Query 021552
Match_columns 311
No_of_seqs 210 out of 1505
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 03:53:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021552.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021552hhsearch_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 1.1E-52 2.5E-57 375.1 19.4 271 15-290 3-277 (367)
2 KOG0834 CDK9 kinase-activating 100.0 2.1E-50 4.6E-55 369.9 23.3 234 5-245 8-250 (323)
3 TIGR00569 ccl1 cyclin ccl1. Un 100.0 1.2E-39 2.7E-44 299.4 21.9 216 4-239 5-251 (305)
4 KOG0794 CDK8 kinase-activating 100.0 1.7E-40 3.7E-45 284.1 13.1 232 4-245 9-243 (264)
5 COG5333 CCL1 Cdk activating ki 100.0 2.8E-32 6E-37 244.6 15.8 188 26-229 36-225 (297)
6 KOG0656 G1/S-specific cyclin D 99.9 3.9E-23 8.5E-28 190.0 18.3 166 23-207 66-239 (335)
7 PRK00423 tfb transcription ini 99.9 2.1E-22 4.6E-27 187.1 20.7 182 36-240 123-304 (310)
8 KOG2496 Cdk activating kinase 99.9 5E-23 1.1E-27 183.5 8.5 189 4-210 6-224 (325)
9 KOG0653 Cyclin B and related k 99.9 2.4E-21 5.1E-26 185.4 15.2 188 31-238 154-343 (391)
10 COG5024 Cyclin [Cell division 99.8 5E-20 1.1E-24 175.3 15.4 191 32-247 210-406 (440)
11 KOG0655 G1/S-specific cyclin E 99.8 4.1E-20 8.9E-25 166.3 11.7 183 29-240 139-335 (408)
12 KOG1597 Transcription initiati 99.7 3E-16 6.4E-21 140.0 17.5 180 35-237 104-285 (308)
13 KOG0654 G2/Mitotic-specific cy 99.7 3.9E-17 8.5E-22 151.7 10.8 205 29-255 131-337 (359)
14 PF00134 Cyclin_N: Cyclin, N-t 99.7 5.7E-17 1.2E-21 131.0 10.5 102 29-150 25-127 (127)
15 COG1405 SUA7 Transcription ini 99.7 2.4E-15 5.1E-20 137.2 17.4 182 35-239 97-278 (285)
16 cd00043 CYCLIN Cyclin box fold 99.4 5.2E-13 1.1E-17 99.6 8.7 87 35-142 2-88 (88)
17 smart00385 CYCLIN domain prese 99.3 5.6E-12 1.2E-16 93.0 6.9 83 40-143 1-83 (83)
18 PF02984 Cyclin_C: Cyclin, C-t 99.2 8.8E-12 1.9E-16 99.0 3.9 91 152-242 1-91 (118)
19 smart00385 CYCLIN domain prese 98.9 8.1E-09 1.8E-13 75.9 8.0 81 156-237 1-82 (83)
20 cd00043 CYCLIN Cyclin box fold 98.7 5.1E-08 1.1E-12 72.3 8.3 85 151-236 2-87 (88)
21 KOG1598 Transcription initiati 98.7 3.8E-08 8.2E-13 95.1 9.0 155 35-212 67-227 (521)
22 PF00382 TFIIB: Transcription 98.7 9.4E-08 2E-12 69.5 8.2 64 42-105 1-64 (71)
23 KOG4164 Cyclin ik3-1/CABLES [C 98.2 1.8E-06 3.9E-11 80.3 6.0 97 38-152 385-482 (497)
24 PF00382 TFIIB: Transcription 98.2 7.1E-06 1.5E-10 59.5 6.7 69 158-227 1-69 (71)
25 PRK00423 tfb transcription ini 97.9 6.9E-05 1.5E-09 70.0 9.5 68 39-106 220-287 (310)
26 PF08613 Cyclin: Cyclin; Inte 97.9 0.00019 4.1E-09 59.8 10.8 90 38-149 54-149 (149)
27 COG1405 SUA7 Transcription ini 96.5 0.012 2.5E-07 54.3 8.5 68 39-106 195-262 (285)
28 PF00134 Cyclin_N: Cyclin, N-t 95.9 0.037 8.1E-07 43.9 7.4 86 155-240 35-122 (127)
29 KOG1597 Transcription initiati 95.7 0.044 9.6E-07 49.9 7.5 69 38-106 203-271 (308)
30 TIGR00569 ccl1 cyclin ccl1. Un 94.7 0.082 1.8E-06 49.2 6.4 56 157-212 62-119 (305)
31 PF01857 RB_B: Retinoblastoma- 93.9 0.41 8.8E-06 39.2 8.2 69 38-106 14-84 (135)
32 PF02984 Cyclin_C: Cyclin, C-t 93.3 0.44 9.5E-06 37.0 7.3 56 39-94 4-59 (118)
33 KOG1674 Cyclin [General functi 92.4 0.6 1.3E-05 41.4 7.6 93 39-152 79-181 (218)
34 KOG0835 Cyclin L [General func 91.5 0.33 7.2E-06 45.0 5.0 57 39-95 142-200 (367)
35 COG5333 CCL1 Cdk activating ki 89.8 0.7 1.5E-05 42.6 5.5 85 155-239 49-140 (297)
36 KOG0834 CDK9 kinase-activating 89.3 0.59 1.3E-05 43.8 4.8 58 155-212 43-100 (323)
37 KOG0794 CDK8 kinase-activating 89.1 0.74 1.6E-05 40.8 4.9 85 155-240 45-144 (264)
38 PF08613 Cyclin: Cyclin; Inte 88.9 2.8 6E-05 34.7 8.1 88 153-240 53-145 (149)
39 KOG1598 Transcription initiati 83.4 1.4 3E-05 43.6 4.1 55 54-108 185-239 (521)
40 PF01857 RB_B: Retinoblastoma- 82.6 3.9 8.5E-05 33.4 5.8 57 155-211 15-73 (135)
41 KOG0656 G1/S-specific cyclin D 81.0 9.4 0.0002 36.0 8.4 84 130-213 48-143 (335)
42 KOG2496 Cdk activating kinase 79.5 4.7 0.0001 37.2 5.8 52 158-209 63-116 (325)
43 KOG1675 Predicted cyclin [Gene 76.2 4.7 0.0001 37.3 4.7 75 58-153 213-290 (343)
44 KOG4557 Origin recognition com 56.5 76 0.0016 28.1 8.0 79 10-93 60-151 (262)
45 KOG1010 Rb (Retinoblastoma tum 51.6 28 0.00061 36.7 5.3 69 39-107 681-751 (920)
46 KOG1567 Ribonucleotide reducta 44.1 93 0.002 28.8 6.9 82 80-164 225-311 (344)
47 PF11357 Spy1: Cell cycle regu 43.1 1.7E+02 0.0038 23.7 7.6 84 48-152 24-110 (131)
48 KOG4557 Origin recognition com 40.1 2.7E+02 0.0058 24.7 14.3 57 187-244 129-185 (262)
49 PF10440 WIYLD: Ubiquitin-bind 36.1 40 0.00087 23.9 2.7 34 219-255 18-51 (65)
50 KOG0653 Cyclin B and related k 35.7 1.6E+02 0.0035 28.3 7.8 83 158-240 165-250 (391)
51 KOG0655 G1/S-specific cyclin E 35.3 1.4E+02 0.0031 28.2 6.8 85 156-240 150-237 (408)
52 COG5024 Cyclin [Cell division 33.2 62 0.0013 31.8 4.3 76 166-241 228-305 (440)
53 PHA02690 hypothetical protein; 32.1 77 0.0017 23.3 3.6 32 155-186 21-52 (90)
54 PF13591 MerR_2: MerR HTH fami 31.8 1.2E+02 0.0027 22.2 4.9 29 40-68 46-74 (84)
55 PF09080 K-cyclin_vir_C: K cyc 27.2 2.7E+02 0.0059 20.9 6.3 66 172-240 26-99 (106)
No 1
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=100.00 E-value=1.1e-52 Score=375.10 Aligned_cols=271 Identities=48% Similarity=0.793 Sum_probs=249.2
Q ss_pred HHhcCCCccCCCCHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccC
Q 021552 15 QLKDSPSRKDGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEES 94 (311)
Q Consensus 15 ~l~~~pS~~~gi~~~~e~~~R~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~ 94 (311)
.|..+||..||++.+.|..+|.-||+||++.|..|+||+.+++|++++|+|||..+++..+++..+++||++||+|+||.
T Consensus 3 ~i~~~~s~qd~l~~e~e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~ 82 (367)
T KOG0835|consen 3 KIDSTPSLQDGLSLETEEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEE 82 (367)
T ss_pred cccCchhhhcccccchHHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccc
Confidence 46678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHhhhhccCCCccccccchHHHHHHHHHHHHHHHHHHHHcCceeeecChHHHHHHHHHHcCCC--HHHH
Q 021552 95 PRKARQVIIVFHRMECRREGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETP--LELR 172 (311)
Q Consensus 95 ~~~l~~i~~v~~~~~~~~~~~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~v~~P~~~l~~~l~~l~~~--~~l~ 172 (311)
|+++++|++|++++.++++..+.++. .....|..++..++.+|+.||++|||+++|.|||+++..|++.|+++ .++.
T Consensus 83 Prr~rdVinVFh~L~~r~~~~~~~~~-~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~~l~ 161 (367)
T KOG0835|consen 83 PRRIRDVINVFHYLEQRRESEAAEHL-ILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNLKLL 161 (367)
T ss_pred cccHhHHHHHHHHHHHHHhccCcchh-hhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCchhHH
Confidence 99999999999999998887777766 56678888999999999999999999999999999999999999986 4579
Q ss_pred HHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHHhhcC--CCCccccc
Q 021552 173 QEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAHLYSL--PKAKYIPV 250 (311)
Q Consensus 173 ~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~~~~~~~l~~~~~~il~ly~~--~k~~~~~~ 250 (311)
|.+|+|+||+++|++|+.|+|+.|||||||+|++.+++++|..++||.+|++++++++++|..++.+|.. ++...+.+
T Consensus 162 Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ic~~l~~lY~~~~p~~~li~~ 241 (367)
T KOG0835|consen 162 QAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEICYRLIPLYKRAKPDETLIEA 241 (367)
T ss_pred HHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHHHHHHHHHHHhcccCHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999998 78888899
Q ss_pred cCCCCcccccCCCCCCCCCCCCcccccCCCCCCCCCcCCC
Q 021552 251 CKDGTSFTFSSKTVDSQPQSTPKEVLQSSPQANNHTTFPI 290 (311)
Q Consensus 251 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 290 (311)
+.+..++.+++-+...+.+..+++.- ++.+.++-++
T Consensus 242 ~vd~~k~~~~da~~k~~~~~ds~~~l----~g~~~a~~~~ 277 (367)
T KOG0835|consen 242 FVDRLKRKFSDASGKAKGANDSASLL----GGFAPAVDPS 277 (367)
T ss_pred HHHHhhHHHHhccCCccchhhHHHhh----cccccccCCC
Confidence 99998888888888777777655543 4455554444
No 2
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=2.1e-50 Score=369.93 Aligned_cols=234 Identities=39% Similarity=0.689 Sum_probs=218.5
Q ss_pred cCCCcccCHHHHh-cCCCccCCCCHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHH
Q 021552 5 AIDNFYLTDEQLK-DSPSRKDGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAAS 83 (311)
Q Consensus 5 ~~~~wl~t~e~l~-~~pS~~~gi~~~~e~~~R~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~a 83 (311)
....|||+++|++ ++||+++|++.+.|...|..++.||+++|.+|++++.|+++|++||||||+.++++.++++.+|++
T Consensus 8 ~~~~w~~s~e~~~~~tpSr~~g~~~~~E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~s 87 (323)
T KOG0834|consen 8 ETSRWYFSKEQLEENTPSRRDGIDLKKELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAAS 87 (323)
T ss_pred cccccccCHHHHccCChhhccCCchhHHHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHH
Confidence 4678999999997 899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhhccCcccHHHHHHHHHHhhhhccCCCccccccchHHHHHHHHHHHHHHHHHHHHcCceeeecChHHHHHHHHH
Q 021552 84 SVWLASKLEESPRKARQVIIVFHRMECRREGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLA 163 (311)
Q Consensus 84 cLfLA~K~EE~~~~l~~i~~v~~~~~~~~~~~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~v~~P~~~l~~~l~ 163 (311)
|||||+|+||+|++++||+.++++..++.+ ....+.|++.++.|+.+|..||++|+|||++.|||+||.+|++
T Consensus 88 clfLAgKvEetp~kl~dIi~~s~~~~~~~~-------~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k 160 (323)
T KOG0834|consen 88 CLFLAGKVEETPRKLEDIIKVSYRYLNPKD-------LELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLK 160 (323)
T ss_pred HHHHHhhcccCcccHHHHHHHHHHHcCccc-------ccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHH
Confidence 999999999999999999999998876533 2356789999999999999999999999999999999999999
Q ss_pred HcCCCH----HHHHHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCCCCCC--Ccccccccc--CCHHHHHHHHHH
Q 021552 164 TLETPL----ELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPE--NPPWWKAFD--AEKSGIDEVCRV 235 (311)
Q Consensus 164 ~l~~~~----~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~~lp~--~~~w~~~~~--~~~~~l~~~~~~ 235 (311)
.++... .+.+.||+++||++++.+||+|+|.+||+|||++|++..|..+|. ...||..++ ++.+++.+++..
T Consensus 161 ~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~ 240 (323)
T KOG0834|consen 161 KLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHE 240 (323)
T ss_pred HhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHH
Confidence 998765 489999999999999999999999999999999999999987764 347999999 999999999999
Q ss_pred HHHhhcCCCC
Q 021552 236 LAHLYSLPKA 245 (311)
Q Consensus 236 il~ly~~~k~ 245 (311)
++++|++...
T Consensus 241 ~l~~y~~~~~ 250 (323)
T KOG0834|consen 241 FLDLYEQTPQ 250 (323)
T ss_pred HHHHHhhccc
Confidence 9999986443
No 3
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=100.00 E-value=1.2e-39 Score=299.40 Aligned_cols=216 Identities=19% Similarity=0.288 Sum_probs=184.4
Q ss_pred ccCCCcccC-HHHHhcCC-------------------CccCCCCHHHHHHHHHHHHHHHHHHHHHcC--CCHHHHHHHHH
Q 021552 4 TAIDNFYLT-DEQLKDSP-------------------SRKDGIDEATETTLRIYGCDLIQESGILLK--LPQAVMATGQV 61 (311)
Q Consensus 4 ~~~~~wl~t-~e~l~~~p-------------------S~~~gi~~~~e~~~R~~~~~~I~~v~~~L~--L~~~t~~tA~~ 61 (311)
||..+|.|| +++|.... ....+++.++|..+|.+++.+|+++|..|+ ||+.|++||++
T Consensus 5 tQ~r~W~F~~~~~L~~~R~~~N~~~~~~~~~~~~~~~~~~~~Lt~eeE~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAiv 84 (305)
T TIGR00569 5 SQKRHWTFTSEEQLQEKRADANAKFREAHEEEEKVLEAKPIFLTPEEELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIM 84 (305)
T ss_pred cccccCcCCCHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHH
Confidence 788899999 88875221 123489999999999999999999999999 99999999999
Q ss_pred HHHHhhhcCCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHHHHhhhhccCCCccccccchHHHHHHHHHHHHHHHHH
Q 021552 62 LFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGLPIEHLDLFSKKFSELKMEMSRTERHI 141 (311)
Q Consensus 62 ~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~~~~~~~~~~~p~~~~~~~~~~y~~~~~~I~~~E~~I 141 (311)
||||||.++++.++++++|++||||||||+||.++++++++.... +.+...+++|+.+|..|
T Consensus 85 yf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~------------------~~~~~~~~~Il~~E~~l 146 (305)
T TIGR00569 85 YFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLK------------------ETPLKALEQVLEYELLL 146 (305)
T ss_pred HHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhcc------------------CCchhhHHHHHHHHHHH
Confidence 999999999999999999999999999999999999998876321 01123668999999999
Q ss_pred HHHcCceeeecChHHHHHHHHHHcC-------CCHHHHHHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCCCCCC
Q 021552 142 LKEMGFVCHVEHPHKFISNYLATLE-------TPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPE 214 (311)
Q Consensus 142 L~~L~F~l~v~~P~~~l~~~l~~l~-------~~~~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~~lp~ 214 (311)
|++|||+|.++|||+++..|+..++ ..+.+.+.||.++||+++|++|+.|+|++||+||||+|++.+|.++|.
T Consensus 147 L~~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAAI~lA~~~~~~~l~~ 226 (305)
T TIGR00569 147 IQQLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAGLNMES 226 (305)
T ss_pred HHHCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHHHHHHHHHHHHHhCCCCcc
Confidence 9999999999999999999997553 235688999999999999999999999999999999999999999987
Q ss_pred CccccccccC--CHHHHHHHHHHHHHh
Q 021552 215 NPPWWKAFDA--EKSGIDEVCRVLAHL 239 (311)
Q Consensus 215 ~~~w~~~~~~--~~~~l~~~~~~il~l 239 (311)
.. | +.++. +.+++..++..|.++
T Consensus 227 ~~-~-e~~~~~~~~~~~~~l~~~~~~~ 251 (305)
T TIGR00569 227 YL-T-EQLSVPGNREELPQLIDIMREL 251 (305)
T ss_pred cc-h-hhhcccccHHHHHHHHHHHHHH
Confidence 54 4 77876 556555544444433
No 4
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=100.00 E-value=1.7e-40 Score=284.11 Aligned_cols=232 Identities=25% Similarity=0.442 Sum_probs=202.1
Q ss_pred ccCCCcccCHHHHh-cCCCccCCCCHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHH
Q 021552 4 TAIDNFYLTDEQLK-DSPSRKDGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAA 82 (311)
Q Consensus 4 ~~~~~wl~t~e~l~-~~pS~~~gi~~~~e~~~R~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~ 82 (311)
|+.-+|+|+++++. ..|--..|++.++..+++.+..+.|+.+|++++++|++++||++||+|||.++|++++++.+++.
T Consensus 9 Sh~~qwl~dk~el~k~r~~D~r~l~~d~~~~l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~ 88 (264)
T KOG0794|consen 9 SHYQQWLLDKTELLKERQLDLRGLSEDEYSKLKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAP 88 (264)
T ss_pred hhhhhHhcCHHHHhhhccchhhcccHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHH
Confidence 45567999999995 33333568999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhccCc-ccHHHHHHHHHHhhhhccCCCccccccchHHHHHHHHHHHHHHHHHHHHcCceeeecChHHHHHHH
Q 021552 83 SSVWLASKLEESP-RKARQVIIVFHRMECRREGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNY 161 (311)
Q Consensus 83 acLfLA~K~EE~~-~~l~~i~~v~~~~~~~~~~~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~v~~P~~~l~~~ 161 (311)
||+|||||+||+| ...+-++..+..+..+-+ .. ++.+......|+++|..+|+.|++-|.|.|||+-|..+
T Consensus 89 TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~-~~-------~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~ 160 (264)
T KOG0794|consen 89 TCLYLACKVEECPIVHIRLLVNEAKVLKTRFS-YW-------PEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQF 160 (264)
T ss_pred HHHHHHhhhhhcchHHHHHHHHHHHHHhhhcc-cc-------hhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHH
Confidence 9999999999998 556666665555433322 11 12222244789999999999999999999999999999
Q ss_pred HHHcCC-CHHHHHHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHHhh
Q 021552 162 LATLET-PLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAHLY 240 (311)
Q Consensus 162 l~~l~~-~~~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~~~~~~~l~~~~~~il~ly 240 (311)
++..|. +.++.+.+|.++||++++++||.|+|..||.|||++|+...|.+.| +.|...+.+|.++|.+|+.+|+++|
T Consensus 161 ~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~~~--~~w~~el~vD~ekV~~~v~~I~~lY 238 (264)
T KOG0794|consen 161 VQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKDIP--KAWFAELSVDMEKVKDIVQEILKLY 238 (264)
T ss_pred HHHhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCChH--HHHHHHHhccHHHHHHHHHHHHHHH
Confidence 999998 6779999999999999999999999999999999999999998877 4699999999999999999999999
Q ss_pred cCCCC
Q 021552 241 SLPKA 245 (311)
Q Consensus 241 ~~~k~ 245 (311)
.+.+.
T Consensus 239 e~wk~ 243 (264)
T KOG0794|consen 239 ELWKI 243 (264)
T ss_pred HHHhh
Confidence 87654
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=2.8e-32 Score=244.65 Aligned_cols=188 Identities=29% Similarity=0.464 Sum_probs=161.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHH
Q 021552 26 IDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVF 105 (311)
Q Consensus 26 i~~~~e~~~R~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~ 105 (311)
++-+.|..+|.++..||+.+|.+|++|+.+++||+.+|+||+.+.++++.+++.++.||+|||||+||+++.++-.....
T Consensus 36 l~~~~e~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~ 115 (297)
T COG5333 36 LTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEA 115 (297)
T ss_pred cchhhhhhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHh
Confidence 66688999999999999999999999999999999999999999999999999999999999999999865554333322
Q ss_pred HHhhhhccCCCccccccchHHHHHHHHHHHHHHHHHHHHcCceeeecChHHHHHHHHHHcCCC--HHHHHHHHHHHHhhh
Q 021552 106 HRMECRREGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETP--LELRQEAWNLANDSL 183 (311)
Q Consensus 106 ~~~~~~~~~~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~v~~P~~~l~~~l~~l~~~--~~l~~~A~~l~~ds~ 183 (311)
+ +..++.++..|++|+.+|..+|++|+||+.|+|||.++..|++.+... .++.+.||.++||++
T Consensus 116 ~--------------~~~se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~ 181 (297)
T COG5333 116 R--------------DLWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDAL 181 (297)
T ss_pred h--------------ccccccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhh
Confidence 2 223456667899999999999999999999999999999999988754 369999999999999
Q ss_pred cCcccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHHHH
Q 021552 184 RTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGI 229 (311)
Q Consensus 184 ~t~~~l~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~~~~~~~l 229 (311)
++++|+.|+|.+||+||+++|+..+|.+.+. .|......+.+++
T Consensus 182 ~t~~~llypphiIA~a~l~ia~~~~~~~~~~--~~~~~s~~~~e~v 225 (297)
T COG5333 182 RTDLCLLYPPHIIALAALLIACEVLGMPIIK--LLDFVSYETKEEV 225 (297)
T ss_pred hceeeeecChHHHHHHHHHHHHHhcCCccch--hhccccccchhHH
Confidence 9999999999999999999999999886653 2433444444433
No 6
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=99.91 E-value=3.9e-23 Score=189.98 Aligned_cols=166 Identities=14% Similarity=0.192 Sum_probs=136.7
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccch---HHHHHHHHHHHhhhhccCc-ccH
Q 021552 23 KDGIDEATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFD---VKIVAASSVWLASKLEESP-RKA 98 (311)
Q Consensus 23 ~~gi~~~~e~~~R~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~---~~lva~acLfLA~K~EE~~-~~l 98 (311)
+-+++...--.+|..+++||.++|..+++...|...|++|+|||++.+.+.+.+ .+++|+|||+||+|+||+. +-+
T Consensus 66 ~~~~~~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll 145 (335)
T KOG0656|consen 66 FLCVQKLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLL 145 (335)
T ss_pred hhhcccccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchh
Confidence 344444444566999999999999999999999999999999999999999988 9999999999999999985 444
Q ss_pred HHHHHHHHHhhhhccCCCccccccchHHHHHHHHHHHHHHHHHHHHcCceeeecChHHHHHHHHHHcCCC----HHHHHH
Q 021552 99 RQVIIVFHRMECRREGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETP----LELRQE 174 (311)
Q Consensus 99 ~~i~~v~~~~~~~~~~~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~v~~P~~~l~~~l~~l~~~----~~l~~~ 174 (311)
-|+.... ..|-...+.|.+||..||.+|+|+++..+|+.|+..|+.+++.. ..+...
T Consensus 146 ~dl~v~~-------------------~~~~feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~~~~~~~ 206 (335)
T KOG0656|consen 146 ADLQVEY-------------------TDNVFEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNKHLFLKH 206 (335)
T ss_pred hhhhhcc-------------------ccccccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcccchHHHHHHH
Confidence 4443311 12334568999999999999999999999999999999999873 456667
Q ss_pred HHHHHHhhhcCcccccCChHHHHHHHHHHHHHH
Q 021552 175 AWNLANDSLRTTLCVRFKSEVVACGVVYAAARR 207 (311)
Q Consensus 175 A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~ 207 (311)
+..++-......-++.|+|++||+|++..+...
T Consensus 207 ~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~~~ 239 (335)
T KOG0656|consen 207 ASLFLLSVITDIKFLEYPPSVIAAAAILSVSAS 239 (335)
T ss_pred HHHHHHHHhhhhhhhcCChHHHHHHHHHHHHHh
Confidence 777776666666799999999999988666543
No 7
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.90 E-value=2.1e-22 Score=187.11 Aligned_cols=182 Identities=15% Similarity=0.195 Sum_probs=165.7
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHHHHhhhhccCC
Q 021552 36 IYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGL 115 (311)
Q Consensus 36 ~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~~~~~~~~~~~ 115 (311)
..+...|.++|..|+||..+..+|..+|++++..+.+++.+...+++||||+|||.|+.|++++|+..+++-
T Consensus 123 ~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~v-------- 194 (310)
T PRK00423 123 AFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRV-------- 194 (310)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCC--------
Confidence 557789999999999999999999999999999999999999999999999999999999999999886541
Q ss_pred CccccccchHHHHHHHHHHHHHHHHHHHHcCceeeecChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcCcccccCChHH
Q 021552 116 PIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEV 195 (311)
Q Consensus 116 p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~v~~P~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~l~~~P~~ 195 (311)
.+.+|.+.++.|++.|++++...+|++|+.+|+..|++++++.+.|+.+++++....++.+..|..
T Consensus 195 --------------~~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~s 260 (310)
T PRK00423 195 --------------SRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTG 260 (310)
T ss_pred --------------CHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHH
Confidence 346888899999999999999999999999999999999999999999999999888899999999
Q ss_pred HHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHHhh
Q 021552 196 VACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAHLY 240 (311)
Q Consensus 196 IA~AaI~lA~~~~~~~lp~~~~w~~~~~~~~~~l~~~~~~il~ly 240 (311)
||+||||+|++.+|.+... +....+.+++...|....+.|....
T Consensus 261 IAAAaIYlA~~~~g~~~t~-keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 261 LAAAAIYIASLLLGERRTQ-REVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred HHHHHHHHHHHHhCCCCCH-HHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 9999999999999987643 3467778899999999888887644
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=99.88 E-value=5e-23 Score=183.54 Aligned_cols=189 Identities=23% Similarity=0.301 Sum_probs=143.0
Q ss_pred ccCCCcccCHHHHhcCC---Ccc-------CC---------CCHHHHHHHHHHHHHHHHHHHHHc--CCCHHHHHHHHHH
Q 021552 4 TAIDNFYLTDEQLKDSP---SRK-------DG---------IDEATETTLRIYGCDLIQESGILL--KLPQAVMATGQVL 62 (311)
Q Consensus 4 ~~~~~wl~t~e~l~~~p---S~~-------~g---------i~~~~e~~~R~~~~~~I~~v~~~L--~L~~~t~~tA~~~ 62 (311)
||-..|.||++||.... +.+ .| +.++.+..+-.....-+.+.+..+ +||..|+.||+.+
T Consensus 6 sq~r~W~fte~qL~e~r~~~N~k~i~~~ee~~~~~~~~e~~v~~~ee~tl~k~~E~~l~~f~~k~~p~lp~~Vv~TA~~f 85 (325)
T KOG2496|consen 6 SQYRKWIFTEEQLAERRVDANQKAIQMLEEEAHNLDENEVFVLEAEELTLTKEEELSLVNFYSKFKPNLPTSVVSTAIEF 85 (325)
T ss_pred hhhhcccccHHHHHHHHHHHHHHHHHHHHHhccCCCccchhccccccccccHHHHHHHHHHHHHhcCCCchHHHHHHHHH
Confidence 56778999999996431 000 01 111222333333334444555544 5899999999999
Q ss_pred HHHhhhcCCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHHHHhhhhccCCCccccccchHHHHHHHHHHHHHHHHHH
Q 021552 63 FHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGLPIEHLDLFSKKFSELKMEMSRTERHIL 142 (311)
Q Consensus 63 ~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~~~~~~~~~~~p~~~~~~~~~~y~~~~~~I~~~E~~IL 142 (311)
|+|||..+++.++++..|.+||+|||||+||..+.+.+++.... |. -+...+.|+..|..+|
T Consensus 86 FkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~-------~~-----------~~k~~e~vLk~E~~ll 147 (325)
T KOG2496|consen 86 FKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMN-------GR-----------KWKTHEIVLKYEFLLL 147 (325)
T ss_pred HHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhcc-------Cc-----------ccccHHHHHhchHHHH
Confidence 99999999999999999999999999999999999999987433 00 1235689999999999
Q ss_pred HHcCceeeecChHHHHHHHHHHcCC------CHH-HHHH--HHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCC
Q 021552 143 KEMGFVCHVEHPHKFISNYLATLET------PLE-LRQE--AWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQI 210 (311)
Q Consensus 143 ~~L~F~l~v~~P~~~l~~~l~~l~~------~~~-l~~~--A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~ 210 (311)
+.|+|++.+.+||+.+..|+..++. +.+ +... ...+++.+++++.++.|+|++||+|||..|....|.
T Consensus 148 qsL~f~L~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a~~~~~~ 224 (325)
T KOG2496|consen 148 QSLKFSLTVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHAAGRTGE 224 (325)
T ss_pred HhhhhhheecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHHhccccc
Confidence 9999999999999999999876542 222 2222 258999999999999999999999999666555554
No 9
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=99.87 E-value=2.4e-21 Score=185.43 Aligned_cols=188 Identities=19% Similarity=0.194 Sum_probs=158.3
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHH-HhhhhccCc-ccHHHHHHHHHHh
Q 021552 31 ETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVW-LASKLEESP-RKARQVIIVFHRM 108 (311)
Q Consensus 31 e~~~R~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLf-LA~K~EE~~-~~l~~i~~v~~~~ 108 (311)
-..+|...++|+.++...++|..+|+++|++++|||+.+..+.....++|+++||| ||||+||.. +.+.|++.+++.
T Consensus 154 ~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~- 232 (391)
T KOG0653|consen 154 RAKMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDG- 232 (391)
T ss_pred cHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCC-
Confidence 35799999999999999999999999999999999999988999999999999977 999999954 446666654432
Q ss_pred hhhccCCCccccccchHHHHHHHHHHHHHHHHHHHHcCceeeecChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcCccc
Q 021552 109 ECRREGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELRQEAWNLANDSLRTTLC 188 (311)
Q Consensus 109 ~~~~~~~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~v~~P~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~ 188 (311)
.| .+++|+.||..||.+|+|++.+++|+.|+++|.+....+.+....+.++++.++...-+
T Consensus 233 -----------------~~--s~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d~~~~~~~k~~~El~l~d~~~ 293 (391)
T KOG0653|consen 233 -----------------AY--SREEILRMEKYILNVLEFDLSVPTPLSFLRRFLKAADYDIKTRTLVKYLLELSLCDYSM 293 (391)
T ss_pred -----------------cc--chHHHHHHHHHHHhccCeeecCCchHHHHHHHHHhhhcchhHHHHHHHHHHHHHhhhHH
Confidence 23 56999999999999999999999999999999999998888888999999999998889
Q ss_pred ccCChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHH
Q 021552 189 VRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAH 238 (311)
Q Consensus 189 l~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~~~~~~~l~~~~~~il~ 238 (311)
+.++|+.+|+|+.+++.++.+.+-.|...-....|....++.++.+.+..
T Consensus 294 ~~~~~s~~aaa~~~~~~~~~~~~~~w~~~~~~~sg~~~~~~~~~~~~~~~ 343 (391)
T KOG0653|consen 294 LSIPPSSSAAASFTLALRMLSKGDVWSPTLEHYSGYSESYLFECARSLSA 343 (391)
T ss_pred hccCcHHHHHHHHHHHHHHhccCCccCCCCeeccCCCcHHHHHHHHHHHH
Confidence 99999999999999999998875433333333445554466666665555
No 10
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=99.84 E-value=5e-20 Score=175.34 Aligned_cols=191 Identities=15% Similarity=0.153 Sum_probs=166.5
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccC-cccHHHHHHHHHHhhh
Q 021552 32 TTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEES-PRKARQVIIVFHRMEC 110 (311)
Q Consensus 32 ~~~R~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~-~~~l~~i~~v~~~~~~ 110 (311)
..+|..+++||.++...|++-++|+++|++++|||++.+.+.-...++||++|||+|||+||. .+.++++..++....
T Consensus 210 ~~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~- 288 (440)
T COG5024 210 WSMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAF- 288 (440)
T ss_pred HhHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccc-
Confidence 489999999999999999999999999999999999999999999999999999999999996 455777777655321
Q ss_pred hccCCCccccccchHHHHHHHHHHHHHHHHHHHHcCceeeecChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcCccccc
Q 021552 111 RREGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVR 190 (311)
Q Consensus 111 ~~~~~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~v~~P~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~l~ 190 (311)
.+++|+.+|+.+|..|+|++..|.|+.|++++-+.-+.+-..+-.+.+++.-+....-+++
T Consensus 289 -------------------t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka~dyd~~srt~~k~~~e~s~~~~~f~~ 349 (440)
T COG5024 289 -------------------TRDDIIRAERYMLEVLDFNISWPSPMSFLRRISKASDYDIFSRTPAKFSSEISPVDYKFIQ 349 (440)
T ss_pred -------------------cHHHHHHHHHHHhhhcccccCCCChHHHHHHHHhhcccchhhhhhHhhhCCchHhhhhhcc
Confidence 5699999999999999999999999999999988887777777788888888888788889
Q ss_pred CChHHHHHHHHHHHHHHcCCCCCCCccccccc----c-CCHHHHHHHHHHHHHhhcCCCCcc
Q 021552 191 FKSEVVACGVVYAAARRFQIPLPENPPWWKAF----D-AEKSGIDEVCRVLAHLYSLPKAKY 247 (311)
Q Consensus 191 ~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~----~-~~~~~l~~~~~~il~ly~~~k~~~ 247 (311)
++|+.+|+||.|+|.+.++..- |-..+ | ++.+++..++..+++....+..++
T Consensus 350 ~~~S~~~aaa~~~s~~~~~~~~-----w~~~l~~ySg~y~~~~l~~~~~~~~~~l~~~~~~~ 406 (440)
T COG5024 350 ISPSWCAAAAMYLSRKILSQNQ-----WDRTLIHYSGNYTNPDLKPLNESNKENLQNPSVHH 406 (440)
T ss_pred CCchHHHHHHHHHHHhhhccCC-----CCccccccCCCCCchhHHHHHHHHHHHhcccchhh
Confidence 9999999999999999998632 44444 4 677789999999999888777664
No 11
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=99.83 E-value=4.1e-20 Score=166.30 Aligned_cols=183 Identities=18% Similarity=0.160 Sum_probs=144.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhc-CCcccchHHHHHHHHHHHhhhhcc-CcccHHHHHHHHH
Q 021552 29 ATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCK-RSFARFDVKIVAASSVWLASKLEE-SPRKARQVIIVFH 106 (311)
Q Consensus 29 ~~e~~~R~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~-~s~~~~~~~lva~acLfLA~K~EE-~~~~l~~i~~v~~ 106 (311)
..+-++|..+.+|+.+||..++|..+|.+.|+-|||||+.. +.+.+..++++++||||+|+|+|| .|+++.++..+..
T Consensus 139 dlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTD 218 (408)
T KOG0655|consen 139 DLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTD 218 (408)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeecc
Confidence 34578999999999999999999999999999999999976 566788999999999999999999 5889988877654
Q ss_pred HhhhhccCCCccccccchHHHHHHHHHHHHHHHHHHHHcCceeeecChHHHHHHHHHHcCCC------------HHHHHH
Q 021552 107 RMECRREGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETP------------LELRQE 174 (311)
Q Consensus 107 ~~~~~~~~~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~v~~P~~~l~~~l~~l~~~------------~~l~~~ 174 (311)
.. ...++|+.||..||++|+|++...+...+|.-|++..+.+ .+..|.
T Consensus 219 gA--------------------cs~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqi 278 (408)
T KOG0655|consen 219 GA--------------------CSEDDILTMELIILKALKWELSPITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQI 278 (408)
T ss_pred Cc--------------------cchHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcCCCCceeccccchHHHHHH
Confidence 22 1448999999999999999999999999999999987542 233444
Q ss_pred HHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHHhh
Q 021552 175 AWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAHLY 240 (311)
Q Consensus 175 A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~~~~~~~l~~~~~~il~ly 240 (311)
|. ++......--++.|+..+|||||++.-....- -.++-|..+..|++|++-+.-+.
T Consensus 279 aq-lLDlc~ldids~~fsYrilaAAal~h~~s~e~--------v~kaSG~~w~~ie~cv~wm~Pf~ 335 (408)
T KOG0655|consen 279 AQ-LLDLCILDIDSLEFSYRILAAAALCHFTSIEV--------VKKASGLEWDSIEECVDWMVPFV 335 (408)
T ss_pred HH-HHHHHHhccccccchHHHHHHHHHHHHhHHHH--------HHHcccccHHHHHHHHHHHHHHH
Confidence 33 34444444458899999999999987654211 23455667778888887665443
No 12
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.72 E-value=3e-16 Score=140.00 Aligned_cols=180 Identities=14% Similarity=0.165 Sum_probs=153.8
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHHHHhhhhccC
Q 021552 35 RIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREG 114 (311)
Q Consensus 35 R~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~~~~~~~~~~ 114 (311)
...+...|..+++.++||..+...|..+|+++...+.+++.+...+++||||+||+-++.||++++|..+.+ +
T Consensus 104 ~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~an-v------ 176 (308)
T KOG1597|consen 104 LKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVAN-V------ 176 (308)
T ss_pred HHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHHc-C------
Confidence 345678899999999999999999999999999999999999999999999999999999999999998876 3
Q ss_pred CCccccccchHHHHHHHHHHHHHHHHHHHHcCceeeec--ChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcCcccccCC
Q 021552 115 LPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVE--HPHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFK 192 (311)
Q Consensus 115 ~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~v~--~P~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~l~~~ 192 (311)
.+++|-++-..|++.|+-+...- +.-+|+.|||..|++++++...|-+++.-+-.-+.+-+..
T Consensus 177 ---------------~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRs 241 (308)
T KOG1597|consen 177 ---------------SKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRS 241 (308)
T ss_pred ---------------CHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCC
Confidence 34667777788888887766544 4789999999999999999999999998887777777799
Q ss_pred hHHHHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHH
Q 021552 193 SEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLA 237 (311)
Q Consensus 193 P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~~~~~~~l~~~~~~il 237 (311)
|-.||+|+||+++++...+.+. ...-++.|+.+-.|...++.|.
T Consensus 242 PiSIAAa~IYmisqls~~kkt~-keI~~vtgVaE~TIr~sYK~Ly 285 (308)
T KOG1597|consen 242 PISIAAAAIYMISQLSDEKKTQ-KEIGEVTGVAEVTIRNSYKDLY 285 (308)
T ss_pred chhHHHHHHHHHHHhccCcccH-HHHHHHhhhhHHHHHHHHHHHh
Confidence 9999999999999998865442 3355667787777877777543
No 13
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=99.71 E-value=3.9e-17 Score=151.75 Aligned_cols=205 Identities=17% Similarity=0.204 Sum_probs=178.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccC-cccHHHHHHHHHH
Q 021552 29 ATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEES-PRKARQVIIVFHR 107 (311)
Q Consensus 29 ~~e~~~R~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~-~~~l~~i~~v~~~ 107 (311)
+....+|..+++|..++++.+++.-++++.+.++.+||+......+...++++.+|.++|+|+||. ++.+.+++...++
T Consensus 131 d~t~smrgilvdwlvevsee~r~~~e~l~ls~~~~drfl~~~~~~~~k~ql~g~s~m~I~sk~ee~~~~~~~ef~~itd~ 210 (359)
T KOG0654|consen 131 DITPSMRGILVDWLVEVSEEYRLTFETLYLSVNYRDRFLSYKEVNKQKLQLVGISAMLIASKYEEIKEPRVEEFCYITDN 210 (359)
T ss_pred CCCcchhhhhhhhhhHHHHHHHhhhhheeecHHHHHHHhccCccHHHHHHHhCcccceeeccchhhcchHHHHHHhhhhh
Confidence 334678999999999999999999999999999999999999999999999999999999999995 5677877775543
Q ss_pred hhhhccCCCccccccchHHHHHHHHHHHHHHHHHHHHcCceeeecChHHHHHHHHHHcC-CCHHHHHHHHHHHHhhhcCc
Q 021552 108 MECRREGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLE-TPLELRQEAWNLANDSLRTT 186 (311)
Q Consensus 108 ~~~~~~~~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~v~~P~~~l~~~l~~l~-~~~~l~~~A~~l~~ds~~t~ 186 (311)
.| ++.++..+|..+|..+.|++..++...|+.+|+.... ...++...+.++.+.++...
T Consensus 211 ------------------ty--~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~~~~~~~~~~e~~~~yl~elsll~~ 270 (359)
T KOG0654|consen 211 ------------------TY--TYWQVLRMEIDILNALTFELVRPTSKTFLRRFLRVAQTPELQVEPLANYLTELSLLDY 270 (359)
T ss_pred ------------------hh--HHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHHhhcchhHHHHHHHHHHHHhhhhhH
Confidence 22 5689999999999999999999999999999987654 34677889999999999888
Q ss_pred ccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHHhhcCCCCccccccCCCC
Q 021552 187 LCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAHLYSLPKAKYIPVCKDGT 255 (311)
Q Consensus 187 ~~l~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~~~~~~~l~~~~~~il~ly~~~k~~~~~~~~~~~ 255 (311)
.+++|.|+.||+||+++|...++ .-||++..++..+++.+++..|+..|. +|.+.++..++..+.+.
T Consensus 271 ~~l~y~PSliAasAv~lA~~~~~-~~pW~~~L~~~T~y~~edl~~~v~~L~-~~l~~~~~~l~air~ky 337 (359)
T KOG0654|consen 271 IFLKYLPSLIAASAVFLARLTLD-FHPWNQTLEDYTGYKAEDLKPCVLDLH-LYLNASGTDLPAIREKY 337 (359)
T ss_pred HHhccChHHHHHHHHHHHHhhcc-CCCCchhhHHhhcccHHHHHHHHHHHh-cccCCCCCchHHHHHHh
Confidence 89999999999999999999888 667777777888999999999999999 88877777665544443
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=99.71 E-value=5.7e-17 Score=131.00 Aligned_cols=102 Identities=29% Similarity=0.420 Sum_probs=85.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccC-cccHHHHHHHHHH
Q 021552 29 ATETTLRIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEES-PRKARQVIIVFHR 107 (311)
Q Consensus 29 ~~e~~~R~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~-~~~l~~i~~v~~~ 107 (311)
+.....|...++||.+++..++++..|.++|+.|||||+.+..+...+++++++||+++|||+||. ++++.+++.....
T Consensus 25 ~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~ 104 (127)
T PF00134_consen 25 EITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDN 104 (127)
T ss_dssp SHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTT
T ss_pred hcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcC
Confidence 445588999999999999999999999999999999999999999999999999999999999997 7788888775421
Q ss_pred hhhhccCCCccccccchHHHHHHHHHHHHHHHHHHHHcCceee
Q 021552 108 MECRREGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCH 150 (311)
Q Consensus 108 ~~~~~~~~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~ 150 (311)
.| .+++++.+|..||++|||+++
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 12 469999999999999999985
No 15
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.67 E-value=2.4e-15 Score=137.21 Aligned_cols=182 Identities=19% Similarity=0.248 Sum_probs=160.8
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHHHHhhhhccC
Q 021552 35 RIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREG 114 (311)
Q Consensus 35 R~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~~~~~~~~~~ 114 (311)
...+...|..++..|+||..+..+|..+|.+.+.++..+..+..-+++||+|+||+.++.|+++.++..+.. +
T Consensus 97 l~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~-V------ 169 (285)
T COG1405 97 LITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALG-V------ 169 (285)
T ss_pred HHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHC-C------
Confidence 345778899999999999999999999999999999999999999999999999999999999999998655 1
Q ss_pred CCccccccchHHHHHHHHHHHHHHHHHHHHcCceeeecChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcCcccccCChH
Q 021552 115 LPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVEHPHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSE 194 (311)
Q Consensus 115 ~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~v~~P~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~l~~~P~ 194 (311)
.+.+|.++.+.+.+.|+-.+....|..|+.+|+..|+++.++...|..++..+....+..+-.|.
T Consensus 170 ---------------~~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~ 234 (285)
T COG1405 170 ---------------SKKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPA 234 (285)
T ss_pred ---------------CHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCch
Confidence 34788889999999999999999999999999999999999999999999999988888899999
Q ss_pred HHHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHHh
Q 021552 195 VVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAHL 239 (311)
Q Consensus 195 ~IA~AaI~lA~~~~~~~lp~~~~w~~~~~~~~~~l~~~~~~il~l 239 (311)
.||+||||+|+.++|.+... ..--.+.++++..|..-...|.+.
T Consensus 235 glAaaaiy~as~l~~~~~tq-~eva~v~~vtevTIrnrykel~~~ 278 (285)
T COG1405 235 GLAAAAIYLASLLLGERRTQ-KEVAKVAGVTEVTIRNRYKELADA 278 (285)
T ss_pred hHHHHHHHHHHHHhCCchHH-HHHHHHhCCeeeHHHHHHHHHHHh
Confidence 99999999999999965432 345567788888777777666543
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=99.44 E-value=5.2e-13 Score=99.62 Aligned_cols=87 Identities=25% Similarity=0.314 Sum_probs=77.2
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHHHHhhhhccC
Q 021552 35 RIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREG 114 (311)
Q Consensus 35 R~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~~~~~~~~~~ 114 (311)
|...++||.+++..++++..+..+|+.+++||+..+.+.+++++++++||||+|||++|.++..+++..+....
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~------ 75 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYA------ 75 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCC------
Confidence 56789999999999999999999999999999999999999999999999999999999999999998755420
Q ss_pred CCccccccchHHHHHHHHHHHHHHHHHH
Q 021552 115 LPIEHLDLFSKKFSELKMEMSRTERHIL 142 (311)
Q Consensus 115 ~p~~~~~~~~~~y~~~~~~I~~~E~~IL 142 (311)
..++|..+|..|+
T Consensus 76 ---------------~~~~i~~~e~~il 88 (88)
T cd00043 76 ---------------TEEEILRMEKLLL 88 (88)
T ss_pred ---------------CHHHHHHHHHHhC
Confidence 3478888888764
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=99.31 E-value=5.6e-12 Score=93.01 Aligned_cols=83 Identities=23% Similarity=0.374 Sum_probs=71.8
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHHHHhhhhccCCCccc
Q 021552 40 DLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREGLPIEH 119 (311)
Q Consensus 40 ~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~~~~~~~~~~~p~~~ 119 (311)
+||.+++..++++.++..+|..+++||+....+.+.+++.+|+||+|+|||++|.++..+++......
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~------------ 68 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGY------------ 68 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC------------
Confidence 48999999999999999999999999999777778999999999999999999988888887664331
Q ss_pred cccchHHHHHHHHHHHHHHHHHHH
Q 021552 120 LDLFSKKFSELKMEMSRTERHILK 143 (311)
Q Consensus 120 ~~~~~~~y~~~~~~I~~~E~~IL~ 143 (311)
..+++|..+|+.||+
T Consensus 69 ---------~~~~~i~~~~~~il~ 83 (83)
T smart00385 69 ---------FTEEEILRMEKLLLE 83 (83)
T ss_pred ---------CCHHHHHHHHHHHhC
Confidence 134789999998873
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=99.21 E-value=8.8e-12 Score=98.95 Aligned_cols=91 Identities=20% Similarity=0.224 Sum_probs=75.6
Q ss_pred cChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHH
Q 021552 152 EHPHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDE 231 (311)
Q Consensus 152 ~~P~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~~~~~~~l~~ 231 (311)
|+|+.||.+|++..+.+.++...++++++.++.+..++.|+|+.||+|||++|...++...++.+.+....|++.+++.+
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 68999999997766667889999999999999999999999999999999999999885344444455567899999999
Q ss_pred HHHHHHHhhcC
Q 021552 232 VCRVLAHLYSL 242 (311)
Q Consensus 232 ~~~~il~ly~~ 242 (311)
|++.|.+++..
T Consensus 81 c~~~i~~~~~~ 91 (118)
T PF02984_consen 81 CIELIQELLSK 91 (118)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHh
Confidence 99999999874
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=98.89 E-value=8.1e-09 Score=75.89 Aligned_cols=81 Identities=20% Similarity=0.229 Sum_probs=72.2
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccC-CHHHHHHHHH
Q 021552 156 KFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDA-EKSGIDEVCR 234 (311)
Q Consensus 156 ~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~~~-~~~~l~~~~~ 234 (311)
+|+.+++..++.++++...|+++++..+....++.++|+.||+||+|+|++..+.+ ++.+.+....+. +.+++.++.+
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 37889999999999999999999999988677788999999999999999999986 566678888888 9999999888
Q ss_pred HHH
Q 021552 235 VLA 237 (311)
Q Consensus 235 ~il 237 (311)
.|+
T Consensus 80 ~il 82 (83)
T smart00385 80 LLL 82 (83)
T ss_pred HHh
Confidence 775
No 20
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.75 E-value=5.1e-08 Score=72.28 Aligned_cols=85 Identities=20% Similarity=0.129 Sum_probs=74.1
Q ss_pred ecChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccC-CHHHH
Q 021552 151 VEHPHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDA-EKSGI 229 (311)
Q Consensus 151 v~~P~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~~~-~~~~l 229 (311)
.++|..|+.+++..++.+.++...|+.+++.++....+..++|+.||+||+++|++..+. .++.+++....+. +.+++
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~-~~~~~~~~~~~~~~~~~~i 80 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEI-PPWLKDLVHVTGYATEEEI 80 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCC-CCCHHHHhHHhCCCCHHHH
Confidence 467899999999999999999999999999999888888999999999999999999998 4445567777788 88888
Q ss_pred HHHHHHH
Q 021552 230 DEVCRVL 236 (311)
Q Consensus 230 ~~~~~~i 236 (311)
..+...+
T Consensus 81 ~~~e~~i 87 (88)
T cd00043 81 LRMEKLL 87 (88)
T ss_pred HHHHHHh
Confidence 8776654
No 21
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.74 E-value=3.8e-08 Score=95.11 Aligned_cols=155 Identities=14% Similarity=0.084 Sum_probs=122.9
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHHHHhhhhccC
Q 021552 35 RIYGCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRMECRREG 114 (311)
Q Consensus 35 R~~~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~~~~~~~~~~ 114 (311)
-..+-..|.+++..|+++. .+.+|..+|.-...++..++.....|.++|+|++|+.|.++.-+-|...+.. +
T Consensus 67 ~~n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~Lq-v------ 138 (521)
T KOG1598|consen 67 IYNARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQ-V------ 138 (521)
T ss_pred HHHHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccceE-E------
Confidence 3345678999999999999 9999999999999999999999999999999999999987644333322100 0
Q ss_pred CCccccccchHHHHHHHHHHHHHHHHHHHHcCce---eeecChHHHHHHHHHHcCC---CHHHHHHHHHHHHhhhcCccc
Q 021552 115 LPIEHLDLFSKKFSELKMEMSRTERHILKEMGFV---CHVEHPHKFISNYLATLET---PLELRQEAWNLANDSLRTTLC 188 (311)
Q Consensus 115 ~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~---l~v~~P~~~l~~~l~~l~~---~~~l~~~A~~l~~ds~~t~~~ 188 (311)
..-++-..=..|.+.|.-+ +....|.-|+.+|...|.. ++++...|..+++...+..+.
T Consensus 139 ---------------~Vy~LG~~~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~ 203 (521)
T KOG1598|consen 139 ---------------SVYDLGSNFLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQ 203 (521)
T ss_pred ---------------ehhhhhHHHHHHHHHhccccccccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHH
Confidence 0011222334556666666 6778999999999988753 367999999999999999999
Q ss_pred ccCChHHHHHHHHHHHHHHcCCCC
Q 021552 189 VRFKSEVVACGVVYAAARRFQIPL 212 (311)
Q Consensus 189 l~~~P~~IA~AaI~lA~~~~~~~l 212 (311)
....|+.|+.|||++|++.+|.+.
T Consensus 204 tGRRPsglcGAaLliAar~h~~~r 227 (521)
T KOG1598|consen 204 TGRRPSGLCGAALLIAARMHGFRR 227 (521)
T ss_pred hCCCccchhHHHHHHHHHHcCccc
Confidence 999999999999999999999764
No 22
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=98.70 E-value=9.4e-08 Score=69.48 Aligned_cols=64 Identities=19% Similarity=0.287 Sum_probs=57.5
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHH
Q 021552 42 IQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVF 105 (311)
Q Consensus 42 I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~ 105 (311)
|.++|..|+||..+..+|..++++....+-.++.++..+++||+|+||+.++.+++++++..+.
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~ 64 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAA 64 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHC
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHh
Confidence 5789999999999999999999999999989999999999999999999999999999998754
No 23
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=98.23 E-value=1.8e-06 Score=80.34 Aligned_cols=97 Identities=18% Similarity=0.237 Sum_probs=81.8
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccCc-ccHHHHHHHHHHhhhhccCCC
Q 021552 38 GCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESP-RKARQVIIVFHRMECRREGLP 116 (311)
Q Consensus 38 ~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~-~~l~~i~~v~~~~~~~~~~~p 116 (311)
.-.-|.+++...++...|+++|.+||.....+.-+.+.+..++|-|||+||+|+.+.. -.++.++.-
T Consensus 385 lKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek------------ 452 (497)
T KOG4164|consen 385 LKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEK------------ 452 (497)
T ss_pred HHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHH------------
Confidence 4456888999999999999999999999999999999999999999999999999643 234444442
Q ss_pred ccccccchHHHHHHHHHHHHHHHHHHHHcCceeeec
Q 021552 117 IEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVE 152 (311)
Q Consensus 117 ~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~v~ 152 (311)
..+.|...|.+++..|.-||-+|.|-|+++
T Consensus 453 ------~Ee~fR~nrrdLia~Ef~VlvaLefaL~~~ 482 (497)
T KOG4164|consen 453 ------LEEQFRLNRRDLIAFEFPVLVALEFALHLP 482 (497)
T ss_pred ------HHHHhcccHHhhhhhhhhHHHhhhhhccCC
Confidence 235666778999999999999999999864
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=98.16 E-value=7.1e-06 Score=59.51 Aligned_cols=69 Identities=19% Similarity=0.202 Sum_probs=53.7
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHH
Q 021552 158 ISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKS 227 (311)
Q Consensus 158 l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~~~~~~ 227 (311)
|.+|+..|++++.+.+.|..+........+.-+..|..||+||||+|++..+.+.+. .+.-+.++++..
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~-~eIa~~~~Vs~~ 69 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTL-KEIAEAAGVSEK 69 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSH-HHHHHHCTSSHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCH-HHHHHHhCCCCC
Confidence 578999999999999999999999888888888999999999999999999987653 223444444443
No 25
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=97.89 E-value=6.9e-05 Score=69.98 Aligned_cols=68 Identities=21% Similarity=0.132 Sum_probs=62.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHHH
Q 021552 39 CDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFH 106 (311)
Q Consensus 39 ~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~~ 106 (311)
.++|.++|..|+|+..+..+|..++++.....-..+.++.-+|+||+|+||+..+.++++++|..+..
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 58999999999999999999999999998877778999999999999999999999999999987643
No 26
>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=97.86 E-value=0.00019 Score=59.83 Aligned_cols=90 Identities=14% Similarity=0.129 Sum_probs=64.1
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHhhh---c--CCcccchHHHHHHHHHHHhhhhccC-cccHHHHHHHHHHhhhh
Q 021552 38 GCDLIQESGILLKLPQAVMATGQVLFHRFYC---K--RSFARFDVKIVAASSVWLASKLEES-PRKARQVIIVFHRMECR 111 (311)
Q Consensus 38 ~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~---~--~s~~~~~~~lva~acLfLA~K~EE~-~~~l~~i~~v~~~~~~~ 111 (311)
..+|+.++.+..+++..++-.|..|++|+.. . ..+.....+-+.++|+.+|+|+-+. ...-+....++.
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 4678899999999999999999999999998 2 2356677899999999999999653 333333333221
Q ss_pred ccCCCccccccchHHHHHHHHHHHHHHHHHHHHcCcee
Q 021552 112 REGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVC 149 (311)
Q Consensus 112 ~~~~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l 149 (311)
. ..+++-.+|+..|..|+|+|
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 34799999999999999986
No 27
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=96.55 E-value=0.012 Score=54.25 Aligned_cols=68 Identities=22% Similarity=0.130 Sum_probs=63.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHHH
Q 021552 39 CDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFH 106 (311)
Q Consensus 39 ~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~~ 106 (311)
.++|.+.+..|+|+.++...|..+.+............+.-+|+||+|+||+....+++-+++..+.+
T Consensus 195 ~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~ 262 (285)
T COG1405 195 SDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAG 262 (285)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhC
Confidence 68899999999999999999999999999998888999999999999999999998888888887655
No 28
>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=95.90 E-value=0.037 Score=43.95 Aligned_cols=86 Identities=17% Similarity=0.089 Sum_probs=63.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCCCCCCCccccccc--cCCHHHHHHH
Q 021552 155 HKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAF--DAEKSGIDEV 232 (311)
Q Consensus 155 ~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~--~~~~~~l~~~ 232 (311)
.+|+......++++......|..++...+.........+..||+||+++|++..+...|.-..|.... .++.+++.++
T Consensus 35 ~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~ 114 (127)
T PF00134_consen 35 IDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILEM 114 (127)
T ss_dssp HHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHH
T ss_pred HHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHHH
Confidence 35677777788888889999999998877666677788999999999999999887555433444443 3578888888
Q ss_pred HHHHHHhh
Q 021552 233 CRVLAHLY 240 (311)
Q Consensus 233 ~~~il~ly 240 (311)
-..++...
T Consensus 115 E~~iL~~L 122 (127)
T PF00134_consen 115 EREILSAL 122 (127)
T ss_dssp HHHHHHHT
T ss_pred HHHHHHHC
Confidence 88887754
No 29
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=95.66 E-value=0.044 Score=49.94 Aligned_cols=69 Identities=14% Similarity=0.129 Sum_probs=63.3
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHHH
Q 021552 38 GCDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFH 106 (311)
Q Consensus 38 ~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~~ 106 (311)
..+||.+.|..|+||.++...|..+-.+.-...-..+..+.-||+|.+|+++-+++.++..++|..+..
T Consensus 203 t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtg 271 (308)
T KOG1597|consen 203 TGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTG 271 (308)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhh
Confidence 578999999999999999999999999998888888899999999999999999999999999877654
No 30
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=94.67 E-value=0.082 Score=49.24 Aligned_cols=56 Identities=7% Similarity=0.157 Sum_probs=49.0
Q ss_pred HHHHHHHHcC--CCHHHHHHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCCCC
Q 021552 157 FISNYLATLE--TPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPL 212 (311)
Q Consensus 157 ~l~~~l~~l~--~~~~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~~l 212 (311)
+|..++..++ +++++...|..++...+...-...|+|..||++|+|+|++.-+.+.
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 5677788888 8999999999999998887777899999999999999999887654
No 31
>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=93.89 E-value=0.41 Score=39.17 Aligned_cols=69 Identities=9% Similarity=0.089 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHhhhc--CCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHHH
Q 021552 38 GCDLIQESGILLKLPQAVMATGQVLFHRFYCK--RSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFH 106 (311)
Q Consensus 38 ~~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~--~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~~ 106 (311)
+..=|+++|.+|+++.+........|+..+.. .-+.+.++.-+.+.|+|.-||+.....+.++++..+.
T Consensus 14 a~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr 84 (135)
T PF01857_consen 14 AAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYR 84 (135)
T ss_dssp HHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHT
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHH
Confidence 45558899999999998888888888888754 3467888999999999999999999999999998664
No 32
>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=93.26 E-value=0.44 Score=36.97 Aligned_cols=56 Identities=18% Similarity=0.228 Sum_probs=44.8
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccC
Q 021552 39 CDLIQESGILLKLPQAVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEES 94 (311)
Q Consensus 39 ~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~ 94 (311)
..||....+..+....+...|..+++-.+....+-++.+..+|+||+++|.+.-+.
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 45666665555556778888999999888888899999999999999999999653
No 33
>KOG1674 consensus Cyclin [General function prediction only]
Probab=92.41 E-value=0.6 Score=41.39 Aligned_cols=93 Identities=14% Similarity=0.176 Sum_probs=65.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcCC---------cccch-HHHHHHHHHHHhhhhccCcccHHHHHHHHHHh
Q 021552 39 CDLIQESGILLKLPQAVMATGQVLFHRFYCKRS---------FARFD-VKIVAASSVWLASKLEESPRKARQVIIVFHRM 108 (311)
Q Consensus 39 ~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~s---------~~~~~-~~lva~acLfLA~K~EE~~~~l~~i~~v~~~~ 108 (311)
-+++.++-+..+....+.-.|.+||+||..... +...+ .+-..++|+-+|+|..+.- ... ...
T Consensus 79 ~~yleri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~------~y~-n~~ 151 (218)
T KOG1674|consen 79 RQYLERIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDV------YYS-NAY 151 (218)
T ss_pred HHHHHHHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccch------hhh-HHH
Confidence 366778888999999999999999999998621 12334 5558899999999998631 110 001
Q ss_pred hhhccCCCccccccchHHHHHHHHHHHHHHHHHHHHcCceeeec
Q 021552 109 ECRREGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFVCHVE 152 (311)
Q Consensus 109 ~~~~~~~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~l~v~ 152 (311)
..+-+|.+ .+++-.+|..+|..++|.+.+.
T Consensus 152 ~a~vggl~--------------~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 152 YAKVGGLT--------------TDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred HHHhCCCC--------------hHhhhhhhHHHHhhCCeEEEec
Confidence 11112332 3566689999999999999985
No 34
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=91.53 E-value=0.33 Score=45.04 Aligned_cols=57 Identities=21% Similarity=0.308 Sum_probs=44.8
Q ss_pred HHHHHHHHHHcCCCHHH--HHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccCc
Q 021552 39 CDLIQESGILLKLPQAV--MATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESP 95 (311)
Q Consensus 39 ~~~I~~v~~~L~L~~~t--~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~ 95 (311)
..+|......|++++.- ...|-+|++--+-..-+..+.+..||+||+|||++.+|.|
T Consensus 142 hklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIp 200 (367)
T KOG0835|consen 142 HKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIP 200 (367)
T ss_pred HHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCC
Confidence 35666667778887655 6677777776666677788999999999999999999955
No 35
>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=89.79 E-value=0.7 Score=42.57 Aligned_cols=85 Identities=15% Similarity=0.078 Sum_probs=60.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcC--CCCC-----CCccccccccCCHH
Q 021552 155 HKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQ--IPLP-----ENPPWWKAFDAEKS 227 (311)
Q Consensus 155 ~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~--~~lp-----~~~~w~~~~~~~~~ 227 (311)
..++..++..|+.+..+...|..+....+.-.-.-.+++..||.+|||+|++.-+ ..+. ....|-+...-+.+
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 3678889999999999999999998887765557789999999999999999877 2221 11234444445555
Q ss_pred HHHHHHHHHHHh
Q 021552 228 GIDEVCRVLAHL 239 (311)
Q Consensus 228 ~l~~~~~~il~l 239 (311)
.|-+.-..+++.
T Consensus 129 ~Il~~E~~lLEa 140 (297)
T COG5333 129 RILEYEFELLEA 140 (297)
T ss_pred HHHHHHHHHHHH
Confidence 555554444443
No 36
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=89.34 E-value=0.59 Score=43.82 Aligned_cols=58 Identities=19% Similarity=0.189 Sum_probs=47.1
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCCCC
Q 021552 155 HKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPL 212 (311)
Q Consensus 155 ~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~~l 212 (311)
..||......|++++.-...|..+....+.-.-+-.|+|..||++|||+|.+..+-+.
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 4678888888888877777777777777766667789999999999999999877654
No 37
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=89.10 E-value=0.74 Score=40.79 Aligned_cols=85 Identities=15% Similarity=0.095 Sum_probs=58.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCCCCC---------------CCcccc
Q 021552 155 HKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLP---------------ENPPWW 219 (311)
Q Consensus 155 ~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~~lp---------------~~~~w~ 219 (311)
..+|..+.+.+++.+++...|.-++...+.-.-.-.+.|..+|..|||+|++....++. .+ -|-
T Consensus 45 ~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~-~~~ 123 (264)
T KOG0794|consen 45 ANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFS-YWP 123 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcc-cch
Confidence 34556666667777888888877776665433466899999999999999998776521 12 466
Q ss_pred ccccCCHHHHHHHHHHHHHhh
Q 021552 220 KAFDAEKSGIDEVCRVLAHLY 240 (311)
Q Consensus 220 ~~~~~~~~~l~~~~~~il~ly 240 (311)
+.+.++..+|-|+--.+++..
T Consensus 124 e~~~~~~~~I~e~Ef~llE~L 144 (264)
T KOG0794|consen 124 EKFPYERKDILEMEFYLLEAL 144 (264)
T ss_pred hhcCCCcCcchhhhhhHHhhh
Confidence 667776666666665555543
No 38
>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=88.86 E-value=2.8 Score=34.68 Aligned_cols=88 Identities=14% Similarity=0.065 Sum_probs=62.3
Q ss_pred ChHHHHHHHHHHcCCCHHHHHHHHHHHHhhhc---C-cccc-cCChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHH
Q 021552 153 HPHKFISNYLATLETPLELRQEAWNLANDSLR---T-TLCV-RFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKS 227 (311)
Q Consensus 153 ~P~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~---t-~~~l-~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~~~~~~ 227 (311)
.-.+|+.++++....+..+.-.|..++..... . ...+ .....-+-++|+.+|.+.+.-..-.+..|-++.|++..
T Consensus 53 ~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~~ 132 (149)
T PF08613_consen 53 SIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISLK 132 (149)
T ss_dssp -HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HH
T ss_pred cHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCHH
Confidence 34678888888888888887777777766555 1 1222 45677899999999999987655557789999999999
Q ss_pred HHHHHHHHHHHhh
Q 021552 228 GIDEVCRVLAHLY 240 (311)
Q Consensus 228 ~l~~~~~~il~ly 240 (311)
+++.+-...+.+.
T Consensus 133 eln~lE~~fL~~l 145 (149)
T PF08613_consen 133 ELNELEREFLKLL 145 (149)
T ss_dssp HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHC
Confidence 9999998888765
No 39
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=83.43 E-value=1.4 Score=43.56 Aligned_cols=55 Identities=15% Similarity=0.106 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHhhhcCCcccchHHHHHHHHHHHhhhhccCcccHHHHHHHHHHh
Q 021552 54 AVMATGQVLFHRFYCKRSFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHRM 108 (311)
Q Consensus 54 ~t~~tA~~~~~Rf~~~~s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~~~~ 108 (311)
.|..+|..+..|----.-.....+.-++.|||++||.+...++++.||+.+.+-.
T Consensus 185 ~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~ 239 (521)
T KOG1598|consen 185 DVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVC 239 (521)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHh
Confidence 3777888887776443334567778899999999999999999999999876643
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=82.63 E-value=3.9 Score=33.40 Aligned_cols=57 Identities=16% Similarity=0.232 Sum_probs=46.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhhhc--CcccccCChHHHHHHHHHHHHHHcCCC
Q 021552 155 HKFISNYLATLETPLELRQEAWNLANDSLR--TTLCVRFKSEVVACGVVYAAARRFQIP 211 (311)
Q Consensus 155 ~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~--t~~~l~~~P~~IA~AaI~lA~~~~~~~ 211 (311)
..-+..+|+.|+++.++.+.+|.+++-++. +.++....-.+|-+.|||..+++.+.+
T Consensus 15 ~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~ 73 (135)
T PF01857_consen 15 AVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEE 73 (135)
T ss_dssp HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCC
Confidence 345677888899999999999999998874 678888889999999999999988743
No 41
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=80.95 E-value=9.4 Score=36.01 Aligned_cols=84 Identities=12% Similarity=0.069 Sum_probs=62.9
Q ss_pred HHHHHHHHHHHHHHHcCceeee---cC------hHHHHHHHHHHcCCCHHHHHHHHHHHHhhhcCcccccCCh---HHHH
Q 021552 130 LKMEMSRTERHILKEMGFVCHV---EH------PHKFISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKS---EVVA 197 (311)
Q Consensus 130 ~~~~I~~~E~~IL~~L~F~l~v---~~------P~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~l~~~P---~~IA 197 (311)
.-..++..|..-....++.+.+ .+ ..+.|...++..+....+.-+|.+++...+...-+-..+| ..||
T Consensus 48 ~i~~ll~kEe~~~p~~~~~~~~~~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlA 127 (335)
T KOG0656|consen 48 VLANLLEKEEQHNPSLDYFLCVQKLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLA 127 (335)
T ss_pred HHHHHHHHHHHhCCCCchhhhcccccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHH
Confidence 3456666777766666633332 22 3477888888899999999999999999887777778884 5789
Q ss_pred HHHHHHHHHHcCCCCC
Q 021552 198 CGVVYAAARRFQIPLP 213 (311)
Q Consensus 198 ~AaI~lA~~~~~~~lp 213 (311)
+||+.+|+++-....|
T Consensus 128 vaCLsLAsKmeE~~vP 143 (335)
T KOG0656|consen 128 VACLSLASKMEETDVP 143 (335)
T ss_pred HHHHHHHHhhcCcCCc
Confidence 9999999998776444
No 42
>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=79.54 E-value=4.7 Score=37.23 Aligned_cols=52 Identities=8% Similarity=0.232 Sum_probs=43.6
Q ss_pred HHHHHHHcC--CCHHHHHHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcC
Q 021552 158 ISNYLATLE--TPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQ 209 (311)
Q Consensus 158 l~~~l~~l~--~~~~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~ 209 (311)
+..|+..+. ++..+...|..+....+.......|.|..|.++|+++|+++-+
T Consensus 63 l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kiee 116 (325)
T KOG2496|consen 63 LVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEE 116 (325)
T ss_pred HHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHh
Confidence 445555543 5788999999999999998888999999999999999999754
No 43
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=76.19 E-value=4.7 Score=37.34 Aligned_cols=75 Identities=16% Similarity=0.143 Sum_probs=47.4
Q ss_pred HHHHHHHHhhh--cCCcccchHHHHHHHHHHHhhhhccCc-ccHHHHHHHHHHhhhhccCCCccccccchHHHHHHHHHH
Q 021552 58 TGQVLFHRFYC--KRSFARFDVKIVAASSVWLASKLEESP-RKARQVIIVFHRMECRREGLPIEHLDLFSKKFSELKMEM 134 (311)
Q Consensus 58 tA~~~~~Rf~~--~~s~~~~~~~lva~acLfLA~K~EE~~-~~l~~i~~v~~~~~~~~~~~p~~~~~~~~~~y~~~~~~I 134 (311)
....|+.|..- ........+..+....+++|+|+=... ..--|.+.++.. ...+++
T Consensus 213 itL~~~erl~~~~e~~~~p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlKd---------------------~tveDm 271 (343)
T KOG1675|consen 213 ITLVYAERLLWLAERDPCPRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILKD---------------------QSVDDM 271 (343)
T ss_pred HHHHhhHhhhhHhhcCCCcchhhhhhhhhheehhhhhhhhhcccHHHHHHHhh---------------------ccHhhH
Confidence 33456666543 233456677777777899999985421 111111111111 146889
Q ss_pred HHHHHHHHHHcCceeeecC
Q 021552 135 SRTERHILKEMGFVCHVEH 153 (311)
Q Consensus 135 ~~~E~~IL~~L~F~l~v~~ 153 (311)
-.+|+++|+.|+|+++++-
T Consensus 272 Ne~ERqfLelLqfNinvp~ 290 (343)
T KOG1675|consen 272 NALERQFLELLQFNINVPS 290 (343)
T ss_pred HHHHHHHHHHHhhccCccH
Confidence 9999999999999999874
No 44
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=56.53 E-value=76 Score=28.08 Aligned_cols=79 Identities=14% Similarity=0.196 Sum_probs=50.6
Q ss_pred ccCHHHHhcCCCccCCCCHHHHHHHHHHHHHH--------HHHHHHHcCCCHHHHHHHHHHHHHhhhc-----CCcccch
Q 021552 10 YLTDEQLKDSPSRKDGIDEATETTLRIYGCDL--------IQESGILLKLPQAVMATGQVLFHRFYCK-----RSFARFD 76 (311)
Q Consensus 10 l~t~e~l~~~pS~~~gi~~~~e~~~R~~~~~~--------I~~v~~~L~L~~~t~~tA~~~~~Rf~~~-----~s~~~~~ 76 (311)
.|++++.- ...|++.+.+..-...+-++ ++++|..|++ .+++-.|..++.-|-.+ +.-.++.
T Consensus 60 ~fDr~~av----KLSGl~k~~Y~~~~~sfe~llgln~~~~VrdlaVQfgc-~evi~~a~~vl~syk~~lpaT~~~~~D~S 134 (262)
T KOG4557|consen 60 IFDRQAAV----KLSGLSKKAYSRSFNSFENLLGLNIKLNVRDLAVQFGC-VEVIKSAQNVLSSYKERLPATRRANADFS 134 (262)
T ss_pred cccHHHHH----HhccccHHHHHHHHHHHHHHhcchhhcCHHHHHHHHhH-HHHHHHHHHHHHHHHhcCchhhhcCCccc
Confidence 35566653 34588777764433333222 3556666665 35677888888888663 2234566
Q ss_pred HHHHHHHHHHHhhhhcc
Q 021552 77 VKIVAASSVWLASKLEE 93 (311)
Q Consensus 77 ~~lva~acLfLA~K~EE 93 (311)
.-..++|++|+|||.--
T Consensus 135 rP~ft~aA~~~ack~lK 151 (262)
T KOG4557|consen 135 RPVFTAAAFYLACKKLK 151 (262)
T ss_pred chHHHHHHHHHHHHHHH
Confidence 77889999999999753
No 45
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=51.65 E-value=28 Score=36.69 Aligned_cols=69 Identities=9% Similarity=0.117 Sum_probs=56.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHhhhcC--CcccchHHHHHHHHHHHhhhhccCcccHHHHHHHHHH
Q 021552 39 CDLIQESGILLKLPQAVMATGQVLFHRFYCKR--SFARFDVKIVAASSVWLASKLEESPRKARQVIIVFHR 107 (311)
Q Consensus 39 ~~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~~~--s~~~~~~~lva~acLfLA~K~EE~~~~l~~i~~v~~~ 107 (311)
.-=|+.+|.+|.+.+++...--.+|+.-+... -+++.++.-+.+.|+|+-+|+++...+.++|+..+.+
T Consensus 681 avRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR~ 751 (920)
T KOG1010|consen 681 AVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYRR 751 (920)
T ss_pred HHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHhc
Confidence 34478999999999988888888888776543 3567778889999999999999999999999886653
No 46
>KOG1567 consensus Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism]
Probab=44.11 E-value=93 Score=28.75 Aligned_cols=82 Identities=16% Similarity=0.261 Sum_probs=53.0
Q ss_pred HHHHHHHHhhhhcc-CcccHHHHHHHHHHhhhh--ccCCCccccccchHHHHHHHHHHHHHHHHHHHHcCce--eeecCh
Q 021552 80 VAASSVWLASKLEE-SPRKARQVIIVFHRMECR--REGLPIEHLDLFSKKFSELKMEMSRTERHILKEMGFV--CHVEHP 154 (311)
Q Consensus 80 va~acLfLA~K~EE-~~~~l~~i~~v~~~~~~~--~~~~p~~~~~~~~~~y~~~~~~I~~~E~~IL~~L~F~--l~v~~P 154 (311)
.--|||+-+--... .+.++.+|+.-+-.+.+. .+.+|...+.++.+...+..+= .--.+|..||++ .++.+|
T Consensus 225 ~dFacll~~~l~~kp~~~ri~eII~eAV~IEqef~~eaLPv~liGMN~~lM~qYIEF---VADrLL~~lG~~K~Yn~~NP 301 (344)
T KOG1567|consen 225 CDFACLLFSHLKKKPNEERIEEIITEAVEIEQEFLTEALPVNLIGMNCDLMSQYIEF---VADRLLVELGNEKYYNAENP 301 (344)
T ss_pred ccHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHHHHhccchhhhccCHHHHHHHHHH---HHHHHHHHhCccceecCCCc
Confidence 34677776643332 345678887765555543 3567877777776655443332 234689999997 468999
Q ss_pred HHHHHHHHHH
Q 021552 155 HKFISNYLAT 164 (311)
Q Consensus 155 ~~~l~~~l~~ 164 (311)
++|+..+--.
T Consensus 302 FdfMEnISl~ 311 (344)
T KOG1567|consen 302 FDFMENISLA 311 (344)
T ss_pred hHHHHHhhhc
Confidence 9999876543
No 47
>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=43.05 E-value=1.7e+02 Score=23.71 Aligned_cols=84 Identities=14% Similarity=0.260 Sum_probs=49.1
Q ss_pred HcCCCHH-HHHHHHHHHHHhhhcC-CcccchHHHHHHHHHHHhhhhccCcccHH-HHHHHHHHhhhhccCCCccccccch
Q 021552 48 LLKLPQA-VMATGQVLFHRFYCKR-SFARFDVKIVAASSVWLASKLEESPRKAR-QVIIVFHRMECRREGLPIEHLDLFS 124 (311)
Q Consensus 48 ~L~L~~~-t~~tA~~~~~Rf~~~~-s~~~~~~~lva~acLfLA~K~EE~~~~l~-~i~~v~~~~~~~~~~~p~~~~~~~~ 124 (311)
.+++++. .++..+.||.|--... .+...+ --.+||||+-+||.....+ ++......
T Consensus 24 ~~~~sDKYLLAmV~~YF~Ragl~~~~Y~ri~----FFlALYLAndmEED~~~~K~~If~f~~G----------------- 82 (131)
T PF11357_consen 24 CLRVSDKYLLAMVIAYFSRAGLFSWQYQRIH----FFLALYLANDMEEDDEEPKYEIFPFLYG----------------- 82 (131)
T ss_pred chhhhhHHHHHHHHHHHHhcccchhhcchHH----HHHHHHHhhHHHhccchHHHHHHHHHHC-----------------
Confidence 4455555 6688889998875421 122222 3468999999999654333 33332221
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCceeeec
Q 021552 125 KKFSELKMEMSRTERHILKEMGFVCHVE 152 (311)
Q Consensus 125 ~~y~~~~~~I~~~E~~IL~~L~F~l~v~ 152 (311)
..+....-...+.=.++.+.+||..-|.
T Consensus 83 ~~w~~~~~~F~klr~~~~~~m~~Ra~Vs 110 (131)
T PF11357_consen 83 KNWRSQIPQFHKLRDQFWRRMDWRAWVS 110 (131)
T ss_pred cchHHHhHHHHHHHHHHHHHcCCceeeC
Confidence 1111223445556667888899988765
No 48
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=40.05 E-value=2.7e+02 Score=24.74 Aligned_cols=57 Identities=12% Similarity=0.207 Sum_probs=44.8
Q ss_pred ccccCChHHHHHHHHHHHHHHcCCCCCCCccccccccCCHHHHHHHHHHHHHhhcCCC
Q 021552 187 LCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFDAEKSGIDEVCRVLAHLYSLPK 244 (311)
Q Consensus 187 ~~l~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~~~~~~~l~~~~~~il~ly~~~k 244 (311)
.-..++-.+-++||+|.|++.+...+.... .....|+.+.+..-++.++-..|.+..
T Consensus 129 ~~~D~SrP~ft~aA~~~ack~lKlKVdK~k-li~~sg~~~s~F~~l~kqler~~~qv~ 185 (262)
T KOG4557|consen 129 ANADFSRPVFTAAAFYLACKKLKLKVDKLK-LIEVSGTSESEFSCLSKQLERNYKQVS 185 (262)
T ss_pred cCCcccchHHHHHHHHHHHHHHHHhhhHhh-cccccCCCHHHHHHHHHHHHHHHHHhc
Confidence 455677788999999999999887654433 556678889999999999999887543
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=36.06 E-value=40 Score=23.88 Aligned_cols=34 Identities=18% Similarity=0.222 Sum_probs=26.5
Q ss_pred cccccCCHHHHHHHHHHHHHhhcCCCCccccccCCCC
Q 021552 219 WKAFDAEKSGIDEVCRVLAHLYSLPKAKYIPVCKDGT 255 (311)
Q Consensus 219 ~~~~~~~~~~l~~~~~~il~ly~~~k~~~~~~~~~~~ 255 (311)
...+|+...++..+.+.++++|... |..+..++.
T Consensus 18 m~~lG~~~~~v~~vl~~LL~lY~~n---W~lIEed~Y 51 (65)
T PF10440_consen 18 MRQLGFSKKQVRPVLKNLLKLYDGN---WELIEEDNY 51 (65)
T ss_pred HHHcCCCHHHHHHHHHHHHHHHcCC---chhhhcccH
Confidence 3457888999999999999999643 776666554
No 50
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=35.73 E-value=1.6e+02 Score=28.34 Aligned_cols=83 Identities=14% Similarity=0.062 Sum_probs=49.3
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHhhhcCcccccCChHHHHHHHHH-HHHHHcCCCCCCCccccccc--cCCHHHHHHHHH
Q 021552 158 ISNYLATLETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVY-AAARRFQIPLPENPPWWKAF--DAEKSGIDEVCR 234 (311)
Q Consensus 158 l~~~l~~l~~~~~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~-lA~~~~~~~lp~~~~w~~~~--~~~~~~l~~~~~ 234 (311)
+...-..+++..+...+|.+++...+....+-.-.=..++++|++ +|++...+..|.-.+.--.. .++.++|..+..
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 333344566777888888888855443322222233466778855 99998666566422222222 257788888777
Q ss_pred HHHHhh
Q 021552 235 VLAHLY 240 (311)
Q Consensus 235 ~il~ly 240 (311)
.|+...
T Consensus 245 ~il~~L 250 (391)
T KOG0653|consen 245 YILNVL 250 (391)
T ss_pred HHHhcc
Confidence 777654
No 51
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=35.28 E-value=1.4e+02 Score=28.18 Aligned_cols=85 Identities=12% Similarity=0.060 Sum_probs=48.5
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHhhhcCc-ccccCChHHHHHHHHHHHHHHcCCCCCCCcccccccc--CCHHHHHHH
Q 021552 156 KFISNYLATLETPLELRQEAWNLANDSLRTT-LCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAFD--AEKSGIDEV 232 (311)
Q Consensus 156 ~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~-~~l~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~~--~~~~~l~~~ 232 (311)
+++...|+..++..+...+|..++..-+.+. -|..-.=..|-.+|+++|+++..+--|.-..+..+.+ .+.++|...
T Consensus 150 DWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddIltm 229 (408)
T KOG0655|consen 150 DWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDILTM 229 (408)
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHHHHHH
Confidence 3444455555555555555555555444432 2333334578899999999999887665433444443 456666555
Q ss_pred HHHHHHhh
Q 021552 233 CRVLAHLY 240 (311)
Q Consensus 233 ~~~il~ly 240 (311)
-.-|++..
T Consensus 230 E~iilkal 237 (408)
T KOG0655|consen 230 ELIILKAL 237 (408)
T ss_pred HHHHHHHh
Confidence 55455443
No 52
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=33.15 E-value=62 Score=31.82 Aligned_cols=76 Identities=14% Similarity=0.069 Sum_probs=54.0
Q ss_pred CCCHHHHHHHHHHHHhhhcCcccccCChHHHHHHHHHHHHHHcCCCCCCCccccccc--cCCHHHHHHHHHHHHHhhc
Q 021552 166 ETPLELRQEAWNLANDSLRTTLCVRFKSEVVACGVVYAAARRFQIPLPENPPWWKAF--DAEKSGIDEVCRVLAHLYS 241 (311)
Q Consensus 166 ~~~~~l~~~A~~l~~ds~~t~~~l~~~P~~IA~AaI~lA~~~~~~~lp~~~~w~~~~--~~~~~~l~~~~~~il~ly~ 241 (311)
++-.+..-+|.++++..+-...+..=.-..+++.|+++|++...+.+|.-...-.++ .++.+++...-+.+++...
T Consensus 228 ~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE~~ml~~l~ 305 (440)
T COG5024 228 GLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERYMLEVLD 305 (440)
T ss_pred cccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHHHHHhhhcc
Confidence 334556667778877766666655556778999999999999988777533333333 3678888888888887754
No 53
>PHA02690 hypothetical protein; Provisional
Probab=32.07 E-value=77 Score=23.28 Aligned_cols=32 Identities=25% Similarity=0.401 Sum_probs=24.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhhhcCc
Q 021552 155 HKFISNYLATLETPLELRQEAWNLANDSLRTT 186 (311)
Q Consensus 155 ~~~l~~~l~~l~~~~~l~~~A~~l~~ds~~t~ 186 (311)
..|+..+...++.+..+...+|.++-|.+.|-
T Consensus 21 rrYLeAIqrhlEgs~plLR~~~RlLfDL~lTv 52 (90)
T PHA02690 21 RRYLEAIQRHLEGSTPLLRQMWRLLFDLLLTV 52 (90)
T ss_pred hHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Confidence 45677777777777778888999988877663
No 54
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=31.76 E-value=1.2e+02 Score=22.19 Aligned_cols=29 Identities=17% Similarity=-0.055 Sum_probs=25.2
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHhhh
Q 021552 40 DLIQESGILLKLPQAVMATGQVLFHRFYC 68 (311)
Q Consensus 40 ~~I~~v~~~L~L~~~t~~tA~~~~~Rf~~ 68 (311)
..+.++...|+++...++.+..+++|...
T Consensus 46 ~~~~rL~~Dl~in~~gi~lil~LLd~i~~ 74 (84)
T PF13591_consen 46 RRIRRLHRDLGINLEGIALILDLLDRIEQ 74 (84)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 45778899999999999999999998754
No 55
>PF09080 K-cyclin_vir_C: K cyclin, C terminal; InterPro: IPR015164 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This domain adopts a secondary structure consisting of a five alpha-helix cyclin fold. Interaction with cyclin dependent kinases (CDKs) at a PSTAIRE sequence motif within the catalytic cleft of CDK results in the regulation of CDK activity []. ; PDB: 1G3N_C.
Probab=27.19 E-value=2.7e+02 Score=20.92 Aligned_cols=66 Identities=11% Similarity=0.134 Sum_probs=40.6
Q ss_pred HHHHHHHHHhhhcCcccccCChHHHHHH-HHHHHHHHcCCCCCC----C---ccccccccCCHHHHHHHHHHHHHhh
Q 021552 172 RQEAWNLANDSLRTTLCVRFKSEVVACG-VVYAAARRFQIPLPE----N---PPWWKAFDAEKSGIDEVCRVLAHLY 240 (311)
Q Consensus 172 ~~~A~~l~~ds~~t~~~l~~~P~~IA~A-aI~lA~~~~~~~lp~----~---~~w~~~~~~~~~~l~~~~~~il~ly 240 (311)
.......+...+..+..-..+|+.||+| |-.+.. +.-.|. + +..-+.+|++...+...++.++.-.
T Consensus 26 H~~V~~~v~KAiV~P~TG~Lp~SlvaAA~CAL~~~---~~~~P~~~~~~~~~~~LA~~~G~~~a~L~AA~E~v~Tt~ 99 (106)
T PF09080_consen 26 HSEVVESVHKAIVNPKTGGLPPSLVAAAGCALFSL---GAAAPPDTHSGGVVPQLAEALGVSAATLQAAAESVATTL 99 (106)
T ss_dssp HHHHHHHHHHHHCSTTGGGS-HHHHHHHHHHHHS----GGGS--------HHHHHHHHHT--HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCcccCCCCHHHHHHhhhhhccc---cccCCCccccccchHHHHHHhCccHHHHHHHHHHHHHHH
Confidence 4455566667777888888999999987 654432 222221 1 3567788999888888887776543
Done!