Query 026635
Match_columns 235
No_of_seqs 152 out of 1485
Neff 8.9
Searched_HMMs 46136
Date Fri Mar 29 10:36:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026635.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026635hhsearch_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 1.7E-38 3.6E-43 277.8 19.4 222 2-223 148-372 (391)
2 COG5024 Cyclin [Cell division 100.0 1.1E-37 2.4E-42 270.1 16.0 221 1-223 202-423 (440)
3 KOG0655 G1/S-specific cyclin E 100.0 2.9E-37 6.3E-42 252.8 16.5 192 1-200 134-337 (408)
4 KOG0654 G2/Mitotic-specific cy 100.0 2.3E-36 4.9E-41 255.5 12.1 222 4-227 129-351 (359)
5 KOG0656 G1/S-specific cyclin D 100.0 9.1E-35 2E-39 243.7 17.6 189 4-192 70-268 (335)
6 TIGR00569 ccl1 cyclin ccl1. Un 99.9 1.5E-25 3.2E-30 188.8 20.2 161 6-167 46-221 (305)
7 KOG0834 CDK9 kinase-activating 99.9 7.3E-25 1.6E-29 184.3 14.4 194 8-202 35-249 (323)
8 PF00134 Cyclin_N: Cyclin, N-t 99.9 1.4E-24 3.1E-29 161.8 10.5 107 2-108 21-127 (127)
9 KOG0835 Cyclin L [General func 99.9 1.9E-22 4.2E-27 165.8 18.6 192 8-200 19-231 (367)
10 PF02984 Cyclin_C: Cyclin, C-t 99.9 1.5E-23 3.2E-28 154.2 10.8 118 110-227 1-118 (118)
11 KOG0794 CDK8 kinase-activating 99.9 9E-23 1.9E-27 160.3 11.7 187 13-203 42-243 (264)
12 COG5333 CCL1 Cdk activating ki 99.8 2.7E-20 5.8E-25 153.2 15.1 165 8-174 41-213 (297)
13 PRK00423 tfb transcription ini 99.8 2.1E-18 4.6E-23 146.9 22.3 182 13-198 123-304 (310)
14 KOG1597 Transcription initiati 99.7 1.3E-15 2.8E-20 124.4 17.1 182 15-200 107-290 (308)
15 COG1405 SUA7 Transcription ini 99.6 2.7E-14 5.9E-19 119.2 19.5 181 14-198 99-279 (285)
16 cd00043 CYCLIN Cyclin box fold 99.6 5.9E-15 1.3E-19 101.9 8.9 87 12-100 2-88 (88)
17 KOG2496 Cdk activating kinase 99.6 2E-14 4.4E-19 117.8 10.9 144 18-162 62-218 (325)
18 smart00385 CYCLIN domain prese 99.5 3.1E-14 6.6E-19 97.2 7.8 83 17-101 1-83 (83)
19 smart00385 CYCLIN domain prese 99.0 3.2E-09 7E-14 72.0 8.7 81 114-195 1-82 (83)
20 cd00043 CYCLIN Cyclin box fold 99.0 7.1E-09 1.5E-13 71.1 9.3 85 109-194 2-87 (88)
21 PF08613 Cyclin: Cyclin; Inte 98.8 8.9E-08 1.9E-12 73.2 10.0 92 14-107 53-149 (149)
22 KOG1598 Transcription initiati 98.4 3E-06 6.5E-11 75.3 10.8 174 18-196 73-252 (521)
23 KOG4164 Cyclin ik3-1/CABLES [C 98.4 9E-07 2E-11 75.5 6.8 99 12-110 382-482 (497)
24 PF00382 TFIIB: Transcription 98.1 1.2E-05 2.6E-10 53.4 6.9 65 19-84 1-65 (71)
25 PF00382 TFIIB: Transcription 97.8 0.00025 5.4E-09 47.0 8.4 71 116-187 1-71 (71)
26 PRK00423 tfb transcription ini 97.5 0.0013 2.8E-08 56.4 10.3 90 15-107 219-308 (310)
27 KOG1674 Cyclin [General functi 96.3 0.024 5.2E-07 46.0 8.0 94 15-110 78-181 (218)
28 COG1405 SUA7 Transcription ini 95.8 0.077 1.7E-06 44.8 8.8 89 14-105 193-281 (285)
29 PF00134 Cyclin_N: Cyclin, N-t 95.7 0.13 2.9E-06 37.4 9.1 86 113-198 35-122 (127)
30 KOG1675 Predicted cyclin [Gene 94.3 0.085 1.8E-06 44.4 4.9 84 36-121 214-299 (343)
31 PF02984 Cyclin_C: Cyclin, C-t 94.1 0.27 5.9E-06 35.1 7.0 87 16-104 4-90 (118)
32 PF08613 Cyclin: Cyclin; Inte 93.8 1.2 2.6E-05 33.8 10.1 91 108-198 50-145 (149)
33 KOG0834 CDK9 kinase-activating 90.8 0.29 6.2E-06 42.1 3.7 75 31-105 171-247 (323)
34 KOG1597 Transcription initiati 89.8 1.3 2.9E-05 37.2 6.6 84 14-100 202-285 (308)
35 TIGR00569 ccl1 cyclin ccl1. Un 88.9 2.8 6.1E-05 35.9 8.2 53 115-167 62-116 (305)
36 PF01857 RB_B: Retinoblastoma- 88.0 3 6.5E-05 31.2 6.9 69 16-85 15-85 (135)
37 PF09241 Herp-Cyclin: Herpesvi 77.5 19 0.00041 24.3 9.1 86 112-197 4-97 (106)
38 KOG1598 Transcription initiati 66.6 6.1 0.00013 36.1 3.2 53 30-83 184-236 (521)
39 KOG0835 Cyclin L [General func 65.4 65 0.0014 27.9 8.8 78 115-204 29-106 (367)
40 KOG0794 CDK8 kinase-activating 65.3 24 0.00051 28.9 6.0 84 114-198 46-144 (264)
41 PF12550 GCR1_C: Transcription 53.7 32 0.00069 23.1 4.3 34 7-43 47-80 (81)
42 COG5333 CCL1 Cdk activating ki 44.3 42 0.00092 28.6 4.4 78 89-166 18-102 (297)
43 PF01527 HTH_Tnp_1: Transposas 41.0 52 0.0011 21.1 3.8 41 1-41 1-48 (76)
44 PF13936 HTH_38: Helix-turn-he 40.1 42 0.0009 19.5 2.8 34 4-37 2-41 (44)
45 PF11919 DUF3437: Domain of un 34.3 73 0.0016 21.9 3.7 77 151-230 8-89 (90)
46 KOG0656 G1/S-specific cyclin D 32.6 1.9E+02 0.0042 25.1 6.8 56 112-167 81-139 (335)
47 PF03261 CDK5_activator: Cycli 30.7 73 0.0016 27.7 3.8 19 50-68 268-286 (346)
48 COG5024 Cyclin [Cell division 29.4 2.2E+02 0.0047 25.9 6.7 72 152-223 256-330 (440)
49 PF13591 MerR_2: MerR HTH fami 27.9 1.2E+02 0.0027 20.3 4.0 30 16-45 45-74 (84)
50 PF01466 Skp1: Skp1 family, di 27.3 1.6E+02 0.0034 19.4 4.4 40 55-95 30-69 (78)
51 PF14502 HTH_41: Helix-turn-he 23.8 1.2E+02 0.0026 18.3 2.9 24 19-42 9-32 (48)
52 cd04447 DEP_BRCC3 DEP (Disheve 23.5 1.6E+02 0.0035 20.4 3.8 37 14-50 34-72 (92)
53 KOG1675 Predicted cyclin [Gene 21.8 1.7E+02 0.0037 25.2 4.4 67 148-215 231-298 (343)
54 PF11357 Spy1: Cell cycle regu 21.2 3.5E+02 0.0077 20.1 6.9 82 24-109 23-109 (131)
55 cd04438 DEP_dishevelled DEP (D 21.2 1.1E+02 0.0023 20.8 2.6 31 14-44 34-64 (84)
56 cd04449 DEP_DEPDC5-like DEP (D 21.1 1.1E+02 0.0023 20.6 2.6 30 13-42 33-62 (83)
57 KOG1257 NADP+-dependent malic 20.4 2.1E+02 0.0045 26.7 4.8 56 7-62 233-294 (582)
58 cd04439 DEP_1_P-Rex DEP (Dishe 20.4 94 0.002 20.9 2.2 29 13-42 32-60 (81)
59 PRK10265 chaperone-modulator p 20.1 2.4E+02 0.0052 19.6 4.3 32 14-45 51-82 (101)
No 1
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.7e-38 Score=277.77 Aligned_cols=222 Identities=51% Similarity=0.774 Sum_probs=207.6
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHH-HhhhccccccccHhhHH
Q 026635 2 TQQFDINEKMRAILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAML-LACKYEEVSVPVVGDLI 80 (235)
Q Consensus 2 ~~q~~i~~~~R~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~-IA~K~ee~~~~~~~~l~ 80 (235)
.+|++++.+||..+++|+.+++..|++..+|+++||+++|||++..++++.++||+|++||+ ||||+||..+|.+.+++
T Consensus 148 ~~~~e~~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv 227 (391)
T KOG0653|consen 148 ISQSEIRAKMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLV 227 (391)
T ss_pred cccccccHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeE
Confidence 47899999999999999999999999999999999999999999999999999999999966 99999999999999999
Q ss_pred HhhcCCCCHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCcchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHH
Q 026635 81 LISDKAYTRKEVLEMESLMLNTLQFNMSVPTPYVFIQRFLKAAQSDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIY 160 (235)
Q Consensus 81 ~~~~~~~~~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~~~~~~~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~ 160 (235)
.++++.|+.++|.+||+.||++|+|+++.|+|+.|++++......+.+...++.++++++++|+.++.++||.+|+|+.+
T Consensus 228 ~isd~~~s~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~ 307 (391)
T KOG0653|consen 228 LITDGAYSREEILRMEKYILNVLEFDLSVPTPLSFLRRFLKAADYDIKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFT 307 (391)
T ss_pred eeeCCccchHHHHHHHHHHHhccCeeecCCchHHHHHHHHHhhhcchhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999989999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCchhhhhhcCCCHHHHHHHHHHHHHHHhhc-CCCChhH-HHHhhCCCCCCcccc
Q 026635 161 AAQCTIYGFKQWSKTCQWHSGYSEDQLLECATLMIGFHQKA-ATGKLTG-VHRKYCTSKFGYISK 223 (235)
Q Consensus 161 la~~~~~~~~~w~~~l~~~t~~~~~~i~~~~~~i~~~~~~~-~~~~~~~-i~~ky~~~~~~~vs~ 223 (235)
+++........|...+..++|+...++.+|.+.+..+.... .++.... +++||.+++++.++.
T Consensus 308 ~~~~~~~~~~~w~~~~~~~sg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ky~~~~~~~~~~ 372 (391)
T KOG0653|consen 308 LALRMLSKGDVWSPTLEHYSGYSESYLFECARSLSALSLSSLQNPSLRASVLNKYNSSKFLPASP 372 (391)
T ss_pred HHHHHhccCCccCCCCeeccCCCcHHHHHHHHHHHHHHHHhcccchhHHHHHHHhcccccchhhh
Confidence 99988776557999999999999999999999999955443 3334454 999999999999984
No 2
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=100.00 E-value=1.1e-37 Score=270.11 Aligned_cols=221 Identities=38% Similarity=0.611 Sum_probs=211.5
Q ss_pred CCCCCCCcHHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHH
Q 026635 1 MTQQFDINEKMRAILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLI 80 (235)
Q Consensus 1 ~~~q~~i~~~~R~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~ 80 (235)
|.+|+.+...+|..+++|+.+++..|++.++|+++|++++|||++...+.-+++||+|++|||||||+||.+.|.++++.
T Consensus 202 l~kq~~~~~~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~ 281 (440)
T COG5024 202 LIKQSLYEWSMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLV 281 (440)
T ss_pred HhhcchhHHhHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCCCCHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCcchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHH
Q 026635 81 LISDKAYTRKEVLEMESLMLNTLQFNMSVPTPYVFIQRFLKAAQSDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIY 160 (235)
Q Consensus 81 ~~~~~~~~~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~~~~~~~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~ 160 (235)
.++++.++.++|+++|+.+|..|+|+++.|+|..|++++......+......+.++++.+..++.|.+++||.+|+||.+
T Consensus 282 ~~t~g~~t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka~dyd~~srt~~k~~~e~s~~~~~f~~~~~S~~~aaa~~ 361 (440)
T COG5024 282 YATDGAFTRDDIIRAERYMLEVLDFNISWPSPMSFLRRISKASDYDIFSRTPAKFSSEISPVDYKFIQISPSWCAAAAMY 361 (440)
T ss_pred HHHcccccHHHHHHHHHHHhhhcccccCCCChHHHHHHHHhhcccchhhhhhHhhhCCchHhhhhhccCCchHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCCCchhhhhhcC-CCHHHHHHHHHHHHHHHhhcCCCChhHHHHhhCCCCCCcccc
Q 026635 161 AAQCTIYGFKQWSKTCQWHSG-YSEDQLLECATLMIGFHQKAATGKLTGVHRKYCTSKFGYISK 223 (235)
Q Consensus 161 la~~~~~~~~~w~~~l~~~t~-~~~~~i~~~~~~i~~~~~~~~~~~~~~i~~ky~~~~~~~vs~ 223 (235)
+++..++..+ |...+..++| |+..++.++...+.+.+.....+. .++.+||.+++|+.++.
T Consensus 362 ~s~~~~~~~~-w~~~l~~ySg~y~~~~l~~~~~~~~~~l~~~~~~~-~~i~~Ky~~~~~~~~s~ 423 (440)
T COG5024 362 LSRKILSQNQ-WDRTLIHYSGNYTNPDLKPLNESNKENLQNPSVHH-DAIFPKYPSPTFGKASS 423 (440)
T ss_pred HHHhhhccCC-CCccccccCCCCCchhHHHHHHHHHHHhcccchhh-hhhhhccccccccccch
Confidence 9998887655 9999999999 999999999999999988877654 89999999999998874
No 3
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2.9e-37 Score=252.82 Aligned_cols=192 Identities=29% Similarity=0.543 Sum_probs=173.2
Q ss_pred CCCCCCCcHHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccc-cccchhHHHHHHHHHHHhhhccccccccHhhH
Q 026635 1 MTQQFDINEKMRAILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQ-QVVRKKLQLVGLVAMLLACKYEEVSVPVVGDL 79 (235)
Q Consensus 1 ~~~q~~i~~~~R~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~-~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l 79 (235)
++++|++.|+||++++|||.++|+-++|.++|+|+|+.|||||+... .+.+.++||+|+||||||+|+||.+||++.+|
T Consensus 134 l~qHpdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eF 213 (408)
T KOG0655|consen 134 LEQHPDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEF 213 (408)
T ss_pred HhhCCCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccce
Confidence 57899999999999999999999999999999999999999999865 79999999999999999999999999999999
Q ss_pred HHhhcCCCCHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCcch-----------HHHHHHHHHHHHHhcchhccC
Q 026635 80 ILISDKAYTRKEVLEMESLMLNTLQFNMSVPTPYVFIQRFLKAAQSDK-----------KLQLLSFFLIELSLVEYEMLK 148 (235)
Q Consensus 80 ~~~~~~~~~~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~~~~~~~~~-----------~~~~~a~~ll~~~l~~~~~~~ 148 (235)
.+++++.+|.++|+.||..||+.|+|++.+.|...|+.-|+......+ ...--...++++|+.+...+.
T Consensus 214 AyvTDgAcs~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqiaqlLDlc~ldids~~ 293 (408)
T KOG0655|consen 214 AYVTDGACSEDDILTMELIILKALKWELSPITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIAQLLDLCILDIDSLE 293 (408)
T ss_pred eeeccCccchHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcCCCCceeccccchHHHHHHHHHHHHHHhcccccc
Confidence 999999999999999999999999999999999999999998875332 111113457899999999999
Q ss_pred CCHHHHHHHHHHHHHHHhcCCCCCchhhhhhcCCCHHHHHHHHHHHHHHHhh
Q 026635 149 FTPSLLAAAAIYAAQCTIYGFKQWSKTCQWHSGYSEDQLLECATLMIGFHQK 200 (235)
Q Consensus 149 ~~ps~iA~a~l~la~~~~~~~~~w~~~l~~~t~~~~~~i~~~~~~i~~~~~~ 200 (235)
|+.+++||||++.... ...+.+.+|+.+.+|.+|+++|.-+.+-
T Consensus 294 fsYrilaAAal~h~~s--------~e~v~kaSG~~w~~ie~cv~wm~Pf~rv 337 (408)
T KOG0655|consen 294 FSYRILAAAALCHFTS--------IEVVKKASGLEWDSIEECVDWMVPFVRV 337 (408)
T ss_pred chHHHHHHHHHHHHhH--------HHHHHHcccccHHHHHHHHHHHHHHHHH
Confidence 9999999999987742 3567788999999999999999987753
No 4
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2.3e-36 Score=255.52 Aligned_cols=222 Identities=41% Similarity=0.680 Sum_probs=215.4
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhh
Q 026635 4 QFDINEKMRAILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILIS 83 (235)
Q Consensus 4 q~~i~~~~R~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~ 83 (235)
|.++|+.||.++++|.+++.+.+++..+++|+++++.|||+....+.+.++|+++.+|.+||+|.+|..+|.+.+++.++
T Consensus 129 q~d~t~smrgilvdwlvevsee~r~~~e~l~ls~~~~drfl~~~~~~~~k~ql~g~s~m~I~sk~ee~~~~~~~ef~~it 208 (359)
T KOG0654|consen 129 QADITPSMRGILVDWLVEVSEEYRLTFETLYLSVNYRDRFLSYKEVNKQKLQLVGISAMLIASKYEEIKEPRVEEFCYIT 208 (359)
T ss_pred ecCCCcchhhhhhhhhhHHHHHHHhhhhheeecHHHHHHHhccCccHHHHHHHhCcccceeeccchhhcchHHHHHHhhh
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhC-cchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHH
Q 026635 84 DKAYTRKEVLEMESLMLNTLQFNMSVPTPYVFIQRFLKAAQ-SDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAA 162 (235)
Q Consensus 84 ~~~~~~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~~~~~~-~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la 162 (235)
++.|+..++.+||..|+..|.|.+..||.-.|+..|+.... ...++..++.|+.++++.++.|+.|.||.|||||+++|
T Consensus 209 d~ty~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~~~~~~~~~~e~~~~yl~elsll~~~~l~y~PSliAasAv~lA 288 (359)
T KOG0654|consen 209 DNTYTYWQVLRMEIDILNALTFELVRPTSKTFLRRFLRVAQTPELQVEPLANYLTELSLLDYIFLKYLPSLIAASAVFLA 288 (359)
T ss_pred hhhhHHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHHhhcchhHHHHHHHHHHHHhhhhhHHHhccChHHHHHHHHHHH
Confidence 99999999999999999999999999999999999988876 56678899999999999999999999999999999999
Q ss_pred HHHhcCCCCCchhhhhhcCCCHHHHHHHHHHHHHHHhhcCCCChhHHHHhhCCCCCCccccCCCc
Q 026635 163 QCTIYGFKQWSKTCQWHSGYSEDQLLECATLMIGFHQKAATGKLTGVHRKYCTSKFGYISKSEPA 227 (235)
Q Consensus 163 ~~~~~~~~~w~~~l~~~t~~~~~~i~~~~~~i~~~~~~~~~~~~~~i~~ky~~~~~~~vs~~~~~ 227 (235)
+.+++ ..+|.+.++.+|||+.+++..|+..|. ++.+.++..+++|++||+.++|++|+.+++|
T Consensus 289 ~~~~~-~~pW~~~L~~~T~y~~edl~~~v~~L~-~~l~~~~~~l~air~ky~~~k~~~Va~~~~p 351 (359)
T KOG0654|consen 289 RLTLD-FHPWNQTLEDYTGYKAEDLKPCVLDLH-LYLNASGTDLPAIREKYKQSKFKEVALLPVP 351 (359)
T ss_pred Hhhcc-CCCCchhhHHhhcccHHHHHHHHHHHh-cccCCCCCchHHHHHHhhhhhhhhhhccCCC
Confidence 98887 799999999999999999999999999 8899999999999999999999999999987
No 5
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=9.1e-35 Score=243.74 Aligned_cols=189 Identities=28% Similarity=0.512 Sum_probs=163.7
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchh---HHHHHHHHHHHhhhccccccccHhhHH
Q 026635 4 QFDINEKMRAILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKK---LQLVGLVAMLLACKYEEVSVPVVGDLI 80 (235)
Q Consensus 4 q~~i~~~~R~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~---l~l~a~tcl~IA~K~ee~~~~~~~~l~ 80 (235)
|..+++.+|...++||.++|.++++.+.++.+|++|||||++..++++++ +||+|++||+||||++|..+|.+.++.
T Consensus 70 ~~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~ 149 (335)
T KOG0656|consen 70 QKLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQ 149 (335)
T ss_pred ccccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhh
Confidence 67789999999999999999999999999999999999999999999999 999999999999999999878877775
Q ss_pred -HhhcCCCCHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCcch----HHHHHHHHHHHHHhcchhccCCCHHHHH
Q 026635 81 -LISDKAYTRKEVLEMESLMLNTLQFNMSVPTPYVFIQRFLKAAQSDK----KLQLLSFFLIELSLVEYEMLKFTPSLLA 155 (235)
Q Consensus 81 -~~~~~~~~~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~~~~~~~~~----~~~~~a~~ll~~~l~~~~~~~~~ps~iA 155 (235)
...++.|.++.|.+||..||++|+|+++.+||++|+++|++.++... ....-+..++-.+..|..|+.|+||+||
T Consensus 150 v~~~~~~feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviA 229 (335)
T KOG0656|consen 150 VEYTDNVFEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIA 229 (335)
T ss_pred hccccccccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHH
Confidence 45688999999999999999999999999999999999999998743 2333455566677899999999999999
Q ss_pred HHHHHHHHHHhcCCCC--CchhhhhhcCCCHHHHHHHHH
Q 026635 156 AAAIYAAQCTIYGFKQ--WSKTCQWHSGYSEDQLLECAT 192 (235)
Q Consensus 156 ~a~l~la~~~~~~~~~--w~~~l~~~t~~~~~~i~~~~~ 192 (235)
+|++..+...+..... ....+..+.+++.+.++.|+.
T Consensus 230 aa~~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 230 AAAILSVSASVDGLDFREYENNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred HHHHHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence 9988777655543221 125666777888888888888
No 6
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.94 E-value=1.5e-25 Score=188.79 Aligned_cols=161 Identities=22% Similarity=0.311 Sum_probs=141.2
Q ss_pred CCcH----HHHHHHHHHHHHHHHHcC--CChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhH
Q 026635 6 DINE----KMRAILIDWLIEVHDKFD--LMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDL 79 (235)
Q Consensus 6 ~i~~----~~R~~~v~wm~~~~~~~~--l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l 79 (235)
.+|+ ..|.--+++|.++|.+++ ++..|+.+|+.||+||+..+++...+.+++++||+|||||+||. +.++.++
T Consensus 46 ~Lt~eeE~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~-~~si~~f 124 (305)
T TIGR00569 46 FLTPEEELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEF-NVSIDQF 124 (305)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhcccc-CcCHHHH
Confidence 4565 677788899999999999 99999999999999999999999999999999999999999999 6678888
Q ss_pred HHhhcCC--CCHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhC-------cchHHHHHHHHHHHHHhcchhccCCC
Q 026635 80 ILISDKA--YTRKEVLEMESLMLNTLQFNMSVPTPYVFIQRFLKAAQ-------SDKKLQLLSFFLIELSLVEYEMLKFT 150 (235)
Q Consensus 80 ~~~~~~~--~~~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~~~~~~-------~~~~~~~~a~~ll~~~l~~~~~~~~~ 150 (235)
+...... ..+++|+++|..||+.|+|++.+++|+.++..|+..+. ..+.+...++.+++.++.+..++.|+
T Consensus 125 v~~~~~~~~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~ 204 (305)
T TIGR00569 125 VGNLKETPLKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYT 204 (305)
T ss_pred HhhccCCchhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCC
Confidence 8755443 35699999999999999999999999999999885432 23456778888888888888899999
Q ss_pred HHHHHHHHHHHHHHHhc
Q 026635 151 PSLLAAAAIYAAQCTIY 167 (235)
Q Consensus 151 ps~iA~a~l~la~~~~~ 167 (235)
|++||+|||++|...++
T Consensus 205 Ps~IAlAAI~lA~~~~~ 221 (305)
T TIGR00569 205 PSQIALAAILHTASRAG 221 (305)
T ss_pred HHHHHHHHHHHHHHHhC
Confidence 99999999999988776
No 7
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.93 E-value=7.3e-25 Score=184.29 Aligned_cols=194 Identities=19% Similarity=0.281 Sum_probs=168.0
Q ss_pred cHHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcCCC
Q 026635 8 NEKMRAILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDKAY 87 (235)
Q Consensus 8 ~~~~R~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~~~ 87 (235)
....|...+.||.+++.+++++..|+.+|+.||+||+...++...+...+|++|+|||+|+||. +.+++|++..+...+
T Consensus 35 E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEet-p~kl~dIi~~s~~~~ 113 (323)
T KOG0834|consen 35 ELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEET-PRKLEDIIKVSYRYL 113 (323)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccC-cccHHHHHHHHHHHc
Confidence 3467999999999999999999999999999999999999999999999999999999999999 999999988775544
Q ss_pred C-------------HHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCcchH----HHHHHHHHHHHHhcchhccCCC
Q 026635 88 T-------------RKEVLEMESLMLNTLQFNMSVPTPYVFIQRFLKAAQSDKK----LQLLSFFLIELSLVEYEMLKFT 150 (235)
Q Consensus 88 ~-------------~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~~~~~~~~~~----~~~~a~~ll~~~l~~~~~~~~~ 150 (235)
+ ++.|...|..+|++|+||+++-+|+.|+-.++..+..+.. ....|+.++..++....+++|+
T Consensus 114 ~~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~ 193 (323)
T KOG0834|consen 114 NPKDLELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYS 193 (323)
T ss_pred CcccccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeec
Confidence 4 4779999999999999999999999999999999987664 8899999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcCC-CCCchh-hhhhcC--CCHHHHHHHHHHHHHHHhhcC
Q 026635 151 PSLLAAAAIYAAQCTIYGF-KQWSKT-CQWHSG--YSEDQLLECATLMIGFHQKAA 202 (235)
Q Consensus 151 ps~iA~a~l~la~~~~~~~-~~w~~~-l~~~t~--~~~~~i~~~~~~i~~~~~~~~ 202 (235)
|..||+|||++|....+.. +.+... .-...+ ++.+.+.+....+++++.+..
T Consensus 194 p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y~~~~ 249 (323)
T KOG0834|consen 194 PHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHEFLDLYEQTP 249 (323)
T ss_pred CcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHHHHHHHhhcc
Confidence 9999999999998765521 111111 122234 899999999999999996543
No 8
>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=99.92 E-value=1.4e-24 Score=161.79 Aligned_cols=107 Identities=48% Similarity=0.785 Sum_probs=97.3
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHH
Q 026635 2 TQQFDINEKMRAILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLIL 81 (235)
Q Consensus 2 ~~q~~i~~~~R~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~ 81 (235)
++|+++++.+|..+++||.+++..+++++.|+++|+.|||||+...++.+.+++++|++|++||+|++|..+|.+.+++.
T Consensus 21 ~~~~~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~ 100 (127)
T PF00134_consen 21 EQQPEITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIR 100 (127)
T ss_dssp TGTSSHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHH
T ss_pred ccChhcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHH
Confidence 56778999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCCCHHHHHHHHHHHHHHcCcccc
Q 026635 82 ISDKAYTRKEVLEMESLMLNTLQFNMS 108 (235)
Q Consensus 82 ~~~~~~~~~~i~~~E~~IL~~L~f~l~ 108 (235)
.+++.++++++.+||+.||+.|+|+++
T Consensus 101 ~~~~~~~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 101 ISDNTFTKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp HTTTSSHHHHHHHHHHHHHHHTTT---
T ss_pred HHcCCCCHHHHHHHHHHHHHHCCCCcC
Confidence 999999999999999999999999985
No 9
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.90 E-value=1.9e-22 Score=165.80 Aligned_cols=192 Identities=21% Similarity=0.263 Sum_probs=168.7
Q ss_pred cHHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcC--
Q 026635 8 NEKMRAILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDK-- 85 (235)
Q Consensus 8 ~~~~R~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~-- 85 (235)
..+.|..-++||.+.|.-++|+..+..++..+|.||+...++.+.++..++.+|++||+|+||. |..+++++.+.+.
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 4567889999999999999999999999999999999999999999999999999999999998 8888888765431
Q ss_pred ------CCC-----------HHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCcch--HHHHHHHHHHHHHhcchhc
Q 026635 86 ------AYT-----------RKEVLEMESLMLNTLQFNMSVPTPYVFIQRFLKAAQSDK--KLQLLSFFLIELSLVEYEM 146 (235)
Q Consensus 86 ------~~~-----------~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~~~~~~~~~--~~~~~a~~ll~~~l~~~~~ 146 (235)
.+. +.+++++|..||+.|+|++++.+|+.++-.|++-++... ++.+.++-+++.++-..-|
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 111 456889999999999999999999999999999988665 4588999999999999999
Q ss_pred cCCCHHHHHHHHHHHHHHHhcCCCCCchhhhhhcCCCHHHHHHHHHHHHHHHhh
Q 026635 147 LKFTPSLLAAAAIYAAQCTIYGFKQWSKTCQWHSGYSEDQLLECATLMIGFHQK 200 (235)
Q Consensus 147 ~~~~ps~iA~a~l~la~~~~~~~~~w~~~l~~~t~~~~~~i~~~~~~i~~~~~~ 200 (235)
..|+|+.|||||+++|.+.++..-+..+.+-.+.+.++++|.+.+..+..++..
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 999999999999999988887433334455566799999999999999999887
No 10
>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=99.90 E-value=1.5e-23 Score=154.16 Aligned_cols=118 Identities=37% Similarity=0.700 Sum_probs=106.2
Q ss_pred CChHHHHHHHHHHhCcchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHHHHHhcCCCCCchhhhhhcCCCHHHHHH
Q 026635 110 PTPYVFIQRFLKAAQSDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAAQCTIYGFKQWSKTCQWHSGYSEDQLLE 189 (235)
Q Consensus 110 ~tp~~fl~~~~~~~~~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la~~~~~~~~~w~~~l~~~t~~~~~~i~~ 189 (235)
|||++|+++|++..+.+.....++.+++++++.+..|++|+||+||+||+++|+..++..+.|...+...+|++.+++.+
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 79999999997777777889999999999999999999999999999999999999887689999999999999999999
Q ss_pred HHHHHHHHHhhcCCCChhHHHHhhCCCCCCccccCCCc
Q 026635 190 CATLMIGFHQKAATGKLTGVHRKYCTSKFGYISKSEPA 227 (235)
Q Consensus 190 ~~~~i~~~~~~~~~~~~~~i~~ky~~~~~~~vs~~~~~ 227 (235)
|++.|.+++.+....+.+++++||++.+|++||.++||
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 99999999998777788999999999999999999988
No 11
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.89 E-value=9e-23 Score=160.32 Aligned_cols=187 Identities=20% Similarity=0.295 Sum_probs=158.6
Q ss_pred HHHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhh---------
Q 026635 13 AILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILIS--------- 83 (235)
Q Consensus 13 ~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~--------- 83 (235)
--.-+.|..+++++++...++.+|+.||.||+.+.++..-++.++|.||+++|||+||.-...++-++..+
T Consensus 42 i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~ 121 (264)
T KOG0794|consen 42 IFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSY 121 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhccc
Confidence 34567788999999999999999999999999999999999999999999999999998434444443221
Q ss_pred ---cCCCCHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCc-chHHHHHHHHHHHHHhcchhccCCCHHHHHHHHH
Q 026635 84 ---DKAYTRKEVLEMESLMLNTLQFNMSVPTPYVFIQRFLKAAQS-DKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAI 159 (235)
Q Consensus 84 ---~~~~~~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~~~~~~~-~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l 159 (235)
...+..++|..+|..+|+.|++.+-+.+|+.=+..+++..+. +.+..++++.+++.++...-.+-|+|..||.||+
T Consensus 122 ~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl 201 (264)
T KOG0794|consen 122 WPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACL 201 (264)
T ss_pred chhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHH
Confidence 124567899999999999999999999999999999999887 6669999999999999999999999999999999
Q ss_pred HHHHHHhcCC--CCCchhhhhhcCCCHHHHHHHHHHHHHHHhhcCC
Q 026635 160 YAAQCTIYGF--KQWSKTCQWHSGYSEDQLLECATLMIGFHQKAAT 203 (235)
Q Consensus 160 ~la~~~~~~~--~~w~~~l~~~t~~~~~~i~~~~~~i~~~~~~~~~ 203 (235)
++|+...+.. ..|... ...+.+.+.+|++.+++++..-..
T Consensus 202 ~Ia~~~~~k~~~~~w~~e----l~vD~ekV~~~v~~I~~lYe~wk~ 243 (264)
T KOG0794|consen 202 YIACVIDEKDIPKAWFAE----LSVDMEKVKDIVQEILKLYELWKI 243 (264)
T ss_pred HHHHhhcCCChHHHHHHH----HhccHHHHHHHHHHHHHHHHHHhh
Confidence 9998665432 234444 478999999999999999876543
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=99.85 E-value=2.7e-20 Score=153.18 Aligned_cols=165 Identities=22% Similarity=0.324 Sum_probs=141.7
Q ss_pred cHHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhc---
Q 026635 8 NEKMRAILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISD--- 84 (235)
Q Consensus 8 ~~~~R~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~--- 84 (235)
+...|..-..|+..+|.+++++..++.+|+.+|+||+.++++.+..++-++.||+++|||.||+ +..+.-.....+
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 3456777779999999999999999999999999999999999999999999999999999996 333333333332
Q ss_pred ---CCCCHHHHHHHHHHHHHHcCccccCCChHHHHHHHHHHhCcchH--HHHHHHHHHHHHhcchhccCCCHHHHHHHHH
Q 026635 85 ---KAYTRKEVLEMESLMLNTLQFNMSVPTPYVFIQRFLKAAQSDKK--LQLLSFFLIELSLVEYEMLKFTPSLLAAAAI 159 (235)
Q Consensus 85 ---~~~~~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~~~~~~~~~~--~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l 159 (235)
..-+++.|..+|..+|+.|+||+.+++|+.++..|+..+..... ..++|+-++..++...-++.|+|..||+||+
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 13468999999999999999999999999999999988866554 8999999999999999999999999999999
Q ss_pred HHHHHHhcCCCCCch
Q 026635 160 YAAQCTIYGFKQWSK 174 (235)
Q Consensus 160 ~la~~~~~~~~~w~~ 174 (235)
..|...++ .+.|..
T Consensus 200 ~ia~~~~~-~~~~~~ 213 (297)
T COG5333 200 LIACEVLG-MPIIKL 213 (297)
T ss_pred HHHHHhcC-Cccchh
Confidence 99987654 345543
No 13
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.83 E-value=2.1e-18 Score=146.90 Aligned_cols=182 Identities=16% Similarity=0.170 Sum_probs=164.9
Q ss_pred HHHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcCCCCHHHH
Q 026635 13 AILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDKAYTRKEV 92 (235)
Q Consensus 13 ~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~~~~~~~i 92 (235)
.....-|.++|..++++..+...|..+|++++....+.+.....++++|+|+|||.++. |.+++++..+++ .+.++|
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 34566788999999999999999999999999998899999999999999999998877 899999988875 589999
Q ss_pred HHHHHHHHHHcCccccCCChHHHHHHHHHHhCcchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHHHHHhcCCCCC
Q 026635 93 LEMESLMLNTLQFNMSVPTPYVFIQRFLKAAQSDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAAQCTIYGFKQW 172 (235)
Q Consensus 93 ~~~E~~IL~~L~f~l~~~tp~~fl~~~~~~~~~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la~~~~~~~~~w 172 (235)
.+.++.|++.|++++...+|.+|+.+|...++.+.++...|..+++.+....-..+.+|..||+||||+|.... +.+.-
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 GRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLL-GERRT 278 (310)
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHh-CCCCC
Confidence 99999999999999999999999999999999999999999999998876666689999999999999997655 44566
Q ss_pred chhhhhhcCCCHHHHHHHHHHHHHHH
Q 026635 173 SKTCQWHSGYSEDQLLECATLMIGFH 198 (235)
Q Consensus 173 ~~~l~~~t~~~~~~i~~~~~~i~~~~ 198 (235)
...+..++|+++.+|...++.|.+.+
T Consensus 279 ~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 279 QREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 77888999999999999999999864
No 14
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.70 E-value=1.3e-15 Score=124.38 Aligned_cols=182 Identities=16% Similarity=0.132 Sum_probs=162.7
Q ss_pred HHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcCCCCHHHHHH
Q 026635 15 LIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDKAYTRKEVLE 94 (235)
Q Consensus 15 ~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~~~~~~~i~~ 94 (235)
...-|..+++.++|+......|-.+|.++-..+...+.+.+-++++|++|||+-++. |++++++..+++ .+++||.+
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 AFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDV-PRTFKEISAVAN--VSKKEIGR 183 (308)
T ss_pred HHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCC-CchHHHHHHHHc--CCHHHHHH
Confidence 345577889999999999999999999999888899999999999999999997777 999999999987 79999999
Q ss_pred HHHHHHHHcCccccCCC--hHHHHHHHHHHhCcchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHHHHHhcCCCCC
Q 026635 95 MESLMLNTLQFNMSVPT--PYVFIQRFLKAAQSDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAAQCTIYGFKQW 172 (235)
Q Consensus 95 ~E~~IL~~L~f~l~~~t--p~~fl~~~~~~~~~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la~~~~~~~~~w 172 (235)
.-..|++.|+-.+...+ ..+|+.+|+..++.+++....|.++.+.+..-....+-+|-.||||+||++... .+...-
T Consensus 184 ~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisql-s~~kkt 262 (308)
T KOG1597|consen 184 CVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQL-SDEKKT 262 (308)
T ss_pred HHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHh-ccCccc
Confidence 99999999987766555 899999999999999999999999999887666677899999999999999764 457778
Q ss_pred chhhhhhcCCCHHHHHHHHHHHHHHHhh
Q 026635 173 SKTCQWHSGYSEDQLLECATLMIGFHQK 200 (235)
Q Consensus 173 ~~~l~~~t~~~~~~i~~~~~~i~~~~~~ 200 (235)
...+..++|+.+..|+..|+.|+.....
T Consensus 263 ~keI~~vtgVaE~TIr~sYK~Lyp~~~~ 290 (308)
T KOG1597|consen 263 QKEIGEVTGVAEVTIRNSYKDLYPHADK 290 (308)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHhhchhh
Confidence 8899999999999999999999876543
No 15
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.65 E-value=2.7e-14 Score=119.22 Aligned_cols=181 Identities=15% Similarity=0.175 Sum_probs=166.9
Q ss_pred HHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcCCCCHHHHH
Q 026635 14 ILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDKAYTRKEVL 93 (235)
Q Consensus 14 ~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~~~~~~~i~ 93 (235)
...+.+-.++..++++..+...|..++-+.+.+.-..+...+-++++|+++||+.... |.++.++....+ .++.+|.
T Consensus 99 ~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~-prtl~eIa~a~~--V~~kei~ 175 (285)
T COG1405 99 TALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGV-PRTLDEIAKALG--VSKKEIG 175 (285)
T ss_pred HHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCC-CccHHHHHHHHC--CCHHHHH
Confidence 5677888899999999999999999999999999999999999999999999999888 999999998877 6789999
Q ss_pred HHHHHHHHHcCccccCCChHHHHHHHHHHhCcchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHHHHHhcCCCCCc
Q 026635 94 EMESLMLNTLQFNMSVPTPYVFIQRFLKAAQSDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAAQCTIYGFKQWS 173 (235)
Q Consensus 94 ~~E~~IL~~L~f~l~~~tp~~fl~~~~~~~~~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la~~~~~~~~~w~ 173 (235)
++.+.+.+.|+=.+.+..|.+|+.+|.+.++.+.+....|..+++.+.....-.+-+|+.+|+||+|+|.... +...-+
T Consensus 176 rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~-~~~~tq 254 (285)
T COG1405 176 RTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLL-GERRTQ 254 (285)
T ss_pred HHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHh-CCchHH
Confidence 9999999999999999999999999999999999999999999999998888889999999999999997655 456667
Q ss_pred hhhhhhcCCCHHHHHHHHHHHHHHH
Q 026635 174 KTCQWHSGYSEDQLLECATLMIGFH 198 (235)
Q Consensus 174 ~~l~~~t~~~~~~i~~~~~~i~~~~ 198 (235)
..+..++|+++..|++-++++.+..
T Consensus 255 ~eva~v~~vtevTIrnrykel~~~~ 279 (285)
T COG1405 255 KEVAKVAGVTEVTIRNRYKELADAL 279 (285)
T ss_pred HHHHHHhCCeeeHHHHHHHHHHHhh
Confidence 8888999999999999998887754
No 16
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=99.60 E-value=5.9e-15 Score=101.87 Aligned_cols=87 Identities=40% Similarity=0.600 Sum_probs=81.3
Q ss_pred HHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcCCCCHHH
Q 026635 12 RAILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDKAYTRKE 91 (235)
Q Consensus 12 R~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~~~~~~~ 91 (235)
|...++||.+++..+++++++.++|+.++|||+....+.+.+++++|++|++||+|+++. ++..+++...++.. +.++
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 678899999999999999999999999999999999999999999999999999999999 89999998887554 8999
Q ss_pred HHHHHHHHH
Q 026635 92 VLEMESLML 100 (235)
Q Consensus 92 i~~~E~~IL 100 (235)
|.++|..|+
T Consensus 80 i~~~e~~il 88 (88)
T cd00043 80 ILRMEKLLL 88 (88)
T ss_pred HHHHHHHhC
Confidence 999999874
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=99.57 E-value=2e-14 Score=117.76 Aligned_cols=144 Identities=28% Similarity=0.401 Sum_probs=117.6
Q ss_pred HHHHHHHHc--CCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhc--CCCCHHHHH
Q 026635 18 WLIEVHDKF--DLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISD--KAYTRKEVL 93 (235)
Q Consensus 18 wm~~~~~~~--~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~--~~~~~~~i~ 93 (235)
-+.+.+..+ .++..++.+|+.+|.||+-.+++...+...+.+||+|+|||++|. ..++.+|+.-.. ..-+.+.++
T Consensus 62 ~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef-~ISieqFvkn~~~~~~k~~e~vL 140 (325)
T KOG2496|consen 62 SLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEF-YISIEQFVKNMNGRKWKTHEIVL 140 (325)
T ss_pred HHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhh-eecHHHHHhhccCcccccHHHHH
Confidence 344455555 579999999999999999999999999999999999999999998 777888877554 234689999
Q ss_pred HHHHHHHHHcCccccCCChHHHHHHHHHHhCc-------chHH--HHHHHHHHHHHhcchhccCCCHHHHHHHHHHHH
Q 026635 94 EMESLMLNTLQFNMSVPTPYVFIQRFLKAAQS-------DKKL--QLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAA 162 (235)
Q Consensus 94 ~~E~~IL~~L~f~l~~~tp~~fl~~~~~~~~~-------~~~~--~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la 162 (235)
..|..+++.|+|++.+.+|+.-++.|+..+.. .+.. ......+++.++....++-|+||+||.|||..|
T Consensus 141 k~E~~llqsL~f~L~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a 218 (325)
T KOG2496|consen 141 KYEFLLLQSLKFSLTVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHA 218 (325)
T ss_pred hchHHHHHhhhhhheecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHH
Confidence 99999999999999999999999998866532 1111 122346677788888888899999999999555
No 18
>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=99.54 E-value=3.1e-14 Score=97.24 Aligned_cols=83 Identities=37% Similarity=0.598 Sum_probs=75.9
Q ss_pred HHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcCCCCHHHHHHHH
Q 026635 17 DWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDKAYTRKEVLEME 96 (235)
Q Consensus 17 ~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~~~~~~~i~~~E 96 (235)
+||.+++..+++++++.++|+.++||++...++.+.+.+++|++|+++|+|+++.. ++..++...++. ++.+++.++|
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 59999999999999999999999999999888888999999999999999999984 677888887765 7999999999
Q ss_pred HHHHH
Q 026635 97 SLMLN 101 (235)
Q Consensus 97 ~~IL~ 101 (235)
+.|++
T Consensus 79 ~~il~ 83 (83)
T smart00385 79 KLLLE 83 (83)
T ss_pred HHHhC
Confidence 99874
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=99.00 E-value=3.2e-09 Score=72.03 Aligned_cols=81 Identities=35% Similarity=0.543 Sum_probs=74.3
Q ss_pred HHHHHHHHHhCcchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHHHHHhcCCCCCchhhhhhcCC-CHHHHHHHHH
Q 026635 114 VFIQRFLKAAQSDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAAQCTIYGFKQWSKTCQWHSGY-SEDQLLECAT 192 (235)
Q Consensus 114 ~fl~~~~~~~~~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la~~~~~~~~~w~~~l~~~t~~-~~~~i~~~~~ 192 (235)
+|+..+...++.+.+...+|.++++.++.+..+.+++|+.+|+||+++|.+..+. +.|...+..++|+ +.+++.++.+
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~-~~~~~~~~~~~~~~~~~~i~~~~~ 79 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEI-PPWTKELVHYTGYFTEEEILRMEK 79 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcC-CCCchhHhHhhCCCCHHHHHHHHH
Confidence 4788999999999999999999999999988999999999999999999887765 5899999999999 9999999998
Q ss_pred HHH
Q 026635 193 LMI 195 (235)
Q Consensus 193 ~i~ 195 (235)
.|+
T Consensus 80 ~il 82 (83)
T smart00385 80 LLL 82 (83)
T ss_pred HHh
Confidence 875
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=98.96 E-value=7.1e-09 Score=71.06 Aligned_cols=85 Identities=33% Similarity=0.484 Sum_probs=78.9
Q ss_pred CCChHHHHHHHHHHhCcchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHHHHHhcCCCCCchhhhhhcCC-CHHHH
Q 026635 109 VPTPYVFIQRFLKAAQSDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAAQCTIYGFKQWSKTCQWHSGY-SEDQL 187 (235)
Q Consensus 109 ~~tp~~fl~~~~~~~~~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la~~~~~~~~~w~~~l~~~t~~-~~~~i 187 (235)
.+++.+|+..+...++.+.+....|.++++.++....+..++|+.+|+||+++|.+..+. +.|...+...+++ +.++|
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 578999999999999999999999999999999999999999999999999999886655 8999999999999 99999
Q ss_pred HHHHHHH
Q 026635 188 LECATLM 194 (235)
Q Consensus 188 ~~~~~~i 194 (235)
.++...+
T Consensus 81 ~~~e~~i 87 (88)
T cd00043 81 LRMEKLL 87 (88)
T ss_pred HHHHHHh
Confidence 9988765
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=98.76 E-value=8.9e-08 Score=73.25 Aligned_cols=92 Identities=21% Similarity=0.296 Sum_probs=71.9
Q ss_pred HHHHHHHHHHHHcCCChhHHHHHHHHHHHhhc---cc--cccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcCCCC
Q 026635 14 ILIDWLIEVHDKFDLMSETLFLSINLIDRFLS---QQ--QVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDKAYT 88 (235)
Q Consensus 14 ~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~---~~--~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~~~~ 88 (235)
.+.+|+.++....+++.+++-.|..|+||+.. .. .+...+.+-+.++|+.+|+|+-+....+-+....+++ ++
T Consensus 53 ~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~g--is 130 (149)
T PF08613_consen 53 SIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGG--IS 130 (149)
T ss_dssp -HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHT--S-
T ss_pred cHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcC--CC
Confidence 47889999999999999999999999999988 22 3667778899999999999997766777778877765 68
Q ss_pred HHHHHHHHHHHHHHcCccc
Q 026635 89 RKEVLEMESLMLNTLQFNM 107 (235)
Q Consensus 89 ~~~i~~~E~~IL~~L~f~l 107 (235)
.+++.+||+..|..|+|++
T Consensus 131 ~~eln~lE~~fL~~l~~~L 149 (149)
T PF08613_consen 131 LKELNELEREFLKLLDYNL 149 (149)
T ss_dssp HHHHHHHHHHHHHHTTT--
T ss_pred HHHHHHHHHHHHHHCCCcC
Confidence 9999999999999999986
No 22
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.40 E-value=3e-06 Score=75.32 Aligned_cols=174 Identities=13% Similarity=0.078 Sum_probs=136.1
Q ss_pred HHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcCCCCHHHHHHHHH
Q 026635 18 WLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDKAYTRKEVLEMES 97 (235)
Q Consensus 18 wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~~~~~~~i~~~E~ 97 (235)
-|.+++..+++.. ....|.++|.-.+..+-.++...+.+.++|+|++|+.+.. ...+-|+..+. ..+.-++-.+-+
T Consensus 73 ~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t-~hlliDfS~~L--qv~Vy~LG~~~l 148 (521)
T KOG1598|consen 73 LIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKT-DHLLIDFSSYL--QVSVYDLGSNFL 148 (521)
T ss_pred HHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCC-ceEEEEeccce--EEehhhhhHHHH
Confidence 6889999999998 9999999999999998899999999999999999998776 33333333322 256777888888
Q ss_pred HHHHHcCcc---ccCCChHHHHHHHHHHhCc---chHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHHHHHhcCCCC
Q 026635 98 LMLNTLQFN---MSVPTPYVFIQRFLKAAQS---DKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAAQCTIYGFKQ 171 (235)
Q Consensus 98 ~IL~~L~f~---l~~~tp~~fl~~~~~~~~~---~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la~~~~~~~~~ 171 (235)
.+-..|.-+ +....|.-|+.+|...+.. ++++...|..++.-...|....+-+|+.|+.|||++|.+..+ ...
T Consensus 149 ~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~-~~r 227 (521)
T KOG1598|consen 149 EVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHG-FRR 227 (521)
T ss_pred HHHHHhccccccccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcC-ccc
Confidence 888888877 6778899999999887743 345677788888888889999999999999999999976544 344
Q ss_pred CchhhhhhcCCCHHHHHHHHHHHHH
Q 026635 172 WSKTCQWHSGYSEDQLLECATLMIG 196 (235)
Q Consensus 172 w~~~l~~~t~~~~~~i~~~~~~i~~ 196 (235)
-...+..+..+.+..|..-+.++.+
T Consensus 228 si~dIv~vvhV~e~Tl~kRl~Ef~~ 252 (521)
T KOG1598|consen 228 TIGDIAKVVHVCESTLSKRLKEFSD 252 (521)
T ss_pred cHHHHHHHHHHhHHHHHHHHHHHhc
Confidence 4555555666666666666655544
No 23
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=98.38 E-value=9e-07 Score=75.51 Aligned_cols=99 Identities=17% Similarity=0.291 Sum_probs=88.7
Q ss_pred HHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcC--CCCH
Q 026635 12 RAILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDK--AYTR 89 (235)
Q Consensus 12 R~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~--~~~~ 89 (235)
-+.+-.-|.++....+++..|+.+|..||.....+..+++.+-.+.|.+|+.+|+|+.+.+-..++.++.-.+. .+++
T Consensus 382 irSlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nr 461 (497)
T KOG4164|consen 382 IRSLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNR 461 (497)
T ss_pred HHHHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccH
Confidence 34556678899999999999999999999999999999999999999999999999999888888888875544 5689
Q ss_pred HHHHHHHHHHHHHcCccccCC
Q 026635 90 KEVLEMESLMLNTLQFNMSVP 110 (235)
Q Consensus 90 ~~i~~~E~~IL~~L~f~l~~~ 110 (235)
.|++..|.-||-+|+|.++.|
T Consensus 462 rdLia~Ef~VlvaLefaL~~~ 482 (497)
T KOG4164|consen 462 RDLIAFEFPVLVALEFALHLP 482 (497)
T ss_pred HhhhhhhhhHHHhhhhhccCC
Confidence 999999999999999999865
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=98.14 E-value=1.2e-05 Score=53.44 Aligned_cols=65 Identities=9% Similarity=0.176 Sum_probs=55.3
Q ss_pred HHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhc
Q 026635 19 LIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISD 84 (235)
Q Consensus 19 m~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~ 84 (235)
|-++|..++|+..+...|..++++.....-..+.+...++++|+++||+.++. +.+++++...++
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 46789999999999999999999998888788888999999999999998876 888899877664
No 25
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=97.79 E-value=0.00025 Score=47.01 Aligned_cols=71 Identities=20% Similarity=0.105 Sum_probs=57.5
Q ss_pred HHHHHHHhCcchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHHHHHhcCCCCCchhhhhhcCCCHHHH
Q 026635 116 IQRFLKAAQSDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAAQCTIYGFKQWSKTCQWHSGYSEDQL 187 (235)
Q Consensus 116 l~~~~~~~~~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la~~~~~~~~~w~~~l~~~t~~~~~~i 187 (235)
++++...++.++.+...|..+...+......-+-+|..+|+||+|+|.+.. +.+.-...+...+|+++.+|
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~-~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLN-GVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHT-TSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHc-CCCcCHHHHHHHhCCCCCcC
Confidence 568899999999999999999999887777788999999999999997654 55667778888888888765
No 26
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=97.47 E-value=0.0013 Score=56.39 Aligned_cols=90 Identities=12% Similarity=0.100 Sum_probs=77.9
Q ss_pred HHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcCCCCHHHHHH
Q 026635 15 LIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDKAYTRKEVLE 94 (235)
Q Consensus 15 ~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~~~~~~~i~~ 94 (235)
-.++|..+|..++++.++...|..++.+.....-..+.+..-+|++|+|+||+..+. +.+.+++..+++ .+...|.+
T Consensus 219 p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~-~~t~keIa~v~~--Vs~~tI~~ 295 (310)
T PRK00423 219 PIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGE-RRTQREVAEVAG--VTEVTVRN 295 (310)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHcC--CCHHHHHH
Confidence 358999999999999999999999999988776678888999999999999998876 678899887764 67888999
Q ss_pred HHHHHHHHcCccc
Q 026635 95 MESLMLNTLQFNM 107 (235)
Q Consensus 95 ~E~~IL~~L~f~l 107 (235)
.-+.+.+.|+..+
T Consensus 296 ~ykel~~~l~~~~ 308 (310)
T PRK00423 296 RYKELAEKLDIKI 308 (310)
T ss_pred HHHHHHHHhCccc
Confidence 8889988877644
No 27
>KOG1674 consensus Cyclin [General function prediction only]
Probab=96.30 E-value=0.024 Score=46.04 Aligned_cols=94 Identities=17% Similarity=0.238 Sum_probs=73.6
Q ss_pred HHHHHHHHHHHcCCChhHHHHHHHHHHHhhcccc---------ccchh-HHHHHHHHHHHhhhccccccccHhhHHHhhc
Q 026635 15 LIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQ---------VVRKK-LQLVGLVAMLLACKYEEVSVPVVGDLILISD 84 (235)
Q Consensus 15 ~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~---------~~~~~-l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~ 84 (235)
+-+++..+....+.+++++-.|-.||||+....+ ++--+ .+-..++|+.+|+|+.+...-.-.-...+
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 4578888999999999999999999999998622 33334 56678999999999986643333333333
Q ss_pred CCCCHHHHHHHHHHHHHHcCccccCC
Q 026635 85 KAYTRKEVLEMESLMLNTLQFNMSVP 110 (235)
Q Consensus 85 ~~~~~~~i~~~E~~IL~~L~f~l~~~ 110 (235)
+..+.+++-.+|...+..++|++.++
T Consensus 156 ggl~~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 156 GGLTTDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred CCCChHhhhhhhHHHHhhCCeEEEec
Confidence 35678999999999999999999875
No 28
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=95.75 E-value=0.077 Score=44.85 Aligned_cols=89 Identities=12% Similarity=0.073 Sum_probs=70.6
Q ss_pred HHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcCCCCHHHHH
Q 026635 14 ILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDKAYTRKEVL 93 (235)
Q Consensus 14 ~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~~~~~~~i~ 93 (235)
.-.+++-..|..|+++.++.-.|..+++.........+....-+|++|+++|+++... ..+-+++..+++- |...|.
T Consensus 193 ~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~-~~tq~eva~v~~v--tevTIr 269 (285)
T COG1405 193 DPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGE-RRTQKEVAKVAGV--TEVTIR 269 (285)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCC-chHHHHHHHHhCC--eeeHHH
Confidence 3467889999999999999999999999998888888899999999999999999885 6666777666643 344455
Q ss_pred HHHHHHHHHcCc
Q 026635 94 EMESLMLNTLQF 105 (235)
Q Consensus 94 ~~E~~IL~~L~f 105 (235)
+--.++...++-
T Consensus 270 nrykel~~~~~i 281 (285)
T COG1405 270 NRYKELADALDI 281 (285)
T ss_pred HHHHHHHHhhcc
Confidence 555555555543
No 29
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=95.71 E-value=0.13 Score=37.41 Aligned_cols=86 Identities=13% Similarity=0.097 Sum_probs=63.6
Q ss_pred HHHHHHHHHHhCcchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHHHHHhcCCCCCchhhhhhc--CCCHHHHHHH
Q 026635 113 YVFIQRFLKAAQSDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAAQCTIYGFKQWSKTCQWHS--GYSEDQLLEC 190 (235)
Q Consensus 113 ~~fl~~~~~~~~~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la~~~~~~~~~w~~~l~~~t--~~~~~~i~~~ 190 (235)
.+|+.......+.+......|..+++.-+.........+..+|+||+++|.+......++...+...+ .++.+++.+.
T Consensus 35 ~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~ 114 (127)
T PF00134_consen 35 IDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILEM 114 (127)
T ss_dssp HHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHH
T ss_pred HHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHHH
Confidence 44666677777888888889999999888777788999999999999999987766555555555554 4677888877
Q ss_pred HHHHHHHH
Q 026635 191 ATLMIGFH 198 (235)
Q Consensus 191 ~~~i~~~~ 198 (235)
-..+++.+
T Consensus 115 E~~iL~~L 122 (127)
T PF00134_consen 115 EREILSAL 122 (127)
T ss_dssp HHHHHHHT
T ss_pred HHHHHHHC
Confidence 77776653
No 30
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=94.29 E-value=0.085 Score=44.40 Aligned_cols=84 Identities=19% Similarity=0.242 Sum_probs=59.0
Q ss_pred HHHHHHHhhcccccc--chhHHHHHHHHHHHhhhccccccccHhhHHHhhcCCCCHHHHHHHHHHHHHHcCccccCCChH
Q 026635 36 SINLIDRFLSQQQVV--RKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDKAYTRKEVLEMESLMLNTLQFNMSVPTPY 113 (235)
Q Consensus 36 Av~l~Dr~l~~~~~~--~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~~~~~~~i~~~E~~IL~~L~f~l~~~tp~ 113 (235)
...|++|-+.-.... +.+...+....+++|+|+-......--+.+.++.. .|.+|+..+|+.+|+.|+|++++|..
T Consensus 214 tL~~~erl~~~~e~~~~p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlKd-~tveDmNe~ERqfLelLqfNinvp~s- 291 (343)
T KOG1675|consen 214 TLVYAERLLWLAERDPCPRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILKD-QSVDDMNALERQFLELLQFNINVPSS- 291 (343)
T ss_pred HHHhhHhhhhHhhcCCCcchhhhhhhhhheehhhhhhhhhcccHHHHHHHhh-ccHhhHHHHHHHHHHHHhhccCccHH-
Confidence 346777776655444 66677777778999999855433333556666543 47899999999999999999999853
Q ss_pred HHHHHHHH
Q 026635 114 VFIQRFLK 121 (235)
Q Consensus 114 ~fl~~~~~ 121 (235)
.|...|..
T Consensus 292 vYAKyYfd 299 (343)
T KOG1675|consen 292 EYAKYYFD 299 (343)
T ss_pred HHHHHHHH
Confidence 34444443
No 31
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=94.15 E-value=0.27 Score=35.10 Aligned_cols=87 Identities=20% Similarity=0.193 Sum_probs=62.0
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcCCCCHHHHHHH
Q 026635 16 IDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDKAYTRKEVLEM 95 (235)
Q Consensus 16 v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~~~~~~~i~~~ 95 (235)
.+|+.......+.+.++..+|-.+++..+....+-....-.+|++|+++|.+..+..++.-..+...+ .++.+++..+
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 45666665545556778889999999888887888888899999999999998654233334455555 3478888887
Q ss_pred HHHHHHHcC
Q 026635 96 ESLMLNTLQ 104 (235)
Q Consensus 96 E~~IL~~L~ 104 (235)
=..|.+.+.
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 777766654
No 32
>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=93.76 E-value=1.2 Score=33.79 Aligned_cols=91 Identities=15% Similarity=0.066 Sum_probs=64.6
Q ss_pred cCCChHHHHHHHHHHhCcchHHHHHHHHHHHHHhc---chh--ccCCCHHHHHHHHHHHHHHHhcCCCCCchhhhhhcCC
Q 026635 108 SVPTPYVFIQRFLKAAQSDKKLQLLSFFLIELSLV---EYE--MLKFTPSLLAAAAIYAAQCTIYGFKQWSKTCQWHSGY 182 (235)
Q Consensus 108 ~~~tp~~fl~~~~~~~~~~~~~~~~a~~ll~~~l~---~~~--~~~~~ps~iA~a~l~la~~~~~~~~~w~~~l~~~t~~ 182 (235)
...+..+|+.++......+....-+|..+++.... ... .-...+.-+-.+|+.+|.+.+.+...+.....+++|+
T Consensus 50 p~i~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gi 129 (149)
T PF08613_consen 50 PSISIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGI 129 (149)
T ss_dssp -SS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS
T ss_pred CCCcHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCC
Confidence 44567789999999888888887777777676554 222 3356677888899999999999988898899999999
Q ss_pred CHHHHHHHHHHHHHHH
Q 026635 183 SEDQLLECATLMIGFH 198 (235)
Q Consensus 183 ~~~~i~~~~~~i~~~~ 198 (235)
+..++...-..++..+
T Consensus 130 s~~eln~lE~~fL~~l 145 (149)
T PF08613_consen 130 SLKELNELEREFLKLL 145 (149)
T ss_dssp -HHHHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHHHHC
Confidence 9999999888877754
No 33
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=90.78 E-value=0.29 Score=42.08 Aligned_cols=75 Identities=15% Similarity=0.110 Sum_probs=54.4
Q ss_pred hHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhH--HHhhcCCCCHHHHHHHHHHHHHHcCc
Q 026635 31 ETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDL--ILISDKAYTRKEVLEMESLMLNTLQF 105 (235)
Q Consensus 31 ~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l--~~~~~~~~~~~~i~~~E~~IL~~L~f 105 (235)
.....|-++....+...-+-....+-+|++|++||+|+.....+...+- ....+...+.+++..+...++....-
T Consensus 171 ~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y~~ 247 (323)
T KOG0834|consen 171 PLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHEFLDLYEQ 247 (323)
T ss_pred cHHHHHHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHHHHHHHhh
Confidence 3666666776666655566677788999999999999977655554444 34455668888888888888877644
No 34
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=89.81 E-value=1.3 Score=37.19 Aligned_cols=84 Identities=4% Similarity=0.007 Sum_probs=65.9
Q ss_pred HHHHHHHHHHHHcCCChhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcCCCCHHHHH
Q 026635 14 ILIDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDKAYTRKEVL 93 (235)
Q Consensus 14 ~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~~~~~~~i~ 93 (235)
..-++|.+.|..|+|+..+...|..+-.++-...-..+...--+|++.+|+++.+.+ ...+.+++..+++- +.-.|.
T Consensus 202 ~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~-~kkt~keI~~vtgV--aE~TIr 278 (308)
T KOG1597|consen 202 STGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSD-EKKTQKEIGEVTGV--AEVTIR 278 (308)
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhcc-CcccHHHHHHHhhh--hHHHHH
Confidence 356899999999999999999999999988777777778888999999999999988 47777888766542 233444
Q ss_pred HHHHHHH
Q 026635 94 EMESLML 100 (235)
Q Consensus 94 ~~E~~IL 100 (235)
..-..++
T Consensus 279 ~sYK~Ly 285 (308)
T KOG1597|consen 279 NSYKDLY 285 (308)
T ss_pred HHHHHHh
Confidence 4444443
No 35
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=88.95 E-value=2.8 Score=35.88 Aligned_cols=53 Identities=8% Similarity=0.139 Sum_probs=40.6
Q ss_pred HHHHHHHHhC--cchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHHHHHhc
Q 026635 115 FIQRFLKAAQ--SDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAAQCTIY 167 (235)
Q Consensus 115 fl~~~~~~~~--~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la~~~~~ 167 (235)
++..+...+. .++.+...|..+..--.....+..|.|-.||++|+++|.+.-.
T Consensus 62 ~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE 116 (305)
T TIGR00569 62 RLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEE 116 (305)
T ss_pred HHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccc
Confidence 4444555556 6677777777777777778888899999999999999986543
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=88.01 E-value=3 Score=31.22 Aligned_cols=69 Identities=19% Similarity=0.205 Sum_probs=52.9
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHHHHHhhcccc--ccchhHHHHHHHHHHHhhhccccccccHhhHHHhhcC
Q 026635 16 IDWLIEVHDKFDLMSETLFLSINLIDRFLSQQQ--VVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILISDK 85 (235)
Q Consensus 16 v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~~~~--~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~ 85 (235)
-.-+.++|..++++++.....-..|+..+.... +...++-.+.++|+++-||+.. ...+.+++......
T Consensus 15 ~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~-~~~sF~~Ii~~Yr~ 85 (135)
T PF01857_consen 15 AVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSK-EELSFKDIIKAYRK 85 (135)
T ss_dssp HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT--S--HHHHHHHHTT
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhc-CCCCHHHHHHHHHh
Confidence 345778999999999988888899999887553 5666788899999999999987 47778888765543
No 37
>PF09241 Herp-Cyclin: Herpesviridae viral cyclin; InterPro: IPR015322 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry represents a domain found in a family of viral cyclins that specifically activate CDK6 of host cells to a very high degree []. This domain adopts a helical structure consisting of five alpha-helices, with one helix surrounded by the others.; PDB: 1XO2_A 1JOW_A 2F2C_A 2EUF_A 1BU2_A.
Probab=77.49 E-value=19 Score=24.28 Aligned_cols=86 Identities=13% Similarity=0.122 Sum_probs=59.8
Q ss_pred hHHHHHHHHHHhCcch----HHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHHHHHhc-CCCCCchhhhh---hcCCC
Q 026635 112 PYVFIQRFLKAAQSDK----KLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAAQCTIY-GFKQWSKTCQW---HSGYS 183 (235)
Q Consensus 112 p~~fl~~~~~~~~~~~----~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la~~~~~-~~~~w~~~l~~---~t~~~ 183 (235)
.-+|+-..++.+..++ ++...+..-+-.++..++..-.+|..|.++.+......-+ ....|..+++. ..+++
T Consensus 4 ~tdflip~c~alkipe~~wpql~e~~s~tickaliqpniall~p~licaggllttiet~ntn~~~wt~yledl~~ilnfs 83 (106)
T PF09241_consen 4 STDFLIPVCHALKIPEDFWPQLFEATSITICKALIQPNIALLPPCLICAGGLLTTIETDNTNCQPWTCYLEDLSCILNFS 83 (106)
T ss_dssp GGGGHHHHHHHTT--GGGHHHHHHHHHHHHHHHTTSGGGGGS-HHHHHHHHHHHHHHTS-TSSSTCHHHHHHHHHHHTCH
T ss_pred hhhhHHHhhhhccCcHHHhHHHHHHHHHHHHHHHcCCCccccCcceeecccceEEEeccCCCCcchhhhHHhhHHHhhcc
Confidence 4567888888887665 4566676667778889999999999999999999876544 34678776654 45666
Q ss_pred HHHHHHHHHHHHHH
Q 026635 184 EDQLLECATLMIGF 197 (235)
Q Consensus 184 ~~~i~~~~~~i~~~ 197 (235)
-..++..-..+.+.
T Consensus 84 tntirt~kdqv~ea 97 (106)
T PF09241_consen 84 TNTIRTVKDQVSEA 97 (106)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred cchhhhHHHHHHHH
Confidence 67766655555443
No 38
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=66.63 E-value=6.1 Score=36.07 Aligned_cols=53 Identities=13% Similarity=0.164 Sum_probs=40.5
Q ss_pred hhHHHHHHHHHHHhhccccccchhHHHHHHHHHHHhhhccccccccHhhHHHhh
Q 026635 30 SETLFLSINLIDRFLSQQQVVRKKLQLVGLVAMLLACKYEEVSVPVVGDLILIS 83 (235)
Q Consensus 30 ~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl~IA~K~ee~~~~~~~~l~~~~ 83 (235)
.++.-+|..++.|.---....+.+.--++.+||+|||+++.. ..++.+++.+.
T Consensus 184 ~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~-~rsi~dIv~vv 236 (521)
T KOG1598|consen 184 EDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGF-RRTIGDIAKVV 236 (521)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCc-cccHHHHHHHH
Confidence 457778888888865544566667778899999999999987 77777776543
No 39
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=65.40 E-value=65 Score=27.88 Aligned_cols=78 Identities=8% Similarity=-0.048 Sum_probs=50.6
Q ss_pred HHHHHHHHhCcchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHHHHHhcCCCCCchhhhhhcCCCHHHHHHHHHHH
Q 026635 115 FIQRFLKAAQSDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAAQCTIYGFKQWSKTCQWHSGYSEDQLLECATLM 194 (235)
Q Consensus 115 fl~~~~~~~~~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la~~~~~~~~~w~~~l~~~t~~~~~~i~~~~~~i 194 (235)
||+.-.-.++.++.....+..|..--.....|..|.--.+|.|||++|.++-.. .-...++..+...|
T Consensus 29 ~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~------------Prr~rdVinVFh~L 96 (367)
T KOG0835|consen 29 LIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEE------------PRRIRDVINVFHYL 96 (367)
T ss_pred HHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccc------------cccHhHHHHHHHHH
Confidence 454444555666665556666666666677788888899999999999875432 12344556666666
Q ss_pred HHHHhhcCCC
Q 026635 195 IGFHQKAATG 204 (235)
Q Consensus 195 ~~~~~~~~~~ 204 (235)
-..+.+...+
T Consensus 97 ~~r~~~~~~~ 106 (367)
T KOG0835|consen 97 EQRRESEAAE 106 (367)
T ss_pred HHHHhccCcc
Confidence 6666554433
No 40
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=65.34 E-value=24 Score=28.95 Aligned_cols=84 Identities=14% Similarity=0.142 Sum_probs=50.1
Q ss_pred HHHHHHHHHhCcchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHHHHHhcCC---------------CCCchhhhh
Q 026635 114 VFIQRFLKAAQSDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYAAQCTIYGF---------------KQWSKTCQW 178 (235)
Q Consensus 114 ~fl~~~~~~~~~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~la~~~~~~~---------------~~w~~~l~~ 178 (235)
.++..+-..+...+++...|.-++.--+.-.++-.+.|-.+|..|+++|++.-... ..|. ....
T Consensus 46 n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~-~~~e 124 (264)
T KOG0794|consen 46 NVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFS-YWPE 124 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcc-cchh
Confidence 34444445555555555555444444444555778999999999999997543311 1122 2233
Q ss_pred hcCCCHHHHHHHHHHHHHHH
Q 026635 179 HSGYSEDQLLECATLMIGFH 198 (235)
Q Consensus 179 ~t~~~~~~i~~~~~~i~~~~ 198 (235)
...+..++|.+|--.+++.+
T Consensus 125 ~~~~~~~~I~e~Ef~llE~L 144 (264)
T KOG0794|consen 125 KFPYERKDILEMEFYLLEAL 144 (264)
T ss_pred hcCCCcCcchhhhhhHHhhh
Confidence 45677777777766666644
No 41
>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=53.71 E-value=32 Score=23.06 Aligned_cols=34 Identities=12% Similarity=0.282 Sum_probs=27.2
Q ss_pred CcHHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHh
Q 026635 7 INEKMRAILIDWLIEVHDKFDLMSETLFLSINLIDRF 43 (235)
Q Consensus 7 i~~~~R~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~ 43 (235)
-+...|..++++|.+++..-++ +...|+..+|.+
T Consensus 47 ~~y~rRK~Ii~~I~~l~~~~g~---~~~~ai~~le~~ 80 (81)
T PF12550_consen 47 RTYSRRKVIIDFIERLANERGI---SEEEAIEILEEI 80 (81)
T ss_pred hhHHHHHHHHHHHHHHHHHcCC---CHHHHHHHHHhc
Confidence 3567899999999999988888 456677777764
No 42
>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=44.30 E-value=42 Score=28.55 Aligned_cols=78 Identities=8% Similarity=0.008 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHHHHcCcccc-----CCC--hHHHHHHHHHHhCcchHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHH
Q 026635 89 RKEVLEMESLMLNTLQFNMS-----VPT--PYVFIQRFLKAAQSDKKLQLLSFFLIELSLVEYEMLKFTPSLLAAAAIYA 161 (235)
Q Consensus 89 ~~~i~~~E~~IL~~L~f~l~-----~~t--p~~fl~~~~~~~~~~~~~~~~a~~ll~~~l~~~~~~~~~ps~iA~a~l~l 161 (235)
.+.....+...+..+.|.+. --+ -..++..+...+..+......|..+..--..-.....+++-.+|.+||++
T Consensus 18 ~~~~q~~~e~~l~~~~p~l~~~~e~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~L 97 (297)
T COG5333 18 FDSSQNAIELDLLVLEPELTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYL 97 (297)
T ss_pred hhHHHHHHHhhHhcCCcccchhhhhhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheee
Confidence 44455555556666666211 111 23577778888888888888888777777776678899999999999999
Q ss_pred HHHHh
Q 026635 162 AQCTI 166 (235)
Q Consensus 162 a~~~~ 166 (235)
|.+.-
T Consensus 98 A~K~e 102 (297)
T COG5333 98 ACKVE 102 (297)
T ss_pred eeecc
Confidence 97543
No 43
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=40.98 E-value=52 Score=21.14 Aligned_cols=41 Identities=12% Similarity=0.137 Sum_probs=27.7
Q ss_pred CCCCCCCcHHHHHHHHHHH-------HHHHHHcCCChhHHHHHHHHHH
Q 026635 1 MTQQFDINEKMRAILIDWL-------IEVHDKFDLMSETLFLSINLID 41 (235)
Q Consensus 1 ~~~q~~i~~~~R~~~v~wm-------~~~~~~~~l~~~t~~~Av~l~D 41 (235)
|.+....+++.+..+|.-. .++|..+|++..+++.=+.-+.
T Consensus 1 m~~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 1 MRKRRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp --SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 5667888999999999887 4789999999999987555554
No 44
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=40.08 E-value=42 Score=19.53 Aligned_cols=34 Identities=12% Similarity=0.105 Sum_probs=17.4
Q ss_pred CCCCcHHHHHHHHHHH------HHHHHHcCCChhHHHHHH
Q 026635 4 QFDINEKMRAILIDWL------IEVHDKFDLMSETLFLSI 37 (235)
Q Consensus 4 q~~i~~~~R~~~v~wm------~~~~~~~~l~~~t~~~Av 37 (235)
.+++|++.|..+-.+. .+++..++.++.|+..-+
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGMSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ----------HHHHHHCS---HHHHHHHTT--HHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcCCCHHHHHHHHCcCcHHHHHHH
Confidence 4678999999988874 578999999999987543
No 45
>PF11919 DUF3437: Domain of unknown function (DUF3437); InterPro: IPR021843 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 142 to 163 amino acids in length. ; PDB: 3L5Q_6 1VSY_5.
Probab=34.30 E-value=73 Score=21.94 Aligned_cols=77 Identities=9% Similarity=0.220 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCchhh-h---hhcCCCHHHHHHHHHHHHHHHhhcCCCChhHHHHhhCCCCCCccccC-C
Q 026635 151 PSLLAAAAIYAAQCTIYGFKQWSKTC-Q---WHSGYSEDQLLECATLMIGFHQKAATGKLTGVHRKYCTSKFGYISKS-E 225 (235)
Q Consensus 151 ps~iA~a~l~la~~~~~~~~~w~~~l-~---~~t~~~~~~i~~~~~~i~~~~~~~~~~~~~~i~~ky~~~~~~~vs~~-~ 225 (235)
..+++++|+..|. -...+.|.+.+ . ..+. +..-|...++..+.-+++.....-....+++....-.....+ .
T Consensus 8 ~~VLGL~Alv~a~--Py~vP~w~P~~l~~La~~~~-~~~~I~~tvk~tl~eFkrtH~D~W~~~~~~Ft~~ql~~l~~~~~ 84 (90)
T PF11919_consen 8 AAVLGLSALVLAF--PYDVPPWMPEVLEELARHAN-DPQPIRTTVKKTLSEFKRTHQDTWHEHKKKFTEDQLEDLEDVLV 84 (90)
T ss_dssp HHHHHHHHHHTT---S--SS-HHHHHHHHHHTTSS-S-SSHHHHTHHHHHHHHHHTSTTHHHHGGG--SSTTGGGSS---
T ss_pred HHHHHHHHHHHHc--CCCCcccHHHHHHHHHHHhC-CCchHHHHHHHHHHHHHHhCcccHHHHHHhCCHHHHHHHHcCCC
Confidence 3566677776663 23556785533 2 3333 556666666666666666555555667777887777777655 4
Q ss_pred Ccccc
Q 026635 226 PAQFL 230 (235)
Q Consensus 226 ~~~~~ 230 (235)
.|+++
T Consensus 85 ~psYy 89 (90)
T PF11919_consen 85 SPSYY 89 (90)
T ss_dssp --TTB
T ss_pred CCCcc
Confidence 55543
No 46
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=32.61 E-value=1.9e+02 Score=25.14 Aligned_cols=56 Identities=18% Similarity=0.096 Sum_probs=43.7
Q ss_pred hHHHHHHHHHHhCcchHHHHHHHHHHHHHhcchhccCCC---HHHHHHHHHHHHHHHhc
Q 026635 112 PYVFIQRFLKAAQSDKKLQLLSFFLIELSLVEYEMLKFT---PSLLAAAAIYAAQCTIY 167 (235)
Q Consensus 112 p~~fl~~~~~~~~~~~~~~~~a~~ll~~~l~~~~~~~~~---ps~iA~a~l~la~~~~~ 167 (235)
+.+|+-......+......-+|--++|--+....+-+.+ --.+|+||+.+|.+.-.
T Consensus 81 A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE 139 (335)
T KOG0656|consen 81 ALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEE 139 (335)
T ss_pred HHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcC
Confidence 456666666667777777778887888888888888888 66899999999987544
No 47
>PF03261 CDK5_activator: Cyclin-dependent kinase 5 activator protein; InterPro: IPR004944 These proteins are neuron specific activators of cyclin-dependent kinase 5 (CDK5) []. They form a heterodimer with the catalytic subunit (CDK5) [].; GO: 0016534 cyclin-dependent protein kinase 5 activator activity, 0016533 cyclin-dependent protein kinase 5 holoenzyme complex; PDB: 3O0G_D 1H4L_E 1UNH_D 1UNL_E 1UNG_E.
Probab=30.67 E-value=73 Score=27.70 Aligned_cols=19 Identities=26% Similarity=0.499 Sum_probs=16.1
Q ss_pred cchhHHHHHHHHHHHhhhc
Q 026635 50 VRKKLQLVGLVAMLLACKY 68 (235)
Q Consensus 50 ~~~~l~l~a~tcl~IA~K~ 68 (235)
...++|.+..|||+||--+
T Consensus 268 ~~~~l~~~~l~cly~sysy 286 (346)
T PF03261_consen 268 SERELQAIVLTCLYLSYSY 286 (346)
T ss_dssp SHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhhh
Confidence 4456999999999999887
No 48
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=29.35 E-value=2.2e+02 Score=25.86 Aligned_cols=72 Identities=11% Similarity=0.043 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHHHhcCCCCCchhhhhh--cCCCHHHHHHHHHHHHHHHhh-cCCCChhHHHHhhCCCCCCcccc
Q 026635 152 SLLAAAAIYAAQCTIYGFKQWSKTCQWH--SGYSEDQLLECATLMIGFHQK-AATGKLTGVHRKYCTSKFGYISK 223 (235)
Q Consensus 152 s~iA~a~l~la~~~~~~~~~w~~~l~~~--t~~~~~~i~~~~~~i~~~~~~-~~~~~~~~i~~ky~~~~~~~vs~ 223 (235)
-.+|++|+++|.+.-....+-...+..+ -.++.++|....+.|+..+.- .+.+.+...-++-+...-.++..
T Consensus 256 QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka~dyd~~s 330 (440)
T COG5024 256 QLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERYMLEVLDFNISWPSPMSFLRRISKASDYDIFS 330 (440)
T ss_pred HHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHHHHHhhhcccccCCCChHHHHHHHHhhcccchhh
Confidence 3678899999976443222223333322 457889999999999987653 55566566555555544444433
No 49
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=27.90 E-value=1.2e+02 Score=20.28 Aligned_cols=30 Identities=20% Similarity=0.391 Sum_probs=26.0
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHHHHHhhc
Q 026635 16 IDWLIEVHDKFDLMSETLFLSINLIDRFLS 45 (235)
Q Consensus 16 v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~ 45 (235)
+.-+..++..|+++.+.+.++..++|+.-.
T Consensus 45 l~~~~rL~~Dl~in~~gi~lil~LLd~i~~ 74 (84)
T PF13591_consen 45 LRRIRRLHRDLGINLEGIALILDLLDRIEQ 74 (84)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 456788899999999999999999998643
No 50
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=27.34 E-value=1.6e+02 Score=19.39 Aligned_cols=40 Identities=20% Similarity=0.161 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhhhccccccccHhhHHHhhcCCCCHHHHHHH
Q 026635 55 QLVGLVAMLLACKYEEVSVPVVGDLILISDKAYTRKEVLEM 95 (235)
Q Consensus 55 ~l~a~tcl~IA~K~ee~~~~~~~~l~~~~~~~~~~~~i~~~ 95 (235)
.|+-.+|-.||.++.+..+-.++.+..+.+ .+++++-.++
T Consensus 30 ~L~~~~~~~iA~~i~gks~eeir~~fgi~~-d~t~eee~~i 69 (78)
T PF01466_consen 30 GLLDLCCKYIANMIKGKSPEEIRKYFGIEN-DLTPEEEEEI 69 (78)
T ss_dssp HHHHHHHHHHHHHHTTS-HHHHHHHHT----TSSHHHHHHH
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHcCCCC-CCCHHHHHHH
Confidence 467788999999998876666777766654 4676655443
No 51
>PF14502 HTH_41: Helix-turn-helix domain
Probab=23.82 E-value=1.2e+02 Score=18.29 Aligned_cols=24 Identities=17% Similarity=0.390 Sum_probs=20.9
Q ss_pred HHHHHHHcCCChhHHHHHHHHHHH
Q 026635 19 LIEVHDKFDLMSETLFLSINLIDR 42 (235)
Q Consensus 19 m~~~~~~~~l~~~t~~~Av~l~Dr 42 (235)
+.+.++.|+++.-|+..|+.++.-
T Consensus 9 I~e~~~~~~vs~GtiQ~Alk~Le~ 32 (48)
T PF14502_consen 9 ISEYSEKFGVSRGTIQNALKFLEE 32 (48)
T ss_pred HHHHHHHhCcchhHHHHHHHHHHH
Confidence 567889999999999999998864
No 52
>cd04447 DEP_BRCC3 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in BBRC3-like proteins. BBRC3, also known as DEPDC1B, is a DEP containing protein of unknown function.
Probab=23.53 E-value=1.6e+02 Score=20.43 Aligned_cols=37 Identities=22% Similarity=0.340 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHcCC--ChhHHHHHHHHHHHhhcccccc
Q 026635 14 ILIDWLIEVHDKFDL--MSETLFLSINLIDRFLSQQQVV 50 (235)
Q Consensus 14 ~~v~wm~~~~~~~~l--~~~t~~~Av~l~Dr~l~~~~~~ 50 (235)
..|||+.+.-..... +..+...||.++.+++..+-+.
T Consensus 34 EAVDwL~~~l~~n~~fg~~vtR~~av~l~qkll~~hVie 72 (92)
T cd04447 34 EAVDWLHELLRSNSNFGPEVTRQQTVQLLKKFLKNHVIE 72 (92)
T ss_pred HHHHHHHHHHHhccccCCCCCHHHHHHHHHHHHHcCCch
Confidence 689999988533221 3668888999999998876553
No 53
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=21.77 E-value=1.7e+02 Score=25.15 Aligned_cols=67 Identities=13% Similarity=0.054 Sum_probs=46.5
Q ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCc-hhhhhhcCCCHHHHHHHHHHHHHHHhhcCCCChhHHHHhhCC
Q 026635 148 KFTPSLLAAAAIYAAQCTIYGFKQWS-KTCQWHSGYSEDQLLECATLMIGFHQKAATGKLTGVHRKYCT 215 (235)
Q Consensus 148 ~~~ps~iA~a~l~la~~~~~~~~~w~-~~l~~~t~~~~~~i~~~~~~i~~~~~~~~~~~~~~i~~ky~~ 215 (235)
.+..+-+..++++++.....+...|. .+++.+-..+.++.++.-+.++++++-.-+. +..+|.||--
T Consensus 231 p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlKd~tveDmNe~ERqfLelLqfNinv-p~svYAKyYf 298 (343)
T KOG1675|consen 231 PRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILKDQSVDDMNALERQFLELLQFNINV-PSSEYAKYYF 298 (343)
T ss_pred cchhhhhhhhhheehhhhhhhhhcccHHHHHHHhhccHhhHHHHHHHHHHHHhhccCc-cHHHHHHHHH
Confidence 44555666667888877777777784 4555666778999999999888877633222 2578888843
No 54
>PF11357 Spy1: Cell cycle regulatory protein; InterPro: IPR020984 Speedy (Spy1) is a cell cycle regulatory protein which activates CDK2, the major kinase that allows progression through G1/S phase and further replication events. Spy1 expression overcomes a p27-induced cell cycle arrest to allow for DNA synthesis, so cell cycle progression occurs due to an interaction between Spy1 and p27 []. Spy1 is also known as Ringo protein A.
Probab=21.22 E-value=3.5e+02 Score=20.09 Aligned_cols=82 Identities=12% Similarity=0.125 Sum_probs=47.1
Q ss_pred HHcCCChh-HHHHHHHHHHHhhccccccchhH-HHHHHHHHHHhhhccccccccHhhHHH-hhcCC--CCHHHHHHHHHH
Q 026635 24 DKFDLMSE-TLFLSINLIDRFLSQQQVVRKKL-QLVGLVAMLLACKYEEVSVPVVGDLIL-ISDKA--YTRKEVLEMESL 98 (235)
Q Consensus 24 ~~~~l~~~-t~~~Av~l~Dr~l~~~~~~~~~l-~l~a~tcl~IA~K~ee~~~~~~~~l~~-~~~~~--~~~~~i~~~E~~ 98 (235)
..+++++. .+...+.||-|- +.....+ ..--..+|+||+-+||.....-.++.. +.+.. -...++.+.-..
T Consensus 23 ~~~~~sDKYLLAmV~~YF~Ra----gl~~~~Y~ri~FFlALYLAndmEED~~~~K~~If~f~~G~~w~~~~~~F~klr~~ 98 (131)
T PF11357_consen 23 KCLRVSDKYLLAMVIAYFSRA----GLFSWQYQRIHFFLALYLANDMEEDDEEPKYEIFPFLYGKNWRSQIPQFHKLRDQ 98 (131)
T ss_pred cchhhhhHHHHHHHHHHHHhc----ccchhhcchHHHHHHHHHhhHHHhccchHHHHHHHHHHCcchHHHhHHHHHHHHH
Confidence 34455544 455566666653 3333322 222346899999999875544344433 33322 223566777778
Q ss_pred HHHHcCccccC
Q 026635 99 MLNTLQFNMSV 109 (235)
Q Consensus 99 IL~~L~f~l~~ 109 (235)
+...++|+..+
T Consensus 99 ~~~~m~~Ra~V 109 (131)
T PF11357_consen 99 FWRRMDWRAWV 109 (131)
T ss_pred HHHHcCCceee
Confidence 88888887654
No 55
>cd04438 DEP_dishevelled DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in dishevelled-like proteins. Dishevelled-like proteins play a key role in the transduction of the Wnt signal from the cell surface to the nucleus, which in turn is an important regulatory pathway for cellular development and growth. They contain an N-terminal DIX domain, a central PDZ domain, and a C-terminal DEP domain.
Probab=21.20 E-value=1.1e+02 Score=20.81 Aligned_cols=31 Identities=19% Similarity=0.235 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHcCCChhHHHHHHHHHHHhh
Q 026635 14 ILIDWLIEVHDKFDLMSETLFLSINLIDRFL 44 (235)
Q Consensus 14 ~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l 44 (235)
.+|+|+.+-.....=..++...+-.+++.=+
T Consensus 34 dlVdWL~~~~~~~~~R~eAv~~g~~Ll~~G~ 64 (84)
T cd04438 34 DLVDWLLSHVEGLTDRREARKYASSLLKLGY 64 (84)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHHHHHCCc
Confidence 5899998876655555677777777776533
No 56
>cd04449 DEP_DEPDC5-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.
Probab=21.10 E-value=1.1e+02 Score=20.58 Aligned_cols=30 Identities=23% Similarity=0.461 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHcCCChhHHHHHHHHHHH
Q 026635 13 AILIDWLIEVHDKFDLMSETLFLSINLIDR 42 (235)
Q Consensus 13 ~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr 42 (235)
..+|+|+.+-.....-..+++..+-.++|.
T Consensus 33 ~e~VdWL~~~~~~~~~r~eAv~lgq~Ll~~ 62 (83)
T cd04449 33 SEAVSWLINNFEDVDTREEAVELGQELMNE 62 (83)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHHHHHC
Confidence 378999997544222233444444444443
No 57
>KOG1257 consensus NADP+-dependent malic enzyme [Energy production and conversion]
Probab=20.36 E-value=2.1e+02 Score=26.69 Aligned_cols=56 Identities=11% Similarity=0.220 Sum_probs=43.0
Q ss_pred CcHHHHHHHHHHHHHHHHHcC------CChhHHHHHHHHHHHhhccccccchhHHHHHHHHH
Q 026635 7 INEKMRAILIDWLIEVHDKFD------LMSETLFLSINLIDRFLSQQQVVRKKLQLVGLVAM 62 (235)
Q Consensus 7 i~~~~R~~~v~wm~~~~~~~~------l~~~t~~~Av~l~Dr~l~~~~~~~~~l~l~a~tcl 62 (235)
-.+++=.-+=+||.-+...++ +.+-..+.|..++++|-.+.-.-.+++|..|++++
T Consensus 233 ~g~eYd~~~dEFm~Av~~~yG~~~lIqFEDF~~~nAfrlL~kYr~~~c~FNDDIQGTaaVal 294 (582)
T KOG1257|consen 233 RGKEYDEFLDEFMEAVVQRYGPNTLIQFEDFANHNAFRLLEKYRNKYCMFNDDIQGTAAVAL 294 (582)
T ss_pred cccHHHHHHHHHHHHHHHHhCcceEEEehhccchhHHHHHHHhccccceecccccchhHHHH
Confidence 345555666778888888885 45566788999999999888777788887776655
No 58
>cd04439 DEP_1_P-Rex DEP (Dishevelled, Egl-10, and Pleckstrin) domain 1 found in P-Rex-like proteins. The P-Rex family is the guanine-nucleotide exchange factor (GEF) for the small GTPase Rac that contains an N-terminal RhoGEF domain, two DEP and PDZ domains. Rac-GEF activity is stimulated by phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3), a lipid second messenger, and by the G beta-gamma subunits of heterotrimeric G proteins. The DEP domains are not involved in mediating these stimuli, but may be of importance for basal and stimulated levels Rac-GEF activity.
Probab=20.36 E-value=94 Score=20.89 Aligned_cols=29 Identities=21% Similarity=0.440 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHcCCChhHHHHHHHHHHH
Q 026635 13 AILIDWLIEVHDKFDLMSETLFLSINLIDR 42 (235)
Q Consensus 13 ~~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr 42 (235)
..+|+||.+....-. ..+++..+-.++|.
T Consensus 32 selVdWL~~~~~~~~-r~eAv~lg~~Ll~~ 60 (81)
T cd04439 32 NEFVSWLLEIGEISK-PEEGVNLGQALLEN 60 (81)
T ss_pred HHHHHHHHHcCCCCC-HHHHHHHHHHHHHC
Confidence 368999997542111 23555555555553
No 59
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=20.07 E-value=2.4e+02 Score=19.65 Aligned_cols=32 Identities=13% Similarity=0.319 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHcCCChhHHHHHHHHHHHhhc
Q 026635 14 ILIDWLIEVHDKFDLMSETLFLSINLIDRFLS 45 (235)
Q Consensus 14 ~~v~wm~~~~~~~~l~~~t~~~Av~l~Dr~l~ 45 (235)
..+.-+.+++..++++.+.+.++..++|+.-.
T Consensus 51 ~r~~~a~rL~~dl~in~~gialvl~LLd~i~~ 82 (101)
T PRK10265 51 IVVQRAVRLRHELALDWPGIAVALTLLDEIAH 82 (101)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 45667888999999999999999999998644
Done!