Query 015212
Match_columns 411
No_of_seqs 224 out of 597
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 04:10:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015212.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015212hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2297 Predicted translation 100.0 2E-129 4E-134 935.8 34.1 407 1-411 2-411 (412)
2 KOG1461 Translation initiation 99.9 9.4E-24 2E-28 220.1 16.8 163 249-411 505-669 (673)
3 smart00515 eIF5C Domain at the 99.9 6.5E-22 1.4E-26 160.4 8.6 83 325-407 1-83 (83)
4 PF02020 W2: eIF4-gamma/eIF5/e 99.8 3.6E-21 7.7E-26 156.6 8.0 76 336-411 2-80 (84)
5 KOG2767 Translation initiation 99.6 3.4E-14 7.3E-19 139.8 14.9 96 316-411 292-393 (400)
6 PF09090 MIF4G_like_2: MIF4G l 97.3 0.0047 1E-07 60.1 13.1 121 253-383 10-135 (253)
7 KOG1104 Nuclear cap-binding co 95.0 0.45 9.8E-06 52.4 14.0 174 182-385 448-623 (759)
8 KOG2140 Uncharacterized conser 94.0 0.34 7.3E-06 51.7 9.8 134 104-242 504-640 (739)
9 KOG0401 Translation initiation 86.6 0.8 1.7E-05 52.9 4.7 75 144-223 871-945 (970)
10 smart00544 MA3 Domain in DAP-5 80.3 5 0.00011 33.5 6.0 59 102-163 52-113 (113)
11 PF02847 MA3: MA3 domain; Int 78.8 6.3 0.00014 32.8 6.1 59 102-163 52-113 (113)
12 PF02847 MA3: MA3 domain; Int 69.5 63 0.0014 26.7 11.4 103 253-372 2-112 (113)
13 KOG2141 Protein involved in hi 46.7 1E+02 0.0022 34.8 8.9 97 106-207 672-768 (822)
14 PF02583 Trns_repr_metal: Meta 46.6 43 0.00093 27.2 4.8 43 257-303 18-60 (85)
15 PF11517 Nab2: Nuclear abundan 45.9 42 0.00092 28.4 4.6 70 129-205 17-90 (107)
16 PF13972 TetR: Bacterial trans 39.8 1.1E+02 0.0024 26.6 6.8 64 99-165 20-86 (146)
17 PRK11352 regulator protein Frm 38.0 1.4E+02 0.0031 24.7 6.6 29 257-285 22-50 (91)
18 PF08362 TetR_C_3: YcdC-like p 36.1 1E+02 0.0022 27.6 6.0 65 97-164 19-87 (143)
19 PF07528 DZF: DZF domain; Int 34.9 38 0.00083 33.1 3.3 49 67-116 182-233 (248)
20 PF14821 Thr_synth_N: Threonin 34.3 40 0.00086 26.9 2.8 46 26-71 10-62 (79)
21 PF10193 Telomere_reg-2: Telom 33.1 1.4E+02 0.003 25.5 6.1 66 99-171 18-90 (114)
22 PF08542 Rep_fac_C: Replicatio 33.0 1.9E+02 0.004 22.8 6.6 46 253-298 20-65 (89)
23 cd01051 Mn_catalase Manganese 32.8 2.4E+02 0.0051 25.5 7.9 102 29-137 20-139 (156)
24 PF04286 DUF445: Protein of un 32.6 5E+02 0.011 25.6 15.1 32 136-170 32-63 (367)
25 KOG2213 Apoptosis inhibitor 5/ 31.0 6.7E+02 0.014 26.6 13.0 118 175-304 87-226 (460)
26 PRK15039 transcriptional repre 30.8 1.8E+02 0.004 24.0 6.2 29 257-285 22-50 (90)
27 PHA02690 hypothetical protein; 30.0 50 0.0011 26.8 2.6 32 41-72 20-51 (90)
28 PF08337 Plexin_cytopl: Plexin 29.9 2.7E+02 0.0059 30.5 8.9 52 99-155 35-86 (539)
29 PF09733 VEFS-Box: VEFS-Box of 28.0 2.3E+02 0.0049 25.3 6.8 62 316-379 67-135 (140)
30 PF14026 DUF4242: Protein of u 27.3 36 0.00078 27.1 1.4 27 81-108 39-65 (77)
31 PF09851 SHOCT: Short C-termin 26.2 62 0.0013 21.2 2.1 20 360-379 5-24 (31)
32 PF03997 VPS28: VPS28 protein; 26.0 5.6E+02 0.012 24.1 10.8 82 104-196 26-108 (188)
33 PF03542 Tuberin: Tuberin; In 25.4 5E+02 0.011 26.8 9.6 100 253-366 181-281 (356)
34 TIGR02923 AhaC ATP synthase A1 24.6 6.9E+02 0.015 24.7 13.8 112 174-296 121-232 (343)
35 TIGR03652 FeS_repair_RIC iron- 24.3 3.4E+02 0.0074 25.6 7.7 62 229-303 12-75 (216)
36 PRK10167 hypothetical protein; 23.1 2E+02 0.0043 26.6 5.6 77 101-182 70-147 (169)
37 PF05537 DUF759: Borrelia burg 22.8 9.3E+02 0.02 25.5 13.1 170 111-299 197-390 (431)
38 cd08330 CARD_ASC_NALP1 Caspase 22.5 2.3E+02 0.005 22.7 5.3 51 358-408 16-74 (82)
39 PF02671 PAH: Paired amphipath 21.9 2.4E+02 0.0052 19.7 4.7 40 322-361 5-44 (47)
40 cd00620 Methyltransferase_Sun 21.9 3.7E+02 0.0081 22.8 6.9 85 103-195 37-125 (126)
41 TIGR02100 glgX_debranch glycog 21.8 2E+02 0.0044 32.3 6.4 95 29-123 401-575 (688)
42 COG1937 Uncharacterized protei 21.8 4.2E+02 0.0091 21.9 6.7 29 257-285 22-50 (89)
43 PF07631 PSD4: Protein of unkn 21.7 5.4E+02 0.012 22.4 7.9 25 250-274 87-111 (128)
44 PF11838 ERAP1_C: ERAP1-like C 20.4 7.8E+02 0.017 23.7 18.7 43 128-174 21-66 (324)
45 smart00544 MA3 Domain in DAP-5 20.4 4.8E+02 0.01 21.3 10.6 100 255-371 4-111 (113)
No 1
>KOG2297 consensus Predicted translation factor, contains W2 domain [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-129 Score=935.76 Aligned_cols=407 Identities=49% Similarity=0.836 Sum_probs=401.1
Q ss_pred CCCCCCCCCCCcccccccccccCCCCchhhHHHHHHHhhcCCCCHHHHHHHh--hcCCccchhhhhhhHHhhhhcCCCCC
Q 015212 1 MSSKEKPTLGGTRIKPRKRNIAAPLDPAAFSDAVVQIYLDNAGDLELIAKCI--ESSDLNFSRYGDTFFEVVFTGGRTQP 78 (411)
Q Consensus 1 ~~~~~kp~l~g~riktrkr~~~~~~dp~~f~d~~~~~~~~~~~dle~~~~~l--~g~~ldy~ry~~~lf~i~~~gg~l~p 78 (411)
|++.+||+|+|+||||||||++++|||++|||++|+||++++||||+|||+| .|++||||||||+||||+|+||+++|
T Consensus 2 ~~k~~kp~lsg~riktrKr~~~e~~dp~~f~da~vq~~~~~~gdle~vak~ldssg~~l~~~rYgd~~fdil~~gg~~~p 81 (412)
T KOG2297|consen 2 SQKTEKPVLSGQRIKTRKRDEAEKLDPTAFRDAVVQGLEDNAGDLELVAKSLDSSGNDLDYRRYGDILFDILFAGGRLQP 81 (412)
T ss_pred CccccCCCCCCccchhhhccccccCCCccHHHHHHHHHHhcCccHHHHHHHHHhccccccHHHHHHHHHHHHHHhcccCC
Confidence 6889999999999999999999999999999999999999999999999999 68899999999999999999999999
Q ss_pred CCcccCCCC-CCCceeeccCcchhhhhhHHHHHHHHHhhhhhhHHHhHHHHHHHHHHhhccChhhhHHHHHHHHHHHhhh
Q 015212 79 GTTKPDEGE-RHSYSIIDCEPQREAILPSVIYIQKILRRRPFLIKNLENVTRRFMQSLELFEENERKKLAIFTALAFSQK 157 (411)
Q Consensus 79 gg~~~~~~~-~~~~~i~~~~~~~~~~~~~~~~~~kl~rr~kyl~k~~e~~~~~~l~~l~~f~~~~r~klA~~~a~~~~~~ 157 (411)
||+.+|||+ +++||||+|++++|+|++|+|||||||||||||+|+|||+|+|+|+||++|++++|+|||++||++++
T Consensus 82 g~~~sddge~~t~~cvfda~e~~E~i~~~~qvf~KliRRykyLeK~fE~e~~k~Llflk~F~e~Er~KLA~~Tal~l~-- 159 (412)
T KOG2297|consen 82 GGVKSDDGERHTSYCVFDAEEKREAIRNSVQVFQKLIRRYKYLEKNFENEMRKFLLFLKLFEENERKKLAMLTALLLS-- 159 (412)
T ss_pred CCccccccCccCceeEeecCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHh--
Confidence 999999997 56799999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCccchhhhhhccccCCCchHHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhcCCCCCCChhhHHHHHHhcCC
Q 015212 158 LSGLPPETVFQPLLKDNLVGKGLVLSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDFFPSSKRSAEGFSEHFTKEGL 237 (411)
Q Consensus 158 ~~g~~~~~~l~~l~~~~Lv~~G~a~~fl~~i~~~~~~~~~~~~l~~~lrksgl~~~l~~f~P~~kr~~e~f~~~f~~~~L 237 (411)
+|++|+++|++|++||||++|++++|++.+|+.|+.|+|++.|+++||+++|++||++|||||+||.|+|.+||.++||
T Consensus 160 -nGt~~~tvl~~L~~d~LVkeGi~l~F~~~lFk~~~~Ek~i~~lis~Lrkg~md~rLmeffPpnkrs~E~Fak~Ft~agL 238 (412)
T KOG2297|consen 160 -NGTLPATVLQSLLNDNLVKEGIALSFAVKLFKEWLVEKDINDLISSLRKGKMDDRLMEFFPPNKRSVEHFAKYFTDAGL 238 (412)
T ss_pred -CCCCCHHHHHHHHHhhHHHHhHHHHHHHHHHHHHHhhccHHHHHHHHHhcChHhHHHHhcCCcchhHHHHHHHHhHhhH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccchhhhhHHhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHHhhhhccchhhhHHHH
Q 015212 238 IPLVEYNEKKIFEVKLKDMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILWDILMDAVQWSGKNQQQNANAA 317 (411)
Q Consensus 238 ~~l~~~~~~~~~~~~~~El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~~alm~~v~~s~k~~~~~~~~~ 317 (411)
.++++|++.|+++..++|+++.|++.+.++.|.++|+..|+..+..+|+|+++||++||+++|+.++||++ ++++++++
T Consensus 239 ~elvey~~~q~~~~a~kElq~~L~~q~s~e~p~~evi~~VKee~k~~nlPe~eVi~ivWs~iMsaveWnKk-eelva~qa 317 (412)
T KOG2297|consen 239 KELVEYHRNQQSEGARKELQKELQEQVSEEDPVKEVILYVKEEMKRNNLPETEVIGIVWSGIMSAVEWNKK-EELVAEQA 317 (412)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcCCCCceEEeeeHhhhhHHHhhchH-HHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999955 88999999
Q ss_pred HHHHHHHHHHHHHHhcChHHHHHHHHHHHHHhhcchHHHhHHHHHHHHhhhhcccchhhHHHhhhcCCCcchHHHHHHhH
Q 015212 318 LRQVKTWAQLLNTFCTNAKLELELMYKVQMQCYEDAKLMKLFPEIVRSLYDQDVLAEDTILYWFRKGTNPKGRQTFVKAL 397 (411)
Q Consensus 318 ~~~lk~~~pLL~~f~~~~~~Ql~lL~alQ~~c~e~~~~~k~f~~IL~~LYd~DVlsEeaIlkW~~~~~~~~Gk~~~lk~~ 397 (411)
++++++|+|||..||+++++++.+|+.+|.|||+|.++|+.|+.|+..||..||++||+|++||.+++.++||++|++++
T Consensus 318 lrhlK~yaPLL~af~s~g~sEL~Ll~KvQe~CYen~~fMKaFqkiV~lfYk~dVLsEe~IL~Wyk~gh~~KGk~~Fleqm 397 (412)
T KOG2297|consen 318 LRHLKQYAPLLAAFCSQGQSELELLLKVQEYCYENIHFMKAFQKIVVLFYKADVLSEETILKWYKEGHVAKGKSVFLEQM 397 (412)
T ss_pred HHHHHhhhHHHHHHhcCChHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhccccccHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhcccCC
Q 015212 398 EPFVKWLEEAEEEE 411 (411)
Q Consensus 398 ~~FV~WLeEAEEEs 411 (411)
+|||+||++|||||
T Consensus 398 kkFVeWL~~AEEEs 411 (412)
T KOG2297|consen 398 KKFVEWLQNAEEES 411 (412)
T ss_pred HHHHHHHHhhhhcc
Confidence 99999999999996
No 2
>KOG1461 consensus Translation initiation factor 2B, epsilon subunit (eIF-2Bepsilon/GCD6) [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=9.4e-24 Score=220.08 Aligned_cols=163 Identities=23% Similarity=0.420 Sum_probs=144.1
Q ss_pred HHhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHHhhhhccch-hhhHHHHHHHHHHHHHH
Q 015212 249 FEVKLKDMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILWDILMDAVQWSGKNQ-QQNANAALRQVKTWAQL 327 (411)
Q Consensus 249 ~~~~~~El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~~alm~~v~~s~k~~-~~~~~~~~~~lk~~~pL 327 (411)
...|.+|+..+|+|++++++.++++++|||++++++|++.++|+.+++.|+|+.+.....+. ..+..++.+.+++|+|+
T Consensus 505 ~~~F~~Ev~~s~~ra~Een~~~D~~vlEINslRla~N~s~~ev~~av~~all~~~~~~~~~~~~~~~~~~~~~~~~w~~l 584 (673)
T KOG1461|consen 505 TKDFEKEVLGSLQRAFEENSDMDNLVLEINSLRLAYNVSLKEVAGAVFMALLKLILHQDHSSMNEVKRAALKVFTQWGPL 584 (673)
T ss_pred hHHHHHHHHHHHHHHHHhccchHHHHHHHhhhHHhhcCCHHHHHHHHHHHHHHHHhcCCCccchhHHHHHHHHHHHhhHH
Confidence 45789999999999999999999999999999999999999999999999999986433221 12566888999999999
Q ss_pred HHHHhcChHHHHHHHHHHHHHhhcchHHHhHHHHHHHHhhhhcccchhhHHHhhhcCCCcch-HHHHHHhHHHHHHHhhh
Q 015212 328 LNTFCTNAKLELELMYKVQMQCYEDAKLMKLFPEIVRSLYDQDVLAEDTILYWFRKGTNPKG-RQTFVKALEPFVKWLEE 406 (411)
Q Consensus 328 L~~f~~~~~~Ql~lL~alQ~~c~e~~~~~k~f~~IL~~LYd~DVlsEeaIlkW~~~~~~~~G-k~~~lk~~~~FV~WLeE 406 (411)
+.+|+.+.+.|+++|.+||.+|.++..+...+.++++.||+.||++||+|++|+...+...+ ..+.++++++||+||+|
T Consensus 585 ~~~y~ks~deqid~l~~led~~~e~~~~~~~~~~~v~~lY~~dil~EdaI~~W~~~~~~~~~~~~~~~~~~k~fv~WL~e 664 (673)
T KOG1461|consen 585 LGNYIKSEDEQIDLLLALEDKCVESEELGPKAAKLVHYLYDYDILQEDAILSWSSQKAGDDEEDAVYNQQLKKFVDWLKE 664 (673)
T ss_pred hhhhhhhHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHhHhhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999976666788999999999999999999999998544333 36788999999999999
Q ss_pred cccCC
Q 015212 407 AEEEE 411 (411)
Q Consensus 407 AEEEs 411 (411)
|+|||
T Consensus 665 aseE~ 669 (673)
T KOG1461|consen 665 ASEEE 669 (673)
T ss_pred ccccc
Confidence 99885
No 3
>smart00515 eIF5C Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5.
Probab=99.86 E-value=6.5e-22 Score=160.42 Aligned_cols=83 Identities=39% Similarity=0.814 Sum_probs=77.7
Q ss_pred HHHHHHHhcChHHHHHHHHHHHHHhhcchHHHhHHHHHHHHhhhhcccchhhHHHhhhcCCCcchHHHHHHhHHHHHHHh
Q 015212 325 AQLLNTFCTNAKLELELMYKVQMQCYEDAKLMKLFPEIVRSLYDQDVLAEDTILYWFRKGTNPKGRQTFVKALEPFVKWL 404 (411)
Q Consensus 325 ~pLL~~f~~~~~~Ql~lL~alQ~~c~e~~~~~k~f~~IL~~LYd~DVlsEeaIlkW~~~~~~~~Gk~~~lk~~~~FV~WL 404 (411)
+|+|.+|+++.+.|+++|+++|.+|+++....+.|+.|++.|||+|||+||+|++||+++++..|+++++++++|||+||
T Consensus 1 ~~ll~~~~~~~~~q~~~L~ale~~~~~~~~~~~~~~~il~~LYd~dileEe~il~W~~~~~~~~~~~~~~~~~~~fv~WL 80 (83)
T smart00515 1 GPLLKFLAKDEEEQIDLLYAIEEFCVELEKLIKLLPKILKSLYDADILEEEAILKWYEKAVSAEGKKKVRKNAKPFVTWL 80 (83)
T ss_pred ChHHHHHHCChHHHHHHHHHHHHHHHHcchHHHHHHHHHHHHhhhccccHHHHHHHHHcCCChHHHHHHHHHHhHHHHHH
Confidence 48999999999999999999999999866688999999999999999999999999999877678899999999999999
Q ss_pred hhc
Q 015212 405 EEA 407 (411)
Q Consensus 405 eEA 407 (411)
+||
T Consensus 81 ~eA 83 (83)
T smart00515 81 QEA 83 (83)
T ss_pred HcC
Confidence 987
No 4
>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=99.84 E-value=3.6e-21 Score=156.60 Aligned_cols=76 Identities=41% Similarity=0.846 Sum_probs=65.8
Q ss_pred HHHHHHHHHHHHHhhcchHHHhHHHHHHHHhhhhcccchhhHHHhhhcCC---CcchHHHHHHhHHHHHHHhhhcccCC
Q 015212 336 KLELELMYKVQMQCYEDAKLMKLFPEIVRSLYDQDVLAEDTILYWFRKGT---NPKGRQTFVKALEPFVKWLEEAEEEE 411 (411)
Q Consensus 336 ~~Ql~lL~alQ~~c~e~~~~~k~f~~IL~~LYd~DVlsEeaIlkW~~~~~---~~~Gk~~~lk~~~~FV~WLeEAEEEs 411 (411)
+.|+++|.|+|.||.+++++++.|+.||+.|||.|||+|++|++||++.. +..|+.+++++++|||+||++|||||
T Consensus 2 ~~Q~~~L~ale~~~~~~~~~~~~~~~il~~LYd~Dil~Eeail~W~~~~~~~~~~~~~~~~r~~~~~fi~WL~eaeeE~ 80 (84)
T PF02020_consen 2 DDQVDLLNALEEFCAENPNLMPLFPKILQQLYDEDILEEEAILEWYEDSKPAVDGEGRAKVRKQAQPFIEWLEEAEEES 80 (84)
T ss_dssp HHHHHHHHHHHHHHHHTCGHGGHHHHHHHHHHHTTSS-HHHHHHHHHC-SSSSCHHHHHHHHHHHHHHHHHHHHCC---
T ss_pred HHHHHHHHHHHHHHHhCccHHHHHHHHHHHHhhhhhccHHHHHHHHHcCCccccchhHHHHHHHHHHHHHHHhccCccC
Confidence 57999999999999999999999999999999999999999999999822 23467889999999999999999985
No 5
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=99.57 E-value=3.4e-14 Score=139.85 Aligned_cols=96 Identities=28% Similarity=0.544 Sum_probs=85.4
Q ss_pred HHHHHHHHHHHHHHHHhcC-hHHHHHHHHHHHHHhhc-chHHHhHHHHHHHHhhhhcccchhhHHHhhhcCCCcc----h
Q 015212 316 AALRQVKTWAQLLNTFCTN-AKLELELMYKVQMQCYE-DAKLMKLFPEIVRSLYDQDVLAEDTILYWFRKGTNPK----G 389 (411)
Q Consensus 316 ~~~~~lk~~~pLL~~f~~~-~~~Ql~lL~alQ~~c~e-~~~~~k~f~~IL~~LYd~DVlsEeaIlkW~~~~~~~~----G 389 (411)
.+.+.|.++.++|.+||.+ ...|..+|..|+.+|.. +..+++..+.||+.|||+||++|+.|++|+++++..+ -
T Consensus 292 ~ivkei~k~~~~l~k~~~~~~k~qr~LLggiE~~~~~~~~el~~kva~ilk~lYd~DI~~e~vi~~w~~K~skk~vsk~~ 371 (400)
T KOG2767|consen 292 KIVKEILKHRALLLKFCTNNEKAQRYLLGGIERFVEKHEAELISKVAGILKELYDEDILEEEVIIKWGEKPSKKYVSKEK 371 (400)
T ss_pred HHHHHHHHHHHHHHHHHhccHHHHHHHHhHHHHHHHhhHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHhcccccccchhh
Confidence 5567899999999999987 58999999999999986 5777899999999999999999999999999988743 2
Q ss_pred HHHHHHhHHHHHHHhhhcccCC
Q 015212 390 RQTFVKALEPFVKWLEEAEEEE 411 (411)
Q Consensus 390 k~~~lk~~~~FV~WLeEAEEEs 411 (411)
.+.+++.++|||+||++||+|+
T Consensus 372 sk~i~e~a~Pfi~WL~~AESe~ 393 (400)
T KOG2767|consen 372 SKKIRENAKPFIEWLKNAESED 393 (400)
T ss_pred hhhhHhhhhHHHHHHHhccccc
Confidence 3678999999999999998764
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=97.26 E-value=0.0047 Score=60.14 Aligned_cols=121 Identities=12% Similarity=0.203 Sum_probs=86.6
Q ss_pred HHHHHHHHHHHHHhcCcHHHHHHHHHHHhhhcCCCh----HHHHHHHHHHHHHHhhhhccchhhhHHHHHHHHHHHHHHH
Q 015212 253 LKDMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPD----IEVVRILWDILMDAVQWSGKNQQQNANAALRQVKTWAQLL 328 (411)
Q Consensus 253 ~~El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~----~evi~~l~~alm~~v~~s~k~~~~~~~~~~~~lk~~~pLL 328 (411)
..++.+.|.+.+....+++++..+++......+-.. .-.+.++++|++.... + +-.-....|.+|.+.|
T Consensus 10 ~~~~a~~l~~~ir~k~~~eei~~~l~~i~~~~~~~~~~~~~~~i~v~~q~ll~~GS---k----S~SH~~~~lery~~~L 82 (253)
T PF09090_consen 10 FHALAQKLLDLIRKKAPPEEISELLEEIEEPAEEHGSDFDKFVIDVFVQCLLHIGS---K----SFSHVLSALERYKEVL 82 (253)
T ss_dssp THHHHHHHHHHHHTT--HHHHHHHHTTS------------HHHHHHHHHHHHHHTT---T----SHHHHHHHHHHTHHHH
T ss_pred cHHHHHHHHHHHHcCCCHHHHHHHHHhccccccccccchhhHHHHHHHHHHHHhcC---c----hHHHHHHHHHHHHHHH
Confidence 346778899999999999999999888766655332 2456666666666532 2 1123456899999999
Q ss_pred HHH-hcChHHHHHHHHHHHHHhhcchHHHhHHHHHHHHhhhhcccchhhHHHhhhc
Q 015212 329 NTF-CTNAKLELELMYKVQMQCYEDAKLMKLFPEIVRSLYDQDVLAEDTILYWFRK 383 (411)
Q Consensus 329 ~~f-~~~~~~Ql~lL~alQ~~c~e~~~~~k~f~~IL~~LYd~DVlsEeaIlkW~~~ 383 (411)
..+ +.+...|..+|.++-.|...+|... .-|+..|=+.+||+-.+|+.|-=+
T Consensus 83 k~l~~~~~~~q~~il~~v~~~W~~~~q~~---~li~dkll~~~ii~~~~Vv~w~f~ 135 (253)
T PF09090_consen 83 KELEAESEEAQFWILDAVFRFWKNNPQMG---FLIIDKLLNYGIISPSAVVNWVFS 135 (253)
T ss_dssp HHH-TSSHHHHHHHHHHHHHHHTT-HHHH---HHHHHHHHHTTSS-HHHHHHHHTS
T ss_pred HHhccCChHHHHHHHHHHHHHHhcCCcee---hHHHHHHHhcCCCCHHHHHHHHcC
Confidence 999 8888999999999999988888763 667899999999999999999844
No 7
>KOG1104 consensus Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]
Probab=95.02 E-value=0.45 Score=52.44 Aligned_cols=174 Identities=9% Similarity=0.131 Sum_probs=114.4
Q ss_pred HHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhcCCCCCCChhhHHHHHHhcCCcccccchhhhhHHhHHHHHHHHHH
Q 015212 182 LSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDFFPSSKRSAEGFSEHFTKEGLIPLVEYNEKKIFEVKLKDMKSTLT 261 (411)
Q Consensus 182 ~~fl~~i~~~~~~~~~~~~l~~~lrksgl~~~l~~f~P~~kr~~e~f~~~f~~~~L~~l~~~~~~~~~~~~~~El~~~L~ 261 (411)
-.|+-++++.=+.......+.+++- . -+.+++|+.. .+ +|. +..++-..+. .+.+..+|.
T Consensus 448 ~~FvreviqkelrLsy~~rI~dslP----~-~~~~l~P~~~-~p-ny~-----y~~Ee~~~~~--------~~~~~~~l~ 507 (759)
T KOG1104|consen 448 PNFVREVIQKELRLSYYQRIKDSLP----T-LLAKLLPPPP-LP-NYK-----YTDEEDPVLP--------QSLVAVQLI 507 (759)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhhh----H-HHHHhCCCCC-CC-cee-----eecccCcccc--------chHHHHHHH
Confidence 3577777777666666666666665 1 2566777653 22 221 1111111111 112567888
Q ss_pred HHHHhcCcHHHHHHHHHHHhhhcCCChH-HHHHHHHHHHHHHhhhhccchhhhHHHHHHHHHHHHHHHHHHhcChH-HHH
Q 015212 262 TQIAEETEMSEVIESVKQRVKDAKLPDI-EVVRILWDILMDAVQWSGKNQQQNANAALRQVKTWAQLLNTFCTNAK-LEL 339 (411)
Q Consensus 262 ~~l~e~~~~~~ii~eIk~~~~~~n~s~~-evi~~l~~alm~~v~~s~k~~~~~~~~~~~~lk~~~pLL~~f~~~~~-~Ql 339 (411)
.++.+..++++++.||++.-.+...+.. =.+.++++++++... |..+ -+...+.+|..+|.++|.+.. .|.
T Consensus 508 ~~~~~k~~~e~~~~iLk~~~~~~~~~~n~~~i~lfvq~~l~lGS---KSfS----H~f~~lek~~~vfk~l~~~~e~~q~ 580 (759)
T KOG1104|consen 508 VAFREKATAEEIVNILKSEDESEIGSFNRLKIILFVQTLLDLGS---KSFS----HAFSALEKYHTVFKKLCEDSETKQI 580 (759)
T ss_pred HHHhccCCHHHHHHHHhcCccccccCCcceehhhHHHHHHHhcc---chhh----hHHHHHHHHHHHHHHHhcCCchhHH
Confidence 9999999999999999933222222222 246667788877642 2122 235678999999999998875 499
Q ss_pred HHHHHHHHHhhcchHHHhHHHHHHHHhhhhcccchhhHHHhhhcCC
Q 015212 340 ELMYKVQMQCYEDAKLMKLFPEIVRSLYDQDVLAEDTILYWFRKGT 385 (411)
Q Consensus 340 ~lL~alQ~~c~e~~~~~k~f~~IL~~LYd~DVlsEeaIlkW~~~~~ 385 (411)
.+|.++=.+...||..+ ..+.+.|-..-||+=.||..|-=+..
T Consensus 581 ~vl~~vft~Wk~n~Qm~---~v~~Dkml~~~ii~~~aVv~WiF~~~ 623 (759)
T KOG1104|consen 581 IVLEAVFTFWKANPQMG---FVLTDKMLKYQIIDCSAVVRWIFSEE 623 (759)
T ss_pred HHHHHHHHHHhcCchhh---HHHHHHHhccccccHHHHHHHhcCHH
Confidence 99999988888777643 44568888899999999999985443
No 8
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=93.98 E-value=0.34 Score=51.69 Aligned_cols=134 Identities=22% Similarity=0.274 Sum_probs=104.9
Q ss_pred hhHHHHHHHHHhhhhhhHHHhHHHHHHHHHHhhccChhhhHHHHHHHHHHHhhhcCCCCCccchhh--hhhccccCCCch
Q 015212 104 LPSVIYIQKILRRRPFLIKNLENVTRRFMQSLELFEENERKKLAIFTALAFSQKLSGLPPETVFQP--LLKDNLVGKGLV 181 (411)
Q Consensus 104 ~~~~~~~~kl~rr~kyl~k~~e~~~~~~l~~l~~f~~~~r~klA~~~a~~~~~~~~g~~~~~~l~~--l~~~~Lv~~G~a 181 (411)
|=|--+-.++++=++-.+-.||+..+.--..|+.++-+.-.-||.|.|.+++ ..-+|..||.- |.-+.-...|.-
T Consensus 504 kFYglL~eRfc~l~r~~q~~fe~~f~q~YstIhr~EtnkLRnlakffahLls---td~lpw~vl~~ikLTEEdTtsssRI 580 (739)
T KOG2140|consen 504 KFYGLLGERFCMLHREWQEAFEKCFKQQYSTIHRYETNKLRNLAKFFAHLLS---TDALPWDVLACIKLTEEDTTSSSRI 580 (739)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhc---ccccchHHHHHhhcccccCCcccee
Confidence 3344455666666677777888876666666999998888999999999999 99999999975 344444455554
Q ss_pred HHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhcCCCCCCChhhHH-HHHHhcCCccccc
Q 015212 182 LSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDFFPSSKRSAEGFS-EHFTKEGLIPLVE 242 (411)
Q Consensus 182 ~~fl~~i~~~~~~~~~~~~l~~~lrksgl~~~l~~f~P~~kr~~e~f~-~~f~~~~L~~l~~ 242 (411)
|+--+|+.++..+|++.|..-+....|...+..+||-.....-.|. .+|+.-||+-+.+
T Consensus 581 --fiKilFqELve~lGl~~L~~RL~dptl~~~l~glFP~dnp~n~RfsINfFTsIGLGgLTe 640 (739)
T KOG2140|consen 581 --FIKILFQELVEALGLDKLNERLNDPTLQPKLEGLFPRDNPRNTRFSINFFTSIGLGGLTE 640 (739)
T ss_pred --hHHHHHHHHHHHhChHHHHHHhcCcchhhhhhccCcCCCcccceeeeehhhhhccccchH
Confidence 8899999999999999999999999998889999997643333443 5889999987754
No 9
>KOG0401 consensus Translation initiation factor 4F, ribosome/mRNA-bridging subunit (eIF-4G) [Translation, ribosomal structure and biogenesis]
Probab=86.58 E-value=0.8 Score=52.89 Aligned_cols=75 Identities=9% Similarity=0.062 Sum_probs=71.4
Q ss_pred HHHHHHHHHHHhhhcCCCCCccchhhhhhccccCCCchHHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhcCCCCCC
Q 015212 144 KKLAIFTALAFSQKLSGLPPETVFQPLLKDNLVGKGLVLSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDFFPSSKR 223 (411)
Q Consensus 144 ~klA~~~a~~~~~~~~g~~~~~~l~~l~~~~Lv~~G~a~~fl~~i~~~~~~~~~~~~l~~~lrksgl~~~l~~f~P~~kr 223 (411)
..++.+.+.++. .|.+..+.+.+.+..+.-+.|.+..++-.++..++++.+..++..+|+++++. |.+|+|++..
T Consensus 871 ~~~~e~~gp~~~---~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s--~~~~~~~~~~ 945 (970)
T KOG0401|consen 871 NYIKEFLGPLIH---QKILDESELVREILKNMRPNGRRSNVLFSVLEIVEKELGRADLGDIQRESFLS--TKTLLQENSQ 945 (970)
T ss_pred hHHHHhhhhHhh---hccccHHHHHHHHhhcCCccccccchHHHHHHHHHHhhhHHHHHHHHHHhccc--chhcccccch
Confidence 678899999999 89999999999999999999999999999999999999999999999999999 9999999863
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=80.28 E-value=5 Score=33.55 Aligned_cols=59 Identities=22% Similarity=0.278 Sum_probs=52.2
Q ss_pred hhhhHHHHHHHHHhhhhhhHHHhHHHHHHHHHHhhccCh---hhhHHHHHHHHHHHhhhcCCCCC
Q 015212 102 AILPSVIYIQKILRRRPFLIKNLENVTRRFMQSLELFEE---NERKKLAIFTALAFSQKLSGLPP 163 (411)
Q Consensus 102 ~~~~~~~~~~kl~rr~kyl~k~~e~~~~~~l~~l~~f~~---~~r~klA~~~a~~~~~~~~g~~~ 163 (411)
.-..|..++..|..+...-...|+.-+.+++..++-.+- .....+|.++|.+++ +|.+|
T Consensus 52 ~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~l~dl~~D~P~a~~~la~~~a~~v~---~~~l~ 113 (113)
T smart00544 52 YREMYSVLLSRLCQANVISTKQFEKGFWRLLEDIEDLELDIPNAWRNLAEFVARLIS---DGILP 113 (113)
T ss_pred HHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhChhhhcccccHHHHHHHHHHHHHH---cCCCC
Confidence 456788899999989999999999999999999998855 688999999999999 99886
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=78.76 E-value=6.3 Score=32.79 Aligned_cols=59 Identities=19% Similarity=0.210 Sum_probs=49.8
Q ss_pred hhhhHHHHHHHHHhhhhhhHHHhHHHHHHHHHHhhccChh---hhHHHHHHHHHHHhhhcCCCCC
Q 015212 102 AILPSVIYIQKILRRRPFLIKNLENVTRRFMQSLELFEEN---ERKKLAIFTALAFSQKLSGLPP 163 (411)
Q Consensus 102 ~~~~~~~~~~kl~rr~kyl~k~~e~~~~~~l~~l~~f~~~---~r~klA~~~a~~~~~~~~g~~~ 163 (411)
.-..|..++..|+.+...-...++.-+.+++..+.-.... .-..+|.++|.+++ +|.+|
T Consensus 52 ~r~~~~~Ll~~L~~~~~~~~~~~~~gf~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~---~~~lp 113 (113)
T PF02847_consen 52 YREYYSKLLSHLCKRKLISKEQFQEGFEDLLESLEDLELDIPKAPEYLAKFLARLIA---DGILP 113 (113)
T ss_dssp HHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHH---TTSS-
T ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhHhhhccccchHHHHHHHHHHHHHHH---cCCcC
Confidence 4567888999999999988888999888999998877555 78999999999999 99887
No 12
>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=69.50 E-value=63 Score=26.66 Aligned_cols=103 Identities=16% Similarity=0.229 Sum_probs=62.8
Q ss_pred HHHHHHHHHHHHHhcCcHHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHHhhhhccchhhhHHHHHHHHHHHHHHHHHHh
Q 015212 253 LKDMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILWDILMDAVQWSGKNQQQNANAALRQVKTWAQLLNTFC 332 (411)
Q Consensus 253 ~~El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~~alm~~v~~s~k~~~~~~~~~~~~lk~~~pLL~~f~ 332 (411)
++.+...|.+.+.. .+.++++..|+++..+ --.++|+..++...++.- + ..-+.+..++..++
T Consensus 2 rk~i~~~l~ey~~~-~d~~ea~~~l~el~~~--~~~~~vv~~~l~~~le~~----~----------~~r~~~~~Ll~~L~ 64 (113)
T PF02847_consen 2 RKKIFSILMEYFSS-GDVDEAVECLKELKLP--SQHHEVVKVILECALEEK----K----------SYREYYSKLLSHLC 64 (113)
T ss_dssp HHHHHHHHHHHHHH-T-HHHHHHHHHHTT-G--GGHHHHHHHHHHHHHTSS----H----------HHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHhcC-CCHHHHHHHHHHhCCC--ccHHHHHHHHHHHHhhcc----H----------HHHHHHHHHHHHHH
Confidence 34555566666644 4788888889887555 345677777777776651 0 11245566677777
Q ss_pred cCh-HHHHHHHHHHHH-------HhhcchHHHhHHHHHHHHhhhhccc
Q 015212 333 TNA-KLELELMYKVQM-------QCYEDAKLMKLFPEIVRSLYDQDVL 372 (411)
Q Consensus 333 ~~~-~~Ql~lL~alQ~-------~c~e~~~~~k~f~~IL~~LYd~DVl 372 (411)
..+ -.+-++..+++. +..+-|+....+..++-.+...|+|
T Consensus 65 ~~~~~~~~~~~~gf~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~~~~l 112 (113)
T PF02847_consen 65 KRKLISKEQFQEGFEDLLESLEDLELDIPKAPEYLAKFLARLIADGIL 112 (113)
T ss_dssp HTTSS-HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTSS
T ss_pred hcCCCCHHHHHHHHHHHHhHhhhccccchHHHHHHHHHHHHHHHcCCc
Confidence 543 333344444444 3344577777888888888888876
No 13
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=46.70 E-value=1e+02 Score=34.76 Aligned_cols=97 Identities=15% Similarity=0.142 Sum_probs=62.9
Q ss_pred HHHHHHHHHhhhhhhHHHhHHHHHHHHHHhhccChhhhHHHHHHHHHHHhhhcCCCCCccchhhhhhccccCCCchHHHH
Q 015212 106 SVIYIQKILRRRPFLIKNLENVTRRFMQSLELFEENERKKLAIFTALAFSQKLSGLPPETVFQPLLKDNLVGKGLVLSFI 185 (411)
Q Consensus 106 ~~~~~~kl~rr~kyl~k~~e~~~~~~l~~l~~f~~~~r~klA~~~a~~~~~~~~g~~~~~~l~~l~~~~Lv~~G~a~~fl 185 (411)
|.-+-+|+--+++-+++.|.=.+=-.+.=++.-+..++.-||.++|-+|+ +-..|++||.+.==-.|-+. ..-|+
T Consensus 672 Ya~lA~KfCe~~~~~~~tfQF~~WD~f~ele~ls~~ri~nLa~l~a~Li~---~~~lsLtVLK~Vdfm~l~~~--~~~fl 746 (822)
T KOG2141|consen 672 YALLALKFCEFNKNLKKTFQFALWDRFKELEQLSLFRISNLAKLLASLIS---NAVLSLTVLKHVDFMELNAR--RTTFL 746 (822)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHhhhcchhhHhHHHHHHHHHHH---hcccceeeeeeccHhhcChH--HHHHH
Confidence 45566667777777777776555444444556677888999999999999 99999999986211122222 22356
Q ss_pred HHHHHHHHHhCChhHHHHHHHh
Q 015212 186 TDFFKEYLVDNSLDDLIAILKR 207 (411)
Q Consensus 186 ~~i~~~~~~~~~~~~l~~~lrk 207 (411)
..+|-.++-+...+.+..++.+
T Consensus 747 ~~~l~~l~l~~~~~~v~~~ftr 768 (822)
T KOG2141|consen 747 KKLLFGLILEPEEKDVFQLFTR 768 (822)
T ss_pred HHHHHHHHhcchHHHHHHHHHH
Confidence 6566666666555555555443
No 14
>PF02583 Trns_repr_metal: Metal-sensitive transcriptional repressor; InterPro: IPR003735 This entry describes proteins of unknown function.; PDB: 2HH7_A 3AAI_A 4ADZ_B.
Probab=46.63 E-value=43 Score=27.15 Aligned_cols=43 Identities=7% Similarity=0.221 Sum_probs=31.6
Q ss_pred HHHHHHHHHhcCcHHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHHh
Q 015212 257 KSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILWDILMDAV 303 (411)
Q Consensus 257 ~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~~alm~~v 303 (411)
...+.++++++.++.+|+..|.+.+.+-+ .+...++..-+..+
T Consensus 18 v~gI~~Miee~~~C~dIl~Qi~Av~~Al~----~~~~~vl~~hl~~c 60 (85)
T PF02583_consen 18 VRGIERMIEEDRDCEDILQQIAAVRSALD----KVGKLVLEDHLEHC 60 (85)
T ss_dssp HHHHHHHHHTTE-HHHHHHHHHHHHHHHH----HHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHH
Confidence 46678899999999999999999888754 55566665555543
No 15
>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=45.93 E-value=42 Score=28.37 Aligned_cols=70 Identities=21% Similarity=0.248 Sum_probs=44.0
Q ss_pred HHHHHHhhccChhhhHHHHHHHHHHHhhhcCCCCCccchhhhhhccccCCCchHHHHHH----HHHHHHHhCChhHHHHH
Q 015212 129 RRFMQSLELFEENERKKLAIFTALAFSQKLSGLPPETVFQPLLKDNLVGKGLVLSFITD----FFKEYLVDNSLDDLIAI 204 (411)
Q Consensus 129 ~~~l~~l~~f~~~~r~klA~~~a~~~~~~~~g~~~~~~l~~l~~~~Lv~~G~a~~fl~~----i~~~~~~~~~~~~l~~~ 204 (411)
-.=|..+.+|++ +-+..|.++-++|+ ||.-+.++++.|. .|- |++.-..++. .|..+-..++-+.+..+
T Consensus 17 aEkL~~l~NFnE-Dv~YVAEyIvlLis---Nggs~esivqELs--sLF-D~vs~~~l~~VVQtaF~ale~Lq~Ge~~e~i 89 (107)
T PF11517_consen 17 AEKLKTLPNFNE-DVNYVAEYIVLLIS---NGGSVESIVQELS--SLF-DSVSTEALTDVVQTAFFALEALQQGETVENI 89 (107)
T ss_dssp HHHHTTSTT--S-SHHHHHHHHHHHHH---TT--HHHHHHHHH--HH--TTS-HHHHHHHHHHHHHHHHHHHTT--HHHH
T ss_pred HHHHccccCccc-cHHHHHHHhheeee---CCCCHHHHHHHHH--HHH-hccCHHHHHHHHHHHHHHHHHHhCCCcHHHH
Confidence 344678888876 46899999999999 9999999998765 233 7777777766 45555555544444444
Q ss_pred H
Q 015212 205 L 205 (411)
Q Consensus 205 l 205 (411)
.
T Consensus 90 v 90 (107)
T PF11517_consen 90 V 90 (107)
T ss_dssp H
T ss_pred H
Confidence 3
No 16
>PF13972 TetR: Bacterial transcriptional repressor; PDB: 3RH2_A 3NNR_A.
Probab=39.77 E-value=1.1e+02 Score=26.64 Aligned_cols=64 Identities=11% Similarity=0.221 Sum_probs=43.8
Q ss_pred chhhhhhHHHHHHHHHhhhhhhHHHhHHHH---HHHHHHhhccChhhhHHHHHHHHHHHhhhcCCCCCcc
Q 015212 99 QREAILPSVIYIQKILRRRPFLIKNLENVT---RRFMQSLELFEENERKKLAIFTALAFSQKLSGLPPET 165 (411)
Q Consensus 99 ~~~~~~~~~~~~~kl~rr~kyl~k~~e~~~---~~~l~~l~~f~~~~r~klA~~~a~~~~~~~~g~~~~~ 165 (411)
+.|.+-.|....-.+|.||+|+-+.+-+-+ +.+-.-...+...-+..+..+...++. +|.+.++
T Consensus 20 ~le~~~~~l~~~f~~~w~YRF~~~dl~~Ll~~~p~L~~~~~~~~~~~~~~~~~l~~~l~~---~g~l~~~ 86 (146)
T PF13972_consen 20 SLEDLWNYLDSVFELMWRYRFFYRDLPDLLRRDPELKKRYRQLQQRRREQLRQLLQSLIE---AGILRID 86 (146)
T ss_dssp SHHHHHHHHHHHHHHHHHTHHHHHSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHH---TTSB---
T ss_pred CHHHHHHHHHHHHHHHHHhhhHHccHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHHH---CCCCCCC
Confidence 788999999999999999999999988855 334333333444445555556666666 7777533
No 17
>PRK11352 regulator protein FrmR; Provisional
Probab=38.03 E-value=1.4e+02 Score=24.66 Aligned_cols=29 Identities=10% Similarity=0.218 Sum_probs=24.5
Q ss_pred HHHHHHHHHhcCcHHHHHHHHHHHhhhcC
Q 015212 257 KSTLTTQIAEETEMSEVIESVKQRVKDAK 285 (411)
Q Consensus 257 ~~~L~~~l~e~~~~~~ii~eIk~~~~~~n 285 (411)
++.+.++++++.++.+|+.-|.+-+.+-+
T Consensus 22 v~gi~~Mie~~~~C~dil~Ql~Avr~Al~ 50 (91)
T PRK11352 22 IDALERSLEGDAECRAILQQIAAVRGAAN 50 (91)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Confidence 45678889999999999999998877754
No 18
>PF08362 TetR_C_3: YcdC-like protein, C-terminal region; InterPro: IPR013573 This entry represents the C-terminal domain found in the hypothetical transcriptional regulators RutR and YcdC (P75899 from SWISSPROT) from Escherichia coli. Both of these proteins are member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. RutR negatively controls the transcription of the rut operon involved in pyrimidine utilization. The C-terminal domains of RutR, YsiA and TetR share a multi-helical, interlocking structure. These proteins also contain helix-turn-helix (HTH) DNA-binding domains.; GO: 0045892 negative regulation of transcription, DNA-dependent; PDB: 3LOC_B.
Probab=36.11 E-value=1e+02 Score=27.57 Aligned_cols=65 Identities=11% Similarity=-0.024 Sum_probs=47.4
Q ss_pred CcchhhhhhHHHHHHHHHhhhhhhHHHhHHHH----HHHHHHhhccChhhhHHHHHHHHHHHhhhcCCCCCc
Q 015212 97 EPQREAILPSVIYIQKILRRRPFLIKNLENVT----RRFMQSLELFEENERKKLAIFTALAFSQKLSGLPPE 164 (411)
Q Consensus 97 ~~~~~~~~~~~~~~~kl~rr~kyl~k~~e~~~----~~~l~~l~~f~~~~r~klA~~~a~~~~~~~~g~~~~ 164 (411)
.++.++++.|+.-.-.+-|.||..-|.|=.|+ +.+-.|++..--..-++.+..+..|+. .|.+.+
T Consensus 19 ~dP~~aL~~YI~~k~~~s~~~P~~Srlfa~Eii~Gap~L~~~l~~~l~~~~~~~~~~I~~Wi~---~G~i~~ 87 (143)
T PF08362_consen 19 DDPAEALRAYIRAKMEYSRDHPEASRLFANEIIQGAPHLKDYLRERLRPWVDRKVAVIERWIA---QGKIAP 87 (143)
T ss_dssp S-HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHTTSTTTHHHHHTHHHHHHHHHHHHHHHHHH---TTSS-S
T ss_pred CCHHHHHHHHHHHHHHHHHHCchhhHHHHHHHHcCchhhHHHHHHHHHHHHHHHHHHHHHHHH---CCCCCC
Confidence 34566999999999999999999999999874 667777754433333344557788999 898854
No 19
>PF07528 DZF: DZF domain; InterPro: IPR006561 This domain is found in proteins containing the double-stranded RNA-binding motif, DSRM (IPR001159 from INTERPRO), or the zinc finger domain C2H2 (IPR007087 from INTERPRO). This domain is found exclusively in the metazoa.
Probab=34.95 E-value=38 Score=33.12 Aligned_cols=49 Identities=24% Similarity=0.357 Sum_probs=37.9
Q ss_pred HHhhhhcCCCCCCCcccCCC-CCCCceeecc--CcchhhhhhHHHHHHHHHhh
Q 015212 67 FEVVFTGGRTQPGTTKPDEG-ERHSYSIIDC--EPQREAILPSVIYIQKILRR 116 (411)
Q Consensus 67 f~i~~~gg~l~pgg~~~~~~-~~~~~~i~~~--~~~~~~~~~~~~~~~kl~rr 116 (411)
|| ++|+|+|-|||.-+.|- ++.++.+.++ ..++|.|-..+|-+-|+|--
T Consensus 182 le-~lasGillp~~~gl~DPcE~~~~~~~~~lt~qq~e~it~sAQ~~LRllaf 233 (248)
T PF07528_consen 182 LE-CLASGILLPGSPGLRDPCEKDPVDVLDTLTLQQREDITSSAQTALRLLAF 233 (248)
T ss_pred HH-HHhCceecCCCCCCcCCCCCCCceeeccCCHHHHHHHHHHHHHHHHHHHh
Confidence 44 47999999999877753 4568888885 66888999999988887743
No 20
>PF14821 Thr_synth_N: Threonine synthase N terminus; PDB: 3V7N_A 1VB3_A 1KL7_A.
Probab=34.32 E-value=40 Score=26.94 Aligned_cols=46 Identities=17% Similarity=0.402 Sum_probs=28.1
Q ss_pred CchhhHHHHHHHhhcCCC-----CHHHHHHH-h-hcCCccchhhhhhhHHhhh
Q 015212 26 DPAAFSDAVVQIYLDNAG-----DLELIAKC-I-ESSDLNFSRYGDTFFEVVF 71 (411)
Q Consensus 26 dp~~f~d~~~~~~~~~~~-----dle~~~~~-l-~g~~ldy~ry~~~lf~i~~ 71 (411)
.+.+|.+||++||...|| .+-.+.+. | .-..++|.--+-.++..++
T Consensus 10 ~~vsf~eAil~GlA~DGGLyvP~~iP~l~~~~l~~l~~~sy~elA~~il~~f~ 62 (79)
T PF14821_consen 10 PPVSFKEAILQGLAPDGGLYVPEEIPKLSKEELEELKNLSYAELAFEILSPFL 62 (79)
T ss_dssp CEE-HHHHHHH-SBTTSB-EEESS-----HHHHHHHTTS-HHHHHHHHHHHHC
T ss_pred CCcCHHHHHHhCCCCCCeeEecCcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 789999999999998887 55555544 4 3456777766666666665
No 21
>PF10193 Telomere_reg-2: Telomere length regulation protein; InterPro: IPR019337 This entry represents a conserved domain found in a group of proteins called telomere-length regulation, or clock abnormal protein-2, which are conserved from plants to humans. These proteins regulate telomere length and contribute to silencing of sub-telomeric regions []. In vitro the protein binds to telomeric DNA repeats. ; PDB: 3O4Z_B.
Probab=33.12 E-value=1.4e+02 Score=25.54 Aligned_cols=66 Identities=24% Similarity=0.340 Sum_probs=38.7
Q ss_pred chhhhhhHHHHHHHHHhhhhh----hHHHhHHHHHHHHHHhh-ccChh--hhHHHHHHHHHHHhhhcCCCCCccchhhhh
Q 015212 99 QREAILPSVIYIQKILRRRPF----LIKNLENVTRRFMQSLE-LFEEN--ERKKLAIFTALAFSQKLSGLPPETVFQPLL 171 (411)
Q Consensus 99 ~~~~~~~~~~~~~kl~rr~ky----l~k~~e~~~~~~l~~l~-~f~~~--~r~klA~~~a~~~~~~~~g~~~~~~l~~l~ 171 (411)
+.+.+..-.....+||||.+= +...-++-+ +.|..|+ .|+.+ +..+...++|++++ .|..+..-|+
T Consensus 18 ~~e~~e~aL~~a~~LIR~k~~fg~el~~~a~eL~-~~Ll~L~~~f~~~~Fe~~R~~alval~v~------~P~~~~~~L~ 90 (114)
T PF10193_consen 18 DYEKFEAALKSAEKLIRRKPDFGTELSEYAEELL-KALLHLQNKFDIENFEELRQNALVALVVA------APEKVAPYLT 90 (114)
T ss_dssp --S-SHHHHHHHHHHHHS-----SSHHHHHHHHH-HHHHH---TT--TTTTHHHHHHHHHHHHH------SGGGHHH-HH
T ss_pred CHHHHHHHHHHHHHHHhcCCCCcchHHHHHHHHH-HHHhhccccCCccCHHHHHHHHHHHHHHH------hhHHHHHHHH
Confidence 567778888899999999998 444444444 4444444 46655 47899999999999 5666555433
No 22
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=33.04 E-value=1.9e+02 Score=22.79 Aligned_cols=46 Identities=17% Similarity=0.362 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHhcCcHHHHHHHHHHHhhhcCCChHHHHHHHHHH
Q 015212 253 LKDMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILWDI 298 (411)
Q Consensus 253 ~~El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~~a 298 (411)
..++...+.+.+.+|.++.+|+..+.......++++.....++...
T Consensus 20 ~~~~~~~~~~l~~~G~s~~~Il~~l~~~l~~~~~~~~~k~~i~~~l 65 (89)
T PF08542_consen 20 FKEARKKLYELLVEGYSASDILKQLHEVLVESDIPDSQKAEILKIL 65 (89)
T ss_dssp HHHHHHHHHHHHHTT--HHHHHHHHHHHHHTSTSSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccHHHHHHHHHHH
No 23
>cd01051 Mn_catalase Manganese catalase, ferritin-like diiron-binding domain. Manganese (Mn) catalase is a member of a broad superfamily of ferritin-like diiron enzymes. While many diiron enzymes catalyze dioxygen-dependent reactions, manganese catalase performs peroxide-dependent oxidation-reduction. Catalases are important antioxidant metalloenzymes that catalyze disproportionation of hydrogen peroxide, forming dioxygen and water. Manganese catalase, a nonheme type II catalase, contains a binuclear manganese cluster that catalyzes the redox dismutation of hydrogen peroxide, interconverting between dimanganese(II) [(2,2)] and dimanganese(III) [(3,3)] oxidation states during turnover. Mn catalases are found in a broad range of microorganisms in microaerophilic environments, including the mesophilic lactic acid bacteria (e.g., Lactobacillus plantarum) and bacterial and archaeal thermophiles (e.g., Thermus thermophilus and Pyrobaculum caldifontis). L. plantarum and T. thermophilus holoenz
Probab=32.75 E-value=2.4e+02 Score=25.48 Aligned_cols=102 Identities=11% Similarity=0.103 Sum_probs=72.0
Q ss_pred hhHHHHHHHhhcCCCCHHHHHHHh-hcCCc-cchhhhhhhHHhhh---------------hcCCCCCCCcccCCCCCCCc
Q 015212 29 AFSDAVVQIYLDNAGDLELIAKCI-ESSDL-NFSRYGDTFFEVVF---------------TGGRTQPGTTKPDEGERHSY 91 (411)
Q Consensus 29 ~f~d~~~~~~~~~~~dle~~~~~l-~g~~l-dy~ry~~~lf~i~~---------------~gg~l~pgg~~~~~~~~~~~ 91 (411)
.|+..|.+.+-.+.|-+.++-.+| .+-.. .+..+.|.|-+|-. -|| .|+|. +- ..+|
T Consensus 20 ~~A~~l~~~~gG~~gEl~ai~qYl~q~~~~~~~~~~~d~l~~ia~eEm~H~e~la~~I~~Lg~--~~~g~-pw---~~~y 93 (156)
T cd01051 20 RFAKLLQEQLGGAFGELSAAMQYLFQSFNFREDPKYRDLLLDIGTEELSHLEMVATLIAMLLK--DSQGV-PW---TAAY 93 (156)
T ss_pred HHHHHHHHHhCCccHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC--CCCCC-cC---CCcc
Confidence 688999999988889999999999 44445 88999999988743 133 56663 22 2344
Q ss_pred eeeccCcchhhhhhHHHHHHHHHhhhhhhHHHhHH-HHHHHHHHhhc
Q 015212 92 SIIDCEPQREAILPSVIYIQKILRRRPFLIKNLEN-VTRRFMQSLEL 137 (411)
Q Consensus 92 ~i~~~~~~~~~~~~~~~~~~kl~rr~kyl~k~~e~-~~~~~l~~l~~ 137 (411)
|-.+.+-.+.++.=+.-=++-+.+|..+.+..+| .++.+|.+|-.
T Consensus 94 -v~~~~d~~~~L~~ni~aE~~Ai~~Y~~l~~~~~Dp~v~~~l~~I~~ 139 (156)
T cd01051 94 -IQSSGNLVADLRSNIAAESRARLTYERLYEMTDDPGVKDTLSFLLV 139 (156)
T ss_pred -cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 2223333445555555567788889999988888 58888888765
No 24
>PF04286 DUF445: Protein of unknown function (DUF445); InterPro: IPR007383 This entry contains proteins of unknown function. They are predicted to be transmembrane proteins with 2 or 3 TM domains.
Probab=32.60 E-value=5e+02 Score=25.64 Aligned_cols=32 Identities=9% Similarity=0.011 Sum_probs=26.5
Q ss_pred hccChhhhHHHHHHHHHHHhhhcCCCCCccchhhh
Q 015212 136 ELFEENERKKLAIFTALAFSQKLSGLPPETVFQPL 170 (411)
Q Consensus 136 ~~f~~~~r~klA~~~a~~~~~~~~g~~~~~~l~~l 170 (411)
-+--|..|+++|..+|-++. +.++++..+..-
T Consensus 32 ~giip~~r~~~~~~~~~~v~---~~ll~~~~i~~~ 63 (367)
T PF04286_consen 32 TGIIPKNRERIAESIGEMVE---NELLTPETIRRK 63 (367)
T ss_pred cccccccHHHHHHHHHHHHH---HHCCCHHHHHHH
Confidence 35668899999999999999 888977776653
No 25
>KOG2213 consensus Apoptosis inhibitor 5/fibroblast growth factor 2-interacting factor 2, and related proteins [Signal transduction mechanisms]
Probab=30.99 E-value=6.7e+02 Score=26.61 Aligned_cols=118 Identities=18% Similarity=0.170 Sum_probs=63.4
Q ss_pred ccCCCchHHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhcCCCCCCChhhHHHHHHhcCCcccccchhhhhHHhHHH
Q 015212 175 LVGKGLVLSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDFFPSSKRSAEGFSEHFTKEGLIPLVEYNEKKIFEVKLK 254 (411)
Q Consensus 175 Lv~~G~a~~fl~~i~~~~~~~~~~~~l~~~lrksgl~~~l~~f~P~~kr~~e~f~~~f~~~~L~~l~~~~~~~~~~~~~~ 254 (411)
+.-.|-+++-+..++.+++. ...++.++.+++.- +....|+-...+..+=++-..++..+..+.....
T Consensus 87 ~fc~~d~~~rv~d~l~qLLn---k~sl~~Lf~~~~~~---------D~~irek~l~fi~tKl~~l~~e~L~kevE~~iv~ 154 (460)
T KOG2213|consen 87 LFCKGDALSRVNDVLVQLLN---KASLTGLFGQIEVG---------DEQIREKVLKFIRTKLITLKGEVLTKEVERHIVD 154 (460)
T ss_pred hhccCchhhhhHHHHHHHHH---HHHHHHHHhhhhhh---------hHHHHHHHHHHHHHHhhcccHHHhhhHHHHHHHH
Confidence 34455777777888888887 45566667666552 1112222222233333333344444444444555
Q ss_pred HHHHHHHHHHHh-----------------cCcH---HHHHHHHHHHh--hhcCCChHHHHHHHHHHHHHHhh
Q 015212 255 DMKSTLTTQIAE-----------------ETEM---SEVIESVKQRV--KDAKLPDIEVVRILWDILMDAVQ 304 (411)
Q Consensus 255 El~~~L~~~l~e-----------------~~~~---~~ii~eIk~~~--~~~n~s~~evi~~l~~alm~~v~ 304 (411)
|+...|.+.-.+ ..+. .+++.++.++. .+-|.|+.++|-=.++|+.-++.
T Consensus 155 eikkal~dVtgeef~lfm~~L~~lk~~~~k~~~a~lqeLa~~~e~~a~ldaf~~sD~d~VdRfisCl~~AvP 226 (460)
T KOG2213|consen 155 EIKKALEDVTGEEFTLFMDILASLKSLQTKAGEARLQELAEEQEGLADLDAFNVSDADYVDRFISCLLMAVP 226 (460)
T ss_pred HHHHHHHhccHHHHHHHHHHHHhhhcccCCCCHHHHHHHHHHHhhhhccCcccCCChHHHHHHHHHHHHhhh
Confidence 555555442111 1122 34444444443 33788999999888888877764
No 26
>PRK15039 transcriptional repressor RcnR to maintain nickel and cobalt homeostasis; Provisional
Probab=30.77 E-value=1.8e+02 Score=24.01 Aligned_cols=29 Identities=14% Similarity=0.185 Sum_probs=24.6
Q ss_pred HHHHHHHHHhcCcHHHHHHHHHHHhhhcC
Q 015212 257 KSTLTTQIAEETEMSEVIESVKQRVKDAK 285 (411)
Q Consensus 257 ~~~L~~~l~e~~~~~~ii~eIk~~~~~~n 285 (411)
++.+.++++++.++.+|+.-|.+-+.+-+
T Consensus 22 v~gI~~Miee~~~C~dIl~Ql~Avr~Al~ 50 (90)
T PRK15039 22 VVALKKMLDEPHECAAVLQQIAAIRGAVN 50 (90)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Confidence 46778899999999999999998877654
No 27
>PHA02690 hypothetical protein; Provisional
Probab=29.95 E-value=50 Score=26.77 Aligned_cols=32 Identities=22% Similarity=0.318 Sum_probs=27.9
Q ss_pred CCCCHHHHHHHhhcCCccchhhhhhhHHhhhh
Q 015212 41 NAGDLELIAKCIESSDLNFSRYGDTFFEVVFT 72 (411)
Q Consensus 41 ~~~dle~~~~~l~g~~ldy~ry~~~lf~i~~~ 72 (411)
..+=|||+-..|+||+.=-|+----|||.+++
T Consensus 20 drrYLeAIqrhlEgs~plLR~~~RlLfDL~lT 51 (90)
T PHA02690 20 DRRYLEAIQRHLEGSTPLLRQMWRLLFDLLLT 51 (90)
T ss_pred hhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Confidence 33689999999999999999999999998875
No 28
>PF08337 Plexin_cytopl: Plexin cytoplasmic RasGAP domain; InterPro: IPR013548 This domain is found at C terminus of various plexins (e.g. P51805 from SWISSPROT). Plexins are receptors for semaphorins, and plexin signalling is important in pathfinding and patterning of both neurons and developing blood vessels [, ]. The cytoplasmic region, which has been called a SEX domain [], and is involved in downstream signalling pathways, by interaction with proteins such as Rac1, RhoD, Rnd1 and other plexins []. ; PDB: 3H6N_A 4E71_A 4E74_A 3IG3_A 2REX_C 2JPH_A 2R2O_A 3HM6_X 3SU8_X 3SUA_E ....
Probab=29.86 E-value=2.7e+02 Score=30.46 Aligned_cols=52 Identities=17% Similarity=0.301 Sum_probs=38.2
Q ss_pred chhhhhhHHHHHHHHHhhhhhhHHHhHHHHHHHHHHhhccChhhhHHHHHHHHHHHh
Q 015212 99 QREAILPSVIYIQKILRRRPFLIKNLENVTRRFMQSLELFEENERKKLAIFTALAFS 155 (411)
Q Consensus 99 ~~~~~~~~~~~~~kl~rr~kyl~k~~e~~~~~~l~~l~~f~~~~r~klA~~~a~~~~ 155 (411)
....+..=...|.+|+....||..- -+.|-.=+.|+..+|-.+|-++-.++.
T Consensus 35 ~~~~~~~~l~~f~~LL~nk~Fl~~f-----i~tlE~q~~fs~rDr~~vASLL~vaL~ 86 (539)
T PF08337_consen 35 RRSTVEQGLRQFSQLLNNKHFLLTF-----IHTLESQRSFSMRDRCNVASLLMVALQ 86 (539)
T ss_dssp THHHHHHHHHHHHHHHTSHHHHHHH-----HHHHHCSSSS-HHHHHHHHHHHHHHTG
T ss_pred cchhHhHHHHHHHHHhcCchHHHHH-----HHHHHhCCCcccccchhhhhHHHHHHc
Confidence 4446667777899999999998754 344445578999999999988776666
No 29
>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=28.00 E-value=2.3e+02 Score=25.34 Aligned_cols=62 Identities=18% Similarity=0.162 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHhhc-------chHHHhHHHHHHHHhhhhcccchhhHHH
Q 015212 316 AALRQVKTWAQLLNTFCTNAKLELELMYKVQMQCYE-------DAKLMKLFPEIVRSLYDQDVLAEDTILY 379 (411)
Q Consensus 316 ~~~~~lk~~~pLL~~f~~~~~~Ql~lL~alQ~~c~e-------~~~~~k~f~~IL~~LYd~DVlsEeaIlk 379 (411)
..++.++.|-..+.+.--.++.| +=.|++.|+.. ++++...|..-+-.||+.++|+..+|..
T Consensus 67 ~EKefM~lWN~fv~k~r~~aD~~--ip~ac~~Fv~~~~~~L~~~~~l~~~f~lHl~~L~d~glLd~~~i~~ 135 (140)
T PF09733_consen 67 EEKEFMKLWNSFVMKQRVIADGH--IPWACEAFVREHGQWLVEKPNLRREFLLHLINLWDFGLLDARTIDE 135 (140)
T ss_pred HHHHHHHHHHHHHHHccCcchHH--HHHHHHHHHHHhHHHHhhChhHHHHHHHHHHHHHHcCCCCHHHHHH
Confidence 44566677777664433323322 33344555542 4678888998899999999999998854
No 30
>PF14026 DUF4242: Protein of unknown function (DUF4242)
Probab=27.34 E-value=36 Score=27.12 Aligned_cols=27 Identities=11% Similarity=0.218 Sum_probs=19.6
Q ss_pred cccCCCCCCCceeeccCcchhhhhhHHH
Q 015212 81 TKPDEGERHSYSIIDCEPQREAILPSVI 108 (411)
Q Consensus 81 ~~~~~~~~~~~~i~~~~~~~~~~~~~~~ 108 (411)
|++.+++..-|||+.|| +.|+|+...+
T Consensus 39 s~v~~d~~k~~Cly~Ap-~~eaV~~~~~ 65 (77)
T PF14026_consen 39 SYVSEDDGKIFCLYEAP-DEEAVREHAR 65 (77)
T ss_pred EEEecCCCeEEEEEECC-CHHHHHHHHH
Confidence 56665556789999999 5577776544
No 31
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=26.15 E-value=62 Score=21.20 Aligned_cols=20 Identities=25% Similarity=0.418 Sum_probs=16.5
Q ss_pred HHHHHHhhhhcccchhhHHH
Q 015212 360 PEIVRSLYDQDVLAEDTILY 379 (411)
Q Consensus 360 ~~IL~~LYd~DVlsEeaIlk 379 (411)
...|+.||+.++|+++-+-+
T Consensus 5 L~~L~~l~~~G~IseeEy~~ 24 (31)
T PF09851_consen 5 LEKLKELYDKGEISEEEYEQ 24 (31)
T ss_pred HHHHHHHHHcCCCCHHHHHH
Confidence 35679999999999998753
No 32
>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=26.00 E-value=5.6e+02 Score=24.08 Aligned_cols=82 Identities=11% Similarity=0.134 Sum_probs=46.9
Q ss_pred hhHHHHHHHHHhhhhhhHHHhHH-HHHHHHHHhhccChhhhHHHHHHHHHHHhhhcCCCCCccchhhhhhccccCCCchH
Q 015212 104 LPSVIYIQKILRRRPFLIKNLEN-VTRRFMQSLELFEENERKKLAIFTALAFSQKLSGLPPETVFQPLLKDNLVGKGLVL 182 (411)
Q Consensus 104 ~~~~~~~~kl~rr~kyl~k~~e~-~~~~~l~~l~~f~~~~r~klA~~~a~~~~~~~~g~~~~~~l~~l~~~~Lv~~G~a~ 182 (411)
+.|..--+|||-+||=+.+.+.. ..+-+=.|.+.|.-.--..+..+ .-.+|.|+-..- .+-...|...
T Consensus 26 ~eYt~~c~kLl~Qyk~~~~~~~~~~~~~le~F~~~y~l~cp~A~~Rl---------~~G~P~Tie~~~--~~~~~~~~~a 94 (188)
T PF03997_consen 26 KEYTTACNKLLNQYKTILKQLKDDEFPDLEEFMKKYNLDCPAALERL---------REGVPATIEHRI--SSSSDKGNSA 94 (188)
T ss_dssp HHHHHHHHHHHHHHHHHHTSTTHHHHHHHHHHHHHTTS-HHHHHHHH---------HCTSS----------------CHH
T ss_pred HHHHHHHHHHHHHHHHHHHHcccccCCCHHHHHHHhcccCChHHHHH---------HcCCCCchhhhc--ccccCCchHH
Confidence 56999999999999999999988 77888888888875432222222 355776665421 1122445555
Q ss_pred HHHHHHHHHHHHhC
Q 015212 183 SFITDFFKEYLVDN 196 (411)
Q Consensus 183 ~fl~~i~~~~~~~~ 196 (411)
..+.++-+-++.-|
T Consensus 95 k~Vae~t~~FIT~m 108 (188)
T PF03997_consen 95 KLVAEATQNFITLM 108 (188)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHhChhhhhh
Confidence 55555555555433
No 33
>PF03542 Tuberin: Tuberin; InterPro: IPR018515 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This domain is found in Tuberin proteins. ; GO: 0005096 GTPase activator activity, 0043547 positive regulation of GTPase activity
Probab=25.45 E-value=5e+02 Score=26.84 Aligned_cols=100 Identities=15% Similarity=0.326 Sum_probs=56.9
Q ss_pred HHHHHHHHHHHHHhcCcHHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHHhhhhccchhhhHHHHHHHHHHHHHHHHHHh
Q 015212 253 LKDMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILWDILMDAVQWSGKNQQQNANAALRQVKTWAQLLNTFC 332 (411)
Q Consensus 253 ~~El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~~alm~~v~~s~k~~~~~~~~~~~~lk~~~pLL~~f~ 332 (411)
.+++...|.+++.+....+.+ ...+.+++-.|+..+++.++-..+.--..-+.+..+..++.+. .-+
T Consensus 181 I~~L~~~Lc~~i~d~~~~~~l------~~~p~~~~~~D~~~~~~~~Ls~LisYh~~~~k~~qd~iV~~l~-------~GL 247 (356)
T PF03542_consen 181 IDQLRNALCSMICDRSFLESL------SNKPTGFKRADLQVCVFPVLSALISYHSHFSKQEQDEIVRALE-------SGL 247 (356)
T ss_pred HHHHHHHHHHHHhcccccccc------cCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCHhHHHHHHHHHH-------HHh
Confidence 345667777777654433222 1244678888988888876665543211001111112222221 111
Q ss_pred cChHHHHHHHHHHHHHhhc-chHHHhHHHHHHHHh
Q 015212 333 TNAKLELELMYKVQMQCYE-DAKLMKLFPEIVRSL 366 (411)
Q Consensus 333 ~~~~~Ql~lL~alQ~~c~e-~~~~~k~f~~IL~~L 366 (411)
.+ +....|+.|+-..|+| +....|.++.|+..|
T Consensus 248 ~s-~~a~~CI~aLtic~~EmP~s~~k~L~~iL~kL 281 (356)
T PF03542_consen 248 GS-KTAKPCIHALTICCYEMPDSMKKLLPSILLKL 281 (356)
T ss_pred cc-CcHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 11 3456799999999999 566677888887766
No 34
>TIGR02923 AhaC ATP synthase A1, C subunit. The A1/A0 ATP synthase is homologous to the V-type (V1/V0, vacuolar) ATPase, but functions in the ATP synthetic direction as does the F1/F0 ATPase of bacteria. The C subunit is part of the hydrophilic A1 "stalk" complex (AhaABCDEFG) which is the site of ATP generation and is coupled to the membrane-embedded proton translocating A0 complex.
Probab=24.64 E-value=6.9e+02 Score=24.68 Aligned_cols=112 Identities=13% Similarity=0.195 Sum_probs=62.8
Q ss_pred cccCCCchHHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhcCCCCCCChhhHHHHHHhcCCcccccchhhhhHHhHH
Q 015212 174 NLVGKGLVLSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDFFPSSKRSAEGFSEHFTKEGLIPLVEYNEKKIFEVKL 253 (411)
Q Consensus 174 ~Lv~~G~a~~fl~~i~~~~~~~~~~~~l~~~lrksgl~~~l~~f~P~~kr~~e~f~~~f~~~~L~~l~~~~~~~~~~~~~ 253 (411)
.|++.|. +-..-|+.++...+.+.+...++......-+.+++ +...+...+...+...-+..+....+. ..
T Consensus 121 ~l~~~g~---~~~~~l~~l~~~~~~~e~~~~L~~t~y~~~l~~~~-~~~~~l~~~E~~Ld~~y~~~l~~~~~~-----~~ 191 (343)
T TIGR02923 121 LLIPAGE---FLEKRIKELAEAKTIEEIVEALEGTPYYGPLQEAL-AGNGDLSPIENELDRMYYEKLLKYVGS-----PS 191 (343)
T ss_pred Hhccccc---cCHHHHHHHHcCCCHHHHHHHcCCCccHHHHHHHH-hcCCCHHHHHHHHHHHHHHHHHHHhcC-----CC
Confidence 4566663 34556888888899999988888877765466666 333455455443333222222221100 00
Q ss_pred HHHHHHHHHHHHhcCcHHHHHHHHHHHhhhcCCChHHHHHHHH
Q 015212 254 KDMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILW 296 (411)
Q Consensus 254 ~El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~ 296 (411)
..-...+...+.......||...+++.+. +++..++...+.
T Consensus 192 ~~~~~~l~~~~~~eiD~~Nl~~ilr~k~~--~~~~e~i~~~li 232 (343)
T TIGR02923 192 DDETKLFTEFIKTEVDIRNLKTLLRLKAA--GLSPDEIMPYTI 232 (343)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHc--CCCHHHHHhhcc
Confidence 01123455555556677778777777643 666655555444
No 35
>TIGR03652 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers.
Probab=24.30 E-value=3.4e+02 Score=25.57 Aligned_cols=62 Identities=11% Similarity=0.110 Sum_probs=34.0
Q ss_pred HHHHHhcCCcccccchhhhhHHhHHHHHHHHHHHHH-HhcCcHHHHHHHHHHHhhhc-CCChHHHHHHHHHHHHHHh
Q 015212 229 SEHFTKEGLIPLVEYNEKKIFEVKLKDMKSTLTTQI-AEETEMSEVIESVKQRVKDA-KLPDIEVVRILWDILMDAV 303 (411)
Q Consensus 229 ~~~f~~~~L~~l~~~~~~~~~~~~~~El~~~L~~~l-~e~~~~~~ii~eIk~~~~~~-n~s~~evi~~l~~alm~~v 303 (411)
..+|.+.|+++=+.- .++|.++. ..|.+++.++.+++...... +.+..++...-..++++++
T Consensus 12 ~~vf~~~gid~cc~g-------------~~~l~~a~~~~g~d~~~~l~~ln~~~~~~~~~~~~~~~~~~~~~Lid~i 75 (216)
T TIGR03652 12 ARIFRKYGIDFCCGG-------------NVSLAEACKEKGLDPDEILAELNALQQEPENSGAKDWREAPLSELIDHI 75 (216)
T ss_pred HHHHHHcCCCccCCC-------------cchHHHHHHHcCCCHHHHHHHHHHHHhccccccccChhhCCHHHHHHHH
Confidence 356777777643332 13455554 34678888888888775222 1222344444445666665
No 36
>PRK10167 hypothetical protein; Provisional
Probab=23.08 E-value=2e+02 Score=26.57 Aligned_cols=77 Identities=13% Similarity=0.024 Sum_probs=0.0
Q ss_pred hhhhhHHHHHHHHHhhhhhhHHHhHHHHHHHHHHhhcc-ChhhhHHHHHHHHHHHhhhcCCCCCccchhhhhhccccCCC
Q 015212 101 EAILPSVIYIQKILRRRPFLIKNLENVTRRFMQSLELF-EENERKKLAIFTALAFSQKLSGLPPETVFQPLLKDNLVGKG 179 (411)
Q Consensus 101 ~~~~~~~~~~~kl~rr~kyl~k~~e~~~~~~l~~l~~f-~~~~r~klA~~~a~~~~~~~~g~~~~~~l~~l~~~~Lv~~G 179 (411)
+-+..|.+.|.+.+.+.+ =.+..=|++..+..|++.. +..||.-+..++.-.-. |.+|..+.-.+++-++.+-+
T Consensus 70 ~~~~~Y~~~lm~al~~~~-t~~~~~NvL~Hi~GYFKk~Ls~~EKq~l~~lI~~Yr~----g~vpl~vpltlL~h~~~~y~ 144 (169)
T PRK10167 70 DFYNQYRQRVIVLLSHPA-NVRDHTNVLMHVQGYFRPHIDSTERQQLAALIDSYRR----GEQPLLAPLMRIKHYMALYP 144 (169)
T ss_pred HHHHHHHHHHHHHHcCCC-CcchhHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHc----CCCCHHHHHHHHHHHHHHCC
Q ss_pred chH
Q 015212 180 LVL 182 (411)
Q Consensus 180 ~a~ 182 (411)
...
T Consensus 145 ~~Y 147 (169)
T PRK10167 145 DAW 147 (169)
T ss_pred cHH
No 37
>PF05537 DUF759: Borrelia burgdorferi protein of unknown function (DUF759); InterPro: IPR008478 This entry consists of several uncharacterised proteins from Borrelia species including Borrelia burgdorferi and Borrelia garinii.
Probab=22.82 E-value=9.3e+02 Score=25.52 Aligned_cols=170 Identities=18% Similarity=0.232 Sum_probs=91.2
Q ss_pred HHHHhhhhhhHHHhHHH--H------HHHHHHhhccCh---hhhHHHHHHHHHHHhhhcCCCCC-ccchhhhhhccccCC
Q 015212 111 QKILRRRPFLIKNLENV--T------RRFMQSLELFEE---NERKKLAIFTALAFSQKLSGLPP-ETVFQPLLKDNLVGK 178 (411)
Q Consensus 111 ~kl~rr~kyl~k~~e~~--~------~~~l~~l~~f~~---~~r~klA~~~a~~~~~~~~g~~~-~~~l~~l~~~~Lv~~ 178 (411)
++.+-+.|=.++.||.+ + +.-|.-|+ +.+ +.-.....+.|.+-| +|+++ ...-..+.++.|--+
T Consensus 197 ~~il~~mkGFER~LEKEdFLr~asvlKg~l~el~-lnd~~~~nl~~AvelAA~LkS---sG~as~ne~Ai~~Vs~~L~Ge 272 (431)
T PF05537_consen 197 NKILKGMKGFERDLEKEDFLRKASVLKGSLRELG-LNDENGENLKNAVELAAMLKS---SGLASDNESAIAAVSSLLKGE 272 (431)
T ss_pred HHHhccccchhhhhhHHHHHHHHHHHHhHHHhcC-CccccchhHHHHHHHHHHHHh---cCCCCccHHHHHHHHHHhcCC
Confidence 34666777777777763 3 44456666 444 455666788999999 99998 444455777888877
Q ss_pred CchH-HHHHHHHHHHHHhCChhHHHH---HH---HhCCCchhhhhcCCCCCCChhhHHHHHHhcCCcccccchhhhhHHh
Q 015212 179 GLVL-SFITDFFKEYLVDNSLDDLIA---IL---KRGKMEDNLLDFFPSSKRSAEGFSEHFTKEGLIPLVEYNEKKIFEV 251 (411)
Q Consensus 179 G~a~-~fl~~i~~~~~~~~~~~~l~~---~l---rksgl~~~l~~f~P~~kr~~e~f~~~f~~~~L~~l~~~~~~~~~~~ 251 (411)
|..+ .++..| ...|.+.+-. .| .+.|-+ ++-..+....+..-|..-||..-++-..+ -..
T Consensus 273 g~~lf~imk~~-----~~~G~KY~E~~K~~~E~ltq~g~~------~~lr~~iL~kMikD~sSlgitk~AdekEk--ikS 339 (431)
T PF05537_consen 273 GDELFDIMKPI-----KKFGEKYLERAKMNWELLTQSGAK------FDLRSRILKKMIKDISSLGITKHADEKEK--IKS 339 (431)
T ss_pred chHHHHHHhcc-----chhhHHHHHHHHHHHHHHhhhccc------cCcchHHHHHHHHHHHhcccccccCcHHH--HHh
Confidence 7442 222111 2223222222 22 111222 12222234455555666676655543322 122
Q ss_pred HHHHHHHHHHHHHHhcCc-----HHHHHHHHHHHhhhcCCChHHHHHHHHHHH
Q 015212 252 KLKDMKSTLTTQIAEETE-----MSEVIESVKQRVKDAKLPDIEVVRILWDIL 299 (411)
Q Consensus 252 ~~~El~~~L~~~l~e~~~-----~~~ii~eIk~~~~~~n~s~~evi~~l~~al 299 (411)
-...+.++|.+....... ...|+.||+......+ ...++..++.++
T Consensus 340 nLasiEQTL~dlTt~vL~PLL~~is~IIe~VkD~i~~Ft--~t~Ii~~i~~gi 390 (431)
T PF05537_consen 340 NLASIEQTLEDLTTNVLKPLLKKISEIIEWVKDYINNFT--ETHIINPIINGI 390 (431)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc--ccccchHHHHHH
Confidence 233444555555544332 3578888887655554 666776665444
No 38
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=22.47 E-value=2.3e+02 Score=22.67 Aligned_cols=51 Identities=18% Similarity=0.190 Sum_probs=33.1
Q ss_pred HHHHHHHHhhhhcccchhhHHHhhhcCCCcchHHHH--------HHhHHHHHHHhhhcc
Q 015212 358 LFPEIVRSLYDQDVLAEDTILYWFRKGTNPKGRQTF--------VKALEPFVKWLEEAE 408 (411)
Q Consensus 358 ~f~~IL~~LYd~DVlsEeaIlkW~~~~~~~~Gk~~~--------lk~~~~FV~WLeEAE 408 (411)
..-.|+..||..+||+++..-.=...++++.-...+ ......|+.+|+|-+
T Consensus 16 ~v~~ilD~L~~~~Vit~e~~~~I~a~~T~~~kar~Lld~l~~kG~~A~~~F~~~L~e~~ 74 (82)
T cd08330 16 NVDPILDKLHGKKVITQEQYSEVRAEKTNQEKMRKLFSFVRSWGASCKDIFYQILREEE 74 (82)
T ss_pred hHHHHHHHHHHCCCCCHHHHHHHHcCCCcHHHHHHHHHHHHccCHHHHHHHHHHHHHhC
Confidence 346688999999999999887766666553211111 122345888887643
No 39
>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=21.90 E-value=2.4e+02 Score=19.74 Aligned_cols=40 Identities=15% Similarity=0.224 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhcChHHHHHHHHHHHHHhhcchHHHhHHHH
Q 015212 322 KTWAQLLNTFCTNAKLELELMYKVQMQCYEDAKLMKLFPE 361 (411)
Q Consensus 322 k~~~pLL~~f~~~~~~Ql~lL~alQ~~c~e~~~~~k~f~~ 361 (411)
+.+-.+|..|..+..+.-++...+..+..++|+++.-|..
T Consensus 5 ~~FL~il~~y~~~~~~~~~v~~~v~~Ll~~hpdLl~~F~~ 44 (47)
T PF02671_consen 5 NEFLKILNDYKKGRISRSEVIEEVSELLRGHPDLLEEFNR 44 (47)
T ss_dssp HHHHHHHHHHHCTCSCHHHHHHHHHHHTTT-HHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHccCHHHHHHHHh
Confidence 4555677777776556666777888888888888766643
No 40
>cd00620 Methyltransferase_Sun N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological role of this domain in Sun is unknown, although it is likely to be involved in sequence-specific RNA binding. The C-terminal methyltransferase domain of Sun has been shown to catalyze formation of m5C at position 967 of 16S rRNA in Escherichia coli.
Probab=21.85 E-value=3.7e+02 Score=22.75 Aligned_cols=85 Identities=7% Similarity=-0.097 Sum_probs=52.7
Q ss_pred hhhHHH-HHHHHHhhhhhhHHHhHHHHHHHHHHhhccChhhhHHHHHHHHHHHhhhcCCCCCccchhhhh---hccccCC
Q 015212 103 ILPSVI-YIQKILRRRPFLIKNLENVTRRFMQSLELFEENERKKLAIFTALAFSQKLSGLPPETVFQPLL---KDNLVGK 178 (411)
Q Consensus 103 ~~~~~~-~~~kl~rr~kyl~k~~e~~~~~~l~~l~~f~~~~r~klA~~~a~~~~~~~~g~~~~~~l~~l~---~~~Lv~~ 178 (411)
-+.|++ ++.-.+|++.+|...++..+++-+ ..-.+..|.-|-+.++-++- .. +|+...-... .+.. ..
T Consensus 37 d~~~~~~lv~g~~r~~~~ld~~i~~~l~~~~---~~~~~~~~~iLr~a~~el~~---~~-~p~~avvneaVelak~~-~~ 108 (126)
T cd00620 37 DRGLATELVYGTLRWLALLDWIINPLLKKPD---VGKDPDVRNLLRLGLYQLLY---LD-VPPHAAVDETVEIAKIR-KD 108 (126)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHhCCCc---cccCHHHHHHHHHHHHHHHh---cC-CCchHHHHHHHHHHHHh-CC
Confidence 466666 899999999999999988765521 22346677777777777766 45 4544432211 1111 23
Q ss_pred CchHHHHHHHHHHHHHh
Q 015212 179 GLVLSFITDFFKEYLVD 195 (411)
Q Consensus 179 G~a~~fl~~i~~~~~~~ 195 (411)
..+..|+-.||+.+.++
T Consensus 109 ~~~~~fVNaVLr~i~r~ 125 (126)
T cd00620 109 LGRAGLVNAVLRRFERE 125 (126)
T ss_pred CchhhHHHHHHHHHhcc
Confidence 34556777777766553
No 41
>TIGR02100 glgX_debranch glycogen debranching enzyme GlgX. This family consists of the GlgX protein from the E. coli glycogen operon and probable equivalogs from other prokaryotic species. GlgX is not required for glycogen biosynthesis, but instead acts as a debranching enzyme for glycogen catabolism. This model distinguishes GlgX from pullanases and other related proteins that also operate on alpha-1,6-glycosidic linkages. In the wide band between the trusted and noise cutoffs are functionally similar enzymes, mostly from plants, that act similarly but usually are termed isoamylase.
Probab=21.80 E-value=2e+02 Score=32.31 Aligned_cols=95 Identities=18% Similarity=0.294 Sum_probs=63.4
Q ss_pred hhHHHHHHHhhcCCCCHHHHHHHhhcCCccchhh-------------hhh--hHHhhh-------hcC------------
Q 015212 29 AFSDAVVQIYLDNAGDLELIAKCIESSDLNFSRY-------------GDT--FFEVVF-------TGG------------ 74 (411)
Q Consensus 29 ~f~d~~~~~~~~~~~dle~~~~~l~g~~ldy~ry-------------~~~--lf~i~~-------~gg------------ 74 (411)
.|||+|..-+....++.+.++..|.||.--|+++ .|. |+|.+- +.|
T Consensus 401 ~frd~ir~f~~g~~~~~~~~~~~l~gs~~~~~~~~~~~~~~iNyv~~HD~~tl~D~~~~~~khn~~nge~n~dg~~~N~S 480 (688)
T TIGR02100 401 RYRDDMRRFWRGDAGMIGELANRLTGSSDLFEHNGRRPWASINFVTAHDGFTLRDLVSYNEKHNEANGENNRDGHNDNYS 480 (688)
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHhCCHhhccccCCCcCEEEEEEeCCCCchHHHHHHhhccchhhcccccccccccccc
Confidence 3999999888877789999999998875445444 443 888754 222
Q ss_pred -----------------------------CCCCCCcccCCCC---------CCCcee------eccC--cchhhhhhHHH
Q 015212 75 -----------------------------RTQPGTTKPDEGE---------RHSYSI------IDCE--PQREAILPSVI 108 (411)
Q Consensus 75 -----------------------------~l~pgg~~~~~~~---------~~~~~i------~~~~--~~~~~~~~~~~ 108 (411)
++.||--.+--|+ ..+||- |.=. .....+..|++
T Consensus 481 ~n~g~eG~~~~~~~~~~r~~~~r~~~a~l~~s~GiP~i~~GdE~g~t~~G~~n~y~~~~~~~~~dW~~~~~~~~l~~~~k 560 (688)
T TIGR02100 481 WNCGVEGPTDDPAINALRRRQQRNLLATLLLSQGTPMLLAGDEFGRTQQGNNNAYCQDNEIGWVDWSLDEGDDELLAFTK 560 (688)
T ss_pred ccccccCCCCCHHHHHHHHHHHHHHHHHHHHcCCCceeeecHhhccCCCCCCCCccCCCcccccCcccccccHHHHHHHH
Confidence 4567755554332 236664 2211 22336888888
Q ss_pred HHHHHHhhhhhhHHH
Q 015212 109 YIQKILRRRPFLIKN 123 (411)
Q Consensus 109 ~~~kl~rr~kyl~k~ 123 (411)
-+.+|.|+|+-|...
T Consensus 561 ~Li~lRk~~~~l~~~ 575 (688)
T TIGR02100 561 KLIALRKAHPVLRRE 575 (688)
T ss_pred HHHHHHHhCchhccc
Confidence 888888888876654
No 42
>COG1937 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.79 E-value=4.2e+02 Score=21.91 Aligned_cols=29 Identities=7% Similarity=0.173 Sum_probs=24.3
Q ss_pred HHHHHHHHHhcCcHHHHHHHHHHHhhhcC
Q 015212 257 KSTLTTQIAEETEMSEVIESVKQRVKDAK 285 (411)
Q Consensus 257 ~~~L~~~l~e~~~~~~ii~eIk~~~~~~n 285 (411)
.+.+.++++++.++.+|...|-+-+.+-|
T Consensus 22 v~gI~rMlEe~~~C~dVl~QIaAVr~Al~ 50 (89)
T COG1937 22 VRGIERMLEEDRDCIDVLQQIAAVRGALN 50 (89)
T ss_pred HHHHHHHHhCCCcHHHHHHHHHHHHHHHH
Confidence 46678899999999999999988777754
No 43
>PF07631 PSD4: Protein of unknown function (DUF1592); InterPro: IPR013042 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013039 from INTERPRO and IPR013043 from INTERPRO.
Probab=21.71 E-value=5.4e+02 Score=22.42 Aligned_cols=25 Identities=16% Similarity=0.274 Sum_probs=17.7
Q ss_pred HhHHHHHHHHHHHHHHhcCcHHHHH
Q 015212 250 EVKLKDMKSTLTTQIAEETEMSEVI 274 (411)
Q Consensus 250 ~~~~~El~~~L~~~l~e~~~~~~ii 274 (411)
...+.|...-+...+++|.+..+++
T Consensus 87 ~~m~~E~~~f~~~vl~~n~~~~~ll 111 (128)
T PF07631_consen 87 EAMREETDEFFEHVLEENGSVSELL 111 (128)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHh
Confidence 4456677777777788887777665
No 44
>PF11838 ERAP1_C: ERAP1-like C-terminal domain; InterPro: IPR024571 This entry represents the uncharacterised C-terminal domain of zinc metallopeptidases belonging to MEROPS peptidase family M1 (aminopeptidase N, clan MA), with a single member characterised in Streptomyces lividans: aminopeptidase G []. The rest of the members of this family are identified as aminopeptidase N of the actinomycete-type. The spectrum of activity may differ somewhat from the aminopeptidase N clade of Escherichia coli and most other proteobacteria, which are well separated phylogenetically within the M1 family. ; PDB: 3MDJ_A 2YD0_A 3QNF_C 3RJO_A 1Z5H_A 3Q7J_A 1Z1W_A 3SE6_B.
Probab=20.45 E-value=7.8e+02 Score=23.74 Aligned_cols=43 Identities=23% Similarity=0.216 Sum_probs=26.9
Q ss_pred HHHHHHHhhc--cChhhhHHHH-HHHHHHHhhhcCCCCCccchhhhhhcc
Q 015212 128 TRRFMQSLEL--FEENERKKLA-IFTALAFSQKLSGLPPETVFQPLLKDN 174 (411)
Q Consensus 128 ~~~~l~~l~~--f~~~~r~klA-~~~a~~~~~~~~g~~~~~~l~~l~~~~ 174 (411)
+.+++..|+. +++.+|-.|- -+.+++ . .|.+|.+.+..++.-.
T Consensus 21 ~~~l~~~L~~~~l~~~~R~~ll~D~~al~-~---~g~~~~~~~l~l~~~~ 66 (324)
T PF11838_consen 21 WDALIKQLQSNHLSPLDRAQLLDDLFALA-R---AGRLSYSDFLDLLEYL 66 (324)
T ss_dssp HHHHHHHHHHHGS-HHHHHHHHHHHHHHH-H---TTSS-HHHHHHHHGGG
T ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHHHHH-H---cCCCCHHHHHHHHHHh
Confidence 4555555543 7899997755 444444 4 5999998888766544
No 45
>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=20.38 E-value=4.8e+02 Score=21.31 Aligned_cols=100 Identities=11% Similarity=0.160 Sum_probs=57.4
Q ss_pred HHHHHHHHHHHhcCcHHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHHhhhhccchhhhHHHHHHHHHHHHHHHHHHhcC
Q 015212 255 DMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILWDILMDAVQWSGKNQQQNANAALRQVKTWAQLLNTFCTN 334 (411)
Q Consensus 255 El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~~alm~~v~~s~k~~~~~~~~~~~~lk~~~pLL~~f~~~ 334 (411)
.+...+.+.+.. .+.++.+.-|.++..+ . -.++++..++...++.- . +.-+.+..++..+++.
T Consensus 4 ~i~~~l~ey~~~-~D~~ea~~~l~~L~~~-~-~~~~vv~~~i~~~le~~----~----------~~~~~~~~Ll~~L~~~ 66 (113)
T smart00544 4 KIFLIIEEYLSS-GDTDEAVHCLLELKLP-E-QHHEVVKVLLTCALEEK----R----------TYREMYSVLLSRLCQA 66 (113)
T ss_pred HHHHHHHHHHHc-CCHHHHHHHHHHhCCC-c-chHHHHHHHHHHHHcCC----c----------cHHHHHHHHHHHHHHc
Confidence 444455555533 3777888888887665 2 36678887777777641 0 1225667778888844
Q ss_pred h-HHHHHHHHHHHHHhhc-------chHHHhHHHHHHHHhhhhcc
Q 015212 335 A-KLELELMYKVQMQCYE-------DAKLMKLFPEIVRSLYDQDV 371 (411)
Q Consensus 335 ~-~~Ql~lL~alQ~~c~e-------~~~~~k~f~~IL~~LYd~DV 371 (411)
+ -.+-++..+++.+... .|+....+..++-.+--.|+
T Consensus 67 ~~~~~~~~~~~f~~~~~~l~dl~~D~P~a~~~la~~~a~~v~~~~ 111 (113)
T smart00544 67 NVISTKQFEKGFWRLLEDIEDLELDIPNAWRNLAEFVARLISDGI 111 (113)
T ss_pred CCcCHHHHHHHHHHHHhhChhhhcccccHHHHHHHHHHHHHHcCC
Confidence 3 4555566666655542 24454455544444444443
Done!