Query 011488
Match_columns 484
No_of_seqs 329 out of 1777
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 01:55:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011488.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011488hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0653 Cyclin B and related k 100.0 4.6E-50 9.9E-55 419.7 21.8 286 182-470 92-384 (391)
2 COG5024 Cyclin [Cell division 100.0 1.1E-46 2.4E-51 393.8 17.4 261 201-463 162-424 (440)
3 KOG0654 G2/Mitotic-specific cy 100.0 3.7E-42 8E-47 351.6 11.3 261 203-466 87-351 (359)
4 KOG0655 G1/S-specific cyclin E 100.0 2.1E-38 4.5E-43 315.1 20.7 210 220-438 113-336 (408)
5 KOG0656 G1/S-specific cyclin D 100.0 1.8E-32 4E-37 278.2 19.8 214 218-431 43-268 (335)
6 PF00134 Cyclin_N: Cyclin, N-t 99.9 1.5E-25 3.2E-30 197.1 13.1 126 222-347 1-127 (127)
7 TIGR00569 ccl1 cyclin ccl1. Un 99.9 1.4E-21 3E-26 198.5 19.6 158 249-407 54-222 (305)
8 PF02984 Cyclin_C: Cyclin, C-t 99.9 4.3E-22 9.3E-27 172.1 9.5 118 349-466 1-118 (118)
9 KOG0834 CDK9 kinase-activating 99.8 9.3E-21 2E-25 192.9 14.8 200 241-441 29-249 (323)
10 KOG0835 Cyclin L [General func 99.8 4.4E-18 9.5E-23 170.4 19.0 192 247-439 19-231 (367)
11 KOG0794 CDK8 kinase-activating 99.8 6.8E-18 1.5E-22 162.2 12.4 186 251-438 41-239 (264)
12 COG5333 CCL1 Cdk activating ki 99.7 1.2E-16 2.7E-21 159.7 13.8 164 247-412 41-212 (297)
13 PRK00423 tfb transcription ini 99.6 3E-13 6.5E-18 138.3 23.8 181 252-436 123-303 (310)
14 cd00043 CYCLIN Cyclin box fold 99.5 3.2E-14 6.9E-19 114.9 8.9 87 251-339 2-88 (88)
15 smart00385 CYCLIN domain prese 99.5 1.6E-13 3.4E-18 109.8 8.1 83 256-340 1-83 (83)
16 KOG2496 Cdk activating kinase 99.2 2E-10 4.3E-15 115.0 16.4 147 254-401 59-218 (325)
17 KOG1597 Transcription initiati 99.2 5.5E-10 1.2E-14 111.5 18.0 180 254-438 107-289 (308)
18 COG1405 SUA7 Transcription ini 99.1 1E-08 2.2E-13 103.8 20.7 183 251-437 97-279 (285)
19 smart00385 CYCLIN domain prese 98.8 5.2E-08 1.1E-12 77.6 9.1 81 353-434 1-82 (83)
20 cd00043 CYCLIN Cyclin box fold 98.7 8.4E-08 1.8E-12 77.1 10.0 85 348-433 2-87 (88)
21 PF08613 Cyclin: Cyclin; Inte 98.5 5.6E-07 1.2E-11 82.8 10.5 91 254-346 54-149 (149)
22 KOG4164 Cyclin ik3-1/CABLES [C 97.7 1.8E-05 3.8E-10 82.2 3.3 102 248-350 380-483 (497)
23 KOG1598 Transcription initiati 97.4 0.00076 1.7E-08 72.9 9.9 147 257-407 73-225 (521)
24 PF00382 TFIIB: Transcription 96.7 0.0081 1.8E-07 48.2 7.6 65 258-323 1-65 (71)
25 PF00382 TFIIB: Transcription 95.8 0.08 1.7E-06 42.4 8.7 71 355-426 1-71 (71)
26 KOG1674 Cyclin [General functi 95.2 0.064 1.4E-06 52.7 7.7 94 254-349 78-181 (218)
27 PRK00423 tfb transcription ini 95.1 0.17 3.7E-06 52.2 10.7 147 178-346 162-308 (310)
28 KOG1675 Predicted cyclin [Gene 93.5 0.12 2.7E-06 52.8 5.4 88 263-351 202-291 (343)
29 PF02984 Cyclin_C: Cyclin, C-t 91.4 0.92 2E-05 38.6 7.6 87 255-343 4-90 (118)
30 PF00134 Cyclin_N: Cyclin, N-t 91.0 2.1 4.6E-05 37.0 9.6 82 354-435 37-120 (127)
31 COG1405 SUA7 Transcription ini 88.2 3.4 7.3E-05 42.4 9.8 146 176-343 135-280 (285)
32 KOG0834 CDK9 kinase-activating 83.8 1.3 2.9E-05 46.1 4.4 93 252-344 153-247 (323)
33 PF08613 Cyclin: Cyclin; Inte 77.2 30 0.00065 31.7 10.5 88 348-435 51-143 (149)
34 KOG0835 Cyclin L [General func 67.9 20 0.00043 37.5 7.6 72 261-334 148-221 (367)
35 TIGR00569 ccl1 cyclin ccl1. Un 55.1 67 0.0015 33.3 9.0 40 367-406 77-116 (305)
36 PF01857 RB_B: Retinoblastoma- 51.6 52 0.0011 30.1 6.7 66 256-322 16-83 (135)
37 KOG1597 Transcription initiati 47.2 67 0.0014 33.3 7.2 129 176-323 142-271 (308)
38 KOG1992 Nuclear export recepto 29.7 5.9E+02 0.013 30.3 11.8 61 250-310 378-440 (960)
39 PLN00064 photosystem II protei 23.4 2E+02 0.0043 27.3 5.7 70 216-285 63-136 (166)
40 KOG1943 Beta-tubulin folding c 21.1 1.6E+03 0.035 27.6 14.6 22 368-389 468-489 (1133)
41 KOG0656 G1/S-specific cyclin D 20.9 3.1E+02 0.0066 29.0 7.1 53 368-420 98-154 (335)
No 1
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.6e-50 Score=419.67 Aligned_cols=286 Identities=45% Similarity=0.658 Sum_probs=261.3
Q ss_pred HHHHhhhhhhhcccCCCCCccccCCCcCCCCCccccccHHHHHHHHHHHHhhcCCCCccCcCccccHHHHHHHHHHHHHH
Q 011488 182 SVLTARSKAACGLAQKPKEQIVDIDAKDANNDLAGVEYVEDIYKFYKLVENESRPCSYIHTQTEITERMRAILVDWLIDV 261 (484)
Q Consensus 182 s~l~~rs~~a~~~~~~p~~~i~diD~~d~~n~l~~~eY~~DIy~~l~~~E~e~~~~dyl~~Q~eIt~~mR~~LVdWLieV 261 (484)
+++...+...|+.... .+.|+|..|..|++++.||++|||.||+..|.++.+..|+..|++++++||.++||||++|
T Consensus 92 ~~~~~~~~~~~~~~~~---~~~dl~~~d~~~~~~~~ey~~di~~~l~~~e~~~~p~~~~~~~~e~~~~mR~iLvdwlvev 168 (391)
T KOG0653|consen 92 SVLESTSKLASGLSDL---SILDLDSEDKSDPSMIVEYVQDIFEYLRQLELEFLPLSYDISQSEIRAKMRAILVDWLVEV 168 (391)
T ss_pred ccchhhhhhhcccccc---CccCcchhcccCcHHHHHHHHHHHHHHHHHHHhhCchhhhcccccccHHHHHHHHHHHHHh
Confidence 5555566667777543 4789999999999999999999999999998777888888999999999999999999999
Q ss_pred HHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHH-HHhhhccccCCCHHHHHHHhccCCCHHHHHHHHHHHHH
Q 011488 262 HQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAML-IASKYEEIWAPEVNDLVRIADNAYSHPEVLAMEKTILG 340 (484)
Q Consensus 262 ~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~-IAsK~EE~~~P~l~dlv~isd~~yt~~~Il~mE~~IL~ 340 (484)
|.+|+|.+|||||||+|+||||+...|++.++||+|++||| |||||||.++|.+.||+++++++||+++|++||+.||+
T Consensus 169 h~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~il~mE~~il~ 248 (391)
T KOG0653|consen 169 HEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREEILRMEKYILN 248 (391)
T ss_pred hhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999977 99999999999999999999999999999999999999
Q ss_pred HcCCcccCCCHHHHHHHHHHhcCCCchhHHHHHHHHHHHhccccccCCcHHHHHHHHHHHHHHHhCCCCCChHHHHhhhC
Q 011488 341 KLEWTLTVPTYYVFLVRFIKASIPDQDMENTVYFLAELGMMHYDTLMFSPSMVAASAVYAARCTLNRSPAWTDTLRFHTG 420 (484)
Q Consensus 341 ~L~w~L~~PTp~~FL~~fl~~~~~d~el~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~lA~~~l~~~p~W~~~L~~~tg 420 (484)
.|+|++.+|||+.||++|+++...+.+...++.|++|++++||.++.++||.+|+|++++++.++.....|..++.+|+|
T Consensus 249 ~L~f~l~~p~~~~FLrr~~ka~~~d~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~~~~~~~w~~~~~~~sg 328 (391)
T KOG0653|consen 249 VLEFDLSVPTPLSFLRRFLKAADYDIKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALRMLSKGDVWSPTLEHYSG 328 (391)
T ss_pred ccCeeecCCchHHHHHHHHHhhhcchhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHHhccCCccCCCCeeccC
Confidence 99999999999999999999988888899999999999999999999999999999999999999877679999999999
Q ss_pred CCHHHHHHHHHHHHHHHhhcCcc-chHH-HHHhhCCCCCCcee----ecCCCCCcc
Q 011488 421 FSETQLMDCARLLVYFHSKASEN-RLQV-VHKKYARTQRGSVS----LLPPAKSLL 470 (484)
Q Consensus 421 ys~~eL~~c~~~L~~l~~~a~~s-~l~a-I~kKYS~~~~~~VA----~~pp~~~l~ 470 (484)
|+..++.+|.+.+..++.....+ .+.. +++||+++.++.++ .++.+....
T Consensus 329 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ky~~~~~~~~~~~~~~~~~~~~~~ 384 (391)
T KOG0653|consen 329 YSESYLFECARSLSALSLSSLQNPSLRASVLNKYNSSKFLPASPHVWILEKITSSA 384 (391)
T ss_pred CCcHHHHHHHHHHHHHHHHhcccchhHHHHHHHhcccccchhhhhcceeccccccc
Confidence 99999999999999876665544 4554 99999999999999 455544433
No 2
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=100.00 E-value=1.1e-46 Score=393.78 Aligned_cols=261 Identities=35% Similarity=0.529 Sum_probs=248.5
Q ss_pred ccccCCCcCCCCCccccccHHHHHHHHHHHHhhcCC-CCccCcCccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 011488 201 QIVDIDAKDANNDLAGVEYVEDIYKFYKLVENESRP-CSYIHTQTEITERMRAILVDWLIDVHQEFELSQETLYLTINII 279 (484)
Q Consensus 201 ~i~diD~~d~~n~l~~~eY~~DIy~~l~~~E~e~~~-~dyl~~Q~eIt~~mR~~LVdWLieV~~~f~L~~eTl~LAV~ll 279 (484)
...|+|+.|.++++++.||..|||.|+..+|....+ .+||..|+.+.+.||.+|+|||+++|.+|+|.++|||+||+|+
T Consensus 162 ~~~dld~~~~~d~~mv~Ey~~~Ife~l~k~e~~~lp~~~yl~kq~~~~~~mR~~Lv~wlvevH~~F~llpeTL~lainii 241 (440)
T COG5024 162 SWQDLDATDQEDPLMVPEYASDIFEYLLKLELIDLPNPNYLIKQSLYEWSMRSILVDWLVEVHGKFGLLPETLFLAINII 241 (440)
T ss_pred CccccccccccCccchHHHHHHHHHHHHHHHHHhcCcHHHHhhcchhHHhHHHHHHHHHHHhcccccccchHHHHHHHHH
Confidence 357899999999999999999999999999999888 6899999999999999999999999999999999999999999
Q ss_pred HHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccCCCHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHH
Q 011488 280 DRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNAYSHPEVLAMEKTILGKLEWTLTVPTYYVFLVRFI 359 (484)
Q Consensus 280 DRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~yt~~~Il~mE~~IL~~L~w~L~~PTp~~FL~~fl 359 (484)
||||+...+.-+++||+|++||||||||||++.|.+.+|++++++.|+.++|+++|+.||..|+|++..|+|+.||+++.
T Consensus 242 DrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriS 321 (440)
T COG5024 242 DRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERYMLEVLDFNISWPSPMSFLRRIS 321 (440)
T ss_pred HHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHHHHHhhhcccccCCCChHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCchhHHHHHHHHHHHhccccccCCcHHHHHHHHHHHHHHHhCCCCCChHHHHhhhC-CCHHHHHHHHHHHHHHHh
Q 011488 360 KASIPDQDMENTVYFLAELGMMHYDTLMFSPSMVAASAVYAARCTLNRSPAWTDTLRFHTG-FSETQLMDCARLLVYFHS 438 (484)
Q Consensus 360 ~~~~~d~el~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~lA~~~l~~~p~W~~~L~~~tg-ys~~eL~~c~~~L~~l~~ 438 (484)
++...+.....++.|+++.+++++.|+.++||.+|++|.++++.+++..+ |...|.+++| |+.+++.++...+.+.+.
T Consensus 322 ka~dyd~~srt~~k~~~e~s~~~~~f~~~~~S~~~aaa~~~s~~~~~~~~-w~~~l~~ySg~y~~~~l~~~~~~~~~~l~ 400 (440)
T COG5024 322 KASDYDIFSRTPAKFSSEISPVDYKFIQISPSWCAAAAMYLSRKILSQNQ-WDRTLIHYSGNYTNPDLKPLNESNKENLQ 400 (440)
T ss_pred hhcccchhhhhhHhhhCCchHhhhhhccCCchHHHHHHHHHHHhhhccCC-CCccccccCCCCCchhHHHHHHHHHHHhc
Confidence 99888888899999999999999999999999999999999999999876 9999999999 999999999999998876
Q ss_pred hcCccchHHHHHhhCCCCCCceeec
Q 011488 439 KASENRLQVVHKKYARTQRGSVSLL 463 (484)
Q Consensus 439 ~a~~s~l~aI~kKYS~~~~~~VA~~ 463 (484)
.... ++.++++||+.+.||.++..
T Consensus 401 ~~~~-~~~~i~~Ky~~~~~~~~s~~ 424 (440)
T COG5024 401 NPSV-HHDAIFPKYPSPTFGKASSP 424 (440)
T ss_pred ccch-hhhhhhhccccccccccchH
Confidence 5443 44999999999999998853
No 3
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=3.7e-42 Score=351.57 Aligned_cols=261 Identities=40% Similarity=0.631 Sum_probs=247.9
Q ss_pred ccCCCcCCCCCccccccHHHHHHHHHHHHhh-cCC-CCccCc-CccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 011488 203 VDIDAKDANNDLAGVEYVEDIYKFYKLVENE-SRP-CSYIHT-QTEITERMRAILVDWLIDVHQEFELSQETLYLTINII 279 (484)
Q Consensus 203 ~diD~~d~~n~l~~~eY~~DIy~~l~~~E~e-~~~-~dyl~~-Q~eIt~~mR~~LVdWLieV~~~f~L~~eTl~LAV~ll 279 (484)
.|||. +..++++|..|..+||++.+..|.. .++ .+||.. |.++++.||.++|||++++.+.+.+..+|||++++++
T Consensus 87 ~~~ds-~~~dp~~c~~~~~~I~~~~r~~ei~~~rp~~~~~e~vq~d~t~smrgilvdwlvevsee~r~~~e~l~ls~~~~ 165 (359)
T KOG0654|consen 87 MRIDS-VGEDPQMCLKIAAKIYNTLRVSDIKSERPLPSKFEFVQADITPSMRGILVDWLVEVSEEYRLTFETLYLSVNYR 165 (359)
T ss_pred cchhh-cccchHHHHHHHHHHhhcccccchhhccCcccceeeeecCCCcchhhhhhhhhhHHHHHHHhhhhheeecHHHH
Confidence 45554 5678899999999999999999977 666 689977 9999999999999999999999999999999999999
Q ss_pred HHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccCCCHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHH
Q 011488 280 DRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNAYSHPEVLAMEKTILGKLEWTLTVPTYYVFLVRFI 359 (484)
Q Consensus 280 DRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~yt~~~Il~mE~~IL~~L~w~L~~PTp~~FL~~fl 359 (484)
||||+...+.+.++|++|++|++||+||||+.+|.+.+|++++|+.|+..++..||..||+.|.|.+..||...|+++|+
T Consensus 166 drfl~~~~~~~~k~ql~g~s~m~I~sk~ee~~~~~~~ef~~itd~ty~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~ 245 (359)
T KOG0654|consen 166 DRFLSYKEVNKQKLQLVGISAMLIASKYEEIKEPRVEEFCYITDNTYTYWQVLRMEIDILNALTFELVRPTSKTFLRRFL 245 (359)
T ss_pred HHHhccCccHHHHHHHhCcccceeeccchhhcchHHHHHHhhhhhhhHHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HhcC-CCchhHHHHHHHHHHHhccccccCCcHHHHHHHHHHHHHHHhCCCCCChHHHHhhhCCCHHHHHHHHHHHHHHHh
Q 011488 360 KASI-PDQDMENTVYFLAELGMMHYDTLMFSPSMVAASAVYAARCTLNRSPAWTDTLRFHTGFSETQLMDCARLLVYFHS 438 (484)
Q Consensus 360 ~~~~-~d~el~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~lA~~~l~~~p~W~~~L~~~tgys~~eL~~c~~~L~~l~~ 438 (484)
.... ...+++.++.||+|++++||.|+.|.||.|||||+++|+.+++ ...|++.|+++|||+.++|..|+..|. ++.
T Consensus 246 ~~~~~~~~~~e~~~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~-~~pW~~~L~~~T~y~~edl~~~v~~L~-~~l 323 (359)
T KOG0654|consen 246 RVAQTPELQVEPLANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLD-FHPWNQTLEDYTGYKAEDLKPCVLDLH-LYL 323 (359)
T ss_pred HhhcchhHHHHHHHHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhcc-CCCCchhhHHhhcccHHHHHHHHHHHh-ccc
Confidence 8766 4667899999999999999999999999999999999999999 568999999999999999999999999 899
Q ss_pred hcCccchHHHHHhhCCCCCCceeecCCC
Q 011488 439 KASENRLQVVHKKYARTQRGSVSLLPPA 466 (484)
Q Consensus 439 ~a~~s~l~aI~kKYS~~~~~~VA~~pp~ 466 (484)
.++...+++|+.||+.++|+.||.+|++
T Consensus 324 ~~~~~~l~air~ky~~~k~~~Va~~~~p 351 (359)
T KOG0654|consen 324 NASGTDLPAIREKYKQSKFKEVALLPVP 351 (359)
T ss_pred CCCCCchHHHHHHhhhhhhhhhhccCCC
Confidence 9999999999999999999999999987
No 4
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2.1e-38 Score=315.08 Aligned_cols=210 Identities=27% Similarity=0.522 Sum_probs=186.9
Q ss_pred HHHHHHHHHHHHhhcCC-CCccCcCccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcc-cccccchhHHHH
Q 011488 220 VEDIYKFYKLVENESRP-CSYIHTQTEITERMRAILVDWLIDVHQEFELSQETLYLTINIIDRFLSV-KVVSRRELQLVG 297 (484)
Q Consensus 220 ~~DIy~~l~~~E~e~~~-~dyl~~Q~eIt~~mR~~LVdWLieV~~~f~L~~eTl~LAV~llDRfLs~-~~V~~~~LQLvg 297 (484)
..++|..|...|..+.. ..|+..||++.++||++|+|||+|||+.++|.+||||||+.||||||.. +.|.+.+|||||
T Consensus 113 ~~eVW~lM~kkee~~l~~~~~l~qHpdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIG 192 (408)
T KOG0655|consen 113 SKEVWLLMLKKEERYLRDKHFLEQHPDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIG 192 (408)
T ss_pred HHHHHHHHHccchhhhhhhHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhh
Confidence 47899988888865544 5788999999999999999999999999999999999999999999975 589999999999
Q ss_pred HHHHHHHhhhccccCCCHHHHHHHhccCCCHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHhcCCCc-----------
Q 011488 298 MGAMLIASKYEEIWAPEVNDLVRIADNAYSHPEVLAMEKTILGKLEWTLTVPTYYVFLVRFIKASIPDQ----------- 366 (484)
Q Consensus 298 iaCL~IAsK~EE~~~P~l~dlv~isd~~yt~~~Il~mE~~IL~~L~w~L~~PTp~~FL~~fl~~~~~d~----------- 366 (484)
+||||||+|+||++||.+.+|.+++|++||.++|+.||+.||+.|+|+|+..|...||..|+.......
T Consensus 193 itsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n~~~k~l~Pq~~~ 272 (408)
T KOG0655|consen 193 ITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDILTMELIILKALKWELSPITIISWLNVYLQVDALNDAPKVLLPQYSQ 272 (408)
T ss_pred HHHHHHHHHHhhccCccccceeeeccCccchHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcCCCCceeccccch
Confidence 999999999999999999999999999999999999999999999999999999999999998654321
Q ss_pred -hhHHHHHHHHHHHhccccccCCcHHHHHHHHHHHHHHHhCCCCCChHHHHhhhCCCHHHHHHHHHHHHHHHh
Q 011488 367 -DMENTVYFLAELGMMHYDTLMFSPSMVAASAVYAARCTLNRSPAWTDTLRFHTGFSETQLMDCARLLVYFHS 438 (484)
Q Consensus 367 -el~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~lA~~~l~~~p~W~~~L~~~tgys~~eL~~c~~~L~~l~~ 438 (484)
+..++ ..|++++++|...+.|+.++||||||+.-.. .+...+.+|+.+.+|.+|+++|..|..
T Consensus 273 ~efiqi-aqlLDlc~ldids~~fsYrilaAAal~h~~s--------~e~v~kaSG~~w~~ie~cv~wm~Pf~r 336 (408)
T KOG0655|consen 273 EEFIQI-AQLLDLCILDIDSLEFSYRILAAAALCHFTS--------IEVVKKASGLEWDSIEECVDWMVPFVR 336 (408)
T ss_pred HHHHHH-HHHHHHHHhccccccchHHHHHHHHHHHHhH--------HHHHHHcccccHHHHHHHHHHHHHHHH
Confidence 12223 3478899999999999999999999987532 456788999999999999999998765
No 5
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.8e-32 Score=278.24 Aligned_cols=214 Identities=23% Similarity=0.398 Sum_probs=178.9
Q ss_pred ccHHHHHHHHHHHHhhcCCC-C-ccCcCccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccch---
Q 011488 218 EYVEDIYKFYKLVENESRPC-S-YIHTQTEITERMRAILVDWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRE--- 292 (484)
Q Consensus 218 eY~~DIy~~l~~~E~e~~~~-d-yl~~Q~eIt~~mR~~LVdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~--- 292 (484)
-+.+|++..+.+.|.++.|. + |+..|..+++.||.+.++||.+||.++++.++|++||||||||||+.+.+++.+
T Consensus 43 ~~~e~~i~~ll~kEe~~~p~~~~~~~~~~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~ 122 (335)
T KOG0656|consen 43 LWDERVLANLLEKEEQHNPSLDYFLCVQKLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWM 122 (335)
T ss_pred cccHHHHHHHHHHHHHhCCCCchhhhcccccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHH
Confidence 46677777777888887774 4 567888999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHhhhccccCCCHHHHH-HHhccCCCHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHhcCCCc----h
Q 011488 293 LQLVGMGAMLIASKYEEIWAPEVNDLV-RIADNAYSHPEVLAMEKTILGKLEWTLTVPTYYVFLVRFIKASIPDQ----D 367 (484)
Q Consensus 293 LQLvgiaCL~IAsK~EE~~~P~l~dlv-~isd~~yt~~~Il~mE~~IL~~L~w~L~~PTp~~FL~~fl~~~~~d~----e 367 (484)
+||+|++||+||||+||+..|.+-|+. ..+++.|..+.|.+||+.||++|+|+++.+||++|+.+|+....... .
T Consensus 123 lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~~~ 202 (335)
T KOG0656|consen 123 LQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNKHL 202 (335)
T ss_pred HHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcccchHHH
Confidence 999999999999999999888888875 66799999999999999999999999999999999999998765422 2
Q ss_pred hHHHHHHHHHHHhccccccCCcHHHHHHHHHHHHHHHhCCCC--CChHHHHhhhCCCHHHHHHHHH
Q 011488 368 MENTVYFLAELGMMHYDTLMFSPSMVAASAVYAARCTLNRSP--AWTDTLRFHTGFSETQLMDCAR 431 (484)
Q Consensus 368 l~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~lA~~~l~~~p--~W~~~L~~~tgys~~eL~~c~~ 431 (484)
+...+.-++-.+..|+.|+.|+||+||+|++.++...+.... .....+..+.+++.+.+..|+.
T Consensus 203 ~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 203 FLKHASLFLLSVITDIKFLEYPPSVIAAAAILSVSASVDGLDFREYENNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred HHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence 444555566567799999999999999998877655443321 1124455666777888888877
No 6
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=99.93 E-value=1.5e-25 Score=197.06 Aligned_cols=126 Identities=41% Similarity=0.743 Sum_probs=114.8
Q ss_pred HHHHHHHHHHhhcCC-CCccCcCccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHH
Q 011488 222 DIYKFYKLVENESRP-CSYIHTQTEITERMRAILVDWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGA 300 (484)
Q Consensus 222 DIy~~l~~~E~e~~~-~dyl~~Q~eIt~~mR~~LVdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaC 300 (484)
|||.++...|....+ .+|++.|++++..+|..+++||++++..++++++|+++|+.|||||+....+.+.+++++|++|
T Consensus 1 ~i~~~~~~~e~~~~~~~~~~~~~~~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~c 80 (127)
T PF00134_consen 1 DIFRYLLEKELKYKPNPDYLEQQPEITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALAC 80 (127)
T ss_dssp HHHHHHHHHHHHTTCCTTHGTGTSSHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHH
T ss_pred CHHHHHHHHHHHHCcCccccccChhcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhH
Confidence 899999999977664 7899988899999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhccccCCCHHHHHHHhccCCCHHHHHHHHHHHHHHcCCccc
Q 011488 301 MLIASKYEEIWAPEVNDLVRIADNAYSHPEVLAMEKTILGKLEWTLT 347 (484)
Q Consensus 301 L~IAsK~EE~~~P~l~dlv~isd~~yt~~~Il~mE~~IL~~L~w~L~ 347 (484)
|+||||+||..+|.+.+++.++++.|+.++|.+||+.||+.|+|+++
T Consensus 81 l~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 81 LFLASKMEEDNPPSISDLIRISDNTFTKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp HHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHHHHHHHHHTTT---
T ss_pred HHHhhhhhccccchHHHHHHHHcCCCCHHHHHHHHHHHHHHCCCCcC
Confidence 99999999999999999999999999999999999999999999985
No 7
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.88 E-value=1.4e-21 Score=198.49 Aligned_cols=158 Identities=16% Similarity=0.224 Sum_probs=138.6
Q ss_pred HHHHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccC-
Q 011488 249 RMRAILVDWLIDVHQEFE--LSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNA- 325 (484)
Q Consensus 249 ~mR~~LVdWLieV~~~f~--L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~- 325 (484)
.+|..-.++|.++|.+|+ |+.+|+.+|+.||+||+..+++...+.++|++||||||||+||.. .++.+|+......
T Consensus 54 ~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~-~si~~fv~~~~~~~ 132 (305)
T TIGR00569 54 DLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFN-VSIDQFVGNLKETP 132 (305)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccC-cCHHHHHhhccCCc
Confidence 567788899999999999 999999999999999999999999999999999999999999985 5789998765543
Q ss_pred -CCHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHhcC-------CCchhHHHHHHHHHHHhccccccCCcHHHHHHHH
Q 011488 326 -YSHPEVLAMEKTILGKLEWTLTVPTYYVFLVRFIKASI-------PDQDMENTVYFLAELGMMHYDTLMFSPSMVAASA 397 (484)
Q Consensus 326 -yt~~~Il~mE~~IL~~L~w~L~~PTp~~FL~~fl~~~~-------~d~el~~lA~yL~ELsL~d~~~l~~~PS~IAAAa 397 (484)
+..++|+.||..||+.|+|+|.+++||.||..|+.... ..+.+...++.++..+++..-++.|+||.||+||
T Consensus 133 ~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAA 212 (305)
T TIGR00569 133 LKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAA 212 (305)
T ss_pred hhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHHHHHH
Confidence 36799999999999999999999999999999885321 1235677888888888877778889999999999
Q ss_pred HHHHHHHhCC
Q 011488 398 VYAARCTLNR 407 (484)
Q Consensus 398 l~lA~~~l~~ 407 (484)
|++|...++.
T Consensus 213 I~lA~~~~~~ 222 (305)
T TIGR00569 213 ILHTASRAGL 222 (305)
T ss_pred HHHHHHHhCC
Confidence 9999988764
No 8
>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=99.87 E-value=4.3e-22 Score=172.08 Aligned_cols=118 Identities=40% Similarity=0.705 Sum_probs=105.4
Q ss_pred CCHHHHHHHHHHhcCCCchhHHHHHHHHHHHhccccccCCcHHHHHHHHHHHHHHHhCCCCCChHHHHhhhCCCHHHHHH
Q 011488 349 PTYYVFLVRFIKASIPDQDMENTVYFLAELGMMHYDTLMFSPSMVAASAVYAARCTLNRSPAWTDTLRFHTGFSETQLMD 428 (484)
Q Consensus 349 PTp~~FL~~fl~~~~~d~el~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~lA~~~l~~~p~W~~~L~~~tgys~~eL~~ 428 (484)
|||++||++|++....+.++..+++||+|++++|+.|+.|+||+||+||+++|+.+++..+.|...|..++||+.++|.+
T Consensus 1 PTp~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~ 80 (118)
T PF02984_consen 1 PTPYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKE 80 (118)
T ss_dssp --HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHH
T ss_pred CcHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHH
Confidence 89999999997765556789999999999999999999999999999999999999987679999999999999999999
Q ss_pred HHHHHHHHHhhcCccchHHHHHhhCCCCCCceeecCCC
Q 011488 429 CARLLVYFHSKASENRLQVVHKKYARTQRGSVSLLPPA 466 (484)
Q Consensus 429 c~~~L~~l~~~a~~s~l~aI~kKYS~~~~~~VA~~pp~ 466 (484)
|++.|..++......++.+|++||++.+|+.||.+++|
T Consensus 81 c~~~i~~~~~~~~~~~~~ai~~Kys~~~~~~vs~~~~~ 118 (118)
T PF02984_consen 81 CIELIQELLSKASNSKLQAIRKKYSSQKFSSVSQIPPP 118 (118)
T ss_dssp HHHHHHHHHHHCCGSSCTHHHHHTTSGGGTTGGGSS--
T ss_pred HHHHHHHHHHhcCCccchHHHHHhCccccCCccCCCCC
Confidence 99999999988778889999999999999999999875
No 9
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.85 E-value=9.3e-21 Score=192.87 Aligned_cols=200 Identities=17% Similarity=0.270 Sum_probs=170.9
Q ss_pred CcCccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHH
Q 011488 241 HTQTEITERMRAILVDWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVR 320 (484)
Q Consensus 241 ~~Q~eIt~~mR~~LVdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~ 320 (484)
....+--...|.....||.+++.+++++..|+.+|+.||+||+..+++.......+|++|||||+|.||. +..++|++.
T Consensus 29 g~~~~~E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEet-p~kl~dIi~ 107 (323)
T KOG0834|consen 29 GIDLKKELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEET-PRKLEDIIK 107 (323)
T ss_pred CCchhHHHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccC-cccHHHHHH
Confidence 3333444567999999999999999999999999999999999999999999999999999999999997 678999987
Q ss_pred HhccCCC-------------HHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHhcCCCc----hhHHHHHHHHHHHhccc
Q 011488 321 IADNAYS-------------HPEVLAMEKTILGKLEWTLTVPTYYVFLVRFIKASIPDQ----DMENTVYFLAELGMMHY 383 (484)
Q Consensus 321 isd~~yt-------------~~~Il~mE~~IL~~L~w~L~~PTp~~FL~~fl~~~~~d~----el~~lA~yL~ELsL~d~ 383 (484)
.+...+. ++.|+..|+.||++|+|++++-+||.||..|++....+. .+..+|+.++..++...
T Consensus 108 ~s~~~~~~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~ 187 (323)
T KOG0834|consen 108 VSYRYLNPKDLELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTT 187 (323)
T ss_pred HHHHHcCcccccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheee
Confidence 7654444 468999999999999999999999999999999876644 48899999999999988
Q ss_pred cccCCcHHHHHHHHHHHHHHHhCC-CCCChHH-HHhhhC--CCHHHHHHHHHHHHHHHhhcC
Q 011488 384 DTLMFSPSMVAASAVYAARCTLNR-SPAWTDT-LRFHTG--FSETQLMDCARLLVYFHSKAS 441 (484)
Q Consensus 384 ~~l~~~PS~IAAAal~lA~~~l~~-~p~W~~~-L~~~tg--ys~~eL~~c~~~L~~l~~~a~ 441 (484)
-+++|+|..||+|||++|....+. .+.|.+. +...++ ++.++|.+++..++.++....
T Consensus 188 ~cL~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y~~~~ 249 (323)
T KOG0834|consen 188 LCLQYSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHEFLDLYEQTP 249 (323)
T ss_pred eeEeecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHHHHHHHhhcc
Confidence 889999999999999999987764 2334333 445556 899999999999999886543
No 10
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.79 E-value=4.4e-18 Score=170.42 Aligned_cols=192 Identities=16% Similarity=0.237 Sum_probs=164.1
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhcc--
Q 011488 247 TERMRAILVDWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADN-- 324 (484)
Q Consensus 247 t~~mR~~LVdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~-- 324 (484)
....|..-++||.+.+.-++|+..+.+.+..||-||+...++-+.++..++++|++||||+||. |-.+.|.+.+..+
T Consensus 19 e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~-Prr~rdVinVFh~L~ 97 (367)
T KOG0835|consen 19 EEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEE-PRRIRDVINVFHYLE 97 (367)
T ss_pred HHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccc-cccHhHHHHHHHHHH
Confidence 4567888899999999999999999999999999999999999999999999999999999996 5567776554321
Q ss_pred ------C-----------CCHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHhcCC--CchhHHHHHHHHHHHhccccc
Q 011488 325 ------A-----------YSHPEVLAMEKTILGKLEWTLTVPTYYVFLVRFIKASIP--DQDMENTVYFLAELGMMHYDT 385 (484)
Q Consensus 325 ------~-----------yt~~~Il~mE~~IL~~L~w~L~~PTp~~FL~~fl~~~~~--d~el~~lA~yL~ELsL~d~~~ 385 (484)
. -.+.+++++|..||+.|+|++++-+|+-++..|+..+.. ..++.+.+|.|+.+++...-|
T Consensus 98 ~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~ 177 (367)
T KOG0835|consen 98 QRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVF 177 (367)
T ss_pred HHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCchhHHHHHHHhhhhcccccee
Confidence 0 124578999999999999999999999999999998765 335789999999999999999
Q ss_pred cCCcHHHHHHHHHHHHHHHhCCCCCChHHHHhhhCCCHHHHHHHHHHHHHHHhh
Q 011488 386 LMFSPSMVAASAVYAARCTLNRSPAWTDTLRFHTGFSETQLMDCARLLVYFHSK 439 (484)
Q Consensus 386 l~~~PS~IAAAal~lA~~~l~~~p~W~~~L~~~tgys~~eL~~c~~~L~~l~~~ 439 (484)
+.|+|+.|||||||||...++..-...+.+..+++.++.+|.+.+..++.+|..
T Consensus 178 vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~~l~~lY~~ 231 (367)
T KOG0835|consen 178 VRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICYRLIPLYKR 231 (367)
T ss_pred eecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHHHHHHHHHh
Confidence 999999999999999999988211122234467799999999998888888887
No 11
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.75 E-value=6.8e-18 Score=162.18 Aligned_cols=186 Identities=19% Similarity=0.227 Sum_probs=155.4
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHh--------
Q 011488 251 RAILVDWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIA-------- 322 (484)
Q Consensus 251 R~~LVdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~is-------- 322 (484)
+--.-+.|..++++++|...++.+|+.||-||+.+.++..-++.|++.||++||||.||--...++-++...
T Consensus 41 ~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~ 120 (264)
T KOG0794|consen 41 KIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFS 120 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcc
Confidence 334457788899999999999999999999999999999999999999999999999997422233332211
Q ss_pred ----ccCCCHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHhcCC-CchhHHHHHHHHHHHhccccccCCcHHHHHHHH
Q 011488 323 ----DNAYSHPEVLAMEKTILGKLEWTLTVPTYYVFLVRFIKASIP-DQDMENTVYFLAELGMMHYDTLMFSPSMVAASA 397 (484)
Q Consensus 323 ----d~~yt~~~Il~mE~~IL~~L~w~L~~PTp~~FL~~fl~~~~~-d~el~~lA~yL~ELsL~d~~~l~~~PS~IAAAa 397 (484)
...|...+|++||..+|+.|++.|-+-+||.-|..|+..++. |+++.++++.+...++...-.+.|+|..||.||
T Consensus 121 ~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAc 200 (264)
T KOG0794|consen 121 YWPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALAC 200 (264)
T ss_pred cchhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHH
Confidence 234678899999999999999999999999999999988776 777999999999999987788899999999999
Q ss_pred HHHHHHHhCCCCCChHHHHhhhCCCHHHHHHHHHHHHHHHh
Q 011488 398 VYAARCTLNRSPAWTDTLRFHTGFSETQLMDCARLLVYFHS 438 (484)
Q Consensus 398 l~lA~~~l~~~p~W~~~L~~~tgys~~eL~~c~~~L~~l~~ 438 (484)
|+.|.+..++.- ...+..-...+.+.+.+|++.+++++.
T Consensus 201 l~Ia~~~~~k~~--~~~w~~el~vD~ekV~~~v~~I~~lYe 239 (264)
T KOG0794|consen 201 LYIACVIDEKDI--PKAWFAELSVDMEKVKDIVQEILKLYE 239 (264)
T ss_pred HHHHHhhcCCCh--HHHHHHHHhccHHHHHHHHHHHHHHHH
Confidence 999998877642 133334446799999999999998765
No 12
>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=99.70 E-value=1.2e-16 Score=159.74 Aligned_cols=164 Identities=20% Similarity=0.244 Sum_probs=139.8
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhc---
Q 011488 247 TERMRAILVDWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIAD--- 323 (484)
Q Consensus 247 t~~mR~~LVdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd--- 323 (484)
....|..-..|+..+|.+++|+..++.+||.+|+||+.+.++....++-++.||++||||.||. +-.+.-.....+
T Consensus 41 e~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~-~~~I~i~~~~~~~~~ 119 (297)
T COG5333 41 ELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDT-PRDISIESFEARDLW 119 (297)
T ss_pred hhhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccc-cchhhHHHHHhhccc
Confidence 3456777779999999999999999999999999999999999999999999999999999995 222222222222
Q ss_pred ---cCCCHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHhcCCCc--hhHHHHHHHHHHHhccccccCCcHHHHHHHHH
Q 011488 324 ---NAYSHPEVLAMEKTILGKLEWTLTVPTYYVFLVRFIKASIPDQ--DMENTVYFLAELGMMHYDTLMFSPSMVAASAV 398 (484)
Q Consensus 324 ---~~yt~~~Il~mE~~IL~~L~w~L~~PTp~~FL~~fl~~~~~d~--el~~lA~yL~ELsL~d~~~l~~~PS~IAAAal 398 (484)
..-+++.|+.+|..||+.|+|++.+++||..+..|++...... ++.+++|-++..++...-++.|+|+.||+||+
T Consensus 120 se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypphiIA~a~l 199 (297)
T COG5333 120 SEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAAL 199 (297)
T ss_pred cccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecChHHHHHHHH
Confidence 2236889999999999999999999999999999998765533 58999999999999999999999999999999
Q ss_pred HHHHHHhCCCCCCh
Q 011488 399 YAARCTLNRSPAWT 412 (484)
Q Consensus 399 ~lA~~~l~~~p~W~ 412 (484)
+.|.+.++. +.|.
T Consensus 200 ~ia~~~~~~-~~~~ 212 (297)
T COG5333 200 LIACEVLGM-PIIK 212 (297)
T ss_pred HHHHHhcCC-ccch
Confidence 999988764 4554
No 13
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.59 E-value=3e-13 Score=138.30 Aligned_cols=181 Identities=14% Similarity=0.109 Sum_probs=159.4
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccCCCHHHH
Q 011488 252 AILVDWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNAYSHPEV 331 (484)
Q Consensus 252 ~~LVdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~yt~~~I 331 (484)
.....-|.+++..++|+..+.-.|..||.+++....+.......++++|||||||.|+ .|.+++|+..+++ .+..+|
T Consensus 123 ~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~-~prtl~eI~~~~~--v~~k~i 199 (310)
T PRK00423 123 AFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCK-VPRTLDEIAEVSR--VSRKEI 199 (310)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcC-CCcCHHHHHHHhC--CCHHHH
Confidence 4455778999999999999999999999999999888889999999999999999766 4789999998875 689999
Q ss_pred HHHHHHHHHHcCCcccCCCHHHHHHHHHHhcCCCchhHHHHHHHHHHHhccccccCCcHHHHHHHHHHHHHHHhCCCCCC
Q 011488 332 LAMEKTILGKLEWTLTVPTYYVFLVRFIKASIPDQDMENTVYFLAELGMMHYDTLMFSPSMVAASAVYAARCTLNRSPAW 411 (484)
Q Consensus 332 l~mE~~IL~~L~w~L~~PTp~~FL~~fl~~~~~d~el~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~lA~~~l~~~p~W 411 (484)
.+.++.|++.|++++...+|.+|+.+|...+..+.++...|.+++..+.-..-....+|..|||||||+|....+. +.-
T Consensus 200 ~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~-~~t 278 (310)
T PRK00423 200 GRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGE-RRT 278 (310)
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCC-CCC
Confidence 9999999999999999999999999999998888889999999998776543345799999999999999887764 344
Q ss_pred hHHHHhhhCCCHHHHHHHHHHHHHH
Q 011488 412 TDTLRFHTGFSETQLMDCARLLVYF 436 (484)
Q Consensus 412 ~~~L~~~tgys~~eL~~c~~~L~~l 436 (484)
...+...+|+++..|...++.|...
T Consensus 279 ~keIa~v~~Vs~~tI~~~ykel~~~ 303 (310)
T PRK00423 279 QREVAEVAGVTEVTVRNRYKELAEK 303 (310)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 5677888999999999999999874
No 14
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=99.53 E-value=3.2e-14 Score=114.90 Aligned_cols=87 Identities=41% Similarity=0.575 Sum_probs=81.7
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccCCCHHH
Q 011488 251 RAILVDWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNAYSHPE 330 (484)
Q Consensus 251 R~~LVdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~yt~~~ 330 (484)
|...++||.+++..++++++|+++|++|+|||+....+.+.+++++|++||+||+|++|. ++..+++..+++.. +.++
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~-~~~~~~~~~~~~~~-~~~~ 79 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEI-PPWLKDLVHVTGYA-TEEE 79 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCC-CCCHHHHhHHhCCC-CHHH
Confidence 678999999999999999999999999999999999999999999999999999999999 88999999888654 9999
Q ss_pred HHHHHHHHH
Q 011488 331 VLAMEKTIL 339 (484)
Q Consensus 331 Il~mE~~IL 339 (484)
|..||+.||
T Consensus 80 i~~~e~~il 88 (88)
T cd00043 80 ILRMEKLLL 88 (88)
T ss_pred HHHHHHHhC
Confidence 999999875
No 15
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=99.47 E-value=1.6e-13 Score=109.83 Aligned_cols=83 Identities=36% Similarity=0.528 Sum_probs=76.5
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccCCCHHHHHHHH
Q 011488 256 DWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNAYSHPEVLAME 335 (484)
Q Consensus 256 dWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~yt~~~Il~mE 335 (484)
+||.+++..++++++|.++|++|+|||+....+.+..++++|++||+||+|++|.. +...++..+++. |+.++|.+||
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~-~~~~~~~~~~~~-~~~~~i~~~~ 78 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIP-PWTKELVHYTGY-FTEEEILRME 78 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCC-CCchhHhHhhCC-CCHHHHHHHH
Confidence 59999999999999999999999999999877878999999999999999999985 577888888776 8999999999
Q ss_pred HHHHH
Q 011488 336 KTILG 340 (484)
Q Consensus 336 ~~IL~ 340 (484)
+.||.
T Consensus 79 ~~il~ 83 (83)
T smart00385 79 KLLLE 83 (83)
T ss_pred HHHhC
Confidence 99974
No 16
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=99.25 E-value=2e-10 Score=115.00 Aligned_cols=147 Identities=21% Similarity=0.314 Sum_probs=114.4
Q ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhc--cCCCHH
Q 011488 254 LVDWLIDVHQEF--ELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIAD--NAYSHP 329 (484)
Q Consensus 254 LVdWLieV~~~f--~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd--~~yt~~ 329 (484)
...-+++.+.+| .|..+++.+|+.+|-||+...+|..-....|..||+|+|||+||.++ ++.+|+.-.. ..-+.+
T Consensus 59 ~E~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~I-SieqFvkn~~~~~~k~~e 137 (325)
T KOG2496|consen 59 EELSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYI-SIEQFVKNMNGRKWKTHE 137 (325)
T ss_pred HHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhhee-cHHHHHhhccCcccccHH
Confidence 334455555555 47899999999999999999999999999999999999999999865 8999986544 235788
Q ss_pred HHHHHHHHHHHHcCCcccCCCHHHHHHHHHHhcCC------Cchh---HHHHHHHHHHHhccccccCCcHHHHHHHHHHH
Q 011488 330 EVLAMEKTILGKLEWTLTVPTYYVFLVRFIKASIP------DQDM---ENTVYFLAELGMMHYDTLMFSPSMVAASAVYA 400 (484)
Q Consensus 330 ~Il~mE~~IL~~L~w~L~~PTp~~FL~~fl~~~~~------d~el---~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~l 400 (484)
.|+..|..+|+.|+|+|.+-+||.-|+-|+..... +.++ .....-++.-+++...++-|+||.||+|||..
T Consensus 138 ~vLk~E~~llqsL~f~L~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~ 217 (325)
T KOG2496|consen 138 IVLKYEFLLLQSLKFSLTVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILH 217 (325)
T ss_pred HHHhchHHHHHhhhhhheecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHH
Confidence 99999999999999999999999988888753221 2211 11123344555665667789999999999955
Q ss_pred H
Q 011488 401 A 401 (484)
Q Consensus 401 A 401 (484)
|
T Consensus 218 a 218 (325)
T KOG2496|consen 218 A 218 (325)
T ss_pred H
Confidence 4
No 17
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.22 E-value=5.5e-10 Score=111.50 Aligned_cols=180 Identities=16% Similarity=0.131 Sum_probs=155.4
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccCCCHHHHHH
Q 011488 254 LVDWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNAYSHPEVLA 333 (484)
Q Consensus 254 LVdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~yt~~~Il~ 333 (484)
-+.-|..+++..+|.....-.|-.+|-++...+....++.+-++++||+|||+-|+ .|.++++++.+++ .+.+||-+
T Consensus 107 a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~-~pRT~kEI~~~an--v~kKEIgr 183 (308)
T KOG1597|consen 107 AFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQED-VPRTFKEISAVAN--VSKKEIGR 183 (308)
T ss_pred HHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcC-CCchHHHHHHHHc--CCHHHHHH
Confidence 34557888999999999999999999999988889999999999999999999555 5889999998887 89999999
Q ss_pred HHHHHHHHcCCcccCCC--HHHHHHHHHHhcCCCchhHHHHHHHHHHHhcccccc-CCcHHHHHHHHHHHHHHHhCCCCC
Q 011488 334 MEKTILGKLEWTLTVPT--YYVFLVRFIKASIPDQDMENTVYFLAELGMMHYDTL-MFSPSMVAASAVYAARCTLNRSPA 410 (484)
Q Consensus 334 mE~~IL~~L~w~L~~PT--p~~FL~~fl~~~~~d~el~~lA~yL~ELsL~d~~~l-~~~PS~IAAAal~lA~~~l~~~p~ 410 (484)
.=+.|+..|+-++...+ ..+|+.||+..+..+.++...|.++.+.+-- ..+. .-.|-.||||+||++..... .+.
T Consensus 184 ~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~-~~~~~gRsPiSIAAa~IYmisqls~-~kk 261 (308)
T KOG1597|consen 184 CVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEE-MDIRAGRSPISIAAAAIYMISQLSD-EKK 261 (308)
T ss_pred HHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHH-hccccCCCchhHHHHHHHHHHHhcc-Ccc
Confidence 99999999987766555 8999999999988899999999999987653 3333 48899999999999987765 445
Q ss_pred ChHHHHhhhCCCHHHHHHHHHHHHHHHh
Q 011488 411 WTDTLRFHTGFSETQLMDCARLLVYFHS 438 (484)
Q Consensus 411 W~~~L~~~tgys~~eL~~c~~~L~~l~~ 438 (484)
-...+...+|+.+..|+..++.|+.+..
T Consensus 262 t~keI~~vtgVaE~TIr~sYK~Lyp~~~ 289 (308)
T KOG1597|consen 262 TQKEIGEVTGVAEVTIRNSYKDLYPHAD 289 (308)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHhhchh
Confidence 5678889999999999999999997643
No 18
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.10 E-value=1e-08 Score=103.76 Aligned_cols=183 Identities=13% Similarity=0.118 Sum_probs=162.4
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccCCCHHH
Q 011488 251 RAILVDWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNAYSHPE 330 (484)
Q Consensus 251 R~~LVdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~yt~~~ 330 (484)
-......|-.++..++|+..+.-.|..|+-..+....+.....+-+.++|+++||+.+.. |.++.++..+.. .+..+
T Consensus 97 l~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~-prtl~eIa~a~~--V~~ke 173 (285)
T COG1405 97 LITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGV-PRTLDEIAKALG--VSKKE 173 (285)
T ss_pred HHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCC-CccHHHHHHHHC--CCHHH
Confidence 345678888899999999999999999999999999999999999999999999998775 778899988877 77899
Q ss_pred HHHHHHHHHHHcCCcccCCCHHHHHHHHHHhcCCCchhHHHHHHHHHHHhccccccCCcHHHHHHHHHHHHHHHhCCCCC
Q 011488 331 VLAMEKTILGKLEWTLTVPTYYVFLVRFIKASIPDQDMENTVYFLAELGMMHYDTLMFSPSMVAASAVYAARCTLNRSPA 410 (484)
Q Consensus 331 Il~mE~~IL~~L~w~L~~PTp~~FL~~fl~~~~~d~el~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~lA~~~l~~~p~ 410 (484)
|.++.+.+...|+=.+....|.+|+.+|...+..+.++...|..|+..+.-.-....-.|+-||+||||+|....+. +.
T Consensus 174 i~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~-~~ 252 (285)
T COG1405 174 IGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGE-RR 252 (285)
T ss_pred HHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCC-ch
Confidence 99999999999999999999999999999999999999999999999887766667899999999999999988773 34
Q ss_pred ChHHHHhhhCCCHHHHHHHHHHHHHHH
Q 011488 411 WTDTLRFHTGFSETQLMDCARLLVYFH 437 (484)
Q Consensus 411 W~~~L~~~tgys~~eL~~c~~~L~~l~ 437 (484)
-......++|.++..|++-++.|.+..
T Consensus 253 tq~eva~v~~vtevTIrnrykel~~~~ 279 (285)
T COG1405 253 TQKEVAKVAGVTEVTIRNRYKELADAL 279 (285)
T ss_pred HHHHHHHHhCCeeeHHHHHHHHHHHhh
Confidence 455678899999999999998887643
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=98.76 E-value=5.2e-08 Score=77.64 Aligned_cols=81 Identities=33% Similarity=0.459 Sum_probs=73.9
Q ss_pred HHHHHHHHhcCCCchhHHHHHHHHHHHhccccccCCcHHHHHHHHHHHHHHHhCCCCCChHHHHhhhCC-CHHHHHHHHH
Q 011488 353 VFLVRFIKASIPDQDMENTVYFLAELGMMHYDTLMFSPSMVAASAVYAARCTLNRSPAWTDTLRFHTGF-SETQLMDCAR 431 (484)
Q Consensus 353 ~FL~~fl~~~~~d~el~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~lA~~~l~~~p~W~~~L~~~tgy-s~~eL~~c~~ 431 (484)
+|+.++......+.++..+|.++++..+.++.++.++|+.||+||+++|.+..+.. .|...+..++|+ +.++|.++.+
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~-~~~~~~~~~~~~~~~~~i~~~~~ 79 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIP-PWTKELVHYTGYFTEEEILRMEK 79 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCC-CCchhHhHhhCCCCHHHHHHHHH
Confidence 47888988888888999999999999999889999999999999999999988865 699999999999 9999999988
Q ss_pred HHH
Q 011488 432 LLV 434 (484)
Q Consensus 432 ~L~ 434 (484)
.|+
T Consensus 80 ~il 82 (83)
T smart00385 80 LLL 82 (83)
T ss_pred HHh
Confidence 775
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=98.74 E-value=8.4e-08 Score=77.15 Aligned_cols=85 Identities=32% Similarity=0.405 Sum_probs=78.6
Q ss_pred CCCHHHHHHHHHHhcCCCchhHHHHHHHHHHHhccccccCCcHHHHHHHHHHHHHHHhCCCCCChHHHHhhhCC-CHHHH
Q 011488 348 VPTYYVFLVRFIKASIPDQDMENTVYFLAELGMMHYDTLMFSPSMVAASAVYAARCTLNRSPAWTDTLRFHTGF-SETQL 426 (484)
Q Consensus 348 ~PTp~~FL~~fl~~~~~d~el~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~lA~~~l~~~p~W~~~L~~~tgy-s~~eL 426 (484)
.+++++|+.++......+.++..+|.++++..+....+..+.|+.||+||+++|.+..+. +.|...+..++++ +.++|
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~-~~~~~~~~~~~~~~~~~~i 80 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEI-PPWLKDLVHVTGYATEEEI 80 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCC-CCCHHHHhHHhCCCCHHHH
Confidence 588999999999998888899999999999999988888999999999999999998877 8999999999999 99999
Q ss_pred HHHHHHH
Q 011488 427 MDCARLL 433 (484)
Q Consensus 427 ~~c~~~L 433 (484)
..+...|
T Consensus 81 ~~~e~~i 87 (88)
T cd00043 81 LRMEKLL 87 (88)
T ss_pred HHHHHHh
Confidence 9887765
No 21
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=98.54 E-value=5.6e-07 Score=82.83 Aligned_cols=91 Identities=20% Similarity=0.291 Sum_probs=72.5
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHhhc---cc--ccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccCCCH
Q 011488 254 LVDWLIDVHQEFELSQETLYLTINIIDRFLS---VK--VVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNAYSH 328 (484)
Q Consensus 254 LVdWLieV~~~f~L~~eTl~LAV~llDRfLs---~~--~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~yt~ 328 (484)
+.+|+.++....+++++++-+|..|+||+.. .. .+...+.+-+-++||.||+|+-+.....-+.+..+++ ++.
T Consensus 54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~g--is~ 131 (149)
T PF08613_consen 54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGG--ISL 131 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHT--S-H
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcC--CCH
Confidence 8899999999999999999999999999998 22 4666778889999999999997776667888888875 799
Q ss_pred HHHHHHHHHHHHHcCCcc
Q 011488 329 PEVLAMEKTILGKLEWTL 346 (484)
Q Consensus 329 ~~Il~mE~~IL~~L~w~L 346 (484)
+++..||+..|..|+|+|
T Consensus 132 ~eln~lE~~fL~~l~~~L 149 (149)
T PF08613_consen 132 KELNELEREFLKLLDYNL 149 (149)
T ss_dssp HHHHHHHHHHHHHTTT--
T ss_pred HHHHHHHHHHHHHCCCcC
Confidence 999999999999999986
No 22
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=97.75 E-value=1.8e-05 Score=82.18 Aligned_cols=102 Identities=17% Similarity=0.332 Sum_probs=88.9
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhc--cC
Q 011488 248 ERMRAILVDWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIAD--NA 325 (484)
Q Consensus 248 ~~mR~~LVdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd--~~ 325 (484)
.++| .|-.-|.++....++..-|+..|..||.....+..+.+.+-.|+|-+||++|+|+-+..--.++.++.-.. ..
T Consensus 380 SKir-SlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR 458 (497)
T KOG4164|consen 380 SKIR-SLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFR 458 (497)
T ss_pred HHHH-HHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhc
Confidence 3555 45677889999999999999999999999999999999999999999999999999887777888876544 35
Q ss_pred CCHHHHHHHHHHHHHHcCCcccCCC
Q 011488 326 YSHPEVLAMEKTILGKLEWTLTVPT 350 (484)
Q Consensus 326 yt~~~Il~mE~~IL~~L~w~L~~PT 350 (484)
+++.|++..|.-||-.|+|.|+.|-
T Consensus 459 ~nrrdLia~Ef~VlvaLefaL~~~~ 483 (497)
T KOG4164|consen 459 LNRRDLIAFEFPVLVALEFALHLPE 483 (497)
T ss_pred ccHHhhhhhhhhHHHhhhhhccCCh
Confidence 6899999999999999999998653
No 23
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=97.40 E-value=0.00076 Score=72.91 Aligned_cols=147 Identities=13% Similarity=0.065 Sum_probs=117.3
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccCCCHHHHHHHHH
Q 011488 257 WLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNAYSHPEVLAMEK 336 (484)
Q Consensus 257 WLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~yt~~~Il~mE~ 336 (484)
-|-+++..++|.. .+-.|.++|--.++.+-......++|-.+||||.|..|-+.. .+-||..+.. .+.-++-.+=+
T Consensus 73 ~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~h-lliDfS~~Lq--v~Vy~LG~~~l 148 (521)
T KOG1598|consen 73 LIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDH-LLIDFSSYLQ--VSVYDLGSNFL 148 (521)
T ss_pred HHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCce-EEEEeccceE--EehhhhhHHHH
Confidence 6888999999999 999999999999999889999999999999999999776532 2334443332 45566666777
Q ss_pred HHHHHcCCc---ccCCCHHHHHHHHHHhcCC---CchhHHHHHHHHHHHhccccccCCcHHHHHHHHHHHHHHHhCC
Q 011488 337 TILGKLEWT---LTVPTYYVFLVRFIKASIP---DQDMENTVYFLAELGMMHYDTLMFSPSMVAASAVYAARCTLNR 407 (484)
Q Consensus 337 ~IL~~L~w~---L~~PTp~~FL~~fl~~~~~---d~el~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~lA~~~l~~ 407 (484)
.+-..|.-+ +-...|.-|+.+|...+.. +.++...+.+|+.-...|.-...-+|+-|+-|||++|.++.+.
T Consensus 149 ~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~ 225 (521)
T KOG1598|consen 149 EVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGF 225 (521)
T ss_pred HHHHHhccccccccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCc
Confidence 777788776 6667788888888875432 4567888899988887887778899999999999999887753
No 24
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=96.69 E-value=0.0081 Score=48.17 Aligned_cols=65 Identities=8% Similarity=0.193 Sum_probs=53.6
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhc
Q 011488 258 LIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIAD 323 (484)
Q Consensus 258 LieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd 323 (484)
|-.+|..++|+.++.-.|..++++.....-+......-++++|+++||+.+.. +.++.|+...++
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~-~~t~~eIa~~~~ 65 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGV-PRTLKEIAEAAG 65 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTS-SSSHHHHHHHCT
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCC-CcCHHHHHHHhC
Confidence 45789999999999999999999998888888888999999999999997654 668888877655
No 25
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=95.77 E-value=0.08 Score=42.39 Aligned_cols=71 Identities=17% Similarity=0.071 Sum_probs=50.7
Q ss_pred HHHHHHhcCCCchhHHHHHHHHHHHhccccccCCcHHHHHHHHHHHHHHHhCCCCCChHHHHhhhCCCHHHH
Q 011488 355 LVRFIKASIPDQDMENTVYFLAELGMMHYDTLMFSPSMVAASAVYAARCTLNRSPAWTDTLRFHTGFSETQL 426 (484)
Q Consensus 355 L~~fl~~~~~d~el~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~lA~~~l~~~p~W~~~L~~~tgys~~eL 426 (484)
+.+|...+..+..+...|..+...+.-..-.-.-+|..||+||||+|.+..+. +.-...+...+|+++.+|
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~-~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGV-PRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTS-SSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCC-CcCHHHHHHHhCCCCCcC
Confidence 45677777777788999999988776544445688999999999999877653 444566777777777654
No 26
>KOG1674 consensus Cyclin [General function prediction only]
Probab=95.21 E-value=0.064 Score=52.72 Aligned_cols=94 Identities=15% Similarity=0.235 Sum_probs=71.8
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccc---------cccch-hHHHHHHHHHHHhhhccccCCCHHHHHHHhc
Q 011488 254 LVDWLIDVHQEFELSQETLYLTINIIDRFLSVKV---------VSRRE-LQLVGMGAMLIASKYEEIWAPEVNDLVRIAD 323 (484)
Q Consensus 254 LVdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~---------V~~~~-LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd 323 (484)
+-+++.++......+++++-+|..|||||..... ++--+ ..-+-++|+.+|+|+.+...-.-.-+..+
T Consensus 78 i~~yleri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~y~n~~~a~v-- 155 (218)
T KOG1674|consen 78 IRQYLERIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVYYSNAYYAKV-- 155 (218)
T ss_pred hHHHHHHHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccchhhhHHHHHHh--
Confidence 5577778888889999999999999999998622 22223 44578899999999987643222222232
Q ss_pred cCCCHHHHHHHHHHHHHHcCCcccCC
Q 011488 324 NAYSHPEVLAMEKTILGKLEWTLTVP 349 (484)
Q Consensus 324 ~~yt~~~Il~mE~~IL~~L~w~L~~P 349 (484)
+..+.+++-.+|...|..++|++.++
T Consensus 156 ggl~~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 156 GGLTTDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred CCCChHhhhhhhHHHHhhCCeEEEec
Confidence 45789999999999999999999875
No 27
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=95.10 E-value=0.17 Score=52.16 Aligned_cols=147 Identities=18% Similarity=0.217 Sum_probs=103.4
Q ss_pred hhhHHHHHhhhhhhhcccCCCCCccccCCCcCCCCCccccccHHHHHHHHHHHHhhcCCCCccCcCccccHHHHHHHHHH
Q 011488 178 QTLTSVLTARSKAACGLAQKPKEQIVDIDAKDANNDLAGVEYVEDIYKFYKLVENESRPCSYIHTQTEITERMRAILVDW 257 (484)
Q Consensus 178 ~~l~s~l~~rs~~a~~~~~~p~~~i~diD~~d~~n~l~~~eY~~DIy~~l~~~E~e~~~~dyl~~Q~eIt~~mR~~LVdW 257 (484)
++...+..+.-..||...+.|. .+.||-.. .+ + -..+|-+.|+.+...... ..+ .++ .-++
T Consensus 162 rs~~~i~AAclYiACR~~~~pr-tl~eI~~~--~~---v--~~k~i~~~~~~l~k~L~~----~~~-~~~------p~~~ 222 (310)
T PRK00423 162 RSIEGVVAAALYAACRRCKVPR-TLDEIAEV--SR---V--SRKEIGRCYRFLLRELNL----KLP-PTD------PIDY 222 (310)
T ss_pred CCHHHHHHHHHHHHHHHcCCCc-CHHHHHHH--hC---C--CHHHHHHHHHHHHHHhCC----CCC-CCC------HHHH
Confidence 3556777777778898877775 33333211 11 1 123555555544443321 111 111 3589
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccCCCHHHHHHHHHH
Q 011488 258 LIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNAYSHPEVLAMEKT 337 (484)
Q Consensus 258 LieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~yt~~~Il~mE~~ 337 (484)
|..++..|+|+.++...|..++.+.....-.......-++++|+||||+.... +.+++++..+++ .+...|...=+.
T Consensus 223 i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~-~~t~keIa~v~~--Vs~~tI~~~yke 299 (310)
T PRK00423 223 VPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGE-RRTQREVAEVAG--VTEVTVRNRYKE 299 (310)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHcC--CCHHHHHHHHHH
Confidence 99999999999999999999999888766677889999999999999998764 468888887764 678888888888
Q ss_pred HHHHcCCcc
Q 011488 338 ILGKLEWTL 346 (484)
Q Consensus 338 IL~~L~w~L 346 (484)
|+..|+..+
T Consensus 300 l~~~l~~~~ 308 (310)
T PRK00423 300 LAEKLDIKI 308 (310)
T ss_pred HHHHhCccc
Confidence 888876543
No 28
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=93.48 E-value=0.12 Score=52.85 Aligned_cols=88 Identities=22% Similarity=0.248 Sum_probs=64.5
Q ss_pred HHcCCCHHHHHHHHHHHHHhhccccc--ccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccCCCHHHHHHHHHHHHH
Q 011488 263 QEFELSQETLYLTINIIDRFLSVKVV--SRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNAYSHPEVLAMEKTILG 340 (484)
Q Consensus 263 ~~f~L~~eTl~LAV~llDRfLs~~~V--~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~yt~~~Il~mE~~IL~ 340 (484)
....|..+.--....|++|.+....+ -..+...+....+++|+|+-....-.--|.+.|+.. .|.+|+..||+.+|.
T Consensus 202 ~~~qlta~~aiitL~~~erl~~~~e~~~~p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlKd-~tveDmNe~ERqfLe 280 (343)
T KOG1675|consen 202 SWAQLTAECDIITLVYAERLLWLAERDPCPRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILKD-QSVDDMNALERQFLE 280 (343)
T ss_pred hhhhhhhccchHHHHhhHhhhhHhhcCCCcchhhhhhhhhheehhhhhhhhhcccHHHHHHHhh-ccHhhHHHHHHHHHH
Confidence 33444555555566788888765544 366777788788999999966544334566777655 589999999999999
Q ss_pred HcCCcccCCCH
Q 011488 341 KLEWTLTVPTY 351 (484)
Q Consensus 341 ~L~w~L~~PTp 351 (484)
.|+|++++|..
T Consensus 281 lLqfNinvp~s 291 (343)
T KOG1675|consen 281 LLQFNINVPSS 291 (343)
T ss_pred HHhhccCccHH
Confidence 99999998754
No 29
>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=91.41 E-value=0.92 Score=38.57 Aligned_cols=87 Identities=17% Similarity=0.133 Sum_probs=59.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccCCCHHHHHHH
Q 011488 255 VDWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNAYSHPEVLAM 334 (484)
Q Consensus 255 VdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~yt~~~Il~m 334 (484)
.+||.......+...++-++|-++++..+....+-.-.--++|++|+++|.+.-...++--..+..++ .|+.++|..+
T Consensus 4 ~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t--~~~~~~l~~c 81 (118)
T PF02984_consen 4 YDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLT--GYDKEDLKEC 81 (118)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHH--TS-HHHHHHH
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhc--CCCHHHHHHH
Confidence 46666664444556678889999999877776677777789999999999998553223334455555 4588888777
Q ss_pred HHHHHHHcC
Q 011488 335 EKTILGKLE 343 (484)
Q Consensus 335 E~~IL~~L~ 343 (484)
=..|.+.+.
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 666665553
No 30
>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=91.03 E-value=2.1 Score=37.01 Aligned_cols=82 Identities=9% Similarity=0.132 Sum_probs=54.5
Q ss_pred HHHHHHHhcCCCchhHHHHHHHHHHHhccccccCCcHHHHHHHHHHHHHHHhCCCCCChHHHHhhh--CCCHHHHHHHHH
Q 011488 354 FLVRFIKASIPDQDMENTVYFLAELGMMHYDTLMFSPSMVAASAVYAARCTLNRSPAWTDTLRFHT--GFSETQLMDCAR 431 (484)
Q Consensus 354 FL~~fl~~~~~d~el~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~lA~~~l~~~p~W~~~L~~~t--gys~~eL~~c~~ 431 (484)
|+.........+..+..+|.++.+.-+....+....+..+|++|+++|.+..+..+.+...+...+ .|+.++|...=.
T Consensus 37 ~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~E~ 116 (127)
T PF00134_consen 37 WIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILEMER 116 (127)
T ss_dssp HHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHHHH
T ss_pred HHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHHHHH
Confidence 344433333445556667777777666555566788999999999999998887666777776666 367788777655
Q ss_pred HHHH
Q 011488 432 LLVY 435 (484)
Q Consensus 432 ~L~~ 435 (484)
.++.
T Consensus 117 ~iL~ 120 (127)
T PF00134_consen 117 EILS 120 (127)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 5554
No 31
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=88.22 E-value=3.4 Score=42.42 Aligned_cols=146 Identities=16% Similarity=0.217 Sum_probs=95.7
Q ss_pred cchhhHHHHHhhhhhhhcccCCCCCccccCCCcCCCCCccccccHHHHHHHHHHHHhhcCCCCccCcCccccHHHHHHHH
Q 011488 176 KSQTLTSVLTARSKAACGLAQKPKEQIVDIDAKDANNDLAGVEYVEDIYKFYKLVENESRPCSYIHTQTEITERMRAILV 255 (484)
Q Consensus 176 ~~~~l~s~l~~rs~~a~~~~~~p~~~i~diD~~d~~n~l~~~eY~~DIy~~l~~~E~e~~~~dyl~~Q~eIt~~mR~~LV 255 (484)
+.++..+++.+.-.++|...+.|+- +.+|-.. .. +.. .+|.+.|+.+-... .+...+ ..-.
T Consensus 135 rGRsie~v~AA~iY~acR~~~~prt-l~eIa~a--~~---V~~--kei~rtyr~~~~~L----~l~~~~-------~~p~ 195 (285)
T COG1405 135 RGRSIESVAAACIYAACRINGVPRT-LDEIAKA--LG---VSK--KEIGRTYRLLVREL----KLKIPP-------VDPS 195 (285)
T ss_pred cCCcHHHHHHHHHHHHHHHcCCCcc-HHHHHHH--HC---CCH--HHHHHHHHHHHHhc----CCCCCC-------CCHH
Confidence 4557788899988999988877753 2222211 11 211 67777776322221 111111 3356
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccCCCHHHHHHHH
Q 011488 256 DWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNAYSHPEVLAME 335 (484)
Q Consensus 256 dWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~yt~~~Il~mE 335 (484)
++|-.++..++|+.++--.|+.|++..............-++++|++|||.+... ..+.++...+++- |..-|..--
T Consensus 196 ~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~-~~tq~eva~v~~v--tevTIrnry 272 (285)
T COG1405 196 DYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGE-RRTQKEVAKVAGV--TEVTIRNRY 272 (285)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCC-chHHHHHHHHhCC--eeeHHHHHH
Confidence 7888999999999999999999999998888777888889999999999998763 3355666655542 333333333
Q ss_pred HHHHHHcC
Q 011488 336 KTILGKLE 343 (484)
Q Consensus 336 ~~IL~~L~ 343 (484)
+.|...|+
T Consensus 273 kel~~~~~ 280 (285)
T COG1405 273 KELADALD 280 (285)
T ss_pred HHHHHhhc
Confidence 44444443
No 32
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=83.82 E-value=1.3 Score=46.11 Aligned_cols=93 Identities=15% Similarity=0.152 Sum_probs=68.4
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHH--HHHhccCCCHH
Q 011488 252 AILVDWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDL--VRIADNAYSHP 329 (484)
Q Consensus 252 ~~LVdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dl--v~isd~~yt~~ 329 (484)
.-|++|+..+-..-+........|.+++-..+...-+-.-..+-||++||+||+|+-....|...+. -...+...|.+
T Consensus 153 ~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e 232 (323)
T KOG0834|consen 153 KYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTNE 232 (323)
T ss_pred HHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCHH
Confidence 3466777666665555555777788888777776677778889999999999999977655544443 45566678889
Q ss_pred HHHHHHHHHHHHcCC
Q 011488 330 EVLAMEKTILGKLEW 344 (484)
Q Consensus 330 ~Il~mE~~IL~~L~w 344 (484)
++..+...+|..++-
T Consensus 233 ~l~~i~~~~l~~y~~ 247 (323)
T KOG0834|consen 233 LLDDICHEFLDLYEQ 247 (323)
T ss_pred HHHHHHHHHHHHHhh
Confidence 888888888877644
No 33
>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=77.16 E-value=30 Score=31.69 Aligned_cols=88 Identities=13% Similarity=-0.016 Sum_probs=57.0
Q ss_pred CCCHHHHHHHHHHhcCCCchhHHHHHHHHHHHhc---c--ccccCCcHHHHHHHHHHHHHHHhCCCCCChHHHHhhhCCC
Q 011488 348 VPTYYVFLVRFIKASIPDQDMENTVYFLAELGMM---H--YDTLMFSPSMVAASAVYAARCTLNRSPAWTDTLRFHTGFS 422 (484)
Q Consensus 348 ~PTp~~FL~~fl~~~~~d~el~~lA~yL~ELsL~---d--~~~l~~~PS~IAAAal~lA~~~l~~~p~W~~~L~~~tgys 422 (484)
..+-.+|+.++++....+..+.-+|.++++--.. . .........-+=.+|+.+|.+.++....|+..+...+|++
T Consensus 51 ~i~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis 130 (149)
T PF08613_consen 51 SISIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGIS 130 (149)
T ss_dssp SS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-
T ss_pred CCcHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCC
Confidence 3456778999998877777666666665554333 1 1223466778889999999999988888899999999999
Q ss_pred HHHHHHHHHHHHH
Q 011488 423 ETQLMDCARLLVY 435 (484)
Q Consensus 423 ~~eL~~c~~~L~~ 435 (484)
..+|...=..++.
T Consensus 131 ~~eln~lE~~fL~ 143 (149)
T PF08613_consen 131 LKELNELEREFLK 143 (149)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 9998876444443
No 34
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=67.93 E-value=20 Score=37.55 Aligned_cols=72 Identities=18% Similarity=0.200 Sum_probs=51.9
Q ss_pred HHHHcCCCHHH--HHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhccCCCHHHHHHH
Q 011488 261 VHQEFELSQET--LYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIADNAYSHPEVLAM 334 (484)
Q Consensus 261 V~~~f~L~~eT--l~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd~~yt~~~Il~m 334 (484)
.-+.+++.+.- +..+-||+.--|-...+.+..-.+|+++|++||+..+|+-.|....+..+.+ ++.++|-..
T Consensus 148 YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd--~~k~eid~i 221 (367)
T KOG0835|consen 148 YLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFD--TTKREIDEI 221 (367)
T ss_pred HHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcC--CcHHHHHHH
Confidence 33455665544 6777788887777777788888999999999999999986666666555543 456655544
No 35
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=55.09 E-value=67 Score=33.31 Aligned_cols=40 Identities=10% Similarity=0.172 Sum_probs=26.0
Q ss_pred hhHHHHHHHHHHHhccccccCCcHHHHHHHHHHHHHHHhC
Q 011488 367 DMENTVYFLAELGMMHYDTLMFSPSMVAASAVYAARCTLN 406 (484)
Q Consensus 367 el~~lA~yL~ELsL~d~~~l~~~PS~IAAAal~lA~~~l~ 406 (484)
++...|..+..--++...+..|.|-.||++|||+|...-+
T Consensus 77 ~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE 116 (305)
T TIGR00569 77 SVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEE 116 (305)
T ss_pred hHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccc
Confidence 3334443333333344455668999999999999987654
No 36
>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=51.64 E-value=52 Score=30.08 Aligned_cols=66 Identities=15% Similarity=0.164 Sum_probs=50.5
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHhhccc--ccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHh
Q 011488 256 DWLIDVHQEFELSQETLYLTINIIDRFLSVK--VVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIA 322 (484)
Q Consensus 256 dWLieV~~~f~L~~eTl~LAV~llDRfLs~~--~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~is 322 (484)
.-|.++|.+++|+.+.......+|+..+..+ -+...++--+-++|+++-||+.. ...+.++++...
T Consensus 16 ~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~-~~~sF~~Ii~~Y 83 (135)
T PF01857_consen 16 VRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSK-EELSFKDIIKAY 83 (135)
T ss_dssp HHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT--S--HHHHHHHH
T ss_pred HHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhc-CCCCHHHHHHHH
Confidence 4577899999999998888889999988754 35677899999999999999876 455667776543
No 37
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=47.21 E-value=67 Score=33.28 Aligned_cols=129 Identities=13% Similarity=0.220 Sum_probs=83.1
Q ss_pred cchhhHHHHHhhhhhhhcccCCCCCccccCCCcCCCCCccccccHHHHHHHHHHHHhhc-CCCCccCcCccccHHHHHHH
Q 011488 176 KSQTLTSVLTARSKAACGLAQKPKEQIVDIDAKDANNDLAGVEYVEDIYKFYKLVENES-RPCSYIHTQTEITERMRAIL 254 (484)
Q Consensus 176 ~~~~l~s~l~~rs~~a~~~~~~p~~~i~diD~~d~~n~l~~~eY~~DIy~~l~~~E~e~-~~~dyl~~Q~eIt~~mR~~L 254 (484)
+.++...+..|.-..||.-...|.- +-+|-. ..| ..- .||=++++.+=... ...+.+ -...
T Consensus 142 rGks~eai~AAclyiACRq~~~pRT-~kEI~~--~an-v~k----KEIgr~~K~i~~~l~~s~~~~----------s~~t 203 (308)
T KOG1597|consen 142 RGKSVEALAAACLYIACRQEDVPRT-FKEISA--VAN-VSK----KEIGRCVKLIGEALETSVDLI----------SIST 203 (308)
T ss_pred cCccHHHHHHHHHHHHHHhcCCCch-HHHHHH--HHc-CCH----HHHHHHHHHHHHHHhccchhh----------hhhH
Confidence 3456777888888888887666642 222221 112 111 22222222211111 111111 1236
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHhhcccccccchhHHHHHHHHHHHhhhccccCCCHHHHHHHhc
Q 011488 255 VDWLIDVHQEFELSQETLYLTINIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEIWAPEVNDLVRIAD 323 (484)
Q Consensus 255 VdWLieV~~~f~L~~eTl~LAV~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~~~P~l~dlv~isd 323 (484)
-|+|..+|..|+|+..+.-.|-.+-..+-....+.....--|+++.+||++-..+ ..-+.+++..+++
T Consensus 204 ~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~-~kkt~keI~~vtg 271 (308)
T KOG1597|consen 204 GDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSD-EKKTQKEIGEVTG 271 (308)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhcc-CcccHHHHHHHhh
Confidence 6999999999999999999999999888777777777888899999999999987 4556777776654
No 38
>KOG1992 consensus Nuclear export receptor CSE1/CAS (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=29.69 E-value=5.9e+02 Score=30.35 Aligned_cols=61 Identities=11% Similarity=0.100 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHH--HHHHHhhcccccccchhHHHHHHHHHHHhhhccc
Q 011488 250 MRAILVDWLIDVHQEFELSQETLYLTI--NIIDRFLSVKVVSRRELQLVGMGAMLIASKYEEI 310 (484)
Q Consensus 250 mR~~LVdWLieV~~~f~L~~eTl~LAV--~llDRfLs~~~V~~~~LQLvgiaCL~IAsK~EE~ 310 (484)
.|+..+|.+..+|..|+-.-.+++.+. .++|.|...-+..=.+-...---|..+|+|-++.
T Consensus 378 RRR~a~dlvrgL~~~fe~~vt~v~~~~v~~~l~~y~~nPS~nWk~kd~aiyL~talaik~~t~ 440 (960)
T KOG1992|consen 378 RRRAAIDLVRGLCKNFEGQVTGVFSSEVQRLLDQYSKNPSGNWKKKDRAIYLVTALAIKGQTA 440 (960)
T ss_pred hHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhccCCCccccccchhhhhhHHHHhhcchh
Confidence 477899999999999987766666543 6788886654433222222333456788887665
No 39
>PLN00064 photosystem II protein Psb27; Provisional
Probab=23.45 E-value=2e+02 Score=27.31 Aligned_cols=70 Identities=16% Similarity=0.203 Sum_probs=50.2
Q ss_pred ccccHHHHHHHHHHHHhhcCCCCccCcCccccHHHHHHHHHHHHHHHHHcCC----CHHHHHHHHHHHHHhhcc
Q 011488 216 GVEYVEDIYKFYKLVENESRPCSYIHTQTEITERMRAILVDWLIDVHQEFEL----SQETLYLTINIIDRFLSV 285 (484)
Q Consensus 216 ~~eY~~DIy~~l~~~E~e~~~~dyl~~Q~eIt~~mR~~LVdWLieV~~~f~L----~~eTl~LAV~llDRfLs~ 285 (484)
..+|++|-......+..-.....+-....+...+.|..+-||+-.-...-.+ +..|+|.|+|-+--+++.
T Consensus 63 ~g~Y~~DT~aVi~~lr~tI~L~~ddp~~a~a~aeaR~~iNdyvSrYRr~~~v~Gl~SFttMyTALNaLAGHY~S 136 (166)
T PLN00064 63 DEEYVKETKDVIGKVRSTINMDKTDPNVADAVAELRETSNSWVAKYRREKALLGRPSFRDMYSALNAVSGHYIS 136 (166)
T ss_pred CCChHHHHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHHHHHHHhcCCCcccCcccHHHHHHHHHHHHHHhhc
Confidence 3579999988777666544333333333456678999999999988776555 778999999988766643
No 40
>KOG1943 consensus Beta-tubulin folding cofactor D [Posttranslational modification, protein turnover, chaperones]
Probab=21.15 E-value=1.6e+03 Score=27.64 Aligned_cols=22 Identities=5% Similarity=0.014 Sum_probs=14.7
Q ss_pred hHHHHHHHHHHHhccccccCCc
Q 011488 368 MENTVYFLAELGMMHYDTLMFS 389 (484)
Q Consensus 368 l~~lA~yL~ELsL~d~~~l~~~ 389 (484)
+..++.-|+-.++.|.+..+-+
T Consensus 468 l~~L~s~LL~~AlFDrevncRR 489 (1133)
T KOG1943|consen 468 LQSLASALLIVALFDREVNCRR 489 (1133)
T ss_pred HHHHHHHHHHHHhcCchhhHhH
Confidence 4557777777788877765443
No 41
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=20.85 E-value=3.1e+02 Score=29.04 Aligned_cols=53 Identities=9% Similarity=-0.123 Sum_probs=28.3
Q ss_pred hHHHHHHHHHHHhccccccCCc---HHHHHHHHHHHHHHHhCCC-CCChHHHHhhhC
Q 011488 368 MENTVYFLAELGMMHYDTLMFS---PSMVAASAVYAARCTLNRS-PAWTDTLRFHTG 420 (484)
Q Consensus 368 l~~lA~yL~ELsL~d~~~l~~~---PS~IAAAal~lA~~~l~~~-p~W~~~L~~~tg 420 (484)
+--+|--+++--|..+.+-..+ --+||+||+.||.++-... |.-.+....++.
T Consensus 98 ~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~ 154 (335)
T KOG0656|consen 98 VFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTD 154 (335)
T ss_pred HHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcccc
Confidence 3333433444334444444455 4568999999998876552 443333334433
Done!