Query 031095
Match_columns 166
No_of_seqs 112 out of 1060
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 09:09:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031095.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031095hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03072 60S ribosomal protein 100.0 7.1E-69 1.5E-73 428.8 18.3 165 1-166 1-166 (166)
2 PRK01143 rpl11p 50S ribosomal 100.0 2.6E-63 5.6E-68 396.0 15.8 149 11-162 3-154 (163)
3 PTZ00105 60S ribosomal protein 100.0 5E-60 1.1E-64 369.1 15.3 140 26-166 1-140 (140)
4 COG0080 RplK Ribosomal protein 100.0 2.2E-59 4.8E-64 363.9 14.8 137 8-147 3-141 (141)
5 TIGR01632 L11_bact 50S ribosom 100.0 4.1E-59 8.9E-64 364.0 15.4 136 8-146 2-140 (140)
6 PRK00140 rplK 50S ribosomal pr 100.0 4E-58 8.6E-63 358.8 15.7 136 8-146 4-141 (141)
7 CHL00127 rpl11 ribosomal prote 100.0 1.8E-57 3.9E-62 354.8 15.0 135 8-145 4-140 (140)
8 smart00649 RL11 Ribosomal prot 100.0 4.1E-57 8.9E-62 349.6 13.7 130 13-145 1-132 (132)
9 cd00349 Ribosomal_L11 Ribosoma 100.0 4.5E-56 9.8E-61 343.4 13.4 129 13-144 1-131 (131)
10 PRK14539 50S ribosomal protein 100.0 3.3E-54 7.1E-59 351.1 15.9 134 8-148 5-140 (196)
11 PTZ00321 ribosomal protein L11 100.0 1.7E-53 3.8E-58 365.4 16.5 142 6-148 46-195 (342)
12 KOG3257 Mitochondrial/chloropl 100.0 5.3E-50 1.1E-54 316.1 11.4 135 9-146 18-157 (168)
13 KOG0886 40S ribosomal protein 100.0 3.1E-46 6.7E-51 291.2 13.0 165 1-166 1-167 (167)
14 PF03946 Ribosomal_L11_N: Ribo 99.9 5.5E-28 1.2E-32 164.4 6.4 58 12-70 1-60 (60)
15 PF00298 Ribosomal_L11: Riboso 99.9 1.2E-27 2.5E-32 166.9 6.7 68 75-144 2-69 (69)
16 PF05164 ZapA: Cell division p 47.1 21 0.00045 24.5 2.7 28 60-87 1-28 (89)
17 COG1437 CyaB Adenylate cyclase 45.3 6.5 0.00014 32.2 -0.2 89 70-158 81-176 (178)
18 COG0051 RpsJ Ribosomal protein 41.1 5.3 0.00012 30.1 -1.2 32 115-146 7-38 (104)
19 COG5106 RPF2 Uncharacterized c 34.2 55 0.0012 28.6 3.7 44 55-98 191-258 (316)
20 PF13817 DDE_Tnp_IS66_C: IS66 30.6 24 0.00053 21.8 0.8 20 132-156 1-20 (39)
21 PF12475 Amdo_NSP: Amdovirus n 26.4 36 0.00079 22.3 1.0 20 67-86 3-23 (48)
22 cd02395 SF1_like-KH Splicing f 26.1 44 0.00094 25.4 1.6 35 15-49 4-38 (120)
23 KOG1196 Predicted NAD-dependen 25.8 19 0.0004 32.4 -0.6 39 108-146 143-183 (343)
24 KOG1088 Uncharacterized conser 25.3 30 0.00066 26.8 0.6 11 155-165 93-103 (124)
25 KOG0455 Homoserine dehydrogena 24.4 77 0.0017 28.2 3.0 42 102-146 192-240 (364)
26 PF03978 Borrelia_REV: Borreli 24.2 59 0.0013 26.3 2.1 34 112-145 94-127 (160)
27 PF10941 DUF2620: Protein of u 22.8 69 0.0015 24.7 2.1 62 100-161 4-96 (117)
28 PF13184 KH_5: NusA-like KH do 22.1 46 0.00099 22.8 0.9 34 13-47 5-38 (69)
29 TIGR01046 S10_Arc_S20_Euk ribo 21.8 20 0.00043 26.5 -1.0 32 115-146 4-35 (99)
30 PF03990 DUF348: Domain of unk 21.7 1.3E+02 0.0028 18.3 2.9 31 60-91 1-32 (43)
31 PF04316 FlgM: Anti-sigma-28 f 21.7 53 0.0012 21.4 1.2 17 148-164 29-45 (57)
32 KOG1588 RNA-binding protein Sa 21.3 1.5E+02 0.0033 25.7 4.1 97 9-118 90-210 (259)
33 PF13727 CoA_binding_3: CoA-bi 20.7 62 0.0014 24.0 1.5 39 106-144 129-171 (175)
34 CHL00137 rps13 ribosomal prote 20.2 1.2E+02 0.0025 23.2 2.9 48 75-130 26-74 (122)
35 PHA02135 hypothetical protein 20.1 42 0.00091 25.5 0.4 18 41-59 32-49 (122)
No 1
>PLN03072 60S ribosomal protein L12; Provisional
Probab=100.00 E-value=7.1e-69 Score=428.80 Aligned_cols=165 Identities=93% Similarity=1.332 Sum_probs=160.0
Q ss_pred CCCCCCCCceEEEEEEEeccccCCCCCCccccCCCCCChhhHHHHHHHHhhcc-CCCceeEEEEEEecCceEEEEeCChH
Q 031095 1 MPPKFDPSQVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKD-WKGLRVTVKLTVQNRQAKVAVVPSAA 79 (166)
Q Consensus 1 m~~k~~~~~~~~ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~~T~~~-~~g~~ipV~Itv~drsf~~~v~Ppts 79 (166)
||||+|++...+|+|+|+||+|+|+|||||+|||+|||+|+||++||++| ++ |+|++|||+|+||+|||+|+++||+|
T Consensus 1 m~~~~~~~~~~~i~l~v~aG~A~P~PplGPaLG~~GvNi~~f~k~fN~~T-~~~~~G~~VpV~Itv~~rsf~~~v~Pp~s 79 (166)
T PLN03072 1 MPPKLDPSQVVEVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKET-AKDWKGLRVTVKLTVQNRQAKVSVVPSAA 79 (166)
T ss_pred CCCCCCCCccEEEEEEEEcCccCCCCCCccccccCCCCHHHHHHHHHHHh-hhhcCCCeEEEEEEEECCeEEEEeCCCHH
Confidence 99999999999999999999999999999999999999999999999999 75 99999999999999999998899999
Q ss_pred HHHHHHhCCCCcCccCccCcceeeeecHHHHHHHHHHhcccCCCcChhhhhhhhhhcccceeeEecCCChHhHHHhhhCc
Q 031095 80 ALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKEILGTCVSVGCTVDGKDPKDLQQEINDG 159 (166)
Q Consensus 80 ~likka~g~~~~~~k~~~~~~~~G~it~~~v~eIAk~K~~d~~~~~l~~~~k~VlGTa~SmGi~V~~~~P~e~~~~i~~g 159 (166)
+||+|+||+++|+++++++.+++|+||++||||||+.|++|+++++|+++||+|+||||||||+|+++||+|++++||+|
T Consensus 80 ~LLkKa~g~~kgs~~~~~~~~~vG~it~~qv~eIA~~K~~dl~a~~l~~avk~VlGTarSmGi~V~gk~pkev~~~i~~G 159 (166)
T PLN03072 80 ALVIKALKEPERDRKKVKNIKHNGNISLDDVIEIAKIMRPRSMAKELAGTVKEILGTCVSVGCTVDGKDPKDLQQEIDDG 159 (166)
T ss_pred HHHHHHhCCCCCCCccCCCCeeeeeecHHHHHHHHHHHHHHhCcccHHHHHHHhHheeeeCeEEEeCCCHHHHHHHHhCC
Confidence 99999999999999865656799999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeccCC
Q 031095 160 DVEIPLD 166 (166)
Q Consensus 160 ~~~~~~~ 166 (166)
+|+||++
T Consensus 160 ~~~~p~~ 166 (166)
T PLN03072 160 EVEIPEA 166 (166)
T ss_pred CeeCCCC
Confidence 9999986
No 2
>PRK01143 rpl11p 50S ribosomal protein L11P; Validated
Probab=100.00 E-value=2.6e-63 Score=396.02 Aligned_cols=149 Identities=37% Similarity=0.677 Sum_probs=146.1
Q ss_pred EEEEEEEeccccCCCCCCccccCCCCCChhhHHHHHHHHhhccCCCceeEEEEEE-e-cCceEEEE-eCChHHHHHHHhC
Q 031095 11 VDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTV-Q-NRQAKVAV-VPSAAALVIKALK 87 (166)
Q Consensus 11 ~~ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~~T~~~~~g~~ipV~Itv-~-drsf~~~v-~Ppts~likka~g 87 (166)
++|+|+|+||+|+|+|||||+|||+|||+|+||++||++| ++|.|++|||+||| | ||+|+|++ +||+||||+|+||
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 KVVEVLVEGGKATPGPPLGPALGPLGLNVKQVVQEINEKT-KDFKGMQVPVKVIVDTDTKKFEIEVGIPPTTALIKKELG 81 (163)
T ss_pred eEEEEEEecCccCCCCCCcccccccCCCHHHHHHHHHHHh-hhcCCCeEeEEEEEEeCCceEEEEECCCCHHHHHHHHhC
Confidence 6899999999999999999999999999999999999999 99999999999999 8 99999999 9999999999999
Q ss_pred CCCcCccCccCcceeeeecHHHHHHHHHHhcccCCCcChhhhhhhhhhcccceeeEecCCChHhHHHhhhCceee
Q 031095 88 EPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKEILGTCVSVGCTVDGKDPKDLQQEINDGDVE 162 (166)
Q Consensus 88 ~~~~~~k~~~~~~~~G~it~~~v~eIAk~K~~d~~~~~l~~~~k~VlGTa~SmGi~V~~~~P~e~~~~i~~g~~~ 162 (166)
+.+|+++++++ ++|+||++||||||+.|++|+++.+|+++||+|+||||||||+|++++|+|++++||+|+|+
T Consensus 82 ~~kgs~~p~~~--~vG~It~~qv~eIA~~K~~d~~~~~l~~~vk~VlGTarSmGi~V~g~~pkev~~~i~~g~~~ 154 (163)
T PRK01143 82 IEKGSGEPGHE--VVGNLSFEQVVKIAIMKKDDLLSYDLKAAVKEVLGTCVSMGVTVEGKDPKEVQKEVDEGKYD 154 (163)
T ss_pred CcCCCCCCCCc--eeeeecHHHHHHHHHHHhhhhccccHHHHHHHHHhhHhhceEEEecCCHHHHHHHcCcccHH
Confidence 99999999886 89999999999999999999999999999999999999999999999999999999999986
No 3
>PTZ00105 60S ribosomal protein L12; Provisional
Probab=100.00 E-value=5e-60 Score=369.14 Aligned_cols=140 Identities=72% Similarity=1.182 Sum_probs=134.9
Q ss_pred CCCccccCCCCCChhhHHHHHHHHhhccCCCceeEEEEEEecCceEEEEeCChHHHHHHHhCCCCcCccCccCcceeeee
Q 031095 26 SSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAKVAVVPSAAALVIKALKEPERDRKKTKNIKHNGNI 105 (166)
Q Consensus 26 PplGp~LG~~Gin~~~fck~fN~~T~~~~~g~~ipV~Itv~drsf~~~v~Ppts~likka~g~~~~~~k~~~~~~~~G~i 105 (166)
++|||+|||+|||+|+||++||++| ++|+|++|||+||||||||+|++.||+|+||+|+||+..++++++++++++|+|
T Consensus 1 ~~lGPaLG~~GvNi~~fck~fN~~T-~~~~G~~vpV~Itv~drsf~~~v~Pp~s~ll~k~ag~~~~~~~~~~~~~~vG~i 79 (140)
T PTZ00105 1 SSLAPKVGPLGLSPKKVGDDIAKAT-KDWKGLKVTVKLTVQNRQATVEVVPTASSLLIKALKEPPRDRKKVKNIKHSGNL 79 (140)
T ss_pred CCCccccccCCCCHHHHHHHHHHHH-hhcCCCeEEEEEEEECCEEEEEECCCHHHHHHHHhCCCCCCCCCCCcceeeeEe
Confidence 5899999999999999999999999 899999999999999999999889999999999999988888887666689999
Q ss_pred cHHHHHHHHHHhcccCCCcChhhhhhhhhhcccceeeEecCCChHhHHHhhhCceeeccCC
Q 031095 106 TLDDVIEIAKIMRPRSMAKELSGTVKEILGTCVSVGCTVDGKDPKDLQQEINDGDVEIPLD 166 (166)
Q Consensus 106 t~~~v~eIAk~K~~d~~~~~l~~~~k~VlGTa~SmGi~V~~~~P~e~~~~i~~g~~~~~~~ 166 (166)
|++||||||+.|++|+++.+|+++||+|+||||||||+|+++||+|++++||+|+||||++
T Consensus 80 t~~qv~eIAk~K~~dl~~~~l~~a~k~V~GTarSmGi~V~gk~pkev~~~i~~G~~~~p~~ 140 (140)
T PTZ00105 80 TFDQVIKIARTMRPKSMAKTFKGTVKEVLGTCVSIGCTVDGESPRDIQEKINNGEIKVPES 140 (140)
T ss_pred eHHHHHHHHHHHHhhhCCCcHHHHHHHHHhhheeeeEEEECCCHHHHHHHHhCCCccCCCC
Confidence 9999999999999999999999999999999999999999999999999999999999985
No 4
>COG0080 RplK Ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.2e-59 Score=363.91 Aligned_cols=137 Identities=39% Similarity=0.515 Sum_probs=133.6
Q ss_pred CceEEEEEEEeccccCCCCCCccccCCCCCChhhHHHHHHHHhhccCCCceeEEEEEEe-cCceEEEE-eCChHHHHHHH
Q 031095 8 SQVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQ-NRQAKVAV-VPSAAALVIKA 85 (166)
Q Consensus 8 ~~~~~ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~~T~~~~~g~~ipV~Itv~-drsf~~~v-~Ppts~likka 85 (166)
+..++|+|+|+||+|+|+|||||+|||+|||+|+|||+||++| ++++|++|||+|||| ||||+|++ +||+|+||+|+
T Consensus 3 k~~~~ikl~v~aGkA~p~PpvGPALG~~Gvni~~f~k~fN~~T-~~~~G~~vPV~Itv~~drsftf~~ktPPas~LlkKa 81 (141)
T COG0080 3 KVVKIIKLQVPAGKANPSPPVGPALGQLGVNIMEFCKEFNAAT-KDEKGLPVPVVITVYEDRSFTFIVKTPPASALLKKA 81 (141)
T ss_pred ccceEEEEEecccccCCCCCCCccccccCCCHHHHHHHHHHHh-hccCCCeeeEEEEEEcCCcEEEEECCCCHHHHHHHH
Confidence 4789999999999999999999999999999999999999999 999999999999999 99999999 99999999999
Q ss_pred hCCCCcCccCccCcceeeeecHHHHHHHHHHhcccCCCcChhhhhhhhhhcccceeeEecCC
Q 031095 86 LKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKEILGTCVSVGCTVDGK 147 (166)
Q Consensus 86 ~g~~~~~~k~~~~~~~~G~it~~~v~eIAk~K~~d~~~~~l~~~~k~VlGTa~SmGi~V~~~ 147 (166)
||+.+|+++|.++ ++|+||++||+|||+.|++||++.+|++++|+|+||||||||+|+|+
T Consensus 82 ~g~~~Gs~~p~k~--~vG~lt~~qv~eIA~~K~~dl~a~~l~aA~k~I~GTa~SMGv~Veg~ 141 (141)
T COG0080 82 AGIEKGSGKPNKN--KVGKLTLAQVREIAKTKMPDLNAKDLEAAVKEILGTARSMGVTVEGK 141 (141)
T ss_pred hCCCCCCCCCCcc--eeeeeeHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhhhhceEEeecC
Confidence 9999999999886 99999999999999999999999999999999999999999999974
No 5
>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=4.1e-59 Score=363.99 Aligned_cols=136 Identities=27% Similarity=0.365 Sum_probs=132.0
Q ss_pred CceEEEEEEEeccccCCCCCCccccCCCCCChhhHHHHHHHHhhcc-CCCceeEEEEEEe-cCceEEEE-eCChHHHHHH
Q 031095 8 SQVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKD-WKGLRVTVKLTVQ-NRQAKVAV-VPSAAALVIK 84 (166)
Q Consensus 8 ~~~~~ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~~T~~~-~~g~~ipV~Itv~-drsf~~~v-~Ppts~likk 84 (166)
+..++|+|+|+||+|+|+|||||+|||+|||+|+||++||++| ++ |+|++|||+|+|| ||+|+|++ +||+||||+|
T Consensus 2 ~~~~~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 2 KIVGIIKLQVPAGQANPAPPVGPALGQRGVNIMEFCKQFNART-ADYEPGLPVPVVITVYEDKSFTFIVKTPPVSYLLKK 80 (140)
T ss_pred ceEEEEEEEEeccccCCCCCCcccccccCCCHHHHHHHHHHHH-hhhcCCCeEEEEEEEeCCCeEEEEEcCCCHHHHHHH
Confidence 4678999999999999999999999999999999999999999 88 7999999999999 99999999 9999999999
Q ss_pred HhCCCCcCccCccCcceeeeecHHHHHHHHHHhcccCCCcChhhhhhhhhhcccceeeEecC
Q 031095 85 ALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKEILGTCVSVGCTVDG 146 (166)
Q Consensus 85 a~g~~~~~~k~~~~~~~~G~it~~~v~eIAk~K~~d~~~~~l~~~~k~VlGTa~SmGi~V~~ 146 (166)
++|+.+|+++++++ ++|+||++||||||+.|++|+++.+|+++||+|+||||||||+|++
T Consensus 81 aag~~~gs~~p~~~--~~G~it~~qv~eIA~~K~~d~~~~~l~~~vk~v~GTarSmGi~V~~ 140 (140)
T TIGR01632 81 AAGVEKGSKNPKKE--KVGKITRKQVREIAEIKMSDLNTKDIEAAMKIIAGTAKSMGIEIVG 140 (140)
T ss_pred HhCCCCCCCCCCCe--EEeEecHHHHHHHHHHHHHHhCcccHHHHHHHhheeHeeceEEEeC
Confidence 99999999999886 8999999999999999999999999999999999999999999985
No 6
>PRK00140 rplK 50S ribosomal protein L11; Validated
Probab=100.00 E-value=4e-58 Score=358.79 Aligned_cols=136 Identities=27% Similarity=0.394 Sum_probs=132.3
Q ss_pred CceEEEEEEEeccccCCCCCCccccCCCCCChhhHHHHHHHHhhccCCCceeEEEEEEe-cCceEEEE-eCChHHHHHHH
Q 031095 8 SQVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQ-NRQAKVAV-VPSAAALVIKA 85 (166)
Q Consensus 8 ~~~~~ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~~T~~~~~g~~ipV~Itv~-drsf~~~v-~Ppts~likka 85 (166)
+..++|+|+++||+|+|+|||||+|||+|||+|+||++||++| ++|+|++|||+|++| ||+|+|++ +||+||||+++
T Consensus 4 ~~~~~ikl~v~aG~A~p~PplgP~LG~~Gini~~f~k~fN~~T-~~~~g~~vpV~i~v~~drsf~~~v~~Pp~s~ll~k~ 82 (141)
T PRK00140 4 KVVGYIKLQIPAGKANPAPPVGPALGQRGVNIMEFCKAFNART-QDQKGLPIPVVITVYEDRSFTFITKTPPASVLLKKA 82 (141)
T ss_pred ccceEEEEEEecCccCCCCCCcccccccCCCHHHHHHHHHHHH-hhcCCCeEEEEEEEecCCeEEEEEcCCCHHHHHHHH
Confidence 4578999999999999999999999999999999999999999 999999999999999 99999999 99999999999
Q ss_pred hCCCCcCccCccCcceeeeecHHHHHHHHHHhcccCCCcChhhhhhhhhhcccceeeEecC
Q 031095 86 LKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKEILGTCVSVGCTVDG 146 (166)
Q Consensus 86 ~g~~~~~~k~~~~~~~~G~it~~~v~eIAk~K~~d~~~~~l~~~~k~VlGTa~SmGi~V~~ 146 (166)
+|+++|+++++++ ++|+||++||||||+.|++|+++.+|+++||+|+|||+||||+|++
T Consensus 83 ~g~~~gs~~p~~~--~vG~it~~~v~eIA~~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~g 141 (141)
T PRK00140 83 AGIEKGSGEPNKE--KVGKITRAQVREIAETKMPDLNAADIEAAMRMIAGTARSMGIVVEG 141 (141)
T ss_pred hCCCCCCCCCCCe--EEeeEcHHHHHHHHHHHHHhhCCCcHHHHHHHhheeeeEeeEEEeC
Confidence 9999999999886 9999999999999999999999999999999999999999999985
No 7
>CHL00127 rpl11 ribosomal protein L11; Validated
Probab=100.00 E-value=1.8e-57 Score=354.75 Aligned_cols=135 Identities=24% Similarity=0.376 Sum_probs=130.5
Q ss_pred CceEEEEEEEeccccCCCCCCccccCCCCCChhhHHHHHHHHhhccCCCceeEEEEEEe-cCceEEEE-eCChHHHHHHH
Q 031095 8 SQVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQ-NRQAKVAV-VPSAAALVIKA 85 (166)
Q Consensus 8 ~~~~~ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~~T~~~~~g~~ipV~Itv~-drsf~~~v-~Ppts~likka 85 (166)
+..++|+|+++||+|+|+|||||+|||+|||+|+||+|||++| ++|.|++|||+|+|| ||+|+|++ +||+||||+||
T Consensus 4 ~~~~~ikl~v~aG~A~p~PplGP~LG~~Gini~~f~k~fN~~T-~~~~g~~vpV~Itv~~drsf~~~v~~Pp~s~ll~ka 82 (140)
T CHL00127 4 KKLAIIKLALPAGKATPAPPVGPALGQHGVNINLFCKEYNART-KDKIGLIIPVEISVYEDKSYTFILKTPPASVLLAKA 82 (140)
T ss_pred ccccEEEEEEecCccCCCCCCcccccccCCCHHHHHHHHHHHh-hhcCCCeEEEEEEEeCCceEEEEEcCCCHHHHHHHH
Confidence 3578999999999999999999999999999999999999999 999999999999999 99999999 99999999999
Q ss_pred hCCCCcCccCccCcceeeeecHHHHHHHHHHhcccCCCcChhhhhhhhhhcccceeeEec
Q 031095 86 LKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKEILGTCVSVGCTVD 145 (166)
Q Consensus 86 ~g~~~~~~k~~~~~~~~G~it~~~v~eIAk~K~~d~~~~~l~~~~k~VlGTa~SmGi~V~ 145 (166)
||+++|+.+++++ ++|+||++||||||+.|++|+++.+|+++||+|+||||||||+|.
T Consensus 83 ~gi~~gs~~p~~~--~~G~it~~~v~eIA~~K~~d~~~~~l~~~vk~v~GTa~SmGi~V~ 140 (140)
T CHL00127 83 AGIKKGSGEPNKK--KVGSITIKQLEEIAQIKLPDLNTISLSKAIKIIEGTAKNMGISIK 140 (140)
T ss_pred hCCCcCCCCCCCe--ecceecHHHHHHHHHHHhhhhccccHHHHHHHhHeeheeceEEeC
Confidence 9999999988875 999999999999999999999999999999999999999999983
No 8
>smart00649 RL11 Ribosomal protein L11/L12.
Probab=100.00 E-value=4.1e-57 Score=349.64 Aligned_cols=130 Identities=40% Similarity=0.585 Sum_probs=127.1
Q ss_pred EEEEEeccccCCCCCCccccCCCCCChhhHHHHHHHHhhccCCCceeEEEEEEe-cCceEEEE-eCChHHHHHHHhCCCC
Q 031095 13 VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQ-NRQAKVAV-VPSAAALVIKALKEPE 90 (166)
Q Consensus 13 ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~~T~~~~~g~~ipV~Itv~-drsf~~~v-~Ppts~likka~g~~~ 90 (166)
|+|+|+||+|+|+|||||+|||+|||+|+||++||++| ++|+|++|||+|++| ||+|+|++ +||+||||+|++|+.+
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 IKLQIPAGKANPAPPLGPALGQLGINIMEFCKEFNART-KDKKGLPIPVKITVYNDKSFTFIIKTPPASFLLKKAAGIEK 79 (132)
T ss_pred CEEEEecCccCCCCCcccccccCCCCHHHHHHHHHHHH-hhcCCCeEeEEEEEeCCCeEEEEEcCCCHHHHHHHHhCCCC
Confidence 58999999999999999999999999999999999999 889999999999999 99999999 9999999999999999
Q ss_pred cCccCccCcceeeeecHHHHHHHHHHhcccCCCcChhhhhhhhhhcccceeeEec
Q 031095 91 RDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKEILGTCVSVGCTVD 145 (166)
Q Consensus 91 ~~~k~~~~~~~~G~it~~~v~eIAk~K~~d~~~~~l~~~~k~VlGTa~SmGi~V~ 145 (166)
|+++|+++ ++|+||++||||||+.|++|+++.+|+++||+|+|||+||||+|+
T Consensus 80 gs~~p~~~--~~g~it~~~v~eIA~~K~~d~~~~~l~~~~k~V~GTa~SmGi~V~ 132 (132)
T smart00649 80 GSKKPGKK--KVGNITLDQVYEIAKIKRPDLNAKDLEAAVKEILGTARSMGITVE 132 (132)
T ss_pred CCCCCCCe--eeeEEcHHHHHHHHHHHHHHhcchhHHHHHHHHHhhHhcceEEeC
Confidence 99999985 999999999999999999999999999999999999999999986
No 9
>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=4.5e-56 Score=343.42 Aligned_cols=129 Identities=44% Similarity=0.605 Sum_probs=125.5
Q ss_pred EEEEEeccccCCCCCCccccCCCCCChhhHHHHHHHHhhccCCCceeEEEEEEe-cCceEEEE-eCChHHHHHHHhCCCC
Q 031095 13 VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQ-NRQAKVAV-VPSAAALVIKALKEPE 90 (166)
Q Consensus 13 ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~~T~~~~~g~~ipV~Itv~-drsf~~~v-~Ppts~likka~g~~~ 90 (166)
|+|+|+||+|+|+|||||+|||+|||+|+||++||++| ++|+|++|||+|+|| ||+|+|++ +||+||||+|++|+.+
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 IKLQVPAGKASPAPPLGPALGQLGVNIMKFCKEFNART-KDYKGLPVPVKITVYNDRSFTFEVKTPPASALLKKAAGIEK 79 (131)
T ss_pred CEEEEecCccCCCCCcccccccCCCCHHHHHHHHHHHH-hhcCCCeEEEEEEEeCCCeEEEEEcCCCHHHHHHHHhCCCC
Confidence 58999999999999999999999999999999999999 899999999999999 99999999 8999999999999999
Q ss_pred cCccCccCcceeeeecHHHHHHHHHHhcccCCCcChhhhhhhhhhcccceeeEe
Q 031095 91 RDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKEILGTCVSVGCTV 144 (166)
Q Consensus 91 ~~~k~~~~~~~~G~it~~~v~eIAk~K~~d~~~~~l~~~~k~VlGTa~SmGi~V 144 (166)
|+.+++++ ++|+||++||||||+.|++|+++.+|+++||+|+|||+||||+|
T Consensus 80 gs~~~~~~--~~g~it~~~v~eIA~~K~~dl~~~~l~~~vk~v~GTa~SmGi~V 131 (131)
T cd00349 80 GSKKPNKE--KVGNITLDQVYEIAKIKLPDLNAKTLKSAVKEILGTARSMGITV 131 (131)
T ss_pred CCCCCCCe--eeeeecHHHHHHHHHHHHhhhcchhHHHHHHHHHhhHhhCeEEC
Confidence 99988775 99999999999999999999999999999999999999999986
No 10
>PRK14539 50S ribosomal protein L11/unknown domain fusion protein; Provisional
Probab=100.00 E-value=3.3e-54 Score=351.09 Aligned_cols=134 Identities=22% Similarity=0.331 Sum_probs=128.7
Q ss_pred CceEEEEEEEeccccCCCCCCccccCCCCCChhhHHHHHHHHhhccCCCceeEEEEEEe-cCceEEEE-eCChHHHHHHH
Q 031095 8 SQVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQ-NRQAKVAV-VPSAAALVIKA 85 (166)
Q Consensus 8 ~~~~~ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~~T~~~~~g~~ipV~Itv~-drsf~~~v-~Ppts~likka 85 (166)
+..++|+|+|+||+|+| ||+|||+|||+|+||++||++| ++|.|++|||+|||| ||||+|++ +||+||||+|+
T Consensus 5 ki~~~Ikl~v~AGkA~P----GPaLG~~GVNi~~FcKefN~~T-k~~~G~~VPV~ItV~~DRsf~f~vktPptS~LLkKa 79 (196)
T PRK14539 5 EVVKVAKLQFNAGQAKP----GPSLAGVGINMPEFTKQFNDAT-RDRGGEPVPVQITVYKDKSFDFKLFTAPASFKIKQA 79 (196)
T ss_pred hhheEEEEEEECCccCC----CCcccccCCCHHHHHHHHHHHh-hhcCCceEEEEEEEecCCeEEEEEeCCCHHHHHHHH
Confidence 46789999999999999 5668899999999999999999 899999999999999 99999988 99999999999
Q ss_pred hCCCCcCccCccCcceeeeecHHHHHHHHHHhcccCCCcChhhhhhhhhhcccceeeEecCCC
Q 031095 86 LKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKEILGTCVSVGCTVDGKD 148 (166)
Q Consensus 86 ~g~~~~~~k~~~~~~~~G~it~~~v~eIAk~K~~d~~~~~l~~~~k~VlGTa~SmGi~V~~~~ 148 (166)
+|+.+|+++|+++ ++|+||++||||||++|++|+++.+|+++||+|+||||||||+|+++|
T Consensus 80 agi~kGs~~p~k~--~vG~Itl~qv~eIAk~K~~Dl~~~~Le~avK~VlGTArSMGI~Veg~d 140 (196)
T PRK14539 80 AKIKSGSANSKTT--IVGTITLSQLEEIAKYKLPDLNTDDVEEAMHTIAGTAKNMGVLVEGYD 140 (196)
T ss_pred hCCCCCCCCCCCe--EEEEecHHHHHHHHHHHhhhhCCCcHHHHHHHHHhhheeCeEEEEccc
Confidence 9999999999986 899999999999999999999999999999999999999999999977
No 11
>PTZ00321 ribosomal protein L11; Provisional
Probab=100.00 E-value=1.7e-53 Score=365.43 Aligned_cols=142 Identities=17% Similarity=0.274 Sum_probs=132.2
Q ss_pred CCCceEEEEEEEeccccCCCCCCccccCCCCCChhhHHHHHHHHhhcc-C-CCceeEEEEEEe-cCceEEEE-eCChHHH
Q 031095 6 DPSQVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKD-W-KGLRVTVKLTVQ-NRQAKVAV-VPSAAAL 81 (166)
Q Consensus 6 ~~~~~~~ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~~T~~~-~-~g~~ipV~Itv~-drsf~~~v-~Ppts~l 81 (166)
++++.+.|||+|+||+|+|+|||||+|||+|||+|+|||+||++| ++ | .|++|||+|+|| ||||+|++ +||+|||
T Consensus 46 ~KkV~~~IKL~VpAGKAtPaPPVGPALGq~GVNImqFCKeFNerT-K~~fk~GvpVPV~ITVy~DKSF~F~IktPPtS~L 124 (342)
T PTZ00321 46 GKRVLHNWRFFIKAGKAATGPPVGQEFSKLGLKAMDFAKSFNDRT-KPHFKDDVELIVRIQVYFDKSYLFTIEPPPTAWF 124 (342)
T ss_pred CCeeeEEEEEEEECCCcCCCCCCcccccccCCCHHHHHHHHHHHH-HhhccCCCeEeEEEEEeCCCeEEEEECCCCHHHH
Confidence 567899999999999999999999999999999999999999999 76 5 799999999999 99999999 9999999
Q ss_pred HHHHhCCCCcCccCccC-cceeeeecHHHHHHHHHHhcccCCC---cChhhhhhhhhhcccceeeEecCCC
Q 031095 82 VIKALKEPERDRKKTKN-IKHNGNITLDDVIEIAKIMRPRSMA---KELSGTVKEILGTCVSVGCTVDGKD 148 (166)
Q Consensus 82 ikka~g~~~~~~k~~~~-~~~~G~it~~~v~eIAk~K~~d~~~---~~l~~~~k~VlGTa~SmGi~V~~~~ 148 (166)
|+|+||+.+|+++++++ -+++|+||++||||||++|++|+++ .+|+++||+|+|||+||||+|+++|
T Consensus 125 LKKAAGI~KGS~~P~~~k~e~VG~ITlkQVyEIAkiK~~DLnal~~~~LesAvK~ViGTARSMGIkVeGKD 195 (342)
T PTZ00321 125 ILRALRKKRRETGPVPLRGHYCALMTLEMAYEIAKMKPRSWGRPEYPLIETRVRRVVGQARRMGVCFIGVD 195 (342)
T ss_pred HHHHhCCCCCCCCCCCCCCceEEeccHHHHHHHHHHhhhccccccccCHHHHHHHHHhhHhcCeEEEeccc
Confidence 99999999999988431 1489999999999999999999775 7999999999999999999999854
No 12
>KOG3257 consensus Mitochondrial/chloroplast ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.3e-50 Score=316.07 Aligned_cols=135 Identities=27% Similarity=0.378 Sum_probs=129.7
Q ss_pred ceEEEEEEEeccccCCCCCCccccCCCCCChhhHHHHHHHHhhccC-CCceeEEEEEEe-cCceEEEE-eCChHHHHHHH
Q 031095 9 QVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDW-KGLRVTVKLTVQ-NRQAKVAV-VPSAAALVIKA 85 (166)
Q Consensus 9 ~~~~ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~~T~~~~-~g~~ipV~Itv~-drsf~~~v-~Ppts~likka 85 (166)
....+|+.++||.|.|+||+||+|||+|+|+++||||||++| ++| +|+|+|++||+. ||||+|++ +||+||||+||
T Consensus 18 h~~~ikl~v~Ag~A~~~pp~gP~Lgqr~l~viafckefnarT-~~~k~~vplp~kiTv~pDrsftf~iktPpts~lL~kA 96 (168)
T KOG3257|consen 18 HSASIKLIVKAGLAAPAPPLGPALGQRGLNVIAFCKEFNART-KKVKPGVPLPGKITVKPDRSFTFIIKTPPTSWLLKKA 96 (168)
T ss_pred ceeEEEEeeccccccCCCCCCchhhhcchhHHHhchhhhhhh-ccccCCCccceeEeecCCCeEEEEecCCChHHHHHHH
Confidence 466899999999999999999999999999999999999999 886 799999999999 99999999 99999999999
Q ss_pred hCCCCcCccCccCcceeeeecHHHHHHHHHHhcccCC--CcChhhhhhhhhhcccceeeEecC
Q 031095 86 LKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSM--AKELSGTVKEILGTCVSVGCTVDG 146 (166)
Q Consensus 86 ~g~~~~~~k~~~~~~~~G~it~~~v~eIAk~K~~d~~--~~~l~~~~k~VlGTa~SmGi~V~~ 146 (166)
||+++|++.|+++ .+|.||++||||||++|..|.+ ..+|+++||+|+|||+||||+|+.
T Consensus 97 agv~KGs~~p~~~--~vG~lTlkhvyeIAkiK~~D~~~q~~~lesi~rsiigtA~smGIkVvp 157 (168)
T KOG3257|consen 97 AGVEKGSKDPGQE--KVGMLTLKHVYEIAKIKLPDPNLQCTTLESICRSIIGTARSMGIKVVP 157 (168)
T ss_pred hCcccCCCCCcce--eeeeEEHHHHHHHHHhhcCCcccccccHHHHHHHHHHHHHhCccccch
Confidence 9999999999886 9999999999999999999966 899999999999999999999986
No 13
>KOG0886 consensus 40S ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.1e-46 Score=291.25 Aligned_cols=165 Identities=76% Similarity=1.201 Sum_probs=161.7
Q ss_pred CCC--CCCCCceEEEEEEEeccccCCCCCCccccCCCCCChhhHHHHHHHHhhccCCCceeEEEEEEecCceEEEEeCCh
Q 031095 1 MPP--KFDPSQVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAKVAVVPSA 78 (166)
Q Consensus 1 m~~--k~~~~~~~~ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~~T~~~~~g~~ipV~Itv~drsf~~~v~Ppt 78 (166)
||+ |||++++++++|+|.||+...+..|+|.+||+|+.++.+.+++.++| +||+|+.|+|+++++||...+++.|++
T Consensus 1 mp~~pkfdP~eiK~vylrc~GgEVgatsaLApKIgPLGLSpKkvGedIaKaT-~dwKgl~vtvkLtIqnR~A~i~VvpSa 79 (167)
T KOG0886|consen 1 MPPKPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGEDIAKAT-GDWKGLRVTVKLTIQNRQAQIEVVPSA 79 (167)
T ss_pred CCCCCCCCccceEEEEEEeecCccccccccccccccccCCccccchHHHHhh-cccccceEEEEEEecCcccceEEcccH
Confidence 455 59999999999999999999999999999999999999999999999 999999999999999999999999999
Q ss_pred HHHHHHHhCCCCcCccCccCcceeeeecHHHHHHHHHHhcccCCCcChhhhhhhhhhcccceeeEecCCChHhHHHhhhC
Q 031095 79 AALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKEILGTCVSVGCTVDGKDPKDLQQEIND 158 (166)
Q Consensus 79 s~likka~g~~~~~~k~~~~~~~~G~it~~~v~eIAk~K~~d~~~~~l~~~~k~VlGTa~SmGi~V~~~~P~e~~~~i~~ 158 (166)
|.||+|+|++++|+||+.+|+.|+|+|+++++.+||+++++.+.+++|++++++|+|||+|+||+|+|++|++++++||+
T Consensus 80 saLiIkaLKEPpRDRKk~knikh~Gni~~deiv~iar~mr~rS~a~~l~gt~keilgt~~svgc~vDgk~Phdi~~~i~~ 159 (167)
T KOG0886|consen 80 SALIIKALKEPPRDRKKQKNIKHSGNITFDEIVEIARIMRPRSLARELSGTVKEILGTAQSVGCTVDGKHPHDIIDEINA 159 (167)
T ss_pred HHHHHHHhcCCcchhhhhccccccCcccHHHHHHHHHHhhhHhhhhhhhhhHHHHhchhhhcccccCCCChHHHHhhhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeccCC
Q 031095 159 GDVEIPLD 166 (166)
Q Consensus 159 g~~~~~~~ 166 (166)
|+++||++
T Consensus 160 Geie~P~~ 167 (167)
T KOG0886|consen 160 GEIEIPAN 167 (167)
T ss_pred CceeCCCC
Confidence 99999985
No 14
>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=99.95 E-value=5.5e-28 Score=164.45 Aligned_cols=58 Identities=41% Similarity=0.693 Sum_probs=55.5
Q ss_pred EEEEEEeccccCCCCCCccccCCCCCChhhHHHHHHHHhhccCC-CceeEEEEEEe-cCce
Q 031095 12 DVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWK-GLRVTVKLTVQ-NRQA 70 (166)
Q Consensus 12 ~ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~~T~~~~~-g~~ipV~Itv~-drsf 70 (166)
+|+|+|+||+|+|+|||||+|||+|||+|+||+|||++| ++|+ |++|||+|+|| ||||
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 VIKLRVPAGKATPAPPLGPALGPLGINIKKFCKDFNKAT-KDYKPGIPVPVKITVYNDKSF 60 (60)
T ss_dssp EEEEEEETTSSSSTTTSTHHHHTTTS-HHHHHHHHHHHT-TTCTTSSEEEEEEEEETTSEE
T ss_pred CEEEEEecCcccCCCCcCcccccCCCCHHHHHHHHHHHH-hcccCCCEEEEEEEEeCCCCC
Confidence 589999999999999999999999999999999999999 9987 99999999999 9998
No 15
>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=99.94 E-value=1.2e-27 Score=166.89 Aligned_cols=68 Identities=37% Similarity=0.452 Sum_probs=66.2
Q ss_pred eCChHHHHHHHhCCCCcCccCccCcceeeeecHHHHHHHHHHhcccCCCcChhhhhhhhhhcccceeeEe
Q 031095 75 VPSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKEILGTCVSVGCTV 144 (166)
Q Consensus 75 ~Ppts~likka~g~~~~~~k~~~~~~~~G~it~~~v~eIAk~K~~d~~~~~l~~~~k~VlGTa~SmGi~V 144 (166)
+||+||||+|+||+.+|+.+|+++ ++|+||++||||||++|+.|+++.+|+++||+|+||||||||+|
T Consensus 2 ~Pp~s~llkkaagi~kGs~~p~~~--~vG~it~~~i~eIAk~K~~d~~~~~l~~~~k~v~Gta~SmGi~V 69 (69)
T PF00298_consen 2 TPPTSWLLKKAAGIKKGSSKPGKE--KVGTITLKQIYEIAKIKQKDLNAKSLESAVKSVIGTARSMGIKV 69 (69)
T ss_dssp SSTHHHHHHHHHTTSSSSSSTTTS--SSEEEEHHHHHHHHHHHTTTSSSSSHHHHHHHHHHHHHTTTEEE
T ss_pred CCChHHHHHHHhCCCCCCCCCCCc--eeeeecHHHHHHHHHHhhcccccCCHHHHHHHHHHHHhcCceEC
Confidence 699999999999999999999987 79999999999999999999999999999999999999999987
No 16
>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=47.15 E-value=21 Score=24.53 Aligned_cols=28 Identities=21% Similarity=0.297 Sum_probs=23.8
Q ss_pred EEEEEEecCceEEEEeCChHHHHHHHhC
Q 031095 60 TVKLTVQNRQAKVAVVPSAAALVIKALK 87 (166)
Q Consensus 60 pV~Itv~drsf~~~v~Ppts~likka~g 87 (166)
.|+|+|.+++|.|.+++.--..+.+++.
T Consensus 1 ~V~v~I~G~~y~i~~~~~~ee~l~~~a~ 28 (89)
T PF05164_consen 1 QVKVTILGREYRIKCPDEDEEYLRKAAE 28 (89)
T ss_dssp -EEEEETTEEEEECETGCGHHHHHHHHH
T ss_pred CeEEEECCEEEEeecCCCCHHHHHHHHH
Confidence 3788899999999888888888888885
No 17
>COG1437 CyaB Adenylate cyclase, class 2 (thermophilic) [Nucleotide transport and metabolism]
Probab=45.33 E-value=6.5 Score=32.25 Aligned_cols=89 Identities=20% Similarity=0.227 Sum_probs=60.6
Q ss_pred eEEEE-eCChHHHHHHHhCCC-CcCccCccCcceee--eecHHHHHHHHHHhc---ccCCCcChhhhhhhhhhcccceee
Q 031095 70 AKVAV-VPSAAALVIKALKEP-ERDRKKTKNIKHNG--NITLDDVIEIAKIMR---PRSMAKELSGTVKEILGTCVSVGC 142 (166)
Q Consensus 70 f~~~v-~Ppts~likka~g~~-~~~~k~~~~~~~~G--~it~~~v~eIAk~K~---~d~~~~~l~~~~k~VlGTa~SmGi 142 (166)
+++++ -|+.+.-|.+.||.. .+.-+|...+...| .|++++|...-.--. ..-...++.++.+.+-..++++|+
T Consensus 81 ~E~~v~D~~~~~~il~~LGF~~~~~VkK~R~iY~~~~~~i~lD~VegLG~F~EIE~~~~d~~e~~~~~~~~~~i~~~lGl 160 (178)
T COG1437 81 IEIEVSDVEKALEILKRLGFKEVAVVKKTREIYKVGNVTIELDAVEGLGDFLEIEVMVDDENEIDGAKEEIEEIARQLGL 160 (178)
T ss_pred EEEEeCCHHHHHHHHHHcCCceeeEEEEEEEEEeeCCEEEEEecccCCcccEEEEEecCCchhhHHHHHHHHHHHHHhCC
Confidence 35666 688999999999954 33434444444455 566777643222110 012446677888999999999999
Q ss_pred EecCCChHhHHHhhhC
Q 031095 143 TVDGKDPKDLQQEIND 158 (166)
Q Consensus 143 ~V~~~~P~e~~~~i~~ 158 (166)
..++.-++-|++.++.
T Consensus 161 ~~~~~~r~sYlELl~~ 176 (178)
T COG1437 161 KEEDLERRSYLELLLE 176 (178)
T ss_pred ChhcccchhHHHHHhc
Confidence 9999999999987764
No 18
>COG0051 RpsJ Ribosomal protein S10 [Translation, ribosomal structure and biogenesis]
Probab=41.13 E-value=5.3 Score=30.08 Aligned_cols=32 Identities=25% Similarity=0.302 Sum_probs=27.8
Q ss_pred HHhcccCCCcChhhhhhhhhhcccceeeEecC
Q 031095 115 KIMRPRSMAKELSGTVKEILGTCVSVGCTVDG 146 (166)
Q Consensus 115 k~K~~d~~~~~l~~~~k~VlGTa~SmGi~V~~ 146 (166)
++++..+....|+..|+.|.-||+.+|+.+-|
T Consensus 7 rI~L~s~d~~~LD~~~~~Ive~akrtg~~v~G 38 (104)
T COG0051 7 RIRLKSFDHRLLDQVCREIVETAKRTGADVKG 38 (104)
T ss_pred EEEEecCCHHHHHHHHHHHHHHHHHhCCeeeC
Confidence 44556677888999999999999999999987
No 19
>COG5106 RPF2 Uncharacterized conserved protein [Function unknown]
Probab=34.18 E-value=55 Score=28.63 Aligned_cols=44 Identities=20% Similarity=0.301 Sum_probs=31.3
Q ss_pred CCceeEEEE-EEe-cC--------------------ceEE-EEeCChHHHHHHHhCCCCc-CccCccC
Q 031095 55 KGLRVTVKL-TVQ-NR--------------------QAKV-AVVPSAAALVIKALKEPER-DRKKTKN 98 (166)
Q Consensus 55 ~g~~ipV~I-tv~-dr--------------------sf~~-~v~Ppts~likka~g~~~~-~~k~~~~ 98 (166)
.+.|+|..+ .|| .+ .|.+ .+.|+.+.++++|+++++. ..||.+|
T Consensus 191 d~~plp~v~fRVyk~k~~kt~~~lpr~elee~GPrldf~i~R~~~~s~d~~~ealkkPk~~e~KpkKN 258 (316)
T COG5106 191 DTYPLPLVVFRVYKTKLLKTKTNLPRLELEECGPRLDFEIVRSYHCSDDLYKEALKKPKTQEPKPKKN 258 (316)
T ss_pred ccccccceeeeeeecccccccCCCCceehhhcccceeeEEEeecCCChHHHHHHhcCccccCCCcccc
Confidence 467888555 887 45 2444 3379999999999999874 5566665
No 20
>PF13817 DDE_Tnp_IS66_C: IS66 C-terminal element
Probab=30.55 E-value=24 Score=21.76 Aligned_cols=20 Identities=20% Similarity=0.521 Sum_probs=14.1
Q ss_pred hhhhcccceeeEecCCChHhHHHhh
Q 031095 132 EILGTCVSVGCTVDGKDPKDLQQEI 156 (166)
Q Consensus 132 ~VlGTa~SmGi~V~~~~P~e~~~~i 156 (166)
++++||+--|+ +|..|+.++
T Consensus 1 SlieTcK~ngv-----~P~~yL~~v 20 (39)
T PF13817_consen 1 SLIETCKLNGV-----NPYAYLTDV 20 (39)
T ss_pred CHHHHHHHcCC-----CHHHHHHHH
Confidence 46788886665 777777654
No 21
>PF12475 Amdo_NSP: Amdovirus non-structural protein ; InterPro: IPR020960 This domain family is found in viruses, and is approximately 50 amino acids in length. This family contains proteins of each of the three types of Amdovirus non-structural protein [].
Probab=26.44 E-value=36 Score=22.27 Aligned_cols=20 Identities=5% Similarity=-0.037 Sum_probs=13.7
Q ss_pred cCceEEEE-eCChHHHHHHHh
Q 031095 67 NRQAKVAV-VPSAAALVIKAL 86 (166)
Q Consensus 67 drsf~~~v-~Ppts~likka~ 86 (166)
|+.=+=.. +||.+|||++.-
T Consensus 3 Dkd~dPkd~t~sL~w~~k~~n 23 (48)
T PF12475_consen 3 DKDNDPKDVTKSLGWFLKTTN 23 (48)
T ss_pred CCCCCccccccchHHHHHHhh
Confidence 44444433 899999998753
No 22
>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=26.09 E-value=44 Score=25.37 Aligned_cols=35 Identities=14% Similarity=0.208 Sum_probs=25.7
Q ss_pred EEEeccccCCCCCCccccCCCCCChhhHHHHHHHH
Q 031095 15 VRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKE 49 (166)
Q Consensus 15 l~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~~ 49 (166)
+.||.=+-.--.-+|-.|||.|-++.+.+++++.+
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 44554444455678999999999999888887643
No 23
>KOG1196 consensus Predicted NAD-dependent oxidoreductase [General function prediction only]
Probab=25.81 E-value=19 Score=32.36 Aligned_cols=39 Identities=26% Similarity=0.434 Sum_probs=30.3
Q ss_pred HHHHHHHHHhccc-CCCcChhhhhhhhhhc-ccceeeEecC
Q 031095 108 DDVIEIAKIMRPR-SMAKELSGTVKEILGT-CVSVGCTVDG 146 (166)
Q Consensus 108 ~~v~eIAk~K~~d-~~~~~l~~~~k~VlGT-a~SmGi~V~~ 146 (166)
-=++||+..|..+ ..-.--.+||-++.|. |+-|||+|+|
T Consensus 143 ~Gf~ei~~pk~geTv~VSaAsGAvGql~GQ~Ak~~Gc~VVG 183 (343)
T KOG1196|consen 143 AGFYEICSPKKGETVFVSAASGAVGQLVGQFAKLMGCYVVG 183 (343)
T ss_pred HHHHHhcCCCCCCEEEEeeccchhHHHHHHHHHhcCCEEEE
Confidence 3467999988876 3334457899999997 7899999996
No 24
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.34 E-value=30 Score=26.78 Aligned_cols=11 Identities=18% Similarity=0.564 Sum_probs=8.8
Q ss_pred hhhCceeeccC
Q 031095 155 EINDGDVEIPL 165 (166)
Q Consensus 155 ~i~~g~~~~~~ 165 (166)
+|-+|+..||+
T Consensus 93 ~v~EG~l~Cpe 103 (124)
T KOG1088|consen 93 DVIEGELVCPE 103 (124)
T ss_pred hhccceEecCC
Confidence 56789998886
No 25
>KOG0455 consensus Homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=24.45 E-value=77 Score=28.16 Aligned_cols=42 Identities=19% Similarity=0.369 Sum_probs=30.7
Q ss_pred eeeecHHHHHHHHHHh-------cccCCCcChhhhhhhhhhcccceeeEecC
Q 031095 102 NGNITLDDVIEIAKIM-------RPRSMAKELSGTVKEILGTCVSVGCTVDG 146 (166)
Q Consensus 102 ~G~it~~~v~eIAk~K-------~~d~~~~~l~~~~k~VlGTa~SmGi~V~~ 146 (166)
-|+++|.||.++|+.- +.|++..+.. |-+.=-+|-.|+.|+.
T Consensus 192 ~~~~sfsdvVk~AKklGYTEPDPRDDLnGmDVA---RKvtIl~Ri~Gv~ves 240 (364)
T KOG0455|consen 192 PGTLSFSDVVKAAKKLGYTEPDPRDDLNGMDVA---RKVTILARILGVRVES 240 (364)
T ss_pred CCcccHHHHHHHHHHcCCCCCCcccccccchhh---hhhhhhhhhccceeec
Confidence 3899999999999954 2358877754 3444447788999885
No 26
>PF03978 Borrelia_REV: Borrelia burgdorferi REV protein; InterPro: IPR007126 This family consists of several REV proteins from Borrelia burgdorferi (Lyme disease spirochete) and Borrelia garinii. The function of REV is unknown although it has been shown that the gene is induced during the ingesting of host blood suggesting a role in the metabolic activation of borreliae to adapt to physiological stimuli [].
Probab=24.19 E-value=59 Score=26.30 Aligned_cols=34 Identities=24% Similarity=0.131 Sum_probs=29.4
Q ss_pred HHHHHhcccCCCcChhhhhhhhhhcccceeeEec
Q 031095 112 EIAKIMRPRSMAKELSGTVKEILGTCVSVGCTVD 145 (166)
Q Consensus 112 eIAk~K~~d~~~~~l~~~~k~VlGTa~SmGi~V~ 145 (166)
+-|+.+..++...+.+..-..+.-+|+|+|++|-
T Consensus 94 KAak~~i~~~~d~d~~~~k~~Iw~eak~~Gv~vk 127 (160)
T PF03978_consen 94 KAAKQKIEGIQDKDQECAKAKIWTEAKLVGVTVK 127 (160)
T ss_pred HHHHHHhcchhhhhHHHHHHHHHHHHHhcCeeee
Confidence 3488888888888888889999999999999987
No 27
>PF10941 DUF2620: Protein of unknown function DUF2620; InterPro: IPR021238 This is a bacterial family of proteins with unknown function.
Probab=22.85 E-value=69 Score=24.65 Aligned_cols=62 Identities=15% Similarity=0.475 Sum_probs=42.0
Q ss_pred ceeeeecHHHHHHHHHHhccc----CCCcChhhhhhhh-------hhcc-------cceeeEecC-------------CC
Q 031095 100 KHNGNITLDDVIEIAKIMRPR----SMAKELSGTVKEI-------LGTC-------VSVGCTVDG-------------KD 148 (166)
Q Consensus 100 ~~~G~it~~~v~eIAk~K~~d----~~~~~l~~~~k~V-------lGTa-------~SmGi~V~~-------------~~ 148 (166)
.+-|.|.-+++.+.-+...++ .-..||+++++.= +|+| .+|-|-+.| .+
T Consensus 4 vigGql~K~ei~~~i~~~~~~~~ev~i~sDmeAAm~vK~G~aDYY~GACnTGgGgALamAIallG~~~C~Tvs~pg~~~~ 83 (117)
T PF10941_consen 4 VIGGQLDKEEIAELIEKLGPGKVEVTIKSDMEAAMAVKSGQADYYLGACNTGGGGALAMAIALLGYGKCATVSMPGKIPS 83 (117)
T ss_pred EEccccCHHHHHHHHHHHCCCcEEEEEechHHHHHHhhcCCcCEeEeecCCCccHHHHHHHHHhCccceeEeecCCCCCC
Confidence 355779999999988877666 3457788877653 3333 333222222 37
Q ss_pred hHhHHHhhhCcee
Q 031095 149 PKDLQQEINDGDV 161 (166)
Q Consensus 149 P~e~~~~i~~g~~ 161 (166)
.+|+.+.|++|+.
T Consensus 84 eeeI~~~v~~GK~ 96 (117)
T PF10941_consen 84 EEEIRKEVAEGKK 96 (117)
T ss_pred HHHHHHHHHcCCe
Confidence 8999999999985
No 28
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=22.08 E-value=46 Score=22.84 Aligned_cols=34 Identities=26% Similarity=0.367 Sum_probs=24.5
Q ss_pred EEEEEeccccCCCCCCccccCCCCCChhhHHHHHH
Q 031095 13 VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIA 47 (166)
Q Consensus 13 ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN 47 (166)
.++-|..+.. ---|+|-..|+.|..+..+.+++|
T Consensus 5 ~kvaV~~~~~-~~d~vG~~iG~~G~rik~i~~~L~ 38 (69)
T PF13184_consen 5 TKVAVKSGDP-NIDPVGACIGKKGSRIKAISEELN 38 (69)
T ss_dssp EEEEEEESST-TS-HHHHHH-CCCCCHHHHHHHTT
T ss_pred EEEEEEcCCC-CcCcceecCccccHHHHHHHHHhC
Confidence 4555665553 235789999999999999999995
No 29
>TIGR01046 S10_Arc_S20_Euk ribosomal protein S10(archaeal)/S20(eukaryotic). its equivalents in eukaryotes.
Probab=21.81 E-value=20 Score=26.46 Aligned_cols=32 Identities=16% Similarity=0.250 Sum_probs=27.3
Q ss_pred HHhcccCCCcChhhhhhhhhhcccceeeEecC
Q 031095 115 KIMRPRSMAKELSGTVKEILGTCVSVGCTVDG 146 (166)
Q Consensus 115 k~K~~d~~~~~l~~~~k~VlGTa~SmGi~V~~ 146 (166)
++++...+...|+.+|+.++-+|+.-|+.+.|
T Consensus 4 rI~L~S~d~~~Ld~~~~~I~~~ak~~g~~~~G 35 (99)
T TIGR01046 4 RIKLTSTNVRSLEKVCAQIKRIAEKTGVRMSG 35 (99)
T ss_pred EEEEEECCHHHHHHHHHHHHHHHHHcCCEEEC
Confidence 44556677788999999999999999999987
No 30
>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=21.69 E-value=1.3e+02 Score=18.34 Aligned_cols=31 Identities=19% Similarity=0.222 Sum_probs=22.3
Q ss_pred EEEEEEecCceEEEE-eCChHHHHHHHhCCCCc
Q 031095 60 TVKLTVQNRQAKVAV-VPSAAALVIKALKEPER 91 (166)
Q Consensus 60 pV~Itv~drsf~~~v-~Ppts~likka~g~~~~ 91 (166)
||.|++..++..+.. ..++..+| +.+|+.-+
T Consensus 1 ~Vtv~~dG~~~~v~T~a~tV~~~L-~~~gI~l~ 32 (43)
T PF03990_consen 1 PVTVTVDGKEKTVYTTASTVGDAL-KELGITLG 32 (43)
T ss_pred CEEEEECCEEEEEEeCCCCHHHHH-HhCCCCCC
Confidence 578888888888866 67777776 46676533
No 31
>PF04316 FlgM: Anti-sigma-28 factor, FlgM; InterPro: IPR007412 FlgM binds and inhibits the activity of the transcription factor sigma 28. Inhibition of sigma 28 prevents the expression of genes from flagellar transcriptional class 3, which include genes for the filament and chemotaxis. Correctly assembled basal body-hook structures export FlgM, relieving inhibition of sigma 28 and allowing expression of class 3 genes. NMR studies show that free FlgM is mostly unfolded, which may facilitate its export. The C-terminal half of FlgM adopts a tertiary structure when it binds to sigma 28. All mutations in FlgM that prevent sigma 28 inhibition affect the C-terminal domain and is the region thought to constitute the binding domain. A minimal binding domain has been identified between Glu 64 and Arg 88 in Salmonella typhimurium (P26477 from SWISSPROT).The N-terminal portion remains unstructured and may be necessary for recognition by the export machinery [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0019861 flagellum; PDB: 1RP3_B 1SC5_B.
Probab=21.67 E-value=53 Score=21.38 Aligned_cols=17 Identities=12% Similarity=0.362 Sum_probs=10.3
Q ss_pred ChHhHHHhhhCceeecc
Q 031095 148 DPKDLQQEINDGDVEIP 164 (166)
Q Consensus 148 ~P~e~~~~i~~g~~~~~ 164 (166)
.-.++.+.|++|+|.+.
T Consensus 29 kV~~ik~~I~~G~Y~vd 45 (57)
T PF04316_consen 29 KVAEIKAAIASGTYKVD 45 (57)
T ss_dssp HHHHHHHHHHTT-----
T ss_pred HHHHHHHHHHcCCCCCC
Confidence 46789999999999875
No 32
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=21.32 E-value=1.5e+02 Score=25.75 Aligned_cols=97 Identities=19% Similarity=0.156 Sum_probs=60.8
Q ss_pred ceEEEEEEEeccccCCCCCCccccCCCCCChhhHHHHHHH------------------Hhhc--cCC--CceeEEEEEEe
Q 031095 9 QVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAK------------------ETAK--DWK--GLRVTVKLTVQ 66 (166)
Q Consensus 9 ~~~~ikl~v~aG~A~p~PplGp~LG~~Gin~~~fck~fN~------------------~T~~--~~~--g~~ipV~Itv~ 66 (166)
.....|+.||-=+..---.+|-.|||+|-.+.+++++--- .. + .|. ..+++|.|++.
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR-~~p~yeHL~epLHVlIe~~ 168 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELR-GDPGYEHLNEPLHVLIETE 168 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhh-cCcchHHhCCCcEEEEEEe
Confidence 4556788888888777778999999999999999887521 11 1 121 46888888864
Q ss_pred cCceEEEEeCChHH--HHHHHhCCCCcCccCccCcceeeeecHHHHHHHHHHhc
Q 031095 67 NRQAKVAVVPSAAA--LVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMR 118 (166)
Q Consensus 67 drsf~~~v~Ppts~--likka~g~~~~~~k~~~~~~~~G~it~~~v~eIAk~K~ 118 (166)
.|+.-+ -|..|+-+-+.==.|-+ .+.+..+|+.|.|.+--
T Consensus 169 --------~p~~ea~~rl~~AleeI~klL~P~~----e~~dk~~QL~ELa~lng 210 (259)
T KOG1588|consen 169 --------APPAEAYARLAYALEEIKKLLVPDH----EDEDKREQLRELAILNG 210 (259)
T ss_pred --------CCHHHHHHHHHHHHHHHHHhcCCCC----CCchHHHHHHHHhhcCC
Confidence 233222 22233322111112432 35668999999998654
No 33
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=20.73 E-value=62 Score=23.97 Aligned_cols=39 Identities=21% Similarity=0.258 Sum_probs=26.6
Q ss_pred cHHHHHHHHHHhccc----CCCcChhhhhhhhhhcccceeeEe
Q 031095 106 TLDDVIEIAKIMRPR----SMAKELSGTVKEILGTCVSVGCTV 144 (166)
Q Consensus 106 t~~~v~eIAk~K~~d----~~~~~l~~~~k~VlGTa~SmGi~V 144 (166)
+++++.++++...-| -...+-+..++.++.-|+++||+|
T Consensus 129 ~~~~l~~~~~~~~id~v~ial~~~~~~~i~~ii~~~~~~~v~v 171 (175)
T PF13727_consen 129 DLDDLPELVREHDIDEVIIALPWSEEEQIKRIIEELENHGVRV 171 (175)
T ss_dssp -GGGHHHHHHHHT--EEEE--TTS-HHHHHHHHHHHHTTT-EE
T ss_pred CHHHHHHHHHhCCCCEEEEEcCccCHHHHHHHHHHHHhCCCEE
Confidence 457899998877666 223344778999999999999987
No 34
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=20.22 E-value=1.2e+02 Score=23.23 Aligned_cols=48 Identities=8% Similarity=0.107 Sum_probs=35.8
Q ss_pred eCChHHHHHHHhCCCCcCccCccCcceeeeecHHHHHHHHHHhccc-CCCcChhhhh
Q 031095 75 VPSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPR-SMAKELSGTV 130 (166)
Q Consensus 75 ~Ppts~likka~g~~~~~~k~~~~~~~~G~it~~~v~eIAk~K~~d-~~~~~l~~~~ 130 (166)
-+.+|.-|.+.+|+.+.. .+|.+|-+|+..|...-..+ ....+|...+
T Consensus 26 G~~~A~~ic~~lgi~~~~--------~~~~Lt~~qi~~l~~~i~~~~~i~~dL~~~~ 74 (122)
T CHL00137 26 GLTSAKEILEKANIDPDI--------RTKDLTDEQISALREIIEENYQVEGDLRRFE 74 (122)
T ss_pred cHHHHHHHHHHcCcCcCc--------CcccCCHHHHHHHHHHHHHhCcchHHHHHHH
Confidence 588999999999988776 38999999999999877543 3333444433
No 35
>PHA02135 hypothetical protein
Probab=20.10 E-value=42 Score=25.50 Aligned_cols=18 Identities=22% Similarity=0.473 Sum_probs=14.6
Q ss_pred hHHHHHHHHhhccCCCcee
Q 031095 41 KIGEDIAKETAKDWKGLRV 59 (166)
Q Consensus 41 ~fck~fN~~T~~~~~g~~i 59 (166)
.+.+.||+.| ++++|.-|
T Consensus 32 kvi~~fn~nt-~~~~~~~v 49 (122)
T PHA02135 32 KVISKFNDNT-SNYPGISV 49 (122)
T ss_pred HHHHHhccCC-cCCCcccc
Confidence 4678999999 99998644
Done!