Query psy8860
Match_columns 374
No_of_seqs 398 out of 2428
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 21:14:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8860.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8860hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00140 rpl6 ribosomal protei 100.0 1.5E-55 3.3E-60 399.1 22.1 168 118-285 1-168 (178)
2 TIGR03654 L6_bact ribosomal pr 100.0 3.5E-54 7.6E-59 389.3 22.4 167 119-285 1-167 (175)
3 PRK05498 rplF 50S ribosomal pr 100.0 9.1E-54 2E-58 387.7 22.5 168 118-285 1-168 (178)
4 COG0097 RplF Ribosomal protein 100.0 2E-53 4.2E-58 380.5 20.4 166 118-284 1-167 (178)
5 PRK05518 rpl6p 50S ribosomal p 100.0 3.2E-44 7E-49 324.7 20.0 149 122-271 6-159 (180)
6 TIGR03653 arch_L6P archaeal ri 100.0 5.3E-44 1.2E-48 320.9 20.7 149 123-272 1-154 (170)
7 KOG3254|consensus 100.0 1.5E-44 3.3E-49 318.7 13.2 166 120-285 33-201 (211)
8 PTZ00027 60S ribosomal protein 100.0 5.3E-43 1.1E-47 319.5 20.2 149 123-271 7-166 (190)
9 PTZ00179 60S ribosomal protein 100.0 5E-43 1.1E-47 319.4 19.1 149 122-270 5-164 (189)
10 COG0096 RpsH Ribosomal protein 100.0 3.8E-42 8.2E-47 293.6 10.0 125 1-126 1-128 (132)
11 CHL00042 rps8 ribosomal protei 100.0 6.6E-40 1.4E-44 283.4 10.6 123 3-126 2-128 (132)
12 PRK00136 rpsH 30S ribosomal pr 100.0 1.9E-38 4.2E-43 273.8 10.2 123 3-126 2-126 (130)
13 PF00410 Ribosomal_S8: Ribosom 100.0 5E-36 1.1E-40 258.6 10.1 122 5-126 1-125 (129)
14 CHL00139 rpl18 ribosomal prote 100.0 2.9E-34 6.3E-39 239.7 12.5 95 276-374 14-109 (109)
15 PTZ00158 40S ribosomal protein 100.0 7.1E-34 1.5E-38 244.0 10.4 114 1-126 1-126 (130)
16 PTZ00032 60S ribosomal protein 100.0 1.4E-33 3.1E-38 254.1 12.4 99 276-374 104-211 (211)
17 COG0256 RplR Ribosomal protein 100.0 2.9E-33 6.3E-38 237.0 12.5 98 275-374 27-125 (125)
18 PLN00146 40S ribosomal protein 100.0 1.7E-33 3.8E-38 242.6 10.1 117 1-126 1-126 (130)
19 TIGR00060 L18_bact ribosomal p 100.0 6E-33 1.3E-37 232.9 12.1 91 276-374 23-114 (114)
20 PRK05593 rplR 50S ribosomal pr 100.0 1.2E-32 2.6E-37 232.9 12.4 95 275-374 22-117 (117)
21 PRK04034 rps8p 30S ribosomal p 100.0 2.3E-32 5E-37 235.9 8.7 117 1-126 1-126 (130)
22 PF00861 Ribosomal_L18p: Ribos 100.0 6.7E-31 1.5E-35 223.6 12.9 97 276-374 22-119 (119)
23 cd00432 Ribosomal_L18_L5e Ribo 100.0 1.4E-28 3E-33 204.3 12.1 95 274-372 8-103 (103)
24 PRK08569 rpl18p 50S ribosomal 100.0 1.2E-28 2.6E-33 223.3 11.7 95 276-374 31-130 (193)
25 KOG1754|consensus 99.9 6.4E-22 1.4E-26 165.6 7.9 116 1-125 1-125 (130)
26 PF00347 Ribosomal_L6: Ribosom 99.7 2.8E-16 6.1E-21 123.1 7.5 72 128-199 1-77 (77)
27 KOG3255|consensus 99.6 2.9E-17 6.2E-22 147.9 0.8 146 123-269 7-164 (179)
28 PTZ00069 60S ribosomal protein 99.3 1.6E-12 3.4E-17 124.2 7.6 98 273-374 43-174 (300)
29 KOG3333|consensus 99.3 4.7E-12 1E-16 110.2 9.0 93 278-374 61-154 (188)
30 PF00347 Ribosomal_L6: Ribosom 98.1 5E-07 1.1E-11 70.5 0.3 70 208-280 2-75 (77)
31 TIGR03632 bact_S11 30S ribosom 97.4 0.0011 2.3E-08 55.7 9.3 87 278-373 1-88 (108)
32 PF00411 Ribosomal_S11: Riboso 97.4 0.0012 2.7E-08 55.5 9.2 87 278-373 1-88 (110)
33 CHL00041 rps11 ribosomal prote 97.3 0.0021 4.5E-08 54.7 9.5 88 277-373 13-101 (116)
34 PRK05309 30S ribosomal protein 96.9 0.0076 1.6E-07 52.2 9.6 88 277-373 17-105 (128)
35 PTZ00090 40S ribosomal protein 96.8 0.011 2.4E-07 55.1 9.7 88 277-374 118-208 (233)
36 PTZ00129 40S ribosomal protein 96.4 0.029 6.4E-07 49.6 9.5 91 277-373 28-125 (149)
37 TIGR03628 arch_S11P archaeal r 96.1 0.048 1E-06 46.3 9.3 89 278-373 3-99 (114)
38 PRK09607 rps11p 30S ribosomal 96.0 0.035 7.6E-07 48.3 7.8 90 277-373 9-106 (132)
39 KOG0875|consensus 95.9 0.0059 1.3E-07 57.8 2.8 101 269-373 39-172 (264)
40 COG0100 RpsK Ribosomal protein 94.8 0.21 4.5E-06 43.2 8.7 95 270-373 11-106 (129)
41 KOG0408|consensus 89.7 2.5 5.3E-05 38.1 8.7 93 273-373 75-167 (190)
42 KOG0407|consensus 68.9 52 0.0011 27.9 8.9 90 278-373 17-113 (139)
43 cd06479 ACD_HspB7_like Alpha c 67.4 14 0.0003 29.3 5.1 43 129-171 21-79 (81)
44 PRK06518 hypothetical protein; 52.2 54 0.0012 29.9 6.9 100 245-372 48-151 (177)
45 PF00011 HSP20: Hsp20/alpha cr 47.2 57 0.0012 26.0 5.7 44 129-172 20-86 (102)
46 cd06470 ACD_IbpA-B_like Alpha- 46.6 42 0.00091 26.7 4.7 18 129-146 24-41 (90)
47 TIGR01917 gly_red_sel_B glycin 45.9 68 0.0015 33.3 7.1 55 319-373 312-366 (431)
48 cd06469 p23_DYX1C1_like p23_li 45.7 95 0.0021 23.3 6.5 44 129-172 19-67 (78)
49 cd06481 ACD_HspB9_like Alpha c 45.6 56 0.0012 26.0 5.3 19 129-147 20-38 (87)
50 cd00298 ACD_sHsps_p23-like Thi 43.6 56 0.0012 23.5 4.8 42 129-170 19-77 (80)
51 PF12970 DUF3858: Domain of Un 41.4 1.6E+02 0.0034 25.2 7.5 44 121-170 38-81 (116)
52 TIGR01918 various_sel_PB selen 40.5 91 0.002 32.4 7.1 55 319-373 312-366 (431)
53 cd06280 PBP1_LacI_like_4 Ligan 39.1 88 0.0019 28.7 6.4 44 331-374 102-147 (263)
54 cd00175 SNc Staphylococcal nuc 38.7 1.1E+02 0.0023 25.4 6.3 102 246-372 18-124 (129)
55 cd06471 ACD_LpsHSP_like Group 37.2 1.1E+02 0.0023 24.2 5.7 17 130-146 24-40 (93)
56 COG0097 RplF Ribosomal protein 35.2 38 0.00082 31.1 3.1 28 124-151 113-141 (178)
57 cd06276 PBP1_FucR_like Ligand- 33.1 1E+02 0.0023 28.4 5.9 44 331-374 102-149 (247)
58 PF09639 YjcQ: YjcQ protein; 33.0 27 0.00059 28.0 1.6 23 31-53 25-47 (88)
59 cd06288 PBP1_sucrose_transcrip 31.6 1.2E+02 0.0026 27.7 6.0 42 332-373 104-148 (269)
60 PF14419 SPOUT_MTase_2: AF2226 31.0 1.3E+02 0.0029 27.2 5.7 49 322-370 10-58 (173)
61 cd02393 PNPase_KH Polynucleoti 30.8 79 0.0017 23.3 3.7 30 236-265 31-60 (61)
62 cd06286 PBP1_CcpB_like Ligand- 30.8 1.3E+02 0.0028 27.4 6.0 42 332-373 102-146 (260)
63 COG0299 PurN Folate-dependent 30.6 81 0.0017 29.5 4.4 38 336-373 43-81 (200)
64 cd06319 PBP1_ABC_sugar_binding 30.6 1.4E+02 0.003 27.4 6.3 51 323-373 102-157 (277)
65 PRK10423 transcriptional repre 29.3 1.4E+02 0.003 28.4 6.2 43 332-374 162-207 (327)
66 smart00481 POLIIIAc DNA polyme 29.2 1.2E+02 0.0027 22.1 4.6 38 333-373 18-56 (67)
67 PF03900 Porphobil_deamC: Porp 29.2 76 0.0017 24.2 3.5 49 278-341 23-74 (74)
68 cd06472 ACD_ScHsp26_like Alpha 28.5 2E+02 0.0044 22.6 6.1 18 129-146 22-40 (92)
69 PF07137 VDE: Violaxanthin de- 28.5 59 0.0013 30.2 3.1 29 346-374 150-178 (198)
70 PF04273 DUF442: Putative phos 28.1 66 0.0014 26.9 3.2 37 338-374 22-60 (110)
71 cd06285 PBP1_LacI_like_7 Ligan 27.9 1.5E+02 0.0032 27.1 6.0 47 324-374 98-147 (265)
72 cd06267 PBP1_LacI_sugar_bindin 27.8 1.7E+02 0.0036 26.2 6.1 42 332-373 104-148 (264)
73 CHL00140 rpl6 ribosomal protei 26.7 65 0.0014 29.3 3.2 30 120-149 106-139 (178)
74 cd06477 ACD_HspB3_Like Alpha c 26.6 44 0.00096 26.5 1.8 19 129-147 20-38 (83)
75 cd01543 PBP1_XylR Ligand-bindi 26.5 1.8E+02 0.004 26.6 6.3 43 331-373 96-140 (265)
76 cd06270 PBP1_GalS_like Ligand 26.5 1.8E+02 0.0039 26.6 6.2 43 332-374 104-149 (268)
77 TIGR03653 arch_L6P archaeal ri 26.3 4.9E+02 0.011 23.5 9.5 57 133-194 93-152 (170)
78 PF00070 Pyr_redox: Pyridine n 25.8 1.7E+02 0.0036 22.1 4.9 44 331-374 10-57 (80)
79 TIGR00725 conserved hypothetic 25.7 2E+02 0.0043 25.5 6.0 39 325-372 17-55 (159)
80 cd06275 PBP1_PurR Ligand-bindi 25.5 2E+02 0.0042 26.3 6.3 44 331-374 104-150 (269)
81 COG1072 CoaA Panthothenate kin 25.4 49 0.0011 32.5 2.2 42 218-260 161-202 (283)
82 PF00875 DNA_photolyase: DNA p 25.4 88 0.0019 27.3 3.7 43 332-374 77-120 (165)
83 PRK09492 treR trehalose repres 24.8 1.9E+02 0.0042 27.3 6.2 46 324-373 159-208 (315)
84 COG1611 Predicted Rossmann fol 24.4 93 0.002 29.0 3.8 39 326-373 34-72 (205)
85 cd06478 ACD_HspB4-5-6 Alpha-cr 24.2 59 0.0013 25.5 2.1 18 129-146 20-37 (83)
86 cd06463 p23_like Proteins cont 24.2 2.9E+02 0.0063 20.2 6.2 43 129-171 19-71 (84)
87 COG0071 IbpA Molecular chapero 24.1 1.7E+02 0.0037 25.3 5.2 44 129-172 63-131 (146)
88 cd06274 PBP1_FruR Ligand bindi 24.0 2E+02 0.0044 26.2 6.0 46 324-373 100-148 (264)
89 cd06498 ACD_alphaB-crystallin_ 23.8 53 0.0012 25.9 1.8 18 129-146 20-37 (84)
90 PTZ00027 60S ribosomal protein 23.8 80 0.0017 29.1 3.2 24 124-147 123-149 (190)
91 TIGR03654 L6_bact ribosomal pr 23.7 81 0.0018 28.6 3.2 29 120-148 105-137 (175)
92 cd01540 PBP1_arabinose_binding 23.5 1.9E+02 0.0042 26.7 5.9 52 322-373 105-162 (289)
93 PRK10703 DNA-binding transcrip 23.4 1.9E+02 0.0042 27.7 6.1 44 331-374 165-211 (341)
94 cd06296 PBP1_CatR_like Ligand- 23.0 2.2E+02 0.0048 25.9 6.1 43 331-373 104-149 (270)
95 COG3603 Uncharacterized conser 22.9 1.4E+02 0.003 25.8 4.1 51 91-147 22-72 (128)
96 cd06480 ACD_HspB8_like Alpha-c 22.7 54 0.0012 26.6 1.7 20 129-148 28-47 (91)
97 cd06476 ACD_HspB2_like Alpha c 22.7 57 0.0012 25.8 1.7 19 129-147 20-38 (83)
98 PF00532 Peripla_BP_1: Peripla 22.6 1.4E+02 0.0029 28.6 4.7 43 331-373 105-151 (279)
99 PRK10727 DNA-binding transcrip 22.1 2.2E+02 0.0047 27.5 6.1 42 332-373 164-208 (343)
100 PF04969 CS: CS domain; Inter 22.0 3.1E+02 0.0067 20.0 5.7 42 129-170 25-76 (79)
101 PF11280 DUF3081: Protein of u 21.8 68 0.0015 25.5 2.0 40 195-234 18-62 (79)
102 PRK05498 rplF 50S ribosomal pr 21.8 93 0.002 28.3 3.2 29 120-148 106-138 (178)
103 cd06497 ACD_alphaA-crystallin_ 21.8 62 0.0013 25.6 1.8 19 129-147 23-41 (86)
104 COG1908 FrhD Coenzyme F420-red 21.7 1.9E+02 0.0042 25.0 4.8 40 334-373 44-93 (132)
105 cd06293 PBP1_LacI_like_11 Liga 21.6 2.5E+02 0.0053 25.7 6.1 42 332-373 104-148 (269)
106 smart00812 Alpha_L_fucos Alpha 21.6 1.1E+02 0.0025 31.2 4.1 42 333-374 84-144 (384)
107 PF13380 CoA_binding_2: CoA bi 21.1 1.1E+02 0.0024 25.5 3.3 39 331-374 67-105 (116)
108 cd06271 PBP1_AglR_RafR_like Li 21.0 2.3E+02 0.0049 25.7 5.8 43 331-373 107-152 (268)
109 cd01545 PBP1_SalR Ligand-bindi 21.0 2.7E+02 0.0058 25.3 6.2 45 330-374 104-151 (270)
110 COG0041 PurE Phosphoribosylcar 20.8 2.6E+02 0.0057 25.2 5.6 40 334-373 20-59 (162)
111 PF07355 GRDB: Glycine/sarcosi 20.7 1.5E+02 0.0032 30.1 4.6 31 319-349 316-346 (349)
112 PF01120 Alpha_L_fucos: Alpha- 20.5 1.3E+02 0.0029 30.0 4.2 43 332-374 93-154 (346)
113 PF13601 HTH_34: Winged helix 20.3 1.4E+02 0.0031 23.3 3.6 35 28-65 27-61 (80)
114 cd06482 ACD_HspB10 Alpha cryst 20.3 68 0.0015 25.7 1.8 19 129-147 21-39 (87)
115 cd06282 PBP1_GntR_like_2 Ligan 20.2 2.4E+02 0.0053 25.4 5.7 44 330-373 102-149 (266)
No 1
>CHL00140 rpl6 ribosomal protein L6; Validated
Probab=100.00 E-value=1.5e-55 Score=399.06 Aligned_cols=168 Identities=43% Similarity=0.724 Sum_probs=164.6
Q ss_pred cccCCcceeecCCCeEEEEeccEEEEEeCCeEEEEEcCCCeEEEEeCCEEEEEEcCCchhHHHHHHHHHHHHhhcceecc
Q psy8860 118 ARSMGKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKNDSNVLYFTAINNSRIAKSMSGTMRSIINNMIIGVT 197 (374)
Q Consensus 118 a~~ig~~~I~IP~~V~v~~~~~~i~vkGp~G~l~~~l~~~v~i~~~~~~l~i~~~~~~k~~~a~~gT~rsli~Nmi~GVt 197 (374)
|+|+|+.||+||+||+|+++++.|+|+||+|+|+++|++.+++..++|.+.+..|+++++++|+|||+||||+|||+||+
T Consensus 1 msrig~~~I~IP~~V~v~i~~~~v~vkGp~G~l~~~~~~~v~i~~~~~~i~v~~~~~~k~~~a~~gt~~slI~Nmi~GVt 80 (178)
T CHL00140 1 MSRIGKLPIKIPDNVNVSIDDQIIKVKGPKGTLSRKIPDLITIEIQDNSLFVSKKDESKKARALHGLYRTLINNMVIGVS 80 (178)
T ss_pred CCcccceeeecCCCCEEEEECCEEEEECCCEEEEEECCCCeEEEEeCCEEEEEcCCCCHHHHHHHHHHHHHHHHHHhhcc
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceEEEEEEEEEEEEEEEeCcEEEEEecceeeEEEeCCCCcEEEcccCCEEEEEecchhhhhhHHHHHHhhcCCCCcCCc
Q psy8860 198 KGFEKKLQLIGVGFRAKIEKNYLNLILGFSHPILYKIPFDIICETPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKGI 277 (374)
Q Consensus 198 ~Gf~~~L~lvGvGyr~~~~g~~L~l~LG~Sh~i~~~IP~gV~v~~~~~t~I~l~G~dke~Vgq~Aa~Ir~~r~pepYkgk 277 (374)
+||+++|+++|+||||.++|+.|.++||||||+.++||+||+|+|+++|+|+|+|+|||+|+||||+||+||||||||||
T Consensus 81 ~Gf~~~L~lvGvGyr~~~~g~~l~l~LG~sh~i~~~IP~gv~v~~~~~t~I~i~G~dke~Vgq~AA~Ir~~r~pepYKGK 160 (178)
T CHL00140 81 EGFEKKLELQGVGYRAQVQGKDLILNLGYSHPVKIKIPPGISVEVENNTNITIKGIDKELVGQFAAKIRSVRPPEPYKGK 160 (178)
T ss_pred cCceEEEEEEEEEEEEEEeCCcEEEEecCCeeEEEECCCCeEEEeCCCCEEEEEECCHHHHHHHHHHHhccCCCCCcCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeecc
Q psy8860 278 NRLMVHRT 285 (374)
Q Consensus 278 giL~V~eS 285 (374)
||+|.+|.
T Consensus 161 GI~y~~e~ 168 (178)
T CHL00140 161 GIRYKGEV 168 (178)
T ss_pred cEeECCEE
Confidence 99998873
No 2
>TIGR03654 L6_bact ribosomal protein L6, bacterial type.
Probab=100.00 E-value=3.5e-54 Score=389.31 Aligned_cols=167 Identities=49% Similarity=0.803 Sum_probs=163.2
Q ss_pred ccCCcceeecCCCeEEEEeccEEEEEeCCeEEEEEcCCCeEEEEeCCEEEEEEcCCchhHHHHHHHHHHHHhhcceeccc
Q psy8860 119 RSMGKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKNDSNVLYFTAINNSRIAKSMSGTMRSIINNMIIGVTK 198 (374)
Q Consensus 119 ~~ig~~~I~IP~~V~v~~~~~~i~vkGp~G~l~~~l~~~v~i~~~~~~l~i~~~~~~k~~~a~~gT~rsli~Nmi~GVt~ 198 (374)
+|+|++||.||++|+|+++++.|+|+||+|+|+++|++.+++..++|.+.++.|+++++++++|||+||||+|||+|||+
T Consensus 1 s~ig~~~I~IP~~V~v~~~~~~v~v~Gp~G~l~~~l~~~i~i~~~~~~i~v~~~~~~kk~~a~~gt~~s~i~Nmi~GVt~ 80 (175)
T TIGR03654 1 SRIGKKPIAIPAGVEVTIDGNVVTVKGPKGELSRTLHPGVTVKVEDGQLTVSRPNDSKEARALHGTTRALINNMVIGVSE 80 (175)
T ss_pred CcccccceecCCCcEEEEeCCEEEEEcCCeEEEEEcCCCeEEEEECCEEEEEecCCCHHHHHHHHHHHHHHHHHhheecc
Confidence 58999999999999999999999999999999999988999999999999999999999999999999999999999999
Q ss_pred ceEEEEEEEEEEEEEEEeCcEEEEEecceeeEEEeCCCCcEEEcccCCEEEEEecchhhhhhHHHHHHhhcCCCCcCCce
Q psy8860 199 GFEKKLQLIGVGFRAKIEKNYLNLILGFSHPILYKIPFDIICETPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKGIN 278 (374)
Q Consensus 199 Gf~~~L~lvGvGyr~~~~g~~L~l~LG~Sh~i~~~IP~gV~v~~~~~t~I~l~G~dke~Vgq~Aa~Ir~~r~pepYkgkg 278 (374)
||+++|+++|+||||.++|+.|.++|||||++.++||+||+++++++|+|+|+|+|||+|+||||+||++||||||||||
T Consensus 81 Gf~~~L~lvGvgyrv~~~g~~l~l~LG~sh~i~~~Ip~~v~v~~~~~t~I~i~G~dke~Vgq~AA~Ir~~r~pepYKgkG 160 (175)
T TIGR03654 81 GFEKKLEIVGVGYRAQLQGKKLNLSLGYSHPVEYEIPEGITVEVPKPTEIVVKGIDKQLVGQVAAEIRAFRKPEPYKGKG 160 (175)
T ss_pred CcEEEEEEEEEEEEEEEeCCeEEEEecCceeEEEECCCCeEEEeCCCCEEEEEECCHHHHHHHHHHHhccCCCCCcCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeecc
Q psy8860 279 RLMVHRT 285 (374)
Q Consensus 279 iL~V~eS 285 (374)
|+|.+|.
T Consensus 161 i~~~~e~ 167 (175)
T TIGR03654 161 IRYAGEV 167 (175)
T ss_pred EeECCEE
Confidence 9998874
No 3
>PRK05498 rplF 50S ribosomal protein L6; Validated
Probab=100.00 E-value=9.1e-54 Score=387.71 Aligned_cols=168 Identities=49% Similarity=0.808 Sum_probs=164.0
Q ss_pred cccCCcceeecCCCeEEEEeccEEEEEeCCeEEEEEcCCCeEEEEeCCEEEEEEcCCchhHHHHHHHHHHHHhhcceecc
Q psy8860 118 ARSMGKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKNDSNVLYFTAINNSRIAKSMSGTMRSIINNMIIGVT 197 (374)
Q Consensus 118 a~~ig~~~I~IP~~V~v~~~~~~i~vkGp~G~l~~~l~~~v~i~~~~~~l~i~~~~~~k~~~a~~gT~rsli~Nmi~GVt 197 (374)
|+++|+.||+||++|+|+++++.|+|+||+|+|+++|++++++..+++.|.+..|+++++++|+|||+||||+|||+||+
T Consensus 1 ms~ig~~~I~IP~~V~v~~~~~~v~vkGp~G~l~~~~~~~v~i~~~~~~i~v~~~~~~k~~~a~~gt~~s~I~Nmi~GVt 80 (178)
T PRK05498 1 MSRIGKKPIAIPAGVEVTINGNVVTVKGPKGELSRTLNPDVTVKVEDNEITVTRPDDSKKARALHGTTRALINNMVVGVT 80 (178)
T ss_pred CCcccccceecCCCCEEEEECCEEEEECCCEEEEEEcCCCeEEEEECCEEEEEcCCCCHHHHHHHHHHHHHHHHHhhhcC
Confidence 68999999999999999999999999999999999998899999999999999999999999999999999999999999
Q ss_pred cceEEEEEEEEEEEEEEEeCcEEEEEecceeeEEEeCCCCcEEEcccCCEEEEEecchhhhhhHHHHHHhhcCCCCcCCc
Q psy8860 198 KGFEKKLQLIGVGFRAKIEKNYLNLILGFSHPILYKIPFDIICETPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKGI 277 (374)
Q Consensus 198 ~Gf~~~L~lvGvGyr~~~~g~~L~l~LG~Sh~i~~~IP~gV~v~~~~~t~I~l~G~dke~Vgq~Aa~Ir~~r~pepYkgk 277 (374)
+||+++|+++|+||+|.++|+.|.++||||||+.++||+||+|+++++|+|+|+|+|+|+|+||||+||++|||||||||
T Consensus 81 ~Gf~~~L~lvGvgyrv~~~g~~l~l~LG~sh~i~~~Ip~gv~v~~~~~t~I~i~G~dke~Vg~~AA~Ir~~r~pe~Ykgk 160 (178)
T PRK05498 81 EGFEKKLEIVGVGYRAQVKGKKLNLSLGYSHPVEYEIPEGITVEVPKPTEIVVKGIDKQLVGQVAAEIRSYRPPEPYKGK 160 (178)
T ss_pred CCeEEEEEEEeEEEEEEEeCCeEEEEecCCEEEEEECCCCeEEEeCCCCEEEEEECCHHHHHHHHHHHhccCCCCCccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeecc
Q psy8860 278 NRLMVHRT 285 (374)
Q Consensus 278 giL~V~eS 285 (374)
||++.++.
T Consensus 161 Gi~~~~e~ 168 (178)
T PRK05498 161 GIRYAGEV 168 (178)
T ss_pred cEeECCEE
Confidence 99998874
No 4
>COG0097 RplF Ribosomal protein L6P/L9E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-53 Score=380.49 Aligned_cols=166 Identities=42% Similarity=0.756 Sum_probs=158.0
Q ss_pred cccCCcceeecCCCeEEEEeccEEEEEeCCeEEEEEcCCCe-EEEEeCCEEEEEEcCCchhHHHHHHHHHHHHhhcceec
Q psy8860 118 ARSMGKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLV-NIKNDSNVLYFTAINNSRIAKSMSGTMRSIINNMIIGV 196 (374)
Q Consensus 118 a~~ig~~~I~IP~~V~v~~~~~~i~vkGp~G~l~~~l~~~v-~i~~~~~~l~i~~~~~~k~~~a~~gT~rsli~Nmi~GV 196 (374)
|+|+|+.||.+|+||+|+++++.++|+||+|+|+++|++.+ .++.+++.+.+..++. ++.+|+|||+||||+||++||
T Consensus 1 Msri~k~~i~~P~gV~V~i~~~~v~vkGpkGeL~~~~~~~~v~v~~~~~~~vv~~~~~-k~~~a~~Gt~rali~Nmv~GV 79 (178)
T COG0097 1 MSRIGKRPIVIPAGVTVSIEGQVVTVKGPKGELTREFHDNVVKVEVEDNILVVRPVDG-KRKRALHGTVRALINNMVKGV 79 (178)
T ss_pred CCceeeccEecCCCeEEEEeccEEEEECCCcEEEEEecCcceEEEecCCEEEEeeccc-chhHHHHHHHHHHHHHHheec
Confidence 68999999999999999999999999999999999999765 8888899888887776 556699999999999999999
Q ss_pred ccceEEEEEEEEEEEEEEEeCcEEEEEecceeeEEEeCCCCcEEEcccCCEEEEEecchhhhhhHHHHHHhhcCCCCcCC
Q psy8860 197 TKGFEKKLQLIGVGFRAKIEKNYLNLILGFSHPILYKIPFDIICETPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKG 276 (374)
Q Consensus 197 t~Gf~~~L~lvGvGyr~~~~g~~L~l~LG~Sh~i~~~IP~gV~v~~~~~t~I~l~G~dke~Vgq~Aa~Ir~~r~pepYkg 276 (374)
|+||+|+|+++|+|||+++.|+.|.|+||||||+.++||+||+++++++|+|+|+|+|||+||||||+||++|+||||||
T Consensus 80 teGf~~kL~ivgvgyra~v~g~~l~l~LG~shp~~~~ip~gi~v~v~~~t~I~v~GidKe~VGQ~AA~Ir~~r~pepykg 159 (178)
T COG0097 80 TEGFEKKLEIVGVGYRAQVVGGNLELFLGYSHPVVIEIPEGITVEVPGPTEIVVEGIDKELVGQVAANIRAARKPEPYKG 159 (178)
T ss_pred ccceEEEEEEEEecceeEEeccEEEEeecccCCeEEECCCCeEEEecCCCEEEEEcCCHHHHhHHHHHHHhccCCCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeeeec
Q psy8860 277 INRLMVHR 284 (374)
Q Consensus 277 kgiL~V~e 284 (374)
||++|.++
T Consensus 160 Kgi~ydge 167 (178)
T COG0097 160 KGIRYDGE 167 (178)
T ss_pred cceEEcCE
Confidence 99988765
No 5
>PRK05518 rpl6p 50S ribosomal protein L6P; Reviewed
Probab=100.00 E-value=3.2e-44 Score=324.72 Aligned_cols=149 Identities=32% Similarity=0.422 Sum_probs=143.4
Q ss_pred CcceeecCCCeEEEEeccEEEEEeCCeEEEEEcCC-CeEEEEeCCEEEEEEcCCchhHHHHHHHHHHHHhhcceecccce
Q psy8860 122 GKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNN-LVNIKNDSNVLYFTAINNSRIAKSMSGTMRSIINNMIIGVTKGF 200 (374)
Q Consensus 122 g~~~I~IP~~V~v~~~~~~i~vkGp~G~l~~~l~~-~v~i~~~~~~l~i~~~~~~k~~~a~~gT~rsli~Nmi~GVt~Gf 200 (374)
-.+||.||++|+|+++++.|+|+||+|+|+++|++ .+++.+++|.+.+..|+++++++|+|||+||||+|||+|||+||
T Consensus 6 ~~~pI~IP~~V~v~i~~~~v~VkGp~G~L~~~~~~~~v~i~~~~~~i~v~~~~~~kk~ra~~gt~rslI~NmI~GVt~Gf 85 (180)
T PRK05518 6 IREEIEIPEGVTVEIEGLVVTVKGPKGELTRDFWYPGVTISVEDGKVVIETEFARKKTKAMVGTFASHIKNMIKGVTEGF 85 (180)
T ss_pred ccccEEcCCCCEEEEECCEEEEECCCeEEEEEecCCcEEEEEECCEEEEEECCCCHHHHHHHHHHHHHHHhhheecccce
Confidence 35799999999999999999999999999999987 99999999999999999999999999999999999999999999
Q ss_pred EEEEEEEEEEE--EEEEeCcEEEE--EecceeeEEEeCCCCcEEEcccCCEEEEEecchhhhhhHHHHHHhhcCC
Q psy8860 201 EKKLQLIGVGF--RAKIEKNYLNL--ILGFSHPILYKIPFDIICETPSQTEILIKGINKQAVGHVAAEIRRYYKP 271 (374)
Q Consensus 201 ~~~L~lvGvGy--r~~~~g~~L~l--~LG~Sh~i~~~IP~gV~v~~~~~t~I~l~G~dke~Vgq~Aa~Ir~~r~p 271 (374)
+++|+++|+|| |+.++|+.|.+ +||||||+.++||+||++++++ |+|+|+|+|||+||||||+||+.++.
T Consensus 86 ~~~LelvGvGypira~~~g~~l~l~n~LG~Sh~v~~~iP~gV~v~~~~-t~I~i~GiDKq~Vgq~AA~Ir~~~~~ 159 (180)
T PRK05518 86 EYKLKIVYSHFPMQVKVQGNEVVIENFLGEKSPRRAKILGGVKVKVKG-EDVIVEGIDKEDVGQTAANIEQATKI 159 (180)
T ss_pred EEEEEEEecCccEEEEEcCCEEEEEeccccceeEEEeCCCCeEEEecC-CEEEEEeCCHHHHHHHHHHHHHhhcc
Confidence 99999999999 88999999987 9999999999999999999999 99999999999999999999998853
No 6
>TIGR03653 arch_L6P archaeal ribosomal protein L6P. Members of this protein family are the archaeal ribosomal protein L6P. The top-scoring proteins not selected by this model are eukaryotic cytosolic ribosomal protein L9. Bacterial ribosomal protein L6 scores lower and is described by a distinct model.
Probab=100.00 E-value=5.3e-44 Score=320.95 Aligned_cols=149 Identities=33% Similarity=0.483 Sum_probs=142.5
Q ss_pred cceeecCCCeEEEEeccEEEEEeCCeEEEEEc-CCCeEEEEeCCEEEEEEcCCchhHHHHHHHHHHHHhhcceecccceE
Q psy8860 123 KMPIFIPPNVEVTLNSNKITLKGPLGILKQNK-NNLVNIKNDSNVLYFTAINNSRIAKSMSGTMRSIINNMIIGVTKGFE 201 (374)
Q Consensus 123 ~~~I~IP~~V~v~~~~~~i~vkGp~G~l~~~l-~~~v~i~~~~~~l~i~~~~~~k~~~a~~gT~rsli~Nmi~GVt~Gf~ 201 (374)
.+||.||++|+|+++++.|+|+||+|+|+++| ++.+++.+++|.+.++.|+++++++++|||+||||+|||+|||+||+
T Consensus 1 ~~pI~IP~~V~v~i~~~~i~vkGp~G~L~~~~~~~~v~i~~~~~~i~v~~~~~~k~~~a~~gt~rsli~NmI~GVt~Gf~ 80 (170)
T TIGR03653 1 REEIEIPEGVSVTIEGNIVTVKGPKGEVTRELWYPGIEISVEDGKVVIETDFARKKDKAMVGTYRSHIKNMIKGVTEGFE 80 (170)
T ss_pred CceEecCCCCEEEEeCCEEEEECCCeEEEEEEeCCcEEEEEeCCEEEEEeCCCCHHHHHHHHHHHHHHHhheeecccCeE
Confidence 36899999999999999999999999999999 78999999999999999999999999999999999999999999999
Q ss_pred EEEEEEEEEE--EEEEeCcEEEE--EecceeeEEEeCCCCcEEEcccCCEEEEEecchhhhhhHHHHHHhhcCCC
Q psy8860 202 KKLQLIGVGF--RAKIEKNYLNL--ILGFSHPILYKIPFDIICETPSQTEILIKGINKQAVGHVAAEIRRYYKPE 272 (374)
Q Consensus 202 ~~L~lvGvGy--r~~~~g~~L~l--~LG~Sh~i~~~IP~gV~v~~~~~t~I~l~G~dke~Vgq~Aa~Ir~~r~pe 272 (374)
++|+++|+|| ||.++|+.|.+ +||||||+.++||+||+++++++ +|+|+|+|||+||||||.||+.++..
T Consensus 81 ~~LeivGvGy~~ra~~~g~~L~l~n~LG~Sh~i~~~iP~gI~v~~~~~-~I~i~G~DKq~Vgq~AA~Ir~~~~~~ 154 (170)
T TIGR03653 81 YKMKVVYSHFPMQVKVEGNKVVIENFLGEKAPRRAKIPGGVKVKVKGE-EVIVTGIDKEDVGQTAANIEQATRIK 154 (170)
T ss_pred EEEEEEeccccEEEEEcCCeEEEeeccccceeEEEECCCCeEEEecCC-EEEEEeCCHHHHHHHHHHHHHhhccc
Confidence 9999999999 88899999887 99999999999999999999985 99999999999999999999988643
No 7
>KOG3254|consensus
Probab=100.00 E-value=1.5e-44 Score=318.73 Aligned_cols=166 Identities=36% Similarity=0.627 Sum_probs=150.6
Q ss_pred cCCcceeecCCCeEEEEeccEEEEEeCCeEEEEEcCCCeEEEEeC---CEEEEEEcCCchhHHHHHHHHHHHHhhcceec
Q psy8860 120 SMGKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKNDS---NVLYFTAINNSRIAKSMSGTMRSIINNMIIGV 196 (374)
Q Consensus 120 ~ig~~~I~IP~~V~v~~~~~~i~vkGp~G~l~~~l~~~v~i~~~~---~~l~i~~~~~~k~~~a~~gT~rsli~Nmi~GV 196 (374)
-+|+++|..|+...-.+++..+.|+||+|+|.+++|.+++++.+. +..........|++++||||+|+|++||+.||
T Consensus 33 ~~~~k~i~~~e~k~~~lege~l~vkGP~gel~l~~P~~l~L~~dkk~~g~~~~~k~~etkkqr~mwgt~R~l~~N~v~GV 112 (211)
T KOG3254|consen 33 YVGKKEIIVKENKQRDLEGEQLQVKGPHGELNLRFPNYLNLSNDKKKSGMDANIKKQETKKQRAMWGTFRALLANNVKGV 112 (211)
T ss_pred eecceeEEeehhhccccccCceEeeCCcceeeccCCccccccchhhhcceeeeecchhhHHHHHHHHHHHHHHhccchhh
Confidence 467777777777777789999999999999999999998885433 22333345567899999999999999999999
Q ss_pred ccceEEEEEEEEEEEEEEEeCcEEEEEecceeeEEEeCCCCcEEEcccCCEEEEEecchhhhhhHHHHHHhhcCCCCcCC
Q psy8860 197 TKGFEKKLQLIGVGFRAKIEKNYLNLILGFSHPILYKIPFDIICETPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKG 276 (374)
Q Consensus 197 t~Gf~~~L~lvGvGyr~~~~g~~L~l~LG~Sh~i~~~IP~gV~v~~~~~t~I~l~G~dke~Vgq~Aa~Ir~~r~pepYkg 276 (374)
|.||.+.|++||+|||+.++|+.|.++|||||++...||++|+|+++.||.|+++|+|||+|+||||.+|+|+|||||||
T Consensus 113 t~g~~k~l~lVGvGYRa~legk~l~lklG~S~~v~l~iP~~v~Vk~p~ptsl~~~G~dKq~V~qFAAkvRsfkpPEPYKG 192 (211)
T KOG3254|consen 113 TMGFLKILKLVGVGYRASLEGKFLHLKLGYSHDVLLSIPTDVQVKNPTPTSLVLRGIDKQKVTQFAAKVRSFKPPEPYKG 192 (211)
T ss_pred hhhhhheeeEEeeeeEEEecCceEEEEeccccceeecCCCceEEecCCCCEEEEecccHHHHHHHHHHHhccCCCCCcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeeeecc
Q psy8860 277 INRLMVHRT 285 (374)
Q Consensus 277 kgiL~V~eS 285 (374)
|||.+.+|.
T Consensus 193 KGIyv~dE~ 201 (211)
T KOG3254|consen 193 KGIYVDDEK 201 (211)
T ss_pred CceEeccce
Confidence 999987764
No 8
>PTZ00027 60S ribosomal protein L6; Provisional
Probab=100.00 E-value=5.3e-43 Score=319.48 Aligned_cols=149 Identities=26% Similarity=0.326 Sum_probs=140.6
Q ss_pred cceeecCCCeEEEEeccEEEEEeCCeEEEEEcCC---CeEEEEeCCEEEEEEcCCchhHHHHHHHHHHHHhhcceecccc
Q psy8860 123 KMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNN---LVNIKNDSNVLYFTAINNSRIAKSMSGTMRSIINNMIIGVTKG 199 (374)
Q Consensus 123 ~~~I~IP~~V~v~~~~~~i~vkGp~G~l~~~l~~---~v~i~~~~~~l~i~~~~~~k~~~a~~gT~rsli~Nmi~GVt~G 199 (374)
..||.||+||+|+++++.|+|+||+|+|+++|++ .+.+..+++.+.++.|.++++.+|+|||+||||+|||+|||+|
T Consensus 7 ~~~I~IP~~V~V~i~~~~v~VkGp~G~L~~~~~~~~~~i~i~~~~~~i~v~~~~~~~k~~a~~Gt~rslI~NmI~GVt~G 86 (190)
T PTZ00027 7 SEKIRIPEGVTVTVKSRKVTVTGKYGELTRSFRHLPVDIKLSKDGKYIKVEMWFGTPSHLACIRTVCSHIKNMMTGVTKK 86 (190)
T ss_pred CCCEecCCCCEEEEECCEEEEECCCceEEEEecCCCceEEEEeCCCEEEEEeCCCCHHHHHHHHHHHHHHHHHhhhhcCC
Confidence 4699999999999999999999999999999997 5667779999999999999999999999999999999999999
Q ss_pred eEEEEEEEEEEEEEE--E--eCcEEEE--EecceeeEEEeCCCCcEEEcccC--CEEEEEecchhhhhhHHHHHHhhcCC
Q psy8860 200 FEKKLQLIGVGFRAK--I--EKNYLNL--ILGFSHPILYKIPFDIICETPSQ--TEILIKGINKQAVGHVAAEIRRYYKP 271 (374)
Q Consensus 200 f~~~L~lvGvGyr~~--~--~g~~L~l--~LG~Sh~i~~~IP~gV~v~~~~~--t~I~l~G~dke~Vgq~Aa~Ir~~r~p 271 (374)
|+++|+++|+||||. + +|+.|.+ +||||||+.++||+||+++++++ |+|+|+|+|||+||||||+||+.++.
T Consensus 87 f~~~LeivGvGyra~~~v~~~g~~L~l~N~LG~Sh~i~~~iP~gv~v~~~~~~~t~I~i~G~DKq~Vgq~AA~I~~~~~~ 166 (190)
T PTZ00027 87 FQYKMRLVYAHFPINSNITDNGKTIEIRNFLGEKRVRTVKMLPGVVVEKSESVKDEIIVTGADLELVSRSAALIHQSTLV 166 (190)
T ss_pred EEEEEEEEEeeeeEEEEEcCCCCEEEEEccCCCceeEEEECCCCeEEEeCCCCCCEEEEEeCCHHHHHHHHHHHHHHhcc
Confidence 999999999999999 6 7888988 99999999999999999999975 89999999999999999999998853
No 9
>PTZ00179 60S ribosomal protein L9; Provisional
Probab=100.00 E-value=5e-43 Score=319.40 Aligned_cols=149 Identities=23% Similarity=0.319 Sum_probs=142.5
Q ss_pred CcceeecCCCeEEEEeccEEEEEeCCeEEEEEcCC---CeEEEEeCCEEEEEEcCCchhHHHHHHHHHHHHhhcceeccc
Q psy8860 122 GKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNN---LVNIKNDSNVLYFTAINNSRIAKSMSGTMRSIINNMIIGVTK 198 (374)
Q Consensus 122 g~~~I~IP~~V~v~~~~~~i~vkGp~G~l~~~l~~---~v~i~~~~~~l~i~~~~~~k~~~a~~gT~rsli~Nmi~GVt~ 198 (374)
-..||+||+||+|+++++.|+|+||+|+|+++|++ .+.+..+++.|.+++|+++++.+|+|||+||||+|||+|||+
T Consensus 5 ~~~pI~IP~~V~V~i~~~~ItVkGpkG~Ls~~~~~~~~~i~i~~~~~~I~v~~~~~~kk~~al~Gt~rslI~NMI~GVt~ 84 (189)
T PTZ00179 5 SQDTITIPEDVTVSVKDRIVTVKGKRGTLTKDLRHLQLDFRVNKKNRTFTAVRWFGSKIPNSTINTALSHVRNMITGVTK 84 (189)
T ss_pred ccccEeCCCCCEEEEeCCEEEEECCCcEEEEEcCCCCcEEEEEecCCEEEEEeCCCCHHHHHHHHHHHHHHHHHhhhhcC
Confidence 35799999999999999999999999999999998 678888889999999999999999999999999999999999
Q ss_pred ceEEEEEEEEEEE--EEEEeCcEEEE--EecceeeEEEeCCCCcEEEcccC----CEEEEEecchhhhhhHHHHHHhhcC
Q psy8860 199 GFEKKLQLIGVGF--RAKIEKNYLNL--ILGFSHPILYKIPFDIICETPSQ----TEILIKGINKQAVGHVAAEIRRYYK 270 (374)
Q Consensus 199 Gf~~~L~lvGvGy--r~~~~g~~L~l--~LG~Sh~i~~~IP~gV~v~~~~~----t~I~l~G~dke~Vgq~Aa~Ir~~r~ 270 (374)
||+++|+++|+|| ||.++|+.|.+ +||||||+.++||+||++++++| |+|+|+|+|||+||||||+|++.++
T Consensus 85 GF~k~L~ivgvgyp~ra~v~g~~l~l~N~LG~sh~~~~~ip~gv~v~~~~~~~~k~~i~i~G~DKq~Vgq~AA~i~~~~~ 164 (189)
T PTZ00179 85 GFRFKVRFAYAHFPISVSVENQLVEIRNFLGEKRVRRQVVADTVKVYRTDPSKVKDELVLEGNDLEQVSREAAVMHQLCL 164 (189)
T ss_pred CEEEEEEEEEeCcceEEEEcCCEEEEEecCCCCccEEEECCCCEEEEecCCcccCCEEEEEeCCHHHHHHHHHHHHHhhc
Confidence 9999999999999 99999999987 99999999999999999999988 8999999999999999999999884
No 10
>COG0096 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.8e-42 Score=293.64 Aligned_cols=125 Identities=50% Similarity=0.801 Sum_probs=119.0
Q ss_pred CCCcchHHHHHHhhhhhhccCCceEEeecchhHHHHHHHHHhCCCcceEEEEeccCCeeEEEEEEEee-cCcceeeeeee
Q psy8860 1 MSMSDPIADMLTYIRNGQIVNKKKIIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELKILLKYY-MNRPVIECLKR 79 (374)
Q Consensus 1 M~~~d~iad~lt~IrNa~~a~~~~v~~p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~LKY~-~~~pvi~~~~~ 79 (374)
|+|+|||||||||||||++++|..|++|+||++.+||++|++||||++|+++|+ ..+..++|+|||+ +++|||+.++|
T Consensus 1 m~~~DpiAdmltrIrNa~~~~~~~v~~P~SKl~~~il~vLk~eGYI~~f~~~~~-~~~~~~~v~Lky~~n~~~vI~~~~r 79 (132)
T COG0096 1 MMMTDPLADMLTRIRNAERAKKEVVSMPASKLKGAILKVLKKEGYIKDFEVIDD-GRKGKLRVQLKYRINGCGVISPIKR 79 (132)
T ss_pred CccccHHHHHHHHhHhHHHhccceeecchHHHHHHHHHHHHHcCCcceEEEEeC-CcceEEEEEEEeccCCCccccccee
Confidence 899999999999999999999999999999999999999999999999999985 5677999999997 77899999999
Q ss_pred eccCCCcccccCCCcccccCCceEEEEEcCCcccccccccc--CCccee
Q psy8860 80 VSRPGLRIYKNKDNIPKIMNGLGLVIISTASGIITDRKARS--MGKMPI 126 (374)
Q Consensus 80 iSkP~~Rvy~~~~~l~~~~~g~G~~ivSTs~Gvmt~~ea~~--ig~~~I 126 (374)
|||||+|+|.+.++||++++|+|++|||||+|||||+||++ +|++.+
T Consensus 80 VSkpg~rvy~~~~~LP~v~~g~Gi~IvSTs~GVMtd~eAr~~~vGGevL 128 (132)
T COG0096 80 VSKPGLRVYEKKRELPAVLNGLGIAIVSTSKGVMTDKEARKKGVGGEVL 128 (132)
T ss_pred cCCCCceeecChhhhhhhhcCceEEEEEcCCCccChHHHHHcCCCcEEE
Confidence 99999999999999999999999999999999999999995 777655
No 11
>CHL00042 rps8 ribosomal protein S8
Probab=100.00 E-value=6.6e-40 Score=283.39 Aligned_cols=123 Identities=45% Similarity=0.753 Sum_probs=115.2
Q ss_pred CcchHHHHHHhhhhhhccCCceEEeecchhHHHHHHHHHhCCCcceEEEEeccCCeeEEEEEEEee--cCcceeeeeeee
Q psy8860 3 MSDPIADMLTYIRNGQIVNKKKIIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELKILLKYY--MNRPVIECLKRV 80 (374)
Q Consensus 3 ~~d~iad~lt~IrNa~~a~~~~v~~p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~LKY~--~~~pvi~~~~~i 80 (374)
|+|||||||||||||++|++.+|.+|+||++.+||++|++||||++|++.++ ++++.++|+|||+ +++|||+.++||
T Consensus 2 ~~d~iad~lt~IrNa~~a~~~~v~ip~Skl~~~il~iL~~eGyI~~~~~~~~-~~~~~i~v~Lky~~~~~~pvi~~i~~i 80 (132)
T CHL00042 2 GNDTIADMLTRIRNANMVKKGTVRIPATNITENIVKILLREGFIENVREHRE-NNKYFLVLTLKYRGNKKKPYITTLKRI 80 (132)
T ss_pred CcchHHHHHHHhHHHHHCCCCEEEEeccHHHHHHHHHHHHCCcccceEEEec-CCeeEEEEEEEeecCCCceeccccEEE
Confidence 4699999999999999999999999999999999999999999999999864 4567899999998 458999999999
Q ss_pred ccCCCcccccCCCcccccCCceEEEEEcCCccccccccc--cCCccee
Q psy8860 81 SRPGLRIYKNKDNIPKIMNGLGLVIISTASGIITDRKAR--SMGKMPI 126 (374)
Q Consensus 81 SkP~~Rvy~~~~~l~~~~~g~G~~ivSTs~Gvmt~~ea~--~ig~~~I 126 (374)
||||+|+|+++++||++.+|+|++|||||+|||||+||+ ++|++.+
T Consensus 81 SkPg~Rvy~~~~~L~~~~~g~G~~IlSTskGimt~~eA~~~~iGGe~L 128 (132)
T CHL00042 81 SKPGLRIYSNYKEIPRVLGGMGIVILSTSKGIMTDREARLKGIGGEIL 128 (132)
T ss_pred cCCCceeEcCHhHHHHHhCCCcEEEEECCCCcccHHHHHHcCCCCEEE
Confidence 999999999999999999999999999999999999999 4888755
No 12
>PRK00136 rpsH 30S ribosomal protein S8; Validated
Probab=100.00 E-value=1.9e-38 Score=273.84 Aligned_cols=123 Identities=54% Similarity=0.895 Sum_probs=115.3
Q ss_pred CcchHHHHHHhhhhhhccCCceEEeecchhHHHHHHHHHhCCCcceEEEEeccCCeeEEEEEEEeecCcceeeeeeeecc
Q psy8860 3 MSDPIADMLTYIRNGQIVNKKKIIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELKILLKYYMNRPVIECLKRVSR 82 (374)
Q Consensus 3 ~~d~iad~lt~IrNa~~a~~~~v~~p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~LKY~~~~pvi~~~~~iSk 82 (374)
|+|+||||||+||||++|++.+|.+|+|+++++||++|++||||++|++.++ .+..+++|.|||++++|||+.+++|||
T Consensus 2 ~~d~i~d~lt~IrNa~~~~~~~v~ip~sk~~~~il~iL~~eGyI~~~~~~~~-~~~~~~~v~Lky~~~~pvi~~i~~ISk 80 (130)
T PRK00136 2 MTDPIADMLTRIRNAQMAKHETVSMPASKLKVAIAEILKEEGYIKDYEVEED-GKQGILRITLKYGEGEPVIEGIKRVSK 80 (130)
T ss_pred CcChHHHHHHHHHHHHHcCCCeEEecccHHHHHHHHHHHHCCcccceEEEec-CCcceEEEEEecCCCCcccccceEecC
Confidence 4699999999999999999999999999999999999999999999998864 334568999999988999999999999
Q ss_pred CCCcccccCCCcccccCCceEEEEEcCCccccccccc--cCCccee
Q psy8860 83 PGLRIYKNKDNIPKIMNGLGLVIISTASGIITDRKAR--SMGKMPI 126 (374)
Q Consensus 83 P~~Rvy~~~~~l~~~~~g~G~~ivSTs~Gvmt~~ea~--~ig~~~I 126 (374)
||+|+|+++++||++.+|+|++|+|||+|||||+||+ ++|++.+
T Consensus 81 Pg~Riy~~~~~l~~~~~g~G~~IlSTs~Gimt~~eA~~~~iGGeiL 126 (130)
T PRK00136 81 PGLRVYKKKDELPKVLNGLGIAIVSTSKGVMTDREARKAGVGGEVL 126 (130)
T ss_pred CCcceEcCHhHHHHHHCCCCEEEEEcCCCeeeHHHHHHhCCCCEEE
Confidence 9999999999999999999999999999999999999 4888754
No 13
>PF00410 Ribosomal_S8: Ribosomal protein S8; InterPro: IPR000630 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S8 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S8 is known to bind directly to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups eubacterial, algal and plant chloroplast, cyanelle, archaebacterial and Marchantia polymorpha mitochondrial S8; mammalian and plant S15A; and yeast S22 (S24) ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1S1H_H 3O30_O 3O2Z_O 3IZB_H 3U5G_W 3U5C_W 3OTO_H 1AN7_A 2HGR_K 3BBN_H ....
Probab=100.00 E-value=5e-36 Score=258.64 Aligned_cols=122 Identities=46% Similarity=0.764 Sum_probs=115.0
Q ss_pred chHHHHHHhhhhhhccCCceEEeecchhHHHHHHHHHhCCCcceEEEEeccCCeeEEEEEEEe-ecCcceeeeeeeeccC
Q psy8860 5 DPIADMLTYIRNGQIVNKKKIIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELKILLKY-YMNRPVIECLKRVSRP 83 (374)
Q Consensus 5 d~iad~lt~IrNa~~a~~~~v~~p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~LKY-~~~~pvi~~~~~iSkP 83 (374)
|||||||++||||+++++..|.+|+|++++++|++|++||||++|++.++..+.++++|+||| .+++|+|+.++++|+|
T Consensus 1 D~lad~l~~I~Na~~~~~~~v~ip~sk~~~~il~iL~~eGyI~~f~~~~~~~~~~~i~I~Lky~~~~~~~i~~i~~iSkp 80 (129)
T PF00410_consen 1 DPLADLLTRIRNASRARKRFVIIPYSKLNLSILKILKKEGYISGFEIIDDNRNGKRIWIELKYRRNGKPVIKKIKRISKP 80 (129)
T ss_dssp SHHHHHHHHHHHHHHTTCSEEEEEHCHHHHHHHHHHHHTTSEEEEEEEESSSSEEEEEEEESBCSSSSBSSSEEEESSBT
T ss_pred CcHHHHHHHhHHHHHCCCCEEEecccHHHHHHHHHHhhccccceeEeeccCCCceEEEEEEccccccchhhhhhhcccCC
Confidence 899999999999999999999999999999999999999999999998864445789999999 7899999999999999
Q ss_pred CCcccccCCCcccccCCceEEEEEcCCcccccccccc--CCccee
Q psy8860 84 GLRIYKNKDNIPKIMNGLGLVIISTASGIITDRKARS--MGKMPI 126 (374)
Q Consensus 84 ~~Rvy~~~~~l~~~~~g~G~~ivSTs~Gvmt~~ea~~--ig~~~I 126 (374)
|+|+|++.++|+++.+|+|++|+|||+||||++||++ +|++.+
T Consensus 81 ~~r~y~~~~~L~~~~~g~g~~IlSTskGImt~~eA~~~~vGGevL 125 (129)
T PF00410_consen 81 GRRVYISYKELPKVKNGLGILILSTSKGIMTHREARKLNVGGEVL 125 (129)
T ss_dssp TCCCEESGTGSHHSCTTTSEEEEEETTEEEEHHHHHHHTSEEEEE
T ss_pred CcceecCHHHHHHHhCCCeEEEEEcCCCcEeHHHHHHcCCCCEEE
Confidence 9999999999999999999999999999999999985 777654
No 14
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=100.00 E-value=2.9e-34 Score=239.71 Aligned_cols=95 Identities=54% Similarity=0.781 Sum_probs=90.3
Q ss_pred CceeeeeecccceEEEEEEeC-CCcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEEEccCCC
Q psy8860 276 GINRLMVHRTNLHIYANIISS-NAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAFDRSGF 354 (374)
Q Consensus 276 gkgiL~V~eSn~hi~aqvi~~-~g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vvfDr~~~ 354 (374)
++++|+|++||+||||||||| +|+||+||||.||+++. |..+++|++||+.||++||+||+++||++|+||||+|
T Consensus 14 ~rpRL~V~rSnkhiyaQvidd~~g~tlasaST~ek~~~~----~~~~~~n~~aA~~vG~lla~ra~~~gi~~vvfDrgg~ 89 (109)
T CHL00139 14 ERPRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKS----SLSSTSTCDASKLVGQKLAKKSLKKGITKVVFDRGGK 89 (109)
T ss_pred CCCEEEEEEeCCeEEEEEEECCCCCEEEEEecCchhhhc----cccCCCCHHHHHHHHHHHHHHHHHCCCCEEEEcCCCC
Confidence 478999999999999999998 68999999999999975 4467999999999999999999999999999999999
Q ss_pred chhhHHHHHHHHHHHcCCCC
Q psy8860 355 RYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 355 ~yhgrv~a~a~~~re~Gl~f 374 (374)
+|||||+||||+|||+||+|
T Consensus 90 ~yhGrV~a~a~~are~GL~f 109 (109)
T CHL00139 90 LYHGRIKALAEAAREAGLQF 109 (109)
T ss_pred ccchHHHHHHHHHHHhCCCC
Confidence 99999999999999999998
No 15
>PTZ00158 40S ribosomal protein S15A; Provisional
Probab=100.00 E-value=7.1e-34 Score=244.00 Aligned_cols=114 Identities=27% Similarity=0.451 Sum_probs=102.8
Q ss_pred CCCcchHHHHHHhhhhhhccCCceEEe-ecchhHHHHHHHHHhCCCcceEEEEeccCCeeEEEEEEEeecCcceeeeeee
Q psy8860 1 MSMSDPIADMLTYIRNGQIVNKKKIIM-PSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELKILLKYYMNRPVIECLKR 79 (374)
Q Consensus 1 M~~~d~iad~lt~IrNa~~a~~~~v~~-p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~LKY~~~~pvi~~~~~ 79 (374)
|++.||||||||+||||++++|.+|.+ |+||++.+||++|++||||.+|++.++ .....+.+.|| .|
T Consensus 1 m~~~~~iadmlt~IrNa~~~~~~~V~v~p~Skl~~~il~IL~~eGyI~~~~~~~~-~~~~~i~v~l~-----------~r 68 (130)
T PTZ00158 1 MVRMSVLADCLRSIVNAEKQGKRQVLIRPSSKVVVKFLQVMQKHGYIGEFEIVDD-HRSGKIVVNLN-----------GR 68 (130)
T ss_pred CCcccHHHHHHHhhhhHHhCCCCeEEEeCCcHHHHHHHHHHHHCCcccceEEEec-CCEEEEEEEEc-----------Cc
Confidence 887899999999999999999999997 999999999999999999999998764 34456777774 67
Q ss_pred eccCCC---cccccCCCcccccC------CceEEEEEcCCccccccccc--cCCccee
Q psy8860 80 VSRPGL---RIYKNKDNIPKIMN------GLGLVIISTASGIITDRKAR--SMGKMPI 126 (374)
Q Consensus 80 iSkP~~---Rvy~~~~~l~~~~~------g~G~~ivSTs~Gvmt~~ea~--~ig~~~I 126 (374)
+||||+ |+|+++++||+|++ |+|++|||||+|||||+||+ ++|++.+
T Consensus 69 Isk~g~IS~RvY~~~~~ip~v~~~~lp~~glGi~IlSTSkGImt~~eAr~~~vGGEvL 126 (130)
T PTZ00158 69 LNKCGVISPRFDVTLGEFEKWANNILPSRQFGHVVLTTSYGIMDHEEARRRHTGGKIL 126 (130)
T ss_pred cccCCCCccceECCcchhhHHhcCCCccccceEEEEECCCCccChHHHHHcCCCceEE
Confidence 888888 99999999999965 89999999999999999999 4888765
No 16
>PTZ00032 60S ribosomal protein L18; Provisional
Probab=100.00 E-value=1.4e-33 Score=254.08 Aligned_cols=99 Identities=35% Similarity=0.533 Sum_probs=90.2
Q ss_pred CceeeeeecccceEEEEEEeC-CCcEEEEEecchHHhhhhcc--------ccCCCCCChHHHHHHHHHHHHHHHHCCCcE
Q psy8860 276 GINRLMVHRTNLHIYANIISS-NAKILISASTLEKEVRLTLN--------TKLGKGGNTFAASIIGQRIAKKALKIGITK 346 (374)
Q Consensus 276 gkgiL~V~eSn~hi~aqvi~~-~g~tl~sast~e~~~~~~l~--------~~~~~~~~~~aa~~vG~~la~r~~~~gi~~ 346 (374)
.++||+|++||+|||||+||| .|+|||||||++++++..+. +....++|++||+.||++||+||+++||++
T Consensus 104 rrPRLsV~RSnkHIYAQIIDD~~~~TLasaSTlek~l~~~~~~~~~~~~n~~~~~g~nieaA~~VGk~IAerAl~kGI~k 183 (211)
T PTZ00032 104 RRPRLTLKNTNNQMYATIVDDYTRHVLCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAYELGKLIGRKALSKGISK 183 (211)
T ss_pred CcceEEEEecCCeEEEEEEECCCCCEEEEecCCCHHHHhhhcccccccccccccCCCcHHHHHHHHHHHHHHHHHCCCCE
Confidence 469999999999999999999 68999999999999976431 112257899999999999999999999999
Q ss_pred EEEccCCCchhhHHHHHHHHHHHcCCCC
Q psy8860 347 VAFDRSGFRYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 347 vvfDr~~~~yhgrv~a~a~~~re~Gl~f 374 (374)
|+||||||+|||||+||||+|||+||+|
T Consensus 184 VvFDRgGy~YHGRVkALAdaARe~GLkF 211 (211)
T PTZ00032 184 VRFDRAHYKYAGKVEALAEGARAVGLQF 211 (211)
T ss_pred EEEeCCCCeehhHHHHHHHHHHHcCCCC
Confidence 9999999999999999999999999998
No 17
>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-33 Score=236.99 Aligned_cols=98 Identities=54% Similarity=0.819 Sum_probs=93.4
Q ss_pred CCceeeeeecccceEEEEEEeC-CCcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEEEccCC
Q psy8860 275 KGINRLMVHRTNLHIYANIISS-NAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAFDRSG 353 (374)
Q Consensus 275 kgkgiL~V~eSn~hi~aqvi~~-~g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vvfDr~~ 353 (374)
-++++|+|++||+||||||||| .+.||++|||.+++++++ +|...++|++||++||+++|+||+++||++|||||++
T Consensus 27 ~~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~--g~~~~~~N~~aA~~vG~lia~ra~~kgi~~vVfdr~g 104 (125)
T COG0256 27 SGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKY--GKKGGGGNTEAAYLVGKLIAERALAKGIEEVVFDRGG 104 (125)
T ss_pred CCCcEEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHHhh--cccCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEcCCC
Confidence 3689999999999999999998 589999999999999875 6777889999999999999999999999999999999
Q ss_pred CchhhHHHHHHHHHHHcCCCC
Q psy8860 354 FRYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 354 ~~yhgrv~a~a~~~re~Gl~f 374 (374)
|+|||||+|+||+|||+||+|
T Consensus 105 ~~yhgRV~Ala~~AreaGL~f 125 (125)
T COG0256 105 YKYHGRVAALADGAREAGLEF 125 (125)
T ss_pred CCcchHHHHHHHHHHHcCcCC
Confidence 999999999999999999998
No 18
>PLN00146 40S ribosomal protein S15a; Provisional
Probab=100.00 E-value=1.7e-33 Score=242.60 Aligned_cols=117 Identities=24% Similarity=0.407 Sum_probs=106.1
Q ss_pred CCCcchHHHHHHhhhhhhccCCceEE-eecchhHHHHHHHHHhCCCcceEEEEeccCCeeEEEEEEEeecCcceeeeeee
Q psy8860 1 MSMSDPIADMLTYIRNGQIVNKKKII-MPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELKILLKYYMNRPVIECLKR 79 (374)
Q Consensus 1 M~~~d~iad~lt~IrNa~~a~~~~v~-~p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~LKY~~~~pvi~~~~~ 79 (374)
|++.|||||||||||||++++|.+|. +|+||++++||++|++||||++|++.++ .....++|+||| +|+.+++
T Consensus 1 m~~~~~iad~lt~IrNa~~a~~~~v~~~p~Skl~~~il~iL~~eGyI~~~~~~~~-~~~~~i~v~Lk~-----~i~~~~~ 74 (130)
T PLN00146 1 MVRRSVLNDALKTMYNAEKRGKRQVLIRPSSKVVIKFLKVMQKHGYIGEFEVVDD-HRSGKIVVELNG-----RLNKCGV 74 (130)
T ss_pred CCCcChHHHHHHHhHhHHHcCCCeEEEEcChHHHHHHHHHHHHCCCCcceEEEec-CCcceEEEEEcc-----cccCCcE
Confidence 77789999999999999999999997 7999999999999999999999998764 444578999986 4667899
Q ss_pred eccCCCcccccCCCccccc------CCceEEEEEcCCcccccccccc--CCccee
Q psy8860 80 VSRPGLRIYKNKDNIPKIM------NGLGLVIISTASGIITDRKARS--MGKMPI 126 (374)
Q Consensus 80 iSkP~~Rvy~~~~~l~~~~------~g~G~~ivSTs~Gvmt~~ea~~--ig~~~I 126 (374)
|| | |+|+++++||+|+ +|+|++|||||+|||||+||++ +|++.+
T Consensus 75 IS-~--Rvy~~~~~l~~v~~~~~~~~g~Gi~IlSTskGimt~~eAr~~~vGGEvL 126 (130)
T PLN00146 75 IS-P--RFDVKVKEIEAWTARLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKVL 126 (130)
T ss_pred EE-c--CEecCcchhhHHHhccCCCCCCEEEEEECCCccccHHHHHHcCCCCEEE
Confidence 98 6 9999999999997 9999999999999999999994 888754
No 19
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=100.00 E-value=6e-33 Score=232.89 Aligned_cols=91 Identities=48% Similarity=0.787 Sum_probs=86.6
Q ss_pred CceeeeeecccceEEEEEEeC-CCcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEEEccCCC
Q psy8860 276 GINRLMVHRTNLHIYANIISS-NAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAFDRSGF 354 (374)
Q Consensus 276 gkgiL~V~eSn~hi~aqvi~~-~g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vvfDr~~~ 354 (374)
.+++|+|++||+||||||||| .++||+||||+|++++ .++|++||+.||++||+||+++||++|+||||||
T Consensus 23 ~rpRL~V~rSnk~iyaQiIdd~~~~tlasaST~ek~~~--------~~~n~~aA~~vG~~la~ra~~~gi~~vvfDrgg~ 94 (114)
T TIGR00060 23 NRPRLVVFRSNRHIYAQVIDDSKSEVLASASTLEKKLK--------YTGNKDAAKKVGKLVAERLKEKGIKDVVFDRGGY 94 (114)
T ss_pred CCcEEEEEEeCCeEEEEEEECCCCEEEEEEecchhhhc--------CCCCHHHHHHHHHHHHHHHHHCCCCEEEEeCCCC
Confidence 377999999999999999999 4799999999999874 4789999999999999999999999999999999
Q ss_pred chhhHHHHHHHHHHHcCCCC
Q psy8860 355 RYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 355 ~yhgrv~a~a~~~re~Gl~f 374 (374)
+|||||+||||+|||+||+|
T Consensus 95 ~YhGrv~A~a~~aRe~Gl~F 114 (114)
T TIGR00060 95 KYHGRVAALAEAAREAGLNF 114 (114)
T ss_pred cchHHHHHHHHHHHHhCCCC
Confidence 99999999999999999998
No 20
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=100.00 E-value=1.2e-32 Score=232.88 Aligned_cols=95 Identities=55% Similarity=0.792 Sum_probs=89.2
Q ss_pred CCceeeeeecccceEEEEEEeCC-CcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEEEccCC
Q psy8860 275 KGINRLMVHRTNLHIYANIISSN-AKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAFDRSG 353 (374)
Q Consensus 275 kgkgiL~V~eSn~hi~aqvi~~~-g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vvfDr~~ 353 (374)
..+++|+|++||+|||||||||+ ++||+||||+|++++.. | .++|++||+.||++||+||+++||++|+||||+
T Consensus 22 ~~rpRL~V~~SnkhiyAQvidd~~~~tl~saST~e~~~k~~---~--~~~n~~aa~~vG~~la~ra~~~gi~~vvfDrg~ 96 (117)
T PRK05593 22 AERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVRAG---L--KGGNKEAAKKVGKLIAERAKAKGIKQVVFDRGG 96 (117)
T ss_pred CCCCEEEEEEeCCeEEEEEEECCCCEEEEEEecCcHhHhcc---c--cCCCHHHHHHHHHHHHHHHHHCCCCEEEEcCCC
Confidence 45899999999999999999994 79999999999999653 3 289999999999999999999999999999999
Q ss_pred CchhhHHHHHHHHHHHcCCCC
Q psy8860 354 FRYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 354 ~~yhgrv~a~a~~~re~Gl~f 374 (374)
|+|||||+||||+|||+||+|
T Consensus 97 ~~yhGrV~a~a~~are~Gl~f 117 (117)
T PRK05593 97 YKYHGRVKALADAAREAGLKF 117 (117)
T ss_pred CcccHHHHHHHHHHHHhCCCC
Confidence 999999999999999999998
No 21
>PRK04034 rps8p 30S ribosomal protein S8P; Reviewed
Probab=99.97 E-value=2.3e-32 Score=235.92 Aligned_cols=117 Identities=32% Similarity=0.539 Sum_probs=103.3
Q ss_pred CCCcchHHHHHHhhhhhhccCCceE-EeecchhHHHHHHHHHhCCCcceEEEEeccCCeeEEEEEEEeecCcceeeeeee
Q psy8860 1 MSMSDPIADMLTYIRNGQIVNKKKI-IMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELKILLKYYMNRPVIECLKR 79 (374)
Q Consensus 1 M~~~d~iad~lt~IrNa~~a~~~~v-~~p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~LKY~~~~pvi~~~~~ 79 (374)
|+|+|+|||||||||||++|++.+| .+|+||++++||++|++||||++|++.++ ..++.+.|.|||..+ .+++
T Consensus 1 m~~~d~iad~lt~IrNa~~a~~~~v~~~p~Sk~~~~il~iL~~eGyI~~~~~~~~-~~~~~~~v~Lk~~~~-----~~~~ 74 (130)
T PRK04034 1 MVLLDPLANALSTIKNAEMVGKKEVIIKPASKLIGNVLRVMQDEGYIGEFEYIDD-GRAGKFKVELLGRIN-----KCGA 74 (130)
T ss_pred CCcccHHHHHHHHhHhHHHcCCceEEEEcccHHHHHHHHHHHHCCCceEEEEEcC-CCccceEEEECCccC-----CCCc
Confidence 8888999999999999999999997 69999999999999999999999998764 335578999998543 2333
Q ss_pred eccCCCcccccCCCccccc------CCceEEEEEcCCccccccccc--cCCccee
Q psy8860 80 VSRPGLRIYKNKDNIPKIM------NGLGLVIISTASGIITDRKAR--SMGKMPI 126 (374)
Q Consensus 80 iSkP~~Rvy~~~~~l~~~~------~g~G~~ivSTs~Gvmt~~ea~--~ig~~~I 126 (374)
| || |+|+++++||++. +|+|++|||||+|||||+||+ ++|++.+
T Consensus 75 I-kP--Rvy~~~~~l~~~~~~~l~~~~lGi~IlSTskGImt~~eA~~~~vGGEvL 126 (130)
T PRK04034 75 I-KP--RYPVKYDEFEKWEKRYLPARDFGILIVSTSKGVMSHKEAREKGIGGVLL 126 (130)
T ss_pred C-CC--CeEcCHhHhHHHHhccCCCCCceEEEEECCCCceeHHHHHHcCCCCEEE
Confidence 4 89 9999999999996 999999999999999999999 4888754
No 22
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=99.97 E-value=6.7e-31 Score=223.60 Aligned_cols=97 Identities=51% Similarity=0.746 Sum_probs=91.6
Q ss_pred CceeeeeecccceEEEEEEeC-CCcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEEEccCCC
Q psy8860 276 GINRLMVHRTNLHIYANIISS-NAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAFDRSGF 354 (374)
Q Consensus 276 gkgiL~V~eSn~hi~aqvi~~-~g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vvfDr~~~ 354 (374)
++++|+|++||+||||||||| .++||++|||.+++++++ +|..+++|++||+.||++||+||+++||+.|+|||+++
T Consensus 22 ~~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~~--~~~~~~~n~~aa~~vG~lla~ra~~~gi~~v~fdr~~~ 99 (119)
T PF00861_consen 22 ERPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKKY--GWKGSTKNVEAAYLVGELLAKRALEKGIAKVVFDRGGY 99 (119)
T ss_dssp SSEEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGGT--T-SSTTSSHHHHHHHHHHHHHHHHHTTSSEEEECTSTS
T ss_pred CCCEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhhh--hhccCCCCEehHHHHHHHHHHHHHHcCCcEEEEcCCCC
Confidence 579999999999999999999 589999999999999986 67788899999999999999999999999999999999
Q ss_pred chhhHHHHHHHHHHHcCCCC
Q psy8860 355 RYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 355 ~yhgrv~a~a~~~re~Gl~f 374 (374)
+|||||+||||+|||+||+|
T Consensus 100 ~y~grv~a~~~~~re~Gl~f 119 (119)
T PF00861_consen 100 KYHGRVKALADGAREGGLEF 119 (119)
T ss_dssp SSSSHHHHHHHHHHHTTCB-
T ss_pred cccHHHHHHHHHHHHcCCCC
Confidence 99999999999999999998
No 23
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=99.96 E-value=1.4e-28 Score=204.32 Aligned_cols=95 Identities=52% Similarity=0.798 Sum_probs=89.4
Q ss_pred cCCceeeeeecccceEEEEEEeCC-CcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEEEccC
Q psy8860 274 YKGINRLMVHRTNLHIYANIISSN-AKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAFDRS 352 (374)
Q Consensus 274 YkgkgiL~V~eSn~hi~aqvi~~~-g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vvfDr~ 352 (374)
+..+++|++++||+|||||||||. ++||++|||.|+++++.+ .+++|++||+.+|++||+||+++|+++|+||||
T Consensus 8 ~~~~~RL~v~~Sn~~i~aqvi~~~~~~vl~sast~e~~~~~~~----~~~~n~~aA~~vG~~la~r~~~~gi~~vv~D~~ 83 (103)
T cd00432 8 TQERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVL----GSGNNVEAAYLVGRLLAKRALEKGIKKVVFDRG 83 (103)
T ss_pred cCCCCEEEEEEeCCEEEEEEEEeCcCeEEEEEecCchhhcccc----cCCCcHHHHHHHHHHHHHHHHHCCCCEEEEeCC
Confidence 346899999999999999999995 899999999999997653 678999999999999999999999999999999
Q ss_pred CCchhhHHHHHHHHHHHcCC
Q psy8860 353 GFRYHGRIKFLADAARKNGL 372 (374)
Q Consensus 353 ~~~yhgrv~a~a~~~re~Gl 372 (374)
+++|||||+||+|++||+||
T Consensus 84 ~~~~~grv~a~~~~~r~~Gl 103 (103)
T cd00432 84 GYRYHGRVKALAKGAREGGL 103 (103)
T ss_pred CcccccHHHHHHHHHHHcCC
Confidence 99999999999999999997
No 24
>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed
Probab=99.96 E-value=1.2e-28 Score=223.27 Aligned_cols=95 Identities=34% Similarity=0.385 Sum_probs=89.3
Q ss_pred CceeeeeecccceEEEEEE--eCC-CcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEEEccC
Q psy8860 276 GINRLMVHRTNLHIYANII--SSN-AKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAFDRS 352 (374)
Q Consensus 276 gkgiL~V~eSn~hi~aqvi--~~~-g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vvfDr~ 352 (374)
+++||+|++||+||||||| ||+ ++||+||||.|++.. +|..+++|++||+.||+++|+||+++||++|+||||
T Consensus 31 ~kpRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~----g~~~~~~N~~AAy~vG~llA~ral~kGi~~vvfDrG 106 (193)
T PRK08569 31 GKPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKY----GWKGDTGNTPAAYLTGLLAGKKALKAGVEEAVLDIG 106 (193)
T ss_pred CCCEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhc----cccCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEecC
Confidence 5799999999999999999 665 699999999999864 566789999999999999999999999999999999
Q ss_pred CCchh--hHHHHHHHHHHHcCCCC
Q psy8860 353 GFRYH--GRIKFLADAARKNGLNF 374 (374)
Q Consensus 353 ~~~yh--grv~a~a~~~re~Gl~f 374 (374)
+++|| |||+||||+|||+||+|
T Consensus 107 g~~yh~gGRV~A~akgArd~GL~f 130 (193)
T PRK08569 107 LHRPTKGSRVFAALKGAIDAGLEI 130 (193)
T ss_pred CccccCCccHHHHHHHHHHcCCcC
Confidence 99999 99999999999999998
No 25
>KOG1754|consensus
Probab=99.86 E-value=6.4e-22 Score=165.59 Aligned_cols=116 Identities=28% Similarity=0.470 Sum_probs=104.1
Q ss_pred CCCcchHHHHHHhhhhhhccCCceEEe-ecchhHHHHHHHHHhCCCcceEEEEeccCCeeEEEEEEEeecCcceeeeeee
Q psy8860 1 MSMSDPIADMLTYIRNGQIVNKKKIIM-PSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELKILLKYYMNRPVIECLKR 79 (374)
Q Consensus 1 M~~~d~iad~lt~IrNa~~a~~~~v~~-p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~LKY~~~~pvi~~~~~ 79 (374)
|.+.+.|||+|..|+||.++++.+|.+ |+|+....||.+|.+||||.+|+++|| ....++.|.|..+-|+ |.
T Consensus 1 m~~~~vLaDalksinNA~krGK~qvlirp~Skvii~FL~vmmkhGyIg~fei~dd-hragkivv~L~gRlNk----cg-- 73 (130)
T KOG1754|consen 1 MVRMNVLADALKSINNAEKRGKRQVLIRPSSKVIIRFLTVMMKHGYIGEFEIIDD-HRAGKIVVNLTGRLNK----CG-- 73 (130)
T ss_pred CchHHHHHHHHHHhhhHHhcCCceEEecccHHHHHHHHHHHHHcCcccceEEecC-CccceEEEeccccccc----cc--
Confidence 666799999999999999999999877 899999999999999999999999996 6667999999888775 66
Q ss_pred eccCCCcccccCCCccccc------CCceEEEEEcCCcccccccccc--CCcce
Q psy8860 80 VSRPGLRIYKNKDNIPKIM------NGLGLVIISTASGIITDRKARS--MGKMP 125 (374)
Q Consensus 80 iSkP~~Rvy~~~~~l~~~~------~g~G~~ivSTs~Gvmt~~ea~~--ig~~~ 125 (374)
+..| |+-|+.++|++|. ++||+.+++||+|+|+|+||++ +|++.
T Consensus 74 ~Isp--rfdV~lkdlek~~n~llpsrqfg~ivltts~Gimdh~ear~k~~gg~i 125 (130)
T KOG1754|consen 74 VISP--RFDVKLKDLEKWTNSLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKI 125 (130)
T ss_pred cccc--ccccccchHHHHHhccCccceeeEEEEecccccccHHHHhHhhcCccc
Confidence 7788 9999999999995 6789999999999999999984 66643
No 26
>PF00347 Ribosomal_L6: Ribosomal protein L6; InterPro: IPR020040 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L6 is a protein from the large (50S) subunit. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of an ancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites []. This entry represents the alpha-beta domain found duplicated in ribosomal L6 proteins. This domain consists of two beta-sheets and one alpha-helix packed around single core [].; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 2HGJ_H 2HGQ_H 2HGU_H 1S1I_H 3O5H_I 3O58_I 3J16_F 3IZS_F 2V47_H 2WDJ_H ....
Probab=99.65 E-value=2.8e-16 Score=123.12 Aligned_cols=72 Identities=42% Similarity=0.624 Sum_probs=68.4
Q ss_pred cCCCeEEEEeccEEEEEeCCeEEEEEcCCCeEEE--EeCCEEEEEEcCCchhHHH---HHHHHHHHHhhcceecccc
Q psy8860 128 IPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIK--NDSNVLYFTAINNSRIAKS---MSGTMRSIINNMIIGVTKG 199 (374)
Q Consensus 128 IP~~V~v~~~~~~i~vkGp~G~l~~~l~~~v~i~--~~~~~l~i~~~~~~k~~~a---~~gT~rsli~Nmi~GVt~G 199 (374)
||+||+|+++++.++|+||+|++++++++.+.+. .+++.+.+..+.+++++++ +|||+|||++||++||++|
T Consensus 1 IP~gV~v~~~~~~i~v~G~~g~l~~~~~~~v~v~~~~~~~~~~~~~~~~~~k~~~~~a~~gt~rsli~n~i~GV~~G 77 (77)
T PF00347_consen 1 IPEGVKVTIKGNIITVKGPKGELSRPIPPGVKVEIKVEDNKITVSVLSGNKKQKAFAAMIGTYRSLINNMIKGVTEG 77 (77)
T ss_dssp SSTTCEEEEETTEEEEESSSSEEEEEETTTEEEEEEEETTSEEEEEEEESHHHHHHHHHHHHHHHHHHHHHHHHHTE
T ss_pred CCCcEEEEEeCcEEEEECCCEeEEEECCCCeeEEEEcCCCceEEEECcccHhHhhhHHhhccccccccCceeEECCC
Confidence 7999999999999999999999999999988887 6799999999988999999 9999999999999999987
No 27
>KOG3255|consensus
Probab=99.64 E-value=2.9e-17 Score=147.94 Aligned_cols=146 Identities=25% Similarity=0.288 Sum_probs=127.5
Q ss_pred cceeecCCCeEEEEeccEEEEEeCCeEEEEEcCC-CeEEEEeCC---EEEEEEcCCchhHHHHHHHHHHHHhhcceeccc
Q psy8860 123 KMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNN-LVNIKNDSN---VLYFTAINNSRIAKSMSGTMRSIINNMIIGVTK 198 (374)
Q Consensus 123 ~~~I~IP~~V~v~~~~~~i~vkGp~G~l~~~l~~-~v~i~~~~~---~l~i~~~~~~k~~~a~~gT~rsli~Nmi~GVt~ 198 (374)
...+.||++|.+++.+..++|+||.|+++.+|.| .+++...++ .+.+..|...|+..+.+.|..|+++||++||+.
T Consensus 7 n~tv~iPe~v~it~k~~v~~v~gprgtl~~d~~hi~~~~~~~~~~~~~ik~~~~~~~Rk~va~l~t~~s~ien~i~gvt~ 86 (179)
T KOG3255|consen 7 NQTVHIPENVDITLKGHVVIVKGPRGTLWRDFNHINVELSLLGKKKKRLKIDKWWGTRKGVACLRTVVSHIENCIKGVTI 86 (179)
T ss_pred ceEEecCCCceEEEeeEEEEEeCCCcceeccccccchhhhhhcchhhhhhhhhhhccchhHHHHHHHHHHHHHHHhcchH
Confidence 4578999999999999999999999999999997 666655444 488889999999999999999999999999999
Q ss_pred ceEEEEEEEEEEEEEEE---eCc---EEEEEecceeeEEEeCCCCcEEEcc--cCCEEEEEecchhhhhhHHHHHHhhc
Q psy8860 199 GFEKKLQLIGVGFRAKI---EKN---YLNLILGFSHPILYKIPFDIICETP--SQTEILIKGINKQAVGHVAAEIRRYY 269 (374)
Q Consensus 199 Gf~~~L~lvGvGyr~~~---~g~---~L~l~LG~Sh~i~~~IP~gV~v~~~--~~t~I~l~G~dke~Vgq~Aa~Ir~~r 269 (374)
||.|++..++.||++.. ++. .+.+|||++.+..+++.+|+..... -+++|+++|+|.+.|++-||. ++.+
T Consensus 87 ~~i~k~~av~a~f~in~~~~~~~~s~~i~n~l~~k~~~~~~~~~Gv~~~~~~~~~~~i~~~~~~~~~vs~~~a~-~~~~ 164 (179)
T KOG3255|consen 87 GFIYKMRAVYAHFPINTVIQENGKSEEIRNFLGEKLVRRVEMRPGVTIVRSSKVKDEIVLEGNDLELVSQSAAL-QQIC 164 (179)
T ss_pred HHHHHhhhHHhhccccceecCCCcchhhhhhhhhhccceEecCCCeEEeeehhcchhheecccchhhhhhHhHh-hccc
Confidence 99999999999999764 231 3568999999999999999998764 468999999999999998887 4443
No 28
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=99.35 E-value=1.6e-12 Score=124.17 Aligned_cols=98 Identities=28% Similarity=0.224 Sum_probs=86.6
Q ss_pred CcCC-ceeeeeecccceEEEEEEeC--CC-cEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHC------
Q psy8860 273 PYKG-INRLMVHRTNLHIYANIISS--NA-KILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKI------ 342 (374)
Q Consensus 273 pYkg-kgiL~V~eSn~hi~aqvi~~--~g-~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~------ 342 (374)
.|.. |.+++|..||++|.|||+.. +| .+|+||+|.|+. ++ ||..+.+|.+|||.+|.++|.|++++
T Consensus 43 KynspK~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S~eL~--ky--G~k~gl~N~~AAY~TGlL~arR~L~kl~ld~~ 118 (300)
T PTZ00069 43 KYNSPKYRLVVRITNKDIICQIVYATIVGDKVLAAAYSHELP--RF--GIPVGLTNYAAAYATGLLLARRLLKKLGLDKQ 118 (300)
T ss_pred ccCCCCceEEEEEECCcEEEEEEEeecCCCEEEEEeehhhHh--hc--CcCCCCccHHHHHHHHHHHHHHHHHhhccccc
Confidence 4444 68999999999999999995 67 999999999976 44 89999999999999999999999999
Q ss_pred --CCc--------------------EEEEccCCCc--hhhHHHHHHHHHHHcCCCC
Q psy8860 343 --GIT--------------------KVAFDRSGFR--YHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 343 --gi~--------------------~vvfDr~~~~--yhgrv~a~a~~~re~Gl~f 374 (374)
|++ ++++|.|..+ .++||+|++.||.|+||+.
T Consensus 119 y~G~~e~~g~~y~v~e~~~~~~rpf~a~LDiGL~rtt~G~RVFaalKGa~DgGl~I 174 (300)
T PTZ00069 119 FEGVKEADGEYYHVDEEDDEERRPFKAILDVGLARTTTGNRVFGALKGAVDGGLHI 174 (300)
T ss_pred ccCcccccCcccccccccccCCCCceEEEeeccccCCCCceeeeehhcccccCccc
Confidence 773 7899999655 5789999999999999974
No 29
>KOG3333|consensus
Probab=99.33 E-value=4.7e-12 Score=110.19 Aligned_cols=93 Identities=26% Similarity=0.323 Sum_probs=84.1
Q ss_pred eeeeeecccceEEEEEEeCCCcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEEEccCCCc-h
Q psy8860 278 NRLMVHRTNLHIYANIISSNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAFDRSGFR-Y 356 (374)
Q Consensus 278 giL~V~eSn~hi~aqvi~~~g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vvfDr~~~~-y 356 (374)
..+-+.++.+|+.+-|.|.+|.+++||||.||+|+++| +++.|+.||..+|++||+||++.||..+++.--..- .
T Consensus 61 h~lev~~~~~hveg~v~H~~~gvvvSAST~EwaIk~qL----Yst~dtsA~~niGRVLAqRCLqsGI~fm~~~~t~ea~~ 136 (188)
T KOG3333|consen 61 HRLEVIRTQHHVEGLVEHQNGGVVVSASTREWAIKKQL----YSTRDTSACENIGRVLAQRCLQSGINFMVYQPTPEAAA 136 (188)
T ss_pred eEEEEeecccceeeeeeEecCCEEEEecccchHHHHHH----hhccchHHHHHHHHHHHHHHHHhCcceeccCCChhhcc
Confidence 57889999999999999999999999999999999998 689999999999999999999999999999854333 4
Q ss_pred hhHHHHHHHHHHHcCCCC
Q psy8860 357 HGRIKFLADAARKNGLNF 374 (374)
Q Consensus 357 hgrv~a~a~~~re~Gl~f 374 (374)
....+-|..++.|+|+.|
T Consensus 137 ~s~~q~l~~a~~e~Gv~l 154 (188)
T KOG3333|consen 137 SSSMQRLQSAMTEGGVVL 154 (188)
T ss_pred chHHHHHHHHHHhCCeee
Confidence 568888999999999865
No 30
>PF00347 Ribosomal_L6: Ribosomal protein L6; InterPro: IPR020040 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L6 is a protein from the large (50S) subunit. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of an ancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites []. This entry represents the alpha-beta domain found duplicated in ribosomal L6 proteins. This domain consists of two beta-sheets and one alpha-helix packed around single core [].; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 2HGJ_H 2HGQ_H 2HGU_H 1S1I_H 3O5H_I 3O58_I 3J16_F 3IZS_F 2V47_H 2WDJ_H ....
Probab=98.14 E-value=5e-07 Score=70.49 Aligned_cols=70 Identities=20% Similarity=0.119 Sum_probs=61.7
Q ss_pred EEEEEEEEeCcEEEEEecceeeEEEeCCCCcEEEcc----cCCEEEEEecchhhhhhHHHHHHhhcCCCCcCCceee
Q psy8860 208 GVGFRAKIEKNYLNLILGFSHPILYKIPFDIICETP----SQTEILIKGINKQAVGHVAAEIRRYYKPEPYKGINRL 280 (374)
Q Consensus 208 GvGyr~~~~g~~L~l~LG~Sh~i~~~IP~gV~v~~~----~~t~I~l~G~dke~Vgq~Aa~Ir~~r~pepYkgkgiL 280 (374)
+.|++|.+++ .+....|+++...+++|++|.+++. +.+...+.+.|++.. +||.++.+|++.+|+.+|+.
T Consensus 2 P~gV~v~~~~-~~i~v~G~~g~l~~~~~~~v~v~~~~~~~~~~~~~~~~~~k~~~--~~a~~gt~rsli~n~i~GV~ 75 (77)
T PF00347_consen 2 PEGVKVTIKG-NIITVKGPKGELSRPIPPGVKVEIKVEDNKITVSVLSGNKKQKA--FAAMIGTYRSLINNMIKGVT 75 (77)
T ss_dssp STTCEEEEET-TEEEEESSSSEEEEEETTTEEEEEEEETTSEEEEEEEESHHHHH--HHHHHHHHHHHHHHHHHHHH
T ss_pred CCcEEEEEeC-cEEEEECCCEeEEEECCCCeeEEEEcCCCceEEEECcccHhHhh--hHHhhccccccccCceeEEC
Confidence 4578899999 7888999999999999999999965 345677899999999 99999999999999999864
No 31
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=97.44 E-value=0.0011 Score=55.73 Aligned_cols=87 Identities=23% Similarity=0.248 Sum_probs=69.0
Q ss_pred eeeeeecccceEEEEEEeCCCcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEEE-ccCCCch
Q psy8860 278 NRLMVHRTNLHIYANIISSNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAF-DRSGFRY 356 (374)
Q Consensus 278 giL~V~eSn~hi~aqvi~~~g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vvf-Dr~~~~y 356 (374)
|+++++-|.++..+.+.|..|.+++.+|+-...++.. ......||..+++.++++|++.|+..+.. =||. -+
T Consensus 1 gi~hI~~s~NNT~itlTd~~g~~~~~~S~G~~gfkg~------rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~~kG~-G~ 73 (108)
T TIGR03632 1 GVAHIHATFNNTIVTITDPQGNVLSWASAGAVGFKGS------KKSTPYAAQLAAEDAAKKAKEFGMKTVDVYVKGP-GA 73 (108)
T ss_pred CEEEEEccCCCEEEEEEcCCCCEEEEEecCceeeCCC------ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECC-CC
Confidence 6899999999999999999998999988776666542 34567899999999999999999998744 4553 22
Q ss_pred hhHHHHHHHHHHHcCCC
Q psy8860 357 HGRIKFLADAARKNGLN 373 (374)
Q Consensus 357 hgrv~a~a~~~re~Gl~ 373 (374)
|| +++..++...||+
T Consensus 74 -gr-~~~ir~l~~~glk 88 (108)
T TIGR03632 74 -GR-ESAIRALQAAGLE 88 (108)
T ss_pred -cH-HHHHHHHHHCCCE
Confidence 44 5666777777875
No 32
>PF00411 Ribosomal_S11: Ribosomal protein S11; InterPro: IPR001971 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S11 [] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. On the basis of sequence similarities, S11 belongs to a family of bacterial, archaeal and eukaryotic ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_K 3U5C_O 3O2Z_H 3IZB_K 3U5G_O 3O30_H 1S1H_K 3BBN_K 2XZN_K 2XZM_K ....
Probab=97.39 E-value=0.0012 Score=55.49 Aligned_cols=87 Identities=21% Similarity=0.258 Sum_probs=69.4
Q ss_pred eeeeeecccceEEEEEEeCCCcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEEEc-cCCCch
Q psy8860 278 NRLMVHRTNLHIYANIISSNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAFD-RSGFRY 356 (374)
Q Consensus 278 giL~V~eSn~hi~aqvi~~~g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vvfD-r~~~~y 356 (374)
|++++.-|.++..+.+.|..|.++.++|+-...++.. ......||+.+++.++++|++.||+.|..- +| .-
T Consensus 1 giihI~~s~NNt~vtlTd~~G~~~~~~S~G~~gfK~~------rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG--~g 72 (110)
T PF00411_consen 1 GIIHIKSSFNNTIVTLTDLKGNVLFWSSAGSLGFKGA------RKSTPYAAQQAAEKIAKKAKELGIKTVRVKIKG--FG 72 (110)
T ss_dssp EEEEEEEESSEEEEEEEETTSEEEEEEETTTSSTTTT------CGSSHHHHHHHHHHHHHHHHCTTEEEEEEEEES--SS
T ss_pred CEEEEEecCCCEEEEEECCCCCEEEEEeccccccccc------cccCHHHHHHHHHHHHHHHHHcCCeEEEEEEcC--CC
Confidence 7899999999999999999999999999887777653 356779999999999999999999987443 44 22
Q ss_pred hhHHHHHHHHHHHcCCC
Q psy8860 357 HGRIKFLADAARKNGLN 373 (374)
Q Consensus 357 hgrv~a~a~~~re~Gl~ 373 (374)
-||- ++..++...|++
T Consensus 73 ~gr~-~~lk~l~~~gl~ 88 (110)
T PF00411_consen 73 PGRE-AALKALKKSGLK 88 (110)
T ss_dssp TTHH-HHHHHHHHTTSE
T ss_pred ccHH-HHHHHHHhcCCE
Confidence 3454 344666777875
No 33
>CHL00041 rps11 ribosomal protein S11
Probab=97.30 E-value=0.0021 Score=54.73 Aligned_cols=88 Identities=14% Similarity=0.228 Sum_probs=71.1
Q ss_pred ceeeeeecccceEEEEEEeCCCcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEE-EccCCCc
Q psy8860 277 INRLMVHRTNLHIYANIISSNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVA-FDRSGFR 355 (374)
Q Consensus 277 kgiL~V~eSn~hi~aqvi~~~g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vv-fDr~~~~ 355 (374)
.|+++++-|-++..+.+.|..|.+++.+|.-...++.. ......||..+++.++++|++.|+..+. +=||. -
T Consensus 13 ~gi~hI~~t~NNTiiTlTd~~G~~l~~~S~G~~gfKg~------rK~T~~Aa~~~a~~~~~~~~~~gi~~v~I~ikG~-G 85 (116)
T CHL00041 13 KGVIHIQASFNNTIVTVTDVRGRVISWSSAGACGFKGA------RKGTPFAAQTAAENAIRTVIDQGMKRAEVMIKGP-G 85 (116)
T ss_pred eEEEEEEcccCCEEEEEEcCCCCEEEEEecCceeeCCC------ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECC-C
Confidence 59999999999999999999999999998877666542 3456789999999999999999999873 33653 2
Q ss_pred hhhHHHHHHHHHHHcCCC
Q psy8860 356 YHGRIKFLADAARKNGLN 373 (374)
Q Consensus 356 yhgrv~a~a~~~re~Gl~ 373 (374)
.|| +++..++...||+
T Consensus 86 -~Gr-~~~ir~l~~~glk 101 (116)
T CHL00041 86 -LGR-DTALRAIRRSGLK 101 (116)
T ss_pred -CcH-HHHHHHHHHCCCE
Confidence 366 5667888888885
No 34
>PRK05309 30S ribosomal protein S11; Validated
Probab=96.93 E-value=0.0076 Score=52.17 Aligned_cols=88 Identities=20% Similarity=0.223 Sum_probs=69.3
Q ss_pred ceeeeeecccceEEEEEEeCCCcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEEE-ccCCCc
Q psy8860 277 INRLMVHRTNLHIYANIISSNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAF-DRSGFR 355 (374)
Q Consensus 277 kgiL~V~eSn~hi~aqvi~~~g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vvf-Dr~~~~ 355 (374)
.|+++++-|.++..+.+.|..|.+++.+|.-...++.. ..+...||..+++.+++.|++.|+..+.. =||. -
T Consensus 17 ~gi~hI~~t~NNTiitlTd~~G~~~~~~S~G~~gfKg~------rK~T~~Aa~~aa~~~~~~~~~~gi~~v~v~ikG~-G 89 (128)
T PRK05309 17 SGVAHIHATFNNTIVTITDRQGNVISWASAGGLGFKGS------RKSTPYAAQVAAEDAAKKAKEHGMKTVEVFVKGP-G 89 (128)
T ss_pred eeEEEEEccCCCEEEEEEcCCCCEEEEEecCccEeCCC------ccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECC-C
Confidence 69999999999999999999999999888766666532 34567899999999999999999998744 3552 2
Q ss_pred hhhHHHHHHHHHHHcCCC
Q psy8860 356 YHGRIKFLADAARKNGLN 373 (374)
Q Consensus 356 yhgrv~a~a~~~re~Gl~ 373 (374)
-|| +++..++...||+
T Consensus 90 -~Gr-~~air~L~~~glk 105 (128)
T PRK05309 90 -SGR-ESAIRALQAAGLE 105 (128)
T ss_pred -CcH-HHHHHHHHHCCCE
Confidence 244 5666667777875
No 35
>PTZ00090 40S ribosomal protein S11; Provisional
Probab=96.76 E-value=0.011 Score=55.09 Aligned_cols=88 Identities=20% Similarity=0.194 Sum_probs=70.1
Q ss_pred ceeeeeecccceEEEEEEeCCCc--EEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEE-EEccCC
Q psy8860 277 INRLMVHRTNLHIYANIISSNAK--ILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKV-AFDRSG 353 (374)
Q Consensus 277 kgiL~V~eSn~hi~aqvi~~~g~--tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~v-vfDr~~ 353 (374)
.-.+++.-|-++..++|.|..|. ||+-+|+-...++.. ..+.--||+.+++.+|++|++.||.+| |+=+|.
T Consensus 118 ~f~~vI~aSfNNTIVTlTD~~GNv~tl~WSSAG~~GFKGs------KKsTpfAAQ~aae~aakka~~~GIk~V~V~vKGp 191 (233)
T PTZ00090 118 RFMLVITTSKNNVHAQVVNKSKNYKTVFGSFAGNVGFRKK------LQQSERCAYRIGENIAKKCRRLGIFAVDIKFRRI 191 (233)
T ss_pred cEEEEEEeccCcEEEEEEeCCCCEEEEEEEcccccCcccC------ccCCHHHHHHHHHHHHHHHHHcCCeEEEEEEeCC
Confidence 34588999999999999999887 477777666666532 335668999999999999999999998 555655
Q ss_pred CchhhHHHHHHHHHHHcCCCC
Q psy8860 354 FRYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 354 ~~yhgrv~a~a~~~re~Gl~f 374 (374)
+| .++++.++..+||++
T Consensus 192 ---Gg-REtALRaL~~~GLkI 208 (233)
T PTZ00090 192 ---MR-VETVLQAFYANGLQV 208 (233)
T ss_pred ---Ch-HHHHHHHHHHCCCEE
Confidence 24 899999999999863
No 36
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=96.37 E-value=0.029 Score=49.60 Aligned_cols=91 Identities=16% Similarity=0.233 Sum_probs=69.6
Q ss_pred ceeeeeecccceEEEEEEeCCCcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEE-EEcc--CC
Q psy8860 277 INRLMVHRTNLHIYANIISSNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKV-AFDR--SG 353 (374)
Q Consensus 277 kgiL~V~eSn~hi~aqvi~~~g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~v-vfDr--~~ 353 (374)
.|+.+++-|-++....|.|..|.+++.+|+-...++.. ...+.--||...++.+|++|++.||+.+ |+=| ||
T Consensus 28 ~Gi~hI~as~NNTiItiTD~~G~~~~w~SsG~~gfKg~-----r~KsTpyAAq~aa~~~a~k~~~~Gi~~v~V~vr~~gg 102 (149)
T PTZ00129 28 FGVAHIFASFNDTFIHVTDLSGRETLVRVTGGMKVKAD-----RDESSPYAAMMAAQDVAARCKELGINALHIKLRATGG 102 (149)
T ss_pred EEEEEEEcccCCeEEEEEcccCCEEEEEecCcceeccc-----ccCCCHHHHHHHHHHHHHHHHHcCCeEEEEEEEecCC
Confidence 59999999999999999999998888888877666532 1134557999999999999999999998 4444 33
Q ss_pred Cchh----hHHHHHHHHHHHcCCC
Q psy8860 354 FRYH----GRIKFLADAARKNGLN 373 (374)
Q Consensus 354 ~~yh----grv~a~a~~~re~Gl~ 373 (374)
..-+ || ++++.++..+||+
T Consensus 103 ~~~kg~GpGr-~~airaL~~~glk 125 (149)
T PTZ00129 103 VRTKTPGPGA-QAALRALARAGLK 125 (149)
T ss_pred CCCCCCCCCH-HHHHHHHHHCCCE
Confidence 3332 34 4556777778875
No 37
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=96.13 E-value=0.048 Score=46.28 Aligned_cols=89 Identities=19% Similarity=0.109 Sum_probs=65.5
Q ss_pred eeeeeecccceEEEEEEeCCC-cEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEE-EccC--C
Q psy8860 278 NRLMVHRTNLHIYANIISSNA-KILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVA-FDRS--G 353 (374)
Q Consensus 278 giL~V~eSn~hi~aqvi~~~g-~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vv-fDr~--~ 353 (374)
|+.+++-|-++....|.|..| .+++-+|.-...++. ...+.--||...++.++++|++.||+.|. +=|| |
T Consensus 3 gi~hI~as~NNTiitvTD~~G~~~~~~~S~G~~g~kg------~kk~TpyAAq~aa~~~~~~~~~~Gi~~v~v~ikG~gg 76 (114)
T TIGR03628 3 GIAHIYSSFNNTIITITDITGAETIARSSGGMVVKAD------RDESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGG 76 (114)
T ss_pred EEEEEEccCCCeEEEEEcCCCCEEEEEecCcceEeCC------CccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCC
Confidence 789999999999999999888 667777766555432 12345679999999999999999999984 4455 3
Q ss_pred Cchh----hHHHHHHHHHHHcCCC
Q psy8860 354 FRYH----GRIKFLADAARKNGLN 373 (374)
Q Consensus 354 ~~yh----grv~a~a~~~re~Gl~ 373 (374)
.+.+ || ++...+++.+||+
T Consensus 77 ~~~~~~G~Gr-~~air~l~~~glk 99 (114)
T TIGR03628 77 NGQKSPGPGA-QAAIRALARAGLR 99 (114)
T ss_pred CCCCCCCCcH-HHHHHHHHHCCCE
Confidence 3322 44 4455677778875
No 38
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=95.97 E-value=0.035 Score=48.26 Aligned_cols=90 Identities=18% Similarity=0.104 Sum_probs=65.8
Q ss_pred ceeeeeecccceEEEEEEeCCC-cEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEEE-ccC--
Q psy8860 277 INRLMVHRTNLHIYANIISSNA-KILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAF-DRS-- 352 (374)
Q Consensus 277 kgiL~V~eSn~hi~aqvi~~~g-~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vvf-Dr~-- 352 (374)
.|+.+++-|-++....|.|..| .|++.+|.-...++. ...+.--||...++.++++|++.||+.|.. =||
T Consensus 9 ~gi~hI~as~NNTivtvTD~~G~~~~~~~S~G~~g~kg------~kK~TpyAAq~aae~~~~~~~~~Gi~~v~v~vkG~G 82 (132)
T PRK09607 9 WGIAHIYASFNNTIITITDLTGAETIAKSSGGMVVKAD------RDESSPYAAMQAAEKAAEDAKEKGITGVHIKVRAPG 82 (132)
T ss_pred eeEEEEEcccCCeEEEEEcCCCCEEEEEecCcceeeCC------CccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecC
Confidence 6899999999999999999888 488777766544332 123455799999999999999999999844 455
Q ss_pred CCc---h-hhHHHHHHHHHHHcCCC
Q psy8860 353 GFR---Y-HGRIKFLADAARKNGLN 373 (374)
Q Consensus 353 ~~~---y-hgrv~a~a~~~re~Gl~ 373 (374)
|.. + -|| ++.+.++..+||+
T Consensus 83 gn~~~~~G~Gr-~~airal~~~glk 106 (132)
T PRK09607 83 GNGQKSPGPGA-QAAIRALARAGLR 106 (132)
T ss_pred CCCCcCCCCcH-HHHHHHHHHCCCE
Confidence 222 2 244 3445667777775
No 39
>KOG0875|consensus
Probab=95.86 E-value=0.0059 Score=57.76 Aligned_cols=101 Identities=22% Similarity=0.139 Sum_probs=76.9
Q ss_pred cCCCCcCC-ceeeeeecccceEEEEEEeC--CC-cEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHH-CC
Q psy8860 269 YKPEPYKG-INRLMVHRTNLHIYANIISS--NA-KILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALK-IG 343 (374)
Q Consensus 269 r~pepYkg-kgiL~V~eSn~hi~aqvi~~--~g-~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~-~g 343 (374)
.-++.|.+ |-++.+..+|+.+.+|+... +| .++++|.+-|+. ++ |....-.|-.||+..|.+||.|+++ .|
T Consensus 39 qdknk~nt~kyR~ivr~~n~~iicqi~~~~i~gd~v~~~a~s~elp--ky--g~~~GLtNyaAay~TglLLarR~l~~~g 114 (264)
T KOG0875|consen 39 QDKNKYNTPKYRMIVRVINKDIICQIAYATIEGDVIVRAAYAHELP--KY--GVKVGLTNYAAAYCTGLLLACRLLKRFG 114 (264)
T ss_pred hcccccCCCceEEEEEEechhhHHHHHhheecceEEEEeecccccc--cc--ccccccchhHHHHhhHHHHHHHHHHHhC
Confidence 35677887 78999999999999999996 67 777888887765 33 3334567899999999999999986 44
Q ss_pred Cc--------------------------EEEEccCCCc--hhhHHHHHHHHHHHcCCC
Q psy8860 344 IT--------------------------KVAFDRSGFR--YHGRIKFLADAARKNGLN 373 (374)
Q Consensus 344 i~--------------------------~vvfDr~~~~--yhgrv~a~a~~~re~Gl~ 373 (374)
.+ ++.+|-|.-+ -+.||+..+++|.++||.
T Consensus 115 mD~~yeg~~e~~gde~~~e~idgq~~aFt~~Ld~GLaRtttg~kvFGAlkga~dGGL~ 172 (264)
T KOG0875|consen 115 MDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLS 172 (264)
T ss_pred cccccccceeecCcccccccccCCCCCeEEEecccccccCCCceeeeeeehhccccee
Confidence 22 3444555333 256899999999999985
No 40
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=94.81 E-value=0.21 Score=43.21 Aligned_cols=95 Identities=21% Similarity=0.184 Sum_probs=70.2
Q ss_pred CCCCcCCceeeeeecccceEEEEEEeCCCcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEE-E
Q psy8860 270 KPEPYKGINRLMVHRTNLHIYANIISSNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKV-A 348 (374)
Q Consensus 270 ~pepYkgkgiL~V~eSn~hi~aqvi~~~g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~v-v 348 (374)
.++.+---|+.+++.|-++-..-+-|.+|..+..+|+=...++.. ..+.-.||...++..|+.|+|.||..+ |
T Consensus 11 ~~~~~i~~GvahI~asfNNTivtitD~~Gn~i~wassG~~gfk~~------rk~tpyAA~~aa~~aa~~a~e~Gi~~v~v 84 (129)
T COG0100 11 KVKKNIADGVAHIHASFNNTIVTITDLTGNVIIWASSGGMGFKGS------RKSTPYAAQLAAEDAAKKAKEHGIKSVEV 84 (129)
T ss_pred eeccccccceEEEEcccCCcEEEecCCCCCEEEEEecCCceEcCC------CCCCHHHHHHHHHHHHHHHHHhCccEEEE
Confidence 445555678888888888888888888999999999988887753 256678888899999999999999988 4
Q ss_pred EccCCCchhhHHHHHHHHHHHcCCC
Q psy8860 349 FDRSGFRYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 349 fDr~~~~yhgrv~a~a~~~re~Gl~ 373 (374)
+=+|. =-|| +|+..+|-.+||+
T Consensus 85 ~vkgp--G~Gr-eaAiraL~~ag~~ 106 (129)
T COG0100 85 KVKGP--GPGR-EAAIRALAAAGLK 106 (129)
T ss_pred EEECC--CCcH-HHHHHHHHHccce
Confidence 44551 1133 3444455566764
No 41
>KOG0408|consensus
Probab=89.70 E-value=2.5 Score=38.08 Aligned_cols=93 Identities=17% Similarity=0.234 Sum_probs=70.0
Q ss_pred CcCCceeeeeecccceEEEEEEeCCCcEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEEEccC
Q psy8860 273 PYKGINRLMVHRTNLHIYANIISSNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAFDRS 352 (374)
Q Consensus 273 pYkgkgiL~V~eSn~hi~aqvi~~~g~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vvfDr~ 352 (374)
+|..-++.++.-|-++...||.|..|.++..+|---..+|.. ..+..-||...|-..+.|+.+.|+..|-.--.
T Consensus 75 ~f~eiPi~hIraS~NNTivtVtd~kg~vi~~~ScgteGFrnt------rkgT~iAaQtaavaa~~r~v~~G~~~vrV~Vk 148 (190)
T KOG0408|consen 75 NFREIPIIHIRASFNNTIVTVTDVKGEVISWSSCGTEGFRNT------RKGTPIAAQTAAVAAIRRAVDQGMQTVRVRVK 148 (190)
T ss_pred cccccceEEEEecCCCeEEEEEccCCcEEEEeeccccccccc------ccCCchhHHHHHHHHHHHHHHhcceEEEEEEe
Confidence 666778999999999999999999898888877665556542 23455788889999999999999998844432
Q ss_pred CCchhhHHHHHHHHHHHcCCC
Q psy8860 353 GFRYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 353 ~~~yhgrv~a~a~~~re~Gl~ 373 (374)
| .=-||..| +.+++-+||.
T Consensus 149 G-lGpGRmsa-~kgl~m~Gl~ 167 (190)
T KOG0408|consen 149 G-LGPGRMSA-LKGLRMGGLL 167 (190)
T ss_pred c-CCccHHHH-HhhhhhcceE
Confidence 2 22377765 4678878764
No 42
>KOG0407|consensus
Probab=68.88 E-value=52 Score=27.86 Aligned_cols=90 Identities=14% Similarity=0.239 Sum_probs=54.8
Q ss_pred eeeeeecccceEEEEEEeCCC-cEEEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHHCCCcEEEEc-c--CC
Q psy8860 278 NRLMVHRTNLHIYANIISSNA-KILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAFD-R--SG 353 (374)
Q Consensus 278 giL~V~eSn~hi~aqvi~~~g-~tl~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~~gi~~vvfD-r--~~ 353 (374)
|+--++-|-+..++.|-|-.| .|++-.+-- ..++.. ...++--||-+.++-.|.+|++.||+.+-+. | ||
T Consensus 17 gvahi~asfndtfvhitdlsg~eti~rvtgg-mkvkad-----rdesspyaamlaaqdva~kck~~gi~alh~klratgg 90 (139)
T KOG0407|consen 17 GVAHIFASFNDTFVHVTDLSGKETIVRVTGG-MKVKAD-----RDESSPYAAMLAAQDVAAKCKELGITALHIKLRATGG 90 (139)
T ss_pred eEEEEEeecccceEEEeccCCceEEEEecCC-eEEecc-----cccCChHHHHHHHHHHHHHHHhcCeeEEEEEEEecCC
Confidence 344445555555555555456 788775432 223322 2345678889999999999999999999886 3 44
Q ss_pred Cch---hhHHHHHHHHHHHcCCC
Q psy8860 354 FRY---HGRIKFLADAARKNGLN 373 (374)
Q Consensus 354 ~~y---hgrv~a~a~~~re~Gl~ 373 (374)
.+. +-=-++.+.++-.+|+.
T Consensus 91 ~ktktpgpgaqsalralar~gmr 113 (139)
T KOG0407|consen 91 TKTKTPGPGAQSALRALARSGMR 113 (139)
T ss_pred cccCCCCccHHHHHHHHHHhcce
Confidence 442 22234445555555654
No 43
>cd06479 ACD_HspB7_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB7, also known as cardiovascular small heat shock protein (cvHsp), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB7 is a 25-kDa protein, preferentially expressed in heart and skeletal muscle. It binds the cytoskeleton protein alpha-filamin (also known as actin-binding protein 280). The expression of HspB7 is increased during rat muscle aging. Its expression is also modulated in obesity implicating this protein in this and related metabolic disorders. As the human gene encoding HspB7 is mapped to chromosome 1p36.23-p34.3 it is a positional candidate for several dystrophies and myopathies.
Probab=67.37 E-value=14 Score=29.30 Aligned_cols=43 Identities=19% Similarity=0.258 Sum_probs=32.0
Q ss_pred CCCeEEEEeccEEEEEeCC--------eEEEEEcC--CC-----eEEEE-eCCEEEEEE
Q psy8860 129 PPNVEVTLNSNKITLKGPL--------GILKQNKN--NL-----VNIKN-DSNVLYFTA 171 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp~--------G~l~~~l~--~~-----v~i~~-~~~~l~i~~ 171 (374)
|++++|+++++.|+|+|-+ |+.++.|. .. ++-.+ +++.|.|..
T Consensus 21 pedi~V~v~~~~L~I~ger~~~~~~~~g~F~R~~~LP~~vd~e~v~A~l~~~GvL~I~~ 79 (81)
T cd06479 21 PEDIIVTTSNNQIEVHAEKLASDGTVMNTFTHKCQLPEDVDPTSVSSSLGEDGTLTIKA 79 (81)
T ss_pred HHHeEEEEECCEEEEEEEEeccCCCEEEEEEEEEECCCCcCHHHeEEEecCCCEEEEEe
Confidence 6789999999999999865 77777765 22 44555 778877754
No 44
>PRK06518 hypothetical protein; Provisional
Probab=52.20 E-value=54 Score=29.90 Aligned_cols=100 Identities=17% Similarity=0.043 Sum_probs=61.4
Q ss_pred CCEEEEEecchhhhhhHHHHHHhhcCCCCcCC--ceeeeeecccceEEEEEEeC-CCcEEEEEecchHHhhhhccccCCC
Q psy8860 245 QTEILIKGINKQAVGHVAAEIRRYYKPEPYKG--INRLMVHRTNLHIYANIISS-NAKILISASTLEKEVRLTLNTKLGK 321 (374)
Q Consensus 245 ~t~I~l~G~dke~Vgq~Aa~Ir~~r~pepYkg--kgiL~V~eSn~hi~aqvi~~-~g~tl~sast~e~~~~~~l~~~~~~ 321 (374)
+..|-|.|||--..+|.|. .-.+++||-- +=.|.-.-.++.+.++...| .|.+++.+..-..
T Consensus 48 ~~~VRL~GIDAPE~~Q~c~---~~~~~wp~G~~A~~~L~~li~gk~V~~~~~~D~ygR~lA~~~~~g~------------ 112 (177)
T PRK06518 48 TRDIRLYGVDTCAPRQKAR---LGDQEWPCGAVATAWLVTKTLNKWLSCRQARMENGVHYAQCFVDGV------------ 112 (177)
T ss_pred CeEEEEEEEcCCCCCCccc---CCCCCCcHHHHHHHHHHHHHCCCeEEEEEecccCCCEEEEEEECCE------------
Confidence 5689999999989999754 2246666632 11122222467788887776 5999999873211
Q ss_pred CCChHHHHHHHHHHHHHHHHCCCcEEEEcc-CCCchhhHHHHHHHHHHHcCC
Q psy8860 322 GGNTFAASIIGQRIAKKALKIGITKVAFDR-SGFRYHGRIKFLADAARKNGL 372 (374)
Q Consensus 322 ~~~~~aa~~vG~~la~r~~~~gi~~vvfDr-~~~~yhgrv~a~a~~~re~Gl 372 (374)
-|.+...+.|.- .+|.+ ..+.+++...++.+.||++++
T Consensus 113 ------------dln~~mV~~G~A-~ay~~~~~~~~~~~y~~aE~~AR~~k~ 151 (177)
T PRK06518 113 ------------DIAALGLAEGMA-VLSKDDHEDPGPAQYASLEEKARKAYR 151 (177)
T ss_pred ------------EHHHHHHhCCCE-EEEeeccCCCCHHHHHHHHHHHHHhCC
Confidence 134445556653 33333 234456777777777877654
No 45
>PF00011 HSP20: Hsp20/alpha crystallin family This prints entry is a subset of the Pfam entry.; InterPro: IPR002068 Prokaryotic and eukaryotic organisms respond to heat shock or other environmental stress by inducing the synthesis of proteins collectively known as heat-shock proteins (hsp) []. Amongst them is a family of proteins with an average molecular weight of 20 Kd, known as the hsp20 proteins []. These seem to act as chaperones that can protect other proteins against heat-induced denaturation and aggregation. Hsp20 proteins seem to form large heterooligomeric aggregates. Structurally, this family is characterised by the presence of a conserved C-terminal domain of about 100 residues.; PDB: 2BOL_B 3N3E_B 2H50_P 2H53_F 2BYU_L 1GME_D 3VQM_J 3VQK_E 3VQL_A 3AAC_A ....
Probab=47.16 E-value=57 Score=25.96 Aligned_cols=44 Identities=14% Similarity=0.224 Sum_probs=30.3
Q ss_pred CCCeEEEEeccEEEEEeCCe------------------EEEEEcCC-----CeEEEEeCCEEEEEEc
Q psy8860 129 PPNVEVTLNSNKITLKGPLG------------------ILKQNKNN-----LVNIKNDSNVLYFTAI 172 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp~G------------------~l~~~l~~-----~v~i~~~~~~l~i~~~ 172 (374)
|++++|++.++.|+|+|... ..++.||. .++..++++.|.|...
T Consensus 20 ~edi~I~~~~~~L~I~g~~~~~~~~~~~~~~~~~~~~f~r~~~lP~~vd~~~i~a~~~~GvL~I~~p 86 (102)
T PF00011_consen 20 KEDIKIKVDDNKLVISGKRKEEEEDDRYYRSERRYGSFERSIRLPEDVDPDKIKASYENGVLTITIP 86 (102)
T ss_dssp GGGEEEEEETTEEEEEEEEEGEECTTCEEEE-S-SEEEEEEEE-STTB-GGG-EEEETTSEEEEEEE
T ss_pred hHHEEEEEecCccceeceeeeeeeeeeeeecccccceEEEEEcCCCcCCcceEEEEecCCEEEEEEE
Confidence 56888898888888888777 33445553 3556778888888743
No 46
>cd06470 ACD_IbpA-B_like Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. IbpA and IbpB are produced during high-level production of various heterologous proteins, specifically human prorenin, renin and bovine insulin-like growth factor 2 (bIGF-2), and are strongly associated with inclusion bodies containing these heterologous proteins. IbpA and IbpB work as an integrated system to stabilize thermally aggregated proteins in a disaggregation competent state. The chaperone activity of IbpB is also significantly elevated as the temperature increases from normal to heat shock. The high temperature results in the disassociation of 2-3-MDa IbpB oligomers into smaller approximately 6
Probab=46.63 E-value=42 Score=26.66 Aligned_cols=18 Identities=22% Similarity=0.584 Sum_probs=14.4
Q ss_pred CCCeEEEEeccEEEEEeC
Q psy8860 129 PPNVEVTLNSNKITLKGP 146 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp 146 (374)
|++++|.++++.|+|+|.
T Consensus 24 kedi~v~~~~~~L~I~g~ 41 (90)
T cd06470 24 EDDLEIEVENNQLTVTGK 41 (90)
T ss_pred HHHeEEEEECCEEEEEEE
Confidence 467888888888888874
No 47
>TIGR01917 gly_red_sel_B glycine reductase, selenoprotein B. Glycine reductase is a complex with two selenoprotein subunits, A and B. This model represents the glycine reductase selenoprotein B. Closely related to it, but excluded from this model, are selenoprotein B subunits of betaine reductase and sarcosine reductase. All contain selenocysteine incorporated during translation at a specific UGA codon.
Probab=45.93 E-value=68 Score=33.34 Aligned_cols=55 Identities=13% Similarity=0.184 Sum_probs=42.9
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHCCCcEEEEccCCCchhhHHHHHHHHHHHcCCC
Q psy8860 319 LGKGGNTFAASIIGQRIAKKALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 319 ~~~~~~~~aa~~vG~~la~r~~~~gi~~vvfDr~~~~yhgrv~a~a~~~re~Gl~ 373 (374)
.+.+.+.+.|+..|..||+++++.|++.|++--.=-.-|=-+...+..+-++||.
T Consensus 312 ~G~gt~~~~a~~~g~eIa~~Lk~dgVDAvILtstCgtCtrcga~m~keiE~~GIP 366 (431)
T TIGR01917 312 TGNGTAVANSKQFAKEFSKELLAAGVDAVILTSTUGTCTRCGATMVKEIERAGIP 366 (431)
T ss_pred cCCCccHHHHHHHHHHHHHHHHHcCCCEEEEcCCCCcchhHHHHHHHHHHHcCCC
Confidence 4556778889999999999999999999999865224555566677777778874
No 48
>cd06469 p23_DYX1C1_like p23_like domain found in proteins similar to dyslexia susceptibility 1 (DYX1) candidate 1 (C1) protein, DYX1C1. The human gene encoding this protein is a positional candidate gene for developmental dyslexia (DD), it is located on 15q21.3 by the DYX1 DD susceptibility locus (15q15-21). Independent association studies have reported conflicting results. However, association of short-term memory, which plays a role in DD, with a variant within the DYX1C1 gene has been reported. Most proteins belonging to this group contain a C-terminal tetratricopeptide repeat (TPR) protein binding region.
Probab=45.70 E-value=95 Score=23.29 Aligned_cols=44 Identities=16% Similarity=0.190 Sum_probs=33.7
Q ss_pred CCCeEEEEeccEEEEEeCCeEEEEEcCCC-----eEEEEeCCEEEEEEc
Q psy8860 129 PPNVEVTLNSNKITLKGPLGILKQNKNNL-----VNIKNDSNVLYFTAI 172 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp~G~l~~~l~~~-----v~i~~~~~~l~i~~~ 172 (374)
|++++|+++++.+.++++.=.+..+|++. ....++++.+.+...
T Consensus 19 ~~~v~v~~~~~~l~i~~~~~~~~~~l~~~I~~e~~~~~~~~~~l~i~L~ 67 (78)
T cd06469 19 TSKVDIFCSDLYLKVNFPPYLFELDLAAPIDDEKSSAKIGNGVLVFTLV 67 (78)
T ss_pred cccceEEEecCEEEEcCCCEEEEEeCcccccccccEEEEeCCEEEEEEE
Confidence 67889999999999999666677777754 445678888877643
No 49
>cd06481 ACD_HspB9_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB9 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB9 is expressed exclusively in the normal testis and in various tumor samples and is a cancer/testis antigen. hHspB9 interacts with TCTEL1 (T-complex testis expressed protein -1), a subunit of dynein. hHspB9 and TCTEL1 are co-expressed in similar cells within the testis and in tumor cells. Included in this group is Xenopus Hsp30, a developmentally-regulated heat-inducible molecular chaperone.
Probab=45.63 E-value=56 Score=25.98 Aligned_cols=19 Identities=21% Similarity=0.543 Sum_probs=15.8
Q ss_pred CCCeEEEEeccEEEEEeCC
Q psy8860 129 PPNVEVTLNSNKITLKGPL 147 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp~ 147 (374)
|++++|+++++.|+|+|-.
T Consensus 20 ~edI~V~v~~~~L~I~g~~ 38 (87)
T cd06481 20 PEDLSVRVDGRKLVVTGKR 38 (87)
T ss_pred hHHeEEEEECCEEEEEEEE
Confidence 6788999999999988853
No 50
>cd00298 ACD_sHsps_p23-like This domain family includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this family is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind
Probab=43.61 E-value=56 Score=23.52 Aligned_cols=42 Identities=17% Similarity=0.168 Sum_probs=29.7
Q ss_pred CCCeEEEEeccEEEEEeCCe------------EEEEEcCCC-----eEEEEeCCEEEEE
Q psy8860 129 PPNVEVTLNSNKITLKGPLG------------ILKQNKNNL-----VNIKNDSNVLYFT 170 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp~G------------~l~~~l~~~-----v~i~~~~~~l~i~ 170 (374)
|+.++|.++++.|.|+|... .+...|++. +...+.++.|.+.
T Consensus 19 ~~~i~v~~~~~~l~v~~~~~~~~~~~~~~~~~~~~~~L~~~i~~~~~~~~~~~~~l~i~ 77 (80)
T cd00298 19 KEDIKVEVEDNVLTISGKREEEEERERSYGEFERSFELPEDVDPEKSKASLENGVLEIT 77 (80)
T ss_pred HHHeEEEEECCEEEEEEEEcCCCcceEeeeeEEEEEECCCCcCHHHCEEEEECCEEEEE
Confidence 57899999999999997654 445555543 3455667777665
No 51
>PF12970 DUF3858: Domain of Unknown Function with PDB structure (DUF3858); InterPro: IPR024544 This domain of unknown function is structurally similar to part of neuropilin-2. The proteins it occurs in have not yet been functionally characterised.; PDB: 3KD4_A.
Probab=41.37 E-value=1.6e+02 Score=25.16 Aligned_cols=44 Identities=16% Similarity=0.289 Sum_probs=29.4
Q ss_pred CCcceeecCCCeEEEEeccEEEEEeCCeEEEEEcCCCeEEEEeCCEEEEE
Q psy8860 121 MGKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKNDSNVLYFT 170 (374)
Q Consensus 121 ig~~~I~IP~~V~v~~~~~~i~vkGp~G~l~~~l~~~v~i~~~~~~l~i~ 170 (374)
--...|.+|+|-++.--...-.++-|-|++++. +..+++.+.|.
T Consensus 38 ~ytyti~~pegm~l~t~~~~K~I~N~~Gk~~is------v~~~~~~~~V~ 81 (116)
T PF12970_consen 38 TYTYTIELPEGMKLVTPPMEKKIDNPVGKVSIS------VKPEGNKIKVT 81 (116)
T ss_dssp EEEEEEEE-TT-EE-S--S-EEEEETTEEEEEE------EEEETTEEEEE
T ss_pred ceEEEEEcCCCCeeecCccceeccCCcceEEEE------EEecCCeEEEE
Confidence 335678999999988888888999999999954 56677776665
No 52
>TIGR01918 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family. This model represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. This model is built in fragment mode to assist in recognizing fragmentary translations. All members are expected to contain an internal TGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon.
Probab=40.48 E-value=91 Score=32.43 Aligned_cols=55 Identities=9% Similarity=0.126 Sum_probs=42.6
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHCCCcEEEEccCCCchhhHHHHHHHHHHHcCCC
Q psy8860 319 LGKGGNTFAASIIGQRIAKKALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 319 ~~~~~~~~aa~~vG~~la~r~~~~gi~~vvfDr~~~~yhgrv~a~a~~~re~Gl~ 373 (374)
.+.+.+...|+..|..||+++++.|++.|++--.=-.-|=-+...+..+-.+||.
T Consensus 312 ~G~gt~~~~a~~~g~eIa~~Lk~dgVDAVILTstCgtC~r~~a~m~keiE~~GiP 366 (431)
T TIGR01918 312 VGNGTTVAESKQFAKEFVVELKQGGVDAVILTSTUGTCTRCGATMVKEIERAGIP 366 (431)
T ss_pred CCCCchHHHHHHHHHHHHHHHHHcCCCEEEEcCCCCcchhHHHHHHHHHHHcCCC
Confidence 3456777888999999999999999999999865224455556677777778874
No 53
>cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=39.06 E-value=88 Score=28.70 Aligned_cols=44 Identities=16% Similarity=0.175 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHCCCcEEEE--ccCCCchhhHHHHHHHHHHHcCCCC
Q psy8860 331 IGQRIAKKALKIGITKVAF--DRSGFRYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 331 vG~~la~r~~~~gi~~vvf--Dr~~~~yhgrv~a~a~~~re~Gl~f 374 (374)
.|+.+|+.+.+.|..++.| ........-|+.+|.+++.+.|+.+
T Consensus 102 ~g~~a~~~L~~~g~~~i~~~~~~~~~~~~~R~~gf~~~~~~~~~~~ 147 (263)
T cd06280 102 AARTLVEHLVAQGYRRIGGLFGNASTTGAERRAGYEDAMRRHGLAP 147 (263)
T ss_pred HHHHHHHHHHHCCCceEEEEeCCCCCCHHHHHHHHHHHHHHcCCCC
Confidence 4556667777789988765 3322233579999999999999763
No 54
>cd00175 SNc Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.
Probab=38.68 E-value=1.1e+02 Score=25.42 Aligned_cols=102 Identities=17% Similarity=0.156 Sum_probs=65.6
Q ss_pred CEEEEEecchhhhhhHHHHHHhhcCCCCcCC--ceeeeeecccceEEEEEEe-C-CCcEEEEEecchHHhhhhccccCCC
Q psy8860 246 TEILIKGINKQAVGHVAAEIRRYYKPEPYKG--INRLMVHRTNLHIYANIIS-S-NAKILISASTLEKEVRLTLNTKLGK 321 (374)
Q Consensus 246 t~I~l~G~dke~Vgq~Aa~Ir~~r~pepYkg--kgiL~V~eSn~hi~aqvi~-~-~g~tl~sast~e~~~~~~l~~~~~~ 321 (374)
..|.|.|+|-....+.+. ....+++||-- +-.+...-.++.+..++.. | .|..|+.+...+
T Consensus 18 ~~vrL~gId~Pe~~~~~~--~~~~~~~~~g~~A~~~l~~~l~~~~V~i~~~~~d~~gr~la~v~~~~------------- 82 (129)
T cd00175 18 ITVRLSGIDAPETARPNK--GKSETDEPFGEEAKEFLKKLLLGKKVQVEVDSKDRYGRTLGTVYLNG------------- 82 (129)
T ss_pred EEEEEEeecCccccCCcc--CCCCCCCchHHHHHHHHHHHhCCCEEEEEEccCCCCCCEEEEEEeCC-------------
Confidence 368888888777766544 23344555532 1122222234667777664 4 589998875321
Q ss_pred CCChHHHHHHHHHHHHHHHHCCCcEEEEccCCC-chhhHHHHHHHHHHHcCC
Q psy8860 322 GGNTFAASIIGQRIAKKALKIGITKVAFDRSGF-RYHGRIKFLADAARKNGL 372 (374)
Q Consensus 322 ~~~~~aa~~vG~~la~r~~~~gi~~vvfDr~~~-~yhgrv~a~a~~~re~Gl 372 (374)
+.-+++.+.+.|.-.+....... .|+.+..++.+.|+++++
T Consensus 83 ----------~~~v~~~Lv~~G~A~~~~~~~~~~~~~~~l~~ae~~Ak~~k~ 124 (129)
T cd00175 83 ----------GENIAEELVKEGLARVYRYYPDDSEYYDELLEAEEAAKKARK 124 (129)
T ss_pred ----------CCcHHHHHHhcCCEEEEEECCCCcHHHHHHHHHHHHHHHhCc
Confidence 33467778888988887766543 688899999999998765
No 55
>cd06471 ACD_LpsHSP_like Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Transcription of the genes encoding Lp HSP 18.5, 18.55 and 19.3 is regulated by a variety of stresses including heat, cold and ethanol. Early growing L. plantarum cells contain elevated levels of these mRNAs which rapidly fall of as the cells enter stationary phase. Also belonging to this group is Bifidobacterium breve (Bb) HSP20 and Oenococcus oenis (syn. Leuconostoc oenos) (Oo) HSP18. Transcription of the gene encoding BbHSP20 is strongly induced following heat or osmotic shock, and that of the gene encoding OoHSP18 following heat, ethanol or acid shock. OoHSP18 is peripherally associated with the cytoplasmic me
Probab=37.16 E-value=1.1e+02 Score=24.17 Aligned_cols=17 Identities=6% Similarity=0.305 Sum_probs=12.2
Q ss_pred CCeEEEEeccEEEEEeC
Q psy8860 130 PNVEVTLNSNKITLKGP 146 (374)
Q Consensus 130 ~~V~v~~~~~~i~vkGp 146 (374)
++++|.+.++.|+|+|-
T Consensus 24 edi~v~~~~~~L~I~g~ 40 (93)
T cd06471 24 EDIKLDYKDGYLTISAK 40 (93)
T ss_pred HHeEEEEECCEEEEEEE
Confidence 66777777777777663
No 56
>COG0097 RplF Ribosomal protein L6P/L9E [Translation, ribosomal structure and biogenesis]
Probab=35.18 E-value=38 Score=31.06 Aligned_cols=28 Identities=25% Similarity=0.313 Sum_probs=22.8
Q ss_pred ceeecCCCeEEEEec-cEEEEEeCCeEEE
Q psy8860 124 MPIFIPPNVEVTLNS-NKITLKGPLGILK 151 (374)
Q Consensus 124 ~~I~IP~~V~v~~~~-~~i~vkGp~G~l~ 151 (374)
..+.||+||+|++.+ ..|+++|+.-+..
T Consensus 113 ~~~~ip~gi~v~v~~~t~I~v~GidKe~V 141 (178)
T COG0097 113 VVIEIPEGITVEVPGPTEIVVEGIDKELV 141 (178)
T ss_pred eEEECCCCeEEEecCCCEEEEEcCCHHHH
Confidence 456899999999998 7899999875544
No 57
>cd06276 PBP1_FucR_like Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability. FcuR acts as an inducer of fucRRIAK and as a corepressor of another locus that regulates production of fucosylated glycans. FcuR and its close homologs in this group are a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes t
Probab=33.11 E-value=1e+02 Score=28.43 Aligned_cols=44 Identities=5% Similarity=-0.095 Sum_probs=31.5
Q ss_pred HHHHHHHHHHH--CCCcEEEEc--cCCCchhhHHHHHHHHHHHcCCCC
Q psy8860 331 IGQRIAKKALK--IGITKVAFD--RSGFRYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 331 vG~~la~r~~~--~gi~~vvfD--r~~~~yhgrv~a~a~~~re~Gl~f 374 (374)
.|..+++.+.+ +|.+++.|= ........|...|.++++++|+.|
T Consensus 102 ~~~~a~~~L~~~~~G~~~Ia~i~~~~~~~~~~R~~gf~~~l~~~g~~~ 149 (247)
T cd06276 102 AIYNALQEGLEKLKKYKKLILVFPNKTAIPKEIKRGFERFCKDYNIET 149 (247)
T ss_pred HHHHHHHHHHHHhcCCCEEEEEecCccHhHHHHHHHHHHHHHHcCCCc
Confidence 44556677777 799998653 222334579999999999999864
No 58
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=33.04 E-value=27 Score=27.96 Aligned_cols=23 Identities=35% Similarity=0.618 Sum_probs=17.7
Q ss_pred hhHHHHHHHHHhCCCcceEEEEe
Q psy8860 31 KIKIAIAKVLKDEGYIKDFFIIK 53 (374)
Q Consensus 31 k~~~~il~iL~~eGyI~~~~~~~ 53 (374)
..-..++.-|+++|||.|+.+.+
T Consensus 25 ~~~~~il~~L~d~GyI~G~~~~~ 47 (88)
T PF09639_consen 25 SYWSDILRMLQDEGYIKGVSVVR 47 (88)
T ss_dssp HHHHHHHHHHHHHTSEE--EESS
T ss_pred HHHHHHHHHHHHCCCccceEEEe
Confidence 55678899999999999998854
No 59
>cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=31.62 E-value=1.2e+02 Score=27.67 Aligned_cols=42 Identities=21% Similarity=0.294 Sum_probs=28.6
Q ss_pred HHHHHHHHHHCCCcEEEEccC--CC-chhhHHHHHHHHHHHcCCC
Q psy8860 332 GQRIAKKALKIGITKVAFDRS--GF-RYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 332 G~~la~r~~~~gi~~vvfDr~--~~-~yhgrv~a~a~~~re~Gl~ 373 (374)
|+.+++.+.++|..++.|=.+ .. ...-|.++|.+++.+.|++
T Consensus 104 ~~~a~~~l~~~g~~~i~~l~~~~~~~~~~~R~~gf~~~~~~~~~~ 148 (269)
T cd06288 104 GYDATRHLLAAGHRRIAFINGEPWMLAAKDRLKGYRQALAEAGIP 148 (269)
T ss_pred HHHHHHHHHHcCCceEEEEeCCccchhHHHHHHHHHHHHHHcCCC
Confidence 445555555668888866322 22 2356999999999999864
No 60
>PF14419 SPOUT_MTase_2: AF2226-like SPOUT RNA Methylase fused to THUMP
Probab=30.98 E-value=1.3e+02 Score=27.19 Aligned_cols=49 Identities=14% Similarity=0.139 Sum_probs=38.1
Q ss_pred CCChHHHHHHHHHHHHHHHHCCCcEEEEccCCCchhhHHHHHHHHHHHc
Q psy8860 322 GGNTFAASIIGQRIAKKALKIGITKVAFDRSGFRYHGRIKFLADAARKN 370 (374)
Q Consensus 322 ~~~~~aa~~vG~~la~r~~~~gi~~vvfDr~~~~yhgrv~a~a~~~re~ 370 (374)
-++.+||+.+|+-++..+....+.+.+----++--.=-+..|++|++++
T Consensus 10 lGd~~a~r~mGerIGRaaQ~FEV~eLiiap~~~vda~eL~~Fl~gV~~G 58 (173)
T PF14419_consen 10 LGDLKACRKMGERIGRAAQAFEVKELIIAPKEKVDAYELMEFLRGVREG 58 (173)
T ss_pred cCCHHHHHHHHHHHhHHHhhcchheEEEeccCccCHHHHHHHHHHHHHh
Confidence 4688999999999999999999999876554433333567788888764
No 61
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=30.83 E-value=79 Score=23.30 Aligned_cols=30 Identities=13% Similarity=0.176 Sum_probs=22.8
Q ss_pred CCcEEEcccCCEEEEEecchhhhhhHHHHH
Q psy8860 236 FDIICETPSQTEILIKGINKQAVGHVAAEI 265 (374)
Q Consensus 236 ~gV~v~~~~~t~I~l~G~dke~Vgq~Aa~I 265 (374)
.|+++.+++...+.++|.|++.+..-.+.|
T Consensus 31 tg~~I~i~~~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 31 TGVKIDIEDDGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred HCCEEEeCCCCEEEEEeCCHHHHHHHHHHh
Confidence 366677776778999999998887765554
No 62
>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.
Probab=30.78 E-value=1.3e+02 Score=27.38 Aligned_cols=42 Identities=24% Similarity=0.244 Sum_probs=29.8
Q ss_pred HHHHHHHHHHCCCcEEEEccC---CCchhhHHHHHHHHHHHcCCC
Q psy8860 332 GQRIAKKALKIGITKVAFDRS---GFRYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 332 G~~la~r~~~~gi~~vvfDr~---~~~yhgrv~a~a~~~re~Gl~ 373 (374)
|..+++.+.+.|..++.|=-+ ....+.|...|.+++++.|++
T Consensus 102 ~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~~~~ 146 (260)
T cd06286 102 FYEALKYLIQKGYRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLT 146 (260)
T ss_pred HHHHHHHHHHCCCceEEEEcCCcccchhHHHHHHHHHHHHHcCCC
Confidence 335556666679999876432 223457999999999999975
No 63
>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]
Probab=30.61 E-value=81 Score=29.45 Aligned_cols=38 Identities=29% Similarity=0.385 Sum_probs=29.2
Q ss_pred HHHHHHCCCcEEEEccCCCch-hhHHHHHHHHHHHcCCC
Q psy8860 336 AKKALKIGITKVAFDRSGFRY-HGRIKFLADAARKNGLN 373 (374)
Q Consensus 336 a~r~~~~gi~~vvfDr~~~~y-hgrv~a~a~~~re~Gl~ 373 (374)
.+||+++||..++|||..|.- .--=.++++.+++.+.+
T Consensus 43 lerA~~~gIpt~~~~~k~~~~r~~~d~~l~~~l~~~~~d 81 (200)
T COG0299 43 LERAAKAGIPTVVLDRKEFPSREAFDRALVEALDEYGPD 81 (200)
T ss_pred HHHHHHcCCCEEEeccccCCCHHHHHHHHHHHHHhcCCC
Confidence 589999999999999987652 12346778888877765
No 64
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=30.56 E-value=1.4e+02 Score=27.41 Aligned_cols=51 Identities=20% Similarity=0.083 Sum_probs=37.6
Q ss_pred CChHHHHHHHHHHHHHHHHC--CCcEEEEccC---CCchhhHHHHHHHHHHHcCCC
Q psy8860 323 GNTFAASIIGQRIAKKALKI--GITKVAFDRS---GFRYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 323 ~~~~aa~~vG~~la~r~~~~--gi~~vvfDr~---~~~yhgrv~a~a~~~re~Gl~ 373 (374)
.+..+++..++.|++++++. |-.++.|=.+ .....-|.++|.+++.+.|++
T Consensus 102 d~~~~g~~~~~~l~~~~~~~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~l~~~~~~ 157 (277)
T cd06319 102 DNYEGAYDLGKFLAAAMKAQGWADGKVGMVAIPQKRKNGQKRTKGFKEAMKEAGCD 157 (277)
T ss_pred ccHHHHHHHHHHHHHHHHhhCCCCCcEEEEeccCCCccHHHHHHHHHHHHHhcCCc
Confidence 46688889999999998876 5567655322 122357899999999999875
No 65
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=29.26 E-value=1.4e+02 Score=28.41 Aligned_cols=43 Identities=21% Similarity=0.240 Sum_probs=30.7
Q ss_pred HHHHHHHHHHCCCcEEEEccCC---CchhhHHHHHHHHHHHcCCCC
Q psy8860 332 GQRIAKKALKIGITKVAFDRSG---FRYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 332 G~~la~r~~~~gi~~vvfDr~~---~~yhgrv~a~a~~~re~Gl~f 374 (374)
|+.+++.+.++|..++.|=-+. .....|..+|.+++.++|+.+
T Consensus 162 ~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~ 207 (327)
T PRK10423 162 GDLATQYLIDKGYTRIACITGPLDKTPARLRLEGYRAAMKRAGLNI 207 (327)
T ss_pred HHHHHHHHHHcCCCeEEEEeCCccccchHHHHHHHHHHHHHcCCCC
Confidence 4555666777899998773221 223569999999999999853
No 66
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=29.24 E-value=1.2e+02 Score=22.12 Aligned_cols=38 Identities=26% Similarity=0.552 Sum_probs=26.8
Q ss_pred HHHHHHHHHCCCcEEEE-ccCCCchhhHHHHHHHHHHHcCCC
Q psy8860 333 QRIAKKALKIGITKVAF-DRSGFRYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 333 ~~la~r~~~~gi~~vvf-Dr~~~~yhgrv~a~a~~~re~Gl~ 373 (374)
+.+.++|++.|++.+.+ |.+ .+.|-. .+.+.+++.|++
T Consensus 18 ~~~~~~a~~~g~~~v~iTDh~--~~~~~~-~~~~~~~~~gi~ 56 (67)
T smart00481 18 EELVKRAKELGLKAIAITDHG--NLFGAV-EFYKAAKKAGIK 56 (67)
T ss_pred HHHHHHHHHcCCCEEEEeeCC--cccCHH-HHHHHHHHcCCe
Confidence 45789999999999976 776 234433 455666777875
No 67
>PF03900 Porphobil_deamC: Porphobilinogen deaminase, C-terminal domain; InterPro: IPR022418 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. Porphobilinogen deaminase (also known as hydroxymethylbilane synthase, 2.5.1.61 from EC) functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the polymerisation of four PBG molecules into the tetrapyrrole structure, preuroporphyrinogen, with the concomitant release of four molecules of ammonia. This enzyme uses a unique dipyrro-methane cofactor made from two molecules of PBG, which is covalently attached to a cysteine side chain. The tetrapyrrole product is synthesized in an ordered, sequential fashion, by initial attachment of the first pyrrole unit (ring A) to the cofactor, followed by subsequent additions of the remaining pyrrole units (rings B, C, D) to the growing pyrrole chain []. The link between the pyrrole ring and the cofactor is broken once all the pyrroles have been added. This enzyme is folded into three distinct domains that enclose a single, large active site that makes use of an aspartic acid as its one essential catalytic residue, acting as a general acid/base during catalysis [, ]. A deficiency of hydroxymethylbilane synthase is implicated in the neuropathic disease, Acute Intermittent Porphyria (AIP) []. This entry represents the C-terminal domain of porphobilinogen deaminase, an enzyme involved in tetrapyrrole biosynthesis. The structure of this alpha/beta domain consists of alpha-beta(3)-alpha in two layers []. Porphobilinogen deaminase has a three-domain structure. Domains 1 (N-terminal) and 2 are duplications with the same structure, resembling the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 (C-terminal), but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins []. The enzyme has a single catalytic site, and the flexibility between domains is thought to aid elongation of the polypyrrole product in the active-site cleft of the enzyme.; GO: 0033014 tetrapyrrole biosynthetic process; PDB: 3EQ1_B 3ECR_A 1GTK_A 1AH5_A 2YPN_A 1PDA_A 1YPN_A.
Probab=29.19 E-value=76 Score=24.25 Aligned_cols=49 Identities=16% Similarity=0.185 Sum_probs=29.1
Q ss_pred eeeeeecccc--eEEEEEEeCCCcE-EEEEecchHHhhhhccccCCCCCChHHHHHHHHHHHHHHHH
Q psy8860 278 NRLMVHRTNL--HIYANIISSNAKI-LISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALK 341 (374)
Q Consensus 278 giL~V~eSn~--hi~aqvi~~~g~t-l~sast~e~~~~~~l~~~~~~~~~~~aa~~vG~~la~r~~~ 341 (374)
|.+.....++ ++.+.+.+.+|.. +..++. +.+.+.|..+|+.+|+..++
T Consensus 23 ga~a~~~~~~~l~l~~~v~~~dG~~~~~~~~~---------------~~~~~~a~~lg~~la~~l~~ 74 (74)
T PF03900_consen 23 GAYAKIEGDERLRLRAMVGSPDGSRIIIRVEI---------------TGPIEDAEELGKKLAEELLA 74 (74)
T ss_dssp EEEEEEETTE-EEEEEEEE-TTSSSEEEEEEE---------------EE-GGGHCCHHHHHHHHHHH
T ss_pred eeEEEEcCCCEEEEEEEEECCCCCEEEEEEEE---------------EcCHHHHHHHHHHHHHHHhC
Confidence 4455555555 7777777767643 443331 12446677789999988764
No 68
>cd06472 ACD_ScHsp26_like Alpha crystallin domain (ACD) found in Saccharomyces cerevisiae (Sc) small heat shock protein (Hsp)26 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. ScHsp26 is temperature-regulated, it switches from an inactive to a chaperone-active form upon elevation in temperature. It associates into large 24-mers storage forms which upon heat shock disassociate into dimers. These dimers initiate the interaction with non-native substrate proteins and re-assemble into large globular assemblies having one monomer of substrate bound per dimer. This group also contains Arabidopsis thaliana (Ath) Hsp15.7, a peroxisomal matrix protein which can complement the morphological phenotype of S. cerevisiae mutants deficient in Hsps26. AthHsp15.7 is minimally expressed under normal conditions and is strongly induced by heat and oxidative st
Probab=28.52 E-value=2e+02 Score=22.55 Aligned_cols=18 Identities=17% Similarity=0.416 Sum_probs=12.2
Q ss_pred CCCeEEEEec-cEEEEEeC
Q psy8860 129 PPNVEVTLNS-NKITLKGP 146 (374)
Q Consensus 129 P~~V~v~~~~-~~i~vkGp 146 (374)
|++++|.+++ +.|+|+|.
T Consensus 22 ~edi~i~v~~~~~L~I~g~ 40 (92)
T cd06472 22 KEDVKVEVEDGRVLRISGE 40 (92)
T ss_pred hHhEEEEEeCCCEEEEEEE
Confidence 4677777765 36777773
No 69
>PF07137 VDE: Violaxanthin de-epoxidase (VDE); InterPro: IPR010788 This family represents a conserved region approximately 350 residues long within plant violaxanthin de-epoxidase (VDE). In higher plants, violaxanthin de-epoxidase forms part of a conserved system that dissipates excess energy as heat in the light-harvesting complexes of photosystem II (PSII), thus protecting them from photo-inhibitory damage [].; GO: 0046422 violaxanthin de-epoxidase activity, 0055114 oxidation-reduction process, 0009507 chloroplast; PDB: 3CQN_B 3CQR_A.
Probab=28.46 E-value=59 Score=30.22 Aligned_cols=29 Identities=31% Similarity=0.405 Sum_probs=22.6
Q ss_pred EEEEccCCCchhhHHHHHHHHHHHcCCCC
Q psy8860 346 KVAFDRSGFRYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 346 ~vvfDr~~~~yhgrv~a~a~~~re~Gl~f 374 (374)
.+||-|.+.....-+..+..+|.++|++|
T Consensus 150 AvVYtrs~~lP~s~~p~l~~aa~k~G~d~ 178 (198)
T PF07137_consen 150 AVVYTRSPTLPESIVPELRRAAKKAGIDF 178 (198)
T ss_dssp EEEEESSSS--GGGHHHHHHHHHHTT--G
T ss_pred eEEEeCCCCCChHHhHHHHHHHHHhCCCH
Confidence 57999999899999999999999999986
No 70
>PF04273 DUF442: Putative phosphatase (DUF442); InterPro: IPR005939 Although this domain is uncharacterised it seems likely that it performs a phosphatase function.; GO: 0016787 hydrolase activity; PDB: 2F46_A 3GXH_B 3GXG_B.
Probab=28.11 E-value=66 Score=26.91 Aligned_cols=37 Identities=24% Similarity=0.146 Sum_probs=17.7
Q ss_pred HHHHCCCcEEEEccC-CCch-hhHHHHHHHHHHHcCCCC
Q psy8860 338 KALKIGITKVAFDRS-GFRY-HGRIKFLADAARKNGLNF 374 (374)
Q Consensus 338 r~~~~gi~~vvfDr~-~~~y-hgrv~a~a~~~re~Gl~f 374 (374)
++.++|++.|+.-|. +... ...-...++.+++.||.|
T Consensus 22 ~la~~GfktVInlRpd~E~~~qp~~~~~~~~a~~~Gl~y 60 (110)
T PF04273_consen 22 QLAAQGFKTVINLRPDGEEPGQPSSAEEAAAAEALGLQY 60 (110)
T ss_dssp HHHHCT--EEEE-S-TTSTTT-T-HHCHHHHHHHCT-EE
T ss_pred HHHHCCCcEEEECCCCCCCCCCCCHHHHHHHHHHcCCeE
Confidence 455677777777773 2222 234555666777777653
No 71
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=27.91 E-value=1.5e+02 Score=27.11 Aligned_cols=47 Identities=13% Similarity=0.232 Sum_probs=31.4
Q ss_pred ChHHHHHHHHHHHHHHHHCCCcEEEEccCCC---chhhHHHHHHHHHHHcCCCC
Q psy8860 324 NTFAASIIGQRIAKKALKIGITKVAFDRSGF---RYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 324 ~~~aa~~vG~~la~r~~~~gi~~vvfDr~~~---~yhgrv~a~a~~~re~Gl~f 374 (374)
|..+++.+ ++.+.+.|..++.|=-+.. ....|.+.|.+++++.|+++
T Consensus 98 ~~~ag~~a----~~~L~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~ 147 (265)
T cd06285 98 DVLGGRLA----TRHLLDLGHRRIAVLAGPDYASTARDRLAGFRAALAEAGIEV 147 (265)
T ss_pred cHHHHHHH----HHHHHHCCCccEEEEeCCcccccHHHHHHHHHHHHHHcCCCC
Confidence 44555544 4455556888887654321 23579999999999999853
No 72
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=27.76 E-value=1.7e+02 Score=26.23 Aligned_cols=42 Identities=14% Similarity=0.275 Sum_probs=28.5
Q ss_pred HHHHHHHHHHCCCcEEEEc--cCCCc-hhhHHHHHHHHHHHcCCC
Q psy8860 332 GQRIAKKALKIGITKVAFD--RSGFR-YHGRIKFLADAARKNGLN 373 (374)
Q Consensus 332 G~~la~r~~~~gi~~vvfD--r~~~~-yhgrv~a~a~~~re~Gl~ 373 (374)
|+.+++.+.++|..++.+= ..... .+.|.++|.+.+++.|++
T Consensus 104 g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~r~~g~~~~~~~~~~~ 148 (264)
T cd06267 104 AYLAVEHLIELGHRRIAFIGGPPDLSTARERLEGYREALEEAGIP 148 (264)
T ss_pred HHHHHHHHHHCCCceEEEecCCCccchHHHHHHHHHHHHHHcCCC
Confidence 4555566666688887652 22323 357999999999999854
No 73
>CHL00140 rpl6 ribosomal protein L6; Validated
Probab=26.69 E-value=65 Score=29.30 Aligned_cols=30 Identities=37% Similarity=0.589 Sum_probs=21.2
Q ss_pred cCCc---ceeecCCCeEEEEecc-EEEEEeCCeE
Q psy8860 120 SMGK---MPIFIPPNVEVTLNSN-KITLKGPLGI 149 (374)
Q Consensus 120 ~ig~---~~I~IP~~V~v~~~~~-~i~vkGp~G~ 149 (374)
.+|- ..++||+||+|+..+. .|.++|..=+
T Consensus 106 ~LG~sh~i~~~IP~gv~v~~~~~t~I~i~G~dke 139 (178)
T CHL00140 106 NLGYSHPVKIKIPPGISVEVENNTNITIKGIDKE 139 (178)
T ss_pred EecCCeeEEEECCCCeEEEeCCCCEEEEEECCHH
Confidence 4553 3458999999988765 6788877533
No 74
>cd06477 ACD_HspB3_Like Alpha crystallin domain (ACD) found in mammalian HspB3, also known as heat-shock protein 27-like protein (HSPL27, 17-kDa) and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB3 is expressed in adult skeletal muscle, smooth muscle, and heart, and in several other fetal tissues. In muscle cells HspB3 forms an oligomeric 150 kDa complex with myotonic dystrophy protein kinase-binding protein (MKBP/ HspB2), this complex may comprise one of two independent muscle-cell specific chaperone systems. The expression of HspB3 is induced during muscle differentiation controlled by the myogenic factor MyoD. HspB3 may also interact with Hsp22 (HspB8).
Probab=26.58 E-value=44 Score=26.51 Aligned_cols=19 Identities=16% Similarity=0.363 Sum_probs=15.9
Q ss_pred CCCeEEEEeccEEEEEeCC
Q psy8860 129 PPNVEVTLNSNKITLKGPL 147 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp~ 147 (374)
|+.++|+++++.|+|+|-.
T Consensus 20 ~edI~V~v~~~~L~I~ge~ 38 (83)
T cd06477 20 PEDIIIQVFEGWLLIKGQH 38 (83)
T ss_pred HHHeEEEEECCEEEEEEEE
Confidence 6788999999999888854
No 75
>cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=26.52 E-value=1.8e+02 Score=26.60 Aligned_cols=43 Identities=23% Similarity=0.268 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHCCCcEEEEccCC-Cc-hhhHHHHHHHHHHHcCCC
Q psy8860 331 IGQRIAKKALKIGITKVAFDRSG-FR-YHGRIKFLADAARKNGLN 373 (374)
Q Consensus 331 vG~~la~r~~~~gi~~vvfDr~~-~~-yhgrv~a~a~~~re~Gl~ 373 (374)
.|+.+++.+.+.|.+++.|=.+. .. ..-|..+|.+++++.|++
T Consensus 96 ~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~R~~gf~~~~~~~~~~ 140 (265)
T cd01543 96 IGRMAAEHFLERGFRHFAFYGLPGARWSDEREEAFRQLVAEAGYE 140 (265)
T ss_pred HHHHHHHHHHHCCCcEEEEEcCCCCHHHHHHHHHHHHHHHHcCCc
Confidence 44455666677899998874321 11 246899999999999875
No 76
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=26.47 E-value=1.8e+02 Score=26.64 Aligned_cols=43 Identities=19% Similarity=0.196 Sum_probs=28.8
Q ss_pred HHHHHHHHHHCCCcEEEEc--cCCC-chhhHHHHHHHHHHHcCCCC
Q psy8860 332 GQRIAKKALKIGITKVAFD--RSGF-RYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 332 G~~la~r~~~~gi~~vvfD--r~~~-~yhgrv~a~a~~~re~Gl~f 374 (374)
|+.+++.+.++|-.++.|= .... .-.-|.++|.+++++.|+.+
T Consensus 104 ~~~~~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~ 149 (268)
T cd06270 104 GYLATEHLIELGHRKIACITGPLTKEDARLRLQGYRDALAEAGIAL 149 (268)
T ss_pred HHHHHHHHHHCCCceEEEEeCCcccccHHHHHHHHHHHHHHcCCCC
Confidence 4455566666788887663 2222 23468999999999998753
No 77
>TIGR03653 arch_L6P archaeal ribosomal protein L6P. Members of this protein family are the archaeal ribosomal protein L6P. The top-scoring proteins not selected by this model are eukaryotic cytosolic ribosomal protein L9. Bacterial ribosomal protein L6 scores lower and is described by a distinct model.
Probab=26.30 E-value=4.9e+02 Score=23.50 Aligned_cols=57 Identities=19% Similarity=0.237 Sum_probs=38.6
Q ss_pred EEEEeccEEEEE---eCCeEEEEEcCCCeEEEEeCCEEEEEEcCCchhHHHHHHHHHHHHhhcce
Q psy8860 133 EVTLNSNKITLK---GPLGILKQNKNNLVNIKNDSNVLYFTAINNSRIAKSMSGTMRSIINNMII 194 (374)
Q Consensus 133 ~v~~~~~~i~vk---Gp~G~l~~~l~~~v~i~~~~~~l~i~~~~~~k~~~a~~gT~rsli~Nmi~ 194 (374)
++.++++.+.++ |=.-...+++|..+.+...++.|.++-. + +..+|.+.+.|++..+
T Consensus 93 ra~~~g~~L~l~n~LG~Sh~i~~~iP~gI~v~~~~~~I~i~G~--D---Kq~Vgq~AA~Ir~~~~ 152 (170)
T TIGR03653 93 QVKVEGNKVVIENFLGEKAPRRAKIPGGVKVKVKGEEVIVTGI--D---KEDVGQTAANIEQATR 152 (170)
T ss_pred EEEEcCCeEEEeeccccceeEEEECCCCeEEEecCCEEEEEeC--C---HHHHHHHHHHHHHhhc
Confidence 455677777774 4444667777778888877766666543 2 3568888999988654
No 78
>PF00070 Pyr_redox: Pyridine nucleotide-disulphide oxidoreductase; InterPro: IPR001327 FAD flavoproteins belonging to the family of pyridine nucleotide-disulphide oxidoreductases (glutathione reductase, trypanothione reductase, lipoamide dehydrogenase, mercuric reductase, thioredoxin reductase, alkyl hydroperoxide reductase) share sequence similarity with a number of other flavoprotein oxidoreductases, in particular with ferredoxin-NAD+ reductases involved in oxidative metabolism of a variety of hydrocarbons (rubredoxin reductase, putidaredoxin reductase, terpredoxin reductase, ferredoxin-NAD+ reductase components of benzene 1,2-dioxygenase, toluene 1,2-dioxygenase, chlorobenzene dioxygenase, biphenyl dioxygenase), NADH oxidase and NADH peroxidase [, , ]. Comparison of the crystal structures of human glutathione reductase and Escherichia coli thioredoxin reductase reveals different locations of their active sites, suggesting that the enzymes diverged from an ancestral FAD/NAD(P)H reductase and acquired their disulphide reductase activities independently []. Despite functional similarities, oxidoreductases of this family show no sequence similarity with adrenodoxin reductases [] and flavoprotein pyridine nucleotide cytochrome reductases (FPNCR) []. Assuming that disulphide reductase activity emerged later, during divergent evolution, the family can be referred to as FAD-dependent pyridine nucleotide reductases, FADPNR. To date, 3D structures of glutathione reductase [], thioredoxin reductase [], mercuric reductase [], lipoamide dehydrogenase [], trypanothione reductase [] and NADH peroxidase [] have been solved. The enzymes share similar tertiary structures based on a doubly-wound alpha/beta fold, but the relative orientations of their FAD- and NAD(P)H-binding domains may vary significantly. By contrast with the FPNCR family, the folds of the FAD- and NAD(P)H-binding domains are similar, suggesting that the domains evolved by gene duplication []. This entry describes a small NADH binding domain within a larger FAD binding domain described by IPR023753 from INTERPRO. It is found in both class I and class II oxidoreductases. ; GO: 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZKQ_A 3DGZ_A 1ZDL_A 2R9Z_B 2RAB_A 2A87_B 1M6I_A 2YVG_A 2GR1_A 2GQW_A ....
Probab=25.79 E-value=1.7e+02 Score=22.14 Aligned_cols=44 Identities=25% Similarity=0.351 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHCCCcEEEEccCCCch----hhHHHHHHHHHHHcCCCC
Q psy8860 331 IGQRIAKKALKIGITKVAFDRSGFRY----HGRIKFLADAARKNGLNF 374 (374)
Q Consensus 331 vG~~la~r~~~~gi~~vvfDr~~~~y----hgrv~a~a~~~re~Gl~f 374 (374)
+|-.+|.-+.+.|.+-.+++|+.... .---+.+.+.+++.|++|
T Consensus 10 ig~E~A~~l~~~g~~vtli~~~~~~~~~~~~~~~~~~~~~l~~~gV~v 57 (80)
T PF00070_consen 10 IGIELAEALAELGKEVTLIERSDRLLPGFDPDAAKILEEYLRKRGVEV 57 (80)
T ss_dssp HHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEE
T ss_pred HHHHHHHHHHHhCcEEEEEeccchhhhhcCHHHHHHHHHHHHHCCCEE
Confidence 66777788888998888999976554 223556678888888764
No 79
>TIGR00725 conserved hypothetical protein, DprA/Smf-related, family 1. This model represents one branch of a subfamily of uncharacterized proteins. Both PSI-BLAST and weak hits by this model show a low level of similarity and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting the branches may have distinct functions. This family is one of several families within the scope of PFAM model pfam03641, several members of which are annotated as lysine decarboxylases. That larger family, and the branch described by this model, have a well-conserved motif PGGXGTXXE.
Probab=25.72 E-value=2e+02 Score=25.51 Aligned_cols=39 Identities=26% Similarity=0.283 Sum_probs=29.8
Q ss_pred hHHHHHHHHHHHHHHHHCCCcEEEEccCCCchhhHHHHHHHHHHHcCC
Q psy8860 325 TFAASIIGQRIAKKALKIGITKVAFDRSGFRYHGRIKFLADAARKNGL 372 (374)
Q Consensus 325 ~~aa~~vG~~la~r~~~~gi~~vvfDr~~~~yhgrv~a~a~~~re~Gl 372 (374)
.++|+.+|+.||+ .|+ .+++ ||. .|--.|+++++.++|-
T Consensus 17 ~~~A~~lg~~La~----~g~-~lv~--Gg~--~GlM~a~a~ga~~~gg 55 (159)
T TIGR00725 17 YEIAYRLGKELAK----KGH-ILIN--GGR--TGVMEAVSKGAREAGG 55 (159)
T ss_pred HHHHHHHHHHHHH----CCC-EEEc--CCc--hhHHHHHHHHHHHCCC
Confidence 3677777777776 487 6777 763 3999999999999874
No 80
>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a
Probab=25.47 E-value=2e+02 Score=26.26 Aligned_cols=44 Identities=14% Similarity=0.158 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHCCCcEEEEc--c-CCCchhhHHHHHHHHHHHcCCCC
Q psy8860 331 IGQRIAKKALKIGITKVAFD--R-SGFRYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 331 vG~~la~r~~~~gi~~vvfD--r-~~~~yhgrv~a~a~~~re~Gl~f 374 (374)
.|+.+++.+.+.|..++.|= . +....+-|.+.|.+++.+.|+++
T Consensus 104 ~~~~~~~~l~~~G~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~~ 150 (269)
T cd06275 104 GGYLATRHLIELGHRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLPV 150 (269)
T ss_pred HHHHHHHHHHHCCCceEEEEeCCCCCccHHHHHHHHHHHHHHcCCCC
Confidence 44455566666798888662 2 22223568999999999998753
No 81
>COG1072 CoaA Panthothenate kinase [Coenzyme metabolism]
Probab=25.42 E-value=49 Score=32.46 Aligned_cols=42 Identities=19% Similarity=0.214 Sum_probs=32.5
Q ss_pred cEEEEEecceeeEEEeCCCCcEEEcccCCEEEEEecchhhhhh
Q psy8860 218 NYLNLILGFSHPILYKIPFDIICETPSQTEILIKGINKQAVGH 260 (374)
Q Consensus 218 ~~L~l~LG~Sh~i~~~IP~gV~v~~~~~t~I~l~G~dke~Vgq 260 (374)
..-..-=.|||.+.-.+|...+| +++++.|+++|++.=+-++
T Consensus 161 ~~~v~aPvysh~~yD~vpd~~~v-~~~pdIlI~EG~nvLq~~~ 202 (283)
T COG1072 161 KPDVFAPVYSHLIYDPVPDAFQV-VPQPDILIVEGNNVLQDGE 202 (283)
T ss_pred CCccccccccccccccCCCceee-cCCCCEEEEechhhhcCCC
Confidence 33345568999999999998888 6678899999998654443
No 82
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=25.36 E-value=88 Score=27.30 Aligned_cols=43 Identities=23% Similarity=0.314 Sum_probs=30.8
Q ss_pred HHHHHHHHHHCCCcEEEEccCCCch-hhHHHHHHHHHHHcCCCC
Q psy8860 332 GQRIAKKALKIGITKVAFDRSGFRY-HGRIKFLADAARKNGLNF 374 (374)
Q Consensus 332 G~~la~r~~~~gi~~vvfDr~~~~y-hgrv~a~a~~~re~Gl~f 374 (374)
...|.+-|.+.|++.|++++..-.+ .-+.+++.+.+.+.|+.+
T Consensus 77 ~~~l~~l~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~ 120 (165)
T PF00875_consen 77 EEVLPELAKEYGATAVYFNEEYTPYERRRDERVRKALKKHGIKV 120 (165)
T ss_dssp HHHHHHHHHHHTESEEEEE---SHHHHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHhcCcCeeEeccccCHHHHHHHHHHHHHHHhcceEE
Confidence 3455566777899999999974444 468899999999988864
No 83
>PRK09492 treR trehalose repressor; Provisional
Probab=24.78 E-value=1.9e+02 Score=27.32 Aligned_cols=46 Identities=9% Similarity=0.049 Sum_probs=31.6
Q ss_pred ChHHHHHHHHHHHHHHHHCCCcEEEEccCC--C--chhhHHHHHHHHHHHcCCC
Q psy8860 324 NTFAASIIGQRIAKKALKIGITKVAFDRSG--F--RYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 324 ~~~aa~~vG~~la~r~~~~gi~~vvfDr~~--~--~yhgrv~a~a~~~re~Gl~ 373 (374)
|..+++ .+++.+.+.|..++.|=.++ . ....|..+|.+++++.|++
T Consensus 159 ~~~~~~----~a~~~L~~~G~~~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~ 208 (315)
T PRK09492 159 DEGAIK----LLMQRLYDQGHRHISYLGVDHSDVTTGKRRHQAYLAFCKQHKLT 208 (315)
T ss_pred cHHHHH----HHHHHHHHcCCCeEEEEcCCcccchhHHHHHHHHHHHHHHcCCC
Confidence 444554 45555567799998774321 1 1257999999999999986
No 84
>COG1611 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]
Probab=24.35 E-value=93 Score=28.98 Aligned_cols=39 Identities=21% Similarity=0.199 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHCCCcEEEEccCCCchhhHHHHHHHHHHHcCCC
Q psy8860 326 FAASIIGQRIAKKALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 326 ~aa~~vG~~la~r~~~~gi~~vvfDr~~~~yhgrv~a~a~~~re~Gl~ 373 (374)
+.|+.+|+.||+|. .+|+-=| ..|-..|.+++|.++|-.
T Consensus 34 ~~a~~lg~~la~~g------~~V~tGG---~~GiMea~~~gA~~~gg~ 72 (205)
T COG1611 34 ELARELGRELAKRG------LLVITGG---GPGVMEAVARGALEAGGL 72 (205)
T ss_pred HHHHHHHHHHHhCC------cEEEeCC---chhhhhHHHHHHHHcCCe
Confidence 67888888888876 5566433 368999999999998853
No 85
>cd06478 ACD_HspB4-5-6 Alpha-crystallin domain found in alphaA-crystallin (HspB4), alphaB-crystallin (HspB5), and the small heat shock protein (sHsp) HspB6, also known as Hsp20. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. Only trace amounts of HspB4 are found in tissues other than the lens. HspB5 on the other hand is also expressed constitutively in other tissues including brain, heart, and type I and type IIa skeletal muscle fibers, and in several cancers including gliomas, renal cell carcinomas, basal-like and metaplastic breast carcinomas, and head and neck cancer. HspB5's functions include effects on the apoptotic pathway and on metastasis. Phosphorylation of HspB5 reduces its ol
Probab=24.24 E-value=59 Score=25.51 Aligned_cols=18 Identities=17% Similarity=0.445 Sum_probs=15.4
Q ss_pred CCCeEEEEeccEEEEEeC
Q psy8860 129 PPNVEVTLNSNKITLKGP 146 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp 146 (374)
|++++|+++++.|+|+|.
T Consensus 20 ~edI~V~v~~~~L~I~g~ 37 (83)
T cd06478 20 PEELSVKVLGDFVEIHGK 37 (83)
T ss_pred HHHeEEEEECCEEEEEEE
Confidence 678899999999999884
No 86
>cd06463 p23_like Proteins containing this p23_like domain include p23 and its Saccharomyces cerevisiae (Sc) homolog Sba1. Both are co-chaperones for the heat shock protein (Hsp) 90. p23 binds Hsp90 and participates in the folding of a number of Hsp90 clients, including the progesterone receptor. p23 also has a passive chaperoning activity and in addition may participate in prostaglandin synthesis. Both p23 and Sba1p can regulate telomerase activity. This group includes domains similar to the C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1). Sgt1 interacts with multiple protein complexes and has the features of a co-chaperone. Human (h) Sgt1 interacts with both Hsp70 and Hsp90, and has been shown to bind Hsp90 through its CS domain. Saccharomyces cerevisiae (Sc) Sgt1 is a subunit of both core kinetochore and SCF (Skp1-Cul1-F-box) ubiquitin ligase complexes. Sgt1 is required for pathogen resistance in plants. This group also includes the p23_like domains of
Probab=24.23 E-value=2.9e+02 Score=20.22 Aligned_cols=43 Identities=12% Similarity=0.091 Sum_probs=30.6
Q ss_pred CCCeEEEEeccEEEEEeCC---e--EEEEEcCCC-----eEEEEeCCEEEEEE
Q psy8860 129 PPNVEVTLNSNKITLKGPL---G--ILKQNKNNL-----VNIKNDSNVLYFTA 171 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp~---G--~l~~~l~~~-----v~i~~~~~~l~i~~ 171 (374)
+++++|.++++.++++... + .+..+|.+. ....++++.+.|..
T Consensus 19 ~~~~~v~~~~~~l~i~~~~~~~~~~~~~~~L~~~I~~~~s~~~~~~~~l~i~L 71 (84)
T cd06463 19 KKDVKVEFTPKSLTVSVKGGGGKEYLLEGELFGPIDPEESKWTVEDRKIEITL 71 (84)
T ss_pred ccceEEEEecCEEEEEeeCCCCCceEEeeEccCccchhhcEEEEeCCEEEEEE
Confidence 6888999999988887653 2 566666643 44567888887764
No 87
>COG0071 IbpA Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=24.09 E-value=1.7e+02 Score=25.27 Aligned_cols=44 Identities=20% Similarity=0.366 Sum_probs=31.1
Q ss_pred CCCeEEEEeccEEEEEeCC------------------eEEEEEc--CCC-----eEEEEeCCEEEEEEc
Q psy8860 129 PPNVEVTLNSNKITLKGPL------------------GILKQNK--NNL-----VNIKNDSNVLYFTAI 172 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp~------------------G~l~~~l--~~~-----v~i~~~~~~l~i~~~ 172 (374)
|++|+|++.++.|+|+|-. |...+.| +.. +.-.++++-|.|...
T Consensus 63 kedI~I~~~~~~l~I~g~~~~~~~~~~~~~~~~e~~~~~f~r~~~Lp~~v~~~~~~A~~~nGvL~I~lp 131 (146)
T COG0071 63 KEDIEITVEGNTLTIRGEREEEEEEEEEGYLRRERAYGEFERTFRLPEKVDPEVIKAKYKNGLLTVTLP 131 (146)
T ss_pred hHHeEEEEECCEEEEEEEecccccccCCceEEEEEEeeeEEEEEECcccccccceeeEeeCcEEEEEEe
Confidence 5789999999999998877 4444444 422 445678888888643
No 88
>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor
Probab=23.98 E-value=2e+02 Score=26.21 Aligned_cols=46 Identities=20% Similarity=0.086 Sum_probs=29.9
Q ss_pred ChHHHHHHHHHHHHHHHHCCCcEEEEccCC---CchhhHHHHHHHHHHHcCCC
Q psy8860 324 NTFAASIIGQRIAKKALKIGITKVAFDRSG---FRYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 324 ~~~aa~~vG~~la~r~~~~gi~~vvfDr~~---~~yhgrv~a~a~~~re~Gl~ 373 (374)
|.++++.+++. +.+.|..++.|=.+. ..-+-|.++|.+++.++|+.
T Consensus 100 ~~~~g~~~~~~----l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 148 (264)
T cd06274 100 NRDGAAELTRE----LLAAPPEEVLFLGGLPELSPSRERLAGFRQALADAGLP 148 (264)
T ss_pred cHHHHHHHHHH----HHHCCCCcEEEEeCCCcccchHHHHHHHHHHHHHcCCC
Confidence 44555555544 445788887664332 22356999999999999864
No 89
>cd06498 ACD_alphaB-crystallin_HspB5 Alpha-crystallin domain found in the small heat shock protein (sHsp) alphaB-crystallin (HspB5, 20kDa). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. HspB4 does not belong to this group. HspB5 shows increased synthesis in response to stress. HspB5 is also expressed constitutively in other tissues including brain, heart, and type I and type IIa skeletal muscle fibers, and in several cancers including gliomas, renal cell carcinomas, basal-like and metaplastic breast carcinomas, and head and neck cancer. Its functions include effects on the apoptotic pathway and on metastasis. Phosphorylation of HspB5 reduces its oligomerization and anti-apoptotic activ
Probab=23.81 E-value=53 Score=25.93 Aligned_cols=18 Identities=22% Similarity=0.481 Sum_probs=16.0
Q ss_pred CCCeEEEEeccEEEEEeC
Q psy8860 129 PPNVEVTLNSNKITLKGP 146 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp 146 (374)
|++++|.++++.|+|+|-
T Consensus 20 ~edi~V~v~~~~L~I~g~ 37 (84)
T cd06498 20 PEELKVKVLGDFIEIHGK 37 (84)
T ss_pred HHHeEEEEECCEEEEEEE
Confidence 788999999999999984
No 90
>PTZ00027 60S ribosomal protein L6; Provisional
Probab=23.75 E-value=80 Score=29.14 Aligned_cols=24 Identities=21% Similarity=0.304 Sum_probs=16.5
Q ss_pred ceeecCCCeEEEEec---cEEEEEeCC
Q psy8860 124 MPIFIPPNVEVTLNS---NKITLKGPL 147 (374)
Q Consensus 124 ~~I~IP~~V~v~~~~---~~i~vkGp~ 147 (374)
..++||+||+++..+ +.|+++|..
T Consensus 123 i~~~iP~gv~v~~~~~~~t~I~i~G~D 149 (190)
T PTZ00027 123 RTVKMLPGVVVEKSESVKDEIIVTGAD 149 (190)
T ss_pred EEEECCCCeEEEeCCCCCCEEEEEeCC
Confidence 345889999998765 356666654
No 91
>TIGR03654 L6_bact ribosomal protein L6, bacterial type.
Probab=23.65 E-value=81 Score=28.58 Aligned_cols=29 Identities=28% Similarity=0.381 Sum_probs=20.3
Q ss_pred cCCc---ceeecCCCeEEEEecc-EEEEEeCCe
Q psy8860 120 SMGK---MPIFIPPNVEVTLNSN-KITLKGPLG 148 (374)
Q Consensus 120 ~ig~---~~I~IP~~V~v~~~~~-~i~vkGp~G 148 (374)
.+|- ..++||+||+|+..+. .|+++|+.=
T Consensus 105 ~LG~sh~i~~~Ip~~v~v~~~~~t~I~i~G~dk 137 (175)
T TIGR03654 105 SLGYSHPVEYEIPEGITVEVPKPTEIVVKGIDK 137 (175)
T ss_pred EecCceeEEEECCCCeEEEeCCCCEEEEEECCH
Confidence 4563 3458899999988765 577777653
No 92
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=23.54 E-value=1.9e+02 Score=26.72 Aligned_cols=52 Identities=19% Similarity=0.089 Sum_probs=37.9
Q ss_pred CCChHHHHHHHHHHHHHHHHCCC--cEEEE-cc---CCCchhhHHHHHHHHHHHcCCC
Q psy8860 322 GGNTFAASIIGQRIAKKALKIGI--TKVAF-DR---SGFRYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 322 ~~~~~aa~~vG~~la~r~~~~gi--~~vvf-Dr---~~~~yhgrv~a~a~~~re~Gl~ 373 (374)
..|..+++..|+.|++.+.++|. .++.| .- ....-.-|...|.+++.+.|+.
T Consensus 105 ~d~~~~g~~~~~~l~~~~~~~g~~~~~i~~i~~~~~~~~~~~~R~~G~~~~l~~~~~~ 162 (289)
T cd01540 105 MSATKIGEQVGEAIADEMKKRGWDPKEVGALRITYDELDTAKPRTDGALEALKAPGFP 162 (289)
T ss_pred CCHHHHHHHHHHHHHHHHHhhcCCCcceEEEEecCCCCcchhhHHHHHHHHHhcCCCC
Confidence 46778899999999999888887 45543 21 1112356999999999988874
No 93
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=23.38 E-value=1.9e+02 Score=27.70 Aligned_cols=44 Identities=11% Similarity=0.088 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHCCCcEEEEccC---CCchhhHHHHHHHHHHHcCCCC
Q psy8860 331 IGQRIAKKALKIGITKVAFDRS---GFRYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 331 vG~~la~r~~~~gi~~vvfDr~---~~~yhgrv~a~a~~~re~Gl~f 374 (374)
.|..+++.+.+.|..++.|=-+ ....+-|..+|.+++.+.|+++
T Consensus 165 ~g~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~~l~~~gi~~ 211 (341)
T PRK10703 165 GGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKV 211 (341)
T ss_pred HHHHHHHHHHHCCCCcEEEEeCCccccchHHHHHHHHHHHHHcCCCC
Confidence 3555566666778888866322 2233579999999999999864
No 94
>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=23.00 E-value=2.2e+02 Score=25.91 Aligned_cols=43 Identities=16% Similarity=0.259 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHCCCcEEEEccC--CCc-hhhHHHHHHHHHHHcCCC
Q psy8860 331 IGQRIAKKALKIGITKVAFDRS--GFR-YHGRIKFLADAARKNGLN 373 (374)
Q Consensus 331 vG~~la~r~~~~gi~~vvfDr~--~~~-yhgrv~a~a~~~re~Gl~ 373 (374)
.|+.+++.+.++|..++.|=.+ ... ...|..+|.+++++.|++
T Consensus 104 ~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~r~~gf~~~~~~~~~~ 149 (270)
T cd06296 104 GGLAATEHLLELGHRRIGFITGPPDLLCSRARLDGYRAALAEAGIP 149 (270)
T ss_pred HHHHHHHHHHHcCCCcEEEEcCCCcchhHHHHHHHHHHHHHHcCCC
Confidence 3455566666679898876333 222 357999999999998874
No 95
>COG3603 Uncharacterized conserved protein [Function unknown]
Probab=22.94 E-value=1.4e+02 Score=25.81 Aligned_cols=51 Identities=18% Similarity=0.288 Sum_probs=36.7
Q ss_pred CCCcccccCCceEEEEEcCCccccccccccCCcceeecCCCeEEEEeccEEEEEeCC
Q psy8860 91 KDNIPKIMNGLGLVIISTASGIITDRKARSMGKMPIFIPPNVEVTLNSNKITLKGPL 147 (374)
Q Consensus 91 ~~~l~~~~~g~G~~ivSTs~Gvmt~~ea~~ig~~~I~IP~~V~v~~~~~~i~vkGp~ 147 (374)
...+|.|.-|-|..=++-..-.|+.-+.-. .+|+.|+++-.=..+++.||+
T Consensus 22 ~~~ip~wa~~~~F~sIt~t~eelsivc~~~------~vp~~V~~~~GW~~lk~~gpf 72 (128)
T COG3603 22 GSAIPAWADGPGFWSITRTPEELSIVCLAD------RVPDVVQIEKGWSCLKFEGPF 72 (128)
T ss_pred CCcCccccCCCceEEEEcCCceEEEEeecc------cCCcceEecCCeEEEEEeccc
Confidence 368999999988765554444444433222 689999998887899999996
No 96
>cd06480 ACD_HspB8_like Alpha-crystallin domain (ACD) found in mammalian 21.6 KDa small heat shock protein (sHsp) HspB8, also denoted as Hsp22 in humans, and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. A chaperone complex formed of HspB8 and Bag3 stimulates degradation of protein complexes by macroautophagy. HspB8 also forms complexes with Hsp27 (HspB1), MKBP (HspB2), HspB3, alphaB-crystallin (HspB5), Hsp20 (HspB6), and cvHsp (HspB7). These latter interactions may depend on phosphorylation of the respective partner sHsp. HspB8 may participate in the regulation of cell proliferation, cardiac hypertrophy, apoptosis, and carcinogenesis. Point mutations in HspB8 have been correlated with the development of several congenital neurological diseases, including Charcot Marie tooth disease and distal motor neuropathy type II.
Probab=22.74 E-value=54 Score=26.58 Aligned_cols=20 Identities=15% Similarity=0.310 Sum_probs=16.8
Q ss_pred CCCeEEEEeccEEEEEeCCe
Q psy8860 129 PPNVEVTLNSNKITLKGPLG 148 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp~G 148 (374)
|+.++|++.++.|+|+|...
T Consensus 28 pEDL~Vkv~~~~L~V~Gkh~ 47 (91)
T cd06480 28 PEELTVKTKDGFVEVSGKHE 47 (91)
T ss_pred HHHcEEEEECCEEEEEEEEC
Confidence 78889999999999988653
No 97
>cd06476 ACD_HspB2_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB2/heat shock 27kDa protein 2 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB2 is preferentially and constitutively expressed in skeletal muscle and heart. HspB2 shows homooligomeric activity and forms aggregates in muscle cytosol. Although its expression is not induced by heat shock, it redistributes to the insoluble fraction in response to heat shock. In the mouse heart, HspB2 plays a role in maintaining energetic balance, by protecting cardiac energetics during ischemia/reperfusion, and allowing for increased work during acute inotropic challenge. hHspB2 [previously also known as myotonic dystrophy protein kinase (DMPK) binding protein (MKBP)] is selectively up-regulated in skeletal muscles from myotonic dystrophy patients.
Probab=22.69 E-value=57 Score=25.77 Aligned_cols=19 Identities=16% Similarity=0.265 Sum_probs=15.8
Q ss_pred CCCeEEEEeccEEEEEeCC
Q psy8860 129 PPNVEVTLNSNKITLKGPL 147 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp~ 147 (374)
|++++|++.++.|+|+|..
T Consensus 20 ~edi~V~v~~~~L~I~g~~ 38 (83)
T cd06476 20 PDEITVRTVDNLLEVSARH 38 (83)
T ss_pred HHHeEEEEECCEEEEEEEE
Confidence 6788999999999988854
No 98
>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....
Probab=22.64 E-value=1.4e+02 Score=28.59 Aligned_cols=43 Identities=23% Similarity=0.278 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHCCCcE-EEEccCCC---chhhHHHHHHHHHHHcCCC
Q psy8860 331 IGQRIAKKALKIGITK-VAFDRSGF---RYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 331 vG~~la~r~~~~gi~~-vvfDr~~~---~yhgrv~a~a~~~re~Gl~ 373 (374)
-|+.+++.+.+.|.++ +.|=.+.. ....|.+.|.+++.++|+.
T Consensus 105 a~~~a~~~Li~~Gh~~~I~~i~~~~~~~~~~~R~~Gy~~Al~~~Gl~ 151 (279)
T PF00532_consen 105 AGYEATEYLIKKGHRRPIAFIGGPEDSSTSRERLQGYRDALKEAGLP 151 (279)
T ss_dssp HHHHHHHHHHHTTCCSTEEEEEESTTTHHHHHHHHHHHHHHHHTTSC
T ss_pred HHHHHHHHHHhcccCCeEEEEecCcchHHHHHHHHHHHHHHHHcCCC
Confidence 4556778888899999 76644322 2356999999999999985
No 99
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=22.09 E-value=2.2e+02 Score=27.50 Aligned_cols=42 Identities=17% Similarity=0.218 Sum_probs=29.6
Q ss_pred HHHHHHHHHHCCCcEEEEccCC---CchhhHHHHHHHHHHHcCCC
Q psy8860 332 GQRIAKKALKIGITKVAFDRSG---FRYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 332 G~~la~r~~~~gi~~vvfDr~~---~~yhgrv~a~a~~~re~Gl~ 373 (374)
|..+++.+.+.|..++.|=.+. .....|...|.+++.+.|+.
T Consensus 164 ~~~a~~~L~~~G~~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gi~ 208 (343)
T PRK10727 164 AWLATRHLIQQGHTRIGYLCSNHSISDAEDRLQGYYDALAESGIP 208 (343)
T ss_pred HHHHHHHHHHCCCccEEEEeCCccccchHHHHHHHHHHHHHCCCC
Confidence 4455566667798888764332 22356999999999999985
No 100
>PF04969 CS: CS domain; InterPro: IPR017447 The function of the CS domain is unknown. The CS domain is sometimes found C-terminal to the CHORD domain (IPR007051 from INTERPRO) in metazoan proteins, but occurs separately from the CHORD domain in plants. This association is thought to be indicative of an functional interaction between CS and CHORD domains [].; PDB: 1WGV_A 2KMW_A 2O30_B 1WH0_A 1EJF_A 2RH0_B 1RL1_A 2CR0_A 1WFI_A 2XCM_D ....
Probab=21.97 E-value=3.1e+02 Score=19.98 Aligned_cols=42 Identities=17% Similarity=0.225 Sum_probs=29.1
Q ss_pred CCCeEEEEeccEEEEEeCCe-----EEEEEcCCCe-----EEEEeCCEEEEE
Q psy8860 129 PPNVEVTLNSNKITLKGPLG-----ILKQNKNNLV-----NIKNDSNVLYFT 170 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp~G-----~l~~~l~~~v-----~i~~~~~~l~i~ 170 (374)
|++++|.++++.+.|+-+.| .+..+|.+.| ...+.++.|.+.
T Consensus 25 ~~dv~v~~~~~~l~v~~~~~~~~~~~~~~~L~~~I~~~~s~~~~~~~~i~i~ 76 (79)
T PF04969_consen 25 KEDVKVDFTDTSLSVSIKSGDGKEYLLEGELFGEIDPDESTWKVKDNKIEIT 76 (79)
T ss_dssp GGGEEEEEETTEEEEEEEETTSCEEEEEEEBSS-BECCCEEEEEETTEEEEE
T ss_pred hHHeEEEEEeeEEEEEEEccCCceEEEEEEEeeeEcchhcEEEEECCEEEEE
Confidence 57899999999999886522 5666666543 456677777664
No 101
>PF11280 DUF3081: Protein of unknown function (DUF3081); InterPro: IPR021432 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=21.83 E-value=68 Score=25.51 Aligned_cols=40 Identities=25% Similarity=0.329 Sum_probs=28.2
Q ss_pred ecccceEEEEEEEEE-----EEEEEEeCcEEEEEecceeeEEEeC
Q psy8860 195 GVTKGFEKKLQLIGV-----GFRAKIEKNYLNLILGFSHPILYKI 234 (374)
Q Consensus 195 GVt~Gf~~~L~lvGv-----Gyr~~~~g~~L~l~LG~Sh~i~~~I 234 (374)
|-.....+.|.=+.+ ||.+++.++.+.+.|||=..-.++=
T Consensus 18 Ge~~~~~y~l~GI~A~~D~DGYtv~L~~~~VtLtl~FHnty~~dy 62 (79)
T PF11280_consen 18 GEKTEGGYELEGITAFSDFDGYTVYLEDNGVTLTLGFHNTYHLDY 62 (79)
T ss_pred CccCCCcEEEccEEEEecCCCcEEEEeCCCEEEEEEeccceecCC
Confidence 444555555555444 8899999999999999976555443
No 102
>PRK05498 rplF 50S ribosomal protein L6; Validated
Probab=21.80 E-value=93 Score=28.26 Aligned_cols=29 Identities=28% Similarity=0.381 Sum_probs=19.9
Q ss_pred cCCc---ceeecCCCeEEEEecc-EEEEEeCCe
Q psy8860 120 SMGK---MPIFIPPNVEVTLNSN-KITLKGPLG 148 (374)
Q Consensus 120 ~ig~---~~I~IP~~V~v~~~~~-~i~vkGp~G 148 (374)
.+|- ..++||+||+|+..+. .|+++|..=
T Consensus 106 ~LG~sh~i~~~Ip~gv~v~~~~~t~I~i~G~dk 138 (178)
T PRK05498 106 SLGYSHPVEYEIPEGITVEVPKPTEIVVKGIDK 138 (178)
T ss_pred EecCCEEEEEECCCCeEEEeCCCCEEEEEECCH
Confidence 4663 3458899999987665 577777653
No 103
>cd06497 ACD_alphaA-crystallin_HspB4 Alpha-crystallin domain found in the small heat shock protein (sHsp) alphaA-crystallin (HspB4, 20kDa). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. Only trace amounts of HspB4 are found in tissues other than the lens. HspB5 does not belong to this group. Mutations inHspB4 have been associated with Autosomal Dominant Congenital Cataract (ADCC). The chaperone-like functions of HspB4 are considered important for maintaining lens transparency and preventing cataract.
Probab=21.76 E-value=62 Score=25.64 Aligned_cols=19 Identities=16% Similarity=0.429 Sum_probs=16.4
Q ss_pred CCCeEEEEeccEEEEEeCC
Q psy8860 129 PPNVEVTLNSNKITLKGPL 147 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp~ 147 (374)
|++++|++.++.|+|+|..
T Consensus 23 ~edi~V~v~~~~L~I~g~~ 41 (86)
T cd06497 23 PEDLTVKVLDDYVEIHGKH 41 (86)
T ss_pred HHHeEEEEECCEEEEEEEE
Confidence 6889999999999999853
No 104
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=21.73 E-value=1.9e+02 Score=24.98 Aligned_cols=40 Identities=20% Similarity=0.414 Sum_probs=31.8
Q ss_pred HHHHHHHHCCCcEE----------EEccCCCchhhHHHHHHHHHHHcCCC
Q psy8860 334 RIAKKALKIGITKV----------AFDRSGFRYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 334 ~la~r~~~~gi~~v----------vfDr~~~~yhgrv~a~a~~~re~Gl~ 373 (374)
.++-+|+..|++-| -|++|.|+-.-|+..+.+.+-|-||+
T Consensus 44 ~fvl~Al~~GaDGV~v~GC~~geCHy~~GN~ka~rR~~~lke~l~elgie 93 (132)
T COG1908 44 EFVLKALRKGADGVLVAGCKIGECHYISGNYKAKRRMELLKELLKELGIE 93 (132)
T ss_pred HHHHHHHHcCCCeEEEecccccceeeeccchHHHHHHHHHHHHHHHhCCC
Confidence 45667778887754 47888888888999999999998875
No 105
>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=21.62 E-value=2.5e+02 Score=25.71 Aligned_cols=42 Identities=14% Similarity=0.214 Sum_probs=28.6
Q ss_pred HHHHHHHHHHCCCcEEEEccC--CC-chhhHHHHHHHHHHHcCCC
Q psy8860 332 GQRIAKKALKIGITKVAFDRS--GF-RYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 332 G~~la~r~~~~gi~~vvfDr~--~~-~yhgrv~a~a~~~re~Gl~ 373 (374)
|+.+++++.++|..++.|=.+ .. .-..|.++|.+++.+.|+.
T Consensus 104 ~~~~~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~ 148 (269)
T cd06293 104 GRLATRHLARAGHRRIAFVGGPDALISARERYAGYREALAEAHIP 148 (269)
T ss_pred HHHHHHHHHHCCCceEEEEecCcccccHHHHHHHHHHHHHHcCCC
Confidence 344555556679999876433 21 2246899999999999875
No 106
>smart00812 Alpha_L_fucos Alpha-L-fucosidase. O-Glycosyl hydrolases (EC 3.2.1.-) 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 PUBMED:. Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in 'clans'. Family 29 encompasses alpha-L-fucosidases, which is a lysosomal enzyme responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Deficiency of alpha-L-fucosidase results in the lysosomal storage disease fucosidosis.
Probab=21.56 E-value=1.1e+02 Score=31.17 Aligned_cols=42 Identities=36% Similarity=0.470 Sum_probs=31.7
Q ss_pred HHHHHHHHHCCCcEEEEccC---CCc--------h-------hh-HHHHHHHHHHHcCCCC
Q psy8860 333 QRIAKKALKIGITKVAFDRS---GFR--------Y-------HG-RIKFLADAARKNGLNF 374 (374)
Q Consensus 333 ~~la~r~~~~gi~~vvfDr~---~~~--------y-------hg-rv~a~a~~~re~Gl~f 374 (374)
+..|+.|+++|.+-+|+--. |+- | +. -|+.|++++|+.||+|
T Consensus 84 ~~Wa~~~k~AGakY~vlTaKHHDGF~lw~S~~t~~n~~~~~pkrDiv~el~~A~rk~Glk~ 144 (384)
T smart00812 84 EEWADLFKKAGAKYVVLTAKHHDGFCLWDSKYSNWNAVDTGPKRDLVGELADAVRKRGLKF 144 (384)
T ss_pred HHHHHHHHHcCCCeEEeeeeecCCccccCCCCCCCcccCCCCCcchHHHHHHHHHHcCCeE
Confidence 56789999999999887532 111 1 11 4999999999999986
No 107
>PF13380 CoA_binding_2: CoA binding domain; PDB: 3FF4_A 2D5A_A 2D59_A 2E6U_X 1IUL_A 1IUK_A 1Y81_A 2DUW_A.
Probab=21.05 E-value=1.1e+02 Score=25.47 Aligned_cols=39 Identities=23% Similarity=0.329 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHCCCcEEEEccCCCchhhHHHHHHHHHHHcCCCC
Q psy8860 331 IGQRIAKKALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLNF 374 (374)
Q Consensus 331 vG~~la~r~~~~gi~~vvfDr~~~~yhgrv~a~a~~~re~Gl~f 374 (374)
....+.+.|.++|+..+.|--| ..-..+.+.++++|+.+
T Consensus 67 ~~~~~v~~~~~~g~~~v~~~~g-----~~~~~~~~~a~~~gi~v 105 (116)
T PF13380_consen 67 KVPEIVDEAAALGVKAVWLQPG-----AESEELIEAAREAGIRV 105 (116)
T ss_dssp HHHHHHHHHHHHT-SEEEE-TT-----S--HHHHHHHHHTT-EE
T ss_pred HHHHHHHHHHHcCCCEEEEEcc-----hHHHHHHHHHHHcCCEE
Confidence 3444567788889999999887 67788999999999863
No 108
>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso
Probab=21.04 E-value=2.3e+02 Score=25.67 Aligned_cols=43 Identities=14% Similarity=0.247 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHCCCcEEEEc--cCCCch-hhHHHHHHHHHHHcCCC
Q psy8860 331 IGQRIAKKALKIGITKVAFD--RSGFRY-HGRIKFLADAARKNGLN 373 (374)
Q Consensus 331 vG~~la~r~~~~gi~~vvfD--r~~~~y-hgrv~a~a~~~re~Gl~ 373 (374)
.|..+++.+.+.|..++.|= +..... ..|.+.|.+++.+.|+.
T Consensus 107 ~~~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~ 152 (268)
T cd06271 107 AAYQAVRRLIALGHRRIALLNPPEDLTFAQHRRAGYRRALAEAGLP 152 (268)
T ss_pred HHHHHHHHHHHcCCCcEEEecCccccchHHHHHHHHHHHHHHhCCC
Confidence 34455555566788888663 222222 46899999999998864
No 109
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=20.96 E-value=2.7e+02 Score=25.28 Aligned_cols=45 Identities=20% Similarity=0.366 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHCCCcEEEEccC--CCch-hhHHHHHHHHHHHcCCCC
Q psy8860 330 IIGQRIAKKALKIGITKVAFDRS--GFRY-HGRIKFLADAARKNGLNF 374 (374)
Q Consensus 330 ~vG~~la~r~~~~gi~~vvfDr~--~~~y-hgrv~a~a~~~re~Gl~f 374 (374)
..|+.+++.+.+.|-+++.+=.+ ++.. .-|...|.+++++.|+++
T Consensus 104 ~~g~~a~~~l~~~g~~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~ 151 (270)
T cd01545 104 AAAREMTRHLIDLGHRRIAFIAGPPDHRASAERLEGYRDALAEAGLPL 151 (270)
T ss_pred HHHHHHHHHHHHCCCceEEEEeCCCCchhHHHHHHHHHHHHHHcCCCC
Confidence 35566666667778888866332 3332 368899999999988753
No 110
>COG0041 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]
Probab=20.81 E-value=2.6e+02 Score=25.18 Aligned_cols=40 Identities=18% Similarity=0.164 Sum_probs=32.9
Q ss_pred HHHHHHHHCCCcEEEEccCCCchhhHHHHHHHHHHHcCCC
Q psy8860 334 RIAKKALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 334 ~la~r~~~~gi~~vvfDr~~~~yhgrv~a~a~~~re~Gl~ 373 (374)
..|+-+.+.||+--+.=-+.++-..++..+|+.+++.|++
T Consensus 20 ~Aa~~L~~fgi~ye~~VvSAHRTPe~m~~ya~~a~~~g~~ 59 (162)
T COG0041 20 KAAEILEEFGVPYEVRVVSAHRTPEKMFEYAEEAEERGVK 59 (162)
T ss_pred HHHHHHHHcCCCeEEEEEeccCCHHHHHHHHHHHHHCCCe
Confidence 3466677889987666667888889999999999999986
No 111
>PF07355 GRDB: Glycine/sarcosine/betaine reductase selenoprotein B (GRDB); InterPro: IPR022787 This entry represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. All members are expected to contain an internal UGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon. ; GO: 0030699 glycine reductase activity, 0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor, 0055114 oxidation-reduction process, 0030700 glycine reductase complex
Probab=20.72 E-value=1.5e+02 Score=30.06 Aligned_cols=31 Identities=29% Similarity=0.426 Sum_probs=27.1
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHCCCcEEEE
Q psy8860 319 LGKGGNTFAASIIGQRIAKKALKIGITKVAF 349 (374)
Q Consensus 319 ~~~~~~~~aa~~vG~~la~r~~~~gi~~vvf 349 (374)
.+.+.+.+.++..|..+|+++++.|++.|++
T Consensus 316 ~G~gt~~~~~~~~g~eIa~~Lk~dgVDAVIL 346 (349)
T PF07355_consen 316 MGNGTAVANAKRFGPEIAKELKEDGVDAVIL 346 (349)
T ss_pred CCCCccHHHHHHHHHHHHHHHHHcCCCEEEE
Confidence 4455678889999999999999999999986
No 112
>PF01120 Alpha_L_fucos: Alpha-L-fucosidase; InterPro: IPR000933 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. Family 29 (GH29 from CAZY) encompasses alpha-L-fucosidases (3.2.1.51 from EC) [], which is a lysosomal enzyme responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Alpha-L-fucosidase is responsible for hydrolysing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Fucosylated glycoconjugates are involved in numerous biological events, making alpha-l-fucosidases, the enzymes responsible for their processing, critically important. Deficiency in alpha-l-fucosidase activity is associated with fucosidosis, a lysosomal storage disorder characterised by rapid neurodegeneration, resulting in severe mental and motor deterioration []. The enzyme is a hexamer and displays a two-domain fold, composed of a catalytic (beta/alpha)(8)-like domain and a C-terminal beta-sandwich domain []. Drosophila melanogaster spermatozoa contains an alpha-l-fucosidase that might be involved in fertilisation by interacting with alpha-l-fucose residues on the micropyle of the eggshell []. In human sperm, membrane-associated alpha-l-fucosidase is stable for extended periods of time, which is made possible by membrane domains and compartmentalisation. These help preserve protein integrity []. ; GO: 0004560 alpha-L-fucosidase activity, 0005975 carbohydrate metabolic process; PDB: 3EYP_B 2ZX6_A 2ZWY_B 2ZX8_B 2WSP_A 2ZXA_A 2ZWZ_B 1ODU_B 1HL9_A 2ZX5_B ....
Probab=20.46 E-value=1.3e+02 Score=30.02 Aligned_cols=43 Identities=40% Similarity=0.505 Sum_probs=29.7
Q ss_pred HHHHHHHHHHCCCcEEEEcc---CCCc--------h-----h-h--HHHHHHHHHHHcCCCC
Q psy8860 332 GQRIAKKALKIGITKVAFDR---SGFR--------Y-----H-G--RIKFLADAARKNGLNF 374 (374)
Q Consensus 332 G~~la~r~~~~gi~~vvfDr---~~~~--------y-----h-g--rv~a~a~~~re~Gl~f 374 (374)
....|+.|+++|-+-+|+-- .||- | + + -|+.|++++|+.||+|
T Consensus 93 ~dqW~~~ak~aGakY~VlTakHHDGF~LW~S~~t~~~v~~~~~krDiv~El~~A~rk~Glk~ 154 (346)
T PF01120_consen 93 ADQWAKLAKDAGAKYVVLTAKHHDGFCLWPSKYTDYNVVNSGPKRDIVGELADACRKYGLKF 154 (346)
T ss_dssp HHHHHHHHHHTT-SEEEEEEE-TT--BSS--TT-SSBGGGGGGTS-HHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHHcCCCEEEeehhhcCccccCCCCCCcccccCCCCCCCHHHHHHHHHHHcCCeE
Confidence 34578999999999999852 1211 1 1 1 4999999999999986
No 113
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=20.32 E-value=1.4e+02 Score=23.26 Aligned_cols=35 Identities=14% Similarity=0.120 Sum_probs=21.1
Q ss_pred ecchhHHHHHHHHHhCCCcceEEEEeccCCeeEEEEEE
Q psy8860 28 PSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELKILL 65 (374)
Q Consensus 28 p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~L 65 (374)
+.+++. .-|+.|.++|||+.-....+ +.++.|+.|
T Consensus 27 t~g~Ls-~hL~~Le~~GyV~~~k~~~~--~~p~t~~~l 61 (80)
T PF13601_consen 27 TDGNLS-KHLKKLEEAGYVEVEKEFEG--RRPRTWYSL 61 (80)
T ss_dssp -HHHHH-HHHHHHHHTTSEEEEEE-SS--S--EEEEEE
T ss_pred CHHHHH-HHHHHHHHCCCEEEEEeccC--CCCeEEEEE
Confidence 444443 45699999999997665432 445666665
No 114
>cd06482 ACD_HspB10 Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB10, also known as sperm outer dense fiber protein (ODFP), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB10 occurs exclusively in the axoneme of sperm cells and may have a cytoskeletal role.
Probab=20.26 E-value=68 Score=25.69 Aligned_cols=19 Identities=21% Similarity=0.443 Sum_probs=14.8
Q ss_pred CCCeEEEEeccEEEEEeCC
Q psy8860 129 PPNVEVTLNSNKITLKGPL 147 (374)
Q Consensus 129 P~~V~v~~~~~~i~vkGp~ 147 (374)
|++|+|+++++.|+|+|-.
T Consensus 21 kedI~V~v~~~~L~I~ger 39 (87)
T cd06482 21 PDQVKVKVKDGKVQVSAER 39 (87)
T ss_pred HHHeEEEEECCEEEEEEEE
Confidence 5678888888888888853
No 115
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=20.21 E-value=2.4e+02 Score=25.45 Aligned_cols=44 Identities=20% Similarity=0.228 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHCCCcEEEEccC---CC-chhhHHHHHHHHHHHcCCC
Q psy8860 330 IIGQRIAKKALKIGITKVAFDRS---GF-RYHGRIKFLADAARKNGLN 373 (374)
Q Consensus 330 ~vG~~la~r~~~~gi~~vvfDr~---~~-~yhgrv~a~a~~~re~Gl~ 373 (374)
..|..+++.+.+.|..++.|=.+ .. ..+.|.++|.+.+.+.|++
T Consensus 102 ~~g~~~~~~l~~~g~~~i~~i~~~~~~~~~~~~r~~gf~~~l~~~~~~ 149 (266)
T cd06282 102 AAARDVAQALAALGHRRIAMLAGRLAASDRARQRYAGYRAAMRAAGLA 149 (266)
T ss_pred HHHHHHHHHHHHcCcccEEEeccccccCchHHHHHHHHHHHHHHcCCC
Confidence 45555566666679888866332 12 2357999999999999875
Done!