Query 016163
Match_columns 394
No_of_seqs 323 out of 1705
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 04:22:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016163.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016163hhsearch_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 4.7E-53 1E-57 411.1 24.2 284 74-388 41-334 (335)
2 KOG0655 G1/S-specific cyclin E 100.0 2.8E-36 6E-41 287.1 20.0 219 73-307 106-338 (408)
3 KOG0653 Cyclin B and related k 100.0 4.2E-33 9.1E-38 281.9 20.0 234 77-322 126-365 (391)
4 COG5024 Cyclin [Cell division 100.0 6.6E-32 1.4E-36 271.9 13.4 245 77-336 180-429 (440)
5 KOG0654 G2/Mitotic-specific cy 100.0 6.1E-29 1.3E-33 244.5 9.2 244 77-333 102-351 (359)
6 KOG0834 CDK9 kinase-activating 99.9 1.7E-23 3.7E-28 204.4 16.6 201 104-309 35-250 (323)
7 TIGR00569 ccl1 cyclin ccl1. Un 99.9 4.9E-23 1.1E-27 201.2 18.8 190 106-303 54-251 (305)
8 KOG0835 Cyclin L [General func 99.9 8.3E-22 1.8E-26 188.4 18.5 195 104-306 19-231 (367)
9 PF00134 Cyclin_N: Cyclin, N-t 99.9 5.4E-22 1.2E-26 169.1 11.4 123 80-208 1-127 (127)
10 KOG0794 CDK8 kinase-activating 99.8 3.9E-20 8.4E-25 169.5 12.0 192 106-307 39-241 (264)
11 COG5333 CCL1 Cdk activating ki 99.8 7.3E-18 1.6E-22 161.5 13.8 163 105-273 42-209 (297)
12 PF02984 Cyclin_C: Cyclin, C-t 99.6 6.6E-16 1.4E-20 129.4 9.7 115 210-330 1-115 (118)
13 PRK00423 tfb transcription ini 99.5 1.1E-12 2.3E-17 129.4 21.1 184 106-304 120-304 (310)
14 cd00043 CYCLIN Cyclin box fold 99.4 9.3E-13 2E-17 103.3 7.9 87 108-200 2-88 (88)
15 KOG2496 Cdk activating kinase 99.4 2.1E-11 4.4E-16 116.6 15.6 151 115-270 63-222 (325)
16 smart00385 CYCLIN domain prese 99.3 8E-12 1.7E-16 97.0 7.7 83 113-201 1-83 (83)
17 COG1405 SUA7 Transcription ini 98.9 1.8E-07 4E-12 90.9 18.3 185 106-304 95-279 (285)
18 KOG1597 Transcription initiati 98.6 1.4E-06 3.1E-11 83.6 16.7 186 107-306 103-290 (308)
19 smart00385 CYCLIN domain prese 98.3 4E-06 8.6E-11 64.6 8.5 81 214-301 1-82 (83)
20 cd00043 CYCLIN Cyclin box fold 98.3 5.5E-06 1.2E-10 64.4 8.8 85 209-300 2-87 (88)
21 PF08613 Cyclin: Cyclin; Inte 98.2 8E-06 1.7E-10 72.2 8.8 92 111-207 54-149 (149)
22 KOG4164 Cyclin ik3-1/CABLES [C 97.9 6.5E-06 1.4E-10 81.6 3.3 98 110-210 384-482 (497)
23 KOG1598 Transcription initiati 97.7 0.00052 1.1E-08 71.1 12.3 147 114-271 73-224 (521)
24 PF00382 TFIIB: Transcription 95.8 0.077 1.7E-06 40.6 8.3 71 216-293 1-71 (71)
25 PF00382 TFIIB: Transcription 95.5 0.052 1.1E-06 41.5 6.4 60 115-178 1-60 (71)
26 KOG1674 Cyclin [General functi 94.1 0.13 2.8E-06 48.5 6.5 96 112-210 79-181 (218)
27 PF09080 K-cyclin_vir_C: K cyc 93.5 1.1 2.4E-05 35.9 9.5 95 212-306 4-101 (106)
28 PRK00423 tfb transcription ini 93.0 0.82 1.8E-05 45.3 10.4 87 212-305 125-211 (310)
29 COG1405 SUA7 Transcription ini 81.4 14 0.00031 36.2 10.3 87 211-305 99-186 (285)
30 PF09241 Herp-Cyclin: Herpesvi 80.9 21 0.00046 28.4 9.0 95 211-305 3-99 (106)
31 PF02984 Cyclin_C: Cyclin, C-t 78.7 5.4 0.00012 32.4 5.6 87 112-204 4-90 (118)
32 KOG0834 CDK9 kinase-activating 77.7 2 4.4E-05 42.8 3.2 89 109-202 153-244 (323)
33 KOG1675 Predicted cyclin [Gene 77.5 3 6.5E-05 41.1 4.1 99 117-220 199-298 (343)
34 PF00134 Cyclin_N: Cyclin, N-t 75.5 25 0.00054 29.0 8.9 67 233-301 51-119 (127)
35 KOG1597 Transcription initiati 69.5 39 0.00085 33.3 9.6 83 216-306 111-194 (308)
36 KOG0835 Cyclin L [General func 51.3 52 0.0011 32.9 7.0 61 129-195 161-221 (367)
37 PF08613 Cyclin: Cyclin; Inte 38.8 2.6E+02 0.0057 24.2 9.8 82 209-296 51-137 (149)
38 TIGR00569 ccl1 cyclin ccl1. Un 37.1 52 0.0011 32.6 4.7 39 233-271 78-116 (305)
39 PF13824 zf-Mss51: Zinc-finger 25.6 19 0.0004 26.5 -0.5 11 18-28 24-34 (55)
40 PF03261 CDK5_activator: Cycli 23.5 1.7E+02 0.0037 29.5 5.6 50 151-201 270-324 (346)
41 PF07226 DUF1422: Protein of u 23.1 1.2E+02 0.0025 25.9 3.7 38 125-166 40-77 (117)
42 PF00524 PPV_E1_N: E1 Protein, 22.7 81 0.0017 27.3 2.8 11 312-322 75-85 (130)
43 KOG3866 DNA-binding protein of 22.1 5E+02 0.011 26.0 8.3 32 63-94 245-278 (442)
No 1
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.7e-53 Score=411.13 Aligned_cols=284 Identities=44% Similarity=0.629 Sum_probs=239.1
Q ss_pred CCCCcHHHHHHHHHhhccCC----ccccCCCCcccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCc
Q 016163 74 DLSWQDDELSTLLSKEVPNR----LYNILKTNPSLSRARSEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDK 149 (394)
Q Consensus 74 d~~~~de~l~~Ll~kE~~~~----~~~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~ 149 (394)
+++|+++.+.+|+++|.++. ++..+++. +++.+|.++++||++|++++++.++|+++||||||||++.+++++.+
T Consensus 41 ~~~~~e~~i~~ll~kEe~~~p~~~~~~~~~~~-~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k 119 (335)
T KOG0656|consen 41 FLLWDERVLANLLEKEEQHNPSLDYFLCVQKL-ILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDK 119 (335)
T ss_pred cccccHHHHHHHHHHHHHhCCCCchhhhcccc-cccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCc
Confidence 37899999999999999866 24455555 88999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHHHHhhhcccccCCCccchhhcccccccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHcCCCCcc
Q 016163 150 PWMAQLAAVACLSLAAKVEETQVPLLLDLQVEDIKFVFEAKTIQRMEILVLSTLQWKMNPVTPLSFLDYIARRLGLKGYL 229 (394)
Q Consensus 150 p~~lqLvavaCL~LAaK~EE~~~p~l~dl~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~l~~~~~~ 229 (394)
||++||+|+|||+||||+||+.+|.+.|+++.+..|.|.+++|+|||++||++|+|||+++||++|+++|+++++..+..
T Consensus 120 ~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~ 199 (335)
T KOG0656|consen 120 PWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHN 199 (335)
T ss_pred hHHHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcccch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998877
Q ss_pred cHHHHHHHHHHHHHhhchhcccCCCHHHHHHHHHHHHHHHhccccCcchhhhhHhHcCCCHHHHHHHHHHHHHHHHhhcc
Q 016163 230 CWEFLKRCDRILLSAISDSSFMQYLPSVMANATMLHVVQNIESSLGVEYEKQLLNILGTDKDKVEHCSKLIMQLAEQVQG 309 (394)
Q Consensus 230 ~~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~~~~~L~~~~~~~~~~l~~C~~~l~~l~~~~~~ 309 (394)
...++.+|..++..+..|.+|+.|+||+||+|++..+...+.+.....+...+..+.+++++.+..|+... +
T Consensus 200 ~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~~~--~------ 271 (335)
T KOG0656|consen 200 KHLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSVSASVDGLDFREYENNLLSLLSLSKEKVNRCYDHF--L------ 271 (335)
T ss_pred HHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhcchhhh--h------
Confidence 78899999999999999999999999999999999999988877666677888889999999999998800 0
Q ss_pred CCchhhhhcccCCCCCCCCCCCcccccccccccCCCCCCCCcC------CccCCCCCCCCCCCCcccccchhhccccccc
Q 016163 310 QGSQSIKRKFGSITVPVVPGSPNGVMDVSFSSSDSSNDSWSVA------SSVSSSPEPLSKKNRSQAQDHDQDQLLLQGA 383 (394)
Q Consensus 310 ~~~~~~~~ky~s~~~~~~p~sP~~Vld~~~ss~~ss~ds~~~~------~s~~ss~~p~~kr~~~~~~~~~~~~~~~~~~ 383 (394)
... ..++.++++..- | +.+|..+ ++.+++++|..|+||.+..++ +.++-.+.
T Consensus 272 ----------~~~-----~~~~~~~l~~~~--~---~~~~~~~~~~~~~~s~~~~~~~~~~~rr~~~~~~--~~~s~~~~ 329 (335)
T KOG0656|consen 272 ----------SKI-----LNSESDCLRGEA--S---NESGEASLRDSSSSSSQSPNSPSLKKRRVSSDKE--RKQSSPPT 329 (335)
T ss_pred ----------hhc-----cCCccccccHHH--H---hhhhcccccccchhccCCCCcccccccccccccc--cccCCCCc
Confidence 001 234445555311 1 1111111 112223467888899988888 77777776
Q ss_pred cCccc
Q 016163 384 TPDFL 388 (394)
Q Consensus 384 ~~~~~ 388 (394)
.++.+
T Consensus 330 ~~~~l 334 (335)
T KOG0656|consen 330 EVRDL 334 (335)
T ss_pred ccccc
Confidence 66543
No 2
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2.8e-36 Score=287.09 Aligned_cols=219 Identities=26% Similarity=0.428 Sum_probs=189.2
Q ss_pred CCCCCc--HHHHHHHHHhhccCC-ccccC-CCCcccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccc-cccC
Q 016163 73 QDLSWQ--DDELSTLLSKEVPNR-LYNIL-KTNPSLSRARSEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSF-QLQR 147 (394)
Q Consensus 73 ~d~~~~--de~l~~Ll~kE~~~~-~~~~~-q~~~i~~~~R~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~-~v~~ 147 (394)
+++.|. .+.+..|+.||+.+. ....+ |.....++||++++|||++||+.|++.++|+|+||.||||||... .+.+
T Consensus 106 p~lswgn~~eVW~lM~kkee~~l~~~~~l~qHpdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~k 185 (408)
T KOG0655|consen 106 PCLSWGNSKEVWLLMLKKEERYLRDKHFLEQHPDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSK 185 (408)
T ss_pred ccccccCHHHHHHHHHccchhhhhhhHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhh
Confidence 566675 489999999999876 22222 334488999999999999999999999999999999999999764 5666
Q ss_pred CcchhHHHHHHHHHHhhhcccccCCCccchh-hcccccccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHcCCC
Q 016163 148 DKPWMAQLAAVACLSLAAKVEETQVPLLLDL-QVEDIKFVFEAKTIQRMEILVLSTLQWKMNPVTPLSFLDYIARRLGLK 226 (394)
Q Consensus 148 ~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl-~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~l~~~ 226 (394)
.. +||||+||||||||+||+++|++.+| +|+++.| +.++|+.||..||++|+|++.++|..++|..|+...+.+
T Consensus 186 t~---lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAc--s~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n 260 (408)
T KOG0655|consen 186 TN---LQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGAC--SEDDILTMELIILKALKWELSPITIISWLNVYLQVDALN 260 (408)
T ss_pred hh---HHHhhHHHHHHHHHHhhccCccccceeeeccCcc--chHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcC
Confidence 66 99999999999999999999999999 8999987 899999999999999999999999999999999987654
Q ss_pred C--------cccHHHHHHHHHHHHHhhchhcccCCCHHHHHHHHHHHHHHHhccccCcchhhhhHhHcCCCHHHHHHHHH
Q 016163 227 G--------YLCWEFLKRCDRILLSAISDSSFMQYLPSVMANATMLHVVQNIESSLGVEYEKQLLNILGTDKDKVEHCSK 298 (394)
Q Consensus 227 ~--------~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~~~~~L~~~~~~~~~~l~~C~~ 298 (394)
+ ....+|++.| .++++++.+..++.|.-++|||||+++-... ....+.+|+.+.+|.+|++
T Consensus 261 ~~~k~l~Pq~~~~efiqia-qlLDlc~ldids~~fsYrilaAAal~h~~s~----------e~v~kaSG~~w~~ie~cv~ 329 (408)
T KOG0655|consen 261 DAPKVLLPQYSQEEFIQIA-QLLDLCILDIDSLEFSYRILAAAALCHFTSI----------EVVKKASGLEWDSIEECVD 329 (408)
T ss_pred CCCceeccccchHHHHHHH-HHHHHHHhccccccchHHHHHHHHHHHHhHH----------HHHHHcccccHHHHHHHHH
Confidence 3 2235788877 8889999999999999999999999886531 2346689999999999999
Q ss_pred HHHHHHHhh
Q 016163 299 LIMQLAEQV 307 (394)
Q Consensus 299 ~l~~l~~~~ 307 (394)
.|.-+++--
T Consensus 330 wm~Pf~rvi 338 (408)
T KOG0655|consen 330 WMVPFVRVI 338 (408)
T ss_pred HHHHHHHHH
Confidence 999887644
No 3
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.2e-33 Score=281.90 Aligned_cols=234 Identities=24% Similarity=0.351 Sum_probs=200.6
Q ss_pred CcHHHHHHHHHhh-ccCC-ccccCCCCcccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHH
Q 016163 77 WQDDELSTLLSKE-VPNR-LYNILKTNPSLSRARSEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQ 154 (394)
Q Consensus 77 ~~de~l~~Ll~kE-~~~~-~~~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lq 154 (394)
|.++++.++..+| .... .... +...++..||.++|||+++|+.+|++.++|+++|||++||||++..++..+ +|
T Consensus 126 y~~di~~~l~~~e~~~~p~~~~~-~~~e~~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~---lq 201 (391)
T KOG0653|consen 126 YVQDIFEYLRQLELEFLPLSYDI-SQSEIRAKMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKK---LQ 201 (391)
T ss_pred HHHHHHHHHHHHHHhhCchhhhc-ccccccHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHH---hh
Confidence 6779999999998 3333 2222 233388899999999999999999999999999999999999998888777 99
Q ss_pred HHHHHHHH-hhhcccccCCCccchh-hcccccccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHcCCCCcccHH
Q 016163 155 LAAVACLS-LAAKVEETQVPLLLDL-QVEDIKFVFEAKTIQRMEILVLSTLQWKMNPVTPLSFLDYIARRLGLKGYLCWE 232 (394)
Q Consensus 155 LvavaCL~-LAaK~EE~~~p~l~dl-~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~l~~~~~~~~~ 232 (394)
|+|++||+ ||+|+||..+|.+.|+ +++++.| ++++|++||+.||++|+|++..|||+.||++|++....+ ..
T Consensus 202 Lvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~--s~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d----~~ 275 (391)
T KOG0653|consen 202 LVGVSALLSIACKYEEISLPSVEDLVLITDGAY--SREEILRMEKYILNVLEFDLSVPTPLSFLRRFLKAADYD----IK 275 (391)
T ss_pred HHhHHHHHHHHHhhhhccCCccceeEeeeCCcc--chHHHHHHHHHHHhccCeeecCCchHHHHHHHHHhhhcc----hh
Confidence 99999966 9999999999999999 5777765 999999999999999999999999999999999998732 23
Q ss_pred HHHHHHHHHHHhhchhcccCCCHHHHHHHHHHHHHHHhccccCcchhhhhHhHcCCCHHHHHHHHHHHHHHHHhhccCC-
Q 016163 233 FLKRCDRILLSAISDSSFMQYLPSVMANATMLHVVQNIESSLGVEYEKQLLNILGTDKDKVEHCSKLIMQLAEQVQGQG- 311 (394)
Q Consensus 233 ~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~~~~~L~~~~~~~~~~l~~C~~~l~~l~~~~~~~~- 311 (394)
......++++.+++|++++.++||.+|+|+++++++..... ..|...+..++|+....+..|.+.+..+.......+
T Consensus 276 ~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~~~~~--~~w~~~~~~~sg~~~~~~~~~~~~~~~~~~~~~~~~~ 353 (391)
T KOG0653|consen 276 TRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALRMLSKG--DVWSPTLEHYSGYSESYLFECARSLSALSLSSLQNPS 353 (391)
T ss_pred HHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHHhccC--CccCCCCeeccCCCcHHHHHHHHHHHHHHHHhcccch
Confidence 44567789999999999999999999999999999988632 269999999999999899999999999666554432
Q ss_pred chh-hhhcccCC
Q 016163 312 SQS-IKRKFGSI 322 (394)
Q Consensus 312 ~~~-~~~ky~s~ 322 (394)
.+. +.+||.+.
T Consensus 354 ~~~~~~~ky~~~ 365 (391)
T KOG0653|consen 354 LRASVLNKYNSS 365 (391)
T ss_pred hHHHHHHHhccc
Confidence 343 89999865
No 4
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=99.97 E-value=6.6e-32 Score=271.90 Aligned_cols=245 Identities=25% Similarity=0.316 Sum_probs=206.9
Q ss_pred CcHHHHHHHHHhhccCCc---cccCCCCcccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhH
Q 016163 77 WQDDELSTLLSKEVPNRL---YNILKTNPSLSRARSEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMA 153 (394)
Q Consensus 77 ~~de~l~~Ll~kE~~~~~---~~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~l 153 (394)
|+.+++.+|+++|....+ + -.+...+...||..+|+|+.+|+.+|++.++|+++|||++||||++..+.-.+ +
T Consensus 180 y~~~Ife~l~k~e~~~lp~~~y-l~kq~~~~~~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k---~ 255 (440)
T COG5024 180 YASDIFEYLLKLELIDLPNPNY-LIKQSLYEWSMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEK---Y 255 (440)
T ss_pred HHHHHHHHHHHHHHHhcCcHHH-HhhcchhHHhHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHH---H
Confidence 688999999999999872 2 22333355599999999999999999999999999999999999999999999 9
Q ss_pred HHHHHHHHHhhhcccccCCCccchh-hcccccccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHcCCCCcccHH
Q 016163 154 QLAAVACLSLAAKVEETQVPLLLDL-QVEDIKFVFEAKTIQRMEILVLSTLQWKMNPVTPLSFLDYIARRLGLKGYLCWE 232 (394)
Q Consensus 154 qLvavaCL~LAaK~EE~~~p~l~dl-~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~l~~~~~~~~~ 232 (394)
||+|++|||||||+||++.|.+.++ +++++.| +.++|+++|+.+|.+|+|++..|+|..|++++.+.-+....
T Consensus 256 QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~--t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka~dyd~~---- 329 (440)
T COG5024 256 QLVGISALFIASKYEEVNCPSIKDLVYATDGAF--TRDDIIRAERYMLEVLDFNISWPSPMSFLRRISKASDYDIF---- 329 (440)
T ss_pred HHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccc--cHHHHHHHHHHHhhhcccccCCCChHHHHHHHHhhcccchh----
Confidence 9999999999999999999999999 5777766 89999999999999999999999999998888776554322
Q ss_pred HHHHHHHHHHHhhchhcccCCCHHHHHHHHHHHHHHHhccccCcchhhhhHhHcC-CCHHHHHHHHHHHHHHHHhhccCC
Q 016163 233 FLKRCDRILLSAISDSSFMQYLPSVMANATMLHVVQNIESSLGVEYEKQLLNILG-TDKDKVEHCSKLIMQLAEQVQGQG 311 (394)
Q Consensus 233 ~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~~~~~L~~~~~-~~~~~l~~C~~~l~~l~~~~~~~~ 311 (394)
-...+.++++.+..+++|.+++||.+|+||++.+++.++.. .|...|..++| |+.+++..++..+.+.+..... .
T Consensus 330 srt~~k~~~e~s~~~~~f~~~~~S~~~aaa~~~s~~~~~~~---~w~~~l~~ySg~y~~~~l~~~~~~~~~~l~~~~~-~ 405 (440)
T COG5024 330 SRTPAKFSSEISPVDYKFIQISPSWCAAAAMYLSRKILSQN---QWDRTLIHYSGNYTNPDLKPLNESNKENLQNPSV-H 405 (440)
T ss_pred hhhhHhhhCCchHhhhhhccCCchHHHHHHHHHHHhhhccC---CCCccccccCCCCCchhHHHHHHHHHHHhcccch-h
Confidence 22357789999999999999999999999999999998743 39999999999 9999999999999998876633 2
Q ss_pred chhhhhcccCCCCCCCCCCCccccc
Q 016163 312 SQSIKRKFGSITVPVVPGSPNGVMD 336 (394)
Q Consensus 312 ~~~~~~ky~s~~~~~~p~sP~~Vld 336 (394)
+.++.+||....+.. ...|++-+.
T Consensus 406 ~~~i~~Ky~~~~~~~-~s~~~~ew~ 429 (440)
T COG5024 406 HDAIFPKYPSPTFGK-ASSPTGEWI 429 (440)
T ss_pred hhhhhhccccccccc-cchHHHHHH
Confidence 367788887654432 233444433
No 5
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=99.95 E-value=6.1e-29 Score=244.46 Aligned_cols=244 Identities=22% Similarity=0.340 Sum_probs=213.9
Q ss_pred CcHHHHHHHHHhhcc-CC----ccccCCCCcccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcch
Q 016163 77 WQDDELSTLLSKEVP-NR----LYNILKTNPSLSRARSEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPW 151 (394)
Q Consensus 77 ~~de~l~~Ll~kE~~-~~----~~~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~ 151 (394)
|..++..++..-|.. .. ++..+|.+ +++.||.++|+|.++|++.+++..+++++++++.|||+....+.+.+
T Consensus 102 ~~~~I~~~~r~~ei~~~rp~~~~~e~vq~d-~t~smrgilvdwlvevsee~r~~~e~l~ls~~~~drfl~~~~~~~~k-- 178 (359)
T KOG0654|consen 102 IAAKIYNTLRVSDIKSERPLPSKFEFVQAD-ITPSMRGILVDWLVEVSEEYRLTFETLYLSVNYRDRFLSYKEVNKQK-- 178 (359)
T ss_pred HHHHHhhcccccchhhccCcccceeeeecC-CCcchhhhhhhhhhHHHHHHHhhhhheeecHHHHHHHhccCccHHHH--
Confidence 455677777666666 33 56677888 99999999999999999999999999999999999999999999988
Q ss_pred hHHHHHHHHHHhhhcccccCCCccchh-hcccccccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHcCCCCccc
Q 016163 152 MAQLAAVACLSLAAKVEETQVPLLLDL-QVEDIKFVFEAKTIQRMEILVLSTLQWKMNPVTPLSFLDYIARRLGLKGYLC 230 (394)
Q Consensus 152 ~lqLvavaCL~LAaK~EE~~~p~l~dl-~v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~l~~~~~~~ 230 (394)
+|++|++|++||+|+||..+|.+.++ .+.++.| +..++.+||..||..|.|.+..||.-.|+..|++.... ..
T Consensus 179 -~ql~g~s~m~I~sk~ee~~~~~~~ef~~itd~ty--~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~~~~~---~~ 252 (359)
T KOG0654|consen 179 -LQLVGISAMLIASKYEEIKEPRVEEFCYITDNTY--TYWQVLRMEIDILNALTFELVRPTSKTFLRRFLRVAQT---PE 252 (359)
T ss_pred -HHHhCcccceeeccchhhcchHHHHHHhhhhhhh--HHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHHhhcc---hh
Confidence 99999999999999999999999999 5777766 78899999999999999999999999999999877543 22
Q ss_pred HHHHHHHHHHHHHhhchhcccCCCHHHHHHHHHHHHHHHhccccCcchhhhhHhHcCCCHHHHHHHHHHHHHHHHhhccC
Q 016163 231 WEFLKRCDRILLSAISDSSFMQYLPSVMANATMLHVVQNIESSLGVEYEKQLLNILGTDKDKVEHCSKLIMQLAEQVQGQ 310 (394)
Q Consensus 231 ~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~~~~~L~~~~~~~~~~l~~C~~~l~~l~~~~~~~ 310 (394)
.+.-..|.++.++++.++.|+.|.||+|||||+++|.-.++ .-+|...|+.++||+.+++..|+..|. ++.+....
T Consensus 253 ~~~e~~~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~---~~pW~~~L~~~T~y~~edl~~~v~~L~-~~l~~~~~ 328 (359)
T KOG0654|consen 253 LQVEPLANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLD---FHPWNQTLEDYTGYKAEDLKPCVLDLH-LYLNASGT 328 (359)
T ss_pred HHHHHHHHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhcc---CCCCchhhHHhhcccHHHHHHHHHHHh-cccCCCCC
Confidence 34456688999999999999999999999999999999887 567999999999999999999999999 77777666
Q ss_pred CchhhhhcccCCCCCCCCCCCcc
Q 016163 311 GSQSIKRKFGSITVPVVPGSPNG 333 (394)
Q Consensus 311 ~~~~~~~ky~s~~~~~~p~sP~~ 333 (394)
..++++.||...++..|+.-|..
T Consensus 329 ~l~air~ky~~~k~~~Va~~~~p 351 (359)
T KOG0654|consen 329 DLPAIREKYKQSKFKEVALLPVP 351 (359)
T ss_pred chHHHHHHhhhhhhhhhhccCCC
Confidence 78999999998777776654443
No 6
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.91 E-value=1.7e-23 Score=204.38 Aligned_cols=201 Identities=19% Similarity=0.222 Sum_probs=173.1
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchhhccc-
Q 016163 104 LSRARSEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDLQVED- 182 (394)
Q Consensus 104 ~~~~R~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl~v~~- 182 (394)
....|...+.||.+++..+|+++.|+++|+.||+||+..+++.... .+.+|++||+||+|+||+ +..+.|+....
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 3579999999999999999999999999999999999999999988 799999999999999999 56677773111
Q ss_pred -----------ccccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhccc
Q 016163 183 -----------IKFVFEAKTIQRMEILVLSTLQWKMNPVTPLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFM 251 (394)
Q Consensus 183 -----------~~~~f~~~~I~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l 251 (394)
..|.-.++.|+..|+.||++|+|++++-+||.||..|+..++............|+.++..++...-++
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 223334789999999999999999999999999999999998776544446677889999999999999
Q ss_pred CCCHHHHHHHHHHHHHHHhccccCcchhh-hhHhHcC--CCHHHHHHHHHHHHHHHHhhcc
Q 016163 252 QYLPSVMANATMLHVVQNIESSLGVEYEK-QLLNILG--TDKDKVEHCSKLIMQLAEQVQG 309 (394)
Q Consensus 252 ~~~PS~IAaAai~lA~~~l~~~~~~~~~~-~L~~~~~--~~~~~l~~C~~~l~~l~~~~~~ 309 (394)
+|+|.+||+|||++|.+..+- ..+.+.. .|+..++ ++.+++.+.+..+..++...+.
T Consensus 191 ~y~p~~IAva~i~lA~~~~~~-~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y~~~~~ 250 (323)
T KOG0834|consen 191 QYSPHSIAVACIHLAAKLLGV-ELPSDTDKRWWREFDETVTNELLDDICHEFLDLYEQTPQ 250 (323)
T ss_pred eecCcEEEeehhhHHHHHcCC-CCCCCcccchhhhhcccCCHHHHHHHHHHHHHHHhhccc
Confidence 999999999999999988775 3333333 5888888 9999999999999999977643
No 7
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.90 E-value=4.9e-23 Score=201.19 Aligned_cols=190 Identities=17% Similarity=0.223 Sum_probs=149.2
Q ss_pred HHHHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchhh-ccc
Q 016163 106 RARSEAVDWMLKVNAHYS--FTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDLQ-VED 182 (394)
Q Consensus 106 ~~R~~lvdWi~~v~~~~~--l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl~-v~~ 182 (394)
..|...+.+|.++|.+++ +++.|+++|+.||+||+.+.++...+ .+++|+|||+||+|+||..+ .+.++. ...
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 99999999999999999999999887 89999999999999999954 566663 222
Q ss_pred ccccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHcCC---CCcccHHHHHHHHHHHHHhhchhcccCCCHHHHH
Q 016163 183 IKFVFEAKTIQRMEILVLSTLQWKMNPVTPLSFLDYIARRLGL---KGYLCWEFLKRCDRILLSAISDSSFMQYLPSVMA 259 (394)
Q Consensus 183 ~~~~f~~~~I~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~l~~---~~~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IA 259 (394)
......+++|++||..||++|+|++.+++|+.++..|+..++. .......+.+.++.++..++...-++.|+||+||
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 2222357999999999999999999999999999998865431 1111124556788888888888889999999999
Q ss_pred HHHHHHHHHHhccccCcchhhhhHhHcCC--CHHHHHHHHHHHHHH
Q 016163 260 NATMLHVVQNIESSLGVEYEKQLLNILGT--DKDKVEHCSKLIMQL 303 (394)
Q Consensus 260 aAai~lA~~~l~~~~~~~~~~~L~~~~~~--~~~~l~~C~~~l~~l 303 (394)
+|||++|.+.++.. .....+.++.. +.+.+..-+..|.++
T Consensus 210 lAAI~lA~~~~~~~----l~~~~~e~~~~~~~~~~~~~l~~~~~~~ 251 (305)
T TIGR00569 210 LAAILHTASRAGLN----MESYLTEQLSVPGNREELPQLIDIMREL 251 (305)
T ss_pred HHHHHHHHHHhCCC----CcccchhhhcccccHHHHHHHHHHHHHH
Confidence 99999999988743 22222344555 555555555555544
No 8
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.88 E-value=8.3e-22 Score=188.43 Aligned_cols=195 Identities=17% Similarity=0.284 Sum_probs=172.3
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchhh-c--
Q 016163 104 LSRARSEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDLQ-V-- 180 (394)
Q Consensus 104 ~~~~R~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl~-v-- 180 (394)
....|.-.++||.+.+.-++|+..+.+++..+|.||+...++.+.+ +..+++||++||+|+||. |-.+.|++ |
T Consensus 19 e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~---~e~vv~ACv~LASKiEE~-Prr~rdVinVFh 94 (367)
T KOG0835|consen 19 EEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHD---FEIVVMACVLLASKIEEE-PRRIRDVINVFH 94 (367)
T ss_pred HHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhcccccccc---HHHHHHHHHHHHhhhccc-cccHhHHHHHHH
Confidence 3578999999999999999999999999999999999999999888 999999999999999997 45555552 1
Q ss_pred ---------------ccccccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhh
Q 016163 181 ---------------EDIKFVFEAKTIQRMEILVLSTLQWKMNPVTPLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAI 245 (394)
Q Consensus 181 ---------------~~~~~~f~~~~I~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl 245 (394)
-+..|.-.+..+.++|+.||++|+|++++.+|+.++-.|+..+++.++. .+++.+|.++..++
T Consensus 95 ~L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~--~l~Q~~wNfmNDsl 172 (367)
T KOG0835|consen 95 YLEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNL--KLLQAAWNFMNDSL 172 (367)
T ss_pred HHHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCch--hHHHHHHHhhhhcc
Confidence 0112222467899999999999999999999999999999999998886 58889999999999
Q ss_pred chhcccCCCHHHHHHHHHHHHHHHhccccCcchhhhhHhHcCCCHHHHHHHHHHHHHHHHh
Q 016163 246 SDSSFMQYLPSVMANATMLHVVQNIESSLGVEYEKQLLNILGTDKDKVEHCSKLIMQLAEQ 306 (394)
Q Consensus 246 ~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~~~~~L~~~~~~~~~~l~~C~~~l~~l~~~ 306 (394)
...-|+.|+|+.||+|||++|.+.++ .+.+..+.|+.+++.++++|...+-.+..+|..
T Consensus 173 RT~v~vry~pe~iACaciyLaAR~~e--IpLp~~P~Wf~~Fd~~k~eid~ic~~l~~lY~~ 231 (367)
T KOG0835|consen 173 RTDVFVRYSPESIACACIYLAARNLE--IPLPFQPHWFKAFDTTKREIDEICYRLIPLYKR 231 (367)
T ss_pred ccceeeecCHHHHHHHHHHHHHhhhc--CCCCCCccHHHHcCCcHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999988 455567788999999999999999999998876
No 9
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=99.87 E-value=5.4e-22 Score=169.14 Aligned_cols=123 Identities=33% Similarity=0.480 Sum_probs=102.2
Q ss_pred HHHHHHHHhhccCC---ccccCCCCcccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHH
Q 016163 80 DELSTLLSKEVPNR---LYNILKTNPSLSRARSEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLA 156 (394)
Q Consensus 80 e~l~~Ll~kE~~~~---~~~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLv 156 (394)
|++.+|+++|.+.. .+-..+. .++...|..+++||.+++.++++++.|+++|+.|||||+.+.++.+.+ ++++
T Consensus 1 ~i~~~~~~~e~~~~~~~~~~~~~~-~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~---~~li 76 (127)
T PF00134_consen 1 DIFRYLLEKELKYKPNPDYLEQQP-EITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSK---LQLI 76 (127)
T ss_dssp HHHHHHHHHHHHTTCCTTHGTGTS-SHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCG---HHHH
T ss_pred CHHHHHHHHHHHHCcCccccccCh-hcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccch---hhhh
Confidence 68899999998865 2222223 488899999999999999999999999999999999999999888777 9999
Q ss_pred HHHHHHhhhcccccCCCccchhh-cccccccccHHHHHHHHHHHHHHcCcccc
Q 016163 157 AVACLSLAAKVEETQVPLLLDLQ-VEDIKFVFEAKTIQRMEILVLSTLQWKMN 208 (394)
Q Consensus 157 avaCL~LAaK~EE~~~p~l~dl~-v~~~~~~f~~~~I~~mE~~IL~~L~w~l~ 208 (394)
|+|||+||+|++|..+|.+.++. +. .+.|++++|.+||+.||++|+|+++
T Consensus 77 ~~~cl~lA~K~~e~~~~~~~~~~~~~--~~~~~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 77 ALACLFLASKMEEDNPPSISDLIRIS--DNTFTKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp HHHHHHHHHHHHTSS--HHHHHHHHT--TTSSHHHHHHHHHHHHHHHTTT---
T ss_pred hhhHHHHhhhhhccccchHHHHHHHH--cCCCCHHHHHHHHHHHHHHCCCCcC
Confidence 99999999999999899999884 43 4467999999999999999999985
No 10
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.83 E-value=3.9e-20 Score=169.53 Aligned_cols=192 Identities=23% Similarity=0.269 Sum_probs=162.1
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchhh-----c
Q 016163 106 RARSEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDLQ-----V 180 (394)
Q Consensus 106 ~~R~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl~-----v 180 (394)
..+--.-+.|.+++.++++.+.++++|+.||-||+.+.++..-. ..|+|.||++||||+||..+...+-+. +
T Consensus 39 ~l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~---p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L 115 (264)
T KOG0794|consen 39 KLKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIE---PRLLAPTCLYLACKVEECPIVHIRLLVNEAKVL 115 (264)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccC---HHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHH
Confidence 45666677899999999999999999999999999999988888 899999999999999998311111110 1
Q ss_pred ------ccccccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcccCCC
Q 016163 181 ------EDIKFVFEAKTIQRMEILVLSTLQWKMNPVTPLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFMQYL 254 (394)
Q Consensus 181 ------~~~~~~f~~~~I~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~ 254 (394)
....+.++.++|..||..+|+.|+.-|-+-+|+.-|..++..+|..+. ..+..++.++..++...-++-|+
T Consensus 116 ~~~f~~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~d~---~~l~~~W~ivNDSyr~Dl~Ll~P 192 (264)
T KOG0794|consen 116 KTRFSYWPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGINDQ---KLLQLAWSIVNDSYRMDLCLLYP 192 (264)
T ss_pred hhhcccchhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcccch---hhhhhhHhhhcchhhcceeeecC
Confidence 233445578999999999999999999999999999999999987443 35677888999999999999999
Q ss_pred HHHHHHHHHHHHHHHhccccCcchhhhhHhHcCCCHHHHHHHHHHHHHHHHhh
Q 016163 255 PSVMANATMLHVVQNIESSLGVEYEKQLLNILGTDKDKVEHCSKLIMQLAEQV 307 (394)
Q Consensus 255 PS~IAaAai~lA~~~l~~~~~~~~~~~L~~~~~~~~~~l~~C~~~l~~l~~~~ 307 (394)
|.+||.|||+.|....+.. -.++|.....++.+.|.+|++.|.++|..-
T Consensus 193 Ph~IalAcl~Ia~~~~~k~----~~~~w~~el~vD~ekV~~~v~~I~~lYe~w 241 (264)
T KOG0794|consen 193 PHQIALACLYIACVIDEKD----IPKAWFAELSVDMEKVKDIVQEILKLYELW 241 (264)
T ss_pred HHHHHHHHHHHHHhhcCCC----hHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Confidence 9999999999999877643 236777788999999999999999999765
No 11
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=99.76 E-value=7.3e-18 Score=161.45 Aligned_cols=163 Identities=16% Similarity=0.251 Sum_probs=139.5
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhccccc--CCCccchhh---
Q 016163 105 SRARSEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEET--QVPLLLDLQ--- 179 (394)
Q Consensus 105 ~~~R~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~--~~p~l~dl~--- 179 (394)
...|.....|+..+|.+++++..++.+||.+|+||+.+.++.... ++-++.||++||+|+||+ ++ .+..+.
T Consensus 42 ~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~---~~~vv~tcv~LA~K~ed~~~~I-~i~~~~~~~ 117 (297)
T COG5333 42 LNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEIS---LYSVVTTCVYLACKVEDTPRDI-SIESFEARD 117 (297)
T ss_pred hhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhccccccc---HHHHHHhheeeeeecccccchh-hHHHHHhhc
Confidence 357888889999999999999999999999999999999988887 999999999999999996 21 111111
Q ss_pred cccccccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcccCCCHHHHH
Q 016163 180 VEDIKFVFEAKTIQRMEILVLSTLQWKMNPVTPLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFMQYLPSVMA 259 (394)
Q Consensus 180 v~~~~~~f~~~~I~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IA 259 (394)
+......-+++.|..+|..||+.|+|++.+++|+.++..|+..+...+. .+..+.|+.++..++...-++.|+|..||
T Consensus 118 ~~se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~--~~~~~~aw~~inDa~~t~~~llypphiIA 195 (297)
T COG5333 118 LWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDK--YKLLQIAWKIINDALRTDLCLLYPPHIIA 195 (297)
T ss_pred cccccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccH--HHHHHHHHHHHHhhhhceeeeecChHHHH
Confidence 1111333479999999999999999999999999999999988866555 46789999999999999999999999999
Q ss_pred HHHHHHHHHHhccc
Q 016163 260 NATMLHVVQNIESS 273 (394)
Q Consensus 260 aAai~lA~~~l~~~ 273 (394)
+||++.|...++..
T Consensus 196 ~a~l~ia~~~~~~~ 209 (297)
T COG5333 196 LAALLIACEVLGMP 209 (297)
T ss_pred HHHHHHHHHhcCCc
Confidence 99999999987643
No 12
>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=99.65 E-value=6.6e-16 Score=129.41 Aligned_cols=115 Identities=25% Similarity=0.359 Sum_probs=93.8
Q ss_pred CChHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcccCCCHHHHHHHHHHHHHHHhccccCcchhhhhHhHcCCC
Q 016163 210 VTPLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFMQYLPSVMANATMLHVVQNIESSLGVEYEKQLLNILGTD 289 (394)
Q Consensus 210 pTp~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~~~~~L~~~~~~~ 289 (394)
|||++||++|++..+. .......+.+++++++.++.|++|+||+||+||+++|+..++ ....|...+..++|++
T Consensus 1 PTp~~Fl~~~~~~~~~----~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~--~~~~~~~~l~~~t~~~ 74 (118)
T PF02984_consen 1 PTPYDFLRRFLKISNA----DQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILG--KEPPWPESLEKLTGYD 74 (118)
T ss_dssp --HHHHHHHHHTSSSH----HHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHH--SSTCSHHHHHHHHTS-
T ss_pred CcHHHHHHHHHHHcCC----cHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhC--ccccCCccchhhcCCC
Confidence 8999999999654332 234667789999999999999999999999999999999987 2347999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhccCCchhhhhcccCCCCCCCCCC
Q 016163 290 KDKVEHCSKLIMQLAEQVQGQGSQSIKRKFGSITVPVVPGS 330 (394)
Q Consensus 290 ~~~l~~C~~~l~~l~~~~~~~~~~~~~~ky~s~~~~~~p~s 330 (394)
+++|.+|++.|.+++.+......+++++||++..+..|...
T Consensus 75 ~~~l~~c~~~i~~~~~~~~~~~~~ai~~Kys~~~~~~vs~~ 115 (118)
T PF02984_consen 75 KEDLKECIELIQELLSKASNSKLQAIRKKYSSQKFSSVSQI 115 (118)
T ss_dssp HHHHHHHHHHHHHHHHHCCGSSCTHHHHHTTSGGGTTGGGS
T ss_pred HHHHHHHHHHHHHHHHhcCCccchHHHHHhCccccCCccCC
Confidence 99999999999999987766678999999998765555443
No 13
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.53 E-value=1.1e-12 Score=129.43 Aligned_cols=184 Identities=17% Similarity=0.168 Sum_probs=155.2
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchhh-ccccc
Q 016163 106 RARSEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDLQ-VEDIK 184 (394)
Q Consensus 106 ~~R~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl~-v~~~~ 184 (394)
+.-..+..-|..++..++++..+.-.|..++.+++....+...+ ...+++|||++|+|.++. |..+.++. +. .
T Consensus 120 r~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs---~~~i~AAclYiACR~~~~-prtl~eI~~~~--~ 193 (310)
T PRK00423 120 RNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRS---IEGVVAAALYAACRRCKV-PRTLDEIAEVS--R 193 (310)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCC---HHHHHHHHHHHHHHHcCC-CcCHHHHHHHh--C
Confidence 34456677899999999999999999999999999987777666 889999999999999888 56778872 32 1
Q ss_pred ccccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcccCCCHHHHHHHHHH
Q 016163 185 FVFEAKTIQRMEILVLSTLQWKMNPVTPLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFMQYLPSVMANATML 264 (394)
Q Consensus 185 ~~f~~~~I~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~ 264 (394)
-++++|.+.++.|++.|+.++.+..|.+|+..|...|++++. +.+.|..++..+....-..+.+|..|||||||
T Consensus 194 --v~~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~----v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIY 267 (310)
T PRK00423 194 --VSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGE----VQKKAIEILQKAKEKGLTSGKGPTGLAAAAIY 267 (310)
T ss_pred --CCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHH----HHHHHHHHHHHHHhcCcccCCCHHHHHHHHHH
Confidence 278999999999999999999999999999999999998764 45667777776665555789999999999999
Q ss_pred HHHHHhccccCcchhhhhHhHcCCCHHHHHHHHHHHHHHH
Q 016163 265 HVVQNIESSLGVEYEKQLLNILGTDKDKVEHCSKLIMQLA 304 (394)
Q Consensus 265 lA~~~l~~~~~~~~~~~L~~~~~~~~~~l~~C~~~l~~l~ 304 (394)
+|.+..+.. .-...+..++|++...|...++.|.+.+
T Consensus 268 lA~~~~g~~---~t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 268 IASLLLGER---RTQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred HHHHHhCCC---CCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 999876632 2456788899999999999999998754
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=99.40 E-value=9.3e-13 Score=103.28 Aligned_cols=87 Identities=39% Similarity=0.536 Sum_probs=75.7
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchhhcccccccc
Q 016163 108 RSEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDLQVEDIKFVF 187 (394)
Q Consensus 108 R~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl~v~~~~~~f 187 (394)
|..+++||.+++..+++++.|.++|+.++|||+....+.+.+ .+++|+||++||+|+++. ++...++. ...++.
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 77778873 122221
Q ss_pred cHHHHHHHHHHHH
Q 016163 188 EAKTIQRMEILVL 200 (394)
Q Consensus 188 ~~~~I~~mE~~IL 200 (394)
+.++|.+||..||
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=99.35 E-value=2.1e-11 Score=116.59 Aligned_cols=151 Identities=17% Similarity=0.293 Sum_probs=113.6
Q ss_pred HHHHHHHc--CCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchhh--cccccccccHH
Q 016163 115 MLKVNAHY--SFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDLQ--VEDIKFVFEAK 190 (394)
Q Consensus 115 i~~v~~~~--~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl~--v~~~~~~f~~~ 190 (394)
+.+.+.++ .++..++.+|+.+|-||+...++.... ...|.+||+++|+|++|-++ .+.+|. +. +.-+-+.+
T Consensus 63 l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~---pk~I~~tc~flA~Kieef~I-SieqFvkn~~-~~~~k~~e 137 (325)
T KOG2496|consen 63 LVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYS---PKIIMATCFFLACKIEEFYI-SIEQFVKNMN-GRKWKTHE 137 (325)
T ss_pred HHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcC---hHHHHHHHHHHHhhhHhhee-cHHHHHhhcc-CcccccHH
Confidence 33444433 678999999999999999999998888 67799999999999999864 456662 22 22234789
Q ss_pred HHHHHHHHHHHHcCccccCCChHHHHHHHHHHcC-----CCCcccHHHHHHHHHHHHHhhchhcccCCCHHHHHHHHHHH
Q 016163 191 TIQRMEILVLSTLQWKMNPVTPLSFLDYIARRLG-----LKGYLCWEFLKRCDRILLSAISDSSFMQYLPSVMANATMLH 265 (394)
Q Consensus 191 ~I~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~l~-----~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~l 265 (394)
.|+..|..+|+.|+|++.+.+|+.-++-|+..+. ..+............++..++....++-|.||+||+|||+.
T Consensus 138 ~vLk~E~~llqsL~f~L~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~ 217 (325)
T KOG2496|consen 138 IVLKYEFLLLQSLKFSLTVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILH 217 (325)
T ss_pred HHHhchHHHHHhhhhhheecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHH
Confidence 9999999999999999999999999988876542 11111111112224667777777778889999999999977
Q ss_pred HHHHh
Q 016163 266 VVQNI 270 (394)
Q Consensus 266 A~~~l 270 (394)
+....
T Consensus 218 a~~~~ 222 (325)
T KOG2496|consen 218 AAGRT 222 (325)
T ss_pred Hhccc
Confidence 65433
No 16
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=99.30 E-value=8e-12 Score=96.99 Aligned_cols=83 Identities=37% Similarity=0.488 Sum_probs=70.7
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchhhcccccccccHHHH
Q 016163 113 DWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDLQVEDIKFVFEAKTI 192 (394)
Q Consensus 113 dWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl~v~~~~~~f~~~~I 192 (394)
+||.+++..+++++++.++|+.++|||+....+.+.+ .+++|+||++||+|++|.. |...++.. ..++ |+.++|
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~---~~~ia~a~l~lA~k~~~~~-~~~~~~~~-~~~~-~~~~~i 74 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYS---PSLIAAAALYLAAKTEEIP-PWTKELVH-YTGY-FTEEEI 74 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCC---HHHHHHHHHHHHHHHhcCC-CCchhHhH-hhCC-CCHHHH
Confidence 5999999999999999999999999999977777666 9999999999999999986 45566631 1222 689999
Q ss_pred HHHHHHHHH
Q 016163 193 QRMEILVLS 201 (394)
Q Consensus 193 ~~mE~~IL~ 201 (394)
.+||+.||.
T Consensus 75 ~~~~~~il~ 83 (83)
T smart00385 75 LRMEKLLLE 83 (83)
T ss_pred HHHHHHHhC
Confidence 999999973
No 17
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=98.86 E-value=1.8e-07 Score=90.94 Aligned_cols=185 Identities=16% Similarity=0.192 Sum_probs=154.6
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchhhcccccc
Q 016163 106 RARSEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDLQVEDIKF 185 (394)
Q Consensus 106 ~~R~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl~v~~~~~ 185 (394)
..-..+..-+-.++..++++..+.-.|..++-+.+.+.-+.... .+-++++|+++|++.... +..+.++.. ..+
T Consensus 95 rnl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRs---ie~v~AA~iY~acR~~~~-prtl~eIa~-a~~- 168 (285)
T COG1405 95 RNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRS---IESVAAACIYAACRINGV-PRTLDEIAK-ALG- 168 (285)
T ss_pred hHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCc---HHHHHHHHHHHHHHHcCC-CccHHHHHH-HHC-
Confidence 44567778888999999999999999999999999988887777 899999999999999887 455666631 122
Q ss_pred cccHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcccCCCHHHHHHHHHHH
Q 016163 186 VFEAKTIQRMEILVLSTLQWKMNPVTPLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFMQYLPSVMANATMLH 265 (394)
Q Consensus 186 ~f~~~~I~~mE~~IL~~L~w~l~~pTp~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~l 265 (394)
-++++|.++.+.+.+.|+=.+.+..|..|+..|...|++++. ....+..++..+...-.-.+-.|+-||+||+|+
T Consensus 169 -V~~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~----v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~ 243 (285)
T COG1405 169 -VSKKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSDE----VRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYL 243 (285)
T ss_pred -CCHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHH----HHHHHHHHHHHHHHhCcccCCCchhHHHHHHHH
Confidence 268999999999999999999999999999999999999854 446677777777777777899999999999999
Q ss_pred HHHHhccccCcchhhhhHhHcCCCHHHHHHHHHHHHHHH
Q 016163 266 VVQNIESSLGVEYEKQLLNILGTDKDKVEHCSKLIMQLA 304 (394)
Q Consensus 266 A~~~l~~~~~~~~~~~L~~~~~~~~~~l~~C~~~l~~l~ 304 (394)
|....+ ...-+.....++|+++..|.+=+..|.+..
T Consensus 244 as~l~~---~~~tq~eva~v~~vtevTIrnrykel~~~~ 279 (285)
T COG1405 244 ASLLLG---ERRTQKEVAKVAGVTEVTIRNRYKELADAL 279 (285)
T ss_pred HHHHhC---CchHHHHHHHHhCCeeeHHHHHHHHHHHhh
Confidence 998776 334567888999999999999887776643
No 18
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.65 E-value=1.4e-06 Score=83.55 Aligned_cols=186 Identities=17% Similarity=0.133 Sum_probs=143.2
Q ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchhhccccccc
Q 016163 107 ARSEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDLQVEDIKFV 186 (394)
Q Consensus 107 ~R~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl~v~~~~~~ 186 (394)
.-..+..-|..++...+|+....-.|-.+|-++-..+.....+ ..-+++|||+||++-++. |..+.++..-..
T Consensus 103 ~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks---~eai~AAclyiACRq~~~-pRT~kEI~~~an--- 175 (308)
T KOG1597|consen 103 VLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKS---VEALAAACLYIACRQEDV-PRTFKEISAVAN--- 175 (308)
T ss_pred HHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCcc---HHHHHHHHHHHHHHhcCC-CchHHHHHHHHc---
Confidence 3344555677899999999999999999999999776666666 899999999999998887 667788742222
Q ss_pred ccHHHHHHHHHHHHHHcCccccCCC--hHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcccCCCHHHHHHHHHH
Q 016163 187 FEAKTIQRMEILVLSTLQWKMNPVT--PLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFMQYLPSVMANATML 264 (394)
Q Consensus 187 f~~~~I~~mE~~IL~~L~w~l~~pT--p~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~ 264 (394)
-++++|-+.=..|+..|+=.....| .-+|+.+|...|+++.... ..|.++.+.+..-....+-.|=.||||+||
T Consensus 176 v~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q----~aA~e~a~ka~~~~~~~gRsPiSIAAa~IY 251 (308)
T KOG1597|consen 176 VSKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQ----EAATEIAEKAEEMDIRAGRSPISIAAAAIY 251 (308)
T ss_pred CCHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHH----HHHHHHHHHHHHhccccCCCchhHHHHHHH
Confidence 2799999999999999998777666 8899999999999887544 233333333221122345789999999999
Q ss_pred HHHHHhccccCcchhhhhHhHcCCCHHHHHHHHHHHHHHHHh
Q 016163 265 HVVQNIESSLGVEYEKQLLNILGTDKDKVEHCSKLIMQLAEQ 306 (394)
Q Consensus 265 lA~~~l~~~~~~~~~~~L~~~~~~~~~~l~~C~~~l~~l~~~ 306 (394)
++..... ...-...+..++|+.+.-|+.-|+.|......
T Consensus 252 misqls~---~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~~~ 290 (308)
T KOG1597|consen 252 MISQLSD---EKKTQKEIGEVTGVAEVTIRNSYKDLYPHADK 290 (308)
T ss_pred HHHHhcc---CcccHHHHHHHhhhhHHHHHHHHHHHhhchhh
Confidence 9987554 23345778889999999999999999875543
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=98.30 E-value=4e-06 Score=64.60 Aligned_cols=81 Identities=26% Similarity=0.434 Sum_probs=68.6
Q ss_pred HHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcccCCCHHHHHHHHHHHHHHHhccccCcchhhhhHhHcCC-CHHH
Q 016163 214 SFLDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFMQYLPSVMANATMLHVVQNIESSLGVEYEKQLLNILGT-DKDK 292 (394)
Q Consensus 214 ~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~~~~~L~~~~~~-~~~~ 292 (394)
+|+..+...++++. +....+.++++..+.+..+.+++|+.||+||+++|.+..+. ..|...+..++|+ +.++
T Consensus 1 ~~l~~~~~~~~~~~----~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~---~~~~~~~~~~~~~~~~~~ 73 (83)
T smart00385 1 DFLRRVCKALNLDP----ETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEI---PPWTKELVHYTGYFTEEE 73 (83)
T ss_pred CHHHHHHHHcCCCH----HHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcC---CCCchhHhHhhCCCCHHH
Confidence 37778888887753 45677888999998888999999999999999999998863 3588999999999 9999
Q ss_pred HHHHHHHHH
Q 016163 293 VEHCSKLIM 301 (394)
Q Consensus 293 l~~C~~~l~ 301 (394)
+.+|...|.
T Consensus 74 i~~~~~~il 82 (83)
T smart00385 74 ILRMEKLLL 82 (83)
T ss_pred HHHHHHHHh
Confidence 999988775
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=98.27 E-value=5.5e-06 Score=64.42 Aligned_cols=85 Identities=28% Similarity=0.379 Sum_probs=73.9
Q ss_pred CCChHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcccCCCHHHHHHHHHHHHHHHhccccCcchhhhhHhHcCC
Q 016163 209 PVTPLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFMQYLPSVMANATMLHVVQNIESSLGVEYEKQLLNILGT 288 (394)
Q Consensus 209 ~pTp~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~~~~~L~~~~~~ 288 (394)
.++|.+|+..+...++.+. +....|..+++..+....+..+.|+.||+||+++|.+..+. +.|...+..++++
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 5789999999999997764 35577888889888888899999999999999999997763 6788999999999
Q ss_pred -CHHHHHHHHHHH
Q 016163 289 -DKDKVEHCSKLI 300 (394)
Q Consensus 289 -~~~~l~~C~~~l 300 (394)
+.+++.++...|
T Consensus 75 ~~~~~i~~~e~~i 87 (88)
T cd00043 75 ATEEEILRMEKLL 87 (88)
T ss_pred CCHHHHHHHHHHh
Confidence 999999987765
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=8e-06 Score=72.23 Aligned_cols=92 Identities=17% Similarity=0.177 Sum_probs=65.3
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhc---cccccCCcchhHHHHHHHHHHhhhcccccCCCccchh-hccccccc
Q 016163 111 AVDWMLKVNAHYSFTALTALLAVNYLDRFLF---SFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDL-QVEDIKFV 186 (394)
Q Consensus 111 lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs---~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl-~v~~~~~~ 186 (394)
+.+|+.++..+-++++.++.+|..|+||+.. ...+.- .+...+-+-++||.||+|+-+........+ .+. +
T Consensus 54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~-~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~--g-- 128 (149)
T PF08613_consen 54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPL-NSSNIHRLFLTALILASKFLDDNTYSNKSWAKVG--G-- 128 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT----STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHH--T--
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhccccccc-ccchhHHHHHHHHHHHHhhcccccccHHHHHhhc--C--
Confidence 7789999999999999999999999999999 222222 233377889999999999965443343444 232 2
Q ss_pred ccHHHHHHHHHHHHHHcCccc
Q 016163 187 FEAKTIQRMEILVLSTLQWKM 207 (394)
Q Consensus 187 f~~~~I~~mE~~IL~~L~w~l 207 (394)
++.+++.+||+..|..|+|+|
T Consensus 129 is~~eln~lE~~fL~~l~~~L 149 (149)
T PF08613_consen 129 ISLKELNELEREFLKLLDYNL 149 (149)
T ss_dssp S-HHHHHHHHHHHHHHTTT--
T ss_pred CCHHHHHHHHHHHHHHCCCcC
Confidence 489999999999999999986
No 22
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=97.92 E-value=6.5e-06 Score=81.58 Aligned_cols=98 Identities=19% Similarity=0.314 Sum_probs=84.5
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchhh-ccccccccc
Q 016163 110 EAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDLQ-VEDIKFVFE 188 (394)
Q Consensus 110 ~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl~-v~~~~~~f~ 188 (394)
.+=.=|.+++...++...|+++|-.||.....+..+.+.+ -.|.|-|||.||+||.+..-..++.++ -.+.++.+.
T Consensus 384 SlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~N---RKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~n 460 (497)
T KOG4164|consen 384 SLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQN---RKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLN 460 (497)
T ss_pred HHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhh---hhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhccc
Confidence 4455688899999999999999999999999998888887 899999999999999876555555653 345678889
Q ss_pred HHHHHHHHHHHHHHcCccccCC
Q 016163 189 AKTIQRMEILVLSTLQWKMNPV 210 (394)
Q Consensus 189 ~~~I~~mE~~IL~~L~w~l~~p 210 (394)
+.+++..|.-||.+|.|.|+++
T Consensus 461 rrdLia~Ef~VlvaLefaL~~~ 482 (497)
T KOG4164|consen 461 RRDLIAFEFPVLVALEFALHLP 482 (497)
T ss_pred HHhhhhhhhhHHHhhhhhccCC
Confidence 9999999999999999999865
No 23
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=97.65 E-value=0.00052 Score=71.08 Aligned_cols=147 Identities=16% Similarity=0.148 Sum_probs=119.4
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchh--hcccccccccHHH
Q 016163 114 WMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDL--QVEDIKFVFEAKT 191 (394)
Q Consensus 114 Wi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl--~v~~~~~~f~~~~ 191 (394)
-|.+++..+++.. .+-.|.++|---+...-.+... .+.+-.+||+|++..|-+. -.+.|+ +... +.-+
T Consensus 73 ~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~---~~~vvasClY~vcR~e~t~-hlliDfS~~Lqv-----~Vy~ 142 (521)
T KOG1598|consen 73 LIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRR---STEVVAACLYLVCRLEKTD-HLLIDFSSYLQV-----SVYD 142 (521)
T ss_pred HHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcc---hHHHHHHHHHHHHHhhCCc-eEEEEeccceEE-----ehhh
Confidence 5778999999999 8899999998888876666656 8999999999999998884 345566 2222 3335
Q ss_pred HHHHHHHHHHHcCcc---ccCCChHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcccCCCHHHHHHHHHHHHHH
Q 016163 192 IQRMEILVLSTLQWK---MNPVTPLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFMQYLPSVMANATMLHVVQ 268 (394)
Q Consensus 192 I~~mE~~IL~~L~w~---l~~pTp~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~lA~~ 268 (394)
+-.+=+.|-..|.-. +..+-|.-|+.+|...+...++. .++...+.+++.....|--...-+|+-|+.|||+.|.+
T Consensus 143 LG~~~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~-~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar 221 (521)
T KOG1598|consen 143 LGSNFLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKT-EDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAAR 221 (521)
T ss_pred hhHHHHHHHHHhccccccccccCcceeeechhHhhhcCCch-HHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHH
Confidence 556666677777777 67888999999999998766555 47888888999999999999999999999999999999
Q ss_pred Hhc
Q 016163 269 NIE 271 (394)
Q Consensus 269 ~l~ 271 (394)
..+
T Consensus 222 ~h~ 224 (521)
T KOG1598|consen 222 MHG 224 (521)
T ss_pred HcC
Confidence 876
No 24
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=95.75 E-value=0.077 Score=40.59 Aligned_cols=71 Identities=17% Similarity=0.208 Sum_probs=49.5
Q ss_pred HHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcccCCCHHHHHHHHHHHHHHHhccccCcchhhhhHhHcCCCHHHH
Q 016163 216 LDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFMQYLPSVMANATMLHVVQNIESSLGVEYEKQLLNILGTDKDKV 293 (394)
Q Consensus 216 L~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~~~~~L~~~~~~~~~~l 293 (394)
+..|...|++++ .+.+.|..+...+....-..+-+|..|||||+|+|.+..+. +.-...+...+|+++.+|
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 356777888776 45577777777666665567788999999999999988762 234567777888887654
No 25
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=95.48 E-value=0.052 Score=41.54 Aligned_cols=60 Identities=13% Similarity=0.134 Sum_probs=47.0
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchh
Q 016163 115 MLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDL 178 (394)
Q Consensus 115 i~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl 178 (394)
|-+++..++|+..+.-.|..++++-....-....+ ..-++++|+++|++.+.. +..+.++
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~---~~~iaAA~iY~acr~~~~-~~t~~eI 60 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRS---PESIAAACIYLACRLNGV-PRTLKEI 60 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS----HHHHHHHHHHHHHHHTTS-SSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCC---HHHHHHHHHHHHHHHcCC-CcCHHHH
Confidence 45789999999999999999999988776665555 788999999999999876 3455665
No 26
>KOG1674 consensus Cyclin [General function prediction only]
Probab=94.10 E-value=0.13 Score=48.45 Aligned_cols=96 Identities=13% Similarity=0.153 Sum_probs=68.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccc---cCC---cchh-HHHHHHHHHHhhhcccccCCCccchhhccccc
Q 016163 112 VDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQL---QRD---KPWM-AQLAAVACLSLAAKVEETQVPLLLDLQVEDIK 184 (394)
Q Consensus 112 vdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v---~~~---~p~~-lqLvavaCL~LAaK~EE~~~p~l~dl~v~~~~ 184 (394)
-+++..+..+-+.++.++.+|..|||||....+. ... +.-+ .+-+-++|+.+|+|+.+..-- -...+..-++
T Consensus 79 ~~yleri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~y-~n~~~a~vgg 157 (218)
T KOG1674|consen 79 RQYLERIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVYY-SNAYYAKVGG 157 (218)
T ss_pred HHHHHHHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccchhh-hHHHHHHhCC
Confidence 3566678888899999999999999999997431 111 1122 455789999999999865311 1222211122
Q ss_pred ccccHHHHHHHHHHHHHHcCccccCC
Q 016163 185 FVFEAKTIQRMEILVLSTLQWKMNPV 210 (394)
Q Consensus 185 ~~f~~~~I~~mE~~IL~~L~w~l~~p 210 (394)
- +.+++..+|...|..++|++.+.
T Consensus 158 l--~~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 158 L--TTDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred C--ChHhhhhhhHHHHhhCCeEEEec
Confidence 2 78999999999999999999875
No 27
>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=93.45 E-value=1.1 Score=35.88 Aligned_cols=95 Identities=14% Similarity=0.128 Sum_probs=60.8
Q ss_pred hHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcccCCCHHHHHHH-HHHHHHHHhcccc--CcchhhhhHhHcCC
Q 016163 212 PLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFMQYLPSVMANA-TMLHVVQNIESSL--GVEYEKQLLNILGT 288 (394)
Q Consensus 212 p~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaA-ai~lA~~~l~~~~--~~~~~~~L~~~~~~ 288 (394)
|-+-+...+-+++........+..+....+..++.|..--..+||.||+| |-+++....-|.. .....++|....|+
T Consensus 4 ~TD~~~~~L~K~~~~~e~L~~~H~~V~~~v~KAiV~P~TG~Lp~SlvaAA~CAL~~~~~~~P~~~~~~~~~~~LA~~~G~ 83 (106)
T PF09080_consen 4 PTDAIGPLLFKSGFTKEQLFAWHSEVVESVHKAIVNPKTGGLPPSLVAAAGCALFSLGAAAPPDTHSGGVVPQLAEALGV 83 (106)
T ss_dssp CHHHHHHHHHHHS-SSTTHHHHHHHHHHHHHHHHCSTTGGGS-HHHHHHHHHHHHS-GGGS--------HHHHHHHHHT-
T ss_pred ccccccHHHHHHcccHHHHHHHHHHHHHHHHHHhcCcccCCCCHHHHHHhhhhhccccccCCCccccccchHHHHHHhCc
Confidence 44444444545554444433444567788888999999999999999998 7666665544322 23456789999999
Q ss_pred CHHHHHHHHHHHHHHHHh
Q 016163 289 DKDKVEHCSKLIMQLAEQ 306 (394)
Q Consensus 289 ~~~~l~~C~~~l~~l~~~ 306 (394)
+...+....+.+..-+++
T Consensus 84 ~~a~L~AA~E~v~Tt~~e 101 (106)
T PF09080_consen 84 SAATLQAAAESVATTLRE 101 (106)
T ss_dssp -HHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHHH
Confidence 999999988888765543
No 28
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=92.98 E-value=0.82 Score=45.30 Aligned_cols=87 Identities=15% Similarity=0.197 Sum_probs=66.4
Q ss_pred hHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcccCCCHHHHHHHHHHHHHHHhccccCcchhhhhHhHcCCCHH
Q 016163 212 PLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFMQYLPSVMANATMLHVVQNIESSLGVEYEKQLLNILGTDKD 291 (394)
Q Consensus 212 p~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~~~~~L~~~~~~~~~ 291 (394)
.+..|..+...+++++. +.+.|..+...+.....+-....-.+||||||+|.+..+ .+--...+..++++++.
T Consensus 125 a~~~I~~~~~~L~Lp~~----v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~---~prtl~eI~~~~~v~~k 197 (310)
T PRK00423 125 ALSELDRIASQLGLPRS----VREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCK---VPRTLDEIAEVSRVSRK 197 (310)
T ss_pred HHHHHHHHHHHcCCCHH----HHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcC---CCcCHHHHHHHhCCCHH
Confidence 34567778888888754 556666666665555556788889999999999999876 23344577888999999
Q ss_pred HHHHHHHHHHHHHH
Q 016163 292 KVEHCSKLIMQLAE 305 (394)
Q Consensus 292 ~l~~C~~~l~~l~~ 305 (394)
+|..+++.|.+.+.
T Consensus 198 ~i~~~~~~l~k~L~ 211 (310)
T PRK00423 198 EIGRCYRFLLRELN 211 (310)
T ss_pred HHHHHHHHHHHHhC
Confidence 99999999988764
No 29
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=81.37 E-value=14 Score=36.21 Aligned_cols=87 Identities=20% Similarity=0.197 Sum_probs=60.4
Q ss_pred ChHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcc-cCCCHHHHHHHHHHHHHHHhccccCcchhhhhHhHcCCC
Q 016163 211 TPLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSF-MQYLPSVMANATMLHVVQNIESSLGVEYEKQLLNILGTD 289 (394)
Q Consensus 211 Tp~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~-l~~~PS~IAaAai~lA~~~l~~~~~~~~~~~L~~~~~~~ 289 (394)
+....|..+...++++.... ..+..+... ..+..+ -.=+...++|||+|.|.+..+ .+--...+...++++
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 TALEELERIASALGLPESVR----ETAARIYRK-AVDKGLLRGRSIESVAAACIYAACRING---VPRTLDEIAKALGVS 170 (285)
T ss_pred HHHHHHHHHHHHhCCCchHH----HHHHHHHHH-HhhcCCCcCCcHHHHHHHHHHHHHHHcC---CCccHHHHHHHHCCC
Confidence 56677888888888886543 333333333 334444 445578899999999998776 233456777888999
Q ss_pred HHHHHHHHHHHHHHHH
Q 016163 290 KDKVEHCSKLIMQLAE 305 (394)
Q Consensus 290 ~~~l~~C~~~l~~l~~ 305 (394)
+.++..+++.|.....
T Consensus 171 ~kei~rtyr~~~~~L~ 186 (285)
T COG1405 171 KKEIGRTYRLLVRELK 186 (285)
T ss_pred HHHHHHHHHHHHHhcC
Confidence 9999999997766543
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=80.88 E-value=21 Score=28.35 Aligned_cols=95 Identities=11% Similarity=0.151 Sum_probs=69.1
Q ss_pred ChHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcccCCCHHHHHHHHHHHHHHHhccc--cCcchhhhhHhHcCC
Q 016163 211 TPLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFMQYLPSVMANATMLHVVQNIESS--LGVEYEKQLLNILGT 288 (394)
Q Consensus 211 Tp~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~lA~~~l~~~--~~~~~~~~L~~~~~~ 288 (394)
..-+|+-...+.+...+.+..+..+.+.-.+-.++......-.+|-.|.|+.++-.+..-+.. .+..+...|..++++
T Consensus 3 l~tdflip~c~alkipe~~wpql~e~~s~tickaliqpniall~p~licaggllttiet~ntn~~~wt~yledl~~ilnf 82 (106)
T PF09241_consen 3 LSTDFLIPVCHALKIPEDFWPQLFEATSITICKALIQPNIALLPPCLICAGGLLTTIETDNTNCQPWTCYLEDLSCILNF 82 (106)
T ss_dssp -GGGGHHHHHHHTT--GGGHHHHHHHHHHHHHHHTTSGGGGGS-HHHHHHHHHHHHHHTS-TSSSTCHHHHHHHHHHHTC
T ss_pred chhhhHHHhhhhccCcHHHhHHHHHHHHHHHHHHHcCCCccccCcceeecccceEEEeccCCCCcchhhhHHhhHHHhhc
Confidence 345788888899999888877777777777778888888888999999999999888755422 133444566678889
Q ss_pred CHHHHHHHHHHHHHHHH
Q 016163 289 DKDKVEHCSKLIMQLAE 305 (394)
Q Consensus 289 ~~~~l~~C~~~l~~l~~ 305 (394)
+-..++....++.+.+.
T Consensus 83 stntirt~kdqv~ea~~ 99 (106)
T PF09241_consen 83 STNTIRTVKDQVSEAFS 99 (106)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHH
Confidence 88888888777776543
No 31
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=78.75 E-value=5.4 Score=32.45 Aligned_cols=87 Identities=16% Similarity=0.181 Sum_probs=54.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchhhcccccccccHHH
Q 016163 112 VDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDLQVEDIKFVFEAKT 191 (394)
Q Consensus 112 vdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl~v~~~~~~f~~~~ 191 (394)
.+||.......+.+..+..+|-.+++-.+....+-..+ --++|+||+++|.++-....+....+. ...++ +.++
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 45555554434446678888888888888777777777 778999999999999553222222221 11233 6777
Q ss_pred HHHHHHHHHHHcC
Q 016163 192 IQRMEILVLSTLQ 204 (394)
Q Consensus 192 I~~mE~~IL~~L~ 204 (394)
|..+=..|.+.+.
T Consensus 78 l~~c~~~i~~~~~ 90 (118)
T PF02984_consen 78 LKECIELIQELLS 90 (118)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 7766555555443
No 32
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=77.72 E-value=2 Score=42.79 Aligned_cols=89 Identities=20% Similarity=0.165 Sum_probs=53.8
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchh--h-cccccc
Q 016163 109 SEAVDWMLKVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDL--Q-VEDIKF 185 (394)
Q Consensus 109 ~~lvdWi~~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl--~-v~~~~~ 185 (394)
.-+++|+..+...-+........|-+++-..+...-.-+.+ .+-||++||+||+|+-...+|...+- . ..+..
T Consensus 153 ~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~---p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~- 228 (323)
T KOG0834|consen 153 KYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYS---PHSIAVACIHLAAKLLGVELPSDTDKRWWREFDET- 228 (323)
T ss_pred HHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeec---CcEEEeehhhHHHHHcCCCCCCCcccchhhhhccc-
Confidence 34555565555555544456777777777776655444455 66799999999999977666654443 1 11111
Q ss_pred cccHHHHHHHHHHHHHH
Q 016163 186 VFEAKTIQRMEILVLST 202 (394)
Q Consensus 186 ~f~~~~I~~mE~~IL~~ 202 (394)
.+.+.+..+-..+|..
T Consensus 229 -vt~e~l~~i~~~~l~~ 244 (323)
T KOG0834|consen 229 -VTNELLDDICHEFLDL 244 (323)
T ss_pred -CCHHHHHHHHHHHHHH
Confidence 3556666555554443
No 33
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=77.45 E-value=3 Score=41.05 Aligned_cols=99 Identities=18% Similarity=0.223 Sum_probs=60.1
Q ss_pred HHHHHcCCCHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchh-hcccccccccHHHHHHH
Q 016163 117 KVNAHYSFTALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDL-QVEDIKFVFEAKTIQRM 195 (394)
Q Consensus 117 ~v~~~~~l~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl-~v~~~~~~f~~~~I~~m 195 (394)
-.+....+..+.......|++|-+........ |.....+.....++|+|+-....-.-.|. ++... -+.+++..|
T Consensus 199 ~l~~~~qlta~~aiitL~~~erl~~~~e~~~~-p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlKd---~tveDmNe~ 274 (343)
T KOG1675|consen 199 ILFSWAQLTAECDIITLVYAERLLWLAERDPC-PRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILKD---QSVDDMNAL 274 (343)
T ss_pred hHhhhhhhhhccchHHHHhhHhhhhHhhcCCC-cchhhhhhhhhheehhhhhhhhhcccHHHHHHHhh---ccHhhHHHH
Confidence 33444455555555566788887765544421 22244555557999999954321111222 22211 168999999
Q ss_pred HHHHHHHcCccccCCChHHHHHHHH
Q 016163 196 EILVLSTLQWKMNPVTPLSFLDYIA 220 (394)
Q Consensus 196 E~~IL~~L~w~l~~pTp~~FL~~~l 220 (394)
|+.+|+.|+|++++|-. .|..+|.
T Consensus 275 ERqfLelLqfNinvp~s-vYAKyYf 298 (343)
T KOG1675|consen 275 ERQFLELLQFNINVPSS-EYAKYYF 298 (343)
T ss_pred HHHHHHHHhhccCccHH-HHHHHHH
Confidence 99999999999998753 3444443
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=75.51 E-value=25 Score=29.03 Aligned_cols=67 Identities=13% Similarity=0.061 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHhhchhcccCCCHHHHHHHHHHHHHHHhccccCcchhhhhHhHc--CCCHHHHHHHHHHHH
Q 016163 233 FLKRCDRILLSAISDSSFMQYLPSVMANATMLHVVQNIESSLGVEYEKQLLNIL--GTDKDKVEHCSKLIM 301 (394)
Q Consensus 233 ~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~~~~~L~~~~--~~~~~~l~~C~~~l~ 301 (394)
.+..|..+++.-+.........+..+|+||+++|.+..+. ...+...+...+ .++.+++...=..+.
T Consensus 51 ~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~--~~~~~~~~~~~~~~~~~~~~i~~~E~~iL 119 (127)
T PF00134_consen 51 TLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEED--NPPSISDLIRISDNTFTKKDILEMEREIL 119 (127)
T ss_dssp HHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTS--S--HHHHHHHHTTTSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhcc--ccchHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 3444555555555555678888999999999999997763 234455555555 356666665444433
No 35
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=69.52 E-value=39 Score=33.25 Aligned_cols=83 Identities=19% Similarity=0.286 Sum_probs=53.8
Q ss_pred HHHHHHHcCCCCcccHHHHHHHHHHHHHhhchhcccCCCH-HHHHHHHHHHHHHHhccccCcchhhhhHhHcCCCHHHHH
Q 016163 216 LDYIARRLGLKGYLCWEFLKRCDRILLSAISDSSFMQYLP-SVMANATMLHVVQNIESSLGVEYEKQLLNILGTDKDKVE 294 (394)
Q Consensus 216 L~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~d~~~l~~~P-S~IAaAai~lA~~~l~~~~~~~~~~~L~~~~~~~~~~l~ 294 (394)
+..+...+++... +..+|.++... +.+.+.++=+- -.|||||||.|.+..+ .+.-...+..+.++++.+|-
T Consensus 111 I~~m~d~~~Lp~~----I~d~A~~ifk~-v~~~k~lrGks~eai~AAclyiACRq~~---~pRT~kEI~~~anv~kKEIg 182 (308)
T KOG1597|consen 111 ITAMCDRLSLPAT----IKDRANEIFKL-VEDSKLLRGKSVEALAAACLYIACRQED---VPRTFKEISAVANVSKKEIG 182 (308)
T ss_pred HHHHHHHhCCchH----HHHHHHHHHHH-HHHhhhhcCccHHHHHHHHHHHHHHhcC---CCchHHHHHHHHcCCHHHHH
Confidence 3444455555432 23444443332 22555554444 4699999999998776 33345677778899999999
Q ss_pred HHHHHHHHHHHh
Q 016163 295 HCSKLIMQLAEQ 306 (394)
Q Consensus 295 ~C~~~l~~l~~~ 306 (394)
+|++.|.+-+..
T Consensus 183 r~~K~i~~~l~~ 194 (308)
T KOG1597|consen 183 RCVKLIGEALET 194 (308)
T ss_pred HHHHHHHHHHhc
Confidence 999999886643
No 36
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=51.26 E-value=52 Score=32.92 Aligned_cols=61 Identities=23% Similarity=0.247 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhcccccCCCccchhhcccccccccHHHHHHH
Q 016163 129 ALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAKVEETQVPLLLDLQVEDIKFVFEAKTIQRM 195 (394)
Q Consensus 129 ~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK~EE~~~p~l~dl~v~~~~~~f~~~~I~~m 195 (394)
...|-||+.--+-..-+.... --.||++|++|||..+|+-.|...... ..+.+++.+|...
T Consensus 161 ~Q~~wNfmNDslRT~v~vry~---pe~iACaciyLaAR~~eIpLp~~P~Wf---~~Fd~~k~eid~i 221 (367)
T KOG0835|consen 161 LQAAWNFMNDSLRTDVFVRYS---PESIACACIYLAARNLEIPLPFQPHWF---KAFDTTKREIDEI 221 (367)
T ss_pred HHHHHHhhhhccccceeeecC---HHHHHHHHHHHHHhhhcCCCCCCccHH---HHcCCcHHHHHHH
Confidence 334444444444334444555 678999999999999997656555442 1133456665543
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=38.77 E-value=2.6e+02 Score=24.24 Aligned_cols=82 Identities=9% Similarity=-0.012 Sum_probs=45.7
Q ss_pred CCChHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHhhc-----hhcccCCCHHHHHHHHHHHHHHHhccccCcchhhhhH
Q 016163 209 PVTPLSFLDYIARRLGLKGYLCWEFLKRCDRILLSAIS-----DSSFMQYLPSVMANATMLHVVQNIESSLGVEYEKQLL 283 (394)
Q Consensus 209 ~pTp~~FL~~~l~~l~~~~~~~~~~l~~a~~ll~~sl~-----d~~~l~~~PS~IAaAai~lA~~~l~~~~~~~~~~~L~ 283 (394)
.++-.+|+..+.+........ +-.+..+++.... ........+.-+-++|+.+|.+.+.. ...+...|.
T Consensus 51 ~i~i~~fl~ri~~~~~~s~~~----~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D--~~~~n~~~a 124 (149)
T PF08613_consen 51 SISIRDFLSRILKYTQCSPEC----LILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDD--NTYSNKSWA 124 (149)
T ss_dssp SS-HHHHHHHHHHHTT--HHH----HHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-S--S---HHHHH
T ss_pred CCcHHHHHHHHHHHcCCChHH----HHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhccc--ccccHHHHH
Confidence 345566777777776655422 2222223332222 22244556677888899999998873 344577888
Q ss_pred hHcCCCHHHHHHH
Q 016163 284 NILGTDKDKVEHC 296 (394)
Q Consensus 284 ~~~~~~~~~l~~C 296 (394)
.++|++..++..-
T Consensus 125 ~v~gis~~eln~l 137 (149)
T PF08613_consen 125 KVGGISLKELNEL 137 (149)
T ss_dssp HHHTS-HHHHHHH
T ss_pred hhcCCCHHHHHHH
Confidence 9999999887764
No 38
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=37.07 E-value=52 Score=32.60 Aligned_cols=39 Identities=13% Similarity=0.160 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHhhchhcccCCCHHHHHHHHHHHHHHHhc
Q 016163 233 FLKRCDRILLSAISDSSFMQYLPSVMANATMLHVVQNIE 271 (394)
Q Consensus 233 ~l~~a~~ll~~sl~d~~~l~~~PS~IAaAai~lA~~~l~ 271 (394)
.+..|..++..-.....+..|.|-.||++|+++|.+.-+
T Consensus 78 viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE 116 (305)
T TIGR00569 78 VVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEE 116 (305)
T ss_pred HHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccc
Confidence 333343344333445567889999999999999998654
No 39
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=25.63 E-value=19 Score=26.52 Aligned_cols=11 Identities=64% Similarity=1.325 Sum_probs=10.0
Q ss_pred cccccccchhh
Q 016163 18 LYCSEENWEDE 28 (394)
Q Consensus 18 ~~~~~~~~~~~ 28 (394)
-||++|+|++|
T Consensus 24 thcS~ehw~~D 34 (55)
T PF13824_consen 24 THCSEEHWEDD 34 (55)
T ss_pred CccCHHHHHHh
Confidence 69999999988
No 40
>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=23.47 E-value=1.7e+02 Score=29.49 Aligned_cols=50 Identities=28% Similarity=0.353 Sum_probs=30.0
Q ss_pred hhHHHHHHHHHHhhhcc--cccCCCccchhhcccccccccHH---HHHHHHHHHHH
Q 016163 151 WMAQLAAVACLSLAAKV--EETQVPLLLDLQVEDIKFVFEAK---TIQRMEILVLS 201 (394)
Q Consensus 151 ~~lqLvavaCL~LAaK~--EE~~~p~l~dl~v~~~~~~f~~~---~I~~mE~~IL~ 201 (394)
..+|-+.++||+||=-+ .|+..| +.-|.|+..+..|+.. -|-+|-..+|+
T Consensus 270 ~~l~~~~l~cly~sysy~gneisyp-lkpflv~~~~~~fw~~~~~~~~~~s~~ml~ 324 (346)
T PF03261_consen 270 RELQAIVLTCLYLSYSYMGNEISYP-LKPFLVEESKEAFWDRCLSIINRLSAKMLR 324 (346)
T ss_dssp HHHHHHHHHHHHHHHHHH-SSS----SGGG--SS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhhcCcccccc-cCCeeecccHHHHHHHHHHHHHHhhHHHhh
Confidence 35999999999999888 677555 4666677776666533 33444444443
No 41
>PF07226 DUF1422: Protein of unknown function (DUF1422); InterPro: IPR009867 This family consists of several hypothetical bacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=23.07 E-value=1.2e+02 Score=25.85 Aligned_cols=38 Identities=21% Similarity=0.268 Sum_probs=29.4
Q ss_pred CHHHHHHHHHHHHHHhccccccCCcchhHHHHHHHHHHhhhc
Q 016163 125 TALTALLAVNYLDRFLFSFQLQRDKPWMAQLAAVACLSLAAK 166 (394)
Q Consensus 125 ~~~T~~lAV~~lDRFLs~~~v~~~~p~~lqLvavaCL~LAaK 166 (394)
+-.++.+|+.-+..-+..+.++.+ .-.+|.+|++|-.=
T Consensus 40 PlIaLvLavy~LyQ~Yl~~~m~eg----~P~~a~acFflG~f 77 (117)
T PF07226_consen 40 PLIALVLAVYCLYQRYLNHPMPEG----TPKLALACFFLGLF 77 (117)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCC----ChHHHHHHHHHHHH
Confidence 456888999988877777777765 66889999998653
No 42
>PF00524 PPV_E1_N: E1 Protein, N terminal domain; InterPro: IPR014000 Papillomaviruses are a large family of DNA tumour viruses which give rise to warts in their host species. The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication []. It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins []. The E1 protein is a 70 kDa polypeptide with a centrally-located DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase []. In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel beta sheet bordered by four loosely packed alpha helices on one side and two tightly packed helices on the other []. Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity []. This entry represents the N-terminal region of E1, which contains the nuclear localisation signal.; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=22.72 E-value=81 Score=27.31 Aligned_cols=11 Identities=36% Similarity=0.486 Sum_probs=8.5
Q ss_pred chhhhhcccCC
Q 016163 312 SQSIKRKFGSI 322 (394)
Q Consensus 312 ~~~~~~ky~s~ 322 (394)
.+++||||..+
T Consensus 75 v~~LKRK~~~S 85 (130)
T PF00524_consen 75 VQALKRKYLGS 85 (130)
T ss_pred HHHHHHHHcCC
Confidence 56789999754
No 43
>KOG3866 consensus DNA-binding protein of the nucleobindin family [General function prediction only]
Probab=22.15 E-value=5e+02 Score=26.04 Aligned_cols=32 Identities=28% Similarity=0.345 Sum_probs=24.8
Q ss_pred CCCCCCccc--CCCCCCcHHHHHHHHHhhccCCc
Q 016163 63 IPVPVPMLH--EQDLSWQDDELSTLLSKEVPNRL 94 (394)
Q Consensus 63 ~~~~~~~l~--~~d~~~~de~l~~Ll~kE~~~~~ 94 (394)
.|-+.+.|| ..|.||++.++.+|+.+|-+..|
T Consensus 245 dPKTFF~LHD~NsDGfldeqELEaLFtkELEKvY 278 (442)
T KOG3866|consen 245 DPKTFFALHDLNSDGFLDEQELEALFTKELEKVY 278 (442)
T ss_pred CcchheeeeccCCcccccHHHHHHHHHHHHHHhc
Confidence 344455555 58999999999999999988664
Done!