Query 017988
Match_columns 362
No_of_seqs 283 out of 1743
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 05:10:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017988.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017988hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0654 G2/Mitotic-specific cy 100.0 4.5E-51 9.8E-56 391.0 13.9 273 78-359 85-358 (359)
2 KOG0653 Cyclin B and related k 100.0 6.9E-45 1.5E-49 360.0 20.9 260 79-346 109-372 (391)
3 COG5024 Cyclin [Cell division 100.0 5E-45 1.1E-49 358.1 18.8 258 80-346 164-423 (440)
4 KOG0655 G1/S-specific cyclin E 100.0 6.1E-41 1.3E-45 310.8 21.7 216 96-322 113-336 (408)
5 KOG0656 G1/S-specific cyclin D 100.0 4.2E-37 9.2E-42 292.4 21.6 221 94-315 43-268 (335)
6 PF00134 Cyclin_N: Cyclin, N-t 99.9 6.6E-27 1.4E-31 195.8 13.3 127 98-225 1-127 (127)
7 TIGR00569 ccl1 cyclin ccl1. Un 99.9 1.3E-22 2.7E-27 193.8 21.2 162 127-289 54-221 (305)
8 KOG0834 CDK9 kinase-activating 99.9 1.2E-21 2.7E-26 186.9 13.8 203 121-325 31-249 (323)
9 PF02984 Cyclin_C: Cyclin, C-t 99.8 4E-21 8.7E-26 158.2 10.3 118 227-350 1-118 (118)
10 KOG0835 Cyclin L [General func 99.8 3.5E-18 7.7E-23 159.6 19.2 194 122-323 16-231 (367)
11 KOG0794 CDK8 kinase-activating 99.8 4.6E-19 1E-23 158.3 10.3 189 129-325 41-242 (264)
12 COG5333 CCL1 Cdk activating ki 99.7 5.7E-17 1.2E-21 151.6 14.2 167 125-297 41-213 (297)
13 PRK00423 tfb transcription ini 99.5 1.3E-12 2.7E-17 126.2 22.9 182 130-321 123-304 (310)
14 cd00043 CYCLIN Cyclin box fold 99.5 2.9E-14 6.3E-19 110.0 8.7 87 129-217 2-88 (88)
15 smart00385 CYCLIN domain prese 99.5 1.9E-13 4.1E-18 104.4 7.8 83 134-218 1-83 (83)
16 KOG2496 Cdk activating kinase 99.5 2.8E-12 6.1E-17 119.3 16.6 153 130-284 57-218 (325)
17 KOG1597 Transcription initiati 99.0 1.8E-08 3.9E-13 93.9 17.1 177 133-320 108-287 (308)
18 COG1405 SUA7 Transcription ini 98.9 1.3E-07 2.8E-12 89.9 20.2 182 129-320 97-278 (285)
19 PF08613 Cyclin: Cyclin; Inte 98.7 1.4E-07 3E-12 81.6 10.4 91 132-224 54-149 (149)
20 smart00385 CYCLIN domain prese 98.7 1.1E-07 2.4E-12 72.0 8.4 81 231-318 1-82 (83)
21 cd00043 CYCLIN Cyclin box fold 98.5 6.5E-07 1.4E-11 68.5 9.5 85 226-317 2-87 (88)
22 KOG4164 Cyclin ik3-1/CABLES [C 97.9 1.1E-05 2.3E-10 78.1 5.2 99 130-228 383-483 (497)
23 KOG1598 Transcription initiati 96.9 0.0088 1.9E-07 60.7 10.8 148 135-288 73-223 (521)
24 PF00382 TFIIB: Transcription 96.7 0.0087 1.9E-07 44.8 7.4 65 136-201 1-65 (71)
25 KOG1674 Cyclin [General functi 96.1 0.021 4.6E-07 52.5 7.6 94 132-227 78-181 (218)
26 PRK00423 tfb transcription ini 95.1 0.2 4.3E-06 48.5 10.7 89 133-224 220-308 (310)
27 PF00382 TFIIB: Transcription 94.0 0.39 8.4E-06 35.7 7.7 58 250-309 13-70 (71)
28 KOG1675 Predicted cyclin [Gene 93.6 0.11 2.3E-06 49.5 4.8 101 136-238 197-299 (343)
29 PF02984 Cyclin_C: Cyclin, C-t 90.5 1.4 3E-05 35.3 7.5 87 133-221 4-90 (118)
30 KOG0834 CDK9 kinase-activating 87.5 0.61 1.3E-05 45.3 3.8 95 129-223 152-248 (323)
31 PF00134 Cyclin_N: Cyclin, N-t 86.9 5 0.00011 32.6 8.6 68 252-320 52-121 (127)
32 COG1405 SUA7 Transcription ini 83.2 7.6 0.00016 37.2 8.9 70 131-201 193-262 (285)
33 KOG0835 Cyclin L [General func 70.5 20 0.00042 34.9 7.6 72 142-215 151-224 (367)
34 PF08613 Cyclin: Cyclin; Inte 69.8 32 0.00069 29.4 8.3 89 226-320 51-144 (149)
35 PF01857 RB_B: Retinoblastoma- 41.2 86 0.0019 26.5 6.0 64 134-198 16-81 (135)
36 KOG1597 Transcription initiati 40.6 1E+02 0.0022 29.7 6.8 66 135-201 206-271 (308)
37 TIGR00569 ccl1 cyclin ccl1. Un 40.1 1.4E+02 0.003 29.0 8.0 28 261-288 88-115 (305)
38 PF12550 GCR1_C: Transcription 32.9 2.1E+02 0.0046 21.6 6.6 33 125-160 48-80 (81)
39 PF09241 Herp-Cyclin: Herpesvi 31.2 2.5E+02 0.0054 21.7 9.0 93 229-322 4-99 (106)
40 cd04438 DEP_dishevelled DEP (D 26.8 56 0.0012 25.3 2.3 40 129-168 32-71 (84)
41 cd04439 DEP_1_P-Rex DEP (Dishe 24.5 65 0.0014 24.7 2.3 30 129-159 31-60 (81)
42 PF15576 DUF4661: Domain of un 24.2 2.4E+02 0.0053 25.5 6.1 33 1-33 17-49 (253)
43 cd04441 DEP_2_DEP6 DEP (Dishev 23.9 71 0.0015 24.8 2.5 34 130-164 36-69 (85)
44 cd04443 DEP_GPR155 DEP (Dishev 22.8 83 0.0018 24.3 2.6 30 129-159 33-62 (83)
45 KOG0794 CDK8 kinase-activating 21.9 4.2E+02 0.009 24.8 7.3 25 167-191 189-213 (264)
46 KOG4557 Origin recognition com 21.7 1.4E+02 0.0031 27.4 4.2 53 271-325 133-185 (262)
47 cd04449 DEP_DEPDC5-like DEP (D 20.8 92 0.002 23.8 2.5 34 129-162 32-65 (83)
No 1
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.5e-51 Score=391.02 Aligned_cols=273 Identities=56% Similarity=0.883 Sum_probs=263.5
Q ss_pred CcccCCCCCCCcchhhhhHHHHHHHHHHHHhh-cCCCcchHhhhcccCCHHHHHHHHHHHHHHHHHcCCchHHHHHHHHH
Q 017988 78 RVVNVDDNYMDPQLCATFACDIYKHLRASEVK-KRPSTDFMEIIQKDINASMRAILIDWLVEVAEEYRLVPDTLYLTVNY 156 (362)
Q Consensus 78 ~~~~id~~~~dp~~~~~y~~dI~~~l~~~E~~-~~p~~~y~~~~q~~i~~~~R~~lvdwl~ev~~~~~l~~eTl~lAv~l 156 (362)
..+++|....||++|..|+.+|++|++..|.+ .+|.++||+.+|.++++.||.++|+|++++++.+++..+++|+++++
T Consensus 85 ~~~~~ds~~~dp~~c~~~~~~I~~~~r~~ei~~~rp~~~~~e~vq~d~t~smrgilvdwlvevsee~r~~~e~l~ls~~~ 164 (359)
T KOG0654|consen 85 FVMRIDSVGEDPQMCLKIAAKIYNTLRVSDIKSERPLPSKFEFVQADITPSMRGILVDWLVEVSEEYRLTFETLYLSVNY 164 (359)
T ss_pred cccchhhcccchHHHHHHHHHHhhcccccchhhccCcccceeeeecCCCcchhhhhhhhhhHHHHHHHhhhhheeecHHH
Confidence 34788999999999999999999999999999 99999999999999999999999999999999999999999999999
Q ss_pred HHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcCCCCHHHHHHHHHHHHHHcCCCccCCCHHHHHHHH
Q 017988 157 IDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDNTYFKEEVLEMESSILNYLKFEMTAPTAKCFLRRF 236 (362)
Q Consensus 157 lDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~~~t~~ei~~mE~~IL~~L~f~l~~pT~~~FL~~~ 236 (362)
.|||+....+.+.++|++|.+|++||+|+||+.+|.+++|+++++++|+..++..||..+|+.|.|.+..||...|+++|
T Consensus 165 ~drfl~~~~~~~~k~ql~g~s~m~I~sk~ee~~~~~~~ef~~itd~ty~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~ 244 (359)
T KOG0654|consen 165 RDRFLSYKEVNKQKLQLVGISAMLIASKYEEIKEPRVEEFCYITDNTYTYWQVLRMEIDILNALTFELVRPTSKTFLRRF 244 (359)
T ss_pred HHHHhccCccHHHHHHHhCcccceeeccchhhcchHHHHHHhhhhhhhHHHHHHHHHHHHHHHhHHHHhCchHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHccCCCCchhHHHHHHHHHHHHhhccccccCccHHHHHHHHHHHHHHhhcCCCCCCcHHHHhhhCCChhhHHHHHHH
Q 017988 237 VRAAQGINEVPSMQLECLANYVTELSLLDYSMLCHAPSLIAASAIFLAKYILLPAKRPWNSTLQHYTLYQPSDLMECVKD 316 (362)
Q Consensus 237 l~~~~~~~~~~~~~~~~la~~l~elsL~d~~~l~y~PS~iAaAai~lA~~~l~~~~~~w~~~L~~~t~~~~~~l~~c~~~ 316 (362)
+.+.+. +..+++.++.|++|++++++.|+.|.||.|||||+++|+.+++ ..+|+..|+++|||+.++++.|+..
T Consensus 245 ~~~~~~----~~~~~e~~~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~--~~pW~~~L~~~T~y~~edl~~~v~~ 318 (359)
T KOG0654|consen 245 LRVAQT----PELQVEPLANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLD--FHPWNQTLEDYTGYKAEDLKPCVLD 318 (359)
T ss_pred HHhhcc----hhHHHHHHHHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhcc--CCCCchhhHHhhcccHHHHHHHHHH
Confidence 998876 5567889999999999999999999999999999999999994 8899999999999999999999999
Q ss_pred HHHHHhcCCCCChhHHHHhhcCCcccccccccCCCCCCccccc
Q 017988 317 LHRLYCNSQSSTLPAIREKYSLHKYKCVAKKYCPPSIPPEFFL 359 (362)
Q Consensus 317 L~~l~~~~~~~~~~~i~~KY~~~~~~~va~~~~p~~~~~~~~~ 359 (362)
|+ ++.+..+..+++||+||+++||++||...+| +|..||.
T Consensus 319 L~-~~l~~~~~~l~air~ky~~~k~~~Va~~~~p--~p~~~~~ 358 (359)
T KOG0654|consen 319 LH-LYLNASGTDLPAIREKYKQSKFKEVALLPVP--LPHTFVE 358 (359)
T ss_pred Hh-cccCCCCCchHHHHHHhhhhhhhhhhccCCC--Ccchhcc
Confidence 99 9999999999999999999999999999888 7888875
No 2
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=6.9e-45 Score=359.95 Aligned_cols=260 Identities=42% Similarity=0.686 Sum_probs=234.6
Q ss_pred cccCC-CCCCCcchhhhhHHHHHHHHHHHHhhcCCCcchHhhhcccCCHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHH
Q 017988 79 VVNVD-DNYMDPQLCATFACDIYKHLRASEVKKRPSTDFMEIIQKDINASMRAILIDWLVEVAEEYRLVPDTLYLTVNYI 157 (362)
Q Consensus 79 ~~~id-~~~~dp~~~~~y~~dI~~~l~~~E~~~~p~~~y~~~~q~~i~~~~R~~lvdwl~ev~~~~~l~~eTl~lAv~ll 157 (362)
+.|+| .+..+|+++.+|+.|||.+++..|....|...+ . .|.+++..||.++||||++|+.+|+|.+||+|+||+++
T Consensus 109 ~~dl~~~d~~~~~~~~ey~~di~~~l~~~e~~~~p~~~~-~-~~~e~~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnli 186 (391)
T KOG0653|consen 109 ILDLDSEDKSDPSMIVEYVQDIFEYLRQLELEFLPLSYD-I-SQSEIRAKMRAILVDWLVEVHEKFGLSPETLYLAVNLI 186 (391)
T ss_pred ccCcchhcccCcHHHHHHHHHHHHHHHHHHHhhCchhhh-c-ccccccHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHH
Confidence 67777 478999999999999999999999755666544 3 48899999999999999999999999999999999999
Q ss_pred HhhccCCcCcchhhHHHHHHHHH-HHhhhccccccCHHHHHHhhcCCCCHHHHHHHHHHHHHHcCCCccCCCHHHHHHHH
Q 017988 158 DRYLSGNPMSRQRLQLLGVACMM-IAAKYEEICAPQVEEFCFITDNTYFKEEVLEMESSILNYLKFEMTAPTAKCFLRRF 236 (362)
Q Consensus 158 DRfLs~~~v~~~~lqLva~tcL~-IAsK~eE~~~p~i~~l~~i~~~~~t~~ei~~mE~~IL~~L~f~l~~pT~~~FL~~~ 236 (362)
||||++..+++.++||+|++||| ||+|+||..+|.+.+|+++++++|++++|++||+.||++|+|+++.|||+.||++|
T Consensus 187 DRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~il~mE~~il~~L~f~l~~p~~~~FLrr~ 266 (391)
T KOG0653|consen 187 DRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREEILRMEKYILNVLEFDLSVPTPLSFLRRF 266 (391)
T ss_pred HHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHHHHHHHHHHHhccCeeecCCchHHHHHHH
Confidence 99999999999999999999966 99999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHccCCCCchhHHHHHHHHHHHHhhccccccCccHHHHHHHHHHHHHHhhcCCCCCCcHHHHhhhCCChhhHHHHHHH
Q 017988 237 VRAAQGINEVPSMQLECLANYVTELSLLDYSMLCHAPSLIAASAIFLAKYILLPAKRPWNSTLQHYTLYQPSDLMECVKD 316 (362)
Q Consensus 237 l~~~~~~~~~~~~~~~~la~~l~elsL~d~~~l~y~PS~iAaAai~lA~~~l~~~~~~w~~~L~~~t~~~~~~l~~c~~~ 316 (362)
+++...+ ...+.+++|++|++++|+.++.++||.+|+|++++++.+...+ ..|..++.+++||...++.+|...
T Consensus 267 ~ka~~~d-----~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~~~~~-~~w~~~~~~~sg~~~~~~~~~~~~ 340 (391)
T KOG0653|consen 267 LKAADYD-----IKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALRMLSKG-DVWSPTLEHYSGYSESYLFECARS 340 (391)
T ss_pred HHhhhcc-----hhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHHhccC-CccCCCCeeccCCCcHHHHHHHHH
Confidence 9998732 3567899999999999999999999999999999999998422 269999999999999999999999
Q ss_pred HHHHHhcCC-CCChh-HHHHhhcCCccccccc
Q 017988 317 LHRLYCNSQ-SSTLP-AIREKYSLHKYKCVAK 346 (362)
Q Consensus 317 L~~l~~~~~-~~~~~-~i~~KY~~~~~~~va~ 346 (362)
+..+..... ..... ++++||+..++..++.
T Consensus 341 ~~~~~~~~~~~~~~~~~~~~ky~~~~~~~~~~ 372 (391)
T KOG0653|consen 341 LSALSLSSLQNPSLRASVLNKYNSSKFLPASP 372 (391)
T ss_pred HHHHHHHhcccchhHHHHHHHhcccccchhhh
Confidence 998554443 33445 4999999999999985
No 3
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=100.00 E-value=5e-45 Score=358.13 Aligned_cols=258 Identities=31% Similarity=0.566 Sum_probs=239.6
Q ss_pred ccCC-CCCCCcchhhhhHHHHHHHHHHHHhhcCCCcchHhhhcccCCHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHH
Q 017988 80 VNVD-DNYMDPQLCATFACDIYKHLRASEVKKRPSTDFMEIIQKDINASMRAILIDWLVEVAEEYRLVPDTLYLTVNYID 158 (362)
Q Consensus 80 ~~id-~~~~dp~~~~~y~~dI~~~l~~~E~~~~p~~~y~~~~q~~i~~~~R~~lvdwl~ev~~~~~l~~eTl~lAv~llD 158 (362)
-|+| .+.+||.++.||+.+|+.+++++|....|.+.||.+ |+.+.+.||.+|++||++++.+|++.++|+++||+++|
T Consensus 164 ~dld~~~~~d~~mv~Ey~~~Ife~l~k~e~~~lp~~~yl~k-q~~~~~~mR~~Lv~wlvevH~~F~llpeTL~lainiiD 242 (440)
T COG5024 164 QDLDATDQEDPLMVPEYASDIFEYLLKLELIDLPNPNYLIK-QSLYEWSMRSILVDWLVEVHGKFGLLPETLFLAINIID 242 (440)
T ss_pred cccccccccCccchHHHHHHHHHHHHHHHHHhcCcHHHHhh-cchhHHhHHHHHHHHHHHhcccccccchHHHHHHHHHH
Confidence 4555 467999999999999999999999999999999886 99999999999999999999999999999999999999
Q ss_pred hhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcCCCCHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHH
Q 017988 159 RYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDNTYFKEEVLEMESSILNYLKFEMTAPTAKCFLRRFVR 238 (362)
Q Consensus 159 RfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~~~t~~ei~~mE~~IL~~L~f~l~~pT~~~FL~~~l~ 238 (362)
|||++.++.-+++||+|++|||||||+||+..|.+++|++++++.|+.++|+++|+.+|.+|+|++..|+|+.||+++.+
T Consensus 243 rfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSk 322 (440)
T COG5024 243 RFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERYMLEVLDFNISWPSPMSFLRRISK 322 (440)
T ss_pred HHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHHHHHhhhcccccCCCChHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHccCCCCchhHHHHHHHHHHHHhhccccccCccHHHHHHHHHHHHHHhhcCCCCCCcHHHHhhhC-CChhhHHHHHHHH
Q 017988 239 AAQGINEVPSMQLECLANYVTELSLLDYSMLCHAPSLIAASAIFLAKYILLPAKRPWNSTLQHYTL-YQPSDLMECVKDL 317 (362)
Q Consensus 239 ~~~~~~~~~~~~~~~la~~l~elsL~d~~~l~y~PS~iAaAai~lA~~~l~~~~~~w~~~L~~~t~-~~~~~l~~c~~~L 317 (362)
+...+ ...+..+.|+++++++++.|++++||.+||||.++|+.+++ ...|...|.+++| |+..++.++...+
T Consensus 323 a~dyd-----~~srt~~k~~~e~s~~~~~f~~~~~S~~~aaa~~~s~~~~~--~~~w~~~l~~ySg~y~~~~l~~~~~~~ 395 (440)
T COG5024 323 ASDYD-----IFSRTPAKFSSEISPVDYKFIQISPSWCAAAAMYLSRKILS--QNQWDRTLIHYSGNYTNPDLKPLNESN 395 (440)
T ss_pred hcccc-----hhhhhhHhhhCCchHhhhhhccCCchHHHHHHHHHHHhhhc--cCCCCccccccCCCCCchhHHHHHHHH
Confidence 75433 34568899999999999999999999999999999999994 4459999999999 9999999999999
Q ss_pred HHHHhcCCCCChhHHHHhhcCCccccccc
Q 017988 318 HRLYCNSQSSTLPAIREKYSLHKYKCVAK 346 (362)
Q Consensus 318 ~~l~~~~~~~~~~~i~~KY~~~~~~~va~ 346 (362)
.+.+.+...+ +.++.+||...+|+.++.
T Consensus 396 ~~~l~~~~~~-~~~i~~Ky~~~~~~~~s~ 423 (440)
T COG5024 396 KENLQNPSVH-HDAIFPKYPSPTFGKASS 423 (440)
T ss_pred HHHhcccchh-hhhhhhccccccccccch
Confidence 9877665544 489999999999998875
No 4
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=6.1e-41 Score=310.82 Aligned_cols=216 Identities=31% Similarity=0.509 Sum_probs=188.9
Q ss_pred HHHHHHHHHHHHhhcCCCcchHhhhcccCCHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHhhccC-CcCcchhhHHH
Q 017988 96 ACDIYKHLRASEVKKRPSTDFMEIIQKDINASMRAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSG-NPMSRQRLQLL 174 (362)
Q Consensus 96 ~~dI~~~l~~~E~~~~p~~~y~~~~q~~i~~~~R~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~-~~v~~~~lqLv 174 (362)
..++|..|..+|..+.-+..++.. ++++.++||++|+|||+|||+.|+|++||||||+.||||||.. +.+.+.++||+
T Consensus 113 ~~eVW~lM~kkee~~l~~~~~l~q-Hpdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLI 191 (408)
T KOG0655|consen 113 SKEVWLLMLKKEERYLRDKHFLEQ-HPDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLI 191 (408)
T ss_pred HHHHHHHHHccchhhhhhhHHHhh-CCCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHh
Confidence 358999999999988777777765 8999999999999999999999999999999999999999986 67999999999
Q ss_pred HHHHHHHHhhhccccccCHHHHHHhhcCCCCHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHccCCCCchh-----
Q 017988 175 GVACMMIAAKYEEICAPQVEEFCFITDNTYFKEEVLEMESSILNYLKFEMTAPTAKCFLRRFVRAAQGINEVPSM----- 249 (362)
Q Consensus 175 a~tcL~IAsK~eE~~~p~i~~l~~i~~~~~t~~ei~~mE~~IL~~L~f~l~~pT~~~FL~~~l~~~~~~~~~~~~----- 249 (362)
|+||||||+|+||++||++.+|+|++|++|+.++|+.||..||+.|+|+|.+.|...||..|+......+ .+.+
T Consensus 192 GitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n~-~~k~l~Pq~ 270 (408)
T KOG0655|consen 192 GITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDILTMELIILKALKWELSPITIISWLNVYLQVDALND-APKVLLPQY 270 (408)
T ss_pred hHHHHHHHHHHhhccCccccceeeeccCccchHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcCC-CCceecccc
Confidence 9999999999999999999999999999999999999999999999999999999999999998754332 2211
Q ss_pred -HHHHH-HHHHHHHhhccccccCccHHHHHHHHHHHHHHhhcCCCCCCcHHHHhhhCCChhhHHHHHHHHHHHHh
Q 017988 250 -QLECL-ANYVTELSLLDYSMLCHAPSLIAASAIFLAKYILLPAKRPWNSTLQHYTLYQPSDLMECVKDLHRLYC 322 (362)
Q Consensus 250 -~~~~l-a~~l~elsL~d~~~l~y~PS~iAaAai~lA~~~l~~~~~~w~~~L~~~t~~~~~~l~~c~~~L~~l~~ 322 (362)
+.+.+ ...|++++++|...+.|+.+.|||||++.-.. ....++.+|+...+|.+|++.|.-++.
T Consensus 271 ~~~efiqiaqlLDlc~ldids~~fsYrilaAAal~h~~s---------~e~v~kaSG~~w~~ie~cv~wm~Pf~r 336 (408)
T KOG0655|consen 271 SQEEFIQIAQLLDLCILDIDSLEFSYRILAAAALCHFTS---------IEVVKKASGLEWDSIEECVDWMVPFVR 336 (408)
T ss_pred chHHHHHHHHHHHHHHhccccccchHHHHHHHHHHHHhH---------HHHHHHcccccHHHHHHHHHHHHHHHH
Confidence 11111 24467899999999999999999999986433 235788999999999999999987654
No 5
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.2e-37 Score=292.39 Aligned_cols=221 Identities=28% Similarity=0.450 Sum_probs=188.5
Q ss_pred hhHHHHHHHHHHHHhhcCCCcchHhhhcccCCHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchh---
Q 017988 94 TFACDIYKHLRASEVKKRPSTDFMEIIQKDINASMRAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQR--- 170 (362)
Q Consensus 94 ~y~~dI~~~l~~~E~~~~p~~~y~~~~q~~i~~~~R~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~--- 170 (362)
-+.++++..|.+.|..+.|..+|...+|..+++.||.++++||.+||+++++.++|+++|+|||||||+.+.+++.+
T Consensus 43 ~~~e~~i~~ll~kEe~~~p~~~~~~~~~~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~ 122 (335)
T KOG0656|consen 43 LWDERVLANLLEKEEQHNPSLDYFLCVQKLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWM 122 (335)
T ss_pred cccHHHHHHHHHHHHHhCCCCchhhhcccccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHH
Confidence 35678999999999999999998888899999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHhhhccccccCHHHHH-HhhcCCCCHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHccCCCCchh
Q 017988 171 LQLLGVACMMIAAKYEEICAPQVEEFC-FITDNTYFKEEVLEMESSILNYLKFEMTAPTAKCFLRRFVRAAQGINEVPSM 249 (362)
Q Consensus 171 lqLva~tcL~IAsK~eE~~~p~i~~l~-~i~~~~~t~~ei~~mE~~IL~~L~f~l~~pT~~~FL~~~l~~~~~~~~~~~~ 249 (362)
+||+|+|||+||||+||+.+|.+.++. ..+++.|.++.|.+||+.||++|+|+++.+||++|+++|+..+.........
T Consensus 123 lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~~~ 202 (335)
T KOG0656|consen 123 LQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNKHL 202 (335)
T ss_pred HHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcccchHHH
Confidence 999999999999999999888877774 7789999999999999999999999999999999999999998776444444
Q ss_pred HHHHHHHHHHHHhhccccccCccHHHHHHHHHHHHHHhhcCCC-CCCcHHHHhhhCCChhhHHHHHH
Q 017988 250 QLECLANYVTELSLLDYSMLCHAPSLIAASAIFLAKYILLPAK-RPWNSTLQHYTLYQPSDLMECVK 315 (362)
Q Consensus 250 ~~~~la~~l~elsL~d~~~l~y~PS~iAaAai~lA~~~l~~~~-~~w~~~L~~~t~~~~~~l~~c~~ 315 (362)
...+...+++ .+..|.+|+.|+||+||+|++.++...+.+.. ......+..+...+.+.+..|+.
T Consensus 203 ~~~~~s~~ll-~~~~d~~Fl~y~pSviAaa~~~~v~~~~~~l~~~~~~~~~~~~~~l~~e~~~~~~~ 268 (335)
T KOG0656|consen 203 FLKHASLFLL-SVITDIKFLEYPPSVIAAAAILSVSASVDGLDFREYENNLLSLLSLSKEKVNRCYD 268 (335)
T ss_pred HHHHHHHHHH-HHhhhhhhhcCChHHHHHHHHHHHHHhhcchhhhhhhHHHHHHHHhhHHhhhcchh
Confidence 4444455555 56789999999999999998887766653221 11234556666677777777777
No 6
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=99.94 E-value=6.6e-27 Score=195.82 Aligned_cols=127 Identities=40% Similarity=0.793 Sum_probs=116.8
Q ss_pred HHHHHHHHHHhhcCCCcchHhhhcccCCHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHH
Q 017988 98 DIYKHLRASEVKKRPSTDFMEIIQKDINASMRAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVA 177 (362)
Q Consensus 98 dI~~~l~~~E~~~~p~~~y~~~~q~~i~~~~R~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~t 177 (362)
||++++++.|.++.|++.|++. |++++..+|..+++||.+++..++++++|+++|+.|||||+.+.++.+.+++++|+|
T Consensus 1 ~i~~~~~~~e~~~~~~~~~~~~-~~~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~ 79 (127)
T PF00134_consen 1 DIFRYLLEKELKYKPNPDYLEQ-QPEITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALA 79 (127)
T ss_dssp HHHHHHHHHHHHTTCCTTHGTG-TSSHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHH
T ss_pred CHHHHHHHHHHHHCcCcccccc-ChhcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhh
Confidence 7999999999999999999985 778999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhccccccCHHHHHHhhcCCCCHHHHHHHHHHHHHHcCCCcc
Q 017988 178 CMMIAAKYEEICAPQVEEFCFITDNTYFKEEVLEMESSILNYLKFEMT 225 (362)
Q Consensus 178 cL~IAsK~eE~~~p~i~~l~~i~~~~~t~~ei~~mE~~IL~~L~f~l~ 225 (362)
||+||+|++|..+|.+.+++.++++.|++++|.+||+.||++|+|+++
T Consensus 80 cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 80 CLFLASKMEEDNPPSISDLIRISDNTFTKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp HHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHHHHHHHHHTTT---
T ss_pred HHHHhhhhhccccchHHHHHHHHcCCCCHHHHHHHHHHHHHHCCCCcC
Confidence 999999999999999999999999999999999999999999999985
No 7
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.90 E-value=1.3e-22 Score=193.78 Aligned_cols=162 Identities=19% Similarity=0.228 Sum_probs=133.1
Q ss_pred HHHHHHHHHHHHHHHHcC--CchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcCC-
Q 017988 127 SMRAILIDWLVEVAEEYR--LVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDNT- 203 (362)
Q Consensus 127 ~~R~~lvdwl~ev~~~~~--l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~~- 203 (362)
..|..-..+|.++|.+++ |+.+|+++|+.||+||+.++++...+.+++|+||||||||+||. +.++.+++......
T Consensus 54 ~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~-~~si~~fv~~~~~~~ 132 (305)
T TIGR00569 54 DLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEF-NVSIDQFVGNLKETP 132 (305)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhcccc-CcCHHHHHhhccCCc
Confidence 568888899999999999 99999999999999999999999999999999999999999996 45889998766543
Q ss_pred -CCHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHccCC--CCchhHHHHHHHHHHHHhhccccccCccHHHHHHHH
Q 017988 204 -YFKEEVLEMESSILNYLKFEMTAPTAKCFLRRFVRAAQGIN--EVPSMQLECLANYVTELSLLDYSMLCHAPSLIAASA 280 (362)
Q Consensus 204 -~t~~ei~~mE~~IL~~L~f~l~~pT~~~FL~~~l~~~~~~~--~~~~~~~~~la~~l~elsL~d~~~l~y~PS~iAaAa 280 (362)
...++|++||..||+.|+|++.+++|+.+|..|+..++... ......+...+..+++-+++..-++.|+||.||+||
T Consensus 133 ~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAA 212 (305)
T TIGR00569 133 LKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAA 212 (305)
T ss_pred hhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHHHHHH
Confidence 35699999999999999999999999999999986554211 011112334444444445544457889999999999
Q ss_pred HHHHHHhhc
Q 017988 281 IFLAKYILL 289 (362)
Q Consensus 281 i~lA~~~l~ 289 (362)
|++|...++
T Consensus 213 I~lA~~~~~ 221 (305)
T TIGR00569 213 ILHTASRAG 221 (305)
T ss_pred HHHHHHHhC
Confidence 999998885
No 8
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.87 E-value=1.2e-21 Score=186.89 Aligned_cols=203 Identities=16% Similarity=0.183 Sum_probs=169.4
Q ss_pred cccCCHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhh
Q 017988 121 QKDINASMRAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFIT 200 (362)
Q Consensus 121 q~~i~~~~R~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~ 200 (362)
...-....|.....||.+++.+++++..|+.+|+.||+||+..+++.....+.+|++|||||+|.|| .+-++++++..+
T Consensus 31 ~~~~E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEe-tp~kl~dIi~~s 109 (323)
T KOG0834|consen 31 DLKKELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEE-TPRKLEDIIKVS 109 (323)
T ss_pred chhHHHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhccc-CcccHHHHHHHH
Confidence 3334456799999999999999999999999999999999999999999999999999999999999 577889988766
Q ss_pred cCCCC-------------HHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHhhcccc
Q 017988 201 DNTYF-------------KEEVLEMESSILNYLKFEMTAPTAKCFLRRFVRAAQGINEVPSMQLECLANYVTELSLLDYS 267 (362)
Q Consensus 201 ~~~~t-------------~~ei~~mE~~IL~~L~f~l~~pT~~~FL~~~l~~~~~~~~~~~~~~~~la~~l~elsL~d~~ 267 (362)
...+. ++.|+..|+.||++|+|++++-.||.||-.|++.++...... ..+..+|+.++..++...-
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~-~~~a~~Aw~~~nD~~~t~~ 188 (323)
T KOG0834|consen 110 YRYLNPKDLELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLK-QPLAQAAWNFVNDSLRTTL 188 (323)
T ss_pred HHHcCcccccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhcc-ccHHHHHHHHhchhheeee
Confidence 54333 467999999999999999999999999999999887654321 2356788888888888888
Q ss_pred ccCccHHHHHHHHHHHHHHhhcCCCCCCcHH-HHhhhC--CChhhHHHHHHHHHHHHhcCC
Q 017988 268 MLCHAPSLIAASAIFLAKYILLPAKRPWNST-LQHYTL--YQPSDLMECVKDLHRLYCNSQ 325 (362)
Q Consensus 268 ~l~y~PS~iAaAai~lA~~~l~~~~~~w~~~-L~~~t~--~~~~~l~~c~~~L~~l~~~~~ 325 (362)
+++|+|..||+|||.+|....+-..+.|... .....+ .+.+++.+.+..+..+|....
T Consensus 189 cL~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y~~~~ 249 (323)
T KOG0834|consen 189 CLQYSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHEFLDLYEQTP 249 (323)
T ss_pred eEeecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHHHHHHHhhcc
Confidence 8999999999999999999886433333322 234445 888999999999999997654
No 9
>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=99.85 E-value=4e-21 Score=158.25 Aligned_cols=118 Identities=42% Similarity=0.682 Sum_probs=101.3
Q ss_pred CCHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHhhccccccCccHHHHHHHHHHHHHHhhcCCCCCCcHHHHhhhCCC
Q 017988 227 PTAKCFLRRFVRAAQGINEVPSMQLECLANYVTELSLLDYSMLCHAPSLIAASAIFLAKYILLPAKRPWNSTLQHYTLYQ 306 (362)
Q Consensus 227 pT~~~FL~~~l~~~~~~~~~~~~~~~~la~~l~elsL~d~~~l~y~PS~iAaAai~lA~~~l~~~~~~w~~~L~~~t~~~ 306 (362)
|||++||++|++..+. ...+..+++|++|++++++.|++|+||+||+||+++|+.+++ ....|...+..++|++
T Consensus 1 PTp~~Fl~~~~~~~~~-----~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~-~~~~~~~~l~~~t~~~ 74 (118)
T PF02984_consen 1 PTPYDFLRRFLKISNA-----DQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILG-KEPPWPESLEKLTGYD 74 (118)
T ss_dssp --HHHHHHHHHTSSSH-----HHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHH-SSTCSHHHHHHHHTS-
T ss_pred CcHHHHHHHHHHHcCC-----cHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhC-ccccCCccchhhcCCC
Confidence 8999999999654222 335789999999999999999999999999999999999984 4468999999999999
Q ss_pred hhhHHHHHHHHHHHHhcCCCCChhHHHHhhcCCcccccccccCC
Q 017988 307 PSDLMECVKDLHRLYCNSQSSTLPAIREKYSLHKYKCVAKKYCP 350 (362)
Q Consensus 307 ~~~l~~c~~~L~~l~~~~~~~~~~~i~~KY~~~~~~~va~~~~p 350 (362)
.+++.+|++.|.+++.+.....+.++++||++++|++||....|
T Consensus 75 ~~~l~~c~~~i~~~~~~~~~~~~~ai~~Kys~~~~~~vs~~~~~ 118 (118)
T PF02984_consen 75 KEDLKECIELIQELLSKASNSKLQAIRKKYSSQKFSSVSQIPPP 118 (118)
T ss_dssp HHHHHHHHHHHHHHHHHCCGSSCTHHHHHTTSGGGTTGGGSS--
T ss_pred HHHHHHHHHHHHHHHHhcCCccchHHHHHhCccccCCccCCCCC
Confidence 99999999999999998777889999999999999999998655
No 10
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.80 E-value=3.5e-18 Score=159.58 Aligned_cols=194 Identities=19% Similarity=0.246 Sum_probs=164.4
Q ss_pred ccCCHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhc
Q 017988 122 KDINASMRAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITD 201 (362)
Q Consensus 122 ~~i~~~~R~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~ 201 (362)
.+-..+.|..-+.||.+.+.-++|+..+.+.+..+|-||+...++-+.++..++.+|++||||+||. |-.+.+++.+..
T Consensus 16 ~e~e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~-Prr~rdVinVFh 94 (367)
T KOG0835|consen 16 LETEEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEE-PRRIRDVINVFH 94 (367)
T ss_pred cchHHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccc-cccHhHHHHHHH
Confidence 3455678999999999999999999999999999999999999999999999999999999999994 556666554432
Q ss_pred C--------C---------C--CHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHh
Q 017988 202 N--------T---------Y--FKEEVLEMESSILNYLKFEMTAPTAKCFLRRFVRAAQGINEVPSMQLECLANYVTELS 262 (362)
Q Consensus 202 ~--------~---------~--t~~ei~~mE~~IL~~L~f~l~~pT~~~FL~~~l~~~~~~~~~~~~~~~~la~~l~els 262 (362)
. . | .+..+.++|..||+.|+|++.+..|+.++-.|+..++.... ..+.+.++-+++.+
T Consensus 95 ~L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~---~~l~Q~~wNfmNDs 171 (367)
T KOG0835|consen 95 YLEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPN---LKLLQAAWNFMNDS 171 (367)
T ss_pred HHHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCc---hhHHHHHHHhhhhc
Confidence 1 0 1 24568899999999999999999999999999998877543 24567788888899
Q ss_pred hccccccCccHHHHHHHHHHHHHHhhc---CCCCCCcHHHHhhhCCChhhHHHHHHHHHHHHhc
Q 017988 263 LLDYSMLCHAPSLIAASAIFLAKYILL---PAKRPWNSTLQHYTLYQPSDLMECVKDLHRLYCN 323 (362)
Q Consensus 263 L~d~~~l~y~PS~iAaAai~lA~~~l~---~~~~~w~~~L~~~t~~~~~~l~~c~~~L~~l~~~ 323 (362)
+-.--|+.|+|+.||||||++|.+.++ +..+.|. .+.+.+.+++.+..-.+..+|..
T Consensus 172 lRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf----~~Fd~~k~eid~ic~~l~~lY~~ 231 (367)
T KOG0835|consen 172 LRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWF----KAFDTTKREIDEICYRLIPLYKR 231 (367)
T ss_pred cccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHH----HHcCCcHHHHHHHHHHHHHHHHh
Confidence 988889999999999999999999886 4566663 45588899999988888888887
No 11
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.79 E-value=4.6e-19 Score=158.25 Aligned_cols=189 Identities=19% Similarity=0.241 Sum_probs=155.0
Q ss_pred HHHHHHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhh--------
Q 017988 129 RAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFIT-------- 200 (362)
Q Consensus 129 R~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~-------- 200 (362)
+--.-+.|..+++++++...++.+|+.||-||+.+.++..-.+.++|.||++||||+||.....++.++..+
T Consensus 41 ~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~ 120 (264)
T KOG0794|consen 41 KIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFS 120 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcc
Confidence 444556788999999999999999999999999999999999999999999999999995323344443221
Q ss_pred ----cCCCCHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHhhccccccCccHHHH
Q 017988 201 ----DNTYFKEEVLEMESSILNYLKFEMTAPTAKCFLRRFVRAAQGINEVPSMQLECLANYVTELSLLDYSMLCHAPSLI 276 (362)
Q Consensus 201 ----~~~~t~~ei~~mE~~IL~~L~f~l~~pT~~~FL~~~l~~~~~~~~~~~~~~~~la~~l~elsL~d~~~l~y~PS~i 276 (362)
...|...+|.+||..+|+.|++-|-+.+|+.-|..++..++..+. ...++++.+.+.++...-.+-|+|..|
T Consensus 121 ~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~d~----~~l~~~W~ivNDSyr~Dl~Ll~PPh~I 196 (264)
T KOG0794|consen 121 YWPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGINDQ----KLLQLAWSIVNDSYRMDLCLLYPPHQI 196 (264)
T ss_pred cchhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcccch----hhhhhhHhhhcchhhcceeeecCHHHH
Confidence 134667889999999999999999999999999999987765322 345788888888887767788999999
Q ss_pred HHHHHHHHHHhhcCCC-CCCcHHHHhhhCCChhhHHHHHHHHHHHHhcCC
Q 017988 277 AASAIFLAKYILLPAK-RPWNSTLQHYTLYQPSDLMECVKDLHRLYCNSQ 325 (362)
Q Consensus 277 AaAai~lA~~~l~~~~-~~w~~~L~~~t~~~~~~l~~c~~~L~~l~~~~~ 325 (362)
|.|||++|....+.+. ..|...+ ..+.+.+.+|++++..+|..-+
T Consensus 197 alAcl~Ia~~~~~k~~~~~w~~el----~vD~ekV~~~v~~I~~lYe~wk 242 (264)
T KOG0794|consen 197 ALACLYIACVIDEKDIPKAWFAEL----SVDMEKVKDIVQEILKLYELWK 242 (264)
T ss_pred HHHHHHHHHhhcCCChHHHHHHHH----hccHHHHHHHHHHHHHHHHHHh
Confidence 9999999999886544 4565554 5788999999999999986533
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=99.73 E-value=5.7e-17 Score=151.57 Aligned_cols=167 Identities=18% Similarity=0.269 Sum_probs=140.9
Q ss_pred CHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcC--
Q 017988 125 NASMRAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDN-- 202 (362)
Q Consensus 125 ~~~~R~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~-- 202 (362)
..+.|..-..|+..+|.+++++..++.+||.+|+||+.+.++....++-++.||++||+|.||. +-.+.-.....++
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 3456777778999999999999999999999999999999999999999999999999999994 3333333333332
Q ss_pred ----CCCHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHhhccccccCccHHHHHH
Q 017988 203 ----TYFKEEVLEMESSILNYLKFEMTAPTAKCFLRRFVRAAQGINEVPSMQLECLANYVTELSLLDYSMLCHAPSLIAA 278 (362)
Q Consensus 203 ----~~t~~ei~~mE~~IL~~L~f~l~~pT~~~FL~~~l~~~~~~~~~~~~~~~~la~~l~elsL~d~~~l~y~PS~iAa 278 (362)
.-+++.|..+|..+|+.|+|++.++.|+..+..|+..++.... .+...+|+-++..++...-++.|+|..||+
T Consensus 120 se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~---~~~~~~aw~~inDa~~t~~~llypphiIA~ 196 (297)
T COG5333 120 SEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDK---YKLLQIAWKIINDALRTDLCLLYPPHIIAL 196 (297)
T ss_pred cccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccH---HHHHHHHHHHHHhhhhceeeeecChHHHHH
Confidence 2368899999999999999999999999999999988776542 345678888888888888899999999999
Q ss_pred HHHHHHHHhhcCCCCCCcH
Q 017988 279 SAIFLAKYILLPAKRPWNS 297 (362)
Q Consensus 279 Aai~lA~~~l~~~~~~w~~ 297 (362)
||+..|...+ +.+.|..
T Consensus 197 a~l~ia~~~~--~~~~~~~ 213 (297)
T COG5333 197 AALLIACEVL--GMPIIKL 213 (297)
T ss_pred HHHHHHHHhc--CCccchh
Confidence 9999999987 4555644
No 13
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.55 E-value=1.3e-12 Score=126.19 Aligned_cols=182 Identities=13% Similarity=0.108 Sum_probs=155.0
Q ss_pred HHHHHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcCCCCHHHH
Q 017988 130 AILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDNTYFKEEV 209 (362)
Q Consensus 130 ~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~~~t~~ei 209 (362)
.....-|-+++..++|+..+.-.|..++.+++....+.......++++|+|+|||.+. .|-++.+++.+++ .++.+|
T Consensus 123 ~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~-~prtl~eI~~~~~--v~~k~i 199 (310)
T PRK00423 123 AFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCK-VPRTLDEIAEVSR--VSRKEI 199 (310)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcC-CCcCHHHHHHHhC--CCHHHH
Confidence 4455678899999999999999999999999999888888999999999999999977 4679999998876 689999
Q ss_pred HHHHHHHHHHcCCCccCCCHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHhhccccccCccHHHHHHHHHHHHHHhhc
Q 017988 210 LEMESSILNYLKFEMTAPTAKCFLRRFVRAAQGINEVPSMQLECLANYVTELSLLDYSMLCHAPSLIAASAIFLAKYILL 289 (362)
Q Consensus 210 ~~mE~~IL~~L~f~l~~pT~~~FL~~~l~~~~~~~~~~~~~~~~la~~l~elsL~d~~~l~y~PS~iAaAai~lA~~~l~ 289 (362)
.+.++.|++.|++++....|.+|+.+|...++... .+...|..+++.+.-..-..+.+|..|||||||+|.+..
T Consensus 200 ~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~-----~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~- 273 (310)
T PRK00423 200 GRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSG-----EVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLL- 273 (310)
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCH-----HHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHh-
Confidence 99999999999999999999999999999887543 355677777765543333467999999999999999887
Q ss_pred CCCCCCcHHHHhhhCCChhhHHHHHHHHHHHH
Q 017988 290 PAKRPWNSTLQHYTLYQPSDLMECVKDLHRLY 321 (362)
Q Consensus 290 ~~~~~w~~~L~~~t~~~~~~l~~c~~~L~~l~ 321 (362)
+.+.-...+...+|.+...+...++.|.+.+
T Consensus 274 -g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 274 -GERRTQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred -CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 3333456788899999999999999988754
No 14
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=99.54 E-value=2.9e-14 Score=109.97 Aligned_cols=87 Identities=36% Similarity=0.553 Sum_probs=81.6
Q ss_pred HHHHHHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcCCCCHHH
Q 017988 129 RAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDNTYFKEE 208 (362)
Q Consensus 129 R~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~~~t~~e 208 (362)
|...++||.+++..++++++|.++|+.++|||+....+.+.+++++|+||++||+|+++. ++...++..+++.. +.++
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 678899999999999999999999999999999999999999999999999999999998 88999999888754 8999
Q ss_pred HHHHHHHHH
Q 017988 209 VLEMESSIL 217 (362)
Q Consensus 209 i~~mE~~IL 217 (362)
|.++|+.|+
T Consensus 80 i~~~e~~il 88 (88)
T cd00043 80 ILRMEKLLL 88 (88)
T ss_pred HHHHHHHhC
Confidence 999999874
No 15
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=99.46 E-value=1.9e-13 Score=104.36 Aligned_cols=83 Identities=37% Similarity=0.557 Sum_probs=76.0
Q ss_pred HHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcCCCCHHHHHHHH
Q 017988 134 DWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDNTYFKEEVLEME 213 (362)
Q Consensus 134 dwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~~~t~~ei~~mE 213 (362)
+||.+++..+++++++.++|+.++||++....+.+.+.+++|++|++||+|++|.. +...++..+++. |+.++|.++|
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 59999999999999999999999999999877778999999999999999999975 677888888776 7999999999
Q ss_pred HHHHH
Q 017988 214 SSILN 218 (362)
Q Consensus 214 ~~IL~ 218 (362)
+.||.
T Consensus 79 ~~il~ 83 (83)
T smart00385 79 KLLLE 83 (83)
T ss_pred HHHhC
Confidence 99874
No 16
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=99.46 E-value=2.8e-12 Score=119.34 Aligned_cols=153 Identities=23% Similarity=0.277 Sum_probs=118.8
Q ss_pred HHHHHHHHHHHHHc--CCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhc--CCCC
Q 017988 130 AILIDWLVEVAEEY--RLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITD--NTYF 205 (362)
Q Consensus 130 ~~lvdwl~ev~~~~--~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~--~~~t 205 (362)
..-..-+++.+.++ .+++.++.+|+.+|-||+-..++..-..+.|.+||+|+|+|++|.+ .++.+|+.-.. ..-+
T Consensus 57 k~~E~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~-ISieqFvkn~~~~~~k~ 135 (325)
T KOG2496|consen 57 KEEELSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFY-ISIEQFVKNMNGRKWKT 135 (325)
T ss_pred HHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhhe-ecHHHHHhhccCccccc
Confidence 34445566777776 4789999999999999999999999999999999999999999965 58999986544 2346
Q ss_pred HHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHccC---CCCchhHHHHHH--HHHHHHhhccccccCccHHHHHHHH
Q 017988 206 KEEVLEMESSILNYLKFEMTAPTAKCFLRRFVRAAQGI---NEVPSMQLECLA--NYVTELSLLDYSMLCHAPSLIAASA 280 (362)
Q Consensus 206 ~~ei~~mE~~IL~~L~f~l~~pT~~~FL~~~l~~~~~~---~~~~~~~~~~la--~~l~elsL~d~~~l~y~PS~iAaAa 280 (362)
.+.|+..|..+++.|+|++.+.+|+.-++-|+..++.. .+++.......- .++-...+.| .++-|+||+||.||
T Consensus 136 ~e~vLk~E~~llqsL~f~L~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltD-a~lLytPsQIALaA 214 (325)
T KOG2496|consen 136 HEIVLKYEFLLLQSLKFSLTVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTD-AYLLYTPSQIALAA 214 (325)
T ss_pred HHHHHhchHHHHHhhhhhheecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhc-cceecChHHHHHHH
Confidence 88999999999999999999999999999998765432 122222222222 4555444555 56669999999999
Q ss_pred HHHH
Q 017988 281 IFLA 284 (362)
Q Consensus 281 i~lA 284 (362)
|..|
T Consensus 215 il~a 218 (325)
T KOG2496|consen 215 ILHA 218 (325)
T ss_pred HHHH
Confidence 9555
No 17
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.02 E-value=1.8e-08 Score=93.91 Aligned_cols=177 Identities=15% Similarity=0.162 Sum_probs=148.2
Q ss_pred HHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcCCCCHHHHHHH
Q 017988 133 IDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDNTYFKEEVLEM 212 (362)
Q Consensus 133 vdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~~~t~~ei~~m 212 (362)
..-|..++...+|+....-.|-.+|-++-..+.......+-+++|||+|||.-++ .|-++++++.+++ .+++||-+.
T Consensus 108 ~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~-~pRT~kEI~~~an--v~kKEIgr~ 184 (308)
T KOG1597|consen 108 FKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQED-VPRTFKEISAVAN--VSKKEIGRC 184 (308)
T ss_pred HHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcC-CCchHHHHHHHHc--CCHHHHHHH
Confidence 3446789999999999999999999999988888888999999999999999877 5779999998888 789999999
Q ss_pred HHHHHHHcCCCccCCC--HHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHhhccccc-cCccHHHHHHHHHHHHHHhhc
Q 017988 213 ESSILNYLKFEMTAPT--AKCFLRRFVRAAQGINEVPSMQLECLANYVTELSLLDYSM-LCHAPSLIAASAIFLAKYILL 289 (362)
Q Consensus 213 E~~IL~~L~f~l~~pT--~~~FL~~~l~~~~~~~~~~~~~~~~la~~l~elsL~d~~~-l~y~PS~iAaAai~lA~~~l~ 289 (362)
=+.|+..|+=.+..-| .-+|+.+|...++.++ +....|..+++.+- +..+ .+-.|=.||||+||++.++.
T Consensus 185 ~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~-----~~q~aA~e~a~ka~-~~~~~~gRsPiSIAAa~IYmisqls- 257 (308)
T KOG1597|consen 185 VKLIGEALETSVDLISISTGDFMPRFCSNLGLPK-----SAQEAATEIAEKAE-EMDIRAGRSPISIAAAAIYMISQLS- 257 (308)
T ss_pred HHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCH-----HHHHHHHHHHHHHH-HhccccCCCchhHHHHHHHHHHHhc-
Confidence 9999999998877666 7899999998887654 44567777776543 2233 34789999999999999887
Q ss_pred CCCCCCcHHHHhhhCCChhhHHHHHHHHHHH
Q 017988 290 PAKRPWNSTLQHYTLYQPSDLMECVKDLHRL 320 (362)
Q Consensus 290 ~~~~~w~~~L~~~t~~~~~~l~~c~~~L~~l 320 (362)
..+.-...+...||..+.-++..++.|+.-
T Consensus 258 -~~kkt~keI~~vtgVaE~TIr~sYK~Lyp~ 287 (308)
T KOG1597|consen 258 -DEKKTQKEIGEVTGVAEVTIRNSYKDLYPH 287 (308)
T ss_pred -cCcccHHHHHHHhhhhHHHHHHHHHHHhhc
Confidence 355567889999999999999999888753
No 18
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=98.94 E-value=1.3e-07 Score=89.86 Aligned_cols=182 Identities=14% Similarity=0.148 Sum_probs=154.4
Q ss_pred HHHHHHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcCCCCHHH
Q 017988 129 RAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDNTYFKEE 208 (362)
Q Consensus 129 R~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~~~t~~e 208 (362)
-.....-|-.++..++|+..+.-.|..++=+.+.+.-+.....+-++++|+++||+... .|-++.++..+.+ .++.+
T Consensus 97 l~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~-~prtl~eIa~a~~--V~~ke 173 (285)
T COG1405 97 LITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRING-VPRTLDEIAKALG--VSKKE 173 (285)
T ss_pred HHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcC-CCccHHHHHHHHC--CCHHH
Confidence 45566778899999999999999999999999999999999999999999999999977 4678888888877 67899
Q ss_pred HHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHhhccccccCccHHHHHHHHHHHHHHhh
Q 017988 209 VLEMESSILNYLKFEMTAPTAKCFLRRFVRAAQGINEVPSMQLECLANYVTELSLLDYSMLCHAPSLIAASAIFLAKYIL 288 (362)
Q Consensus 209 i~~mE~~IL~~L~f~l~~pT~~~FL~~~l~~~~~~~~~~~~~~~~la~~l~elsL~d~~~l~y~PS~iAaAai~lA~~~l 288 (362)
|.++.+.+.+.|+=.+.+..|.+|+.+|...++.+. .+...|..|+..+.-.-...+-.|+-+|+||+|+|..+.
T Consensus 174 i~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~-----~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~ 248 (285)
T COG1405 174 IGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSD-----EVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLL 248 (285)
T ss_pred HHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCH-----HHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHh
Confidence 999999999999999999999999999999987664 345667777766665555568999999999999999988
Q ss_pred cCCCCCCcHHHHhhhCCChhhHHHHHHHHHHH
Q 017988 289 LPAKRPWNSTLQHYTLYQPSDLMECVKDLHRL 320 (362)
Q Consensus 289 ~~~~~~w~~~L~~~t~~~~~~l~~c~~~L~~l 320 (362)
+...-.....+++|.++..|+.=++.|.+-
T Consensus 249 --~~~~tq~eva~v~~vtevTIrnrykel~~~ 278 (285)
T COG1405 249 --GERRTQKEVAKVAGVTEVTIRNRYKELADA 278 (285)
T ss_pred --CCchHHHHHHHHhCCeeeHHHHHHHHHHHh
Confidence 344456678899999998888877776653
No 19
>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=98.69 E-value=1.4e-07 Score=81.62 Aligned_cols=91 Identities=19% Similarity=0.355 Sum_probs=72.7
Q ss_pred HHHHHHHHHHHcCCchHHHHHHHHHHHhhcc---C--CcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcCCCCH
Q 017988 132 LIDWLVEVAEEYRLVPDTLYLTVNYIDRYLS---G--NPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDNTYFK 206 (362)
Q Consensus 132 lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs---~--~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~~~t~ 206 (362)
+.+|+.++....+++++++-+|..|+||+.. . ..+.....+-+-++|+.+|+|+-+.....-+.+..+++ ++.
T Consensus 54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~g--is~ 131 (149)
T PF08613_consen 54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGG--ISL 131 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHT--S-H
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcC--CCH
Confidence 7789999999999999999999999999998 2 23667778999999999999998887778888888876 799
Q ss_pred HHHHHHHHHHHHHcCCCc
Q 017988 207 EEVLEMESSILNYLKFEM 224 (362)
Q Consensus 207 ~ei~~mE~~IL~~L~f~l 224 (362)
+|+.+||+..|..|+|+|
T Consensus 132 ~eln~lE~~fL~~l~~~L 149 (149)
T PF08613_consen 132 KELNELEREFLKLLDYNL 149 (149)
T ss_dssp HHHHHHHHHHHHHTTT--
T ss_pred HHHHHHHHHHHHHCCCcC
Confidence 999999999999999986
No 20
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.67 E-value=1.1e-07 Score=72.04 Aligned_cols=81 Identities=36% Similarity=0.448 Sum_probs=69.0
Q ss_pred HHHHHHHHHHccCCCCchhHHHHHHHHHHHHhhccccccCccHHHHHHHHHHHHHHhhcCCCCCCcHHHHhhhCC-Chhh
Q 017988 231 CFLRRFVRAAQGINEVPSMQLECLANYVTELSLLDYSMLCHAPSLIAASAIFLAKYILLPAKRPWNSTLQHYTLY-QPSD 309 (362)
Q Consensus 231 ~FL~~~l~~~~~~~~~~~~~~~~la~~l~elsL~d~~~l~y~PS~iAaAai~lA~~~l~~~~~~w~~~L~~~t~~-~~~~ 309 (362)
+|+.++...++.+. .+..+|.++++..+.++.+.+++|+.||+||+++|.+.. +..+|...+..++|+ +.++
T Consensus 1 ~~l~~~~~~~~~~~-----~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~--~~~~~~~~~~~~~~~~~~~~ 73 (83)
T smart00385 1 DFLRRVCKALNLDP-----ETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTE--EIPPWTKELVHYTGYFTEEE 73 (83)
T ss_pred CHHHHHHHHcCCCH-----HHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHh--cCCCCchhHhHhhCCCCHHH
Confidence 37777777765532 467889999999999889999999999999999999998 345799999999999 9999
Q ss_pred HHHHHHHHH
Q 017988 310 LMECVKDLH 318 (362)
Q Consensus 310 l~~c~~~L~ 318 (362)
+.+|...|.
T Consensus 74 i~~~~~~il 82 (83)
T smart00385 74 ILRMEKLLL 82 (83)
T ss_pred HHHHHHHHh
Confidence 999988775
No 21
>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=98.55 E-value=6.5e-07 Score=68.47 Aligned_cols=85 Identities=36% Similarity=0.480 Sum_probs=73.8
Q ss_pred CCCHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHhhccccccCccHHHHHHHHHHHHHHhhcCCCCCCcHHHHhhhCC
Q 017988 226 APTAKCFLRRFVRAAQGINEVPSMQLECLANYVTELSLLDYSMLCHAPSLIAASAIFLAKYILLPAKRPWNSTLQHYTLY 305 (362)
Q Consensus 226 ~pT~~~FL~~~l~~~~~~~~~~~~~~~~la~~l~elsL~d~~~l~y~PS~iAaAai~lA~~~l~~~~~~w~~~L~~~t~~ 305 (362)
.|++.+|+.++...++... ....+|.++.+..+....+..+.|+.||+||+++|.+.. +...|...+..++++
T Consensus 2 ~~~~~~~l~~~~~~~~~~~-----~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~--~~~~~~~~~~~~~~~ 74 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSP-----ETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVE--EIPPWLKDLVHVTGY 74 (88)
T ss_pred cchHHHHHHHHHHHcCCCH-----HHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHc--CCCCCHHHHhHHhCC
Confidence 5789999999998875432 456889999999999888999999999999999999988 348899999999999
Q ss_pred -ChhhHHHHHHHH
Q 017988 306 -QPSDLMECVKDL 317 (362)
Q Consensus 306 -~~~~l~~c~~~L 317 (362)
+.+++..+...|
T Consensus 75 ~~~~~i~~~e~~i 87 (88)
T cd00043 75 ATEEEILRMEKLL 87 (88)
T ss_pred CCHHHHHHHHHHh
Confidence 999998887765
No 22
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=97.94 E-value=1.1e-05 Score=78.06 Aligned_cols=99 Identities=19% Similarity=0.319 Sum_probs=86.9
Q ss_pred HHHHHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcC--CCCHH
Q 017988 130 AILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDN--TYFKE 207 (362)
Q Consensus 130 ~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~--~~t~~ 207 (362)
+.+-.-|.++++..++..-|+.+|-.||.....+..+++.+-+|.|.|||++|+|+.+..--.++.++.-.+. .+.+.
T Consensus 383 rSlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrr 462 (497)
T KOG4164|consen 383 RSLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRR 462 (497)
T ss_pred HHHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHH
Confidence 3455668889999999999999999999999999999999999999999999999998777778887765543 46899
Q ss_pred HHHHHHHHHHHHcCCCccCCC
Q 017988 208 EVLEMESSILNYLKFEMTAPT 228 (362)
Q Consensus 208 ei~~mE~~IL~~L~f~l~~pT 228 (362)
|++..|.-||-.|+|.|..|-
T Consensus 463 dLia~Ef~VlvaLefaL~~~~ 483 (497)
T KOG4164|consen 463 DLIAFEFPVLVALEFALHLPE 483 (497)
T ss_pred hhhhhhhhHHHhhhhhccCCh
Confidence 999999999999999998753
No 23
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=96.86 E-value=0.0088 Score=60.68 Aligned_cols=148 Identities=13% Similarity=0.093 Sum_probs=109.8
Q ss_pred HHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcCCCCHHHHHHHHH
Q 017988 135 WLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDNTYFKEEVLEMES 214 (362)
Q Consensus 135 wl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~~~t~~ei~~mE~ 214 (362)
-|-+++..+++.. .+-.|.++|---+..+-.+....+.|-.+||||+|..|-..... -||..+.. .+.-++-.+=+
T Consensus 73 ~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hll-iDfS~~Lq--v~Vy~LG~~~l 148 (521)
T KOG1598|consen 73 LIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLL-IDFSSYLQ--VSVYDLGSNFL 148 (521)
T ss_pred HHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEE-EEeccceE--EehhhhhHHHH
Confidence 5788999999999 99999999999998888888999999999999999987653322 22222211 23334444555
Q ss_pred HHHHHcCCC---ccCCCHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHhhccccccCccHHHHHHHHHHHHHHhh
Q 017988 215 SILNYLKFE---MTAPTAKCFLRRFVRAAQGINEVPSMQLECLANYVTELSLLDYSMLCHAPSLIAASAIFLAKYIL 288 (362)
Q Consensus 215 ~IL~~L~f~---l~~pT~~~FL~~~l~~~~~~~~~~~~~~~~la~~l~elsL~d~~~l~y~PS~iAaAai~lA~~~l 288 (362)
.|-..|.-+ +-...|.-|+-+|...+...... ..+-..|.+|+.-..-|.-...-+|+-|+.|||++|.++.
T Consensus 149 ~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~--~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h 223 (521)
T KOG1598|consen 149 EVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKT--EDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMH 223 (521)
T ss_pred HHHHHhccccccccccCcceeeechhHhhhcCCch--HHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHc
Confidence 666666666 56677778888888776443322 3445667888777667777788999999999999999987
No 24
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=96.72 E-value=0.0087 Score=44.76 Aligned_cols=65 Identities=9% Similarity=0.166 Sum_probs=53.2
Q ss_pred HHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhc
Q 017988 136 LVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITD 201 (362)
Q Consensus 136 l~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~ 201 (362)
|-+++..++|+..+.-.|..++++-....-.......-++++|+++||+.+. .+-++.++...++
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~-~~~t~~eIa~~~~ 65 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNG-VPRTLKEIAEAAG 65 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTT-SSSSHHHHHHHCT
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcC-CCcCHHHHHHHhC
Confidence 4578999999999999999999999888777778899999999999999876 4567888876655
No 25
>KOG1674 consensus Cyclin [General function prediction only]
Probab=96.11 E-value=0.021 Score=52.48 Aligned_cols=94 Identities=15% Similarity=0.300 Sum_probs=72.8
Q ss_pred HHHHHHHHHHHcCCchHHHHHHHHHHHhhccCCc---------Ccchh-hHHHHHHHHHHHhhhccccccCHHHHHHhhc
Q 017988 132 LIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNP---------MSRQR-LQLLGVACMMIAAKYEEICAPQVEEFCFITD 201 (362)
Q Consensus 132 lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~---------v~~~~-lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~ 201 (362)
+-+++..+.+..+.+++++-+|..|||||..+.. ++--+ ..-+-++|+.+|+|+.+..--.-.-+.++
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 3456777888889999999999999999998622 22333 55678999999999987544344444444
Q ss_pred CCCCHHHHHHHHHHHHHHcCCCccCC
Q 017988 202 NTYFKEEVLEMESSILNYLKFEMTAP 227 (362)
Q Consensus 202 ~~~t~~ei~~mE~~IL~~L~f~l~~p 227 (362)
+..+.+++..+|...|..++|++.++
T Consensus 156 ggl~~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 156 GGLTTDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred CCCChHhhhhhhHHHHhhCCeEEEec
Confidence 34788999999999999999999875
No 26
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=95.12 E-value=0.2 Score=48.54 Aligned_cols=89 Identities=15% Similarity=0.108 Sum_probs=73.4
Q ss_pred HHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcCCCCHHHHHHH
Q 017988 133 IDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDNTYFKEEVLEM 212 (362)
Q Consensus 133 vdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~~~t~~ei~~m 212 (362)
-++|..++..++|+..+.-.|..++.+.....-....+..-+|+||+|||++.... +.+.+++..+++ .+...|.+.
T Consensus 220 ~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~-~~t~keIa~v~~--Vs~~tI~~~ 296 (310)
T PRK00423 220 IDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGE-RRTQREVAEVAG--VTEVTVRNR 296 (310)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHcC--CCHHHHHHH
Confidence 48899999999999999999999999887766667788999999999999998763 457888887765 567778877
Q ss_pred HHHHHHHcCCCc
Q 017988 213 ESSILNYLKFEM 224 (362)
Q Consensus 213 E~~IL~~L~f~l 224 (362)
=+.+++.|+..+
T Consensus 297 ykel~~~l~~~~ 308 (310)
T PRK00423 297 YKELAEKLDIKI 308 (310)
T ss_pred HHHHHHHhCccc
Confidence 777777776543
No 27
>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=93.98 E-value=0.39 Score=35.72 Aligned_cols=58 Identities=14% Similarity=0.016 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHhhccccccCccHHHHHHHHHHHHHHhhcCCCCCCcHHHHhhhCCChhh
Q 017988 250 QLECLANYVTELSLLDYSMLCHAPSLIAASAIFLAKYILLPAKRPWNSTLQHYTLYQPSD 309 (362)
Q Consensus 250 ~~~~la~~l~elsL~d~~~l~y~PS~iAaAai~lA~~~l~~~~~~w~~~L~~~t~~~~~~ 309 (362)
.+...|..+.....-..-.-+-+|..+||||||+|.+.. +.+.-...+...+|.+..+
T Consensus 13 ~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~--~~~~t~~eIa~~~~Vs~~t 70 (71)
T PF00382_consen 13 DVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLN--GVPRTLKEIAEAAGVSEKT 70 (71)
T ss_dssp HHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHT--TSSSSHHHHHHHCTSSHHH
T ss_pred HHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHc--CCCcCHHHHHHHhCCCCCc
Confidence 445667777665544433456789999999999999987 4444455666666766543
No 28
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=93.57 E-value=0.11 Score=49.53 Aligned_cols=101 Identities=13% Similarity=0.210 Sum_probs=71.5
Q ss_pred HHHHHHHcCCchHHHHHHHHHHHhhccCCcCc--chhhHHHHHHHHHHHhhhccccccCHHHHHHhhcCCCCHHHHHHHH
Q 017988 136 LVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMS--RQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDNTYFKEEVLEME 213 (362)
Q Consensus 136 l~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~--~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~~~t~~ei~~mE 213 (362)
..-.+....|..+.--....|++|.+.-..+. ..+...+..-..++|+|+-....-.-.+.+.++.. .|.+|+..||
T Consensus 197 v~~l~~~~qlta~~aiitL~~~erl~~~~e~~~~p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlKd-~tveDmNe~E 275 (343)
T KOG1675|consen 197 VRILFSWAQLTAECDIITLVYAERLLWLAERDPCPRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILKD-QSVDDMNALE 275 (343)
T ss_pred hhhHhhhhhhhhccchHHHHhhHhhhhHhhcCCCcchhhhhhhhhheehhhhhhhhhcccHHHHHHHhh-ccHhhHHHHH
Confidence 34444455555555566677888887754443 66777777778999999877544444566666554 4799999999
Q ss_pred HHHHHHcCCCccCCCHHHHHHHHHH
Q 017988 214 SSILNYLKFEMTAPTAKCFLRRFVR 238 (362)
Q Consensus 214 ~~IL~~L~f~l~~pT~~~FL~~~l~ 238 (362)
+.+|..|+|++++|.. .|-.+|..
T Consensus 276 RqfLelLqfNinvp~s-vYAKyYfd 299 (343)
T KOG1675|consen 276 RQFLELLQFNINVPSS-EYAKYYFD 299 (343)
T ss_pred HHHHHHHhhccCccHH-HHHHHHHH
Confidence 9999999999999875 34455543
No 29
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=90.48 E-value=1.4 Score=35.31 Aligned_cols=87 Identities=18% Similarity=0.146 Sum_probs=57.5
Q ss_pred HHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcCCCCHHHHHHH
Q 017988 133 IDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDNTYFKEEVLEM 212 (362)
Q Consensus 133 vdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~~~t~~ei~~m 212 (362)
.+||.......+...++-.+|-.+++..+....+-....-++|++|+++|.+.-...++--..+..+++ ++.+++...
T Consensus 4 ~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~--~~~~~l~~c 81 (118)
T PF02984_consen 4 YDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTG--YDKEDLKEC 81 (118)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHT--S-HHHHHHH
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcC--CCHHHHHHH
Confidence 345555533344466788888888887777767777888999999999999996633334444556663 578887776
Q ss_pred HHHHHHHcC
Q 017988 213 ESSILNYLK 221 (362)
Q Consensus 213 E~~IL~~L~ 221 (362)
=..|.+.+.
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 555555443
No 30
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=87.53 E-value=0.61 Score=45.33 Aligned_cols=95 Identities=17% Similarity=0.174 Sum_probs=70.5
Q ss_pred HHHHHHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHH--HHhhcCCCCH
Q 017988 129 RAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEF--CFITDNTYFK 206 (362)
Q Consensus 129 R~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l--~~i~~~~~t~ 206 (362)
-.-|++|+..+...-+........|-+++...+...-.-....+-||++||+||+|+-....|...+- ....+...+.
T Consensus 152 y~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~ 231 (323)
T KOG0834|consen 152 YKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTN 231 (323)
T ss_pred hHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCH
Confidence 45566666666665555556777788888777766667778899999999999999977655544444 4556777899
Q ss_pred HHHHHHHHHHHHHcCCC
Q 017988 207 EEVLEMESSILNYLKFE 223 (362)
Q Consensus 207 ~ei~~mE~~IL~~L~f~ 223 (362)
+++..+...+|....-+
T Consensus 232 e~l~~i~~~~l~~y~~~ 248 (323)
T KOG0834|consen 232 ELLDDICHEFLDLYEQT 248 (323)
T ss_pred HHHHHHHHHHHHHHhhc
Confidence 99999988888877544
No 31
>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=86.95 E-value=5 Score=32.58 Aligned_cols=68 Identities=22% Similarity=0.232 Sum_probs=46.4
Q ss_pred HHHHHHHHHHhhccccccCccHHHHHHHHHHHHHHhhcCCCCCCcHHHHhhhC--CChhhHHHHHHHHHHH
Q 017988 252 ECLANYVTELSLLDYSMLCHAPSLIAASAIFLAKYILLPAKRPWNSTLQHYTL--YQPSDLMECVKDLHRL 320 (362)
Q Consensus 252 ~~la~~l~elsL~d~~~l~y~PS~iAaAai~lA~~~l~~~~~~w~~~L~~~t~--~~~~~l~~c~~~L~~l 320 (362)
-..|..+.+..+.........+..+|+||+++|.++. ....++...+...++ ++.+++...-..+.+.
T Consensus 52 ~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~-e~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~ 121 (127)
T PF00134_consen 52 LHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKME-EDNPPSISDLIRISDNTFTKKDILEMEREILSA 121 (127)
T ss_dssp HHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHH-TSS--HHHHHHHHTTTSSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhh-ccccchHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence 3556666666666556777899999999999999987 345566777766664 6677777665555543
No 32
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=83.18 E-value=7.6 Score=37.22 Aligned_cols=70 Identities=10% Similarity=0.064 Sum_probs=57.7
Q ss_pred HHHHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhc
Q 017988 131 ILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITD 201 (362)
Q Consensus 131 ~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~ 201 (362)
.-.+++-..+..++|+.++--.|+.+++..............-+|++|+++||+.... .-+-++...+++
T Consensus 193 ~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~-~~tq~eva~v~~ 262 (285)
T COG1405 193 DPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGE-RRTQKEVAKVAG 262 (285)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCC-chHHHHHHHHhC
Confidence 4457888999999999999999999999998887777888999999999999998762 334445555544
No 33
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=70.47 E-value=20 Score=34.92 Aligned_cols=72 Identities=24% Similarity=0.294 Sum_probs=48.8
Q ss_pred HcCCchH--HHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhcCCCCHHHHHHHHHH
Q 017988 142 EYRLVPD--TLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITDNTYFKEEVLEMESS 215 (362)
Q Consensus 142 ~~~l~~e--Tl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~~~~t~~ei~~mE~~ 215 (362)
.+++.+. .+-.|-+|+.--+-.....+..-..||++|+++|+.-+|+..|.-..+..+.+ +++.+|-..=..
T Consensus 151 tL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd--~~k~eid~ic~~ 224 (367)
T KOG0835|consen 151 TLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFD--TTKREIDEICYR 224 (367)
T ss_pred HhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcC--CcHHHHHHHHHH
Confidence 3444443 25556677766666667778889999999999999999976666555555444 556666554333
No 34
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=69.84 E-value=32 Score=29.37 Aligned_cols=89 Identities=17% Similarity=0.129 Sum_probs=50.2
Q ss_pred CCCHHHHHHHHHHHHccCCCCchhHHHHHHHHHHH-Hhh----ccccccCccHHHHHHHHHHHHHHhhcCCCCCCcHHHH
Q 017988 226 APTAKCFLRRFVRAAQGINEVPSMQLECLANYVTE-LSL----LDYSMLCHAPSLIAASAIFLAKYILLPAKRPWNSTLQ 300 (362)
Q Consensus 226 ~pT~~~FL~~~l~~~~~~~~~~~~~~~~la~~l~e-lsL----~d~~~l~y~PS~iAaAai~lA~~~l~~~~~~w~~~L~ 300 (362)
..+..+|+.++.+..+... ...-+|.++++ +.- .....-.....-+=++|+.+|.+.+ .+...|+....
T Consensus 51 ~i~i~~fl~ri~~~~~~s~-----~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~-~D~~~~n~~~a 124 (149)
T PF08613_consen 51 SISIRDFLSRILKYTQCSP-----ECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFL-DDNTYSNKSWA 124 (149)
T ss_dssp SS-HHHHHHHHHHHTT--H-----HHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH--SS---HHHHH
T ss_pred CCcHHHHHHHHHHHcCCCh-----HHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhc-ccccccHHHHH
Confidence 3455678888876654432 11223333332 222 1122334667788888999999998 46677899999
Q ss_pred hhhCCChhhHHHHHHHHHHH
Q 017988 301 HYTLYQPSDLMECVKDLHRL 320 (362)
Q Consensus 301 ~~t~~~~~~l~~c~~~L~~l 320 (362)
+++|++..++...=..+..+
T Consensus 125 ~v~gis~~eln~lE~~fL~~ 144 (149)
T PF08613_consen 125 KVGGISLKELNELEREFLKL 144 (149)
T ss_dssp HHHTS-HHHHHHHHHHHHHH
T ss_pred hhcCCCHHHHHHHHHHHHHH
Confidence 99999999887655544443
No 35
>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=41.17 E-value=86 Score=26.52 Aligned_cols=64 Identities=13% Similarity=0.097 Sum_probs=47.4
Q ss_pred HHHHHHHHHcCCchHHHHHHHHHHHhhccCCc--CcchhhHHHHHHHHHHHhhhccccccCHHHHHH
Q 017988 134 DWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNP--MSRQRLQLLGVACMMIAAKYEEICAPQVEEFCF 198 (362)
Q Consensus 134 dwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~--v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~ 198 (362)
.-|.++|.+++++.+.....-..|+..+..+. +...++--+-+.|+++-+|+.. ..++.+++..
T Consensus 16 ~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~-~~~sF~~Ii~ 81 (135)
T PF01857_consen 16 VRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSK-EELSFKDIIK 81 (135)
T ss_dssp HHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT--S--HHHHHH
T ss_pred HHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhc-CCCCHHHHHH
Confidence 34678999999999888888888888886533 4566788899999999999876 4556666654
No 36
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=40.57 E-value=1e+02 Score=29.69 Aligned_cols=66 Identities=6% Similarity=0.047 Sum_probs=30.5
Q ss_pred HHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcchhhHHHHHHHHHHHhhhccccccCHHHHHHhhc
Q 017988 135 WLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSRQRLQLLGVACMMIAAKYEEICAPQVEEFCFITD 201 (362)
Q Consensus 135 wl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~~~lqLva~tcL~IAsK~eE~~~p~i~~l~~i~~ 201 (362)
+|...|..++|+..+.-.|..+--+.--...+.....--||++.+|+++-..+ ..-..+++..+++
T Consensus 206 ~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~-~kkt~keI~~vtg 271 (308)
T KOG1597|consen 206 FMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSD-EKKTQKEIGEVTG 271 (308)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhcc-CcccHHHHHHHhh
Confidence 33344444444444444443333333322233333445566666666666655 3344455544443
No 37
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=40.07 E-value=1.4e+02 Score=28.96 Aligned_cols=28 Identities=25% Similarity=0.322 Sum_probs=22.5
Q ss_pred HhhccccccCccHHHHHHHHHHHHHHhh
Q 017988 261 LSLLDYSMLCHAPSLIAASAIFLAKYIL 288 (362)
Q Consensus 261 lsL~d~~~l~y~PS~iAaAai~lA~~~l 288 (362)
-.++..++..|.|-.||++|+++|.+.-
T Consensus 88 RFy~~~Sv~~~~p~~Ia~tclfLA~KvE 115 (305)
T TIGR00569 88 RFYLNNSVMEYHPKIIMLTCVFLACKVE 115 (305)
T ss_pred HHhccCchhhcCHHHHHHHHHHHHHhcc
Confidence 3344556677999999999999998876
No 38
>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=32.92 E-value=2.1e+02 Score=21.60 Aligned_cols=33 Identities=18% Similarity=0.393 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHhh
Q 017988 125 NASMRAILIDWLVEVAEEYRLVPDTLYLTVNYIDRY 160 (362)
Q Consensus 125 ~~~~R~~lvdwl~ev~~~~~l~~eTl~lAv~llDRf 160 (362)
.-..|..+|++|..++..-+++.+ .|+..+|.+
T Consensus 48 ~y~rRK~Ii~~I~~l~~~~g~~~~---~ai~~le~~ 80 (81)
T PF12550_consen 48 TYSRRKVIIDFIERLANERGISEE---EAIEILEEI 80 (81)
T ss_pred hHHHHHHHHHHHHHHHHHcCCCHH---HHHHHHHhc
Confidence 445699999999999888777665 466666654
No 39
>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=31.25 E-value=2.5e+02 Score=21.73 Aligned_cols=93 Identities=14% Similarity=0.155 Sum_probs=57.7
Q ss_pred HHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHhhccccccCccHHHHHHHHHHHHHHhhcCCCCCCcHHHHh---hhCC
Q 017988 229 AKCFLRRFVRAAQGINEVPSMQLECLANYVTELSLLDYSMLCHAPSLIAASAIFLAKYILLPAKRPWNSTLQH---YTLY 305 (362)
Q Consensus 229 ~~~FL~~~l~~~~~~~~~~~~~~~~la~~l~elsL~d~~~l~y~PS~iAaAai~lA~~~l~~~~~~w~~~L~~---~t~~ 305 (362)
+-+|+--...++....+. -.|+..++..-.--.|......-.+|-.|.|+.+......-+.+..+|...|+. +.++
T Consensus 4 ~tdflip~c~alkipe~~-wpql~e~~s~tickaliqpniall~p~licaggllttiet~ntn~~~wt~yledl~~ilnf 82 (106)
T PF09241_consen 4 STDFLIPVCHALKIPEDF-WPQLFEATSITICKALIQPNIALLPPCLICAGGLLTTIETDNTNCQPWTCYLEDLSCILNF 82 (106)
T ss_dssp GGGGHHHHHHHTT--GGG-HHHHHHHHHHHHHHHTTSGGGGGS-HHHHHHHHHHHHHHTS-TSSSTCHHHHHHHHHHHTC
T ss_pred hhhhHHHhhhhccCcHHH-hHHHHHHHHHHHHHHHcCCCccccCcceeecccceEEEeccCCCCcchhhhHHhhHHHhhc
Confidence 346777666666554332 113333333333345667777778999999999999988877777889776544 4566
Q ss_pred ChhhHHHHHHHHHHHHh
Q 017988 306 QPSDLMECVKDLHRLYC 322 (362)
Q Consensus 306 ~~~~l~~c~~~L~~l~~ 322 (362)
+-..++..-+++.+.+.
T Consensus 83 stntirt~kdqv~ea~~ 99 (106)
T PF09241_consen 83 STNTIRTVKDQVSEAFS 99 (106)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHH
Confidence 66677766666665543
No 40
>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=26.78 E-value=56 Score=25.27 Aligned_cols=40 Identities=13% Similarity=0.189 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHcCCchHHHHHHHHHHHhhccCCcCcc
Q 017988 129 RAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGNPMSR 168 (362)
Q Consensus 129 R~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~~v~~ 168 (362)
=..+|+||++-.+...=..+++..+-.+++.=+-.+..++
T Consensus 32 GsdlVdWL~~~~~~~~~R~eAv~~g~~Ll~~G~i~HV~~~ 71 (84)
T cd04438 32 GSDLVDWLLSHVEGLTDRREARKYASSLLKLGYIRHTVNK 71 (84)
T ss_pred chHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCcEEecCCC
Confidence 4679999998665444456888888888876554444333
No 41
>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=24.51 E-value=65 Score=24.69 Aligned_cols=30 Identities=17% Similarity=0.401 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHcCCchHHHHHHHHHHHh
Q 017988 129 RAILIDWLVEVAEEYRLVPDTLYLTVNYIDR 159 (362)
Q Consensus 129 R~~lvdwl~ev~~~~~l~~eTl~lAv~llDR 159 (362)
=..+|+||++... ..-..|.+.++-.++|.
T Consensus 31 GselVdWL~~~~~-~~~r~eAv~lg~~Ll~~ 60 (81)
T cd04439 31 GNEFVSWLLEIGE-ISKPEEGVNLGQALLEN 60 (81)
T ss_pred hHHHHHHHHHcCC-CCCHHHHHHHHHHHHHC
Confidence 3679999998652 22234778888877775
No 42
>PF15576 DUF4661: Domain of unknown function (DUF4661)
Probab=24.19 E-value=2.4e+02 Score=25.49 Aligned_cols=33 Identities=27% Similarity=0.245 Sum_probs=27.4
Q ss_pred CCCCCCCCCCCcccccCCCCccCCCCCCccccc
Q 017988 1 MDVSPSKSDANSVSMDESMSVCDSFKSPEVEYL 33 (362)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 (362)
||-||++|++.-=|+-|+|..-...++-+.--.
T Consensus 17 ~dSS~EnSGSDWDSAPetmgD~g~pktkdsg~~ 49 (253)
T PF15576_consen 17 MDSSPENSGSDWDSAPETMGDVGPPKTKDSGTQ 49 (253)
T ss_pred CCCCcccCCCccccccccccCCCCCCCCCcccc
Confidence 688999999999999999998877776655443
No 43
>cd04441 DEP_2_DEP6 DEP (Dishevelled, Egl-10, and Pleckstrin) domain 2 found in DEP6-like proteins. DEP6 proteins contain two DEP and a PDZ domain. Their function is unknown.
Probab=23.94 E-value=71 Score=24.81 Aligned_cols=34 Identities=18% Similarity=0.342 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHcCCchHHHHHHHHHHHhhccCC
Q 017988 130 AILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLSGN 164 (362)
Q Consensus 130 ~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs~~ 164 (362)
..+||||++.+ ...=..+++.++..++|.=+-.+
T Consensus 36 sElVdWL~~~~-~~~sR~eAv~lgq~Ll~~gii~H 69 (85)
T cd04441 36 SEFIDWLLQEG-EAESRREAVQLCRRLLEHGIIQH 69 (85)
T ss_pred hHHHHHHHHcC-CCCCHHHHHHHHHHHHHCCCEEe
Confidence 68999999966 23334567777777777644333
No 44
>cd04443 DEP_GPR155 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in GPR155-like proteins. GRP155-like proteins, also known as PGR22, contain an N-terminal permease domain, a central transmembrane region and a C-terminal DEP domain. They are orphan receptors of the class B G protein-coupled receptors. Their function is unknown.
Probab=22.82 E-value=83 Score=24.27 Aligned_cols=30 Identities=17% Similarity=0.290 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHcCCchHHHHHHHHHHHh
Q 017988 129 RAILIDWLVEVAEEYRLVPDTLYLTVNYIDR 159 (362)
Q Consensus 129 R~~lvdwl~ev~~~~~l~~eTl~lAv~llDR 159 (362)
=..+|+||++... ..=..|++.+|-.++|.
T Consensus 33 GselVdWL~~~~~-~~sR~eAv~lg~~Ll~~ 62 (83)
T cd04443 33 GCDLVSWLIEVGL-AQDRGEAVLYGRRLLQG 62 (83)
T ss_pred HHHHHHHHHHcCC-CCCHHHHHHHHHHHHHC
Confidence 4679999998532 22234777787777775
No 45
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=21.92 E-value=4.2e+02 Score=24.81 Aligned_cols=25 Identities=24% Similarity=0.325 Sum_probs=19.9
Q ss_pred cchhhHHHHHHHHHHHhhhcccccc
Q 017988 167 SRQRLQLLGVACMMIAAKYEEICAP 191 (362)
Q Consensus 167 ~~~~lqLva~tcL~IAsK~eE~~~p 191 (362)
--.....+|+|||+||+=..|...|
T Consensus 189 Ll~PPh~IalAcl~Ia~~~~~k~~~ 213 (264)
T KOG0794|consen 189 LLYPPHQIALACLYIACVIDEKDIP 213 (264)
T ss_pred eecCHHHHHHHHHHHHHhhcCCChH
Confidence 3455788999999999998886554
No 46
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=21.68 E-value=1.4e+02 Score=27.43 Aligned_cols=53 Identities=21% Similarity=0.134 Sum_probs=40.0
Q ss_pred ccHHHHHHHHHHHHHHhhcCCCCCCcHHHHhhhCCChhhHHHHHHHHHHHHhcCC
Q 017988 271 HAPSLIAASAIFLAKYILLPAKRPWNSTLQHYTLYQPSDLMECVKDLHRLYCNSQ 325 (362)
Q Consensus 271 y~PS~iAaAai~lA~~~l~~~~~~w~~~L~~~t~~~~~~l~~c~~~L~~l~~~~~ 325 (362)
+.--+-++||+++|++.+. ...-...|..++|..++++....+++.+.+...+
T Consensus 133 ~SrP~ft~aA~~~ack~lK--lKVdK~kli~~sg~~~s~F~~l~kqler~~~qv~ 185 (262)
T KOG4557|consen 133 FSRPVFTAAAFYLACKKLK--LKVDKLKLIEVSGTSESEFSCLSKQLERNYKQVS 185 (262)
T ss_pred ccchHHHHHHHHHHHHHHH--HhhhHhhcccccCCCHHHHHHHHHHHHHHHHHhc
Confidence 3444667889999998883 3333456778899999999999999999887544
No 47
>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=20.77 E-value=92 Score=23.80 Aligned_cols=34 Identities=15% Similarity=0.262 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHcCCchHHHHHHHHHHHhhcc
Q 017988 129 RAILIDWLVEVAEEYRLVPDTLYLTVNYIDRYLS 162 (362)
Q Consensus 129 R~~lvdwl~ev~~~~~l~~eTl~lAv~llDRfLs 162 (362)
=..+|+||++-.....=..+++.++-.++|.=+-
T Consensus 32 G~e~VdWL~~~~~~~~~r~eAv~lgq~Ll~~g~I 65 (83)
T cd04449 32 GSEAVSWLINNFEDVDTREEAVELGQELMNEGLI 65 (83)
T ss_pred hHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCCE
Confidence 4789999998554333345677777777775443
Done!