Query 036944
Match_columns 370
No_of_seqs 252 out of 1540
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 06:59:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036944.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036944hhsearch_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 7.4E-39 1.6E-43 310.3 21.7 215 13-231 45-268 (335)
2 KOG0655 G1/S-specific cyclin E 100.0 6.5E-35 1.4E-39 277.0 17.7 207 13-238 113-336 (408)
3 KOG0653 Cyclin B and related k 100.0 4.7E-33 1E-37 279.5 19.4 221 5-238 117-346 (391)
4 COG5024 Cyclin [Cell division 100.0 1.8E-32 4E-37 274.5 16.5 222 5-239 171-401 (440)
5 KOG0654 G2/Mitotic-specific cy 100.0 4.1E-29 8.9E-34 244.5 9.1 221 7-240 95-325 (359)
6 TIGR00569 ccl1 cyclin ccl1. Un 99.9 1.2E-26 2.6E-31 225.2 19.3 195 39-244 53-260 (305)
7 KOG0834 CDK9 kinase-activating 99.9 1.9E-24 4.1E-29 210.0 17.1 193 39-239 36-247 (323)
8 KOG0794 CDK8 kinase-activating 99.9 9.4E-25 2E-29 199.2 12.9 197 39-246 38-248 (264)
9 KOG0835 Cyclin L [General func 99.9 1.3E-22 2.9E-27 193.3 18.0 192 39-239 20-231 (367)
10 PF00134 Cyclin_N: Cyclin, N-t 99.9 7.2E-23 1.6E-27 173.0 13.8 123 15-144 1-127 (127)
11 COG5333 CCL1 Cdk activating ki 99.8 9.2E-20 2E-24 173.8 13.0 160 39-206 42-209 (297)
12 KOG2496 Cdk activating kinase 99.7 5.1E-16 1.1E-20 147.3 14.0 154 45-205 59-224 (325)
13 PRK00423 tfb transcription ini 99.6 3E-13 6.6E-18 132.4 22.6 182 43-237 123-304 (310)
14 PF02984 Cyclin_C: Cyclin, C-t 99.5 7.3E-14 1.6E-18 115.9 10.2 93 146-241 1-93 (118)
15 cd00043 CYCLIN Cyclin box fold 99.4 4.3E-13 9.3E-18 104.2 8.0 86 42-136 2-88 (88)
16 smart00385 CYCLIN domain prese 99.4 1.7E-12 3.8E-17 99.8 7.7 83 47-137 1-83 (83)
17 COG1405 SUA7 Transcription ini 98.9 1.1E-07 2.4E-12 92.0 19.7 184 40-236 95-278 (285)
18 KOG1597 Transcription initiati 98.8 1.8E-07 3.8E-12 89.4 17.0 178 46-236 108-287 (308)
19 smart00385 CYCLIN domain prese 98.4 1.3E-06 2.8E-11 66.8 8.4 80 151-234 2-82 (83)
20 cd00043 CYCLIN Cyclin box fold 98.4 2.9E-06 6.3E-11 65.4 10.1 85 145-233 2-87 (88)
21 PF08613 Cyclin: Cyclin; Inte 98.2 9.6E-06 2.1E-10 71.3 9.3 93 44-143 53-149 (149)
22 KOG4164 Cyclin ik3-1/CABLES [C 97.8 1.6E-05 3.4E-10 78.7 4.4 100 39-146 380-482 (497)
23 KOG1598 Transcription initiati 97.4 0.0016 3.5E-08 67.2 11.4 171 48-234 73-251 (521)
24 PF00382 TFIIB: Transcription 96.5 0.017 3.8E-07 44.0 7.8 61 49-115 1-61 (71)
25 PF00382 TFIIB: Transcription 96.3 0.04 8.6E-07 42.0 8.7 70 153-226 2-71 (71)
26 KOG1674 Cyclin [General functi 95.2 0.076 1.6E-06 49.7 7.8 99 45-146 78-181 (218)
27 PRK00423 tfb transcription ini 94.3 0.33 7.1E-06 47.8 10.0 88 46-142 220-307 (310)
28 PF00134 Cyclin_N: Cyclin, N-t 82.3 17 0.00037 29.8 9.9 83 151-236 37-121 (127)
29 COG1405 SUA7 Transcription ini 80.9 19 0.00042 35.1 11.0 102 132-237 76-185 (285)
30 PF02984 Cyclin_C: Cyclin, C-t 80.0 5.2 0.00011 32.3 5.9 85 46-139 4-89 (118)
31 PF09080 K-cyclin_vir_C: K cyc 79.1 23 0.00051 28.5 8.8 75 163-237 22-99 (106)
32 KOG1597 Transcription initiati 78.7 15 0.00033 35.9 9.3 68 165-236 123-191 (308)
33 KOG0834 CDK9 kinase-activating 74.3 5.3 0.00011 39.7 5.0 87 43-138 153-244 (323)
34 PF09241 Herp-Cyclin: Herpesvi 66.7 53 0.0012 26.1 8.1 90 148-237 4-98 (106)
35 KOG1675 Predicted cyclin [Gene 66.5 8.9 0.00019 37.7 4.5 87 59-155 207-297 (343)
36 TIGR00569 ccl1 cyclin ccl1. Un 53.1 97 0.0021 30.5 9.3 40 165-204 77-116 (305)
37 PF08613 Cyclin: Cyclin; Inte 41.9 2.3E+02 0.005 24.5 10.9 88 146-236 52-144 (149)
38 COG5225 RRS1 Uncharacterized p 41.5 4.2 9.1E-05 35.4 -1.9 54 267-320 42-96 (172)
39 KOG1992 Nuclear export recepto 31.8 8.1E+02 0.018 27.8 12.9 189 39-236 376-597 (960)
40 KOG0835 Cyclin L [General func 31.7 1.9E+02 0.0042 28.9 7.4 24 87-110 179-202 (367)
41 PF03261 CDK5_activator: Cycli 31.5 1.2E+02 0.0027 30.4 6.2 64 87-155 269-336 (346)
42 PF01857 RB_B: Retinoblastoma- 26.0 2.4E+02 0.0053 24.3 6.4 65 46-114 15-79 (135)
No 1
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=7.4e-39 Score=310.34 Aligned_cols=215 Identities=28% Similarity=0.514 Sum_probs=193.6
Q ss_pred HHHHHHHHHHHHHhhcCCCCcccCCc----HHHHHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccc
Q 036944 13 EQQALEKFFNEERESMAAEGYAVSKE----ATLRKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRD 88 (370)
Q Consensus 13 ~~dil~~Ll~~E~~~~p~~~y~~~~q----~~~R~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~ 88 (370)
.+|++.+|+++|+++.|..+|+...+ +.+|...++||.+||.++++.++|+++|+||||||++...++.+++|+
T Consensus 45 ~e~~i~~ll~kEe~~~p~~~~~~~~~~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~-- 122 (335)
T KOG0656|consen 45 DERVLANLLEKEEQHNPSLDYFLCVQKLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWM-- 122 (335)
T ss_pred cHHHHHHHHHHHHHhCCCCchhhhcccccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHH--
Confidence 48999999999999999998665554 889999999999999999999999999999999999999999999999
Q ss_pred cchhhHHHHHHHHHHhhccCCch-hHHhhcC-CCCCCcHHHHHHHHHHHHHHcCCcccccChHHHHHHHHhhCCC---Ch
Q 036944 89 DIVLAAICCLTLAWKVRNQAFRF-IYFERDN-NLNEDYKRHILSMELQILKGINWRLRAVTAMYFKEFFVGKIPV---GK 163 (370)
Q Consensus 89 ~lqLiavtCL~IAsKvEE~~~pl-~~l~~~~-~~~yt~~~~Il~mE~~IL~~L~w~L~~pTp~~Fl~~fl~~l~~---~~ 163 (370)
+||+|+|||+||||+||+.+|+ .+++... .+.|. ++.|.+||..||.+|+|+++.+||++|+++|+.+++. ..
T Consensus 123 -lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~fe-aktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~ 200 (335)
T KOG0656|consen 123 -LQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFE-AKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNK 200 (335)
T ss_pred -HHHHHHHHHHHHHhhcCcCCchhhhhhhcccccccc-HHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcccchH
Confidence 9999999999999999999875 8888766 47899 9999999999999999999999999999999999954 24
Q ss_pred HHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHHhCCCCCCcchHHHHhhcCCCHHHHHHHHH
Q 036944 164 GIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRLLYPNEYNQCERDILATKHIKEEELESCLK 231 (370)
Q Consensus 164 ~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~~~~~e~L~~C~~ 231 (370)
..+...+..++..+..|..|+.|+||+||+|++..+...+...........+..+++++.+.+..|+.
T Consensus 201 ~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 201 HLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSVSASVDGLDFREYENNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred HHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence 56788999999999999999999999999999988888766655444456677788899999999998
No 2
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=6.5e-35 Score=277.00 Aligned_cols=207 Identities=17% Similarity=0.296 Sum_probs=179.2
Q ss_pred HHHHHHHHHHHHHhhcCCCCcccCCc---HHHHHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcC-CccCCcccCccc
Q 036944 13 EQQALEKFFNEERESMAAEGYAVSKE---ATLRKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISR-NQLPNVLGRVRD 88 (370)
Q Consensus 13 ~~dil~~Ll~~E~~~~p~~~y~~~~q---~~~R~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~-~~v~~~~~~~~~ 88 (370)
..|.+..|+.+|+.|.....++..+. ++||++++|||.+||+.++|++||||+|+-|||||+.. ..+. +.
T Consensus 113 ~~eVW~lM~kkee~~l~~~~~l~qHpdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~------kt 186 (408)
T KOG0655|consen 113 SKEVWLLMLKKEERYLRDKHFLEQHPDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVS------KT 186 (408)
T ss_pred HHHHHHHHHccchhhhhhhHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhh------hh
Confidence 38999999999999887666666655 99999999999999999999999999999999999954 4555 88
Q ss_pred cchhhHHHHHHHHHHhhccCCc-hhHH--hhcCCCCCCcHHHHHHHHHHHHHHcCCcccccChHHHHHHHHhhCCC----
Q 036944 89 DIVLAAICCLTLAWKVRNQAFR-FIYF--ERDNNLNEDYKRHILSMELQILKGINWRLRAVTAMYFKEFFVGKIPV---- 161 (370)
Q Consensus 89 ~lqLiavtCL~IAsKvEE~~~p-l~~l--~~~~~~~yt~~~~Il~mE~~IL~~L~w~L~~pTp~~Fl~~fl~~l~~---- 161 (370)
++||||+||||||||+||++|| +.+| .++++ ++ .++|+.||..||++|+|+|.+.|...+|..|+.....
T Consensus 187 ~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgA--cs-~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n~~~ 263 (408)
T KOG0655|consen 187 NLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGA--CS-EDDILTMELIILKALKWELSPITIISWLNVYLQVDALNDAP 263 (408)
T ss_pred hHHHhhHHHHHHHHHHhhccCccccceeeeccCc--cc-hHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcCCCC
Confidence 9999999999999999999997 5777 46766 88 9999999999999999999999999999999987621
Q ss_pred ------ChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHHhCCCCCCcchHHHHhhcCCCHHHHHHHHHHHHH
Q 036944 162 ------GKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRLLYPNEYNQCERDILATKHIKEEELESCLKRTYE 235 (370)
Q Consensus 162 ------~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~~~~~e~L~~C~~~m~~ 235 (370)
......-....|+++++++..++.|+-+++|||||+.... ...+.+.+|+...+|.+|++.|.-
T Consensus 264 k~l~Pq~~~~efiqiaqlLDlc~ldids~~fsYrilaAAal~h~~s----------~e~v~kaSG~~w~~ie~cv~wm~P 333 (408)
T KOG0655|consen 264 KVLLPQYSQEEFIQIAQLLDLCILDIDSLEFSYRILAAAALCHFTS----------IEVVKKASGLEWDSIEECVDWMVP 333 (408)
T ss_pred ceeccccchHHHHHHHHHHHHHHhccccccchHHHHHHHHHHHHhH----------HHHHHHcccccHHHHHHHHHHHHH
Confidence 1122233455788999999999999999999999997665 256678899999999999999998
Q ss_pred HHh
Q 036944 236 MCM 238 (370)
Q Consensus 236 l~~ 238 (370)
+.+
T Consensus 334 f~r 336 (408)
T KOG0655|consen 334 FVR 336 (408)
T ss_pred HHH
Confidence 854
No 3
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.7e-33 Score=279.46 Aligned_cols=221 Identities=20% Similarity=0.269 Sum_probs=192.8
Q ss_pred CCCCCc--CcHHHHHHHHHHHHHhhcCCCCcccCCc---HHHHHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCcc
Q 036944 5 SGNPLH--SFEQQALEKFFNEERESMAAEGYAVSKE---ATLRKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQL 79 (370)
Q Consensus 5 ~~~pl~--~~~~dil~~Ll~~E~~~~p~~~y~~~~q---~~~R~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v 79 (370)
-+||.. ++.+|++.++...|..+.|...+ ..+. ..||.++|||+++||.+|++..||+|+||+++||||++..+
T Consensus 117 ~~~~~~~~ey~~di~~~l~~~e~~~~p~~~~-~~~~e~~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v 195 (391)
T KOG0653|consen 117 KSDPSMIVEYVQDIFEYLRQLELEFLPLSYD-ISQSEIRAKMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKV 195 (391)
T ss_pred ccCcHHHHHHHHHHHHHHHHHHHhhCchhhh-cccccccHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcc
Confidence 345644 45699999999999766665544 3332 78999999999999999999999999999999999999888
Q ss_pred CCcccCccccchhhHHHHHH-HHHHhhccCCc-hhHHh--hcCCCCCCcHHHHHHHHHHHHHHcCCcccccChHHHHHHH
Q 036944 80 PNVLGRVRDDIVLAAICCLT-LAWKVRNQAFR-FIYFE--RDNNLNEDYKRHILSMELQILKGINWRLRAVTAMYFKEFF 155 (370)
Q Consensus 80 ~~~~~~~~~~lqLiavtCL~-IAsKvEE~~~p-l~~l~--~~~~~~yt~~~~Il~mE~~IL~~L~w~L~~pTp~~Fl~~f 155 (370)
+ +.++||+|++||| ||+|+||..+| +.+|. .++. |+ +++|++||+.||++|+|++..|||+.|++.|
T Consensus 196 ~------~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~--~s-~~~il~mE~~il~~L~f~l~~p~~~~FLrr~ 266 (391)
T KOG0653|consen 196 P------LKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGA--YS-REEILRMEKYILNVLEFDLSVPTPLSFLRRF 266 (391)
T ss_pred c------HHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCc--cc-hHHHHHHHHHHHhccCeeecCCchHHHHHHH
Confidence 8 8999999999977 99999998888 57774 4544 99 9999999999999999999999999999999
Q ss_pred HhhCCCChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHHhCCCCCCcchHHHHhhcCCCHHHHHHHHHHHHH
Q 036944 156 VGKIPVGKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRLLYPNEYNQCERDILATKHIKEEELESCLKRTYE 235 (370)
Q Consensus 156 l~~l~~~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~~~~~e~L~~C~~~m~~ 235 (370)
+.....+. ..+..+.++++++++|+.++.++||.+|+|++++++.....+. .|...+..++|+...++.+|.+.+..
T Consensus 267 ~ka~~~d~-~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~~~~~~--~w~~~~~~~sg~~~~~~~~~~~~~~~ 343 (391)
T KOG0653|consen 267 LKAADYDI-KTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALRMLSKGD--VWSPTLEHYSGYSESYLFECARSLSA 343 (391)
T ss_pred HHhhhcch-hHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHHhccCC--ccCCCCeeccCCCcHHHHHHHHHHHH
Confidence 98876443 5678999999999999999999999999999999999887653 48888999999988899999999988
Q ss_pred HHh
Q 036944 236 MCM 238 (370)
Q Consensus 236 l~~ 238 (370)
+..
T Consensus 344 ~~~ 346 (391)
T KOG0653|consen 344 LSL 346 (391)
T ss_pred HHH
Confidence 643
No 4
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=100.00 E-value=1.8e-32 Score=274.48 Aligned_cols=222 Identities=17% Similarity=0.195 Sum_probs=198.9
Q ss_pred CCCCCcCc--HHHHHHHHHHHHHhhcCCCCcccCCc---HHHHHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCcc
Q 036944 5 SGNPLHSF--EQQALEKFFNEERESMAAEGYAVSKE---ATLRKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQL 79 (370)
Q Consensus 5 ~~~pl~~~--~~dil~~Ll~~E~~~~p~~~y~~~~q---~~~R~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v 79 (370)
.++|+.+. +.||+.+|+.+|..+.|...|+..++ ..||.++++|+++||.+|++.++|+++||+++|||++...+
T Consensus 171 ~~d~~mv~Ey~~~Ife~l~k~e~~~lp~~~yl~kq~~~~~~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v 250 (440)
T COG5024 171 QEDPLMVPEYASDIFEYLLKLELIDLPNPNYLIKQSLYEWSMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVV 250 (440)
T ss_pred ccCccchHHHHHHHHHHHHHHHHHhcCcHHHHhhcchhHHhHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCcc
Confidence 45777744 59999999999999999999977766 79999999999999999999999999999999999999999
Q ss_pred CCcccCccccchhhHHHHHHHHHHhhccCCch-hHHh--hcCCCCCCcHHHHHHHHHHHHHHcCCcccccChHHHHHHHH
Q 036944 80 PNVLGRVRDDIVLAAICCLTLAWKVRNQAFRF-IYFE--RDNNLNEDYKRHILSMELQILKGINWRLRAVTAMYFKEFFV 156 (370)
Q Consensus 80 ~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl-~~l~--~~~~~~yt~~~~Il~mE~~IL~~L~w~L~~pTp~~Fl~~fl 156 (370)
. -+.+||+|++||||||||||...|. .+|. .+++ |+ .++|+++|+.+|.+|+|++..|+|+.|++.+.
T Consensus 251 ~------l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~--~t-~~~i~~aE~~ml~~l~f~is~P~P~sFLRriS 321 (440)
T COG5024 251 S------LEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGA--FT-RDDIIRAERYMLEVLDFNISWPSPMSFLRRIS 321 (440)
T ss_pred c------HHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHccc--cc-HHHHHHHHHHHhhhcccccCCCChHHHHHHHH
Confidence 8 8889999999999999999999874 6664 4555 89 99999999999999999999999999988887
Q ss_pred hhCCCChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHHhCCCCCCcchHHHHhhcC-CCHHHHHHHHHHHHH
Q 036944 157 GKIPVGKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRLLYPNEYNQCERDILATKH-IKEEELESCLKRTYE 235 (370)
Q Consensus 157 ~~l~~~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~~-~~~e~L~~C~~~m~~ 235 (370)
..-..+ ...+..+.++++.+..++.|.+++||.+|+||.+.|++.++... |...+..++| |+.+++..++..+.+
T Consensus 322 ka~dyd-~~srt~~k~~~e~s~~~~~f~~~~~S~~~aaa~~~s~~~~~~~~---w~~~l~~ySg~y~~~~l~~~~~~~~~ 397 (440)
T COG5024 322 KASDYD-IFSRTPAKFSSEISPVDYKFIQISPSWCAAAAMYLSRKILSQNQ---WDRTLIHYSGNYTNPDLKPLNESNKE 397 (440)
T ss_pred hhcccc-hhhhhhHhhhCCchHhhhhhccCCchHHHHHHHHHHHhhhccCC---CCccccccCCCCCchhHHHHHHHHHH
Confidence 664433 35677899999999999999999999999999999999988754 7888889998 999999999999988
Q ss_pred HHhc
Q 036944 236 MCMD 239 (370)
Q Consensus 236 l~~~ 239 (370)
....
T Consensus 398 ~l~~ 401 (440)
T COG5024 398 NLQN 401 (440)
T ss_pred Hhcc
Confidence 7654
No 5
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=99.96 E-value=4.1e-29 Score=244.49 Aligned_cols=221 Identities=19% Similarity=0.236 Sum_probs=199.8
Q ss_pred CCCcCc--HHHHHHHHHHHHHh-hcCCCCcccCCc----HHHHHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCcc
Q 036944 7 NPLHSF--EQQALEKFFNEERE-SMAAEGYAVSKE----ATLRKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQL 79 (370)
Q Consensus 7 ~pl~~~--~~dil~~Ll~~E~~-~~p~~~y~~~~q----~~~R~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v 79 (370)
+|.... ..+|+.++...|.+ .+|..+|+...| +.||.++|+|+++|++.+++..+|+|+++++.|||+....+
T Consensus 95 dp~~c~~~~~~I~~~~r~~ei~~~rp~~~~~e~vq~d~t~smrgilvdwlvevsee~r~~~e~l~ls~~~~drfl~~~~~ 174 (359)
T KOG0654|consen 95 DPQMCLKIAAKIYNTLRVSDIKSERPLPSKFEFVQADITPSMRGILVDWLVEVSEEYRLTFETLYLSVNYRDRFLSYKEV 174 (359)
T ss_pred chHHHHHHHHHHhhcccccchhhccCcccceeeeecCCCcchhhhhhhhhhHHHHHHHhhhhheeecHHHHHHHhccCcc
Confidence 555533 58999999999999 999999998866 99999999999999999999999999999999999999998
Q ss_pred CCcccCccccchhhHHHHHHHHHHhhccCCc-hhHHh--hcCCCCCCcHHHHHHHHHHHHHHcCCcccccChHHHHHHHH
Q 036944 80 PNVLGRVRDDIVLAAICCLTLAWKVRNQAFR-FIYFE--RDNNLNEDYKRHILSMELQILKGINWRLRAVTAMYFKEFFV 156 (370)
Q Consensus 80 ~~~~~~~~~~lqLiavtCL~IAsKvEE~~~p-l~~l~--~~~~~~yt~~~~Il~mE~~IL~~L~w~L~~pTp~~Fl~~fl 156 (370)
. +..+|++|.+|++||+|+||..+| +.+|. .+++ |+ ..++..||..||..|.|.+..||.-.|+..|+
T Consensus 175 ~------~~k~ql~g~s~m~I~sk~ee~~~~~~~ef~~itd~t--y~-~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~ 245 (359)
T KOG0654|consen 175 N------KQKLQLVGISAMLIASKYEEIKEPRVEEFCYITDNT--YT-YWQVLRMEIDILNALTFELVRPTSKTFLRRFL 245 (359)
T ss_pred H------HHHHHHhCcccceeeccchhhcchHHHHHHhhhhhh--hH-HHHHHHHHHHHHHHhHHHHhCchHHHHHHHHH
Confidence 8 889999999999999999999987 46664 5555 88 99999999999999999999999999999998
Q ss_pred hhCCCChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHHhCCCCCCcchHHHHhhcCCCHHHHHHHHHHHHHH
Q 036944 157 GKIPVGKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRLLYPNEYNQCERDILATKHIKEEELESCLKRTYEM 236 (370)
Q Consensus 157 ~~l~~~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~~~~~e~L~~C~~~m~~l 236 (370)
.........+..++.|+.++++.++.|+.|.||.|||||+++|.-+++. ..|.+.+.+++||+.+++..|+..|+ +
T Consensus 246 ~~~~~~~~~~e~~~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~~---~pW~~~L~~~T~y~~edl~~~v~~L~-~ 321 (359)
T KOG0654|consen 246 RVAQTPELQVEPLANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLDF---HPWNQTLEDYTGYKAEDLKPCVLDLH-L 321 (359)
T ss_pred HhhcchhHHHHHHHHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhccC---CCCchhhHHhhcccHHHHHHHHHHHh-c
Confidence 8876444468899999999999999999999999999999999998873 34899999999999999999999999 7
Q ss_pred Hhcc
Q 036944 237 CMDK 240 (370)
Q Consensus 237 ~~~~ 240 (370)
+...
T Consensus 322 ~l~~ 325 (359)
T KOG0654|consen 322 YLNA 325 (359)
T ss_pred ccCC
Confidence 5443
No 6
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.95 E-value=1.2e-26 Score=225.17 Aligned_cols=195 Identities=18% Similarity=0.192 Sum_probs=162.2
Q ss_pred HHHHHHHHHHHHHhHHhcC--CCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCchhHHhh
Q 036944 39 ATLRKVALNVILKNSKCFN--FDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRFIYFER 116 (370)
Q Consensus 39 ~~~R~~lvdWl~~V~~~~~--l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl~~l~~ 116 (370)
..+|...++.|.++|..|+ ++++|+++|++||+||+.++++. ..++++||+||||||||+||..+++.+|..
T Consensus 53 ~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~------~~~p~~Ia~tclfLA~KvEE~~~si~~fv~ 126 (305)
T TIGR00569 53 LDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVM------EYHPKIIMLTCVFLACKVEEFNVSIDQFVG 126 (305)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchh------hcCHHHHHHHHHHHHHhccccCcCHHHHHh
Confidence 7899999999999999999 99999999999999999999988 778999999999999999999988887753
Q ss_pred c--CCCCCCcHHHHHHHHHHHHHHcCCcccccChHHHHHHHHhhCC------CChHHHHHHHHHHHHHhcccccccCcch
Q 036944 117 D--NNLNEDYKRHILSMELQILKGINWRLRAVTAMYFKEFFVGKIP------VGKGIMRRTLNEIIIQAQGDINFTQYKP 188 (370)
Q Consensus 117 ~--~~~~yt~~~~Il~mE~~IL~~L~w~L~~pTp~~Fl~~fl~~l~------~~~~~l~~~a~~ll~~sl~d~~~l~y~P 188 (370)
. ...... +++|++||..||+.|+|+|.+++|++++..|+..+. ...+.+.+.||.++++++++..++.|+|
T Consensus 127 ~~~~~~~~~-~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~P 205 (305)
T TIGR00569 127 NLKETPLKA-LEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTP 205 (305)
T ss_pred hccCCchhh-HHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCH
Confidence 2 222235 799999999999999999999999999999986542 2234688999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCCcchHHHHhhcCC--CHHHHHHHHHHHHHH-HhccCCch
Q 036944 189 SVMAASSLLTACRLLYPNEYNQCERDILATKHI--KEEELESCLKRTYEM-CMDKQILL 244 (370)
Q Consensus 189 S~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~~~--~~e~L~~C~~~m~~l-~~~~~~~~ 244 (370)
|+||+|||++|.+.++.. .+... +..++. +.+.+...+..|+++ ...++...
T Consensus 206 s~IAlAAI~lA~~~~~~~-l~~~~---~e~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 260 (305)
T TIGR00569 206 SQIALAAILHTASRAGLN-MESYL---TEQLSVPGNREELPQLIDIMRELRILVKKYEE 260 (305)
T ss_pred HHHHHHHHHHHHHHhCCC-Ccccc---hhhhcccccHHHHHHHHHHHHHHHHHHHcCCC
Confidence 999999999999998764 32211 234544 667777777777777 33344443
No 7
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.92 E-value=1.9e-24 Score=209.97 Aligned_cols=193 Identities=16% Similarity=0.175 Sum_probs=169.6
Q ss_pred HHHHHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCchhHHhh--
Q 036944 39 ATLRKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRFIYFER-- 116 (370)
Q Consensus 39 ~~~R~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl~~l~~-- 116 (370)
...|...+.||.+++.++++++.|+++|+.||+||+...++. ..+.+.+|++|||||+|+||...++.|++.
T Consensus 36 ~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~------~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s 109 (323)
T KOG0834|consen 36 LRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFK------KFDPYTVAASCLFLAGKVEETPRKLEDIIKVS 109 (323)
T ss_pred HHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccc------cCcHHHHHHHHHHHHhhcccCcccHHHHHHHH
Confidence 889999999999999999999999999999999999999998 788999999999999999999888766521
Q ss_pred ----c-------CCCCCCcHHHHHHHHHHHHHHcCCcccccChHHHHHHHHhhCCCChH---HHHHHHHHHHHHhccccc
Q 036944 117 ----D-------NNLNEDYKRHILSMELQILKGINWRLRAVTAMYFKEFFVGKIPVGKG---IMRRTLNEIIIQAQGDIN 182 (370)
Q Consensus 117 ----~-------~~~~yt~~~~Il~mE~~IL~~L~w~L~~pTp~~Fl~~fl~~l~~~~~---~l~~~a~~ll~~sl~d~~ 182 (370)
. ..| ...++.|+..|..||++|+|++++-+||.||..|+..+..... .+.+.||+++++++....
T Consensus 110 ~~~~~~~~~~~~~~~-~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~ 188 (323)
T KOG0834|consen 110 YRYLNPKDLELEEVY-WELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTL 188 (323)
T ss_pred HHHcCcccccHHHHH-HHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeee
Confidence 1 111 1127899999999999999999999999999999999965432 588999999999999999
Q ss_pred ccCcchHHHHHHHHHHHHHHhCCCCCCcchH-HHHhhcC--CCHHHHHHHHHHHHHHHhc
Q 036944 183 FTQYKPSVMAASSLLTACRLLYPNEYNQCER-DILATKH--IKEEELESCLKRTYEMCMD 239 (370)
Q Consensus 183 ~l~y~PS~IAaAaI~lA~~~l~~~~~~~~~~-~l~~~~~--~~~e~L~~C~~~m~~l~~~ 239 (370)
+++|+|.+||+|||++|+...+. ..+.+.. .|+..++ ++.++|.+.+..+..++..
T Consensus 189 cL~y~p~~IAva~i~lA~~~~~~-~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y~~ 247 (323)
T KOG0834|consen 189 CLQYSPHSIAVACIHLAAKLLGV-ELPSDTDKRWWREFDETVTNELLDDICHEFLDLYEQ 247 (323)
T ss_pred eEeecCcEEEeehhhHHHHHcCC-CCCCCcccchhhhhcccCCHHHHHHHHHHHHHHHhh
Confidence 99999999999999999998877 4444444 4788888 9999999999999999854
No 8
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.92 E-value=9.4e-25 Score=199.24 Aligned_cols=197 Identities=19% Similarity=0.205 Sum_probs=170.1
Q ss_pred HHHHHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCc-h------
Q 036944 39 ATLRKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFR-F------ 111 (370)
Q Consensus 39 ~~~R~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~p-l------ 111 (370)
...+--..+.+..++.++++.+.++++|+.||.||+.++++. .-++.++|.||+|||||+||..+. .
T Consensus 38 ~~l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k------~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~ 111 (264)
T KOG0794|consen 38 SKLKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLK------EIEPRLLAPTCLYLACKVEECPIVHIRLLVNE 111 (264)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh------ccCHHHHHHHHHHHHhhhhhcchHHHHHHHHH
Confidence 445556667788999999999999999999999999999987 677999999999999999998632 1
Q ss_pred -hHH-----hhcCCCCCCcHHHHHHHHHHHHHHcCCcccccChHHHHHHHHhhCCCChHHHHHHHHHHHHHhcccccccC
Q 036944 112 -IYF-----ERDNNLNEDYKRHILSMELQILKGINWRLRAVTAMYFKEFFVGKIPVGKGIMRRTLNEIIIQAQGDINFTQ 185 (370)
Q Consensus 112 -~~l-----~~~~~~~yt~~~~Il~mE~~IL~~L~w~L~~pTp~~Fl~~fl~~l~~~~~~l~~~a~~ll~~sl~d~~~l~ 185 (370)
..+ .....+.|. .+.|++||..+|+.|++.|.+.+|++.|..+++..+.....+.+.+|.++++++....++.
T Consensus 112 a~~L~~~f~~~~e~~~~~-~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll 190 (264)
T KOG0794|consen 112 AKVLKTRFSYWPEKFPYE-RKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLL 190 (264)
T ss_pred HHHHhhhcccchhhcCCC-cCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcccchhhhhhhHhhhcchhhcceeee
Confidence 122 123345688 9999999999999999999999999999999999987666789999999999999999999
Q ss_pred cchHHHHHHHHHHHHHHhCCCCCCcchHHHHhhcCCCHHHHHHHHHHHHHHH-hccCCchhh
Q 036944 186 YKPSVMAASSLLTACRLLYPNEYNQCERDILATKHIKEEELESCLKRTYEMC-MDKQILLER 246 (370)
Q Consensus 186 y~PS~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~~~~~e~L~~C~~~m~~l~-~~~~~~~~~ 246 (370)
|+|.+||.|||++|+...+... .+.|...+.+|.+.+.+|++.+.++| .++.++..+
T Consensus 191 ~PPh~IalAcl~Ia~~~~~k~~----~~~w~~el~vD~ekV~~~v~~I~~lYe~wk~~~E~~ 248 (264)
T KOG0794|consen 191 YPPHQIALACLYIACVIDEKDI----PKAWFAELSVDMEKVKDIVQEILKLYELWKIFDEKK 248 (264)
T ss_pred cCHHHHHHHHHHHHHhhcCCCh----HHHHHHHHhccHHHHHHHHHHHHHHHHHHhhhhHHH
Confidence 9999999999999999877642 37788889999999999999999994 566666544
No 9
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.90 E-value=1.3e-22 Score=193.29 Aligned_cols=192 Identities=14% Similarity=0.176 Sum_probs=166.9
Q ss_pred HHHHHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCchhHH----
Q 036944 39 ATLRKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRFIYF---- 114 (370)
Q Consensus 39 ~~~R~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl~~l---- 114 (370)
...|...++||.+-+..++|++.+.+++..+|-||+...++. +.++..++++|++||+|+||....+.++
T Consensus 20 ~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v------~~~~e~vv~ACv~LASKiEE~Prr~rdVinVF 93 (367)
T KOG0835|consen 20 EELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFV------RHDFEIVVMACVLLASKIEEEPRRIRDVINVF 93 (367)
T ss_pred HHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccc------cccHHHHHHHHHHHHhhhccccccHhHHHHHH
Confidence 789999999999999999999999999999999999999888 8889999999999999999987543322
Q ss_pred ------hh---------cCCCCCCcHHHHHHHHHHHHHHcCCcccccChHHHHHHHHhhCCCC-hHHHHHHHHHHHHHhc
Q 036944 115 ------ER---------DNNLNEDYKRHILSMELQILKGINWRLRAVTAMYFKEFFVGKIPVG-KGIMRRTLNEIIIQAQ 178 (370)
Q Consensus 115 ------~~---------~~~~~yt~~~~Il~mE~~IL~~L~w~L~~pTp~~Fl~~fl~~l~~~-~~~l~~~a~~ll~~sl 178 (370)
.. ...+.-. +.+++++|..||..|||++++.+|+.++-.|++.++-. ...+.+.+|.|+++++
T Consensus 94 h~L~~r~~~~~~~~~~~~~~~~~l-k~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDsl 172 (367)
T KOG0835|consen 94 HYLEQRRESEAAEHLILARLYINL-KMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSL 172 (367)
T ss_pred HHHHHHHhccCcchhhhhhHHhhh-hhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCchhHHHHHHHhhhhcc
Confidence 00 1111112 67889999999999999999999999999999999543 2358999999999999
Q ss_pred ccccccCcchHHHHHHHHHHHHHHhCCCCCCcchHHHHhhcCCCHHHHHHHHHHHHHHHhc
Q 036944 179 GDINFTQYKPSVMAASSLLTACRLLYPNEYNQCERDILATKHIKEEELESCLKRTYEMCMD 239 (370)
Q Consensus 179 ~d~~~l~y~PS~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~~~~~e~L~~C~~~m~~l~~~ 239 (370)
.+..|..|+|+.||+|||++|.+.++.... ..+.|+.+++.++++|.+.+..+..+|..
T Consensus 173 RT~v~vry~pe~iACaciyLaAR~~eIpLp--~~P~Wf~~Fd~~k~eid~ic~~l~~lY~~ 231 (367)
T KOG0835|consen 173 RTDVFVRYSPESIACACIYLAARNLEIPLP--FQPHWFKAFDTTKREIDEICYRLIPLYKR 231 (367)
T ss_pred ccceeeecCHHHHHHHHHHHHHhhhcCCCC--CCccHHHHcCCcHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999885422 34678999999999999999999999887
No 10
>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=99.90 E-value=7.2e-23 Score=173.03 Aligned_cols=123 Identities=23% Similarity=0.357 Sum_probs=105.9
Q ss_pred HHHHHHHHHHHhhcCCCCcccCCc---HHHHHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccch
Q 036944 15 QALEKFFNEERESMAAEGYAVSKE---ATLRKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIV 91 (370)
Q Consensus 15 dil~~Ll~~E~~~~p~~~y~~~~q---~~~R~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lq 91 (370)
||+.+|+++|.++.|...|++.++ ...|..+++||.+++..++++++|+++|+.|||||+.+..+. +.+++
T Consensus 1 ~i~~~~~~~e~~~~~~~~~~~~~~~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~------~~~~~ 74 (127)
T PF00134_consen 1 DIFRYLLEKELKYKPNPDYLEQQPEITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVN------RSKLQ 74 (127)
T ss_dssp HHHHHHHHHHHHTTCCTTHGTGTSSHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TT------CCGHH
T ss_pred CHHHHHHHHHHHHCcCccccccChhcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccc------cchhh
Confidence 799999999999998899998554 899999999999999999999999999999999999999887 88899
Q ss_pred hhHHHHHHHHHHhhccCCc-hhHHhhcCCCCCCcHHHHHHHHHHHHHHcCCccc
Q 036944 92 LAAICCLTLAWKVRNQAFR-FIYFERDNNLNEDYKRHILSMELQILKGINWRLR 144 (370)
Q Consensus 92 LiavtCL~IAsKvEE~~~p-l~~l~~~~~~~yt~~~~Il~mE~~IL~~L~w~L~ 144 (370)
++|+|||+||+|++|..+| +.++.......|+ +++|++||+.||++|+|+++
T Consensus 75 li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~-~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 75 LIALACLFLASKMEEDNPPSISDLIRISDNTFT-KKDILEMEREILSALNFDLN 127 (127)
T ss_dssp HHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSH-HHHHHHHHHHHHHHTTT---
T ss_pred hhhhhHHHHhhhhhccccchHHHHHHHHcCCCC-HHHHHHHHHHHHHHCCCCcC
Confidence 9999999999999999765 6676433334599 99999999999999999985
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=99.82 E-value=9.2e-20 Score=173.75 Aligned_cols=160 Identities=21% Similarity=0.298 Sum_probs=139.9
Q ss_pred HHHHHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhcc--CCchhHHh-
Q 036944 39 ATLRKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQ--AFRFIYFE- 115 (370)
Q Consensus 39 ~~~R~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~--~~pl~~l~- 115 (370)
...|-....|+..+|.+++++..|+.+||.+|+||+.++++. ...++-++.||++||+|+||. ...+..+.
T Consensus 42 ~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~------e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~ 115 (297)
T COG5333 42 LNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVE------EISLYSVVTTCVYLACKVEDTPRDISIESFEA 115 (297)
T ss_pred hhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccc------cccHHHHHHhheeeeeecccccchhhHHHHHh
Confidence 678888899999999999999999999999999999999987 667999999999999999995 33333332
Q ss_pred ----hcCCCCCCcHHHHHHHHHHHHHHcCCcccccChHHHHHHHHhhCCCC-hHHHHHHHHHHHHHhcccccccCcchHH
Q 036944 116 ----RDNNLNEDYKRHILSMELQILKGINWRLRAVTAMYFKEFFVGKIPVG-KGIMRRTLNEIIIQAQGDINFTQYKPSV 190 (370)
Q Consensus 116 ----~~~~~~yt~~~~Il~mE~~IL~~L~w~L~~pTp~~Fl~~fl~~l~~~-~~~l~~~a~~ll~~sl~d~~~l~y~PS~ 190 (370)
.+.- +++++.|..+|..+|+.|+|++++++|+..+..|+..+... ...+.+.||.++++++.+..++.|+|+.
T Consensus 116 ~~~~se~~--~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypphi 193 (297)
T COG5333 116 RDLWSEEP--KSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHI 193 (297)
T ss_pred hccccccc--cccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecChHH
Confidence 2222 33499999999999999999999999999999999988443 2368899999999999999999999999
Q ss_pred HHHHHHHHHHHHhCCC
Q 036944 191 MAASSLLTACRLLYPN 206 (370)
Q Consensus 191 IAaAaI~lA~~~l~~~ 206 (370)
||+||++.|++.++..
T Consensus 194 IA~a~l~ia~~~~~~~ 209 (297)
T COG5333 194 IALAALLIACEVLGMP 209 (297)
T ss_pred HHHHHHHHHHHhcCCc
Confidence 9999999999987654
No 12
>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=99.68 E-value=5.1e-16 Score=147.31 Aligned_cols=154 Identities=18% Similarity=0.214 Sum_probs=123.3
Q ss_pred HHHHHHHhHHhc--CCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCchhHHhhcCC--C
Q 036944 45 ALNVILKNSKCF--NFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRFIYFERDNN--L 120 (370)
Q Consensus 45 lvdWl~~V~~~~--~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl~~l~~~~~--~ 120 (370)
...-+++.+.+| .+++.++.+|+.+|.||+..+++. .-+.+.|.+||+|+|+|++|.++++.+|..... .
T Consensus 59 ~E~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvm------e~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~~~ 132 (325)
T KOG2496|consen 59 EELSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVM------EYSPKIIMATCFFLACKIEEFYISIEQFVKNMNGRK 132 (325)
T ss_pred HHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchh------hcChHHHHHHHHHHHhhhHhheecHHHHHhhccCcc
Confidence 334445555544 568999999999999999999987 666999999999999999999999988864321 1
Q ss_pred CCCcHHHHHHHHHHHHHHcCCcccccChHHHHHHHHhhCC------CChHHHHHHHH--HHHHHhcccccccCcchHHHH
Q 036944 121 NEDYKRHILSMELQILKGINWRLRAVTAMYFKEFFVGKIP------VGKGIMRRTLN--EIIIQAQGDINFTQYKPSVMA 192 (370)
Q Consensus 121 ~yt~~~~Il~mE~~IL~~L~w~L~~pTp~~Fl~~fl~~l~------~~~~~l~~~a~--~ll~~sl~d~~~l~y~PS~IA 192 (370)
.=+ .+.|+..|..+|+.|+|+|.+.+|++.++.|+..+. .+...++.... .+++.++++..++.|+||+||
T Consensus 133 ~k~-~e~vLk~E~~llqsL~f~L~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIA 211 (325)
T KOG2496|consen 133 WKT-HEIVLKYEFLLLQSLKFSLTVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIA 211 (325)
T ss_pred ccc-HHHHHhchHHHHHhhhhhheecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHH
Confidence 234 899999999999999999999999999999988772 12223344444 788889999999999999999
Q ss_pred HHHHHHHHHHhCC
Q 036944 193 ASSLLTACRLLYP 205 (370)
Q Consensus 193 aAaI~lA~~~l~~ 205 (370)
+|||+.|....+.
T Consensus 212 LaAil~a~~~~~~ 224 (325)
T KOG2496|consen 212 LAAILHAAGRTGE 224 (325)
T ss_pred HHHHHHHhccccc
Confidence 9999666554443
No 13
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.58 E-value=3e-13 Score=132.36 Aligned_cols=182 Identities=13% Similarity=0.111 Sum_probs=158.0
Q ss_pred HHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCchhHHhhcCCCCC
Q 036944 43 KVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRFIYFERDNNLNE 122 (370)
Q Consensus 43 ~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl~~l~~~~~~~y 122 (370)
.....-|.+++..++++..+.-.|..++.+++....+. ......++++|+|+|+|.++...++.++..-.. .
T Consensus 123 ~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~r------grs~~~i~AAclYiACR~~~~prtl~eI~~~~~--v 194 (310)
T PRK00423 123 AFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIR------GRSIEGVVAAALYAACRRCKVPRTLDEIAEVSR--V 194 (310)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccc------CCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhC--C
Confidence 45567788899999999999999999999999888776 666899999999999999888778888854322 4
Q ss_pred CcHHHHHHHHHHHHHHcCCcccccChHHHHHHHHhhCCCChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHH
Q 036944 123 DYKRHILSMELQILKGINWRLRAVTAMYFKEFFVGKIPVGKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRL 202 (370)
Q Consensus 123 t~~~~Il~mE~~IL~~L~w~L~~pTp~~Fl~~fl~~l~~~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~ 202 (370)
+ +++|-+.++.|++.|+.++...+|.+|+..|...++-.. .+...|.+++..+..........|..|||||||+|++.
T Consensus 195 ~-~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~-~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~ 272 (310)
T PRK00423 195 S-RKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSG-EVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLL 272 (310)
T ss_pred C-HHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCH-HHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHH
Confidence 6 999999999999999999999999999999999997654 67889999999888766678999999999999999998
Q ss_pred hCCCCCCcchHHHHhhcCCCHHHHHHHHHHHHHHH
Q 036944 203 LYPNEYNQCERDILATKHIKEEELESCLKRTYEMC 237 (370)
Q Consensus 203 l~~~~~~~~~~~l~~~~~~~~e~L~~C~~~m~~l~ 237 (370)
.+... -.+.+...+|++...|...++.|.+..
T Consensus 273 ~g~~~---t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 273 LGERR---TQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred hCCCC---CHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 76543 267889999999999999999888753
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=99.52 E-value=7.3e-14 Score=115.94 Aligned_cols=93 Identities=22% Similarity=0.277 Sum_probs=77.6
Q ss_pred cChHHHHHHHHhhCCCChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHHhCCCCCCcchHHHHhhcCCCHHH
Q 036944 146 VTAMYFKEFFVGKIPVGKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRLLYPNEYNQCERDILATKHIKEEE 225 (370)
Q Consensus 146 pTp~~Fl~~fl~~l~~~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~~~~~e~ 225 (370)
|||++||++|++. ......+...+++++++++.++.|++|+||+||+||+++|+..++.. ..|...+..++|++.++
T Consensus 1 PTp~~Fl~~~~~~-~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~--~~~~~~l~~~t~~~~~~ 77 (118)
T PF02984_consen 1 PTPYDFLRRFLKI-SNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKE--PPWPESLEKLTGYDKED 77 (118)
T ss_dssp --HHHHHHHHHTS-SSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSS--TCSHHHHHHHHTS-HHH
T ss_pred CcHHHHHHHHHHH-cCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCcc--ccCCccchhhcCCCHHH
Confidence 7999999999554 33345789999999999999999999999999999999999998742 25889999999999999
Q ss_pred HHHHHHHHHHHHhccC
Q 036944 226 LESCLKRTYEMCMDKQ 241 (370)
Q Consensus 226 L~~C~~~m~~l~~~~~ 241 (370)
|.+|++.|.+++....
T Consensus 78 l~~c~~~i~~~~~~~~ 93 (118)
T PF02984_consen 78 LKECIELIQELLSKAS 93 (118)
T ss_dssp HHHHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHHhcC
Confidence 9999999999976433
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=99.43 E-value=4.3e-13 Score=104.23 Aligned_cols=86 Identities=23% Similarity=0.223 Sum_probs=76.2
Q ss_pred HHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCchhHHhhcCCCC
Q 036944 42 RKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRFIYFERDNNLN 121 (370)
Q Consensus 42 R~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl~~l~~~~~~~ 121 (370)
|...++||.+++..++++++|.++|+.++|||+....+. +.+++++|++|++||+|++|..+...++.....
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~------~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~-- 73 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVL------GRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTG-- 73 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccc------cCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhC--
Confidence 678999999999999999999999999999999998887 777999999999999999999556677754433
Q ss_pred C-CcHHHHHHHHHHHH
Q 036944 122 E-DYKRHILSMELQIL 136 (370)
Q Consensus 122 y-t~~~~Il~mE~~IL 136 (370)
+ + .++|.++|+.|+
T Consensus 74 ~~~-~~~i~~~e~~il 88 (88)
T cd00043 74 YAT-EEEILRMEKLLL 88 (88)
T ss_pred CCC-HHHHHHHHHHhC
Confidence 5 7 999999999875
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=99.37 E-value=1.7e-12 Score=99.83 Aligned_cols=83 Identities=24% Similarity=0.221 Sum_probs=71.6
Q ss_pred HHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCchhHHhhcCCCCCCcHH
Q 036944 47 NVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRFIYFERDNNLNEDYKR 126 (370)
Q Consensus 47 dWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl~~l~~~~~~~yt~~~ 126 (370)
+||.+++..++++++|.++|+.++|||+....+. +..++++|++|++||+|++|..++..++....++ |+ .+
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~------~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~-~~-~~ 72 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFL------KYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGY-FT-EE 72 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcc------cCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC-CC-HH
Confidence 5999999999999999999999999999976666 6779999999999999999988766666433332 58 99
Q ss_pred HHHHHHHHHHH
Q 036944 127 HILSMELQILK 137 (370)
Q Consensus 127 ~Il~mE~~IL~ 137 (370)
+|.++|+.||+
T Consensus 73 ~i~~~~~~il~ 83 (83)
T smart00385 73 EILRMEKLLLE 83 (83)
T ss_pred HHHHHHHHHhC
Confidence 99999999874
No 17
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=98.93 E-value=1.1e-07 Score=91.97 Aligned_cols=184 Identities=14% Similarity=0.159 Sum_probs=157.0
Q ss_pred HHHHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCchhHHhhcCC
Q 036944 40 TLRKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRFIYFERDNN 119 (370)
Q Consensus 40 ~~R~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl~~l~~~~~ 119 (370)
..-.....-+-.++..++++..+.-.|..++-+.+...-+. ....+-++++|+|+|++.......+.++.....
T Consensus 95 rnl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~r------GRsie~v~AA~iY~acR~~~~prtl~eIa~a~~ 168 (285)
T COG1405 95 RNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLR------GRSIESVAAACIYAACRINGVPRTLDEIAKALG 168 (285)
T ss_pred hHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCc------CCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHC
Confidence 34445667777889999999999999999999999988877 666899999999999999988778777754333
Q ss_pred CCCCcHHHHHHHHHHHHHHcCCcccccChHHHHHHHHhhCCCChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHH
Q 036944 120 LNEDYKRHILSMELQILKGINWRLRAVTAMYFKEFFVGKIPVGKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTA 199 (370)
Q Consensus 120 ~~yt~~~~Il~mE~~IL~~L~w~L~~pTp~~Fl~~fl~~l~~~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA 199 (370)
-+ +.+|.++.+.+...|+=.+.+..|..|+..|...++-. ..+...|..++..+...-.-..-.|+-+|+||+|+|
T Consensus 169 --V~-~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~-~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~a 244 (285)
T COG1405 169 --VS-KKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLS-DEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLA 244 (285)
T ss_pred --CC-HHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCC-HHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHH
Confidence 45 99999999999999998888899999999999999776 478889999999998877778999999999999999
Q ss_pred HHHhCCCCCCcchHHHHhhcCCCHHHHHHHHHHHHHH
Q 036944 200 CRLLYPNEYNQCERDILATKHIKEEELESCLKRTYEM 236 (370)
Q Consensus 200 ~~~l~~~~~~~~~~~l~~~~~~~~e~L~~C~~~m~~l 236 (370)
....+... -.+.+..++|+++..|+.-++.|.+-
T Consensus 245 s~l~~~~~---tq~eva~v~~vtevTIrnrykel~~~ 278 (285)
T COG1405 245 SLLLGERR---TQKEVAKVAGVTEVTIRNRYKELADA 278 (285)
T ss_pred HHHhCCch---HHHHHHHHhCCeeeHHHHHHHHHHHh
Confidence 99887432 36778899999999999888766553
No 18
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.84 E-value=1.8e-07 Score=89.38 Aligned_cols=178 Identities=17% Similarity=0.153 Sum_probs=144.5
Q ss_pred HHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCchhHHhhcCCCCCCcH
Q 036944 46 LNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRFIYFERDNNLNEDYK 125 (370)
Q Consensus 46 vdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl~~l~~~~~~~yt~~ 125 (370)
..-+..+++..+|+....-.|-.+|.++-..+... .....-++++||+||++-++....+.++..-.+ -+ +
T Consensus 108 ~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lr------Gks~eai~AAclyiACRq~~~pRT~kEI~~~an--v~-k 178 (308)
T KOG1597|consen 108 FKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLR------GKSVEALAAACLYIACRQEDVPRTFKEISAVAN--VS-K 178 (308)
T ss_pred HHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhc------CccHHHHHHHHHHHHHHhcCCCchHHHHHHHHc--CC-H
Confidence 34456779999999999999999999999776665 666899999999999998887777888764433 46 9
Q ss_pred HHHHHHHHHHHHHcCCcccccC--hHHHHHHHHhhCCCChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHHh
Q 036944 126 RHILSMELQILKGINWRLRAVT--AMYFKEFFVGKIPVGKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRLL 203 (370)
Q Consensus 126 ~~Il~mE~~IL~~L~w~L~~pT--p~~Fl~~fl~~l~~~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~l 203 (370)
++|-+.=+.|++.|+=.+...+ .-+|+.+|...+.-.. .....|.++.+.+-.-.....-.|=.||||+||++....
T Consensus 179 KEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~-~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls 257 (308)
T KOG1597|consen 179 KEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPK-SAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLS 257 (308)
T ss_pred HHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCH-HHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhc
Confidence 9999999999999988877666 8899999999987655 455677777777664444556889999999999999876
Q ss_pred CCCCCCcchHHHHhhcCCCHHHHHHHHHHHHHH
Q 036944 204 YPNEYNQCERDILATKHIKEEELESCLKRTYEM 236 (370)
Q Consensus 204 ~~~~~~~~~~~l~~~~~~~~e~L~~C~~~m~~l 236 (370)
.... -.+.+...+|+.+..|+.-++.|...
T Consensus 258 ~~kk---t~keI~~vtgVaE~TIr~sYK~Lyp~ 287 (308)
T KOG1597|consen 258 DEKK---TQKEIGEVTGVAEVTIRNSYKDLYPH 287 (308)
T ss_pred cCcc---cHHHHHHHhhhhHHHHHHHHHHHhhc
Confidence 5333 26788889999999999999888764
No 19
>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=98.43 E-value=1.3e-06 Score=66.78 Aligned_cols=80 Identities=18% Similarity=0.187 Sum_probs=68.9
Q ss_pred HHHHHHhhCCCChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHHhCCCCCCcchHHHHhhcCC-CHHHHHHH
Q 036944 151 FKEFFVGKIPVGKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRLLYPNEYNQCERDILATKHI-KEEELESC 229 (370)
Q Consensus 151 Fl~~fl~~l~~~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~~~-~~e~L~~C 229 (370)
|+..+...++... .+...|.++++.++.+..+..++|+.||+||+++|.+..+.. .|.+.+..++|+ +.++|.+|
T Consensus 2 ~l~~~~~~~~~~~-~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~---~~~~~~~~~~~~~~~~~i~~~ 77 (83)
T smart00385 2 FLRRVCKALNLDP-ETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIP---PWTKELVHYTGYFTEEEILRM 77 (83)
T ss_pred HHHHHHHHcCCCH-HHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCC---CCchhHhHhhCCCCHHHHHHH
Confidence 6777777776544 688899999999999889999999999999999999988754 377888999999 99999999
Q ss_pred HHHHH
Q 036944 230 LKRTY 234 (370)
Q Consensus 230 ~~~m~ 234 (370)
.+.|.
T Consensus 78 ~~~il 82 (83)
T smart00385 78 EKLLL 82 (83)
T ss_pred HHHHh
Confidence 88764
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=98.41 E-value=2.9e-06 Score=65.39 Aligned_cols=85 Identities=16% Similarity=0.095 Sum_probs=74.8
Q ss_pred ccChHHHHHHHHhhCCCChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHHhCCCCCCcchHHHHhhcCC-CH
Q 036944 145 AVTAMYFKEFFVGKIPVGKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRLLYPNEYNQCERDILATKHI-KE 223 (370)
Q Consensus 145 ~pTp~~Fl~~fl~~l~~~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~~~-~~ 223 (370)
.+++.+|+..+...++... .....|.++++.++....+..+.|+.||+||+++|.+..+. +.|.+.+..++++ +.
T Consensus 2 ~~~~~~~l~~~~~~~~~~~-~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~---~~~~~~~~~~~~~~~~ 77 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSP-ETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEI---PPWLKDLVHVTGYATE 77 (88)
T ss_pred cchHHHHHHHHHHHcCCCH-HHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCC---CCCHHHHhHHhCCCCH
Confidence 5789999999999986654 67789999999999999999999999999999999998765 3478999999999 99
Q ss_pred HHHHHHHHHH
Q 036944 224 EELESCLKRT 233 (370)
Q Consensus 224 e~L~~C~~~m 233 (370)
++|.++.+.+
T Consensus 78 ~~i~~~e~~i 87 (88)
T cd00043 78 EEILRMEKLL 87 (88)
T ss_pred HHHHHHHHHh
Confidence 9999888765
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=98.18 E-value=9.6e-06 Score=71.27 Aligned_cols=93 Identities=16% Similarity=0.177 Sum_probs=67.4
Q ss_pred HHHHHHHHhHHhcCCCchHHHHHHHHHHHHhc---CCccCCcccCccccchhhHHHHHHHHHHhhccCC-chhHHhhcCC
Q 036944 44 VALNVILKNSKCFNFDAFIPYLAMNYFDLFIS---RNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAF-RFIYFERDNN 119 (370)
Q Consensus 44 ~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs---~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~-pl~~l~~~~~ 119 (370)
.+.+|+.++...-+++++++.+|..|+||+.. ...+. .. ....+-+-++|+.+|+|+-+-.. +...+..-.+
T Consensus 53 ~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~-~~---~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~g 128 (149)
T PF08613_consen 53 SIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIP-LN---SSNIHRLFLTALILASKFLDDNTYSNKSWAKVGG 128 (149)
T ss_dssp -HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT----S---TTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHT
T ss_pred cHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccc-cc---cchhHHHHHHHHHHHHhhcccccccHHHHHhhcC
Confidence 37889999999999999999999999999998 22222 11 45577889999999999987664 5455543333
Q ss_pred CCCCcHHHHHHHHHHHHHHcCCcc
Q 036944 120 LNEDYKRHILSMELQILKGINWRL 143 (370)
Q Consensus 120 ~~yt~~~~Il~mE~~IL~~L~w~L 143 (370)
++ .+++-+||+..|..|+|+|
T Consensus 129 --is-~~eln~lE~~fL~~l~~~L 149 (149)
T PF08613_consen 129 --IS-LKELNELEREFLKLLDYNL 149 (149)
T ss_dssp --S--HHHHHHHHHHHHHHTTT--
T ss_pred --CC-HHHHHHHHHHHHHHCCCcC
Confidence 67 9999999999999999986
No 22
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=97.83 E-value=1.6e-05 Score=78.69 Aligned_cols=100 Identities=17% Similarity=0.291 Sum_probs=83.3
Q ss_pred HHHHHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCC-chhHHh--
Q 036944 39 ATLRKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAF-RFIYFE-- 115 (370)
Q Consensus 39 ~~~R~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~-pl~~l~-- 115 (370)
+++|. +=.-|.+++..-++...|+++|.+||.....+..+. +.+-.|.|-+||++|+|+.+..- .++.++
T Consensus 380 SKirS-lKREMr~l~~d~~id~~TVa~AyVYFEKliLkglis------K~NRKlcAGAclLlaaKmnD~Kks~vKslIek 452 (497)
T KOG4164|consen 380 SKIRS-LKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLIS------KQNRKLCAGACLLLAAKMNDLKKSTVKSLIEK 452 (497)
T ss_pred HHHHH-HHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhh------hhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHH
Confidence 45554 344577888888999999999999999999999888 89999999999999999997654 355553
Q ss_pred hcCCCCCCcHHHHHHHHHHHHHHcCCccccc
Q 036944 116 RDNNLNEDYKRHILSMELQILKGINWRLRAV 146 (370)
Q Consensus 116 ~~~~~~yt~~~~Il~mE~~IL~~L~w~L~~p 146 (370)
.++.+.+. +.+++..|.-||.+|.|.|+.|
T Consensus 453 ~Ee~fR~n-rrdLia~Ef~VlvaLefaL~~~ 482 (497)
T KOG4164|consen 453 LEEQFRLN-RRDLIAFEFPVLVALEFALHLP 482 (497)
T ss_pred HHHHhccc-HHhhhhhhhhHHHhhhhhccCC
Confidence 34456678 9999999999999999999875
No 23
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=97.36 E-value=0.0016 Score=67.16 Aligned_cols=171 Identities=20% Similarity=0.187 Sum_probs=124.2
Q ss_pred HHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCchhHH---hhcCCCCCCc
Q 036944 48 VILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRFIYF---ERDNNLNEDY 124 (370)
Q Consensus 48 Wl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl~~l---~~~~~~~yt~ 124 (370)
-|-+++..+++.. .+-.|.++|.--+..+-.+ ....+++-.+||||++..|-+..=+.|| ..- + .|.
T Consensus 73 ~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftk------Gr~~~~vvasClY~vcR~e~t~hlliDfS~~Lqv-~-Vy~- 142 (521)
T KOG1598|consen 73 LIEELTERLNLGN-KTEVAFNFFKLAPDRNFTK------GRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQV-S-VYD- 142 (521)
T ss_pred HHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCC------CcchHHHHHHHHHHHHHhhCCceEEEEeccceEE-e-hhh-
Confidence 5678899999999 8889999999999888777 5668999999999999988765433333 111 1 122
Q ss_pred HHHHHHHHHHHHHHcCCc---ccccChHHHHHHHHhhCC--CChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHH
Q 036944 125 KRHILSMELQILKGINWR---LRAVTAMYFKEFFVGKIP--VGKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTA 199 (370)
Q Consensus 125 ~~~Il~mE~~IL~~L~w~---L~~pTp~~Fl~~fl~~l~--~~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA 199 (370)
+=.+=+.+...|.=. +-...|.-|+..|...+. ...+.+...|..|+.....|.-...-+|+-|.-|||++|
T Consensus 143 ---LG~~~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliA 219 (521)
T KOG1598|consen 143 ---LGSNFLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIA 219 (521)
T ss_pred ---hhHHHHHHHHHhccccccccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHH
Confidence 222223444555544 556778889999988872 233568889999999999999999999999999999999
Q ss_pred HHHhCCCCCCcchHHHHhhcCCCHHHHHHHHHHHH
Q 036944 200 CRLLYPNEYNQCERDILATKHIKEEELESCLKRTY 234 (370)
Q Consensus 200 ~~~l~~~~~~~~~~~l~~~~~~~~e~L~~C~~~m~ 234 (370)
++..+... -...+..+..+....|.+=+..+.
T Consensus 220 ar~h~~~r---si~dIv~vvhV~e~Tl~kRl~Ef~ 251 (521)
T KOG1598|consen 220 ARMHGFRR---TIGDIAKVVHVCESTLSKRLKEFS 251 (521)
T ss_pred HHHcCccc---cHHHHHHHHHHhHHHHHHHHHHHh
Confidence 99876532 245566666666666655554443
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=96.48 E-value=0.017 Score=43.99 Aligned_cols=61 Identities=13% Similarity=0.077 Sum_probs=49.8
Q ss_pred HHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCchhHHh
Q 036944 49 ILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRFIYFE 115 (370)
Q Consensus 49 l~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl~~l~ 115 (370)
|-+++..++|+..+.-.|..++++-....-.. .....-++++|+++|++.+....++.++.
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~------Gr~~~~iaAA~iY~acr~~~~~~t~~eIa 61 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLK------GRSPESIAAACIYLACRLNGVPRTLKEIA 61 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTST------TS-HHHHHHHHHHHHHHHTTSSSSHHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcc------cCCHHHHHHHHHHHHHHHcCCCcCHHHHH
Confidence 35789999999999999999999998877665 55588999999999999998877877774
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=96.26 E-value=0.04 Score=41.98 Aligned_cols=70 Identities=21% Similarity=0.252 Sum_probs=51.8
Q ss_pred HHHHhhCCCChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHHhCCCCCCcchHHHHhhcCCCHHHH
Q 036944 153 EFFVGKIPVGKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRLLYPNEYNQCERDILATKHIKEEEL 226 (370)
Q Consensus 153 ~~fl~~l~~~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~~~~~e~L 226 (370)
..|...++-.. .+...|..+...+......-.-+|..||+||||+|++..+... -.+.+...+|++..+|
T Consensus 2 ~r~~~~L~L~~-~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~---t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 2 PRICSKLGLPE-DVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPR---TLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHTT--H-HHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSS---SHHHHHHHCTSSHHHH
T ss_pred hHHHhHcCCCH-HHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCc---CHHHHHHHhCCCCCcC
Confidence 45555655443 6788999998888766666678899999999999999876543 2678888899887654
No 26
>KOG1674 consensus Cyclin [General function prediction only]
Probab=95.21 E-value=0.076 Score=49.73 Aligned_cols=99 Identities=16% Similarity=0.161 Sum_probs=70.7
Q ss_pred HHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCc---cCCcccCcccc-chhhHHHHHHHHHHhhccCC-chhHHhhcCC
Q 036944 45 ALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQ---LPNVLGRVRDD-IVLAAICCLTLAWKVRNQAF-RFIYFERDNN 119 (370)
Q Consensus 45 lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~---v~~~~~~~~~~-lqLiavtCL~IAsKvEE~~~-pl~~l~~~~~ 119 (370)
+-+++..+..+-+.+++++.+|..|||||..+.. +.......-.. ..=+-++|+.+|+|+.+..- .-..+..-++
T Consensus 78 i~~yleri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~y~n~~~a~vgg 157 (218)
T KOG1674|consen 78 IRQYLERIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVYYSNAYYAKVGG 157 (218)
T ss_pred hHHHHHHHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccchhhhHHHHHHhCC
Confidence 4456678888888999999999999999998733 11111110112 33478999999999996543 3333333233
Q ss_pred CCCCcHHHHHHHHHHHHHHcCCccccc
Q 036944 120 LNEDYKRHILSMELQILKGINWRLRAV 146 (370)
Q Consensus 120 ~~yt~~~~Il~mE~~IL~~L~w~L~~p 146 (370)
.+ .+++-.+|...|..++|++.+.
T Consensus 158 --l~-~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 158 --LT-TDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred --CC-hHhhhhhhHHHHhhCCeEEEec
Confidence 56 8999999999999999999985
No 27
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=94.26 E-value=0.33 Score=47.78 Aligned_cols=88 Identities=3% Similarity=-0.039 Sum_probs=69.1
Q ss_pred HHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCchhHHhhcCCCCCCcH
Q 036944 46 LNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRFIYFERDNNLNEDYK 125 (370)
Q Consensus 46 vdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl~~l~~~~~~~yt~~ 125 (370)
-+++...+..++++..+.-.|..++.+.....-.. ...+.-||++|+|||++..+...++.++..-.. -+ .
T Consensus 220 ~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~------Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~--Vs-~ 290 (310)
T PRK00423 220 IDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTS------GKGPTGLAAAAIYIASLLLGERRTQREVAEVAG--VT-E 290 (310)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccc------CCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcC--CC-H
Confidence 58888999999999999999999999887655444 556899999999999999887767777743322 45 7
Q ss_pred HHHHHHHHHHHHHcCCc
Q 036944 126 RHILSMELQILKGINWR 142 (370)
Q Consensus 126 ~~Il~mE~~IL~~L~w~ 142 (370)
..|.+.=+.|.+.|+..
T Consensus 291 ~tI~~~ykel~~~l~~~ 307 (310)
T PRK00423 291 VTVRNRYKELAEKLDIK 307 (310)
T ss_pred HHHHHHHHHHHHHhCcc
Confidence 77777777777777653
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=82.30 E-value=17 Score=29.80 Aligned_cols=83 Identities=7% Similarity=0.055 Sum_probs=51.8
Q ss_pred HHHHHHhhCCCChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHHhCCCCCCcchHHHHhhc--CCCHHHHHH
Q 036944 151 FKEFFVGKIPVGKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRLLYPNEYNQCERDILATK--HIKEEELES 228 (370)
Q Consensus 151 Fl~~fl~~l~~~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~--~~~~e~L~~ 228 (370)
|+......++... .....|..+++.-+.........+..+|+||+++|.+..+... -+...+.... .++.++|.+
T Consensus 37 ~i~~~~~~~~l~~-~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~--~~~~~~~~~~~~~~~~~~i~~ 113 (127)
T PF00134_consen 37 WIIELCQRLKLSP-ETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNP--PSISDLIRISDNTFTKKDILE 113 (127)
T ss_dssp HHHHHHHHTT-BH-HHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS----HHHHHHHHTTTSSHHHHHHH
T ss_pred HHHHHHHhcccch-hHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhcccc--chHHHHHHHHcCCCCHHHHHH
Confidence 4444444443333 4556777777777776678889999999999999999865521 1345554444 356677766
Q ss_pred HHHHHHHH
Q 036944 229 CLKRTYEM 236 (370)
Q Consensus 229 C~~~m~~l 236 (370)
.-..+...
T Consensus 114 ~E~~iL~~ 121 (127)
T PF00134_consen 114 MEREILSA 121 (127)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 65555443
No 29
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=80.90 E-value=19 Score=35.09 Aligned_cols=102 Identities=17% Similarity=0.137 Sum_probs=68.1
Q ss_pred HHHHHHHcCCccccc--------ChHHHHHHHHhhCCCChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHHh
Q 036944 132 ELQILKGINWRLRAV--------TAMYFKEFFVGKIPVGKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRLL 203 (370)
Q Consensus 132 E~~IL~~L~w~L~~p--------Tp~~Fl~~fl~~l~~~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~l 203 (370)
+..-|...+....+. +....+..+...++-.. .+...|..+.-.++-.-..-.-+...++|||+|+|++..
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 KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPE-SVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRIN 154 (285)
T ss_pred HHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHhCCCc-hHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHc
Confidence 444455554445554 34455555555554333 456667766666654444445668999999999999987
Q ss_pred CCCCCCcchHHHHhhcCCCHHHHHHHHHHHHHHH
Q 036944 204 YPNEYNQCERDILATKHIKEEELESCLKRTYEMC 237 (370)
Q Consensus 204 ~~~~~~~~~~~l~~~~~~~~e~L~~C~~~m~~l~ 237 (370)
+.... ...+...++++..++..+.+.|.+..
T Consensus 155 ~~prt---l~eIa~a~~V~~kei~rtyr~~~~~L 185 (285)
T COG1405 155 GVPRT---LDEIAKALGVSKKEIGRTYRLLVREL 185 (285)
T ss_pred CCCcc---HHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 65432 67788889999999999999776654
No 30
>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=80.03 E-value=5.2 Score=32.30 Aligned_cols=85 Identities=16% Similarity=0.092 Sum_probs=51.9
Q ss_pred HHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCch-hHHhhcCCCCCCc
Q 036944 46 LNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRF-IYFERDNNLNEDY 124 (370)
Q Consensus 46 vdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl-~~l~~~~~~~yt~ 124 (370)
.+||.......+.+.++..+|-.+++-.+....+- .-..-+||++|+++|.+.-....+. ..+....+ |+
T Consensus 4 ~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl------~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~--~~- 74 (118)
T PF02984_consen 4 YDFLRRFLKISNADQEVRNLARYLLELSLLDYEFL------QYPPSVIAAAAILLARKILGKEPPWPESLEKLTG--YD- 74 (118)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHT------TS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHT--S--
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhcccc------CCCHHHHHHHHHHHHHHHhCccccCCccchhhcC--CC-
Confidence 34555553333445668888888888777666554 4458899999999999997642332 22222112 56
Q ss_pred HHHHHHHHHHHHHHc
Q 036944 125 KRHILSMELQILKGI 139 (370)
Q Consensus 125 ~~~Il~mE~~IL~~L 139 (370)
.++|..+=..|.+.+
T Consensus 75 ~~~l~~c~~~i~~~~ 89 (118)
T PF02984_consen 75 KEDLKECIELIQELL 89 (118)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 777777655555444
No 31
>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=79.10 E-value=23 Score=28.46 Aligned_cols=75 Identities=12% Similarity=0.055 Sum_probs=52.1
Q ss_pred hHHHHHHHHHHHHHhcccccccCcchHHHHHH-HHHHHHHHhCCCCCC--cchHHHHhhcCCCHHHHHHHHHHHHHHH
Q 036944 163 KGIMRRTLNEIIIQAQGDINFTQYKPSVMAAS-SLLTACRLLYPNEYN--QCERDILATKHIKEEELESCLKRTYEMC 237 (370)
Q Consensus 163 ~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaA-aI~lA~~~l~~~~~~--~~~~~l~~~~~~~~e~L~~C~~~m~~l~ 237 (370)
...+......++..++.+..--..+||.||+| |-++......+.... .....+...+|++...+...++.+..-.
T Consensus 22 L~~~H~~V~~~v~KAiV~P~TG~Lp~SlvaAA~CAL~~~~~~~P~~~~~~~~~~~LA~~~G~~~a~L~AA~E~v~Tt~ 99 (106)
T PF09080_consen 22 LFAWHSEVVESVHKAIVNPKTGGLPPSLVAAAGCALFSLGAAAPPDTHSGGVVPQLAEALGVSAATLQAAAESVATTL 99 (106)
T ss_dssp HHHHHHHHHHHHHHHHCSTTGGGS-HHHHHHHHHHHHS-GGGS--------HHHHHHHHHT--HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhcCcccCCCCHHHHHHhhhhhccccccCCCccccccchHHHHHHhCccHHHHHHHHHHHHHHH
Confidence 34567778889999999999999999999999 777766554443111 1345788899999999999988876643
No 32
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=78.73 E-value=15 Score=35.85 Aligned_cols=68 Identities=24% Similarity=0.317 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHHhccccccc-CcchHHHHHHHHHHHHHHhCCCCCCcchHHHHhhcCCCHHHHHHHHHHHHHH
Q 036944 165 IMRRTLNEIIIQAQGDINFT-QYKPSVMAASSLLTACRLLYPNEYNQCERDILATKHIKEEELESCLKRTYEM 236 (370)
Q Consensus 165 ~l~~~a~~ll~~sl~d~~~l-~y~PS~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~~~~~e~L~~C~~~m~~l 236 (370)
.+...|.++....- +..++ .-.--.||||||+.|++..+... -.+.+..+.+++..+|-+|++.+.+-
T Consensus 123 ~I~d~A~~ifk~v~-~~k~lrGks~eai~AAclyiACRq~~~pR---T~kEI~~~anv~kKEIgr~~K~i~~~ 191 (308)
T KOG1597|consen 123 TIKDRANEIFKLVE-DSKLLRGKSVEALAAACLYIACRQEDVPR---TFKEISAVANVSKKEIGRCVKLIGEA 191 (308)
T ss_pred HHHHHHHHHHHHHH-HhhhhcCccHHHHHHHHHHHHHHhcCCCc---hHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 45666766655543 44344 34556799999999999866532 24677778999999999999988765
No 33
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=74.28 E-value=5.3 Score=39.68 Aligned_cols=87 Identities=15% Similarity=0.019 Sum_probs=54.6
Q ss_pred HHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCchh-HH--h--hc
Q 036944 43 KVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRFI-YF--E--RD 117 (370)
Q Consensus 43 ~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl~-~l--~--~~ 117 (370)
.-+++++..+-...+.......+|-+++...+...-+- +-..+-||++|++||+|+-....|.. +- . .+
T Consensus 153 ~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL------~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d 226 (323)
T KOG0834|consen 153 KYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCL------QYSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFD 226 (323)
T ss_pred HHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeE------eecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhc
Confidence 34666666666555555556677888887777555443 44588899999999999988765531 11 1 12
Q ss_pred CCCCCCcHHHHHHHHHHHHHH
Q 036944 118 NNLNEDYKRHILSMELQILKG 138 (370)
Q Consensus 118 ~~~~yt~~~~Il~mE~~IL~~ 138 (370)
.+ .+ .+.+.++...+|..
T Consensus 227 ~~--vt-~e~l~~i~~~~l~~ 244 (323)
T KOG0834|consen 227 ET--VT-NELLDDICHEFLDL 244 (323)
T ss_pred cc--CC-HHHHHHHHHHHHHH
Confidence 12 45 66666655554443
No 34
>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=66.75 E-value=53 Score=26.14 Aligned_cols=90 Identities=13% Similarity=0.075 Sum_probs=65.1
Q ss_pred hHHHHHHHHhhCCC---ChHHHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHHhCCC--CCCcchHHHHhhcCCC
Q 036944 148 AMYFKEFFVGKIPV---GKGIMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRLLYPN--EYNQCERDILATKHIK 222 (370)
Q Consensus 148 p~~Fl~~fl~~l~~---~~~~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~l~~~--~~~~~~~~l~~~~~~~ 222 (370)
..+|+-...+.+.- ....+...+..-+..++...+....+|-.|.|+.++...+.-+.+ .|..+.+.+..++++.
T Consensus 4 ~tdflip~c~alkipe~~wpql~e~~s~tickaliqpniall~p~licaggllttiet~ntn~~~wt~yledl~~ilnfs 83 (106)
T PF09241_consen 4 STDFLIPVCHALKIPEDFWPQLFEATSITICKALIQPNIALLPPCLICAGGLLTTIETDNTNCQPWTCYLEDLSCILNFS 83 (106)
T ss_dssp GGGGHHHHHHHTT--GGGHHHHHHHHHHHHHHHTTSGGGGGS-HHHHHHHHHHHHHHTS-TSSSTCHHHHHHHHHHHTCH
T ss_pred hhhhHHHhhhhccCcHHHhHHHHHHHHHHHHHHHcCCCccccCcceeecccceEEEeccCCCCcchhhhHHhhHHHhhcc
Confidence 34666666666632 234577777777888899999999999999999999999875443 4445566667788898
Q ss_pred HHHHHHHHHHHHHHH
Q 036944 223 EEELESCLKRTYEMC 237 (370)
Q Consensus 223 ~e~L~~C~~~m~~l~ 237 (370)
-..++..-+++.+..
T Consensus 84 tntirt~kdqv~ea~ 98 (106)
T PF09241_consen 84 TNTIRTVKDQVSEAF 98 (106)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred cchhhhHHHHHHHHH
Confidence 888888887777653
No 35
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=66.46 E-value=8.9 Score=37.72 Aligned_cols=87 Identities=11% Similarity=0.158 Sum_probs=54.3
Q ss_pred CchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCC--chh--HHhhcCCCCCCcHHHHHHHHHH
Q 036944 59 DAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAF--RFI--YFERDNNLNEDYKRHILSMELQ 134 (370)
Q Consensus 59 ~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~--pl~--~l~~~~~~~yt~~~~Il~mE~~ 134 (370)
..+.--....|++|-+--..... - ......+.....++|+|+-.... .+. .+..+ -+ .+++.+||+.
T Consensus 207 ta~~aiitL~~~erl~~~~e~~~-~---p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlKd----~t-veDmNe~ERq 277 (343)
T KOG1675|consen 207 TAECDIITLVYAERLLWLAERDP-C---PRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILKD----QS-VDDMNALERQ 277 (343)
T ss_pred hhccchHHHHhhHhhhhHhhcCC-C---cchhhhhhhhhheehhhhhhhhhcccHHHHHHHhh----cc-HhhHHHHHHH
Confidence 33333445688888774332220 0 22244455556999999976542 232 22344 34 9999999999
Q ss_pred HHHHcCCcccccChHHHHHHH
Q 036944 135 ILKGINWRLRAVTAMYFKEFF 155 (370)
Q Consensus 135 IL~~L~w~L~~pTp~~Fl~~f 155 (370)
+|+.|+|++++|..- |..+|
T Consensus 278 fLelLqfNinvp~sv-YAKyY 297 (343)
T KOG1675|consen 278 FLELLQFNINVPSSE-YAKYY 297 (343)
T ss_pred HHHHHhhccCccHHH-HHHHH
Confidence 999999999988643 34444
No 36
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=53.14 E-value=97 Score=30.54 Aligned_cols=40 Identities=13% Similarity=0.193 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHhcccccccCcchHHHHHHHHHHHHHHhC
Q 036944 165 IMRRTLNEIIIQAQGDINFTQYKPSVMAASSLLTACRLLY 204 (370)
Q Consensus 165 ~l~~~a~~ll~~sl~d~~~l~y~PS~IAaAaI~lA~~~l~ 204 (370)
.+...|..+...-.....+..|.|..||++|+++|.+.-+
T Consensus 77 ~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE 116 (305)
T TIGR00569 77 SVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEE 116 (305)
T ss_pred hHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccc
Confidence 4556666666666666777889999999999999998654
No 37
>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=41.86 E-value=2.3e+02 Score=24.46 Aligned_cols=88 Identities=10% Similarity=0.072 Sum_probs=51.2
Q ss_pred cChHHHHHHHHhhCCCChHHHHHHHHHHHHHhcc-----cccccCcchHHHHHHHHHHHHHHhCCCCCCcchHHHHhhcC
Q 036944 146 VTAMYFKEFFVGKIPVGKGIMRRTLNEIIIQAQG-----DINFTQYKPSVMAASSLLTACRLLYPNEYNQCERDILATKH 220 (370)
Q Consensus 146 pTp~~Fl~~fl~~l~~~~~~l~~~a~~ll~~sl~-----d~~~l~y~PS~IAaAaI~lA~~~l~~~~~~~~~~~l~~~~~ 220 (370)
.+-.+|+..+..........+ -.|-.+++.... ....-.....-+-++|+.+|.+.+.... .+.+.|..+.|
T Consensus 52 i~i~~fl~ri~~~~~~s~~~~-i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~--~~n~~~a~v~g 128 (149)
T PF08613_consen 52 ISIRDFLSRILKYTQCSPECL-ILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNT--YSNKSWAKVGG 128 (149)
T ss_dssp S-HHHHHHHHHHHTT--HHHH-HHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS-----HHHHHHHHT
T ss_pred CcHHHHHHHHHHHcCCChHHH-HHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhccccc--ccHHHHHhhcC
Confidence 445567888777765544333 333333333222 1223355677889999999999986543 35788999999
Q ss_pred CCHHHHHHHHHHHHHH
Q 036944 221 IKEEELESCLKRTYEM 236 (370)
Q Consensus 221 ~~~e~L~~C~~~m~~l 236 (370)
++.++|...=..+..+
T Consensus 129 is~~eln~lE~~fL~~ 144 (149)
T PF08613_consen 129 ISLKELNELEREFLKL 144 (149)
T ss_dssp S-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHH
Confidence 9988887665555444
No 38
>COG5225 RRS1 Uncharacterized protein involved in ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=41.55 E-value=4.2 Score=35.43 Aligned_cols=54 Identities=24% Similarity=0.442 Sum_probs=47.2
Q ss_pred ccCCCcchhccCCCCCCCcccccccc-ccCccccCCCCCCCCCCcceeEEeeeec
Q 036944 267 MLSKDPLQDILHRPGKGPIQEISEIV-LEIPETRMEPDESDNEPGLSFELKWRLW 320 (370)
Q Consensus 267 ~~s~d~~~~~~~~~g~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 320 (370)
+++.|++|+..+..-+-|+-..|.+| +|.||+-..---++.+|--+.|-||.-+
T Consensus 42 sL~rdnVQ~l~nql~slp~~rtsd~VllqLPe~tt~lPR~kplpk~k~eTkWerF 96 (172)
T COG5225 42 SLKRDNVQELKNQLCSLPARRTSDLVLLQLPESTTALPREKPLPKEKIETKWERF 96 (172)
T ss_pred hhhHHHHHHHHHHHhcCchhcccceeEEeCCCccccCcccccccccchHHHHHHH
Confidence 34568999999999999999999999 9999998877778889999999999654
No 39
>KOG1992 consensus Nuclear export receptor CSE1/CAS (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=31.81 E-value=8.1e+02 Score=27.83 Aligned_cols=189 Identities=15% Similarity=0.111 Sum_probs=98.9
Q ss_pred HHHHHHHHHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccC--C----c--
Q 036944 39 ATLRKVALNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQA--F----R-- 110 (370)
Q Consensus 39 ~~~R~~lvdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~--~----p-- 110 (370)
-.-|+..+|.+..++..|.-.-.+++. .++.|.+...+-.....|.+++.-+.- |.-+|.|.++.. + +
T Consensus 376 dTRRR~a~dlvrgL~~~fe~~vt~v~~--~~v~~~l~~y~~nPS~nWk~kd~aiyL--~talaik~~t~~~Gvtstn~lv 451 (960)
T KOG1992|consen 376 DTRRRAAIDLVRGLCKNFEGQVTGVFS--SEVQRLLDQYSKNPSGNWKKKDRAIYL--VTALAIKGQTAKHGVTSTNELV 451 (960)
T ss_pred chhHHHHHHHHHHHHHHhcchhHHHHH--HHHHHHHHHhccCCCccccccchhhhh--hHHHHhhcchhhcceeeccccc
Confidence 456999999999999999766555554 455666654444444556555544433 445788877653 2 1
Q ss_pred -hhHHhhcCCCCCCcHHHHHH---HHHHHHH--HcCC------cccccChHHHHHHHHhhCCCChHHHHHHHHHHHHHhc
Q 036944 111 -FIYFERDNNLNEDYKRHILS---MELQILK--GINW------RLRAVTAMYFKEFFVGKIPVGKGIMRRTLNEIIIQAQ 178 (370)
Q Consensus 111 -l~~l~~~~~~~yt~~~~Il~---mE~~IL~--~L~w------~L~~pTp~~Fl~~fl~~l~~~~~~l~~~a~~ll~~sl 178 (370)
+.+|....- ..++.. .|.-||+ .++| .+........+...+..+......++.+|..-++.-+
T Consensus 452 dv~~Ff~~~i-----lp~L~s~~vn~~pilka~aIKy~~~FR~ql~~~~lm~~~p~li~~L~a~s~vvhsYAA~aiEkil 526 (960)
T KOG1992|consen 452 DVVDFFANQI-----LPDLLSPNVNEFPILKADAIKYIYTFRNQLGKEHLMALLPRLIRFLEAESRVVHSYAAIAIEKLL 526 (960)
T ss_pred cHHHHHHHHh-----hHHhccCccccccchhhcccceeeeecccCChHHHHHHHHHHHHhccCcchHHHHHHHHHHHhcc
Confidence 223311000 111111 1111221 1222 3444455566666666666655578888888887765
Q ss_pred cccc---ccCcchHHHH---HHHHHHHHHHhCCC--CCCc-chHHHHhhcCCCHHHH----HHHHHHHHHH
Q 036944 179 GDIN---FTQYKPSVMA---ASSLLTACRLLYPN--EYNQ-CERDILATKHIKEEEL----ESCLKRTYEM 236 (370)
Q Consensus 179 ~d~~---~l~y~PS~IA---aAaI~lA~~~l~~~--~~~~-~~~~l~~~~~~~~e~L----~~C~~~m~~l 236 (370)
.-.. -..|.|-.|| .-.+.-..+.+... .-++ ..+.+...+++..+.+ -.|+..+.++
T Consensus 527 ~vre~~~~~if~~~~iap~~~~ll~nLf~a~s~p~~~EneylmKaImRii~i~~~~i~p~~~~~l~~Ltei 597 (960)
T KOG1992|consen 527 TVRENSNAKIFGAEDIAPFVEILLTNLFKALSLPGKAENEYLMKAIMRIISILQSAIIPHAPELLRQLTEI 597 (960)
T ss_pred ccccCccccccchhhcchHHHHHHHHHHHhccCCcccccHHHHHHHHHHHHhCHHhhhhhhhHHHHHHHHH
Confidence 4222 2345555555 22222222332222 1112 2455667777777766 3555556555
No 40
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=31.66 E-value=1.9e+02 Score=28.93 Aligned_cols=24 Identities=21% Similarity=0.151 Sum_probs=20.4
Q ss_pred cccchhhHHHHHHHHHHhhccCCc
Q 036944 87 RDDIVLAAICCLTLAWKVRNQAFR 110 (370)
Q Consensus 87 ~~~lqLiavtCL~IAsKvEE~~~p 110 (370)
+.....||++|.++|+..+|+..|
T Consensus 179 ry~pe~iACaciyLaAR~~eIpLp 202 (367)
T KOG0835|consen 179 RYSPESIACACIYLAARNLEIPLP 202 (367)
T ss_pred ecCHHHHHHHHHHHHHhhhcCCCC
Confidence 556789999999999999996644
No 41
>PF03261 CDK5_activator: Cyclin-dependent kinase 5 activator protein; InterPro: IPR004944 These proteins are neuron specific activators of cyclin-dependent kinase 5 (CDK5) []. They form a heterodimer with the catalytic subunit (CDK5) [].; GO: 0016534 cyclin-dependent protein kinase 5 activator activity, 0016533 cyclin-dependent protein kinase 5 holoenzyme complex; PDB: 3O0G_D 1H4L_E 1UNH_D 1UNL_E 1UNG_E.
Probab=31.51 E-value=1.2e+02 Score=30.37 Aligned_cols=64 Identities=16% Similarity=0.356 Sum_probs=36.6
Q ss_pred cccchhhHHHHHHHHHHhhccC--CchhHHhhcCCCCCCcHHHHHHHHHHHHHHcCCccc--ccChHHHHHHH
Q 036944 87 RDDIVLAAICCLTLAWKVRNQA--FRFIYFERDNNLNEDYKRHILSMELQILKGINWRLR--AVTAMYFKEFF 155 (370)
Q Consensus 87 ~~~lqLiavtCL~IAsKvEE~~--~pl~~l~~~~~~~yt~~~~Il~mE~~IL~~L~w~L~--~pTp~~Fl~~f 155 (370)
..++|-+-.|||+||--|-... .|++-|..+.+ ++.+.+-=..|+..+.=++- -..|..|-+-|
T Consensus 269 ~~~l~~~~l~cly~sysy~gneisyplkpflv~~~-----~~~fw~~~~~~~~~~s~~ml~~n~~~~~ft~~~ 336 (346)
T PF03261_consen 269 ERELQAIVLTCLYLSYSYMGNEISYPLKPFLVEES-----KEAFWDRCLSIINRLSAKMLRINADPHFFTEVF 336 (346)
T ss_dssp HHHHHHHHHHHHHHHHHHH-SSS---SGGG--SS------HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhhcCcccccccCCeeeccc-----HHHHHHHHHHHHHHhhHHHhhhcCCCchHHHHH
Confidence 5679999999999999987655 47877766644 55555544455544433322 13355555544
No 42
>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=25.99 E-value=2.4e+02 Score=24.30 Aligned_cols=65 Identities=8% Similarity=0.094 Sum_probs=45.9
Q ss_pred HHHHHHhHHhcCCCchHHHHHHHHHHHHhcCCccCCcccCccccchhhHHHHHHHHHHhhccCCchhHH
Q 036944 46 LNVILKNSKCFNFDAFIPYLAMNYFDLFISRNQLPNVLGRVRDDIVLAAICCLTLAWKVRNQAFRFIYF 114 (370)
Q Consensus 46 vdWl~~V~~~~~l~~eTl~lAv~y~DRfLs~~~v~~~~~~~~~~lqLiavtCL~IAsKvEE~~~pl~~l 114 (370)
..-+.++|..++++.+..-..-..|+..+.... .--+ ..++--+-++|+++-+|+....++..++
T Consensus 15 ~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t-~L~~---dRHLDQiilCaiY~i~Kv~~~~~sF~~I 79 (135)
T PF01857_consen 15 AVRLQDLCERLDLSSDLREKIWTCFEHSLTHHT-ELMK---DRHLDQIILCAIYGICKVSKEELSFKDI 79 (135)
T ss_dssp HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSG-GGGT---TS-HHHHHHHHHHHHHHHTT-S--HHHH
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhH-HHHh---cchHHHHHHHHHHHHHHhhcCCCCHHHH
Confidence 344678899999999988888888888885432 1011 5569999999999999998755554554
Done!