Query 023880
Match_columns 276
No_of_seqs 188 out of 1506
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 07:19:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023880.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023880hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0835 Cyclin L [General func 100.0 2.2E-51 4.7E-56 361.5 18.9 238 3-241 26-267 (367)
2 KOG0834 CDK9 kinase-activating 100.0 4.2E-47 9E-52 342.4 19.6 204 1-211 40-251 (323)
3 KOG0794 CDK8 kinase-activating 100.0 1.4E-38 3.1E-43 268.5 10.5 198 3-210 44-243 (264)
4 TIGR00569 ccl1 cyclin ccl1. Un 100.0 7.3E-37 1.6E-41 276.2 18.5 181 2-202 58-249 (305)
5 COG5333 CCL1 Cdk activating ki 100.0 3E-33 6.4E-38 246.9 13.6 178 1-194 46-225 (297)
6 PRK00423 tfb transcription ini 99.9 1.4E-23 3.1E-28 191.3 19.2 181 2-205 124-304 (310)
7 KOG0656 G1/S-specific cyclin D 99.9 1.2E-21 2.6E-26 177.2 15.0 153 2-173 80-240 (335)
8 KOG2496 Cdk activating kinase 99.9 2.6E-21 5.6E-26 170.1 9.8 155 3-175 59-224 (325)
9 COG5024 Cyclin [Cell division 99.8 1.1E-20 2.4E-25 176.7 12.4 211 3-238 216-432 (440)
10 KOG0653 Cyclin B and related k 99.8 5E-20 1.1E-24 173.0 14.0 177 3-203 161-343 (391)
11 KOG0655 G1/S-specific cyclin E 99.7 2.4E-17 5.1E-22 146.4 10.9 175 3-206 148-336 (408)
12 COG1405 SUA7 Transcription ini 99.7 2.2E-16 4.8E-21 141.5 17.2 180 2-204 99-278 (285)
13 KOG1597 Transcription initiati 99.7 4E-16 8.7E-21 137.1 17.0 179 2-203 106-286 (308)
14 PF00134 Cyclin_N: Cyclin, N-t 99.7 3E-16 6.6E-21 124.3 9.2 94 2-115 33-127 (127)
15 KOG0654 G2/Mitotic-specific cy 99.6 6.8E-15 1.5E-19 134.6 11.1 197 3-221 140-339 (359)
16 cd00043 CYCLIN Cyclin box fold 99.5 2E-13 4.4E-18 99.9 8.4 85 2-107 4-88 (88)
17 smart00385 CYCLIN domain prese 99.4 1.5E-12 3.3E-17 94.2 7.1 83 5-108 1-83 (83)
18 PF02984 Cyclin_C: Cyclin, C-t 99.4 5.1E-13 1.1E-17 104.0 4.1 115 117-231 1-116 (118)
19 smart00385 CYCLIN domain prese 98.9 9.1E-09 2E-13 74.1 8.3 81 121-202 1-82 (83)
20 PF00382 TFIIB: Transcription 98.8 1.8E-08 3.8E-13 72.1 8.1 65 7-71 1-65 (71)
21 cd00043 CYCLIN Cyclin box fold 98.7 7.7E-08 1.7E-12 69.9 8.4 85 116-201 2-87 (88)
22 KOG1598 Transcription initiati 98.5 2.5E-07 5.4E-12 88.0 7.5 150 5-177 72-227 (521)
23 KOG4164 Cyclin ik3-1/CABLES [C 98.3 1.1E-06 2.3E-11 80.6 6.6 95 5-117 387-482 (497)
24 PF00382 TFIIB: Transcription 98.2 6.5E-06 1.4E-10 58.7 6.8 70 123-193 1-70 (71)
25 PF08613 Cyclin: Cyclin; Inte 98.2 2E-05 4.4E-10 64.5 10.4 90 3-114 54-149 (149)
26 PRK00423 tfb transcription ini 98.1 1.5E-05 3.3E-10 72.9 9.7 68 4-71 220-287 (310)
27 COG1405 SUA7 Transcription ini 97.1 0.0023 4.9E-08 57.9 8.7 70 2-71 193-262 (285)
28 KOG1597 Transcription initiati 96.8 0.0056 1.2E-07 54.8 7.6 70 3-72 203-272 (308)
29 PF00134 Cyclin_N: Cyclin, N-t 95.9 0.037 8.1E-07 43.1 7.4 85 121-205 36-122 (127)
30 PF01857 RB_B: Retinoblastoma- 95.1 0.1 2.3E-06 41.9 7.2 69 4-72 15-85 (135)
31 TIGR00569 ccl1 cyclin ccl1. Un 94.0 0.15 3.2E-06 46.7 6.3 56 122-177 62-119 (305)
32 KOG1674 Cyclin [General functi 92.6 0.5 1.1E-05 41.1 7.2 92 4-117 79-181 (218)
33 PF02984 Cyclin_C: Cyclin, C-t 91.6 0.82 1.8E-05 34.7 6.7 56 4-59 4-59 (118)
34 KOG0834 CDK9 kinase-activating 89.1 0.66 1.4E-05 42.7 4.8 58 120-177 43-100 (323)
35 PF08613 Cyclin: Cyclin; Inte 88.7 3.2 6.8E-05 33.7 8.2 88 119-206 54-146 (149)
36 KOG1598 Transcription initiati 88.3 0.71 1.5E-05 44.8 4.7 68 6-73 169-239 (521)
37 KOG0835 Cyclin L [General func 88.1 0.89 1.9E-05 41.6 4.9 55 6-60 144-200 (367)
38 COG5333 CCL1 Cdk activating ki 87.5 1.3 2.8E-05 40.2 5.6 86 120-205 49-141 (297)
39 KOG0794 CDK8 kinase-activating 87.0 1.2 2.7E-05 38.8 4.9 86 121-206 46-145 (264)
40 PF01857 RB_B: Retinoblastoma- 86.7 2.3 5E-05 34.2 6.1 55 121-175 16-72 (135)
41 KOG1675 Predicted cyclin [Gene 80.9 3.4 7.4E-05 37.6 5.2 74 24-118 214-290 (343)
42 KOG0656 G1/S-specific cyclin D 80.5 11 0.00025 34.8 8.7 83 96-178 49-143 (335)
43 KOG2496 Cdk activating kinase 69.9 12 0.00027 34.0 5.8 51 123-173 63-115 (325)
44 KOG1010 Rb (Retinoblastoma tum 53.7 29 0.00063 36.0 5.8 68 5-72 682-751 (920)
45 KOG4557 Origin recognition com 44.7 2.2E+02 0.0047 24.9 14.6 176 6-211 2-187 (262)
46 KOG4557 Origin recognition com 41.2 61 0.0013 28.2 5.0 50 7-57 96-150 (262)
47 KOG0653 Cyclin B and related k 35.4 1.9E+02 0.004 27.4 7.9 84 123-206 165-251 (391)
48 KOG1567 Ribonucleotide reducta 34.3 1.7E+02 0.0036 26.7 6.8 79 47-128 227-310 (344)
49 PF10440 WIYLD: Ubiquitin-bind 29.5 61 0.0013 22.6 2.6 24 185-208 19-42 (65)
50 PHA02690 hypothetical protein; 29.4 1.1E+02 0.0024 22.2 4.0 33 120-152 21-53 (90)
51 PF11357 Spy1: Cell cycle regu 24.2 3.7E+02 0.0081 21.4 6.9 85 13-117 24-110 (131)
52 COG5024 Cyclin [Cell division 23.5 1.2E+02 0.0026 29.4 4.3 75 132-206 229-305 (440)
53 TIGR00873 gnd 6-phosphoglucona 22.2 1.2E+02 0.0025 29.6 4.1 31 3-33 400-430 (467)
54 PF00376 MerR: MerR family reg 21.8 1.3E+02 0.0027 18.4 2.8 15 7-21 2-16 (38)
No 1
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=100.00 E-value=2.2e-51 Score=361.52 Aligned_cols=238 Identities=46% Similarity=0.734 Sum_probs=221.8
Q ss_pred hhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHHhhhhccCCCc
Q 023880 3 YAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGLPI 82 (276)
Q Consensus 3 ~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~i~~~~~~~p~ 82 (276)
+|+||++.|.+|+||+.+++|++++|+|||..+++..+|...+++||++||+|+||.|++++||++|++++.++.+..+.
T Consensus 26 G~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~~~~~~ 105 (367)
T KOG0835|consen 26 GCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRRESEAA 105 (367)
T ss_pred hHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHHhccCc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999988887777
Q ss_pred cccccchHHHHHHHHHHHHHHHHHHHHhCccccccChHHHHHHHHHHcCCCH--HHHHHHHHHHHhhhcccccccCChHH
Q 023880 83 EHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPL--ELRQEAWNLANDSLRTTLCVRFKSEV 160 (276)
Q Consensus 83 ~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~~P~~~L~~~l~~l~~~~--~l~~~A~~~l~ds~~t~l~l~~~P~~ 160 (276)
++. .....|..++..++.+|+.||++|||+++|.|||+++..|++.|++++ +|.|.+|+|+||+++|++|++|+|+.
T Consensus 106 ~~~-~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~ 184 (367)
T KOG0835|consen 106 EHL-ILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPES 184 (367)
T ss_pred chh-hhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHH
Confidence 665 556778889999999999999999999999999999999999999864 57999999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHHhhcC--CCCccccccCCCCcccccCCCCCCCCCCCCc
Q 023880 161 VACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAHLYSL--PKAKYIPVCKDGTSFTFSSKTVDSQPQSTPK 238 (276)
Q Consensus 161 IAaAaI~lA~~~~~~~lp~~~~W~~~~~~~~~~v~~i~~~ll~ly~~--~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 (276)
|||||||+|++.++++||..++||..|++++++|+++|..++.+|.. ++..++..+.+...+.++..+...+.+..++
T Consensus 185 iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~~l~~lY~~~~p~~~li~~~vd~~k~~~~da~~k~~~~~ds~ 264 (367)
T KOG0835|consen 185 IACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICYRLIPLYKRAKPDETLIEAFVDRLKRKFSDASGKAKGANDSA 264 (367)
T ss_pred HHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHHHHHHHHHhcccCHHHHHHHHHHhhHHHHhccCCccchhhHH
Confidence 99999999999999999999999999999999999999999999998 7778888888888888888777777776655
Q ss_pred cCC
Q 023880 239 EVL 241 (276)
Q Consensus 239 ~~~ 241 (276)
+..
T Consensus 265 ~~l 267 (367)
T KOG0835|consen 265 SLL 267 (367)
T ss_pred Hhh
Confidence 544
No 2
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.2e-47 Score=342.36 Aligned_cols=204 Identities=36% Similarity=0.607 Sum_probs=189.3
Q ss_pred CchhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHHhhhhccCC
Q 023880 1 MQYAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGL 80 (276)
Q Consensus 1 ~~~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~i~~~~~~~ 80 (276)
+++|+||+++|.+||+++.+++||++||||||+.+++++++++.+|++|||||+|+||+|++++||+.++++..++.+
T Consensus 40 ~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~-- 117 (323)
T KOG0834|consen 40 QEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKD-- 117 (323)
T ss_pred HHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCccc--
Confidence 368999999999999999999999999999999999999999999999999999999999999999999999887643
Q ss_pred CccccccchHHHHHHHHHHHHHHHHHHHHhCccccccChHHHHHHHHHHcCCCH----HHHHHHHHHHHhhhcccccccC
Q 023880 81 PIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPL----ELRQEAWNLANDSLRTTLCVRF 156 (276)
Q Consensus 81 p~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~~P~~~L~~~l~~l~~~~----~l~~~A~~~l~ds~~t~l~l~~ 156 (276)
....+.|++.+++|+..|+.||++|+||++|.|||.||.+|++.++.+. .+.+.||.++||++++.+||+|
T Consensus 118 -----~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y 192 (323)
T KOG0834|consen 118 -----LELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQY 192 (323)
T ss_pred -----ccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEee
Confidence 2346789999999999999999999999999999999999999998765 4999999999999999999999
Q ss_pred ChHHHHHHHHHHHHHHcCCCCCC--Ccccccccc--CCHHHHHHHHHHHHHhhcCCCCc
Q 023880 157 KSEVVACGVVYAAARRFQIPLPE--NPPWWKAFD--AEKSGIDEVCRVLAHLYSLPKAK 211 (276)
Q Consensus 157 ~P~~IAaAaI~lA~~~~~~~lp~--~~~W~~~~~--~~~~~v~~i~~~ll~ly~~~k~~ 211 (276)
+|.+||+|||++|++..|.++|. ...||..++ ++.+++++++.+++++|......
T Consensus 193 ~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~l~~y~~~~~~ 251 (323)
T KOG0834|consen 193 SPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHEFLDLYEQTPQR 251 (323)
T ss_pred cCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHHHHHHHhhcccc
Confidence 99999999999999999998774 337999999 99999999999999999865433
No 3
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=100.00 E-value=1.4e-38 Score=268.47 Aligned_cols=198 Identities=24% Similarity=0.427 Sum_probs=175.9
Q ss_pred hhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCC-cCHHHHHHHHHHhhhhccCCC
Q 023880 3 YAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESP-RKARQVIIVFHRMECRREGLP 81 (276)
Q Consensus 3 ~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~-~~l~dii~v~~~i~~~~~~~p 81 (276)
++++|+.+|.+|+|.|.|++||++||+|||.++|++++++.+++.||||||||+||+| ..+|-+++....+.++-.
T Consensus 44 ~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~--- 120 (264)
T KOG0794|consen 44 MANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFS--- 120 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcc---
Confidence 5789999999999999999999999999999999999999999999999999999998 667777766555433211
Q ss_pred ccccccchHHHHHHHHHHHHHHHHHHHHhCccccccChHHHHHHHHHHcCC-CHHHHHHHHHHHHhhhcccccccCChHH
Q 023880 82 IEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLET-PLELRQEAWNLANDSLRTTLCVRFKSEV 160 (276)
Q Consensus 82 ~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~~P~~~L~~~l~~l~~-~~~l~~~A~~~l~ds~~t~l~l~~~P~~ 160 (276)
.-++.+......|+++|+.+|..|++-+-|.||++-|..+++..|. +.++.+.+|.++||++++++||.|+|.+
T Consensus 121 -----~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~ 195 (264)
T KOG0794|consen 121 -----YWPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQ 195 (264)
T ss_pred -----cchhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHH
Confidence 1122333346789999999999999999999999999999999998 6779999999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHHhhcCCCC
Q 023880 161 VACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAHLYSLPKA 210 (276)
Q Consensus 161 IAaAaI~lA~~~~~~~lp~~~~W~~~~~~~~~~v~~i~~~ll~ly~~~k~ 210 (276)
||.||+++|+...+.+.|. .|...+.+|++.|.+|+++|+++|..+|.
T Consensus 196 IalAcl~Ia~~~~~k~~~~--~w~~el~vD~ekV~~~v~~I~~lYe~wk~ 243 (264)
T KOG0794|consen 196 IALACLYIACVIDEKDIPK--AWFAELSVDMEKVKDIVQEILKLYELWKI 243 (264)
T ss_pred HHHHHHHHHHhhcCCChHH--HHHHHHhccHHHHHHHHHHHHHHHHHHhh
Confidence 9999999999999988763 69999999999999999999999998753
No 4
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=100.00 E-value=7.3e-37 Score=276.17 Aligned_cols=181 Identities=19% Similarity=0.311 Sum_probs=157.0
Q ss_pred chhHHHHHHHHHhC--CCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHHhhhhccC
Q 023880 2 QYAGSIVSFICVVY--RPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREG 79 (276)
Q Consensus 2 ~~~~~I~~v~~~L~--L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~i~~~~~~ 79 (276)
.||.+|.++|.+|+ ||+.|++||++||||||.++|+.++++++|++||||||||+||.++++++++.....
T Consensus 58 ~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~------- 130 (305)
T TIGR00569 58 YYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKE------- 130 (305)
T ss_pred HHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccC-------
Confidence 68999999999999 999999999999999999999999999999999999999999999999998864321
Q ss_pred CCccccccchHHHHHHHHHHHHHHHHHHHHhCccccccChHHHHHHHHHHcC-------CCHHHHHHHHHHHHhhhcccc
Q 023880 80 LPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLE-------TPLELRQEAWNLANDSLRTTL 152 (276)
Q Consensus 80 ~p~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~~P~~~L~~~l~~l~-------~~~~l~~~A~~~l~ds~~t~l 152 (276)
.+...+++|+.+|+.||++|||++.+.|||++|..|+..++ ..+.+.+.||.++||+++|++
T Consensus 131 -----------~~~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~ 199 (305)
T TIGR00569 131 -----------TPLKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDA 199 (305)
T ss_pred -----------CchhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCc
Confidence 11246799999999999999999999999999999987553 235789999999999999999
Q ss_pred cccCChHHHHHHHHHHHHHHcCCCCCCCccccccccC--CHHHHHHHHHHHH
Q 023880 153 CVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDA--EKSGIDEVCRVLA 202 (276)
Q Consensus 153 ~l~~~P~~IAaAaI~lA~~~~~~~lp~~~~W~~~~~~--~~~~v~~i~~~ll 202 (276)
|+.|+|++||+||||+|.+.++.++|+.. | +.+++ +.+.+..++..|.
T Consensus 200 ~L~y~Ps~IAlAAI~lA~~~~~~~l~~~~-~-e~~~~~~~~~~~~~l~~~~~ 249 (305)
T TIGR00569 200 YLLYTPSQIALAAILHTASRAGLNMESYL-T-EQLSVPGNREELPQLIDIMR 249 (305)
T ss_pred eecCCHHHHHHHHHHHHHHHhCCCCcccc-h-hhhcccccHHHHHHHHHHHH
Confidence 99999999999999999999999998743 4 77876 5554444443333
No 5
>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=100.00 E-value=3e-33 Score=246.94 Aligned_cols=178 Identities=28% Similarity=0.459 Sum_probs=152.5
Q ss_pred CchhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHHhhhhccCC
Q 023880 1 MQYAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGL 80 (276)
Q Consensus 1 ~~~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~i~~~~~~~ 80 (276)
|+|+.||+.+|.+|+||+.+++||+.+|+||+.+.++++++++.|+.||||||||+||+++.++-.....+
T Consensus 46 i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~--------- 116 (297)
T COG5333 46 IYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEAR--------- 116 (297)
T ss_pred HHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhh---------
Confidence 67999999999999999999999999999999999999999999999999999999999666553332222
Q ss_pred CccccccchHHHHHHHHHHHHHHHHHHHHhCccccccChHHHHHHHHHHcCCC--HHHHHHHHHHHHhhhcccccccCCh
Q 023880 81 PIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETP--LELRQEAWNLANDSLRTTLCVRFKS 158 (276)
Q Consensus 81 p~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~~P~~~L~~~l~~l~~~--~~l~~~A~~~l~ds~~t~l~l~~~P 158 (276)
|+.++.++.+|++|+.+|+.+|+.|+||+.|+|||.++..|++.+... .++.+.||.++||++++.+|+.|+|
T Consensus 117 -----~~~se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypp 191 (297)
T COG5333 117 -----DLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPP 191 (297)
T ss_pred -----ccccccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecCh
Confidence 234456677899999999999999999999999999999999988754 3699999999999999999999999
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCccccccccCCHHHH
Q 023880 159 EVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGI 194 (276)
Q Consensus 159 ~~IAaAaI~lA~~~~~~~lp~~~~W~~~~~~~~~~v 194 (276)
..||+||+++|+...|.+.+. .|......+.+.+
T Consensus 192 hiIA~a~l~ia~~~~~~~~~~--~~~~~s~~~~e~v 225 (297)
T COG5333 192 HIIALAALLIACEVLGMPIIK--LLDFVSYETKEEV 225 (297)
T ss_pred HHHHHHHHHHHHHhcCCccch--hhccccccchhHH
Confidence 999999999999998876553 2444444444433
No 6
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.92 E-value=1.4e-23 Score=191.34 Aligned_cols=181 Identities=14% Similarity=0.162 Sum_probs=165.0
Q ss_pred chhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHHhhhhccCCC
Q 023880 2 QYAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGLP 81 (276)
Q Consensus 2 ~~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~i~~~~~~~p 81 (276)
++...|.++|..|+||..+..+|..+|++++..+.+++.+...+++||||+|||.|+.|++++||..+++.
T Consensus 124 ~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~v--------- 194 (310)
T PRK00423 124 FALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRV--------- 194 (310)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCC---------
Confidence 45678999999999999999999999999999999999999999999999999999999999999887641
Q ss_pred ccccccchHHHHHHHHHHHHHHHHHHHHhCccccccChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCChHHH
Q 023880 82 IEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVV 161 (276)
Q Consensus 82 ~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~~P~~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~P~~I 161 (276)
.+.+|.+.++.|++.||+++.+.+|++|+.+|+..|+++.++.+.|+.+++++....++-+.+|..|
T Consensus 195 -------------~~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sI 261 (310)
T PRK00423 195 -------------SRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGL 261 (310)
T ss_pred -------------CHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHH
Confidence 2567888999999999999999999999999999999999999999999999998899999999999
Q ss_pred HHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHHhh
Q 023880 162 ACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAHLY 205 (276)
Q Consensus 162 AaAaI~lA~~~~~~~lp~~~~W~~~~~~~~~~v~~i~~~ll~ly 205 (276)
|+||||+|++.+|.+... +.-....+++...|...+++|....
T Consensus 262 AAAaIYlA~~~~g~~~t~-keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 262 AAAAIYIASLLLGERRTQ-REVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred HHHHHHHHHHHhCCCCCH-HHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 999999999999887542 3466778899999999999888754
No 7
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=99.87 E-value=1.2e-21 Score=177.20 Aligned_cols=153 Identities=14% Similarity=0.190 Sum_probs=130.4
Q ss_pred chhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccch---HHHHHHHHHHHhhhcccCC-cCHHHHHHHHHHhhhhc
Q 023880 2 QYAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFD---VKIVAASSVWLASKLEESP-RKARQVIIVFHRMECRR 77 (276)
Q Consensus 2 ~~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~---~~~va~acLfLA~K~EE~~-~~l~dii~v~~~i~~~~ 77 (276)
|+++||.++|..++....|...|++|++||...+.+.+.+ .+++|+|||+||+|+||.. +-+-|+....
T Consensus 80 ~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~------- 152 (335)
T KOG0656|consen 80 QALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEY------- 152 (335)
T ss_pred HHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcc-------
Confidence 6899999999999999999999999999999999999988 8999999999999999985 4444443221
Q ss_pred cCCCccccccchHHHHHHHHHHHHHHHHHHHHhCccccccChHHHHHHHHHHcCCC----HHHHHHHHHHHHhhhccccc
Q 023880 78 EGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETP----LELRQEAWNLANDSLRTTLC 153 (276)
Q Consensus 78 ~~~p~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~~P~~~L~~~l~~l~~~----~~l~~~A~~~l~ds~~t~l~ 153 (276)
-.|....+.|.+||..||.+|+|+++..+|+.|+..|+.+++.. ..+...+..++-..-...-+
T Consensus 153 ------------~~~~feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~F 220 (335)
T KOG0656|consen 153 ------------TDNVFEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKF 220 (335)
T ss_pred ------------ccccccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhh
Confidence 12333578999999999999999999999999999999999873 45677777777777777789
Q ss_pred ccCChHHHHHHHHHHHHHHc
Q 023880 154 VRFKSEVVACGVVYAAARRF 173 (276)
Q Consensus 154 l~~~P~~IAaAaI~lA~~~~ 173 (276)
+.|+|++||+|++..+....
T Consensus 221 l~y~pSviAaa~~~~v~~~~ 240 (335)
T KOG0656|consen 221 LEYPPSVIAAAAILSVSASV 240 (335)
T ss_pred hcCChHHHHHHHHHHHHHhh
Confidence 99999999999887666643
No 8
>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=99.85 E-value=2.6e-21 Score=170.05 Aligned_cols=155 Identities=22% Similarity=0.288 Sum_probs=127.8
Q ss_pred hhHHHHHHHHHh--CCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHHhhhhccCC
Q 023880 3 YAGSIVSFICVV--YRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGL 80 (276)
Q Consensus 3 ~~~~I~~v~~~L--~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~i~~~~~~~ 80 (276)
+-......+.++ +||..|..||+.+|+|||..+|+.++++..|++||+|||||+||....+.++++-+..
T Consensus 59 ~E~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~-------- 130 (325)
T KOG2496|consen 59 EELSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMNG-------- 130 (325)
T ss_pred HHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhccC--------
Confidence 344555666655 4899999999999999999999999999999999999999999999999999875430
Q ss_pred CccccccchHHHHHHHHHHHHHHHHHHHHhCccccccChHHHHHHHHHHcCC------C-HHHHHHH--HHHHHhhhccc
Q 023880 81 PIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLET------P-LELRQEA--WNLANDSLRTT 151 (276)
Q Consensus 81 p~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~~P~~~L~~~l~~l~~------~-~~l~~~A--~~~l~ds~~t~ 151 (276)
.-|...+.|+..|..+|+.|+|++.+.+|++-+..|+..+.. + .-+++.. ..+++..+.|+
T Consensus 131 ----------~~~k~~e~vLk~E~~llqsL~f~L~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltD 200 (325)
T KOG2496|consen 131 ----------RKWKTHEIVLKYEFLLLQSLKFSLTVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTD 200 (325)
T ss_pred ----------cccccHHHHHhchHHHHHhhhhhheecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhc
Confidence 112468899999999999999999999999999998866542 2 2233333 48999999999
Q ss_pred ccccCChHHHHHHHHHHHHHHcCC
Q 023880 152 LCVRFKSEVVACGVVYAAARRFQI 175 (276)
Q Consensus 152 l~l~~~P~~IAaAaI~lA~~~~~~ 175 (276)
.++.|+|++||+|||..|.-..|.
T Consensus 201 a~lLytPsQIALaAil~a~~~~~~ 224 (325)
T KOG2496|consen 201 AYLLYTPSQIALAAILHAAGRTGE 224 (325)
T ss_pred cceecChHHHHHHHHHHHhccccc
Confidence 999999999999999666555554
No 9
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=99.84 E-value=1.1e-20 Score=176.72 Aligned_cols=211 Identities=13% Similarity=0.120 Sum_probs=183.0
Q ss_pred hhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccC-CcCHHHHHHHHHHhhhhccCCC
Q 023880 3 YAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEES-PRKARQVIIVFHRMECRREGLP 81 (276)
Q Consensus 3 ~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~-~~~l~dii~v~~~i~~~~~~~p 81 (276)
..+||.+++..|+|.+.|+..|+.+++||+..+...-...++||++|||||||+||. .+.+++++.++...
T Consensus 216 Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~-------- 287 (440)
T COG5024 216 LVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGA-------- 287 (440)
T ss_pred HHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHccc--------
Confidence 368999999999999999999999999999999988889999999999999999997 55678888776632
Q ss_pred ccccccchHHHHHHHHHHHHHHHHHHHHhCccccccChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCChHHH
Q 023880 82 IEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVV 161 (276)
Q Consensus 82 ~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~~P~~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~P~~I 161 (276)
..+++|+.+|+.+|.+|+|++.++.|+.||+++-+..+.+..-+..+.+++.-+....-++.++|+.+
T Consensus 288 ------------~t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka~dyd~~srt~~k~~~e~s~~~~~f~~~~~S~~ 355 (440)
T COG5024 288 ------------FTRDDIIRAERYMLEVLDFNISWPSPMSFLRRISKASDYDIFSRTPAKFSSEISPVDYKFIQISPSWC 355 (440)
T ss_pred ------------ccHHHHHHHHHHHhhhcccccCCCChHHHHHHHHhhcccchhhhhhHhhhCCchHhhhhhccCCchHH
Confidence 25899999999999999999999999999999999988888888899999999888888889999999
Q ss_pred HHHHHHHHHHHcCCCCCCCccccccc----c-CCHHHHHHHHHHHHHhhcCCCCccccccCCCCcccccCCCCCCCCCCC
Q 023880 162 ACGVVYAAARRFQIPLPENPPWWKAF----D-AEKSGIDEVCRVLAHLYSLPKAKYIPVCKDGTSFTFSSKTVDSQPQST 236 (276)
Q Consensus 162 AaAaI~lA~~~~~~~lp~~~~W~~~~----~-~~~~~v~~i~~~ll~ly~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ 236 (276)
|+||.|+|.+.++.. +|-..+ | ++..++..++..+++....+...+-...++++..++...+.+++++..
T Consensus 356 ~aaa~~~s~~~~~~~-----~w~~~l~~ySg~y~~~~l~~~~~~~~~~l~~~~~~~~~i~~Ky~~~~~~~~s~~~~ew~~ 430 (440)
T COG5024 356 AAAAMYLSRKILSQN-----QWDRTLIHYSGNYTNPDLKPLNESNKENLQNPSVHHDAIFPKYPSPTFGKASSPTGEWIR 430 (440)
T ss_pred HHHHHHHHHhhhccC-----CCCccccccCCCCCchhHHHHHHHHHHHhcccchhhhhhhhccccccccccchHHHHHHh
Confidence 999999999999863 365555 3 566789999999999999999998888888886666666666665554
Q ss_pred Cc
Q 023880 237 PK 238 (276)
Q Consensus 237 ~~ 238 (276)
.+
T Consensus 431 ~~ 432 (440)
T COG5024 431 SN 432 (440)
T ss_pred hc
Confidence 44
No 10
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=99.83 E-value=5e-20 Score=172.98 Aligned_cols=177 Identities=19% Similarity=0.190 Sum_probs=151.5
Q ss_pred hhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHH-HhhhcccCC-cCHHHHHHHHHHhhhhccCC
Q 023880 3 YAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVW-LASKLEESP-RKARQVIIVFHRMECRREGL 80 (276)
Q Consensus 3 ~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLf-LA~K~EE~~-~~l~dii~v~~~i~~~~~~~ 80 (276)
-++|+.+++.+++|..+|+..|+.+++||+.+..+...+.++|+++||| ||||+||.. +.+.|++.+++.
T Consensus 161 Lvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~-------- 232 (391)
T KOG0653|consen 161 LVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDG-------- 232 (391)
T ss_pred HHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCC--------
Confidence 4789999999999999999999999999999988999999999999977 999999964 447777765442
Q ss_pred CccccccchHHHHHHHHHHHHHHHHHHHHhCccccccChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCChHH
Q 023880 81 PIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEV 160 (276)
Q Consensus 81 p~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~~P~~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~P~~ 160 (276)
. ..+++|+.||+.||.+|+|++.+++|+.||.++.+..+.+.+....+.++++.++...-.+.++|+.
T Consensus 233 ----------~--~s~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d~~~~~~~k~~~El~l~d~~~~~~~~s~ 300 (391)
T KOG0653|consen 233 ----------A--YSREEILRMEKYILNVLEFDLSVPTPLSFLRRFLKAADYDIKTRTLVKYLLELSLCDYSMLSIPPSS 300 (391)
T ss_pred ----------c--cchHHHHHHHHHHHhccCeeecCCchHHHHHHHHHhhhcchhHHHHHHHHHHHHHhhhHHhccCcHH
Confidence 2 2589999999999999999999999999999999999988889999999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCCCCCCccccccc----cCCHHHHHHHHHHHHH
Q 023880 161 VACGVVYAAARRFQIPLPENPPWWKAF----DAEKSGIDEVCRVLAH 203 (276)
Q Consensus 161 IAaAaI~lA~~~~~~~lp~~~~W~~~~----~~~~~~v~~i~~~ll~ 203 (276)
+|+|+.+++.++.+.+- .|...+ |.....+.++.+.+..
T Consensus 301 ~aaa~~~~~~~~~~~~~----~w~~~~~~~sg~~~~~~~~~~~~~~~ 343 (391)
T KOG0653|consen 301 SAAASFTLALRMLSKGD----VWSPTLEHYSGYSESYLFECARSLSA 343 (391)
T ss_pred HHHHHHHHHHHHhccCC----ccCCCCeeccCCCcHHHHHHHHHHHH
Confidence 99999999999987643 355544 4444455555555555
No 11
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=99.73 E-value=2.4e-17 Score=146.45 Aligned_cols=175 Identities=16% Similarity=0.129 Sum_probs=139.6
Q ss_pred hhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhc-cccccchHHHHHHHHHHHhhhcccC-CcCHHHHHHHHHHhhhhccCC
Q 023880 3 YAGSIVSFICVVYRPQAVMATGQVLFHRFYCK-RSFARFDVKIVAASSVWLASKLEES-PRKARQVIIVFHRMECRREGL 80 (276)
Q Consensus 3 ~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~-~s~~~~~~~~va~acLfLA~K~EE~-~~~l~dii~v~~~i~~~~~~~ 80 (276)
-.+|+.++|+-++|-.+|.+.|+-||+||+.. +...+...++++.||||+|+|+||. |+++.++..|.+..
T Consensus 148 LlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgA------- 220 (408)
T KOG0655|consen 148 LLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGA------- 220 (408)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCc-------
Confidence 46899999999999999999999999999875 4566788999999999999999996 89999998876532
Q ss_pred CccccccchHHHHHHHHHHHHHHHHHHHHhCccccccChHHHHHHHHHHcCCC-----------H-HHHHHHHHHHHhhh
Q 023880 81 PIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETP-----------L-ELRQEAWNLANDSL 148 (276)
Q Consensus 81 p~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~~P~~~L~~~l~~l~~~-----------~-~l~~~A~~~l~ds~ 148 (276)
-.-++|+.||..||+.|||++...+-..+|.-|++..++. + +..|. -.+++.+.
T Consensus 221 -------------cs~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqi-aqlLDlc~ 286 (408)
T KOG0655|consen 221 -------------CSEDDILTMELIILKALKWELSPITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQI-AQLLDLCI 286 (408)
T ss_pred -------------cchHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcCCCCceeccccchHHHHHH-HHHHHHHH
Confidence 1478999999999999999999999999999999887542 2 33344 34555555
Q ss_pred cccccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHHhhc
Q 023880 149 RTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAHLYS 206 (276)
Q Consensus 149 ~t~l~l~~~P~~IAaAaI~lA~~~~~~~lp~~~~W~~~~~~~~~~v~~i~~~ll~ly~ 206 (276)
..--++.|+..+|||||++.-....- --+.-|....+|++|++-|.-+..
T Consensus 287 ldids~~fsYrilaAAal~h~~s~e~--------v~kaSG~~w~~ie~cv~wm~Pf~r 336 (408)
T KOG0655|consen 287 LDIDSLEFSYRILAAAALCHFTSIEV--------VKKASGLEWDSIEECVDWMVPFVR 336 (408)
T ss_pred hccccccchHHHHHHHHHHHHhHHHH--------HHHcccccHHHHHHHHHHHHHHHH
Confidence 56678899999999999986544211 113455667788888887766554
No 12
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.72 E-value=2.2e-16 Score=141.45 Aligned_cols=180 Identities=17% Similarity=0.225 Sum_probs=160.7
Q ss_pred chhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHHhhhhccCCC
Q 023880 2 QYAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGLP 81 (276)
Q Consensus 2 ~~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~i~~~~~~~p 81 (276)
++...|.+++..|+||..+..+|..+|.+.+.++..++.+..-+++||+|+||+.++.|+++.++..+.. +
T Consensus 99 ~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~-V-------- 169 (285)
T COG1405 99 TALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALG-V-------- 169 (285)
T ss_pred HHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHC-C--------
Confidence 3567899999999999999999999999999999999999999999999999999999999999998765 2
Q ss_pred ccccccchHHHHHHHHHHHHHHHHHHHHhCccccccChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCChHHH
Q 023880 82 IEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVV 161 (276)
Q Consensus 82 ~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~~P~~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~P~~I 161 (276)
.+.+|.++.+.+.+.|+=.+....|..|+.+|+..|+++.++...|..++..+....+..+-.|..|
T Consensus 170 -------------~~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~gl 236 (285)
T COG1405 170 -------------SKKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGL 236 (285)
T ss_pred -------------CHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhH
Confidence 2467788888999999999999999999999999999999999999999999999999899999999
Q ss_pred HHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHHh
Q 023880 162 ACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAHL 204 (276)
Q Consensus 162 AaAaI~lA~~~~~~~lp~~~~W~~~~~~~~~~v~~i~~~ll~l 204 (276)
|+||||+|+.+++.+... ..--...|+++..|.+-..+|.+-
T Consensus 237 Aaaaiy~as~l~~~~~tq-~eva~v~~vtevTIrnrykel~~~ 278 (285)
T COG1405 237 AAAAIYLASLLLGERRTQ-KEVAKVAGVTEVTIRNRYKELADA 278 (285)
T ss_pred HHHHHHHHHHHhCCchHH-HHHHHHhCCeeeHHHHHHHHHHHh
Confidence 999999999999965432 345567788888888877766553
No 13
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.71 E-value=4e-16 Score=137.08 Aligned_cols=179 Identities=13% Similarity=0.162 Sum_probs=153.8
Q ss_pred chhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHHhhhhccCCC
Q 023880 2 QYAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGLP 81 (276)
Q Consensus 2 ~~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~i~~~~~~~p 81 (276)
++-..|..+|++++||..+...|..+|+++...+.+++.+...+++|||++||+-++.||++++|..+.+ +
T Consensus 106 ~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~an-v-------- 176 (308)
T KOG1597|consen 106 AAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVAN-V-------- 176 (308)
T ss_pred HHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHHc-C--------
Confidence 4567899999999999999999999999999999999999999999999999999999999999998876 3
Q ss_pred ccccccchHHHHHHHHHHHHHHHHHHHHhCccccc--cChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCChH
Q 023880 82 IEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHV--EHPHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSE 159 (276)
Q Consensus 82 ~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v--~~P~~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~P~ 159 (276)
.+.+|-++=..|++.|+-+... .+.-+|+.+||..|++++++...|..++.-+-.-+.+-+..|-
T Consensus 177 -------------~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPi 243 (308)
T KOG1597|consen 177 -------------SKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPI 243 (308)
T ss_pred -------------CHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCch
Confidence 2456666777788888766554 4588999999999999999999999999998877888889999
Q ss_pred HHHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHH
Q 023880 160 VVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAH 203 (276)
Q Consensus 160 ~IAaAaI~lA~~~~~~~lp~~~~W~~~~~~~~~~v~~i~~~ll~ 203 (276)
.||+|+|||++.+...+.+. +..-...|+.+..|...+++|..
T Consensus 244 SIAAa~IYmisqls~~kkt~-keI~~vtgVaE~TIr~sYK~Lyp 286 (308)
T KOG1597|consen 244 SIAAAAIYMISQLSDEKKTQ-KEIGEVTGVAEVTIRNSYKDLYP 286 (308)
T ss_pred hHHHHHHHHHHHhccCcccH-HHHHHHhhhhHHHHHHHHHHHhh
Confidence 99999999999998854332 34556778888889888886543
No 14
>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=99.67 E-value=3e-16 Score=124.29 Aligned_cols=94 Identities=26% Similarity=0.397 Sum_probs=78.9
Q ss_pred chhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccC-CcCHHHHHHHHHHhhhhccCC
Q 023880 2 QYAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEES-PRKARQVIIVFHRMECRREGL 80 (276)
Q Consensus 2 ~~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~-~~~l~dii~v~~~i~~~~~~~ 80 (276)
..++||.+++..++++..|.++|+.|||||+.+.++...+++++++||+++|||+||. +.++.+++..+..
T Consensus 33 ~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~-------- 104 (127)
T PF00134_consen 33 IIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDN-------- 104 (127)
T ss_dssp HHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTT--------
T ss_pred HHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcC--------
Confidence 3679999999999999999999999999999999999999999999999999999998 7788888876531
Q ss_pred CccccccchHHHHHHHHHHHHHHHHHHHHhCcccc
Q 023880 81 PIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCH 115 (276)
Q Consensus 81 p~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~ 115 (276)
.| .+++++++|+.||++|||+++
T Consensus 105 ----------~~--~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 105 ----------TF--TKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp ----------SS--HHHHHHHHHHHHHHHTTT---
T ss_pred ----------CC--CHHHHHHHHHHHHHHCCCCcC
Confidence 11 488999999999999999975
No 15
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=99.59 E-value=6.8e-15 Score=134.60 Aligned_cols=197 Identities=15% Similarity=0.154 Sum_probs=167.7
Q ss_pred hhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccC-CcCHHHHHHHHHHhhhhccCCC
Q 023880 3 YAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEES-PRKARQVIIVFHRMECRREGLP 81 (276)
Q Consensus 3 ~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~-~~~l~dii~v~~~i~~~~~~~p 81 (276)
.++|..++++..++...+.+.+.++.+||+......+...++++.+|.++|+|.||. ++++++++..+++
T Consensus 140 lvdwlvevsee~r~~~e~l~ls~~~~drfl~~~~~~~~k~ql~g~s~m~I~sk~ee~~~~~~~ef~~itd~--------- 210 (359)
T KOG0654|consen 140 LVDWLVEVSEEYRLTFETLYLSVNYRDRFLSYKEVNKQKLQLVGISAMLIASKYEEIKEPRVEEFCYITDN--------- 210 (359)
T ss_pred hhhhhhHHHHHHHhhhhheeecHHHHHHHhccCccHHHHHHHhCcccceeeccchhhcchHHHHHHhhhhh---------
Confidence 579999999999999999999999999999999999999999999999999999997 6678888776553
Q ss_pred ccccccchHHHHHHHHHHHHHHHHHHHHhCccccccChHHHHHHHHHHcC-CCHHHHHHHHHHHHhhhcccccccCChHH
Q 023880 82 IEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLE-TPLELRQEAWNLANDSLRTTLCVRFKSEV 160 (276)
Q Consensus 82 ~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~~P~~~L~~~l~~l~-~~~~l~~~A~~~l~ds~~t~l~l~~~P~~ 160 (276)
. .++.++..+|..+|..+.|++..++...|+.+|+.... ...++..++.++.+.++....+++|.|+.
T Consensus 211 ---------t--y~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~~~~~~~~~~e~~~~yl~elsll~~~~l~y~PSl 279 (359)
T KOG0654|consen 211 ---------T--YTYWQVLRMEIDILNALTFELVRPTSKTFLRRFLRVAQTPELQVEPLANYLTELSLLDYIFLKYLPSL 279 (359)
T ss_pred ---------h--hHHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHHhhcchhHHHHHHHHHHHHhhhhhHHHhccChHH
Confidence 2 35788999999999999999999999999999977654 45678889999999999887899999999
Q ss_pred HHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHHhhcCCCCccc-cccCCCCc
Q 023880 161 VACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAHLYSLPKAKYI-PVCKDGTS 221 (276)
Q Consensus 161 IAaAaI~lA~~~~~~~lp~~~~W~~~~~~~~~~v~~i~~~ll~ly~~~k~~~~-~~~~~~~~ 221 (276)
||++|+++|...++ .-|+.+.-++..+++.+++..|+..|. +|.+.+.... .+-.+++-
T Consensus 280 iAasAv~lA~~~~~-~~pW~~~L~~~T~y~~edl~~~v~~L~-~~l~~~~~~l~air~ky~~ 339 (359)
T KOG0654|consen 280 IAASAVFLARLTLD-FHPWNQTLEDYTGYKAEDLKPCVLDLH-LYLNASGTDLPAIREKYKQ 339 (359)
T ss_pred HHHHHHHHHHhhcc-CCCCchhhHHhhcccHHHHHHHHHHHh-cccCCCCCchHHHHHHhhh
Confidence 99999999999988 334334445556789999999999998 8887766554 55556653
No 16
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=99.47 E-value=2e-13 Score=99.89 Aligned_cols=85 Identities=21% Similarity=0.220 Sum_probs=76.0
Q ss_pred chhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHHhhhhccCCC
Q 023880 2 QYAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGLP 81 (276)
Q Consensus 2 ~~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~i~~~~~~~p 81 (276)
+..+||.+++..++++..+..+|+.+++||+..+.+.+++++.+++||||+|||++|.++.++++..+....
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~-------- 75 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYA-------- 75 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCC--------
Confidence 468999999999999999999999999999999999999999999999999999999999999998765420
Q ss_pred ccccccchHHHHHHHHHHHHHHHHHH
Q 023880 82 IEHLDLFSKKFSELKMEMSRTERHIL 107 (276)
Q Consensus 82 ~~~~d~~~~~y~~~k~~Il~~E~~IL 107 (276)
.+++|..+|..++
T Consensus 76 -------------~~~~i~~~e~~il 88 (88)
T cd00043 76 -------------TEEEILRMEKLLL 88 (88)
T ss_pred -------------CHHHHHHHHHHhC
Confidence 3677888888764
No 17
>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=99.37 E-value=1.5e-12 Score=94.21 Aligned_cols=83 Identities=19% Similarity=0.288 Sum_probs=72.6
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHHhhhhccCCCccc
Q 023880 5 GSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGLPIEH 84 (276)
Q Consensus 5 ~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~i~~~~~~~p~~~ 84 (276)
+||.+++..++++..+..+|..+++||+....+.+++++.+|+||+|+|||.+|.++...++..++..
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~------------ 68 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGY------------ 68 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC------------
Confidence 58999999999999999999999999999778888999999999999999999998888887765431
Q ss_pred cccchHHHHHHHHHHHHHHHHHHH
Q 023880 85 LDLFSKKFSELKMEMSRTERHILK 108 (276)
Q Consensus 85 ~d~~~~~y~~~k~~Il~~E~~IL~ 108 (276)
..+++|..+|+.||+
T Consensus 69 ---------~~~~~i~~~~~~il~ 83 (83)
T smart00385 69 ---------FTEEEILRMEKLLLE 83 (83)
T ss_pred ---------CCHHHHHHHHHHHhC
Confidence 136788999998873
No 18
>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=99.36 E-value=5.1e-13 Score=104.05 Aligned_cols=115 Identities=21% Similarity=0.210 Sum_probs=92.1
Q ss_pred cChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHH
Q 023880 117 EHPHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDE 196 (276)
Q Consensus 117 ~~P~~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~P~~IAaAaI~lA~~~~~~~lp~~~~W~~~~~~~~~~v~~ 196 (276)
++|+.||.+|++..+.+.++...++++++.++.+..++.|+|+.||+||+++|...++...++.+.+....|++.+++.+
T Consensus 1 PTp~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~ 80 (118)
T PF02984_consen 1 PTPYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKE 80 (118)
T ss_dssp --HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHH
T ss_pred CcHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHH
Confidence 57999999997766667889999999999999999999999999999999999999874222222344456889999999
Q ss_pred HHHHHHHhhcCCC-CccccccCCCCcccccCCCCCC
Q 023880 197 VCRVLAHLYSLPK-AKYIPVCKDGTSFTFSSKTVDS 231 (276)
Q Consensus 197 i~~~ll~ly~~~k-~~~~~~~~~~~~~~~~~~~~~~ 231 (276)
|+..|.+++.+.. .++..+.+++.+..+++.|..+
T Consensus 81 c~~~i~~~~~~~~~~~~~ai~~Kys~~~~~~vs~~~ 116 (118)
T PF02984_consen 81 CIELIQELLSKASNSKLQAIRKKYSSQKFSSVSQIP 116 (118)
T ss_dssp HHHHHHHHHHHCCGSSCTHHHHHTTSGGGTTGGGSS
T ss_pred HHHHHHHHHHhcCCccchHHHHHhCccccCCccCCC
Confidence 9999999998544 7777888888877777777665
No 19
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.90 E-value=9.1e-09 Score=74.14 Aligned_cols=81 Identities=20% Similarity=0.229 Sum_probs=71.6
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccC-CHHHHHHHHH
Q 023880 121 KFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDA-EKSGIDEVCR 199 (276)
Q Consensus 121 ~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~P~~IAaAaI~lA~~~~~~~lp~~~~W~~~~~~-~~~~v~~i~~ 199 (276)
+|+.++++.+++++++...|+++++..+...-+++++|+.||+||+|+|++..+.+ +..+.|....+. +.+++.++.+
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~-~~~~~~~~~~~~~~~~~i~~~~~ 79 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIP-PWTKELVHYTGYFTEEEILRMEK 79 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCC-CCchhHhHhhCCCCHHHHHHHHH
Confidence 37889999999999999999999999998777888999999999999999999886 444567777888 9999999988
Q ss_pred HHH
Q 023880 200 VLA 202 (276)
Q Consensus 200 ~ll 202 (276)
.|+
T Consensus 80 ~il 82 (83)
T smart00385 80 LLL 82 (83)
T ss_pred HHh
Confidence 876
No 20
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=98.84 E-value=1.8e-08 Score=72.11 Aligned_cols=65 Identities=15% Similarity=0.238 Sum_probs=58.4
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHH
Q 023880 7 IVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFH 71 (276)
Q Consensus 7 I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~ 71 (276)
|.++|..|+||..+..+|..++++....+-.++.++..+++||||+||+.++.+++++||..+.+
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~ 65 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAG 65 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCT
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhC
Confidence 67899999999999999999999999999999999999999999999999999999999987654
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=98.72 E-value=7.7e-08 Score=69.90 Aligned_cols=85 Identities=21% Similarity=0.167 Sum_probs=72.9
Q ss_pred ccChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccC-CHHHH
Q 023880 116 VEHPHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDA-EKSGI 194 (276)
Q Consensus 116 v~~P~~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~P~~IAaAaI~lA~~~~~~~lp~~~~W~~~~~~-~~~~v 194 (276)
.++|.+|+.++++.++++.++...|+.+++.++....+..++|+.||+||+++|++..+.+ +..++|....+. +.+++
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~-~~~~~~~~~~~~~~~~~i 80 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIP-PWLKDLVHVTGYATEEEI 80 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCC-CCHHHHhHHhCCCCHHHH
Confidence 3678999999999999999999999999999998888889999999999999999998873 333456667778 88888
Q ss_pred HHHHHHH
Q 023880 195 DEVCRVL 201 (276)
Q Consensus 195 ~~i~~~l 201 (276)
..+...+
T Consensus 81 ~~~e~~i 87 (88)
T cd00043 81 LRMEKLL 87 (88)
T ss_pred HHHHHHh
Confidence 7776654
No 22
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.51 E-value=2.5e-07 Score=88.04 Aligned_cols=150 Identities=11% Similarity=0.074 Sum_probs=119.4
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHHhhhhccCCCccc
Q 023880 5 GSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGLPIEH 84 (276)
Q Consensus 5 ~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~i~~~~~~~p~~~ 84 (276)
+.|.+++..|+|+. .+.+|..+|.--..++--++.....|.++|+|++|+.|.++.-+-|+..+.. +
T Consensus 72 ~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~Lq-v----------- 138 (521)
T KOG1598|consen 72 RLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQ-V----------- 138 (521)
T ss_pred hHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccceE-E-----------
Confidence 47899999999999 9999999999999999999999999999999999999987654433332111 0
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHhCcc---ccccChHHHHHHHHHHcCC---CHHHHHHHHHHHHhhhcccccccCCh
Q 023880 85 LDLFSKKFSELKMEMSRTERHILKEMGFV---CHVEHPHKFISNYLATLET---PLELRQEAWNLANDSLRTTLCVRFKS 158 (276)
Q Consensus 85 ~d~~~~~y~~~k~~Il~~E~~IL~~L~Fd---l~v~~P~~~L~~~l~~l~~---~~~l~~~A~~~l~ds~~t~l~l~~~P 158 (276)
+ -| ++-.+=..|.+.|.-+ +....|.-|+.+|...|.. +.++...|..+++...+..+..+..|
T Consensus 139 -~----Vy-----~LG~~~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRP 208 (521)
T KOG1598|consen 139 -S----VY-----DLGSNFLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRP 208 (521)
T ss_pred -e----hh-----hhhHHHHHHHHHhccccccccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence 0 00 1122333455566666 6677899999999887753 35799999999999999999999999
Q ss_pred HHHHHHHHHHHHHHcCCCC
Q 023880 159 EVVACGVVYAAARRFQIPL 177 (276)
Q Consensus 159 ~~IAaAaI~lA~~~~~~~l 177 (276)
+.|.-||+++|++.+|.+.
T Consensus 209 sglcGAaLliAar~h~~~r 227 (521)
T KOG1598|consen 209 SGLCGAALLIAARMHGFRR 227 (521)
T ss_pred cchhHHHHHHHHHHcCccc
Confidence 9999999999999998864
No 23
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=98.33 E-value=1.1e-06 Score=80.62 Aligned_cols=95 Identities=16% Similarity=0.217 Sum_probs=80.0
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCc-CHHHHHHHHHHhhhhccCCCcc
Q 023880 5 GSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPR-KARQVIIVFHRMECRREGLPIE 83 (276)
Q Consensus 5 ~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~-~l~dii~v~~~i~~~~~~~p~~ 83 (276)
+.|.+++...++...|+++|.+||.+...+.-+.+.+..++|-|||+||+|+.|... .++.+|.-..
T Consensus 387 REMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~E------------ 454 (497)
T KOG4164|consen 387 REMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLE------------ 454 (497)
T ss_pred HHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHH------------
Confidence 457888888999999999999999999999999999999999999999999997533 3555554333
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHHhCcccccc
Q 023880 84 HLDLFSKKFSELKMEMSRTERHILKEMGFVCHVE 117 (276)
Q Consensus 84 ~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~ 117 (276)
+.|..-|.+++..|.-||.+|.|-|+++
T Consensus 455 ------e~fR~nrrdLia~Ef~VlvaLefaL~~~ 482 (497)
T KOG4164|consen 455 ------EQFRLNRRDLIAFEFPVLVALEFALHLP 482 (497)
T ss_pred ------HHhcccHHhhhhhhhhHHHhhhhhccCC
Confidence 3455568899999999999999998864
No 24
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=98.18 E-value=6.5e-06 Score=58.72 Aligned_cols=70 Identities=19% Similarity=0.194 Sum_probs=54.3
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHHH
Q 023880 123 ISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSG 193 (276)
Q Consensus 123 L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~P~~IAaAaI~lA~~~~~~~lp~~~~W~~~~~~~~~~ 193 (276)
+.+++..|++++.+.+.|..+........+.-+.+|..||+||||+|++..+.+.+. .+.-...++++.+
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~-~eIa~~~~Vs~~t 70 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTL-KEIAEAAGVSEKT 70 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSH-HHHHHHCTSSHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCH-HHHHHHhCCCCCc
Confidence 468999999999999999999999988888889999999999999999999887542 1233444555443
No 25
>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=98.17 E-value=2e-05 Score=64.47 Aligned_cols=90 Identities=13% Similarity=0.130 Sum_probs=65.4
Q ss_pred hhHHHHHHHHHhCCCHHHHHHHHHHHHHhHh---c--cccccchHHHHHHHHHHHhhhccc-CCcCHHHHHHHHHHhhhh
Q 023880 3 YAGSIVSFICVVYRPQAVMATGQVLFHRFYC---K--RSFARFDVKIVAASSVWLASKLEE-SPRKARQVIIVFHRMECR 76 (276)
Q Consensus 3 ~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~---~--~s~~~~~~~~va~acLfLA~K~EE-~~~~l~dii~v~~~i~~~ 76 (276)
.-+|+.++.+..+++..+.-.|..|++|+.. . ..+.....+.+.++||.+|+|+-+ ....-+....+..
T Consensus 54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~g----- 128 (149)
T PF08613_consen 54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGG----- 128 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHT-----
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcC-----
Confidence 5679999999999999999999999999998 2 224567889999999999999954 3444444444432
Q ss_pred ccCCCccccccchHHHHHHHHHHHHHHHHHHHHhCccc
Q 023880 77 REGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVC 114 (276)
Q Consensus 77 ~~~~p~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl 114 (276)
. ..+++-.||+..|..|+|+|
T Consensus 129 ---i--------------s~~eln~lE~~fL~~l~~~L 149 (149)
T PF08613_consen 129 ---I--------------SLKELNELEREFLKLLDYNL 149 (149)
T ss_dssp ---S---------------HHHHHHHHHHHHHHTTT--
T ss_pred ---C--------------CHHHHHHHHHHHHHHCCCcC
Confidence 1 35688999999999999986
No 26
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=98.12 E-value=1.5e-05 Score=72.94 Aligned_cols=68 Identities=18% Similarity=0.091 Sum_probs=63.2
Q ss_pred hHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHH
Q 023880 4 AGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFH 71 (276)
Q Consensus 4 ~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~ 71 (276)
.+||.++|..|+|+..+..+|..++++.....-..+.++..+|+||||+||+..+.++++++|..++.
T Consensus 220 ~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~ 287 (310)
T PRK00423 220 IDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAG 287 (310)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcC
Confidence 58999999999999999999999999998877778999999999999999999999999999987754
No 27
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=97.15 E-value=0.0023 Score=57.87 Aligned_cols=70 Identities=19% Similarity=0.077 Sum_probs=65.2
Q ss_pred chhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHH
Q 023880 2 QYAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFH 71 (276)
Q Consensus 2 ~~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~ 71 (276)
...+||-++|..|+|+..+...|..+.+.........+.++.-+|+||+|+||+..+.+++-+++..+.+
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 DPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAG 262 (285)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhC
Confidence 4568999999999999999999999999999998888999999999999999999999999998888765
No 28
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=96.77 E-value=0.0056 Score=54.78 Aligned_cols=70 Identities=11% Similarity=0.080 Sum_probs=64.2
Q ss_pred hhHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHH
Q 023880 3 YAGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHR 72 (276)
Q Consensus 3 ~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~ 72 (276)
..+||.++|..|+||..+...|..+-.+.-...-..+..+..|++|.+|+++-+++.++..++|..+...
T Consensus 203 t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgV 272 (308)
T KOG1597|consen 203 TGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGV 272 (308)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhh
Confidence 5689999999999999999999999999988888888999999999999999999999999998876553
No 29
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=95.93 E-value=0.037 Score=43.08 Aligned_cols=85 Identities=18% Similarity=0.098 Sum_probs=62.9
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCChHHHHHHHHHHHHHHcCCCCCCCccccccc--cCCHHHHHHHH
Q 023880 121 KFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAF--DAEKSGIDEVC 198 (276)
Q Consensus 121 ~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~P~~IAaAaI~lA~~~~~~~lp~~~~W~~~~--~~~~~~v~~i~ 198 (276)
+++......++++......|..+++..+....+....+..||+||+++|++..+...|.-..|.... ..+.+++.++-
T Consensus 36 ~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~E 115 (127)
T PF00134_consen 36 DWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILEME 115 (127)
T ss_dssp HHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHHH
T ss_pred HHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHHHH
Confidence 4566677788888899999999998887766677888999999999999999877544433444433 35778888888
Q ss_pred HHHHHhh
Q 023880 199 RVLAHLY 205 (276)
Q Consensus 199 ~~ll~ly 205 (276)
..|+...
T Consensus 116 ~~iL~~L 122 (127)
T PF00134_consen 116 REILSAL 122 (127)
T ss_dssp HHHHHHT
T ss_pred HHHHHHC
Confidence 8887754
No 30
>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=95.08 E-value=0.1 Score=41.93 Aligned_cols=69 Identities=6% Similarity=0.053 Sum_probs=55.2
Q ss_pred hHHHHHHHHHhCCCHHHHHHHHHHHHHhHhc--cccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHH
Q 023880 4 AGSIVSFICVVYRPQAVMATGQVLFHRFYCK--RSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHR 72 (276)
Q Consensus 4 ~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~--~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~ 72 (276)
+.=|+++|.+|+|+.......-+.|...... .-+.+.+..-+.+.|+|.-||+.....+.++|+..+..
T Consensus 15 ~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~ 85 (135)
T PF01857_consen 15 AVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRK 85 (135)
T ss_dssp HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTT
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHh
Confidence 4457899999999998888888888888754 34678999999999999999999999999999987753
No 31
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=93.95 E-value=0.15 Score=46.71 Aligned_cols=56 Identities=7% Similarity=0.157 Sum_probs=48.8
Q ss_pred HHHHHHHHcC--CCHHHHHHHHHHHHhhhcccccccCChHHHHHHHHHHHHHHcCCCC
Q 023880 122 FISNYLATLE--TPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPL 177 (276)
Q Consensus 122 ~L~~~l~~l~--~~~~l~~~A~~~l~ds~~t~l~l~~~P~~IAaAaI~lA~~~~~~~l 177 (276)
+|..++..++ +++.+...|..++...+...-...|+|..||++|+|+|++.-+.+.
T Consensus 62 ~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~ 119 (305)
T TIGR00569 62 RLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNV 119 (305)
T ss_pred HHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCc
Confidence 5666778888 8999999999999998887778899999999999999999876654
No 32
>KOG1674 consensus Cyclin [General function prediction only]
Probab=92.56 E-value=0.5 Score=41.11 Aligned_cols=92 Identities=13% Similarity=0.156 Sum_probs=66.7
Q ss_pred hHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccc---------cccch-HHHHHHHHHHHhhhcccCC-cCHHHHHHHHHH
Q 023880 4 AGSIVSFICVVYRPQAVMATGQVLFHRFYCKRS---------FARFD-VKIVAASSVWLASKLEESP-RKARQVIIVFHR 72 (276)
Q Consensus 4 ~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s---------~~~~~-~~~va~acLfLA~K~EE~~-~~l~dii~v~~~ 72 (276)
-+|..++-+..+....+.-.|.+||+||..+.. +...+ .+-..++|+-+|+|..+.. -+-.-..
T Consensus 79 ~~yleri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~y~n~~~a----- 153 (218)
T KOG1674|consen 79 RQYLERIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVYYSNAYYA----- 153 (218)
T ss_pred HHHHHHHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccchhhhHHHHH-----
Confidence 357788889999999999999999999988622 22345 6668999999999998632 1111111
Q ss_pred hhhhccCCCccccccchHHHHHHHHHHHHHHHHHHHHhCcccccc
Q 023880 73 MECRREGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVE 117 (276)
Q Consensus 73 i~~~~~~~p~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~ 117 (276)
+-.+.+ .+++-.+|..+|..++|.+.+.
T Consensus 154 ---~vggl~--------------~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 154 ---KVGGLT--------------TDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred ---HhCCCC--------------hHhhhhhhHHHHhhCCeEEEec
Confidence 112332 4566699999999999999885
No 33
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=91.55 E-value=0.82 Score=34.67 Aligned_cols=56 Identities=18% Similarity=0.233 Sum_probs=44.9
Q ss_pred hHHHHHHHHHhCCCHHHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccC
Q 023880 4 AGSIVSFICVVYRPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEES 59 (276)
Q Consensus 4 ~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~ 59 (276)
..|+..+.+..+....+...|..+..-......+-++.+-.+|+||+++|.+.-+.
T Consensus 4 ~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~ 59 (118)
T PF02984_consen 4 YDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGK 59 (118)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCc
Confidence 35677775555556778889999999888888899999999999999999998653
No 34
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=89.08 E-value=0.66 Score=42.75 Aligned_cols=58 Identities=19% Similarity=0.189 Sum_probs=48.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCChHHHHHHHHHHHHHHcCCCC
Q 023880 120 HKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPL 177 (276)
Q Consensus 120 ~~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~P~~IAaAaI~lA~~~~~~~l 177 (276)
-.||......|++++.-...|..+....+.-.-+-.|+|..||++|+++|.+.-+.+.
T Consensus 43 ~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~ 100 (323)
T KOG0834|consen 43 AKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPR 100 (323)
T ss_pred HHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcc
Confidence 3678888888988877778888888887777777889999999999999999876654
No 35
>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=88.74 E-value=3.2 Score=33.71 Aligned_cols=88 Identities=14% Similarity=0.066 Sum_probs=63.0
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHHHHHhhhc---cc-ccc-cCChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHHH
Q 023880 119 PHKFISNYLATLETPLELRQEAWNLANDSLR---TT-LCV-RFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSG 193 (276)
Q Consensus 119 P~~~L~~~l~~l~~~~~l~~~A~~~l~ds~~---t~-l~l-~~~P~~IAaAaI~lA~~~~~~~lp~~~~W~~~~~~~~~~ 193 (276)
-.+|+.++.+....+....-.|..++..... .+ ..+ .....-+-++|+.+|.|.+.-.--.++.|-+..|++..+
T Consensus 54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~e 133 (149)
T PF08613_consen 54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLKE 133 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHH
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHHH
Confidence 4778888888888888888888887776655 12 222 456778999999999999865444467899999999999
Q ss_pred HHHHHHHHHHhhc
Q 023880 194 IDEVCRVLAHLYS 206 (276)
Q Consensus 194 v~~i~~~ll~ly~ 206 (276)
+..+-.+++.+..
T Consensus 134 ln~lE~~fL~~l~ 146 (149)
T PF08613_consen 134 LNELEREFLKLLD 146 (149)
T ss_dssp HHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHCC
Confidence 9999998887653
No 36
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=88.31 E-value=0.71 Score=44.80 Aligned_cols=68 Identities=18% Similarity=0.217 Sum_probs=50.5
Q ss_pred HHHHHHHH-hCCCH--HHHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHHh
Q 023880 6 SIVSFICV-VYRPQ--AVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRM 73 (276)
Q Consensus 6 ~I~~v~~~-L~L~~--~t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~i 73 (276)
||.+.+-+ +..+. .|..+|..+..|----.-..+..+--++.|||++||.+.+.++++.||+++.+..
T Consensus 169 ~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~ 239 (521)
T KOG1598|consen 169 YIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVC 239 (521)
T ss_pred eeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHh
Confidence 34444443 33443 3788888888887544445667778899999999999999999999999887743
No 37
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=88.06 E-value=0.89 Score=41.62 Aligned_cols=55 Identities=16% Similarity=0.342 Sum_probs=37.8
Q ss_pred HHHHHHHHhCCCHHH--HHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCC
Q 023880 6 SIVSFICVVYRPQAV--MATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESP 60 (276)
Q Consensus 6 ~I~~v~~~L~L~~~t--~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~ 60 (276)
+|.--...|++++.- ...|-+|+.--.-..-+..+.+..||+||+|||++.+|.|
T Consensus 144 lii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIp 200 (367)
T KOG0835|consen 144 LIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIP 200 (367)
T ss_pred HHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCC
Confidence 444555667777655 3444444443333455678999999999999999999854
No 38
>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=87.54 E-value=1.3 Score=40.18 Aligned_cols=86 Identities=15% Similarity=0.074 Sum_probs=62.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCChHHHHHHHHHHHHHHcCC--CCCC-----CccccccccCCHH
Q 023880 120 HKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQI--PLPE-----NPPWWKAFDAEKS 192 (276)
Q Consensus 120 ~~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~P~~IAaAaI~lA~~~~~~--~lp~-----~~~W~~~~~~~~~ 192 (276)
..++..++..|+++..+...|..+....+.-.-.-.+++..||.+|||+|++.-+. .+-. ...|-+...-+.+
T Consensus 49 ~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~sr~ 128 (297)
T COG5333 49 LKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKSSRE 128 (297)
T ss_pred HHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccccccHH
Confidence 36788899999999999999999988877655577899999999999999998763 2110 1235555555666
Q ss_pred HHHHHHHHHHHhh
Q 023880 193 GIDEVCRVLAHLY 205 (276)
Q Consensus 193 ~v~~i~~~ll~ly 205 (276)
.|-+.-..+++..
T Consensus 129 ~Il~~E~~lLEaL 141 (297)
T COG5333 129 RILEYEFELLEAL 141 (297)
T ss_pred HHHHHHHHHHHHc
Confidence 6655555555543
No 39
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=87.04 E-value=1.2 Score=38.85 Aligned_cols=86 Identities=15% Similarity=0.100 Sum_probs=60.2
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCChHHHHHHHHHHHHHHcCCCCC-------------C-Ccccccc
Q 023880 121 KFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLP-------------E-NPPWWKA 186 (276)
Q Consensus 121 ~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~P~~IAaAaI~lA~~~~~~~lp-------------~-~~~W~~~ 186 (276)
.++..+.+.+++.+.+...|.-++...+.-.-.-.+.|..+|..|+|+|++.-..++. . -..|.+.
T Consensus 46 n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~~e~ 125 (264)
T KOG0794|consen 46 NVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYWPEK 125 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccchhh
Confidence 4455555666667777777777766665433466899999999999999998766521 1 0157777
Q ss_pred ccCCHHHHHHHHHHHHHhhc
Q 023880 187 FDAEKSGIDEVCRVLAHLYS 206 (276)
Q Consensus 187 ~~~~~~~v~~i~~~ll~ly~ 206 (276)
+.++..+|.|+--.+++...
T Consensus 126 ~~~~~~~I~e~Ef~llE~Ld 145 (264)
T KOG0794|consen 126 FPYERKDILEMEFYLLEALD 145 (264)
T ss_pred cCCCcCcchhhhhhHHhhhc
Confidence 77888888777777766654
No 40
>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=86.67 E-value=2.3 Score=34.16 Aligned_cols=55 Identities=16% Similarity=0.248 Sum_probs=46.1
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHhhhc--ccccccCChHHHHHHHHHHHHHHcCC
Q 023880 121 KFISNYLATLETPLELRQEAWNLANDSLR--TTLCVRFKSEVVACGVVYAAARRFQI 175 (276)
Q Consensus 121 ~~L~~~l~~l~~~~~l~~~A~~~l~ds~~--t~l~l~~~P~~IAaAaI~lA~~~~~~ 175 (276)
.=+..+|+.|++++++.+..|.+.+-++. +.+.....-.+|-++|||..++..+.
T Consensus 16 ~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~ 72 (135)
T PF01857_consen 16 VRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKE 72 (135)
T ss_dssp HHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcC
Confidence 34566888889998999999999999984 78888899999999999999998763
No 41
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=80.87 E-value=3.4 Score=37.61 Aligned_cols=74 Identities=16% Similarity=0.150 Sum_probs=46.4
Q ss_pred HHHHHHHhHh--ccccccchHHHHHHHHHHHhhhcccC-CcCHHHHHHHHHHhhhhccCCCccccccchHHHHHHHHHHH
Q 023880 24 GQVLFHRFYC--KRSFARFDVKIVAASSVWLASKLEES-PRKARQVIIVFHRMECRREGLPIEHLDLFSKKFSELKMEMS 100 (276)
Q Consensus 24 A~~~f~RF~~--~~s~~~~~~~~va~acLfLA~K~EE~-~~~l~dii~v~~~i~~~~~~~p~~~~d~~~~~y~~~k~~Il 100 (276)
...|+.|-.. ...+..+.+..+....+++|+|+=+. ...=-|-+.++.. .+.+++-
T Consensus 214 tL~~~erl~~~~e~~~~p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlKd---------------------~tveDmN 272 (343)
T KOG1675|consen 214 TLVYAERLLWLAERDPCPRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILKD---------------------QSVDDMN 272 (343)
T ss_pred HHHhhHhhhhHhhcCCCcchhhhhhhhhheehhhhhhhhhcccHHHHHHHhh---------------------ccHhhHH
Confidence 3455655533 23344667778888889999997432 1111122221111 1477889
Q ss_pred HHHHHHHHHhCccccccC
Q 023880 101 RTERHILKEMGFVCHVEH 118 (276)
Q Consensus 101 ~~E~~IL~~L~Fdl~v~~ 118 (276)
.+||++|+.|+|+++++-
T Consensus 273 e~ERqfLelLqfNinvp~ 290 (343)
T KOG1675|consen 273 ALERQFLELLQFNINVPS 290 (343)
T ss_pred HHHHHHHHHHhhccCccH
Confidence 999999999999999864
No 42
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=80.52 E-value=11 Score=34.85 Aligned_cols=83 Identities=12% Similarity=0.065 Sum_probs=61.9
Q ss_pred HHHHHHHHHHHHHHhCccccc---c------ChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCC---hHHHHH
Q 023880 96 KMEMSRTERHILKEMGFVCHV---E------HPHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFK---SEVVAC 163 (276)
Q Consensus 96 k~~Il~~E~~IL~~L~Fdl~v---~------~P~~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~---P~~IAa 163 (276)
-..++..|..-....++.+.+ . ...+.|.+.++..+......-+|.++++..+...-+-..+ -..+|+
T Consensus 49 i~~ll~kEe~~~p~~~~~~~~~~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAv 128 (335)
T KOG0656|consen 49 LANLLEKEEQHNPSLDYFLCVQKLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAV 128 (335)
T ss_pred HHHHHHHHHHhCCCCchhhhcccccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHH
Confidence 446667777666666533332 2 3446788888888999999999999999988777777888 556899
Q ss_pred HHHHHHHHHcCCCCC
Q 023880 164 GVVYAAARRFQIPLP 178 (276)
Q Consensus 164 AaI~lA~~~~~~~lp 178 (276)
||+.+|+|+-....|
T Consensus 129 aCLsLAsKmeE~~vP 143 (335)
T KOG0656|consen 129 ACLSLASKMEETDVP 143 (335)
T ss_pred HHHHHHHhhcCcCCc
Confidence 999999998765433
No 43
>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=69.91 E-value=12 Score=34.02 Aligned_cols=51 Identities=8% Similarity=0.223 Sum_probs=43.3
Q ss_pred HHHHHHHc--CCCHHHHHHHHHHHHhhhcccccccCChHHHHHHHHHHHHHHc
Q 023880 123 ISNYLATL--ETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRF 173 (276)
Q Consensus 123 L~~~l~~l--~~~~~l~~~A~~~l~ds~~t~l~l~~~P~~IAaAaI~lA~~~~ 173 (276)
+..|+..+ .++..++..|..+....+..+....|+|..|-++|+++|++.-
T Consensus 63 l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kie 115 (325)
T KOG2496|consen 63 LVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIE 115 (325)
T ss_pred HHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhH
Confidence 44455444 4688999999999999999999999999999999999999974
No 44
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=53.74 E-value=29 Score=35.95 Aligned_cols=68 Identities=6% Similarity=0.072 Sum_probs=54.7
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHhHhcc--ccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHH
Q 023880 5 GSIVSFICVVYRPQAVMATGQVLFHRFYCKR--SFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHR 72 (276)
Q Consensus 5 ~~I~~v~~~L~L~~~t~~tA~~~f~RF~~~~--s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~ 72 (276)
.=|+.+|.+|.|.+.....--++|+.-+... -+++.+..=+.+.|+|+-+|+++...+.++|+..+.+
T Consensus 682 vRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR~ 751 (920)
T KOG1010|consen 682 VRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYRR 751 (920)
T ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHhc
Confidence 3478999999999987776666776655432 3567788889999999999999999999999987764
No 45
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=44.71 E-value=2.2e+02 Score=24.94 Aligned_cols=176 Identities=11% Similarity=0.076 Sum_probs=97.2
Q ss_pred HHHHHHHHhCCC--HHHHHHHHHHHHHhHh--ccccccchHHHHHHHHHHHhhhcccCCcCHHHHHHHHHHhhhhccCCC
Q 023880 6 SIVSFICVVYRP--QAVMATGQVLFHRFYC--KRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGLP 81 (276)
Q Consensus 6 ~I~~v~~~L~L~--~~t~~tA~~~f~RF~~--~~s~~~~~~~~va~acLfLA~K~EE~~~~l~dii~v~~~i~~~~~~~p 81 (276)
.|.+++.+|+|. +.++-.|-.|.+-.-. ..+..+..-.-=++-|+=||+-.-.++-.-...+...
T Consensus 2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avKLS----------- 70 (262)
T KOG4557|consen 2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVKLS----------- 70 (262)
T ss_pred cHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHHhc-----------
Confidence 588999999995 5666667666543322 2334444445556667777764433322222222211
Q ss_pred ccccccchHHHHHHHHHHHHHHHHHHHHhCccccccChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcc------ccccc
Q 023880 82 IEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELRQEAWNLANDSLRT------TLCVR 155 (276)
Q Consensus 82 ~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fdl~v~~P~~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t------~l~l~ 155 (276)
.+..+.|..-. -..|.. -.|+-.++| ..++-.+|. -++.+.|..++.. |.. ..-..
T Consensus 71 ----Gl~k~~Y~~~~---~sfe~l--lgln~~~~V-------rdlaVQfgc-~evi~~a~~vl~s-yk~~lpaT~~~~~D 132 (262)
T KOG4557|consen 71 ----GLSKKAYSRSF---NSFENL--LGLNIKLNV-------RDLAVQFGC-VEVIKSAQNVLSS-YKERLPATRRANAD 132 (262)
T ss_pred ----cccHHHHHHHH---HHHHHH--hcchhhcCH-------HHHHHHHhH-HHHHHHHHHHHHH-HHhcCchhhhcCCc
Confidence 12334443222 122221 112222222 122222232 2455556665533 322 24467
Q ss_pred CChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHHhhcCCCCc
Q 023880 156 FKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAHLYSLPKAK 211 (276)
Q Consensus 156 ~~P~~IAaAaI~lA~~~~~~~lp~~~~W~~~~~~~~~~v~~i~~~ll~ly~~~k~~ 211 (276)
++-.+-++||+|.|++.+...+... .....-|+.+.+.+-++.++-.+|.+....
T Consensus 133 ~SrP~ft~aA~~~ack~lKlKVdK~-kli~~sg~~~s~F~~l~kqler~~~qv~~e 187 (262)
T KOG4557|consen 133 FSRPVFTAAAFYLACKKLKLKVDKL-KLIEVSGTSESEFSCLSKQLERNYKQVSTE 187 (262)
T ss_pred ccchHHHHHHHHHHHHHHHHhhhHh-hcccccCCCHHHHHHHHHHHHHHHHHhcCC
Confidence 7888899999999999987655332 244566788999999999999999875544
No 46
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=41.16 E-value=61 Score=28.22 Aligned_cols=50 Identities=18% Similarity=0.232 Sum_probs=35.8
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHHhHhc-----cccccchHHHHHHHHHHHhhhcc
Q 023880 7 IVSFICVVYRPQAVMATGQVLFHRFYCK-----RSFARFDVKIVAASSVWLASKLE 57 (276)
Q Consensus 7 I~~v~~~L~L~~~t~~tA~~~f~RF~~~-----~s~~~~~~~~va~acLfLA~K~E 57 (276)
|+++|..|++- +++-.|..++.-|-.+ .--.++..-.+.++++|+|||.-
T Consensus 96 VrdlaVQfgc~-evi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~l 150 (262)
T KOG4557|consen 96 VRDLAVQFGCV-EVIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKL 150 (262)
T ss_pred HHHHHHHHhHH-HHHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHH
Confidence 45666666653 4566788888877653 22346778899999999999964
No 47
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=35.39 E-value=1.9e+02 Score=27.42 Aligned_cols=84 Identities=14% Similarity=0.062 Sum_probs=50.0
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHhhhcccccccCChHHHHHHHHH-HHHHHcCCCCCCCccccccc--cCCHHHHHHHHH
Q 023880 123 ISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVY-AAARRFQIPLPENPPWWKAF--DAEKSGIDEVCR 199 (276)
Q Consensus 123 L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l~l~~~P~~IAaAaI~-lA~~~~~~~lp~~~~W~~~~--~~~~~~v~~i~~ 199 (276)
+...-..+++..+...+|.++++..+....+-.-.=.-++++|++ +|++.-.+.+|...+.--.. .++.++|..+-.
T Consensus 165 lvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~il~mE~ 244 (391)
T KOG0653|consen 165 LVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREEILRMEK 244 (391)
T ss_pred HHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHHHHHHHH
Confidence 333345567778889999999955443323333344456777855 99998555555321111111 157778877777
Q ss_pred HHHHhhc
Q 023880 200 VLAHLYS 206 (276)
Q Consensus 200 ~ll~ly~ 206 (276)
.|++...
T Consensus 245 ~il~~L~ 251 (391)
T KOG0653|consen 245 YILNVLE 251 (391)
T ss_pred HHHhccC
Confidence 7766543
No 48
>KOG1567 consensus Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism]
Probab=34.32 E-value=1.7e+02 Score=26.71 Aligned_cols=79 Identities=16% Similarity=0.276 Sum_probs=47.7
Q ss_pred HHHHHHhhhccc-CCcCHHHHHHHHHHhhhh--ccCCCccccccchHHHHHHHHHHHHHHHHHHHHhCcc--ccccChHH
Q 023880 47 ASSVWLASKLEE-SPRKARQVIIVFHRMECR--REGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFV--CHVEHPHK 121 (276)
Q Consensus 47 ~acLfLA~K~EE-~~~~l~dii~v~~~i~~~--~~~~p~~~~d~~~~~y~~~k~~Il~~E~~IL~~L~Fd--l~v~~P~~ 121 (276)
-|||+-+--... .+.++++|+.-+-.+.+. .+.+|...+.++.+...+..+=| --.+|..||++ .++.+|++
T Consensus 227 Facll~~~l~~kp~~~ri~eII~eAV~IEqef~~eaLPv~liGMN~~lM~qYIEFV---ADrLL~~lG~~K~Yn~~NPFd 303 (344)
T KOG1567|consen 227 FACLLFSHLKKKPNEERIEEIITEAVEIEQEFLTEALPVNLIGMNCDLMSQYIEFV---ADRLLVELGNEKYYNAENPFD 303 (344)
T ss_pred HHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHHHHhccchhhhccCHHHHHHHHHHH---HHHHHHHhCccceecCCCchH
Confidence 467766543332 345677877655445432 35677766666555433222211 22589999997 57899999
Q ss_pred HHHHHHH
Q 023880 122 FISNYLA 128 (276)
Q Consensus 122 ~L~~~l~ 128 (276)
|...+--
T Consensus 304 fMEnISl 310 (344)
T KOG1567|consen 304 FMENISL 310 (344)
T ss_pred HHHHhhh
Confidence 9887653
No 49
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=29.49 E-value=61 Score=22.63 Aligned_cols=24 Identities=21% Similarity=0.278 Sum_probs=20.6
Q ss_pred ccccCCHHHHHHHHHHHHHhhcCC
Q 023880 185 KAFDAEKSGIDEVCRVLAHLYSLP 208 (276)
Q Consensus 185 ~~~~~~~~~v~~i~~~ll~ly~~~ 208 (276)
..+|++..+|..+...|+++|..+
T Consensus 19 ~~lG~~~~~v~~vl~~LL~lY~~n 42 (65)
T PF10440_consen 19 RQLGFSKKQVRPVLKNLLKLYDGN 42 (65)
T ss_pred HHcCCCHHHHHHHHHHHHHHHcCC
Confidence 457889999999999999999743
No 50
>PHA02690 hypothetical protein; Provisional
Probab=29.36 E-value=1.1e+02 Score=22.18 Aligned_cols=33 Identities=24% Similarity=0.409 Sum_probs=25.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhhhcccc
Q 023880 120 HKFISNYLATLETPLELRQEAWNLANDSLRTTL 152 (276)
Q Consensus 120 ~~~L~~~l~~l~~~~~l~~~A~~~l~ds~~t~l 152 (276)
..|+..+...++.+..+...+|.++-|.+.|-+
T Consensus 21 rrYLeAIqrhlEgs~plLR~~~RlLfDL~lTvf 53 (90)
T PHA02690 21 RRYLEAIQRHLEGSTPLLRQMWRLLFDLLLTVF 53 (90)
T ss_pred hHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH
Confidence 467777777777777788889999999877653
No 51
>PF11357 Spy1: Cell cycle regulatory protein; InterPro: IPR020984 Speedy (Spy1) is a cell cycle regulatory protein which activates CDK2, the major kinase that allows progression through G1/S phase and further replication events. Spy1 expression overcomes a p27-induced cell cycle arrest to allow for DNA synthesis, so cell cycle progression occurs due to an interaction between Spy1 and p27 []. Spy1 is also known as Ringo protein A.
Probab=24.20 E-value=3.7e+02 Score=21.45 Aligned_cols=85 Identities=13% Similarity=0.177 Sum_probs=48.1
Q ss_pred HhCCCHH-HHHHHHHHHHHhHhccccccchHHHHHHHHHHHhhhcccCCcCH-HHHHHHHHHhhhhccCCCccccccchH
Q 023880 13 VVYRPQA-VMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKA-RQVIIVFHRMECRREGLPIEHLDLFSK 90 (276)
Q Consensus 13 ~L~L~~~-t~~tA~~~f~RF~~~~s~~~~~~~~va~acLfLA~K~EE~~~~l-~dii~v~~~i~~~~~~~p~~~~d~~~~ 90 (276)
.++.++. .++..+.||.|--.... .+.. .=-..+|+||.-+||..... .+|...... +
T Consensus 24 ~~~~sDKYLLAmV~~YF~Ragl~~~--~Y~r-i~FFlALYLAndmEED~~~~K~~If~f~~G-----------------~ 83 (131)
T PF11357_consen 24 CLRVSDKYLLAMVIAYFSRAGLFSW--QYQR-IHFFLALYLANDMEEDDEEPKYEIFPFLYG-----------------K 83 (131)
T ss_pred chhhhhHHHHHHHHHHHHhcccchh--hcch-HHHHHHHHHhhHHHhccchHHHHHHHHHHC-----------------c
Confidence 3556655 66888889888743211 1222 22346899999999875433 344433221 1
Q ss_pred HHHHHHHHHHHHHHHHHHHhCcccccc
Q 023880 91 KFSELKMEMSRTERHILKEMGFVCHVE 117 (276)
Q Consensus 91 ~y~~~k~~Il~~E~~IL~~L~Fdl~v~ 117 (276)
......-...+.=..+.+.+||..-|.
T Consensus 84 ~w~~~~~~F~klr~~~~~~m~~Ra~Vs 110 (131)
T PF11357_consen 84 NWRSQIPQFHKLRDQFWRRMDWRAWVS 110 (131)
T ss_pred chHHHhHHHHHHHHHHHHHcCCceeeC
Confidence 111123344455566788888876654
No 52
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=23.48 E-value=1.2e+02 Score=29.36 Aligned_cols=75 Identities=16% Similarity=0.095 Sum_probs=53.0
Q ss_pred CCHHHHHHHHHHHHhhhcccccccCChHHHHHHHHHHHHHHcCCCCCCCcccccccc--CCHHHHHHHHHHHHHhhc
Q 023880 132 TPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFD--AEKSGIDEVCRVLAHLYS 206 (276)
Q Consensus 132 ~~~~l~~~A~~~l~ds~~t~l~l~~~P~~IAaAaI~lA~~~~~~~lp~~~~W~~~~~--~~~~~v~~i~~~ll~ly~ 206 (276)
+-++-.-+|..+++..+-...+..-.-..+++.|+++|++.-.+.+|.....--+++ .+.+++...-+.|++...
T Consensus 229 llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE~~ml~~l~ 305 (440)
T COG5024 229 LLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERYMLEVLD 305 (440)
T ss_pred ccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHHHHHhhhcc
Confidence 345666777777777666666666777889999999999998887765332222332 577888888887777654
No 53
>TIGR00873 gnd 6-phosphogluconate dehydrogenase, decarboxylating. This model does not specify whether the cofactor is NADP only (EC 1.1.1.44), NAD only, or both. The model does not assign an EC number for that reason.
Probab=22.15 E-value=1.2e+02 Score=29.58 Aligned_cols=31 Identities=6% Similarity=0.072 Sum_probs=28.5
Q ss_pred hhHHHHHHHHHhCCCHHHHHHHHHHHHHhHh
Q 023880 3 YAGSIVSFICVVYRPQAVMATGQVLFHRFYC 33 (276)
Q Consensus 3 ~~~~I~~v~~~L~L~~~t~~tA~~~f~RF~~ 33 (276)
..+|+...+...++|..++..|+.||++|-.
T Consensus 400 ~~r~vV~~a~~~gip~P~ls~aL~y~~~~~s 430 (467)
T TIGR00873 400 GWRRVVALAIEYGIPVPAFSAALSFYDGYRT 430 (467)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHhhc
Confidence 3489999999999999999999999999976
No 54
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=21.78 E-value=1.3e+02 Score=18.36 Aligned_cols=15 Identities=7% Similarity=-0.055 Sum_probs=12.6
Q ss_pred HHHHHHHhCCCHHHH
Q 023880 7 IVSFICVVYRPQAVM 21 (276)
Q Consensus 7 I~~v~~~L~L~~~t~ 21 (276)
|.++++.++++..|+
T Consensus 2 i~e~A~~~gvs~~tl 16 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTL 16 (38)
T ss_dssp HHHHHHHHTS-HHHH
T ss_pred HHHHHHHHCCCHHHH
Confidence 678999999999987
Done!