Query 001866
Match_columns 1002
No_of_seqs 187 out of 299
Neff 6.2
Searched_HMMs 46136
Date Thu Mar 28 11:08:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001866.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001866hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5113 UFD2 Ubiquitin fusion 100.0 2E-161 5E-166 1348.5 58.1 871 11-990 3-893 (929)
2 KOG2042 Ubiquitin fusion degra 100.0 8E-151 2E-155 1346.3 53.0 847 39-990 51-909 (943)
3 PF10408 Ufd2P_core: Ubiquitin 100.0 4E-150 9E-155 1360.2 56.7 606 266-936 1-629 (629)
4 KOG4692 Predicted E3 ubiquitin 97.2 0.045 9.8E-07 61.1 20.9 265 593-885 19-325 (489)
5 PF04564 U-box: U-box domain; 97.2 9.8E-05 2.1E-09 65.7 0.1 43 951-994 1-47 (73)
6 smart00504 Ubox Modified RING 54.1 6.2 0.00014 33.4 1.1 39 954-993 1-42 (63)
7 KOG4642 Chaperone-dependent E3 47.1 26 0.00056 38.6 4.5 45 949-993 206-253 (284)
8 PRK09458 pspB phage shock prot 28.5 1.4E+02 0.003 27.2 5.3 36 918-953 35-71 (75)
9 cd04790 HTH_Cfa-like_unk Helix 27.3 1.7E+02 0.0036 30.6 6.7 87 897-992 35-134 (172)
10 PF12726 SEN1_N: SEN1 N termin 25.4 1.5E+03 0.033 28.9 18.9 79 683-769 229-308 (727)
11 PF11672 DUF3268: Protein of u 25.3 1.1E+02 0.0023 29.4 4.4 42 313-354 58-100 (102)
12 PF11635 Med16: Mediator compl 22.5 2.1E+02 0.0045 36.9 7.6 175 802-992 465-679 (753)
No 1
>COG5113 UFD2 Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.1e-161 Score=1348.51 Aligned_cols=871 Identities=21% Similarity=0.309 Sum_probs=775.3
Q ss_pred HHHHHHHHHHhhhhhccCCcCCCCCCeeehhhhHHHHhhcCCccccChhhhhHHHHHHHhCCCCCCCChhhHHHHHHH-H
Q 001866 11 EEIEDIILRKIFLVTLNEATTDADPRIAYLELTAAELLSEGKDMRLSRDLMERVLVDRLSGNFPAAEPPFLYLINCYR-R 89 (1002)
Q Consensus 11 ~~~~~~~l~~if~vtl~~~~~~~~~~~~~L~~~~~el~~~~~~~~l~~d~ld~~l~~rl~~~~~~~~~~~~YL~~c~~-R 89 (1002)
.+|.+++-..+++||.+|+ +.+-++| +.+++..+|.+ |..+.+|.+|+.+|+... ..+|.||.+||+ +
T Consensus 3 ~~~M~~ie~~~l~it~~p~----D~~~y~l--fk~~e~~~gS~--l~~n~~d~~LL~~l~~~~---nn~fsYl~~s~~fl 71 (929)
T COG5113 3 YPGMNRIELYELFITGMPA----DMDPYEL--FKEAECIRGSY--LTNNSSDNILLTLLPRYK---NNTFSYLQESAKFL 71 (929)
T ss_pred CcccchhhhhhhhcccCcc----ccchhhh--cchhhccccCc--cccccHHHHHHHHccccC---CCchHHHHHHHHHH
Confidence 4699999989999999998 4455777 45555566664 677799999999999863 788999999999 5
Q ss_pred HHHHHHhhcCCCccchhhHHHHHHHHHHHHHHhhhHHhhcCCcccCCCCCCcccccccCCCCCCCCchHHHHhhcCCCCC
Q 001866 90 AHDELKKIGNMKDKNLRSELEAVVKQAKKMIVSYCRIHLANPDFFGSNNDNNYEINNSNNKSSISPLLPFIFAEVGGGID 169 (1002)
Q Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~l~~i~~l~vsy~~~~l~~Pd~F~~~~~~~~~~~~~~~~~~~~~ll~~~l~~~~~~~~ 169 (1002)
.+..+|.. + .+.......+-++.|.+++++|+|.+..+||-|.... ..++.-|...
T Consensus 72 ~q~~kri~-k--n~~~a~s~hs~~~li~~l~~~y~g~v~~~~e~FN~e~---------------i~~ieg~~~~------ 127 (929)
T COG5113 72 IQTIKRIV-K--NPEMAGSAHSPVALIPLLTNTYGGSVFDVMECFNSEK---------------ISEIEGMARK------ 127 (929)
T ss_pred HHHHHHhc-C--CccccccccchHHHHHHHHhhccceEeehHhhcchhH---------------HHHHHHHHHh------
Confidence 55554443 3 2333345566889999999999999999999993211 1112122221
Q ss_pred CCCCCCCCCCCCChHHHHHHHHh--hccCChHHHHHHHHHHHHHHhhccCcccccchHHHHHHHhhCChhHHHHhhcCCC
Q 001866 170 GFGNSTSSGSQCPPGFLKEFFEE--ADFDTLDPILKGLYENLRGSVLNVSALGNFQQPLRALLYLVSFPVGVKSLVNHQW 247 (1002)
Q Consensus 170 ~~~~s~~~~~~~~~~Fl~eli~~--~~~d~~~~if~~i~~~l~~~~~~~s~~~~~~~~l~~l~~L~~~k~ia~~l~~~~~ 247 (1002)
- .+|-.|+.+++.| ++..+++..|.++++.+....+.+........++.+...|++.||||.++.+.|.
T Consensus 128 -------~--~~p~~fls~f~qr~l~e~~nld~lF~~~LE~l~~~~g~~~~dtV~~NVm~I~~~lv~~kPia~v~~k~p~ 198 (929)
T COG5113 128 -------M--LLPMIFLSSFKQRQLDEASNLDNLFTSALEALTGLHGVLEEDTVLKNVMEIYWGLVNTKPIADVILKFPI 198 (929)
T ss_pred -------c--ccHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHhhhcccchHHHHHHHHHHHHHHHhcCccHHHHhhcCcc
Confidence 1 1577999999999 4666699999999999988777666533345589999999999999999999999
Q ss_pred CCCCccCCCcchhhhhcccccccccCCCCCCccccCCChhhhhccCCCcCCChhhHHhHHHHHHHHHHHHHHHHHHHHHH
Q 001866 248 WIPKSVYLNGRVIEMTSILGPFFHVSALPDHAIFKSQPDVGQQCFSEASTRRPADLLSSFTTIKTVMRGLYKDLGDVLLA 327 (1002)
Q Consensus 248 f~p~~~~~~G~~~E~~SlLGp~l~lS~l~~~~~f~~~p~v~~~~F~~~~~~~~~~i~~~~~slr~~l~~~~~~L~~I~~~ 327 (1002)
|.|.. .+.+||.+|+|||+.++|++ .-+||-.+|++...|+.+.+..+..+||.++..+++.||+|+++
T Consensus 199 ~~~t~---~p~~fe~kt~lG~i~sls~~--------~~dvA~r~~~~~~~rs~q~v~~s~~Sl~~t~s~~~d~lfqIi~~ 267 (929)
T COG5113 199 YSGTN---FPCGFEYKTLLGFIESLSYK--------KCDVAARALDYLGIRSRQVVEKSRRSLRLTLSDHSDKLFQIIHS 267 (929)
T ss_pred cCCCC---CCCCCcceeecccccccchh--------hhhhhhhhccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99864 33479999999999999999 45788999999999999999999999999999999999999999
Q ss_pred Hhc-ChhhHHHHHHHHHHHHHhchhhhhcccCCCccCChhhHHHHHHHHHHhhhhhcCCCccCcCccCccCcccCCCcCC
Q 001866 328 LLK-NTDTRENVLEYLAEVINRNSSRAHIQVEPLSCASSGMFVNLSAVMLRLCDPFLDANLTKRDKIDPKYVFYSSRLDL 406 (1002)
Q Consensus 328 Llr-~~~sRe~vL~w~a~vl~~N~~R~k~~~d~~~~aSDGFmlNl~~VLlrL~~PF~d~~~~KidkID~~Y~~~~~~vdi 406 (1002)
|+| |.+.|+.+++|||+|+|+||+|++.+++.+...|||||.|++.||.||++||+|.+++|||+||..|++ ++|||+
T Consensus 268 lvr~S~~lr~~~~~yfa~v~n~nh~R~~~~~~~~e~~Sdgfm~N~s~vlsRfs~pflDi~~sKID~vd~~YFn-NP~vDi 346 (929)
T COG5113 268 LVRSSKELRANFMKYFAKVINVNHERSKTIFSWRENISDGFMYNMSMVLSRFSRPFLDIGCSKIDMVDKIYFN-NPRVDI 346 (929)
T ss_pred HHhccHHHHHHHHHHHHHHhccchhhccccCCHhhhcchHHHHHHHHHHHHhcccccccccchhhhHhHHhhc-CCcccc
Confidence 999 789999999999999999999999999999999999999999999999999999999999999999999 779999
Q ss_pred CccccccCCHHHHHHHHhcCCCCCCCCCCCCCcchhhhhhhhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCcchhHHH
Q 001866 407 RSLTALHASSEEVSEWINKGNPAKADGSKHFSDGENQLLQSQEATSSSGGASEPSLPAGRPASIGGGKSKYPFICECFFM 486 (1002)
Q Consensus 407 ~~eTri~a~~~e~~~~~~~~~p~~~~~~~~~~~~e~~~l~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~nFItecFFL 486 (1002)
++|||+|+|+.+++.||.+ | .++.+||||+||||
T Consensus 347 k~ETklN~d~k~~dsFy~K--~--------------------------------------------Ae~s~NFISD~FFl 380 (929)
T COG5113 347 KEETKLNVDEKSLDSFYTK--P--------------------------------------------AEGSNNFISDIFFL 380 (929)
T ss_pred ccchhcchhhhhhhccccC--c--------------------------------------------cccCCccchhhHHh
Confidence 9999999999999999963 1 46688999999999
Q ss_pred HHHHHHhchHHHHHHHHHHHHHHHHHHHHHHHHHhhcC-CCCchHHHHHHHHHHHHHHHHHHhHHHHhhhhccChHHHHH
Q 001866 487 TARVLNLGLLKAFSDFKHLVQDISRAEDTLATLKATQG-QTPSSQLNLEITRIEKEIELSSQEKLCYEAQILRDGDLIQH 565 (1002)
Q Consensus 487 T~~~lhlG~~~~~~~~~~l~r~i~~~~~~l~~~~~~~~-~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~L~dp~l~~~ 565 (1002)
++..+|||+++++.--+++.+.|+.++++++.-..... .-...++.+++.|+++.++...+...|+++ .|...++..+
T Consensus 381 ~lt~~HyGv~~tf~~~ek~g~~IrkLKE~le~e~~~~~gs~~At~lTaqlsrme~~lk~~~S~~~al~g-fl~~tsl~~~ 459 (929)
T COG5113 381 YLTKIHYGVNATFTSCEKFGEYIRKLKESLEYECRLLDGSFQATRLTAQLSRMEAYLKGIDSKMSALNG-FLFMTSLFAD 459 (929)
T ss_pred HHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHhcCchhhhhHHhHHHHHHHHHhhhHHHHHHHHH-HHHHhhhhhh
Confidence 99999999999999999999999988887765332111 111334678899999999999999999999 8999999999
Q ss_pred HHHHHHHHHHHHHHHhcC--------CcCCCCCCCCcccccchhHHHHhHHHHHHHHhhc--CccccccchHHHHHHHHH
Q 001866 566 ALSFYRLMIVWLVDLVGG--------FKMPLPDTCPMEFACMPEHFVEDAMELLIFASRI--PKALDGVLLDDFMNFIIM 635 (1002)
Q Consensus 566 ~~~F~~~~~~wL~~l~~~--------~~lPLp~~~p~~f~~lPE~~iEdi~d~~~f~~r~--p~~l~~~~~~~l~~f~i~ 635 (1002)
.+.|.++++.||.|+++| .++|+-+.+|.+|+|+|||+||++++|..++.+. .+++- ..++++++||++
T Consensus 460 ~f~F~~f~t~~l~rv~dp~~typf~~~~Lp~~ENap~~fk~~pe~~ie~~~ny~l~~~k~~~Spif~-~~L~~l~Ef~~~ 538 (929)
T COG5113 460 EFPFTDFMTEYLARVEDPWPTYPFYYKTLPWMENAPMTFKLIPEATIENALNYVLESIKDWRSPIFK-KELEPLCEFVKI 538 (929)
T ss_pred ccchHHHHHHHHHHhcCCCCCCCccccccchhcCCcchhhhchHHHhccHHHHHHHHHhcccCchhh-ccccchhhhhhh
Confidence 999999999999999987 4567778899999999999999999999999887 44433 338999999999
Q ss_pred HhCCCCCccChhhHhhHHHHHH-hhcCCCCCCchhhHHhhhcchhhHHHHHHHHHHHhhhhhccCCCccchhhhhhhhhH
Q 001866 636 FMASPKYIRNPYLRSKMVEVLN-CWMPRRSGSSSATATLFEGHQMSLEYLVRNLLKLYVDIEFTGSHTQFYDKFNIRHNI 714 (1002)
Q Consensus 636 ~l~s~~~ikNPhLraklvevL~-~~~p~~~~~~~~~~~lf~~~~la~~~L~~aLm~fYidvE~TG~~~qFYdKFn~R~~I 714 (1002)
++++|++||||||++|++++|+ +.+|....++|.+.++|...+++.++|+||||.|||+||+||+|+|||||||+||.|
T Consensus 539 vl~~~~~iknp~L~~kl~~~ls~G~~~~~~~s~~~~~dif~~~kv~~r~LL~ALmaFYi~iEsTGqStqfydkfNirf~i 618 (929)
T COG5113 539 VLHRSSAIKNPMLNRKLDYYLSLGRDEMRMESRSIIHDIFKEGKVFSRWLLPALMAFYIEIESTGQSTQFYDKFNIRFII 618 (929)
T ss_pred hcccHhhhccHHHHHHHHHHHhcCcchhccCchHHHHHHHHhhhhhhhhhHHHHHhHheeeeccCcccceeeeccceeeh
Confidence 9999999999999999999997 577776666789999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCChhhHHHHHHHHHhhccchhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhccchhhcCCCHHHHHHHHH
Q 001866 715 AELLEYLWQVPSHRNAWRQIAKEEEKGVYLNFLNFLINDSIYLLDESLNKILELKVIEAEMSNTAEWERRPAQERQERTR 794 (1002)
Q Consensus 715 ~~Ilk~LW~~~~yr~~l~~~a~~~~~~~FvrFvnlLiND~tfLLDE~L~~L~~I~~~q~e~~d~~~w~~l~~eer~e~~~ 794 (1002)
+.+++.+|+.|.|.+++.++.+.| -++||||...|+||+||||||++.+|.++|++|.+++|....+ ...|+-+|.+.
T Consensus 619 c~~~~~~yK~Psy~~~L~~~~~tN-~~FFVkfda~mlndlt~lLDEal~~l~E~hniqs~Lad~~s~s-n~~e~~~elq~ 696 (929)
T COG5113 619 CMMKDFEYKQPSYSEGLSSIKDTN-LPFFVKFDAKMLNDLTRLLDEALKELVEEHNIQSLLADAISNS-NISERIGELQK 696 (929)
T ss_pred hHHHHHHhcCchhhhhhhhhhccC-CchhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhhccC-chhhHHHHHHH
Confidence 999999999999999999998875 8999999999999999999999999999999999999876544 44566788899
Q ss_pred HHHHhhhhhhhhhhcHHHHHHHHHHHHHhccCCCCchHHHHHHHHHHHHHHhhhcCccccCccccCCcccCCChHHHHHH
Q 001866 795 LFHSQENIIRIDMKLANEDVSMLAFTSEQIVAPFLLPEMIERVASMLNYFLLQLVGPQRKSLTLKDPEKYEFRPKQLLKQ 874 (1002)
Q Consensus 795 ~l~~~er~ars~~~La~etv~ml~~~T~~i~~~Fl~peivdRLA~MLNynL~~LvGPk~~~LKVknpekY~F~Pk~LL~~ 874 (1002)
.++.++||||++++|++++++||..++++||++|+.||||+|||+||||||+.||||||.+||||||++|+|+||.||+.
T Consensus 697 ~la~a~rqA~~sc~l~d~~~~lf~~~~~~iP~aF~~~EiV~rla~mLNyNL~~l~GPKC~~LkVkdP~~Y~FnaK~LL~~ 776 (929)
T COG5113 697 SLAFAKRQARNSCLLVDGCFDLFTHILDEIPDAFLVDEIVSRLARMLNYNLKILTGPKCTDLKVKDPEQYGFNAKNLLRR 776 (929)
T ss_pred HHHHHHHhhcchheecccHHHHHHHHhhccchhhhhHHHHHHHHHHHhCcchhccCCCccceeecChhhcCCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcccccccchhhHhhhhCCCCCCHHHHHHHHHHHHHhCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 001866 875 IVCIYVHLARGDTQNLFPAAISSDGRSYNEQLFSAAADVLWKIGE-DGRIIQEFIELGAKAKAAASEAMDAEAALGDIPD 953 (1002)
Q Consensus 875 i~~IYlnL~~~~~~~~F~~AVa~DgRSY~~elF~~A~~il~r~~l-~~~~i~~f~~l~~kv~~~~~~~~~~E~~l~diPD 953 (1002)
++++|+||+. +++||.|||.|||||+.++|.+|++||.++.+ ++.+|+++.+|++|+|+.+..++.||||+|||||
T Consensus 777 ~~~VYinl~~---es~FveaVA~D~rsf~~~~F~rA~~I~~~k~L~s~~~IE~l~~f~nr~E~~r~~ea~EeED~GDvPD 853 (929)
T COG5113 777 MVMVYINLRS---ESKFVEAVASDKRSFDIDFFRRALRICENKYLISESQIEELRSFINRLEKVRVIEAVEEEDMGDVPD 853 (929)
T ss_pred HHHHhhhhcc---hHHHHHHHHcccccccHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCch
Confidence 9999999995 46899999999999999999999999999999 9999999999999999999888899999999999
Q ss_pred cccChhHHHHHH---hhccCcceehhhhHHHhhhhhcccC
Q 001866 954 EFLDPIQVCFTC---LLSSLVRTVLRTMVIVSFVAVHFDE 990 (1002)
Q Consensus 954 EFlDPLM~tlM~---~LPsS~~~vDR~ti~~~~~~~~~~~ 990 (1002)
|||||||+|+|+ +||+|+++||||||++||+.--.||
T Consensus 854 eFlDPLmftimkdPV~Lp~S~i~IDRSTikahllsd~tDP 893 (929)
T COG5113 854 EFLDPLMFTIMKDPVKLPTSRITIDRSTIKAHLLSDGTDP 893 (929)
T ss_pred hhhCchhhhcccCCeecccccccccHHHHHHHHhcCCCCc
Confidence 999999999999 9999999999999999999888887
No 2
>KOG2042 consensus Ubiquitin fusion degradation protein-2 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.4e-151 Score=1346.28 Aligned_cols=847 Identities=36% Similarity=0.556 Sum_probs=720.7
Q ss_pred ehhhhHHHHhhcCCccccChhhhhHHHHHHHhCCCCCCCChhhHHHHHHHHHHHHHHhhcCCCccchhhHHHHHHHHHHH
Q 001866 39 YLELTAAELLSEGKDMRLSRDLMERVLVDRLSGNFPAAEPPFLYLINCYRRAHDELKKIGNMKDKNLRSELEAVVKQAKK 118 (1002)
Q Consensus 39 ~L~~~~~el~~~~~~~~l~~d~ld~~l~~rl~~~~~~~~~~~~YL~~c~~R~~~~~~~~~~~~~~~~~~~~~~~l~~i~~ 118 (1002)
+.+.+..++..+|.+.+++.+ |...+.-..+.+ ....++.|+..||.+.....++...++. + +. .
T Consensus 51 ~~~~~~~~~~~~g~~~~~~~~--~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~p~----------~-~~-~ 115 (943)
T KOG2042|consen 51 SYELFSSDLPADGLSHRFNEA--ESDTLALCTEND-ALNILFIYLYRCKSELSQYKRKECRKPT----------L-EQ-N 115 (943)
T ss_pred HHHhccccccccCCccccchh--hhHHHHhhccch-HHHHHHHHHHHHHHHHHHHhHHHhcCcc----------h-hh-c
Confidence 333344444444555545444 444443343332 3457788999999988766665433211 1 11 4
Q ss_pred HHHhhhHHhhcCCcccCCCCCCcccccccCCCCCCCCchHHHHhhcCCCCCCCCCCCCCCCCCChHHHHHHHHhhccCCh
Q 001866 119 MIVSYCRIHLANPDFFGSNNDNNYEINNSNNKSSISPLLPFIFAEVGGGIDGFGNSTSSGSQCPPGFLKEFFEEADFDTL 198 (1002)
Q Consensus 119 l~vsy~~~~l~~Pd~F~~~~~~~~~~~~~~~~~~~~~ll~~~l~~~~~~~~~~~~s~~~~~~~~~~Fl~eli~~~~~d~~ 198 (1002)
+.++++.++...++.+..+... +. . ..+....++..+. ..|...|..|+.++...++.|.+
T Consensus 116 ~~~~~~~~~~~~~~~l~~~~~~-----~~-~---~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~d~l 176 (943)
T KOG2042|consen 116 LKLAGSSFVMITLGVLAPQLRL-----QP-A---SLQDISGLLELMN----------SEGFARPLLFLLEVTEHFDLDAL 176 (943)
T ss_pred hhhccchheeeehhhccchhhh-----hh-h---hhhhHHHHHHHhh----------hhhcccchhHHHHHhhhhhhHHH
Confidence 6666666666666666532200 00 0 0111111111110 12333567899999999999999
Q ss_pred HHHHHHHHHHHHHHhh--ccCcccccchHHHHHHHhhCChhHHHHhhcCCCCCCCccCCCcchhhhhcccccccccCCCC
Q 001866 199 DPILKGLYENLRGSVL--NVSALGNFQQPLRALLYLVSFPVGVKSLVNHQWWIPKSVYLNGRVIEMTSILGPFFHVSALP 276 (1002)
Q Consensus 199 ~~if~~i~~~l~~~~~--~~s~~~~~~~~l~~l~~L~~~k~ia~~l~~~~~f~p~~~~~~G~~~E~~SlLGp~l~lS~l~ 276 (1002)
+.+|+|+++.+..++. +.+....+..++.++..+++.||+|.+++++|+|.|++ +|++++..|+|||||++|+++
T Consensus 177 ~~if~~vl~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~kp~a~l~~~~~~~~p~~---~g~e~~~~s~LGpfls~S~~~ 253 (943)
T KOG2042|consen 177 DAIFNPVLERLESNLDILKLNVLVLENLVLLILLYFVSTKPIADLLVKLPDFLPPP---CGREFELKSFLGPFLSISCLP 253 (943)
T ss_pred HHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHhcCCCcHHHHHhhccccCCCC---CCcchhhhhhhccceeeeecc
Confidence 9999999977764443 33333456788999999999999999999999999986 799999999999999999999
Q ss_pred CCccccCCChhhhhccCCCcCCChhhHHhHHHHHHHHHHHHHHHHHHHHHHHhc-ChhhHHHHHHHHHHHHHhchhhhhc
Q 001866 277 DHAIFKSQPDVGQQCFSEASTRRPADLLSSFTTIKTVMRGLYKDLGDVLLALLK-NTDTRENVLEYLAEVINRNSSRAHI 355 (1002)
Q Consensus 277 ~~~~f~~~p~v~~~~F~~~~~~~~~~i~~~~~slr~~l~~~~~~L~~I~~~Llr-~~~sRe~vL~w~a~vl~~N~~R~k~ 355 (1002)
.+++ .--.+|...+..+++.+. .+++..++ ....+++|++.+|+ |+++|+++|+|+|.||++|++|+++
T Consensus 254 ~~~~------~~y~~~~e~s~~~~~~~~---~s~~~~~~-~~~~~~~~v~~ll~~s~etr~~~L~~~a~vi~aN~~R~~~ 323 (943)
T KOG2042|consen 254 AAPA------KRYGDFSERSRKNTSEVS---SSLLLYHQ-MDRKMLQIVKHLLRLSPETREKTLSYVANVINANDKRASI 323 (943)
T ss_pred ccch------hhhcccchhhhcchHHHH---HHHHHHHH-HHHHHHHHHHHHHhcChhhHHHHHHHHHHHhhcccccccc
Confidence 7742 112233444444444444 44555555 55899999999999 8999999999999999999999999
Q ss_pred ccCCCccCChhhHHHHHHHHHHhhhhhcCCCccCcCccCccCcccCCCcCCCccccccCCHHHHHHHHhcCCCCCCCCCC
Q 001866 356 QVEPLSCASSGMFVNLSAVMLRLCDPFLDANLTKRDKIDPKYVFYSSRLDLRSLTALHASSEEVSEWINKGNPAKADGSK 435 (1002)
Q Consensus 356 ~~d~~~~aSDGFmlNl~~VLlrL~~PF~d~~~~KidkID~~Y~~~~~~vdi~~eTri~a~~~e~~~~~~~~~p~~~~~~~ 435 (1002)
++|+..++|||||+|+++||+|||+||+|++..|+|||||+|+....+.+..++|+++++.+++. |++
T Consensus 324 ~~~~~~~~sDgfm~Nl~~Vl~rls~p~~~~~~~~~~~~~p~y~~~~~~~~~~~~t~~~~~~~~t~-~~~----------- 391 (943)
T KOG2042|consen 324 QVDPREVASDGFMLNLSAVLSRLSEPFLDPSIKKIDKIDPEYLINISKETRSKETELNADDKETC-FYD----------- 391 (943)
T ss_pred cCCHHHhhchHHHHHHHHHHHHhcccccccccccccccChHHhcCccHhhhhhhhhhccchhhhh-ccC-----------
Confidence 99999999999999999999999999999999999999999999888899999999999988877 773
Q ss_pred CCCcchhhhhhhhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCcchhHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHH
Q 001866 436 HFSDGENQLLQSQEATSSSGGASEPSLPAGRPASIGGGKSKYPFICECFFMTARVLNLGLLKAFSDFKHLVQDISRAEDT 515 (1002)
Q Consensus 436 ~~~~~e~~~l~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~nFItecFFLT~~~lhlG~~~~~~~~~~l~r~i~~~~~~ 515 (1002)
..+++||+|+|||||+++||+|+.+++..|.++.+.|.+++..
T Consensus 392 -------------------------------------~~~~~~F~t~cfFltl~~~~l~~~~~~~~~~~i~~~i~~l~~~ 434 (943)
T KOG2042|consen 392 -------------------------------------KPGEPNFPTECFFLTLAALHLGLLPTCSAFSEINRSLPELKPL 434 (943)
T ss_pred -------------------------------------CCCCCCcchHHHHHHHHHHHhchhHHHHHHHHHHHHhHHHHHH
Confidence 2357899999999999999999999999999999999999999
Q ss_pred HHHHHhhcCCCC-chHHHHHHHHHHHHHHHHHHhHHHHhhhhccChHHHHHHHHHHHHHHHHHHHHhc-C-CcC-CCCCC
Q 001866 516 LATLKATQGQTP-SSQLNLEITRIEKEIELSSQEKLCYEAQILRDGDLIQHALSFYRLMIVWLVDLVG-G-FKM-PLPDT 591 (1002)
Q Consensus 516 l~~~~~~~~~~~-~~~~~~~l~~~~~~~~~l~~~~~~~~~~~L~dp~l~~~~~~F~~~~~~wL~~l~~-~-~~l-PLp~~ 591 (1002)
++..+..+++.. .......+.|++++++.+...+.|+++ .+.+|.+.++++.|+.+++.|+.++++ + ... ++|-.
T Consensus 435 i~~lk~~~d~~~~a~~~~~~l~r~e~~lk~~~~~k~~~~~-~~~~p~l~~~~~~f~~~~s~~l~~~~~~~~~~~~~~p~~ 513 (943)
T KOG2042|consen 435 IETLKVIADGYSVANLESADLTRLEKGLKLLSSIKPCLEI-TLLFPSLLQRCLNFYDFMSEGLLRVVDLEMPDSSTLPLN 513 (943)
T ss_pred HHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHhhhhhhhh-hhcCcHHHHHhhccHHHHHHHHHHHhhccCCcccCCCCC
Confidence 998877655432 234557889999999999999999999 789999999999999999999999997 2 222 45557
Q ss_pred CCcccccchhHHHHhHHHHHHHHhhc-CccccccchHHHHHHHHHHhCCCCCccChhhHhhHHHHHHhhcCCCCCCchhh
Q 001866 592 CPMEFACMPEHFVEDAMELLIFASRI-PKALDGVLLDDFMNFIIMFMASPKYIRNPYLRSKMVEVLNCWMPRRSGSSSAT 670 (1002)
Q Consensus 592 ~p~~f~~lPE~~iEdi~d~~~f~~r~-p~~l~~~~~~~l~~f~i~~l~s~~~ikNPhLraklvevL~~~~p~~~~~~~~~ 670 (1002)
+|..|+|+|||++||+.+|+.|+.++ +..+....++.+++||+.+|++++|+||||||||+||+++ +|....+...+
T Consensus 514 ~p~~f~~lPE~~vedi~efllf~~~~~~~~l~~~~~~~~~~f~~~~~~~~~~ikNP~l~aKlvevl~--~~~~~~s~~~v 591 (943)
T KOG2042|consen 514 APCRFSALPEFFVEDIEEFLLFARKLGKMALDLQRLADIVTFLTVFMTSSMYIKNPYLRAKLVEVLS--MPKPSLSFNAV 591 (943)
T ss_pred CccccccCchhhcCCHHHHHHHHHHhchhhhccccchhHHHHHHHhcccHhhhcChHHHHHHHHHHh--ccCcccCchHH
Confidence 88999999999999999999999999 5667788889999999999999999999999999999999 44444444568
Q ss_pred HHhhhcchhhHHHHHHHHHHHhhhhhccCCCccchhhhhhhhhHHHHHHHHhCChhhHHHHHHHHHhhccchhHHHHHHH
Q 001866 671 ATLFEGHQMSLEYLVRNLLKLYVDIEFTGSHTQFYDKFNIRHNIAELLEYLWQVPSHRNAWRQIAKEEEKGVYLNFLNFL 750 (1002)
Q Consensus 671 ~~lf~~~~la~~~L~~aLm~fYidvE~TG~~~qFYdKFn~R~~I~~Ilk~LW~~~~yr~~l~~~a~~~~~~~FvrFvnlL 750 (1002)
..+|+.++.+. |+|+||+||||||.||+++|||||||+||+|+.|++++|.+|.|+.++.+.++++ ++.|+||+|+|
T Consensus 592 ~~v~~~~~~~~--L~~~llr~yv~ie~tg~s~qfydKfnvr~~i~~i~~~mw~~pa~~~~~~~~~~~~-~~~f~rfvn~l 668 (943)
T KOG2042|consen 592 SRVIEAHENGG--LVPCLLRFYVDIESTGQSSQFYDKFNVRRNISEILEYMWQDPAYRGEFMDEAKDA-PPVFVRFVNML 668 (943)
T ss_pred HHHHHhccccc--cchhhhhheeeeecCCCchhHHHHhHHHhhHHHHHHHHhcCccccchhhhhcccc-chHHHHHHHHH
Confidence 88999888765 9999999999999999999999999999999999999999999999999999876 89999999999
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHhccchhhcCCCHHHHHHHHHHHHHhhhhhhhhhhcHHHHHHHHHHHHHhccCCCCc
Q 001866 751 INDSIYLLDESLNKILELKVIEAEMSNTAEWERRPAQERQERTRLFHSQENIIRIDMKLANEDVSMLAFTSEQIVAPFLL 830 (1002)
Q Consensus 751 iND~tfLLDE~L~~L~~I~~~q~e~~d~~~w~~l~~eer~e~~~~l~~~er~ars~~~La~etv~ml~~~T~~i~~~Fl~ 830 (1002)
+||+||||||++++|.+||++|..++|.++|..++.++|+++.+.+++++|+||+|+.++++|+.||+++|++||++|++
T Consensus 669 ~Nd~t~lLDE~l~~L~~i~~iq~~~kn~~q~~~~~~~~~e~~~~~l~s~~r~art~~~la~et~~ll~~~tk~i~~~Fl~ 748 (943)
T KOG2042|consen 669 LNDATFLLDESLSELMEIHQIQPSGKNIDQWTKLKREEREAKWGRLASDERQARTGLALANETIDLLHLLTKAIPEPFLL 748 (943)
T ss_pred hhhHHHHHhHHHHHhhhhhhhhhhhhhhhhccCCcHHHHHHHHhccccchhhhcccceeccchhhHHHHHHhhcchhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHhhhcCccccCccccCCcccCCChHHHHHHHHHHHHhcccccccchhhHhhhhCCCCCCHHHHHHH
Q 001866 831 PEMIERVASMLNYFLLQLVGPQRKSLTLKDPEKYEFRPKQLLKQIVCIYVHLARGDTQNLFPAAISSDGRSYNEQLFSAA 910 (1002)
Q Consensus 831 peivdRLA~MLNynL~~LvGPk~~~LKVknpekY~F~Pk~LL~~i~~IYlnL~~~~~~~~F~~AVa~DgRSY~~elF~~A 910 (1002)
||+|+|+|+||||||.+||||||++||||||++|+|+||++|++|++||+||++ ++.|+.|||.|||||++++|..|
T Consensus 749 ~elv~rla~MLN~nL~~lvGPK~~~Lkvkdp~~y~fePk~ll~~i~~iYlnl~~---~~~F~~avA~D~RSys~~lF~~a 825 (943)
T KOG2042|consen 749 PELVERLAAMLNYNLSQLVGPKCSDLKVKDPEKYGFEPKQLLSQLSDIYLNLSS---EPSFVEAVAKDGRSYSEELFNHA 825 (943)
T ss_pred hhHHHHHHHHHhhhHHHhhCCcccccccCCccccCCChHHHHHHHHHHHHhhcc---chhHHHHHhccccccCHHHHhhh
Confidence 999999999999999999999999999999999999999999999999999995 35899999999999999999999
Q ss_pred HHHHHHhCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcccChhHHHHHH---hhccCcceehhhhHHHhhhhh
Q 001866 911 ADVLWKIGE-DGRIIQEFIELGAKAKAAASEAMDAEAALGDIPDEFLDPIQVCFTC---LLSSLVRTVLRTMVIVSFVAV 986 (1002)
Q Consensus 911 ~~il~r~~l-~~~~i~~f~~l~~kv~~~~~~~~~~E~~l~diPDEFlDPLM~tlM~---~LPsS~~~vDR~ti~~~~~~~ 986 (1002)
+++++|.++ +..+|++|..||.++++.+..++++|++||||||||+||||+|+|+ .||+|+++|||+||.|||+..
T Consensus 826 ~~~~~k~~l~~~~~Ie~~s~la~~~~~~~~~~~~eee~l~dvpdef~DPlm~Tlm~dPV~LP~Srv~vDRsti~rhlLs~ 905 (943)
T KOG2042|consen 826 ISILRKRILKSSRQIEEFSELAERVEATASIDAEEEEELGDVPDEFLDPLMSTLMSDPVVLPSSRVTVDRSTIERHLLSD 905 (943)
T ss_pred HHHHHHhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCchhhhCccccccCCCCccCCcccccccHHHHHHHHhcC
Confidence 999988888 8889999999999999999999999999999999999999999999 999999999999999999999
Q ss_pred cccC
Q 001866 987 HFDE 990 (1002)
Q Consensus 987 ~~~~ 990 (1002)
..|+
T Consensus 906 ~tdP 909 (943)
T KOG2042|consen 906 CTDP 909 (943)
T ss_pred CCCc
Confidence 9887
No 3
>PF10408 Ufd2P_core: Ubiquitin elongating factor core; InterPro: IPR019474 This entry represents the most conserved part of the core region of ubiquitin conjugation factor E4 (or Ub elongating factor, or Ufd2P), running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C terminus, (IPR003613 from INTERPRO), which has ligase activity. Ubiquitin conjugation factor E4 is involved in N-terminal ubiquitin fusion degradation proteolytic pathway (UFD pathway). E4 binds to the ubiquitin moieties of preformed conjugates and catalyses ubiquitin chain assembly in conjunction with E1, E2, and E3. E4 appears to influence the formation and topology of the multi-Ub chain as it enhances ubiquitination at 'Lys-48' but not at 'Lys-29' of the N-terminal Ub moiety.; GO: 0034450 ubiquitin-ubiquitin ligase activity, 0006511 ubiquitin-dependent protein catabolic process, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 2KRE_A 3M63_A 2QIZ_A 2QJ0_A 3M62_A.
Probab=100.00 E-value=4.4e-150 Score=1360.19 Aligned_cols=606 Identities=42% Similarity=0.768 Sum_probs=519.2
Q ss_pred cccccccCCCCCCccccCCChhhhhccCCCcCCChhhHHhHHHHHHHHHHHHHHHHHHHHHHHhc-ChhhHHHHHHHHHH
Q 001866 266 LGPFFHVSALPDHAIFKSQPDVGQQCFSEASTRRPADLLSSFTTIKTVMRGLYKDLGDVLLALLK-NTDTRENVLEYLAE 344 (1002)
Q Consensus 266 LGp~l~lS~l~~~~~f~~~p~v~~~~F~~~~~~~~~~i~~~~~slr~~l~~~~~~L~~I~~~Llr-~~~sRe~vL~w~a~ 344 (1002)
|||||++||+|++ +|.++..||.+...++++++++++.+||+.++.+++.||+|+++||| |+++|+++|+|||.
T Consensus 1 LGp~l~~S~~~~~-----~~~~~~~~F~~~~~~~~~~~~~~~~~lr~~l~~~~~~l~~i~~~LLr~s~~sR~~~L~w~a~ 75 (629)
T PF10408_consen 1 LGPFLSLSPLPDD-----QPEVAEQFFSNPSKRNQQDVESSISSLRQELQNIQDQLHQIFKSLLRASPESRERVLSWFAQ 75 (629)
T ss_dssp THHHHT--TTS--------HHHHHHHTTT-TT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
T ss_pred CCCCeecCCCCCC-----ccHHHHHhcCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHH
Confidence 8999999999988 48899999999999999999999999999999999999999999999 89999999999999
Q ss_pred HHHhchhhhhc--ccCCCccCChhhHHHHHHHHHHhhhhhcCCCccCcCccCccC----ccc--CCCcCCCccccccCCH
Q 001866 345 VINRNSSRAHI--QVEPLSCASSGMFVNLSAVMLRLCDPFLDANLTKRDKIDPKY----VFY--SSRLDLRSLTALHASS 416 (1002)
Q Consensus 345 vl~~N~~R~k~--~~d~~~~aSDGFmlNl~~VLlrL~~PF~d~~~~KidkID~~Y----~~~--~~~vdi~~eTri~a~~ 416 (1002)
|++.|++|+|| ++++..+||||||+|+++||++||+||+|+..+|++||||+| +.+ ++++|+++|||++++.
T Consensus 76 ~l~~N~~R~k~~~~~~~~~~aSDGFmlNl~~VLl~L~~Pf~~~~~~K~~kID~~Y~~~~~~~~~~~~vd~~~eT~l~~~~ 155 (629)
T PF10408_consen 76 ILNANAKRAKMWLQVDPRTVASDGFMLNLTAVLLRLCQPFMDPSFSKIDKIDPDYCAHPLLRPRNSRVDISEETRLNATE 155 (629)
T ss_dssp HHHT-GGGGSS--S--GGGS--HHHHHHHHHHHHHHHGGGGSTT-TTGGGS-TTT-----TSS--SSS--TT--BSSB-H
T ss_pred HHHhchhhhhhhhccccccCCCcHHHHHHHHHHHHHHHhhhhhhhhhHhhcCcchhhhhhccccccccCcccccccCCCh
Confidence 99999999999 999999999999999999999999999999899999999999 455 7899999999999999
Q ss_pred HHHHHHHhcCCCCCCCCCCCCCcchhhhhhhhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCcchhHHHHHHHHHhchH
Q 001866 417 EEVSEWINKGNPAKADGSKHFSDGENQLLQSQEATSSSGGASEPSLPAGRPASIGGGKSKYPFICECFFMTARVLNLGLL 496 (1002)
Q Consensus 417 ~e~~~~~~~~~p~~~~~~~~~~~~e~~~l~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~nFItecFFLT~~~lhlG~~ 496 (1002)
+++++|++... ..+++||||||||||++|+|||+.
T Consensus 156 ~e~~~~~~~~~---------------------------------------------~~~~~nFiTe~FFLT~~a~hlg~~ 190 (629)
T PF10408_consen 156 EESEEWYEDLP---------------------------------------------NPGPPNFITECFFLTLRALHLGLL 190 (629)
T ss_dssp HHHHHHHHHCT---------------------------------------------TSTS--HHHHHHHHHHHHHHHTHH
T ss_pred hHHhhhhcccc---------------------------------------------cCCCCCchHHHHHHHHHHHHHhHH
Confidence 99999997542 233499999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHHHHHhHHHHhhhhccChHHHHHHHHHHHHHHHH
Q 001866 497 KAFSDFKHLVQDISRAEDTLATLKATQGQTPSSQLNLEITRIEKEIELSSQEKLCYEAQILRDGDLIQHALSFYRLMIVW 576 (1002)
Q Consensus 497 ~~~~~~~~l~r~i~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~L~dp~l~~~~~~F~~~~~~w 576 (1002)
|++++|+++.|+++++++.++++++. ..+++++++++.+.+.++|++| +|+||++++++++|+++++.|
T Consensus 191 ~~~~~~~~~~r~l~~lq~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~e~-~L~~p~~~~~~~~F~~~~~~w 259 (629)
T PF10408_consen 191 PAIQRYKRLLRELRRLQRELEELEAS----------AQLKRLKEQLDKLMSEKLSLEA-VLLDPDFLSRCLQFYNFVAQW 259 (629)
T ss_dssp HHHHHHHTHHHHHHHHHHHHHHHTT-----------HHHHHHHHHHHHHHHHHHHHHH-HHT-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhH----------HHHHHHHHHHHHHHHHHHHHHH-HhcCHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999987642 5678999999999999999999 799999999999999999999
Q ss_pred HHHHhc---------CCcCCCCCCCCcccccchhHHHHhHHHHHHHHhhc---CccccccchHHHHHHHHHHhCCCCCcc
Q 001866 577 LVDLVG---------GFKMPLPDTCPMEFACMPEHFVEDAMELLIFASRI---PKALDGVLLDDFMNFIIMFMASPKYIR 644 (1002)
Q Consensus 577 L~~l~~---------~~~lPLp~~~p~~f~~lPE~~iEdi~d~~~f~~r~---p~~l~~~~~~~l~~f~i~~l~s~~~ik 644 (1002)
|+++++ +.++|||+++|+.|++||||+||||+||+.|+.|+ |..+.+..++++++|||+||++|+||+
T Consensus 260 L~~~~~~~~~~~~~~~~~~Plp~~~p~~f~~lPE~~iedi~d~~~f~~~~~~~~~~l~~~~~~~l~~f~i~fm~s~~~ik 339 (629)
T PF10408_consen 260 LLRLADPSNQYPENKPPKLPLPEEPPPQFAYLPEFFIEDIVDFLLFLRRFNNSPDLLSSQDLDELVTFCITFMGSPEYIK 339 (629)
T ss_dssp HHHHHSTT--TTS-S---S-SS----TTGGGSBTHHHHHHHHHHHHHTTSTT-TTTT-T-THHHHHHHHHHHHH-TTS--
T ss_pred HHHHhcccccccccCCcCCCCCCCCChHHHhCCHHHHHHHHHHHHHHHHhcCChhhhhhhhHHHHHHHHHHHhCChhhcC
Confidence 999993 36789999999999999999999999999999998 788889999999999999999999999
Q ss_pred ChhhHhhHHHHHHhhcCCCC-CCchhhHHhhhcchhhHHHHHHHHHHHhhhhhccCCCccchhhhhhhhhHHHHHHHHhC
Q 001866 645 NPYLRSKMVEVLNCWMPRRS-GSSSATATLFEGHQMSLEYLVRNLLKLYVDIEFTGSHTQFYDKFNIRHNIAELLEYLWQ 723 (1002)
Q Consensus 645 NPhLraklvevL~~~~p~~~-~~~~~~~~lf~~~~la~~~L~~aLm~fYidvE~TG~~~qFYdKFn~R~~I~~Ilk~LW~ 723 (1002)
|||||||+||+|+.++|... +.++.+.++|++||++++||+||||+||||||+||+|+|||||||+||+|+.||++||+
T Consensus 340 NP~LraklvevL~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~sLm~~yidvE~Tg~~~qfydKFn~R~~i~~il~~lw~ 419 (629)
T PF10408_consen 340 NPHLRAKLVEVLFSLLPPDRDGRRGVLGSLFESHPLAQEHLVPSLMKFYIDVEKTGASTQFYDKFNIRYHISQILKYLWK 419 (629)
T ss_dssp -HHHHHHHHHHHHHCCS--TTS---TTHHHHHH-HHHHCCHHHHHHHHHHHCCCT-SSSSSTCHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHhcCcccccccccHHHHHHcCHHHHHHHHHHHHHHHHHHHhcCCCccchhcccchhhHHHHHHHHcC
Confidence 99999999999999988776 55677888999999999999999999999999999999999999999999999999999
Q ss_pred ChhhHHHHHHHHHhhccchhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhccchhhcCCCHHHHHHHHHHHHHhhhhh
Q 001866 724 VPSHRNAWRQIAKEEEKGVYLNFLNFLINDSIYLLDESLNKILELKVIEAEMSNTAEWERRPAQERQERTRLFHSQENII 803 (1002)
Q Consensus 724 ~~~yr~~l~~~a~~~~~~~FvrFvnlLiND~tfLLDE~L~~L~~I~~~q~e~~d~~~w~~l~~eer~e~~~~l~~~er~a 803 (1002)
+|.||++|+++++++ +++|+|||||||||+||||||||++|++||++|.+++|.++|+++++|+|+++++.++++||+|
T Consensus 420 ~~~~r~~~~~~~~~~-~~~F~rFvn~liND~~~llDE~l~~L~~I~~~q~~~~d~~~w~~~~~~~r~~~~~~l~~~e~~~ 498 (629)
T PF10408_consen 420 NPEYREQFIKEAKEN-PPLFVRFVNMLINDTTFLLDESLSKLKEIKELQEEMADQSEWNALSQEERQEKESQLEQAERQA 498 (629)
T ss_dssp -HHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS---------HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCHHHHHHHHHHHHHHHHHH
Confidence 999999999999985 7899999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhcHHHHHHHHHHHHHhccCCCCchHHHHHHHHHHHHHHhhhcCccccCccccCCcccCCChHHHHHHHHHHHHhcc
Q 001866 804 RIDMKLANEDVSMLAFTSEQIVAPFLLPEMIERVASMLNYFLLQLVGPQRKSLTLKDPEKYEFRPKQLLKQIVCIYVHLA 883 (1002)
Q Consensus 804 rs~~~La~etv~ml~~~T~~i~~~Fl~peivdRLA~MLNynL~~LvGPk~~~LKVknpekY~F~Pk~LL~~i~~IYlnL~ 883 (1002)
|||++||++|++||.+||+++|+||++||||+|||+||||||++||||||++||||||++|||+||+||.+||+||+||+
T Consensus 499 rs~~~l~~~t~~~l~~lt~~~~~~Fl~~elv~RlA~MLn~~L~~L~Gpk~~~LkVk~~~~y~F~P~~ll~~i~~iy~~l~ 578 (629)
T PF10408_consen 499 RSYLQLANETLKMLNYLTSEIPEPFLRPELVDRLAAMLNYNLDQLVGPKCSELKVKNPEKYGFDPKELLSQIVDIYLNLS 578 (629)
T ss_dssp HHHHHHHHHHHHHHHHHHHH-GGGGCSHHHHHHHHHHHHHHHHHHHSHHHHT---SSGGGGT--HHHHHHHHHHHHHHCT
T ss_pred HHHHHHHHHHHHHHHHHHHhCchhhhhHHHHHHHHHHHHHHHHHHcCCchhcccCCChhhcCCcHHHHHHHHHHHHhhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cccccchhhHhhhhCCCCCCHHHHHHHHHHHHHhCC-CHHHHHHHHHHHHHHHH
Q 001866 884 RGDTQNLFPAAISSDGRSYNEQLFSAAADVLWKIGE-DGRIIQEFIELGAKAKA 936 (1002)
Q Consensus 884 ~~~~~~~F~~AVa~DgRSY~~elF~~A~~il~r~~l-~~~~i~~f~~l~~kv~~ 936 (1002)
+. ++|++|||+|||||++++|++|++||+|+|+ +++++++|++|+++|++
T Consensus 579 ~~---~~F~~ava~D~Rsy~~~lf~~a~~~l~~~~l~~~~~i~~f~~l~~~ve~ 629 (629)
T PF10408_consen 579 DS---DKFVQAVANDGRSYSPELFEKAVRILRRIGLKSEDEIEKFEELAKKVEE 629 (629)
T ss_dssp T----HHHHHHHHH-TTT--HHHHHHHHHHHTTSTSSTHHHHHHHHHHCCHHHH
T ss_pred Cc---hHHHHHHHhCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhC
Confidence 64 4799999999999999999999999999998 99999999999999985
No 4
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.20 E-value=0.045 Score=61.06 Aligned_cols=265 Identities=20% Similarity=0.205 Sum_probs=160.8
Q ss_pred CcccccchhHHHHhHHHHHHHHhhc--Cc-c-ccc----cchHHHHHHHHHHhCCCCCccChhhHhhHHHHHHhhcCCCC
Q 001866 593 PMEFACMPEHFVEDAMELLIFASRI--PK-A-LDG----VLLDDFMNFIIMFMASPKYIRNPYLRSKMVEVLNCWMPRRS 664 (1002)
Q Consensus 593 p~~f~~lPE~~iEdi~d~~~f~~r~--p~-~-l~~----~~~~~l~~f~i~~l~s~~~ikNPhLraklvevL~~~~p~~~ 664 (1002)
-..|+.+||+++......+.-+..| |- . .+. ..+....+|.-+-...| .|--...|..+.+.|..+...+.
T Consensus 19 gslfsfvpe~yvn~~~~~~~av~d~~~~l~a~~e~~~~e~sv~~~a~~l~~h~ad~-riv~a~~kdsllqal~t~~c~~~ 97 (489)
T KOG4692|consen 19 GSLFSFVPEVYVNTLPILLDAVMDFSHDLKAQFEASDAECSVNAAAEFLGIHSADP-RIVLASCKDSLLQALGTLTCHKS 97 (489)
T ss_pred cchhhhchHHHHHhhHHHHHHHHHhCcchhhhhcCCCchhhHHHHHHHHhhccCCc-eeeechhHHHHHHHhhheeechh
Confidence 3569999999999999888888776 21 1 122 22344455554444445 56666778888888877655544
Q ss_pred CCchhhHHhhhcchhhHHHHHHHHHHHhhhhhc-----------cCCCccchhhhhhhhhH-HHHHHHHhCCh-------
Q 001866 665 GSSSATATLFEGHQMSLEYLVRNLLKLYVDIEF-----------TGSHTQFYDKFNIRHNI-AELLEYLWQVP------- 725 (1002)
Q Consensus 665 ~~~~~~~~lf~~~~la~~~L~~aLm~fYidvE~-----------TG~~~qFYdKFn~R~~I-~~Ilk~LW~~~------- 725 (1002)
| +..+=...+-.+-.++.+|+.-|-.--. -|. .| .||++= .++++.=-.+.
T Consensus 98 ~----vraler~~k~sq~smvraLLapyenR~W~q~nwillRlw~G~--Gf----~y~~~r~phl~rsr~~n~~~~sl~~ 167 (489)
T KOG4692|consen 98 G----VRALERTSKRSQASMVRALLAPYENRSWIQVNWILLRLWKGS--GF----SYLKNREPHLCRSRSRNETHTSLSS 167 (489)
T ss_pred h----hhHHHhccHhhHHHHHHHHhhhhhcCCchhhhHHHHHHHccC--Cc----cccccCCchhhhhhhcccccccccC
Confidence 3 2222223344455566777766632111 021 11 222211 01222222221
Q ss_pred ----hhHHHHHHHHHhhccchhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhccchhhcCCCHHHHHHHHHHHHHhhh
Q 001866 726 ----SHRNAWRQIAKEEEKGVYLNFLNFLINDSIYLLDESLNKILELKVIEAEMSNTAEWERRPAQERQERTRLFHSQEN 801 (1002)
Q Consensus 726 ----~yr~~l~~~a~~~~~~~FvrFvnlLiND~tfLLDE~L~~L~~I~~~q~e~~d~~~w~~l~~eer~e~~~~l~~~er 801 (1002)
.+-+++..-+--+++++-.-|+|.++|-.+|-+.|-+..+.||.+.-+.|+++- .-..+.+
T Consensus 168 p~pst~fQ~ll~a~ll~dgp~a~tFLNsvlnqLnWafsEFi~~vqEiQ~~aqr~E~~~---------------~e~~Qlk 232 (489)
T KOG4692|consen 168 PAPSTVFQALLRAALLNDGPLASTFLNSVLNQLNWAFSEFIVSVQEIQEKAQRMENTL---------------FEPFQLK 232 (489)
T ss_pred CCchHHHHHHHHHHHhccCchHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHhhc---------------cCHHHHh
Confidence 122223221111246788999999999999999999988877766554444221 1112235
Q ss_pred hhhhhhhcHHHHHHHHHHHHHhccCCCCc------hHHHHHHHHHHHHHHhhhcCccc-cCccc----cCCcccCCChHH
Q 001866 802 IIRIDMKLANEDVSMLAFTSEQIVAPFLL------PEMIERVASMLNYFLLQLVGPQR-KSLTL----KDPEKYEFRPKQ 870 (1002)
Q Consensus 802 ~ars~~~La~etv~ml~~~T~~i~~~Fl~------peivdRLA~MLNynL~~LvGPk~-~~LKV----knpekY~F~Pk~ 870 (1002)
.|-.-+.|+-.-++.|++.+...|+.|+. .-+.+||+..||..|.....|.- ....| .+-++..=- -
T Consensus 233 ~C~~cFeLsvsL~RvLEm~it~~Peifld~trpns~~Ll~ri~qllnqvlsrVt~e~~lf~rvv~~~~~~le~V~hy--p 310 (489)
T KOG4692|consen 233 KCCVCFELSVSLARVLEMCITAMPEIFLDGTRPNSRRLLERILQLLNQVLSRVTDEFFLFVRVVRRQGQPLEKVSHY--P 310 (489)
T ss_pred HhhhhHHHHHHHHHHHHHHHHhhhHHHhcCCCCcHHHHHHHHHHHHHHHHHhhccccchhHHHHHhhcCChhhhccc--c
Confidence 67778889999999999999999999984 34689999999999988775543 22111 122333322 3
Q ss_pred HHHHHHHHHHhcccc
Q 001866 871 LLKQIVCIYVHLARG 885 (1002)
Q Consensus 871 LL~~i~~IYlnL~~~ 885 (1002)
+|..++.|.+||-..
T Consensus 311 il~a~~GIll~Ll~~ 325 (489)
T KOG4692|consen 311 ILAALVGILLNLLEA 325 (489)
T ss_pred hHHHHHHHHHHHHHh
Confidence 789999999999654
No 5
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=97.16 E-value=9.8e-05 Score=65.71 Aligned_cols=43 Identities=30% Similarity=0.240 Sum_probs=34.8
Q ss_pred CCCcccChhHHHHHH---hhccCcceehhhhHHHhhhh-hcccCCCcc
Q 001866 951 IPDEFLDPIQVCFTC---LLSSLVRTVLRTMVIVSFVA-VHFDEGSGH 994 (1002)
Q Consensus 951 iPDEFlDPLM~tlM~---~LPsS~~~vDR~ti~~~~~~-~~~~~~~~~ 994 (1002)
|||+|+|||...||+ ++|+. .|.||++|...+.. -+.|+-+|.
T Consensus 1 iP~~f~CpIt~~lM~dPVi~~~G-~tyer~~I~~~l~~~~~~~P~t~~ 47 (73)
T PF04564_consen 1 IPDEFLCPITGELMRDPVILPSG-HTYERSAIERWLEQNGGTDPFTRQ 47 (73)
T ss_dssp SSGGGB-TTTSSB-SSEEEETTS-EEEEHHHHHHHHCTTSSB-TTT-S
T ss_pred CCcccCCcCcCcHhhCceeCCcC-CEEcHHHHHHHHHcCCCCCCCCCC
Confidence 799999999999999 66655 99999999999999 778887764
No 6
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=54.14 E-value=6.2 Score=33.37 Aligned_cols=39 Identities=26% Similarity=0.242 Sum_probs=32.4
Q ss_pred cccChhHHHHHH---hhccCcceehhhhHHHhhhhhcccCCCc
Q 001866 954 EFLDPIQVCFTC---LLSSLVRTVLRTMVIVSFVAVHFDEGSG 993 (1002)
Q Consensus 954 EFlDPLM~tlM~---~LPsS~~~vDR~ti~~~~~~~~~~~~~~ 993 (1002)
||.+||...+|+ ++| ++.+.+|+.|..++.....||=.|
T Consensus 1 ~~~Cpi~~~~~~~Pv~~~-~G~v~~~~~i~~~~~~~~~cP~~~ 42 (63)
T smart00504 1 EFLCPISLEVMKDPVILP-SGQTYERRAIEKWLLSHGTDPVTG 42 (63)
T ss_pred CcCCcCCCCcCCCCEECC-CCCEEeHHHHHHHHHHCCCCCCCc
Confidence 689999999999 665 579999999999998855666544
No 7
>KOG4642 consensus Chaperone-dependent E3 ubiquitin protein ligase (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]
Probab=47.12 E-value=26 Score=38.55 Aligned_cols=45 Identities=20% Similarity=0.230 Sum_probs=38.7
Q ss_pred CCCCCcccChhHHHHHH--hhccCcceehhhhHHHhhhhh-cccCCCc
Q 001866 949 GDIPDEFLDPIQVCFTC--LLSSLVRTVLRTMVIVSFVAV-HFDEGSG 993 (1002)
Q Consensus 949 ~diPDEFlDPLM~tlM~--~LPsS~~~vDR~ti~~~~~~~-~~~~~~~ 993 (1002)
-|+||--.--|...||+ -.--|++|-||.-|+-|+.|| |||+-.+
T Consensus 206 rEvpd~lcgkIt~el~~~pvi~psgIty~ra~I~Ehl~rvghfdpvtr 253 (284)
T KOG4642|consen 206 REVPDYLCGKITLELMREPVITPSGITYDRADIEEHLQRVGHFDPVTR 253 (284)
T ss_pred ccccchhhhhhhHHhhcCCccCccccchhHHHHHHHHHHhccCCchhc
Confidence 58999999999999999 444579999999999999998 6777544
No 8
>PRK09458 pspB phage shock protein B; Provisional
Probab=28.50 E-value=1.4e+02 Score=27.19 Aligned_cols=36 Identities=25% Similarity=0.281 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCCC
Q 001866 918 GEDGRIIQEFIELGAKAKAAASEAMDAEAAL-GDIPD 953 (1002)
Q Consensus 918 ~l~~~~i~~f~~l~~kv~~~~~~~~~~E~~l-~diPD 953 (1002)
|++.++.+.++++.++++.+.+..+..|..+ .|.|+
T Consensus 35 ~Ls~~d~~~L~~L~~~A~rm~~RI~tLE~ILDae~P~ 71 (75)
T PRK09458 35 GLSQEEQQRLAQLTEKAERMRERIQALEAILDAEHPN 71 (75)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCC
Confidence 4589999999999999999998888888887 56774
No 9
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=27.31 E-value=1.7e+02 Score=30.57 Aligned_cols=87 Identities=16% Similarity=0.121 Sum_probs=49.2
Q ss_pred hCCCCCCHHHHHHHHHHH--HHhCCCHHHHHHHHH---------HHHHHHHHHHHHHHHHHhcCCCCCcccChhHHHHHH
Q 001866 897 SDGRSYNEQLFSAAADVL--WKIGEDGRIIQEFIE---------LGAKAKAAASEAMDAEAALGDIPDEFLDPIQVCFTC 965 (1002)
Q Consensus 897 ~DgRSY~~elF~~A~~il--~r~~l~~~~i~~f~~---------l~~kv~~~~~~~~~~E~~l~diPDEFlDPLM~tlM~ 965 (1002)
+.-|.|+.+-..+...|. +..|++-.+|..+-. +.++.++..++.++...... .+..+..
T Consensus 35 ~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~~~~~~~~L~~~~~~l~~ei~~L~~~~~---------~l~~ll~ 105 (172)
T cd04790 35 SNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDATDVLRRRLAELNREIQRLRQQQR---------AIATLLK 105 (172)
T ss_pred CCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHH
Confidence 345889998777665544 667777777776653 33333333322222111111 0122222
Q ss_pred --hhccCcceehhhhHHHhhhhhcccCCC
Q 001866 966 --LLSSLVRTVLRTMVIVSFVAVHFDEGS 992 (1002)
Q Consensus 966 --~LPsS~~~vDR~ti~~~~~~~~~~~~~ 992 (1002)
.+-..+..||+.-.+..+.+.++|+.+
T Consensus 106 ~~~~~~~~~~V~~~~w~~l~~~~g~~~~~ 134 (172)
T cd04790 106 QPTLLKEQRLVTKEKWVAILKAAGMDEAD 134 (172)
T ss_pred HHhhccccccCCHHHHHHHHHHcCCChHH
Confidence 222455667888888888999998876
No 10
>PF12726 SEN1_N: SEN1 N terminal; InterPro: IPR024481 The yeast helicase Sen1 is an RNA polymerase II termination factor for noncoding RNA genes []. The C-terminal domain of Sen1 is essential for cell growth, while the N-terminal domain appears to be dispensible []. This entry represents the N-terminal domain.
Probab=25.36 E-value=1.5e+03 Score=28.94 Aligned_cols=79 Identities=15% Similarity=0.202 Sum_probs=50.0
Q ss_pred HHHHHHHHHhhh-hhccCCCccchhhhhhhhhHHHHHHHHhCChhhHHHHHHHHHhhccchhHHHHHHHHHhHHHHHHHH
Q 001866 683 YLVRNLLKLYVD-IEFTGSHTQFYDKFNIRHNIAELLEYLWQVPSHRNAWRQIAKEEEKGVYLNFLNFLINDSIYLLDES 761 (1002)
Q Consensus 683 ~L~~aLm~fYid-vE~TG~~~qFYdKFn~R~~I~~Ilk~LW~~~~yr~~l~~~a~~~~~~~FvrFvnlLiND~tfLLDE~ 761 (1002)
--++.+++.+.- .|+.| +.|++...- +.-..|++.+..+|.|++.+.+...++ ......+ ++|..--+..-
T Consensus 229 ~~l~~lL~~l~~lL~k~~--~~FW~~~~~-~~p~~ild~If~np~f~~~L~~~~~~~---~~~~~~~--~~~~~sWi~pf 300 (727)
T PF12726_consen 229 PPLPILLRCLSILLEKLG--SDFWDAMGP-ISPQVILDQIFDNPAFKKLLLQSQEDE---ISESDDD--LPDLLSWISPF 300 (727)
T ss_pred hhHHHHHHHHHHHHHhCH--HHHhcccCC-CCHHHHHHHHhCChHHHHHHHhhccCC---ccccchh--hHHHHHHHHHH
Confidence 344566677765 47777 569986643 233489999999999999998876542 2322222 55555555555
Q ss_pred HHHHHHHH
Q 001866 762 LNKILELK 769 (1002)
Q Consensus 762 L~~L~~I~ 769 (1002)
+..|+..+
T Consensus 301 ~~SL~~~~ 308 (727)
T PF12726_consen 301 LRSLSPSQ 308 (727)
T ss_pred HHHhcccc
Confidence 55555444
No 11
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=25.35 E-value=1.1e+02 Score=29.44 Aligned_cols=42 Identities=17% Similarity=0.216 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHhc-ChhhHHHHHHHHHHHHHhchhhhh
Q 001866 313 VMRGLYKDLGDVLLALLK-NTDTRENVLEYLAEVINRNSSRAH 354 (1002)
Q Consensus 313 ~l~~~~~~L~~I~~~Llr-~~~sRe~vL~w~a~vl~~N~~R~k 354 (1002)
+|...+...|..|+.|-+ +.-+|.+.-.|+|..+..+.....
T Consensus 58 ~lR~~R~~ah~~fd~lw~~~~~~R~~aY~wLA~~lgi~~~~cH 100 (102)
T PF11672_consen 58 ELRRARKAAHRAFDPLWQSGHMSRSDAYRWLAKKLGIPVEECH 100 (102)
T ss_pred HHHHHHHHHHHHHHHHHHhCcccHHHHHHHHHHHcCCChHhcc
Confidence 455677788999999999 567899999999999988766543
No 12
>PF11635 Med16: Mediator complex subunit 16; InterPro: IPR021665 Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression []. Several members including the human protein, Q9Y2X0 from SWISSPROT, have one or more WD40 domains on them, PF00400 from PFAM.
Probab=22.54 E-value=2.1e+02 Score=36.89 Aligned_cols=175 Identities=20% Similarity=0.229 Sum_probs=94.5
Q ss_pred hhhhhhhcHHHHHHHHHHHHHhcc-------CCCCchHHHHHHHHH----------HHHHHhhhc-CccccCccccCC--
Q 001866 802 IIRIDMKLANEDVSMLAFTSEQIV-------APFLLPEMIERVASM----------LNYFLLQLV-GPQRKSLTLKDP-- 861 (1002)
Q Consensus 802 ~ars~~~La~etv~ml~~~T~~i~-------~~Fl~peivdRLA~M----------LNynL~~Lv-GPk~~~LKVknp-- 861 (1002)
.++--+.|-+.++ |..+-..++ .++..||.++=|... |+-.|-.|. -|+. |+.+|-
T Consensus 465 ia~v~LnLR~~~f--L~~~~~~~~~~~~~~~~~~~~~e~l~sL~g~~kW~~Dl~~yL~~~L~~L~~~~~~--l~~~~sv~ 540 (753)
T PF11635_consen 465 IAWVILNLRNISF--LSTIYRQISNKEKTFQNSFDEPEVLQSLIGNIKWVLDLMAYLLQELFELSNDPES--LTLPNSVV 540 (753)
T ss_pred HHHHHHhhhhhhh--hHHHHHHcccccccccCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccc--cCCccchh
Confidence 3344444444444 444444444 449999999888766 333333332 2221 222221
Q ss_pred --cccCCChHHHHHHHHHHHHhcccccccchhhHhhhhCCCCCCHHHHHHHHHHHHHhCC-CHHHHHHHHHHHHHHHHHH
Q 001866 862 --EKYEFRPKQLLKQIVCIYVHLARGDTQNLFPAAISSDGRSYNEQLFSAAADVLWKIGE-DGRIIQEFIELGAKAKAAA 938 (1002)
Q Consensus 862 --ekY~F~Pk~LL~~i~~IYlnL~~~~~~~~F~~AVa~DgRSY~~elF~~A~~il~r~~l-~~~~i~~f~~l~~kv~~~~ 938 (1002)
---+=.||.+|..+|.---+|. ++.... |.|.+ .+.+...+.+.-- ++..++.|+.|-.++...-
T Consensus 541 l~~ll~~~~r~fL~~~~r~l~~l~------~~l~~~----~~~~~--l~~s~~~~~~~~~~s~v~~~~fe~lL~~~~~~i 608 (753)
T PF11635_consen 541 LPLLLSSSPRSFLLYACRSLRKLR------ELLKKI----RIWPL--LNESCQPLFTITSDSPVKLSLFEKLLTELDNDI 608 (753)
T ss_pred hhhhcccCcHHHHHHHHHHHHHHH------HHHHHH----hcccc--cChHHHHHHHHHhcCCccHHHHHHHHHHHHHHH
Confidence 0111247888887775555553 133222 33333 1333444443333 6667788887777773211
Q ss_pred -------------HHHHHHHHhc-CCCCCcccChhHHHHHHhhccCcceehhhhH---HHhhhhhcccCCC
Q 001866 939 -------------SEAMDAEAAL-GDIPDEFLDPIQVCFTCLLSSLVRTVLRTMV---IVSFVAVHFDEGS 992 (1002)
Q Consensus 939 -------------~~~~~~E~~l-~diPDEFlDPLM~tlM~~LPsS~~~vDR~ti---~~~~~~~~~~~~~ 992 (1002)
+...+-+.+. |++|++|+-|++.=+-..+|..+-.+|++.+ +...+.++.|+-+
T Consensus 609 ~~~~~~~~~~~~~~~~~E~~ll~~~~iP~~l~~~~~~~~~~~~~~~~~~~d~~~L~F~d~~~L~i~~~~~~ 679 (753)
T PF11635_consen 609 RQAYQLDGFEKQPRLPDEQSLLECGEIPPQLLPPAKKLLTKTLPAIRSEIDPSKLYFYDTSWLGIGDDKRS 679 (753)
T ss_pred HHHhhhhhcccCcCCchHHHHHhcCCCCHHHHHHHHHhcCccchhhhcCCChhheeecccccccCcccccc
Confidence 1112233333 8999999988877666677777777888765 4556666666544
Done!