Query 016851
Match_columns 381
No_of_seqs 215 out of 1335
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 03:23:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016851.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016851hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0834 CDK9 kinase-activating 100.0 3.3E-45 7.1E-50 354.1 17.0 230 146-381 9-245 (323)
2 KOG0835 Cyclin L [General func 100.0 3E-38 6.6E-43 298.5 19.9 224 158-381 5-229 (367)
3 TIGR00569 ccl1 cyclin ccl1. Un 100.0 2.8E-35 6E-40 285.2 21.9 215 145-378 6-249 (305)
4 KOG0794 CDK8 kinase-activating 100.0 4.4E-36 9.6E-41 271.8 14.7 226 147-381 12-238 (264)
5 KOG0655 G1/S-specific cyclin E 100.0 1.9E-30 4.2E-35 245.5 12.7 202 109-347 95-309 (408)
6 COG5333 CCL1 Cdk activating ki 100.0 1.4E-27 3E-32 226.4 14.8 175 167-354 36-211 (297)
7 KOG0656 G1/S-specific cyclin D 99.9 4.5E-25 9.7E-30 214.0 15.2 173 159-350 59-241 (335)
8 KOG0653 Cyclin B and related k 99.9 3E-23 6.4E-28 208.8 14.3 197 158-378 140-342 (391)
9 COG5024 Cyclin [Cell division 99.9 6.4E-22 1.4E-26 198.4 13.4 191 165-380 202-398 (440)
10 PRK00423 tfb transcription ini 99.8 2.2E-19 4.8E-24 175.6 22.1 185 171-379 118-302 (310)
11 KOG2496 Cdk activating kinase 99.8 2.4E-20 5.3E-25 175.8 14.4 154 183-353 63-226 (325)
12 KOG0654 G2/Mitotic-specific cy 99.8 7.8E-19 1.7E-23 172.0 9.3 199 158-381 119-322 (359)
13 PF00134 Cyclin_N: Cyclin, N-t 99.8 1.4E-18 3E-23 147.2 9.3 121 151-290 6-127 (127)
14 COG1405 SUA7 Transcription ini 99.6 2.9E-13 6.2E-18 130.3 18.9 185 171-379 93-277 (285)
15 KOG1597 Transcription initiati 99.5 1.7E-12 3.7E-17 122.7 22.2 178 178-378 106-285 (308)
16 cd00043 CYCLIN Cyclin box fold 99.4 6.1E-13 1.3E-17 103.7 8.2 87 176-282 2-88 (88)
17 smart00385 CYCLIN domain prese 99.3 6.6E-12 1.4E-16 96.9 7.1 83 181-283 1-83 (83)
18 PF02984 Cyclin_C: Cyclin, C-t 99.0 6.1E-10 1.3E-14 92.5 6.1 88 292-380 1-88 (118)
19 smart00385 CYCLIN domain prese 98.6 3.2E-07 6.9E-12 70.4 8.9 82 296-379 1-83 (83)
20 cd00043 CYCLIN Cyclin box fold 98.5 1.2E-06 2.5E-11 67.9 9.5 86 291-378 2-88 (88)
21 KOG1598 Transcription initiati 98.3 4.8E-06 1E-10 85.2 10.5 154 178-353 69-227 (521)
22 PF00382 TFIIB: Transcription 98.3 3.8E-06 8.3E-11 64.3 7.4 64 183-246 1-64 (71)
23 PF08613 Cyclin: Cyclin; Inte 98.1 2.7E-05 5.8E-10 68.4 9.7 91 178-289 53-149 (149)
24 KOG4164 Cyclin ik3-1/CABLES [C 98.0 1.2E-05 2.6E-10 79.2 7.1 98 178-292 384-482 (497)
25 PF00382 TFIIB: Transcription 97.8 0.00015 3.2E-09 55.5 8.4 71 298-370 1-71 (71)
26 PRK00423 tfb transcription ini 97.3 0.0012 2.7E-08 64.8 9.4 67 180-246 220-286 (310)
27 PF00134 Cyclin_N: Cyclin, N-t 95.8 0.076 1.6E-06 44.3 9.3 85 295-380 35-121 (127)
28 COG1405 SUA7 Transcription ini 95.2 0.065 1.4E-06 52.1 7.4 69 178-246 193-261 (285)
29 KOG1597 Transcription initiati 92.9 0.38 8.3E-06 46.5 7.5 68 179-246 203-270 (308)
30 KOG1674 Cyclin [General functi 92.2 0.38 8.2E-06 45.0 6.4 92 181-292 80-181 (218)
31 TIGR00569 ccl1 cyclin ccl1. Un 89.3 0.94 2E-05 44.6 6.5 56 297-353 62-119 (305)
32 PF01857 RB_B: Retinoblastoma- 88.4 1.4 3E-05 38.1 6.2 69 179-247 14-84 (135)
33 PF02984 Cyclin_C: Cyclin, C-t 87.5 1.6 3.4E-05 35.5 5.8 56 180-235 4-59 (118)
34 PF08613 Cyclin: Cyclin; Inte 82.0 15 0.00033 31.9 9.8 87 293-380 53-144 (149)
35 KOG0834 CDK9 kinase-activating 77.5 7.8 0.00017 38.4 7.2 59 295-354 43-101 (323)
36 KOG0656 G1/S-specific cyclin D 75.9 17 0.00037 36.2 9.0 84 270-354 48-143 (335)
37 KOG0835 Cyclin L [General func 75.9 4.3 9.3E-05 40.0 4.7 57 183-239 145-203 (367)
38 KOG1675 Predicted cyclin [Gene 74.4 5.8 0.00012 38.8 5.1 92 181-293 195-290 (343)
39 COG5333 CCL1 Cdk activating ki 68.8 11 0.00023 36.9 5.6 83 296-379 50-139 (297)
40 KOG0794 CDK8 kinase-activating 66.8 12 0.00026 35.3 5.3 48 329-376 78-139 (264)
41 KOG1598 Transcription initiati 63.8 8.6 0.00019 40.3 4.1 54 194-247 184-237 (521)
42 PF01857 RB_B: Retinoblastoma- 53.6 51 0.0011 28.4 6.6 58 295-353 15-74 (135)
43 KOG0653 Cyclin B and related k 44.6 79 0.0017 32.1 7.5 84 296-380 163-249 (391)
44 PF13591 MerR_2: MerR HTH fami 35.3 1.2E+02 0.0025 23.7 5.6 41 147-208 33-73 (84)
45 COG5024 Cyclin [Cell division 33.8 96 0.0021 32.2 6.1 74 305-379 227-302 (440)
46 PF09241 Herp-Cyclin: Herpesvi 32.0 2.6E+02 0.0056 22.2 7.4 61 294-354 4-67 (106)
47 COG5552 Uncharacterized conser 31.2 94 0.002 24.1 4.1 46 333-379 16-61 (88)
48 KOG2496 Cdk activating kinase 30.4 1.2E+02 0.0025 29.9 5.7 46 307-353 74-119 (325)
49 PF11671 Apis_Csd: Complementa 29.1 32 0.00068 29.5 1.4 8 65-72 75-82 (146)
50 PF11357 Spy1: Cell cycle regu 23.6 4.6E+02 0.0099 22.6 7.5 87 187-292 22-110 (131)
51 KOG0655 G1/S-specific cyclin E 21.3 3.4E+02 0.0073 27.3 7.0 44 336-379 190-235 (408)
52 KOG1010 Rb (Retinoblastoma tum 21.0 1.4E+02 0.003 33.5 4.6 68 180-247 681-750 (920)
No 1
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=3.3e-45 Score=354.08 Aligned_cols=230 Identities=38% Similarity=0.672 Sum_probs=215.9
Q ss_pred CCCccccHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHH
Q 016851 146 DEPVFMSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAA 225 (381)
Q Consensus 146 ~~~~yft~~e~~~~sPs~~~~i~~~~e~~~R~~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~ac 225 (381)
..+|||+++++++.+||+..|++.+.|...|..++.||+++|.+|++++.|+++|++||||||+.+++++++++.||++|
T Consensus 9 ~~~w~~s~e~~~~~tpSr~~g~~~~~E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sc 88 (323)
T KOG0834|consen 9 TSRWYFSKEQLEENTPSRRDGIDLKKELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASC 88 (323)
T ss_pred ccccccCHHHHccCChhhccCCchhHHHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHH
Confidence 45799999999989999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhccCCCCChHHHHHHHHHHHhhhhhhhhcccCChhHHhHHHHHHHHHHHHHHHHcCcccccCChHHHHHHHHHHc
Q 016851 226 LFLAAKSEETPRPLNDVLRASSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKL 305 (381)
Q Consensus 226 LfLA~K~EE~p~~l~dii~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~tP~~~L~~~l~~l 305 (381)
||||+|+||+|++++||+.++++.+++.+ ....+.|+..++.|+.+|++||++|+|||.+.+||.||.+|++.+
T Consensus 89 lfLAgKvEetp~kl~dIi~~s~~~~~~~~------~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l 162 (323)
T KOG0834|consen 89 LFLAGKVEETPRKLEDIIKVSYRYLNPKD------LELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKL 162 (323)
T ss_pred HHHHhhcccCcccHHHHHHHHHHHcCccc------ccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHh
Confidence 99999999999999999999999887644 234567999999999999999999999999999999999999999
Q ss_pred CCCHH---HHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCccc--hhhhhhhcc--cCHHHHHHHHHHHH
Q 016851 306 GLSQT---VLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDLAA--YQNIWHEFQ--TTPAILQDVAQQLM 378 (381)
Q Consensus 306 ~~~~~---~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~~--~~~w~~~~~--~~~~~I~e~~~~Ll 378 (381)
+.... .+.+.||.+++|++.+.+||+|+|.+||+|||++|+++.++..+. .+.||+.++ ++.++|++++.+++
T Consensus 163 ~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l 242 (323)
T KOG0834|consen 163 KADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHEFL 242 (323)
T ss_pred hhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHHHH
Confidence 87654 589999999999999999999999999999999999999997664 347999999 99999999999999
Q ss_pred hhC
Q 016851 379 ELF 381 (381)
Q Consensus 379 ~Ly 381 (381)
++|
T Consensus 243 ~~y 245 (323)
T KOG0834|consen 243 DLY 245 (323)
T ss_pred HHH
Confidence 987
No 2
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=100.00 E-value=3e-38 Score=298.46 Aligned_cols=224 Identities=31% Similarity=0.502 Sum_probs=203.1
Q ss_pred HhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCC
Q 016851 158 RFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPR 237 (381)
Q Consensus 158 ~~sPs~~~~i~~~~e~~~R~~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~ 237 (381)
..+|+..+|++.+.|..+|.-+|.||++.|..|+||+.+.++++++|+||+...++..+++..|++||++||+|+||.|+
T Consensus 5 ~~~~s~qd~l~~e~e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Pr 84 (367)
T KOG0835|consen 5 DSTPSLQDGLSLETEEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPR 84 (367)
T ss_pred cCchhhhcccccchHHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccc
Confidence 46788899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChHHHHHHHHHHHhhhhhhhhcccCChhHHhHHHHHHHHHHHHHHHHcCcccccCChHHHHHHHHHHcCCCHH-HHHHHH
Q 016851 238 PLNDVLRASSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQT-VLVNLA 316 (381)
Q Consensus 238 ~l~dii~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~tP~~~L~~~l~~l~~~~~-~i~~lA 316 (381)
++++|++|...+-...........+-...+...+..++.+|..||+.|||++.+.+||.++..|++.+++++. ++.|.+
T Consensus 85 r~rdVinVFh~L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~~l~Q~~ 164 (367)
T KOG0835|consen 85 RIRDVINVFHYLEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNLKLLQAA 164 (367)
T ss_pred cHhHHHHHHHHHHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCchhHHHHH
Confidence 9999999988765443322111112223345567889999999999999999999999999999999998764 489999
Q ss_pred HHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCccchhhhhhhcccCHHHHHHHHHHHHhhC
Q 016851 317 LNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQTTPAILQDVAQQLMELF 381 (381)
Q Consensus 317 ~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~~~~~~I~e~~~~Ll~Ly 381 (381)
|+++||++++.+|+.|+|..||+||||||++.+++++|..+.||..|++++++|++++.+++.||
T Consensus 165 wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~~l~~lY 229 (367)
T KOG0835|consen 165 WNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICYRLIPLY 229 (367)
T ss_pred HHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999989999999999999999999999997
No 3
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=100.00 E-value=2.8e-35 Score=285.16 Aligned_cols=215 Identities=20% Similarity=0.296 Sum_probs=181.8
Q ss_pred CCCCcccc-HHHHHHhC------------------CCCcCCCCHHHHHHHHHHHHHHHHHHHHhcC--CCHHHHHHHHHH
Q 016851 145 DDEPVFMS-RDEIERFS------------------PSRKDGIDALRETHLRYSYCAFIQNLGLRLE--LPQTTIGTAMVL 203 (381)
Q Consensus 145 ~~~~~yft-~~e~~~~s------------------Ps~~~~i~~~~e~~~R~~~v~~I~~v~~~L~--L~~~t~~~Ai~~ 203 (381)
+.+.|.|+ ++++.+.. +....++++++|..+|..++.+|.++|.+|+ ||+.|++||++|
T Consensus 6 Q~r~W~F~~~~~L~~~R~~~N~~~~~~~~~~~~~~~~~~~~Lt~eeE~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivy 85 (305)
T TIGR00569 6 QKRHWTFTSEEQLQEKRADANAKFREAHEEEEKVLEAKPIFLTPEEELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMY 85 (305)
T ss_pred ccccCcCCCHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHH
Confidence 45679999 77775421 1235589999999999999999999999999 999999999999
Q ss_pred HHHHhccCCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHHHHHHhhhhhhhhcccCChhHHhHHHHHHHHHHHHHHH
Q 016851 204 CHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILT 283 (381)
Q Consensus 204 fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~Il~~E~~IL~ 283 (381)
|||||+++++..+++++|++||||||||+||.++++.+++...... ...++++|+++|..||+
T Consensus 86 f~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~~-----------------~~~~~~~Il~~E~~lL~ 148 (305)
T TIGR00569 86 FKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKET-----------------PLKALEQVLEYELLLIQ 148 (305)
T ss_pred HhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccCC-----------------chhhHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999887643210 11357899999999999
Q ss_pred HcCcccccCChHHHHHHHHHHcC------CCHHHHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCccchh
Q 016851 284 TLNFELNVQHPYDPLTSILNKLG------LSQTVLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDLAAYQ 357 (381)
Q Consensus 284 ~L~FdL~v~tP~~~L~~~l~~l~------~~~~~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~~~~ 357 (381)
+|+|+|.+++||.+|..|+..++ ...+.+.+.||.++++++++++|+.|+|++||+|||++|++.++++++++
T Consensus 149 ~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAAI~lA~~~~~~~l~~~- 227 (305)
T TIGR00569 149 QLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAGLNMESY- 227 (305)
T ss_pred HCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHHHHHHHHHHHHHhCCCCccc-
Confidence 99999999999999999987553 12345889999999999999999999999999999999999999999874
Q ss_pred hhhhhccc--CHHHHHHHHHHHH
Q 016851 358 NIWHEFQT--TPAILQDVAQQLM 378 (381)
Q Consensus 358 ~w~~~~~~--~~~~I~e~~~~Ll 378 (381)
. |+.+++ +++++..+...|.
T Consensus 228 ~-~e~~~~~~~~~~~~~l~~~~~ 249 (305)
T TIGR00569 228 L-TEQLSVPGNREELPQLIDIMR 249 (305)
T ss_pred c-hhhhcccccHHHHHHHHHHHH
Confidence 3 477776 5555555544443
No 4
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=100.00 E-value=4.4e-36 Score=271.81 Aligned_cols=226 Identities=25% Similarity=0.422 Sum_probs=198.5
Q ss_pred CCccccHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHH
Q 016851 147 EPVFMSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAAL 226 (381)
Q Consensus 147 ~~~yft~~e~~~~sPs~~~~i~~~~e~~~R~~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acL 226 (381)
.+|.|+++++.+-.|.+..+++.+.-..++-...+.|+.+|++++|.+.+++||++||.|||.++|+++.++.++|.|||
T Consensus 12 ~qwl~dk~el~k~r~~D~r~l~~d~~~~l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TCl 91 (264)
T KOG0794|consen 12 QQWLLDKTELLKERQLDLRGLSEDEYSKLKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCL 91 (264)
T ss_pred hhHhcCHHHHhhhccchhhcccHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHH
Confidence 56899999999988988899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhccCCC-CChHHHHHHHHHHHhhhhhhhhcccCChhHHhHHHHHHHHHHHHHHHHcCcccccCChHHHHHHHHHHc
Q 016851 227 FLAAKSEETP-RPLNDVLRASSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKL 305 (381)
Q Consensus 227 fLA~K~EE~p-~~l~dii~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~tP~~~L~~~l~~l 305 (381)
|||||+||+| ..++-++..+..+..+-. ...+.+......|+++|..||+.|++-|.+.||++.|..++++.
T Consensus 92 yLAcKvEE~~i~~~r~l~~~a~~L~~~f~-------~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~ 164 (264)
T KOG0794|consen 92 YLACKVEECPIVHIRLLVNEAKVLKTRFS-------YWPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDM 164 (264)
T ss_pred HHHhhhhhcchHHHHHHHHHHHHHhhhcc-------cchhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHh
Confidence 9999999998 334444444433311111 01111222367899999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCccchhhhhhhcccCHHHHHHHHHHHHhhC
Q 016851 306 GLSQTVLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQTTPAILQDVAQQLMELF 381 (381)
Q Consensus 306 ~~~~~~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~~~~~~I~e~~~~Ll~Ly 381 (381)
|+...+..+++|.++||+++.++||.|+|..||+|||++|+...+.+.+ +.|+.+.++|.+.+.+|+++|+++|
T Consensus 165 gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~~~--~~w~~el~vD~ekV~~~v~~I~~lY 238 (264)
T KOG0794|consen 165 GINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKDIP--KAWFAELSVDMEKVKDIVQEILKLY 238 (264)
T ss_pred cccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCChH--HHHHHHHhccHHHHHHHHHHHHHHH
Confidence 9866568999999999999999999999999999999999999999887 4799999999999999999999997
No 5
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=99.97 E-value=1.9e-30 Score=245.55 Aligned_cols=202 Identities=20% Similarity=0.169 Sum_probs=172.0
Q ss_pred cccccCCCCCCCCCCCCCCCCCCCCcccccccCCCCCCCCccccHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHH
Q 016851 109 ETAVSSSNKTLVPPVSISNIEVSTSMSCKRDRSKLEDDEPVFMSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGL 188 (381)
Q Consensus 109 ~~~~ss~~~~~~p~~~~s~~~~~~s~~~~~~~~~~~~~~~~yft~~e~~~~sPs~~~~i~~~~e~~~R~~~v~~I~~v~~ 188 (381)
-.+..++-+|+|-++|+++.++|.-|..+... |+...-++..+| ..+++||++++|||++||+
T Consensus 95 ~v~apsr~splp~lswgn~~eVW~lM~kkee~---------~l~~~~~l~qHp--------dlqp~mRaILlDWlmEVCE 157 (408)
T KOG0655|consen 95 MVIAPSRLSPLPCLSWGNSKEVWLLMLKKEER---------YLRDKHFLEQHP--------DLQPQMRAILLDWLMEVCE 157 (408)
T ss_pred cccccccCCCCccccccCHHHHHHHHHccchh---------hhhhhHHHhhCC--------CCCHHHHHHHHHHHHHHHH
Confidence 34456777888889999999999999775542 445445554444 4578899999999999999
Q ss_pred hcCCCHHHHHHHHHHHHHHhcc-CCcCccchhhhhHHHHHHhhhccCC-CCChHHHHHHHHHHHhhhhhhhhcccCChhH
Q 016851 189 RLELPQTTIGTAMVLCHRFFVR-RSHACHDRFIIATAALFLAAKSEET-PRPLNDVLRASSELYHKQNITLLSYLLPIDW 266 (381)
Q Consensus 189 ~L~L~~~t~~~Ai~~fdRF~~~-~si~~~~~~lva~acLfLA~K~EE~-p~~l~dii~~~~~~~~k~~~~~~~~~~~~~~ 266 (381)
.++|+++|+++|+.|||||+.. +.+.+..+||||+||||||+|+||. |+++-+++++++..
T Consensus 158 vykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgA----------------- 220 (408)
T KOG0655|consen 158 VYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGA----------------- 220 (408)
T ss_pred HHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCc-----------------
Confidence 9999999999999999999965 6677899999999999999999997 88899999988643
Q ss_pred HhHHHHHHHHHHHHHHHHcCcccccCChHHHHHHHHHHcCC-----------CHHHHHHHHHHHHHHHhccccccCcCHH
Q 016851 267 FEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGL-----------SQTVLVNLALNLVSEGLRSSLWLQFKPN 335 (381)
Q Consensus 267 ~~~~~~~Il~~E~~IL~~L~FdL~v~tP~~~L~~~l~~l~~-----------~~~~i~~lA~~ll~dsl~t~~~L~y~Ps 335 (381)
++.++|+.||.+||++|+|+|.+.|...||..|++..+. ++..+.|+|+ +++.++.+.-++.|+..
T Consensus 221 --cs~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqiaq-lLDlc~ldids~~fsYr 297 (408)
T KOG0655|consen 221 --CSEDDILTMELIILKALKWELSPITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIAQ-LLDLCILDIDSLEFSYR 297 (408)
T ss_pred --cchHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcCCCCceeccccchHHHHHHHH-HHHHHHhccccccchHH
Confidence 468899999999999999999999999999999997643 3456788886 88999999999999999
Q ss_pred HHHHHHHHHHHH
Q 016851 336 HIAAGAAYLAAK 347 (381)
Q Consensus 336 ~IAaAaI~lA~~ 347 (381)
+|||||++.-..
T Consensus 298 ilaAAal~h~~s 309 (408)
T KOG0655|consen 298 ILAAAALCHFTS 309 (408)
T ss_pred HHHHHHHHHHhH
Confidence 999999985443
No 6
>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=99.95 E-value=1.4e-27 Score=226.36 Aligned_cols=175 Identities=30% Similarity=0.488 Sum_probs=152.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHH
Q 016851 167 IDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRAS 246 (381)
Q Consensus 167 i~~~~e~~~R~~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~ 246 (381)
+.-+.|..+|-.++.||+.+|.+|+||+.+++||+.+|+||+.+.++.+.+++.|+.||+|||||+||+|+-+.-.....
T Consensus 36 l~~~~e~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~ 115 (297)
T COG5333 36 LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEA 115 (297)
T ss_pred cchhhhhhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHh
Confidence 66688999999999999999999999999999999999999999999999999999999999999999855443222222
Q ss_pred HHHHhhhhhhhhcccCChhHHhHHHHHHHHHHHHHHHHcCcccccCChHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHhc
Q 016851 247 SELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQT-VLVNLALNLVSEGLR 325 (381)
Q Consensus 247 ~~~~~k~~~~~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~tP~~~L~~~l~~l~~~~~-~i~~lA~~ll~dsl~ 325 (381)
..+ ..+..+.+++.|+++|..||++|+||+.+++||.++..|++++..... ++.++||.+++|++.
T Consensus 116 ~~~-------------~se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~ 182 (297)
T COG5333 116 RDL-------------WSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALR 182 (297)
T ss_pred hcc-------------ccccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhh
Confidence 111 122345679999999999999999999999999999999998865543 589999999999999
Q ss_pred cccccCcCHHHHHHHHHHHHHHHcCCCcc
Q 016851 326 SSLWLQFKPNHIAAGAAYLAAKFLNWDLA 354 (381)
Q Consensus 326 t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~ 354 (381)
+..|+.|+|++||+||+++|+...|.+.+
T Consensus 183 t~~~llypphiIA~a~l~ia~~~~~~~~~ 211 (297)
T COG5333 183 TDLCLLYPPHIIALAALLIACEVLGMPII 211 (297)
T ss_pred ceeeeecChHHHHHHHHHHHHHhcCCccc
Confidence 99999999999999999999999887654
No 7
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=99.93 E-value=4.5e-25 Score=213.95 Aligned_cols=173 Identities=21% Similarity=0.262 Sum_probs=145.8
Q ss_pred hCCCC--cCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccc---hhhhhHHHHHHhhhcc
Q 016851 159 FSPSR--KDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHD---RFIIATAALFLAAKSE 233 (381)
Q Consensus 159 ~sPs~--~~~i~~~~e~~~R~~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~---~~lva~acLfLA~K~E 233 (381)
..|.. ...++...-..+|.++++||.+||+++++..+|+.+|++|||||++.+++.+.+ .||+|+|||+||+|+|
T Consensus 59 ~~p~~~~~~~~~~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKme 138 (335)
T KOG0656|consen 59 HNPSLDYFLCVQKLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKME 138 (335)
T ss_pred hCCCCchhhhcccccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhc
Confidence 45554 567777788889999999999999999999999999999999999999999998 9999999999999999
Q ss_pred CCCCC-hHHHHHH-HHHHHhhhhhhhhcccCChhHHhHHHHHHHHHHHHHHHHcCcccccCChHHHHHHHHHHcCCCH--
Q 016851 234 ETPRP-LNDVLRA-SSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQ-- 309 (381)
Q Consensus 234 E~p~~-l~dii~~-~~~~~~k~~~~~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~tP~~~L~~~l~~l~~~~-- 309 (381)
|+..+ +.|+.-. +.. -...+.|.+||..||.+|+|++...||++|+..|+.+++...
T Consensus 139 E~~vPll~dl~v~~~~~-------------------~feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~ 199 (335)
T KOG0656|consen 139 ETDVPLLADLQVEYTDN-------------------VFEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHN 199 (335)
T ss_pred CcCCchhhhhhhccccc-------------------cccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcccch
Confidence 98533 4443221 111 234788999999999999999999999999999999998743
Q ss_pred -HHHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcC
Q 016851 310 -TVLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLN 350 (381)
Q Consensus 310 -~~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~ 350 (381)
..+...|..++-.+..+..++.|+|++||+|++..+.....
T Consensus 200 ~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~~~~~ 241 (335)
T KOG0656|consen 200 KHLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSVSASVD 241 (335)
T ss_pred HHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHHHHhhc
Confidence 34666777787778888999999999999998877666543
No 8
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=99.90 E-value=3e-23 Score=208.83 Aligned_cols=197 Identities=22% Similarity=0.268 Sum_probs=165.8
Q ss_pred HhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHH-HhhhccCC-
Q 016851 158 RFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALF-LAAKSEET- 235 (381)
Q Consensus 158 ~~sPs~~~~i~~~~e~~~R~~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLf-LA~K~EE~- 235 (381)
...|.....-+.+....||..+++||.+|+..|+|..+|+++|+.++|||+....+...++|+||++||| ||||+||.
T Consensus 140 ~~~p~~~~~~~~e~~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~ 219 (391)
T KOG0653|consen 140 EFLPLSYDISQSEIRAKMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEIS 219 (391)
T ss_pred hhCchhhhcccccccHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhcc
Confidence 3455554455666677899999999999999999999999999999999999988999999999999977 99999997
Q ss_pred CCChHHHHHHHHHHHhhhhhhhhcccCChhHHhHHHHHHHHHHHHHHHHcCcccccCChHHHHHHHHHHcCCCHHHHHHH
Q 016851 236 PRPLNDVLRASSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQTVLVNL 315 (381)
Q Consensus 236 p~~l~dii~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~tP~~~L~~~l~~l~~~~~~i~~l 315 (381)
++.++|++.++++.+ ++++|+.||+.||.+|+|++.+++|+.||.++.+..+.+.+ ...+
T Consensus 220 ~P~v~dlv~isd~~~-------------------s~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d~~-~~~~ 279 (391)
T KOG0653|consen 220 LPSVEDLVLITDGAY-------------------SREEILRMEKYILNVLEFDLSVPTPLSFLRRFLKAADYDIK-TRTL 279 (391)
T ss_pred CCccceeEeeeCCcc-------------------chHHHHHHHHHHHhccCeeecCCchHHHHHHHHHhhhcchh-HHHH
Confidence 444888888776443 68999999999999999999999999999999998875543 6678
Q ss_pred HHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCccchhhhhhhcc----cCHHHHHHHHHHHH
Q 016851 316 ALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQ----TTPAILQDVAQQLM 378 (381)
Q Consensus 316 A~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~----~~~~~I~e~~~~Ll 378 (381)
+.+++++++.+...+.++|+.+|+|+++++..+...+. .|-..+. ....++.++.+.+.
T Consensus 280 ~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~~~~~~----~w~~~~~~~sg~~~~~~~~~~~~~~ 342 (391)
T KOG0653|consen 280 VKYLLELSLCDYSMLSIPPSSSAAASFTLALRMLSKGD----VWSPTLEHYSGYSESYLFECARSLS 342 (391)
T ss_pred HHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHHhccCC----ccCCCCeeccCCCcHHHHHHHHHHH
Confidence 99999999999999999999999999999999988763 3444333 34446666666554
No 9
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=99.87 E-value=6.4e-22 Score=198.40 Aligned_cols=191 Identities=21% Similarity=0.226 Sum_probs=163.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCC-CCChHHHH
Q 016851 165 DGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEET-PRPLNDVL 243 (381)
Q Consensus 165 ~~i~~~~e~~~R~~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~-p~~l~dii 243 (381)
..-+++.+..||..+++||.+++..|+|-++|+++|+.++|||+..+.+.-..+||||++|||||||+||. .+.+++++
T Consensus 202 l~kq~~~~~~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~ 281 (440)
T COG5024 202 LIKQSLYEWSMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLV 281 (440)
T ss_pred HhhcchhHHhHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHH
Confidence 33455666789999999999999999999999999999999999999999999999999999999999997 45588888
Q ss_pred HHHHHHHhhhhhhhhcccCChhHHhHHHHHHHHHHHHHHHHcCcccccCChHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Q 016851 244 RASSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQTVLVNLALNLVSEG 323 (381)
Q Consensus 244 ~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~tP~~~L~~~l~~l~~~~~~i~~lA~~ll~ds 323 (381)
.++...+ ++++|+.+|+-+|.+|+|++..|.|..||+++.+..+.+.. -+..+.+++..+
T Consensus 282 ~~t~g~~-------------------t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka~dyd~~-srt~~k~~~e~s 341 (440)
T COG5024 282 YATDGAF-------------------TRDDIIRAERYMLEVLDFNISWPSPMSFLRRISKASDYDIF-SRTPAKFSSEIS 341 (440)
T ss_pred HHHcccc-------------------cHHHHHHHHHHHhhhcccccCCCChHHHHHHHHhhcccchh-hhhhHhhhCCch
Confidence 8876443 68999999999999999999999999999988887766543 455788888888
Q ss_pred hccccccCcCHHHHHHHHHHHHHHHcCCCccchhhhhhhcc-----cCHHHHHHHHHHHHhh
Q 016851 324 LRSSLWLQFKPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQ-----TTPAILQDVAQQLMEL 380 (381)
Q Consensus 324 l~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~-----~~~~~I~e~~~~Ll~L 380 (381)
....-++.++|+.+|+||.|+|.++++.+- |=..+. ++.+++..++..++++
T Consensus 342 ~~~~~f~~~~~S~~~aaa~~~s~~~~~~~~-----w~~~l~~ySg~y~~~~l~~~~~~~~~~ 398 (440)
T COG5024 342 PVDYKFIQISPSWCAAAAMYLSRKILSQNQ-----WDRTLIHYSGNYTNPDLKPLNESNKEN 398 (440)
T ss_pred HhhhhhccCCchHHHHHHHHHHHhhhccCC-----CCccccccCCCCCchhHHHHHHHHHHH
Confidence 888888999999999999999999998752 333332 5666888888877764
No 10
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.84 E-value=2.2e-19 Score=175.63 Aligned_cols=185 Identities=21% Similarity=0.263 Sum_probs=166.6
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHHHHHH
Q 016851 171 RETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELY 250 (381)
Q Consensus 171 ~e~~~R~~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~~~~~ 250 (381)
.|..+ ..+...|.++|..|+||..+..+|+.+|++++....+++.....+++||||+|||.++.|+++++|..++.
T Consensus 118 ~er~l-~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~--- 193 (310)
T PRK00423 118 AERNL-AFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSR--- 193 (310)
T ss_pred HhHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhC---
Confidence 44555 46779999999999999999999999999999999999999999999999999999999999999987753
Q ss_pred hhhhhhhhcccCChhHHhHHHHHHHHHHHHHHHHcCcccccCChHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcccccc
Q 016851 251 HKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQTVLVNLALNLVSEGLRSSLWL 330 (381)
Q Consensus 251 ~k~~~~~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~tP~~~L~~~l~~l~~~~~~i~~lA~~ll~dsl~t~~~L 330 (381)
..+.+|...++.|++.|++++.+.+|.+|+.+|+..++++.+ +.+.|+.+++.+....+..
T Consensus 194 ------------------v~~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~-v~~~A~~i~~~a~~~~l~~ 254 (310)
T PRK00423 194 ------------------VSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGE-VQKKAIEILQKAKEKGLTS 254 (310)
T ss_pred ------------------CCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHhcCccc
Confidence 136678889999999999999999999999999999999985 8899999999998888888
Q ss_pred CcCHHHHHHHHHHHHHHHcCCCccchhhhhhhcccCHHHHHHHHHHHHh
Q 016851 331 QFKPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQTTPAILQDVAQQLME 379 (381)
Q Consensus 331 ~y~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~~~~~~I~e~~~~Ll~ 379 (381)
..+|..||+||||+|+++.+.+.. .++.....++++..|....++|..
T Consensus 255 Gr~P~sIAAAaIYlA~~~~g~~~t-~keIa~v~~Vs~~tI~~~ykel~~ 302 (310)
T PRK00423 255 GKGPTGLAAAAIYIASLLLGERRT-QREVAEVAGVTEVTVRNRYKELAE 302 (310)
T ss_pred CCCHHHHHHHHHHHHHHHhCCCCC-HHHHHHHcCCCHHHHHHHHHHHHH
Confidence 999999999999999999998854 367888889999999998888864
No 11
>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=99.84 E-value=2.4e-20 Score=175.81 Aligned_cols=154 Identities=26% Similarity=0.377 Sum_probs=126.4
Q ss_pred HHHHHHhc--CCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHHHHHHhhhhhhhhcc
Q 016851 183 IQNLGLRL--ELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELYHKQNITLLSY 260 (381)
Q Consensus 183 I~~v~~~L--~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~~~~~~k~~~~~~~~ 260 (381)
+.+.+..+ +||..|+.||+.+|.|||...++.++++..|++||+|+|||+||....++++++...
T Consensus 63 l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~------------- 129 (325)
T KOG2496|consen 63 LVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMN------------- 129 (325)
T ss_pred HHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhcc-------------
Confidence 33444443 589999999999999999999999999999999999999999999999999988653
Q ss_pred cCChhHHhHHHHHHHHHHHHHHHHcCcccccCChHHHHHHHHHHcC------CCHHHHHH--HHHHHHHHHhccccccCc
Q 016851 261 LLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLG------LSQTVLVN--LALNLVSEGLRSSLWLQF 332 (381)
Q Consensus 261 ~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~tP~~~L~~~l~~l~------~~~~~i~~--lA~~ll~dsl~t~~~L~y 332 (381)
+.-++..+.|+..|..+|+.|+|+|.+.+|+..++.|+.+++ .+.+...+ ....+++..+.+++++.|
T Consensus 130 ----~~~~k~~e~vLk~E~~llqsL~f~L~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLy 205 (325)
T KOG2496|consen 130 ----GRKWKTHEIVLKYEFLLLQSLKFSLTVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLY 205 (325)
T ss_pred ----CcccccHHHHHhchHHHHHhhhhhheecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceec
Confidence 112456899999999999999999999999999999987642 11221222 234788889999999999
Q ss_pred CHHHHHHHHHHHHHHHcCCCc
Q 016851 333 KPNHIAAGAAYLAAKFLNWDL 353 (381)
Q Consensus 333 ~Ps~IAaAaI~lA~~~~~~~l 353 (381)
+|++||+|||..|....|.-+
T Consensus 206 tPsQIALaAil~a~~~~~~~l 226 (325)
T KOG2496|consen 206 TPSQIALAAILHAAGRTGETL 226 (325)
T ss_pred ChHHHHHHHHHHHhccccchH
Confidence 999999999977766666654
No 12
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=99.77 E-value=7.8e-19 Score=172.02 Aligned_cols=199 Identities=21% Similarity=0.232 Sum_probs=175.4
Q ss_pred HhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCC-C
Q 016851 158 RFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEET-P 236 (381)
Q Consensus 158 ~~sPs~~~~i~~~~e~~~R~~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~-p 236 (381)
+..|+...-++.+....||..+|+|+.++++.+++..++++++.++.|||+....+.+...++++.+|.+||+|.||. +
T Consensus 119 rp~~~~~e~vq~d~t~smrgilvdwlvevsee~r~~~e~l~ls~~~~drfl~~~~~~~~k~ql~g~s~m~I~sk~ee~~~ 198 (359)
T KOG0654|consen 119 RPLPSKFEFVQADITPSMRGILVDWLVEVSEEYRLTFETLYLSVNYRDRFLSYKEVNKQKLQLVGISAMLIASKYEEIKE 198 (359)
T ss_pred cCcccceeeeecCCCcchhhhhhhhhhHHHHHHHhhhhheeecHHHHHHHhccCccHHHHHHHhCcccceeeccchhhcc
Confidence 345556667788888999999999999999999999999999999999999999999999999999999999999997 5
Q ss_pred CChHHHHHHHHHHHhhhhhhhhcccCChhHHhHHHHHHHHHHHHHHHHcCcccccCChHHHHHHHHHHcCCCHHHHHHHH
Q 016851 237 RPLNDVLRASSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQTVLVNLA 316 (381)
Q Consensus 237 ~~l~dii~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~tP~~~L~~~l~~l~~~~~~i~~lA 316 (381)
+.+++++..+++.+ +..++..||..||..|.|++..++...|+..++........++..+|
T Consensus 199 ~~~~ef~~itd~ty-------------------~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~~~~~~~~~~e~~~ 259 (359)
T KOG0654|consen 199 PRVEEFCYITDNTY-------------------TYWQVLRMEIDILNALTFELVRPTSKTFLRRFLRVAQTPELQVEPLA 259 (359)
T ss_pred hHHHHHHhhhhhhh-------------------HHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHHhhcchhHHHHHHH
Confidence 66888888876554 58899999999999999999999999999999887664444577889
Q ss_pred HHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCccchhhhhhhcc----cCHHHHHHHHHHHHhhC
Q 016851 317 LNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQ----TTPAILQDVAQQLMELF 381 (381)
Q Consensus 317 ~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~----~~~~~I~e~~~~Ll~Ly 381 (381)
.++.+.++.+..++.|.||.||+||+++|...++. .+|-+.+. ++.++++.|...|. +|
T Consensus 260 ~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~~-----~pW~~~L~~~T~y~~edl~~~v~~L~-~~ 322 (359)
T KOG0654|consen 260 NYLTELSLLDYIFLKYLPSLIAASAVFLARLTLDF-----HPWNQTLEDYTGYKAEDLKPCVLDLH-LY 322 (359)
T ss_pred HHHHHhhhhhHHHhccChHHHHHHHHHHHHhhccC-----CCCchhhHHhhcccHHHHHHHHHHHh-cc
Confidence 99999999999999999999999999999999882 35655544 88999999999987 65
No 13
>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=99.77 E-value=1.4e-18 Score=147.16 Aligned_cols=121 Identities=30% Similarity=0.405 Sum_probs=94.4
Q ss_pred ccHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhh
Q 016851 151 MSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAA 230 (381)
Q Consensus 151 ft~~e~~~~sPs~~~~i~~~~e~~~R~~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~ 230 (381)
+...|.....+..-...+++.....|..+++||.+++..++++..|+++|+.|||||+.+.++...+++++++|||+|||
T Consensus 6 ~~~~e~~~~~~~~~~~~~~~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~ 85 (127)
T PF00134_consen 6 LLEKELKYKPNPDYLEQQPEITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLAS 85 (127)
T ss_dssp HHHHHHHTTCCTTHGTGTSSHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHH
T ss_pred HHHHHHHHCcCccccccChhcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhh
Confidence 34444433333333334446777999999999999999999999999999999999999999999999999999999999
Q ss_pred hccCC-CCChHHHHHHHHHHHhhhhhhhhcccCChhHHhHHHHHHHHHHHHHHHHcCcccc
Q 016851 231 KSEET-PRPLNDVLRASSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELN 290 (381)
Q Consensus 231 K~EE~-p~~l~dii~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~ 290 (381)
|+||. ++.+.+++..+... .++++|++||+.||++|+|+++
T Consensus 86 K~~e~~~~~~~~~~~~~~~~-------------------~~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 86 KMEEDNPPSISDLIRISDNT-------------------FTKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp HHHTSS--HHHHHHHHTTTS-------------------SHHHHHHHHHHHHHHHTTT---
T ss_pred hhhccccchHHHHHHHHcCC-------------------CCHHHHHHHHHHHHHHCCCCcC
Confidence 99998 77788887766321 2589999999999999999984
No 14
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.55 E-value=2.9e-13 Score=130.32 Aligned_cols=185 Identities=19% Similarity=0.287 Sum_probs=164.0
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHHHHHH
Q 016851 171 RETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELY 250 (381)
Q Consensus 171 ~e~~~R~~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~~~~~ 250 (381)
.|..+. .+...|..++..|+||..+.-+|+.+|.+.+...-+++....-+++||+|+||+.+..|+.+.++..+.. +
T Consensus 93 ~ernl~-~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~-V- 169 (285)
T COG1405 93 KERNLI-TALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALG-V- 169 (285)
T ss_pred hhhHHH-HHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHC-C-
Confidence 344444 6788999999999999999999999999999999999999999999999999999999999999988763 1
Q ss_pred hhhhhhhhcccCChhHHhHHHHHHHHHHHHHHHHcCcccccCChHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcccccc
Q 016851 251 HKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQTVLVNLALNLVSEGLRSSLWL 330 (381)
Q Consensus 251 ~k~~~~~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~tP~~~L~~~l~~l~~~~~~i~~lA~~ll~dsl~t~~~L 330 (381)
.+.+|....+.+.+.|+=.+.+..|..|+.+|+..|+++.+ +...|..++..+.....-.
T Consensus 170 -------------------~~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~-v~~~a~ei~~~~~~~g~~~ 229 (285)
T COG1405 170 -------------------SKKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSDE-VRRKAIEIVKKAKRAGLTA 229 (285)
T ss_pred -------------------CHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHHhCccc
Confidence 25778888999999999999999999999999999999964 8889999999998888778
Q ss_pred CcCHHHHHHHHHHHHHHHcCCCccchhhhhhhcccCHHHHHHHHHHHHh
Q 016851 331 QFKPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQTTPAILQDVAQQLME 379 (381)
Q Consensus 331 ~y~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~~~~~~I~e~~~~Ll~ 379 (381)
.-.|..||+||||+|+.+++..... ++.-...++++..|..--++|.+
T Consensus 230 Gk~P~glAaaaiy~as~l~~~~~tq-~eva~v~~vtevTIrnrykel~~ 277 (285)
T COG1405 230 GKSPAGLAAAAIYLASLLLGERRTQ-KEVAKVAGVTEVTIRNRYKELAD 277 (285)
T ss_pred CCCchhHHHHHHHHHHHHhCCchHH-HHHHHHhCCeeeHHHHHHHHHHH
Confidence 9999999999999999999976543 57788888999999888887765
No 15
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.54 E-value=1.7e-12 Score=122.70 Aligned_cols=178 Identities=16% Similarity=0.201 Sum_probs=147.9
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHHHHHHhhhhhhh
Q 016851 178 SYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELYHKQNITL 257 (381)
Q Consensus 178 ~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~~~~~~k~~~~~ 257 (381)
....-|..++++++||..+.-.|..+|.++...+.++......+++|||++||+.++.|+.+++|..++. .
T Consensus 106 ~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~an--v------- 176 (308)
T KOG1597|consen 106 AAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVAN--V------- 176 (308)
T ss_pred HHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHHc--C-------
Confidence 4556678999999999999999999999999989999999999999999999999999999999888765 2
Q ss_pred hcccCChhHHhHHHHHHHHHHHHHHHHcCcccccCC--hHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccccccCcCHH
Q 016851 258 LSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQH--PYDPLTSILNKLGLSQTVLVNLALNLVSEGLRSSLWLQFKPN 335 (381)
Q Consensus 258 ~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~t--P~~~L~~~l~~l~~~~~~i~~lA~~ll~dsl~t~~~L~y~Ps 335 (381)
.+++|-++=+.|++.|+=....-+ .-+|+.+|+..|+++.. +...|..++..+.--..+-.-+|-
T Consensus 177 ------------~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~-~q~aA~e~a~ka~~~~~~~gRsPi 243 (308)
T KOG1597|consen 177 ------------SKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKS-AQEAATEIAEKAEEMDIRAGRSPI 243 (308)
T ss_pred ------------CHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHH-HHHHHHHHHHHHHHhccccCCCch
Confidence 245555666777777776655444 78899999999999986 677788888877655666668999
Q ss_pred HHHHHHHHHHHHHcCCCccchhhhhhhcccCHHHHHHHHHHHH
Q 016851 336 HIAAGAAYLAAKFLNWDLAAYQNIWHEFQTTPAILQDVAQQLM 378 (381)
Q Consensus 336 ~IAaAaI~lA~~~~~~~l~~~~~w~~~~~~~~~~I~e~~~~Ll 378 (381)
.||+|+|||++++.+...+. ++.-+..++++..|+...+.|.
T Consensus 244 SIAAa~IYmisqls~~kkt~-keI~~vtgVaE~TIr~sYK~Ly 285 (308)
T KOG1597|consen 244 SIAAAAIYMISQLSDEKKTQ-KEIGEVTGVAEVTIRNSYKDLY 285 (308)
T ss_pred hHHHHHHHHHHHhccCcccH-HHHHHHhhhhHHHHHHHHHHHh
Confidence 99999999999998855443 5677778888988888887765
No 16
>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=99.42 E-value=6.1e-13 Score=103.73 Aligned_cols=87 Identities=30% Similarity=0.418 Sum_probs=77.9
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHHHHHHhhhhh
Q 016851 176 RYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELYHKQNI 255 (381)
Q Consensus 176 R~~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~~~~~~k~~~ 255 (381)
|...++||.+++..++++.+|..+|+.++|||+....+.+.+++++|+||||||||++|.++.++++...+...
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~------ 75 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYA------ 75 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCC------
Confidence 55789999999999999999999999999999999999999999999999999999999988999988766310
Q ss_pred hhhcccCChhHHhHHHHHHHHHHHHHH
Q 016851 256 TLLSYLLPIDWFEQYRERVIEAEQMIL 282 (381)
Q Consensus 256 ~~~~~~~~~~~~~~~~~~Il~~E~~IL 282 (381)
+.++|..+|..||
T Consensus 76 --------------~~~~i~~~e~~il 88 (88)
T cd00043 76 --------------TEEEILRMEKLLL 88 (88)
T ss_pred --------------CHHHHHHHHHHhC
Confidence 4778889998874
No 17
>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=99.29 E-value=6.6e-12 Score=96.87 Aligned_cols=83 Identities=28% Similarity=0.385 Sum_probs=72.3
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHHHHHHhhhhhhhhcc
Q 016851 181 AFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELYHKQNITLLSY 260 (381)
Q Consensus 181 ~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~~~~~~k~~~~~~~~ 260 (381)
+||.+++..++++.++..+|+.++||++....+.+..++++|+||||+|||++|.++..+++...+..
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~------------ 68 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGY------------ 68 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC------------
Confidence 48999999999999999999999999999777778999999999999999999988788777665421
Q ss_pred cCChhHHhHHHHHHHHHHHHHHH
Q 016851 261 LLPIDWFEQYRERVIEAEQMILT 283 (381)
Q Consensus 261 ~~~~~~~~~~~~~Il~~E~~IL~ 283 (381)
.+.++|..+|+.||+
T Consensus 69 --------~~~~~i~~~~~~il~ 83 (83)
T smart00385 69 --------FTEEEILRMEKLLLE 83 (83)
T ss_pred --------CCHHHHHHHHHHHhC
Confidence 147789999999874
No 18
>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=99.00 E-value=6.1e-10 Score=92.49 Aligned_cols=88 Identities=27% Similarity=0.266 Sum_probs=67.8
Q ss_pred CChHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCccchhhhhhhcccCHHHHH
Q 016851 292 QHPYDPLTSILNKLGLSQTVLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQTTPAILQ 371 (381)
Q Consensus 292 ~tP~~~L~~~l~~l~~~~~~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~~~~~~I~ 371 (381)
|||+.||..|++..+.+ ..+..+|+++++.++.+..++.|+|+.||+|||++|..+++.............+++.++|.
T Consensus 1 PTp~~Fl~~~~~~~~~~-~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~ 79 (118)
T PF02984_consen 1 PTPYDFLRRFLKISNAD-QEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLK 79 (118)
T ss_dssp --HHHHHHHHHTSSSHH-HHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHH
T ss_pred CcHHHHHHHHHHHcCCc-HHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHH
Confidence 68999999996654443 35889999999999999999999999999999999999988422211223344568999999
Q ss_pred HHHHHHHhh
Q 016851 372 DVAQQLMEL 380 (381)
Q Consensus 372 e~~~~Ll~L 380 (381)
+|++.|.++
T Consensus 80 ~c~~~i~~~ 88 (118)
T PF02984_consen 80 ECIELIQEL 88 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 999999876
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=98.59 E-value=3.2e-07 Score=70.41 Aligned_cols=82 Identities=30% Similarity=0.338 Sum_probs=70.6
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCccchhhhhhhccc-CHHHHHHHH
Q 016851 296 DPLTSILNKLGLSQTVLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQT-TPAILQDVA 374 (381)
Q Consensus 296 ~~L~~~l~~l~~~~~~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~~-~~~~I~e~~ 374 (381)
+|+.++...++++.+ +..+|+.+++..+....++.++|+.||+|||++|+++.+.+. ..+++....++ ++++|.++.
T Consensus 1 ~~l~~~~~~~~~~~~-~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~-~~~~~~~~~~~~~~~~i~~~~ 78 (83)
T smart00385 1 DFLRRVCKALNLDPE-TLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPP-WTKELVHYTGYFTEEEILRME 78 (83)
T ss_pred CHHHHHHHHcCCCHH-HHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCC-CchhHhHhhCCCCHHHHHHHH
Confidence 378889999999875 899999999999887778889999999999999999998873 33567777777 999999999
Q ss_pred HHHHh
Q 016851 375 QQLME 379 (381)
Q Consensus 375 ~~Ll~ 379 (381)
++|++
T Consensus 79 ~~il~ 83 (83)
T smart00385 79 KLLLE 83 (83)
T ss_pred HHHhC
Confidence 98874
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=98.48 E-value=1.2e-06 Score=67.90 Aligned_cols=86 Identities=29% Similarity=0.305 Sum_probs=73.9
Q ss_pred cCChHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCccchhhhhhhccc-CHHH
Q 016851 291 VQHPYDPLTSILNKLGLSQTVLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQT-TPAI 369 (381)
Q Consensus 291 v~tP~~~L~~~l~~l~~~~~~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~~-~~~~ 369 (381)
.++|..|+.+++..++++.+ +..+|..+++..+....+..+.|+.||+|||++|+++.+.. +...++....+. ++++
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~-~~~~~~~~~~~~~~~~~ 79 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPE-TLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIP-PWLKDLVHVTGYATEEE 79 (88)
T ss_pred cchHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCC-CCHHHHhHHhCCCCHHH
Confidence 46899999999999999986 88899999999998888889999999999999999999883 333567777778 9999
Q ss_pred HHHHHHHHH
Q 016851 370 LQDVAQQLM 378 (381)
Q Consensus 370 I~e~~~~Ll 378 (381)
|..+.++|+
T Consensus 80 i~~~e~~il 88 (88)
T cd00043 80 ILRMEKLLL 88 (88)
T ss_pred HHHHHHHhC
Confidence 998887763
No 21
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.27 E-value=4.8e-06 Score=85.19 Aligned_cols=154 Identities=16% Similarity=0.106 Sum_probs=121.5
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHHHHHHhhhhhhh
Q 016851 178 SYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELYHKQNITL 257 (381)
Q Consensus 178 ~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~~~~~~k~~~~~ 257 (381)
..-..|.+++..|+|+. .+-+|..+|.--...+-.++.....|.++|||++|..|-++.-+=|+.....
T Consensus 69 n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~Lq---------- 137 (521)
T KOG1598|consen 69 NARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQ---------- 137 (521)
T ss_pred HHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccceE----------
Confidence 44557889999999999 9999999999988888888889999999999999999988666544322210
Q ss_pred hcccCChhHHhHHHHHHHHHHHHHHHHcCcc---cccCChHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHhccccccCc
Q 016851 258 LSYLLPIDWFEQYRERVIEAEQMILTTLNFE---LNVQHPYDPLTSILNKLGLS--QTVLVNLALNLVSEGLRSSLWLQF 332 (381)
Q Consensus 258 ~~~~~~~~~~~~~~~~Il~~E~~IL~~L~Fd---L~v~tP~~~L~~~l~~l~~~--~~~i~~lA~~ll~dsl~t~~~L~y 332 (381)
.+ .=++-.+=+.|...|.-+ +....|.-|+.+|...+... .+++...|..++.-..++.+...-
T Consensus 138 ------v~-----Vy~LG~~~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGR 206 (521)
T KOG1598|consen 138 ------VS-----VYDLGSNFLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGR 206 (521)
T ss_pred ------Ee-----hhhhhHHHHHHHHHhccccccccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCC
Confidence 01 111222334555666666 66778999999998877543 346888999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHcCCCc
Q 016851 333 KPNHIAAGAAYLAAKFLNWDL 353 (381)
Q Consensus 333 ~Ps~IAaAaI~lA~~~~~~~l 353 (381)
+|+.|+-|||++|++++|+..
T Consensus 207 RPsglcGAaLliAar~h~~~r 227 (521)
T KOG1598|consen 207 RPSGLCGAALLIAARMHGFRR 227 (521)
T ss_pred CccchhHHHHHHHHHHcCccc
Confidence 999999999999999999874
No 22
>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=98.26 E-value=3.8e-06 Score=64.32 Aligned_cols=64 Identities=23% Similarity=0.311 Sum_probs=56.5
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHH
Q 016851 183 IQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRAS 246 (381)
Q Consensus 183 I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~ 246 (381)
|.++|..|+||..+.-.|..++++-....-..+..+..+++||||+||+.+..++++++|..++
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~ 64 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAA 64 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHC
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHh
Confidence 5689999999999999999999999988888889999999999999999999999999987754
No 23
>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=98.06 E-value=2.7e-05 Score=68.44 Aligned_cols=91 Identities=15% Similarity=0.136 Sum_probs=64.3
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhc---c--CCcCccchhhhhHHHHHHhhhcc-CCCCChHHHHHHHHHHHh
Q 016851 178 SYCAFIQNLGLRLELPQTTIGTAMVLCHRFFV---R--RSHACHDRFIIATAALFLAAKSE-ETPRPLNDVLRASSELYH 251 (381)
Q Consensus 178 ~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~---~--~si~~~~~~lva~acLfLA~K~E-E~p~~l~dii~~~~~~~~ 251 (381)
.+.+|+.++.+..+++.+++..|++|++|+.. . ..+.....+-+.++||.+|+|+- |....-+...+++.
T Consensus 53 ~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~g---- 128 (149)
T PF08613_consen 53 SIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGG---- 128 (149)
T ss_dssp -HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHT----
T ss_pred cHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcC----
Confidence 45678889999999999999999999999998 2 23455667888999999999965 44444444444321
Q ss_pred hhhhhhhcccCChhHHhHHHHHHHHHHHHHHHHcCccc
Q 016851 252 KQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFEL 289 (381)
Q Consensus 252 k~~~~~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL 289 (381)
-..+++-.||+..|..|+|+|
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 136789999999999999986
No 24
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=98.02 E-value=1.2e-05 Score=79.19 Aligned_cols=98 Identities=23% Similarity=0.331 Sum_probs=82.3
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCC-ChHHHHHHHHHHHhhhhhh
Q 016851 178 SYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPR-PLNDVLRASSELYHKQNIT 256 (381)
Q Consensus 178 ~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~-~l~dii~~~~~~~~k~~~~ 256 (381)
.+-.-|.++++..++..-|++.|-+||.....+.-+.+....++|-|||+||+|+.|... .++.+|....+.
T Consensus 384 SlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~------- 456 (497)
T KOG4164|consen 384 SLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQ------- 456 (497)
T ss_pred HHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHH-------
Confidence 445566789999999999999999999999999999999999999999999999997533 367766655433
Q ss_pred hhcccCChhHHhHHHHHHHHHHHHHHHHcCcccccC
Q 016851 257 LLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQ 292 (381)
Q Consensus 257 ~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~ 292 (381)
+...+.+++..|.-||-+|.|.|.++
T Consensus 457 ----------fR~nrrdLia~Ef~VlvaLefaL~~~ 482 (497)
T KOG4164|consen 457 ----------FRLNRRDLIAFEFPVLVALEFALHLP 482 (497)
T ss_pred ----------hcccHHhhhhhhhhHHHhhhhhccCC
Confidence 33357889999999999999999765
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=97.79 E-value=0.00015 Score=55.46 Aligned_cols=71 Identities=21% Similarity=0.265 Sum_probs=56.6
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCccchhhhhhhcccCHHHH
Q 016851 298 LTSILNKLGLSQTVLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQTTPAIL 370 (381)
Q Consensus 298 L~~~l~~l~~~~~~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~~~~~~I 370 (381)
+.+++..++++.. +...|..+........+.-.-+|..||+||||+|++..+.+.+. .+.-+..++++.+|
T Consensus 1 I~r~~~~L~L~~~-v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~-~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPED-VRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTL-KEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HH-HHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSH-HHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCCHH-HHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCH-HHHHHHhCCCCCcC
Confidence 4678999999985 88999999998887777778899999999999999999988654 46677777777654
No 26
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=97.29 E-value=0.0012 Score=64.84 Aligned_cols=67 Identities=13% Similarity=0.149 Sum_probs=61.2
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHH
Q 016851 180 CAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRAS 246 (381)
Q Consensus 180 v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~ 246 (381)
.++|.+++..|+|+..+.-+|..++.+.....-..+..+.-|++||+|+||+..+.++.+++|..++
T Consensus 220 ~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~ 286 (310)
T PRK00423 220 IDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVA 286 (310)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHc
Confidence 5899999999999999999999999998876666789999999999999999999999999987765
No 27
>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=95.81 E-value=0.076 Score=44.28 Aligned_cols=85 Identities=18% Similarity=0.169 Sum_probs=62.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCccchhhhhhhcc--cCHHHHHH
Q 016851 295 YDPLTSILNKLGLSQTVLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQ--TTPAILQD 372 (381)
Q Consensus 295 ~~~L~~~l~~l~~~~~~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~--~~~~~I~e 372 (381)
..|+......++++.. ....|..+++..+.........+..+|+||+++|+++.+...+.-.+|....+ ++.++|.+
T Consensus 35 ~~~i~~~~~~~~l~~~-~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~ 113 (127)
T PF00134_consen 35 IDWIIELCQRLKLSPE-TLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILE 113 (127)
T ss_dssp HHHHHHHHHHTT-BHH-HHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHH
T ss_pred HHHHHHHHHhcccchh-HHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHH
Confidence 3456667777888875 67788888888776666777889999999999999999886665556655544 78899988
Q ss_pred HHHHHHhh
Q 016851 373 VAQQLMEL 380 (381)
Q Consensus 373 ~~~~Ll~L 380 (381)
+-..|+..
T Consensus 114 ~E~~iL~~ 121 (127)
T PF00134_consen 114 MEREILSA 121 (127)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 88888753
No 28
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=95.16 E-value=0.065 Score=52.08 Aligned_cols=69 Identities=17% Similarity=0.175 Sum_probs=61.5
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHH
Q 016851 178 SYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRAS 246 (381)
Q Consensus 178 ~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~ 246 (381)
.-.++|.+++..|+|+.++.-.|..+++............+.-+|+||+|+||++...++.-+++..++
T Consensus 193 ~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~ 261 (285)
T COG1405 193 DPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVA 261 (285)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHh
Confidence 346788999999999999999999999999988888899999999999999999998777777776655
No 29
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=92.89 E-value=0.38 Score=46.48 Aligned_cols=68 Identities=15% Similarity=0.220 Sum_probs=59.4
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHH
Q 016851 179 YCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRAS 246 (381)
Q Consensus 179 ~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~ 246 (381)
..+||.+.|..|+|+..+.-.|..+-.+.-...-..+..+.-|+++++|+++-+++.++..++|..++
T Consensus 203 t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vt 270 (308)
T KOG1597|consen 203 TGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVT 270 (308)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHh
Confidence 56888999999999999999999999988877777788899999999999999999888888875544
No 30
>KOG1674 consensus Cyclin [General function prediction only]
Probab=92.16 E-value=0.38 Score=45.00 Aligned_cols=92 Identities=14% Similarity=0.134 Sum_probs=63.5
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHhccCC---------cCccc-hhhhhHHHHHHhhhccCCCCChHHHHHHHHHHH
Q 016851 181 AFIQNLGLRLELPQTTIGTAMVLCHRFFVRRS---------HACHD-RFIIATAALFLAAKSEETPRPLNDVLRASSELY 250 (381)
Q Consensus 181 ~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~s---------i~~~~-~~lva~acLfLA~K~EE~p~~l~dii~~~~~~~ 250 (381)
+++.++-+..+...+++.+|.+|||||..... +.-.. ..-..++|+-+|+|..+..-- ....+
T Consensus 80 ~yleri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~y-------~n~~~ 152 (218)
T KOG1674|consen 80 QYLERIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVYY-------SNAYY 152 (218)
T ss_pred HHHHHHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccchhh-------hHHHH
Confidence 45667788889999999999999999988622 11223 344789999999999863110 00111
Q ss_pred hhhhhhhhcccCChhHHhHHHHHHHHHHHHHHHHcCcccccC
Q 016851 251 HKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQ 292 (381)
Q Consensus 251 ~k~~~~~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~ 292 (381)
.+. +. -..+++-.+|..+|..++|.+.+.
T Consensus 153 a~v-----gg--------l~~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 153 AKV-----GG--------LTTDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred HHh-----CC--------CChHhhhhhhHHHHhhCCeEEEec
Confidence 110 00 035667799999999999999886
No 31
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=89.35 E-value=0.94 Score=44.56 Aligned_cols=56 Identities=14% Similarity=0.266 Sum_probs=44.6
Q ss_pred HHHHHHHHcC--CCHHHHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCc
Q 016851 297 PLTSILNKLG--LSQTVLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDL 353 (381)
Q Consensus 297 ~L~~~l~~l~--~~~~~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l 353 (381)
+|..+...++ +++. +...|..+....+...-...|.|..||++|||+|++..+.+.
T Consensus 62 ~i~~~~~~lkp~Lpq~-viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~ 119 (305)
T TIGR00569 62 RLLDFCSAFKPTMPTS-VVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNV 119 (305)
T ss_pred HHHHHHHHhcCCCCch-HHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCc
Confidence 4555566777 7775 667788788777777777889999999999999999987764
No 32
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=88.38 E-value=1.4 Score=38.13 Aligned_cols=69 Identities=14% Similarity=0.107 Sum_probs=52.6
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcc--CCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHHH
Q 016851 179 YCAFIQNLGLRLELPQTTIGTAMVLCHRFFVR--RSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASS 247 (381)
Q Consensus 179 ~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~--~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~~ 247 (381)
+..-|.++|++|+|+.++....-..|+..+.. .-+.+.++.-+.+.|+|.-||+.....+.++|+....
T Consensus 14 a~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr 84 (135)
T PF01857_consen 14 AAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYR 84 (135)
T ss_dssp HHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHT
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHH
Confidence 44557899999999998877777777777654 3356677888999999999999988889999888653
No 33
>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=87.46 E-value=1.6 Score=35.51 Aligned_cols=56 Identities=20% Similarity=0.077 Sum_probs=43.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCC
Q 016851 180 CAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEET 235 (381)
Q Consensus 180 v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~ 235 (381)
.+||....+..+...++...|..+++-.+....+-++.+-.||+||+++|.++.+.
T Consensus 4 ~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~ 59 (118)
T PF02984_consen 4 YDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGK 59 (118)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCc
Confidence 45666665555556778888999998888777788899999999999999998553
No 34
>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=81.99 E-value=15 Score=31.88 Aligned_cols=87 Identities=18% Similarity=0.116 Sum_probs=56.9
Q ss_pred ChHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhc---c-cc-ccCcCHHHHHHHHHHHHHHHcCCCccchhhhhhhcccCH
Q 016851 293 HPYDPLTSILNKLGLSQTVLVNLALNLVSEGLR---S-SL-WLQFKPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQTTP 367 (381)
Q Consensus 293 tP~~~L~~~l~~l~~~~~~i~~lA~~ll~dsl~---t-~~-~L~y~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~~~~ 367 (381)
.-.+|+.++++....+.+ +.-+|..+++.... . .. .-.....-+-++|+.+|.++++-.....+.|-+..|++.
T Consensus 53 ~i~~fl~ri~~~~~~s~~-~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~ 131 (149)
T PF08613_consen 53 SIRDFLSRILKYTQCSPE-CLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISL 131 (149)
T ss_dssp -HHHHHHHHHHHTT--HH-HHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-H
T ss_pred cHHHHHHHHHHHcCCChH-HHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCH
Confidence 456688888887777775 44455555554443 1 12 123567789999999999998765555678999999999
Q ss_pred HHHHHHHHHHHhh
Q 016851 368 AILQDVAQQLMEL 380 (381)
Q Consensus 368 ~~I~e~~~~Ll~L 380 (381)
.+|..+-.+++.+
T Consensus 132 ~eln~lE~~fL~~ 144 (149)
T PF08613_consen 132 KELNELEREFLKL 144 (149)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 9999998888765
No 35
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=77.51 E-value=7.8 Score=38.41 Aligned_cols=59 Identities=17% Similarity=0.180 Sum_probs=43.0
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCcc
Q 016851 295 YDPLTSILNKLGLSQTVLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDLA 354 (381)
Q Consensus 295 ~~~L~~~l~~l~~~~~~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~ 354 (381)
..||..+...|++++.. ...|..+....++-.-.-.|+|..+|++||+||.+..+.+..
T Consensus 43 ~~fI~elg~~L~~~~~t-i~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~k 101 (323)
T KOG0834|consen 43 AKFIQELGVRLKMPQKT-IATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRK 101 (323)
T ss_pred HHHHHHHHHHcCCCccc-hhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCccc
Confidence 35677777888887653 334555555555556667789999999999999999887643
No 36
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=75.94 E-value=17 Score=36.22 Aligned_cols=84 Identities=21% Similarity=0.199 Sum_probs=62.1
Q ss_pred HHHHHHHHHHHHHHHcCcccccC---C------hHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccccccCcC---HHHH
Q 016851 270 YRERVIEAEQMILTTLNFELNVQ---H------PYDPLTSILNKLGLSQTVLVNLALNLVSEGLRSSLWLQFK---PNHI 337 (381)
Q Consensus 270 ~~~~Il~~E~~IL~~L~FdL~v~---t------P~~~L~~~l~~l~~~~~~i~~lA~~ll~dsl~t~~~L~y~---Ps~I 337 (381)
....++..|..-...+++.+.+. + ..+|+.+.++..+.+.. +.-+|.+.++..+...-+-..+ -..|
T Consensus 48 ~i~~ll~kEe~~~p~~~~~~~~~~~~~~~~R~~A~~WIl~V~~~~~~~~~-~~~LA~NYlDRFls~~~l~k~k~W~lQLl 126 (335)
T KOG0656|consen 48 VLANLLEKEEQHNPSLDYFLCVQKLILSSMRKQALDWILKVCEEYNFEPL-VFLLAMNYLDRFLSSQKLPKDKPWMLQLL 126 (335)
T ss_pred HHHHHHHHHHHhCCCCchhhhcccccccHHHHHHHHHHHHHHHHhCCchH-HHHHHHHHHHHhhcccccCCCchHHHHHH
Confidence 34566677777666666444322 3 44678888888888875 7778999999888777777777 5689
Q ss_pred HHHHHHHHHHHcCCCcc
Q 016851 338 AAGAAYLAAKFLNWDLA 354 (381)
Q Consensus 338 AaAaI~lA~~~~~~~l~ 354 (381)
|+||+.+|+++...+.|
T Consensus 127 AvaCLsLAsKmeE~~vP 143 (335)
T KOG0656|consen 127 AVACLSLASKMEETDVP 143 (335)
T ss_pred HHHHHHHHHhhcCcCCc
Confidence 99999999999887654
No 37
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=75.89 E-value=4.3 Score=40.05 Aligned_cols=57 Identities=25% Similarity=0.254 Sum_probs=36.4
Q ss_pred HHHHHHhcCCCHHH--HHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCCh
Q 016851 183 IQNLGLRLELPQTT--IGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPL 239 (381)
Q Consensus 183 I~~v~~~L~L~~~t--~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l 239 (381)
|+.....|++++.- .-.|=+|+.--+-..-+..+.+..||.||++||+..+|.|.+-
T Consensus 145 ii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~ 203 (367)
T KOG0835|consen 145 IIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPF 203 (367)
T ss_pred HHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCC
Confidence 33444455665444 3444444444333344556888999999999999999976553
No 38
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=74.42 E-value=5.8 Score=38.84 Aligned_cols=92 Identities=18% Similarity=0.213 Sum_probs=59.1
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHhc--cCCcCccchhhhhHHHHHHhhhccCC--CCChHHHHHHHHHHHhhhhhh
Q 016851 181 AFIQNLGLRLELPQTTIGTAMVLCHRFFV--RRSHACHDRFIIATAALFLAAKSEET--PRPLNDVLRASSELYHKQNIT 256 (381)
Q Consensus 181 ~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~--~~si~~~~~~lva~acLfLA~K~EE~--p~~l~dii~~~~~~~~k~~~~ 256 (381)
.++...+....|.-+.-...++|++|-.- ...+....+..+....+++|+|+=.. .-.+ | .+++++.
T Consensus 195 k~v~~l~~~~qlta~~aiitL~~~erl~~~~e~~~~p~~w~r~~~g~il~sskv~~dqs~wnv-d----ycqIlKd---- 265 (343)
T KOG1675|consen 195 KFVRILFSWAQLTAECDIITLVYAERLLWLAERDPCPRNWSRAVLGEILLSSKVYDDQSVWNV-D----YCEILKD---- 265 (343)
T ss_pred hhhhhHhhhhhhhhccchHHHHhhHhhhhHhhcCCCcchhhhhhhhhheehhhhhhhhhcccH-H----HHHHHhh----
Confidence 34444444455555555556777777743 34445667777778889999997642 1111 1 2233321
Q ss_pred hhcccCChhHHhHHHHHHHHHHHHHHHHcCcccccCC
Q 016851 257 LLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQH 293 (381)
Q Consensus 257 ~~~~~~~~~~~~~~~~~Il~~E~~IL~~L~FdL~v~t 293 (381)
.+.+++-+||+.+|+.|+|+++++-
T Consensus 266 ------------~tveDmNe~ERqfLelLqfNinvp~ 290 (343)
T KOG1675|consen 266 ------------QSVDDMNALERQFLELLQFNINVPS 290 (343)
T ss_pred ------------ccHhhHHHHHHHHHHHHhhccCccH
Confidence 2478899999999999999998874
No 39
>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=68.75 E-value=11 Score=36.91 Aligned_cols=83 Identities=17% Similarity=0.182 Sum_probs=56.5
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcC--CCccc-----hhhhhhhcccCHH
Q 016851 296 DPLTSILNKLGLSQTVLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLN--WDLAA-----YQNIWHEFQTTPA 368 (381)
Q Consensus 296 ~~L~~~l~~l~~~~~~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~--~~l~~-----~~~w~~~~~~~~~ 368 (381)
.++..++..+.+++. +...|..+....+.-.-.-.+++..||.+||+||++..+ .++.- ...|-+...-+++
T Consensus 50 k~i~~l~~~L~lp~~-~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~sr~ 128 (297)
T COG5333 50 KLIMDLCTRLNLPQT-VLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKSSRE 128 (297)
T ss_pred HHHHHHHHhcCCCcc-hHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccccccHH
Confidence 467777788888886 666777666665555556789999999999999999988 44321 1124444445666
Q ss_pred HHHHHHHHHHh
Q 016851 369 ILQDVAQQLME 379 (381)
Q Consensus 369 ~I~e~~~~Ll~ 379 (381)
.|-++--+|++
T Consensus 129 ~Il~~E~~lLE 139 (297)
T COG5333 129 RILEYEFELLE 139 (297)
T ss_pred HHHHHHHHHHH
Confidence 66666555554
No 40
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=66.83 E-value=12 Score=35.32 Aligned_cols=48 Identities=15% Similarity=0.189 Sum_probs=32.5
Q ss_pred ccCcCHHHHHHHHHHHHHHHcCCCccc--------------hhhhhhhcccCHHHHHHHHHH
Q 016851 329 WLQFKPNHIAAGAAYLAAKFLNWDLAA--------------YQNIWHEFQTTPAILQDVAQQ 376 (381)
Q Consensus 329 ~L~y~Ps~IAaAaI~lA~~~~~~~l~~--------------~~~w~~~~~~~~~~I~e~~~~ 376 (381)
.-.+.|..+|..|||+|++....++.. +.-|.+.+.+....|-||-=.
T Consensus 78 ~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~~e~~~~~~~~I~e~Ef~ 139 (264)
T KOG0794|consen 78 LKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYWPEKFPYERKDILEMEFY 139 (264)
T ss_pred hhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccchhhcCCCcCcchhhhhh
Confidence 557899999999999999998776221 223555566655555554333
No 41
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=63.81 E-value=8.6 Score=40.27 Aligned_cols=54 Identities=20% Similarity=0.199 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCChHHHHHHHH
Q 016851 194 QTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASS 247 (381)
Q Consensus 194 ~~t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~~ 247 (381)
.+|+.+|.-++.|--.---.....+--++.|||+|||.+...++++.+|+.+.+
T Consensus 184 ~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvh 237 (521)
T KOG1598|consen 184 EDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVH 237 (521)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHH
Confidence 447788888887753222223445567889999999999999999999987754
No 42
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=53.62 E-value=51 Score=28.44 Aligned_cols=58 Identities=21% Similarity=0.164 Sum_probs=42.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhc--cccccCcCHHHHHHHHHHHHHHHcCCCc
Q 016851 295 YDPLTSILNKLGLSQTVLVNLALNLVSEGLR--SSLWLQFKPNHIAAGAAYLAAKFLNWDL 353 (381)
Q Consensus 295 ~~~L~~~l~~l~~~~~~i~~lA~~ll~dsl~--t~~~L~y~Ps~IAaAaI~lA~~~~~~~l 353 (381)
..-+..++..++++.+ +...+|.+.+.++. +.++..-.-.+|-++|||..+++.+.++
T Consensus 15 ~~Rl~~LC~~L~l~~~-~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~ 74 (135)
T PF01857_consen 15 AVRLQDLCERLDLSSD-LREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEEL 74 (135)
T ss_dssp HHHHHHHHHHHTTSTT-HHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S-
T ss_pred HHHHHHHHHHcCCcHH-HHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCC
Confidence 3345667777888775 77778888888874 4566666778999999999999988653
No 43
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=44.60 E-value=79 Score=32.11 Aligned_cols=84 Identities=19% Similarity=0.214 Sum_probs=48.6
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHhccccccCcCHHHHHHHHHH-HHHHHcCCCccchhhhhhhcc--cCHHHHHH
Q 016851 296 DPLTSILNKLGLSQTVLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAY-LAAKFLNWDLAAYQNIWHEFQ--TTPAILQD 372 (381)
Q Consensus 296 ~~L~~~l~~l~~~~~~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~-lA~~~~~~~l~~~~~w~~~~~--~~~~~I~e 372 (381)
+|+...-..+++..+ ...+|.++++..+....+-.-.=..++++|++ +|++...+..|...+.--..+ ++.++|..
T Consensus 163 dwlvevh~~F~L~~E-TL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~il~ 241 (391)
T KOG0653|consen 163 DWLVEVHEKFGLSPE-TLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREEILR 241 (391)
T ss_pred HHHHHhhhhcCcCHH-HHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHHHHH
Confidence 344455555666665 55677778755443323222233367778856 999986655554222111122 68888888
Q ss_pred HHHHHHhh
Q 016851 373 VAQQLMEL 380 (381)
Q Consensus 373 ~~~~Ll~L 380 (381)
+-+.|++.
T Consensus 242 mE~~il~~ 249 (391)
T KOG0653|consen 242 MEKYILNV 249 (391)
T ss_pred HHHHHHhc
Confidence 87777653
No 44
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=35.35 E-value=1.2e+02 Score=23.71 Aligned_cols=41 Identities=22% Similarity=0.267 Sum_probs=34.2
Q ss_pred CCccccHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 016851 147 EPVFMSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFF 208 (381)
Q Consensus 147 ~~~yft~~e~~~~sPs~~~~i~~~~e~~~R~~~v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~ 208 (381)
..|||+..++.+ +..+.++...|++..+.+.++..++||.-
T Consensus 33 ~~~~f~~~~l~r---------------------l~~~~rL~~Dl~in~~gi~lil~LLd~i~ 73 (84)
T PF13591_consen 33 EEWYFSEEDLAR---------------------LRRIRRLHRDLGINLEGIALILDLLDRIE 73 (84)
T ss_pred CeeeECHHHHHH---------------------HHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 568999988852 34566889999999999999999999974
No 45
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=33.77 E-value=96 Score=32.19 Aligned_cols=74 Identities=18% Similarity=0.204 Sum_probs=50.7
Q ss_pred cCCCHHHHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCccchhhhhhhcc--cCHHHHHHHHHHHHh
Q 016851 305 LGLSQTVLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQ--TTPAILQDVAQQLME 379 (381)
Q Consensus 305 l~~~~~~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~--~~~~~I~e~~~~Ll~ 379 (381)
+++..+ -.-+|..|++-.+....+..=.-..++++|+++|++...+..|..++.--+++ ++.++|...-+.+++
T Consensus 227 F~llpe-TL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE~~ml~ 302 (440)
T COG5024 227 FGLLPE-TLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERYMLE 302 (440)
T ss_pred ccccch-HHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHHHHHhh
Confidence 344333 34467777777666666666667789999999999999998876444333333 778887777666654
No 46
>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=32.01 E-value=2.6e+02 Score=22.15 Aligned_cols=61 Identities=16% Similarity=0.122 Sum_probs=40.5
Q ss_pred hHHHHHHHHHHcCCCHH---HHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCcc
Q 016851 294 PYDPLTSILNKLGLSQT---VLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDLA 354 (381)
Q Consensus 294 P~~~L~~~l~~l~~~~~---~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l~ 354 (381)
..+|+...+..++++++ ++...+-.-+...+..+.....+|..|.++.+.-....-+-+..
T Consensus 4 ~tdflip~c~alkipe~~wpql~e~~s~tickaliqpniall~p~licaggllttiet~ntn~~ 67 (106)
T PF09241_consen 4 STDFLIPVCHALKIPEDFWPQLFEATSITICKALIQPNIALLPPCLICAGGLLTTIETDNTNCQ 67 (106)
T ss_dssp GGGGHHHHHHHTT--GGGHHHHHHHHHHHHHHHTTSGGGGGS-HHHHHHHHHHHHHHTS-TSSS
T ss_pred hhhhHHHhhhhccCcHHHhHHHHHHHHHHHHHHHcCCCccccCcceeecccceEEEeccCCCCc
Confidence 34678888888888764 34555554555566677777789999999999888877665543
No 47
>COG5552 Uncharacterized conserved protein [Function unknown]
Probab=31.18 E-value=94 Score=24.11 Aligned_cols=46 Identities=15% Similarity=0.189 Sum_probs=34.3
Q ss_pred CHHHHHHHHHHHHHHHcCCCccchhhhhhhcccCHHHHHHHHHHHHh
Q 016851 333 KPNHIAAGAAYLAAKFLNWDLAAYQNIWHEFQTTPAILQDVAQQLME 379 (381)
Q Consensus 333 ~Ps~IAaAaI~lA~~~~~~~l~~~~~w~~~~~~~~~~I~e~~~~Ll~ 379 (381)
+|..|+.||+.+..++.|...|+. .--+.|+.-.++|-.++.+|+|
T Consensus 16 T~~EvrdAAlQfVRKlSGtT~PS~-~n~~AFe~AV~~iaA~areLLD 61 (88)
T COG5552 16 TPVEVRDAALQFVRKLSGTTHPSA-ANAEAFEAAVAEIAATARELLD 61 (88)
T ss_pred CcHHHHHHHHHHHHHhcCCCCcch-hhHHHHHHHHHHHHHHHHHHHH
Confidence 466888999999999988877762 3345566666778888888876
No 48
>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=30.44 E-value=1.2e+02 Score=29.95 Aligned_cols=46 Identities=20% Similarity=0.342 Sum_probs=36.0
Q ss_pred CCHHHHHHHHHHHHHHHhccccccCcCHHHHHHHHHHHHHHHcCCCc
Q 016851 307 LSQTVLVNLALNLVSEGLRSSLWLQFKPNHIAAGAAYLAAKFLNWDL 353 (381)
Q Consensus 307 ~~~~~i~~lA~~ll~dsl~t~~~L~y~Ps~IAaAaI~lA~~~~~~~l 353 (381)
++.. +...|..+....+.....+.|+|.+|-++|+++|++.-+..+
T Consensus 74 lp~~-Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~I 119 (325)
T KOG2496|consen 74 LPTS-VVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYI 119 (325)
T ss_pred CchH-HHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhhee
Confidence 4443 666777777777777777899999999999999999876543
No 49
>PF11671 Apis_Csd: Complementary sex determiner protein; InterPro: IPR021007 Sex determination proteins are found in eukaryotes. Proteins in this family are typically between 168 and 410 amino acids in length. It plays a role in the gender determination of around 20% of all animals. In the honeybee, the mechanism of sex determination depends on the complementary sex determiner (csd) gene which produces an SR-type protein. Males are homozygous while females are homozygous for the csd gene. Heterozygosity generates an active protein which initiates female development []. This entry represents the C-terminal end of the sex determination protein.
Probab=29.09 E-value=32 Score=29.52 Aligned_cols=8 Identities=50% Similarity=0.783 Sum_probs=4.3
Q ss_pred cCCCCccc
Q 016851 65 YDNPSYIT 72 (381)
Q Consensus 65 ~~~~~~~~ 72 (381)
++|..||.
T Consensus 75 yyninyIE 82 (146)
T PF11671_consen 75 YYNINYIE 82 (146)
T ss_pred ccchhcee
Confidence 45555554
No 50
>PF11357 Spy1: Cell cycle regulatory protein; InterPro: IPR020984 Speedy (Spy1) is a cell cycle regulatory protein which activates CDK2, the major kinase that allows progression through G1/S phase and further replication events. Spy1 expression overcomes a p27-induced cell cycle arrest to allow for DNA synthesis, so cell cycle progression occurs due to an interaction between Spy1 and p27 []. Spy1 is also known as Ringo protein A.
Probab=23.60 E-value=4.6e+02 Score=22.62 Aligned_cols=87 Identities=14% Similarity=0.101 Sum_probs=48.5
Q ss_pred HHhcCCCHH-HHHHHHHHHHHHhccCCcCccchhhhhHHHHHHhhhccCCCCCh-HHHHHHHHHHHhhhhhhhhcccCCh
Q 016851 187 GLRLELPQT-TIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPL-NDVLRASSELYHKQNITLLSYLLPI 264 (381)
Q Consensus 187 ~~~L~L~~~-t~~~Ai~~fdRF~~~~si~~~~~~lva~acLfLA~K~EE~p~~l-~dii~~~~~~~~k~~~~~~~~~~~~ 264 (381)
-..+++++. .++..+.||.|--... ..+.. .--..||+||+-+||..... .+|..-..+ +.
T Consensus 22 D~~~~~sDKYLLAmV~~YF~Ragl~~--~~Y~r-i~FFlALYLAndmEED~~~~K~~If~f~~G---~~----------- 84 (131)
T PF11357_consen 22 DKCLRVSDKYLLAMVIAYFSRAGLFS--WQYQR-IHFFLALYLANDMEEDDEEPKYEIFPFLYG---KN----------- 84 (131)
T ss_pred CcchhhhhHHHHHHHHHHHHhcccch--hhcch-HHHHHHHHHhhHHHhccchHHHHHHHHHHC---cc-----------
Confidence 344556655 5678888888753211 11222 22367899999999864432 333333221 10
Q ss_pred hHHhHHHHHHHHHHHHHHHHcCcccccC
Q 016851 265 DWFEQYRERVIEAEQMILTTLNFELNVQ 292 (381)
Q Consensus 265 ~~~~~~~~~Il~~E~~IL~~L~FdL~v~ 292 (381)
-....-....+=..+.+.+||+..|.
T Consensus 85 --w~~~~~~F~klr~~~~~~m~~Ra~Vs 110 (131)
T PF11357_consen 85 --WRSQIPQFHKLRDQFWRRMDWRAWVS 110 (131)
T ss_pred --hHHHhHHHHHHHHHHHHHcCCceeeC
Confidence 00123445566667888899987654
No 51
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=21.26 E-value=3.4e+02 Score=27.30 Aligned_cols=44 Identities=9% Similarity=0.026 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHcCCCccchhhhhhhcc--cCHHHHHHHHHHHHh
Q 016851 336 HIAAGAAYLAAKFLNWDLAAYQNIWHEFQ--TTPAILQDVAQQLME 379 (381)
Q Consensus 336 ~IAaAaI~lA~~~~~~~l~~~~~w~~~~~--~~~~~I~e~~~~Ll~ 379 (381)
.|.++|+++|+++..+=.|.-.++.-.-+ .++++|..+-.-|++
T Consensus 190 LIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddIltmE~iilk 235 (408)
T KOG0655|consen 190 LIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDILTMELIILK 235 (408)
T ss_pred HhhHHHHHHHHHHhhccCccccceeeeccCccchHHHHHHHHHHHH
Confidence 57889999999988775554333333333 577777666555543
No 52
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=21.00 E-value=1.4e+02 Score=33.52 Aligned_cols=68 Identities=16% Similarity=0.152 Sum_probs=51.6
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHhccCC--cCccchhhhhHHHHHHhhhccCCCCChHHHHHHHH
Q 016851 180 CAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRS--HACHDRFIIATAALFLAAKSEETPRPLNDVLRASS 247 (381)
Q Consensus 180 v~~I~~v~~~L~L~~~t~~~Ai~~fdRF~~~~s--i~~~~~~lva~acLfLA~K~EE~p~~l~dii~~~~ 247 (381)
.--|..+|++|.+.+++...-=.+|+.-+.... +.+.++.-+.+.|+|+-+|+.+...+..+|+....
T Consensus 681 avRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR 750 (920)
T KOG1010|consen 681 AVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYR 750 (920)
T ss_pred HHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHh
Confidence 344778999999998777766666666554422 34566667889999999999998899999887654
Done!