Query psy13547
Match_columns 165
No_of_seqs 149 out of 1043
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 22:03:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13547.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13547hhsearch_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 1.9E-68 4.1E-73 425.9 18.3 163 1-165 1-166 (166)
2 PRK01143 rpl11p 50S ribosomal 100.0 9.5E-63 2.1E-67 392.3 15.8 147 11-161 3-154 (163)
3 PTZ00105 60S ribosomal protein 100.0 4.2E-59 9.2E-64 363.5 15.4 140 26-165 1-140 (140)
4 COG0080 RplK Ribosomal protein 100.0 1.1E-58 2.5E-63 359.5 14.7 134 9-146 4-141 (141)
5 TIGR01632 L11_bact 50S ribosom 100.0 2.1E-57 4.6E-62 353.9 14.8 132 10-145 4-140 (140)
6 PRK00140 rplK 50S ribosomal pr 100.0 1.8E-56 3.8E-61 349.1 15.3 132 10-145 6-141 (141)
7 CHL00127 rpl11 ribosomal prote 100.0 2.6E-56 5.6E-61 347.8 15.0 131 10-144 6-140 (140)
8 smart00649 RL11 Ribosomal prot 100.0 8.9E-56 1.9E-60 341.8 13.5 128 13-144 1-132 (132)
9 KOG0886|consensus 100.0 3.2E-55 6.9E-60 341.2 13.1 164 2-165 4-167 (167)
10 cd00349 Ribosomal_L11 Ribosoma 100.0 3.9E-55 8.3E-60 337.8 13.3 127 13-143 1-131 (131)
11 PRK14539 50S ribosomal protein 100.0 7.1E-53 1.5E-57 342.9 15.9 130 10-147 7-140 (196)
12 PTZ00321 ribosomal protein L11 100.0 1.6E-51 3.5E-56 352.9 16.1 137 10-147 50-195 (342)
13 KOG3257|consensus 100.0 8.6E-49 1.9E-53 308.8 11.6 132 10-145 19-157 (168)
14 PF03946 Ribosomal_L11_N: Ribo 99.9 2.2E-27 4.7E-32 161.3 6.3 58 12-69 1-60 (60)
15 PF00298 Ribosomal_L11: Riboso 99.9 5.8E-27 1.3E-31 163.2 7.0 66 74-143 2-69 (69)
16 cd02395 SF1_like-KH Splicing f 64.4 42 0.00091 25.4 7.0 33 15-47 4-36 (120)
17 COG0051 RpsJ Ribosomal protein 42.5 5.2 0.00011 30.1 -1.1 33 115-147 8-40 (104)
18 PF03990 DUF348: Domain of unk 38.3 48 0.001 20.3 3.0 27 59-86 1-28 (43)
19 PF05164 ZapA: Cell division p 32.2 52 0.0011 22.4 2.8 27 60-86 2-28 (89)
20 cd02393 PNPase_KH Polynucleoti 29.0 49 0.0011 21.7 2.1 24 24-47 9-32 (61)
21 PF13727 CoA_binding_3: CoA-bi 28.2 45 0.00098 24.7 2.0 40 105-144 129-172 (175)
22 KOG0455|consensus 27.5 67 0.0015 28.5 3.1 44 101-147 192-242 (364)
23 KOG4093|consensus 27.1 1.1E+02 0.0023 24.3 3.9 47 39-86 83-131 (144)
24 PF13184 KH_5: NusA-like KH do 27.0 58 0.0013 22.3 2.2 56 13-86 5-60 (69)
25 PF04319 NifZ: NifZ domain; I 26.3 1.2E+02 0.0025 21.5 3.7 35 1-36 1-36 (75)
26 PF03487 IL13: Interleukin-13; 25.5 33 0.00071 21.8 0.7 36 11-52 7-42 (43)
27 PF03780 Asp23: Asp23 family; 25.3 95 0.0021 21.9 3.2 33 34-66 69-106 (108)
28 PF03978 Borrelia_REV: Borreli 24.7 64 0.0014 26.1 2.4 34 111-144 94-127 (160)
29 COG0081 RplA Ribosomal protein 24.1 27 0.00059 29.7 0.2 27 28-54 128-158 (228)
30 PF02401 LYTB: LytB protein; 23.3 1.5E+02 0.0034 25.6 4.7 51 106-156 224-275 (281)
31 COG1437 CyaB Adenylate cyclase 22.8 23 0.00049 29.0 -0.5 88 69-156 81-175 (178)
32 TIGR01046 S10_Arc_S20_Euk ribo 20.9 24 0.00051 26.0 -0.8 33 115-147 5-37 (99)
33 COG4953 PbpC Membrane carboxyp 20.8 94 0.002 30.7 3.0 68 14-86 418-487 (733)
34 PRK05424 rplA 50S ribosomal pr 20.5 70 0.0015 26.8 1.9 28 27-54 125-156 (230)
35 PF04316 FlgM: Anti-sigma-28 f 20.3 65 0.0014 20.9 1.3 19 146-164 28-46 (57)
36 COG2080 CoxS Aerobic-type carb 20.1 1.7E+02 0.0037 23.5 3.9 29 58-86 2-32 (156)
No 1
>PLN03072 60S ribosomal protein L12; Provisional
Probab=100.00 E-value=1.9e-68 Score=425.88 Aligned_cols=163 Identities=65% Similarity=1.107 Sum_probs=155.2
Q ss_pred CCCCCCCCceeEEEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcC-CCCceeEEEEEEeccceEEEEeCCHHH
Q psy13547 1 MPPKFDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGD-WKGLKITVCLTIQNRQAAISVVPSAAS 79 (165)
Q Consensus 1 m~~k~~~~~~~~vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~-~~G~~vpV~itv~drsf~~~v~Pp~s~ 79 (165)
||||||+++.++|+|+|+||+|+|+|||||+|||+|||+|+||++||++|++ |+|++|||+|||.+|+|+|+++||+|+
T Consensus 1 m~~~~~~~~~~~i~l~v~aG~A~P~PplGPaLG~~GvNi~~f~k~fN~~T~~~~~G~~VpV~Itv~~rsf~~~v~Pp~s~ 80 (166)
T PLN03072 1 MPPKLDPSQVVEVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAKVSVVPSAAA 80 (166)
T ss_pred CCCCCCCCccEEEEEEEEcCccCCCCCCccccccCCCCHHHHHHHHHHHhhhhcCCCeEEEEEEEECCeEEEEeCCCHHH
Confidence 9999999999999999999999999999999999999999999999999996 999999999999779999999999999
Q ss_pred HHHHHhC--CCCCCCCCcccccceeeecHHHHHHHHHHhcccccCcChhhhhhHHhhccccceeEecCCChHHHHHHhhC
Q psy13547 80 LIIKALK--EPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVLGTCQSVGATVEGRSARDIIEAIDN 157 (165)
Q Consensus 80 Li~ka~g--kgs~~~~k~~n~~~~G~it~~~v~eIA~~k~~~~~~~~l~~~vk~VlGTa~SmGi~V~g~~p~ev~~~i~~ 157 (165)
||+|+|| ++++++ ..|.+++|+||++||+|||+.|++|+++++|+++||+|+||||||||+|+|++|+||+++||+
T Consensus 81 LLkKa~g~~kgs~~~--~~~~~~vG~it~~qv~eIA~~K~~dl~a~~l~~avk~VlGTarSmGi~V~gk~pkev~~~i~~ 158 (166)
T PLN03072 81 LVIKALKEPERDRKK--VKNIKHNGNISLDDVIEIAKIMRPRSMAKELAGTVKEILGTCVSVGCTVDGKDPKDLQQEIDD 158 (166)
T ss_pred HHHHHhCCCCCCCcc--CCCCeeeeeecHHHHHHHHHHHHHHhCcccHHHHHHHhHheeeeCeEEEeCCCHHHHHHHHhC
Confidence 9999999 566653 223489999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeccCC
Q psy13547 158 GEIEVPEE 165 (165)
Q Consensus 158 G~~~~p~~ 165 (165)
|+|+||++
T Consensus 159 G~~~~p~~ 166 (166)
T PLN03072 159 GEVEIPEA 166 (166)
T ss_pred CCeeCCCC
Confidence 99999985
No 2
>PRK01143 rpl11p 50S ribosomal protein L11P; Validated
Probab=100.00 E-value=9.5e-63 Score=392.30 Aligned_cols=147 Identities=31% Similarity=0.573 Sum_probs=144.3
Q ss_pred eEEEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcCCCCceeEEEEEE--eccceEEEE-eCCHHHHHHHHhC-
Q psy13547 11 KKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTI--QNRQAAISV-VPSAASLIIKALK- 86 (165)
Q Consensus 11 ~~vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~~~G~~vpV~itv--~drsf~~~v-~Pp~s~Li~ka~g- 86 (165)
++|+|+|+||+|+|+|||||+|||+|||+|+||++||++|++|+|++|||+||| +||+|+|++ +||+||||+|++|
T Consensus 3 ~~ikl~v~aG~A~p~PplGPaLG~~Gini~~f~k~fN~~T~~~~g~~vpV~Itv~~~drsf~~~vk~Pp~s~ll~kaag~ 82 (163)
T PRK01143 3 KVVEVLVEGGKATPGPPLGPALGPLGLNVKQVVQEINEKTKDFKGMQVPVKVIVDTDTKKFEIEVGIPPTTALIKKELGI 82 (163)
T ss_pred eEEEEEEecCccCCCCCCcccccccCCCHHHHHHHHHHHhhhcCCCeEeEEEEEEeCCceEEEEECCCCHHHHHHHHhCC
Confidence 589999999999999999999999999999999999999999999999999999 699999999 9999999999999
Q ss_pred -CCCCCCCCcccccceeeecHHHHHHHHHHhcccccCcChhhhhhHHhhccccceeEecCCChHHHHHHhhCceee
Q psy13547 87 -EPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVLGTCQSVGATVEGRSARDIIEAIDNGEIE 161 (165)
Q Consensus 87 -kgs~~~~k~~n~~~~G~it~~~v~eIA~~k~~~~~~~~l~~~vk~VlGTa~SmGi~V~g~~p~ev~~~i~~G~~~ 161 (165)
+|+++|++ +++|+||++||||||+.|++|+++.+|+++||+|+||||||||+|+|++|+||+++||+|+|+
T Consensus 83 ~kgs~~p~~----~~vG~It~~qv~eIA~~K~~d~~~~~l~~~vk~VlGTarSmGi~V~g~~pkev~~~i~~g~~~ 154 (163)
T PRK01143 83 EKGSGEPGH----EVVGNLSFEQVVKIAIMKKDDLLSYDLKAAVKEVLGTCVSMGVTVEGKDPKEVQKEVDEGKYD 154 (163)
T ss_pred cCCCCCCCC----ceeeeecHHHHHHHHHHHhhhhccccHHHHHHHHHhhHhhceEEEecCCHHHHHHHcCcccHH
Confidence 79999998 889999999999999999999999999999999999999999999999999999999999996
No 3
>PTZ00105 60S ribosomal protein L12; Provisional
Probab=100.00 E-value=4.2e-59 Score=363.48 Aligned_cols=140 Identities=74% Similarity=1.154 Sum_probs=129.7
Q ss_pred CCCccccCCCCCChHHHHHHHHHHhcCCCCceeEEEEEEeccceEEEEeCCHHHHHHHHhCCCCCCCCCcccccceeeec
Q psy13547 26 SSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVP 105 (165)
Q Consensus 26 PplgP~LG~~Gin~~~f~k~fN~~T~~~~G~~vpV~itv~drsf~~~v~Pp~s~Li~ka~gkgs~~~~k~~n~~~~G~it 105 (165)
++|||+|||+|||+|+||++||++|++|+|++|||+|||.||+|+|++.||+|+||+|++|..++.+++.++++++|+||
T Consensus 1 ~~lGPaLG~~GvNi~~fck~fN~~T~~~~G~~vpV~Itv~drsf~~~v~Pp~s~ll~k~ag~~~~~~~~~~~~~~vG~it 80 (140)
T PTZ00105 1 SSLAPKVGPLGLSPKKVGDDIAKATKDWKGLKVTVKLTVQNRQATVEVVPTASSLLIKALKEPPRDRKKVKNIKHSGNLT 80 (140)
T ss_pred CCCccccccCCCCHHHHHHHHHHHHhhcCCCeEEEEEEEECCEEEEEECCCHHHHHHHHhCCCCCCCCCCCcceeeeEee
Confidence 68999999999999999999999999999999999999999999998899999999999994333333333334899999
Q ss_pred HHHHHHHHHHhcccccCcChhhhhhHHhhccccceeEecCCChHHHHHHhhCceeeccCC
Q psy13547 106 IDEIYNISRTMRPRSMARKFVGTVKEVLGTCQSVGATVEGRSARDIIEAIDNGEIEVPEE 165 (165)
Q Consensus 106 ~~~v~eIA~~k~~~~~~~~l~~~vk~VlGTa~SmGi~V~g~~p~ev~~~i~~G~~~~p~~ 165 (165)
++||||||+.|++|+++++|+++||+|+||||||||+|+|++||||+++||+|+||||++
T Consensus 81 ~~qv~eIAk~K~~dl~~~~l~~a~k~V~GTarSmGi~V~gk~pkev~~~i~~G~~~~p~~ 140 (140)
T PTZ00105 81 FDQVIKIARTMRPKSMAKTFKGTVKEVLGTCVSIGCTVDGESPRDIQEKINNGEIKVPES 140 (140)
T ss_pred HHHHHHHHHHHHhhhCCCcHHHHHHHHHhhheeeeEEEECCCHHHHHHHHhCCCccCCCC
Confidence 999999999999999999999999999999999999999999999999999999999985
No 4
>COG0080 RplK Ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-58 Score=359.48 Aligned_cols=134 Identities=31% Similarity=0.509 Sum_probs=131.3
Q ss_pred ceeEEEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcCCCCceeEEEEEE-eccceEEEE-eCCHHHHHHHHhC
Q psy13547 9 EVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTI-QNRQAAISV-VPSAASLIIKALK 86 (165)
Q Consensus 9 ~~~~vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~~~G~~vpV~itv-~drsf~~~v-~Pp~s~Li~ka~g 86 (165)
..++|+|+++||+|+|+|||||+|||+|||+|+||++||++|++|+|++|||+||| +||||+|++ +||+|+||+|++|
T Consensus 4 ~~~~ikl~v~aGkA~p~PpvGPALG~~Gvni~~f~k~fN~~T~~~~G~~vPV~Itv~~drsftf~~ktPPas~LlkKa~g 83 (141)
T COG0080 4 VVKIIKLQVPAGKANPSPPVGPALGQLGVNIMEFCKEFNAATKDEKGLPVPVVITVYEDRSFTFIVKTPPASALLKKAAG 83 (141)
T ss_pred cceEEEEEecccccCCCCCCCccccccCCCHHHHHHHHHHHhhccCCCeeeEEEEEEcCCcEEEEECCCCHHHHHHHHhC
Confidence 57899999999999999999999999999999999999999999999999999999 799999999 9999999999999
Q ss_pred --CCCCCCCCcccccceeeecHHHHHHHHHHhcccccCcChhhhhhHHhhccccceeEecCC
Q psy13547 87 --EPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVLGTCQSVGATVEGR 146 (165)
Q Consensus 87 --kgs~~~~k~~n~~~~G~it~~~v~eIA~~k~~~~~~~~l~~~vk~VlGTa~SmGi~V~g~ 146 (165)
+||++|++ +++|+||++||+|||+.|++||++.+|++|+|+|+||||||||+|+|+
T Consensus 84 ~~~Gs~~p~k----~~vG~lt~~qv~eIA~~K~~dl~a~~l~aA~k~I~GTa~SMGv~Veg~ 141 (141)
T COG0080 84 IEKGSGKPNK----NKVGKLTLAQVREIAKTKMPDLNAKDLEAAVKEILGTARSMGVTVEGK 141 (141)
T ss_pred CCCCCCCCCc----ceeeeeeHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhhhhceEEeecC
Confidence 89999999 999999999999999999999999999999999999999999999985
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=2.1e-57 Score=353.95 Aligned_cols=132 Identities=20% Similarity=0.369 Sum_probs=128.5
Q ss_pred eeEEEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcC-CCCceeEEEEEE-eccceEEEE-eCCHHHHHHHHhC
Q psy13547 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGD-WKGLKITVCLTI-QNRQAAISV-VPSAASLIIKALK 86 (165)
Q Consensus 10 ~~~vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~-~~G~~vpV~itv-~drsf~~~v-~Pp~s~Li~ka~g 86 (165)
.++|+|+++||+|+|+|||||+|||+|||+|+||++||++|++ |+|++|||+||| +||+|+|++ +||+||||+|++|
T Consensus 4 ~~~ikl~v~aG~A~p~PplGP~LG~~Gini~~f~k~fN~~T~~~~~G~~vpV~Itv~~drsf~~~v~~Pp~s~ll~kaag 83 (140)
T TIGR01632 4 VGIIKLQVPAGQANPAPPVGPALGQRGVNIMEFCKQFNARTADYEPGLPVPVVITVYEDKSFTFIVKTPPVSYLLKKAAG 83 (140)
T ss_pred EEEEEEEEeccccCCCCCCcccccccCCCHHHHHHHHHHHHhhhcCCCeEEEEEEEeCCCeEEEEEcCCCHHHHHHHHhC
Confidence 6789999999999999999999999999999999999999999 699999999999 799999999 9999999999999
Q ss_pred --CCCCCCCCcccccceeeecHHHHHHHHHHhcccccCcChhhhhhHHhhccccceeEecC
Q psy13547 87 --EPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVLGTCQSVGATVEG 145 (165)
Q Consensus 87 --kgs~~~~k~~n~~~~G~it~~~v~eIA~~k~~~~~~~~l~~~vk~VlGTa~SmGi~V~g 145 (165)
+|+++|++ +++|+||++||||||+.|++|+++.+|+++||+|+||||||||+|++
T Consensus 84 ~~~gs~~p~~----~~~G~it~~qv~eIA~~K~~d~~~~~l~~~vk~v~GTarSmGi~V~~ 140 (140)
T TIGR01632 84 VEKGSKNPKK----EKVGKITRKQVREIAEIKMSDLNTKDIEAAMKIIAGTAKSMGIEIVG 140 (140)
T ss_pred CCCCCCCCCC----eEEeEecHHHHHHHHHHHHHHhCcccHHHHHHHhheeHeeceEEEeC
Confidence 78999998 89999999999999999999999999999999999999999999986
No 6
>PRK00140 rplK 50S ribosomal protein L11; Validated
Probab=100.00 E-value=1.8e-56 Score=349.11 Aligned_cols=132 Identities=25% Similarity=0.400 Sum_probs=128.8
Q ss_pred eeEEEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcCCCCceeEEEEEE-eccceEEEE-eCCHHHHHHHHhC-
Q psy13547 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTI-QNRQAAISV-VPSAASLIIKALK- 86 (165)
Q Consensus 10 ~~~vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~~~G~~vpV~itv-~drsf~~~v-~Pp~s~Li~ka~g- 86 (165)
.++|+|+++||+|+|+|||||+|||+|||+|+||++||++|++|+|++|||+|+| +||+|+|++ +||+||||+|++|
T Consensus 6 ~~~ikl~v~aG~A~p~PplgP~LG~~Gini~~f~k~fN~~T~~~~g~~vpV~i~v~~drsf~~~v~~Pp~s~ll~k~~g~ 85 (141)
T PRK00140 6 VGYIKLQIPAGKANPAPPVGPALGQRGVNIMEFCKAFNARTQDQKGLPIPVVITVYEDRSFTFITKTPPASVLLKKAAGI 85 (141)
T ss_pred ceEEEEEEecCccCCCCCCcccccccCCCHHHHHHHHHHHHhhcCCCeEEEEEEEecCCeEEEEEcCCCHHHHHHHHhCC
Confidence 5689999999999999999999999999999999999999999999999999999 799999999 9999999999999
Q ss_pred -CCCCCCCCcccccceeeecHHHHHHHHHHhcccccCcChhhhhhHHhhccccceeEecC
Q psy13547 87 -EPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVLGTCQSVGATVEG 145 (165)
Q Consensus 87 -kgs~~~~k~~n~~~~G~it~~~v~eIA~~k~~~~~~~~l~~~vk~VlGTa~SmGi~V~g 145 (165)
+|+++|++ +++|+||++||||||+.|++|+++++|+++||+|+||||||||+|+|
T Consensus 86 ~~gs~~p~~----~~vG~it~~~v~eIA~~K~~d~~~~~l~~~vk~VlGTa~SmGi~V~g 141 (141)
T PRK00140 86 EKGSGEPNK----EKVGKITRAQVREIAETKMPDLNAADIEAAMRMIAGTARSMGIVVEG 141 (141)
T ss_pred CCCCCCCCC----eEEeeEcHHHHHHHHHHHHHhhCCCcHHHHHHHhheeeeEeeEEEeC
Confidence 78889988 89999999999999999999999999999999999999999999986
No 7
>CHL00127 rpl11 ribosomal protein L11; Validated
Probab=100.00 E-value=2.6e-56 Score=347.81 Aligned_cols=131 Identities=20% Similarity=0.346 Sum_probs=127.5
Q ss_pred eeEEEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcCCCCceeEEEEEE-eccceEEEE-eCCHHHHHHHHhC-
Q psy13547 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTI-QNRQAAISV-VPSAASLIIKALK- 86 (165)
Q Consensus 10 ~~~vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~~~G~~vpV~itv-~drsf~~~v-~Pp~s~Li~ka~g- 86 (165)
..+|+|+++||+|+|+|||||+|||+|||+|+||+|||++|++|+|++|||+|+| +||+|+|++ +||+||||+|++|
T Consensus 6 ~~~ikl~v~aG~A~p~PplGP~LG~~Gini~~f~k~fN~~T~~~~g~~vpV~Itv~~drsf~~~v~~Pp~s~ll~ka~gi 85 (140)
T CHL00127 6 LAIIKLALPAGKATPAPPVGPALGQHGVNINLFCKEYNARTKDKIGLIIPVEISVYEDKSYTFILKTPPASVLLAKAAGI 85 (140)
T ss_pred ccEEEEEEecCccCCCCCCcccccccCCCHHHHHHHHHHHhhhcCCCeEEEEEEEeCCceEEEEEcCCCHHHHHHHHhCC
Confidence 5689999999999999999999999999999999999999999999999999999 799999999 9999999999999
Q ss_pred -CCCCCCCCcccccceeeecHHHHHHHHHHhcccccCcChhhhhhHHhhccccceeEec
Q psy13547 87 -EPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVLGTCQSVGATVE 144 (165)
Q Consensus 87 -kgs~~~~k~~n~~~~G~it~~~v~eIA~~k~~~~~~~~l~~~vk~VlGTa~SmGi~V~ 144 (165)
+|+++|++ +++|+||++||||||+.|++|+++.+|+++||+|+||||||||+|.
T Consensus 86 ~~gs~~p~~----~~~G~it~~~v~eIA~~K~~d~~~~~l~~~vk~v~GTa~SmGi~V~ 140 (140)
T CHL00127 86 KKGSGEPNK----KKVGSITIKQLEEIAQIKLPDLNTISLSKAIKIIEGTAKNMGISIK 140 (140)
T ss_pred CcCCCCCCC----eecceecHHHHHHHHHHHhhhhccccHHHHHHHhHeeheeceEEeC
Confidence 78888888 9999999999999999999999999999999999999999999983
No 8
>smart00649 RL11 Ribosomal protein L11/L12.
Probab=100.00 E-value=8.9e-56 Score=341.76 Aligned_cols=128 Identities=32% Similarity=0.542 Sum_probs=125.3
Q ss_pred EEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcCCCCceeEEEEEE-eccceEEEE-eCCHHHHHHHHhC--CC
Q psy13547 13 VYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTI-QNRQAAISV-VPSAASLIIKALK--EP 88 (165)
Q Consensus 13 vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~~~G~~vpV~itv-~drsf~~~v-~Pp~s~Li~ka~g--kg 88 (165)
|+|+|+||+|+|+|||||+|||+|||+|+||++||++|++|+|++|||+|+| +||+|+|++ +||+||||+|++| +|
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~~kg 80 (132)
T smart00649 1 IKLQIPAGKANPAPPLGPALGQLGINIMEFCKEFNARTKDKKGLPIPVKITVYNDKSFTFIIKTPPASFLLKKAAGIEKG 80 (132)
T ss_pred CEEEEecCccCCCCCcccccccCCCCHHHHHHHHHHHHhhcCCCeEeEEEEEeCCCeEEEEEcCCCHHHHHHHHhCCCCC
Confidence 6899999999999999999999999999999999999999999999999999 799999999 9999999999999 79
Q ss_pred CCCCCCcccccceeeecHHHHHHHHHHhcccccCcChhhhhhHHhhccccceeEec
Q psy13547 89 PRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVLGTCQSVGATVE 144 (165)
Q Consensus 89 s~~~~k~~n~~~~G~it~~~v~eIA~~k~~~~~~~~l~~~vk~VlGTa~SmGi~V~ 144 (165)
+++|++ +++|+||++||||||+.|++|+++.+|+++||+|+||||||||+|+
T Consensus 81 s~~p~~----~~~g~it~~~v~eIA~~K~~d~~~~~l~~~~k~V~GTa~SmGi~V~ 132 (132)
T smart00649 81 SKKPGK----KKVGNITLDQVYEIAKIKRPDLNAKDLEAAVKEILGTARSMGITVE 132 (132)
T ss_pred CCCCCC----eeeeEEcHHHHHHHHHHHHHHhcchhHHHHHHHHHhhHhcceEEeC
Confidence 999998 9999999999999999999999999999999999999999999986
No 9
>KOG0886|consensus
Probab=100.00 E-value=3.2e-55 Score=341.20 Aligned_cols=164 Identities=74% Similarity=1.173 Sum_probs=161.3
Q ss_pred CCCCCCCceeEEEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcCCCCceeEEEEEEeccceEEEEeCCHHHHH
Q psy13547 2 PPKFDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQAAISVVPSAASLI 81 (165)
Q Consensus 2 ~~k~~~~~~~~vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~~~G~~vpV~itv~drsf~~~v~Pp~s~Li 81 (165)
+|||||+++++|||||.||++.+++.|+|.+||+|++++++++++.++|++|+|++|+|+++|+||+..++|.|++|+||
T Consensus 4 ~pkfdP~eiK~vylrc~GgEVgatsaLApKIgPLGLSpKkvGedIaKaT~dwKgl~vtvkLtIqnR~A~i~VvpSasaLi 83 (167)
T KOG0886|consen 4 KPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGEDIAKATGDWKGLRVTVKLTIQNRQAQIEVVPSASALI 83 (167)
T ss_pred CCCCCccceEEEEEEeecCccccccccccccccccCCccccchHHHHhhcccccceEEEEEEecCcccceEEcccHHHHH
Confidence 34599999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCCCCCCCcccccceeeecHHHHHHHHHHhcccccCcChhhhhhHHhhccccceeEecCCChHHHHHHhhCceee
Q psy13547 82 IKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVLGTCQSVGATVEGRSARDIIEAIDNGEIE 161 (165)
Q Consensus 82 ~ka~gkgs~~~~k~~n~~~~G~it~~~v~eIA~~k~~~~~~~~l~~~vk~VlGTa~SmGi~V~g~~p~ev~~~i~~G~~~ 161 (165)
+|+|++++|+++++||++|+|||+|++|.+||++|++.+++++|++++++|+|||+|+||+|||++|||++++||+|+++
T Consensus 84 IkaLKEPpRDRKk~knikh~Gni~~deiv~iar~mr~rS~a~~l~gt~keilgt~~svgc~vDgk~Phdi~~~i~~Geie 163 (167)
T KOG0886|consen 84 IKALKEPPRDRKKQKNIKHSGNITFDEIVEIARIMRPRSLARELSGTVKEILGTAQSVGCTVDGKHPHDIIDEINAGEIE 163 (167)
T ss_pred HHHhcCCcchhhhhccccccCcccHHHHHHHHHHhhhHhhhhhhhhhHHHHhchhhhcccccCCCChHHHHhhhcCCcee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCC
Q psy13547 162 VPEE 165 (165)
Q Consensus 162 ~p~~ 165 (165)
||++
T Consensus 164 ~P~~ 167 (167)
T KOG0886|consen 164 IPAN 167 (167)
T ss_pred CCCC
Confidence 9985
No 10
>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=3.9e-55 Score=337.85 Aligned_cols=127 Identities=31% Similarity=0.562 Sum_probs=124.3
Q ss_pred EEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcCCCCceeEEEEEE-eccceEEEE-eCCHHHHHHHHhC--CC
Q psy13547 13 VYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTI-QNRQAAISV-VPSAASLIIKALK--EP 88 (165)
Q Consensus 13 vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~~~G~~vpV~itv-~drsf~~~v-~Pp~s~Li~ka~g--kg 88 (165)
|+|+|+||+|+|+|||||+|||+|||+|+||++||++|++|+|++|||+|+| +||+|+|++ +||+||||+|++| +|
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~~kg 80 (131)
T cd00349 1 IKLQVPAGKASPAPPLGPALGQLGVNIMKFCKEFNARTKDYKGLPVPVKITVYNDRSFTFEVKTPPASALLKKAAGIEKG 80 (131)
T ss_pred CEEEEecCccCCCCCcccccccCCCCHHHHHHHHHHHHhhcCCCeEEEEEEEeCCCeEEEEEcCCCHHHHHHHHhCCCCC
Confidence 5899999999999999999999999999999999999999999999999999 799999999 9999999999999 89
Q ss_pred CCCCCCcccccceeeecHHHHHHHHHHhcccccCcChhhhhhHHhhccccceeEe
Q psy13547 89 PRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVLGTCQSVGATV 143 (165)
Q Consensus 89 s~~~~k~~n~~~~G~it~~~v~eIA~~k~~~~~~~~l~~~vk~VlGTa~SmGi~V 143 (165)
+++|++ +++|+||++||||||+.|++|+++.+|+++||+|+||||||||+|
T Consensus 81 s~~~~~----~~~g~it~~~v~eIA~~K~~dl~~~~l~~~vk~v~GTa~SmGi~V 131 (131)
T cd00349 81 SKKPNK----EKVGNITLDQVYEIAKIKLPDLNAKTLKSAVKEILGTARSMGITV 131 (131)
T ss_pred CCCCCC----eeeeeecHHHHHHHHHHHHhhhcchhHHHHHHHHHhhHhhCeEEC
Confidence 999988 999999999999999999999999999999999999999999986
No 11
>PRK14539 50S ribosomal protein L11/unknown domain fusion protein; Provisional
Probab=100.00 E-value=7.1e-53 Score=342.86 Aligned_cols=130 Identities=20% Similarity=0.325 Sum_probs=125.8
Q ss_pred eeEEEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcCCCCceeEEEEEE-eccceEEEE-eCCHHHHHHHHhC-
Q psy13547 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTI-QNRQAAISV-VPSAASLIIKALK- 86 (165)
Q Consensus 10 ~~~vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~~~G~~vpV~itv-~drsf~~~v-~Pp~s~Li~ka~g- 86 (165)
.++|+|+++||+|+| ||+|||+|||+|+||++||++|++|.|++|||+||| +||+|+|++ +||+||||+|++|
T Consensus 7 ~~~Ikl~v~AGkA~P----GPaLG~~GVNi~~FcKefN~~Tk~~~G~~VPV~ItV~~DRsf~f~vktPptS~LLkKaagi 82 (196)
T PRK14539 7 VKVAKLQFNAGQAKP----GPSLAGVGINMPEFTKQFNDATRDRGGEPVPVQITVYKDKSFDFKLFTAPASFKIKQAAKI 82 (196)
T ss_pred heEEEEEEECCccCC----CCcccccCCCHHHHHHHHHHHhhhcCCceEEEEEEEecCCeEEEEEeCCCHHHHHHHHhCC
Confidence 679999999999999 667899999999999999999999999999999999 899999999 9999999999999
Q ss_pred -CCCCCCCCcccccceeeecHHHHHHHHHHhcccccCcChhhhhhHHhhccccceeEecCCC
Q psy13547 87 -EPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVLGTCQSVGATVEGRS 147 (165)
Q Consensus 87 -kgs~~~~k~~n~~~~G~it~~~v~eIA~~k~~~~~~~~l~~~vk~VlGTa~SmGi~V~g~~ 147 (165)
+||++|++ +++|+||++||||||+.|++|+++.+|+++||+|+||||||||+|+|+|
T Consensus 83 ~kGs~~p~k----~~vG~Itl~qv~eIAk~K~~Dl~~~~Le~avK~VlGTArSMGI~Veg~d 140 (196)
T PRK14539 83 KSGSANSKT----TIVGTITLSQLEEIAKYKLPDLNTDDVEEAMHTIAGTAKNMGVLVEGYD 140 (196)
T ss_pred CCCCCCCCC----eEEEEecHHHHHHHHHHHhhhhCCCcHHHHHHHHHhhheeCeEEEEccc
Confidence 89999999 8899999999999999999999999999999999999999999999987
No 12
>PTZ00321 ribosomal protein L11; Provisional
Probab=100.00 E-value=1.6e-51 Score=352.87 Aligned_cols=137 Identities=13% Similarity=0.241 Sum_probs=127.5
Q ss_pred eeEEEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcC-C-CCceeEEEEEE-eccceEEEE-eCCHHHHHHHHh
Q psy13547 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGD-W-KGLKITVCLTI-QNRQAAISV-VPSAASLIIKAL 85 (165)
Q Consensus 10 ~~~vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~-~-~G~~vpV~itv-~drsf~~~v-~Pp~s~Li~ka~ 85 (165)
...|||+|+||+|+|+|||||+|||+|||+|+|||+||++|++ | .|++|||+||| +||||+|++ +||+||||+|++
T Consensus 50 ~~~IKL~VpAGKAtPaPPVGPALGq~GVNImqFCKeFNerTK~~fk~GvpVPV~ITVy~DKSF~F~IktPPtS~LLKKAA 129 (342)
T PTZ00321 50 LHNWRFFIKAGKAATGPPVGQEFSKLGLKAMDFAKSFNDRTKPHFKDDVELIVRIQVYFDKSYLFTIEPPPTAWFILRAL 129 (342)
T ss_pred eEEEEEEEECCCcCCCCCCcccccccCCCHHHHHHHHHHHHHhhccCCCeEeEEEEEeCCCeEEEEECCCCHHHHHHHHh
Confidence 7789999999999999999999999999999999999999998 6 59999999999 899999999 999999999999
Q ss_pred C--CCCCCCCCcccccceeeecHHHHHHHHHHhcccccC---cChhhhhhHHhhccccceeEecCCC
Q psy13547 86 K--EPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMA---RKFVGTVKEVLGTCQSVGATVEGRS 147 (165)
Q Consensus 86 g--kgs~~~~k~~n~~~~G~it~~~v~eIA~~k~~~~~~---~~l~~~vk~VlGTa~SmGi~V~g~~ 147 (165)
| +|+++|++.+ -+++|+||++||||||++|++|+++ .+|+++||+|+||||||||+|+|+|
T Consensus 130 GI~KGS~~P~~~k-~e~VG~ITlkQVyEIAkiK~~DLnal~~~~LesAvK~ViGTARSMGIkVeGKD 195 (342)
T PTZ00321 130 RKKRRETGPVPLR-GHYCALMTLEMAYEIAKMKPRSWGRPEYPLIETRVRRVVGQARRMGVCFIGVD 195 (342)
T ss_pred CCCCCCCCCCCCC-CceEEeccHHHHHHHHHHhhhccccccccCHHHHHHHHHhhHhcCeEEEeccc
Confidence 9 7888883211 1689999999999999999999875 7999999999999999999999975
No 13
>KOG3257|consensus
Probab=100.00 E-value=8.6e-49 Score=308.80 Aligned_cols=132 Identities=20% Similarity=0.349 Sum_probs=128.2
Q ss_pred eeEEEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcCCC-CceeEEEEEE-eccceEEEE-eCCHHHHHHHHhC
Q psy13547 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWK-GLKITVCLTI-QNRQAAISV-VPSAASLIIKALK 86 (165)
Q Consensus 10 ~~~vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~~~-G~~vpV~itv-~drsf~~~v-~Pp~s~Li~ka~g 86 (165)
...+|+.++||.|.|+||+||+|||+|||+++||+|||++|++|+ |+|+|++||+ .||||+|++ +||+||||+||||
T Consensus 19 ~~~ikl~v~Ag~A~~~pp~gP~Lgqr~l~viafckefnarT~~~k~~vplp~kiTv~pDrsftf~iktPpts~lL~kAag 98 (168)
T KOG3257|consen 19 SASIKLIVKAGLAAPAPPLGPALGQRGLNVIAFCKEFNARTKKVKPGVPLPGKITVKPDRSFTFIIKTPPTSWLLKKAAG 98 (168)
T ss_pred eeEEEEeeccccccCCCCCCchhhhcchhHHHhchhhhhhhccccCCCccceeEeecCCCeEEEEecCCChHHHHHHHhC
Confidence 568999999999999999999999999999999999999999996 9999999999 899999999 9999999999999
Q ss_pred --CCCCCCCCcccccceeeecHHHHHHHHHHhccccc--CcChhhhhhHHhhccccceeEecC
Q psy13547 87 --EPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSM--ARKFVGTVKEVLGTCQSVGATVEG 145 (165)
Q Consensus 87 --kgs~~~~k~~n~~~~G~it~~~v~eIA~~k~~~~~--~~~l~~~vk~VlGTa~SmGi~V~g 145 (165)
+|+++|++ +.+|.||++||||||++|.+|.+ ..+|+++||+|+||||||||+|+.
T Consensus 99 v~KGs~~p~~----~~vG~lTlkhvyeIAkiK~~D~~~q~~~lesi~rsiigtA~smGIkVvp 157 (168)
T KOG3257|consen 99 VEKGSKDPGQ----EKVGMLTLKHVYEIAKIKLPDPNLQCTTLESICRSIIGTARSMGIKVVP 157 (168)
T ss_pred cccCCCCCcc----eeeeeEEHHHHHHHHHhhcCCcccccccHHHHHHHHHHHHHhCccccch
Confidence 99999999 89999999999999999999977 789999999999999999999987
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=99.94 E-value=2.2e-27 Score=161.33 Aligned_cols=58 Identities=34% Similarity=0.630 Sum_probs=55.5
Q ss_pred EEEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcCCC-CceeEEEEEE-eccce
Q psy13547 12 KVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWK-GLKITVCLTI-QNRQA 69 (165)
Q Consensus 12 ~vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~~~-G~~vpV~itv-~drsf 69 (165)
+|||+|+||+|+|+|||||+|||+|||+++||+|||++|++|+ |++|||+|+| +||||
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 6899999999999999999999999999999999999999998 9999999999 79988
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=5.8e-27 Score=163.19 Aligned_cols=66 Identities=27% Similarity=0.451 Sum_probs=64.3
Q ss_pred eCCHHHHHHHHhC--CCCCCCCCcccccceeeecHHHHHHHHHHhcccccCcChhhhhhHHhhccccceeEe
Q psy13547 74 VPSAASLIIKALK--EPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVLGTCQSVGATV 143 (165)
Q Consensus 74 ~Pp~s~Li~ka~g--kgs~~~~k~~n~~~~G~it~~~v~eIA~~k~~~~~~~~l~~~vk~VlGTa~SmGi~V 143 (165)
+||+||||+|++| +||++|++ +++|+||++||||||++|+.|+++.+|+++||+|+||||||||+|
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 TPPTSWLLKKAAGIKKGSSKPGK----EKVGTITLKQIYEIAKIKQKDLNAKSLESAVKSVIGTARSMGIKV 69 (69)
T ss_dssp SSTHHHHHHHHHTTSSSSSSTTT----SSSEEEEHHHHHHHHHHHTTTSSSSSHHHHHHHHHHHHHTTTEEE
T ss_pred CCChHHHHHHHhCCCCCCCCCCC----ceeeeecHHHHHHHHHHhhcccccCCHHHHHHHHHHHHhcCceEC
Confidence 6999999999999 89999999 889999999999999999999999999999999999999999987
No 16
>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=64.40 E-value=42 Score=25.43 Aligned_cols=33 Identities=12% Similarity=0.121 Sum_probs=25.5
Q ss_pred EEEeccccCCCCCCccccCCCCCChHHHHHHHH
Q psy13547 15 LRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIA 47 (165)
Q Consensus 15 l~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN 47 (165)
+.+|.=+-+--.-+|-.|||.|-++++.+++.+
T Consensus 4 i~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg 36 (120)
T cd02395 4 VYIPVKQYPKYNFVGLILGPRGNTLKQLEKETG 36 (120)
T ss_pred EEcCcccCCCCCeeEEEECCCChHHHHHHHHHC
Confidence 444544554456789999999999999999886
No 17
>COG0051 RpsJ Ribosomal protein S10 [Translation, ribosomal structure and biogenesis]
Probab=42.53 E-value=5.2 Score=30.11 Aligned_cols=33 Identities=21% Similarity=0.214 Sum_probs=27.5
Q ss_pred HhcccccCcChhhhhhHHhhccccceeEecCCC
Q psy13547 115 TMRPRSMARKFVGTVKEVLGTCQSVGATVEGRS 147 (165)
Q Consensus 115 ~k~~~~~~~~l~~~vk~VlGTa~SmGi~V~g~~ 147 (165)
+++.....+.|+..|++|.-||+.+|+.|.|--
T Consensus 8 I~L~s~d~~~LD~~~~~Ive~akrtg~~v~GPi 40 (104)
T COG0051 8 IRLKSFDHRLLDQVCREIVETAKRTGADVKGPI 40 (104)
T ss_pred EEEecCCHHHHHHHHHHHHHHHHHhCCeeeCCc
Confidence 445556678899999999999999999999843
No 18
>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=38.35 E-value=48 Score=20.35 Aligned_cols=27 Identities=11% Similarity=0.286 Sum_probs=20.9
Q ss_pred EEEEEEeccceEEEE-eCCHHHHHHHHhC
Q psy13547 59 TVCLTIQNRQAAISV-VPSAASLIIKALK 86 (165)
Q Consensus 59 pV~itv~drsf~~~v-~Pp~s~Li~ka~g 86 (165)
||.|+++.++..+.. ......+|. .+|
T Consensus 1 ~Vtv~~dG~~~~v~T~a~tV~~~L~-~~g 28 (43)
T PF03990_consen 1 PVTVTVDGKEKTVYTTASTVGDALK-ELG 28 (43)
T ss_pred CEEEEECCEEEEEEeCCCCHHHHHH-hCC
Confidence 578888899999988 777777775 445
No 19
>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=32.21 E-value=52 Score=22.45 Aligned_cols=27 Identities=26% Similarity=0.236 Sum_probs=22.8
Q ss_pred EEEEEeccceEEEEeCCHHHHHHHHhC
Q psy13547 60 VCLTIQNRQAAISVVPSAASLIIKALK 86 (165)
Q Consensus 60 V~itv~drsf~~~v~Pp~s~Li~ka~g 86 (165)
|+|+|-+|+|.|.+++.--..+.+++.
T Consensus 2 V~v~I~G~~y~i~~~~~~ee~l~~~a~ 28 (89)
T PF05164_consen 2 VKVTILGREYRIKCPDEDEEYLRKAAE 28 (89)
T ss_dssp EEEEETTEEEEECETGCGHHHHHHHHH
T ss_pred eEEEECCEEEEeecCCCCHHHHHHHHH
Confidence 678889999999998877778887776
No 20
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=29.01 E-value=49 Score=21.69 Aligned_cols=24 Identities=25% Similarity=0.394 Sum_probs=20.6
Q ss_pred CCCCCccccCCCCCChHHHHHHHH
Q psy13547 24 ATSSLAPKIGPLGLSPKKVGDDIA 47 (165)
Q Consensus 24 p~PplgP~LG~~Gin~~~f~k~fN 47 (165)
|..-+|-.+|.-|-++.++.++++
T Consensus 9 p~~~ig~iIGkgG~~ik~I~~~tg 32 (61)
T cd02393 9 PPDKIRDVIGPGGKTIKKIIEETG 32 (61)
T ss_pred ChhheeeeECCCchHHHHHHHHHC
Confidence 345678899999999999999997
No 21
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=28.15 E-value=45 Score=24.72 Aligned_cols=40 Identities=13% Similarity=0.245 Sum_probs=27.3
Q ss_pred cHHHHHHHHHHhccc----ccCcChhhhhhHHhhccccceeEec
Q psy13547 105 PIDEIYNISRTMRPR----SMARKFVGTVKEVLGTCQSVGATVE 144 (165)
Q Consensus 105 t~~~v~eIA~~k~~~----~~~~~l~~~vk~VlGTa~SmGi~V~ 144 (165)
+++++.++++...-| ....+-+..+++++.-|+++||+|-
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 568899998876655 2234447789999999999999873
No 22
>KOG0455|consensus
Probab=27.48 E-value=67 Score=28.48 Aligned_cols=44 Identities=14% Similarity=0.242 Sum_probs=31.6
Q ss_pred eeeecHHHHHHHHHHh-------cccccCcChhhhhhHHhhccccceeEecCCC
Q psy13547 101 NGNVPIDEIYNISRTM-------RPRSMARKFVGTVKEVLGTCQSVGATVEGRS 147 (165)
Q Consensus 101 ~G~it~~~v~eIA~~k-------~~~~~~~~l~~~vk~VlGTa~SmGi~V~g~~ 147 (165)
.|+++|.||+++|+.- +.|++..+...-+- =-+|-.|+.|+..+
T Consensus 192 ~~~~sfsdvVk~AKklGYTEPDPRDDLnGmDVARKvt---Il~Ri~Gv~ves~~ 242 (364)
T KOG0455|consen 192 PGTLSFSDVVKAAKKLGYTEPDPRDDLNGMDVARKVT---ILARILGVRVESMD 242 (364)
T ss_pred CCcccHHHHHHHHHHcCCCCCCcccccccchhhhhhh---hhhhhccceeeccc
Confidence 5789999999999963 34688877654433 33677888888543
No 23
>KOG4093|consensus
Probab=27.11 E-value=1.1e+02 Score=24.26 Aligned_cols=47 Identities=15% Similarity=0.250 Sum_probs=32.9
Q ss_pred hHHHHHHHHHHhcCCC-CceeEEEEEEeccceEEEE-eCCHHHHHHHHhC
Q psy13547 39 PKKVGDDIAKATGDWK-GLKITVCLTIQNRQAAISV-VPSAASLIIKALK 86 (165)
Q Consensus 39 ~~~f~k~fN~~T~~~~-G~~vpV~itv~drsf~~~v-~Pp~s~Li~ka~g 86 (165)
.-+||..||+...||. |.-+...-+- .-+-+-.+ .|-.-+|-+..+.
T Consensus 83 WR~F~~~f~~kvdDyn~GTLlR~daS~-ey~~e~TifvpRiqflAiEiAR 131 (144)
T KOG4093|consen 83 WRPFCEKFEKKVDDYNFGTLLRIDASK-EYSQETTIFVPRIQFLAIEIAR 131 (144)
T ss_pred HHHHHHHHHhhhcccccceeeeecccc-ccCCCceEEEeehhhHHHHHHh
Confidence 5689999999999997 8665533222 22223344 8999998888876
No 24
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=26.98 E-value=58 Score=22.27 Aligned_cols=56 Identities=21% Similarity=0.291 Sum_probs=33.9
Q ss_pred EEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcCCCCceeEEEEEEeccceEEEEeCCHHHHHHHHhC
Q psy13547 13 VYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQAAISVVPSAASLIIKALK 86 (165)
Q Consensus 13 vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~~~G~~vpV~itv~drsf~~~v~Pp~s~Li~ka~g 86 (165)
.++-|..+.. ---|+|-.+|+.|..+..+.+++| |.+|-|... ++-...|+.+++-
T Consensus 5 ~kvaV~~~~~-~~d~vG~~iG~~G~rik~i~~~L~-------gekIdvV~~----------s~d~~~fI~nal~ 60 (69)
T PF13184_consen 5 TKVAVKSGDP-NIDPVGACIGKKGSRIKAISEELN-------GEKIDVVEY----------SDDPKEFIKNALS 60 (69)
T ss_dssp EEEEEEESST-TS-HHHHHH-CCCCCHHHHHHHTT-------T-EEEEEE------------SSHHHHHHHHTT
T ss_pred EEEEEEcCCC-CcCcceecCccccHHHHHHHHHhC-------CCeEEEEEc----------CCCHHHHHHHhCC
Confidence 3455555552 235789999999999999999996 444433222 5555666666654
No 25
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=26.34 E-value=1.2e+02 Score=21.53 Aligned_cols=35 Identities=20% Similarity=0.281 Sum_probs=24.8
Q ss_pred CCCCCCCCc-eeEEEEEEeccccCCCCCCccccCCCC
Q psy13547 1 MPPKFDPTE-VKKVYLRCVGGEVGATSSLAPKIGPLG 36 (165)
Q Consensus 1 m~~k~~~~~-~~~vkl~v~aG~A~p~PplgP~LG~~G 36 (165)
|||+|+..+ ++..+-...=|.- |.-+.|-.|-..|
T Consensus 1 ~~p~f~~G~~V~a~~~irNDGt~-Pg~~~g~lLv~~G 36 (75)
T PF04319_consen 1 MPPRFEWGDKVRARKDIRNDGTF-PGKEIGELLVRKG 36 (75)
T ss_pred CCCccCCCCEEEEEEEeEcCCCC-CCCCCCCEEEcCC
Confidence 899999987 5566666666765 5566777776555
No 26
>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=25.53 E-value=33 Score=21.77 Aligned_cols=36 Identities=17% Similarity=0.334 Sum_probs=11.5
Q ss_pred eEEEEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcC
Q psy13547 11 KKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGD 52 (165)
Q Consensus 11 ~~vkl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~ 52 (165)
.+|-|.|-||-|+|+|---+. ..++..+|.-+-|++
T Consensus 7 ~vialtClggLasPgPvp~~~------alkELIeELvNITqn 42 (43)
T PF03487_consen 7 VVIALTCLGGLASPGPVPSST------ALKELIEELVNITQN 42 (43)
T ss_dssp ----------------S-HHH------HHHHHHHHHHHHHHS
T ss_pred HHHHHHHhcccCCCCCCCchH------HHHHHHHHHHhhccC
Confidence 467799999999997732222 467777777777664
No 27
>PF03780 Asp23: Asp23 family; InterPro: IPR005531 This entry represents the alkaline shock protein 23 family. These small proteins are involved in alkaline pH tolerance of Staphylococcus aureus [,].
Probab=25.33 E-value=95 Score=21.92 Aligned_cols=33 Identities=15% Similarity=0.457 Sum_probs=25.8
Q ss_pred CCCCChHHHHHHHHHHhcC----CCCcee-EEEEEEec
Q psy13547 34 PLGLSPKKVGDDIAKATGD----WKGLKI-TVCLTIQN 66 (165)
Q Consensus 34 ~~Gin~~~f~k~fN~~T~~----~~G~~v-pV~itv~d 66 (165)
.+|.|+.++|+++.++-++ +.|+.+ .|.|+|+|
T Consensus 69 ~~g~~i~~v~~~iq~~V~~~v~~~tg~~v~~V~V~V~~ 106 (108)
T PF03780_consen 69 EYGVNIPEVAEEIQEKVKEAVEEMTGIEVSEVNVHVED 106 (108)
T ss_pred ECCccHHHHHHHHHHHHHHHHHHHHCCeeEEEEEEEEe
Confidence 6889999999999999874 358877 47777643
No 28
>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=24.73 E-value=64 Score=26.05 Aligned_cols=34 Identities=12% Similarity=0.101 Sum_probs=29.9
Q ss_pred HHHHHhcccccCcChhhhhhHHhhccccceeEec
Q psy13547 111 NISRTMRPRSMARKFVGTVKEVLGTCQSVGATVE 144 (165)
Q Consensus 111 eIA~~k~~~~~~~~l~~~vk~VlGTa~SmGi~V~ 144 (165)
+-|+.+..++...+.+..-..|--+|+|+|++|-
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 3488888888888888899999999999999997
No 29
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=24.14 E-value=27 Score=29.67 Aligned_cols=27 Identities=52% Similarity=0.822 Sum_probs=19.6
Q ss_pred CccccCCCCC--ChHH--HHHHHHHHhcCCC
Q psy13547 28 LAPKIGPLGL--SPKK--VGDDIAKATGDWK 54 (165)
Q Consensus 28 lgP~LG~~Gi--n~~~--f~k~fN~~T~~~~ 54 (165)
|||.|||+|+ |+.- +..|++++-.+++
T Consensus 128 LG~vLGPRGlMP~Pk~gTvt~Dv~~av~~~K 158 (228)
T COG0081 128 LGKVLGPRGLMPNPKTGTVTDDVAKAVEELK 158 (228)
T ss_pred HhhhcCCCCCCCCCCCCCCCcCHHHHHHHHh
Confidence 7999999998 4444 5666666666664
No 30
>PF02401 LYTB: LytB protein; InterPro: IPR003451 Terpenes are among the largest groups of natural products and include compounds such as vitamins, cholesterol and carotenoids. The biosynthesis of all terpenoids begins with one or both of the two C5 precursors of the pathway: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In animals, fungi, and certain bacteria, the synthesis of IPP and DMAPP occurs via the well-known mevalonate pathway, however, a second, nonmevalonate terpenoid pathway has been identified in many eubacteria, algae and the chloroplasts of higher plants []. LytB(IspH) catalyses the conversion of 1-hydroy-2-methyl-2-(E)-butenyl 4-diphosphate into IPP and DMAPP in this second pathway The enzyme appears to be responsible for a branch-step in the nonmevalonate pathway, in that IPP and DMAPP are produced in parallel from a single precursor although the exact mechanism of this is not currently fully understood []. Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response [].; GO: 0019288 isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway, 0055114 oxidation-reduction process; PDB: 3DNF_B 3SZL_B 3KE8_B 3KEF_B 3SZU_A 3KEL_A 3F7T_B 3KE9_B 3KEM_B 3T0G_A ....
Probab=23.35 E-value=1.5e+02 Score=25.62 Aligned_cols=51 Identities=18% Similarity=0.096 Sum_probs=34.5
Q ss_pred HHHHHHHHHHhccc-ccCcChhhhhhHHhhccccceeEecCCChHHHHHHhh
Q psy13547 106 IDEIYNISRTMRPR-SMARKFVGTVKEVLGTCQSVGATVEGRSARDIIEAID 156 (165)
Q Consensus 106 ~~~v~eIA~~k~~~-~~~~~l~~~vk~VlGTa~SmGi~V~g~~p~ev~~~i~ 156 (165)
=.+|+|||+..-.+ ..-.+.+..-.+.+--++++||+----.|..+++++-
T Consensus 224 T~kL~eia~~~~~~t~~Ie~~~el~~~~l~~~~~VGItaGASTP~~ii~eVi 275 (281)
T PF02401_consen 224 TRKLAEIAKEHGKPTYHIETADELDPEWLKGVKKVGITAGASTPDWIIEEVI 275 (281)
T ss_dssp HHHHHHHHHHCTTCEEEESSGGG--HHHHTT-SEEEEEE-TTS-HHHHHHHH
T ss_pred HHHHHHHHHHhCCCEEEeCCccccCHhHhCCCCEEEEEccCCCCHHHHHHHH
Confidence 46899999975443 3334455555778888999999998899999998874
No 31
>COG1437 CyaB Adenylate cyclase, class 2 (thermophilic) [Nucleotide transport and metabolism]
Probab=22.85 E-value=23 Score=29.05 Aligned_cols=88 Identities=19% Similarity=0.225 Sum_probs=57.0
Q ss_pred eEEEE-eCCHHHHHHHHhC-CCCCCCCCcccccceee--ecHHHHHHHHHHhc---ccccCcChhhhhhHHhhcccccee
Q psy13547 69 AAISV-VPSAASLIIKALK-EPPRDRKKVKNVKHNGN--VPIDEIYNISRTMR---PRSMARKFVGTVKEVLGTCQSVGA 141 (165)
Q Consensus 69 f~~~v-~Pp~s~Li~ka~g-kgs~~~~k~~n~~~~G~--it~~~v~eIA~~k~---~~~~~~~l~~~vk~VlGTa~SmGi 141 (165)
+++++ -|+...-|.+.|| +....=+|..-+.+.|+ |++|+|-..-.--- ..-...++.++.+.+-..++++|+
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 46777 7889999999999 54433333333344554 67777754222100 012446677888999999999999
Q ss_pred EecCCChHHHHHHhh
Q psy13547 142 TVEGRSARDIIEAID 156 (165)
Q Consensus 142 ~V~g~~p~ev~~~i~ 156 (165)
..++.-++--+..++
T Consensus 161 ~~~~~~r~sYlELl~ 175 (178)
T COG1437 161 KEEDLERRSYLELLL 175 (178)
T ss_pred ChhcccchhHHHHHh
Confidence 888777766555544
No 32
>TIGR01046 S10_Arc_S20_Euk ribosomal protein S10(archaeal)/S20(eukaryotic). its equivalents in eukaryotes.
Probab=20.86 E-value=24 Score=26.01 Aligned_cols=33 Identities=9% Similarity=0.153 Sum_probs=26.9
Q ss_pred HhcccccCcChhhhhhHHhhccccceeEecCCC
Q psy13547 115 TMRPRSMARKFVGTVKEVLGTCQSVGATVEGRS 147 (165)
Q Consensus 115 ~k~~~~~~~~l~~~vk~VlGTa~SmGi~V~g~~ 147 (165)
+++.......|+.+|++|+-+|+.-|+.+.|-.
T Consensus 5 I~L~S~d~~~Ld~~~~~I~~~ak~~g~~~~GPi 37 (99)
T TIGR01046 5 IKLTSTNVRSLEKVCAQIKRIAEKTGVRMSGPV 37 (99)
T ss_pred EEEEECCHHHHHHHHHHHHHHHHHcCCEEECCc
Confidence 344556677899999999999999999998843
No 33
>COG4953 PbpC Membrane carboxypeptidase/penicillin-binding protein PbpC [Cell envelope biogenesis, outer membrane]
Probab=20.79 E-value=94 Score=30.65 Aligned_cols=68 Identities=19% Similarity=0.215 Sum_probs=56.8
Q ss_pred EEEEeccccCCCCCCccccCCCCCChHHHHHHHHHHhcCCCCceeEEEEEE-eccceEEEE-eCCHHHHHHHHhC
Q psy13547 14 YLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTI-QNRQAAISV-VPSAASLIIKALK 86 (165)
Q Consensus 14 kl~v~aG~A~p~PplgP~LG~~Gin~~~f~k~fN~~T~~~~G~~vpV~itv-~drsf~~~v-~Pp~s~Li~ka~g 86 (165)
+|+.+.++ +|-|+=.||-.|++..+...-|...-. .|..-|.+-+. +|+.-+-.+ .|.++|++..-+.
T Consensus 418 ~L~~P~~~---~~GLsLiLGg~gi~L~dLa~lYa~lAn--~G~~~~L~~~~~~~~~~~~~l~s~~Aaw~i~dIl~ 487 (733)
T COG4953 418 HLYLPEGA---APGLSLILGGAGITLEDLAQLYAALAN--QGKAGPLRDTLDDDPLTERTLLSPGAAWQILDILS 487 (733)
T ss_pred CCCCCCcc---CCCeeEEecCCcccHHHHHHHHHHHhc--CCceecccccCCCCCCCCccccCcchHHHHHHHHh
Confidence 67777776 477899999999999999999865432 38888899999 588888888 9999999999887
No 34
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=20.51 E-value=70 Score=26.80 Aligned_cols=28 Identities=43% Similarity=0.592 Sum_probs=19.2
Q ss_pred CCccccCCCCCChHH----HHHHHHHHhcCCC
Q psy13547 27 SLAPKIGPLGLSPKK----VGDDIAKATGDWK 54 (165)
Q Consensus 27 plgP~LG~~Gin~~~----f~k~fN~~T~~~~ 54 (165)
+||+.|||+|+=|.- +++++-+.-.+++
T Consensus 125 ~Lg~iLGPrGlMP~pk~gTv~~di~~~I~~~k 156 (230)
T PRK05424 125 KLGRILGPRGLMPNPKTGTVTMDVAKAVKEAK 156 (230)
T ss_pred HhccccccccCCCCCCCCCcchhHHHHHHHHh
Confidence 499999999964433 5566666666653
No 35
>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=20.26 E-value=65 Score=20.93 Aligned_cols=19 Identities=26% Similarity=0.375 Sum_probs=11.2
Q ss_pred CChHHHHHHhhCceeeccC
Q psy13547 146 RSARDIIEAIDNGEIEVPE 164 (165)
Q Consensus 146 ~~p~ev~~~i~~G~~~~p~ 164 (165)
..-.++.+.|++|+|.+..
T Consensus 28 ~kV~~ik~~I~~G~Y~vd~ 46 (57)
T PF04316_consen 28 EKVAEIKAAIASGTYKVDA 46 (57)
T ss_dssp HHHHHHHHHHHTT-----H
T ss_pred HHHHHHHHHHHcCCCCCCH
Confidence 4567899999999998753
No 36
>COG2080 CoxS Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]
Probab=20.09 E-value=1.7e+02 Score=23.52 Aligned_cols=29 Identities=14% Similarity=0.290 Sum_probs=24.9
Q ss_pred eEEEEEEeccceEEEE--eCCHHHHHHHHhC
Q psy13547 58 ITVCLTIQNRQAAISV--VPSAASLIIKALK 86 (165)
Q Consensus 58 vpV~itv~drsf~~~v--~Pp~s~Li~ka~g 86 (165)
+++.++|+.+++++++ .-+..|+|+..++
T Consensus 2 ~~i~ltvNG~~~~~~~~p~~~Ll~~LRd~l~ 32 (156)
T COG2080 2 MPITLTVNGEPVELDVDPRTPLLDVLRDELG 32 (156)
T ss_pred CcEEEEECCeEEEEEeCCCChHHHHHHHhcC
Confidence 5788999999999999 5577899999998
Done!