Query psy998
Match_columns 380
No_of_seqs 222 out of 1111
Neff 5.7
Searched_HMMs 46136
Date Sat Aug 17 00:35:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy998.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/998hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3015|consensus 100.0 2.8E-51 6.1E-56 387.3 16.6 175 195-369 44-283 (283)
2 COG5387 Chaperone required for 100.0 8.9E-45 1.9E-49 337.5 13.6 167 195-361 32-259 (264)
3 TIGR01049 rpsJ_bact ribosomal 100.0 2.3E-29 5E-34 209.6 10.7 98 48-149 1-98 (99)
4 PRK00596 rpsJ 30S ribosomal pr 100.0 2.5E-29 5.5E-34 210.5 10.7 99 47-149 3-101 (102)
5 CHL00135 rps10 ribosomal prote 100.0 1.1E-28 2.5E-33 205.9 10.7 96 47-146 6-101 (101)
6 COG0051 RpsJ Ribosomal protein 100.0 1.6E-28 3.4E-33 204.5 11.2 101 47-151 3-103 (104)
7 KOG3321|consensus 99.9 2.4E-29 5.2E-34 222.1 -0.3 124 42-166 41-164 (175)
8 PF00338 Ribosomal_S10: Riboso 99.9 5.1E-27 1.1E-31 193.8 12.1 97 50-150 1-97 (97)
9 PRK12271 rps10p 30S ribosomal 99.9 2.9E-26 6.2E-31 191.8 13.0 99 48-151 2-101 (102)
10 TIGR01046 S10_Arc_S20_Euk ribo 99.9 8.2E-26 1.8E-30 188.2 12.6 98 48-150 1-99 (99)
11 PTZ00039 40S ribosomal protein 99.9 9.6E-26 2.1E-30 192.1 12.4 100 46-150 15-115 (115)
12 PF07542 ATP12: ATP12 chaperon 99.9 1.2E-25 2.7E-30 193.8 4.4 87 196-287 1-89 (122)
13 KOG4060|consensus 99.9 2E-22 4.2E-27 176.5 8.4 136 35-173 36-175 (176)
14 KOG0900|consensus 99.4 7.2E-14 1.6E-18 119.0 2.4 102 45-151 17-119 (121)
15 COG1638 DctP TRAP-type C4-dica 50.6 93 0.002 31.4 9.0 111 208-323 146-299 (332)
16 PF01781 Ribosomal_L38e: Ribos 36.0 1.2E+02 0.0025 24.1 5.5 47 93-147 21-67 (69)
17 PF14277 DUF4364: Domain of un 35.4 37 0.0008 30.9 3.0 43 206-248 109-152 (163)
18 PF11469 Ribonucleas_3_2: Ribo 31.4 49 0.0011 28.4 2.9 21 307-327 64-84 (120)
19 PF06236 MelC1: Tyrosinase co- 30.1 24 0.00051 31.0 0.8 37 208-244 68-115 (125)
20 PF01929 Ribosomal_L14e: Ribos 26.8 63 0.0014 26.0 2.7 33 320-357 28-60 (77)
21 KOG3499|consensus 26.0 3.1E+02 0.0066 21.4 6.1 37 107-147 31-67 (69)
No 1
>KOG3015|consensus
Probab=100.00 E-value=2.8e-51 Score=387.32 Aligned_cols=175 Identities=49% Similarity=0.799 Sum_probs=170.9
Q ss_pred CCccceeeeeEEeC--CcEEEEeCCCcCCCCCCCeeeeCcHHHHHHHHHHHhhcc-cccCCCcccc--------------
Q psy998 195 PKRFYKKVGILESN--GDYEISLDHRKLKTPNGVLFKVSSEPLALAIAAEWDAQH-ETIQRSTMHL-------------- 257 (380)
Q Consensus 195 ~kRFyk~v~v~~~~--gg~~V~LDgR~lkTP~~~~l~vPs~~LA~aiA~EW~~Q~-e~I~p~~MPL-------------- 257 (380)
.|||||+|++...+ |||.|.||||++|||.|+++.||+++||.+||.||+.|. +.|+|++|||
T Consensus 44 ~krF~kkvs~~~g~~~g~~~v~LD~R~lKTP~g~~f~v~s~~LA~~ia~Ewdsq~s~~i~~~~mplt~L~~taid~~~~~ 123 (283)
T KOG3015|consen 44 SKRFYKKVSTLTGDAFGGQEVQLDGRTLKTPKGNPFKVRSEKLAIAIALEWDSQKSTSIRPFTMPLTSLVFTAIDNPSEL 123 (283)
T ss_pred HHHHHhhhhheecccCCceEEecccccccCCCCCeeecccHHHHHHHHHHHhhcccccccccccHHHHHHHHHhhccCcc
Confidence 58999999998876 999999999999999999999999999999999999998 8999999999
Q ss_pred ------------------------------------------------ccCceeeeecCCCCCCCCHHHHHHHHHHHhcC
Q psy998 258 ------------------------------------------------RYNTSISYSNDIAGPSVDPKDRATIQRHFLSY 289 (380)
Q Consensus 258 ------------------------------------------------~~gv~l~~~~gi~~~~q~~~~~~~l~~~l~~l 289 (380)
+|||++.++++|+++.|++.+++++++||.++
T Consensus 124 ~kd~i~~~llrfldtDTvlf~~pe~e~l~~l~~~Q~e~w~Plie~~e~~lgvkl~~~~~I~~~~q~e~~ke~i~~~l~s~ 203 (283)
T KOG3015|consen 124 NKDTISNQLLRFLDTDTVLFFSPESEDLGRLRDLQVEEWDPLIEWFENRLGVKLQPSDNILGGKQAEKDKEAIDKWLSSL 203 (283)
T ss_pred cHHHHHHHHHHHhccCeEEEecCChhhhhHHHHHHHHhhHHHHHHHHHHhCcceeecccccCCcccHHHHHHHHHHHHhc
Confidence 79999999999999999999999999999999
Q ss_pred ChhhhHHHHHHHHhhhHHHHHHHHHcCCCCHHHHHHHhhhhHHHhhhhhcCcCCCcCHhHHHHHHHHHHHHHHHHhcccc
Q psy998 290 NFETVMGVNFAVETLKSIVLTLACIDRKLSIEEAVHLSKLEEEYQIGHWGRVEWAHDLHQQELQARLAAAIFYVHVNTLK 369 (380)
Q Consensus 290 ~~~~L~al~~~~~~~kS~vlalal~~g~l~~e~A~~~a~lEe~~Q~~~WG~VE~~HD~e~~~~~~~l~aa~lf~~l~~~~ 369 (380)
|+|+|+||+.+|..+||||||+++++|++++|+|+++|||||+||+++||+|||+||+|.+|++++++||.+|+++++++
T Consensus 204 n~w~Lagle~~v~s~KSfVia~~ii~~~l~~d~Av~larLEe~yQvekWG~VEwaHdi~~~eL~~r~~aa~lf~~l~~~~ 283 (283)
T KOG3015|consen 204 NFWALAGLEFAVASLKSFVIALGIIEGKLDVDKAVALARLEEEYQVEKWGNVEWAHDIEKQELRARLSAATLFVHLNSEN 283 (283)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHhcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999854
No 2
>COG5387 Chaperone required for the assembly of the mitochondrial F1-ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.9e-45 Score=337.47 Aligned_cols=167 Identities=31% Similarity=0.465 Sum_probs=159.3
Q ss_pred CCccceeeeeEEeC-CcEEEEeCCCcCCCCCCCeeeeCcHHHHHHHHHHHhhcccccCCCcccc----------------
Q psy998 195 PKRFYKKVGILESN-GDYEISLDHRKLKTPNGVLFKVSSEPLALAIAAEWDAQHETIQRSTMHL---------------- 257 (380)
Q Consensus 195 ~kRFyk~v~v~~~~-gg~~V~LDgR~lkTP~~~~l~vPs~~LA~aiA~EW~~Q~e~I~p~~MPL---------------- 257 (380)
+|||||++++.+.+ |||.|+||||++|||.|++|+||+++||+.||.||++|.+.|+|+.||+
T Consensus 32 pkrfyk~a~aa~ve~Gg~aiqLDGR~~KtPa~k~l~vpt~~LA~lla~EWdaqs~~I~~~~mP~TrlV~taID~ia~~~~ 111 (264)
T COG5387 32 PKRFYKKATAADVEKGGFAIQLDGRTLKTPAGKPLVVPTEALAYLLALEWDAQSESIDPHSMPLTRLVNTAIDGIAEDSQ 111 (264)
T ss_pred hHHHHHHhhcCccccCceEEEeCCCCCCCCCCCceeCcHHHHHHHHHHHhhcchhccCcccCcHHHHHHHHHHhhcccHH
Confidence 89999999999865 9999999999999999999999999999999999999999999999999
Q ss_pred ------------------------------------------ccCceeeeecCCCCCCCCHHHHHHHHHHHhcC-Chhhh
Q psy998 258 ------------------------------------------RYNTSISYSNDIAGPSVDPKDRATIQRHFLSY-NFETV 294 (380)
Q Consensus 258 ------------------------------------------~~gv~l~~~~gi~~~~q~~~~~~~l~~~l~~l-~~~~L 294 (380)
.+|++|...+|+++..||++++++++.++.++ +||+|
T Consensus 112 ~v~~~ilrf~~tDlLcYra~sp~eLv~rQ~e~w~Piidw~e~~lg~rf~~vdgvih~~Qp~E~va~~a~~l~s~~sp~~L 191 (264)
T COG5387 112 AVFEQILRFLDTDLLCYRAESPFELVERQNENWDPIIDWAENFLGARFILVDGVIHGEQPREAVAAFAVKLMSLDSPWAL 191 (264)
T ss_pred HHHHHHHHHccCCeeEecCCCHHHHHHHHHhhhHHHHHHHHHhhCceEEeehhhhcCCCcHHHHHHHHHHHhhcCCHHHH
Confidence 58999999999999999999999999999999 56999
Q ss_pred HHHHHHHHhhhHHHHHHHHHcCCCCHHHHHHHhhhhHHHhhhhhc-CcCCCcCHhHHHHHHHHHHHHH
Q psy998 295 MGVNFAVETLKSIVLTLACIDRKLSIEEAVHLSKLEEEYQIGHWG-RVEWAHDLHQQELQARLAAAIF 361 (380)
Q Consensus 295 ~al~~~~~~~kS~vlalal~~g~l~~e~A~~~a~lEe~~Q~~~WG-~VE~~HD~e~~~~~~~l~aa~l 361 (380)
+||+.+|.++||+|||+|+.+|.++.|+||++|+|||+||+|+|| .+|+.||.+..++++.+.+.++
T Consensus 192 A~l~~~~sl~gS~Il~lal~~g~l~~e~a~ala~lde~~q~EqWG~d~Ea~~r~~~r~i~~~i~~r~i 259 (264)
T COG5387 192 AALETMVSLTGSFILALALLEGELSAEKAWALAHLDEDWQAEQWGSDEEATERRKNRLIEMAIAARVI 259 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCcccHHHHHHHHhHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999 7788889999988888876654
No 3
>TIGR01049 rpsJ_bact ribosomal protein S10, bacterial/organelle. This model describes bacterial 30S ribosomal protein S10. In species that have a transcription antitermination complex, or N utilization substance, with NusA, NusB, NusG, and NusE, this ribosomal protein is responsible for NusE activity. Included in the family are one member each from Saccharomyces cerevisiae and Schizosaccharomyces pombe. These proteins lack an N-terminal mitochondrial transit peptide but contain additional sequence C-terminal to the ribosomal S10 protein region.
Probab=99.96 E-value=2.3e-29 Score=209.64 Aligned_cols=98 Identities=28% Similarity=0.435 Sum_probs=94.6
Q ss_pred eEEEEEEEEcChhhHHHHHHHHHHHHHHcCCeecccccCCceeeEEEEEecccCCCcccceeeEEEEEEEEEEEecCCHH
Q psy998 48 SRICCELRANDPEVMNSYSKFATAAAQHLNIEIGECYAQKKAHHERYTLLRSVHVVKRCRVQYEVRTYFRWMNFHKLTGS 127 (380)
Q Consensus 48 ~~I~I~LkS~D~~~Le~~~~~I~~~ak~l~i~v~g~~a~LPTk~~~~TvlRSPhv~KKSreqFElrtykR~I~I~~~~~~ 127 (380)
++|+|+|+|||...||+|+++|.++|+.+|++++||+ ||||++++||++||||+|||||||||+|+|+|+|+|.++++.
T Consensus 1 ~~irI~l~s~d~~~L~~~~~~i~~~a~~~gi~~~gpi-~LPtk~~~~tvlrSPhv~kksreqfE~r~hkR~i~i~~~~~~ 79 (99)
T TIGR01049 1 QKIRIKLKSYDHRLLDQSTKKIVETAKRTGAQVKGPI-PLPTKKERYTVLRSPHVNKDSREQFEIRTHKRLIDIIDPNPK 79 (99)
T ss_pred CeEEEEEEECCHHHHHHHHHHHHHHHHHcCCceeccc-CCCCEEEEEEEeeCCCCCCCHHHHhhhhhheEEEEEeCCCHH
Confidence 4799999999999999999999999999999999999 999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHccCCCCceEEEE
Q psy998 128 TADTFLEYIQRNLPEGVALKVT 149 (380)
Q Consensus 128 ~~~~fl~~l~~~lP~GV~i~Ik 149 (380)
+++.|+ +.++|+||+|+|+
T Consensus 80 ~~~~l~---~~~lp~gV~iei~ 98 (99)
T TIGR01049 80 TIDALM---KLDLPAGVDIEIK 98 (99)
T ss_pred HHHHHH---cCCCCCCcEEEEE
Confidence 999998 5699999999986
No 4
>PRK00596 rpsJ 30S ribosomal protein S10; Reviewed
Probab=99.96 E-value=2.5e-29 Score=210.46 Aligned_cols=99 Identities=28% Similarity=0.416 Sum_probs=95.8
Q ss_pred eeEEEEEEEEcChhhHHHHHHHHHHHHHHcCCeecccccCCceeeEEEEEecccCCCcccceeeEEEEEEEEEEEecCCH
Q psy998 47 YSRICCELRANDPEVMNSYSKFATAAAQHLNIEIGECYAQKKAHHERYTLLRSVHVVKRCRVQYEVRTYFRWMNFHKLTG 126 (380)
Q Consensus 47 ~~~I~I~LkS~D~~~Le~~~~~I~~~ak~l~i~v~g~~a~LPTk~~~~TvlRSPhv~KKSreqFElrtykR~I~I~~~~~ 126 (380)
.++|+|+|+|||...||++|++|.++|+.+|++++||+ ||||++++||++||||+|||||||||+|+|+|+|+|.++++
T Consensus 3 ~~~irI~l~S~d~~~L~~~~~~i~~~a~~~~i~v~Gpi-pLPtk~~r~tvlrSPhv~KksreqfE~r~hkR~i~i~~~~~ 81 (102)
T PRK00596 3 KQKIRIRLKAFDHRLLDQSAKKIVETAKRTGAQVRGPI-PLPTKKERFTVLRSPHVNKDSREQFEIRTHKRLIDIVDPTP 81 (102)
T ss_pred CcEEEEEEEECCHHHHHHHHHHHHHHHHHcCCeEECCc-CCCcEEEEEEEeeCCCCCCCHHHHhhhhhheEEEEEECCCH
Confidence 46899999999999999999999999999999999999 99999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHccCCCCceEEEE
Q psy998 127 STADTFLEYIQRNLPEGVALKVT 149 (380)
Q Consensus 127 ~~~~~fl~~l~~~lP~GV~i~Ik 149 (380)
.+++.|+ +.++|+||+|+|+
T Consensus 82 ~~~~~l~---~~~lp~gV~iev~ 101 (102)
T PRK00596 82 KTVDALM---KLDLPAGVDVEIK 101 (102)
T ss_pred HHHHHHh---cCCCCCCcEEEEE
Confidence 9999887 7899999999996
No 5
>CHL00135 rps10 ribosomal protein S10; Validated
Probab=99.96 E-value=1.1e-28 Score=205.92 Aligned_cols=96 Identities=27% Similarity=0.353 Sum_probs=92.5
Q ss_pred eeEEEEEEEEcChhhHHHHHHHHHHHHHHcCCeecccccCCceeeEEEEEecccCCCcccceeeEEEEEEEEEEEecCCH
Q psy998 47 YSRICCELRANDPEVMNSYSKFATAAAQHLNIEIGECYAQKKAHHERYTLLRSVHVVKRCRVQYEVRTYFRWMNFHKLTG 126 (380)
Q Consensus 47 ~~~I~I~LkS~D~~~Le~~~~~I~~~ak~l~i~v~g~~a~LPTk~~~~TvlRSPhv~KKSreqFElrtykR~I~I~~~~~ 126 (380)
.++|+|+|+|||...||+++++|.++|+..|+.+.||+ ||||++++|||+||||+|||||||||+|+|||+|+|.++++
T Consensus 6 ~~kirI~LkS~d~~~L~~~~~~I~~~~k~~~~~~~Gpi-pLPtk~~~~TvlrSPhv~KkSrEqfE~r~hKRlI~i~~~~~ 84 (101)
T CHL00135 6 NAKIRIKLKSFNHELLNSSCKKIIDTASRTNATAVGPI-PLPTKRRIYCVLRSPHVDKDSREHFEIRTHKRIIDIYYPSS 84 (101)
T ss_pred cCeEEEEEEECCHHHHHHHHHHHHHHHHHcCCeEeCCc-CCCcEEEEEEEecCCCCCCchHHhhhheeeeEEEEEeCCCH
Confidence 36899999999999999999999999999999999999 99999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHccCCCCceE
Q psy998 127 STADTFLEYIQRNLPEGVAL 146 (380)
Q Consensus 127 ~~~~~fl~~l~~~lP~GV~i 146 (380)
.+++.|+ +.++|+||+|
T Consensus 85 ~~i~~l~---~~~lp~gV~i 101 (101)
T CHL00135 85 ETIDSLM---KLDLPPGVDI 101 (101)
T ss_pred HHHHHHH---cCCCCCCCcC
Confidence 9999988 7899999975
No 6
>COG0051 RpsJ Ribosomal protein S10 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=1.6e-28 Score=204.52 Aligned_cols=101 Identities=25% Similarity=0.340 Sum_probs=97.5
Q ss_pred eeEEEEEEEEcChhhHHHHHHHHHHHHHHcCCeecccccCCceeeEEEEEecccCCCcccceeeEEEEEEEEEEEecCCH
Q psy998 47 YSRICCELRANDPEVMNSYSKFATAAAQHLNIEIGECYAQKKAHHERYTLLRSVHVVKRCRVQYEVRTYFRWMNFHKLTG 126 (380)
Q Consensus 47 ~~~I~I~LkS~D~~~Le~~~~~I~~~ak~l~i~v~g~~a~LPTk~~~~TvlRSPhv~KKSreqFElrtykR~I~I~~~~~ 126 (380)
.++++|+|+|||+..||.+|.+|.+.|+..|+.++||+ |||||+.+||++||||++|+||||||||+|||+|+|.++++
T Consensus 3 ~~kirI~L~s~d~~~LD~~~~~Ive~akrtg~~v~GPi-PLPTk~~~~tvlrsP~~~k~s~e~fEmr~HkRlidi~~~~~ 81 (104)
T COG0051 3 KQKIRIRLKSFDHRLLDQVCREIVETAKRTGADVKGPI-PLPTKRERVTVLRSPHGEKDSREQFEMRTHKRLIDIVDPTP 81 (104)
T ss_pred CceEEEEEecCCHHHHHHHHHHHHHHHHHhCCeeeCCc-cCCCceEEEEEEeCCCCCCchHHHhhhheeeeEEEeecCCH
Confidence 35899999999999999999999999999999999999 99999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHccCCCCceEEEEEE
Q psy998 127 STADTFLEYIQRNLPEGVALKVTKY 151 (380)
Q Consensus 127 ~~~~~fl~~l~~~lP~GV~i~Ik~~ 151 (380)
.+++.++ +..+|+||+|+|+..
T Consensus 82 ~~~~~Lm---~i~~p~gV~vei~~~ 103 (104)
T COG0051 82 KTVDALM---RLDLPAGVDVEIKLE 103 (104)
T ss_pred HHHHHHh---cccCCCCceEEEEEc
Confidence 9999998 899999999999864
No 7
>KOG3321|consensus
Probab=99.95 E-value=2.4e-29 Score=222.09 Aligned_cols=124 Identities=44% Similarity=0.625 Sum_probs=120.3
Q ss_pred CCccceeEEEEEEEEcChhhHHHHHHHHHHHHHHcCCeecccccCCceeeEEEEEecccCCCcccceeeEEEEEEEEEEE
Q psy998 42 VPDKLYSRICCELRANDPEVMNSYSKFATAAAQHLNIEIGECYAQKKAHHERYTLLRSVHVVKRCRVQYEVRTYFRWMNF 121 (380)
Q Consensus 42 ~~d~~~~~I~I~LkS~D~~~Le~~~~~I~~~ak~l~i~v~g~~a~LPTk~~~~TvlRSPhv~KKSreqFElrtykR~I~I 121 (380)
.||++|..+.|+++|||..+|++|..||.+.|..+||.++|++ |||+++.+||++||||||||+++|||+|||.|.|++
T Consensus 41 ~Pdkly~~~ai~lrg~D~avLdsYt~Fi~~ta~~LgIp~~~~~-plp~~~Er~TlLrS~fIhKK~k~~yE~rTH~R~i~l 119 (175)
T KOG3321|consen 41 LPDKLYSLVAIELRGHDKAVLDSYTDFICRTAYYLGIPIKGPE-PLPKKRERWTLLRSPFIHKKSKENYERRTHSRLIEL 119 (175)
T ss_pred CchhhcceeeEEeccCchHHHHHHHHHHHHHHHHhCCccCCCC-CCchhhhhhhhhhchhhhhHHhhhHHHHHHHHHHHH
Confidence 7999999999999999999999999999999999999999999 999999999999999999999999999999999999
Q ss_pred ecCCHHHHHHHHHHHHccCCCCceEEEEEEecccCCCCCCCcccc
Q psy998 122 HKLTGSTADTFLEYIQRNLPEGVALKVTKYELQKLPSHFVPPTLL 166 (380)
Q Consensus 122 ~~~~~~~~~~fl~~l~~~lP~GV~i~Ik~~~~e~~~~r~~~~~~~ 166 (380)
.+++++++++|++||++|+|+||.|+++-++.+.+|.+++...|+
T Consensus 120 ~~~tgsTl~tfleYI~rn~pegV~mq~~~tele~ip~~lkk~~de 164 (175)
T KOG3321|consen 120 YSVTGSTLDTFLEYIQRNLPEGVGMQAKFTELEEIPLHLKKNIDE 164 (175)
T ss_pred hhcCchHHHHHHHHHHhhChhhhcceeceeecccchHhHhcCHHH
Confidence 999999999999999999999999999999999999999866543
No 8
>PF00338 Ribosomal_S10: Ribosomal protein S10p/S20e; InterPro: IPR001848 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S10 consists of about 100 amino acid residues. In Escherichia coli, S10 is involved in binding tRNA to the ribosome, and also operates as a transcriptional elongation factor []. Experimental evidence [] has revealed that S10 has virtually no groups exposed on the ribosomal surface, and is one of the "split proteins": these are a discrete group that are selectively removed from 30S subunits under low salt conditions and are required for the formation of activated 30S reconstitution intermediate (RI*) particles. S10 belongs to a family of proteins [] that includes: bacteria S10; algal chloroplast S10; cyanelle S10; archaebacterial S10; Marchantia polymorpha and Prototheca wickerhamii mitochondrial S10; Arabidopsis thaliana mitochondrial S10 (nuclear encoded); vertebrate S20; plant S20; and yeast URP2.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1S1H_J 3U5G_U 3O30_N 3O2Z_N 3IZB_J 3U5C_U 3R2C_J 3R2D_J 2ZKQ_j 2XQD_J ....
Probab=99.94 E-value=5.1e-27 Score=193.80 Aligned_cols=97 Identities=34% Similarity=0.541 Sum_probs=92.3
Q ss_pred EEEEEEEcChhhHHHHHHHHHHHHHHcCCeecccccCCceeeEEEEEecccCCCcccceeeEEEEEEEEEEEecCCHHHH
Q psy998 50 ICCELRANDPEVMNSYSKFATAAAQHLNIEIGECYAQKKAHHERYTLLRSVHVVKRCRVQYEVRTYFRWMNFHKLTGSTA 129 (380)
Q Consensus 50 I~I~LkS~D~~~Le~~~~~I~~~ak~l~i~v~g~~a~LPTk~~~~TvlRSPhv~KKSreqFElrtykR~I~I~~~~~~~~ 129 (380)
|+|+|+|||+..||+|+++|+++|+.+|++++|++ +|||++++||++||||+|||||||||+++|+|+|+|.+.++.++
T Consensus 1 i~I~l~s~d~~~l~~~~~~i~~~~~~~~~~~~~~~-~lPtk~~~~tvlrSPhv~kks~eqfe~~~~kr~i~i~~~~~~~~ 79 (97)
T PF00338_consen 1 IRIKLKSYDKKLLESYVKFIHKLAKNLGIKVSGPI-PLPTKKKRFTVLRSPHVDKKSREQFEIRTHKRLIQIKNLNSELA 79 (97)
T ss_dssp EEEEEEESSHHHHHHHHHHHHHHHHCTSSCEEEEE-EEEEEEEEEEEESSSSSSTTSEEEEEEEEEEEEEEESSSSHHHH
T ss_pred CEEEEEECCHHHHHHHHHHHHHHHHHhCCcccccc-cCCccEEEEEEeecCcCCcchhhheeeeeeEEEEEEeCCCHHHH
Confidence 68999999999999999999999999999999999 99999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHccCCCCceEEEEE
Q psy998 130 DTFLEYIQRNLPEGVALKVTK 150 (380)
Q Consensus 130 ~~fl~~l~~~lP~GV~i~Ik~ 150 (380)
+.|+ ...+|+||+|+|++
T Consensus 80 ~~~l---~~~~p~gV~i~i~i 97 (97)
T PF00338_consen 80 DKLL---YIQLPEGVQIEIKI 97 (97)
T ss_dssp HHHH---HSSTSSSSEEEEEE
T ss_pred HHHh---CcCCCCCCEEEEEC
Confidence 9998 44559999999974
No 9
>PRK12271 rps10p 30S ribosomal protein S10P; Reviewed
Probab=99.94 E-value=2.9e-26 Score=191.79 Aligned_cols=99 Identities=11% Similarity=0.160 Sum_probs=92.8
Q ss_pred eEEEEEEEEcChhhHHHHHHHHHHHHHHcCCeecccccCCceeeEEEEEecccCCC-cccceeeEEEEEEEEEEEecCCH
Q psy998 48 SRICCELRANDPEVMNSYSKFATAAAQHLNIEIGECYAQKKAHHERYTLLRSVHVV-KRCRVQYEVRTYFRWMNFHKLTG 126 (380)
Q Consensus 48 ~~I~I~LkS~D~~~Le~~~~~I~~~ak~l~i~v~g~~a~LPTk~~~~TvlRSPhv~-KKSreqFElrtykR~I~I~~~~~ 126 (380)
++|+|+|+|||...||.+|+.|.+.++..|+.++||+ |||||+.+||++||||++ ||||||||+|+|||+|+|. .+.
T Consensus 2 ~~irI~L~S~d~~~Ld~~~~~I~~~~k~~g~~~~GPi-pLPtk~~~~tv~rSPh~~gk~sreqfE~r~hKRlidi~-~~~ 79 (102)
T PRK12271 2 QKARIRLSSTNPEDLDEVCDQIKEIAEKTGVDMSGPI-PLPTKRLVVPTRKSPDGEGTATWDHWEMRIHKRLIDID-ADE 79 (102)
T ss_pred ceEEEEEEeCCHHHHHHHHHHHHHHHHHcCCeEECCC-cCCceeEEEEeeeCCCCCCCcchHHeEEEEeEEEEEee-CCH
Confidence 4799999999999999999999999999999999999 999999999999999986 9999999999999999995 677
Q ss_pred HHHHHHHHHHHccCCCCceEEEEEE
Q psy998 127 STADTFLEYIQRNLPEGVALKVTKY 151 (380)
Q Consensus 127 ~~~~~fl~~l~~~lP~GV~i~Ik~~ 151 (380)
.+++.++ +..+|+||+|+|++.
T Consensus 80 ~~~~~l~---~~~lp~gV~iei~~~ 101 (102)
T PRK12271 80 RALRQLM---RIRVPEDVQIEIELI 101 (102)
T ss_pred HHHHHHh---CCCCCCCcEEEEEEc
Confidence 7887777 789999999999864
No 10
>TIGR01046 S10_Arc_S20_Euk ribosomal protein S10(archaeal)/S20(eukaryotic). its equivalents in eukaryotes.
Probab=99.93 E-value=8.2e-26 Score=188.20 Aligned_cols=98 Identities=11% Similarity=0.142 Sum_probs=90.7
Q ss_pred eEEEEEEEEcChhhHHHHHHHHHHHHHHcCCeecccccCCceeeEEEEEecccCCC-cccceeeEEEEEEEEEEEecCCH
Q psy998 48 SRICCELRANDPEVMNSYSKFATAAAQHLNIEIGECYAQKKAHHERYTLLRSVHVV-KRCRVQYEVRTYFRWMNFHKLTG 126 (380)
Q Consensus 48 ~~I~I~LkS~D~~~Le~~~~~I~~~ak~l~i~v~g~~a~LPTk~~~~TvlRSPhv~-KKSreqFElrtykR~I~I~~~~~ 126 (380)
++|+|+|+|||...||++|+.|.+.|+..|+.+.||+ |||||+.+||++||||++ +|||||||+|+|||+|+|.+. .
T Consensus 1 ~~irI~L~S~d~~~Ld~~~~~I~~~ak~~g~~~~GPi-pLPtk~~~~tv~rsPh~~~~ks~e~fE~r~hKRlidi~~~-~ 78 (99)
T TIGR01046 1 HKARIKLTSTNVRSLEKVCAQIKRIAEKTGVRMSGPV-PLPTKRLRVPTRKSPDGEGSKTWDRWEMRIHKRLIDIEAD-E 78 (99)
T ss_pred CcEEEEEEECCHHHHHHHHHHHHHHHHHcCCEEECCc-cCCcceEEEEeeeCCCCCCCcchHheEEEEEEEEEEEECC-H
Confidence 3689999999999999999999999999999999999 999999999999999976 599999999999999999875 5
Q ss_pred HHHHHHHHHHHccCCCCceEEEEE
Q psy998 127 STADTFLEYIQRNLPEGVALKVTK 150 (380)
Q Consensus 127 ~~~~~fl~~l~~~lP~GV~i~Ik~ 150 (380)
.+++.++ +.++|+||+++|++
T Consensus 79 ~~~~~l~---~~~lp~gV~vei~~ 99 (99)
T TIGR01046 79 RALRQIM---RISVPEDVEIEITL 99 (99)
T ss_pred HHHHHHh---CCCCCCCcEEEEEC
Confidence 6777776 78999999999973
No 11
>PTZ00039 40S ribosomal protein S20; Provisional
Probab=99.93 E-value=9.6e-26 Score=192.06 Aligned_cols=100 Identities=15% Similarity=0.166 Sum_probs=92.8
Q ss_pred ceeEEEEEEEEcChhhHHHHHHHHHHHHHHcCCeecccccCCceeeEEEEEecccCCC-cccceeeEEEEEEEEEEEecC
Q psy998 46 LYSRICCELRANDPEVMNSYSKFATAAAQHLNIEIGECYAQKKAHHERYTLLRSVHVV-KRCRVQYEVRTYFRWMNFHKL 124 (380)
Q Consensus 46 ~~~~I~I~LkS~D~~~Le~~~~~I~~~ak~l~i~v~g~~a~LPTk~~~~TvlRSPhv~-KKSreqFElrtykR~I~I~~~ 124 (380)
.-++|+|+|+|||...||.+|+.|.+.|+..|+.+.||+ |||||+.+||++||||++ ||||||||+|+|||+|+|++
T Consensus 15 ~~~kirI~L~S~d~~~Ld~~~~~Ii~~ak~~g~~v~GPi-pLPtK~~~~tvlrSPhg~~kksreqfE~RiHKRlIdI~~- 92 (115)
T PTZ00039 15 RLHKIRITLTSKNLKSIEKVCADIITGAKEKNLKVTGPV-RMPVKTLRITTRKSPCGEGTNTWDRFEMRIYKRVIDLYS- 92 (115)
T ss_pred eeeEEEEEEEECCHHHHHHHHHHHHHHHHHcCCEeECCc-cCCceeEEEEeeeCCCCCCCchHHHheeeeeeEEEEEeC-
Confidence 347899999999999999999999999999999999999 999999999999999975 99999999999999999987
Q ss_pred CHHHHHHHHHHHHccCCCCceEEEEE
Q psy998 125 TGSTADTFLEYIQRNLPEGVALKVTK 150 (380)
Q Consensus 125 ~~~~~~~fl~~l~~~lP~GV~i~Ik~ 150 (380)
+..+++.++ +.++|+||+++|++
T Consensus 93 ~~~~v~~l~---~~~lp~GV~Iei~~ 115 (115)
T PTZ00039 93 SSDVVTQIT---SINIDPGVEVEVII 115 (115)
T ss_pred CHHHHHHHh---CCCCCCCcEEEEeC
Confidence 566777776 78999999999863
No 12
>PF07542 ATP12: ATP12 chaperone protein; InterPro: IPR011419 This entry represents a group of ATPase F1F0-assembly proteins, including ATP12 and ATPAF2 (ATP synthase mitochondrial F1 complex assembly factor 2). These proteins are essential for the assembly of the mitochondrial F1-F0 complex. Mitochondrial F1-ATPase is an oligomeric enzyme composed of five distinct subunit polypeptides. The alpha and beta subunits make up the bulk of protein mass of F1. In Saccharomyces cerevisiae both subunits are synthesised as precursors with N-terminal targeting signals that are removed upon translocation of the proteins to the matrix compartment []. These proteins include examples from eukaryotes and bacteria and may have chaperone activity, being involved in F1 ATPase complex assembly. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0043461 proton-transporting ATP synthase complex assembly; PDB: 2R6I_B 2ZD2_B 2P4X_B 2R31_A.
Probab=99.91 E-value=1.2e-25 Score=193.75 Aligned_cols=87 Identities=44% Similarity=0.581 Sum_probs=61.6
Q ss_pred CccceeeeeEEeCCcEEEEeCCCcCCCCCCCeeeeCcHHHHHHHHHHHhhcccccCCCccccccCceeee--ecCCCCCC
Q psy998 196 KRFYKKVGILESNGDYEISLDHRKLKTPNGVLFKVSSEPLALAIAAEWDAQHETIQRSTMHLRYNTSISY--SNDIAGPS 273 (380)
Q Consensus 196 kRFyk~v~v~~~~gg~~V~LDgR~lkTP~~~~l~vPs~~LA~aiA~EW~~Q~e~I~p~~MPL~~gv~l~~--~~gi~~~~ 273 (380)
|||||+|+|.+.+|||+|+||||+||||+|++|+|||++||.+||+||++|++.|+|++|||. .+.. .+.+..
T Consensus 1 KRFyk~v~v~~~~~g~~V~LDgR~lkTP~~~~l~vps~~LA~avA~EW~~Q~~~i~p~~MPLT---~L~~taiD~~~~-- 75 (122)
T PF07542_consen 1 KRFYKEVSVEENDGGFQVLLDGRPLKTPAGNPLVVPSEALAEAVAAEWDAQGEYIKPHTMPLT---SLANTAIDRVAE-- 75 (122)
T ss_dssp B---S-EEEEEETTSEEEEETTEE-BETTSEB--BSSHHHHHHHHHHHHT-SSB--GGG-HHH---HHHHHHHHTTCC--
T ss_pred CCCcceeeEEecCCCEEEEeCCCCCCCCCCCeeEcCcHHHHHHHHHHHHhhhcccCcccccHH---HHHHHHHhccch--
Confidence 799999999999999999999999999999999999999999999999999999999999991 1110 111111
Q ss_pred CCHHHHHHHHHHHh
Q psy998 274 VDPKDRATIQRHFL 287 (380)
Q Consensus 274 q~~~~~~~l~~~l~ 287 (380)
+..+.++.|-+|++
T Consensus 76 ~r~~~~~~il~yl~ 89 (122)
T PF07542_consen 76 DREAVIDEILRYLD 89 (122)
T ss_dssp CHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHcC
Confidence 46667777777775
No 13
>KOG4060|consensus
Probab=99.87 E-value=2e-22 Score=176.50 Aligned_cols=136 Identities=23% Similarity=0.320 Sum_probs=119.1
Q ss_pred eecccCCCCc----cceeEEEEEEEEcChhhHHHHHHHHHHHHHHcCCeecccccCCceeeEEEEEecccCCCcccceee
Q psy998 35 ISQEKEPVPD----KLYSRICCELRANDPEVMNSYSKFATAAAQHLNIEIGECYAQKKAHHERYTLLRSVHVVKRCRVQY 110 (380)
Q Consensus 35 ~~~~k~~~~d----~~~~~I~I~LkS~D~~~Le~~~~~I~~~ak~l~i~v~g~~a~LPTk~~~~TvlRSPhv~KKSreqF 110 (380)
+...+|+.++ .+|..+|++|+|||...||+|+.|+|++|+.++++|.+++ .+|+++...--+ --..+++...+
T Consensus 36 ~~~~ePKf~~~re~~ey~~lNV~i~gyD~~~lEsYq~yvH~la~~l~~~V~dsY-A~p~qt~~v~~l--~p~stv~ese~ 112 (176)
T KOG4060|consen 36 IKAEEPKFKKEREINEYGVLNVHITGYDMTLLESYQQYVHNLANSLSIKVEDSY-AMPTQTIEVLQL--QPQSTVMESES 112 (176)
T ss_pred hhhhCCcccchhcccccceEEEEEEecccchHHHHHHHHHHHHHHcCceeEeee-ccCccceeEEEe--cCCceeeehhh
Confidence 3445666665 5788899999999999999999999999999999999999 677765533323 23337889999
Q ss_pred EEEEEEEEEEEecCCHHHHHHHHHHHHccCCCCceEEEEEEecccCCCCCCCcccccCCCCCC
Q psy998 111 EVRTYFRWMNFHKLTGSTADTFLEYIQRNLPEGVALKVTKYELQKLPSHFVPPTLLESGSPET 173 (380)
Q Consensus 111 ElrtykR~I~I~~~~~~~~~~fl~~l~~~lP~GV~i~Ik~~~~e~~~~r~~~~~~~e~~~~e~ 173 (380)
.|.||.|++++++++...+++|+++++.++|+||.+.|+.|+.++++.||+||.+++...+|+
T Consensus 113 ~ltTyeRvvqls~v~Ap~~~~Fl~iiqa~lPeGV~l~VkEht~~de~~Ry~pd~eL~~l~~eL 175 (176)
T KOG4060|consen 113 VLTTYERVVQLSGVSAPFAEIFLEIIQASLPEGVRLSVKEHTEEDEKGRYKPDPELEELLAEL 175 (176)
T ss_pred hhhhhhheeeecccCchhHHHHHHHHHHhCCcceEEEeeeccccccccccCCCHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999999999877764
No 14
>KOG0900|consensus
Probab=99.41 E-value=7.2e-14 Score=118.97 Aligned_cols=102 Identities=13% Similarity=0.118 Sum_probs=90.3
Q ss_pred cceeEEEEEEEEcChhhHHHHHHHHHHHHHHcCCeecccccCCceeeEEEEEecccCC-CcccceeeEEEEEEEEEEEec
Q psy998 45 KLYSRICCELRANDPEVMNSYSKFATAAAQHLNIEIGECYAQKKAHHERYTLLRSVHV-VKRCRVQYEVRTYFRWMNFHK 123 (380)
Q Consensus 45 ~~~~~I~I~LkS~D~~~Le~~~~~I~~~ak~l~i~v~g~~a~LPTk~~~~TvlRSPhv-~KKSreqFElrtykR~I~I~~ 123 (380)
....+++|.+.|-....|++.|..|.+.|+..|.++.|++ +||||.+++|++|+||+ ++|.|+.|+||+|+|+|++..
T Consensus 17 ~~~~~~~it~~~~~~kslekvC~dl~~~ak~~nl~~kg~v-r~Ptk~~~itt~k~p~g~g~k~w~~f~mRiH~R~idl~s 95 (121)
T KOG0900|consen 17 PEIHKIRITLTSQKVKSLEKVCADLVRGAKEKNLKVKGPV-RLPTKVLKITTRKTPCGEGSKTWDRFEMRVHKRLIDLHS 95 (121)
T ss_pred hhhhccceeeeHHHHHHHHHHHHHHHHHHhhcCCcccCcc-cCCceeEEEEEeecCCcCCccHHHHHHHHHHHHHhccCC
Confidence 3566788999999999999999999999999999999999 99999999999999994 799999999999999999987
Q ss_pred CCHHHHHHHHHHHHccCCCCceEEEEEE
Q psy998 124 LTGSTADTFLEYIQRNLPEGVALKVTKY 151 (380)
Q Consensus 124 ~~~~~~~~fl~~l~~~lP~GV~i~Ik~~ 151 (380)
++.. ++... +..+++||++++++.
T Consensus 96 ~se~-vkqit---si~~epgVevev~i~ 119 (121)
T KOG0900|consen 96 PSEI-VKQIT---SISIEPGVEVEVTIA 119 (121)
T ss_pred hHHH-HHHhh---hhccCCCceEEEEec
Confidence 6543 55554 567789999999864
No 15
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=50.60 E-value=93 Score=31.41 Aligned_cols=111 Identities=17% Similarity=0.135 Sum_probs=75.1
Q ss_pred CCcEEEEeCCC-cCCCCC---CCeeeeCcHHHHHHHHHHHhhcccccCCCcccc--------------------------
Q psy998 208 NGDYEISLDHR-KLKTPN---GVLFKVSSEPLALAIAAEWDAQHETIQRSTMHL-------------------------- 257 (380)
Q Consensus 208 ~gg~~V~LDgR-~lkTP~---~~~l~vPs~~LA~aiA~EW~~Q~e~I~p~~MPL-------------------------- 257 (380)
++||.-..-++ ||+||. |..+.||..++..+....+-+. |..||.
T Consensus 146 ~~G~R~~t~~k~PI~~peDlkGlkiRv~~s~~~~~~~~a~GA~-----P~pm~f~Evy~aLqtGvVDGqEnp~~~i~~~k 220 (332)
T COG1638 146 ENGFRQFTSNKRPIKTPEDLKGLKIRVPQSPLLLAMFKALGAN-----PTPMPFAEVYTALQTGVVDGQENPLSNIYSAK 220 (332)
T ss_pred cCceeeeecCCCCCCChHHhCCCeeecCCCHHHHHHHHHcCCC-----CCCCCHHHHHHHHHcCCcccccCCHHHHhhcc
Confidence 57888888866 999998 9999999988888888777764 566666
Q ss_pred -------------ccCceeeeecCCCCCCCCHHHHHHHHHHHhcCChhhhHHHHHHHHhhhHHHHHHHHHcCCCCHHHH
Q psy998 258 -------------RYNTSISYSNDIAGPSVDPKDRATIQRHFLSYNFETVMGVNFAVETLKSIVLTLACIDRKLSIEEA 323 (380)
Q Consensus 258 -------------~~gv~l~~~~gi~~~~q~~~~~~~l~~~l~~l~~~~L~al~~~~~~~kS~vlalal~~g~l~~e~A 323 (380)
.+..-+.+.+.-.=...|++..+++++.....-.|+....+..-..+...+..-.+---..+.+++
T Consensus 221 ~~EVqky~t~tnH~~~~~~~~~s~~~w~~L~~e~q~il~~aa~e~~~~~~~~~~~~e~~~~e~lk~~Gv~v~~~~~~~~ 299 (332)
T COG1638 221 LYEVQKYLTLTNHIYLPLAVLVSKAFWDSLPEEDQTILLEAAKEAAEEQRKLVEELEDELLEKLKEAGVEVVEPDAAEA 299 (332)
T ss_pred HHHHhHHhhhccccccceeeEEcHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEecCCchHH
Confidence 111122222222236789999999999998877777776666666666666554333223344443
No 16
>PF01781 Ribosomal_L38e: Ribosomal L38e protein family; InterPro: IPR002675 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 L38e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_n 3IZR_n 4A1D_P 4A19_P 4A18_P 4A1B_P.
Probab=35.97 E-value=1.2e+02 Score=24.10 Aligned_cols=47 Identities=15% Similarity=0.250 Sum_probs=35.8
Q ss_pred EEEEecccCCCcccceeeEEEEEEEEEEEecCCHHHHHHHHHHHHccCCCCceEE
Q psy998 93 RYTLLRSVHVVKRCRVQYEVRTYFRWMNFHKLTGSTADTFLEYIQRNLPEGVALK 147 (380)
Q Consensus 93 ~~TvlRSPhv~KKSreqFElrtykR~I~I~~~~~~~~~~fl~~l~~~lP~GV~i~ 147 (380)
-+++.|++... ..|.+|..+.+..+.-.+...++.+ +..||+|+.+.
T Consensus 21 sv~iKk~~~~~----tKFKvRcsryLYTLvv~d~~KAekl----kqSLPp~l~v~ 67 (69)
T PF01781_consen 21 SVKIKKNKDNG----TKFKVRCSRYLYTLVVKDKEKAEKL----KQSLPPGLKVK 67 (69)
T ss_dssp EEEEECESSST----EEEEEECSS-EEEESS-SHHHHHHH----HHSSSSSSEEE
T ss_pred eEEEEecCCCe----eEEEEEecceEEEEEEcCHHHHHHH----HhhCCCCCeEe
Confidence 45556655542 7899999999999988888888887 58999999864
No 17
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=35.41 E-value=37 Score=30.92 Aligned_cols=43 Identities=28% Similarity=0.425 Sum_probs=31.0
Q ss_pred EeCCcEEEEeCCCcCCCCC-CCeeeeCcHHHHHHHHHHHhhccc
Q psy998 206 ESNGDYEISLDHRKLKTPN-GVLFKVSSEPLALAIAAEWDAQHE 248 (380)
Q Consensus 206 ~~~gg~~V~LDgR~lkTP~-~~~l~vPs~~LA~aiA~EW~~Q~e 248 (380)
..+|||.|.|-=+--.++. .=.|.||++.-|.+|+.-|.....
T Consensus 109 ~~~~~y~V~l~i~e~~~~Li~l~l~vp~~~qA~~ic~nwk~n~~ 152 (163)
T PF14277_consen 109 NSNGEYIVRLQIIENDSDLIDLKLNVPSEEQAEAICNNWKKNSQ 152 (163)
T ss_pred cCCCCEEEEEEEEeCCceEEEEEEeCCCHHHHHHHHHHHhhCHH
Confidence 3467788876443333443 446899999999999999997654
No 18
>PF11469 Ribonucleas_3_2: Ribonuclease III; InterPro: IPR021568 This archaeal family of proteins has no known function. ; PDB: 1ZTD_A.
Probab=31.38 E-value=49 Score=28.36 Aligned_cols=21 Identities=33% Similarity=0.570 Sum_probs=17.9
Q ss_pred HHHHHHHHcCCCCHHHHHHHh
Q psy998 307 IVLTLACIDRKLSIEEAVHLS 327 (380)
Q Consensus 307 ~vlalal~~g~l~~e~A~~~a 327 (380)
.+||.|.++|.++.|+|++.-
T Consensus 64 A~iAyAWLeg~it~eEaveil 84 (120)
T PF11469_consen 64 ALIAYAWLEGKITIEEAVEIL 84 (120)
T ss_dssp HHHHHHHHTTSS-HHHHHHHH
T ss_pred HHHHHHHHhccccHHHHHHHH
Confidence 579999999999999999864
No 19
>PF06236 MelC1: Tyrosinase co-factor MelC1; InterPro: IPR010928 This family consists of several tyrosinase co-factor MELC1 proteins from a number of Streptomyces species. The melanin operon (melC) of Streptomyces antibioticus contains two genes, melC1 and melC2 (apotyrosinase). It is thought that MelC1 forms a transient binary complex with the downstream apotyrosinase MelC2 to facilitate the incorporation of copper ion and the secretion of tyrosinase indicating that MelC1 is a chaperone for the apotyrosinase MelC2 [].; GO: 0005507 copper ion binding, 0042438 melanin biosynthetic process; PDB: 1WX4_B 2ZWD_B 2ZMZ_B 1WX2_B 1WX5_D 3AWX_B 3AWS_B 2ZMY_B 3AX0_B 2ZWG_B ....
Probab=30.06 E-value=24 Score=31.01 Aligned_cols=37 Identities=27% Similarity=0.436 Sum_probs=23.7
Q ss_pred CCcEEEEeCCCcCCC---CCCCeee-------eCc-HHHHHHHHHHHh
Q psy998 208 NGDYEISLDHRKLKT---PNGVLFK-------VSS-EPLALAIAAEWD 244 (380)
Q Consensus 208 ~gg~~V~LDgR~lkT---P~~~~l~-------vPs-~~LA~aiA~EW~ 244 (380)
.++|.|++|||+|.- -.|.-|+ +|+ .++|.+.-.|-.
T Consensus 68 ~~~~~V~IDGr~LhvMr~ADGswlS~V~HYe~~pTpl~aARAAVdeL~ 115 (125)
T PF06236_consen 68 GGGYEVTIDGRPLHVMRRADGSWLSVVNHYESYPTPLEAARAAVDELG 115 (125)
T ss_dssp --SEEEEETTEEE-EEE-TTS-EEETTEEEEEESSHHHHHHHHHHHHT
T ss_pred CCceEEEECCeEeeeEEcCCCCEEeeeecccCCCCHHHHHHHHHHHhC
Confidence 356999999998754 3465554 465 567777777765
No 20
>PF01929 Ribosomal_L14e: Ribosomal protein L14; InterPro: IPR002784 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 [, ]. This entry includes the eukaryotic ribosomal protein L14, which binds to the 60S ribosomal subunit, and archaebacterial ribosomal protein L14E, which binds to the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_N 3O5H_N 3O58_N 2KDS_A 2JOY_A 4A1B_F 4A19_F 4A18_F 4A1D_F 3IZR_N.
Probab=26.75 E-value=63 Score=25.96 Aligned_cols=33 Identities=18% Similarity=0.484 Sum_probs=27.9
Q ss_pred HHHHHHHhhhhHHHhhhhhcCcCCCcCHhHHHHHHHHH
Q psy998 320 IEEAVHLSKLEEEYQIGHWGRVEWAHDLHQQELQARLA 357 (380)
Q Consensus 320 ~e~A~~~a~lEe~~Q~~~WG~VE~~HD~e~~~~~~~l~ 357 (380)
+..||+.+.+.+.|....||. -++..+.++.|+
T Consensus 28 vkka~~~~~i~~kw~~s~waK-----k~~~~~~Ra~lt 60 (77)
T PF01929_consen 28 VKKAWEKADIDEKWAESAWAK-----KIAAREKRANLT 60 (77)
T ss_dssp HHHHHHHHTCHHHHHHHHCSC-----HHHHHHHHHSHH
T ss_pred HHHHHHHccHHHHHHHhHHHH-----HHHHHHHHhcCC
Confidence 678999999999999999999 777777666553
No 21
>KOG3499|consensus
Probab=26.00 E-value=3.1e+02 Score=21.42 Aligned_cols=37 Identities=22% Similarity=0.415 Sum_probs=29.5
Q ss_pred ceeeEEEEEEEEEEEecCCHHHHHHHHHHHHccCCCCceEE
Q psy998 107 RVQYEVRTYFRWMNFHKLTGSTADTFLEYIQRNLPEGVALK 147 (380)
Q Consensus 107 reqFElrtykR~I~I~~~~~~~~~~fl~~l~~~lP~GV~i~ 147 (380)
...|.+|-.+.+..+-..+...++.+ +..+|+|.+++
T Consensus 31 ~~KFKvRcsryLYTLvv~D~~KAeKl----kQSLPP~l~V~ 67 (69)
T KOG3499|consen 31 NVKFKVRCSRYLYTLVVADAEKAEKL----KQSLPPGLTVK 67 (69)
T ss_pred ceeEEEEeeeeeeeeeeccHHHHHHH----HhcCCCCceee
Confidence 46788888888877777788888887 58999998764
Done!