Query 031693
Match_columns 155
No_of_seqs 142 out of 1043
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 04:03:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031693.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031693hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0080 RplK Ribosomal protein 100.0 7.2E-63 1.6E-67 378.6 15.2 140 11-153 2-141 (141)
2 TIGR01632 L11_bact 50S ribosom 100.0 1.2E-62 2.6E-67 379.0 15.7 140 11-152 1-140 (140)
3 CHL00127 rpl11 ribosomal prote 100.0 2.7E-61 5.8E-66 371.5 15.2 138 11-151 3-140 (140)
4 PRK00140 rplK 50S ribosomal pr 100.0 3.5E-61 7.6E-66 371.3 15.3 139 11-152 3-141 (141)
5 PRK01143 rpl11p 50S ribosomal 100.0 9.9E-60 2.1E-64 370.7 16.3 136 15-153 3-139 (163)
6 smart00649 RL11 Ribosomal prot 100.0 7.3E-60 1.6E-64 360.4 14.6 132 17-151 1-132 (132)
7 cd00349 Ribosomal_L11 Ribosoma 100.0 3.8E-59 8.2E-64 356.0 14.3 131 17-150 1-131 (131)
8 PTZ00321 ribosomal protein L11 100.0 1.1E-58 2.3E-63 392.5 17.0 153 1-153 32-194 (342)
9 PLN03072 60S ribosomal protein 100.0 4E-57 8.7E-62 356.6 15.0 134 15-153 11-147 (166)
10 PRK14539 50S ribosomal protein 100.0 4.7E-57 1E-61 363.1 15.6 138 9-153 2-139 (196)
11 KOG3257 Mitochondrial/chloropl 100.0 3.8E-57 8.3E-62 352.1 13.5 147 7-153 12-158 (168)
12 PTZ00105 60S ribosomal protein 100.0 1.8E-50 3.8E-55 311.4 13.5 119 30-153 1-121 (140)
13 KOG0886 40S ribosomal protein 100.0 8.7E-31 1.9E-35 202.1 10.0 136 13-153 11-148 (167)
14 PF00298 Ribosomal_L11: Riboso 100.0 5.4E-30 1.2E-34 176.4 8.1 69 80-150 1-69 (69)
15 PF03946 Ribosomal_L11_N: Ribo 100.0 8.6E-30 1.9E-34 171.2 7.0 60 16-75 1-60 (60)
16 COG0051 RpsJ Ribosomal protein 41.7 21 0.00046 26.5 2.1 27 127-153 13-39 (104)
17 COG4953 PbpC Membrane carboxyp 41.1 33 0.00072 33.3 3.7 76 17-98 417-492 (733)
18 cd02742 GH20_hexosaminidase Be 40.5 85 0.0018 26.5 5.9 67 43-120 14-80 (303)
19 PF13184 KH_5: NusA-like KH do 40.1 21 0.00045 24.2 1.7 56 17-93 5-60 (69)
20 cd02395 SF1_like-KH Splicing f 36.6 36 0.00078 25.5 2.7 35 19-53 4-38 (120)
21 PRK05424 rplA 50S ribosomal pr 34.7 39 0.00085 28.0 2.8 31 30-60 124-158 (230)
22 PF05164 ZapA: Cell division p 32.9 63 0.0014 21.8 3.2 27 65-93 2-28 (89)
23 cd06562 GH20_HexA_HexB-like Be 32.1 2.9E+02 0.0063 23.9 7.9 61 44-119 17-77 (348)
24 KOG1588 RNA-binding protein Sa 28.3 1E+02 0.0022 26.5 4.3 98 11-122 88-210 (259)
25 KOG1196 Predicted NAD-dependen 27.6 28 0.0006 30.8 0.8 42 111-153 142-184 (343)
26 CHL00129 rpl1 ribosomal protei 26.7 48 0.001 27.5 2.1 12 31-42 125-136 (229)
27 TIGR01046 S10_Arc_S20_Euk ribo 24.9 57 0.0012 23.7 2.0 26 128-153 11-36 (99)
28 CHL00135 rps10 ribosomal prote 23.2 63 0.0014 23.6 1.9 26 128-153 17-42 (101)
29 PF03990 DUF348: Domain of unk 22.3 1.6E+02 0.0035 17.7 3.4 34 64-99 1-34 (43)
30 PRK04053 rps13p 30S ribosomal 21.6 1.7E+02 0.0036 22.9 4.1 36 81-122 34-69 (149)
31 TIGR01049 rpsJ_bact ribosomal 20.9 58 0.0013 23.4 1.3 25 129-153 12-36 (99)
32 PTZ00039 40S ribosomal protein 20.8 75 0.0016 23.8 1.9 33 119-153 20-52 (115)
33 PRK12271 rps10p 30S ribosomal 20.8 76 0.0016 23.2 1.9 26 128-153 12-37 (102)
34 PF13727 CoA_binding_3: CoA-bi 20.0 66 0.0014 23.5 1.5 42 110-151 129-172 (175)
35 PF03487 IL13: Interleukin-13; 20.0 52 0.0011 20.6 0.8 38 13-56 5-42 (43)
No 1
>COG0080 RplK Ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.2e-63 Score=378.61 Aligned_cols=140 Identities=47% Similarity=0.760 Sum_probs=135.3
Q ss_pred cceeeEEEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhCCCCCCceEEEEEecCCCeEEEEEeCCCHHHHHHH
Q 031693 11 RPVAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPSVTWYLKK 90 (155)
Q Consensus 11 k~~~~~ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf~~~v~~Ppts~likk 90 (155)
+++.++|+|+++||+|+|+|||||+|||+|||+|+|||+||++|+++ +|++|||+||||+||||+|++++||+|+||+|
T Consensus 2 ~k~~~~ikl~v~aGkA~p~PpvGPALG~~Gvni~~f~k~fN~~T~~~-~G~~vPV~Itv~~drsftf~~ktPPas~LlkK 80 (141)
T COG0080 2 KKVVKIIKLQVPAGKANPSPPVGPALGQLGVNIMEFCKEFNAATKDE-KGLPVPVVITVYEDRSFTFIVKTPPASALLKK 80 (141)
T ss_pred CccceEEEEEecccccCCCCCCCccccccCCCHHHHHHHHHHHhhcc-CCCeeeEEEEEEcCCcEEEEECCCCHHHHHHH
Confidence 34889999999999999999999999999999999999999999995 59999999999999999999999999999999
Q ss_pred HhCCCCCCCCCCCeeeecccHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHhhhhcCeEEecc
Q 031693 91 AAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESICKSIIGTAATMGIKVVKE 153 (155)
Q Consensus 91 a~g~~~gs~~p~~~~vG~It~~~v~eIAk~K~~d~~~~~~~l~~~~k~VlGTa~SmGi~V~~~ 153 (155)
++|+++||++|+++++|+||++||+|||++|++|++ +.+|++++|+|+||||||||+|++.
T Consensus 81 a~g~~~Gs~~p~k~~vG~lt~~qv~eIA~~K~~dl~--a~~l~aA~k~I~GTa~SMGv~Veg~ 141 (141)
T COG0080 81 AAGIEKGSGKPNKNKVGKLTLAQVREIAKTKMPDLN--AKDLEAAVKEILGTARSMGVTVEGK 141 (141)
T ss_pred HhCCCCCCCCCCcceeeeeeHHHHHHHHHHhhhhhh--hHHHHHHHHHHhhhhhhceEEeecC
Confidence 999999999999999999999999999999999965 8899999999999999999999974
No 2
>TIGR01632 L11_bact 50S ribosomal protein L11. This model represents bacterial, chloroplast, and most mitochondrial forms of 50S ribosomal protein L11.
Probab=100.00 E-value=1.2e-62 Score=379.05 Aligned_cols=140 Identities=49% Similarity=0.828 Sum_probs=135.2
Q ss_pred cceeeEEEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhCCCCCCceEEEEEecCCCeEEEEEeCCCHHHHHHH
Q 031693 11 RPVAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPSVTWYLKK 90 (155)
Q Consensus 11 k~~~~~ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf~~~v~~Ppts~likk 90 (155)
|++.++|+|+++||+|+|+|||||+|||+|||+|+||||||++|++|..|++|||+|+||+||+|+|++++||+||||+|
T Consensus 1 k~~~~~ikl~v~aG~A~p~PplGP~LG~~Gini~~f~k~fN~~T~~~~~G~~vpV~Itv~~drsf~~~v~~Pp~s~ll~k 80 (140)
T TIGR01632 1 KKIVGIIKLQVPAGQANPAPPVGPALGQRGVNIMEFCKQFNARTADYEPGLPVPVVITVYEDKSFTFIVKTPPVSYLLKK 80 (140)
T ss_pred CceEEEEEEEEeccccCCCCCCcccccccCCCHHHHHHHHHHHHhhhcCCCeEEEEEEEeCCCeEEEEEcCCCHHHHHHH
Confidence 35789999999999999999999999999999999999999999996669999999999999999999999999999999
Q ss_pred HhCCCCCCCCCCCeeeecccHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHhhhhcCeEEec
Q 031693 91 AAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESICKSIIGTAATMGIKVVK 152 (155)
Q Consensus 91 a~g~~~gs~~p~~~~vG~It~~~v~eIAk~K~~d~~~~~~~l~~~~k~VlGTa~SmGi~V~~ 152 (155)
++|+++||++|+++++|+||++||||||+.|++|++ +.+|+++||+|+||||||||+|++
T Consensus 81 aag~~~gs~~p~~~~~G~it~~qv~eIA~~K~~d~~--~~~l~~~vk~v~GTarSmGi~V~~ 140 (140)
T TIGR01632 81 AAGVEKGSKNPKKEKVGKITRKQVREIAEIKMSDLN--TKDIEAAMKIIAGTAKSMGIEIVG 140 (140)
T ss_pred HhCCCCCCCCCCCeEEeEecHHHHHHHHHHHHHHhC--cccHHHHHHHhheeHeeceEEEeC
Confidence 999999999999999999999999999999999965 889999999999999999999985
No 3
>CHL00127 rpl11 ribosomal protein L11; Validated
Probab=100.00 E-value=2.7e-61 Score=371.54 Aligned_cols=138 Identities=41% Similarity=0.688 Sum_probs=133.5
Q ss_pred cceeeEEEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhCCCCCCceEEEEEecCCCeEEEEEeCCCHHHHHHH
Q 031693 11 RPVAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPSVTWYLKK 90 (155)
Q Consensus 11 k~~~~~ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf~~~v~~Ppts~likk 90 (155)
|++.++|+|+++||+|+|+|||||+|||+|||+|+||||||++|++|+ |++|||+|+||+||+|+|++++||+||||+|
T Consensus 3 k~~~~~ikl~v~aG~A~p~PplGP~LG~~Gini~~f~k~fN~~T~~~~-g~~vpV~Itv~~drsf~~~v~~Pp~s~ll~k 81 (140)
T CHL00127 3 KKKLAIIKLALPAGKATPAPPVGPALGQHGVNINLFCKEYNARTKDKI-GLIIPVEISVYEDKSYTFILKTPPASVLLAK 81 (140)
T ss_pred cccccEEEEEEecCccCCCCCCcccccccCCCHHHHHHHHHHHhhhcC-CCeEEEEEEEeCCceEEEEEcCCCHHHHHHH
Confidence 457889999999999999999999999999999999999999999985 9999999999999999999999999999999
Q ss_pred HhCCCCCCCCCCCeeeecccHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHhhhhcCeEEe
Q 031693 91 AAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESICKSIIGTAATMGIKVV 151 (155)
Q Consensus 91 a~g~~~gs~~p~~~~vG~It~~~v~eIAk~K~~d~~~~~~~l~~~~k~VlGTa~SmGi~V~ 151 (155)
++|+++||++|+++++|+||++||||||+.|++|++ +.+|+++||+|+||||||||+|.
T Consensus 82 a~gi~~gs~~p~~~~~G~it~~~v~eIA~~K~~d~~--~~~l~~~vk~v~GTa~SmGi~V~ 140 (140)
T CHL00127 82 AAGIKKGSGEPNKKKVGSITIKQLEEIAQIKLPDLN--TISLSKAIKIIEGTAKNMGISIK 140 (140)
T ss_pred HhCCCcCCCCCCCeecceecHHHHHHHHHHHhhhhc--cccHHHHHHHhHeeheeceEEeC
Confidence 999999999999999999999999999999999965 88999999999999999999984
No 4
>PRK00140 rplK 50S ribosomal protein L11; Validated
Probab=100.00 E-value=3.5e-61 Score=371.26 Aligned_cols=139 Identities=46% Similarity=0.727 Sum_probs=134.9
Q ss_pred cceeeEEEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhCCCCCCceEEEEEecCCCeEEEEEeCCCHHHHHHH
Q 031693 11 RPVAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPSVTWYLKK 90 (155)
Q Consensus 11 k~~~~~ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf~~~v~~Ppts~likk 90 (155)
|++.++|+|+++||+|+|+|||||+|||+|||+|+||||||++|++| .|++|||+|+||+||+|+|++++||+||||+|
T Consensus 3 k~~~~~ikl~v~aG~A~p~PplgP~LG~~Gini~~f~k~fN~~T~~~-~g~~vpV~i~v~~drsf~~~v~~Pp~s~ll~k 81 (141)
T PRK00140 3 KKVVGYIKLQIPAGKANPAPPVGPALGQRGVNIMEFCKAFNARTQDQ-KGLPIPVVITVYEDRSFTFITKTPPASVLLKK 81 (141)
T ss_pred cccceEEEEEEecCccCCCCCCcccccccCCCHHHHHHHHHHHHhhc-CCCeEEEEEEEecCCeEEEEEcCCCHHHHHHH
Confidence 45788999999999999999999999999999999999999999999 59999999999999999999999999999999
Q ss_pred HhCCCCCCCCCCCeeeecccHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHhhhhcCeEEec
Q 031693 91 AAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESICKSIIGTAATMGIKVVK 152 (155)
Q Consensus 91 a~g~~~gs~~p~~~~vG~It~~~v~eIAk~K~~d~~~~~~~l~~~~k~VlGTa~SmGi~V~~ 152 (155)
++|+++||++|+++++|+||++||||||+.|++|++ +.+|+++||+|+|||+||||+|++
T Consensus 82 ~~g~~~gs~~p~~~~vG~it~~~v~eIA~~K~~d~~--~~~l~~~vk~VlGTa~SmGi~V~g 141 (141)
T PRK00140 82 AAGIEKGSGEPNKEKVGKITRAQVREIAETKMPDLN--AADIEAAMRMIAGTARSMGIVVEG 141 (141)
T ss_pred HhCCCCCCCCCCCeEEeeEcHHHHHHHHHHHHHhhC--CCcHHHHHHHhheeeeEeeEEEeC
Confidence 999999999999999999999999999999999965 889999999999999999999985
No 5
>PRK01143 rpl11p 50S ribosomal protein L11P; Validated
Probab=100.00 E-value=9.9e-60 Score=370.68 Aligned_cols=136 Identities=32% Similarity=0.583 Sum_probs=132.6
Q ss_pred eEEEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhCCCCCCceEEEEEe-cCCCeEEEEEeCCCHHHHHHHHhC
Q 031693 15 ATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITA-FKDNTFEFTVKSPSVTWYLKKAAG 93 (155)
Q Consensus 15 ~~ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~~~~g~~vpV~i~v-~~drsf~~~v~~Ppts~likka~g 93 (155)
++|+|+|+||+|+|+|||||+|||+|||+|+|||+||++|++|+ |++|||+|+| |+||+|+|++++||+||||+|++|
T Consensus 3 ~~ikl~v~aG~A~p~PplGPaLG~~Gini~~f~k~fN~~T~~~~-g~~vpV~Itv~~~drsf~~~vk~Pp~s~ll~kaag 81 (163)
T PRK01143 3 KVVEVLVEGGKATPGPPLGPALGPLGLNVKQVVQEINEKTKDFK-GMQVPVKVIVDTDTKKFEIEVGIPPTTALIKKELG 81 (163)
T ss_pred eEEEEEEecCccCCCCCCcccccccCCCHHHHHHHHHHHhhhcC-CCeEeEEEEEEeCCceEEEEECCCCHHHHHHHHhC
Confidence 68999999999999999999999999999999999999999995 9999999999 999999999999999999999999
Q ss_pred CCCCCCCCCCeeeecccHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHhhhhcCeEEecc
Q 031693 94 IESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESICKSIIGTAATMGIKVVKE 153 (155)
Q Consensus 94 ~~~gs~~p~~~~vG~It~~~v~eIAk~K~~d~~~~~~~l~~~~k~VlGTa~SmGi~V~~~ 153 (155)
+++||++|+++++|+||++||||||+.|++|++ +.+|+++||+|+||||||||+|+++
T Consensus 82 ~~kgs~~p~~~~vG~It~~qv~eIA~~K~~d~~--~~~l~~~vk~VlGTarSmGi~V~g~ 139 (163)
T PRK01143 82 IEKGSGEPGHEVVGNLSFEQVVKIAIMKKDDLL--SYDLKAAVKEVLGTCVSMGVTVEGK 139 (163)
T ss_pred CcCCCCCCCCceeeeecHHHHHHHHHHHhhhhc--cccHHHHHHHHHhhHhhceEEEecC
Confidence 999999999999999999999999999999966 8899999999999999999999875
No 6
>smart00649 RL11 Ribosomal protein L11/L12.
Probab=100.00 E-value=7.3e-60 Score=360.40 Aligned_cols=132 Identities=52% Similarity=0.903 Sum_probs=128.6
Q ss_pred EEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhCCCCCCceEEEEEecCCCeEEEEEeCCCHHHHHHHHhCCCC
Q 031693 17 IRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPSVTWYLKKAAGIES 96 (155)
Q Consensus 17 ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf~~~v~~Ppts~likka~g~~~ 96 (155)
|+|+|+||+|+|+|||||+|||+|||+|+||||||++|++|+ |++|||+|+||+||+|+|++++||+||||+|++|+++
T Consensus 1 ikl~v~aG~A~p~PplgP~LG~~Gini~~f~k~fN~~T~~~~-g~~vpV~I~v~~dksf~~~v~~P~~s~ll~k~~g~~k 79 (132)
T smart00649 1 IKLQIPAGKANPAPPLGPALGQLGINIMEFCKEFNARTKDKK-GLPIPVKITVYNDKSFTFIIKTPPASFLLKKAAGIEK 79 (132)
T ss_pred CEEEEecCccCCCCCcccccccCCCCHHHHHHHHHHHHhhcC-CCeEeEEEEEeCCCeEEEEEcCCCHHHHHHHHhCCCC
Confidence 689999999999999999999999999999999999999975 9999999999999999999999999999999999999
Q ss_pred CCCCCCCeeeecccHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHhhhhcCeEEe
Q 031693 97 GSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESICKSIIGTAATMGIKVV 151 (155)
Q Consensus 97 gs~~p~~~~vG~It~~~v~eIAk~K~~d~~~~~~~l~~~~k~VlGTa~SmGi~V~ 151 (155)
||++|+++++|+||++||||||+.|++|++ +.+|+++||+|+|||+||||+|+
T Consensus 80 gs~~p~~~~~g~it~~~v~eIA~~K~~d~~--~~~l~~~~k~V~GTa~SmGi~V~ 132 (132)
T smart00649 80 GSKKPGKKKVGNITLDQVYEIAKIKRPDLN--AKDLEAAVKEILGTARSMGITVE 132 (132)
T ss_pred CCCCCCCeeeeEEcHHHHHHHHHHHHHHhc--chhHHHHHHHHHhhHhcceEEeC
Confidence 999999999999999999999999999955 88999999999999999999985
No 7
>cd00349 Ribosomal_L11 Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal protein L12, which is distinct from the L12 involved in the formation of the L7/L12 stalk. The C-terminal domain (CTD) of L11 is essential for binding 23S rRNA, while the N-terminal domain (NTD) contains the binding site for the antibiotics thiostrepton and micrococcin. L11 and 23S rRNA form an essential part of the GTPase-associated region (GAR). Based on differences in the relative positions of the L11 NTD and CTD during the translational cycle, L11 is proposed to play a significant role in the binding of initiation factors, elongation factors, and release factors to the ribosome. Several factors, including the class I release factors RF1 and RF2, are known to interact directly with L11. In eukaryotes, L11 has been im
Probab=100.00 E-value=3.8e-59 Score=356.05 Aligned_cols=131 Identities=53% Similarity=0.881 Sum_probs=127.9
Q ss_pred EEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhCCCCCCceEEEEEecCCCeEEEEEeCCCHHHHHHHHhCCCC
Q 031693 17 IRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPSVTWYLKKAAGIES 96 (155)
Q Consensus 17 ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf~~~v~~Ppts~likka~g~~~ 96 (155)
|+|+|+||+|+|+|||||+|||+|||+|+|||+||++|++| .|++|||+|+||+||+|+|++++||+||||+|++|+++
T Consensus 1 ikl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~~-~g~~vpV~itv~~dksf~~~v~~Pp~s~ll~ka~g~~k 79 (131)
T cd00349 1 IKLQVPAGKASPAPPLGPALGQLGVNIMKFCKEFNARTKDY-KGLPVPVKITVYNDRSFTFEVKTPPASALLKKAAGIEK 79 (131)
T ss_pred CEEEEecCccCCCCCcccccccCCCCHHHHHHHHHHHHhhc-CCCeEEEEEEEeCCCeEEEEEcCCCHHHHHHHHhCCCC
Confidence 58999999999999999999999999999999999999999 59999999999999999999999999999999999999
Q ss_pred CCCCCCCeeeecccHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHhhhhcCeEE
Q 031693 97 GSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESICKSIIGTAATMGIKV 150 (155)
Q Consensus 97 gs~~p~~~~vG~It~~~v~eIAk~K~~d~~~~~~~l~~~~k~VlGTa~SmGi~V 150 (155)
||++|+++++|+||++||||||+.|++|++ +.+|+++||+|+|||+||||+|
T Consensus 80 gs~~~~~~~~g~it~~~v~eIA~~K~~dl~--~~~l~~~vk~v~GTa~SmGi~V 131 (131)
T cd00349 80 GSKKPNKEKVGNITLDQVYEIAKIKLPDLN--AKTLKSAVKEILGTARSMGITV 131 (131)
T ss_pred CCCCCCCeeeeeecHHHHHHHHHHHHhhhc--chhHHHHHHHHHhhHhhCeEEC
Confidence 999999999999999999999999999955 8899999999999999999986
No 8
>PTZ00321 ribosomal protein L11; Provisional
Probab=100.00 E-value=1.1e-58 Score=392.55 Aligned_cols=153 Identities=29% Similarity=0.510 Sum_probs=143.3
Q ss_pred ChhhHhhhhc-----cceeeEEEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhC-CCCCCceEEEEEecCCCe
Q 031693 1 MATLKEILTR-----RPVAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQK-YKPETPMSVTITAFKDNT 74 (155)
Q Consensus 1 ~~~~~~~~~~-----k~~~~~ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~-~~~g~~vpV~i~v~~drs 74 (155)
|+++++|+.. |++.+.|||+|+||+|+|+|||||+|||+|||+|+|||+||++|++ |+.|++|||+|+||+|||
T Consensus 32 ~~~~~~~~~~~~~~~KkV~~~IKL~VpAGKAtPaPPVGPALGq~GVNImqFCKeFNerTK~~fk~GvpVPV~ITVy~DKS 111 (342)
T PTZ00321 32 MAKAKDIFAVPEFPGKRVLHNWRFFIKAGKAATGPPVGQEFSKLGLKAMDFAKSFNDRTKPHFKDDVELIVRIQVYFDKS 111 (342)
T ss_pred HHhhhhcccCCCCCCCeeeEEEEEEEECCCcCCCCCCcccccccCCCHHHHHHHHHHHHHhhccCCCeEeEEEEEeCCCe
Confidence 4677888855 7899999999999999999999999999999999999999999997 788999999999999999
Q ss_pred EEEEEeCCCHHHHHHHHhCCCCCCCCC--CC-eeeecccHHHHHHHHHhcccCCC-CCCCCHHHHHHHHHHhhhhcCeEE
Q 031693 75 FEFTVKSPSVTWYLKKAAGIESGSSRP--GH-VTASTVTLKHIYEIAKVKQSDPY-CQYMPLESICKSIIGTAATMGIKV 150 (155)
Q Consensus 75 f~~~v~~Ppts~likka~g~~~gs~~p--~~-~~vG~It~~~v~eIAk~K~~d~~-~~~~~l~~~~k~VlGTa~SmGi~V 150 (155)
|+|++++||+||||+|++|+++||++| ++ +++|+||++||||||++|++|++ +++.+|+++||+|+|||+||||+|
T Consensus 112 F~F~IktPPtS~LLKKAAGI~KGS~~P~~~k~e~VG~ITlkQVyEIAkiK~~DLnal~~~~LesAvK~ViGTARSMGIkV 191 (342)
T PTZ00321 112 YLFTIEPPPTAWFILRALRKKRRETGPVPLRGHYCALMTLEMAYEIAKMKPRSWGRPEYPLIETRVRRVVGQARRMGVCF 191 (342)
T ss_pred EEEEECCCCHHHHHHHHhCCCCCCCCCCCCCCceEEeccHHHHHHHHHHhhhccccccccCHHHHHHHHHhhHhcCeEEE
Confidence 999999999999999999999999999 33 89999999999999999999976 345799999999999999999999
Q ss_pred ecc
Q 031693 151 VKE 153 (155)
Q Consensus 151 ~~~ 153 (155)
++.
T Consensus 192 eGK 194 (342)
T PTZ00321 192 IGV 194 (342)
T ss_pred ecc
Confidence 974
No 9
>PLN03072 60S ribosomal protein L12; Provisional
Probab=100.00 E-value=4e-57 Score=356.58 Aligned_cols=134 Identities=22% Similarity=0.313 Sum_probs=128.7
Q ss_pred eEEEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhC-CCCCCceEEEEEecCCCeEEEEEeCCCHHHHHHHHhC
Q 031693 15 ATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQK-YKPETPMSVTITAFKDNTFEFTVKSPSVTWYLKKAAG 93 (155)
Q Consensus 15 ~~ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~-~~~g~~vpV~i~v~~drsf~~~v~~Ppts~likka~g 93 (155)
.+|+|+|+||+|+|+|||||+|||+|||+|+||++||++|++ |+ |++|||+|+||+ |||+|++ +||+|+||+|+||
T Consensus 11 ~~i~l~v~aG~A~P~PplGPaLG~~GvNi~~f~k~fN~~T~~~~~-G~~VpV~Itv~~-rsf~~~v-~Pp~s~LLkKa~g 87 (166)
T PLN03072 11 VEVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWK-GLRVTVKLTVQN-RQAKVSV-VPSAAALVIKALK 87 (166)
T ss_pred EEEEEEEEcCccCCCCCCccccccCCCCHHHHHHHHHHHhhhhcC-CCeEEEEEEEEC-CeEEEEe-CCCHHHHHHHHhC
Confidence 389999999999999999999999999999999999999996 85 999999999997 9999999 9999999999999
Q ss_pred CCCCCCC--CCCeeeecccHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHhhhhcCeEEecc
Q 031693 94 IESGSSR--PGHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESICKSIIGTAATMGIKVVKE 153 (155)
Q Consensus 94 ~~~gs~~--p~~~~vG~It~~~v~eIAk~K~~d~~~~~~~l~~~~k~VlGTa~SmGi~V~~~ 153 (155)
+++||++ |+++++|+||++||||||+.|++|++ +.+|+++||+|+||||||||+|+++
T Consensus 88 ~~kgs~~~~~~~~~vG~it~~qv~eIA~~K~~dl~--a~~l~~avk~VlGTarSmGi~V~gk 147 (166)
T PLN03072 88 EPERDRKKVKNIKHNGNISLDDVIEIAKIMRPRSM--AKELAGTVKEILGTCVSVGCTVDGK 147 (166)
T ss_pred CCCCCCccCCCCeeeeeecHHHHHHHHHHHHHHhC--cccHHHHHHHhHheeeeCeEEEeCC
Confidence 9999998 78899999999999999999999965 8899999999999999999999985
No 10
>PRK14539 50S ribosomal protein L11/unknown domain fusion protein; Provisional
Probab=100.00 E-value=4.7e-57 Score=363.13 Aligned_cols=138 Identities=34% Similarity=0.522 Sum_probs=131.1
Q ss_pred hccceeeEEEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhCCCCCCceEEEEEecCCCeEEEEEeCCCHHHHH
Q 031693 9 TRRPVAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPSVTWYL 88 (155)
Q Consensus 9 ~~k~~~~~ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf~~~v~~Ppts~li 88 (155)
++|++.++|+|+|+||+|+| ||+|||+|||+|+||++||++|++|. |++|||+|+||+||||+|++++||+||||
T Consensus 2 m~kki~~~Ikl~v~AGkA~P----GPaLG~~GVNi~~FcKefN~~Tk~~~-G~~VPV~ItV~~DRsf~f~vktPptS~LL 76 (196)
T PRK14539 2 AKKEVVKVAKLQFNAGQAKP----GPSLAGVGINMPEFTKQFNDATRDRG-GEPVPVQITVYKDKSFDFKLFTAPASFKI 76 (196)
T ss_pred ccchhheEEEEEEECCccCC----CCcccccCCCHHHHHHHHHHHhhhcC-CceEEEEEEEecCCeEEEEEeCCCHHHHH
Confidence 44668899999999999999 56688999999999999999999984 99999999999999999999999999999
Q ss_pred HHHhCCCCCCCCCCCeeeecccHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHhhhhcCeEEecc
Q 031693 89 KKAAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESICKSIIGTAATMGIKVVKE 153 (155)
Q Consensus 89 kka~g~~~gs~~p~~~~vG~It~~~v~eIAk~K~~d~~~~~~~l~~~~k~VlGTa~SmGi~V~~~ 153 (155)
+|++|+++||++|+++++|+||++||||||++|++|++ +.+|+++||+|+||||||||+|++.
T Consensus 77 kKaagi~kGs~~p~k~~vG~Itl~qv~eIAk~K~~Dl~--~~~Le~avK~VlGTArSMGI~Veg~ 139 (196)
T PRK14539 77 KQAAKIKSGSANSKTTIVGTITLSQLEEIAKYKLPDLN--TDDVEEAMHTIAGTAKNMGVLVEGY 139 (196)
T ss_pred HHHhCCCCCCCCCCCeEEEEecHHHHHHHHHHHhhhhC--CCcHHHHHHHHHhhheeCeEEEEcc
Confidence 99999999999999999999999999999999999965 7899999999999999999999874
No 11
>KOG3257 consensus Mitochondrial/chloroplast ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.8e-57 Score=352.12 Aligned_cols=147 Identities=55% Similarity=0.898 Sum_probs=141.5
Q ss_pred hhhccceeeEEEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhCCCCCCceEEEEEecCCCeEEEEEeCCCHHH
Q 031693 7 ILTRRPVAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPSVTW 86 (155)
Q Consensus 7 ~~~~k~~~~~ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf~~~v~~Ppts~ 86 (155)
-+.+..+...+||.++||.|.|+||+||+|||+|+|+++||||||++|++|++|+|+|++||+.+||||+|++++||+||
T Consensus 12 ~~~k~~h~~~ikl~v~Ag~A~~~pp~gP~Lgqr~l~viafckefnarT~~~k~~vplp~kiTv~pDrsftf~iktPpts~ 91 (168)
T KOG3257|consen 12 PISKLSHSASIKLIVKAGLAAPAPPLGPALGQRGLNVIAFCKEFNARTKKVKPGVPLPGKITVKPDRSFTFIIKTPPTSW 91 (168)
T ss_pred ccccccceeEEEEeeccccccCCCCCCchhhhcchhHHHhchhhhhhhccccCCCccceeEeecCCCeEEEEecCCChHH
Confidence 34456678899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCCCCCCCCCCeeeecccHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHhhhhcCeEEecc
Q 031693 87 YLKKAAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESICKSIIGTAATMGIKVVKE 153 (155)
Q Consensus 87 likka~g~~~gs~~p~~~~vG~It~~~v~eIAk~K~~d~~~~~~~l~~~~k~VlGTa~SmGi~V~~~ 153 (155)
||+||||+++||.+|+++.+|.||++||||||++|.+|+++...+|+++||+|+|||+||||+|+..
T Consensus 92 lL~kAagv~KGs~~p~~~~vG~lTlkhvyeIAkiK~~D~~~q~~~lesi~rsiigtA~smGIkVvp~ 158 (168)
T KOG3257|consen 92 LLKKAAGVEKGSKDPGQEKVGMLTLKHVYEIAKIKLPDPNLQCTTLESICRSIIGTARSMGIKVVPP 158 (168)
T ss_pred HHHHHhCcccCCCCCcceeeeeEEHHHHHHHHHhhcCCcccccccHHHHHHHHHHHHHhCccccchh
Confidence 9999999999999999999999999999999999999999888999999999999999999999863
No 12
>PTZ00105 60S ribosomal protein L12; Provisional
Probab=100.00 E-value=1.8e-50 Score=311.45 Aligned_cols=119 Identities=18% Similarity=0.291 Sum_probs=113.0
Q ss_pred CCCCcccCcCCCChhHHHHHHHHHhhCCCCCCceEEEEEecCCCeEEEEEeCCCHHHHHHHHhCCCCCCCCCCCe--eee
Q 031693 30 PPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPSVTWYLKKAAGIESGSSRPGHV--TAS 107 (155)
Q Consensus 30 PplGP~LG~~Gin~~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf~~~v~~Ppts~likka~g~~~gs~~p~~~--~vG 107 (155)
+||||+|||+|||+|+|||+||++|++|+ |++|||+|+|| ||||+|++ .||+|+||+|++|++.++.+++++ ++|
T Consensus 1 ~~lGPaLG~~GvNi~~fck~fN~~T~~~~-G~~vpV~Itv~-drsf~~~v-~Pp~s~ll~k~ag~~~~~~~~~~~~~~vG 77 (140)
T PTZ00105 1 SSLAPKVGPLGLSPKKVGDDIAKATKDWK-GLKVTVKLTVQ-NRQATVEV-VPTASSLLIKALKEPPRDRKKVKNIKHSG 77 (140)
T ss_pred CCCccccccCCCCHHHHHHHHHHHHhhcC-CCeEEEEEEEE-CCEEEEEE-CCCHHHHHHHHhCCCCCCCCCCCcceeee
Confidence 68999999999999999999999999985 99999999999 89999999 599999999999988888888876 999
Q ss_pred cccHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHhhhhcCeEEecc
Q 031693 108 TVTLKHIYEIAKVKQSDPYCQYMPLESICKSIIGTAATMGIKVVKE 153 (155)
Q Consensus 108 ~It~~~v~eIAk~K~~d~~~~~~~l~~~~k~VlGTa~SmGi~V~~~ 153 (155)
+||++||||||+.|++|++ +.+|+++||+|+||||||||+|+++
T Consensus 78 ~it~~qv~eIAk~K~~dl~--~~~l~~a~k~V~GTarSmGi~V~gk 121 (140)
T PTZ00105 78 NLTFDQVIKIARTMRPKSM--AKTFKGTVKEVLGTCVSIGCTVDGE 121 (140)
T ss_pred EeeHHHHHHHHHHHHhhhC--CCcHHHHHHHHHhhheeeeEEEECC
Confidence 9999999999999999965 8899999999999999999999985
No 13
>KOG0886 consensus 40S ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=8.7e-31 Score=202.06 Aligned_cols=136 Identities=21% Similarity=0.291 Sum_probs=129.0
Q ss_pred eeeEEEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhCCCCCCceEEEEEecCCCeEEEEEeCCCHHHHHHHHh
Q 031693 13 VAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPSVTWYLKKAA 92 (155)
Q Consensus 13 ~~~~ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf~~~v~~Ppts~likka~ 92 (155)
-..+|+|+|.||+...+..|+|.+||+|+.+..+.+++-++|++|+ |..+.|.++|+ ||...+++ .|++|.||+|+|
T Consensus 11 eiK~vylrc~GgEVgatsaLApKIgPLGLSpKkvGedIaKaT~dwK-gl~vtvkLtIq-nR~A~i~V-vpSasaLiIkaL 87 (167)
T KOG0886|consen 11 EIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGEDIAKATGDWK-GLRVTVKLTIQ-NRQAQIEV-VPSASALIIKAL 87 (167)
T ss_pred ceEEEEEEeecCccccccccccccccccCCccccchHHHHhhcccc-cceEEEEEEec-CcccceEE-cccHHHHHHHHh
Confidence 3578999999999999999999999999999999999999999998 99999999998 99999999 899999999999
Q ss_pred CCCCCCCCC--CCeeeecccHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHhhhhcCeEEecc
Q 031693 93 GIESGSSRP--GHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESICKSIIGTAATMGIKVVKE 153 (155)
Q Consensus 93 g~~~gs~~p--~~~~vG~It~~~v~eIAk~K~~d~~~~~~~l~~~~k~VlGTa~SmGi~V~~~ 153 (155)
++++++++. +..|.|+|+|+++.+||+++.+.++ ++.|.+++++|+|||+|+||+|++.
T Consensus 88 KEPpRDRKk~knikh~Gni~~deiv~iar~mr~rS~--a~~l~gt~keilgt~~svgc~vDgk 148 (167)
T KOG0886|consen 88 KEPPRDRKKQKNIKHSGNITFDEIVEIARIMRPRSL--ARELSGTVKEILGTAQSVGCTVDGK 148 (167)
T ss_pred cCCcchhhhhccccccCcccHHHHHHHHHHhhhHhh--hhhhhhhHHHHhchhhhcccccCCC
Confidence 999998765 4589999999999999999999887 7899999999999999999999975
No 14
>PF00298 Ribosomal_L11: Ribosomal protein L11, RNA binding domain; InterPro: IPR020783 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 L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown [] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 1VQN_I 2OTJ_I 3G6E_I 3CME_I 1YIJ_I 1YI2_I 3G4S_I 3CMA_I 3I55_I 1VQ7_I ....
Probab=99.96 E-value=5.4e-30 Score=176.42 Aligned_cols=69 Identities=61% Similarity=0.900 Sum_probs=67.0
Q ss_pred eCCCHHHHHHHHhCCCCCCCCCCCeeeecccHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHhhhhcCeEE
Q 031693 80 KSPSVTWYLKKAAGIESGSSRPGHVTASTVTLKHIYEIAKVKQSDPYCQYMPLESICKSIIGTAATMGIKV 150 (155)
Q Consensus 80 ~~Ppts~likka~g~~~gs~~p~~~~vG~It~~~v~eIAk~K~~d~~~~~~~l~~~~k~VlGTa~SmGi~V 150 (155)
++||+||||+|++|+++||++|+++.+|+||++||||||++|++|++ +.+|+++||+|+||||||||+|
T Consensus 1 K~Pp~s~llkkaagi~kGs~~p~~~~vG~it~~~i~eIAk~K~~d~~--~~~l~~~~k~v~Gta~SmGi~V 69 (69)
T PF00298_consen 1 KTPPTSWLLKKAAGIKKGSSKPGKEKVGTITLKQIYEIAKIKQKDLN--AKSLESAVKSVIGTARSMGIKV 69 (69)
T ss_dssp SSSTHHHHHHHHHTTSSSSSSTTTSSSEEEEHHHHHHHHHHHTTTSS--SSSHHHHHHHHHHHHHTTTEEE
T ss_pred CCCChHHHHHHHhCCCCCCCCCCCceeeeecHHHHHHHHHHhhcccc--cCCHHHHHHHHHHHHhcCceEC
Confidence 58999999999999999999999999999999999999999999975 8899999999999999999987
No 15
>PF03946 Ribosomal_L11_N: Ribosomal protein L11, N-terminal domain; InterPro: IPR020784 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 L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown [] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.; PDB: 2ZJQ_F 2ZJP_F 3CF5_F 2WRJ_K 2WH4_K 2WRL_K 3FIN_L 2X9U_K 3I8I_L 2XUX_K ....
Probab=99.96 E-value=8.6e-30 Score=171.19 Aligned_cols=60 Identities=55% Similarity=1.053 Sum_probs=58.0
Q ss_pred EEEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhCCCCCCceEEEEEecCCCeE
Q 031693 16 TIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTF 75 (155)
Q Consensus 16 ~ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf 75 (155)
+|||+|+||+|+|+|||||+|||+|||+|+||+|||++|++|++|++|||+|+||+||||
T Consensus 1 ~i~l~v~aG~A~p~pplgp~LG~~Gin~~~f~k~fN~~T~~~k~G~~v~V~i~v~~d~sf 60 (60)
T PF03946_consen 1 VIKLRVPAGKATPAPPLGPALGPLGINIKKFCKDFNKATKDYKPGIPVPVKITVYNDKSF 60 (60)
T ss_dssp EEEEEEETTSSSSTTTSTHHHHTTTS-HHHHHHHHHHHTTTCTTSSEEEEEEEEETTSEE
T ss_pred CEEEEEecCcccCCCCcCcccccCCCCHHHHHHHHHHHHhcccCCCEEEEEEEEeCCCCC
Confidence 589999999999999999999999999999999999999999999999999999999998
No 16
>COG0051 RpsJ Ribosomal protein S10 [Translation, ribosomal structure and biogenesis]
Probab=41.74 E-value=21 Score=26.49 Aligned_cols=27 Identities=26% Similarity=0.429 Sum_probs=24.1
Q ss_pred CCCCCHHHHHHHHHHhhhhcCeEEecc
Q 031693 127 CQYMPLESICKSIIGTAATMGIKVVKE 153 (155)
Q Consensus 127 ~~~~~l~~~~k~VlGTa~SmGi~V~~~ 153 (155)
++...|+..|+.|.-||+.+|+.|.|-
T Consensus 13 ~d~~~LD~~~~~Ive~akrtg~~v~GP 39 (104)
T COG0051 13 FDHRLLDQVCREIVETAKRTGADVKGP 39 (104)
T ss_pred CCHHHHHHHHHHHHHHHHHhCCeeeCC
Confidence 447899999999999999999999874
No 17
>COG4953 PbpC Membrane carboxypeptidase/penicillin-binding protein PbpC [Cell envelope biogenesis, outer membrane]
Probab=41.08 E-value=33 Score=33.26 Aligned_cols=76 Identities=21% Similarity=0.270 Sum_probs=63.0
Q ss_pred EEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhCCCCCCceEEEEEecCCCeEEEEEeCCCHHHHHHHHhCCCC
Q 031693 17 IRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPSVTWYLKKAAGIES 96 (155)
Q Consensus 17 ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf~~~v~~Ppts~likka~g~~~ 96 (155)
+.|..+.+. +|=|+=.||-.|++..|..+-|-.-..+ |.+-|.+-+..+|+.-+-.+-+|.++|++...+.-..
T Consensus 417 ~~L~~P~~~---~~GLsLiLGg~gi~L~dLa~lYa~lAn~---G~~~~L~~~~~~~~~~~~~l~s~~Aaw~i~dIl~~~~ 490 (733)
T COG4953 417 VHLYLPEGA---APGLSLILGGAGITLEDLAQLYAALANQ---GKAGPLRDTLDDDPLTERTLLSPGAAWQILDILSDVA 490 (733)
T ss_pred CCCCCCCcc---CCCeeEEecCCcccHHHHHHHHHHHhcC---CceecccccCCCCCCCCccccCcchHHHHHHHHhccC
Confidence 477778777 4568889999999999999999877754 9999999999878777777779999999999887554
Q ss_pred CC
Q 031693 97 GS 98 (155)
Q Consensus 97 gs 98 (155)
+.
T Consensus 491 ~P 492 (733)
T COG4953 491 RP 492 (733)
T ss_pred CC
Confidence 44
No 18
>cd02742 GH20_hexosaminidase Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides. These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself.
Probab=40.50 E-value=85 Score=26.55 Aligned_cols=67 Identities=13% Similarity=0.082 Sum_probs=37.3
Q ss_pred hhHHHHHHHHHhhCCCCCCceEEEEEecCCCeEEEEEeCCCHHHHHHHHhCCCCCCCCCCCeeeecccHHHHHHHHHh
Q 031693 43 LMAFCKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPSVTWYLKKAAGIESGSSRPGHVTASTVTLKHIYEIAKV 120 (155)
Q Consensus 43 ~~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf~~~v~~Ppts~likka~g~~~gs~~p~~~~vG~It~~~v~eIAk~ 120 (155)
.++..|++=+.-+.+| --. ..+.+.+|-+|.++++.=|- |- ++|+........|..|.+|+.||.+.
T Consensus 14 ~~~~lk~~id~ma~~K-~N~--lhlHl~D~~~~~le~~~~p~--l~------~~g~~~~~~~~~~~yT~~di~elv~y 80 (303)
T cd02742 14 SVESIKRTIDVLARYK-INT--FHWHLTDDQAWRIESKKFPE--LA------EKGGQINPRSPGGFYTYAQLKDIIEY 80 (303)
T ss_pred CHHHHHHHHHHHHHhC-CcE--EEEeeecCCCceEeeCccch--hh------hhcccccCCCCCCeECHHHHHHHHHH
Confidence 4566666666666555 223 34566688999998864222 11 11211111122467888888888753
No 19
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=40.10 E-value=21 Score=24.21 Aligned_cols=56 Identities=20% Similarity=0.367 Sum_probs=35.4
Q ss_pred EEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhCCCCCCceEEEEEecCCCeEEEEEeCCCHHHHHHHHhC
Q 031693 17 IRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPSVTWYLKKAAG 93 (155)
Q Consensus 17 ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf~~~v~~Ppts~likka~g 93 (155)
.++-|..+.. ---|+|-.+|+.|..+..+.+++| | +..++...++....|+..++-
T Consensus 5 ~kvaV~~~~~-~~d~vG~~iG~~G~rik~i~~~L~--------g------------ekIdvV~~s~d~~~fI~nal~ 60 (69)
T PF13184_consen 5 TKVAVKSGDP-NIDPVGACIGKKGSRIKAISEELN--------G------------EKIDVVEYSDDPKEFIKNALS 60 (69)
T ss_dssp EEEEEEESST-TS-HHHHHH-CCCCCHHHHHHHTT--------T-------------EEEEEE--SSHHHHHHHHTT
T ss_pred EEEEEEcCCC-CcCcceecCccccHHHHHHHHHhC--------C------------CeEEEEEcCCCHHHHHHHhCC
Confidence 4556666663 235689999999999999999995 2 222333345667777777764
No 20
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. 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=36.55 E-value=36 Score=25.48 Aligned_cols=35 Identities=23% Similarity=0.198 Sum_probs=25.8
Q ss_pred EEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHH
Q 031693 19 LTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNAR 53 (155)
Q Consensus 19 l~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~ 53 (155)
+.||.=+-.--.-+|-.|||.|-++.+.+++++.+
T Consensus 4 i~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~k 38 (120)
T cd02395 4 VYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAK 38 (120)
T ss_pred EEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCE
Confidence 44444444344568999999999999999998644
No 21
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=34.66 E-value=39 Score=27.98 Aligned_cols=31 Identities=19% Similarity=0.159 Sum_probs=17.6
Q ss_pred CCCCcccCcCCCChhH----HHHHHHHHhhCCCCC
Q 031693 30 PPVGPALGQYRLNLMA----FCKDFNARTQKYKPE 60 (155)
Q Consensus 30 PplGP~LG~~Gin~~~----fck~fN~~T~~~~~g 60 (155)
++||+.|||+|+=+.- ++.++-+.-.+++.|
T Consensus 124 ~~Lg~iLGPrGlMP~pk~gTv~~di~~~I~~~k~g 158 (230)
T PRK05424 124 GKLGRILGPRGLMPNPKTGTVTMDVAKAVKEAKAG 158 (230)
T ss_pred HHhccccccccCCCCCCCCCcchhHHHHHHHHhcC
Confidence 3499999999952221 334444444444434
No 22
>PF05164 ZapA: Cell division protein ZapA; InterPro: IPR007838 This entry a structural domain found in the cell division protein ZapA, as well as in related proteins. This domain has a core structure consisting of two layers alpha/beta, and has a long C-terminal helix that forms dimeric parallel and tetrameric antiparallel coiled coils []. ZapA interacts with FtsZ, where FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. ZapA drives the polymerisation and filament bundling of FtsZ, thereby contributing to the spatio-temporal tuning of the Z-ring.; PDB: 1T3U_B 1W2E_B 3HNW_A.
Probab=32.92 E-value=63 Score=21.75 Aligned_cols=27 Identities=26% Similarity=0.390 Sum_probs=20.3
Q ss_pred EEEEecCCCeEEEEEeCCCHHHHHHHHhC
Q 031693 65 VTITAFKDNTFEFTVKSPSVTWYLKKAAG 93 (155)
Q Consensus 65 V~i~v~~drsf~~~v~~Ppts~likka~g 93 (155)
|+|+|+ +++|.|.+ ++.--..+.+++.
T Consensus 2 V~v~I~-G~~y~i~~-~~~~ee~l~~~a~ 28 (89)
T PF05164_consen 2 VKVTIL-GREYRIKC-PDEDEEYLRKAAE 28 (89)
T ss_dssp EEEEET-TEEEEECE-TGCGHHHHHHHHH
T ss_pred eEEEEC-CEEEEeec-CCCCHHHHHHHHH
Confidence 788888 89999987 5666666666654
No 23
>cd06562 GH20_HexA_HexB-like Beta-N-acetylhexosaminidases catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides. The hexA and hexB genes encode the alpha- and beta-subunits of the two major beta-N-acetylhexosaminidase isoenzymes, N-acetyl-beta-D-hexosaminidase A (HexA) and beta-N-acetylhexosaminidase B (HexB). Both the alpha and the beta catalytic subunits have a TIM-barrel fold and belong to the glycosyl hydrolase family 20 (GH20). The HexA enzyme is a heterodimer containing one alpha and one beta subunit while the HexB enzyme is a homodimer containing two beta-subunits. Hexosaminidase mutations cause an inability to properly hydrolyze certain sphingolipids which accumulate in lysosomes within the brain, resulting in the lipid storage disorders Tay-Sachs and Sandhoff. Mutations in the alpha subunit cause in a deficiency in the HexA enzyme and result in
Probab=32.14 E-value=2.9e+02 Score=23.91 Aligned_cols=61 Identities=15% Similarity=0.103 Sum_probs=36.8
Q ss_pred hHHHHHHHHHhhCCCCCCceEEEEEecCCCeEEEEEeCCCHHHHHHHHhCCCCCCCCCCCeeeecccHHHHHHHHH
Q 031693 44 MAFCKDFNARTQKYKPETPMSVTITAFKDNTFEFTVKSPSVTWYLKKAAGIESGSSRPGHVTASTVTLKHIYEIAK 119 (155)
Q Consensus 44 ~~fck~fN~~T~~~~~g~~vpV~i~v~~drsf~~~v~~Ppts~likka~g~~~gs~~p~~~~vG~It~~~v~eIAk 119 (155)
++..|++=+.-+.+|-. . ..+.+.+|-+|.++++.=|- |- +.|+..+ .|-.|.+++.||-+
T Consensus 17 ~~~ik~~Id~ma~~KlN-~--lh~HltDd~~~rle~~~~P~--Lt------~~ga~~~----~~~YT~~di~eiv~ 77 (348)
T cd06562 17 VDSIKRTIDAMAYNKLN-V--LHWHITDSQSFPLESPSYPE--LS------KKGAYSP----SEVYTPEDVKEIVE 77 (348)
T ss_pred HHHHHHHHHHHHHhCCc-E--EEEeEEcCCCceEeeCCCch--hh------hccCcCC----CceECHHHHHHHHH
Confidence 56677777777766522 2 45666688999999864442 11 2233222 36677777777764
No 24
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=28.25 E-value=1e+02 Score=26.48 Aligned_cols=98 Identities=21% Similarity=0.244 Sum_probs=62.0
Q ss_pred cceeeEEEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHH---------------h--------hCCCCCCceEEEE
Q 031693 11 RPVAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNAR---------------T--------QKYKPETPMSVTI 67 (155)
Q Consensus 11 k~~~~~ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~---------------T--------~~~~~g~~vpV~i 67 (155)
+.+.-..|+.|+-=+..---.||-.|||+|-.+.+++++.--+ - .|+ ..++.|.|
T Consensus 88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL--~epLHVlI 165 (259)
T KOG1588|consen 88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHL--NEPLHVLI 165 (259)
T ss_pred CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHh--CCCcEEEE
Confidence 5566677888887776556679999999999999999875211 0 122 25888888
Q ss_pred EecCCCeEEEEEeCCCHHHH--HHHHhCCCCCCCCCCCeeeecccHHHHHHHHHhcc
Q 031693 68 TAFKDNTFEFTVKSPSVTWY--LKKAAGIESGSSRPGHVTASTVTLKHIYEIAKVKQ 122 (155)
Q Consensus 68 ~v~~drsf~~~v~~Ppts~l--ikka~g~~~gs~~p~~~~vG~It~~~v~eIAk~K~ 122 (155)
++. .|+.-.. |..|+-+-+.=-.|-++ +.+..+|+.|.|.+--
T Consensus 166 e~~----------~p~~ea~~rl~~AleeI~klL~P~~e--~~dk~~QL~ELa~lng 210 (259)
T KOG1588|consen 166 ETE----------APPAEAYARLAYALEEIKKLLVPDHE--DEDKREQLRELAILNG 210 (259)
T ss_pred EEe----------CCHHHHHHHHHHHHHHHHHhcCCCCC--CchHHHHHHHHhhcCC
Confidence 875 2333222 22333322222235433 5568999999997543
No 25
>KOG1196 consensus Predicted NAD-dependent oxidoreductase [General function prediction only]
Probab=27.56 E-value=28 Score=30.84 Aligned_cols=42 Identities=24% Similarity=0.329 Sum_probs=31.7
Q ss_pred HHHHHHHHHhcccCCCCCCCCHHHHHHHHHHh-hhhcCeEEecc
Q 031693 111 LKHIYEIAKVKQSDPYCQYMPLESICKSIIGT-AATMGIKVVKE 153 (155)
Q Consensus 111 ~~~v~eIAk~K~~d~~~~~~~l~~~~k~VlGT-a~SmGi~V~~~ 153 (155)
.-=++||+..|..+..+- .--.+||-+++|. |+-|||.|++-
T Consensus 142 y~Gf~ei~~pk~geTv~V-SaAsGAvGql~GQ~Ak~~Gc~VVGs 184 (343)
T KOG1196|consen 142 YAGFYEICSPKKGETVFV-SAASGAVGQLVGQFAKLMGCYVVGS 184 (343)
T ss_pred HHHHHHhcCCCCCCEEEE-eeccchhHHHHHHHHHhcCCEEEEe
Confidence 345779998888765432 3346899999996 89999999974
No 26
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=26.74 E-value=48 Score=27.52 Aligned_cols=12 Identities=33% Similarity=0.457 Sum_probs=10.1
Q ss_pred CCCcccCcCCCC
Q 031693 31 PVGPALGQYRLN 42 (155)
Q Consensus 31 plGP~LG~~Gin 42 (155)
+||+.|||+|+=
T Consensus 125 kLgriLGprGlM 136 (229)
T CHL00129 125 KLGRVLGPRGLM 136 (229)
T ss_pred HhcCcccccCCC
Confidence 499999999863
No 27
>TIGR01046 S10_Arc_S20_Euk ribosomal protein S10(archaeal)/S20(eukaryotic). its equivalents in eukaryotes.
Probab=24.91 E-value=57 Score=23.67 Aligned_cols=26 Identities=23% Similarity=0.437 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHHHHhhhhcCeEEecc
Q 031693 128 QYMPLESICKSIIGTAATMGIKVVKE 153 (155)
Q Consensus 128 ~~~~l~~~~k~VlGTa~SmGi~V~~~ 153 (155)
+...|+.+|+.++-+|+.-|+.+.|-
T Consensus 11 d~~~Ld~~~~~I~~~ak~~g~~~~GP 36 (99)
T TIGR01046 11 NVRSLEKVCAQIKRIAEKTGVRMSGP 36 (99)
T ss_pred CHHHHHHHHHHHHHHHHHcCCEEECC
Confidence 46789999999999999999999874
No 28
>CHL00135 rps10 ribosomal protein S10; Validated
Probab=23.16 E-value=63 Score=23.58 Aligned_cols=26 Identities=35% Similarity=0.376 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHHHHhhhhcCeEEecc
Q 031693 128 QYMPLESICKSIIGTAATMGIKVVKE 153 (155)
Q Consensus 128 ~~~~l~~~~k~VlGTa~SmGi~V~~~ 153 (155)
+...|+.+|+.+.-+|+..|+.+.|-
T Consensus 17 d~~~L~~~~~~I~~~~k~~~~~~~Gp 42 (101)
T CHL00135 17 NHELLNSSCKKIIDTASRTNATAVGP 42 (101)
T ss_pred CHHHHHHHHHHHHHHHHHcCCeEeCC
Confidence 36799999999999999999998874
No 29
>PF03990 DUF348: Domain of unknown function (DUF348) ; InterPro: IPR007137 This domain normally occurs as tandem repeats; however it is found as a single copy in the Saccharomyces cerevisiae (Baker's yeast) DNA-binding nuclear protein YCR593 (P25357 from SWISSPROT).
Probab=22.27 E-value=1.6e+02 Score=17.68 Aligned_cols=34 Identities=26% Similarity=0.223 Sum_probs=25.1
Q ss_pred EEEEEecCCCeEEEEEeCCCHHHHHHHHhCCCCCCC
Q 031693 64 SVTITAFKDNTFEFTVKSPSVTWYLKKAAGIESGSS 99 (155)
Q Consensus 64 pV~i~v~~drsf~~~v~~Ppts~likka~g~~~gs~ 99 (155)
||.|++. .++..+.....++..+| +.+|+.-+..
T Consensus 1 ~Vtv~~d-G~~~~v~T~a~tV~~~L-~~~gI~l~~~ 34 (43)
T PF03990_consen 1 PVTVTVD-GKEKTVYTTASTVGDAL-KELGITLGEE 34 (43)
T ss_pred CEEEEEC-CEEEEEEeCCCCHHHHH-HhCCCCCCCC
Confidence 4677774 78889988777777765 5788876654
No 30
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=21.59 E-value=1.7e+02 Score=22.90 Aligned_cols=36 Identities=8% Similarity=0.181 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHhCCCCCCCCCCCeeeecccHHHHHHHHHhcc
Q 031693 81 SPSVTWYLKKAAGIESGSSRPGHVTASTVTLKHIYEIAKVKQ 122 (155)
Q Consensus 81 ~Ppts~likka~g~~~gs~~p~~~~vG~It~~~v~eIAk~K~ 122 (155)
-+..|..|.+.+|+.+.. .+|.+|-+|+.+|...-.
T Consensus 34 G~~~a~~Ic~~lgi~~~~------~~~~Lt~~qi~~l~~~i~ 69 (149)
T PRK04053 34 GRRTARAIARKLGLDPNA------KLGYLSDEEIEKIEEALE 69 (149)
T ss_pred cHHHHHHHHHHcCcCCCC------ccCcCCHHHHHHHHHHHH
Confidence 478899999999987543 479999999999998874
No 31
>TIGR01049 rpsJ_bact ribosomal protein S10, bacterial/organelle. This model describes bacterial 30S ribosomal protein S10. In species that have a transcription antitermination complex, or N utilization substance, with NusA, NusB, NusG, and NusE, this ribosomal protein is responsible for NusE activity. Included in the family are one member each from Saccharomyces cerevisiae and Schizosaccharomyces pombe. These proteins lack an N-terminal mitochondrial transit peptide but contain additional sequence C-terminal to the ribosomal S10 protein region.
Probab=20.95 E-value=58 Score=23.38 Aligned_cols=25 Identities=28% Similarity=0.256 Sum_probs=22.4
Q ss_pred CCCHHHHHHHHHHhhhhcCeEEecc
Q 031693 129 YMPLESICKSIIGTAATMGIKVVKE 153 (155)
Q Consensus 129 ~~~l~~~~k~VlGTa~SmGi~V~~~ 153 (155)
...|+..|+.+...|+..|+.+.|-
T Consensus 12 ~~~L~~~~~~i~~~a~~~gi~~~gp 36 (99)
T TIGR01049 12 HRLLDQSTKKIVETAKRTGAQVKGP 36 (99)
T ss_pred HHHHHHHHHHHHHHHHHcCCceecc
Confidence 5689999999999999999998764
No 32
>PTZ00039 40S ribosomal protein S20; Provisional
Probab=20.83 E-value=75 Score=23.83 Aligned_cols=33 Identities=21% Similarity=0.394 Sum_probs=26.4
Q ss_pred HhcccCCCCCCCCHHHHHHHHHHhhhhcCeEEecc
Q 031693 119 KVKQSDPYCQYMPLESICKSIIGTAATMGIKVVKE 153 (155)
Q Consensus 119 k~K~~d~~~~~~~l~~~~k~VlGTa~SmGi~V~~~ 153 (155)
++++.. ++...|+.+|+.++-+|+..|+.|.|-
T Consensus 20 rI~L~S--~d~~~Ld~~~~~Ii~~ak~~g~~v~GP 52 (115)
T PTZ00039 20 RITLTS--KNLKSIEKVCADIITGAKEKNLKVTGP 52 (115)
T ss_pred EEEEEE--CCHHHHHHHHHHHHHHHHHcCCEeECC
Confidence 344443 346799999999999999999999874
No 33
>PRK12271 rps10p 30S ribosomal protein S10P; Reviewed
Probab=20.80 E-value=76 Score=23.20 Aligned_cols=26 Identities=19% Similarity=0.369 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHHHHhhhhcCeEEecc
Q 031693 128 QYMPLESICKSIIGTAATMGIKVVKE 153 (155)
Q Consensus 128 ~~~~l~~~~k~VlGTa~SmGi~V~~~ 153 (155)
+...|+.+|+.++-+|+.-|+.+.|-
T Consensus 12 d~~~Ld~~~~~I~~~~k~~g~~~~GP 37 (102)
T PRK12271 12 NPEDLDEVCDQIKEIAEKTGVDMSGP 37 (102)
T ss_pred CHHHHHHHHHHHHHHHHHcCCeEECC
Confidence 46789999999999999999999874
No 34
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=20.03 E-value=66 Score=23.51 Aligned_cols=42 Identities=21% Similarity=0.230 Sum_probs=27.1
Q ss_pred cHHHHHHHHHhcccCCCCCC--CCHHHHHHHHHHhhhhcCeEEe
Q 031693 110 TLKHIYEIAKVKQSDPYCQY--MPLESICKSIIGTAATMGIKVV 151 (155)
Q Consensus 110 t~~~v~eIAk~K~~d~~~~~--~~l~~~~k~VlGTa~SmGi~V~ 151 (155)
+++++.++++...-|.-.-+ .+-+..++.++.-|+++||+|-
T Consensus 129 ~~~~l~~~~~~~~id~v~ial~~~~~~~i~~ii~~~~~~~v~v~ 172 (175)
T PF13727_consen 129 DLDDLPELVREHDIDEVIIALPWSEEEQIKRIIEELENHGVRVR 172 (175)
T ss_dssp -GGGHHHHHHHHT--EEEE--TTS-HHHHHHHHHHHHTTT-EEE
T ss_pred CHHHHHHHHHhCCCCEEEEEcCccCHHHHHHHHHHHHhCCCEEE
Confidence 35788888877655542222 2346788999999999999873
No 35
>PF03487 IL13: Interleukin-13; InterPro: IPR020470 Interleukin-13 (IL-13) is a pleiotropic cytokine which may be important in the regulation of the inflammatory and immune responses []. It inhibits inflammatory cytokine production and synergises with IL-2 in regulating interferon-gamma synthesis. The sequences of IL-4 and IL-13 are distantly related.; PDB: 3G6D_A 3L5W_J 3BPO_A 1GA3_A 1IK0_A 3L5X_A 3L5Y_A 1IJZ_A 3LB6_B.
Probab=20.00 E-value=52 Score=20.61 Aligned_cols=38 Identities=29% Similarity=0.378 Sum_probs=11.9
Q ss_pred eeeEEEEEeeccCCCCCCCCCcccCcCCCChhHHHHHHHHHhhC
Q 031693 13 VAATIRLTVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQK 56 (155)
Q Consensus 13 ~~~~ikl~v~aG~A~p~PplGP~LG~~Gin~~~fck~fN~~T~~ 56 (155)
+..+|-|.|.||-|+|+| +.+. -...|..+|.-+-|++
T Consensus 5 lt~vialtClggLasPgP-vp~~-----~alkELIeELvNITqn 42 (43)
T PF03487_consen 5 LTVVIALTCLGGLASPGP-VPSS-----TALKELIEELVNITQN 42 (43)
T ss_dssp -------------------S-HH-----HHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHhcccCCCCC-CCch-----HHHHHHHHHHHhhccC
Confidence 345678999999999976 2221 1467888888777764
Done!