Query 028181
Match_columns 212
No_of_seqs 183 out of 1129
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 07:31:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028181.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028181hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0794 CDK8 kinase-activating 100.0 2.1E-37 4.5E-42 259.4 7.5 159 53-211 1-174 (264)
2 KOG0834 CDK9 kinase-activating 100.0 2.6E-32 5.6E-37 241.7 11.9 146 61-206 10-167 (323)
3 TIGR00569 ccl1 cyclin ccl1. Un 100.0 5.1E-29 1.1E-33 220.3 13.4 141 57-202 1-171 (305)
4 KOG0835 Cyclin L [General func 99.9 2.3E-24 5.1E-29 188.6 11.1 131 77-207 16-158 (367)
5 COG5333 CCL1 Cdk activating ki 99.9 3.7E-24 8.1E-29 186.4 8.8 125 81-206 42-166 (297)
6 KOG2496 Cdk activating kinase 99.8 3.6E-19 7.8E-24 154.8 9.1 98 99-202 73-171 (325)
7 KOG0656 G1/S-specific cyclin D 99.8 6.4E-18 1.4E-22 150.3 12.5 120 80-205 74-197 (335)
8 PF00134 Cyclin_N: Cyclin, N-t 99.7 1.5E-17 3.3E-22 127.5 8.9 101 79-186 26-127 (127)
9 PRK00423 tfb transcription ini 99.7 1.1E-15 2.5E-20 135.7 13.5 113 85-206 123-235 (310)
10 cd00043 CYCLIN Cyclin box fold 99.5 7.1E-14 1.5E-18 98.7 9.1 86 84-178 2-88 (88)
11 KOG0653 Cyclin B and related k 99.5 8.2E-14 1.8E-18 127.4 7.7 117 80-203 154-272 (391)
12 KOG0655 G1/S-specific cyclin E 99.4 2.3E-13 4.9E-18 120.0 7.7 123 77-206 138-262 (408)
13 smart00385 CYCLIN domain prese 99.4 5.7E-13 1.2E-17 93.2 7.5 83 89-179 1-83 (83)
14 COG5024 Cyclin [Cell division 99.4 1.8E-12 3.9E-17 119.4 9.2 115 82-203 211-326 (440)
15 COG1405 SUA7 Transcription ini 99.3 1.9E-10 4.1E-15 101.2 15.9 114 84-206 97-210 (285)
16 KOG1597 Transcription initiati 99.3 1.2E-10 2.5E-15 101.6 14.3 115 83-206 103-219 (308)
17 PF00382 TFIIB: Transcription 98.9 3E-09 6.6E-14 74.6 6.9 64 91-154 1-64 (71)
18 KOG4164 Cyclin ik3-1/CABLES [C 98.6 2.4E-08 5.2E-13 90.2 4.4 95 88-187 386-481 (497)
19 PRK00423 tfb transcription ini 98.4 2.2E-06 4.8E-11 76.3 10.2 89 88-185 220-308 (310)
20 PF08613 Cyclin: Cyclin; Inte 97.9 0.00012 2.7E-09 58.4 10.2 90 87-185 54-149 (149)
21 KOG0654 G2/Mitotic-specific cy 97.7 2.9E-05 6.3E-10 70.3 3.7 115 80-201 133-248 (359)
22 COG1405 SUA7 Transcription ini 97.5 0.00066 1.4E-08 60.0 9.2 88 88-184 195-282 (285)
23 KOG1598 Transcription initiati 97.1 0.00085 1.8E-08 63.2 5.2 111 86-206 69-182 (521)
24 KOG1597 Transcription initiati 96.8 0.0052 1.1E-07 54.3 7.5 67 88-154 204-270 (308)
25 PF02984 Cyclin_C: Cyclin, C-t 94.3 0.11 2.5E-06 38.3 5.3 56 88-143 4-59 (118)
26 PF01857 RB_B: Retinoblastoma- 93.6 0.15 3.3E-06 40.3 5.0 70 87-156 14-85 (135)
27 KOG0835 Cyclin L [General func 89.8 0.49 1.1E-05 42.7 4.4 57 89-145 143-201 (367)
28 KOG1674 Cyclin [General functi 86.3 3.7 8E-05 34.9 7.5 92 88-188 79-181 (218)
29 KOG0834 CDK9 kinase-activating 86.3 0.49 1.1E-05 42.7 2.2 58 89-146 153-214 (323)
30 KOG1598 Transcription initiati 85.1 1.3 2.7E-05 42.3 4.4 49 104-155 186-237 (521)
31 TIGR00569 ccl1 cyclin ccl1. Un 78.4 5.6 0.00012 35.6 5.9 55 88-142 164-221 (305)
32 KOG0794 CDK8 kinase-activating 63.6 37 0.00081 29.5 7.2 56 88-146 158-213 (264)
33 KOG1675 Predicted cyclin [Gene 56.9 25 0.00054 31.7 5.3 75 107-189 213-290 (343)
34 KOG4557 Origin recognition com 55.6 23 0.0005 30.5 4.6 51 91-142 96-151 (262)
35 KOG1010 Rb (Retinoblastoma tum 47.5 29 0.00064 35.3 4.6 71 87-157 680-752 (920)
36 PF11357 Spy1: Cell cycle regu 30.9 58 0.0013 25.7 3.1 87 95-188 22-110 (131)
37 smart00435 TOPEUc DNA Topoisom 27.1 97 0.0021 28.8 4.3 21 100-120 111-131 (391)
38 KOG0213 Splicing factor 3b, su 23.4 7.2E+02 0.016 25.8 9.6 66 79-144 648-716 (1172)
39 COG5333 CCL1 Cdk activating ki 21.8 1.5E+02 0.0033 26.5 4.4 45 102-146 167-211 (297)
40 PF02315 MDH: Methanol dehydro 21.1 52 0.0011 24.2 1.1 26 31-57 23-49 (93)
41 PF14502 HTH_41: Helix-turn-he 20.6 1.5E+02 0.0034 19.2 3.1 25 90-114 8-32 (48)
No 1
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=100.00 E-value=2.1e-37 Score=259.38 Aligned_cols=159 Identities=48% Similarity=0.815 Sum_probs=138.9
Q ss_pred ccccccccc---ccch-HHhH-hHHhhcccccCHHH----HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCC
Q 028181 53 TTNSFWTKK---TWMW-RNLL-TEKRASLLKITSSL----RCRCPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTE 123 (212)
Q Consensus 53 ~a~~fw~s~---~W~f-~e~l-~~~r~~~~~~~~e~----r~~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~ 123 (212)
||+|||+|+ ||+| ++.| .++..|...++.++ +..+.++|+.+|++++|+|+|+|||++||+|||.+.|+++
T Consensus 1 MA~NFW~SSh~~qwl~dk~el~k~r~~D~r~l~~d~~~~l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~ 80 (264)
T KOG0794|consen 1 MAGNFWTSSHYQQWLLDKTELLKERQLDLRGLSEDEYSKLKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKE 80 (264)
T ss_pred CCcchhhhhhhhhHhcCHHHHhhhccchhhcccHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 899999996 8999 4444 44444545555543 4456899999999999999999999999999999999999
Q ss_pred CCchhhhHHHHHHhhccCCCC-ccHHHHHHHHHHhc-----ccccccccHHHHHHHHHHHHHHcCCcceecChHHHHHHH
Q 028181 124 YDPHLVAPTCLYLASKAEEST-VQARLLVFYIKKIY-----SDEKYRYEVKDILEMEMKILEALNYYLVVFHPYRSLVQF 197 (212)
Q Consensus 124 ~~~~lvaaAcLfLA~KvEE~~-~~i~~ii~~~~~~~-----~d~~~~~~~~~I~~~E~~LL~~L~Fdl~v~~P~~~L~~~ 197 (212)
++|.++|+||||||||+||++ ..++.++..++.+. .++.++++..+|.++|+.||+.|++.|.|.|||+.|.++
T Consensus 81 ~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~ 160 (264)
T KOG0794|consen 81 IEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYWPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQF 160 (264)
T ss_pred cCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccchhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHH
Confidence 999999999999999999998 67899999887762 466778888999999999999999999999999999999
Q ss_pred HHHcCCCCcccccC
Q 028181 198 LQDAGMNDINMTHL 211 (212)
Q Consensus 198 l~~l~l~~~~~~~~ 211 (212)
+++.|+++.++.|+
T Consensus 161 ~qd~gi~d~~~l~~ 174 (264)
T KOG0794|consen 161 VQDMGINDQKLLQL 174 (264)
T ss_pred HHHhcccchhhhhh
Confidence 99999988877765
No 2
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.98 E-value=2.6e-32 Score=241.74 Aligned_cols=146 Identities=26% Similarity=0.485 Sum_probs=130.1
Q ss_pred cccch-HHhHh---HHhhcccccCHH--HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHH
Q 028181 61 KTWMW-RNLLT---EKRASLLKITSS--LRCRCPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCL 134 (212)
Q Consensus 61 ~~W~f-~e~l~---~~r~~~~~~~~e--~r~~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcL 134 (212)
+.|+| ++++. +.|.+....+.| .|.++++||+++|.+||+++.+++||++||||||+.++++++|++.+|++||
T Consensus 10 ~~w~~s~e~~~~~tpSr~~g~~~~~E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~scl 89 (323)
T KOG0834|consen 10 SRWYFSKEQLEENTPSRRDGIDLKKELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCL 89 (323)
T ss_pred cccccCHHHHccCChhhccCCchhHHHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHH
Confidence 79999 77776 567776666655 4889999999999999999999999999999999999999999999999999
Q ss_pred HHhhccCCCCccHHHHHHHHHHhccc---c--cccc-cHHHHHHHHHHHHHHcCCcceecChHHHHHHHHHHcCCCCc
Q 028181 135 YLASKAEESTVQARLLVFYIKKIYSD---E--KYRY-EVKDILEMEMKILEALNYYLVVFHPYRSLVQFLQDAGMNDI 206 (212)
Q Consensus 135 fLA~KvEE~~~~i~~ii~~~~~~~~d---~--~~~~-~~~~I~~~E~~LL~~L~Fdl~v~~P~~~L~~~l~~l~l~~~ 206 (212)
|||+|+||++++++|||.+++++.+. + ...+ ..+.|+.+|.+||++|+|||+|+|||+||.+++++++.+.+
T Consensus 90 fLAgKvEetp~kl~dIi~~s~~~~~~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~l~~~~~ 167 (323)
T KOG0834|consen 90 FLAGKVEETPRKLEDIIKVSYRYLNPKDLELEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKKLKADEN 167 (323)
T ss_pred HHHhhcccCcccHHHHHHHHHHHcCcccccHHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHHhhhhhh
Confidence 99999999999999999999888753 1 1122 35899999999999999999999999999999999987765
No 3
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.96 E-value=5.1e-29 Score=220.25 Aligned_cols=141 Identities=31% Similarity=0.531 Sum_probs=119.6
Q ss_pred ccccc---ccch--HHhHhHHhhcc-------------------cccCHH----HHHHHHHHHHHHHHHcC--CCHHHHH
Q 028181 57 FWTKK---TWMW--RNLLTEKRASL-------------------LKITSS----LRCRCPTIYRNLAQHVK--VRQRVVA 106 (212)
Q Consensus 57 fw~s~---~W~f--~e~l~~~r~~~-------------------~~~~~e----~r~~~~~~I~~l~~~L~--L~~~t~a 106 (212)
||.|+ .|+| +++|...|... ..++.+ .|..++++|+++|.+|+ ||+.|++
T Consensus 1 y~~StQ~r~W~F~~~~~L~~~R~~~N~~~~~~~~~~~~~~~~~~~~Lt~eeE~~l~~~y~~~i~~~~~~lkp~Lpq~via 80 (305)
T TIGR00569 1 YRNSSQKRHWTFTSEEQLQEKRADANAKFREAHEEEEKVLEAKPIFLTPEEELDLVKYYEKRLLDFCSAFKPTMPTSVVG 80 (305)
T ss_pred CCCCcccccCcCCCHHHHHHHHHHHHHHHHHHHhhhccccccccCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHH
Confidence 78886 6999 47787766421 112332 37788999999999999 9999999
Q ss_pred HHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHcCCcce
Q 028181 107 TAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIKKIYSDEKYRYEVKDILEMEMKILEALNYYLV 186 (212)
Q Consensus 107 TA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~~~~~d~~~~~~~~~I~~~E~~LL~~L~Fdl~ 186 (212)
||++||||||+++|+.++|+++|++||||||||+||+++++++++..+.. + .....++|+++|+.||++|+|+|.
T Consensus 81 TAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~---~--~~~~~~~Il~~E~~lL~~L~F~L~ 155 (305)
T TIGR00569 81 TAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKE---T--PLKALEQVLEYELLLIQQLNFHLI 155 (305)
T ss_pred HHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccC---C--chhhHHHHHHHHHHHHHHCCCcEE
Confidence 99999999999999999999999999999999999999999999886532 1 112358999999999999999999
Q ss_pred ecChHHHHHHHHHHcC
Q 028181 187 VFHPYRSLVQFLQDAG 202 (212)
Q Consensus 187 v~~P~~~L~~~l~~l~ 202 (212)
|+|||++|..|+.+++
T Consensus 156 V~hPyr~L~~~l~dl~ 171 (305)
T TIGR00569 156 VHNPYRPLEGFLIDIK 171 (305)
T ss_pred eeCccHHHHHHHHHHH
Confidence 9999999999998764
No 4
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.91 E-value=2.3e-24 Score=188.55 Aligned_cols=131 Identities=23% Similarity=0.280 Sum_probs=116.4
Q ss_pred cccCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHHH
Q 028181 77 LKITSSLRCRCPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIKK 156 (212)
Q Consensus 77 ~~~~~e~r~~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~~ 156 (212)
..++++.|..++.||++.|..|+|||.+.+|+.|+|+|||...|+..+|...+++|||.||+|+||.|+++++|+++++.
T Consensus 16 ~e~e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~ 95 (367)
T KOG0835|consen 16 LETEEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHY 95 (367)
T ss_pred cchHHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHH
Confidence 34456789999999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred hc---ccc---------cccccHHHHHHHHHHHHHHcCCcceecChHHHHHHHHHHcCCCCcc
Q 028181 157 IY---SDE---------KYRYEVKDILEMEMKILEALNYYLVVFHPYRSLVQFLQDAGMNDIN 207 (212)
Q Consensus 157 ~~---~d~---------~~~~~~~~I~~~E~~LL~~L~Fdl~v~~P~~~L~~~l~~l~l~~~~ 207 (212)
+. .+. .+......++.+|..||.+|||+++|.|||+++..|++.|++++..
T Consensus 96 L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~ 158 (367)
T KOG0835|consen 96 LEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYLQTLQLPPNL 158 (367)
T ss_pred HHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHHHHhcCCCch
Confidence 53 111 1111246899999999999999999999999999999999999875
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=99.90 E-value=3.7e-24 Score=186.44 Aligned_cols=125 Identities=32% Similarity=0.504 Sum_probs=111.3
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHHHhccc
Q 028181 81 SSLRCRCPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIKKIYSD 160 (212)
Q Consensus 81 ~e~r~~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~~~~~d 160 (212)
...|..+..+|+.+|.+|+||+.|.+||+.||+||+.++++++++++.++.||||||||+||+++.+.-....++.++++
T Consensus 42 ~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se 121 (297)
T COG5333 42 LNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSE 121 (297)
T ss_pred hhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccc
Confidence 34688999999999999999999999999999999999999999999999999999999999988887666667666644
Q ss_pred ccccccHHHHHHHHHHHHHHcCCcceecChHHHHHHHHHHcCCCCc
Q 028181 161 EKYRYEVKDILEMEMKILEALNYYLVVFHPYRSLVQFLQDAGMNDI 206 (212)
Q Consensus 161 ~~~~~~~~~I~~~E~~LL~~L~Fdl~v~~P~~~L~~~l~~l~l~~~ 206 (212)
. ..-+++.|.++|+.||++|+||++|+|||.++..+++++...+.
T Consensus 122 ~-~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~~q~~~~ 166 (297)
T COG5333 122 E-PKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKDLQEKDK 166 (297)
T ss_pred c-ccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHHHHhccH
Confidence 3 23347899999999999999999999999999999998876654
No 6
>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=99.79 E-value=3.6e-19 Score=154.78 Aligned_cols=98 Identities=31% Similarity=0.588 Sum_probs=90.0
Q ss_pred CCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHHHhcccccccc-cHHHHHHHHHHH
Q 028181 99 KVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIKKIYSDEKYRY-EVKDILEMEMKI 177 (212)
Q Consensus 99 ~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~~~~~d~~~~~-~~~~I~~~E~~L 177 (212)
++|..|..||+.||+|||..+|..+++|..|++||+|||||+||..+++.+++..++ +-++ ..+.|+++|+.+
T Consensus 73 ~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~------~~~~k~~e~vLk~E~~l 146 (325)
T KOG2496|consen 73 NLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMN------GRKWKTHEIVLKYEFLL 146 (325)
T ss_pred CCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhcc------CcccccHHHHHhchHHH
Confidence 689999999999999999999999999999999999999999999999999999864 1122 358999999999
Q ss_pred HHHcCCcceecChHHHHHHHHHHcC
Q 028181 178 LEALNYYLVVFHPYRSLVQFLQDAG 202 (212)
Q Consensus 178 L~~L~Fdl~v~~P~~~L~~~l~~l~ 202 (212)
|+.|+|+|.|++||++|..|+.++.
T Consensus 147 lqsL~f~L~vh~PyRPleGFl~D~k 171 (325)
T KOG2496|consen 147 LQSLKFSLTVHNPYRPLEGFLLDMK 171 (325)
T ss_pred HHhhhhhheecCCCCchHHHHHHHH
Confidence 9999999999999999999998773
No 7
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=99.76 E-value=6.4e-18 Score=150.34 Aligned_cols=120 Identities=26% Similarity=0.362 Sum_probs=104.8
Q ss_pred CHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCC---chhhhHHHHHHhhccCCCCcc-HHHHHHHHH
Q 028181 80 TSSLRCRCPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYD---PHLVAPTCLYLASKAEESTVQ-ARLLVFYIK 155 (212)
Q Consensus 80 ~~e~r~~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~---~~lvaaAcLfLA~KvEE~~~~-i~~ii~~~~ 155 (212)
.+.+|.++++||.++|...++...|...|+.||+||...+++.+.. .+++|+|||+||+|+||..++ +-|+....
T Consensus 74 ~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~- 152 (335)
T KOG0656|consen 74 LSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEY- 152 (335)
T ss_pred ccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcc-
Confidence 3456999999999999999999999999999999999999998888 899999999999999998654 33443321
Q ss_pred HhcccccccccHHHHHHHHHHHHHHcCCcceecChHHHHHHHHHHcCCCC
Q 028181 156 KIYSDEKYRYEVKDILEMEMKILEALNYYLVVFHPYRSLVQFLQDAGMND 205 (212)
Q Consensus 156 ~~~~d~~~~~~~~~I~~~E~~LL~~L~Fdl~v~~P~~~L~~~l~~l~l~~ 205 (212)
..+.+.++.|.++|.+||.+|+|+++..+|+.|+..|+.+++..+
T Consensus 153 -----~~~~feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ki~~~~ 197 (335)
T KOG0656|consen 153 -----TDNVFEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLSKISQKD 197 (335)
T ss_pred -----ccccccHHHHHHHHHHHHhhccccccCCCchHHHHHHHHHcCccc
Confidence 123456899999999999999999999999999999999999863
No 8
>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=99.73 E-value=1.5e-17 Score=127.51 Aligned_cols=101 Identities=32% Similarity=0.418 Sum_probs=86.0
Q ss_pred cCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCC-CccHHHHHHHHHHh
Q 028181 79 ITSSLRCRCPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEES-TVQARLLVFYIKKI 157 (212)
Q Consensus 79 ~~~e~r~~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~-~~~i~~ii~~~~~~ 157 (212)
++.+.|...++||.+++..++++..|+.+|+.||+||+.+.++...+++++++||+++|||+||. +.++.+++..+.
T Consensus 26 ~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~-- 103 (127)
T PF00134_consen 26 ITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISD-- 103 (127)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTT--
T ss_pred cCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHc--
Confidence 44577999999999999999999999999999999999999999999999999999999999998 667888888752
Q ss_pred cccccccccHHHHHHHHHHHHHHcCCcce
Q 028181 158 YSDEKYRYEVKDILEMEMKILEALNYYLV 186 (212)
Q Consensus 158 ~~d~~~~~~~~~I~~~E~~LL~~L~Fdl~ 186 (212)
..++.++|.++|+.||++|+|+++
T Consensus 104 -----~~~~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 104 -----NTFTKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp -----TSSHHHHHHHHHHHHHHHTTT---
T ss_pred -----CCCCHHHHHHHHHHHHHHCCCCcC
Confidence 245689999999999999999985
No 9
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.66 E-value=1.1e-15 Score=135.71 Aligned_cols=113 Identities=15% Similarity=0.131 Sum_probs=106.1
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHHHhccccccc
Q 028181 85 CRCPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIKKIYSDEKYR 164 (212)
Q Consensus 85 ~~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~~~~~d~~~~ 164 (212)
..+++.|.++|..|+||+.++.+|..+|++++..+.+++.+...+++||||+|||.|+.|+++++|...++
T Consensus 123 ~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~--------- 193 (310)
T PRK00423 123 AFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSR--------- 193 (310)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhC---------
Confidence 56789999999999999999999999999999999999999999999999999999999999999998763
Q ss_pred ccHHHHHHHHHHHHHHcCCcceecChHHHHHHHHHHcCCCCc
Q 028181 165 YEVKDILEMEMKILEALNYYLVVFHPYRSLVQFLQDAGMNDI 206 (212)
Q Consensus 165 ~~~~~I~~~E~~LL~~L~Fdl~v~~P~~~L~~~l~~l~l~~~ 206 (212)
.+.++|...++.|++.|++++.+.+|+.||.+|+..|+++..
T Consensus 194 v~~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~ 235 (310)
T PRK00423 194 VSRKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGE 235 (310)
T ss_pred CCHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHH
Confidence 357899999999999999999999999999999999999864
No 10
>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=99.52 E-value=7.1e-14 Score=98.73 Aligned_cols=86 Identities=30% Similarity=0.363 Sum_probs=78.1
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHHHhcccccc
Q 028181 84 RCRCPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIKKIYSDEKY 163 (212)
Q Consensus 84 r~~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~~~~~d~~~ 163 (212)
|....+||.+++..++++..+..+|..|++||+..+.+.+++++.+|+||+|+|||+++.+..+++++..+.
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~-------- 73 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTG-------- 73 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhC--------
Confidence 446789999999999999999999999999999999999999999999999999999999889999988762
Q ss_pred cc-cHHHHHHHHHHHH
Q 028181 164 RY-EVKDILEMEMKIL 178 (212)
Q Consensus 164 ~~-~~~~I~~~E~~LL 178 (212)
. +.++|..+|..|+
T Consensus 74 -~~~~~~i~~~e~~il 88 (88)
T cd00043 74 -YATEEEILRMEKLLL 88 (88)
T ss_pred -CCCHHHHHHHHHHhC
Confidence 2 5788999998874
No 11
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=99.47 E-value=8.2e-14 Score=127.44 Aligned_cols=117 Identities=24% Similarity=0.301 Sum_probs=103.9
Q ss_pred CHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHH-HhhccCCCCcc-HHHHHHHHHHh
Q 028181 80 TSSLRCRCPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLY-LASKAEESTVQ-ARLLVFYIKKI 157 (212)
Q Consensus 80 ~~e~r~~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLf-LA~KvEE~~~~-i~~ii~~~~~~ 157 (212)
...+|...++|+.++...++|...|+..|+.+++||.....+...+.++++++||| +|||.||...+ +.+++..+.
T Consensus 154 ~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd-- 231 (391)
T KOG0653|consen 154 RAKMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITD-- 231 (391)
T ss_pred cHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeC--
Confidence 34689999999999999999999999999999999999988888899999999977 99999997666 666665542
Q ss_pred cccccccccHHHHHHHHHHHHHHcCCcceecChHHHHHHHHHHcCC
Q 028181 158 YSDEKYRYEVKDILEMEMKILEALNYYLVVFHPYRSLVQFLQDAGM 203 (212)
Q Consensus 158 ~~d~~~~~~~~~I~~~E~~LL~~L~Fdl~v~~P~~~L~~~l~~l~l 203 (212)
..++.++|+.+|..||..|+|++.+++|+.||.++.+....
T Consensus 232 -----~~~s~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ka~~~ 272 (391)
T KOG0653|consen 232 -----GAYSREEILRMEKYILNVLEFDLSVPTPLSFLRRFLKAADY 272 (391)
T ss_pred -----CccchHHHHHHHHHHHhccCeeecCCchHHHHHHHHHhhhc
Confidence 24678999999999999999999999999999999988763
No 12
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=99.44 E-value=2.3e-13 Score=120.04 Aligned_cols=123 Identities=24% Similarity=0.308 Sum_probs=107.0
Q ss_pred cccCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhc-CCCCCCCCchhhhHHHHHHhhccCCC-CccHHHHHHHH
Q 028181 77 LKITSSLRCRCPTIYRNLAQHVKVRQRVVATAVTYMRRCYT-RKSMTEYDPHLVAPTCLYLASKAEES-TVQARLLVFYI 154 (212)
Q Consensus 77 ~~~~~e~r~~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~-~~s~~~~~~~lvaaAcLfLA~KvEE~-~~~i~~ii~~~ 154 (212)
.+..+++|...++|+.++|+-.+|-..|+..|.-||+||.. .+...+.+.++|+.||||+|+|+||. |.++-++..++
T Consensus 138 pdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvT 217 (408)
T KOG0655|consen 138 PDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVT 217 (408)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeec
Confidence 44568899999999999999999999999999999999985 45667789999999999999999997 55687777654
Q ss_pred HHhcccccccccHHHHHHHHHHHHHHcCCcceecChHHHHHHHHHHcCCCCc
Q 028181 155 KKIYSDEKYRYEVKDILEMEMKILEALNYYLVVFHPYRSLVQFLQDAGMNDI 206 (212)
Q Consensus 155 ~~~~~d~~~~~~~~~I~~~E~~LL~~L~Fdl~v~~P~~~L~~~l~~l~l~~~ 206 (212)
|. ..+-++|+.+|..||++|+|++...+.-..|.-|++..++++.
T Consensus 218 -----Dg--Acs~ddIltmE~iilkal~W~l~PiTii~WL~vylQv~~~n~~ 262 (408)
T KOG0655|consen 218 -----DG--ACSEDDILTMELIILKALKWELSPITIISWLNVYLQVDALNDA 262 (408)
T ss_pred -----cC--ccchHHHHHHHHHHHHHhcccccceehHHHHHHHHHHHhcCCC
Confidence 22 2345899999999999999999999999999999999888764
No 13
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=99.42 E-value=5.7e-13 Score=93.23 Aligned_cols=83 Identities=29% Similarity=0.481 Sum_probs=73.7
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHHHhcccccccccHH
Q 028181 89 TIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIKKIYSDEKYRYEVK 168 (212)
Q Consensus 89 ~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~~~~~d~~~~~~~~ 168 (212)
+||.+++..++++..+..+|..+++||+..+.+...+++.+|+||+|+|||++|.++..+++...+.. ++.+
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~--------~~~~ 72 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGY--------FTEE 72 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC--------CCHH
Confidence 48999999999999999999999999999777888999999999999999999998888888776521 3678
Q ss_pred HHHHHHHHHHH
Q 028181 169 DILEMEMKILE 179 (212)
Q Consensus 169 ~I~~~E~~LL~ 179 (212)
+|.++|+.||+
T Consensus 73 ~i~~~~~~il~ 83 (83)
T smart00385 73 EILRMEKLLLE 83 (83)
T ss_pred HHHHHHHHHhC
Confidence 99999999873
No 14
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=99.37 E-value=1.8e-12 Score=119.37 Aligned_cols=115 Identities=19% Similarity=0.251 Sum_probs=101.8
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCcc-HHHHHHHHHHhccc
Q 028181 82 SLRCRCPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQ-ARLLVFYIKKIYSD 160 (212)
Q Consensus 82 e~r~~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~-i~~ii~~~~~~~~d 160 (212)
.+|...++||.++...|++-+.|+..|+.+++||...+...--..++++++|||+|||.||...+ +++++-++..
T Consensus 211 ~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g---- 286 (440)
T COG5024 211 SMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDG---- 286 (440)
T ss_pred hHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcc----
Confidence 45777899999999999999999999999999999998888888999999999999999998664 7888777632
Q ss_pred ccccccHHHHHHHHHHHHHHcCCcceecChHHHHHHHHHHcCC
Q 028181 161 EKYRYEVKDILEMEMKILEALNYYLVVFHPYRSLVQFLQDAGM 203 (212)
Q Consensus 161 ~~~~~~~~~I~~~E~~LL~~L~Fdl~v~~P~~~L~~~l~~l~l 203 (212)
.++.++|+.+|+.+|..|+|++..+.|..||.++-+.-..
T Consensus 287 ---~~t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSka~dy 326 (440)
T COG5024 287 ---AFTRDDIIRAERYMLEVLDFNISWPSPMSFLRRISKASDY 326 (440)
T ss_pred ---cccHHHHHHHHHHHhhhcccccCCCChHHHHHHHHhhccc
Confidence 4578999999999999999999999999998887665543
No 15
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.27 E-value=1.9e-10 Score=101.24 Aligned_cols=114 Identities=15% Similarity=0.175 Sum_probs=106.9
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHHHhcccccc
Q 028181 84 RCRCPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIKKIYSDEKY 163 (212)
Q Consensus 84 r~~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~~~~~d~~~ 163 (212)
-..+.+.|..++..|+||..+..+|+.+|++.+..+.+++.+...+++||+|.||+.++.|+++.+|..++.
T Consensus 97 l~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~-------- 168 (285)
T COG1405 97 LITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALG-------- 168 (285)
T ss_pred HHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHC--------
Confidence 456789999999999999999999999999999999999999999999999999999999999999999874
Q ss_pred cccHHHHHHHHHHHHHHcCCcceecChHHHHHHHHHHcCCCCc
Q 028181 164 RYEVKDILEMEMKILEALNYYLVVFHPYRSLVQFLQDAGMNDI 206 (212)
Q Consensus 164 ~~~~~~I~~~E~~LL~~L~Fdl~v~~P~~~L~~~l~~l~l~~~ 206 (212)
.++++|..+.+.+.+.|+-.+....|..|+.+|+.+||+++.
T Consensus 169 -V~~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~ 210 (285)
T COG1405 169 -VSKKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASKLGLSDE 210 (285)
T ss_pred -CCHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHH
Confidence 246899999999999999999999999999999999999953
No 16
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.27 E-value=1.2e-10 Score=101.63 Aligned_cols=115 Identities=14% Similarity=0.132 Sum_probs=103.9
Q ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHHHhccccc
Q 028181 83 LRCRCPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIKKIYSDEK 162 (212)
Q Consensus 83 ~r~~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~~~~~d~~ 162 (212)
.-..+...|..|+++++||..+..+|..+|+++.....+++.+...+++||||+||.-++.||++++|..+++
T Consensus 103 ~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~an------- 175 (308)
T KOG1597|consen 103 VLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVAN------- 175 (308)
T ss_pred HHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHHc-------
Confidence 3456789999999999999999999999999999999999999999999999999999999999999999884
Q ss_pred ccccHHHHHHHHHHHHHHcCCcceec--ChHHHHHHHHHHcCCCCc
Q 028181 163 YRYEVKDILEMEMKILEALNYYLVVF--HPYRSLVQFLQDAGMNDI 206 (212)
Q Consensus 163 ~~~~~~~I~~~E~~LL~~L~Fdl~v~--~P~~~L~~~l~~l~l~~~ 206 (212)
.+.++|.++=..|++.|+-..... +--+|+.+||..|+++..
T Consensus 176 --v~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~ 219 (308)
T KOG1597|consen 176 --VSKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKS 219 (308)
T ss_pred --CCHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHH
Confidence 257899999999999998876644 588999999999999854
No 17
>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=98.94 E-value=3e-09 Score=74.59 Aligned_cols=64 Identities=14% Similarity=0.249 Sum_probs=57.9
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHH
Q 028181 91 YRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYI 154 (212)
Q Consensus 91 I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~ 154 (212)
|.++|..|+||..+..+|..++++-...+-.++.++..+++||||+||+.++.++++++|..++
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 6789999999999999999999999999988999999999999999999999999999998875
No 18
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=98.64 E-value=2.4e-08 Score=90.23 Aligned_cols=95 Identities=22% Similarity=0.400 Sum_probs=83.4
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCcc-HHHHHHHHHHhccccccccc
Q 028181 88 PTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQ-ARLLVFYIKKIYSDEKYRYE 166 (212)
Q Consensus 88 ~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~-i~~ii~~~~~~~~d~~~~~~ 166 (212)
-..|.+++...++...|+++|.|||.+..+++-+.+.+..+.|-|||.||+|+.+..++ ++.+|..+-. .+...
T Consensus 386 KREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee-----~fR~n 460 (497)
T KOG4164|consen 386 KREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEE-----QFRLN 460 (497)
T ss_pred HHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHH-----Hhccc
Confidence 36778899999999999999999999999999999999999999999999999976553 8888887633 34555
Q ss_pred HHHHHHHHHHHHHHcCCccee
Q 028181 167 VKDILEMEMKILEALNYYLVV 187 (212)
Q Consensus 167 ~~~I~~~E~~LL~~L~Fdl~v 187 (212)
..+++..|+-||-+|.|.|++
T Consensus 461 rrdLia~Ef~VlvaLefaL~~ 481 (497)
T KOG4164|consen 461 RRDLIAFEFPVLVALEFALHL 481 (497)
T ss_pred HHhhhhhhhhHHHhhhhhccC
Confidence 789999999999999999985
No 19
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=98.40 E-value=2.2e-06 Score=76.34 Aligned_cols=89 Identities=12% Similarity=0.109 Sum_probs=77.7
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHHHhcccccccccH
Q 028181 88 PTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIKKIYSDEKYRYEV 167 (212)
Q Consensus 88 ~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~~~~~d~~~~~~~ 167 (212)
.+||.++|..|+|+..+..+|..++++.....-..+.+|..+|+||||+||+..+.+++.++|..++. .+.
T Consensus 220 ~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~---------Vs~ 290 (310)
T PRK00423 220 IDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAG---------VTE 290 (310)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcC---------CCH
Confidence 48999999999999999999999999988777778999999999999999999999999999988762 234
Q ss_pred HHHHHHHHHHHHHcCCcc
Q 028181 168 KDILEMEMKILEALNYYL 185 (212)
Q Consensus 168 ~~I~~~E~~LL~~L~Fdl 185 (212)
..|....+.|++.|+..+
T Consensus 291 ~tI~~~ykel~~~l~~~~ 308 (310)
T PRK00423 291 VTVRNRYKELAEKLDIKI 308 (310)
T ss_pred HHHHHHHHHHHHHhCccc
Confidence 678888888888887654
No 20
>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=97.92 E-value=0.00012 Score=58.40 Aligned_cols=90 Identities=20% Similarity=0.245 Sum_probs=65.9
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhc---C--CCCCCCCchhhhHHHHHHhhccCC-CCccHHHHHHHHHHhccc
Q 028181 87 CPTIYRNLAQHVKVRQRVVATAVTYMRRCYT---R--KSMTEYDPHLVAPTCLYLASKAEE-STVQARLLVFYIKKIYSD 160 (212)
Q Consensus 87 ~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~---~--~s~~~~~~~lvaaAcLfLA~KvEE-~~~~i~~ii~~~~~~~~d 160 (212)
...|+.++.+..+++..++-.|.+|++|+.. . ..+...+.+-+-++|+.+|+|.-+ ..-+-+....++
T Consensus 54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~------ 127 (149)
T PF08613_consen 54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVG------ 127 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHH------
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhc------
Confidence 5678999999999999999999999999988 2 224567788899999999999744 455556555554
Q ss_pred ccccccHHHHHHHHHHHHHHcCCcc
Q 028181 161 EKYRYEVKDILEMEMKILEALNYYL 185 (212)
Q Consensus 161 ~~~~~~~~~I~~~E~~LL~~L~Fdl 185 (212)
....+++-.+|+..|..|+|+|
T Consensus 128 ---gis~~eln~lE~~fL~~l~~~L 149 (149)
T PF08613_consen 128 ---GISLKELNELEREFLKLLDYNL 149 (149)
T ss_dssp ---TS-HHHHHHHHHHHHHHTTT--
T ss_pred ---CCCHHHHHHHHHHHHHHCCCcC
Confidence 2357899999999999999986
No 21
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=97.71 E-value=2.9e-05 Score=70.34 Aligned_cols=115 Identities=24% Similarity=0.309 Sum_probs=100.9
Q ss_pred CHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCc-cHHHHHHHHHHhc
Q 028181 80 TSSLRCRCPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTV-QARLLVFYIKKIY 158 (212)
Q Consensus 80 ~~e~r~~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~-~i~~ii~~~~~~~ 158 (212)
++.+|-.++.|..++++..++...++..+..+.+||...........+++..+|.++|+|-||... .+++++..+.+
T Consensus 133 t~smrgilvdwlvevsee~r~~~e~l~ls~~~~drfl~~~~~~~~k~ql~g~s~m~I~sk~ee~~~~~~~ef~~itd~-- 210 (359)
T KOG0654|consen 133 TPSMRGILVDWLVEVSEEYRLTFETLYLSVNYRDRFLSYKEVNKQKLQLVGISAMLIASKYEEIKEPRVEEFCYITDN-- 210 (359)
T ss_pred CcchhhhhhhhhhHHHHHHHhhhhheeecHHHHHHHhccCccHHHHHHHhCcccceeeccchhhcchHHHHHHhhhhh--
Confidence 456788999999999999999999999999999999998888888888999999999999999755 47888876633
Q ss_pred ccccccccHHHHHHHHHHHHHHcCCcceecChHHHHHHHHHHc
Q 028181 159 SDEKYRYEVKDILEMEMKILEALNYYLVVFHPYRSLVQFLQDA 201 (212)
Q Consensus 159 ~d~~~~~~~~~I~~~E~~LL~~L~Fdl~v~~P~~~L~~~l~~l 201 (212)
.+...++..+|..+|..+.|++..+....|+..++...
T Consensus 211 -----ty~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~~~ 248 (359)
T KOG0654|consen 211 -----TYTYWQVLRMEIDILNALTFELVRPTSKTFLRRFLRVA 248 (359)
T ss_pred -----hhHHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHHhh
Confidence 34568999999999999999999999999999986543
No 22
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=97.49 E-value=0.00066 Score=60.00 Aligned_cols=88 Identities=14% Similarity=0.107 Sum_probs=74.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHHHhcccccccccH
Q 028181 88 PTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIKKIYSDEKYRYEV 167 (212)
Q Consensus 88 ~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~~~~~d~~~~~~~ 167 (212)
.++|.+.+..|+|+..|...|..+.+..-..+...+.+|..+|+||+|+||+..+..++-+++..++.. +.
T Consensus 195 ~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~v---------te 265 (285)
T COG1405 195 SDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAGV---------TE 265 (285)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhCC---------ee
Confidence 589999999999999999999999999999999999999999999999999999988889999888632 22
Q ss_pred HHHHHHHHHHHHHcCCc
Q 028181 168 KDILEMEMKILEALNYY 184 (212)
Q Consensus 168 ~~I~~~E~~LL~~L~Fd 184 (212)
-.|.+-.+.|.+.++..
T Consensus 266 vTIrnrykel~~~~~i~ 282 (285)
T COG1405 266 VTIRNRYKELADALDIE 282 (285)
T ss_pred eHHHHHHHHHHHhhccc
Confidence 34555556666666543
No 23
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=97.06 E-value=0.00085 Score=63.22 Aligned_cols=111 Identities=15% Similarity=0.217 Sum_probs=88.9
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHHHhcccccccc
Q 028181 86 RCPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIKKIYSDEKYRY 165 (212)
Q Consensus 86 ~~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~~~~~d~~~~~ 165 (212)
.+-+.|.+++.+|+++. ++.+|..||+--..++-.++.....+.++|+|++|..|.++.-+=|+..+. ..
T Consensus 69 n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~L---------qv 138 (521)
T KOG1598|consen 69 NARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSYL---------QV 138 (521)
T ss_pred HHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccce---------EE
Confidence 34579999999999999 999999999999999988999999999999999999998766543333321 12
Q ss_pred cHHHHHHHHHHHHHHcCCc---ceecChHHHHHHHHHHcCCCCc
Q 028181 166 EVKDILEMEMKILEALNYY---LVVFHPYRSLVQFLQDAGMNDI 206 (212)
Q Consensus 166 ~~~~I~~~E~~LL~~L~Fd---l~v~~P~~~L~~~l~~l~l~~~ 206 (212)
+.-+|...-+.|...|..+ +....|.-|+.+|...|-.-+.
T Consensus 139 ~Vy~LG~~~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~ 182 (521)
T KOG1598|consen 139 SVYDLGSNFLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDK 182 (521)
T ss_pred ehhhhhHHHHHHHHHhccccccccccCcceeeechhHhhhcCCc
Confidence 3445666777888888888 6677899999999888755443
No 24
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=96.79 E-value=0.0052 Score=54.27 Aligned_cols=67 Identities=7% Similarity=0.104 Sum_probs=59.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHH
Q 028181 88 PTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYI 154 (212)
Q Consensus 88 ~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~ 154 (212)
.+||.+.|..|+||.++...|..+-++.-...-..+.+|..||+|++|++|-.++.+++.++|..++
T Consensus 204 ~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vt 270 (308)
T KOG1597|consen 204 GDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVT 270 (308)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHh
Confidence 4788899999999999999999888888776667778999999999999999999999999998775
No 25
>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=94.27 E-value=0.11 Score=38.27 Aligned_cols=56 Identities=18% Similarity=0.208 Sum_probs=41.5
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCC
Q 028181 88 PTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEES 143 (212)
Q Consensus 88 ~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~ 143 (212)
..||....+..+....+...|..+..-......+.++.|-.+|+||+++|.++.+.
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 34555554445556667777777777777777788899999999999999998553
No 26
>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=93.59 E-value=0.15 Score=40.29 Aligned_cols=70 Identities=10% Similarity=0.154 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCC--CCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHHH
Q 028181 87 CPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRK--SMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIKK 156 (212)
Q Consensus 87 ~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~--s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~~ 156 (212)
+..=|.++|.+|+++..+....-+.|......+ -+.+.+.--+.+.|+|.-||+.....+.++|+...++
T Consensus 14 a~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~ 85 (135)
T PF01857_consen 14 AAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRK 85 (135)
T ss_dssp HHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTT
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHh
Confidence 456678999999999988777777777766433 3356667779999999999999988899999997644
No 27
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=89.81 E-value=0.49 Score=42.71 Aligned_cols=57 Identities=19% Similarity=0.399 Sum_probs=41.7
Q ss_pred HHHHHHHHHcCCCHHH--HHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCc
Q 028181 89 TIYRNLAQHVKVRQRV--VATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTV 145 (212)
Q Consensus 89 ~~I~~l~~~L~L~~~t--~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~ 145 (212)
.+|..-...|++++.- ..+|=.|+.--.-..-+..+.+..||.||+|||+..+|.|.
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 5566666778888765 44555565555555556678999999999999999998543
No 28
>KOG1674 consensus Cyclin [General function prediction only]
Probab=86.28 E-value=3.7 Score=34.91 Aligned_cols=92 Identities=12% Similarity=0.185 Sum_probs=64.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCC------C---CCCC-chhhhHHHHHHhhccCCCCc-cHHHHHHHHHH
Q 028181 88 PTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKS------M---TEYD-PHLVAPTCLYLASKAEESTV-QARLLVFYIKK 156 (212)
Q Consensus 88 ~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s------~---~~~~-~~lvaaAcLfLA~KvEE~~~-~i~~ii~~~~~ 156 (212)
.+++.++-+..+....++-.|.+||.||-.+.. - ...+ ..-...+|+-+|||..+..- .-.....+.
T Consensus 79 ~~yleri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~y~n~~~a~vg-- 156 (218)
T KOG1674|consen 79 RQYLERIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVYYSNAYYAKVG-- 156 (218)
T ss_pred HHHHHHHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccchhhhHHHHHHhC--
Confidence 467777888999999999999999999988622 1 1223 23368899999999875421 222122111
Q ss_pred hcccccccccHHHHHHHHHHHHHHcCCcceec
Q 028181 157 IYSDEKYRYEVKDILEMEMKILEALNYYLVVF 188 (212)
Q Consensus 157 ~~~d~~~~~~~~~I~~~E~~LL~~L~Fdl~v~ 188 (212)
....+++-.+|..+|..++|++.+.
T Consensus 157 -------gl~~~eln~lE~~~l~~~~~~l~i~ 181 (218)
T KOG1674|consen 157 -------GLTTDELNKLELDLLFLLDFRLIIS 181 (218)
T ss_pred -------CCChHhhhhhhHHHHhhCCeEEEec
Confidence 2345777799999999999999973
No 29
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=86.26 E-value=0.49 Score=42.67 Aligned_cols=58 Identities=17% Similarity=0.316 Sum_probs=44.9
Q ss_pred HHHHHHHHHcCCCHH----HHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCcc
Q 028181 89 TIYRNLAQHVKVRQR----VVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQ 146 (212)
Q Consensus 89 ~~I~~l~~~L~L~~~----t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~ 146 (212)
.++.+.++.++-... +.-+|-++.+..+...-.-.+.+..||+|||+||+|.-+...+
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 556666666666654 7778888888888766556799999999999999998877544
No 30
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=85.07 E-value=1.3 Score=42.34 Aligned_cols=49 Identities=16% Similarity=0.157 Sum_probs=39.5
Q ss_pred HHHHHHHHHHH---HhcCCCCCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHH
Q 028181 104 VVATAVTYMRR---CYTRKSMTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIK 155 (212)
Q Consensus 104 t~aTA~vyf~R---Fy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~ 155 (212)
|..+|.-+..| -|+. .+.-|..++.|||++||.+.+..+++.+|+.+++
T Consensus 186 Vv~~a~~L~~rMkrdwm~---tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvh 237 (521)
T KOG1598|consen 186 VAKTATRLAQRMKRDWMQ---TGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVH 237 (521)
T ss_pred HHHHHHHHHHHHHHHHHH---hCCCccchhHHHHHHHHHHcCccccHHHHHHHHH
Confidence 67777766655 3443 4567889999999999999999999999999864
No 31
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=78.40 E-value=5.6 Score=35.58 Aligned_cols=55 Identities=9% Similarity=0.172 Sum_probs=39.6
Q ss_pred HHHHHHHHHHc---CCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCC
Q 028181 88 PTIYRNLAQHV---KVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEE 142 (212)
Q Consensus 88 ~~~I~~l~~~L---~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE 142 (212)
..++.++...+ .-+..+...|-.|+...+...-.-.+.|..||+||||+|++...
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 34666665544 22344667778888888776666679999999999999998543
No 32
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=63.59 E-value=37 Score=29.51 Aligned_cols=56 Identities=21% Similarity=0.403 Sum_probs=33.2
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCcc
Q 028181 88 PTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQ 146 (212)
Q Consensus 88 ~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~ 146 (212)
.++++++|. .++.....+-.+..--|...-.--++|+.+|.||||+||=..|.+.+
T Consensus 158 ~q~~qd~gi---~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~~~ 213 (264)
T KOG0794|consen 158 LQFVQDMGI---NDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKDIP 213 (264)
T ss_pred HHHHHHhcc---cchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCChH
Confidence 466666665 23333333333333333222223478999999999999988776653
No 33
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=56.90 E-value=25 Score=31.72 Aligned_cols=75 Identities=19% Similarity=0.181 Sum_probs=49.3
Q ss_pred HHHHHHHHHh--cCCCCCCCCchhhhHHHHHHhhccCCC-CccHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHcCC
Q 028181 107 TAVTYMRRCY--TRKSMTEYDPHLVAPTCLYLASKAEES-TVQARLLVFYIKKIYSDEKYRYEVKDILEMEMKILEALNY 183 (212)
Q Consensus 107 TA~vyf~RFy--~~~s~~~~~~~lvaaAcLfLA~KvEE~-~~~i~~ii~~~~~~~~d~~~~~~~~~I~~~E~~LL~~L~F 183 (212)
...+|+.|-. ........++..+....+.+|+|+=.. ...--|.+..++.+ +++++-++|+..|+-|+|
T Consensus 213 itL~~~erl~~~~e~~~~p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlKd~--------tveDmNe~ERqfLelLqf 284 (343)
T KOG1675|consen 213 ITLVYAERLLWLAERDPCPRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILKDQ--------SVDDMNALERQFLELLQF 284 (343)
T ss_pred HHHHhhHhhhhHhhcCCCcchhhhhhhhhheehhhhhhhhhcccHHHHHHHhhc--------cHhhHHHHHHHHHHHHhh
Confidence 3446777753 333344566666777779999997543 22223455554432 468999999999999999
Q ss_pred cceecC
Q 028181 184 YLVVFH 189 (212)
Q Consensus 184 dl~v~~ 189 (212)
+++++-
T Consensus 285 Ninvp~ 290 (343)
T KOG1675|consen 285 NINVPS 290 (343)
T ss_pred ccCccH
Confidence 998653
No 34
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=55.56 E-value=23 Score=30.46 Aligned_cols=51 Identities=20% Similarity=0.315 Sum_probs=36.3
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHhcCCCC-----CCCCchhhhHHHHHHhhccCC
Q 028181 91 YRNLAQHVKVRQRVVATAVTYMRRCYTRKSM-----TEYDPHLVAPTCLYLASKAEE 142 (212)
Q Consensus 91 I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s~-----~~~~~~lvaaAcLfLA~KvEE 142 (212)
+.++|.+|++ ..|+..|..++.-|=.+-+- .+++.-..++|++|+|||.-.
T Consensus 96 VrdlaVQfgc-~evi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lK 151 (262)
T KOG4557|consen 96 VRDLAVQFGC-VEVIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLK 151 (262)
T ss_pred HHHHHHHHhH-HHHHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHH
Confidence 4667777775 45777888888877653222 356677889999999998643
No 35
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=47.50 E-value=29 Score=35.26 Aligned_cols=71 Identities=8% Similarity=0.151 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCC--CCCCCchhhhHHHHHHhhccCCCCccHHHHHHHHHHh
Q 028181 87 CPTIYRNLAQHVKVRQRVVATAVTYMRRCYTRKS--MTEYDPHLVAPTCLYLASKAEESTVQARLLVFYIKKI 157 (212)
Q Consensus 87 ~~~~I~~l~~~L~L~~~t~aTA~vyf~RFy~~~s--~~~~~~~lvaaAcLfLA~KvEE~~~~i~~ii~~~~~~ 157 (212)
+.-=|+.+|.+|.+.+++...--++|..-+.... +++.|.--+.+.|+|+-+|+++...+.++|+...++.
T Consensus 680 AavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR~Q 752 (920)
T KOG1010|consen 680 AAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYRRQ 752 (920)
T ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHhcC
Confidence 4455789999999998776666666665544332 2345555689999999999999999999999887653
No 36
>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=30.93 E-value=58 Score=25.67 Aligned_cols=87 Identities=15% Similarity=0.257 Sum_probs=52.6
Q ss_pred HHHcCCCHH-HHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCccH-HHHHHHHHHhcccccccccHHHHHH
Q 028181 95 AQHVKVRQR-VVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQA-RLLVFYIKKIYSDEKYRYEVKDILE 172 (212)
Q Consensus 95 ~~~L~L~~~-t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~i-~~ii~~~~~~~~d~~~~~~~~~I~~ 172 (212)
-..++++.. .+|..++||.|--... ..+++... -.+||||+-+||..... .+|..-+... + ..-.......
T Consensus 22 D~~~~~sDKYLLAmV~~YF~Ragl~~--~~Y~ri~F-FlALYLAndmEED~~~~K~~If~f~~G~---~-w~~~~~~F~k 94 (131)
T PF11357_consen 22 DKCLRVSDKYLLAMVIAYFSRAGLFS--WQYQRIHF-FLALYLANDMEEDDEEPKYEIFPFLYGK---N-WRSQIPQFHK 94 (131)
T ss_pred CcchhhhhHHHHHHHHHHHHhcccch--hhcchHHH-HHHHHHhhHHHhccchHHHHHHHHHHCc---c-hHHHhHHHHH
Confidence 345555555 6789999999964321 12333322 45899999999986543 3444433221 0 0111245666
Q ss_pred HHHHHHHHcCCcceec
Q 028181 173 MEMKILEALNYYLVVF 188 (212)
Q Consensus 173 ~E~~LL~~L~Fdl~v~ 188 (212)
.=..+.+.|||...|.
T Consensus 95 lr~~~~~~m~~Ra~Vs 110 (131)
T PF11357_consen 95 LRDQFWRRMDWRAWVS 110 (131)
T ss_pred HHHHHHHHcCCceeeC
Confidence 7778889999988764
No 37
>smart00435 TOPEUc DNA Topoisomerase I (eukaryota). DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras
Probab=27.09 E-value=97 Score=28.84 Aligned_cols=21 Identities=24% Similarity=0.252 Sum_probs=18.0
Q ss_pred CCHHHHHHHHHHHHHHhcCCC
Q 028181 100 VRQRVVATAVTYMRRCYTRKS 120 (212)
Q Consensus 100 L~~~t~aTA~vyf~RFy~~~s 120 (212)
+...++|+|+.++++++++..
T Consensus 111 ~r~rqlAvav~LID~~alRvG 131 (391)
T smart00435 111 MKVRQRATALYLIDKLALRAG 131 (391)
T ss_pred hhhhHHHHHHHHHHHhcccCC
Confidence 467899999999999998754
No 38
>KOG0213 consensus Splicing factor 3b, subunit 1 [RNA processing and modification]
Probab=23.38 E-value=7.2e+02 Score=25.80 Aligned_cols=66 Identities=8% Similarity=0.068 Sum_probs=49.9
Q ss_pred cCHHHHHHHHHHHHHHHHHcCCCHHHHHH--HHHHHHHHhcCCCCC-CCCchhhhHHHHHHhhccCCCC
Q 028181 79 ITSSLRCRCPTIYRNLAQHVKVRQRVVAT--AVTYMRRCYTRKSMT-EYDPHLVAPTCLYLASKAEEST 144 (212)
Q Consensus 79 ~~~e~r~~~~~~I~~l~~~L~L~~~t~aT--A~vyf~RFy~~~s~~-~~~~~lvaaAcLfLA~KvEE~~ 144 (212)
-++|+....+....++|..-+....-+.+ .-.||+.||.+..-. ..++.-+.-+.+-+|.|+--.+
T Consensus 648 PDeemkkivLKVv~qcc~t~Gv~~~y~r~dilp~ff~~fw~rrmA~drr~ykqlv~ttv~ia~KvG~~~ 716 (1172)
T KOG0213|consen 648 PDEEMKKIVLKVVKQCCATDGVEPAYIRFDILPEFFFSFWGRRMALDRRNYKQLVDTTVEIAAKVGSDP 716 (1172)
T ss_pred ChHHHHHHHHHHHHHHhcccCCCHHHHhhhhhHHHHhhhhhhhhhccccchhhHHHHHHHHHHHhCchH
Confidence 35566666788899999999988886654 446999999887654 4566677788999999986544
No 39
>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=21.83 E-value=1.5e+02 Score=26.51 Aligned_cols=45 Identities=16% Similarity=0.251 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCCchhhhHHHHHHhhccCCCCcc
Q 028181 102 QRVVATAVTYMRRCYTRKSMTEYDPHLVAPTCLYLASKAEESTVQ 146 (212)
Q Consensus 102 ~~t~aTA~vyf~RFy~~~s~~~~~~~lvaaAcLfLA~KvEE~~~~ 146 (212)
-.+...|=.+..--+...-.--+.|..+|+||+++||++-+.+..
T Consensus 167 ~~~~~~aw~~inDa~~t~~~llypphiIA~a~l~ia~~~~~~~~~ 211 (297)
T COG5333 167 YKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPII 211 (297)
T ss_pred HHHHHHHHHHHHhhhhceeeeecChHHHHHHHHHHHHHhcCCccc
Confidence 446666666666666555555689999999999999999776653
No 40
>PF02315 MDH: Methanol dehydrogenase beta subunit; InterPro: IPR003420 Methanol dehydrogenase (MDH) (1.1.99.8 from EC), found in Gram-negative bacteria, is a pyrroloquinoline quinone (PQQ)-containing enzyme which oxidises methanol to formaldehyde. It is located in the periplasmic space and passes electrons derived from the oxidation of methanol to the soluble cytochrome cL []. The enzyme is a tetramer composed of two large alpha subunits and two smaller beta subunits. The alpha subunit binds the PQQ cofactor and contains the active site, while the function of the beta subunit is currently unknown []. The alpha subunit forms an eight-bladed propeller structure, with several novel tryptophan-docking motifs linking the individual blades together. This entry represents the beta subunit of methanol dehydrogenase.; GO: 0004022 alcohol dehydrogenase (NAD) activity, 0015946 methanol oxidation, 0055114 oxidation-reduction process; PDB: 1LRW_B 2D0V_J 2AD6_B 1G72_B 4AAH_D 2AD8_D 2AD7_D 1H4J_D 1H4I_B 1W6S_B ....
Probab=21.06 E-value=52 Score=24.20 Aligned_cols=26 Identities=27% Similarity=0.296 Sum_probs=10.4
Q ss_pred cCcccCCCCCCcccCCCCCccc-ccccc
Q 028181 31 KDYSNSGKGGVKKWLPISGHRR-TTNSF 57 (212)
Q Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~-~a~~f 57 (212)
=|-++|..||+ +|.|.|||.. +|+..
T Consensus 23 YDGt~CkapG~-CWEpkPGyPekiaGSK 49 (93)
T PF02315_consen 23 YDGTNCKAPGN-CWEPKPGYPEKIAGSK 49 (93)
T ss_dssp --S---SBTTB------TTS-SS-TTST
T ss_pred ccCcccCCCcc-ccCCCCCCcccccccc
Confidence 56677778888 6888999986 66543
No 41
>PF14502 HTH_41: Helix-turn-helix domain
Probab=20.60 E-value=1.5e+02 Score=19.21 Aligned_cols=25 Identities=8% Similarity=0.294 Sum_probs=21.4
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHH
Q 028181 90 IYRNLAQHVKVRQRVVATAVTYMRR 114 (212)
Q Consensus 90 ~I~~l~~~L~L~~~t~aTA~vyf~R 114 (212)
-|.++.+.++++.-|+..|..++..
T Consensus 8 tI~e~~~~~~vs~GtiQ~Alk~Le~ 32 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQNALKFLEE 32 (48)
T ss_pred CHHHHHHHhCcchhHHHHHHHHHHH
Confidence 3678889999999999999988764
Done!