Query psy9484
Match_columns 407
No_of_seqs 152 out of 214
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 20:35:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9484.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9484hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1010|consensus 100.0 1.4E-75 3E-80 621.2 20.0 330 10-373 35-374 (920)
2 PF11934 DUF3452: Domain of un 100.0 8.2E-41 1.8E-45 296.1 9.7 134 65-206 1-136 (136)
3 KOG1010|consensus 99.7 3.9E-18 8.5E-23 183.5 4.9 156 123-310 435-605 (920)
4 PF01858 RB_A: Retinoblastoma- 99.7 7.7E-18 1.7E-22 157.7 2.4 80 194-295 115-194 (194)
5 PF00382 TFIIB: Transcription 97.2 0.0013 2.7E-08 51.7 7.2 68 14-93 2-70 (71)
6 PRK00423 tfb transcription ini 96.6 0.028 6.1E-07 56.5 12.2 83 12-106 128-211 (310)
7 COG1405 SUA7 Transcription ini 96.4 0.015 3.2E-07 58.1 8.6 113 9-122 100-222 (285)
8 PF01857 RB_B: Retinoblastoma- 96.1 0.013 2.8E-07 52.4 5.9 68 9-88 14-84 (135)
9 smart00385 CYCLIN domain prese 94.0 0.3 6.5E-06 37.2 7.4 50 13-62 3-53 (83)
10 KOG1597|consensus 93.1 0.72 1.6E-05 46.3 10.0 118 5-122 100-231 (308)
11 PRK00423 tfb transcription ini 92.7 0.62 1.3E-05 46.9 9.2 80 9-100 219-299 (310)
12 cd00043 CYCLIN Cyclin box fold 82.8 12 0.00027 28.3 8.6 73 9-93 5-79 (88)
13 PF00134 Cyclin_N: Cyclin, N-t 52.2 1.4E+02 0.003 24.8 9.4 67 10-87 35-102 (127)
14 PHA00666 putative protease 45.4 38 0.00082 33.1 4.9 38 1-38 93-130 (233)
15 KOG1598|consensus 45.3 1.9E+02 0.0042 31.5 10.7 55 10-65 71-126 (521)
16 PF15150 PMAIP1: Phorbol-12-my 37.0 4.6 0.0001 30.3 -2.0 23 383-405 20-44 (54)
17 COG1405 SUA7 Transcription ini 35.7 58 0.0013 32.8 4.8 54 10-63 195-249 (285)
18 TIGR00569 ccl1 cyclin ccl1. Un 30.7 1.3E+02 0.0027 30.6 6.3 49 11-59 61-112 (305)
19 PF11047 SopD: Salmonella oute 27.4 18 0.00038 36.5 -0.5 34 329-362 274-310 (319)
20 smart00342 HTH_ARAC helix_turn 25.7 1.7E+02 0.0037 21.7 5.0 26 78-103 2-27 (84)
21 PHA01623 hypothetical protein 25.2 1.5E+02 0.0033 22.5 4.4 32 6-37 21-53 (56)
22 KOG2475|consensus 22.9 85 0.0018 34.3 3.5 80 47-137 295-380 (587)
23 PF11315 Med30: Mediator compl 21.8 2.4E+02 0.0052 25.9 5.8 41 99-139 24-71 (150)
24 KOG1598|consensus 21.6 2.6E+02 0.0055 30.7 6.8 70 24-106 184-255 (521)
25 PF02796 HTH_7: Helix-turn-hel 21.2 62 0.0013 23.0 1.5 26 76-101 20-45 (45)
No 1
>KOG1010|consensus
Probab=100.00 E-value=1.4e-75 Score=621.23 Aligned_cols=330 Identities=39% Similarity=0.737 Sum_probs=311.4
Q ss_pred HHHHHHHhhhcCCCHHHHHHHHHHHHHhhcccCccccchhhhHHHHhhhhhccccCccCCCccccC-CcccHHHHHhhhC
Q psy9484 10 AHQHQELCMALNIDSTTAKEAWNAYKEMSHHYTLEGSQLHWLGCSLYVSCRKATVPTVNSNRTIEG-NLVCLTSLLKHCK 88 (407)
Q Consensus 10 ~~~f~~lC~~LnlD~~t~~~Aw~~~~~~~~~~tlEg~~~~W~aCaLY~a~r~~~~~tv~~~~~~~~-n~vsLt~LLr~~~ 88 (407)
.+.|.++|+.||+|++++.+||++|.++++.+++||++.||+|||+|++||++++||||+ +.++| |+||||+|||+++
T Consensus 35 ~q~~~~~c~~lnld~~~~~ea~d~yta~~q~~slegs~~hW~~cAlY~~~r~S~~~~v~~-~~~~~~n~vsL~~Ilrs~k 113 (920)
T KOG1010|consen 35 EQDSDELCRPLNLDEQTETEAWDTYTAVSQRLSLEGSESHWLACALYTACRRSSVPTVGG-GIVEGKNEVSLTRILRSFK 113 (920)
T ss_pred hhhhhhhhhhhcccchhhhhhHHHHHHHHhHhCCCccHHHHHHHHHHHHHHhccCCccCc-ceeeecceehHHHHHHHHH
Confidence 789999999999999999999999999999999999999999999999999999999998 77777 9999999999999
Q ss_pred CChHHHHHHHHHHHHhcCCChHHHHHHHHHHHhhhHHHHHHHHhHHHHhccCCCCCCchhhhhhhcccccccccchhhHH
Q psy9484 89 MSLNQFLNKCRKWADMRKLPDSFRSKIARLERNFAVSKVIFTKYLPMFKEMFKPPDLDELLMHVRHNKKKMIHCTSTKVF 168 (407)
Q Consensus 89 lsi~~Ff~kl~kw~~~~~L~~e~~~~i~~Le~~f~v~~vLfkky~~iF~~iF~~p~~~~~~~~~r~~k~~~~~c~~~~lf 168 (407)
+|++|||+||+||++|++++.+||+++++||++|.|+++|||||++||..||+.|. ++....++.+++++.+|++.++|
T Consensus 114 ~sv~eff~km~~w~~ma~s~~~f~~~ieel~~~f~vssvl~KkY~~iF~~iF~~p~-~e~~~~~~~~n~~~~~~~~~~l~ 192 (920)
T KOG1010|consen 114 MSVIEFFTKMKQWVDMANSPQEFREEIEELQRNFKVSSVLFKKYKRIFRDIFKLPR-EELGYLNRPSNHARTPCSYAELF 192 (920)
T ss_pred HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhccceehhHHHHHHHHHHHHHhCcc-cccccCCCcccccCCcccHHHHH
Confidence 99999999999999999999999999999999999999999999999999999998 66677888889999999999999
Q ss_pred HHHHHHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhhcccccccCCCCCCCCCCCCCCCCCCCCCCchHHHHhhhc
Q psy9484 169 EFTWILFVLTKAEYLDVSNDLVNSFHLLIATCDLIYANVIQSKLRDIVNPDFEGMPSNFLDSHFAPLDDPPCIISILCKH 248 (407)
Q Consensus 169 ~f~WlLFL~~K~~~~~~~~DLV~s~~LLlC~Ldlvi~n~~~~~~~~lln~~F~~~~~~~~~~~f~~~~~~~~ILe~LC~~ 248 (407)
+|||+|||++||++|++.||||+|||||+||||++|+|++.+.|.+++||+|.|++++|+..+|.+...++|||+.||+.
T Consensus 193 ~f~W~lFL~~Kn~~~~~~dDLV~syqlllc~LDlv~~n~lc~~R~~~v~p~f~gl~~n~~~~d~~~s~n~~cii~~lce~ 272 (920)
T KOG1010|consen 193 KFCWLLFLVAKNEFPSIEDDLVNSYQLLLCILDLVYKNLLCSPRKDLVNPSFKGLPKNWTARDFKPSENPPCIIEVLCEL 272 (920)
T ss_pred HHHHHHHHHHhcccchhhhhHHhhhhHHHHHHHHHHHHhccccccccccccccCCCCCCchhhccccCCCcchhHHhhhh
Confidence 99999999999999999999999999999999999999988999999999999999999999999889999999999999
Q ss_pred CCCccchhhhhhhhhhhHHHHHHHHHHHHHHHhhhhhccCCchhhhhhhcCCCCCchhhhccCcccccccccCCCchhhh
Q psy9484 249 HDGCKLCVIVRAEASLSRDIVKHLNLTEEQVLDSLAWVSNSPLWKNIEDSGQEIPGCEQKLRGNIEDLSAILEPENFDYN 328 (407)
Q Consensus 249 ~~~~vie~~~~~E~~L~r~~~Khln~IEe~ile~l~w~~~s~l~~~~~~~~~~~p~~~~~~~g~~~~~~~l~~~~~l~~n 328 (407)
|++++.|+++..| +.|.++.++.. ..+.+.||...++|++++++|.+|
T Consensus 273 h~~li~eak~~k~----------------------------~~fk~~~~~l~----~~ktl~g~~~~~~gll~~~~f~~~ 320 (920)
T KOG1010|consen 273 HEGLIDEAKNMKE----------------------------TNFKPFMSSLY----EVKTLKGDYLLMRGLLDEGNFLPN 320 (920)
T ss_pred hhhHHHhhcchHH----------------------------HhHHHHHHHHH----hhhhhhcccccccccccccccchh
Confidence 9999999999999 88888887766 336888999999999999999999
Q ss_pred HHHHHHHHHHHhhccCCcccccccCCCCCCCC---------CCCCCCCCCCCCC
Q psy9484 329 FKVVNKMYEEYILSVGDFDERIFLPKFQSFDE---------TAPGSSGPGLDDL 373 (407)
Q Consensus 329 ~~~Lnk~Yee~~l~~Gd~DERiFL~~d~~e~~---------~tp~~~~~~~~~~ 373 (407)
+++|||.||+||+++||+|||||++.|+.+++ .+|-++++.-..+
T Consensus 321 ~~~lnk~yeeyvl~vgelDeRifl~~Da~~~t~~~~s~~~~r~~~~~~~~~~~~ 374 (920)
T KOG1010|consen 321 VKNLNKSYEEYVLDVGELDERIFLGEDAEEETKSSDSFESERLAVKSSLAQEFL 374 (920)
T ss_pred HHHHhhhHHHHhccccchhhhhhcccchhhhhccCCccchhccccccccchhhc
Confidence 99999999999999999999999999998775 3555666655555
No 2
>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=8.2e-41 Score=296.07 Aligned_cols=134 Identities=44% Similarity=0.849 Sum_probs=93.5
Q ss_pred CccCCCccccCCcccHHHHHhhhCCChHHHHHHHHHHH-HhcCCC-hHHHHHHHHHHHhhhHHHHHHHHhHHHHhccCCC
Q psy9484 65 PTVNSNRTIEGNLVCLTSLLKHCKMSLNQFLNKCRKWA-DMRKLP-DSFRSKIARLERNFAVSKVIFTKYLPMFKEMFKP 142 (407)
Q Consensus 65 ~tv~~~~~~~~n~vsLt~LLr~~~lsi~~Ff~kl~kw~-~~~~L~-~e~~~~i~~Le~~f~v~~vLfkky~~iF~~iF~~ 142 (407)
||||+ +.++|||||||||||+++||++|||++|+||+ +|++++ +.++.++++||++|+|+++|||||+++|++||..
T Consensus 1 ~~~~~-~~~~~n~vsLt~lLr~~~is~~~Ff~~l~~~~~~m~~~~~~~~~~~~~~L~~~f~v~~~l~kky~~~f~~lF~~ 79 (136)
T PF11934_consen 1 PTVGK-GVVEGNGVSLTQLLRACKISLVEFFKKLKKWAVDMANILSKRFRAQVKELERNFVVSTVLFKKYERIFQELFKP 79 (136)
T ss_dssp ---------T---S-HHHHHHHHT--HHHHHHHHCCS--------HHHHHH-HHHHHHHHHHHHHHHHHHHHHHCCCB--
T ss_pred CCccc-cccCCCcCcHHHHHHHcCCCHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 56765 78899999999999999999999999999999 778777 5777889999999999999999999999999999
Q ss_pred CCCchhhhhhhcccccccccchhhHHHHHHHHHHHHHhhccccccchhhhhhHHHHHHHHHHHh
Q psy9484 143 PDLDELLMHVRHNKKKMIHCTSTKVFEFTWILFVLTKAEYLDVSNDLVNSFHLLIATCDLIYAN 206 (407)
Q Consensus 143 p~~~~~~~~~r~~k~~~~~c~~~~lf~f~WlLFL~~K~~~~~~~~DLV~s~~LLlC~Ldlvi~n 206 (407)
|+++. +. +++.+|+++++|+|||+|||++|++++++++|||+|||||+||||++|+|
T Consensus 80 ~~~~~-~~------~~~~~~~~~~l~~f~W~LFL~~K~~~~~~~~DLV~s~~LLlc~ld~~~~n 136 (136)
T PF11934_consen 80 PPESP-PK------SRSSPCSYSDLFRFGWLLFLAAKGKFPSIFDDLVTSYHLLLCVLDLVYTN 136 (136)
T ss_dssp B---S----------SS--B-CHHHHHHHHHHHHHHHHHH-SSS--HHHHHHHHHHHHHHHHH-
T ss_pred CCccc-cc------ccCCCCCHHHHHHHHHHHHHHHhCCCCcccccHHHHHHHHHHHHHHHHhC
Confidence 97332 21 34568999999999999999999999999999999999999999999986
No 3
>KOG1010|consensus
Probab=99.71 E-value=3.9e-18 Score=183.50 Aligned_cols=156 Identities=28% Similarity=0.388 Sum_probs=113.6
Q ss_pred hHHHHHHHHhHHHHhccCCCCCCchhhhhhhccccccccc--chhhHHHHHHHHHH-----HHHhhccccc-cchh----
Q psy9484 123 AVSKVIFTKYLPMFKEMFKPPDLDELLMHVRHNKKKMIHC--TSTKVFEFTWILFV-----LTKAEYLDVS-NDLV---- 190 (407)
Q Consensus 123 ~v~~vLfkky~~iF~~iF~~p~~~~~~~~~r~~k~~~~~c--~~~~lf~f~WlLFL-----~~K~~~~~~~-~DLV---- 190 (407)
+.+-.|-++-+.||+.++..-....+.+ +.| -.+..|+++=.||. .++.+.-... -||-
T Consensus 435 ~p~e~Il~r~~~i~e~~~q~f~~~~~~g---------~~~~e~~~~r~k~a~~LYykvLE~il~aE~~rl~~~dl~~LL~ 505 (920)
T KOG1010|consen 435 DPTESILKRLKEIFEIFEQKFSAAEGSG---------NSCIEIASQRFKLAERLYYKVLEKILKAELKRLPDMDLSKLLE 505 (920)
T ss_pred ChHHHHHHHHHHHHHHHHHHhhhhccCC---------ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHH
Confidence 4456677777777777664322011001 011 13345777777773 3344332211 2332
Q ss_pred -hhh--hHHHHHHHHHHHhhhhcccccccCCCCCCCCCCCCCCCCCCCCCCchHHHHhhhcCCCccchhhhhhhhhhhHH
Q psy9484 191 -NSF--HLLIATCDLIYANVIQSKLRDIVNPDFEGMPSNFLDSHFAPLDDPPCIISILCKHHDGCKLCVIVRAEASLSRD 267 (407)
Q Consensus 191 -~s~--~LLlC~Ldlvi~n~~~~~~~~lln~~F~~~~~~~~~~~f~~~~~~~~ILe~LC~~~~~~vie~~~~~E~~L~r~ 267 (407)
.-| .||+||+|+|++ +|.++ ..|||++++|+.++|+ ++ +|||++||+|++|+|+
T Consensus 506 q~~Fh~sLlACclElVL~----ty~~~---l~FPwvle~~~l~aFd----F~------------KVIE~~IRhE~~L~Re 562 (920)
T KOG1010|consen 506 QEIFHRSLLACCLELVLA----TYKTD---LSFPWVLECFGLKAFD----FY------------KVIESFIRHEGGLSRE 562 (920)
T ss_pred HHHHHHHHHHHHHHHHHH----HhCCC---CCCchhhhhcCCcHHH----HH------------HHHHHHHHhcccccHH
Confidence 223 399999999999 55655 7899999999999998 54 7789999999999999
Q ss_pred HHHHHHHHHHHHHhhhhhccCCchhhhhhhcCCCCCchhhhcc
Q psy9484 268 IVKHLNLTEEQVLDSLAWVSNSPLWKNIEDSGQEIPGCEQKLR 310 (407)
Q Consensus 268 ~~Khln~IEe~ile~l~w~~~s~l~~~~~~~~~~~p~~~~~~~ 310 (407)
|+||||.|||+|||+|||.++|++|+++..+....|+|.++.-
T Consensus 563 miKHLn~iEE~iLEslaW~~dS~Lw~~i~~~~~~~~~~~~~~~ 605 (920)
T KOG1010|consen 563 MIKHLNSIEERILESLAWKSDSPLWEMIKQAKPRLPTEEGVDP 605 (920)
T ss_pred HHHHHHHHHHHHHHHHhhccCCcHHHHHHhccccccccccccc
Confidence 9999999999999999999999999999999999999996543
No 4
>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=99.68 E-value=7.7e-18 Score=157.69 Aligned_cols=80 Identities=38% Similarity=0.514 Sum_probs=65.4
Q ss_pred hHHHHHHHHHHHhhhhcccccccCCCCCCCCCCCCCCCCCCCCCCchHHHHhhhcCCCccchhhhhhhhhhhHHHHHHHH
Q psy9484 194 HLLIATCDLIYANVIQSKLRDIVNPDFEGMPSNFLDSHFAPLDDPPCIISILCKHHDGCKLCVIVRAEASLSRDIVKHLN 273 (407)
Q Consensus 194 ~LLlC~Ldlvi~n~~~~~~~~lln~~F~~~~~~~~~~~f~~~~~~~~ILe~LC~~~~~~vie~~~~~E~~L~r~~~Khln 273 (407)
.|++||+|+|+. +|+. .+..|||+++.+++++|+ + ++|||+++|+|++|+|+|+||||
T Consensus 115 sL~ACclEiVl~----sy~~--~~~~FPwiL~~~~i~~f~----f------------~KvIE~~Vr~~~~Lpr~lvkHL~ 172 (194)
T PF01858_consen 115 SLLACCLEIVLF----SYKS--VSLSFPWILEVFDIHPFD----F------------YKVIESFVRHEDGLPRELVKHLN 172 (194)
T ss_dssp HHHHHHHHHHHH----HTCT--SSSSTTHHHHHTT--HHH----H------------HTTHHHHHHH-TT--HHHHHHHH
T ss_pred HHHHHHHHHHHH----HcCC--CCCcchHHHHhcCCChhh----H------------hhHHHHHHHccccCCHHHHHHHH
Confidence 499999999999 4443 347899999999999887 4 57899999999999999999999
Q ss_pred HHHHHHHhhhhhccCCchhhhh
Q psy9484 274 LTEEQVLDSLAWVSNSPLWKNI 295 (407)
Q Consensus 274 ~IEe~ile~l~w~~~s~l~~~~ 295 (407)
.|||+|||++||+++||+|+.+
T Consensus 173 ~IEE~iLeslaW~~~S~Lw~~l 194 (194)
T PF01858_consen 173 SIEEQILESLAWKSDSPLWEML 194 (194)
T ss_dssp HHHHHHHHTGGGSTT-THHHHH
T ss_pred HHHHHHHHHHHhcCCChhhhhC
Confidence 9999999999999999999864
No 5
>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=97.24 E-value=0.0013 Score=51.70 Aligned_cols=68 Identities=19% Similarity=0.307 Sum_probs=54.1
Q ss_pred HHHhhhcCCCHHHHHHHHHHHHHhhcccCccc-cchhhhHHHHhhhhhccccCccCCCccccCCcccHHHHHhhhCCChH
Q psy9484 14 QELCMALNIDSTTAKEAWNAYKEMSHHYTLEG-SQLHWLGCSLYVSCRKATVPTVNSNRTIEGNLVCLTSLLKHCKMSLN 92 (407)
Q Consensus 14 ~~lC~~LnlD~~t~~~Aw~~~~~~~~~~tlEg-~~~~W~aCaLY~a~r~~~~~tv~~~~~~~~n~vsLt~LLr~~~lsi~ 92 (407)
..+|..|+|++.+.+.|.++|+......-..| ......|.++|.+||... ...|+.+|-..++++-.
T Consensus 2 ~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~------------~~~t~~eIa~~~~Vs~~ 69 (71)
T PF00382_consen 2 PRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNG------------VPRTLKEIAEAAGVSEK 69 (71)
T ss_dssp HHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTT------------SSSSHHHHHHHCTSSHH
T ss_pred hHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcC------------CCcCHHHHHHHhCCCCC
Confidence 46899999999999999999999987665544 478999999999999873 44688899888888754
Q ss_pred H
Q psy9484 93 Q 93 (407)
Q Consensus 93 ~ 93 (407)
+
T Consensus 70 t 70 (71)
T PF00382_consen 70 T 70 (71)
T ss_dssp H
T ss_pred c
Confidence 3
No 6
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=96.57 E-value=0.028 Score=56.48 Aligned_cols=83 Identities=14% Similarity=0.169 Sum_probs=64.7
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHHHHhhcccCc-cccchhhhHHHHhhhhhccccCccCCCccccCCcccHHHHHhhhCCC
Q psy9484 12 QHQELCMALNIDSTTAKEAWNAYKEMSHHYTL-EGSQLHWLGCSLYVSCRKATVPTVNSNRTIEGNLVCLTSLLKHCKMS 90 (407)
Q Consensus 12 ~f~~lC~~LnlD~~t~~~Aw~~~~~~~~~~tl-Eg~~~~W~aCaLY~a~r~~~~~tv~~~~~~~~n~vsLt~LLr~~~ls 90 (407)
...++|..|||++.+.++|..+|+.+.....+ ........|++||.|||+.. .+.||-+|...++++
T Consensus 128 ~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~------------~prtl~eI~~~~~v~ 195 (310)
T PRK00423 128 ELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCK------------VPRTLDEIAEVSRVS 195 (310)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcC------------CCcCHHHHHHHhCCC
Confidence 34568999999999999999999999754444 45678899999999999964 445788888888888
Q ss_pred hHHHHHHHHHHHHhcC
Q psy9484 91 LNQFLNKCRKWADMRK 106 (407)
Q Consensus 91 i~~Ff~kl~kw~~~~~ 106 (407)
..++-+..+......+
T Consensus 196 ~k~i~~~~~~l~k~L~ 211 (310)
T PRK00423 196 RKEIGRCYRFLLRELN 211 (310)
T ss_pred HHHHHHHHHHHHHHhC
Confidence 8877666555554444
No 7
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=96.36 E-value=0.015 Score=58.09 Aligned_cols=113 Identities=17% Similarity=0.221 Sum_probs=77.8
Q ss_pred HHHHHHHHhhhcCCCHHHHHHHHHHHHHhhcccCcc-ccchhhhHHHHhhhhhccccCccCCCccccCCcc-------cH
Q psy9484 9 TAHQHQELCMALNIDSTTAKEAWNAYKEMSHHYTLE-GSQLHWLGCSLYVSCRKATVPTVNSNRTIEGNLV-------CL 80 (407)
Q Consensus 9 ~~~~f~~lC~~LnlD~~t~~~Aw~~~~~~~~~~tlE-g~~~~W~aCaLY~a~r~~~~~tv~~~~~~~~n~v-------sL 80 (407)
.......+|..|+|+..+.+.|..+|...-....+- .+...-.|.++|++||+...|...+ ....-..| +.
T Consensus 100 a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~-eIa~a~~V~~kei~rty 178 (285)
T COG1405 100 ALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPRTLD-EIAKALGVSKKEIGRTY 178 (285)
T ss_pred HHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHH-HHHHHHCCCHHHHHHHH
Confidence 455667789999999999999999999988666554 4477888999999999987774322 00000111 22
Q ss_pred HHHHhhhCCChH--HHHHHHHHHHHhcCCChHHHHHHHHHHHhh
Q psy9484 81 TSLLKHCKMSLN--QFLNKCRKWADMRKLPDSFRSKIARLERNF 122 (407)
Q Consensus 81 t~LLr~~~lsi~--~Ff~kl~kw~~~~~L~~e~~~~i~~Le~~f 122 (407)
.-+.+..++.+. ++...+++|+...+|+.+++..+.+|=+..
T Consensus 179 r~~~~~L~l~~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~ 222 (285)
T COG1405 179 RLLVRELKLKIPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKA 222 (285)
T ss_pred HHHHHhcCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 234444444444 777778888888888887777776665443
No 8
>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=96.07 E-value=0.013 Score=52.37 Aligned_cols=68 Identities=19% Similarity=0.465 Sum_probs=51.2
Q ss_pred HHHHHHHHhhhcCCCHHHHHHHHHHHHHhhcc-cCc--cccchhhhHHHHhhhhhccccCccCCCccccCCcccHHHHHh
Q psy9484 9 TAHQHQELCMALNIDSTTAKEAWNAYKEMSHH-YTL--EGSQLHWLGCSLYVSCRKATVPTVNSNRTIEGNLVCLTSLLK 85 (407)
Q Consensus 9 ~~~~f~~lC~~LnlD~~t~~~Aw~~~~~~~~~-~tl--Eg~~~~W~aCaLY~a~r~~~~~tv~~~~~~~~n~vsLt~LLr 85 (407)
...|..+||+.|++++++.++.|.+|+.+-.+ ..| +.--.+++.|++|++|+.+. ..+|+.+|++
T Consensus 14 a~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~------------~~~sF~~Ii~ 81 (135)
T PF01857_consen 14 AAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSK------------EELSFKDIIK 81 (135)
T ss_dssp HHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-------------S--HHHHHH
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhc------------CCCCHHHHHH
Confidence 35688999999999999999999999998742 233 34456899999999997651 4568888887
Q ss_pred hhC
Q psy9484 86 HCK 88 (407)
Q Consensus 86 ~~~ 88 (407)
+-+
T Consensus 82 ~Yr 84 (135)
T PF01857_consen 82 AYR 84 (135)
T ss_dssp HHT
T ss_pred HHH
Confidence 765
No 9
>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=94.02 E-value=0.3 Score=37.17 Aligned_cols=50 Identities=24% Similarity=0.279 Sum_probs=42.9
Q ss_pred HHHHhhhcCCCHHHHHHHHHHHHHhhc-ccCccccchhhhHHHHhhhhhcc
Q psy9484 13 HQELCMALNIDSTTAKEAWNAYKEMSH-HYTLEGSQLHWLGCSLYVSCRKA 62 (407)
Q Consensus 13 f~~lC~~LnlD~~t~~~Aw~~~~~~~~-~~tlEg~~~~W~aCaLY~a~r~~ 62 (407)
...+|+.++++..+...||.+++..-. ...+........++++|.||+..
T Consensus 3 l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~ 53 (83)
T smart00385 3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTE 53 (83)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHh
Confidence 357899999999999999999999987 33456788899999999998775
No 10
>KOG1597|consensus
Probab=93.10 E-value=0.72 Score=46.26 Aligned_cols=118 Identities=18% Similarity=0.280 Sum_probs=73.3
Q ss_pred cchHHHHHHHH---HhhhcCCCHHHHHHHHHHHHHhhcccCcccc-chhhhHHHHhhhhhccccCc-cCC-----Ccccc
Q psy9484 5 ADNETAHQHQE---LCMALNIDSTTAKEAWNAYKEMSHHYTLEGS-QLHWLGCSLYVSCRKATVPT-VNS-----NRTIE 74 (407)
Q Consensus 5 ~~~~~~~~f~~---lC~~LnlD~~t~~~Aw~~~~~~~~~~tlEg~-~~~W~aCaLY~a~r~~~~~t-v~~-----~~~~~ 74 (407)
.+..+...|.+ +|..|+|+..+.+.|=++|+.+...=.+.|. ..--+|..||.|||+...|. +.. +....
T Consensus 100 ~d~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~~pRT~kEI~~~anv~kK 179 (308)
T KOG1597|consen 100 SDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDVPRTFKEISAVANVSKK 179 (308)
T ss_pred ccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCCCchHHHHHHHHcCCHH
Confidence 34456666654 5888999999999999999998844344443 45567777999999986661 110 00000
Q ss_pred CCcccHHHHHhhhCCChHHH----HHHHHHHHHhcCCChHHHHHHHHHHHhh
Q psy9484 75 GNLVCLTSLLKHCKMSLNQF----LNKCRKWADMRKLPDSFRSKIARLERNF 122 (407)
Q Consensus 75 ~n~vsLt~LLr~~~lsi~~F----f~kl~kw~~~~~L~~e~~~~i~~Le~~f 122 (407)
.-+=.+-.|+++.++|+..- -.-|++|+.+.+||...+..+.++=++.
T Consensus 180 EIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka 231 (308)
T KOG1597|consen 180 EIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKA 231 (308)
T ss_pred HHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 11113344555555443222 2348888888888887777766655443
No 11
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=92.73 E-value=0.62 Score=46.88 Aligned_cols=80 Identities=8% Similarity=0.059 Sum_probs=59.9
Q ss_pred HHHHHHHHhhhcCCCHHHHHHHHHHHHHhhccc-CccccchhhhHHHHhhhhhccccCccCCCccccCCcccHHHHHhhh
Q psy9484 9 TAHQHQELCMALNIDSTTAKEAWNAYKEMSHHY-TLEGSQLHWLGCSLYVSCRKATVPTVNSNRTIEGNLVCLTSLLKHC 87 (407)
Q Consensus 9 ~~~~f~~lC~~LnlD~~t~~~Aw~~~~~~~~~~-tlEg~~~~W~aCaLY~a~r~~~~~tv~~~~~~~~n~vsLt~LLr~~ 87 (407)
+..=...+|..|+|+..+.+.||.+++.+.... +-.-...-..|.++|.||+... ...|+.+|-+.+
T Consensus 219 p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g------------~~~t~keIa~v~ 286 (310)
T PRK00423 219 PIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLG------------ERRTQREVAEVA 286 (310)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhC------------CCCCHHHHHHHc
Confidence 344456779999999999999999999997544 3456688899999999998752 335788888888
Q ss_pred CCChHHHHHHHHH
Q psy9484 88 KMSLNQFLNKCRK 100 (407)
Q Consensus 88 ~lsi~~Ff~kl~k 100 (407)
+++-...-+..+.
T Consensus 287 ~Vs~~tI~~~yke 299 (310)
T PRK00423 287 GVTEVTVRNRYKE 299 (310)
T ss_pred CCCHHHHHHHHHH
Confidence 8776554433333
No 12
>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=82.77 E-value=12 Score=28.29 Aligned_cols=73 Identities=15% Similarity=0.137 Sum_probs=51.3
Q ss_pred HHHHHHHHhhhcCCCHHHHHHHHHHHHHhhcccCc-cccchhhhHHHHhhhhhccccCccCCCccccCCcccHHHHHhhh
Q psy9484 9 TAHQHQELCMALNIDSTTAKEAWNAYKEMSHHYTL-EGSQLHWLGCSLYVSCRKATVPTVNSNRTIEGNLVCLTSLLKHC 87 (407)
Q Consensus 9 ~~~~f~~lC~~LnlD~~t~~~Aw~~~~~~~~~~tl-Eg~~~~W~aCaLY~a~r~~~~~tv~~~~~~~~n~vsLt~LLr~~ 87 (407)
+..-...+|+.++++..+...|+.+++..-..... ..+...=.++++|.|++.. +...++.++.+.+
T Consensus 5 ~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~------------~~~~~~~~~~~~~ 72 (88)
T cd00043 5 PLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVE------------EIPPWLKDLVHVT 72 (88)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHc------------CCCCCHHHHhHHh
Confidence 34456788999999999999999999999765544 3445566677888886554 1244566666666
Q ss_pred CC-ChHH
Q psy9484 88 KM-SLNQ 93 (407)
Q Consensus 88 ~l-si~~ 93 (407)
+. +..+
T Consensus 73 ~~~~~~~ 79 (88)
T cd00043 73 GYATEEE 79 (88)
T ss_pred CCCCHHH
Confidence 66 4444
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=52.17 E-value=1.4e+02 Score=24.83 Aligned_cols=67 Identities=18% Similarity=0.265 Sum_probs=41.6
Q ss_pred HHHHHHHhhhcCCCHHHHHHHHHHHHHhhcccCccccchh-hhHHHHhhhhhccccCccCCCccccCCcccHHHHHhhh
Q psy9484 10 AHQHQELCMALNIDSTTAKEAWNAYKEMSHHYTLEGSQLH-WLGCSLYVSCRKATVPTVNSNRTIEGNLVCLTSLLKHC 87 (407)
Q Consensus 10 ~~~f~~lC~~LnlD~~t~~~Aw~~~~~~~~~~tlEg~~~~-W~aCaLY~a~r~~~~~tv~~~~~~~~n~vsLt~LLr~~ 87 (407)
-.-...+|..++++..|..-|+.++.+.-..........+ =++++++.|++.. +...+++.++...+
T Consensus 35 ~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~-----------e~~~~~~~~~~~~~ 102 (127)
T PF00134_consen 35 IDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKME-----------EDNPPSISDLIRIS 102 (127)
T ss_dssp HHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHH-----------TSS--HHHHHHHHT
T ss_pred HHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhh-----------ccccchHHHHHHHH
Confidence 3445567788999999999999999999866654444333 3556666665432 22445666666655
No 14
>PHA00666 putative protease
Probab=45.35 E-value=38 Score=33.12 Aligned_cols=38 Identities=16% Similarity=0.243 Sum_probs=32.7
Q ss_pred CCCccchHHHHHHHHHhhhcCCCHHHHHHHHHHHHHhh
Q psy9484 1 MGQLADNETAHQHQELCMALNIDSTTAKEAWNAYKEMS 38 (407)
Q Consensus 1 ~~~~~~~~~~~~f~~lC~~LnlD~~t~~~Aw~~~~~~~ 38 (407)
+|..-+.++..+|+.+|++|||+...+.++...|-++.
T Consensus 93 EG~elD~~~l~~F~~~a~ElgLtqEQAQklvD~y~ki~ 130 (233)
T PHA00666 93 EGVELDTGALGAFEPVARELNLTNEQAQKVVDLYTKIL 130 (233)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhh
Confidence 35666788999999999999999999999999885554
No 15
>KOG1598|consensus
Probab=45.26 E-value=1.9e+02 Score=31.54 Aligned_cols=55 Identities=22% Similarity=0.351 Sum_probs=46.2
Q ss_pred HHHHHHHhhhcCCCHHHHHHHHHHHHHhh-cccCccccchhhhHHHHhhhhhccccC
Q psy9484 10 AHQHQELCMALNIDSTTAKEAWNAYKEMS-HHYTLEGSQLHWLGCSLYVSCRKATVP 65 (407)
Q Consensus 10 ~~~f~~lC~~LnlD~~t~~~Aw~~~~~~~-~~~tlEg~~~~W~aCaLY~a~r~~~~~ 65 (407)
+-...+++..|++.+ ..+-|.+.|+-.- .+++-...-.+=++..+|++||+.+++
T Consensus 71 r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~ 126 (521)
T KOG1598|consen 71 RRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTD 126 (521)
T ss_pred HhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCc
Confidence 346678899999999 8899999998766 678888888888999999999998655
No 16
>PF15150 PMAIP1: Phorbol-12-myristate-13-acetate-induced; PDB: 2ROD_B 2JM6_A 2NLA_B 3MQP_B.
Probab=36.98 E-value=4.6 Score=30.27 Aligned_cols=23 Identities=35% Similarity=0.468 Sum_probs=13.4
Q ss_pred CCccccccchhHHh--HhhhhhccC
Q psy9484 383 PPEVDFGIDFTSFR--RNLRQKLVP 405 (407)
Q Consensus 383 ~~~~~~~~~~~~~~--~~~~~~~~~ 405 (407)
.|||.+.|.+.-|- -|+||||+-
T Consensus 20 ~~~vEca~QlRriGDklnfrqKLLn 44 (54)
T PF15150_consen 20 ELEVECAIQLRRIGDKLNFRQKLLN 44 (54)
T ss_dssp THHHHHHHHHHHHHHHHHHHHHCCH
T ss_pred ccchHHHHHHHHHhhHHHHHHHHHH
Confidence 34556665544332 378999864
No 17
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=35.68 E-value=58 Score=32.75 Aligned_cols=54 Identities=11% Similarity=0.095 Sum_probs=42.1
Q ss_pred HHHHHHHhhhcCCCHHHHHHHHHHHHHhhccc-CccccchhhhHHHHhhhhhccc
Q psy9484 10 AHQHQELCMALNIDSTTAKEAWNAYKEMSHHY-TLEGSQLHWLGCSLYVSCRKAT 63 (407)
Q Consensus 10 ~~~f~~lC~~LnlD~~t~~~Aw~~~~~~~~~~-tlEg~~~~W~aCaLY~a~r~~~ 63 (407)
..--..+|+.||+++.+..+|.++-+.++..+ +..-.+.--.|.++|.|++...
T Consensus 195 ~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~ 249 (285)
T COG1405 195 SDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLG 249 (285)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhC
Confidence 34445679999999999999999999998655 4445566677888888877753
No 18
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=30.71 E-value=1.3e+02 Score=30.63 Aligned_cols=49 Identities=12% Similarity=0.277 Sum_probs=40.5
Q ss_pred HHHHHHhhhcC--CCHHHHHHHHHHHHHhhcccCc-cccchhhhHHHHhhhh
Q psy9484 11 HQHQELCMALN--IDSTTAKEAWNAYKEMSHHYTL-EGSQLHWLGCSLYVSC 59 (407)
Q Consensus 11 ~~f~~lC~~Ln--lD~~t~~~Aw~~~~~~~~~~tl-Eg~~~~W~aCaLY~a~ 59 (407)
..-.++|..|+ |.+.|...|.-.|++.-...++ +-+.+.=++.+||.||
T Consensus 61 ~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~ 112 (305)
T TIGR00569 61 KRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLAC 112 (305)
T ss_pred HHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHH
Confidence 34567888999 9999999999999998864444 6778888999999995
No 19
>PF11047 SopD: Salmonella outer protein D; InterPro: IPR022747 The proteins in this entry are also known as secreted effector proteins. Effector proteins function to alter host cell physiology and promote bacterial survival in host tissues. They contribute to the formation of Salmonella-induced filaments (Sifs) in infected epithelial cells and to replication in macrophages []. SopD is a type III virulence effector protein whose structure consists of 38% alpha-helix and 26% beta-strand [].; GO: 0009405 pathogenesis, 0033644 host cell membrane
Probab=27.41 E-value=18 Score=36.50 Aligned_cols=34 Identities=24% Similarity=0.404 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhhccCCcc---cccccCCCCCCCCCC
Q psy9484 329 FKVVNKMYEEYILSVGDFD---ERIFLPKFQSFDETA 362 (407)
Q Consensus 329 ~~~Lnk~Yee~~l~~Gd~D---ERiFL~~d~~e~~~t 362 (407)
++.||++|++|.-++.+|| |||++.++-+-.||.
T Consensus 274 ~~~ln~dy~dy~~nk~~id~ile~iy~sh~~sl~i~k 310 (319)
T PF11047_consen 274 LNKLNQDYDDYHNNKREIDPILEKIYLSHNNSLFIGK 310 (319)
T ss_pred HHHhccchhhHhcchhhHHHHHHHHHHhcCCcEEEcC
Confidence 4689999999999999999 899999887777664
No 20
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=25.70 E-value=1.7e+02 Score=21.74 Aligned_cols=26 Identities=19% Similarity=0.157 Sum_probs=21.0
Q ss_pred ccHHHHHhhhCCChHHHHHHHHHHHH
Q psy9484 78 VCLTSLLKHCKMSLNQFLNKCRKWAD 103 (407)
Q Consensus 78 vsLt~LLr~~~lsi~~Ff~kl~kw~~ 103 (407)
+|+.+|.+.+++|...|...++++..
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~~ 27 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETG 27 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHhC
Confidence 57888899999998888877777653
No 21
>PHA01623 hypothetical protein
Probab=25.23 E-value=1.5e+02 Score=22.46 Aligned_cols=32 Identities=19% Similarity=0.353 Sum_probs=26.8
Q ss_pred chHHHHHHHHHhhhcCCC-HHHHHHHHHHHHHh
Q psy9484 6 DNETAHQHQELCMALNID-STTAKEAWNAYKEM 37 (407)
Q Consensus 6 ~~~~~~~f~~lC~~LnlD-~~t~~~Aw~~~~~~ 37 (407)
++++..++..+|...|++ ..+..+|.+.|-.-
T Consensus 21 deel~~~Ld~y~~~~g~~rSe~IreAI~~yL~~ 53 (56)
T PHA01623 21 DKDLKTRLKVYCAKNNLQLTQAIEEAIKEYLQK 53 (56)
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 567899999999999998 45888999988653
No 22
>KOG2475|consensus
Probab=22.88 E-value=85 Score=34.34 Aligned_cols=80 Identities=23% Similarity=0.350 Sum_probs=59.1
Q ss_pred chhh-----hHHHHhhhhhccccCccCCCccccCCcccHHHHHhhhCCChHHHHHHHHHHHHhcC-CChHHHHHHHHHHH
Q psy9484 47 QLHW-----LGCSLYVSCRKATVPTVNSNRTIEGNLVCLTSLLKHCKMSLNQFLNKCRKWADMRK-LPDSFRSKIARLER 120 (407)
Q Consensus 47 ~~~W-----~aCaLY~a~r~~~~~tv~~~~~~~~n~vsLt~LLr~~~lsi~~Ff~kl~kw~~~~~-L~~e~~~~i~~Le~ 120 (407)
-+|| ++|+-|++++.+.=. +..-..|-.||...++.+++= =++|.-|.. +-.++++.+++.-.
T Consensus 295 yrHWsL~dSm~~S~Y~~~klklWs--------~~G~KrLh~lLA~MGl~L~e~---kQkf~aMd~~lk~~l~~~~er~a~ 363 (587)
T KOG2475|consen 295 YRHWSLFDSMLYSSYVSAKLKLWS--------ENGDKRLHKLLARMGLPLVEA---KQKFEAMDLELKRELKSMFERFAP 363 (587)
T ss_pred eecccHHHHHHHHHHHHhHhhhhh--------hhhHHHHHHHHHHhCCcHHHH---HHHhhhcCHHHHHHHHHHHHhhcc
Confidence 4799 789999999887322 122257999999999999885 456776633 55678888888888
Q ss_pred hhhHHHHHHHHhHHHHh
Q psy9484 121 NFAVSKVIFTKYLPMFK 137 (407)
Q Consensus 121 ~f~v~~vLfkky~~iF~ 137 (407)
+|+..-++|+-|-+.|.
T Consensus 364 ~ygl~D~~~~tF~rt~G 380 (587)
T KOG2475|consen 364 KYGLMDIIFATFTRTLG 380 (587)
T ss_pred cccchhhhhhhhhhhcc
Confidence 88888888887766643
No 23
>PF11315 Med30: Mediator complex subunit 30; InterPro: IPR021019 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med30 is a metazoan-specific subunit of Mediator [], having no homologues in yeasts.
Probab=21.83 E-value=2.4e+02 Score=25.88 Aligned_cols=41 Identities=17% Similarity=0.310 Sum_probs=28.1
Q ss_pred HHHHHhcCCCh-------HHHHHHHHHHHhhhHHHHHHHHhHHHHhcc
Q psy9484 99 RKWADMRKLPD-------SFRSKIARLERNFAVSKVIFTKYLPMFKEM 139 (407)
Q Consensus 99 ~kw~~~~~L~~-------e~~~~i~~Le~~f~v~~vLfkky~~iF~~i 139 (407)
=+|+....+|. -...+..+|+..+....+||+|-+-||+..
T Consensus 24 F~~lk~~QlPng~t~~~~~aqdr~~kl~e~lr~i~~LFkkLRlIYekC 71 (150)
T PF11315_consen 24 FQALKNPQLPNGSTQQQNMAQDRRNKLQEQLRTIKVLFKKLRLIYEKC 71 (150)
T ss_pred HHHHhcccCCCCccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555652 345556688888888888999888777653
No 24
>KOG1598|consensus
Probab=21.59 E-value=2.6e+02 Score=30.67 Aligned_cols=70 Identities=14% Similarity=0.174 Sum_probs=48.8
Q ss_pred HHHHHHHHHHHHHhhcccCccc--cchhhhHHHHhhhhhccccCccCCCccccCCcccHHHHHhhhCCChHHHHHHHHHH
Q psy9484 24 STTAKEAWNAYKEMSHHYTLEG--SQLHWLGCSLYVSCRKATVPTVNSNRTIEGNLVCLTSLLKHCKMSLNQFLNKCRKW 101 (407)
Q Consensus 24 ~~t~~~Aw~~~~~~~~~~tlEg--~~~~W~aCaLY~a~r~~~~~tv~~~~~~~~n~vsLt~LLr~~~lsi~~Ff~kl~kw 101 (407)
+.+...|.++-..++...--.| -.-..+|| ||.|||. .|-..|.+.|.+-..++..-+=+++.+|
T Consensus 184 ~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAa-LliAar~------------h~~~rsi~dIv~vvhV~e~Tl~kRl~Ef 250 (521)
T KOG1598|consen 184 EDVAKTATRLAQRMKRDWMQTGRRPSGLCGAA-LLIAARM------------HGFRRTIGDIAKVVHVCESTLSKRLKEF 250 (521)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCccchhHHH-HHHHHHH------------cCccccHHHHHHHHHHhHHHHHHHHHHH
Confidence 4588888888888876442222 23344455 4555444 3455789999999999999999999999
Q ss_pred HHhcC
Q psy9484 102 ADMRK 106 (407)
Q Consensus 102 ~~~~~ 106 (407)
.+...
T Consensus 251 ~~T~s 255 (521)
T KOG1598|consen 251 SDTLS 255 (521)
T ss_pred hcccc
Confidence 97733
No 25
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=21.25 E-value=62 Score=23.00 Aligned_cols=26 Identities=12% Similarity=0.068 Sum_probs=19.3
Q ss_pred CcccHHHHHhhhCCChHHHHHHHHHH
Q psy9484 76 NLVCLTSLLKHCKMSLNQFLNKCRKW 101 (407)
Q Consensus 76 n~vsLt~LLr~~~lsi~~Ff~kl~kw 101 (407)
.+.|..+|.+.+++|...+.+.+++|
T Consensus 20 ~G~si~~IA~~~gvsr~TvyR~l~~~ 45 (45)
T PF02796_consen 20 EGMSIAEIAKQFGVSRSTVYRYLNKN 45 (45)
T ss_dssp TT--HHHHHHHTTS-HHHHHHHHCC-
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 44899999999999999999888766
Done!