Query 015100
Match_columns 413
No_of_seqs 155 out of 1200
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 03:06:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015100.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015100hhsearch_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 2.8E-48 6.1E-53 385.6 10.9 302 10-312 10-338 (343)
2 PTZ00029 60S ribosomal protein 100.0 1.5E-40 3.2E-45 315.6 20.0 208 16-249 1-209 (216)
3 PTZ00225 60S ribosomal protein 100.0 2.7E-39 5.9E-44 306.6 20.0 206 16-249 1-207 (214)
4 PRK04203 rpl1P 50S ribosomal p 100.0 5.2E-39 1.1E-43 304.7 20.1 204 19-249 2-207 (215)
5 PF00687 Ribosomal_L1: Ribosom 100.0 2.1E-38 4.6E-43 298.1 17.6 210 28-249 1-217 (220)
6 cd00403 Ribosomal_L1 Ribosomal 100.0 2.8E-37 6.1E-42 288.8 18.3 200 24-249 1-202 (208)
7 CHL00129 rpl1 ribosomal protei 100.0 9E-29 2E-33 237.0 18.6 190 24-249 22-217 (229)
8 COG0081 RplA Ribosomal protein 100.0 9.8E-29 2.1E-33 234.9 17.2 196 19-249 18-219 (228)
9 PRK05424 rplA 50S ribosomal pr 100.0 2.5E-28 5.4E-33 234.1 18.3 190 24-249 22-217 (230)
10 TIGR01169 rplA_bact ribosomal 100.0 3.3E-28 7.2E-33 232.8 18.7 190 24-249 21-216 (227)
11 KOG1570 60S ribosomal protein 99.9 5.5E-27 1.2E-31 219.0 7.5 211 16-251 2-213 (218)
12 TIGR01170 rplA_mito ribosomal 99.7 5.1E-16 1.1E-20 139.3 12.1 137 24-192 3-141 (141)
13 KOG1569 50S ribosomal protein 99.6 1.4E-15 3.1E-20 149.3 13.8 167 52-239 114-289 (323)
14 PF13003 MRL1: Ribosomal prote 88.8 1 2.2E-05 40.6 5.7 60 23-93 71-133 (133)
15 KOG3130 Uncharacterized conser 53.9 8 0.00017 40.9 1.9 21 317-337 288-308 (514)
16 KOG2652 RNA polymerase II tran 44.1 17 0.00037 37.6 2.5 13 324-336 289-301 (348)
17 PF06524 NOA36: NOA36 protein; 41.1 20 0.00044 36.0 2.5 13 52-64 53-65 (314)
18 KOG0923 mRNA splicing factor A 38.4 35 0.00075 38.8 3.9 80 167-248 438-525 (902)
19 KOG3241 Uncharacterized conser 27.3 48 0.001 31.8 2.4 21 303-323 195-215 (227)
20 KOG2422 Uncharacterized conser 26.5 33 0.0007 38.2 1.3 74 317-391 67-141 (665)
21 KOG0526 Nucleosome-binding fac 25.2 54 0.0012 36.1 2.7 49 284-332 450-500 (615)
22 PLN02347 GMP synthetase 24.8 6.7E+02 0.015 27.6 10.9 147 88-239 256-458 (536)
23 TIGR00853 pts-lac PTS system, 22.7 2.4E+02 0.0052 23.6 5.6 76 87-175 3-80 (95)
24 KOG1513 Nuclear helicase MOP-3 22.5 35 0.00075 39.6 0.6 114 198-334 598-718 (1300)
No 1
>KOG1685 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.8e-48 Score=385.65 Aligned_cols=302 Identities=42% Similarity=0.588 Sum_probs=254.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCCCcceeeeEeCCCCCCCCCCC--CC
Q 015100 10 SLPPSAGSRVSPKTVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQVSRTNAFKIPLPHSLLGNDSD--NP 87 (413)
Q Consensus 10 ~~~~~~~s~Vd~eqV~kAVkALlk~~~k~~~~~K~~Lf~Ede~V~L~ItLKkIp~k~r~~p~~I~LPHpl~~~~~~--~~ 87 (413)
..++.+++++++..+..|++++.++.........+++++++..+|.....++++.....+...|++||++..+. . .+
T Consensus 10 ~~~~~~~~~v~~~~~e~~~k~~~~~~~~~~k~~~~~~~~~~k~~~~~~~~k~~~~~~~~n~~~IP~k~~~~~~~-~~~~~ 88 (343)
T KOG1685|consen 10 SSTAIPRESVSPKNVESAVKALDKEREKKSKAENPQLLEALKNVYKVVLQKNTPQKVGTNKLKIPLKHLLKKLL-LKHDD 88 (343)
T ss_pred ccccccccccCchhhhHHHhhhhhhhHHHHHhhhhhhhhhhhhhHHHHHHHhcccccccccccccCcchhcccc-cCCCC
Confidence 35667888999999999999999988776554457788877777777777677776666777888999887664 2 37
Q ss_pred CEEEEEecCCCCCchhHHHHHHhhhcCCCC-cceeeechhHHhhcccHHHHHhhhhccCEEEEcCCchhhhhhhhccccc
Q 015100 88 PEICLIMDDRPKSNLTKDAVMKKIKNDNLP-ITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFF 166 (413)
Q Consensus 88 ~kICLIvkD~~~~~~t~~~ake~L~~~gi~-i~kVI~lkkLkkeyKsfEakRKL~~sYDlFLAD~rI~p~LpklLGK~F~ 166 (413)
.+||||++|+++.++|+++|+++|.++|++ +++||++++|+.+|++||++|+|+++||+||||+||+|+||++|||.||
T Consensus 89 ~~vcLIvkD~~~~~~t~~~~~d~l~~~gi~~itkVI~~~~LK~~yksyeaKr~L~~sfDlflaD~RV~~~LP~llGK~f~ 168 (343)
T KOG1685|consen 89 TDVCLIVKDLQQSYLTEEDAEDLLESEGIKSITKVISLSKLKRDYKSYEAKRKLLSSFDLFLADDRVIPLLPKLLGKEFY 168 (343)
T ss_pred CceEEEecCchhccccHHHHHHHHHHcCCccceeeeehHHHHHHHHHHHHHHHHHhhccEEEEcchhHhHHHHHhhhhhc
Confidence 899999999999999999999999999999 9999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCccccCCccc--HHHHHHHHHcccEEEccCCCEEEEEEecCCCCHHHHHHHHHHHHHHHH---------------
Q 015100 167 KKKKIPVPVDLKHQN--WKEQIEKVCGSALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGLL--------------- 229 (413)
Q Consensus 167 kkkK~PipV~l~~~d--Lk~~Ieka~~st~f~l~~G~~~sVkVG~~sMs~eqIvENI~Avl~~L~--------------- 229 (413)
++++.|+||++.+.+ |..+|++||++|+|+++.|+|++|+|||++|+.++|+|||.++++.+.
T Consensus 169 q~kk~Pv~i~l~k~~~~l~~qi~~a~~~t~~~~~~g~~~~i~vg~l~~~~~~l~ENv~~vlk~l~e~~P~~~~~Irsl~l 248 (343)
T KOG1685|consen 169 QKKKVPVSIRLSKKNELLKQQIENACGSTYFRLRKGTSSAIKVGHLGNTSEELAENVVAVLKGLSEILPGGWKNIRSLHL 248 (343)
T ss_pred ccccCceEEEecccchHHHHHHHHHhhhheeeccCCceeEEEeccccccHHHHHHHHHHHHHHHHHHccchHhHhHHHhh
Confidence 999999999998767 999999999999999999999999999999999999999999999963
Q ss_pred ---hhccCCCeeecCcceeeeccccCCCCCCccc--cccccccccccc--ccchhhhcccccceeEEEeecCcccccccc
Q 015100 230 ---ESLALPVYQAVPDLKLKIEGVKENEGEGQDK--DSEKENAEDVND--HGSKKKLKKKKGRIHEVRYMDSTIGEVLDE 302 (413)
Q Consensus 230 ---~SlaLPiYqni~~v~iKi~~~~~~~~~~~~~--~~~~~~~~~~~~--~~~~~~~~~k~~~i~~~~~~~~~~~~~~~~ 302 (413)
+|++||+|++...+...+..++...+-.+.. .+..++.+.+.. ....++.+.++|+||+++|||++..|.+|.
T Consensus 249 Kt~~s~aLPly~s~~~~~~~~~~~~~i~~~~~~k~~~~~~~k~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~e~~~~ 328 (343)
T KOG1685|consen 249 KTSRSPALPLYVSVISLKEIASKRGSIRDFVELKETQKKERKSDLSLFGKGKKEIKIKVKKGSIDSKQQNDSNKAEVLDL 328 (343)
T ss_pred hccCCcccceeecccchhhhhcccCchhhhhHHHhhhhhhhhccccccchhhhHhhhhhhccchhhHHhccchhhhhccc
Confidence 4899999999998888888776544322221 222333333322 233346677889999999999999999999
Q ss_pred cccCCCCCCC
Q 015100 303 DELGSDDDGE 312 (413)
Q Consensus 303 ~~~~~~~~~~ 312 (413)
|+...|.|.+
T Consensus 329 d~~~~~~d~~ 338 (343)
T KOG1685|consen 329 DEEKKDSDAN 338 (343)
T ss_pred ccccccccch
Confidence 9998865543
No 2
>PTZ00029 60S ribosomal protein L10a; Provisional
Probab=100.00 E-value=1.5e-40 Score=315.60 Aligned_cols=208 Identities=25% Similarity=0.363 Sum_probs=185.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCC-CcceeeeEeCCCCCCCCCCCCCCEEEEEe
Q 015100 16 GSRVSPKTVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQV-SRTNAFKIPLPHSLLGNDSDNPPEICLIM 94 (413)
Q Consensus 16 ~s~Vd~eqV~kAVkALlk~~~k~~~~~K~~Lf~Ede~V~L~ItLKkIp~k-~r~~p~~I~LPHpl~~~~~~~~~kICLIv 94 (413)
||.++++++++||++|++|. ..+.+.|.| +|+|+|+|++|+++ .+..++.|.|||++++ ..+||||+
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 56789999999999999872 235677887 99999999999554 5667789999999986 68999999
Q ss_pred cCCCCCchhHHHHHHhhhcCCCCcceeeechhHHhhcccHHHHHhhhhccCEEEEcCCchhhhhhhhcccccCCCCCCcc
Q 015100 95 DDRPKSNLTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVP 174 (413)
Q Consensus 95 kD~~~~~~t~~~ake~L~~~gi~i~kVI~lkkLkkeyKsfEakRKL~~sYDlFLAD~rI~p~LpklLGK~F~kkkK~Pip 174 (413)
++... ++| ++.|+ +|++.++|...|+.|+.+|+|+.+||+||||+++||.||++||+.||+++|+|+|
T Consensus 69 ~~~~~-----~~A----k~aGa---~vvg~edL~~~~k~~k~~kkl~~~fD~flA~~~im~~l~riLGp~l~p~~K~P~~ 136 (216)
T PTZ00029 69 DAVHC-----DEA----KKLGL---DFMDIEGLKKFNKNKKLVKKLAKKYDAFLASQSLLPQIPRLLGPGLNKAGKFPTL 136 (216)
T ss_pred CcHHH-----HHH----HHcCC---CEecHHHHHHhhhhHHHHhcccccCCEEEECHHHHHHHHHHhccccccCCCCCCc
Confidence 87643 244 34566 4999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCcccHHHHHHHHHcccEEEccCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHhhccCCCeeecCcceeeecc
Q 015100 175 VDLKHQNWKEQIEKVCGSALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGLLESLALPVYQAVPDLKLKIEG 249 (413)
Q Consensus 175 V~l~~~dLk~~Ieka~~st~f~l~~G~~~sVkVG~~sMs~eqIvENI~Avl~~L~~SlaLPiYqni~~v~iKi~~ 249 (413)
++.+ .+|...|+++++++.|++++++|++++||+++|+++||+|||.|++++|...+ ..+|+++.++|||+|.
T Consensus 137 v~~~-~d~~~~i~~~k~~v~~r~~k~~~i~v~VG~~~~~~e~l~eNi~avl~~i~~~~-~kg~~~Iksv~lktTm 209 (216)
T PTZ00029 137 ITHN-DDIEDKINELKSSVKFQLKKVLCLGVAVGNVEMTEEQLRQNIVLSINFLVSLL-KKNWQNIKTLHIKSTM 209 (216)
T ss_pred ccCc-cCHHHHHHHHHheEEEEECCCCEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHh-ccccccEeEEEEECCC
Confidence 9875 68999999999999999999999999999999999999999999999996665 4679999999999876
No 3
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=100.00 E-value=2.7e-39 Score=306.63 Aligned_cols=206 Identities=25% Similarity=0.408 Sum_probs=180.6
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccC-CCCCcceeeeEeCCCCCCCCCCCCCCEEEEEe
Q 015100 16 GSRVSPKTVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKI-PQVSRTNAFKIPLPHSLLGNDSDNPPEICLIM 94 (413)
Q Consensus 16 ~s~Vd~eqV~kAVkALlk~~~k~~~~~K~~Lf~Ede~V~L~ItLKkI-p~k~r~~p~~I~LPHpl~~~~~~~~~kICLIv 94 (413)
||.|+++++.+||++|+++. +.+.|.| +|+|+|+|++| |.+.+..++.|.|||++++ ..+||||+
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 56799999999999998743 3456877 99999999999 5556777899999999986 68999999
Q ss_pred cCCCCCchhHHHHHHhhhcCCCCcceeeechhHHhhcccHHHHHhhhhccCEEEEcCCchhhhhhhhcccccCCCCCCcc
Q 015100 95 DDRPKSNLTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVP 174 (413)
Q Consensus 95 kD~~~~~~t~~~ake~L~~~gi~i~kVI~lkkLkkeyKsfEakRKL~~sYDlFLAD~rI~p~LpklLGK~F~kkkK~Pip 174 (413)
++... ++| +++|++ +++..+|.+..+.++++|+||.+||+|||++++||.||++||+.|++++|||+|
T Consensus 67 ~~~~~-----~~A----k~aGad---~v~~e~l~~l~k~~~~~kkl~~~fD~fiA~~~~m~~lgk~LGp~~~p~gK~P~~ 134 (214)
T PTZ00225 67 DLVHE-----DIA----KKEGVP---TMNQEELKKLNKNKKLVKKMCNQYDAFLCSESIIKTVPRLVGPHMHRMGKFPTV 134 (214)
T ss_pred ChHHH-----HHH----HHCCCC---EECHHHHHHHHhccHHHHHHHhhCCEEEECHHHHHhhhhhcCCCCCcCCCCCcc
Confidence 98754 345 346774 777777777777777999999999999999999999999999999999999999
Q ss_pred ccCCcccHHHHHHHHHcccEEEccCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHhhccCCCeeecCcceeeecc
Q 015100 175 VDLKHQNWKEQIEKVCGSALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGLLESLALPVYQAVPDLKLKIEG 249 (413)
Q Consensus 175 V~l~~~dLk~~Ieka~~st~f~l~~G~~~sVkVG~~sMs~eqIvENI~Avl~~L~~SlaLPiYqni~~v~iKi~~ 249 (413)
++.+ .||...|+++.+++.|++++..|++++||+++|+++||+||+.|++++|...+. ..|+|+.++|||+|-
T Consensus 135 ~~~~-~dl~~~i~~~k~~v~~r~~k~~~~~~~VGk~~m~~e~i~eNi~a~l~~l~~~~p-~k~~nIksv~iktTM 207 (214)
T PTZ00225 135 CSPS-ESLPDKVVELRSTVKFQLKKVLCLGTCVGHVEMTEEQLRQNVVMAINFLVSLLK-KNWQNLKSAYIKSTM 207 (214)
T ss_pred cCCc-cCHHHHHHHHhheeEEEecCccEEEeEEccCCCCHHHHHHHHHHHHHHHHHhCC-cCCceEeEEEEECCC
Confidence 9886 799999999999999999999999999999999999999999999999955544 579999999999987
No 4
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=100.00 E-value=5.2e-39 Score=304.72 Aligned_cols=204 Identities=24% Similarity=0.301 Sum_probs=181.3
Q ss_pred CCHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCC--CcceeeeEeCCCCCCCCCCCCCCEEEEEecC
Q 015100 19 VSPKTVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQV--SRTNAFKIPLPHSLLGNDSDNPPEICLIMDD 96 (413)
Q Consensus 19 Vd~eqV~kAVkALlk~~~k~~~~~K~~Lf~Ede~V~L~ItLKkIp~k--~r~~p~~I~LPHpl~~~~~~~~~kICLIvkD 96 (413)
++++++.+||+.|+++ .+.+.|.| +|+|+|+||+|+.+ ++..++.|.|||+++. ..+||||+++
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 6889999999999873 24567888 99999999999885 3556889999999986 6899999998
Q ss_pred CCCCchhHHHHHHhhhcCCCCcceeeechhHHhhcccHHHHHhhhhccCEEEEcCCchhhhhhhhcccccCCCCCCcccc
Q 015100 97 RPKSNLTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVD 176 (413)
Q Consensus 97 ~~~~~~t~~~ake~L~~~gi~i~kVI~lkkLkkeyKsfEakRKL~~sYDlFLAD~rI~p~LpklLGK~F~kkkK~PipV~ 176 (413)
++. ++| +++|+ ..|++.+.|.+-++.|+++|+|+.+||+||||+++|+.||++||++||+|++||+|++
T Consensus 68 ~~~-----~~A----k~aGa--~~v~~~e~L~~i~~~~k~~rkl~~~fD~~lA~~~im~~l~k~LGk~lgprgkmP~p~~ 136 (215)
T PRK04203 68 ELA-----LQA----KEAGA--DYVITREELEELGGDKRAAKKLANEYDFFIAEADLMPLIGRYLGPVLGPRGKMPTPLP 136 (215)
T ss_pred HhH-----HHH----HHcCC--CEEeCHHHHHHHhcChHHHhhhhhcCCEEEECHHHHHHHHHHHhhhcCcCCCCCCCcC
Confidence 653 345 24565 4589999999888889999999999999999999999999999999999999999999
Q ss_pred CCcccHHHHHHHHHcccEEEccCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHhhccCCCeeecCcceeeecc
Q 015100 177 LKHQNWKEQIEKVCGSALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGLLESLALPVYQAVPDLKLKIEG 249 (413)
Q Consensus 177 l~~~dLk~~Ieka~~st~f~l~~G~~~sVkVG~~sMs~eqIvENI~Avl~~L~~SlaLPiYqni~~v~iKi~~ 249 (413)
++. ||...|++++++++|++++++|++++||+++|+++||+|||.++++++...+ ..+|+++.++|||+|.
T Consensus 137 ~t~-di~~~i~~~~~~~~~r~~k~~~i~v~VG~~~m~~e~l~eNi~avl~~i~~~~-p~g~~~Iksi~lktTm 207 (215)
T PRK04203 137 PNA-DIKPLVERLKNTVRIRTKDQPTFHVRVGTEDMSPEELAENIDAVLNRIESKL-EKGRQNIKSVYVKTTM 207 (215)
T ss_pred CCC-CHHHHHHHHhhceEEEeCCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhC-ccccccEEEEEEECCC
Confidence 874 9999999999999999999999999999999999999999999999996554 4789999999999987
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=2.1e-38 Score=298.13 Aligned_cols=210 Identities=40% Similarity=0.616 Sum_probs=173.7
Q ss_pred HHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCCC--cceeeeEeCCCCCCCCCCCCCCEEEEEecCCCCCchhHH
Q 015100 28 VKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQVS--RTNAFKIPLPHSLLGNDSDNPPEICLIMDDRPKSNLTKD 105 (413)
Q Consensus 28 VkALlk~~~k~~~~~K~~Lf~Ede~V~L~ItLKkIp~k~--r~~p~~I~LPHpl~~~~~~~~~kICLIvkD~~~~~~t~~ 105 (413)
|+||++|+++..+ .......+++|+|+|+++++|.+. +..++.|.||||++. ...+||||++|+++.
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 5789999987532 122333455999999999998875 444899999999982 278999999998652
Q ss_pred HHHH--hhhcCCC-CcceeeechhHHhhcccHHHHHhhhhccCEEEEcCCchhhhhhhhcccc-cCCCCCCccccCCccc
Q 015100 106 AVMK--KIKNDNL-PITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHF-FKKKKIPVPVDLKHQN 181 (413)
Q Consensus 106 ~ake--~L~~~gi-~i~kVI~lkkLkkeyKsfEakRKL~~sYDlFLAD~rI~p~LpklLGK~F-~kkkK~PipV~l~~~d 181 (413)
+++ ++.+.+. .+.+|+++++|+++|++|+++|+|+.+||+||||+||++.||++||+.| +++++||+||+++..+
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 221 1111111 2457999999999999999999999999999999999999999999999 5788999999875479
Q ss_pred HHHHHHHHHcccEEEcc-CCCEEEEEEecCCCCHHHHHHHHHHHHHHHHhhccCCCeeecCcceeeecc
Q 015100 182 WKEQIEKVCGSALLYLR-TGTCSVLKVGKVSMGAEDIAENVIAAINGLLESLALPVYQAVPDLKLKIEG 249 (413)
Q Consensus 182 Lk~~Ieka~~st~f~l~-~G~~~sVkVG~~sMs~eqIvENI~Avl~~L~~SlaLPiYqni~~v~iKi~~ 249 (413)
|.++|+++++++.|+.+ .|+|++|+||+++|+.+||+|||.++++++.......+|.+|.++|||++.
T Consensus 149 l~~~i~~~~~~~~~~~~~~~~~~~v~VG~~~~~~~~i~eNi~~~i~~i~~~~~~~g~~~I~~i~ikst~ 217 (220)
T PF00687_consen 149 LKEQIEKALNSTKFRLSGKGGCISVKVGHLSMTDEQIVENIKAVIKAIVSKPLPKGWKNIKSIYIKSTM 217 (220)
T ss_dssp HHHHHHHHHTEEEEEETBTSSEEEEEEEETTSCHHHHHHHHHHHHHHHHHTTTSSSSGSEEEEEEEESS
T ss_pred HHHHHHHHHCCEEEEeeccCCeeecCccCCCCCHHHHHHHHHHHHHHHHHhhhccCcceEEEEEEECCC
Confidence 99999999999999988 899999999999999999999999999999665245789999999999876
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=2.8e-37 Score=288.81 Aligned_cols=200 Identities=33% Similarity=0.433 Sum_probs=173.2
Q ss_pred HHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCC-CcceeeeEeCCCCCCCCCCCCCCEEEEEecCCCCCch
Q 015100 24 VERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQV-SRTNAFKIPLPHSLLGNDSDNPPEICLIMDDRPKSNL 102 (413)
Q Consensus 24 V~kAVkALlk~~~k~~~~~K~~Lf~Ede~V~L~ItLKkIp~k-~r~~p~~I~LPHpl~~~~~~~~~kICLIvkD~~~~~~ 102 (413)
+.+|+++|.+|.. ....|. ++|+|+|+|+.++.+ ....++.|.||||++. +.+||||++|++..
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 3579999988653 223344 499999999998633 4456679999999984 78999999987652
Q ss_pred hHHHHHHhhhcCCCCcceeeechhHHhhcccHHHHHhhhhccCEEEEcCCchhhhhhhhcccccCCCCCCccccCC-ccc
Q 015100 103 TKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVDLK-HQN 181 (413)
Q Consensus 103 t~~~ake~L~~~gi~i~kVI~lkkLkkeyKsfEakRKL~~sYDlFLAD~rI~p~LpklLGK~F~kkkK~PipV~l~-~~d 181 (413)
.|+ +.+ .+|+++++|+.+|++|+++ +|+.+||+||||+++++.+|++||+.||+|++||+++.++ ..+
T Consensus 66 ---~a~----~~~---a~vig~~~L~~~~~~~~~~-~l~~~~D~fla~~~~~~~~~~~lgk~~~~k~k~P~~~~~t~~~~ 134 (208)
T cd00403 66 ---EAK----AAG---ADVVGGEDLKKKIKNGEAK-KLAKDFDLFLADPRIMMLLPKLLGKVLGPRGKMPNPKTGTVTED 134 (208)
T ss_pred ---HHH----HcC---CCEEcHHHHHHHhhcchhh-hhhhcCCEEEECHHHHHHHHHHhccccccCCCCCcCCCCCCccc
Confidence 332 123 3699999999999999999 9999999999999999999999999999999999999985 579
Q ss_pred HHHHHHHHHcccEEEccCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHhhccCCCeeecCcceeeecc
Q 015100 182 WKEQIEKVCGSALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGLLESLALPVYQAVPDLKLKIEG 249 (413)
Q Consensus 182 Lk~~Ieka~~st~f~l~~G~~~sVkVG~~sMs~eqIvENI~Avl~~L~~SlaLPiYqni~~v~iKi~~ 249 (413)
|.++|++++++++|+++.+.|++++||+++|+++||+|||.++++++...+....|+++.++|||++.
T Consensus 135 l~~~i~~~~~~~~~~~~~~~~~~v~VG~~~m~~~~l~eNi~~vi~~i~~~~~~~~~~~i~~v~lktt~ 202 (208)
T cd00403 135 LAKAIEEAKSSVEFRLDKGGCIHVPVGKVSMSPEQLVENIEAVINALVKKLPSKKGQNIKSIYLKTTM 202 (208)
T ss_pred HHHHHHHHHhCeEEEECCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCCcccCeEEEEEEEECCC
Confidence 99999999999999999999999999999999999999999999999766655789999999999985
No 7
>CHL00129 rpl1 ribosomal protein L1; Reviewed
Probab=99.96 E-value=9e-29 Score=236.98 Aligned_cols=190 Identities=15% Similarity=0.157 Sum_probs=160.0
Q ss_pred HHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCC--CcceeeeEeCCCCCCCCCCCCCCEEEEEecCCCCCc
Q 015100 24 VERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQV--SRTNAFKIPLPHSLLGNDSDNPPEICLIMDDRPKSN 101 (413)
Q Consensus 24 V~kAVkALlk~~~k~~~~~K~~Lf~Ede~V~L~ItLKkIp~k--~r~~p~~I~LPHpl~~~~~~~~~kICLIvkD~~~~~ 101 (413)
+.+||+.|+++ +...|.| +|+|+|+| +++.+ .....+.|.|||++++ ..+||||+++...
T Consensus 22 l~eAi~~~k~~--------~~~kF~e--svel~i~L-~id~kk~~~~irg~v~LP~~~gk-----~~kV~Vfa~~~~~-- 83 (229)
T CHL00129 22 PEEAINLLKET--------ATAKFIE--TAEAHISL-NIDPKYADQQLRTTVTLPKGTGK-----TIRIAVLTNEEKI-- 83 (229)
T ss_pred HHHHHHHHHHh--------CcCCCCc--cEEEEEEE-CCCCCCCCCceeeEEECCCCCCC-----CcEEEEECChHhH--
Confidence 67888888751 3456887 99999999 88665 4566789999999976 6899999998643
Q ss_pred hhHHHHHHhhhcCCCCcceeeechhHHhhcccHHHHHhhhhccCEEEEcCCchhhhhhhhcccccCCCCCCccccCC-cc
Q 015100 102 LTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVDLK-HQ 180 (413)
Q Consensus 102 ~t~~~ake~L~~~gi~i~kVI~lkkLkkeyKsfEakRKL~~sYDlFLAD~rI~p~LpklLGK~F~kkkK~PipV~l~-~~ 180 (413)
++| ++.|+ .+++.++|...+ ++++.+||+|||++++|+.|++ ||+.|+|||+||.|..++ ..
T Consensus 84 ---~eA----k~aGa---d~vg~edLi~~i------k~~~~~fd~~iAt~d~m~~l~k-LgriLGprGlMP~pk~gTvt~ 146 (229)
T CHL00129 84 ---TEA----KNAGA---DIVGSDDLIEEI------TKGNLDFDLLIATPDMMPKLAK-LGRVLGPRGLMPSPKSGTVTT 146 (229)
T ss_pred ---HHH----HHcCC---CEeCHHHHHHHH------HcCcccCCEEEECHHHHHHHHH-hcCcccccCCCCCCCCCCccc
Confidence 245 34666 489999997744 5678899999999999999999 999999999999999987 57
Q ss_pred cHHHHHHHHHc-ccEEEccCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHhhccCCCee--ecCcceeeecc
Q 015100 181 NWKEQIEKVCG-SALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGLLESLALPVYQ--AVPDLKLKIEG 249 (413)
Q Consensus 181 dLk~~Ieka~~-st~f~l~~G~~~sVkVG~~sMs~eqIvENI~Avl~~L~~SlaLPiYq--ni~~v~iKi~~ 249 (413)
|+.+.|+++.+ ++.|+..+..+++++||+++|+++||+|||.++++++... ....|. ++.++||++|-
T Consensus 147 di~~~V~~~k~G~v~~r~dk~g~i~~~VG~~~m~~~~l~eNi~a~l~~i~~~-~p~~~kg~~ik~v~issTM 217 (229)
T CHL00129 147 DLASAINEFKKGKLEYRADKTGIVHVLFGKSNFTEEDLLENLQAIYESIEQN-RPSGVKGKYWKSFYICSTM 217 (229)
T ss_pred cHHHHHHHHhcCcEEEEecCCcEEEEEEeCCCCCHHHHHHHHHHHHHHHHHh-CcccccCceEEEEEEECCC
Confidence 99999999987 6899999999999999999999999999999999999543 323455 78999998886
No 8
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=9.8e-29 Score=234.85 Aligned_cols=196 Identities=19% Similarity=0.243 Sum_probs=161.4
Q ss_pred CCHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCC--CcceeeeEeCCCCCCCCCCCCCCEEEEEecC
Q 015100 19 VSPKTVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQV--SRTNAFKIPLPHSLLGNDSDNPPEICLIMDD 96 (413)
Q Consensus 19 Vd~eqV~kAVkALlk~~~k~~~~~K~~Lf~Ede~V~L~ItLKkIp~k--~r~~p~~I~LPHpl~~~~~~~~~kICLIvkD 96 (413)
.....+.+||+.+.+ . ..+.|.+ +|+++|+|+ ++++ ++...+.+.|||++++ ..+||||+++
T Consensus 18 ~~~~~i~eai~~~ke-------~-~~~kF~e--tVevav~L~-vD~~k~dq~vrg~VvLP~g~gk-----~vrV~Vfa~g 81 (228)
T COG0081 18 NKLYSLEEAVKLLKE-------T-SKRKFDE--TVEVAVNLK-VDPRKPDQRVRGSVVLPNGTGK-----TVRVAVFADG 81 (228)
T ss_pred hhhhhHHHHHHHHHh-------c-cccCcce--EEEEEEEcc-cCCCCcccccceeEECCCCCCC-----ccEEEEEcCh
Confidence 345567777777766 2 3477988 999999997 8664 4667789999999987 6899999976
Q ss_pred CCCCchhHHHHHHhhhcCCCCcceeeechhHHhhcccHHHHHhhhhccCEEEEcCCchhhhhhhhcccccCCCCCCcccc
Q 015100 97 RPKSNLTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVD 176 (413)
Q Consensus 97 ~~~~~~t~~~ake~L~~~gi~i~kVI~lkkLkkeyKsfEakRKL~~sYDlFLAD~rI~p~LpklLGK~F~kkkK~PipV~ 176 (413)
... ++| .+.|+ . +++..+|....+ ..| +.+||+|||++++|+.+ +.||+.|+|||+||.|+.
T Consensus 82 ~~~-----~~A----~~AGa--d-~Vg~edl~e~ik---~~r--~~~fD~~IAtpdmM~~v-~~LG~vLGPRGlMP~Pk~ 143 (228)
T COG0081 82 EKA-----EEA----KAAGA--D-YVGGEDLIELIK---NGR--AKDFDVFIATPDMMPLV-GKLGKVLGPRGLMPNPKT 143 (228)
T ss_pred HhH-----HHH----HHcCC--C-EecHHHHHHHHh---Ccc--hhcCCEEEECchHHHHH-HHHhhhcCCCCCCCCCCC
Confidence 543 244 34565 3 444488877766 333 88999999999999999 779999999999999999
Q ss_pred CC-cccHHHHHHHHHc-ccEEEccCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHhhccCCC--eeecCcceeeecc
Q 015100 177 LK-HQNWKEQIEKVCG-SALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGLLESLALPV--YQAVPDLKLKIEG 249 (413)
Q Consensus 177 l~-~~dLk~~Ieka~~-st~f~l~~G~~~sVkVG~~sMs~eqIvENI~Avl~~L~~SlaLPi--Yqni~~v~iKi~~ 249 (413)
+| +.|+...|+++.+ ++.||.++..|+|+.||+++|++++|+|||.++++.+.. ..... ++++.++|+++|-
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~vstTM 219 (228)
T COG0081 144 GTVTDDVAKAVEELKKGTVEFRADKAGVIHVPIGKVSFDDEKLAENIEALLNAIVK-AKPAGAKGQYIKSVYVSTTM 219 (228)
T ss_pred CCCCcCHHHHHHHHhcCcEEEEECCCceEEEEecCCCCCHHHHHHHHHHHHHHHHH-hCcCCcccceEeEEEEecCC
Confidence 76 5799999999999 789999999999999999999999999999999999943 33233 9999999999987
No 9
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=99.96 E-value=2.5e-28 Score=234.09 Aligned_cols=190 Identities=14% Similarity=0.184 Sum_probs=159.0
Q ss_pred HHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCC--CcceeeeEeCCCCCCCCCCCCCCEEEEEecCCCCCc
Q 015100 24 VERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQV--SRTNAFKIPLPHSLLGNDSDNPPEICLIMDDRPKSN 101 (413)
Q Consensus 24 V~kAVkALlk~~~k~~~~~K~~Lf~Ede~V~L~ItLKkIp~k--~r~~p~~I~LPHpl~~~~~~~~~kICLIvkD~~~~~ 101 (413)
+.+||+.|+++ +.+.|.| +|+|+|+| +++.+ .....+.|.|||++++ ..+||||+++...
T Consensus 22 l~eAi~~lk~~--------~~~kF~e--svel~v~L-~id~kK~~~~irg~v~LP~~~gk-----~~kI~Vfa~~~~~-- 83 (230)
T PRK05424 22 LEEAIALVKET--------ATAKFDE--TVDVAVNL-GVDPRKADQQVRGAVVLPHGTGK-----TVRVAVFAKGEKA-- 83 (230)
T ss_pred HHHHHHHHHhh--------ccCCCCC--cEEEEEEe-CCCCCCCCCeeeEEEECCCCCCC-----CcEEEEECChHhH--
Confidence 67888888762 2456877 99999999 88554 3566789999999986 6899999976543
Q ss_pred hhHHHHHHhhhcCCCCcceeeechhHHhhcccHHHHHhhhhccCEEEEcCCchhhhhhhhcccccCCCCCCccccCC-cc
Q 015100 102 LTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVDLK-HQ 180 (413)
Q Consensus 102 ~t~~~ake~L~~~gi~i~kVI~lkkLkkeyKsfEakRKL~~sYDlFLAD~rI~p~LpklLGK~F~kkkK~PipV~l~-~~ 180 (413)
++| .+.|+ .+++.++|....+ +.++ +||+|||++++||.|++ ||+.|+|||+||.|..++ ..
T Consensus 84 ---~~A----k~aGa---~~vg~eeLi~~ik-----~~~~-~fd~~iat~~~m~~l~~-Lg~iLGPrGlMP~pk~gTv~~ 146 (230)
T PRK05424 84 ---EEA----KAAGA---DIVGGEDLIEKIK-----GGWL-DFDVVIATPDMMGKVGK-LGRILGPRGLMPNPKTGTVTM 146 (230)
T ss_pred ---HHH----HHcCC---CEeCHHHHHHHHh-----cCCC-cCCEEEECHHHHHHHHH-hccccccccCCCCCCCCCcch
Confidence 244 34676 3889999987664 3444 89999999999999999 999999999999999976 46
Q ss_pred cHHHHHHHHHc-ccEEEccCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHhhccCCCe--eecCcceeeecc
Q 015100 181 NWKEQIEKVCG-SALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGLLESLALPVY--QAVPDLKLKIEG 249 (413)
Q Consensus 181 dLk~~Ieka~~-st~f~l~~G~~~sVkVG~~sMs~eqIvENI~Avl~~L~~SlaLPiY--qni~~v~iKi~~ 249 (413)
|+.+.|+++.+ ++.|+..+..|++++||+++|+++||+|||.++++++. +.....| +++.++||++|.
T Consensus 147 di~~~I~~~k~g~v~~r~~k~g~i~~~IG~~~m~~e~i~eNi~a~l~~i~-~~~p~~~kg~~Ik~v~lssTm 217 (230)
T PRK05424 147 DVAKAVKEAKAGKVEFRVDKAGIIHAPIGKVSFDAEKLKENLKALIDAIK-KAKPATAKGTYIKSVSLSSTM 217 (230)
T ss_pred hHHHHHHHHhcCcEEEEecCCCEEEEEEeCCCCCHHHHHHHHHHHHHHHH-HhCccccCCCEEEEEEEECCC
Confidence 99999999987 57999999999999999999999999999999999995 4444567 789999999987
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=99.96 E-value=3.3e-28 Score=232.81 Aligned_cols=190 Identities=14% Similarity=0.171 Sum_probs=160.2
Q ss_pred HHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCC--CcceeeeEeCCCCCCCCCCCCCCEEEEEecCCCCCc
Q 015100 24 VERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQV--SRTNAFKIPLPHSLLGNDSDNPPEICLIMDDRPKSN 101 (413)
Q Consensus 24 V~kAVkALlk~~~k~~~~~K~~Lf~Ede~V~L~ItLKkIp~k--~r~~p~~I~LPHpl~~~~~~~~~kICLIvkD~~~~~ 101 (413)
+.+||+.|.++ +.+.|.| +|+|+|+| +++.+ .....+.|.|||+++. ..+||||+++.+.
T Consensus 21 l~eAi~~lk~~--------~~~~f~e--svel~i~L-~id~kK~~~~irg~v~LP~~~gk-----~~kV~Vfa~~~~~-- 82 (227)
T TIGR01169 21 LDEAIALLKET--------ATAKFDE--TVEVAIRL-GIDPRKSDQQVRGTVVLPHGTGK-----TVRVAVFAKGEKA-- 82 (227)
T ss_pred HHHHHHHHHhh--------ccCCCCC--CEEEEEEE-CcCCCcCCCeeeEEEECCCCCCC-----CcEEEEEcCchhH--
Confidence 67888888762 2456877 99999999 88554 4567789999999976 6899999986543
Q ss_pred hhHHHHHHhhhcCCCCcceeeechhHHhhcccHHHHHhhhhccCEEEEcCCchhhhhhhhcccccCCCCCCccccCC-cc
Q 015100 102 LTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVDLK-HQ 180 (413)
Q Consensus 102 ~t~~~ake~L~~~gi~i~kVI~lkkLkkeyKsfEakRKL~~sYDlFLAD~rI~p~LpklLGK~F~kkkK~PipV~l~-~~ 180 (413)
++| .+.|+ .+++.++|... .++++.+||+|||++++||.|+ .||+.|+|||+||.|..++ ..
T Consensus 83 ---~~A----k~aGa---~~vg~~eLi~~------ik~~~~~fd~~iat~~~m~~l~-~Lg~iLGPrGlMP~~k~gtv~~ 145 (227)
T TIGR01169 83 ---EEA----KAAGA---DYVGSDDLIEK------IKKGWLDFDVVIATPDMMRVVG-KLGRILGPRGLMPNPKTGTVTA 145 (227)
T ss_pred ---HHH----HHcCC---CEeCHHHHHHH------HHcCCccCCEEEECHHHHHHHH-HhccccccccCCCCCCCCCccc
Confidence 244 34566 38999999774 4567899999999999999999 7999999999999999987 57
Q ss_pred cHHHHHHHHHc-ccEEEccCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHhhccCCCe--eecCcceeeecc
Q 015100 181 NWKEQIEKVCG-SALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGLLESLALPVY--QAVPDLKLKIEG 249 (413)
Q Consensus 181 dLk~~Ieka~~-st~f~l~~G~~~sVkVG~~sMs~eqIvENI~Avl~~L~~SlaLPiY--qni~~v~iKi~~ 249 (413)
|+.+.|+++.+ ++.|+..+..|++++||+++|+++||.|||.++++++. +.....| +++.++||++|.
T Consensus 146 di~~~I~~~k~g~v~~r~~k~g~i~~~VG~~~m~~e~i~eNi~a~l~~i~-~~~p~~~kg~~Ik~v~lssTm 216 (227)
T TIGR01169 146 DVAKAVKNAKKGQVEFRADKAGNIHASIGKVSFDSEKLKENLEALLDAIK-KAKPSGAKGQYIKNIALSSTM 216 (227)
T ss_pred cHHHHHHHHHcCcEEEEeCCCCEEEEEEecCCCCHHHHHHHHHHHHHHHH-HhCccccCCCEEEEEEEECCC
Confidence 99999999997 58999999999999999999999999999999999995 4444556 789999999977
No 11
>KOG1570 consensus 60S ribosomal protein L10A [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=5.5e-27 Score=218.98 Aligned_cols=211 Identities=27% Similarity=0.364 Sum_probs=182.4
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccC-CCCCcceeeeEeCCCCCCCCCCCCCCEEEEEe
Q 015100 16 GSRVSPKTVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKI-PQVSRTNAFKIPLPHSLLGNDSDNPPEICLIM 94 (413)
Q Consensus 16 ~s~Vd~eqV~kAVkALlk~~~k~~~~~K~~Lf~Ede~V~L~ItLKkI-p~k~r~~p~~I~LPHpl~~~~~~~~~kICLIv 94 (413)
+|.++++++..||..++.+.. ..+++.|-+ +|++||+|++| |.+..++.+.+.|||..+. ..++|+|.
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 457899999999999987543 235566776 99999999999 4557778899999999875 78999999
Q ss_pred cCCCCCchhHHHHHHhhhcCCCCcceeeechhHHhhcccHHHHHhhhhccCEEEEcCCchhhhhhhhcccccCCCCCCcc
Q 015100 95 DDRPKSNLTKDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVP 174 (413)
Q Consensus 95 kD~~~~~~t~~~ake~L~~~gi~i~kVI~lkkLkkeyKsfEakRKL~~sYDlFLAD~rI~p~LpklLGK~F~kkkK~Pip 174 (413)
+..++. .| .+-++|...+-.+++|.+..+ .+++|++.||.|||..+++.+||++||+.+.+.|++|.+
T Consensus 71 d~~h~~-----~a----k~~~~p~m~~d~lkklnk~Kk---lvkklakky~~flase~~ikQlpr~lgp~l~kaGkfps~ 138 (218)
T KOG1570|consen 71 DQQHCD-----EA----KAIDLPAMDIDALKKLNKNKK---LVKKLAKKYDAFLASESLIKQLPRILGPGLSKAGKFPSL 138 (218)
T ss_pred hHHHHH-----Hh----hcCCCCCcCHHHHhcCcccch---HHHHHHHHhhhHHhhHHHHHHhhhhhcccccccccCCcc
Confidence 876652 44 345677666667777766665 789999999999999999999999999999999999999
Q ss_pred ccCCcccHHHHHHHHHcccEEEccCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHhhccCCCeeecCcceeeecccc
Q 015100 175 VDLKHQNWKEQIEKVCGSALLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGLLESLALPVYQAVPDLKLKIEGVK 251 (413)
Q Consensus 175 V~l~~~dLk~~Ieka~~st~f~l~~G~~~sVkVG~~sMs~eqIvENI~Avl~~L~~SlaLPiYqni~~v~iKi~~~~ 251 (413)
+... +++.+.++..+.+..|++++-.|++|.|||+.|++++|++||.-.++++ .|+.+..|||++.++||+|.-+
T Consensus 139 l~~~-d~l~akv~evk~t~k~q~kkvKOGavaVGhv~M~d~el~~nI~l~vnFl-VSlLKknwQNvral~iKst~g~ 213 (218)
T KOG1570|consen 139 LVHG-DSLYAKVEEVKSTIKFQMKKVLCLAVAVGHVGMTDEELVYNIHLAVNFL-VSLLKKNWQNVRALYIKSTMGK 213 (218)
T ss_pred ccch-HHHHHHHHHHHhhHHHHHHhhhheeeeecCCCCCHHHHHHhhhhhhhhH-HHHHhhcccchhheeeccCCCC
Confidence 9864 7999999999999999999999999999999999999999999999988 8999999999999999999743
No 12
>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=99.67 E-value=5.1e-16 Score=139.26 Aligned_cols=137 Identities=18% Similarity=0.162 Sum_probs=102.9
Q ss_pred HHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCCCcceeeeEeCCCCCCCCCCCCCCEEEEEecCCCCCchh
Q 015100 24 VERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQVSRTNAFKIPLPHSLLGNDSDNPPEICLIMDDRPKSNLT 103 (413)
Q Consensus 24 V~kAVkALlk~~~k~~~~~K~~Lf~Ede~V~L~ItLKkIp~k~r~~p~~I~LPHpl~~~~~~~~~kICLIvkD~~~~~~t 103 (413)
+.+|++-|.++. ... -.|.+ +|+|+|+| ++........+.|.|||++.+ +.+||||+++.+..
T Consensus 3 i~eA~~~lk~~~-----~~~-~~~~e--tvel~i~L-~~~~~~~~irg~v~LP~~~~k-----~~kV~Vf~~~~~~~--- 65 (141)
T TIGR01170 3 VIKAFVYLKTKS-----ISM-YVPKQ--SVNLDIGL-LMELGKESVQGMFSFPHPFGK-----EPKIAVFTKGASEV--- 65 (141)
T ss_pred HHHHHHHHHHhc-----ccC-CCCCc--eEEEEEEE-CCCCCCCCceEEEECCCCCCC-----CCEEEEECCChHHH---
Confidence 456666665532 111 25666 99999999 554432235689999999986 57999999987531
Q ss_pred HHHHHHhhhcCCCCcceeeechhHHhhcccHHHHHhhhhc-cCEEEEcCCchhhhhhhhcccccCCCCCCccccCC-ccc
Q 015100 104 KDAVMKKIKNDNLPITKVIKITKLKTDYRPFEAKRKLCDS-YDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVDLK-HQN 181 (413)
Q Consensus 104 ~~~ake~L~~~gi~i~kVI~lkkLkkeyKsfEakRKL~~s-YDlFLAD~rI~p~LpklLGK~F~kkkK~PipV~l~-~~d 181 (413)
++| ++.|+ .+++.++|..+++. .+ .. ||+|||++++|+.|+ .||+.|++||+||.|...+ ..|
T Consensus 66 -~~A----k~aGa---~~vg~edLi~~i~~----g~--~~~fd~~iA~~~~m~~l~-~Lg~iLGprGlMP~~k~gTv~~d 130 (141)
T TIGR01170 66 -EEA----REAGA---DYVGGDDLIKKIED----GE--IKPFDYLIAHPDIVPELA-QLRRLLGPKGLMPSPKRGTVGDN 130 (141)
T ss_pred -HHH----HHcCC---CEeCHHHHHHHHhc----CC--cccccEEEECHHHHHHHH-HhhcccccCcCCCCCCCCCcccC
Confidence 234 34565 48999999777652 11 23 999999999999999 7999999999999999987 579
Q ss_pred HHHHHHHHHcc
Q 015100 182 WKEQIEKVCGS 192 (413)
Q Consensus 182 Lk~~Ieka~~s 192 (413)
+...|+++.++
T Consensus 131 i~~~I~~~k~G 141 (141)
T TIGR01170 131 LLSMIETFKKG 141 (141)
T ss_pred HHHHHHHHhCc
Confidence 99999988753
No 13
>KOG1569 consensus 50S ribosomal protein L1 [Translation, ribosomal structure and biogenesis]
Probab=99.65 E-value=1.4e-15 Score=149.31 Aligned_cols=167 Identities=22% Similarity=0.266 Sum_probs=130.3
Q ss_pred eEEEEEEecc----CCCCCcceeeeEeCCCCCCCCCCCCCCEEEEEecCCCCCchhHHHHHHhhhcCCCCcceeeechhH
Q 015100 52 FVYLILTLKK----IPQVSRTNAFKIPLPHSLLGNDSDNPPEICLIMDDRPKSNLTKDAVMKKIKNDNLPITKVIKITKL 127 (413)
Q Consensus 52 ~V~L~ItLKk----Ip~k~r~~p~~I~LPHpl~~~~~~~~~kICLIvkD~~~~~~t~~~ake~L~~~gi~i~kVI~lkkL 127 (413)
+++|.|.|.. ........++.+.+|||+... +...|++|+.|.... ++| .+.|+ .++|...|
T Consensus 114 ~~~l~i~l~~~a~~~~k~~~~~~~~v~vP~Pf~~g---e~r~IavFtn~~~kv----eeA----rEaGA---~l~GG~dL 179 (323)
T KOG1569|consen 114 PVNLRIELNMLAEKETKGVAPLQGSVTVPHPFAHG---EIRKIAVFTNDASKV----EEA----REAGA---ALAGGTDL 179 (323)
T ss_pred ceeeeEEeeeeeeeeccccCCCceeEeccccCCCC---ceEEEEEecCChHHH----HHH----Hhccc---cccccHHH
Confidence 5666665533 211123456789999999875 366799999996542 344 34565 58888899
Q ss_pred HhhcccHHHHHhhhhccCEEEEcCCchhhhhhhhcccccCCCCCCccccCC-cccHHHHHHHHHcc--cEEEccCCCEEE
Q 015100 128 KTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKHFFKKKKIPVPVDLK-HQNWKEQIEKVCGS--ALLYLRTGTCSV 204 (413)
Q Consensus 128 kkeyKsfEakRKL~~sYDlFLAD~rI~p~LpklLGK~F~kkkK~PipV~l~-~~dLk~~Ieka~~s--t~f~l~~G~~~s 204 (413)
.++++.-+ +.-+||+++|.++||+.|.+ |++.+++| ||.|...+ ..||.+.|+++.++ +.|+....+.++
T Consensus 180 IkkI~~Ge----i~~Dyd~~vA~Pdim~~l~~-Lr~iL~~r--~Pn~k~gtvg~nipemieeFk~G~~i~~d~~~~~~~~ 252 (323)
T KOG1569|consen 180 IKKIKSGE----IVADYDFYVAHPDIMPELNR-LRKILGPR--FPNPKRGTVGRNIPEMIEEFKNGHEIKFDEERENILQ 252 (323)
T ss_pred HHHhhcCe----EEEeeceeeecchHHHHHHH-HHHHhccc--CCCcccCccccchHHHHHHhhCCcccccccccCceee
Confidence 88887543 56669999999999999998 88888877 99999988 78999999999999 677766556679
Q ss_pred EEEecCCCCHHHHHHHHHHHHHHHH--hhccCCCeee
Q 015100 205 LKVGKVSMGAEDIAENVIAAINGLL--ESLALPVYQA 239 (413)
Q Consensus 205 VkVG~~sMs~eqIvENI~Avl~~L~--~SlaLPiYqn 239 (413)
+.||+++|+.+||.+||.+++..+. ...++|.|.+
T Consensus 253 ~~vGkl~mt~e~i~~Ni~a~i~av~t~rp~~~G~fv~ 289 (323)
T KOG1569|consen 253 IKVGKLDMTSEQILANIQAVIAAVCTHRPKALGPFVV 289 (323)
T ss_pred eeeeeecCCHHHHHHHHHHHHHHHHhcCCcccCceee
Confidence 9999999999999999999999974 3557777754
No 14
>PF13003 MRL1: Ribosomal protein L1; InterPro: IPR024663 This entry represents a ribosomal protein L1 domain found mainly in chordates.
Probab=88.76 E-value=1 Score=40.62 Aligned_cols=60 Identities=25% Similarity=0.248 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHhccCCCCCCCCCCCCeEEEEEEeccCCCCC---cceeeeEeCCCCCCCCCCCCCCEEEEE
Q 015100 23 TVERAVKALLKWLKSNSQTQKPQLLEQDDFVYLILTLKKIPQVS---RTNAFKIPLPHSLLGNDSDNPPEICLI 93 (413)
Q Consensus 23 qV~kAVkALlk~~~k~~~~~K~~Lf~Ede~V~L~ItLKkIp~k~---r~~p~~I~LPHpl~~~~~~~~~kICLI 93 (413)
.|++||.-|.+|. .-+.-.+.+.|||.++|...-.+. -.++..|.||||+... -.+|+||
T Consensus 71 eve~Ai~mLKkfQ-------~lDfT~pkQ~VYldL~Ldm~l~KKkkVePF~s~i~lPypF~~e----iNKv~VF 133 (133)
T PF13003_consen 71 EVEKAIDMLKKFQ-------ILDFTSPKQPVYLDLTLDMKLEKKKKVEPFASVILLPYPFTSE----INKVLVF 133 (133)
T ss_pred HHHHHHHHHHhcc-------cccCCCCCCcEEEeeeehhhhccccccCCCccceecccccccc----cceeeeC
Confidence 5889999998864 233334456999999996654442 3356789999999763 5677765
No 15
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=53.85 E-value=8 Score=40.94 Aligned_cols=21 Identities=19% Similarity=0.248 Sum_probs=15.8
Q ss_pred CCCCCCCccccccCCCccccc
Q 015100 317 ESEDGEDSEDGKMSSGDILGK 337 (413)
Q Consensus 317 ~~~~~~~~~~~~~~~~~~~~~ 337 (413)
.|++++|++....|+|++.=+
T Consensus 288 ~ddd~~d~d~e~~~v~dN~~p 308 (514)
T KOG3130|consen 288 IDDDDGDNDHEALGVGDNSIP 308 (514)
T ss_pred ccccccccchhhhccCCCcCc
Confidence 467777788888899887644
No 16
>KOG2652 consensus RNA polymerase II transcription initiation factor TFIIA, large chain [Transcription]
Probab=44.11 E-value=17 Score=37.65 Aligned_cols=13 Identities=23% Similarity=0.312 Sum_probs=8.8
Q ss_pred ccccccCCCcccc
Q 015100 324 SEDGKMSSGDILG 336 (413)
Q Consensus 324 ~~~~~~~~~~~~~ 336 (413)
.|+..+.||+=++
T Consensus 289 ~EeeplnsedDvs 301 (348)
T KOG2652|consen 289 VEEEPLNSEDDVS 301 (348)
T ss_pred cccccccCccccc
Confidence 3667777776665
No 17
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=41.06 E-value=20 Score=36.05 Aligned_cols=13 Identities=23% Similarity=0.794 Sum_probs=5.4
Q ss_pred eEEEEEEeccCCC
Q 015100 52 FVYLILTLKKIPQ 64 (413)
Q Consensus 52 ~V~L~ItLKkIp~ 64 (413)
|-|.--++.++|.
T Consensus 53 FCYFC~s~qrlp~ 65 (314)
T PF06524_consen 53 FCYFCQSVQRLPM 65 (314)
T ss_pred eeehhhhhhcCch
Confidence 3343334444443
No 18
>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]
Probab=38.44 E-value=35 Score=38.75 Aligned_cols=80 Identities=21% Similarity=0.293 Sum_probs=54.7
Q ss_pred CCCCCCccccCCcccHHHHHHHHHccc---EEEccCCCEEEEEEecCCCCHHHHHHHHHHHHHHHHh----hccCCCeee
Q 015100 167 KKKKIPVPVDLKHQNWKEQIEKVCGSA---LLYLRTGTCSVLKVGKVSMGAEDIAENVIAAINGLLE----SLALPVYQA 239 (413)
Q Consensus 167 kkkK~PipV~l~~~dLk~~Ieka~~st---~f~l~~G~~~sVkVG~~sMs~eqIvENI~Avl~~L~~----SlaLPiYqn 239 (413)
|-+++|+-+-.+...=+..|+.|+.++ ++..+-|..+.+-.|.-. .+-.-||+...+..|.. =+.+|||.|
T Consensus 438 PGRRyPVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeE--IEt~~e~l~~~~~~LGski~eliv~PiYaN 515 (902)
T KOG0923|consen 438 PGRRYPVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEE--IETVKENLKERCRRLGSKIRELIVLPIYAN 515 (902)
T ss_pred cCcccceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHH--HHHHHHHHHHHHHHhccccceEEEeecccc
Confidence 678899888777555566777777764 333455777777767654 55566788888877743 478999999
Q ss_pred cCc-ceeeec
Q 015100 240 VPD-LKLKIE 248 (413)
Q Consensus 240 i~~-v~iKi~ 248 (413)
+|+ +..||=
T Consensus 516 LPselQakIF 525 (902)
T KOG0923|consen 516 LPSELQAKIF 525 (902)
T ss_pred CChHHHHhhc
Confidence 875 455553
No 19
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.29 E-value=48 Score=31.76 Aligned_cols=21 Identities=33% Similarity=0.604 Sum_probs=12.7
Q ss_pred cccCCCCCCCCCCCCCCCCCC
Q 015100 303 DELGSDDDGEGDVGESEDGED 323 (413)
Q Consensus 303 ~~~~~~~~~~~~~~~~~~~~~ 323 (413)
|.+|.|.|.|+.+|.|+-++|
T Consensus 195 Dd~d~d~D~eD~~gD~e~~~e 215 (227)
T KOG3241|consen 195 DDSDPDSDEEDNVGDDEHDLE 215 (227)
T ss_pred cccCCccccccccCccccccc
Confidence 345556677777776664443
No 20
>KOG2422 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.53 E-value=33 Score=38.18 Aligned_cols=74 Identities=27% Similarity=0.197 Sum_probs=44.0
Q ss_pred CCCCCCCccccccCCCccccccccccchHHhhhchhhhh-hhhhhhcccccccchhhhhhhhhcccccccCccccc
Q 015100 317 ESEDGEDSEDGKMSSGDILGKKRKKGDKERAQKLPKKVA-KVKKDELSSDMKNEDVGKQKKQKKVGLSLKNDEEKS 391 (413)
Q Consensus 317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 391 (413)
.++-|+++ ++--.+++.+.|.-|-|.+++.++.-|+.+ +.-+.+.+.+-+..+.++--|.|.+-.+.+..-..|
T Consensus 67 ~ee~de~~-~~~es~~~~~~~~sk~k~KKK~krkkKk~~~~~d~~e~s~deq~~a~l~~~k~K~d~~~e~~~~t~s 141 (665)
T KOG2422|consen 67 AEERDEPS-VGQESRITLASKSSKNKKKKKKKRKKKKSTAEVDKDEGSDDEQKLAILKYGKTKNDDKNEEGFFTAS 141 (665)
T ss_pred hhcccCcc-cCCcccccccchhhccccchhhhhccccccCccccccCCchHHHHHHHHhhccchhhhhcccCCccc
Confidence 34444443 333456777777777776666665555543 333447777767777777777777666665543333
No 21
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=25.21 E-value=54 Score=36.10 Aligned_cols=49 Identities=29% Similarity=0.186 Sum_probs=23.5
Q ss_pred cceeEEEeecCcccccccccccCC--CCCCCCCCCCCCCCCCccccccCCC
Q 015100 284 GRIHEVRYMDSTIGEVLDEDELGS--DDDGEGDVGESEDGEDSEDGKMSSG 332 (413)
Q Consensus 284 ~~i~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~ 332 (413)
||..|.--||+.+.|+.++||.=. .||.+...+-|.++.||++.+-+|+
T Consensus 450 ~~~~edd~~d~~~de~~e~Dedf~~~~~~d~vaee~dS~~~ds~~~eg~S~ 500 (615)
T KOG0526|consen 450 DRDEEDDSDDSSTDEDEEEDEDFKPGEEDDDVAEEFDSDEADSSDEEGDSD 500 (615)
T ss_pred cchhhhcccccccccchhhhhhcccCccccccccccCCcccccccccCCcc
Confidence 444455456666655555554322 1332333333444556565564444
No 22
>PLN02347 GMP synthetase
Probab=24.75 E-value=6.7e+02 Score=27.61 Aligned_cols=147 Identities=20% Similarity=0.272 Sum_probs=74.0
Q ss_pred CEEEEEecCCCCCchhHHHHHHhh-hcCCCCcceeeechh--HHh--hcccHHHHHhhhhc----------------c--
Q 015100 88 PEICLIMDDRPKSNLTKDAVMKKI-KNDNLPITKVIKITK--LKT--DYRPFEAKRKLCDS----------------Y-- 144 (413)
Q Consensus 88 ~kICLIvkD~~~~~~t~~~ake~L-~~~gi~i~kVI~lkk--Lkk--eyKsfEakRKL~~s----------------Y-- 144 (413)
.=+|||++......-..+++...+ ...|+++. ++.+++ |.. .+...++||+.|.. +
T Consensus 256 ~v~av~id~g~~~~~E~~~~~~~~a~~lgi~~~-vvd~~e~fl~~l~~~~~pe~k~~~~~~~f~~~f~~~~~~~~~~~~~ 334 (536)
T PLN02347 256 RLHCVFVDNGLLRYKEQERVMETFKRDLHLPVT-CVDASERFLSKLKGVTDPEKKRKIIGAEFIEVFDEFAHKLEQKLGK 334 (536)
T ss_pred cEEEEEEeCCCCChhHHHHHHHHHHHHcCCcEE-EEeCcHHHHhhCCCCCChHHhcchhCchHHHHHHHHHHHHHHhhCC
Confidence 457899986544321222332333 34677643 666666 443 34345555544444 1
Q ss_pred -CEEEEcCCchhhhhhh---hcc-----ccc---------C---CCCCCccccCCcccHHHHHHHHHccc------EEEc
Q 015100 145 -DIFLADKRVVPLLPKL---LGK-----HFF---------K---KKKIPVPVDLKHQNWKEQIEKVCGSA------LLYL 197 (413)
Q Consensus 145 -DlFLAD~rI~p~Lpkl---LGK-----~F~---------k---kkK~PipV~l~~~dLk~~Ieka~~st------~f~l 197 (413)
..||++..++|-+..- .|. ... + -.++-.|+. .=.+.+|+++.+.. ..+.
T Consensus 335 ~~~~l~qGt~~~D~~es~~r~g~~~~~~~~ik~hhn~~~l~~~~~~~ii~PL~---~l~K~eVR~la~~lgl~~~~~~~~ 411 (536)
T PLN02347 335 KPAFLVQGTLYPDVIESCPPPGSGRTHSHTIKSHHNVGGLPKDMKLKLIEPLK---LLFKDEVRKLGRLLGVPEAFLKRH 411 (536)
T ss_pred CCcEEccCCcccccccccCCCCCccccccceeeecccccChHHHHCccccchh---hCcHHHHHHHHHHcCCCHHHhcCC
Confidence 1488888887766431 121 000 0 011222221 11244555543322 2333
Q ss_pred -cCCCEEEEEEecCCCCHHH---HHHHHHHHHHHHHh--hccCCCeee
Q 015100 198 -RTGTCSVLKVGKVSMGAED---IAENVIAAINGLLE--SLALPVYQA 239 (413)
Q Consensus 198 -~~G~~~sVkVG~~sMs~eq---IvENI~Avl~~L~~--SlaLPiYqn 239 (413)
..|+|++++| .-.-+.++ +++-+.+++..... .+--.+||.
T Consensus 412 p~p~p~La~Ri-~g~~~~~~~l~~~~~ad~i~~~~~~~~~~~~~~~q~ 458 (536)
T PLN02347 412 PFPGPGLAVRV-LGDVTEGNALDILRQVDEIFINSIKDAGLYDEIWQA 458 (536)
T ss_pred CcCCCCEEeee-CCccCCHHHHHHHHHHHHHHHHHHHHcCCcccccee
Confidence 5799999999 44456666 66666666555322 344556666
No 23
>TIGR00853 pts-lac PTS system, lactose/cellobiose family IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Lac family includes several sequenced lactose (b-galactoside) permeases of Gram-positive bacteria as well as those in E. coli. While the Lac family usually consists of two polypeptide components IIA and IICB, the Chb permease of E. coli consists of three IIA, IIB and IIC. This family is specific for the IIB subunit of the Lac PTS family.
Probab=22.69 E-value=2.4e+02 Score=23.57 Aligned_cols=76 Identities=24% Similarity=0.297 Sum_probs=43.9
Q ss_pred CCEEEEEecCCCCCchhHHHHHHhhhcCCCCcceee--echhHHhhcccHHHHHhhhhccCEEEEcCCchhhhhhhhccc
Q 015100 87 PPEICLIMDDRPKSNLTKDAVMKKIKNDNLPITKVI--KITKLKTDYRPFEAKRKLCDSYDIFLADKRVVPLLPKLLGKH 164 (413)
Q Consensus 87 ~~kICLIvkD~~~~~~t~~~ake~L~~~gi~i~kVI--~lkkLkkeyKsfEakRKL~~sYDlFLAD~rI~p~LpklLGK~ 164 (413)
..+|+|+|..-..+.+=-...++.+.+.|+++. |. ++.++. ....+||++|..+.+...+..+-.
T Consensus 3 ~~~ILl~C~~G~sSS~l~~k~~~~~~~~gi~~~-v~a~~~~~~~----------~~~~~~Dvill~pqi~~~~~~i~~-- 69 (95)
T TIGR00853 3 ETNILLLCAAGMSTSLLVNKMNKAAEEYGVPVK-IAAGSYGAAG----------EKLDDADVVLLAPQVAYMLPDLKK-- 69 (95)
T ss_pred ccEEEEECCCchhHHHHHHHHHHHHHHCCCcEE-EEEecHHHHH----------hhcCCCCEEEECchHHHHHHHHHH--
Confidence 467888887653321111234455667788642 33 333332 234679999999999887777532
Q ss_pred ccCCCCCCccc
Q 015100 165 FFKKKKIPVPV 175 (413)
Q Consensus 165 F~kkkK~PipV 175 (413)
+......|+.+
T Consensus 70 ~~~~~~ipv~~ 80 (95)
T TIGR00853 70 ETDKKGIPVEV 80 (95)
T ss_pred HhhhcCCCEEE
Confidence 23344466643
No 24
>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]
Probab=22.52 E-value=35 Score=39.58 Aligned_cols=114 Identities=21% Similarity=0.204 Sum_probs=53.2
Q ss_pred cCCCEEEEEEecCC--CCHHHHHHHHHHHHHHHHhhccCCCeeec-----CcceeeeccccCCCCCCccccccccccccc
Q 015100 198 RTGTCSVLKVGKVS--MGAEDIAENVIAAINGLLESLALPVYQAV-----PDLKLKIEGVKENEGEGQDKDSEKENAEDV 270 (413)
Q Consensus 198 ~~G~~~sVkVG~~s--Ms~eqIvENI~Avl~~L~~SlaLPiYqni-----~~v~iKi~~~~~~~~~~~~~~~~~~~~~~~ 270 (413)
+.|-|+.|-.-.++ -+.++|-+|=-.+-.++ |.|+.+++.+ |+-.=+...+-++-
T Consensus 598 k~~KcVVIGLQSTGEsrTle~Le~~~G~Ln~FV--StAk~v~~s~iekHFPa~~r~~~~~tt~~---------------- 659 (1300)
T KOG1513|consen 598 KRGKCVVIGLQSTGESRTLEVLEENDGELNCFV--STAKGVFQSLIEKHFPAPKRKSDRVTTGA---------------- 659 (1300)
T ss_pred hcCceEEEeeccccchhHHHHHHhcCCchhHHH--HHHHHHHHHHHHHhCCCcccccccccccc----------------
Confidence 45888655554554 46788888733333333 4444444432 22222222222211
Q ss_pred ccccchhhhcccccceeEEEeecCcccccccccccCCCCCCCCCCCCCCCCCCccccccCCCcc
Q 015100 271 NDHGSKKKLKKKKGRIHEVRYMDSTIGEVLDEDELGSDDDGEGDVGESEDGEDSEDGKMSSGDI 334 (413)
Q Consensus 271 ~~~~~~~~~~~k~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 (413)
.+.+..+.+||=.|-.-|-.+...++.+|+.|+ |..+.|-|.+.|-+++.+...++|+-
T Consensus 660 ----G~r~g~~~~~Rs~e~~~~k~~~~tdg~~~~~d~-d~~~sd~~~~~d~~sa~ee~~~~~d~ 718 (1300)
T KOG1513|consen 660 ----GSRRGRRPRGRSNEAKAPKLACETDGVIDISDD-DSTESDPGLDSDFNSAPEELVGQDDD 718 (1300)
T ss_pred ----ccccccCcccCCCcccccchhcccccccccccc-cccccCcccccccccchHhhhccccc
Confidence 122223455555555555555555555555443 33444444455544444444444443
Done!