Query 025012
Match_columns 259
No_of_seqs 177 out of 1481
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 09:14:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025012.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025012hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0656 G1/S-specific cyclin D 100.0 9E-45 1.9E-49 316.7 22.8 248 10-258 9-262 (335)
2 KOG0655 G1/S-specific cyclin E 100.0 6.6E-38 1.4E-42 267.3 13.2 203 39-251 112-322 (408)
3 KOG0653 Cyclin B and related k 100.0 9.7E-34 2.1E-38 257.8 16.3 187 39-236 126-313 (391)
4 COG5024 Cyclin [Cell division 100.0 4.6E-33 9.9E-38 251.5 13.1 189 38-236 179-367 (440)
5 PF00134 Cyclin_N: Cyclin, N-t 99.9 8.9E-27 1.9E-31 180.2 14.0 127 42-174 1-127 (127)
6 KOG0654 G2/Mitotic-specific cy 99.9 2.4E-27 5.2E-32 209.1 8.6 191 39-237 102-293 (359)
7 TIGR00569 ccl1 cyclin ccl1. Un 99.9 1.8E-23 3.9E-28 183.4 16.6 162 72-237 54-221 (305)
8 KOG0834 CDK9 kinase-activating 99.9 1.6E-22 3.4E-27 177.3 10.7 182 69-256 34-227 (323)
9 KOG0835 Cyclin L [General func 99.8 5.9E-20 1.3E-24 157.5 15.9 179 69-257 18-214 (367)
10 COG5333 CCL1 Cdk activating ki 99.8 1.9E-18 4E-23 148.3 12.8 189 40-240 17-212 (297)
11 KOG0794 CDK8 kinase-activating 99.7 3.7E-17 8E-22 134.2 10.1 173 72-256 39-222 (264)
12 cd00043 CYCLIN Cyclin box fold 99.5 7.8E-14 1.7E-18 99.6 8.7 86 74-166 2-88 (88)
13 PRK00423 tfb transcription ini 99.5 5.1E-12 1.1E-16 112.1 19.1 153 73-236 121-273 (310)
14 KOG2496 Cdk activating kinase 99.5 1.9E-12 4E-17 110.8 14.4 153 75-232 57-218 (325)
15 smart00385 CYCLIN domain prese 99.4 7.2E-13 1.6E-17 93.6 8.1 83 79-167 1-83 (83)
16 PF02984 Cyclin_C: Cyclin, C-t 98.9 1.2E-09 2.5E-14 82.8 5.3 57 176-236 1-57 (118)
17 COG1405 SUA7 Transcription ini 98.9 1.4E-07 3.1E-12 82.3 18.4 156 71-237 94-249 (285)
18 PF08613 Cyclin: Cyclin; Inte 98.8 7.2E-08 1.6E-12 76.7 9.8 92 76-173 53-149 (149)
19 KOG1597 Transcription initiati 98.7 2E-06 4.3E-11 74.0 16.3 152 73-235 103-256 (308)
20 KOG4164 Cyclin ik3-1/CABLES [C 97.9 5.3E-06 1.1E-10 73.8 3.0 105 69-176 377-482 (497)
21 KOG1598 Transcription initiati 97.7 0.0009 2E-08 62.3 12.7 172 56-236 44-223 (521)
22 cd00043 CYCLIN Cyclin box fold 97.5 0.00053 1.1E-08 48.1 6.9 59 175-237 2-60 (88)
23 smart00385 CYCLIN domain prese 97.2 0.0013 2.8E-08 45.5 6.4 53 181-237 2-54 (83)
24 KOG1674 Cyclin [General functi 97.0 0.003 6.5E-08 53.3 7.9 97 77-176 78-181 (218)
25 PF00382 TFIIB: Transcription 96.8 0.016 3.5E-07 39.7 8.7 62 81-146 1-62 (71)
26 PRK00423 tfb transcription ini 95.2 0.24 5.1E-06 44.2 10.7 89 78-173 220-308 (310)
27 PF00382 TFIIB: Transcription 93.8 0.24 5.1E-06 33.8 5.8 51 183-237 2-52 (71)
28 KOG1675 Predicted cyclin [Gene 93.2 0.12 2.6E-06 45.3 4.1 100 81-186 197-298 (343)
29 PF02984 Cyclin_C: Cyclin, C-t 89.4 2 4.3E-05 31.6 7.0 87 78-170 4-90 (118)
30 COG1405 SUA7 Transcription ini 85.9 6.4 0.00014 34.7 9.0 57 76-135 193-249 (285)
31 KOG0834 CDK9 kinase-activating 82.9 1.7 3.7E-05 38.9 4.1 95 75-172 153-248 (323)
32 PF09080 K-cyclin_vir_C: K cyc 76.7 13 0.00029 26.5 6.1 54 180-233 6-60 (106)
33 PF09241 Herp-Cyclin: Herpesvi 65.0 42 0.00091 23.6 6.4 57 179-235 5-61 (106)
34 TIGR00569 ccl1 cyclin ccl1. Un 62.3 11 0.00023 33.6 4.0 39 198-236 77-115 (305)
35 PF01857 RB_B: Retinoblastoma- 60.3 57 0.0012 25.3 7.3 64 79-145 16-80 (135)
36 PF00134 Cyclin_N: Cyclin, N-t 58.8 51 0.0011 24.3 6.8 39 200-238 52-90 (127)
37 KOG0835 Cyclin L [General func 56.9 80 0.0017 28.4 8.3 66 96-167 162-227 (367)
38 KOG1925 Rac1 GTPase effector F 56.5 13 0.00028 35.1 3.6 72 39-110 547-618 (817)
39 cd03197 GST_C_mPGES2 GST_C fam 53.4 1E+02 0.0022 24.4 7.7 41 93-133 29-69 (149)
40 KOG4112 Signal peptidase subun 38.0 24 0.00052 25.5 1.7 33 220-253 52-84 (101)
41 KOG1597 Transcription initiati 36.4 1.5E+02 0.0033 26.2 6.7 17 119-135 242-258 (308)
42 KOG0794 CDK8 kinase-activating 32.4 70 0.0015 27.3 3.9 39 196-234 58-96 (264)
43 cd04441 DEP_2_DEP6 DEP (Dishev 29.0 58 0.0013 23.1 2.6 29 75-104 36-64 (85)
44 PF07226 DUF1422: Protein of u 27.2 1.5E+02 0.0034 22.3 4.6 39 91-133 40-78 (117)
45 cd04439 DEP_1_P-Rex DEP (Dishe 24.9 66 0.0014 22.6 2.2 29 75-104 32-60 (81)
46 cd04449 DEP_DEPDC5-like DEP (D 24.5 75 0.0016 22.2 2.5 30 75-104 33-62 (83)
47 cd04443 DEP_GPR155 DEP (Dishev 24.2 82 0.0018 22.2 2.6 29 75-104 34-62 (83)
48 cd04438 DEP_dishevelled DEP (D 22.8 84 0.0018 22.2 2.4 30 75-104 33-62 (84)
49 cd04442 DEP_1_DEP6 DEP (Dishev 22.2 84 0.0018 22.1 2.3 29 75-104 32-60 (82)
50 PF14502 HTH_41: Helix-turn-he 20.5 1.5E+02 0.0033 18.6 2.9 24 81-104 9-32 (48)
51 TIGR01446 DnaD_dom DnaD and ph 20.3 2E+02 0.0044 19.1 3.9 30 68-101 12-41 (73)
52 PRK11056 hypothetical protein; 20.2 2.5E+02 0.0055 21.3 4.6 39 91-133 40-78 (120)
53 cd04444 DEP_PLEK2 DEP (Disheve 20.2 89 0.0019 23.4 2.2 29 75-104 35-63 (109)
No 1
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=9e-45 Score=316.66 Aligned_cols=248 Identities=44% Similarity=0.644 Sum_probs=214.2
Q ss_pred cccccccccccccC---CCCCCCCCCCC---CCCCchHHHHHHHHHHHHhhCCCCCccccccCCCCCHHHHHHHHHHHHH
Q 025012 10 PDLLCGEDSGIFAG---ESSPACSSSDL---ESSASIEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILK 83 (259)
Q Consensus 10 ~~l~c~e~~~~~~~---~~~~~~~~~~~---~~~~~~~e~l~~ll~~E~~~~~~~~y~~~~q~~~i~~~~R~~lvdwl~~ 83 (259)
+.|+|+|.+....+ .+++.-...++ ++..+++|.+.+|+++|+++.|..+|+..+|. .+++.+|.++++||.+
T Consensus 9 ~~l~c~E~~~~~~~~~~~~D~~~~~~~~~~~~~~~~~e~~i~~ll~kEe~~~p~~~~~~~~~~-~~~~~~R~~A~~WIl~ 87 (335)
T KOG0656|consen 9 SQLLCHEESTSDEQDRADNDESSTESSIPQLGFLLWDERVLANLLEKEEQHNPSLDYFLCVQK-LILSSMRKQALDWILK 87 (335)
T ss_pred cccccCCCCcccccccccCCcccccccccccccccccHHHHHHHHHHHHHhCCCCchhhhccc-ccccHHHHHHHHHHHH
Confidence 45899996555432 11121111111 12357889999999999999999997776664 5899999999999999
Q ss_pred HHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhhccCccccHHHHHHHHH
Q 025012 84 VQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMEL 163 (259)
Q Consensus 84 v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~~~~~s~~~i~~~E~ 163 (259)
|+.++++.++|+++|+||||||++..++++.++|-+||+|+|||+||||++|+.+|.+.++.....++.|.++.|.+||.
T Consensus 88 V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~feaktI~rmEL 167 (335)
T KOG0656|consen 88 VCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAKTIQRMEL 167 (335)
T ss_pred HHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccHHHHHHHHH
Confidence 99999999999999999999999999999998899999999999999999999999999999888899999999999999
Q ss_pred HHHHHcCCccccCCHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcchhccCccHHHHHHHHHHHHHhcCCCCCCCC
Q 025012 164 LVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPNLSLVN 243 (259)
Q Consensus 164 ~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la~~~~~~~~~~~ 243 (259)
.||++|+|++..+||++|+++|+++++..+.....+...+..++..+..|..|+.|+||+||+|++.++...+..-..+.
T Consensus 168 LVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~~~~~~l~~~~ 247 (335)
T KOG0656|consen 168 LVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSVSASVDGLDFRE 247 (335)
T ss_pred HHHhhccccccCCCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHHHHhhcchhhhh
Confidence 99999999999999999999999999998888889999999999999999999999999999999988877776555555
Q ss_pred CCchhhHhhhhhccc
Q 025012 244 PEHAESWCDGLSKVS 258 (259)
Q Consensus 244 ~~~~~~w~~~l~~~~ 258 (259)
-++...++..+.+++
T Consensus 248 ~~~~~~~~~~l~~e~ 262 (335)
T KOG0656|consen 248 YENNLLSLLSLSKEK 262 (335)
T ss_pred hhHHHHHHHHhhHHh
Confidence 456777777776664
No 2
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=6.6e-38 Score=267.31 Aligned_cols=203 Identities=22% Similarity=0.375 Sum_probs=174.2
Q ss_pred chHHHHHHHHHHHHhhCCCCCccccccCCCCCHHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCC-ccCCCCCC
Q 025012 39 SIEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSR-RLPDNNGW 117 (259)
Q Consensus 39 ~~~e~l~~ll~~E~~~~~~~~y~~~~q~~~i~~~~R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~-~i~~~~~~ 117 (259)
...++|..|+.+|+.+..+..++.. ++.+.++||++++|||++||+.+++++||+|+|+.||||||... .+.+.
T Consensus 112 n~~eVW~lM~kkee~~l~~~~~l~q--Hpdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt--- 186 (408)
T KOG0655|consen 112 NSKEVWLLMLKKEERYLRDKHFLEQ--HPDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKT--- 186 (408)
T ss_pred CHHHHHHHHHccchhhhhhhHHHhh--CCCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhh---
Confidence 5569999999999999888888877 99999999999999999999999999999999999999999765 57777
Q ss_pred chHHHHHHHHHHHHHhhcccCCchhhhhhhccCccccHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHhcCCC-----
Q 025012 118 PWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPT----- 192 (259)
Q Consensus 118 ~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~~~~~s~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~l~~l~~~----- 192 (259)
.+||+|+||||||+|+||++||++.+|.+. +++.+|.++|+.||..||+.|+|+|++.|...||..|+......
T Consensus 187 ~lQLIGitsLFIAAK~EEIYpPKl~eFAyv-TDgAcs~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n~~~k~ 265 (408)
T KOG0655|consen 187 NLQLIGITSLFIAAKLEEIYPPKLIEFAYV-TDGACSEDDILTMELIILKALKWELSPITIISWLNVYLQVDALNDAPKV 265 (408)
T ss_pred hHHHhhHHHHHHHHHHhhccCccccceeee-ccCccchHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcCCCCce
Confidence 799999999999999999999999999865 88999999999999999999999999999999999999654332
Q ss_pred --CChHHHHHHHHHHHHHHHhcchhccCccHHHHHHHHHHHHHhcCCCCCCCCCCchhhHh
Q 025012 193 --GTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPNLSLVNPEHAESWC 251 (259)
Q Consensus 193 --~~~~~~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la~~~~~~~~~~~~~~~~~w~ 251 (259)
.+..+...-....++++|+.|...+.|+-++||||||+.... -..+...+|..|.
T Consensus 266 l~Pq~~~~efiqiaqlLDlc~ldids~~fsYrilaAAal~h~~s----~e~v~kaSG~~w~ 322 (408)
T KOG0655|consen 266 LLPQYSQEEFIQIAQLLDLCILDIDSLEFSYRILAAAALCHFTS----IEVVKKASGLEWD 322 (408)
T ss_pred eccccchHHHHHHHHHHHHHHhccccccchHHHHHHHHHHHHhH----HHHHHHcccccHH
Confidence 123333334456789999999999999999999999987632 1133444555554
No 3
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=9.7e-34 Score=257.79 Aligned_cols=187 Identities=29% Similarity=0.393 Sum_probs=166.2
Q ss_pred chHHHHHHHHHHHHhhCCCCCccccccCCCCCHHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCc
Q 025012 39 SIEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWP 118 (259)
Q Consensus 39 ~~~e~l~~ll~~E~~~~~~~~y~~~~q~~~i~~~~R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~ 118 (259)
+.+|+...|.++|..+.|.. |... +.+++..||.+++||+++|+.+|++.+||+++||+++||||++..+++. +
T Consensus 126 y~~di~~~l~~~e~~~~p~~-~~~~--~~e~~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~---~ 199 (391)
T KOG0653|consen 126 YVQDIFEYLRQLELEFLPLS-YDIS--QSEIRAKMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLK---K 199 (391)
T ss_pred HHHHHHHHHHHHHHhhCchh-hhcc--cccccHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHH---H
Confidence 55678888888876666765 4443 6789999999999999999999999999999999999999999998888 8
Q ss_pred hHHHHHHHHH-HHHHhhcccCCchhhhhhhccCccccHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHhcCCCCChHH
Q 025012 119 WQLLSVACLS-LAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMG 197 (259)
Q Consensus 119 lqL~a~acL~-IAsK~eE~~~p~~~~l~~~~~~~~~s~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~~~~ 197 (259)
+||+|++||+ ||+|+||..+|.+.+++.. +++.||+++|++||+.||++|+|+++.|+|+.|+++|++..... .
T Consensus 200 lqLvgvsalf~IA~K~EE~~~P~v~dlv~i-sd~~~s~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d----~ 274 (391)
T KOG0653|consen 200 LQLVGVSALLSIACKYEEISLPSVEDLVLI-TDGAYSREEILRMEKYILNVLEFDLSVPTPLSFLRRFLKAADYD----I 274 (391)
T ss_pred hhHHhHHHHHHHHHhhhhccCCccceeEee-eCCccchHHHHHHHHHHHhccCeeecCCchHHHHHHHHHhhhcc----h
Confidence 9999999966 9999999999999999764 78899999999999999999999999999999999998766521 2
Q ss_pred HHHHHHHHHHHHHhcchhccCccHHHHHHHHHHHHHhcC
Q 025012 198 FLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEI 236 (259)
Q Consensus 198 ~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la~~~~ 236 (259)
.....+.++++++++|+.++.++||.+|+|+.+++++..
T Consensus 275 ~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~~ 313 (391)
T KOG0653|consen 275 KTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALRML 313 (391)
T ss_pred hHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHHh
Confidence 345668899999999999999999999999999998755
No 4
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=100.00 E-value=4.6e-33 Score=251.45 Aligned_cols=189 Identities=28% Similarity=0.365 Sum_probs=172.7
Q ss_pred CchHHHHHHHHHHHHhhCCCCCccccccCCCCCHHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCC
Q 025012 38 ASIEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGW 117 (259)
Q Consensus 38 ~~~~e~l~~ll~~E~~~~~~~~y~~~~q~~~i~~~~R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~ 117 (259)
++..+++..|+++|..+.|.++|+.+ ++.+...||.++++|+.+++.+|++.++|+++|++++|||+++..+.-.
T Consensus 179 Ey~~~Ife~l~k~e~~~lp~~~yl~k--q~~~~~~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~--- 253 (440)
T COG5024 179 EYASDIFEYLLKLELIDLPNPNYLIK--QSLYEWSMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLE--- 253 (440)
T ss_pred HHHHHHHHHHHHHHHHhcCcHHHHhh--cchhHHhHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHH---
Confidence 47779999999999999999999877 8888899999999999999999999999999999999999999999988
Q ss_pred chHHHHHHHHHHHHHhhcccCCchhhhhhhccCccccHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHhcCCCCChHH
Q 025012 118 PWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMG 197 (259)
Q Consensus 118 ~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~~~~~s~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~~~~ 197 (259)
++||+|++|||||+|+||++.|.+.++... +++.|++++|+++|+.+|.+|+|+++.|+|..|++++.+.-+.. .
T Consensus 254 k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~-t~g~~t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka~dyd----~ 328 (440)
T COG5024 254 KYQLVGISALFIASKYEEVNCPSIKDLVYA-TDGAFTRDDIIRAERYMLEVLDFNISWPSPMSFLRRISKASDYD----I 328 (440)
T ss_pred HHHHHHHHHHHHHHhHhHhcCHHHHHHHHH-HcccccHHHHHHHHHHHhhhcccccCCCChHHHHHHHHhhcccc----h
Confidence 899999999999999999999999999865 78899999999999999999999999999999988885433222 2
Q ss_pred HHHHHHHHHHHHHhcchhccCccHHHHHHHHHHHHHhcC
Q 025012 198 FLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEI 236 (259)
Q Consensus 198 ~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la~~~~ 236 (259)
..+..+.++++.+..++.|++++||.+|+||.++++...
T Consensus 329 ~srt~~k~~~e~s~~~~~f~~~~~S~~~aaa~~~s~~~~ 367 (440)
T COG5024 329 FSRTPAKFSSEISPVDYKFIQISPSWCAAAAMYLSRKIL 367 (440)
T ss_pred hhhhhHhhhCCchHhhhhhccCCchHHHHHHHHHHHhhh
Confidence 334458899999999999999999999999999998755
No 5
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=99.95 E-value=8.9e-27 Score=180.23 Aligned_cols=127 Identities=32% Similarity=0.502 Sum_probs=113.7
Q ss_pred HHHHHHHHHHHhhCCCCCccccccCCCCCHHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHH
Q 025012 42 ESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQL 121 (259)
Q Consensus 42 e~l~~ll~~E~~~~~~~~y~~~~q~~~i~~~~R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL 121 (259)
|++++|+++|.++.|++.|++. ++.++..+|..+++||.+++..++++++|+++|+.|||||+.+.++.+. ++++
T Consensus 1 ~i~~~~~~~e~~~~~~~~~~~~--~~~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~---~~~l 75 (127)
T PF00134_consen 1 DIFRYLLEKELKYKPNPDYLEQ--QPEITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRS---KLQL 75 (127)
T ss_dssp HHHHHHHHHHHHTTCCTTHGTG--TSSHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCC---GHHH
T ss_pred CHHHHHHHHHHHHCcCcccccc--ChhcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccc---hhhh
Confidence 6899999999999999999996 6679999999999999999999999999999999999999999998887 8999
Q ss_pred HHHHHHHHHHHhhcccCCchhhhhhhccCccccHHHHHHHHHHHHHHcCCccc
Q 025012 122 LSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLR 174 (259)
Q Consensus 122 ~a~acL~IAsK~eE~~~p~~~~l~~~~~~~~~s~~~i~~~E~~IL~~L~f~l~ 174 (259)
+|++|++||+|++|..+|.+.+++.. +++.+++++|.+||+.||++|+|+++
T Consensus 76 i~~~cl~lA~K~~e~~~~~~~~~~~~-~~~~~~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 76 IALACLFLASKMEEDNPPSISDLIRI-SDNTFTKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp HHHHHHHHHHHHHTSS--HHHHHHHH-TTTSSHHHHHHHHHHHHHHHTTT---
T ss_pred hhhhHHHHhhhhhccccchHHHHHHH-HcCCCCHHHHHHHHHHHHHHCCCCcC
Confidence 99999999999999999999999876 47789999999999999999999985
No 6
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=99.94 E-value=2.4e-27 Score=209.11 Aligned_cols=191 Identities=24% Similarity=0.278 Sum_probs=174.5
Q ss_pred chHHHHHHHHHHHHh-hCCCCCccccccCCCCCHHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCC
Q 025012 39 SIEESIAGFIEDERN-FVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGW 117 (259)
Q Consensus 39 ~~~e~l~~ll~~E~~-~~~~~~y~~~~q~~~i~~~~R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~ 117 (259)
+..++.+++..-|.+ .+|.++|++.+|. ++|+.||.++++|.+++++.+++..+++|+++++.|||+....+.+.
T Consensus 102 ~~~~I~~~~r~~ei~~~rp~~~~~e~vq~-d~t~smrgilvdwlvevsee~r~~~e~l~ls~~~~drfl~~~~~~~~--- 177 (359)
T KOG0654|consen 102 IAAKIYNTLRVSDIKSERPLPSKFEFVQA-DITPSMRGILVDWLVEVSEEYRLTFETLYLSVNYRDRFLSYKEVNKQ--- 177 (359)
T ss_pred HHHHHhhcccccchhhccCcccceeeeec-CCCcchhhhhhhhhhHHHHHHHhhhhheeecHHHHHHHhccCccHHH---
Confidence 444777777888888 9999999999885 69999999999999999999999999999999999999999999998
Q ss_pred chHHHHHHHHHHHHHhhcccCCchhhhhhhccCccccHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHhcCCCCChHH
Q 025012 118 PWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMG 197 (259)
Q Consensus 118 ~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~~~~~s~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~~~~ 197 (259)
++|++|.+|++||+|++|..+|.+.+|+.. .++.|+..++..||..||+.|.|.+..||.-.|++.|+..... ...
T Consensus 178 k~ql~g~s~m~I~sk~ee~~~~~~~ef~~i-td~ty~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~~~~~---~~~ 253 (359)
T KOG0654|consen 178 KLQLVGISAMLIASKYEEIKEPRVEEFCYI-TDNTYTYWQVLRMEIDILNALTFELVRPTSKTFLRRFLRVAQT---PEL 253 (359)
T ss_pred HHHHhCcccceeeccchhhcchHHHHHHhh-hhhhhHHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHHhhcc---hhH
Confidence 899999999999999999999999999875 7889999999999999999999999999999999999866544 234
Q ss_pred HHHHHHHHHHHHHhcchhccCccHHHHHHHHHHHHHhcCC
Q 025012 198 FLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIP 237 (259)
Q Consensus 198 ~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la~~~~~ 237 (259)
.+...+.++.++++.|+.|++|.||.|||||+++|.-++.
T Consensus 254 ~~e~~~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~ 293 (359)
T KOG0654|consen 254 QVEPLANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLD 293 (359)
T ss_pred HHHHHHHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhcc
Confidence 5667799999999999999999999999999999987764
No 7
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.91 E-value=1.8e-23 Score=183.40 Aligned_cols=162 Identities=20% Similarity=0.245 Sum_probs=135.5
Q ss_pred HHHHHHHHHHHHHHHHhC--CchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhhcc
Q 025012 72 SAREESVAWILKVQAYYN--FLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGA 149 (259)
Q Consensus 72 ~~R~~lvdwl~~v~~~~~--l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~ 149 (259)
..|..-.+.|.+++..++ ++..|+.+|+.||+||+.++++... +.+++++||+|||+|+||.. .++.+++....
T Consensus 54 ~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~---~p~~Ia~tclfLA~KvEE~~-~si~~fv~~~~ 129 (305)
T TIGR00569 54 DLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEY---HPKIIMLTCVFLACKVEEFN-VSIDQFVGNLK 129 (305)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhc---CHHHHHHHHHHHHHhccccC-cCHHHHHhhcc
Confidence 778888999999999999 9999999999999999999999888 79999999999999999984 57888875322
Q ss_pred C-ccccHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHhcCC---CCChHHHHHHHHHHHHHHHhcchhccCccHHHHH
Q 025012 150 K-YIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDP---TGTFMGFLISRATKIILSNIQEASFLEYRPSSIA 225 (259)
Q Consensus 150 ~-~~~s~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~l~~l~~---~~~~~~~~~~~a~~~l~~~l~d~~~~~~~PS~iA 225 (259)
. ....+++|+++|..||++|+|++.+++|+.++..|+..+.. .......+.+.+..++..++...-++.|+||.||
T Consensus 130 ~~~~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IA 209 (305)
T TIGR00569 130 ETPLKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIA 209 (305)
T ss_pred CCchhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHHH
Confidence 2 12356999999999999999999999999999988743321 1122345667788888777776668889999999
Q ss_pred HHHHHHHHhcCC
Q 025012 226 AAAILCAANEIP 237 (259)
Q Consensus 226 aAai~la~~~~~ 237 (259)
+|||++|.+.++
T Consensus 210 lAAI~lA~~~~~ 221 (305)
T TIGR00569 210 LAAILHTASRAG 221 (305)
T ss_pred HHHHHHHHHHhC
Confidence 999999987554
No 8
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.88 E-value=1.6e-22 Score=177.29 Aligned_cols=182 Identities=23% Similarity=0.314 Sum_probs=152.2
Q ss_pred CCHHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhhc
Q 025012 69 LDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEG 148 (259)
Q Consensus 69 i~~~~R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~ 148 (259)
-....|.....||.+++..++++..|+.+|+.|++||+...+.... +.+.+|++|+|+|+|+||. |.++++++...
T Consensus 34 ~E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~---~~~~vA~sclfLAgKvEet-p~kl~dIi~~s 109 (323)
T KOG0834|consen 34 KELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKF---DPYTVAASCLFLAGKVEET-PRKLEDIIKVS 109 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccC---cHHHHHHHHHHHHhhcccC-cccHHHHHHHH
Confidence 3467899999999999999999999999999999999999999998 7899999999999999987 67788876321
Q ss_pred cCcc------------ccHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcchhc
Q 025012 149 AKYI------------FETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASF 216 (259)
Q Consensus 149 ~~~~------------~s~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~~~l~d~~~ 216 (259)
.... -.++.|+..|+.||++|+|++++-.|+.||-.|+..++...+....+...|+.++.-++...-+
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~c 189 (323)
T KOG0834|consen 110 YRYLNPKDLELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLC 189 (323)
T ss_pred HHHcCcccccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeee
Confidence 1111 1278899999999999999999999999999999988877665456778899999999988888
Q ss_pred cCccHHHHHHHHHHHHHhcCCCCCCCCCCchhhHhhhhhc
Q 025012 217 LEYRPSSIAAAAILCAANEIPNLSLVNPEHAESWCDGLSK 256 (259)
Q Consensus 217 ~~~~PS~iAaAai~la~~~~~~~~~~~~~~~~~w~~~l~~ 256 (259)
++|+|..||+|||++|....+. ........ .||+.+++
T Consensus 190 L~y~p~~IAva~i~lA~~~~~~-~~~~~~~~-~w~~~~d~ 227 (323)
T KOG0834|consen 190 LQYSPHSIAVACIHLAAKLLGV-ELPSDTDK-RWWREFDE 227 (323)
T ss_pred EeecCcEEEeehhhHHHHHcCC-CCCCCccc-chhhhhcc
Confidence 9999999999999999865543 33333333 68877664
No 9
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.84 E-value=5.9e-20 Score=157.55 Aligned_cols=179 Identities=21% Similarity=0.336 Sum_probs=150.4
Q ss_pred CCHHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhh-
Q 025012 69 LDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVE- 147 (259)
Q Consensus 69 i~~~~R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~- 147 (259)
-..+.|..=+.||.+-+..++|+..+.+++..+|-||+...++.+. ++..++++|++||||+||. |-.+++.+..
T Consensus 18 ~e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~---~~e~vv~ACv~LASKiEE~-Prr~rdVinVF 93 (367)
T KOG0835|consen 18 TEEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRH---DFEIVVMACVLLASKIEEE-PRRIRDVINVF 93 (367)
T ss_pred hHHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccc---cHHHHHHHHHHHHhhhccc-cccHhHHHHHH
Confidence 4567788889999999999999999999999999999999999888 7999999999999999986 4455554310
Q ss_pred -----------------ccCccccHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHH
Q 025012 148 -----------------GAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSN 210 (259)
Q Consensus 148 -----------------~~~~~~s~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~~~ 210 (259)
.-.+.-.+.++.++|+.||+.|+|++.+.+|+.++-.|+..++.++.. .+.+.++++...+
T Consensus 94 h~L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~--~l~Q~~wNfmNDs 171 (367)
T KOG0835|consen 94 HYLEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNL--KLLQAAWNFMNDS 171 (367)
T ss_pred HHHHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCch--hHHHHHHHhhhhc
Confidence 000111367789999999999999999999999999999999988764 6788899999999
Q ss_pred hcchhccCccHHHHHHHHHHHHHhcCCCCCCCCCCchhhHhhhhhcc
Q 025012 211 IQEASFLEYRPSSIAAAAILCAANEIPNLSLVNPEHAESWCDGLSKV 257 (259)
Q Consensus 211 l~d~~~~~~~PS~iAaAai~la~~~~~~~~~~~~~~~~~w~~~l~~~ 257 (259)
+-..-|..|+|+.||||||++|.+.+. .+-+..+ .|+..+.-.
T Consensus 172 lRT~v~vry~pe~iACaciyLaAR~~e---IpLp~~P-~Wf~~Fd~~ 214 (367)
T KOG0835|consen 172 LRTDVFVRYSPESIACACIYLAARNLE---IPLPFQP-HWFKAFDTT 214 (367)
T ss_pred cccceeeecCHHHHHHHHHHHHHhhhc---CCCCCCc-cHHHHcCCc
Confidence 999999999999999999999998875 3445555 788776543
No 10
>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=99.78 E-value=1.9e-18 Score=148.28 Aligned_cols=189 Identities=21% Similarity=0.233 Sum_probs=149.3
Q ss_pred hHHHHHHHHHHHHhhCCCCCccccccCCCCCHHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCch
Q 025012 40 IEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPW 119 (259)
Q Consensus 40 ~~e~l~~ll~~E~~~~~~~~y~~~~q~~~i~~~~R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~l 119 (259)
..+-.++.+++...-.++. +. -+-+.+.|..-..|+..+|.+++++..++.+|+.+|+||+.+.++... .+
T Consensus 17 ~~~~~q~~~e~~l~~~~p~--l~----~~~e~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~---~~ 87 (297)
T COG5333 17 SFDSSQNAIELDLLVLEPE--LT----LEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEI---SL 87 (297)
T ss_pred chhHHHHHHHhhHhcCCcc--cc----hhhhhhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccc---cH
Confidence 3455666666666544431 21 123557777888999999999999999999999999999999999888 79
Q ss_pred HHHHHHHHHHHHHhhcccCC--chhhhhhh---ccCccccHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHhcCCCCC
Q 025012 120 QLLSVACLSLAAKMEETVVP--SLLDLQVE---GAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGT 194 (259)
Q Consensus 120 qL~a~acL~IAsK~eE~~~p--~~~~l~~~---~~~~~~s~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~ 194 (259)
+-++.||+++|+|+||. +. .+..+... .....-+++.|..+|..+|+.|+|++.+++|+.++..|+..+...+.
T Consensus 88 ~~vv~tcv~LA~K~ed~-~~~I~i~~~~~~~~~se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~ 166 (297)
T COG5333 88 YSVVTTCVYLACKVEDT-PRDISIESFEARDLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDK 166 (297)
T ss_pred HHHHHhheeeeeecccc-cchhhHHHHHhhccccccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccH
Confidence 99999999999999995 22 22222211 00223579999999999999999999999999999999876655443
Q ss_pred hHHHHHHHHHHHHHHHhcchhccCccHHHHHHHHHHHHHhc--CCCCC
Q 025012 195 FMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANE--IPNLS 240 (259)
Q Consensus 195 ~~~~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la~~~--~~~~~ 240 (259)
....+.|+.++.-++...-++.|+|..||+||++.|.+. .|.|.
T Consensus 167 --~~~~~~aw~~inDa~~t~~~llypphiIA~a~l~ia~~~~~~~~~~ 212 (297)
T COG5333 167 --YKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPIIK 212 (297)
T ss_pred --HHHHHHHHHHHHhhhhceeeeecChHHHHHHHHHHHHHhcCCccch
Confidence 567788999999999999999999999999999999764 34443
No 11
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.72 E-value=3.7e-17 Score=134.24 Aligned_cols=173 Identities=24% Similarity=0.284 Sum_probs=136.9
Q ss_pred HHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhh----
Q 025012 72 SAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVE---- 147 (259)
Q Consensus 72 ~~R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~---- 147 (259)
+.+--.-+.|..+++++++...++.+|+.||-||+.+.+...- .+.+++.||+++|||+||.-...++.++..
T Consensus 39 ~l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~---~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L 115 (264)
T KOG0794|consen 39 KLKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEI---EPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVL 115 (264)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc---CHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHH
Confidence 4455667789999999999999999999999999999998877 799999999999999999742222222210
Q ss_pred -------ccCccccHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcchhccCcc
Q 025012 148 -------GAKYIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYR 220 (259)
Q Consensus 148 -------~~~~~~s~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~~~l~d~~~~~~~ 220 (259)
.....+...+|..||..+|+.|++-|-+.+|+.-|..++...+..+ ..+...+..++.-++...-.+-|+
T Consensus 116 ~~~f~~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~d---~~~l~~~W~ivNDSyr~Dl~Ll~P 192 (264)
T KOG0794|consen 116 KTRFSYWPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGIND---QKLLQLAWSIVNDSYRMDLCLLYP 192 (264)
T ss_pred hhhcccchhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcccc---hhhhhhhHhhhcchhhcceeeecC
Confidence 1123467899999999999999999999999999999987665532 335566888888888888888999
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCCCCchhhHhhhhhc
Q 025012 221 PSSIAAAAILCAANEIPNLSLVNPEHAESWCDGLSK 256 (259)
Q Consensus 221 PS~iAaAai~la~~~~~~~~~~~~~~~~~w~~~l~~ 256 (259)
|..||.|||+.|....+. .-+..|...+..
T Consensus 193 Ph~IalAcl~Ia~~~~~k------~~~~~w~~el~v 222 (264)
T KOG0794|consen 193 PHQIALACLYIACVIDEK------DIPKAWFAELSV 222 (264)
T ss_pred HHHHHHHHHHHHHhhcCC------ChHHHHHHHHhc
Confidence 999999999999765432 223667655543
No 12
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=99.51 E-value=7.8e-14 Score=99.61 Aligned_cols=86 Identities=35% Similarity=0.443 Sum_probs=78.0
Q ss_pred HHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhhccCccc
Q 025012 74 REESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIF 153 (259)
Q Consensus 74 R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~~~~~ 153 (259)
|...++||.+++..++++++|.++|+.++|||+....+.+. .++++|++|++||+|+++. ++..+++... ++ +
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~---~~~~ia~a~l~lA~k~~~~-~~~~~~~~~~-~~--~ 74 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGR---SPSLVAAAALYLAAKVEEI-PPWLKDLVHV-TG--Y 74 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccC---ChHHHHHHHHHHHHHHcCC-CCCHHHHhHH-hC--C
Confidence 67889999999999999999999999999999999888766 7999999999999999999 8899998754 33 4
Q ss_pred -cHHHHHHHHHHHH
Q 025012 154 -ETKTIRRMELLVL 166 (259)
Q Consensus 154 -s~~~i~~~E~~IL 166 (259)
+.++|.++|+.|+
T Consensus 75 ~~~~~i~~~e~~il 88 (88)
T cd00043 75 ATEEEILRMEKLLL 88 (88)
T ss_pred CCHHHHHHHHHHhC
Confidence 9999999999874
No 13
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.48 E-value=5.1e-12 Score=112.15 Aligned_cols=153 Identities=16% Similarity=0.152 Sum_probs=130.2
Q ss_pred HHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhhccCcc
Q 025012 73 AREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYI 152 (259)
Q Consensus 73 ~R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~~~~ 152 (259)
.-.....-|-+++..++++..+.-.|..++.++.....+... ....++++|+|+|+|.++. |.++.++... .+
T Consensus 121 ~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgr---s~~~i~AAclYiACR~~~~-prtl~eI~~~-~~-- 193 (310)
T PRK00423 121 NLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGR---SIEGVVAAALYAACRRCKV-PRTLDEIAEV-SR-- 193 (310)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCC---CHHHHHHHHHHHHHHHcCC-CcCHHHHHHH-hC--
Confidence 335566778999999999999999999999999998777666 6999999999999997655 7899998754 32
Q ss_pred ccHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcchhccCccHHHHHHHHHHHH
Q 025012 153 FETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCA 232 (259)
Q Consensus 153 ~s~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la 232 (259)
.++++|.+.++.|++.|++++...+|.+|+..|.+.++.+. .+...|..++..+....-....+|..|||||||+|
T Consensus 194 v~~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~----~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA 269 (310)
T PRK00423 194 VSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSG----EVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIA 269 (310)
T ss_pred CCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCH----HHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999998864 45667888887776555557899999999999999
Q ss_pred HhcC
Q 025012 233 ANEI 236 (259)
Q Consensus 233 ~~~~ 236 (259)
.+..
T Consensus 270 ~~~~ 273 (310)
T PRK00423 270 SLLL 273 (310)
T ss_pred HHHh
Confidence 7544
No 14
>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=1.9e-12 Score=110.75 Aligned_cols=153 Identities=20% Similarity=0.302 Sum_probs=116.2
Q ss_pred HHHHHHHHHHHHHh--CCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhhcc-Cc
Q 025012 75 EESVAWILKVQAYY--NFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGA-KY 151 (259)
Q Consensus 75 ~~lvdwl~~v~~~~--~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~-~~ 151 (259)
.....-+.+.+.+| .++++++.+|+.+|-||+...++... +.+.|.+||+|+|+|++|-+ .++.+|+.... +.
T Consensus 57 k~~E~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~---~pk~I~~tc~flA~Kieef~-ISieqFvkn~~~~~ 132 (325)
T KOG2496|consen 57 KEEELSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEY---SPKIIMATCFFLACKIEEFY-ISIEQFVKNMNGRK 132 (325)
T ss_pred HHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhc---ChHHHHHHHHHHHhhhHhhe-ecHHHHHhhccCcc
Confidence 34444556666666 47899999999999999999998888 79999999999999999875 58899874322 22
Q ss_pred cccHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHhc----CCCCChHHHHHHH--HHHHHHHHhcchhccCccHHHHH
Q 025012 152 IFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKL----DPTGTFMGFLISR--ATKIILSNIQEASFLEYRPSSIA 225 (259)
Q Consensus 152 ~~s~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~l~~l----~~~~~~~~~~~~~--a~~~l~~~l~d~~~~~~~PS~iA 225 (259)
.-+.+.|+..|..+++.|+|++.+.+|+.=++-|+--+ ..-.+ ....... ...+++.+++..-++-|+||.||
T Consensus 133 ~k~~e~vLk~E~~llqsL~f~L~vh~PyRPleGFl~D~kt~l~~~~n-~d~~~~~~d~~~fl~~~lltDa~lLytPsQIA 211 (325)
T KOG2496|consen 133 WKTHEIVLKYEFLLLQSLKFSLTVHNPYRPLEGFLLDMKTRLPALEN-PDILRKHDDSKKFLDRALLTDAYLLYTPSQIA 211 (325)
T ss_pred cccHHHHHhchHHHHHhhhhhheecCCCCchHHHHHHHHHHHHhccC-HHHHhhhhhHHHHHHHHHHhccceecChHHHH
Confidence 35789999999999999999999999999998887321 11111 1111111 24566666666667779999999
Q ss_pred HHHHHHH
Q 025012 226 AAAILCA 232 (259)
Q Consensus 226 aAai~la 232 (259)
+|||..|
T Consensus 212 LaAil~a 218 (325)
T KOG2496|consen 212 LAAILHA 218 (325)
T ss_pred HHHHHHH
Confidence 9999655
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=99.42 E-value=7.2e-13 Score=93.60 Aligned_cols=83 Identities=36% Similarity=0.435 Sum_probs=72.0
Q ss_pred HHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhhccCccccHHHH
Q 025012 79 AWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTI 158 (259)
Q Consensus 79 dwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~~~~~s~~~i 158 (259)
+||.+++..+++++++.++|+.++||++....+.+. ..+++|++|+++|+|+++.. |...++... +++ ++.++|
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~---~~~~ia~a~l~lA~k~~~~~-~~~~~~~~~-~~~-~~~~~i 74 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKY---SPSLIAAAALYLAAKTEEIP-PWTKELVHY-TGY-FTEEEI 74 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccC---CHHHHHHHHHHHHHHHhcCC-CCchhHhHh-hCC-CCHHHH
Confidence 599999999999999999999999999997666665 79999999999999999985 566777544 343 699999
Q ss_pred HHHHHHHHH
Q 025012 159 RRMELLVLS 167 (259)
Q Consensus 159 ~~~E~~IL~ 167 (259)
.++|+.||+
T Consensus 75 ~~~~~~il~ 83 (83)
T smart00385 75 LRMEKLLLE 83 (83)
T ss_pred HHHHHHHhC
Confidence 999999873
No 16
>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=98.95 E-value=1.2e-09 Score=82.80 Aligned_cols=57 Identities=32% Similarity=0.356 Sum_probs=46.7
Q ss_pred CCHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcchhccCccHHHHHHHHHHHHHhcC
Q 025012 176 VTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEI 236 (259)
Q Consensus 176 ~tp~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la~~~~ 236 (259)
|||++|+++|++.. .....+...+.+++++++.|+.|++|+||+||+||+++|+..+
T Consensus 1 PTp~~Fl~~~~~~~----~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~ 57 (118)
T PF02984_consen 1 PTPYDFLRRFLKIS----NADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKIL 57 (118)
T ss_dssp --HHHHHHHHHTSS----SHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHc----CCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHh
Confidence 89999999995432 2245678889999999999999999999999999999999875
No 17
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=98.93 E-value=1.4e-07 Score=82.25 Aligned_cols=156 Identities=17% Similarity=0.185 Sum_probs=133.6
Q ss_pred HHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhhccC
Q 025012 71 ASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAK 150 (259)
Q Consensus 71 ~~~R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~~ 150 (259)
.+.-......+-.++..++++..+.-.|..++-+.+.+.-+..- ..+-++++|+|+|++.... |.++.++... .+
T Consensus 94 ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGR---sie~v~AA~iY~acR~~~~-prtl~eIa~a-~~ 168 (285)
T COG1405 94 ERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGR---SIESVAAACIYAACRINGV-PRTLDEIAKA-LG 168 (285)
T ss_pred hhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCC---cHHHHHHHHHHHHHHHcCC-CccHHHHHHH-HC
Confidence 34456778888999999999999999999999999998877766 6999999999999998776 6777787654 23
Q ss_pred ccccHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcchhccCccHHHHHHHHHH
Q 025012 151 YIFETKTIRRMELLVLSVLDWRLRSVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAIL 230 (259)
Q Consensus 151 ~~~s~~~i~~~E~~IL~~L~f~l~~~tp~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~ 230 (259)
.++++|.++.+.+.+.|+=.+.+..|.+|+..|.+.|+.+++ +...|..++..+........-.|+.+|+||||
T Consensus 169 --V~~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~----v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy 242 (285)
T COG1405 169 --VSKKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSDE----VRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIY 242 (285)
T ss_pred --CCHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHH----HHHHHHHHHHHHHHhCcccCCCchhHHHHHHH
Confidence 678999999999999999999999999999999999999843 55567788888877777789999999999999
Q ss_pred HHHhcCC
Q 025012 231 CAANEIP 237 (259)
Q Consensus 231 la~~~~~ 237 (259)
+|....+
T Consensus 243 ~as~l~~ 249 (285)
T COG1405 243 LASLLLG 249 (285)
T ss_pred HHHHHhC
Confidence 9965543
No 18
>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=98.75 E-value=7.2e-08 Score=76.67 Aligned_cols=92 Identities=21% Similarity=0.250 Sum_probs=70.5
Q ss_pred HHHHHHHHHHHHhCCchhHHHHHHHHHHHHhc---CCc--cCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhhccC
Q 025012 76 ESVAWILKVQAYYNFLPLTSYLSVNYMDRFLY---SRR--LPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAK 150 (259)
Q Consensus 76 ~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~---~~~--i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~~ 150 (259)
.+.+|+.++...-+++++++.+|+.|+||+.. ... +... ..+.+-++|+.+|+|+-+......+.+... ++
T Consensus 53 ~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~---~~~Rl~l~alilA~K~~~D~~~~n~~~a~v-~g 128 (149)
T PF08613_consen 53 SIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSS---NIHRLFLTALILASKFLDDNTYSNKSWAKV-GG 128 (149)
T ss_dssp -HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STT---THHHHHHHHHHHHHHHH-SS---HHHHHHH-HT
T ss_pred cHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccc---hhHHHHHHHHHHHHhhcccccccHHHHHhh-cC
Confidence 38899999999999999999999999999999 222 3334 688999999999999988877777777654 33
Q ss_pred ccccHHHHHHHHHHHHHHcCCcc
Q 025012 151 YIFETKTIRRMELLVLSVLDWRL 173 (259)
Q Consensus 151 ~~~s~~~i~~~E~~IL~~L~f~l 173 (259)
++.+++.+||+..|..|+|+|
T Consensus 129 --is~~eln~lE~~fL~~l~~~L 149 (149)
T PF08613_consen 129 --ISLKELNELEREFLKLLDYNL 149 (149)
T ss_dssp --S-HHHHHHHHHHHHHHTTT--
T ss_pred --CCHHHHHHHHHHHHHHCCCcC
Confidence 799999999999999999986
No 19
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.66 E-value=2e-06 Score=73.96 Aligned_cols=152 Identities=19% Similarity=0.150 Sum_probs=120.1
Q ss_pred HHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhhccCcc
Q 025012 73 AREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYI 152 (259)
Q Consensus 73 ~R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~~~~ 152 (259)
.-.....-|..+++..+|+....-.|-.+|.++-..+..... ..+-+++||++||++-++. |.++++++.. .+
T Consensus 103 ~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGk---s~eai~AAclyiACRq~~~-pRT~kEI~~~-an-- 175 (308)
T KOG1597|consen 103 VLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGK---SVEALAAACLYIACRQEDV-PRTFKEISAV-AN-- 175 (308)
T ss_pred HHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCc---cHHHHHHHHHHHHHHhcCC-CchHHHHHHH-Hc--
Confidence 334455567889999999999999999999999976666655 6999999999999995554 8888888754 33
Q ss_pred ccHHHHHHHHHHHHHHcCCccccCC--HHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcchhccCccHHHHHHHHHH
Q 025012 153 FETKTIRRMELLVLSVLDWRLRSVT--PFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAIL 230 (259)
Q Consensus 153 ~s~~~i~~~E~~IL~~L~f~l~~~t--p~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~ 230 (259)
.+++||-+.=..|++.|+=.+...+ .-+|+.+|.+.++.+.. +...|.++.+.+..-.....-.|=.||||+||
T Consensus 176 v~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~----~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IY 251 (308)
T KOG1597|consen 176 VSKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKS----AQEAATEIAEKAEEMDIRAGRSPISIAAAAIY 251 (308)
T ss_pred CCHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHH----HHHHHHHHHHHHHHhccccCCCchhHHHHHHH
Confidence 7899999999999999988777665 88999999998888743 44556666666543333345789999999999
Q ss_pred HHHhc
Q 025012 231 CAANE 235 (259)
Q Consensus 231 la~~~ 235 (259)
++.+.
T Consensus 252 misql 256 (308)
T KOG1597|consen 252 MISQL 256 (308)
T ss_pred HHHHh
Confidence 98543
No 20
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=97.95 E-value=5.3e-06 Score=73.78 Aligned_cols=105 Identities=18% Similarity=0.229 Sum_probs=86.7
Q ss_pred CCHHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhh-hh
Q 025012 69 LDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQ-VE 147 (259)
Q Consensus 69 i~~~~R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~-~~ 147 (259)
+|..-=+.+-.-|.++....++..-|+.+|..||.....+..+.+. .-.|.|-||+++|+|+.+..--.++.++ ..
T Consensus 377 LTLSKirSlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~---NRKlcAGAclLlaaKmnD~Kks~vKslIek~ 453 (497)
T KOG4164|consen 377 LTLSKIRSLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQ---NRKLCAGACLLLAAKMNDLKKSTVKSLIEKL 453 (497)
T ss_pred EeHHHHHHHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhh---hhhHHHHHHHHHHHHhhhhhhHHHHHHHHHH
Confidence 3433333445557788888999999999999999999999999988 4899999999999999987777777776 23
Q ss_pred ccCccccHHHHHHHHHHHHHHcCCccccC
Q 025012 148 GAKYIFETKTIRRMELLVLSVLDWRLRSV 176 (259)
Q Consensus 148 ~~~~~~s~~~i~~~E~~IL~~L~f~l~~~ 176 (259)
.....+++.|++..|.-||-.|.|.|..|
T Consensus 454 Ee~fR~nrrdLia~Ef~VlvaLefaL~~~ 482 (497)
T KOG4164|consen 454 EEQFRLNRRDLIAFEFPVLVALEFALHLP 482 (497)
T ss_pred HHHhcccHHhhhhhhhhHHHhhhhhccCC
Confidence 34556889999999999999999999875
No 21
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=97.66 E-value=0.0009 Score=62.26 Aligned_cols=172 Identities=19% Similarity=0.151 Sum_probs=132.5
Q ss_pred CCCCccccccCCCC-CHHHHHHHHH----HHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHH
Q 025012 56 PGFDYLTRFQTHSL-DASAREESVA----WILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLA 130 (259)
Q Consensus 56 ~~~~y~~~~q~~~i-~~~~R~~lvd----wl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IA 130 (259)
+..+|...-|.+.- ..+.|...+. -|-+++..+++.. ..-.|.++|.--+..+-.+.. ..+.+-.+|+|++
T Consensus 44 ~~G~~v~~~~~g~~~s~e~r~~t~~n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr---~~~~vvasClY~v 119 (521)
T KOG1598|consen 44 AQGQFVRVGQSGAGSSLESREKTIYNARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGR---RSTEVVAACLYLV 119 (521)
T ss_pred cceeEEeccccCCccchHHHHHHHHHHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCc---chHHHHHHHHHHH
Confidence 45556655444322 3455555444 4788999999999 999999999999888877776 6999999999999
Q ss_pred HHhhcccCCchhhhhhhccCccccHHHHHHHHHHHHHHcCCc---cccCCHHHHHHHHHHhcCCCCChHHHHHHHHHHHH
Q 025012 131 AKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLSVLDWR---LRSVTPFSFIYFFACKLDPTGTFMGFLISRATKII 207 (259)
Q Consensus 131 sK~eE~~~p~~~~l~~~~~~~~~s~~~i~~~E~~IL~~L~f~---l~~~tp~~fl~~~l~~l~~~~~~~~~~~~~a~~~l 207 (259)
+..+-... .+-+|... -..+.-++-.+=+.+-..|.-. +....|.-|+.+|..++...+.. ..+...+..++
T Consensus 120 cR~e~t~h-lliDfS~~---Lqv~Vy~LG~~~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~-~~Vv~~a~~L~ 194 (521)
T KOG1598|consen 120 CRLEKTDH-LLIDFSSY---LQVSVYDLGSNFLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKT-EDVAKTATRLA 194 (521)
T ss_pred HHhhCCce-EEEEeccc---eEEehhhhhHHHHHHHHHhccccccccccCcceeeechhHhhhcCCch-HHHHHHHHHHH
Confidence 99776643 44444321 2256778888888888888887 66788999999999887665544 77888899999
Q ss_pred HHHhcchhccCccHHHHHHHHHHHHHhcC
Q 025012 208 LSNIQEASFLEYRPSSIAAAAILCAANEI 236 (259)
Q Consensus 208 ~~~l~d~~~~~~~PS~iAaAai~la~~~~ 236 (259)
....-|--...-+|+-|+-|||+.|.+..
T Consensus 195 ~rMkrdwm~tGRRPsglcGAaLliAar~h 223 (521)
T KOG1598|consen 195 QRMKRDWMQTGRRPSGLCGAALLIAARMH 223 (521)
T ss_pred HHHHHHHHHhCCCccchhHHHHHHHHHHc
Confidence 98888888888999999999999997654
No 22
>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=97.47 E-value=0.00053 Score=48.06 Aligned_cols=59 Identities=27% Similarity=0.240 Sum_probs=50.7
Q ss_pred cCCHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcchhccCccHHHHHHHHHHHHHhcCC
Q 025012 175 SVTPFSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIP 237 (259)
Q Consensus 175 ~~tp~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la~~~~~ 237 (259)
.+++.+|+..+...++.+ ..+...|..+++.++....+..+.|+.+|+||+++|.+..+
T Consensus 2 ~~~~~~~l~~~~~~~~~~----~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~ 60 (88)
T cd00043 2 RPTPLDFLRRVAKALGLS----PETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEE 60 (88)
T ss_pred cchHHHHHHHHHHHcCCC----HHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcC
Confidence 578999999999888665 34667799999999999999999999999999999987554
No 23
>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=97.22 E-value=0.0013 Score=45.50 Aligned_cols=53 Identities=28% Similarity=0.320 Sum_probs=44.0
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcchhccCccHHHHHHHHHHHHHhcCC
Q 025012 181 FIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIP 237 (259)
Q Consensus 181 fl~~~l~~l~~~~~~~~~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la~~~~~ 237 (259)
|+..+...++.+ ..+...|.++++.++.+..+.+++|+.+|+||+++|.+..+
T Consensus 2 ~l~~~~~~~~~~----~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~ 54 (83)
T smart00385 2 FLRRVCKALNLD----PETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEE 54 (83)
T ss_pred HHHHHHHHcCCC----HHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhc
Confidence 667777666664 45677899999999998999999999999999999987654
No 24
>KOG1674 consensus Cyclin [General function prediction only]
Probab=97.04 E-value=0.003 Score=53.32 Aligned_cols=97 Identities=21% Similarity=0.233 Sum_probs=75.4
Q ss_pred HHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCc------cCCCCCCc-hHHHHHHHHHHHHHhhcccCCchhhhhhhcc
Q 025012 77 SVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRR------LPDNNGWP-WQLLSVACLSLAAKMEETVVPSLLDLQVEGA 149 (259)
Q Consensus 77 lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~------i~~~~~~~-lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~ 149 (259)
+-+++.++.+..+.+++++..|..|||||..+.+ -..-+... .+-+-++|+.+|+|+.+...-....+...
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 4567888888999999999999999999999733 11111113 66788999999999987754444444433
Q ss_pred CccccHHHHHHHHHHHHHHcCCccccC
Q 025012 150 KYIFETKTIRRMELLVLSVLDWRLRSV 176 (259)
Q Consensus 150 ~~~~s~~~i~~~E~~IL~~L~f~l~~~ 176 (259)
+..+.+++..+|...|..++|++.++
T Consensus 156 -ggl~~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 156 -GGLTTDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred -CCCChHhhhhhhHHHHhhCCeEEEec
Confidence 34789999999999999999999885
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=96.79 E-value=0.016 Score=39.74 Aligned_cols=62 Identities=11% Similarity=0.117 Sum_probs=48.8
Q ss_pred HHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhh
Q 025012 81 ILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQV 146 (259)
Q Consensus 81 l~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~ 146 (259)
|-+++..++++.++.-.|..++++-....-.... ...-++++|+|+|++.... +.++.++..
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr---~~~~iaAA~iY~acr~~~~-~~t~~eIa~ 62 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGR---SPESIAAACIYLACRLNGV-PRTLKEIAE 62 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS----HHHHHHHHHHHHHHHTTS-SSSHHHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccC---CHHHHHHHHHHHHHHHcCC-CcCHHHHHH
Confidence 4578999999999999999999998887655544 6999999999999997654 667777754
No 26
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=95.24 E-value=0.24 Score=44.16 Aligned_cols=89 Identities=9% Similarity=0.028 Sum_probs=70.5
Q ss_pred HHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhhccCccccHHH
Q 025012 78 VAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKT 157 (259)
Q Consensus 78 vdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~~~~~s~~~ 157 (259)
-++|-+.+..++++.++.-.|..++.+.....-.... ...-++++|+|+|++.... +.+.+++... . ..+...
T Consensus 220 ~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr---~P~sIAAAaIYlA~~~~g~-~~t~keIa~v-~--~Vs~~t 292 (310)
T PRK00423 220 IDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGK---GPTGLAAAAIYIASLLLGE-RRTQREVAEV-A--GVTEVT 292 (310)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCC---CHHHHHHHHHHHHHHHhCC-CCCHHHHHHH-c--CCCHHH
Confidence 4889999999999999999999999888765433333 7999999999999998764 4677777543 3 368888
Q ss_pred HHHHHHHHHHHcCCcc
Q 025012 158 IRRMELLVLSVLDWRL 173 (259)
Q Consensus 158 i~~~E~~IL~~L~f~l 173 (259)
|.+.=+.+.+.|+..+
T Consensus 293 I~~~ykel~~~l~~~~ 308 (310)
T PRK00423 293 VRNRYKELAEKLDIKI 308 (310)
T ss_pred HHHHHHHHHHHhCccc
Confidence 8888888888876543
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=93.85 E-value=0.24 Score=33.83 Aligned_cols=51 Identities=25% Similarity=0.133 Sum_probs=36.3
Q ss_pred HHHHHhcCCCCChHHHHHHHHHHHHHHHhcchhccCccHHHHHHHHHHHHHhcCC
Q 025012 183 YFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIP 237 (259)
Q Consensus 183 ~~~l~~l~~~~~~~~~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la~~~~~ 237 (259)
..|.+.++.+. .+.+.|..+...+....-.-+-+|..+|+||||+|.+..+
T Consensus 2 ~r~~~~L~L~~----~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~ 52 (71)
T PF00382_consen 2 PRICSKLGLPE----DVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNG 52 (71)
T ss_dssp HHHHHHTT--H----HHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTT
T ss_pred hHHHhHcCCCH----HHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcC
Confidence 45556666654 5677788888777666666678999999999999977653
No 28
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=93.19 E-value=0.12 Score=45.26 Aligned_cols=100 Identities=10% Similarity=0.178 Sum_probs=66.6
Q ss_pred HHHHHHHhCCchhHHHHHHHHHHHHhcCCccC--CCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhhccCccccHHHH
Q 025012 81 ILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLP--DNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTI 158 (259)
Q Consensus 81 l~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~--~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~~~~~s~~~i 158 (259)
....+....+..+--...+.|++|-+.-.... +. ....+..-..++|+|+-......--+.+...- -.|.+|+
T Consensus 197 v~~l~~~~qlta~~aiitL~~~erl~~~~e~~~~p~---~w~r~~~g~il~sskv~~dqs~wnvdycqIlK--d~tveDm 271 (343)
T KOG1675|consen 197 VRILFSWAQLTAECDIITLVYAERLLWLAERDPCPR---NWSRAVLGEILLSSKVYDDQSVWNVDYCEILK--DQSVDDM 271 (343)
T ss_pred hhhHhhhhhhhhccchHHHHhhHhhhhHhhcCCCcc---hhhhhhhhhheehhhhhhhhhcccHHHHHHHh--hccHhhH
Confidence 33344444555555556678888877655444 33 35556666799999996654433344433322 2579999
Q ss_pred HHHHHHHHHHcCCccccCCHHHHHHHHH
Q 025012 159 RRMELLVLSVLDWRLRSVTPFSFIYFFA 186 (259)
Q Consensus 159 ~~~E~~IL~~L~f~l~~~tp~~fl~~~l 186 (259)
..|||.+|+.|+|++++|.. -|-.+|.
T Consensus 272 Ne~ERqfLelLqfNinvp~s-vYAKyYf 298 (343)
T KOG1675|consen 272 NALERQFLELLQFNINVPSS-EYAKYYF 298 (343)
T ss_pred HHHHHHHHHHHhhccCccHH-HHHHHHH
Confidence 99999999999999999875 4555554
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=89.36 E-value=2 Score=31.64 Aligned_cols=87 Identities=14% Similarity=0.140 Sum_probs=56.9
Q ss_pred HHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhhccCccccHHH
Q 025012 78 VAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKT 157 (259)
Q Consensus 78 vdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~~~~~s~~~ 157 (259)
.+|+....+..+.+.++..+|-.+++..+....+-.. ..-.+|++|+++|.+.-...++--..+... ++ ++.++
T Consensus 4 ~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~---~PS~iAaAai~lA~~~~~~~~~~~~~l~~~-t~--~~~~~ 77 (118)
T PF02984_consen 4 YDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQY---PPSVIAAAAILLARKILGKEPPWPESLEKL-TG--YDKED 77 (118)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS----HHHHHHHHHHHHHHHHHSSTCSHHHHHHH-HT--S-HHH
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCC---CHHHHHHHHHHHHHHHhCccccCCccchhh-cC--CCHHH
Confidence 3455555333444667888899999988877776666 689999999999999966323333333322 32 57888
Q ss_pred HHHHHHHHHHHcC
Q 025012 158 IRRMELLVLSVLD 170 (259)
Q Consensus 158 i~~~E~~IL~~L~ 170 (259)
|..+=..|.+.+.
T Consensus 78 l~~c~~~i~~~~~ 90 (118)
T PF02984_consen 78 LKECIELIQELLS 90 (118)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 8777666665554
No 30
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=85.94 E-value=6.4 Score=34.66 Aligned_cols=57 Identities=9% Similarity=0.044 Sum_probs=49.5
Q ss_pred HHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhc
Q 025012 76 ESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEE 135 (259)
Q Consensus 76 ~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE 135 (259)
.-.+++-..+..++++.++--.|+.+++....+...... ...-+|++|+|+|++...
T Consensus 193 ~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk---~P~glAaaaiy~as~l~~ 249 (285)
T COG1405 193 DPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGK---SPAGLAAAAIYLASLLLG 249 (285)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCC---CchhHHHHHHHHHHHHhC
Confidence 345788899999999999999999999999887765544 588899999999999876
No 31
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=82.87 E-value=1.7 Score=38.85 Aligned_cols=95 Identities=17% Similarity=0.152 Sum_probs=63.2
Q ss_pred HHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhh-hhccCccc
Q 025012 75 EESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQ-VEGAKYIF 153 (259)
Q Consensus 75 ~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~-~~~~~~~~ 153 (259)
.-+++++..+-...+........|-+++-..+...-.-.. ..+.||++|++||+|+.....|...+.. ....+...
T Consensus 153 ~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y---~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~v 229 (323)
T KOG0834|consen 153 KYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQY---SPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETV 229 (323)
T ss_pred HHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEee---cCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccC
Confidence 4556666665555555445666777777666655444444 6889999999999999877555544441 22234447
Q ss_pred cHHHHHHHHHHHHHHcCCc
Q 025012 154 ETKTIRRMELLVLSVLDWR 172 (259)
Q Consensus 154 s~~~i~~~E~~IL~~L~f~ 172 (259)
+.+++.++.-.+|....-.
T Consensus 230 t~e~l~~i~~~~l~~y~~~ 248 (323)
T KOG0834|consen 230 TNELLDDICHEFLDLYEQT 248 (323)
T ss_pred CHHHHHHHHHHHHHHHhhc
Confidence 8899999988888877543
No 32
>PF09080 K-cyclin_vir_C: K cyclin, C terminal; InterPro: IPR015164 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 domain adopts a secondary structure consisting of a five alpha-helix cyclin fold. Interaction with cyclin dependent kinases (CDKs) at a PSTAIRE sequence motif within the catalytic cleft of CDK results in the regulation of CDK activity []. ; PDB: 1G3N_C.
Probab=76.68 E-value=13 Score=26.46 Aligned_cols=54 Identities=20% Similarity=0.017 Sum_probs=37.9
Q ss_pred HHHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcchhccCccHHHHHHH-HHHHHH
Q 025012 180 SFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAA-AILCAA 233 (259)
Q Consensus 180 ~fl~~~l~~l~~~~~~~~~~~~~a~~~l~~~l~d~~~~~~~PS~iAaA-ai~la~ 233 (259)
+-+...+-+.....+....+.......+..++-|...-..+||.+|+| |-++..
T Consensus 6 D~~~~~L~K~~~~~e~L~~~H~~V~~~v~KAiV~P~TG~Lp~SlvaAA~CAL~~~ 60 (106)
T PF09080_consen 6 DAIGPLLFKSGFTKEQLFAWHSEVVESVHKAIVNPKTGGLPPSLVAAAGCALFSL 60 (106)
T ss_dssp HHHHHHHHHHS-SSTTHHHHHHHHHHHHHHHHCSTTGGGS-HHHHHHHHHHHHS-
T ss_pred ccccHHHHHHcccHHHHHHHHHHHHHHHHHHhcCcccCCCCHHHHHHhhhhhccc
Confidence 444444444455556667778888889999999999999999999998 554443
No 33
>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=65.00 E-value=42 Score=23.65 Aligned_cols=57 Identities=16% Similarity=0.190 Sum_probs=45.4
Q ss_pred HHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcchhccCccHHHHHHHHHHHHHhc
Q 025012 179 FSFIYFFACKLDPTGTFMGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANE 235 (259)
Q Consensus 179 ~~fl~~~l~~l~~~~~~~~~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la~~~ 235 (259)
.+|+-...+.+..+++...++.+.+.--+-.++......-.+|..|.++.+......
T Consensus 5 tdflip~c~alkipe~~wpql~e~~s~tickaliqpniall~p~licaggllttiet 61 (106)
T PF09241_consen 5 TDFLIPVCHALKIPEDFWPQLFEATSITICKALIQPNIALLPPCLICAGGLLTTIET 61 (106)
T ss_dssp GGGHHHHHHHTT--GGGHHHHHHHHHHHHHHHTTSGGGGGS-HHHHHHHHHHHHHHT
T ss_pred hhhHHHhhhhccCcHHHhHHHHHHHHHHHHHHHcCCCccccCcceeecccceEEEec
Confidence 467777778888899999999988888888888888888899999999999887654
No 34
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=62.30 E-value=11 Score=33.59 Aligned_cols=39 Identities=18% Similarity=0.214 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHhcchhccCccHHHHHHHHHHHHHhcC
Q 025012 198 FLISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEI 236 (259)
Q Consensus 198 ~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la~~~~ 236 (259)
.+...|..+...-.....+..|.|..||++|+++|.+--
T Consensus 77 ~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvE 115 (305)
T TIGR00569 77 SVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVE 115 (305)
T ss_pred hHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhcc
Confidence 344556666666677777888999999999999996543
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=60.33 E-value=57 Score=25.30 Aligned_cols=64 Identities=8% Similarity=0.005 Sum_probs=47.1
Q ss_pred HHHHHHHHHhCCchhHHHHHHHHHHHHhcCC-ccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhh
Q 025012 79 AWILKVQAYYNFLPLTSYLSVNYMDRFLYSR-RLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQ 145 (259)
Q Consensus 79 dwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~-~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~ 145 (259)
.-+.++|..++++.+.....-..|+..+... ..-.+. ++--+-++|+|+-+|+.. ..++..++.
T Consensus 16 ~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dR--HLDQiilCaiY~i~Kv~~-~~~sF~~Ii 80 (135)
T PF01857_consen 16 VRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDR--HLDQIILCAIYGICKVSK-EELSFKDII 80 (135)
T ss_dssp HHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS---HHHHHHHHHHHHHHHTT--S--HHHHH
T ss_pred HHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcc--hHHHHHHHHHHHHHHhhc-CCCCHHHHH
Confidence 3467899999999998888888999988754 344443 899999999999999876 345555554
No 36
>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=58.78 E-value=51 Score=24.31 Aligned_cols=39 Identities=13% Similarity=0.066 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhcchhccCccHHHHHHHHHHHHHhcCCC
Q 025012 200 ISRATKIILSNIQEASFLEYRPSSIAAAAILCAANEIPN 238 (259)
Q Consensus 200 ~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la~~~~~~ 238 (259)
...|..+++.-+.........+..+|+||+++|.+....
T Consensus 52 ~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~ 90 (127)
T PF00134_consen 52 LHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEED 90 (127)
T ss_dssp HHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhcc
Confidence 344555555555555566778889999999999875543
No 37
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=56.91 E-value=80 Score=28.40 Aligned_cols=66 Identities=17% Similarity=0.181 Sum_probs=38.9
Q ss_pred HHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHhhcccCCchhhhhhhccCccccHHHHHHHHHHHHH
Q 025012 96 YLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKMEETVVPSLLDLQVEGAKYIFETKTIRRMELLVLS 167 (259)
Q Consensus 96 ~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~eE~~~p~~~~l~~~~~~~~~s~~~i~~~E~~IL~ 167 (259)
..|-+|+.--+-..-.... .-..||++|+++|+...|+--|....+-.. ...++.+|-..=..++.
T Consensus 162 Q~~wNfmNDslRT~v~vry---~pe~iACaciyLaAR~~eIpLp~~P~Wf~~---Fd~~k~eid~ic~~l~~ 227 (367)
T KOG0835|consen 162 QAAWNFMNDSLRTDVFVRY---SPESIACACIYLAARNLEIPLPFQPHWFKA---FDTTKREIDEICYRLIP 227 (367)
T ss_pred HHHHHhhhhccccceeeec---CHHHHHHHHHHHHHhhhcCCCCCCccHHHH---cCCcHHHHHHHHHHHHH
Confidence 3333444433333333344 689999999999999999654555554332 23566666655444433
No 38
>KOG1925 consensus Rac1 GTPase effector FHOS [Signal transduction mechanisms; Cytoskeleton]
Probab=56.55 E-value=13 Score=35.14 Aligned_cols=72 Identities=15% Similarity=0.187 Sum_probs=56.0
Q ss_pred chHHHHHHHHHHHHhhCCCCCccccccCCCCCHHHHHHHHHHHHHHHHHhCCchhHHHHHHHHHHHHhcCCc
Q 025012 39 SIEESIAGFIEDERNFVPGFDYLTRFQTHSLDASAREESVAWILKVQAYYNFLPLTSYLSVNYMDRFLYSRR 110 (259)
Q Consensus 39 ~~~e~l~~ll~~E~~~~~~~~y~~~~q~~~i~~~~R~~lvdwl~~v~~~~~l~~~t~~~Av~l~DRfl~~~~ 110 (259)
+-++...||.+.|.+...+.+-+..+..+++.+..|+++..|+-+++++..+-.-+.-..++=|+-||.-..
T Consensus 547 Df~qL~DNL~qlErrCKaSWe~L~~Iakhe~~p~l~~r~~~fl~~cA~RI~~LKivhrr~~NRfHSFLLy~G 618 (817)
T KOG1925|consen 547 DFEQLTDNLGQLERRCKASWESLRSIAKHELAPALRARLTHFLDQCARRIAMLKIVHRRVCNRFHSFLLYLG 618 (817)
T ss_pred cHHHHHHHHHHHHHHhhHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 334677899999999888888888888889999999999999999998765544444455566676665443
No 39
>cd03197 GST_C_mPGES2 GST_C family; microsomal Prostaglandin E synthase Type 2 (mPGES2) subfamily; mPGES2 is a membrane-anchored dimeric protein containing a CXXC motif which catalyzes the isomerization of PGH2 to PGE2. Unlike cytosolic PGE synthase (cPGES) and microsomal PGES Type 1 (mPGES1), mPGES2 does not require glutathione (GSH) for its activity, although its catalytic rate is increased two- to four-fold in the presence of DTT, GSH, or other thiol compounds. PGE2 is widely distributed in various tissues and is implicated in the sleep/wake cycle, relaxation/contraction of smooth muscle, excretion of sodium ions, maintenance of body temperature, and mediation of inflammation. mPGES2 contains an N-terminal hydrophobic domain which is membrane associated and a C-terminal soluble domain with a GST-like structure. The C-terminus contains two structural domains a N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain. The GST active site is located in a cleft between t
Probab=53.38 E-value=1e+02 Score=24.37 Aligned_cols=41 Identities=15% Similarity=-0.011 Sum_probs=30.9
Q ss_pred hHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHh
Q 025012 93 LTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKM 133 (259)
Q Consensus 93 ~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~ 133 (259)
.|+.-|+.=||-+.....+...++.-.+.+|+++||+.||.
T Consensus 29 rt~~ea~~~f~yi~~~~~f~~~er~~~~~~Ga~aM~~isk~ 69 (149)
T cd03197 29 RTWSEALASFDYITPSGYFGYWEKFFAKYVGAAAMYLISKY 69 (149)
T ss_pred CCHHHHHHhhhhHhcCCCccHHHHHHHHHhhHHHHHHHHHH
Confidence 36777888888888777764333236899999999999996
No 40
>KOG4112 consensus Signal peptidase subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.98 E-value=24 Score=25.54 Aligned_cols=33 Identities=9% Similarity=0.178 Sum_probs=26.0
Q ss_pred cHHHHHHHHHHHHHhcCCCCCCCCCCchhhHhhh
Q 025012 220 RPSSIAAAAILCAANEIPNLSLVNPEHAESWCDG 253 (259)
Q Consensus 220 ~PS~iAaAai~la~~~~~~~~~~~~~~~~~w~~~ 253 (259)
.=..+.+++.+.++..+|+||.... ++..|...
T Consensus 52 tvy~vg~~~v~t~li~LPpwP~y~r-n~LkW~~P 84 (101)
T KOG4112|consen 52 TVYIVGAGFVFTLLITLPPWPWYRR-NPLKWAQP 84 (101)
T ss_pred HHHHHHHHHHHHHHhcCCCchhhhc-CcccccCC
Confidence 3446778888899999999987777 88889753
No 41
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=36.44 E-value=1.5e+02 Score=26.23 Aligned_cols=17 Identities=6% Similarity=0.180 Sum_probs=9.4
Q ss_pred hHHHHHHHHHHHHHhhc
Q 025012 119 WQLLSVACLSLAAKMEE 135 (259)
Q Consensus 119 lqL~a~acL~IAsK~eE 135 (259)
.--++++.+|+++.+..
T Consensus 242 PiSIAAa~IYmisqls~ 258 (308)
T KOG1597|consen 242 PISIAAAAIYMISQLSD 258 (308)
T ss_pred chhHHHHHHHHHHHhcc
Confidence 44455566666665544
No 42
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=32.39 E-value=70 Score=27.31 Aligned_cols=39 Identities=18% Similarity=0.136 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHhcchhccCccHHHHHHHHHHHHHh
Q 025012 196 MGFLISRATKIILSNIQEASFLEYRPSSIAAAAILCAAN 234 (259)
Q Consensus 196 ~~~~~~~a~~~l~~~l~d~~~~~~~PS~iAaAai~la~~ 234 (259)
.+.+...|.-++...+.-..+-.+.|-.+|..|+|+|-+
T Consensus 58 RQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcK 96 (264)
T KOG0794|consen 58 RQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACK 96 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhh
Confidence 344444444444555555567789999999999999953
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=29.05 E-value=58 Score=23.13 Aligned_cols=29 Identities=14% Similarity=0.198 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHhCCchhHHHHHHHHHHH
Q 025012 75 EESVAWILKVQAYYNFLPLTSYLSVNYMDR 104 (259)
Q Consensus 75 ~~lvdwl~~v~~~~~l~~~t~~~Av~l~DR 104 (259)
..+||||++.. ...-..+++.++..++|.
T Consensus 36 sElVdWL~~~~-~~~sR~eAv~lgq~Ll~~ 64 (85)
T cd04441 36 SEFIDWLLQEG-EAESRREAVQLCRRLLEH 64 (85)
T ss_pred hHHHHHHHHcC-CCCCHHHHHHHHHHHHHC
Confidence 57999999975 233445566666666654
No 44
>PF07226 DUF1422: Protein of unknown function (DUF1422); InterPro: IPR009867 This family consists of several hypothetical bacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=27.20 E-value=1.5e+02 Score=22.30 Aligned_cols=39 Identities=18% Similarity=0.218 Sum_probs=29.6
Q ss_pred chhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHh
Q 025012 91 LPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKM 133 (259)
Q Consensus 91 ~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~ 133 (259)
+--++.+|++-+..-+.+++++.. ...++.+|+++..=.
T Consensus 40 PlIaLvLavy~LyQ~Yl~~~m~eg----~P~~a~acFflG~f~ 78 (117)
T PF07226_consen 40 PLIALVLAVYCLYQRYLNHPMPEG----TPKLALACFFLGLFG 78 (117)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCC----ChHHHHHHHHHHHHH
Confidence 455788888777666666677765 899999999997643
No 45
>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=24.91 E-value=66 Score=22.56 Aligned_cols=29 Identities=17% Similarity=0.308 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHhCCchhHHHHHHHHHHH
Q 025012 75 EESVAWILKVQAYYNFLPLTSYLSVNYMDR 104 (259)
Q Consensus 75 ~~lvdwl~~v~~~~~l~~~t~~~Av~l~DR 104 (259)
..+|+||++.... .-..+++.++-.++|.
T Consensus 32 selVdWL~~~~~~-~~r~eAv~lg~~Ll~~ 60 (81)
T cd04439 32 NEFVSWLLEIGEI-SKPEEGVNLGQALLEN 60 (81)
T ss_pred HHHHHHHHHcCCC-CCHHHHHHHHHHHHHC
Confidence 5699999976421 1134666666666654
No 46
>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=24.52 E-value=75 Score=22.22 Aligned_cols=30 Identities=17% Similarity=0.262 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHhCCchhHHHHHHHHHHH
Q 025012 75 EESVAWILKVQAYYNFLPLTSYLSVNYMDR 104 (259)
Q Consensus 75 ~~lvdwl~~v~~~~~l~~~t~~~Av~l~DR 104 (259)
..+|+||.+-.....-..+++.++-.++|.
T Consensus 33 ~e~VdWL~~~~~~~~~r~eAv~lgq~Ll~~ 62 (83)
T cd04449 33 SEAVSWLINNFEDVDTREEAVELGQELMNE 62 (83)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHHHHHC
Confidence 579999998544333344566666666654
No 47
>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=24.24 E-value=82 Score=22.19 Aligned_cols=29 Identities=10% Similarity=0.148 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHhCCchhHHHHHHHHHHH
Q 025012 75 EESVAWILKVQAYYNFLPLTSYLSVNYMDR 104 (259)
Q Consensus 75 ~~lvdwl~~v~~~~~l~~~t~~~Av~l~DR 104 (259)
..+|+||.+... ..-..+++.++-.++|.
T Consensus 34 selVdWL~~~~~-~~sR~eAv~lg~~Ll~~ 62 (83)
T cd04443 34 CDLVSWLIEVGL-AQDRGEAVLYGRRLLQG 62 (83)
T ss_pred HHHHHHHHHcCC-CCCHHHHHHHHHHHHHC
Confidence 579999998522 22234666666666654
No 48
>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=22.85 E-value=84 Score=22.18 Aligned_cols=30 Identities=10% Similarity=0.091 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHhCCchhHHHHHHHHHHH
Q 025012 75 EESVAWILKVQAYYNFLPLTSYLSVNYMDR 104 (259)
Q Consensus 75 ~~lvdwl~~v~~~~~l~~~t~~~Av~l~DR 104 (259)
..+|+||.+-.....-..+++..+-.+++.
T Consensus 33 sdlVdWL~~~~~~~~~R~eAv~~g~~Ll~~ 62 (84)
T cd04438 33 SDLVDWLLSHVEGLTDRREARKYASSLLKL 62 (84)
T ss_pred hHHHHHHHHhCCCCCCHHHHHHHHHHHHHC
Confidence 569999998665545556777777777765
No 49
>cd04442 DEP_1_DEP6 DEP (Dishevelled, Egl-10, and Pleckstrin) domain 1 found in DEP6-like proteins. DEP6 proteins contain two DEP and a PDZ domain. Their function is unknown.
Probab=22.25 E-value=84 Score=22.12 Aligned_cols=29 Identities=10% Similarity=0.251 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHhCCchhHHHHHHHHHHH
Q 025012 75 EESVAWILKVQAYYNFLPLTSYLSVNYMDR 104 (259)
Q Consensus 75 ~~lvdwl~~v~~~~~l~~~t~~~Av~l~DR 104 (259)
..+||||++.... .-..+++.++..++|.
T Consensus 32 selVdWL~~~~~~-~sR~eAv~lgq~Ll~~ 60 (82)
T cd04442 32 KELIDWLIEHKEA-SDRETAIKIMQKLLDH 60 (82)
T ss_pred HHHHHHHHHcCCC-CCHHHHHHHHHHHHHC
Confidence 4699999976441 2234455555555543
No 50
>PF14502 HTH_41: Helix-turn-helix domain
Probab=20.52 E-value=1.5e+02 Score=18.65 Aligned_cols=24 Identities=8% Similarity=0.127 Sum_probs=20.5
Q ss_pred HHHHHHHhCCchhHHHHHHHHHHH
Q 025012 81 ILKVQAYYNFLPLTSYLSVNYMDR 104 (259)
Q Consensus 81 l~~v~~~~~l~~~t~~~Av~l~DR 104 (259)
+-+.++.|+++.-|+..|+.++.-
T Consensus 9 I~e~~~~~~vs~GtiQ~Alk~Le~ 32 (48)
T PF14502_consen 9 ISEYSEKFGVSRGTIQNALKFLEE 32 (48)
T ss_pred HHHHHHHhCcchhHHHHHHHHHHH
Confidence 457788999999999999988764
No 51
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=20.28 E-value=2e+02 Score=19.05 Aligned_cols=30 Identities=13% Similarity=0.128 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHhCCchhHHHHHHHH
Q 025012 68 SLDASAREESVAWILKVQAYYNFLPLTSYLSVNY 101 (259)
Q Consensus 68 ~i~~~~R~~lvdwl~~v~~~~~l~~~t~~~Av~l 101 (259)
.+++.....+.+|+ ..++++++++..|+.+
T Consensus 12 ~ls~~e~~~i~~~~----~~~~~~~evI~~ai~~ 41 (73)
T TIGR01446 12 MLSPFEMEDLKYWL----DEFGNSPELIKEALKE 41 (73)
T ss_pred CCCHHHHHHHHHHH----HHhCCCHHHHHHHHHH
Confidence 47888889988887 5667889999888876
No 52
>PRK11056 hypothetical protein; Provisional
Probab=20.24 E-value=2.5e+02 Score=21.28 Aligned_cols=39 Identities=21% Similarity=0.335 Sum_probs=27.9
Q ss_pred chhHHHHHHHHHHHHhcCCccCCCCCCchHHHHHHHHHHHHHh
Q 025012 91 LPLTSYLSVNYMDRFLYSRRLPDNNGWPWQLLSVACLSLAAKM 133 (259)
Q Consensus 91 ~~~t~~~Av~l~DRfl~~~~i~~~~~~~lqL~a~acL~IAsK~ 133 (259)
+--++-+|++-+..=+.+++++.. ...++.+|+++..=.
T Consensus 40 PlIaLvLavycLyQ~Yl~~~m~eg----~P~~a~acFflG~f~ 78 (120)
T PRK11056 40 PLIALVLAVYCLHQRYLNRPMPEG----LPGLAAACFFLGVFL 78 (120)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCC----ChHHHHHHHHHHHHH
Confidence 445777888766555555566665 889999999997653
No 53
>cd04444 DEP_PLEK2 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in pleckstrin 2-like proteins. Pleckstrin 2 is found in a wide variety of cell types, which suggest a more general role in signaling than pleckstrin 1. Pleckstrin-like proteins contain a central DEP domain, flanked by 2 PH (pleckstrin homology) domains.
Probab=20.23 E-value=89 Score=23.36 Aligned_cols=29 Identities=14% Similarity=0.109 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHhCCchhHHHHHHHHHHH
Q 025012 75 EESVAWILKVQAYYNFLPLTSYLSVNYMDR 104 (259)
Q Consensus 75 ~~lvdwl~~v~~~~~l~~~t~~~Av~l~DR 104 (259)
..+||||++-...- -..+++.+|-.+||.
T Consensus 35 se~VDWLv~~~~~i-~R~EAv~l~q~Lmd~ 63 (109)
T cd04444 35 SALVDWLISNSFAA-SRLEAVTLASMLMEE 63 (109)
T ss_pred hHHHHHHHHCCCCC-CHHHHHHHHHHHHhC
Confidence 57899999986643 467788888888876
Done!