Query psy8413
Match_columns 796
No_of_seqs 198 out of 247
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 18:09:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8413.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8413hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1104|consensus 100.0 4E-189 8E-194 1581.1 69.4 755 1-796 1-759 (759)
2 PF09088 MIF4G_like: MIF4G lik 100.0 2.9E-65 6.4E-70 508.0 13.2 166 310-475 1-191 (191)
3 PF09090 MIF4G_like_2: MIF4G l 100.0 2E-51 4.2E-56 434.4 24.0 248 489-760 1-253 (253)
4 smart00543 MIF4G Middle domain 99.7 3.4E-16 7.4E-21 158.5 16.9 173 32-210 2-178 (200)
5 KOG2140|consensus 99.7 1.3E-14 2.8E-19 159.9 27.1 376 66-485 194-619 (739)
6 PF02854 MIF4G: MIF4G domain; 99.6 9.5E-14 2.1E-18 140.7 19.2 197 32-246 2-209 (209)
7 KOG2141|consensus 97.9 0.0015 3.2E-08 76.4 22.9 385 29-460 318-753 (822)
8 KOG2051|consensus 96.7 0.0095 2.1E-07 72.5 11.5 128 67-203 459-591 (1128)
9 KOG2051|consensus 86.5 22 0.00048 44.7 16.7 173 34-210 634-816 (1128)
10 smart00544 MA3 Domain in DAP-5 74.4 36 0.00079 31.2 10.5 97 323-423 4-105 (113)
11 PF02847 MA3: MA3 domain; Int 66.6 48 0.001 30.3 9.4 101 321-425 2-107 (113)
12 PF09403 FadA: Adhesion protei 65.4 1E+02 0.0023 29.6 11.5 103 651-795 24-126 (126)
13 KOG1760|consensus 61.2 33 0.00072 32.6 7.1 82 645-726 21-125 (131)
14 PF03378 CAS_CSE1: CAS/CSE pro 55.8 1.2E+02 0.0027 35.2 12.2 120 90-213 97-218 (435)
15 PF02847 MA3: MA3 domain; Int 52.1 96 0.0021 28.2 8.8 92 52-143 17-112 (113)
16 smart00544 MA3 Domain in DAP-5 48.3 1.1E+02 0.0024 28.0 8.5 92 52-143 17-112 (113)
17 COG5215 KAP95 Karyopherin (imp 47.7 3.2E+02 0.007 32.8 13.5 114 21-137 585-709 (858)
18 smart00515 eIF5C Domain at the 45.8 39 0.00085 29.6 4.8 53 574-627 2-57 (83)
19 COG1422 Predicted membrane pro 44.6 1.1E+02 0.0023 31.8 8.2 27 695-721 97-123 (201)
20 PF04054 Not1: CCR4-Not comple 43.8 92 0.002 35.5 8.6 138 503-654 185-352 (379)
21 cd07600 BAR_Gvp36 The Bin/Amph 41.2 4.2E+02 0.0091 28.4 12.5 59 694-773 182-240 (242)
22 PF03962 Mnd1: Mnd1 family; I 39.2 84 0.0018 32.2 6.7 88 558-676 7-98 (188)
23 KOG1077|consensus 38.7 5.5E+02 0.012 31.7 13.8 425 117-615 81-566 (938)
24 KOG2140|consensus 37.3 72 0.0016 37.5 6.3 100 62-168 478-579 (739)
25 PF02020 W2: eIF4-gamma/eIF5/e 36.4 65 0.0014 28.3 4.8 45 585-629 2-49 (84)
26 PF13801 Metal_resist: Heavy-m 34.3 3.4E+02 0.0075 24.3 10.1 73 643-729 48-120 (125)
27 PF14500 MMS19_N: Dos2-interac 34.2 2.9E+02 0.0062 29.9 10.1 106 55-180 3-109 (262)
28 PF07064 RIC1: RIC1; InterPro 32.4 1.5E+02 0.0033 31.9 7.6 70 72-142 183-254 (258)
29 COG1579 Zn-ribbon protein, pos 32.2 4.6E+02 0.0099 28.1 10.9 37 640-676 45-81 (239)
30 cd04378 RhoGAP_GMIP_PARG1 RhoG 31.6 27 0.00058 36.1 1.7 36 380-417 5-40 (203)
31 cd07594 BAR_Endophilin_B The B 31.4 6.3E+02 0.014 26.8 11.9 155 547-773 71-227 (229)
32 PF05004 IFRD: Interferon-rela 31.4 6.4E+02 0.014 27.8 12.5 97 27-123 38-142 (309)
33 cd07439 FANCE_c-term Fanconi a 27.4 8.1E+02 0.018 26.4 12.1 131 72-209 103-247 (254)
34 KOG4403|consensus 26.8 1.1E+02 0.0023 35.1 5.4 9 779-787 394-402 (575)
35 PF14225 MOR2-PAG1_C: Cell mor 26.3 8.3E+02 0.018 26.4 12.0 98 143-241 77-179 (262)
36 KOG2025|consensus 24.9 3.8E+02 0.0083 33.0 9.6 109 33-159 24-135 (892)
37 PF10274 ParcG: Parkin co-regu 24.5 3.4E+02 0.0074 27.8 8.1 95 64-160 36-130 (183)
38 PF14327 CSTF2_hinge: Hinge do 24.3 1E+02 0.0022 27.4 3.8 44 575-625 37-80 (84)
39 KOG3942|consensus 24.2 2.9E+02 0.0064 30.5 7.9 135 101-253 199-339 (348)
40 PF07571 DUF1546: Protein of u 24.0 1.9E+02 0.0041 26.0 5.6 42 64-111 41-84 (92)
41 PF10455 BAR_2: Bin/amphiphysi 22.6 1.1E+03 0.023 26.1 12.5 133 552-718 112-251 (289)
42 PF04844 Ovate: Transcriptiona 22.5 2.4E+02 0.0051 23.6 5.3 54 500-559 4-59 (59)
43 KOG2213|consensus 22.4 1.2E+03 0.027 26.8 15.6 80 105-184 146-229 (460)
44 PTZ00429 beta-adaptin; Provisi 22.4 1.1E+03 0.024 29.5 13.5 224 378-630 201-468 (746)
45 PF07889 DUF1664: Protein of u 22.0 4E+02 0.0087 25.7 7.6 70 645-717 41-110 (126)
46 PF08146 BP28CT: BP28CT (NUC21 22.0 2.1E+02 0.0046 28.2 6.0 79 350-428 36-120 (153)
47 PF07889 DUF1664: Protein of u 21.9 3.1E+02 0.0067 26.4 6.8 32 639-670 53-84 (126)
48 PF15188 CCDC-167: Coiled-coil 21.8 2.4E+02 0.0051 25.4 5.5 74 648-725 6-80 (85)
49 PF13324 GCIP: Grap2 and cycli 21.7 7.8E+02 0.017 26.5 10.9 20 758-777 231-250 (275)
50 PF05529 Bap31: B-cell recepto 21.3 1.5E+02 0.0033 30.1 5.0 23 692-714 157-179 (192)
51 PF14838 INTS5_C: Integrator c 20.6 1E+03 0.022 29.4 12.3 119 82-207 194-338 (696)
52 cd07595 BAR_RhoGAP_Rich-like T 20.3 4.9E+02 0.011 27.9 8.7 62 648-714 122-183 (244)
53 KOG2141|consensus 20.1 3.5E+02 0.0075 33.3 8.0 105 34-139 616-721 (822)
No 1
>KOG1104|consensus
Probab=100.00 E-value=3.6e-189 Score=1581.09 Aligned_cols=755 Identities=53% Similarity=0.906 Sum_probs=716.3
Q ss_pred CCCCCCCCCCCCchhhhcccccCCCCchhHHHHHHHHHHhhcCCCCcchhhhHHHHHHHHHHhhHhhHHHHHHHHHHHHH
Q psy8413 1 MSNRRRPHEEDDGYERAYKKRRRVPENQELEDRFEVLIVKVGERSTTSLESHLDGLAKVLETDLATYRVKILRILTDCAT 80 (796)
Q Consensus 1 m~~rrR~~d~~d~~d~~~~kr~r~~~~~~~~~~l~~~I~~ige~~~~s~e~~l~~La~~l~~d~~~~~~~i~~~l~~~v~ 80 (796)
|| |||+.||+|++ ++.+|||.++.+++++||+++|+++||.+++++|+||++|+.+|.+|++++++.|++++..||.
T Consensus 1 ms-rRrr~d~edE~--y~~rr~r~~~~e~l~krl~~~i~~vg~~s~ss~e~~l~~l~~~l~~~~~~~~~~iL~~L~~ca~ 77 (759)
T KOG1104|consen 1 MS-RRRRGDDEDEN--YDDRRRRISPAETLEKRLESLIREVGEPSGSSVEDNLENLVAVLEADLENFKSKILDILNTCAV 77 (759)
T ss_pred CC-CCccCCccccc--cccccccCCcHHHHHHHHHHHHHhhcCCCCCcHHHhHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 44 55666655543 4667889999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCCchHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHhhcccccccChhhHHHHHHHHHHhhh
Q psy8413 81 KYPEKCCIYTTLVGLLNAKNYNFGGEFVELMVKTFKDALKNCQWNAARYALRFLADLVNCHVISTNSLLQLLENMLDASK 160 (796)
Q Consensus 81 e~P~K~p~yAtLVgllN~kn~~~g~~iv~~l~~~lq~~l~~~~w~~~kl~lrFLa~L~n~~Vi~~~sl~~ll~~ll~~a~ 160 (796)
++|+|+|+||||||++|+||++||+++|++++.++|+++++|+|++||.++|||++|+||+|+++++++++|++|++++.
T Consensus 78 ~lP~K~~~yaTLvgllN~kn~~fg~~~v~~~~~~~q~sl~~~~~n~ar~llrfL~dL~~~~vl~~~sli~l~esl~~~~~ 157 (759)
T KOG1104|consen 78 YLPEKITAYATLVGLLNLKNFNFGGEFVEYMIEELQESLKSGNWNEARYLLRFLSDLSNCHVLQADSLINLFESLLDAAI 157 (759)
T ss_pred HcccchhHHHHHHHHHhccchhhHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHhcCCccChHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCccchhhHHHHHHhhchhccHHhHHhhHHHHHHHHHHHHHHHhhcccccccccccccCCCCCChhhHHHHHHHHHH
Q psy8413 161 EDGVPNVRKDWYVYAVLSCLPWVGRELYEKKEQALALLLLNIELYLNKRSKKHVAALQVWSSDKPHPQEEYLDCLWAQIV 240 (796)
Q Consensus 161 e~~~~q~R~d~~vy~vL~~LP~~G~~L~e~~~~~l~~ll~~i~~yl~~r~~~~~~ll~~~~~~~~~~~~d~l~~L~~qi~ 240 (796)
|+++||+|+|||+||+|++|||+|++|++++++++++|+..|+.|+++|+++|.+++++|+++.|++|+|||++||+||+
T Consensus 158 e~~~Pqvr~D~~v~~vLs~lPw~g~el~e~~~~~~e~ll~~ie~Yl~~R~~shi~lL~vw~~~~~~~qeeyle~L~~qI~ 237 (759)
T KOG1104|consen 158 EENVPQVRRDYYVYCVLSSLPWFGRELNEKKPTEMEELLVYIEIYLKKRKKSHINLLNVWSGEPDHPQEEYLELLWAQIQ 237 (759)
T ss_pred hhcCcchhhhHHHHHHHhccchhhhhhcccchHHHHHHHHHHHHHHHHhcccccchhhcCCCCCCchHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCccccccCCCcchhhhhhhhhhcCCCCCCCCCCCCCCCCCCCCeeEEEeccCCCC-CCCCCCCCCCCCcchHHHH
Q psy8413 241 KLRQDNWTDHHIYRPYTVFDSRLSVALQHNLPNIILPPHHDSLIYPMPSVVFRMFDYTDC-PEEPSISPLPGAHSIERFL 319 (796)
Q Consensus 241 ~l~~~~w~~~~i~rpy~~f~~~L~~a~~h~Lp~~~~p~~~~~~~y~~P~~~frlf~~~~~-~~~~~~~~lP~~~sier~l 319 (796)
++++|+|++++|||||.+|+++|++|.+|+||+|..|+|+.++.||+|+++||+|++++| +++ +++||.+||||||
T Consensus 238 ~lr~n~w~e~hIprPy~~Fes~L~~~~~h~Lp~~~~pph~~~~~yp~p~v~fR~f~~~~~~~e~---p~mp~~ssi~rfl 314 (759)
T KOG1104|consen 238 KLRQNDWAENHIPRPYLGFESTLVHALQHNLPSFVSPPHTEDSEYPMPRVVFRMFQYTDCGFEI---PTMPGASSIERFL 314 (759)
T ss_pred HHHhcCcccccCCCchhhHHHHHHHhcccCCCCCCCCCCcccccCCcchhhhhcccccccCCCC---CCCCCchhHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999 487 9999999999999
Q ss_pred HHHHHHHHHHHhccCHHHHHHHHhcCC---CCCCchhHHHHHHHHHhhcCCCCCccchhHHHHHHHHhccCCCChhHHHH
Q psy8413 320 IEEHLLQIIEMNYFERKDCATQLLKYN---MKIPLEYCIVEIIFGELFRLPTPKYLEIFYGSVLIELCKMKPDTMPQVLA 396 (796)
Q Consensus 320 ~ee~i~Dii~~~~~nRkecA~~Ll~lp---~~~~~E~~ivEtIfs~lf~LP~p~~~~iyY~slLielCk~~P~~i~pv~~ 396 (796)
|||+|+|||+.+++||||||+||++|| ..+|+||+|||||||+||+||+||+++|||||||+||||++|+++|||||
T Consensus 315 fe~~i~dii~sl~fnRKecA~~l~~l~~~f~~~p~eylivEtIfgell~LP~~~~~~iyy~slLiElCK~~P~~lpqV~a 394 (759)
T KOG1104|consen 315 FEEIILDIIESLEFNRKECARQLLSLPVKFKAIPIEYLIVETIFGELLRLPTPPYKTIYYTSLLIELCKLQPKALPQVLA 394 (759)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHcCcccccCccHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHhCccchhHHHH
Confidence 999999999999999999999999999 45889999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcCccccHHHHHHHHHHHHHHhhccCCcccchhhhhhhcCCCCCChHHHHHHHHHHHHhhcchHHHhhhCccc
Q psy8413 397 QATVILFMRIESMNTACFDRFVAWFAYHLSNFQFQWSWEDWESALKLDLEHPKPKFIHEVLNKCVRLSYHQRIKEIVPPQ 476 (796)
Q Consensus 397 ~Air~ly~~l~~mD~e~~~Rf~dWFS~hLSNF~F~W~W~eW~~~l~~~~~~Pk~~Fi~~~l~KeiRLSy~~rIk~~lPe~ 476 (796)
||+|+||+++++||++|++||+||||||||||||+|+|+||++|+++|.+|||++|+|++|+||+|||||+||+++||+-
T Consensus 395 qa~r~lY~rldsm~~~c~dR~idWFShHLSNF~F~w~W~eW~~~l~~d~~~pk~~FvreviqkelrLsy~~rI~dslP~~ 474 (759)
T KOG1104|consen 395 QAVRILYMRLDSMDTECFDRFIDWFSHHLSNFQFRWKWNEWADCLGLDFEHPKPNFVREVIQKELRLSYYQRIKDSLPTL 474 (759)
T ss_pred HHHHHHHHHhccCCHHHHHHHHHHHHHHhccCcceechhhhhhhcCCCCcCcchhHHHHHHHHHHHHHHHHHHHHhhhHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCCCCcccCCCCCCCCCchHHHHHHHHHHHhcCCCHHHHHHHHhhCCCCCCCCCCCCCCChhHHHHHHHHHHh
Q psy8413 477 FAPLLPLKPEPHFKYNQEGGEHLPGFVYAQELINAIKKKQSSPNEIMAILNKIPSSSMDEDGADPINPLKIDVFTQVLLY 556 (796)
Q Consensus 477 ~~~llp~~p~p~fky~~e~~~~~p~~~~a~~l~~~i~~k~~~~eev~~~l~~i~~~~~~~~~~~~~~~~~i~v~~q~ll~ 556 (796)
+..|+|++|+|+|+|++|+....|++..+.++..+++.|+ ++|++..+|++- ++....++|.++|.+||||+++
T Consensus 475 ~~~l~P~~~~pny~y~~Ee~~~~~~~~~~~~l~~~~~~k~-~~e~~~~iLk~~-----~~~~~~~~n~~~i~lfvq~~l~ 548 (759)
T KOG1104|consen 475 LAKLLPPPPLPNYKYTDEEDPVLPQSLVAVQLIVAFREKA-TAEEIVNILKSE-----DESEIGSFNRLKIILFVQTLLD 548 (759)
T ss_pred HHHhCCCCCCCceeeecccCccccchHHHHHHHHHHhccC-CHHHHHHHHhcC-----ccccccCCcceehhhHHHHHHH
Confidence 9999999999999999999988899888999999999999 999999999921 1111156789999999999999
Q ss_pred hccchHHhHHHHHHhHHHHHHhhhCCChHHHHHHHHHHHHHHhhCcCeeHHHHHHHHhCCCCChhhhhhhhcccCCcchh
Q psy8413 557 LGSKSFSHSFAALSKFYKVLKEHIGHTEESQSYVLKSLFELWHDHQQMMAVLIDKMLKTQLLHCSSVANWIFSKEMQPEF 636 (796)
Q Consensus 557 ~GsKSfSH~~~~iery~~~Lk~l~~~~~~~q~~il~~v~~~W~~~~Q~~~iiidkll~~~iv~p~~Vv~w~F~~~~~~~~ 636 (796)
+|||||||++++++||+++||+++.+++..|.++|++|++||++||||+++++|||++|+||+|.+||+|+|+++|..+|
T Consensus 549 lGSKSfSH~f~~lek~~~vfk~l~~~~e~~q~~vl~~vft~Wk~n~Qm~~v~~Dkml~~~ii~~~aVv~WiF~~~m~~~~ 628 (759)
T KOG1104|consen 549 LGSKSFSHAFSALEKYHTVFKKLCEDSETKQIIVLEAVFTFWKANPQMGFVLTDKMLKYQIIDCSAVVRWIFSEEMVNEF 628 (759)
T ss_pred hccchhhhHHHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHhcCchhhHHHHHHHhccccccHHHHHHHhcCHHhhhhH
Confidence 99999999999999999999999997887899999999999999999999999999999999999999999999999999
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCcccccCCCCCccccccCHHHHHHHHHHHHHHHHHHHHHH
Q psy8413 637 TKLYVWEILHLTIKKMSKYVNRVGKELLDAKERLKHVSSESEEESDGEGGKKNEEKISEEVVEKIEEKLEAAQADQKNLF 716 (796)
Q Consensus 637 ~~~~~Weil~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~a~~eqk~l~ 716 (796)
++.|+||+||+|++|+++|+.+++++++++.+++..+.++...+++... ..+++..++.+|...++++.+..++|..|
T Consensus 629 ~r~~~wEil~~al~K~~~~~~~~~k~ie~~~e~~~~~~~~~~d~~~~~~--~~~~~~~~e~~e~~~~~~E~~~~~~k~~~ 706 (759)
T KOG1104|consen 629 TRLYLWEILHSALNKLNKHLNRSQKNIEEVTEKLETAEKSEIDLEDDLS--AERDEIKEENVEGDPEDLEDANLKEKWLF 706 (759)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhhcccccchhhhhh--hhhhhhhHHHhccChhhhhhhhHHHHHHH
Confidence 9999999999999999999999999999999999776655532222111 22356667888888999999999999999
Q ss_pred HHHHHHHHHHhcccccccCCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchhHHHHHHHHHhccC
Q psy8413 717 LIIFQRFIMILSEHLVRCDTDGVDFNTHWYKWTIGRLQQVLLAHHEQVQKYSSTLETLLFTQDLEPHILDVFHQFLALNA 796 (796)
Q Consensus 717 ~~i~~~fv~~Lse~~~~~~~~~~~~~~~W~~~~~gr~~~~~~~~~~~~~~~~~~L~~~~ft~~~d~~i~~vf~qf~al~~ 796 (796)
..+||+|+ ++++.|..|++...+|+.++++.+||+|+||+|+++|+||+++++
T Consensus 707 ~~v~~k~~---------------------------~le~~f~~~~e~~~k~~~~i~~~~~te~l~psi~~~~~~f~~~~~ 759 (759)
T KOG1104|consen 707 FVVFQKFI---------------------------ILEAYFLEHEELAQKYSSTIENLVFTEDLDPSISNVFQQFVALRA 759 (759)
T ss_pred HHHhhhhH---------------------------HHHHHHHHHHHHHHHHHHHhhccccccccChHHHHHHHHHhhhcC
Confidence 99999998 889999999999999999999999999999999999999999985
No 2
>PF09088 MIF4G_like: MIF4G like; InterPro: IPR015172 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 1", and is found in nuclear cap-binding proteins and eIF4G. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA.; GO: 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A.
Probab=100.00 E-value=2.9e-65 Score=508.03 Aligned_cols=166 Identities=48% Similarity=0.861 Sum_probs=113.2
Q ss_pred CCCcchHHHHHHHHHHHHHHHhccCHHHHHHHHhcCC-------------------------CCCCchhHHHHHHHHHhh
Q psy8413 310 PGAHSIERFLIEEHLLQIIEMNYFERKDCATQLLKYN-------------------------MKIPLEYCIVEIIFGELF 364 (796)
Q Consensus 310 P~~~sier~l~ee~i~Dii~~~~~nRkecA~~Ll~lp-------------------------~~~~~E~~ivEtIfs~lf 364 (796)
|+.++|+|+|+||+|.|||+.+++||||||+||+++| +++++||+|||||||+||
T Consensus 1 P~~~si~~~l~rd~i~Dii~~~~~NRke~A~~Ll~l~~~f~~~~F~~~~~~~~~l~~~~~~~~~~~~e~~ivE~ifs~mf 80 (191)
T PF09088_consen 1 PPITSIAGFLLRDIIVDIIEILEFNRKECARQLLDLDCYFAPGTFKKRGTSFDQLREEDPSKSTWKIEDLIVETIFSQMF 80 (191)
T ss_dssp -------------------------------------------------------------SS---HHHHHHHHHHHHHT
T ss_pred CcccccccccccccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCcHHHHHHHHHHHHHH
Confidence 7888999999999999999999999999999999875 478999999999999999
Q ss_pred cCCCCCccchhHHHHHHHHhccCCCChhHHHHHHHHHHHhcCccccHHHHHHHHHHHHHHhhccCCcccchhhhhhhcCC
Q psy8413 365 RLPTPKYLEIFYGSVLIELCKMKPDTMPQVLAQATVILFMRIESMNTACFDRFVAWFAYHLSNFQFQWSWEDWESALKLD 444 (796)
Q Consensus 365 ~LP~p~~~~iyY~slLielCk~~P~~i~pv~~~Air~ly~~l~~mD~e~~~Rf~dWFS~hLSNF~F~W~W~eW~~~l~~~ 444 (796)
+||+|+|+.+||+|||+||||++|++||||+|||||+||+|+++||+||++||+||||||||||||+|+|+||++|++++
T Consensus 81 ~LP~p~~~~iyY~sllielCk~~P~~i~pv~~~air~ly~~l~~md~e~~~Rf~dWfS~hLSNF~f~W~W~eW~~~~~l~ 160 (191)
T PF09088_consen 81 QLPSPPHKLIYYHSLLIELCKLSPSAIPPVLGRAIRFLYRNLDSMDFELRDRFVDWFSHHLSNFGFQWKWDEWVDDLELP 160 (191)
T ss_dssp -SS--SS-HHHHHHHHHHHHHHSTTTHHHHHHHHHHHHHHGGGGB-HHHHHHHHHHHHHHHHTTTT---GGGGGGGTTS-
T ss_pred hCCCCCCchhHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHhcCCceeeHHHhhhhhhCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCChHHHHHHHHHHHHhhcchHHHhhhCcc
Q psy8413 445 LEHPKPKFIHEVLNKCVRLSYHQRIKEIVPP 475 (796)
Q Consensus 445 ~~~Pk~~Fi~~~l~KeiRLSy~~rIk~~lPe 475 (796)
+.|||++||+++|+||+||||++||+++|||
T Consensus 161 ~~~pk~~Fi~~~l~k~iRLSy~~rIk~~LPe 191 (191)
T PF09088_consen 161 PLHPKRVFIREVLEKEIRLSYYDRIKESLPE 191 (191)
T ss_dssp TTSHHHHHHHHHHHHHHHTS-HHHHHHHS--
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHHhCCC
Confidence 9999999999999999999999999999997
No 3
>PF09090 MIF4G_like_2: MIF4G like; InterPro: IPR015174 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 2", and is found in nuclear cap-binding proteins and eIF4G. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA.; GO: 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A.
Probab=100.00 E-value=2e-51 Score=434.43 Aligned_cols=248 Identities=45% Similarity=0.773 Sum_probs=211.3
Q ss_pred cccCCCCCCCCCchHHHHHHHHHHHhcCCCHHHHHHHHhhCCCCCCCCCCCCCCChhHHHHHHHHHHhhccchHHhHHHH
Q psy8413 489 FKYNQEGGEHLPGFVYAQELINAIKKKQSSPNEIMAILNKIPSSSMDEDGADPINPLKIDVFTQVLLYLGSKSFSHSFAA 568 (796)
Q Consensus 489 fky~~e~~~~~p~~~~a~~l~~~i~~k~~~~eev~~~l~~i~~~~~~~~~~~~~~~~~i~v~~q~ll~~GsKSfSH~~~~ 568 (796)
|+|.+|++ |+++.|++|+++||+|+ +++|+.++++++++...+++. +++.+++++|+||+|++|||||||++++
T Consensus 1 fky~~e~~---P~~~~a~~l~~~ir~k~-~~eei~~~l~~i~~~~~~~~~--~~~~~~i~v~~q~ll~~GSkS~SH~~~~ 74 (253)
T PF09090_consen 1 FKYENESL---PFHALAQKLLDLIRKKA-PPEEISELLEEIEEPAEEHGS--DFDKFVIDVFVQCLLHIGSKSFSHVLSA 74 (253)
T ss_dssp -TTS-TTS---TTHHHHHHHHHHHHTT---HHHHHHHHTTS--------------HHHHHHHHHHHHHHTTTSHHHHHHH
T ss_pred CCCCCCCC---ccHHHHHHHHHHHHcCC-CHHHHHHHHHhcccccccccc--chhhHHHHHHHHHHHHhcCchHHHHHHH
Confidence 78987766 99999999999999998 999999999999988765432 6778999999999999999999999999
Q ss_pred HHhHHHHHHhhhCCChHHHHHHHHHHHHHHhhCcCeeHHHHHHHHhCCCCChhhhhhhhcccCC-cchhhhhhHHHHHHH
Q psy8413 569 LSKFYKVLKEHIGHTEESQSYVLKSLFELWHDHQQMMAVLIDKMLKTQLLHCSSVANWIFSKEM-QPEFTKLYVWEILHL 647 (796)
Q Consensus 569 iery~~~Lk~l~~~~~~~q~~il~~v~~~W~~~~Q~~~iiidkll~~~iv~p~~Vv~w~F~~~~-~~~~~~~~~Weil~~ 647 (796)
|+||+++||++...++++|.+||++|++||++||||+++|+|||++||||+|.+||+|+|++++ ...|++.|+||++++
T Consensus 75 lery~~~Lk~l~~~~~~~q~~il~~v~~~W~~~~q~~~li~dkll~~~ii~~~~Vv~w~f~~~~~~~~~~~~~~wE~l~~ 154 (253)
T PF09090_consen 75 LERYKEVLKELEAESEEAQFWILDAVFRFWKNNPQMGFLIIDKLLNYGIISPSAVVNWVFSPENGNQELTRSYVWEILNR 154 (253)
T ss_dssp HHHTHHHHHHH-TSSHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTTSS-HHHHHHHHTSGGG-TTTTTSHHHHHHHHH
T ss_pred HHHHHHHHHHhccCChHHHHHHHHHHHHHHhcCCceehHHHHHHHhcCCCCHHHHHHHHcCccccccchhhchHHHHHHH
Confidence 9999999999944499999999999999999999999999999999999999999999999999 889999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhccCCcccccCCCCCccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy8413 648 TIKKMSKYVNRVGKELLDAKERLKHVSSESEEESDGEGGKKNEEKISEEVVEKIEEKLEAAQADQKNLFLIIFQRFIMIL 727 (796)
Q Consensus 648 ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~a~~eqk~l~~~i~~~fv~~L 727 (796)
|++||++|++++++++++++. ++.++.. + +++++.++++|+++..+|+++|..++++|+++|
T Consensus 155 tl~k~~~rv~~~~~~~~~~~~----------~e~~~~~------~--~~~~~~~~~~L~~~~~e~~~~l~~~~~~fv~~l 216 (253)
T PF09090_consen 155 TLRKVTKRVRQVRKELEEAKA----------EENSSEE------D--EEELESLEEKLERALEEQKNLLLLIFQRFVMVL 216 (253)
T ss_dssp HHHHHHHHHHHHHHHHHHHH------------------------H--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhcc----------cccchhh------h--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999982 1101100 1 788999999999999999999999999999999
Q ss_pred ---cccccccCCCCCCccchh-HHHHHHHHHHHHHHH
Q psy8413 728 ---SEHLVRCDTDGVDFNTHW-YKWTIGRLQQVLLAH 760 (796)
Q Consensus 728 ---se~~~~~~~~~~~~~~~W-~~~~~gr~~~~~~~~ 760 (796)
++|...|+.++.++++.| |+|++||+|+|+|+|
T Consensus 217 ~~~~~~~~~~~~~~~~~~~~W~~~~~~g~~k~~~rky 253 (253)
T PF09090_consen 217 VIESEHLVECEQDLRDWDTRWLFRWYVGRLKSFLRKY 253 (253)
T ss_dssp ---HHHHHHHHHHT--SS-HH-HHHHHHHHHHHHHHT
T ss_pred hccCCcccchhhhhHHhccCcHHHHHHHHHHHHHHhC
Confidence 999999999999999999 999999999999998
No 4
>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)
Probab=99.70 E-value=3.4e-16 Score=158.53 Aligned_cols=173 Identities=29% Similarity=0.424 Sum_probs=151.0
Q ss_pred HHHHHHHHhhcCCCCcchhhhHHHHHHHHHHhhHhhHHHHHHHHHHHHHhCCCCchHHHHHHHHHhccCcccHHHHHHHH
Q psy8413 32 DRFEVLIVKVGERSTTSLESHLDGLAKVLETDLATYRVKILRILTDCATKYPEKCCIYTTLVGLLNAKNYNFGGEFVELM 111 (796)
Q Consensus 32 ~~l~~~I~~ige~~~~s~e~~l~~La~~l~~d~~~~~~~i~~~l~~~v~e~P~K~p~yAtLVgllN~kn~~~g~~iv~~l 111 (796)
+++++.+-++++. .++.-+..+.+... +.++.++.+++++++++..+|.++|+||+|++.+|...++||+.+++.+
T Consensus 2 ~~v~~~lnkLs~~---n~~~~~~~l~~~~~-~~~~~~~~l~~~i~~~~~~~~~~~~~ya~L~~~l~~~~~~f~~~ll~~~ 77 (200)
T smart00543 2 KKVKGLINKLSPS---NFESIIKELLKLNN-SDKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLLERL 77 (200)
T ss_pred hHHHHHHhhCCHH---HHHHHHHHHHHHHc-cCHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4688888888753 23333444443332 2357899999999999999999999999999999999999999999999
Q ss_pred HHHHHH---HHhcCChhhHHHHHHHHhhcccccccChhhHHHHHHHHHHhhhcCCCCccchhhHHHHHHhhchhccHHhH
Q psy8413 112 VKTFKD---ALKNCQWNAARYALRFLADLVNCHVISTNSLLQLLENMLDASKEDGVPNVRKDWYVYAVLSCLPWVGRELY 188 (796)
Q Consensus 112 ~~~lq~---~l~~~~w~~~kl~lrFLa~L~n~~Vi~~~sl~~ll~~ll~~a~e~~~~q~R~d~~vy~vL~~LP~~G~~L~ 188 (796)
...|+. ..+.+.|++++..+||||+|++.+|++...+++++..|++...+.+.+ |+++.+++++..|+++|+.+.
T Consensus 78 ~~~f~~~~e~~~~~~~~~~~~~i~fl~eL~~~~~i~~~~i~~~l~~ll~~~~~~~~~--~~~~~ve~l~~lL~~~G~~l~ 155 (200)
T smart00543 78 QEEFEKGLESEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLTKLDPP--RSDFSVECLLSLLPTCGKDLE 155 (200)
T ss_pred HHHHHHHHHHHHHHhhhhHHhHHHHHHHHHHcccCcHHHHHHHHHHHHhccCCCCCC--CcHHHHHHHHHHHHHhhHHHc
Confidence 999999 666789999999999999999999999999999999999988665543 889999999999999999999
Q ss_pred -HhhHHHHHHHHHHHHHHHhhcc
Q psy8413 189 -EKKEQALALLLLNIELYLNKRS 210 (796)
Q Consensus 189 -e~~~~~l~~ll~~i~~yl~~r~ 210 (796)
...+..++.+++.++.|...++
T Consensus 156 ~~~~~~~~~~~l~~l~~~~~~~~ 178 (200)
T smart00543 156 REKSPKLLDEILERLQDYLLKKD 178 (200)
T ss_pred CcccHHHHHHHHHHHHHHHhccc
Confidence 7899999999999999998765
No 5
>KOG2140|consensus
Probab=99.68 E-value=1.3e-14 Score=159.89 Aligned_cols=376 Identities=19% Similarity=0.285 Sum_probs=245.4
Q ss_pred hhHHHHHHHHHHHHHhCCCCchHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHhhcccccccCh
Q psy8413 66 TYRVKILRILTDCATKYPEKCCIYTTLVGLLNAKNYNFGGEFVELMVKTFKDALKNCQWNAARYALRFLADLVNCHVIST 145 (796)
Q Consensus 66 ~~~~~i~~~l~~~v~e~P~K~p~yAtLVgllN~kn~~~g~~iv~~l~~~lq~~l~~~~w~~~kl~lrFLa~L~n~~Vi~~ 145 (796)
.+|+.+++.+++++...|..+|+|||||+|+|+|.|.+|+.++.+++.+|++.++.++.-.|-.++.|+|||+|+.|++.
T Consensus 194 rgRgl~crsv~~aq~asp~ft~vyaALvAviNskfP~IgElLlkrLilqf~r~f~RnDk~~c~~~~kfiahLinq~VahE 273 (739)
T KOG2140|consen 194 RGRGLLCRSVMQAQAASPGFTPVYAALVAVINSKFPQIGELLLKRLILQFKRSFRRNDKVSCLNASKFIAHLINQQVAHE 273 (739)
T ss_pred hccchhHHHHHHHHhcCCCCcHHHHHHHHHHccCCchHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHH
Confidence 37999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHhhhcCCCCccchhhHHHHHHhhchhccHHhHHhhHHHHHHHHHHHHHHHhhcccccccccccccCCCC
Q psy8413 146 NSLLQLLENMLDASKEDGVPNVRKDWYVYAVLSCLPWVGRELYEKKEQALALLLLNIELYLNKRSKKHVAALQVWSSDKP 225 (796)
Q Consensus 146 ~sl~~ll~~ll~~a~e~~~~q~R~d~~vy~vL~~LP~~G~~L~e~~~~~l~~ll~~i~~yl~~r~~~~~~ll~~~~~~~~ 225 (796)
.-.++++..||+.++++++ .++...|..||..|.+-++.++++|+++++..+..-.
T Consensus 274 Iv~Leil~lLLe~PTddSv---------evaI~flkecGakL~~VSpr~~n~IfErlR~ILhe~E--------------- 329 (739)
T KOG2140|consen 274 IVALEILTLLLERPTDDSV---------EVAIAFLKECGAKLAEVSPRALNGIFERLRYILHEGE--------------- 329 (739)
T ss_pred HHHHHHHHHHhcCCCCchH---------HHHHHHHHHHHHHHHHhChHHHhHHHHHHHHHHhHhh---------------
Confidence 9999999999999999998 9999999999999999999999999999997663211
Q ss_pred CChhhHHHHHHHHHHHHHhCCccccccCCCcchhhhhhhh---hhcCCCC------------CCCCCCC-C-CCCCCCCC
Q psy8413 226 HPQEEYLDCLWAQIVKLRQDNWTDHHIYRPYTVFDSRLSV---ALQHNLP------------NIILPPH-H-DSLIYPMP 288 (796)
Q Consensus 226 ~~~~d~l~~L~~qi~~l~~~~w~~~~i~rpy~~f~~~L~~---a~~h~Lp------------~~~~p~~-~-~~~~y~~P 288 (796)
-+..+.-+..-+=..++++++....-.+-+ .|.+ --.|.|+ .|..-|. . ...+|..
T Consensus 330 --ld~rvqy~iEtlf~iRkdkfk~~p~v~~~L----Dlvee~dq~tH~l~l~de~dpe~~L~vFk~dp~f~ene~kyda- 402 (739)
T KOG2140|consen 330 --LDRRVQYMIETLFQIRKDKFKSHPAVLEEL----DLVEEEDQITHSLSLEDEDDPEKELGVFKKDPNFEENEEKYDA- 402 (739)
T ss_pred --HHHHHHHHHHHHHHHHHHhhccCCcccccc----CccchhhheeeeeecccccChhhhhcccccCccHHHHHHHHHH-
Confidence 112233333333344566665421111111 0000 0112221 1110000 0 0000000
Q ss_pred eeEEEeccCCCC---------------CCCCC---C---CCCCCCcchHHHHHHHHHHHHHHHhccCHHHHHHHHhcC--
Q psy8413 289 SVVFRMFDYTDC---------------PEEPS---I---SPLPGAHSIERFLIEEHLLQIIEMNYFERKDCATQLLKY-- 345 (796)
Q Consensus 289 ~~~frlf~~~~~---------------~~~~~---~---~~lP~~~sier~l~ee~i~Dii~~~~~nRkecA~~Ll~l-- 345 (796)
.-=.+...++. +++.. . ..+-+.++..=.=|+.-|.=+|.+ ..+=.|||..||-+
T Consensus 403 -ikkeiLgn~dsen~d~~~~s~E~~~eee~e~~ee~~e~~qI~D~T~~Nlv~frr~IYLti~S-SldfeEaaHKLLKmki 480 (739)
T KOG2140|consen 403 -IKKEILGNEDSENEDDEDGSSEDDDEEEDESVEEDEEKLQIIDMTETNLVNFRRTIYLTIQS-SLDFEEAAHKLLKMKI 480 (739)
T ss_pred -HHHHHhcCCcccccccccccccccccccccccccccccceeeccccchhHHhhhhheeeeec-cCcHHHHHHHHHhccC
Confidence 00000111111 00000 0 011111122222334444433332 35567999999875
Q ss_pred CCC--CCchhHHHHHHHHHhhcCCCCCccchhHHHHHHHHhccCCCChhHHHHHHHHHHHhcCccccHHHHHHHHHHHHH
Q psy8413 346 NMK--IPLEYCIVEIIFGELFRLPTPKYLEIFYGSVLIELCKMKPDTMPQVLAQATVILFMRIESMNTACFDRFVAWFAY 423 (796)
Q Consensus 346 p~~--~~~E~~ivEtIfs~lf~LP~p~~~~iyY~slLielCk~~P~~i~pv~~~Air~ly~~l~~mD~e~~~Rf~dWFS~ 423 (796)
|.. ..+=++|+++-.-+ ....=||+.|.-..|++.- .--..+.+++.--|..|..++..-.+-++-+|+|
T Consensus 481 p~~q~~elc~mii~cc~Qe-------rTy~kFYglL~eRfc~l~r-~~q~~fe~~f~q~YstIhr~EtnkLRnlakffah 552 (739)
T KOG2140|consen 481 PESQEKELCNMIIDCCAQE-------RTYEKFYGLLGERFCMLHR-EWQEAFEKCFKQQYSTIHRYETNKLRNLAKFFAH 552 (739)
T ss_pred CchhhHHHHHHHHHHhhhH-------HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 432 33445667765433 1335689999899999874 3456788888888888888988877888999999
Q ss_pred HhhccCCcccchhhhhhhcC---CCCCChHHHHHHHHHHHHhh----cchHHHhh-hCcccccccCCCCC
Q psy8413 424 HLSNFQFQWSWEDWESALKL---DLEHPKPKFIHEVLNKCVRL----SYHQRIKE-IVPPQFAPLLPLKP 485 (796)
Q Consensus 424 hLSNF~F~W~W~eW~~~l~~---~~~~Pk~~Fi~~~l~KeiRL----Sy~~rIk~-~lPe~~~~llp~~p 485 (796)
-||-=-.-|. --.|+.+ +....-|.||+=+..-.+-- .-+.|+.+ +|-+.|+.++|-..
T Consensus 553 Llstd~lpw~---vl~~ikLTEEdTtsssRIfiKilFqELve~lGl~~L~~RL~dptl~~~l~glFP~dn 619 (739)
T KOG2140|consen 553 LLSTDALPWD---VLACIKLTEEDTTSSSRIFIKILFQELVEALGLDKLNERLNDPTLQPKLEGLFPRDN 619 (739)
T ss_pred HhcccccchH---HHHHhhcccccCCccceehHHHHHHHHHHHhChHHHHHHhcCcchhhhhhccCcCCC
Confidence 9986555554 3344333 33334478877665544432 33455554 56667888998753
No 6
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=99.58 E-value=9.5e-14 Score=140.74 Aligned_cols=197 Identities=19% Similarity=0.306 Sum_probs=167.6
Q ss_pred HHHHHHHHhhcCCCCcchhhhHHHHHHHHHHhhHhhHHHHHHHHHHHHHhCCCCchHHHHHHHHHhccCc-ccHHHHHHH
Q psy8413 32 DRFEVLIVKVGERSTTSLESHLDGLAKVLETDLATYRVKILRILTDCATKYPEKCCIYTTLVGLLNAKNY-NFGGEFVEL 110 (796)
Q Consensus 32 ~~l~~~I~~ige~~~~s~e~~l~~La~~l~~d~~~~~~~i~~~l~~~v~e~P~K~p~yAtLVgllN~kn~-~~g~~iv~~ 110 (796)
++++..|-++.+. .++.-++.+.+....+.++..+.+++++++++.++|+++|+||.|++.++...+ +||..++++
T Consensus 2 r~v~~~lnklt~~---n~~~~~~~l~~~~~~~~~~~~~~i~~~i~~~a~~~~~~~~~~a~l~~~l~~~~~~~f~~~ll~~ 78 (209)
T PF02854_consen 2 RKVRGILNKLTPS---NFESIIDELIKLNWSDDPETLKEIVKLIFEKAVEEPNFSPLYARLCAALNSRFPSEFRSLLLNR 78 (209)
T ss_dssp HHHHHHHHHCSST---THHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSGGGHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_pred chHHHHHHHCCHH---HHHHHHHHHHHHHhhccHHHHHHHHHHHhhhhhcCchHHHHHHHHHHHHhccchhhHHHHHHHH
Confidence 5788999999854 255555555555544446789999999999999999999999999999999999 999999999
Q ss_pred HHHHHHH--------HHhcCChhhHHHHHHHHhhcccccccChhhHHHHHHHHHHhhhcCCCCccchhhHHHHHHhhchh
Q psy8413 111 MVKTFKD--------ALKNCQWNAARYALRFLADLVNCHVISTNSLLQLLENMLDASKEDGVPNVRKDWYVYAVLSCLPW 182 (796)
Q Consensus 111 l~~~lq~--------~l~~~~w~~~kl~lrFLa~L~n~~Vi~~~sl~~ll~~ll~~a~e~~~~q~R~d~~vy~vL~~LP~ 182 (796)
+...|+. ......+.+.+..+||+|+|.+.+|+++..+++++..|+....+... +.+.+..+++++..|++
T Consensus 79 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~fl~eL~~~~vv~~~~i~~~l~~ll~~~~~~~~-~~~~~~~ie~~~~lL~~ 157 (209)
T PF02854_consen 79 CQEEFEERYSNEELEENRQSSKQRRRGNIRFLAELFNFGVVSEKIIFDILRELLSDGTDECQ-PPPDEENIECLCTLLKT 157 (209)
T ss_dssp HHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHTSHHCC-HHTCHHHHHHHHHHHHH
T ss_pred HHHHHHHhhhhhhHHHHHHHHHHHHhhhhhHHHhhHhhccccchhHHHHHHHHHhccccccc-CCCcHhHHHHHHHHHHH
Confidence 9999999 66678899999999999999999999999999999999998877554 67788899999999999
Q ss_pred ccHHhH--HhhHHHHHHHHHHHHHHHhhcccccccccccccCCCCCChhhHHHHHHHHHHHHHhCC
Q psy8413 183 VGRELY--EKKEQALALLLLNIELYLNKRSKKHVAALQVWSSDKPHPQEEYLDCLWAQIVKLRQDN 246 (796)
Q Consensus 183 ~G~~L~--e~~~~~l~~ll~~i~~yl~~r~~~~~~ll~~~~~~~~~~~~d~l~~L~~qi~~l~~~~ 246 (796)
+|+.+. +..+..++.+++.++.|...... ......+..++..+-.+++|+
T Consensus 158 ~G~~l~~~~~~~~~l~~~~~~~~~~~~~~~~--------------~~~~~r~~~~l~~l~~lr~~~ 209 (209)
T PF02854_consen 158 CGKKLENSEESPKALDEIFERLQKYANSKKD--------------PNLSSRIRFMLEDLIELRNNK 209 (209)
T ss_dssp HHHHHHHCHHHHHHHHHHHHHHHHHHHHCHS--------------SSSSHHHHHHHHHHHHHHHTC
T ss_pred HHHHHhcCCCchhHHHHHHHHHHHHHHhhcc--------------cCCCHHHHHHHHHHHHHhcCC
Confidence 999999 88899999999999999877530 011245777888888888764
No 7
>KOG2141|consensus
Probab=97.92 E-value=0.0015 Score=76.39 Aligned_cols=385 Identities=15% Similarity=0.199 Sum_probs=222.0
Q ss_pred hHHHHHHHHHHhhcCCCCcchhhhHHHHHHHHHHhh--HhhHHHHHHHHHHHHHhCCCCchHHHHHHHHHhccC-cccHH
Q psy8413 29 ELEDRFEVLIVKVGERSTTSLESHLDGLAKVLETDL--ATYRVKILRILTDCATKYPEKCCIYTTLVGLLNAKN-YNFGG 105 (796)
Q Consensus 29 ~~~~~l~~~I~~ige~~~~s~e~~l~~La~~l~~d~--~~~~~~i~~~l~~~v~e~P~K~p~yAtLVgllN~kn-~~~g~ 105 (796)
.+..++.+.|-++.|.....+--+|+.|..-+.+.. ..+-..+.++++.-..-+-.-+..||+|..-|.+.- -++|.
T Consensus 318 rl~rkv~g~LNKLSdaNi~~I~~~i~~Ly~~~sr~~v~~sLtk~l~~~~~~~~~~ld~~~~~y~AL~~~l~~~vg~eiga 397 (822)
T KOG2141|consen 318 RLRRKVNGSLNKLSDANIIKIIAGIAELYMNNSRYDVTSSLTKLLLKALLGPFRLLDSLLTTYAALAAMLHTMVGNEIGA 397 (822)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHH
Confidence 344455556666666532222223333332221111 123445556665555556667789999999998865 68999
Q ss_pred HHHHHHHHHHHHHHhcCChh-----hHHHHHHHHhhcccccccChhhHHHHHHHHHHhhhcCCCCccchhhHHHHHHhhc
Q psy8413 106 EFVELMVKTFKDALKNCQWN-----AARYALRFLADLVNCHVISTNSLLQLLENMLDASKEDGVPNVRKDWYVYAVLSCL 180 (796)
Q Consensus 106 ~iv~~l~~~lq~~l~~~~w~-----~~kl~lrFLa~L~n~~Vi~~~sl~~ll~~ll~~a~e~~~~q~R~d~~vy~vL~~L 180 (796)
-+++.++..|-.++++-.-. .+-.++-|+|.|+|-+|++..-++.++..|.+..+|.++ .++|..+
T Consensus 398 hf~q~~ve~f~~~~~~~~~~~~~~K~~~Nl~~~l~ylynF~ivs~~LiydiI~kl~~~l~e~~v---------e~ll~ii 468 (822)
T KOG2141|consen 398 HFLQTFVEDFLKSYKEEEEMDLKDKSLNNIVLFLSYLYNFGIVSCSLIYDIIRKLAENLNETNV---------EALLTII 468 (822)
T ss_pred HHHHHHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHhhcccHHHHHHHHHHHHhchhhhhH---------HHHHHHH
Confidence 99999999998888864333 377889999999999999999999999999999999998 9999999
Q ss_pred hhccHHhHHhhHHHHHHHHHHHHHHHhhcccccccccccccCCCCCChhhHHHHHHHHHHHHHhCCccccccCCCcchhh
Q psy8413 181 PWVGRELYEKKEQALALLLLNIELYLNKRSKKHVAALQVWSSDKPHPQEEYLDCLWAQIVKLRQDNWTDHHIYRPYTVFD 260 (796)
Q Consensus 181 P~~G~~L~e~~~~~l~~ll~~i~~yl~~r~~~~~~ll~~~~~~~~~~~~d~l~~L~~qi~~l~~~~w~~~~i~rpy~~f~ 260 (796)
-+||..|-.+.+.++..++..+..-.++-+... .+ -.+--++.-+..|..|+.+-....-|.. ++
T Consensus 469 ~~~G~~LRkDDp~alk~~i~eiq~~a~~a~~s~---~~-----------pR~rFmleti~aLKnN~~kki~~~d~e~-ve 533 (822)
T KOG2141|consen 469 ANCGFSLRKDDPLALKDIITEIQSKAASAKISA---IS-----------PRLRFMLETISALKNNKLKKIPYADPER-VE 533 (822)
T ss_pred HHccchhcCCChHHHHHHHHHHHHHhhcCCccc---cc-----------hHHHHHHHHHHHHhcCCCcCCCcCChHH-HH
Confidence 999999999999999999999998665443321 11 1233334444444444433211001100 10
Q ss_pred hhhh--------hh-hcCCCC------CCCCCCCC-----CCCCCCCCeeEEEeccCCC--CCCCCCC-CCCCC------
Q psy8413 261 SRLS--------VA-LQHNLP------NIILPPHH-----DSLIYPMPSVVFRMFDYTD--CPEEPSI-SPLPG------ 311 (796)
Q Consensus 261 ~~L~--------~a-~~h~Lp------~~~~p~~~-----~~~~y~~P~~~frlf~~~~--~~~~~~~-~~lP~------ 311 (796)
.|. .+ ....+| .+..++.. -|+.|..|.- |-.+..+. ...++.. -+.|+
T Consensus 534 -~lrk~~k~l~~~~~s~~~~~l~vTledll~ae~kGrWWlVGsaw~g~~~-~~~s~~~~~d~~~~k~~~gs~~~kmL~lA 611 (822)
T KOG2141|consen 534 -NLRKLKKALGSSASSSVSLPLSVTLEDLLHAEQKGRWWLVGSAWRGNEQ-FMGSINTASDSAKSKKAEGSFADKMLELA 611 (822)
T ss_pred -HHHHHHHHHHhccchhhhccccccHHHhhChHhcCceEEecchhcCCcc-cccccchHhHHhhhhcccCCccHHHHHHH
Confidence 010 11 001111 11112111 1333332211 11111110 0000000 00000
Q ss_pred -----CcchHHHHHHHHHH--HHHHHhccCHHHHHHHHhcCC--C-C-CCchhHHHHHHHHHhhcCCCCCccchhHHHHH
Q psy8413 312 -----AHSIERFLIEEHLL--QIIEMNYFERKDCATQLLKYN--M-K-IPLEYCIVEIIFGELFRLPTPKYLEIFYGSVL 380 (796)
Q Consensus 312 -----~~sier~l~ee~i~--Dii~~~~~nRkecA~~Ll~lp--~-~-~~~E~~ivEtIfs~lf~LP~p~~~~iyY~slL 380 (796)
.++|-|.||=.+.. |-|+.| ..|+-|. . + --|-|+++.+.+.+=. .--||..|.
T Consensus 612 rkqrMNTdiRr~IFcsImsaeDyiDAF--------EklLkL~LK~~Q~rEI~~VllhC~l~EK~-------yNpfYa~lA 676 (822)
T KOG2141|consen 612 RKQRMNTDIRRAIFCSIMSAEDYIDAF--------EKLLKLSLKGKQEREIARVLLHCCLNEKT-------YNPFYALLA 676 (822)
T ss_pred HHhhcchHhhhhheeeeecchHHHHHH--------HHHHhccCCCcchHHHHHHHHHHHhhhcc-------cchHHHHHH
Confidence 01121111111110 222222 2343332 1 1 2356788887776533 346999999
Q ss_pred HHHhccCCCChhHHHHHHHHHHHhcCccccHHHHHHHHHHHHHHhhccCCccc---chhhhhhhcCCCCCChHHHHHHHH
Q psy8413 381 IELCKMKPDTMPQVLAQATVILFMRIESMNTACFDRFVAWFAYHLSNFQFQWS---WEDWESALKLDLEHPKPKFIHEVL 457 (796)
Q Consensus 381 ielCk~~P~~i~pv~~~Air~ly~~l~~mD~e~~~Rf~dWFS~hLSNF~F~W~---W~eW~~~l~~~~~~Pk~~Fi~~~l 457 (796)
.-+|...- .+--.|.-|+==.|+.++.|-.--+.-++-.++|-++|+..+.. =-+|. +++ .+...|++.++
T Consensus 677 ~KfCe~~~-~~~~tfQF~~WD~f~ele~ls~~ri~nLa~l~a~Li~~~~lsLtVLK~Vdfm---~l~--~~~~~fl~~~l 750 (822)
T KOG2141|consen 677 LKFCEFNK-NLKKTFQFALWDRFKELEQLSLFRISNLAKLLASLISNAVLSLTVLKHVDFM---ELN--ARRTTFLKKLL 750 (822)
T ss_pred HHHHHHhh-hhHHHHHHHHHHHHHHhhhcchhhHhHHHHHHHHHHHhcccceeeeeeccHh---hcC--hHHHHHHHHHH
Confidence 99999764 34556666776678888888888888899999999999998854 24444 332 35577877666
Q ss_pred HHH
Q psy8413 458 NKC 460 (796)
Q Consensus 458 ~Ke 460 (796)
-..
T Consensus 751 ~~l 753 (822)
T KOG2141|consen 751 FGL 753 (822)
T ss_pred HHH
Confidence 443
No 8
>KOG2051|consensus
Probab=96.71 E-value=0.0095 Score=72.53 Aligned_cols=128 Identities=18% Similarity=0.267 Sum_probs=105.7
Q ss_pred hHHHHHHHHHHHHHhCCCCchHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhcCCh--hhHH-HHHHHHhhccccccc
Q psy8413 67 YRVKILRILTDCATKYPEKCCIYTTLVGLLNAKNYNFGGEFVELMVKTFKDALKNCQW--NAAR-YALRFLADLVNCHVI 143 (796)
Q Consensus 67 ~~~~i~~~l~~~v~e~P~K~p~yAtLVgllN~kn~~~g~~iv~~l~~~lq~~l~~~~w--~~~k-l~lrFLa~L~n~~Vi 143 (796)
.|+.++++++.....+=...|+|+.+|+.+..-.+++..++|..+-..|+..+.+.+- ...| .++||++.|+--+++
T Consensus 459 ~RkrLvKal~~vprt~ldllPyYsRlVAtl~~~M~dvat~lv~~L~~eFr~~~hkK~q~~ietk~~~VrfIsEL~KF~lv 538 (1128)
T KOG2051|consen 459 NRKRLVKALFVVPRTRLDLLPYYSRLVATLSKCMPDVATELVTMLRKEFRSHLHKKAQINIETKLKIVRFISELCKFQLV 538 (1128)
T ss_pred HHHHHHHhhhcccchhhhhhhHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhHHhhhhhCcc
Confidence 6889999998888888899999999999999999999999999999999999998733 2333 569999999999999
Q ss_pred ChhhHHHHHHHHHHhhhcCCCCccchhhHHHHHHhhchhccHHhHHhhHH--HHHHHHHHHH
Q psy8413 144 STNSLLQLLENMLDASKEDGVPNVRKDWYVYAVLSCLPWVGRELYEKKEQ--ALALLLLNIE 203 (796)
Q Consensus 144 ~~~sl~~ll~~ll~~a~e~~~~q~R~d~~vy~vL~~LP~~G~~L~e~~~~--~l~~ll~~i~ 203 (796)
+...++..|+.|+.--.--++ .++...|--+|++|+..-.. -+..+++.+.
T Consensus 539 ~~~~if~cLk~ll~dF~~hnI---------Em~c~lLE~~GrfLlr~pEt~lrM~~~Le~i~ 591 (1128)
T KOG2051|consen 539 PKFEIFSCLKMLLNDFTHHNI---------EMACVLLESCGRFLLRSPETKLRMRVFLEQIK 591 (1128)
T ss_pred ChHHHHHHHHHHHHhcccccH---------HHHHHHHHhcchhhhcChhHHHHHHHHHHHHH
Confidence 999999999999885554444 67777778899999985433 3445555554
No 9
>KOG2051|consensus
Probab=86.47 E-value=22 Score=44.66 Aligned_cols=173 Identities=13% Similarity=0.205 Sum_probs=112.6
Q ss_pred HHHHHH-hhcCCCCcchhhhHHHHHHHHHHhhHhhHHHHHHHHHHHHHhCCCCchHHHHHHHHHhccCcccHHHHHHHHH
Q psy8413 34 FEVLIV-KVGERSTTSLESHLDGLAKVLETDLATYRVKILRILTDCATKYPEKCCIYTTLVGLLNAKNYNFGGEFVELMV 112 (796)
Q Consensus 34 l~~~I~-~ige~~~~s~e~~l~~La~~l~~d~~~~~~~i~~~l~~~v~e~P~K~p~yAtLVgllN~kn~~~g~~iv~~l~ 112 (796)
+|.+|. .|.+. ++. .+-++-+-+.+..++.+.-++.+|++.=.--=.-++..|.|++=|-+-.++||--||+.+.
T Consensus 634 iR~Li~~dL~k~---tvd-~~lkllRkl~W~D~e~~~yli~~~~k~w~iky~~i~~lA~llaGL~~y~~~fvi~VID~vl 709 (1128)
T KOG2051|consen 634 IRYLIRSDLSKD---TVD-RVLKLLRKLDWSDPEVKQYLISCFSKPWKIKYQNIHALASLLAGLSSYHPEFVIHVIDHVL 709 (1128)
T ss_pred HHHHHHHHhccc---cHH-HHHHHHHhcccccHHHHHHHHHHhhhhhccccccHHHHHHHHHHHHhhchhhhhhhHHHHH
Confidence 566665 44443 122 2333334444565666777777666543333334677888887777889999999999999
Q ss_pred HHHHHHHhcCCh---hhHHHHHHHHhhcccccccChhhHHHHHHHHHHhhhcCC-CCc---cchh-hHHHHHHhhchhcc
Q psy8413 113 KTFKDALKNCQW---NAARYALRFLADLVNCHVISTNSLLQLLENMLDASKEDG-VPN---VRKD-WYVYAVLSCLPWVG 184 (796)
Q Consensus 113 ~~lq~~l~~~~w---~~~kl~lrFLa~L~n~~Vi~~~sl~~ll~~ll~~a~e~~-~~q---~R~d-~~vy~vL~~LP~~G 184 (796)
+.++..|.-++. .+....+|||+.|.|-.++..+.|+..|-.++....-.+ .|. +-.| +=+..|...|--||
T Consensus 710 E~Ir~glEin~~~~nQrriA~aryL~ELynfemvds~vIl~tLy~~i~~g~~~~~~~~~ldppddlFRirlV~~lL~tc~ 789 (1128)
T KOG2051|consen 710 EDIRPGLEINDYVSNQRRIALARYLGELYNFEMVDSDVILNTLYHLISLGHFENLTPSALDPPDDLFRIRLVCMLLQTCG 789 (1128)
T ss_pred HHHHhhhhcCcHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHhcccccCCCCcccCCChHHHHHHHHHHHHHHHcc
Confidence 999999995543 466788999999999999999999999999988663333 332 2222 23334444444455
Q ss_pred HHhHHh-hHHHHHHHHHHHHHHHhhcc
Q psy8413 185 RELYEK-KEQALALLLLNIELYLNKRS 210 (796)
Q Consensus 185 ~~L~e~-~~~~l~~ll~~i~~yl~~r~ 210 (796)
+++-.. ...-+...+-.++-|+-.-+
T Consensus 790 ~yf~rgs~kkkl~~fL~~fq~Y~~iKk 816 (1128)
T KOG2051|consen 790 PYFTRGSTKKKLDQFLVAFQRYILIKK 816 (1128)
T ss_pred cccccchhHHHHHHHHHHHHHHhhccc
Confidence 533221 22346677778888875544
No 10
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=74.38 E-value=36 Score=31.19 Aligned_cols=97 Identities=14% Similarity=0.247 Sum_probs=71.8
Q ss_pred HHHHHHHHhc--cCHHHHHHHHhcCCCCCCchhHHHHHHHHHhhcCCCCCccchhHHHHHHHHhccCCCChhHHHHHHHH
Q psy8413 323 HLLQIIEMNY--FERKDCATQLLKYNMKIPLEYCIVEIIFGELFRLPTPKYLEIFYGSVLIELCKMKPDTMPQVLAQATV 400 (796)
Q Consensus 323 ~i~Dii~~~~--~nRkecA~~Ll~lp~~~~~E~~ivEtIfs~lf~LP~p~~~~iyY~slLielCk~~P~~i~pv~~~Air 400 (796)
.|..+|..|- .|=.|+++-|..++.+ ...+-+|..++...+.- .+...=||+.|+..||+... ..+..|.+++.
T Consensus 4 ~i~~~l~ey~~~~D~~ea~~~l~~L~~~-~~~~~vv~~~i~~~le~--~~~~~~~~~~Ll~~L~~~~~-~~~~~~~~~f~ 79 (113)
T smart00544 4 KIFLIIEEYLSSGDTDEAVHCLLELKLP-EQHHEVVKVLLTCALEE--KRTYREMYSVLLSRLCQANV-ISTKQFEKGFW 79 (113)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhCCC-cchHHHHHHHHHHHHcC--CccHHHHHHHHHHHHHHcCC-cCHHHHHHHHH
Confidence 3444554442 3788999999998855 58888999999998874 23345689999999998775 45678999999
Q ss_pred HHHhcCccccHH---HHHHHHHHHHH
Q psy8413 401 ILFMRIESMNTA---CFDRFVAWFAY 423 (796)
Q Consensus 401 ~ly~~l~~mD~e---~~~Rf~dWFS~ 423 (796)
-+|+.++.+.++ ....++..++.
T Consensus 80 ~~~~~l~dl~~D~P~a~~~la~~~a~ 105 (113)
T smart00544 80 RLLEDIEDLELDIPNAWRNLAEFVAR 105 (113)
T ss_pred HHHhhChhhhcccccHHHHHHHHHHH
Confidence 999999987663 45555555544
No 11
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=66.61 E-value=48 Score=30.30 Aligned_cols=101 Identities=14% Similarity=0.229 Sum_probs=71.8
Q ss_pred HHHHHHHHHHhc--cCHHHHHHHHhcCCCCCCchhHHHHHHHHHhhcCCCCCccchhHHHHHHHHhccCCCChhHHHHHH
Q psy8413 321 EEHLLQIIEMNY--FERKDCATQLLKYNMKIPLEYCIVEIIFGELFRLPTPKYLEIFYGSVLIELCKMKPDTMPQVLAQA 398 (796)
Q Consensus 321 ee~i~Dii~~~~--~nRkecA~~Ll~lp~~~~~E~~ivEtIfs~lf~LP~p~~~~iyY~slLielCk~~P~~i~pv~~~A 398 (796)
+..+..+|..|- .|-.|++..|..+..+ ....-+|..++...+.- .+..-=||+.|+..||+..- .-...+.+|
T Consensus 2 rk~i~~~l~ey~~~~d~~ea~~~l~el~~~-~~~~~vv~~~l~~~le~--~~~~r~~~~~Ll~~L~~~~~-~~~~~~~~g 77 (113)
T PF02847_consen 2 RKKIFSILMEYFSSGDVDEAVECLKELKLP-SQHHEVVKVILECALEE--KKSYREYYSKLLSHLCKRKL-ISKEQFQEG 77 (113)
T ss_dssp HHHHHHHHHHHHHHT-HHHHHHHHHHTT-G-GGHHHHHHHHHHHHHTS--SHHHHHHHHHHHHHHHHTTS-S-HHHHHHH
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHhCCC-ccHHHHHHHHHHHHhhc--cHHHHHHHHHHHHHHHhcCC-CCHHHHHHH
Confidence 344555555442 4788999999988755 78889999999999986 23334689999999998653 445679999
Q ss_pred HHHHHhcCccccHH---HHHHHHHHHHHHh
Q psy8413 399 TVILFMRIESMNTA---CFDRFVAWFAYHL 425 (796)
Q Consensus 399 ir~ly~~l~~mD~e---~~~Rf~dWFS~hL 425 (796)
+.-+++.++.+... ....++..+++=+
T Consensus 78 f~~~l~~l~Dl~~D~P~~~~~la~~~~~~i 107 (113)
T PF02847_consen 78 FEDLLESLEDLELDIPKAPEYLAKFLARLI 107 (113)
T ss_dssp HHHHHHHHHHHHHHSTTHHHHHHHHHHHHH
T ss_pred HHHHHhHhhhccccchHHHHHHHHHHHHHH
Confidence 99999999876666 5555555555433
No 12
>PF09403 FadA: Adhesion protein FadA; InterPro: IPR018543 FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices. ; PDB: 3ETZ_B 3ETY_A 2GL2_B 3ETX_C 3ETW_A.
Probab=65.41 E-value=1e+02 Score=29.60 Aligned_cols=103 Identities=18% Similarity=0.304 Sum_probs=65.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhccCCcccccCCCCCccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Q psy8413 651 KMSKYVNRVGKELLDAKERLKHVSSESEEESDGEGGKKNEEKISEEVVEKIEEKLEAAQADQKNLFLIIFQRFIMILSEH 730 (796)
Q Consensus 651 kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~a~~eqk~l~~~i~~~fv~~Lse~ 730 (796)
-|-+++.++..+++.+..+... .-.......+.++....+++++...+-.+.-.+-.
T Consensus 24 ~v~~~l~~LEae~q~L~~kE~~---------------------r~~~~k~~ae~a~~~L~~~~~~~~~i~e~~~kl~~-- 80 (126)
T PF09403_consen 24 SVESELNQLEAEYQQLEQKEEA---------------------RYNEEKQEAEAAEAELAELKELYAEIEEKIEKLKQ-- 80 (126)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH---------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHHHHHHHH---------------------HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH--
Confidence 3666788888888877653211 11122233445555666666766666555544432
Q ss_pred ccccCCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchhHHHHHHHHHhcc
Q psy8413 731 LVRCDTDGVDFNTHWYKWTIGRLQQVLLAHHEQVQKYSSTLETLLFTQDLEPHILDVFHQFLALN 795 (796)
Q Consensus 731 ~~~~~~~~~~~~~~W~~~~~gr~~~~~~~~~~~~~~~~~~L~~~~ft~~~d~~i~~vf~qf~al~ 795 (796)
+.++-||+ +-++++.-+|.+...+.-..+... ..+.+-|+++.|||
T Consensus 81 ---------~~~~r~yk---~eYk~llk~y~~~~~~L~k~I~~~-------e~iI~~fe~i~~~~ 126 (126)
T PF09403_consen 81 ---------DSKVRWYK---DEYKELLKKYKDLLNKLDKEIAEQ-------EQIIDNFEKIQSLR 126 (126)
T ss_dssp ---------HGGGSTTH---HHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHH
T ss_pred ---------hcchhHHH---HHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhcC
Confidence 12366887 668888888877777766666653 68889999999886
No 13
>KOG1760|consensus
Probab=61.19 E-value=33 Score=32.58 Aligned_cols=82 Identities=16% Similarity=0.304 Sum_probs=51.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCC------cccccCC---CCC--------------ccccccCHHHHHHH
Q psy8413 645 LHLTIKKMSKYVNRVGKELLDAKERLKHVSSES------EEESDGE---GGK--------------KNEEKISEEVVEKI 701 (796)
Q Consensus 645 l~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~------~~~~~~~---~~~--------------~~~~~~~~~~~e~~ 701 (796)
.-|-+.+.+.|+.++..+++.+|.+..--+..+ +.++++- .|. ++..+..+..++.+
T Consensus 21 ~iN~Fsrl~~R~~~lk~dik~~k~~~enledA~~EieL~Dedd~~Ip~~vGdvF~~~~~~~~~~~LEe~ke~l~k~i~~l 100 (131)
T KOG1760|consen 21 NINEFSRLNSRKDDLKADIKEAKTEIENLEDASNEIELLDEDDEDIPFKVGDVFIHVKLDKLQDQLEEKKETLEKEIEEL 100 (131)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhhHhhcCccccccceehhhhheeccHHHHHHHHHHHHHHHHHHHHHH
Confidence 446788899999999999999998874432222 1111110 000 01122234566667
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8413 702 EEKLEAAQADQKNLFLIIFQRFIMI 726 (796)
Q Consensus 702 ~~~l~~a~~eqk~l~~~i~~~fv~~ 726 (796)
+.+++...+...+|=..++.+|-.-
T Consensus 101 es~~e~I~~~m~~LK~~LYaKFgdn 125 (131)
T KOG1760|consen 101 ESELESISARMDELKKVLYAKFGDN 125 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccc
Confidence 7777777777777888888888653
No 14
>PF03378 CAS_CSE1: CAS/CSE protein, C-terminus; InterPro: IPR005043 Mammalian cellular apoptosis susceptibility (CAS) proteins and the yeast chromosome-segregation protein, CSE1 are homologous []. CAS is involved in both cellular apoptosis and proliferation [, ]. Apoptosis is inhibited in CAS-depleted cells, while the expression of CAS correlates to the degree of cellular proliferation. Like CSE1, it is essential for the mitotic checkpoint in the cell cycle (CAS depletion blocks the cell in the G2 phase), and has been shown to be associated with the microtubule network and the mitotic spindle [], as is the protein MEK, which is thought to regulate the intracellular localization (predominantly nuclear vs. predominantly cytosolic) of CAS. In the nucleus, CAS acts as a nuclear transport factor in the importin pathway []. The importin pathway mediates the nuclear transport of several proteins that are necessary for mitosis and further progression. CAS is therefore thought to affect the cell cycle through its effect on the nuclear transport of these proteins []. Since apoptosis also requires the nuclear import of several proteins (such as P53 and transcription factors), it has been suggested that CAS also enables apoptosis by facilitating the nuclear import of at least a subset of these essential proteins []. This entry represents the C-terminal portion of these proteins. Structural studies of the yeast CSE1 protein indicate that this domain binds to both the transport-orchestrating protein RanGTP and the cargo molecule that is being exported [].; GO: 0005515 protein binding; PDB: 1Z3H_B 1WA5_C.
Probab=55.83 E-value=1.2e+02 Score=35.18 Aligned_cols=120 Identities=13% Similarity=0.163 Sum_probs=49.4
Q ss_pred HHHHHHHhccCcccHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHhhcccccccChhhHHHHHHHHHHhhhcCCCCccch
Q psy8413 90 TTLVGLLNAKNYNFGGEFVELMVKTFKDALKNCQWNAARYALRFLADLVNCHVISTNSLLQLLENMLDASKEDGVPNVRK 169 (796)
Q Consensus 90 AtLVgllN~kn~~~g~~iv~~l~~~lq~~l~~~~w~~~kl~lrFLa~L~n~~Vi~~~sl~~ll~~ll~~a~e~~~~q~R~ 169 (796)
|+||..+...+++....+-+.+.--|+.-|.+.-=.=+=.++..||-|...+- ...+=+.|..|+.....+.....|+
T Consensus 97 ~~lir~~~~~~~~~v~~~E~~L~P~f~~ILq~dV~EF~PYvfQIla~Lle~~~--~~~~p~~y~~L~~~Ll~p~lWe~~g 174 (435)
T PF03378_consen 97 GALIRFVCEADPEAVSQFEEALFPPFQEILQQDVQEFIPYVFQILAQLLELRP--SSPLPDAYKQLFPPLLSPALWERRG 174 (435)
T ss_dssp HHHHHHS-GGGHH---HHHHHHHHHHHHHHHTT-TTTHHHHHHHHHHHHHHSS----S--TTTGGGHHHHTSGGGGGSTT
T ss_pred HHHHHhccCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC--CCCCcHHHHHHHHHHcCcchhccCC
Confidence 55666666666666666667777777766665433323334444444443332 1222222222222222222222222
Q ss_pred h--hHHHHHHhhchhccHHhHHhhHHHHHHHHHHHHHHHhhccccc
Q psy8413 170 D--WYVYAVLSCLPWVGRELYEKKEQALALLLLNIELYLNKRSKKH 213 (796)
Q Consensus 170 d--~~vy~vL~~LP~~G~~L~e~~~~~l~~ll~~i~~yl~~r~~~~ 213 (796)
. -++...-..+.-.+.+.. ....++.++.-++..++++...+
T Consensus 175 niPalvrLL~a~i~k~~~~i~--~~~~l~~iLgvFQkLi~sk~~D~ 218 (435)
T PF03378_consen 175 NIPALVRLLQAYIKKDPSFIV--ANNQLEPILGVFQKLIASKANDH 218 (435)
T ss_dssp THHHHHHHHHHHHHHHGGG------S-CHHHHHHHHHHHT-TTCHH
T ss_pred CcCcHHHHHHHHHHhCchhhc--chhhHHHHHHHHHHHHCCCCcch
Confidence 1 133333333333333331 23445667777777777765443
No 15
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=52.10 E-value=96 Score=28.25 Aligned_cols=92 Identities=17% Similarity=0.257 Sum_probs=61.1
Q ss_pred hHHHHHHHHHH-hhHhhHHHHHHHHHHHHHhC-CCCchHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHh--cCChhhH
Q psy8413 52 HLDGLAKVLET-DLATYRVKILRILTDCATKY-PEKCCIYTTLVGLLNAKNYNFGGEFVELMVKTFKDALK--NCQWNAA 127 (796)
Q Consensus 52 ~l~~La~~l~~-d~~~~~~~i~~~l~~~v~e~-P~K~p~yAtLVgllN~kn~~~g~~iv~~l~~~lq~~l~--~~~w~~~ 127 (796)
|.+.....|.. ..+.+...++..++.|+.+. +..-+.|+.|+.-+..++.-....+.+.+..-++..=+ ...=...
T Consensus 17 d~~ea~~~l~el~~~~~~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~~~~~~~~~~~gf~~~l~~l~Dl~~D~P~~~ 96 (113)
T PF02847_consen 17 DVDEAVECLKELKLPSQHHEVVKVILECALEEKKSYREYYSKLLSHLCKRKLISKEQFQEGFEDLLESLEDLELDIPKAP 96 (113)
T ss_dssp -HHHHHHHHHHTT-GGGHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHSTTHH
T ss_pred CHHHHHHHHHHhCCCccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhHhhhccccchHHH
Confidence 45555555543 45578899999999999998 88899999999999888776666665555544443211 1222245
Q ss_pred HHHHHHHhhccccccc
Q psy8413 128 RYALRFLADLVNCHVI 143 (796)
Q Consensus 128 kl~lrFLa~L~n~~Vi 143 (796)
..+-+|+++++..+++
T Consensus 97 ~~la~~~~~~i~~~~l 112 (113)
T PF02847_consen 97 EYLAKFLARLIADGIL 112 (113)
T ss_dssp HHHHHHHHHHHHTTSS
T ss_pred HHHHHHHHHHHHcCCc
Confidence 6778888888766554
No 16
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=48.28 E-value=1.1e+02 Score=27.97 Aligned_cols=92 Identities=20% Similarity=0.200 Sum_probs=61.2
Q ss_pred hHHHHHHHHHH-hhHhhHHHHHHHHHHHHHhC-CCCchHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhc--CChhhH
Q psy8413 52 HLDGLAKVLET-DLATYRVKILRILTDCATKY-PEKCCIYTTLVGLLNAKNYNFGGEFVELMVKTFKDALKN--CQWNAA 127 (796)
Q Consensus 52 ~l~~La~~l~~-d~~~~~~~i~~~l~~~v~e~-P~K~p~yAtLVgllN~kn~~~g~~iv~~l~~~lq~~l~~--~~w~~~ 127 (796)
|......-|.. ..+++...++..++.|+.+. +..-+.|+.|+.-+..++.-....+...+...++..=+- ..=+..
T Consensus 17 D~~ea~~~l~~L~~~~~~~~vv~~~i~~~le~~~~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~l~dl~~D~P~a~ 96 (113)
T smart00544 17 DTDEAVHCLLELKLPEQHHEVVKVLLTCALEEKRTYREMYSVLLSRLCQANVISTKQFEKGFWRLLEDIEDLELDIPNAW 96 (113)
T ss_pred CHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhChhhhcccccHH
Confidence 44444444432 33468888999999999987 678899999999988887766666655555544443221 111456
Q ss_pred HHHHHHHhhccccccc
Q psy8413 128 RYALRFLADLVNCHVI 143 (796)
Q Consensus 128 kl~lrFLa~L~n~~Vi 143 (796)
..+-+|+|.++..+++
T Consensus 97 ~~la~~~a~~v~~~~l 112 (113)
T smart00544 97 RNLAEFVARLISDGIL 112 (113)
T ss_pred HHHHHHHHHHHHcCCC
Confidence 6777888888766654
No 17
>COG5215 KAP95 Karyopherin (importin) beta [Intracellular trafficking and secretion]
Probab=47.70 E-value=3.2e+02 Score=32.82 Aligned_cols=114 Identities=19% Similarity=0.334 Sum_probs=61.7
Q ss_pred ccCCCCchhHHHHHHHHHHhhcCCC-Ccchhhh----HHHHHHHHHHhhHhhHHHHHHHHHHHHHhCCCCchHHHHHHHH
Q psy8413 21 RRRVPENQELEDRFEVLIVKVGERS-TTSLESH----LDGLAKVLETDLATYRVKILRILTDCATKYPEKCCIYTTLVGL 95 (796)
Q Consensus 21 r~r~~~~~~~~~~l~~~I~~ige~~-~~s~e~~----l~~La~~l~~d~~~~~~~i~~~l~~~v~e~P~K~p~yAtLVgl 95 (796)
|+|.++...+++.|+.+..|+-|+. .+..++| |-.|+..|+..++.+-..|+..+....-+ .--++-.+.||+
T Consensus 585 r~~~~~ie~v~D~lm~Lf~r~les~~~t~~~~dV~~aIsal~~sl~e~Fe~y~~~fiPyl~~aln~--~d~~v~~~avgl 662 (858)
T COG5215 585 RTRRRDIEDVEDQLMELFIRILESTKPTTAFGDVYTAISALSTSLEERFEQYASKFIPYLTRALNC--TDRFVLNSAVGL 662 (858)
T ss_pred HhcCCCcccHHHHHHHHHHHHHhccCCchhhhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHhcc--hhHHHHHHHHHH
Confidence 3444445667788999999998875 3345555 44556666666777777777766655422 223444455554
Q ss_pred H----hccCcccHHHHHHHHHHHHHHHHhc-CChhhHH-HHHHHHhhc
Q psy8413 96 L----NAKNYNFGGEFVELMVKTFKDALKN-CQWNAAR-YALRFLADL 137 (796)
Q Consensus 96 l----N~kn~~~g~~iv~~l~~~lq~~l~~-~~w~~~k-l~lrFLa~L 137 (796)
+ |+-+..|-... ..+...+-.+|.+ ..-++.| .+|-.|++.
T Consensus 663 vgdlantl~~df~~y~-d~~ms~LvQ~lss~~~~R~lKPaiLSvFgDI 709 (858)
T COG5215 663 VGDLANTLGTDFNIYA-DVLMSSLVQCLSSEATHRDLKPAILSVFGDI 709 (858)
T ss_pred HHHHHHHhhhhHHHHH-HHHHHHHHHHhcChhhccccchHHHHHHHHH
Confidence 4 55554443322 1222222233332 2333444 345566665
No 18
>smart00515 eIF5C Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5.
Probab=45.80 E-value=39 Score=29.55 Aligned_cols=53 Identities=17% Similarity=0.337 Sum_probs=43.1
Q ss_pred HHHHhhhCCChHHHHHHHHHHHHHHhhCcCe---eHHHHHHHHhCCCCChhhhhhhh
Q psy8413 574 KVLKEHIGHTEESQSYVLKSLFELWHDHQQM---MAVLIDKMLKTQLLHCSSVANWI 627 (796)
Q Consensus 574 ~~Lk~l~~~~~~~q~~il~~v~~~W~~~~Q~---~~iiidkll~~~iv~p~~Vv~w~ 627 (796)
.+|+.+.. +.+.|..+|.++-++-..++.. ...++..|.+..||+-.+|++|-
T Consensus 2 ~ll~~~~~-~~~~q~~~L~ale~~~~~~~~~~~~~~~il~~LYd~dileEe~il~W~ 57 (83)
T smart00515 2 PLLKFLAK-DEEEQIDLLYAIEEFCVELEKLIKLLPKILKSLYDADILEEEAILKWY 57 (83)
T ss_pred hHHHHHHC-ChHHHHHHHHHHHHHHHHcchHHHHHHHHHHHHhhhccccHHHHHHHH
Confidence 46778887 8889999999999999765432 34466888899999999999997
No 19
>COG1422 Predicted membrane protein [Function unknown]
Probab=44.60 E-value=1.1e+02 Score=31.81 Aligned_cols=27 Identities=26% Similarity=0.409 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8413 695 EEVVEKIEEKLEAAQADQKNLFLIIFQ 721 (796)
Q Consensus 695 ~~~~e~~~~~l~~a~~eqk~l~~~i~~ 721 (796)
...++++|++-.++..+|.+++..-|+
T Consensus 97 ~~~lkkLq~~qmem~~~Q~elmk~qfk 123 (201)
T COG1422 97 MKKLKKLQEKQMEMMDDQRELMKMQFK 123 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 467889999999999999999887665
No 20
>PF04054 Not1: CCR4-Not complex component, Not1; InterPro: IPR007196 The Ccr4-Not complex is a global regulator of gene expression that is conserved from yeast to human. It affects genes positively and negatively and is thought to regulate transcription factor IID function. In Saccharomyces cerevisiae, it exists in two prominent forms and consists of at least nine core subunits: the five Not proteins (Not1p to Not5p), Caf1p, Caf40p, Caf130p and Ccr4p []. The Ccr4-Not complex regulates many different cellular functions, including RNA degradation and transcription initiation. It may be a regulatory platform that senses nutrient levels and stress []. Caf1p and Ccr4p, are directly involved in mRNA deadenylation, and Caf1p is associated with Dhh1p, a putative RNA helicase thought to be a component of the decapping complex []. Pop2, a component of the Ccr4-Not complex, functions as a deadenylase []. The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID [].
Probab=43.83 E-value=92 Score=35.52 Aligned_cols=138 Identities=20% Similarity=0.202 Sum_probs=81.3
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHhhCCCCCCCCCC-----CCCCCh-----hHHHHHHHHHHhhccchHHhHHHHHHhH
Q psy8413 503 VYAQELINAIKKKQSSPNEIMAILNKIPSSSMDEDG-----ADPINP-----LKIDVFTQVLLYLGSKSFSHSFAALSKF 572 (796)
Q Consensus 503 ~~a~~l~~~i~~k~~~~eev~~~l~~i~~~~~~~~~-----~~~~~~-----~~i~v~~q~ll~~GsKSfSH~~~~iery 572 (796)
.+-+.+-++++... +.+-+..+...+..+..+... ....|. +++-+-++++...+++|-+..++--+-+
T Consensus 185 ~lk~~vd~~l~~~~-~~~~l~~i~~~l~~~~~~~~~~~g~~~~~~n~~linalVlyvg~~a~~~~~~~~~~~~f~~~s~~ 263 (379)
T PF04054_consen 185 GLKKPVDQYLRNGP-SESLLAQILHKLQLPEPEETNGFGFDGVKYNVKLINALVLYVGIQAVAEAQKKSSAPSFNTKSPH 263 (379)
T ss_pred HHHHHHHHHHHhCC-CHHHHHHHHHHhcCCccccccccCCCCccccHHHHHHHHHHHhHHHHHHHhccCCCccccccChH
Confidence 36666777888865 777777777777665433211 123332 3444445555555555555555554566
Q ss_pred HHHHHhhhC-CChHHHHHHHHHHHHHHhh-CcCeeHHHHHHHHhCCCCChhhhhhhhcccCCc-------c-h-------
Q psy8413 573 YKVLKEHIG-HTEESQSYVLKSLFELWHD-HQQMMAVLIDKMLKTQLLHCSSVANWIFSKEMQ-------P-E------- 635 (796)
Q Consensus 573 ~~~Lk~l~~-~~~~~q~~il~~v~~~W~~-~~Q~~~iiidkll~~~iv~p~~Vv~w~F~~~~~-------~-~------- 635 (796)
...|..|+. .+.|+|..++.++..-=+. |.++-+ . ..++-|+|+.++. + +
T Consensus 264 ~~ll~~Li~~ld~E~RY~ll~aiaNqLRYPN~HT~~--F-----------s~~lL~lF~~~~~~~~~~~IqEqItRVLLE 330 (379)
T PF04054_consen 264 VTLLSKLIHELDPEGRYYLLSAIANQLRYPNSHTHF--F-----------SCVLLNLFSSDMNDPNDEDIQEQITRVLLE 330 (379)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHcCCCchhHHH--H-----------HHHHHHHhcCCCCccchhhhHHHHHHHHHH
Confidence 777877764 6889999999999875544 222211 1 2234677773221 1 1
Q ss_pred ---hhhhhHHHHHHHHHHHHHH
Q psy8413 636 ---FTKLYVWEILHLTIKKMSK 654 (796)
Q Consensus 636 ---~~~~~~Weil~~ti~kv~~ 654 (796)
-.++|.|-++-.-++-+++
T Consensus 331 Rliv~rPHPWGllitfiELikN 352 (379)
T PF04054_consen 331 RLIVNRPHPWGLLITFIELIKN 352 (379)
T ss_pred HHhcCCCCCccHHHHHHHHHhC
Confidence 1378888888877777654
No 21
>cd07600 BAR_Gvp36 The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Golgi vesicle protein of 36 kDa and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Proteomic analysis shows that Golgi vesicle protein of 36 kDa (Gvp36) may be involved in vesicular trafficking and nutritional adaptation. A Saccharomyces cerevisiae strain deficient in Gvp36 shows defects in growth, in actin cytoskeleton polarization, in endocytosis, in vacuolar biogenesis, and in the cell cycle. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=41.21 E-value=4.2e+02 Score=28.36 Aligned_cols=59 Identities=17% Similarity=0.160 Sum_probs=37.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccCCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8413 694 SEEVVEKIEEKLEAAQADQKNLFLIIFQRFIMILSEHLVRCDTDGVDFNTHWYKWTIGRLQQVLLAHHEQVQKYSSTLET 773 (796)
Q Consensus 694 ~~~~~e~~~~~l~~a~~eqk~l~~~i~~~fv~~Lse~~~~~~~~~~~~~~~W~~~~~gr~~~~~~~~~~~~~~~~~~L~~ 773 (796)
...++|.+|++++.++++-..++..|... .. +...+.-|.+.=+.||++..+.++.|-.
T Consensus 182 ~~~e~E~aEdef~~a~E~a~~~M~~il~~-~e--------------------~i~~L~~fv~AQl~Yh~~~~e~L~~l~~ 240 (242)
T cd07600 182 ARVEVETAEDEFVSATEEAVELMKEVLDN-PE--------------------PLQLLKELVKAQLAYHKTAAELLEELLS 240 (242)
T ss_pred hHHHHHHHHHHHHHhHHHHHHHHHHHHhh-hH--------------------HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 46778889999998887765555444332 11 2233344555567888888888776654
No 22
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=39.24 E-value=84 Score=32.22 Aligned_cols=88 Identities=18% Similarity=0.321 Sum_probs=50.1
Q ss_pred ccchHHhHHHHHHhHHHHHHhhhCCChHHHHHHHHHHHHHHhhCcCeeHHHHHHHHhCCCCCh----hhhhhhhcccCCc
Q psy8413 558 GSKSFSHSFAALSKFYKVLKEHIGHTEESQSYVLKSLFELWHDHQQMMAVLIDKMLKTQLLHC----SSVANWIFSKEMQ 633 (796)
Q Consensus 558 GsKSfSH~~~~iery~~~Lk~l~~~~~~~q~~il~~v~~~W~~~~Q~~~iiidkll~~~iv~p----~~Vv~w~F~~~~~ 633 (796)
.+++| |.+.=||+..+.-+.+.+ |.+-=++.-|+.-|+|.. ++.+-|.|.....
T Consensus 7 e~~~~-y~lKELEK~~pK~~gI~~---------------------~~VKdvlq~LvDDglV~~EKiGssn~YWsFps~~~ 64 (188)
T PF03962_consen 7 ESKDF-YTLKELEKLAPKEKGIVS---------------------MSVKDVLQSLVDDGLVHVEKIGSSNYYWSFPSQAK 64 (188)
T ss_pred hcCCc-ccHHHHHHHcccccCCch---------------------hhHHHHHHHHhccccchhhhccCeeEEEecChHHH
Confidence 45566 466666766665554444 112224445555666665 3456788876532
Q ss_pred chhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccC
Q psy8413 634 PEFTKLYVWEILHLTIKKMSKYVNRVGKELLDAKERLKHVSSE 676 (796)
Q Consensus 634 ~~~~~~~~Weil~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~ 676 (796)
. .+.+.+++....+..++.+++++++++......
T Consensus 65 ~---------~~~~~~~~l~~~~~~~~~~i~~l~~~i~~~~~~ 98 (188)
T PF03962_consen 65 Q---------KRQNKLEKLQKEIEELEKKIEELEEKIEEAKKG 98 (188)
T ss_pred H---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 2 445566666666666666666666666554333
No 23
>KOG1077|consensus
Probab=38.68 E-value=5.5e+02 Score=31.73 Aligned_cols=425 Identities=16% Similarity=0.212 Sum_probs=220.1
Q ss_pred HHHhcCChhhHHHHHHHHhhcccccccChhhHHHHHHHHHHhhhcCCCCccchhhHHHHHHhhchhc-cHHhHHhhHHHH
Q psy8413 117 DALKNCQWNAARYALRFLADLVNCHVISTNSLLQLLENMLDASKEDGVPNVRKDWYVYAVLSCLPWV-GRELYEKKEQAL 195 (796)
Q Consensus 117 ~~l~~~~w~~~kl~lrFLa~L~n~~Vi~~~sl~~ll~~ll~~a~e~~~~q~R~d~~vy~vL~~LP~~-G~~L~e~~~~~l 195 (796)
+.|.++.+.+-..---|+++|+|.+ ..++. .... ....+. +.|++.++-.+|.++--+ |+++.+.-..++
T Consensus 81 ~LLss~kysEKqIGYl~is~L~n~n----~dl~k---lvin-~iknDL-~srn~~fv~LAL~~I~niG~re~~ea~~~DI 151 (938)
T KOG1077|consen 81 NLLSSNKYSEKQIGYLFISLLLNEN----SDLMK---LVIN-SIKNDL-SSRNPTFVCLALHCIANIGSREMAEAFADDI 151 (938)
T ss_pred HHhhcCCccHHHHhHHHHHHHHhcc----hHHHH---HHHH-HHHhhh-hcCCcHHHHHHHHHHHhhccHhHHHHhhhhh
Confidence 4566777777777778899998876 22221 1111 112222 467888888899998865 455555555555
Q ss_pred HHHHHH--HHHHHhhcccccccccccccC-------------------CC----------------CCChhhHHHHHHHH
Q psy8413 196 ALLLLN--IELYLNKRSKKHVAALQVWSS-------------------DK----------------PHPQEEYLDCLWAQ 238 (796)
Q Consensus 196 ~~ll~~--i~~yl~~r~~~~~~ll~~~~~-------------------~~----------------~~~~~d~l~~L~~q 238 (796)
-.|+-. ...|+++- +--.+|+.|.+ |. ..++++|-.|+-.|
T Consensus 152 ~KlLvS~~~~~~vkqk--aALclL~L~r~spDl~~~~~W~~riv~LL~D~~~gv~ta~~sLi~~lvk~~p~~yk~~~~~a 229 (938)
T KOG1077|consen 152 PKLLVSGSSMDYVKQK--AALCLLRLFRKSPDLVNPGEWAQRIVHLLDDQHMGVVTAATSLIEALVKKNPESYKTCLPLA 229 (938)
T ss_pred HHHHhCCcchHHHHHH--HHHHHHHHHhcCccccChhhHHHHHHHHhCccccceeeehHHHHHHHHHcCCHHHhhhHHHH
Confidence 555432 23333322 11122333311 00 14566777888888
Q ss_pred HHHHHhC---------CccccccCCCcchhhhhhhhhhcCCCCCCCCCCCCCCCCCCCCeeEEEecc-CCCCCCCCCCCC
Q psy8413 239 IVKLRQD---------NWTDHHIYRPYTVFDSRLSVALQHNLPNIILPPHHDSLIYPMPSVVFRMFD-YTDCPEEPSISP 308 (796)
Q Consensus 239 i~~l~~~---------~w~~~~i~rpy~~f~~~L~~a~~h~Lp~~~~p~~~~~~~y~~P~~~frlf~-~~~~~~~~~~~~ 308 (796)
|..|... ++.--.+|-||+.- .|...+|- +|+ +.+++.+-..-++.=++.+ .+++|.. .
T Consensus 230 vs~L~riv~~~~t~~qdYTyy~vP~PWL~v--Kl~rlLq~-~p~----~~D~~~r~~l~evl~~iLnk~~~~~~~----k 298 (938)
T KOG1077|consen 230 VSRLSRIVVVVGTSLQDYTYYFVPAPWLQV--KLLRLLQI-YPT----PEDPSTRARLNEVLERILNKAQEPPKS----K 298 (938)
T ss_pred HHHHHHHHhhcccchhhceeecCCChHHHH--HHHHHHHh-CCC----CCCchHHHHHHHHHHHHHhccccCccc----c
Confidence 8877632 22334578888642 33333322 122 2222222222222222222 2223221 0
Q ss_pred CCCCcchHHH-HHHHHHHHHHHHhccCHH---HHHHHHhcCC--CCCCchhHHHHHHHHHhhcCCCCCccch-hHHHHHH
Q psy8413 309 LPGAHSIERF-LIEEHLLQIIEMNYFERK---DCATQLLKYN--MKIPLEYCIVEIIFGELFRLPTPKYLEI-FYGSVLI 381 (796)
Q Consensus 309 lP~~~sier~-l~ee~i~Dii~~~~~nRk---ecA~~Ll~lp--~~~~~E~~ivEtIfs~lf~LP~p~~~~i-yY~slLi 381 (796)
- ..|+.+.- ++.|.|.=++ .++.... .|..||-.+- +..-+.|+..|++--++-. .+.|-.| +|..+++
T Consensus 299 ~-vq~~na~naVLFeaI~l~~-h~D~e~~ll~~~~~~Lg~fls~rE~NiRYLaLEsm~~L~ss--~~s~davK~h~d~Ii 374 (938)
T KOG1077|consen 299 K-VQHSNAKNAVLFEAISLAI-HLDSEPELLSRAVNQLGQFLSHRETNIRYLALESMCKLASS--EFSIDAVKKHQDTII 374 (938)
T ss_pred c-hHhhhhHHHHHHHHHHHHH-HcCCcHHHHHHHHHHHHHHhhcccccchhhhHHHHHHHHhc--cchHHHHHHHHHHHH
Confidence 0 12333332 4445544232 2333322 2555665543 5677999999998766655 3444444 6778999
Q ss_pred HHhccCCCChhHHHHHHHHHHHhcCccccHHHHHHHHHHHHHHhhccCCcccchhhhhh--hcCCCCCChHHHHHHHHHH
Q psy8413 382 ELCKMKPDTMPQVLAQATVILFMRIESMNTACFDRFVAWFAYHLSNFQFQWSWEDWESA--LKLDLEHPKPKFIHEVLNK 459 (796)
Q Consensus 382 elCk~~P~~i~pv~~~Air~ly~~l~~mD~e~~~Rf~dWFS~hLSNF~F~W~W~eW~~~--l~~~~~~Pk~~Fi~~~l~K 459 (796)
..-|..++. .+--||++.||..-|.=+.. -.++=+-.+|+-=+|+.+ +|-+-. +=...+.+.-..--.++-+
T Consensus 375 ~sLkterDv--SirrravDLLY~mcD~~Nak---~IV~elLqYL~tAd~sir-eeivlKvAILaEKyAtDy~WyVdviLq 448 (938)
T KOG1077|consen 375 NSLKTERDV--SIRRRAVDLLYAMCDVSNAK---QIVAELLQYLETADYSIR-EEIVLKVAILAEKYATDYSWYVDVILQ 448 (938)
T ss_pred HHhccccch--HHHHHHHHHHHHHhchhhHH---HHHHHHHHHHhhcchHHH-HHHHHHHHHHHHHhcCCcchhHHHHHH
Confidence 999988874 47889999999876554443 223333333333444433 111111 0013455555555566667
Q ss_pred HHhhcchHHHhhhCcccccccCCCCCCCCcccCCCCCCCC-CchHHHHHHHHHHHhcCCCHHHHHHHHhhCCCCCCCCCC
Q psy8413 460 CVRLSYHQRIKEIVPPQFAPLLPLKPEPHFKYNQEGGEHL-PGFVYAQELINAIKKKQSSPNEIMAILNKIPSSSMDEDG 538 (796)
Q Consensus 460 eiRLSy~~rIk~~lPe~~~~llp~~p~p~fky~~e~~~~~-p~~~~a~~l~~~i~~k~~~~eev~~~l~~i~~~~~~~~~ 538 (796)
.+|+.- +.+-++... ....+-.++|+ + +| +|+++.+++.+++ -.|.+...=.=|-
T Consensus 449 Liriag-----d~vsdeVW~-----RvvQiVvNned---lq~y--aak~~fe~Lq~~a-~hE~mVKvggyiL-------- 504 (938)
T KOG1077|consen 449 LIRIAG-----DYVSDEVWY-----RVVQIVVNNED---LQGY--AAKRLFEYLQKPA-CHENMVKVGGYIL-------- 504 (938)
T ss_pred HHHHhc-----ccccHHHHH-----HhheeEecchh---hhHH--HHHHHHHHHhhhH-HHHHHHHhhhhhh--------
Confidence 777653 111111100 00111122222 2 34 7889999999988 7766654311110
Q ss_pred CCCCChhHHHHHHHHHHhhc--cchHHhHHHHH-HhHHHHHHhhhCCChHHHHHHHHHHHHHHhhCcCeeHHHHHHHHhC
Q psy8413 539 ADPINPLKIDVFTQVLLYLG--SKSFSHSFAAL-SKFYKVLKEHIGHTEESQSYVLKSLFELWHDHQQMMAVLIDKMLKT 615 (796)
Q Consensus 539 ~~~~~~~~i~v~~q~ll~~G--sKSfSH~~~~i-ery~~~Lk~l~~~~~~~q~~il~~v~~~W~~~~Q~~~iiidkll~~ 615 (796)
..+.. |..| .-|-.|.|+.| +||+ .. +...+..+|.+...+-+..|-+.-.|.+-|-.|
T Consensus 505 -GEfg~----------LIa~~prss~~~qFsllh~K~~------~~-s~~tr~lLLtTyiKl~nl~PEi~~~v~~vFq~~ 566 (938)
T KOG1077|consen 505 -GEFGN----------LIADDPRSSPAVQFSLLHEKLH------LC-SPVTRALLLTTYIKLINLFPEIKSNVQKVFQLY 566 (938)
T ss_pred -hhhhh----------hhcCCCCCChHHHHHHHHHHhc------cC-ChhHHHHHHHHHHHHHhhChhhhHHHHHHHHhh
Confidence 00111 1122 23445666655 3443 22 666888888998899988888888887777644
No 24
>KOG2140|consensus
Probab=37.28 E-value=72 Score=37.55 Aligned_cols=100 Identities=19% Similarity=0.282 Sum_probs=56.7
Q ss_pred HhhHh-hHHHHHHHHHHHHHhCCCCchHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHhhcccc
Q psy8413 62 TDLAT-YRVKILRILTDCATKYPEKCCIYTTLVGLLNAKNYNFGGEFVELMVKTFKDALKNCQWNAARYALRFLADLVNC 140 (796)
Q Consensus 62 ~d~~~-~~~~i~~~l~~~v~e~P~K~p~yAtLVgllN~kn~~~g~~iv~~l~~~lq~~l~~~~w~~~kl~lrFLa~L~n~ 140 (796)
=++++ ....++.++++|..++--..-+|+.|..---.-+-+.-... +.+.++--.-+..-+=++.|.+.+|+|||.
T Consensus 478 mkip~~q~~elc~mii~cc~QerTy~kFYglL~eRfc~l~r~~q~~f-e~~f~q~YstIhr~EtnkLRnlakffahLl-- 554 (739)
T KOG2140|consen 478 MKIPESQEKELCNMIIDCCAQERTYEKFYGLLGERFCMLHREWQEAF-EKCFKQQYSTIHRYETNKLRNLAKFFAHLL-- 554 (739)
T ss_pred ccCCchhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhHHHHHHHHHHHHHHh--
Confidence 35554 67889999999999998888888877543222111111111 111111111122344578899999999994
Q ss_pred cccChhhH-HHHHHHHHHhhhcCCCCccc
Q psy8413 141 HVISTNSL-LQLLENMLDASKEDGVPNVR 168 (796)
Q Consensus 141 ~Vi~~~sl-~~ll~~ll~~a~e~~~~q~R 168 (796)
+.+++ ..+| .-+....|+..++.|
T Consensus 555 ---std~lpw~vl-~~ikLTEEdTtsssR 579 (739)
T KOG2140|consen 555 ---STDALPWDVL-ACIKLTEEDTTSSSR 579 (739)
T ss_pred ---cccccchHHH-HHhhcccccCCccce
Confidence 33433 2223 334566677776654
No 25
>PF02020 W2: eIF4-gamma/eIF5/eIF2-epsilon; InterPro: IPR003307 This entry represents the W2 domain (two invariant tryptophans) and is a region of ~165 amino acids which is found in the C terminus of the following eIFs [, , , ]: Eukaryotic translation initiation factor 2B epsilon (eIF-2B-epsilon) Eukaryotic translation initiation factor 4 gamma (eIF-4-gamma) Eukaryotic translation initiation factor 5 (eIF-5), a GTPase-activating protein (GAP) specific for eIF2 Translation initiation is a sophisticated, well regulated and highly coordinated cellular process in eukaryotes, in which at least 11 eukayrotic initiation factors (eIFs) are included []. The W2 domain has a globular fold and is exclusively composed out of alpha-helices [, , ]. The structure can be divided into a structural C-terminal core onto which the two N-terminal helices are attached. The core contains two aromatic/acidic residue-rich regions (AA boxes), which are important for mediating protein-protein interactions. For example, the W2 domain of H. sapiens eIF5 binds eIF2-beta, eIF3 and eIF1 [], and therefore plays an important role in multifactor complex assembly. The entry covers the entire W2 domain.; GO: 0005488 binding; PDB: 3D3M_A 3L6A_A 1PAQ_A 2FUL_D 2IU1_A 1UG3_B 3JUI_A.
Probab=36.40 E-value=65 Score=28.31 Aligned_cols=45 Identities=13% Similarity=0.383 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHhhCcC---eeHHHHHHHHhCCCCChhhhhhhhcc
Q psy8413 585 ESQSYVLKSLFELWHDHQQ---MMAVLIDKMLKTQLLHCSSVANWIFS 629 (796)
Q Consensus 585 ~~q~~il~~v~~~W~~~~Q---~~~iiidkll~~~iv~p~~Vv~w~F~ 629 (796)
+.|..+|.++-.+=.+++. ....|+-.|.+..||+-.+|+.|-=+
T Consensus 2 ~~Q~~~L~ale~~~~~~~~~~~~~~~il~~LYd~Dil~Eeail~W~~~ 49 (84)
T PF02020_consen 2 DDQVDLLNALEEFCAENPNLMPLFPKILQQLYDEDILEEEAILEWYED 49 (84)
T ss_dssp HHHHHHHHHHHHHHHHTCGHGGHHHHHHHHHHHTTSS-HHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHhCccHHHHHHHHHHHHhhhhhccHHHHHHHHHc
Confidence 5788999999999988887 56778889999999999999999865
No 26
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=34.35 E-value=3.4e+02 Score=24.30 Aligned_cols=73 Identities=18% Similarity=0.241 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCcccccCCCCCccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8413 643 EILHLTIKKMSKYVNRVGKELLDAKERLKHVSSESEEESDGEGGKKNEEKISEEVVEKIEEKLEAAQADQKNLFLIIFQR 722 (796)
Q Consensus 643 eil~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~a~~eqk~l~~~i~~~ 722 (796)
+.++...++....++.++.++.+++.++... -..+.++++.++++-+++..+..+........+-.
T Consensus 48 ~~l~~~~~~~~~~~~~~r~~~~~~r~~l~~l--------------l~~~~~D~~~i~a~~~~~~~~~~~l~~~~~~~~~~ 113 (125)
T PF13801_consen 48 AKLRALMDEFRQEMRALRQELRAARQELRAL--------------LAAPPPDEAAIEALLEEIREAQAELRQERLEHLLE 113 (125)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HCCSSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444555555555666666666666555331 11245667888888888888888888888888777
Q ss_pred HHHHhcc
Q psy8413 723 FIMILSE 729 (796)
Q Consensus 723 fv~~Lse 729 (796)
+..+|++
T Consensus 114 ~~~~Ltp 120 (125)
T PF13801_consen 114 IRAVLTP 120 (125)
T ss_dssp HHHTT-G
T ss_pred HHHcCCH
Confidence 7777764
No 27
>PF14500 MMS19_N: Dos2-interacting transcription regulator of RNA-Pol-II
Probab=34.22 E-value=2.9e+02 Score=29.87 Aligned_cols=106 Identities=21% Similarity=0.313 Sum_probs=65.3
Q ss_pred HHHHHHHHhhHhhHHHHHHHHHHHHHhCCCCchHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhcCChhhHHHHHHHH
Q psy8413 55 GLAKVLETDLATYRVKILRILTDCATKYPEKCCIYTTLVGLLNAKNYNFGGEFVELMVKTFKDALKNCQWNAARYALRFL 134 (796)
Q Consensus 55 ~La~~l~~d~~~~~~~i~~~l~~~v~e~P~K~p~yAtLVgllN~kn~~~g~~iv~~l~~~lq~~l~~~~w~~~kl~lrFL 134 (796)
.|...|..+.+..|..-+..|-.+..+.|... +.+.=++.+..-+.+.+ .++..+.-.++=+
T Consensus 3 ~Lg~~Ltsed~~~R~ka~~~Ls~vL~~lp~~~----------------L~~~ev~~L~~F~~~rl--~D~~~~~~~l~gl 64 (262)
T PF14500_consen 3 SLGEYLTSEDPIIRAKALELLSEVLERLPPDF----------------LSRQEVQVLLDFFCSRL--DDHACVQPALKGL 64 (262)
T ss_pred chhhhhCCCCHHHHHHHHHHHHHHHHhCCHhh----------------ccHHHHHHHHHHHHHHh--ccHhhHHHHHHHH
Confidence 45555666666778888888877777777443 22222333333333344 4666677777777
Q ss_pred hhcccccccChhhHHHHHHHHHHhhhcCCCCccchhh-HHHHHHhhc
Q psy8413 135 ADLVNCHVISTNSLLQLLENMLDASKEDGVPNVRKDW-YVYAVLSCL 180 (796)
Q Consensus 135 a~L~n~~Vi~~~sl~~ll~~ll~~a~e~~~~q~R~d~-~vy~vL~~L 180 (796)
..|++.+-++++....+++.+++...-.. +.+++. .+|.++.++
T Consensus 65 ~~L~~~~~~~~~~~~~i~~~l~~~~~~q~--~~q~~R~~~~~ll~~l 109 (262)
T PF14500_consen 65 LALVKMKNFSPESAVKILRSLFQNVDVQS--LPQSTRYAVYQLLDSL 109 (262)
T ss_pred HHHHhCcCCChhhHHHHHHHHHHhCChhh--hhHHHHHHHHHHHHHH
Confidence 77777788888899999998887332222 344554 445555544
No 28
>PF07064 RIC1: RIC1; InterPro: IPR009771 This entry represents RIC1 (Ribosomal control protein1) and has been identified in yeast as a Golgi protein involved in retrograde transport to the cis-Golgi network. It forms a heterodimer with Rgp1 and functions as a guanyl-nucleotide exchange factor [] which activates YPT6 by exchanging bound GDP for free GTP. RIC1 is thereby required for efficient fusion of endosome-derived vesicles with the Golgi. The RIC1-RGP1 complex participates in the recycling of SNC1, presumably by mediating fusion of endosomal vesicles with the Golgi compartment and may also be indirectly involved in the transcription of both ribosomal protein genes and ribosomal RNA [, , ].
Probab=32.36 E-value=1.5e+02 Score=31.93 Aligned_cols=70 Identities=19% Similarity=0.193 Sum_probs=48.8
Q ss_pred HHHHHHHHHhCCCCchHHHHHHHHHhccCccc--HHHHHHHHHHHHHHHHhcCChhhHHHHHHHHhhcccccc
Q psy8413 72 LRILTDCATKYPEKCCIYTTLVGLLNAKNYNF--GGEFVELMVKTFKDALKNCQWNAARYALRFLADLVNCHV 142 (796)
Q Consensus 72 ~~~l~~~v~e~P~K~p~yAtLVgllN~kn~~~--g~~iv~~l~~~lq~~l~~~~w~~~kl~lrFLa~L~n~~V 142 (796)
.+++-+|...--.| .++.-|+-+-|....+. .++..+.+++-++.++++++|.-|+-++|||..|-.++.
T Consensus 183 ~dLf~~cl~~~~l~-tAa~yLlVl~~~e~~~~~~~~~~~~~al~LL~~a~~~~~w~Lc~eL~RFL~~ld~~~~ 254 (258)
T PF07064_consen 183 RDLFEECLENGNLK-TAASYLLVLQNLEGSSVVKDEESRQCALRLLVMALESGDWDLCFELVRFLKALDPEGN 254 (258)
T ss_pred HHHHHHHHHcCcHH-HHHHHHHHHHhcCCcchhhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCcccC
Confidence 46666677665555 34444554545554433 344667777788889999999999999999999866553
No 29
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=32.20 E-value=4.6e+02 Score=28.08 Aligned_cols=37 Identities=19% Similarity=0.422 Sum_probs=25.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccC
Q psy8413 640 YVWEILHLTIKKMSKYVNRVGKELLDAKERLKHVSSE 676 (796)
Q Consensus 640 ~~Weil~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~ 676 (796)
-..+-+..++..+.+.|.++..++.+++++.++.+..
T Consensus 45 ~~~~~~~~e~e~le~qv~~~e~ei~~~r~r~~~~e~k 81 (239)
T COG1579 45 KALEALEIELEDLENQVSQLESEIQEIRERIKRAEEK 81 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455666777777788888888888877777554443
No 30
>cd04378 RhoGAP_GMIP_PARG1 RhoGAP_GMIP_PARG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of GMIP (Gem interacting protein) and PARG1 (PTPL1-associated RhoGAP1). GMIP plays important roles in neurite growth and axonal guidance, and interacts with Gem, a member of the RGK subfamily of the Ras small GTPase superfamily, through the N-terminal half of the protein. GMIP contains a C-terminal RhoGAP domain. GMIP inhibits RhoA function, but is inactive towards Rac1 and Cdc41. PARG1 interacts with Rap2, also a member of the Ras small GTPase superfamily whose exact function is unknown, and shows strong preference for Rho. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases ge
Probab=31.57 E-value=27 Score=36.06 Aligned_cols=36 Identities=17% Similarity=0.266 Sum_probs=30.8
Q ss_pred HHHHhccCCCChhHHHHHHHHHHHhcCccccHHHHHHH
Q psy8413 380 LIELCKMKPDTMPQVLAQATVILFMRIESMNTACFDRF 417 (796)
Q Consensus 380 LielCk~~P~~i~pv~~~Air~ly~~l~~mD~e~~~Rf 417 (796)
|.++|+..|+.+|.++-+++++++.+ .++.|-..|-
T Consensus 5 L~~~~~~~~~~vP~iv~~ci~~i~~~--gl~~eGIfR~ 40 (203)
T cd04378 5 FSQVPRDFPDEVPFIIKKCTSEIENR--ALGVQGIYRV 40 (203)
T ss_pred hHHHHHHCCCCCChHHHHHHHHHHhc--CCCCccceeC
Confidence 67899999999999999999999986 6777766553
No 31
>cd07594 BAR_Endophilin_B The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. They are classified into two types, A and B. Vertebrates contain two endophilin-B isoforms. Endophilin-B proteins are cytoplasmic proteins expressed mainly in the heart, placenta, and skeletal muscle.
Probab=31.40 E-value=6.3e+02 Score=26.80 Aligned_cols=155 Identities=17% Similarity=0.112 Sum_probs=81.2
Q ss_pred HHHHHHHHHhhccch--HHhHHHHHHhHHHHHHhhhCCChHHHHHHHHHHHHHHhhCcCeeHHHHHHHHhCCCCChhhhh
Q psy8413 547 IDVFTQVLLYLGSKS--FSHSFAALSKFYKVLKEHIGHTEESQSYVLKSLFELWHDHQQMMAVLIDKMLKTQLLHCSSVA 624 (796)
Q Consensus 547 i~v~~q~ll~~GsKS--fSH~~~~iery~~~Lk~l~~~~~~~q~~il~~v~~~W~~~~Q~~~iiidkll~~~iv~p~~Vv 624 (796)
.+.+=+|++..|.-- =|..=.+|.+|++..+.++. .|......|-. ++++|..
T Consensus 71 ~e~Lg~~M~~~g~~lg~~S~~g~aL~~~g~a~~kia~----~~~~~~~~i~~-------------------~fl~pL~-- 125 (229)
T cd07594 71 LEQLGQAMIEAGNDFGPGTAYGSALIKVGQAQKKLGQ----AEREFIQTSSS-------------------NFLQPLR-- 125 (229)
T ss_pred HHHHHHHHHHHHhhCCCCCchHHHHHHHHHHHHHHHH----HHHHHHHHHHH-------------------HHHHHHH--
Confidence 346666666654432 24466788888888888887 33333333322 1111211
Q ss_pred hhhcccCCcchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCcccccCCCCCccccccCHHHHHHHHHH
Q psy8413 625 NWIFSKEMQPEFTKLYVWEILHLTIKKMSKYVNRVGKELLDAKERLKHVSSESEEESDGEGGKKNEEKISEEVVEKIEEK 704 (796)
Q Consensus 625 ~w~F~~~~~~~~~~~~~Weil~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 704 (796)
.+. +---..+.|..+.+...|-++..+|.++.++++. ++....+++|+..+++
T Consensus 126 ----------~~l-----~~dik~i~k~RKkLe~rRLd~D~~k~r~~kAk~~------------~~~~~~e~elr~Ae~k 178 (229)
T cd07594 126 ----------NFL-----EGDMKTISKERKLLENKRLDLDACKTRVKKAKSA------------EAIEQAEQDLRVAQSE 178 (229)
T ss_pred ----------HHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCc------------cchhhhHHHHHHHHHH
Confidence 000 0001133344455555566666666655433211 1123446778888889
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcccccccCCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8413 705 LEAAQADQKNLFLIIFQRFIMILSEHLVRCDTDGVDFNTHWYKWTIGRLQQVLLAHHEQVQKYSSTLET 773 (796)
Q Consensus 705 l~~a~~eqk~l~~~i~~~fv~~Lse~~~~~~~~~~~~~~~W~~~~~gr~~~~~~~~~~~~~~~~~~L~~ 773 (796)
++...++-+.++..|....+.-+ .-+.-|-+-=+.||.+..+++..|-.
T Consensus 179 F~~~~E~a~~~M~~i~~~~~~~~--------------------~~L~~lv~AQl~Yh~q~~e~L~~l~~ 227 (229)
T cd07594 179 FDRQAEITKLLLEGISSTHANHL--------------------RCLRDFVEAQMTYYAQCYQYMDDLQR 227 (229)
T ss_pred HHHHHHHHHHHHHHHHhcCchHH--------------------HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 88888776666655543222111 11223333446788888887776654
No 32
>PF05004 IFRD: Interferon-related developmental regulator (IFRD); InterPro: IPR007701 Interferon-related developmental regulator (IFRD1) is the human homologue of the Rattus norvegicus early response protein PC4 and its murine homologue TIS7 []. The exact function of IFRD1 is unknown but it has been shown that PC4 is necessary for muscle differentiation and that it might have a role in signal transduction. This entry also contains IFRD2 and its murine equivalent SKMc15, which are highly expressed soon after gastrulation and in the hepatic primordium, suggesting an involvement in early hematopoiesis [].
Probab=31.38 E-value=6.4e+02 Score=27.83 Aligned_cols=97 Identities=21% Similarity=0.243 Sum_probs=71.6
Q ss_pred chhHHHHHHHHHHhhcCCCCcchhhhHHHHHHHHHH-----hhHhhHHHHHHHHHHHHHhCCCCchHHH-HHHHHHhcc-
Q psy8413 27 NQELEDRFEVLIVKVGERSTTSLESHLDGLAKVLET-----DLATYRVKILRILTDCATKYPEKCCIYT-TLVGLLNAK- 99 (796)
Q Consensus 27 ~~~~~~~l~~~I~~ige~~~~s~e~~l~~La~~l~~-----d~~~~~~~i~~~l~~~v~e~P~K~p~yA-tLVgllN~k- 99 (796)
...++++|...|-.+.||..+.=+.-|+.+.+.+.. .+.+.+..+++.+.+|+..-..+--..| .+++|+-..
T Consensus 38 ~~~~e~~L~~~Id~l~eK~~~~Re~aL~~l~~~l~~~~~~d~v~~~~~tL~~~~~k~lkkg~~~E~~lA~~~l~Ll~ltl 117 (309)
T PF05004_consen 38 QEDLEDKLKEAIDLLTEKSSSTREAALEALIRALSSRYLPDFVEDRRETLLDALLKSLKKGKSEEQALAARALALLALTL 117 (309)
T ss_pred hhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHhhhc
Confidence 356778899999999999766666777777777753 4456788899999999966433445554 556776555
Q ss_pred -CcccHHHHHHHHHHHHHHHHhcCC
Q psy8413 100 -NYNFGGEFVELMVKTFKDALKNCQ 123 (796)
Q Consensus 100 -n~~~g~~iv~~l~~~lq~~l~~~~ 123 (796)
...-..++.+.+...|+..+..+.
T Consensus 118 g~g~~~~ei~~~~~~~L~~~l~d~s 142 (309)
T PF05004_consen 118 GAGEDSEEIFEELKPVLKRILTDSS 142 (309)
T ss_pred CCCccHHHHHHHHHHHHHHHHhCCc
Confidence 446678999999999998888653
No 33
>cd07439 FANCE_c-term Fanconi anemia complementation group E protein, C-terminal domain. Fanconi Anemia (FA) is an autosomal recessive disorder associated with increased susceptibility to various cancers, bone marrow failure, cardiac, renal, and limb malformations, and other characteristics. Cells are highly sensitive to DNA damaging agents. A multi-subunit protein complex, the FA core complex, is responsible for ubiquitination of the protein FANCD2 in response to DNA damage. This monoubiquitination results in a downstream effect on homology-directed DNA repair. FANCE is part of the FA core complex and its C-terminal domain, which is modeled here, has been shown to directly interact with FANCD2. The domain contains a five-fold repeat of a structural unit similar to ARM and HEAT repeats. FANCE appears conserved in metazoa and in plants.
Probab=27.42 E-value=8.1e+02 Score=26.44 Aligned_cols=131 Identities=19% Similarity=0.276 Sum_probs=77.1
Q ss_pred HHHHHHHHHhCCCCchHHHHHHHHHhccC-cccHHHHHHHHHHHH----------HHHHhcC--ChhhHHHHHHHHhhcc
Q psy8413 72 LRILTDCATKYPEKCCIYTTLVGLLNAKN-YNFGGEFVELMVKTF----------KDALKNC--QWNAARYALRFLADLV 138 (796)
Q Consensus 72 ~~~l~~~v~e~P~K~p~yAtLVgllN~kn-~~~g~~iv~~l~~~l----------q~~l~~~--~w~~~kl~lrFLa~L~ 138 (796)
...+...+...| ..-++|.++-++..+. ..+--+++.++++.- ++.+... .|++.- +-.+-++.
T Consensus 103 ~~al~~f~~r~~-~~~ceall~PLl~~~~~~~~q~ell~rlike~~~~~~~~l~~~q~L~~~~~~W~E~~--~~v~q~lL 179 (254)
T cd07439 103 VAALASFAKRYP-RPFCEALLRPLLQCPHPGPFQAELLCRLVKECFEPDAVLLLLHQILISPNLVWTEET--FTVIQALL 179 (254)
T ss_pred HHHHHHHHHhCC-hhHHHHHHHHHHHCCCCCHHHHHHHHHHHhccccHHHHHHHHHHHHccccccccHHH--HHHHHHHH
Confidence 344444455566 4445666677777765 344444555544432 2333333 287653 33344455
Q ss_pred cccc-cChhhHHHHHHHHHHhhhcCCCCccchhhHHHHHHhhchhccHHhHHhhHHHHHHHHHHHHHHHhhc
Q psy8413 139 NCHV-ISTNSLLQLLENMLDASKEDGVPNVRKDWYVYAVLSCLPWVGRELYEKKEQALALLLLNIELYLNKR 209 (796)
Q Consensus 139 n~~V-i~~~sl~~ll~~ll~~a~e~~~~q~R~d~~vy~vL~~LP~~G~~L~e~~~~~l~~ll~~i~~yl~~r 209 (796)
|.++ ++++.+-.+.+.+-+.+..-+- +-.|...++..+--.|+.........+.+++++.+.+++|-
T Consensus 180 ~~~~~lte~~~~~Lv~~L~~~a~~~sk----SlkFa~lll~~itky~~~~~~~~~~~L~~~~~~~~TflkKs 247 (254)
T cd07439 180 NRKPPLSEESFSELVSKLQEQAEAFSK----SLKFAKLLLAVITKYGPQMSPAHKQSLSEALERNKTFLKKS 247 (254)
T ss_pred hcCCCCCHHHHHHHHHHHHHHHHHhhc----cccHHHHHHHHHHHccHhhcHHHHHHHHHHHHhcchHHHHH
Confidence 5555 5666655555555555433332 33477777887877888766667788999999999988763
No 34
>KOG4403|consensus
Probab=26.83 E-value=1.1e+02 Score=35.10 Aligned_cols=9 Identities=33% Similarity=0.722 Sum_probs=5.1
Q ss_pred CCchhHHHH
Q psy8413 779 DLEPHILDV 787 (796)
Q Consensus 779 ~~d~~i~~v 787 (796)
|+|..|++.
T Consensus 394 dVD~kIlea 402 (575)
T KOG4403|consen 394 DVDHKILEA 402 (575)
T ss_pred hHHHHHHHH
Confidence 566666543
No 35
>PF14225 MOR2-PAG1_C: Cell morphogenesis C-terminal
Probab=26.29 E-value=8.3e+02 Score=26.39 Aligned_cols=98 Identities=9% Similarity=0.170 Sum_probs=56.5
Q ss_pred cChhhHHHHHHHHHHhhhcCCCCccchhhHHHHHHhhchhccHHhHHhh----HHHHHHHHHHHHHHHhhccc-cccccc
Q psy8413 143 ISTNSLLQLLENMLDASKEDGVPNVRKDWYVYAVLSCLPWVGRELYEKK----EQALALLLLNIELYLNKRSK-KHVAAL 217 (796)
Q Consensus 143 i~~~sl~~ll~~ll~~a~e~~~~q~R~d~~vy~vL~~LP~~G~~L~e~~----~~~l~~ll~~i~~yl~~r~~-~~~~ll 217 (796)
.+.+.-++++..|.....+.=+... -+.+.++++.++||+-..+-+.. .......-+.+-...+.... .....+
T Consensus 77 ~t~e~tl~lL~~L~~~~~~~lig~~-~~rll~~~la~LP~ll~~~d~~~~i~~~~~~~~~A~~La~~a~~~~~~~La~il 155 (262)
T PF14225_consen 77 STYELTLRLLSRLTPLPDDPLIGDS-QSRLLFLLLALLPRLLHAFDDPNPIQPDQECIEIAEALAQVAEAQGLPNLARIL 155 (262)
T ss_pred CcHHHHHHHHHHHhcCCCccccCCC-CccHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHhCCCccHHHHH
Confidence 4556667888888777655433221 12688999999999877665544 13333333344332222111 123445
Q ss_pred ccccCCCCCChhhHHHHHHHHHHH
Q psy8413 218 QVWSSDKPHPQEEYLDCLWAQIVK 241 (796)
Q Consensus 218 ~~~~~~~~~~~~d~l~~L~~qi~~ 241 (796)
+-|..+.--..+|++.++.+.|+.
T Consensus 156 ~~ya~~~fr~~~dfl~~v~~~l~~ 179 (262)
T PF14225_consen 156 SSYAKGRFRDKDDFLSQVVSYLRE 179 (262)
T ss_pred HHHHhcCCCCHHHHHHHHHHHHHH
Confidence 556555545677888887776653
No 36
>KOG2025|consensus
Probab=24.90 E-value=3.8e+02 Score=33.04 Aligned_cols=109 Identities=10% Similarity=0.095 Sum_probs=71.7
Q ss_pred HHHHHHHhhcCCCCcchhhhHHHHHHHHH--HhhHhhHHHHHHHHHHHHHhCCCCchHHHHHHHHHhccCcccHHHHHHH
Q psy8413 33 RFEVLIVKVGERSTTSLESHLDGLAKVLE--TDLATYRVKILRILTDCATKYPEKCCIYTTLVGLLNAKNYNFGGEFVEL 110 (796)
Q Consensus 33 ~l~~~I~~ige~~~~s~e~~l~~La~~l~--~d~~~~~~~i~~~l~~~v~e~P~K~p~yAtLVgllN~kn~~~g~~iv~~ 110 (796)
++.+-..+.|.. ..++++..++.+.+. ..=+-..+.|++++.+-+..+| +...+..+|..
T Consensus 24 kl~~k~~em~t~--~~F~eeflr~vn~il~vkKresi~dRIl~fla~fv~sl~----------------q~d~e~DlV~~ 85 (892)
T KOG2025|consen 24 KLLAKVMEMLTA--HEFSEEFLRVVNYILLVKKRESIPDRILSFLARFVESLP----------------QLDKEEDLVAG 85 (892)
T ss_pred HHHHHHHHhhhH--hhhHHHHHHHHHHheeeccCCCcHHHHHHHHHHHHHhhh----------------ccCchhhHHHH
Confidence 345555566665 336666666666442 2222355667777766666666 55677778998
Q ss_pred HHHHHHHHHhcCChhhHHHHHHHHhhcccccccChhhHHHHHH-HHHHhh
Q psy8413 111 MVKTFKDALKNCQWNAARYALRFLADLVNCHVISTNSLLQLLE-NMLDAS 159 (796)
Q Consensus 111 l~~~lq~~l~~~~w~~~kl~lrFLa~L~n~~Vi~~~sl~~ll~-~ll~~a 159 (796)
+...+-+...+.+.+.=..++..|+-|+++.+.-++++++.+. .++.+.
T Consensus 86 ~f~hlLRg~Eskdk~VRfrvlqila~l~d~~~eidd~vfn~l~e~l~~Rl 135 (892)
T KOG2025|consen 86 TFYHLLRGTESKDKKVRFRVLQILALLSDENAEIDDDVFNKLNEKLLIRL 135 (892)
T ss_pred HHHHHHhcccCcchhHHHHHHHHHHHHhccccccCHHHHHHHHHHHHHHH
Confidence 8888888888888776667777888888877777777776554 444444
No 37
>PF10274 ParcG: Parkin co-regulated protein; InterPro: IPR019399 This family of proteins is transcribed anti-sense along the DNA to the Parkin gene product and the two appear to be transcribed under the same promoter. The protein has predicted alpha-helical and beta-sheet domains which suggest its function is in the ubiquitin/proteasome system []. Mutations in parkin are the genetic cause of early-onset and autosomal recessive juvenile parkinsonism.
Probab=24.49 E-value=3.4e+02 Score=27.84 Aligned_cols=95 Identities=16% Similarity=0.113 Sum_probs=70.1
Q ss_pred hHhhHHHHHHHHHHHHHhCCCCchHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHhhccccccc
Q psy8413 64 LATYRVKILRILTDCATKYPEKCCIYTTLVGLLNAKNYNFGGEFVELMVKTFKDALKNCQWNAARYALRFLADLVNCHVI 143 (796)
Q Consensus 64 ~~~~~~~i~~~l~~~v~e~P~K~p~yAtLVgllN~kn~~~g~~iv~~l~~~lq~~l~~~~w~~~kl~lrFLa~L~n~~Vi 143 (796)
++.+-..+++.+. =++.|+..=+....--++-....+-.--++-.++.-++++|++.+-......|+-|-.||.+.=.
T Consensus 36 y~~~Lpif~dGL~--Et~~Py~flA~~g~~dll~~~~~~kilPvlPqLI~plk~AL~tr~~~V~~~~L~~Lq~Lv~~~~~ 113 (183)
T PF10274_consen 36 YHHYLPIFFDGLR--ETEHPYRFLARQGIKDLLERGGGEKILPVLPQLIIPLKRALNTRDPEVFCATLKALQQLVTSSDM 113 (183)
T ss_pred hhhHHHHHHhhhh--ccCccHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhhhh
Confidence 3334444444432 23477776666666666666666667778889999999999999999999999999999766666
Q ss_pred ChhhHHHHHHHHHHhhh
Q psy8413 144 STNSLLQLLENMLDASK 160 (796)
Q Consensus 144 ~~~sl~~ll~~ll~~a~ 160 (796)
-+..+...|..|+-...
T Consensus 114 vG~aLvPyyrqLLp~ln 130 (183)
T PF10274_consen 114 VGEALVPYYRQLLPVLN 130 (183)
T ss_pred hhHHHHHHHHHHHHHHH
Confidence 77888888888887664
No 38
>PF14327 CSTF2_hinge: Hinge domain of cleavage stimulation factor subunit 2; PDB: 4EBA_G.
Probab=24.31 E-value=1e+02 Score=27.35 Aligned_cols=44 Identities=14% Similarity=0.191 Sum_probs=31.0
Q ss_pred HHHhhhCCChHHHHHHHHHHHHHHhhCcCeeHHHHHHHHhCCCCChhhhhh
Q psy8413 575 VLKEHIGHTEESQSYVLKSLFELWHDHQQMMAVLIDKMLKTQLLHCSSVAN 625 (796)
Q Consensus 575 ~Lk~l~~~~~~~q~~il~~v~~~W~~~~Q~~~iiidkll~~~iv~p~~Vv~ 625 (796)
-+|.++..++ +.+.++-..|||..+-++.-++.+|+|++..|-.
T Consensus 37 ~mK~l~~~~p-------~~ar~lL~~nPqLa~Al~qa~l~lg~vd~~v~~~ 80 (84)
T PF14327_consen 37 QMKQLAQQNP-------EQARQLLQQNPQLAYALFQALLLLGMVDPDVVQS 80 (84)
T ss_dssp HHHHHHC-----------HHHHHHHS-THHHHHHHHHHHHTSS-SSSCHHH
T ss_pred HHHHHHHhCH-------HHHHHHHHHCcHHHHHHHHHHHHhCCCCHHHHHh
Confidence 3566666344 3466777899999999999999999999987654
No 39
>KOG3942|consensus
Probab=24.23 E-value=2.9e+02 Score=30.54 Aligned_cols=135 Identities=13% Similarity=0.119 Sum_probs=75.3
Q ss_pred cccHHHHHHHHHHHHHHHHh------cCChhhHHHHHHHHhhcccccccChhhHHHHHHHHHHhhhcCCCCccchhhHHH
Q psy8413 101 YNFGGEFVELMVKTFKDALK------NCQWNAARYALRFLADLVNCHVISTNSLLQLLENMLDASKEDGVPNVRKDWYVY 174 (796)
Q Consensus 101 ~~~g~~iv~~l~~~lq~~l~------~~~w~~~kl~lrFLa~L~n~~Vi~~~sl~~ll~~ll~~a~e~~~~q~R~d~~vy 174 (796)
+..|.++++.+...+++.+. +.+....-..+-||+.|.+. +....-..+...+...+.+.--|+.+....+.
T Consensus 199 ~~~gt~f~~~Lln~lrq~f~~r~gl~s~~~~rw~~fisfltelf~n--lgs~p~~vL~~~l~~cl~~llrspd~~~~e~e 276 (348)
T KOG3942|consen 199 WRNGTQFMDELLNLLRQGFLLRTGLSSLASCRWWRFISFLTELFDN--LGSCPQVVLQRSLRLCLQILLRSPDWPEFEYE 276 (348)
T ss_pred hhccchHHHHHHHHHHHhhccchhccchhHHHHHHHHHHHHHHHhh--cCCCChhhHHHHHHHHHHHHccCCCcchHHHH
Confidence 34455566666666655554 33344444455566665532 23333333443444444443345555555556
Q ss_pred HHHhhchhccHHhHHhhHHHHHHHHHHHHHHHhhcccccccccccccCCCCCChhhHHHHHHHHHHHHHhCCccccccC
Q psy8413 175 AVLSCLPWVGRELYEKKEQALALLLLNIELYLNKRSKKHVAALQVWSSDKPHPQEEYLDCLWAQIVKLRQDNWTDHHIY 253 (796)
Q Consensus 175 ~vL~~LP~~G~~L~e~~~~~l~~ll~~i~~yl~~r~~~~~~ll~~~~~~~~~~~~d~l~~L~~qi~~l~~~~w~~~~i~ 253 (796)
|...-|--.|..+-++-|..+..++..+++=+--+..+ +-+ ..++..++-.|.++.|+.+.-|
T Consensus 277 cl~~~L~~~g~dle~qlP~ql~lL~~s~rDafL~~sep----~a~------------~r~~lllliel~As~wqlpt~p 339 (348)
T KOG3942|consen 277 CLSMKLAVEGLDLEKQLPFQLLLLFPSRRDAFLVRSEP----LAP------------WRCPLLLLIELPASAWQLPTTP 339 (348)
T ss_pred HHHHHHHHcCccchhhhhHHHHHHHHHHHHhhhccccc----ccc------------ccchhhhccccCccccCCCCCh
Confidence 66666667788888888888888888777633333221 011 2345556677888999875444
No 40
>PF07571 DUF1546: Protein of unknown function (DUF1546); InterPro: IPR011442 These proteins are associated with IPR004823 from INTERPRO in transcription initiation factor TFIID subunit 6 (TAF6).; GO: 0051090 regulation of sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=23.95 E-value=1.9e+02 Score=26.02 Aligned_cols=42 Identities=31% Similarity=0.449 Sum_probs=29.9
Q ss_pred hHhhHHHHHHHHHHHHHhCCCC--chHHHHHHHHHhccCcccHHHHHHHH
Q psy8413 64 LATYRVKILRILTDCATKYPEK--CCIYTTLVGLLNAKNYNFGGEFVELM 111 (796)
Q Consensus 64 ~~~~~~~i~~~l~~~v~e~P~K--~p~yAtLVgllN~kn~~~g~~iv~~l 111 (796)
.++++..|.+++.+.... |.| ...|++++|+.. +|.++|+.+
T Consensus 41 ~~~L~~Ri~~tl~k~l~d-~~~~~~t~YGAi~gL~~-----lG~~~vr~~ 84 (92)
T PF07571_consen 41 YPTLQPRITRTLLKALLD-PKKPLGTHYGAIVGLSA-----LGPEAVRAL 84 (92)
T ss_pred cchHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHH-----HHHHHHHHh
Confidence 345788888888876653 444 458999999975 577776654
No 41
>PF10455 BAR_2: Bin/amphiphysin/Rvs domain for vesicular trafficking; InterPro: IPR018859 Endocytosis and intracellular transport involve several mechanistic steps: (1) for the internalisation of cargo molecules, the membrane needs to bend to form a vesicular structure, which requires membrane curvature and a rearrangement of the cytoskeleton; (2) following its formation, the vesicle has to be pinched off the membrane; (3) the cargo has to be subsequently transported through the cell and the vesicle must fuse with the correct cellular compartment. Members of the Amphiphysin protein family are key regulators in the early steps of endocytosis, involved in the formation of clathrin-coated vesicles by promoting the assembly of a protein complex at the plasma membrane and directly assist in the induction of the high curvature of the membrane at the neck of the vesicle. Amphiphysins contain a characteristic domain, known as the BAR (Bin-Amphiphysin-Rvs)-domain, which is required for their in vivo function and their ability to tubulate membranes []. The crystal structure of these proteins suggest the domain forms a crescent-shaped dimer of a three-helix coiled coil with a characteristic set of conserved hydrophobic, aromatic and hydrophilic amino acids. Proteins containing this domain have been shown to homodimerise, heterodimerise or, in a few cases, interact with small GTPases. This entry identifies several fungal BAR domain proteins, such as Gvp36, that are not found by IPR004148 from INTERPRO [].
Probab=22.59 E-value=1.1e+03 Score=26.11 Aligned_cols=133 Identities=19% Similarity=0.187 Sum_probs=63.5
Q ss_pred HHHHhhccchHHhHHHHH-HhHHHHHHhhhC-CChHHH-HHHHHHHHHHHhhCcCeeHHHHHHHHhCCCCChhhhhhhhc
Q psy8413 552 QVLLYLGSKSFSHSFAAL-SKFYKVLKEHIG-HTEESQ-SYVLKSLFELWHDHQQMMAVLIDKMLKTQLLHCSSVANWIF 628 (796)
Q Consensus 552 q~ll~~GsKSfSH~~~~i-ery~~~Lk~l~~-~~~~~q-~~il~~v~~~W~~~~Q~~~iiidkll~~~iv~p~~Vv~w~F 628 (796)
|.---.--|||+|.++-. ......|..+.. .+.... ..++......|.+=.+ +=+--|.+|..
T Consensus 112 ~~~~~~~PKTl~~ALSraa~~ss~~l~~l~~~~~~~~~L~~aL~~~S~~~~~I~~-aRL~qD~~I~~------------- 177 (289)
T PF10455_consen 112 QETSPSQPKTLYHALSRAALTSSEILEELKSSDEDEDPLSKALLKYSSAYEKIAQ-ARLEQDQLIQK------------- 177 (289)
T ss_pred cccccCCCccHHHHHHHHHHHhHHHHHhcccCCCcccHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH-------------
Confidence 333445678999988755 455556666622 111111 2333333333332111 12223333322
Q ss_pred ccCCcchhhhhhHH-HHHHHHHHHHH---HHHHHHHHHHHHHHHHhhhhccCCcccccCCCCCccccccCHHHHHHHHHH
Q psy8413 629 SKEMQPEFTKLYVW-EILHLTIKKMS---KYVNRVGKELLDAKERLKHVSSESEEESDGEGGKKNEEKISEEVVEKIEEK 704 (796)
Q Consensus 629 ~~~~~~~~~~~~~W-eil~~ti~kv~---~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 704 (796)
+| ..-| +.|+.-+.+++ ++|...|-++..+|.++... + +.+.++.....||.+|++
T Consensus 178 ------~F--n~~l~~~Ln~~~~~a~k~RkkV~~sRL~~D~~R~~~k~~------~------~pekee~~r~~lE~aEDe 237 (289)
T PF10455_consen 178 ------EF--NKKLQTTLNTDFKKANKARKKVENSRLQFDAARANLKNK------A------KPEKEEQLRVELEQAEDE 237 (289)
T ss_pred ------HH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc------C------CcccCHHHHHHHHHHHHH
Confidence 22 1234 56776666544 44555555555555443221 0 022223345677888888
Q ss_pred HHHHHHHHHHHHHH
Q psy8413 705 LEAAQADQKNLFLI 718 (796)
Q Consensus 705 l~~a~~eqk~l~~~ 718 (796)
+-.+.++--.++-.
T Consensus 238 Fv~aTeeAv~~Mk~ 251 (289)
T PF10455_consen 238 FVSATEEAVEVMKE 251 (289)
T ss_pred HHHHHHHHHHHHHH
Confidence 87777774444433
No 42
>PF04844 Ovate: Transcriptional repressor, ovate; InterPro: IPR006458 This group of sequences contain an uncharacterised domain of about 70 residues found exclusively in plants, generally toward the C terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana (Mouse-ear cress). Other regions of these proteins tend to consist largely of low-complexity sequence. Function is not known.
Probab=22.52 E-value=2.4e+02 Score=23.62 Aligned_cols=54 Identities=15% Similarity=0.246 Sum_probs=36.2
Q ss_pred CchHHHHHHHHHHHhcC-CCHHHHHHHHhh-CCCCCCCCCCCCCCChhHHHHHHHHHHhhcc
Q psy8413 500 PGFVYAQELINAIKKKQ-SSPNEIMAILNK-IPSSSMDEDGADPINPLKIDVFTQVLLYLGS 559 (796)
Q Consensus 500 p~~~~a~~l~~~i~~k~-~~~eev~~~l~~-i~~~~~~~~~~~~~~~~~i~v~~q~ll~~Gs 559 (796)
|+.+.-+...++|.++. ...+++.++|.- +.-+..+ .-..++.+|.+....++|
T Consensus 4 P~~DFr~SM~EMI~~~~i~~~~~LeeLL~cYL~LN~~~------~H~~Iv~aF~dv~~~l~s 59 (59)
T PF04844_consen 4 PYEDFRESMVEMIEENGIRDWDDLEELLACYLSLNSPE------HHKFIVEAFVDVWVELFS 59 (59)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCChh------hhhHHHHHHHHHHHHHhC
Confidence 88888899999998876 566777777764 2112111 125788888887766654
No 43
>KOG2213|consensus
Probab=22.37 E-value=1.2e+03 Score=26.84 Aligned_cols=80 Identities=19% Similarity=0.233 Sum_probs=52.4
Q ss_pred HHHHHHHHHHHHHHHhcCChhhHHHHHHHHhhccccc-ccChhhHHHHHHHHHHhhhcCCC--C-ccchhhHHHHHHhhc
Q psy8413 105 GEFVELMVKTFKDALKNCQWNAARYALRFLADLVNCH-VISTNSLLQLLENMLDASKEDGV--P-NVRKDWYVYAVLSCL 180 (796)
Q Consensus 105 ~~iv~~l~~~lq~~l~~~~w~~~kl~lrFLa~L~n~~-Vi~~~sl~~ll~~ll~~a~e~~~--~-q~R~d~~vy~vL~~L 180 (796)
+++=.+++.....+|.--.-.+..+++.||+.|---+ +-....+..+-+.+-..+.-+.. + ..--|.++.|.+.++
T Consensus 146 kevE~~iv~eikkal~dVtgeef~lfm~~L~~lk~~~~k~~~a~lqeLa~~~e~~a~ldaf~~sD~d~VdRfisCl~~Av 225 (460)
T KOG2213|consen 146 KEVERHIVDEIKKALEDVTGEEFTLFMDILASLKSLQTKAGEARLQELAEEQEGLADLDAFNVSDADYVDRFISCLLMAV 225 (460)
T ss_pred hHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhhcccCCCCHHHHHHHHHHHhhhhccCcccCCChHHHHHHHHHHHHhh
Confidence 6666667777777777544458899999999985433 44455566666555555533321 1 122456899999999
Q ss_pred hhcc
Q psy8413 181 PWVG 184 (796)
Q Consensus 181 P~~G 184 (796)
|++.
T Consensus 226 PfFa 229 (460)
T KOG2213|consen 226 PFFA 229 (460)
T ss_pred hhhh
Confidence 9963
No 44
>PTZ00429 beta-adaptin; Provisional
Probab=22.36 E-value=1.1e+03 Score=29.52 Aligned_cols=224 Identities=13% Similarity=0.195 Sum_probs=0.0
Q ss_pred HHHHHHhccCCCChhHHHHHHHHHHHhcCccccHHHHHHHHHHHHHHhhccCCcccchhhhhh------hcCCCCCChHH
Q psy8413 378 SVLIELCKMKPDTMPQVLAQATVILFMRIESMNTACFDRFVAWFAYHLSNFQFQWSWEDWESA------LKLDLEHPKPK 451 (796)
Q Consensus 378 slLielCk~~P~~i~pv~~~Air~ly~~l~~mD~e~~~Rf~dWFS~hLSNF~F~W~W~eW~~~------l~~~~~~Pk~~ 451 (796)
++|.|+|...|+.+ ......++.|+++++.++ +|.-..+-+.=-.++=++-.+. +..--.|....
T Consensus 201 ~aL~eI~~~~~~~l-~l~~~~~~~Ll~~L~e~~--------EW~Qi~IL~lL~~y~P~~~~e~~~il~~l~~~Lq~~N~A 271 (746)
T PTZ00429 201 AIVCEVNDYGSEKI-ESSNEWVNRLVYHLPECN--------EWGQLYILELLAAQRPSDKESAETLLTRVLPRMSHQNPA 271 (746)
T ss_pred HHHHHHHHhCchhh-HHHHHHHHHHHHHhhcCC--------hHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHhcCCCHH
Q ss_pred HHHHHHHHHHhhcch------HHHhhhCcccccccCCCCCCCC--------------------------cccCCCCCCCC
Q psy8413 452 FIHEVLNKCVRLSYH------QRIKEIVPPQFAPLLPLKPEPH--------------------------FKYNQEGGEHL 499 (796)
Q Consensus 452 Fi~~~l~KeiRLSy~------~rIk~~lPe~~~~llp~~p~p~--------------------------fky~~e~~~~~ 499 (796)
-+-+++.-.+.|+.+ +.+-.-+-.++..+.-.+|... .+|++...
T Consensus 272 VVl~Aik~il~l~~~~~~~~~~~~~~rl~~pLv~L~ss~~eiqyvaLr~I~~i~~~~P~lf~~~~~~Ff~~~~Dp~y--- 348 (746)
T PTZ00429 272 VVMGAIKVVANLASRCSQELIERCTVRVNTALLTLSRRDAETQYIVCKNIHALLVIFPNLLRTNLDSFYVRYSDPPF--- 348 (746)
T ss_pred HHHHHHHHHHHhcCcCCHHHHHHHHHHHHHHHHHhhCCCccHHHHHHHHHHHHHHHCHHHHHHHHHhhhcccCCcHH---
Q ss_pred CchHHHHHHHHHHHhcCCCHHHHHHHHhhCCCCCCCCCCCCCCChhHHHHHHHHHHhhccchHHhHHHHHHhHHHHHHhh
Q psy8413 500 PGFVYAQELINAIKKKQSSPNEIMAILNKIPSSSMDEDGADPINPLKIDVFTQVLLYLGSKSFSHSFAALSKFYKVLKEH 579 (796)
Q Consensus 500 p~~~~a~~l~~~i~~k~~~~eev~~~l~~i~~~~~~~~~~~~~~~~~i~v~~q~ll~~GsKSfSH~~~~iery~~~Lk~l 579 (796)
+...=++.+-.=+ +.+.+..+++++..-. .+.+.....-.++++-.++.|- -...+.+-+.|..+
T Consensus 349 ----IK~~KLeIL~~La-ne~Nv~~IL~EL~eYa------~d~D~ef~r~aIrAIg~lA~k~----~~~a~~cV~~Ll~l 413 (746)
T PTZ00429 349 ----VKLEKLRLLLKLV-TPSVAPEILKELAEYA------SGVDMVFVVEVVRAIASLAIKV----DSVAPDCANLLLQI 413 (746)
T ss_pred ----HHHHHHHHHHHHc-CcccHHHHHHHHHHHh------hcCCHHHHHHHHHHHHHHHHhC----hHHHHHHHHHHHHH
Q ss_pred hCCChHHHHHHHHHHHHHHhhCcCeeHHHHHHHHh----CCCCChhhhhh--hhccc
Q psy8413 580 IGHTEESQSYVLKSLFELWHDHQQMMAVLIDKMLK----TQLLHCSSVAN--WIFSK 630 (796)
Q Consensus 580 ~~~~~~~q~~il~~v~~~W~~~~Q~~~iiidkll~----~~iv~p~~Vv~--w~F~~ 630 (796)
.+.+.+-....+..+..+-+..|+.. ++.+|+. ..|-+|.+-+. |++++
T Consensus 414 l~~~~~~v~e~i~vik~IlrkyP~~~--il~~L~~~~~~~~i~e~~AKaaiiWILGE 468 (746)
T PTZ00429 414 VDRRPELLPQVVTAAKDIVRKYPELL--MLDTLVTDYGADEVVEEEAKVSLLWMLGE 468 (746)
T ss_pred hcCCchhHHHHHHHHHHHHHHCccHH--HHHHHHHhhcccccccHHHHHHHHHHHHh
No 45
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=22.00 E-value=4e+02 Score=25.66 Aligned_cols=70 Identities=19% Similarity=0.264 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCcccccCCCCCccccccCHHHHHHHHHHHHHHHHHHHHHHH
Q psy8413 645 LHLTIKKMSKYVNRVGKELLDAKERLKHVSSESEEESDGEGGKKNEEKISEEVVEKIEEKLEAAQADQKNLFL 717 (796)
Q Consensus 645 l~~ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~a~~eqk~l~~ 717 (796)
|.+++.-|.+++.++...|+.+|+++..+-.+.+.--+ +. .+--....++|..+...++....+.+.+..
T Consensus 41 m~~A~~~v~kql~~vs~~l~~tKkhLsqRId~vd~klD-e~--~ei~~~i~~eV~~v~~dv~~i~~dv~~v~~ 110 (126)
T PF07889_consen 41 MSDAVASVSKQLEQVSESLSSTKKHLSQRIDRVDDKLD-EQ--KEISKQIKDEVTEVREDVSQIGDDVDSVQQ 110 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHH-HH--HHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 45566666666666666666666655332221111000 00 001122345555666666666666555443
No 46
>PF08146 BP28CT: BP28CT (NUC211) domain; InterPro: IPR012954 This C-terminal domain is found in BAP28-like nucleolar proteins []. The bap28 mutation leads to abnormalities in the brain, starting at midsomitogenesis stages. Mutant zebrafish embryos display excessive apoptosis, especially in the central nervous system (CNS) that results in death. The mutation affects a gene that encodes a large protein with high similarity to the uncharacterised human protein BAP28 and lower similarity to yeast Utp10. Utp10 is a component of a nucleolar U3 small nucleolar RNA-containing RNP complex that is required for transcription of ribosomal DNA and for processing of 18 S rRNA. Zebrafish Bap28 is also required for rRNA transcription and processing, with a major effect on 18S rRNA maturation. Bap28 is therefore required for cell survival in the CNS through its role in rRNA synthesis and processing [].
Probab=21.96 E-value=2.1e+02 Score=28.20 Aligned_cols=79 Identities=13% Similarity=0.165 Sum_probs=52.7
Q ss_pred CchhHHHHHHHHHhhcCCCCCccchhHHHHHHHHhccCCCChhH------HHHHHHHHHHhcCccccHHHHHHHHHHHHH
Q psy8413 350 PLEYCIVEIIFGELFRLPTPKYLEIFYGSVLIELCKMKPDTMPQ------VLAQATVILFMRIESMNTACFDRFVAWFAY 423 (796)
Q Consensus 350 ~~E~~ivEtIfs~lf~LP~p~~~~iyY~slLielCk~~P~~i~p------v~~~Air~ly~~l~~mD~e~~~Rf~dWFS~ 423 (796)
.+|..++++.....++|..+.++|+|+..+=-..-.+..+.-++ +|-+-+.-|++++.++=+--...+++=...
T Consensus 36 ~vE~~v~~~~~~lV~KLnE~~FRPlF~~l~dWA~~~l~~~~~~~~~~R~itfy~l~~~l~e~LKslf~~Y~~~ll~~~~~ 115 (153)
T PF08146_consen 36 EVESSVISAFVSLVLKLNEATFRPLFLKLVDWATSGLPKSDSSGSRARLITFYRLLNALAEKLKSLFTPYFSYLLDNAVD 115 (153)
T ss_pred HHHHHHHHHHHHHHHHcccchhHhHHHHHHHHHcccCCcccCcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57999999999999999999999999876543332222221222 244555666666666655555566666666
Q ss_pred Hhhcc
Q psy8413 424 HLSNF 428 (796)
Q Consensus 424 hLSNF 428 (796)
.|.++
T Consensus 116 ~L~~~ 120 (153)
T PF08146_consen 116 LLKQF 120 (153)
T ss_pred HHHHh
Confidence 67666
No 47
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=21.91 E-value=3.1e+02 Score=26.44 Aligned_cols=32 Identities=34% Similarity=0.293 Sum_probs=27.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy8413 639 LYVWEILHLTIKKMSKYVNRVGKELLDAKERL 670 (796)
Q Consensus 639 ~~~Weil~~ti~kv~~rv~~~~~~l~~~~~~~ 670 (796)
..+||-|..|=++++.||..+..++++..+-.
T Consensus 53 ~~vs~~l~~tKkhLsqRId~vd~klDe~~ei~ 84 (126)
T PF07889_consen 53 EQVSESLSSTKKHLSQRIDRVDDKLDEQKEIS 84 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence 57999999999999999999999998776544
No 48
>PF15188 CCDC-167: Coiled-coil domain-containing protein 167
Probab=21.85 E-value=2.4e+02 Score=25.39 Aligned_cols=74 Identities=16% Similarity=0.254 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhccCCcccccCCCCCccccccCHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH
Q psy8413 648 TIKKMSKYVNRVGKELLDAKERLKHVSSESEEESDGEGGKKNEEKISEEVVEKIEEKLEAAQADQK-NLFLIIFQRFIM 725 (796)
Q Consensus 648 ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~a~~eqk-~l~~~i~~~fv~ 725 (796)
=|+++..++.+++.+|+.+.+++...+=..++=.+. +++.......++..|++|..+..|.+ ++++.+.=-|+.
T Consensus 6 eId~lEekl~~cr~~le~ve~rL~~~eLs~e~R~~l----E~E~~~l~~~l~~~E~eL~~LrkENrK~~~ls~~l~~v~ 80 (85)
T PF15188_consen 6 EIDGLEEKLAQCRRRLEAVESRLRRRELSPEARRSL----EKELNELKEKLENNEKELKLLRKENRKSMLLSVALFFVC 80 (85)
T ss_pred HHhhHHHHHHHHHHHHHHHHHHHcccCCChHHHHHH----HHHHHHHHHHhhccHHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 467788889999999999988885532221110000 00112223455566777777776654 444444333443
No 49
>PF13324 GCIP: Grap2 and cyclin-D-interacting; PDB: 3AY5_A.
Probab=21.68 E-value=7.8e+02 Score=26.50 Aligned_cols=20 Identities=15% Similarity=0.280 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHHHhhcC
Q psy8413 758 LAHHEQVQKYSSTLETLLFT 777 (796)
Q Consensus 758 ~~~~~~~~~~~~~L~~~~ft 777 (796)
..++.+|....+.|-.-++.
T Consensus 231 ~~~~~~i~~~VDel~~slYp 250 (275)
T PF13324_consen 231 LDLCQEISPSVDELASSLYP 250 (275)
T ss_dssp HHHHHHHHHHHHHHHHHHSS
T ss_pred HHHHHHhhhHHHHHHHHhcC
Confidence 35556666666777666663
No 50
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=21.29 E-value=1.5e+02 Score=30.15 Aligned_cols=23 Identities=26% Similarity=0.393 Sum_probs=14.2
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHH
Q psy8413 692 KISEEVVEKIEEKLEAAQADQKN 714 (796)
Q Consensus 692 ~~~~~~~e~~~~~l~~a~~eqk~ 714 (796)
...+++++.++++|+.++.|-.+
T Consensus 157 ~~~~~ei~~lk~el~~~~~~~~~ 179 (192)
T PF05529_consen 157 KKLSEEIEKLKKELEKKEKEIEA 179 (192)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHH
Confidence 44456677777777766665443
No 51
>PF14838 INTS5_C: Integrator complex subunit 5 C-terminus
Probab=20.57 E-value=1e+03 Score=29.44 Aligned_cols=119 Identities=18% Similarity=0.177 Sum_probs=75.6
Q ss_pred CCCCchHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHhhccc----------------------
Q psy8413 82 YPEKCCIYTTLVGLLNAKNYNFGGEFVELMVKTFKDALKNCQWNAARYALRFLADLVN---------------------- 139 (796)
Q Consensus 82 ~P~K~p~yAtLVgllN~kn~~~g~~iv~~l~~~lq~~l~~~~w~~~kl~lrFLa~L~n---------------------- 139 (796)
-+-+.--...|++++-..+|.++-+.+.++..+ +..=.+.-+++|.++.+.+
T Consensus 194 n~~r~~w~~rLL~lL~~~~Psi~~~~~~~lL~~------A~~~~~l~lli~L~~~~~~~~~~~~~~l~~~vle~~l~~i~ 267 (696)
T PF14838_consen 194 NRKRQQWAHRLLCLLSSQHPSIAIEAISYLLTK------AQNPEHLALLIRLYAGLSVVNFPSLPGLFPAVLEQCLRQIH 267 (696)
T ss_pred chHHHHHHHHHHHHHhcCCCchHHHHHHHHHHh------cCCHHHHHHHHHHHhcccCCccccccchHHHHHHHHHHHHh
Confidence 344444455667777788999999888888776 3344566677888888776
Q ss_pred ccccChhhHHHHHHHHHHhhh-cCC--CC-ccchhhHHHHHHhhchhccHHhHHhhHHHHHHHHHHHHHHHh
Q psy8413 140 CHVISTNSLLQLLENMLDASK-EDG--VP-NVRKDWYVYAVLSCLPWVGRELYEKKEQALALLLLNIELYLN 207 (796)
Q Consensus 140 ~~Vi~~~sl~~ll~~ll~~a~-e~~--~~-q~R~d~~vy~vL~~LP~~G~~L~e~~~~~l~~ll~~i~~yl~ 207 (796)
.+.+++....++|..|.-.+. |.+ .+ ...+-.+...+.++|+-+++-| ...+.++..++.++-.++.
T Consensus 268 ~~~lt~~e~~qLl~NL~~L~k~eks~~~~~~~~~~~l~~Al~~~L~~i~~lL-~~~~~~~~~~~v~lL~~l~ 338 (696)
T PF14838_consen 268 TNTLTPTEATQLLQNLALLAKWEKSGNVPPASMSSQLTQALSSHLPDIAQLL-LHSDPEVAHAAVKLLDLLP 338 (696)
T ss_pred cCCCCcHHHHHHHHHHHHHHHHhhcCCccchhHHHHHHHHHHHHHHHHHHHH-cCCChhHHHHHHHHHHhCC
Confidence 356667777777777777662 222 22 3455556677888888777766 4344444444555544443
No 52
>cd07595 BAR_RhoGAP_Rich-like The Bin/Amphiphysin/Rvs (BAR) domain of Rich-like Rho GTPase Activating Proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of Rho and Rac GTPase activating proteins (GAPs) with similarity to GAP interacting with CIP4 homologs proteins (Rich). Members contain an N-terminal BAR domain, followed by a Rho GAP domain, and a C-terminal prolin-rich region. Vertebrates harbor at least three Rho GAPs in this subfamily including Rich1, Rich2, and SH3-domain binding protein 1 (SH3BP1). Rich1 and Rich2 play complementary roles in the establishment and maintenance of cell polarity. Rich1 is a Cdc42- and Rac-specific GAP that binds to polarity proteins through the scaffold protein angiomotin and plays a role in maintaining the integrity of tight junctions. Rich2 is a Rac GAP that interacts with CD317 and plays a role in actin cytoskeleton organization and
Probab=20.28 E-value=4.9e+02 Score=27.85 Aligned_cols=62 Identities=19% Similarity=0.244 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhccCCcccccCCCCCccccccCHHHHHHHHHHHHHHHHHHHH
Q psy8413 648 TIKKMSKYVNRVGKELLDAKERLKHVSSESEEESDGEGGKKNEEKISEEVVEKIEEKLEAAQADQKN 714 (796)
Q Consensus 648 ti~kv~~rv~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~a~~eqk~ 714 (796)
++.|-.+++...+-++..+|.++.++.+.+... .. ..+.....++++.++.+++..+.+--.
T Consensus 122 ~i~k~RKkLe~~RLd~D~~k~r~~ka~k~~~~~--~~---~~K~~~l~eE~e~ae~k~e~~~e~~~~ 183 (244)
T cd07595 122 NIQKQKKRLSKLVLDMDSARSRYNAAHKSSGGQ--GA---AAKVDALKDEYEEAELKLEQCRDALAT 183 (244)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHHhcccccccc--cc---ccccchHHHHHHHHHHHHHHHHHHHHH
Confidence 556777788888888888888887654433210 00 112223467788888888887766333
No 53
>KOG2141|consensus
Probab=20.09 E-value=3.5e+02 Score=33.34 Aligned_cols=105 Identities=21% Similarity=0.190 Sum_probs=66.3
Q ss_pred HHHHHHhhcCCCCcchhhhHHHHHHHHHHhhHh-hHHHHHHHHHHHHHhCCCCchHHHHHHHHHhccCcccHHHHHHHHH
Q psy8413 34 FEVLIVKVGERSTTSLESHLDGLAKVLETDLAT-YRVKILRILTDCATKYPEKCCIYTTLVGLLNAKNYNFGGEFVELMV 112 (796)
Q Consensus 34 l~~~I~~ige~~~~s~e~~l~~La~~l~~d~~~-~~~~i~~~l~~~v~e~P~K~p~yAtLVgllN~kn~~~g~~iv~~l~ 112 (796)
|-.+|+|==.-+.-+.++-|....+.+.=.+.. ---.|...++.|+.+--..-|+||+|..-+-.-+..+...+==.++
T Consensus 616 MNTdiRr~IFcsImsaeDyiDAFEklLkL~LK~~Q~rEI~~VllhC~l~EK~yNpfYa~lA~KfCe~~~~~~~tfQF~~W 695 (822)
T KOG2141|consen 616 MNTDIRRAIFCSIMSAEDYIDAFEKLLKLSLKGKQEREIARVLLHCCLNEKTYNPFYALLALKFCEFNKNLKKTFQFALW 695 (822)
T ss_pred cchHhhhhheeeeecchHHHHHHHHHHhccCCCcchHHHHHHHHHHHhhhcccchHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence 444444433323344454555555555433321 2356899999999999999999999988777766666665555556
Q ss_pred HHHHHHHhcCChhhHHHHHHHHhhccc
Q psy8413 113 KTFKDALKNCQWNAARYALRFLADLVN 139 (796)
Q Consensus 113 ~~lq~~l~~~~w~~~kl~lrFLa~L~n 139 (796)
..|+++=. -.-.++..+.+|+++|+-
T Consensus 696 D~f~ele~-ls~~ri~nLa~l~a~Li~ 721 (822)
T KOG2141|consen 696 DRFKELEQ-LSLFRISNLAKLLASLIS 721 (822)
T ss_pred HHHHHhhh-cchhhHhHHHHHHHHHHH
Confidence 66665433 334567788888888863
Done!