Query 001701
Match_columns 1024
No_of_seqs 185 out of 211
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 07:15:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001701.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001701hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1010 Rb (Retinoblastoma tum 100.0 8E-198 2E-202 1707.8 64.1 854 25-1014 35-917 (920)
2 PF01858 RB_A: Retinoblastoma- 100.0 5.9E-61 1.3E-65 499.9 17.1 194 418-619 1-194 (194)
3 PF01857 RB_B: Retinoblastoma- 100.0 2.8E-51 6E-56 403.6 11.5 131 741-871 1-135 (135)
4 PF11934 DUF3452: Domain of un 100.0 1.3E-36 2.8E-41 300.9 9.9 136 90-236 1-136 (136)
5 PF08934 Rb_C: Rb C-terminal d 99.7 3.6E-19 7.8E-24 171.9 2.6 79 901-984 8-95 (155)
6 PRK00423 tfb transcription ini 97.1 0.0019 4.1E-08 73.2 9.3 73 749-823 120-192 (310)
7 PF00382 TFIIB: Transcription 97.0 0.0028 6.1E-08 56.2 7.7 63 758-822 1-63 (71)
8 smart00385 CYCLIN domain prese 95.8 0.032 7E-07 48.7 7.0 63 758-822 3-65 (83)
9 cd00043 CYCLIN Cyclin box fold 95.3 0.095 2.1E-06 46.2 8.5 69 754-824 5-73 (88)
10 PF00382 TFIIB: Transcription 95.0 0.14 3E-06 45.4 8.5 67 29-118 2-69 (71)
11 KOG1597 Transcription initiati 94.7 0.098 2.1E-06 58.3 8.1 73 749-823 102-174 (308)
12 PRK00423 tfb transcription ini 93.4 0.19 4.1E-06 57.2 7.5 62 758-821 223-284 (310)
13 PF01857 RB_B: Retinoblastoma- 91.0 0.42 9.1E-06 48.2 5.7 71 24-114 14-84 (135)
14 COG1405 SUA7 Transcription ini 87.9 2.3 5E-05 48.1 9.2 76 749-826 95-170 (285)
15 smart00385 CYCLIN domain prese 80.4 9.7 0.00021 32.9 8.1 52 28-89 3-54 (83)
16 PF00134 Cyclin_N: Cyclin, N-t 73.2 20 0.00043 34.4 8.7 72 749-822 29-101 (127)
17 COG1405 SUA7 Transcription ini 55.7 57 0.0012 37.2 9.2 56 23-88 99-154 (285)
18 TIGR00569 ccl1 cyclin ccl1. Un 54.5 49 0.0011 38.0 8.6 67 755-823 60-128 (305)
19 cd00043 CYCLIN Cyclin box fold 53.8 1E+02 0.0022 26.7 8.8 55 24-88 5-59 (88)
20 KOG1992 Nuclear export recepto 40.1 1.5E+02 0.0032 38.3 9.9 101 105-232 201-323 (960)
21 KOG1598 Transcription initiati 37.5 98 0.0021 37.9 7.7 55 754-811 70-124 (521)
22 KOG1598 Transcription initiati 35.4 3.6E+02 0.0077 33.3 11.9 55 23-88 69-123 (521)
23 PF07340 Herpes_IE1: Cytomegal 26.0 1.2E+03 0.026 27.9 20.2 73 533-608 198-281 (392)
24 KOG1597 Transcription initiati 24.6 2E+02 0.0044 33.0 7.0 63 758-822 207-269 (308)
No 1
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=8.3e-198 Score=1707.83 Aligned_cols=854 Identities=34% Similarity=0.499 Sum_probs=707.0
Q ss_pred HHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHhhccccCCCCCchHHHHHHHHHHHHHHHhcc-cccCCCCCCCcCC-C
Q 001701 25 EARLTDLCKNGLSVDENTYKEIIKLFRETKHLLLANISAIGNGMPEEAERFWFAFVLYLVRRLS-EKNGENLQQGSND-N 102 (1024)
Q Consensus 25 ~~rf~~lC~~~LnlD~~t~~~A~~~f~~~~~~~~~~~~~~~~~t~E~~~~~W~acaLY~a~r~~-~~tv~~~~~~~~g-n 102 (1024)
.+.|.++|+. ||||++++.+||++|.++++.| |+||++.||+|||+|++||.+ +++|+| +.++| |
T Consensus 35 ~q~~~~~c~~-lnld~~~~~ea~d~yta~~q~~----------slegs~~hW~~cAlY~~~r~S~~~~v~~--~~~~~~n 101 (920)
T KOG1010|consen 35 EQDSDELCRP-LNLDEQTETEAWDTYTAVSQRL----------SLEGSESHWLACALYTACRRSSVPTVGG--GIVEGKN 101 (920)
T ss_pred hhhhhhhhhh-hcccchhhhhhHHHHHHHHhHh----------CCCccHHHHHHHHHHHHHHhccCCccCc--ceeeecc
Confidence 7899999998 9999999999999999999654 999999999999999999998 689986 45667 9
Q ss_pred cccHHHHHHhhCCCHHHHHHhhHHHHHhhcCcccccCCchHHhHHHHHhHhhhhhhHHHHHHHHHHHHhccccCCCCCcc
Q 001701 103 EFNLCHILRVMKLNIVDFFKELPQFLVKSGPILSNIYGADWENRLEAKELQANFVHLSILSKSYKRIYREFFLPSDANGD 182 (1024)
Q Consensus 103 ~vsLT~lLr~~~lsl~~Ff~km~~w~~~~~~~l~~l~~~~~e~rl~~keLe~nF~v~~vL~kky~~iF~~iF~~p~~~~~ 182 (1024)
+||||+|||++++|++|||+||+||.+|++ + +. ++|++++|||+||+|+++|||||++||.+||+.|..+.+
T Consensus 102 ~vsL~~Ilrs~k~sv~eff~km~~w~~ma~-----s-~~--~f~~~ieel~~~f~vssvl~KkY~~iF~~iF~~p~~e~~ 173 (920)
T KOG1010|consen 102 EVSLTRILRSFKMSVIEFFTKMKQWVDMAN-----S-PQ--EFREEIEELQRNFKVSSVLFKKYKRIFRDIFKLPREELG 173 (920)
T ss_pred eehHHHHHHHHHHHHHHHHHHHHHHHHHhc-----C-HH--HHHHHHHHHHhccceehhHHHHHHHHHHHHHhCcccccc
Confidence 999999999999999999999999999984 3 44 557779999999999999999999999999999996655
Q ss_pred ccccccc---CCCChhhHHHHHHHHHHHHHhhhcccCchHHHHhhHHHHHHHHHHhcCCcccc----ccccCC-Ccccc-
Q 001701 183 KQSAAAS---TSGYISDYHRFGWLLFLALRIHAFSRFKDLVTCTNGLVSILAILIIHVPVRFR----NFNIHD-SSRFV- 253 (1024)
Q Consensus 183 ~~~~~~~---~~~~~~d~~~f~W~LFL~aK~~~~~~f~DLV~s~~LLlc~Ldll~~n~p~~~~----~~~~~~-~~~~~- 253 (1024)
..++.++ .+|++.++|+|||+|||++|+++++++||||+||||||||||++|+|++.+.| ++.++| +.++.
T Consensus 174 ~~~~~~n~~~~~~~~~~l~~f~W~lFL~~Kn~~~~~~dDLV~syqlllc~LDlv~~n~lc~~R~~~v~p~f~gl~~n~~~ 253 (920)
T KOG1010|consen 174 YLNRPSNHARTPCSYAELFKFCWLLFLVAKNEFPSIEDDLVNSYQLLLCILDLVYKNLLCSPRKDLVNPSFKGLPKNWTA 253 (920)
T ss_pred cCCCcccccCCcccHHHHHHHHHHHHHHHhcccchhhhhHHhhhhHHHHHHHHHHHHhccccccccccccccCCCCCCch
Confidence 4444333 78999999999999999999999999999999999999999999999776644 567776 33332
Q ss_pred ---cccCCcchhHHHhhhhcCCCHHHHHHHHHH-HHHHHHHHhccCCccccccccccCCCCCCCcccccccCCCCcchhH
Q 001701 254 ---KKSNKGVDLIASLCSIYDTSEDDLRKIMEK-TNTLIADILKKKPCEASECKSENLENIDTDGLIYFENLMDDSSLSS 329 (1024)
Q Consensus 254 ---k~~~~~~~il~~LC~~~~~~~~e~k~~~~~-~~~~I~~lf~k~~l~~~~~~~~~l~~~~~~~~~~~~gLl~~~~f~~ 329 (1024)
+++.+++|||+.||++|+++.+|+|+|+++ |++++..+|..+.+.+ +.. .++||++.++|..
T Consensus 254 ~d~~~s~n~~cii~~lce~h~~li~eak~~k~~~fk~~~~~l~~~ktl~g---~~~-----------~~~gll~~~~f~~ 319 (920)
T KOG1010|consen 254 RDFKPSENPPCIIEVLCELHEGLIDEAKNMKETNFKPFMSSLYEVKTLKG---DYL-----------LMRGLLDEGNFLP 319 (920)
T ss_pred hhccccCCCcchhHHhhhhhhhHHHhhcchHHHhHHHHHHHHHhhhhhhc---ccc-----------cccccccccccch
Confidence 456788999999999999999999999999 5999999999877663 222 2589999999999
Q ss_pred HHHHHHHHHHHHhhccCCCcccccccCCCccccCCCCCCCccccccccccccccCCCcccCCCCCCCCCCCCCCCCCCCC
Q 001701 330 SLNILEKDYDNATRNKGELDERVFINEDDSLLGSGSLSGGAVNITGAKRKFDSLASPVKTITSPLSPHRSSASHPNGIAG 409 (1024)
Q Consensus 330 nl~~Lnk~YEe~vl~~GdlDERiFL~~d~~~ig~~~~s~~~~~~~~~~~k~~~~~sp~k~~~tplt~~~sp~s~~~g~~~ 409 (1024)
|+++|||.||+||+++|||||||||+.|+++.+..+ .++..++.+...++++..-.+.+ + ..++.+|.+|
T Consensus 320 ~~~~lnk~yeeyvl~vgelDeRifl~~Da~~~t~~~-------~s~~~~r~~~~~~~~~~~~~~~s-~--~~p~~~~~~y 389 (920)
T KOG1010|consen 320 NVKNLNKSYEEYVLDVGELDERIFLGEDAEEETKSS-------DSFESERLAVKSSLAQEFLKTQS-K--KSPPHTGVRY 389 (920)
T ss_pred hHHHHhhhHHHHhccccchhhhhhcccchhhhhccC-------Cccchhccccccccchhhccccc-c--cCCCCccccc
Confidence 999999999999999999999999999988765221 12222222222233221111222 1 2345678899
Q ss_pred CCCccccCchhhhHHhHHHHHHHHhCCCCCCCcHHHHHHHhhcCCChHHHHHHHHHHHHHhhccCCCCCccccccCCCCC
Q 001701 410 GATSKMVVTPVSTAMTTAKWLRTVICPLPSKPSAELERFLKSCDKDVTTDVMRRAHIILEAIFPSSGLGERCVTGSLQGA 489 (1024)
Q Consensus 410 ~~~~~~~~TPVs~Am~s~~wL~~~l~~l~~~PS~~L~~~~~sC~~d~~~~i~~rv~~i~e~~f~~~~~~~~~~~~~~~~~ 489 (1024)
..+.....|||++||++++||++++.|+.++||++|++||++|++||+++|++|+++|++.|+++...+..+ + .
T Consensus 390 ~~e~~~~~tPvsta~~sik~l~t~i~g~~~~psdkLe~~~~tc~r~p~e~Il~r~~~i~e~~~q~f~~~~~~-----g-~ 463 (920)
T KOG1010|consen 390 NLELGNYPTPVSTATNSIKQLMTILNGLKKEPSDKLEQYLNTCSRDPTESILKRLKEIFEIFEQKFSAAEGS-----G-N 463 (920)
T ss_pred ccccccCCCcchhHHHHHHHHHHHHhccccCCcHHHHHHHhhcccChHHHHHHHHHHHHHHHHHHhhhhccC-----C-c
Confidence 999999999999999999999999999999999999999999999999999999999999999876543311 1 2
Q ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccchHHhhchhhHHHHHHHHHHHHHHhhccCCccchhHHhhhcCC
Q 001701 490 NLMDNIWAEQRRLEALKLYYRVLEAMCTAEAQVLHAKNLTSLLTNERFHRCMLACSAELVLATHKTVTMLFPAVLERTGI 569 (1024)
Q Consensus 490 ~~~d~~~a~qR~~~a~~LYYrvLE~Il~~E~~rl~~~dls~LL~~d~FhrsLlACclEiVl~ty~~~~~~FPwILe~~~i 569 (1024)
..++ ++.||+++|++|||||||+||++|.+|++..||+.||+|++||+||||||+|+||++|++ ++.|||||++|||
T Consensus 464 ~~~e--~~~~r~k~a~~LYykvLE~il~aE~~rl~~~dl~~LL~q~~Fh~sLlACclElVL~ty~~-~l~FPwvle~~~l 540 (920)
T KOG1010|consen 464 SCIE--IASQRFKLAERLYYKVLEKILKAELKRLPDMDLSKLLEQEIFHRSLLACCLELVLATYKT-DLSFPWVLECFGL 540 (920)
T ss_pred cchH--HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CCCCchhhhhcCC
Confidence 3455 799999999999999999999999999999999999999999999999999999999997 5999999999999
Q ss_pred CcchHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHhhhhccCCCchhHhhhhhccchhhhhhhcccCCCCCCchhhhhhc
Q 001701 570 TAFDLSKVIESFIRHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSLTVARPVLSAEINRLGLLADPMPSLDAIATH 649 (1024)
Q Consensus 570 ~afdf~KVIE~fVR~e~~LpRelvkHLn~IEE~ILEslAW~~~S~Lw~~L~~a~~~~~~ei~~~~~~~e~~p~~~~i~~~ 649 (1024)
+|||||||||+|||||++|+||||||||+|||+|||||||++|||||++|++++ ++++++++++|+.+ ++..
T Consensus 541 ~aFdF~KVIE~~IRhE~~L~RemiKHLn~iEE~iLEslaW~~dS~Lw~~i~~~~-------~~~~~~~~~~~~~~-le~~ 612 (920)
T KOG1010|consen 541 KAFDFYKVIESFIRHEGGLSREMIKHLNSIEERILESLAWKSDSPLWEMIKQAK-------PRLPTEEGVDPPDN-LESA 612 (920)
T ss_pred cHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccCCcHHHHHHhcc-------cccccccccccccc-cccc
Confidence 999999999999999999999999999999999999999999999999999987 46667777777665 2210
Q ss_pred cccCCCCCCCcccCCccc----CCCCCCCCCCCCCCCcccccccccccccccCcccccccccCCCCCCCCCCCcccccCC
Q 001701 650 INFSSGGLSPVHSLHKHE----TSPGQNGDIRSPKRPCTDYRSVLVERNNFTSPVKDRLLGLNNLKSKPLPPPLQSAFAS 725 (1024)
Q Consensus 650 ~~~~~~~~p~~p~~~~~~----~~~~~~~~~~sp~~~~~~~~~~~~~~~~~~sP~k~~l~~~~~~~~k~~p~~~~s~~~s 725 (1024)
. ..| -.|...++. ++|++ +|+..|+ ++|++++.. .
T Consensus 613 ~---~~~--~~p~~~~~~~~~~~sp~~-----~Pk~~~~------------t~pv~~~an-------------------~ 651 (920)
T KOG1010|consen 613 C---IAG--LLPLRVNHVRARYSSPVL-----EPKDKGT------------TIPVNGTAN-------------------A 651 (920)
T ss_pred c---ccc--cCCccccccccccCCCCC-----Ccccccc------------ccccccccc-------------------c
Confidence 0 011 122122221 11221 2333322 445555332 1
Q ss_pred CCCCCCCCCCCcccchhHHHHHHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHH
Q 001701 726 PTRPNPGGGGETCAETGINIFFCKINKLAAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYG 805 (1024)
Q Consensus 726 p~~~~~~~~~e~~~~t~l~lFfrKvy~LAa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~ 805 (1024)
++..++.+++.++++++|+|||||||+|||+||++||+||+++++++++|||||||+|+|+|+||+|||||||||||||+
T Consensus 652 ~qe~~~~~~~~~~~stsLsIF~rKvY~LAavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~ 731 (920)
T KOG1010|consen 652 GQEVTAFGVNKPRKSTSLSIFLRKVYHLAAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYG 731 (920)
T ss_pred cccCCcccCCCcccccchHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHh
Confidence 23445556778889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhccCccCHHHHHHHhhcCCCCCcceeeEEEecccccccCCCcc--cccccccchhhhccHHhhHHHHHHhcCCCCcc
Q 001701 806 VAKISQLNLTFREIIYNYRKQPQCKPQVFRSVFVDWASARQSGRSE--QDHVDIITFYNKIFVPAVKPLLVELGPAGTAM 883 (1024)
Q Consensus 806 i~Kv~k~~~sFk~Ii~~Yr~QPqa~~~VyRsVli~~~~~~~~g~~~--~e~gDII~FYN~VFvp~mK~f~l~~~~~~~~~ 883 (1024)
||||++++++|++||++||+||||.++|||+|+|+....+..|..| ++++|||+|||.||||.||+|+++|..+.+
T Consensus 732 i~KV~~~~ltF~eIm~~YR~QPqa~~~vyRsV~i~~~~~~~~~~~~P~~~~~diI~fyN~iyV~~~k~~~i~~~~~~~-- 809 (920)
T KOG1010|consen 732 IAKVKKEDLTFSEIMRAYRRQPQAVSLVYRSVLIKDKTNRDQGPSGPKEERSDIITFYNNIYVPPMKTFAIEYGLATT-- 809 (920)
T ss_pred heehhcccchHHHHHHHHhcCchhhhhhhhheeecccccccccCCCCcccccceeccccceehhhhhhhhhhhccCCC--
Confidence 9999999999999999999999999999999999832222233223 489999999999999999999999998631
Q ss_pred ccccccccCCCCCCCCCCCCCCCCCCCCC--CCCCcccccCCcEEEecCCCCCcccccCCCCceEEEEeccccccCCCCC
Q 001701 884 KTNRVSEVNHNNDGPCPGSPKVSVFPALP--DMSPKKVSATHNVYVSPLRTSKMDALISHSSKSYYACVGESTHAYQSPS 961 (1024)
Q Consensus 884 ~~~~~~~~~~~~d~~~~~sP~lSp~P~~~--~~SP~rvs~~~nvyvSP~k~~k~~~~lsp~s~~~y~~~Ges~~~~~SPs 961 (1024)
++.++++|.|++. ..+|++||++||||||||+++ +.+++++.+.||+| .|||
T Consensus 810 ----------------~~~~~lsp~~~i~~~~~e~~~~S~~h~v~is~~~~~--~~l~s~s~~~y~~~--------~sps 863 (920)
T KOG1010|consen 810 ----------------MDAKPLSPSPSIKVSIGEPRRLSQRHNVYISPHKNS--DRLQSRSTAEYYFC--------NSPS 863 (920)
T ss_pred ----------------CCCCCCCCCccccccCCCCcchhhhcceeecCCCch--hhhcCcchhhcccc--------CCCC
Confidence 2345666666654 458889999999999999887 34444444555555 3799
Q ss_pred ccHHHHHHHhhcCCCcccceecCCCcccccccchhHhhhhccc------cCCCCCcCCC
Q 001701 962 KDLTDINHRLNSNRRVRGTLNFDDVDVDVGLVSDSMVANSLYL------QNGSAAASTC 1014 (1024)
Q Consensus 962 kdL~~IN~~i~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~ 1014 (1024)
|+|++||.||+++....+..++.+ | +++++.+||.+-. |+++.+++++
T Consensus 864 k~L~ain~~i~~ss~~~~~~~~~~---e--s~~Es~~ani~~~~~~~~~~r~~D~~~~~ 917 (920)
T KOG1010|consen 864 KDLPAINNLIRGSSERTKKKHIPG---E--SKSESKRANILQERTRMQLQRLQDAMSTR 917 (920)
T ss_pred cchHHHHHHhhcCcccccccCCCc---c--chhhhhHhhhhhhhhHHHHhhhhhhhhcc
Confidence 999999999998544334444554 3 8999999998865 6666666553
No 2
>PF01858 RB_A: Retinoblastoma-associated protein A domain; InterPro: IPR002720 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and Simian virus 40 (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 appears to be required for the stable folding of the B box (see IPR002719 from INTERPRO). 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 A-box is on N-terminal side of the B-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1O9K_A 3POM_A 1GH6_B 1N4M_A 4ELL_B 1AD6_A 1GUX_A 2R7G_C 4ELJ_A.
Probab=100.00 E-value=5.9e-61 Score=499.87 Aligned_cols=194 Identities=45% Similarity=0.738 Sum_probs=167.7
Q ss_pred chhhhHHhHHHHHHHHhCCCCCCCcHHHHHHHhhcCCChHHHHHHHHHHHHHhhccCCCCCccccccCCCCCCccchHHH
Q 001701 418 TPVSTAMTTAKWLRTVICPLPSKPSAELERFLKSCDKDVTTDVMRRAHIILEAIFPSSGLGERCVTGSLQGANLMDNIWA 497 (1024)
Q Consensus 418 TPVs~Am~s~~wL~~~l~~l~~~PS~~L~~~~~sC~~d~~~~i~~rv~~i~e~~f~~~~~~~~~~~~~~~~~~~~d~~~a 497 (1024)
||||+||++++||+++++|+++.||++|.++|++|++||+++|++||++|++.|++.+..+.. . . ..+..++
T Consensus 1 TPVs~A~~~~~~L~~~l~~~~~~PS~~L~~~~~~c~~~p~~~i~~rv~~l~~~~~~~~~~~~~----~-~---~~~~~~~ 72 (194)
T PF01858_consen 1 TPVSSAMQSVSWLQALLSGLSDEPSEELLRIFKSCSRDPTESILKRVKQLLEKFCQKYTEAEG----E-Q---SSNSDFA 72 (194)
T ss_dssp -HHHHHHHHHHHHHHHHHHS-SS--HHHHHHHHTSSS--HHHHHHHHHHHHHHHHHHHHHHHS----G-G-----GHHHH
T ss_pred CchHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHhccccc----c-c---cccchHH
Confidence 899999999999999999999999999999999999999999999999999999876542110 0 0 2334489
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcccchHHhhchhhHHHHHHHHHHHHHHhhccCCccchhHHhhhcCCCcchHHHH
Q 001701 498 EQRRLEALKLYYRVLEAMCTAEAQVLHAKNLTSLLTNERFHRCMLACSAELVLATHKTVTMLFPAVLERTGITAFDLSKV 577 (1024)
Q Consensus 498 ~qR~~~a~~LYYrvLE~Il~~E~~rl~~~dls~LL~~d~FhrsLlACclEiVl~ty~~~~~~FPwILe~~~i~afdf~KV 577 (1024)
++|+++|++|||++||+||.+|.+|++..|++.||+||+|||||+|||+|||+|+|+++++.|||||++|+|+|||||||
T Consensus 73 ~~r~~~~~~LYY~~LE~Il~~E~~r~~~~~ls~LL~~~~FhrsL~ACclEiVl~sy~~~~~~FPwiL~~~~i~~f~f~Kv 152 (194)
T PF01858_consen 73 EQRFNLAEKLYYKVLEKILKAEEKRLPTNDLSSLLSQEIFHRSLLACCLEIVLFSYKSVSLSFPWILEVFDIHPFDFYKV 152 (194)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHSCSHHHHHHT-HHHHHHHHHHHHHHHHHHTCTSSSSTTHHHHHTT--HHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccccHhHHHHHhhhhHHHHHHHHHHHHHHHHHcCCCCCcchHHHHhcCCChhhHhhH
Confidence 99999999999999999999999999999999999999999999999999999999987899999999999999999999
Q ss_pred HHHHHhhcCCCCHHHHHHHHHHHHHHHhhhhccCCCchhHhh
Q 001701 578 IESFIRHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSL 619 (1024)
Q Consensus 578 IE~fVR~e~~LpRelvkHLn~IEE~ILEslAW~~~S~Lw~~L 619 (1024)
||+|||||++|||+||||||+|||||||+|||++|||||++|
T Consensus 153 IE~~Vr~~~~Lpr~lvkHL~~IEE~iLeslaW~~~S~Lw~~l 194 (194)
T PF01858_consen 153 IESFVRHEDGLPRELVKHLNSIEEQILESLAWKSDSPLWEML 194 (194)
T ss_dssp HHHHHHH-TT--HHHHHHHHHHHHHHHHTGGGSTT-THHHHH
T ss_pred HHHHHHccccCCHHHHHHHHHHHHHHHHHHHhcCCChhhhhC
Confidence 999999999999999999999999999999999999999865
No 3
>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=100.00 E-value=2.8e-51 Score=403.58 Aligned_cols=131 Identities=49% Similarity=0.867 Sum_probs=111.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhhhhccCccCHHHHH
Q 001701 741 TGINIFFCKINKLAAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREII 820 (1024)
Q Consensus 741 t~l~lFfrKvy~LAa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~sFk~Ii 820 (1024)
++|++||||||+||++||++||++|+++++++++|||+|||+|+|+|+||+|||||||||||||++|||++.++||++||
T Consensus 1 ~sl~iFfrKvy~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii 80 (135)
T PF01857_consen 1 GSLNIFFRKVYKLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDII 80 (135)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHH
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCCcceeeEEEecccccccC---C-CcccccccccchhhhccHHhhHH
Q 001701 821 YNYRKQPQCKPQVFRSVFVDWASARQS---G-RSEQDHVDIITFYNKIFVPAVKP 871 (1024)
Q Consensus 821 ~~Yr~QPqa~~~VyRsVli~~~~~~~~---g-~~~~e~gDII~FYN~VFvp~mK~ 871 (1024)
++||+|||++++|||+|+|+....+.+ | .+++++||||+|||+||||+||+
T Consensus 81 ~~Yr~qpq~~~~Vyr~V~i~~~~~~~~~~~~~~~~~~~gDII~FYN~vFvp~mK~ 135 (135)
T PF01857_consen 81 KAYRKQPQASSHVYRSVLIRSRSDNRNNDSGERSEEERGDIIKFYNKVFVPRMKS 135 (135)
T ss_dssp HHHTTSTT--THHHHSEEESS--------------SEEE-HHHHHHHTHHHHHHH
T ss_pred HHHHhcccccccceEEEEECCcccccccccccccCCCCCCeeeeehHhHHhhcCC
Confidence 999999999999999999987543322 1 23479999999999999999996
No 4
>PF11934 DUF3452: Domain of unknown function (DUF3452); InterPro: IPR024599 This domain is found in proteins of the retinoblastoma protein family. It is found in association with Pfam:PF01858 and Pfam:PF01857. This domain is typically between 124 to 150 amino acids in length and has a single completely conserved residue W that may be functionally important.; PDB: 2QDJ_A 4ELJ_A.
Probab=100.00 E-value=1.3e-36 Score=300.92 Aligned_cols=136 Identities=37% Similarity=0.578 Sum_probs=91.6
Q ss_pred ccCCCCCCCcCCCcccHHHHHHhhCCCHHHHHHhhHHHHHhhcCcccccCCchHHhHHHHHhHhhhhhhHHHHHHHHHHH
Q 001701 90 KNGENLQQGSNDNEFNLCHILRVMKLNIVDFFKELPQFLVKSGPILSNIYGADWENRLEAKELQANFVHLSILSKSYKRI 169 (1024)
Q Consensus 90 ~tv~~~~~~~~gn~vsLT~lLr~~~lsl~~Ff~km~~w~~~~~~~l~~l~~~~~e~rl~~keLe~nF~v~~vL~kky~~i 169 (1024)
|||+ +++++|||||||||||+|+||++|||++|++|+.++++.++ ..+ +.++++||++|+|+++|||||+++
T Consensus 1 ~~~~--~~~~~~n~vsLt~lLr~~~is~~~Ff~~l~~~~~~m~~~~~----~~~--~~~~~~L~~~f~v~~~l~kky~~~ 72 (136)
T PF11934_consen 1 PTVG--KGVVEGNGVSLTQLLRACKISLVEFFKKLKKWAVDMANILS----KRF--RAQVKELERNFVVSTVLFKKYERI 72 (136)
T ss_dssp ----------T---S-HHHHHHHHT--HHHHHHHHCCS--------H----HHH--HH-HHHHHHHHHHHHHHHHHHHHH
T ss_pred CCcc--ccccCCCcCcHHHHHHHcCCCHHHHHHHHHHHHHHhccCcH----HHH--HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4564 46789999999999999999999999999999954433322 233 335999999999999999999999
Q ss_pred HhccccCCCCCcccccccccCCCChhhHHHHHHHHHHHHHhhhcccCchHHHHhhHHHHHHHHHHhc
Q 001701 170 YREFFLPSDANGDKQSAAASTSGYISDYHRFGWLLFLALRIHAFSRFKDLVTCTNGLVSILAILIIH 236 (1024)
Q Consensus 170 F~~iF~~p~~~~~~~~~~~~~~~~~~d~~~f~W~LFL~aK~~~~~~f~DLV~s~~LLlc~Ldll~~n 236 (1024)
|++||..|++++++ .++.+|+++++++|||+|||++|+++++.++|||+||||||||||++|+|
T Consensus 73 f~~lF~~~~~~~~~---~~~~~~~~~~l~~f~W~LFL~~K~~~~~~~~DLV~s~~LLlc~ld~~~~n 136 (136)
T PF11934_consen 73 FQELFKPPPESPPK---SRSSPCSYSDLFRFGWLLFLAAKGKFPSIFDDLVTSYHLLLCVLDLVYTN 136 (136)
T ss_dssp HCCCB--B---S------SS--B-CHHHHHHHHHHHHHHHHHH-SSS--HHHHHHHHHHHHHHHHH-
T ss_pred HHHHhCCCCccccc---ccCCCCCHHHHHHHHHHHHHHHhCCCCcccccHHHHHHHHHHHHHHHHhC
Confidence 99999999877655 22358999999999999999999999999999999999999999999987
No 5
>PF08934 Rb_C: Rb C-terminal domain; InterPro: IPR015030 The Rb C-terminal domain is required for high-affinity binding to E2F-DP complexes and for maximal repression of E2F-responsive promoters, thereby acting as a growth suppressor by blocking the G1-S transition of the cell cycle. This domain has a strand-loop-helix structure, which directly interacts with both E2F1 and DP1, followed by a tail segment that lacks regular secondary structure []. ; PDB: 1H25_E 1GUX_B 3POM_A 1GH6_B 2AZE_C 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A ....
Probab=99.75 E-value=3.6e-19 Score=171.90 Aligned_cols=79 Identities=35% Similarity=0.603 Sum_probs=26.2
Q ss_pred CCCCCCCCCCCCC------CCCcccccCCcEEEecCCC-CCc-ccccCCCCceEEEEeccccccCCCCCccHHHHHHHhh
Q 001701 901 GSPKVSVFPALPD------MSPKKVSATHNVYVSPLRT-SKM-DALISHSSKSYYACVGESTHAYQSPSKDLTDINHRLN 972 (1024)
Q Consensus 901 ~sP~lSp~P~~~~------~SP~rvs~~~nvyvSP~k~-~k~-~~~lsp~s~~~y~~~Ges~~~~~SPskdL~~IN~~i~ 972 (1024)
..|+|||||.+|. .||+||+++|||||||||+ .|. ...||||+++| ||||||+ ++|++|++||+||+
T Consensus 8 ~~p~LSPiP~iprSPy~~~~SP~RVp~s~NVYISPlK~~~k~s~~~mTPRSr~L-y~iGeS~----~~s~~lq~IN~mv~ 82 (155)
T PF08934_consen 8 RPPTLSPIPHIPRSPYKFPNSPRRVPQSHNVYISPLKNPYKMSPSKMTPRSRML-YSIGESF----GSSEKLQKINQMVN 82 (155)
T ss_dssp S-TT-----------------------------------------------EEE-EESS-TT----THHHHHHHHHHHHH
T ss_pred CCCCCCCCCCCCCCcccCCCCCccccCccceEeccccccccCCCcccCccchhh-eeecCCc----chHHHHHHHHHHHc
Confidence 3478888888763 3999999999999999999 443 35899999999 5899988 48999999999999
Q ss_pred c-CCCcccceecC
Q 001701 973 S-NRRVRGTLNFD 984 (1024)
Q Consensus 973 ~-~~~~~~~l~~~ 984 (1024)
+ .|.+||.++.+
T Consensus 83 ~~~Rs~KR~~~~~ 95 (155)
T PF08934_consen 83 SGERSKKRSLDSS 95 (155)
T ss_dssp --TT-----STT-
T ss_pred cchhhhhhhccCC
Confidence 8 67788876643
No 6
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=97.07 E-value=0.0019 Score=73.20 Aligned_cols=73 Identities=16% Similarity=0.345 Sum_probs=65.2
Q ss_pred HHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhhhhccCccCHHHHHHHh
Q 001701 749 KINKLAAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYNY 823 (1024)
Q Consensus 749 Kvy~LAa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~sFk~Ii~~Y 823 (1024)
|.+.-|...|+++|.+|+|++.+.+..-.+|..+..+ .++++|.++.++.+|+|+.||..+...||+||...-
T Consensus 120 r~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~--~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~ 192 (310)
T PRK00423 120 RNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEK--GLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVS 192 (310)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhc--CcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHh
Confidence 3456688999999999999999999999999887665 689999999999999999999999999999997664
No 7
>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=96.99 E-value=0.0028 Score=56.21 Aligned_cols=63 Identities=21% Similarity=0.402 Sum_probs=53.2
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhhhhccCccCHHHHHHH
Q 001701 758 INAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYN 822 (1024)
Q Consensus 758 L~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~sFk~Ii~~ 822 (1024)
|..+|++|+|++++.+..-.+++.+.. ..+.++|..+.|.-.|||..|+.++..+|.+||-+.
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~--~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~ 63 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQE--RGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEA 63 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHH--TTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHH--cCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHH
Confidence 578999999999998888888877644 459999999999999999999999999999999765
No 8
>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=95.76 E-value=0.032 Score=48.72 Aligned_cols=63 Identities=14% Similarity=0.187 Sum_probs=54.3
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhhhhccCccCHHHHHHH
Q 001701 758 INAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYN 822 (1024)
Q Consensus 758 L~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~sFk~Ii~~ 822 (1024)
|..+|.++++++++....|.+++..+.. ..+++ ++...|..+|+|+-||+.....+.++|...
T Consensus 3 l~~~~~~~~~~~~~~~~a~~~~~~~l~~-~~~~~-~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~ 65 (83)
T smart00385 3 LRRVCKALNLDPETLNLAVNLLDRFLSD-YKFLK-YSPSLIAAAALYLAAKTEEIPPWTKELVHY 65 (83)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHH-hhccc-CCHHHHHHHHHHHHHHHhcCCCCchhHhHh
Confidence 6789999999999999999999999875 34554 999999999999999999877777777544
No 9
>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=95.32 E-value=0.095 Score=46.17 Aligned_cols=69 Identities=13% Similarity=0.155 Sum_probs=59.9
Q ss_pred HHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhhhhccCccCHHHHHHHhh
Q 001701 754 AAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYNYR 824 (1024)
Q Consensus 754 Aa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~sFk~Ii~~Yr 824 (1024)
+...|+.+|+.++++.++....|.+++..+... .+..++...|.++|+|.-||+.+...+.++|.+.-.
T Consensus 5 ~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~ 73 (88)
T cd00043 5 PLDFLRRVAKALGLSPETLTLAVNLLDRFLLDY--SVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTG 73 (88)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhc--ccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhC
Confidence 456688999999999999999999999998754 456999999999999999999988888888876543
No 10
>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=95.01 E-value=0.14 Score=45.40 Aligned_cols=67 Identities=15% Similarity=0.251 Sum_probs=48.8
Q ss_pred HHHHhcccCCCHHHHHHHHHHHHHHHHHHhhccccCCCCCchH-HHHHHHHHHHHHHHhcccccCCCCCCCcCCCcccHH
Q 001701 29 TDLCKNGLSVDENTYKEIIKLFRETKHLLLANISAIGNGMPEE-AERFWFAFVLYLVRRLSEKNGENLQQGSNDNEFNLC 107 (1024)
Q Consensus 29 ~~lC~~~LnlD~~t~~~A~~~f~~~~~~~~~~~~~~~~~t~E~-~~~~W~acaLY~a~r~~~~tv~~~~~~~~gn~vsLT 107 (1024)
..+|.. |+|.+.+.+.|.++|+..... + -.-| ......|.++|.|||+. +...|+.
T Consensus 2 ~r~~~~-L~L~~~v~~~A~~i~~~~~~~---------~-~~~Gr~~~~iaAA~iY~acr~~------------~~~~t~~ 58 (71)
T PF00382_consen 2 PRICSK-LGLPEDVRERAKEIYKKAQER---------G-LLKGRSPESIAAACIYLACRLN------------GVPRTLK 58 (71)
T ss_dssp HHHHHH-TT--HHHHHHHHHHHHHHHHT---------T-TSTTS-HHHHHHHHHHHHHHHT------------TSSSSHH
T ss_pred hHHHhH-cCCCHHHHHHHHHHHHHHHHc---------C-CcccCCHHHHHHHHHHHHHHHc------------CCCcCHH
Confidence 468998 999999999999999998632 1 1222 35678899999999983 4556888
Q ss_pred HHHHhhCCCHH
Q 001701 108 HILRVMKLNIV 118 (1024)
Q Consensus 108 ~lLr~~~lsl~ 118 (1024)
+|-..++++-.
T Consensus 59 eIa~~~~Vs~~ 69 (71)
T PF00382_consen 59 EIAEAAGVSEK 69 (71)
T ss_dssp HHHHHCTSSHH
T ss_pred HHHHHhCCCCC
Confidence 88888877644
No 11
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=94.71 E-value=0.098 Score=58.31 Aligned_cols=73 Identities=23% Similarity=0.427 Sum_probs=61.0
Q ss_pred HHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhhhhccCccCHHHHHHHh
Q 001701 749 KINKLAAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYNY 823 (1024)
Q Consensus 749 Kvy~LAa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~sFk~Ii~~Y 823 (1024)
++...|..-|..+|++|+|+..+..+.-.+|+.+ +...++++|..|-|.--|||+-||-.++..|||||-..-
T Consensus 102 ~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v--~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~a 174 (308)
T KOG1597|consen 102 RVLKAAFKEITAMCDRLSLPATIKDRANEIFKLV--EDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVA 174 (308)
T ss_pred HHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHH--HHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHH
Confidence 4677899999999999999987666655555543 356699999999999999999999999999999995543
No 12
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=93.41 E-value=0.19 Score=57.21 Aligned_cols=62 Identities=15% Similarity=0.156 Sum_probs=55.7
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhhhhccCccCHHHHHH
Q 001701 758 INAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIY 821 (1024)
Q Consensus 758 L~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~sFk~Ii~ 821 (1024)
|..+|++|+|+.++.+..|.+++.+.. ..|..+|+..-|.-.|||+.|++++..+|+++|-.
T Consensus 223 i~r~~~~L~L~~~v~~~A~~i~~~a~~--~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~ 284 (310)
T PRK00423 223 VPRFASELGLSGEVQKKAIEILQKAKE--KGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAE 284 (310)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHh--cCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence 347899999999999999999998754 57999999999999999999999999999999844
No 13
>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=91.02 E-value=0.42 Score=48.24 Aligned_cols=71 Identities=17% Similarity=0.345 Sum_probs=49.5
Q ss_pred HHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHhhccccCCCCCchHHHHHHHHHHHHHHHhcccccCCCCCCCcCCCc
Q 001701 24 TEARLTDLCKNGLSVDENTYKEIIKLFRETKHLLLANISAIGNGMPEEAERFWFAFVLYLVRRLSEKNGENLQQGSNDNE 103 (1024)
Q Consensus 24 ~~~rf~~lC~~~LnlD~~t~~~A~~~f~~~~~~~~~~~~~~~~~t~E~~~~~W~acaLY~a~r~~~~tv~~~~~~~~gn~ 103 (1024)
.-.|.++||.. |+|+++..++.|..|+.+-.. ...-+-+ ----.++.|++|+.|+.. ...
T Consensus 14 a~~Rl~~LC~~-L~l~~~~~~~iwt~fe~~l~~---~t~L~~d----RHLDQiilCaiY~i~Kv~------------~~~ 73 (135)
T PF01857_consen 14 AAVRLQDLCER-LDLSSDLREKIWTCFEHSLTH---HTELMKD----RHLDQIILCAIYGICKVS------------KEE 73 (135)
T ss_dssp HHHHHHHHHHH-HTTSTTHHHHHHHHHHHHHHH---SGGGGTT----S-HHHHHHHHHHHHHHHT------------T-S
T ss_pred HHHHHHHHHHH-cCCcHHHHHHHHHHHHHHHHh---hHHHHhc----chHHHHHHHHHHHHHHhh------------cCC
Confidence 34689999997 999999999999999998522 1111111 123468999999999872 245
Q ss_pred ccHHHHHHhhC
Q 001701 104 FNLCHILRVMK 114 (1024)
Q Consensus 104 vsLT~lLr~~~ 114 (1024)
+|+.+|+++-+
T Consensus 74 ~sF~~Ii~~Yr 84 (135)
T PF01857_consen 74 LSFKDIIKAYR 84 (135)
T ss_dssp --HHHHHHHHT
T ss_pred CCHHHHHHHHH
Confidence 68888888764
No 14
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=87.88 E-value=2.3 Score=48.08 Aligned_cols=76 Identities=18% Similarity=0.341 Sum_probs=63.5
Q ss_pred HHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhhhhccCccCHHHHHHHhhcC
Q 001701 749 KINKLAAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYNYRKQ 826 (1024)
Q Consensus 749 Kvy~LAa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~sFk~Ii~~Yr~Q 826 (1024)
+-...|..-|..+|..|+|+..+++..-.++.-++ ...|.++|-+-.++--|+|+.|+..+...|+++|....+-.
T Consensus 95 rnl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~--~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V~ 170 (285)
T COG1405 95 RNLITALEELERIASALGLPESVRETAARIYRKAV--DKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGVS 170 (285)
T ss_pred hHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHh--hcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCCC
Confidence 44556888899999999999987776655555444 45699999999999999999999999999999999988643
No 15
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=80.39 E-value=9.7 Score=32.90 Aligned_cols=52 Identities=23% Similarity=0.324 Sum_probs=40.2
Q ss_pred HHHHHhcccCCCHHHHHHHHHHHHHHHHHHhhccccCCCCCchHHHHHHHHHHHHHHHhccc
Q 001701 28 LTDLCKNGLSVDENTYKEIIKLFRETKHLLLANISAIGNGMPEEAERFWFAFVLYLVRRLSE 89 (1024)
Q Consensus 28 f~~lC~~~LnlD~~t~~~A~~~f~~~~~~~~~~~~~~~~~t~E~~~~~W~acaLY~a~r~~~ 89 (1024)
+..+|+. ++++.++...|+.+++...... . -.........|+++|.||+...
T Consensus 3 l~~~~~~-~~~~~~~~~~a~~~~~~~l~~~--~-------~~~~~~~~ia~a~l~lA~k~~~ 54 (83)
T smart00385 3 LRRVCKA-LNLDPETLNLAVNLLDRFLSDY--K-------FLKYSPSLIAAAALYLAAKTEE 54 (83)
T ss_pred HHHHHHH-cCCCHHHHHHHHHHHHHHHHHh--h-------cccCCHHHHHHHHHHHHHHHhc
Confidence 4578997 9999999999999999996421 1 1224567788999999999853
No 16
>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=73.24 E-value=20 Score=34.45 Aligned_cols=72 Identities=19% Similarity=0.355 Sum_probs=56.8
Q ss_pred HHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhhhhccC-ccCHHHHHHH
Q 001701 749 KINKLAAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQL-NLTFREIIYN 822 (1024)
Q Consensus 749 Kvy~LAa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~-~~sFk~Ii~~ 822 (1024)
+.-..+...+..+|..++++++.....+.+|+..+.... +...++..|.++|+|+-||+... ..+.++++..
T Consensus 29 ~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~--~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~ 101 (127)
T PF00134_consen 29 EMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRP--VNRSKLQLIALACLFLASKMEEDNPPSISDLIRI 101 (127)
T ss_dssp HHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS---TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcc--cccchhhhhhhhHHHHhhhhhccccchHHHHHHH
Confidence 344556677888999999999999999999998877663 88899999999999999999876 4666666554
No 17
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=55.74 E-value=57 Score=37.19 Aligned_cols=56 Identities=13% Similarity=0.202 Sum_probs=41.6
Q ss_pred hHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHhhccccCCCCCchHHHHHHHHHHHHHHHhcc
Q 001701 23 ATEARLTDLCKNGLSVDENTYKEIIKLFRETKHLLLANISAIGNGMPEEAERFWFAFVLYLVRRLS 88 (1024)
Q Consensus 23 ~~~~rf~~lC~~~LnlD~~t~~~A~~~f~~~~~~~~~~~~~~~~~t~E~~~~~W~acaLY~a~r~~ 88 (1024)
.....+..+|.. |+|.+...+.|..+|...- +-....+-+. .--+|.++|+|||+.
T Consensus 99 ~a~~~l~~~~~~-l~LP~~v~e~A~~iyr~a~-----~~~l~rGRsi----e~v~AA~iY~acR~~ 154 (285)
T COG1405 99 TALEELERIASA-LGLPESVRETAARIYRKAV-----DKGLLRGRSI----ESVAAACIYAACRIN 154 (285)
T ss_pred HHHHHHHHHHHH-hCCCchHHHHHHHHHHHHh-----hcCCCcCCcH----HHHHHHHHHHHHHHc
Confidence 455667778998 9999999999999999874 1112233333 446789999999994
No 18
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=54.49 E-value=49 Score=37.99 Aligned_cols=67 Identities=15% Similarity=0.355 Sum_probs=47.6
Q ss_pred HHHHHHHHHHhC--CChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhhhhccCccCHHHHHHHh
Q 001701 755 AVRINAMVERLQ--LSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYNY 823 (1024)
Q Consensus 755 a~RL~~LC~~L~--l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~sFk~Ii~~Y 823 (1024)
...|+++|.+|+ +++++..-.=..|.--.. ... +++-|.-.|++.|+|.-||+....++-.++...-
T Consensus 60 ~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~-~~S-v~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~ 128 (305)
T TIGR00569 60 EKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYL-NNS-VMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNL 128 (305)
T ss_pred HHHHHHHHHHhcCCCCchHHHHHHHHHhHHhc-cCc-hhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhc
Confidence 458899999999 988654433334422222 223 4467999999999999999998777777776643
No 19
>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=53.81 E-value=1e+02 Score=26.70 Aligned_cols=55 Identities=16% Similarity=0.152 Sum_probs=39.3
Q ss_pred HHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHhhccccCCCCCchHHHHHHHHHHHHHHHhcc
Q 001701 24 TEARLTDLCKNGLSVDENTYKEIIKLFRETKHLLLANISAIGNGMPEEAERFWFAFVLYLVRRLS 88 (1024)
Q Consensus 24 ~~~rf~~lC~~~LnlD~~t~~~A~~~f~~~~~~~~~~~~~~~~~t~E~~~~~W~acaLY~a~r~~ 88 (1024)
...-...+|+. ++++..+..-|+..|+...... . + .......-.+++||.||+..
T Consensus 5 ~~~~l~~~~~~-~~~~~~~~~~A~~~~~~~~~~~---~--~----~~~~~~~ia~a~l~lA~k~~ 59 (88)
T cd00043 5 PLDFLRRVAKA-LGLSPETLTLAVNLLDRFLLDY---S--V----LGRSPSLVAAAALYLAAKVE 59 (88)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHHHHHHHHHhc---c--c----ccCChHHHHHHHHHHHHHHc
Confidence 44557789998 9999999999999999985321 1 1 12233445578888888873
No 20
>KOG1992 consensus Nuclear export receptor CSE1/CAS (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=40.07 E-value=1.5e+02 Score=38.34 Aligned_cols=101 Identities=21% Similarity=0.393 Sum_probs=60.9
Q ss_pred cHHHHHH----hhC-------CCHHHHH-HhhHHHHHh-------hcCcccccCCchHHhHHHHHhHhhhhhhHHHHH-H
Q 001701 105 NLCHILR----VMK-------LNIVDFF-KELPQFLVK-------SGPILSNIYGADWENRLEAKELQANFVHLSILS-K 164 (1024)
Q Consensus 105 sLT~lLr----~~~-------lsl~~Ff-~km~~w~~~-------~~~~l~~l~~~~~e~rl~~keLe~nF~v~~vL~-k 164 (1024)
+|..|++ .|| ..|-+|| +.|+.|+.. .++.+. + |-+.--.+.++.+...=...|| +
T Consensus 201 ~l~~lf~vlll~~klfysLn~QDiPEFFEdnm~~wM~~F~k~l~~~~p~le---~-~~ee~~~l~~lka~ICEi~~LY~~ 276 (960)
T KOG1992|consen 201 ALNILFGVLLLICKLFYSLNFQDIPEFFEDNMKTWMGAFHKLLTYDNPLLE---S-DEEEATVLDKLKAQICEIFNLYAT 276 (960)
T ss_pred HHHHHHHHHHHHHHHHHhhhcccchHHHHhhHHHHHHHHHHHHhccCcccc---c-CcccccHHHHHHHHHHHHHHHHHH
Confidence 7777777 233 5678999 589998543 233333 2 2122222555655555555566 8
Q ss_pred HHHHHHhccccCCCCCcccccccccCCCChhhHHHHHHHHHHHHHhhhc-ccCchHH-HHhhHHHHHHHH
Q 001701 165 SYKRIYREFFLPSDANGDKQSAAASTSGYISDYHRFGWLLFLALRIHAF-SRFKDLV-TCTNGLVSILAI 232 (1024)
Q Consensus 165 ky~~iF~~iF~~p~~~~~~~~~~~~~~~~~~d~~~f~W~LFL~aK~~~~-~~f~DLV-~s~~LLlc~Ldl 232 (1024)
||++.|+.+. .|.....|.|-.. -.+ ..+|-|| +.+..|..|...
T Consensus 277 kYeEef~~fl--------------------~~fv~~~W~LL~~---~s~~~kyD~Lvs~Al~FLt~V~~r 323 (960)
T KOG1992|consen 277 KYEEEFQPFL--------------------PDFVTATWNLLVS---TSPDTKYDYLVSKALQFLTSVSRR 323 (960)
T ss_pred hhHHHHHhhH--------------------HHHHHHHHHHHHh---cCCCccHHHHHHHHHHHHHHHHhh
Confidence 9999888765 3466678988773 122 2457787 567777666554
No 21
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=37.47 E-value=98 Score=37.94 Aligned_cols=55 Identities=22% Similarity=0.440 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhhhhcc
Q 001701 754 AAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQ 811 (1024)
Q Consensus 754 Aa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k 811 (1024)
|-..|.+++.+|+|.+ ..+-+..-|+-++.++ +-++|----+|--|+|++|+..+
T Consensus 70 ~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~n--ftkGr~~~~vvasClY~vcR~e~ 124 (521)
T KOG1598|consen 70 ARRLIEELTERLNLGN-KTEVAFNFFKLAPDRN--FTKGRRSTEVVAACLYLVCRLEK 124 (521)
T ss_pred HHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCC--CCCCcchHHHHHHHHHHHHHhhC
Confidence 6678999999999988 6777777777776654 88999999999999999999876
No 22
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=35.38 E-value=3.6e+02 Score=33.35 Aligned_cols=55 Identities=20% Similarity=0.211 Sum_probs=43.8
Q ss_pred hHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHhhccccCCCCCchHHHHHHHHHHHHHHHhcc
Q 001701 23 ATEARLTDLCKNGLSVDENTYKEIIKLFRETKHLLLANISAIGNGMPEEAERFWFAFVLYLVRRLS 88 (1024)
Q Consensus 23 ~~~~rf~~lC~~~LnlD~~t~~~A~~~f~~~~~~~~~~~~~~~~~t~E~~~~~W~acaLY~a~r~~ 88 (1024)
..+...+++|.. |++.+ -.+-|...|.-.- .+|++.-.-..+=+|..||++||+.
T Consensus 69 n~r~~i~~~~~~-l~l~~-~~~~a~~~~k~a~---------~~nftkGr~~~~vvasClY~vcR~e 123 (521)
T KOG1598|consen 69 NARRLIEELTER-LNLGN-KTEVAFNFFKLAP---------DRNFTKGRRSTEVVAACLYLVCRLE 123 (521)
T ss_pred HHHhHHHHHHHh-cCcch-HHHHHHHHHHHHh---------hCCCCCCcchHHHHHHHHHHHHHhh
Confidence 345578899998 99999 8888888887763 3666665567788899999999996
No 23
>PF07340 Herpes_IE1: Cytomegalovirus IE1 protein; InterPro: IPR010855 Expression from a human cytomegalovirus early promoter (E1.7) has been shown to be activated in trans by the IE2 gene product. Although the IE1 gene product alone had no effect on this early viral promoter, maximal early promoter activity was detected when both IE1 and IE2 gene products were present []. The IE1 protein from cytomegalovirus is also known as UL123.; GO: 0050792 regulation of viral reproduction, 0042025 host cell nucleus
Probab=25.97 E-value=1.2e+03 Score=27.89 Aligned_cols=73 Identities=18% Similarity=0.230 Sum_probs=50.1
Q ss_pred chhhHHHHHHHHHHHHHHhhccCCccchh--------HHhhhcCCCcchHHHHHHHHHhhcCCCC---HHHHHHHHHHHH
Q 001701 533 TNERFHRCMLACSAELVLATHKTVTMLFP--------AVLERTGITAFDLSKVIESFIRHEESLP---RELRRHLNSLEE 601 (1024)
Q Consensus 533 ~~d~FhrsLlACclEiVl~ty~~~~~~FP--------wILe~~~i~afdf~KVIE~fVR~e~~Lp---RelvkHLn~IEE 601 (1024)
.++.--|+.++|--=+|.+..+. .|| +++-.-+++-+|---|++.-.+--..|- .++.=|++.+=-
T Consensus 198 kddL~~k~~Yt~~Ky~e~~mk~~---~~PKttn~~sQA~~fL~nlp~~d~d~v~~~g~~iik~LD~Eq~~Vl~~id~~f~ 274 (392)
T PF07340_consen 198 KDDLKRKCTYTCLKYIEMFMKNL---CMPKTTNGQSQAKAFLRNLPQCDPDEVNEYGQKIIKTLDKEQKEVLFHIDNVFM 274 (392)
T ss_pred HHHHHHHHHHHHHHHHHHHHccC---CCCCCcccHHHHHHHHhccccCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence 36667788999988888888754 577 5555567777777667665444434444 445558888777
Q ss_pred HHHhhhh
Q 001701 602 RLLESMV 608 (1024)
Q Consensus 602 ~ILEslA 608 (1024)
.||++.+
T Consensus 275 ~ll~~~~ 281 (392)
T PF07340_consen 275 DLLTTCV 281 (392)
T ss_pred HHHHHHH
Confidence 8888764
No 24
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=24.62 E-value=2e+02 Score=32.97 Aligned_cols=63 Identities=16% Similarity=0.162 Sum_probs=50.6
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhhhhccCccCHHHHHHH
Q 001701 758 INAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYN 822 (1024)
Q Consensus 758 L~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~sFk~Ii~~ 822 (1024)
+...|..|+|+.+.++-+=.+.|-+ +.-++..+|.-.-|.--+||.++.+.....+-++|.+.
T Consensus 207 m~RFCs~L~L~~~~q~aA~e~a~ka--~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~v 269 (308)
T KOG1597|consen 207 MPRFCSNLGLPKSAQEAATEIAEKA--EEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEV 269 (308)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHHH--HHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHH
Confidence 4457999999987666554444443 45678889999999999999999999998999998654
Done!