Query 002530
Match_columns 912
No_of_seqs 177 out of 204
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 01:51:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002530.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002530hhsearch_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 1E-180 2E-185 1548.6 55.8 776 1-902 112-917 (920)
2 PF01858 RB_A: Retinoblastoma- 100.0 9.3E-62 2E-66 499.7 17.1 194 306-507 1-194 (194)
3 PF01857 RB_B: Retinoblastoma- 100.0 5.9E-52 1.3E-56 403.3 11.5 131 629-759 1-135 (135)
4 PF11934 DUF3452: Domain of un 100.0 3.3E-31 7.1E-36 259.2 8.7 115 1-124 22-136 (136)
5 PF08934 Rb_C: Rb C-terminal d 99.8 1.1E-19 2.4E-24 173.3 2.6 79 789-872 8-95 (155)
6 PRK00423 tfb transcription ini 97.1 0.0016 3.5E-08 72.8 9.3 73 637-711 120-192 (310)
7 PF00382 TFIIB: Transcription 97.1 0.0022 4.8E-08 56.0 7.8 63 646-710 1-63 (71)
8 smart00385 CYCLIN domain prese 95.9 0.026 5.5E-07 48.6 7.0 63 646-710 3-65 (83)
9 cd00043 CYCLIN Cyclin box fold 95.6 0.074 1.6E-06 46.2 8.5 69 642-712 5-73 (88)
10 KOG1597 Transcription initiati 94.9 0.083 1.8E-06 58.1 8.1 72 637-710 102-173 (308)
11 PRK00423 tfb transcription ini 93.8 0.15 3.2E-06 57.2 7.5 62 646-709 223-284 (310)
12 COG1405 SUA7 Transcription ini 88.6 2 4.3E-05 47.9 9.2 75 637-713 95-169 (285)
13 PF00134 Cyclin_N: Cyclin, N-t 75.7 16 0.00036 34.5 8.8 72 637-710 29-101 (127)
14 TIGR00569 ccl1 cyclin ccl1. Un 56.6 44 0.00095 37.8 8.5 67 643-711 60-128 (305)
15 KOG1992 Nuclear export recepto 45.0 1E+02 0.0022 39.1 9.5 95 4-120 223-323 (960)
16 KOG1598 Transcription initiati 36.1 97 0.0021 37.4 7.4 55 642-699 70-124 (521)
17 KOG1597 Transcription initiati 26.9 1.8E+02 0.0039 32.9 7.0 63 646-710 207-269 (308)
18 PRK14102 nifW nitrogenase stab 23.4 93 0.002 30.0 3.6 35 207-242 53-87 (105)
19 KOG1010 Rb (Retinoblastoma tum 22.8 1E+02 0.0022 39.2 4.7 54 643-699 35-88 (920)
20 cd08768 Cdc6_C Winged-helix do 21.2 1.1E+02 0.0024 27.2 3.5 30 685-714 5-35 (87)
No 1
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1e-180 Score=1548.57 Aligned_cols=776 Identities=34% Similarity=0.507 Sum_probs=636.1
Q ss_pred CCccHHHHhHhhHHHHHhhcCcccccCChhHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhhcCCCCCCCCccccccc---
Q 002530 1 MKLNIVDFFKELPQFLVKSGPILSNIYGADWENRLEAKELQANFVHLSILSKSYKRIYREFFLPSDANGDKQSAAAS--- 77 (912)
Q Consensus 1 ~~lsl~~Ff~km~~w~~~~~~~l~~~~~~~~~~rl~~~~Le~~F~v~~vl~kky~~iF~~iF~~p~~~~~~~~~~~~--- 77 (912)
||||++|||+||+||++|+ + .+++| |++++|||+||+|+++|||||++||.+||+.|.++++..++.++
T Consensus 112 ~k~sv~eff~km~~w~~ma-----~-s~~~f--~~~ieel~~~f~vssvl~KkY~~iF~~iF~~p~~e~~~~~~~~n~~~ 183 (920)
T KOG1010|consen 112 FKMSVIEFFTKMKQWVDMA-----N-SPQEF--REEIEELQRNFKVSSVLFKKYKRIFRDIFKLPREELGYLNRPSNHAR 183 (920)
T ss_pred HHHHHHHHHHHHHHHHHHh-----c-CHHHH--HHHHHHHHhccceehhHHHHHHHHHHHHHhCcccccccCCCcccccC
Confidence 5899999999999999998 4 48855 66699999999999999999999999999999976665555444
Q ss_pred CCCChhhHHhHHHHHHHHHHhhhccccchHHHHhhHHHHHHHHHHhccCccc----cccccCCC-cccc----cccCCcc
Q 002530 78 TSGYISDYHRFGWLLFLALRIHAFSRFKDLVTCTNGLVSILAILIIHVPVRF----RNFNIHDS-SRFV----KKSNKGV 148 (912)
Q Consensus 78 ~~~~~~d~~~f~W~LFl~~k~~~~~~f~DLV~s~~LLlc~ldll~~n~p~~~----~n~~~~~~-~~~~----k~~~~~~ 148 (912)
++|++.++|+|||+|||++|+++++++||||+||||||||||++|+|++.+. .||+|+|. .++. +.+..++
T Consensus 184 ~~~~~~~l~~f~W~lFL~~Kn~~~~~~dDLV~syqlllc~LDlv~~n~lc~~R~~~v~p~f~gl~~n~~~~d~~~s~n~~ 263 (920)
T KOG1010|consen 184 TPCSYAELFKFCWLLFLVAKNEFPSIEDDLVNSYQLLLCILDLVYKNLLCSPRKDLVNPSFKGLPKNWTARDFKPSENPP 263 (920)
T ss_pred CcccHHHHHHHHHHHHHHHhcccchhhhhHHhhhhHHHHHHHHHHHHhccccccccccccccCCCCCCchhhccccCCCc
Confidence 7999999999999999999999999999999999999999999999966654 47888873 4443 4557889
Q ss_pred hhHHHhhhhcCCCHHHHHHHHHH-hHHHHHHHhccCcccccccccccCCCCCCCcccccccCCCCCchHHHHHHHHHHHH
Q 002530 149 DLIASLCSIYDTSEDDLRKIMEK-TNTLIADILKKKPCEASECKSENLENIDTDGLIYFENLMDDSSLSSSLNILEKDYD 227 (912)
Q Consensus 149 ~il~~LC~~~~~~~~e~k~~~~~-~~~~I~~~f~k~~l~~~~~~~~~l~~~~~~~~~~~~gLl~~~~f~~nl~~Lnk~YE 227 (912)
|||+.||++|+++.+|||+|+++ |++++..+|..+.+. |+..+ ++||++.++|..|+++|||.||
T Consensus 264 cii~~lce~h~~li~eak~~k~~~fk~~~~~l~~~ktl~---g~~~~-----------~~gll~~~~f~~~~~~lnk~ye 329 (920)
T KOG1010|consen 264 CIIEVLCELHEGLIDEAKNMKETNFKPFMSSLYEVKTLK---GDYLL-----------MRGLLDEGNFLPNVKNLNKSYE 329 (920)
T ss_pred chhHHhhhhhhhHHHhhcchHHHhHHHHHHHHHhhhhhh---ccccc-----------ccccccccccchhHHHHhhhHH
Confidence 99999999999999999999999 599999999887652 22222 5899999999999999999999
Q ss_pred HHhccCCCCcccccccCCCccccCCCCCCC--cccc-ccccccccccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 002530 228 NATRNKGELDERVFINEDDSLLGSGSLSGG--AVNI-TGAKRKFDSLASPVKTITSPLSPHRSSASHPNGIAGGATSKMV 304 (912)
Q Consensus 228 ~~vl~~GdlDERiFL~~d~~~ig~~~~s~~--~~~~-~~~~~~~~~~~sp~~~~~~plt~~~sp~s~~~g~~~~~~~~~~ 304 (912)
+||+++|||||||||+.|+++.+..+.++- ..++ +.+.+++.+..| . .+++..|++|.++.+..
T Consensus 330 eyvl~vgelDeRifl~~Da~~~t~~~~s~~~~r~~~~~~~~~~~~~~~s-~------------~~p~~~~~~y~~e~~~~ 396 (920)
T KOG1010|consen 330 EYVLDVGELDERIFLGEDAEEETKSSDSFESERLAVKSSLAQEFLKTQS-K------------KSPPHTGVRYNLELGNY 396 (920)
T ss_pred HHhccccchhhhhhcccchhhhhccCCccchhccccccccchhhccccc-c------------cCCCCcccccccccccC
Confidence 999999999999999999887763221111 1111 222333332222 1 12345599999999999
Q ss_pred CchhhhHHhHHHHHHHHhCCCCCCCcHHHHHHHhhcCCChHHHHHHHHHHHHHhhcCCCCCCCcccccCCCCCcccchHH
Q 002530 305 VTPVSTAMTTAKWLRTVICPLPSKPSAELERFLKSCDKDVTTDVMRRAHIILEAIFPSSGLGERCVTGSLQGANLMDNIW 384 (912)
Q Consensus 305 ~TPVs~Am~s~~~L~~~l~~l~~~PS~~L~~~f~~C~~d~~~~i~~rv~~i~e~~f~~~~~~~~~~~~~~~~~~~~d~~~ 384 (912)
.|||++||++++||++++.|+..+||++|++||++|++||+++|++|+++|++.|+++...+..+ + ...++ +
T Consensus 397 ~tPvsta~~sik~l~t~i~g~~~~psdkLe~~~~tc~r~p~e~Il~r~~~i~e~~~q~f~~~~~~-----g-~~~~e--~ 468 (920)
T KOG1010|consen 397 PTPVSTATNSIKQLMTILNGLKKEPSDKLEQYLNTCSRDPTESILKRLKEIFEIFEQKFSAAEGS-----G-NSCIE--I 468 (920)
T ss_pred CCcchhHHHHHHHHHHHHhccccCCcHHHHHHHhhcccChHHHHHHHHHHHHHHHHHHhhhhccC-----C-ccchH--H
Confidence 99999999999999999999999999999999999999999999999999999998876533311 1 23455 7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcccchHhhhchhHHHHHHHHHHHHHHHhhccCCccchhHHhhhcCCCcchhhh
Q 002530 385 AEQRRLEALKLYYRVLEAMCTAEAQVLHAKNLTSLLTNERFHRCMLACSAELVLATHKTVTMLFPAVLERTGITAFDLSK 464 (912)
Q Consensus 385 a~qR~~~a~~LYYrvLE~Il~~E~~rl~~~dls~LL~~d~FhrsLlACclEiVl~ty~~~~~~FPwILe~~~i~afdf~K 464 (912)
+.||+++|++|||||||+||++|.+|++..||+.||+|++||+||||||+|+||++|++ ++.|||||++|||+||||||
T Consensus 469 ~~~r~k~a~~LYykvLE~il~aE~~rl~~~dl~~LL~q~~Fh~sLlACclElVL~ty~~-~l~FPwvle~~~l~aFdF~K 547 (920)
T KOG1010|consen 469 ASQRFKLAERLYYKVLEKILKAELKRLPDMDLSKLLEQEIFHRSLLACCLELVLATYKT-DLSFPWVLECFGLKAFDFYK 547 (920)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CCCCchhhhhcCCcHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999997 59999999999999999999
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhhcCCCCchhHHHhhhccchhhhhhhcCCCCCCCCchhhhhhccccCCCC
Q 002530 465 VIESFIRHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSLTVARPVLSAEINRLGLLADPMPSLDAIATHINFSSGG 544 (912)
Q Consensus 465 VIE~fIR~e~~LpRelvkHLn~IEE~ILEslAW~~~S~Lw~~L~~~~~~~~~e~~~~~~~~e~~p~~~~i~~~~~~~~~~ 544 (912)
|||+|||||++|+||||||||+|||+|||||||++|||||++|++++ +|++++.+++|+.+ .+... ..|
T Consensus 548 VIE~~IRhE~~L~RemiKHLn~iEE~iLEslaW~~dS~Lw~~i~~~~-------~~~~~~~~~~~~~~-le~~~---~~~ 616 (920)
T KOG1010|consen 548 VIESFIRHEGGLSREMIKHLNSIEERILESLAWKSDSPLWEMIKQAK-------PRLPTEEGVDPPDN-LESAC---IAG 616 (920)
T ss_pred HHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccCCcHHHHHHhcc-------cccccccccccccc-ccccc---ccc
Confidence 99999999999999999999999999999999999999999999887 45666666666654 21100 011
Q ss_pred CCCcccCCcCCC----CCCCCCCCCCCCCCCcCccccccccccccCcccccccccCCCCCCCCCCCcccccCCCCCCCCC
Q 002530 545 LSPVHSLHKHET----SPGQNGDIRSPKRPCTDYRSVLVERNNFTSPVKDRLLGLNNLKSKPLPPPLQSAFASPTRPNPG 620 (912)
Q Consensus 545 ~p~~p~~~~~~~----~~~~~~~~~sp~~~~~~~~s~~~~~~~~~sP~k~~l~~~~~~~~k~~p~~~~s~~~sp~~~~~~ 620 (912)
-.|.+.++.+ +|++ .|++. +.++|++++.. .++..++.
T Consensus 617 --~~p~~~~~~~~~~~sp~~-----~Pk~~------------~~t~pv~~~an-------------------~~qe~~~~ 658 (920)
T KOG1010|consen 617 --LLPLRVNHVRARYSSPVL-----EPKDK------------GTTIPVNGTAN-------------------AGQEVTAF 658 (920)
T ss_pred --cCCccccccccccCCCCC-----Ccccc------------ccccccccccc-------------------ccccCCcc
Confidence 1222222111 1111 12221 12334444321 22445556
Q ss_pred CCCCcccchhHHHHHHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhHhhccC
Q 002530 621 GGGETCAETGINIFFCKINKLAAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQL 700 (912)
Q Consensus 621 ~~~e~~~~t~l~lFfrKvy~LAa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~ 700 (912)
+++.++++|+|+|||||||+|||+||++||+||+++++++++|||||||+|+|+|+||+||||||||||||||||||+++
T Consensus 659 ~~~~~~~stsLsIF~rKvY~LAavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~ 738 (920)
T KOG1010|consen 659 GVNKPRKSTSLSIFLRKVYHLAAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKE 738 (920)
T ss_pred cCCCcccccchHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcc
Confidence 67788899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCHHHHHHHHhcCCCCCCceeEEEEecccccccCCCcc--cccccccchhhhccHhhhHHHHHHhcCCCCcCccCcccc
Q 002530 701 NLTFREIIYNYRKQPQCKPQVFRSVFVDWASARQSGRSE--QDHVDIITFYNKIFVPAVKPLLVELGPAGTAMKTNRVSE 778 (912)
Q Consensus 701 ~~tFk~Ii~~Yr~QPqa~~~VyRsVli~~~~~~~~g~~~--~e~gDII~FYN~VFvp~mK~f~l~~~~~~~~~~~~~~~~ 778 (912)
++||++||++||+||||.++|||+|+|+....++.|..| ++++|||+|||.||||.||+|+++|....+
T Consensus 739 ~ltF~eIm~~YR~QPqa~~~vyRsV~i~~~~~~~~~~~~P~~~~~diI~fyN~iyV~~~k~~~i~~~~~~~--------- 809 (920)
T KOG1010|consen 739 DLTFSEIMRAYRRQPQAVSLVYRSVLIKDKTNRDQGPSGPKEERSDIITFYNNIYVPPMKTFAIEYGLATT--------- 809 (920)
T ss_pred cchHHHHHHHHhcCchhhhhhhhheeecccccccccCCCCcccccceeccccceehhhhhhhhhhhccCCC---------
Confidence 999999999999999999999999999832222233222 489999999999999999999999998621
Q ss_pred cCCCCCCCCCCCCCCCCCCCCC--CCCCcccccCCcEEEecCCCCCcccccCCCCceEEEEeccccccCCCCCccHHHHH
Q 002530 779 VNHNNDGPCPGSPKVSVFPALP--DMSPKKVSATHNVYVSPLRTSKMDALISHSSKSYYACVGESTHAYQSPSKDLTDIN 856 (912)
Q Consensus 779 ~~~~~d~~~~~sP~lSp~p~l~--~~sP~rvs~~hnvyvSPlk~~k~~~~lsp~s~~~y~~~ges~~~~~SPskdL~~IN 856 (912)
++.++++|.|++. ..+|+++|++||||||||+++ +.+++++++.||+| .||||+|++||
T Consensus 810 ---------~~~~~lsp~~~i~~~~~e~~~~S~~h~v~is~~~~~--~~l~s~s~~~y~~~--------~spsk~L~ain 870 (920)
T KOG1010|consen 810 ---------MDAKPLSPSPSIKVSIGEPRRLSQRHNVYISPHKNS--DRLQSRSTAEYYFC--------NSPSKDLPAIN 870 (920)
T ss_pred ---------CCCCCCCCCccccccCCCCcchhhhcceeecCCCch--hhhcCcchhhcccc--------CCCCcchHHHH
Confidence 3456777777765 458899999999999999887 34444444555555 37999999999
Q ss_pred HHhhcCCCcccceecCCCcccccccchhhhhhhccc------cCCCCCcCCC
Q 002530 857 HRLNSNRRVRGTLNFDDVDVDVGLVSDSMVANSLYL------QNGSAAASTC 902 (912)
Q Consensus 857 ~~i~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~ 902 (912)
+||+++....+..++.+ | .++++.+||.+-. |+++.+++++
T Consensus 871 ~~i~~ss~~~~~~~~~~---e--s~~Es~~ani~~~~~~~~~~r~~D~~~~~ 917 (920)
T KOG1010|consen 871 NLIRGSSERTKKKHIPG---E--SKSESKRANILQERTRMQLQRLQDAMSTR 917 (920)
T ss_pred HHhhcCcccccccCCCc---c--chhhhhHhhhhhhhhHHHHhhhhhhhhcc
Confidence 99998433333444554 2 8999999998865 5666666553
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=9.3e-62 Score=499.72 Aligned_cols=194 Identities=45% Similarity=0.734 Sum_probs=167.6
Q ss_pred chhhhHHhHHHHHHHHhCCCCCCCcHHHHHHHhhcCCChHHHHHHHHHHHHHhhcCCCCCCCcccccCCCCCcccchHHH
Q 002530 306 TPVSTAMTTAKWLRTVICPLPSKPSAELERFLKSCDKDVTTDVMRRAHIILEAIFPSSGLGERCVTGSLQGANLMDNIWA 385 (912)
Q Consensus 306 TPVs~Am~s~~~L~~~l~~l~~~PS~~L~~~f~~C~~d~~~~i~~rv~~i~e~~f~~~~~~~~~~~~~~~~~~~~d~~~a 385 (912)
||||+||++++||+++++|+++.||++|.++|++|++||+++|++||++|++.|++.+..+.. . ...+..++
T Consensus 1 TPVs~A~~~~~~L~~~l~~~~~~PS~~L~~~~~~c~~~p~~~i~~rv~~l~~~~~~~~~~~~~----~----~~~~~~~~ 72 (194)
T PF01858_consen 1 TPVSSAMQSVSWLQALLSGLSDEPSEELLRIFKSCSRDPTESILKRVKQLLEKFCQKYTEAEG----E----QSSNSDFA 72 (194)
T ss_dssp -HHHHHHHHHHHHHHHHHHS-SS--HHHHHHHHTSSS--HHHHHHHHHHHHHHHHHHHHHHHS----G----G--GHHHH
T ss_pred CchHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHhccccc----c----ccccchHH
Confidence 899999999999999999999999999999999999999999999999999999775541110 0 02334489
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcccchHhhhchhHHHHHHHHHHHHHHHhhccCCccchhHHhhhcCCCcchhhhH
Q 002530 386 EQRRLEALKLYYRVLEAMCTAEAQVLHAKNLTSLLTNERFHRCMLACSAELVLATHKTVTMLFPAVLERTGITAFDLSKV 465 (912)
Q Consensus 386 ~qR~~~a~~LYYrvLE~Il~~E~~rl~~~dls~LL~~d~FhrsLlACclEiVl~ty~~~~~~FPwILe~~~i~afdf~KV 465 (912)
++|+++|++|||++||+||.+|.+|++..|++.||+||+|||||+|||+|||+|+|+++++.|||||++|+|+|||||||
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 HHHHHhcCCCCCHHHHHHHHHHHHHHHhhhhcCCCCchhHHH
Q 002530 466 IESFIRHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSL 507 (912)
Q Consensus 466 IE~fIR~e~~LpRelvkHLn~IEE~ILEslAW~~~S~Lw~~L 507 (912)
||+|||||++|||+||||||+|||||||+|||++|||||++|
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 999999999999999999999999999999999999999875
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=5.9e-52 Score=403.34 Aligned_cols=131 Identities=49% Similarity=0.867 Sum_probs=111.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhHhhccCccCHHHHH
Q 002530 629 TGINIFFCKINKLAAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREII 708 (912)
Q Consensus 629 t~l~lFfrKvy~LAa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~tFk~Ii 708 (912)
++|++||||||+||++||++||++|+++++++++|||+|||+|+|+|+||+|||||||||||||++|||++.++||++||
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 002530 709 YNYRKQPQCKPQVFRSVFVDWASARQS---G-RSEQDHVDIITFYNKIFVPAVKP 759 (912)
Q Consensus 709 ~~Yr~QPqa~~~VyRsVli~~~~~~~~---g-~~~~e~gDII~FYN~VFvp~mK~ 759 (912)
++||+||||+++|||+|+|+..+.+.+ | .+++++||||+|||+||||+||+
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=99.97 E-value=3.3e-31 Score=259.22 Aligned_cols=115 Identities=39% Similarity=0.642 Sum_probs=82.6
Q ss_pred CCccHHHHhHhhHHHHHhhcCcccccCChhHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhhcCCCCCCCCcccccccCCC
Q 002530 1 MKLNIVDFFKELPQFLVKSGPILSNIYGADWENRLEAKELQANFVHLSILSKSYKRIYREFFLPSDANGDKQSAAASTSG 80 (912)
Q Consensus 1 ~~lsl~~Ff~km~~w~~~~~~~l~~~~~~~~~~rl~~~~Le~~F~v~~vl~kky~~iF~~iF~~p~~~~~~~~~~~~~~~ 80 (912)
|+||++|||+||+||+..++ +..+..+ +.++++||++|+|+++|||||+++|+++|..|++++++ .++.+|
T Consensus 22 ~~is~~~Ff~~l~~~~~~m~----~~~~~~~--~~~~~~L~~~f~v~~~l~kky~~~f~~lF~~~~~~~~~---~~~~~~ 92 (136)
T PF11934_consen 22 CKISLVEFFKKLKKWAVDMA----NILSKRF--RAQVKELERNFVVSTVLFKKYERIFQELFKPPPESPPK---SRSSPC 92 (136)
T ss_dssp HT--HHHHHHHHCCS------------HHHH--HH-HHHHHHHHHHHHHHHHHHHHHHCCCB--B---S------SS--B
T ss_pred cCCCHHHHHHHHHHHHHHhc----cCcHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccccc---ccCCCC
Confidence 58999999999999994443 3223433 44599999999999999999999999999999877654 233589
Q ss_pred ChhhHHhHHHHHHHHHHhhhccccchHHHHhhHHHHHHHHHHhc
Q 002530 81 YISDYHRFGWLLFLALRIHAFSRFKDLVTCTNGLVSILAILIIH 124 (912)
Q Consensus 81 ~~~d~~~f~W~LFl~~k~~~~~~f~DLV~s~~LLlc~ldll~~n 124 (912)
+..++|+|||+|||++|++.++.|+|||+||||||||||++|+|
T Consensus 93 ~~~~l~~f~W~LFL~~K~~~~~~~~DLV~s~~LLlc~ld~~~~n 136 (136)
T PF11934_consen 93 SYSDLFRFGWLLFLAAKGKFPSIFDDLVTSYHLLLCVLDLVYTN 136 (136)
T ss_dssp -CHHHHHHHHHHHHHHHHHH-SSS--HHHHHHHHHHHHHHHHH-
T ss_pred CHHHHHHHHHHHHHHHhCCCCcccccHHHHHHHHHHHHHHHHhC
Confidence 99999999999999999999999999999999999999999987
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=99.76 E-value=1.1e-19 Score=173.35 Aligned_cols=79 Identities=35% Similarity=0.603 Sum_probs=26.4
Q ss_pred CCCCCCCCCCCCC------CCCcccccCCcEEEecCCC-CCc-ccccCCCCceEEEEeccccccCCCCCccHHHHHHHhh
Q 002530 789 GSPKVSVFPALPD------MSPKKVSATHNVYVSPLRT-SKM-DALISHSSKSYYACVGESTHAYQSPSKDLTDINHRLN 860 (912)
Q Consensus 789 ~sP~lSp~p~l~~------~sP~rvs~~hnvyvSPlk~-~k~-~~~lsp~s~~~y~~~ges~~~~~SPskdL~~IN~~i~ 860 (912)
..|+|||||.+|. .||+||+++|||||||||+ .|. ...||||+++| ||||||+ ++|++|++||+||+
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 4578899998873 3999999999999999999 443 36899999999 5799987 48999999999999
Q ss_pred c-CCCcccceecC
Q 002530 861 S-NRRVRGTLNFD 872 (912)
Q Consensus 861 ~-~~~~~~~l~~~ 872 (912)
+ .|.+||.++.+
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 67888887644
No 6
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=97.13 E-value=0.0016 Score=72.81 Aligned_cols=73 Identities=16% Similarity=0.345 Sum_probs=65.1
Q ss_pred HHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhHhhccCccCHHHHHHHH
Q 002530 637 KINKLAAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYNY 711 (912)
Q Consensus 637 Kvy~LAa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~tFk~Ii~~Y 711 (912)
|.+.-|...|+++|++|+|+..+.+..-.+|..+..+ .++++|.++.++.+|+|+.||..+..+||+||...-
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 3456688899999999999999999999998887655 689999999999999999999999999999997654
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=97.07 E-value=0.0022 Score=56.04 Aligned_cols=63 Identities=21% Similarity=0.402 Sum_probs=53.1
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhHhhccCccCHHHHHHH
Q 002530 646 INAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYN 710 (912)
Q Consensus 646 L~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~tFk~Ii~~ 710 (912)
|..+|++|+|++++.+..-.+++.+.. ..+.++|..+.|.-.|||..|+.++..+|.+||-+.
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 578999999999988888888877644 469999999999999999999999999999999765
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=95.93 E-value=0.026 Score=48.63 Aligned_cols=63 Identities=14% Similarity=0.187 Sum_probs=54.3
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhHhhccCccCHHHHHHH
Q 002530 646 INAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYN 710 (912)
Q Consensus 646 L~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~tFk~Ii~~ 710 (912)
|..+|.++++++++....|.+++..+.. ..+++ ++...|..+|+|+-||+.....+.++|...
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=95.55 E-value=0.074 Score=46.16 Aligned_cols=69 Identities=13% Similarity=0.155 Sum_probs=59.9
Q ss_pred HHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhHhhccCccCHHHHHHHHh
Q 002530 642 AAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYNYR 712 (912)
Q Consensus 642 Aa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~tFk~Ii~~Yr 712 (912)
+...|..+|+.++++.++....|.+++..+... .+..++...|.++|+|.-||+.+...+.+++.+.-.
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
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=94.91 E-value=0.083 Score=58.11 Aligned_cols=72 Identities=24% Similarity=0.443 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhHhhccCccCHHHHHHH
Q 002530 637 KINKLAAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYN 710 (912)
Q Consensus 637 Kvy~LAa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~tFk~Ii~~ 710 (912)
++...|..-+..+|++|+|+..+..+.-.+|+.+ +...++++|..|-|.--|+|+-||=.++..|||||-..
T Consensus 102 ~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v--~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~ 173 (308)
T KOG1597|consen 102 RVLKAAFKEITAMCDRLSLPATIKDRANEIFKLV--EDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAV 173 (308)
T ss_pred HHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHH--HHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHH
Confidence 4677899999999999999987666555555443 35669999999999999999999999999999999544
No 11
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=93.83 E-value=0.15 Score=57.22 Aligned_cols=62 Identities=15% Similarity=0.156 Sum_probs=55.7
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhHhhccCccCHHHHHH
Q 002530 646 INAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIY 709 (912)
Q Consensus 646 L~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~tFk~Ii~ 709 (912)
|..+|++|+|+.++.+..|.+++.+.. ..|..+|+..-|.-.|||+.|++++..+|++||-.
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 12
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=88.64 E-value=2 Score=47.91 Aligned_cols=75 Identities=19% Similarity=0.330 Sum_probs=63.0
Q ss_pred HHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhHhhccCccCHHHHHHHHhc
Q 002530 637 KINKLAAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYNYRK 713 (912)
Q Consensus 637 Kvy~LAa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~tFk~Ii~~Yr~ 713 (912)
+-...|..-|..+|..|+|+..+++..-.++.-+ ..-.|.++|-+-.++--|+|+.|+..+...|+++|....+-
T Consensus 95 rnl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a--~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V 169 (285)
T COG1405 95 RNLITALEELERIASALGLPESVRETAARIYRKA--VDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGV 169 (285)
T ss_pred hHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHH--hhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCC
Confidence 4455688889999999999998777665555444 44569999999999999999999999999999999998863
No 13
>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=75.74 E-value=16 Score=34.45 Aligned_cols=72 Identities=19% Similarity=0.355 Sum_probs=56.7
Q ss_pred HHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhHhhccC-ccCHHHHHHH
Q 002530 637 KINKLAAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQL-NLTFREIIYN 710 (912)
Q Consensus 637 Kvy~LAa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~-~~tFk~Ii~~ 710 (912)
+.-..+...+..+|..++++.+.....+.+|+..+.... +...++..|.++|+|+-||+... ..+.++++..
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 334556677888999999999999999999998887663 88899999999999999999876 4666666554
No 14
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=56.58 E-value=44 Score=37.82 Aligned_cols=67 Identities=15% Similarity=0.355 Sum_probs=47.4
Q ss_pred HHHHHHHHHHhC--CChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhHhhccCccCHHHHHHHH
Q 002530 643 AVRINAMVERLQ--LSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYNY 711 (912)
Q Consensus 643 a~RL~~LC~~L~--l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~tFk~Ii~~Y 711 (912)
...|+++|.+|+ +++++..-.=..|.--.. ... +++-|.-.|+++|+|.-||+....++-.++...-
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 988654333333422222 223 4467999999999999999998777777776543
No 15
>KOG1992 consensus Nuclear export receptor CSE1/CAS (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=44.95 E-value=1e+02 Score=39.12 Aligned_cols=95 Identities=19% Similarity=0.324 Sum_probs=57.7
Q ss_pred cHHHHhH-hhHHHHHhhcCcccccCC---hhHHhHHHHHHHHhhHHHHHHHH-HHHHHHHHhhcCCCCCCCCcccccccC
Q 002530 4 NIVDFFK-ELPQFLVKSGPILSNIYG---ADWENRLEAKELQANFVHLSILS-KSYKRIYREFFLPSDANGDKQSAAAST 78 (912)
Q Consensus 4 sl~~Ff~-km~~w~~~~~~~l~~~~~---~~~~~rl~~~~Le~~F~v~~vl~-kky~~iF~~iF~~p~~~~~~~~~~~~~ 78 (912)
-|-|||. .|+.|+-.=-++|+--.| .|=+.--.+.+|.+..+=...|| +||++.|+.+.
T Consensus 223 DiPEFFEdnm~~wM~~F~k~l~~~~p~le~~~ee~~~l~~lka~ICEi~~LY~~kYeEef~~fl---------------- 286 (960)
T KOG1992|consen 223 DIPEFFEDNMKTWMGAFHKLLTYDNPLLESDEEEATVLDKLKAQICEIFNLYATKYEEEFQPFL---------------- 286 (960)
T ss_pred cchHHHHhhHHHHHHHHHHHHhccCcccccCcccccHHHHHHHHHHHHHHHHHHhhHHHHHhhH----------------
Confidence 3568887 899996543333321011 12233334677777777667777 89999988765
Q ss_pred CCChhhHHhHHHHHHHHHHhhhccccchHH-HHhhHHHHHHHH
Q 002530 79 SGYISDYHRFGWLLFLALRIHAFSRFKDLV-TCTNGLVSILAI 120 (912)
Q Consensus 79 ~~~~~d~~~f~W~LFl~~k~~~~~~f~DLV-~s~~LLlc~ldl 120 (912)
.|.....|.|-+..-.+ ..+|-|| +.+..|..|...
T Consensus 287 ----~~fv~~~W~LL~~~s~~--~kyD~Lvs~Al~FLt~V~~r 323 (960)
T KOG1992|consen 287 ----PDFVTATWNLLVSTSPD--TKYDYLVSKALQFLTSVSRR 323 (960)
T ss_pred ----HHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHhh
Confidence 33666789987732211 2467788 667777666554
No 16
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=36.15 E-value=97 Score=37.43 Aligned_cols=55 Identities=22% Similarity=0.440 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhHhhcc
Q 002530 642 AAVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQ 699 (912)
Q Consensus 642 Aa~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k 699 (912)
|-..|.++|.+|+|.+ ..+-+..-|+-++.++ +-++|----+|--|+|++|+..+
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 17
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=26.93 E-value=1.8e+02 Score=32.93 Aligned_cols=63 Identities=16% Similarity=0.162 Sum_probs=50.7
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhHhhccCccCHHHHHHH
Q 002530 646 INAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQLNLTFREIIYN 710 (912)
Q Consensus 646 L~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k~~~tFk~Ii~~ 710 (912)
+...|..|+|+.+..+-+=.+.|-+ +.-++..+|.-.-|.--+||.++.+.....+-+||.+.
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 55678889999999999999999999988999998654
No 18
>PRK14102 nifW nitrogenase stabilizing/protective protein; Provisional
Probab=23.42 E-value=93 Score=30.02 Aligned_cols=35 Identities=20% Similarity=0.338 Sum_probs=26.5
Q ss_pred ccCCCCCchHHHHHHHHHHHHHHhccCCCCcccccc
Q 002530 207 ENLMDDSSLSSSLNILEKDYDNATRNKGELDERVFI 242 (912)
Q Consensus 207 ~gLl~~~~f~~nl~~Lnk~YE~~vl~~GdlDERiFL 242 (912)
.|+-+.+.+..-=.+|.++|+..+.+ .=++||+|=
T Consensus 53 ~~~~e~~~~~~yr~~L~~AY~dF~~S-tp~~ekvFK 87 (105)
T PRK14102 53 PDLSEEEKLEKYQLALEEAYQVFLTS-TPLEQKLFK 87 (105)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHccC-ChhhhhhHH
Confidence 34445566777778899999996655 779999994
No 19
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=22.84 E-value=1e+02 Score=39.18 Aligned_cols=54 Identities=11% Similarity=0.196 Sum_probs=43.6
Q ss_pred HHHHHHHHHHhCCChHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHhHhhcc
Q 002530 643 AVRINAMVERLQLSQQIRESVYCLFQQILNQRTSLFFNRHIDQIILCCFYGVAKISQ 699 (912)
Q Consensus 643 a~RL~~LC~~L~l~~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~i~Kv~k 699 (912)
..++..+|..|.++.......|..|.++-...+-=+- -+..+.||+|..||.+.
T Consensus 35 ~q~~~~~c~~lnld~~~~~ea~d~yta~~q~~slegs---~~hW~~cAlY~~~r~S~ 88 (920)
T KOG1010|consen 35 EQDSDELCRPLNLDEQTETEAWDTYTAVSQRLSLEGS---ESHWLACALYTACRRSS 88 (920)
T ss_pred hhhhhhhhhhhcccchhhhhhHHHHHHHHhHhCCCcc---HHHHHHHHHHHHHHhcc
Confidence 5678899999999999999999999887554432233 56789999999999984
No 20
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=21.15 E-value=1.1e+02 Score=27.23 Aligned_cols=30 Identities=17% Similarity=0.174 Sum_probs=25.4
Q ss_pred HHHHHHHHHhHhhc-cCccCHHHHHHHHhcC
Q 002530 685 QIILCCFYGVAKIS-QLNLTFREIIYNYRKQ 714 (912)
Q Consensus 685 QiiLCaiY~i~Kv~-k~~~tFk~Ii~~Yr~Q 714 (912)
+++|||+=...+-+ ..+.++.+|.+.|+..
T Consensus 5 Kl~L~Al~~~~~~~~~~~~~~~~vy~~Y~~~ 35 (87)
T cd08768 5 KLVLLALLLLFKRGGEEEATTGEVYEVYEEL 35 (87)
T ss_pred HHHHHHHHHHHhcCCCCCccHHHHHHHHHHH
Confidence 78999998888766 4579999999999875
Done!