Query 014066
Match_columns 431
No_of_seqs 156 out of 1152
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 01:31:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014066.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014066hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1685 Uncharacterized conser 100.0 2.6E-54 5.6E-59 430.7 10.7 318 10-328 10-336 (343)
2 PTZ00029 60S ribosomal protein 100.0 9.7E-47 2.1E-51 360.0 21.9 215 16-255 1-216 (216)
3 PRK04203 rpl1P 50S ribosomal p 100.0 1.6E-45 3.5E-50 351.3 20.5 212 19-256 2-215 (215)
4 PTZ00225 60S ribosomal protein 100.0 3.6E-45 7.8E-50 348.7 21.4 213 16-255 1-214 (214)
5 PF00687 Ribosomal_L1: Ribosom 100.0 2.8E-43 6.1E-48 333.6 17.5 212 28-251 1-220 (220)
6 cd00403 Ribosomal_L1 Ribosomal 100.0 7.7E-43 1.7E-47 328.7 20.0 205 24-254 1-208 (208)
7 COG0081 RplA Ribosomal protein 100.0 5.2E-34 1.1E-38 272.0 20.3 207 18-257 17-228 (228)
8 CHL00129 rpl1 ribosomal protei 100.0 2.5E-33 5.4E-38 269.9 21.5 200 23-257 21-226 (229)
9 PRK05424 rplA 50S ribosomal pr 100.0 1.1E-32 2.4E-37 265.6 21.0 200 23-257 21-226 (230)
10 TIGR01169 rplA_bact ribosomal 100.0 2E-32 4.2E-37 263.4 21.6 200 23-257 20-225 (227)
11 KOG1570 60S ribosomal protein 100.0 9.8E-30 2.1E-34 238.3 8.4 216 16-255 2-218 (218)
12 KOG1569 50S ribosomal protein 99.8 5.2E-19 1.1E-23 174.0 16.1 185 52-257 114-306 (323)
13 TIGR01170 rplA_mito ribosomal 99.7 7.3E-16 1.6E-20 139.0 12.4 137 24-191 3-140 (141)
14 PF13003 MRL1: Ribosomal prote 89.3 0.97 2.1E-05 40.9 6.0 61 22-93 70-133 (133)
15 PF00370 FGGY_N: FGGY family o 21.9 1.4E+02 0.0031 28.3 4.7 52 208-259 39-90 (245)
No 1
>KOG1685 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.6e-54 Score=430.74 Aligned_cols=318 Identities=43% Similarity=0.616 Sum_probs=273.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCCCccceeeEeCCCCCCCCCCC-CCC
Q 014066 10 SLPPSAGSRVSPKTVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQVSRTNAFKIPLPHSLLGNDSD-NPP 88 (431)
Q Consensus 10 ~~~~~~~s~v~~e~V~kAVkaLlk~~~~~~~~~K~~Lfeed~~V~L~VtLKkip~k~k~~p~~I~LPHpl~~~~~~-~~~ 88 (431)
..++++++++++..+.-|+.++..+.......+.+++++++..+|.....++++.....+...||+||++...... .+.
T Consensus 10 ~~~~~~~~~v~~~~~e~~~k~~~~~~~~~~k~~~~~~~~~~k~~~~~~~~k~~~~~~~~n~~~IP~k~~~~~~~~~~~~~ 89 (343)
T KOG1685|consen 10 SSTAIPRESVSPKNVESAVKALDKEREKKSKAENPQLLEALKNVYKVVLQKNTPQKVGTNKLKIPLKHLLKKLLLKHDDT 89 (343)
T ss_pred ccccccccccCchhhhHHHhhhhhhhHHHHHhhhhhhhhhhhhhHHHHHHHhcccccccccccccCcchhcccccCCCCC
Confidence 3567788899999999999999998777665555788887777777766667677666677788899988765411 378
Q ss_pred EEEEEecCCCCCchhHHHHHHHhhhCCCC-cceeeehhhhhhhcchHHHHhhccccccEEEEcCCchhhhhhhhcccccC
Q 014066 89 EICLIMDDRPKSNLTKDAVMKKIKNDNLP-ITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFK 167 (431)
Q Consensus 89 kICLIvkD~~~~~~t~~e~kekl~a~~i~-i~kVI~lkkLk~kyKsfE~kRKL~~sYDlFLAD~rI~~~LpklLGK~F~k 167 (431)
+||||++|+++..+|.++|++++.++|++ |.+||++++|+.+|++||++|+|+++||+||||+||+|+||++|||.||+
T Consensus 90 ~vcLIvkD~~~~~~t~~~~~d~l~~~gi~~itkVI~~~~LK~~yksyeaKr~L~~sfDlflaD~RV~~~LP~llGK~f~q 169 (343)
T KOG1685|consen 90 DVCLIVKDLQQSYLTEEDAEDLLESEGIKSITKVISLSKLKRDYKSYEAKRKLLSSFDLFLADDRVIPLLPKLLGKEFYQ 169 (343)
T ss_pred ceEEEecCchhccccHHHHHHHHHHcCCccceeeeehHHHHHHHHHHHHHHHHHhhccEEEEcchhHhHHHHHhhhhhcc
Confidence 99999999999989999999999999999 99999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeecCCccc--HHHHHHHHHccceEEccCCCEEEEEEecCCCChhHHHHHHHHHHHHHHHhcCCCCCCccEEEEE
Q 014066 168 KKKIPVPVDLKHQN--WKEQIEKVCGSALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGVAEIVPRKWGNVRSFHLK 245 (431)
Q Consensus 168 kkK~PipV~lt~~d--Lk~~Ieka~~St~~~l~kG~~~sVkVG~~sMs~eqIvENI~avl~~l~~~lPkg~~NIksI~LK 245 (431)
+++.|+||++.+.+ |..+|++||++|+|+++.|+|+.|+|||++|+.++|+|||.++++.+.+.+|+||.||++||||
T Consensus 170 ~kk~Pv~i~l~k~~~~l~~qi~~a~~~t~~~~~~g~~~~i~vg~l~~~~~~l~ENv~~vlk~l~e~~P~~~~~Irsl~lK 249 (343)
T KOG1685|consen 170 KKKVPVSIRLSKKNELLKQQIENACGSTYFRLRKGTSSAIKVGHLGNTSEELAENVVAVLKGLSEILPGGWKNIRSLHLK 249 (343)
T ss_pred cccCceEEEecccchHHHHHHHHHhhhheeeccCCceeEEEeccccccHHHHHHHHHHHHHHHHHHccchHhHhHHHhhh
Confidence 99999999998777 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCcceEEeccCCCCcccccccccCCCCCCCcccccc---ccccccc--ccccccccccCceeeEEEeecccccccccc
Q 014066 246 LLESLALPVYQAVPDLKLKIEGVKENEGEGQDKDSEKE---NAEDVND--HGSKKKLKKKKGRIHEVRYMDSTIGEVLDE 320 (431)
Q Consensus 246 tt~S~aLPIY~s~~~~~~~i~~~~~~~~~~~~~~~~~~---~~~~~~~--~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~ 320 (431)
|..|++||||++++.+++.+...+..++-. +..++.. ....... .....+.+.++|+||+++|||.+..+.++.
T Consensus 250 t~~s~aLPly~s~~~~~~~~~~~~~i~~~~-~~k~~~~~~~k~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~e~~~~ 328 (343)
T KOG1685|consen 250 TSRSPALPLYVSVISLKEIASKRGSIRDFV-ELKETQKKERKSDLSLFGKGKKEIKIKVKKGSIDSKQQNDSNKAEVLDL 328 (343)
T ss_pred ccCCcccceeecccchhhhhcccCchhhhh-HHHhhhhhhhhccccccchhhhHhhhhhhccchhhHHhccchhhhhccc
Confidence 999999999999999999888877555311 1111111 1122111 334456678889999999999999999999
Q ss_pred cccCCCCC
Q 014066 321 DELGSDDD 328 (431)
Q Consensus 321 ~~~~~~~~ 328 (431)
|....|.|
T Consensus 329 d~~~~~~d 336 (343)
T KOG1685|consen 329 DEEKKDSD 336 (343)
T ss_pred cccccccc
Confidence 98877654
No 2
>PTZ00029 60S ribosomal protein L10a; Provisional
Probab=100.00 E-value=9.7e-47 Score=359.97 Aligned_cols=215 Identities=24% Similarity=0.400 Sum_probs=194.0
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccC-CCCCccceeeEeCCCCCCCCCCCCCCEEEEEe
Q 014066 16 GSRVSPKTVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKI-PQVSRTNAFKIPLPHSLLGNDSDNPPEICLIM 94 (431)
Q Consensus 16 ~s~v~~e~V~kAVkaLlk~~~~~~~~~K~~Lfeed~~V~L~VtLKki-p~k~k~~p~~I~LPHpl~~~~~~~~~kICLIv 94 (431)
||.++++++++||++|++|. ..+...|.| +|+++|+|+++ |.+.+..++.|.|||++++ ..+||||+
T Consensus 1 m~~~~~~~~~~av~~~~~~~-----~~~~~~f~e--sv~~~i~Lk~id~~~~~~ir~~v~LP~~~gk-----~~~v~V~a 68 (216)
T PTZ00029 1 MSKLSSEALRKAIAEILEGS-----EEKKRKFVE--TVELQIGLKDYDTQKDKRFSGSVKLPNVPKP-----NLKVCVLG 68 (216)
T ss_pred CCcCCHHHHHHHHHHHHhhc-----cccccCCce--EEEEEEEcCCCCCCcCcccceeEecCCCCCC-----CcEEEEEC
Confidence 45789999999999999872 234567776 99999999998 4445667889999999986 68999999
Q ss_pred cCCCCCchhHHHHHHHhhhCCCCcceeeehhhhhhhcchHHHHhhccccccEEEEcCCchhhhhhhhcccccCCCCCCee
Q 014066 95 DDRPKSNLTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVP 174 (431)
Q Consensus 95 kD~~~~~~t~~e~kekl~a~~i~i~kVI~lkkLk~kyKsfE~kRKL~~sYDlFLAD~rI~~~LpklLGK~F~kkkK~Pip 174 (431)
+++.. +.++++|+ +|++.++|...|+.++.+|+|+.+||+||||+++|+.||++||+.||+++|+|+|
T Consensus 69 ~~~~~---------~~Ak~aGa---~vvg~edL~~~~k~~k~~kkl~~~fD~flA~~~im~~l~riLGp~l~p~~K~P~~ 136 (216)
T PTZ00029 69 DAVHC---------DEAKKLGL---DFMDIEGLKKFNKNKKLVKKLAKKYDAFLASQSLLPQIPRLLGPGLNKAGKFPTL 136 (216)
T ss_pred CcHHH---------HHHHHcCC---CEecHHHHHHhhhhHHHHhcccccCCEEEECHHHHHHHHHHhccccccCCCCCCc
Confidence 88742 22456676 4999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCcccHHHHHHHHHccceEEccCCCEEEEEEecCCCChhHHHHHHHHHHHHHHHhcCCCCCCccEEEEEcCCCcceEE
Q 014066 175 VDLKHQNWKEQIEKVCGSALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGVAEIVPRKWGNVRSFHLKLLESLALPV 254 (431)
Q Consensus 175 V~lt~~dLk~~Ieka~~St~~~l~kG~~~sVkVG~~sMs~eqIvENI~avl~~l~~~lPkg~~NIksI~LKtt~S~aLPI 254 (431)
++.+ .+|...|+++++++.|++++++|++++||+++|+++||+|||.+++++|.+.+|+||+||++|||||||||++||
T Consensus 137 v~~~-~d~~~~i~~~k~~v~~r~~k~~~i~v~VG~~~~~~e~l~eNi~avl~~i~~~~~kg~~~Iksv~lktTmgp~v~v 215 (216)
T PTZ00029 137 ITHN-DDIEDKINELKSSVKFQLKKVLCLGVAVGNVEMTEEQLRQNIVLSINFLVSLLKKNWQNIKTLHIKSTMGKPQRI 215 (216)
T ss_pred ccCc-cCHHHHHHHHHheEEEEECCCCEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHhccccccEeEEEEECCCCCCEeC
Confidence 9875 689999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred e
Q 014066 255 Y 255 (431)
Q Consensus 255 Y 255 (431)
|
T Consensus 216 ~ 216 (216)
T PTZ00029 216 Y 216 (216)
T ss_pred C
Confidence 7
No 3
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=100.00 E-value=1.6e-45 Score=351.25 Aligned_cols=212 Identities=24% Similarity=0.305 Sum_probs=190.6
Q ss_pred CCHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCC--CccceeeEeCCCCCCCCCCCCCCEEEEEecC
Q 014066 19 VSPKTVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQV--SRTNAFKIPLPHSLLGNDSDNPPEICLIMDD 96 (431)
Q Consensus 19 v~~e~V~kAVkaLlk~~~~~~~~~K~~Lfeed~~V~L~VtLKkip~k--~k~~p~~I~LPHpl~~~~~~~~~kICLIvkD 96 (431)
++++++.+||+.|+++ .+.+.|.| +|+|+|+||+++.+ .+..++.|.|||++++ ..+||||+++
T Consensus 2 ~~~~~~~eai~~~k~~-------~~~~kf~e--svel~v~Lk~id~~k~~~~irg~i~LP~~~~k-----~~~V~vf~~~ 67 (215)
T PRK04203 2 MDREKIEEAVKEALEE-------APKRNFTQ--SVDLIVNLKDIDLKKPENRIDEEVVLPHGRGK-----EVKIAVIAKG 67 (215)
T ss_pred CcHHHHHHHHHHHHHh-------cccCCCCc--eEEEEEEecCCCCCccCceeeEEEECCCCCCC-----CcEEEEEcCh
Confidence 6889999999999863 24566877 99999999999775 2455789999999976 6899999998
Q ss_pred CCCCchhHHHHHHHhhhCCCCcceeeehhhhhhhcchHHHHhhccccccEEEEcCCchhhhhhhhcccccCCCCCCeeec
Q 014066 97 RPKSNLTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVD 176 (431)
Q Consensus 97 ~~~~~~t~~e~kekl~a~~i~i~kVI~lkkLk~kyKsfE~kRKL~~sYDlFLAD~rI~~~LpklLGK~F~kkkK~PipV~ 176 (431)
++. ++ ++++|+ ..|++.+.|++.++.|+++|+|+.+||+||||+++|+.||++||+.||++++||+|+.
T Consensus 68 ~~~-----~~----Ak~aGa--~~v~~~e~L~~i~~~~k~~rkl~~~fD~~lA~~~im~~l~k~LGk~lgprgkmP~p~~ 136 (215)
T PRK04203 68 ELA-----LQ----AKEAGA--DYVITREELEELGGDKRAAKKLANEYDFFIAEADLMPLIGRYLGPVLGPRGKMPTPLP 136 (215)
T ss_pred HhH-----HH----HHHcCC--CEEeCHHHHHHHhcChHHHhhhhhcCCEEEECHHHHHHHHHHHhhhcCcCCCCCCCcC
Confidence 742 22 335565 3589999999888889999999999999999999999999999999999999999999
Q ss_pred CCcccHHHHHHHHHccceEEccCCCEEEEEEecCCCChhHHHHHHHHHHHHHHHhcCCCCCCccEEEEEcCCCcceEEec
Q 014066 177 LKHQNWKEQIEKVCGSALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGVAEIVPRKWGNVRSFHLKLLESLALPVYQ 256 (431)
Q Consensus 177 lt~~dLk~~Ieka~~St~~~l~kG~~~sVkVG~~sMs~eqIvENI~avl~~l~~~lPkg~~NIksI~LKtt~S~aLPIY~ 256 (431)
++. ||...|++++++++|++++++|++++||+++|+++||+|||.+++++|.+.+|+||+||++|||||||||++|||.
T Consensus 137 ~t~-di~~~i~~~~~~~~~r~~k~~~i~v~VG~~~m~~e~l~eNi~avl~~i~~~~p~g~~~Iksi~lktTmgp~i~i~~ 215 (215)
T PRK04203 137 PNA-DIKPLVERLKNTVRIRTKDQPTFHVRVGTEDMSPEELAENIDAVLNRIESKLEKGRQNIKSVYVKTTMGPAVKVEL 215 (215)
T ss_pred CCC-CHHHHHHHHhhceEEEeCCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCccccccEEEEEEECCCCCCEEeeC
Confidence 875 9999999999999999999999999999999999999999999999999999999999999999999999999984
No 4
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=100.00 E-value=3.6e-45 Score=348.73 Aligned_cols=213 Identities=24% Similarity=0.426 Sum_probs=190.2
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccC-CCCCccceeeEeCCCCCCCCCCCCCCEEEEEe
Q 014066 16 GSRVSPKTVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKI-PQVSRTNAFKIPLPHSLLGNDSDNPPEICLIM 94 (431)
Q Consensus 16 ~s~v~~e~V~kAVkaLlk~~~~~~~~~K~~Lfeed~~V~L~VtLKki-p~k~k~~p~~I~LPHpl~~~~~~~~~kICLIv 94 (431)
||.|+++++.+||++|+++. +.+.|.| +|+|+|+|+++ |.+.+..++.|.|||++++ ..+||||+
T Consensus 1 m~k~~~~~i~~Av~~~lk~~-------~~~kF~E--tvdl~v~Lk~iDp~kd~~irg~v~LPhg~gk-----~~kV~v~~ 66 (214)
T PTZ00225 1 MSKIPPQTLSEAIQAVLKVD-------KERKFKE--SIDLQVNLKNYDPQKDKRFSGSLKLPNVCRP-----RMTVCLLC 66 (214)
T ss_pred CCcCCHHHHHHHHHHHHHhc-------ccCCCCc--eEEEEEeccCcCCCcCcccceeEECCCCCCC-----CcEEEEEC
Confidence 46789999999999998743 3345766 99999999998 6666777899999999986 68999999
Q ss_pred cCCCCCchhHHHHHHHhhhCCCCcceeeehhhhhhhcchHHHHhhccccccEEEEcCCchhhhhhhhcccccCCCCCCee
Q 014066 95 DDRPKSNLTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVP 174 (431)
Q Consensus 95 kD~~~~~~t~~e~kekl~a~~i~i~kVI~lkkLk~kyKsfE~kRKL~~sYDlFLAD~rI~~~LpklLGK~F~kkkK~Pip 174 (431)
+++.. +.++++|++ +++.++|....+.+++.|+||.+||+|||++++|+.||++||+.|++++|||+|
T Consensus 67 ~~~~~---------~~Ak~aGad---~v~~e~l~~l~k~~~~~kkl~~~fD~fiA~~~~m~~lgk~LGp~~~p~gK~P~~ 134 (214)
T PTZ00225 67 DLVHE---------DIAKKEGVP---TMNQEELKKLNKNKKLVKKMCNQYDAFLCSESIIKTVPRLVGPHMHRMGKFPTV 134 (214)
T ss_pred ChHHH---------HHHHHCCCC---EECHHHHHHHHhccHHHHHHHhhCCEEEECHHHHHhhhhhcCCCCCcCCCCCcc
Confidence 98753 224567775 777777777777778899999999999999999999999999999999999999
Q ss_pred ecCCcccHHHHHHHHHccceEEccCCCEEEEEEecCCCChhHHHHHHHHHHHHHHHhcCCCCCCccEEEEEcCCCcceEE
Q 014066 175 VDLKHQNWKEQIEKVCGSALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGVAEIVPRKWGNVRSFHLKLLESLALPV 254 (431)
Q Consensus 175 V~lt~~dLk~~Ieka~~St~~~l~kG~~~sVkVG~~sMs~eqIvENI~avl~~l~~~lPkg~~NIksI~LKtt~S~aLPI 254 (431)
++++ .|+...|+++.+++.|++++..|++++||+++|+++||+||+.++++.|.+.+|.+|+||++|||||||||++.|
T Consensus 135 ~~~~-~dl~~~i~~~k~~v~~r~~k~~~~~~~VGk~~m~~e~i~eNi~a~l~~l~~~~p~k~~nIksv~iktTMGp~~~~ 213 (214)
T PTZ00225 135 CSPS-ESLPDKVVELRSTVKFQLKKVLCLGTCVGHVEMTEEQLRQNVVMAINFLVSLLKKNWQNLKSAYIKSTMGKPQRI 213 (214)
T ss_pred cCCc-cCHHHHHHHHhheeEEEecCccEEEeEEccCCCCHHHHHHHHHHHHHHHHHhCCcCCceEeEEEEECCCCCCEeC
Confidence 9876 699999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred e
Q 014066 255 Y 255 (431)
Q Consensus 255 Y 255 (431)
|
T Consensus 214 ~ 214 (214)
T PTZ00225 214 Y 214 (214)
T ss_pred C
Confidence 7
No 5
>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-43 Score=333.62 Aligned_cols=212 Identities=42% Similarity=0.661 Sum_probs=179.0
Q ss_pred HHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCCC--ccceeeEeCCCCCCCCCCCCCCEEEEEecCCCCCchhHH
Q 014066 28 VKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQVS--RTNAFKIPLPHSLLGNDSDNPPEICLIMDDRPKSNLTKD 105 (431)
Q Consensus 28 VkaLlk~~~~~~~~~K~~Lfeed~~V~L~VtLKkip~k~--k~~p~~I~LPHpl~~~~~~~~~kICLIvkD~~~~~~t~~ 105 (431)
|+||++|+++..+ .......+++|+|+|+++.+|.+. +..++.|+||||++. +..+||||++|++..
T Consensus 1 ~~aL~k~~~~~~~--~~~~~~~~~~v~l~i~~~~~~~~~~~~~~~~~i~LPh~~~~----~~~~vcli~~d~~~~----- 69 (220)
T PF00687_consen 1 IKALKKYIKKKKE--ENEDDNFDESVYLQITLKKIPKKKDKSFKPGRIPLPHPLYI----KNSKVCLIVKDPQKK----- 69 (220)
T ss_dssp HTCHHHHHHHHHH--CCCCSSSSTEEEEEEEESSSTTSSCTST-EEEEEBSTSSS-----SSSBEEEEESCHHHH-----
T ss_pred ChHHHHHHHHHHh--hcccCCCCcEEEEEEEeCcCCCccccccccceeeecCCCCC----CccEEEEEecCcchh-----
Confidence 6789999887532 122334456999999999998875 334899999999982 278999999998642
Q ss_pred HHHH--HhhhCCC-CcceeeehhhhhhhcchHHHHhhccccccEEEEcCCchhhhhhhhcccc-cCCCCCCeeecCCccc
Q 014066 106 AVMK--KIKNDNL-PITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHF-FKKKKIPVPVDLKHQN 181 (431)
Q Consensus 106 e~ke--kl~a~~i-~i~kVI~lkkLk~kyKsfE~kRKL~~sYDlFLAD~rI~~~LpklLGK~F-~kkkK~PipV~lt~~d 181 (431)
+.+ ++.+.+. .+.+||++++|+++|++|+++|+|+.+||+||||+||++.||++||+.| +++++||+||.++..+
T Consensus 70 -~~~~~~~~~~~~~~~~~vi~~~~L~~~~~~~~~~r~l~~~~d~flad~~i~~~l~~~Lgk~~~~~k~k~P~~v~~~~~~ 148 (220)
T PF00687_consen 70 -AKEKEKLEEKAVEAGAKVIGGEELKKKYKTIEAKRKLAKSYDFFLADPRIMPKLPKLLGKIFYGKKGKMPIPVTLSKED 148 (220)
T ss_dssp -HH-------HHHHTTCSEEECHHHHHHHCHHHHCHHHHHCSSEEEEEGGGHHHHHHHTHHHH-CCTTTSCEEBSSHTSC
T ss_pred -hhhhhhhhhhhhhcccceecHHHHHHHHHHHHHHHHHHhhcCEEEECHHHHHHHHHhhhhheecccCCcceEEeccchh
Confidence 211 1111111 2346999999999999999999999999999999999999999999999 5788999999875579
Q ss_pred HHHHHHHHHccceEEcc-CCCEEEEEEecCCCChhHHHHHHHHHHHHHHHh-cCCCCCCccEEEEEcCCCcc
Q 014066 182 WKEQIEKVCGSALLYLR-TGTCSVLKVGKVSMGAEDIAENVIAAINGVAEI-VPRKWGNVRSFHLKLLESLA 251 (431)
Q Consensus 182 Lk~~Ieka~~St~~~l~-kG~~~sVkVG~~sMs~eqIvENI~avl~~l~~~-lPkg~~NIksI~LKtt~S~a 251 (431)
|.++|+++++++.|+++ .|+|++|+||+++|+.+||+|||.+++++|.++ +|+||.||++||||||||||
T Consensus 149 l~~~i~~~~~~~~~~~~~~~~~~~v~VG~~~~~~~~i~eNi~~~i~~i~~~~~~~g~~~I~~i~ikst~s~~ 220 (220)
T PF00687_consen 149 LKEQIEKALNSTKFRLSGKGGCISVKVGHLSMTDEQIVENIKAVIKAIVSKPLPKGWKNIKSIYIKSTMSPS 220 (220)
T ss_dssp HHHHHHHHHTEEEEEETBTSSEEEEEEEETTSCHHHHHHHHHHHHHHHHHTTTSSSSGSEEEEEEEESSSEE
T ss_pred HHHHHHHHHCCEEEEeeccCCeeecCccCCCCCHHHHHHHHHHHHHHHHHhhhccCcceEEEEEEECCCCCC
Confidence 99999999999999988 999999999999999999999999999999999 99999999999999999986
No 6
>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=7.7e-43 Score=328.66 Aligned_cols=205 Identities=34% Similarity=0.465 Sum_probs=181.1
Q ss_pred HHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCC-CccceeeEeCCCCCCCCCCCCCCEEEEEecCCCCCch
Q 014066 24 VERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQV-SRTNAFKIPLPHSLLGNDSDNPPEICLIMDDRPKSNL 102 (431)
Q Consensus 24 V~kAVkaLlk~~~~~~~~~K~~Lfeed~~V~L~VtLKkip~k-~k~~p~~I~LPHpl~~~~~~~~~kICLIvkD~~~~~~ 102 (431)
+.+|+++|.+|.. ....|. ++|+|+|+|+.++.+ ....++.|.||||++. ..+||||++|++..
T Consensus 1 ~~~Ai~~l~~~~~------~~~~~~--~~v~l~i~l~~~~~~~~~~~~~~i~LPh~~~~-----~~~i~v~~~d~~~~-- 65 (208)
T cd00403 1 LEEAIKALKKTSV------KKRKFD--ETVELQINLKKDDRKKDQRIRGTVILPHGLGK-----DVKVCVFAKDEQAK-- 65 (208)
T ss_pred CHHHHHHHHHhcc------ccCCCC--ceEEEEEEeCCCCCccccccceeEECCCCCCC-----CeEEEEEcChHhHH--
Confidence 3589999988643 222333 499999999998633 3456789999999984 78999999988642
Q ss_pred hHHHHHHHhhhCCCCcceeeehhhhhhhcchHHHHhhccccccEEEEcCCchhhhhhhhcccccCCCCCCeeecCC-ccc
Q 014066 103 TKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVDLK-HQN 181 (431)
Q Consensus 103 t~~e~kekl~a~~i~i~kVI~lkkLk~kyKsfE~kRKL~~sYDlFLAD~rI~~~LpklLGK~F~kkkK~PipV~lt-~~d 181 (431)
+. .+.++ +|+++++|+.+|++|+++ +|+.+||+||||+++++.+|+.||+.||++++||+++.++ ..+
T Consensus 66 ----~a---~~~~a---~vig~~~L~~~~~~~~~~-~l~~~~D~fla~~~~~~~~~~~lgk~~~~k~k~P~~~~~t~~~~ 134 (208)
T cd00403 66 ----EA---KAAGA---DVVGGEDLKKKIKNGEAK-KLAKDFDLFLADPRIMMLLPKLLGKVLGPRGKMPNPKTGTVTED 134 (208)
T ss_pred ----HH---HHcCC---CEEcHHHHHHHhhcchhh-hhhhcCCEEEECHHHHHHHHHHhccccccCCCCCcCCCCCCccc
Confidence 21 22343 699999999999999999 9999999999999999999999999999999999999985 679
Q ss_pred HHHHHHHHHccceEEccCCCEEEEEEecCCCChhHHHHHHHHHHHHHHHhcC-CCCCCccEEEEEcCCCcceEE
Q 014066 182 WKEQIEKVCGSALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGVAEIVP-RKWGNVRSFHLKLLESLALPV 254 (431)
Q Consensus 182 Lk~~Ieka~~St~~~l~kG~~~sVkVG~~sMs~eqIvENI~avl~~l~~~lP-kg~~NIksI~LKtt~S~aLPI 254 (431)
|.++|++++++++|++++++|++++||+++|+++||+|||.+++++|.+++| +||+||++|||||+||++|||
T Consensus 135 l~~~i~~~~~~~~~~~~~~~~~~v~VG~~~m~~~~l~eNi~~vi~~i~~~~~~~~~~~i~~v~lktt~~~~lpI 208 (208)
T cd00403 135 LAKAIEEAKSSVEFRLDKGGCIHVPVGKVSMSPEQLVENIEAVINALVKKLPSKKGQNIKSIYLKTTMGPSLPI 208 (208)
T ss_pred HHHHHHHHHhCeEEEECCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCCcccCeEEEEEEEECCCCCCeEC
Confidence 9999999999999999999999999999999999999999999999999999 999999999999999999997
No 7
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.2e-34 Score=271.99 Aligned_cols=207 Identities=20% Similarity=0.252 Sum_probs=175.6
Q ss_pred CCCHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCC-CccceeeEeCCCCCCCCCCCCCCEEEEEecC
Q 014066 18 RVSPKTVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQV-SRTNAFKIPLPHSLLGNDSDNPPEICLIMDD 96 (431)
Q Consensus 18 ~v~~e~V~kAVkaLlk~~~~~~~~~K~~Lfeed~~V~L~VtLKkip~k-~k~~p~~I~LPHpl~~~~~~~~~kICLIvkD 96 (431)
+.....+.+||+.+.+ .. ...|++ +|+++|+|+-.|.+ .+...+.|.|||+.++ ..+||||+++
T Consensus 17 ~~~~~~i~eai~~~ke-------~~-~~kF~e--tVevav~L~vD~~k~dq~vrg~VvLP~g~gk-----~vrV~Vfa~g 81 (228)
T COG0081 17 RNKLYSLEEAVKLLKE-------TS-KRKFDE--TVEVAVNLKVDPRKPDQRVRGSVVLPNGTGK-----TVRVAVFADG 81 (228)
T ss_pred hhhhhhHHHHHHHHHh-------cc-ccCcce--EEEEEEEcccCCCCcccccceeEECCCCCCC-----ccEEEEEcCh
Confidence 3455667888887766 22 367887 99999999943434 4667789999999987 6899999976
Q ss_pred CCCCchhHHHHHHHhhhCCCCcceeeehhhhhhhcchHHHHhhccccccEEEEcCCchhhhhhhhcccccCCCCCCeeec
Q 014066 97 RPKSNLTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVD 176 (431)
Q Consensus 97 ~~~~~~t~~e~kekl~a~~i~i~kVI~lkkLk~kyKsfE~kRKL~~sYDlFLAD~rI~~~LpklLGK~F~kkkK~PipV~ 176 (431)
... +.+.++|++ +++.++|....+. .| +.+||+|||++++|+.+ +.||+.|+|||+||+|+.
T Consensus 82 ~~~---------~~A~~AGad---~Vg~edl~e~ik~---~r--~~~fD~~IAtpdmM~~v-~~LG~vLGPRGlMP~Pk~ 143 (228)
T COG0081 82 EKA---------EEAKAAGAD---YVGGEDLIELIKN---GR--AKDFDVFIATPDMMPLV-GKLGKVLGPRGLMPNPKT 143 (228)
T ss_pred HhH---------HHHHHcCCC---EecHHHHHHHHhC---cc--hhcCCEEEECchHHHHH-HHHhhhcCCCCCCCCCCC
Confidence 542 223456663 4444888887765 34 88999999999999999 789999999999999999
Q ss_pred CC-cccHHHHHHHHHc-cceEEccCCCEEEEEEecCCCChhHHHHHHHHHHHHHHHhcCCC--CCCccEEEEEcCCCcce
Q 014066 177 LK-HQNWKEQIEKVCG-SALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGVAEIVPRK--WGNVRSFHLKLLESLAL 252 (431)
Q Consensus 177 lt-~~dLk~~Ieka~~-St~~~l~kG~~~sVkVG~~sMs~eqIvENI~avl~~l~~~lPkg--~~NIksI~LKtt~S~aL 252 (431)
+| +.|+...|+++.+ ++.||.++.+|+|+.||+++|++++|+|||.++++.|...+|.+ |+||++|||+|||||++
T Consensus 144 gTvt~Dv~~av~~~K~g~v~~R~dk~g~ih~~iGk~sf~~e~L~eNi~a~l~~i~~~~p~~~kg~~ik~v~vstTMGP~v 223 (228)
T COG0081 144 GTVTDDVAKAVEELKKGTVEFRADKAGVIHVPIGKVSFDDEKLAENIEALLNAIVKAKPAGAKGQYIKSVYVSTTMGPGV 223 (228)
T ss_pred CCCCcCHHHHHHHHhcCcEEEEECCCceEEEEecCCCCCHHHHHHHHHHHHHHHHHhCcCCcccceEeEEEEecCCCCCE
Confidence 76 6899999999999 88999999999999999999999999999999999999999987 99999999999999999
Q ss_pred EEecc
Q 014066 253 PVYQA 257 (431)
Q Consensus 253 PIY~s 257 (431)
.||.+
T Consensus 224 ~v~~~ 228 (228)
T COG0081 224 KVDLA 228 (228)
T ss_pred EeccC
Confidence 99863
No 8
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=100.00 E-value=2.5e-33 Score=269.86 Aligned_cols=200 Identities=17% Similarity=0.187 Sum_probs=172.1
Q ss_pred HHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCC--CccceeeEeCCCCCCCCCCCCCCEEEEEecCCCCC
Q 014066 23 TVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQV--SRTNAFKIPLPHSLLGNDSDNPPEICLIMDDRPKS 100 (431)
Q Consensus 23 ~V~kAVkaLlk~~~~~~~~~K~~Lfeed~~V~L~VtLKkip~k--~k~~p~~I~LPHpl~~~~~~~~~kICLIvkD~~~~ 100 (431)
.+.+||+.|++ . +...|.| +|+|+|+| +++.+ .....+.|.|||++++ ..+||||+++...
T Consensus 21 ~l~eAi~~~k~-------~-~~~kF~e--svel~i~L-~id~kk~~~~irg~v~LP~~~gk-----~~kV~Vfa~~~~~- 83 (229)
T CHL00129 21 SPEEAINLLKE-------T-ATAKFIE--TAEAHISL-NIDPKYADQQLRTTVTLPKGTGK-----TIRIAVLTNEEKI- 83 (229)
T ss_pred CHHHHHHHHHH-------h-CcCCCCc--cEEEEEEE-CCCCCCCCCceeeEEECCCCCCC-----CcEEEEECChHhH-
Confidence 46788888875 1 2355776 99999999 66444 3566789999999976 6899999998642
Q ss_pred chhHHHHHHHhhhCCCCcceeeehhhhhhhcchHHHHhhccccccEEEEcCCchhhhhhhhcccccCCCCCCeeecCC-c
Q 014066 101 NLTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVDLK-H 179 (431)
Q Consensus 101 ~~t~~e~kekl~a~~i~i~kVI~lkkLk~kyKsfE~kRKL~~sYDlFLAD~rI~~~LpklLGK~F~kkkK~PipV~lt-~ 179 (431)
++ +.++|+. +++.++|...+ ++++.+||+|||++++|+.|++ ||+.|++||+||+|..+| .
T Consensus 84 ----~e----Ak~aGad---~vg~edLi~~i------k~~~~~fd~~iAt~d~m~~l~k-LgriLGprGlMP~pk~gTvt 145 (229)
T CHL00129 84 ----TE----AKNAGAD---IVGSDDLIEEI------TKGNLDFDLLIATPDMMPKLAK-LGRVLGPRGLMPSPKSGTVT 145 (229)
T ss_pred ----HH----HHHcCCC---EeCHHHHHHHH------HcCcccCCEEEECHHHHHHHHH-hcCcccccCCCCCCCCCCcc
Confidence 22 3466763 89999998754 5678899999999999999999 999999999999999987 5
Q ss_pred ccHHHHHHHHHc-cceEEccCCCEEEEEEecCCCChhHHHHHHHHHHHHHHHhcCCCCC--CccEEEEEcCCCcceEEec
Q 014066 180 QNWKEQIEKVCG-SALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGVAEIVPRKWG--NVRSFHLKLLESLALPVYQ 256 (431)
Q Consensus 180 ~dLk~~Ieka~~-St~~~l~kG~~~sVkVG~~sMs~eqIvENI~avl~~l~~~lPkg~~--NIksI~LKtt~S~aLPIY~ 256 (431)
.|+.+.|+++.+ ++.|+.++.++++++||+++|+++||+|||.+++++|.+..|.+|. ||++|||+|||||+++|-.
T Consensus 146 ~di~~~V~~~k~G~v~~r~dk~g~i~~~VG~~~m~~~~l~eNi~a~l~~i~~~~p~~~kg~~ik~v~issTMGp~v~i~~ 225 (229)
T CHL00129 146 TDLASAINEFKKGKLEYRADKTGIVHVLFGKSNFTEEDLLENLQAIYESIEQNRPSGVKGKYWKSFYICSTMGPSIQIDI 225 (229)
T ss_pred ccHHHHHHHHhcCcEEEEecCCcEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCcccccCceEEEEEEECCCCCCEEecc
Confidence 799999999987 7899999999999999999999999999999999999999999988 9999999999999999865
Q ss_pred c
Q 014066 257 A 257 (431)
Q Consensus 257 s 257 (431)
+
T Consensus 226 ~ 226 (229)
T CHL00129 226 S 226 (229)
T ss_pred c
Confidence 4
No 9
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=100.00 E-value=1.1e-32 Score=265.58 Aligned_cols=200 Identities=16% Similarity=0.214 Sum_probs=169.9
Q ss_pred HHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccC-CCC-CccceeeEeCCCCCCCCCCCCCCEEEEEecCCCCC
Q 014066 23 TVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKI-PQV-SRTNAFKIPLPHSLLGNDSDNPPEICLIMDDRPKS 100 (431)
Q Consensus 23 ~V~kAVkaLlk~~~~~~~~~K~~Lfeed~~V~L~VtLKki-p~k-~k~~p~~I~LPHpl~~~~~~~~~kICLIvkD~~~~ 100 (431)
.+.+||+.|+++ +...|.| +|+|+|+| .+ +.+ .....+.|.|||++++ ..+||||+++...
T Consensus 21 ~l~eAi~~lk~~--------~~~kF~e--svel~v~L-~id~kK~~~~irg~v~LP~~~gk-----~~kI~Vfa~~~~~- 83 (230)
T PRK05424 21 SLEEAIALVKET--------ATAKFDE--TVDVAVNL-GVDPRKADQQVRGAVVLPHGTGK-----TVRVAVFAKGEKA- 83 (230)
T ss_pred CHHHHHHHHHhh--------ccCCCCC--cEEEEEEe-CCCCCCCCCeeeEEEECCCCCCC-----CcEEEEECChHhH-
Confidence 477888888751 2355776 99999999 66 444 3566789999999976 6899999976532
Q ss_pred chhHHHHHHHhhhCCCCcceeeehhhhhhhcchHHHHhhccccccEEEEcCCchhhhhhhhcccccCCCCCCeeecCC-c
Q 014066 101 NLTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVDLK-H 179 (431)
Q Consensus 101 ~~t~~e~kekl~a~~i~i~kVI~lkkLk~kyKsfE~kRKL~~sYDlFLAD~rI~~~LpklLGK~F~kkkK~PipV~lt-~ 179 (431)
++ +++.|+. +++.++|....+ +.++ +||+|||++++|+.|++ ||+.|++||+||+|+.+| .
T Consensus 84 ----~~----Ak~aGa~---~vg~eeLi~~ik-----~~~~-~fd~~iat~~~m~~l~~-Lg~iLGPrGlMP~pk~gTv~ 145 (230)
T PRK05424 84 ----EE----AKAAGAD---IVGGEDLIEKIK-----GGWL-DFDVVIATPDMMGKVGK-LGRILGPRGLMPNPKTGTVT 145 (230)
T ss_pred ----HH----HHHcCCC---EeCHHHHHHHHh-----cCCC-cCCEEEECHHHHHHHHH-hccccccccCCCCCCCCCcc
Confidence 22 3466764 889999987765 2343 89999999999999998 999999999999999987 4
Q ss_pred ccHHHHHHHHHc-cceEEccCCCEEEEEEecCCCChhHHHHHHHHHHHHHHHhcCCCC--CCccEEEEEcCCCcceEEec
Q 014066 180 QNWKEQIEKVCG-SALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGVAEIVPRKW--GNVRSFHLKLLESLALPVYQ 256 (431)
Q Consensus 180 ~dLk~~Ieka~~-St~~~l~kG~~~sVkVG~~sMs~eqIvENI~avl~~l~~~lPkg~--~NIksI~LKtt~S~aLPIY~ 256 (431)
.|+.+.|+++.+ ++.|+.++.++++++||+++|+++||+|||.+++++|.+..|.+| ++|++|||+|||||++.|-.
T Consensus 146 ~di~~~I~~~k~g~v~~r~~k~g~i~~~IG~~~m~~e~i~eNi~a~l~~i~~~~p~~~kg~~Ik~v~lssTmGp~~~i~~ 225 (230)
T PRK05424 146 MDVAKAVKEAKAGKVEFRVDKAGIIHAPIGKVSFDAEKLKENLKALIDAIKKAKPATAKGTYIKSVSLSSTMGPGVKVDP 225 (230)
T ss_pred hhHHHHHHHHhcCcEEEEecCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCccccCCCEEEEEEEECCCCCCEEech
Confidence 699999999987 689999999999999999999999999999999999999999999 79999999999999998765
Q ss_pred c
Q 014066 257 A 257 (431)
Q Consensus 257 s 257 (431)
.
T Consensus 226 ~ 226 (230)
T PRK05424 226 S 226 (230)
T ss_pred H
Confidence 4
No 10
>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=2e-32 Score=263.44 Aligned_cols=200 Identities=15% Similarity=0.195 Sum_probs=171.1
Q ss_pred HHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccC-CCC-CccceeeEeCCCCCCCCCCCCCCEEEEEecCCCCC
Q 014066 23 TVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKI-PQV-SRTNAFKIPLPHSLLGNDSDNPPEICLIMDDRPKS 100 (431)
Q Consensus 23 ~V~kAVkaLlk~~~~~~~~~K~~Lfeed~~V~L~VtLKki-p~k-~k~~p~~I~LPHpl~~~~~~~~~kICLIvkD~~~~ 100 (431)
.+.+||+.|.++ +...|.| +|+|+|+| ++ +.+ .....+.|.|||++++ ..+||||+++...
T Consensus 20 ~l~eAi~~lk~~--------~~~~f~e--svel~i~L-~id~kK~~~~irg~v~LP~~~gk-----~~kV~Vfa~~~~~- 82 (227)
T TIGR01169 20 SLDEAIALLKET--------ATAKFDE--TVEVAIRL-GIDPRKSDQQVRGTVVLPHGTGK-----TVRVAVFAKGEKA- 82 (227)
T ss_pred CHHHHHHHHHhh--------ccCCCCC--CEEEEEEE-CcCCCcCCCeeeEEEECCCCCCC-----CcEEEEEcCchhH-
Confidence 467888888751 2355776 99999999 66 444 3567789999999976 6899999986532
Q ss_pred chhHHHHHHHhhhCCCCcceeeehhhhhhhcchHHHHhhccccccEEEEcCCchhhhhhhhcccccCCCCCCeeecCC-c
Q 014066 101 NLTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVDLK-H 179 (431)
Q Consensus 101 ~~t~~e~kekl~a~~i~i~kVI~lkkLk~kyKsfE~kRKL~~sYDlFLAD~rI~~~LpklLGK~F~kkkK~PipV~lt-~ 179 (431)
++ +.+.|+. +++.++|... .++++.+||+|||++++|+.|+ .||+.|++||+||+|..+| .
T Consensus 83 ----~~----Ak~aGa~---~vg~~eLi~~------ik~~~~~fd~~iat~~~m~~l~-~Lg~iLGPrGlMP~~k~gtv~ 144 (227)
T TIGR01169 83 ----EE----AKAAGAD---YVGSDDLIEK------IKKGWLDFDVVIATPDMMRVVG-KLGRILGPRGLMPNPKTGTVT 144 (227)
T ss_pred ----HH----HHHcCCC---EeCHHHHHHH------HHcCCccCCEEEECHHHHHHHH-HhccccccccCCCCCCCCCcc
Confidence 22 3456764 8899999875 4567899999999999999999 7999999999999999987 5
Q ss_pred ccHHHHHHHHHc-cceEEccCCCEEEEEEecCCCChhHHHHHHHHHHHHHHHhcCCCC--CCccEEEEEcCCCcceEEec
Q 014066 180 QNWKEQIEKVCG-SALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGVAEIVPRKW--GNVRSFHLKLLESLALPVYQ 256 (431)
Q Consensus 180 ~dLk~~Ieka~~-St~~~l~kG~~~sVkVG~~sMs~eqIvENI~avl~~l~~~lPkg~--~NIksI~LKtt~S~aLPIY~ 256 (431)
.|+.+.|+++.+ ++.|+.++.++++++||+++|+++||+|||.+++++|.+..|.+| ++|++|||+|||||++.|-.
T Consensus 145 ~di~~~I~~~k~g~v~~r~~k~g~i~~~VG~~~m~~e~i~eNi~a~l~~i~~~~p~~~kg~~Ik~v~lssTmGp~~~i~~ 224 (227)
T TIGR01169 145 ADVAKAVKNAKKGQVEFRADKAGNIHASIGKVSFDSEKLKENLEALLDAIKKAKPSGAKGQYIKNIALSSTMGPGIKVDL 224 (227)
T ss_pred ccHHHHHHHHHcCcEEEEeCCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHhCccccCCCEEEEEEEECCCCCCEEecc
Confidence 799999999997 689999999999999999999999999999999999999999999 89999999999999998754
Q ss_pred c
Q 014066 257 A 257 (431)
Q Consensus 257 s 257 (431)
.
T Consensus 225 ~ 225 (227)
T TIGR01169 225 S 225 (227)
T ss_pred C
Confidence 3
No 11
>KOG1570 consensus 60S ribosomal protein L10A [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=9.8e-30 Score=238.27 Aligned_cols=216 Identities=25% Similarity=0.398 Sum_probs=184.1
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccC-CCCCccceeeEeCCCCCCCCCCCCCCEEEEEe
Q 014066 16 GSRVSPKTVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKI-PQVSRTNAFKIPLPHSLLGNDSDNPPEICLIM 94 (431)
Q Consensus 16 ~s~v~~e~V~kAVkaLlk~~~~~~~~~K~~Lfeed~~V~L~VtLKki-p~k~k~~p~~I~LPHpl~~~~~~~~~kICLIv 94 (431)
++.++++++..||..++.+.. ..|++.|-+ +|++|++|++| |.+...+.+.+.|||..+. ..++|+|.
T Consensus 2 ~sk~~~~~l~~~v~~i~~~~~----~~k~~~~~~--tielQi~Lk~ydp~Kdkr~s~~~~l~~~~~p-----~~k~cv~g 70 (218)
T KOG1570|consen 2 SSKVEEEALREAVAEILLRSK----EFKNRNFVE--TIELQINLKNYDPQKDKRFSGSVKLPHAPRP-----KMKVCVIG 70 (218)
T ss_pred CcchhHHHHHHHHHHHHhccc----cccCcccee--eeeeeecccccChhHhCcccceEecCCCCCc-----cceeeeec
Confidence 356889999999999887542 234455555 99999999998 5667778899999999875 78999999
Q ss_pred cCCCCCchhHHHHHHHhhhCCCCcceeeehhhhhhhcchHHHHhhccccccEEEEcCCchhhhhhhhcccccCCCCCCee
Q 014066 95 DDRPKSNLTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVP 174 (431)
Q Consensus 95 kD~~~~~~t~~e~kekl~a~~i~i~kVI~lkkLk~kyKsfE~kRKL~~sYDlFLAD~rI~~~LpklLGK~F~kkkK~Pip 174 (431)
+..+. +...+-++|...+-.+++|.+..+- ..+|+++||+|||..+++.+||++||+.+-+.|++|.+
T Consensus 71 d~~h~---------~~ak~~~~p~m~~d~lkklnk~Kkl---vkklakky~~flase~~ikQlpr~lgp~l~kaGkfps~ 138 (218)
T KOG1570|consen 71 DQQHC---------DEAKAIDLPAMDIDALKKLNKNKKL---VKKLAKKYDAFLASESLIKQLPRILGPGLSKAGKFPSL 138 (218)
T ss_pred hHHHH---------HHhhcCCCCCcCHHHHhcCcccchH---HHHHHHHhhhHHhhHHHHHHhhhhhcccccccccCCcc
Confidence 86543 1234556765555556666554444 88999999999999999999999999999999999999
Q ss_pred ecCCcccHHHHHHHHHccceEEccCCCEEEEEEecCCCChhHHHHHHHHHHHHHHHhcCCCCCCccEEEEEcCCCcceEE
Q 014066 175 VDLKHQNWKEQIEKVCGSALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGVAEIVPRKWGNVRSFHLKLLESLALPV 254 (431)
Q Consensus 175 V~lt~~dLk~~Ieka~~St~~~l~kG~~~sVkVG~~sMs~eqIvENI~avl~~l~~~lPkg~~NIksI~LKtt~S~aLPI 254 (431)
+.- .+++.+.++..+.+..|++++--|++|.|||+.|++++|+.||.-.++++++.+.++|+|+++++||+||+++.-+
T Consensus 139 l~~-~d~l~akv~evk~t~k~q~kkvKOGavaVGhv~M~d~el~~nI~l~vnFlVSlLKknwQNvral~iKst~g~p~~l 217 (218)
T KOG1570|consen 139 LVH-GDSLYAKVEEVKSTIKFQMKKVLCLAVAVGHVGMTDEELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMGKPQRL 217 (218)
T ss_pred ccc-hHHHHHHHHHHHhhHHHHHHhhhheeeeecCCCCCHHHHHHhhhhhhhhHHHHHhhcccchhheeeccCCCCceec
Confidence 975 4799999999999999999999999999999999999999999999999999999999999999999999998766
Q ss_pred e
Q 014066 255 Y 255 (431)
Q Consensus 255 Y 255 (431)
|
T Consensus 218 y 218 (218)
T KOG1570|consen 218 Y 218 (218)
T ss_pred C
Confidence 5
No 12
>KOG1569 consensus 50S ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=99.81 E-value=5.2e-19 Score=174.03 Aligned_cols=185 Identities=20% Similarity=0.230 Sum_probs=149.2
Q ss_pred eEEEEEEecc----CCCCCccceeeEeCCCCCCCCCCCCCCEEEEEecCCCCCchhHHHHHHHhhhCCCCcceeeehhhh
Q 014066 52 FVYLILTLKK----IPQVSRTNAFKIPLPHSLLGNDSDNPPEICLIMDDRPKSNLTKDAVMKKIKNDNLPITKVIKITKL 127 (431)
Q Consensus 52 ~V~L~VtLKk----ip~k~k~~p~~I~LPHpl~~~~~~~~~kICLIvkD~~~~~~t~~e~kekl~a~~i~i~kVI~lkkL 127 (431)
++++.|.|.. ........++.+++|||+.+. +...|.+|++|.... +.++++|+ .++|..+|
T Consensus 114 ~~~l~i~l~~~a~~~~k~~~~~~~~v~vP~Pf~~g---e~r~IavFtn~~~kv--------eeArEaGA---~l~GG~dL 179 (323)
T KOG1569|consen 114 PVNLRIELNMLAEKETKGVAPLQGSVTVPHPFAHG---EIRKIAVFTNDASKV--------EEAREAGA---ALAGGTDL 179 (323)
T ss_pred ceeeeEEeeeeeeeeccccCCCceeEeccccCCCC---ceEEEEEecCChHHH--------HHHHhccc---cccccHHH
Confidence 5555555544 222223456789999999874 367799999997542 22445565 47888899
Q ss_pred hhhcchHHHHhhccccccEEEEcCCchhhhhhhhcccccCCCCCCeeecCC-cccHHHHHHHHHcc--ceEEccCCCEEE
Q 014066 128 KTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVDLK-HQNWKEQIEKVCGS--ALLYLRTGTCSV 204 (431)
Q Consensus 128 k~kyKsfE~kRKL~~sYDlFLAD~rI~~~LpklLGK~F~kkkK~PipV~lt-~~dLk~~Ieka~~S--t~~~l~kG~~~s 204 (431)
.++++. -.+.-+||+++|.++||+.|-+ |++.+++| ||+|..++ +.||.+.|+++.++ +.|+....+.++
T Consensus 180 IkkI~~----Gei~~Dyd~~vA~Pdim~~l~~-Lr~iL~~r--~Pn~k~gtvg~nipemieeFk~G~~i~~d~~~~~~~~ 252 (323)
T KOG1569|consen 180 IKKIKS----GEIVADYDFYVAHPDIMPELNR-LRKILGPR--FPNPKRGTVGRNIPEMIEEFKNGHEIKFDEERENILQ 252 (323)
T ss_pred HHHhhc----CeEEEeeceeeecchHHHHHHH-HHHHhccc--CCCcccCccccchHHHHHHhhCCcccccccccCceee
Confidence 999886 4566669999999999999988 78888877 99999988 78999999999998 777776666679
Q ss_pred EEEecCCCChhHHHHHHHHHHHHHHHhcCCCC-CCccEEEEEcCCCcceEEecc
Q 014066 205 LKVGKVSMGAEDIAENVIAAINGVAEIVPRKW-GNVRSFHLKLLESLALPVYQA 257 (431)
Q Consensus 205 VkVG~~sMs~eqIvENI~avl~~l~~~lPkg~-~NIksI~LKtt~S~aLPIY~s 257 (431)
++||+++|+.+||.+||.++++.+..+.|... .+|.+.+|+|++|+.+-|-+.
T Consensus 253 ~~vGkl~mt~e~i~~Ni~a~i~av~t~rp~~~G~fv~ra~L~Ss~g~~i~l~i~ 306 (323)
T KOG1569|consen 253 IKVGKLDMTSEQILANIQAVIAAVCTHRPKALGPFVVRALLRSSPGEGILLKID 306 (323)
T ss_pred eeeeeecCCHHHHHHHHHHHHHHHHhcCCcccCceeeeeEeecCCCCceeEecc
Confidence 99999999999999999999999999999764 479999999999998776655
No 13
>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=99.66 E-value=7.3e-16 Score=138.97 Aligned_cols=137 Identities=18% Similarity=0.142 Sum_probs=103.3
Q ss_pred HHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCCCccceeeEeCCCCCCCCCCCCCCEEEEEecCCCCCchh
Q 014066 24 VERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQVSRTNAFKIPLPHSLLGNDSDNPPEICLIMDDRPKSNLT 103 (431)
Q Consensus 24 V~kAVkaLlk~~~~~~~~~K~~Lfeed~~V~L~VtLKkip~k~k~~p~~I~LPHpl~~~~~~~~~kICLIvkD~~~~~~t 103 (431)
+.+|++-|.++.. .. -.|.+ +|+|+|+|.--+.+.+ ..+.|.|||++++ +.+||||+++.+..
T Consensus 3 i~eA~~~lk~~~~-----~~-~~~~e--tvel~i~L~~~~~~~~-irg~v~LP~~~~k-----~~kV~Vf~~~~~~~--- 65 (141)
T TIGR01170 3 VIKAFVYLKTKSI-----SM-YVPKQ--SVNLDIGLLMELGKES-VQGMFSFPHPFGK-----EPKIAVFTKGASEV--- 65 (141)
T ss_pred HHHHHHHHHHhcc-----cC-CCCCc--eEEEEEEECCCCCCCC-ceEEEECCCCCCC-----CCEEEEECCChHHH---
Confidence 4567776665421 11 24665 9999999954343444 6789999999976 57999999987521
Q ss_pred HHHHHHHhhhCCCCcceeeehhhhhhhcchHHHHhhccccccEEEEcCCchhhhhhhhcccccCCCCCCeeecCC-cccH
Q 014066 104 KDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVDLK-HQNW 182 (431)
Q Consensus 104 ~~e~kekl~a~~i~i~kVI~lkkLk~kyKsfE~kRKL~~sYDlFLAD~rI~~~LpklLGK~F~kkkK~PipV~lt-~~dL 182 (431)
+.+++.|+ .+++.++|..+++. .++.. ||+|||++++|+.|+ .||+.|++||+||+|+.+| ..|+
T Consensus 66 -----~~Ak~aGa---~~vg~edLi~~i~~----g~~~~-fd~~iA~~~~m~~l~-~Lg~iLGprGlMP~~k~gTv~~di 131 (141)
T TIGR01170 66 -----EEAREAGA---DYVGGDDLIKKIED----GEIKP-FDYLIAHPDIVPELA-QLRRLLGPKGLMPSPKRGTVGDNL 131 (141)
T ss_pred -----HHHHHcCC---CEeCHHHHHHHHhc----CCccc-ccEEEECHHHHHHHH-HhhcccccCcCCCCCCCCCcccCH
Confidence 22345666 38999999777763 22211 999999999999999 8999999999999999987 5799
Q ss_pred HHHHHHHHc
Q 014066 183 KEQIEKVCG 191 (431)
Q Consensus 183 k~~Ieka~~ 191 (431)
...|+++.+
T Consensus 132 ~~~I~~~k~ 140 (141)
T TIGR01170 132 LSMIETFKK 140 (141)
T ss_pred HHHHHHHhC
Confidence 999998865
No 14
>PF13003 MRL1: Ribosomal protein L1; InterPro: IPR024663 This entry represents a ribosomal protein L1 domain found mainly in chordates.
Probab=89.33 E-value=0.97 Score=40.91 Aligned_cols=61 Identities=25% Similarity=0.233 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCCC---ccceeeEeCCCCCCCCCCCCCCEEEEE
Q 014066 22 KTVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQVS---RTNAFKIPLPHSLLGNDSDNPPEICLI 93 (431)
Q Consensus 22 e~V~kAVkaLlk~~~~~~~~~K~~Lfeed~~V~L~VtLKkip~k~---k~~p~~I~LPHpl~~~~~~~~~kICLI 93 (431)
-.|++||.-|.+|.. .+.-.+.+.|||.++|.....+. -.++..|.||||+-.. -.++.||
T Consensus 70 yeve~Ai~mLKkfQ~-------lDfT~pkQ~VYldL~Ldm~l~KKkkVePF~s~i~lPypF~~e----iNKv~VF 133 (133)
T PF13003_consen 70 YEVEKAIDMLKKFQI-------LDFTSPKQPVYLDLTLDMKLEKKKKVEPFASVILLPYPFTSE----INKVLVF 133 (133)
T ss_pred HHHHHHHHHHHhccc-------ccCCCCCCcEEEeeeehhhhccccccCCCccceecccccccc----cceeeeC
Confidence 468999999998642 23333456999999997765542 2466789999999753 5666665
No 15
>PF00370 FGGY_N: FGGY family of carbohydrate kinases, N-terminal domain; InterPro: IPR018484 It has been shown [] that four different type of carbohydrate kinases seem to be evolutionary related. These enzymes include L-fucolokinase (2.7.1.51 from EC) (gene fucK); gluconokinase (2.7.1.12 from EC) (gene gntK); glycerol kinase (2.7.1.30 from EC) (gene glpK); xylulokinase (2.7.1.17 from EC) (gene xylB); and L-xylulose kinase (2.7.1.53 from EC) (gene lyxK). These enzymes are proteins of from 480 to 520 amino acid residues. This entry represents the N-terminal domain of these proteins. It adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain [, ].; GO: 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 3G25_D 3GE1_D 2NLX_A 2ITM_A 2ZF5_Y 3L0Q_B 3GG4_B 3I8B_A 3H3O_C 3FLC_X ....
Probab=21.90 E-value=1.4e+02 Score=28.33 Aligned_cols=52 Identities=8% Similarity=0.016 Sum_probs=42.1
Q ss_pred ecCCCChhHHHHHHHHHHHHHHHhcCCCCCCccEEEEEcCCCcceEEeccCC
Q 014066 208 GKVSMGAEDIAENVIAAINGVAEIVPRKWGNVRSFHLKLLESLALPVYQAVP 259 (431)
Q Consensus 208 G~~sMs~eqIvENI~avl~~l~~~lPkg~~NIksI~LKtt~S~aLPIY~s~~ 259 (431)
|...++++++.+-+..++..+.+.++.....|.+|.+.+.+.-.+++-..-.
T Consensus 39 g~~e~d~~~~~~~~~~~~~~~~~~~~~~~~~I~aI~is~~~~~~v~~D~~~~ 90 (245)
T PF00370_consen 39 GWAEQDPDEIWEAICEALKELLSQAGIDPEQIKAIGISGQGHGLVLLDKDGK 90 (245)
T ss_dssp TEEEE-HHHHHHHHHHHHHHHHHHCTSCGGGEEEEEEEE-SSEEEEEETTSS
T ss_pred cccccChHHHHHHHHHHHHHHHhhcCcccceeEEEEeccccCCcceeccccc
Confidence 5667899999999999999999988666779999999998877777766653
Done!