Query 046343
Match_columns 633
No_of_seqs 161 out of 187
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 11:08:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046343.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046343hhsearch_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 4E-122 8E-127 1026.1 34.2 494 9-623 353-917 (920)
2 PF01858 RB_A: Retinoblastoma- 100.0 1.3E-56 2.8E-61 441.5 14.7 156 46-201 1-194 (194)
3 PF01857 RB_B: Retinoblastoma- 100.0 2.8E-53 6.1E-58 396.2 9.0 117 372-489 1-135 (135)
4 PF08934 Rb_C: Rb C-terminal d 99.8 1.6E-19 3.5E-24 167.4 2.6 78 512-593 9-95 (155)
5 PRK00423 tfb transcription ini 97.5 0.00029 6.3E-09 74.9 8.4 73 381-456 121-193 (310)
6 PF00382 TFIIB: Transcription 97.3 0.00081 1.8E-08 56.1 7.1 64 389-455 1-64 (71)
7 cd00043 CYCLIN Cyclin box fold 96.6 0.0061 1.3E-07 50.0 6.6 70 385-457 5-74 (88)
8 smart00385 CYCLIN domain prese 96.6 0.0055 1.2E-07 49.9 6.0 65 389-456 3-67 (83)
9 KOG1597 Transcription initiati 95.9 0.019 4.1E-07 60.7 7.0 74 380-456 102-175 (308)
10 PRK00423 tfb transcription ini 95.0 0.049 1.1E-06 58.1 6.5 64 388-454 222-285 (310)
11 COG1405 SUA7 Transcription ini 90.4 1 2.2E-05 48.1 8.1 75 381-458 96-170 (285)
12 PF00134 Cyclin_N: Cyclin, N-t 82.6 7 0.00015 35.0 8.1 72 381-455 30-102 (127)
13 TIGR00569 ccl1 cyclin ccl1. Un 75.4 10 0.00022 40.9 7.9 67 387-456 61-129 (305)
14 KOG1598 Transcription initiati 47.8 45 0.00097 38.6 6.7 66 373-443 59-124 (521)
15 KOG0834 CDK9 kinase-activating 34.9 63 0.0014 35.3 5.2 65 385-455 42-109 (323)
16 cd08768 Cdc6_C Winged-helix do 33.6 46 0.001 28.2 3.2 30 429-458 5-35 (87)
17 PRK09239 chorismate mutase; Pr 33.3 34 0.00074 31.3 2.5 37 385-421 60-96 (104)
18 PF02671 PAH: Paired amphipath 28.8 8.4 0.00018 29.7 -1.9 35 447-481 6-44 (47)
19 KOG1010 Rb (Retinoblastoma tum 27.9 56 0.0012 39.9 3.6 54 386-443 35-88 (920)
20 PRK10885 cca multifunctional t 24.6 96 0.0021 34.8 4.6 34 384-417 276-309 (409)
21 KOG1597 Transcription initiati 24.1 1.8E+02 0.0038 31.7 6.1 68 385-455 203-270 (308)
22 PHA03002 Hypothetical protein; 23.1 55 0.0012 38.9 2.4 67 429-497 133-244 (679)
23 PF13150 DUF3989: Protein of u 22.5 94 0.002 27.6 3.2 32 377-410 3-35 (85)
24 cd07923 Gallate_dioxygenase_C 22.1 1.7E+02 0.0036 26.7 4.7 71 386-457 5-83 (94)
25 PF03359 GKAP: Guanylate-kinas 21.4 1.6E+02 0.0036 32.5 5.5 81 375-485 171-258 (357)
26 PF09263 PEX-2N: Peroxisome bi 21.4 14 0.00031 32.9 -2.1 34 170-204 18-51 (87)
27 TIGR01795 CM_mono_cladeE monof 21.1 80 0.0017 28.3 2.5 34 387-420 55-88 (94)
No 1
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=3.8e-122 Score=1026.12 Aligned_cols=494 Identities=35% Similarity=0.479 Sum_probs=403.1
Q ss_pred cccccccccccccccCCcccccCCCCCCCCCC---------CCCCCChHHHHHHHHHHHHHHhCCCCCCCCcccc-----
Q 046343 9 AVNITGAKRKFDSLASPVKTITSPLSPHHSST---------SKMVVTPVSTAMTTAKWLRTIICPLPSKPSADLQ----- 74 (633)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~TPVs~Am~s~~~L~~~la~l~~~PS~~l~----- 74 (633)
.++.++.++|.+...+++++--.+.| +.+|. .+...|||++||++++||++++.|+.++||+++.
T Consensus 353 ~~~~s~~~~r~~~~~~~~~~~~~~~s-~~~p~~~~~~y~~e~~~~~tPvsta~~sik~l~t~i~g~~~~psdkLe~~~~t 431 (920)
T KOG1010|consen 353 KSSDSFESERLAVKSSLAQEFLKTQS-KKSPPHTGVRYNLELGNYPTPVSTATNSIKQLMTILNGLKKEPSDKLEQYLNT 431 (920)
T ss_pred ccCCccchhccccccccchhhccccc-ccCCCCcccccccccccCCCcchhHHHHHHHHHHHHhccccCCcHHHHHHHhh
Confidence 55778889999999999998888777 55551 3567899999999999999999999999999943
Q ss_pred C-CCCCCh---------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCchHHH-----HHH
Q 046343 75 G-ANLMDN---------------------------IWAEQRRLEALKLNYKVLETMCTAEAQVLHAKNLTSL-----FHR 121 (633)
Q Consensus 75 ~-~~~~d~---------------------------~~a~qR~~~a~~LYYkvLE~Il~~E~krl~~~~ls~L-----FHr 121 (633)
| .+.+++ .+|.|||++|++|||||||+||++|.+|++..||+.| ||+
T Consensus 432 c~r~p~e~Il~r~~~i~e~~~q~f~~~~~~g~~~~e~~~~r~k~a~~LYykvLE~il~aE~~rl~~~dl~~LL~q~~Fh~ 511 (920)
T KOG1010|consen 432 CSRDPTESILKRLKEIFEIFEQKFSAAEGSGNSCIEIASQRFKLAERLYYKVLEKILKAELKRLPDMDLSKLLEQEIFHR 511 (920)
T ss_pred cccChHHHHHHHHHHHHHHHHHHhhhhccCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHH
Confidence 1 112211 1578999999999999999999999999999999998 999
Q ss_pred HHHHHHHHHHHHHhCCCccchHHHHHhhCCCcchhhchhhhhhhcCCCCCHHHHHHHHHHHHHHHHhhhcCCCCchhHhH
Q 046343 122 CMLACSAELVLATHKTVTMLFLAVLERIGITAFNLSKVIQSFIRHEESLPRELRRHLNSLEERLLESMVWEKGSSMYNSL 201 (633)
Q Consensus 122 sLlACclEiVl~sy~~~~~~FPwILe~~~l~aFdf~KVIE~fIRae~~LpRelvKHLn~IEEqILEslAW~~~SpLw~~L 201 (633)
||||||+|+||++|++ ++.||||||+|||+|||||||||+|||||++|+||||||||+|||+|||||||++|||||++|
T Consensus 512 sLlACclElVL~ty~~-~l~FPwvle~~~l~aFdF~KVIE~~IRhE~~L~RemiKHLn~iEE~iLEslaW~~dS~Lw~~i 590 (920)
T KOG1010|consen 512 SLLACCLELVLATYKT-DLSFPWVLECFGLKAFDFYKVIESFIRHEGGLSREMIKHLNSIEERILESLAWKSDSPLWEMI 590 (920)
T ss_pred HHHHHHHHHHHHHhCC-CCCCchhhhhcCCcHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccCCcHHHHH
Confidence 9999999999999997 599999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhCCcchhhhccCcccccccccccchhhhccccCCCCCCCCCccccCCCCCCCCCCccccchhhcCCCCchhhhhhhcc
Q 046343 202 TVARPALSAEINLGFTDILFQDSQDSWEEFTSILTVPPTDSPTRQHYENLPWWKEPFTEVDSIFLLIPMPSLDAIAMHIN 281 (633)
Q Consensus 202 ~~a~p~~~~ev~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~~~~~~~~~k~~~~~~~~~~l~~~~~s~~~ia~~~~ 281 (633)
+++++.++-|.+ ..|.+. . ++ +.|+. +
T Consensus 591 ~~~~~~~~~~~~------------~~~~~~------------------------------------l--e~-~~~~~--~ 617 (920)
T KOG1010|consen 591 KQAKPRLPTEEG------------VDPPDN------------------------------------L--ES-ACIAG--L 617 (920)
T ss_pred Hhcccccccccc------------cccccc------------------------------------c--cc-ccccc--c
Confidence 999876533322 111100 0 00 00100 0
Q ss_pred ccCCCCCCCcccccccCCCcccccccccccccCCcccccccccchhccccccccccccccccCCCCCCCCCCCCCCCCCC
Q 046343 282 FSSGGLSPVHSLHKHETSPVCSIFNFQFYANCYGELVTDDYRSVLVERNNFTSLVKDCLLGLNNLKSKPLPPPLYPTRSN 361 (633)
Q Consensus 282 ~s~~~l~p~ps~~~~~ssp~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~sP~k~~~~~~~~~~~k~~~~~l~p~~~~ 361 (633)
++ .+.-+ ...++++|+ . .|++.+ .|+|+++... .++..+
T Consensus 618 ~p-~~~~~---~~~~~~sp~---------~--~Pk~~~------------~t~pv~~~an--------------~~qe~~ 656 (920)
T KOG1010|consen 618 LP-LRVNH---VRARYSSPV---------L--EPKDKG------------TTIPVNGTAN--------------AGQEVT 656 (920)
T ss_pred CC-ccccc---cccccCCCC---------C--Cccccc------------cccccccccc--------------ccccCC
Confidence 00 00001 122566665 1 255432 3788876321 123344
Q ss_pred CCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHhCCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhh
Q 046343 362 PGGGGEPCAETGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKI 441 (633)
Q Consensus 362 p~~~~~~~~~t~L~lFfRKVy~LAa~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV 441 (633)
+.+.++++++++|+||||||||||++||+|||+||+++++++++||||| ||+|+|+|+||||||||||||||||+||||
T Consensus 657 ~~~~~~~~~stsLsIF~rKvY~LAavRL~~Lc~rL~l~~e~r~~IWtlF-ehsl~~et~Lm~dRHLDQillCaiy~i~KV 735 (920)
T KOG1010|consen 657 AFGVNKPRKSTSLSIFLRKVYHLAAVRLNDLCERLSLSDELREQIWTLF-EHSLTNETELMRDRHLDQILLCAIYGIAKV 735 (920)
T ss_pred cccCCCcccccchHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHH-HHHHhccHHHHHhhhHHHHHHHHHHhheeh
Confidence 5566788889999999999999999999999999999999999999999 999999999999999999999999999999
Q ss_pred ccCccCHHHHHHHHhcCCCCCCcceeeec----------------cccceeehhhhcchhhhHHHHHHhcCCCcccccCC
Q 046343 442 SQLNLTFKEIIYNYGKQPQCKPQVFRSVF----------------DHVDIITFYNKIFAPTVKPLLVELGPVGTAMKTNR 505 (633)
Q Consensus 442 ~k~~~tFk~Ii~~YR~QPQa~s~VyRsVl----------------ergDII~FYN~VFvp~mK~F~l~~~~~~~~~~~~~ 505 (633)
+++++||++||++||+||||.++|||+|+ +++|||+|||.|||+.||+|+++|....+
T Consensus 736 ~~~~ltF~eIm~~YR~QPqa~~~vyRsV~i~~~~~~~~~~~~P~~~~~diI~fyN~iyV~~~k~~~i~~~~~~~------ 809 (920)
T KOG1010|consen 736 KKEDLTFSEIMRAYRRQPQAVSLVYRSVLIKDKTNRDQGPSGPKEERSDIITFYNNIYVPPMKTFAIEYGLATT------ 809 (920)
T ss_pred hcccchHHHHHHHHhcCchhhhhhhhheeecccccccccCCCCcccccceeccccceehhhhhhhhhhhccCCC------
Confidence 99999999999999999999999999999 37899999999999999999999998732
Q ss_pred CcccCCCCCCCCCCCCC--CCCCCccccCCcEEEecCCCCcccccCCCCCceEEEEeCCcccCCCCccchHHHHHHhhcC
Q 046343 506 DSEVNHNNDASVFPALP--DMSPKKVSATHSVYVSPLRTSEMDALISHSSKSYYACVGESTHAYSPFKDLTDINHRLNSN 583 (633)
Q Consensus 506 ~~~~~~~~~lSP~P~~~--~~SP~rvs~~hnVyVSPlk~~~~~~~lsP~s~~ly~~~gest~a~SPsKdL~~IN~~i~~~ 583 (633)
.+.++++|.|++. ..+|+++|++||||||||+++ ..+.+++.+.|||++ ||+|+|++||.|++++
T Consensus 810 ----~~~~~lsp~~~i~~~~~e~~~~S~~h~v~is~~~~~---~~l~s~s~~~y~~~~------spsk~L~ain~~i~~s 876 (920)
T KOG1010|consen 810 ----MDAKPLSPSPSIKVSIGEPRRLSQRHNVYISPHKNS---DRLQSRSTAEYYFCN------SPSKDLPAINNLIRGS 876 (920)
T ss_pred ----CCCCCCCCCccccccCCCCcchhhhcceeecCCCch---hhhcCcchhhccccC------CCCcchHHHHHHhhcC
Confidence 1257899999876 468999999999999999987 445556655566666 8999999999999985
Q ss_pred cCcccceeccCCCCcccccccchhhccccc------cCCCCCCCCC
Q 046343 584 RRVRGALNFDDVDVDVGLVSDSMVVNSLYL------QNGSAAASTC 623 (633)
Q Consensus 584 ~~~kr~l~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~ 623 (633)
....+..++.+ | .+++++++|.+-. |+++.+.++.
T Consensus 877 s~~~~~~~~~~---e--s~~Es~~ani~~~~~~~~~~r~~D~~~~~ 917 (920)
T KOG1010|consen 877 SERTKKKHIPG---E--SKSESKRANILQERTRMQLQRLQDAMSTR 917 (920)
T ss_pred cccccccCCCc---c--chhhhhHhhhhhhhhHHHHhhhhhhhhcc
Confidence 44344445554 3 7899999998865 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=1.3e-56 Score=441.52 Aligned_cols=156 Identities=46% Similarity=0.743 Sum_probs=136.1
Q ss_pred ChHHHHHHHHHHHHHHhCCCCCCCCcccc-----CC----------------------------CCCChHHHHHHHHHHH
Q 046343 46 TPVSTAMTTAKWLRTIICPLPSKPSADLQ-----GA----------------------------NLMDNIWAEQRRLEAL 92 (633)
Q Consensus 46 TPVs~Am~s~~~L~~~la~l~~~PS~~l~-----~~----------------------------~~~d~~~a~qR~~~a~ 92 (633)
||||+||++++||+++++|++++||+++. |. ..++..++++|+++|+
T Consensus 1 TPVs~A~~~~~~L~~~l~~~~~~PS~~L~~~~~~c~~~p~~~i~~rv~~l~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~ 80 (194)
T PF01858_consen 1 TPVSSAMQSVSWLQALLSGLSDEPSEELLRIFKSCSRDPTESILKRVKQLLEKFCQKYTEAEGEQSSNSDFAEQRFNLAE 80 (194)
T ss_dssp -HHHHHHHHHHHHHHHHHHS-SS--HHHHHHHHTSSS--HHHHHHHHHHHHHHHHHHHHHHHSGG--GHHHHHHHHHHHH
T ss_pred CchHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHhccccccccccchHHHHHHHHHH
Confidence 89999999999999999999999999932 11 0234458899999999
Q ss_pred HHHHHHHHHHHHHHHHhhccCchHHH-----HHHHHHHHHHHHHHHHhCCCccchHHHHHhhCCCcchhhchhhhhhhcC
Q 046343 93 KLNYKVLETMCTAEAQVLHAKNLTSL-----FHRCMLACSAELVLATHKTVTMLFLAVLERIGITAFNLSKVIQSFIRHE 167 (633)
Q Consensus 93 ~LYYkvLE~Il~~E~krl~~~~ls~L-----FHrsLlACclEiVl~sy~~~~~~FPwILe~~~l~aFdf~KVIE~fIRae 167 (633)
+|||++||+||.+|.+|++..|++.| |||||||||+|||+|+|+++++.|||||++|+|+|||||||||+|||||
T Consensus 81 ~LYY~~LE~Il~~E~~r~~~~~ls~LL~~~~FhrsL~ACclEiVl~sy~~~~~~FPwiL~~~~i~~f~f~KvIE~~Vr~~ 160 (194)
T PF01858_consen 81 KLYYKVLEKILKAEEKRLPTNDLSSLLSQEIFHRSLLACCLEIVLFSYKSVSLSFPWILEVFDIHPFDFYKVIESFVRHE 160 (194)
T ss_dssp HHHHHHHHHHHHHHHHHHSCSHHHHHHT-HHHHHHHHHHHHHHHHHHTCTSSSSTTHHHHHTT--HHHHHTTHHHHHHH-
T ss_pred HHHHHHHHHHHHHHhccccHhHHHHHhhhhHHHHHHHHHHHHHHHHHcCCCCCcchHHHHhcCCChhhHhhHHHHHHHcc
Confidence 99999999999999999999999988 9999999999999999998789999999999999999999999999999
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhhcCCCCchhHhH
Q 046343 168 ESLPRELRRHLNSLEERLLESMVWEKGSSMYNSL 201 (633)
Q Consensus 168 ~~LpRelvKHLn~IEEqILEslAW~~~SpLw~~L 201 (633)
++||||||||||+|||||||+|||++|||||++|
T Consensus 161 ~~Lpr~lvkHL~~IEE~iLeslaW~~~S~Lw~~l 194 (194)
T PF01858_consen 161 DGLPRELVKHLNSIEEQILESLAWKSDSPLWEML 194 (194)
T ss_dssp TT--HHHHHHHHHHHHHHHHTGGGSTT-THHHHH
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHhcCCChhhhhC
Confidence 9999999999999999999999999999999975
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-53 Score=396.20 Aligned_cols=117 Identities=47% Similarity=0.827 Sum_probs=107.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhCCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhccCccCHHHH
Q 046343 372 TGINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEI 451 (633)
Q Consensus 372 t~L~lFfRKVy~LAa~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k~~~tFk~I 451 (633)
++|++||||||+||++||++||++|+++++++++|||+| ||+|+|+|+||+|||||||||||||++|||++.++||+||
T Consensus 1 ~sl~iFfrKvy~la~~Rl~~LC~~L~l~~~~~~~iwt~f-e~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~I 79 (135)
T PF01857_consen 1 GSLNIFFRKVYKLAAVRLQDLCERLDLSSDLREKIWTCF-EHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDI 79 (135)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTTSTTHHHHHHHHH-HHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHH
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHH-HHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHH
Confidence 479999999999999999999999999999999999999 9999999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCCCcceeeec------------------cccceeehhhhcchhhhHH
Q 046343 452 IYNYGKQPQCKPQVFRSVF------------------DHVDIITFYNKIFAPTVKP 489 (633)
Q Consensus 452 i~~YR~QPQa~s~VyRsVl------------------ergDII~FYN~VFvp~mK~ 489 (633)
|++||+|||++++|||+|+ ++||||+|||+||||+||+
T Consensus 80 i~~Yr~qpq~~~~Vyr~V~i~~~~~~~~~~~~~~~~~~~gDII~FYN~vFvp~mK~ 135 (135)
T PF01857_consen 80 IKAYRKQPQASSHVYRSVLIRSRSDNRNNDSGERSEEERGDIIKFYNKVFVPRMKS 135 (135)
T ss_dssp HHHHTTSTT--THHHHSEEESS--------------SEEE-HHHHHHHTHHHHHHH
T ss_pred HHHHHhcccccccceEEEEECCcccccccccccccCCCCCCeeeeehHhHHhhcCC
Confidence 9999999999999999999 5799999999999999996
No 4
>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=1.6e-19 Score=167.43 Aligned_cols=78 Identities=31% Similarity=0.552 Sum_probs=25.4
Q ss_pred CCCCCCCCCCCC------CCCCccccCCcEEEecCCC-Cccc-ccCCCCCceEEEEeCCcccCCCCccchHHHHHHhhc-
Q 046343 512 NNDASVFPALPD------MSPKKVSATHSVYVSPLRT-SEMD-ALISHSSKSYYACVGESTHAYSPFKDLTDINHRLNS- 582 (633)
Q Consensus 512 ~~~lSP~P~~~~------~SP~rvs~~hnVyVSPlk~-~~~~-~~lsP~s~~ly~~~gest~a~SPsKdL~~IN~~i~~- 582 (633)
.|+|||||++|. .||+||++.|||||||||+ .++. ..||||+++| ||+||| ++++++|++||+||++
T Consensus 9 ~p~LSPiP~iprSPy~~~~SP~RVp~s~NVYISPlK~~~k~s~~~mTPRSr~L-y~iGeS---~~~s~~lq~IN~mv~~~ 84 (155)
T PF08934_consen 9 PPTLSPIPHIPRSPYKFPNSPRRVPQSHNVYISPLKNPYKMSPSKMTPRSRML-YSIGES---FGSSEKLQKINQMVNSG 84 (155)
T ss_dssp -TT-----------------------------------------------EEE-EESS-T---TTHHHHHHHHHHHHH--
T ss_pred CCCCCCCCCCCCCcccCCCCCccccCccceEeccccccccCCCcccCccchhh-eeecCC---cchHHHHHHHHHHHccc
Confidence 478999999885 4999999999999999998 4433 5899999999 578997 3789999999999998
Q ss_pred CcCcccceecc
Q 046343 583 NRRVRGALNFD 593 (633)
Q Consensus 583 ~~~~kr~l~~~ 593 (633)
.+.+||.|+.+
T Consensus 85 ~Rs~KR~~~~~ 95 (155)
T PF08934_consen 85 ERSKKRSLDSS 95 (155)
T ss_dssp TT-----STT-
T ss_pred hhhhhhhccCC
Confidence 56778876543
No 5
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=97.50 E-value=0.00029 Score=74.89 Aligned_cols=73 Identities=15% Similarity=0.292 Sum_probs=64.1
Q ss_pred HHHHHHHHHHHHHHHhCCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhccCccCHHHHHHHHh
Q 046343 381 INKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYG 456 (633)
Q Consensus 381 Vy~LAa~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k~~~tFk~Ii~~YR 456 (633)
.+.-|...|+++|++|+|++.+.+..-.+| +....+ .++++|.++.++.+|+|+.||..+..+||+||...-+
T Consensus 121 ~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iy-k~~~~~--~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~ 193 (310)
T PRK00423 121 NLAFALSELDRIASQLGLPRSVREEAAVIY-RKAVEK--GLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSR 193 (310)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHH-HHHHhc--CcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhC
Confidence 345688899999999999999999998888 665543 8899999999999999999999999999999977654
No 6
>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=97.31 E-value=0.00081 Score=56.14 Aligned_cols=64 Identities=22% Similarity=0.341 Sum_probs=53.1
Q ss_pred HHHHHHHhCCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhccCccCHHHHHHHH
Q 046343 389 INAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNY 455 (633)
Q Consensus 389 L~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k~~~tFk~Ii~~Y 455 (633)
|..+|++|+|++++++..-.++ +... ...+.++|..+-|.-.|||..|+.++..+|++||-+.-
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~-~~~~--~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~ 64 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIY-KKAQ--ERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAA 64 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHH-HHHH--HTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHC
T ss_pred ChHHHhHcCCCHHHHHHHHHHH-HHHH--HcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHh
Confidence 5689999999999988888888 5543 45799999999999999999999999999999997653
No 7
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=96.64 E-value=0.0061 Score=50.05 Aligned_cols=70 Identities=16% Similarity=0.130 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHhCCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhccCccCHHHHHHHHhc
Q 046343 385 AAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYGK 457 (633)
Q Consensus 385 Aa~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k~~~tFk~Ii~~YR~ 457 (633)
+...|+.+|+.++++++.....|.++ +..+.. ..+..++...|.++|+|.-||+.+...+.+++.+.-..
T Consensus 5 ~~~~l~~~~~~~~~~~~~~~~A~~~~-~~~~~~--~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~ 74 (88)
T cd00043 5 PLDFLRRVAKALGLSPETLTLAVNLL-DRFLLD--YSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGY 74 (88)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHH-HHHHHh--cccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCC
Confidence 45668899999999999999999999 877764 34569999999999999999999989999999776654
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=96.58 E-value=0.0055 Score=49.88 Aligned_cols=65 Identities=18% Similarity=0.194 Sum_probs=55.7
Q ss_pred HHHHHHHhCCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhccCccCHHHHHHHHh
Q 046343 389 INAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYG 456 (633)
Q Consensus 389 L~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k~~~tFk~Ii~~YR 456 (633)
|+.+|.++++++++....|.++ +..+.. ..+++ ++...|..+|+|+-||+.....+.++|....+
T Consensus 3 l~~~~~~~~~~~~~~~~a~~~~-~~~l~~-~~~~~-~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~ 67 (83)
T smart00385 3 LRRVCKALNLDPETLNLAVNLL-DRFLSD-YKFLK-YSPSLIAAAALYLAAKTEEIPPWTKELVHYTG 67 (83)
T ss_pred HHHHHHHcCCCHHHHHHHHHHH-HHHHHH-hhccc-CCHHHHHHHHHHHHHHHhcCCCCchhHhHhhC
Confidence 6789999999999999999999 888774 44555 99999999999999999998888888865443
No 9
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=95.90 E-value=0.019 Score=60.75 Aligned_cols=74 Identities=26% Similarity=0.375 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHHHHHHhCCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhccCccCHHHHHHHHh
Q 046343 380 KINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYG 456 (633)
Q Consensus 380 KVy~LAa~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k~~~tFk~Ii~~YR 456 (633)
+++..|..-+..+|++|+|+.-+..+.-.+| + +++...++++|..|-|+--|+|+-||=.++..|||||-..-+
T Consensus 102 ~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~if-k--~v~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~an 175 (308)
T KOG1597|consen 102 RVLKAAFKEITAMCDRLSLPATIKDRANEIF-K--LVEDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVAN 175 (308)
T ss_pred HHHHHHHHHHHHHHHHhCCchHHHHHHHHHH-H--HHHHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHHc
Confidence 3567788899999999999876655555555 2 234678999999999999999999999999999999965544
No 10
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=94.96 E-value=0.049 Score=58.10 Aligned_cols=64 Identities=11% Similarity=0.078 Sum_probs=56.9
Q ss_pred HHHHHHHHhCCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhccCccCHHHHHHH
Q 046343 388 RINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYN 454 (633)
Q Consensus 388 RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k~~~tFk~Ii~~ 454 (633)
=|..+|++|+|+.++.+..|.++ +... +..|..+|+..-|.-.|||..|++.+..+|++||-..
T Consensus 222 ~i~r~~~~L~L~~~v~~~A~~i~-~~a~--~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v 285 (310)
T PRK00423 222 YVPRFASELGLSGEVQKKAIEIL-QKAK--EKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEV 285 (310)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHH-HHHH--hcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence 35689999999999999999999 7665 3579999999999999999999999999999998544
No 11
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=90.37 E-value=1 Score=48.06 Aligned_cols=75 Identities=19% Similarity=0.280 Sum_probs=62.9
Q ss_pred HHHHHHHHHHHHHHHhCCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhccCccCHHHHHHHHhcC
Q 046343 381 INKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYGKQ 458 (633)
Q Consensus 381 Vy~LAa~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k~~~tFk~Ii~~YR~Q 458 (633)
-...|..-|..+|+.|+|+..+++..-.++ -......|.++|-+-.++--|+|+.|+..+..+||++|....+..
T Consensus 96 nl~~a~~~l~~~~~~l~LP~~v~e~A~~iy---r~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V~ 170 (285)
T COG1405 96 NLITALEELERIASALGLPESVRETAARIY---RKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGVS 170 (285)
T ss_pred HHHHHHHHHHHHHHHhCCCchHHHHHHHHH---HHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCCC
Confidence 344577789999999999988877655555 233567899999999999999999999999999999999998743
No 12
>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=82.55 E-value=7 Score=35.01 Aligned_cols=72 Identities=19% Similarity=0.294 Sum_probs=55.5
Q ss_pred HHHHHHHHHHHHHHHhCCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhccC-ccCHHHHHHHH
Q 046343 381 INKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQL-NLTFKEIIYNY 455 (633)
Q Consensus 381 Vy~LAa~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k~-~~tFk~Ii~~Y 455 (633)
.-......+..+|..++++++.....+.+| +..+... .+...++..|.++|+|+-||+... ..+.++++..-
T Consensus 30 ~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~-dr~~~~~--~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~ 102 (127)
T PF00134_consen 30 MRQIIIDWIIELCQRLKLSPETLHLAIYLF-DRFLSKR--PVNRSKLQLIALACLFLASKMEEDNPPSISDLIRIS 102 (127)
T ss_dssp HHHHHHHHHHHHHHHTT-BHHHHHHHHHHH-HHHHTTS---TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHT
T ss_pred HHHHHHHHHHHHHHhcccchhHHHHHHHHH-HHHHhhc--ccccchhhhhhhhHHHHhhhhhccccchHHHHHHHH
Confidence 334566678889999999999999999999 7766654 388899999999999999999876 56667666543
No 13
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=75.44 E-value=10 Score=40.88 Aligned_cols=67 Identities=16% Similarity=0.330 Sum_probs=49.1
Q ss_pred HHHHHHHHHhC--CChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhccCccCHHHHHHHHh
Q 046343 387 VRINAMVERLQ--LSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNYG 456 (633)
Q Consensus 387 ~RL~dLC~rL~--ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k~~~tFk~Ii~~YR 456 (633)
..|+++|.+|+ +++++..-.=..| +.... ... +++-|.-.|+++|+|.-|||....++-.++...-.
T Consensus 61 ~~i~~~~~~lkp~Lpq~viaTAivyf-~RFy~-~~S-v~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~ 129 (305)
T TIGR00569 61 KRLLDFCSAFKPTMPTSVVGTAIMYF-KRFYL-NNS-VMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLK 129 (305)
T ss_pred HHHHHHHHHhcCCCCchHHHHHHHHH-hHHhc-cCc-hhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhcc
Confidence 47889999999 9988754444445 33332 223 44679999999999999999888887777776443
No 14
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=47.81 E-value=45 Score=38.57 Aligned_cols=66 Identities=18% Similarity=0.285 Sum_probs=52.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhcc
Q 046343 373 GINICFCKINKLAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQ 443 (633)
Q Consensus 373 ~L~lFfRKVy~LAa~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k 443 (633)
++--=.+++|. |-.+|.++|.+|+|.+ ..+-+..-| +-.+. -.+-++|----+|--|+|++|+..+
T Consensus 59 s~e~r~~t~~n-~r~~i~~~~~~l~l~~-~~~~a~~~~-k~a~~--~nftkGr~~~~vvasClY~vcR~e~ 124 (521)
T KOG1598|consen 59 SLESREKTIYN-ARRLIEELTERLNLGN-KTEVAFNFF-KLAPD--RNFTKGRRSTEVVAACLYLVCRLEK 124 (521)
T ss_pred chHHHHHHHHH-HHhHHHHHHHhcCcch-HHHHHHHHH-HHHhh--CCCCCCcchHHHHHHHHHHHHHhhC
Confidence 44444555555 7889999999999988 667777777 55553 4688999999999999999999876
No 15
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=34.92 E-value=63 Score=35.34 Aligned_cols=65 Identities=17% Similarity=0.230 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHhCCChHHHHHHhhhcchhhhhccccc-ccccchhH--HHHHHHHHhhhhccCccCHHHHHHHH
Q 046343 385 AAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSL-FFNCHIDQ--IILCCFYGVAKISQLNLTFKEIIYNY 455 (633)
Q Consensus 385 Aa~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~L-m~dRHLDQ--IiLCaiY~icKV~k~~~tFk~Ii~~Y 455 (633)
++.=|.+|+.+|+++..- |-|.. ++.|+.-+ ..-+.-|- +-++|||.-+||....++++|||..=
T Consensus 42 ~~~fI~elg~~L~~~~~t---i~tA~---~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s 109 (323)
T KOG0834|consen 42 GAKFIQELGVRLKMPQKT---IATAI---VIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVS 109 (323)
T ss_pred HHHHHHHHHHHcCCCccc---hhhhh---hhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHH
Confidence 445589999999997654 22222 33444322 22233343 88999999999999999999999753
No 16
>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=33.57 E-value=46 Score=28.18 Aligned_cols=30 Identities=17% Similarity=0.160 Sum_probs=25.2
Q ss_pred HHHHHHHHHhhhhc-cCccCHHHHHHHHhcC
Q 046343 429 QIILCCFYGVAKIS-QLNLTFKEIIYNYGKQ 458 (633)
Q Consensus 429 QIiLCaiY~icKV~-k~~~tFk~Ii~~YR~Q 458 (633)
+|+|||+-...+-+ ..+++|.+|.+.|+..
T Consensus 5 Kl~L~Al~~~~~~~~~~~~~~~~vy~~Y~~~ 35 (87)
T cd08768 5 KLVLLALLLLFKRGGEEEATTGEVYEVYEEL 35 (87)
T ss_pred HHHHHHHHHHHhcCCCCCccHHHHHHHHHHH
Confidence 78999998888766 4579999999999854
No 17
>PRK09239 chorismate mutase; Provisional
Probab=33.30 E-value=34 Score=31.26 Aligned_cols=37 Identities=11% Similarity=0.226 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhCCChHHHHHHhhhcchhhhhccccc
Q 046343 385 AAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSL 421 (633)
Q Consensus 385 Aa~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~L 421 (633)
-.-|++.++..++|++++.+.||..+.++++.++.+.
T Consensus 60 vl~~~~~~a~~~gl~p~~~~~i~~~ii~esir~q~~i 96 (104)
T PRK09239 60 QIERLRQLAKDANLDPDFAEKFLNFIIKEVIRHHERI 96 (104)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457888999999999999999999878888877654
No 18
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=28.78 E-value=8.4 Score=29.69 Aligned_cols=35 Identities=26% Similarity=0.500 Sum_probs=27.1
Q ss_pred CHHHHHHHHhcCCCCCCcceeeec----cccceeehhhh
Q 046343 447 TFKEIIYNYGKQPQCKPQVFRSVF----DHVDIITFYNK 481 (633)
Q Consensus 447 tFk~Ii~~YR~QPQa~s~VyRsVl----ergDII~FYN~ 481 (633)
.|-+||+.|++.-.....|+..|- ++-|++.-+|.
T Consensus 6 ~FL~il~~y~~~~~~~~~v~~~v~~Ll~~hpdLl~~F~~ 44 (47)
T PF02671_consen 6 EFLKILNDYKKGRISRSEVIEEVSELLRGHPDLLEEFNR 44 (47)
T ss_dssp HHHHHHHHHHCTCSCHHHHHHHHHHHTTT-HHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHccCHHHHHHHHh
Confidence 588999999987777788888776 66787777665
No 19
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=27.92 E-value=56 Score=39.86 Aligned_cols=54 Identities=13% Similarity=0.194 Sum_probs=43.2
Q ss_pred HHHHHHHHHHhCCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhcc
Q 046343 386 AVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQ 443 (633)
Q Consensus 386 a~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k 443 (633)
..++..+|..|.+.++.....|..| .++-...+ |=.+ -+..+.||+|..||.+.
T Consensus 35 ~q~~~~~c~~lnld~~~~~ea~d~y-ta~~q~~s-legs--~~hW~~cAlY~~~r~S~ 88 (920)
T KOG1010|consen 35 EQDSDELCRPLNLDEQTETEAWDTY-TAVSQRLS-LEGS--ESHWLACALYTACRRSS 88 (920)
T ss_pred hhhhhhhhhhhcccchhhhhhHHHH-HHHHhHhC-CCcc--HHHHHHHHHHHHHHhcc
Confidence 5678899999999999999999999 77655433 3322 56789999999999984
No 20
>PRK10885 cca multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed
Probab=24.64 E-value=96 Score=34.76 Aligned_cols=34 Identities=9% Similarity=0.192 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHhCCChHHHHHHhhhcchhhhhc
Q 046343 384 LAAVRINAMVERLQLSQQIRESVYCLCPKRTLNQ 417 (633)
Q Consensus 384 LAa~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~ 417 (633)
..+.-.+.+|+||.++.+.++.++.++++|...+
T Consensus 276 ~Ga~~a~~i~~RLk~p~~~~~~~~~lv~~H~~~~ 309 (409)
T PRK10885 276 RGVKLVEQLCQRLRVPNECRDLALLVAEEHDNIH 309 (409)
T ss_pred hHHHHHHHHHHHcCcCHHHHHHHHHHHHHhhccc
Confidence 3566689999999999999999988885665444
No 21
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=24.06 E-value=1.8e+02 Score=31.72 Aligned_cols=68 Identities=15% Similarity=0.109 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHhCCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhccCccCHHHHHHHH
Q 046343 385 AAVRINAMVERLQLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLTFKEIIYNY 455 (633)
Q Consensus 385 Aa~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k~~~tFk~Ii~~Y 455 (633)
++.=+...|..|+|+.+.++-+=... |.. ++-++..+|.-.-|.--+||.++.+..+..+-+||...-
T Consensus 203 t~~~m~RFCs~L~L~~~~q~aA~e~a-~ka--~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vt 270 (308)
T KOG1597|consen 203 TGDFMPRFCSNLGLPKSAQEAATEIA-EKA--EEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVT 270 (308)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHH-HHH--HHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHh
Confidence 44556778999999988766665555 332 456788899999999999999999999999999997654
No 22
>PHA03002 Hypothetical protein; Provisional
Probab=23.09 E-value=55 Score=38.85 Aligned_cols=67 Identities=22% Similarity=0.303 Sum_probs=48.9
Q ss_pred HHHHHHHHHhhhhccCccCHHHHHHHHhcCC-CCCCcceeeec-------------------------------------
Q 046343 429 QIILCCFYGVAKISQLNLTFKEIIYNYGKQP-QCKPQVFRSVF------------------------------------- 470 (633)
Q Consensus 429 QIiLCaiY~icKV~k~~~tFk~Ii~~YR~QP-Qa~s~VyRsVl------------------------------------- 470 (633)
||+.|.=+..|+ +..+|=.||++-.+.-| .+-.+.|.+..
T Consensus 133 ~ilkinP~la~~--~m~ls~~Ei~~v~~~ip~~~~~~LY~~L~i~l~tlLylsD~fnIpP~n~sL~~L~D~~k~i~LVkk 210 (679)
T PHA03002 133 YLLKINPMLASK--KMILSKDEIIDLVKDIPSYATPYLYNNLSIDLDTLLYISDTFNIPPTNDSLLKLTDEEKAIELVKK 210 (679)
T ss_pred HHHhcCHHhhcC--CCCCCHHHHHHHHHhCCHHHHHHHHHhcCCCHHHHHHHhhccCCCchhHHHHHhhhHHHHHHHHHh
Confidence 445555555554 56788889999887655 45566777643
Q ss_pred -cccceeeh------hhhcchhhhHHHHHHhcCC
Q 046343 471 -DHVDIITF------YNKIFAPTVKPLLVELGPV 497 (633)
Q Consensus 471 -ergDII~F------YN~VFvp~mK~F~l~~~~~ 497 (633)
-..|||.| ||+.|+..|++++...-|.
T Consensus 211 yP~~nII~yis~~vK~~~~Fi~~i~e~V~~~~P~ 244 (679)
T PHA03002 211 YPNDNIINYISDDIKYNKTFIEKIHEIVNENFPN 244 (679)
T ss_pred CChhhhHhhcCHHhhhhHHHHHHHHHHHHHhCCc
Confidence 26789998 7889999999999988775
No 23
>PF13150 DUF3989: Protein of unknown function (DUF3989)
Probab=22.49 E-value=94 Score=27.64 Aligned_cols=32 Identities=25% Similarity=0.260 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCChHHH-HHHhhhc
Q 046343 377 CFCKINKLAAVRINAMVERLQLSQQIR-ESVYCLC 410 (633)
Q Consensus 377 FfRKVy~LAa~RL~dLC~rL~ls~el~-~kIWt~f 410 (633)
.|+|+-.-|-.||+.+|.+|- ++-| .-|++.|
T Consensus 3 ~~~~~~~~~~~~Lr~~c~~Ls--p~~R~~vvl~ml 35 (85)
T PF13150_consen 3 KIRKIKDRADDRLRRYCGRLS--PKQRLRVVLVML 35 (85)
T ss_pred hHHHHHHHHHHHHHHHHhcCC--HHHHHHHHHHHH
Confidence 478888999999999999984 4432 3455555
No 24
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=22.12 E-value=1.7e+02 Score=26.75 Aligned_cols=71 Identities=21% Similarity=0.265 Sum_probs=52.7
Q ss_pred HHHHHHHHHHhCCChHHHHHHh----hhcchhhhh-cccccccccchhHHHH--HHHHHhhhhccC-ccCHHHHHHHHhc
Q 046343 386 AVRINAMVERLQLSQQIRESVY----CLCPKRTLN-QRTSLFFNCHIDQIIL--CCFYGVAKISQL-NLTFKEIIYNYGK 457 (633)
Q Consensus 386 a~RL~dLC~rL~ls~el~~kIW----t~f~e~~L~-~~t~Lm~dRHLDQIiL--CaiY~icKV~k~-~~tFk~Ii~~YR~ 457 (633)
.-||+++|..|. .++.|+.-= ..++++-|+ ++.+++++|-+=.+|= +.||...|+-.. .++|++|-..-+-
T Consensus 5 gy~LN~f~~sL~-~a~~RerF~~D~ea~~~e~gLt~Ee~~av~~rD~~~li~~G~n~y~L~K~a~~~G~~~~~~~a~m~G 83 (94)
T cd07923 5 AYRINRFLHRLI-EPAHRERFLEDPEALFDEAGLTEEERTLIRNRDWIGMIRYGVIFFVLEKLAAVVGVSNLHVYAAMRG 83 (94)
T ss_pred hHHHHHHHHHHC-CHHHHHHHHhCHHHHHHHcCCCHHHHHHHHcchHHHHHHccCcHHHHHHHHHHcCCCHHHHHHHhhC
Confidence 568999999995 666654321 233456666 5568999998877764 789999999886 6999999877664
No 25
>PF03359 GKAP: Guanylate-kinase-associated protein (GKAP) protein; InterPro: IPR005026 The protein called postsynaptic density (PSD) is a specialised submembranous structure within which synaptic membrane proteins are linked to cytoskeleton and signalling proteins. Guanylate-kinase-associated protein (PSD-95/synapse-associated protein 90) is one of the major components of PSD, and functions as a scaffold protein for various ion channels and associated signalling molecules.; GO: 0007267 cell-cell signaling
Probab=21.41 E-value=1.6e+02 Score=32.48 Aligned_cols=81 Identities=12% Similarity=0.281 Sum_probs=56.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh-------CCChHHHHHHhhhcchhhhhcccccccccchhHHHHHHHHHhhhhccCccC
Q 046343 375 NICFCKINKLAAVRINAMVERL-------QLSQQIRESVYCLCPKRTLNQRTSLFFNCHIDQIILCCFYGVAKISQLNLT 447 (633)
Q Consensus 375 ~lFfRKVy~LAa~RL~dLC~rL-------~ls~el~~kIWt~f~e~~L~~~t~Lm~dRHLDQIiLCaiY~icKV~k~~~t 447 (633)
..||||+++---.||..||... +|++|+...|=+++ -++.||+..- =.-
T Consensus 171 g~yF~~ll~~E~~RL~~lC~~~e~~~~~~~lpee~~~~ir~av------Gqa~LL~~qK------------------f~Q 226 (357)
T PF03359_consen 171 GHYFRKLLQSETERLEGLCAEWEKEEEENDLPEEAKGLIRSAV------GQARLLMSQK------------------FKQ 226 (357)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccccCCChhHHHHHHHHH------hHHHHHHHHH------------------HHH
Confidence 5689999999999999999854 56777777777666 3455444332 234
Q ss_pred HHHHHHHHhcCCCCCCcceeeeccccceeehhhhcchh
Q 046343 448 FKEIIYNYGKQPQCKPQVFRSVFDHVDIITFYNKIFAP 485 (633)
Q Consensus 448 Fk~Ii~~YR~QPQa~s~VyRsVlergDII~FYN~VFvp 485 (633)
|..+++.+.+ |.+...| .--|+--|.--||+.
T Consensus 227 F~~L~~~~~~-~~~~~~~-----t~~DL~GFWDmv~lq 258 (357)
T PF03359_consen 227 FEGLCQQNEN-PSGEPPT-----TCQDLAGFWDMVYLQ 258 (357)
T ss_pred HHHHHHHhcC-cccCCCc-----chhhhhhHHHHHHHH
Confidence 6666666665 5444433 235999999999875
No 26
>PF09263 PEX-2N: Peroxisome biogenesis factor 1, N-terminal ; InterPro: IPR015343 This domain adopts a Cdc48 domain 2-like fold, with a beta-alpha-beta(3) arrangement. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation []. ; PDB: 1WLF_A.
Probab=21.35 E-value=14 Score=32.88 Aligned_cols=34 Identities=24% Similarity=0.452 Sum_probs=21.0
Q ss_pred CCHHHHHHHHHHHHHHHHhhhcCCCCchhHhHhhh
Q 046343 170 LPRELRRHLNSLEERLLESMVWEKGSSMYNSLTVA 204 (633)
Q Consensus 170 LpRelvKHLn~IEEqILEslAW~~~SpLw~~L~~a 204 (633)
||+.++.||.--|.|.+| ++|...+|.|=.....
T Consensus 18 Lp~~l~~~L~L~q~qAvE-vsWg~~~pvfLSW~e~ 51 (87)
T PF09263_consen 18 LPSRLASQLHLQQNQAVE-VSWGHQSPVFLSWVEG 51 (87)
T ss_dssp E-HHHHHHTT--TT--EE-EESSS---EEE-EEE-
T ss_pred CCHHHHHHHHHhhCceEE-EEeCCCCcEEEEeecc
Confidence 899999999999999987 8999999998765433
No 27
>TIGR01795 CM_mono_cladeE monofunctional chorismate mutase, alpha proteobacterial type. The alpha proteobacterial members are trusted because the pathways of CM are evident and there is only one plausible CM in the genome. In S. coelicolor, however, there is another aparrent monofunctional CM.
Probab=21.05 E-value=80 Score=28.33 Aligned_cols=34 Identities=9% Similarity=0.179 Sum_probs=28.3
Q ss_pred HHHHHHHHHhCCChHHHHHHhhhcchhhhhcccc
Q 046343 387 VRINAMVERLQLSQQIRESVYCLCPKRTLNQRTS 420 (633)
Q Consensus 387 ~RL~dLC~rL~ls~el~~kIWt~f~e~~L~~~t~ 420 (633)
.|++.++..++|++++.+.||..+-++++..+.+
T Consensus 55 ~~~~~~a~~~gl~p~~~e~i~~~i~~esir~q~~ 88 (94)
T TIGR01795 55 ARLRRLAIDAGLDPEFAEKFLNFIVTEVIKHHER 88 (94)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4778899999999999999999886777766543
Done!