Query 017247
Match_columns 375
No_of_seqs 326 out of 1812
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 06:54:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017247.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017247hhsearch_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 1.9E-55 4.1E-60 422.5 23.1 261 13-282 7-268 (335)
2 KOG0655 G1/S-specific cyclin E 100.0 1E-35 2.3E-40 279.4 19.1 214 58-289 113-336 (408)
3 KOG0653 Cyclin B and related k 100.0 9.3E-33 2E-37 276.2 20.7 238 57-308 126-367 (391)
4 COG5024 Cyclin [Cell division 100.0 8.3E-32 1.8E-36 267.8 13.5 234 57-305 180-415 (440)
5 KOG0654 G2/Mitotic-specific cy 99.9 4.3E-28 9.4E-33 235.4 6.6 234 58-304 103-338 (359)
6 TIGR00569 ccl1 cyclin ccl1. Un 99.9 1.1E-22 2.4E-27 196.2 18.2 191 90-288 54-252 (305)
7 PF00134 Cyclin_N: Cyclin, N-t 99.9 1.3E-22 2.8E-27 171.2 11.5 126 60-192 1-127 (127)
8 KOG0834 CDK9 kinase-activating 99.9 8.3E-22 1.8E-26 190.2 14.5 200 88-292 35-249 (323)
9 KOG0835 Cyclin L [General func 99.8 8.3E-20 1.8E-24 172.5 17.6 196 87-290 18-231 (367)
10 KOG0794 CDK8 kinase-activating 99.8 6.3E-20 1.4E-24 165.8 11.3 224 56-291 5-241 (264)
11 COG5333 CCL1 Cdk activating ki 99.7 2E-17 4.3E-22 156.4 13.2 163 89-258 42-210 (297)
12 PRK00423 tfb transcription ini 99.6 3.7E-14 8E-19 138.2 20.5 185 89-288 119-304 (310)
13 PF02984 Cyclin_C: Cyclin, C-t 99.5 1.3E-14 2.7E-19 120.4 5.5 106 194-305 1-106 (118)
14 cd00043 CYCLIN Cyclin box fold 99.4 6.7E-13 1.4E-17 103.1 7.7 87 92-184 2-88 (88)
15 KOG2496 Cdk activating kinase 99.4 1.6E-12 3.4E-17 122.4 9.7 150 98-254 62-222 (325)
16 smart00385 CYCLIN domain prese 99.3 3.5E-12 7.5E-17 98.1 7.4 83 97-185 1-83 (83)
17 COG1405 SUA7 Transcription ini 99.2 1.2E-09 2.5E-14 104.9 16.9 186 89-288 94-279 (285)
18 KOG1597 Transcription initiati 98.9 2.6E-08 5.6E-13 94.0 15.4 186 90-289 102-289 (308)
19 cd00043 CYCLIN Cyclin box fold 98.4 2.3E-06 4.9E-11 66.0 8.8 85 193-284 2-87 (88)
20 smart00385 CYCLIN domain prese 98.4 1.7E-06 3.7E-11 66.0 7.9 81 198-285 1-82 (83)
21 PF08613 Cyclin: Cyclin; Inte 98.2 3.9E-06 8.4E-11 73.4 7.8 93 94-191 53-149 (149)
22 KOG1598 Transcription initiati 98.1 3E-05 6.4E-10 79.0 11.6 176 97-286 72-252 (521)
23 KOG4164 Cyclin ik3-1/CABLES [C 97.9 3.3E-06 7.2E-11 82.5 1.7 101 91-194 381-482 (497)
24 PF00382 TFIIB: Transcription 96.6 0.01 2.2E-07 44.9 7.2 71 200-277 1-71 (71)
25 PF00382 TFIIB: Transcription 96.2 0.016 3.4E-07 43.9 6.1 60 99-162 1-60 (71)
26 PRK00423 tfb transcription ini 94.7 0.21 4.5E-06 48.9 9.7 87 196-289 125-211 (310)
27 KOG1674 Cyclin [General functi 94.6 0.062 1.3E-06 50.0 5.3 97 95-194 78-181 (218)
28 PF09080 K-cyclin_vir_C: K cyc 90.8 2.1 4.6E-05 33.7 8.1 92 198-289 6-100 (106)
29 COG1405 SUA7 Transcription ini 87.7 4.6 9.9E-05 39.1 9.9 86 195-288 99-185 (285)
30 PF09241 Herp-Cyclin: Herpesvi 84.7 7.3 0.00016 30.4 7.6 93 196-289 4-99 (106)
31 KOG0834 CDK9 kinase-activating 82.9 1.3 2.8E-05 43.6 3.6 90 92-185 152-243 (323)
32 PF02984 Cyclin_C: Cyclin, C-t 81.1 2.7 5.8E-05 33.9 4.5 86 96-187 4-89 (118)
33 KOG1597 Transcription initiati 79.0 13 0.00028 36.0 8.7 83 199-289 110-193 (308)
34 PF00134 Cyclin_N: Cyclin, N-t 77.6 15 0.00032 30.1 8.0 82 198-285 36-119 (127)
35 KOG1675 Predicted cyclin [Gene 73.9 2.8 6E-05 40.7 2.8 97 103-204 201-298 (343)
36 KOG0835 Cyclin L [General func 65.0 23 0.00049 34.9 7.0 60 115-180 163-222 (367)
37 TIGR00569 ccl1 cyclin ccl1. Un 63.9 18 0.00038 35.5 6.1 40 216-255 77-116 (305)
38 PF08613 Cyclin: Cyclin; Inte 38.1 1.6E+02 0.0035 25.3 7.5 83 192-280 50-137 (149)
39 KOG3866 DNA-binding protein of 27.5 4.6E+02 0.01 25.9 9.1 24 51-74 255-278 (442)
40 PF13824 zf-Mss51: Zinc-finger 23.1 19 0.00041 26.1 -0.8 11 17-27 24-34 (55)
41 KOG0794 CDK8 kinase-activating 22.3 97 0.0021 29.2 3.4 40 216-255 60-99 (264)
No 1
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.9e-55 Score=422.46 Aligned_cols=261 Identities=44% Similarity=0.717 Sum_probs=230.3
Q ss_pred cccccccccccccchhc-cccccccccCCCCCCCccccccccCCCCcHHHHHHHHHHHHhccCCcccccccCCCcchHHH
Q 017247 13 LLDALYCEEEELEDEVI-DQEDDECSQNKNPACLFSLLLLEQDLFWEDEELLSLFSKEEQQLLKQETQTHYKDSDVLVVA 91 (375)
Q Consensus 13 ~~~~l~c~e~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~e~l~~Ll~kE~~~~~~~~y~~~lq~~~~~~~~ 91 (375)
..|.|+|.|+.+.++-+ ..++ +... ..+. .-.+.++|++|.+.+|+++|.++.|..+|..++++. +++.+
T Consensus 7 ~e~~l~c~E~~~~~~~~~~~~D------~~~~-~~~~-~~~~~~~~~e~~i~~ll~kEe~~~p~~~~~~~~~~~-~~~~~ 77 (335)
T KOG0656|consen 7 MESQLLCHEESTSDEQDRADND------ESST-ESSI-PQLGFLLWDERVLANLLEKEEQHNPSLDYFLCVQKL-ILSSM 77 (335)
T ss_pred cccccccCCCCcccccccccCC------cccc-cccc-cccccccccHHHHHHHHHHHHHhCCCCchhhhcccc-cccHH
Confidence 45679999987765421 1111 0111 1111 111227899999999999999999988888888766 89999
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccceeeeCCCccc
Q 017247 92 RSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDLQVEGAKYVF 171 (375)
Q Consensus 92 R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl~v~~~~~~f 171 (375)
|..+++||++|++++++.++|++||+||||||++.+++++.+|||+||+|+|||+||||+||+.+|.+.|+++.+.+|.|
T Consensus 78 R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~f 157 (335)
T KOG0656|consen 78 RKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVF 157 (335)
T ss_pred HHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHH
Q 017247 172 ETKAIQRMELLVLSTLEWKMHPVTPISFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHII 251 (375)
Q Consensus 172 ~~~~I~~mE~~IL~~L~w~l~~~Tp~~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~ 251 (375)
.+++|+|||++||++|+|||+.+||++|+++|+++++..++....++.+|..++..+..|.+|++|+||+||+|++..+.
T Consensus 158 eaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~ 237 (335)
T KOG0656|consen 158 EAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSVS 237 (335)
T ss_pred cHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999888778899999999999999999999999999999999999
Q ss_pred HHhCCCCCCCcccchhhccCCCHHHHHHHHH
Q 017247 252 DQVEPVNPVDYQNQLLGVLKISKEKVSDCYK 282 (375)
Q Consensus 252 ~~l~~~~~~~~~~~L~~~~~i~~~~l~~C~~ 282 (375)
..+.+.....+...+..+++++++.+.+|+.
T Consensus 238 ~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 238 ASVDGLDFREYENNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred HhhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence 8888777666778888899999999999988
No 2
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1e-35 Score=279.36 Aligned_cols=214 Identities=25% Similarity=0.437 Sum_probs=186.3
Q ss_pred cHHHHHHHHHHHHhccCCcccccccCCCcchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhc-cccccCCchh
Q 017247 58 EDEELLSLFSKEEQQLLKQETQTHYKDSDVLVVARSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRS-FHFQIDKPWM 136 (375)
Q Consensus 58 ~~e~l~~Ll~kE~~~~~~~~y~~~lq~~~~~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~-~~v~~~~~~~ 136 (375)
..|++..|+.||+.+.....++. |..++.+++|++++|||.+||+.|+|.++|+||||.||||||.. ..+.+..
T Consensus 113 ~~eVW~lM~kkee~~l~~~~~l~--qHpdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~--- 187 (408)
T KOG0655|consen 113 SKEVWLLMLKKEERYLRDKHFLE--QHPDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTN--- 187 (408)
T ss_pred HHHHHHHHHccchhhhhhhHHHh--hCCCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhh---
Confidence 45899999999998876542222 34458899999999999999999999999999999999999976 4566666
Q ss_pred HHHHHHHHHHhhhhhcccCCCcccce-eeeCCCccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCCCC----
Q 017247 137 IQLLAVTCLSLAAKVEETQVPLLLDL-QVEGAKYVFETKAIQRMELLVLSTLEWKMHPVTPISFLDHIIRRLGLKT---- 211 (375)
Q Consensus 137 lqLvavaCL~LAaK~eE~~vp~l~dl-~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~FL~~fl~~l~~~~---- 211 (375)
+||+|+||||||||+||+++|.+.+| +++++.| +.++|++||+.||++|+|++.++|..++|..|+...+.++
T Consensus 188 lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAc--s~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n~~~k~ 265 (408)
T KOG0655|consen 188 LQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGAC--SEDDILTMELIILKALKWELSPITIISWLNVYLQVDALNDAPKV 265 (408)
T ss_pred HHHhhHHHHHHHHHHhhccCccccceeeeccCcc--chHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcCCCCce
Confidence 99999999999999999999999999 9999876 8999999999999999999999999999999999876554
Q ss_pred ----cchHHHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHHHhCCCCCCCcccchhhccCCCHHHHHHHHHHHHHH
Q 017247 212 ----SLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHIIDQVEPVNPVDYQNQLLGVLKISKEKVSDCYKLILEL 287 (375)
Q Consensus 212 ----~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L~~~~~i~~~~l~~C~~~i~~l 287 (375)
....+|++.| .+++.++.+...+.|..++|||||+++-... ..+.+.+|+.+..|.+|++.|.-+
T Consensus 266 l~Pq~~~~efiqia-qlLDlc~ldids~~fsYrilaAAal~h~~s~----------e~v~kaSG~~w~~ie~cv~wm~Pf 334 (408)
T KOG0655|consen 266 LLPQYSQEEFIQIA-QLLDLCILDIDSLEFSYRILAAAALCHFTSI----------EVVKKASGLEWDSIEECVDWMVPF 334 (408)
T ss_pred eccccchHHHHHHH-HHHHHHHhccccccchHHHHHHHHHHHHhHH----------HHHHHcccccHHHHHHHHHHHHHH
Confidence 2334677777 7888899999999999999999999987642 245678999999999999999887
Q ss_pred HH
Q 017247 288 AN 289 (375)
Q Consensus 288 ~~ 289 (375)
..
T Consensus 335 ~r 336 (408)
T KOG0655|consen 335 VR 336 (408)
T ss_pred HH
Confidence 64
No 3
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=9.3e-33 Score=276.22 Aligned_cols=238 Identities=23% Similarity=0.324 Sum_probs=200.7
Q ss_pred CcHHHHHHHHHHHHhccCCcccccccCCCcchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchh
Q 017247 57 WEDEELLSLFSKEEQQLLKQETQTHYKDSDVLVVARSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWM 136 (375)
Q Consensus 57 ~~~e~l~~Ll~kE~~~~~~~~y~~~lq~~~~~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~ 136 (375)
|.++++..+..+|....|...+ .+...++..+|.++||||++|+.+|++.++|+++|||++||||++..++..+
T Consensus 126 y~~di~~~l~~~e~~~~p~~~~---~~~~e~~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~--- 199 (391)
T KOG0653|consen 126 YVQDIFEYLRQLELEFLPLSYD---ISQSEIRAKMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKK--- 199 (391)
T ss_pred HHHHHHHHHHHHHHhhCchhhh---cccccccHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHH---
Confidence 4567888888888544443322 2333488899999999999999999999999999999999999998888888
Q ss_pred HHHHHHHHHH-hhhhhcccCCCcccce-eeeCCCccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCCCCcch
Q 017247 137 IQLLAVTCLS-LAAKVEETQVPLLLDL-QVEGAKYVFETKAIQRMELLVLSTLEWKMHPVTPISFLDHIIRRLGLKTSLH 214 (375)
Q Consensus 137 lqLvavaCL~-LAaK~eE~~vp~l~dl-~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~FL~~fl~~l~~~~~~~ 214 (375)
+||+|++||+ ||+|+||..+|.+.|+ +++++. |++++|++||+.||.+|+|++..|||+.||++|++....+.
T Consensus 200 lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~--~s~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d~--- 274 (391)
T KOG0653|consen 200 LQLVGVSALLSIACKYEEISLPSVEDLVLITDGA--YSREEILRMEKYILNVLEFDLSVPTPLSFLRRFLKAADYDI--- 274 (391)
T ss_pred hhHHhHHHHHHHHHhhhhccCCccceeEeeeCCc--cchHHHHHHHHHHHhccCeeecCCchHHHHHHHHHhhhcch---
Confidence 9999999966 9999999999999999 777766 59999999999999999999999999999999999987332
Q ss_pred HHHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHHHhCCCCCCCcccchhhccCCCHHHHHHHHHHHHHHHHhcCCC
Q 017247 215 WEFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHIIDQVEPVNPVDYQNQLLGVLKISKEKVSDCYKLILELANAKTNA 294 (375)
Q Consensus 215 ~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L~~~~~i~~~~l~~C~~~i~~l~~~~~~~ 294 (375)
.......++++..++|++++.++||.+|+|+++++++...... .|...+..++|+....+..|...+..+.......
T Consensus 275 -~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~~~~~~--~w~~~~~~~sg~~~~~~~~~~~~~~~~~~~~~~~ 351 (391)
T KOG0653|consen 275 -KTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALRMLSKGD--VWSPTLEHYSGYSESYLFECARSLSALSLSSLQN 351 (391)
T ss_pred -hHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHHhccCC--ccCCCCeeccCCCcHHHHHHHHHHHHHHHHhccc
Confidence 3445577889999999999999999999999999998876432 6999999999999999999999999966655444
Q ss_pred C-CCc-cccccCCCCC
Q 017247 295 N-SNP-HKRKFEAIPG 308 (375)
Q Consensus 295 ~-~~~-~~~k~~s~p~ 308 (375)
+ ... +.+||.+.+-
T Consensus 352 ~~~~~~~~~ky~~~~~ 367 (391)
T KOG0653|consen 352 PSLRASVLNKYNSSKF 367 (391)
T ss_pred chhHHHHHHHhccccc
Confidence 3 333 7888876443
No 4
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=99.97 E-value=8.3e-32 Score=267.82 Aligned_cols=234 Identities=21% Similarity=0.246 Sum_probs=201.8
Q ss_pred CcHHHHHHHHHHHHhccCCcccccccCCCcchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchh
Q 017247 57 WEDEELLSLFSKEEQQLLKQETQTHYKDSDVLVVARSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWM 136 (375)
Q Consensus 57 ~~~e~l~~Ll~kE~~~~~~~~y~~~lq~~~~~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~ 136 (375)
|..+++..|+++|....|...|+.. ...+...+|..+|+||.+|+..|++.++|+++|||++||||++..+.-.+
T Consensus 180 y~~~Ife~l~k~e~~~lp~~~yl~k--q~~~~~~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k--- 254 (440)
T COG5024 180 YASDIFEYLLKLELIDLPNPNYLIK--QSLYEWSMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEK--- 254 (440)
T ss_pred HHHHHHHHHHHHHHHhcCcHHHHhh--cchhHHhHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHH---
Confidence 4789999999999999998877543 23355599999999999999999999999999999999999999999888
Q ss_pred HHHHHHHHHHhhhhhcccCCCcccce-eeeCCCccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCCCCcchH
Q 017247 137 IQLLAVTCLSLAAKVEETQVPLLLDL-QVEGAKYVFETKAIQRMELLVLSTLEWKMHPVTPISFLDHIIRRLGLKTSLHW 215 (375)
Q Consensus 137 lqLvavaCL~LAaK~eE~~vp~l~dl-~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~FL~~fl~~l~~~~~~~~ 215 (375)
+||+|++|||||||+||++.|.+.++ +++++.| +.++|+++|+.+|.+|+|++..|+|..||+++.+.-..+-
T Consensus 255 ~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~--t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka~dyd~---- 328 (440)
T COG5024 255 YQLVGISALFIASKYEEVNCPSIKDLVYATDGAF--TRDDIIRAERYMLEVLDFNISWPSPMSFLRRISKASDYDI---- 328 (440)
T ss_pred HHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccc--cHHHHHHHHHHHhhhcccccCCCChHHHHHHHHhhcccch----
Confidence 99999999999999999999999999 6777655 8999999999999999999999999999888777654432
Q ss_pred HHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHHHhCCCCCCCcccchhhccC-CCHHHHHHHHHHHHHHHHhcCCC
Q 017247 216 EFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHIIDQVEPVNPVDYQNQLLGVLK-ISKEKVSDCYKLILELANAKTNA 294 (375)
Q Consensus 216 ~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L~~~~~-i~~~~l~~C~~~i~~l~~~~~~~ 294 (375)
.-...+.+++..+..++.|.+++||.+||||++.+++.++..+ |...|..++| |+.+++..+++.+.+...+....
T Consensus 329 ~srt~~k~~~e~s~~~~~f~~~~~S~~~aaa~~~s~~~~~~~~---w~~~l~~ySg~y~~~~l~~~~~~~~~~l~~~~~~ 405 (440)
T COG5024 329 FSRTPAKFSSEISPVDYKFIQISPSWCAAAAMYLSRKILSQNQ---WDRTLIHYSGNYTNPDLKPLNESNKENLQNPSVH 405 (440)
T ss_pred hhhhhHhhhCCchHhhhhhccCCchHHHHHHHHHHHhhhccCC---CCccccccCCCCCchhHHHHHHHHHHHhcccchh
Confidence 1223477888889999999999999999999999999987543 9999999999 99999999999999988655321
Q ss_pred CCCccccccCC
Q 017247 295 NSNPHKRKFEA 305 (375)
Q Consensus 295 ~~~~~~~k~~s 305 (375)
..+..+||.+
T Consensus 406 -~~~i~~Ky~~ 415 (440)
T COG5024 406 -HDAIFPKYPS 415 (440)
T ss_pred -hhhhhhcccc
Confidence 1345677754
No 5
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=99.94 E-value=4.3e-28 Score=235.43 Aligned_cols=234 Identities=19% Similarity=0.268 Sum_probs=204.5
Q ss_pred cHHHHHHHHHHHHh-ccCCcccccccCCCcchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchh
Q 017247 58 EDEELLSLFSKEEQ-QLLKQETQTHYKDSDVLVVARSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWM 136 (375)
Q Consensus 58 ~~e~l~~Ll~kE~~-~~~~~~y~~~lq~~~~~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~ 136 (375)
..++..++..-|.. ..|..+|+..+|.+ +++.||.++|+|.++|++.+++..+|+++++++.|||+....+.+.+
T Consensus 103 ~~~I~~~~r~~ei~~~rp~~~~~e~vq~d-~t~smrgilvdwlvevsee~r~~~e~l~ls~~~~drfl~~~~~~~~k--- 178 (359)
T KOG0654|consen 103 AAKIYNTLRVSDIKSERPLPSKFEFVQAD-ITPSMRGILVDWLVEVSEEYRLTFETLYLSVNYRDRFLSYKEVNKQK--- 178 (359)
T ss_pred HHHHhhcccccchhhccCcccceeeeecC-CCcchhhhhhhhhhHHHHHHHhhhhheeecHHHHHHHhccCccHHHH---
Confidence 34556666666666 77788899999987 99999999999999999999999999999999999999999999888
Q ss_pred HHHHHHHHHHhhhhhcccCCCcccce-eeeCCCccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCCCCcchH
Q 017247 137 IQLLAVTCLSLAAKVEETQVPLLLDL-QVEGAKYVFETKAIQRMELLVLSTLEWKMHPVTPISFLDHIIRRLGLKTSLHW 215 (375)
Q Consensus 137 lqLvavaCL~LAaK~eE~~vp~l~dl-~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~FL~~fl~~l~~~~~~~~ 215 (375)
+|++|++|++||+|+||...|.+.+| .+.+..| +..++.+||..||..|.|++..||.-.|+..|+..... ...
T Consensus 179 ~ql~g~s~m~I~sk~ee~~~~~~~ef~~itd~ty--~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~~~~~---~~~ 253 (359)
T KOG0654|consen 179 LQLVGISAMLIASKYEEIKEPRVEEFCYITDNTY--TYWQVLRMEIDILNALTFELVRPTSKTFLRRFLRVAQT---PEL 253 (359)
T ss_pred HHHhCcccceeeccchhhcchHHHHHHhhhhhhh--HHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHHhhcc---hhH
Confidence 99999999999999999999999998 6666655 78899999999999999999999999999999877543 122
Q ss_pred HHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHHHhCCCCCCCcccchhhccCCCHHHHHHHHHHHHHHHHhcCCCC
Q 017247 216 EFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHIIDQVEPVNPVDYQNQLLGVLKISKEKVSDCYKLILELANAKTNAN 295 (375)
Q Consensus 216 ~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L~~~~~i~~~~l~~C~~~i~~l~~~~~~~~ 295 (375)
+.-..|.++.+.++.++.|+.|.||+|||||+++|...++ ...|.+.|..++||+.++++.|+..|. ++.+.....
T Consensus 254 ~~e~~~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~---~~pW~~~L~~~T~y~~edl~~~v~~L~-~~l~~~~~~ 329 (359)
T KOG0654|consen 254 QVEPLANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLD---FHPWNQTLEDYTGYKAEDLKPCVLDLH-LYLNASGTD 329 (359)
T ss_pred HHHHHHHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhcc---CCCCchhhHHhhcccHHHHHHHHHHHh-cccCCCCCc
Confidence 4445688999999999999999999999999999998887 456999999999999999999999999 776665555
Q ss_pred CCccccccC
Q 017247 296 SNPHKRKFE 304 (375)
Q Consensus 296 ~~~~~~k~~ 304 (375)
.++++.||.
T Consensus 330 l~air~ky~ 338 (359)
T KOG0654|consen 330 LPAIREKYK 338 (359)
T ss_pred hHHHHHHhh
Confidence 666666664
No 6
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.90 E-value=1.1e-22 Score=196.24 Aligned_cols=191 Identities=18% Similarity=0.223 Sum_probs=148.3
Q ss_pred HHHHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccce-eeeC
Q 017247 90 VARSEAVEWVLKVNAHYG--FSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDL-QVEG 166 (375)
Q Consensus 90 ~~R~~~v~Wi~~v~~~~~--l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl-~v~~ 166 (375)
..|.-.+.+|.+++.+++ ++..|+++|+.||+||+...++...+ .+++|+|||+||+|+||..+ .+.++ ....
T Consensus 54 ~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~---p~~Ia~tclfLA~KvEE~~~-si~~fv~~~~ 129 (305)
T TIGR00569 54 DLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYH---PKIIMLTCVFLACKVEEFNV-SIDQFVGNLK 129 (305)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcC---HHHHHHHHHHHHHhccccCc-CHHHHHhhcc
Confidence 789999999999999999 99999999999999999999998888 99999999999999999854 45666 2222
Q ss_pred CCccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCCC---CcchHHHHHHHHHHHHhhcccccccCCCHHHHH
Q 017247 167 AKYVFETKAIQRMELLVLSTLEWKMHPVTPISFLDHIIRRLGLK---TSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLA 243 (375)
Q Consensus 167 ~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~FL~~fl~~l~~~---~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IA 243 (375)
......+++|.+||..||++|+|++.+++|+.+|..|+..++.. ......+.+.++.++..++...-++.|+||.||
T Consensus 130 ~~~~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IA 209 (305)
T TIGR00569 130 ETPLKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIA 209 (305)
T ss_pred CCchhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHHH
Confidence 22223568999999999999999999999999999988654311 011123557788888888777779999999999
Q ss_pred HHHHHHHHHHhCCCCCCCcccchhhccCC--CHHHHHHHHHHHHHHH
Q 017247 244 TATMMHIIDQVEPVNPVDYQNQLLGVLKI--SKEKVSDCYKLILELA 288 (375)
Q Consensus 244 aAal~~a~~~l~~~~~~~~~~~L~~~~~i--~~~~l~~C~~~i~~l~ 288 (375)
+|||++|.+.++-. .......+.+. +.+.+..-+..|.++.
T Consensus 210 lAAI~lA~~~~~~~----l~~~~~e~~~~~~~~~~~~~l~~~~~~~~ 252 (305)
T TIGR00569 210 LAAILHTASRAGLN----MESYLTEQLSVPGNREELPQLIDIMRELR 252 (305)
T ss_pred HHHHHHHHHHhCCC----CcccchhhhcccccHHHHHHHHHHHHHHH
Confidence 99999999988642 22222244555 5555555555555543
No 7
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=99.88 E-value=1.3e-22 Score=171.25 Aligned_cols=126 Identities=29% Similarity=0.448 Sum_probs=106.9
Q ss_pred HHHHHHHHHHHhccCCcccccccCCCcchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHH
Q 017247 60 EELLSLFSKEEQQLLKQETQTHYKDSDVLVVARSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQL 139 (375)
Q Consensus 60 e~l~~Ll~kE~~~~~~~~y~~~lq~~~~~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqL 139 (375)
|++..|+++|.++.+...|... ..+++...|..+++||.+++.++++++.|+++|+.|||||+....+.+.+ +++
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 6889999999999877766653 22588999999999999999999999999999999999999999888777 999
Q ss_pred HHHHHHHhhhhhcccCCCcccce-eeeCCCccccHHHHHHHHHHHHHHcCcccc
Q 017247 140 LAVTCLSLAAKVEETQVPLLLDL-QVEGAKYVFETKAIQRMELLVLSTLEWKMH 192 (375)
Q Consensus 140 vavaCL~LAaK~eE~~vp~l~dl-~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~ 192 (375)
+|+|||+||+|++|..+|.+.++ .+. .+.|++++|.+||+.||++|+|+++
T Consensus 76 i~~~cl~lA~K~~e~~~~~~~~~~~~~--~~~~~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 76 IALACLFLASKMEEDNPPSISDLIRIS--DNTFTKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp HHHHHHHHHHHHHTSS--HHHHHHHHT--TTSSHHHHHHHHHHHHHHHTTT---
T ss_pred hhhhHHHHhhhhhccccchHHHHHHHH--cCCCCHHHHHHHHHHHHHHCCCCcC
Confidence 99999999999999988999888 333 4567999999999999999999985
No 8
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.87 E-value=8.3e-22 Score=190.16 Aligned_cols=200 Identities=21% Similarity=0.265 Sum_probs=167.9
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCccccee-e--
Q 017247 88 LVVARSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDLQ-V-- 164 (375)
Q Consensus 88 ~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl~-v-- 164 (375)
....|..++.||.+++..+|++..|+++|+.|++||+..+++.... .+.+|++||+||+|+||+ +..+.|+. +
T Consensus 35 E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~---~~~vA~sclfLAgKvEet-p~kl~dIi~~s~ 110 (323)
T KOG0834|consen 35 ELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFD---PYTVAASCLFLAGKVEET-PRKLEDIIKVSY 110 (323)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCc---HHHHHHHHHHHHhhcccC-cccHHHHHHHHH
Confidence 3578999999999999999999999999999999999999999888 899999999999999998 55666662 1
Q ss_pred ---eC------CCccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhhccccccc
Q 017247 165 ---EG------AKYVFETKAIQRMELLVLSTLEWKMHPVTPISFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSV 235 (375)
Q Consensus 165 ---~~------~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l 235 (375)
.. ..|.=.++.|...|+.||++|+|++++-+||.||..|+..++...+........|+.++..++...-++
T Consensus 111 ~~~~~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL 190 (323)
T KOG0834|consen 111 RYLNPKDLELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCL 190 (323)
T ss_pred HHcCcccccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeE
Confidence 10 112223678999999999999999999999999999999998776654456677899999999999999
Q ss_pred CCCHHHHHHHHHHHHHHHhCCCCCCCccc-chhhccC--CCHHHHHHHHHHHHHHHHhcC
Q 017247 236 SYLPSVLATATMMHIIDQVEPVNPVDYQN-QLLGVLK--ISKEKVSDCYKLILELANAKT 292 (375)
Q Consensus 236 ~~~PS~IAaAal~~a~~~l~~~~~~~~~~-~L~~~~~--i~~~~l~~C~~~i~~l~~~~~ 292 (375)
+|+|..||+|||++|.+..+- ..+.+.. .+....+ ++.+.|.+.++.+.+++...+
T Consensus 191 ~y~p~~IAva~i~lA~~~~~~-~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y~~~~ 249 (323)
T KOG0834|consen 191 QYSPHSIAVACIHLAAKLLGV-ELPSDTDKRWWREFDETVTNELLDDICHEFLDLYEQTP 249 (323)
T ss_pred eecCcEEEeehhhHHHHHcCC-CCCCCcccchhhhhcccCCHHHHHHHHHHHHHHHhhcc
Confidence 999999999999999987764 2222222 3455677 999999999999999997654
No 9
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.84 E-value=8.3e-20 Score=172.47 Aligned_cols=196 Identities=17% Similarity=0.262 Sum_probs=166.2
Q ss_pred chHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCccccee---
Q 017247 87 VLVVARSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDLQ--- 163 (375)
Q Consensus 87 ~~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl~--- 163 (375)
.....|...++||.+.+.-++|+..+.+++..+|-||+...++.+.+ +..+++||++||+|+||. |-.+.|++
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 34578999999999999999999999999999999999999998888 999999999999999997 44444431
Q ss_pred ---------------eeCCCccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhh
Q 017247 164 ---------------VEGAKYVFETKAIQRMELLVLSTLEWKMHPVTPISFLDHIIRRLGLKTSLHWEFLKRCERLLLTL 228 (375)
Q Consensus 164 ---------------v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~ 228 (375)
+.+..|.-.+..+.++|+.||+.|+|++++.+|+.++-.|+..+++.++. .+++.++.++..+
T Consensus 94 h~L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~--~l~Q~~wNfmNDs 171 (367)
T KOG0835|consen 94 HYLEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNL--KLLQAAWNFMNDS 171 (367)
T ss_pred HHHHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCch--hHHHHHHHhhhhc
Confidence 00111222356799999999999999999999999999999999998876 6789999999999
Q ss_pred cccccccCCCHHHHHHHHHHHHHHHhCCCCCCCcccchhhccCCCHHHHHHHHHHHHHHHHh
Q 017247 229 VSDSRSVSYLPSVLATATMMHIIDQVEPVNPVDYQNQLLGVLKISKEKVSDCYKLILELANA 290 (375)
Q Consensus 229 l~d~~~l~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L~~~~~i~~~~l~~C~~~i~~l~~~ 290 (375)
+...-|..|+|+.||+||+++|.+.++ .+...++.+..+++.++++|.+.+-.+..+|..
T Consensus 172 lRT~v~vry~pe~iACaciyLaAR~~e--IpLp~~P~Wf~~Fd~~k~eid~ic~~l~~lY~~ 231 (367)
T KOG0835|consen 172 LRTDVFVRYSPESIACACIYLAARNLE--IPLPFQPHWFKAFDTTKREIDEICYRLIPLYKR 231 (367)
T ss_pred cccceeeecCHHHHHHHHHHHHHhhhc--CCCCCCccHHHHcCCcHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999887 222344456678999999999977777777765
No 10
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.82 E-value=6.3e-20 Score=165.83 Aligned_cols=224 Identities=23% Similarity=0.259 Sum_probs=172.5
Q ss_pred CCcHHHHHH-HHHHHHhccCCc-ccccccCCCcchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCC
Q 017247 56 FWEDEELLS-LFSKEEQQLLKQ-ETQTHYKDSDVLVVARSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDK 133 (375)
Q Consensus 56 ~~~~e~l~~-Ll~kE~~~~~~~-~y~~~lq~~~~~~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~ 133 (375)
||....++. ++.++.-..-.. | +..+..+ -....+--.-+.|..++.++++...++++|+.||.||+.+.++..-.
T Consensus 5 FW~SSh~~qwl~dk~el~k~r~~D-~r~l~~d-~~~~l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~ 82 (264)
T KOG0794|consen 5 FWTSSHYQQWLLDKTELLKERQLD-LRGLSED-EYSKLKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIE 82 (264)
T ss_pred hhhhhhhhhHhcCHHHHhhhccch-hhcccHH-HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccC
Confidence 566655555 666554332111 1 1111111 12234555667889999999999999999999999999999988878
Q ss_pred chhHHHHHHHHHHhhhhhcccCCCcccce-----------eeeCCCccccHHHHHHHHHHHHHHcCccccCCChHHHHHH
Q 017247 134 PWMIQLLAVTCLSLAAKVEETQVPLLLDL-----------QVEGAKYVFETKAIQRMELLVLSTLEWKMHPVTPISFLDH 202 (375)
Q Consensus 134 ~~~lqLvavaCL~LAaK~eE~~vp~l~dl-----------~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~FL~~ 202 (375)
+.|+|.||++||||+||..+...+-+ ......+.++.++|..||..+|+.|+.-|-+.+|+.-|..
T Consensus 83 ---p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q 159 (264)
T KOG0794|consen 83 ---PRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYWPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQ 159 (264)
T ss_pred ---HHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccchhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHH
Confidence 99999999999999999732111111 1233445567889999999999999999999999999999
Q ss_pred HHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHHHhCCCCCCCcccchhhccCCCHHHHHHHHH
Q 017247 203 IIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHIIDQVEPVNPVDYQNQLLGVLKISKEKVSDCYK 282 (375)
Q Consensus 203 fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L~~~~~i~~~~l~~C~~ 282 (375)
++...|..+. ..+..++.++..+....-++-|+|.+||.||++.|....+... .+++...+.+|.+.|.+|++
T Consensus 160 ~~qd~gi~d~---~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~~----~~~w~~el~vD~ekV~~~v~ 232 (264)
T KOG0794|consen 160 FVQDMGINDQ---KLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKDI----PKAWFAELSVDMEKVKDIVQ 232 (264)
T ss_pred HHHHhcccch---hhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCCh----HHHHHHHHhccHHHHHHHHH
Confidence 9999998553 4678899999999999999999999999999999997766432 24555667999999999999
Q ss_pred HHHHHHHhc
Q 017247 283 LILELANAK 291 (375)
Q Consensus 283 ~i~~l~~~~ 291 (375)
.|.+++...
T Consensus 233 ~I~~lYe~w 241 (264)
T KOG0794|consen 233 EILKLYELW 241 (264)
T ss_pred HHHHHHHHH
Confidence 999998654
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=99.74 E-value=2e-17 Score=156.42 Aligned_cols=163 Identities=17% Similarity=0.278 Sum_probs=138.7
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhccc--CCCcc----cce
Q 017247 89 VVARSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEET--QVPLL----LDL 162 (375)
Q Consensus 89 ~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~--~vp~l----~dl 162 (375)
...|.....||..+|.+++++..++.+||.+|+||+.+..+.... ++-++.||++||+|+||+ ++... +++
T Consensus 42 ~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~---~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~ 118 (297)
T COG5333 42 LNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEIS---LYSVVTTCVYLACKVEDTPRDISIESFEARDL 118 (297)
T ss_pred hhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhccccccc---HHHHHHhheeeeeecccccchhhHHHHHhhcc
Confidence 346777889999999999999999999999999999999988887 999999999999999995 22111 111
Q ss_pred eeeCCCccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHH
Q 017247 163 QVEGAKYVFETKAIQRMELLVLSTLEWKMHPVTPISFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVL 242 (375)
Q Consensus 163 ~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~I 242 (375)
+ -....-+++.|..+|..||+.|+|++++++|+.++.+|+..+...+. .+..+.|+.++..++...-++.|+|..|
T Consensus 119 ~--se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~--~~~~~~aw~~inDa~~t~~~llypphiI 194 (297)
T COG5333 119 W--SEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDK--YKLLQIAWKIINDALRTDLCLLYPPHII 194 (297)
T ss_pred c--cccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccH--HHHHHHHHHHHHhhhhceeeeecChHHH
Confidence 1 11223378999999999999999999999999999999998876654 3678999999999999999999999999
Q ss_pred HHHHHHHHHHHhCCCC
Q 017247 243 ATATMMHIIDQVEPVN 258 (375)
Q Consensus 243 AaAal~~a~~~l~~~~ 258 (375)
|+||++.|.+.++...
T Consensus 195 A~a~l~ia~~~~~~~~ 210 (297)
T COG5333 195 ALAALLIACEVLGMPI 210 (297)
T ss_pred HHHHHHHHHHhcCCcc
Confidence 9999999998876443
No 12
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.62 E-value=3.7e-14 Score=138.20 Aligned_cols=185 Identities=18% Similarity=0.168 Sum_probs=158.1
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccce-eeeCC
Q 017247 89 VVARSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDL-QVEGA 167 (375)
Q Consensus 89 ~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl-~v~~~ 167 (375)
.+.-..+..-|.+++..++++..+.-.|..++.+++....+.... ...+++|||++|||.++. +..+.++ .+.
T Consensus 119 er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs---~~~i~AAclYiACR~~~~-prtl~eI~~~~-- 192 (310)
T PRK00423 119 ERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRS---IEGVVAAALYAACRRCKV-PRTLDEIAEVS-- 192 (310)
T ss_pred hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCC---HHHHHHHHHHHHHHHcCC-CcCHHHHHHHh--
Confidence 345567778899999999999999999999999999987777777 899999999999999888 5677887 222
Q ss_pred CccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHHHHHHH
Q 017247 168 KYVFETKAIQRMELLVLSTLEWKMHPVTPISFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATATM 247 (375)
Q Consensus 168 ~~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal 247 (375)
..+.++|.+.++.|++.|+.++.+.+|.+|+..|...|+++. .+.+.|.+++..+....-..+.+|..||||||
T Consensus 193 --~v~~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~----~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaI 266 (310)
T PRK00423 193 --RVSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSG----EVQKKAIEILQKAKEKGLTSGKGPTGLAAAAI 266 (310)
T ss_pred --CCCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCH----HHHHHHHHHHHHHHhcCcccCCCHHHHHHHHH
Confidence 237899999999999999999999999999999999999876 45677777777766555567999999999999
Q ss_pred HHHHHHhCCCCCCCcccchhhccCCCHHHHHHHHHHHHHHH
Q 017247 248 MHIIDQVEPVNPVDYQNQLLGVLKISKEKVSDCYKLILELA 288 (375)
Q Consensus 248 ~~a~~~l~~~~~~~~~~~L~~~~~i~~~~l~~C~~~i~~l~ 288 (375)
|+|.+..+.. --+..+..++|+++..|+.+|+.|.+.+
T Consensus 267 YlA~~~~g~~---~t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 267 YIASLLLGER---RTQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred HHHHHHhCCC---CCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 9999876532 3567888999999999999999998854
No 13
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=99.52 E-value=1.3e-14 Score=120.42 Aligned_cols=106 Identities=23% Similarity=0.332 Sum_probs=85.3
Q ss_pred CChHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHHHhCCCCCCCcccchhhccCCC
Q 017247 194 VTPISFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHIIDQVEPVNPVDYQNQLLGVLKIS 273 (375)
Q Consensus 194 ~Tp~~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L~~~~~i~ 273 (375)
|||++||++|++..+. ..+....+.++++.++.++.|++|+||+||+||+++|+..++. ...|...+..++|++
T Consensus 1 PTp~~Fl~~~~~~~~~----~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~--~~~~~~~l~~~t~~~ 74 (118)
T PF02984_consen 1 PTPYDFLRRFLKISNA----DQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGK--EPPWPESLEKLTGYD 74 (118)
T ss_dssp --HHHHHHHHHTSSSH----HHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHS--STCSHHHHHHHHTS-
T ss_pred CcHHHHHHHHHHHcCC----cHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCc--cccCCccchhhcCCC
Confidence 7999999999654332 2246677889999999999999999999999999999999862 236999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCCccccccCC
Q 017247 274 KEKVSDCYKLILELANAKTNANSNPHKRKFEA 305 (375)
Q Consensus 274 ~~~l~~C~~~i~~l~~~~~~~~~~~~~~k~~s 305 (375)
+++|.+|++.|.+++.+......+++++||.+
T Consensus 75 ~~~l~~c~~~i~~~~~~~~~~~~~ai~~Kys~ 106 (118)
T PF02984_consen 75 KEDLKECIELIQELLSKASNSKLQAIRKKYSS 106 (118)
T ss_dssp HHHHHHHHHHHHHHHHHCCGSSCTHHHHHTTS
T ss_pred HHHHHHHHHHHHHHHHhcCCccchHHHHHhCc
Confidence 99999999999999986654456678888864
No 14
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=99.41 E-value=6.7e-13 Score=103.13 Aligned_cols=87 Identities=39% Similarity=0.516 Sum_probs=75.5
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccceeeeCCCccc
Q 017247 92 RSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDLQVEGAKYVF 171 (375)
Q Consensus 92 R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl~v~~~~~~f 171 (375)
|..+++||.+++..+++++.|.++|+.|+|||+....+.+.+ ++++|+||++||+|+++. ++...++. ...++.
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~---~~~ia~a~l~lA~k~~~~-~~~~~~~~-~~~~~~- 75 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRS---PSLVAAAALYLAAKVEEI-PPWLKDLV-HVTGYA- 75 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCC---hHHHHHHHHHHHHHHcCC-CCCHHHHh-HHhCCC-
Confidence 678999999999999999999999999999999998887666 999999999999999999 77778872 122221
Q ss_pred cHHHHHHHHHHHH
Q 017247 172 ETKAIQRMELLVL 184 (375)
Q Consensus 172 ~~~~I~~mE~~IL 184 (375)
+.++|.+||+.|+
T Consensus 76 ~~~~i~~~e~~il 88 (88)
T cd00043 76 TEEEILRMEKLLL 88 (88)
T ss_pred CHHHHHHHHHHhC
Confidence 7999999999875
No 15
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=99.38 E-value=1.6e-12 Score=122.45 Aligned_cols=150 Identities=17% Similarity=0.309 Sum_probs=113.8
Q ss_pred HHHHHHHHc--CCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccce--eeeCCCccccH
Q 017247 98 WVLKVNAHY--GFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDL--QVEGAKYVFET 173 (375)
Q Consensus 98 Wi~~v~~~~--~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl--~v~~~~~~f~~ 173 (375)
-+++.+..+ .+++.+..+|+.||-||+...++.... ...|.+||+++|+|++|.++ .+.+| .+. +.-.-+.
T Consensus 62 ~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~---pk~I~~tc~flA~Kieef~I-SieqFvkn~~-~~~~k~~ 136 (325)
T KOG2496|consen 62 SLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYS---PKIIMATCFFLACKIEEFYI-SIEQFVKNMN-GRKWKTH 136 (325)
T ss_pred HHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcC---hHHHHHHHHHHHhhhHhhee-cHHHHHhhcc-CcccccH
Confidence 344444444 579999999999999999999998888 88999999999999999865 44555 122 2222378
Q ss_pred HHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhC----CCCcchHHHH---HHHHHHHHhhcccccccCCCHHHHHHHH
Q 017247 174 KAIQRMELLVLSTLEWKMHPVTPISFLDHIIRRLG----LKTSLHWEFL---KRCERLLLTLVSDSRSVSYLPSVLATAT 246 (375)
Q Consensus 174 ~~I~~mE~~IL~~L~w~l~~~Tp~~FL~~fl~~l~----~~~~~~~~~l---~~~~~ll~~~l~d~~~l~~~PS~IAaAa 246 (375)
+.|+..|..+++.|+|++.+.+|+.-++.|+.-+. ...+. +++ .....++..++..--++-|.||.||+||
T Consensus 137 e~vLk~E~~llqsL~f~L~vh~PyRPleGFl~D~kt~l~~~~n~--d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaA 214 (325)
T KOG2496|consen 137 EIVLKYEFLLLQSLKFSLTVHNPYRPLEGFLLDMKTRLPALENP--DILRKHDDSKKFLDRALLTDAYLLYTPSQIALAA 214 (325)
T ss_pred HHHHhchHHHHHhhhhhheecCCCCchHHHHHHHHHHHHhccCH--HHHhhhhhHHHHHHHHHHhccceecChHHHHHHH
Confidence 89999999999999999999999999999885542 11111 122 1124677777777778899999999999
Q ss_pred HHHHHHHh
Q 017247 247 MMHIIDQV 254 (375)
Q Consensus 247 l~~a~~~l 254 (375)
|+.+....
T Consensus 215 il~a~~~~ 222 (325)
T KOG2496|consen 215 ILHAAGRT 222 (325)
T ss_pred HHHHhccc
Confidence 97775443
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=99.33 E-value=3.5e-12 Score=98.09 Aligned_cols=83 Identities=36% Similarity=0.498 Sum_probs=70.4
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccceeeeCCCccccHHHH
Q 017247 97 EWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDLQVEGAKYVFETKAI 176 (375)
Q Consensus 97 ~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl~v~~~~~~f~~~~I 176 (375)
+||.+++..+++++++.++|++++|||+....+.+.+ ++++|+||++||+|++|.. |...++. ...++ |+.++|
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~---~~~ia~a~l~lA~k~~~~~-~~~~~~~-~~~~~-~~~~~i 74 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYS---PSLIAAAALYLAAKTEEIP-PWTKELV-HYTGY-FTEEEI 74 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCC---HHHHHHHHHHHHHHHhcCC-CCchhHh-HhhCC-CCHHHH
Confidence 5999999999999999999999999999977777666 9999999999999999985 5556662 11222 589999
Q ss_pred HHHHHHHHH
Q 017247 177 QRMELLVLS 185 (375)
Q Consensus 177 ~~mE~~IL~ 185 (375)
.+||+.||.
T Consensus 75 ~~~~~~il~ 83 (83)
T smart00385 75 LRMEKLLLE 83 (83)
T ss_pred HHHHHHHhC
Confidence 999999873
No 17
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.17 E-value=1.2e-09 Score=104.87 Aligned_cols=186 Identities=16% Similarity=0.208 Sum_probs=159.7
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccceeeeCCC
Q 017247 89 VVARSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDLQVEGAK 168 (375)
Q Consensus 89 ~~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl~v~~~~ 168 (375)
.+.-..+...|-.++..++++..+.-.|..++-+.+...-+.... .+-+++||+++|++.... +..+.++.. ..+
T Consensus 94 ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRs---ie~v~AA~iY~acR~~~~-prtl~eIa~-a~~ 168 (285)
T COG1405 94 ERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRS---IESVAAACIYAACRINGV-PRTLDEIAK-ALG 168 (285)
T ss_pred hhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCc---HHHHHHHHHHHHHHHcCC-CccHHHHHH-HHC
Confidence 345667888899999999999999999999999999988888888 999999999999999887 455666521 122
Q ss_pred ccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHHHHHHHH
Q 017247 169 YVFETKAIQRMELLVLSTLEWKMHPVTPISFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATATMM 248 (375)
Q Consensus 169 ~~f~~~~I~~mE~~IL~~L~w~l~~~Tp~~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~ 248 (375)
.++++|.++.+.+...|+=.+.+..|.+|+..|...|++++ +....+..++..+.....-.+-.|+.||+||+|
T Consensus 169 --V~~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~----~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy 242 (285)
T COG1405 169 --VSKKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSD----EVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIY 242 (285)
T ss_pred --CCHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCH----HHHHHHHHHHHHHHHhCcccCCCchhHHHHHHH
Confidence 37899999999999999999999999999999999999986 556778888888877777789999999999999
Q ss_pred HHHHHhCCCCCCCcccchhhccCCCHHHHHHHHHHHHHHH
Q 017247 249 HIIDQVEPVNPVDYQNQLLGVLKISKEKVSDCYKLILELA 288 (375)
Q Consensus 249 ~a~~~l~~~~~~~~~~~L~~~~~i~~~~l~~C~~~i~~l~ 288 (375)
+|....+ ....+..+..++|+++..|++-|+.|.+..
T Consensus 243 ~as~l~~---~~~tq~eva~v~~vtevTIrnrykel~~~~ 279 (285)
T COG1405 243 LASLLLG---ERRTQKEVAKVAGVTEVTIRNRYKELADAL 279 (285)
T ss_pred HHHHHhC---CchHHHHHHHHhCCeeeHHHHHHHHHHHhh
Confidence 9998775 334678899999999999999998887654
No 18
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.95 E-value=2.6e-08 Score=94.01 Aligned_cols=186 Identities=16% Similarity=0.166 Sum_probs=145.4
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccceeeeCCCc
Q 017247 90 VARSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDLQVEGAKY 169 (375)
Q Consensus 90 ~~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl~v~~~~~ 169 (375)
..-..+..-|..++...+|+....-.|-.+|.++-..+...... ..-+++|||+||++-++. +..+.++..-..
T Consensus 102 ~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks---~eai~AAclyiACRq~~~-pRT~kEI~~~an-- 175 (308)
T KOG1597|consen 102 RVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKS---VEALAAACLYIACRQEDV-PRTFKEISAVAN-- 175 (308)
T ss_pred HHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCcc---HHHHHHHHHHHHHHhcCC-CchHHHHHHHHc--
Confidence 34455666678899999999999999999999999777777677 999999999999998887 667788732222
Q ss_pred cccHHHHHHHHHHHHHHcCccccCCC--hHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHHHHHHH
Q 017247 170 VFETKAIQRMELLVLSTLEWKMHPVT--PISFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATATM 247 (375)
Q Consensus 170 ~f~~~~I~~mE~~IL~~L~w~l~~~T--p~~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal 247 (375)
.++++|-+.=..|+..|+=.....| .-+|+.+|...|+++...+ ..|.++...+..-....+-.|-.||||+|
T Consensus 176 -v~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q----~aA~e~a~ka~~~~~~~gRsPiSIAAa~I 250 (308)
T KOG1597|consen 176 -VSKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQ----EAATEIAEKAEEMDIRAGRSPISIAAAAI 250 (308)
T ss_pred -CCHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHH----HHHHHHHHHHHHhccccCCCchhHHHHHH
Confidence 3799999999999999988776665 8899999999999986433 33333333332222244688999999999
Q ss_pred HHHHHHhCCCCCCCcccchhhccCCCHHHHHHHHHHHHHHHH
Q 017247 248 MHIIDQVEPVNPVDYQNQLLGVLKISKEKVSDCYKLILELAN 289 (375)
Q Consensus 248 ~~a~~~l~~~~~~~~~~~L~~~~~i~~~~l~~C~~~i~~l~~ 289 (375)
|++....... ..+..+..++|+.+..|+.-|+.|.....
T Consensus 251 Ymisqls~~k---kt~keI~~vtgVaE~TIr~sYK~Lyp~~~ 289 (308)
T KOG1597|consen 251 YMISQLSDEK---KTQKEIGEVTGVAEVTIRNSYKDLYPHAD 289 (308)
T ss_pred HHHHHhccCc---ccHHHHHHHhhhhHHHHHHHHHHHhhchh
Confidence 9998765432 35678889999999999999999987554
No 19
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.38 E-value=2.3e-06 Score=65.98 Aligned_cols=85 Identities=26% Similarity=0.340 Sum_probs=74.3
Q ss_pred CCChHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHHHhCCCCCCCcccchhhccCC
Q 017247 193 PVTPISFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHIIDQVEPVNPVDYQNQLLGVLKI 272 (375)
Q Consensus 193 ~~Tp~~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L~~~~~i 272 (375)
.+++.+|+..+...++.+. .....|..+++..+....+.++.|+.||+||+++|.+..+. ..|...+..++++
T Consensus 2 ~~~~~~~l~~~~~~~~~~~----~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~---~~~~~~~~~~~~~ 74 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSP----ETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEI---PPWLKDLVHVTGY 74 (88)
T ss_pred cchHHHHHHHHHHHcCCCH----HHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCC---CCCHHHHhHHhCC
Confidence 5789999999999998765 56677888999988888899999999999999999987764 5688899999999
Q ss_pred -CHHHHHHHHHHH
Q 017247 273 -SKEKVSDCYKLI 284 (375)
Q Consensus 273 -~~~~l~~C~~~i 284 (375)
+.++|.++...|
T Consensus 75 ~~~~~i~~~e~~i 87 (88)
T cd00043 75 ATEEEILRMEKLL 87 (88)
T ss_pred CCHHHHHHHHHHh
Confidence 999999988765
No 20
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.37 E-value=1.7e-06 Score=66.01 Aligned_cols=81 Identities=26% Similarity=0.371 Sum_probs=69.2
Q ss_pred HHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHHHhCCCCCCCcccchhhccCC-CHHH
Q 017247 198 SFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHIIDQVEPVNPVDYQNQLLGVLKI-SKEK 276 (375)
Q Consensus 198 ~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L~~~~~i-~~~~ 276 (375)
+|+..+...++.+. +....+.++++..+.+..+.+++|+.||+||+++|.+..+.. .|...+..++|+ +.++
T Consensus 1 ~~l~~~~~~~~~~~----~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~---~~~~~~~~~~~~~~~~~ 73 (83)
T smart00385 1 DFLRRVCKALNLDP----ETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIP---PWTKELVHYTGYFTEEE 73 (83)
T ss_pred CHHHHHHHHcCCCH----HHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCC---CCchhHhHhhCCCCHHH
Confidence 47888888888864 566788889999888888999999999999999999987642 488889999999 9999
Q ss_pred HHHHHHHHH
Q 017247 277 VSDCYKLIL 285 (375)
Q Consensus 277 l~~C~~~i~ 285 (375)
|.+|...|.
T Consensus 74 i~~~~~~il 82 (83)
T smart00385 74 ILRMEKLLL 82 (83)
T ss_pred HHHHHHHHh
Confidence 999988775
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=98.23 E-value=3.9e-06 Score=73.36 Aligned_cols=93 Identities=22% Similarity=0.245 Sum_probs=65.1
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhh---ccccccCCchhHHHHHHHHHHhhhhhcccCCCcccce-eeeCCCc
Q 017247 94 EAVEWVLKVNAHYGFSTLTAILAINYLDRFLR---SFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDL-QVEGAKY 169 (375)
Q Consensus 94 ~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs---~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl-~v~~~~~ 169 (375)
.+.+|+.++..+-++++.++.+|..|+||+.. ...+.- .+.-.+-+-++||.+|+|+-+.....-..+ .+ +
T Consensus 53 ~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~-~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v--~-- 127 (149)
T PF08613_consen 53 SIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPL-NSSNIHRLFLTALILASKFLDDNTYSNKSWAKV--G-- 127 (149)
T ss_dssp -HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT----STTTHHHHHHHHHHHHHHHH-SS---HHHHHHH--H--
T ss_pred cHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhccccccc-ccchhHHHHHHHHHHHHhhcccccccHHHHHhh--c--
Confidence 37789999999999999999999999999998 222221 133388899999999999966543333433 23 2
Q ss_pred cccHHHHHHHHHHHHHHcCccc
Q 017247 170 VFETKAIQRMELLVLSTLEWKM 191 (375)
Q Consensus 170 ~f~~~~I~~mE~~IL~~L~w~l 191 (375)
.++.+++.+||+..|..|+|+|
T Consensus 128 gis~~eln~lE~~fL~~l~~~L 149 (149)
T PF08613_consen 128 GISLKELNELEREFLKLLDYNL 149 (149)
T ss_dssp TS-HHHHHHHHHHHHHHTTT--
T ss_pred CCCHHHHHHHHHHHHHHCCCcC
Confidence 2489999999999999999986
No 22
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.08 E-value=3e-05 Score=79.04 Aligned_cols=176 Identities=16% Similarity=0.158 Sum_probs=138.6
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccce--eeeCCCccccHH
Q 017247 97 EWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDL--QVEGAKYVFETK 174 (375)
Q Consensus 97 ~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl--~v~~~~~~f~~~ 174 (375)
.-|-+++..+++.. ..-.|.++|---+...-.+... .+.+..+||+|+|+.|-+. ..+.|+ +... +.-
T Consensus 72 ~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~---~~~vvasClY~vcR~e~t~-hlliDfS~~Lqv-----~Vy 141 (521)
T KOG1598|consen 72 RLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRR---STEVVAACLYLVCRLEKTD-HLLIDFSSYLQV-----SVY 141 (521)
T ss_pred hHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcc---hHHHHHHHHHHHHHhhCCc-eEEEEeccceEE-----ehh
Confidence 36788999999999 9999999999988887777777 9999999999999988873 455566 2222 334
Q ss_pred HHHHHHHHHHHHcCcc---ccCCChHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHH
Q 017247 175 AIQRMELLVLSTLEWK---MHPVTPISFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHII 251 (375)
Q Consensus 175 ~I~~mE~~IL~~L~w~---l~~~Tp~~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~ 251 (375)
++-.+=+.|-..|.-. +..+.|.-|+.+|...|...+.. .+++..+.+++.....|.-..+-+|+.|+-|||+.|+
T Consensus 142 ~LG~~~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~-~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAa 220 (521)
T KOG1598|consen 142 DLGSNFLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKT-EDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAA 220 (521)
T ss_pred hhhHHHHHHHHHhccccccccccCcceeeechhHhhhcCCch-HHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHH
Confidence 6666667777777777 77889999999999998766655 3788888899988888988999999999999999999
Q ss_pred HHhCCCCCCCcccchhhccCCCHHHHHHHHHHHHH
Q 017247 252 DQVEPVNPVDYQNQLLGVLKISKEKVSDCYKLILE 286 (375)
Q Consensus 252 ~~l~~~~~~~~~~~L~~~~~i~~~~l~~C~~~i~~ 286 (375)
+..+.. --...+.++..+....+..-+..+.+
T Consensus 221 r~h~~~---rsi~dIv~vvhV~e~Tl~kRl~Ef~~ 252 (521)
T KOG1598|consen 221 RMHGFR---RTIGDIAKVVHVCESTLSKRLKEFSD 252 (521)
T ss_pred HHcCcc---ccHHHHHHHHHHhHHHHHHHHHHHhc
Confidence 887522 23345666677777777777666644
No 23
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=97.94 E-value=3.3e-06 Score=82.49 Aligned_cols=101 Identities=19% Similarity=0.286 Sum_probs=84.9
Q ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccce-eeeCCCc
Q 017247 91 ARSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDL-QVEGAKY 169 (375)
Q Consensus 91 ~R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl-~v~~~~~ 169 (375)
.-+.+=.-|.+++...++..-|+++|..||.....+..+.+.+ -.|.|-|||.||+||.+.+--.++.+ .-.+.++
T Consensus 381 KirSlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~N---RKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~f 457 (497)
T KOG4164|consen 381 KIRSLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQN---RKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQF 457 (497)
T ss_pred HHHHHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhh---hhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHh
Confidence 3344566788899999999999999999999999988888887 89999999999999987654455555 2234668
Q ss_pred cccHHHHHHHHHHHHHHcCccccCC
Q 017247 170 VFETKAIQRMELLVLSTLEWKMHPV 194 (375)
Q Consensus 170 ~f~~~~I~~mE~~IL~~L~w~l~~~ 194 (375)
.+.+++++..|.-||.+|.|.|+++
T Consensus 458 R~nrrdLia~Ef~VlvaLefaL~~~ 482 (497)
T KOG4164|consen 458 RLNRRDLIAFEFPVLVALEFALHLP 482 (497)
T ss_pred cccHHhhhhhhhhHHHhhhhhccCC
Confidence 8899999999999999999999875
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=96.60 E-value=0.01 Score=44.91 Aligned_cols=71 Identities=13% Similarity=0.153 Sum_probs=51.5
Q ss_pred HHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHHHhCCCCCCCcccchhhccCCCHHHH
Q 017247 200 LDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHIIDQVEPVNPVDYQNQLLGVLKISKEKV 277 (375)
Q Consensus 200 L~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L~~~~~i~~~~l 277 (375)
+..|...|++++ .+.+.|..+...+....-..+-+|..|||||+|+|.+..+. +--...+...+|+++.+|
T Consensus 1 I~r~~~~L~L~~----~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~---~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPE----DVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGV---PRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--H----HHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTS---SSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCCH----HHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCC---CcCHHHHHHHhCCCCCcC
Confidence 456778888876 56677777777766666667899999999999999988753 235567778888887664
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=96.20 E-value=0.016 Score=43.88 Aligned_cols=60 Identities=12% Similarity=0.165 Sum_probs=47.5
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccce
Q 017247 99 VLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDL 162 (375)
Q Consensus 99 i~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl 162 (375)
|-+++..++|+..+.-.|..++++-....-....+ ..-++++|+++|++.+... ..+.++
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 45789999999999999999999988877666666 8999999999999998763 344554
No 26
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=94.72 E-value=0.21 Score=48.90 Aligned_cols=87 Identities=17% Similarity=0.269 Sum_probs=68.6
Q ss_pred hHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHHHhCCCCCCCcccchhhccCCCHH
Q 017247 196 PISFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHIIDQVEPVNPVDYQNQLLGVLKISKE 275 (375)
Q Consensus 196 p~~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L~~~~~i~~~ 275 (375)
.+..|..+...|++++ .+...|..+...+.....+-+...-.+||||||+|.+..+. +-....+..++++++.
T Consensus 125 a~~~I~~~~~~L~Lp~----~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~---prtl~eI~~~~~v~~k 197 (310)
T PRK00423 125 ALSELDRIASQLGLPR----SVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKV---PRTLDEIAEVSRVSRK 197 (310)
T ss_pred HHHHHHHHHHHcCCCH----HHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCC---CcCHHHHHHHhCCCHH
Confidence 4567788888888876 56677777776666555566889999999999999988652 2345677888999999
Q ss_pred HHHHHHHHHHHHHH
Q 017247 276 KVSDCYKLILELAN 289 (375)
Q Consensus 276 ~l~~C~~~i~~l~~ 289 (375)
+|..+++.|.+.+.
T Consensus 198 ~i~~~~~~l~k~L~ 211 (310)
T PRK00423 198 EIGRCYRFLLRELN 211 (310)
T ss_pred HHHHHHHHHHHHhC
Confidence 99999999998763
No 27
>KOG1674 consensus Cyclin [General function prediction only]
Probab=94.55 E-value=0.062 Score=49.99 Aligned_cols=97 Identities=16% Similarity=0.230 Sum_probs=68.1
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccc---cccC---Cchh-HHHHHHHHHHhhhhhcccCCCcccceeeeCC
Q 017247 95 AVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFH---FQID---KPWM-IQLLAVTCLSLAAKVEETQVPLLLDLQVEGA 167 (375)
Q Consensus 95 ~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~---v~~~---~~~~-lqLvavaCL~LAaK~eE~~vp~l~dl~v~~~ 167 (375)
+-+++.++..+-+.+++++.+|..|||||..... +... +..+ ..-+-++|+.+|+|+.+..--. ...+-.-+
T Consensus 78 i~~yleri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~y~-n~~~a~vg 156 (218)
T KOG1674|consen 78 IRQYLERIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVYYS-NAYYAKVG 156 (218)
T ss_pred hHHHHHHHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccchhhh-HHHHHHhC
Confidence 3456667777888999999999999999998633 1111 1122 4457899999999998752111 11111112
Q ss_pred CccccHHHHHHHHHHHHHHcCccccCC
Q 017247 168 KYVFETKAIQRMELLVLSTLEWKMHPV 194 (375)
Q Consensus 168 ~~~f~~~~I~~mE~~IL~~L~w~l~~~ 194 (375)
..+.+++..+|+..|..++|++.+.
T Consensus 157 --gl~~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 157 --GLTTDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred --CCChHhhhhhhHHHHhhCCeEEEec
Confidence 2378899999999999999999875
No 28
>PF09080 K-cyclin_vir_C: K cyclin, C terminal; InterPro: IPR015164 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This domain adopts a secondary structure consisting of a five alpha-helix cyclin fold. Interaction with cyclin dependent kinases (CDKs) at a PSTAIRE sequence motif within the catalytic cleft of CDK results in the regulation of CDK activity []. ; PDB: 1G3N_C.
Probab=90.81 E-value=2.1 Score=33.75 Aligned_cols=92 Identities=11% Similarity=0.174 Sum_probs=57.2
Q ss_pred HHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHHHHH-HHHHHHHHhCCCC--CCCcccchhhccCCCH
Q 017247 198 SFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATA-TMMHIIDQVEPVN--PVDYQNQLLGVLKISK 274 (375)
Q Consensus 198 ~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaA-al~~a~~~l~~~~--~~~~~~~L~~~~~i~~ 274 (375)
+-+-..+-+++........+..+....+..++.|..--+.+||.|||| |-+++.....|.. .....++|..++|++.
T Consensus 6 D~~~~~L~K~~~~~e~L~~~H~~V~~~v~KAiV~P~TG~Lp~SlvaAA~CAL~~~~~~~P~~~~~~~~~~~LA~~~G~~~ 85 (106)
T PF09080_consen 6 DAIGPLLFKSGFTKEQLFAWHSEVVESVHKAIVNPKTGGLPPSLVAAAGCALFSLGAAAPPDTHSGGVVPQLAEALGVSA 85 (106)
T ss_dssp HHHHHHHHHHS-SSTTHHHHHHHHHHHHHHHHCSTTGGGS-HHHHHHHHHHHHS-GGGS--------HHHHHHHHHT--H
T ss_pred ccccHHHHHHcccHHHHHHHHHHHHHHHHHHhcCcccCCCCHHHHHHhhhhhccccccCCCccccccchHHHHHHhCccH
Confidence 334444444444333332444667788888999999999999999998 6666655443322 2234568999999999
Q ss_pred HHHHHHHHHHHHHHH
Q 017247 275 EKVSDCYKLILELAN 289 (375)
Q Consensus 275 ~~l~~C~~~i~~l~~ 289 (375)
..+....+.+..-+.
T Consensus 86 a~L~AA~E~v~Tt~~ 100 (106)
T PF09080_consen 86 ATLQAAAESVATTLR 100 (106)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 999888888876554
No 29
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=87.72 E-value=4.6 Score=39.13 Aligned_cols=86 Identities=19% Similarity=0.215 Sum_probs=61.3
Q ss_pred ChHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccc-cCCCHHHHHHHHHHHHHHHhCCCCCCCcccchhhccCCC
Q 017247 195 TPISFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRS-VSYLPSVLATATMMHIIDQVEPVNPVDYQNQLLGVLKIS 273 (375)
Q Consensus 195 Tp~~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~-l~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L~~~~~i~ 273 (375)
+.+..+..+...++++... ...+..+...+ .+..+ -+-+...++|||+|.|.+..+. +-....+...++++
T Consensus 99 ~a~~~l~~~~~~l~LP~~v----~e~A~~iyr~a-~~~~l~rGRsie~v~AA~iY~acR~~~~---prtl~eIa~a~~V~ 170 (285)
T COG1405 99 TALEELERIASALGLPESV----RETAARIYRKA-VDKGLLRGRSIESVAAACIYAACRINGV---PRTLDEIAKALGVS 170 (285)
T ss_pred HHHHHHHHHHHHhCCCchH----HHHHHHHHHHH-hhcCCCcCCcHHHHHHHHHHHHHHHcCC---CccHHHHHHHHCCC
Confidence 5566778888888887643 34443444333 34444 4677899999999999987652 33556778889999
Q ss_pred HHHHHHHHHHHHHHH
Q 017247 274 KEKVSDCYKLILELA 288 (375)
Q Consensus 274 ~~~l~~C~~~i~~l~ 288 (375)
..+|.++++.|....
T Consensus 171 ~kei~rtyr~~~~~L 185 (285)
T COG1405 171 KKEIGRTYRLLVREL 185 (285)
T ss_pred HHHHHHHHHHHHHhc
Confidence 999999999777655
No 30
>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=84.68 E-value=7.3 Score=30.44 Aligned_cols=93 Identities=11% Similarity=0.176 Sum_probs=69.7
Q ss_pred hHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHHHhCCCCCCCcc---cchhhccCC
Q 017247 196 PISFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHIIDQVEPVNPVDYQ---NQLLGVLKI 272 (375)
Q Consensus 196 p~~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~~~l~~~~~~~~~---~~L~~~~~i 272 (375)
.-+|+-.....+...+....+..+.+.-.+..++......-.+|-.|.|+.++..++.-+ .+...|. ..|..++++
T Consensus 4 ~tdflip~c~alkipe~~wpql~e~~s~tickaliqpniall~p~licaggllttiet~n-tn~~~wt~yledl~~ilnf 82 (106)
T PF09241_consen 4 STDFLIPVCHALKIPEDFWPQLFEATSITICKALIQPNIALLPPCLICAGGLLTTIETDN-TNCQPWTCYLEDLSCILNF 82 (106)
T ss_dssp GGGGHHHHHHHTT--GGGHHHHHHHHHHHHHHHTTSGGGGGS-HHHHHHHHHHHHHHTS--TSSSTCHHHHHHHHHHHTC
T ss_pred hhhhHHHhhhhccCcHHHhHHHHHHHHHHHHHHHcCCCccccCcceeecccceEEEeccC-CCCcchhhhHHhhHHHhhc
Confidence 457888888899998887766777777778888888888899999999999999886543 2334454 566678899
Q ss_pred CHHHHHHHHHHHHHHHH
Q 017247 273 SKEKVSDCYKLILELAN 289 (375)
Q Consensus 273 ~~~~l~~C~~~i~~l~~ 289 (375)
+.+.|+..-+++.+...
T Consensus 83 stntirt~kdqv~ea~~ 99 (106)
T PF09241_consen 83 STNTIRTVKDQVSEAFS 99 (106)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHH
Confidence 99999998888877653
No 31
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=82.92 E-value=1.3 Score=43.65 Aligned_cols=90 Identities=19% Similarity=0.176 Sum_probs=57.7
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccceeeeCCCcc-
Q 017247 92 RSEAVEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDLQVEGAKYV- 170 (375)
Q Consensus 92 R~~~v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl~v~~~~~~- 170 (375)
-.-+++|+..+...-+........|-+++-..+...-.-+.+ .+-||++||+||+|+-...+|...+- .--..+.
T Consensus 152 y~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~---p~~IAva~i~lA~~~~~~~~~~~~~~-~w~~~~d~ 227 (323)
T KOG0834|consen 152 YKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYS---PHSIAVACIHLAAKLLGVELPSDTDK-RWWREFDE 227 (323)
T ss_pred hHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeec---CcEEEeehhhHHHHHcCCCCCCCccc-chhhhhcc
Confidence 455677777776666655567777888877776655445556 78899999999999987766665544 0001111
Q ss_pred -ccHHHHHHHHHHHHH
Q 017247 171 -FETKAIQRMELLVLS 185 (375)
Q Consensus 171 -f~~~~I~~mE~~IL~ 185 (375)
.+.+.+..+...+|.
T Consensus 228 ~vt~e~l~~i~~~~l~ 243 (323)
T KOG0834|consen 228 TVTNELLDDICHEFLD 243 (323)
T ss_pred cCCHHHHHHHHHHHHH
Confidence 356666555544443
No 32
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=81.09 E-value=2.7 Score=33.92 Aligned_cols=86 Identities=16% Similarity=0.165 Sum_probs=53.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccceeeeCCCccccHHH
Q 017247 96 VEWVLKVNAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDLQVEGAKYVFETKA 175 (375)
Q Consensus 96 v~Wi~~v~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl~v~~~~~~f~~~~ 175 (375)
.+||.......+.+..+..+|-.+++-.+....+-... .-++|+||+++|.++-....+....+. ...++ +.++
T Consensus 4 ~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~---PS~iAaAai~lA~~~~~~~~~~~~~l~-~~t~~--~~~~ 77 (118)
T PF02984_consen 4 YDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYP---PSVIAAAAILLARKILGKEPPWPESLE-KLTGY--DKED 77 (118)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS----HHHHHHHHHHHHHHHHHSSTCSHHHHH-HHHTS---HHH
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCC---HHHHHHHHHHHHHHHhCccccCCccch-hhcCC--CHHH
Confidence 45566654444456678888888888877777777777 889999999999999553122212221 11223 6777
Q ss_pred HHHHHHHHHHHc
Q 017247 176 IQRMELLVLSTL 187 (375)
Q Consensus 176 I~~mE~~IL~~L 187 (375)
+...=..|.+.+
T Consensus 78 l~~c~~~i~~~~ 89 (118)
T PF02984_consen 78 LKECIELIQELL 89 (118)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 766555555444
No 33
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=79.00 E-value=13 Score=36.04 Aligned_cols=83 Identities=23% Similarity=0.280 Sum_probs=55.5
Q ss_pred HHHHHHHHhCCCCcchHHHHHHHHHHHHhhccccccc-CCCHHHHHHHHHHHHHHHhCCCCCCCcccchhhccCCCHHHH
Q 017247 199 FLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSV-SYLPSVLATATMMHIIDQVEPVNPVDYQNQLLGVLKISKEKV 277 (375)
Q Consensus 199 FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l-~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L~~~~~i~~~~l 277 (375)
=+..+..++++.. -+..++.++... +.|...+ +-.--.|||||||.|.+..+ .+-....+..+.++++.+|
T Consensus 110 ~I~~m~d~~~Lp~----~I~d~A~~ifk~-v~~~k~lrGks~eai~AAclyiACRq~~---~pRT~kEI~~~anv~kKEI 181 (308)
T KOG1597|consen 110 EITAMCDRLSLPA----TIKDRANEIFKL-VEDSKLLRGKSVEALAAACLYIACRQED---VPRTFKEISAVANVSKKEI 181 (308)
T ss_pred HHHHHHHHhCCch----HHHHHHHHHHHH-HHHhhhhcCccHHHHHHHHHHHHHHhcC---CCchHHHHHHHHcCCHHHH
Confidence 3445556666653 233444444333 2355555 45556899999999998764 2335566777889999999
Q ss_pred HHHHHHHHHHHH
Q 017247 278 SDCYKLILELAN 289 (375)
Q Consensus 278 ~~C~~~i~~l~~ 289 (375)
.+|++.|.+-+.
T Consensus 182 gr~~K~i~~~l~ 193 (308)
T KOG1597|consen 182 GRCVKLIGEALE 193 (308)
T ss_pred HHHHHHHHHHHh
Confidence 999999988654
No 34
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=77.58 E-value=15 Score=30.08 Aligned_cols=82 Identities=17% Similarity=0.163 Sum_probs=48.8
Q ss_pred HHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHHHhCCCCCCCcccchhhcc--CCCHH
Q 017247 198 SFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHIIDQVEPVNPVDYQNQLLGVL--KISKE 275 (375)
Q Consensus 198 ~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L~~~~--~i~~~ 275 (375)
+|+......+++.. ..+..|..+++..+.........+..+|+||+++|.+..+.. ..+...+..+. .++.+
T Consensus 36 ~~i~~~~~~~~l~~----~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~--~~~~~~~~~~~~~~~~~~ 109 (127)
T PF00134_consen 36 DWIIELCQRLKLSP----ETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDN--PPSISDLIRISDNTFTKK 109 (127)
T ss_dssp HHHHHHHHHTT-BH----HHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS----HHHHHHHHTTTSSHHH
T ss_pred HHHHHHHHhcccch----hHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccc--cchHHHHHHHHcCCCCHH
Confidence 34444555555543 445556666666666666888999999999999999977531 22334444443 35666
Q ss_pred HHHHHHHHHH
Q 017247 276 KVSDCYKLIL 285 (375)
Q Consensus 276 ~l~~C~~~i~ 285 (375)
++..-=..|.
T Consensus 110 ~i~~~E~~iL 119 (127)
T PF00134_consen 110 DILEMEREIL 119 (127)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 6665444443
No 35
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=73.87 E-value=2.8 Score=40.72 Aligned_cols=97 Identities=13% Similarity=0.150 Sum_probs=58.0
Q ss_pred HHHcCCCHHHHHHHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccce-eeeCCCccccHHHHHHHHH
Q 017247 103 NAHYGFSTLTAILAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDL-QVEGAKYVFETKAIQRMEL 181 (375)
Q Consensus 103 ~~~~~l~~~T~~lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl-~v~~~~~~f~~~~I~~mE~ 181 (375)
+....+..+.......|++|-+........ |.....+.....++|+|+-....-.-.|. ++... -+.+++..||+
T Consensus 201 ~~~~qlta~~aiitL~~~erl~~~~e~~~~-p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlKd---~tveDmNe~ER 276 (343)
T KOG1675|consen 201 FSWAQLTAECDIITLVYAERLLWLAERDPC-PRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILKD---QSVDDMNALER 276 (343)
T ss_pred hhhhhhhhccchHHHHhhHhhhhHhhcCCC-cchhhhhhhhhheehhhhhhhhhcccHHHHHHHhh---ccHhhHHHHHH
Confidence 334445555555566888888765544321 22244444456899999844321111121 22211 26899999999
Q ss_pred HHHHHcCccccCCChHHHHHHHH
Q 017247 182 LVLSTLEWKMHPVTPISFLDHII 204 (375)
Q Consensus 182 ~IL~~L~w~l~~~Tp~~FL~~fl 204 (375)
.+|+.|+|+++.|-. .|..+|.
T Consensus 277 qfLelLqfNinvp~s-vYAKyYf 298 (343)
T KOG1675|consen 277 QFLELLQFNINVPSS-EYAKYYF 298 (343)
T ss_pred HHHHHHhhccCccHH-HHHHHHH
Confidence 999999999998853 3444443
No 36
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=64.98 E-value=23 Score=34.90 Aligned_cols=60 Identities=22% Similarity=0.280 Sum_probs=37.0
Q ss_pred HHHHHHHHHhhccccccCCchhHHHHHHHHHHhhhhhcccCCCcccceeeeCCCccccHHHHHHHH
Q 017247 115 LAINYLDRFLRSFHFQIDKPWMIQLLAVTCLSLAAKVEETQVPLLLDLQVEGAKYVFETKAIQRME 180 (375)
Q Consensus 115 lAV~ylDRfLs~~~v~~~~~~~lqLvavaCL~LAaK~eE~~vp~l~dl~v~~~~~~f~~~~I~~mE 180 (375)
.|-||+.--+-..-+.... ...||++|++|||+.+|+..|...+.. ..+.+++.+|...=
T Consensus 163 ~~wNfmNDslRT~v~vry~---pe~iACaciyLaAR~~eIpLp~~P~Wf---~~Fd~~k~eid~ic 222 (367)
T KOG0835|consen 163 AAWNFMNDSLRTDVFVRYS---PESIACACIYLAARNLEIPLPFQPHWF---KAFDTTKREIDEIC 222 (367)
T ss_pred HHHHhhhhccccceeeecC---HHHHHHHHHHHHHhhhcCCCCCCccHH---HHcCCcHHHHHHHH
Confidence 3334444333333344556 789999999999999997666655442 12444666665443
No 37
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=63.87 E-value=18 Score=35.49 Aligned_cols=40 Identities=8% Similarity=0.142 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHHHhC
Q 017247 216 EFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHIIDQVE 255 (375)
Q Consensus 216 ~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~~~l~ 255 (375)
..+..|..++........+..|.|-.||++|+++|.+.-+
T Consensus 77 ~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE 116 (305)
T TIGR00569 77 SVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEE 116 (305)
T ss_pred hHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccc
Confidence 4556666666666667778899999999999999998654
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=38.13 E-value=1.6e+02 Score=25.26 Aligned_cols=83 Identities=14% Similarity=0.032 Sum_probs=46.2
Q ss_pred cCCChHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhhcc-----cccccCCCHHHHHHHHHHHHHHHhCCCCCCCcccch
Q 017247 192 HPVTPISFLDHIIRRLGLKTSLHWEFLKRCERLLLTLVS-----DSRSVSYLPSVLATATMMHIIDQVEPVNPVDYQNQL 266 (375)
Q Consensus 192 ~~~Tp~~FL~~fl~~l~~~~~~~~~~l~~~~~ll~~~l~-----d~~~l~~~PS~IAaAal~~a~~~l~~~~~~~~~~~L 266 (375)
..++-.+|+..+.+...... ..+-.+..+++.... ...........+=++|+.+|.+.+... ..+...+
T Consensus 50 p~i~i~~fl~ri~~~~~~s~----~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~--~~~n~~~ 123 (149)
T PF08613_consen 50 PSISIRDFLSRILKYTQCSP----ECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDN--TYSNKSW 123 (149)
T ss_dssp -SS-HHHHHHHHHHHTT--H----HHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS-----HHHH
T ss_pred CCCcHHHHHHHHHHHcCCCh----HHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccc--cccHHHH
Confidence 34456678888887766644 222233333333322 222345667778888999999988743 3356678
Q ss_pred hhccCCCHHHHHHH
Q 017247 267 LGVLKISKEKVSDC 280 (375)
Q Consensus 267 ~~~~~i~~~~l~~C 280 (375)
.++.|++..++..-
T Consensus 124 a~v~gis~~eln~l 137 (149)
T PF08613_consen 124 AKVGGISLKELNEL 137 (149)
T ss_dssp HHHHTS-HHHHHHH
T ss_pred HhhcCCCHHHHHHH
Confidence 88999998887653
No 39
>KOG3866 consensus DNA-binding protein of the nucleobindin family [General function prediction only]
Probab=27.50 E-value=4.6e+02 Score=25.92 Aligned_cols=24 Identities=38% Similarity=0.642 Sum_probs=20.9
Q ss_pred cccCCCCcHHHHHHHHHHHHhccC
Q 017247 51 LEQDLFWEDEELLSLFSKEEQQLL 74 (375)
Q Consensus 51 l~~~~~~~~e~l~~Ll~kE~~~~~ 74 (375)
+..|-||++-+|.+|+.+|.+...
T Consensus 255 ~NsDGfldeqELEaLFtkELEKvY 278 (442)
T KOG3866|consen 255 LNSDGFLDEQELEALFTKELEKVY 278 (442)
T ss_pred cCCcccccHHHHHHHHHHHHHHhc
Confidence 678999999999999999977653
No 40
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=23.10 E-value=19 Score=26.05 Aligned_cols=11 Identities=45% Similarity=0.791 Sum_probs=9.9
Q ss_pred cccccccccch
Q 017247 17 LYCEEEELEDE 27 (375)
Q Consensus 17 l~c~e~~~~~~ 27 (375)
-||.+|+|++|
T Consensus 24 thcS~ehw~~D 34 (55)
T PF13824_consen 24 THCSEEHWEDD 34 (55)
T ss_pred CccCHHHHHHh
Confidence 69999999877
No 41
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=22.31 E-value=97 Score=29.22 Aligned_cols=40 Identities=10% Similarity=0.042 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHHHhC
Q 017247 216 EFLKRCERLLLTLVSDSRSVSYLPSVLATATMMHIIDQVE 255 (375)
Q Consensus 216 ~~l~~~~~ll~~~l~d~~~l~~~PS~IAaAal~~a~~~l~ 255 (375)
.+++.|.-++.....-..+-.+.|-.+|..|+++|.+.-+
T Consensus 60 ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE 99 (264)
T KOG0794|consen 60 RVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEE 99 (264)
T ss_pred HHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhh
Confidence 4444454444444444457899999999999999997543
Done!