Query psy3925
Match_columns 210
No_of_seqs 202 out of 580
Neff 6.7
Searched_HMMs 46136
Date Fri Aug 16 20:52:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3925.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3925hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2297|consensus 100.0 4.9E-58 1.1E-62 397.5 21.9 200 7-207 91-412 (412)
2 KOG1461|consensus 100.0 1.7E-30 3.7E-35 241.9 17.6 167 35-210 503-673 (673)
3 PF02020 W2: eIF4-gamma/eIF5/e 99.9 9.2E-26 2E-30 164.1 8.5 80 131-210 2-84 (84)
4 smart00515 eIF5C Domain at the 99.9 3.5E-24 7.6E-29 155.3 9.3 83 119-202 1-83 (83)
5 KOG2767|consensus 99.9 2.1E-20 4.6E-25 164.3 17.4 169 21-209 214-396 (400)
6 PF09090 MIF4G_like_2: MIF4G l 96.2 0.12 2.5E-06 44.7 12.1 119 46-178 12-135 (253)
7 PF06109 HlyE: Haemolysin E (H 79.1 12 0.00027 31.6 7.7 59 17-75 4-68 (299)
8 PRK11376 hlyE hemolysin E; Pro 73.1 11 0.00024 32.4 6.0 72 18-89 8-85 (303)
9 KOG1104|consensus 66.0 20 0.00043 35.8 6.8 65 112-179 558-622 (759)
10 PF14026 DUF4242: Protein of u 44.1 16 0.00035 25.8 1.7 21 7-28 45-65 (77)
11 PF09851 SHOCT: Short C-termin 43.6 32 0.00068 19.9 2.6 19 155-173 5-23 (31)
12 PF00123 Hormone_2: Peptide ho 42.5 20 0.00044 20.5 1.6 11 190-200 17-27 (28)
13 PF02847 MA3: MA3 domain; Int 39.4 1E+02 0.0022 22.4 5.5 59 21-79 51-112 (113)
14 PF09733 VEFS-Box: VEFS-Box of 37.9 2E+02 0.0044 22.7 7.6 60 112-174 69-135 (140)
15 COG5215 KAP95 Karyopherin (imp 36.0 4.6E+02 0.0099 26.2 10.8 38 21-58 571-609 (858)
16 PF03997 VPS28: VPS28 protein; 32.5 1.4E+02 0.0031 24.8 5.8 44 24-67 26-70 (188)
17 smart00070 GLUCA Glucagon like 32.0 36 0.00078 19.3 1.5 11 190-200 17-27 (27)
18 PF14178 YppF: YppF-like prote 30.8 60 0.0013 22.1 2.7 31 16-46 17-51 (60)
19 PF02671 PAH: Paired amphipath 30.4 1.3E+02 0.0027 18.6 4.1 38 117-155 6-43 (47)
20 PHA01399 membrane protein P6 29.0 3.5E+02 0.0077 22.8 10.0 61 110-178 35-95 (242)
21 COG5587 Uncharacterized conser 26.7 39 0.00084 28.3 1.5 19 186-204 207-225 (228)
22 PF10474 DUF2451: Protein of u 26.4 4.1E+02 0.0088 22.6 9.7 82 77-179 115-202 (234)
23 smart00544 MA3 Domain in DAP-5 26.1 2.2E+02 0.0048 20.5 5.5 59 21-79 51-112 (113)
24 PF09674 DUF2400: Protein of u 26.1 4.2E+02 0.0091 22.7 7.8 96 53-155 4-99 (232)
25 PF07749 ERp29: Endoplasmic re 24.5 2.8E+02 0.0061 20.1 6.3 32 21-53 41-73 (95)
26 PF02854 MIF4G: MIF4G domain; 24.2 3.4E+02 0.0074 21.0 13.1 148 12-163 41-204 (209)
27 PF02970 TBCA: Tubulin binding 23.6 2.9E+02 0.0062 19.9 6.7 35 23-57 2-36 (90)
28 PF13972 TetR: Bacterial trans 23.6 3.3E+02 0.0073 20.7 9.6 30 19-48 20-49 (146)
29 KOG2676|consensus 23.5 6.2E+02 0.013 23.7 9.5 33 130-162 110-142 (478)
30 PF11517 Nab2: Nuclear abundan 22.0 52 0.0011 24.7 1.3 33 54-87 22-54 (107)
No 1
>KOG2297|consensus
Probab=100.00 E-value=4.9e-58 Score=397.51 Aligned_cols=200 Identities=63% Similarity=1.054 Sum_probs=195.8
Q ss_pred CCCCcceecccccHHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHhhHHHhcCCCchhHHHH
Q psy3925 7 VQTTACIFEAQEDMQSLKNFEQVFIKLMRRYKYLEKMFDEEMKKVLVFIKGFNETERIKLARMTALWITNGSVPPTVLQV 86 (210)
Q Consensus 7 ~~~~~~v~~~~~~~~~i~~~~~v~~kl~rr~~~l~k~~ee~~~~~l~~l~~~~~~~~~~llEl~~Lrms~n~~~~~v~~a 86 (210)
.||+||||+|++++|+|++|+|||+|||||||||+|.||++|.++|.|+++|++..|+++|.++||.+|+|.+|+.|+.+
T Consensus 91 ~~t~~cvfda~e~~E~i~~~~qvf~KliRRykyLeK~fE~e~~k~Llflk~F~e~Er~KLA~~Tal~l~nGt~~~tvl~~ 170 (412)
T KOG2297|consen 91 RHTSYCVFDAEEKREAIRNSVQVFQKLIRRYKYLEKNFENEMRKFLLFLKLFEENERKKLAMLTALLLSNGTLPATVLQS 170 (412)
T ss_pred ccCceeEeecCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence 57789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHH-----------------------------------------------------------------------------
Q psy3925 87 LIN----------------------------------------------------------------------------- 89 (210)
Q Consensus 87 l~~----------------------------------------------------------------------------- 89 (210)
++|
T Consensus 171 L~~d~LVkeGi~l~F~~~lFk~~~~Ek~i~~lis~Lrkg~md~rLmeffPpnkrs~E~Fak~Ft~agL~elvey~~~q~~ 250 (412)
T KOG2297|consen 171 LLNDNLVKEGIALSFAVKLFKEWLVEKDINDLISSLRKGKMDDRLMEFFPPNKRSVEHFAKYFTDAGLKELVEYHRNQQS 250 (412)
T ss_pred HHHhhHHHHhHHHHHHHHHHHHHHhhccHHHHHHHHHhcChHhHHHHhcCCcchhHHHHHHHHhHhhHHHHHHHHHHHHH
Confidence 988
Q ss_pred ---------------------------------------------HHHHHHhhhhhcchhhhHHHHHHHHHhhHHHHHHH
Q psy3925 90 ---------------------------------------------IWSTVMAQVEWNKKEELVAEQALKHLKQFTPLFGA 124 (210)
Q Consensus 90 ---------------------------------------------i~~a~m~~v~~~~~~~l~~~~~~~~l~~~~~ll~~ 124 (210)
+|+++|+.++||+++++.++++.++++.|+|||..
T Consensus 251 ~~a~kElq~~L~~q~s~e~p~~evi~~VKee~k~~nlPe~eVi~ivWs~iMsaveWnKkeelva~qalrhlK~yaPLL~a 330 (412)
T KOG2297|consen 251 EGARKELQKELQEQVSEEDPVKEVILYVKEEMKRNNLPETEVIGIVWSGIMSAVEWNKKEELVAEQALRHLKQYAPLLAA 330 (412)
T ss_pred HHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcCCCCceEEeeeHhhhhHHHhhchHHHHHHHHHHHHHHhhhHHHHH
Confidence 89999999999999999999999999999999999
Q ss_pred hccCCcHhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhhccCCChHHHHHHhhcCCCchhHHHHHHHHHHHHHHHccCCC
Q psy3925 125 FTDTAPRAELALMLKVQEFCYENMNLMRVFQKIILLFYKTDVISEEVILKWYKEGHSIKGKIMFLEQMKKFVEWLQSAEE 204 (210)
Q Consensus 125 ~~~~~~~~Q~~lL~alq~~c~~~~~~~~~f~~Il~~LYd~DIleEe~Il~W~~~~~~~~~~~~~~~~~~~FIeWL~eAEE 204 (210)
||++ +..++.+|+.+|.|||++..+|+.|+.|+..||..||++||.|++||++++.++|+++|.++++|||+||++|||
T Consensus 331 f~s~-g~sEL~Ll~KvQe~CYen~~fMKaFqkiV~lfYk~dVLsEe~IL~Wyk~gh~~KGk~~FleqmkkFVeWL~~AEE 409 (412)
T KOG2297|consen 331 FCSQ-GQSELELLLKVQEYCYENIHFMKAFQKIVVLFYKADVLSEETILKWYKEGHVAKGKSVFLEQMKKFVEWLQNAEE 409 (412)
T ss_pred HhcC-ChHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhccccccHHHHHHHHHHHHHHHHhhhh
Confidence 9999 999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCC
Q psy3925 205 GMS 207 (210)
Q Consensus 205 Esd 207 (210)
||+
T Consensus 410 EsE 412 (412)
T KOG2297|consen 410 ESE 412 (412)
T ss_pred ccC
Confidence 975
No 2
>KOG1461|consensus
Probab=99.97 E-value=1.7e-30 Score=241.95 Aligned_cols=167 Identities=22% Similarity=0.391 Sum_probs=148.1
Q ss_pred HhhHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHhhHHHhcCCCchhHHHHHHHHHHHHHhhhh---hcchhhhHHHHH
Q psy3925 35 RRYKYLEKMFDEEMKKVLVFIKGFNETERIKLARMTALWITNGSVPPTVLQVLINIWSTVMAQVE---WNKKEELVAEQA 111 (210)
Q Consensus 35 rr~~~l~k~~ee~~~~~l~~l~~~~~~~~~~llEl~~Lrms~n~~~~~v~~al~~i~~a~m~~v~---~~~~~~l~~~~~ 111 (210)
..+++|+|++.++|++.+. ++. ..|++++|+|+||||+|++.++|++|+ +.++|+.+. .++..+ +..++
T Consensus 503 ~d~~~F~~Ev~~s~~ra~E--en~--~~D~~vlEINslRla~N~s~~ev~~av---~~all~~~~~~~~~~~~~-~~~~~ 574 (673)
T KOG1461|consen 503 DDTKDFEKEVLGSLQRAFE--ENS--DMDNLVLEINSLRLAYNVSLKEVAGAV---FMALLKLILHQDHSSMNE-VKRAA 574 (673)
T ss_pred chhHHHHHHHHHHHHHHHH--hcc--chHHHHHHHhhhHHhhcCCHHHHHHHH---HHHHHHHHhcCCCccchh-HHHHH
Confidence 4899999999999999985 443 459999999999999999999999999 999999983 333223 45688
Q ss_pred HHHHhhHHHHHHHhccCCcHhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhhccCCChHHHHHHhhcCCCch-hHHHHHH
Q psy3925 112 LKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYENMNLMRVFQKIILLFYKTDVISEEVILKWYKEGHSIK-GKIMFLE 190 (210)
Q Consensus 112 ~~~l~~~~~ll~~~~~~~~~~Q~~lL~alq~~c~~~~~~~~~f~~Il~~LYd~DIleEe~Il~W~~~~~~~~-~~~~~~~ 190 (210)
.+++++|+|++.+|+++ .+.|+++|.+||++|.++..+.+.+.++++.||+.|||+|++|++||...+... ..++.+.
T Consensus 575 ~~~~~~w~~l~~~y~ks-~deqid~l~~led~~~e~~~~~~~~~~~v~~lY~~dil~EdaI~~W~~~~~~~~~~~~~~~~ 653 (673)
T KOG1461|consen 575 LKVFTQWGPLLGNYIKS-EDEQIDLLLALEDKCVESEELGPKAAKLVHYLYDYDILQEDAILSWSSQKAGDDEEDAVYNQ 653 (673)
T ss_pred HHHHHHhhHHhhhhhhh-HHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHhHhhHHHHHHhhhccccchHHHHHHHH
Confidence 89999999999999999 999999999999999999888899999999999999999999999998844443 3468899
Q ss_pred HHHHHHHHHccCCCCCCCCC
Q psy3925 191 QMKKFVEWLQSAEEGMSSEA 210 (210)
Q Consensus 191 ~~~~FIeWL~eAEEEsdeed 210 (210)
++++||+||++|+||||+||
T Consensus 654 ~~k~fv~WL~easeE~~~ee 673 (673)
T KOG1461|consen 654 QLKKFVDWLKEASEEEESEE 673 (673)
T ss_pred HHHHHHHHHhhcccccccCC
Confidence 99999999999999999886
No 3
>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=99.93 E-value=9.2e-26 Score=164.12 Aligned_cols=80 Identities=38% Similarity=0.737 Sum_probs=65.9
Q ss_pred HhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhhccCCChHHHHHHhhcCC---CchhHHHHHHHHHHHHHHHccCCCCCC
Q psy3925 131 RAELALMLKVQEFCYENMNLMRVFQKIILLFYKTDVISEEVILKWYKEGH---SIKGKIMFLEQMKKFVEWLQSAEEGMS 207 (210)
Q Consensus 131 ~~Q~~lL~alq~~c~~~~~~~~~f~~Il~~LYd~DIleEe~Il~W~~~~~---~~~~~~~~~~~~~~FIeWL~eAEEEsd 207 (210)
++|+++|.++|.+|.+++.+++.|++||+.|||.|||+|++|++||++.. .+++++++|++++|||+||++||||||
T Consensus 2 ~~Q~~~L~ale~~~~~~~~~~~~~~~il~~LYd~Dil~Eeail~W~~~~~~~~~~~~~~~~r~~~~~fi~WL~eaeeE~~ 81 (84)
T PF02020_consen 2 DDQVDLLNALEEFCAENPNLMPLFPKILQQLYDEDILEEEAILEWYEDSKPAVDGEGRAKVRKQAQPFIEWLEEAEEESD 81 (84)
T ss_dssp HHHHHHHHHHHHHHHHTCGHGGHHHHHHHHHHHTTSS-HHHHHHHHHC-SSSSCHHHHHHHHHHHHHHHHHHHHCC----
T ss_pred HHHHHHHHHHHHHHHhCccHHHHHHHHHHHHhhhhhccHHHHHHHHHcCCccccchhHHHHHHHHHHHHHHHhccCccCC
Confidence 68999999999999999999999999999999999999999999999822 234678899999999999999999999
Q ss_pred CCC
Q psy3925 208 SEA 210 (210)
Q Consensus 208 eed 210 (210)
+||
T Consensus 82 eed 84 (84)
T PF02020_consen 82 EED 84 (84)
T ss_dssp ---
T ss_pred CCC
Confidence 886
No 4
>smart00515 eIF5C Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5.
Probab=99.91 E-value=3.5e-24 Score=155.28 Aligned_cols=83 Identities=35% Similarity=0.699 Sum_probs=77.2
Q ss_pred HHHHHHhccCCcHhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhhccCCChHHHHHHhhcCCCchhHHHHHHHHHHHHHH
Q psy3925 119 TPLFGAFTDTAPRAELALMLKVQEFCYENMNLMRVFQKIILLFYKTDVISEEVILKWYKEGHSIKGKIMFLEQMKKFVEW 198 (210)
Q Consensus 119 ~~ll~~~~~~~~~~Q~~lL~alq~~c~~~~~~~~~f~~Il~~LYd~DIleEe~Il~W~~~~~~~~~~~~~~~~~~~FIeW 198 (210)
+|+|.+++++ .++|+++|.++|.+|.+++.+.+.|+.|++.|||.|||+||+|++||+++++++++++++++++|||+|
T Consensus 1 ~~ll~~~~~~-~~~q~~~L~ale~~~~~~~~~~~~~~~il~~LYd~dileEe~il~W~~~~~~~~~~~~~~~~~~~fv~W 79 (83)
T smart00515 1 GPLLKFLAKD-EEEQIDLLYAIEEFCVELEKLIKLLPKILKSLYDADILEEEAILKWYEKAVSAEGKKKVRKNAKPFVTW 79 (83)
T ss_pred ChHHHHHHCC-hHHHHHHHHHHHHHHHHcchHHHHHHHHHHHHhhhccccHHHHHHHHHcCCChHHHHHHHHHHhHHHHH
Confidence 4789999998 899999999999999987668899999999999999999999999999987666889999999999999
Q ss_pred HccC
Q psy3925 199 LQSA 202 (210)
Q Consensus 199 L~eA 202 (210)
|++|
T Consensus 80 L~eA 83 (83)
T smart00515 80 LQEA 83 (83)
T ss_pred HHcC
Confidence 9986
No 5
>KOG2767|consensus
Probab=99.86 E-value=2.1e-20 Score=164.33 Aligned_cols=169 Identities=25% Similarity=0.347 Sum_probs=124.9
Q ss_pred HHhHHHHHHHH---HHHHhhHHHHHHHHHHHHHHHHHHhcCChhH------HHHHHHHhhHHHhcCCCchhHHHHHHHHH
Q psy3925 21 QSLKNFEQVFI---KLMRRYKYLEKMFDEEMKKVLVFIKGFNETE------RIKLARMTALWITNGSVPPTVLQVLINIW 91 (210)
Q Consensus 21 ~~i~~~~~v~~---kl~rr~~~l~k~~ee~~~~~l~~l~~~~~~~------~~~llEl~~Lrms~n~~~~~v~~al~~i~ 91 (210)
++++..+|-+. +-+--..++++.=++....+.++.+...++. ...+.++..|-+.+ ..|...+
T Consensus 214 ea~r~R~~~Ls~~~~~~~~~sd~e~~E~~~~~~~~d~~~~~~~en~~~~~~kEi~~~a~~l~i~~-k~p~vl~------- 285 (400)
T KOG2767|consen 214 EAIRARMQELSANAKEMLLLSDLEKSEEEREDILYDFVKKKKEENVPDKSDKEIVKEAERLDIKN-KAPLVLA------- 285 (400)
T ss_pred HHHHHHHHHHhhhhhhhhhhhhhhhhHHHHHHHHHHhhhhcccccCCCccHHHHHHHHHHHhhcc-cchHHHH-------
Confidence 56666666332 3333457788876777788887777766422 12233333222222 1111111
Q ss_pred HHHHhhhhhcchhhhHHHHHHHHHhhHHHHHHHhccCCcHhHHHHHHHHHHHHHhh-hhhHHHHHHHHHHHhhccCCChH
Q psy3925 92 STVMAQVEWNKKEELVAEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYEN-MNLMRVFQKIILLFYKTDVISEE 170 (210)
Q Consensus 92 ~a~m~~v~~~~~~~l~~~~~~~~l~~~~~ll~~~~~~~~~~Q~~lL~alq~~c~~~-~~~~~~f~~Il~~LYd~DIleEe 170 (210)
+.||.+.+.+.|.+++++|.+||.++.+.|..||.+|+++|..+ ..+++..+.||+.|||+||++|+
T Consensus 286 ------------~~Lf~e~ivkei~k~~~~l~k~~~~~~k~qr~LLggiE~~~~~~~~el~~kva~ilk~lYd~DI~~e~ 353 (400)
T KOG2767|consen 286 ------------EVLFDEKIVKEILKHRALLLKFCTNNEKAQRYLLGGIERFVEKHEAELISKVAGILKELYDEDILEEE 353 (400)
T ss_pred ------------HHHhhhHHHHHHHHHHHHHHHHHhccHHHHHHHHhHHHHHHHhhHHHHHHHHHHHHHHHHhhhhhhHH
Confidence 23567788899999999999999987889999999999999874 78899999999999999999999
Q ss_pred HHHHHhhcCCC---chh-HHHHHHHHHHHHHHHccCCCCCCCC
Q psy3925 171 VILKWYKEGHS---IKG-KIMFLEQMKKFVEWLQSAEEGMSSE 209 (210)
Q Consensus 171 ~Il~W~~~~~~---~~~-~~~~~~~~~~FIeWL~eAEEEsdee 209 (210)
+|++|+.++++ ++. .+.+++.++|||+||++||+|+++|
T Consensus 354 vi~~w~~K~skk~vsk~~sk~i~e~a~Pfi~WL~~AESe~eeE 396 (400)
T KOG2767|consen 354 VIIKWGEKPSKKYVSKEKSKKIRENAKPFIEWLKNAESEDEEE 396 (400)
T ss_pred HHHHHHhcccccccchhhhhhhHhhhhHHHHHHHhcccccccc
Confidence 99999999885 343 4689999999999999998776655
No 6
>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=96.17 E-value=0.12 Score=44.71 Aligned_cols=119 Identities=16% Similarity=0.201 Sum_probs=74.5
Q ss_pred HHHHHHHHHHhcCChhHHHHHHHHhhHHHh---cCCCchh-HHHHHHHHHHHHHhhhhhcchhhhHHHHHHHHHhhHHHH
Q psy3925 46 EEMKKVLVFIKGFNETERIKLARMTALWIT---NGSVPPT-VLQVLINIWSTVMAQVEWNKKEELVAEQALKHLKQFTPL 121 (210)
Q Consensus 46 e~~~~~l~~l~~~~~~~~~~llEl~~Lrms---~n~~~~~-v~~al~~i~~a~m~~v~~~~~~~l~~~~~~~~l~~~~~l 121 (210)
+...++++++++.. +.+....-++.+.-. .|..+.. ++..+ +++++-.+ ++. +. -+...|++|++.
T Consensus 12 ~~a~~l~~~ir~k~-~~eei~~~l~~i~~~~~~~~~~~~~~~i~v~---~q~ll~~G---SkS--~S-H~~~~lery~~~ 81 (253)
T PF09090_consen 12 ALAQKLLDLIRKKA-PPEEISELLEEIEEPAEEHGSDFDKFVIDVF---VQCLLHIG---SKS--FS-HVLSALERYKEV 81 (253)
T ss_dssp HHHHHHHHHHHTT---HHHHHHHHTTS------------HHHHHHH---HHHHHHHT---TTS--HH-HHHHHHHHTHHH
T ss_pred HHHHHHHHHHHcCC-CHHHHHHHHHhccccccccccchhhHHHHHH---HHHHHHhc---Cch--HH-HHHHHHHHHHHH
Confidence 44577888888865 444444444433322 2221111 22222 55555332 221 23 244589999999
Q ss_pred HHHh-ccCCcHhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhhccCCChHHHHHHhhc
Q psy3925 122 FGAF-TDTAPRAELALMLKVQEFCYENMNLMRVFQKIILLFYKTDVISEEVILKWYKE 178 (210)
Q Consensus 122 l~~~-~~~~~~~Q~~lL~alq~~c~~~~~~~~~f~~Il~~LYd~DIleEe~Il~W~~~ 178 (210)
|+.+ +.+ ...|..+|.++-.+...+|.. ..-|+..|-..+||+-.+|+.|-=+
T Consensus 82 Lk~l~~~~-~~~q~~il~~v~~~W~~~~q~---~~li~dkll~~~ii~~~~Vv~w~f~ 135 (253)
T PF09090_consen 82 LKELEAES-EEAQFWILDAVFRFWKNNPQM---GFLIIDKLLNYGIISPSAVVNWVFS 135 (253)
T ss_dssp HHHH-TSS-HHHHHHHHHHHHHHHTT-HHH---HHHHHHHHHHTTSS-HHHHHHHHTS
T ss_pred HHHhccCC-hHHHHHHHHHHHHHHhcCCce---ehHHHHHHHhcCCCCHHHHHHHHcC
Confidence 9999 776 889999999999999888874 4678889999999999999999843
No 7
>PF06109 HlyE: Haemolysin E (HlyE); InterPro: IPR010356 This family consists of several enterobacterial haemolysin (HlyE) proteins. Haemolysin E (HlyE) is a novel pore-forming toxin of Escherichia coli, Salmonella typhi, and Shigella flexneri. HlyE is unrelated to the well characterised pore-forming E. coli haemolysins of the RTX family, haemolysin A (HlyA), and the enterohaemolysin encoded by the plasmid borne ehxA gene of E. coli 0157. However, it is evident that expression of HlyE in the absence of the RTX toxins is sufficient to give a haemolytic phenotype in E. coli. HlyE is a protein of 34 kDa that is expressed during anaerobic growth of E. coli. Anaerobic expression is controlled by the transcription factor, FNR, such that, upon ingestion and entry into the anaerobic mammalian intestine, HlyE is produced and may then contribute to the colonisation of the host [].; PDB: 2WCD_P 1QOY_A.
Probab=79.15 E-value=12 Score=31.55 Aligned_cols=59 Identities=19% Similarity=0.425 Sum_probs=43.2
Q ss_pred cccHHHhHHHHHHHHHHHHhh-HHHH-----HHHHHHHHHHHHHHhcCChhHHHHHHHHhhHHHh
Q psy3925 17 QEDMQSLKNFEQVFIKLMRRY-KYLE-----KMFDEEMKKVLVFIKGFNETERIKLARMTALWIT 75 (210)
Q Consensus 17 ~~~~~~i~~~~~v~~kl~rr~-~~l~-----k~~ee~~~~~l~~l~~~~~~~~~~llEl~~Lrms 75 (210)
..++|.+++-.+--.+-+..| |||. .+|.++++.+-+|-+.++......+.++.+|.|-
T Consensus 4 d~tve~vk~ai~tad~aldlynk~ldqvipw~tf~~tikelsrfk~eysq~as~lvg~ik~llm~ 68 (299)
T PF06109_consen 4 DQTVETVKNAIDTADKALDLYNKYLDQVIPWQTFNDTIKELSRFKQEYSQSASTLVGDIKSLLMN 68 (299)
T ss_dssp HHHTHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chhHHHHHHHHHhccchHHHHHHHHhhhCCchhHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Confidence 335566666655555555555 4554 4688899999888888888888999999999984
No 8
>PRK11376 hlyE hemolysin E; Provisional
Probab=73.06 E-value=11 Score=32.39 Aligned_cols=72 Identities=17% Similarity=0.305 Sum_probs=51.2
Q ss_pred ccHHHhHHHHHHHHHHHHhhH-HHH-----HHHHHHHHHHHHHHhcCChhHHHHHHHHhhHHHhcCCCchhHHHHHHH
Q psy3925 18 EDMQSLKNFEQVFIKLMRRYK-YLE-----KMFDEEMKKVLVFIKGFNETERIKLARMTALWITNGSVPPTVLQVLIN 89 (210)
Q Consensus 18 ~~~~~i~~~~~v~~kl~rr~~-~l~-----k~~ee~~~~~l~~l~~~~~~~~~~llEl~~Lrms~n~~~~~v~~al~~ 89 (210)
.++|.++.-.+--.+-+..|. +|+ .+|.+++..+=+|+.++....++.+-++.+|-+.....+..|.+.++.
T Consensus 8 ~tve~vk~ai~tad~ald~Yr~ELDqkVkf~eLQeAIdeIDRaMlgYqG~AK~~Ld~IRsLnSdAr~kYqecV~pVFE 85 (303)
T PRK11376 8 KTVEVVKNAIETADGALDLYNKYLDQVIPWQTFDETIKELSRFKQEYSQAASVLVGDIKTLLMDSQDKYFEATQTVYE 85 (303)
T ss_pred hhHHHHHHHHHhhhhHHHHHHHHHhccCCHHHHHHHHHHHHHHhhhhhhHHHHhhhHHHHHHHHHHHHHHHhhHHHHH
Confidence 355555555544444443332 233 256777777777888999899999999999999999999999888754
No 9
>KOG1104|consensus
Probab=66.03 E-value=20 Score=35.75 Aligned_cols=65 Identities=12% Similarity=0.274 Sum_probs=52.7
Q ss_pred HHHHhhHHHHHHHhccCCcHhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhhccCCChHHHHHHhhcC
Q psy3925 112 LKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYENMNLMRVFQKIILLFYKTDVISEEVILKWYKEG 179 (210)
Q Consensus 112 ~~~l~~~~~ll~~~~~~~~~~Q~~lL~alq~~c~~~~~~~~~f~~Il~~LYd~DIleEe~Il~W~~~~ 179 (210)
..++.+|+..|+.+|.++...|+.+|.++=.+...||+.+ ..++-.|-...||+-.+|..|-=+.
T Consensus 558 f~~lek~~~vfk~l~~~~e~~q~~vl~~vft~Wk~n~Qm~---~v~~Dkml~~~ii~~~aVv~WiF~~ 622 (759)
T KOG1104|consen 558 FSALEKYHTVFKKLCEDSETKQIIVLEAVFTFWKANPQMG---FVLTDKMLKYQIIDCSAVVRWIFSE 622 (759)
T ss_pred HHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHhcCchhh---HHHHHHHhccccccHHHHHHHhcCH
Confidence 4478999999999999845559999999999988887743 4456666778999999999998443
No 10
>PF14026 DUF4242: Protein of unknown function (DUF4242)
Probab=44.11 E-value=16 Score=25.76 Aligned_cols=21 Identities=19% Similarity=0.490 Sum_probs=16.4
Q ss_pred CCCCcceecccccHHHhHHHHH
Q psy3925 7 VQTTACIFEAQEDMQSLKNFEQ 28 (210)
Q Consensus 7 ~~~~~~v~~~~~~~~~i~~~~~ 28 (210)
...-|||+.|| |-|+|+.+.+
T Consensus 45 ~~k~~Cly~Ap-~~eaV~~~~~ 65 (77)
T PF14026_consen 45 DGKIFCLYEAP-DEEAVREHAR 65 (77)
T ss_pred CCeEEEEEECC-CHHHHHHHHH
Confidence 44479999999 6778888765
No 11
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=43.64 E-value=32 Score=19.92 Aligned_cols=19 Identities=26% Similarity=0.212 Sum_probs=16.3
Q ss_pred HHHHHHHhhccCCChHHHH
Q psy3925 155 QKIILLFYKTDVISEEVIL 173 (210)
Q Consensus 155 ~~Il~~LYd~DIleEe~Il 173 (210)
...|+.||+.++++++-+-
T Consensus 5 L~~L~~l~~~G~IseeEy~ 23 (31)
T PF09851_consen 5 LEKLKELYDKGEISEEEYE 23 (31)
T ss_pred HHHHHHHHHcCCCCHHHHH
Confidence 3578999999999999875
No 12
>PF00123 Hormone_2: Peptide hormone; InterPro: IPR000532 A number of polypeptidic hormones, mainly expressed in the intestine or the pancreas, belong to a group of structurally related peptides [, ]. Once such hormone, glucagon is widely distributed and produced in the alpha-cells of pancreatic islets []. It affects glucose metabolism in the liver [] by inhibiting glycogen synthesis, stimulating glycogenolysis and enchancing gluconeogenesis. It also increases mobilisation of glucose, free fatty acids and ketone bodies, which are metabolites produced in excess in diabetes mellitus. Glucagon is produced, like other peptide hormones, as part of a larger precursor (preproglucagon), which is cleaved to produce glucagon, glucagon-like protein I and glucagon-like protein II []. The structure of glucagon itself is fully conserved in all known mammalian species []. Other members of the structurally similar group include glicentin precursor, secretin, gastric inhibitory protein, vasoactive intestinal peptide (VIP), prealbumin, peptide HI-27 and growth hormone releasing factor.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1T5Q_A 2OBU_A 2QKH_B 2L70_A 2L71_A 2B4N_A 1GCN_A 1D0R_A 3IOL_B 2RRI_A ....
Probab=42.52 E-value=20 Score=20.54 Aligned_cols=11 Identities=45% Similarity=0.921 Sum_probs=9.0
Q ss_pred HHHHHHHHHHc
Q psy3925 190 EQMKKFVEWLQ 200 (210)
Q Consensus 190 ~~~~~FIeWL~ 200 (210)
..+++||.||.
T Consensus 17 ~aak~fl~~L~ 27 (28)
T PF00123_consen 17 LAAKKFLQWLM 27 (28)
T ss_dssp HHHHHHHHHHC
T ss_pred HHHHHHHHHHh
Confidence 36888999995
No 13
>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=39.43 E-value=1e+02 Score=22.38 Aligned_cols=59 Identities=17% Similarity=0.262 Sum_probs=35.3
Q ss_pred HHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCChh---HHHHHHHHhhHHHhcCCC
Q psy3925 21 QSLKNFEQVFIKLMRRYKYLEKMFDEEMKKVLVFIKGFNET---ERIKLARMTALWITNGSV 79 (210)
Q Consensus 21 ~~i~~~~~v~~kl~rr~~~l~k~~ee~~~~~l~~l~~~~~~---~~~~llEl~~Lrms~n~~ 79 (210)
..-.-|.+++..|+.+...-...++.-+..+++.+.....+ .-.-++.+.+-.++.|..
T Consensus 51 ~~r~~~~~Ll~~L~~~~~~~~~~~~~gf~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~~~~l 112 (113)
T PF02847_consen 51 SYREYYSKLLSHLCKRKLISKEQFQEGFEDLLESLEDLELDIPKAPEYLAKFLARLIADGIL 112 (113)
T ss_dssp HHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTSS
T ss_pred HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhHhhhccccchHHHHHHHHHHHHHHHcCCc
Confidence 33455667888888776666666666666666655554433 455666666666655544
No 14
>PF09733 VEFS-Box: VEFS-Box of polycomb protein; InterPro: IPR019135 The VEFS-Box is found in the the C-terminal region of the VRN2, EMF2, FIS2, and Su(z)12 polycomb proteins. This domain is characterised by an acidic cluster and a tryptophan/methionine-rich sequence, the acidic-W/M domain []. In some proteins the VEFS-Box is associated with a zinc-finger domain located roughly 100 residues towards the N terminus. These proteins are part of the polycomb cluster of proteins which control HOX gene transcription as it functions in heterochromatin-mediated repression [].
Probab=37.87 E-value=2e+02 Score=22.66 Aligned_cols=60 Identities=13% Similarity=0.184 Sum_probs=39.4
Q ss_pred HHHHhhHHHHHHHhccCCcHhHHHHHHHHHHHHHh-------hhhhHHHHHHHHHHHhhccCCChHHHHH
Q psy3925 112 LKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYE-------NMNLMRVFQKIILLFYKTDVISEEVILK 174 (210)
Q Consensus 112 ~~~l~~~~~ll~~~~~~~~~~Q~~lL~alq~~c~~-------~~~~~~~f~~Il~~LYd~DIleEe~Il~ 174 (210)
++.+..|...+.+.-.. ++.| +=.+++.|+.. ++.+...|..-+-.||+.++|+..+|..
T Consensus 69 KefM~lWN~fv~k~r~~-aD~~--ip~ac~~Fv~~~~~~L~~~~~l~~~f~lHl~~L~d~glLd~~~i~~ 135 (140)
T PF09733_consen 69 KEFMKLWNSFVMKQRVI-ADGH--IPWACEAFVREHGQWLVEKPNLRREFLLHLINLWDFGLLDARTIDE 135 (140)
T ss_pred HHHHHHHHHHHHHccCc-chHH--HHHHHHHHHHHhHHHHhhChhHHHHHHHHHHHHHHcCCCCHHHHHH
Confidence 34566677666554433 4444 33344444443 3577788888899999999999998863
No 15
>COG5215 KAP95 Karyopherin (importin) beta [Intracellular trafficking and secretion]
Probab=35.98 E-value=4.6e+02 Score=26.20 Aligned_cols=38 Identities=11% Similarity=0.183 Sum_probs=25.8
Q ss_pred HHhHHHHHHHHHHHHhhHHHHHHHHHH-HHHHHHHHhcC
Q psy3925 21 QSLKNFEQVFIKLMRRYKYLEKMFDEE-MKKVLVFIKGF 58 (210)
Q Consensus 21 ~~i~~~~~v~~kl~rr~~~l~k~~ee~-~~~~l~~l~~~ 58 (210)
|-..+|..|+.-+||+++-=.+.+++. |.-+++-++.-
T Consensus 571 elqSN~~~vl~aiir~~~~~ie~v~D~lm~Lf~r~les~ 609 (858)
T COG5215 571 ELQSNYIGVLEAIIRTRRRDIEDVEDQLMELFIRILEST 609 (858)
T ss_pred HHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHhcc
Confidence 345688889999998887766677775 44444544443
No 16
>PF03997 VPS28: VPS28 protein; InterPro: IPR007143 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ].; PDB: 2J9W_B 2J9U_C 2G3K_A 2F66_E 2F6M_D 2J9V_A 2CAZ_E 2P22_B.
Probab=32.46 E-value=1.4e+02 Score=24.77 Aligned_cols=44 Identities=25% Similarity=0.400 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHH-HHHHHHHHHhcCChhHHHHHH
Q psy3925 24 KNFEQVFIKLMRRYKYLEKMFDE-EMKKVLVFIKGFNETERIKLA 67 (210)
Q Consensus 24 ~~~~~v~~kl~rr~~~l~k~~ee-~~~~~l~~l~~~~~~~~~~ll 67 (210)
+.|..-.+|||.+||-+.+.+.. .+..+=.|.++|..+-..++-
T Consensus 26 ~eYt~~c~kLl~Qyk~~~~~~~~~~~~~le~F~~~y~l~cp~A~~ 70 (188)
T PF03997_consen 26 KEYTTACNKLLNQYKTILKQLKDDEFPDLEEFMKKYNLDCPAALE 70 (188)
T ss_dssp HHHHHHHHHHHHHHHHHHTSTTHHHHHHHHHHHHHTTS-HHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHcccccCCCHHHHHHHhcccCChHHH
Confidence 56999999999999999999888 788888899998865444443
No 17
>smart00070 GLUCA Glucagon like hormones.
Probab=31.95 E-value=36 Score=19.34 Aligned_cols=11 Identities=45% Similarity=0.921 Sum_probs=8.6
Q ss_pred HHHHHHHHHHc
Q psy3925 190 EQMKKFVEWLQ 200 (210)
Q Consensus 190 ~~~~~FIeWL~ 200 (210)
..+++||.||.
T Consensus 17 ~~ar~fl~~L~ 27 (27)
T smart00070 17 LAAKKFLQWLM 27 (27)
T ss_pred HHHHHHHHHhC
Confidence 35888999983
No 18
>PF14178 YppF: YppF-like protein
Probab=30.78 E-value=60 Score=22.09 Aligned_cols=31 Identities=23% Similarity=0.492 Sum_probs=19.6
Q ss_pred ccccHHHhHHHHH---HHHHH-HHhhHHHHHHHHH
Q psy3925 16 AQEDMQSLKNFEQ---VFIKL-MRRYKYLEKMFDE 46 (210)
Q Consensus 16 ~~~~~~~i~~~~~---v~~kl-~rr~~~l~k~~ee 46 (210)
.|.+++.+.+|++ +.+++ |++|+.|-|++|-
T Consensus 17 ~p~~~NeLLDFar~~Yi~gei~i~eYR~lvreLE~ 51 (60)
T PF14178_consen 17 EPEDMNELLDFARKLYIQGEISINEYRNLVRELEA 51 (60)
T ss_pred CcccHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence 3567777777776 33332 6677777777664
No 19
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=30.36 E-value=1.3e+02 Score=18.63 Aligned_cols=38 Identities=13% Similarity=0.301 Sum_probs=20.7
Q ss_pred hHHHHHHHhccCCcHhHHHHHHHHHHHHHhhhhhHHHHH
Q psy3925 117 QFTPLFGAFTDTAPRAELALMLKVQEFCYENMNLMRVFQ 155 (210)
Q Consensus 117 ~~~~ll~~~~~~~~~~Q~~lL~alq~~c~~~~~~~~~f~ 155 (210)
.+-.++..|..+ ..+.-++...+......||.++.-|.
T Consensus 6 ~FL~il~~y~~~-~~~~~~v~~~v~~Ll~~hpdLl~~F~ 43 (47)
T PF02671_consen 6 EFLKILNDYKKG-RISRSEVIEEVSELLRGHPDLLEEFN 43 (47)
T ss_dssp HHHHHHHHHHCT-CSCHHHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHhc-CCCHHHHHHHHHHHHccCHHHHHHHH
Confidence 333455555554 44555566666666666666655543
No 20
>PHA01399 membrane protein P6
Probab=29.02 E-value=3.5e+02 Score=22.80 Aligned_cols=61 Identities=8% Similarity=0.219 Sum_probs=29.9
Q ss_pred HHHHHHhhHHHHHHHhccCCcHhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhhccCCChHHHHHHhhc
Q psy3925 110 QALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYENMNLMRVFQKIILLFYKTDVISEEVILKWYKE 178 (210)
Q Consensus 110 ~~~~~l~~~~~ll~~~~~~~~~~Q~~lL~alq~~c~~~~~~~~~f~~Il~~LYd~DIleEe~Il~W~~~ 178 (210)
++.+.+++-..++..|++. -=+-+.+++.+--...-.=.+.|.|..++|.|. +.|..|...
T Consensus 35 a~vk~ikkivsvi~~fisk-ifs~ig~il~~il~~~~awf~fpa~IAIIKNLW-------EGIrnwv~e 95 (242)
T PHA01399 35 AIVKIIKKIVSVILDFISK-IFSKIGIILIIILIIIAAWFFFPAFAAFLQSAW-------ASFVNFFQT 95 (242)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHhccHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHH
Confidence 4555666666555555532 111122221111111111234566778888876 777777754
No 21
>COG5587 Uncharacterized conserved protein [Function unknown]
Probab=26.67 E-value=39 Score=28.25 Aligned_cols=19 Identities=32% Similarity=0.852 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHccCCC
Q psy3925 186 IMFLEQMKKFVEWLQSAEE 204 (210)
Q Consensus 186 ~~~~~~~~~FIeWL~eAEE 204 (210)
..+...++|||+|+..+|+
T Consensus 207 vdf~~ra~PliDw~ra~e~ 225 (228)
T COG5587 207 VDFLHRAAPLIDWLRAAED 225 (228)
T ss_pred HHHHHHhhhHHHHHHHHhc
Confidence 3678889999999998875
No 22
>PF10474 DUF2451: Protein of unknown function C-terminus (DUF2451); InterPro: IPR019514 This protein is found in eukaryotes but its function is not known. The N-terminal domain of some members is PF10475 from PFAM (DUF2450).
Probab=26.43 E-value=4.1e+02 Score=22.63 Aligned_cols=82 Identities=21% Similarity=0.425 Sum_probs=44.7
Q ss_pred CCCchhHHHHHHHHHHHHHhhhhhcchhhhHHHHHHHHHhhHHHHHHHhccCCcHhHHH-----HHHHHHHHHHhh-hhh
Q psy3925 77 GSVPPTVLQVLINIWSTVMAQVEWNKKEELVAEQALKHLKQFTPLFGAFTDTAPRAELA-----LMLKVQEFCYEN-MNL 150 (210)
Q Consensus 77 n~~~~~v~~al~~i~~a~m~~v~~~~~~~l~~~~~~~~l~~~~~ll~~~~~~~~~~Q~~-----lL~alq~~c~~~-~~~ 150 (210)
+..|.++...+ |..++..+ .+. .++-|+.+ ++.... +++++. ++..+|...... +.-
T Consensus 115 ~~i~~~~~~~l---w~~~i~~~---------~~~---Lveg~s~v-kKCs~e-GRalM~lD~q~~~~~le~l~~~~~~p~ 177 (234)
T PF10474_consen 115 GPIPPEVQNVL---WDRLIFFA---------FET---LVEGYSRV-KKCSNE-GRALMQLDFQQLQNKLEKLSGIRPIPN 177 (234)
T ss_pred CCCCHHHHHHH---HHHHHHHH---------HHH---HHHHHHhc-cCCChh-hHHHHHHHHHHHHHHHHHHcCCCCCcc
Confidence 45566666666 66665443 111 23444442 344434 666543 233333333222 122
Q ss_pred HHHHHHHHHHHhhccCCChHHHHHHhhcC
Q psy3925 151 MRVFQKIILLFYKTDVISEEVILKWYKEG 179 (210)
Q Consensus 151 ~~~f~~Il~~LYd~DIleEe~Il~W~~~~ 179 (210)
....-..+|++| +.|+.+.+|-..-
T Consensus 178 ~~~Ve~YIKAyY----l~e~e~~~W~~~h 202 (234)
T PF10474_consen 178 REYVENYIKAYY----LPEEELEEWIRTH 202 (234)
T ss_pred HHHHHHHHHHHc----CCHHHHHHHHHhC
Confidence 345667789999 7889999999774
No 23
>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=26.13 E-value=2.2e+02 Score=20.54 Aligned_cols=59 Identities=17% Similarity=0.221 Sum_probs=37.0
Q ss_pred HHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCh---hHHHHHHHHhhHHHhcCCC
Q psy3925 21 QSLKNFEQVFIKLMRRYKYLEKMFDEEMKKVLVFIKGFNE---TERIKLARMTALWITNGSV 79 (210)
Q Consensus 21 ~~i~~~~~v~~kl~rr~~~l~k~~ee~~~~~l~~l~~~~~---~~~~~llEl~~Lrms~n~~ 79 (210)
..-..|.+++..|.++..-....++.-+.++++.+....- ..-..++.+-|-.++.|..
T Consensus 51 ~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~l~dl~~D~P~a~~~la~~~a~~v~~~~l 112 (113)
T smart00544 51 TYREMYSVLLSRLCQANVISTKQFEKGFWRLLEDIEDLELDIPNAWRNLAEFVARLISDGIL 112 (113)
T ss_pred cHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhChhhhcccccHHHHHHHHHHHHHHcCCC
Confidence 3455666788888877777777777777777776666543 2345555555555555543
No 24
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=26.06 E-value=4.2e+02 Score=22.70 Aligned_cols=96 Identities=14% Similarity=0.241 Sum_probs=45.5
Q ss_pred HHHhcCChhHHHHHHHHhhHHHhcCCCchhHHHHHHHHHHHHHhhhhhcchhhhHHHHHHHHHhhHHHHHHHhccCCcHh
Q psy3925 53 VFIKGFNETERIKLARMTALWITNGSVPPTVLQVLINIWSTVMAQVEWNKKEELVAEQALKHLKQFTPLFGAFTDTAPRA 132 (210)
Q Consensus 53 ~~l~~~~~~~~~~llEl~~Lrms~n~~~~~v~~al~~i~~a~m~~v~~~~~~~l~~~~~~~~l~~~~~ll~~~~~~~~~~ 132 (210)
++.+.+++..|.-++=+-+-.+|+|.. ..+... ...+++..+.++-.-+.........+......-||.+ ..+
T Consensus 4 ~f~h~y~~~~D~Ei~afiaA~lAyG~~-~~I~~~----~~~ll~~~~~~P~~~v~~~~~~~~~~~~~~~~yRf~~--~~D 76 (232)
T PF09674_consen 4 QFPHRYKDKEDIEIAAFIAALLAYGNR-KQIIKK----LERLLDLMGPSPYDFVLSGDEKDDRKDLEGFFYRFQN--GED 76 (232)
T ss_pred cchhhcCCchhhHHHHHHHHHHHccCH-HHHHHH----HHHHHHHhCCCHHHHHHcCCHhhhHHHccCCCcCCCC--HHH
Confidence 456667766666566666667888843 233322 2333433321111111111111122222233334443 566
Q ss_pred HHHHHHHHHHHHHhhhhhHHHHH
Q psy3925 133 ELALMLKVQEFCYENMNLMRVFQ 155 (210)
Q Consensus 133 Q~~lL~alq~~c~~~~~~~~~f~ 155 (210)
-..++.+++....++..+...|.
T Consensus 77 ~~~~~~~l~~i~~~~gsLe~~f~ 99 (232)
T PF09674_consen 77 MYAFFIALKRIYQEYGSLEEAFA 99 (232)
T ss_pred HHHHHHHHHHHHHccCCHHHHHH
Confidence 66788888887666544444443
No 25
>PF07749 ERp29: Endoplasmic reticulum protein ERp29, C-terminal domain; InterPro: IPR011679 ERp29 is a ubiquitously expressed endoplasmic reticulum protein found in mammals []. This protein is found associated with an N-terminal thioredoxin-like domain (IPR006662 from INTERPRO), which is homologous to the domain of human protein disulphide isomerase (PDI). ERp29 may help mediate the chaperone function of PDI. The C-terminal Erp29 domain has a 5-helical bundle fold. ERp29 is thought to form part of the thyroglobulin folding complex []. ; GO: 0005783 endoplasmic reticulum; PDB: 2QC7_B 1G7D_A 2C0G_B 1OVN_A 2C0F_A 2C0E_A 2C1Y_A.
Probab=24.46 E-value=2.8e+02 Score=20.09 Aligned_cols=32 Identities=16% Similarity=0.341 Sum_probs=27.1
Q ss_pred HHhHHHHHHHHHHHHh-hHHHHHHHHHHHHHHHH
Q psy3925 21 QSLKNFEQVFIKLMRR-YKYLEKMFDEEMKKVLV 53 (210)
Q Consensus 21 ~~i~~~~~v~~kl~rr-~~~l~k~~ee~~~~~l~ 53 (210)
..-+-|++|+.|++-. ..|++++ -+.++++|.
T Consensus 41 ~~a~~Yvkvm~Ki~~~g~~fv~~E-~~RL~~lL~ 73 (95)
T PF07749_consen 41 KYAKYYVKVMEKIIEKGEEFVAKE-IARLERLLE 73 (95)
T ss_dssp HHHHHHHHHHHHHHHSGTHHHHHH-HHHHHHHHH
T ss_pred HhHHHHHHHHHHHHHccchHHHHH-HHHHHHHHh
Confidence 4567799999999999 9999999 567888886
No 26
>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=24.24 E-value=3.4e+02 Score=21.04 Aligned_cols=148 Identities=14% Similarity=0.121 Sum_probs=71.0
Q ss_pred ceecc-cccHHHhHHHHHHHHHHHHhhH-HHHHHHHHHHHHHHHH---------HhcCChhHHHHHHHHhhHHHhcCCCc
Q psy3925 12 CIFEA-QEDMQSLKNFEQVFIKLMRRYK-YLEKMFDEEMKKVLVF---------IKGFNETERIKLARMTALWITNGSVP 80 (210)
Q Consensus 12 ~v~~~-~~~~~~i~~~~~v~~kl~rr~~-~l~k~~ee~~~~~l~~---------l~~~~~~~~~~llEl~~Lrms~n~~~ 80 (210)
+||+. -.+..-+.-|+++...+..+.+ .|-..+-+....-+.. .......-....+-+-|-....|+.+
T Consensus 41 ~i~~~a~~~~~~~~~~a~l~~~l~~~~~~~f~~~ll~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~fl~eL~~~~vv~ 120 (209)
T PF02854_consen 41 LIFEKAVEEPNFSPLYARLCAALNSRFPSEFRSLLLNRCQEEFEERYSNEELEENRQSSKQRRRGNIRFLAELFNFGVVS 120 (209)
T ss_dssp HHHHHHHHSGGGHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSC
T ss_pred HHhhhhhcCchHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHhhhhhHHHhhHhhcccc
Confidence 34553 3344678889999998888888 5555554444333332 00100011222333334344467777
Q ss_pred hhHHHHHHHHHHHHHhhhhhcc---hhhhHHHHHHHHHhhHHHHHHHhccCCcHhHHHHHHHHHHHHHhh--hhhHHHHH
Q psy3925 81 PTVLQVLINIWSTVMAQVEWNK---KEELVAEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYEN--MNLMRVFQ 155 (210)
Q Consensus 81 ~~v~~al~~i~~a~m~~v~~~~---~~~l~~~~~~~~l~~~~~ll~~~~~~~~~~Q~~lL~alq~~c~~~--~~~~~~f~ 155 (210)
..+...+ +..++....... +....-+.+...++.-+..+..-..+ .+.--.++..++.++... +...+-..
T Consensus 121 ~~~i~~~---l~~ll~~~~~~~~~~~~~~~ie~~~~lL~~~G~~l~~~~~~-~~~l~~~~~~~~~~~~~~~~~~~~~r~~ 196 (209)
T PF02854_consen 121 EKIIFDI---LRELLSDGTDECQPPPDEENIECLCTLLKTCGKKLENSEES-PKALDEIFERLQKYANSKKDPNLSSRIR 196 (209)
T ss_dssp HHHHHHH---HHHHHHHTSHHCCHHTCHHHHHHHHHHHHHHHHHHHHCHHH-HHHHHHHHHHHHHHHHHCHSSSSSHHHH
T ss_pred chhHHHH---HHHHHhcccccccCCCcHhHHHHHHHHHHHHHHHHhcCCCc-hhHHHHHHHHHHHHHHhhcccCCCHHHH
Confidence 7766555 555555532100 00111123333444444444411111 333445777777777653 34434455
Q ss_pred HHHHHHhh
Q psy3925 156 KIILLFYK 163 (210)
Q Consensus 156 ~Il~~LYd 163 (210)
.+++.+.+
T Consensus 197 ~~l~~l~~ 204 (209)
T PF02854_consen 197 FMLEDLIE 204 (209)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 55554443
No 27
>PF02970 TBCA: Tubulin binding cofactor A; InterPro: IPR004226 The folding pathway of tubulins includes highly specific interactions with a series of cofactors (A, B, C, D and E) after they are released from the eukaryotic chaperonin CCT. Cofactors A and D capture and stabilise tubulin in a quasi-native conformation. Cofactor E binds to the cofactor D-tubulin complex, and interaction with cofactor C then causes the release of tubulin poypeptides in the native state. This family is the tubulin-specific chaperone A.; GO: 0051082 unfolded protein binding, 0007021 tubulin complex assembly, 0005874 microtubule; PDB: 3MXZ_A 1QSD_A 1H7C_A.
Probab=23.61 E-value=2.9e+02 Score=19.92 Aligned_cols=35 Identities=20% Similarity=0.171 Sum_probs=28.3
Q ss_pred hHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhc
Q psy3925 23 LKNFEQVFIKLMRRYKYLEKMFDEEMKKVLVFIKG 57 (210)
Q Consensus 23 i~~~~~v~~kl~rr~~~l~k~~ee~~~~~l~~l~~ 57 (210)
|+-...++.+|+..+.|.++++++.-.++-.+-..
T Consensus 2 LkIkt~~vkRL~KE~~~Y~kE~~~q~~rle~~k~~ 36 (90)
T PF02970_consen 2 LKIKTGVVKRLLKEEASYEKEVEEQEARLEKMKAE 36 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred ceehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 45667799999999999999999988777544444
No 28
>PF13972 TetR: Bacterial transcriptional repressor; PDB: 3RH2_A 3NNR_A.
Probab=23.57 E-value=3.3e+02 Score=20.68 Aligned_cols=30 Identities=20% Similarity=0.493 Sum_probs=25.6
Q ss_pred cHHHhHHHHHHHHHHHHhhHHHHHHHHHHH
Q psy3925 19 DMQSLKNFEQVFIKLMRRYKYLEKMFDEEM 48 (210)
Q Consensus 19 ~~~~i~~~~~v~~kl~rr~~~l~k~~ee~~ 48 (210)
+.+++-.|...+-.+|.+|.+|.+-+-+=+
T Consensus 20 ~le~~~~~l~~~f~~~w~YRF~~~dl~~Ll 49 (146)
T PF13972_consen 20 SLEDLWNYLDSVFELMWRYRFFYRDLPDLL 49 (146)
T ss_dssp SHHHHHHHHHHHHHHHHHTHHHHHSHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHhhhHHccHHHHH
Confidence 789999999988889999999998765543
No 29
>KOG2676|consensus
Probab=23.49 E-value=6.2e+02 Score=23.72 Aligned_cols=33 Identities=18% Similarity=0.354 Sum_probs=23.7
Q ss_pred cHhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHh
Q psy3925 130 PRAELALMLKVQEFCYENMNLMRVFQKIILLFY 162 (210)
Q Consensus 130 ~~~Q~~lL~alq~~c~~~~~~~~~f~~Il~~LY 162 (210)
..-.++++...|+...+....++.|+.-++.|.
T Consensus 110 p~~~vdlIll~~cl~~eq~~~lT~fr~~lQfL~ 142 (478)
T KOG2676|consen 110 PMNPVDLILLAQCLALEQALWLTLFRVDLQFLF 142 (478)
T ss_pred CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344556776777666666777888888888888
No 30
>PF11517 Nab2: Nuclear abundant poly(A) RNA-bind protein 2 (Nab2); InterPro: IPR021083 Nab2 is a yeast heterogeneous nuclear ribonucleoprotein that modulates poly(A) tail length and mRNA. This is the N-terminal domain of the protein which mediates interactions with the C-terminal globular domain, Myosin-like protein 1 and the mRNA export factor, Gfd1 []. The N-terminal domain of Nab2 shows a structure of a helical fold. The N-terminal domain of Nab2 is thought to mediate protein:protein interactions that facilitate the nuclear export of mRNA []. An essential hydrophobic Phe73 patch on the N-terminal domain is thought to be an important component of the interface between Nab2 and Mlp1 [].; PDB: 3LCN_B 2V75_A 2JPS_A.
Probab=22.00 E-value=52 Score=24.74 Aligned_cols=33 Identities=27% Similarity=0.388 Sum_probs=24.2
Q ss_pred HHhcCChhHHHHHHHHhhHHHhcCCCchhHHHHH
Q psy3925 54 FIKGFNETERIKLARMTALWITNGSVPPTVLQVL 87 (210)
Q Consensus 54 ~l~~~~~~~~~~llEl~~Lrms~n~~~~~v~~al 87 (210)
.+.+|. ++-+-++|.--|.||+|-++.++..-+
T Consensus 22 ~l~NFn-EDv~YVAEyIvlLisNggs~esivqEL 54 (107)
T PF11517_consen 22 TLPNFN-EDVNYVAEYIVLLISNGGSVESIVQEL 54 (107)
T ss_dssp TSTT---SSHHHHHHHHHHHHHTT--HHHHHHHH
T ss_pred cccCcc-ccHHHHHHHhheeeeCCCCHHHHHHHH
Confidence 456777 456788999999999999999998877
Done!