Query 009199
Match_columns 540
No_of_seqs 41 out of 43
Neff 2.5
Searched_HMMs 46136
Date Thu Mar 28 21:38:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009199.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009199hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04278 Tic22: Tic22-like fam 100.0 2.1E-30 4.5E-35 252.0 12.7 114 159-278 97-225 (274)
2 TIGR00995 3a0901s06TIC22 chlor 100.0 4.7E-29 1E-33 244.3 14.1 128 115-278 84-218 (270)
3 PF04278 Tic22: Tic22-like fam 95.3 0.026 5.7E-07 56.4 5.4 80 134-220 182-272 (274)
4 TIGR00995 3a0901s06TIC22 chlor 90.1 0.82 1.8E-05 46.6 6.7 64 159-222 194-269 (270)
5 PLN02701 alpha-mannosidase 72.0 2.2 4.7E-05 50.2 1.9 77 314-390 101-183 (1050)
6 PF01074 Glyco_hydro_38: Glyco 67.5 3.3 7.1E-05 39.8 1.8 124 263-394 17-145 (275)
7 cd03195 GST_C_4 GST_C family, 53.8 2 4.3E-05 36.4 -2.0 42 107-150 61-102 (114)
8 PF06506 PrpR_N: Propionate ca 49.9 1.4E+02 0.0031 27.4 9.2 118 159-292 53-176 (176)
9 cd06389 PBP1_iGluR_AMPA_GluR2 48.3 94 0.002 31.5 8.4 72 117-190 49-152 (370)
10 PRK06756 flavodoxin; Provision 46.9 1.4E+02 0.003 26.3 8.3 77 136-224 58-143 (148)
11 PF15652 Tox-SHH: HNH/Endo VII 46.3 30 0.00065 31.4 4.0 55 280-344 41-98 (100)
12 PF11360 DUF3110: Protein of u 45.6 64 0.0014 28.0 5.8 51 160-210 23-76 (86)
13 KOG0700 Protein phosphatase 2C 41.2 29 0.00063 37.5 3.7 51 471-521 166-223 (390)
14 cd03194 GST_C_3 GST_C family, 40.7 4.2 9.2E-05 34.6 -2.0 43 107-151 62-104 (114)
15 cd08057 MPN_euk_non_mb Mpr1p, 40.6 90 0.002 28.3 6.3 60 108-170 22-86 (157)
16 COG0050 TufB GTPases - transla 40.6 35 0.00077 36.7 4.2 35 316-350 153-200 (394)
17 PRK15429 formate hydrogenlyase 40.1 77 0.0017 35.2 6.9 85 225-323 109-206 (686)
18 cd06388 PBP1_iGluR_AMPA_GluR4 39.5 1.3E+02 0.0028 30.8 7.9 106 117-226 55-200 (371)
19 KOG1276 Protoporphyrinogen oxi 37.6 46 0.001 37.0 4.6 66 459-526 384-474 (491)
20 PF04392 ABC_sub_bind: ABC tra 36.9 1.9E+02 0.004 28.3 8.2 74 162-243 133-219 (294)
21 PRK07764 DNA polymerase III su 36.3 2.5E+02 0.0053 33.0 10.2 58 167-224 132-195 (824)
22 PRK13294 F420-0--gamma-glutamy 33.9 46 0.00099 36.0 3.9 113 183-309 162-281 (448)
23 PF08755 YccV-like: Hemimethyl 32.6 4.9 0.00011 34.8 -2.9 83 111-199 5-90 (100)
24 PF04305 DUF455: Protein of un 32.6 88 0.0019 31.7 5.4 50 308-362 162-211 (253)
25 KOG0922 DEAH-box RNA helicase 32.6 5.8E+02 0.013 29.9 12.1 158 159-340 380-594 (674)
26 PF07862 Nif11: Nitrogen fixat 31.4 19 0.00041 27.1 0.4 39 167-205 1-43 (49)
27 cd06387 PBP1_iGluR_AMPA_GluR3 30.8 1.8E+02 0.0038 30.3 7.3 92 132-226 85-201 (372)
28 PF02829 3H: 3H domain; Inter 30.8 57 0.0012 28.9 3.3 49 168-225 45-95 (98)
29 KOG1579 Homocysteine S-methylt 30.2 80 0.0017 33.5 4.8 45 189-241 141-195 (317)
30 PLN03083 E3 UFM1-protein ligas 28.2 84 0.0018 37.0 4.9 179 124-362 132-331 (803)
31 PF11859 DUF3379: Protein of u 27.7 67 0.0015 32.6 3.6 49 290-353 7-65 (232)
32 TIGR02196 GlrX_YruB Glutaredox 27.4 1E+02 0.0022 22.5 3.7 42 195-243 17-58 (74)
33 PF01323 DSBA: DSBA-like thior 26.2 1.7E+02 0.0036 26.0 5.5 44 265-308 87-134 (193)
34 cd08045 TAF4 TATA Binding Prot 26.1 86 0.0019 30.2 3.9 54 306-359 39-99 (212)
35 PRK15113 glutathione S-transfe 25.8 11 0.00024 34.7 -2.0 42 107-150 156-197 (214)
36 COG4058 McrA Methyl coenzyme M 25.8 2.1E+02 0.0046 31.7 7.0 99 213-326 43-141 (553)
37 PRK10329 glutaredoxin-like pro 25.6 1.7E+02 0.0036 24.2 5.0 59 193-272 16-74 (81)
38 TIGR01165 cbiN cobalt transpor 25.2 61 0.0013 29.0 2.5 25 297-321 37-70 (91)
39 PRK05569 flavodoxin; Provision 24.7 4.1E+02 0.009 22.9 7.5 67 144-223 67-138 (141)
40 COG3935 DnaD Putative primosom 24.4 2.5E+02 0.0055 28.8 7.0 70 285-357 115-191 (246)
41 COG1105 FruK Fructose-1-phosph 24.4 27 0.00059 36.5 0.2 88 115-216 160-247 (310)
42 PRK00377 cbiT cobalt-precorrin 23.9 1.3E+02 0.0029 27.8 4.6 58 169-226 98-163 (198)
43 TIGR03537 DapC succinyldiamino 23.6 1.9E+02 0.004 28.7 5.8 50 171-223 300-349 (350)
44 PRK09756 PTS system N-acetylga 23.5 1.3E+02 0.0029 28.2 4.6 41 149-189 69-110 (158)
45 KOG0698 Serine/threonine prote 23.3 1E+02 0.0022 31.4 4.1 10 512-521 154-163 (330)
46 PF00481 PP2C: Protein phospha 22.8 58 0.0013 31.0 2.1 17 456-472 29-45 (254)
47 cd03204 GST_C_GDAP1 GST_C fami 22.8 16 0.00035 32.3 -1.5 48 104-151 54-107 (111)
48 PF00043 GST_C: Glutathione S- 22.8 13 0.00028 29.2 -1.9 45 107-151 46-93 (95)
49 PRK15088 PTS system mannose-sp 22.5 1.9E+02 0.004 30.2 5.8 43 147-189 225-269 (322)
50 TIGR00854 pts-sorbose PTS syst 21.5 1.2E+02 0.0026 28.3 3.8 56 160-222 76-134 (151)
51 PRK09819 alpha-mannosidase; Pr 20.6 63 0.0014 37.2 2.2 50 342-392 97-147 (875)
52 cd02976 NrdH NrdH-redoxin (Nrd 20.1 2E+02 0.0044 20.9 4.1 47 193-246 15-61 (73)
No 1
>PF04278 Tic22: Tic22-like family; InterPro: IPR007378 Chloroplast function requires the import of nuclear encoded proteins from the cytoplasm across the chloroplast double membrane. This is accompished by two protein complexes, the Toc complex located at the outer membrane and the Tic complex loacted at the inner membrane []. The Toc complex recognises specific proteins by a cleavable N-terminal sequence and is primarily responsible for translocation through the outer membrane, while the Tic complex translocates the protein through the inner membrane. This entry represents Tic22, a core member of the Tic complex. It is believed to act as a link between both protein complexes, contacting the translocated protein in the intermembrane space after transport through the Toc complex, and directing it to the Tic complex [].; PDB: 4EV1_A.
Probab=99.97 E-value=2.1e-30 Score=252.00 Aligned_cols=114 Identities=35% Similarity=0.493 Sum_probs=93.7
Q ss_pred CCceEEEEeehhHHHHHHHHhCCC------CceEEEeehhHHHHhhh-----cCCceeeEecCHHHHHHHHHHHHHCCCC
Q 009199 159 NGPVFRFFMDLGDAVTYVKQLNIP------SGVVGACRLDLAYEHFK-----EKPHLFQFVPNEKQVKAANKLLRTIPDS 227 (540)
Q Consensus 159 n~sV~~fFms~~DA~AyV~rLkkp------s~kVgpVSLd~aYE~~K-----ekpv~FrFVPdekQVKaAkkLLK~~GQg 227 (540)
+.+|+.|||+++||++||++|++. +++|+||+||+|||+++ .+++.|+|+|+++||++|++||++.|+
T Consensus 97 ~~~v~~~F~s~~dA~~~L~~lk~~~p~~~~~~kV~pvsL~~vY~l~~~~~~k~~~~~F~~vP~~~qV~~A~~ll~~~g~- 175 (274)
T PF04278_consen 97 GKSVGLFFFSQQDAEAFLAQLKKSNPELASGAKVVPVSLGKVYQLAQENKKKPEGLQFRFVPDPKQVEAALELLKKQGQ- 175 (274)
T ss_dssp -SEEEEEES-HHHHHHHHHHHHH-SSHHHTT-EEEEEEHHHHHHHHHHTTT-TT-EEEEEE--HHHHHHHHHHHHTTT--
T ss_pred CceEEEEEecHHHHHHHHHHHhhhCccccCceEEEEecHHHHHHHHHHhhcCCcCceEEEcCCHHHHHHHHHHHHhcCC-
Confidence 788999999999999999999874 78999999999999955 679999999999999999999999999
Q ss_pred CCCCCcCCceeeeeec----eeeeeeccCCCeeeeecccchhhHHHHHHHHHHHH
Q 009199 228 GRKKKVDGVPVFSAQN----LDIAIATADGIKWYTPYFFDKNMLDNILEESVDQH 278 (540)
Q Consensus 228 ~~~kqF~GVPVF~Ar~----LtIavat~dGnK~yiPlFFdKEDLD~iLEqsKdQ~ 278 (540)
.+++|+|||||++++ |+| +++++||||+||+||||+++|+++++|+
T Consensus 176 -~~~~f~GVPvF~~~~~~~~Lti----~~~~~~~iPlFF~kedL~~~l~k~~kq~ 225 (274)
T PF04278_consen 176 -KVKQFQGVPVFYAEGGKGYLTI----KQDNKRIIPLFFDKEDLQAALEKAKKQQ 225 (274)
T ss_dssp ---S---S-EEEEEESST-B-EE----TTTTEEEEEEESSHHHHHHHHHHHTTT-
T ss_pred -CcccCCCeEEEEEcCCCceEEE----eeCCeEEEEEEecHHHHHHHHHHHHHhC
Confidence 669999999999999 988 6899999999999999999999998886
No 2
>TIGR00995 3a0901s06TIC22 chloroplast protein import component, Tic22 family. Two families of proteins are involved in the chloroplast envelope import appartus.They are the three proteins of the outer membrane (TOC) and four proteins in the inner membrane (TIC). This family is specific for the Tic22 protein.
Probab=99.96 E-value=4.7e-29 Score=244.26 Aligned_cols=128 Identities=23% Similarity=0.340 Sum_probs=113.2
Q ss_pred eeeecccCCCceeeeeeccccCcccccCHHHHHHHHhHHhccCCCCceEEEEeehhH-HHHHHHHhCCC------CceEE
Q 009199 115 VFSMCDLSGTGLMAVSTHFDIPFISKRTPEWLKKLFATITKSERNGPVFRFFMDLGD-AVTYVKQLNIP------SGVVG 187 (540)
Q Consensus 115 vfsmcd~sg~glmavst~f~iPfi~krt~~w~k~~~~~l~~se~n~sV~~fFms~~D-A~AyV~rLkkp------s~kVg 187 (540)
|||++|-.|.-|.+... +++.++++||+++| |++||++||+. +++|+
T Consensus 84 VFtItn~~G~pvl~s~~--------------------------~~~~~~gvf~s~qedA~afL~~lk~~~p~l~~~~kV~ 137 (270)
T TIGR00995 84 VFTVSNAQNEFVLASDN--------------------------DGEKSIGLLCFRQEDAEAFLAQLRKRKPEVGSQAKVV 137 (270)
T ss_pred eEEEEcCCCCeEEEECC--------------------------CCCceEEEEECCHHHHHHHHHHHHhhCccccCCceEE
Confidence 79999999998887633 35678899999886 99999999774 67999
Q ss_pred EeehhHHHHhhhcCCceeeEecCHHHHHHHHHHHHHCCCCCCCCCcCCceeeeeeceeeeeeccCCCeeeeecccchhhH
Q 009199 188 ACRLDLAYEHFKEKPHLFQFVPNEKQVKAANKLLRTIPDSGRKKKVDGVPVFSAQNLDIAIATADGIKWYTPYFFDKNML 267 (540)
Q Consensus 188 pVSLd~aYE~~Kekpv~FrFVPdekQVKaAkkLLK~~GQg~~~kqF~GVPVF~Ar~LtIavat~dGnK~yiPlFFdKEDL 267 (540)
||+||+|||+ +.+++.|+|+|+++||++|++|+ +.++ +.|+|||||++..||| +++|++|||+||+||||
T Consensus 138 pvsL~~vYkl-~~e~l~F~fiP~~~qV~~A~~ll-~~~~----~~~~GVPlF~~~~Lti----~~~n~~~iP~FF~Kedl 207 (270)
T TIGR00995 138 PITLDQVYKL-KVEGIGFRFLPDPAQIKNALELP-AANS----EYFDGVPVFQSGLLVV----QKKNERYCPVYFSKEDI 207 (270)
T ss_pred EEEHHHHHHH-hhcCccEEEeCCHHHHHHHHHHH-hcCc----cCCCCccEEeecceEE----EeCCeEEEeeEeeHHHH
Confidence 9999999999 45559999999999999999999 3334 6678999999999999 69999999999999999
Q ss_pred HHHHHHHHHHH
Q 009199 268 DNILEESVDQH 278 (540)
Q Consensus 268 D~iLEqsKdQ~ 278 (540)
|++|+++++|+
T Consensus 208 q~~L~~~kkq~ 218 (270)
T TIGR00995 208 EQELSKFKRES 218 (270)
T ss_pred HHHHHHHhHhC
Confidence 99999999885
No 3
>PF04278 Tic22: Tic22-like family; InterPro: IPR007378 Chloroplast function requires the import of nuclear encoded proteins from the cytoplasm across the chloroplast double membrane. This is accompished by two protein complexes, the Toc complex located at the outer membrane and the Tic complex loacted at the inner membrane []. The Toc complex recognises specific proteins by a cleavable N-terminal sequence and is primarily responsible for translocation through the outer membrane, while the Tic complex translocates the protein through the inner membrane. This entry represents Tic22, a core member of the Tic complex. It is believed to act as a link between both protein complexes, contacting the translocated protein in the intermembrane space after transport through the Toc complex, and directing it to the Tic complex [].; PDB: 4EV1_A.
Probab=95.34 E-value=0.026 Score=56.37 Aligned_cols=80 Identities=15% Similarity=0.276 Sum_probs=59.0
Q ss_pred ccC-cccccCHHHHHHHHhHHhccCCCCceEEEEeehhHHHHHHHHhCCC------CceEEEeehhHHHHhhhcC----C
Q 009199 134 DIP-FISKRTPEWLKKLFATITKSERNGPVFRFFMDLGDAVTYVKQLNIP------SGVVGACRLDLAYEHFKEK----P 202 (540)
Q Consensus 134 ~iP-fi~krt~~w~k~~~~~l~~se~n~sV~~fFms~~DA~AyV~rLkkp------s~kVgpVSLd~aYE~~Kek----p 202 (540)
+|| |+.+-.+ .-|+....+..+.=+||+++|+++.+++.++. +.+|..++|..+-+.++++ -
T Consensus 182 GVPvF~~~~~~-------~~Lti~~~~~~~iPlFF~kedL~~~l~k~~kq~p~~~~~~~I~V~~Le~vI~~m~~~~d~~~ 254 (274)
T PF04278_consen 182 GVPVFYAEGGK-------GYLTIKQDNKRIIPLFFDKEDLQAALEKAKKQQPDLAKEPKIQVVSLEDVIKTMEESDDSDL 254 (274)
T ss_dssp S-EEEEEESST--------B-EETTTTEEEEEEESSHHHHHHHHHHHTTT-TT-----EEEEEEHHHHHHHHHH---GGG
T ss_pred CeEEEEEcCCC-------ceEEEeeCCeEEEEEEecHHHHHHHHHHHHHhCCCCcCCceEEEEcHHHHHHHHhcCCCCCc
Confidence 499 8888877 22344445778899999999999999999774 5789999999999998833 4
Q ss_pred ceeeEecCHHHHHHHHHH
Q 009199 203 HLFQFVPNEKQVKAANKL 220 (540)
Q Consensus 203 v~FrFVPdekQVKaAkkL 220 (540)
-.|.|||..+.++-++++
T Consensus 255 ~~i~fiP~~es~~~i~~~ 272 (274)
T PF04278_consen 255 KKIVFIPPGESLEFIQSL 272 (274)
T ss_dssp GGEEEE--HHHHHHHHTS
T ss_pred ceEEEECCHHHHHHHHHh
Confidence 489999999988877554
No 4
>TIGR00995 3a0901s06TIC22 chloroplast protein import component, Tic22 family. Two families of proteins are involved in the chloroplast envelope import appartus.They are the three proteins of the outer membrane (TOC) and four proteins in the inner membrane (TIC). This family is specific for the Tic22 protein.
Probab=90.07 E-value=0.82 Score=46.63 Aligned_cols=64 Identities=9% Similarity=0.160 Sum_probs=51.6
Q ss_pred CCceEEEEeehhHHHHHHHHhCCC------CceEEEeehhHHHHhhhcC------CceeeEecCHHHHHHHHHHHH
Q 009199 159 NGPVFRFFMDLGDAVTYVKQLNIP------SGVVGACRLDLAYEHFKEK------PHLFQFVPNEKQVKAANKLLR 222 (540)
Q Consensus 159 n~sV~~fFms~~DA~AyV~rLkkp------s~kVgpVSLd~aYE~~Kek------pv~FrFVPdekQVKaAkkLLK 222 (540)
|..+.=|||+++|+++.|+++++. +.+|..++|+.+-+.+++. --.-.|+|.+.-++-..++.+
T Consensus 194 n~~~iP~FF~Kedlq~~L~~~kkq~p~l~~~~~I~V~~Le~vi~~m~~~~~~~~~~~~I~l~Ps~e~~~~iq~~~~ 269 (270)
T TIGR00995 194 NERYCPVYFSKEDIEQELSKFKRESPGMADSQVIMVGSMEDVLSKMETSEKDSGWEDQIFIPPGQEAIQHMQSLIA 269 (270)
T ss_pred CeEEEeeEeeHHHHHHHHHHHhHhCcCcCCCccEEEEeHHHHHHHHhccCCCCcccceEEECCCHHHHHHHHHHhc
Confidence 455677999999999999999773 6789999999999999852 225679999988887766643
No 5
>PLN02701 alpha-mannosidase
Probab=72.04 E-value=2.2 Score=50.22 Aligned_cols=77 Identities=21% Similarity=0.359 Sum_probs=55.8
Q ss_pred ChhHHHHHHHhCCCC-----CchHHHHHHHHHHHHHHHHHHhhcchHHHHhhCCCCCCcccccccchh-hhHhhhhhccc
Q 009199 314 PPEVQEMMDEIGHPA-----IPLSVISKAAEIQLLYAVDRVLLGNRWLRKATGIQPKFPYMVDSFENR-SAASFLRASES 387 (540)
Q Consensus 314 ppEvqe~~~e~g~~~-----i~~sv~~kaae~q~~~~vdrvllgn~w~rk~~giqp~fp~~vDSFErr-sa~s~~ras~s 387 (540)
.||.++-+..+=..| .|.=|+.-.|-....+++|.++.|++|+++.+|+-|+.=+.+|+|=-= +-..|.+-..=
T Consensus 101 ~pe~~~~vk~LV~~GrLE~vgGgwvm~DEa~~~~esiI~Ql~~G~~~l~~~fG~~P~~~W~iDpFGhs~~~P~Ll~~~G~ 180 (1050)
T PLN02701 101 SPSKKEAFTKLVKNGQLEIVGGGWVMNDEANSHYFAIIEQITEGNMWLNDTIGVAPKNSWAIDPFGYSSTMAYLLRRMGF 180 (1050)
T ss_pred CHHHHHHHHHHHHcCCEEEECCceecccccccCHHHHHHHHHhhhHHHHhhcCCCCCcCccCCCCCCCHHHHHHHHhCCC
Confidence 466666554442222 344566677888889999999999999999999999999999999765 45555555544
Q ss_pred ccc
Q 009199 388 TSC 390 (540)
Q Consensus 388 ~s~ 390 (540)
...
T Consensus 181 ~~~ 183 (1050)
T PLN02701 181 ENM 183 (1050)
T ss_pred ceE
Confidence 443
No 6
>PF01074 Glyco_hydro_38: Glycosyl hydrolases family 38 N-terminal domain; InterPro: IPR000602 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 38 GH38 from CAZY comprises enzymes with only one known activity; alpha-mannosidase (3.2.1.24 from EC) (3.2.1.114 from EC). Lysosomal alpha-mannosidase is necessary for the catabolism of N-linked carbohydrates released during glycoprotein turnover. The enzyme catalyses the hydrolysis of terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides, and can cleave all known types of alpha-mannosidic linkages. Defects in the gene cause lysosomal alpha-mannosidosis (AM), a lysosomal storage disease characterised by the accumulation of unbranched oligo-saccharide chains.; GO: 0004559 alpha-mannosidase activity, 0005975 carbohydrate metabolic process; PDB: 2WYI_A 2WYH_A 1O7D_A 3CZN_A 2FYV_A 3D50_A 3EJU_A 3EJS_A 3DX3_A 3BVX_A ....
Probab=67.46 E-value=3.3 Score=39.84 Aligned_cols=124 Identities=19% Similarity=0.221 Sum_probs=67.7
Q ss_pred chhhHHHHHHHHHHHHHHHHHhhhhhhhccccccchhhHHHHHHhccCCCCChhHHHHHHHhCCCCC----chHHHHHHH
Q 009199 263 DKNMLDNILEESVDQHFHALIQTRHMQRRRDVIDDNLAAEVVEEIGDSIWEPPEVQEMMDEIGHPAI----PLSVISKAA 338 (540)
Q Consensus 263 dKEDLD~iLEqsKdQ~fh~liq~Rh~qRrrdv~ddn~~~Ev~ee~~dslleppEvqe~~~e~g~~~i----~~sv~~kaa 338 (540)
.-++....+.+..++....|-+.- +++ .++ ....++|+..+. .|.+..++.+-+-.+-| |.-+..=.+
T Consensus 17 t~~~~~~~~~~~~~~~l~~l~~~~---~~~-f~~--~~~~~~~~~~~~--~p~~~~~~~~lv~~Gri~~vgg~~~~~D~~ 88 (275)
T PF01074_consen 17 TFEEYRRYLVNILDSVLDLLEEDP---DFR-FID--GQTAYLEDYLED--APEEFKRIKKLVKEGRIEIVGGWYVQPDEN 88 (275)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHH-T---T---EEC--TBCHHHHHHHHC--SGHHHHHHHHHHHTTSEEESSSBSS-B-SS
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCC---cce-Eee--chhHHHHHHHHh--CCHHHHHHHHHHHhceeEEeCceeeecccc
Confidence 344445555555555544443222 222 344 335566666665 66666555443322221 222223333
Q ss_pred HHHHHHHHHHHhhcchHHHHhhCCCCCCcccccccchh-hhHhhhhhcccccccccC
Q 009199 339 EIQLLYAVDRVLLGNRWLRKATGIQPKFPYMVDSFENR-SAASFLRASESTSCLANS 394 (540)
Q Consensus 339 e~q~~~~vdrvllgn~w~rk~~giqp~fp~~vDSFErr-sa~s~~ras~s~s~~~~s 394 (540)
-...-.+++..+.|.+|+|+..|..|+.=|++|+|=-= .-..|.+.+.-...+.+-
T Consensus 89 l~~~Eslirql~~G~~~~~~~fg~~~~~~~~~D~FG~~~~lP~il~~~Gi~~~v~~r 145 (275)
T PF01074_consen 89 LPSGESLIRQLLYGHKYLRKEFGVRPKVAWQPDSFGHSAQLPQILKQFGIKYFVIWR 145 (275)
T ss_dssp SS-HHHHHHHHHHHHHHHHHHHTG--SEEEESSSSSB-TCHHHHHHTTT-SEEEESS
T ss_pred CCCHHHHHHHHhhhHHHHHHhcCCCCCeEEeCCCCCCchhhHHHHhccCcceEEEec
Confidence 34445678889999999999999999999999999765 455666666665554443
No 7
>cd03195 GST_C_4 GST_C family, unknown subfamily 4; composed of uncharacterized proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain.
Probab=53.76 E-value=2 Score=36.36 Aligned_cols=42 Identities=12% Similarity=0.297 Sum_probs=26.1
Q ss_pred CCccceeeeeeecccCCCceeeeeeccccCcccccCHHHHHHHH
Q 009199 107 GGPAFVGQVFSMCDLSGTGLMAVSTHFDIPFISKRTPEWLKKLF 150 (540)
Q Consensus 107 ggpafvgqvfsmcd~sg~glmavst~f~iPfi~krt~~w~k~~~ 150 (540)
|+|-++|+ ||++|+.=.-+..-..+++++. +...-.|++||+
T Consensus 61 ~~~~l~G~-fSiAD~~l~~~~~~~~~~g~~l-~p~l~ay~~r~~ 102 (114)
T cd03195 61 GAANLFGE-WCIADTDLALMLNRLVLNGDPV-PERLRDYARRQW 102 (114)
T ss_pred CCCcccCC-ccHHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHH
Confidence 56899996 9999987544443334555543 234445666654
No 8
>PF06506 PrpR_N: Propionate catabolism activator; InterPro: IPR010524 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate. In Salmonella enterica subsp. enterica serovar Typhimurium, PrpR acts as a sensor of 2-methylcitrate (2-MC), an intermediate of the 2-methylcitric acid cycle used by this bacterium to convert propionate to pyruvate []. ; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay); PDB: 2Q5C_A 2PJU_A.
Probab=49.92 E-value=1.4e+02 Score=27.45 Aligned_cols=118 Identities=14% Similarity=0.102 Sum_probs=73.7
Q ss_pred CCceEEEEeehhHHHHHHHHhCCCCceEEEeehhHHHHhhh------cCCceeeEecCHHHHHHHHHHHHHCCCCCCCCC
Q 009199 159 NGPVFRFFMDLGDAVTYVKQLNIPSGVVGACRLDLAYEHFK------EKPHLFQFVPNEKQVKAANKLLRTIPDSGRKKK 232 (540)
Q Consensus 159 n~sV~~fFms~~DA~AyV~rLkkps~kVgpVSLd~aYE~~K------ekpv~FrFVPdekQVKaAkkLLK~~GQg~~~kq 232 (540)
+.||..+=++-.|-...|.+.+..+-+|+-|.......-+. .-.+.+..+-++.++..+.+-++..
T Consensus 53 ~iPVV~I~~s~~Dil~al~~a~~~~~~Iavv~~~~~~~~~~~~~~ll~~~i~~~~~~~~~e~~~~i~~~~~~-------- 124 (176)
T PF06506_consen 53 SIPVVEIPISGFDILRALAKAKKYGPKIAVVGYPNIIPGLESIEELLGVDIKIYPYDSEEEIEAAIKQAKAE-------- 124 (176)
T ss_dssp SS-EEEE---HHHHHHHHHHCCCCTSEEEEEEESS-SCCHHHHHHHHT-EEEEEEESSHHHHHHHHHHHHHT--------
T ss_pred CCCEEEECCCHhHHHHHHHHHHhcCCcEEEEecccccHHHHHHHHHhCCceEEEEECCHHHHHHHHHHHHHc--------
Confidence 67788888888888888888877777888777655543222 2245555667788888877766663
Q ss_pred cCCceeeeeeceeeeeeccCCCeeeeecccchhhHHHHHHHHHHHHHHHHHhhhhhhhcc
Q 009199 233 VDGVPVFSAQNLDIAIATADGIKWYTPYFFDKNMLDNILEESVDQHFHALIQTRHMQRRR 292 (540)
Q Consensus 233 F~GVPVF~Ar~LtIavat~dGnK~yiPlFFdKEDLD~iLEqsKdQ~fh~liq~Rh~qRrr 292 (540)
|+=||.--+++..++-+-|-+ ++++.=.++-+...|+++.. +++.++.+|+|
T Consensus 125 --G~~viVGg~~~~~~A~~~gl~-~v~i~sg~esi~~Al~eA~~-----i~~~~~~ek~r 176 (176)
T PF06506_consen 125 --GVDVIVGGGVVCRLARKLGLP-GVLIESGEESIRRALEEALR-----IARARRREKER 176 (176)
T ss_dssp --T--EEEESHHHHHHHHHTTSE-EEESS--HHHHHHHHHHHHH-----HHHHHHH----
T ss_pred --CCcEEECCHHHHHHHHHcCCc-EEEEEecHHHHHHHHHHHHH-----HHHHHHHhccC
Confidence 444666666666666666666 89998889999999998864 56666666654
No 9
>cd06389 PBP1_iGluR_AMPA_GluR2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=48.27 E-value=94 Score=31.52 Aligned_cols=72 Identities=15% Similarity=0.247 Sum_probs=41.7
Q ss_pred eecccCCCceeeee---------------eccccCcccc-------------cCHHHHHHHHhHHhccCCCCceEEEEee
Q 009199 117 SMCDLSGTGLMAVS---------------THFDIPFISK-------------RTPEWLKKLFATITKSERNGPVFRFFMD 168 (540)
Q Consensus 117 smcd~sg~glmavs---------------t~f~iPfi~k-------------rt~~w~k~~~~~l~~se~n~sV~~fFms 168 (540)
.+|++-..|++||- ..++||||.- ..|. +-+.+..+.+.-.-..|+-+| +
T Consensus 49 ~~C~~~~~GV~AI~Gp~ss~~~~~v~~i~~~~~IP~I~~~~~~~~~~~f~~~~~p~-~~~ai~d~i~~~~wk~vailY-d 126 (370)
T cd06389 49 AFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQMRPD-LKGALLSLIEYYQWDKFAYLY-D 126 (370)
T ss_pred HHHHHhhcCcEEEEecCCHHHHHHHHHhhccCCCCeeeecCCCCCCCceEEEecch-hhhHHHHHHHhcCCcEEEEEe-c
Confidence 35777777777653 3788888863 3455 555555666555556677777 4
Q ss_pred hhHHH----HHHHHhCCCCceEEEee
Q 009199 169 LGDAV----TYVKQLNIPSGVVGACR 190 (540)
Q Consensus 169 ~~DA~----AyV~rLkkps~kVgpVS 190 (540)
-++.. ++++.++..+.+|..+.
T Consensus 127 sd~gl~~lq~l~~~~~~~g~~V~~~~ 152 (370)
T cd06389 127 SDRGLSTLQAVLDSAAEKKWQVTAIN 152 (370)
T ss_pred CchHHHHHHHHHHhhccCCceEEEEE
Confidence 33333 44444444565555433
No 10
>PRK06756 flavodoxin; Provisional
Probab=46.89 E-value=1.4e+02 Score=26.27 Aligned_cols=77 Identities=13% Similarity=0.149 Sum_probs=47.5
Q ss_pred Cccc-ccCHHHHHHHHhHHhccCCCCceEEEEee----h---hHHHHHHH-HhCCCCceEEEeehhHHHHhhhcCCceee
Q 009199 136 PFIS-KRTPEWLKKLFATITKSERNGPVFRFFMD----L---GDAVTYVK-QLNIPSGVVGACRLDLAYEHFKEKPHLFQ 206 (540)
Q Consensus 136 Pfi~-krt~~w~k~~~~~l~~se~n~sV~~fFms----~---~DA~AyV~-rLkkps~kVgpVSLd~aYE~~Kekpv~Fr 206 (540)
|.+. .+.|.-++..+..|.....++....+|.+ + .+|...+. .|.+...+|. .+++.+.
T Consensus 58 pt~~~g~~p~~~~~fl~~l~~~~l~~k~~~~fgt~~~~y~~~~~a~~~l~~~l~~~g~~~v------------~~~~~~~ 125 (148)
T PRK06756 58 YTWGDGDLPDDFLDFYDAMDSIDLTGKKAAVFGSCDSAYPKYGVAVDILIEKLQERGAAVV------------LEGLKVE 125 (148)
T ss_pred CCCCCCCCcHHHHHHHHHHhcCCCCCCEEEEEeCCCCchHHHHHHHHHHHHHHHHCCCEEc------------CCCeEEe
Confidence 5443 44555466666667655556667777766 2 24444333 4444444443 3367888
Q ss_pred EecCHHHHHHHHHHHHHC
Q 009199 207 FVPNEKQVKAANKLLRTI 224 (540)
Q Consensus 207 FVPdekQVKaAkkLLK~~ 224 (540)
+-|++..++.+.++.++.
T Consensus 126 ~~p~~~d~~~~~~~~~~~ 143 (148)
T PRK06756 126 LTPEDEDVEKCLQFGAEF 143 (148)
T ss_pred cCCCHHHHHHHHHHHHHH
Confidence 999999999988887654
No 11
>PF15652 Tox-SHH: HNH/Endo VII superfamily toxin with a SHH signature
Probab=46.30 E-value=30 Score=31.40 Aligned_cols=55 Identities=22% Similarity=0.294 Sum_probs=38.0
Q ss_pred HHHHhh-hhhhhccccccch--hhHHHHHHhccCCCCChhHHHHHHHhCCCCCchHHHHHHHHHHHHH
Q 009199 280 HALIQT-RHMQRRRDVIDDN--LAAEVVEEIGDSIWEPPEVQEMMDEIGHPAIPLSVISKAAEIQLLY 344 (540)
Q Consensus 280 h~liq~-Rh~qRrrdv~ddn--~~~Ev~ee~~dslleppEvqe~~~e~g~~~i~~sv~~kaae~q~~~ 344 (540)
|+.|.+ -++||.|....-+ ...-+-+ |+|++.+||=..|+|-+...||.+.|..|
T Consensus 41 Ha~isaa~~~~r~~r~~~g~gkw~t~~~~----------Ef~~~~~eM~dAGV~~~~~~~~l~~~Yky 98 (100)
T PF15652_consen 41 HAIISAAQNAQRDERTAKGGGKWSTTLQE----------EFNNSYREMFDAGVSKECRKKALKAQYKY 98 (100)
T ss_pred hHHHHHHHHHHHHHHhcCCCCCccchHHH----------HHHHHHHHHHHcCCCHHHHHHHHHHHHhh
Confidence 788876 3344444443322 2333333 48999999888999999999999988765
No 12
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=45.65 E-value=64 Score=28.02 Aligned_cols=51 Identities=22% Similarity=0.216 Sum_probs=45.2
Q ss_pred CceEEEEeehhHHHHHHHHhCCC---CceEEEeehhHHHHhhhcCCceeeEecC
Q 009199 160 GPVFRFFMDLGDAVTYVKQLNIP---SGVVGACRLDLAYEHFKEKPHLFQFVPN 210 (540)
Q Consensus 160 ~sV~~fFms~~DA~AyV~rLkkp---s~kVgpVSLd~aYE~~Kekpv~FrFVPd 210 (540)
..+..+|=+++||+.|-..|... .-.|..|...+|..+-++-+..+++||.
T Consensus 23 ~~~Vl~FE~edDA~RYa~lLEAqd~~~p~Ve~id~~~i~~fC~~~gy~~~iv~~ 76 (86)
T PF11360_consen 23 RNVVLMFEDEDDAERYAGLLEAQDFPDPTVEEIDPEEIEEFCRSAGYEYEIVPP 76 (86)
T ss_pred CCEEEEEccHHHHHHHHHHHHhcCCCCCCeEEECHHHHHHHHHHCCceEEEECC
Confidence 45788999999999999999653 5589999999999999999999999985
No 13
>KOG0700 consensus Protein phosphatase 2C/pyruvate dehydrogenase (lipoamide) phosphatase [Signal transduction mechanisms]
Probab=41.23 E-value=29 Score=37.54 Aligned_cols=51 Identities=24% Similarity=0.231 Sum_probs=28.8
Q ss_pred cccchHHHHHHHHHHHHHH----HhhhhcccCCCCCCCc---ccCCCCceEEeecCcc
Q 009199 471 GQMTKANLKKTMENLTKEL----EQTDQENATSSGSNEY---IIEDRDPLFVANVGGY 521 (540)
Q Consensus 471 gqmskanlkktMedltkel----E~~~~~~~~~~gs~~~---~~~drdPLFvANvg~y 521 (540)
.+++..-|+|+.+.+.+++ ++..+.+..-.-++.| -.-..+=|+|||+||=
T Consensus 166 ~~~v~~al~~Af~~tee~fl~~v~~~~~~~p~lA~~GSC~Lv~~i~~~~LyVaN~GDS 223 (390)
T KOG0700|consen 166 HGDVLEALSKAFEATEEDFLEMVDKQLQENPELALVGSCCLVGLIKGGDLYVANVGDS 223 (390)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHhhccchhhhhhcceEEEEEEeCCeEEEEecCcc
Confidence 3566666666655555444 6666665432222223 2233445999999995
No 14
>cd03194 GST_C_3 GST_C family, unknown subfamily 3; composed of uncharacterized proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain.
Probab=40.67 E-value=4.2 Score=34.57 Aligned_cols=43 Identities=23% Similarity=0.488 Sum_probs=28.3
Q ss_pred CCccceeeeeeecccCCCceeeeeeccccCcccccCHHHHHHHHh
Q 009199 107 GGPAFVGQVFSMCDLSGTGLMAVSTHFDIPFISKRTPEWLKKLFA 151 (540)
Q Consensus 107 ggpafvgqvfsmcd~sg~glmavst~f~iPfi~krt~~w~k~~~~ 151 (540)
||+-++|. ||.+|+.=-+++.-...++++.. ...-.|++|+.+
T Consensus 62 ~~~yl~Gd-~T~ADi~l~~~~~~~~~~~~~~~-P~l~~~~~rv~~ 104 (114)
T cd03194 62 GGPFLFGD-FSIADAFFAPVVTRFRTYGLPLS-PAAQAYVDALLA 104 (114)
T ss_pred CCCCCCCC-CcHHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHC
Confidence 56789999 99999875555443345555522 455567777654
No 15
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=40.62 E-value=90 Score=28.34 Aligned_cols=60 Identities=17% Similarity=0.313 Sum_probs=48.0
Q ss_pred CccceeeeeeecccCCCceeeeeeccccCccccc-----CHHHHHHHHhHHhccCCCCceEEEEeehh
Q 009199 108 GPAFVGQVFSMCDLSGTGLMAVSTHFDIPFISKR-----TPEWLKKLFATITKSERNGPVFRFFMDLG 170 (540)
Q Consensus 108 gpafvgqvfsmcd~sg~glmavst~f~iPfi~kr-----t~~w~k~~~~~l~~se~n~sV~~fFms~~ 170 (540)
.+..+|+.+-..+ .|-+-|++-|.+|+-... -.+++++|+.-+.+--.+-.+.|+|-.-.
T Consensus 22 ~~~v~G~LlG~~~---~~~veV~nsF~lp~~~~~~~~~~d~~y~~~m~~~~~~v~~~~~vVGWY~~~~ 86 (157)
T cd08057 22 IKRVIGVLLGYVD---GDKIEVTNSFELPFDEEEESIFIDTEYLEKRYNLHKKVYPQEKIVGWYSIGS 86 (157)
T ss_pred CCeEEEEEEeEEe---CCEEEEEEeEEccccCCCcchhhhHHHHHHHHHHHHHhCCCCCEEEEEeecC
Confidence 4567888888887 568889999999985543 38899999999988887878888886554
No 16
>COG0050 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]
Probab=40.62 E-value=35 Score=36.68 Aligned_cols=35 Identities=40% Similarity=0.589 Sum_probs=27.0
Q ss_pred hHHHHHHHhCCCCC--ch--HHHHHHHH---------HHHHHHHHHHh
Q 009199 316 EVQEMMDEIGHPAI--PL--SVISKAAE---------IQLLYAVDRVL 350 (540)
Q Consensus 316 Evqe~~~e~g~~~i--~~--sv~~kaae---------~q~~~~vdrvl 350 (540)
||.||+++.|-+|- |. .--.||.| ..||++||.-|
T Consensus 153 EvreLLs~y~f~gd~~Pii~gSal~ale~~~~~~~~i~eLm~avd~yi 200 (394)
T COG0050 153 EVRELLSEYGFPGDDTPIIRGSALKALEGDAKWEAKIEELMDAVDSYI 200 (394)
T ss_pred HHHHHHHHcCCCCCCcceeechhhhhhcCCcchHHHHHHHHHHHHhcC
Confidence 69999999999853 33 33568888 88999998754
No 17
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=40.07 E-value=77 Score=35.18 Aligned_cols=85 Identities=11% Similarity=0.179 Sum_probs=48.5
Q ss_pred CCCCCCCCcCCceeeeeec----eeeeeeccCCCeeeeecccchhhHHHH------HH---HHHHHHHHHHHhhhhhhhc
Q 009199 225 PDSGRKKKVDGVPVFSAQN----LDIAIATADGIKWYTPYFFDKNMLDNI------LE---ESVDQHFHALIQTRHMQRR 291 (540)
Q Consensus 225 GQg~~~kqF~GVPVF~Ar~----LtIavat~dGnK~yiPlFFdKEDLD~i------LE---qsKdQ~fh~liq~Rh~qRr 291 (540)
+...+...|=||||....- |.+ ..|.+--|+.+|+.-+ +. +-...+.++..+.|+.+|+
T Consensus 109 ~~~~~~~~~lgvPl~~~~~v~G~l~l--------~~~~~~~Ft~~d~~ll~~la~~a~~aie~~~~~e~~~~~~~~L~~~ 180 (686)
T PRK15429 109 GLYPKFGHYCLMPLAAEGHIFGGCEF--------IRYDDRPWSEKEFNRLQTFTQIVSVVTEQIQSRVVNNVDYELLCRE 180 (686)
T ss_pred ccccCccceEEeceeeCCeeEEEEEE--------EEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4445667789999998442 555 1245778999995444 11 1224455666667777888
Q ss_pred cccccchhhHHHHHHhccCCCCChhHHHHHHH
Q 009199 292 RDVIDDNLAAEVVEEIGDSIWEPPEVQEMMDE 323 (540)
Q Consensus 292 rdv~ddn~~~Ev~ee~~dslleppEvqe~~~e 323 (540)
|+- -+++-|+...|+--.+..|+++.
T Consensus 181 r~~------~~~L~eIs~~l~s~~dl~ell~~ 206 (686)
T PRK15429 181 RDN------FRILVAITNAVLSRLDMDELVSE 206 (686)
T ss_pred HHH------HHHHHHHHHHHccCCCHHHHHHH
Confidence 854 22344444444444444444443
No 18
>cd06388 PBP1_iGluR_AMPA_GluR4 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=39.49 E-value=1.3e+02 Score=30.80 Aligned_cols=106 Identities=13% Similarity=0.197 Sum_probs=53.4
Q ss_pred eecccCCCceeeeee---------------ccccCcccc-------------cCHHHHHHHHhHHhccCCCCceEEEEee
Q 009199 117 SMCDLSGTGLMAVST---------------HFDIPFISK-------------RTPEWLKKLFATITKSERNGPVFRFFMD 168 (540)
Q Consensus 117 smcd~sg~glmavst---------------~f~iPfi~k-------------rt~~w~k~~~~~l~~se~n~sV~~fFms 168 (540)
.+|++-..|+.||-. .++||+|+- ..|. +.+.+..+.+.-.-..++-+| +
T Consensus 55 ~~C~~~~~gV~AI~Gp~ss~~~~~v~~i~~~~~IP~I~~~~~~~~~~~f~i~~~p~-~~~a~~~~i~~~~wk~vaiiY-d 132 (371)
T cd06388 55 AFCSQYSRGVFAIFGLYDKRSVHTLTSFCSALHISLITPSFPTEGESQFVLQLRPS-LRGALLSLLDHYEWNRFVFLY-D 132 (371)
T ss_pred HHHHHHhCCceEEEecCCHHHHHHHHHHhhCCCCCeeecCccccCCCceEEEeChh-hhhHHHHHHHhcCceEEEEEe-c
Confidence 357777777766532 788888863 2444 333344454444345555555 4
Q ss_pred hhH----HHHHHHHhCCCCceEEEeeh----h-HHHHhhh---cCCceeeEecCHHHHHHHHHHHHHCCC
Q 009199 169 LGD----AVTYVKQLNIPSGVVGACRL----D-LAYEHFK---EKPHLFQFVPNEKQVKAANKLLRTIPD 226 (540)
Q Consensus 169 ~~D----A~AyV~rLkkps~kVgpVSL----d-~aYE~~K---ekpv~FrFVPdekQVKaAkkLLK~~GQ 226 (540)
.+| +++|++.++..+++|..+.. + +.-..++ ..+--.-+++.. .+.|..++++..+
T Consensus 133 ~~~~~~~lq~l~~~~~~~g~~v~~~~~~~~~~~d~~~~L~~ik~~~~~~iil~~~--~~~~~~il~qa~~ 200 (371)
T cd06388 133 TDRGYSILQAIMEKAGQNGWQVSAICVENFNDASYRRLLEDLDRRQEKKFVIDCE--IERLQNILEQIVS 200 (371)
T ss_pred CCccHHHHHHHHHhhHhcCCeeeeEEeccCCcHHHHHHHHHhcccccEEEEEECC--HHHHHHHHHHHHh
Confidence 333 45555555555655554221 1 1222222 223333355555 3445567766544
No 19
>KOG1276 consensus Protoporphyrinogen oxidase [Coenzyme transport and metabolism]
Probab=37.64 E-value=46 Score=36.98 Aligned_cols=66 Identities=21% Similarity=0.330 Sum_probs=44.0
Q ss_pred eee-EEeeecCcccccchHHHHHHHHHHHHHHHhhhhcccCCCCCCCc----------------------ccCCCC--ce
Q 009199 459 KVT-MVGISTGEAGQMTKANLKKTMENLTKELEQTDQENATSSGSNEY----------------------IIEDRD--PL 513 (540)
Q Consensus 459 KiT-MvGiS~ge~gqmskanlkktMedltkelE~~~~~~~~~~gs~~~----------------------~~~drd--PL 513 (540)
|+| |+|+++-.-+-.-+.+=+.+.+..|+.|.+....-..-..++.+ ...+.. ||
T Consensus 384 ~vtvm~gg~~~~n~~~~~~S~ee~~~~v~~alq~~Lgi~~~P~~~~v~l~~~ciPqy~vGh~~~le~a~~~l~~~~g~~l 463 (491)
T KOG1276|consen 384 KVTVMMGGGGSTNTSLAVPSPEELVNAVTSALQKMLGISNKPVSVNVHLWKNCIPQYTVGHDDVLEAAKSMLTDSPGLGL 463 (491)
T ss_pred eEEEEecccccccCcCCCCCHHHHHHHHHHHHHHHhCCCCCcccccceehhhcccceecchHHHHHHHHHHHHhCCCCce
Confidence 777 88999887666777777888888888888776553322222221 223333 88
Q ss_pred EEeecCccccccc
Q 009199 514 FVANVGGYYSGLA 526 (540)
Q Consensus 514 FvANvg~y~s~~~ 526 (540)
|+| |.||+|.+
T Consensus 464 ~l~--G~~y~Gv~ 474 (491)
T KOG1276|consen 464 FLG--GNHYGGVS 474 (491)
T ss_pred Eee--ccccCCCC
Confidence 886 88888853
No 20
>PF04392 ABC_sub_bind: ABC transporter substrate binding protein; InterPro: IPR007487 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.; PDB: 3LFT_A 3LKV_A.
Probab=36.94 E-value=1.9e+02 Score=28.32 Aligned_cols=74 Identities=19% Similarity=0.298 Sum_probs=32.6
Q ss_pred eEEEEeehhHH--HHHHHHhCC----CCceEEEeehh------HHHHhhhcCCceeeEecCHHHHHHH-HHHHHHCCCCC
Q 009199 162 VFRFFMDLGDA--VTYVKQLNI----PSGVVGACRLD------LAYEHFKEKPHLFQFVPNEKQVKAA-NKLLRTIPDSG 228 (540)
Q Consensus 162 V~~fFms~~DA--~AyV~rLkk----ps~kVgpVSLd------~aYE~~Kekpv~FrFVPdekQVKaA-kkLLK~~GQg~ 228 (540)
-.+++++..++ ...++.++. ..+++..+... .+.+.+.++.-.+-..++. -+.++ ..+++..-.
T Consensus 133 ~igvl~~~~~~~~~~~~~~~~~~a~~~g~~l~~~~v~~~~~~~~~~~~l~~~~da~~~~~~~-~~~~~~~~i~~~~~~-- 209 (294)
T PF04392_consen 133 RIGVLYDPSEPNSVAQIEQLRKAAKKLGIELVEIPVPSSEDLEQALEALAEKVDALYLLPDN-LVDSNFEAILQLANE-- 209 (294)
T ss_dssp EEEEEEETT-HHHHHHHHHHHHHHHHTT-EEEEEEESSGGGHHHHHHHHCTT-SEEEE-S-H-HHHHTHHHHHHHCCC--
T ss_pred EEEEEecCCCccHHHHHHHHHHHHHHcCCEEEEEecCcHhHHHHHHHHhhccCCEEEEECCc-chHhHHHHHHHHHHh--
Confidence 34455565544 444444433 35555544433 3333333554455444444 45444 344444322
Q ss_pred CCCCcCCceeeeeec
Q 009199 229 RKKKVDGVPVFSAQN 243 (540)
Q Consensus 229 ~~kqF~GVPVF~Ar~ 243 (540)
.+||||....
T Consensus 210 -----~~iPv~~~~~ 219 (294)
T PF04392_consen 210 -----AKIPVFGSSD 219 (294)
T ss_dssp -----TT--EEESSH
T ss_pred -----cCCCEEECCH
Confidence 6899997654
No 21
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=36.34 E-value=2.5e+02 Score=33.01 Aligned_cols=58 Identities=9% Similarity=0.054 Sum_probs=35.4
Q ss_pred eehhHHHHHHHHhCCC--CceEEEee--hhHHHHhhhcCCceeeEecC-HHHHH-HHHHHHHHC
Q 009199 167 MDLGDAVTYVKQLNIP--SGVVGACR--LDLAYEHFKEKPHLFQFVPN-EKQVK-AANKLLRTI 224 (540)
Q Consensus 167 ms~~DA~AyV~rLkkp--s~kVgpVS--Ld~aYE~~Kekpv~FrFVPd-ekQVK-aAkkLLK~~ 224 (540)
|+.+-+.++|+-|.++ .+.++-|. .+++|+-+++.-..|.|-+- ..++. -..++++.+
T Consensus 132 lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~~E 195 (824)
T PRK07764 132 VTPQGFNALLKIVEEPPEHLKFIFATTEPDKVIGTIRSRTHHYPFRLVPPEVMRGYLERICAQE 195 (824)
T ss_pred cCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhheeEEEeeCCCHHHHHHHHHHHHHHc
Confidence 3455567888888875 44444333 56777777778777777654 44443 344555554
No 22
>PRK13294 F420-0--gamma-glutamyl ligase; Provisional
Probab=33.95 E-value=46 Score=36.01 Aligned_cols=113 Identities=19% Similarity=0.196 Sum_probs=69.4
Q ss_pred CceEEEeehhHHHHhhh-----cCCceeeEecCHHHHHHHHHHHHHCCCCCCCCCcCCceeeeeeceeeeeeccCCCeee
Q 009199 183 SGVVGACRLDLAYEHFK-----EKPHLFQFVPNEKQVKAANKLLRTIPDSGRKKKVDGVPVFSAQNLDIAIATADGIKWY 257 (540)
Q Consensus 183 s~kVgpVSLd~aYE~~K-----ekpv~FrFVPdekQVKaAkkLLK~~GQg~~~kqF~GVPVF~Ar~LtIavat~dGnK~y 257 (540)
.+-|+..=+.-++.+-- -+++.-..+-.-.++.+|-.|+.. + . +||||-..||+.... .+. --
T Consensus 162 ~vaig~~g~~~~~~~~g~~d~~g~~l~~t~~a~aD~la~aa~l~mg--~-----~-~~~p~~~vrg~~~~~---~~~-~~ 229 (448)
T PRK13294 162 DAAIGAAGLAVLHDYAGAVDAYGNELVVTEVAVADEIAAAADLVKG--K-----L-TGVPVAVVRGLGLLD---DGS-TA 229 (448)
T ss_pred ceEEEecCChHHHhcCCCcCCCCCEeeeeHHHHHHHHHHHHHHhcc--c-----C-CCccEEEEeCCCCCC---CCc-ch
Confidence 34455555555555522 234455666666679999999765 2 1 489999999988831 111 23
Q ss_pred eecccch-hhHHHH-HHHHHHHHHHHHHhhhhhhhccccccchhhHHHHHHhcc
Q 009199 258 TPYFFDK-NMLDNI-LEESVDQHFHALIQTRHMQRRRDVIDDNLAAEVVEEIGD 309 (540)
Q Consensus 258 iPlFFdK-EDLD~i-LEqsKdQ~fh~liq~Rh~qRrrdv~ddn~~~Ev~ee~~d 309 (540)
.+++..+ +||=.. ..++..+-++.+|++||.-|+ .-++.++.|.|+++.+
T Consensus 230 ~~l~r~~~~d~f~~~~~~~~~~~~~eaI~~RRSvR~--F~~~pVp~E~I~~ILe 281 (448)
T PRK13294 230 RDLVRPGEEDLFRLGTAEALELGRREAVLLRRSVRE--FSDDPVDPEAVRRAVA 281 (448)
T ss_pred HhhcCCCccceeccchHHHHHHhHHHhhhcCCcccc--CCCCCCCHHHHHHHHH
Confidence 4555443 344222 336677778889999999865 3355677777766543
No 23
>PF08755 YccV-like: Hemimethylated DNA-binding protein YccV like; InterPro: IPR011722 This entry describes the small protein from Escherichia coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein []. The model entry describes a domain in longer eukaryotic proteins.; PDB: 1VBV_A.
Probab=32.64 E-value=4.9 Score=34.80 Aligned_cols=83 Identities=25% Similarity=0.362 Sum_probs=27.7
Q ss_pred ceeeeeeecccCCCceeeeeeccccCcccccCHHHHHHHHhHHhccCCCCceEEEEeehhHH--HHHHHHhCC-CCceEE
Q 009199 111 FVGQVFSMCDLSGTGLMAVSTHFDIPFISKRTPEWLKKLFATITKSERNGPVFRFFMDLGDA--VTYVKQLNI-PSGVVG 187 (540)
Q Consensus 111 fvgqvfsmcd~sg~glmavst~f~iPfi~krt~~w~k~~~~~l~~se~n~sV~~fFms~~DA--~AyV~rLkk-ps~kVg 187 (540)
.|||||.=.-. |..+|-.-.|.. -+.+++|+++|...-... ++.|--.++++-.|. .+||.+-+. +...-.
T Consensus 5 ~vGqvv~Hr~~---~y~GVIvgwD~~--~~~~~~W~~~~~~~~~~~-~~qPfY~vLv~~~~~~~~~YVaEenL~~~~~~~ 78 (100)
T PF08755_consen 5 RVGQVVRHRRY---GYRGVIVGWDPE--CQAPEEWIEQMGVDNLPR-RNQPFYHVLVDDRDSPPVRYVAEENLEPDSTPE 78 (100)
T ss_dssp -TT-EEEETTT-----EEEEEEEE---------------------------EEEEEEE-SS--EEEEEEGGGEEE---S-
T ss_pred ccCCEEEEeee---CccEEEECcccc--cCCCchHHHhcccccccc-CCCCcEEEEEecCCccceEEecccccccCCCCC
Confidence 58999975444 555665555544 468899999987663333 788888888888775 456655333 222333
Q ss_pred EeehhHHHHhhh
Q 009199 188 ACRLDLAYEHFK 199 (540)
Q Consensus 188 pVSLd~aYE~~K 199 (540)
++.-..+-++|+
T Consensus 79 ~i~hp~i~~yF~ 90 (100)
T PF08755_consen 79 PINHPEIGRYFK 90 (100)
T ss_dssp -TT-HHHHHHHH
T ss_pred CcCChHHHHHHH
Confidence 444444444444
No 24
>PF04305 DUF455: Protein of unknown function (DUF455); InterPro: IPR007402 This is a family of uncharacterised proteins.
Probab=32.64 E-value=88 Score=31.75 Aligned_cols=50 Identities=24% Similarity=0.326 Sum_probs=41.3
Q ss_pred ccCCCCChhHHHHHHHhCCCCCchHHHHHHHHHHHHHHHHHHhhcchHHHHhhCC
Q 009199 308 GDSIWEPPEVQEMMDEIGHPAIPLSVISKAAEIQLLYAVDRVLLGNRWLRKATGI 362 (540)
Q Consensus 308 ~dslleppEvqe~~~e~g~~~i~~sv~~kaae~q~~~~vdrvllgn~w~rk~~gi 362 (540)
+-+|=--|.+.+-++..|.. -.+++.++-+-|=+.-|-+|+||+|.+..-
T Consensus 162 ArGLD~~p~~~~k~~~~gD~-----~sa~iL~~I~~DEi~HV~~G~rWf~~~c~~ 211 (253)
T PF04305_consen 162 ARGLDVTPFIIEKFRSAGDE-----ESAAILEIILRDEIGHVAIGNRWFRYLCEQ 211 (253)
T ss_pred hhCCCCCHHHHHHHHHCCCH-----HHHHHHHHHHHHHHHHHHhhHHHHHHHHHh
Confidence 56666678888888888886 566777888899999999999999998763
No 25
>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]
Probab=32.61 E-value=5.8e+02 Score=29.94 Aligned_cols=158 Identities=18% Similarity=0.316 Sum_probs=104.2
Q ss_pred CCceEEEEeehhHHHHHHHHhCCC-CceEEEeehhHHHHhhh----cCCceeeEe--cCHHHHHHHHHHHHHCCCCCCCC
Q 009199 159 NGPVFRFFMDLGDAVTYVKQLNIP-SGVVGACRLDLAYEHFK----EKPHLFQFV--PNEKQVKAANKLLRTIPDSGRKK 231 (540)
Q Consensus 159 n~sV~~fFms~~DA~AyV~rLkkp-s~kVgpVSLd~aYE~~K----ekpv~FrFV--PdekQVKaAkkLLK~~GQg~~~k 231 (540)
+|..++.|-- .+| +++... .-.|..|.|..+.=.+| .|.+.|-|+ |...-+..|++.|-..|.-+...
T Consensus 380 pGkcyRLYte----~~~-~~~~~~~~PEI~R~~Ls~~vL~Lkalgi~d~l~F~f~d~P~~~~l~~AL~~L~~lgald~~g 454 (674)
T KOG0922|consen 380 PGKCYRLYTE----SAY-DKMPLQTVPEIQRVNLSSAVLQLKALGINDPLRFPFIDPPPPEALEEALEELYSLGALDDRG 454 (674)
T ss_pred CceEEEeeeH----HHH-hhcccCCCCceeeechHHHHHHHHhcCCCCcccCCCCCCCChHHHHHHHHHHHhcCcccCcC
Confidence 4666777652 345 776665 44889999999998888 678899997 78888999999998877654443
Q ss_pred CcCC--------cee---e-----eeec-------eeeeeeccCCCeeeeecccchhhHHH-----------------HH
Q 009199 232 KVDG--------VPV---F-----SAQN-------LDIAIATADGIKWYTPYFFDKNMLDN-----------------IL 271 (540)
Q Consensus 232 qF~G--------VPV---F-----~Ar~-------LtIavat~dGnK~yiPlFFdKEDLD~-----------------iL 271 (540)
.+.- .|+ + .+.. |+|+-.+.-++.++.|....+++.+. +.
T Consensus 455 ~lt~p~G~~ma~~Pl~p~lsk~ll~s~~~gc~~e~l~i~a~Lsv~~~f~~p~~~~~~~a~~~~~kf~~~eGDh~tlL~vy 534 (674)
T KOG0922|consen 455 KLTSPLGRQMAELPLEPHLSKMLLKSSELGCSEEILTIAAMLSVQSVFSRPKDKKAEDADRKRAKFANPEGDHLTLLNVY 534 (674)
T ss_pred CcCchHHhhhhhcCCCcchhhhhhhccccCCcchhhhheeeeeccceecCccchhhhhhhHHHHhhcCcccCHHHHHHHH
Confidence 3332 121 1 1111 78877777889999999998884332 22
Q ss_pred HHHHHH------HHHHHHhhhhhhhccccccchhhHHHHHHhccCCCCChhHHHHHHHhC----CCCCchHHHHHHHHH
Q 009199 272 EESVDQ------HFHALIQTRHMQRRRDVIDDNLAAEVVEEIGDSIWEPPEVQEMMDEIG----HPAIPLSVISKAAEI 340 (540)
Q Consensus 272 EqsKdQ------~fh~liq~Rh~qRrrdv~ddn~~~Ev~ee~~dslleppEvqe~~~e~g----~~~i~~sv~~kaae~ 340 (540)
++++.. =...-|+.||+.|=.||-+ .+-++|++++ ..+.-++.|.|+.-.
T Consensus 535 ~~~~~~~~~~~wC~en~i~~r~l~~a~~ir~-------------------QL~~i~~~~~~~~~s~~~d~~~i~k~l~a 594 (674)
T KOG0922|consen 535 ESWKENGTSKKWCKENFINARSLKRAKDIRK-------------------QLRRILDKFGLPVSSCGGDMEKIRKCLCA 594 (674)
T ss_pred HHHHhcCChhhHHHHhcccHHHHHHHHHHHH-------------------HHHHHHHHcCCCccCCCCCHHHHHHHHHH
Confidence 232222 1345678888887666554 2556677777 455566677777644
No 26
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=31.40 E-value=19 Score=27.10 Aligned_cols=39 Identities=13% Similarity=0.212 Sum_probs=28.6
Q ss_pred eehhHHHHHHHHhCCC---CceEEEe-ehhHHHHhhhcCCcee
Q 009199 167 MDLGDAVTYVKQLNIP---SGVVGAC-RLDLAYEHFKEKPHLF 205 (540)
Q Consensus 167 ms~~DA~AyV~rLkkp---s~kVgpV-SLd~aYE~~Kekpv~F 205 (540)
||.+++.+||.+++.. .-++..| +..++-+++++.|..|
T Consensus 1 MS~~~l~~Fl~~~~~d~~l~~~l~~~~~~~e~~~lA~~~Gy~f 43 (49)
T PF07862_consen 1 MSIESLKAFLEKVKSDPELREQLKACQNPEEVVALAREAGYDF 43 (49)
T ss_pred CCHHHHHHHHHHHhcCHHHHHHHHhcCCHHHHHHHHHHcCCCC
Confidence 7899999999998764 2355556 7777777777666544
No 27
>cd06387 PBP1_iGluR_AMPA_GluR3 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=30.82 E-value=1.8e+02 Score=30.30 Aligned_cols=92 Identities=12% Similarity=0.164 Sum_probs=55.5
Q ss_pred ccccCccc-------------ccCHHHHHHHHhHHhccCCCCceEEEEeehhHHHHHHHHh----CCCCceEEEeeh---
Q 009199 132 HFDIPFIS-------------KRTPEWLKKLFATITKSERNGPVFRFFMDLGDAVTYVKQL----NIPSGVVGACRL--- 191 (540)
Q Consensus 132 ~f~iPfi~-------------krt~~w~k~~~~~l~~se~n~sV~~fFms~~DA~AyV~rL----kkps~kVgpVSL--- 191 (540)
-++||||. ...|. |.+++..|++.-.=..++-+| +-+++..-|..| ...+.+|..+++
T Consensus 85 ~~~iP~i~~~~~~~~~~~~~l~l~P~-l~~Ai~diI~~~~Wr~~~~iY-d~d~gl~~Lq~L~~~~~~~~~~V~~~~v~~~ 162 (372)
T cd06387 85 ALHTSFITPSFPTDADVQFVIQMRPA-LKGAILSLLAHYKWEKFVYLY-DTERGFSILQAIMEAAVQNNWQVTARSVGNI 162 (372)
T ss_pred cccCCeeeeCCCCCCCCceEEEEChh-HHHHHHHHHHhcCCCEEEEEe-cCchhHHHHHHHHHhhccCCceEEEEEeccC
Confidence 68888886 34455 888999999888778888888 777776655544 333555544443
Q ss_pred ---hHHHHhhh--cCCceeeEecCHHHHHHHHHHHHHCCC
Q 009199 192 ---DLAYEHFK--EKPHLFQFVPNEKQVKAANKLLRTIPD 226 (540)
Q Consensus 192 ---d~aYE~~K--ekpv~FrFVPdekQVKaAkkLLK~~GQ 226 (540)
+....++| .+.-..+||=+-. .+.|..+|++..+
T Consensus 163 ~~~~~~~~~l~el~~~~~r~iIld~s-~~~~~~il~~a~e 201 (372)
T cd06387 163 KDVQEFRRIIEEMDRRQEKRYLIDCE-VERINTILEQVVI 201 (372)
T ss_pred CchHHHHHHHHHhccccceEEEEECC-HHHHHHHHHHHHH
Confidence 22233333 2223344553332 2567778877644
No 28
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=30.76 E-value=57 Score=28.90 Aligned_cols=49 Identities=10% Similarity=0.149 Sum_probs=36.8
Q ss_pred ehhHHHHHHHHhCCCCceEEEeehhHHHHhhhcCCceee--EecCHHHHHHHHHHHHHCC
Q 009199 168 DLGDAVTYVKQLNIPSGVVGACRLDLAYEHFKEKPHLFQ--FVPNEKQVKAANKLLRTIP 225 (540)
Q Consensus 168 s~~DA~AyV~rLkkps~kVgpVSLd~aYE~~Kekpv~Fr--FVPdekQVKaAkkLLK~~G 225 (540)
++.|.+.|+++|++...+ ..|.+ ++++.+- -.|+++.++.+.+-|++.|
T Consensus 45 sr~Dv~~Fi~~l~~~~~~-------~Ls~L--T~GvH~HtI~a~~~e~l~~I~~~L~~~G 95 (98)
T PF02829_consen 45 SRRDVDKFIEKLEKSKAK-------PLSSL--TGGVHYHTIEAPDEEDLDKIEEALKKKG 95 (98)
T ss_dssp SHHHHHHHHHHHHH--S---------STTG--GGGEEEEEEEESSHHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHHhccCCc-------chHHh--cCCEeeEEEEECCHHHHHHHHHHHHHCC
Confidence 889999999999887666 33444 6666554 6799999999999999875
No 29
>KOG1579 consensus Homocysteine S-methyltransferase [Amino acid transport and metabolism]
Probab=30.24 E-value=80 Score=33.52 Aligned_cols=45 Identities=27% Similarity=0.439 Sum_probs=36.9
Q ss_pred eehhHHHHhhh----------cCCceeeEecCHHHHHHHHHHHHHCCCCCCCCCcCCceeeee
Q 009199 189 CRLDLAYEHFK----------EKPHLFQFVPNEKQVKAANKLLRTIPDSGRKKKVDGVPVFSA 241 (540)
Q Consensus 189 VSLd~aYE~~K----------ekpv~FrFVPdekQVKaAkkLLK~~GQg~~~kqF~GVPVF~A 241 (540)
+++.++|+++| -+-++|-.+|+..+-++|.++|+.. +...|+|.+
T Consensus 141 ~~~~el~~~~k~qle~~~~~gvD~L~fETip~~~EA~a~l~~l~~~--------~~~~p~~is 195 (317)
T KOG1579|consen 141 VEFEELYDFFKQQLEVFLEAGVDLLAFETIPNVAEAKAALELLQEL--------GPSKPFWIS 195 (317)
T ss_pred cCHHHHHHHHHHHHHHHHhCCCCEEEEeecCCHHHHHHHHHHHHhc--------CCCCcEEEE
Confidence 57888999998 2466999999999999999999986 245677764
No 30
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=28.21 E-value=84 Score=36.96 Aligned_cols=179 Identities=13% Similarity=0.269 Sum_probs=105.4
Q ss_pred Cceeeee---eccccC--cccccCHHHHHHHHhHHhccCCCCceEEEEeehhHHHHHHHHhCCC-----CceEEEeehhH
Q 009199 124 TGLMAVS---THFDIP--FISKRTPEWLKKLFATITKSERNGPVFRFFMDLGDAVTYVKQLNIP-----SGVVGACRLDL 193 (540)
Q Consensus 124 ~glmavs---t~f~iP--fi~krt~~w~k~~~~~l~~se~n~sV~~fFms~~DA~AyV~rLkkp-----s~kVgpVSLd~ 193 (540)
.|.++|+ .+|++| |+...-- +| +..+.++..++.+ +|- .+||++.+.. ..-..|+++..
T Consensus 132 ~G~isI~eLa~~~~Lpsefl~~~l~---~r-lG~iI~g~~~g~~--lyT-----~aYv~r~~a~vRG~l~AiT~Pt~~s~ 200 (803)
T PLN03083 132 CSQIALAELARQLQVGSELVTSMLE---PR-LGTIVKARLEGGQ--LYT-----PAYVARVTAMVRGAARGITVPTNLSS 200 (803)
T ss_pred cCcChHHHHHHhcCChHHHHHHHHH---HH-hccceEEEecCCE--Eec-----HHHHHHHHHHHHHHHHHhcccccHHH
Confidence 3445544 499999 3332221 12 3455666555433 343 7899986553 55778999999
Q ss_pred HHHhhhc-----C---CceeeEecCHHHHHHH-HHHHHHCCCCCCCCCcCCceeeeeeceeeeeeccCCCeeeeecccch
Q 009199 194 AYEHFKE-----K---PHLFQFVPNEKQVKAA-NKLLRTIPDSGRKKKVDGVPVFSAQNLDIAIATADGIKWYTPYFFDK 264 (540)
Q Consensus 194 aYE~~Ke-----k---pv~FrFVPdekQVKaA-kkLLK~~GQg~~~kqF~GVPVF~Ar~LtIavat~dGnK~yiPlFFdK 264 (540)
++..++. + ++.|+ .+-+... .+|++. |+ +.| +-+|+-.|+|.-|.+
T Consensus 201 l~~~~q~~l~~~~~~~~v~~~----~~lf~~~l~~Li~~-~~------l~G--------------~~~~~~~yvP~vy~~ 255 (803)
T PLN03083 201 LWNSLQQLLREMDGAGGVTVE----GSFFQSIFNGLVKE-EE------VLG--------------SLRAGTHWTPAVFAH 255 (803)
T ss_pred HHHHHHHhhccccccccccch----HHHHHHHHHHHHhc-Cc------ccc--------------eeecCcEEccHHHHH
Confidence 9887752 1 22332 1222222 233333 22 122 135556799999998
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhhhhhccccccchhhHHHHHHhccCCCCChhHHHHHHHhCCCCCchHH--HHHHHHHHH
Q 009199 265 NMLDNILEESVDQHFHALIQTRHMQRRRDVIDDNLAAEVVEEIGDSIWEPPEVQEMMDEIGHPAIPLSV--ISKAAEIQL 342 (540)
Q Consensus 265 EDLD~iLEqsKdQ~fh~liq~Rh~qRrrdv~ddn~~~Ev~ee~~dslleppEvqe~~~e~g~~~i~~sv--~~kaae~q~ 342 (540)
.+-+-+-.-|.+--| |+ =+.+-..+= ++..+++.++-+.+|+|.- |.+..--|+
T Consensus 256 ~Q~~~V~sfy~QNgy---------------Ie----yd~l~kLgI-----sdpk~~l~~~~~~~v~L~s~fv~~~Lieql 311 (803)
T PLN03083 256 AQKESVDAFFSQNSY---------------IT----YDTLQKLGI-----SQPKQFLQSRYPDGIALDAVFVHSSMIEML 311 (803)
T ss_pred HHHHHHHHHHHhcCc---------------Ee----HHHHHHhCC-----CchHHHHHHhCcCCccchhhhccHHHHHHH
Confidence 776554444333333 11 122222222 2568888888888898863 777776699
Q ss_pred HHHHHHHhhcchHHHHhhCC
Q 009199 343 LYAVDRVLLGNRWLRKATGI 362 (540)
Q Consensus 343 ~~~vdrvllgn~w~rk~~gi 362 (540)
-.+|.-+|=.+.|+.-.+=+
T Consensus 312 ~~av~Eai~~~sw~Dl~~iL 331 (803)
T PLN03083 312 DSAAEDAIEGGSWIDSLSVL 331 (803)
T ss_pred HHHHHHHHhcCCeEehHhhc
Confidence 99999999999998755433
No 31
>PF11859 DUF3379: Protein of unknown function (DUF3379); InterPro: IPR021806 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 234 to 251 amino acids in length.
Probab=27.73 E-value=67 Score=32.62 Aligned_cols=49 Identities=31% Similarity=0.428 Sum_probs=35.3
Q ss_pred hccccccc-hhhHHHHHHhccCCCCChhHHHHHHHhCCCCCchHHHHHHHHHHHH---------HHHHHHhhcc
Q 009199 290 RRRDVIDD-NLAAEVVEEIGDSIWEPPEVQEMMDEIGHPAIPLSVISKAAEIQLL---------YAVDRVLLGN 353 (540)
Q Consensus 290 Rrrdv~dd-n~~~Ev~ee~~dslleppEvqe~~~e~g~~~i~~sv~~kaae~q~~---------~~vdrvllgn 353 (540)
|||-+.|= +.+.|+++-+ -+.|+=|++++|| |+...||. |++||+||..
T Consensus 7 RRr~~aDP~~~d~e~l~a~----~~~~~~~~F~~d~-----------~~lD~~l~~Al~VdVPddLAdkiLl~Q 65 (232)
T PF11859_consen 7 RRRIYADPNDQDPEFLEAA----KASPANQKFVDDL-----------KQLDAQLEQALKVDVPDDLADKILLRQ 65 (232)
T ss_pred HHHHHcCCccCCHHHHHHH----HhCHHHHHHHHHH-----------HHHHHHHHHHcCCCCCccHHHHHHhhc
Confidence 56666663 3557777764 4569999999997 55555554 5689999988
No 32
>TIGR02196 GlrX_YruB Glutaredoxin-like protein, YruB-family. This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon. Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system.
Probab=27.42 E-value=1e+02 Score=22.49 Aligned_cols=42 Identities=26% Similarity=0.364 Sum_probs=26.1
Q ss_pred HHhhhcCCceeeEecCHHHHHHHHHHHHHCCCCCCCCCcCCceeeeeec
Q 009199 195 YEHFKEKPHLFQFVPNEKQVKAANKLLRTIPDSGRKKKVDGVPVFSAQN 243 (540)
Q Consensus 195 YE~~Kekpv~FrFVPdekQVKaAkkLLK~~GQg~~~kqF~GVPVF~Ar~ 243 (540)
...+++.++.|..+-..+.-+.+.++++..|. .+||+|...+
T Consensus 17 ~~~l~~~~i~~~~vdi~~~~~~~~~~~~~~~~-------~~vP~~~~~~ 58 (74)
T TIGR02196 17 KEYLTSKGIAFEEIDVEKDSAAREEVLKVLGQ-------RGVPVIVIGH 58 (74)
T ss_pred HHHHHHCCCeEEEEeccCCHHHHHHHHHHhCC-------CcccEEEECC
Confidence 34455567777777544333445567666543 6899998654
No 33
>PF01323 DSBA: DSBA-like thioredoxin domain; InterPro: IPR001853 DSBA is a sub-family of the Thioredoxin family []. The efficient and correct folding of bacterial disulphide bonded proteins in vivo is dependent upon a class of periplasmic oxidoreductase proteins called DsbA, after the Escherichia coli enzyme. The bacterial protein-folding factor DsbA is the most oxidizing of the thioredoxin family. DsbA catalyses disulphide-bond formation during the folding of secreted proteins. The extremely oxidizing nature of DsbA has been proposed to result from either domain motion or stabilising active-site interactions in the reduced form. DsbA's highly oxidizing nature is a result of hydrogen bond, electrostatic and helix-dipole interactions that favour the thiolate over the disulphide at the active site []. In the pathogenic bacterium Vibrio cholerae, the DsbA homologue (TcpG) is responsible for the folding, maturation and secretion of virulence factors. While the overall architecture of TcpG and DsbA is similar and the surface features are retained in TcpG, there are significant differences. For example, the kinked active site helix results from a three-residue loop in DsbA, but is caused by a proline in TcpG (making TcpG more similar to thioredoxin in this respect). Furthermore, the proposed peptide binding groove of TcpG is substantially shortened compared with that of DsbA due to a six-residue deletion. Also, the hydrophobic pocket of TcpG is more shallow and the acidic patch is much less extensive than that of E. coli DsbA [].; GO: 0015035 protein disulfide oxidoreductase activity; PDB: 3GL5_A 3DKS_D 3RPP_C 3RPN_B 1YZX_A 3L9V_C 2IMD_A 2IME_A 2IMF_A 2B3S_B ....
Probab=26.16 E-value=1.7e+02 Score=25.96 Aligned_cols=44 Identities=23% Similarity=0.289 Sum_probs=31.4
Q ss_pred hhHHHHHHHHHHH----HHHHHHhhhhhhhccccccchhhHHHHHHhc
Q 009199 265 NMLDNILEESVDQ----HFHALIQTRHMQRRRDVIDDNLAAEVVEEIG 308 (540)
Q Consensus 265 EDLD~iLEqsKdQ----~fh~liq~Rh~qRrrdv~ddn~~~Ev~ee~~ 308 (540)
..+..++...+.+ .|+..|...+..+.++|-|...-.+++++.|
T Consensus 87 ~~a~~~~~~a~~~~~~~~~~~al~~a~~~~~~~i~~~~vl~~~~~~~G 134 (193)
T PF01323_consen 87 RPAHRAAYAAQEQGKADAFADALFRAYFVEGRDISDPDVLAEIAEEAG 134 (193)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHTSST-TSSHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHhcccCCCCHHHHHHHHHHcC
Confidence 4455555544444 7888888888999999999887777877754
No 34
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=26.11 E-value=86 Score=30.25 Aligned_cols=54 Identities=17% Similarity=0.233 Sum_probs=41.9
Q ss_pred HhccCCCCChhHHHHHHHhCCC-CC------chHHHHHHHHHHHHHHHHHHhhcchHHHHh
Q 009199 306 EIGDSIWEPPEVQEMMDEIGHP-AI------PLSVISKAAEIQLLYAVDRVLLGNRWLRKA 359 (540)
Q Consensus 306 e~~dslleppEvqe~~~e~g~~-~i------~~sv~~kaae~q~~~~vdrvllgn~w~rk~ 359 (540)
....++|++..++..|..++.. |+ -++.|+.|+|.++.+++++++-=-++-+..
T Consensus 39 ~~~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~ 99 (212)
T cd08045 39 QKDPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDS 99 (212)
T ss_pred cchhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 3456799999999999999884 33 245599999999999999998655554433
No 35
>PRK15113 glutathione S-transferase; Provisional
Probab=25.84 E-value=11 Score=34.75 Aligned_cols=42 Identities=12% Similarity=0.244 Sum_probs=24.8
Q ss_pred CCccceeeeeeecccCCCceeeeeeccccCcccccCHHHHHHHH
Q 009199 107 GGPAFVGQVFSMCDLSGTGLMAVSTHFDIPFISKRTPEWLKKLF 150 (540)
Q Consensus 107 ggpafvgqvfsmcd~sg~glmavst~f~iPfi~krt~~w~k~~~ 150 (540)
+|+.++|+ ||++|+.--.....-.++++++ ....-.|++||.
T Consensus 156 ~~~~l~G~-~TlADi~l~~~l~~~~~~~~~~-~p~l~~~~~r~~ 197 (214)
T PRK15113 156 GQPNLFGE-WCIADTDLALMLNRLVLHGDEV-PERLADYATFQW 197 (214)
T ss_pred CCCEeeCC-ccHHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHh
Confidence 46788998 9999987443332222344442 234556777764
No 36
>COG4058 McrA Methyl coenzyme M reductase, alpha subunit [Coenzyme metabolism]
Probab=25.82 E-value=2.1e+02 Score=31.66 Aligned_cols=99 Identities=21% Similarity=0.263 Sum_probs=61.1
Q ss_pred HHHHHHHHHHHCCCCCCCCCcCCceeeeeeceeeeeeccCCCeeeeecccchhhHHHHHHHHHHHHHHHHHhhhhhhhcc
Q 009199 213 QVKAANKLLRTIPDSGRKKKVDGVPVFSAQNLDIAIATADGIKWYTPYFFDKNMLDNILEESVDQHFHALIQTRHMQRRR 292 (540)
Q Consensus 213 QVKaAkkLLK~~GQg~~~kqF~GVPVF~Ar~LtIavat~dGnK~yiPlFFdKEDLD~iLEqsKdQ~fh~liq~Rh~qRrr 292 (540)
=|++|+++.++.|-- -++-=-|||+=|-.-..-.|.+.+ .|-+-.||-=+=.++++|....+ ||-
T Consensus 43 FvkaakkiaEkRGIp-fYNPdiG~plgqr~lm~y~vsgtd-------~~vegddlhfvnnaamqqmwddi-------rrt 107 (553)
T COG4058 43 FVKAAKKIAEKRGIP-FYNPDIGVPLGQRKLMPYQVSGTD-------AFVEGDDLHFVNNAAMQQMWDDI-------RRT 107 (553)
T ss_pred HHHHHHHHHHhcCCC-ccCCCCCCccccceeeeeEecCcc-------eeeccccceeecHHHHHHHHHHh-------hhh
Confidence 389999999998751 333334999877666555544433 34555566544445555555443 455
Q ss_pred ccccchhhHHHHHHhccCCCCChhHHHHHHHhCC
Q 009199 293 DVIDDNLAAEVVEEIGDSIWEPPEVQEMMDEIGH 326 (540)
Q Consensus 293 dv~ddn~~~Ev~ee~~dslleppEvqe~~~e~g~ 326 (540)
-||-=+-+-+|+|.-.--=.-|--+-|.||-+.|
T Consensus 108 vivgmd~ah~vlekrlg~evtpetin~ymet~nh 141 (553)
T COG4058 108 VIVGMDTAHAVLEKRLGKEVTPETINEYMETLNH 141 (553)
T ss_pred eEeccchHHHHHHHHhCCccCHHHHHHHHHHhhc
Confidence 5666566667777655555556666677777666
No 37
>PRK10329 glutaredoxin-like protein; Provisional
Probab=25.62 E-value=1.7e+02 Score=24.21 Aligned_cols=59 Identities=17% Similarity=0.234 Sum_probs=37.0
Q ss_pred HHHHhhhcCCceeeEecCHHHHHHHHHHHHHCCCCCCCCCcCCceeeeeeceeeeeeccCCCeeeeecccchhhHHHHHH
Q 009199 193 LAYEHFKEKPHLFQFVPNEKQVKAANKLLRTIPDSGRKKKVDGVPVFSAQNLDIAIATADGIKWYTPYFFDKNMLDNILE 272 (540)
Q Consensus 193 ~aYE~~Kekpv~FrFVPdekQVKaAkkLLK~~GQg~~~kqF~GVPVF~Ar~LtIavat~dGnK~yiPlFFdKEDLD~iLE 272 (540)
.+-++++++++.|..+.....=++ .+.++..|. ..|||....+..| ..|+.+.|+.++-
T Consensus 16 ~ak~~L~~~gI~~~~idi~~~~~~-~~~~~~~g~-------~~vPvv~i~~~~~-------------~Gf~~~~l~~~~~ 74 (81)
T PRK10329 16 ATKRAMESRGFDFEMINVDRVPEA-AETLRAQGF-------RQLPVVIAGDLSW-------------SGFRPDMINRLHP 74 (81)
T ss_pred HHHHHHHHCCCceEEEECCCCHHH-HHHHHHcCC-------CCcCEEEECCEEE-------------ecCCHHHHHHHHH
Confidence 355666778888888766543333 444454444 5899987655444 1678877776653
No 38
>TIGR01165 cbiN cobalt transport protein. This model describes the cobalt transporter in bacteria and its equivalents in archaea. It principally functions in the ion uptake mechanism. It is a multisubunit transporter with two integral membrane proteins and two closely associated cytoplasmic subunits. This transporter belongs to the ABC transporter superfamily (ATP stands for ATP Binding Cassette). This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.
Probab=25.18 E-value=61 Score=29.04 Aligned_cols=25 Identities=52% Similarity=1.128 Sum_probs=18.3
Q ss_pred chhhHHHHHHhc-------cCCCCCh--hHHHHH
Q 009199 297 DNLAAEVVEEIG-------DSIWEPP--EVQEMM 321 (540)
Q Consensus 297 dn~~~Ev~ee~~-------dsllepp--Evqe~~ 321 (540)
|..+.|+|+|.. +.+|||| ||.-++
T Consensus 37 D~~A~~~I~ei~p~Y~PWf~PlwEPpsGEiESlL 70 (91)
T TIGR01165 37 DGQAEEVIEEIGPDYKPWFSPLWEPPSGEIESLL 70 (91)
T ss_pred chHHHHHHHHhCCCCcccccccccCCcchHHHHH
Confidence 567788888876 5899998 554443
No 39
>PRK05569 flavodoxin; Provisional
Probab=24.70 E-value=4.1e+02 Score=22.93 Aligned_cols=67 Identities=13% Similarity=0.123 Sum_probs=38.3
Q ss_pred HHHHHHHhHHhccCCCCceEEEEeehh----HHHHHHHH-hCCCCceEEEeehhHHHHhhhcCCceeeEecCHHHHHHHH
Q 009199 144 EWLKKLFATITKSERNGPVFRFFMDLG----DAVTYVKQ-LNIPSGVVGACRLDLAYEHFKEKPHLFQFVPNEKQVKAAN 218 (540)
Q Consensus 144 ~w~k~~~~~l~~se~n~sV~~fFms~~----DA~AyV~r-Lkkps~kVgpVSLd~aYE~~Kekpv~FrFVPdekQVKaAk 218 (540)
..++.++..|.....+++...+|.+.. ++...+++ |+....+|.. ++.+.+.|+++..+.|.
T Consensus 67 ~~~~~~~~~l~~~~~~~K~v~~f~t~g~~~~~~~~~~~~~l~~~g~~~~~-------------~~~~~~~p~~~~~~~~~ 133 (141)
T PRK05569 67 EEMAPFLDQFKLTPNENKKCILFGSYGWDNGEFMKLWKDRMKDYGFNVIG-------------DLAVNESPNKEELNSAK 133 (141)
T ss_pred HHHHHHHHHhhccCcCCCEEEEEeCCCCCCCcHHHHHHHHHHHCCCeEee-------------eEEEccCCCHHHHHHHH
Confidence 455566666644333455666666543 34444432 3333333321 35566889999999998
Q ss_pred HHHHH
Q 009199 219 KLLRT 223 (540)
Q Consensus 219 kLLK~ 223 (540)
++-++
T Consensus 134 ~~g~~ 138 (141)
T PRK05569 134 ELGKK 138 (141)
T ss_pred HHHHH
Confidence 88654
No 40
>COG3935 DnaD Putative primosome component and related proteins [DNA replication, recombination, and repair]
Probab=24.42 E-value=2.5e+02 Score=28.80 Aligned_cols=70 Identities=16% Similarity=0.258 Sum_probs=51.1
Q ss_pred hhhhhhccc-cccchhhHHHHHHhccCCCCChhHHHHHHHhCCCCCchHHHHHHHHHHHH------HHHHHHhhcchHHH
Q 009199 285 TRHMQRRRD-VIDDNLAAEVVEEIGDSIWEPPEVQEMMDEIGHPAIPLSVISKAAEIQLL------YAVDRVLLGNRWLR 357 (540)
Q Consensus 285 ~Rh~qRrrd-v~ddn~~~Ev~ee~~dslleppEvqe~~~e~g~~~i~~sv~~kaae~q~~------~~vdrvllgn~w~r 357 (540)
.+--+++.+ -=-+.+....-+|.|- +|-|+|.++|.--+..-+.+.++|-+|.+.-+. -.+|++|+ .|.-
T Consensus 115 ~~~~e~~~~~~~~k~l~~~F~~e~Gr-~lsP~e~E~L~~wld~d~~~~elI~~ALkeAv~~gK~n~~YI~~IL~--nW~k 191 (246)
T COG3935 115 LEDNELKNQNEDKKELFRDFEEEFGR-MLSPFEIEDLQKWLDEDSHDPELIKAALKEAVENGKLNFKYIDAILR--NWKK 191 (246)
T ss_pred ccHHHhccchhHHHHHHHHHHHHcCC-cCCchhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCccHHHHHHHHH--HHHH
Confidence 344455555 2223345666777777 999999999999999988899999999987664 56888885 5753
No 41
>COG1105 FruK Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]
Probab=24.37 E-value=27 Score=36.47 Aligned_cols=88 Identities=20% Similarity=0.191 Sum_probs=62.0
Q ss_pred eeeecccCCCceeeeeeccccCcccccCHHHHHHHHhHHhccCCCCceEEEEeehhHHHHHHHHhCCCCceEEEeehhHH
Q 009199 115 VFSMCDLSGTGLMAVSTHFDIPFISKRTPEWLKKLFATITKSERNGPVFRFFMDLGDAVTYVKQLNIPSGVVGACRLDLA 194 (540)
Q Consensus 115 vfsmcd~sg~glmavst~f~iPfi~krt~~w~k~~~~~l~~se~n~sV~~fFms~~DA~AyV~rLkkps~kVgpVSLd~a 194 (540)
++-+||.||..|.++-.- . |++.|---+-|+-+|..=.+ +.+|+.++..+|....++.+-|||+.-
T Consensus 160 ~~vilD~Sg~~L~~~L~~-~-P~lIKPN~~EL~~~~g~~~~------------~~~d~i~~a~~l~~~g~~~ViVSlG~~ 225 (310)
T COG1105 160 AKVILDTSGEALLAALEA-K-PWLIKPNREELEALFGRELT------------TLEDVIKAARELLAEGIENVIVSLGAD 225 (310)
T ss_pred CeEEEECChHHHHHHHcc-C-CcEEecCHHHHHHHhCCCCC------------ChHHHHHHHHHHHHCCCCEEEEEecCc
Confidence 678999999999876442 2 99998877777776654322 344999999999889999999999875
Q ss_pred HHhhhcCCceeeEecCHHHHHH
Q 009199 195 YEHFKEKPHLFQFVPNEKQVKA 216 (540)
Q Consensus 195 YE~~Kekpv~FrFVPdekQVKa 216 (540)
=-++..+.-.|...|-+-||.+
T Consensus 226 Gal~~~~~~~~~a~~p~~~vvs 247 (310)
T COG1105 226 GALLVTAEGVYFASPPKVQVVS 247 (310)
T ss_pred ccEEEccCCeEEEeCCCcceec
Confidence 5555544444444444445544
No 42
>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Probab=23.91 E-value=1.3e+02 Score=27.77 Aligned_cols=58 Identities=16% Similarity=0.039 Sum_probs=40.6
Q ss_pred hhHHHHHHHHhCC-CCceEEEe-------ehhHHHHhhhcCCceeeEecCHHHHHHHHHHHHHCCC
Q 009199 169 LGDAVTYVKQLNI-PSGVVGAC-------RLDLAYEHFKEKPHLFQFVPNEKQVKAANKLLRTIPD 226 (540)
Q Consensus 169 ~~DA~AyV~rLkk-ps~kVgpV-------SLd~aYE~~Kekpv~FrFVPdekQVKaAkkLLK~~GQ 226 (540)
..|+..++..+.. .+..+... -|..+++++|..+..+-..++..++..+.++|++.|-
T Consensus 98 ~~d~~~~l~~~~~~~D~V~~~~~~~~~~~~l~~~~~~LkpgG~lv~~~~~~~~~~~~~~~l~~~g~ 163 (198)
T PRK00377 98 KGEAPEILFTINEKFDRIFIGGGSEKLKEIISASWEIIKKGGRIVIDAILLETVNNALSALENIGF 163 (198)
T ss_pred EechhhhHhhcCCCCCEEEECCCcccHHHHHHHHHHHcCCCcEEEEEeecHHHHHHHHHHHHHcCC
Confidence 4677777776532 34444311 2566777778888877778899999999999988653
No 43
>TIGR03537 DapC succinyldiaminopimelate transaminase. Note: the detailed information included in the EC:2.6.1.17 record includes the assertions that the enzyme uses the pyridoxal pyrophosphate cofactor, which is consistent with the pfam00155 family, and the assertion that the amino group donor is L-glutamate, which is undetermined for the sequences in this clade.
Probab=23.56 E-value=1.9e+02 Score=28.67 Aligned_cols=50 Identities=22% Similarity=0.166 Sum_probs=34.6
Q ss_pred HHHHHHHHhCCCCceEEEeehhHHHHhhhcCCceeeEecCHHHHHHHHHHHHH
Q 009199 171 DAVTYVKQLNIPSGVVGACRLDLAYEHFKEKPHLFQFVPNEKQVKAANKLLRT 223 (540)
Q Consensus 171 DA~AyV~rLkkps~kVgpVSLd~aYE~~Kekpv~FrFVPdekQVKaAkkLLK~ 223 (540)
++.+++++|.+.++.|.|.+. |..-..+-+-+.|.+++++++.|.+.+++
T Consensus 300 ~~~~l~~~L~~~gv~v~~g~~---f~~~~~~~~Ri~~~~~~~~~~~~l~~~~~ 349 (350)
T TIGR03537 300 DAKDYALRLLENGIVVAPGEN---FGSGEEGYVRVALVPTLEECEEALRLWER 349 (350)
T ss_pred CHHHHHHHHHHCCEEEcCchh---hCCCCCCEEEEEecCCHHHHHHHHHHHhc
Confidence 588999999888888887643 21101122334466899999999988875
No 44
>PRK09756 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=23.53 E-value=1.3e+02 Score=28.23 Aligned_cols=41 Identities=15% Similarity=0.174 Sum_probs=27.6
Q ss_pred HHhHHhccCCCCceEEEEeehhHHHHHHH-HhCCCCceEEEe
Q 009199 149 LFATITKSERNGPVFRFFMDLGDAVTYVK-QLNIPSGVVGAC 189 (540)
Q Consensus 149 ~~~~l~~se~n~sV~~fFms~~DA~AyV~-rLkkps~kVgpV 189 (540)
+...|.+...+..++-+|=+-+||.++++ -+..+++.||.+
T Consensus 69 a~~~l~~~~~~~~vlvl~~~~~da~~l~~~g~~i~~iNiG~m 110 (158)
T PRK09756 69 TINVIGKAAPHQKIFLICRTPQTVRKLVEGGIDLKDVNVGNM 110 (158)
T ss_pred HHHHHHhccCCceEEEEECCHHHHHHHHHcCCCCCEEEECCC
Confidence 33334332334568889999999999998 566666666665
No 45
>KOG0698 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=23.35 E-value=1e+02 Score=31.44 Aligned_cols=10 Identities=60% Similarity=0.876 Sum_probs=9.1
Q ss_pred ceEEeecCcc
Q 009199 512 PLFVANVGGY 521 (540)
Q Consensus 512 PLFvANvg~y 521 (540)
=||||||||=
T Consensus 154 ~l~vaN~GDS 163 (330)
T KOG0698|consen 154 KLYVANVGDS 163 (330)
T ss_pred EEEEEEcCCC
Confidence 8999999993
No 46
>PF00481 PP2C: Protein phosphatase 2C; InterPro: IPR001932 This domain is found in protein phosphatase 2C, as well as other proteins eg. pyruvate dehydrogenase (lipoamide)-phosphatase (3.1.3.43 from EC), adenylate cyclase (4.6.1.1 from EC) and some bacterial stage II sporulation E proteins (3.1.3.16 from EC). Protein phosphatase 2C (PP2C) is one of the four major classes of mammalian serine/threonine specific protein phosphatases (3.1.3.16 from EC). PP2C [] is a monomeric enzyme of about 42 Kd which shows broad substrate specificity and is dependent on divalent cations (mainly manganese and magnesium) for its activity. Its exact physiological role is still unclear. Three isozymes are currently known in mammals: PP2C-alpha, -beta and -gamma. In yeast, there are at least four PP2C homologs: phosphatase PTC1 [], which has weak tyrosine phosphatase activity in addition to its activity on serines, phosphatases PTC2 and PTC3, and hypothetical protein YBR125c. Isozymes of PP2C are also known from Arabidopsis thaliana (ABI1, PPH1), Caenorhabditis elegans (FEM-2, F42G9.1, T23F11.1), Leishmania chagasi and Paramecium tetraurelia. In A. thaliana, the kinase associated protein phosphatase (KAPP) [] is an enzyme that dephosphorylates the Ser/Thr receptor-like kinase RLK5 and which contains a C-terminal PP2C domain. PP2C does not seem to be evolutionary related to the main family of serine/ threonine phosphatases: PP1, PP2A and PP2B. However, it is significantly similar to the catalytic subunit of pyruvate dehydrogenase phosphatase 3.1.3.43 from EC (PDPC) [], which catalyzes dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex. PDPC is a mitochondrial enzyme and, like PP2C, is magnesium-dependent.; GO: 0003824 catalytic activity; PDB: 2I0O_A 2POP_C 2POM_A 2J4O_A 2I44_B 3MQ3_A 3N3C_A 2PNQ_B 2P8E_A 2IQ1_A ....
Probab=22.77 E-value=58 Score=30.99 Aligned_cols=17 Identities=24% Similarity=0.411 Sum_probs=11.4
Q ss_pred CCceeeEEeeecCcccc
Q 009199 456 FLPKVTMVGISTGEAGQ 472 (540)
Q Consensus 456 flPKiTMvGiS~ge~gq 472 (540)
-.++..++||--|-||.
T Consensus 29 ~~~~~~l~~V~DGhgG~ 45 (254)
T PF00481_consen 29 GNDNVSLFGVFDGHGGS 45 (254)
T ss_dssp TEEEEEEEEEEEEESSS
T ss_pred CCCCcEEEEEecCCCCh
Confidence 34667777777776664
No 47
>cd03204 GST_C_GDAP1 GST_C family, Ganglioside-induced differentiation-associated protein 1 (GDAP1) subfamily; GDAP1 was originally identified as a highly expressed gene at the differentiated stage of GD3 synthase-transfected cells. More recently, mutations in GDAP1 have been reported to cause both axonal and demyelinating autosomal-recessive Charcot-Marie-Tooth (CMT) type 4A neuropathy. CMT is characterized by slow and progressive weakness and atrophy of muscles. Sequence analysis of GDAP1 shows similarities and differences with GSTs; it appears to contain both N-terminal thioredoxin-fold and C-terminal alpha helical domains of GSTs, however, it also contains additional C-terminal transmembrane domains unlike GSTs. GDAP1 is mainly expressed in neuronal cells and is localized in the mitochondria through its transmembrane domains. It does not exhibit GST activity using standard substrates.
Probab=22.77 E-value=16 Score=32.29 Aligned_cols=48 Identities=8% Similarity=0.155 Sum_probs=28.5
Q ss_pred CCCCCccceeeeeeecccCCCceeeeee--ccccCcc----cccCHHHHHHHHh
Q 009199 104 GKGGGPAFVGQVFSMCDLSGTGLMAVST--HFDIPFI----SKRTPEWLKKLFA 151 (540)
Q Consensus 104 ~~~ggpafvgqvfsmcd~sg~glmavst--~f~iPfi----~krt~~w~k~~~~ 151 (540)
+.+++|-++|.-||.+|+.--..+..-. .|++++. -...-.|++||.+
T Consensus 54 ~~~~~~yL~Gd~~TlADi~l~~~l~~~~~~~~~~~~~~~~~~P~l~~w~~rv~a 107 (111)
T cd03204 54 EQKCQLWLCGDTFTLADISLGVTLHRLKFLGLSRRYWGNGKRPNLEAYFERVLQ 107 (111)
T ss_pred cccCCCccCCCCCCHHHHHHHHHHHHHHHcCccccccccccChHHHHHHHHHHc
Confidence 3445699999999999998655443222 3444321 1223467777643
No 48
>PF00043 GST_C: Glutathione S-transferase, C-terminal domain; InterPro: IPR004046 In eukaryotes, glutathione S-transferases (GSTs) participate in the detoxification of reactive electrophillic compounds by catalysing their conjugation to glutathione. The GST domain is also found in S-crystallins from squid, and proteins with no known GST activity, such as eukaryotic elongation factors 1-gamma and the HSP26 family of stress-related proteins, which include auxin-regulated proteins in plants and stringent starvation proteins in Escherichia coli. The major lens polypeptide of cephalopods is also a GST [, , , ]. Bacterial GSTs of known function often have a specific, growth-supporting role in biodegradative metabolism: epoxide ring opening and tetrachlorohydroquinone reductive dehalogenation are two examples of the reactions catalysed by these bacterial GSTs. Some regulatory proteins, like the stringent starvation proteins, also belong to the GST family [, ]. GST seems to be absent from Archaea in which gamma-glutamylcysteine substitute to glutathione as major thiol. Glutathione S-transferases form homodimers, but in eukaryotes can also form heterodimers of the A1 and A2 or YC1 and YC2 subunits. The homodimeric enzymes display a conserved structural fold. Each monomer is composed of a distinct N-terminal sub-domain, which adopts the thioredoxin fold, and a C-terminal all-helical sub-domain. This entry is the C-terminal domain.; PDB: 3UAP_A 3UAR_A 3QAV_A 3QAW_A 1Y6E_A 1U88_B 4AI6_B 1UA5_A 4AKH_A 3QMZ_S ....
Probab=22.76 E-value=13 Score=29.20 Aligned_cols=45 Identities=24% Similarity=0.626 Sum_probs=30.9
Q ss_pred CCccceeeeeeecccCCCceeeeeeccccCcccccCH---HHHHHHHh
Q 009199 107 GGPAFVGQVFSMCDLSGTGLMAVSTHFDIPFISKRTP---EWLKKLFA 151 (540)
Q Consensus 107 ggpafvgqvfsmcd~sg~glmavst~f~iPfi~krt~---~w~k~~~~ 151 (540)
||+-++|.-+|++|+.=-+.+..-..++..+.....| .|+++|++
T Consensus 46 ~~~~l~G~~~t~ADi~~~~~~~~~~~~~~~~~~~~~P~l~~w~~~~~~ 93 (95)
T PF00043_consen 46 GGPYLVGDKLTIADIALFPMLDWLERLGPDFLFEKFPKLKKWYERMFA 93 (95)
T ss_dssp TSSSSSBSS-CHHHHHHHHHHHHHHHHTTTTTHTTSHHHHHHHHHHHT
T ss_pred CCCeeeccCCchhHHHHHHHHHHHHHhCCCcccccCHHHHHHHHHHHc
Confidence 8899999999999987666655555666655434444 57777654
No 49
>PRK15088 PTS system mannose-specific transporter subunits IIAB; Provisional
Probab=22.52 E-value=1.9e+02 Score=30.17 Aligned_cols=43 Identities=19% Similarity=0.275 Sum_probs=26.9
Q ss_pred HHHHhHHhccC-CCCceEEEEeehhHHHHHHH-HhCCCCceEEEe
Q 009199 147 KKLFATITKSE-RNGPVFRFFMDLGDAVTYVK-QLNIPSGVVGAC 189 (540)
Q Consensus 147 k~~~~~l~~se-~n~sV~~fFms~~DA~AyV~-rLkkps~kVgpV 189 (540)
+++...|.+.+ .+..++-+|=+-+||.++++ -++.+++.||.+
T Consensus 225 ~~a~~~l~~~~~~~~~vlil~k~p~d~~~l~~~g~~i~~iNvG~m 269 (322)
T PRK15088 225 AKMIRVYNNPKYAGERVMLLFTNPTDVERLVEGGVKITSVNIGGM 269 (322)
T ss_pred HHHHHHHhCCCCCCCeEEEEECCHHHHHHHHHcCCCCCeEEECCc
Confidence 34455555432 24458888888888888888 455555544444
No 50
>TIGR00854 pts-sorbose PTS system, mannose/fructose/sorbose family, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families.It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIB components of this family of PTS transporters.
Probab=21.54 E-value=1.2e+02 Score=28.30 Aligned_cols=56 Identities=18% Similarity=0.261 Sum_probs=29.8
Q ss_pred CceEEEEeehhHHHHHHH-HhCCCCceEEEeehhHHHHhhhcCCc--eeeEecCHHHHHHHHHHHH
Q 009199 160 GPVFRFFMDLGDAVTYVK-QLNIPSGVVGACRLDLAYEHFKEKPH--LFQFVPNEKQVKAANKLLR 222 (540)
Q Consensus 160 ~sV~~fFms~~DA~AyV~-rLkkps~kVgpVSLd~aYE~~Kekpv--~FrFVPdekQVKaAkkLLK 222 (540)
..++-+|=+-.||.++++ -+..+++.||.+.- ++... .-...=+++++++-++|..
T Consensus 76 ~~v~vl~k~~~da~~l~~~g~~i~~iniG~~~~-------~~g~~~v~~~v~l~~~e~~~l~~l~~ 134 (151)
T TIGR00854 76 QTIFLLFRNPQDVLTLVEGGVPIKTVNVGGMHF-------SNGKKQITKKVSVDDQDITAFRFLKQ 134 (151)
T ss_pred ceEEEEECCHHHHHHHHHcCCCCCEEEECCccc-------CCCCEEEecceeeCHHHHHHHHHHHH
Confidence 456777777777777776 45555555555521 11111 1112225667777666643
No 51
>PRK09819 alpha-mannosidase; Provisional
Probab=20.61 E-value=63 Score=37.20 Aligned_cols=50 Identities=24% Similarity=0.187 Sum_probs=38.5
Q ss_pred HHHHHHHHhhcchHHHHhhCCCCCCcccccccchh-hhHhhhhhcccccccc
Q 009199 342 LLYAVDRVLLGNRWLRKATGIQPKFPYMVDSFENR-SAASFLRASESTSCLA 392 (540)
Q Consensus 342 ~~~~vdrvllgn~w~rk~~giqp~fp~~vDSFErr-sa~s~~ras~s~s~~~ 392 (540)
--.+|+-.++|.||+ +..|.-|+.=|+.|+|=-= .-..|.+-+.=..++.
T Consensus 97 gEsliRqll~G~~~~-~~fG~~~~vgwlpD~FG~s~~lPqIl~~~Gi~~~~~ 147 (875)
T PRK09819 97 GESIVRNLLYGIRDC-REFGEPMKIGYLPDSFGQSGQMPQIYNGFGITRTLF 147 (875)
T ss_pred HHHHHHHHHHHHHHH-HHcCCCCceeeecCCCCCcHHHHHHHHhCCCCeEEE
Confidence 345788899999999 5799999999999999765 4555666666555443
No 52
>cd02976 NrdH NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase activity that is dependent on TRX reductase, not glutathione (GSH). It is part of the NrdHIEF operon, where NrdEF codes for class Ib ribonucleotide reductase (RNR-Ib), an efficient enzyme at low oxygen levels. Under these conditions when GSH is mostly conjugated to spermidine, NrdH can still function and act as a hydrogen donor for RNR-Ib. It has been suggested that the NrdHEF system may be the oldest RNR reducing system, capable of functioning in a microaerophilic environment, where GSH was not yet available. NrdH from Corynebacterium ammoniagenes can form domain-swapped dimers, although it is unknown if this happens in vivo. Domain-swapped dimerization, which results in the blocking of the TRX reductase binding site, cou
Probab=20.08 E-value=2e+02 Score=20.93 Aligned_cols=47 Identities=17% Similarity=0.185 Sum_probs=28.8
Q ss_pred HHHHhhhcCCceeeEecCHHHHHHHHHHHHHCCCCCCCCCcCCceeeeeeceee
Q 009199 193 LAYEHFKEKPHLFQFVPNEKQVKAANKLLRTIPDSGRKKKVDGVPVFSAQNLDI 246 (540)
Q Consensus 193 ~aYE~~Kekpv~FrFVPdekQVKaAkkLLK~~GQg~~~kqF~GVPVF~Ar~LtI 246 (540)
.+.+.+++.++.|..+.....-+.+.++.+-. ...+||++.-.+..|
T Consensus 15 ~~~~~l~~~~i~~~~~~i~~~~~~~~~~~~~~-------~~~~vP~i~~~~~~i 61 (73)
T cd02976 15 ATKRFLDERGIPFEEVDVDEDPEALEELKKLN-------GYRSVPVVVIGDEHL 61 (73)
T ss_pred HHHHHHHHCCCCeEEEeCCCCHHHHHHHHHHc-------CCcccCEEEECCEEE
Confidence 45666667777777776543333444444332 347899998777555
Done!