Query 048703
Match_columns 361
No_of_seqs 232 out of 1470
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 12:12:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048703.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048703hhsearch_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-34 1E-38 286.5 8.6 158 202-361 108-267 (391)
2 COG5024 Cyclin [Cell division 100.0 1.8E-33 3.8E-38 282.4 8.0 161 200-361 160-321 (440)
3 KOG0655 G1/S-specific cyclin E 100.0 2E-32 4.4E-37 261.5 6.9 144 216-360 109-253 (408)
4 KOG0656 G1/S-specific cyclin D 100.0 6.7E-30 1.5E-34 248.7 11.4 144 217-360 42-189 (335)
5 PF00134 Cyclin_N: Cyclin, N-t 99.9 1.3E-26 2.7E-31 195.5 8.6 127 222-349 1-127 (127)
6 KOG0654 G2/Mitotic-specific cy 99.9 3.2E-26 6.9E-31 224.8 3.6 157 204-360 87-244 (359)
7 TIGR00569 ccl1 cyclin ccl1. Un 99.6 1.4E-15 3.1E-20 148.1 7.1 109 251-360 54-166 (305)
8 cd00043 CYCLIN Cyclin box fold 99.5 1.9E-14 4.2E-19 111.4 5.4 87 253-341 2-88 (88)
9 smart00385 CYCLIN domain prese 99.4 1.2E-13 2.5E-18 106.1 4.5 83 258-342 1-83 (83)
10 KOG0834 CDK9 kinase-activating 99.4 5.9E-13 1.3E-17 130.2 5.2 122 238-360 24-158 (323)
11 COG5333 CCL1 Cdk activating ki 99.1 9.2E-11 2E-15 112.8 6.7 113 247-360 39-157 (297)
12 KOG0835 Cyclin L [General func 99.0 6E-10 1.3E-14 107.7 5.4 114 246-360 16-148 (367)
13 PF08613 Cyclin: Cyclin; Inte 98.7 2.4E-08 5.1E-13 87.9 6.4 91 256-348 54-149 (149)
14 KOG0794 CDK8 kinase-activating 98.7 5.3E-09 1.1E-13 97.1 2.2 107 251-357 39-157 (264)
15 PRK00423 tfb transcription ini 98.3 2.2E-06 4.7E-11 84.2 8.8 105 254-361 123-227 (310)
16 KOG4164 Cyclin ik3-1/CABLES [C 98.2 3.1E-07 6.7E-12 90.9 0.2 141 211-351 339-482 (497)
17 KOG2496 Cdk activating kinase 98.1 8.3E-06 1.8E-10 78.7 6.9 101 254-355 57-161 (325)
18 KOG1597 Transcription initiati 96.9 0.0014 2.9E-08 63.5 5.6 102 257-361 108-211 (308)
19 KOG1674 Cyclin [General functi 96.6 0.0029 6.4E-08 59.3 4.8 94 256-351 78-181 (218)
20 COG1405 SUA7 Transcription ini 96.2 0.019 4.1E-07 56.0 8.0 107 252-361 96-202 (285)
21 KOG1675 Predicted cyclin [Gene 95.4 0.02 4.4E-07 55.8 4.9 99 260-360 197-297 (343)
22 PF00382 TFIIB: Transcription 95.2 0.022 4.7E-07 43.6 3.3 65 260-325 1-65 (71)
23 PRK00423 tfb transcription ini 91.7 0.43 9.2E-06 47.0 6.5 89 257-348 220-308 (310)
24 KOG0834 CDK9 kinase-activating 91.4 0.45 9.8E-06 47.3 6.3 94 253-346 152-247 (323)
25 PF02984 Cyclin_C: Cyclin, C-t 88.0 0.68 1.5E-05 37.6 3.9 87 257-345 4-90 (118)
26 COG1405 SUA7 Transcription ini 73.1 4.6 0.0001 39.5 4.3 69 256-325 194-262 (285)
27 KOG1598 Transcription initiati 49.9 16 0.00034 38.6 3.4 121 236-360 44-173 (521)
28 KOG0835 Cyclin L [General func 31.8 55 0.0012 32.8 3.8 61 274-336 161-221 (367)
29 KOG1597 Transcription initiati 25.2 1E+02 0.0023 30.4 4.3 68 256-324 203-270 (308)
30 PF12550 GCR1_C: Transcription 23.4 3E+02 0.0065 21.4 6.0 34 248-284 47-80 (81)
31 KOG2145 Cytoplasmic tryptophan 23.0 35 0.00075 33.9 0.6 49 8-63 238-287 (397)
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-34 Score=286.52 Aligned_cols=158 Identities=47% Similarity=0.786 Sum_probs=148.3
Q ss_pred CcccCCC-CCCCcchhhccHHHHHHHHHHHHhccCCCCCccccccccCCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHH
Q 048703 202 DHVDIDS-DHTDPQLCSLYAADIYSNLQVAELNRRPFPNFMETVQRDITQAMRGILVDWLVEVSEEYKLVPDTLYMTVYL 280 (361)
Q Consensus 202 ~~~did~-~~~dp~~~~eY~~dI~~~L~~~E~~~~p~~~yl~~~Q~~It~~~R~~lIdwL~~v~~~~~L~~eTl~lAV~l 280 (361)
.+.|+|. +..+|+++.+|..+||.+|+..|..+.|. .|+. -|.++++.||.++||||++||..|+|.+|||||||+|
T Consensus 108 ~~~dl~~~d~~~~~~~~ey~~di~~~l~~~e~~~~p~-~~~~-~~~e~~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnl 185 (391)
T KOG0653|consen 108 SILDLDSEDKSDPSMIVEYVQDIFEYLRQLELEFLPL-SYDI-SQSEIRAKMRAILVDWLVEVHEKFGLSPETLYLAVNL 185 (391)
T ss_pred CccCcchhcccCcHHHHHHHHHHHHHHHHHHHhhCch-hhhc-ccccccHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHH
Confidence 6889988 88999999999999999999999755564 4444 3889999999999999999999999999999999999
Q ss_pred HHHhhhcCccCccCeEEEeeeehh-hhhhhhccCCCCHHHHHHhhcCCCCHHHHHHHHHHHHHHcCceecCCCHHHHHHh
Q 048703 281 IDWFLCQNYIERQRLQLLGITCML-IASKYEEICAPRAEEFCFITDNTYSREEVLKMESQVLKCLGFQLFVPTTKTFLRY 359 (361)
Q Consensus 281 ~DRfLs~~~v~~~~lqLvgitCL~-IASK~EE~~~p~l~~l~~i~~~~yt~~eI~~mE~~IL~~L~w~L~~pTp~~FL~~ 359 (361)
+||||++..+.+.++||+|++||| ||+||||+++|.+.+|++++++.||.+||++||+.||.+|+|++..|+|+.||++
T Consensus 186 iDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~il~mE~~il~~L~f~l~~p~~~~FLrr 265 (391)
T KOG0653|consen 186 IDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREEILRMEKYILNVLEFDLSVPTPLSFLRR 265 (391)
T ss_pred HHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHHHHHHHHHHHhccCeeecCCchHHHHHH
Confidence 999999988999999999999966 9999999999999999999999999999999999999999999999999999999
Q ss_pred hC
Q 048703 360 FN 361 (361)
Q Consensus 360 Fs 361 (361)
|+
T Consensus 266 ~~ 267 (391)
T KOG0653|consen 266 FL 267 (391)
T ss_pred HH
Confidence 84
No 2
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=100.00 E-value=1.8e-33 Score=282.39 Aligned_cols=161 Identities=36% Similarity=0.690 Sum_probs=155.8
Q ss_pred CCCcccCCC-CCCCcchhhccHHHHHHHHHHHHhccCCCCCccccccccCCHHHHHHHHHHHHHHHHHhcCchHHHHHHH
Q 048703 200 YPDHVDIDS-DHTDPQLCSLYAADIYSNLQVAELNRRPFPNFMETVQRDITQAMRGILVDWLVEVSEEYKLVPDTLYMTV 278 (361)
Q Consensus 200 ~~~~~did~-~~~dp~~~~eY~~dI~~~L~~~E~~~~p~~~yl~~~Q~~It~~~R~~lIdwL~~v~~~~~L~~eTl~lAV 278 (361)
...+.|+|. +..||.|+.||..+|+.+|+..|..+.|.++||.. |+.+.+.||.+|++||+++|..|+|.++|+|+||
T Consensus 160 ~~~~~dld~~~~~d~~mv~Ey~~~Ife~l~k~e~~~lp~~~yl~k-q~~~~~~mR~~Lv~wlvevH~~F~llpeTL~lai 238 (440)
T COG5024 160 SQSWQDLDATDQEDPLMVPEYASDIFEYLLKLELIDLPNPNYLIK-QSLYEWSMRSILVDWLVEVHGKFGLLPETLFLAI 238 (440)
T ss_pred ccCccccccccccCccchHHHHHHHHHHHHHHHHHhcCcHHHHhh-cchhHHhHHHHHHHHHHHhcccccccchHHHHHH
Confidence 347789997 88999999999999999999999999999999886 8899999999999999999999999999999999
Q ss_pred HHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcCCCCHHHHHHHHHHHHHHcCceecCCCHHHHHH
Q 048703 279 YLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDNTYSREEVLKMESQVLKCLGFQLFVPTTKTFLR 358 (361)
Q Consensus 279 ~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~~yt~~eI~~mE~~IL~~L~w~L~~pTp~~FL~ 358 (361)
+|+||||+...+.-.++||+|++||||||||||+++|.+.+|++++++.|+.++|+++|+.+|..|+|+|..|+|+.||+
T Consensus 239 niiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE~~ml~~l~f~is~P~P~sFLR 318 (440)
T COG5024 239 NIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERYMLEVLDFNISWPSPMSFLR 318 (440)
T ss_pred HHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHHHHHhhhcccccCCCChHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhC
Q 048703 359 YFN 361 (361)
Q Consensus 359 ~Fs 361 (361)
+++
T Consensus 319 riS 321 (440)
T COG5024 319 RIS 321 (440)
T ss_pred HHH
Confidence 875
No 3
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=99.97 E-value=2e-32 Score=261.46 Aligned_cols=144 Identities=35% Similarity=0.559 Sum_probs=135.3
Q ss_pred hhccHHHHHHHHHHHHhccCCCCCccccccccCCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhh-cCccCccC
Q 048703 216 CSLYAADIYSNLQVAELNRRPFPNFMETVQRDITQAMRGILVDWLVEVSEEYKLVPDTLYMTVYLIDWFLC-QNYIERQR 294 (361)
Q Consensus 216 ~~eY~~dI~~~L~~~E~~~~p~~~yl~~~Q~~It~~~R~~lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs-~~~v~~~~ 294 (361)
..-...+++..|+.+|..|.-..+++.. ++++.+.||++|+|||++||+-|+|..||||||+.||||||. ...+.+.+
T Consensus 109 swgn~~eVW~lM~kkee~~l~~~~~l~q-Hpdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~ 187 (408)
T KOG0655|consen 109 SWGNSKEVWLLMLKKEERYLRDKHFLEQ-HPDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTN 187 (408)
T ss_pred cccCHHHHHHHHHccchhhhhhhHHHhh-CCCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhh
Confidence 3455789999999999999887777775 789999999999999999999999999999999999999995 46799999
Q ss_pred eEEEeeeehhhhhhhhccCCCCHHHHHHhhcCCCCHHHHHHHHHHHHHHcCceecCCCHHHHHHhh
Q 048703 295 LQLLGITCMLIASKYEEICAPRAEEFCFITDNTYSREEVLKMESQVLKCLGFQLFVPTTKTFLRYF 360 (361)
Q Consensus 295 lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~~yt~~eI~~mE~~IL~~L~w~L~~pTp~~FL~~F 360 (361)
|||||+||||||+|+||+++|.+.+|.+++|+.||.++|+.||+.||++|+|+|+..|...||.-|
T Consensus 188 lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddIltmE~iilkal~W~l~PiTii~WL~vy 253 (408)
T KOG0655|consen 188 LQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDILTMELIILKALKWELSPITIISWLNVY 253 (408)
T ss_pred HHHhhHHHHHHHHHHhhccCccccceeeeccCccchHHHHHHHHHHHHHhcccccceehHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999866
No 4
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=99.96 E-value=6.7e-30 Score=248.67 Aligned_cols=144 Identities=30% Similarity=0.512 Sum_probs=137.1
Q ss_pred hccHHHHHHHHHHHHhccCCCCCccccccccCCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccC--
Q 048703 217 SLYAADIYSNLQVAELNRRPFPNFMETVQRDITQAMRGILVDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQR-- 294 (361)
Q Consensus 217 ~eY~~dI~~~L~~~E~~~~p~~~yl~~~Q~~It~~~R~~lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~-- 294 (361)
..+.++++.+|+..|..+.|..+|+..+|..+.+.||...++||.+||.++++.++|++||+|||||||+...+++.+
T Consensus 42 ~~~~e~~i~~ll~kEe~~~p~~~~~~~~~~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W 121 (335)
T KOG0656|consen 42 LLWDERVLANLLEKEEQHNPSLDYFLCVQKLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPW 121 (335)
T ss_pred ccccHHHHHHHHHHHHHhCCCCchhhhcccccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchH
Confidence 567889999999999999999998888899999999999999999999999999999999999999999999999999
Q ss_pred -eEEEeeeehhhhhhhhccCCCCHHHH-HHhhcCCCCHHHHHHHHHHHHHHcCceecCCCHHHHHHhh
Q 048703 295 -LQLLGITCMLIASKYEEICAPRAEEF-CFITDNTYSREEVLKMESQVLKCLGFQLFVPTTKTFLRYF 360 (361)
Q Consensus 295 -lqLvgitCL~IASK~EE~~~p~l~~l-~~i~~~~yt~~eI~~mE~~IL~~L~w~L~~pTp~~FL~~F 360 (361)
+||+|++||+||||+||...|.+.|+ +..+++.|-.+.|.+||+.||++|+|++..+||++|++||
T Consensus 122 ~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~feaktI~rmELLVLstL~Wrl~aVTP~sF~~~f 189 (335)
T KOG0656|consen 122 MLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHF 189 (335)
T ss_pred HHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccHHHHHHHHHHHHhhccccccCCCchHHHHHH
Confidence 99999999999999999987888776 5777999999999999999999999999999999999998
No 5
>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=1.3e-26 Score=195.45 Aligned_cols=127 Identities=39% Similarity=0.773 Sum_probs=116.6
Q ss_pred HHHHHHHHHHhccCCCCCccccccccCCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeee
Q 048703 222 DIYSNLQVAELNRRPFPNFMETVQRDITQAMRGILVDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGIT 301 (361)
Q Consensus 222 dI~~~L~~~E~~~~p~~~yl~~~Q~~It~~~R~~lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgit 301 (361)
||+.+|++.|.++.+++.|++. |++++..+|..+++||.+++..+++++.|+++|+.|||||+....+.+.+++++|++
T Consensus 1 ~i~~~~~~~e~~~~~~~~~~~~-~~~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~ 79 (127)
T PF00134_consen 1 DIFRYLLEKELKYKPNPDYLEQ-QPEITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALA 79 (127)
T ss_dssp HHHHHHHHHHHHTTCCTTHGTG-TSSHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHH
T ss_pred CHHHHHHHHHHHHCcCcccccc-ChhcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhh
Confidence 7999999999999999999985 778999999999999999999999999999999999999999999999999999999
Q ss_pred ehhhhhhhhccCCCCHHHHHHhhcCCCCHHHHHHHHHHHHHHcCceec
Q 048703 302 CMLIASKYEEICAPRAEEFCFITDNTYSREEVLKMESQVLKCLGFQLF 349 (361)
Q Consensus 302 CL~IASK~EE~~~p~l~~l~~i~~~~yt~~eI~~mE~~IL~~L~w~L~ 349 (361)
||+||+|++|..+|.+.+++.++++.|+.++|++||..||+.|+|+|+
T Consensus 80 cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 80 CLFLASKMEEDNPPSISDLIRISDNTFTKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp HHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHHHHHHHHHTTT---
T ss_pred HHHHhhhhhccccchHHHHHHHHcCCCCHHHHHHHHHHHHHHCCCCcC
Confidence 999999999999999999999999999999999999999999999985
No 6
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=99.92 E-value=3.2e-26 Score=224.79 Aligned_cols=157 Identities=57% Similarity=0.925 Sum_probs=154.6
Q ss_pred ccCCCCCCCcchhhccHHHHHHHHHHHHhc-cCCCCCccccccccCCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHH
Q 048703 204 VDIDSDHTDPQLCSLYAADIYSNLQVAELN-RRPFPNFMETVQRDITQAMRGILVDWLVEVSEEYKLVPDTLYMTVYLID 282 (361)
Q Consensus 204 ~did~~~~dp~~~~eY~~dI~~~L~~~E~~-~~p~~~yl~~~Q~~It~~~R~~lIdwL~~v~~~~~L~~eTl~lAV~l~D 282 (361)
.|||.+..||++|..|..+|++|++..|.. .+|.++||+.+|.++++.||+++|||++++++++++..+|||++++++|
T Consensus 87 ~~~ds~~~dp~~c~~~~~~I~~~~r~~ei~~~rp~~~~~e~vq~d~t~smrgilvdwlvevsee~r~~~e~l~ls~~~~d 166 (359)
T KOG0654|consen 87 MRIDSVGEDPQMCLKIAAKIYNTLRVSDIKSERPLPSKFEFVQADITPSMRGILVDWLVEVSEEYRLTFETLYLSVNYRD 166 (359)
T ss_pred cchhhcccchHHHHHHHHHHhhcccccchhhccCcccceeeeecCCCcchhhhhhhhhhHHHHHHHhhhhheeecHHHHH
Confidence 799999999999999999999999999999 9999999999999999999999999999999999999999999999999
Q ss_pred HhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcCCCCHHHHHHHHHHHHHHcCceecCCCHHHHHHhh
Q 048703 283 WFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDNTYSREEVLKMESQVLKCLGFQLFVPTTKTFLRYF 360 (361)
Q Consensus 283 RfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~~yt~~eI~~mE~~IL~~L~w~L~~pTp~~FL~~F 360 (361)
||++...+.+.++|++|++|++||+||||+.+|.+++|+++++++|+..++..||..||+.|.|.+..||...||+.|
T Consensus 167 rfl~~~~~~~~k~ql~g~s~m~I~sk~ee~~~~~~~ef~~itd~ty~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~ 244 (359)
T KOG0654|consen 167 RFLSYKEVNKQKLQLVGISAMLIASKYEEIKEPRVEEFCYITDNTYTYWQVLRMEIDILNALTFELVRPTSKTFLRRF 244 (359)
T ss_pred HHhccCccHHHHHHHhCcccceeeccchhhcchHHHHHHhhhhhhhHHHHHHHHHHHHHHHhHHHHhCchHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999887
No 7
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.59 E-value=1.4e-15 Score=148.12 Aligned_cols=109 Identities=20% Similarity=0.302 Sum_probs=99.7
Q ss_pred HHHHHHHHHHHHHHHHhc--CchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcCC-
Q 048703 251 AMRGILVDWLVEVSEEYK--LVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDNT- 327 (361)
Q Consensus 251 ~~R~~lIdwL~~v~~~~~--L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~~- 327 (361)
.+|..-..+|.++|..|+ |+.+|++.|+.||+||+..+.+...+.++|++||||||+|+||.. .++.+|+......
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 788888999999999999 999999999999999999999999999999999999999999964 5789998766544
Q ss_pred -CCHHHHHHHHHHHHHHcCceecCCCHHHHHHhh
Q 048703 328 -YSREEVLKMESQVLKCLGFQLFVPTTKTFLRYF 360 (361)
Q Consensus 328 -yt~~eI~~mE~~IL~~L~w~L~~pTp~~FL~~F 360 (361)
...++|++||..||+.|+|+|.+++|+.||..|
T Consensus 133 ~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~ 166 (305)
T TIGR00569 133 LKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGF 166 (305)
T ss_pred hhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHH
Confidence 366999999999999999999999999988765
No 8
>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=99.51 E-value=1.9e-14 Score=111.41 Aligned_cols=87 Identities=31% Similarity=0.507 Sum_probs=81.6
Q ss_pred HHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcCCCCHHH
Q 048703 253 RGILVDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDNTYSREE 332 (361)
Q Consensus 253 R~~lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~~yt~~e 332 (361)
|..+++||.+++..++++++|.++|+.|+|||+....+...+++++|++||+||+|+++. ++..+++..+++.. +.++
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 677899999999999999999999999999999999999999999999999999999998 88999999887554 9999
Q ss_pred HHHHHHHHH
Q 048703 333 VLKMESQVL 341 (361)
Q Consensus 333 I~~mE~~IL 341 (361)
|.+||..||
T Consensus 80 i~~~e~~il 88 (88)
T cd00043 80 ILRMEKLLL 88 (88)
T ss_pred HHHHHHHhC
Confidence 999999885
No 9
>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=99.43 E-value=1.2e-13 Score=106.07 Aligned_cols=83 Identities=33% Similarity=0.526 Sum_probs=76.2
Q ss_pred HHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcCCCCHHHHHHHH
Q 048703 258 DWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDNTYSREEVLKME 337 (361)
Q Consensus 258 dwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~~yt~~eI~~mE 337 (361)
+||.+++..++++.++.++|++|+|||+....+.+.+.+++|++||+||+|++|.. +...++..+++. |+.++|.+||
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 59999999999999999999999999999777778999999999999999999975 677888888776 8999999999
Q ss_pred HHHHH
Q 048703 338 SQVLK 342 (361)
Q Consensus 338 ~~IL~ 342 (361)
+.||.
T Consensus 79 ~~il~ 83 (83)
T smart00385 79 KLLLE 83 (83)
T ss_pred HHHhC
Confidence 99974
No 10
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.35 E-value=5.9e-13 Score=130.23 Aligned_cols=122 Identities=17% Similarity=0.315 Sum_probs=105.7
Q ss_pred CCccccccccCCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCH
Q 048703 238 PNFMETVQRDITQAMRGILVDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRA 317 (361)
Q Consensus 238 ~~yl~~~Q~~It~~~R~~lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l 317 (361)
+.-..++..+-....|.....||++++..++++..|+..|+.||+||+....+...+.+.+|++|||||+|.|| .+..+
T Consensus 24 pSr~~g~~~~~E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEe-tp~kl 102 (323)
T KOG0834|consen 24 PSRRDGIDLKKELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEE-TPRKL 102 (323)
T ss_pred hhhccCCchhHHHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhccc-CcccH
Confidence 33444434444458899999999999999999999999999999999999999999999999999999999999 47789
Q ss_pred HHHHHhhcCCCC-------------HHHHHHHHHHHHHHcCceecCCCHHHHHHhh
Q 048703 318 EEFCFITDNTYS-------------REEVLKMESQVLKCLGFQLFVPTTKTFLRYF 360 (361)
Q Consensus 318 ~~l~~i~~~~yt-------------~~eI~~mE~~IL~~L~w~L~~pTp~~FL~~F 360 (361)
+|++..+...+. +++|+..|+.||++|+|++++-.||.||-.|
T Consensus 103 ~dIi~~s~~~~~~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~ 158 (323)
T KOG0834|consen 103 EDIIKVSYRYLNPKDLELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKY 158 (323)
T ss_pred HHHHHHHHHHcCcccccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHH
Confidence 998876654443 3679999999999999999999999999876
No 11
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=99.12 E-value=9.2e-11 Score=112.84 Aligned_cols=113 Identities=21% Similarity=0.326 Sum_probs=96.1
Q ss_pred cCCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcC
Q 048703 247 DITQAMRGILVDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDN 326 (361)
Q Consensus 247 ~It~~~R~~lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~ 326 (361)
+-+...|..-..|+..+|.+++++..++..||.+|+||+.++.+....++-|+.||++||+|.||. +-.+.-.....++
T Consensus 39 ~~e~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~-~~~I~i~~~~~~~ 117 (297)
T COG5333 39 EKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDT-PRDISIESFEARD 117 (297)
T ss_pred hhhhhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccc-cchhhHHHHHhhc
Confidence 344577777789999999999999999999999999999999999999999999999999999994 3233333333332
Q ss_pred ------CCCHHHHHHHHHHHHHHcCceecCCCHHHHHHhh
Q 048703 327 ------TYSREEVLKMESQVLKCLGFQLFVPTTKTFLRYF 360 (361)
Q Consensus 327 ------~yt~~eI~~mE~~IL~~L~w~L~~pTp~~FL~~F 360 (361)
.-+++.|..+|..||+.|+|++.+..|+.++..|
T Consensus 118 ~~se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f 157 (297)
T COG5333 118 LWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGF 157 (297)
T ss_pred cccccccccHHHHHHHHHHHHHHcccceEeccccHHHHHH
Confidence 2357889999999999999999999999999876
No 12
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=98.96 E-value=6e-10 Score=107.75 Aligned_cols=114 Identities=19% Similarity=0.341 Sum_probs=96.3
Q ss_pred ccCCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhc
Q 048703 246 RDITQAMRGILVDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITD 325 (361)
Q Consensus 246 ~~It~~~R~~lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~ 325 (361)
.+-....|..-+.||.+.+.-++|+..+.+.+..||.||+....+-..++..++.+|++||||+||. |-.+++++.+.+
T Consensus 16 ~e~e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~-Prr~rdVinVFh 94 (367)
T KOG0835|consen 16 LETEEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEE-PRRIRDVINVFH 94 (367)
T ss_pred cchHHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccc-cccHhHHHHHHH
Confidence 3445688999999999999999999999999999999999999999999999999999999999994 556666654432
Q ss_pred C--------C---------C--CHHHHHHHHHHHHHHcCceecCCCHHHHHHhh
Q 048703 326 N--------T---------Y--SREEVLKMESQVLKCLGFQLFVPTTKTFLRYF 360 (361)
Q Consensus 326 ~--------~---------y--t~~eI~~mE~~IL~~L~w~L~~pTp~~FL~~F 360 (361)
+ . | .+..+.++|..||..|+|++++-.|+-++-.|
T Consensus 95 ~L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~Y 148 (367)
T KOG0835|consen 95 YLEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMY 148 (367)
T ss_pred HHHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHH
Confidence 1 0 1 13468899999999999999999999877655
No 13
>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=98.71 E-value=2.4e-08 Score=87.89 Aligned_cols=91 Identities=19% Similarity=0.311 Sum_probs=72.7
Q ss_pred HHHHHHHHHHHhcCchHHHHHHHHHHHHhhh---c--CccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcCCCCH
Q 048703 256 LVDWLVEVSEEYKLVPDTLYMTVYLIDWFLC---Q--NYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDNTYSR 330 (361)
Q Consensus 256 lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs---~--~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~~yt~ 330 (361)
+.+|+.++....+++++++.+|..|+||+.. . ..+.....+-+-++||.||+|+-+......+.+..+++ ++.
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 7789999999999999999999999999998 2 23567778889999999999999988888888988874 799
Q ss_pred HHHHHHHHHHHHHcCcee
Q 048703 331 EEVLKMESQVLKCLGFQL 348 (361)
Q Consensus 331 ~eI~~mE~~IL~~L~w~L 348 (361)
.||.+||+.+|..|+|+|
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 14
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=98.71 E-value=5.3e-09 Score=97.09 Aligned_cols=107 Identities=20% Similarity=0.285 Sum_probs=87.5
Q ss_pred HHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhh------
Q 048703 251 AMRGILVDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFIT------ 324 (361)
Q Consensus 251 ~~R~~lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~------ 324 (361)
..+--..+.|..++.++++...++..|+.||-||+-+..+..-.+.|++.||++||||.||.....++-++...
T Consensus 39 ~l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~ 118 (264)
T KOG0794|consen 39 KLKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTR 118 (264)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhh
Confidence 44555567788999999999999999999999999999999999999999999999999996433444443322
Q ss_pred ------cCCCCHHHHHHHHHHHHHHcCceecCCCHHHHH
Q 048703 325 ------DNTYSREEVLKMESQVLKCLGFQLFVPTTKTFL 357 (361)
Q Consensus 325 ------~~~yt~~eI~~mE~~IL~~L~w~L~~pTp~~FL 357 (361)
...|...+|.+||..+|..|++-|-+-.|+.=|
T Consensus 119 f~~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL 157 (264)
T KOG0794|consen 119 FSYWPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSL 157 (264)
T ss_pred cccchhhcCCCcCcchhhhhhHHhhhceeEEEecCCccH
Confidence 124567889999999999999999887776544
No 15
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=98.31 E-value=2.2e-06 Score=84.17 Aligned_cols=105 Identities=11% Similarity=0.126 Sum_probs=94.9
Q ss_pred HHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcCCCCHHHH
Q 048703 254 GILVDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDNTYSREEV 333 (361)
Q Consensus 254 ~~lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~~yt~~eI 333 (361)
......|.+++..++|+..+.-.|..||.+++....+.......++++|||||++.+.. |-++.+|..+++ .+..+|
T Consensus 123 ~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~-prtl~eI~~~~~--v~~k~i 199 (310)
T PRK00423 123 AFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKV-PRTLDEIAEVSR--VSRKEI 199 (310)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCC-CcCHHHHHHHhC--CCHHHH
Confidence 34556688999999999999999999999999998888888999999999999999874 679999998874 689999
Q ss_pred HHHHHHHHHHcCceecCCCHHHHHHhhC
Q 048703 334 LKMESQVLKCLGFQLFVPTTKTFLRYFN 361 (361)
Q Consensus 334 ~~mE~~IL~~L~w~L~~pTp~~FL~~Fs 361 (361)
-+.++.|++.|++++....|.+|+.+|+
T Consensus 200 ~~~~~~l~k~L~~~~~~~~p~~~i~r~~ 227 (310)
T PRK00423 200 GRCYRFLLRELNLKLPPTDPIDYVPRFA 227 (310)
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHH
Confidence 9999999999999999999999999984
No 16
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=98.20 E-value=3.1e-07 Score=90.93 Aligned_cols=141 Identities=18% Similarity=0.275 Sum_probs=104.4
Q ss_pred CCcchhhccHHHHHHHHHHHHhccCCCCCccccccc-cCCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCc
Q 048703 211 TDPQLCSLYAADIYSNLQVAELNRRPFPNFMETVQR-DITQAMRGILVDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNY 289 (361)
Q Consensus 211 ~dp~~~~eY~~dI~~~L~~~E~~~~p~~~yl~~~Q~-~It~~~R~~lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~ 289 (361)
.++..++.|...++.|.+-...+...+..|-+.+.+ .+|..-=+.|=.-|.+++...++..-|+..|..||...+-+..
T Consensus 339 k~~l~F~symttvidyVrpsdlKkdmNe~FreKfP~IkLTLSKirSlKREMr~l~~d~~id~~TVa~AyVYFEKliLkgl 418 (497)
T KOG4164|consen 339 KRVLIFSSYMTTVIDYVRPSDLKKDMNETFREKFPHIKLTLSKIRSLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGL 418 (497)
T ss_pred cceeEeccccceeEEEechHHHHHHHhHHHHHhCCeeEEeHHHHHHHHHHHHHhhhccCccceeehhHHHHHHHHHHhhh
Confidence 333344555555555444443333333333333211 2343222334556888999999999999999999999999999
Q ss_pred cCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhc--CCCCHHHHHHHHHHHHHHcCceecCC
Q 048703 290 IERQRLQLLGITCMLIASKYEEICAPRAEEFCFITD--NTYSREEVLKMESQVLKCLGFQLFVP 351 (361)
Q Consensus 290 v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~--~~yt~~eI~~mE~~IL~~L~w~L~~p 351 (361)
+.+.+=.|.|.+||++|+|+.+..--.++.|+.-+. ..++..|++..|.-||.+|+|.|+.|
T Consensus 419 isK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrrdLia~Ef~VlvaLefaL~~~ 482 (497)
T KOG4164|consen 419 ISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRRDLIAFEFPVLVALEFALHLP 482 (497)
T ss_pred hhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHHhhhhhhhhHHHhhhhhccCC
Confidence 999999999999999999999988888888886553 47789999999999999999999865
No 17
>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=98.06 E-value=8.3e-06 Score=78.74 Aligned_cols=101 Identities=24% Similarity=0.264 Sum_probs=84.6
Q ss_pred HHHHHHHHHHHHHhc--CchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcC--CCC
Q 048703 254 GILVDWLVEVSEEYK--LVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDN--TYS 329 (361)
Q Consensus 254 ~~lIdwL~~v~~~~~--L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~--~yt 329 (361)
......+++.+..|. +++.++-.|+.+|-||+-.+.+...+...|.+||+|+|+|.+|. ..++++|+.-..+ .=+
T Consensus 57 k~~E~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef-~ISieqFvkn~~~~~~k~ 135 (325)
T KOG2496|consen 57 KEEELSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEF-YISIEQFVKNMNGRKWKT 135 (325)
T ss_pred HHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhh-eecHHHHHhhccCccccc
Confidence 334455666666664 78899999999999999999999999999999999999999995 5599999865542 246
Q ss_pred HHHHHHHHHHHHHHcCceecCCCHHH
Q 048703 330 REEVLKMESQVLKCLGFQLFVPTTKT 355 (361)
Q Consensus 330 ~~eI~~mE~~IL~~L~w~L~~pTp~~ 355 (361)
.+.|+..|..+|+.|+|+|..-+|+-
T Consensus 136 ~e~vLk~E~~llqsL~f~L~vh~PyR 161 (325)
T KOG2496|consen 136 HEIVLKYEFLLLQSLKFSLTVHNPYR 161 (325)
T ss_pred HHHHHhchHHHHHhhhhhheecCCCC
Confidence 78899999999999999999888875
No 18
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=96.94 E-value=0.0014 Score=63.49 Aligned_cols=102 Identities=13% Similarity=0.189 Sum_probs=90.6
Q ss_pred HHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcCCCCHHHHHHH
Q 048703 257 VDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDNTYSREEVLKM 336 (361)
Q Consensus 257 IdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~~yt~~eI~~m 336 (361)
+.-|..++..++|+....-.|-.+|-+|-..+...-...+-++++||+||+..++ .+-++++++.+++ .+..||-+.
T Consensus 108 ~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~-~pRT~kEI~~~an--v~kKEIgr~ 184 (308)
T KOG1597|consen 108 FKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQED-VPRTFKEISAVAN--VSKKEIGRC 184 (308)
T ss_pred HHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcC-CCchHHHHHHHHc--CCHHHHHHH
Confidence 3446789999999999999999999999988888888899999999999998777 5889999999987 899999999
Q ss_pred HHHHHHHcCceecCCC--HHHHHHhhC
Q 048703 337 ESQVLKCLGFQLFVPT--TKTFLRYFN 361 (361)
Q Consensus 337 E~~IL~~L~w~L~~pT--p~~FL~~Fs 361 (361)
=..|+..|+=.+...+ .-+|+.+|+
T Consensus 185 ~K~i~~~l~~s~~~~s~~t~~~m~RFC 211 (308)
T KOG1597|consen 185 VKLIGEALETSVDLISISTGDFMPRFC 211 (308)
T ss_pred HHHHHHHHhccchhhhhhHHHHHHHHH
Confidence 9999999998887666 889999996
No 19
>KOG1674 consensus Cyclin [General function prediction only]
Probab=96.56 E-value=0.0029 Score=59.29 Aligned_cols=94 Identities=20% Similarity=0.313 Sum_probs=73.5
Q ss_pred HHHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCc---------cCccC-eEEEeeeehhhhhhhhccCCCCHHHHHHhhc
Q 048703 256 LVDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNY---------IERQR-LQLLGITCMLIASKYEEICAPRAEEFCFITD 325 (361)
Q Consensus 256 lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~---------v~~~~-lqLvgitCL~IASK~EE~~~p~l~~l~~i~~ 325 (361)
+-+++.++..+.+.+++++.+|..|||||..+.. +.--. +.-+-++|+.+|+|+.+...-...-+..+
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 3467778888999999999999999999998622 12222 34456899999999998655444444444
Q ss_pred CCCCHHHHHHHHHHHHHHcCceecCC
Q 048703 326 NTYSREEVLKMESQVLKCLGFQLFVP 351 (361)
Q Consensus 326 ~~yt~~eI~~mE~~IL~~L~w~L~~p 351 (361)
++.+.+|+..+|...|..++|++.++
T Consensus 156 ggl~~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 156 GGLTTDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred CCCChHhhhhhhHHHHhhCCeEEEec
Confidence 67899999999999999999999864
No 20
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=96.16 E-value=0.019 Score=56.00 Aligned_cols=107 Identities=8% Similarity=0.123 Sum_probs=95.6
Q ss_pred HHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcCCCCHH
Q 048703 252 MRGILVDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDNTYSRE 331 (361)
Q Consensus 252 ~R~~lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~~yt~~ 331 (361)
.-......|-.++..++|+..+.-.|..++=..+.+..+.....+-+.++|+|+|++.... +-++.++..+.+ .+..
T Consensus 96 nl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~-prtl~eIa~a~~--V~~k 172 (285)
T COG1405 96 NLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGV-PRTLDEIAKALG--VSKK 172 (285)
T ss_pred HHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCC-CccHHHHHHHHC--CCHH
Confidence 3445667788899999999999999999999999998888888999999999999998874 778889988876 7889
Q ss_pred HHHHHHHHHHHHcCceecCCCHHHHHHhhC
Q 048703 332 EVLKMESQVLKCLGFQLFVPTTKTFLRYFN 361 (361)
Q Consensus 332 eI~~mE~~IL~~L~w~L~~pTp~~FL~~Fs 361 (361)
+|.++.+.+...|+=.+....|.+|+.+|+
T Consensus 173 ei~rtyr~~~~~L~l~~~~~~p~~yi~rf~ 202 (285)
T COG1405 173 EIGRTYRLLVRELKLKIPPVDPSDYIPRFA 202 (285)
T ss_pred HHHHHHHHHHHhcCCCCCCCCHHHHHHHHH
Confidence 999999999999998888889999999985
No 21
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=95.45 E-value=0.02 Score=55.83 Aligned_cols=99 Identities=17% Similarity=0.229 Sum_probs=71.2
Q ss_pred HHHHHHHhcCchHHHHHHHHHHHHhhhcCc--cCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcCCCCHHHHHHHH
Q 048703 260 LVEVSEEYKLVPDTLYMTVYLIDWFLCQNY--IERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDNTYSREEVLKME 337 (361)
Q Consensus 260 L~~v~~~~~L~~eTl~lAV~l~DRfLs~~~--v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~~yt~~eI~~mE 337 (361)
+.-.+....|..+.--....|++|.+.-.. +.+.+...+....+|+|+|......-.-.|++.++. ..|.+|+..||
T Consensus 197 v~~l~~~~qlta~~aiitL~~~erl~~~~e~~~~p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlK-d~tveDmNe~E 275 (343)
T KOG1675|consen 197 VRILFSWAQLTAECDIITLVYAERLLWLAERDPCPRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILK-DQSVDDMNALE 275 (343)
T ss_pred hhhHhhhhhhhhccchHHHHhhHhhhhHhhcCCCcchhhhhhhhhheehhhhhhhhhcccHHHHHHHh-hccHhhHHHHH
Confidence 334444555555555556678888875433 346667777777899999998765555577887775 45889999999
Q ss_pred HHHHHHcCceecCCCHHHHHHhh
Q 048703 338 SQVLKCLGFQLFVPTTKTFLRYF 360 (361)
Q Consensus 338 ~~IL~~L~w~L~~pTp~~FL~~F 360 (361)
+++|..|+|+++.|-. .|-.||
T Consensus 276 RqfLelLqfNinvp~s-vYAKyY 297 (343)
T KOG1675|consen 276 RQFLELLQFNINVPSS-EYAKYY 297 (343)
T ss_pred HHHHHHHhhccCccHH-HHHHHH
Confidence 9999999999999843 555554
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=95.16 E-value=0.022 Score=43.56 Aligned_cols=65 Identities=8% Similarity=0.115 Sum_probs=52.7
Q ss_pred HHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhc
Q 048703 260 LVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITD 325 (361)
Q Consensus 260 L~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~ 325 (361)
|-+++..++|+..+.-.|..++++........-....-++++|+|+|++.+. .+.++.++...++
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~-~~~t~~eIa~~~~ 65 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNG-VPRTLKEIAEAAG 65 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTT-SSSSHHHHHHHCT
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcC-CCcCHHHHHHHhC
Confidence 3578999999999999999999999888777777788899999999998886 4668888876654
No 23
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=91.70 E-value=0.43 Score=47.01 Aligned_cols=89 Identities=11% Similarity=0.083 Sum_probs=73.5
Q ss_pred HHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcCCCCHHHHHHH
Q 048703 257 VDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDNTYSREEVLKM 336 (361)
Q Consensus 257 IdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~~yt~~eI~~m 336 (361)
-+||..++..++|+..+.-.|..++.+..........+..-|+++|+|||++.... +.+.+++..++ ..+...|.+.
T Consensus 220 ~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~-~~t~keIa~v~--~Vs~~tI~~~ 296 (310)
T PRK00423 220 IDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGE-RRTQREVAEVA--GVTEVTVRNR 296 (310)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHc--CCCHHHHHHH
Confidence 48899999999999999999999999888766667778889999999999998864 56888887775 4677788877
Q ss_pred HHHHHHHcCcee
Q 048703 337 ESQVLKCLGFQL 348 (361)
Q Consensus 337 E~~IL~~L~w~L 348 (361)
=.+|+..|+..+
T Consensus 297 ykel~~~l~~~~ 308 (310)
T PRK00423 297 YKELAEKLDIKI 308 (310)
T ss_pred HHHHHHHhCccc
Confidence 777777776543
No 24
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=91.44 E-value=0.45 Score=47.26 Aligned_cols=94 Identities=13% Similarity=0.109 Sum_probs=71.2
Q ss_pred HHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHH--HHhhcCCCCH
Q 048703 253 RGILVDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEF--CFITDNTYSR 330 (361)
Q Consensus 253 R~~lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l--~~i~~~~yt~ 330 (361)
-.-|++|+..+-..-+........|-+++...+...-+-....+-||++||+||+|+-....|...+- ....+...|.
T Consensus 152 y~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~ 231 (323)
T KOG0834|consen 152 YKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTN 231 (323)
T ss_pred hHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCH
Confidence 34566777766666665556777888888777765566788889999999999999987755544444 5666778999
Q ss_pred HHHHHHHHHHHHHcCc
Q 048703 331 EEVLKMESQVLKCLGF 346 (361)
Q Consensus 331 ~eI~~mE~~IL~~L~w 346 (361)
++|..+..++|..+.-
T Consensus 232 e~l~~i~~~~l~~y~~ 247 (323)
T KOG0834|consen 232 ELLDDICHEFLDLYEQ 247 (323)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 9999999999987753
No 25
>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=88.05 E-value=0.68 Score=37.55 Aligned_cols=87 Identities=16% Similarity=0.190 Sum_probs=59.9
Q ss_pred HHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcCCCCHHHHHHH
Q 048703 257 VDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDNTYSREEVLKM 336 (361)
Q Consensus 257 IdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~~yt~~eI~~m 336 (361)
.+||.......+...++.++|-++++..+....+-...--+||++|+++|.+.-....+.-..+..++ +|+.++|...
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 45666665545556778889999999777666666666778999999999999764344444566666 5588888776
Q ss_pred HHHHHHHcC
Q 048703 337 ESQVLKCLG 345 (361)
Q Consensus 337 E~~IL~~L~ 345 (361)
=..|...+.
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 666665543
No 26
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=73.08 E-value=4.6 Score=39.49 Aligned_cols=69 Identities=9% Similarity=0.044 Sum_probs=56.9
Q ss_pred HHHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhc
Q 048703 256 LVDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITD 325 (361)
Q Consensus 256 lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~ 325 (361)
-.+|+-.++..++|+.++--.|+.|++.........-....=+|++|++|||..... ..+-+++..+++
T Consensus 194 p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~-~~tq~eva~v~~ 262 (285)
T COG1405 194 PSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGE-RRTQKEVAKVAG 262 (285)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCC-chHHHHHHHHhC
Confidence 467888999999999999999999999999888777788888999999999998762 334455555543
No 27
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=49.90 E-value=16 Score=38.60 Aligned_cols=121 Identities=12% Similarity=0.102 Sum_probs=75.7
Q ss_pred CCCCccccccccCC--HHHHHHHHH----HHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhh
Q 048703 236 PFPNFMETVQRDIT--QAMRGILVD----WLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKY 309 (361)
Q Consensus 236 p~~~yl~~~Q~~It--~~~R~~lId----wL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~ 309 (361)
++.+|+..-|...+ ...|..-+. -|.+++..+++.. .+-.|+++|---++.+-..-...++|-.+||||++..
T Consensus 44 ~~G~~v~~~~~g~~~s~e~r~~t~~n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~ 122 (521)
T KOG1598|consen 44 AQGQFVRVGQSGAGSSLESREKTIYNARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRL 122 (521)
T ss_pred cceeEEeccccCCccchHHHHHHHHHHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHh
Confidence 44566665555554 244444443 4778999999999 9999999999999988888888999999999999988
Q ss_pred hccCCCCHHHHHHhhcCCCCHHHHHHHHHHHHHHcCce---ecCCCHHHHHHhh
Q 048703 310 EEICAPRAEEFCFITDNTYSREEVLKMESQVLKCLGFQ---LFVPTTKTFLRYF 360 (361)
Q Consensus 310 EE~~~p~l~~l~~i~~~~yt~~eI~~mE~~IL~~L~w~---L~~pTp~~FL~~F 360 (361)
|-.....+ ||..+.. .+.-+|=.+=+.|-..|.-. +-...|.-|+-+|
T Consensus 123 e~t~hlli-DfS~~Lq--v~Vy~LG~~~l~l~~~L~i~en~~plvDpsL~i~Rf 173 (521)
T KOG1598|consen 123 EKTDHLLI-DFSSYLQ--VSVYDLGSNFLEVTDSLSIGENVSPLVDPSLYIVRF 173 (521)
T ss_pred hCCceEEE-EeccceE--EehhhhhHHHHHHHHHhccccccccccCcceeeech
Confidence 76533222 2222111 22223333333444444444 3344455555555
No 28
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=31.77 E-value=55 Score=32.82 Aligned_cols=61 Identities=15% Similarity=0.181 Sum_probs=37.1
Q ss_pred HHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhhcCCCCHHHHHHH
Q 048703 274 LYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFITDNTYSREEVLKM 336 (361)
Q Consensus 274 l~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~~~~yt~~eI~~m 336 (361)
+..+-||+.--+-...+-+..-..|+++|+++|+.-+|+-.|...++..+ ..++..+|-..
T Consensus 161 ~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~--Fd~~k~eid~i 221 (367)
T KOG0835|consen 161 LQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKA--FDTTKREIDEI 221 (367)
T ss_pred HHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHH--cCCcHHHHHHH
Confidence 33444555444433444566678899999999999999755555444433 24455554433
No 29
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=25.19 E-value=1e+02 Score=30.42 Aligned_cols=68 Identities=7% Similarity=0.010 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHhcCchHHHHHHHHHHHHhhhcCccCccCeEEEeeeehhhhhhhhccCCCCHHHHHHhh
Q 048703 256 LVDWLVEVSEEYKLVPDTLYMTVYLIDWFLCQNYIERQRLQLLGITCMLIASKYEEICAPRAEEFCFIT 324 (361)
Q Consensus 256 lIdwL~~v~~~~~L~~eTl~lAV~l~DRfLs~~~v~~~~lqLvgitCL~IASK~EE~~~p~l~~l~~i~ 324 (361)
.-++|...|..|+|+..+.-.|-.+-..+-....+.....--|+++.+|+++-... ...+.+++..++
T Consensus 203 t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~-~kkt~keI~~vt 270 (308)
T KOG1597|consen 203 TGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSD-EKKTQKEIGEVT 270 (308)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhcc-CcccHHHHHHHh
Confidence 34555566666666666666666555555544444444455567777777777766 445566665554
No 30
>PF12550 GCR1_C: Transcriptional activator of glycolytic enzymes; InterPro: IPR022210 This domain family is found in eukaryotes, and is approximately 80 amino acids in length. This family is activates the transcription of glycolytic enzymes.
Probab=23.45 E-value=3e+02 Score=21.37 Aligned_cols=34 Identities=12% Similarity=0.267 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHh
Q 048703 248 ITQAMRGILVDWLVEVSEEYKLVPDTLYMTVYLIDWF 284 (361)
Q Consensus 248 It~~~R~~lIdwL~~v~~~~~L~~eTl~lAV~l~DRf 284 (361)
-...-|..+|++|..++...+++. ..||.++|.|
T Consensus 47 ~~y~rRK~Ii~~I~~l~~~~g~~~---~~ai~~le~~ 80 (81)
T PF12550_consen 47 RTYSRRKVIIDFIERLANERGISE---EEAIEILEEI 80 (81)
T ss_pred hhHHHHHHHHHHHHHHHHHcCCCH---HHHHHHHHhc
Confidence 355789999999999988877764 4677777764
No 31
>KOG2145 consensus Cytoplasmic tryptophanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=22.96 E-value=35 Score=33.85 Aligned_cols=49 Identities=24% Similarity=0.140 Sum_probs=34.4
Q ss_pred ccccCCCCCcchHHHHHhhccccCCccCCCCCCch-hhhhhhcccCCCccccccccc
Q 048703 8 AANVGDSTGIMTRSRAATLASQSSGFVASSRAPSV-QTRKRVLRENPKKAASDENNI 63 (361)
Q Consensus 8 ~~~~~~~~~r~tra~A~a~~~~~~g~~~~~~~p~~-~~~k~~~~~~~Kr~a~d~~~~ 63 (361)
++-.|+|--|+||--|..++ .+. |.+=..++ .. -.++++|.+|||+|++
T Consensus 238 cAiDQDPyFRmtRDvA~rlg--~~K--pali~stffpa---LqG~~~KMSASdpns~ 287 (397)
T KOG2145|consen 238 CAIDQDPYFRMTRDVAPRLG--YPK--PALIHSTFFPA---LQGAQTKMSASDPNSA 287 (397)
T ss_pred eeccCChHHHhhhhhhhhhC--CCC--cceeehhhchh---hhCcccccccCCCCce
Confidence 44558899999999999888 422 33323333 21 1357999999999998
Done!