Query 022545
Match_columns 295
No_of_seqs 184 out of 1202
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 04:21:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022545.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022545hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0081 RplA Ribosomal protein 100.0 8.9E-71 1.9E-75 496.0 24.4 225 59-283 2-227 (228)
2 CHL00129 rpl1 ribosomal protei 100.0 5.2E-70 1.1E-74 496.3 27.0 226 60-286 3-228 (229)
3 TIGR01169 rplA_bact ribosomal 100.0 9.8E-68 2.1E-72 481.0 27.3 225 61-285 2-226 (227)
4 PRK05424 rplA 50S ribosomal pr 100.0 1.1E-67 2.4E-72 481.6 27.0 228 60-287 2-229 (230)
5 PRK04203 rpl1P 50S ribosomal p 100.0 9.1E-57 2E-61 406.1 24.3 200 79-283 6-215 (215)
6 PTZ00225 60S ribosomal protein 100.0 5.9E-54 1.3E-58 387.5 22.6 198 79-282 8-214 (214)
7 PTZ00029 60S ribosomal protein 100.0 4.9E-52 1.1E-56 375.6 22.7 198 79-282 8-216 (216)
8 cd00403 Ribosomal_L1 Ribosomal 100.0 2E-46 4.4E-51 334.8 23.1 198 81-281 2-208 (208)
9 TIGR01170 rplA_mito ribosomal 100.0 1E-42 2.2E-47 296.0 15.7 137 78-216 1-141 (141)
10 KOG1569 50S ribosomal protein 100.0 8E-43 1.7E-47 323.1 16.2 211 76-289 88-311 (323)
11 PF00687 Ribosomal_L1: Ribosom 100.0 6.7E-37 1.5E-41 275.1 20.4 185 90-278 15-220 (220)
12 KOG1570 60S ribosomal protein 100.0 1.1E-28 2.4E-33 218.9 7.8 201 76-282 6-218 (218)
13 KOG1685 Uncharacterized conser 99.7 1E-17 2.2E-22 159.6 9.0 155 128-286 87-263 (343)
14 PF13003 MRL1: Ribosomal prote 96.7 0.0027 5.9E-08 53.7 5.0 58 78-135 70-133 (133)
15 PTZ00029 60S ribosomal protein 85.3 0.44 9.5E-06 43.5 1.5 22 181-203 116-137 (216)
16 PTZ00225 60S ribosomal protein 73.1 2.2 4.8E-05 39.0 1.9 21 181-202 114-134 (214)
17 COG1064 AdhP Zn-dependent alco 64.6 10 0.00022 37.2 4.5 58 130-191 191-252 (339)
18 TIGR00853 pts-lac PTS system, 54.8 28 0.00061 27.5 4.9 64 129-192 3-75 (95)
19 cd05565 PTS_IIB_lactose PTS_II 51.1 28 0.0006 28.0 4.3 63 131-193 2-73 (99)
20 PRK01189 V-type ATP synthase s 43.2 81 0.0018 25.5 5.9 83 131-214 4-97 (104)
21 PRK13958 N-(5'-phosphoribosyl) 41.4 13 0.00029 33.5 1.2 25 130-154 3-27 (207)
22 COG0135 TrpF Phosphoribosylant 39.3 15 0.00032 33.5 1.1 25 129-153 3-27 (208)
23 PF00697 PRAI: N-(5'phosphorib 35.9 23 0.0005 31.4 1.8 25 130-154 1-25 (197)
24 PF10944 DUF2630: Protein of u 34.4 22 0.00047 27.9 1.2 9 4-12 45-53 (81)
25 PRK01222 N-(5'-phosphoribosyl) 32.8 21 0.00044 32.3 1.0 26 129-154 4-29 (210)
26 cd00405 PRAI Phosphoribosylant 31.8 68 0.0015 28.2 4.1 25 130-154 1-25 (203)
27 PLN02363 phosphoribosylanthran 31.2 24 0.00052 33.1 1.1 27 128-154 47-73 (256)
28 COG1436 NtpG Archaeal/vacuolar 30.3 1.2E+02 0.0026 24.7 5.0 84 130-214 3-98 (104)
29 PRK01395 V-type ATP synthase s 27.4 1.6E+02 0.0035 23.8 5.2 82 130-214 4-99 (104)
30 PF00107 ADH_zinc_N: Zinc-bind 25.9 76 0.0017 25.0 3.1 64 130-193 15-84 (130)
31 KOG1198 Zinc-binding oxidoredu 25.7 1.1E+02 0.0024 29.8 4.7 45 129-173 183-231 (347)
32 PRK02228 V-type ATP synthase s 25.2 1.4E+02 0.0031 23.7 4.5 81 131-214 2-94 (100)
33 PF05991 NYN_YacP: YacP-like N 24.2 89 0.0019 27.1 3.4 36 129-164 94-130 (166)
34 PF01990 ATP-synt_F: ATP synth 23.3 1.1E+02 0.0025 23.7 3.6 56 132-187 1-63 (95)
35 COG4844 Uncharacterized protei 22.3 71 0.0015 24.4 2.1 17 236-252 58-74 (78)
36 PF00281 Ribosomal_L5: Ribosom 22.0 1.4E+02 0.0031 21.4 3.5 31 227-259 12-42 (56)
No 1
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.9e-71 Score=496.04 Aligned_cols=225 Identities=52% Similarity=0.866 Sum_probs=220.9
Q ss_pred cccchhHHHHHhhccCCCCCCHHHHHHHHHhhccCCCCCcEEEEEEeCcCCCCCCccceeeeecCCCCCCceEEEEEcCc
Q 022545 59 ETGSKRFLEIQNLREGKKEYDLKTAISLLKQMSSTKFTETAEAHFRLNIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQG 138 (295)
Q Consensus 59 ~~~~k~~~~~~~~~~~~~~y~l~eAI~~lk~~~~~~F~EsVel~i~L~id~kk~~~~irg~V~LPh~~gk~~kV~Vfa~~ 138 (295)
.|++|+++++.+..+..+.|++.|||+++++.+.++|+||||++++|++|+++++|++||+|.|||++|+..||||||++
T Consensus 2 ~k~~k~~~~~~~~~d~~~~~~i~eai~~~ke~~~~kF~etVevav~L~vD~~k~dq~vrg~VvLP~g~gk~vrV~Vfa~g 81 (228)
T COG0081 2 AKKSKRYRAASEKVDRNKLYSLEEAVKLLKETSKRKFDETVEVAVNLKVDPRKPDQRVRGSVVLPNGTGKTVRVAVFADG 81 (228)
T ss_pred chhHHHHHHHHHhhhhhhhhhHHHHHHHHHhccccCcceEEEEEEEcccCCCCcccccceeEECCCCCCCccEEEEEcCh
Confidence 35799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccHHHHHHcCCCccccHHHHHHHHcC-cccccEEEeCccchHHhHhhchhccCCCCCCCCCCCCCCCCHHHHHHHHhcCe
Q 022545 139 EKFNEAKNAGADLVGGDDLIEQIKGG-FMEFDKLIASPDMMVKVASLGKILGPRGLMPNPKAGTVTTNIPQAIEEFKKGK 217 (295)
Q Consensus 139 ~~~eeAk~aGAd~VG~~eLi~kIk~g-~~~fD~~lAt~d~m~~l~~LgriLGPrGlMP~pk~GTvt~di~~~I~~~k~G~ 217 (295)
+.+++|++||||+||++||+++|+++ |.+||+|||||||||.++.||++||||||||||++||++.|+.++|+++++|+
T Consensus 82 ~~~~~A~~AGad~Vg~edl~e~ik~~r~~~fD~~IAtpdmM~~v~~LG~vLGPRGlMP~Pk~gTvt~Dv~~av~~~K~g~ 161 (228)
T COG0081 82 EKAEEAKAAGADYVGGEDLIELIKNGRAKDFDVFIATPDMMPLVGKLGKVLGPRGLMPNPKTGTVTDDVAKAVEELKKGT 161 (228)
T ss_pred HhHHHHHHcCCCEecHHHHHHHHhCcchhcCCEEEECchHHHHHHHHhhhcCCCCCCCCCCCCCCCcCHHHHHHHHhcCc
Confidence 99999999999999999999999999 99999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEcCCCeeeEeeeCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCceeeEEEEeCCCCCcEEeec
Q 022545 218 VEYRADKTGIVHIPFGKADFSEDDLLINFLAAVKSIEANKPKGAKGVYWKSAYICSSMGPSIRLNI 283 (295)
Q Consensus 218 v~~r~dk~g~i~v~IGk~sm~~e~L~ENi~avl~~I~~~~p~~~kg~~Ik~i~IssTmGp~i~I~~ 283 (295)
++||+|+.|++|++||+++|++|+|.||+.++++.|.+.+|.+.++.||+++||||||||+++|+.
T Consensus 162 v~~R~dk~g~ih~~iGk~sf~~e~L~eNi~a~l~~i~~~~p~~~kg~~ik~v~vstTMGP~v~v~~ 227 (228)
T COG0081 162 VEFRADKAGVIHVPIGKVSFDDEKLAENIEALLNAIVKAKPAGAKGQYIKSVYVSTTMGPGVKVDL 227 (228)
T ss_pred EEEEECCCceEEEEecCCCCCHHHHHHHHHHHHHHHHHhCcCCcccceEeEEEEecCCCCCEEecc
Confidence 999999999999999999999999999999999999999999999999999999999999999986
No 2
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=100.00 E-value=5.2e-70 Score=496.26 Aligned_cols=226 Identities=63% Similarity=1.006 Sum_probs=221.1
Q ss_pred ccchhHHHHHhhccCCCCCCHHHHHHHHHhhccCCCCCcEEEEEEeCcCCCCCCccceeeeecCCCCCCceEEEEEcCcc
Q 022545 60 TGSKRFLEIQNLREGKKEYDLKTAISLLKQMSSTKFTETAEAHFRLNIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGE 139 (295)
Q Consensus 60 ~~~k~~~~~~~~~~~~~~y~l~eAI~~lk~~~~~~F~EsVel~i~L~id~kk~~~~irg~V~LPh~~gk~~kV~Vfa~~~ 139 (295)
+++|||+++.+.++ .+.|++.|||+++++.+.++|+||||++++|++|++++++++||+|.|||++|++.+|||||+++
T Consensus 3 ~~~k~~~~~~~~~~-~~~y~l~eAi~~~k~~~~~kF~esvel~i~L~id~kk~~~~irg~v~LP~~~gk~~kV~Vfa~~~ 81 (229)
T CHL00129 3 KLSRRTKELRSKIE-KKLYSPEEAINLLKETATAKFIETAEAHISLNIDPKYADQQLRTTVTLPKGTGKTIRIAVLTNEE 81 (229)
T ss_pred cccHHHHHHHHhcc-ccccCHHHHHHHHHHhCcCCCCccEEEEEEECCCCCCCCCceeeEEECCCCCCCCcEEEEECChH
Confidence 56899999999999 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHcCCCccccHHHHHHHHcCcccccEEEeCccchHHhHhhchhccCCCCCCCCCCCCCCCCHHHHHHHHhcCeEE
Q 022545 140 KFNEAKNAGADLVGGDDLIEQIKGGFMEFDKLIASPDMMVKVASLGKILGPRGLMPNPKAGTVTTNIPQAIEEFKKGKVE 219 (295)
Q Consensus 140 ~~eeAk~aGAd~VG~~eLi~kIk~g~~~fD~~lAt~d~m~~l~~LgriLGPrGlMP~pk~GTvt~di~~~I~~~k~G~v~ 219 (295)
.+++|++|||++||++||+++|++|+.+||+|||||||||+|++|||+||||||||+|++|||++|+.++|+++++|+++
T Consensus 82 ~~~eAk~aGad~vg~edLi~~ik~~~~~fd~~iAt~d~m~~l~kLgriLGprGlMP~pk~gTvt~di~~~V~~~k~G~v~ 161 (229)
T CHL00129 82 KITEAKNAGADIVGSDDLIEEITKGNLDFDLLIATPDMMPKLAKLGRVLGPRGLMPSPKSGTVTTDLASAINEFKKGKLE 161 (229)
T ss_pred hHHHHHHcCCCEeCHHHHHHHHHcCcccCCEEEECHHHHHHHHHhcCcccccCCCCCCCCCCccccHHHHHHHHhcCcEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCeeeEeeeCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCceeeEEEEeCCCCCcEEeecccc
Q 022545 220 YRADKTGIVHIPFGKADFSEDDLLINFLAAVKSIEANKPKGAKGVYWKSAYICSSMGPSIRLNIKEM 286 (295)
Q Consensus 220 ~r~dk~g~i~v~IGk~sm~~e~L~ENi~avl~~I~~~~p~~~kg~~Ik~i~IssTmGp~i~I~~~~~ 286 (295)
||+|+.|++|++||+++|++|||.||+.+++++|.+++|.+++|.||+++|||||||||++|+.+++
T Consensus 162 ~r~dk~g~i~~~VG~~~m~~~~l~eNi~a~l~~i~~~~p~~~kg~~ik~v~issTMGp~v~i~~~~~ 228 (229)
T CHL00129 162 YRADKTGIVHVLFGKSNFTEEDLLENLQAIYESIEQNRPSGVKGKYWKSFYICSTMGPSIQIDISLL 228 (229)
T ss_pred EEecCCcEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCcccccCceEEEEEEECCCCCCEEeccccc
Confidence 9999999999999999999999999999999999999999999999999999999999999998765
No 3
>TIGR01169 rplA_bact ribosomal protein L1, bacterial/chloroplast. This model describes bacterial (and chloroplast) ribosomal protein L1. The apparent mitochondrial L1 is sufficiently diverged to be the subject of a separate model.
Probab=100.00 E-value=9.8e-68 Score=481.04 Aligned_cols=225 Identities=52% Similarity=0.843 Sum_probs=219.9
Q ss_pred cchhHHHHHhhccCCCCCCHHHHHHHHHhhccCCCCCcEEEEEEeCcCCCCCCccceeeeecCCCCCCceEEEEEcCccc
Q 022545 61 GSKRFLEIQNLREGKKEYDLKTAISLLKQMSSTKFTETAEAHFRLNIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGEK 140 (295)
Q Consensus 61 ~~k~~~~~~~~~~~~~~y~l~eAI~~lk~~~~~~F~EsVel~i~L~id~kk~~~~irg~V~LPh~~gk~~kV~Vfa~~~~ 140 (295)
++||++.+.+.++..+.|++.|||+.+++.+.++|+||||++++|++|++++++++||+|.|||+++++.+|||||++++
T Consensus 2 ~~k~~~~~~~~~~~~~~y~l~eAi~~lk~~~~~~f~esvel~i~L~id~kK~~~~irg~v~LP~~~gk~~kV~Vfa~~~~ 81 (227)
T TIGR01169 2 LSKRYRAAREKVDRNKLYSLDEAIALLKETATAKFDETVEVAIRLGIDPRKSDQQVRGTVVLPHGTGKTVRVAVFAKGEK 81 (227)
T ss_pred CchHHHHHHHhcccCCccCHHHHHHHHHhhccCCCCCCEEEEEEECcCCCcCCCeeeEEEECCCCCCCCcEEEEEcCchh
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCCccccHHHHHHHHcCcccccEEEeCccchHHhHhhchhccCCCCCCCCCCCCCCCCHHHHHHHHhcCeEEE
Q 022545 141 FNEAKNAGADLVGGDDLIEQIKGGFMEFDKLIASPDMMVKVASLGKILGPRGLMPNPKAGTVTTNIPQAIEEFKKGKVEY 220 (295)
Q Consensus 141 ~eeAk~aGAd~VG~~eLi~kIk~g~~~fD~~lAt~d~m~~l~~LgriLGPrGlMP~pk~GTvt~di~~~I~~~k~G~v~~ 220 (295)
+++|++|||++||++||+++|++|+.+||+|||||++||+|+.|||+||||||||+|+.|||++|+.++|+++++|+++|
T Consensus 82 ~~~Ak~aGa~~vg~~eLi~~ik~~~~~fd~~iat~~~m~~l~~Lg~iLGPrGlMP~~k~gtv~~di~~~I~~~k~g~v~~ 161 (227)
T TIGR01169 82 AEEAKAAGADYVGSDDLIEKIKKGWLDFDVVIATPDMMRVVGKLGRILGPRGLMPNPKTGTVTADVAKAVKNAKKGQVEF 161 (227)
T ss_pred HHHHHHcCCCEeCHHHHHHHHHcCCccCCEEEECHHHHHHHHHhccccccccCCCCCCCCCccccHHHHHHHHHcCcEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEcCCCeeeEeeeCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCceeeEEEEeCCCCCcEEeeccc
Q 022545 221 RADKTGIVHIPFGKADFSEDDLLINFLAAVKSIEANKPKGAKGVYWKSAYICSSMGPSIRLNIKE 285 (295)
Q Consensus 221 r~dk~g~i~v~IGk~sm~~e~L~ENi~avl~~I~~~~p~~~kg~~Ik~i~IssTmGp~i~I~~~~ 285 (295)
|+|+.|++|++||+++|++|||.|||.+++++|.+++|.+++|.||+++||||||||+++|+..+
T Consensus 162 r~~k~g~i~~~VG~~~m~~e~i~eNi~a~l~~i~~~~p~~~kg~~Ik~v~lssTmGp~~~i~~~~ 226 (227)
T TIGR01169 162 RADKAGNIHASIGKVSFDSEKLKENLEALLDAIKKAKPSGAKGQYIKNIALSSTMGPGIKVDLSS 226 (227)
T ss_pred EeCCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHhCccccCCCEEEEEEEECCCCCCEEeccCC
Confidence 99999999999999999999999999999999999999999999999999999999999998875
No 4
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=100.00 E-value=1.1e-67 Score=481.58 Aligned_cols=228 Identities=50% Similarity=0.844 Sum_probs=222.0
Q ss_pred ccchhHHHHHhhccCCCCCCHHHHHHHHHhhccCCCCCcEEEEEEeCcCCCCCCccceeeeecCCCCCCceEEEEEcCcc
Q 022545 60 TGSKRFLEIQNLREGKKEYDLKTAISLLKQMSSTKFTETAEAHFRLNIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGE 139 (295)
Q Consensus 60 ~~~k~~~~~~~~~~~~~~y~l~eAI~~lk~~~~~~F~EsVel~i~L~id~kk~~~~irg~V~LPh~~gk~~kV~Vfa~~~ 139 (295)
+++||++.+.+.++..+.|++.|||+.+++.+.++|+||||++++|++|++++++++||+|.|||++|++.+|||||+++
T Consensus 2 ~~~k~~~~~~~~~~~~~~y~l~eAi~~lk~~~~~kF~esvel~v~L~id~kK~~~~irg~v~LP~~~gk~~kI~Vfa~~~ 81 (230)
T PRK05424 2 KLSKRYRAAAEKVDRTKLYSLEEAIALVKETATAKFDETVDVAVNLGVDPRKADQQVRGAVVLPHGTGKTVRVAVFAKGE 81 (230)
T ss_pred CccHHHHHHHHhccccCccCHHHHHHHHHhhccCCCCCcEEEEEEeCCCCCCCCCeeeEEEECCCCCCCCcEEEEECChH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHcCCCccccHHHHHHHHcCcccccEEEeCccchHHhHhhchhccCCCCCCCCCCCCCCCCHHHHHHHHhcCeEE
Q 022545 140 KFNEAKNAGADLVGGDDLIEQIKGGFMEFDKLIASPDMMVKVASLGKILGPRGLMPNPKAGTVTTNIPQAIEEFKKGKVE 219 (295)
Q Consensus 140 ~~eeAk~aGAd~VG~~eLi~kIk~g~~~fD~~lAt~d~m~~l~~LgriLGPrGlMP~pk~GTvt~di~~~I~~~k~G~v~ 219 (295)
.+++|+++||++||++||+++|++++.+||+|||||++||+|++|||+||||||||+|+.|||++|+.++|+++++|+++
T Consensus 82 ~~~~Ak~aGa~~vg~eeLi~~ik~~~~~fd~~iat~~~m~~l~~Lg~iLGPrGlMP~pk~gTv~~di~~~I~~~k~g~v~ 161 (230)
T PRK05424 82 KAEEAKAAGADIVGGEDLIEKIKGGWLDFDVVIATPDMMGKVGKLGRILGPRGLMPNPKTGTVTMDVAKAVKEAKAGKVE 161 (230)
T ss_pred hHHHHHHcCCCEeCHHHHHHHHhcCCCcCCEEEECHHHHHHHHHhccccccccCCCCCCCCCcchhHHHHHHHHhcCcEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCCeeeEeeeCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCceeeEEEEeCCCCCcEEeeccccc
Q 022545 220 YRADKTGIVHIPFGKADFSEDDLLINFLAAVKSIEANKPKGAKGVYWKSAYICSSMGPSIRLNIKEML 287 (295)
Q Consensus 220 ~r~dk~g~i~v~IGk~sm~~e~L~ENi~avl~~I~~~~p~~~kg~~Ik~i~IssTmGp~i~I~~~~~~ 287 (295)
||+|+.|++|++||+++|++|||.||+.+++++|.+++|.+++|.||+++|||||||||++|+..++.
T Consensus 162 ~r~~k~g~i~~~IG~~~m~~e~i~eNi~a~l~~i~~~~p~~~kg~~Ik~v~lssTmGp~~~i~~~~~~ 229 (230)
T PRK05424 162 FRVDKAGIIHAPIGKVSFDAEKLKENLKALIDAIKKAKPATAKGTYIKSVSLSSTMGPGVKVDPSSLA 229 (230)
T ss_pred EEecCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCccccCCCEEEEEEEECCCCCCEEechHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999998764
No 5
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=100.00 E-value=9.1e-57 Score=406.14 Aligned_cols=200 Identities=34% Similarity=0.560 Sum_probs=190.3
Q ss_pred CHHHHHHHHHhh-ccCCCCCcEEEEEEe-CcCCCCCCccceeeeecCCCCCCceEEEEEcCcccHHHHHHcCCCccccHH
Q 022545 79 DLKTAISLLKQM-SSTKFTETAEAHFRL-NIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGEKFNEAKNAGADLVGGDD 156 (295)
Q Consensus 79 ~l~eAI~~lk~~-~~~~F~EsVel~i~L-~id~kk~~~~irg~V~LPh~~gk~~kV~Vfa~~~~~eeAk~aGAd~VG~~e 156 (295)
.+.|||+.+++. +.++|+||||++++| ++|++++++++||+|.|||+++++.+|||||+++++++|++|||++||+.|
T Consensus 6 ~~~eai~~~k~~~~~~kf~esvel~v~Lk~id~~k~~~~irg~i~LP~~~~k~~~V~vf~~~~~~~~Ak~aGa~~v~~~e 85 (215)
T PRK04203 6 KIEEAVKEALEEAPKRNFTQSVDLIVNLKDIDLKKPENRIDEEVVLPHGRGKEVKIAVIAKGELALQAKEAGADYVITRE 85 (215)
T ss_pred HHHHHHHHHHHhcccCCCCceEEEEEEecCCCCCccCceeeEEEECCCCCCCCcEEEEEcChHhHHHHHHcCCCEEeCHH
Confidence 478999999984 699999999999999 999999999999999999999999999999999999999999999888888
Q ss_pred HHHHHHcC-------cccccEEEeCccchHHhHh-hchhccCCCCCCCCCCCCCCCCHHHHHHHHhcCeEEEEEcCCCee
Q 022545 157 LIEQIKGG-------FMEFDKLIASPDMMVKVAS-LGKILGPRGLMPNPKAGTVTTNIPQAIEEFKKGKVEYRADKTGIV 228 (295)
Q Consensus 157 Li~kIk~g-------~~~fD~~lAt~d~m~~l~~-LgriLGPrGlMP~pk~GTvt~di~~~I~~~k~G~v~~r~dk~g~i 228 (295)
.+++|.++ +.+||+|||||++||.|++ ||++|||||+||+|++||+ |+.++|+++++ +++||.++++++
T Consensus 86 ~L~~i~~~~k~~rkl~~~fD~~lA~~~im~~l~k~LGk~lgprgkmP~p~~~t~--di~~~i~~~~~-~~~~r~~k~~~i 162 (215)
T PRK04203 86 ELEELGGDKRAAKKLANEYDFFIAEADLMPLIGRYLGPVLGPRGKMPTPLPPNA--DIKPLVERLKN-TVRIRTKDQPTF 162 (215)
T ss_pred HHHHHhcChHHHhhhhhcCCEEEECHHHHHHHHHHHhhhcCcCCCCCCCcCCCC--CHHHHHHHHhh-ceEEEeCCCCEE
Confidence 88998776 7899999999999999996 9999999999999999996 99999999986 799999999999
Q ss_pred eEeeeCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCceeeEEEEeCCCCCcEEeec
Q 022545 229 HIPFGKADFSEDDLLINFLAAVKSIEANKPKGAKGVYWKSAYICSSMGPSIRLNI 283 (295)
Q Consensus 229 ~v~IGk~sm~~e~L~ENi~avl~~I~~~~p~~~kg~~Ik~i~IssTmGp~i~I~~ 283 (295)
|++||+++|++|||.||+.+++++|.+.+|.+|+ ||+++|||||||||++|+.
T Consensus 163 ~v~VG~~~m~~e~l~eNi~avl~~i~~~~p~g~~--~Iksi~lktTmgp~i~i~~ 215 (215)
T PRK04203 163 HVRVGTEDMSPEELAENIDAVLNRIESKLEKGRQ--NIKSVYVKTTMGPAVKVEL 215 (215)
T ss_pred EEEEeCCCCCHHHHHHHHHHHHHHHHHhCccccc--cEEEEEEECCCCCCEEeeC
Confidence 9999999999999999999999999999999996 7999999999999999873
No 6
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=100.00 E-value=5.9e-54 Score=387.48 Aligned_cols=198 Identities=23% Similarity=0.345 Sum_probs=184.1
Q ss_pred CHHHHHHHHH-hhccCCCCCcEEEEEEe-CcCCCCCCccceeeeecCCCCCCceEEEEEcCcccHHHHHHcCCCccccHH
Q 022545 79 DLKTAISLLK-QMSSTKFTETAEAHFRL-NIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGEKFNEAKNAGADLVGGDD 156 (295)
Q Consensus 79 ~l~eAI~~lk-~~~~~~F~EsVel~i~L-~id~kk~~~~irg~V~LPh~~gk~~kV~Vfa~~~~~eeAk~aGAd~VG~~e 156 (295)
.+.|||+.+. +.+.++|+||||++++| |+||++ ++++||+|.|||++|+..+|||||+++++++|++||||++|.+|
T Consensus 8 ~i~~Av~~~lk~~~~~kF~Etvdl~v~Lk~iDp~k-d~~irg~v~LPhg~gk~~kV~v~~~~~~~~~Ak~aGad~v~~e~ 86 (214)
T PTZ00225 8 TLSEAIQAVLKVDKERKFKESIDLQVNLKNYDPQK-DKRFSGSLKLPNVCRPRMTVCLLCDLVHEDIAKKEGVPTMNQEE 86 (214)
T ss_pred HHHHHHHHHHHhcccCCCCceEEEEEeccCcCCCc-CcccceeEECCCCCCCCcEEEEECChHHHHHHHHCCCCEECHHH
Confidence 4789999955 67799999999999999 999996 99999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCc------ccccEEEeCccchHHhHh-hchhccCCCCCCCCCCCCCCCCHHHHHHHHhcCeEEEEEcCCCeee
Q 022545 157 LIEQIKGGF------MEFDKLIASPDMMVKVAS-LGKILGPRGLMPNPKAGTVTTNIPQAIEEFKKGKVEYRADKTGIVH 229 (295)
Q Consensus 157 Li~kIk~g~------~~fD~~lAt~d~m~~l~~-LgriLGPrGlMP~pk~GTvt~di~~~I~~~k~G~v~~r~dk~g~i~ 229 (295)
|++.+++++ .+||+||||||+||.|++ ||+.|||+|+||++. ++++|+.++|+++++ +++||+++.+++|
T Consensus 87 l~~l~k~~~~~kkl~~~fD~fiA~~~~m~~lgk~LGp~~~p~gK~P~~~--~~~~dl~~~i~~~k~-~v~~r~~k~~~~~ 163 (214)
T PTZ00225 87 LKKLNKNKKLVKKMCNQYDAFLCSESIIKTVPRLVGPHMHRMGKFPTVC--SPSESLPDKVVELRS-TVKFQLKKVLCLG 163 (214)
T ss_pred HHHHHhccHHHHHHHhhCCEEEECHHHHHhhhhhcCCCCCcCCCCCccc--CCccCHHHHHHHHhh-eeEEEecCccEEE
Confidence 999998874 899999999999999873 777777779999864 567999999999997 9999999999999
Q ss_pred EeeeCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCceeeEEEEeCCCCCcEEee
Q 022545 230 IPFGKADFSEDDLLINFLAAVKSIEANKPKGAKGVYWKSAYICSSMGPSIRLN 282 (295)
Q Consensus 230 v~IGk~sm~~e~L~ENi~avl~~I~~~~p~~~kg~~Ik~i~IssTmGp~i~I~ 282 (295)
++||+++|++|||+||+.++++.|.+.+|.+|+ ||+++||||||||+++|+
T Consensus 164 ~~VGk~~m~~e~i~eNi~a~l~~l~~~~p~k~~--nIksv~iktTMGp~~~~~ 214 (214)
T PTZ00225 164 TCVGHVEMTEEQLRQNVVMAINFLVSLLKKNWQ--NLKSAYIKSTMGKPQRIY 214 (214)
T ss_pred eEEccCCCCHHHHHHHHHHHHHHHHHhCCcCCc--eEeEEEEECCCCCCEeCC
Confidence 999999999999999999999999999998776 799999999999999874
No 7
>PTZ00029 60S ribosomal protein L10a; Provisional
Probab=100.00 E-value=4.9e-52 Score=375.57 Aligned_cols=198 Identities=25% Similarity=0.385 Sum_probs=176.6
Q ss_pred CHHHHHHHHHh---hccCCCCCcEEEEEEe-CcCCCCCCccceeeeecCCCCCCceEEEEEcCcccHHHHHHcCCCcccc
Q 022545 79 DLKTAISLLKQ---MSSTKFTETAEAHFRL-NIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGEKFNEAKNAGADLVGG 154 (295)
Q Consensus 79 ~l~eAI~~lk~---~~~~~F~EsVel~i~L-~id~kk~~~~irg~V~LPh~~gk~~kV~Vfa~~~~~eeAk~aGAd~VG~ 154 (295)
.+.+||+.+++ .+.++|+||||++++| ++||++ ++++||+|.||||+|++.+|||||+|+.+++|++|||++||.
T Consensus 8 ~~~~av~~~~~~~~~~~~~f~esv~~~i~Lk~id~~~-~~~ir~~v~LP~~~gk~~~v~V~a~~~~~~~Ak~aGa~vvg~ 86 (216)
T PTZ00029 8 ALRKAIAEILEGSEEKKRKFVETVELQIGLKDYDTQK-DKRFSGSVKLPNVPKPNLKVCVLGDAVHCDEAKKLGLDFMDI 86 (216)
T ss_pred HHHHHHHHHHhhccccccCCceEEEEEEEcCCCCCCc-CcccceeEecCCCCCCCcEEEEECCcHHHHHHHHcCCCEecH
Confidence 36899999886 3489999999999999 999996 999999999999999999999999999999999999999999
Q ss_pred HHHHH-----HHHcC-cccccEEEeCccchHHhHh-hchhccCCCCCCCCCCCCCCCCHHHHHHHHhcCeEEEEEcCCCe
Q 022545 155 DDLIE-----QIKGG-FMEFDKLIASPDMMVKVAS-LGKILGPRGLMPNPKAGTVTTNIPQAIEEFKKGKVEYRADKTGI 227 (295)
Q Consensus 155 ~eLi~-----kIk~g-~~~fD~~lAt~d~m~~l~~-LgriLGPrGlMP~pk~GTvt~di~~~I~~~k~G~v~~r~dk~g~ 227 (295)
+||++ +++.+ ..+||+|||||++||.|++ ||+.|+|+|+||.+. |+++|+.++|+++++ +++||+++.++
T Consensus 87 edL~~~~k~~k~~kkl~~~fD~flA~~~im~~l~riLGp~l~p~~K~P~~v--~~~~d~~~~i~~~k~-~v~~r~~k~~~ 163 (216)
T PTZ00029 87 EGLKKFNKNKKLVKKLAKKYDAFLASQSLLPQIPRLLGPGLNKAGKFPTLI--THNDDIEDKINELKS-SVKFQLKKVLC 163 (216)
T ss_pred HHHHHhhhhHHHHhcccccCCEEEECHHHHHHHHHHhccccccCCCCCCcc--cCccCHHHHHHHHHh-eEEEEECCCCE
Confidence 99998 44444 4799999999999999863 455555555555554 457899999999985 89999999999
Q ss_pred eeEeeeCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCceeeEEEEeCCCCCcEEee
Q 022545 228 VHIPFGKADFSEDDLLINFLAAVKSIEANKPKGAKGVYWKSAYICSSMGPSIRLN 282 (295)
Q Consensus 228 i~v~IGk~sm~~e~L~ENi~avl~~I~~~~p~~~kg~~Ik~i~IssTmGp~i~I~ 282 (295)
+|++||+++|++|||.||+.+++++|.+.+|+||. ||+++|||||||||++|+
T Consensus 164 i~v~VG~~~~~~e~l~eNi~avl~~i~~~~~kg~~--~Iksv~lktTmgp~v~v~ 216 (216)
T PTZ00029 164 LGVAVGNVEMTEEQLRQNIVLSINFLVSLLKKNWQ--NIKTLHIKSTMGKPQRIY 216 (216)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHHHHHHHHhccccc--cEeEEEEECCCCCCEeCC
Confidence 99999999999999999999999999999998887 799999999999999975
No 8
>cd00403 Ribosomal_L1 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA. Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity. L1 is one of the largest ribosomal proteins. It is composed of two domains that cycle between open and closed conformations via a hinge motion. The RNA-binding site of L1 is highly conserved, with both mRNA and rRNA binding the same binding site.
Probab=100.00 E-value=2e-46 Score=334.77 Aligned_cols=198 Identities=47% Similarity=0.758 Sum_probs=187.3
Q ss_pred HHHHHHHHhhc--cCCCCCcEEEEEEeCcCCCCCCccceeeeecCCCCCCceEEEEEcCcccHHHHHHcCCCccccHHHH
Q 022545 81 KTAISLLKQMS--STKFTETAEAHFRLNIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGEKFNEAKNAGADLVGGDDLI 158 (295)
Q Consensus 81 ~eAI~~lk~~~--~~~F~EsVel~i~L~id~kk~~~~irg~V~LPh~~gk~~kV~Vfa~~~~~eeAk~aGAd~VG~~eLi 158 (295)
.||++.+++.+ ...|+|+|+++++++..++++++++++.|.|||++++..+|||||+++++++|+++||+++|+++|+
T Consensus 2 ~~Ai~~l~~~~~~~~~~~~~v~l~i~l~~~~~~~~~~~~~~i~LPh~~~~~~~i~v~~~d~~~~~a~~~~a~vig~~~L~ 81 (208)
T cd00403 2 EEAIKALKKTSVKKRKFDETVELQINLKKDDRKKDQRIRGTVILPHGLGKDVKVCVFAKDEQAKEAKAAGADVVGGEDLK 81 (208)
T ss_pred HHHHHHHHHhccccCCCCceEEEEEEeCCCCCccccccceeEECCCCCCCCeEEEEEcChHhHHHHHHcCCCEEcHHHHH
Confidence 68999999988 8999999999999966666678999999999999999999999999999999999999999999999
Q ss_pred HHHHcCc-----ccccEEEeCccchHHhH-hhchhccCCCCCCCCCCCCCCCCHHHHHHHHhcCeEEEEEcCCCeeeEee
Q 022545 159 EQIKGGF-----MEFDKLIASPDMMVKVA-SLGKILGPRGLMPNPKAGTVTTNIPQAIEEFKKGKVEYRADKTGIVHIPF 232 (295)
Q Consensus 159 ~kIk~g~-----~~fD~~lAt~d~m~~l~-~LgriLGPrGlMP~pk~GTvt~di~~~I~~~k~G~v~~r~dk~g~i~v~I 232 (295)
+++++++ .+||+||||+++|+.++ .||++|||||+||+++.||+++|+.++|+++++ ++.|+.+++|+++++|
T Consensus 82 ~~~~~~~~~~l~~~~D~fla~~~~~~~~~~~lgk~~~~k~k~P~~~~~t~~~~l~~~i~~~~~-~~~~~~~~~~~~~v~V 160 (208)
T cd00403 82 KKIKNGEAKKLAKDFDLFLADPRIMMLLPKLLGKVLGPRGKMPNPKTGTVTEDLAKAIEEAKS-SVEFRLDKGGCIHVPV 160 (208)
T ss_pred HHhhcchhhhhhhcCCEEEECHHHHHHHHHHhccccccCCCCCcCCCCCCcccHHHHHHHHHh-CeEEEECCCCEEEEEE
Confidence 9999887 89999999999999887 699999999999999999999999999999996 7999999999999999
Q ss_pred eCCCCCHHHHHHHHHHHHHHHHHhCC-CCCCCceeeEEEEeCCCCCcEEe
Q 022545 233 GKADFSEDDLLINFLAAVKSIEANKP-KGAKGVYWKSAYICSSMGPSIRL 281 (295)
Q Consensus 233 Gk~sm~~e~L~ENi~avl~~I~~~~p-~~~kg~~Ik~i~IssTmGp~i~I 281 (295)
|+++|+++||+||+.++++++.+++| .+|+ ||+++||||||||+++|
T Consensus 161 G~~~m~~~~l~eNi~~vi~~i~~~~~~~~~~--~i~~v~lktt~~~~lpI 208 (208)
T cd00403 161 GKVSMSPEQLVENIEAVINALVKKLPSKKGQ--NIKSIYLKTTMGPSLPI 208 (208)
T ss_pred eCCCCCHHHHHHHHHHHHHHHHHhCCcccCe--EEEEEEEECCCCCCeEC
Confidence 99999999999999999999999999 6665 79999999999999986
No 9
>TIGR01170 rplA_mito ribosomal protein L1, mitochondrial. This model represents the mitochondrial homolog of bacterial ribosomal protein L1. Unlike chloroplast L1, this form was not sufficiently similar to bacterial forms to include in a single bacterial/organellar L1.
Probab=100.00 E-value=1e-42 Score=295.99 Aligned_cols=137 Identities=42% Similarity=0.687 Sum_probs=131.0
Q ss_pred CCHHHHHHHHHhhccC--CCCCcEEEEEEeCcCCCCCCccceeeeecCCCCCCceEEEEEcCccc-HHHHHHcCCCcccc
Q 022545 78 YDLKTAISLLKQMSST--KFTETAEAHFRLNIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGEK-FNEAKNAGADLVGG 154 (295)
Q Consensus 78 y~l~eAI~~lk~~~~~--~F~EsVel~i~L~id~kk~~~~irg~V~LPh~~gk~~kV~Vfa~~~~-~eeAk~aGAd~VG~ 154 (295)
|++.||++++|+.+.+ +|+||||++++|++++++++ +||+|.|||+++++.+|||||++++ +++|++|||+++|+
T Consensus 1 y~i~eA~~~lk~~~~~~~~~~etvel~i~L~~~~~~~~--irg~v~LP~~~~k~~kV~Vf~~~~~~~~~Ak~aGa~~vg~ 78 (141)
T TIGR01170 1 YKVIKAFVYLKTKSISMYVPKQSVNLDIGLLMELGKES--VQGMFSFPHPFGKEPKIAVFTKGASEVEEAREAGADYVGG 78 (141)
T ss_pred CCHHHHHHHHHHhcccCCCCCceEEEEEEECCCCCCCC--ceEEEECCCCCCCCCEEEEECCChHHHHHHHHcCCCEeCH
Confidence 8999999999999988 99999999999998876444 9999999999999999999999987 68899999999999
Q ss_pred HHHHHHHHcCccc-ccEEEeCccchHHhHhhchhccCCCCCCCCCCCCCCCCHHHHHHHHhcC
Q 022545 155 DDLIEQIKGGFME-FDKLIASPDMMVKVASLGKILGPRGLMPNPKAGTVTTNIPQAIEEFKKG 216 (295)
Q Consensus 155 ~eLi~kIk~g~~~-fD~~lAt~d~m~~l~~LgriLGPrGlMP~pk~GTvt~di~~~I~~~k~G 216 (295)
+|||++|++|+.+ ||+|||||+|||+|+.|||+||||||||+|++|||++|+.++|+++++|
T Consensus 79 edLi~~i~~g~~~~fd~~iA~~~~m~~l~~Lg~iLGprGlMP~~k~gTv~~di~~~I~~~k~G 141 (141)
T TIGR01170 79 DDLIKKIEDGEIKPFDYLIAHPDIVPELAQLRRLLGPKGLMPSPKRGTVGDNLLSMIETFKKG 141 (141)
T ss_pred HHHHHHHhcCCcccccEEEECHHHHHHHHHhhcccccCcCCCCCCCCCcccCHHHHHHHHhCc
Confidence 9999999999999 9999999999999999999999999999999999999999999999986
No 10
>KOG1569 consensus 50S ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8e-43 Score=323.07 Aligned_cols=211 Identities=36% Similarity=0.616 Sum_probs=189.8
Q ss_pred CCCCHHHHHHHHHhhccC----CCCCcEEEEEEeCcCCCC---CCccceeeeecCCCC--CCceEEEEEcCc-ccHHHHH
Q 022545 76 KEYDLKTAISLLKQMSST----KFTETAEAHFRLNIDPKY---NDQQLRATVSLPKGT--GKSVKVAVLAQG-EKFNEAK 145 (295)
Q Consensus 76 ~~y~l~eAI~~lk~~~~~----~F~EsVel~i~L~id~kk---~~~~irg~V~LPh~~--gk~~kV~Vfa~~-~~~eeAk 145 (295)
+.|.+.+|+...|++... ...+++.+.+++++-..+ ....+.+.+..|||. |+.++|+|||+| +..++|+
T Consensus 88 ~~y~vq~a~~~~ke~~~~sa~~~pk~~~~l~i~l~~~a~~~~k~~~~~~~~v~vP~Pf~~ge~r~IavFtn~~~kveeAr 167 (323)
T KOG1569|consen 88 QIYEVQKAVHLHKELQILSAYNVPKQPVNLRIELNMLAEKETKGVAPLQGSVTVPHPFAHGEIRKIAVFTNDASKVEEAR 167 (323)
T ss_pred chhhHHHHHHHHHHhccchhhhCCCCceeeeEEeeeeeeeeccccCCCceeEeccccCCCCceEEEEEecCChHHHHHHH
Confidence 459999999999997632 446888888888775432 344566778888876 567889999999 5689999
Q ss_pred HcCCCccccHHHHHHHHcCcc--cccEEEeCccchHHhHhhchhccCCCCCCCCCCCCCCCCHHHHHHHHhcC-eEEEEE
Q 022545 146 NAGADLVGGDDLIEQIKGGFM--EFDKLIASPDMMVKVASLGKILGPRGLMPNPKAGTVTTNIPQAIEEFKKG-KVEYRA 222 (295)
Q Consensus 146 ~aGAd~VG~~eLi~kIk~g~~--~fD~~lAt~d~m~~l~~LgriLGPrGlMP~pk~GTvt~di~~~I~~~k~G-~v~~r~ 222 (295)
++||+++||.|||++|++|.+ |||+++|+|||||.|..|+++|||| |||+++|||++||+++|++|++| .++|+.
T Consensus 168 EaGA~l~GG~dLIkkI~~Gei~~Dyd~~vA~Pdim~~l~~Lr~iL~~r--~Pn~k~gtvg~nipemieeFk~G~~i~~d~ 245 (323)
T KOG1569|consen 168 EAGAALAGGTDLIKKIKSGEIVADYDFYVAHPDIMPELNRLRKILGPR--FPNPKRGTVGRNIPEMIEEFKNGHEIKFDE 245 (323)
T ss_pred hccccccccHHHHHHhhcCeEEEeeceeeecchHHHHHHHHHHHhccc--CCCcccCccccchHHHHHHhhCCccccccc
Confidence 999999999999999999976 5669999999999999999999999 99999999999999999999998 789999
Q ss_pred cCCCeeeEeeeCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCceeeEEEEeCCCCCcEEeeccccccc
Q 022545 223 DKTGIVHIPFGKADFSEDDLLINFLAAVKSIEANKPKGAKGVYWKSAYICSSMGPSIRLNIKEMLDY 289 (295)
Q Consensus 223 dk~g~i~v~IGk~sm~~e~L~ENi~avl~~I~~~~p~~~kg~~Ik~i~IssTmGp~i~I~~~~~~~~ 289 (295)
++.++++++||+++|++|||++||.+++++++.++|+ .+|.||.+++|+|+|||++.|+++.+..+
T Consensus 246 ~~~~~~~~~vGkl~mt~e~i~~Ni~a~i~av~t~rp~-~~G~fv~ra~L~Ss~g~~i~l~i~p~i~~ 311 (323)
T KOG1569|consen 246 ERENILQIKVGKLDMTSEQILANIQAVIAAVCTHRPK-ALGPFVVRALLRSSPGEGILLKIDPLIPK 311 (323)
T ss_pred ccCceeeeeeeeecCCHHHHHHHHHHHHHHHHhcCCc-ccCceeeeeEeecCCCCceeEecccccce
Confidence 9999999999999999999999999999999999998 68999999999999999999999999877
No 11
>PF00687 Ribosomal_L1: Ribosomal protein L1p/L10e family; InterPro: IPR002143 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 L1 is the largest protein from the large ribosomal subunit. The L1 protein contains two domains: 2-layer alpha/beta domain and a 3-layer alpha/beta domain (interrupts the first domain). In Escherichia coli, L1 is known to bind to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L1. Algal and plant chloroplast L1. Cyanelle L1. Archaebacterial L1. Vertebrate L10A. Yeast SSM1. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3QOY_A 3BBO_D 1VSA_A 1VSP_A 2NOQ_G 3IZS_A 1S1I_A 3O5H_A 3O58_A 2WRL_C ....
Probab=100.00 E-value=6.7e-37 Score=275.08 Aligned_cols=185 Identities=30% Similarity=0.509 Sum_probs=164.2
Q ss_pred hccCCCCCcEEEEEEeCcCCCCCCccc-eeeeecCCCCC-CceEEEEEcCcccHHH---------HHHcCCCccccHHHH
Q 022545 90 MSSTKFTETAEAHFRLNIDPKYNDQQL-RATVSLPKGTG-KSVKVAVLAQGEKFNE---------AKNAGADLVGGDDLI 158 (295)
Q Consensus 90 ~~~~~F~EsVel~i~L~id~kk~~~~i-rg~V~LPh~~g-k~~kV~Vfa~~~~~ee---------Ak~aGAd~VG~~eLi 158 (295)
....+|+++|++++.+...+.+.++++ ++.|.|||++. +..+||||++|++.+. +.++|++++|+++|.
T Consensus 15 ~~~~~~~~~v~l~i~~~~~~~~~~~~~~~~~i~LPh~~~~~~~~vcli~~d~~~~~~~~~~~~~~~~~~~~~vi~~~~L~ 94 (220)
T PF00687_consen 15 NEDDNFDESVYLQITLKKIPKKKDKSFKPGRIPLPHPLYIKNSKVCLIVKDPQKKAKEKEKLEEKAVEAGAKVIGGEELK 94 (220)
T ss_dssp CCCSSSSTEEEEEEEESSSTTSSCTST-EEEEEBSTSSS-SSSBEEEEESCHHHHHH-------HHHHTTCSEEECHHHH
T ss_pred cccCCCCcEEEEEEEeCcCCCccccccccceeeecCCCCCCccEEEEEecCcchhhhhhhhhhhhhhhcccceecHHHHH
Confidence 357799999999999966666566777 99999999998 8899999998876433 467899999999999
Q ss_pred HH---HHcCc---ccccEEEeCccchHHhHh-hchhc-cCCCCCCCCCCCCCCCCHHHHHHHHhcCeEEEEEc-CCCeee
Q 022545 159 EQ---IKGGF---MEFDKLIASPDMMVKVAS-LGKIL-GPRGLMPNPKAGTVTTNIPQAIEEFKKGKVEYRAD-KTGIVH 229 (295)
Q Consensus 159 ~k---Ik~g~---~~fD~~lAt~d~m~~l~~-LgriL-GPrGlMP~pk~GTvt~di~~~I~~~k~G~v~~r~d-k~g~i~ 229 (295)
++ ++.++ .+||+|||++++|+.+++ ||++| ||||+||+|...+ .+|+.+.|+++.+| +.|+.. ++++++
T Consensus 95 ~~~~~~~~~r~l~~~~d~flad~~i~~~l~~~Lgk~~~~~k~k~P~~v~~~-~~~l~~~i~~~~~~-~~~~~~~~~~~~~ 172 (220)
T PF00687_consen 95 KKYKTIEAKRKLAKSYDFFLADPRIMPKLPKLLGKIFYGKKGKMPIPVTLS-KEDLKEQIEKALNS-TKFRLSGKGGCIS 172 (220)
T ss_dssp HHHCHHHHCHHHHHCSSEEEEEGGGHHHHHHHTHHHH-CCTTTSCEEBSSH-TSCHHHHHHHHHTE-EEEEETBTSSEEE
T ss_pred HHHHHHHHHHHHHhhcCEEEECHHHHHHHHHhhhhheecccCCcceEEecc-chhHHHHHHHHHCC-EEEEeeccCCeee
Confidence 98 77776 899999999999999997 99999 9999999996422 37999999999974 567777 999999
Q ss_pred EeeeCCCCCHHHHHHHHHHHHHHHHHh-CCCCCCCceeeEEEEeCCCCCc
Q 022545 230 IPFGKADFSEDDLLINFLAAVKSIEAN-KPKGAKGVYWKSAYICSSMGPS 278 (295)
Q Consensus 230 v~IGk~sm~~e~L~ENi~avl~~I~~~-~p~~~kg~~Ik~i~IssTmGp~ 278 (295)
++||+++|+++||+|||.++++++.++ .|+||+ +|+++||+||||||
T Consensus 173 v~VG~~~~~~~~i~eNi~~~i~~i~~~~~~~g~~--~I~~i~ikst~s~~ 220 (220)
T PF00687_consen 173 VKVGHLSMTDEQIVENIKAVIKAIVSKPLPKGWK--NIKSIYIKSTMSPS 220 (220)
T ss_dssp EEEEETTSCHHHHHHHHHHHHHHHHHTTTSSSSG--SEEEEEEEESSSEE
T ss_pred cCccCCCCCHHHHHHHHHHHHHHHHHhhhccCcc--eEEEEEEECCCCCC
Confidence 999999999999999999999999999 888887 59999999999996
No 12
>KOG1570 consensus 60S ribosomal protein L10A [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=1.1e-28 Score=218.92 Aligned_cols=201 Identities=24% Similarity=0.385 Sum_probs=174.1
Q ss_pred CCCCHHHHHHHHHh----hccCCCCCcEEEEEEe-CcCCCCCCccceeeeecCCCCCCceEEEEEcCcccHHHHHHcCCC
Q 022545 76 KEYDLKTAISLLKQ----MSSTKFTETAEAHFRL-NIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGEKFNEAKNAGAD 150 (295)
Q Consensus 76 ~~y~l~eAI~~lk~----~~~~~F~EsVel~i~L-~id~kk~~~~irg~V~LPh~~gk~~kV~Vfa~~~~~eeAk~aGAd 150 (295)
.++.+.+||..+.- ...++|.|||+++++| |+||. ++.++.|++.|||..++..++|||++..+..+|++.|.+
T Consensus 6 ~~~~l~~~v~~i~~~~~~~k~~~~~~tielQi~Lk~ydp~-Kdkr~s~~~~l~~~~~p~~k~cv~gd~~h~~~ak~~~~p 84 (218)
T KOG1570|consen 6 EEEALREAVAEILLRSKEFKNRNFVETIELQINLKNYDPQ-KDKRFSGSVKLPHAPRPKMKVCVIGDQQHCDEAKAIDLP 84 (218)
T ss_pred hHHHHHHHHHHHHhccccccCccceeeeeeeecccccChh-HhCcccceEecCCCCCccceeeeechHHHHHHhhcCCCC
Confidence 35677888877753 3478999999999999 99998 689999999999999999999999999999999999999
Q ss_pred ccccHHHHH-----H-HHcCcccccEEEeCccchHHhHh-hchhccCCCCCCCCCCCCCCCCHHHHHHHHhcCeEEEEEc
Q 022545 151 LVGGDDLIE-----Q-IKGGFMEFDKLIASPDMMVKVAS-LGKILGPRGLMPNPKAGTVTTNIPQAIEEFKKGKVEYRAD 223 (295)
Q Consensus 151 ~VG~~eLi~-----k-Ik~g~~~fD~~lAt~d~m~~l~~-LgriLGPrGlMP~pk~GTvt~di~~~I~~~k~G~v~~r~d 223 (295)
+..-++|.+ + +++....||+|||+.+...+|++ ||.-|..-|++|+++.. .+|+.+.+++.++ +.+|+.+
T Consensus 85 ~m~~d~lkklnk~Kklvkklakky~~flase~~ikQlpr~lgp~l~kaGkfps~l~~--~d~l~akv~evk~-t~k~q~k 161 (218)
T KOG1570|consen 85 AMDIDALKKLNKNKKLVKKLAKKYDAFLASESLIKQLPRILGPGLSKAGKFPSLLVH--GDSLYAKVEEVKS-TIKFQMK 161 (218)
T ss_pred CcCHHHHhcCcccchHHHHHHHHhhhHHhhHHHHHHhhhhhcccccccccCCccccc--hHHHHHHHHHHHh-hHHHHHH
Confidence 988655543 1 23346799999999999999882 34444455999999954 4899999999998 6899999
Q ss_pred CCCeeeEeeeCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCceeeEEEEeCCCCCcEEee
Q 022545 224 KTGIVHIPFGKADFSEDDLLINFLAAVKSIEANKPKGAKGVYWKSAYICSSMGPSIRLN 282 (295)
Q Consensus 224 k~g~i~v~IGk~sm~~e~L~ENi~avl~~I~~~~p~~~kg~~Ik~i~IssTmGp~i~I~ 282 (295)
+.-|..|.||++.|++|+|.+||.-.++++++.+.++|+ |+++.||+|||||+.++|
T Consensus 162 kvKOGavaVGhv~M~d~el~~nI~l~vnFlVSlLKknwQ--Nvral~iKst~g~p~~ly 218 (218)
T KOG1570|consen 162 KVLCLAVAVGHVGMTDEELVYNIHLAVNFLVSLLKKNWQ--NVRALYIKSTMGKPQRLY 218 (218)
T ss_pred hhhheeeeecCCCCCHHHHHHhhhhhhhhHHHHHhhccc--chhheeeccCCCCceecC
Confidence 999999999999999999999999999999999999999 599999999999998875
No 13
>KOG1685 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.72 E-value=1e-17 Score=159.57 Aligned_cols=155 Identities=21% Similarity=0.289 Sum_probs=133.1
Q ss_pred CceEEEEEcCcccH-----HHH----HHcCCC----ccccHHHHHHHHc------CcccccEEEeCccchHHhHh-hchh
Q 022545 128 KSVKVAVLAQGEKF-----NEA----KNAGAD----LVGGDDLIEQIKG------GFMEFDKLIASPDMMVKVAS-LGKI 187 (295)
Q Consensus 128 k~~kV~Vfa~~~~~-----eeA----k~aGAd----~VG~~eLi~kIk~------g~~~fD~~lAt~d~m~~l~~-Lgri 187 (295)
.+..||+|.+|.+. +.| .++|.+ +++..+|..+.++ +..+||+|+|+.+++|.|+. |||.
T Consensus 87 ~~~~vcLIvkD~~~~~~t~~~~~d~l~~~gi~~itkVI~~~~LK~~yksyeaKr~L~~sfDlflaD~RV~~~LP~llGK~ 166 (343)
T KOG1685|consen 87 DDTDVCLIVKDLQQSYLTEEDAEDLLESEGIKSITKVISLSKLKRDYKSYEAKRKLLSSFDLFLADDRVIPLLPKLLGKE 166 (343)
T ss_pred CCCceEEEecCchhccccHHHHHHHHHHcCCccceeeeehHHHHHHHHHHHHHHHHHhhccEEEEcchhHhHHHHHhhhh
Confidence 46799999998552 223 457887 6788887776654 45799999999999999995 8999
Q ss_pred ccCCCCCCCCCCCCCCCC--HHHHHHHHhcCeEEEEEcCCCeeeEeeeCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCce
Q 022545 188 LGPRGLMPNPKAGTVTTN--IPQAIEEFKKGKVEYRADKTGIVHIPFGKADFSEDDLLINFLAAVKSIEANKPKGAKGVY 265 (295)
Q Consensus 188 LGPrGlMP~pk~GTvt~d--i~~~I~~~k~G~v~~r~dk~g~i~v~IGk~sm~~e~L~ENi~avl~~I~~~~p~~~kg~~ 265 (295)
|..+.+.|.+.+ ....+ +...|+++. |.+.|++.+..+..+.+|+++|+.++|.|||.++++.+.+..|.+|. +
T Consensus 167 f~q~kk~Pv~i~-l~k~~~~l~~qi~~a~-~~t~~~~~~g~~~~i~vg~l~~~~~~l~ENv~~vlk~l~e~~P~~~~--~ 242 (343)
T KOG1685|consen 167 FYQKKKVPVSIR-LSKKNELLKQQIENAC-GSTYFRLRKGTSSAIKVGHLGNTSEELAENVVAVLKGLSEILPGGWK--N 242 (343)
T ss_pred hcccccCceEEE-ecccchHHHHHHHHHh-hhheeeccCCceeEEEeccccccHHHHHHHHHHHHHHHHHHccchHh--H
Confidence 999999999974 22244 799999998 57899998888899999999999999999999999999999999999 5
Q ss_pred eeEEEEeCCCCCcEEeecccc
Q 022545 266 WKSAYICSSMGPSIRLNIKEM 286 (295)
Q Consensus 266 Ik~i~IssTmGp~i~I~~~~~ 286 (295)
|+++|++|.-||++|||.+..
T Consensus 243 Irsl~lKt~~s~aLPly~s~~ 263 (343)
T KOG1685|consen 243 IRSLHLKTSRSPALPLYVSVI 263 (343)
T ss_pred hHHHhhhccCCcccceeeccc
Confidence 999999999999999999875
No 14
>PF13003 MRL1: Ribosomal protein L1; InterPro: IPR024663 This entry represents a ribosomal protein L1 domain found mainly in chordates.
Probab=96.71 E-value=0.0027 Score=53.73 Aligned_cols=58 Identities=24% Similarity=0.381 Sum_probs=46.3
Q ss_pred CCHHHHHHHHHhhccCCCC---CcEEEEEEeCcC--CCCCCccceeeeecCCCCC-CceEEEEE
Q 022545 78 YDLKTAISLLKQMSSTKFT---ETAEAHFRLNID--PKYNDQQLRATVSLPKGTG-KSVKVAVL 135 (295)
Q Consensus 78 y~l~eAI~~lk~~~~~~F~---EsVel~i~L~id--~kk~~~~irg~V~LPh~~g-k~~kV~Vf 135 (295)
|.+++||.+|+.+...+|+ +.|.+.++|++. .++...++-+.|.|||+.- +..+|+||
T Consensus 70 yeve~Ai~mLKkfQ~lDfT~pkQ~VYldL~Ldm~l~KKkkVePF~s~i~lPypF~~eiNKv~VF 133 (133)
T PF13003_consen 70 YEVEKAIDMLKKFQILDFTSPKQPVYLDLTLDMKLEKKKKVEPFASVILLPYPFTSEINKVLVF 133 (133)
T ss_pred HHHHHHHHHHHhcccccCCCCCCcEEEeeeehhhhccccccCCCccceecccccccccceeeeC
Confidence 7799999999999977774 678888888664 3444568889999999974 45788887
No 15
>PTZ00029 60S ribosomal protein L10a; Provisional
Probab=85.31 E-value=0.44 Score=43.52 Aligned_cols=22 Identities=32% Similarity=0.548 Sum_probs=18.9
Q ss_pred hHhhchhccCCCCCCCCCCCCCC
Q 022545 181 VASLGKILGPRGLMPNPKAGTVT 203 (295)
Q Consensus 181 l~~LgriLGPrGlMP~pk~GTvt 203 (295)
++.|||+||| |+||++|.|++.
T Consensus 116 m~~l~riLGp-~l~p~~K~P~~v 137 (216)
T PTZ00029 116 LPQIPRLLGP-GLNKAGKFPTLI 137 (216)
T ss_pred HHHHHHHhcc-ccccCCCCCCcc
Confidence 3579999999 999999998854
No 16
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=73.14 E-value=2.2 Score=38.97 Aligned_cols=21 Identities=24% Similarity=0.344 Sum_probs=18.3
Q ss_pred hHhhchhccCCCCCCCCCCCCC
Q 022545 181 VASLGKILGPRGLMPNPKAGTV 202 (295)
Q Consensus 181 l~~LgriLGPrGlMP~pk~GTv 202 (295)
++.|||+|||+|. |++|.||+
T Consensus 114 m~~lgk~LGp~~~-p~gK~P~~ 134 (214)
T PTZ00225 114 IKTVPRLVGPHMH-RMGKFPTV 134 (214)
T ss_pred HHhhhhhcCCCCC-cCCCCCcc
Confidence 3579999999997 99999985
No 17
>COG1064 AdhP Zn-dependent alcohol dehydrogenases [General function prediction only]
Probab=64.58 E-value=10 Score=37.20 Aligned_cols=58 Identities=28% Similarity=0.283 Sum_probs=41.0
Q ss_pred eEEEEEcCcc-cHHHHHHcCCCcccc---HHHHHHHHcCcccccEEEeCccchHHhHhhchhccCC
Q 022545 130 VKVAVLAQGE-KFNEAKNAGADLVGG---DDLIEQIKGGFMEFDKLIASPDMMVKVASLGKILGPR 191 (295)
Q Consensus 130 ~kV~Vfa~~~-~~eeAk~aGAd~VG~---~eLi~kIk~g~~~fD~~lAt~d~m~~l~~LgriLGPr 191 (295)
.+|.+|+.++ +.+.|++.|||++-. ++..+.+++. ||.+|.|.. -+.+...-+.|.+.
T Consensus 191 a~Via~~~~~~K~e~a~~lGAd~~i~~~~~~~~~~~~~~---~d~ii~tv~-~~~~~~~l~~l~~~ 252 (339)
T COG1064 191 AEVIAITRSEEKLELAKKLGADHVINSSDSDALEAVKEI---ADAIIDTVG-PATLEPSLKALRRG 252 (339)
T ss_pred CeEEEEeCChHHHHHHHHhCCcEEEEcCCchhhHHhHhh---CcEEEECCC-hhhHHHHHHHHhcC
Confidence 5788888764 467899999997654 5666666653 999998877 55555444666555
No 18
>TIGR00853 pts-lac PTS system, lactose/cellobiose family IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Lac family includes several sequenced lactose (b-galactoside) permeases of Gram-positive bacteria as well as those in E. coli. While the Lac family usually consists of two polypeptide components IIA and IICB, the Chb permease of E. coli consists of three IIA, IIB and IIC. This family is specific for the IIB subunit of the Lac PTS family.
Probab=54.77 E-value=28 Score=27.49 Aligned_cols=64 Identities=13% Similarity=0.153 Sum_probs=39.4
Q ss_pred ceEEEEEcCccc---------HHHHHHcCCCccccHHHHHHHHcCcccccEEEeCccchHHhHhhchhccCCC
Q 022545 129 SVKVAVLAQGEK---------FNEAKNAGADLVGGDDLIEQIKGGFMEFDKLIASPDMMVKVASLGKILGPRG 192 (295)
Q Consensus 129 ~~kV~Vfa~~~~---------~eeAk~aGAd~VG~~eLi~kIk~g~~~fD~~lAt~d~m~~l~~LgriLGPrG 192 (295)
..+|+++|..-. .+.|++.|.++--..--+.++.+...+||+++.+|.+-.....+-+.+.+.|
T Consensus 3 ~~~ILl~C~~G~sSS~l~~k~~~~~~~~gi~~~v~a~~~~~~~~~~~~~Dvill~pqi~~~~~~i~~~~~~~~ 75 (95)
T TIGR00853 3 ETNILLLCAAGMSTSLLVNKMNKAAEEYGVPVKIAAGSYGAAGEKLDDADVVLLAPQVAYMLPDLKKETDKKG 75 (95)
T ss_pred ccEEEEECCCchhHHHHHHHHHHHHHHCCCcEEEEEecHHHHHhhcCCCCEEEECchHHHHHHHHHHHhhhcC
Confidence 457888886411 2446677876421111122333334579999999999888877766665443
No 19
>cd05565 PTS_IIB_lactose PTS_IIB_lactose: subunit IIB of enzyme II (EII) of the lactose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) found in Firmicutes as well as Actinobacteria. In this system, EII is a lactose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIC and IIB domains are expressed as a single protein from the lac operon. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include lactose, chitobiose/lichenan, ascorbate, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.
Probab=51.08 E-value=28 Score=28.00 Aligned_cols=63 Identities=24% Similarity=0.253 Sum_probs=40.0
Q ss_pred EEEEEcCcc--------c-HHHHHHcCCCccccHHHHHHHHcCcccccEEEeCccchHHhHhhchhccCCCC
Q 022545 131 KVAVLAQGE--------K-FNEAKNAGADLVGGDDLIEQIKGGFMEFDKLIASPDMMVKVASLGKILGPRGL 193 (295)
Q Consensus 131 kV~Vfa~~~--------~-~eeAk~aGAd~VG~~eLi~kIk~g~~~fD~~lAt~d~m~~l~~LgriLGPrGl 193 (295)
+|+++|.+= . .+.|++.|.++--..-=..++.+-..+||+++.+|.+--.+..+.+..++.|.
T Consensus 2 ~Ill~C~~GaSSs~la~km~~~a~~~gi~~~i~a~~~~e~~~~~~~~Dvill~PQv~~~~~~i~~~~~~~~i 73 (99)
T cd05565 2 NVLVLCAGGGTSGLLANALNKGAKERGVPLEAAAGAYGSHYDMIPDYDLVILAPQMASYYDELKKDTDRLGI 73 (99)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEeeHHHHHHhccCCCEEEEcChHHHHHHHHHHHhhhcCC
Confidence 577777531 1 24577788874211111223334456899999999998888878788877653
No 20
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=43.22 E-value=81 Score=25.54 Aligned_cols=83 Identities=12% Similarity=0.081 Sum_probs=54.8
Q ss_pred EEEEEcCcccHHHHHHcCCC---ccccHHHHHHHHc-C-cccccEEEeCccchHHhH-hhchhccCCCCCCCCC----CC
Q 022545 131 KVAVLAQGEKFNEAKNAGAD---LVGGDDLIEQIKG-G-FMEFDKLIASPDMMVKVA-SLGKILGPRGLMPNPK----AG 200 (295)
Q Consensus 131 kV~Vfa~~~~~eeAk~aGAd---~VG~~eLi~kIk~-g-~~~fD~~lAt~d~m~~l~-~LgriLGPrGlMP~pk----~G 200 (295)
+|+|+.+.+..---+-+|.+ .+..++..+++.+ . ..+|=.++-|.++...++ .+-..+. ....|.-. +|
T Consensus 4 kIaVvGd~DtilGFrlaGi~~v~~~~~~e~~~~~~~~l~~~~~gII~iTE~~a~~i~~~~i~~~~-~~~~P~II~Ipipg 82 (104)
T PRK01189 4 CITVIGERDVVLGFRLLGIGDTIEAEGKDLVKKFLEIFNNPKCKYIFVSESTKNMFDKNTLRSLE-SSSKPLVVFIPLPG 82 (104)
T ss_pred eEEEEcCHHHHHHHHHcCCceEEEcCCHHHHHHHHHHHhcCCeEEEEEEHHHHhhCCHHHHHHHh-ccCCCeEEEEeCCC
Confidence 79999998877767778996 4455665566554 2 347888999999988887 3444444 44444322 22
Q ss_pred CC-CCCHHHHHHHHh
Q 022545 201 TV-TTNIPQAIEEFK 214 (295)
Q Consensus 201 Tv-t~di~~~I~~~k 214 (295)
+- .+.+.+.|+++.
T Consensus 83 ~~~~~~i~~~ik~ai 97 (104)
T PRK01189 83 ISEEESIEEMAKRIL 97 (104)
T ss_pred CccchhHHHHHHHHh
Confidence 10 346888888876
No 21
>PRK13958 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional
Probab=41.42 E-value=13 Score=33.46 Aligned_cols=25 Identities=16% Similarity=0.139 Sum_probs=23.0
Q ss_pred eEEEEEcCcccHHHHHHcCCCcccc
Q 022545 130 VKVAVLAQGEKFNEAKNAGADLVGG 154 (295)
Q Consensus 130 ~kV~Vfa~~~~~eeAk~aGAd~VG~ 154 (295)
.|||=+++.++++.|.++|||++|.
T Consensus 3 vKICGit~~eda~~~~~~GaD~iGf 27 (207)
T PRK13958 3 LKFCGFTTIKDVTAASQLPIDAIGF 27 (207)
T ss_pred EEEcCCCcHHHHHHHHHcCCCEEEE
Confidence 7999999999999999999999985
No 22
>COG0135 TrpF Phosphoribosylanthranilate isomerase [Amino acid transport and metabolism]
Probab=39.28 E-value=15 Score=33.55 Aligned_cols=25 Identities=40% Similarity=0.533 Sum_probs=22.9
Q ss_pred ceEEEEEcCcccHHHHHHcCCCccc
Q 022545 129 SVKVAVLAQGEKFNEAKNAGADLVG 153 (295)
Q Consensus 129 ~~kV~Vfa~~~~~eeAk~aGAd~VG 153 (295)
..|||=+++.++++.|.++|||++|
T Consensus 3 ~vKICGlt~~eda~~a~~~gad~iG 27 (208)
T COG0135 3 KVKICGLTRLEDAKAAAKAGADYIG 27 (208)
T ss_pred ceEECCCCCHHHHHHHHHcCCCEEE
Confidence 4799999999999999999999998
No 23
>PF00697 PRAI: N-(5'phosphoribosyl)anthranilate (PRA) isomerase; InterPro: IPR001240 Indole-3-glycerol phosphate synthase (IGPS) (see IPR001468 from INTERPRO) catalyzes the fourth step in the biosynthesis of tryptophan, the ring closure of 1-(2-carboxy-phenylamino)-1-deoxyribulose into indol-3-glycerol-phosphate. In some bacteria, IGPS is a single chain enzyme. In others, such as Escherichia coli, it is the N-terminal domain of a bifunctional enzyme that also catalyzes N-(5-phosphoribosyl)anthranilate isomerase (PRAI) activity, the third step of tryptophan biosynthesis. In fungi, IGPS is the central domain of a trifunctional enzyme that contains a PRAI C-terminal domain and a glutamine amidotransferase (GATase) N-terminal domain (see IPR000991 from INTERPRO). Phosphoribosylanthranilate isomerase (PRAI) is monomeric and labile in most mesophilic microorganisms, but dimeric and stable in the hyperthermophile Thermotoga maritima (tPRAI) []. The comparison to the known 2.0 A structure of PRAI from Escherichia coli (ePRAI) shows that tPRAI has the complete TIM- or (beta alp ha)8-barrel fold, whereas helix alpha5 in ePRAI is replaced by a loop. The subunits of tPRAI associate via the N-terminal faces of their central beta-barrels. Two long, symmetry-related loops that protrude reciprocally into cavities of the other subunit provide for multiple hydrophobic interactions. Moreover, the side chains of the N-terminal methionines and the C-terminal leucines of both subunits are immobilized in a hydrophobic cluster, and the number of salt bridges is increased in tPRAI. These features appear to be mainly responsible for the high thermostability of tPRAI []. ; GO: 0004640 phosphoribosylanthranilate isomerase activity, 0006568 tryptophan metabolic process; PDB: 1V5X_A 1PII_A 1JCM_P 2KZH_A 1LBM_A 1DL3_A 1NSJ_A.
Probab=35.90 E-value=23 Score=31.42 Aligned_cols=25 Identities=32% Similarity=0.376 Sum_probs=19.9
Q ss_pred eEEEEEcCcccHHHHHHcCCCcccc
Q 022545 130 VKVAVLAQGEKFNEAKNAGADLVGG 154 (295)
Q Consensus 130 ~kV~Vfa~~~~~eeAk~aGAd~VG~ 154 (295)
+|||=+++.+++..|.++|+|++|.
T Consensus 1 vKICGi~~~~da~~~~~~g~d~~Gf 25 (197)
T PF00697_consen 1 VKICGITRPEDARLAAELGADYLGF 25 (197)
T ss_dssp EEEE---SHHHHHHHHHHTSSEEEE
T ss_pred CeECCCCcHHHHHHHHHcCCCEEee
Confidence 5899999999999999999999995
No 24
>PF10944 DUF2630: Protein of unknown function (DUF2630); InterPro: IPR020311 This entry contains proteins with no known function.
Probab=34.37 E-value=22 Score=27.90 Aligned_cols=9 Identities=67% Similarity=1.475 Sum_probs=7.3
Q ss_pred hHHHHHHHH
Q 022545 4 LDTCWRLLL 12 (295)
Q Consensus 4 ~~~~~~~~~ 12 (295)
||-||-||-
T Consensus 45 LDQCWDLLR 53 (81)
T PF10944_consen 45 LDQCWDLLR 53 (81)
T ss_pred HHHHHHHHH
Confidence 799998874
No 25
>PRK01222 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional
Probab=32.83 E-value=21 Score=32.27 Aligned_cols=26 Identities=31% Similarity=0.385 Sum_probs=23.2
Q ss_pred ceEEEEEcCcccHHHHHHcCCCcccc
Q 022545 129 SVKVAVLAQGEKFNEAKNAGADLVGG 154 (295)
Q Consensus 129 ~~kV~Vfa~~~~~eeAk~aGAd~VG~ 154 (295)
..|||=+++-++++.|.++|||++|.
T Consensus 4 ~vKICGi~~~eda~~~~~~Gad~iGf 29 (210)
T PRK01222 4 RVKICGITTPEDAEAAAELGADAIGF 29 (210)
T ss_pred eEEECCCCcHHHHHHHHHcCCCEEEE
Confidence 37999999888899999999999996
No 26
>cd00405 PRAI Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric, monofunctional and thermolabile, but in some thermophile organisms PRAI is dimeric for reasons of stability and in others it is fused to other components of the tryptophan biosynthesis pathway to form multifunctional enzymes.
Probab=31.85 E-value=68 Score=28.23 Aligned_cols=25 Identities=36% Similarity=0.361 Sum_probs=21.8
Q ss_pred eEEEEEcCcccHHHHHHcCCCcccc
Q 022545 130 VKVAVLAQGEKFNEAKNAGADLVGG 154 (295)
Q Consensus 130 ~kV~Vfa~~~~~eeAk~aGAd~VG~ 154 (295)
.|||=+++.++++.|.++||+++|-
T Consensus 1 vKiCGi~~~ed~~~a~~~Gvd~ig~ 25 (203)
T cd00405 1 VKICGITTLEDALAAAEAGADAIGF 25 (203)
T ss_pred CEECCCCCHHHHHHHHHcCCCEEEE
Confidence 4788888888899999999999885
No 27
>PLN02363 phosphoribosylanthranilate isomerase
Probab=31.17 E-value=24 Score=33.08 Aligned_cols=27 Identities=30% Similarity=0.359 Sum_probs=24.1
Q ss_pred CceEEEEEcCcccHHHHHHcCCCcccc
Q 022545 128 KSVKVAVLAQGEKFNEAKNAGADLVGG 154 (295)
Q Consensus 128 k~~kV~Vfa~~~~~eeAk~aGAd~VG~ 154 (295)
...|||=+++-++++.|.++|||++|.
T Consensus 47 ~~VKICGit~~eda~~a~~~GaD~iGf 73 (256)
T PLN02363 47 PLVKMCGITSARDAAMAVEAGADFIGM 73 (256)
T ss_pred ceEEECCCCcHHHHHHHHHcCCCEEEE
Confidence 358999999989999999999999996
No 28
>COG1436 NtpG Archaeal/vacuolar-type H+-ATPase subunit F [Energy production and conversion]
Probab=30.26 E-value=1.2e+02 Score=24.68 Aligned_cols=84 Identities=14% Similarity=0.263 Sum_probs=52.5
Q ss_pred eEEEEEcCcccHHHHHHcCCCc---cccHH--HHHHHHcCc-ccccEEEeCccchHHhH-hhchhc--cCCC---CCCCC
Q 022545 130 VKVAVLAQGEKFNEAKNAGADL---VGGDD--LIEQIKGGF-MEFDKLIASPDMMVKVA-SLGKIL--GPRG---LMPNP 197 (295)
Q Consensus 130 ~kV~Vfa~~~~~eeAk~aGAd~---VG~~e--Li~kIk~g~-~~fD~~lAt~d~m~~l~-~LgriL--GPrG---lMP~p 197 (295)
.+|||+.+.+-+---+=+|+.. +..++ +.+.+.... .+|+.++-|.+++..+. .+-++. +..- ..|+|
T Consensus 3 ~~I~VIGd~dtvtGFrLaGv~~~~v~~~~~~~~~~~~~~l~~~~~~iIiite~~a~~i~~~i~~~~~~~~~P~iv~IPs~ 82 (104)
T COG1436 3 MKIAVIGDRDTVTGFRLAGVRVVYVADDEEDELRAALRVLAEDDVGIILITEDLAEKIREEIRRIIRSSVLPAIVEIPSP 82 (104)
T ss_pred eEEEEEEccchhhceeeecceeEEEecChhHHHHHHHHhhccCCceEEEEeHHHHhhhHHHHHHHhhccCccEEEEeCCC
Confidence 4799999987766556678753 44443 333333322 28999999999999997 455552 2111 14664
Q ss_pred CCCCCCCCHHHHHHHHh
Q 022545 198 KAGTVTTNIPQAIEEFK 214 (295)
Q Consensus 198 k~GTvt~di~~~I~~~k 214 (295)
.+.-.+++.+.|+++.
T Consensus 83 -~~~~~~~~~~~I~k~v 98 (104)
T COG1436 83 -GKEEEEPLRELIRRAV 98 (104)
T ss_pred -CCCccchHHHHHHHHH
Confidence 2233367888887765
No 29
>PRK01395 V-type ATP synthase subunit F; Provisional
Probab=27.42 E-value=1.6e+02 Score=23.76 Aligned_cols=82 Identities=12% Similarity=0.333 Sum_probs=53.2
Q ss_pred eEEEEEcCcccHHHHHHcCCCc---cccHHHHHHHHcC-cccccEEEeCccchHHhHh-hchhccCCCC------CCCCC
Q 022545 130 VKVAVLAQGEKFNEAKNAGADL---VGGDDLIEQIKGG-FMEFDKLIASPDMMVKVAS-LGKILGPRGL------MPNPK 198 (295)
Q Consensus 130 ~kV~Vfa~~~~~eeAk~aGAd~---VG~~eLi~kIk~g-~~~fD~~lAt~d~m~~l~~-LgriLGPrGl------MP~pk 198 (295)
.||+|+++.+.+.=.+-+|++. ...++..+.+... ..+|-.++-|.++...++. +-++ . +.. .|+.
T Consensus 4 ~kIaVIGD~dtv~GFrLaGi~~~~v~~~ee~~~~i~~l~~~d~gII~Ite~~a~~i~~~i~~~-~-~~~~P~Il~IP~~- 80 (104)
T PRK01395 4 YKIGVVGDKDSILPFKALGIDVFPVIDEQEAINTLRKLAMEDYGIIYITEQIAADIPETIERY-D-NQVLPAIILIPSN- 80 (104)
T ss_pred eeEEEEECHHHHHHHHHcCCeeEEecChHHHHHHHHHHhcCCcEEEEEcHHHHHHhHHHHHHh-c-CCCCCEEEEeCCC-
Confidence 4899999976666677789863 3555655555553 4578999999999998873 4443 2 222 3443
Q ss_pred CCCCC---CCHHHHHHHHh
Q 022545 199 AGTVT---TNIPQAIEEFK 214 (295)
Q Consensus 199 ~GTvt---~di~~~I~~~k 214 (295)
.|+.. +.+.+.|+++.
T Consensus 81 ~g~~~~g~~~i~~~v~kAI 99 (104)
T PRK01395 81 QGSLGIGLSRIQDNVEKAV 99 (104)
T ss_pred CCCccccHHHHHHHHHHHh
Confidence 35532 24777777765
No 30
>PF00107 ADH_zinc_N: Zinc-binding dehydrogenase; InterPro: IPR013149 Alcohol dehydrogenase (1.1.1.1 from EC) (ADH) catalyzes the reversible oxidation of alcohols to their corresponding acetaldehyde or ketone with the concomitant reduction of NAD: alcohol + NAD = aldehyde or ketone + NADH Currently three structurally and catalytically different types of alcohol dehydrogenases are known: Zinc-containing 'long-chain' alcohol dehydrogenases. Insect-type, or 'short-chain' alcohol dehydrogenases. Iron-containing alcohol dehydrogenases. Zinc-containing ADH's [, ] are dimeric or tetrameric enzymes that bind two atoms of zinc per subunit. One of the zinc atom is essential for catalytic activity while the other is not. Both zinc atoms are coordinated by either cysteine or histidine residues; the catalytic zinc is coordinated by two cysteines and one histidine. Zinc-containing ADH's are found in bacteria, mammals, plants, and in fungi. In many species there is more than one isozyme (for example, humans have at least six isozymes, yeast have three, etc.). A number of other zinc-dependent dehydrogenases are closely related to zinc ADH [] and are included in this family. Sorbitol dehydrogenase (1.1.1.14 from EC) L-threonine 3-dehydrogenase (1.1.1.103 from EC) Glutathione-dependent formaldehyde dehydrogenase (1.1.1.284 from EC) Mannitol dehydrogenase (1.1.1.255 from EC) In addition, this family includes NADP-dependent quinone oxidoreductase (1.6.5.5 from EC), an enzyme found in bacteria (gene qor), in yeast and in mammals where, in some species such as rodents, it has been recruited as an eye lens protein and is known as zeta-crystallin []. The sequence of quinone oxidoreductase is distantly related to that other zinc-containing alcohol dehydrogenases and it lacks the zinc-ligand residues. The torpedo fish and mammalian synaptic vesicle membrane protein vat-1 is related to qor. This entry represents the cofactor-binding domain of these enzymes, which is normally found towards the C terminus. Structural studies indicate that it forms a classical Rossman fold that reversibly binds NAD(H) [, , ].; GO: 0008270 zinc ion binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3PI7_A 3COS_D 1VJ1_A 2ZB3_A 1PIW_B 1Q1N_A 1PS0_A 2EER_B 3KRT_A 1ZSY_A ....
Probab=25.94 E-value=76 Score=24.98 Aligned_cols=64 Identities=33% Similarity=0.326 Sum_probs=39.4
Q ss_pred eEEEEEcCcc-cHHHHHHcCCCcccc---HHHHHHHHcCc--ccccEEEeCccchHHhHhhchhccCCCC
Q 022545 130 VKVAVLAQGE-KFNEAKNAGADLVGG---DDLIEQIKGGF--MEFDKLIASPDMMVKVASLGKILGPRGL 193 (295)
Q Consensus 130 ~kV~Vfa~~~-~~eeAk~aGAd~VG~---~eLi~kIk~g~--~~fD~~lAt~d~m~~l~~LgriLGPrGl 193 (295)
.+|.+++.++ ..+.|++.||+++-. +++.+++++.. ..+|.+|=+...-..+..--..+.|.|.
T Consensus 15 ~~vi~~~~~~~k~~~~~~~Ga~~~~~~~~~~~~~~i~~~~~~~~~d~vid~~g~~~~~~~~~~~l~~~G~ 84 (130)
T PF00107_consen 15 AKVIATDRSEEKLELAKELGADHVIDYSDDDFVEQIRELTGGRGVDVVIDCVGSGDTLQEAIKLLRPGGR 84 (130)
T ss_dssp SEEEEEESSHHHHHHHHHTTESEEEETTTSSHHHHHHHHTTTSSEEEEEESSSSHHHHHHHHHHEEEEEE
T ss_pred CEEEEEECCHHHHHHHHhhcccccccccccccccccccccccccceEEEEecCcHHHHHHHHHHhccCCE
Confidence 4676777665 467899999986532 34777777644 4699988555433333332355555543
No 31
>KOG1198 consensus Zinc-binding oxidoreductase [Energy production and conversion; General function prediction only]
Probab=25.72 E-value=1.1e+02 Score=29.82 Aligned_cols=45 Identities=29% Similarity=0.344 Sum_probs=34.6
Q ss_pred ceEEEEEcCcccHHHHHHcCCCcc---ccHHHHHHHHcC-cccccEEEe
Q 022545 129 SVKVAVLAQGEKFNEAKNAGADLV---GGDDLIEQIKGG-FMEFDKLIA 173 (295)
Q Consensus 129 ~~kV~Vfa~~~~~eeAk~aGAd~V---G~~eLi~kIk~g-~~~fD~~lA 173 (295)
-.+|.+.|..+..+-+++.|||.+ ..++.++++++- ...||+++-
T Consensus 183 ~~~v~t~~s~e~~~l~k~lGAd~vvdy~~~~~~e~~kk~~~~~~DvVlD 231 (347)
T KOG1198|consen 183 AIKVVTACSKEKLELVKKLGADEVVDYKDENVVELIKKYTGKGVDVVLD 231 (347)
T ss_pred CcEEEEEcccchHHHHHHcCCcEeecCCCHHHHHHHHhhcCCCccEEEE
Confidence 467888888888899999999865 346777777764 457888773
No 32
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=25.19 E-value=1.4e+02 Score=23.69 Aligned_cols=81 Identities=20% Similarity=0.216 Sum_probs=52.1
Q ss_pred EEEEEcCcccHHHHHHcCCC--c-ccc-HHHHHHHHcC--cccccEEEeCccchHHhH-hhchhccCCCCCC----CC-C
Q 022545 131 KVAVLAQGEKFNEAKNAGAD--L-VGG-DDLIEQIKGG--FMEFDKLIASPDMMVKVA-SLGKILGPRGLMP----NP-K 198 (295)
Q Consensus 131 kV~Vfa~~~~~eeAk~aGAd--~-VG~-~eLi~kIk~g--~~~fD~~lAt~d~m~~l~-~LgriLGPrGlMP----~p-k 198 (295)
||+|+++.+.+.-.+-+|++ + +.. ++..+.+.+. ..+|-.++-|.++...++ .+-+....+ ..| .| .
T Consensus 2 kIaVIGD~dtv~GFrLaGi~~~~~~~~~ee~~~~l~~l~~~~d~gII~Ite~~~~~i~e~i~~~~~~~-~~P~ii~IP~~ 80 (100)
T PRK02228 2 EIAVIGSPEFTTGFRLAGIRKVYEVPDDEKLDEAVEEVLEDDDVGILVMHDDDLEKLPRRLRRTLEES-VEPTVVTLGGG 80 (100)
T ss_pred EEEEEeCHHHHHHHHHcCCceEEeeCCHHHHHHHHHHHhhCCCEEEEEEehhHhHhhHHHHHHHHhcC-CCCEEEEECCC
Confidence 79999997777777888996 3 344 4455555553 457999999999988887 455534322 222 22 1
Q ss_pred CCCCCCCHHHHHHHHh
Q 022545 199 AGTVTTNIPQAIEEFK 214 (295)
Q Consensus 199 ~GTvt~di~~~I~~~k 214 (295)
.|+ +.+.+.|+++.
T Consensus 81 ~~~--~~i~~~v~raI 94 (100)
T PRK02228 81 GGS--GGLREKIKRAI 94 (100)
T ss_pred ccc--hHHHHHHHHHh
Confidence 222 45777777765
No 33
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=24.16 E-value=89 Score=27.09 Aligned_cols=36 Identities=17% Similarity=0.448 Sum_probs=29.4
Q ss_pred ceEEEEEcCcccH-HHHHHcCCCccccHHHHHHHHcC
Q 022545 129 SVKVAVLAQGEKF-NEAKNAGADLVGGDDLIEQIKGG 164 (295)
Q Consensus 129 ~~kV~Vfa~~~~~-eeAk~aGAd~VG~~eLi~kIk~g 164 (295)
...|+|.++|... ..|...||..+..+++...+...
T Consensus 94 ~~~v~VVTSD~~iq~~~~~~GA~~iss~ef~~~l~~~ 130 (166)
T PF05991_consen 94 PRQVTVVTSDREIQRAARGRGAKRISSEEFLRELKAA 130 (166)
T ss_pred CCeEEEEeCCHHHHHHHhhCCCEEEcHHHHHHHHHHH
Confidence 4789999988554 56788999999999999988653
No 34
>PF01990 ATP-synt_F: ATP synthase (F/14-kDa) subunit; InterPro: IPR008218 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit F found in the V1 complex of V-ATPases (both eukaryotic and bacterial), as well as in the A1 complex of A-ATPases. Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 2D00_E 3A5C_P 3J0J_H 3A5D_H 2OV6_A 2QAI_B 3AON_B 2I4R_A.
Probab=23.28 E-value=1.1e+02 Score=23.66 Aligned_cols=56 Identities=20% Similarity=0.306 Sum_probs=39.2
Q ss_pred EEEEcCcccHHHHHHcCCC--cc--ccHHHHHHHHcCc--ccccEEEeCccchHHhH-hhchh
Q 022545 132 VAVLAQGEKFNEAKNAGAD--LV--GGDDLIEQIKGGF--MEFDKLIASPDMMVKVA-SLGKI 187 (295)
Q Consensus 132 V~Vfa~~~~~eeAk~aGAd--~V--G~~eLi~kIk~g~--~~fD~~lAt~d~m~~l~-~Lgri 187 (295)
|+|+++.+.+.--+-+|++ ++ ..++..+.+++.. .++-+++-|.+++..+. .+-+.
T Consensus 1 IavIGd~~~v~gFrLaGv~~~~~~~~~ee~~~~l~~l~~~~~~gIIii~e~~~~~~~~~l~~~ 63 (95)
T PF01990_consen 1 IAVIGDRDTVLGFRLAGVEGVYVNTDPEEAEEALKELLKDEDVGIIIITEDLAEKIRDELDEY 63 (95)
T ss_dssp EEEEE-HHHHHHHHHTTSEEEEESHSHHHHHHHHHHHHHHTTEEEEEEEHHHHTTHHHHHHHH
T ss_pred CEEEeCHHHHHHHHHcCCCCccCCCCHHHHHHHHHHHhcCCCccEEEeeHHHHHHHHHHHHHH
Confidence 6788887766667778986 33 4456666666654 68889999999999887 34444
No 35
>COG4844 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.29 E-value=71 Score=24.43 Aligned_cols=17 Identities=12% Similarity=0.262 Sum_probs=13.9
Q ss_pred CCCHHHHHHHHHHHHHH
Q 022545 236 DFSEDDLLINFLAAVKS 252 (295)
Q Consensus 236 sm~~e~L~ENi~avl~~ 252 (295)
+-++|||+|||-+.++.
T Consensus 58 Get~eeLv~NIY~~i~E 74 (78)
T COG4844 58 GETPEELVENIYTFIEE 74 (78)
T ss_pred CCCHHHHHHHHHHHHhc
Confidence 34799999999998763
No 36
>PF00281 Ribosomal_L5: Ribosomal protein L5; InterPro: IPR002132 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 L5, ~180 amino acids in length, is one of the proteins from the large ribosomal subunit. In Escherichia coli, L5 is known to be involved in binding 5S RNA to the large ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , , ], groups: Eubacterial L5. Algal chloroplast L5. Cyanelle L5. Archaebacterial L5. Mammalian L11. Tetrahymena thermophila L21. Dictyostelium discoideum (Slime mold) L5 Saccharomyces cerevisiae (Baker's yeast) L16 (39A). Plant mitochondrial L5. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1IQ4_B 4A1A_D 4A1C_D 4A17_D 4A1E_D 3BBO_H 3O5H_K 1S1I_J 3O58_K 3IZS_E ....
Probab=22.02 E-value=1.4e+02 Score=21.38 Aligned_cols=31 Identities=23% Similarity=0.358 Sum_probs=25.1
Q ss_pred eeeEeeeCCCCCHHHHHHHHHHHHHHHHHhCCC
Q 022545 227 IVHIPFGKADFSEDDLLINFLAAVKSIEANKPK 259 (295)
Q Consensus 227 ~i~v~IGk~sm~~e~L~ENi~avl~~I~~~~p~ 259 (295)
++|+.+|....+ +..++....+..|...+|.
T Consensus 12 vin~gvg~~~~~--k~l~~a~~~L~~ItGQkp~ 42 (56)
T PF00281_consen 12 VINIGVGEAGDD--KVLEKAKKELEQITGQKPV 42 (56)
T ss_dssp EEEEESSTTSST--HHHHHHHHHHHHHHSS--E
T ss_pred EEECCCCccccc--hHHHHHHHHHHHHhCCcee
Confidence 688899988776 7889999999999998884
Done!