Query 019442
Match_columns 341
No_of_seqs 192 out of 1309
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 09:30:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019442.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019442hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0834 CDK9 kinase-activating 100.0 1.2E-42 2.6E-47 335.4 13.6 190 145-340 8-205 (323)
2 KOG0835 Cyclin L [General func 100.0 6E-35 1.3E-39 277.3 16.0 183 158-340 5-193 (367)
3 TIGR00569 ccl1 cyclin ccl1. Un 100.0 1.4E-34 3E-39 278.9 18.1 179 145-340 6-216 (305)
4 KOG0794 CDK8 kinase-activating 100.0 1.7E-32 3.8E-37 250.1 11.0 188 146-340 11-204 (264)
5 COG5333 CCL1 Cdk activating ki 100.0 2.3E-28 5E-33 231.9 13.6 161 167-340 36-202 (297)
6 PRK00423 tfb transcription ini 99.8 1.3E-19 2.7E-24 175.7 18.0 148 170-340 117-269 (310)
7 KOG2496 Cdk activating kinase 99.8 2.8E-20 6.2E-25 176.0 11.8 178 146-340 8-218 (325)
8 KOG0656 G1/S-specific cyclin D 99.8 2E-19 4.3E-24 174.5 15.3 164 159-340 59-236 (335)
9 PF00134 Cyclin_N: Cyclin, N-t 99.7 1.7E-16 3.6E-21 132.4 9.7 102 170-290 25-127 (127)
10 KOG0653 Cyclin B and related k 99.7 2.6E-16 5.7E-21 157.1 12.0 151 171-341 153-310 (391)
11 KOG0655 G1/S-specific cyclin E 99.6 5.7E-15 1.2E-19 141.5 10.0 149 170-339 139-306 (408)
12 COG5024 Cyclin [Cell division 99.6 9E-15 1.9E-19 146.8 11.5 152 170-341 207-364 (440)
13 COG1405 SUA7 Transcription ini 99.5 2E-13 4.4E-18 130.9 16.9 147 171-340 93-244 (285)
14 KOG1597 Transcription initiati 99.5 3.8E-13 8.1E-18 127.5 15.1 142 177-340 105-253 (308)
15 cd00043 CYCLIN Cyclin box fold 99.4 9.7E-13 2.1E-17 100.8 8.4 87 176-282 2-88 (88)
16 smart00385 CYCLIN domain prese 99.3 1.4E-11 3.1E-16 93.4 7.1 83 181-283 1-83 (83)
17 KOG0654 G2/Mitotic-specific cy 99.0 1.3E-09 2.8E-14 107.3 8.3 153 170-341 131-289 (359)
18 PF00382 TFIIB: Transcription 98.6 1.5E-07 3.2E-12 72.0 7.5 64 183-246 1-64 (71)
19 KOG1598 Transcription initiati 98.5 8.8E-07 1.9E-11 90.4 10.6 141 178-340 69-219 (521)
20 KOG4164 Cyclin ik3-1/CABLES [C 97.9 2E-05 4.4E-10 78.0 5.9 95 181-292 387-482 (497)
21 PRK00423 tfb transcription ini 97.8 9.9E-05 2.2E-09 71.9 9.8 67 180-246 220-286 (310)
22 PF08613 Cyclin: Cyclin; Inte 97.4 0.001 2.3E-08 58.0 9.4 90 179-289 54-149 (149)
23 PF02984 Cyclin_C: Cyclin, C-t 97.1 0.00048 1E-08 56.0 3.7 49 292-341 1-54 (118)
24 cd00043 CYCLIN Cyclin box fold 96.9 0.0028 6.1E-08 47.8 6.4 49 291-340 2-55 (88)
25 PF00382 TFIIB: Transcription 96.8 0.0035 7.6E-08 47.7 5.9 42 298-340 1-47 (71)
26 smart00385 CYCLIN domain prese 96.6 0.0056 1.2E-07 45.8 5.6 43 297-340 2-49 (83)
27 COG1405 SUA7 Transcription ini 96.1 0.018 4E-07 55.7 7.5 69 179-247 194-262 (285)
28 KOG1597 Transcription initiati 95.6 0.051 1.1E-06 52.5 7.9 68 179-246 203-270 (308)
29 PF01857 RB_B: Retinoblastoma- 93.6 0.43 9.2E-06 41.3 8.3 69 179-247 14-84 (135)
30 PF02984 Cyclin_C: Cyclin, C-t 91.0 0.68 1.5E-05 37.2 6.1 56 180-235 4-59 (118)
31 KOG0835 Cyclin L [General func 89.7 0.52 1.1E-05 46.4 4.9 57 181-237 143-201 (367)
32 KOG1674 Cyclin [General functi 81.9 4.3 9.4E-05 37.8 6.6 92 181-292 80-181 (218)
33 KOG0834 CDK9 kinase-activating 81.8 1.6 3.5E-05 43.1 3.9 58 181-238 153-214 (323)
34 KOG1598 Transcription initiati 81.0 1.8 3.9E-05 45.1 4.0 54 195-248 185-238 (521)
35 TIGR00569 ccl1 cyclin ccl1. Un 74.3 25 0.00053 34.5 9.6 55 180-234 164-221 (305)
36 PF00134 Cyclin_N: Cyclin, N-t 71.8 13 0.00028 30.3 6.1 44 296-340 36-84 (127)
37 KOG1675 Predicted cyclin [Gene 63.0 14 0.00031 36.4 5.2 93 182-293 196-290 (343)
38 KOG0794 CDK8 kinase-activating 56.7 88 0.0019 29.8 9.1 55 180-237 158-212 (264)
39 KOG1010 Rb (Retinoblastoma tum 49.7 46 0.001 37.0 6.9 69 179-247 680-750 (920)
40 PF13591 MerR_2: MerR HTH fami 34.9 1.2E+02 0.0026 23.7 5.6 43 146-209 32-74 (84)
41 KOG4557 Origin recognition com 32.2 82 0.0018 29.7 4.8 50 183-233 96-150 (262)
42 KOG1103 Predicted coiled-coil 30.9 84 0.0018 31.7 4.8 50 73-122 373-423 (561)
43 PHA02956 hypothetical protein; 27.7 82 0.0018 27.7 3.7 45 149-197 140-184 (189)
44 KOG3088 Secretory carrier memb 24.6 2.5E+02 0.0054 27.6 6.7 14 274-287 207-220 (313)
45 COG5333 CCL1 Cdk activating ki 24.6 1.8E+02 0.0039 28.6 5.8 43 195-237 168-210 (297)
46 PF01857 RB_B: Retinoblastoma- 21.5 2.4E+02 0.0052 24.3 5.5 44 295-339 15-65 (135)
47 PHA02690 hypothetical protein; 20.5 4E+02 0.0086 21.3 5.9 31 296-327 22-52 (90)
No 1
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.2e-42 Score=335.37 Aligned_cols=190 Identities=37% Similarity=0.641 Sum_probs=178.1
Q ss_pred CCCCccccHHHHHHhCCCccCCCCHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHH
Q 019442 145 DDEPVFMSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATA 224 (341)
Q Consensus 145 ~~~~w~ft~eEl~~~sPS~~~GIs~e~E~~lR~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaA 224 (341)
....|+|+++|+++.|||+++|++.+.|...|..++.||+++|.+|++++.+++||++||||||+.++++.++++.||++
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 35689999999988999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhccCCCCCChhHHHHHHHHHhhhhchhhhcccCChhHHHHHHHHHHHHHHHHHHHcCCCcccCCcHHHHHHHHHH
Q 019442 225 ALFLAAKSEETPRPLNDVLRASSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNK 304 (341)
Q Consensus 225 cLFLA~KvEE~prkLrdIi~v~~~l~~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~~P~~~L~~~l~~ 304 (341)
|||||||+||+|++++|||.++++++++.+ ....+.||+.++.|+.+|.+||++|+|||+|+|||.||.+++++
T Consensus 88 clfLAgKvEetp~kl~dIi~~s~~~~~~~~------~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~ 161 (323)
T KOG0834|consen 88 CLFLAGKVEETPRKLEDIIKVSYRYLNPKD------LELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKK 161 (323)
T ss_pred HHHHHhhcccCcccHHHHHHHHHHHcCccc------ccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHH
Confidence 999999999999999999999999887643 13457899999999999999999999999999999999999999
Q ss_pred cCCCHH---HHHHHHHHHHHHHHhhhH-----HHHHHHHHHHHh
Q 019442 305 LGLSQT---VLVNLALNLVSEGFASCL-----QHGLATGALKHA 340 (341)
Q Consensus 305 L~ls~~---~l~q~A~~ilnDsl~T~L-----Ps~IAaAaIyLA 340 (341)
++.+.. .+.++||.+++|+++|.+ |++||+|||+||
T Consensus 162 l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA 205 (323)
T KOG0834|consen 162 LKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLA 205 (323)
T ss_pred hhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEeehhhHH
Confidence 987653 589999999999999865 999999999998
No 2
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=100.00 E-value=6e-35 Score=277.29 Aligned_cols=183 Identities=30% Similarity=0.455 Sum_probs=164.3
Q ss_pred HhCCCccCCCCHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCC
Q 019442 158 RFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPR 237 (341)
Q Consensus 158 ~~sPS~~~GIs~e~E~~lR~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~pr 237 (341)
..+||..+|++.+.|..+|.-||.||++.|..|+|||.+++|++++|+|||..+++..+|...|++|||+||+|+||.|+
T Consensus 5 ~~~~s~qd~l~~e~e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Pr 84 (367)
T KOG0835|consen 5 DSTPSLQDGLSLETEEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPR 84 (367)
T ss_pred cCchhhhcccccchHHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccc
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChhHHHHHHHHHhhhhchhhhcccCChhHHHHHHHHHHHHHHHHHHHcCCCcccCCcHHHHHHHHHHcCCCHH-HHHHHH
Q 019442 238 PLNDVLRASSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQT-VLVNLA 316 (341)
Q Consensus 238 kLrdIi~v~~~l~~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~~P~~~L~~~l~~L~ls~~-~l~q~A 316 (341)
++++|++|+..+-...+....+.......+...+..++.+|..||++|||+++|+|||.++..|++.|++++. +|.|.+
T Consensus 85 r~rdVinVFh~L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~~l~Q~~ 164 (367)
T KOG0835|consen 85 RIRDVINVFHYLEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNLKLLQAA 164 (367)
T ss_pred cHhHHHHHHHHHHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCchhHHHHH
Confidence 9999999998775543322112112233455678999999999999999999999999999999999999764 489999
Q ss_pred HHHHHHHHhhhH-----HHHHHHHHHHHh
Q 019442 317 LNLVSEGFASCL-----QHGLATGALKHA 340 (341)
Q Consensus 317 ~~ilnDsl~T~L-----Ps~IAaAaIyLA 340 (341)
|+|+||+++|++ |+.||+||||||
T Consensus 165 wNfmNDslRT~v~vry~pe~iACaciyLa 193 (367)
T KOG0835|consen 165 WNFMNDSLRTDVFVRYSPESIACACIYLA 193 (367)
T ss_pred HHhhhhccccceeeecCHHHHHHHHHHHH
Confidence 999999999987 999999999998
No 3
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=100.00 E-value=1.4e-34 Score=278.92 Aligned_cols=179 Identities=22% Similarity=0.305 Sum_probs=155.7
Q ss_pred CCCCcccc-HHHHHHhC------------------CCccCCCCHHHHHHHHHHHHHHHHHHHHHcC--CCHHHHHHHHHH
Q 019442 145 DDEPVFMS-RDEIERFS------------------PSRKDGIDALRETHLRYSYCAFIQNLGLRLE--LPQTTIGTAMVL 203 (341)
Q Consensus 145 ~~~~w~ft-~eEl~~~s------------------PS~~~GIs~e~E~~lR~~~~~~I~~lg~~L~--Lp~~tiaTA~v~ 203 (341)
+-..|.|| ++||.+.- +....+|++++|..+|.+++.+|+++|.+|+ ||+.|++||++|
T Consensus 6 Q~r~W~F~~~~~L~~~R~~~N~~~~~~~~~~~~~~~~~~~~Lt~eeE~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivy 85 (305)
T TIGR00569 6 QKRHWTFTSEEQLQEKRADANAKFREAHEEEEKVLEAKPIFLTPEEELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMY 85 (305)
T ss_pred ccccCcCCCHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHH
Confidence 34679999 88876421 1234589999999999999999999999999 999999999999
Q ss_pred HHHHhhcCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHHHHHhhhhchhhhcccCChhHHHHHHHHHHHHHHHHHH
Q 019442 204 CHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILT 283 (341)
Q Consensus 204 fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~~~l~~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~ 283 (341)
|||||+++|+..+++++|++||||||||+||+++++++++..... ....++++|+++|+.||+
T Consensus 86 f~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~-----------------~~~~~~~~Il~~E~~lL~ 148 (305)
T TIGR00569 86 FKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKE-----------------TPLKALEQVLEYELLLIQ 148 (305)
T ss_pred HhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccC-----------------CchhhHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999998864210 011457899999999999
Q ss_pred HcCCCcccCCcHHHHHHHHHHcC-----C-CHHHHHHHHHHHHHHHHhhhH-----HHHHHHHHHHHh
Q 019442 284 TLNFELNVQHPYDPLTSILNKLG-----L-SQTVLVNLALNLVSEGFASCL-----QHGLATGALKHA 340 (341)
Q Consensus 284 tL~FdL~v~~P~~~L~~~l~~L~-----l-s~~~l~q~A~~ilnDsl~T~L-----Ps~IAaAaIyLA 340 (341)
+|+|+|.|.|||++|..|+..++ . +.+.+.+.||.+++|+++|++ |+.||+||||+|
T Consensus 149 ~L~F~L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAAI~lA 216 (305)
T TIGR00569 149 QLNFHLIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHT 216 (305)
T ss_pred HCCCcEEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHHHHHHHHHH
Confidence 99999999999999999987653 1 234688999999999999986 999999999998
No 4
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.98 E-value=1.7e-32 Score=250.07 Aligned_cols=188 Identities=27% Similarity=0.406 Sum_probs=161.0
Q ss_pred CCCccccHHHHHHhCCCccCCCCHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHH
Q 019442 146 DEPVFMSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAA 225 (341)
Q Consensus 146 ~~~w~ft~eEl~~~sPS~~~GIs~e~E~~lR~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAc 225 (341)
-.+|+|++.|+.+--|--..|++.++-.+++....++|+.+|++|+|.|.|+|||++||+|||.++|++++++.++|.||
T Consensus 11 ~~qwl~dk~el~k~r~~D~r~l~~d~~~~l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TC 90 (264)
T KOG0794|consen 11 YQQWLLDKTELLKERQLDLRGLSEDEYSKLKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTC 90 (264)
T ss_pred hhhHhcCHHHHhhhccchhhcccHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHH
Confidence 46899999999886665677899888889999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhccCCCC-CChhHHHHHHHHHhhhhchhhhcccCChhHHHHHHHHHHHHHHHHHHHcCCCcccCCcHHHHHHHHHH
Q 019442 226 LFLAAKSEETP-RPLNDVLRASSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNK 304 (341)
Q Consensus 226 LFLA~KvEE~p-rkLrdIi~v~~~l~~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~~P~~~L~~~l~~ 304 (341)
||||||+||++ ..++-++..+..+..+-+ + ..+.+---...|+++|+.||+.|++-|.|.|||+.|.++++.
T Consensus 91 lyLAcKvEE~~i~~~r~l~~~a~~L~~~f~-----~--~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~qd 163 (264)
T KOG0794|consen 91 LYLACKVEECPIVHIRLLVNEAKVLKTRFS-----Y--WPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQD 163 (264)
T ss_pred HHHHhhhhhcchHHHHHHHHHHHHHhhhcc-----c--chhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHHH
Confidence 99999999998 566666665544422211 0 001111124689999999999999999999999999999999
Q ss_pred cCCCHHHHHHHHHHHHHHHHhhhH-----HHHHHHHHHHHh
Q 019442 305 LGLSQTVLVNLALNLVSEGFASCL-----QHGLATGALKHA 340 (341)
Q Consensus 305 L~ls~~~l~q~A~~ilnDsl~T~L-----Ps~IAaAaIyLA 340 (341)
+|+..+++.+.+|.++||++++++ |+.||+|||++|
T Consensus 164 ~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia 204 (264)
T KOG0794|consen 164 MGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIA 204 (264)
T ss_pred hcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHH
Confidence 999555689999999999999986 999999999998
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=99.95 E-value=2.3e-28 Score=231.92 Aligned_cols=161 Identities=30% Similarity=0.465 Sum_probs=140.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHH
Q 019442 167 IDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRAS 246 (341)
Q Consensus 167 Is~e~E~~lR~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~ 246 (341)
+.-+.|..+|.+++.||.++|.+|+||+.+++||+.+|+||+.+.++++++++.|++||||||||+||+++.+.-..-..
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 67789999999999999999999999999999999999999999999999999999999999999999855543222221
Q ss_pred HHHhhhhchhhhcccCChhHHHHHHHHHHHHHHHHHHHcCCCcccCCcHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHHh
Q 019442 247 SELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQT-VLVNLALNLVSEGFA 325 (341)
Q Consensus 247 ~~l~~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~~P~~~L~~~l~~L~ls~~-~l~q~A~~ilnDsl~ 325 (341)
.. ...+..+.+|++|+.+|+.||++|+|||.|+|||.++..+++.+..... ++.+.||.+++|+++
T Consensus 116 ~~-------------~~se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~ 182 (297)
T COG5333 116 RD-------------LWSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALR 182 (297)
T ss_pred hc-------------cccccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhh
Confidence 11 1123445689999999999999999999999999999999999876442 589999999999999
Q ss_pred hhH-----HHHHHHHHHHHh
Q 019442 326 SCL-----QHGLATGALKHA 340 (341)
Q Consensus 326 T~L-----Ps~IAaAaIyLA 340 (341)
+++ |++||+||+++|
T Consensus 183 t~~~llypphiIA~a~l~ia 202 (297)
T COG5333 183 TDLCLLYPPHIIALAALLIA 202 (297)
T ss_pred ceeeeecChHHHHHHHHHHH
Confidence 875 999999999987
No 6
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.83 E-value=1.3e-19 Score=175.74 Aligned_cols=148 Identities=22% Similarity=0.296 Sum_probs=133.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHHHHH
Q 019442 170 LRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSEL 249 (341)
Q Consensus 170 e~E~~lR~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~~~l 249 (341)
..|+.+ ..+...|.++|..|+||+.++.+|+.+|++++..+.+++.....+++||||+|||.|+.|++++||..++..
T Consensus 117 ~~er~l-~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~v- 194 (310)
T PRK00423 117 AAERNL-AFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRV- 194 (310)
T ss_pred hHhHHH-HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCC-
Confidence 455666 458899999999999999999999999999999999999999999999999999999999999999876431
Q ss_pred hhhhchhhhcccCChhHHHHHHHHHHHHHHHHHHHcCCCcccCCcHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhH-
Q 019442 250 YHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQTVLVNLALNLVSEGFASCL- 328 (341)
Q Consensus 250 ~~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~~P~~~L~~~l~~L~ls~~~l~q~A~~ilnDsl~T~L- 328 (341)
.+++|...++.|++.|++++.+.+|++||.+|+..|+++.+ +.+.|+.++.++....+
T Consensus 195 --------------------~~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~-v~~~A~~i~~~a~~~~l~ 253 (310)
T PRK00423 195 --------------------SRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGE-VQKKAIEILQKAKEKGLT 253 (310)
T ss_pred --------------------CHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHhcCcc
Confidence 14578889999999999999999999999999999999974 89999999998877665
Q ss_pred ----HHHHHHHHHHHh
Q 019442 329 ----QHGLATGALKHA 340 (341)
Q Consensus 329 ----Ps~IAaAaIyLA 340 (341)
|..||+||||+|
T Consensus 254 ~Gr~P~sIAAAaIYlA 269 (310)
T PRK00423 254 SGKGPTGLAAAAIYIA 269 (310)
T ss_pred cCCCHHHHHHHHHHHH
Confidence 999999999998
No 7
>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=99.83 E-value=2.8e-20 Score=176.02 Aligned_cols=178 Identities=21% Similarity=0.288 Sum_probs=134.4
Q ss_pred CCCccccHHHHHHhC------------------CCccCCCCHHHHHHHHHHHHHHHHHHHHHc--CCCHHHHHHHHHHHH
Q 019442 146 DEPVFMSRDEIERFS------------------PSRKDGIDALRETHLRYSYCAFIQNLGLRL--ELPQTTIGTAMVLCH 205 (341)
Q Consensus 146 ~~~w~ft~eEl~~~s------------------PS~~~GIs~e~E~~lR~~~~~~I~~lg~~L--~Lp~~tiaTA~v~fh 205 (341)
.-.|.||+++|.+.- +--..-+.+++|..+-.+...-+.+.+..+ .||..|++||+.+|+
T Consensus 8 ~r~W~fte~qL~e~r~~~N~k~i~~~ee~~~~~~~~e~~v~~~ee~tl~k~~E~~l~~f~~k~~p~lp~~Vv~TA~~fFk 87 (325)
T KOG2496|consen 8 YRKWIFTEEQLAERRVDANQKAIQMLEEEAHNLDENEVFVLEAEELTLTKEEELSLVNFYSKFKPNLPTSVVSTAIEFFK 87 (325)
T ss_pred hhcccccHHHHHHHHHHHHHHHHHHHHHhccCCCccchhccccccccccHHHHHHHHHHHHHhcCCCchHHHHHHHHHHH
Confidence 346999999987520 111122333444444444444455555554 599999999999999
Q ss_pred HHhhcCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHHHHHhhhhchhhhcccCChhHHHHHHHHHHHHHHHHHHHc
Q 019442 206 RFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTL 285 (341)
Q Consensus 206 RFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~~~l~~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL 285 (341)
|||...|..++++..|.+||+|||||+||..+++.++++... ..-|+..+.|+.+|..+|+.|
T Consensus 88 RffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~-----------------~~~~k~~e~vLk~E~~llqsL 150 (325)
T KOG2496|consen 88 RFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMN-----------------GRKWKTHEIVLKYEFLLLQSL 150 (325)
T ss_pred HHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhcc-----------------CcccccHHHHHhchHHHHHhh
Confidence 999999999999999999999999999999999999987542 011245789999999999999
Q ss_pred CCCcccCCcHHHHHHHHHHcC-----C-CHHHHHHHH--HHHHHHHHhhhH-----HHHHHHHHHHHh
Q 019442 286 NFELNVQHPYDPLTSILNKLG-----L-SQTVLVNLA--LNLVSEGFASCL-----QHGLATGALKHA 340 (341)
Q Consensus 286 ~FdL~v~~P~~~L~~~l~~L~-----l-s~~~l~q~A--~~ilnDsl~T~L-----Ps~IAaAaIyLA 340 (341)
.|+|.+.+||+.|+.|+.++. + ..+.+.+.. ..+++..++|+. |+.||+|||..|
T Consensus 151 ~f~L~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a 218 (325)
T KOG2496|consen 151 KFSLTVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHA 218 (325)
T ss_pred hhhheecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHH
Confidence 999999999999999987763 1 222233333 377788888874 999999999554
No 8
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=99.82 E-value=2e-19 Score=174.46 Aligned_cols=164 Identities=20% Similarity=0.207 Sum_probs=126.9
Q ss_pred hCCCc--cCCCCHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccc---hhHHHHHHHHHhhccC
Q 019442 159 FSPSR--KDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHD---RFIIATAALFLAAKSE 233 (341)
Q Consensus 159 ~sPS~--~~GIs~e~E~~lR~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d---~~lVAaAcLFLA~KvE 233 (341)
..|+. ..+++...--..|..+++||.++|..+++...|...|++||+||...+.+.+.+ .+++|+|||+||+|+|
T Consensus 59 ~~p~~~~~~~~~~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKme 138 (335)
T KOG0656|consen 59 HNPSLDYFLCVQKLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKME 138 (335)
T ss_pred hCCCCchhhhcccccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhc
Confidence 44554 345555444456999999999999999999999999999999999999998888 9999999999999999
Q ss_pred CCC-CChhHHHHHHHHHhhhhchhhhcccCChhHHHHHHHHHHHHHHHHHHHcCCCcccCCcHHHHHHHHHHcCCCH---
Q 019442 234 ETP-RPLNDVLRASSELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQ--- 309 (341)
Q Consensus 234 E~p-rkLrdIi~v~~~l~~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~~P~~~L~~~l~~L~ls~--- 309 (341)
|+. +-+-|+..... ... -..+.|.+||.+||.+|+|++...+|+.|+..|+.+++...
T Consensus 139 E~~vPll~dl~v~~~----------------~~~--feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~~~~ 200 (335)
T KOG0656|consen 139 ETDVPLLADLQVEYT----------------DNV--FEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKDHNK 200 (335)
T ss_pred CcCCchhhhhhhccc----------------ccc--ccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCcccchH
Confidence 985 34444432210 011 12578999999999999999999999999999999998743
Q ss_pred HHHHHHHHHHHHHHHhhh--H---HHHHHHHHHHHh
Q 019442 310 TVLVNLALNLVSEGFASC--L---QHGLATGALKHA 340 (341)
Q Consensus 310 ~~l~q~A~~ilnDsl~T~--L---Ps~IAaAaIyLA 340 (341)
..+...+..++-...... + |++||+|++.++
T Consensus 201 ~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v 236 (335)
T KOG0656|consen 201 HLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSV 236 (335)
T ss_pred HHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHH
Confidence 234555665554433321 1 999999988654
No 9
>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=99.68 E-value=1.7e-16 Score=132.44 Aligned_cols=102 Identities=34% Similarity=0.493 Sum_probs=84.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCC-CCChhHHHHHHHH
Q 019442 170 LRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEET-PRPLNDVLRASSE 248 (341)
Q Consensus 170 e~E~~lR~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~-prkLrdIi~v~~~ 248 (341)
+.....|...++||.+++..++++..|+++|+.||+||+.+.++...+++++++|||+||||+||. +..+.+++..+..
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 455678999999999999999999999999999999999999999999999999999999999998 6778888776421
Q ss_pred HhhhhchhhhcccCChhHHHHHHHHHHHHHHHHHHHcCCCcc
Q 019442 249 LYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELN 290 (341)
Q Consensus 249 l~~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~ 290 (341)
. -.+++|+++|..||++|+|+++
T Consensus 105 ~-------------------~~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 105 T-------------------FTKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp S-------------------SHHHHHHHHHHHHHHHTTT---
T ss_pred C-------------------CCHHHHHHHHHHHHHHCCCCcC
Confidence 1 1368999999999999999985
No 10
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=99.67 E-value=2.6e-16 Score=157.09 Aligned_cols=151 Identities=21% Similarity=0.303 Sum_probs=124.9
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHH-HhhccCCCCC-ChhHHHHHHHH
Q 019442 171 RETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALF-LAAKSEETPR-PLNDVLRASSE 248 (341)
Q Consensus 171 ~E~~lR~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLF-LA~KvEE~pr-kLrdIi~v~~~ 248 (341)
.-..+|...++||.+|...++|..+|+..|+.+++||+.+..+...+.++|+++||| ||||.||... .+.|++.++..
T Consensus 153 ~~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~ 232 (391)
T KOG0653|consen 153 IRAKMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDG 232 (391)
T ss_pred ccHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCC
Confidence 334789999999999999999999999999999999999988888899999999977 9999999644 46666654432
Q ss_pred HhhhhchhhhcccCChhHHHHHHHHHHHHHHHHHHHcCCCcccCCcHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhh-
Q 019442 249 LYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQTVLVNLALNLVSEGFASC- 327 (341)
Q Consensus 249 l~~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~~P~~~L~~~l~~L~ls~~~l~q~A~~ilnDsl~T~- 327 (341)
. | .+++|+.||..||.+|+|++.+++|+.||.++.+..+.+.+ ...++..++..++...
T Consensus 233 ~-----------------~--s~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~d~~-~~~~~k~~~El~l~d~~ 292 (391)
T KOG0653|consen 233 A-----------------Y--SREEILRMEKYILNVLEFDLSVPTPLSFLRRFLKAADYDIK-TRTLVKYLLELSLCDYS 292 (391)
T ss_pred c-----------------c--chHHHHHHHHHHHhccCeeecCCchHHHHHHHHHhhhcchh-HHHHHHHHHHHHHhhhH
Confidence 1 1 36899999999999999999999999999999998886543 4556666666666543
Q ss_pred -H---HHHHHHHHHHHhC
Q 019442 328 -L---QHGLATGALKHAK 341 (341)
Q Consensus 328 -L---Ps~IAaAaIyLA~ 341 (341)
+ |+.+|+|+.++|+
T Consensus 293 ~~~~~~s~~aaa~~~~~~ 310 (391)
T KOG0653|consen 293 MLSIPPSSSAAASFTLAL 310 (391)
T ss_pred HhccCcHHHHHHHHHHHH
Confidence 2 7888888888763
No 11
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=99.58 E-value=5.7e-15 Score=141.52 Aligned_cols=149 Identities=23% Similarity=0.213 Sum_probs=118.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhc-CCCCccchhHHHHHHHHHhhccCC-CCCChhHHHHHHH
Q 019442 170 LRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVR-RSHACHDRFIIATAALFLAAKSEE-TPRPLNDVLRASS 247 (341)
Q Consensus 170 e~E~~lR~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r-~Sl~~~d~~lVAaAcLFLA~KvEE-~prkLrdIi~v~~ 247 (341)
..+..+|....+|+.+||+-.+|-.+|...|+-||+||+.. +...+...++|+.||||+|+|+|| .|+++-++..++.
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 34556799999999999999999999999999999999875 344567799999999999999999 4888888876543
Q ss_pred HHhhhhchhhhcccCChhHHHHHHHHHHHHHHHHHHHcCCCcccCCcHHHHHHHHHHcCC-----------CHHHHHHHH
Q 019442 248 ELYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGL-----------SQTVLVNLA 316 (341)
Q Consensus 248 ~l~~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~~P~~~L~~~l~~L~l-----------s~~~l~q~A 316 (341)
.- -.-++|+.||.+||++|+|+|...+--..|.-|++..++ +++..+|+|
T Consensus 219 gA-------------------cs~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqia 279 (408)
T KOG0655|consen 219 GA-------------------CSEDDILTMELIILKALKWELSPITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIA 279 (408)
T ss_pred Cc-------------------cchHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcCCCCceeccccchHHHHHHH
Confidence 21 124689999999999999999999999999988887643 334456666
Q ss_pred HHHHHHHHhhh---H---HHHHHHHHHHH
Q 019442 317 LNLVSEGFASC---L---QHGLATGALKH 339 (341)
Q Consensus 317 ~~ilnDsl~T~---L---Ps~IAaAaIyL 339 (341)
.-+ |.+..+ + ..+||||||+-
T Consensus 280 qlL--Dlc~ldids~~fsYrilaAAal~h 306 (408)
T KOG0655|consen 280 QLL--DLCILDIDSLEFSYRILAAAALCH 306 (408)
T ss_pred HHH--HHHHhccccccchHHHHHHHHHHH
Confidence 533 333222 2 79999999863
No 12
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=99.58 E-value=9e-15 Score=146.78 Aligned_cols=152 Identities=20% Similarity=0.225 Sum_probs=122.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCC-CChhHHHHHHHH
Q 019442 170 LRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETP-RPLNDVLRASSE 248 (341)
Q Consensus 170 e~E~~lR~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~p-rkLrdIi~v~~~ 248 (341)
+-+..+|...++||.++...|+|-++|+.+|+.|++||+......-...++|+++|||||||+||.. +.+++++.++..
T Consensus 207 ~~~~~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g 286 (440)
T COG5024 207 LYEWSMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDG 286 (440)
T ss_pred hhHHhHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcc
Confidence 3445789999999999999999999999999999999999988887889999999999999999964 456777766432
Q ss_pred HhhhhchhhhcccCChhHHHHHHHHHHHHHHHHHHHcCCCcccCCcHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhh--
Q 019442 249 LYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQTVLVNLALNLVSEGFAS-- 326 (341)
Q Consensus 249 l~~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~~P~~~L~~~l~~L~ls~~~l~q~A~~ilnDsl~T-- 326 (341)
. -.++.|+.+|+.+|.+|+|++..+.|.-||.++-+..+.+.. -...+..++.-+...
T Consensus 287 ~-------------------~t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka~dyd~~-srt~~k~~~e~s~~~~~ 346 (440)
T COG5024 287 A-------------------FTRDDIIRAERYMLEVLDFNISWPSPMSFLRRISKASDYDIF-SRTPAKFSSEISPVDYK 346 (440)
T ss_pred c-------------------ccHHHHHHHHHHHhhhcccccCCCChHHHHHHHHhhcccchh-hhhhHhhhCCchHhhhh
Confidence 1 136899999999999999999999999998888777666542 223444444433322
Q ss_pred --hH-HHHHHHHHHHHhC
Q 019442 327 --CL-QHGLATGALKHAK 341 (341)
Q Consensus 327 --~L-Ps~IAaAaIyLA~ 341 (341)
.+ |+.+|+||.|+|+
T Consensus 347 f~~~~~S~~~aaa~~~s~ 364 (440)
T COG5024 347 FIQISPSWCAAAAMYLSR 364 (440)
T ss_pred hccCCchHHHHHHHHHHH
Confidence 12 9999999999985
No 13
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.54 E-value=2e-13 Score=130.90 Aligned_cols=147 Identities=20% Similarity=0.290 Sum_probs=131.9
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHHHHHh
Q 019442 171 RETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELY 250 (341)
Q Consensus 171 ~E~~lR~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~~~l~ 250 (341)
.|..+.. +...|..++..|+||..+..+|+.+|.+.+....+++.....+++||+|+||+.++.|+++.+|..+...
T Consensus 93 ~ernl~~-a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V-- 169 (285)
T COG1405 93 KERNLIT-ALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGV-- 169 (285)
T ss_pred hhhHHHH-HHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCC--
Confidence 4444444 7889999999999999999999999999999999999999999999999999999999999999987530
Q ss_pred hhhchhhhcccCChhHHHHHHHHHHHHHHHHHHHcCCCcccCCcHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhH--
Q 019442 251 HKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQTVLVNLALNLVSEGFASCL-- 328 (341)
Q Consensus 251 ~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~~P~~~L~~~l~~L~ls~~~l~q~A~~ilnDsl~T~L-- 328 (341)
.+++|..+.+.+.+.|+-.+....|..|+.+|+++|+++. ++...|..++..+....+
T Consensus 170 -------------------~~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~-~v~~~a~ei~~~~~~~g~~~ 229 (285)
T COG1405 170 -------------------SKKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSD-EVRRKAIEIVKKAKRAGLTA 229 (285)
T ss_pred -------------------CHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCH-HHHHHHHHHHHHHHHhCccc
Confidence 1367888899999999999999999999999999999996 488999999998877655
Q ss_pred ---HHHHHHHHHHHh
Q 019442 329 ---QHGLATGALKHA 340 (341)
Q Consensus 329 ---Ps~IAaAaIyLA 340 (341)
|..||+||||+|
T Consensus 230 Gk~P~glAaaaiy~a 244 (285)
T COG1405 230 GKSPAGLAAAAIYLA 244 (285)
T ss_pred CCCchhHHHHHHHHH
Confidence 999999999998
No 14
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.51 E-value=3.8e-13 Score=127.54 Aligned_cols=142 Identities=16% Similarity=0.193 Sum_probs=120.3
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHHHHHhhhhchh
Q 019442 177 YSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELYHKQNIT 256 (341)
Q Consensus 177 ~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~~~l~~k~~~~ 256 (341)
..+...|..++++++||..+.-.|..+|+++...+.+++.....+++||||+||+.|+.||++++|..++. +.
T Consensus 105 ~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~an--v~----- 177 (308)
T KOG1597|consen 105 KAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVAN--VS----- 177 (308)
T ss_pred HHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHHc--CC-----
Confidence 34778899999999999999999999999999999999999999999999999999999999999998765 22
Q ss_pred hhcccCChhHHHHHHHHHHHHHHHHHHHcCCCcccC--CcHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhH-----H
Q 019442 257 LLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQ--HPYDPLTSILNKLGLSQTVLVNLALNLVSEGFASCL-----Q 329 (341)
Q Consensus 257 ~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~--~P~~~L~~~l~~L~ls~~~l~q~A~~ilnDsl~T~L-----P 329 (341)
+++|-++=..|++.|+-....- +--+|+.+||..|+++.+ +.+.|-.++..+-.-++ |
T Consensus 178 --------------kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~-~q~aA~e~a~ka~~~~~~~gRsP 242 (308)
T KOG1597|consen 178 --------------KKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKS-AQEAATEIAEKAEEMDIRAGRSP 242 (308)
T ss_pred --------------HHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHH-HHHHHHHHHHHHHHhccccCCCc
Confidence 3466667778888887655443 477999999999999985 67777777766544333 9
Q ss_pred HHHHHHHHHHh
Q 019442 330 HGLATGALKHA 340 (341)
Q Consensus 330 s~IAaAaIyLA 340 (341)
-.||||+|||+
T Consensus 243 iSIAAa~IYmi 253 (308)
T KOG1597|consen 243 ISIAAAAIYMI 253 (308)
T ss_pred hhHHHHHHHHH
Confidence 99999999997
No 15
>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=99.41 E-value=9.7e-13 Score=100.83 Aligned_cols=87 Identities=30% Similarity=0.418 Sum_probs=76.8
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHHHHHhhhhch
Q 019442 176 RYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELYHKQNI 255 (341)
Q Consensus 176 R~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~~~l~~k~~~ 255 (341)
|...++||.+++..++++..+..+|+.+++||+....+.+.+++.+|+||||||||++|.++.+++++..+...
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~------ 75 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYA------ 75 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCC------
Confidence 45688999999999999999999999999999999999999999999999999999999999999998765310
Q ss_pred hhhcccCChhHHHHHHHHHHHHHHHHH
Q 019442 256 TLLSYLLPIDWFEQYRERVIEAEQMIL 282 (341)
Q Consensus 256 ~~~~~~~~~~~~~~~re~Il~~E~~IL 282 (341)
..++|..+|..||
T Consensus 76 --------------~~~~i~~~e~~il 88 (88)
T cd00043 76 --------------TEEEILRMEKLLL 88 (88)
T ss_pred --------------CHHHHHHHHHHhC
Confidence 2567888888764
No 16
>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=99.26 E-value=1.4e-11 Score=93.44 Aligned_cols=83 Identities=28% Similarity=0.385 Sum_probs=71.5
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHHHHHhhhhchhhhcc
Q 019442 181 AFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELYHKQNITLLSY 260 (341)
Q Consensus 181 ~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~~~l~~k~~~~~~~~ 260 (341)
+||.+++..++++..+..+|+.+++||+....+.+.+++.+|+||||+|||.+|.++..+++...+..
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~------------ 68 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGY------------ 68 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC------------
Confidence 48999999999999999999999999999777778999999999999999999998888888765421
Q ss_pred cCChhHHHHHHHHHHHHHHHHHH
Q 019442 261 LLPIDWFEQYRERVIEAEQMILT 283 (341)
Q Consensus 261 ~~~~~~~~~~re~Il~~E~~IL~ 283 (341)
...++|..+|..||+
T Consensus 69 --------~~~~~i~~~~~~il~ 83 (83)
T smart00385 69 --------FTEEEILRMEKLLLE 83 (83)
T ss_pred --------CCHHHHHHHHHHHhC
Confidence 024689999998873
No 17
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=98.98 E-value=1.3e-09 Score=107.31 Aligned_cols=153 Identities=18% Similarity=0.161 Sum_probs=126.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCC-CCChhHHHHHHHH
Q 019442 170 LRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEET-PRPLNDVLRASSE 248 (341)
Q Consensus 170 e~E~~lR~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~-prkLrdIi~v~~~ 248 (341)
+..-.+|...++|..++++...+.-++++.+..+.+||...........+++..+|+++|+|.||. +..+.+++..+..
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 333456999999999999999999999999999999999998888888899999999999999996 4567777665432
Q ss_pred HhhhhchhhhcccCChhHHHHHHHHHHHHHHHHHHHcCCCcccCCcHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhh-
Q 019442 249 LYHKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQHPYDPLTSILNKLGLSQTVLVNLALNLVSEGFASC- 327 (341)
Q Consensus 249 l~~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~~P~~~L~~~l~~L~ls~~~l~q~A~~ilnDsl~T~- 327 (341)
. | .+.++..+|..+|..|.|++..+....|+.+++........++..++-.+...++...
T Consensus 211 t-----------------y--~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~~~~~~~~~~e~~~~yl~elsll~~~ 271 (359)
T KOG0654|consen 211 T-----------------Y--TYWQVLRMEIDILNALTFELVRPTSKTFLRRFLRVAQTPELQVEPLANYLTELSLLDYI 271 (359)
T ss_pred h-----------------h--HHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHHhhcchhHHHHHHHHHHHHhhhhhHH
Confidence 2 1 3578999999999999999999999999999987655443346666766666665532
Q ss_pred -H---HHHHHHHHHHHhC
Q 019442 328 -L---QHGLATGALKHAK 341 (341)
Q Consensus 328 -L---Ps~IAaAaIyLA~ 341 (341)
+ |+.||+||+++|+
T Consensus 272 ~l~y~PSliAasAv~lA~ 289 (359)
T KOG0654|consen 272 FLKYLPSLIAASAVFLAR 289 (359)
T ss_pred HhccChHHHHHHHHHHHH
Confidence 2 9999999999996
No 18
>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=98.62 E-value=1.5e-07 Score=71.97 Aligned_cols=64 Identities=23% Similarity=0.311 Sum_probs=57.4
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHH
Q 019442 183 IQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRAS 246 (341)
Q Consensus 183 I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~ 246 (341)
|.++|..|+||..+..+|..++++.....-..+..+..+++||||+||+.++.+++++||..++
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 6789999999999999999999999999888899999999999999999999999999998764
No 19
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.47 E-value=8.8e-07 Score=90.44 Aligned_cols=141 Identities=18% Similarity=0.132 Sum_probs=110.2
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHHHHHhhhhchhh
Q 019442 178 SYCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELYHKQNITL 257 (341)
Q Consensus 178 ~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~~~l~~k~~~~~ 257 (341)
.+-..|.+++.+|+|+. ++.+|..+|..-..++-.++.....|.++|||++|+.|.++.-+-|+..+
T Consensus 69 n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~------------ 135 (521)
T KOG1598|consen 69 NARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSY------------ 135 (521)
T ss_pred HHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccc------------
Confidence 36678999999999999 99999999999999988888889999999999999999887655444332
Q ss_pred hcccCChhHHHHHHHHHHHHHHHHHHHcCCC---cccCCcHHHHHHHHHHcCCC--HHHHHHHHHHHHH----HHHhhhH
Q 019442 258 LSYLLPIDWFEQYRERVIEAEQMILTTLNFE---LNVQHPYDPLTSILNKLGLS--QTVLVNLALNLVS----EGFASCL 328 (341)
Q Consensus 258 ~~~~~~~~~~~~~re~Il~~E~~IL~tL~Fd---L~v~~P~~~L~~~l~~L~ls--~~~l~q~A~~iln----Dsl~T~L 328 (341)
...+.| ++...-..|...|.-+ +...+|.-|+.+|...|... .++++..|..+++ |.+.|.-
T Consensus 136 ----Lqv~Vy-----~LG~~~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGR 206 (521)
T KOG1598|consen 136 ----LQVSVY-----DLGSNFLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGR 206 (521)
T ss_pred ----eEEehh-----hhhHHHHHHHHHhccccccccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCC
Confidence 112223 3444555677788877 77889999999999888542 2457777777766 4454554
Q ss_pred -HHHHHHHHHHHh
Q 019442 329 -QHGLATGALKHA 340 (341)
Q Consensus 329 -Ps~IAaAaIyLA 340 (341)
|+.|+.|||++|
T Consensus 207 RPsglcGAaLliA 219 (521)
T KOG1598|consen 207 RPSGLCGAALLIA 219 (521)
T ss_pred CccchhHHHHHHH
Confidence 999999999997
No 20
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=97.88 E-value=2e-05 Score=77.97 Aligned_cols=95 Identities=22% Similarity=0.336 Sum_probs=79.2
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCC-ChhHHHHHHHHHhhhhchhhhc
Q 019442 181 AFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPR-PLNDVLRASSELYHKQNITLLS 259 (341)
Q Consensus 181 ~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~pr-kLrdIi~v~~~l~~k~~~~~~~ 259 (341)
.-|.+++...+|...|+++|-+||-....+.-+.+..+.++|-|||+||+|+.+... .++.+|....
T Consensus 387 REMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~E------------ 454 (497)
T KOG4164|consen 387 REMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLE------------ 454 (497)
T ss_pred HHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHH------------
Confidence 458889999999999999999999999999999999999999999999999996432 3455554332
Q ss_pred ccCChhHHHHHHHHHHHHHHHHHHHcCCCcccC
Q 019442 260 YLLPIDWFEQYRERVIEAEQMILTTLNFELNVQ 292 (341)
Q Consensus 260 ~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~ 292 (341)
+.|...|.+++..|+-||-+|.|.|+++
T Consensus 455 -----e~fR~nrrdLia~Ef~VlvaLefaL~~~ 482 (497)
T KOG4164|consen 455 -----EQFRLNRRDLIAFEFPVLVALEFALHLP 482 (497)
T ss_pred -----HHhcccHHhhhhhhhhHHHhhhhhccCC
Confidence 3344568899999999999999999875
No 21
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=97.82 E-value=9.9e-05 Score=71.94 Aligned_cols=67 Identities=13% Similarity=0.149 Sum_probs=62.1
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHH
Q 019442 180 CAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRAS 246 (341)
Q Consensus 180 ~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~ 246 (341)
.++|.++|..|+|+..+..+|..++++.....-..+..+..||+||||+||+..+.++++++|..++
T Consensus 220 ~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~ 286 (310)
T PRK00423 220 IDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVA 286 (310)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHc
Confidence 5899999999999999999999999999877767889999999999999999999999999998764
No 22
>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=97.42 E-value=0.001 Score=57.98 Aligned_cols=90 Identities=14% Similarity=0.133 Sum_probs=62.7
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhh---cC--CCCccchhHHHHHHHHHhhccCCC-CCChhHHHHHHHHHhhh
Q 019442 179 YCAFIQNLGLRLELPQTTIGTAMVLCHRFFV---RR--SHACHDRFIIATAALFLAAKSEET-PRPLNDVLRASSELYHK 252 (341)
Q Consensus 179 ~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~---r~--Sl~~~d~~lVAaAcLFLA~KvEE~-prkLrdIi~v~~~l~~k 252 (341)
..+|+.++....+++..++-.|.+|++|+.. .. .+.....+-+-++||.||.|.-+. ...-+....++.
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 4578999999999999999999999999998 22 234556778899999999999754 333333333221
Q ss_pred hchhhhcccCChhHHHHHHHHHHHHHHHHHHHcCCCc
Q 019442 253 QNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFEL 289 (341)
Q Consensus 253 ~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL 289 (341)
-..+++-.+|..+|..|+|+|
T Consensus 129 ----------------is~~eln~lE~~fL~~l~~~L 149 (149)
T PF08613_consen 129 ----------------ISLKELNELEREFLKLLDYNL 149 (149)
T ss_dssp ----------------S-HHHHHHHHHHHHHHTTT--
T ss_pred ----------------CCHHHHHHHHHHHHHHCCCcC
Confidence 024689999999999999986
No 23
>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=97.11 E-value=0.00048 Score=56.02 Aligned_cols=49 Identities=27% Similarity=0.295 Sum_probs=37.9
Q ss_pred CCcHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhh-H----HHHHHHHHHHHhC
Q 019442 292 QHPYDPLTSILNKLGLSQTVLVNLALNLVSEGFASC-L----QHGLATGALKHAK 341 (341)
Q Consensus 292 ~~P~~~L~~~l~~L~ls~~~l~q~A~~ilnDsl~T~-L----Ps~IAaAaIyLA~ 341 (341)
++|+.||..|++..+.+. .+..+|+.++..++.+. + |+.||+|||++|+
T Consensus 1 PTp~~Fl~~~~~~~~~~~-~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~ 54 (118)
T PF02984_consen 1 PTPYDFLRRFLKISNADQ-EVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLAR 54 (118)
T ss_dssp --HHHHHHHHHTSSSHHH-HHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHcCCcH-HHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHH
Confidence 479999999955444433 58899999999888764 2 9999999999984
No 24
>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=96.94 E-value=0.0028 Score=47.84 Aligned_cols=49 Identities=31% Similarity=0.320 Sum_probs=42.6
Q ss_pred cCCcHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhH-----HHHHHHHHHHHh
Q 019442 291 VQHPYDPLTSILNKLGLSQTVLVNLALNLVSEGFASCL-----QHGLATGALKHA 340 (341)
Q Consensus 291 v~~P~~~L~~~l~~L~ls~~~l~q~A~~ilnDsl~T~L-----Ps~IAaAaIyLA 340 (341)
.++|..+|.+++..++++.+ +..+|+.++...+.... |+.||+|||++|
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~-~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA 55 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPE-TLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLA 55 (88)
T ss_pred cchHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHHhcccccCChHHHHHHHHHHH
Confidence 35789999999999999985 88999999998776432 999999999998
No 25
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=96.81 E-value=0.0035 Score=47.67 Aligned_cols=42 Identities=21% Similarity=0.295 Sum_probs=34.7
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHhhhH-----HHHHHHHHHHHh
Q 019442 298 LTSILNKLGLSQTVLVNLALNLVSEGFASCL-----QHGLATGALKHA 340 (341)
Q Consensus 298 L~~~l~~L~ls~~~l~q~A~~ilnDsl~T~L-----Ps~IAaAaIyLA 340 (341)
|.+++..|+++.. +.+.|..+........+ |..||+||||+|
T Consensus 1 I~r~~~~L~L~~~-v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~a 47 (71)
T PF00382_consen 1 IPRICSKLGLPED-VRERAKEIYKKAQERGLLKGRSPESIAAACIYLA 47 (71)
T ss_dssp HHHHHHHTT--HH-HHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHH
T ss_pred ChHHHhHcCCCHH-HHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHH
Confidence 5789999999984 89999999888776655 999999999997
No 26
>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=96.58 E-value=0.0056 Score=45.75 Aligned_cols=43 Identities=28% Similarity=0.291 Sum_probs=37.4
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHhh-hH----HHHHHHHHHHHh
Q 019442 297 PLTSILNKLGLSQTVLVNLALNLVSEGFAS-CL----QHGLATGALKHA 340 (341)
Q Consensus 297 ~L~~~l~~L~ls~~~l~q~A~~ilnDsl~T-~L----Ps~IAaAaIyLA 340 (341)
+|.+++..++++.+ +..+|+.++...+.. .+ |+.||+|||++|
T Consensus 2 ~l~~~~~~~~~~~~-~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA 49 (83)
T smart00385 2 FLRRVCKALNLDPE-TLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLA 49 (83)
T ss_pred HHHHHHHHcCCCHH-HHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHH
Confidence 68899999999875 889999999988763 33 999999999998
No 27
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=96.10 E-value=0.018 Score=55.70 Aligned_cols=69 Identities=17% Similarity=0.175 Sum_probs=62.9
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHHH
Q 019442 179 YCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASS 247 (341)
Q Consensus 179 ~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~~ 247 (341)
-.++|.+.+..|+|+.++...|.-+.+..-......+..+.-+|+||||+||+..+..+.-+++..++.
T Consensus 194 p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~ 262 (285)
T COG1405 194 PSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAG 262 (285)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhC
Confidence 467899999999999999999999999999998888999999999999999999998888888877653
No 28
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=95.56 E-value=0.051 Score=52.53 Aligned_cols=68 Identities=15% Similarity=0.220 Sum_probs=61.8
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHH
Q 019442 179 YCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRAS 246 (341)
Q Consensus 179 ~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~ 246 (341)
..+||.+.|..|+||..+...|..+-++.-...-..+..+..||+|++|+++-.++.++.+++|..++
T Consensus 203 t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vt 270 (308)
T KOG1597|consen 203 TGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVT 270 (308)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHh
Confidence 56899999999999999999999999998887777778899999999999999999999999988765
No 29
>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=93.62 E-value=0.43 Score=41.34 Aligned_cols=69 Identities=14% Similarity=0.107 Sum_probs=53.5
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhc--CCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHHH
Q 019442 179 YCAFIQNLGLRLELPQTTIGTAMVLCHRFFVR--RSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASS 247 (341)
Q Consensus 179 ~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r--~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~~ 247 (341)
+..-|.++|++|+|+.++..-..+.|...... .-+.+.+..-+.+.|+|.-||+.....+.++|+..+.
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 45569999999999998877777777777653 3446677888999999999999999999999998764
No 30
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=91.05 E-value=0.68 Score=37.22 Aligned_cols=56 Identities=20% Similarity=0.077 Sum_probs=44.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCC
Q 019442 180 CAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEET 235 (341)
Q Consensus 180 ~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~ 235 (341)
..||....+..+..+.+...|..++.-......+..+.+-.||+||+++|.+.-+.
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 46677775555566778889999998888887888999999999999999998553
No 31
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=89.68 E-value=0.52 Score=46.45 Aligned_cols=57 Identities=23% Similarity=0.207 Sum_probs=41.1
Q ss_pred HHHHHHHHHcCCCHHH--HHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCC
Q 019442 181 AFIQNLGLRLELPQTT--IGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPR 237 (341)
Q Consensus 181 ~~I~~lg~~L~Lp~~t--iaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~pr 237 (341)
.+|......|++++.- ..+|.+|+.--.-..-+..+.+..||+||+|||++.+|.|.
T Consensus 143 klii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpL 201 (367)
T KOG0835|consen 143 KLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPL 201 (367)
T ss_pred HHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCC
Confidence 4566666777777654 56666665554444555678899999999999999999553
No 32
>KOG1674 consensus Cyclin [General function prediction only]
Probab=81.94 E-value=4.3 Score=37.82 Aligned_cols=92 Identities=15% Similarity=0.158 Sum_probs=63.7
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCC------C---Cccc-hhHHHHHHHHHhhccCCCCCChhHHHHHHHHHh
Q 019442 181 AFIQNLGLRLELPQTTIGTAMVLCHRFFVRRS------H---ACHD-RFIIATAALFLAAKSEETPRPLNDVLRASSELY 250 (341)
Q Consensus 181 ~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~S------l---~~~d-~~lVAaAcLFLA~KvEE~prkLrdIi~v~~~l~ 250 (341)
+++.++-+..+....+.-+|.+||+||-.... - .... .+-..++|+-+|+|..+..--- +. .+
T Consensus 80 ~yleri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~y~----n~---~~ 152 (218)
T KOG1674|consen 80 QYLERIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVYYS----NA---YY 152 (218)
T ss_pred HHHHHHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccchhhh----HH---HH
Confidence 57788888999999999999999999998622 1 1222 3336789999999998642111 11 11
Q ss_pred hhhchhhhcccCChhHHHHHHHHHHHHHHHHHHHcCCCcccC
Q 019442 251 HKQNITLLSYLLPIDWFEQYRERVIEAEQMILTTLNFELNVQ 292 (341)
Q Consensus 251 ~k~~~~~~~~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~ 292 (341)
.+-+ . . ..+++-.+|..+|..++|.+.+.
T Consensus 153 a~vg-----g-l-------~~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 153 AKVG-----G-L-------TTDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred HHhC-----C-C-------ChHhhhhhhHHHHhhCCeEEEec
Confidence 1110 0 1 14567799999999999999985
No 33
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=81.81 E-value=1.6 Score=43.12 Aligned_cols=58 Identities=17% Similarity=0.095 Sum_probs=43.1
Q ss_pred HHHHHHHHHcCCCH----HHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCCC
Q 019442 181 AFIQNLGLRLELPQ----TTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRP 238 (341)
Q Consensus 181 ~~I~~lg~~L~Lp~----~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prk 238 (341)
.++.+.++.|+-.. .+.-+|.++....+...-.-.+.++.||+|||+||+|.-+....
T Consensus 153 ~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~~~~ 214 (323)
T KOG0834|consen 153 KYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGVELP 214 (323)
T ss_pred HHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCCCCC
Confidence 34555555555444 47788888888888766556788999999999999999876433
No 34
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=80.99 E-value=1.8 Score=45.14 Aligned_cols=54 Identities=20% Similarity=0.177 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHHHH
Q 019442 195 TTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSE 248 (341)
Q Consensus 195 ~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~~~ 248 (341)
.|+.+|..+..|.-----..+..+--++-|||++||.+.+..+++.||+.+++.
T Consensus 185 ~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV 238 (521)
T KOG1598|consen 185 DVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHV 238 (521)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHH
Confidence 488888888877522111245567789999999999999999999999998753
No 35
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=74.34 E-value=25 Score=34.54 Aligned_cols=55 Identities=20% Similarity=0.146 Sum_probs=38.9
Q ss_pred HHHHHHHHHHc-C--CCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCC
Q 019442 180 CAFIQNLGLRL-E--LPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEE 234 (341)
Q Consensus 180 ~~~I~~lg~~L-~--Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE 234 (341)
..++.++...+ + -+..+...|..++...+..--.-.+.+..||+|||++|++...
T Consensus 164 ~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAAI~lA~~~~~ 221 (305)
T TIGR00569 164 EGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAG 221 (305)
T ss_pred HHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHHHHHHHHHHHHHhC
Confidence 34555665554 2 2234566777888777766555678999999999999998665
No 36
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=71.81 E-value=13 Score=30.25 Aligned_cols=44 Identities=23% Similarity=0.215 Sum_probs=29.5
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHHhh-hH----HHHHHHHHHHHh
Q 019442 296 DPLTSILNKLGLSQTVLVNLALNLVSEGFAS-CL----QHGLATGALKHA 340 (341)
Q Consensus 296 ~~L~~~l~~L~ls~~~l~q~A~~ilnDsl~T-~L----Ps~IAaAaIyLA 340 (341)
.++..++..++++.. ....|..++..-+.. .+ +..||+||+++|
T Consensus 36 ~~i~~~~~~~~l~~~-~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA 84 (127)
T PF00134_consen 36 DWIIELCQRLKLSPE-TLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLA 84 (127)
T ss_dssp HHHHHHHHHTT-BHH-HHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHH
T ss_pred HHHHHHHHhcccchh-HHHHHHHHHHHHHhhcccccchhhhhhhhHHHHh
Confidence 356667777777775 666777776654432 22 889999999987
No 37
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=62.98 E-value=14 Score=36.36 Aligned_cols=93 Identities=18% Similarity=0.200 Sum_probs=52.9
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHhh--cCCCCccchhHHHHHHHHHhhccCCCCCChhHHHHHHHHHhhhhchhhhc
Q 019442 182 FIQNLGLRLELPQTTIGTAMVLCHRFFV--RRSHACHDRFIIATAALFLAAKSEETPRPLNDVLRASSELYHKQNITLLS 259 (341)
Q Consensus 182 ~I~~lg~~L~Lp~~tiaTA~v~fhRFy~--r~Sl~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~~~l~~k~~~~~~~ 259 (341)
++..++....|.-..-....+++.|-.- ........+..+....+++|+|+=...---. .-+++++..
T Consensus 196 ~v~~l~~~~qlta~~aiitL~~~erl~~~~e~~~~p~~w~r~~~g~il~sskv~~dqs~wn---vdycqIlKd------- 265 (343)
T KOG1675|consen 196 FVRILFSWAQLTAECDIITLVYAERLLWLAERDPCPRNWSRAVLGEILLSSKVYDDQSVWN---VDYCEILKD------- 265 (343)
T ss_pred hhhhHhhhhhhhhccchHHHHhhHhhhhHhhcCCCcchhhhhhhhhheehhhhhhhhhccc---HHHHHHHhh-------
Confidence 3444444444443333344566666532 2233355566677777888988754210000 012222221
Q ss_pred ccCChhHHHHHHHHHHHHHHHHHHHcCCCcccCC
Q 019442 260 YLLPIDWFEQYRERVIEAEQMILTTLNFELNVQH 293 (341)
Q Consensus 260 ~~~~~~~~~~~re~Il~~E~~IL~tL~FdL~v~~ 293 (341)
...+++-++|+.+|+.|+|+++++.
T Consensus 266 ---------~tveDmNe~ERqfLelLqfNinvp~ 290 (343)
T KOG1675|consen 266 ---------QSVDDMNALERQFLELLQFNINVPS 290 (343)
T ss_pred ---------ccHhhHHHHHHHHHHHHhhccCccH
Confidence 1357899999999999999999863
No 38
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=56.73 E-value=88 Score=29.85 Aligned_cols=55 Identities=20% Similarity=0.225 Sum_probs=31.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCC
Q 019442 180 CAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPR 237 (341)
Q Consensus 180 ~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~pr 237 (341)
.++++++|. ..+.....|..+..--|...-.--++++.+|.|||++||=..|.+.
T Consensus 158 ~q~~qd~gi---~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~~ 212 (264)
T KOG0794|consen 158 LQFVQDMGI---NDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKDI 212 (264)
T ss_pred HHHHHHhcc---cchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCCh
Confidence 345555554 2333333333333332322222357899999999999998877543
No 39
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=49.67 E-value=46 Score=37.02 Aligned_cols=69 Identities=16% Similarity=0.140 Sum_probs=54.4
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhcCC--CCccchhHHHHHHHHHhhccCCCCCChhHHHHHHH
Q 019442 179 YCAFIQNLGLRLELPQTTIGTAMVLCHRFFVRRS--HACHDRFIIATAALFLAAKSEETPRPLNDVLRASS 247 (341)
Q Consensus 179 ~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~S--l~~~d~~lVAaAcLFLA~KvEE~prkLrdIi~v~~ 247 (341)
+..-|+.+|++|.|.+++...-..+|..-+.... +++.+..-+.+.|+|+-+|++....+.++|+..+.
T Consensus 680 AavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR 750 (920)
T KOG1010|consen 680 AAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYR 750 (920)
T ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHh
Confidence 3445999999999999887777777776665433 34455666899999999999999999999988764
No 40
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=34.94 E-value=1.2e+02 Score=23.66 Aligned_cols=43 Identities=21% Similarity=0.264 Sum_probs=35.7
Q ss_pred CCCccccHHHHHHhCCCccCCCCHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhh
Q 019442 146 DEPVFMSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTIGTAMVLCHRFFV 209 (341)
Q Consensus 146 ~~~w~ft~eEl~~~sPS~~~GIs~e~E~~lR~~~~~~I~~lg~~L~Lp~~tiaTA~v~fhRFy~ 209 (341)
+..|+|+.+++.+ +..+.++...|++...-++.+..+++|...
T Consensus 32 ~~~~~f~~~~l~r---------------------l~~~~rL~~Dl~in~~gi~lil~LLd~i~~ 74 (84)
T PF13591_consen 32 EEEWYFSEEDLAR---------------------LRRIRRLHRDLGINLEGIALILDLLDRIEQ 74 (84)
T ss_pred CCeeeECHHHHHH---------------------HHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 4689999999853 266888999999999999999999988653
No 41
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=32.21 E-value=82 Score=29.73 Aligned_cols=50 Identities=22% Similarity=0.290 Sum_probs=34.6
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHhhcCCC-----CccchhHHHHHHHHHhhccC
Q 019442 183 IQNLGLRLELPQTTIGTAMVLCHRFFVRRSH-----ACHDRFIIATAALFLAAKSE 233 (341)
Q Consensus 183 I~~lg~~L~Lp~~tiaTA~v~fhRFy~r~Sl-----~~~d~~lVAaAcLFLA~KvE 233 (341)
+.++|..|++ .+++-.|..++.-|=.+-.- .++.+-..++|++|+|||.-
T Consensus 96 VrdlaVQfgc-~evi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~l 150 (262)
T KOG4557|consen 96 VRDLAVQFGC-VEVIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKL 150 (262)
T ss_pred HHHHHHHHhH-HHHHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHH
Confidence 5677777776 35677788888777653221 24555677899999999864
No 42
>KOG1103 consensus Predicted coiled-coil protein [Function unknown]
Probab=30.86 E-value=84 Score=31.73 Aligned_cols=50 Identities=12% Similarity=0.024 Sum_probs=34.0
Q ss_pred ccccCCCCCccccccccccccccccccccccCCCCCCCCCC-CCCCCCCCC
Q 019442 73 ASYVQPNNAPSFKRRKFSASAWGDSARNYLQVPNEYETAVS-SSNKTLVPP 122 (341)
Q Consensus 73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~ 122 (341)
+|-+.+.++|--+|--.++..=-+.+.--.++||+||.|.| +|--|.-.|
T Consensus 373 ~nN~en~~PP~e~~lala~e~P~E~ggcP~~ie~~VpmPsPl~S~Gsslsp 423 (561)
T KOG1103|consen 373 ANNRENPAPPPEARLALAAEFPTEKGGCPRAIEPAVPMPSPLMSIGSSLSP 423 (561)
T ss_pred cccccCCCCCchhcccccccCccccCCCCCCCCCCCCCCCcccccccccCC
Confidence 34455667777787777776666666666689999999988 554443333
No 43
>PHA02956 hypothetical protein; Provisional
Probab=27.74 E-value=82 Score=27.72 Aligned_cols=45 Identities=22% Similarity=0.340 Sum_probs=34.4
Q ss_pred ccccHHHHHHhCCCccCCCCHHHHHHHHHHHHHHHHHHHHHcCCCHHHH
Q 019442 149 VFMSRDEIERFSPSRKDGIDALRETHLRYSYCAFIQNLGLRLELPQTTI 197 (341)
Q Consensus 149 w~ft~eEl~~~sPS~~~GIs~e~E~~lR~~~~~~I~~lg~~L~Lp~~ti 197 (341)
-+||++|+.. ..-|+++-++.-+|..--..-.+.|+.|.||...+
T Consensus 140 klfsedeii~----hl~gvq~lkdicik~i~~tv~kd~~dkl~lp~sll 184 (189)
T PHA02956 140 KLFSEDEIIN----HLVGVQKLKDICIKMINKTVKKDDCDKLELPRSLL 184 (189)
T ss_pred hccCHHHHHH----HHHccccHHHHHHHHHHhhhchhhhhhhcCcHHHH
Confidence 4899999975 46788887777777655566678899999997653
No 44
>KOG3088 consensus Secretory carrier membrane protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.62 E-value=2.5e+02 Score=27.63 Aligned_cols=14 Identities=7% Similarity=0.275 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHcCC
Q 019442 274 VIEAEQMILTTLNF 287 (341)
Q Consensus 274 Il~~E~~IL~tL~F 287 (341)
+...=..|++++||
T Consensus 207 ~~q~~~~v~qAvgf 220 (313)
T KOG3088|consen 207 FFQIVFCVFQAVGF 220 (313)
T ss_pred HHHHHHHHHHHHcc
Confidence 44555678888886
No 45
>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=24.61 E-value=1.8e+02 Score=28.62 Aligned_cols=43 Identities=21% Similarity=0.128 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHhhcCCCCccchhHHHHHHHHHhhccCCCCC
Q 019442 195 TTIGTAMVLCHRFFVRRSHACHDRFIIATAALFLAAKSEETPR 237 (341)
Q Consensus 195 ~tiaTA~v~fhRFy~r~Sl~~~d~~lVAaAcLFLA~KvEE~pr 237 (341)
++...|..+..--+...-.--++++.||+|||++||++-+.+.
T Consensus 168 ~~~~~aw~~inDa~~t~~~llypphiIA~a~l~ia~~~~~~~~ 210 (297)
T COG5333 168 KLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPI 210 (297)
T ss_pred HHHHHHHHHHHhhhhceeeeecChHHHHHHHHHHHHHhcCCcc
Confidence 3555666665555544444567899999999999999977553
No 46
>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=21.48 E-value=2.4e+02 Score=24.31 Aligned_cols=44 Identities=16% Similarity=0.128 Sum_probs=31.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHh--hhH-----HHHHHHHHHHH
Q 019442 295 YDPLTSILNKLGLSQTVLVNLALNLVSEGFA--SCL-----QHGLATGALKH 339 (341)
Q Consensus 295 ~~~L~~~l~~L~ls~~~l~q~A~~ilnDsl~--T~L-----Ps~IAaAaIyL 339 (341)
..-|..+|..|+++.+ +.+.+|.++.-++. +.| -..|-+.|||.
T Consensus 15 ~~Rl~~LC~~L~l~~~-~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~ 65 (135)
T PF01857_consen 15 AVRLQDLCERLDLSSD-LREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYG 65 (135)
T ss_dssp HHHHHHHHHHHTTSTT-HHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCcHH-HHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHH
Confidence 3456778888888874 77889998887765 455 66666677764
No 47
>PHA02690 hypothetical protein; Provisional
Probab=20.55 E-value=4e+02 Score=21.25 Aligned_cols=31 Identities=19% Similarity=0.121 Sum_probs=21.4
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhh
Q 019442 296 DPLTSILNKLGLSQTVLVNLALNLVSEGFASC 327 (341)
Q Consensus 296 ~~L~~~l~~L~ls~~~l~q~A~~ilnDsl~T~ 327 (341)
.|++.+...+..+. -+...+|.++-|.+.|-
T Consensus 22 rYLeAIqrhlEgs~-plLR~~~RlLfDL~lTv 52 (90)
T PHA02690 22 RYLEAIQRHLEGST-PLLRQMWRLLFDLLLTV 52 (90)
T ss_pred HHHHHHHHHHhcCC-HHHHHHHHHHHHHHHHH
Confidence 46666666666554 36777888888877663
Done!