Query psy7622
Match_columns 179
No_of_seqs 163 out of 1028
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 23:04:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7622.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7622hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00027 60S ribosomal protein 100.0 1.5E-55 3.2E-60 364.6 17.9 154 5-163 24-186 (190)
2 PTZ00179 60S ribosomal protein 100.0 2.9E-55 6.2E-60 362.6 16.5 153 5-165 23-187 (189)
3 PRK05518 rpl6p 50S ribosomal p 100.0 4E-55 8.6E-60 359.5 16.7 149 5-162 24-178 (180)
4 TIGR03653 arch_L6P archaeal ri 100.0 1.4E-54 3.1E-59 353.2 17.1 148 4-160 17-170 (170)
5 COG0097 RplF Ribosomal protein 100.0 2.5E-49 5.4E-54 324.6 15.4 142 5-161 23-173 (178)
6 CHL00140 rpl6 ribosomal protei 100.0 1.7E-46 3.7E-51 307.2 15.8 136 4-146 22-165 (178)
7 TIGR03654 L6_bact ribosomal pr 100.0 2E-45 4.2E-50 300.1 16.2 135 5-146 22-164 (175)
8 PRK05498 rplF 50S ribosomal pr 100.0 1E-44 2.2E-49 296.4 16.3 136 4-146 22-165 (178)
9 KOG3254|consensus 100.0 1.2E-40 2.6E-45 274.1 11.4 133 4-143 52-195 (211)
10 KOG3255|consensus 99.9 7.6E-24 1.6E-28 174.3 -0.9 145 5-162 24-178 (179)
11 PF00347 Ribosomal_L6: Ribosom 99.4 1.8E-13 3.9E-18 96.3 2.5 55 5-59 13-77 (77)
12 PF00347 Ribosomal_L6: Ribosom 97.7 2E-05 4.2E-10 55.2 1.6 53 80-137 10-65 (77)
13 cd02393 PNPase_KH Polynucleoti 68.2 14 0.00029 25.0 4.5 41 91-132 20-60 (61)
14 PRK05498 rplF 50S ribosomal pr 61.2 8.6 0.00019 31.5 2.9 47 102-150 39-101 (178)
15 PTZ00179 60S ribosomal protein 61.0 8.7 0.00019 32.1 3.0 13 124-136 67-79 (189)
16 PRK05518 rpl6p 50S ribosomal p 58.6 10 0.00022 31.5 3.0 32 103-136 42-78 (180)
17 CHL00140 rpl6 ribosomal protei 56.5 61 0.0013 26.6 7.2 75 71-150 11-101 (178)
18 TIGR03654 L6_bact ribosomal pr 49.0 73 0.0016 26.0 6.5 74 72-150 11-100 (175)
19 TIGR03653 arch_L6P archaeal ri 45.5 1.2E+02 0.0025 24.9 7.2 74 72-150 7-99 (170)
20 PTZ00027 60S ribosomal protein 44.2 1.2E+02 0.0025 25.4 7.1 73 72-146 13-101 (190)
21 PF05137 PilN: Fimbrial assemb 39.7 76 0.0017 21.3 4.6 42 98-139 8-52 (78)
22 cd02394 vigilin_like_KH K homo 38.1 70 0.0015 20.8 4.0 30 102-132 29-61 (62)
23 cd06477 ACD_HspB3_Like Alpha c 36.0 74 0.0016 22.9 4.2 29 93-121 51-83 (83)
24 PF00013 KH_1: KH domain syndr 34.0 1E+02 0.0022 19.9 4.3 28 103-132 30-60 (60)
25 PF14250 AbrB-like: AbrB-like 29.9 26 0.00056 25.3 0.9 14 81-96 56-69 (71)
26 COG0097 RplF Ribosomal protein 27.9 62 0.0014 27.0 2.9 61 72-136 12-76 (178)
27 TIGR01212 radical SAM protein, 25.1 34 0.00074 29.9 1.0 14 148-161 32-47 (302)
28 PF00338 Ribosomal_S10: Riboso 24.2 1.4E+02 0.0031 21.3 4.0 30 114-143 2-31 (97)
29 PRK09502 iscA iron-sulfur clus 23.4 58 0.0013 24.2 1.8 19 139-157 22-41 (107)
30 COG1072 CoaA Panthothenate kin 23.3 56 0.0012 29.3 2.0 36 90-127 167-202 (283)
31 PF02741 FTR_C: FTR, proximal 22.2 2.3E+02 0.0049 23.2 5.1 50 97-153 88-138 (150)
32 TIGR03119 one_C_fhcD formylmet 20.8 1.8E+02 0.0039 26.2 4.6 50 97-153 225-275 (287)
33 cd06478 ACD_HspB4-5-6 Alpha-cr 20.5 1.7E+02 0.0037 20.6 3.7 18 101-120 20-37 (83)
34 cd01231 PH_Lnk LNK-family Plec 20.3 2.2E+02 0.0047 22.1 4.4 39 96-134 66-106 (107)
35 COG1242 Predicted Fe-S oxidore 20.2 59 0.0013 29.5 1.5 26 138-163 19-55 (312)
No 1
>PTZ00027 60S ribosomal protein L6; Provisional
Probab=100.00 E-value=1.5e-55 Score=364.58 Aligned_cols=154 Identities=49% Similarity=0.688 Sum_probs=143.7
Q ss_pred ccccccCCcEEEEEeee--------ccCCeEEEEccCCChhhhhHhhhHHHHHhcceeecccCeEEEEEEEEEEeceeEE
Q psy7622 5 NLNPGGGGGCLYLNKTY--------RWEETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCV 76 (179)
Q Consensus 5 ~~~~~Gp~G~l~~~~~~--------~~~~~l~V~~~~~~kk~~a~~GT~rSlI~NMI~GVt~Gf~~kL~ivgvgyra~v~ 76 (179)
.|.++||+|+|++.+.. .++++|.|++|.++++.+|+|||+||||+|||+|||+||+|+|+++|+||||+++
T Consensus 24 ~v~VkGp~G~L~~~~~~~~~~i~i~~~~~~i~v~~~~~~~k~~a~~Gt~rslI~NmI~GVt~Gf~~~LeivGvGyra~~~ 103 (190)
T PTZ00027 24 KVTVTGKYGELTRSFRHLPVDIKLSKDGKYIKVEMWFGTPSHLACIRTVCSHIKNMMTGVTKKFQYKMRLVYAHFPINSN 103 (190)
T ss_pred EEEEECCCceEEEEecCCCceEEEEeCCCEEEEEeCCCCHHHHHHHHHHHHHHHHHhhhhcCCEEEEEEEEEeeeeEEEE
Confidence 47899999999999842 3788999999999999999999999999999999999999999999999999976
Q ss_pred eccCCceeEEeccCCceeeEEEeCCCCcEEEec-CCCCEEEEEEccHHHHHHHHHHHhhhccccCCceeecCCCCCCceE
Q psy7622 77 TSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNS-KQKDELIIEGNDIENVSRSAALIQQSTTVKNKDIHLNPGGGGGGCL 155 (179)
Q Consensus 77 i~~~G~~l~i~NfLG~shpi~~~IP~GV~v~v~-~~~t~IiI~GiDKe~Vgq~AA~Ir~~~~~KgKdiR~FlDG~~~~~~ 155 (179)
++++|+.|+|+||||||||+.++||+||+++++ ..+|+|+|+|+|||+||||||+||++|++|+||+|+|||| |
T Consensus 104 v~~~g~~L~l~N~LG~Sh~i~~~iP~gv~v~~~~~~~t~I~i~G~DKq~Vgq~AA~I~~~~~~~~~d~r~f~dg-----i 178 (190)
T PTZ00027 104 ITDNGKTIEIRNFLGEKRVRTVKMLPGVVVEKSESVKDEIIVTGADLELVSRSAALIHQSTLVRNKDIRKFLDG-----I 178 (190)
T ss_pred EcCCCCEEEEEccCCCceeEEEECCCCeEEEeCCCCCCEEEEEeCCHHHHHHHHHHHHHHhcccCCCccEeecC-----E
Confidence 666799999999999999999999999999998 2348999999999999999999999999999999999999 9
Q ss_pred Eeccccce
Q psy7622 156 YLNKTYRW 163 (179)
Q Consensus 156 ~~~~~~~~ 163 (179)
|+++++..
T Consensus 179 y~~~k~~~ 186 (190)
T PTZ00027 179 YVSEKGTV 186 (190)
T ss_pred EEEEeeee
Confidence 99999944
No 2
>PTZ00179 60S ribosomal protein L9; Provisional
Probab=100.00 E-value=2.9e-55 Score=362.59 Aligned_cols=153 Identities=43% Similarity=0.607 Sum_probs=142.0
Q ss_pred ccccccCCcEEEEEeee--------ccCCeEEEEccCCChhhhhHhhhHHHHHhcceeecccCeEEEEEEEEEEeceeEE
Q psy7622 5 NLNPGGGGGCLYLNKTY--------RWEETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCV 76 (179)
Q Consensus 5 ~~~~~Gp~G~l~~~~~~--------~~~~~l~V~~~~~~kk~~a~~GT~rSlI~NMI~GVt~Gf~~kL~ivgvgyra~v~ 76 (179)
.|.++||+|+|++.+.+ .++++|.|.+|.++++.+|+|||+||||+|||+|||+||+|+|+++|+|||+.++
T Consensus 23 ~ItVkGpkG~Ls~~~~~~~~~i~i~~~~~~I~v~~~~~~kk~~al~Gt~rslI~NMI~GVt~GF~k~L~ivgvgyp~ra~ 102 (189)
T PTZ00179 23 IVTVKGKRGTLTKDLRHLQLDFRVNKKNRTFTAVRWFGSKIPNSTINTALSHVRNMITGVTKGFRFKVRFAYAHFPISVS 102 (189)
T ss_pred EEEEECCCcEEEEEcCCCCcEEEEEecCCEEEEEeCCCCHHHHHHHHHHHHHHHHHhhhhcCCEEEEEEEEEeCcceEEE
Confidence 47899999999998853 4778999999999999999999999999999999999999999999999977665
Q ss_pred eccCCceeEEeccCCceeeEEEeCCCCcEEEecCCC----CEEEEEEccHHHHHHHHHHHhhhccccCCceeecCCCCCC
Q psy7622 77 TSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQK----DELIIEGNDIENVSRSAALIQQSTTVKNKDIHLNPGGGGG 152 (179)
Q Consensus 77 i~~~G~~l~i~NfLG~shpi~~~IP~GV~v~v~~~~----t~IiI~GiDKe~Vgq~AA~Ir~~~~~KgKdiR~FlDG~~~ 152 (179)
+ +|+.|+|+||||||||+.++||+||+++++ ++ |+|+|+|+|||+|||+||+|+++|++|+||+|+||||
T Consensus 103 v--~g~~l~l~N~LG~sh~~~~~ip~gv~v~~~-~~~~~k~~i~i~G~DKq~Vgq~AA~i~~~~~~~~~d~r~f~dg--- 176 (189)
T PTZ00179 103 V--ENQLVEIRNFLGEKRVRRQVVADTVKVYRT-DPSKVKDELVLEGNDLEQVSREAAVMHQLCLVKKKDIRKFLDG--- 176 (189)
T ss_pred E--cCCEEEEEecCCCCccEEEECCCCEEEEec-CCcccCCEEEEEeCCHHHHHHHHHHHHHhhcccCCCccEeecC---
Confidence 5 588999999999999999999999999997 66 8999999999999999999999999999999999999
Q ss_pred ceEEeccccceee
Q psy7622 153 GCLYLNKTYRWEE 165 (179)
Q Consensus 153 ~~~~~~~~~~~~~ 165 (179)
||++.++....
T Consensus 177 --iy~~~k~~~~~ 187 (189)
T PTZ00179 177 --IYVQTKTNVEA 187 (189)
T ss_pred --EEEEEeecccc
Confidence 99999995443
No 3
>PRK05518 rpl6p 50S ribosomal protein L6P; Reviewed
Probab=100.00 E-value=4e-55 Score=359.50 Aligned_cols=149 Identities=37% Similarity=0.533 Sum_probs=139.3
Q ss_pred ccccccCCcEEEEEeee------ccCCeEEEEccCCChhhhhHhhhHHHHHhcceeecccCeEEEEEEEEEEeceeEEec
Q psy7622 5 NLNPGGGGGCLYLNKTY------RWEETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVTS 78 (179)
Q Consensus 5 ~~~~~Gp~G~l~~~~~~------~~~~~l~V~~~~~~kk~~a~~GT~rSlI~NMI~GVt~Gf~~kL~ivgvgyra~v~i~ 78 (179)
.++++||+|+|++.+.. .++++|.+++|+++++++|+|||+||||+|||+|||+||+|+|+++|+|||+.+++
T Consensus 24 ~v~VkGp~G~L~~~~~~~~v~i~~~~~~i~v~~~~~~kk~ra~~gt~rslI~NmI~GVt~Gf~~~LelvGvGypira~~- 102 (180)
T PRK05518 24 VVTVKGPKGELTRDFWYPGVTISVEDGKVVIETEFARKKTKAMVGTFASHIKNMIKGVTEGFEYKLKIVYSHFPMQVKV- 102 (180)
T ss_pred EEEEECCCeEEEEEecCCcEEEEEECCEEEEEECCCCHHHHHHHHHHHHHHHhhheecccceEEEEEEEecCccEEEEE-
Confidence 47999999999999842 58889999999999999999999999999999999999999999999999666544
Q ss_pred cCCceeEEeccCCceeeEEEeCCCCcEEEecCCCCEEEEEEccHHHHHHHHHHHhhhccccCCceeecCCCCCCceEEec
Q psy7622 79 ENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAALIQQSTTVKNKDIHLNPGGGGGGCLYLN 158 (179)
Q Consensus 79 ~~G~~l~i~NfLG~shpi~~~IP~GV~v~v~~~~t~IiI~GiDKe~Vgq~AA~Ir~~~~~KgKdiR~FlDG~~~~~~~~~ 158 (179)
+|+.|+|+|+||||||+.++||+||+++++ + |+|+|+|+|||+||||||+||+.|+.|+||+|+|||| |||+
T Consensus 103 -~g~~l~l~n~LG~Sh~v~~~iP~gV~v~~~-~-t~I~i~GiDKq~Vgq~AA~Ir~~~~~~~kd~r~f~dg-----iyv~ 174 (180)
T PRK05518 103 -QGNEVVIENFLGEKSPRRAKILGGVKVKVK-G-EDVIVEGIDKEDVGQTAANIEQATKIKGFDRRVFQDG-----IYIV 174 (180)
T ss_pred -cCCEEEEEeccccceeEEEeCCCCeEEEec-C-CEEEEEeCCHHHHHHHHHHHHHhhcccCCCCCEeecC-----EEEE
Confidence 588899999999999999999999999997 7 9999999999999999999999999999999999999 9999
Q ss_pred cccc
Q psy7622 159 KTYR 162 (179)
Q Consensus 159 ~~~~ 162 (179)
+++.
T Consensus 175 ~k~~ 178 (180)
T PRK05518 175 EKEV 178 (180)
T ss_pred Eecc
Confidence 8763
No 4
>TIGR03653 arch_L6P archaeal ribosomal protein L6P. Members of this protein family are the archaeal ribosomal protein L6P. The top-scoring proteins not selected by this model are eukaryotic cytosolic ribosomal protein L9. Bacterial ribosomal protein L6 scores lower and is described by a distinct model.
Probab=100.00 E-value=1.4e-54 Score=353.21 Aligned_cols=148 Identities=37% Similarity=0.539 Sum_probs=137.2
Q ss_pred cccccccCCcEEEEEe-ee-----ccCCeEEEEccCCChhhhhHhhhHHHHHhcceeecccCeEEEEEEEEEEeceeEEe
Q psy7622 4 RNLNPGGGGGCLYLNK-TY-----RWEETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVT 77 (179)
Q Consensus 4 ~~~~~~Gp~G~l~~~~-~~-----~~~~~l~V~~~~~~kk~~a~~GT~rSlI~NMI~GVt~Gf~~kL~ivgvgyra~v~i 77 (179)
+.+.++||+|+|++++ ++ .++++|.+++|+++++++|+|||+||||+|||+|||+||+++|+++|+|||+.+++
T Consensus 17 ~~i~vkGp~G~L~~~~~~~~v~i~~~~~~i~v~~~~~~k~~~a~~gt~rsli~NmI~GVt~Gf~~~LeivGvGy~~ra~~ 96 (170)
T TIGR03653 17 NIVTVKGPKGEVTRELWYPGIEISVEDGKVVIETDFARKKDKAMVGTYRSHIKNMIKGVTEGFEYKMKVVYSHFPMQVKV 96 (170)
T ss_pred CEEEEECCCeEEEEEEeCCcEEEEEeCCEEEEEeCCCCHHHHHHHHHHHHHHHhheeecccCeEEEEEEEeccccEEEEE
Confidence 3589999999999998 42 58889999999999999999999999999999999999999999999999665544
Q ss_pred ccCCceeEEeccCCceeeEEEeCCCCcEEEecCCCCEEEEEEccHHHHHHHHHHHhhhccccCCceeecCCCCCCceEEe
Q psy7622 78 SENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAALIQQSTTVKNKDIHLNPGGGGGGCLYL 157 (179)
Q Consensus 78 ~~~G~~l~i~NfLG~shpi~~~IP~GV~v~v~~~~t~IiI~GiDKe~Vgq~AA~Ir~~~~~KgKdiR~FlDG~~~~~~~~ 157 (179)
+|+.|+|+|+||||||+.++||+||+++++ + ++|+|+|+|||+||||||+||++|+.|+||+|+|||| ||+
T Consensus 97 --~g~~L~l~n~LG~Sh~i~~~iP~gI~v~~~-~-~~I~i~G~DKq~Vgq~AA~Ir~~~~~~~~d~r~f~dg-----iy~ 167 (170)
T TIGR03653 97 --EGNKVVIENFLGEKAPRRAKIPGGVKVKVK-G-EEVIVTGIDKEDVGQTAANIEQATRIKGRDPRVFQDG-----IYI 167 (170)
T ss_pred --cCCeEEEeeccccceeEEEECCCCeEEEec-C-CEEEEEeCCHHHHHHHHHHHHHhhcccCCCccEeecC-----EEE
Confidence 588899999999999999999999999997 5 4999999999999999999999999999999999999 999
Q ss_pred ccc
Q psy7622 158 NKT 160 (179)
Q Consensus 158 ~~~ 160 (179)
+++
T Consensus 168 ~~~ 170 (170)
T TIGR03653 168 VEK 170 (170)
T ss_pred EeC
Confidence 864
No 5
>COG0097 RplF Ribosomal protein L6P/L9E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-49 Score=324.62 Aligned_cols=142 Identities=27% Similarity=0.308 Sum_probs=125.9
Q ss_pred ccccccCCcEEEEEeee------ccCCeEEEEccCCChhhhhHhhhHHHHHhcceeecccCeEEEEEEEEEEeceeEEec
Q psy7622 5 NLNPGGGGGCLYLNKTY------RWEETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVTS 78 (179)
Q Consensus 5 ~~~~~Gp~G~l~~~~~~------~~~~~l~V~~~~~~kk~~a~~GT~rSlI~NMI~GVt~Gf~~kL~ivgvgyra~v~i~ 78 (179)
.++++||+|+|++.|.. .+|+.+.+.+++. ++.+|||||+||||+|||+|||+||+|+|+++|+||||++ +
T Consensus 23 ~v~vkGpkGeL~~~~~~~~v~v~~~~~~~vv~~~~~-k~~~a~~Gt~rali~Nmv~GVteGf~~kL~ivgvgyra~v--~ 99 (178)
T COG0097 23 VVTVKGPKGELTREFHDNVVKVEVEDNILVVRPVDG-KRKRALHGTVRALINNMVKGVTEGFEKKLEIVGVGYRAQV--V 99 (178)
T ss_pred EEEEECCCcEEEEEecCcceEEEecCCEEEEeeccc-chhHHHHHHHHHHHHHHheecccceEEEEEEEEecceeEE--e
Confidence 57899999999999942 3678788888777 6666999999999999999999999999999999999998 2
Q ss_pred cCCceeEEeccCCceeeEEEeCCCCcEEEecCCCCEEEEEEccHHHHHHHHHHHhhhcc---ccCCceeecCCCCCCceE
Q psy7622 79 ENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAALIQQSTT---VKNKDIHLNPGGGGGGCL 155 (179)
Q Consensus 79 ~~G~~l~i~NfLG~shpi~~~IP~GV~v~v~~~~t~IiI~GiDKe~Vgq~AA~Ir~~~~---~KgKdiR~FlDG~~~~~~ 155 (179)
|+.|+ ||||||||+.++||+||+++++ .+|+|+|+|+|||+||||||+||++|+ ||||+ +|+|| +
T Consensus 100 --g~~l~--l~LG~shp~~~~ip~gi~v~v~-~~t~I~v~GidKe~VGQ~AA~Ir~~r~pepykgKg--i~ydg-----e 167 (178)
T COG0097 100 --GGNLE--LFLGYSHPVVIEIPEGITVEVP-GPTEIVVEGIDKELVGQVAANIRAARKPEPYKGKG--IRYDG-----E 167 (178)
T ss_pred --ccEEE--EeecccCCeEEECCCCeEEEec-CCCEEEEEcCCHHHHhHHHHHHHhccCCCCCCCcc--eEEcC-----E
Confidence 55655 4899999999999999999998 889999999999999999999999997 55555 38999 9
Q ss_pred Eecccc
Q psy7622 156 YLNKTY 161 (179)
Q Consensus 156 ~~~~~~ 161 (179)
|+..|.
T Consensus 168 ~I~~K~ 173 (178)
T COG0097 168 YIRRKE 173 (178)
T ss_pred EEEEec
Confidence 998664
No 6
>CHL00140 rpl6 ribosomal protein L6; Validated
Probab=100.00 E-value=1.7e-46 Score=307.24 Aligned_cols=136 Identities=24% Similarity=0.272 Sum_probs=127.2
Q ss_pred cccccccCCcEEEEEee-----eccCCeEEEEccCCChhhhhHhhhHHHHHhcceeecccCeEEEEEEEEEEeceeEEec
Q psy7622 4 RNLNPGGGGGCLYLNKT-----YRWEETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVTS 78 (179)
Q Consensus 4 ~~~~~~Gp~G~l~~~~~-----~~~~~~l~V~~~~~~kk~~a~~GT~rSlI~NMI~GVt~Gf~~kL~ivgvgyra~v~i~ 78 (179)
+.|.++||+|+|++.+. ..++++|.|.+|+++|+++|+|||+||||+|||+|||+||+|+|+++|+||+|++
T Consensus 22 ~~v~vkGp~G~l~~~~~~~v~i~~~~~~i~v~~~~~~k~~~a~~gt~~slI~Nmi~GVt~Gf~~~L~lvGvGyr~~~--- 98 (178)
T CHL00140 22 QIIKVKGPKGTLSRKIPDLITIEIQDNSLFVSKKDESKKARALHGLYRTLINNMVIGVSEGFEKKLELQGVGYRAQV--- 98 (178)
T ss_pred CEEEEECCCEEEEEECCCCeEEEEeCCEEEEEcCCCCHHHHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEEEEEE---
Confidence 35899999999999984 2588899999999999999999999999999999999999999999999999987
Q ss_pred cCCceeEEeccCCceeeEEEeCCCCcEEEecCCCCEEEEEEccHHHHHHHHHHHhhhcc---ccCCceeec
Q psy7622 79 ENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAALIQQSTT---VKNKDIHLN 146 (179)
Q Consensus 79 ~~G~~l~i~NfLG~shpi~~~IP~GV~v~v~~~~t~IiI~GiDKe~Vgq~AA~Ir~~~~---~KgKdiR~F 146 (179)
+|+.|.| |||||||+.++||+||+|+++ ++|+|+|+|+|||+||||||+||++|+ |||||||.+
T Consensus 99 -~g~~l~l--~LG~sh~i~~~IP~gv~v~~~-~~t~I~i~G~dke~Vgq~AA~Ir~~r~pepYKGKGI~y~ 165 (178)
T CHL00140 99 -QGKDLIL--NLGYSHPVKIKIPPGISVEVE-NNTNITIKGIDKELVGQFAAKIRSVRPPEPYKGKGIRYK 165 (178)
T ss_pred -eCCcEEE--EecCCeeEEEECCCCeEEEeC-CCCEEEEEECCHHHHHHHHHHHhccCCCCCcCCccEeEC
Confidence 4778999 699999999999999999998 889999999999999999999999995 999999875
No 7
>TIGR03654 L6_bact ribosomal protein L6, bacterial type.
Probab=100.00 E-value=2e-45 Score=300.10 Aligned_cols=135 Identities=23% Similarity=0.248 Sum_probs=126.5
Q ss_pred ccccccCCcEEEEEee-----eccCCeEEEEccCCChhhhhHhhhHHHHHhcceeecccCeEEEEEEEEEEeceeEEecc
Q psy7622 5 NLNPGGGGGCLYLNKT-----YRWEETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVTSE 79 (179)
Q Consensus 5 ~~~~~Gp~G~l~~~~~-----~~~~~~l~V~~~~~~kk~~a~~GT~rSlI~NMI~GVt~Gf~~kL~ivgvgyra~v~i~~ 79 (179)
.|.++||+|+|++.++ +.+++.|.++.|+++++++|||||+||||+|||+|||+||+|+|+++|+||++++
T Consensus 22 ~v~v~Gp~G~l~~~l~~~i~i~~~~~~i~v~~~~~~kk~~a~~gt~~s~i~Nmi~GVt~Gf~~~L~lvGvgyrv~~---- 97 (175)
T TIGR03654 22 VVTVKGPKGELSRTLHPGVTVKVEDGQLTVSRPNDSKEARALHGTTRALINNMVIGVSEGFEKKLEIVGVGYRAQL---- 97 (175)
T ss_pred EEEEEcCCeEEEEEcCCCeEEEEECCEEEEEecCCCHHHHHHHHHHHHHHHHHhheeccCcEEEEEEEEEEEEEEE----
Confidence 4789999999999984 2588899999999999999999999999999999999999999999999999976
Q ss_pred CCceeEEeccCCceeeEEEeCCCCcEEEecCCCCEEEEEEccHHHHHHHHHHHhhhcc---ccCCceeec
Q psy7622 80 NNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAALIQQSTT---VKNKDIHLN 146 (179)
Q Consensus 80 ~G~~l~i~NfLG~shpi~~~IP~GV~v~v~~~~t~IiI~GiDKe~Vgq~AA~Ir~~~~---~KgKdiR~F 146 (179)
+|+.|+| |||||||+.++||+||+++++ ++|+|+|+|+|||+||||||+||++|+ |||||||..
T Consensus 98 ~g~~l~l--~LG~sh~i~~~Ip~~v~v~~~-~~t~I~i~G~dke~Vgq~AA~Ir~~r~pepYKgkGi~~~ 164 (175)
T TIGR03654 98 QGKKLNL--SLGYSHPVEYEIPEGITVEVP-KPTEIVVKGIDKQLVGQVAAEIRAFRKPEPYKGKGIRYA 164 (175)
T ss_pred eCCeEEE--EecCceeEEEECCCCeEEEeC-CCCEEEEEECCHHHHHHHHHHHhccCCCCCcCCCcEeEC
Confidence 4788999 699999999999999999998 889999999999999999999999996 999999875
No 8
>PRK05498 rplF 50S ribosomal protein L6; Validated
Probab=100.00 E-value=1e-44 Score=296.36 Aligned_cols=136 Identities=24% Similarity=0.260 Sum_probs=126.5
Q ss_pred cccccccCCcEEEEEee-----eccCCeEEEEccCCChhhhhHhhhHHHHHhcceeecccCeEEEEEEEEEEeceeEEec
Q psy7622 4 RNLNPGGGGGCLYLNKT-----YRWEETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVTS 78 (179)
Q Consensus 4 ~~~~~~Gp~G~l~~~~~-----~~~~~~l~V~~~~~~kk~~a~~GT~rSlI~NMI~GVt~Gf~~kL~ivgvgyra~v~i~ 78 (179)
+.|.|+||+|+|++.++ +.+++.|.++.|.++++++|+|||+||||+|||+|||+||+|+|+++|+||+|++
T Consensus 22 ~~v~vkGp~G~l~~~~~~~v~i~~~~~~i~v~~~~~~k~~~a~~gt~~s~I~Nmi~GVt~Gf~~~L~lvGvgyrv~~--- 98 (178)
T PRK05498 22 NVVTVKGPKGELSRTLNPDVTVKVEDNEITVTRPDDSKKARALHGTTRALINNMVVGVTEGFEKKLEIVGVGYRAQV--- 98 (178)
T ss_pred CEEEEECCCEEEEEEcCCCeEEEEECCEEEEEcCCCCHHHHHHHHHHHHHHHHHhhhcCCCeEEEEEEEeEEEEEEE---
Confidence 34789999999999984 2578899999999999999999999999999999999999999999999999976
Q ss_pred cCCceeEEeccCCceeeEEEeCCCCcEEEecCCCCEEEEEEccHHHHHHHHHHHhhhcc---ccCCceeec
Q psy7622 79 ENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAALIQQSTT---VKNKDIHLN 146 (179)
Q Consensus 79 ~~G~~l~i~NfLG~shpi~~~IP~GV~v~v~~~~t~IiI~GiDKe~Vgq~AA~Ir~~~~---~KgKdiR~F 146 (179)
+|+.|+| |||||||+.++||+||+|+++ ++|+|+|+|+|||+||||||+||++|+ |||||||.+
T Consensus 99 -~g~~l~l--~LG~sh~i~~~Ip~gv~v~~~-~~t~I~i~G~dke~Vg~~AA~Ir~~r~pe~YkgkGi~~~ 165 (178)
T PRK05498 99 -KGKKLNL--SLGYSHPVEYEIPEGITVEVP-KPTEIVVKGIDKQLVGQVAAEIRSYRPPEPYKGKGIRYA 165 (178)
T ss_pred -eCCeEEE--EecCCEEEEEECCCCeEEEeC-CCCEEEEEECCHHHHHHHHHHHhccCCCCCccCCcEeEC
Confidence 4788999 699999999999999999997 888999999999999999999999996 999998865
No 9
>KOG3254|consensus
Probab=100.00 E-value=1.2e-40 Score=274.11 Aligned_cols=133 Identities=25% Similarity=0.267 Sum_probs=119.6
Q ss_pred cccccccCCcEEEEEeee-------c-cCCeEEEEccCCChhhhhHhhhHHHHHhcceeecccCeEEEEEEEEEEeceeE
Q psy7622 4 RNLNPGGGGGCLYLNKTY-------R-WEETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINC 75 (179)
Q Consensus 4 ~~~~~~Gp~G~l~~~~~~-------~-~~~~l~V~~~~~~kk~~a~~GT~rSlI~NMI~GVt~Gf~~kL~ivgvgyra~v 75 (179)
.|+++|||+|+|++.++. . ..+.+......++|++++||||+|||++|||+|||+||.+.|++||+||||++
T Consensus 52 e~l~vkGP~gel~l~~P~~l~L~~dkk~~g~~~~~k~~etkkqr~mwgt~R~l~~N~v~GVt~g~~k~l~lVGvGYRa~l 131 (211)
T KOG3254|consen 52 EQLQVKGPHGELNLRFPNYLNLSNDKKKSGMDANIKKQETKKQRAMWGTFRALLANNVKGVTMGFLKILKLVGVGYRASL 131 (211)
T ss_pred CceEeeCCcceeeccCCccccccchhhhcceeeeecchhhHHHHHHHHHHHHHHhccchhhhhhhhheeeEEeeeeEEEe
Confidence 478999999999999852 1 22223333456789999999999999999999999999999999999999988
Q ss_pred EeccCCceeEEeccCCceeeEEEeCCCCcEEEecCCCCEEEEEEccHHHHHHHHHHHhhhcc---ccCCce
Q psy7622 76 VTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAALIQQSTT---VKNKDI 143 (179)
Q Consensus 76 ~i~~~G~~l~i~NfLG~shpi~~~IP~GV~v~v~~~~t~IiI~GiDKe~Vgq~AA~Ir~~~~---~KgKdi 143 (179)
+|+.|.++ |||||++.+.||++|.|++| .+|.|+++|+|||.|+||||.+|+++| ||||||
T Consensus 132 ----egk~l~lk--lG~S~~v~l~iP~~v~Vk~p-~ptsl~~~G~dKq~V~qFAAkvRsfkpPEPYKGKGI 195 (211)
T KOG3254|consen 132 ----EGKFLHLK--LGYSHDVLLSIPTDVQVKNP-TPTSLVLRGIDKQKVTQFAAKVRSFKPPEPYKGKGI 195 (211)
T ss_pred ----cCceEEEE--eccccceeecCCCceEEecC-CCCEEEEecccHHHHHHHHHHHhccCCCCCcCCCce
Confidence 59999998 99999999999999999998 999999999999999999999999996 999984
No 10
>KOG3255|consensus
Probab=99.87 E-value=7.6e-24 Score=174.31 Aligned_cols=145 Identities=52% Similarity=0.734 Sum_probs=131.8
Q ss_pred ccccccCCcEEEEEeee-------ccC--CeEEEEccCCChhhhhHhhhHHHHHhcceeecccCeEEEEEEEEEEeceeE
Q psy7622 5 NLNPGGGGGCLYLNKTY-------RWE--ETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINC 75 (179)
Q Consensus 5 ~~~~~Gp~G~l~~~~~~-------~~~--~~l~V~~~~~~kk~~a~~GT~rSlI~NMI~GVt~Gf~~kL~ivgvgyra~v 75 (179)
=+.++||+|+|...+.. ..+ +.+.++.|+..|+..|..-|..|||+||++||+.||.|+|+.++.|||++.
T Consensus 24 v~~v~gprgtl~~d~~hi~~~~~~~~~~~~~ik~~~~~~~Rk~va~l~t~~s~ien~i~gvt~~~i~k~~av~a~f~in~ 103 (179)
T KOG3255|consen 24 VVIVKGPRGTLWRDFNHINVELSLLGKKKKRLKIDKWWGTRKGVACLRTVVSHIENCIKGVTIGFIYKMRAVYAHFPINT 103 (179)
T ss_pred EEEEeCCCcceeccccccchhhhhhcchhhhhhhhhhhccchhHHHHHHHHHHHHHHHhcchHHHHHHhhhHHhhccccc
Confidence 36789999999998831 122 358999999999999999999999999999999999999999999999999
Q ss_pred EeccCCceeEEeccCCceeeEEEeCCCCcEEEec-CCCCEEEEEEccHHHHHHHHHHHhhhccccCCceeecCCCCCCce
Q psy7622 76 VTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNS-KQKDELIIEGNDIENVSRSAALIQQSTTVKNKDIHLNPGGGGGGC 154 (179)
Q Consensus 76 ~i~~~G~~l~i~NfLG~shpi~~~IP~GV~v~v~-~~~t~IiI~GiDKe~Vgq~AA~Ir~~~~~KgKdiR~FlDG~~~~~ 154 (179)
+++++++..++.||||++.++++++++|+..... ..+++|+++|+|.|.|+|.||. ++.|..+++ ||
T Consensus 104 ~~~~~~~s~~i~n~l~~k~~~~~~~~~Gv~~~~~~~~~~~i~~~~~~~~~vs~~~a~-~~~~~~~~~-----ld------ 171 (179)
T KOG3255|consen 104 VIQENGKSEEIRNFLGEKLVRRVEMRPGVTIVRSSKVKDEIVLEGNDLELVSQSAAL-QQICTVKNK-----LD------ 171 (179)
T ss_pred eecCCCcchhhhhhhhhhccceEecCCCeEEeeehhcchhheecccchhhhhhHhHh-hccceehhh-----cc------
Confidence 9988899999999999999999999999999987 6789999999999999999998 999998877 66
Q ss_pred EEeccccc
Q psy7622 155 LYLNKTYR 162 (179)
Q Consensus 155 ~~~~~~~~ 162 (179)
||+.+++
T Consensus 172 -yv~~k~~ 178 (179)
T KOG3255|consen 172 -YVSEKGT 178 (179)
T ss_pred -hhhhccc
Confidence 8888775
No 11
>PF00347 Ribosomal_L6: Ribosomal protein L6; InterPro: IPR020040 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L6 is a protein from the large (50S) subunit. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of an ancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites []. This entry represents the alpha-beta domain found duplicated in ribosomal L6 proteins. This domain consists of two beta-sheets and one alpha-helix packed around single core [].; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 2HGJ_H 2HGQ_H 2HGU_H 1S1I_H 3O5H_I 3O58_I 3J16_F 3IZS_F 2V47_H 2WDJ_H ....
Probab=99.38 E-value=1.8e-13 Score=96.27 Aligned_cols=55 Identities=33% Similarity=0.331 Sum_probs=49.8
Q ss_pred ccccccCCcEEEEEee-----e--ccCCeEEEEccCCChhhhh---HhhhHHHHHhcceeecccC
Q psy7622 5 NLNPGGGGGCLYLNKT-----Y--RWEETFDVDCDNGTKKEIA---AVRTVCSHISNMLKGVTKG 59 (179)
Q Consensus 5 ~~~~~Gp~G~l~~~~~-----~--~~~~~l~V~~~~~~kk~~a---~~GT~rSlI~NMI~GVt~G 59 (179)
.+.++||+|+|++.++ + .+++.+.+..+.+++++++ +|||+|||++||++||++|
T Consensus 13 ~i~v~G~~g~l~~~~~~~v~v~~~~~~~~~~~~~~~~~~k~~~~~a~~gt~rsli~n~i~GV~~G 77 (77)
T PF00347_consen 13 IITVKGPKGELSRPIPPGVKVEIKVEDNKITVSVLSGNKKQKAFAAMIGTYRSLINNMIKGVTEG 77 (77)
T ss_dssp EEEEESSSSEEEEEETTTEEEEEEEETTSEEEEEEEESHHHHHHHHHHHHHHHHHHHHHHHHHTE
T ss_pred EEEEECCCEeEEEECCCCeeEEEEcCCCceEEEECcccHhHhhhHHhhccccccccCceeEECCC
Confidence 4789999999999993 2 4688999999999999999 9999999999999999987
No 12
>PF00347 Ribosomal_L6: Ribosomal protein L6; InterPro: IPR020040 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L6 is a protein from the large (50S) subunit. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of an ancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites []. This entry represents the alpha-beta domain found duplicated in ribosomal L6 proteins. This domain consists of two beta-sheets and one alpha-helix packed around single core [].; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 2HGJ_H 2HGQ_H 2HGU_H 1S1I_H 3O5H_I 3O58_I 3J16_F 3IZS_F 2V47_H 2WDJ_H ....
Probab=97.67 E-value=2e-05 Score=55.19 Aligned_cols=53 Identities=23% Similarity=0.323 Sum_probs=43.7
Q ss_pred CCceeEEeccCCceeeEEEeCCCCcEEEec---CCCCEEEEEEccHHHHHHHHHHHhhhcc
Q psy7622 80 NNTLLEIRNFLGEKYIRRVKMAPGVKVSNS---KQKDELIIEGNDIENVSRSAALIQQSTT 137 (179)
Q Consensus 80 ~G~~l~i~NfLG~shpi~~~IP~GV~v~v~---~~~t~IiI~GiDKe~Vgq~AA~Ir~~~~ 137 (179)
++..+.+ .|+++...+++|++|.++++ .+.+...+++.|++.+ +||.++.+|.
T Consensus 10 ~~~~i~v---~G~~g~l~~~~~~~v~v~~~~~~~~~~~~~~~~~~k~~~--~~a~~gt~rs 65 (77)
T PF00347_consen 10 KGNIITV---KGPKGELSRPIPPGVKVEIKVEDNKITVSVLSGNKKQKA--FAAMIGTYRS 65 (77)
T ss_dssp ETTEEEE---ESSSSEEEEEETTTEEEEEEEETTSEEEEEEEESHHHHH--HHHHHHHHHH
T ss_pred eCcEEEE---ECCCEeEEEECCCCeeEEEEcCCCceEEEECcccHhHhh--hHHhhccccc
Confidence 4656665 89999999999999999953 2235677899999999 9999999986
No 13
>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=68.16 E-value=14 Score=24.95 Aligned_cols=41 Identities=24% Similarity=0.438 Sum_probs=30.2
Q ss_pred CceeeEEEeCCCCcEEEecCCCCEEEEEEccHHHHHHHHHHH
Q psy7622 91 GEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAALI 132 (179)
Q Consensus 91 G~shpi~~~IP~GV~v~v~~~~t~IiI~GiDKe~Vgq~AA~I 132 (179)
|-++...++--.|+++.++ +...+.|+|.|++.|-...+.|
T Consensus 20 gG~~ik~I~~~tg~~I~i~-~~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 20 GGKTIKKIIEETGVKIDIE-DDGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred CchHHHHHHHHHCCEEEeC-CCCEEEEEeCCHHHHHHHHHHh
Confidence 3345555555568888887 6678999999999987766655
No 14
>PRK05498 rplF 50S ribosomal protein L6; Validated
Probab=61.16 E-value=8.6 Score=31.55 Aligned_cols=47 Identities=17% Similarity=0.259 Sum_probs=27.0
Q ss_pred CCcEEEecCCCCEEEEE--EccHH---HHHHHHHHHhhhcc-----------ccCCceeecCCCC
Q psy7622 102 PGVKVSNSKQKDELIIE--GNDIE---NVSRSAALIQQSTT-----------VKNKDIHLNPGGG 150 (179)
Q Consensus 102 ~GV~v~v~~~~t~IiI~--GiDKe---~Vgq~AA~Ir~~~~-----------~KgKdiR~FlDG~ 150 (179)
.++.+.. +++.|.++ ..++. .+|-++|.|++.-. ..|-|.|+.++|.
T Consensus 39 ~~v~i~~--~~~~i~v~~~~~~k~~~a~~gt~~s~I~Nmi~GVt~Gf~~~L~lvGvgyrv~~~g~ 101 (178)
T PRK05498 39 PDVTVKV--EDNEITVTRPDDSKKARALHGTTRALINNMVVGVTEGFEKKLEIVGVGYRAQVKGK 101 (178)
T ss_pred CCeEEEE--ECCEEEEEcCCCCHHHHHHHHHHHHHHHHHhhhcCCCeEEEEEEEeEEEEEEEeCC
Confidence 3444444 33456665 22343 67888888887542 4556667777763
No 15
>PTZ00179 60S ribosomal protein L9; Provisional
Probab=61.03 E-value=8.7 Score=32.08 Aligned_cols=13 Identities=0% Similarity=0.174 Sum_probs=9.0
Q ss_pred HHHHHHHHHhhhc
Q psy7622 124 NVSRSAALIQQST 136 (179)
Q Consensus 124 ~Vgq~AA~Ir~~~ 136 (179)
+.|-++|.|++.-
T Consensus 67 l~Gt~rslI~NMI 79 (189)
T PTZ00179 67 TINTALSHVRNMI 79 (189)
T ss_pred HHHHHHHHHHHHh
Confidence 5677777777654
No 16
>PRK05518 rpl6p 50S ribosomal protein L6P; Reviewed
Probab=58.64 E-value=10 Score=31.45 Aligned_cols=32 Identities=25% Similarity=0.281 Sum_probs=18.1
Q ss_pred CcEEEecCCCCEEEEEEcc-----HHHHHHHHHHHhhhc
Q psy7622 103 GVKVSNSKQKDELIIEGND-----IENVSRSAALIQQST 136 (179)
Q Consensus 103 GV~v~v~~~~t~IiI~GiD-----Ke~Vgq~AA~Ir~~~ 136 (179)
.+++.+ ++++|.++-.+ +...|-+.|.|++.-
T Consensus 42 ~v~i~~--~~~~i~v~~~~~~kk~ra~~gt~rslI~NmI 78 (180)
T PRK05518 42 GVTISV--EDGKVVIETEFARKKTKAMVGTFASHIKNMI 78 (180)
T ss_pred cEEEEE--ECCEEEEEECCCCHHHHHHHHHHHHHHHhhh
Confidence 344444 33456666433 236688888888743
No 17
>CHL00140 rpl6 ribosomal protein L6; Validated
Probab=56.53 E-value=61 Score=26.61 Aligned_cols=75 Identities=15% Similarity=0.192 Sum_probs=52.9
Q ss_pred eceeEEeccCCceeEEeccCCceeeEEEeCCCCcEEEecCCCCEEEEEEcc--H---HHHHHHHHHHhhhcc--------
Q psy7622 71 FPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGND--I---ENVSRSAALIQQSTT-------- 137 (179)
Q Consensus 71 yra~v~i~~~G~~l~i~NfLG~shpi~~~IP~GV~v~v~~~~t~IiI~GiD--K---e~Vgq~AA~Ir~~~~-------- 137 (179)
.|..|+++-+++.|.+++=+| -....+|..+++.. +++.|.++-.+ + ...|-++|.|++.-.
T Consensus 11 IP~~V~v~i~~~~v~vkGp~G---~l~~~~~~~v~i~~--~~~~i~v~~~~~~k~~~a~~gt~~slI~Nmi~GVt~Gf~~ 85 (178)
T CHL00140 11 IPDNVNVSIDDQIIKVKGPKG---TLSRKIPDLITIEI--QDNSLFVSKKDESKKARALHGLYRTLINNMVIGVSEGFEK 85 (178)
T ss_pred cCCCCEEEEECCEEEEECCCE---EEEEECCCCeEEEE--eCCEEEEEcCCCCHHHHHHHHHHHHHHHHHHhhcccCceE
Confidence 455555555688899875555 55678888999887 45578887443 3 358999999998542
Q ss_pred ---ccCCceeecCCCC
Q psy7622 138 ---VKNKDIHLNPGGG 150 (179)
Q Consensus 138 ---~KgKdiR~FlDG~ 150 (179)
..|-|.|..++|.
T Consensus 86 ~L~lvGvGyr~~~~g~ 101 (178)
T CHL00140 86 KLELQGVGYRAQVQGK 101 (178)
T ss_pred EEEEEEEEEEEEEeCC
Confidence 5677788888774
No 18
>TIGR03654 L6_bact ribosomal protein L6, bacterial type.
Probab=48.96 E-value=73 Score=26.01 Aligned_cols=74 Identities=15% Similarity=0.219 Sum_probs=50.0
Q ss_pred ceeEEeccCCceeEEeccCCceeeEEEeCCCCcEEEecCCCCEEEEEEcc--H---HHHHHHHHHHhhhcc---------
Q psy7622 72 PINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGND--I---ENVSRSAALIQQSTT--------- 137 (179)
Q Consensus 72 ra~v~i~~~G~~l~i~NfLG~shpi~~~IP~GV~v~v~~~~t~IiI~GiD--K---e~Vgq~AA~Ir~~~~--------- 137 (179)
|-.|+++-+++.|.+++=+| -....+|+.+.+.+ +++.|.++-.+ + ..+|-++|.|++.-.
T Consensus 11 P~~V~v~~~~~~v~v~Gp~G---~l~~~l~~~i~i~~--~~~~i~v~~~~~~kk~~a~~gt~~s~i~Nmi~GVt~Gf~~~ 85 (175)
T TIGR03654 11 PAGVEVTIDGNVVTVKGPKG---ELSRTLHPGVTVKV--EDGQLTVSRPNDSKEARALHGTTRALINNMVIGVSEGFEKK 85 (175)
T ss_pred CCCcEEEEeCCEEEEEcCCe---EEEEEcCCCeEEEE--ECCEEEEEecCCCHHHHHHHHHHHHHHHHHhheeccCcEEE
Confidence 33344444578899976677 44466688999988 45678887443 2 377888999888542
Q ss_pred --ccCCceeecCCCC
Q psy7622 138 --VKNKDIHLNPGGG 150 (179)
Q Consensus 138 --~KgKdiR~FlDG~ 150 (179)
.-|-|.|+.++|.
T Consensus 86 L~lvGvgyrv~~~g~ 100 (175)
T TIGR03654 86 LEIVGVGYRAQLQGK 100 (175)
T ss_pred EEEEEEEEEEEEeCC
Confidence 4566668888774
No 19
>TIGR03653 arch_L6P archaeal ribosomal protein L6P. Members of this protein family are the archaeal ribosomal protein L6P. The top-scoring proteins not selected by this model are eukaryotic cytosolic ribosomal protein L9. Bacterial ribosomal protein L6 scores lower and is described by a distinct model.
Probab=45.48 E-value=1.2e+02 Score=24.88 Aligned_cols=74 Identities=15% Similarity=0.253 Sum_probs=49.4
Q ss_pred ceeEEeccCCceeEEeccCCceeeEEEeC-CCCcEEEecCCCCEEEEEEcc--H---HHHHHHHHHHhhhcc--------
Q psy7622 72 PINCVTSENNTLLEIRNFLGEKYIRRVKM-APGVKVSNSKQKDELIIEGND--I---ENVSRSAALIQQSTT-------- 137 (179)
Q Consensus 72 ra~v~i~~~G~~l~i~NfLG~shpi~~~I-P~GV~v~v~~~~t~IiI~GiD--K---e~Vgq~AA~Ir~~~~-------- 137 (179)
|..|++.-+++.+.+++=+| -...++ |+.+++.+ +++.|.++-.+ + ...|-+.|.|++.-.
T Consensus 7 P~~V~v~i~~~~i~vkGp~G---~L~~~~~~~~v~i~~--~~~~i~v~~~~~~k~~~a~~gt~rsli~NmI~GVt~Gf~~ 81 (170)
T TIGR03653 7 PEGVSVTIEGNIVTVKGPKG---EVTRELWYPGIEISV--EDGKVVIETDFARKKDKAMVGTYRSHIKNMIKGVTEGFEY 81 (170)
T ss_pred CCCCEEEEeCCEEEEECCCe---EEEEEEeCCcEEEEE--eCCEEEEEeCCCCHHHHHHHHHHHHHHHhheeecccCeEE
Confidence 44444444678899976666 444677 88899988 45678888544 3 367888888887442
Q ss_pred ---ccCCce--eecCCCC
Q psy7622 138 ---VKNKDI--HLNPGGG 150 (179)
Q Consensus 138 ---~KgKdi--R~FlDG~ 150 (179)
+.|-|. |..++|.
T Consensus 82 ~LeivGvGy~~ra~~~g~ 99 (170)
T TIGR03653 82 KMKVVYSHFPMQVKVEGN 99 (170)
T ss_pred EEEEEeccccEEEEEcCC
Confidence 344455 7777774
No 20
>PTZ00027 60S ribosomal protein L6; Provisional
Probab=44.22 E-value=1.2e+02 Score=25.38 Aligned_cols=73 Identities=12% Similarity=0.117 Sum_probs=46.2
Q ss_pred ceeEEeccCCceeEEeccCCceeeEEEeCCCCcEEEecCCCCEEEEEEcc-----HHHHHHHHHHHhhhcc---------
Q psy7622 72 PINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGND-----IENVSRSAALIQQSTT--------- 137 (179)
Q Consensus 72 ra~v~i~~~G~~l~i~NfLG~shpi~~~IP~GV~v~v~~~~t~IiI~GiD-----Ke~Vgq~AA~Ir~~~~--------- 137 (179)
|..|++.-+++.+.+++=+|.-.--.-..|..+.+.. +++.|.++-.+ +...|-++|.|++.-.
T Consensus 13 P~~V~V~i~~~~v~VkGp~G~L~~~~~~~~~~i~i~~--~~~~i~v~~~~~~~k~~a~~Gt~rslI~NmI~GVt~Gf~~~ 90 (190)
T PTZ00027 13 PEGVTVTVKSRKVTVTGKYGELTRSFRHLPVDIKLSK--DGKYIKVEMWFGTPSHLACIRTVCSHIKNMMTGVTKKFQYK 90 (190)
T ss_pred CCCCEEEEECCEEEEECCCceEEEEecCCCceEEEEe--CCCEEEEEeCCCCHHHHHHHHHHHHHHHHHhhhhcCCEEEE
Confidence 4444555467889998777744422222334777766 45578887443 2377999999988653
Q ss_pred --ccCCceeec
Q psy7622 138 --VKNKDIHLN 146 (179)
Q Consensus 138 --~KgKdiR~F 146 (179)
+-|-|.|..
T Consensus 91 LeivGvGyra~ 101 (190)
T PTZ00027 91 MRLVYAHFPIN 101 (190)
T ss_pred EEEEEeeeeEE
Confidence 456666766
No 21
>PF05137 PilN: Fimbrial assembly protein (PilN); InterPro: IPR007813 PilN is a plasmid-encoded, lipoprotein which locates to the outer membrane of bacteria and are part of a thin pilus required only for liquid mating [].
Probab=39.72 E-value=76 Score=21.26 Aligned_cols=42 Identities=19% Similarity=0.210 Sum_probs=30.0
Q ss_pred EeCCCCcEEEec-CCCCEEEEEEc--cHHHHHHHHHHHhhhcccc
Q psy7622 98 VKMAPGVKVSNS-KQKDELIIEGN--DIENVSRSAALIQQSTTVK 139 (179)
Q Consensus 98 ~~IP~GV~v~v~-~~~t~IiI~Gi--DKe~Vgq~AA~Ir~~~~~K 139 (179)
-.+|+||.++-- .+.+.|.|+|. |-+.|.+|-.++++.--++
T Consensus 8 ~~~P~~v~l~~l~~~~~~l~i~G~a~~~~~v~~f~~~L~~~~~f~ 52 (78)
T PF05137_consen 8 RALPEGVWLTSLSINGNTLSISGYADSYQSVAAFLRNLEQSPFFS 52 (78)
T ss_pred hhCCCCEEEEEEEEeCCEEEEEEEECCHHHHHHHHHHHhhCCCcc
Confidence 357999998864 35678888885 6777888877777654333
No 22
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=38.10 E-value=70 Score=20.78 Aligned_cols=30 Identities=33% Similarity=0.494 Sum_probs=20.2
Q ss_pred CCcEEEec-C--CCCEEEEEEccHHHHHHHHHHH
Q psy7622 102 PGVKVSNS-K--QKDELIIEGNDIENVSRSAALI 132 (179)
Q Consensus 102 ~GV~v~v~-~--~~t~IiI~GiDKe~Vgq~AA~I 132 (179)
.|+++.+| . ..+.|+|.|. .+.|-...+.|
T Consensus 29 ~g~~I~i~~~~~~~~~v~I~G~-~~~v~~A~~~i 61 (62)
T cd02394 29 TGVKIRFPDPGSKSDTITITGP-KENVEKAKEEI 61 (62)
T ss_pred hCCEEEcCCCCCCCCEEEEEcC-HHHHHHHHHHh
Confidence 36666665 1 2578999999 66776665554
No 23
>cd06477 ACD_HspB3_Like Alpha crystallin domain (ACD) found in mammalian HspB3, also known as heat-shock protein 27-like protein (HSPL27, 17-kDa) and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB3 is expressed in adult skeletal muscle, smooth muscle, and heart, and in several other fetal tissues. In muscle cells HspB3 forms an oligomeric 150 kDa complex with myotonic dystrophy protein kinase-binding protein (MKBP/ HspB2), this complex may comprise one of two independent muscle-cell specific chaperone systems. The expression of HspB3 is induced during muscle differentiation controlled by the myogenic factor MyoD. HspB3 may also interact with Hsp22 (HspB8).
Probab=35.96 E-value=74 Score=22.93 Aligned_cols=29 Identities=21% Similarity=0.460 Sum_probs=20.6
Q ss_pred eeeEEEeCCCCcEEEec-C---CCCEEEEEEcc
Q psy7622 93 KYIRRVKMAPGVKVSNS-K---QKDELIIEGND 121 (179)
Q Consensus 93 shpi~~~IP~GV~v~v~-~---~~t~IiI~GiD 121 (179)
+.-+.|.+|++|...-- + ++.-|.|++.|
T Consensus 51 ~F~R~~~LP~~Vd~~~v~A~~~~dGvL~I~~~~ 83 (83)
T cd06477 51 SFTRQYQLPDGVEHKDLSAMLCHDGILVVETKD 83 (83)
T ss_pred EEEEEEECCCCcchheEEEEEcCCCEEEEEecC
Confidence 67788999987766532 1 45678888865
No 24
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=34.00 E-value=1e+02 Score=19.89 Aligned_cols=28 Identities=32% Similarity=0.564 Sum_probs=19.9
Q ss_pred CcEEEecCC---CCEEEEEEccHHHHHHHHHHH
Q psy7622 103 GVKVSNSKQ---KDELIIEGNDIENVSRSAALI 132 (179)
Q Consensus 103 GV~v~v~~~---~t~IiI~GiDKe~Vgq~AA~I 132 (179)
|+.+.++ . .+.+.|+| +.+.|-+..+.|
T Consensus 30 ~~~I~i~-~~~~~~~v~I~G-~~~~v~~A~~~I 60 (60)
T PF00013_consen 30 GVKIQIP-DDDERDIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp TSEEEEE-STTEEEEEEEEE-SHHHHHHHHHHH
T ss_pred CeEEEEc-CCCCcEEEEEEe-CHHHHHHHHhhC
Confidence 5666665 3 35799999 888887766554
No 25
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=29.93 E-value=26 Score=25.30 Aligned_cols=14 Identities=43% Similarity=0.631 Sum_probs=7.9
Q ss_pred CceeEEeccCCceeeE
Q psy7622 81 NTLLEIRNFLGEKYIR 96 (179)
Q Consensus 81 G~~l~i~NfLG~shpi 96 (179)
|+..+|+ ||++|++
T Consensus 56 GdEFeI~--LgrKhI~ 69 (71)
T PF14250_consen 56 GDEFEIK--LGRKHIH 69 (71)
T ss_pred CCEEEEE--eCcceEE
Confidence 5555565 6666643
No 26
>COG0097 RplF Ribosomal protein L6P/L9E [Translation, ribosomal structure and biogenesis]
Probab=27.87 E-value=62 Score=27.04 Aligned_cols=61 Identities=18% Similarity=0.168 Sum_probs=35.9
Q ss_pred ceeEEeccCCceeEEeccCCceeeEEEeCCCCcEEEecCCCCEEEEEEcc----HHHHHHHHHHHhhhc
Q psy7622 72 PINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGND----IENVSRSAALIQQST 136 (179)
Q Consensus 72 ra~v~i~~~G~~l~i~NfLG~shpi~~~IP~GV~v~v~~~~t~IiI~GiD----Ke~Vgq~AA~Ir~~~ 136 (179)
|..|++.-++..+.+ -|-+--....++.-+ +.+..+.+.+++.=.| ....|-++|.|.+.-
T Consensus 12 P~gV~V~i~~~~v~v---kGpkGeL~~~~~~~~-v~v~~~~~~~vv~~~~~k~~~a~~Gt~rali~Nmv 76 (178)
T COG0097 12 PAGVTVSIEGQVVTV---KGPKGELTREFHDNV-VKVEVEDNILVVRPVDGKRKRALHGTVRALINNMV 76 (178)
T ss_pred CCCeEEEEeccEEEE---ECCCcEEEEEecCcc-eEEEecCCEEEEeecccchhHHHHHHHHHHHHHHh
Confidence 544444445777776 477767777777666 4443023434443332 356788888888754
No 27
>TIGR01212 radical SAM protein, TIGR01212 family. This uncharacterized protein family shows significant similarity to TIGR01211, a longer protein that is a histone acetyltransferase at its C-terminus and is a subunit of RNA polymerase II (in yeast). This family lacks the GNAT acetyltransferase domain.
Probab=25.08 E-value=34 Score=29.93 Aligned_cols=14 Identities=43% Similarity=1.006 Sum_probs=10.8
Q ss_pred CC--CCCceEEecccc
Q psy7622 148 GG--GGGGCLYLNKTY 161 (179)
Q Consensus 148 DG--~~~~~~~~~~~~ 161 (179)
|| ..|||+||+..+
T Consensus 32 dg~~~~~gC~FC~~~~ 47 (302)
T TIGR01212 32 DGTKGRGGCTFCNDAS 47 (302)
T ss_pred CCCCCCCCcccCCCCC
Confidence 56 458999999655
No 28
>PF00338 Ribosomal_S10: Ribosomal protein S10p/S20e; InterPro: IPR001848 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S10 consists of about 100 amino acid residues. In Escherichia coli, S10 is involved in binding tRNA to the ribosome, and also operates as a transcriptional elongation factor []. Experimental evidence [] has revealed that S10 has virtually no groups exposed on the ribosomal surface, and is one of the "split proteins": these are a discrete group that are selectively removed from 30S subunits under low salt conditions and are required for the formation of activated 30S reconstitution intermediate (RI*) particles. S10 belongs to a family of proteins [] that includes: bacteria S10; algal chloroplast S10; cyanelle S10; archaebacterial S10; Marchantia polymorpha and Prototheca wickerhamii mitochondrial S10; Arabidopsis thaliana mitochondrial S10 (nuclear encoded); vertebrate S20; plant S20; and yeast URP2.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1S1H_J 3U5G_U 3O30_N 3O2Z_N 3IZB_J 3U5C_U 3R2C_J 3R2D_J 2ZKQ_j 2XQD_J ....
Probab=24.22 E-value=1.4e+02 Score=21.33 Aligned_cols=30 Identities=7% Similarity=0.107 Sum_probs=25.3
Q ss_pred EEEEEEccHHHHHHHHHHHhhhccccCCce
Q psy7622 114 ELIIEGNDIENVSRSAALIQQSTTVKNKDI 143 (179)
Q Consensus 114 ~IiI~GiDKe~Vgq~AA~Ir~~~~~KgKdi 143 (179)
.|.|+|.|...+-.++..|..+.+..|-.+
T Consensus 2 ~I~l~s~d~~~l~~~~~~i~~~~~~~~~~~ 31 (97)
T PF00338_consen 2 RIKLKSYDKKLLESYVKFIHKLAKNLGIKV 31 (97)
T ss_dssp EEEEEESSHHHHHHHHHHHHHHHHCTSSCE
T ss_pred EEEEEECCHHHHHHHHHHHHHHHHHhCCcc
Confidence 488999999999999999999986555443
No 29
>PRK09502 iscA iron-sulfur cluster assembly protein; Provisional
Probab=23.40 E-value=58 Score=24.17 Aligned_cols=19 Identities=26% Similarity=0.454 Sum_probs=13.2
Q ss_pred cCCceeecCCCCC-CceEEe
Q psy7622 139 KNKDIHLNPGGGG-GGCLYL 157 (179)
Q Consensus 139 KgKdiR~FlDG~~-~~~~~~ 157 (179)
++.++|+|+++.+ +|.-|.
T Consensus 22 ~~~~LRi~v~~~GCsG~~Y~ 41 (107)
T PRK09502 22 KGFGLRLGVRTSGCSGMAYV 41 (107)
T ss_pred CCceEEEEEECCCcCCeeeE
Confidence 4557999999855 555454
No 30
>COG1072 CoaA Panthothenate kinase [Coenzyme metabolism]
Probab=23.28 E-value=56 Score=29.25 Aligned_cols=36 Identities=22% Similarity=0.185 Sum_probs=29.4
Q ss_pred CCceeeEEEeCCCCcEEEecCCCCEEEEEEccHHHHHH
Q psy7622 90 LGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSR 127 (179)
Q Consensus 90 LG~shpi~~~IP~GV~v~v~~~~t~IiI~GiDKe~Vgq 127 (179)
..|||-+.-.+|....|.- +++.|++||++.=+-++
T Consensus 167 Pvysh~~yD~vpd~~~v~~--~pdIlI~EG~nvLq~~~ 202 (283)
T COG1072 167 PVYSHLIYDPVPDAFQVVP--QPDILIVEGNNVLQDGE 202 (283)
T ss_pred ccccccccccCCCceeecC--CCCEEEEechhhhcCCC
Confidence 7999999999988777754 78999999998655544
No 31
>PF02741 FTR_C: FTR, proximal lobe; InterPro: IPR002770 Formylmethanofuran:tetrahyromethanopterin formyltransferase (Ftr) is involved in C1 metabolism in methanogenic archaea, sulphate-reducing archaea and methylotrophic bacteria. It catalyses the following reversible reaction: N-formylmethanofuran + 5,6,7,8-tetrahydromethanopterin = methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterin Ftr from the thermophilic methanogen Methanopyrus kandleri (optimum growth temperature 98 degrees C) is a hyperthermophilic enzyme that is absolutely dependent on the presence of lyotropic salts for activity and thermostability. The crystal structure of Ftr, determined to a reveals a homotetramer composed essentially of two dimers. Each subunit is subdivided into two tightly associated lobes both consisting of a predominantly antiparallel beta sheet flanked by alpha helices forming an alpha/beta sandwich structure. The approximate location of the active site was detected in a region close to the dimer interface []. Ftr from the mesophilic methanogen Methanosarcina barkeri and the sulphate-reducing archaeon Archaeoglobus fulgidus have a similar structure []. In the methylotrophic bacterium Methylobacterium extorquens, Ftr interacts with three other polypeptides to form an Ftr/cyclohydrolase complex which catalyses the hydrolysis of formyl-tetrahydromethanopterin to formate during growth on C1 substrates [].; GO: 0016740 transferase activity, 0006730 one-carbon metabolic process; PDB: 1M5S_B 1M5H_E 1FTR_C 2FHJ_B 2FHK_D.
Probab=22.21 E-value=2.3e+02 Score=23.24 Aligned_cols=50 Identities=24% Similarity=0.328 Sum_probs=28.9
Q ss_pred EEeCCCCcEEEecCCCCEEEEEEccHHHHHH-HHHHHhhhccccCCceeecCCCCCCc
Q psy7622 97 RVKMAPGVKVSNSKQKDELIIEGNDIENVSR-SAALIQQSTTVKNKDIHLNPGGGGGG 153 (179)
Q Consensus 97 ~~~IP~GV~v~v~~~~t~IiI~GiDKe~Vgq-~AA~Ir~~~~~KgKdiR~FlDG~~~~ 153 (179)
.-.+|+||.... ||+|-|.|-+.|.+ +-+=|+.++ +.-|+..---|.-||
T Consensus 88 ~S~lp~~v~~V~-----EIVIdGl~~~av~~Amr~Gi~Aa~--~~~Gv~~IsAGNYGG 138 (150)
T PF02741_consen 88 DSELPEGVNAVY-----EIVIDGLSEEAVAEAMRAGIEAAC--AVPGVVRISAGNYGG 138 (150)
T ss_dssp T-S--TT--EEE-----EEEEEESSHHHHHHHHHHHHHHHT--TSTTEEEEE---STT
T ss_pred cccCCCCCCeEE-----EEEEcCCCHHHHHHHHHHHHHHHh--cCCCeEEEecCCcCC
Confidence 357899999877 59999999999976 456677777 333444444443333
No 32
>TIGR03119 one_C_fhcD formylmethanofuran--tetrahydromethanopterin N-formyltransferase. Members of this protein family are the FhcD protein of tetrahydromethanopterin (H4MPT)-dependent C-1 carrier metabolism. In the archaea, FhcD is designated formylmethanofuran--tetrahydromethanopterin N-formyltransferase, while in bacteria it is commonly designated as formyltransferase/hydrolase complex subunit D. FhcD is essential for one-carbon metabolism in at least three groups of prokaryotes: methanogenic archaea, sulfate-reducing archaea, and methylotrophic bacteria.
Probab=20.80 E-value=1.8e+02 Score=26.20 Aligned_cols=50 Identities=20% Similarity=0.337 Sum_probs=34.9
Q ss_pred EEeCCCCcEEEecCCCCEEEEEEccHHHHHH-HHHHHhhhccccCCceeecCCCCCCc
Q psy7622 97 RVKMAPGVKVSNSKQKDELIIEGNDIENVSR-SAALIQQSTTVKNKDIHLNPGGGGGG 153 (179)
Q Consensus 97 ~~~IP~GV~v~v~~~~t~IiI~GiDKe~Vgq-~AA~Ir~~~~~KgKdiR~FlDG~~~~ 153 (179)
.-++|+||.... ||+|-|.|-+.|.+ +.+=|+.++.. .|+..---|.-||
T Consensus 225 ~S~lp~~v~~V~-----EIVIdGl~~~aV~~Amr~Gi~Aa~~~--~Gv~~IsAGNYGG 275 (287)
T TIGR03119 225 ESELPEGVNAVY-----EIVIDGLNEAAIAEAMRVGILAATEI--PGVVKITAGNYGG 275 (287)
T ss_pred cccCCCCCCeEE-----EEEEcCCCHHHHHHHHHHHHHHHhcC--CCeEEEecCccCC
Confidence 456888888766 59999999999987 56678887753 3444444443333
No 33
>cd06478 ACD_HspB4-5-6 Alpha-crystallin domain found in alphaA-crystallin (HspB4), alphaB-crystallin (HspB5), and the small heat shock protein (sHsp) HspB6, also known as Hsp20. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. Only trace amounts of HspB4 are found in tissues other than the lens. HspB5 on the other hand is also expressed constitutively in other tissues including brain, heart, and type I and type IIa skeletal muscle fibers, and in several cancers including gliomas, renal cell carcinomas, basal-like and metaplastic breast carcinomas, and head and neck cancer. HspB5's functions include effects on the apoptotic pathway and on metastasis. Phosphorylation of HspB5 reduces its ol
Probab=20.52 E-value=1.7e+02 Score=20.65 Aligned_cols=18 Identities=22% Similarity=0.209 Sum_probs=14.7
Q ss_pred CCCcEEEecCCCCEEEEEEc
Q psy7622 101 APGVKVSNSKQKDELIIEGN 120 (179)
Q Consensus 101 P~GV~v~v~~~~t~IiI~Gi 120 (179)
|+.|+|++ .++.|+|+|-
T Consensus 20 ~edI~V~v--~~~~L~I~g~ 37 (83)
T cd06478 20 PEELSVKV--LGDFVEIHGK 37 (83)
T ss_pred HHHeEEEE--ECCEEEEEEE
Confidence 47889998 4679999994
No 34
>cd01231 PH_Lnk LNK-family Pleckstrin homology (PH) domain. LNK-family Pleckstrin homology (PH) domain. The Lnk family of proteins consists of Lnk, APS and SH2B. They are adaptor proteins consisting of a PH domain and an SH2 domain, which mediates signaling through growth factor receptors. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. The lnk family PH domain is likely involved in targeting of the adaptor proteins to the plasma membrane.
Probab=20.27 E-value=2.2e+02 Score=22.10 Aligned_cols=39 Identities=15% Similarity=0.193 Sum_probs=29.5
Q ss_pred EEEeCCCCcEEEec--CCCCEEEEEEccHHHHHHHHHHHhh
Q psy7622 96 RRVKMAPGVKVSNS--KQKDELIIEGNDIENVSRSAALIQQ 134 (179)
Q Consensus 96 i~~~IP~GV~v~v~--~~~t~IiI~GiDKe~Vgq~AA~Ir~ 134 (179)
-.++||+-...-+. +.+++++++-.|-|++.+--|.||.
T Consensus 66 t~LEmPD~~nTFvLK~~~~~eyI~Ea~d~~q~~SWla~Ir~ 106 (107)
T cd01231 66 TRLEMPDNLYTFVLKVDDNTDIIFEVGDEQQLNSWLAELRY 106 (107)
T ss_pred ccccccCcccEEEEEecCCceEEEEcCCHHHHHHHHHHHhc
Confidence 34567765544443 3678999999999999999999873
No 35
>COG1242 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=20.24 E-value=59 Score=29.49 Aligned_cols=26 Identities=23% Similarity=0.367 Sum_probs=17.7
Q ss_pred ccCCceeecCCCCC-----------CceEEeccccce
Q psy7622 138 VKNKDIHLNPGGGG-----------GGCLYLNKTYRW 163 (179)
Q Consensus 138 ~KgKdiR~FlDG~~-----------~~~~~~~~~~~~ 163 (179)
|.-|=.++-+||+- |||+|||..|+-
T Consensus 19 fg~Kv~Kv~ld~GF~CPNRDGti~rGGCtFC~~~g~~ 55 (312)
T COG1242 19 FGEKVFKVTLDGGFSCPNRDGTIGRGGCTFCSVAGSG 55 (312)
T ss_pred hCCeeEEEeccCCCCCCCCCCcccCCceeeecCCCCC
Confidence 44555566666642 899999977764
Done!