Query 029373
Match_columns 194
No_of_seqs 154 out of 1046
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 11:53:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029373.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029373hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05518 rpl6p 50S ribosomal p 100.0 2.1E-66 4.6E-71 425.5 21.9 178 1-189 1-178 (180)
2 PTZ00027 60S ribosomal protein 100.0 1.2E-65 2.6E-70 424.3 22.8 188 1-192 1-188 (190)
3 PTZ00179 60S ribosomal protein 100.0 8.7E-66 1.9E-70 424.8 21.9 182 4-191 3-186 (189)
4 TIGR03653 arch_L6P archaeal ri 100.0 7.5E-65 1.6E-69 413.2 21.8 170 7-187 1-170 (170)
5 COG0097 RplF Ribosomal protein 100.0 5.1E-58 1.1E-62 373.4 20.7 174 2-190 1-175 (178)
6 CHL00140 rpl6 ribosomal protei 100.0 7.9E-56 1.7E-60 362.6 21.3 170 2-188 1-173 (178)
7 TIGR03654 L6_bact ribosomal pr 100.0 6.6E-54 1.4E-58 350.4 21.7 168 3-187 1-171 (175)
8 PRK05498 rplF 50S ribosomal pr 100.0 1.7E-53 3.6E-58 348.8 21.6 170 2-188 1-173 (178)
9 KOG3254 Mitochondrial/chloropl 100.0 6.8E-45 1.5E-49 294.8 12.9 165 5-188 34-201 (211)
10 KOG3255 60S ribosomal protein 99.9 4E-28 8.6E-33 198.3 2.1 179 1-190 1-179 (179)
11 PF00347 Ribosomal_L6: Ribosom 99.8 1.1E-18 2.3E-23 123.6 7.1 74 12-90 1-77 (77)
12 PF00347 Ribosomal_L6: Ribosom 98.2 7.6E-07 1.7E-11 62.6 2.1 63 100-171 3-67 (77)
13 cd06479 ACD_HspB7_like Alpha c 71.8 10 0.00022 27.0 4.8 27 13-39 21-55 (81)
14 TIGR03653 arch_L6P archaeal ri 57.9 12 0.00026 30.6 3.2 21 9-29 114-134 (170)
15 COG0097 RplF Ribosomal protein 54.9 14 0.00031 30.6 3.2 24 8-31 113-137 (178)
16 TIGR03654 L6_bact ribosomal pr 53.1 77 0.0017 25.8 7.3 56 105-168 15-75 (175)
17 cd06470 ACD_IbpA-B_like Alpha- 53.1 25 0.00054 25.1 3.9 18 13-30 24-41 (90)
18 cd02393 PNPase_KH Polynucleoti 50.2 41 0.00089 22.4 4.4 29 134-164 32-60 (61)
19 PRK05518 rpl6p 50S ribosomal p 49.5 20 0.00044 29.5 3.3 22 9-30 120-141 (180)
20 PF12970 DUF3858: Domain of Un 49.1 46 0.001 25.7 5.0 33 8-40 41-73 (116)
21 CHL00140 rpl6 ribosomal protei 47.7 1.3E+02 0.0029 24.4 7.9 57 105-169 16-77 (178)
22 PF00011 HSP20: Hsp20/alpha cr 44.3 62 0.0013 23.0 5.0 20 13-32 20-39 (102)
23 PTZ00179 60S ribosomal protein 41.8 29 0.00063 28.8 3.1 13 156-168 67-79 (189)
24 cd06477 ACD_HspB3_Like Alpha c 39.9 19 0.0004 25.9 1.5 19 13-31 20-38 (83)
25 cd06478 ACD_HspB4-5-6 Alpha-cr 38.7 24 0.00051 25.0 1.9 18 13-30 20-37 (83)
26 cd06480 ACD_HspB8_like Alpha-c 38.6 20 0.00043 26.3 1.5 19 13-31 28-46 (91)
27 PRK11597 heat shock chaperone 38.5 43 0.00094 26.5 3.5 19 13-31 56-74 (142)
28 cd06498 ACD_alphaB-crystallin_ 38.4 20 0.00044 25.5 1.5 18 13-30 20-37 (84)
29 cd06476 ACD_HspB2_like Alpha c 38.4 20 0.00044 25.5 1.5 19 13-31 20-38 (83)
30 PF00338 Ribosomal_S10: Riboso 37.8 69 0.0015 22.9 4.3 30 146-175 2-31 (97)
31 cd06469 p23_DYX1C1_like p23_li 37.8 1E+02 0.0023 20.6 5.1 28 13-40 19-46 (78)
32 cd06471 ACD_LpsHSP_like Group 36.5 36 0.00078 24.1 2.6 18 14-31 24-41 (93)
33 cd06497 ACD_alphaA-crystallin_ 35.1 24 0.00053 25.2 1.5 19 13-31 23-41 (86)
34 cd06481 ACD_HspB9_like Alpha c 34.6 28 0.0006 24.9 1.7 19 13-31 20-38 (87)
35 PRK14434 acylphosphatase; Prov 33.7 24 0.00052 25.8 1.3 55 96-168 11-66 (92)
36 COG1072 CoaA Panthothenate kin 33.3 31 0.00067 30.6 2.1 36 121-159 167-202 (283)
37 cd06482 ACD_HspB10 Alpha cryst 32.5 29 0.00062 25.1 1.5 18 13-30 21-38 (87)
38 cd06526 metazoan_ACD Alpha-cry 31.9 30 0.00065 24.1 1.5 20 13-32 20-39 (83)
39 cd00298 ACD_sHsps_p23-like Thi 31.4 48 0.001 21.2 2.4 20 13-32 19-38 (80)
40 PTZ00027 60S ribosomal protein 31.2 3E+02 0.0064 22.8 7.5 57 105-169 17-81 (190)
41 cd07429 Cby_like Chibby, a nuc 30.9 25 0.00055 26.8 1.0 14 176-189 52-65 (108)
42 cd06475 ACD_HspB1_like Alpha c 29.2 38 0.00081 24.2 1.7 19 13-31 23-41 (86)
43 PF14506 CppA_N: CppA N-termin 27.5 2.5E+02 0.0055 22.0 6.0 41 138-178 57-99 (125)
44 COG0071 IbpA Molecular chapero 26.5 87 0.0019 24.3 3.5 20 13-32 63-82 (146)
45 PRK14446 acylphosphatase; Prov 24.6 58 0.0013 23.6 2.0 51 96-166 11-62 (88)
46 PF05137 PilN: Fimbrial assemb 24.3 1.5E+02 0.0033 19.7 4.0 40 129-168 8-49 (78)
47 PRK14440 acylphosphatase; Prov 24.3 23 0.0005 25.7 -0.2 52 96-166 12-63 (90)
48 PRK14449 acylphosphatase; Prov 23.9 28 0.0006 25.2 0.2 53 96-167 12-64 (90)
49 PRK14447 acylphosphatase; Prov 23.3 37 0.00081 24.8 0.7 53 96-166 13-65 (95)
50 PRK13781 paaB phenylacetate-Co 23.1 29 0.00063 25.9 0.1 16 121-136 78-93 (95)
51 cd02394 vigilin_like_KH K homo 23.1 1.7E+02 0.0036 18.8 3.9 19 145-164 43-61 (62)
52 PRK14450 acylphosphatase; Prov 22.9 35 0.00075 24.7 0.5 53 96-166 11-63 (91)
53 PRK14421 acylphosphatase; Prov 22.9 27 0.00059 25.9 -0.1 55 92-166 9-64 (99)
54 PRK14420 acylphosphatase; Prov 22.2 22 0.00048 25.6 -0.6 53 96-167 11-63 (91)
55 PRK14433 acylphosphatase; Prov 22.0 30 0.00066 24.9 0.0 52 96-166 10-61 (87)
56 PF00013 KH_1: KH domain syndr 20.4 2.4E+02 0.0053 17.9 4.3 19 145-164 42-60 (60)
57 PRK10743 heat shock protein Ib 20.4 63 0.0014 25.3 1.5 18 13-30 58-75 (137)
58 PRK14445 acylphosphatase; Prov 20.0 54 0.0012 23.7 1.0 56 91-166 8-64 (91)
No 1
>PRK05518 rpl6p 50S ribosomal protein L6P; Reviewed
Probab=100.00 E-value=2.1e-66 Score=425.49 Aligned_cols=178 Identities=38% Similarity=0.666 Sum_probs=169.6
Q ss_pred CccccceeeEEcCCCcEEEEeCcEEEEEcCCcEEEEEecCceEEEEeccccccCCcEEEEEeccCChhhhhhHHhHHHHH
Q 029373 1 MKTILSSETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSAAIRTALSHV 80 (194)
Q Consensus 1 m~~~~~~~~I~IP~~V~v~i~~~~i~VkGp~G~l~~~l~~~~v~i~~~~~~~~~~~~i~v~~~~~~k~~~a~~Gt~rsli 80 (194)
|-.++.+.||.||++|+|+++++.|+|+||+|+|+++|+++.+++. .+++++.+++|+++++++|+|||+||||
T Consensus 1 ~~~~~~~~pI~IP~~V~v~i~~~~v~VkGp~G~L~~~~~~~~v~i~------~~~~~i~v~~~~~~kk~ra~~gt~rslI 74 (180)
T PRK05518 1 MVAAYIREEIEIPEGVTVEIEGLVVTVKGPKGELTRDFWYPGVTIS------VEDGKVVIETEFARKKTKAMVGTFASHI 74 (180)
T ss_pred CccccccccEEcCCCCEEEEECCEEEEECCCeEEEEEecCCcEEEE------EECCEEEEEECCCCHHHHHHHHHHHHHH
Confidence 6678899999999999999999999999999999999986678887 5568999999999999999999999999
Q ss_pred hhceeeecceeEEEEEEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHH
Q 029373 81 GNLITGVTKGYRYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRS 160 (194)
Q Consensus 81 ~Nmi~GVt~Gf~~~L~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~ 160 (194)
+|||+|||+||+++|+++|+||||||++ +|+.|.|+|+||||||+.++||+||++++++ | +|+|+|+|||+||||
T Consensus 75 ~NmI~GVt~Gf~~~LelvGvGypira~~--~g~~l~l~n~LG~Sh~v~~~iP~gV~v~~~~-t--~I~i~GiDKq~Vgq~ 149 (180)
T PRK05518 75 KNMIKGVTEGFEYKLKIVYSHFPMQVKV--QGNEVVIENFLGEKSPRRAKILGGVKVKVKG-E--DVIVEGIDKEDVGQT 149 (180)
T ss_pred HhhheecccceEEEEEEEecCccEEEEE--cCCEEEEEeccccceeEEEeCCCCeEEEecC-C--EEEEEeCCHHHHHHH
Confidence 9999999999999999999999999999 7889999999999999999999999999998 4 799999999999999
Q ss_pred HHHHhcccccCCCceeeeeceEEEeeeee
Q 029373 161 AALINQKCHVKNKDIRKFLDGIYVSERGT 189 (194)
Q Consensus 161 AA~Ir~~~~~K~kd~r~f~DGiyv~~k~~ 189 (194)
||+||+.|+.|+||+|+|+|||||+||+-
T Consensus 150 AA~Ir~~~~~~~kd~r~f~dgiyv~~k~~ 178 (180)
T PRK05518 150 AANIEQATKIKGFDRRVFQDGIYIVEKEV 178 (180)
T ss_pred HHHHHHhhcccCCCCCEeecCEEEEEecc
Confidence 99999999999999999999999999974
No 2
>PTZ00027 60S ribosomal protein L6; Provisional
Probab=100.00 E-value=1.2e-65 Score=424.26 Aligned_cols=188 Identities=57% Similarity=0.939 Sum_probs=170.8
Q ss_pred CccccceeeEEcCCCcEEEEeCcEEEEEcCCcEEEEEecCceEEEEeccccccCCcEEEEEeccCChhhhhhHHhHHHHH
Q 029373 1 MKTILSSETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSAAIRTALSHV 80 (194)
Q Consensus 1 m~~~~~~~~I~IP~~V~v~i~~~~i~VkGp~G~l~~~l~~~~v~i~~~~~~~~~~~~i~v~~~~~~k~~~a~~Gt~rsli 80 (194)
|+.++...||.||++|+|+++++.|+|+||+|+|+++|+++.+.+.++ .++++|.+++|.++++.+|+|||+||||
T Consensus 1 ~~~~~~~~~I~IP~~V~V~i~~~~v~VkGp~G~L~~~~~~~~~~i~i~----~~~~~i~v~~~~~~~k~~a~~Gt~rslI 76 (190)
T PTZ00027 1 MKTIFSSEKIRIPEGVTVTVKSRKVTVTGKYGELTRSFRHLPVDIKLS----KDGKYIKVEMWFGTPSHLACIRTVCSHI 76 (190)
T ss_pred CcccccCCCEecCCCCEEEEECCEEEEECCCceEEEEecCCCceEEEE----eCCCEEEEEeCCCCHHHHHHHHHHHHHH
Confidence 788899999999999999999999999999999999999754455533 3568899999988999999999999999
Q ss_pred hhceeeecceeEEEEEEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHH
Q 029373 81 GNLITGVTKGYRYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRS 160 (194)
Q Consensus 81 ~Nmi~GVt~Gf~~~L~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~ 160 (194)
+|||+|||+||+++|+++|+|||+.+.++++|+.|.|+|+||||||+.++||+||+++++++.+++|+|+|+|||+||||
T Consensus 77 ~NmI~GVt~Gf~~~LeivGvGyra~~~v~~~g~~L~l~N~LG~Sh~i~~~iP~gv~v~~~~~~~t~I~i~G~DKq~Vgq~ 156 (190)
T PTZ00027 77 KNMMTGVTKKFQYKMRLVYAHFPINSNITDNGKTIEIRNFLGEKRVRTVKMLPGVVVEKSESVKDEIIVTGADLELVSRS 156 (190)
T ss_pred HHHhhhhcCCEEEEEEEEEeeeeEEEEEcCCCCEEEEEccCCCceeEEEECCCCeEEEeCCCCCCEEEEEeCCHHHHHHH
Confidence 99999999999999999999995433366689999999999999999999999999999986446899999999999999
Q ss_pred HHHHhcccccCCCceeeeeceEEEeeeeeeee
Q 029373 161 AALINQKCHVKNKDIRKFLDGIYVSERGTIFE 192 (194)
Q Consensus 161 AA~Ir~~~~~K~kd~r~f~DGiyv~~k~~~~~ 192 (194)
||+||+.|+.|+||+|+|||||||++|++..+
T Consensus 157 AA~I~~~~~~~~~d~r~f~dgiy~~~k~~~~~ 188 (190)
T PTZ00027 157 AALIHQSTLVRNKDIRKFLDGIYVSEKGTVDK 188 (190)
T ss_pred HHHHHHHhcccCCCccEeecCEEEEEeeeecc
Confidence 99999999999999999999999999996533
No 3
>PTZ00179 60S ribosomal protein L9; Provisional
Probab=100.00 E-value=8.7e-66 Score=424.79 Aligned_cols=182 Identities=53% Similarity=0.915 Sum_probs=168.3
Q ss_pred ccceeeEEcCCCcEEEEeCcEEEEEcCCcEEEEEecCceEEEEeccccccCCcEEEEEeccCChhhhhhHHhHHHHHhhc
Q 029373 4 ILSSETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSAAIRTALSHVGNL 83 (194)
Q Consensus 4 ~~~~~~I~IP~~V~v~i~~~~i~VkGp~G~l~~~l~~~~v~i~~~~~~~~~~~~i~v~~~~~~k~~~a~~Gt~rsli~Nm 83 (194)
++...||+||+||+|+++++.|+|+||+|+|+++|++..+.+.++ .++++|.+++|.++++.+|+|||+||||+||
T Consensus 3 ~~~~~pI~IP~~V~V~i~~~~ItVkGpkG~Ls~~~~~~~~~i~i~----~~~~~I~v~~~~~~kk~~al~Gt~rslI~NM 78 (189)
T PTZ00179 3 IKSQDTITIPEDVTVSVKDRIVTVKGKRGTLTKDLRHLQLDFRVN----KKNRTFTAVRWFGSKIPNSTINTALSHVRNM 78 (189)
T ss_pred ccccccEeCCCCCEEEEeCCEEEEECCCcEEEEEcCCCCcEEEEE----ecCCEEEEEeCCCCHHHHHHHHHHHHHHHHH
Confidence 455789999999999999999999999999999999864555543 4568999999988999999999999999999
Q ss_pred eeeecceeEEEEEEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCC--cccEEEEEeccHhHHHHHH
Q 029373 84 ITGVTKGYRYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEK--VKDELILDGNDIELVSRSA 161 (194)
Q Consensus 84 i~GVt~Gf~~~L~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~--~k~~I~i~G~Dkq~Vgq~A 161 (194)
|+|||+||+++|+++|+||||||++ +|+.|.|+|+||||||+.++||+|+++++++| .+++|+|+|+|||+|||||
T Consensus 79 I~GVt~GF~k~L~ivgvgyp~ra~v--~g~~l~l~N~LG~sh~~~~~ip~gv~v~~~~~~~~k~~i~i~G~DKq~Vgq~A 156 (189)
T PTZ00179 79 ITGVTKGFRFKVRFAYAHFPISVSV--ENQLVEIRNFLGEKRVRRQVVADTVKVYRTDPSKVKDELVLEGNDLEQVSREA 156 (189)
T ss_pred hhhhcCCEEEEEEEEEeCcceEEEE--cCCEEEEEecCCCCccEEEECCCCEEEEecCCcccCCEEEEEeCCHHHHHHHH
Confidence 9999999999999999999999999 89999999999999999999999999999977 2347999999999999999
Q ss_pred HHHhcccccCCCceeeeeceEEEeeeeeee
Q 029373 162 ALINQKCHVKNKDIRKFLDGIYVSERGTIF 191 (194)
Q Consensus 162 A~Ir~~~~~K~kd~r~f~DGiyv~~k~~~~ 191 (194)
|+|+++|+.|+||+|+|||||||++|++..
T Consensus 157 A~i~~~~~~~~~d~r~f~dgiy~~~k~~~~ 186 (189)
T PTZ00179 157 AVMHQLCLVKKKDIRKFLDGIYVQTKTNVE 186 (189)
T ss_pred HHHHHhhcccCCCccEeecCEEEEEeeccc
Confidence 999999999999999999999999999654
No 4
>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=7.5e-65 Score=413.16 Aligned_cols=170 Identities=38% Similarity=0.686 Sum_probs=161.1
Q ss_pred eeeEEcCCCcEEEEeCcEEEEEcCCcEEEEEecCceEEEEeccccccCCcEEEEEeccCChhhhhhHHhHHHHHhhceee
Q 029373 7 SETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSAAIRTALSHVGNLITG 86 (194)
Q Consensus 7 ~~~I~IP~~V~v~i~~~~i~VkGp~G~l~~~l~~~~v~i~~~~~~~~~~~~i~v~~~~~~k~~~a~~Gt~rsli~Nmi~G 86 (194)
++||.||++|+|+++++.|+|+||+|+|+++|+++.+++. .+++++.+++|.++++++|+|||+||||+|||+|
T Consensus 1 ~~pI~IP~~V~v~i~~~~i~vkGp~G~L~~~~~~~~v~i~------~~~~~i~v~~~~~~k~~~a~~gt~rsli~NmI~G 74 (170)
T TIGR03653 1 REEIEIPEGVSVTIEGNIVTVKGPKGEVTRELWYPGIEIS------VEDGKVVIETDFARKKDKAMVGTYRSHIKNMIKG 74 (170)
T ss_pred CceEecCCCCEEEEeCCEEEEECCCeEEEEEEeCCcEEEE------EeCCEEEEEeCCCCHHHHHHHHHHHHHHHhheee
Confidence 4699999999999999999999999999999933488887 5568999999988899999999999999999999
Q ss_pred ecceeEEEEEEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHHHHHHhc
Q 029373 87 VTKGYRYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSAALINQ 166 (194)
Q Consensus 87 Vt~Gf~~~L~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~AA~Ir~ 166 (194)
||+||+++|+++|+|||+||++ +|+.|.|+|+||||||+.++||+||+++++++ +|+|+|+|||+||||||+||+
T Consensus 75 Vt~Gf~~~LeivGvGy~~ra~~--~g~~L~l~n~LG~Sh~i~~~iP~gI~v~~~~~---~I~i~G~DKq~Vgq~AA~Ir~ 149 (170)
T TIGR03653 75 VTEGFEYKMKVVYSHFPMQVKV--EGNKVVIENFLGEKAPRRAKIPGGVKVKVKGE---EVIVTGIDKEDVGQTAANIEQ 149 (170)
T ss_pred cccCeEEEEEEEeccccEEEEE--cCCeEEEeeccccceeEEEECCCCeEEEecCC---EEEEEeCCHHHHHHHHHHHHH
Confidence 9999999999999999999999 78899999999999999999999999999983 799999999999999999999
Q ss_pred ccccCCCceeeeeceEEEeee
Q 029373 167 KCHVKNKDIRKFLDGIYVSER 187 (194)
Q Consensus 167 ~~~~K~kd~r~f~DGiyv~~k 187 (194)
+|+.|+||+|+|+|||||+||
T Consensus 150 ~~~~~~~d~r~f~dgiy~~~~ 170 (170)
T TIGR03653 150 ATRIKGRDPRVFQDGIYIVEK 170 (170)
T ss_pred hhcccCCCccEeecCEEEEeC
Confidence 999999999999999999986
No 5
>COG0097 RplF Ribosomal protein L6P/L9E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.1e-58 Score=373.40 Aligned_cols=174 Identities=25% Similarity=0.442 Sum_probs=156.8
Q ss_pred ccccceeeEEcCCCcEEEEeCcEEEEEcCCcEEEEEecCceEEEEeccccccCCcEEEEEeccCChhhhhhHHhHHHHHh
Q 029373 2 KTILSSETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSAAIRTALSHVG 81 (194)
Q Consensus 2 ~~~~~~~~I~IP~~V~v~i~~~~i~VkGp~G~l~~~l~~~~v~i~~~~~~~~~~~~i~v~~~~~~k~~~a~~Gt~rsli~ 81 (194)
++++++.||.+|+||+|+++++.++|+||+|+|+++|++..+.++ .+++.+.+.+++. ++.+|||||+||||+
T Consensus 1 Msri~k~~i~~P~gV~V~i~~~~v~vkGpkGeL~~~~~~~~v~v~------~~~~~~vv~~~~~-k~~~a~~Gt~rali~ 73 (178)
T COG0097 1 MSRIGKRPIVIPAGVTVSIEGQVVTVKGPKGELTREFHDNVVKVE------VEDNILVVRPVDG-KRKRALHGTVRALIN 73 (178)
T ss_pred CCceeeccEecCCCeEEEEeccEEEEECCCcEEEEEecCcceEEE------ecCCEEEEeeccc-chhHHHHHHHHHHHH
Confidence 467899999999999999999999999999999999998444666 5567777777666 666799999999999
Q ss_pred hceeeecceeEEEEEEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHHH
Q 029373 82 NLITGVTKGYRYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSA 161 (194)
Q Consensus 82 Nmi~GVt~Gf~~~L~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~A 161 (194)
||++|||+||+|+|+++|+|| ||++ .|+.|.+ |||||||+.++||+|+++++++| |+|+|+|+|||+|||||
T Consensus 74 Nmv~GVteGf~~kL~ivgvgy--ra~v--~g~~l~l--~LG~shp~~~~ip~gi~v~v~~~--t~I~v~GidKe~VGQ~A 145 (178)
T COG0097 74 NMVKGVTEGFEKKLEIVGVGY--RAQV--VGGNLEL--FLGYSHPVVIEIPEGITVEVPGP--TEIVVEGIDKELVGQVA 145 (178)
T ss_pred HHheecccceEEEEEEEEecc--eeEE--eccEEEE--eecccCCeEEECCCCeEEEecCC--CEEEEEcCCHHHHhHHH
Confidence 999999999999999999999 6788 5667777 89999999999999999999999 68999999999999999
Q ss_pred HHHhcccccCCCceee-eeceEEEeeeeee
Q 029373 162 ALINQKCHVKNKDIRK-FLDGIYVSERGTI 190 (194)
Q Consensus 162 A~Ir~~~~~K~kd~r~-f~DGiyv~~k~~~ 190 (194)
|+||++|+++.+|.|. |+||+||.+|+..
T Consensus 146 A~Ir~~r~pepykgKgi~ydge~I~~K~gK 175 (178)
T COG0097 146 ANIRAARKPEPYKGKGIRYDGEYIRRKEGK 175 (178)
T ss_pred HHHHhccCCCCCCCcceEEcCEEEEEeccc
Confidence 9999999977777777 8999999999854
No 6
>CHL00140 rpl6 ribosomal protein L6; Validated
Probab=100.00 E-value=7.9e-56 Score=362.63 Aligned_cols=170 Identities=25% Similarity=0.400 Sum_probs=159.0
Q ss_pred ccccceeeEEcCCCcEEEEeCcEEEEEcCCcEEEEEecCceEEEEeccccccCCcEEEEEeccCChhhhhhHHhHHHHHh
Q 029373 2 KTILSSETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSAAIRTALSHVG 81 (194)
Q Consensus 2 ~~~~~~~~I~IP~~V~v~i~~~~i~VkGp~G~l~~~l~~~~v~i~~~~~~~~~~~~i~v~~~~~~k~~~a~~Gt~rsli~ 81 (194)
++++|+.||+||+||+|+++++.|+|+||+|+|+++|++ .+++. .+++.+.++.|.++++++|+|||+||||+
T Consensus 1 msrig~~~I~IP~~V~v~i~~~~v~vkGp~G~l~~~~~~-~v~i~------~~~~~i~v~~~~~~k~~~a~~gt~~slI~ 73 (178)
T CHL00140 1 MSRIGKLPIKIPDNVNVSIDDQIIKVKGPKGTLSRKIPD-LITIE------IQDNSLFVSKKDESKKARALHGLYRTLIN 73 (178)
T ss_pred CCcccceeeecCCCCEEEEECCEEEEECCCEEEEEECCC-CeEEE------EeCCEEEEEcCCCCHHHHHHHHHHHHHHH
Confidence 378999999999999999999999999999999999998 88887 55688999999889999999999999999
Q ss_pred hceeeecceeEEEEEEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHHH
Q 029373 82 NLITGVTKGYRYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSA 161 (194)
Q Consensus 82 Nmi~GVt~Gf~~~L~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~A 161 (194)
|||+|||+||+++|+++|+|| ||++ +|+.|.| +||||||+.++||+||+|+|++| ++|+|+|+|||+|||||
T Consensus 74 Nmi~GVt~Gf~~~L~lvGvGy--r~~~--~g~~l~l--~LG~sh~i~~~IP~gv~v~~~~~--t~I~i~G~dke~Vgq~A 145 (178)
T CHL00140 74 NMVIGVSEGFEKKLELQGVGY--RAQV--QGKDLIL--NLGYSHPVKIKIPPGISVEVENN--TNITIKGIDKELVGQFA 145 (178)
T ss_pred HHHhhcccCceEEEEEEEEEE--EEEE--eCCcEEE--EecCCeeEEEECCCCeEEEeCCC--CEEEEEECCHHHHHHHH
Confidence 999999999999999999999 8999 7888999 79999999999999999999998 58999999999999999
Q ss_pred HHHhcccc---cCCCceeeeeceEEEeeee
Q 029373 162 ALINQKCH---VKNKDIRKFLDGIYVSERG 188 (194)
Q Consensus 162 A~Ir~~~~---~K~kd~r~f~DGiyv~~k~ 188 (194)
|+||++|+ |||||+| .+|.+|..|+
T Consensus 146 A~Ir~~r~pepYKGKGI~--y~~e~i~~K~ 173 (178)
T CHL00140 146 AKIRSVRPPEPYKGKGIR--YKGEVIRRKA 173 (178)
T ss_pred HHHhccCCCCCcCCccEe--ECCEEEEEec
Confidence 99999996 9999987 6777776665
No 7
>TIGR03654 L6_bact ribosomal protein L6, bacterial type.
Probab=100.00 E-value=6.6e-54 Score=350.39 Aligned_cols=168 Identities=26% Similarity=0.454 Sum_probs=154.7
Q ss_pred cccceeeEEcCCCcEEEEeCcEEEEEcCCcEEEEEecCceEEEEeccccccCCcEEEEEeccCChhhhhhHHhHHHHHhh
Q 029373 3 TILSSETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSAAIRTALSHVGN 82 (194)
Q Consensus 3 ~~~~~~~I~IP~~V~v~i~~~~i~VkGp~G~l~~~l~~~~v~i~~~~~~~~~~~~i~v~~~~~~k~~~a~~Gt~rsli~N 82 (194)
+++|+.||.||++|+|+++++.|+|+||+|+|+++|++ .+.+. .+++.+.++.|+++++++|+|||+||||+|
T Consensus 1 s~ig~~~I~IP~~V~v~~~~~~v~v~Gp~G~l~~~l~~-~i~i~------~~~~~i~v~~~~~~kk~~a~~gt~~s~i~N 73 (175)
T TIGR03654 1 SRIGKKPIAIPAGVEVTIDGNVVTVKGPKGELSRTLHP-GVTVK------VEDGQLTVSRPNDSKEARALHGTTRALINN 73 (175)
T ss_pred CcccccceecCCCcEEEEeCCEEEEEcCCeEEEEEcCC-CeEEE------EECCEEEEEecCCCHHHHHHHHHHHHHHHH
Confidence 57899999999999999999999999999999999975 88887 456889999998889999999999999999
Q ss_pred ceeeecceeEEEEEEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHHHH
Q 029373 83 LITGVTKGYRYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSAA 162 (194)
Q Consensus 83 mi~GVt~Gf~~~L~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~AA 162 (194)
||.|||+||+++|+++|+|| ||++ +|+.|.| +||||||+.++||+|++|++++| ++|+|+|+|||+||||||
T Consensus 74 mi~GVt~Gf~~~L~lvGvgy--rv~~--~g~~l~l--~LG~sh~i~~~Ip~~v~v~~~~~--t~I~i~G~dke~Vgq~AA 145 (175)
T TIGR03654 74 MVIGVSEGFEKKLEIVGVGY--RAQL--QGKKLNL--SLGYSHPVEYEIPEGITVEVPKP--TEIVVKGIDKQLVGQVAA 145 (175)
T ss_pred HhheeccCcEEEEEEEEEEE--EEEE--eCCeEEE--EecCceeEEEECCCCeEEEeCCC--CEEEEEECCHHHHHHHHH
Confidence 99999999999999999999 8999 7889999 79999999999999999999998 589999999999999999
Q ss_pred HHhcccc---cCCCceeeeeceEEEeee
Q 029373 163 LINQKCH---VKNKDIRKFLDGIYVSER 187 (194)
Q Consensus 163 ~Ir~~~~---~K~kd~r~f~DGiyv~~k 187 (194)
+||++|+ |||||+| .+|-+|--|
T Consensus 146 ~Ir~~r~pepYKgkGi~--~~~e~I~~K 171 (175)
T TIGR03654 146 EIRAFRKPEPYKGKGIR--YAGEVVRRK 171 (175)
T ss_pred HHhccCCCCCcCCCcEe--ECCEEEEEe
Confidence 9999996 9999887 345554433
No 8
>PRK05498 rplF 50S ribosomal protein L6; Validated
Probab=100.00 E-value=1.7e-53 Score=348.84 Aligned_cols=170 Identities=26% Similarity=0.455 Sum_probs=157.5
Q ss_pred ccccceeeEEcCCCcEEEEeCcEEEEEcCCcEEEEEecCceEEEEeccccccCCcEEEEEeccCChhhhhhHHhHHHHHh
Q 029373 2 KTILSSETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSAAIRTALSHVG 81 (194)
Q Consensus 2 ~~~~~~~~I~IP~~V~v~i~~~~i~VkGp~G~l~~~l~~~~v~i~~~~~~~~~~~~i~v~~~~~~k~~~a~~Gt~rsli~ 81 (194)
++++|+.||.||++|+|+++++.|+|+||+|+|+++|++ .+++. .+++.|.++.|.++++++|+|||+||||+
T Consensus 1 ms~ig~~~I~IP~~V~v~~~~~~v~vkGp~G~l~~~~~~-~v~i~------~~~~~i~v~~~~~~k~~~a~~gt~~s~I~ 73 (178)
T PRK05498 1 MSRIGKKPIAIPAGVEVTINGNVVTVKGPKGELSRTLNP-DVTVK------VEDNEITVTRPDDSKKARALHGTTRALIN 73 (178)
T ss_pred CCcccccceecCCCCEEEEECCEEEEECCCEEEEEEcCC-CeEEE------EECCEEEEEcCCCCHHHHHHHHHHHHHHH
Confidence 467899999999999999999999999999999999975 78887 45588999999889999999999999999
Q ss_pred hceeeecceeEEEEEEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHHH
Q 029373 82 NLITGVTKGYRYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSA 161 (194)
Q Consensus 82 Nmi~GVt~Gf~~~L~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~A 161 (194)
|||.||++||+++|+++|+|| ||++ +|+.|.| +||||||+.++||+|++|++++| ++|+|+|+|||+|||||
T Consensus 74 Nmi~GVt~Gf~~~L~lvGvgy--rv~~--~g~~l~l--~LG~sh~i~~~Ip~gv~v~~~~~--t~I~i~G~dke~Vg~~A 145 (178)
T PRK05498 74 NMVVGVTEGFEKKLEIVGVGY--RAQV--KGKKLNL--SLGYSHPVEYEIPEGITVEVPKP--TEIVVKGIDKQLVGQVA 145 (178)
T ss_pred HHhhhcCCCeEEEEEEEeEEE--EEEE--eCCeEEE--EecCCEEEEEECCCCeEEEeCCC--CEEEEEECCHHHHHHHH
Confidence 999999999999999999999 8999 7889999 79999999999999999999998 58999999999999999
Q ss_pred HHHhcccc---cCCCceeeeeceEEEeeee
Q 029373 162 ALINQKCH---VKNKDIRKFLDGIYVSERG 188 (194)
Q Consensus 162 A~Ir~~~~---~K~kd~r~f~DGiyv~~k~ 188 (194)
|+||++|+ |||||+| .+|.+|-.|+
T Consensus 146 A~Ir~~r~pe~YkgkGi~--~~~e~i~~K~ 173 (178)
T PRK05498 146 AEIRSYRPPEPYKGKGIR--YAGEVVRRKE 173 (178)
T ss_pred HHHhccCCCCCccCCcEe--ECCEEEEEec
Confidence 99999996 8999877 5677776664
No 9
>KOG3254 consensus Mitochondrial/chloroplast ribosomal protein L6 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.8e-45 Score=294.82 Aligned_cols=165 Identities=22% Similarity=0.278 Sum_probs=144.8
Q ss_pred cceeeEEcCCCcEEEEeCcEEEEEcCCcEEEEEecCceEEEEeccccccCCcEEEEEeccCChhhhhhHHhHHHHHhhce
Q 029373 5 LSSETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSAAIRTALSHVGNLI 84 (194)
Q Consensus 5 ~~~~~I~IP~~V~v~i~~~~i~VkGp~G~l~~~l~~~~v~i~~~~~~~~~~~~i~v~~~~~~k~~~a~~Gt~rsli~Nmi 84 (194)
+++..|..|++..-++++..++|+||+|+|++++|+ +++++-+. .+.+........++|++++||||+|||++||+
T Consensus 34 ~~~k~i~~~e~k~~~lege~l~vkGP~gel~l~~P~-~l~L~~dk---k~~g~~~~~k~~etkkqr~mwgt~R~l~~N~v 109 (211)
T KOG3254|consen 34 VGKKEIIVKENKQRDLEGEQLQVKGPHGELNLRFPN-YLNLSNDK---KKSGMDANIKKQETKKQRAMWGTFRALLANNV 109 (211)
T ss_pred ecceeEEeehhhccccccCceEeeCCcceeeccCCc-cccccchh---hhcceeeeecchhhHHHHHHHHHHHHHHhccc
Confidence 567888888888888889999999999999999997 66665111 23344443344678999999999999999999
Q ss_pred eeecceeEEEEEEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHHHHHH
Q 029373 85 TGVTKGYRYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSAALI 164 (194)
Q Consensus 85 ~GVt~Gf~~~L~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~AA~I 164 (194)
.|||.||.+.|++||+|| ||++ +|+.|.| .|||||++.+.||++++|+++.| |.++++|+|||+|+||||.+
T Consensus 110 ~GVt~g~~k~l~lVGvGY--Ra~l--egk~l~l--klG~S~~v~l~iP~~v~Vk~p~p--tsl~~~G~dKq~V~qFAAkv 181 (211)
T KOG3254|consen 110 KGVTMGFLKILKLVGVGY--RASL--EGKFLHL--KLGYSHDVLLSIPTDVQVKNPTP--TSLVLRGIDKQKVTQFAAKV 181 (211)
T ss_pred hhhhhhhhheeeEEeeee--EEEe--cCceEEE--EeccccceeecCCCceEEecCCC--CEEEEecccHHHHHHHHHHH
Confidence 999999999999999999 8999 7999999 59999999999999999999999 68999999999999999999
Q ss_pred hcccc---cCCCceeeeeceEEEeeee
Q 029373 165 NQKCH---VKNKDIRKFLDGIYVSERG 188 (194)
Q Consensus 165 r~~~~---~K~kd~r~f~DGiyv~~k~ 188 (194)
|+|+| |||| |||++++-
T Consensus 182 RsfkpPEPYKGK-------GIyv~dE~ 201 (211)
T KOG3254|consen 182 RSFKPPEPYKGK-------GIYVDDEK 201 (211)
T ss_pred hccCCCCCcCCC-------ceEeccce
Confidence 99986 9999 78887653
No 10
>KOG3255 consensus 60S ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=4e-28 Score=198.32 Aligned_cols=179 Identities=61% Similarity=0.983 Sum_probs=163.7
Q ss_pred CccccceeeEEcCCCcEEEEeCcEEEEEcCCcEEEEEecCceEEEEeccccccCCcEEEEEeccCChhhhhhHHhHHHHH
Q 029373 1 MKTILSSETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSAAIRTALSHV 80 (194)
Q Consensus 1 m~~~~~~~~I~IP~~V~v~i~~~~i~VkGp~G~l~~~l~~~~v~i~~~~~~~~~~~~i~v~~~~~~k~~~a~~Gt~rsli 80 (194)
|+.++....+.||++|++++++..++|+||+|+|.++|.|..+++.+..+ +.+.+.+..|...|+..|..-|..|++
T Consensus 1 mk~Ilsn~tv~iPe~v~it~k~~v~~v~gprgtl~~d~~hi~~~~~~~~~---~~~~ik~~~~~~~Rk~va~l~t~~s~i 77 (179)
T KOG3255|consen 1 MKTILSNQTVHIPENVDITLKGHVVIVKGPRGTLWRDFNHINVELSLLGK---KKKRLKIDKWWGTRKGVACLRTVVSHI 77 (179)
T ss_pred CceEEeceEEecCCCceEEEeeEEEEEeCCCcceeccccccchhhhhhcc---hhhhhhhhhhhccchhHHHHHHHHHHH
Confidence 88999999999999999999999999999999999999997777774332 114588888999999999999999999
Q ss_pred hhceeeecceeEEEEEEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHH
Q 029373 81 GNLITGVTKGYRYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRS 160 (194)
Q Consensus 81 ~Nmi~GVt~Gf~~~L~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~ 160 (194)
+||+.||+.||.+++..++.|||+...+.+++....+.||||.+.+..+++.+|+........+++|+++|+|.+.|+|.
T Consensus 78 en~i~gvt~~~i~k~~av~a~f~in~~~~~~~~s~~i~n~l~~k~~~~~~~~~Gv~~~~~~~~~~~i~~~~~~~~~vs~~ 157 (179)
T KOG3255|consen 78 ENCIKGVTIGFIYKMRAVYAHFPINTVIQENGKSEEIRNFLGEKLVRRVEMRPGVTIVRSSKVKDEIVLEGNDLELVSQS 157 (179)
T ss_pred HHHHhcchHHHHHHhhhHHhhccccceecCCCcchhhhhhhhhhccceEecCCCeEEeeehhcchhheecccchhhhhhH
Confidence 99999999999999999999999999998788899999999999999999999999988776668999999999999999
Q ss_pred HHHHhcccccCCCceeeeeceEEEeeeeee
Q 029373 161 AALINQKCHVKNKDIRKFLDGIYVSERGTI 190 (194)
Q Consensus 161 AA~Ir~~~~~K~kd~r~f~DGiyv~~k~~~ 190 (194)
||. ++.|+.+++ +| ||+||+++
T Consensus 158 ~a~-~~~~~~~~~-----ld--yv~~k~~~ 179 (179)
T KOG3255|consen 158 AAL-QQICTVKNK-----LD--YVSEKGTI 179 (179)
T ss_pred hHh-hccceehhh-----cc--hhhhcccC
Confidence 888 999998877 88 99999863
No 11
>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=99.77 E-value=1.1e-18 Score=123.62 Aligned_cols=74 Identities=38% Similarity=0.656 Sum_probs=66.0
Q ss_pred cCCCcEEEEeCcEEEEEcCCcEEEEEecCceEEEEeccccccCCcEEEEEeccCChhhhh---hHHhHHHHHhhceeeec
Q 029373 12 IPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSA---AIRTALSHVGNLITGVT 88 (194)
Q Consensus 12 IP~~V~v~i~~~~i~VkGp~G~l~~~l~~~~v~i~~~~~~~~~~~~i~v~~~~~~k~~~a---~~Gt~rsli~Nmi~GVt 88 (194)
||+||+|+++++.++|+||+|+|++++|+ .+.+.++. +++.+.+..+.+.+++++ +|||+|||++||++||+
T Consensus 1 IP~gV~v~~~~~~i~v~G~~g~l~~~~~~-~v~v~~~~----~~~~~~~~~~~~~~k~~~~~a~~gt~rsli~n~i~GV~ 75 (77)
T PF00347_consen 1 IPEGVKVTIKGNIITVKGPKGELSRPIPP-GVKVEIKV----EDNKITVSVLSGNKKQKAFAAMIGTYRSLINNMIKGVT 75 (77)
T ss_dssp SSTTCEEEEETTEEEEESSSSEEEEEETT-TEEEEEEE----ETTSEEEEEEEESHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCcEEEEEeCcEEEEECCCEeEEEECCC-CeeEEEEc----CCCceEEEECcccHhHhhhHHhhccccccccCceeEEC
Confidence 79999999999999999999999999997 57666432 357888888888888998 99999999999999999
Q ss_pred ce
Q 029373 89 KG 90 (194)
Q Consensus 89 ~G 90 (194)
+|
T Consensus 76 ~G 77 (77)
T PF00347_consen 76 EG 77 (77)
T ss_dssp TE
T ss_pred CC
Confidence 97
No 12
>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=98.20 E-value=7.6e-07 Score=62.61 Aligned_cols=63 Identities=21% Similarity=0.190 Sum_probs=51.3
Q ss_pred EEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEc--CCcccEEEEEeccHhHHHHHHHHHhcccccC
Q 029373 100 AHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRS--EKVKDELILDGNDIELVSRSAALINQKCHVK 171 (194)
Q Consensus 100 vGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~--~~~k~~I~i~G~Dkq~Vgq~AA~Ir~~~~~K 171 (194)
.|+ ++++ +++.+.+ .|++|...+++|+++++++. +...+...+++.|+++. +||.++.+|..-
T Consensus 3 ~gV--~v~~--~~~~i~v---~G~~g~l~~~~~~~v~v~~~~~~~~~~~~~~~~~~k~~~--~~a~~gt~rsli 67 (77)
T PF00347_consen 3 EGV--KVTI--KGNIITV---KGPKGELSRPIPPGVKVEIKVEDNKITVSVLSGNKKQKA--FAAMIGTYRSLI 67 (77)
T ss_dssp TTC--EEEE--ETTEEEE---ESSSSEEEEEETTTEEEEEEEETTSEEEEEEEESHHHHH--HHHHHHHHHHHH
T ss_pred CcE--EEEE--eCcEEEE---ECCCEeEEEECCCCeeEEEEcCCCceEEEECcccHhHhh--hHHhhccccccc
Confidence 456 7888 6666666 99999999999999999965 43335677899999999 999999999743
No 13
>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=71.79 E-value=10 Score=27.04 Aligned_cols=27 Identities=15% Similarity=0.413 Sum_probs=21.5
Q ss_pred CCCcEEEEeCcEEEEEcCC--------cEEEEEec
Q 029373 13 PDGVKIKINAKIIEVEGPR--------GKLSRDFK 39 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp~--------G~l~~~l~ 39 (194)
|++++|++.++.|+|+|-+ |+.++.|.
T Consensus 21 pedi~V~v~~~~L~I~ger~~~~~~~~g~F~R~~~ 55 (81)
T cd06479 21 PEDIIVTTSNNQIEVHAEKLASDGTVMNTFTHKCQ 55 (81)
T ss_pred HHHeEEEEECCEEEEEEEEeccCCCEEEEEEEEEE
Confidence 5789999999999999965 56655554
No 14
>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=57.88 E-value=12 Score=30.55 Aligned_cols=21 Identities=38% Similarity=0.699 Sum_probs=11.7
Q ss_pred eEEcCCCcEEEEeCcEEEEEc
Q 029373 9 TMDIPDGVKIKINAKIIEVEG 29 (194)
Q Consensus 9 ~I~IP~~V~v~i~~~~i~VkG 29 (194)
.++||+||+++..+..|+++|
T Consensus 114 ~~~iP~gI~v~~~~~~I~i~G 134 (170)
T TIGR03653 114 RAKIPGGVKVKVKGEEVIVTG 134 (170)
T ss_pred EEECCCCeEEEecCCEEEEEe
Confidence 456666666655444444544
No 15
>COG0097 RplF Ribosomal protein L6P/L9E [Translation, ribosomal structure and biogenesis]
Probab=54.93 E-value=14 Score=30.56 Aligned_cols=24 Identities=29% Similarity=0.620 Sum_probs=20.2
Q ss_pred eeEEcCCCcEEEEeC-cEEEEEcCC
Q 029373 8 ETMDIPDGVKIKINA-KIIEVEGPR 31 (194)
Q Consensus 8 ~~I~IP~~V~v~i~~-~~i~VkGp~ 31 (194)
..+.||+|+++++.+ ..|.|+|+.
T Consensus 113 ~~~~ip~gi~v~v~~~t~I~v~Gid 137 (178)
T COG0097 113 VVIEIPEGITVEVPGPTEIVVEGID 137 (178)
T ss_pred eEEECCCCeEEEecCCCEEEEEcCC
Confidence 457899999999988 679999975
No 16
>TIGR03654 L6_bact ribosomal protein L6, bacterial type.
Probab=53.13 E-value=77 Score=25.77 Aligned_cols=56 Identities=21% Similarity=0.287 Sum_probs=39.8
Q ss_pred eeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEecc--H---hHHHHHHHHHhccc
Q 029373 105 NASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGND--I---ELVSRSAALINQKC 168 (194)
Q Consensus 105 ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~D--k---q~Vgq~AA~Ir~~~ 168 (194)
.+++ +++.|.++.-+| -....+|+++.+...+ +.|.++-.+ + ...|.++|.|++.-
T Consensus 15 ~v~~--~~~~v~v~Gp~G---~l~~~l~~~i~i~~~~---~~i~v~~~~~~kk~~a~~gt~~s~i~Nmi 75 (175)
T TIGR03654 15 EVTI--DGNVVTVKGPKG---ELSRTLHPGVTVKVED---GQLTVSRPNDSKEARALHGTTRALINNMV 75 (175)
T ss_pred EEEE--eCCEEEEEcCCe---EEEEEcCCCeEEEEEC---CEEEEEecCCCHHHHHHHHHHHHHHHHHh
Confidence 3445 678899977777 4456668999998866 468876443 2 36788888888754
No 17
>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=53.09 E-value=25 Score=25.10 Aligned_cols=18 Identities=22% Similarity=0.503 Sum_probs=15.9
Q ss_pred CCCcEEEEeCcEEEEEcC
Q 029373 13 PDGVKIKINAKIIEVEGP 30 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp 30 (194)
|++++|+++++.|+|+|.
T Consensus 24 kedi~v~~~~~~L~I~g~ 41 (90)
T cd06470 24 EDDLEIEVENNQLTVTGK 41 (90)
T ss_pred HHHeEEEEECCEEEEEEE
Confidence 468999999999999985
No 18
>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=50.18 E-value=41 Score=22.35 Aligned_cols=29 Identities=17% Similarity=0.362 Sum_probs=22.2
Q ss_pred CeEEEEcCCcccEEEEEeccHhHHHHHHHHH
Q 029373 134 GVTVVRSEKVKDELILDGNDIELVSRSAALI 164 (194)
Q Consensus 134 gi~v~~~~~~k~~I~i~G~Dkq~Vgq~AA~I 164 (194)
|+++.+++. ..+.|+|.|++.+.+..+.|
T Consensus 32 g~~I~i~~~--g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 32 GVKIDIEDD--GTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred CCEEEeCCC--CEEEEEeCCHHHHHHHHHHh
Confidence 666677665 57999999999888766655
No 19
>PRK05518 rpl6p 50S ribosomal protein L6P; Reviewed
Probab=49.50 E-value=20 Score=29.51 Aligned_cols=22 Identities=36% Similarity=0.518 Sum_probs=13.2
Q ss_pred eEEcCCCcEEEEeCcEEEEEcC
Q 029373 9 TMDIPDGVKIKINAKIIEVEGP 30 (194)
Q Consensus 9 ~I~IP~~V~v~i~~~~i~VkGp 30 (194)
.+.||+||+++..+..|+++|.
T Consensus 120 ~~~iP~gV~v~~~~t~I~i~Gi 141 (180)
T PRK05518 120 RAKILGGVKVKVKGEDVIVEGI 141 (180)
T ss_pred EEeCCCCeEEEecCCEEEEEeC
Confidence 4566777777655444555554
No 20
>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=49.10 E-value=46 Score=25.73 Aligned_cols=33 Identities=27% Similarity=0.509 Sum_probs=22.3
Q ss_pred eeEEcCCCcEEEEeCcEEEEEcCCcEEEEEecC
Q 029373 8 ETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKH 40 (194)
Q Consensus 8 ~~I~IP~~V~v~i~~~~i~VkGp~G~l~~~l~~ 40 (194)
..|.+|+|-++..-.-.-.++.|-|++++.+..
T Consensus 41 yti~~pegm~l~t~~~~K~I~N~~Gk~~isv~~ 73 (116)
T PF12970_consen 41 YTIELPEGMKLVTPPMEKKIDNPVGKVSISVKP 73 (116)
T ss_dssp EEEEE-TT-EE-S--S-EEEEETTEEEEEEEEE
T ss_pred EEEEcCCCCeeecCccceeccCCcceEEEEEEe
Confidence 468899999887766778899999999888764
No 21
>CHL00140 rpl6 ribosomal protein L6; Validated
Probab=47.75 E-value=1.3e+02 Score=24.45 Aligned_cols=57 Identities=23% Similarity=0.285 Sum_probs=40.6
Q ss_pred eeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEecc--Hh---HHHHHHHHHhcccc
Q 029373 105 NASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGND--IE---LVSRSAALINQKCH 169 (194)
Q Consensus 105 ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~D--kq---~Vgq~AA~Ir~~~~ 169 (194)
.+++ +++.|.++.-+| -....+|..+.+...+ +.|.++-.+ ++ ..|.++|.|++.-.
T Consensus 16 ~v~i--~~~~v~vkGp~G---~l~~~~~~~v~i~~~~---~~i~v~~~~~~k~~~a~~gt~~slI~Nmi~ 77 (178)
T CHL00140 16 NVSI--DDQIIKVKGPKG---TLSRKIPDLITIEIQD---NSLFVSKKDESKKARALHGLYRTLINNMVI 77 (178)
T ss_pred EEEE--ECCEEEEECCCE---EEEEECCCCeEEEEeC---CEEEEEcCCCCHHHHHHHHHHHHHHHHHHh
Confidence 3455 688899965565 5667888899988865 468877443 32 48999999998643
No 22
>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=44.31 E-value=62 Score=22.99 Aligned_cols=20 Identities=25% Similarity=0.554 Sum_probs=17.7
Q ss_pred CCCcEEEEeCcEEEEEcCCc
Q 029373 13 PDGVKIKINAKIIEVEGPRG 32 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp~G 32 (194)
|++++|++.++.|+|+|...
T Consensus 20 ~edi~I~~~~~~L~I~g~~~ 39 (102)
T PF00011_consen 20 KEDIKIKVDDNKLVISGKRK 39 (102)
T ss_dssp GGGEEEEEETTEEEEEEEEE
T ss_pred hHHEEEEEecCccceeceee
Confidence 46899999999999999776
No 23
>PTZ00179 60S ribosomal protein L9; Provisional
Probab=41.76 E-value=29 Score=28.81 Aligned_cols=13 Identities=0% Similarity=0.084 Sum_probs=8.8
Q ss_pred HHHHHHHHHhccc
Q 029373 156 LVSRSAALINQKC 168 (194)
Q Consensus 156 ~Vgq~AA~Ir~~~ 168 (194)
..|.++|.|+..-
T Consensus 67 l~Gt~rslI~NMI 79 (189)
T PTZ00179 67 TINTALSHVRNMI 79 (189)
T ss_pred HHHHHHHHHHHHh
Confidence 5677777777653
No 24
>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=39.89 E-value=19 Score=25.86 Aligned_cols=19 Identities=16% Similarity=0.445 Sum_probs=15.7
Q ss_pred CCCcEEEEeCcEEEEEcCC
Q 029373 13 PDGVKIKINAKIIEVEGPR 31 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp~ 31 (194)
|+.++|++.++.|+|+|..
T Consensus 20 ~edI~V~v~~~~L~I~ge~ 38 (83)
T cd06477 20 PEDIIIQVFEGWLLIKGQH 38 (83)
T ss_pred HHHeEEEEECCEEEEEEEE
Confidence 5788899999999998854
No 25
>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=38.72 E-value=24 Score=24.99 Aligned_cols=18 Identities=22% Similarity=0.667 Sum_probs=15.3
Q ss_pred CCCcEEEEeCcEEEEEcC
Q 029373 13 PDGVKIKINAKIIEVEGP 30 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp 30 (194)
|++++|++.++.++|+|.
T Consensus 20 ~edI~V~v~~~~L~I~g~ 37 (83)
T cd06478 20 PEELSVKVLGDFVEIHGK 37 (83)
T ss_pred HHHeEEEEECCEEEEEEE
Confidence 578899999999999884
No 26
>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=38.57 E-value=20 Score=26.27 Aligned_cols=19 Identities=26% Similarity=0.604 Sum_probs=16.4
Q ss_pred CCCcEEEEeCcEEEEEcCC
Q 029373 13 PDGVKIKINAKIIEVEGPR 31 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp~ 31 (194)
|+.++|++.++.|+|+|..
T Consensus 28 pEDL~Vkv~~~~L~V~Gkh 46 (91)
T cd06480 28 PEELTVKTKDGFVEVSGKH 46 (91)
T ss_pred HHHcEEEEECCEEEEEEEE
Confidence 7889999999999998864
No 27
>PRK11597 heat shock chaperone IbpB; Provisional
Probab=38.54 E-value=43 Score=26.49 Aligned_cols=19 Identities=16% Similarity=0.447 Sum_probs=16.3
Q ss_pred CCCcEEEEeCcEEEEEcCC
Q 029373 13 PDGVKIKINAKIIEVEGPR 31 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp~ 31 (194)
|++++|+++++.++|+|-.
T Consensus 56 kedi~V~v~~~~LtI~ge~ 74 (142)
T PRK11597 56 QEDLDIQLEGTRLTVKGTP 74 (142)
T ss_pred HHHeEEEEECCEEEEEEEE
Confidence 4689999999999999964
No 28
>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=38.43 E-value=20 Score=25.52 Aligned_cols=18 Identities=33% Similarity=0.741 Sum_probs=16.0
Q ss_pred CCCcEEEEeCcEEEEEcC
Q 029373 13 PDGVKIKINAKIIEVEGP 30 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp 30 (194)
|+.++|++.++.++|+|.
T Consensus 20 ~edi~V~v~~~~L~I~g~ 37 (84)
T cd06498 20 PEELKVKVLGDFIEIHGK 37 (84)
T ss_pred HHHeEEEEECCEEEEEEE
Confidence 678999999999999984
No 29
>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=38.42 E-value=20 Score=25.53 Aligned_cols=19 Identities=21% Similarity=0.548 Sum_probs=16.1
Q ss_pred CCCcEEEEeCcEEEEEcCC
Q 029373 13 PDGVKIKINAKIIEVEGPR 31 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp~ 31 (194)
|+.++|++.++.|+|+|..
T Consensus 20 ~edi~V~v~~~~L~I~g~~ 38 (83)
T cd06476 20 PDEITVRTVDNLLEVSARH 38 (83)
T ss_pred HHHeEEEEECCEEEEEEEE
Confidence 5788999999999999854
No 30
>PF00338 Ribosomal_S10: Ribosomal protein S10p/S20e; InterPro: IPR001848 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 [, ]. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S10 consists of about 100 amino acid residues. In Escherichia coli, S10 is involved in binding tRNA to the ribosome, and also operates as a transcriptional elongation factor []. Experimental evidence [] has revealed that S10 has virtually no groups exposed on the ribosomal surface, and is one of the "split proteins": these are a discrete group that are selectively removed from 30S subunits under low salt conditions and are required for the formation of activated 30S reconstitution intermediate (RI*) particles. S10 belongs to a family of proteins [] that includes: bacteria S10; algal chloroplast S10; cyanelle S10; archaebacterial S10; Marchantia polymorpha and Prototheca wickerhamii mitochondrial S10; Arabidopsis thaliana mitochondrial S10 (nuclear encoded); vertebrate S20; plant S20; and yeast URP2.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1S1H_J 3U5G_U 3O30_N 3O2Z_N 3IZB_J 3U5C_U 3R2C_J 3R2D_J 2ZKQ_j 2XQD_J ....
Probab=37.81 E-value=69 Score=22.94 Aligned_cols=30 Identities=13% Similarity=0.194 Sum_probs=25.9
Q ss_pred EEEEEeccHhHHHHHHHHHhcccccCCCce
Q 029373 146 ELILDGNDIELVSRSAALINQKCHVKNKDI 175 (194)
Q Consensus 146 ~I~i~G~Dkq~Vgq~AA~Ir~~~~~K~kd~ 175 (194)
+|.|+|.|...+-.+|..|..+.+..|-++
T Consensus 2 ~I~l~s~d~~~l~~~~~~i~~~~~~~~~~~ 31 (97)
T PF00338_consen 2 RIKLKSYDKKLLESYVKFIHKLAKNLGIKV 31 (97)
T ss_dssp EEEEEESSHHHHHHHHHHHHHHHHCTSSCE
T ss_pred EEEEEECCHHHHHHHHHHHHHHHHHhCCcc
Confidence 489999999999999999999987665554
No 31
>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=37.80 E-value=1e+02 Score=20.59 Aligned_cols=28 Identities=18% Similarity=0.121 Sum_probs=22.5
Q ss_pred CCCcEEEEeCcEEEEEcCCcEEEEEecC
Q 029373 13 PDGVKIKINAKIIEVEGPRGKLSRDFKH 40 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp~G~l~~~l~~ 40 (194)
|++++|+++++.+++.|+.=.++.+|++
T Consensus 19 ~~~v~v~~~~~~l~i~~~~~~~~~~l~~ 46 (78)
T cd06469 19 TSKVDIFCSDLYLKVNFPPYLFELDLAA 46 (78)
T ss_pred cccceEEEecCEEEEcCCCEEEEEeCcc
Confidence 5788899999999999965566667775
No 32
>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=36.49 E-value=36 Score=24.08 Aligned_cols=18 Identities=11% Similarity=0.390 Sum_probs=15.7
Q ss_pred CCcEEEEeCcEEEEEcCC
Q 029373 14 DGVKIKINAKIIEVEGPR 31 (194)
Q Consensus 14 ~~V~v~i~~~~i~VkGp~ 31 (194)
++++|++.++.++|+|-+
T Consensus 24 edi~v~~~~~~L~I~g~~ 41 (93)
T cd06471 24 EDIKLDYKDGYLTISAKR 41 (93)
T ss_pred HHeEEEEECCEEEEEEEE
Confidence 788999999999998854
No 33
>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=35.11 E-value=24 Score=25.17 Aligned_cols=19 Identities=21% Similarity=0.614 Sum_probs=16.0
Q ss_pred CCCcEEEEeCcEEEEEcCC
Q 029373 13 PDGVKIKINAKIIEVEGPR 31 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp~ 31 (194)
|+.++|++.++.|+|+|..
T Consensus 23 ~edi~V~v~~~~L~I~g~~ 41 (86)
T cd06497 23 PEDLTVKVLDDYVEIHGKH 41 (86)
T ss_pred HHHeEEEEECCEEEEEEEE
Confidence 5788999999999999853
No 34
>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=34.56 E-value=28 Score=24.94 Aligned_cols=19 Identities=21% Similarity=0.691 Sum_probs=16.2
Q ss_pred CCCcEEEEeCcEEEEEcCC
Q 029373 13 PDGVKIKINAKIIEVEGPR 31 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp~ 31 (194)
|+.++|++.++.|+|+|-.
T Consensus 20 ~edI~V~v~~~~L~I~g~~ 38 (87)
T cd06481 20 PEDLSVRVDGRKLVVTGKR 38 (87)
T ss_pred hHHeEEEEECCEEEEEEEE
Confidence 6789999999999999853
No 35
>PRK14434 acylphosphatase; Provisional
Probab=33.68 E-value=24 Score=25.76 Aligned_cols=55 Identities=20% Similarity=0.178 Sum_probs=34.4
Q ss_pred EEEEEEecceeEeccCCCeEE-EecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHHHHHHhccc
Q 029373 96 RFVYAHFPINASIGNANKSIE-IRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSAALINQKC 168 (194)
Q Consensus 96 ~lvGvGyp~ra~~~~~g~~l~-lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~AA~Ir~~~ 168 (194)
++.|||| |..+......+. | -||- ...++| + =+|.++|.+.+.|-+|.+.|++-.
T Consensus 11 ~VQGVGF--R~fv~~~A~~lg~l---~G~V----~N~~dG--------s-Vei~~qG~~~~~l~~f~~~l~~g~ 66 (92)
T PRK14434 11 RVQGVGF--RYSVYSLALEIGDI---YGRV----WNNDDG--------T-VEILAQSDDSAKLAKFIQEIRKGP 66 (92)
T ss_pred eecceeE--hHHHHHHHHHcCCc---EEEE----EECCCC--------C-EEEEEEcCCHHHHHHHHHHHhcCC
Confidence 5679999 677743444555 5 3332 223333 1 157778877677999999887743
No 36
>COG1072 CoaA Panthothenate kinase [Coenzyme metabolism]
Probab=33.27 E-value=31 Score=30.60 Aligned_cols=36 Identities=19% Similarity=0.162 Sum_probs=29.0
Q ss_pred cCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHH
Q 029373 121 LGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSR 159 (194)
Q Consensus 121 LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq 159 (194)
=.|||.+.-.+|+..++ ++.| +.++++|++.=+-++
T Consensus 167 Pvysh~~yD~vpd~~~v-~~~p--dIlI~EG~nvLq~~~ 202 (283)
T COG1072 167 PVYSHLIYDPVPDAFQV-VPQP--DILIVEGNNVLQDGE 202 (283)
T ss_pred ccccccccccCCCceee-cCCC--CEEEEechhhhcCCC
Confidence 68999999999998777 5666 689999998654444
No 37
>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=32.49 E-value=29 Score=25.12 Aligned_cols=18 Identities=33% Similarity=0.612 Sum_probs=14.7
Q ss_pred CCCcEEEEeCcEEEEEcC
Q 029373 13 PDGVKIKINAKIIEVEGP 30 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp 30 (194)
|++++|++.++.|+|+|.
T Consensus 21 kedI~V~v~~~~L~I~ge 38 (87)
T cd06482 21 PDQVKVKVKDGKVQVSAE 38 (87)
T ss_pred HHHeEEEEECCEEEEEEE
Confidence 367888888888888885
No 38
>cd06526 metazoan_ACD Alpha-crystallin domain (ACD) of metazoan alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (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.
Probab=31.93 E-value=30 Score=24.13 Aligned_cols=20 Identities=30% Similarity=0.615 Sum_probs=16.7
Q ss_pred CCCcEEEEeCcEEEEEcCCc
Q 029373 13 PDGVKIKINAKIIEVEGPRG 32 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp~G 32 (194)
|++++|++.++.|+|+|.+.
T Consensus 20 ~edI~v~v~~~~L~I~g~~~ 39 (83)
T cd06526 20 PEELKVKVSDNKLVVEGKHE 39 (83)
T ss_pred HHHcEEEEECCEEEEEEEEe
Confidence 47899999999999998743
No 39
>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=31.45 E-value=48 Score=21.23 Aligned_cols=20 Identities=15% Similarity=0.606 Sum_probs=16.7
Q ss_pred CCCcEEEEeCcEEEEEcCCc
Q 029373 13 PDGVKIKINAKIIEVEGPRG 32 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp~G 32 (194)
|+.+.|+++++.+.|+|...
T Consensus 19 ~~~i~v~~~~~~l~v~~~~~ 38 (80)
T cd00298 19 KEDIKVEVEDNVLTISGKRE 38 (80)
T ss_pred HHHeEEEEECCEEEEEEEEc
Confidence 46789999999999998654
No 40
>PTZ00027 60S ribosomal protein L6; Provisional
Probab=31.17 E-value=3e+02 Score=22.80 Aligned_cols=57 Identities=5% Similarity=0.128 Sum_probs=37.7
Q ss_pred eeEeccCCCeEEEecccCceeeEEEeCCC---CeEEEEcCCcccEEEEEecc-----HhHHHHHHHHHhcccc
Q 029373 105 NASIGNANKSIEIRNFLGEKKVRKVDMLD---GVTVVRSEKVKDELILDGND-----IELVSRSAALINQKCH 169 (194)
Q Consensus 105 ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~---gi~v~~~~~~k~~I~i~G~D-----kq~Vgq~AA~Ir~~~~ 169 (194)
.+++ +++.+.++.-+|.-. .++|. ++.+...+ +.|.++-.+ +...|.++|.|+..-.
T Consensus 17 ~V~i--~~~~v~VkGp~G~L~---~~~~~~~~~i~i~~~~---~~i~v~~~~~~~k~~a~~Gt~rslI~NmI~ 81 (190)
T PTZ00027 17 TVTV--KSRKVTVTGKYGELT---RSFRHLPVDIKLSKDG---KYIKVEMWFGTPSHLACIRTVCSHIKNMMT 81 (190)
T ss_pred EEEE--ECCEEEEECCCceEE---EEecCCCceEEEEeCC---CEEEEEeCCCCHHHHHHHHHHHHHHHHHhh
Confidence 3455 678889987777433 45544 77776665 468887443 2367889999988654
No 41
>cd07429 Cby_like Chibby, a nuclear inhibitor of Wnt/beta-catenin mediated transcription, and similar proteins. Chibby(Cby) is a well-conserved nuclear protein that functions as part of the Wnt/beta-catenin signaling pathway. Specifically, Cby binds directly to beta-catenin by interacting with its central region, which harbors armadillo repeats. Cby-beta-catenin interactions may also involve 14-3-3 proteins. By competing with other binding partners of beta-catenin, the Tcf/Lef transcription factors, Cby inhibits transcriptional activation. Cby has been shown to play a role in adipocyte differentiation. The C-terminal region of Cby appears to contain an alpha-helical coiled-coil motif.
Probab=30.85 E-value=25 Score=26.81 Aligned_cols=14 Identities=43% Similarity=0.655 Sum_probs=12.2
Q ss_pred eeeeceEEEeeeee
Q 029373 176 RKFLDGIYVSERGT 189 (194)
Q Consensus 176 r~f~DGiyv~~k~~ 189 (194)
-+|.||.|++|.+.
T Consensus 52 l~F~dG~W~~e~~~ 65 (108)
T cd07429 52 LVFEDGRWISESGG 65 (108)
T ss_pred EEeeCCEEecCCCC
Confidence 57999999999875
No 42
>cd06475 ACD_HspB1_like Alpha crystallin domain (ACD) found in mammalian small (s)heat shock protein (Hsp)-27 (also denoted HspB1 in human) 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. Hsp27 shows enhanced synthesis in response to stress. It is a molecular chaperone which interacts with a large number of different proteins. It is found in many types of human cells including breast, uterus, cervix, platelets and cancer cells. Hsp27 has diverse cellular functions including, chaperoning, regulation of actin polymerization, keratinocyte differentiation, regulation of inflammatory pathways in keratinocytes, and protection from oxidative stress through modulating glutathione levels. It is also a subunit of AUF1-containing protein complexes. It has been linked to several transduction pathways regulating cellular functions including differentiat
Probab=29.17 E-value=38 Score=24.18 Aligned_cols=19 Identities=21% Similarity=0.599 Sum_probs=15.0
Q ss_pred CCCcEEEEeCcEEEEEcCC
Q 029373 13 PDGVKIKINAKIIEVEGPR 31 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp~ 31 (194)
|++++|++.++.++|+|-.
T Consensus 23 ~edi~V~v~~~~L~I~g~~ 41 (86)
T cd06475 23 PEELVVKTKDGVVEITGKH 41 (86)
T ss_pred HHHEEEEEECCEEEEEEEE
Confidence 4688888888888888853
No 43
>PF14506 CppA_N: CppA N-terminal; PDB: 3E0R_D.
Probab=27.54 E-value=2.5e+02 Score=21.96 Aligned_cols=41 Identities=15% Similarity=0.043 Sum_probs=26.5
Q ss_pred EEcCCcc-cEEEEEeccHhHHHHHHHHHhcccc-cCCCceeee
Q 029373 138 VRSEKVK-DELILDGNDIELVSRSAALINQKCH-VKNKDIRKF 178 (194)
Q Consensus 138 ~~~~~~k-~~I~i~G~Dkq~Vgq~AA~Ir~~~~-~K~kd~r~f 178 (194)
.+.++-| ++|+|+-.|-+.+-+..|+..++.+ |||++=+-|
T Consensus 57 ~V~G~KKl~~ivIkv~~~~EIe~LLar~~~~~~l~kg~~gyAf 99 (125)
T PF14506_consen 57 AVEGPKKLNRIVIKVPNPKEIEALLARGAQYDRLYKGKNGYAF 99 (125)
T ss_dssp --SSS-SEEEEEEEESSHHHHHHHHHC-S--SEEEE-SSSEEE
T ss_pred cccCcceeeEEEEEcCCHHHHHHHHhcccccceeEEcCCceEE
Confidence 4444433 6899999999999999999988765 788764433
No 44
>COG0071 IbpA Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=26.51 E-value=87 Score=24.29 Aligned_cols=20 Identities=15% Similarity=0.526 Sum_probs=17.2
Q ss_pred CCCcEEEEeCcEEEEEcCCc
Q 029373 13 PDGVKIKINAKIIEVEGPRG 32 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp~G 32 (194)
|++++|++.++.++|+|-.-
T Consensus 63 kedI~I~~~~~~l~I~g~~~ 82 (146)
T COG0071 63 KEDIEITVEGNTLTIRGERE 82 (146)
T ss_pred hHHeEEEEECCEEEEEEEec
Confidence 37899999999999998773
No 45
>PRK14446 acylphosphatase; Provisional
Probab=24.63 E-value=58 Score=23.59 Aligned_cols=51 Identities=20% Similarity=0.267 Sum_probs=30.5
Q ss_pred EEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCC-eEEEEcCCcccEEEEEeccHhHHHHHHHHHhc
Q 029373 96 RFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDG-VTVVRSEKVKDELILDGNDIELVSRSAALINQ 166 (194)
Q Consensus 96 ~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~g-i~v~~~~~~k~~I~i~G~Dkq~Vgq~AA~Ir~ 166 (194)
.+.|||| |..+...-..+.| -||= -..|+| | +|.++| |.+.+.+|.+.+++
T Consensus 11 ~VQGVGF--R~fv~~~A~~lgl---~G~V----~N~~dGsV----------ei~~qG-~~~~l~~f~~~l~~ 62 (88)
T PRK14446 11 VVQGVWY--RASTRERAVALGL---VGHA----RNQADGSV----------EVVAAG-SAAALEALEAWLWQ 62 (88)
T ss_pred ecCCeeE--hHHHHHHHeeCCe---EEEE----EECCCCCE----------EEEEEe-CHHHHHHHHHHHhh
Confidence 5678999 6776333345555 2221 123333 2 567777 45678999988874
No 46
>PF05137 PilN: Fimbrial assembly protein (PilN); InterPro: IPR007813 PilN is a plasmid-encoded, lipoprotein which locates to the outer membrane of bacteria and are part of a thin pilus required only for liquid mating [].
Probab=24.35 E-value=1.5e+02 Score=19.70 Aligned_cols=40 Identities=15% Similarity=0.116 Sum_probs=28.1
Q ss_pred EeCCCCeEEEEcCCcccEEEEEec--cHhHHHHHHHHHhccc
Q 029373 129 VDMLDGVTVVRSEKVKDELILDGN--DIELVSRSAALINQKC 168 (194)
Q Consensus 129 ~~iP~gi~v~~~~~~k~~I~i~G~--Dkq~Vgq~AA~Ir~~~ 168 (194)
-.+|+|+.++--..+.+.+.|+|. |.+.|.+|...+++..
T Consensus 8 ~~~P~~v~l~~l~~~~~~l~i~G~a~~~~~v~~f~~~L~~~~ 49 (78)
T PF05137_consen 8 RALPEGVWLTSLSINGNTLSISGYADSYQSVAAFLRNLEQSP 49 (78)
T ss_pred hhCCCCEEEEEEEEeCCEEEEEEEECCHHHHHHHHHHHhhCC
Confidence 357999988875444367888886 5677777777776643
No 47
>PRK14440 acylphosphatase; Provisional
Probab=24.30 E-value=23 Score=25.71 Aligned_cols=52 Identities=21% Similarity=0.232 Sum_probs=32.9
Q ss_pred EEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHHHHHHhc
Q 029373 96 RFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSAALINQ 166 (194)
Q Consensus 96 ~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~AA~Ir~ 166 (194)
.+.|||| |..+......+.| -||- ...++| + =+|.++|.+ +.|-+|.+.|++
T Consensus 12 ~VQGVGF--R~~v~~~A~~~gl---~G~V----~N~~dG--------~-Vei~~~G~~-~~v~~f~~~l~~ 63 (90)
T PRK14440 12 LVQGVGF--RKFVQIHAIRLGI---KGYA----KNLPDG--------S-VEVVAEGYE-EALSKLLERIKQ 63 (90)
T ss_pred eEeccCc--hHHHHHHHHHcCC---EEEE----EECCCC--------C-EEEEEEcCH-HHHHHHHHHHhh
Confidence 5678999 6776434445555 3332 233444 1 167888866 779999998874
No 48
>PRK14449 acylphosphatase; Provisional
Probab=23.89 E-value=28 Score=25.16 Aligned_cols=53 Identities=19% Similarity=0.270 Sum_probs=32.3
Q ss_pred EEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHHHHHHhcc
Q 029373 96 RFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSAALINQK 167 (194)
Q Consensus 96 ~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~AA~Ir~~ 167 (194)
++.|||| |..+...-..+.| -||- -..++| + =+|.++|.+ +.|.+|.+.|++-
T Consensus 12 ~VQGVGF--R~fv~~~A~~lgl---~G~V----~N~~dG--------~-Vei~~~G~~-~~v~~f~~~l~~~ 64 (90)
T PRK14449 12 HVQGVGL--RYSVYQKAVSLGI---TGYA----ENLYDG--------S-VEVVAEGDE-ENIKELINFIKTG 64 (90)
T ss_pred eecCcCh--HHHHHHHHHHcCC---EEEE----EECCCC--------e-EEEEEEeCH-HHHHHHHHHHhhC
Confidence 4578999 6666323334555 3332 344444 1 157778844 6699999999874
No 49
>PRK14447 acylphosphatase; Provisional
Probab=23.30 E-value=37 Score=24.81 Aligned_cols=53 Identities=21% Similarity=0.225 Sum_probs=32.0
Q ss_pred EEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHHHHHHhc
Q 029373 96 RFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSAALINQ 166 (194)
Q Consensus 96 ~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~AA~Ir~ 166 (194)
.+.|||| |..+......+.| -||- -..|+|-.| +|.++| +.+.|-+|-..|++
T Consensus 13 ~VQGVGF--R~~~~~~A~~~gl---~G~V----~N~~dG~~V--------ei~~qG-~~~~l~~f~~~l~~ 65 (95)
T PRK14447 13 KVQGVFF--RQSMKEVANRNGV---RGWV----RNRSDGRTV--------EAVLEG-PRDAVLKVIEWARV 65 (95)
T ss_pred ecCCccc--hHHHHHHHhhcCe---EEEE----EECCCCCEE--------EEEEEe-CHHHHHHHHHHHhh
Confidence 5678999 6776434455555 3443 233555222 455666 46778888888874
No 50
>PRK13781 paaB phenylacetate-CoA oxygenase subunit PaaB; Provisional
Probab=23.12 E-value=29 Score=25.92 Aligned_cols=16 Identities=13% Similarity=-0.091 Sum_probs=13.7
Q ss_pred cCceeeEEEeCCCCeE
Q 029373 121 LGEKKVRKVDMLDGVT 136 (194)
Q Consensus 121 LG~Sh~i~~~iP~gi~ 136 (194)
==|.||-.|.+|++|.
T Consensus 78 K~YRh~tfy~~p~~v~ 93 (95)
T PRK13781 78 KVYRHPTFYTLPDEVG 93 (95)
T ss_pred CcccCcccccCccccC
Confidence 3589999999999974
No 51
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=23.11 E-value=1.7e+02 Score=18.81 Aligned_cols=19 Identities=26% Similarity=0.387 Sum_probs=13.7
Q ss_pred cEEEEEeccHhHHHHHHHHH
Q 029373 145 DELILDGNDIELVSRSAALI 164 (194)
Q Consensus 145 ~~I~i~G~Dkq~Vgq~AA~I 164 (194)
+.++|+|. .+.|-...+.|
T Consensus 43 ~~v~I~G~-~~~v~~A~~~i 61 (62)
T cd02394 43 DTITITGP-KENVEKAKEEI 61 (62)
T ss_pred CEEEEEcC-HHHHHHHHHHh
Confidence 58999999 56666655554
No 52
>PRK14450 acylphosphatase; Provisional
Probab=22.93 E-value=35 Score=24.68 Aligned_cols=53 Identities=15% Similarity=0.249 Sum_probs=31.9
Q ss_pred EEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHHHHHHhc
Q 029373 96 RFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSAALINQ 166 (194)
Q Consensus 96 ~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~AA~Ir~ 166 (194)
++.|||| |..+.+.-..+.| -||- -.+++|-.| +|.++| |.+.|-+|.+.+++
T Consensus 11 ~VQGVGF--R~~v~~~A~~~~l---~G~V----~N~~dG~~V--------ei~~~G-~~~~v~~f~~~l~~ 63 (91)
T PRK14450 11 KVQGVYF--RDFTRTQATRLGL---CGYA----KNLANGNEV--------EVVAEG-DKDSLLEFLDLLRS 63 (91)
T ss_pred EecCcCc--HHHHHHHHHHcCC---EEEE----EECCCCCEE--------EEEEEe-CHHHHHHHHHHHhh
Confidence 5679999 6776433445555 3432 234455112 456777 45668999888874
No 53
>PRK14421 acylphosphatase; Provisional
Probab=22.90 E-value=27 Score=25.95 Aligned_cols=55 Identities=18% Similarity=0.234 Sum_probs=33.2
Q ss_pred EEEEEEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCC-eEEEEcCCcccEEEEEeccHhHHHHHHHHHhc
Q 029373 92 RYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDG-VTVVRSEKVKDELILDGNDIELVSRSAALINQ 166 (194)
Q Consensus 92 ~~~L~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~g-i~v~~~~~~k~~I~i~G~Dkq~Vgq~AA~Ir~ 166 (194)
...=.+.|||| |..+...-..+.| -||- -..++| | +|.++|.+ +.|-+|.+.|++
T Consensus 9 ~v~G~VQGVGF--R~fv~~~A~~lgL---~G~V----~N~~dG~V----------ei~~~G~~-~~i~~f~~~l~~ 64 (99)
T PRK14421 9 TIRGRVQGVGY--RAWVARTAEALGL---EGWV----RNRRDGSV----------EALFAGPA-DAVAEMIARCRR 64 (99)
T ss_pred EEEEeEcCccc--hHHHHHHHHHhCC---EEEE----EECCCCEE----------EEEEeCCH-HHHHHHHHHHHh
Confidence 33446779999 6777433344555 3433 345555 3 45666655 458889988874
No 54
>PRK14420 acylphosphatase; Provisional
Probab=22.15 E-value=22 Score=25.61 Aligned_cols=53 Identities=17% Similarity=0.129 Sum_probs=31.8
Q ss_pred EEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHHHHHHhcc
Q 029373 96 RFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSAALINQK 167 (194)
Q Consensus 96 ~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~AA~Ir~~ 167 (194)
.+.|||| |..+...-..+.| -||- -..|+| + =+|.++|.+ +.|-+|...|++-
T Consensus 11 ~VQGVGF--R~~~~~~A~~~gl---~G~V----~N~~dG--------~-Vei~~qG~~-~~i~~f~~~l~~~ 63 (91)
T PRK14420 11 RVQGVGF--RYFVQMEADKRKL---TGWV----KNRDDG--------T-VEIEAEGPE-EALQLFLDAIEKG 63 (91)
T ss_pred eeCCcCC--hHHHHHHHHHcCC---EEEE----EECCCC--------c-EEEEEEECH-HHHHHHHHHHHhC
Confidence 4568999 6666323334445 3331 122222 1 167888865 7799999999875
No 55
>PRK14433 acylphosphatase; Provisional
Probab=21.97 E-value=30 Score=24.90 Aligned_cols=52 Identities=15% Similarity=0.273 Sum_probs=31.9
Q ss_pred EEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCCeEEEEcCCcccEEEEEeccHhHHHHHHHHHhc
Q 029373 96 RFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSAALINQ 166 (194)
Q Consensus 96 ~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~gi~v~~~~~~k~~I~i~G~Dkq~Vgq~AA~Ir~ 166 (194)
.+.|||| |..+...-..+.| -||- -.+|+| . =+|.++|.+. .|-+|...|++
T Consensus 10 ~VQGVGF--R~~v~~~A~~~~l---~G~V----~N~~dG-~--------Vei~~~G~~~-~i~~f~~~l~~ 61 (87)
T PRK14433 10 RVQGVGY--RAFVQKKARELGL---SGYA----ENLSDG-R--------VEVVAEGPKE-ALERLLHWLRR 61 (87)
T ss_pred eeeCcCc--hHHHHHHHHHcCC---EEEE----EECCCC-C--------EEEEEEECHH-HHHHHHHHHhh
Confidence 5679999 6666333344555 3432 344555 1 1577777664 78888888864
No 56
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=20.36 E-value=2.4e+02 Score=17.87 Aligned_cols=19 Identities=26% Similarity=0.464 Sum_probs=14.6
Q ss_pred cEEEEEeccHhHHHHHHHHH
Q 029373 145 DELILDGNDIELVSRSAALI 164 (194)
Q Consensus 145 ~~I~i~G~Dkq~Vgq~AA~I 164 (194)
+.+.|+| +.+.|.+..+.|
T Consensus 42 ~~v~I~G-~~~~v~~A~~~I 60 (60)
T PF00013_consen 42 DIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEE-SHHHHHHHHHHH
T ss_pred EEEEEEe-CHHHHHHHHhhC
Confidence 4799999 888887766554
No 57
>PRK10743 heat shock protein IbpA; Provisional
Probab=20.35 E-value=63 Score=25.29 Aligned_cols=18 Identities=17% Similarity=0.407 Sum_probs=14.5
Q ss_pred CCCcEEEEeCcEEEEEcC
Q 029373 13 PDGVKIKINAKIIEVEGP 30 (194)
Q Consensus 13 P~~V~v~i~~~~i~VkGp 30 (194)
|++++|+++++.++|+|-
T Consensus 58 kedi~V~v~~~~LtI~ge 75 (137)
T PRK10743 58 ESELEITAQDNLLVVKGA 75 (137)
T ss_pred HHHeEEEEECCEEEEEEE
Confidence 367788888889999884
No 58
>PRK14445 acylphosphatase; Provisional
Probab=20.04 E-value=54 Score=23.65 Aligned_cols=56 Identities=16% Similarity=0.176 Sum_probs=33.0
Q ss_pred eEEEEEEEEEEecceeEeccCCCeEEEecccCceeeEEEeCCCC-eEEEEcCCcccEEEEEeccHhHHHHHHHHHhc
Q 029373 91 YRYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDMLDG-VTVVRSEKVKDELILDGNDIELVSRSAALINQ 166 (194)
Q Consensus 91 f~~~L~lvGvGyp~ra~~~~~g~~l~lkn~LG~Sh~i~~~iP~g-i~v~~~~~~k~~I~i~G~Dkq~Vgq~AA~Ir~ 166 (194)
+...=.+.|||| |..+.+....+.| -||- -..++| | +|.++|.+ +.|-+|-+.+++
T Consensus 8 ~~v~G~VQGVGF--R~~v~~~A~~~gl---~G~V----~N~~dG~V----------ei~~qG~~-~~l~~f~~~l~~ 64 (91)
T PRK14445 8 LIVSGLVQGVGF--RMFIDRAASELNL---SGWV----RNLPDGTV----------EIEAQGSS-GMIDELIKQAER 64 (91)
T ss_pred EEEEEEEcCcCC--hHHHHHHHhhCCC---EEEE----EECCCCeE----------EEEEEECH-HHHHHHHHHHHh
Confidence 333446789999 6777434444555 2332 223333 2 57777855 558999998874
Done!