Query 011786
Match_columns 477
No_of_seqs 151 out of 180
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 05:13:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011786.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011786hhsearch_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 2E-116 4E-121 949.8 32.0 402 17-477 380-794 (920)
2 PF01858 RB_A: Retinoblastoma- 100.0 5.2E-68 1.1E-72 505.5 16.8 194 31-233 1-194 (194)
3 PF01857 RB_B: Retinoblastoma- 100.0 3.6E-54 7.9E-59 388.4 9.5 125 353-477 1-130 (135)
4 PRK00423 tfb transcription ini 97.7 0.00018 4E-09 73.8 9.3 73 362-436 121-193 (310)
5 PF00382 TFIIB: Transcription 97.6 0.00033 7.1E-09 56.3 7.8 63 370-434 1-63 (71)
6 smart00385 CYCLIN domain prese 96.9 0.0038 8.3E-08 49.1 7.3 63 370-434 3-65 (83)
7 cd00043 CYCLIN Cyclin box fold 96.7 0.012 2.7E-07 46.6 8.6 70 366-437 5-74 (88)
8 KOG1597 Transcription initiati 96.1 0.021 4.7E-07 58.0 8.4 72 361-434 102-173 (308)
9 PRK00423 tfb transcription ini 95.7 0.031 6.6E-07 57.5 7.5 62 370-433 223-284 (310)
10 COG1405 SUA7 Transcription ini 92.0 0.86 1.9E-05 46.6 9.2 77 361-439 95-171 (285)
11 PF00134 Cyclin_N: Cyclin, N-t 87.3 4.6 9.9E-05 34.8 8.9 70 363-434 31-101 (127)
12 TIGR00569 ccl1 cyclin ccl1. Un 79.8 8.2 0.00018 40.0 8.4 67 367-435 60-128 (305)
13 KOG1598 Transcription initiati 57.9 36 0.00078 37.7 7.8 61 359-423 64-124 (521)
14 KOG0834 CDK9 kinase-activating 43.3 46 0.00099 34.9 5.6 67 366-436 42-111 (323)
15 KOG1597 Transcription initiati 37.6 1.1E+02 0.0025 31.7 7.2 63 370-434 207-269 (308)
16 cd08768 Cdc6_C Winged-helix do 36.8 44 0.00096 27.1 3.5 30 409-438 5-35 (87)
17 PF07340 Herpes_IE1: Cytomegal 35.7 5.9E+02 0.013 27.4 18.4 72 148-222 199-281 (392)
18 KOG1010 Rb (Retinoblastoma tum 35.1 50 0.0011 38.7 4.6 54 367-423 35-88 (920)
19 COG1405 SUA7 Transcription ini 27.4 2.2E+02 0.0047 29.3 7.4 61 370-432 198-258 (285)
20 PF09263 PEX-2N: Peroxisome bi 24.9 13 0.00028 31.5 -1.6 32 202-234 18-49 (87)
21 PRK09239 chorismate mutase; Pr 23.6 1.3E+02 0.0027 26.3 4.2 36 366-401 60-96 (104)
22 PF06972 DUF1296: Protein of u 23.5 2.3E+02 0.0051 22.6 5.2 36 37-76 6-41 (60)
23 PF08630 Dfp1_Him1_M: Dfp1/Him 23.1 30 0.00065 31.4 0.2 34 119-153 18-60 (125)
24 KOG2389 Predicted bromodomain 20.5 1.8E+02 0.004 30.8 5.3 19 363-381 28-46 (353)
No 1
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.9e-116 Score=949.80 Aligned_cols=402 Identities=33% Similarity=0.502 Sum_probs=341.0
Q ss_pred CCCCCCCCC----CCCCCCchHHHHHHHHHHHHHHhCCCCCCCcHHHHHHHhhCCCChHHHHHHHHHHHHhhhccccccc
Q 011786 17 PASQSNGSM----AKMTPTPVRTAQNTASNWLKTVIAPLPSKPSAELEKFLSLGSVSIANEVESGANIVLEAIFPSIKLG 92 (477)
Q Consensus 17 p~tp~~g~~----~~~~~TPVs~A~~s~~~~L~~~l~~~~~~PS~~L~~~f~sC~~dp~~~i~~rv~~i~e~~f~~~~~~ 92 (477)
+++|+||++ .+...|||++||+++ +||++++.|++++||++|++||++|++||+++|++|+++|++.|+++...+
T Consensus 380 ~~p~~~~~~y~~e~~~~~tPvsta~~si-k~l~t~i~g~~~~psdkLe~~~~tc~r~p~e~Il~r~~~i~e~~~q~f~~~ 458 (920)
T KOG1010|consen 380 KSPPHTGVRYNLELGNYPTPVSTATNSI-KQLMTILNGLKKEPSDKLEQYLNTCSRDPTESILKRLKEIFEIFEQKFSAA 458 (920)
T ss_pred cCCCCcccccccccccCCCcchhHHHHH-HHHHHHHhccccCCcHHHHHHHhhcccChHHHHHHHHHHHHHHHHHHhhhh
Confidence 567899975 677789999999999 999999999999999999999999999999999999999999999987654
Q ss_pred ccccccccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhcccCCCchhhhccchHHHHHHHHHHHHHHHHHhcCCCc
Q 011786 93 ERLFNWSLLNVNLMDSLWSGQERTEALKLYYKVLESICASEAGKSSSRDLSGLLTNEKFHRCMLACSAELVSMARTRVSI 172 (477)
Q Consensus 93 ~~~~~~~~~~~~~~d~~~a~~R~~~a~~LYYkvLE~Il~~E~~rl~~~~ls~LL~~e~FhrsLlACclEiVl~~y~~~~~ 172 (477)
..++ .++++ .+.||+++|++|||||||+||++|.+|++..||+.||+|++||+||||||+|+||++|+ .++
T Consensus 459 ~~~g------~~~~e--~~~~r~k~a~~LYykvLE~il~aE~~rl~~~dl~~LL~q~~Fh~sLlACclElVL~ty~-~~l 529 (920)
T KOG1010|consen 459 EGSG------NSCIE--IASQRFKLAERLYYKVLEKILKAELKRLPDMDLSKLLEQEIFHRSLLACCLELVLATYK-TDL 529 (920)
T ss_pred ccCC------ccchH--HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhC-CCC
Confidence 3221 34566 79999999999999999999999999999999999999999999999999999999998 558
Q ss_pred chhHHHHhhCCCceehhhhhhHhhhcCCCCCHHHHHHHHHHHHHHHhhhhccCCCcchHHHHhcCCChHHHHHHhhhhcC
Q 011786 173 LFPLILERAGITAFDMCKVTESFIRHEDSLPRELMRHLNSLEETMLESMVWEKGSSLYNSLIASRPDLQEEIKRLKLLAE 252 (477)
Q Consensus 173 ~FPwiL~~~~i~afdf~KVIE~fIR~e~~LpRelvkHLn~IEE~ILEslAW~~~S~L~~~L~~a~~~~~~ei~r~g~~~~ 252 (477)
.|||||++|||+|||||||||+|||||++|+||||||||+|||+|||||||++|||||++|+++++
T Consensus 530 ~FPwvle~~~l~aFdF~KVIE~~IRhE~~L~RemiKHLn~iEE~iLEslaW~~dS~Lw~~i~~~~~-------------- 595 (920)
T KOG1010|consen 530 SFPWVLECFGLKAFDFYKVIESFIRHEGGLSREMIKHLNSIEERILESLAWKSDSPLWEMIKQAKP-------------- 595 (920)
T ss_pred CCchhhhhcCCcHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHhhccCCcHHHHHHhccc--------------
Confidence 999999999999999999999999999999999999999999999999999999999999998774
Q ss_pred CCCchhhhhccccccC----Cccccc-ccccCCCCCCCCCCCccccccCCCccccccccccccccCCCccccccccCCCC
Q 011786 253 PMPSLHEISMNNHLAS----GVLAYQ-HNLHKHKPSTGNNGMKRLCDENGSKLTKHNSYATAMKVDSPVVDSHQVKLQPV 327 (477)
Q Consensus 253 ~~Ps~~~v~~~~~~~~----~~~p~~-p~~~~~~~sp~~~~~kr~~~~~~~~~~~~~s~~~p~~~~sp~k~~~~~~~~~~ 327 (477)
++|.++++..+.++.+ |.+|+. ....+++.+|+. +||+.++ ++|+++.....
T Consensus 596 ~~~~~~~~~~~~~le~~~~~~~~p~~~~~~~~~~~sp~~-~Pk~~~~------------------t~pv~~~an~~---- 652 (920)
T KOG1010|consen 596 RLPTEEGVDPPDNLESACIAGLLPLRVNHVRARYSSPVL-EPKDKGT------------------TIPVNGTANAG---- 652 (920)
T ss_pred ccccccccccccccccccccccCCccccccccccCCCCC-Ccccccc------------------ccccccccccc----
Confidence 4455555544444322 112211 012234556665 4665443 55666544211
Q ss_pred CCCccccccCCCCCCCCCCCCCc-hhhHHHHHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCc
Q 011786 328 TPSSQTAFMSPVQSKTPKDGGIK-MDAAVTFLFNKMTKLGAVRINSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRH 406 (477)
Q Consensus 328 ~~~~qs~~~sp~~~~~p~~~~~~-~~~sl~lFfrKvy~LAa~RL~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRH 406 (477)
+..++.+++++ +.++|+|||||||+||++||++||+||+++++++++|||||||+|+|+|+||+|||
T Consensus 653 ------------qe~~~~~~~~~~~stsLsIF~rKvY~LAavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRH 720 (920)
T KOG1010|consen 653 ------------QEVTAFGVNKPRKSTSLSIFLRKVYHLAAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRH 720 (920)
T ss_pred ------------ccCCcccCCCcccccchHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhh
Confidence 11113334444 67799999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHhcCCCcCHHHHHHHHhcCCCCCCcceeeEEeccc-cccCCCc--cccccccccccccccC
Q 011786 407 IDLIILCCFCGVAKINKLKLKFEEITDNYVKEPQCRSQDFGFVFAGWL-SKHKGKN--RENYKSIDAFYNKYSF 477 (477)
Q Consensus 407 LDQiiLCaiY~icKv~k~~~tFk~Ii~~Yr~QPqa~~~Vyr~Vli~~~-~~~~g~~--~~e~~DII~FYN~VFv 477 (477)
|||||||||||||||++++++|++||++||+||||+++|||+|+|+.. ....|.. .++++|||.|||.+||
T Consensus 721 LDQillCaiy~i~KV~~~~ltF~eIm~~YR~QPqa~~~vyRsV~i~~~~~~~~~~~~P~~~~~diI~fyN~iyV 794 (920)
T KOG1010|consen 721 LDQILLCAIYGIAKVKKEDLTFSEIMRAYRRQPQAVSLVYRSVLIKDKTNRDQGPSGPKEERSDIITFYNNIYV 794 (920)
T ss_pred HHHHHHHHHHhheehhcccchHHHHHHHHhcCchhhhhhhhheeecccccccccCCCCcccccceeccccceeh
Confidence 999999999999999999999999999999999999999999999722 2222222 4589999999999997
No 2
>PF01858 RB_A: Retinoblastoma-associated protein A domain; InterPro: IPR002720 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and Simian virus 40 (SV40) large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion appears to be required for the stable folding of the B box (see IPR002719 from INTERPRO). Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the A-box is on N-terminal side of the B-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1O9K_A 3POM_A 1GH6_B 1N4M_A 4ELL_B 1AD6_A 1GUX_A 2R7G_C 4ELJ_A.
Probab=100.00 E-value=5.2e-68 Score=505.52 Aligned_cols=194 Identities=41% Similarity=0.632 Sum_probs=168.6
Q ss_pred CchHHHHHHHHHHHHHHhCCCCCCCcHHHHHHHhhCCCChHHHHHHHHHHHHhhhcccccccccccccccccccccchhh
Q 011786 31 TPVRTAQNTASNWLKTVIAPLPSKPSAELEKFLSLGSVSIANEVESGANIVLEAIFPSIKLGERLFNWSLLNVNLMDSLW 110 (477)
Q Consensus 31 TPVs~A~~s~~~~L~~~l~~~~~~PS~~L~~~f~sC~~dp~~~i~~rv~~i~e~~f~~~~~~~~~~~~~~~~~~~~d~~~ 110 (477)
||||+||+++ +||+++++|++++||++|.++|++|++||+++|.+||++|++.|++.+..+. +.+ ..+..+
T Consensus 1 TPVs~A~~~~-~~L~~~l~~~~~~PS~~L~~~~~~c~~~p~~~i~~rv~~l~~~~~~~~~~~~-----~~~---~~~~~~ 71 (194)
T PF01858_consen 1 TPVSSAMQSV-SWLQALLSGLSDEPSEELLRIFKSCSRDPTESILKRVKQLLEKFCQKYTEAE-----GEQ---SSNSDF 71 (194)
T ss_dssp -HHHHHHHHH-HHHHHHHHHS-SS--HHHHHHHHTSSS--HHHHHHHHHHHHHHHHHHHHHHH-----SGG-----GHHH
T ss_pred CchHHHHHHH-HHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHhcccc-----ccc---cccchH
Confidence 8999999999 9999999999999999999999999999999999999999999988754221 111 233348
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcccCCCchhhhccchHHHHHHHHHHHHHHHHHhcCCCcchhHHHHhhCCCceehhh
Q 011786 111 SGQERTEALKLYYKVLESICASEAGKSSSRDLSGLLTNEKFHRCMLACSAELVSMARTRVSILFPLILERAGITAFDMCK 190 (477)
Q Consensus 111 a~~R~~~a~~LYYkvLE~Il~~E~~rl~~~~ls~LL~~e~FhrsLlACclEiVl~~y~~~~~~FPwiL~~~~i~afdf~K 190 (477)
+++|+++|++|||++||+||.+|.+|++..|++.||+||+|||||+|||+|||+|+|+++++.|||||++|||+||||||
T Consensus 72 ~~~r~~~~~~LYY~~LE~Il~~E~~r~~~~~ls~LL~~~~FhrsL~ACclEiVl~sy~~~~~~FPwiL~~~~i~~f~f~K 151 (194)
T PF01858_consen 72 AEQRFNLAEKLYYKVLEKILKAEEKRLPTNDLSSLLSQEIFHRSLLACCLEIVLFSYKSVSLSFPWILEVFDIHPFDFYK 151 (194)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHSCSHHHHHHT-HHHHHHHHHHHHHHHHHHTCTSSSSTTHHHHHTT--HHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccHhHHHHHhhhhHHHHHHHHHHHHHHHHHcCCCCCcchHHHHhcCCChhhHhh
Confidence 99999999999999999999999999999999999999999999999999999999999889999999999999999999
Q ss_pred hhhHhhhcCCCCCHHHHHHHHHHHHHHHhhhhccCCCcchHHH
Q 011786 191 VTESFIRHEDSLPRELMRHLNSLEETMLESMVWEKGSSLYNSL 233 (477)
Q Consensus 191 VIE~fIR~e~~LpRelvkHLn~IEE~ILEslAW~~~S~L~~~L 233 (477)
|||+|||||++||||||||||+|||||||||||++|||||++|
T Consensus 152 vIE~~Vr~~~~Lpr~lvkHL~~IEE~iLeslaW~~~S~Lw~~l 194 (194)
T PF01858_consen 152 VIESFVRHEDGLPRELVKHLNSIEEQILESLAWKSDSPLWEML 194 (194)
T ss_dssp THHHHHHH-TT--HHHHHHHHHHHHHHHHTGGGSTT-THHHHH
T ss_pred HHHHHHHccccCCHHHHHHHHHHHHHHHHHHHhcCCChhhhhC
Confidence 9999999999999999999999999999999999999999875
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=3.6e-54 Score=388.35 Aligned_cols=125 Identities=36% Similarity=0.596 Sum_probs=106.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCchhHHHHHHHHHHHHhcCCCcCHHHHH
Q 011786 353 AAVTFLFNKMTKLGAVRINSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEIT 432 (477)
Q Consensus 353 ~sl~lFfrKvy~LAa~RL~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~icKv~k~~~tFk~Ii 432 (477)
++|++||||||+||++||++||++|+++++++++|||+|||+|.|+|+||+|||||||||||||++|||++.++||++||
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 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCCCCCCcceeeEEeccccccC-----CCccccccccccccccccC
Q 011786 433 DNYVKEPQCRSQDFGFVFAGWLSKHK-----GKNRENYKSIDAFYNKYSF 477 (477)
Q Consensus 433 ~~Yr~QPqa~~~Vyr~Vli~~~~~~~-----g~~~~e~~DII~FYN~VFv 477 (477)
++||+|||++++|||+|+|+..+.+. ...++++||||+|||+|||
T Consensus 81 ~~Yr~qpq~~~~Vyr~V~i~~~~~~~~~~~~~~~~~~~gDII~FYN~vFv 130 (135)
T PF01857_consen 81 KAYRKQPQASSHVYRSVLIRSRSDNRNNDSGERSEEERGDIIKFYNKVFV 130 (135)
T ss_dssp HHHTTSTT--THHHHSEEESS--------------SEEE-HHHHHHHTHH
T ss_pred HHHHhcccccccceEEEEECCcccccccccccccCCCCCCeeeeehHhHH
Confidence 99999999999999999998754321 1346899999999999996
No 4
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=97.67 E-value=0.00018 Score=73.76 Aligned_cols=73 Identities=16% Similarity=0.313 Sum_probs=65.0
Q ss_pred HHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCchhHHHHHHHHHHHHhcCCCcCHHHHHHHHh
Q 011786 362 MTKLGAVRINSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEITDNYV 436 (477)
Q Consensus 362 vy~LAa~RL~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~icKv~k~~~tFk~Ii~~Yr 436 (477)
.+.-|...|+++|++|+|++.+.+..-.+|..+..+ .++++|.++.++.+|+|+.||..+..+||+||...-+
T Consensus 121 ~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~--~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~ 193 (310)
T PRK00423 121 NLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEK--GLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSR 193 (310)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhc--CcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhC
Confidence 456688999999999999999999999999888765 7899999999999999999999999999999976543
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=97.59 E-value=0.00033 Score=56.28 Aligned_cols=63 Identities=19% Similarity=0.369 Sum_probs=53.0
Q ss_pred HHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCchhHHHHHHHHHHHHhcCCCcCHHHHHHH
Q 011786 370 INSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEITDN 434 (477)
Q Consensus 370 L~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~icKv~k~~~tFk~Ii~~ 434 (477)
|..+|++|+|++++.+..-.+++.+.. ..+.++|..+-|.-.|+|..|+.++..+|++||-+.
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 568999999999998888777777644 479999999999999999999999999999999765
No 6
>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=96.92 E-value=0.0038 Score=49.13 Aligned_cols=63 Identities=14% Similarity=0.148 Sum_probs=54.5
Q ss_pred HHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCchhHHHHHHHHHHHHhcCCCcCHHHHHHH
Q 011786 370 INSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEITDN 434 (477)
Q Consensus 370 L~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~icKv~k~~~tFk~Ii~~ 434 (477)
|..+|+++++++++....|.+++..+.. ..+++ ++...|..+|+|.-||+...+.+.++|...
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 6789999999999999999999999885 34444 999999999999999999887777777544
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=96.69 E-value=0.012 Score=46.61 Aligned_cols=70 Identities=14% Similarity=0.136 Sum_probs=60.2
Q ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCchhHHHHHHHHHHHHhcCCCcCHHHHHHHHhc
Q 011786 366 GAVRINSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEITDNYVK 437 (477)
Q Consensus 366 Aa~RL~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~icKv~k~~~tFk~Ii~~Yr~ 437 (477)
+...|+.+|+.++++.+.....|.+|+..+... .+.+++...|.++|+|.-||+.+...+.+++...-..
T Consensus 5 ~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~ 74 (88)
T cd00043 5 PLDFLRRVAKALGLSPETLTLAVNLLDRFLLDY--SVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGY 74 (88)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhc--ccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCC
Confidence 456688999999999999999999999988753 3559999999999999999999988899988766543
No 8
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=96.14 E-value=0.021 Score=57.97 Aligned_cols=72 Identities=19% Similarity=0.421 Sum_probs=59.7
Q ss_pred HHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCchhHHHHHHHHHHHHhcCCCcCHHHHHHH
Q 011786 361 KMTKLGAVRINSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEITDN 434 (477)
Q Consensus 361 Kvy~LAa~RL~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~icKv~k~~~tFk~Ii~~ 434 (477)
+++..|..-+..+|++|+|+.-+..+.-.+|+.+ +...++++|..|-|.--|+|+-|+=.++..|||||-..
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 3567799999999999999987665555555533 36679999999999999999999999999999999544
No 9
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=95.68 E-value=0.031 Score=57.53 Aligned_cols=62 Identities=11% Similarity=0.091 Sum_probs=55.4
Q ss_pred HHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCchhHHHHHHHHHHHHhcCCCcCHHHHHH
Q 011786 370 INSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEITD 433 (477)
Q Consensus 370 L~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~icKv~k~~~tFk~Ii~ 433 (477)
+..+|++|+|+.++.+..|.+++.+.. ..|..+|+..-|.-.|||..|++.+..+|++||-.
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 347899999999999999999998764 57999999999999999999999999899998844
No 10
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=91.96 E-value=0.86 Score=46.65 Aligned_cols=77 Identities=18% Similarity=0.303 Sum_probs=64.3
Q ss_pred HHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCchhHHHHHHHHHHHHhcCCCcCHHHHHHHHhcCC
Q 011786 361 KMTKLGAVRINSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEITDNYVKEP 439 (477)
Q Consensus 361 Kvy~LAa~RL~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~icKv~k~~~tFk~Ii~~Yr~QP 439 (477)
+-+..|..-|..+|..|+|+..+++..-.++.-+ ..-.|.++|-+-.++--|+|+.|+..+...|+++|....+-.+
T Consensus 95 rnl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a--~~~~l~rGRsie~v~AA~iY~acR~~~~prtl~eIa~a~~V~~ 171 (285)
T COG1405 95 RNLITALEELERIASALGLPESVRETAARIYRKA--VDKGLLRGRSIESVAAACIYAACRINGVPRTLDEIAKALGVSK 171 (285)
T ss_pred hHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHH--hhcCCCcCCcHHHHHHHHHHHHHHHcCCCccHHHHHHHHCCCH
Confidence 4445688889999999999998876655544444 4568999999999999999999999999999999999887544
No 11
>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=87.32 E-value=4.6 Score=34.83 Aligned_cols=70 Identities=20% Similarity=0.299 Sum_probs=55.6
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCchhHHHHHHHHHHHHhcCC-CcCHHHHHHH
Q 011786 363 TKLGAVRINSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINKL-KLKFEEITDN 434 (477)
Q Consensus 363 y~LAa~RL~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~icKv~k~-~~tFk~Ii~~ 434 (477)
-..+...+..+|..++++++.....+.+|+..+.... +...++..|.++|+|+-||+... ..+.++++..
T Consensus 31 r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~--~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~ 101 (127)
T PF00134_consen 31 RQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRP--VNRSKLQLIALACLFLASKMEEDNPPSISDLIRI 101 (127)
T ss_dssp HHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS---TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHH
T ss_pred HHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcc--cccchhhhhhhhHHHHhhhhhccccchHHHHHHH
Confidence 3446667888999999999999999999998887664 88899999999999999999876 4566666554
No 12
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=79.80 E-value=8.2 Score=39.97 Aligned_cols=67 Identities=13% Similarity=0.391 Sum_probs=49.5
Q ss_pred HHHHHHHHHHcC--CChHHHHHHHHHHHHHHhhhhhccccCchhHHHHHHHHHHHHhcCCCcCHHHHHHHH
Q 011786 367 AVRINSMAERLK--LSQQIREKTYLLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEITDNY 435 (477)
Q Consensus 367 a~RL~~LC~~L~--ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~icKv~k~~~tFk~Ii~~Y 435 (477)
...|+++|.+|+ +++++..-.=..|.-....+ . +++-|.-.|++.|+|.-||+....++-.++...-
T Consensus 60 ~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~-S-v~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~ 128 (305)
T TIGR00569 60 EKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNN-S-VMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNL 128 (305)
T ss_pred HHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccC-c-hhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhc
Confidence 357889999999 99876555555555433322 3 4467999999999999999998777777666543
No 13
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=57.92 E-value=36 Score=37.73 Aligned_cols=61 Identities=18% Similarity=0.282 Sum_probs=49.5
Q ss_pred HHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCchhHHHHHHHHHHHHhcC
Q 011786 359 FNKMTKLGAVRINSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINK 423 (477)
Q Consensus 359 frKvy~LAa~RL~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~icKv~k 423 (477)
.+++|. |-..|.+++.+|+|.+ ..+-+..-|+-++.+ .+-++|----+|--|+|++|+..+
T Consensus 64 ~~t~~n-~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~--nftkGr~~~~vvasClY~vcR~e~ 124 (521)
T KOG1598|consen 64 EKTIYN-ARRLIEELTERLNLGN-KTEVAFNFFKLAPDR--NFTKGRRSTEVVAACLYLVCRLEK 124 (521)
T ss_pred HHHHHH-HHhHHHHHHHhcCcch-HHHHHHHHHHHHhhC--CCCCCcchHHHHHHHHHHHHHhhC
Confidence 445554 7889999999999988 666666666666643 677999999999999999999877
No 14
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=43.28 E-value=46 Score=34.90 Aligned_cols=67 Identities=22% Similarity=0.369 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCchhH--HHHHHHHHHHHhcCCCcCHHHHHHH-Hh
Q 011786 366 GAVRINSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRHIDL--IILCCFCGVAKINKLKLKFEEITDN-YV 436 (477)
Q Consensus 366 Aa~RL~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQ--iiLCaiY~icKv~k~~~tFk~Ii~~-Yr 436 (477)
++.=|.+|+.+|+++..-..-.-+.|......+ .-+.-|- +-++|+|.-+||....++.+|||.. ||
T Consensus 42 ~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~----s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~ 111 (323)
T KOG0834|consen 42 GAKFIQELGVRLKMPQKTIATAIVIFHRFYMFH----SFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYR 111 (323)
T ss_pred HHHHHHHHHHHcCCCccchhhhhhhhhhhhhhc----ccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHH
Confidence 445589999999998754222222333222211 2233333 8899999999999999999999975 44
No 15
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=37.56 E-value=1.1e+02 Score=31.67 Aligned_cols=63 Identities=14% Similarity=0.126 Sum_probs=48.7
Q ss_pred HHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCchhHHHHHHHHHHHHhcCCCcCHHHHHHH
Q 011786 370 INSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEITDN 434 (477)
Q Consensus 370 L~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~icKv~k~~~tFk~Ii~~ 434 (477)
+...|..|+|+.+..+-.=...|-+ ++-++..+|.-.-|.--+||.++.+..+..+-+||.+.
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 3457999999987665444333332 45678889999999999999999999988888887653
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=36.78 E-value=44 Score=27.07 Aligned_cols=30 Identities=13% Similarity=0.099 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHhc-CCCcCHHHHHHHHhcC
Q 011786 409 LIILCCFCGVAKIN-KLKLKFEEITDNYVKE 438 (477)
Q Consensus 409 QiiLCaiY~icKv~-k~~~tFk~Ii~~Yr~Q 438 (477)
+|+|||+=...+-+ ..+.+|.+|.+.|+..
T Consensus 5 Kl~L~Al~~~~~~~~~~~~~~~~vy~~Y~~~ 35 (87)
T cd08768 5 KLVLLALLLLFKRGGEEEATTGEVYEVYEEL 35 (87)
T ss_pred HHHHHHHHHHHhcCCCCCccHHHHHHHHHHH
Confidence 78999998888766 4579999999999975
No 17
>PF07340 Herpes_IE1: Cytomegalovirus IE1 protein; InterPro: IPR010855 Expression from a human cytomegalovirus early promoter (E1.7) has been shown to be activated in trans by the IE2 gene product. Although the IE1 gene product alone had no effect on this early viral promoter, maximal early promoter activity was detected when both IE1 and IE2 gene products were present []. The IE1 protein from cytomegalovirus is also known as UL123.; GO: 0050792 regulation of viral reproduction, 0042025 host cell nucleus
Probab=35.67 E-value=5.9e+02 Score=27.43 Aligned_cols=72 Identities=15% Similarity=0.251 Sum_probs=49.0
Q ss_pred chHHHHHHHHHHHHHHHHHhcCCCcchh--------HHHHhhCCCceehhhhhhHhhhcCCCCCH---HHHHHHHHHHHH
Q 011786 148 NEKFHRCMLACSAELVSMARTRVSILFP--------LILERAGITAFDMCKVTESFIRHEDSLPR---ELMRHLNSLEET 216 (477)
Q Consensus 148 ~e~FhrsLlACclEiVl~~y~~~~~~FP--------wiL~~~~i~afdf~KVIE~fIR~e~~LpR---elvkHLn~IEE~ 216 (477)
+|.--|+.++|--=+|++..+ +.|| +++-.-+++-+|---|++.-.+--..|-. ++.=|++.+=-.
T Consensus 199 ddL~~k~~Yt~~Ky~e~~mk~---~~~PKttn~~sQA~~fL~nlp~~d~d~v~~~g~~iik~LD~Eq~~Vl~~id~~f~~ 275 (392)
T PF07340_consen 199 DDLKRKCTYTCLKYIEMFMKN---LCMPKTTNGQSQAKAFLRNLPQCDPDEVNEYGQKIIKTLDKEQKEVLFHIDNVFMD 275 (392)
T ss_pred HHHHHHHHHHHHHHHHHHHcc---CCCCCCcccHHHHHHHHhccccCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence 667778899999989999875 4677 45555677777766666554433344444 444588887777
Q ss_pred HHhhhh
Q 011786 217 MLESMV 222 (477)
Q Consensus 217 ILEslA 222 (477)
||++.+
T Consensus 276 ll~~~~ 281 (392)
T PF07340_consen 276 LLTTCV 281 (392)
T ss_pred HHHHHH
Confidence 888763
No 18
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=35.06 E-value=50 Score=38.71 Aligned_cols=54 Identities=7% Similarity=0.118 Sum_probs=44.0
Q ss_pred HHHHHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCchhHHHHHHHHHHHHhcC
Q 011786 367 AVRINSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINK 423 (477)
Q Consensus 367 a~RL~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~icKv~k 423 (477)
..++..+|..|.++++.....|..|.++-...+-=+- -+..+.||+|..||.+.
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 5677889999999999988999999988665443333 56689999999999984
No 19
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=27.36 E-value=2.2e+02 Score=29.35 Aligned_cols=61 Identities=15% Similarity=0.126 Sum_probs=49.6
Q ss_pred HHHHHHHcCCChHHHHHHHHHHHHHHhhhhhccccCchhHHHHHHHHHHHHhcCCCcCHHHHH
Q 011786 370 INSMAERLKLSQQIREKTYLLFRQILVEKTYLFFNRHIDLIILCCFCGVAKINKLKLKFEEIT 432 (477)
Q Consensus 370 L~~LC~~L~ls~~l~~kIWt~fe~~L~~~t~Lm~dRHLDQiiLCaiY~icKv~k~~~tFk~Ii 432 (477)
+..+|+.|+|+++...++=.+++.+... .+.-+|+-.-|---|+|..+++.+..+|=++|-
T Consensus 198 i~rf~s~L~l~~~v~~~a~ei~~~~~~~--g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva 258 (285)
T COG1405 198 IPRFASKLGLSDEVRRKAIEIVKKAKRA--GLTAGKSPAGLAAAAIYLASLLLGERRTQKEVA 258 (285)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHh--CcccCCCchhHHHHHHHHHHHHhCCchHHHHHH
Confidence 4478999999999988888888876543 444499999999999999999999766666653
No 20
>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=24.93 E-value=13 Score=31.52 Aligned_cols=32 Identities=25% Similarity=0.517 Sum_probs=19.9
Q ss_pred CCHHHHHHHHHHHHHHHhhhhccCCCcchHHHH
Q 011786 202 LPRELMRHLNSLEETMLESMVWEKGSSLYNSLI 234 (477)
Q Consensus 202 LpRelvkHLn~IEE~ILEslAW~~~S~L~~~L~ 234 (477)
||+.++.||.--|.|.+| ++|...+|.|=+..
T Consensus 18 Lp~~l~~~L~L~q~qAvE-vsWg~~~pvfLSW~ 49 (87)
T PF09263_consen 18 LPSRLASQLHLQQNQAVE-VSWGHQSPVFLSWV 49 (87)
T ss_dssp E-HHHHHHTT--TT--EE-EESSS---EEE-EE
T ss_pred CCHHHHHHHHHhhCceEE-EEeCCCCcEEEEee
Confidence 899999999999999998 78999999875443
No 21
>PRK09239 chorismate mutase; Provisional
Probab=23.55 E-value=1.3e+02 Score=26.31 Aligned_cols=36 Identities=14% Similarity=0.236 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHH-HHHhhhhhc
Q 011786 366 GAVRINSMAERLKLSQQIREKTYLLFR-QILVEKTYL 401 (477)
Q Consensus 366 Aa~RL~~LC~~L~ls~~l~~kIWt~fe-~~L~~~t~L 401 (477)
-..|++.++..++|++++.+.||..+- +++.++...
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 345778888999999999999997654 777776653
No 22
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=23.51 E-value=2.3e+02 Score=22.59 Aligned_cols=36 Identities=14% Similarity=0.216 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHhCCCCCCCcHHHHHHHhhCCCChHHHHHH
Q 011786 37 QNTASNWLKTVIAPLPSKPSAELEKFLSLGSVSIANEVES 76 (477)
Q Consensus 37 ~~s~~~~L~~~l~~~~~~PS~~L~~~f~sC~~dp~~~i~~ 76 (477)
-.++ +-|+.++.+ .+-++....|..|..||-+.+.+
T Consensus 6 rk~V-Q~iKEiv~~---hse~eIya~L~ecnMDpnea~qr 41 (60)
T PF06972_consen 6 RKTV-QSIKEIVGC---HSEEEIYAMLKECNMDPNEAVQR 41 (60)
T ss_pred HHHH-HHHHHHhcC---CCHHHHHHHHHHhCCCHHHHHHH
Confidence 3455 666777643 57789999999999999988844
No 23
>PF08630 Dfp1_Him1_M: Dfp1/Him1, central region; InterPro: IPR013939 This region, together with the C-terminal zinc finger (IPR006572 from INTERPRO) is essential for the mitotic and kinase activation functions of Dfp1/Him1 []. ; PDB: 3OQ0_J 3OQ4_D 3QBZ_A.
Probab=23.09 E-value=30 Score=31.38 Aligned_cols=34 Identities=35% Similarity=0.504 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHh---------cccCCCchhhhccchHHHH
Q 011786 119 LKLYYKVLESICASEA---------GKSSSRDLSGLLTNEKFHR 153 (477)
Q Consensus 119 ~~LYYkvLE~Il~~E~---------~rl~~~~ls~LL~~e~Fhr 153 (477)
+|| .|+|++++..+. +.....+|+.||.+|..|-
T Consensus 18 eKl-~r~L~~l~~~~~~~~~~~~~~~~~~~~~L~~LL~~Ek~~G 60 (125)
T PF08630_consen 18 EKL-QRFLKNLLDPDSPDEASSARTKGTPEPDLSQLLQNEKLHG 60 (125)
T ss_dssp HHH-HHHHHHTT--CHHHHHS---SSTT---HHHHHHHHH----
T ss_pred HHH-HHHHHHhCCCCcccccccccccCCCcchHHHHHHhhhhhC
Confidence 455 577777776665 2244669999999999864
No 24
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=20.53 E-value=1.8e+02 Score=30.77 Aligned_cols=19 Identities=21% Similarity=0.307 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHcCCCh
Q 011786 363 TKLGAVRINSMAERLKLSQ 381 (477)
Q Consensus 363 y~LAa~RL~~LC~~L~ls~ 381 (477)
+.||-++...+|+.|+.+.
T Consensus 28 ~sla~~avaQIcqslg~~~ 46 (353)
T KOG2389|consen 28 FSLARVAVAQICQSLGYSS 46 (353)
T ss_pred HHHHHHHHHHHHHhcCCcc
Confidence 4778899999999998764
Done!