Query 046473
Match_columns 120
No_of_seqs 114 out of 801
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 12:30:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046473.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046473hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00084 40S ribosomal protein 100.0 7E-45 1.5E-49 286.4 10.8 114 2-115 72-188 (220)
2 COG0092 RpsC Ribosomal protein 100.0 1.1E-44 2.3E-49 287.0 9.5 107 2-112 79-186 (233)
3 TIGR01008 rpsC_E_A ribosomal p 100.0 2.8E-44 6.1E-49 278.7 10.6 112 2-115 66-180 (195)
4 PRK04191 rps3p 30S ribosomal p 100.0 3.2E-44 7E-49 279.7 10.7 112 2-115 68-182 (207)
5 CHL00048 rps3 ribosomal protei 100.0 7.1E-39 1.5E-43 251.0 11.0 112 2-115 94-209 (214)
6 TIGR01009 rpsC_bact ribosomal 100.0 4.6E-37 1E-41 240.2 9.9 109 2-115 90-202 (211)
7 PRK00310 rpsC 30S ribosomal pr 100.0 1.6E-36 3.4E-41 240.2 9.0 109 2-115 90-202 (232)
8 KOG3181 40S ribosomal protein 100.0 9.8E-34 2.1E-38 221.2 6.1 112 1-112 71-182 (244)
9 PF00189 Ribosomal_S3_C: Ribos 99.9 7.9E-25 1.7E-29 149.2 5.3 77 34-112 1-79 (85)
10 PF07650 KH_2: KH domain syndr 70.5 2.1 4.6E-05 27.7 0.9 24 3-26 54-78 (78)
11 TIGR02722 lp_ uncharacterized 63.4 34 0.00073 26.1 6.4 94 16-120 72-187 (189)
12 PF13036 DUF3897: Protein of u 61.5 45 0.00097 24.7 6.7 96 14-120 63-180 (180)
13 PHA03303 envelope glycoprotein 44.2 74 0.0016 24.4 5.4 53 6-58 76-132 (159)
14 PF13653 GDPD_2: Glycerophosph 36.4 39 0.00084 18.9 2.1 15 51-65 11-25 (30)
15 PF14698 ASL_C2: Argininosucci 35.8 42 0.0009 21.8 2.6 34 27-63 3-36 (70)
16 PF02355 SecD_SecF: Protein ex 30.1 73 0.0016 24.4 3.5 31 28-58 101-133 (189)
17 PF06069 PerC: PerC transcript 23.1 1.1E+02 0.0025 21.2 3.1 25 32-56 3-27 (90)
18 PRK10753 transcriptional regul 22.0 1.5E+02 0.0032 19.9 3.4 48 45-94 21-69 (90)
19 PF06213 CobT: Cobalamin biosy 20.5 1.1E+02 0.0025 24.5 3.1 27 43-71 10-36 (282)
No 1
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=100.00 E-value=7e-45 Score=286.42 Aligned_cols=114 Identities=68% Similarity=1.028 Sum_probs=109.3
Q ss_pred ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccchhhhhhcc
Q 046473 2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMK 81 (120)
Q Consensus 2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~GerAR~e~ 81 (120)
.|++.|++++++|+|+|.||++|++||.++|++||+|||+|++|||||+++|+++|++||+||||+|||||+|||||+||
T Consensus 72 ~L~k~~~~~~~~i~i~v~ev~~P~l~A~lvA~~IA~qLe~rv~FRRa~k~ai~~~m~aGakGikI~iSGRL~~EiARtE~ 151 (220)
T PTZ00084 72 LLQKRFGFPEGKVELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESGAKGCEVIVSGKLRAQRAKSMK 151 (220)
T ss_pred HHHHHhCCCCceEEEEEEEecCCCcCHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHcCCceEEEEEccchhhHHHHhhH
Confidence 47889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473 82 FKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC 115 (120)
Q Consensus 82 ~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~ 115 (120)
|+||+|.|||+++++||||++.||+|+|| |+||-
T Consensus 152 ~~eGrVl~Tg~~~~~~idy~~~~a~t~yGviGVKVwI 188 (220)
T PTZ00084 152 FRDGYMISTGQPKKDFVDSAVRHVLMRQGVIGVKVKI 188 (220)
T ss_pred hhccEEEecCchHHHheehheEEEcccCceeeEEEEE
Confidence 99999999999999999999999999886 56663
No 2
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-44 Score=287.04 Aligned_cols=107 Identities=23% Similarity=0.277 Sum_probs=100.5
Q ss_pred ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccch-hhhhhc
Q 046473 2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRA-QRATSM 80 (120)
Q Consensus 2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~G-erAR~e 80 (120)
.|++.|+.+ +++|+|+||++|+|||+++|++||.|||+|++|||||++||+++|++||+||||+|||||+| +|||+|
T Consensus 79 ~l~k~~g~~--~v~I~i~EV~~peL~A~lvA~~IA~qLErrv~FRRA~k~ai~~~M~aGAkGiki~vSGRL~GaeiAR~E 156 (233)
T COG0092 79 ELEKLFGKE--NVQINIEEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGAEIARTE 156 (233)
T ss_pred HHHHHhCCC--CceEEEEEcCCCCcCHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcCCceeEEEEecccchHHHHhHH
Confidence 477889875 67777999999999999999999999999999999999999999999999999999999999 779999
Q ss_pred cccceeeeccchhhhhhhheeeeEeCcCCeeE
Q 046473 81 KFKDGYMISSGYPVKEYIDSAVRHVLXRQASS 112 (120)
Q Consensus 81 ~~~eG~vp~sG~~~~~~idy~~~~a~tk~Gv~ 112 (120)
||+||+|||| |++++|||++++|+|+||++
T Consensus 157 ~y~eG~vplh--tlrAdIDyg~a~A~ttyGii 186 (233)
T COG0092 157 KYREGRVPLH--TLRADIDYGTAEAHTTYGVI 186 (233)
T ss_pred HHhcceeEcc--ccceeeeeeeEEEEecCceE
Confidence 9999999996 68999999999999999764
No 3
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=100.00 E-value=2.8e-44 Score=278.66 Aligned_cols=112 Identities=35% Similarity=0.498 Sum_probs=105.0
Q ss_pred ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccchhhhhhcc
Q 046473 2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMK 81 (120)
Q Consensus 2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~GerAR~e~ 81 (120)
.|+++|+.. +++|+|.||++|++||.++|++||+|||+|++|||||+++|+++|++||+||||+|||||+|||||+||
T Consensus 66 ~l~k~~~~~--~~~I~v~ev~~p~l~A~lvA~~Ia~qLe~rv~fRra~k~ai~~~m~aGakGikI~iSGRL~GeiARtE~ 143 (195)
T TIGR01008 66 KLQKKFGLE--NPQIDVEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRIMEAGAKGVEVTISGKLTGERARTEK 143 (195)
T ss_pred HHHHHhCCC--ceEEEEEEEeCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCceEEEEEcccccchhhhhhh
Confidence 467778763 578889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473 82 FKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC 115 (120)
Q Consensus 82 ~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~ 115 (120)
|+||+||+||||+..+||||+++|+|+|| |+||-
T Consensus 144 ~~eG~v~~sG~Pl~t~IDya~~~a~t~yGviGIKVwI 180 (195)
T TIGR01008 144 FAAGYLKHSGEPAEELVDKGFAIALLKLGVLGVKVKI 180 (195)
T ss_pred eeccEEecCCCcchheeeeEEEEEecCCceEEEEEEE
Confidence 99999999999999999999999999997 56774
No 4
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=100.00 E-value=3.2e-44 Score=279.72 Aligned_cols=112 Identities=29% Similarity=0.401 Sum_probs=104.4
Q ss_pred ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccchhhhhhcc
Q 046473 2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMK 81 (120)
Q Consensus 2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~GerAR~e~ 81 (120)
+|++.|+.. ++.|+|.||++|++||.++|++||+|||+|++|||||+++|+++|++||+||||+|||||+|||||+||
T Consensus 68 ~Lkk~~~~~--~v~I~v~ev~~p~~~a~~vA~~ia~qLe~r~~fRra~k~~i~~~~~agakGiki~iSGrL~Ge~AR~e~ 145 (207)
T PRK04191 68 ILEKKFGLE--NPQIDVKEVENPELNARVVAFRLANALERGWHFRRAAHSAIRRIMEAGALGVEIIISGKLTGERARTEK 145 (207)
T ss_pred HHHHHhCCC--ceeEEEEEEeCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCCeeEEEEEccccchHHHHhhh
Confidence 466677654 467779999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473 82 FKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC 115 (120)
Q Consensus 82 ~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~ 115 (120)
|+||+||+||||+..+||||+++|+|+|| |+||-
T Consensus 146 ~~eG~v~~~G~pl~tlIdya~~~a~t~~GviGIKVwI 182 (207)
T PRK04191 146 FTEGYIKKSGEPAEELVDRGFAIAKLKLGIIGVEVRI 182 (207)
T ss_pred hhcceEeccCCcchheeeeEEEEEecCCeeEEEEEEE
Confidence 99999999999999999999999999997 56774
No 5
>CHL00048 rps3 ribosomal protein S3
Probab=100.00 E-value=7.1e-39 Score=251.00 Aligned_cols=112 Identities=14% Similarity=0.118 Sum_probs=105.8
Q ss_pred ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccch-hhhhhc
Q 046473 2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRA-QRATSM 80 (120)
Q Consensus 2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~G-erAR~e 80 (120)
.|++.|+++++++.|+|.||++|++||.++|++||+|||+|++||||++++++++|++||+||||+|||||+| ||||+|
T Consensus 94 ~L~k~~~~~~~~i~I~v~ev~~p~~~A~~iA~~ia~~Le~r~~fRra~~~~i~~~~~~ga~GikI~iSGRL~Gae~AR~e 173 (214)
T CHL00048 94 NLQKELNSVNRKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQISGRLNGAEIARVE 173 (214)
T ss_pred HHHHHhCCCCceEEEEEEEecCCCcCHHHHHHHHHHHHhcChhHHHHHHHHHHHHHHhCCcEEEEEEecccCccchheEE
Confidence 3677888888899999999999999999999999999999999999999999999999999999999999999 999999
Q ss_pred cccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473 81 KFKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC 115 (120)
Q Consensus 81 ~~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~ 115 (120)
||++|+||+ ||++++|||++++|+|+|| |+||-
T Consensus 174 ~~~~G~vpl--~tl~a~Idy~~~~a~t~~G~~GVKVwI 209 (214)
T CHL00048 174 WIREGRVPL--QTLRAKIDYCSYPARTIYGVLGIKIWI 209 (214)
T ss_pred EEecceeEC--CcchhheEEEEEEEecCCceEEEEEEE
Confidence 999999998 4899999999999999986 56774
No 6
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=100.00 E-value=4.6e-37 Score=240.22 Aligned_cols=109 Identities=22% Similarity=0.257 Sum_probs=101.1
Q ss_pred ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccch-hhhhhc
Q 046473 2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRA-QRATSM 80 (120)
Q Consensus 2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~G-erAR~e 80 (120)
.|+++|+ +++.|+|.+|++|++||.++|++||+|||+|++|||+++++++++|++||+||||+|||||+| ||||+|
T Consensus 90 ~l~~~~~---~~~~i~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRr~~~~~i~~~~~~g~~GikI~isGRl~g~e~Ar~e 166 (211)
T TIGR01009 90 DLQKLTG---KEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGAEIARTE 166 (211)
T ss_pred HHHHHhC---CceEEEEEEecCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHhcCCcEEEEEEecccCchhhhhee
Confidence 3566775 468888999999999999999999999999999999999999999999999999999999999 999999
Q ss_pred cccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473 81 KFKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC 115 (120)
Q Consensus 81 ~~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~ 115 (120)
||++|+||++ |++++|||++++|+|+|| |+||-
T Consensus 167 ~~~~G~vpl~--t~~~~Idy~~~~a~T~~G~~GvKVwI 202 (211)
T TIGR01009 167 WYKEGRVPLH--TLRADIDYATAEAHTTYGIIGVKVWI 202 (211)
T ss_pred eeeeCccCcc--cchhhcEEEEEEEEcCCceEEEEEEE
Confidence 9999999984 799999999999999987 56664
No 7
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=100.00 E-value=1.6e-36 Score=240.17 Aligned_cols=109 Identities=21% Similarity=0.243 Sum_probs=101.0
Q ss_pred ccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccch-hhhhhc
Q 046473 2 AVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRA-QRATSM 80 (120)
Q Consensus 2 ~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~G-erAR~e 80 (120)
.|++.|+ ++++|+|.||++|++||.++|++||+|||+|++|||+++++|+++|++||+||+|+|||||+| ||||+|
T Consensus 90 ~L~~~~~---~~~~i~v~ev~~p~~~a~~iA~~ia~~Le~r~~fRr~~~~~i~~~~~~g~~GikI~isGRl~g~e~Ar~e 166 (232)
T PRK00310 90 ELEKLTG---KPVQINIVEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKVQVSGRLGGAEIARTE 166 (232)
T ss_pred HHHHHhC---CceEEEEEEecCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCCcEEEEEEcCCCCcceeeeEE
Confidence 3566665 478888999999999999999999999999999999999999999999999999999999999 999999
Q ss_pred cccceeeeccchhhhhhhheeeeEeCcCCe---eEEec
Q 046473 81 KFKDGYMISSGYPVKEYIDSAVRHVLXRQA---SSIFC 115 (120)
Q Consensus 81 ~~~eG~vp~sG~~~~~~idy~~~~a~tk~G---v~~~~ 115 (120)
||++|+||++ |++++|||++++|+|+|| |+||-
T Consensus 167 ~~~~G~vpl~--t~~~~Idy~~~~a~T~~Gv~GVKVwI 202 (232)
T PRK00310 167 WYREGRVPLH--TLRADIDYGTAEAHTTYGIIGVKVWI 202 (232)
T ss_pred Eeeecccccc--eeeeeeEEEEEEEecCCceEEEEEEE
Confidence 9999999984 799999999999999986 56663
No 8
>KOG3181 consensus 40S ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.8e-34 Score=221.25 Aligned_cols=112 Identities=77% Similarity=1.123 Sum_probs=110.0
Q ss_pred CccccccCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCceeEEEEecccchhhhhhc
Q 046473 1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSM 80 (120)
Q Consensus 1 ~~l~k~~~~~~~~i~i~v~eV~~p~l~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkGikI~ISGrL~GerAR~e 80 (120)
+++||||++++..|++++++|.+.+|||..+||+|+++|..+.++|||++.+++.+|++|||||+|++||||+|+||+++
T Consensus 71 ~lvqkRf~f~~~svelyaEkV~~rGLcAiaQaeslryKllgGlavRRA~ygvlr~vmesgAkGceviVSGKLrgqRAKsm 150 (244)
T KOG3181|consen 71 SLVQKRFKFPEGSVELYAEKVANRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGAKGCEVIVSGKLRGQRAKSM 150 (244)
T ss_pred HHHHHhcCCCCCcEEEehhhhhccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHccCCccEEEEeccchhhhhhcc
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccceeeeccchhhhhhhheeeeEeCcCCeeE
Q 046473 81 KFKDGYMISSGYPVKEYIDSAVRHVLXRQASS 112 (120)
Q Consensus 81 ~~~eG~vp~sG~~~~~~idy~~~~a~tk~Gv~ 112 (120)
||.+|.|.|||||..+|||.|++|++++|||+
T Consensus 151 KF~DG~mIhSG~pv~dyi~ta~rhVllrQGVl 182 (244)
T KOG3181|consen 151 KFVDGLMIHSGQPVKDYIDTAVRHVLLRQGVL 182 (244)
T ss_pred ccccceEEecCCcHHHHHHHHHHhhhhhccee
Confidence 99999999999999999999999999999986
No 9
>PF00189 Ribosomal_S3_C: Ribosomal protein S3, C-terminal domain; InterPro: IPR001351 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 S3 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S3 is known to be involved in the binding of initiator Met-tRNA. This family of ribosomal proteins includes S3 from bacteria, algae and plant chloroplast, cyanelle, archaebacteria, plant mitochondria, vertebrates, insects, Caenorhabditis elegans and yeast []. This entry is the C-terminal domain.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_C 2XZM_C 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C ....
Probab=99.91 E-value=7.9e-25 Score=149.16 Aligned_cols=77 Identities=27% Similarity=0.348 Sum_probs=72.8
Q ss_pred HHHHHhhhhhHHHHHHHHHHHHH-HHhCCceeEEEEecccch-hhhhhccccceeeeccchhhhhhhheeeeEeCcCCee
Q 046473 34 SLRKEGLAVIVCKMACYGVLRFI-MESGAKGCEVIVSGKLRA-QRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQAS 111 (120)
Q Consensus 34 ~ia~qLe~r~~fRra~~~ai~~~-m~aGAkGikI~ISGrL~G-erAR~e~~~eG~vp~sG~~~~~~idy~~~~a~tk~Gv 111 (120)
+|+++||++.+|||+++.+++.+ |++|++||+|++||||+| +|||+|+|.+|.+|+ +++.++|||++.+++|++|+
T Consensus 1 ~i~~~l~k~~~~r~~i~~~~~~i~~~~~~~GikI~isGRl~g~~rar~~~~~~G~i~~--~~~~~~Idy~~~~~~tk~G~ 78 (85)
T PF00189_consen 1 FIAQKLEKRISFRRIIKKIIRRIMMNKGIKGIKIQISGRLNGAERARTEKFKKGKISL--QTFKSNIDYASSHAKTKYGV 78 (85)
T ss_dssp HHHHHHHTTSTHHHHHHHHHHHHHHCTTSSEEEEEEESSGGGTSSSEEEEEEEESSSS--SSSTTEEEEEEEEEEESSSE
T ss_pred ChHHHHhcCcHHHHHHHHHHHHHHhhcccceEEEEEeecCCCCccceEEEEECCCCcc--ccceeeeeEEEEEEEcCCee
Confidence 58999999999999999999999 788999999999999999 999999999999976 68999999999999999875
Q ss_pred E
Q 046473 112 S 112 (120)
Q Consensus 112 ~ 112 (120)
.
T Consensus 79 ~ 79 (85)
T PF00189_consen 79 I 79 (85)
T ss_dssp E
T ss_pred E
Confidence 3
No 10
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=70.50 E-value=2.1 Score=27.66 Aligned_cols=24 Identities=21% Similarity=0.182 Sum_probs=18.1
Q ss_pred cccccC-CCCCeEEEEEEEecCCCc
Q 046473 3 VQKRFK-FPENSVELYAEKVNNRGL 26 (120)
Q Consensus 3 l~k~~~-~~~~~i~i~v~eV~~p~l 26 (120)
+++.+. +.+++|.|++.+|++|++
T Consensus 54 ~~k~l~~~~~~~V~l~v~~V~~~~~ 78 (78)
T PF07650_consen 54 LRKELEKLLNKKVFLNVVKVKKPWR 78 (78)
T ss_dssp HHHHHHHHCSSSEEEEEEEESSCGG
T ss_pred HHHHHhhcCCCcEEEEEEEecCCCC
Confidence 344553 457889999999999975
No 11
>TIGR02722 lp_ uncharacterized proteobacterial lipoprotein. Members of this protein family are restricted to the Proteobacteria, and all are predicted lipoproteins. In genomes that contain the thiK gene for the salvage enzyme thiamin kinase, the member of this family is encoded nearby.
Probab=63.43 E-value=34 Score=26.10 Aligned_cols=94 Identities=15% Similarity=0.174 Sum_probs=61.0
Q ss_pred EEEEEecCC---CcCHHHHHHHHHHHhhhhhHHHH-------HHHHHHHHHHHhC------------CceeEEEEecccc
Q 046473 16 LYAEKVNNR---GLCAIAQAESLRKEGLAVIVCKM-------ACYGVLRFIMESG------------AKGCEVIVSGKLR 73 (120)
Q Consensus 16 i~v~eV~~p---~l~a~i~A~~ia~qLe~r~~fRr-------a~~~ai~~~m~aG------------AkGikI~ISGrL~ 73 (120)
+.|..|+|- .+|+..+.+.|..+|.+.-.|+= ++.+.++.-.++| -.|..-.++|++.
T Consensus 72 l~V~~vkN~T~~~idt~~~t~~i~~~L~~sGkf~~v~~~~~~~~~~e~~~~~~~~~~~~~t~~~~g~~~gADy~L~G~I~ 151 (189)
T TIGR02722 72 LLVDSIKNDTNEHIDTESLTDKIRTALLQSGKFVLTDAQALDRMREQLGYQAESGLVNQSTAIKKGRLVGADYSLYGKIS 151 (189)
T ss_pred EEEecccCCCCCcccHHHHHHHHHHHHHhCCCEEEEcHHHHHHHHHHHHHhhhcCCcCHHHHHHHHHhhCCCEEEEEEEE
Confidence 346777775 68999999999999988744432 2222222111121 1688999999999
Q ss_pred hhhhhhccccceeeeccchhhhhhhheeeeEeCcCCeeEEecceeeC
Q 046473 74 AQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQASSIFCGYVKI 120 (120)
Q Consensus 74 GerAR~e~~~eG~vp~sG~~~~~~idy~~~~a~tk~Gv~~~~~~~~~ 120 (120)
+-..+ .|.+-..++........++-|.++|.|..+|
T Consensus 152 ~~~~~-----------~~~~~~~~~~~~l~Lvd~~TG~ivWs~~~~I 187 (189)
T TIGR02722 152 SIVKS-----------DGSRKLVYYKFTMQLMDLKTGLIVWSDEKPI 187 (189)
T ss_pred EEEee-----------cCCCceEEEEEEEEEEEcCcceEEEecceEe
Confidence 74333 1222334456666777789999999997664
No 12
>PF13036 DUF3897: Protein of unknown function (DUF3897)
Probab=61.52 E-value=45 Score=24.74 Aligned_cols=96 Identities=18% Similarity=0.173 Sum_probs=59.8
Q ss_pred EEEEEEEecCC---CcCHHHHHHHHHHHhhhhhHH-------HHHHHHHHHHHHHhC------------CceeEEEEecc
Q 046473 14 VELYAEKVNNR---GLCAIAQAESLRKEGLAVIVC-------KMACYGVLRFIMESG------------AKGCEVIVSGK 71 (120)
Q Consensus 14 i~i~v~eV~~p---~l~a~i~A~~ia~qLe~r~~f-------Rra~~~ai~~~m~aG------------AkGikI~ISGr 71 (120)
-.|.|..|+|. .++...+.+.|..+|.+.-.| |-.+..-++.-.+.+ -.|..-.++|+
T Consensus 63 ~vv~v~~v~N~T~~~idt~~lt~~I~~~L~~sgk~~~v~~~~~~~~~~e~~~~~~~~~~~~~t~~~~g~~~gady~L~G~ 142 (180)
T PF13036_consen 63 PVVAVSPVKNDTSEHIDTEQLTNKIRTALLNSGKFRFVSGGQRDAMRQELRLQQEDGLVDQSTAIKLGRQLGADYMLSGK 142 (180)
T ss_pred eEEEEeccccCCCCccCHHHHHHHHHHHHHHCCCEEEEchHHHHHHHHHHhhcccccccCHHHHHHHhhccCCCEEEEEE
Confidence 44557777776 788999999999999876322 233444443332222 35888999999
Q ss_pred cchhhhhhccccceeeeccchhhhhhhheeeeEeCcCCeeEEecceeeC
Q 046473 72 LRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQASSIFCGYVKI 120 (120)
Q Consensus 72 L~GerAR~e~~~eG~vp~sG~~~~~~idy~~~~a~tk~Gv~~~~~~~~~ 120 (120)
+.+.+.+... .-.-+.......+..+-|.+||.|..+|
T Consensus 143 I~~~~~~~~~-----------~~~~~y~~~l~L~d~~tg~ivW~~~~~I 180 (180)
T PF13036_consen 143 ISSIVKRNGG-----------KQQVYYQFTLQLVDLETGEIVWSGEKEI 180 (180)
T ss_pred EEEeEeecCC-----------ceeEEEEEEEEEEEcCCCcEEecccccC
Confidence 9865321111 1111224445566679999999998765
No 13
>PHA03303 envelope glycoprotein L; Provisional
Probab=44.15 E-value=74 Score=24.44 Aligned_cols=53 Identities=9% Similarity=-0.068 Sum_probs=40.9
Q ss_pred ccCCCCCeEEEEEEEecCCC-cCHHHHHHHHHHHhhhh---hHHHHHHHHHHHHHHH
Q 046473 6 RFKFPENSVELYAEKVNNRG-LCAIAQAESLRKEGLAV---IVCKMACYGVLRFIME 58 (120)
Q Consensus 6 ~~~~~~~~i~i~v~eV~~p~-l~a~i~A~~ia~qLe~r---~~fRra~~~ai~~~m~ 58 (120)
+.+++.+...+..+.-+.++ .||.+++.-+++.+... --+|+|..++++.+..
T Consensus 76 r~hCp~PE~ILWy~~~~rAyWVNPf~~~~Glaedv~~~~~e~d~r~aL~~al~~al~ 132 (159)
T PHA03303 76 KSKCPIPELIIWFKDKHMAYWTNPYVMLHGLANSIGEEEKEDDIRDALLDALSGALQ 132 (159)
T ss_pred eccCCCCcEEEEeCCCCeeeEeCHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHh
Confidence 45666777777777666664 68888888888888743 5689999999998874
No 14
>PF13653 GDPD_2: Glycerophosphoryl diester phosphodiesterase family; PDB: 3RLG_A 2F9R_B 1XX1_A 3RLH_A.
Probab=36.42 E-value=39 Score=18.89 Aligned_cols=15 Identities=20% Similarity=0.368 Sum_probs=10.9
Q ss_pred HHHHHHHHhCCceeE
Q 046473 51 GVLRFIMESGAKGCE 65 (120)
Q Consensus 51 ~ai~~~m~aGAkGik 65 (120)
.+++.+|++|+.||-
T Consensus 11 ~~~~~~l~~GVDgI~ 25 (30)
T PF13653_consen 11 ASWRELLDLGVDGIM 25 (30)
T ss_dssp HHHHHHHHHT-SEEE
T ss_pred HHHHHHHHcCCCEee
Confidence 456788999999874
No 15
>PF14698 ASL_C2: Argininosuccinate lyase C-terminal; PDB: 1XWO_A 2E9F_A 1TJW_C 1TJU_A 1DCN_B 1K7W_B 1HY1_C 1TJV_B 1AUW_A 1U15_B ....
Probab=35.85 E-value=42 Score=21.76 Aligned_cols=34 Identities=24% Similarity=0.140 Sum_probs=18.3
Q ss_pred CHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhCCce
Q 046473 27 CAIAQAESLRKEGLAVIVCKMACYGVLRFIMESGAKG 63 (120)
Q Consensus 27 ~a~i~A~~ia~qLe~r~~fRra~~~ai~~~m~aGAkG 63 (120)
.|-=+|+.+..+ ++|||.|=+-+=+.+..+-..|
T Consensus 3 ~ATdlAD~LVr~---GipFR~AH~iVg~~V~~a~~~~ 36 (70)
T PF14698_consen 3 TATDLADYLVRK---GIPFREAHHIVGRLVRLAEEEG 36 (70)
T ss_dssp GHHHHHHHHHHT---TS-HHHHHHHHHHHHHHHHHTT
T ss_pred cHHHHHHHHHHc---CCCHHHHHHHHHHHHHHHHHcC
Confidence 344566666655 8999987555443333333333
No 16
>PF02355 SecD_SecF: Protein export membrane protein; InterPro: IPR022813 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains []. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. The SecD and SecF equivalents of the Gram-positive bacterium Bacillus subtilis are jointly present in one polypeptide, denoted SecDF, that is required to maintain a high capacity for protein secretion. Unlike the SecD subunit of the pre-protein translocase of E. coli, SecDF of B. subtilis was not required for the release of a mature secretory protein from the membrane, indicating that SecDF is involved in earlier translocation steps []. Comparison with SecD and SecF proteins from other organisms revealed the presence of 10 conserved regions in SecDF, some of which appear to be important for SecDF function. Interestingly, the SecDF protein of B. subtilis has 12 putative transmembrane domains. Thus, SecDF does not only show sequence similarity but also structural similarity to secondary solute transporters []. This entry represents bacterial SecD and SecF protein export membrane proteins and their archaeal homologues []. It is found in association with PF07549 from PFAM SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC []. SecD and SecF are required to maintain a proton motive force []. ; PDB: 3AQP_A 2RRN_A 3AQO_B.
Probab=30.05 E-value=73 Score=24.38 Aligned_cols=31 Identities=16% Similarity=0.032 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHhhh--hhHHHHHHHHHHHHHHH
Q 046473 28 AIAQAESLRKEGLA--VIVCKMACYGVLRFIME 58 (120)
Q Consensus 28 a~i~A~~ia~qLe~--r~~fRra~~~ai~~~m~ 58 (120)
..++-|+|.+.+.+ +.+++++++.++.+++.
T Consensus 101 ~IVifdRIre~~~~~~~~~~~~~~~~s~~~tl~ 133 (189)
T PF02355_consen 101 NIVIFDRIREELRASRGKSLREAINISIKQTLS 133 (189)
T ss_dssp HHHHHHHHHHHHCC-STS-HHHHHHHHHHHHHH
T ss_pred ceeehHHHHHHhhhCCCCCHHHHHHHHHHHHHH
Confidence 45788999999877 78999999998877654
No 17
>PF06069 PerC: PerC transcriptional activator; InterPro: IPR024684 This family includes PerC, which is a transcriptional activator of EaeA/BfpA expression in enteropathogenic bacteria []. It also includes a number of uncharacterised proteins, such as Orf40 from bacteriophage SfV.
Probab=23.10 E-value=1.1e+02 Score=21.20 Aligned_cols=25 Identities=16% Similarity=-0.007 Sum_probs=20.5
Q ss_pred HHHHHHHhhhhhHHHHHHHHHHHHH
Q 046473 32 AESLRKEGLAVIVCKMACYGVLRFI 56 (120)
Q Consensus 32 A~~ia~qLe~r~~fRra~~~ai~~~ 56 (120)
-+.+|++||.+--||||...=+.-.
T Consensus 3 ~d~~Ae~LE~kGl~RRAA~rW~evm 27 (90)
T PF06069_consen 3 HDKKAEELEAKGLWRRAATRWLEVM 27 (90)
T ss_pred chHHHHHHHHcccHHHHHHHHHHHH
Confidence 4789999999999999998765533
No 18
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=22.00 E-value=1.5e+02 Score=19.89 Aligned_cols=48 Identities=23% Similarity=0.193 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHhCCceeEEEEecccch-hhhhhccccceeeeccchhh
Q 046473 45 CKMACYGVLRFIMESGAKGCEVIVSGKLRA-QRATSMKFKDGYMISSGYPV 94 (120)
Q Consensus 45 fRra~~~ai~~~m~aGAkGikI~ISGrL~G-erAR~e~~~eG~vp~sG~~~ 94 (120)
...++...+..+.++=.+|=+|.|+| ++- +. +.-+-|.|+=|.||++.
T Consensus 21 ~~~~v~~~~~~i~~~L~~g~~V~i~g-fG~F~v-~~r~~R~grNP~Tge~i 69 (90)
T PRK10753 21 AKAALESTLAAITESLKEGDAVQLVG-FGTFKV-NHRAERTGRNPQTGKEI 69 (90)
T ss_pred HHHHHHHHHHHHHHHHHcCCeEEEcC-CEEEEE-eeeCCccccCCCCCCEE
Confidence 33444444444445556777899998 444 32 33345679999998764
No 19
>PF06213 CobT: Cobalamin biosynthesis protein CobT; InterPro: IPR006538 These proteins are CobT subunits of the aerobic cobalt chelatase (aerobic cobalamin biosynthesis pathway). Pseudomonas denitrificans CobT has been experimentally characterised [, ]. Aerobic cobalt chelatase consists of three subunits, CobT, CobN (IPR003672 from INTERPRO) and CobS (IPR006537 from INTERPRO). Cobalamin (vitamin B12) can be complexed with metal via the ATP-dependent reactions (aerobic pathway) (e.g., in P. denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in Salmonella typhimurium) [, ]. The corresponding cobalt chelatases are not homologous. However, aerobic cobalt chelatase subunits CobN and CobS are homologous to Mg-chelatase subunits BchH and BchI, respectively []. CobT, too, has been found to be remotely related to the third subunit of Mg-chelatase, BchD (involved in bacteriochlorophyll synthesis, e.g., in Rhodobacter capsulatus) []. Nomenclature note: CobT of the aerobic pathway P. denitrificans is not a homologue of CobT of the anaerobic pathway (Salmonella typhimurium, Escherichia coli). Therefore, annotation of any members of this family as nicotinate-mononucleotide--5,6-dimethylbenzimidazole phosphoribosyltransferases is erroneous.
Probab=20.51 E-value=1.1e+02 Score=24.52 Aligned_cols=27 Identities=33% Similarity=0.224 Sum_probs=21.7
Q ss_pred hHHHHHHHHHHHHHHHhCCceeEEEEecc
Q 046473 43 IVCKMACYGVLRFIMESGAKGCEVIVSGK 71 (120)
Q Consensus 43 ~~fRra~~~ai~~~m~aGAkGikI~ISGr 71 (120)
-+||+|+-.+++.+ +|-.|++|.++|-
T Consensus 10 e~fk~Al~~~~rAi--a~~~~l~V~~~~~ 36 (282)
T PF06213_consen 10 EPFKRALAAVARAI--AGDFELEVRFGGD 36 (282)
T ss_pred HHHHHHHHHHHHHH--cCCCCceEEeCCC
Confidence 36999998888754 6778999999774
Done!