Query 024105
Match_columns 272
No_of_seqs 193 out of 1102
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 09:00:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024105.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024105hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00070 40S ribosomal protein 100.0 4E-101 9E-106 699.1 24.9 253 1-258 2-255 (257)
2 KOG0877 40S ribosomal protein 100.0 8.5E-85 1.8E-89 574.0 12.1 210 36-245 4-213 (213)
3 TIGR01020 rpsE_arch ribosomal 100.0 3.2E-83 7E-88 570.6 20.6 205 36-242 3-210 (212)
4 PRK04044 rps5p 30S ribosomal p 100.0 2.1E-79 4.6E-84 546.3 21.1 203 37-240 5-209 (211)
5 COG0098 RpsE Ribosomal protein 100.0 3.4E-57 7.4E-62 394.2 18.1 172 52-242 1-172 (181)
6 TIGR01021 rpsE_bact ribosomal 100.0 2E-50 4.4E-55 345.7 17.8 147 82-240 1-147 (154)
7 PRK00550 rpsE 30S ribosomal pr 100.0 1.6E-49 3.5E-54 344.3 17.5 148 81-240 11-158 (168)
8 CHL00138 rps5 ribosomal protei 100.0 5.4E-43 1.2E-47 296.7 15.5 122 81-209 22-143 (143)
9 KOG2646 Ribosomal protein S5 [ 99.9 1.3E-27 2.9E-32 226.3 3.4 147 83-240 182-331 (396)
10 PF03719 Ribosomal_S5_C: Ribos 99.9 5.8E-24 1.3E-28 162.3 7.5 71 165-239 1-71 (74)
11 PF00333 Ribosomal_S5: Ribosom 99.9 2.9E-23 6.2E-28 155.9 7.6 67 82-148 1-67 (67)
12 cd01684 Tet_like_IV EF-G_domai 41.0 92 0.002 25.0 5.9 62 167-254 21-84 (115)
13 PF10957 DUF2758: Protein of u 32.6 1.3E+02 0.0028 22.4 5.0 39 71-110 16-57 (60)
14 cd01434 EFG_mtEFG1_IV EFG_mtEF 30.9 1.6E+02 0.0035 23.3 5.8 20 167-186 23-42 (116)
15 smart00358 DSRM Double-strande 29.7 1.6E+02 0.0034 20.1 5.0 39 100-142 27-65 (67)
16 PTZ00146 fibrillarin; Provisio 29.2 62 0.0013 31.0 3.6 8 141-148 181-188 (293)
17 PRK13186 lpxC UDP-3-O-[3-hydro 27.6 44 0.00095 32.1 2.3 58 171-228 23-117 (295)
18 TIGR00325 lpxC UDP-3-0-acyl N- 26.7 47 0.001 31.9 2.3 16 171-186 22-37 (297)
19 PF06207 DUF1002: Protein of u 26.6 1.6E+02 0.0035 27.1 5.7 58 169-228 52-122 (225)
20 PF03331 LpxC: UDP-3-O-acyl N- 22.8 59 0.0013 30.9 2.1 16 171-186 22-37 (277)
21 KOG3973 Uncharacterized conser 21.4 75 0.0016 31.7 2.6 22 6-27 360-383 (465)
22 PF05866 RusA: Endodeoxyribonu 20.4 73 0.0016 25.0 2.0 16 213-228 72-87 (118)
No 1
>PTZ00070 40S ribosomal protein S2; Provisional
Probab=100.00 E-value=4.3e-101 Score=699.09 Aligned_cols=253 Identities=72% Similarity=1.191 Sum_probs=235.7
Q ss_pred CCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCceeeccCCchhhhcCCcCCHHHHHhcCCCCCchhhhhhhcC
Q 024105 1 MAERGGERGAFGRGFGRGGRGDRGGPRGRRRAGRREEEEKWVPVTKLGRLVREGKIRSLEQIYLHSLPIKEYQIIDTLIG 80 (272)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~p~tklG~lVk~~kiksleei~~~slpIkE~eIiD~~lg 80 (272)
|.+++++++|||++ +||+||++ |++.+++ ++|+++|+|+|+||||||||||+||||||+|||||||+||||+||+
T Consensus 2 ~~~~~~~~~~~g~~-~~~~~g~~---~~~~~~~-~~~~~~W~P~TklGrlVk~gki~s~eei~~~~lpikE~eIvd~ll~ 76 (257)
T PTZ00070 2 AAARGGEGRGFGRR-GRGGRGRG---RGRGRGG-EGEEKEWVPVTKLGRLVKAGKITSLEEIFLFSIPIKEYQIVDHFFA 76 (257)
T ss_pred CcccCCcccCCCCC-CCCCCCCC---CCCCCCC-ccccCceeeccchhhhhhcCccccHHHHHhcCCCccchhhHHHHcc
Confidence 45778888889753 33334433 2212333 5789999999999999999999999999999999999999999996
Q ss_pred -CCcceeEEEEeeEEEeccCCeeeEEEEEEEeCCCCCceecccccchhHHHHHHHHHHHHHhCceEEecCcccCcCCCCc
Q 024105 81 -HKLKDEVMKIMPVQKQTRAGQRTRFKAFVVVGDTDGHVGLGVKCSKEVATAIRGAIILAKLSVIPVRRGYWGNKIGRPH 159 (272)
Q Consensus 81 -~~lk~eVl~i~~Vqk~Tk~Grr~rFkAlVvVGd~nG~VGlGvgkakev~~AI~kAi~~Ak~niipV~rgyw~~~~g~~h 159 (272)
++|+|+||+|++|||||++||++||+|||||||+|||||||++||+||++||++|+++||+||+||+||||+|+|+++|
T Consensus 77 ~~~L~eeVl~I~rVqK~TkgGrr~rF~AlVVVGd~nG~VGlG~gKakEV~~AIrKAi~~AK~nii~V~rgyW~~~~g~~h 156 (257)
T PTZ00070 77 ESKLKDEVMKIMPVQKQTSAGQRTRFKAFVVVGDGNGHIGLGAKVAKEVATAIRGAIIAAKLNLVPVRRGYWGNKIGEPH 156 (257)
T ss_pred CccchheEEEEeeeEEEecCCcEEEEEEEEEEeCCCCcEecceeechhHHHHHHHHHHHHHhCeEEEecccccccCCCCC
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeEEeEEeeEEEEeeeCCCCcceeecCchHHHhhhcCcceeeeeccCCCCChhhHHHHHHHHHHhhccCCChHHHhh
Q 024105 160 TVPCKVTGKCGSVTVRMVPAPRGAGIVAARVPKKVLQFAGIDDVFTSSRGSTKTLGNFVKATFECLLKTYGFLTPDFWRE 239 (272)
Q Consensus 160 TIp~~v~Gk~gsv~V~L~PAPrGtGiva~~v~kkiL~lAGI~D~~tk~~Gst~t~~N~aKAtf~AL~kt~s~~TP~~w~~ 239 (272)
||||+|+|||||++|.|+|||+|+||+|++++++||+||||+|||++++|||+|++||+||||+||++||+|+|||+|++
T Consensus 157 TIp~~V~GK~GSv~V~L~PAP~GtGivAg~~vk~VLelAGIkDv~tks~GsTrt~~N~aKATf~AL~~t~~~~tp~~w~~ 236 (257)
T PTZ00070 157 TVPMKVTGKCGSVRVRLVPAPRGTGIVAAPTPKKILEFAGVEDVFTSSRGKTRTRGNFLKATFYALRKTYGFLTPDLWKE 236 (257)
T ss_pred CeeeeEEEEeCeEEEEEEeCCCCccEEeCcHHHHHHHHcCccceeeecccCCCChHHHHHHHHHHHHHHhcccCHhHccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCCChhhhhhcccCCc
Q 024105 240 TRFVKSPYQEYTDLLTPKP 258 (272)
Q Consensus 240 ~~~~~~p~~~~~d~l~~~~ 258 (272)
+.|+++|||||+|||.+..
T Consensus 237 ~~~~~~p~~~~~~~l~~~~ 255 (257)
T PTZ00070 237 TELSRSPYDEHSEFLAEKK 255 (257)
T ss_pred cccCCCchHHHHHHHhhhc
Confidence 9999999999999997654
No 2
>KOG0877 consensus 40S ribosomal protein S2/30S ribosomal protein S5 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.5e-85 Score=573.98 Aligned_cols=210 Identities=76% Similarity=1.251 Sum_probs=207.6
Q ss_pred cccCceeeccCCchhhhcCCcCCHHHHHhcCCCCCchhhhhhhcCCCcceeEEEEeeEEEeccCCeeeEEEEEEEeCCCC
Q 024105 36 EEEEKWVPVTKLGRLVREGKIRSLEQIYLHSLPIKEYQIIDTLIGHKLKDEVMKIMPVQKQTRAGQRTRFKAFVVVGDTD 115 (272)
Q Consensus 36 ~~~~~w~p~tklG~lVk~~kiksleei~~~slpIkE~eIiD~~lg~~lk~eVl~i~~Vqk~Tk~Grr~rFkAlVvVGd~n 115 (272)
.|+++|+|+|+||+||++|||+|+||||+||+||+|+||||+||+++|+||||+||+|||||++||++||||||+|||+|
T Consensus 4 ~~~~~~~p~t~lG~lv~~~ki~sleeiyl~slpike~eiid~~lg~slkdeVLkImpVqKqtrAGQrtRfKAfVaigD~~ 83 (213)
T KOG0877|consen 4 PEEKEWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYN 83 (213)
T ss_pred CccCcCCCcccccccchhchhhhhhhhhccCccccchhhhhhhhccchHhhhheeeecccccccccccceEEEEEEeecC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceecccccchhHHHHHHHHHHHHHhCceEEecCcccCcCCCCceeeeeEEeEEeeEEEEeeeCCCCcceeecCchHHHh
Q 024105 116 GHVGLGVKCSKEVATAIRGAIILAKLSVIPVRRGYWGNKIGRPHTVPCKVTGKCGSVTVRMVPAPRGAGIVAARVPKKVL 195 (272)
Q Consensus 116 G~VGlGvgkakev~~AI~kAi~~Ak~niipV~rgyw~~~~g~~hTIp~~v~Gk~gsv~V~L~PAPrGtGiva~~v~kkiL 195 (272)
||||+|++|+|||++||++|+++|++|++||+||||+|++|+|||+||+|+|+|+|++|+|+|||||+||++.|++|++|
T Consensus 84 ghVGlgvk~sKeva~airgaiilaklsivpvrrgyw~~~~g~pHt~~~kvtg~~~svlv~l~papRgtGivs~p~~kkll 163 (213)
T KOG0877|consen 84 GHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGDCGSVLVRLIPAPRGTGIVSAPVPKKLL 163 (213)
T ss_pred CceeeeeeehHHHHHHHhHHHhhhheeeeeeeccccccccCCCccccCcccccCCcceEEEeecCCCCceeeccccHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCcceeeeeccCCCCChhhHHHHHHHHHHhhccCCChHHHhhhcCCCC
Q 024105 196 QFAGIDDVFTSSRGSTKTLGNFVKATFECLLKTYGFLTPDFWRETRFVKS 245 (272)
Q Consensus 196 ~lAGI~D~~tk~~Gst~t~~N~aKAtf~AL~kt~s~~TP~~w~~~~~~~~ 245 (272)
+||||+|||++++|||+|++||+||+|+|+++||+|+|||+|+|+.|+++
T Consensus 164 ~mAGi~d~~t~~~G~t~tl~n~~ka~~~a~~~ty~~ltp~~w~e~~~~~~ 213 (213)
T KOG0877|consen 164 MMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKS 213 (213)
T ss_pred HhccccccchhhcccchhhccHHHHHHHHHHhhhhhhChhhccccccccC
Confidence 99999999999999999999999999999999999999999999998764
No 3
>TIGR01020 rpsE_arch ribosomal protein S5(archaeal type)/S2(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S2 as well as archaeal ribosomal protein S5.
Probab=100.00 E-value=3.2e-83 Score=570.57 Aligned_cols=205 Identities=62% Similarity=1.035 Sum_probs=199.7
Q ss_pred cccCceeeccCCchhhhcCCcCCHHHHHhcCCCCCchhhhhhhcCCCc-ceeEEEEeeEEEeccCCeeeEEEEEEEeCCC
Q 024105 36 EEEEKWVPVTKLGRLVREGKIRSLEQIYLHSLPIKEYQIIDTLIGHKL-KDEVMKIMPVQKQTRAGQRTRFKAFVVVGDT 114 (272)
Q Consensus 36 ~~~~~w~p~tklG~lVk~~kiksleei~~~slpIkE~eIiD~~lg~~l-k~eVl~i~~Vqk~Tk~Grr~rFkAlVvVGd~ 114 (272)
.|+++|+|+|+||||||+|||+||||||+||+||+|+||||+|| ++| +|+||+|++|||||++||++||+|+|||||+
T Consensus 3 ~~~~~w~p~t~lgrlV~~g~i~s~~ei~~~~~~i~E~eivd~ll-~~l~~e~vl~I~rV~K~tkgGr~~~F~alVvVGn~ 81 (212)
T TIGR01020 3 AELEEWVPRTKLGRLVKEGKIKSIDEIFLRNLPIKEPEIVDYLL-PDLNEEEVLDVSLVQRMTDSGRRTRFRAFVVVGNR 81 (212)
T ss_pred ccccCeeecchhhhhhhcCCcccHHHHHHcCCCccchhhHHHHh-hhcCcceEEEEEeeEEEecCCcEEEEEEEEEEeCC
Confidence 46788999999999999999999999999999999999999999 699 7799999999999999999999999999999
Q ss_pred CCceecccccchhHHHHHHHHHHHHHhCceEEec--CcccCcCCCCceeeeeEEeEEeeEEEEeeeCCCCcceeecCchH
Q 024105 115 DGHVGLGVKCSKEVATAIRGAIILAKLSVIPVRR--GYWGNKIGRPHTVPCKVTGKCGSVTVRMVPAPRGAGIVAARVPK 192 (272)
Q Consensus 115 nG~VGlGvgkakev~~AI~kAi~~Ak~niipV~r--gyw~~~~g~~hTIp~~v~Gk~gsv~V~L~PAPrGtGiva~~v~k 192 (272)
||+||+|++||+||++||++|+.+||+||+||+| |||+|.|+++|||||+|+|||||++|.|+|||+|+||+|+++++
T Consensus 82 ~G~vG~G~GKa~ev~~AI~kA~~~Ak~n~i~V~rg~g~w~~~~~~~hTIp~~v~Gk~gs~~V~L~PAP~GtGliag~~~r 161 (212)
T TIGR01020 82 DGYVGLGIGKAKEVAPAIRKAIINAKLNIIPVRRGCGSWECGCGRPHSVPFKVTGKCGSVRVRLIPAPRGLGLVAGDVAK 161 (212)
T ss_pred CCeEeeceeecchHHHHHHHHHHHHHhCEEEEecccccccccCCCCCcEeEEEEEEEccEEEEEEeCCCCCceecCcHHH
Confidence 9999999999999999999999999999999999 89999999999999999999999999999999999999999999
Q ss_pred HHhhhcCcceeeeeccCCCCChhhHHHHHHHHHHhhccCCChHHHhhhcC
Q 024105 193 KVLQFAGIDDVFTSSRGSTKTLGNFVKATFECLLKTYGFLTPDFWRETRF 242 (272)
Q Consensus 193 kiL~lAGI~D~~tk~~Gst~t~~N~aKAtf~AL~kt~s~~TP~~w~~~~~ 242 (272)
+||++|||+|||+|++|||+|++||+||||+||+++| |+||++|.+..+
T Consensus 162 ~ilelAGIkDv~tk~~Gstrn~~N~~kAtf~AL~~~~-~~~~~~~~~~~~ 210 (212)
T TIGR01020 162 KVLRLAGIDDVWTQTRGETRTTVNFAKATFDALKKTY-YVTPDLWAEERL 210 (212)
T ss_pred HHHHHcCccceeeeccCCCCChhHHHHHHHHHHHhcc-ccCcchhccccc
Confidence 9999999999999999999999999999999999999 999999977543
No 4
>PRK04044 rps5p 30S ribosomal protein S5P; Reviewed
Probab=100.00 E-value=2.1e-79 Score=546.27 Aligned_cols=203 Identities=54% Similarity=0.844 Sum_probs=199.8
Q ss_pred ccCceeeccCCchhhhcCCcCCHHHHHhcCCCCCchhhhhhhcCCCcceeEEEEeeEEEeccCCeeeEEEEEEEeCCCCC
Q 024105 37 EEEKWVPVTKLGRLVREGKIRSLEQIYLHSLPIKEYQIIDTLIGHKLKDEVMKIMPVQKQTRAGQRTRFKAFVVVGDTDG 116 (272)
Q Consensus 37 ~~~~w~p~tklG~lVk~~kiksleei~~~slpIkE~eIiD~~lg~~lk~eVl~i~~Vqk~Tk~Grr~rFkAlVvVGd~nG 116 (272)
+.++|+|+|+||+|||+|+|+||||||.+++||+|+||||+|| ++|+|+||+|++|||||++||+++|+|+|||||+||
T Consensus 5 ~~~~w~p~t~lg~lv~~~~i~s~e~i~~~~~~i~e~eivd~ll-~~l~e~vv~i~rV~kvtkgGr~~sf~alVvVGn~~G 83 (211)
T PRK04044 5 NIEEWEPKTRLGRLVKEGKITSIDEIFDSGLPIKEPEIVDVLL-PDLEDEVLDINMVQRMTDSGRRVRFRVVVVVGNRDG 83 (211)
T ss_pred cccCccccchhhhhhhcCCcccHHHHHhcCCCcccchhhhhhh-ccceeEEEEEEeEEeeecCCcEEEEEEEEEEeCCCC
Confidence 6778999999999999999999999999999999999999999 799999999999999999999999999999999999
Q ss_pred ceecccccchhHHHHHHHHHHHHHhCceEEecC--cccCcCCCCceeeeeEEeEEeeEEEEeeeCCCCcceeecCchHHH
Q 024105 117 HVGLGVKCSKEVATAIRGAIILAKLSVIPVRRG--YWGNKIGRPHTVPCKVTGKCGSVTVRMVPAPRGAGIVAARVPKKV 194 (272)
Q Consensus 117 ~VGlGvgkakev~~AI~kAi~~Ak~niipV~rg--yw~~~~g~~hTIp~~v~Gk~gsv~V~L~PAPrGtGiva~~v~kki 194 (272)
+||+|++||+|+++||++|+.+|++||++|+|+ ||||.|+++|||||+|+|||||++|.|+|||+|+||+|++.+++|
T Consensus 84 ~vG~G~GKa~ev~~Ai~kA~~~Akknli~V~r~~g~We~~~~~~~TI~h~v~gk~gs~~V~l~Pap~GtGiiag~~vr~v 163 (211)
T PRK04044 84 YVGVGQGKAKQVGPAIRKAIRNAKLNIIKVRRGCGSWECGCGEPHSVPFKVTGKAGSVEVTLKPAPRGLGLVAGDVAKKV 163 (211)
T ss_pred eEeeeeeeccchHHHHHHHHHHHHhCeEEEEcccccccccCCCCCcCCeEEEEEEccEEEEEEECCCCCeEEECcHHHHH
Confidence 999999999999999999999999999999996 899999999999999999999999999999999999999999999
Q ss_pred hhhcCcceeeeeccCCCCChhhHHHHHHHHHHhhccCCChHHHhhh
Q 024105 195 LQFAGIDDVFTSSRGSTKTLGNFVKATFECLLKTYGFLTPDFWRET 240 (272)
Q Consensus 195 L~lAGI~D~~tk~~Gst~t~~N~aKAtf~AL~kt~s~~TP~~w~~~ 240 (272)
|++|||+||++|++|||+|++|++||||+||+++|+++||++|++.
T Consensus 164 lelaGIkDv~aK~~Gstrn~~N~vkAt~~AL~~~~~~~~p~~~~~~ 209 (211)
T PRK04044 164 LELAGIKDVWTRTFGETRTTVNFAKATFNALKNTYKVRTPPDWAEK 209 (211)
T ss_pred HHHcCcceEEEEccCCCCChhHHHHHHHHHHHHHHcccCHHHHHhh
Confidence 9999999999999999999999999999999999999999999874
No 5
>COG0098 RpsE Ribosomal protein S5 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.4e-57 Score=394.17 Aligned_cols=172 Identities=47% Similarity=0.703 Sum_probs=163.7
Q ss_pred hcCCcCCHHHHHhcCCCCCchhhhhhhcCCCcceeEEEEeeEEEeccCCeeeEEEEEEEeCCCCCceecccccchhHHHH
Q 024105 52 REGKIRSLEQIYLHSLPIKEYQIIDTLIGHKLKDEVMKIMPVQKQTRAGQRTRFKAFVVVGDTDGHVGLGVKCSKEVATA 131 (272)
Q Consensus 52 k~~kiksleei~~~slpIkE~eIiD~~lg~~lk~eVl~i~~Vqk~Tk~Grr~rFkAlVvVGd~nG~VGlGvgkakev~~A 131 (272)
++++|+++| |..++|++|+| +|.|+ ++||+|++|||||++||++||+|+|||||.||+||||.|||+||+.|
T Consensus 1 ~~~~~~~~~--~~~~~~~~e~~-~~~l~-----e~vv~inrV~K~~kgGRr~~F~alvVVGd~~G~VG~G~GKA~EV~~A 72 (181)
T COG0098 1 KEGKIATIE--FKSGLPIKEPE-VDELL-----EKVVDINRVSKVVKGGRRFRFSALVVVGDRNGRVGFGIGKAKEVPEA 72 (181)
T ss_pred CCccccchh--hhhccCcCCch-hhhcc-----eeeeEEEEEEEeecCceEEEEEEEEEEeCCCCeEeeeecchhhhHHH
Confidence 467899998 99999999999 87776 67999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhCceEEecCcccCcCCCCceeeeeEEeEEeeEEEEeeeCCCCcceeecCchHHHhhhcCcceeeeeccCCC
Q 024105 132 IRGAIILAKLSVIPVRRGYWGNKIGRPHTVPCKVTGKCGSVTVRMVPAPRGAGIVAARVPKKVLQFAGIDDVFTSSRGST 211 (272)
Q Consensus 132 I~kAi~~Ak~niipV~rgyw~~~~g~~hTIp~~v~Gk~gsv~V~L~PAPrGtGiva~~v~kkiL~lAGI~D~~tk~~Gst 211 (272)
|+||+..||+||++|+++ ++|||||+|.|+||+++|.|+|||+||||+|+++++.||++|||+|||++++||
T Consensus 73 IrKAi~~Ak~nii~V~~~-------~~~Tiph~v~Gk~g~~~V~L~PA~~GtGiiAGg~~r~vlelAGi~Dv~tks~GS- 144 (181)
T COG0098 73 IRKAIEDAKKNIIEVPRG-------NGHTIPHEVIGKHGAVKVLLKPAPEGTGIIAGGAVRAVLELAGIKDVLAKSLGS- 144 (181)
T ss_pred HHHHHHHHHhCeEEEecC-------CCceeeeEEEEEECcEEEEEEECCCCceEEeCcHHHHHHHHcCchhhhhhccCC-
Confidence 999999999999999996 899999999999999999999999999999999999999999999999999995
Q ss_pred CChhhHHHHHHHHHHhhccCCChHHHhhhcC
Q 024105 212 KTLGNFVKATFECLLKTYGFLTPDFWRETRF 242 (272)
Q Consensus 212 ~t~~N~aKAtf~AL~kt~s~~TP~~w~~~~~ 242 (272)
+|++||+||||+||.++. ||++|++..-
T Consensus 145 ~n~~N~vrAt~~aL~~~~---~p~~ia~~Rg 172 (181)
T COG0098 145 RNPINVVRATFDALKKLR---TPEDVAAKRG 172 (181)
T ss_pred CChhHHHHHHHHHHHHcc---CHHHHHHHcC
Confidence 699999999999999666 9999999643
No 6
>TIGR01021 rpsE_bact ribosomal protein S5, bacterial/organelle type. This model finds chloroplast ribosomal protein S5 as well as bacterial ribosomal protein S5. A candidate mitochondrial form (Saccharomyces cerevisiae YBR251W and its homolog) differs substantially and is not included in this model.
Probab=100.00 E-value=2e-50 Score=345.72 Aligned_cols=147 Identities=36% Similarity=0.580 Sum_probs=142.0
Q ss_pred CcceeEEEEeeEEEeccCCeeeEEEEEEEeCCCCCceecccccchhHHHHHHHHHHHHHhCceEEecCcccCcCCCCcee
Q 024105 82 KLKDEVMKIMPVQKQTRAGQRTRFKAFVVVGDTDGHVGLGVKCSKEVATAIRGAIILAKLSVIPVRRGYWGNKIGRPHTV 161 (272)
Q Consensus 82 ~lk~eVl~i~~Vqk~Tk~Grr~rFkAlVvVGd~nG~VGlGvgkakev~~AI~kAi~~Ak~niipV~rgyw~~~~g~~hTI 161 (272)
+|+|+||+|++|||||++||+++|+|+|+|||+||+||+|++|++|+.+||++|+.+|++||++|+++ ++ ||
T Consensus 1 ~l~e~vl~i~rv~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~kA~~~Ak~nl~~V~~~-------~~-Ti 72 (154)
T TIGR01021 1 ELEERLIAVNRVSKVVKGGRRFSFSALVVVGDGKGRVGFGFGKAKEVPDAIKKAVEKARKNLINVPLT-------KG-TI 72 (154)
T ss_pred CceeEEEEEeeeeEEecCCcEEEEEEEEEEECCCCeEeeeeeecchHHHHHHHHHHHHHhCeEEEecC-------CC-cc
Confidence 47899999999999999999999999999999999999999999999999999999999999999994 45 99
Q ss_pred eeeEEeEEeeEEEEeeeCCCCcceeecCchHHHhhhcCcceeeeeccCCCCChhhHHHHHHHHHHhhccCCChHHHhhh
Q 024105 162 PCKVTGKCGSVTVRMVPAPRGAGIVAARVPKKVLQFAGIDDVFTSSRGSTKTLGNFVKATFECLLKTYGFLTPDFWRET 240 (272)
Q Consensus 162 p~~v~Gk~gsv~V~L~PAPrGtGiva~~v~kkiL~lAGI~D~~tk~~Gst~t~~N~aKAtf~AL~kt~s~~TP~~w~~~ 240 (272)
||+++|||||++|.|+|||+|+||+|++.++.||++|||+|||++++||+ |++|++||||+||.+++ ||++.++.
T Consensus 73 ~~~v~gk~gs~~V~l~Pap~G~Gi~a~~~~~~il~laGI~Dv~~k~~Gs~-n~~n~vkAt~~aL~~~~---s~~~ia~~ 147 (154)
T TIGR01021 73 PHEVIGVSGAAKVLLKPASPGTGVIAGGAVRAILELAGVKDILAKSLGSN-NPINVVRATFDALLKLK---SPEDVAEL 147 (154)
T ss_pred ceEEEEEECcEEEEEEECCCCCceEeCcHHHHHHHHcCcceEEEEccCCC-ChHHHHHHHHHHHHcCC---CHHHHHHH
Confidence 99999999999999999999999999999999999999999999999998 78999999999999998 99988774
No 7
>PRK00550 rpsE 30S ribosomal protein S5; Validated
Probab=100.00 E-value=1.6e-49 Score=344.33 Aligned_cols=148 Identities=38% Similarity=0.553 Sum_probs=143.8
Q ss_pred CCcceeEEEEeeEEEeccCCeeeEEEEEEEeCCCCCceecccccchhHHHHHHHHHHHHHhCceEEecCcccCcCCCCce
Q 024105 81 HKLKDEVMKIMPVQKQTRAGQRTRFKAFVVVGDTDGHVGLGVKCSKEVATAIRGAIILAKLSVIPVRRGYWGNKIGRPHT 160 (272)
Q Consensus 81 ~~lk~eVl~i~~Vqk~Tk~Grr~rFkAlVvVGd~nG~VGlGvgkakev~~AI~kAi~~Ak~niipV~rgyw~~~~g~~hT 160 (272)
.+|+++||+|++|||||++||+++|+|+|+|||+||++|+|++|++|+++||++|+..|++||++|+++ +||
T Consensus 11 ~~l~~~vl~v~rv~k~tk~Gr~~~f~alvvvGn~~G~vG~G~gKa~ev~~Ai~kA~~~A~~nl~~V~~~--------~~T 82 (168)
T PRK00550 11 LELEEKVVAINRVTKVVKGGRRFSFSALVVVGDGKGRVGFGYGKAREVPEAIRKAVEDAKKNMIKVPLV--------GGT 82 (168)
T ss_pred CCceEEEEEEeeeEEEecCCcEEEEEEEEEEECCCCeEeeeeeecchHHHHHHHHHHHHHhCEEEEecC--------CCc
Confidence 489999999999999999999999999999999999999999999999999999999999999999993 899
Q ss_pred eeeeEEeEEeeEEEEeeeCCCCcceeecCchHHHhhhcCcceeeeeccCCCCChhhHHHHHHHHHHhhccCCChHHHhhh
Q 024105 161 VPCKVTGKCGSVTVRMVPAPRGAGIVAARVPKKVLQFAGIDDVFTSSRGSTKTLGNFVKATFECLLKTYGFLTPDFWRET 240 (272)
Q Consensus 161 Ip~~v~Gk~gsv~V~L~PAPrGtGiva~~v~kkiL~lAGI~D~~tk~~Gst~t~~N~aKAtf~AL~kt~s~~TP~~w~~~ 240 (272)
|||+++|||||++|.|+|||+|+||+|++.++.||++|||+|||+|++||+ |++|++||||+||.+++ ||++.++.
T Consensus 83 i~~~v~gk~gs~kV~l~Pap~G~Gl~a~~~i~~il~laGI~dv~~k~~Gs~-n~~n~vkA~~~aL~~~~---s~~~ia~~ 158 (168)
T PRK00550 83 IPHEVIGKFGAAKVLLKPASEGTGVIAGGAVRAVLELAGVKDVLAKSLGSN-NPINVVRATFDALKQLR---SPEEVAAK 158 (168)
T ss_pred cceeEEEEEceEEEEEEeCCCCCceEeChHHHHHHHHcCccceeeeccCCC-ChHHHHHHHHHHHHhCC---CHHHHHHH
Confidence 999999999999999999999999999999999999999999999999985 89999999999999998 99998885
No 8
>CHL00138 rps5 ribosomal protein S5; Validated
Probab=100.00 E-value=5.4e-43 Score=296.68 Aligned_cols=122 Identities=30% Similarity=0.597 Sum_probs=119.8
Q ss_pred CCcceeEEEEeeEEEeccCCeeeEEEEEEEeCCCCCceecccccchhHHHHHHHHHHHHHhCceEEecCcccCcCCCCce
Q 024105 81 HKLKDEVMKIMPVQKQTRAGQRTRFKAFVVVGDTDGHVGLGVKCSKEVATAIRGAIILAKLSVIPVRRGYWGNKIGRPHT 160 (272)
Q Consensus 81 ~~lk~eVl~i~~Vqk~Tk~Grr~rFkAlVvVGd~nG~VGlGvgkakev~~AI~kAi~~Ak~niipV~rgyw~~~~g~~hT 160 (272)
++|+|+||+|++|||||++||+++|+|+|+|||+||+||+|++|++|+++||++|+.+|++||++|+++ ++||
T Consensus 22 ~~l~ekvl~i~rV~k~tkgGR~~~f~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknl~~V~~~-------~~~T 94 (143)
T CHL00138 22 NKWEERVIQIKRVSKVVKGGKKLSFRAIVVIGNENGWVGVGVGKADDVQNAVKKAVTDAKKNLITIPLT-------KSNS 94 (143)
T ss_pred CCceEEEEEEeeeeEEecCCcEEEEEEEEEEECCCCeEEEeeEecchHHHHHHHHHHHHHhCeEEEEcC-------CCCe
Confidence 689999999999999999999999999999999999999999999999999999999999999999995 8999
Q ss_pred eeeeEEeEEeeEEEEeeeCCCCcceeecCchHHHhhhcCcceeeeeccC
Q 024105 161 VPCKVTGKCGSVTVRMVPAPRGAGIVAARVPKKVLQFAGIDDVFTSSRG 209 (272)
Q Consensus 161 Ip~~v~Gk~gsv~V~L~PAPrGtGiva~~v~kkiL~lAGI~D~~tk~~G 209 (272)
|||+++|||||++|.|+|||+|+||+|++.++.+|++|||+||++|+.|
T Consensus 95 I~~~v~gk~gs~~V~l~Pap~G~Gi~a~~~i~~vlelaGI~Dv~aK~~G 143 (143)
T CHL00138 95 IPHNITGIFGAAKVILRPSAPGSGVIAGGSVRIVLELAGIKNILAKQLG 143 (143)
T ss_pred EeeEEEEEEeeEEEEEEECCCCCcEEECcHHHHHHHHcCcceeEeeecC
Confidence 9999999999999999999999999999999999999999999999886
No 9
>KOG2646 consensus Ribosomal protein S5 [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=1.3e-27 Score=226.30 Aligned_cols=147 Identities=27% Similarity=0.341 Sum_probs=137.0
Q ss_pred cceeEEEE--eeEEEeccCCeeeEEEEEEEeCCCCCceecccccch-hHHHHHHHHHHHHHhCceEEecCcccCcCCCCc
Q 024105 83 LKDEVMKI--MPVQKQTRAGQRTRFKAFVVVGDTDGHVGLGVKCSK-EVATAIRGAIILAKLSVIPVRRGYWGNKIGRPH 159 (272)
Q Consensus 83 lk~eVl~i--~~Vqk~Tk~Grr~rFkAlVvVGd~nG~VGlGvgkak-ev~~AI~kAi~~Ak~niipV~rgyw~~~~g~~h 159 (272)
++...|.+ ++|..||+.|++-+|.|||||||+||.+|||+||+. +...||.+|+.+|.+||..|+| | +.|
T Consensus 182 fe~r~l~lvrr~~~~~~r~Gki~s~~~LVvvGn~nGaaG~~eGKa~~~~s~A~~ka~~rAv~~l~~ieR-y------E~r 254 (396)
T KOG2646|consen 182 FELRHLELVRRRVENQNRKGKIASMYALVVVGNGNGAAGLGEGKAADPNSPAIYKAIGRAVRNLGYIER-Y------ERR 254 (396)
T ss_pred hhHHHHHHHHhhhhccccccceeeEEEEEEEecCCcceeeccccCcCccCHHHHHHHHHHHhhcCcccc-c------cCc
Confidence 34445554 556788999999999999999999999999999999 8999999999999999999999 7 999
Q ss_pred eeeeeEEeEEeeEEEEeeeCCCCcceeecCchHHHhhhcCcceeeeeccCCCCChhhHHHHHHHHHHhhccCCChHHHhh
Q 024105 160 TVPCKVTGKCGSVTVRMVPAPRGAGIVAARVPKKVLQFAGIDDVFTSSRGSTKTLGNFVKATFECLLKTYGFLTPDFWRE 239 (272)
Q Consensus 160 TIp~~v~Gk~gsv~V~L~PAPrGtGiva~~v~kkiL~lAGI~D~~tk~~Gst~t~~N~aKAtf~AL~kt~s~~TP~~w~~ 239 (272)
||++++.-+|..|+++|+.+|+|+|+.|+|++.+||++|||+|+|.++.|+ +|.+|++||+|+||.++. ||++.+.
T Consensus 255 TiygDi~~r~~~~~l~mk~rp~GfGLrcn~il~kIC~~~GIKDis~kv~Gs-rN~m~i~k~~~e~l~~qe---t~qqlA~ 330 (396)
T KOG2646|consen 255 TIYGDIDDRFHEVRLDMKSRPDGFGLRCNPILIKICECAGIKDISGKVKGS-RNEMNITKAAFEALALQE---THQQLAY 330 (396)
T ss_pred cccccchhhhhhhhhhhhhCCCcccccccHHHHHHHHHhccccccceeecc-chHHHHHHHHHHHHhhhh---hhHHHHH
Confidence 999999999999999999999999999999999999999999999999996 689999999999999999 9988776
Q ss_pred h
Q 024105 240 T 240 (272)
Q Consensus 240 ~ 240 (272)
.
T Consensus 331 r 331 (396)
T KOG2646|consen 331 R 331 (396)
T ss_pred h
Confidence 4
No 10
>PF03719 Ribosomal_S5_C: Ribosomal protein S5, C-terminal domain; InterPro: IPR005324 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of proteins related to the 30S ribosomal protein S5P from Sulfolobus acidocaldarius (O05641 from SWISSPROT). Ribosomal protein S5 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_E 2XZM_E 2WDK_E 3KNJ_E 3HUY_E 2B9M_E 2Y18_E 1XMQ_E 1IBM_E 3TVF_H ....
Probab=99.90 E-value=5.8e-24 Score=162.27 Aligned_cols=71 Identities=44% Similarity=0.687 Sum_probs=67.6
Q ss_pred EEeEEeeEEEEeeeCCCCcceeecCchHHHhhhcCcceeeeeccCCCCChhhHHHHHHHHHHhhccCCChHHHhh
Q 024105 165 VTGKCGSVTVRMVPAPRGAGIVAARVPKKVLQFAGIDDVFTSSRGSTKTLGNFVKATFECLLKTYGFLTPDFWRE 239 (272)
Q Consensus 165 v~Gk~gsv~V~L~PAPrGtGiva~~v~kkiL~lAGI~D~~tk~~Gst~t~~N~aKAtf~AL~kt~s~~TP~~w~~ 239 (272)
|+||||+++|.|+|||+|+||+|++.++.||++|||+|||+|++| ++|++|++||||+||.+++ ||++.++
T Consensus 1 V~gk~g~~~V~l~Pap~G~Gl~a~~~vr~il~laGI~Dv~~K~~G-s~n~~n~v~A~~~aL~~~~---s~~~ia~ 71 (74)
T PF03719_consen 1 VTGKFGATKVFLKPAPPGTGLVAGGAVRAILELAGIKDVYAKSRG-SRNPINVVKATFKALKNQR---SPEDIAE 71 (74)
T ss_dssp EEEEETTEEEEEEESCTTSCEESSHHHHHHHHHTTESSEEEEEES-BSSHHHHHHHHHHHHHTSC---SHHHHHH
T ss_pred CEEEEeeEEEEEEeCCCCcceeechhHHHHHHhcccccEEeeccC-CCChhhHHHHHHHHHHhcC---CHHHHHH
Confidence 689999999999999999999999999999999999999999999 5699999999999999999 8877765
No 11
>PF00333 Ribosomal_S5: Ribosomal protein S5, N-terminal domain; InterPro: IPR013810 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 S5 is one of the proteins from the small ribosomal subunit, and is a protein of 166 to 254 amino-acid residues. In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacterial, cyanelle, red algal chloroplast, archaeal and fungal mitochondrial S5; mammalian, Caenorhabditis elegans, Drosophila and plant S2; and yeast S4 (SUP44). This entry represents the N-terminal domain of ribosomal protein S5, which has an alpha-beta(3)-alpha structure that folds into two layers, alpha/beta.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZKQ_e 2XZN_E 2XZM_E 3O30_B 1S1H_E 3IZB_E 3U5C_C 3U5G_C 3O2Z_B 3BBN_E ....
Probab=99.89 E-value=2.9e-23 Score=155.92 Aligned_cols=67 Identities=43% Similarity=0.604 Sum_probs=64.6
Q ss_pred CcceeEEEEeeEEEeccCCeeeEEEEEEEeCCCCCceecccccchhHHHHHHHHHHHHHhCceEEec
Q 024105 82 KLKDEVMKIMPVQKQTRAGQRTRFKAFVVVGDTDGHVGLGVKCSKEVATAIRGAIILAKLSVIPVRR 148 (272)
Q Consensus 82 ~lk~eVl~i~~Vqk~Tk~Grr~rFkAlVvVGd~nG~VGlGvgkakev~~AI~kAi~~Ak~niipV~r 148 (272)
+|+++||++.+|++||++|++++|+|+|+|||+||+||||++|+.|+.+||++|..+|++||++|+|
T Consensus 1 ~l~~~vl~v~rv~k~tk~Gr~~~~~alvvvGn~~G~vG~G~gKa~~~~~Ai~kA~~~A~knl~~V~R 67 (67)
T PF00333_consen 1 DLEEKVLEVKRVSKMTKGGRIFSFRALVVVGNGNGLVGFGVGKAKEVPDAIRKAKRKAKKNLIYVPR 67 (67)
T ss_dssp SHEEEEEEEEEEEEEETTEEEEEEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHHHCSEEE-SC
T ss_pred CceEEEEEEEEEEEEecCCceeEEEEEEEEecCCCcEecCcccchhHHHHHHHHHHHHHhCCEECcC
Confidence 5789999999999999999999999999999999999999999999999999999999999999986
No 12
>cd01684 Tet_like_IV EF-G_domain IV_RPP domain is a part of bacterial ribosomal protected proteins (RPP) family. RPPs such as tetracycline resistance proteins Tet(M) and Tet(O) mediate tetracycline resistance in both gram-positive and -negative species. Tetracyclines inhibit the accommodation of aminoacyl-tRNA into ribosomal A site and therefore prevent the addition of new amino acids to the growing polypeptide. RPPs Tet(M) confer tetracycline resistance by releasing tetracycline from the ribosome and thereby freeing the ribosome from inhibitory effects of the drug, such that aa-tRNA can bind to the A site and protein synthesis can continue.
Probab=40.95 E-value=92 Score=25.01 Aligned_cols=62 Identities=19% Similarity=0.238 Sum_probs=37.2
Q ss_pred eE--EeeEEEEeeeCCCCcceeecCchHHHhhhcCcceeeeeccCCCCChhhHHHHHHHHHHhhccCCChHHHhhhcCCC
Q 024105 167 GK--CGSVTVRMVPAPRGAGIVAARVPKKVLQFAGIDDVFTSSRGSTKTLGNFVKATFECLLKTYGFLTPDFWRETRFVK 244 (272)
Q Consensus 167 Gk--~gsv~V~L~PAPrGtGiva~~v~kkiL~lAGI~D~~tk~~Gst~t~~N~aKAtf~AL~kt~s~~TP~~w~~~~~~~ 244 (272)
++ |+.+.+.|.|.|+|.|+. +..++.|-. -+-+|+.|+-+++... .....+ -
T Consensus 21 ~~~~~a~v~l~veP~~~g~g~~----------------f~~~~~~~~-ip~~~~~aie~g~~~a--------l~~G~l-G 74 (115)
T cd01684 21 PNPFWATVGLRVEPLPRGSGLQ----------------YESEVSLGS-LPRSFQNAVEETVRET--------LQQGLY-G 74 (115)
T ss_pred CCcEEEEEEEEEEECCCCCCcE----------------EEEEecCCc-CCHHHHHHHHHHHHHH--------HhcCCC-C
Confidence 55 999999999999986543 111222322 4556666666555443 345556 6
Q ss_pred CChhhhhhcc
Q 024105 245 SPYQEYTDLL 254 (272)
Q Consensus 245 ~p~~~~~d~l 254 (272)
+|..+..=.|
T Consensus 75 ~pv~dv~V~l 84 (115)
T cd01684 75 WEVTDCKVTL 84 (115)
T ss_pred CCEeeEEEEE
Confidence 7776654444
No 13
>PF10957 DUF2758: Protein of unknown function (DUF2758); InterPro: IPR020296 Cse60 is expressed during sporulation in Bacillus subtilis. Transcription commences around 2h after the start of sporulation and had an absolute requirement for the transcription factor sigmaE. Maximal expression of cse60 further depended on the DNA-binding protein SpoIIID. Cse60 is an acidic product of only 60 residues, whose function is not known [].
Probab=32.59 E-value=1.3e+02 Score=22.37 Aligned_cols=39 Identities=26% Similarity=0.200 Sum_probs=28.2
Q ss_pred chhhhhhhcCCCcceeEEEEeeEEEecc---CCeeeEEEEEEE
Q 024105 71 EYQIIDTLIGHKLKDEVMKIMPVQKQTR---AGQRTRFKAFVV 110 (272)
Q Consensus 71 E~eIiD~~lg~~lk~eVl~i~~Vqk~Tk---~Grr~rFkAlVv 110 (272)
|.+|-+||-+ .=.++|++|+-....+. .-|.+.|+|+|+
T Consensus 16 e~~vN~fL~~-~~~~~viDIKy~va~~~~~~~eq~y~fSamIi 57 (60)
T PF10957_consen 16 EDQVNDFLAK-LDDDQVIDIKYQVAASCDDEDEQIYCFSAMII 57 (60)
T ss_pred HHHHHHHHHh-CCCCcEEEEEEEEEEeccCCcceeEEEEEEEE
Confidence 6778887742 23568999987766552 457789999987
No 14
>cd01434 EFG_mtEFG1_IV EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provi
Probab=30.89 E-value=1.6e+02 Score=23.29 Aligned_cols=20 Identities=40% Similarity=0.871 Sum_probs=16.9
Q ss_pred eEEeeEEEEeeeCCCCccee
Q 024105 167 GKCGSVTVRMVPAPRGAGIV 186 (272)
Q Consensus 167 Gk~gsv~V~L~PAPrGtGiv 186 (272)
++|+.+.+.|.|+++|.|+.
T Consensus 23 ~~~a~v~l~v~P~~~g~g~~ 42 (116)
T cd01434 23 GQYGHVVLEIEPLPRGSGFE 42 (116)
T ss_pred CeEEEEEEEEEECCCCCCCE
Confidence 46999999999999997654
No 15
>smart00358 DSRM Double-stranded RNA binding motif.
Probab=29.74 E-value=1.6e+02 Score=20.14 Aligned_cols=39 Identities=33% Similarity=0.282 Sum_probs=23.8
Q ss_pred CeeeEEEEEEEeCCCCCceecccccchhHHHHHHHHHHHHHhC
Q 024105 100 GQRTRFKAFVVVGDTDGHVGLGVKCSKEVATAIRGAIILAKLS 142 (272)
Q Consensus 100 Grr~rFkAlVvVGd~nG~VGlGvgkakev~~AI~kAi~~Ak~n 142 (272)
+....|.+-|.+++. .++-|.+.++. .|-+.|-..|...
T Consensus 27 ~~~~~f~~~v~i~~~--~~~~g~g~sKk--~Ak~~AA~~al~~ 65 (67)
T smart00358 27 DHAPRFTVTVKVGGE--YTGEGEGSSKK--EAKQRAAEAALRS 65 (67)
T ss_pred CCCCcEEEEEEECCE--EEEEeccCCHH--HHHHHHHHHHHHh
Confidence 344589998888653 55666665554 4555565555543
No 16
>PTZ00146 fibrillarin; Provisional
Probab=29.23 E-value=62 Score=30.98 Aligned_cols=8 Identities=13% Similarity=0.563 Sum_probs=4.9
Q ss_pred hCceEEec
Q 024105 141 LSVIPVRR 148 (272)
Q Consensus 141 ~niipV~r 148 (272)
.|++++.-
T Consensus 181 ~NI~~I~~ 188 (293)
T PTZ00146 181 PNIVPIIE 188 (293)
T ss_pred CCCEEEEC
Confidence 47777643
No 17
>PRK13186 lpxC UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed
Probab=27.64 E-value=44 Score=32.07 Aligned_cols=58 Identities=24% Similarity=0.299 Sum_probs=35.8
Q ss_pred eEEEEeeeCCCCcceeecC-------c-----------------------------hHHHhhhcCcceeeeeccCCCCC-
Q 024105 171 SVTVRMVPAPRGAGIVAAR-------V-----------------------------PKKVLQFAGIDDVFTSSRGSTKT- 213 (272)
Q Consensus 171 sv~V~L~PAPrGtGiva~~-------v-----------------------------~kkiL~lAGI~D~~tk~~Gst~t- 213 (272)
.|.|+|.|||.++||+=-. . ....|...||+||....-|.--.
T Consensus 23 ~v~v~~~PA~~~tGI~F~R~dl~~~~~I~a~~~~v~~t~~~T~l~~~~~~V~TVEHllAAL~glgIDN~~Ievdg~EvPI 102 (295)
T PRK13186 23 KVTLTLRPAPANTGIVFRRTDLPPPVEIPARAENVGDTRLCTTLGNGGVRVSTVEHLMAALAGLGIDNALIEVDGPEVPI 102 (295)
T ss_pred EEEEEEEcCCCCCEEEEEEccCCCCceEEecHHHcccCcceeEEecCCeEEEeHHHHHHHHHhCCCceEEEEeCCCCCCC
Confidence 6889999999999976311 1 12345678999998888764211
Q ss_pred hhhHHHHHHHHHHhh
Q 024105 214 LGNFVKATFECLLKT 228 (272)
Q Consensus 214 ~~N~aKAtf~AL~kt 228 (272)
+---++..+++|.+.
T Consensus 103 lDGSA~~fv~~i~~a 117 (295)
T PRK13186 103 MDGSAAPFVFLIQSA 117 (295)
T ss_pred ccCCHHHHHHHHHHC
Confidence 111244555555543
No 18
>TIGR00325 lpxC UDP-3-0-acyl N-acetylglucosamine deacetylase. UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc deacetylase from E. coli, LpxC, was previously designated EnvA. This enzyme is involved in lipid-A precursor biosynthesis. It is essential for cell viability.
Probab=26.66 E-value=47 Score=31.91 Aligned_cols=16 Identities=38% Similarity=0.671 Sum_probs=14.5
Q ss_pred eEEEEeeeCCCCccee
Q 024105 171 SVTVRMVPAPRGAGIV 186 (272)
Q Consensus 171 sv~V~L~PAPrGtGiv 186 (272)
.+.|.|.|||.++||+
T Consensus 22 ~v~ltl~PA~~~tGI~ 37 (297)
T TIGR00325 22 KVTLTLRPAAANTGVV 37 (297)
T ss_pred EEEEEEEcCCCCCcEE
Confidence 6889999999999976
No 19
>PF06207 DUF1002: Protein of unknown function (DUF1002); InterPro: IPR009343 This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.
Probab=26.62 E-value=1.6e+02 Score=27.13 Aligned_cols=58 Identities=19% Similarity=0.226 Sum_probs=37.1
Q ss_pred EeeEEEEeeeCCCCcceeecC------------chHHHhhhcCcceeeeeccCCCCChhhHHHH-HHHHHHhh
Q 024105 169 CGSVTVRMVPAPRGAGIVAAR------------VPKKVLQFAGIDDVFTSSRGSTKTLGNFVKA-TFECLLKT 228 (272)
Q Consensus 169 ~gsv~V~L~PAPrGtGiva~~------------v~kkiL~lAGI~D~~tk~~Gst~t~~N~aKA-tf~AL~kt 228 (272)
|.|+ .+.|...|.||...- ...--|..|||+||...+-....-.+--|-| .++|+..+
T Consensus 52 ~SSa--~V~~~~~g~Gi~V~i~tp~NIt~VT~~mY~NAl~TAGv~da~I~Vasp~~VsG~sALtGVyKA~E~~ 122 (225)
T PF06207_consen 52 YSSA--YVTPTDKGSGIKVEIVTPNNITWVTEEMYANALITAGVTDADIYVASPFPVSGESALTGVYKAYEAT 122 (225)
T ss_pred EEEE--EEEECCCCCCeEEEEeccCcceeecHHHHHHHHHHcCCCcceEEEeccccCcchHHHHHHHHHHHHc
Confidence 3444 457888898887543 4556788899999977765544434443333 56666643
No 20
>PF03331 LpxC: UDP-3-O-acyl N-acetylglycosamine deacetylase; InterPro: IPR004463 UDP-3-O-N-acetylglucosamine deacetylases are zinc-dependent metalloamidases that catalyse the second and committed step in the biosynthesis of lipid A. Lipid A anchors lipopolysaccharide (the major constituent of the outer membrane) into the membrane in Gram negative bacteria. LpxC shows no homology to mammalian metalloamidases and is essential for cell viability, making it an important target for the development of novel antibacterial compounds []. The structure of UDP-3-O-N-acetylglucosamine deacetylase (LpxC) from Aquifex aeolicus has a two-layer alpha/beta structure similar to that of the second domain of ribosomal protein S5, only in LpxC there is a duplication giving two structural repeats of this fold, each repeat being elaborated with additional structures forming the active site. LpxC contains a zinc-binding motif, which resides at the base of an active site cleft and adjacent to a hydrophobic tunnel occupied by a fatty acid []. This tunnel accounts for the specificity of LpxC toward substrates and inhibitors bearing appropriately positioned 3-O-fatty acid substituents []. This entry represents the UDP-3-O-N-acetylglucosamine deacetylase family of proteins.; GO: 0008759 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity, 0009245 lipid A biosynthetic process; PDB: 2VES_C 3U1Y_A 3P3E_A 3UHM_A 1XXE_A 2IER_A 1YH8_B 2GO4_A 2O3Z_B 2GO3_B ....
Probab=22.80 E-value=59 Score=30.88 Aligned_cols=16 Identities=50% Similarity=0.848 Sum_probs=11.4
Q ss_pred eEEEEeeeCCCCccee
Q 024105 171 SVTVRMVPAPRGAGIV 186 (272)
Q Consensus 171 sv~V~L~PAPrGtGiv 186 (272)
.+.|.|.|||.++||+
T Consensus 22 ~v~l~l~PA~~~~Gi~ 37 (277)
T PF03331_consen 22 PVTLTLRPAPANTGIV 37 (277)
T ss_dssp EEEEEEEE--TT-EEE
T ss_pred EEEEEEEECCCCCCEE
Confidence 6889999999999975
No 21
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=21.39 E-value=75 Score=31.74 Aligned_cols=22 Identities=55% Similarity=0.903 Sum_probs=0.0
Q ss_pred CCCCC--CCCCCCCCCCCCCCCCC
Q 024105 6 GERGA--FGRGFGRGGRGDRGGPR 27 (272)
Q Consensus 6 ~~~~~--~~~~~~~~~~~~~~~~~ 27 (272)
+++|+ .|+|+||||+|+++++.
T Consensus 360 gg~Gg~~gGrGgGRGggG~GGGgg 383 (465)
T KOG3973|consen 360 GGSGGNWGGRGGGRGGGGRGGGGG 383 (465)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCC
No 22
>PF05866 RusA: Endodeoxyribonuclease RusA; InterPro: IPR008822 This family consists of several bacterial and phage Holliday junction resolvase (RusA) like proteins. The RusA protein of Escherichia coli is an endonuclease that can resolve Holliday intermediates and correct the defects in genetic recombination and DNA repair associated with inactivation of RuvAB or RuvC [].; GO: 0000287 magnesium ion binding, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1Q8R_A 2H8C_A 2H8E_A.
Probab=20.36 E-value=73 Score=25.04 Aligned_cols=16 Identities=31% Similarity=0.503 Sum_probs=14.0
Q ss_pred ChhhHHHHHHHHHHhh
Q 024105 213 TLGNFVKATFECLLKT 228 (272)
Q Consensus 213 t~~N~aKAtf~AL~kt 228 (272)
-+.|++||++|||...
T Consensus 72 D~DN~~K~i~Dal~~~ 87 (118)
T PF05866_consen 72 DLDNLLKAILDALTGA 87 (118)
T ss_dssp -HHHHHHHHHHHHHHT
T ss_pred CchhHHHHHHHHHhCc
Confidence 4789999999999987
Done!