Query 015333
Match_columns 409
No_of_seqs 157 out of 1193
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 05:19:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015333.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015333hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00129 rpl1 ribosomal protei 100.0 2.5E-60 5.5E-65 453.2 24.7 214 177-397 15-228 (229)
2 COG0081 RplA Ribosomal protein 100.0 2.5E-60 5.3E-65 449.9 22.6 214 175-394 13-227 (228)
3 PRK05424 rplA 50S ribosomal pr 100.0 8.3E-59 1.8E-63 443.0 25.4 215 177-397 14-228 (230)
4 TIGR01169 rplA_bact ribosomal 100.0 1.4E-58 3.1E-63 440.7 24.9 214 177-396 13-226 (227)
5 PRK04203 rpl1P 50S ribosomal p 100.0 3.1E-52 6.7E-57 394.0 24.3 201 184-394 6-215 (215)
6 PTZ00225 60S ribosomal protein 100.0 1.4E-49 3.1E-54 376.0 21.7 198 184-393 8-214 (214)
7 PTZ00029 60S ribosomal protein 100.0 1.7E-48 3.7E-53 369.0 22.3 199 184-393 8-216 (216)
8 cd00403 Ribosomal_L1 Ribosomal 100.0 3.8E-44 8.3E-49 333.7 22.4 199 186-392 2-208 (208)
9 KOG1569 50S ribosomal protein 100.0 9.7E-38 2.1E-42 304.1 19.8 211 178-397 85-308 (323)
10 TIGR01170 rplA_mito ribosomal 100.0 3.6E-38 7.9E-43 281.4 15.5 137 183-322 1-141 (141)
11 PF00687 Ribosomal_L1: Ribosom 100.0 2.8E-35 6E-40 275.8 21.7 185 197-389 17-220 (220)
12 KOG1570 60S ribosomal protein 100.0 3.8E-29 8.3E-34 233.6 7.7 200 182-393 7-218 (218)
13 KOG1685 Uncharacterized conser 99.7 2.4E-18 5.2E-23 172.1 7.5 156 233-397 87-263 (343)
14 PF13003 MRL1: Ribosomal prote 95.9 0.014 3E-07 52.4 5.1 62 179-240 66-133 (133)
15 PTZ00029 60S ribosomal protein 68.5 3.1 6.7E-05 40.1 1.9 21 288-309 117-137 (216)
16 PRK01189 V-type ATP synthase s 55.3 36 0.00078 29.3 5.9 86 236-326 4-101 (104)
17 PRK02228 V-type ATP synthase s 53.3 79 0.0017 26.8 7.6 84 235-322 1-95 (100)
18 PRK01395 V-type ATP synthase s 51.4 83 0.0018 27.0 7.5 85 235-322 4-100 (104)
19 COG1064 AdhP Zn-dependent alco 45.2 44 0.00096 34.6 5.7 58 235-297 191-252 (339)
20 PTZ00225 60S ribosomal protein 40.8 17 0.00038 35.1 1.9 20 288-308 115-134 (214)
21 TIGR00853 pts-lac PTS system, 33.6 1.3E+02 0.0028 25.2 5.8 63 234-297 3-74 (95)
22 COG1436 NtpG Archaeal/vacuolar 27.6 1.9E+02 0.0042 25.0 6.0 84 235-320 3-98 (104)
23 PRK13958 N-(5'-phosphoribosyl) 25.9 42 0.0009 32.0 1.8 25 235-259 3-27 (207)
24 PF12270 Cyt_c_ox_IV: Cytochro 24.3 42 0.00092 30.6 1.4 16 117-132 60-75 (137)
25 COG0135 TrpF Phosphoribosylant 22.6 53 0.0012 31.8 1.8 25 234-258 3-27 (208)
26 cd05565 PTS_IIB_lactose PTS_II 22.5 2.2E+02 0.0047 24.4 5.3 59 236-299 2-73 (99)
27 PF05991 NYN_YacP: YacP-like N 22.2 3.2E+02 0.007 25.0 6.8 35 234-268 94-129 (166)
28 PF00697 PRAI: N-(5'phosphorib 21.5 70 0.0015 29.9 2.4 25 235-259 1-25 (197)
No 1
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=100.00 E-value=2.5e-60 Score=453.23 Aligned_cols=214 Identities=42% Similarity=0.675 Sum_probs=206.2
Q ss_pred CCCCCccCHHHHHHHHHHHcccCCCccEEEEEEeCCCCCCCCCceeeeEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCe
Q 015333 177 KESRPVLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADI 256 (409)
Q Consensus 177 ~~~~~~~~l~EAI~~lK~~ak~kF~ETVeL~V~L~id~kK~~~~IRG~V~LPH~~~k~~kIcVFadd~~aeeAkeaGAd~ 256 (409)
.+ ...|++.|||+++|+.+.++|+||||++|+|++|++|+++++||+|.|||++++..+|||||+++.+++|+++||++
T Consensus 15 ~~-~~~y~l~eAi~~~k~~~~~kF~esvel~i~L~id~kk~~~~irg~v~LP~~~gk~~kV~Vfa~~~~~~eAk~aGad~ 93 (229)
T CHL00129 15 IE-KKLYSPEEAINLLKETATAKFIETAEAHISLNIDPKYADQQLRTTVTLPKGTGKTIRIAVLTNEEKITEAKNAGADI 93 (229)
T ss_pred cc-ccccCHHHHHHHHHHhCcCCCCccEEEEEEECCCCCCCCCceeeEEECCCCCCCCcEEEEECChHhHHHHHHcCCCE
Confidence 45 67999999999999988999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccHhHHHHHHhcCcccccEEEEcCcchhhHHhhhhhhhcCCCCCCCCCCCccccHHHHHHHHHcCceEEEecCCCeEEE
Q 015333 257 VGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLMPNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHA 336 (409)
Q Consensus 257 VGgeeLIekI~~~~kL~fD~fLAtpd~mp~L~kLGriLGpKGkMP~pK~GTVt~DI~~~I~~~k~Gsv~fr~~k~g~i~V 336 (409)
||++||+++|+ +++++||+||||++||+.|++||++||||||||+++.|||++||.++|+++++|++.||+++.|++|+
T Consensus 94 vg~edLi~~ik-~~~~~fd~~iAt~d~m~~l~kLgriLGprGlMP~pk~gTvt~di~~~V~~~k~G~v~~r~dk~g~i~~ 172 (229)
T CHL00129 94 VGSDDLIEEIT-KGNLDFDLLIATPDMMPKLAKLGRVLGPRGLMPSPKSGTVTTDLASAINEFKKGKLEYRADKTGIVHV 172 (229)
T ss_pred eCHHHHHHHHH-cCcccCCEEEECHHHHHHHHHhcCcccccCCCCCCCCCCccccHHHHHHHHhcCcEEEEecCCcEEEE
Confidence 99999999998 58999999999999999999999999999999999999999999999999998899999999999999
Q ss_pred EecccCCChHHHHHhHHHHHHHHHHhCCCCCCCCcccccceeEEEEecCCCCceEEehhhh
Q 015333 337 GLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSL 397 (409)
Q Consensus 337 ~IGklsms~eeL~ENI~Avi~aL~~~kP~~lKk~sk~~~nIksVyLkSTmGP~i~I~~~~~ 397 (409)
+||+++|+++||.|||.+++++|.+++|.+.||. ||+++||||||||+++|++.++
T Consensus 173 ~VG~~~m~~~~l~eNi~a~l~~i~~~~p~~~kg~-----~ik~v~issTMGp~v~i~~~~~ 228 (229)
T CHL00129 173 LFGKSNFTEEDLLENLQAIYESIEQNRPSGVKGK-----YWKSFYICSTMGPSIQIDISLL 228 (229)
T ss_pred EEeCCCCCHHHHHHHHHHHHHHHHHhCcccccCc-----eEEEEEEECCCCCCEEeccccc
Confidence 9999999999999999999999999999987764 9999999999999999998765
No 2
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-60 Score=449.91 Aligned_cols=214 Identities=47% Similarity=0.748 Sum_probs=205.6
Q ss_pred ccCCCCCccCHHHHHHHHHHHcccCCCccEEEEEEeCCCCCCCCCceeeeEEcCCCCCCCcEEEEEcCchhHHHHHHcCC
Q 015333 175 KKKESRPVLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGA 254 (409)
Q Consensus 175 ~k~~~~~~~~l~EAI~~lK~~ak~kF~ETVeL~V~L~id~kK~~~~IRG~V~LPH~~~k~~kIcVFadd~~aeeAkeaGA 254 (409)
.+.+....|+|.|||+++++.+.++|+||||++|+|++|++|++++|||.|.|||++|+..||||||+++.+++|+++||
T Consensus 13 ~~~d~~~~~~i~eai~~~ke~~~~kF~etVevav~L~vD~~k~dq~vrg~VvLP~g~gk~vrV~Vfa~g~~~~~A~~AGa 92 (228)
T COG0081 13 EKVDRNKLYSLEEAVKLLKETSKRKFDETVEVAVNLKVDPRKPDQRVRGSVVLPNGTGKTVRVAVFADGEKAEEAKAAGA 92 (228)
T ss_pred HhhhhhhhhhHHHHHHHHHhccccCcceEEEEEEEcccCCCCcccccceeEECCCCCCCccEEEEEcChHhHHHHHHcCC
Confidence 34566778999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeeccHhHHHHHHhcC-cccccEEEEcCcchhhHHhhhhhhhcCCCCCCCCCCCccccHHHHHHHHHcCceEEEecCCCe
Q 015333 255 DIVGGLELIEEIASSG-KLDVEKCFSTRQFMPRLFKISKILNQHGLMPNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSN 333 (409)
Q Consensus 255 d~VGgeeLIekI~~~~-kL~fD~fLAtpd~mp~L~kLGriLGpKGkMP~pK~GTVt~DI~~~I~~~k~Gsv~fr~~k~g~ 333 (409)
|+||++||+++|+ ++ |.+||+|||+|+||+.+++||++||||||||+|+.||++.|+.++|+++++|+++||+++.++
T Consensus 93 d~Vg~edl~e~ik-~~r~~~fD~~IAtpdmM~~v~~LG~vLGPRGlMP~Pk~gTvt~Dv~~av~~~K~g~v~~R~dk~g~ 171 (228)
T COG0081 93 DYVGGEDLIELIK-NGRAKDFDVFIATPDMMPLVGKLGKVLGPRGLMPNPKTGTVTDDVAKAVEELKKGTVEFRADKAGV 171 (228)
T ss_pred CEecHHHHHHHHh-CcchhcCCEEEECchHHHHHHHHhhhcCCCCCCCCCCCCCCCcCHHHHHHHHhcCcEEEEECCCce
Confidence 9999999999998 46 899999999999999998899999999999999999999999999999999999999999999
Q ss_pred EEEEecccCCChHHHHHhHHHHHHHHHHhCCCCCCCCcccccceeEEEEecCCCCceEEeh
Q 015333 334 VHAGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSI 394 (409)
Q Consensus 334 i~V~IGklsms~eeL~ENI~Avi~aL~~~kP~~lKk~sk~~~nIksVyLkSTmGP~i~I~~ 394 (409)
+|+.||+++|++++|.|||.++++.|.+++|.+.|+ +||++|||||||||+++|+.
T Consensus 172 ih~~iGk~sf~~e~L~eNi~a~l~~i~~~~p~~~kg-----~~ik~v~vstTMGP~v~v~~ 227 (228)
T COG0081 172 IHVPIGKVSFDDEKLAENIEALLNAIVKAKPAGAKG-----QYIKSVYVSTTMGPGVKVDL 227 (228)
T ss_pred EEEEecCCCCCHHHHHHHHHHHHHHHHHhCcCCccc-----ceEeEEEEecCCCCCEEecc
Confidence 999999999999999999999999999999998774 59999999999999999985
No 3
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=100.00 E-value=8.3e-59 Score=443.04 Aligned_cols=215 Identities=50% Similarity=0.751 Sum_probs=206.9
Q ss_pred CCCCCccCHHHHHHHHHHHcccCCCccEEEEEEeCCCCCCCCCceeeeEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCe
Q 015333 177 KESRPVLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADI 256 (409)
Q Consensus 177 ~~~~~~~~l~EAI~~lK~~ak~kF~ETVeL~V~L~id~kK~~~~IRG~V~LPH~~~k~~kIcVFadd~~aeeAkeaGAd~ 256 (409)
.+....|++.|||+.+|+.+.++|+||||++|+|++|++|++++|||+|.|||++++..+|||||+++.+++|+++||++
T Consensus 14 ~~~~~~y~l~eAi~~lk~~~~~kF~esvel~v~L~id~kK~~~~irg~v~LP~~~gk~~kI~Vfa~~~~~~~Ak~aGa~~ 93 (230)
T PRK05424 14 VDRTKLYSLEEAIALVKETATAKFDETVDVAVNLGVDPRKADQQVRGAVVLPHGTGKTVRVAVFAKGEKAEEAKAAGADI 93 (230)
T ss_pred ccccCccCHHHHHHHHHhhccCCCCCcEEEEEEeCCCCCCCCCeeeEEEECCCCCCCCcEEEEECChHhHHHHHHcCCCE
Confidence 45567999999999999988999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccHhHHHHHHhcCcccccEEEEcCcchhhHHhhhhhhhcCCCCCCCCCCCccccHHHHHHHHHcCceEEEecCCCeEEE
Q 015333 257 VGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLMPNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHA 336 (409)
Q Consensus 257 VGgeeLIekI~~~~kL~fD~fLAtpd~mp~L~kLGriLGpKGkMP~pK~GTVt~DI~~~I~~~k~Gsv~fr~~k~g~i~V 336 (409)
||++||+++|+ +++++||+||||+++|+.|++||++||||||||+++.|||++||.++|+++++|+++||+++.|++|+
T Consensus 94 vg~eeLi~~ik-~~~~~fd~~iat~~~m~~l~~Lg~iLGPrGlMP~pk~gTv~~di~~~I~~~k~g~v~~r~~k~g~i~~ 172 (230)
T PRK05424 94 VGGEDLIEKIK-GGWLDFDVVIATPDMMGKVGKLGRILGPRGLMPNPKTGTVTMDVAKAVKEAKAGKVEFRVDKAGIIHA 172 (230)
T ss_pred eCHHHHHHHHh-cCCCcCCEEEECHHHHHHHHHhccccccccCCCCCCCCCcchhHHHHHHHHhcCcEEEEecCCCEEEE
Confidence 99999999998 58999999999999999999999999999999999999999999999999998999999999999999
Q ss_pred EecccCCChHHHHHhHHHHHHHHHHhCCCCCCCCcccccceeEEEEecCCCCceEEehhhh
Q 015333 337 GLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSL 397 (409)
Q Consensus 337 ~IGklsms~eeL~ENI~Avi~aL~~~kP~~lKk~sk~~~nIksVyLkSTmGP~i~I~~~~~ 397 (409)
+||+++|+++||.|||.+++++|.+++|.+.||. ||++|||||||||+++|+..++
T Consensus 173 ~IG~~~m~~e~i~eNi~a~l~~i~~~~p~~~kg~-----~Ik~v~lssTmGp~~~i~~~~~ 228 (230)
T PRK05424 173 PIGKVSFDAEKLKENLKALIDAIKKAKPATAKGT-----YIKSVSLSSTMGPGVKVDPSSL 228 (230)
T ss_pred EEeCCCCCHHHHHHHHHHHHHHHHHhCccccCCC-----EEEEEEEECCCCCCEEechHHh
Confidence 9999999999999999999999999999987764 9999999999999999998876
No 4
>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=1.4e-58 Score=440.67 Aligned_cols=214 Identities=49% Similarity=0.758 Sum_probs=205.3
Q ss_pred CCCCCccCHHHHHHHHHHHcccCCCccEEEEEEeCCCCCCCCCceeeeEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCe
Q 015333 177 KESRPVLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADI 256 (409)
Q Consensus 177 ~~~~~~~~l~EAI~~lK~~ak~kF~ETVeL~V~L~id~kK~~~~IRG~V~LPH~~~k~~kIcVFadd~~aeeAkeaGAd~ 256 (409)
.+....|++.|||+.+|+.+.++|+||||++|+|++|++|++++|||+|.|||++++..+|||||+++++++|+++||++
T Consensus 13 ~~~~~~y~l~eAi~~lk~~~~~~f~esvel~i~L~id~kK~~~~irg~v~LP~~~gk~~kV~Vfa~~~~~~~Ak~aGa~~ 92 (227)
T TIGR01169 13 VDRNKLYSLDEAIALLKETATAKFDETVEVAIRLGIDPRKSDQQVRGTVVLPHGTGKTVRVAVFAKGEKAEEAKAAGADY 92 (227)
T ss_pred cccCCccCHHHHHHHHHhhccCCCCCCEEEEEEECcCCCcCCCeeeEEEECCCCCCCCcEEEEEcCchhHHHHHHcCCCE
Confidence 34556899999999999988999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccHhHHHHHHhcCcccccEEEEcCcchhhHHhhhhhhhcCCCCCCCCCCCccccHHHHHHHHHcCceEEEecCCCeEEE
Q 015333 257 VGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLMPNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHA 336 (409)
Q Consensus 257 VGgeeLIekI~~~~kL~fD~fLAtpd~mp~L~kLGriLGpKGkMP~pK~GTVt~DI~~~I~~~k~Gsv~fr~~k~g~i~V 336 (409)
||++||+++|+ +++++||+||||+++|++|++||++||||||||+++.|||++||.++|+++++|+++||+++.|++|+
T Consensus 93 vg~~eLi~~ik-~~~~~fd~~iat~~~m~~l~~Lg~iLGPrGlMP~~k~gtv~~di~~~I~~~k~g~v~~r~~k~g~i~~ 171 (227)
T TIGR01169 93 VGSDDLIEKIK-KGWLDFDVVIATPDMMRVVGKLGRILGPRGLMPNPKTGTVTADVAKAVKNAKKGQVEFRADKAGNIHA 171 (227)
T ss_pred eCHHHHHHHHH-cCCccCCEEEECHHHHHHHHHhccccccccCCCCCCCCCccccHHHHHHHHHcCcEEEEeCCCCEEEE
Confidence 99999999998 58999999999999999999999999999999999999999999999999998899999999999999
Q ss_pred EecccCCChHHHHHhHHHHHHHHHHhCCCCCCCCcccccceeEEEEecCCCCceEEehhh
Q 015333 337 GLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQS 396 (409)
Q Consensus 337 ~IGklsms~eeL~ENI~Avi~aL~~~kP~~lKk~sk~~~nIksVyLkSTmGP~i~I~~~~ 396 (409)
+||+++|+++||.|||.+++++|.+++|.+.||. ||++|||||||||+++|++.+
T Consensus 172 ~VG~~~m~~e~i~eNi~a~l~~i~~~~p~~~kg~-----~Ik~v~lssTmGp~~~i~~~~ 226 (227)
T TIGR01169 172 SIGKVSFDSEKLKENLEALLDAIKKAKPSGAKGQ-----YIKNIALSSTMGPGIKVDLSS 226 (227)
T ss_pred EEecCCCCHHHHHHHHHHHHHHHHHhCccccCCC-----EEEEEEEECCCCCCEEeccCC
Confidence 9999999999999999999999999999987764 999999999999999998765
No 5
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=100.00 E-value=3.1e-52 Score=394.01 Aligned_cols=201 Identities=27% Similarity=0.424 Sum_probs=188.1
Q ss_pred CHHHHHHHHHHH-cccCCCccEEEEEEe-CCCCCCCCCceeeeEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCeeccHh
Q 015333 184 DLMDAIKQVKAN-AKATFDETVEAHVRL-AIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADIVGGLE 261 (409)
Q Consensus 184 ~l~EAI~~lK~~-ak~kF~ETVeL~V~L-~id~kK~~~~IRG~V~LPH~~~k~~kIcVFadd~~aeeAkeaGAd~VGgee 261 (409)
.+.|||+.+++. .+++|+||||++|+| ++|++|+++++||+|.|||++++..+|||||+++++++|+++||++||+.|
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 388999999985 589999999999999 999999999999999999999999999999999999999999999888888
Q ss_pred HHHHHHhc----C--cccccEEEEcCcchhhHHh-hhhhhhcCCCCCCCCCCCccccHHHHHHHHHcCceEEEecCCCeE
Q 015333 262 LIEEIASS----G--KLDVEKCFSTRQFMPRLFK-ISKILNQHGLMPNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNV 334 (409)
Q Consensus 262 LIekI~~~----~--kL~fD~fLAtpd~mp~L~k-LGriLGpKGkMP~pK~GTVt~DI~~~I~~~k~Gsv~fr~~k~g~i 334 (409)
++++|..+ + +.+||+||||++||+.|++ ||++||||||||+++.||+ ||.++|++++ +++.|++++++++
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--DIKPLVERLK-NTVRIRTKDQPTF 162 (215)
T ss_pred HHHHHhcChHHHhhhhhcCCEEEECHHHHHHHHHHHhhhcCcCCCCCCCcCCCC--CHHHHHHHHh-hceEEEeCCCCEE
Confidence 88998641 1 3499999999999999998 9999999999999999996 9999999999 5799999999999
Q ss_pred EEEecccCCChHHHHHhHHHHHHHHHHhCCCCCCCCcccccceeEEEEecCCCCceEEeh
Q 015333 335 HAGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSI 394 (409)
Q Consensus 335 ~V~IGklsms~eeL~ENI~Avi~aL~~~kP~~lKk~sk~~~nIksVyLkSTmGP~i~I~~ 394 (409)
+++||+++|+++||+|||.+++++|.+.+|.+ |+||++|||||||||+++|+.
T Consensus 163 ~v~VG~~~m~~e~l~eNi~avl~~i~~~~p~g-------~~~Iksi~lktTmgp~i~i~~ 215 (215)
T PRK04203 163 HVRVGTEDMSPEELAENIDAVLNRIESKLEKG-------RQNIKSVYVKTTMGPAVKVEL 215 (215)
T ss_pred EEEEeCCCCCHHHHHHHHHHHHHHHHHhCccc-------cccEEEEEEECCCCCCEEeeC
Confidence 99999999999999999999999999998866 889999999999999999873
No 6
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=100.00 E-value=1.4e-49 Score=376.03 Aligned_cols=198 Identities=20% Similarity=0.306 Sum_probs=184.1
Q ss_pred CHHHHHHHHH-HHcccCCCccEEEEEEe-CCCCCCCCCceeeeEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCeeccHh
Q 015333 184 DLMDAIKQVK-ANAKATFDETVEAHVRL-AIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADIVGGLE 261 (409)
Q Consensus 184 ~l~EAI~~lK-~~ak~kF~ETVeL~V~L-~id~kK~~~~IRG~V~LPH~~~k~~kIcVFadd~~aeeAkeaGAd~VGgee 261 (409)
.+.|||+.++ ..++++|+||||++|+| |+|+++ ++++||+|.|||++++..+|||||+++.+++|+++||+++|.+|
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 4889999966 55589999999999999 999998 99999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCc------ccccEEEEcCcchhhHHh-hhhhhhcCCCCCCCCCCCccccHHHHHHHHHcCceEEEecCCCeE
Q 015333 262 LIEEIASSGK------LDVEKCFSTRQFMPRLFK-ISKILNQHGLMPNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNV 334 (409)
Q Consensus 262 LIekI~~~~k------L~fD~fLAtpd~mp~L~k-LGriLGpKGkMP~pK~GTVt~DI~~~I~~~k~Gsv~fr~~k~g~i 334 (409)
|++.++. ++ .+||+|||+++||+.|++ ||+.|||+||||++. +++.||.++|+++++ ++.||+++.+++
T Consensus 87 l~~l~k~-~~~~kkl~~~fD~fiA~~~~m~~lgk~LGp~~~p~gK~P~~~--~~~~dl~~~i~~~k~-~v~~r~~k~~~~ 162 (214)
T PTZ00225 87 LKKLNKN-KKLVKKMCNQYDAFLCSESIIKTVPRLVGPHMHRMGKFPTVC--SPSESLPDKVVELRS-TVKFQLKKVLCL 162 (214)
T ss_pred HHHHHhc-cHHHHHHHhhCCEEEECHHHHHhhhhhcCCCCCcCCCCCccc--CCccCHHHHHHHHhh-eeEEEecCccEE
Confidence 9988864 43 499999999999999999 999999999999965 667899999999995 899999999999
Q ss_pred EEEecccCCChHHHHHhHHHHHHHHHHhCCCCCCCCcccccceeEEEEecCCCCceEEe
Q 015333 335 HAGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS 393 (409)
Q Consensus 335 ~V~IGklsms~eeL~ENI~Avi~aL~~~kP~~lKk~sk~~~nIksVyLkSTmGP~i~I~ 393 (409)
|++||+++|+++||+||+.+++++|.+.+|.+ |+||+++||||||||+++|+
T Consensus 163 ~~~VGk~~m~~e~i~eNi~a~l~~l~~~~p~k-------~~nIksv~iktTMGp~~~~~ 214 (214)
T PTZ00225 163 GTCVGHVEMTEEQLRQNVVMAINFLVSLLKKN-------WQNLKSAYIKSTMGKPQRIY 214 (214)
T ss_pred EeEEccCCCCHHHHHHHHHHHHHHHHHhCCcC-------CceEeEEEEECCCCCCEeCC
Confidence 99999999999999999999999999998853 89999999999999999874
No 7
>PTZ00029 60S ribosomal protein L10a; Provisional
Probab=100.00 E-value=1.7e-48 Score=368.99 Aligned_cols=199 Identities=23% Similarity=0.359 Sum_probs=181.4
Q ss_pred CHHHHHHHHHH--Hc-ccCCCccEEEEEEe-CCCCCCCCCceeeeEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCeecc
Q 015333 184 DLMDAIKQVKA--NA-KATFDETVEAHVRL-AIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADIVGG 259 (409)
Q Consensus 184 ~l~EAI~~lK~--~a-k~kF~ETVeL~V~L-~id~kK~~~~IRG~V~LPH~~~k~~kIcVFadd~~aeeAkeaGAd~VGg 259 (409)
.+.+||+.+++ .. +++|+||||++|+| ++|+++ ++++||+|.|||++++..+|||||+++.+++|+++||++||+
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 47899999996 33 89999999999999 999998 999999999999999999999999999999999999999999
Q ss_pred HhHHHHHHh----cCc-ccccEEEEcCcchhhHHh-hhhhhhcCCCCCCCCCCCccccHHHHHHHHHcCceEEEecCCCe
Q 015333 260 LELIEEIAS----SGK-LDVEKCFSTRQFMPRLFK-ISKILNQHGLMPNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSN 333 (409)
Q Consensus 260 eeLIekI~~----~~k-L~fD~fLAtpd~mp~L~k-LGriLGpKGkMP~pK~GTVt~DI~~~I~~~k~Gsv~fr~~k~g~ 333 (409)
+||++.++. ++. .+||+||||+++|+.|++ ||+.|+|++|||++. |++.|+.++|++++ +++.||+++++|
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--THNDDIEDKINELK-SSVKFQLKKVLC 163 (216)
T ss_pred HHHHHhhhhHHHHhcccccCCEEEECHHHHHHHHHHhccccccCCCCCCcc--cCccCHHHHHHHHH-heEEEEECCCCE
Confidence 999985442 233 399999999999999988 888888888888876 66789999999998 589999999999
Q ss_pred EEEEecccCCChHHHHHhHHHHHHHHHHhCCCCCCCCcccccceeEEEEecCCCCceEEe
Q 015333 334 VHAGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS 393 (409)
Q Consensus 334 i~V~IGklsms~eeL~ENI~Avi~aL~~~kP~~lKk~sk~~~nIksVyLkSTmGP~i~I~ 393 (409)
+|++||+++|+++||.|||.+++++|.+.++.+ |.||++|||||||||+++|+
T Consensus 164 i~v~VG~~~~~~e~l~eNi~avl~~i~~~~~kg-------~~~Iksv~lktTmgp~v~v~ 216 (216)
T PTZ00029 164 LGVAVGNVEMTEEQLRQNIVLSINFLVSLLKKN-------WQNIKTLHIKSTMGKPQRIY 216 (216)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHHHHHHHHhccc-------cccEeEEEEECCCCCCEeCC
Confidence 999999999999999999999999999987533 89999999999999999975
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=3.8e-44 Score=333.72 Aligned_cols=199 Identities=44% Similarity=0.685 Sum_probs=185.8
Q ss_pred HHHHHHHHHHc--ccCCCccEEEEEEeCCCCCCCCCceeeeEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCeeccHhHH
Q 015333 186 MDAIKQVKANA--KATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADIVGGLELI 263 (409)
Q Consensus 186 ~EAI~~lK~~a--k~kF~ETVeL~V~L~id~kK~~~~IRG~V~LPH~~~k~~kIcVFadd~~aeeAkeaGAd~VGgeeLI 263 (409)
.+||+.+++.+ ...|+++|+|+|.|+..+.+++.+++|.|.|||++++..+|||||+++++++|+++|++++|+++|+
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 8999999999999966656668899999999999998999999999999999999999999999999
Q ss_pred HHHHhcCc-----ccccEEEEcCcchhhHHh-hhhhhhcCCCCCCCCCCCccccHHHHHHHHHcCceEEEecCCCeEEEE
Q 015333 264 EEIASSGK-----LDVEKCFSTRQFMPRLFK-ISKILNQHGLMPNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAG 337 (409)
Q Consensus 264 ekI~~~~k-----L~fD~fLAtpd~mp~L~k-LGriLGpKGkMP~pK~GTVt~DI~~~I~~~k~Gsv~fr~~k~g~i~V~ 337 (409)
+++++ ++ .+||+||||+++|+.+.+ ||++||+||+||+++.||+++||.++|+++++ ++.|+.+++++++++
T Consensus 82 ~~~~~-~~~~~l~~~~D~fla~~~~~~~~~~~lgk~~~~k~k~P~~~~~t~~~~l~~~i~~~~~-~~~~~~~~~~~~~v~ 159 (208)
T cd00403 82 KKIKN-GEAKKLAKDFDLFLADPRIMMLLPKLLGKVLGPRGKMPNPKTGTVTEDLAKAIEEAKS-SVEFRLDKGGCIHVP 159 (208)
T ss_pred HHhhc-chhhhhhhcCCEEEECHHHHHHHHHHhccccccCCCCCcCCCCCCcccHHHHHHHHHh-CeEEEECCCCEEEEE
Confidence 99986 44 499999999999999988 99999999999999999999999999999994 789999999999999
Q ss_pred ecccCCChHHHHHhHHHHHHHHHHhCCCCCCCCcccccceeEEEEecCCCCceEE
Q 015333 338 LGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPV 392 (409)
Q Consensus 338 IGklsms~eeL~ENI~Avi~aL~~~kP~~lKk~sk~~~nIksVyLkSTmGP~i~I 392 (409)
||+++|+++||+|||.+++++|.+++|. +| |+||++|||||||||+++|
T Consensus 160 VG~~~m~~~~l~eNi~~vi~~i~~~~~~--~~----~~~i~~v~lktt~~~~lpI 208 (208)
T cd00403 160 VGKVSMSPEQLVENIEAVINALVKKLPS--KK----GQNIKSIYLKTTMGPSLPI 208 (208)
T ss_pred EeCCCCCHHHHHHHHHHHHHHHHHhCCc--cc----CeEEEEEEEECCCCCCeEC
Confidence 9999999999999999999999999884 22 8899999999999999986
No 9
>KOG1569 consensus 50S ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.7e-38 Score=304.09 Aligned_cols=211 Identities=27% Similarity=0.460 Sum_probs=188.6
Q ss_pred CCCCccCHHHHHHHHHHHc----ccCCCccEEEEEEeCCCCC---CCCCceeeeEEcCCCCCC--CcEEEEEcCc-hhHH
Q 015333 178 ESRPVLDLMDAIKQVKANA----KATFDETVEAHVRLAIPPR---KTELIVRGTMNLPHGDKK--AVRVAFFAEG-ADAE 247 (409)
Q Consensus 178 ~~~~~~~l~EAI~~lK~~a----k~kF~ETVeL~V~L~id~k---K~~~~IRG~V~LPH~~~k--~~kIcVFadd-~~ae 247 (409)
-+++.|.+.+|+...|++. .....+++.+.+.|++... |+...+.+.+..||+++- ..+|+||+.| ...+
T Consensus 85 ~kr~~y~vq~a~~~~ke~~~~sa~~~pk~~~~l~i~l~~~a~~~~k~~~~~~~~v~vP~Pf~~ge~r~IavFtn~~~kve 164 (323)
T KOG1569|consen 85 YKRQIYEVQKAVHLHKELQILSAYNVPKQPVNLRIELNMLAEKETKGVAPLQGSVTVPHPFAHGEIRKIAVFTNDASKVE 164 (323)
T ss_pred cCcchhhHHHHHHHHHHhccchhhhCCCCceeeeEEeeeeeeeeccccCCCceeEeccccCCCCceEEEEEecCChHHHH
Confidence 4457899999999999876 4466788888888877643 345678889999999964 5679999999 5689
Q ss_pred HHHHcCCCeeccHhHHHHHHhcCcc--cccEEEEcCcchhhHHhhhhhhhcCCCCCCCCCCCccccHHHHHHHHHcC-ce
Q 015333 248 EARAAGADIVGGLELIEEIASSGKL--DVEKCFSTRQFMPRLFKISKILNQHGLMPNPKQGTVTNDVARAVQEAKQG-HI 324 (409)
Q Consensus 248 eAkeaGAd~VGgeeLIekI~~~~kL--~fD~fLAtpd~mp~L~kLGriLGpKGkMP~pK~GTVt~DI~~~I~~~k~G-sv 324 (409)
+|+++||++|||.|||++|. .|.+ +||+|||+||||+.|..|+++||+| ||++++|||++||.++|++|++| .+
T Consensus 165 eArEaGA~l~GG~dLIkkI~-~Gei~~Dyd~~vA~Pdim~~l~~Lr~iL~~r--~Pn~k~gtvg~nipemieeFk~G~~i 241 (323)
T KOG1569|consen 165 EAREAGAALAGGTDLIKKIK-SGEIVADYDFYVAHPDIMPELNRLRKILGPR--FPNPKRGTVGRNIPEMIEEFKNGHEI 241 (323)
T ss_pred HHHhccccccccHHHHHHhh-cCeEEEeeceeeecchHHHHHHHHHHHhccc--CCCcccCccccchHHHHHHhhCCccc
Confidence 99999999999999999998 4876 7889999999999999999999996 99999999999999999999988 68
Q ss_pred EEEecCCCeEEEEecccCCChHHHHHhHHHHHHHHHHhCCCCCCCCcccccceeEEEEecCCCCceEEehhhh
Q 015333 325 KFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVSIQSL 397 (409)
Q Consensus 325 ~fr~~k~g~i~V~IGklsms~eeL~ENI~Avi~aL~~~kP~~lKk~sk~~~nIksVyLkSTmGP~i~I~~~~~ 397 (409)
.|+-.+.++++++||+++|++++|.+||.+++++++.++|. .+|. ||.+++|+|+||+++.|+++.+
T Consensus 242 ~~d~~~~~~~~~~vGkl~mt~e~i~~Ni~a~i~av~t~rp~-~~G~-----fv~ra~L~Ss~g~~i~l~i~p~ 308 (323)
T KOG1569|consen 242 KFDEERENILQIKVGKLDMTSEQILANIQAVIAAVCTHRPK-ALGP-----FVVRALLRSSPGEGILLKIDPL 308 (323)
T ss_pred ccccccCceeeeeeeeecCCHHHHHHHHHHHHHHHHhcCCc-ccCc-----eeeeeEeecCCCCceeEecccc
Confidence 89988899999999999999999999999999999999997 3554 9999999999999999999876
No 10
>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=3.6e-38 Score=281.40 Aligned_cols=137 Identities=31% Similarity=0.569 Sum_probs=129.5
Q ss_pred cCHHHHHHHHHHHccc--CCCccEEEEEEeCCCCCCCCCceeeeEEcCCCCCCCcEEEEEcCchh-HHHHHHcCCCeecc
Q 015333 183 LDLMDAIKQVKANAKA--TFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGAD-AEEARAAGADIVGG 259 (409)
Q Consensus 183 ~~l~EAI~~lK~~ak~--kF~ETVeL~V~L~id~kK~~~~IRG~V~LPH~~~k~~kIcVFadd~~-aeeAkeaGAd~VGg 259 (409)
|++.||++++|+.+.. +|+|||+++|+|++++++. .|||+|.|||++++..+|||||++++ +++|+++||++||+
T Consensus 1 y~i~eA~~~lk~~~~~~~~~~etvel~i~L~~~~~~~--~irg~v~LP~~~~k~~kV~Vf~~~~~~~~~Ak~aGa~~vg~ 78 (141)
T TIGR01170 1 YKVIKAFVYLKTKSISMYVPKQSVNLDIGLLMELGKE--SVQGMFSFPHPFGKEPKIAVFTKGASEVEEAREAGADYVGG 78 (141)
T ss_pred CCHHHHHHHHHHhcccCCCCCceEEEEEEECCCCCCC--CceEEEECCCCCCCCCEEEEECCChHHHHHHHHcCCCEeCH
Confidence 7899999999999976 9999999999999887664 49999999999999999999999987 68899999999999
Q ss_pred HhHHHHHHhcCccc-ccEEEEcCcchhhHHhhhhhhhcCCCCCCCCCCCccccHHHHHHHHHcC
Q 015333 260 LELIEEIASSGKLD-VEKCFSTRQFMPRLFKISKILNQHGLMPNPKQGTVTNDVARAVQEAKQG 322 (409)
Q Consensus 260 eeLIekI~~~~kL~-fD~fLAtpd~mp~L~kLGriLGpKGkMP~pK~GTVt~DI~~~I~~~k~G 322 (409)
+|||++|+ +++++ ||+||||++||+.|++||++||||||||+++.|||++||.++|+++++|
T Consensus 79 edLi~~i~-~g~~~~fd~~iA~~~~m~~l~~Lg~iLGprGlMP~~k~gTv~~di~~~I~~~k~G 141 (141)
T TIGR01170 79 DDLIKKIE-DGEIKPFDYLIAHPDIVPELAQLRRLLGPKGLMPSPKRGTVGDNLLSMIETFKKG 141 (141)
T ss_pred HHHHHHHh-cCCcccccEEEECHHHHHHHHHhhcccccCcCCCCCCCCCcccCHHHHHHHHhCc
Confidence 99999998 58999 9999999999999999999999999999999999999999999999876
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=2.8e-35 Score=275.79 Aligned_cols=185 Identities=29% Similarity=0.483 Sum_probs=159.7
Q ss_pred ccCCCccEEEEEEeCCCCCCCCCce-eeeEEcCCCCC-CCcEEEEEcCchhHHH---------HHHcCCCeeccHhHHHH
Q 015333 197 KATFDETVEAHVRLAIPPRKTELIV-RGTMNLPHGDK-KAVRVAFFAEGADAEE---------ARAAGADIVGGLELIEE 265 (409)
Q Consensus 197 k~kF~ETVeL~V~L~id~kK~~~~I-RG~V~LPH~~~-k~~kIcVFadd~~aee---------AkeaGAd~VGgeeLIek 265 (409)
..+++++|+|+|.+...+.+.+.++ +|.|.|||++. +..+||||++|++..+ +.++|++++|+++|+++
T Consensus 17 ~~~~~~~v~l~i~~~~~~~~~~~~~~~~~i~LPh~~~~~~~~vcli~~d~~~~~~~~~~~~~~~~~~~~~vi~~~~L~~~ 96 (220)
T PF00687_consen 17 DDNFDESVYLQITLKKIPKKKDKSFKPGRIPLPHPLYIKNSKVCLIVKDPQKKAKEKEKLEEKAVEAGAKVIGGEELKKK 96 (220)
T ss_dssp CSSSSTEEEEEEEESSSTTSSCTST-EEEEEBSTSSS-SSSBEEEEESCHHHHHH-------HHHHTTCSEEECHHHHHH
T ss_pred cCCCCcEEEEEEEeCcCCCccccccccceeeecCCCCCCccEEEEEecCcchhhhhhhhhhhhhhhcccceecHHHHHHH
Confidence 6789999999999966566656677 99999999998 8899999999876443 46789999999999999
Q ss_pred ---HHhcCcc--cccEEEEcCcchhhHHh-hhhhh-hcCCCCCCCCCCCccccHHHHHHHHHcCceEEEec-CCCeEEEE
Q 015333 266 ---IASSGKL--DVEKCFSTRQFMPRLFK-ISKIL-NQHGLMPNPKQGTVTNDVARAVQEAKQGHIKFKMD-NTSNVHAG 337 (409)
Q Consensus 266 ---I~~~~kL--~fD~fLAtpd~mp~L~k-LGriL-GpKGkMP~pK~GTVt~DI~~~I~~~k~Gsv~fr~~-k~g~i~V~ 337 (409)
+...+++ +||+||||+++++.|++ ||++| |++|+||++...+ .+||.+.|+++..+ +.|+.. ++++++|+
T Consensus 97 ~~~~~~~r~l~~~~d~flad~~i~~~l~~~Lgk~~~~~k~k~P~~v~~~-~~~l~~~i~~~~~~-~~~~~~~~~~~~~v~ 174 (220)
T PF00687_consen 97 YKTIEAKRKLAKSYDFFLADPRIMPKLPKLLGKIFYGKKGKMPIPVTLS-KEDLKEQIEKALNS-TKFRLSGKGGCISVK 174 (220)
T ss_dssp HCHHHHCHHHHHCSSEEEEEGGGHHHHHHHTHHHH-CCTTTSCEEBSSH-TSCHHHHHHHHHTE-EEEEETBTSSEEEEE
T ss_pred HHHHHHHHHHHhhcCEEEECHHHHHHHHHhhhhheecccCCcceEEecc-chhHHHHHHHHHCC-EEEEeeccCCeeecC
Confidence 5432333 99999999999999999 99999 9999999996332 37999999999954 567777 99999999
Q ss_pred ecccCCChHHHHHhHHHHHHHHHHhCCCCCCCCcccccceeEEEEecCCCCc
Q 015333 338 LGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPS 389 (409)
Q Consensus 338 IGklsms~eeL~ENI~Avi~aL~~~kP~~lKk~sk~~~nIksVyLkSTmGP~ 389 (409)
||+++|+++||+|||.+++++|.++ | +.++ |.||++|||+||||||
T Consensus 175 VG~~~~~~~~i~eNi~~~i~~i~~~-~--~~~g---~~~I~~i~ikst~s~~ 220 (220)
T PF00687_consen 175 VGHLSMTDEQIVENIKAVIKAIVSK-P--LPKG---WKNIKSIYIKSTMSPS 220 (220)
T ss_dssp EEETTSCHHHHHHHHHHHHHHHHHT-T--TSSS---SGSEEEEEEEESSSEE
T ss_pred ccCCCCCHHHHHHHHHHHHHHHHHh-h--hccC---cceEEEEEEECCCCCC
Confidence 9999999999999999999999998 2 2333 8999999999999986
No 12
>KOG1570 consensus 60S ribosomal protein L10A [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=3.8e-29 Score=233.58 Aligned_cols=200 Identities=24% Similarity=0.348 Sum_probs=179.2
Q ss_pred ccCHHHHHHHHHHHc----ccCCCccEEEEEEe-CCCCCCCCCceeeeEEcCCCCCCCcEEEEEcCchhHHHHHHcCCCe
Q 015333 182 VLDLMDAIKQVKANA----KATFDETVEAHVRL-AIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADI 256 (409)
Q Consensus 182 ~~~l~EAI~~lK~~a----k~kF~ETVeL~V~L-~id~kK~~~~IRG~V~LPH~~~k~~kIcVFadd~~aeeAkeaGAd~ 256 (409)
.+.+.+||+.+...+ .++|.+||+++++| |+|+.| +.++.|.+.|||..++..++|||++..++.+|++.|.+.
T Consensus 7 ~~~l~~~v~~i~~~~~~~k~~~~~~tielQi~Lk~ydp~K-dkr~s~~~~l~~~~~p~~k~cv~gd~~h~~~ak~~~~p~ 85 (218)
T KOG1570|consen 7 EEALREAVAEILLRSKEFKNRNFVETIELQINLKNYDPQK-DKRFSGSVKLPHAPRPKMKVCVIGDQQHCDEAKAIDLPA 85 (218)
T ss_pred HHHHHHHHHHHHhccccccCccceeeeeeeecccccChhH-hCcccceEecCCCCCccceeeeechHHHHHHhhcCCCCC
Confidence 456788888887554 68999999999999 999999 899999999999999999999999999999999999998
Q ss_pred eccHhHHHHHHhcCcc------cccEEEEcCcchhhHHh-hhhhhhcCCCCCCCCCCCccccHHHHHHHHHcCceEEEec
Q 015333 257 VGGLELIEEIASSGKL------DVEKCFSTRQFMPRLFK-ISKILNQHGLMPNPKQGTVTNDVARAVQEAKQGHIKFKMD 329 (409)
Q Consensus 257 VGgeeLIekI~~~~kL------~fD~fLAtpd~mp~L~k-LGriLGpKGkMP~pK~GTVt~DI~~~I~~~k~Gsv~fr~~ 329 (409)
.-.++| ++..++++| .||.|||+.+++.+|++ ||+.|...|++|+++. -.+|+.+.+++.+. +++|+++
T Consensus 86 m~~d~l-kklnk~Kklvkklakky~~flase~~ikQlpr~lgp~l~kaGkfps~l~--~~d~l~akv~evk~-t~k~q~k 161 (218)
T KOG1570|consen 86 MDIDAL-KKLNKNKKLVKKLAKKYDAFLASESLIKQLPRILGPGLSKAGKFPSLLV--HGDSLYAKVEEVKS-TIKFQMK 161 (218)
T ss_pred cCHHHH-hcCcccchHHHHHHHHhhhHHhhHHHHHHhhhhhcccccccccCCcccc--chHHHHHHHHHHHh-hHHHHHH
Confidence 886554 555444444 79999999999999999 8999999999999994 45899999999985 6899999
Q ss_pred CCCeEEEEecccCCChHHHHHhHHHHHHHHHHhCCCCCCCCcccccceeEEEEecCCCCceEEe
Q 015333 330 NTSNVHAGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGPSFPVS 393 (409)
Q Consensus 330 k~g~i~V~IGklsms~eeL~ENI~Avi~aL~~~kP~~lKk~sk~~~nIksVyLkSTmGP~i~I~ 393 (409)
+.-|++|.||++.|++++|++||.-.++++++- +|++ |+|++++||+||||++.++|
T Consensus 162 kvKOGavaVGhv~M~d~el~~nI~l~vnFlVSl----LKkn---wQNvral~iKst~g~p~~ly 218 (218)
T KOG1570|consen 162 KVLCLAVAVGHVGMTDEELVYNIHLAVNFLVSL----LKKN---WQNVRALYIKSTMGKPQRLY 218 (218)
T ss_pred hhhheeeeecCCCCCHHHHHHhhhhhhhhHHHH----Hhhc---ccchhheeeccCCCCceecC
Confidence 999999999999999999999999999999995 6776 99999999999999998875
No 13
>KOG1685 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.74 E-value=2.4e-18 Score=172.07 Aligned_cols=156 Identities=20% Similarity=0.337 Sum_probs=134.1
Q ss_pred CCcEEEEEcCchhH-----HHH----HHcCCC----eeccHhHHHHHHh---cCcc--cccEEEEcCcchhhHHh-hhhh
Q 015333 233 KAVRVAFFAEGADA-----EEA----RAAGAD----IVGGLELIEEIAS---SGKL--DVEKCFSTRQFMPRLFK-ISKI 293 (409)
Q Consensus 233 k~~kIcVFadd~~a-----eeA----keaGAd----~VGgeeLIekI~~---~~kL--~fD~fLAtpd~mp~L~k-LGri 293 (409)
+...||+|++|.+. +.| .+.|.. +++..+|..++++ .++| +||+|||+.++++.|++ |||.
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 46789999999642 223 457877 7889999877765 3445 89999999999999999 8999
Q ss_pred hhcCCCCCCCCCCCcccc--HHHHHHHHHcCceEEEecCCCeEEEEecccCCChHHHHHhHHHHHHHHHHhCCCCCCCCc
Q 015333 294 LNQHGLMPNPKQGTVTND--VARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTS 371 (409)
Q Consensus 294 LGpKGkMP~pK~GTVt~D--I~~~I~~~k~Gsv~fr~~k~g~i~V~IGklsms~eeL~ENI~Avi~aL~~~kP~~lKk~s 371 (409)
|..+.+.|.+.+-. ..+ +..+|+++. |.+.|++..+.|..+.||+++|+.++|.|||.++++.|....|.+
T Consensus 167 f~q~kk~Pv~i~l~-k~~~~l~~qi~~a~-~~t~~~~~~g~~~~i~vg~l~~~~~~l~ENv~~vlk~l~e~~P~~----- 239 (343)
T KOG1685|consen 167 FYQKKKVPVSIRLS-KKNELLKQQIENAC-GSTYFRLRKGTSSAIKVGHLGNTSEELAENVVAVLKGLSEILPGG----- 239 (343)
T ss_pred hcccccCceEEEec-ccchHHHHHHHHHh-hhheeeccCCceeEEEeccccccHHHHHHHHHHHHHHHHHHccch-----
Confidence 99999999998533 234 899999999 678899998889999999999999999999999999999888877
Q ss_pred ccccceeEEEEecCCCCceEEehhhh
Q 015333 372 KFAGYVNSFHMCSTMGPSFPVSIQSL 397 (409)
Q Consensus 372 k~~~nIksVyLkSTmGP~i~I~~~~~ 397 (409)
|.||+++||++..++++|||.+..
T Consensus 240 --~~~Irsl~lKt~~s~aLPly~s~~ 263 (343)
T KOG1685|consen 240 --WKNIRSLHLKTSRSPALPLYVSVI 263 (343)
T ss_pred --HhHhHHHhhhccCCcccceeeccc
Confidence 999999999999999999998754
No 14
>PF13003 MRL1: Ribosomal protein L1; InterPro: IPR024663 This entry represents a ribosomal protein L1 domain found mainly in chordates.
Probab=95.89 E-value=0.014 Score=52.45 Aligned_cols=62 Identities=19% Similarity=0.208 Sum_probs=48.4
Q ss_pred CCCccCHHHHHHHHHHHcc---cCCCccEEEEEEeCCCCC--CCCCceeeeEEcCCCCCCC-cEEEEE
Q 015333 179 SRPVLDLMDAIKQVKANAK---ATFDETVEAHVRLAIPPR--KTELIVRGTMNLPHGDKKA-VRVAFF 240 (409)
Q Consensus 179 ~~~~~~l~EAI~~lK~~ak---~kF~ETVeL~V~L~id~k--K~~~~IRG~V~LPH~~~k~-~kIcVF 240 (409)
.++.|.++.||.+|+.+.. +...|.|.+.++|++... |.-.++-+.|.|||++..+ .+|+||
T Consensus 66 Pr~Iyeve~Ai~mLKkfQ~lDfT~pkQ~VYldL~Ldm~l~KKkkVePF~s~i~lPypF~~eiNKv~VF 133 (133)
T PF13003_consen 66 PRPIYEVEKAIDMLKKFQILDFTSPKQPVYLDLTLDMKLEKKKKVEPFASVILLPYPFTSEINKVLVF 133 (133)
T ss_pred cccHHHHHHHHHHHHhcccccCCCCCCcEEEeeeehhhhccccccCCCccceecccccccccceeeeC
Confidence 3578999999999999874 455678999999966543 3345888999999999644 588887
No 15
>PTZ00029 60S ribosomal protein L10a; Provisional
Probab=68.50 E-value=3.1 Score=40.09 Aligned_cols=21 Identities=29% Similarity=0.325 Sum_probs=18.0
Q ss_pred HhhhhhhhcCCCCCCCCCCCcc
Q 015333 288 FKISKILNQHGLMPNPKQGTVT 309 (409)
Q Consensus 288 ~kLGriLGpKGkMP~pK~GTVt 309 (409)
+.||++||| |+||++|.||+.
T Consensus 117 ~~l~riLGp-~l~p~~K~P~~v 137 (216)
T PTZ00029 117 PQIPRLLGP-GLNKAGKFPTLI 137 (216)
T ss_pred HHHHHHhcc-ccccCCCCCCcc
Confidence 448999999 999999998753
No 16
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=55.26 E-value=36 Score=29.35 Aligned_cols=86 Identities=13% Similarity=0.149 Sum_probs=58.1
Q ss_pred EEEEEcCchhHHHHHHcCCC---eeccHhHHHHHHhcCcc---cccEEEEcCcchhhHH-hhhhhhhcCCCCCCCC----
Q 015333 236 RVAFFAEGADAEEARAAGAD---IVGGLELIEEIASSGKL---DVEKCFSTRQFMPRLF-KISKILNQHGLMPNPK---- 304 (409)
Q Consensus 236 kIcVFadd~~aeeAkeaGAd---~VGgeeLIekI~~~~kL---~fD~fLAtpd~mp~L~-kLGriLGpKGkMP~pK---- 304 (409)
+|+|+.+.+..---+.+|.+ .+..++..+++.. .+ +|-+++.|.++...++ .+-..+. ....|.-.
T Consensus 4 kIaVvGd~DtilGFrlaGi~~v~~~~~~e~~~~~~~--~l~~~~~gII~iTE~~a~~i~~~~i~~~~-~~~~P~II~Ipi 80 (104)
T PRK01189 4 CITVIGERDVVLGFRLLGIGDTIEAEGKDLVKKFLE--IFNNPKCKYIFVSESTKNMFDKNTLRSLE-SSSKPLVVFIPL 80 (104)
T ss_pred eEEEEcCHHHHHHHHHcCCceEEEcCCHHHHHHHHH--HHhcCCeEEEEEEHHHHhhCCHHHHHHHh-ccCCCeEEEEeC
Confidence 79999998877777788996 3455565556542 33 7999999999999998 3444444 45555433
Q ss_pred CCCc-cccHHHHHHHHHcCceEE
Q 015333 305 QGTV-TNDVARAVQEAKQGHIKF 326 (409)
Q Consensus 305 ~GTV-t~DI~~~I~~~k~Gsv~f 326 (409)
+|+- .+.|.+.|+++. | +..
T Consensus 81 pg~~~~~~i~~~ik~ai-G-vd~ 101 (104)
T PRK01189 81 PGISEEESIEEMAKRIL-G-IDI 101 (104)
T ss_pred CCCccchhHHHHHHHHh-c-ccc
Confidence 2321 246888999887 6 443
No 17
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=53.30 E-value=79 Score=26.80 Aligned_cols=84 Identities=18% Similarity=0.239 Sum_probs=54.4
Q ss_pred cEEEEEcCchhHHHHHHcCCC-e--ecc-HhHHHHHHh-cCcccccEEEEcCcchhhHHh-hhhhhhcCCCCCC----C-
Q 015333 235 VRVAFFAEGADAEEARAAGAD-I--VGG-LELIEEIAS-SGKLDVEKCFSTRQFMPRLFK-ISKILNQHGLMPN----P- 303 (409)
Q Consensus 235 ~kIcVFadd~~aeeAkeaGAd-~--VGg-eeLIekI~~-~~kL~fD~fLAtpd~mp~L~k-LGriLGpKGkMP~----p- 303 (409)
.||+|+++.+.+.--+-+|++ + +.. +++.+.|.+ -..=+|.+++.|.++...+.. +.+.+.. ...|. |
T Consensus 1 mkIaVIGD~dtv~GFrLaGi~~~~~~~~~ee~~~~l~~l~~~~d~gII~Ite~~~~~i~e~i~~~~~~-~~~P~ii~IP~ 79 (100)
T PRK02228 1 MEIAVIGSPEFTTGFRLAGIRKVYEVPDDEKLDEAVEEVLEDDDVGILVMHDDDLEKLPRRLRRTLEE-SVEPTVVTLGG 79 (100)
T ss_pred CEEEEEeCHHHHHHHHHcCCceEEeeCCHHHHHHHHHHHhhCCCEEEEEEehhHhHhhHHHHHHHHhc-CCCCEEEEECC
Confidence 379999997767777888997 2 344 344444432 012279999999999998877 6664432 23332 2
Q ss_pred CCCCccccHHHHHHHHHcC
Q 015333 304 KQGTVTNDVARAVQEAKQG 322 (409)
Q Consensus 304 K~GTVt~DI~~~I~~~k~G 322 (409)
..| ++.+.+.|+++. |
T Consensus 80 ~~~--~~~i~~~v~raI-G 95 (100)
T PRK02228 80 GGG--SGGLREKIKRAI-G 95 (100)
T ss_pred Ccc--chHHHHHHHHHh-C
Confidence 223 256888888887 6
No 18
>PRK01395 V-type ATP synthase subunit F; Provisional
Probab=51.43 E-value=83 Score=27.04 Aligned_cols=85 Identities=19% Similarity=0.339 Sum_probs=55.6
Q ss_pred cEEEEEcCchhHHHHHHcCCCee---ccHhHHHHHHhcCcccccEEEEcCcchhhHHh-hhhhhhcCCCCCC----C-CC
Q 015333 235 VRVAFFAEGADAEEARAAGADIV---GGLELIEEIASSGKLDVEKCFSTRQFMPRLFK-ISKILNQHGLMPN----P-KQ 305 (409)
Q Consensus 235 ~kIcVFadd~~aeeAkeaGAd~V---GgeeLIekI~~~~kL~fD~fLAtpd~mp~L~k-LGriLGpKGkMP~----p-K~ 305 (409)
.+|+|++|.+.+.--+-+|++.+ ..+++.+.+.+-..=+|-+++.|.++...+.. +.+. . ...+|. | +.
T Consensus 4 ~kIaVIGD~dtv~GFrLaGi~~~~v~~~ee~~~~i~~l~~~d~gII~Ite~~a~~i~~~i~~~-~-~~~~P~Il~IP~~~ 81 (104)
T PRK01395 4 YKIGVVGDKDSILPFKALGIDVFPVIDEQEAINTLRKLAMEDYGIIYITEQIAADIPETIERY-D-NQVLPAIILIPSNQ 81 (104)
T ss_pred eeEEEEECHHHHHHHHHcCCeeEEecChHHHHHHHHHHhcCCcEEEEEcHHHHHHhHHHHHHh-c-CCCCCEEEEeCCCC
Confidence 47999999776666777898743 44555444442011279999999999999977 5544 3 334432 2 35
Q ss_pred CCcc---ccHHHHHHHHHcC
Q 015333 306 GTVT---NDVARAVQEAKQG 322 (409)
Q Consensus 306 GTVt---~DI~~~I~~~k~G 322 (409)
|+.. +.|.+.|+++. |
T Consensus 82 g~~~~g~~~i~~~v~kAI-G 100 (104)
T PRK01395 82 GSLGIGLSRIQDNVEKAV-G 100 (104)
T ss_pred CCccccHHHHHHHHHHHh-C
Confidence 6543 35888888887 5
No 19
>COG1064 AdhP Zn-dependent alcohol dehydrogenases [General function prediction only]
Probab=45.15 E-value=44 Score=34.64 Aligned_cols=58 Identities=21% Similarity=0.145 Sum_probs=39.0
Q ss_pred cEEEEEcCch-hHHHHHHcCCCeecc---HhHHHHHHhcCcccccEEEEcCcchhhHHhhhhhhhcC
Q 015333 235 VRVAFFAEGA-DAEEARAAGADIVGG---LELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQH 297 (409)
Q Consensus 235 ~kIcVFadd~-~aeeAkeaGAd~VGg---eeLIekI~~~~kL~fD~fLAtpd~mp~L~kLGriLGpK 297 (409)
.+|.+|+.++ ..+.|++.||+++-. ++..+.++. .||.+|.|-. -..+...-+.|.+.
T Consensus 191 a~Via~~~~~~K~e~a~~lGAd~~i~~~~~~~~~~~~~----~~d~ii~tv~-~~~~~~~l~~l~~~ 252 (339)
T COG1064 191 AEVIAITRSEEKLELAKKLGADHVINSSDSDALEAVKE----IADAIIDTVG-PATLEPSLKALRRG 252 (339)
T ss_pred CeEEEEeCChHHHHHHHHhCCcEEEEcCCchhhHHhHh----hCcEEEECCC-hhhHHHHHHHHhcC
Confidence 5788887764 467788999987643 556666642 2999999887 66665544555444
No 20
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=40.84 E-value=17 Score=35.06 Aligned_cols=20 Identities=20% Similarity=0.145 Sum_probs=16.9
Q ss_pred HhhhhhhhcCCCCCCCCCCCc
Q 015333 288 FKISKILNQHGLMPNPKQGTV 308 (409)
Q Consensus 288 ~kLGriLGpKGkMP~pK~GTV 308 (409)
+.|||+|||++. |++|.||+
T Consensus 115 ~~lgk~LGp~~~-p~gK~P~~ 134 (214)
T PTZ00225 115 KTVPRLVGPHMH-RMGKFPTV 134 (214)
T ss_pred HhhhhhcCCCCC-cCCCCCcc
Confidence 448999999986 99998884
No 21
>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=33.64 E-value=1.3e+02 Score=25.24 Aligned_cols=63 Identities=10% Similarity=0.037 Sum_probs=39.0
Q ss_pred CcEEEEEcCchh---------HHHHHHcCCCeeccHhHHHHHHhcCcccccEEEEcCcchhhHHhhhhhhhcC
Q 015333 234 AVRVAFFAEGAD---------AEEARAAGADIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQH 297 (409)
Q Consensus 234 ~~kIcVFadd~~---------aeeAkeaGAd~VGgeeLIekI~~~~kL~fD~fLAtpd~mp~L~kLGriLGpK 297 (409)
..+|+++|..-. .+.|++.|.++--..-=+.++.. .--+||++|.+|.+.-.+..+.+.+...
T Consensus 3 ~~~ILl~C~~G~sSS~l~~k~~~~~~~~gi~~~v~a~~~~~~~~-~~~~~Dvill~pqi~~~~~~i~~~~~~~ 74 (95)
T TIGR00853 3 ETNILLLCAAGMSTSLLVNKMNKAAEEYGVPVKIAAGSYGAAGE-KLDDADVVLLAPQVAYMLPDLKKETDKK 74 (95)
T ss_pred ccEEEEECCCchhHHHHHHHHHHHHHHCCCcEEEEEecHHHHHh-hcCCCCEEEECchHHHHHHHHHHHhhhc
Confidence 457888988521 24567788765211111122321 1126899999999998888888777554
No 22
>COG1436 NtpG Archaeal/vacuolar-type H+-ATPase subunit F [Energy production and conversion]
Probab=27.60 E-value=1.9e+02 Score=25.04 Aligned_cols=84 Identities=15% Similarity=0.270 Sum_probs=52.3
Q ss_pred cEEEEEcCchhHHHHHHcCCCe---eccHh-HHHHHHh--cCcccccEEEEcCcchhhHHh-hhhhhhcC--C---CCCC
Q 015333 235 VRVAFFAEGADAEEARAAGADI---VGGLE-LIEEIAS--SGKLDVEKCFSTRQFMPRLFK-ISKILNQH--G---LMPN 302 (409)
Q Consensus 235 ~kIcVFadd~~aeeAkeaGAd~---VGgee-LIekI~~--~~kL~fD~fLAtpd~mp~L~k-LGriLGpK--G---kMP~ 302 (409)
.+|||+.+.+-+.--+-+|+.. +..++ ++.+... .+. +|+++|-|.+++..+.. +.+..... - ..|+
T Consensus 3 ~~I~VIGd~dtvtGFrLaGv~~~~v~~~~~~~~~~~~~~l~~~-~~~iIiite~~a~~i~~~i~~~~~~~~~P~iv~IPs 81 (104)
T COG1436 3 MKIAVIGDRDTVTGFRLAGVRVVYVADDEEDELRAALRVLAED-DVGIILITEDLAEKIREEIRRIIRSSVLPAIVEIPS 81 (104)
T ss_pred eEEEEEEccchhhceeeecceeEEEecChhHHHHHHHHhhccC-CceEEEEeHHHHhhhHHHHHHHhhccCccEEEEeCC
Confidence 4799999988655555567764 34433 2333322 223 99999999999999987 66663111 0 1455
Q ss_pred CCCCCccccHHHHHHHHH
Q 015333 303 PKQGTVTNDVARAVQEAK 320 (409)
Q Consensus 303 pK~GTVt~DI~~~I~~~k 320 (409)
+ ...-.+.+.+.|+++.
T Consensus 82 ~-~~~~~~~~~~~I~k~v 98 (104)
T COG1436 82 P-GKEEEEPLRELIRRAV 98 (104)
T ss_pred C-CCCccchHHHHHHHHH
Confidence 3 2222367888888876
No 23
>PRK13958 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional
Probab=25.91 E-value=42 Score=31.99 Aligned_cols=25 Identities=20% Similarity=0.189 Sum_probs=23.0
Q ss_pred cEEEEEcCchhHHHHHHcCCCeecc
Q 015333 235 VRVAFFAEGADAEEARAAGADIVGG 259 (409)
Q Consensus 235 ~kIcVFadd~~aeeAkeaGAd~VGg 259 (409)
.|||=+++-++++.|.++|||++|.
T Consensus 3 vKICGit~~eda~~~~~~GaD~iGf 27 (207)
T PRK13958 3 LKFCGFTTIKDVTAASQLPIDAIGF 27 (207)
T ss_pred EEEcCCCcHHHHHHHHHcCCCEEEE
Confidence 6899999999999999999999985
No 24
>PF12270 Cyt_c_ox_IV: Cytochrome c oxidase subunit IV; InterPro: IPR021050 This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. This family is the fourth subunit of the cytochrome c oxidase complex. This subunit does not have a catalytic capacity but instead, is required for assembly and/or stability of the complex []. ; GO: 0004129 cytochrome-c oxidase activity, 0055114 oxidation-reduction process, 0016021 integral to membrane
Probab=24.27 E-value=42 Score=30.62 Aligned_cols=16 Identities=38% Similarity=0.509 Sum_probs=13.8
Q ss_pred CcccCCCCCCCCCCCC
Q 015333 117 SRVAPLPEAGEPASGE 132 (409)
Q Consensus 117 ~~~~~~~~~~~~~~~~ 132 (409)
.|+-++|||++.+|.+
T Consensus 60 rr~~~rPED~~daEI~ 75 (137)
T PF12270_consen 60 RRIGPRPEDREDAEIA 75 (137)
T ss_pred hhCCCCCccccccccc
Confidence 4688999999999777
No 25
>COG0135 TrpF Phosphoribosylanthranilate isomerase [Amino acid transport and metabolism]
Probab=22.63 E-value=53 Score=31.77 Aligned_cols=25 Identities=36% Similarity=0.501 Sum_probs=22.8
Q ss_pred CcEEEEEcCchhHHHHHHcCCCeec
Q 015333 234 AVRVAFFAEGADAEEARAAGADIVG 258 (409)
Q Consensus 234 ~~kIcVFadd~~aeeAkeaGAd~VG 258 (409)
..|||=++.-++++.|.++||+++|
T Consensus 3 ~vKICGlt~~eda~~a~~~gad~iG 27 (208)
T COG0135 3 KVKICGLTRLEDAKAAAKAGADYIG 27 (208)
T ss_pred ceEECCCCCHHHHHHHHHcCCCEEE
Confidence 4689999999999999999999988
No 26
>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=22.50 E-value=2.2e+02 Score=24.35 Aligned_cols=59 Identities=14% Similarity=0.153 Sum_probs=39.1
Q ss_pred EEEEEcCchh---------HHHHHHcCCCe----eccHhHHHHHHhcCcccccEEEEcCcchhhHHhhhhhhhcCCC
Q 015333 236 RVAFFAEGAD---------AEEARAAGADI----VGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGL 299 (409)
Q Consensus 236 kIcVFadd~~---------aeeAkeaGAd~----VGgeeLIekI~~~~kL~fD~fLAtpd~mp~L~kLGriLGpKGk 299 (409)
+|+++|.+-. .+.|++.|.++ ++..++- .. .-+||++|.+|.+--.+..+.+.+.++|.
T Consensus 2 ~Ill~C~~GaSSs~la~km~~~a~~~gi~~~i~a~~~~e~~-~~----~~~~Dvill~PQv~~~~~~i~~~~~~~~i 73 (99)
T cd05565 2 NVLVLCAGGGTSGLLANALNKGAKERGVPLEAAAGAYGSHY-DM----IPDYDLVILAPQMASYYDELKKDTDRLGI 73 (99)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEeeHHHHH-Hh----ccCCCEEEEcChHHHHHHHHHHHhhhcCC
Confidence 5888886411 24577888875 2333322 11 12799999999998888888888877543
No 27
>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=22.20 E-value=3.2e+02 Score=25.05 Aligned_cols=35 Identities=20% Similarity=0.366 Sum_probs=28.6
Q ss_pred CcEEEEEcCchh-HHHHHHcCCCeeccHhHHHHHHh
Q 015333 234 AVRVAFFAEGAD-AEEARAAGADIVGGLELIEEIAS 268 (409)
Q Consensus 234 ~~kIcVFadd~~-aeeAkeaGAd~VGgeeLIekI~~ 268 (409)
...|+|.+.|.. ...|+..||..+..++|+..+..
T Consensus 94 ~~~v~VVTSD~~iq~~~~~~GA~~iss~ef~~~l~~ 129 (166)
T PF05991_consen 94 PRQVTVVTSDREIQRAARGRGAKRISSEEFLRELKA 129 (166)
T ss_pred CCeEEEEeCCHHHHHHHhhCCCEEEcHHHHHHHHHH
Confidence 368999999854 45678899999999999988864
No 28
>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=21.47 E-value=70 Score=29.95 Aligned_cols=25 Identities=32% Similarity=0.353 Sum_probs=20.0
Q ss_pred cEEEEEcCchhHHHHHHcCCCeecc
Q 015333 235 VRVAFFAEGADAEEARAAGADIVGG 259 (409)
Q Consensus 235 ~kIcVFadd~~aeeAkeaGAd~VGg 259 (409)
.|||=++..+++..|.++|++++|.
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 4899999999999999999999996
Done!