Query gi|254781066|ref|YP_003065479.1| putative lysyl-tRNA synthetase protein [Candidatus Liberibacter asiaticus str. psy62] Match_columns 355 No_of_seqs 141 out of 3606 Neff 7.6 Searched_HMMs 39220 Date Mon May 30 04:07:58 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781066.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK00484 lysS lysyl-tRNA synth 100.0 0 0 743.2 27.7 340 1-352 137-491 (491) 2 COG1190 LysU Lysyl-tRNA synthe 100.0 0 0 728.1 21.7 340 1-352 146-502 (502) 3 PRK02983 lysS lysyl-tRNA synth 100.0 0 0 712.2 24.5 338 1-351 742-1099(1099) 4 PRK12445 lysyl-tRNA synthetase 100.0 0 0 708.1 23.0 340 1-352 150-505 (505) 5 KOG1885 consensus 100.0 0 0 684.4 21.6 348 1-354 191-560 (560) 6 PRK09350 lysyl-tRNA synthetase 100.0 0 0 655.9 22.0 317 8-350 5-325 (325) 7 cd00775 LysRS_core Lys_tRNA sy 100.0 0 0 655.3 22.1 325 17-350 3-329 (329) 8 pfam00152 tRNA-synt_2 tRNA syn 100.0 0 0 622.8 17.9 317 18-350 18-341 (341) 9 COG2269 Truncated, possibly in 100.0 0 0 605.2 24.7 321 4-350 1-322 (322) 10 PRK05159 aspC aspartyl-tRNA sy 100.0 0 0 587.7 17.8 291 19-352 134-432 (434) 11 PRK00476 aspS aspartyl-tRNA sy 100.0 0 0 564.2 20.0 327 3-353 111-563 (587) 12 cd00776 AsxRS_core Asx tRNA sy 100.0 0 0 570.0 11.9 289 18-348 20-320 (322) 13 PRK03932 asnC asparaginyl-tRNA 100.0 0 0 560.4 17.9 311 20-352 133-460 (462) 14 cd00669 Asp_Lys_Asn_RS_core As 100.0 0 0 563.4 15.0 265 22-349 1-268 (269) 15 PRK12820 bifunctional aspartyl 100.0 0 0 555.5 21.3 315 12-353 136-579 (706) 16 PRK06462 asparagine synthetase 100.0 0 0 546.2 16.1 294 18-352 25-329 (332) 17 TIGR00459 aspS_bact aspartyl-t 100.0 0 0 535.9 13.5 316 21-350 150-622 (653) 18 TIGR00457 asnS asparaginyl-tRN 100.0 0 0 532.3 15.2 304 14-348 133-489 (495) 19 TIGR00462 genX lysyl-tRNA synt 100.0 0 0 527.7 18.5 321 4-350 6-330 (330) 20 cd00777 AspRS_core Asp tRNA sy 100.0 0 0 509.7 12.2 276 22-350 1-280 (280) 21 COG0017 AsnS Aspartyl/asparagi 100.0 0 0 506.6 14.3 288 20-351 132-432 (435) 22 COG0173 AspS Aspartyl-tRNA syn 100.0 0 0 493.5 22.9 308 21-352 140-560 (585) 23 TIGR00458 aspS_arch aspartyl-t 100.0 0 0 469.1 12.5 295 19-352 152-464 (466) 24 TIGR00499 lysS_bact lysyl-tRNA 100.0 0 0 447.5 20.1 345 1-351 156-537 (538) 25 KOG2411 consensus 100.0 0 0 439.1 21.5 313 19-353 175-602 (628) 26 KOG0554 consensus 100.0 0 0 430.1 11.4 294 14-348 119-440 (446) 27 KOG0556 consensus 100.0 0 0 415.0 12.9 297 20-349 226-528 (533) 28 KOG0555 consensus 100.0 0 0 346.1 12.3 287 20-347 241-538 (545) 29 cd00496 PheRS_alpha_core Pheny 99.6 2.8E-14 7.1E-19 104.0 10.2 112 26-143 4-131 (218) 30 pfam01409 tRNA-synt_2d tRNA sy 99.5 1.8E-13 4.5E-18 99.3 11.1 114 26-142 20-150 (243) 31 PRK04172 pheS phenylalanyl-tRN 99.5 3.1E-13 8E-18 97.8 11.8 115 26-142 248-412 (501) 32 PTZ00326 phenylalanyl-tRNA syn 99.5 3.2E-13 8.1E-18 97.7 11.2 48 95-142 369-418 (505) 33 cd00768 class_II_aaRS-like_cor 99.5 1.8E-13 4.5E-18 99.2 7.2 116 24-142 1-124 (211) 34 PRK09537 pylS pyrolysyl-tRNA s 99.4 3E-14 7.6E-19 103.8 2.1 93 26-126 210-317 (420) 35 COG0016 PheS Phenylalanyl-tRNA 99.4 4.8E-12 1.2E-16 90.8 10.9 115 26-143 114-243 (335) 36 PRK00488 pheS phenylalanyl-tRN 99.2 2.5E-10 6.5E-15 80.6 9.8 112 26-144 110-236 (338) 37 CHL00201 syh histidine-tRNA sy 99.2 9.9E-11 2.5E-15 83.0 6.8 112 8-128 7-136 (424) 38 PRK12292 hisZ ATP phosphoribos 99.1 1.4E-09 3.7E-14 76.1 12.4 103 21-128 16-132 (388) 39 PRK12293 hisZ ATP phosphoribos 99.1 4E-10 1E-14 79.4 9.1 126 1-143 4-139 (281) 40 PRK00037 hisS histidyl-tRNA sy 99.1 2.6E-09 6.5E-14 74.6 12.8 111 7-128 6-137 (417) 41 PRK12325 prolyl-tRNA synthetas 99.1 2.1E-09 5.4E-14 75.1 10.8 118 22-142 47-180 (438) 42 cd00773 HisRS-like_core Class 99.1 9.9E-09 2.5E-13 71.1 14.2 100 23-128 3-116 (261) 43 COG0124 HisS Histidyl-tRNA syn 99.0 7.8E-09 2E-13 71.8 10.2 134 8-150 7-157 (429) 44 PRK12420 histidyl-tRNA synthet 99.0 3.8E-09 9.8E-14 73.6 8.4 117 21-148 17-153 (421) 45 TIGR02367 PylS pyrrolysyl-tRNA 98.9 3E-10 7.6E-15 80.1 0.4 115 26-141 243-367 (453) 46 PRK12295 hisZ ATP phosphoribos 98.8 1.4E-07 3.6E-12 64.3 13.0 97 22-127 4-112 (373) 47 pfam00587 tRNA-synt_2b tRNA sy 98.8 1.6E-08 4.2E-13 69.9 7.6 119 24-143 1-132 (170) 48 cd00779 ProRS_core_prok Prolyl 98.8 3.2E-08 8.2E-13 68.1 7.2 122 22-143 31-165 (255) 49 cd00771 ThrRS_core Threonyl-tR 98.7 3.9E-08 9.8E-13 67.6 7.5 133 5-146 20-166 (298) 50 PRK12421 ATP phosphoribosyltra 98.7 4E-07 1E-11 61.7 11.8 122 20-148 19-155 (391) 51 cd00778 ProRS_core_arch_euk Pr 98.6 3.6E-07 9.3E-12 61.9 9.6 130 4-143 21-171 (261) 52 cd00670 Gly_His_Pro_Ser_Thr_tR 98.6 2.2E-07 5.6E-12 63.2 6.8 121 23-144 3-140 (235) 53 cd00772 ProRS_core Prolyl-tRNA 98.5 1.9E-06 4.9E-11 57.6 11.3 122 22-143 32-171 (264) 54 PRK05425 asparagine synthetase 98.5 1.5E-05 3.8E-10 52.4 15.1 267 22-344 8-308 (327) 55 cd00774 GlyRS-like_core Glycyl 98.4 5.1E-07 1.3E-11 61.0 5.8 99 22-130 32-145 (254) 56 cd00645 AsnA Asparagine synthe 98.4 2.6E-05 6.6E-10 50.9 13.2 262 28-344 3-298 (309) 57 PRK12305 thrS threonyl-tRNA sy 98.3 5.6E-06 1.4E-10 54.8 9.1 130 5-145 198-344 (576) 58 PRK03772 threonyl-tRNA synthet 98.2 1.9E-05 4.9E-10 51.7 9.9 130 5-145 261-406 (642) 59 PRK06253 O-phosphoseryl-tRNA s 98.2 9.5E-07 2.4E-11 59.4 2.6 48 96-143 208-258 (527) 60 cd00770 SerRS_core Seryl-tRNA 98.1 3.3E-06 8.3E-11 56.2 4.8 122 21-145 51-188 (297) 61 PRK12304 thrS threonyl-tRNA sy 98.1 4.9E-05 1.3E-09 49.3 10.1 132 5-147 229-376 (604) 62 PTZ00213 asparagine synthetase 98.1 9.8E-05 2.5E-09 47.5 11.3 294 22-344 8-336 (350) 63 PRK04483 threonyl-tRNA synthet 98.1 2.5E-05 6.3E-10 51.1 8.0 133 5-148 261-412 (634) 64 PRK00413 thrS threonyl-tRNA sy 98.0 4.3E-05 1.1E-09 49.6 8.8 130 5-145 258-404 (639) 65 PRK12444 threonyl-tRNA synthet 98.0 8.8E-05 2.3E-09 47.8 9.8 130 5-145 264-409 (639) 66 COG0442 ProS Prolyl-tRNA synth 97.9 2.8E-05 7.2E-10 50.7 6.2 123 22-145 47-183 (500) 67 TIGR00469 pheS_mito phenylalan 97.9 7.3E-05 1.8E-09 48.3 7.6 129 9-147 31-194 (460) 68 PRK03991 threonyl-tRNA synthet 97.8 3.8E-05 9.7E-10 49.9 5.7 123 23-147 228-366 (613) 69 COG0441 ThrS Threonyl-tRNA syn 97.8 7.2E-05 1.8E-09 48.3 6.2 114 23-147 221-357 (589) 70 PRK08661 prolyl-tRNA synthetas 97.7 0.0002 5.1E-09 45.7 7.7 122 22-143 45-183 (478) 71 KOG2784 consensus 97.7 5.7E-05 1.4E-09 48.9 4.6 59 83-143 322-384 (483) 72 PRK04173 glycyl-tRNA synthetas 97.6 0.00018 4.5E-09 46.0 6.5 33 97-131 192-228 (460) 73 COG2502 AsnA Asparagine synthe 97.6 0.002 5E-08 39.8 11.5 106 22-130 5-127 (330) 74 TIGR00418 thrS threonyl-tRNA s 97.5 0.00012 3.2E-09 46.9 4.6 133 7-147 204-352 (595) 75 COG0423 GRS1 Glycyl-tRNA synth 97.4 0.00017 4.3E-09 46.1 4.2 31 22-52 40-72 (558) 76 PRK09194 prolyl-tRNA synthetas 97.4 0.00085 2.2E-08 42.0 7.1 123 22-148 47-189 (570) 77 PRK05431 seryl-tRNA synthetase 97.3 0.00059 1.5E-08 42.9 5.4 122 23-147 171-308 (422) 78 KOG2324 consensus 97.1 0.0018 4.5E-08 40.0 6.5 125 22-150 52-197 (457) 79 COG0172 SerS Seryl-tRNA synthe 96.8 0.0016 4E-08 40.4 3.8 113 29-144 181-309 (429) 80 TIGR00442 hisS histidyl-tRNA s 96.3 0.0081 2.1E-07 36.1 4.8 128 21-149 17-159 (446) 81 TIGR00389 glyS_dimeric glycyl- 95.7 0.0013 3.3E-08 40.8 -1.4 30 23-52 38-69 (606) 82 KOG1035 consensus 95.3 0.073 1.9E-06 30.5 6.5 110 24-144 934-1056(1351) 83 COG3705 HisZ ATP phosphoribosy 95.3 0.02 5.1E-07 33.8 3.5 100 21-127 16-128 (390) 84 cd00673 AlaRS_core Alanyl-tRNA 94.6 0.34 8.7E-06 26.5 11.3 95 27-147 3-107 (232) 85 TIGR00468 pheS phenylalanyl-tR 94.3 0.018 4.5E-07 34.1 1.2 119 25-143 83-256 (362) 86 KOG1936 consensus 94.2 0.018 4.7E-07 34.0 1.0 108 21-137 73-194 (518) 87 PRK00252 alaS alanyl-tRNA synt 94.1 0.43 1.1E-05 25.9 8.6 99 26-145 5-108 (864) 88 KOG2783 consensus 93.9 0.031 8E-07 32.7 1.9 98 28-127 77-184 (436) 89 KOG2509 consensus 93.9 0.038 9.6E-07 32.2 2.3 122 21-143 184-328 (455) 90 PRK13902 alaS lanyl-tRNA synth 93.8 0.033 8.4E-07 32.5 1.7 32 96-128 117-153 (898) 91 cd00769 PheRS_beta_core Phenyl 93.6 0.08 2E-06 30.3 3.4 81 25-109 2-93 (198) 92 PRK09348 glyQ glycyl-tRNA synt 93.4 0.058 1.5E-06 31.1 2.5 20 26-45 5-24 (291) 93 TIGR00408 proS_fam_I prolyl-tR 93.3 0.11 2.9E-06 29.3 3.9 214 22-260 39-301 (533) 94 PRK09616 pheT phenylalanyl-tRN 93.3 0.29 7.3E-06 27.0 5.9 13 123-135 228-240 (546) 95 COG0013 AlaS Alanyl-tRNA synth 92.9 0.7 1.8E-05 24.7 7.4 45 96-146 64-113 (879) 96 COG0752 GlyQ Glycyl-tRNA synth 90.2 0.24 6.1E-06 27.4 2.7 20 26-45 8-27 (298) 97 TIGR00389 glyS_dimeric glycyl- 90.0 0.28 7.2E-06 27.0 2.8 64 62-129 171-248 (606) 98 TIGR00470 sepS O-phosphoseryl- 89.8 0.14 3.7E-06 28.8 1.2 33 314-347 329-362 (558) 99 COG2024 Phenylalanyl-tRNA synt 89.2 0.26 6.6E-06 27.3 2.2 32 314-346 319-351 (536) 100 KOG0188 consensus 86.8 2.3 5.8E-05 21.6 10.9 102 26-144 5-117 (895) 101 pfam02091 tRNA-synt_2e Glycyl- 86.8 0.42 1.1E-05 26.0 2.0 21 26-46 2-22 (284) 102 KOG2298 consensus 85.8 0.2 5.1E-06 27.9 -0.0 30 24-53 48-78 (599) 103 cd00733 GlyRS_alpha_core Class 85.0 0.55 1.4E-05 25.3 1.9 29 316-344 150-178 (279) 104 CHL00192 syfB phenylalanyl-tRN 83.3 3.1 8E-05 20.8 5.2 113 25-143 396-526 (702) 105 TIGR00468 pheS phenylalanyl-tR 81.8 0.58 1.5E-05 25.2 1.0 27 318-344 323-349 (362) 106 TIGR00669 asnA aspartate--ammo 77.1 3.3 8.4E-05 20.7 3.6 47 297-344 268-315 (330) 107 COG2160 AraA L-arabinose isome 71.6 7.5 0.00019 18.6 5.1 53 94-147 175-233 (497) 108 cd00768 class_II_aaRS-like_cor 69.7 0.32 8.2E-06 26.7 -3.0 52 258-329 153-211 (211) 109 pfam10026 DUF2268 Predicted Zn 68.7 3 7.8E-05 20.9 1.8 88 257-346 99-189 (195) 110 PRK02929 L-arabinose isomerase 68.5 8.8 0.00022 18.2 4.3 14 259-272 399-412 (499) 111 pfam02610 Arabinose_Isome L-ar 66.5 9.6 0.00024 18.0 4.5 50 1-50 1-55 (359) 112 PRK00629 pheT phenylalanyl-tRN 64.5 7.5 0.00019 18.6 3.1 115 25-143 486-617 (786) 113 PRK01584 alanyl-tRNA synthetas 63.5 4.6 0.00012 19.9 1.9 101 27-148 5-109 (593) 114 PRK07080 hypothetical protein; 62.9 5.9 0.00015 19.2 2.3 42 101-143 160-202 (318) 115 KOG0903 consensus 60.9 5 0.00013 19.6 1.7 14 37-50 312-325 (847) 116 pfam01411 tRNA-synt_2c tRNA sy 58.2 8.7 0.00022 18.2 2.5 91 30-140 4-106 (545) 117 PRK13384 delta-aminolevulinic 44.9 11 0.00029 17.6 1.3 15 87-101 69-83 (323) 118 TIGR02151 IPP_isom_2 isopenten 44.6 12 0.00031 17.4 1.5 19 328-346 326-344 (349) 119 PRK09283 delta-aminolevulinic 37.8 23 0.00059 15.7 2.1 11 87-97 66-76 (321) 120 pfam05830 NodZ Nodulation prot 37.5 11 0.00027 17.7 0.3 21 304-324 267-290 (322) 121 cd04823 ALAD_PBGS_aspartate_ri 37.0 21 0.00053 16.0 1.7 11 87-97 61-71 (320) 122 pfam03590 AsnA Aspartate-ammon 35.5 32 0.00081 14.9 7.3 120 22-144 3-139 (244) 123 TIGR00614 recQ_fam ATP-depende 34.8 12 0.00032 17.3 0.3 20 80-99 110-130 (497) 124 TIGR00409 proS_fam_II prolyl-t 34.6 33 0.00083 14.8 2.8 123 22-150 48-197 (620) 125 TIGR00414 serS seryl-tRNA synt 34.0 34 0.00085 14.7 4.2 119 24-143 204-345 (460) 126 cd00384 ALAD_PBGS Porphobilino 33.7 24 0.0006 15.6 1.6 11 87-97 58-68 (314) 127 TIGR01226 phe_am_lyase phenyla 33.2 14 0.00035 17.1 0.3 14 72-85 340-354 (714) 128 COG4302 EutC Ethanolamine ammo 32.2 36 0.00091 14.6 3.5 13 28-40 6-18 (294) 129 pfam00490 ALAD Delta-aminolevu 30.6 31 0.0008 14.9 1.8 10 30-39 13-22 (322) 130 KOG1637 consensus 29.9 39 0.001 14.3 3.1 120 23-148 193-333 (560) 131 TIGR02400 trehalose_OtsA alpha 29.4 40 0.001 14.3 3.0 23 116-138 239-261 (476) 132 TIGR02764 spore_ybaN_pdaB poly 28.7 13 0.00034 17.1 -0.4 10 264-273 58-67 (198) 133 cd03557 L-arabinose_isomerase 28.7 41 0.0011 14.2 5.0 16 259-274 393-408 (484) 134 pfam09743 DUF2042 Uncharacteri 28.5 29 0.00074 15.1 1.3 17 88-104 63-80 (272) 135 TIGR01184 ntrCD nitrate ABC tr 28.5 17 0.00044 16.5 0.1 38 302-353 172-210 (230) 136 TIGR01733 AA-adenyl-dom amino 28.0 33 0.00084 14.8 1.5 26 263-290 357-382 (452) 137 PRK05776 DNA topoisomerase III 25.7 47 0.0012 13.9 3.8 23 276-299 538-560 (675) 138 TIGR02676 cas_provis_2 CRISPR- 25.4 47 0.0012 13.9 3.1 93 28-124 87-193 (1104) 139 COG1304 idi Isopentenyl diphos 21.7 52 0.0013 13.6 1.6 20 328-347 329-348 (360) 140 TIGR02708 L_lactate_ox L-lacta 21.1 46 0.0012 13.9 1.2 21 328-348 340-360 (368) 141 TIGR02653 Lon_rel_chp conserve 21.1 50 0.0013 13.7 1.3 17 255-271 344-360 (677) 142 pfam12109 CXCR4_N CXCR4 Chemok 21.0 31 0.00078 15.0 0.2 10 101-110 21-30 (33) 143 COG0113 HemB Delta-aminolevuli 20.4 60 0.0015 13.3 1.9 15 128-142 98-112 (330) 144 COG3919 Predicted ATP-grasp en 20.1 61 0.0015 13.2 3.0 40 89-138 76-115 (415) No 1 >PRK00484 lysS lysyl-tRNA synthetase; Reviewed Probab=100.00 E-value=0 Score=743.15 Aligned_cols=340 Identities=31% Similarity=0.513 Sum_probs=313.1 Q ss_pred CCCCCCCCCC--CHHHCCCHH-----------HHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECC Q ss_conf 9988987478--831261548-----------999999999999999999879889847821056898544541241024 Q gi|254781066|r 1 MHQIPSQPWW--NRDFHYRRR-----------PFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELI 67 (355) Q Consensus 1 ~~~~p~~~~~--~~~~~~r~R-----------~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~ 67 (355) ++|||..+.+ +.+.|+|+| .+++.||+|+++||+||+++||+||+||+|++++||++ |+||.|+ T Consensus 137 l~plP~k~~g~~d~e~r~r~RyLDLi~n~~~~~~f~~Rs~ii~~iR~~l~~~gF~EVeTPiL~~~~gGA~-ArpF~t~-- 213 (491) T PRK00484 137 LRPLPDKFHGLSDQETRYRQRYLDLIVNEESRETFRKRSKIISAIRRFLDNRGFLEVETPMLQPIPGGAA-ARPFITH-- 213 (491) T ss_pred CCCCCCCCCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCCCC-CCCCCCC-- T ss_conf 8899854445567556311330210279999999999999999999999867689986787766688756-6765564-- Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 78867832000028589999898744688999886424567775448430020001157765787775578887766641 Q gi|254781066|r 68 IQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA 147 (355) Q Consensus 68 ~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~ 147 (355) +|++++++||+||||||||+||+||++||||||||||||+++++|+||||||||||||+|++|+|+++|+||+++++.+ T Consensus 214 -~n~l~~~~yL~~SPqLylk~l~vgG~ervfeI~r~FR~E~~~~rH~pEFT~lE~e~af~d~~dvm~l~E~li~~v~~~v 292 (491) T PRK00484 214 -HNALDIDLYLRIAPELYLKRLIVGGFERVFEIGRNFRNEGIDTRHNPEFTMIEFYQAYADYNDMMDLTEELIRHLAKEV 292 (491) T ss_pred -CCCCCCCEEECCCHHHHHHHHHHCCCHHHEEHHHHHHCCCCCCCCCCCEEEEEEEEECCCHHHHHHHHHHHHHHHHHHH T ss_conf -4566855442068789877787627202222487662575543418401021367724799999999999999999996 Q ss_pred -CCCEECCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEE Q ss_conf -8830002234332467732078888656660876532345556232799999999768877876534789876643003 Q gi|254781066|r 148 -NQKIFSFQNVNCNPFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKI 226 (355) Q Consensus 148 -~~~~~~~~~~~~~~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~i 226 (355) ++..+.+.+..++...+|++++|.+++++++++++.... ....+...+++.+.++...++|+++++.++++++ T Consensus 293 ~g~~~~~~~~~~idl~~pf~rit~~eai~~~~g~d~~~~~------~~~~l~~~~~~~g~~~~~~~~~g~l~~~lfe~~v 366 (491) T PRK00484 293 LGTTKITYGGTEIDFGKPFKRLTMVDAIKEYTGVDFTPQD------EEEEARAIAKELGVEVEKSWGLGKLINELFEEFV 366 (491) T ss_pred CCCCEEEECCEEECCCCCCEECCHHHHHHHHCCCCCCCCC------CHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHH T ss_conf 1995673287763378995022399999997099876556------7899999999869987887787899999888776 Q ss_pred CCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHH Q ss_conf 62237675443257688886413678778363302202236712256402106999999999999999972888530101 Q gi|254781066|r 227 EPNLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPID 306 (355) Q Consensus 227 e~~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D 306 (355) ++++ ..|+||+|||.++|||||.+++||++++|||||++|+||||||+|||||.+|++||++|+..|+.+++|++++| T Consensus 367 e~~l--~~PtFV~d~P~e~sPlak~~~~dp~~~erfdL~i~G~Ei~ng~~el~Dp~~Q~~rf~~q~~~k~~gd~ea~~~D 444 (491) T PRK00484 367 EPKL--IQPTFITDYPVEISPLAKRHRSNPGFTERFELFIGGRELANAFSELNDPIDQRERFEAQVEAKEAGDDEAMFYD 444 (491) T ss_pred HHHC--CCCEECCCCCCCCCCCCCCCCCCCCCEEEECEEECCEEECCCCHHHCCHHHHHHHHHHHHHHHHCCCCHHHHCC T ss_conf 5411--46400136722158755668889670367564348899736503317999999999999999864883233240 Q ss_pred HHHHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCC Q ss_conf 8999986-188963245315999989981559713111585648743 Q gi|254781066|r 307 EDFLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQ 352 (355) Q Consensus 307 ~~fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~ 352 (355) ++||+|| +|||||||||||||||||+|||++|||||||||.|||++ T Consensus 445 edfl~Al~yG~PPhgG~GlGiDRLvMlLtg~~sIRdVI~FP~~kp~~ 491 (491) T PRK00484 445 EDFLRALEYGMPPTGGLGIGIDRLVMLLTNSPSIRDVILFPAMRPEK 491 (491) T ss_pred HHHHHHHHCCCCCCCEEEEHHHHHHHHHCCCCCHHHCCCCCCCCCCC T ss_conf 99999977799998526556999999983999577501688889999 No 2 >COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=0 Score=728.12 Aligned_cols=340 Identities=31% Similarity=0.518 Sum_probs=316.4 Q ss_pred CCCCCCCCCC--CHHHCCCHHH-----------HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECC Q ss_conf 9988987478--8312615489-----------99999999999999999879889847821056898544541241024 Q gi|254781066|r 1 MHQIPSQPWW--NRDFHYRRRP-----------FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELI 67 (355) Q Consensus 1 ~~~~p~~~~~--~~~~~~r~R~-----------~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~ 67 (355) |+|||..+.| +++.|+|+|. .++.||+|+++||+||+++||+||+||+|++.+||++ |+||.|+ T Consensus 146 L~pLPeK~hgL~D~E~RyR~RylDLi~N~e~r~~f~~Rs~ii~~iR~fl~~~gFlEVETP~lq~i~GGA~-ArPF~Th-- 222 (502) T COG1190 146 LRPLPEKFHGLTDKEIRYRQRYLDLIVNPESRQTFIKRSKIIRAIREFLDDRGFLEVETPMLQPIPGGAA-ARPFITH-- 222 (502) T ss_pred CCCCCHHHCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCC-CCCCEEE-- T ss_conf 7779745437863888999888898659999999999999999999999877975841600035578732-2650122-- Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 78867832000028589999898744688999886424567775448430020001157765787775578887766641 Q gi|254781066|r 68 IQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA 147 (355) Q Consensus 68 ~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~ 147 (355) ||.++.++||++|||||||+|+++|++|||+||++||||+.|++|||||||||+|+||+|++|+|+++|++|+++++.+ T Consensus 223 -hNald~dlyLRIApELyLKRliVGG~erVfEIgr~FRNEGid~tHNPEFTmlE~Y~AYaDy~D~m~ltE~Li~~~a~~v 301 (502) T COG1190 223 -HNALDMDLYLRIAPELYLKRLIVGGFERVFEIGRNFRNEGIDTTHNPEFTMLEFYQAYADYEDLMDLTEELIKELAKEV 301 (502) T ss_pred -ECCCCCCEEEEECCHHHHHHHHHCCCHHHEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf -0236775687624189999887537214223055200378766648423568999998579999999999999999995 Q ss_pred C-CCEECCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCC--CCHHHHHHHHHHC Q ss_conf 8-830002234332467732078888656660876532345556232799999999768877876--5347898766430 Q gi|254781066|r 148 N-QKIFSFQNVNCNPFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHD--DTWSDIFSRILIE 224 (355) Q Consensus 148 ~-~~~~~~~~~~~~~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~l~~~ 224 (355) . +..+.|.+..+++.++|+++++.+++++++++++. ...+...+...+++.++++... +++|.++.++|++ T Consensus 302 ~gt~~v~y~~~~id~~~pf~ri~m~dal~e~~g~~~~------~~~~~e~~~~~ak~~~i~~~~~~~~~~g~ll~~lFe~ 375 (502) T COG1190 302 NGTTKVTYGGQEIDFSKPFKRITMVDALKEYLGVDFD------DLFDDEEAKELAKKHGIEVEKYGTWGLGHLLNELFEE 375 (502) T ss_pred CCCEEEEECCEEEECCCCEEEEEHHHHHHHHHCCCCC------CCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHH T ss_conf 4973787899767548972256648999987186655------4588799999999808975765553678999999987 Q ss_pred EECCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCH Q ss_conf 03622376754432576888864136787783633022022367122564021069999999999999999728885301 Q gi|254781066|r 225 KIEPNLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYP 304 (355) Q Consensus 225 ~ie~~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~ 304 (355) .+|++| .+|+||+|||.++|||||.++++|++++||||||+|.||||||+|||||.+|++||++|...++.|++|++. T Consensus 376 ~vE~~l--iqPTFv~d~P~eiSPLak~~~~~p~~teRFElfi~g~EiaNaysELNDP~dQ~~RF~~Q~~~k~~Gddea~~ 453 (502) T COG1190 376 LVEAKL--IQPTFVTDHPVEISPLAKRHRSNPGLTERFELFIGGKEIANAYSELNDPVDQRERFEAQVEEKEAGDDEAME 453 (502) T ss_pred HHHHHH--CCCCEEECCCCCCCCCCCCCCCCCCHHHHHEEEECCEEEEECCCHHCCHHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 765641--488246168543686656798886513221013545876311222069999999999999998729930011 Q ss_pred HHHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCC Q ss_conf 0189999861-88963245315999989981559713111585648743 Q gi|254781066|r 305 IDEDFLACLT-EMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQ 352 (355) Q Consensus 305 ~D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~ 352 (355) +|++|++||+ ||||+||+|||||||||+|||+.||||||+||.||+.+ T Consensus 454 ~Dedfv~ALeyGmPPTgG~GiGIDRLvMllT~~~sIRdVilFP~mr~~~ 502 (502) T COG1190 454 LDEDFVEALEYGMPPTGGLGIGIDRLVMLLTNSPSIRDVILFPAMRPEK 502 (502) T ss_pred CCHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCCHHHEECCCCCCCCC T ss_conf 5799999986699998875125777777773998554222156557889 No 3 >PRK02983 lysS lysyl-tRNA synthetase; Provisional Probab=100.00 E-value=0 Score=712.22 Aligned_cols=338 Identities=29% Similarity=0.414 Sum_probs=305.4 Q ss_pred CCCCCCCCCC--CHHHCCCHHH-----------HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECC Q ss_conf 9988987478--8312615489-----------99999999999999999879889847821056898544541241024 Q gi|254781066|r 1 MHQIPSQPWW--NRDFHYRRRP-----------FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELI 67 (355) Q Consensus 1 ~~~~p~~~~~--~~~~~~r~R~-----------~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~ 67 (355) |+|||..+.+ +.+.|+|+|. +++.||+|+++||+||+++||+|||||||++.+||+. |+||.|+. T Consensus 742 L~PLP~k~~gl~d~E~RlR~RYLDLr~npe~r~~~~~RS~Vi~aiR~~L~~~GFlEVETPiLq~~~GGA~-ARPFlThs- 819 (1099) T PRK02983 742 LRPLPDKWKGLTDPEARVRARYLDLAVNPEARDLIRARSAVLRAVRETLVAKGFLEVETPILQQIHGGAN-ARPFLTHI- 819 (1099) T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCC-CCCCCCCC- T ss_conf 6799976779887767556455651589899999999999999999999878988955754677888756-78530103- Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 78867832000028589999898744688999886424567775448430020001157765787775578887766641 Q gi|254781066|r 68 IQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA 147 (355) Q Consensus 68 ~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~ 147 (355) |.++.++||+||||||||+||++|++||||||||||||+.+.+||||||||||||||+|++++|+++|+|++.+++.+ T Consensus 820 --na~d~~~YLriAPELflKRLmVGGfeRVFEI~RcFRNEglradHnPEFTmLE~Y~Ay~Dyedmm~ltEeLi~~~a~~~ 897 (1099) T PRK02983 820 --NAYDLDLYLRIAPELYLKRLCVGGVERVFELGRAFRNEGVDFSHNPEFTLLEAYQAHADYLVMRDLCRELIQNAAQAA 897 (1099) T ss_pred --CCCCCCCEEECCHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH T ss_conf --367866145148089999998648631134325446799998749407999999984789999999999999999995 Q ss_pred CC-CEEC-----CCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHH Q ss_conf 88-3000-----22343324677320788886566608765323455562327999999997688778765347898766 Q gi|254781066|r 148 NQ-KIFS-----FQNVNCNPFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRI 221 (355) Q Consensus 148 ~~-~~~~-----~~~~~~~~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 221 (355) .. .++. +....+|...+|+++++.+++++.++.++... .....+...+++.++.....+++|+++.++ T Consensus 898 ~G~~v~~~pd~~~~~~~iDls~~w~~~t~~eai~e~~G~di~~~------~~~e~L~~~a~~~gi~~~~~~~~G~lv~eL 971 (1099) T PRK02983 898 NGEPVVMRPGTDGVLEPVDISGEWPVKTVHEAVSEALGEEIDAD------TPLETLRRLCDAAGIPYLTHWDAGAVVLEL 971 (1099) T ss_pred HCCEEEECCCCCCCCEEEECCCCCEEEEHHHHHHHHHCCCCCCC------CCHHHHHHHHHHCCCCCCCCCCHHHHHHHH T ss_conf 19657861687788768656999526539999999838878999------999999999997799778999977999999 Q ss_pred HHCEECCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCC Q ss_conf 43003622376754432576888864136787783633022022367122564021069999999999999999728885 Q gi|254781066|r 222 LIEKIEPNLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNE 301 (355) Q Consensus 222 ~~~~ie~~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e 301 (355) +++.+++++ ..|+||+|||.+++||+|++++||++++|||||+||+||+|||+|||||.+|++||++|+.++.+++.| T Consensus 972 ~e~lVE~~l--~~PtFV~DfP~e~sPLarp~~~dp~lAeRfDLvinG~ELgnGysELnDP~eQR~Rf~eQ~~~~~ggD~E 1049 (1099) T PRK02983 972 YEHLVEDRT--TEPTFYTDFPTSVSPLTRPHRSDPGVAERWDLVAWGVELGTAYSELTDPVEQRRRLTEQSLLAAGGDPE 1049 (1099) T ss_pred HHHHCCCCC--CCCEEEECCCCCCCCCCCCCCCCCCEEEEEEEEECCEEEECCHHHHCCHHHHHHHHHHHHHHHHCCCCH T ss_conf 998527376--677899899722390417789996827877255558997021035169999999999999998679900 Q ss_pred CCHHHHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCC Q ss_conf 3010189999861-8896324531599998998155971311158564874 Q gi|254781066|r 302 TYPIDEDFLACLT-EMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSN 351 (355) Q Consensus 302 ~~~~D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~ 351 (355) ++++|++||+||+ |||||||+|+|||||||+|||. ||||||+||++||. T Consensus 1050 am~~DEdFL~ALeYGmPPhGGialGIDRLVMLLTG~-SIREVIaFPl~kP~ 1099 (1099) T PRK02983 1050 AMELDEDFLQALEYAMPPTGGLGMGVDRLVMLITGR-SIRETLPFPLAKPR 1099 (1099) T ss_pred HHHCHHHHHHHHCCCCCCCCCEEEHHHHHHHHHCCC-CHHHHCCCCCCCCC T ss_conf 233217899984318997364754499999996299-75987438787998 No 4 >PRK12445 lysyl-tRNA synthetase; Reviewed Probab=100.00 E-value=0 Score=708.05 Aligned_cols=340 Identities=27% Similarity=0.457 Sum_probs=304.7 Q ss_pred CCCCCCCCCC--CHHHCCCHHH-----------HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECC Q ss_conf 9988987478--8312615489-----------99999999999999999879889847821056898544541241024 Q gi|254781066|r 1 MHQIPSQPWW--NRDFHYRRRP-----------FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELI 67 (355) Q Consensus 1 ~~~~p~~~~~--~~~~~~r~R~-----------~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~ 67 (355) ++|||..+.+ +.+.|+|+|. +++.||+|+++||+||+++||+||+||+|+++|||++ |+||.|+ T Consensus 150 l~plP~k~~g~~d~e~R~r~RyLDLir~~~~~~~~~~Rs~ii~~iR~~l~~~gF~EVeTPil~~~~gGa~-Arpf~t~-- 226 (505) T PRK12445 150 LRPLPDKFHGLQDQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGAS-ARPFITH-- 226 (505) T ss_pred CCCCCCCCCCCCCHHHHHHHHEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCC-CCEEEEC-- T ss_conf 7898974557878877634111143659999999999999999999999977938997887555458766-6103304-- Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 78867832000028589999898744688999886424567775448430020001157765787775578887766641 Q gi|254781066|r 68 IQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA 147 (355) Q Consensus 68 ~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~ 147 (355) +++++.++||+||||||||+||+|||+||||||||||||+++++|+||||||||||||+|++|+|+++|+||+++++.+ T Consensus 227 -~~~~~~~~yL~qSPQLykk~LmvgGfdRvfeI~r~FRnE~~~~~H~PEFT~lE~e~af~d~~dvm~l~E~li~~i~~~v 305 (505) T PRK12445 227 -HNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEV 305 (505) T ss_pred -CCCCCCCEEECCCCHHHHHHHHHCCCCCEEEHHHHHHCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH T ss_conf -6678867434169399999998579744576278760788886654445435687632789899999999999999984 Q ss_pred -CCCEECCCCCCCCCCCCCCCCCHHHHHHHHCC-CCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCE Q ss_conf -88300022343324677320788886566608-7653234555623279999999976887787653478987664300 Q gi|254781066|r 148 -NQKIFSFQNVNCNPFSEPEYITVAEAFARYAN-IDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEK 225 (355) Q Consensus 148 -~~~~~~~~~~~~~~~~~~~~i~~~e~~~~~~~-~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 225 (355) +...++|.+...+...+|+++++.++++++.. .+... ..........+.+.+......+.++.++..++.+. T Consensus 306 ~g~~~i~y~~~~~d~~~pf~rlt~~eai~~~~~~~~~~~------~~~~~~~~~~~~~~g~~~~~~~~~g~l~~~~~~e~ 379 (505) T PRK12445 306 LGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMAD------LDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEV 379 (505) T ss_pred CCCCEEEECCCHHCCCCCCCCCCHHHHHHHHCCCCCHHH------CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHH T ss_conf 488358665201201698410349999998568887453------34469999999985985344434427999998877 Q ss_pred ECCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHH Q ss_conf 36223767544325768888641367877836330220223671225640210699999999999999997288853010 Q gi|254781066|r 226 IEPNLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPI 305 (355) Q Consensus 226 ie~~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~ 305 (355) +++++ ..|+||+|||.+++||||.++++|.+++|||||++|.||||||+|||||.+|++||++|...+..++++++.+ T Consensus 380 ~e~~l--~~P~fv~d~P~e~splak~~~~~p~~t~rfdl~i~G~Ei~nG~~el~Dp~~Q~~rf~~q~~~k~~g~~e~~~~ 457 (505) T PRK12445 380 AEAHL--IQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFY 457 (505) T ss_pred HHHCC--CCCCCCCCCCCCCCCHHCCCCCCHHHHHEEEEEECCEEEEECEECCCCHHHHHHHHHHHHHHHHCCCCCHHHC T ss_conf 77505--5554244775445830016799841401453511899987460226899999999999887775476600012 Q ss_pred HHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCC Q ss_conf 189999861-88963245315999989981559713111585648743 Q gi|254781066|r 306 DEDFLACLT-EMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQ 352 (355) Q Consensus 306 D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~ 352 (355) |++||+||+ |||||||||||||||||+|||++||||||+||.|||++ T Consensus 458 de~fl~Al~yG~PPhgG~glGiDRLvMlLtg~~sIRdVI~FP~~rp~~ 505 (505) T PRK12445 458 DEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRPQK 505 (505) T ss_pred HHHHHHHHHCCCCCHHCCHHHHHHHHHHHCCCCCHHEECCCCCCCCCC T ss_conf 288999965699850034379999999981999564071699989999 No 5 >KOG1885 consensus Probab=100.00 E-value=0 Score=684.38 Aligned_cols=348 Identities=27% Similarity=0.445 Sum_probs=323.4 Q ss_pred CCCCCCCCCC--CHHHCCCHHH-----------HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECC Q ss_conf 9988987478--8312615489-----------99999999999999999879889847821056898544541241024 Q gi|254781066|r 1 MHQIPSQPWW--NRDFHYRRRP-----------FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELI 67 (355) Q Consensus 1 ~~~~p~~~~~--~~~~~~r~R~-----------~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~ 67 (355) |||||+.|++ +.+.|+|+|. .|++||+|++.||.||+++||+||+||+|+..+||++ |+||+|+ T Consensus 191 Lh~lP~~~~gLkD~EtRyrqRylDlilN~~~r~~f~~RakII~~iRkfld~rgFlEVETPmmn~iaGGA~-AkPFIT~-- 267 (560) T KOG1885 191 LHMLPHEHFGLKDKETRYRKRYLDLILNPEVRDRFRIRAKIISYIRKFLDSRGFLEVETPMMNMIAGGAT-AKPFITH-- 267 (560) T ss_pred HCCCCHHHCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCHHHCCCCCCCC-CCCEEEC-- T ss_conf 1348766517776888999888998708889999999999999999986544956844465525468632-5760431-- Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 78867832000028589999898744688999886424567775448430020001157765787775578887766641 Q gi|254781066|r 68 IQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA 147 (355) Q Consensus 68 ~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~ 147 (355) ||.++.++||+++||||+|+|+++|++|||+||+.||||++|.+||||||.+|+||||+|++|+|+.+|+|++.+++.+ T Consensus 268 -hndldm~LylRiAPEL~lK~LvVGGldrVYEIGr~FRNEGIDlTHNPEFTTcEfY~AYady~dlm~~TE~l~s~mv~~i 346 (560) T KOG1885 268 -HNDLDMDLYLRIAPELYLKMLVVGGLDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYEDLMDMTEELLSGMVKNI 346 (560) T ss_pred -CCCCCCCEEEEECHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf -4556755145636599999898601789999878763057665458774218999987538889999999999999960 Q ss_pred CC-CEECCCC-------CCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHH Q ss_conf 88-3000223-------433246773207888865666087653234555623279999999976887787653478987 Q gi|254781066|r 148 NQ-KIFSFQN-------VNCNPFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFS 219 (355) Q Consensus 148 ~~-~~~~~~~-------~~~~~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 219 (355) .. ..++|+. ..+++..+|+++++.+.+++.+++++..............+...+.+.+++++...+.+.+++ T Consensus 347 ~G~~~i~y~p~~~~~~~~eldf~~pfrri~mi~~L~k~lgi~l~~~~~l~~~e~~~~L~~~~~~~~v~~p~p~t~arlLd 426 (560) T KOG1885 347 TGSYKITYHPNGPEEPELELDFTRPFRRIEMIEELEKELGIKLPPGSTLHTEETRELLKSLCVDEAVECPPPRTTARLLD 426 (560) T ss_pred CCCEEEEECCCCCCCCCEEEECCCCEEEEEHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHH T ss_conf 37436752688988874366236872545078999999588789833357531689999987753667898310899999 Q ss_pred HHHHCEECCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCC Q ss_conf 66430036223767544325768888641367877836330220223671225640210699999999999999997288 Q gi|254781066|r 220 RILIEKIEPNLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIY 299 (355) Q Consensus 220 ~l~~~~ie~~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~ 299 (355) +++++++|++|. .|+||.++|..+|||||.+++++|+++||||||+|.||||+|+|||||..||+||++|.+.+..|+ T Consensus 427 KLvg~flE~~cv--nPTFi~~hP~imSPLAK~hrs~~glteRFElFi~~kEicNAYtElNdP~~Qr~rFe~Q~~~k~~GD 504 (560) T KOG1885 427 KLVGEFLEPTCV--NPTFIIDHPQIMSPLAKYHRSKAGLTERFELFIAGKEICNAYTELNDPVDQRQRFEQQARDKDAGD 504 (560) T ss_pred HHHHHHHCCCCC--CCEEECCCCHHCCCCCCCCCCCCCHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCC T ss_conf 987676410357--970672781331842224565400456778754108875466660688999999999987764498 Q ss_pred CCCCHHHHHHHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCCCC Q ss_conf 85301018999986-18896324531599998998155971311158564874334 Q gi|254781066|r 300 NETYPIDEDFLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQEE 354 (355) Q Consensus 300 ~e~~~~D~~fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~~~ 354 (355) +|++.+|++|++|| ||+||+||||||||||+|+||+++|||||++||.||+++.+ T Consensus 505 DEa~~~De~Fc~ALEYGlPPtgGwGmGIDRL~MllTds~~I~EVL~Fp~mkp~~~~ 560 (560) T KOG1885 505 DEAQMVDEDFCTALEYGLPPTGGWGMGIDRLVMLLTDSNNIREVLLFPAMKPEDRQ 560 (560) T ss_pred CCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCCHHHEEECCCCCHHCCC T ss_conf 31136528788897707999776653664653321377653223524656711049 No 6 >PRK09350 lysyl-tRNA synthetase; Provisional Probab=100.00 E-value=0 Score=655.93 Aligned_cols=317 Identities=33% Similarity=0.567 Sum_probs=286.2 Q ss_pred CCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCC-CCCCCCCCCCCCHHHHH Q ss_conf 47883126154899999999999999999987988984782105689854454124102478-86783200002858999 Q gi|254781066|r 8 PWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQ-DHIRKPLYLQTSPEFSC 86 (355) Q Consensus 8 ~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~-~~~~~~~yL~~SPql~l 86 (355) --|.|++ ++..|++||+|+++||+||+++||+||+||+|+.++.+++++.||.|.+... +..++++||+||||+|| T Consensus 5 ~~w~~~a---s~~~l~~Rs~i~~~iR~ff~~~gFlEVeTP~L~~~t~~~~~~~~f~~~~~~~~~~~~~~~yL~~SPql~~ 81 (325) T PRK09350 5 ASWQPSA---SIKNLLKRAAIIAEIRRFFADRGVLEVETPAMSQATVTDIHLVPFETRFVGPGHSQGKTLWLMTSPEYHM 81 (325) T ss_pred CCCCCHH---HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEECCHHHHH T ss_conf 8777714---7999999999999999999988968977984257788764676222102565545676645507919999 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCC Q ss_conf 98987446889998864245677754484300200011577657877755788877666418830002234332467732 Q gi|254781066|r 87 KKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPFSEPE 166 (355) Q Consensus 87 K~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~~~~~ 166 (355) |+||++|++||||||||||||+++++|+|||||||||++|+|++|+|+++|++++.+++ ..+|+ T Consensus 82 k~l~~~G~~rvfqI~~~FR~E~~~~~H~pEFtmlE~~~~~~d~~d~m~~~e~ll~~~~~----------------~~~~~ 145 (325) T PRK09350 82 KRLLAAGSGPIFQLCRSFRNEEAGRYHNPEFTMLEWYRPHYDMYRLMNEVDDLLQQVLD----------------CPPAE 145 (325) T ss_pred HHHHHCCCCCEEEEEHHHCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC----------------CCCCC T ss_conf 99986678855896113228999876573778889998154899999999999999974----------------89852 Q ss_pred CCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCC--CCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHH Q ss_conf 07888865666087653234555623279999999976887--7876534789876643003622376754432576888 Q gi|254781066|r 167 YITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIR--VAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAP 244 (355) Q Consensus 167 ~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~ 244 (355) ++++.+++.++++++.... ....+...+++.+.. .....+|+.+++.++...|+++++.+.|+||+|||++ T Consensus 146 ~~~~~~~~~~~~~~~~~~~-------~~~~l~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~ve~~l~~~~P~fv~d~P~~ 218 (325) T PRK09350 146 SLSYQQAFLRYLGIDPLSA-------DKTQLREVAAKLDLSNIADTEEDRDTLLQLLFTFGVEPNIGKEKPTFVYHFPAS 218 (325) T ss_pred EEEHHHHHHHHHCCCCCCC-------CHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCC T ss_conf 6419999999819996548-------889999999974997566753478799999999988875076587699558433 Q ss_pred HHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-CCCCCCCEEE Q ss_conf 864136787783633022022367122564021069999999999999999728885301018999986-1889632453 Q gi|254781066|r 245 ESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACL-TEMPQSSGIA 323 (355) Q Consensus 245 ~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al-~G~PPhgG~g 323 (355) ++|||+.+++|+++|+|||||++|+||+|||+|++||.+|++||+.++..++..+.+..++|++||+|| +|+||||||| T Consensus 219 ~~~~~~~~~~d~~~a~rfdl~~~G~El~~G~~el~d~~~~~~r~~~~~~~~~~~g~~~~~~d~~~l~a~~yG~PPhgG~g 298 (325) T PRK09350 219 QAALAQISTEDHRVAERFEVYFKGIELANGFHELTDAREQLQRFEQDNRKRAARGLPQQPIDQNLIAALKAGLPDCSGVA 298 (325) T ss_pred CCHHHCCCCCCCCHHHHHHCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCEEE T ss_conf 37032358789852232101048789667645668999999999999999985799800558999999667999983576 Q ss_pred CCHHHHHHHHHCCCCHHHHCCCCCCCC Q ss_conf 159999899815597131115856487 Q gi|254781066|r 324 MGFDRLVMLVTGANNINEVIWTPFSQS 350 (355) Q Consensus 324 lGidRLvm~l~g~~~Irdvi~FP~~r~ 350 (355) ||||||||++||.+|||||||||++|| T Consensus 299 lGlDRLvm~l~g~~~IRdvi~FP~dR~ 325 (325) T PRK09350 299 LGVDRLIMLALGAESIAEVIAFPVDRA 325 (325) T ss_pred EHHHHHHHHHHCCCCHHHEECCCCCCC T ss_conf 559999999818993887107885549 No 7 >cd00775 LysRS_core Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three characteristic sequence motifs in the core domain. It is found in eukaryotes as well as some prokaryotes and archaea. However, LysRS belongs to class I aaRS's in some prokaryotes and archaea. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Probab=100.00 E-value=0 Score=655.32 Aligned_cols=325 Identities=29% Similarity=0.478 Sum_probs=291.9 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 54899999999999999999987988984782105689854454124102478867832000028589999898744688 Q gi|254781066|r 17 RRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEK 96 (355) Q Consensus 17 r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~r 96 (355) +.|.++++||+|+++||+||.++||+||+||||++++||+ .++||.|++ ++++.++||+||||+|||+||++|++| T Consensus 3 ~~~~~~~~Rs~i~~~iR~ff~~~gF~Ev~TPiL~~~~~g~-~~~~f~~~~---~~~~~~~yL~qSpQl~~q~l~~~g~~r 78 (329) T cd00775 3 EVRQTFIVRSKIISYIRKFLDDRGFLEVETPMLQPIAGGA-AARPFITHH---NALDMDLYLRIAPELYLKRLIVGGFER 78 (329) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCC-CCCCEEECC---CCCCCCCCCCCCHHHHHHHHHHCCCCC T ss_conf 8999999999999999999998898899798655668875-675313224---467867230689899999998567776 Q ss_pred HHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHC-CCEECCCCCCCCCCCCCCCCCHHHHHH Q ss_conf 9998864245677754484300200011577657877755788877666418-830002234332467732078888656 Q gi|254781066|r 97 IFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVAN-QKIFSFQNVNCNPFSEPEYITVAEAFA 175 (355) Q Consensus 97 vyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~-~~~~~~~~~~~~~~~~~~~i~~~e~~~ 175 (355) |||||||||||+++++|+||||||||||+|+|++|+|+++|+||+++++.+. .....+.....+...+|+++++.++++ T Consensus 79 vfqI~p~FR~E~~~~rHl~EFtmle~E~~f~d~~dvm~~~E~li~~i~~~~~~~~~~~~~~~~~d~~~pf~rit~~ea~~ 158 (329) T cd00775 79 VYEIGRNFRNEGIDLTHNPEFTMIEFYEAYADYNDMMDLTEDLFSGLVKKINGKTKIEYGGKELDFTPPFKRVTMVDALK 158 (329) T ss_pred EEEEEECCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHH T ss_conf 79981022479999774734563457774479999999999999999999838875314661235689974376999999 Q ss_pred HHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHCCCCCCC Q ss_conf 66087653234555623279999999976887787653478987664300362237675443257688886413678778 Q gi|254781066|r 176 RYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESALANIYPAD 255 (355) Q Consensus 176 ~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~plak~~~~~ 255 (355) +++++++...... .............+.....+..|++++++++++++++++ ..|+||+|||.+++|||+.++++ T Consensus 159 ~~~g~~~~~~~~~---~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ie~~~--~~p~fi~dyP~~~~pf~~~~~~~ 233 (329) T cd00775 159 EKTGIDFPELDLE---QPEELAKLLAKLIKEKIEKPRTLGKLLDKLFEEFVEPTL--IQPTFIIDHPVEISPLAKRHRSN 233 (329) T ss_pred HHHCCCCCCCCCC---CHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHC--CCCEEEECCHHHCCCHHHCCCCC T ss_conf 9858998766732---389999998775686656787789999999999997513--79689947701118443129999 Q ss_pred CCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC-CCCCCCEEECCHHHHHHHHH Q ss_conf 36330220223671225640210699999999999999997288853010189999861-88963245315999989981 Q gi|254781066|r 256 PRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACLT-EMPQSSGIAMGFDRLVMLVT 334 (355) Q Consensus 256 ~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al~-G~PPhgG~glGidRLvm~l~ 334 (355) +++++|||||++|+||||||+|++||.+|++||++|++.++.++.+...+|++||+|++ |+|||||||||+|||||++| T Consensus 234 ~~~~~~fdl~~~G~Ei~~G~~el~d~~~q~~r~~~~~~~~~~~~~~~~~~de~yl~a~k~G~pPhgG~glGldRLvm~l~ 313 (329) T cd00775 234 PGLTERFELFICGKEIANAYTELNDPFDQRERFEEQAKQKEAGDDEAMMMDEDFVTALEYGMPPTGGLGIGIDRLVMLLT 313 (329) T ss_pred CCEEEECCCCCCCEEEECCEEEECCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHH T ss_conf 77010012456877984153311799999999999999985467511242399999966799986114099999999993 Q ss_pred CCCCHHHHCCCCCCCC Q ss_conf 5597131115856487 Q gi|254781066|r 335 GANNINEVIWTPFSQS 350 (355) Q Consensus 335 g~~~Irdvi~FP~~r~ 350 (355) |++|||||||||.+|| T Consensus 314 g~~nIRdvi~FP~~r~ 329 (329) T cd00775 314 DSNSIRDVILFPAMRP 329 (329) T ss_pred CCCHHHHCCCCCCCCC T ss_conf 8981875137999897 No 8 >pfam00152 tRNA-synt_2 tRNA synthetases class II (D, K and N). Probab=100.00 E-value=0 Score=622.84 Aligned_cols=317 Identities=26% Similarity=0.299 Sum_probs=261.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 48999999999999999999879889847821056898544541241024788678320000285899998987446889 Q gi|254781066|r 18 RRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKI 97 (355) Q Consensus 18 ~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rv 97 (355) .+.++++||+|+++||+||.++||+||+||+|+++++++ .+++|.|+ .++++++||+||||+|||+||++|++|| T Consensus 18 ~~~~l~~Rs~i~~~iR~ff~~~~f~EV~TP~L~~~~~e~-~a~~F~~~----~~~~~~~yL~~Spel~~k~ll~~g~~rV 92 (341) T pfam00152 18 MQANLKLRSKIIRAIREFLDERGFLEVETPILTKSTPEG-GARDFLVP----KFYAKEAYLPQSPQLYKQLLMVAGFDRV 92 (341) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCC-CCCEEEEC----CCCCCCEEECCCHHHHHHHHHHCCCCCC T ss_conf 899999999999999999998898998798200558987-77664502----6789823405488999999986588763 Q ss_pred HHHHHHHCCCCC-CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCC-EECCCCCCCCCCCCCCCCCHHHHHH Q ss_conf 998864245677-75448430020001157765787775578887766641883-0002234332467732078888656 Q gi|254781066|r 98 FCFAHAWRNGEQ-GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQK-IFSFQNVNCNPFSEPEYITVAEAFA 175 (355) Q Consensus 98 yqig~~FRaE~~-~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~-~~~~~~~~~~~~~~~~~i~~~e~~~ 175 (355) ||||||||||++ ++||+||||||||||+|+|++++|+++|+||+++++.+... .........+...+|++++|.++++ T Consensus 93 fei~~~FR~E~~~t~rH~~EFtmlE~y~a~~d~~d~m~~~E~li~~i~~~v~~~~~~~~~~~~~~~~~~f~rity~ea~~ 172 (341) T pfam00152 93 FQIAPCFRDEDLRTDRHPPEFTQLDLEMSFVDYEDVMDLTEDLIKYVFKEVKGKTEKGELLLGIELPEPFPRITYAEAIE 172 (341) T ss_pred EEEECHHCCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCCCCCCCCEEEEHHHHHH T ss_conf 79723202798988655077887767553599999999999999999999863440244124554789844742999999 Q ss_pred HHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCC---CCCCCCCCCCCHHHHHHCCCC Q ss_conf 66087653234555623279999999976887787653478987664300362237---675443257688886413678 Q gi|254781066|r 176 RYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLG---INCCTILDRYPAPESALANIY 252 (355) Q Consensus 176 ~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~---~~~pvfi~~yP~~~~plak~~ 252 (355) ++.+++..... ...+.....+..........+...++.++.+.+++.++ .+.||||+|||.+++|||+.. T Consensus 173 ~~~~~~~~~~~-------~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~~~~~~p~fv~dyP~~~~pf~~~~ 245 (341) T pfam00152 173 RYGSDKPDLRF-------GLELKDVTEIKFEDAALNGGSNKLLGALRSELGERLLGDENLDNPVFVTDFPLFKRPFYMPK 245 (341) T ss_pred HHCCCCCCCCC-------HHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCC T ss_conf 97199988688-------79999999984422333455244899999999888755303786199988884438666867 Q ss_pred -CCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC-CCCCCCEEECCHHHHH Q ss_conf -77836330220223671225640210699999999999999997288853010189999861-8896324531599998 Q gi|254781066|r 253 -PADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACLT-EMPQSSGIAMGFDRLV 330 (355) Q Consensus 253 -~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al~-G~PPhgG~glGidRLv 330 (355) ++++++|+|||||++|+||||||+|+|||++|++||++|.. ..+++++.|++||+|++ |+|||||||||||||+ T Consensus 246 ~~~~~~~a~rFel~~~G~Ei~nG~~el~d~~~~~~rf~~~~~----~~~~~~~~d~~yl~a~~~G~PP~~G~glGidRL~ 321 (341) T pfam00152 246 DEDPPGLAERFDLVLNGGEIGGGSIRIHDPEEQRKRFEELGL----DPEEAEEKFGFYLDALKYGMPPHGGIGLGLDRLV 321 (341) T ss_pred CCCCCCCHHEEEECCCCEEEECCCCCCCCHHHHHHHHHHHCC----CHHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHH T ss_conf 877765012157526974982575345999999999998198----9023356589999998669799705657899999 Q ss_pred HHHHCCCCHHHHCCCCCCCC Q ss_conf 99815597131115856487 Q gi|254781066|r 331 MLVTGANNINEVIWTPFSQS 350 (355) Q Consensus 331 m~l~g~~~Irdvi~FP~~r~ 350 (355) |++||.+||||||+||.+|. T Consensus 322 m~l~g~~~Irdv~~FPr~~~ 341 (341) T pfam00152 322 MLLTGLESIREVIAFPKTRK 341 (341) T ss_pred HHHCCCCCHHHCCCCCCCCC T ss_conf 99808994887267899999 No 9 >COG2269 Truncated, possibly inactive, lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=0 Score=605.23 Aligned_cols=321 Identities=42% Similarity=0.732 Sum_probs=304.3 Q ss_pred CCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCC-CCCCCCCCCH Q ss_conf 898747883126154899999999999999999987988984782105689854454124102478867-8320000285 Q gi|254781066|r 4 IPSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHI-RKPLYLQTSP 82 (355) Q Consensus 4 ~p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~-~~~~yL~~SP 82 (355) ++..+||.|+++..+ +..|++|+++||.||.++||+||+||+|+.+++++.|+.+|.|++..+.+- .+++||+||| T Consensus 1 ~~~~~~W~p~~~~~~---ll~Ra~i~~~iR~FF~erg~lEVeTp~Ls~a~vtd~hL~~F~Te~~~~~~~~~~~l~L~TSP 77 (322) T COG2269 1 MSETPWWQPSASIDN---LLKRAAIIAAIRRFFAERGVLEVETPALSVAPVTDIHLHPFETEFLGPGGAKGKPLWLHTSP 77 (322) T ss_pred CCCCCCCCCCCCHHH---HHHHHHHHHHHHHHHHHCCCEEECCHHHHCCCCCCCCEEEEEEEEECCCCCCCCEEEEECCC T ss_conf 998876888888899---99899999999999987692585336765078986423445667654676665303665680 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCC Q ss_conf 89999898744688999886424567775448430020001157765787775578887766641883000223433246 Q gi|254781066|r 83 EFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPF 162 (355) Q Consensus 83 ql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~ 162 (355) |++||+|||+|.++|||||+||||++.+++|+|||||||||+++.|++.+|+.+-++++.+++. T Consensus 78 Ey~mKrLLAag~~~ifql~kvfRN~E~G~~H~PEFTMLEWYrv~~d~~~lm~e~~~Ll~~vl~~---------------- 141 (322) T COG2269 78 EYHMKRLLAAGSGPIFQLGKVFRNEEMGRLHNPEFTMLEWYRVGCDYYRLMNEVDDLLQLVLEC---------------- 141 (322) T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHC---------------- T ss_conf 7778999975488601454777263325667984367651006785999999999999999703---------------- Q ss_pred CCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCC Q ss_conf 77320788886566608765323455562327999999997688778765347898766430036223767544325768 Q gi|254781066|r 163 SEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYP 242 (355) Q Consensus 163 ~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP 242 (355) .+++++||.++|++|+|+|+.. ++...+...+.+.++....+++|.+++..++.+.|||++|.+.|+||+||| T Consensus 142 ~~~E~ls~~eaF~r~~gid~l~-------~~~~~L~~~~~~~~l~~~~~~~~d~L~~~lf~~~VEP~lg~~rpt~ly~fP 214 (322) T COG2269 142 VEAERLSYQEAFLRYLGIDPLS-------ADKTELREAAAKLGLSAATDEDWDTLLQLLFVEGVEPNLGKERPTFLYHFP 214 (322) T ss_pred CCCCEEEHHHHHHHHHCCCCCC-------CCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECC T ss_conf 7853555999999983889452-------429999999985587777755899999998886407566888844887272 Q ss_pred HHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCEE Q ss_conf 88864136787783633022022367122564021069999999999999999728885301018999986188963245 Q gi|254781066|r 243 APESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACLTEMPQSSGI 322 (355) Q Consensus 243 ~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al~G~PPhgG~ 322 (355) +++++||+++++||+|++|||||++|+||+|||+||+|+.+|++||+.+|+.|.+.+.+.+++|++||.||+.||||+|+ T Consensus 215 ~~qaaLA~i~~~D~rVAERFElY~kGiELaNgf~EltDa~EqrrRfe~dn~~r~~~~l~~~piDe~fl~Al~~mP~cSGv 294 (322) T COG2269 215 ASQAALAQISTGDPRVAERFELYYKGIELANGFHELTDAAEQRRRFEQDNKERARRGLPQYPIDEDFLAALARMPPCSGV 294 (322) T ss_pred HHHHHHHCCCCCCCCHHHHHHHEEEEEEECCCCHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCC T ss_conf 77887604677896256664320100221024000178899999999988999863788777887899999858986541 Q ss_pred ECCHHHHHHHHHCCCCHHHHCCCCCCCC Q ss_conf 3159999899815597131115856487 Q gi|254781066|r 323 AMGFDRLVMLVTGANNINEVIWTPFSQS 350 (355) Q Consensus 323 glGidRLvm~l~g~~~Irdvi~FP~~r~ 350 (355) |||||||||+++|.++|.|||+||+.++ T Consensus 295 ALG~DRLvmLalg~~~i~~Vi~f~v~~a 322 (322) T COG2269 295 ALGFDRLVMLALGAESIDDVIAFPVARA 322 (322) T ss_pred EECHHHHHHHHCCCCHHHHHHHCCCCCC T ss_conf 3238899999818214877761311469 No 10 >PRK05159 aspC aspartyl-tRNA synthetase; Provisional Probab=100.00 E-value=0 Score=587.74 Aligned_cols=291 Identities=20% Similarity=0.323 Sum_probs=231.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEC-CCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 899999999999999999987988984782105-6898544541241024788678320000285899998987446889 Q gi|254781066|r 19 RPFLLKRNMIQSSLREYFVENQFIEIDSMSLQY-SPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKI 97 (355) Q Consensus 19 R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~-~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rv 97 (355) +.+++.||+++++||+||.++||+||+||+|++ +++|+ ++.|.+ +++++++||+||||||||+||++|++|| T Consensus 134 ~~~~r~Rs~i~~~iR~fl~~~gF~EVeTP~l~~~~~eGg--a~~f~~-----~~~~~~~yL~~Spqly~q~li~~G~~rv 206 (434) T PRK05159 134 QAIFKIRSEVLRAFREFLYEEGFTEIFTPKIVATGTEGG--TELFPV-----KYFEKEAFLAQSPQLYKQMMMAAGFERV 206 (434) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCC--CCCCCE-----EECCCEEEECCCCHHHHHHHHHCCCCCE T ss_conf 999999999999999999877919997874325678875--565861-----3127533414683799999876356855 Q ss_pred HHHHHHHCCCCCC-CCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCE---ECCCCCCC-CCCCCCCCCCHHH Q ss_conf 9988642456777-54484300200011577657877755788877666418830---00223433-2467732078888 Q gi|254781066|r 98 FCFAHAWRNGEQG-CLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKI---FSFQNVNC-NPFSEPEYITVAE 172 (355) Q Consensus 98 yqig~~FRaE~~~-~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~---~~~~~~~~-~~~~~~~~i~~~e 172 (355) ||||||||||+++ +|||||||||||||||+|++|+|+++|+||+++++.+.... +...+.+. ....+|+++++.| T Consensus 207 feI~~~FR~E~~~t~RH~pEFT~lE~e~af~d~~d~m~~~E~li~~i~~~v~~~~~~~~~~~~~~~~~~~~~~~rit~~e 286 (434) T PRK05159 207 FEIGPAFRAEEHNTTRHLNEAISIDVEMGFIDEEDVMDLLENLLKYVYEDVAENCEKELELLGIELPVPETPIPRITYDE 286 (434) T ss_pred EEECCCEECCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCCCCCCCCCCCCCEEEHHH T ss_conf 99660102365875445356765666631068999999999999999999986564778635865566799864778999 Q ss_pred HHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHH-CCC Q ss_conf 6566608765323455562327999999997688778765347898766430036223767544325768888641-367 Q gi|254781066|r 173 AFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESAL-ANI 251 (355) Q Consensus 173 ~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~pl-ak~ 251 (355) +++.. .+.+.+. .|++.+....++.+.+.+....|+||+|||++++|| ++. T Consensus 287 ai~~l------------------------~~~~~~~----~~g~dl~~~~e~~l~~~~~~~~~~fI~d~P~~~~pfy~~~ 338 (434) T PRK05159 287 AIEIL------------------------KSKGVEI----SWGDDLDTEGERLLGKYVKESDFYFITDWPTEIRPFYTMP 338 (434) T ss_pred HHHHH------------------------HHCCCCC----CCCCCCCHHHHHHHHHHHCCCCCEEEECCCHHCCCCCCCC T ss_conf 99999------------------------8519987----8555537899999999847589889989970008654677 Q ss_pred CCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC-CCCCCCEEECCHHHHH Q ss_conf 877836330220223671225640210699999999999999997288853010189999861-8896324531599998 Q gi|254781066|r 252 YPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACLT-EMPQSSGIAMGFDRLV 330 (355) Q Consensus 252 ~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al~-G~PPhgG~glGidRLv 330 (355) ++++|++++|||||++|+||||||+|+|||++|+++|+++ +.+.+.+ ++||+||+ |+|||||||||||||+ T Consensus 339 ~~~~~~~~~~fdl~~~G~Ei~~G~~r~~d~~~l~~~~~~~-----g~~~~~~---~~yl~al~yG~PP~gG~glGiDRLv 410 (434) T PRK05159 339 YEDDPEITKSFDLMYRGLEITSGAQRIHDYDMLVESIKEK-----GLNPESF---EFYLEAFKYGMPPHAGWGLGLERLT 410 (434) T ss_pred CCCCCCEEEEEEEEECCEEEEEEEEECCCHHHHHHHHHHC-----CCCHHHH---HHHHHHHHCCCCCCCEEEEHHHHHH T ss_conf 7888320014326776699843101117899999999974-----9898999---9999996679998755878799999 Q ss_pred HHHHCCCCHHHHCCCCCCCCCC Q ss_conf 9981559713111585648743 Q gi|254781066|r 331 MLVTGANNINEVIWTPFSQSNQ 352 (355) Q Consensus 331 m~l~g~~~Irdvi~FP~~r~~~ 352 (355) |++||++|||||||||.++.+- T Consensus 411 m~l~g~~sIrdvi~FPr~~~rl 432 (434) T PRK05159 411 MKLLGLENVREAVLFPRDRTRL 432 (434) T ss_pred HHHCCCCCHHEEECCCCCCCCC T ss_conf 9981999665481488998989 No 11 >PRK00476 aspS aspartyl-tRNA synthetase; Validated Probab=100.00 E-value=0 Score=564.20 Aligned_cols=327 Identities=23% Similarity=0.294 Sum_probs=231.1 Q ss_pred CCCCCCCC--CHHHCCCHH----------HHHHHHHHHHHHHHHHHHHCCCEEEECCCEE-CCCCCCCCCCCEEEECCCC Q ss_conf 88987478--831261548----------9999999999999999998798898478210-5689854454124102478 Q gi|254781066|r 3 QIPSQPWW--NRDFHYRRR----------PFLLKRNMIQSSLREYFVENQFIEIDSMSLQ-YSPGNETHIRAFSTELIIQ 69 (355) Q Consensus 3 ~~p~~~~~--~~~~~~r~R----------~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~-~~~~g~~~~~~f~t~~~~~ 69 (355) |+|....+ ..+.|+|.| .++++||+++++||+||+++||+||+||+|+ ++++| |++|.|+...+ T Consensus 111 P~~~~~~~~~~e~~Rl~~RyLDLr~~~~~~~fr~Rs~i~~~iR~fl~~~gFiEVeTPiL~~s~~eG---A~~F~vpsr~~ 187 (587) T PRK00476 111 PFQIDDETNVSEELRLKYRYLDLRRPEMQNNLKLRSKVTSAIRNFLDDNGFLEIETPILTKSTPEG---ARDYLVPSRVH 187 (587) T ss_pred CCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCEECCCCCCCCCCCC---CCCCCCCCCCC T ss_conf 988655667778886554788872177889999999999999999997597400475432568666---64430131057 Q ss_pred CCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHC Q ss_conf 86783200-00285899998987446889998864245677754484300200011577657877755788877666418 Q gi|254781066|r 70 DHIRKPLY-LQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVAN 148 (355) Q Consensus 70 ~~~~~~~y-L~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~ 148 (355) ..++| |+||||||||+|||||++||||||||||||++++.|+|||||||+||||+|++|+|+++|+||+++++.+. T Consensus 188 ---~~~fyaL~qSPQLykq~L~vgG~erVyeig~~FRnE~~~t~r~pEFt~lE~E~af~d~~dvm~~~E~li~~v~~~v~ 264 (587) T PRK00476 188 ---PGKFYALPQSPQLFKQLLMVAGFDRYYQIARCFRDEDLRADRQPEFTQIDIEMSFVTQEDVMDLMEGLIRHVFKEVL 264 (587) T ss_pred ---CCCEECCCCCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCHHHEEEHHHHCCCHHHHHHHHHHHHHHHHHHHC T ss_conf ---88551356797999999885175527996431238888766682342311111116899999999999999999971 Q ss_pred CCEECCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC--------CC-------------------------CCC-----C Q ss_conf 830002234332467732078888656660876532--------34-------------------------555-----6 Q gi|254781066|r 149 QKIFSFQNVNCNPFSEPEYITVAEAFARYANIDLGT--------TL-------------------------DNP-----D 190 (355) Q Consensus 149 ~~~~~~~~~~~~~~~~~~~i~~~e~~~~~~~~d~~~--------~~-------------------------~~~-----~ 190 (355) . .+...+|++++|.|++++|....... .. ..+ . T Consensus 265 ~---------~~l~~pf~rit~~eai~~yG~DKPDlR~~~~l~d~~~~~~~~~~~~f~~~~~~~~~~v~~i~~p~~~~~~ 335 (587) T PRK00476 265 G---------VDLTKPFPRMTYAEAMRRYGSDKPDLRFPLELVDVTDLFKDSGFKVFAGAANDPGGRVKAIRVPGGASLS 335 (587) T ss_pred C---------CCCCCCCCEEEHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHCCCCEEEEEECCCCCCCC T ss_conf 9---------7478884245699999985799965457621546688761564167899986058869999746867666 Q ss_pred CCCHHHHHHHHHHCCCC------CCCCCC--------------------------------------H---HHHHHHHHH Q ss_conf 23279999999976887------787653--------------------------------------4---789876643 Q gi|254781066|r 191 QPDRHLLYLQAQQAGIR------VAHDDT--------------------------------------W---SDIFSRILI 223 (355) Q Consensus 191 ~~~~~~~~~~~~~~~~~------~~~~~~--------------------------------------~---~~~~~~l~~ 223 (355) ......+...+++.+.+ ...... + |.+..++.. T Consensus 336 r~~id~l~~~~~~~~~~~l~~i~~~~~~~~spi~k~~~~~~~~~l~~~~~~~~gd~~~f~~~~~~~~~~~lg~~r~~~~~ 415 (587) T PRK00476 336 RKQIDELTEFAKIYGAKGLAYIKVNEDGLKGPIAKFLSEEELEALLERTGAKDGDLIFFGADKKKVVNDALGALRLKLGK 415 (587) T ss_pred HHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHCCHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHCHHHHHHHH T ss_conf 66799999999981887733799805556560776469999999999848877877999359607888763317999988 Q ss_pred --CEECCCCCCCCCCCCCCCCH-----H-------HHHHCCCCCCC-------CC--CCCCCEEEECCEECCCCCHHCCC Q ss_conf --00362237675443257688-----8-------86413678778-------36--33022022367122564021069 Q gi|254781066|r 224 --EKIEPNLGINCCTILDRYPA-----P-------ESALANIYPAD-------PR--FTKRFELYACNIELCNACDELLD 280 (355) Q Consensus 224 --~~ie~~l~~~~pvfi~~yP~-----~-------~~plak~~~~~-------~~--va~rfdl~i~G~El~ng~~El~d 280 (355) ..++++. ..|+||+|||. + ..||+++++++ |+ .+++|||+++|+||+|||+|+|| T Consensus 416 ~~~li~~~~--~~p~fV~dfPlfe~~~~~~~~~a~hhPFt~P~~~~~~~~~~dp~~~~~~~yDLv~~G~El~~Gs~Ri~d 493 (587) T PRK00476 416 ELGLIDEDK--FAFLWVVDFPMFEYDEEEGRYVAAHHPFTMPKDEDLELLETDPGKALAYAYDLVLNGYELGGGSIRIHR 493 (587) T ss_pred HHCCCCCCC--CCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCHHHHHEEEEEEEECCEEECCCEEECCC T ss_conf 846666666--642689814531144202563102177458885378877538123234674053077895135032279 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHH---HHHHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCCC Q ss_conf 99999999999999972888530101---8999986-1889632453159999899815597131115856487433 Q gi|254781066|r 281 PIEQRHRFEKEMQEKKKIYNETYPID---EDFLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQE 353 (355) Q Consensus 281 ~~~q~~rf~~q~~~k~~~~~e~~~~D---~~fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~~ 353 (355) |++|+++|+. .+.++. .++ .+||+|| +|||||||||||||||||+|||++|||||||||.+...++ T Consensus 494 ~~~q~~~~~~------~gl~~~-~~~~~F~~yl~al~yG~PPhgG~GlGiDRLvmlltg~~nIRDVI~FPkt~~g~d 563 (587) T PRK00476 494 PEIQEKVFEI------LGISEE-EAEEKFGFLLDALKYGAPPHGGIAFGLDRLVMLLAGADSIRDVIAFPKTQSAAD 563 (587) T ss_pred HHHHHHHHHH------CCCCHH-HHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHCCCCCHHEEEECCCCCCCCC T ss_conf 9999999998------599989-998888899999767999976376149999999759995530650789999877 No 12 >cd00776 AsxRS_core Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as a subgroup of AspRS. AsnRS and AspRS are homodimers, which attach either asparagine or aspartate to the 3'OH group of ribose of the appropriate tRNA. While archaea lack asnRS, they possess a non-discriminating aspRS, which can mischarge Asp-tRNA with Asn. Subsequently, a tRNA-dependent aspartate amidotransferase converts the bound aspartate to asparagine. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Probab=100.00 E-value=0 Score=569.96 Aligned_cols=289 Identities=22% Similarity=0.324 Sum_probs=228.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 48999999999999999999879889847821056898544541241024788678320000285899998987446889 Q gi|254781066|r 18 RRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKI 97 (355) Q Consensus 18 ~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rv 97 (355) .+.+++.||+|+++||+||+++||+||+||+|+++++ +.++++|.++ ++++++||+|||||| ||||++|++|| T Consensus 20 ~~~~l~~Rs~i~~~iR~fl~~~gF~EVeTP~L~~~~~-eg~a~~f~~~-----~~~~~~yL~~Spel~-Kqlli~G~~rV 92 (322) T cd00776 20 VQAIFRIRSEVLRAFREFLRENGFTEVHTPKITSTDT-EGGAELFKVS-----YFGKPAYLAQSPQLY-KEMLIAALERV 92 (322) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCC-CCCCCCCCCC-----CCCCCEEECCCHHHH-HHHHHCCCCCE T ss_conf 9999999999999999999988999997984007889-8654667621-----058760015485889-99975342443 Q ss_pred HHHHHHHCCCCCC-CCCCCCEEEECEEECCC-CHHHHHHHHHHHHHHHHHHHCCCEEC-------CCCCCCCCCCCCCCC Q ss_conf 9988642456777-54484300200011577-65787775578887766641883000-------223433246773207 Q gi|254781066|r 98 FCFAHAWRNGEQG-CLHQPEFTMLEWYRAHE-SYEQLMKDCMNIIRCAAEVANQKIFS-------FQNVNCNPFSEPEYI 168 (355) Q Consensus 98 yqig~~FRaE~~~-~rHlpEFtmLE~e~af~-d~~dlm~~~E~li~~~~~~~~~~~~~-------~~~~~~~~~~~~~~i 168 (355) ||||||||||+++ +|||||||||||||||+ |++++|+++|++|+++++.+...... +.........+|.++ T Consensus 93 fei~~~FR~E~~~t~rH~pEFTmlE~e~af~~d~~d~m~~~E~li~~i~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~r~ 172 (322) T cd00776 93 YEIGPVFRAEKSNTRRHLSEFWMLEAEMAFIEDYNEVMDLIEELIKYIFKRVLERCAKELELVNQLNRELLKPLEPFPRI 172 (322) T ss_pred EEECCEEECCCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC T ss_conf 88726140799987534788876525552332899999999999999999998652678899875121100247996424 Q ss_pred CHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHH Q ss_conf 88886566608765323455562327999999997688778765347898766430036223767544325768888641 Q gi|254781066|r 169 TVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESAL 248 (355) Q Consensus 169 ~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~pl 248 (355) ++.+++.. ..+.+.. .+..|+..+....+..+.+.+. +.||||+|||.+++|| T Consensus 173 ~~~ea~~~------------------------l~~~~~~--~~~~~~~dl~~~~e~~l~~~~~-~~p~fv~d~P~~~~pf 225 (322) T cd00776 173 TYDEAIEL------------------------LREKGVE--EEVKWGEDLSTEHERLLGEIVK-GDPVFVTDYPKEIKPF 225 (322) T ss_pred CHHHHHHH------------------------HHHCCCC--CCCCCCCCCCHHHHHHHHHHHC-CCCEEEECCHHHCCCC T ss_conf 19999999------------------------9856996--6877666337699999999965-8988997974421976 Q ss_pred -CCCCCCCCCCCCCCEEEECCE-ECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC-CCCCCCEEECC Q ss_conf -367877836330220223671-225640210699999999999999997288853010189999861-88963245315 Q gi|254781066|r 249 -ANIYPADPRFTKRFELYACNI-ELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACLT-EMPQSSGIAMG 325 (355) Q Consensus 249 -ak~~~~~~~va~rfdl~i~G~-El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al~-G~PPhgG~glG 325 (355) ++.++++|++++|||||++|+ ||+|||+|++||++|++||+++ +.++. .+++|++|++ |+||||||||| T Consensus 226 y~~~~~~~~~~~~rfel~~~G~~El~~g~~r~~d~~~l~~r~~~~------g~~~~--~~~~yl~al~~G~PP~gG~glG 297 (322) T cd00776 226 YMKPDDDNPETVESFDLLMPGVGEIVGGSQRIHDYDELEERIKEH------GLDPE--SFEWYLDLRKYGMPPHGGFGLG 297 (322) T ss_pred CCCCCCCCHHHHHHHHEECCCCEEECCHHHHHCCHHHHHHHHHHC------CCCHH--HHHHHHHHHHCCCCCCCEEEEH T ss_conf 588668854554542001289278677666408999999999985------99978--9999999976699997245438 Q ss_pred HHHHHHHHHCCCCHHHHCCCCCC Q ss_conf 99998998155971311158564 Q gi|254781066|r 326 FDRLVMLVTGANNINEVIWTPFS 348 (355) Q Consensus 326 idRLvm~l~g~~~Irdvi~FP~~ 348 (355) ||||+|++||++||||||+||.+ T Consensus 298 iDRLvmll~g~~~Irdvi~FPr~ 320 (322) T cd00776 298 LERLVMWLLGLDNIREAILFPRD 320 (322) T ss_pred HHHHHHHHCCCCCHHHEECCCCC T ss_conf 99999998299727605138999 No 13 >PRK03932 asnC asparaginyl-tRNA synthetase; Validated Probab=100.00 E-value=0 Score=560.37 Aligned_cols=311 Identities=18% Similarity=0.198 Sum_probs=239.5 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEEC--------------CCCCCCCCCCCCCCCHHHH Q ss_conf 99999999999999999987988984782105689854454124102--------------4788678320000285899 Q gi|254781066|r 20 PFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTEL--------------IIQDHIRKPLYLQTSPEFS 85 (355) Q Consensus 20 ~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~--------------~~~~~~~~~~yL~~SPql~ 85 (355) .+++.||+|+++||+||+++||+||+||+|++++++++ +++|.|.. ...+|+++++||+|||||| T Consensus 133 ~ifr~RS~i~~~iR~~l~~~~F~EVeTP~L~~~~~eGa-a~~F~v~~~~~~~~~~~~~~~~~~~~yf~~~~yL~~SpqLy 211 (462) T PRK03932 133 AVMRVRNTLAQAIHEFFQENGFVWVHTPIITASDCEGA-GELFRVTTLDLENLPRTDGKVDFSKDFFGKEAFLTVSGQLY 211 (462) T ss_pred HHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCC-CCCEEECCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHHH T ss_conf 99999999999999999767967997886535687645-57404214543445433444331145427762026576899 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCC-CCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCC Q ss_conf 9989874468899988642456777-544843002000115776578777557888776664188300022343324677 Q gi|254781066|r 86 CKKLLAAGEEKIFCFAHAWRNGEQG-CLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPFSE 164 (355) Q Consensus 86 lK~ll~~G~~rvyqig~~FRaE~~~-~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~~~ 164 (355) || +|++|++||||||||||||+++ +||||||||||+||||+|++|+|+++|+|++++++.+.+ .....++..++ T Consensus 212 lq-~li~G~erVfeIg~~FRnE~~~t~RH~pEFT~lE~e~a~~d~~d~m~l~E~li~~i~~~v~~----~~~~el~~~~~ 286 (462) T PRK03932 212 AE-AYAMALSKVYTFGPTFRAENSNTRRHLAEFWMIEPEMAFADLEDNMDLAEDMLKYVIKAVLE----ECPDDLEFLNR 286 (462) T ss_pred HH-HHHHHCCCEEEEEHHHHHCCCCCCCCCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHH----HCHHHHHHHCC T ss_conf 99-98752064899733232056775445430025553110068999999999999999999987----58677876245 Q ss_pred CCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHH Q ss_conf 32078888656660876532345556232799999999768877876534789876643003622376754432576888 Q gi|254781066|r 165 PEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAP 244 (355) Q Consensus 165 ~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~ 244 (355) +......+.++..++.++... .........++.+.+......||+.+....+.++.+.. .+.|+||+|||++ T Consensus 287 ~~~~~~~~~l~~~~~~~~~~i-------t~~eai~~l~~~~~~~~~~~~~g~dl~~~~E~~l~e~~-~~~P~fi~d~P~~ 358 (462) T PRK03932 287 DVDKGLIERLENFIESPFPRI-------TYTEAIEILQKSGKKFEFPVEWGDDLGSEHERYLTEEH-FKKPVFVTNYPKD 358 (462) T ss_pred CCCHHHHHHHHHHCCCCCCEE-------EHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHH-CCCCEEEECCCCC T ss_conf 478368899998628997264-------69999999996496456772111203548888888886-5878899776201 Q ss_pred HHHHCCCCCCCCCCCCCCEEEECCE-ECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-CCCCCCCEE Q ss_conf 8641367877836330220223671-22564021069999999999999999728885301018999986-188963245 Q gi|254781066|r 245 ESALANIYPADPRFTKRFELYACNI-ELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACL-TEMPQSSGI 322 (355) Q Consensus 245 ~~plak~~~~~~~va~rfdl~i~G~-El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al-~G~PPhgG~ 322 (355) ++|||+..++++..+.+|||+++|+ ||+||+.++++++++.+++. +.+.++. .+ ++||+|+ +|||||||| T Consensus 359 ~~Pfy~~~~~d~~~~~~~dll~~G~~Ei~~G~~R~~~~~~l~~~~~------~~g~~~e-~~-~~yl~~~~yG~PP~gG~ 430 (462) T PRK03932 359 IKAFYMRLNPDGKTVAAMDLLAPGIGEIIGGSQREERLDVLDARMK------ELGLDKE-DY-WWYLDLRRYGSVPHSGF 430 (462) T ss_pred CCCCCCCCCCCCCEEEEEEEEECCCEEEECHHHHCCCHHHHHHHHH------HCCCCHH-HH-HHHHHHHHCCCCCCCEE T ss_conf 3853356588977467776773586476065553379999999999------8699989-99-99999976799987737 Q ss_pred ECCHHHHHHHHHCCCCHHHHCCCCCCCCCC Q ss_conf 315999989981559713111585648743 Q gi|254781066|r 323 AMGFDRLVMLVTGANNINEVIWTPFSQSNQ 352 (355) Q Consensus 323 glGidRLvm~l~g~~~Irdvi~FP~~r~~~ 352 (355) |||||||||++||++||||||+||.+..+- T Consensus 431 GiGiDRLvm~l~~~~sIRdvi~FPr~~~r~ 460 (462) T PRK03932 431 GLGFERLVAYVTGLENIRDVIPFPRTPGRA 460 (462) T ss_pred EEHHHHHHHHHCCCCCHHEEECCCCCCCCC T ss_conf 677999999982999654586488987757 No 14 >cd00669 Asp_Lys_Asn_RS_core Asp_Lys_Asn_tRNA synthetase class II core domain. This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. Probab=100.00 E-value=0 Score=563.40 Aligned_cols=265 Identities=27% Similarity=0.408 Sum_probs=228.4 Q ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999998798898478210568985445412410247886783200002858999989874468899988 Q gi|254781066|r 22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFA 101 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig 101 (355) |++||+++++||+||.++||+||+||+|+++++++ ++++|.++++ +.++++||+||||+|||+||++|++|||||| T Consensus 1 lr~Rs~i~~~iR~ff~~~~f~EV~TP~l~~~~~~~-~~~~f~~~~~---~~~~~~~L~~Spel~~k~ll~~g~~~if~i~ 76 (269) T cd00669 1 FKVRSKIIKAIRDFMDDRGFLEVETPMLQKITGGA-GARPFLVKYN---ALGLDYYLRISPQLFKKRLMVGGLDRVFEIN 76 (269) T ss_pred CCHHHHHHHHHHHHHHHCCCEEEECCEEECCCCCC-CCCEEEEECC---CCCCEEEECCCHHHHHHHHHHCCCCCEEEEE T ss_conf 91699999999999998898998798530578987-6742573137---8994077343889999999865888679984 Q ss_pred HHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCC-EECCCCCCCCCCCCCCCCCHHHHHHHHCCC Q ss_conf 6424567775448430020001157765787775578887766641883-000223433246773207888865666087 Q gi|254781066|r 102 HAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQK-IFSFQNVNCNPFSEPEYITVAEAFARYANI 180 (355) Q Consensus 102 ~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~-~~~~~~~~~~~~~~~~~i~~~e~~~~~~~~ 180 (355) ||||||++++||+|||||||||++|+|++++|+++|++|+++++.+... .........++..+|+++++.++++++ T Consensus 77 ~~FR~e~~~~rH~~EFtmlE~y~~~~d~~~~m~~~e~li~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~ea~e~~--- 153 (269) T cd00669 77 RNFRNEDLRARHQPEFTMMDLEMAFADYEDVIELTERLVRHLAREVLGVTAVTYGFELEDFGLPFPRLTYREALERY--- 153 (269) T ss_pred CCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCCCEEEHHHHHHHH--- T ss_conf 62107898655434877578751489999999999999999999996555245355444458998785799999984--- Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHH-HCCCCCCCCCCC Q ss_conf 6532345556232799999999768877876534789876643003622376754432576888864-136787783633 Q gi|254781066|r 181 DLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESA-LANIYPADPRFT 259 (355) Q Consensus 181 d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~p-lak~~~~~~~va 259 (355) ..|+||+|||++++| +++.++++++++ T Consensus 154 ----------------------------------------------------~~p~fi~dyP~~~~~~~~~~~~~~~~~a 181 (269) T cd00669 154 ----------------------------------------------------GQPLFLTDYPAEMHSPLASPHDVNPEIA 181 (269) T ss_pred ----------------------------------------------------CCCEEEECCCHHCCCCCCCCCCCCCCHH T ss_conf ----------------------------------------------------9978998985010780209079996676 Q ss_pred CCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCCC Q ss_conf 0220223671225640210699999999999999997288853010189999861-889632453159999899815597 Q gi|254781066|r 260 KRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACLT-EMPQSSGIAMGFDRLVMLVTGANN 338 (355) Q Consensus 260 ~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~~ 338 (355) +|||||++|+||||||+|++||++|++||+++...++ +....|++||+|++ |+|||||+|||+|||+|+++|++| T Consensus 182 ~rfdl~~~G~El~nG~~r~~d~~~~~~r~~~~~~~~~----~~~~~~~~yl~a~~~G~pp~~G~glG~dRL~m~~~g~~~ 257 (269) T cd00669 182 DAFDLFINGVEVGNGSSRLHDPDIQAEVFQEQGINKE----AGMEYFEFYLKALEYGLPPHGGLGIGIDRLIMLMTNSPT 257 (269) T ss_pred HHCCCCCCCEEECCCCCCCCCHHHHHHHHHHHCCCHH----HHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHHCCCC T ss_conf 6502467860670325204888999999998560744----556658999999877999971663479999999808996 Q ss_pred HHHHCCCCCCC Q ss_conf 13111585648 Q gi|254781066|r 339 INEVIWTPFSQ 349 (355) Q Consensus 339 Irdvi~FP~~r 349 (355) |||||+||++| T Consensus 258 Irdv~~FPr~r 268 (269) T cd00669 258 IREVIAFPKMR 268 (269) T ss_pred HHHCCCCCCCC T ss_conf 88624789988 No 15 >PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional Probab=100.00 E-value=0 Score=555.49 Aligned_cols=315 Identities=22% Similarity=0.243 Sum_probs=226.7 Q ss_pred HHHCCCHHH----------HHHHHHHHHHHHHHHHHHCCCEEEECCCEE-CCCCCCCCCCCEEEECCCCCCCCCCCC-CC Q ss_conf 312615489----------999999999999999998798898478210-568985445412410247886783200-00 Q gi|254781066|r 12 RDFHYRRRP----------FLLKRNMIQSSLREYFVENQFIEIDSMSLQ-YSPGNETHIRAFSTELIIQDHIRKPLY-LQ 79 (355) Q Consensus 12 ~~~~~r~R~----------~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~-~~~~g~~~~~~f~t~~~~~~~~~~~~y-L~ 79 (355) .+.|+|.|. +++.||+++++||+||+++||+||+||+|+ ++|+| |++|.|+...+ +..+| |+ T Consensus 136 ee~RLkyRyLDLRr~~~~~~~~~Rskv~~~iR~~l~~~gF~EVETP~L~~stpEG---ArdflvPsr~~---~~~fyaLp 209 (706) T PRK12820 136 EDLRLQYRYLDIRRPAMQDHLAKRHRIIKCARDFLDSRGFLEIETPILTKSTPEG---ARDYLVPSRIH---PKEFYALP 209 (706) T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCEECCCCCCC---CCCCCCCEECC---CCCEECCC T ss_conf 8887665677647998999999999999999999987798896687044567532---45750024458---87650056 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCC Q ss_conf 28589999898744688999886424567775448430020001157765787775578887766641883000223433 Q gi|254781066|r 80 TSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNC 159 (355) Q Consensus 80 ~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~ 159 (355) ||||+|||+||+||++||||||||||||++++.|+|||||||+||||+|++|+|+++|+|++++++..+ . T Consensus 210 QSPQlyKQlLMvgG~dRyFqIarcFRdEd~r~dRqPEFTqlDiEmSF~d~edvm~l~E~li~~~~~~~~----------~ 279 (706) T PRK12820 210 QSPQLFKQLLMIAGFERYFQLARCFRDEDLRPNRQPEFTQLDIEASFIDEEFIFELIEELTARMFAIGG----------I 279 (706) T ss_pred CCHHHHHHHHHHCCCCEEEEEEEEECCCCCCCCCCCCEEEEEEEHHCCCHHHHHHHHHHHHHHHHHHCC----------C T ss_conf 682999999986286617996001128999988798340687421348999999999999999998538----------4 Q ss_pred CCCCCCCCCCHHHHHHHHCCCCCCCC--------CCCCCCCCHHH--------------------------------HHH Q ss_conf 24677320788886566608765323--------45556232799--------------------------------999 Q gi|254781066|r 160 NPFSEPEYITVAEAFARYANIDLGTT--------LDNPDQPDRHL--------------------------------LYL 199 (355) Q Consensus 160 ~~~~~~~~i~~~e~~~~~~~~d~~~~--------~~~~~~~~~~~--------------------------------~~~ 199 (355) +...+|++++|.+++.+|........ ........... ... T Consensus 280 ~l~~pFprmtY~eAm~~YGsDKPDlRf~lel~d~t~if~~~~f~vF~~~l~~gg~Vk~I~v~~~~~~~s~~~i~~e~~~e 359 (706) T PRK12820 280 ALPRPFPRMPYAEAMDTTGSDRPDLRFDLKFADATDIFENTRYGIFKQILQRGGRIKGINIKGQSEKLSKNVLQNEYAKE 359 (706) T ss_pred CCCCCCCCCCHHHHHHHHCCCCCCCCCCHHHCCCCHHHCCCCCHHHHHHHHHCCEEEEEECCCCHHHHHHHHHHHHHHHH T ss_conf 54687453419999998689874310230102330122155405899988508868899768835665666656699998 Q ss_pred HHHHCCCCCCCCCCH------------HH-----HHHHHH------------------------------------HCEE Q ss_conf 999768877876534------------78-----987664------------------------------------3003 Q gi|254781066|r 200 QAQQAGIRVAHDDTW------------SD-----IFSRIL------------------------------------IEKI 226 (355) Q Consensus 200 ~~~~~~~~~~~~~~~------------~~-----~~~~l~------------------------------------~~~i 226 (355) .+.+.+.+ +..| .+ ....+. ...+ T Consensus 360 ia~~~gak---Gl~w~k~~~~~l~~~i~kf~see~~~~l~~~~~~~~GD~i~~~ad~~~~~v~~~LG~lR~~la~~l~Li 436 (706) T PRK12820 360 IAPSFGAK---GMTWMRAEAGGLDSNIVQFFSADEKEALKRRFHAEDGDVIIMIADASCAIVLSALGQLRLHLADRLGLI 436 (706) T ss_pred HHHHCCCC---CCEEEEEECCCCCCHHHHCCCHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 62430656---625898616864631443079999999999848788988999727506689988626789999984887 Q ss_pred CCCCCCCCCCCCCCCC-----------HHHHHHCCCCCCC--CC--------CCCCCEEEECCEECCCCCHHCCCHHHHH Q ss_conf 6223767544325768-----------8886413678778--36--------3302202236712256402106999999 Q gi|254781066|r 227 EPNLGINCCTILDRYP-----------APESALANIYPAD--PR--------FTKRFELYACNIELCNACDELLDPIEQR 285 (355) Q Consensus 227 e~~l~~~~pvfi~~yP-----------~~~~plak~~~~~--~~--------va~rfdl~i~G~El~ng~~El~d~~~q~ 285 (355) .++. ..|+||+||| ....||++++.++ +. .+.+|||++||.||+||+.|+|||+.|+ T Consensus 437 ~~~~--~~flWVtDFPLFE~~ee~~~~s~HHPFT~P~~ed~d~~~~~~~~~v~a~aYDLVlNG~ElggGSiRIHd~~iQ~ 514 (706) T PRK12820 437 PEGV--FHPLWITDFPLFEATDDGGVTSSHHPFTAPDREDFDPGDIEELLDLRSRAYDLVVNGEELGGGSIRINDKDIQL 514 (706) T ss_pred CCCC--CEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCEEEEEECCEEEEEEEEECCCHHHHH T ss_conf 8786--31688516742234544465335489778882336832245532000364606899999614022038999999 Q ss_pred HHHHHHHHHHHCCCCCC-C-HHHHHHHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCCC Q ss_conf 99999999997288853-0-1018999986-1889632453159999899815597131115856487433 Q gi|254781066|r 286 HRFEKEMQEKKKIYNET-Y-PIDEDFLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQE 353 (355) Q Consensus 286 ~rf~~q~~~k~~~~~e~-~-~~D~~fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~~ 353 (355) ++|+. .|..+. . .-..+||+|| ||+|||||+|||||||||+|||.+|||||||||.+.+.++ T Consensus 515 ~if~~------lGl~~ee~~~kFgf~LeAf~YGaPPHGGialGlDRLvMlLtg~~sIRDVIaFPKt~~g~d 579 (706) T PRK12820 515 RIFAA------LGLSEEDIEDKFGFFLRAFDFAAPPHGGIALGLDRVVSMILQTPSIREVIAFPKNRSAAC 579 (706) T ss_pred HHHHH------CCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEHHHHHHHHHCCCCCHHHEECCCCCCCCCC T ss_conf 99997------599978988899999999866999867031039999999769982650522789988786 No 16 >PRK06462 asparagine synthetase A; Reviewed Probab=100.00 E-value=0 Score=546.21 Aligned_cols=294 Identities=16% Similarity=0.136 Sum_probs=220.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 48999999999999999999879889847821056898544541241024788678320000285899998987446889 Q gi|254781066|r 18 RRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKI 97 (355) Q Consensus 18 ~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rv 97 (355) .|.++++||+|+++||+||+++||+||+||+|+++.+++. +.+|.++ .+++++++||+||||||||+|+++|++|| T Consensus 25 ~~~ifriRs~i~~~iR~f~~~~gF~EV~TPiL~~~~~~~~-~~~~~~~---~~~~~~~~~L~~Spql~lk~li~~g~~rV 100 (332) T PRK06462 25 YSLVLKIQSSILRYTREFLDGRGFVEVLPPIISPSTDPLM-GDAKPAS---IDFYGVEYYLADSMIFHKQLMLRLLKGKV 100 (332) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCC-CCCCCCE---EECCCCCEEECCCHHHHHHHHHHCCCCCE T ss_conf 9999999999999999999888999987972367788766-7760105---84489863314586999999986389977 Q ss_pred HHHHHHHCCCCCC---CCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCE---E-CCCC-CCCCCCCCCCCCC Q ss_conf 9988642456777---54484300200011577657877755788877666418830---0-0223-4332467732078 Q gi|254781066|r 98 FCFAHAWRNGEQG---CLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKI---F-SFQN-VNCNPFSEPEYIT 169 (355) Q Consensus 98 yqig~~FRaE~~~---~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~---~-~~~~-~~~~~~~~~~~i~ 169 (355) ||||||||||++| +|||||||||||||||+|++|+|+++|++|+++++.+.... + ...+ ...+...+|++++ T Consensus 101 feIg~~FR~E~~d~~t~rHlpEFt~lE~y~a~~d~~d~m~~~E~li~~i~~~v~~~~~~~~~~~~~~~~~~~~~~~~ri~ 180 (332) T PRK06462 101 FYLSPNFRLEPVDKDTGRHLYEFTQLDIEIEGADLEEVMSLAEDLIKYLVKELLREHSAELEFFLGRDLPEIKRPFKRIT 180 (332) T ss_pred EEECCHHHCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCC T ss_conf 99745231687776777654577765587873899999999999999999999986679999870777523598114546 Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHC Q ss_conf 88865666087653234555623279999999976887787653478987664300362237675443257688886413 Q gi|254781066|r 170 VAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESALA 249 (355) Q Consensus 170 ~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~pla 249 (355) +.++++.... .+........++...+ ..+++++ ..||||+|||++++||| T Consensus 181 ~~eai~~l~~------------------------~~~~~~~~~~~~~~~e----~~l~~~~--~~P~fv~d~P~~~~Pfy 230 (332) T PRK06462 181 HKEAIEILNE------------------------EGCSGEELEEIGSEGE----KSLSEHF--EEPVWIINIPKGSREFY 230 (332) T ss_pred HHHHHHHHHH------------------------CCCCCCHHHHHHHHHH----HHHHHHH--CCCEEEECCHHHHCHHH T ss_conf 9999999986------------------------2765660767545999----9999980--89789975625529586 Q ss_pred CCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHH-HHHHCCCCCCCHHHHHHHHHH-CCCC-CCCEEECCH Q ss_conf 6787783633022022367122564021069999999999999-999728885301018999986-1889-632453159 Q gi|254781066|r 250 NIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEM-QEKKKIYNETYPIDEDFLACL-TEMP-QSSGIAMGF 326 (355) Q Consensus 250 k~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~-~~k~~~~~e~~~~D~~fl~al-~G~P-PhgG~glGi 326 (355) +.+++++++++||||++ +|||+|++|+.+|+++++++. ++++.+.++... +|||+|+ +|+| ||||||||| T Consensus 231 ~~~~~~~~~~~~fdl~~-----~~g~~El~~g~~r~~~~~~l~~~~~~~g~~~~~~--~~yl~~~~~G~P~P~gG~GiGi 303 (332) T PRK06462 231 DREDERPGVLRDYDLLL-----PEGIGEAVSGGEREYEYEEIVERIREHGVDPENY--KWYLEMAKEGYPLPTAGFGIGV 303 (332) T ss_pred HCCCCCCCEEEECCHHH-----HCCCEEECCHHHHHHHHHHHHHHHHHCCCCHHHH--HHHHHHHHHCCCCCCCEEEEHH T ss_conf 64899988487536033-----0666222251767855999999999769997899--9999999828999987761489 Q ss_pred HHHHHHHHCCCCHHHHCCCCCCCCCC Q ss_conf 99989981559713111585648743 Q gi|254781066|r 327 DRLVMLVTGANNINEVIWTPFSQSNQ 352 (355) Q Consensus 327 dRLvm~l~g~~~Irdvi~FP~~r~~~ 352 (355) |||||++||.+||||||+||++.... T Consensus 304 DRLvm~l~~~~~Irdvi~FPR~pg~~ 329 (332) T PRK06462 304 ERLTRYICGLRDIREVQPFPRVPGIV 329 (332) T ss_pred HHHHHHHHCCCCHHEEEECCCCCCCC T ss_conf 99999980898576174179998988 No 17 >TIGR00459 aspS_bact aspartyl-tRNA synthetase; InterPro: IPR004524 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Aspartyl tRNA synthetase 6.1.1.12 from EC is an alpha2 dimer that belongs to class IIb. Structural analysis combined with mutagenesis and enzymology data on the yeast enzyme point to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module . This family represents aspartyl-tRNA synthetases from the bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). ; GO: 0000166 nucleotide binding, 0004815 aspartate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006422 aspartyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=100.00 E-value=0 Score=535.94 Aligned_cols=316 Identities=21% Similarity=0.277 Sum_probs=225.5 Q ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCEE-CCCCCCCCCCCEEEECCCC-CCCCCCCC-CCCCHHHHHHHHHHHHHHHH Q ss_conf 999999999999999998798898478210-5689854454124102478-86783200-00285899998987446889 Q gi|254781066|r 21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQ-YSPGNETHIRAFSTELIIQ-DHIRKPLY-LQTSPEFSCKKLLAAGEEKI 97 (355) Q Consensus 21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~-~~~~g~~~~~~f~t~~~~~-~~~~~~~y-L~~SPql~lK~ll~~G~~rv 97 (355) .|..||+|..+||+||+++||+|||||||+ +||+| |+.|.|+.+.+ .....+|| |+||||||||.||+||++|| T Consensus 150 ~L~lR~~v~~~~Rn~l~~~gFleiETP~LtKsTPEG---ARDyLVPsRv~rsdG~g~FYALpQSPQlfKQLLMvsG~drY 226 (653) T TIGR00459 150 RLKLRHKVTKAVRNFLDQQGFLEIETPILTKSTPEG---ARDYLVPSRVHRSDGKGEFYALPQSPQLFKQLLMVSGVDRY 226 (653) T ss_pred HHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCC---HHHCCCCCCCCCCCCCCCEECCCCCHHHHHHHHHHCCCCCC T ss_conf 986688989999866642787065067777888431---10157755300368588451468975689998751255531 Q ss_pred HHHHHHHCCCCC--CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCC---CCC----- Q ss_conf 998864245677--7544843002000115776578777557888776664188300022343324677---320----- Q gi|254781066|r 98 FCFAHAWRNGEQ--GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPFSE---PEY----- 167 (355) Q Consensus 98 yqig~~FRaE~~--~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~~~---~~~----- 167 (355) |||++||||||+ ||| |||||+|+||||++.++||+++|+|+.+|++.+... ...++...+ |++ T Consensus 227 yQIArCFRDEDLRADRQ--PEFTQiD~E~SF~~~~~vm~l~E~l~~~vf~~v~~k-----rGl~~L~~~GtlfP~kkenG 299 (653) T TIGR00459 227 YQIARCFRDEDLRADRQ--PEFTQIDMEMSFMTQEDVMDLIEKLVSGVFKEVKGK-----RGLIDLKKPGTLFPVKKENG 299 (653) T ss_pred EEEEEEECCCCCCCCCC--CCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCC-----CCEEEECCCCCEEEEECCCC T ss_conf 35788976625666577--873244263112893568999999999999997078-----51375078852411221676 Q ss_pred ------CCHHHHHHHHCCCCCCCCCCCCC--------------------------------------------CCCHHHH Q ss_conf ------78888656660876532345556--------------------------------------------2327999 Q gi|254781066|r 168 ------ITVAEAFARYANIDLGTTLDNPD--------------------------------------------QPDRHLL 197 (355) Q Consensus 168 ------i~~~e~~~~~~~~d~~~~~~~~~--------------------------------------------~~~~~~~ 197 (355) +||.||+.+|....++.....+. ......+ T Consensus 300 tvsifrmty~EAm~~yGsDKPDLR~~~el~dv~d~f~afshld~~F~vF~~~~~~P~g~v~~i~v~~~~~~ls~~~i~~l 379 (653) T TIGR00459 300 TVSIFRMTYQEAMERYGSDKPDLRFGLELIDVSDLFKAFSHLDSEFKVFSNLINAPGGRVKAIRVKGGDAELSRKSIKEL 379 (653) T ss_pred EEEEEECCHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEECCCCCCCCCHHHHHHH T ss_conf 07998556799986167768778888346777667777664067534579998488855775772786422550212220 Q ss_pred H---HHHHHCCCCC-----------------------------------------------CCCCC-HHHHHHHHHH--- Q ss_conf 9---9999768877-----------------------------------------------87653-4789876643--- Q gi|254781066|r 198 Y---LQAQQAGIRV-----------------------------------------------AHDDT-WSDIFSRILI--- 223 (355) Q Consensus 198 ~---~~~~~~~~~~-----------------------------------------------~~~~~-~~~~~~~l~~--- 223 (355) . ..+...|.+- -.... +......+-+ T Consensus 380 ~~~~~~a~~~GakGlAy~~v~~~~~~~~~~~~~i~kfL~~~~~~~~~~~t~a~~gdillnPfg~~~l~~~v~~~lgGkal 459 (653) T TIGR00459 380 RVLIKFAKEYGAKGLAYLKVNEDAEGLEEVKSPIKKFLDEKKLKKLLERTDAQEGDILLNPFGAGDLKKIVLDALGGKAL 459 (653) T ss_pred CHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCHHHHCCCHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHCCHHH T ss_conf 11445676658631566565216741024531012024735778899874212687865577860589999985041688 Q ss_pred -CEECCCCC--C-----CCCCCCCC---------CCHH------------HHHHCCCCCCCC---------CCCCCCEEE Q ss_conf -00362237--6-----75443257---------6888------------864136787783---------633022022 Q gi|254781066|r 224 -EKIEPNLG--I-----NCCTILDR---------YPAP------------ESALANIYPADP---------RFTKRFELY 265 (355) Q Consensus 224 -~~ie~~l~--~-----~~pvfi~~---------yP~~------------~~plak~~~~~~---------~va~rfdl~ 265 (355) ..+..+++ . -.|+||+| ||.- --||+++.+.+. -.|+.|||+ T Consensus 460 Rl~l~~~l~sWL~d~~~~~flWv~DksGkkeklaFP~fE~d~~E~~~~a~HHpFT~Pk~~~~~~lE~~p~~a~a~aYDlV 539 (653) T TIGR00459 460 RLKLGKDLGSWLVDPDAFSFLWVVDKSGKKEKLAFPLFEKDEEEGRLVAAHHPFTMPKPEDLEDLETAPEEALAEAYDLV 539 (653) T ss_pred HHHHHHHHHCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCHHHHHCCHHHHHHHCCCEE T ss_conf 99987653000235231471789837887023427656677652755840578898751227877407455412028768 Q ss_pred ECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHC Q ss_conf 367122564021069999999999999999728885-301018999986-188963245315999989981559713111 Q gi|254781066|r 266 ACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNE-TYPIDEDFLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVI 343 (355) Q Consensus 266 i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e-~~~~D~~fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi 343 (355) +||+||++|+.+++||..|...|+.-. +.+++ +.+-=-++|+|+ +|+|||||+|+|||||+|+||+.+|||||| T Consensus 540 lNG~ElGGGSiRIh~~~~Q~~~F~d~L----gid~eea~EkFGFLLeA~~yGaPPHgG~A~GlDRL~Mll~~~~nIRDVI 615 (653) T TIGR00459 540 LNGVELGGGSIRIHDPEVQEKVFEDIL----GIDPEEAREKFGFLLEAFKYGAPPHGGLALGLDRLVMLLTGTDNIRDVI 615 (653) T ss_pred EEEEEECCCEEEECCHHHHHHHHHHHH----CCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCEEC T ss_conf 830698871046428789999998762----8898998776356875873576851015555899999980899722001 Q ss_pred CCCCCCC Q ss_conf 5856487 Q gi|254781066|r 344 WTPFSQS 350 (355) Q Consensus 344 ~FP~~r~ 350 (355) |||.+.. T Consensus 616 AFPKt~~ 622 (653) T TIGR00459 616 AFPKTAQ 622 (653) T ss_pred CCCCCCC T ss_conf 7887601 No 18 >TIGR00457 asnS asparaginyl-tRNA synthetase; InterPro: IPR004522 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . AsparaginyltRNA synthetase (6.1.1.22 from EC) is an alpha2 dimer that belongs to class IIb. There is a striking similarity between asparaginyl-tRNA synthetases and archaeal/eukaryotic type aspartyl-tRNA synthetases (IPR004523 from INTERPRO) and a striking divergence of bacterial type aspartyl-tRNA synthetases (IPR004524 from INTERPRO). This family, AsnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.; GO: 0000166 nucleotide binding, 0004816 asparagine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006421 asparaginyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=100.00 E-value=0 Score=532.32 Aligned_cols=304 Identities=20% Similarity=0.242 Sum_probs=243.5 Q ss_pred HCCCHHH-----HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC-CCCCCCCCEEEEC--------------CCCCCCC Q ss_conf 2615489-----999999999999999998798898478210568-9854454124102--------------4788678 Q gi|254781066|r 14 FHYRRRP-----FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP-GNETHIRAFSTEL--------------IIQDHIR 73 (355) Q Consensus 14 ~~~r~R~-----~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~-~g~~~~~~f~t~~--------------~~~~~~~ 73 (355) +|||-|+ ++++||.+.++||+||+++||+.|+||||+++. +|+. +-|.|.. +..+||+ T Consensus 133 ~HLr~Rt~~~~AvmrvR~~l~~ai~~yF~~~gF~~V~~PilT~~d~EGAG--ElF~v~TLdl~~lp~~~g~~df~~~fFg 210 (495) T TIGR00457 133 AHLRLRTNTLGAVMRVRNALSQAIHEYFQKNGFVKVSPPILTSNDCEGAG--ELFKVSTLDLEKLPRNDGKIDFSKDFFG 210 (495) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCEEECCCCCCCC--CCCEEEEHHHHCCCCCCCCCCCCCCCCC T ss_conf 63777898877899999999999998760478678688631136888875--4332200324215332688876302488 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCE- Q ss_conf 3200002858999989874468899988642456777-54484300200011577657877755788877666418830- Q gi|254781066|r 74 KPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQG-CLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKI- 151 (355) Q Consensus 74 ~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~-~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~- 151 (355) +++||+||.||++ +.+|..|+|||+||||||||.|+ +|||+||||||.||||++++|+++++|++|+++++.+-... T Consensus 211 k~ayLTVSGQL~~-E~~A~AL~kvyTfGPTFRAEkS~T~RHLsEFWMiEPE~AF~~l~d~~~~~E~~~k~~~k~VL~~~q 289 (495) T TIGR00457 211 KEAYLTVSGQLYA-EAYALALSKVYTFGPTFRAEKSNTSRHLSEFWMIEPEMAFANLNDLLQLIETLIKYIIKAVLENQQ 289 (495) T ss_pred CEEEEEECCHHHH-HHHHHHHCCCEECCCCEECCCCCCCCCHHHHHHHHHHEEECCHHHHHHHHHHHHHHHHHHHHCCHH T ss_conf 6012330227899-999997478144587400428648701112210112000001333389999999999999830524 Q ss_pred --ECCC---CCC---CC-----------------CCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCC Q ss_conf --0022---343---32-----------------4677320788886566608765323455562327999999997688 Q gi|254781066|r 152 --FSFQ---NVN---CN-----------------PFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGI 206 (355) Q Consensus 152 --~~~~---~~~---~~-----------------~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~ 206 (355) +.-+ ..+ .+ ..++|.+|+|.+|+. +|.....+... T Consensus 290 ellPkqfi~~~enn~~~~L~~~~~~~~~~~l~~~i~~~F~~i~Y~~Ai~--------------------iL~~~~~~~~~ 349 (495) T TIGR00457 290 ELLPKQFICSQENNLLKFLEKNFDKDLIKKLENIINNKFARITYTDAIE--------------------ILKESDNKEKK 349 (495) T ss_pred HHCCHHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHHCCCCEECHHHHHH--------------------HHHHHHHCCCC T ss_conf 5042010377713799986641275677522566622676004789999--------------------98742111464 Q ss_pred CCCCCCC-HHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHCCCCC-CCCCCCCCCEEEECC-E-ECCCCCHHCCCHH Q ss_conf 7787653-4789876643003622376754432576888864136787-783633022022367-1-2256402106999 Q gi|254781066|r 207 RVAHDDT-WSDIFSRILIEKIEPNLGINCCTILDRYPAPESALANIYP-ADPRFTKRFELYACN-I-ELCNACDELLDPI 282 (355) Q Consensus 207 ~~~~~~~-~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~plak~~~-~~~~va~rfdl~i~G-~-El~ng~~El~d~~ 282 (355) +++.++. ||..+...+|.++.++....+||||+|||+++|||||... +|++++.++||++.+ + ||++|+.|+.|-+ T Consensus 350 ~Fe~~d~~wG~DL~~eHER~LaE~~Fk~qPvfV~~YPk~~KaFYMk~NS~D~~tV~a~DlL~P~GiGEIiGGS~Re~dld 429 (495) T TIGR00457 350 NFEYEDFEWGIDLQTEHERFLAEEYFKPQPVFVTDYPKDIKAFYMKLNSDDGKTVAAVDLLAPKGIGEIIGGSEREDDLD 429 (495) T ss_pred CCCCCCCCCCCCCCHHHHHHHHHCCCCCCCEEEECCCCCCCCHHCCCCCCCCCEEEEEEEECCCCEEEEECCCCCHHHHH T ss_conf 35888613488863368998763158988889973885558010536678887478999837896266516754322689 Q ss_pred HHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCC Q ss_conf 99999999999997288853-01018999986-18896324531599998998155971311158564 Q gi|254781066|r 283 EQRHRFEKEMQEKKKIYNET-YPIDEDFLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFS 348 (355) Q Consensus 283 ~q~~rf~~q~~~k~~~~~e~-~~~D~~fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~ 348 (355) ++.+|+.+ .|-+.. .. +||++-. +|..||||||||+||||+|+||..|||||||||++ T Consensus 430 ~L~~r~k~------~g~d~~G~l--~WY~DlRKyGs~PH~GFGLGfERl~ay~~G~~niRD~IPFPR~ 489 (495) T TIGR00457 430 KLEERMKE------MGLDTDGAL--NWYLDLRKYGSVPHSGFGLGFERLVAYITGLENIRDAIPFPRT 489 (495) T ss_pred HHHHHHHH------CCCCCCCCC--HHHHHHCCEECCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCC T ss_conf 99999996------486887750--4326415120566466432489999998178744416677877 No 19 >TIGR00462 genX lysyl-tRNA synthetase homolog GenX; InterPro: IPR004525 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . This entry represents lysyl-tRNA synthetases from bacteria, as well as other related proteins. Escherichia coli, Haemophilus influenzae, and Aquifex aeolicus each have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS, so they appear to be orthologous. The protein is termed PoxA or GenX after its designation in E. coli. Its function is unknown.; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=100.00 E-value=0 Score=527.68 Aligned_cols=321 Identities=36% Similarity=0.593 Sum_probs=296.4 Q ss_pred CCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCC-CCCCCCCCCCCH Q ss_conf 8987478831261548999999999999999999879889847821056898544541241024788-678320000285 Q gi|254781066|r 4 IPSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQD-HIRKPLYLQTSP 82 (355) Q Consensus 4 ~p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~-~~~~~~yL~~SP 82 (355) |-.-.-|+|++-. ....+|++|+..||.||.++|++||+||+|...+..+.++.||.|...... .-++..+|.||| T Consensus 6 M~~l~~W~Psa~i---~n~LkRa~~i~~iR~FF~e~G~~EV~TP~l~~~~~~D~~l~p~~~~~l~~g~~~~~~~WL~TSP 82 (330) T TIGR00462 6 MDLLDAWQPSADI---KNLLKRAKIIAEIRKFFKERGLLEVETPLLSDFPVTDLHLEPFKTEFLEPGGEQNKVLWLSTSP 82 (330) T ss_pred CHHHHCCCCCCCH---HHHHHHHHHHHHHHHHHHHCCCEEECCCCHHCCCCCCEEEEEEEEEEECCCCCCCCEECCCCCC T ss_conf 1033357865224---6778899999999998861784253263010156443022136888842665333312114587 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCC Q ss_conf 89999898744688999886424567775448430020001157765787775578887766641883000223433246 Q gi|254781066|r 83 EFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPF 162 (355) Q Consensus 83 ql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~ 162 (355) |++||+||++|.+.||||+++||||+.+++|+|||||||||++..|+.-+|+.+.++++.++. + T Consensus 83 EY~MK~LL~~~~~~iFQi~k~FRN~E~G~~H~~EF~MLEWY~~~~d~~~Li~E~~~LL~~~ld----------------~ 146 (330) T TIGR00462 83 EYHMKRLLSAGKGPIFQITKVFRNEEAGRLHNPEFTMLEWYRPHYDMLRLINEVDDLLQQLLD----------------C 146 (330) T ss_pred CHHHHHHHHHCCCCEEEEEEHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC----------------C T ss_conf 278999986217862310000100024675775310011121102389999999999999728----------------8 Q ss_pred CCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCC--CCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCC Q ss_conf 773207888865666087653234555623279999999976887--787653478987664300362237675443257 Q gi|254781066|r 163 SEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIR--VAHDDTWSDIFSRILIEKIEPNLGINCCTILDR 240 (355) Q Consensus 163 ~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~ 240 (355) .+++.+||.++|++|.++|+.. .++..+...+.+.++. ...+.+|..++..+|.+.||+++|.+.|+||+| T Consensus 147 ~~~E~l~~~~~F~~y~g~d~l~-------~e~s~l~E~~~k~~~~~~~~~~ED~~TLl~~~F~~~VE~~~G~~rP~~~~~ 219 (330) T TIGR00462 147 PEAESLSYQEAFKRYLGLDPLS-------AEKSELKELAEKKDLDNVAEEDEDRDTLLQLLFIEVVEPQIGKERPTFVYH 219 (330) T ss_pred CCCCEECHHHHHHHHHCCCCCC-------HHHHHHHHHHHHCCCHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEE T ss_conf 6300001899999984479873-------025789999985473233203444799999999876401037778757880 Q ss_pred CCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC-CCCCC Q ss_conf 68888641367877836330220223671225640210699999999999999997288853010189999861-88963 Q gi|254781066|r 241 YPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACLT-EMPQS 319 (355) Q Consensus 241 yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al~-G~PPh 319 (355) ||..+++||+..++|.++|+|||+|+.|+||||||+|++||.+|++||+.+++.|.+.+.+..++|++|+.|++ |||.| T Consensus 220 FP~~~aaLA~v~~eD~~~AERFE~y~KGiELANGf~E~t~a~E~r~R~E~~~~kR~~~~~P~~~~D~~~i~A~~~GMP~c 299 (330) T TIGR00462 220 FPERQAALAQVSTEDNRVAERFELYYKGIELANGFHELTDAEEQRKRFERDNKKRAKRELPTLPIDEDFIKALEDGMPDC 299 (330) T ss_pred CCHHHHHHHCCCCCCCCCCHHEEHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCC T ss_conf 70455555204513363200100100100002775322584889988768877788625898514599999985478741 Q ss_pred CEEECCHHHHHHHHHCCCCHHHHCCCCCCCC Q ss_conf 2453159999899815597131115856487 Q gi|254781066|r 320 SGIAMGFDRLVMLVTGANNINEVIWTPFSQS 350 (355) Q Consensus 320 gG~glGidRLvm~l~g~~~Irdvi~FP~~r~ 350 (355) +|++||||||+|+.+|++.|-+||.|-.++| T Consensus 300 sGvaLGiDRL~~l~Lg~E~l~~~~~~avD~a 330 (330) T TIGR00462 300 SGVALGIDRLVMLALGKEELVEVIAFAVDRA 330 (330) T ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHHHHCCC T ss_conf 4402557899998707326888998863159 No 20 >cd00777 AspRS_core Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. AspRS in this family differ from those found in the AsxRS family by a GAD insert in the core domain. Probab=100.00 E-value=0 Score=509.74 Aligned_cols=276 Identities=25% Similarity=0.315 Sum_probs=204.6 Q ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCEECC-CCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999879889847821056-898544541241024788678320000285899998987446889998 Q gi|254781066|r 22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYS-PGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCF 100 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqi 100 (355) |++||+|+++||+||+++||+||+||+|+++ ++| +.+|.+... .+.+..+||+||||+|||+||++|++||||| T Consensus 1 lr~Rs~i~~~iR~ff~~~gflEV~TPiL~~~~~eg---a~~f~~~~~--~~~~~~~~L~~Spel~~k~l~~~g~~rvf~i 75 (280) T cd00777 1 LRLRSRVIKAIRNFLDEQGFVEIETPILTKSTPEG---ARDFLVPSR--LHPGKFYALPQSPQLFKQLLMVSGFDRYFQI 75 (280) T ss_pred CCHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCC---CCCCEECCC--CCCCCCCCCCCCHHHHHHHHHHCCCCCCEEE T ss_conf 96699999999999998898998798106878776---766442441--6887603688798999999985687775798 Q ss_pred HHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCHHHHHHHHCCC Q ss_conf 86424567775448430020001157765787775578887766641883000223433246773207888865666087 Q gi|254781066|r 101 AHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPFSEPEYITVAEAFARYANI 180 (355) Q Consensus 101 g~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~e~~~~~~~~ 180 (355) |||||||+++++|+||||||||||+|+|++|+|+++|+||+++++.+.. .+...+|++++|.++++++ +. T Consensus 76 ~~~FR~E~~~~~h~~EFtmLE~e~~~~~~~d~m~~~E~li~~i~~~~~~---------~~~~~~~~rity~ea~~~~-g~ 145 (280) T cd00777 76 ARCFRDEDLRADRQPEFTQIDIEMSFVDQEDIMSLIEGLLKYVFKEVLG---------VELTTPFPRMTYAEAMERY-GF 145 (280) T ss_pred ECEECCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHC---------CCCCCCCCEEEHHHHHHHH-CC T ss_conf 4517478888766347762344226888999999999999999999819---------8779997577688999986-89 Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHH-CCCCCCCCCCC Q ss_conf 65323455562327999999997688778765347898766430036223767544325768888641-36787783633 Q gi|254781066|r 181 DLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESAL-ANIYPADPRFT 259 (355) Q Consensus 181 d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~pl-ak~~~~~~~va 259 (355) +.....+.+. ..+..... ..+.. ..| |. .|....+. ...++ +..++ T Consensus 146 ~~~~~~d~~~---------------------~~~~~~~~----~~~~~----~~p-f~--~p~~~~~~~~~~~p-~~~~~ 192 (280) T cd00777 146 KFLWIVDFPL---------------------FEWDEEEG----RLVSA----HHP-FT--APKEEDLDLLEKDP-EDARA 192 (280) T ss_pred CCCCCCCCCC---------------------CCCCHHHC----CCCCC----CCC-CC--CCCHHHHHHHHCCC-HHHHH T ss_conf 7331135753---------------------34624425----52222----077-34--78244167763380-24567 Q ss_pred CCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCC Q ss_conf 0220223671225640210699999999999999997288853-010189999861-88963245315999989981559 Q gi|254781066|r 260 KRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNET-YPIDEDFLACLT-EMPQSSGIAMGFDRLVMLVTGAN 337 (355) Q Consensus 260 ~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~-~~~D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~ 337 (355) +|||||++|+||||||+|++||++|++||+... .+.+. ..-+++||+|++ |+|||||||||||||||++||++ T Consensus 193 ~~fdl~~~G~El~nG~~r~~d~~~~~~~~~~~~-----~~~~~~~~~~~~~l~a~~~G~pP~~G~glGiDRLvm~l~g~~ 267 (280) T cd00777 193 QAYDLVLNGVELGGGSIRIHDPDIQEKVFEILG-----LSEEEAEEKFGFLLEAFKYGAPPHGGIALGLDRLVMLLTGSE 267 (280) T ss_pred HHHCCCCCCEEECCCCCEECCHHHHHHHHHHCC-----CCHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHCCC T ss_conf 774135686442353102279999999999859-----896677888999999976699987435158999999992898 Q ss_pred CHHHHCCCCCCCC Q ss_conf 7131115856487 Q gi|254781066|r 338 NINEVIWTPFSQS 350 (355) Q Consensus 338 ~Irdvi~FP~~r~ 350 (355) |||||||||+++. T Consensus 268 ~Irdvi~FPR~~n 280 (280) T cd00777 268 SIRDVIAFPKTQN 280 (280) T ss_pred CHHEEECCCCCCC T ss_conf 2870734799998 No 21 >COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=0 Score=506.62 Aligned_cols=288 Identities=24% Similarity=0.285 Sum_probs=230.7 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC-CCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999998798898478210568-985445412410247886783200002858999989874468899 Q gi|254781066|r 20 PFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP-GNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKIF 98 (355) Q Consensus 20 ~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~-~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rvy 98 (355) .++++||.+++++|+||.++||+||+||+|++++ +|+ ..+|.+ +|++.++||+||||||+ ++++++++||| T Consensus 132 Av~kirs~i~~a~~eff~~~gF~eV~tP~i~~~~~EGg--~elF~v-----~yf~~~a~LtqS~QLyk-e~~~~al~rVf 203 (435) T COG0017 132 AVFKIRSSILRAIREFFYENGFTEVHTPIITASATEGG--GELFKV-----DYFDKEAYLTQSPQLYK-EALAAALERVF 203 (435) T ss_pred HHHHHHHHHHHHHHHHHHHCCCEEECCCEEECCCCCCC--CEEEEE-----EECCCCEEEECCHHHHH-HHHHHHHCCEE T ss_conf 78949999999999999758958965946853478998--505777-----50685667714788999-99999857648 Q ss_pred HHHHHHCCCCCC-CCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCC---EECCC---CCCCCC--CCCCCCCC Q ss_conf 988642456777-5448430020001157765787775578887766641883---00022---343324--67732078 Q gi|254781066|r 99 CFAHAWRNGEQG-CLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQK---IFSFQ---NVNCNP--FSEPEYIT 169 (355) Q Consensus 99 qig~~FRaE~~~-~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~---~~~~~---~~~~~~--~~~~~~i~ 169 (355) +|||+||||+++ +|||+||||+|+||||+|++|+|+++|+||+++++.+... .+... +..... ..+|+|++ T Consensus 204 ~igP~FRAE~s~T~RHL~EF~~ld~Emaf~~~~d~m~l~E~~i~~i~~~v~e~~~~el~~l~~~~~~l~~~~~~pf~rit 283 (435) T COG0017 204 TIGPTFRAEKSNTRRHLSEFWMLDPEMAFADLNDVMDLAEELIKYLFKKVLEECADELEFLGRDNSELKRPESAPFPRIT 283 (435) T ss_pred EECCCEECCCCCCCCHHHHHHEECCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCEEE T ss_conf 95672554778970036667330211136768889999999999999999997189888761461110344468963777 Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHC Q ss_conf 88865666087653234555623279999999976887787653478987664300362237675443257688886413 Q gi|254781066|r 170 VAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESALA 249 (355) Q Consensus 170 ~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~pla 249 (355) |.||++-. .+.+.+. ..||+.+....+.++.++... +||||+|||++++||| T Consensus 284 Y~eAieiL------------------------~~~~~e~---~~~GdDl~~e~Er~l~e~~~~-~~vfv~~yP~~~kpFY 335 (435) T COG0017 284 YKEAIEIL------------------------EEKGFEK---VEWGDDLGTEHERYLGEEYFK-PPVFVTNYPKEIKPFY 335 (435) T ss_pred HHHHHHHH------------------------HHCCCCC---CCCCCCCCCHHHHHHHHHHCC-CCEEEEECCCCCCCCC T ss_conf 99999999------------------------8647765---677775688999999987579-9499981764446650 Q ss_pred C-CCCCCCCCCCCCEEEECC-EECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-CCCCCCCEEECCH Q ss_conf 6-787783633022022367-122564021069999999999999999728885301018999986-1889632453159 Q gi|254781066|r 250 N-IYPADPRFTKRFELYACN-IELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACL-TEMPQSSGIAMGF 326 (355) Q Consensus 250 k-~~~~~~~va~rfdl~i~G-~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al-~G~PPhgG~glGi 326 (355) + .++++|+++.+|||++.| .||++|+++++|.+.+.+|+ ++.|-++... +|||+++ +|+|||||||||+ T Consensus 336 m~~~~d~p~~~~~~Dll~p~~gEIigGsqRe~~~d~L~~ri------~~~gl~~e~~--~wYld~~kyG~~PHaGfGlG~ 407 (435) T COG0017 336 MRPDPDNPGTVASFDLLAPGGGEIIGGSQREHDYDLLVERI------KEKGLDPESY--EWYLDLRKYGMPPHAGFGLGL 407 (435) T ss_pred CCCCCCCCCEEEEEEEECCCCEEEECCEECCCCHHHHHHHH------HHCCCCHHHH--HHHHHHHHCCCCCCCCCCCCH T ss_conf 33379988769987652478705603623043099999999------9809996881--899999873899986003379 Q ss_pred HHHHHHHHCCCCHHHHCCCCCCCCC Q ss_conf 9998998155971311158564874 Q gi|254781066|r 327 DRLVMLVTGANNINEVIWTPFSQSN 351 (355) Q Consensus 327 dRLvm~l~g~~~Irdvi~FP~~r~~ 351 (355) |||+|++||++|||||||||+++.. T Consensus 408 ERlv~~i~gl~nIRea~pFPR~~~r 432 (435) T COG0017 408 ERLVMYILGLDNIREAIPFPRDPGR 432 (435) T ss_pred HHHHHHHHCCCCCEECCCCCCCCCC T ss_conf 9999999488832012447777787 No 22 >COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=0 Score=493.48 Aligned_cols=308 Identities=23% Similarity=0.304 Sum_probs=224.0 Q ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCEE-CCCCCCCCCCCEEEECCCCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999998798898478210-568985445412410247886783200-002858999989874468899 Q gi|254781066|r 21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQ-YSPGNETHIRAFSTELIIQDHIRKPLY-LQTSPEFSCKKLLAAGEEKIF 98 (355) Q Consensus 21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~-~~~~g~~~~~~f~t~~~~~~~~~~~~y-L~~SPql~lK~ll~~G~~rvy 98 (355) .++.||++.++||+||+++||+||+||+|+ ++|+| |+.|.|++..+.. +|| |+||||+|||.||++||+||| T Consensus 140 ~l~lR~kv~~~iR~~ld~~gF~EiETPiLtkSTPEG---ARDfLVPSRv~~G---~FYALPQSPQlfKQLLMvsGfdRYy 213 (585) T COG0173 140 NLKLRSKVTKAIRNFLDDQGFLEIETPILTKSTPEG---ARDFLVPSRVHPG---KFYALPQSPQLFKQLLMVAGFDRYY 213 (585) T ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCC---CCCCCCCCCCCCC---CEEECCCCHHHHHHHHHHHCCCCEE T ss_conf 999999999999997765498573467414679865---5443013455899---6530688879999999880533002 Q ss_pred HHHHHHCCCCC--CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCHHHHHHH Q ss_conf 98864245677--7544843002000115776578777557888776664188300022343324677320788886566 Q gi|254781066|r 99 CFAHAWRNGEQ--GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPFSEPEYITVAEAFAR 176 (355) Q Consensus 99 qig~~FRaE~~--~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~e~~~~ 176 (355) ||+||||||++ ||+ |||||||+||||+|.+|+|+++|+|++++++.+.. ++...+|++|+|.+|+.+ T Consensus 214 QIarCFRDEDlRaDRQ--PEFTQiD~EmSF~~~edv~~~~E~l~~~vf~~~~~---------i~l~~pFprmtY~eAm~~ 282 (585) T COG0173 214 QIARCFRDEDLRADRQ--PEFTQIDLEMSFVDEEDVMELIEKLLRYVFKEVKG---------IELKTPFPRMTYAEAMRR 282 (585) T ss_pred EEEEEECCCCCCCCCC--CCCEEEEEEEECCCHHHHHHHHHHHHHHHHHHHCC---------CCCCCCCCCCCHHHHHHH T ss_conf 3565404664444468--75336767764388999999999999999998509---------754898561059999997 Q ss_pred HCCCCCCCCCC--------------------------------CCC-----CCCHHHHHHHHHHCCCCCC------CCC- Q ss_conf 60876532345--------------------------------556-----2327999999997688778------765- Q gi|254781066|r 177 YANIDLGTTLD--------------------------------NPD-----QPDRHLLYLQAQQAGIRVA------HDD- 212 (355) Q Consensus 177 ~~~~d~~~~~~--------------------------------~~~-----~~~~~~~~~~~~~~~~~~~------~~~- 212 (355) |.......... .+. ......+...++..|.+.- .+. T Consensus 283 YGSDKPDlRf~lel~dvt~~~~~~~F~vF~~~~~~~~~v~ai~vp~~~~~sRk~id~~~~~ak~~gakGLa~ikv~~~~~ 362 (585) T COG0173 283 YGSDKPDLRFPLELIDVTDLFKDSEFKVFSNALANGGRVKAIVVPGGASLSRKQIDELTEFAKIYGAKGLAYIKVEEDGL 362 (585) T ss_pred HCCCCCCCCCCCEEHHHHHHHCCCCCCEEHHHHHCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEECCCC T ss_conf 38999855688352127987447885130314506982799984786646889999999999974987438999716876 Q ss_pred --CHH-----HHHHHHHH-----------------------------------CEECCCCCCCCCCCCCCCCHH------ Q ss_conf --347-----89876643-----------------------------------003622376754432576888------ Q gi|254781066|r 213 --TWS-----DIFSRILI-----------------------------------EKIEPNLGINCCTILDRYPAP------ 244 (355) Q Consensus 213 --~~~-----~~~~~l~~-----------------------------------~~ie~~l~~~~pvfi~~yP~~------ 244 (355) ... ..+..+.. ..+.+.. -.++||+|||.- T Consensus 363 ~gpi~kfl~e~~~~~l~~~~~~~~gD~iff~A~~~~~~~~~lGalR~~l~~~l~li~~~~--~~f~WVvDFPlfE~~ee~ 440 (585) T COG0173 363 KGPIAKFLSEEILEELIERLGAEDGDIIFFVADKKKVVNKALGALRLKLGKELGLIDKDQ--FKFLWVVDFPLFEWDEEE 440 (585) T ss_pred CCHHHHHCCHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCC--CEEEEEEECCCCCCCCCC T ss_conf 661776447899999999828777888999669488999988999999888738778343--248999706766775345 Q ss_pred ------HHHHCCCCCCCCC---------CCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCC-CCHHHHH Q ss_conf ------8641367877836---------33022022367122564021069999999999999999728885-3010189 Q gi|254781066|r 245 ------ESALANIYPADPR---------FTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNE-TYPIDED 308 (355) Q Consensus 245 ------~~plak~~~~~~~---------va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e-~~~~D~~ 308 (355) --||+++.+++.. .+..|||++||.||++|+.++|+|+.|...|+.- +.+.+ +..-=-. T Consensus 441 ~~~~a~HHPFT~P~~~~~~~l~~~p~~~~a~aYDlVlNG~ElggGSiRIh~~eiQ~~vF~~l-----g~~~eea~ekFGF 515 (585) T COG0173 441 GRYVAAHHPFTMPKPEDLELLEADPESVRARAYDLVLNGYELGGGSIRIHDPEIQEKVFEIL-----GISPEEAEEKFGF 515 (585) T ss_pred CCEECCCCCCCCCCCCCHHHHHCCHHHHHHHHCCEEECCEEECCCEEEECCHHHHHHHHHHC-----CCCHHHHHHHHHH T ss_conf 86740448878998442445416977764532567760275135436407889999999981-----9998999988778 Q ss_pred HHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCC Q ss_conf 99986-188963245315999989981559713111585648743 Q gi|254781066|r 309 FLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQ 352 (355) Q Consensus 309 fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~ 352 (355) +|+|| +|+|||||+|+|+|||||+|+|.+|||||||||.+...+ T Consensus 516 ll~Af~yGaPPHgGiA~GlDRlvmll~g~~sIReVIAFPKt~~a~ 560 (585) T COG0173 516 LLEAFKYGAPPHGGIAFGLDRLVMLLTGAESIRDVIAFPKTQQAA 560 (585) T ss_pred HHHHHHCCCCCCCCEECCHHHHHHHHCCCCCHHHEEECCCCCCCC T ss_conf 999976589997624245999999982897444213147886555 No 23 >TIGR00458 aspS_arch aspartyl-tRNA synthetase; InterPro: IPR004523 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Aspartyl tRNA synthetase 6.1.1.12 from EC is an alpha2 dimer that belongs to class IIb. Structural analysis combined with mutagenesis and enzymology data on the yeast enzyme point to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module . This family represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). ; GO: 0000166 nucleotide binding, 0004815 aspartate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006422 aspartyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=100.00 E-value=0 Score=469.12 Aligned_cols=295 Identities=22% Similarity=0.290 Sum_probs=239.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECC-CCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 8999999999999999999879889847821056-898544541241024788678320000285899998987446889 Q gi|254781066|r 19 RPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYS-PGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKI 97 (355) Q Consensus 19 R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rv 97 (355) ..++++|+++++++|+||.++||+||+||.|.++ .+|++ ++|...||.+++||.||||||||.||++||+|| T Consensus 152 ~AIF~I~~~~~~~vR~~L~~~~F~Ev~TPKlv~~~tEGGt-------~lF~i~YF~~~AfL~QSPQlyKQ~l~~~g~~rV 224 (466) T TIGR00458 152 QAIFRIRSEVLESVREFLAEEGFIEVHTPKLVASATEGGT-------ELFPITYFEREAFLGQSPQLYKQVLMAAGLERV 224 (466) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEECCCCCCC-------CCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCE T ss_conf 2125568999999999873088256307621421668885-------332012212300013570356687765265203 Q ss_pred HHHHHHHCCCCCCC-CCCCCEEEECEEECCCCH-HHHHHHHHHHHHHHHHHHCCC----------EECCCCCCC-CCCCC Q ss_conf 99886424567775-448430020001157765-787775578887766641883----------000223433-24677 Q gi|254781066|r 98 FCFAHAWRNGEQGC-LHQPEFTMLEWYRAHESY-EQLMKDCMNIIRCAAEVANQK----------IFSFQNVNC-NPFSE 164 (355) Q Consensus 98 yqig~~FRaE~~~~-rHlpEFtmLE~e~af~d~-~dlm~~~E~li~~~~~~~~~~----------~~~~~~~~~-~~~~~ 164 (355) |+|||+||||+++| ||+.|++.||+||||.|. +++|+..|+++..++..+... .+...+... .+..+ T Consensus 225 yEI~PiFRAE~~nT~RHl~E~~siDiE~~F~dhy~~v~d~L~~lv~~~~~dv~~~~~~e~el~r~~~~~~~~~le~P~~~ 304 (466) T TIGR00458 225 YEIGPIFRAEEHNTRRHLNEAISIDIEMAFEDHYEDVMDILEELVVRVFEDVAEKCAKEIELVRKELETLEVKLEVPEEK 304 (466) T ss_pred EEECCEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCC T ss_conf 55055220566652145544444224444275378999999999999999999887888999987521023132488875 Q ss_pred CCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCC-CCH Q ss_conf 3207888865666087653234555623279999999976887787653478987664300362237675443257-688 Q gi|254781066|r 165 PEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDR-YPA 243 (355) Q Consensus 165 ~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~-yP~ 243 (355) +.|++|.|++ ..+...|..+....+.+..-.+.+++.+.+.. +..+||++ ||. T Consensus 305 ~~Rl~Y~Ea~------------------------e~~~~~G~ei~~gEDLs~~a~K~~G~l~re~~--~g~yfI~d~wP~ 358 (466) T TIGR00458 305 FERLTYDEAI------------------------EIANAKGKEIKWGEDLSTEAEKALGKLVREEM--DGLYFITDKWPT 358 (466) T ss_pred CCCCCCHHHH------------------------HHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHH--CCCEEEEECCCC T ss_conf 5532207789------------------------99986597155546654357887647887742--761687405876 Q ss_pred HHHHHC-CCC-CCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-CCCCCCC Q ss_conf 886413-678-7783633022022367122564021069999999999999999728885301018999986-1889632 Q gi|254781066|r 244 PESALA-NIY-PADPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACL-TEMPQSS 320 (355) Q Consensus 244 ~~~pla-k~~-~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al-~G~PPhg 320 (355) +++||| |++ .++|..+++|||+.++.||.+|-+++|+.+.+.++ +|+.|-++.-+-=..||+|+ ||||||| T Consensus 359 ei~PFY~MPd~E~~P~~s~~fDl~~~~~Ei~SGA~RiH~~dlL~E~------iK~~Gl~P~dp~~~~Yl~aF~YG~PPHA 432 (466) T TIGR00458 359 EIRPFYTMPDDEDNPEISKSFDLMYRDLEISSGAQRIHLYDLLVEK------IKAKGLNPEDPGFKDYLEAFKYGMPPHA 432 (466) T ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHCCCHHCCHHHHHHHHHHHHHH------HHHCCCCCCCCCHHHHHHHCCCCCCCCC T ss_conf 4676213888656786001444333110110003454458888999------9845889885336878733047847888 Q ss_pred EEECCHHHHHHHHHCCCCHHHHCCCCCCCCCC Q ss_conf 45315999989981559713111585648743 Q gi|254781066|r 321 GIAMGFDRLVMLVTGANNINEVIWTPFSQSNQ 352 (355) Q Consensus 321 G~glGidRLvm~l~g~~~Irdvi~FP~~r~~~ 352 (355) |||||.||++|.+++++|||++++||++|.+. T Consensus 433 GwGlG~eR~~M~~~~lkNiR~~~LFPRDr~RL 464 (466) T TIGR00458 433 GWGLGAERLVMVLLGLKNIREAVLFPRDRKRL 464 (466) T ss_pred CCCCHHHHHHHHHHCCHHHHHHCCCCCCCCCC T ss_conf 76410678888774010112200488886568 No 24 >TIGR00499 lysS_bact lysyl-tRNA synthetase; InterPro: IPR002313 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and some eubacteria . Moreover in some eubacteria there is a gene X, which is similar to a part of lysyl-tRNA synthetase from class II. Lysyl-tRNA synthetase is duplicated in some species with, for example in E. coli, as a constitutive gene (lysS) and an induced one (lysU). No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. Lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. The refined crystal structures give "snapshots" of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding .; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=100.00 E-value=0 Score=447.54 Aligned_cols=345 Identities=31% Similarity=0.514 Sum_probs=298.0 Q ss_pred CCCCCCCCCC--CHHHCCCHHH-----------HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECC Q ss_conf 9988987478--8312615489-----------99999999999999999879889847821056898544541241024 Q gi|254781066|r 1 MHQIPSQPWW--NRDFHYRRRP-----------FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELI 67 (355) Q Consensus 1 ~~~~p~~~~~--~~~~~~r~R~-----------~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~ 67 (355) ++++|..+.+ +.+.++|+|. .++.|+++++++|.|++.+||+||+||++...+||+. ++||.|+ T Consensus 156 ~~~~p~~~~gl~d~e~~~~~~~~d~~~n~~~~~~~~~~~~~~~~~~~~~~~~g~~e~e~p~~~~~~gg~~-~~pf~~~-- 232 (538) T TIGR00499 156 LRPLPDKWHGLTDQETRYRQRYLDLIVNPDSRDTFLKRSKIIAAIRRFLDDRGFLEVETPLLQVIPGGAN-ARPFITH-- 232 (538) T ss_pred HHCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCHHHCCCCCCC-CCCCEEC-- T ss_conf 4226510046651567777655433105024667788999999999987624842211310101267654-4650100-- Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 78867832000028589999898744688999886424567775448430020001157765787775578887766641 Q gi|254781066|r 68 IQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA 147 (355) Q Consensus 68 ~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~ 147 (355) ++.++.++||+++||+|+|+|+++|+++||++|+.||+|+.+.+|+||||++|+|++|+|++++|+.+|.+++.+++.+ T Consensus 233 -~n~~~~~~~~~~~~e~~l~~l~~gg~~~~~e~g~~f~neg~~~~hnpef~~~e~y~~~~~~~~~~~~~~~l~~~~~~~~ 311 (538) T TIGR00499 233 -HNALDLDLYLRIAPELYLKRLVVGGLEKVYEIGRNFRNEGVDTTHNPEFTSLEFYQAYADYEDLLDLTENLFKFLAKEL 311 (538) T ss_pred -CCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf -2322442121122577887776401367787643331046654457530245567765108899998999999999875 Q ss_pred C-CCEE------------CCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCC---CC-CC Q ss_conf 8-8300------------022343324677320788886566608765323455562327999999997688---77-87 Q gi|254781066|r 148 N-QKIF------------SFQNVNCNPFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGI---RV-AH 210 (355) Q Consensus 148 ~-~~~~------------~~~~~~~~~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~ 210 (355) . ...+ .+.....+...+|+++++.+++.++........ .....+.......+.+.+. .. .. T Consensus 312 ~~~~~~~~~p~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~ 389 (538) T TIGR00499 312 LGTTKITRLPVPKTFPELTYGDLELDLKKPWKRITMLDALKKYDLLETGID--FDDLKDDETAKALAKELGIKYFEVAED 389 (538) T ss_pred HHHHHEEECCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCC--CHHCCHHHHHHHHHHHHHHHHHCCCCC T ss_conf 321100112566543112203210023554002245677765200004654--001002578888888754332022345 Q ss_pred C--CCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHH Q ss_conf 6--53478987664300362237675443257688886413678778363302202236712256402106999999999 Q gi|254781066|r 211 D--DTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNIELCNACDELLDPIEQRHRF 288 (355) Q Consensus 211 ~--~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf 288 (355) . +..+.++..++++.++.++....|+|+++||..++|+++.++.+|++++||++|++|.|++|||+|++||..|++|| T Consensus 390 ~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~p~~~~pl~~~~~~~p~~~~~fe~f~~g~e~~n~~~e~~~p~~~~~~~ 469 (538) T TIGR00499 390 SGPLTLGHILNELFEEFLEHTLIQTLPTFITGYPAEISPLAKRNPSNPELTDRFELFIGGKEIANAFSELNDPLDQRERF 469 (538) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCHHCCCCCCCCHHHHHHHEECCHHHHCCHHHHCCHHHHHHHH T ss_conf 77420688999988887755666532143404641222100057777530111110010112201012204627889999 Q ss_pred HHHHHHHHCC----CCCCCHHHHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCC Q ss_conf 9999999728----8853010189999861-8896324531599998998155971311158564874 Q gi|254781066|r 289 EKEMQEKKKI----YNETYPIDEDFLACLT-EMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSN 351 (355) Q Consensus 289 ~~q~~~k~~~----~~e~~~~D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~ 351 (355) +.|...++.+ ++++..+|++|+.|++ |+||.||+|+|+|||+|++|++++||||++||.+|+. T Consensus 470 ~~~~~~~~~gg~~~~~~~~~~d~~~~~~l~~g~pp~~g~g~g~d~l~~l~~~~~~~~~~~~fp~~~~~ 537 (538) T TIGR00499 470 EAQLAEKEAGGNKTDDEAPLLDEDFVEALEYGLPPTGGLGIGIDRLVMLLTDSPSIRDVLLFPALRPD 537 (538) T ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHCCCCCCC T ss_conf 99888875067754103444336788888716886565443277787766167510133202531357 No 25 >KOG2411 consensus Probab=100.00 E-value=0 Score=439.15 Aligned_cols=313 Identities=23% Similarity=0.347 Sum_probs=224.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHC-CCEEEECCCE-ECCCCCCCCCCCEEEECCCCCCCCCCCC-CCCCHHHHHHHHHHHHHH Q ss_conf 899999999999999999987-9889847821-0568985445412410247886783200-002858999989874468 Q gi|254781066|r 19 RPFLLKRNMIQSSLREYFVEN-QFIEIDSMSL-QYSPGNETHIRAFSTELIIQDHIRKPLY-LQTSPEFSCKKLLAAGEE 95 (355) Q Consensus 19 R~~l~~Rs~i~~~iR~ff~~~-gF~EV~TPiL-~~~~~g~~~~~~f~t~~~~~~~~~~~~y-L~~SPql~lK~ll~~G~~ 95 (355) +..++.||.+...||+||.++ ||+||+||.| ..+||| |+.|.|+....+ ..|| |+||||+|+|.||++|++ T Consensus 175 q~nLrlRS~~v~~iR~yl~n~~GFvevETPtLFkrTPgG---A~EFvVPtr~~~---g~FYaLpQSPQQfKQlLMvsGid 248 (628) T KOG2411 175 QNNLRLRSNVVKKIRRYLNNRHGFVEVETPTLFKRTPGG---AREFVVPTRTPR---GKFYALPQSPQQFKQLLMVSGID 248 (628) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCEEECCCCCHHCCCCCC---CCEEECCCCCCC---CCEEECCCCHHHHHHHHHHHCHH T ss_conf 878999999999999998610473551572020148886---412322367898---85553688989999999872303 Q ss_pred HHHHHHHHHCCCCC--CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCHHHH Q ss_conf 89998864245677--7544843002000115776578777557888776664188300022343324677320788886 Q gi|254781066|r 96 KIFCFAHAWRNGEQ--GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPFSEPEYITVAEA 173 (355) Q Consensus 96 rvyqig~~FRaE~~--~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~e~ 173 (355) ||||||+|||+|++ ||+ |||||+|+||||+|.+|+|+++|+++++++..... +..-.+|++|||.+| T Consensus 249 rYyQiARCfRDEdlR~DRQ--PEFTQvD~EMsF~~~~dim~liEdll~~~ws~~k~---------~~l~~PF~riTY~~A 317 (628) T KOG2411 249 RYYQIARCFRDEDLRADRQ--PEFTQVDMEMSFTDQEDIMKLIEDLLRYVWSEDKG---------IQLPVPFPRITYADA 317 (628) T ss_pred HHHHHHHHHCCCCCCCCCC--CCCEEEEEEEECCCHHHHHHHHHHHHHHHCHHHCC---------CCCCCCCCCCCHHHH T ss_conf 6776776641345676568--76435444785367787899999999973624219---------988888664239999 Q ss_pred HHHHCCCCCCCCCCCCCC---------------------------------C---CHHHHHHHHHHC---CC----CCCC Q ss_conf 566608765323455562---------------------------------3---279999999976---88----7787 Q gi|254781066|r 174 FARYANIDLGTTLDNPDQ---------------------------------P---DRHLLYLQAQQA---GI----RVAH 210 (355) Q Consensus 174 ~~~~~~~d~~~~~~~~~~---------------------------------~---~~~~~~~~~~~~---~~----~~~~ 210 (355) +.+|.............. . ..........+. +. .... T Consensus 318 m~~YG~DKPD~Rf~l~l~dv~~~~~~~~~~~~~~d~l~~~~~vv~~~~~~~~s~~~~rk~~e~~~~~~~~~~~f~~~~~~ 397 (628) T KOG2411 318 MDKYGSDKPDTRFPLKLKDVSESISKSFEEALLSDGLISVEIVVLGAKKYSNSNYKKRKIYESLGKSGFVGLPFPIEHDA 397 (628) T ss_pred HHHHCCCCCCCCCCCEECCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCC T ss_conf 99738999866577673226776566555554148854058999514344412567767999875434666300153262 Q ss_pred CCCHHHHHHHHHHCEE--------------------CC---------------------CC---CCCCCCCCCCCCHHH- Q ss_conf 6534789876643003--------------------62---------------------23---767544325768888- Q gi|254781066|r 211 DDTWSDIFSRILIEKI--------------------EP---------------------NL---GINCCTILDRYPAPE- 245 (355) Q Consensus 211 ~~~~~~~~~~l~~~~i--------------------e~---------------------~l---~~~~pvfi~~yP~~~- 245 (355) ...|-+.+..+..+.+ .+ ++ ......||+|||.-. T Consensus 398 ~~~w~~~~~~l~~e~~~~el~~~~~l~~~Div~~~~g~~~~~~~~LgrlRL~l~~l~~~~l~d~~~~~~lWVvDFPLF~p 477 (628) T KOG2411 398 NKNWFKKFSSLTDEAVAIELIKQLGLAEGDIVLLCVGPKVSVNTPLGRLRLVLQDLLVKNLRDKSKFSFLWVVDFPLFSP 477 (628) T ss_pred HHHHHHHCHHHCCCHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCC T ss_conf 01154413242242378999998588878889993268766777237789999998751643666534899983355676 Q ss_pred ------------HHHCCCCCCCCC---------CCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCH Q ss_conf ------------641367877836---------33022022367122564021069999999999999999728885301 Q gi|254781066|r 246 ------------SALANIYPADPR---------FTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYP 304 (355) Q Consensus 246 ------------~plak~~~~~~~---------va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~ 304 (355) -||+.++++|-. ....|||++||+||++|+.+++||+.|+..++.-. |.- +.+. T Consensus 478 ~~E~~q~L~StHHPFTaP~~~Di~~L~s~p~~~rgqhYDlV~NGvElGGGSiRIhn~diQr~vLe~iL--k~p---~~~~ 552 (628) T KOG2411 478 WEEKNQRLESTHHPFTAPHPKDIDLLESAPEKIRGQHYDLVVNGVELGGGSIRIHNPDIQRYVLEDIL--KIP---EDAE 552 (628) T ss_pred CCCCCCEECCCCCCCCCCCHHHHHHHHCCCHHHHCCEEEEEECCEEECCCEEEECCHHHHHHHHHHHH--CCC---HHHH T ss_conf 56677530002588778885566676518166524300167714762473467528889999999985--596---6666 Q ss_pred HHHHHHHHHC-CCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCCCCCCC Q ss_conf 0189999861-889632453159999899815597131115856487433 Q gi|254781066|r 305 IDEDFLACLT-EMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFSQSNQE 353 (355) Q Consensus 305 ~D~~fl~al~-G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~r~~~~ 353 (355) .-..+|+||. |+|||||||+|+|||||++||..|||||||||.+...++ T Consensus 553 s~gHLL~ALd~GaPPHGGiAlGlDRlvaml~~a~sIRDVIAFPKt~~G~D 602 (628) T KOG2411 553 SKGHLLNALDMGAPPHGGIALGLDRLVAMLTGAPSIRDVIAFPKTTTGAD 602 (628) T ss_pred HHHHHHHHHHCCCCCCCCEEECHHHHHHHHCCCCCHHEEEECCCCCCCCC T ss_conf 67789988626999987444127889999808975222564466577543 No 26 >KOG0554 consensus Probab=100.00 E-value=0 Score=430.09 Aligned_cols=294 Identities=20% Similarity=0.246 Sum_probs=229.9 Q ss_pred HCCCHHH-----HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC-CCCCCCCCEEEEC---CCCCCCCCCCCCCCCHHH Q ss_conf 2615489-----999999999999999998798898478210568-9854454124102---478867832000028589 Q gi|254781066|r 14 FHYRRRP-----FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP-GNETHIRAFSTEL---IIQDHIRKPLYLQTSPEF 84 (355) Q Consensus 14 ~~~r~R~-----~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~-~g~~~~~~f~t~~---~~~~~~~~~~yL~~SPql 84 (355) .|+|.|+ ++|.||.+..++|.||++++|++|+||||+++. +|+ -+.|.|.. ...+++++++||++|.|| T Consensus 119 ~HLR~Rt~~~~av~RvRs~~~~a~h~ffq~~~F~~i~tPiiTtnDCEGa--GE~F~Vtt~~d~~~~fFgrp~fLTVSgQL 196 (446) T KOG0554 119 LHLRSRTAKVGAVLRVRSALAFATHSFFQSHDFTYINTPIITTNDCEGA--GEVFQVTTLTDYSKDFFGRPAFLTVSGQL 196 (446) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCEEECCCCCCC--CCEEEEEECCCCCCCCCCCCEEEEEECEE T ss_conf 3321002578999999989999999999875946733867634577787--40589874686543314885079971321 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCCCEEEECEEECCCC-HHHHHHHHHHHHHHHHHHHCCCE---ECCCCCCC Q ss_conf 9998987446889998864245677-7544843002000115776-57877755788877666418830---00223433 Q gi|254781066|r 85 SCKKLLAAGEEKIFCFAHAWRNGEQ-GCLHQPEFTMLEWYRAHES-YEQLMKDCMNIIRCAAEVANQKI---FSFQNVNC 159 (355) Q Consensus 85 ~lK~ll~~G~~rvyqig~~FRaE~~-~~rHlpEFtmLE~e~af~d-~~dlm~~~E~li~~~~~~~~~~~---~~~~~~~~ 159 (355) ++ ..|++++.|||++||+||||++ ++|||+||||+|.|+||++ ++|+|..+|.+++++++.+.+.- .+...... T Consensus 197 hl-Ea~a~aLsrvyt~gP~FRAE~s~t~rHLaEFwmlE~E~af~~sl~d~~~~~e~~~k~m~k~~le~~~Edm~l~~~~~ 275 (446) T KOG0554 197 HL-EAMACALSRVYTFGPTFRAENSHTSRHLAEFWMLEAELAFAESLDDLMSCAEAYIKHMIKYLLEKCIEDMELMHKNE 275 (446) T ss_pred HH-HHHHHHHCCEEEECCCEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHEEECCCC T ss_conf 59-98875523237616613226787546776565242788788888888899999999999999860511010100114 Q ss_pred CC----------CCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCC-CCCCCCCCHHHHHHHHHHCEECC Q ss_conf 24----------67732078888656660876532345556232799999999768-87787653478987664300362 Q gi|254781066|r 160 NP----------FSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAG-IRVAHDDTWSDIFSRILIEKIEP 228 (355) Q Consensus 160 ~~----------~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~ie~ 228 (355) +. ..+|.+++|.+|+.. .++.. .++.....||..+...++.++.+ T Consensus 276 ~~~~~~rl~~~~~~~~~~itYteAie~------------------------L~~a~t~~fk~~~kwG~~lstehe~yL~~ 331 (446) T KOG0554 276 DPGSIDRLELVAKENLLRITYTEAIEL------------------------LQKAVTKKFKTPPKWGIDLSTEHEKYLVE 331 (446) T ss_pred CCCCCCHHHHHHHHHHHHEEHHHHHHH------------------------HHHHCCCCCCCCCCCCCCCCHHHHHHHHH T ss_conf 777531577720102332028999999------------------------99840244356720154400456878999 Q ss_pred CCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCEEEECCE-ECCCCCHHCCCHHHHHHHHHHHHHHHHCC-CCCCCHHH Q ss_conf 23767544325768888641367877836330220223671-22564021069999999999999999728-88530101 Q gi|254781066|r 229 NLGINCCTILDRYPAPESALANIYPADPRFTKRFELYACNI-ELCNACDELLDPIEQRHRFEKEMQEKKKI-YNETYPID 306 (355) Q Consensus 229 ~l~~~~pvfi~~yP~~~~plak~~~~~~~va~rfdl~i~G~-El~ng~~El~d~~~q~~rf~~q~~~k~~~-~~e~~~~D 306 (355) .+. +.||||+|||+.++||||..++++..+.+|||+|.|+ ||++|+.++-++ .++++.+ ..+.. T Consensus 332 ~~~-~~PVfV~dYP~~iKpFYMr~n~~~~tVaa~DlLVP~vGELiGGSlREe~~----------~~l~e~g~~~~~~--- 397 (446) T KOG0554 332 ECF-KKPVFVTDYPKGIKPFYMRLNDDGKTVAAFDLLVPGVGELIGGSLREERK----------ARLKERGLTREEL--- 397 (446) T ss_pred HHC-CCCEEEEECCCCCCCEEEEECCCCCEEEEEEEECCCCHHHCCCCCCHHHH----------HHHHHCCCCCCCC--- T ss_conf 856-89779970644466448885599972689986136631122765312358----------9998659995121--- Q ss_pred HHHHHHH-CCCCCCCEEECCHHHHHHHHHCCCCHHHHCCCCCC Q ss_conf 8999986-18896324531599998998155971311158564 Q gi|254781066|r 307 EDFLACL-TEMPQSSGIAMGFDRLVMLVTGANNINEVIWTPFS 348 (355) Q Consensus 307 ~~fl~al-~G~PPhgG~glGidRLvm~l~g~~~Irdvi~FP~~ 348 (355) +|||+-. +|.+|||||||||||++.+++|.+|||||||||+. T Consensus 398 eWYldLRryG~vphgGFGlGfERmlq~~tG~~nIkd~IPFpR~ 440 (446) T KOG0554 398 EWYLDLRRYGSVPHGGFGLGFERMLQYLTGNDNIKDVIPFPRY 440 (446) T ss_pred CEEHHHHHCCCCCCCCCCCCHHHHHHHHHCCCCHHHCEECCCC T ss_conf 0001155438999873140599999998577654220005788 No 27 >KOG0556 consensus Probab=100.00 E-value=0 Score=414.98 Aligned_cols=297 Identities=19% Similarity=0.298 Sum_probs=235.8 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCEEEECCCEECC-CCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999879889847821056-8985445412410247886783200002858999989874468899 Q gi|254781066|r 20 PFLLKRNMIQSSLREYFVENQFIEIDSMSLQYS-PGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKIF 98 (355) Q Consensus 20 ~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rvy 98 (355) .++++.+.+..+.|+||..+||+||+||.|.++ .+| ++..|.+. |+++++||.||||||+|++++++|+||| T Consensus 226 AiFriq~gvc~~FRe~L~~kgF~EIhTpKli~asSEG--GanvF~v~-----Yfk~~A~LAQSPQLyKQMaI~gdf~rVy 298 (533) T KOG0556 226 AIFRIQAGVCFAFREYLRSKGFVEIHTPKLIGASSEG--GANVFRVS-----YFKQKAYLAQSPQLYKQMAICGDFERVY 298 (533) T ss_pred HEEEHHHHHHHHHHHHHHHCCCCEECCCCCCCCCCCC--CCEEEEEE-----ECCCCCHHHCCHHHHHHHHHHCCHHHEE T ss_conf 1000688899999999975686043263201466777--72268998-----6067503205858887788760611046 Q ss_pred HHHHHHCCCCCCC-CCCCCEEEECEEECCC-CHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCHHHHHH- Q ss_conf 9886424567775-4484300200011577-657877755788877666418830002234332467732078888656- Q gi|254781066|r 99 CFAHAWRNGEQGC-LHQPEFTMLEWYRAHE-SYEQLMKDCMNIIRCAAEVANQKIFSFQNVNCNPFSEPEYITVAEAFA- 175 (355) Q Consensus 99 qig~~FRaE~~~~-rHlpEFtmLE~e~af~-d~~dlm~~~E~li~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~e~~~- 175 (355) +|||+||||++++ ||++||+-||+||+|- +|+++|+.+.+++-++++.+....-.. .+++. T Consensus 299 eIGpVfRAEdSnthRhltEFvGLD~EMaf~~hYhEVm~~i~~lfv~IF~~l~ery~~E----------------ie~Vr~ 362 (533) T KOG0556 299 EIGPVFRAEDSNTHRHLTEFVGLDLEMAFNEHYHEVMDTIGELFVFIFKGLRERYAKE----------------IETVRK 362 (533) T ss_pred EECCEEECCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------HHHHHH T ss_conf 5235566044641666677617422547777799999999999999998788888999----------------999861 Q ss_pred HHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHC-CCCCC Q ss_conf 66087653234555623279999999976887787653478987664300362237675443257688886413-67877 Q gi|254781066|r 176 RYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESALA-NIYPA 254 (355) Q Consensus 176 ~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~pla-k~~~~ 254 (355) +|...++ .....+............++.|++.+...+....-++.++..|.++++.+ ..++..||.+++||| |++++ T Consensus 363 qyp~e~f-kf~~~~lrl~~~e~v~mLreaGvE~g~~dDlsTe~Ek~LG~lV~eky~td-fyildkyP~avRPFYTmpd~~ 440 (533) T KOG0556 363 QYPFEPF-KFLEPPLRLTFKEGVAMLREAGVEMGDEDDLSTESEKKLGQLVREKYDTD-FYILDKYPLAVRPFYTMPDPE 440 (533) T ss_pred CCCCCCC-CCCCCCEEEEHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC-EEEECCCCCCCCCCCCCCCCC T ss_conf 0888633-35787557655889999997286358722358865889999999871784-799714754446643367888 Q ss_pred CCCCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-CCCCCCCEEECCHHHHHHHH Q ss_conf 83633022022367122564021069999999999999999728885301018999986-18896324531599998998 Q gi|254781066|r 255 DPRFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACL-TEMPQSSGIAMGFDRLVMLV 333 (355) Q Consensus 255 ~~~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al-~G~PPhgG~glGidRLvm~l 333 (355) ||.++++||+|++|.||.+|-++++||+.+.+|. ++-|-+. ..+ ..|++++ +|+|||||+|+|+||++|+. T Consensus 441 ~p~ySnSyD~fmRGeEIlSGAQRIhdpe~L~era------~~hGid~-~~i-~~YidsFryG~PPHaGgGIGLERvvmly 512 (533) T KOG0556 441 NPRYSNSYDFFMRGEEILSGAQRIHDPELLVERA------KEHGIDP-SKI-STYIDSFRYGAPPHAGGGIGLERVVMLY 512 (533) T ss_pred CCCCCCCHHHEECHHHHHCCCCCCCCHHHHHHHH------HHCCCCH-HHH-HHHHHHHCCCCCCCCCCCCCHHHHHHHH T ss_conf 8773441432234666634430037889999999------9739887-899-9888874058998778751599999998 Q ss_pred HCCCCHHHHCCCCCCC Q ss_conf 1559713111585648 Q gi|254781066|r 334 TGANNINEVIWTPFSQ 349 (355) Q Consensus 334 ~g~~~Irdvi~FP~~r 349 (355) +|++|||-+.+||++- T Consensus 513 l~L~nIR~~SlFPRDP 528 (533) T KOG0556 513 LGLNNIRKTSLFPRDP 528 (533) T ss_pred HCCCCCHHHCCCCCCC T ss_conf 1677500102578882 No 28 >KOG0555 consensus Probab=100.00 E-value=0 Score=346.07 Aligned_cols=287 Identities=17% Similarity=0.263 Sum_probs=223.6 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCEEEECCCEEC--CCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999987988984782105--6898544541241024788678320000285899998987446889 Q gi|254781066|r 20 PFLLKRNMIQSSLREYFVENQFIEIDSMSLQY--SPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKI 97 (355) Q Consensus 20 ~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~--~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rv 97 (355) .+++.|+.+.+++|++|.++|++||.+|+|.. ..||.+ +|..||+++++||+||.|||+..++++ +++| T Consensus 241 ~vLK~Ra~~lr~~Rd~y~~~~ytEVtPPtmVQTQVEGGsT--------LFkldYyGEeAyLTQSSQLYLEtclpA-lgdv 311 (545) T KOG0555 241 KVLKARAALLRAMRDHYFERGYTEVTPPTMVQTQVEGGST--------LFKLDYYGEEAYLTQSSQLYLETCLPA-LGDV 311 (545) T ss_pred HHHHHHHHHHHHHHHHHHHCCCEECCCCCEEEEEECCCCE--------EEEECCCCCHHHCCCHHHHHHHHHHHH-CCCE T ss_conf 9999999999999988874484245797157887517604--------873113574033022358889876552-0762 Q ss_pred HHHHHHHCCCC-CCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCEECC-----CCCCCCCCCCCCCCCHH Q ss_conf 99886424567-7754484300200011577657877755788877666418830002-----23433246773207888 Q gi|254781066|r 98 FCFAHAWRNGE-QGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKIFSF-----QNVNCNPFSEPEYITVA 171 (355) Q Consensus 98 yqig~~FRaE~-~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~~~~-----~~~~~~~~~~~~~i~~~ 171 (355) |+|.++||||. .+||||+|||++|+|++|.+++++|+.+|++|...++.+....+.. +..-..+..||.|++|. T Consensus 312 y~I~~SyRAEkSrTRRHLsEytHVEaE~afltfd~ll~~iE~lvc~~vdr~l~dp~~~li~~lnP~f~~P~~PFkRm~Y~ 391 (545) T KOG0555 312 YCIQQSYRAEKSRTRRHLSEYTHVEAECAFLTFDDLLDRIEALVCDSVDRLLEDPIAPLIKQLNPDFKAPKRPFKRMNYS 391 (545) T ss_pred EEECHHHHHHHHHHHHHHHHHEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCCCCCCCHHCCCHH T ss_conf 67327566556666665533111023246364889999999999999999986701566887498988888812107889 Q ss_pred HHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHHHCCC Q ss_conf 86566608765323455562327999999997688778765347898766430036223767544325768888641367 Q gi|254781066|r 172 EAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESALANI 251 (355) Q Consensus 172 e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~plak~ 251 (355) +|++-....++. ++.|-+...+++..+.-++.+.+ .. +.|+|+++||.++++|||. T Consensus 392 dAI~wLke~~vk------------------~edg~~fefGdDI~eAaER~mtd----tI--g~PIfLtrFpveiKsFYM~ 447 (545) T KOG0555 392 DAIEWLKEHDVK------------------KEDGTDFEFGDDIPEAAERKMTD----TI--GVPIFLTRFPVEIKSFYMK 447 (545) T ss_pred HHHHHHHHCCCC------------------CCCCCCCCCCCCHHHHHHHHHHH----HC--CCCEEEEECCCCCCCEEEE T ss_conf 999999863976------------------76676020466425678876555----22--8814786333334451331 Q ss_pred -CCCCCCCCCCCEEEECCE-ECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-CCCCCCCEEECCHHH Q ss_conf -877836330220223671-22564021069999999999999999728885301018999986-188963245315999 Q gi|254781066|r 252 -YPADPRFTKRFELYACNI-ELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACL-TEMPQSSGIAMGFDR 328 (355) Q Consensus 252 -~~~~~~va~rfdl~i~G~-El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al-~G~PPhgG~glGidR 328 (355) ..+|++++++.|+.+.|+ ||++|+-++-|.++...-| .|++.+...+ .||++.. +|..||||+|||+|| T Consensus 448 rc~dd~~lTESvD~LmPnVGEIvGGSMRi~d~eeLlagf-----kRegId~~pY---YWy~DqrkyGt~pHGGyGLGlER 519 (545) T KOG0555 448 RCEDDPRLTESVDVLMPNVGEIVGGSMRIDDSEELLAGF-----KREGIDPDPY---YWYTDQRKYGTCPHGGYGLGLER 519 (545) T ss_pred CCCCCCCCCEEEEEECCCCCCCCCCEEEECCHHHHHHHH-----HHCCCCCCCC---EEEEECCCCCCCCCCCCCCCHHH T ss_conf 166765543001111478610036604516599999888-----6558998870---47740100266898851314999 Q ss_pred HHHHHHCCCCHHHHCCCCC Q ss_conf 9899815597131115856 Q gi|254781066|r 329 LVMLVTGANNINEVIWTPF 347 (355) Q Consensus 329 Lvm~l~g~~~Irdvi~FP~ 347 (355) ++||||+..+||||-+||+ T Consensus 520 fL~wL~~r~~vre~cLyPR 538 (545) T KOG0555 520 FLAWLCDRYHVREVCLYPR 538 (545) T ss_pred HHHHHHCCCCHHHEEECCH T ss_conf 9998722231523121231 No 29 >cd00496 PheRS_alpha_core Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer. Probab=99.57 E-value=2.8e-14 Score=104.01 Aligned_cols=112 Identities=24% Similarity=0.381 Sum_probs=69.3 Q ss_pred HHHHHHHHHHHHHCCCEEEECCCEECCCCC-CC------C-CCCEEEECCCCCCCCCC--CCC--CCCHHHHHHHHHHH- Q ss_conf 999999999999879889847821056898-54------4-54124102478867832--000--02858999989874- Q gi|254781066|r 26 NMIQSSLREYFVENQFIEIDSMSLQYSPGN-ET------H-IRAFSTELIIQDHIRKP--LYL--QTSPEFSCKKLLAA- 92 (355) Q Consensus 26 s~i~~~iR~ff~~~gF~EV~TPiL~~~~~g-~~------~-~~~f~t~~~~~~~~~~~--~yL--~~SPql~lK~ll~~- 92 (355) ++++..|+++|.+.||.+++.|.+.+.--. ++ | ++... +.+ |.+.+ .-| +|||=.. +.|.. T Consensus 4 ~~~~~~i~~~f~~~GF~~~~gp~ie~~~~NFD~Ln~P~dHPaR~~~-DTf---y~~~~~~~lLRtHTS~~q~--r~l~~~ 77 (218) T cd00496 4 NKVIEEIEDIFVSMGFTEVEGPEVETDFYNFDALNIPQDHPARDMQ-DTF---YINDPARLLLRTHTSAVQA--RALAKL 77 (218) T ss_pred HHHHHHHHHHHHHCCCEEECCCCCCCCHHHHHHHCCCCCCCCCCCC-CEE---EECCCCCCEECCCCCHHHH--HHHHHC T ss_conf 8999999999987798682289512310304533859887553724-327---8637766021578756679--999745 Q ss_pred -HHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCC--CHHHHHHHHHHHHHHH Q ss_conf -46889998864245677754484300200011577--6578777557888776 Q gi|254781066|r 93 -GEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHE--SYEQLMKDCMNIIRCA 143 (355) Q Consensus 93 -G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~--d~~dlm~~~E~li~~~ 143 (355) .--|++.+|+|||+|..|.+|.|+|.|+|.-..+- +..++...++.+++.+ T Consensus 78 ~~p~~~~~~G~VyR~D~iDatH~~~FhQ~Eg~~v~~~~~~~~Lk~~l~~~~~~l 131 (218) T cd00496 78 KPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGLTFADLKGTLEEFAKEL 131 (218) T ss_pred CCCCEEEECCCEEECCCCCCCCCCEEEEEEEEEEECCCCHHHHHHHHHHHHHHH T ss_conf 898179942504653889843153125763799956511999999999999997 No 30 >pfam01409 tRNA-synt_2d tRNA synthetases class II core domain (F). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only phenylalanyl-tRNA synthetases. This is the core catalytic domain. Probab=99.52 E-value=1.8e-13 Score=99.26 Aligned_cols=114 Identities=22% Similarity=0.358 Sum_probs=67.7 Q ss_pred HHHHHHHHHHHHHCCCEEEECCCEECC---------CCCCCCCCCEE-EECCCCCCCCCCCCC--CCCHHHHHHHHHHHH Q ss_conf 999999999999879889847821056---------89854454124-102478867832000--028589999898744 Q gi|254781066|r 26 NMIQSSLREYFVENQFIEIDSMSLQYS---------PGNETHIRAFS-TELIIQDHIRKPLYL--QTSPEFSCKKLLAAG 93 (355) Q Consensus 26 s~i~~~iR~ff~~~gF~EV~TPiL~~~---------~~g~~~~~~f~-t~~~~~~~~~~~~yL--~~SPql~lK~ll~~G 93 (355) ++++..|+++|.+.||.+++.|.+.+. |..-+ |+... |-+......++..-| ++|+=.. +.|... T Consensus 20 ~~~~~~i~~~f~~~GF~~~~g~eves~~~NFDaLn~P~dHP-aR~~~DTfy~~~~~~~~~~vLRtHTS~~q~--r~l~~~ 96 (243) T pfam01409 20 TRVLEEIRDIFLSMGFEEVEGPEVESDFYNFDALNIPQDHP-ARDMQDTFYLKKPLKARRLLLRTHTTPVQA--RTLAEK 96 (243) T ss_pred HHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHCCCCCCC-CCCCCCEEEECCCCCCCCEEECCCCCHHHH--HHHHHC T ss_conf 99999999999877986876983564277777557898898-767676034336666768657687988999--999742 Q ss_pred HH---HHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCHHHHHHHHHHHHHH Q ss_conf 68---8999886424567775448430020001157--7657877755788877 Q gi|254781066|r 94 EE---KIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESYEQLMKDCMNIIRC 142 (355) Q Consensus 94 ~~---rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~~dlm~~~E~li~~ 142 (355) -+ |++.+|+|||+|..|.+|+|+|.|+|.-... +++.+++..++.+++. T Consensus 97 ~~~p~r~~~~grvyR~d~~DatH~~~FhQ~Eg~vvd~~it~~~Lk~~l~~~~~~ 150 (243) T pfam01409 97 NKPPIKIFSIGRVFRRDQVDATHLPEFHQVEGLVVDENVSFADLKGVLEEFLRK 150 (243) T ss_pred CCCCEEEECCCEEEECCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHHH T ss_conf 799848981431332588984315310575578965777899999999999999 No 31 >PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional Probab=99.51 E-value=3.1e-13 Score=97.78 Aligned_cols=115 Identities=21% Similarity=0.235 Sum_probs=68.4 Q ss_pred HHHHHHHHHHHHHCCCEEEECCCEECC---------CC--CCC-CCCCEEEECCCC------------------------ Q ss_conf 999999999999879889847821056---------89--854-454124102478------------------------ Q gi|254781066|r 26 NMIQSSLREYFVENQFIEIDSMSLQYS---------PG--NET-HIRAFSTELIIQ------------------------ 69 (355) Q Consensus 26 s~i~~~iR~ff~~~gF~EV~TPiL~~~---------~~--g~~-~~~~f~t~~~~~------------------------ 69 (355) .+++..||+.|-+-||.|++.|.+.++ |- ++. .-+.|-+..... T Consensus 248 ~~~~~~~r~i~~~mGF~e~~g~~ve~~fwNfdaLf~Pq~HPARd~~Dtf~l~~~~~~~lp~~~~~~Vk~~HE~Gg~~gS~ 327 (501) T PRK04172 248 REFIEEVRDILVEMGFEEVKGPIVETEFWNFDALFQPQDHPAREMQDTFYLKYPSKGELPEELVERVKEVHEHGGDTGSR 327 (501) T ss_pred HHHHHHHHHHHHHCCCEEEECCCEECCCCCHHHHCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCC T ss_conf 99999999999978976853661010000334305898998555445378657654557378898899987427767887 Q ss_pred --CC-CC----CCCCC--CCCHHHHHHHHHHH---HHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCHHHHHHH Q ss_conf --86-78----32000--02858999989874---4688999886424567775448430020001157--765787775 Q gi|254781066|r 70 --DH-IR----KPLYL--QTSPEFSCKKLLAA---GEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESYEQLMKD 135 (355) Q Consensus 70 --~~-~~----~~~yL--~~SPql~lK~ll~~---G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~~dlm~~ 135 (355) +| .+ +..-| +||+=.. +.|+. .=-|||.||+|||+|..|.+|+|||.|+|--.+. +++.+++.. T Consensus 328 Gw~y~w~~~~~~~~~lRthtt~~~~--r~l~~~~~~p~~~f~~~rvfR~e~~d~tH~~~F~Q~eg~v~~~~~~~~~L~g~ 405 (501) T PRK04172 328 GWGYKWDEDIAKRLVLRTHTTALSA--RYLAERPEPPGKYFSIGRVFRPETIDATHLPEFYQLEGIVMGEDVSFRHLLGI 405 (501) T ss_pred CCCCCCCHHHHHHHCCCCCCCHHHH--HHHHHCCCCCEEEECCCCEEECCCCCCCCCCEEEEEEEEEECCCCCHHHHHHH T ss_conf 7677778556643010436746679--99974689983573565054268888654413322248998488879999999 Q ss_pred HHHHHHH Q ss_conf 5788877 Q gi|254781066|r 136 CMNIIRC 142 (355) Q Consensus 136 ~E~li~~ 142 (355) .+.+.+. T Consensus 406 l~~f~~~ 412 (501) T PRK04172 406 LKEFYKR 412 (501) T ss_pred HHHHHHH T ss_conf 9999998 No 32 >PTZ00326 phenylalanyl-tRNA synthetase; Provisional Probab=99.50 E-value=3.2e-13 Score=97.72 Aligned_cols=48 Identities=25% Similarity=0.292 Sum_probs=39.3 Q ss_pred HHHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCHHHHHHHHHHHHHH Q ss_conf 88999886424567775448430020001157--7657877755788877 Q gi|254781066|r 95 EKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESYEQLMKDCMNIIRC 142 (355) Q Consensus 95 ~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~~dlm~~~E~li~~ 142 (355) .|||.||+|||+|..|.+|+|||.|+|--.+. +++.+++...+.+++. T Consensus 369 ~k~fsi~rv~R~e~~d~th~~~f~Q~eg~~~~~~~~~~~l~~~l~~f~~~ 418 (505) T PTZ00326 369 KKYFSIDRVFRNETLDATHLAEFHQVEGVVIDRNLSLGDLMGTLREFFRR 418 (505) T ss_pred CEEEECCCEEECCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHHH T ss_conf 14752372641577776534045543578964888899999999999998 No 33 >cd00768 class_II_aaRS-like_core Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial ATP phosphoribosyltransferase regulatory subunit HisZ. Probab=99.46 E-value=1.8e-13 Score=99.24 Aligned_cols=116 Identities=22% Similarity=0.223 Sum_probs=81.9 Q ss_pred HHHHHHHHHHHHHHHCCCEEEECCCEECCC--CCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHH----HHH Q ss_conf 999999999999998798898478210568--98544541241024788678320000285899998987446----889 Q gi|254781066|r 24 KRNMIQSSLREYFVENQFIEIDSMSLQYSP--GNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGE----EKI 97 (355) Q Consensus 24 ~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~----~rv 97 (355) .|++|.+.+|+++.++||.||.||+|.... .+..+...+. ....+..+.++||+.+.+..+..+++... -|+ T Consensus 1 ~r~~ie~~~r~~~~~~G~~ev~~P~l~~~~~~~~sg~~~~~~--~~~~~~~~~~~~L~pt~e~~~~~~~~~~~~dLP~r~ 78 (211) T cd00768 1 IRSKIEQKLRRFMAELGFQEVETPIVEREPLLEKAGHEPKDL--LPVGAENEEDLYLRPTLEPGLVRLFVSHIRKLPLRL 78 (211) T ss_pred CHHHHHHHHHHHHHHCCCEEEECCEECCHHHHHHCCCCHHHH--HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHCCHHH T ss_conf 978999999999998699899998342799997506762223--011046797699951684999999752476577786 Q ss_pred HHHHHHHCCCCCCC--CCCCCEEEECEEECCCCHHHHHHHHHHHHHH Q ss_conf 99886424567775--4484300200011577657877755788877 Q gi|254781066|r 98 FCFAHAWRNGEQGC--LHQPEFTMLEWYRAHESYEQLMKDCMNIIRC 142 (355) Q Consensus 98 yqig~~FRaE~~~~--rHlpEFtmLE~e~af~d~~dlm~~~E~li~~ 142 (355) |++++|||+|..++ .|.-||+|.|.+....+.+ .-+..++++.. T Consensus 79 ~~~~~~fR~E~~~~Gl~RvreF~~~e~~~f~~~~~-~~~~~~~~~~~ 124 (211) T cd00768 79 AEIGPAFRNEGGRRGLRRVREFTQLEGEVFGEDGE-EASEFEELIEL 124 (211) T ss_pred HEECCEECCCCCCCCCCCCCCEEEEEEEEEECCHH-HHHHHHHHHHH T ss_conf 43200560578888844604688984799988488-89999999999 No 34 >PRK09537 pylS pyrolysyl-tRNA synthetase; Reviewed Probab=99.44 E-value=3e-14 Score=103.81 Aligned_cols=93 Identities=29% Similarity=0.491 Sum_probs=61.9 Q ss_pred HHHHHHHHHHHHHCCCEEEECCCEECCC-----C--CCCCC--CCEEEECCCCCCCCCCCCCC--CCHHHH--HHHHHHH Q ss_conf 9999999999998798898478210568-----9--85445--41241024788678320000--285899--9989874 Q gi|254781066|r 26 NMIQSSLREYFVENQFIEIDSMSLQYSP-----G--NETHI--RAFSTELIIQDHIRKPLYLQ--TSPEFS--CKKLLAA 92 (355) Q Consensus 26 s~i~~~iR~ff~~~gF~EV~TPiL~~~~-----~--g~~~~--~~f~t~~~~~~~~~~~~yL~--~SPql~--lK~ll~~ 92 (355) .++-+.|-+||-.+||+||..|||.+.. | .++.+ .-|.+ ++.+.|+ -+|-|| ++.|.-. T Consensus 210 gkler~it~ffvdrgfleikspilip~eyiermgid~d~elskQiFrv--------d~n~CLRPMLAPnLYnylrkL~R~ 281 (420) T PRK09537 210 GKLERDITKFFVDRGFLEIKSPILIPAEYIERMGIDNDTELSKQIFRV--------DKNFCLRPMLAPNLYNYLRKLDRA 281 (420) T ss_pred HHHHHHHHHHHHCCCCEEECCCEECCHHHHHHHCCCCHHHHHHHHEEE--------CCCCCCCCCCCHHHHHHHHHHHHH T ss_conf 677888899854145135148504219999985788605655451674--------345332410142699999999861 Q ss_pred --HHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECC Q ss_conf --4688999886424567775448430020001157 Q gi|254781066|r 93 --GEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH 126 (355) Q Consensus 93 --G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af 126 (355) .==|||+||||||-|+-+..|+.|||||-+-+-+ T Consensus 282 lpdPIrIFEIGpCyRKESdG~~HLeEFTMlNfcqmg 317 (420) T PRK09537 282 LPDPIKIFEIGPCYRKESDGKEHLEEFTMVNFCQMG 317 (420) T ss_pred CCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHC T ss_conf 688715886204303444106788777777688644 No 35 >COG0016 PheS Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis] Probab=99.39 E-value=4.8e-12 Score=90.76 Aligned_cols=115 Identities=21% Similarity=0.299 Sum_probs=67.8 Q ss_pred HHHHHHHHHHHHHCCCEEEECCCEECC-CCCCC-C------CCCEEEECCCCCCCCCCCCC--CCCHHHHHHHHHHHH-- Q ss_conf 999999999999879889847821056-89854-4------54124102478867832000--028589999898744-- Q gi|254781066|r 26 NMIQSSLREYFVENQFIEIDSMSLQYS-PGNET-H------IRAFSTELIIQDHIRKPLYL--QTSPEFSCKKLLAAG-- 93 (355) Q Consensus 26 s~i~~~iR~ff~~~gF~EV~TPiL~~~-~~g~~-~------~~~f~t~~~~~~~~~~~~yL--~~SPql~lK~ll~~G-- 93 (355) .+++..|+++|-+-||.+++.|.+.+. -.=++ + |+... +.+..+.-....-| ++||=.. +.|... T Consensus 114 ~~~~e~i~~iF~~mGF~~~~gp~IE~d~~NFDaLn~P~dHPARdmq-DTFy~~~~~~~~lLRTHTs~vq~--R~l~~~~~ 190 (335) T COG0016 114 TQTIEEIEDIFLGMGFTEVEGPEIETDFYNFDALNIPQDHPARDMQ-DTFYLKDDREKLLLRTHTSPVQA--RTLAENAK 190 (335) T ss_pred HHHHHHHHHHHHHCCCEECCCCCCCCCCCCHHHHCCCCCCCCCCCC-CEEEECCCCCCEEECCCCCHHHH--HHHHHCCC T ss_conf 9999999999997496664588213202252432499999841244-43787688773002366827659--99984799 Q ss_pred -HHHHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCHHHHHHHHHHHHHHH Q ss_conf -688999886424567775448430020001157--76578777557888776 Q gi|254781066|r 94 -EEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESYEQLMKDCMNIIRCA 143 (355) Q Consensus 94 -~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~~dlm~~~E~li~~~ 143 (355) =-|++.+|+|||++..|.+|+|||.|+|-=.+. .+..++.-..+++++.+ T Consensus 191 ~P~k~~~~grvyR~D~~DaTHs~~FhQiEGlvvd~~~s~~~Lkg~L~~f~~~~ 243 (335) T COG0016 191 IPIKIFSPGRVYRNDTVDATHSPEFHQIEGLVVDKNISFADLKGTLEEFAKKF 243 (335) T ss_pred CCCEEECCCCEECCCCCCCCCCHHEEEEEEEEEECCCCHHHHHHHHHHHHHHH T ss_conf 99158456634117887764261013367899958956999999999999996 No 36 >PRK00488 pheS phenylalanyl-tRNA synthetase subunit alpha; Validated Probab=99.18 E-value=2.5e-10 Score=80.56 Aligned_cols=112 Identities=18% Similarity=0.271 Sum_probs=72.2 Q ss_pred HHHHHHHHHHHHHCCCEEEECCCEECC---------CCCCCCCCCEEEECCCCCCCCCCCCC--CCCHHHHHHHHHHHHH Q ss_conf 999999999999879889847821056---------89854454124102478867832000--0285899998987446 Q gi|254781066|r 26 NMIQSSLREYFVENQFIEIDSMSLQYS---------PGNETHIRAFSTELIIQDHIRKPLYL--QTSPEFSCKKLLAAGE 94 (355) Q Consensus 26 s~i~~~iR~ff~~~gF~EV~TPiL~~~---------~~g~~~~~~f~t~~~~~~~~~~~~yL--~~SPql~lK~ll~~G~ 94 (355) ++++..|+++|.+-||..++-|-+-+. |..-+ |+.-. +.+ |++...-| +|||=.- +.|..+- T Consensus 110 t~~~~ei~~iF~~~Gf~v~~GpeiE~~~~NFdaLn~P~~HP-AR~~~-DTF---y~~~~~lLRTHTS~~qi--r~m~~~~ 182 (338) T PRK00488 110 TRTIERIEDIFVGLGFEVAEGPEIEDDYYNFEALNIPKDHP-ARDMQ-DTF---YIDDRLLLRTHTSPVQI--RTMEKQK 182 (338) T ss_pred HHHHHHHHHHHHHCCCEEECCCCEEEHHHHHHHHCCCCCCC-CCCCC-CEE---EECCCCEECCCCCHHHH--HHHHHCC T ss_conf 99999999999986976961883100454688756997885-43646-628---97687134356878889--9997269 Q ss_pred --HHHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCHHHHHHHHHHHHHHHH Q ss_conf --88999886424567775448430020001157--765787775578887766 Q gi|254781066|r 95 --EKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESYEQLMKDCMNIIRCAA 144 (355) Q Consensus 95 --~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~~dlm~~~E~li~~~~ 144 (355) =||+..|+|||+|..|.+|.|+|.|+|--+.. +++.++....+.+++.++ T Consensus 183 pp~~~i~~GrvyR~d~~DatH~~~FhQ~Egl~vd~~it~~~Lk~~l~~f~~~~f 236 (338) T PRK00488 183 PPIRIIAPGRVYRNDSDDATHSPMFHQVEGLVVDKNISFADLKGTLEDFLKAFF 236 (338) T ss_pred CCEEEEECCCCCCCCCCCCCCCEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHC T ss_conf 986999526631589998753504664005897178879999999999999972 No 37 >CHL00201 syh histidine-tRNA synthetase; Provisional Probab=99.15 E-value=9.9e-11 Score=82.99 Aligned_cols=112 Identities=12% Similarity=0.110 Sum_probs=67.6 Q ss_pred CCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECC-----CCCCC-CC---CCEEEECCCCCCCCCCCCC Q ss_conf 478831261548999999999999999999879889847821056-----89854-45---4124102478867832000 Q gi|254781066|r 8 PWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYS-----PGNET-HI---RAFSTELIIQDHIRKPLYL 78 (355) Q Consensus 8 ~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-----~~g~~-~~---~~f~t~~~~~~~~~~~~yL 78 (355) +.|.+|... +-...|..+...+++.|...||-+|+||++-.. .+|+. .+ ..|. ..+..++.+-| T Consensus 7 ~kG~rD~lp---~e~~~~~~i~~~i~~~f~~~Gf~~I~TP~lE~~e~~~~~~g~~~d~i~k~~y~----f~D~~g~~l~L 79 (424) T CHL00201 7 LRGTKDILP---DEIEYWQFIHEKAATLLKLANYQEIRTPIFENTELFDRGIGEETDIVNKEMYR----FFDRGNRSITL 79 (424) T ss_pred CCCCCCCCH---HHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHCCCCCCCCHHHHHHHEE----EECCCCCEEEE T ss_conf 999987899---99999999999999999985992504754041988623578742056665325----45599988886 Q ss_pred CC--CHHHHHHHHHHHH-------HHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCC Q ss_conf 02--8589999898744-------68899988642456777544843002000115776 Q gi|254781066|r 79 QT--SPEFSCKKLLAAG-------EEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHES 128 (355) Q Consensus 79 ~~--SPql~lK~ll~~G-------~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d 128 (355) +- .+.+. |.+++. --|.|++|||||+|...+-..-||||+.+|..+.+ T Consensus 80 RpD~T~pia--R~~~~~~~~~~~~P~r~~y~g~vfR~e~pq~GR~REF~Q~gvEiiG~~ 136 (424) T CHL00201 80 RPEGTASIV--RAFIENRMAYHMRPQRLWYSGPMFRYERPQSGRQRQFHQLGIEFIGSS 136 (424) T ss_pred CCCCHHHHH--HHHHHCCCCCCCCCEEEEEECCEEECCCCCCCCCCHHHHCCEEEECCC T ss_conf 787709999--999974765579987899875478058987886421041462000689 No 38 >PRK12292 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional Probab=99.14 E-value=1.4e-09 Score=76.09 Aligned_cols=103 Identities=17% Similarity=0.220 Sum_probs=63.8 Q ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCEECC-----CCCC-CCCCCEEEECCCCCCCCCCCCCC--CCHHHHHHHHHHH Q ss_conf 99999999999999999879889847821056-----8985-44541241024788678320000--2858999989874 Q gi|254781066|r 21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQYS-----PGNE-THIRAFSTELIIQDHIRKPLYLQ--TSPEFSCKKLLAA 92 (355) Q Consensus 21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-----~~g~-~~~~~f~t~~~~~~~~~~~~yL~--~SPql~lK~ll~~ 92 (355) -...|..+.+.+++.|.+.||-||+||++-.+ ..|+ .....|.. ....-++.+-|+ ..++.. |+++. T Consensus 16 e~~~~~~i~~~~~~~f~~~Gy~~I~tP~lE~~e~f~~~~g~~~~~~~~~f---~D~~~Gr~l~LRpD~T~~ia--R~~~~ 90 (388) T PRK12292 16 EARKIEEIRRRLLDVFRLWGYEEVITPTLEYLDTLLTGGGADLDLRTFKL---VDQLSGRTLGLRPDMTPQIA--RIAAT 90 (388) T ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHCCCCCCCCCHHEEEE---EECCCCCEEEECCCCCHHHH--HHHHH T ss_conf 99999999999999999879967357660629885445775021104899---82699978985687719999--99997 Q ss_pred HH------HHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCC Q ss_conf 46------8899988642456777544843002000115776 Q gi|254781066|r 93 GE------EKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHES 128 (355) Q Consensus 93 G~------~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d 128 (355) .+ -|+|.+|+|||.|....-..-||||+.+|.-+.+ T Consensus 91 ~~~~~~~p~r~~Y~g~vfR~e~pq~Gr~REf~Q~G~EiiG~~ 132 (388) T PRK12292 91 RLANRPGPLRLCYAGNVFRAQPRGLGRSREFLQSGVELIGDA 132 (388) T ss_pred HHHCCCCCEEEEEEEEEEEECCCCCCCCCEEEECCEEEECCC T ss_conf 310467876899852268705898996102342575531788 No 39 >PRK12293 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional Probab=99.13 E-value=4e-10 Score=79.41 Aligned_cols=126 Identities=16% Similarity=0.187 Sum_probs=75.5 Q ss_pred CCCCCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC-CCCCCCCCEEEECCCCCCCCCCCCCC Q ss_conf 99889874788312615489999999999999999998798898478210568-98544541241024788678320000 Q gi|254781066|r 1 MHQIPSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP-GNETHIRAFSTELIIQDHIRKPLYLQ 79 (355) Q Consensus 1 ~~~~p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~-~g~~~~~~f~t~~~~~~~~~~~~yL~ 79 (355) +||+| .|.+|.-. +-...+..|...+|+.|.+.||-||.||++--.. .++..-+.. +.-.|..++.+-|+ T Consensus 4 ~~~lP---~GtrD~~p---~~~~~~~~Ie~~~~~~f~~~Gy~eI~TP~~E~~e~~~~~~~kem---y~f~D~~gr~l~LR 74 (281) T PRK12293 4 EHEIP---QGSRLYFG---KSAKLKRDIENVASEILYKEGFEEIVTPSFSYHQHLSVADEKEL---LRFSDEKNHEISLR 74 (281) T ss_pred CCCCC---CCCCCCCH---HHHHHHHHHHHHHHHHHHHCCCEEEECCCEEEEECCCCCCCCEE---EEEECCCCCEEEEC T ss_conf 67899---97816681---99999999999999999985994853785686443466563017---99987999879977 Q ss_pred C--CHHHHHHHHHHHH------HHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCC-CHHHHHHHHHHHHHHH Q ss_conf 2--8589999898744------6889998864245677754484300200011577-6578777557888776 Q gi|254781066|r 80 T--SPEFSCKKLLAAG------EEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHE-SYEQLMKDCMNIIRCA 143 (355) Q Consensus 80 ~--SPql~lK~ll~~G------~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~-d~~dlm~~~E~li~~~ 143 (355) . .++.. |+++.. --|+|.+|||||.|. .||+|+-+|.-+. +..+++.++-++++.+ T Consensus 75 Pd~Ta~ia--R~v~~~l~~~~~p~rl~Y~g~vFRye~------rEf~Q~GvEliG~~s~~Evi~la~~~l~~l 139 (281) T PRK12293 75 ADSTVDVV--RIITKRLGRSTEHKKWFYIQPVFRYPT------TEIYQIGAEIIGESDLSKVLNIAAEIFNEL 139 (281) T ss_pred CCCCHHHH--HHHHHCCCCCCCCEEEEEECCEEECCC------CCCEEECEEEECCCCHHHHHHHHHHHHHHC T ss_conf 88878999--999965544689757998756353467------774684748877999999999999999976 No 40 >PRK00037 hisS histidyl-tRNA synthetase; Reviewed Probab=99.12 E-value=2.6e-09 Score=74.61 Aligned_cols=111 Identities=18% Similarity=0.257 Sum_probs=66.7 Q ss_pred CCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECC-----CCCCC-C-CC--CEEEECCCCCCCCCCCC Q ss_conf 7478831261548999999999999999999879889847821056-----89854-4-54--12410247886783200 Q gi|254781066|r 7 QPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYS-----PGNET-H-IR--AFSTELIIQDHIRKPLY 77 (355) Q Consensus 7 ~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-----~~g~~-~-~~--~f~t~~~~~~~~~~~~y 77 (355) .+.|.+|.-. +-.+.|..+...+|+-|.+.||-||+||+|... ..|+. . +. .|.. .+.-++.+- T Consensus 6 ~p~G~rD~lP---~~~~~~~~i~~~i~~~~~~~Gy~~I~tP~lE~~d~~~~~~g~~~d~~~k~~y~f----~D~~g~~l~ 78 (417) T PRK00037 6 APRGTRDILP---EESAKWQYVEDTIREVFERYGFSEIRTPIFEYTELFKRKIGESTDIVEKEMYTF----QDKGGRSLT 78 (417) T ss_pred CCCCCCCCCH---HHHHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHCCCCCCCCCHHHHHEEEE----ECCCCCEEE T ss_conf 9998776798---899999999999999999859958577521509886245776322013320567----759998898 Q ss_pred CCC--CHHHHHHHHHHHHH--------HHHHHHHHHHCCCCC--CCCCCCCEEEECEEECCCC Q ss_conf 002--85899998987446--------889998864245677--7544843002000115776 Q gi|254781066|r 78 LQT--SPEFSCKKLLAAGE--------EKIFCFAHAWRNGEQ--GCLHQPEFTMLEWYRAHES 128 (355) Q Consensus 78 L~~--SPql~lK~ll~~G~--------~rvyqig~~FRaE~~--~~rHlpEFtmLE~e~af~d 128 (355) |+- .|+.. |.++... =|.|++|+|||+|.. +| .-||||+++|..+.+ T Consensus 79 LRpD~T~~ia--R~~~~~~~~~~~~~P~r~~y~g~vfR~e~p~~GR--~REf~Q~g~eiiG~~ 137 (417) T PRK00037 79 LRPEGTAPVV--RAVIENKLYNELPKPFKLYYIGPMFRYERPQKGR--YRQFHQFGVEVIGSD 137 (417) T ss_pred ECCCCCHHHH--HHHHHHHHHCCCCCCEEEEEECCEEECCCCCCCC--CCCEEECCHHHHCCC T ss_conf 5677672999--9999721010688765899872466047898876--352456352774664 No 41 >PRK12325 prolyl-tRNA synthetase; Provisional Probab=99.07 E-value=2.1e-09 Score=75.11 Aligned_cols=118 Identities=15% Similarity=0.192 Sum_probs=74.1 Q ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CCCCCCCCEEEECCC-CCCCCCCCCCCC-CH----HHHHHHHHH Q ss_conf 99999999999999998798898478210568----985445412410247-886783200002-85----899998987 Q gi|254781066|r 22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GNETHIRAFSTELII-QDHIRKPLYLQT-SP----EFSCKKLLA 91 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g~~~~~~f~t~~~~-~~~~~~~~yL~~-SP----ql~lK~ll~ 91 (355) .+++.+|...+|+-+.+.||-||.||.|.+.. +| |.+-|.-+.+. .+--++++.|.. .- ++| |.-+- T Consensus 47 ~~i~~~le~~ir~e~~~~G~~eV~tP~l~~~~Lw~~SG--h~~~y~~~mf~~~d~~~~~~~l~Pmnc~~~~~i~-~~~~~ 123 (438) T PRK12325 47 LKVLKKIENIVREEQNRAGAIEILMPTIQPADLWRESG--RYDAYGKEMLRIKDRHDREMLYGPTNEEMITDIF-RSYVK 123 (438) T ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHC--CHHHHHHHHCEEECCCCCEECCCCCCCHHHHHHH-HHCCC T ss_conf 99999999999999997499799877658778998628--7645557421213477774313899849999999-74034 Q ss_pred HHHH---HHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHH Q ss_conf 4468---8999886424567775---4484300200011577657877755788877 Q gi|254781066|r 92 AGEE---KIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRC 142 (355) Q Consensus 92 ~G~~---rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~ 142 (355) |.-+ |+||||.+||+|-+.+ .-.-||||-|.|.-..+.++..+..+.+... T Consensus 124 SYRdLPlrl~q~g~~~R~E~sp~~GLlRvReF~m~Dah~F~~~~e~~~~~~~~v~~~ 180 (438) T PRK12325 124 SYKDLPLNLYHIQWKFRDEIRPRFGVMRGREFLMKDAYSFDLDEEGARKSYNRMFVA 180 (438) T ss_pred CHHHCCHHHHHHHHEECCCCCCCCCCCEEEEEECCCHHHCCCCHHHHHHHHHHHHHH T ss_conf 265425788764440112026764410122333041543246889999999999999 No 42 >cd00773 HisRS-like_core Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ. HisZ along with HisG catalyze the first reaction in histidine biosynthesis. HisZ is found only in a subset of bacteria and differs from HisRS in lacking a C-terminal anti-codon binding domain. Probab=99.07 E-value=9.9e-09 Score=71.14 Aligned_cols=100 Identities=18% Similarity=0.238 Sum_probs=63.1 Q ss_pred HHHHHHHHHHHHHHHHCCCEEEECCCEECCC-----CCCC-CCCCEEEECCCCCCCCCCCCCC--CCHHHHHHHHHHHHH Q ss_conf 9999999999999998798898478210568-----9854-4541241024788678320000--285899998987446 Q gi|254781066|r 23 LKRNMIQSSLREYFVENQFIEIDSMSLQYSP-----GNET-HIRAFSTELIIQDHIRKPLYLQ--TSPEFSCKKLLAAGE 94 (355) Q Consensus 23 ~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~-----~g~~-~~~~f~t~~~~~~~~~~~~yL~--~SPql~lK~ll~~G~ 94 (355) +.|..|.+.+++.|.+.||-+|+||++-... .|+. .-..|... +.-++.+-|+ ..++.. |.++... T Consensus 3 ~~r~~i~~~l~~~f~~~Gy~~I~~P~lE~~d~~~~~~~~~~~~~~~~f~----D~~g~~l~LRpD~T~~ia--R~~~~~~ 76 (261) T cd00773 3 ALRRYIEDTLREVFERYGYEEIDTPVFEYTELFLRKSGDEVSKEMYRFK----DKGGRDLALRPDLTAPVA--RAVAENL 76 (261) T ss_pred HHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHCCCCCCCCHHCEEEEE----CCCCCEEEECCCCCHHHH--HHHHHHH T ss_conf 8999999999999998699786677645276752446531021169999----799998976786627999--9999741 Q ss_pred ------HHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCC Q ss_conf ------8899988642456777544843002000115776 Q gi|254781066|r 95 ------EKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHES 128 (355) Q Consensus 95 ------~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d 128 (355) -|+|.+|+|||.+....-..-||+|+.+|.-+.+ T Consensus 77 ~~~~~p~r~~Y~g~VfR~~~~~~g~~rE~~Q~G~EiiG~~ 116 (261) T cd00773 77 LSLPLPLKLYYIGPVFRYERPQKGRYREFYQVGVEIIGSD 116 (261) T ss_pred CCCCCCEEEEEECCEEEECCCCCCCCCCCCCEEEEEECCC T ss_conf 5378885899973189976899998443221469997289 No 43 >COG0124 HisS Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] Probab=98.97 E-value=7.8e-09 Score=71.77 Aligned_cols=134 Identities=19% Similarity=0.248 Sum_probs=76.5 Q ss_pred CCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC-----CCCC-CCCCEEEECCCCCCCCCCCCCC-- Q ss_conf 4788312615489999999999999999998798898478210568-----9854-4541241024788678320000-- Q gi|254781066|r 8 PWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP-----GNET-HIRAFSTELIIQDHIRKPLYLQ-- 79 (355) Q Consensus 8 ~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~-----~g~~-~~~~f~t~~~~~~~~~~~~yL~-- 79 (355) +.|.+|.-. .-...|..|...+|+-+.+-||.||+||++-.+. .|+. ..-.-....+ .|..++..-|+ T Consensus 7 prG~~D~lp---~d~~~~~~i~~~~~~v~~~yGf~eI~TPifE~telf~r~~Ge~td~v~kemY~F-~Dkggr~laLRpe 82 (429) T COG0124 7 PRGTRDFLP---EDMALREYIESTIRKVFESYGFSEIRTPIFEYTELFARKSGEETDVVEKEMYTF-KDKGGRSLALRPE 82 (429) T ss_pred CCCCCCCCH---HHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCHHHHHHCCCCCCCCCCCCEEEE-EECCCCEEEECCC T ss_conf 998665586---778999999999999999809976557551116676201697433332102899-9489988984466 Q ss_pred -CCHHHHHHHHHHHH------HHHHHHHHHHHCCCCC--CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCC Q ss_conf -28589999898744------6889998864245677--75448430020001157765787775578887766641883 Q gi|254781066|r 80 -TSPEFSCKKLLAAG------EEKIFCFAHAWRNGEQ--GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQK 150 (355) Q Consensus 80 -~SPql~lK~ll~~G------~~rvyqig~~FRaE~~--~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~ 150 (355) |+| .=|..+.. --|.|.+|||||.|.. +|. -||||+++|..+.+--..=..+-.|+...++.++-. T Consensus 83 ~Tap---v~R~~~en~~~~~~p~k~yy~g~vfRyErPQ~GR~--RqF~Q~g~E~iG~~~~~~DAEvi~l~~~~l~~lGi~ 157 (429) T COG0124 83 LTAP---VARAVAENKLDLPKPLKLYYFGPVFRYERPQKGRY--RQFYQFGVEVIGSDSPDADAEVIALAVEILEALGIG 157 (429) T ss_pred CCHH---HHHHHHHCCCCCCCCEEEEEECCEECCCCCCCCCC--EEEEECCEEEECCCCCCCCHHHHHHHHHHHHHCCCC T ss_conf 7499---99999956220368725998335623788888875--036876767767998653899999999999974998 No 44 >PRK12420 histidyl-tRNA synthetase; Provisional Probab=98.96 E-value=3.8e-09 Score=73.58 Aligned_cols=117 Identities=21% Similarity=0.255 Sum_probs=69.7 Q ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCEECC------CCCCCCC--CCEEEECCCCCCCCCCCCCC---CCHHHHHHHH Q ss_conf 99999999999999999879889847821056------8985445--41241024788678320000---2858999989 Q gi|254781066|r 21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQYS------PGNETHI--RAFSTELIIQDHIRKPLYLQ---TSPEFSCKKL 89 (355) Q Consensus 21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~------~~g~~~~--~~f~t~~~~~~~~~~~~yL~---~SPql~lK~l 89 (355) -...|..+.+.+|+.|...||-||+||++-.+ .|+++.+ ..|. -.+..+..+-|+ |+| +. |. T Consensus 17 e~~~~~~i~~~~~~~~~~~Gy~~I~tP~~E~~elf~~~~g~~~~i~kemy~----f~D~~gr~l~LRPe~Ta~-ia--R~ 89 (421) T PRK12420 17 EQVLRNKIKRACEDTFERYGCKPLETPTLNMYELMSYKYGGGDEILKEIYT----LQDQGKRDLALRYDLTIP-FA--KV 89 (421) T ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHCCCCCCCCHHHHHEEE----EECCCCCEEEECCCCCHH-HH--HH T ss_conf 999999999999999998599472476501187642447884422411078----881899879856776589-99--99 Q ss_pred HHHH--H---HHHHHHHHHHCCCCC--CCCCCCCEEEECEEECCCCHHHHHHHHH--HHHHHHHHHHC Q ss_conf 8744--6---889998864245677--7544843002000115776578777557--88877666418 Q gi|254781066|r 90 LAAG--E---EKIFCFAHAWRNGEQ--GCLHQPEFTMLEWYRAHESYEQLMKDCM--NIIRCAAEVAN 148 (355) Q Consensus 90 l~~G--~---~rvyqig~~FRaE~~--~~rHlpEFtmLE~e~af~d~~dlm~~~E--~li~~~~~~~~ 148 (355) ++.. . -|.|.+|||||.|.- +|. -||||+.+|.-+.+-- ..++| .+...+++.++ T Consensus 90 ~a~~~~~~~P~k~~y~g~vfR~erpq~GR~--ReF~Q~GvEiiG~~~~--~aDaEiI~la~~~l~~lg 153 (421) T PRK12420 90 VAMNPNIRLPFKRYEIGKVFRDGPIKQGRF--REFIQCDVDIVGVESV--MAEAELMSMAFELFRTLN 153 (421) T ss_pred HHHCCCCCCCEEEEEECCEEECCCCCCCCC--CEEEECCEEEECCCCH--HHHHHHHHHHHHHHHHCC T ss_conf 997757778745888767785389878855--5134357542078877--889999999999999659 No 45 >TIGR02367 PylS pyrrolysyl-tRNA synthetase; InterPro: IPR012739 PylS is the archaeal enzyme responsible for charging the pyrrolysine tRNA, PylT, by ligating a free molecule of pyrrolysine. Pyrrolysine is encoded at an in-frame UAG (amber) at least in several corrinoid-dependent methyltransferases of the archaeal genera Methanosarcina and Methanococcoides, e.g. trimethylamine methyltransferase. . Probab=98.88 E-value=3e-10 Score=80.15 Aligned_cols=115 Identities=27% Similarity=0.346 Sum_probs=70.3 Q ss_pred HHHHHHHHHHHHHCCCEEEECCCEECCCCCCC-CCCCEEEECCCCC-CCCCCCCCC--CCHHHH--HHHH--HHHHHHHH Q ss_conf 99999999999987988984782105689854-4541241024788-678320000--285899--9989--87446889 Q gi|254781066|r 26 NMIQSSLREYFVENQFIEIDSMSLQYSPGNET-HIRAFSTELIIQD-HIRKPLYLQ--TSPEFS--CKKL--LAAGEEKI 97 (355) Q Consensus 26 s~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~-~~~~f~t~~~~~~-~~~~~~yL~--~SPql~--lK~l--l~~G~~rv 97 (355) .++-+.|-.||-.+||+||..|||.+..--+. +++ -.|++...- -.++.+.|+ -+|.|| +.+| +..+==|| T Consensus 243 Gkler~it~ffvdrGfleiksPiliP~ey~ermGi~-ndtelskqifrvdkn~ClrPmlaP~lynylrkldr~lP~Pik~ 321 (453) T TIGR02367 243 GKLEREITKFFVDRGFLEIKSPILIPLEYVERMGID-NDTELSKQIFRVDKNLCLRPMLAPTLYNYLRKLDRILPDPIKV 321 (453) T ss_pred HHHHHHHHHHHHHCCEEEECCCCCCCHHHHHHCCCC-CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCEEE T ss_conf 467666766653124023236310105688650776-4025666666441001012100056899999987537896479 Q ss_pred HHHHHHHCCCCCCCCCCCCEEEECEEECC--CCHHHHHHHHHHHHH Q ss_conf 99886424567775448430020001157--765787775578887 Q gi|254781066|r 98 FCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESYEQLMKDCMNIIR 141 (355) Q Consensus 98 yqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~~dlm~~~E~li~ 141 (355) |+||||||.|+-+..|+-||||+.+=+.+ .+-+.+-.++.+++. T Consensus 322 fe~GPCyrkesdGkehleeftm~nfCqmGsGCtrenle~~i~~fl~ 367 (453) T TIGR02367 322 FEVGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLEALIKEFLD 367 (453) T ss_pred EEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH T ss_conf 8606752435653356666665554314787326779999999887 No 46 >PRK12295 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional Probab=98.84 E-value=1.4e-07 Score=64.32 Aligned_cols=97 Identities=19% Similarity=0.193 Sum_probs=58.7 Q ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCEECC-----CCCCC-CCCCEEEECCCCCCCCCCCCCC--CCHHHHHHHH-HHH Q ss_conf 9999999999999999879889847821056-----89854-4541241024788678320000--2858999989-874 Q gi|254781066|r 22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYS-----PGNET-HIRAFSTELIIQDHIRKPLYLQ--TSPEFSCKKL-LAA 92 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-----~~g~~-~~~~f~t~~~~~~~~~~~~yL~--~SPql~lK~l-l~~ 92 (355) +.+|-.+...|++-|.+.||-+|+||++-.. ..|+. -...|.. .+..++..-|+ -.+++. |. +.. T Consensus 4 ~~r~~~~~~~i~~~f~~~Gy~~I~tP~lE~~d~~~~~~Ge~~~~~~y~f----~D~~g~~l~LRpDlT~pia--R~~~~~ 77 (373) T PRK12295 4 LSRSAALAEALLASFEAAGAVRVDPPILQPAEPFLDLSGEDIRRRIFVT----SDENGEELCLRPDFTIPVC--RRHLAS 77 (373) T ss_pred HHHHHHHHHHHHHHHHHCCCEEECCCCCCCHHHHCCCCCCHHHEEEEEE----ECCCCCEEEEECCCCHHHH--HHHHHH T ss_conf 6779999999999999869968568760417764143563311004889----9899898998178889999--999983 Q ss_pred H---HHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCC Q ss_conf 4---6889998864245677754484300200011577 Q gi|254781066|r 93 G---EEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHE 127 (355) Q Consensus 93 G---~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~ 127 (355) + --|+|.+|+|||.. .++. -||||+.+|.-+. T Consensus 78 ~~~~p~R~~Y~G~VfR~q-~gr~--rEf~Q~GvEiiG~ 112 (373) T PRK12295 78 NAGEPARYSYLGEVFRQR-RDRA--SEFLQAGIESFGR 112 (373) T ss_pred CCCCCEEEEEECCEEECC-CCCC--CCEEEEEEEEECC T ss_conf 899980078773322457-9998--8516701578578 No 47 >pfam00587 tRNA-synt_2b tRNA synthetase class II core domain (G, H, P, S and T). Other tRNA synthetase sub-families are too dissimilar to be included. This domain is the core catalytic domain of tRNA synthetases and includes glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases. Probab=98.82 E-value=1.6e-08 Score=69.86 Aligned_cols=119 Identities=19% Similarity=0.282 Sum_probs=69.0 Q ss_pred HHHHHHHHHHHHHHHCCCEEEECCCEECCC--CCCCCCCCEEEECCC-CCCCCCCCCCCCCHHHHHHHHHHH----HHH- Q ss_conf 999999999999998798898478210568--985445412410247-886783200002858999989874----468- Q gi|254781066|r 24 KRNMIQSSLREYFVENQFIEIDSMSLQYSP--GNETHIRAFSTELII-QDHIRKPLYLQTSPEFSCKKLLAA----GEE- 95 (355) Q Consensus 24 ~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~~~~~f~t~~~~-~~~~~~~~yL~~SPql~lK~ll~~----G~~- 95 (355) .|.+|.+.+|+.+.+.||.||.||+|.... .+..+...|.-+.+. .+..+...+|+-.-+..+-++.+. .-+ T Consensus 1 l~~~l~~~~~~~~~~~G~~~i~tP~l~~~~~~~~sg~~~~~~~~my~~~d~~~~~l~Lrp~~~~~~~~~~~~~~~~~~~l 80 (170) T pfam00587 1 LRNALENFIRDLFKRYGYQEVDTPILEPKELWEGSGHWDDYFDEMYRFKDRGGEELYLRPTAEVGITRLFKNEILSYRDL 80 (170) T ss_pred CHHHHHHHHHHHHHHCCCEEEECCEEEEHHHHHHCCCCCCCHHHEEEEECCCCCEEEEECCCCHHHHHHHHHHCCCCCCC T ss_conf 97999999999999859989999917567898344776557531256735899768873257458889988620032358 Q ss_pred --HHHHHHHHHCCCCCCCC---CCCCEEEECEEECCCCHHHHHHHHHHHHHHH Q ss_conf --89998864245677754---4843002000115776578777557888776 Q gi|254781066|r 96 --KIFCFAHAWRNGEQGCL---HQPEFTMLEWYRAHESYEQLMKDCMNIIRCA 143 (355) Q Consensus 96 --rvyqig~~FRaE~~~~r---HlpEFtmLE~e~af~d~~dlm~~~E~li~~~ 143 (355) |+|++|+|||+|-..++ -.-||||.|++....+ ++..+..++++..+ T Consensus 81 P~r~~~~~~~fR~E~~~~~Gl~R~reF~q~d~~~~~~~-e~s~~~~~e~~~~~ 132 (170) T pfam00587 81 PLKLYQIGPCFRYEARPRRGLGRVREFTQVDAEIFGTP-EQSEEEDEELLKLA 132 (170) T ss_pred CCEEECCCCCCCCCCCCCCCCCEEEEEEEECEEEEECC-CHHHHHHHHHHHHH T ss_conf 60133065300677776667743678898047999670-04299999999999 No 48 >cd00779 ProRS_core_prok Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from prokaryotes and from the mitochondria of eukaryotes. Probab=98.75 E-value=3.2e-08 Score=68.13 Aligned_cols=122 Identities=20% Similarity=0.178 Sum_probs=80.6 Q ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCEECCCC--CCCCCCCEEEECCC-CCCCCCCCCCCCCHHHHHHHHHH----HHH Q ss_conf 999999999999999987988984782105689--85445412410247-88678320000285899998987----446 Q gi|254781066|r 22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSPG--NETHIRAFSTELII-QDHIRKPLYLQTSPEFSCKKLLA----AGE 94 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~--g~~~~~~f~t~~~~-~~~~~~~~yL~~SPql~lK~ll~----~G~ 94 (355) .+.+.+|.+.||+-+++.|+-||.||+|++..- ...+.+-|..+.+. .+..+.+++|+...|-.+-.+.. +-- T Consensus 31 ~~i~~~i~~~i~~~~~~~G~~ev~~P~l~~~~l~~~sg~~~~f~~emf~v~d~~~~~~~L~PT~E~~~~~~~~~~i~Syr 110 (255) T cd00779 31 LRVLKKIENIIREEMNKIGAQEILMPILQPAELWKESGRWDAYGPELLRLKDRHGKEFLLGPTHEEVITDLVANEIKSYK 110 (255) T ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHCCCCCCCCCEEEEECCCCCEEEECCCCHHHHHHHHHHHCCCHH T ss_conf 99999999999999998599899765347388874425301368731544537887773168874889999986503612 Q ss_pred H---HHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHHH Q ss_conf 8---8999886424567775---44843002000115776578777557888776 Q gi|254781066|r 95 E---KIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCA 143 (355) Q Consensus 95 ~---rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~ 143 (355) + ++||+++|||+|-+++ .-.-||+|-|.|....|.++..+..+.+.... T Consensus 111 dLPl~~~q~~~~fR~E~r~~~GllR~rEF~~~d~hsf~~~~e~a~~~~~~~~~~y 165 (255) T cd00779 111 QLPLNLYQIQTKFRDEIRPRFGLMRGREFLMKDAYSFDIDEESLEETYEKMYQAY 165 (255) T ss_pred HCCEEEECCCCEECCCCCCCCCCCEEEEEEEEHHHCCCCCHHHHHHHHHHHHHHH T ss_conf 2574541353354256678866324313770022035699899999999999999 No 49 >cd00771 ThrRS_core Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. Probab=98.75 E-value=3.9e-08 Score=67.65 Aligned_cols=133 Identities=14% Similarity=0.178 Sum_probs=85.7 Q ss_pred CCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC--CCCCCCCCEEEECCCCCCCCCCCCCCCCH Q ss_conf 9874788312615489999999999999999998798898478210568--98544541241024788678320000285 Q gi|254781066|r 5 PSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP--GNETHIRAFSTELIIQDHIRKPLYLQTSP 82 (355) Q Consensus 5 p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~~~~~f~t~~~~~~~~~~~~yL~~SP 82 (355) |-.++|+|. =.++|..+...+|+-..++||.||.||.|.... ....|.+-|.-..+....-+++++|.-.. T Consensus 20 ~G~~~w~P~-------G~~i~~~L~~~ir~~~~~~Gy~eV~tP~i~~~~Lw~~SGH~~~y~e~mf~~~~~~~~~~LkPmn 92 (298) T cd00771 20 PGLPFWLPK-------GAIIRNELEDFLRELQRKRGYQEVETPIIYNKELWETSGHWDHYRENMFPFEEEDEEYGLKPMN 92 (298) T ss_pred CCCEEECCC-------HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCCCCCCCCEEEEEECCCCEEEECCC T ss_conf 765788388-------8999999999999999986998998861266556754776311368568888625416885068 Q ss_pred -----HHHHHHHHHHHHH---HHHHHHHHHCCCCCCC----CCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHH Q ss_conf -----8999989874468---8999886424567775----44843002000115776578777557888776664 Q gi|254781066|r 83 -----EFSCKKLLAAGEE---KIFCFAHAWRNGEQGC----LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEV 146 (355) Q Consensus 83 -----ql~lK~ll~~G~~---rvyqig~~FRaE~~~~----rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~ 146 (355) ++|. .-+-|.-+ |++++|.|||+|-++. .-+-+|||-|... |...+++.+.+.++++.+.+. T Consensus 93 Cp~h~~i~~-~~~~SYrdLPlR~~E~g~~~R~E~sG~L~GL~RvR~FtqdDaHi-Fc~~eQ~~~E~~~~~~~~~~v 166 (298) T cd00771 93 CPGHCLIFK-SKPRSYRDLPLRLAEFGTVHRYEQSGALHGLTRVRGFTQDDAHI-FCTPDQIKEEIKGVLDLIKEV 166 (298) T ss_pred CHHHHHHHH-CCCCCHHHCCHHHHCCCCEECCCCCCCCCCCCCCCCCCCCCCEE-ECCHHHHHHHHHHHHHHHHHH T ss_conf 688999986-35567343467652075055476776755744555674576324-416889999999999999999 No 50 >PRK12421 ATP phosphoribosyltransferase regulatory subunit; Provisional Probab=98.71 E-value=4e-07 Score=61.67 Aligned_cols=122 Identities=11% Similarity=0.092 Sum_probs=71.5 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCEEEECCCEECC-----CCC-CCCCCCEEEECCCCCC-CCCCCCCC--CCHHHHHHHHH Q ss_conf 999999999999999999879889847821056-----898-5445412410247886-78320000--28589999898 Q gi|254781066|r 20 PFLLKRNMIQSSLREYFVENQFIEIDSMSLQYS-----PGN-ETHIRAFSTELIIQDH-IRKPLYLQ--TSPEFSCKKLL 90 (355) Q Consensus 20 ~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-----~~g-~~~~~~f~t~~~~~~~-~~~~~yL~--~SPql~lK~ll 90 (355) +-...+..+.+.+.+.|.+.||-+|.||++-.. ..| +.....|+. .+. -++.+-|+ ..||.. |+. T Consensus 19 ~ea~~~~~l~~~l~~~f~~~Gy~~V~tP~lE~~e~l~~~~g~~~~~~~f~~----~D~~sGr~l~LRpD~T~~vA--Ri~ 92 (391) T PRK12421 19 EEAQKIERLRRRLLDLFASRGYQLVMPPFIEYLESLLTGAGQDLDLQTFKL----IDQLSGRLMGVRADITPQVA--RID 92 (391) T ss_pred HHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHCCCCCCCCCEEEEEE----EECCCCCEEEECCCCCHHHH--HHH T ss_conf 999999999999999999869976216760728785656687341479999----61799978655653206889--999 Q ss_pred H-----HHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCC-HHHHHHHHHHHHHHHHHHHC Q ss_conf 7-----4468899988642456777544843002000115776-57877755788877666418 Q gi|254781066|r 91 A-----AGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHES-YEQLMKDCMNIIRCAAEVAN 148 (355) Q Consensus 91 ~-----~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d-~~dlm~~~E~li~~~~~~~~ 148 (355) + .+--|+|.+|++||.+....--.-||+|+.+|.-+.+ .+.=.+++ .++..+.+.++ T Consensus 93 a~~~~~~~p~Rl~Y~G~V~R~~~~~~gr~Ref~Q~G~EliG~~~~~aD~EvI-~l~~~~L~~lG 155 (391) T PRK12421 93 AHLLNREGVARYCYAGSVLHTLPQGLNASRAPLQLGAELYGHAGIEADIEII-DLMLGLLRNAG 155 (391) T ss_pred HHHCCCCCCEEEEEECEEEECCCCCCCCCCCCEECCEEEECCCCHHHHHHHH-HHHHHHHHHCC T ss_conf 8740468865799965177516888887665215058985699879899999-99999999769 No 51 >cd00778 ProRS_core_arch_euk Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from archaea, the cytoplasm of eukaryotes and some bacteria. Probab=98.63 E-value=3.6e-07 Score=61.87 Aligned_cols=130 Identities=17% Similarity=0.108 Sum_probs=82.9 Q ss_pred CCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECC-----CCCCCCCCC-----EEEECCCCCCCC Q ss_conf 8987478831261548999999999999999999879889847821056-----898544541-----241024788678 Q gi|254781066|r 4 IPSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYS-----PGNETHIRA-----FSTELIIQDHIR 73 (355) Q Consensus 4 ~p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-----~~g~~~~~~-----f~t~~~~~~~~~ 73 (355) .|-.+.|+|- =.+.+.+|.+.+|+-+.+.|+-||.||+|.+. .+| |.+- |.+........+ T Consensus 21 v~G~~~~lP~-------G~~i~~~l~~~~r~~~~~~G~~ev~~P~l~~~~~~~k~sg--h~~~y~~emf~v~~~g~~~~d 91 (261) T cd00778 21 VKGCMVFRPY-------GYAIWENIQKILDKEIKETGHENVYFPLLIPESELEKEKE--HIEGFAPEVAWVTHGGLEELE 91 (261) T ss_pred CCCEEEECCC-------HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHC--HHHCCCCCCEEEECCCCCCCC T ss_conf 9830888632-------8999999999999999986996998833278899997428--143057653355216852013 Q ss_pred CCCCCCCCH-----HHHHHHHHHHHHH---HHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHH Q ss_conf 320000285-----8999989874468---8999886424567775---4484300200011577657877755788877 Q gi|254781066|r 74 KPLYLQTSP-----EFSCKKLLAAGEE---KIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRC 142 (355) Q Consensus 74 ~~~yL~~SP-----ql~lK~ll~~G~~---rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~ 142 (355) .++.|...- ++|. .-+-|.-+ |+||+|.+||+|-+++ .-.-||+|-|.|..|.+.+++.+.+..++.. T Consensus 92 ~~y~LkPmne~~~~~i~~-~~~~SYRdLPlrl~q~g~~~R~E~s~~~gL~RvReF~~dDahs~~~t~eq~~~e~~~~~~~ 170 (261) T cd00778 92 EPLALRPTSETAIYPMFS-KWIRSYRDLPLKINQWVNVFRWETKTTRPFLRTREFLWQEGHTAHATEEEAEEEVLQILDL 170 (261) T ss_pred CCCCCCCCCHHHHHHHHH-HHHCCCCCCCHHHHHCCCEECCCCCCCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHH T ss_conf 560347888699999997-3505402278255530422437788887653254252342336558999999999999999 Q ss_pred H Q ss_conf 6 Q gi|254781066|r 143 A 143 (355) Q Consensus 143 ~ 143 (355) . T Consensus 171 y 171 (261) T cd00778 171 Y 171 (261) T ss_pred H T ss_conf 9 No 52 >cd00670 Gly_His_Pro_Ser_Thr_tRS_core Gly_His_Pro_Ser_Thr_tRNA synthetase class II core domain. This domain is the core catalytic domain of tRNA synthetases of the subgroup containing glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. These enzymes belong to class II aminoacyl-tRNA synthetases (aaRS) based upon their structure and the presence of three characteristic sequence motifs in the core domain. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ and the accessory subunit of mitochondrial polymerase gamma (Pol gamma b) . Most class II tRNA synthetases are dimers, with this subgroup consisting of mostly homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. Probab=98.56 E-value=2.2e-07 Score=63.17 Aligned_cols=121 Identities=14% Similarity=0.104 Sum_probs=76.7 Q ss_pred HHHHHHHHHHHHHHHHCCCEEEECCCEECCC--CCCCCCCCEE-----EECCCCCCCCCCCCCCCCHH-----HHHHHHH Q ss_conf 9999999999999998798898478210568--9854454124-----10247886783200002858-----9999898 Q gi|254781066|r 23 LKRNMIQSSLREYFVENQFIEIDSMSLQYSP--GNETHIRAFS-----TELIIQDHIRKPLYLQTSPE-----FSCKKLL 90 (355) Q Consensus 23 ~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~~~~~f~-----t~~~~~~~~~~~~yL~~SPq-----l~lK~ll 90 (355) +++.++.+.+++.+.+.||.||.||.|.+.. .+..+..-|. +........+.++||.-..| +|.+..+ T Consensus 3 ~L~~aL~~~~~~~~~~~G~~~v~~P~l~~~~~~~~sg~~~~f~~~~y~v~~~~~~~~~~~~~L~PTsE~~~~~~~~~~i~ 82 (235) T cd00670 3 ALWRALERFLDDRMAEYGYQEILFPFLAPTVLFFKGGHLDGYRKEMYTFEDKGRELRDTDLVLRPAACEPIYQIFSGEIL 82 (235) T ss_pred HHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCEEEEECCCHHHHHHHHCCCC T ss_conf 89999999999999986998998985578999922386754520528982377666787389930786999999948328 Q ss_pred HH-HH-HHHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHHHH Q ss_conf 74-46-88999886424567775---448430020001157765787775578887766 Q gi|254781066|r 91 AA-GE-EKIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAA 144 (355) Q Consensus 91 ~~-G~-~rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~ 144 (355) .. -+ =|++++++|||+|-.++ .-.-||+|.|.+. |.+-++..+..+.++.... T Consensus 83 s~~dLPlr~~~~s~~fR~E~~~~~Gl~Rv~eF~k~E~~~-~~~~e~~~~~~~~~~~~~~ 140 (235) T cd00670 83 SYRALPLRLDQIGPCFRHEPSGRRGLMRVREFRQVEYVV-FGEPEEAEEERREWLELAE 140 (235) T ss_pred CHHHCCEEEEEECCEECCCCCCCCCCEEEEEEEEEEEEE-EECHHHHHHHHHHHHHHHH T ss_conf 768799545445653336789999983678999850799-9688999999999999999 No 53 >cd00772 ProRS_core Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. Probab=98.54 E-value=1.9e-06 Score=57.63 Aligned_cols=122 Identities=13% Similarity=0.116 Sum_probs=79.7 Q ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CCC--CCC--CCEEEECCCCCCCCCCCCCCCCHHHHHHHH---- Q ss_conf 99999999999999998798898478210568----985--445--412410247886783200002858999989---- Q gi|254781066|r 22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GNE--THI--RAFSTELIIQDHIRKPLYLQTSPEFSCKKL---- 89 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g~--~~~--~~f~t~~~~~~~~~~~~yL~~SPql~lK~l---- 89 (355) ++++.+|...||+-+++.|+-||-+|+|++.. +|. .+. .-|.+..........++.|+...|-.+-.+ T Consensus 32 ~~i~~ki~~~i~~e~~~~G~qev~~P~l~p~~lw~ksgr~~~~~~~e~~~~~~~~~~~~e~~~~L~PT~Ee~~~~~~~~~ 111 (264) T cd00772 32 KAILDKIENVLDKMFKEHGAQNALFPFFILASFLEKEAEHDEGFSKELAVFKDAGDEELEEDFALRPTLEENIGEIAAKF 111 (264) T ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCHHHCCCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHH T ss_conf 99999999999999998299498125679989999769844437852379973487421235201677868999999864 Q ss_pred HHHHHH---HHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHHH Q ss_conf 874468---8999886424567775---44843002000115776578777557888776 Q gi|254781066|r 90 LAAGEE---KIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCA 143 (355) Q Consensus 90 l~~G~~---rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~ 143 (355) +-|--+ ++|||+.+||+|-+.+ --.-||+|-|.|..++|.++..+..+.++..- T Consensus 112 i~SyrdLPl~lyQ~~~~fR~E~r~r~GllR~REFlmkDahsf~~t~e~a~~~y~~~~~~Y 171 (264) T cd00772 112 IKSWKDLPQHLNQIGNKFRDEIRPRFGFLRAREFIMKDGHSAHADAEEADEEFLNMLSAY 171 (264) T ss_pred CCCHHHCCHHHHHHHHHHHCCCCCCCCCHHHEEEEEEEEEECCCCHHHHHHHHHHHHHHH T ss_conf 076655797787655786057885543323204341103532599999999999999999 No 54 >PRK05425 asparagine synthetase AsnA; Provisional Probab=98.51 E-value=1.5e-05 Score=52.36 Aligned_cols=267 Identities=14% Similarity=0.145 Sum_probs=122.6 Q ss_pred HHHHHHHHHHHHHHHH-----HCCCEEEECCCEECC-CCCCCCC----CCEEEECCCCCCCCCCCCCCCCHHHHHHHH-H Q ss_conf 9999999999999999-----879889847821056-8985445----412410247886783200002858999989-8 Q gi|254781066|r 22 LLKRNMIQSSLREYFV-----ENQFIEIDSMSLQYS-PGNETHI----RAFSTELIIQDHIRKPLYLQTSPEFSCKKL-L 90 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~-----~~gF~EV~TPiL~~~-~~g~~~~----~~f~t~~~~~~~~~~~~yL~~SPql~lK~l-l 90 (355) ++.....++.|+++|. +-+.+.|..|+++.. .|---++ +|.... ..+.-+..+--.+|--=| ||. | T Consensus 8 ~~etq~aI~~iK~~F~~~L~~~LnL~rVsAPLfv~~~sGlNDnLnG~ErpV~F~--vk~~~~~~~EiVhSLAKW-KR~aL 84 (327) T PRK05425 8 FIETQQAISFVKNFFERQLAKKLNLIRVSAPLFVRVGSGLNDNLNGVEKPVSFK--VKDLPDATFEVVHSLAKW-KRLAL 84 (327) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCEEECCCEEECCCCCCCCCCCCEEEEEEEE--CCCCCCCEEEEEEEHHHH-HHHHH T ss_conf 999999999999999999999709079557858737888667777726336986--568888706886106889-99999 Q ss_pred H-HHHH---HHHHHHHHHC-CCCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCC---E-ECCCCCCCCC Q ss_conf 7-4468---8999886424-567775448430020001157765787775578887766641883---0-0022343324 Q gi|254781066|r 91 A-AGEE---KIFCFAHAWR-NGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQK---I-FSFQNVNCNP 161 (355) Q Consensus 91 ~-~G~~---rvyqig~~FR-aE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~---~-~~~~~~~~~~ 161 (355) . -||. -+|+=-.+.| +|+.|..|+-=.-|.|||..-...+-.++...+.++.+.+.+... + ..|.... .. T Consensus 85 ~~y~f~~geGlyTdMnAiR~DE~ldn~HSiyVDQWDWEkvI~~edRnl~~LK~tV~~Iy~~ik~tE~~v~~~yp~~~-~L 163 (327) T PRK05425 85 KRYGFSAGEGLYTDMNAIRPDEDLDNTHSVYVDQWDWEKVIDKEERNLDFLKETVNKIYKAIKATELAVSEKYPLAK-FL 163 (327) T ss_pred HHCCCCCCCEECCCCCCCCCCCCCCCCEEEEECCCCHHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CC T ss_conf 96599989532016762546755687601898400364536853267899999999999999999999999686311-48 Q ss_pred CCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCC Q ss_conf 67732078888656660876532345556232799999999768877876534789876643003622376754432576 Q gi|254781066|r 162 FSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRY 241 (355) Q Consensus 162 ~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~y 241 (355) -.+.-.++-.+....|...+ ...-....+++. +.|||++- T Consensus 164 p~~I~FitsqeL~~~YP~Ls-----------~keRE~~i~ke~-----------------------------gAVFl~~I 203 (327) T PRK05425 164 PEKITFIHSQELEDRYPDLT-----------PKEREDAIAKEY-----------------------------GAVFLIGI 203 (327) T ss_pred CCCCEEECHHHHHHHCCCCC-----------HHHHHHHHHHHH-----------------------------CCEEEEEC T ss_conf 76116864899997675899-----------789999999983-----------------------------94999944 Q ss_pred CHHHHHHC--CCCC----CCCCCCCCCEEEE------CCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHH Q ss_conf 88886413--6787----7836330220223------6712256402106999999999999999972888530101899 Q gi|254781066|r 242 PAPESALA--NIYP----ADPRFTKRFELYA------CNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDF 309 (355) Q Consensus 242 P~~~~pla--k~~~----~~~~va~rfdl~i------~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~f 309 (355) =- +|+ ++++ +-......=|+++ ...||++-+.+.+ +..+..|.......+....+ | T Consensus 204 G~---~L~~g~~Hd~RApDYDDW~LNGDilvw~~vl~~a~ElSSMGIRVd-----~~sL~~QL~~~~~~dr~~l~----~ 271 (327) T PRK05425 204 GG---KLSDGKPHDGRAPDYDDWGLNGDILVWNPVLDRAFELSSMGIRVD-----EEALKKQLKLTGDEDRLELE----W 271 (327) T ss_pred CC---CCCCCCCCCCCCCCCCCCCCCCEEEEEEHHCCCEEEEECCEEEEC-----HHHHHHHHHHCCCHHHHCCH----H T ss_conf 88---689989677779998676667549996023073246623547888-----99999999973973543498----9 Q ss_pred HHHH-CC-CCCCCEEECCHHHHHHHHHCCCCHHHHCC Q ss_conf 9986-18-89632453159999899815597131115 Q gi|254781066|r 310 LACL-TE-MPQSSGIAMGFDRLVMLVTGANNINEVIW 344 (355) Q Consensus 310 l~al-~G-~PPhgG~glGidRLvm~l~g~~~Irdvi~ 344 (355) -.++ .| +|-+=|.|||=.||||+|++...|-||.+ T Consensus 272 H~~ll~~~LP~TIGGGIGQSRlcM~lL~KaHIGEVQ~ 308 (327) T PRK05425 272 HQALLNGELPLTIGGGIGQSRLCMLLLRKAHIGEVQA 308 (327) T ss_pred HHHHHCCCCCCCCCCCCCHHHHHHHHHCCCCCCCEEE T ss_conf 9999749998431276239999999973252211576 No 55 >cd00774 GlyRS-like_core Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP binding and hydrolysis. This alignment contains only sequences from the GlyRS form which homodimerizes. The heterotetramer glyQ is in a different family of class II aaRS. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the N-terminus of the accessory subunit of mitochondrial polymerase gamma (Pol gamma b). Pol gamma b stimulates processive DNA synthesis and is functional as a homodimer, which can associate with the catalytic subunit Pol gamma alpha to form a heterotrimer. Despite significant both structural and sequence similarity with Gly Probab=98.42 E-value=5.1e-07 Score=60.99 Aligned_cols=99 Identities=28% Similarity=0.267 Sum_probs=64.3 Q ss_pred HHHHHHHHHHHHHHHH--HCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHH----H--HHHHHHH Q ss_conf 9999999999999999--879889847821056898544541241024788678320000285899----9--9898744 Q gi|254781066|r 22 LLKRNMIQSSLREYFV--ENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFS----C--KKLLAAG 93 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~--~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~----l--K~ll~~G 93 (355) ...+..|.++-|+.|- +.+++|||||++.+. -.|.|.....+..+..+||+ ||.. . |.++-.. T Consensus 32 ~~LK~Ni~~~W~~~fv~~~~~~~~id~~ii~p~-------LmF~T~iG~~~~~~~~~yLR--PETAQGifvnFk~~~~~~ 102 (254) T cd00774 32 VELKNNIKSAWRKSFVLEEEDMLEIDSPIITPE-------LMFKTSIGPVESGGNLGYLR--PETAQGIFVNFKNLLEFN 102 (254) T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCC-------CCEECCCCCCCCCCCCEEEC--HHHHHHHHHHHHHHHHHC T ss_conf 999999999999998743798799541003663-------22001215655898603536--345347798789999964 Q ss_pred HHH----HHHHHHHHCCCCCCCCCC---CCEEEECEEECCCCHH Q ss_conf 688----999886424567775448---4300200011577657 Q gi|254781066|r 94 EEK----IFCFAHAWRNGEQGCLHQ---PEFTMLEWYRAHESYE 130 (355) Q Consensus 94 ~~r----vyqig~~FRaE~~~~rHl---pEFtmLE~e~af~d~~ 130 (355) -.| |-|||+|||||=+-++.+ -||||+|+|. |++-+ T Consensus 103 r~kLPFGiaQIGk~FRNEIsPr~~l~R~REF~q~EiE~-F~~P~ 145 (254) T cd00774 103 RRKLPFGVAQIGKSFRNEISPRNGLFRVREFTQAEIEF-FVDPE 145 (254) T ss_pred CCCCCEEEEEEEECCCCCCCCCCCCCCHHCHHHHEEEE-EECCC T ss_conf 88888445654202267347776754000002125788-85798 No 56 >cd00645 AsnA Asparagine synthetase (aspartate-ammonia ligase) (AsnA) catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia. AsnA is a homodimeric enzyme which is structurally similiar to the catalytic core domain of class II aminoacyl-tRNA synthetases. Ammonia-dependent AsnA is not homologous to the glutamine-dependent asparagine synthetase AsnB. Probab=98.35 E-value=2.6e-05 Score=50.91 Aligned_cols=262 Identities=16% Similarity=0.170 Sum_probs=122.1 Q ss_pred HHHHHHHHHH-----HCCCEEEECCCEECC-CC-CCC---CCCCEEEECCCCCCCCCCCCCCCCHHHHHHHH-HH-HHHH Q ss_conf 9999999999-----879889847821056-89-854---45412410247886783200002858999989-87-4468 Q gi|254781066|r 28 IQSSLREYFV-----ENQFIEIDSMSLQYS-PG-NET---HIRAFSTELIIQDHIRKPLYLQTSPEFSCKKL-LA-AGEE 95 (355) Q Consensus 28 i~~~iR~ff~-----~~gF~EV~TPiL~~~-~~-g~~---~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~l-l~-~G~~ 95 (355) .|+.|+++|. +-+.+.|..|+++.. .| .+- .-+|..... .+.-+..+=-.+|--=+ ||+ |. -||. T Consensus 3 aI~~iK~~F~~~L~~~LnL~rVsAPLfv~~~sGlND~LnG~ErpV~F~i--k~~~~~~~EIVhSLAKW-KR~aL~~y~f~ 79 (309) T cd00645 3 AIKFIKDFFQDNLAKELNLIRVSAPLFVEKGSGLNDNLNGVEKPVSFKV--KALPDATLEVVHSLAKW-KRLALARYGFS 79 (309) T ss_pred HHHHHHHHHHHHHHHHHCCEEECCCEEECCCCCCCCCCCCEEECEEEEC--CCCCCCEEEEEEEHHHH-HHHHHHHCCCC T ss_conf 4999999999999997392796666177079887768787460228635--78899726997135888-99999966998 Q ss_pred ---HHHHHHHHHCC-CCCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCCE----ECCCCCCCCCCCCCCC Q ss_conf ---89998864245-677754484300200011577657877755788877666418830----0022343324677320 Q gi|254781066|r 96 ---KIFCFAHAWRN-GEQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQKI----FSFQNVNCNPFSEPEY 167 (355) Q Consensus 96 ---rvyqig~~FRa-E~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~~----~~~~~~~~~~~~~~~~ 167 (355) -+|+=-.+-|- |+.|..|+-=.-|-|||..-...+-.++...+.++.+.+.+...- ..|.......-.+.-. T Consensus 80 ~geGlytdMnAiR~DE~ldn~HSiyVDQWDWEkvI~~~dRnl~~Lk~tV~~Iy~~ik~tE~~v~~~yp~l~~~Lp~~I~F 159 (309) T cd00645 80 LGEGLYTDMNAIRPDEDLDNIHSIYVDQWDWEKVISKGERNLETLKETVNKIYKAIKETELEVNEKYPQLEPILPEEITF 159 (309) T ss_pred CCCEECCCCCCCCCCCCCCCCCEEEECCCCHHHHCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCEEE T ss_conf 99430127762557755687612898500353427852258999999999999999999999999762034408886089 Q ss_pred CCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCEECCCCCCCCCCCCCCCCHHHHH Q ss_conf 78888656660876532345556232799999999768877876534789876643003622376754432576888864 Q gi|254781066|r 168 ITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIFSRILIEKIEPNLGINCCTILDRYPAPESA 247 (355) Q Consensus 168 i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ie~~l~~~~pvfi~~yP~~~~p 247 (355) ++-.+....|.... ...-....+++. +.|||++-=. + T Consensus 160 itsqeL~~~YP~Lt-----------~keRE~~i~ke~-----------------------------gaVFi~~IG~---~ 196 (309) T cd00645 160 ITSQELEDRYPDLT-----------PKEREDAICKEH-----------------------------GAVFIIGIGG---K 196 (309) T ss_pred ECHHHHHHHCCCCC-----------HHHHHHHHHHHH-----------------------------CCEEEEECCC---C T ss_conf 62899997777999-----------789999999972-----------------------------9399994488---5 Q ss_pred HC--CCCC----CCCCCCCCCEEEE------CCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH-C Q ss_conf 13--6787----7836330220223------67122564021069999999999999999728885301018999986-1 Q gi|254781066|r 248 LA--NIYP----ADPRFTKRFELYA------CNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLACL-T 314 (355) Q Consensus 248 la--k~~~----~~~~va~rfdl~i------~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~al-~ 314 (355) |+ ++++ +-......=|+++ ...||++-+.+.+ +..+..|.......+....+ |-.++ . T Consensus 197 L~~g~~Hd~RApDYDDW~LNGDilvw~~vl~~a~ElSSMGIRVd-----~~~L~~QL~~~~~~dr~~l~----~Hk~ll~ 267 (309) T cd00645 197 LSDGKKHDGRAPDYDDWTLNGDILVWNPVLQRAFELSSMGIRVD-----EESLQKQLKLAGDEDRLELP----FHKMLLN 267 (309) T ss_pred CCCCCCCCCCCCCCCCCCCCCEEEEECHHCCCEEEEECCEEEEC-----HHHHHHHHHHCCCHHHHCCH----HHHHHHC T ss_conf 78989566779998675447648997023073225634646888-----99999999975983543598----9999974 Q ss_pred C-CCCCCEEECCHHHHHHHHHCCCCHHHHCC Q ss_conf 8-89632453159999899815597131115 Q gi|254781066|r 315 E-MPQSSGIAMGFDRLVMLVTGANNINEVIW 344 (355) Q Consensus 315 G-~PPhgG~glGidRLvm~l~g~~~Irdvi~ 344 (355) | +|-+=|.|||=.||||+|+....|-||.+ T Consensus 268 ~~LP~TIGGGIGQSRlcM~lL~KaHIGEVQ~ 298 (309) T cd00645 268 GELPQTIGGGIGQSRLCMFLLQKAHIGEVQA 298 (309) T ss_pred CCCCCCCCCCCCHHHHHHHHHCCCCCCCEEE T ss_conf 9998452376039999999975373223675 No 57 >PRK12305 thrS threonyl-tRNA synthetase; Reviewed Probab=98.32 E-value=5.6e-06 Score=54.83 Aligned_cols=130 Identities=12% Similarity=0.165 Sum_probs=80.3 Q ss_pred CCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CCCCCCCCEEEECCCC-CCCCCCCCCC Q ss_conf 9874788312615489999999999999999998798898478210568----9854454124102478-8678320000 Q gi|254781066|r 5 PSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GNETHIRAFSTELIIQ-DHIRKPLYLQ 79 (355) Q Consensus 5 p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g~~~~~~f~t~~~~~-~~~~~~~yL~ 79 (355) |-.++|+|. =.++|..+...+|+-..+.||.||.||.+.... +| |.+-+.-..+.. ..-++.+.|. T Consensus 198 pG~~~wlP~-------G~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SG--H~~~Y~e~Mf~~~~~~~e~~~lK 268 (576) T PRK12305 198 QGFPIWLEN-------GMIIKNAIRKFILELDRKYGFDEVLTPHFGEKKLYKTSG--HLDHYKDDMFKPLKIENEELIPR 268 (576) T ss_pred CCCEEECCC-------HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCC--CHHHHHHHCCCCEECCCCEEEEC T ss_conf 876467476-------789999999999999998699898464214288997666--46556642573063156416535 Q ss_pred -----CCHHHHHHHHHHHHHH---HHHHHHHHHCCCCCCCC----CCCCEEEECEEECCCCHHHHHHHHHHHHHHHHH Q ss_conf -----2858999989874468---89998864245677754----484300200011577657877755788877666 Q gi|254781066|r 80 -----TSPEFSCKKLLAAGEE---KIFCFAHAWRNGEQGCL----HQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAE 145 (355) Q Consensus 80 -----~SPql~lK~ll~~G~~---rvyqig~~FRaE~~~~r----HlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~ 145 (355) ..-++|. .-.-|.-+ |++++|.|||+|-++.- -.-.|||=|.. .|.+.+++.+.+.++++.+.. T Consensus 269 PMNCP~H~~if~-~~~rSYRdLPlR~aEfg~~~R~E~SG~L~GL~RvR~FtqDDAH-IFct~dQi~~Ei~~~l~~i~~ 344 (576) T PRK12305 269 PMTCPHHIILYS-NELRSYRDLPIRLSEQSRLYRYEKSGALTGLERVRAMDLTEGH-IFVRKDQIESEVKHLFKMIQE 344 (576) T ss_pred CCCCHHHHHHHH-CCCCCHHHCCHHHHCCCCEECCCCCCCCCCCCCCCCCCCCCCC-EEECHHHHHHHHHHHHHHHHH T ss_conf 778632677764-2775444324220004435447888655575546688768712-120899999999999999999 No 58 >PRK03772 threonyl-tRNA synthetase; Validated Probab=98.21 E-value=1.9e-05 Score=51.70 Aligned_cols=130 Identities=14% Similarity=0.189 Sum_probs=79.3 Q ss_pred CCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECC----CCCCCCCCCEEEECCCCCCCCCCCCCCC Q ss_conf 987478831261548999999999999999999879889847821056----8985445412410247886783200002 Q gi|254781066|r 5 PSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYS----PGNETHIRAFSTELIIQDHIRKPLYLQT 80 (355) Q Consensus 5 p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~----~~g~~~~~~f~t~~~~~~~~~~~~yL~~ 80 (355) |-.++|+|.- .++|..+...+|+-..++||.||.||.+... .+| |.+-+.-..+....-+++++|.. T Consensus 261 pG~~fwlP~G-------~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SG--H~~~Y~e~Mf~~~~e~~ey~lKP 331 (642) T PRK03772 261 PGMVFWHNDG-------WTIFRELEVFVRSKLKEYQYQEVKGPFMMDRVLWEKTG--HWDNYADAMFTTSSENREYAIKP 331 (642) T ss_pred CCCEEECCCH-------HHHHHHHHHHHHHHHHHCCCEEEECCHHCCHHHHHHCC--HHHHHHCCCCCCCCCHHHHCCCC T ss_conf 8763665858-------89999999999999998698598554321377887344--47664103422342014430467 Q ss_pred -----CHHHHHHHHHHHHHH---HHHHHHHHHCCCCCCC----CCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHH Q ss_conf -----858999989874468---8999886424567775----4484300200011577657877755788877666 Q gi|254781066|r 81 -----SPEFSCKKLLAAGEE---KIFCFAHAWRNGEQGC----LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAE 145 (355) Q Consensus 81 -----SPql~lK~ll~~G~~---rvyqig~~FRaE~~~~----rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~ 145 (355) .-++|+ .-.-|.-+ |++++|.|+|+|-++. .-.-.|||=|.. .|...+++-+.+.++++.+.+ T Consensus 332 MNCP~H~~iy~-~~~rSYRdLPlR~aEfg~~~R~E~SG~L~GL~RVR~FtqdDaH-IFC~~dQi~~Ei~~~l~~~~~ 406 (642) T PRK03772 332 MNCPGHVQIFN-QGLKSYRDLPLRMAEFGSCHRNEPSGSLHGLMRVRGFTQDDAH-IFCTEEQIRDEVNSCIKMVYD 406 (642) T ss_pred CCCHHHHHHHH-CCCCCHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCE-EECCHHHHHHHHHHHHHHHHH T ss_conf 78734889986-1664344365455541134316666553474568899878843-553789999999999999999 No 59 >PRK06253 O-phosphoseryl-tRNA synthetase; Reviewed Probab=98.18 E-value=9.5e-07 Score=59.42 Aligned_cols=48 Identities=8% Similarity=0.089 Sum_probs=30.6 Q ss_pred HHHHHHHHHCCC-CCCCCCCCCEEEECEEECC--CCHHHHHHHHHHHHHHH Q ss_conf 899988642456-7775448430020001157--76578777557888776 Q gi|254781066|r 96 KIFCFAHAWRNG-EQGCLHQPEFTMLEWYRAH--ESYEQLMKDCMNIIRCA 143 (355) Q Consensus 96 rvyqig~~FRaE-~~~~rHlpEFtmLE~e~af--~d~~dlm~~~E~li~~~ 143 (355) |+|.|.+|||.| ..|..||+||.+.+.=.+. +++++.....+.+++.. T Consensus 208 klFSIDRcFRrEq~eD~~hL~~yhsascvv~~edVn~d~gkav~~~lL~~f 258 (527) T PRK06253 208 KLFSIDRCFRREQKEDASRLMTYHSASCVVAGEDVTVDDGKAVAEGLLSQF 258 (527) T ss_pred EEEEEEHEEECHHHCCHHHHHHHHEEEEEEECCCCCHHHHHHHHHHHHHHH T ss_conf 687410102200002455634544322699759866777799999999970 No 60 >cd00770 SerRS_core Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. SerRS synthetase is a homodimer. Probab=98.14 E-value=3.3e-06 Score=56.24 Aligned_cols=122 Identities=15% Similarity=0.202 Sum_probs=70.9 Q ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC--CCCCCCCCEEEECCCCCCCCCCCCCCCCHH-----HHHHHHHHH- Q ss_conf 999999999999999998798898478210568--985445412410247886783200002858-----999989874- Q gi|254781066|r 21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP--GNETHIRAFSTELIIQDHIRKPLYLQTSPE-----FSCKKLLAA- 92 (355) Q Consensus 21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~~~~~f~t~~~~~~~~~~~~yL~~SPq-----l~lK~ll~~- 92 (355) ..+....+++.+++++.++||.||.||.|.... .|..+..-|.-..+... +.+.||.-.-| +|..+.+.. T Consensus 51 ga~Le~AL~~f~~d~~~~~Gy~eV~tP~iv~~~~~~~sG~~~~~~e~~y~i~--~~~~~Li~tae~~l~~~~~~~~~~~~ 128 (297) T cd00770 51 GALLERALINFALDFLTKRGFTPVIPPFLVRKEVMEGTGQLPKFDEQLYKVE--GEDLYLIATAEVPLAALHRDEILEEE 128 (297) T ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHCCCCCCHHHHHCCC--CHHHHHHHCCCCCEEEEEEEEECCHH T ss_conf 9999999999999999987998998853013899854357876356521035--50555544056662234420031775 Q ss_pred HH-HHHHHHHHHHCCC-CC---CC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHH Q ss_conf 46-8899988642456-77---75---4484300200011577657877755788877666 Q gi|254781066|r 93 GE-EKIFCFAHAWRNG-EQ---GC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAE 145 (355) Q Consensus 93 G~-~rvyqig~~FRaE-~~---~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~ 145 (355) -+ =|++.+++|||+| ++ ++ ...-.|+++|.. ++.+-++..+..|+|+..+.+ T Consensus 129 dLPlr~~~~s~cfR~Eags~G~d~~GL~RvhqF~kvE~~-~~c~pe~s~~~~e~~~~~~e~ 188 (297) T cd00770 129 ELPLKYAGYSPCFRKEAGSAGRDTRGLFRVHQFEKVEQF-VFTKPEESWEELEELISNAEE 188 (297) T ss_pred HCCCCEEECCCHHHHCCCCCCCCCCCEEEEEECCEEEEE-EECCHHHHHHHHHHHHHHHHH T ss_conf 588650224634132037777555545788721100377-616878899999999999999 No 61 >PRK12304 thrS threonyl-tRNA synthetase; Reviewed Probab=98.10 E-value=4.9e-05 Score=49.26 Aligned_cols=132 Identities=16% Similarity=0.151 Sum_probs=80.2 Q ss_pred CCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CCCCCCCC-----EEEECCCCCCCCCC Q ss_conf 9874788312615489999999999999999998798898478210568----98544541-----24102478867832 Q gi|254781066|r 5 PSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GNETHIRA-----FSTELIIQDHIRKP 75 (355) Q Consensus 5 p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g~~~~~~-----f~t~~~~~~~~~~~ 75 (355) |-.++|+|.= .++|..+...+|+-..+.||.||.||.+.... +| |.+- |.+......+.=+| T Consensus 229 ~G~~~wlP~G-------~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SG--H~~~Y~e~Mf~~~~d~~~y~lKP 299 (604) T PRK12304 229 AGLPIWLPKG-------ARLRSKLEHLLYKAHRLRGYEPVRGPEILKSDVWKISG--HYANYKENMYFTTIDEQEYGIKP 299 (604) T ss_pred CCCEEECCCH-------HHHHHHHHHHHHHHHHHCCCEEECCCCCCCHHHHHCCC--HHHHHCCCCCEEECCCCEEECCC T ss_conf 8753683775-------49999999999999998299680386545588873055--15321057644505774330367 Q ss_pred CCCCCCHHHHHHHHHHHHHH---HHHHHHHHHCCCCCCCC----CCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 00002858999989874468---89998864245677754----48430020001157765787775578887766641 Q gi|254781066|r 76 LYLQTSPEFSCKKLLAAGEE---KIFCFAHAWRNGEQGCL----HQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA 147 (355) Q Consensus 76 ~yL~~SPql~lK~ll~~G~~---rvyqig~~FRaE~~~~r----HlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~ 147 (355) +--+..-++|+ .-.-|.-+ |++++|.|||+|.++.- -.-.|||=|.. .|...+++-+.+.++++.+.+.. T Consensus 300 MNCP~H~~if~-~~~rSYRdLPlR~aEfg~~hR~E~SG~L~GL~RvR~FtqDDaH-IFc~~dQi~~Ei~~~l~~~~~vy 376 (604) T PRK12304 300 MNCVGHIKVYQ-SDLRSYRDLPLKFFEYGVVHRHEKSGVLHGLFRVREFTQDDAH-IFCMPSQIKEEVLEILDFVDKIM 376 (604) T ss_pred CCCHHHHHHHH-CCCCCHHHCCHHHHHCCCEECCCCCCCCCCCCCCCCCCCCCCE-EECCHHHHHHHHHHHHHHHHHHH T ss_conf 79574999986-2774444355554543532026777663464557789778844-65489999999999999999999 No 62 >PTZ00213 asparagine synthetase A; Provisional Probab=98.08 E-value=9.8e-05 Score=47.50 Aligned_cols=294 Identities=12% Similarity=0.125 Sum_probs=131.9 Q ss_pred HHHHHHHHHHHHHHHH-----HCCCEEEECCCEECCCCC--CC---CCCCEEEECCCCCCCCCCCCCCCCHHHHHHHH-H Q ss_conf 9999999999999999-----879889847821056898--54---45412410247886783200002858999989-8 Q gi|254781066|r 22 LLKRNMIQSSLREYFV-----ENQFIEIDSMSLQYSPGN--ET---HIRAFSTELIIQDHIRKPLYLQTSPEFSCKKL-L 90 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~-----~~gF~EV~TPiL~~~~~g--~~---~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~l-l 90 (355) ++...+.|+.|+++|. +-+.++|..|+++....| +- .-+|...+... --+..+=-.+|--=| ||. | T Consensus 8 ~~~tq~aI~~iK~~F~~~L~~~LnL~rVsAPLfv~~~sGlND~LnG~ErpV~f~ik~--~p~~~~EIVhSLAKW-KR~aL 84 (350) T PTZ00213 8 YIDLQEQILTVKQIFSEALAKELNLVEVEAPILARVGDGTQDNLSGVEKAVQVHVKE--IPDAKFEVVHSLAKW-KRQTL 84 (350) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCEEECCCEEEECCCCCCCCCCCEECCEEEECCC--CCCCCEEEEEEHHHH-HHHHH T ss_conf 999999999999999999999739179645638707988766878725131654477--899715997133888-99999 Q ss_pred H-HHH---HHHHHHHHHHCCC-CCCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCCC---E-ECCCCCCCCC Q ss_conf 7-446---8899988642456-7775448430020001157765787775578887766641883---0-0022343324 Q gi|254781066|r 91 A-AGE---EKIFCFAHAWRNG-EQGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQK---I-FSFQNVNCNP 161 (355) Q Consensus 91 ~-~G~---~rvyqig~~FRaE-~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~~---~-~~~~~~~~~~ 161 (355) . -|| +-+|+=-.+-|.+ +.|..|+-=.-|-|||..-...+-.++...+.|+.+.+.+... + ..|. ..... T Consensus 85 ~~y~f~~geGlyTdMnAIR~De~lDn~HSiYVDQWDWEkvI~~e~R~l~~LK~tV~~Iy~~ik~tE~~v~~~y~-~~~~L 163 (350) T PTZ00213 85 GNHKFPVGQGIYTHMKALRVEETLDNIHSVYVDQWDWERVMAPADRNLEFLKATVRSLYAAIRQTEEALCSKYD-IDPIL 163 (350) T ss_pred HHCCCCCCCEEEECCCCCCCCCCCCCCCCEEECCCCHHCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCC T ss_conf 96599899555424440257655687631898520420006842268999999999999999999999998668-65668 Q ss_pred CCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCC----CHHHHHHHHHHCEECCCCCCCC-CC Q ss_conf 677320788886566608765323455562327999999997688778765----3478987664300362237675-44 Q gi|254781066|r 162 FSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDD----TWSDIFSRILIEKIEPNLGINC-CT 236 (355) Q Consensus 162 ~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~l~~~~ie~~l~~~~-pv 236 (355) -.+.-.++-.|....|... +...-....+++.|.-+-.+. .-|+..+. =.|.+.... |+ T Consensus 164 P~~I~FitsqeL~~~YP~L-----------t~keRE~~i~ke~gAVFl~gIG~~L~~G~~HD~-----RAPDYDDW~t~~ 227 (350) T PTZ00213 164 PESIQFVHAEHLLKRYPEL-----------DPKEREREIVKKYGAVFLIGIGCKLSSGDPHDA-----RAPDYDDWSSPV 227 (350) T ss_pred CCCCEEECHHHHHHHCCCC-----------CHHHHHHHHHHHHCCEEEEECCCCCCCCCCCCC-----CCCCCCCCCCCC T ss_conf 8752686289999777799-----------878899999998395999943786789895777-----799876454655 Q ss_pred --CCCCCCHHHHHHCCCCCCCCCCCCCCEEEE------CCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHH Q ss_conf --325768888641367877836330220223------671225640210699999999999999997288853010189 Q gi|254781066|r 237 --ILDRYPAPESALANIYPADPRFTKRFELYA------CNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDED 308 (355) Q Consensus 237 --fi~~yP~~~~plak~~~~~~~va~rfdl~i------~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~ 308 (355) --..||..-.+--..|.-+.--...=|+++ +..||.+-+.+.+ +..+..|.......+....+ T Consensus 228 ~~~~~g~~~~~~~~~~~~~~~~~~GLNGDIlvw~pvL~~a~ElSSMGIRVd-----~~sL~~QL~~~~~~dr~~l~---- 298 (350) T PTZ00213 228 SASKIGFPTADDEKPTMNSLMSLQGLNGDILVYNPVLDDVLELSSMGIRVD-----AEALRRQLELTGNEDRLKCV---- 298 (350) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECHHCCCEEEEECCEEEEC-----HHHHHHHHHHCCCHHHHCCH---- T ss_conf 444344444333333332222345666618996113075125634647888-----99999999875983554498---- Q ss_pred HHHHH-CC-CCCCCEEECCHHHHHHHHHCCCCHHHHCC Q ss_conf 99986-18-89632453159999899815597131115 Q gi|254781066|r 309 FLACL-TE-MPQSSGIAMGFDRLVMLVTGANNINEVIW 344 (355) Q Consensus 309 fl~al-~G-~PPhgG~glGidRLvm~l~g~~~Irdvi~ 344 (355) |-.++ .| +|-+=|.|||--||||+|+....|-||.+ T Consensus 299 ~Hk~ll~geLP~TIGGGIGQSRlcM~lL~KaHIGEVQa 336 (350) T PTZ00213 299 WHQCLLNGEFPQTIGGGIGQSRMVMFMLRKKHIGEVQC 336 (350) T ss_pred HHHHHHCCCCCCCCCCCCCHHHHHHHHHCCCCCCCEEE T ss_conf 99999759998432276219999999973262222664 No 63 >PRK04483 threonyl-tRNA synthetase; Validated Probab=98.07 E-value=2.5e-05 Score=51.05 Aligned_cols=133 Identities=11% Similarity=0.154 Sum_probs=78.8 Q ss_pred CCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CCCCCCCCEEEECCCCCCCCCCCCCCC Q ss_conf 9874788312615489999999999999999998798898478210568----985445412410247886783200002 Q gi|254781066|r 5 PSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GNETHIRAFSTELIIQDHIRKPLYLQT 80 (355) Q Consensus 5 p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g~~~~~~f~t~~~~~~~~~~~~yL~~ 80 (355) |-.++|+|.= .++|..+...+|+-..++||.||.||.+.... +| |.+-+.-..+....-++.+.|.. T Consensus 261 pG~~~wlP~G-------~~i~~~le~~~r~~~~~~Gy~eV~tP~i~~~~Lw~~SG--H~~~Y~e~Mf~~~~~~~~~~lKP 331 (634) T PRK04483 261 PGLVFWHPKG-------WSLWQVVEQYMRKVYRDSGYGEVRCPQILDVSLWQKSG--HWDNYQDAMFFTESEKRTYAVKP 331 (634) T ss_pred CCCEEECCCH-------HHHHHHHHHHHHHHHHHCCCEEEECCEECCHHHHHHCC--CHHHHHHCCCEECCCCCEEEECC T ss_conf 8643881668-------99999999999999998299599886251377876256--16455303713425540355157 Q ss_pred -----CHHHHHHHHHHHHHH---HHHHHHHHHCCCCCCCC----CCCCEEEECEEECCCCHHHHHHHHHHHHH---HHHH Q ss_conf -----858999989874468---89998864245677754----48430020001157765787775578887---7666 Q gi|254781066|r 81 -----SPEFSCKKLLAAGEE---KIFCFAHAWRNGEQGCL----HQPEFTMLEWYRAHESYEQLMKDCMNIIR---CAAE 145 (355) Q Consensus 81 -----SPql~lK~ll~~G~~---rvyqig~~FRaE~~~~r----HlpEFtmLE~e~af~d~~dlm~~~E~li~---~~~~ 145 (355) --++|. .-.-|.-+ |++++|.|||+|-++.- -.-.|||=|.. .|...+++-+.+.++++ .+.+ T Consensus 332 MNCP~H~~if~-~~~rSYRdLPlR~aE~g~~~R~E~SG~L~GL~RvR~FtqdDaH-IFc~~dQi~~Ei~~~l~~~~~vy~ 409 (634) T PRK04483 332 MNCPGHVQVFN-QGLHSYRDLPIRYGEFGACHRNEPSGALHGILRVRGFTQDDGH-VFCLESQIEAEVTAFHQQALAVYT 409 (634) T ss_pred CCCHHHHHHHH-CCCCCHHHCCHHHHHCCCEEECCCCCCCCCCCCCCCCCCCCCE-EECCHHHHHHHHHHHHHHHHHHHH T ss_conf 68564879987-1774444343665543302205677654574568899889833-563899999999999999999998 Q ss_pred HHC Q ss_conf 418 Q gi|254781066|r 146 VAN 148 (355) Q Consensus 146 ~~~ 148 (355) .++ T Consensus 410 ~fG 412 (634) T PRK04483 410 AFG 412 (634) T ss_pred HCC T ss_conf 639 No 64 >PRK00413 thrS threonyl-tRNA synthetase; Reviewed Probab=98.04 E-value=4.3e-05 Score=49.61 Aligned_cols=130 Identities=15% Similarity=0.207 Sum_probs=79.4 Q ss_pred CCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CCCCCCCCEEEECCCCCCC-CCCCCCC Q ss_conf 9874788312615489999999999999999998798898478210568----9854454124102478867-8320000 Q gi|254781066|r 5 PSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GNETHIRAFSTELIIQDHI-RKPLYLQ 79 (355) Q Consensus 5 p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g~~~~~~f~t~~~~~~~~-~~~~yL~ 79 (355) |-.++|+|.= .++|..+...+|+-..++||-||.||.+.... +| |.+-+.-..+..... +..++|. T Consensus 258 pGl~~w~P~G-------~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SG--Hw~~Y~e~Mf~~~~~~~~~~~lK 328 (639) T PRK00413 258 PGLPFWHPKG-------WIIRNELEDYMRRRHLKAGYQEVNTPHILDRSLWETSG--HWDHYRENMFPTMSDDGEDYALK 328 (639) T ss_pred CCCEEECCCH-------HHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCC--CHHHHCCCCCCCEECCCCEEEEC T ss_conf 8764663768-------99999999999999998698598364134688996547--42232254223240152103204 Q ss_pred -----CCHHHHHHHHHHHHHH---HHHHHHHHHCCCCCCCC----CCCCEEEECEEECCCCHHHHHHHHHHHHHHHHH Q ss_conf -----2858999989874468---89998864245677754----484300200011577657877755788877666 Q gi|254781066|r 80 -----TSPEFSCKKLLAAGEE---KIFCFAHAWRNGEQGCL----HQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAE 145 (355) Q Consensus 80 -----~SPql~lK~ll~~G~~---rvyqig~~FRaE~~~~r----HlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~ 145 (355) .--++|. .-.-|.-+ |++++|.|+|+|.++.- -.-.|||=|.. .|...+++.+.+.++++.+.+ T Consensus 329 PMNCP~H~~if~-~~~~SYRdLPlR~aEfg~~~R~E~SG~L~GL~RvR~FtqdDaH-IFc~~dQi~~Ei~~~l~~~~~ 404 (639) T PRK00413 329 PMNCPGHILIFK-SGLRSYRELPLRLAEFGTVHRYEKSGALHGLMRVRGFTQDDAH-IFCTPEQIKDELLSVLDLILS 404 (639) T ss_pred CCCCCCHHHHHH-CCCCCHHHCCHHHHHHHHHHCCCCCCCCCCEEEEEEEECCCCE-EECCHHHHHHHHHHHHHHHHH T ss_conf 668700335644-3553555475566641132056778744564233000015841-324789999999999999999 No 65 >PRK12444 threonyl-tRNA synthetase; Reviewed Probab=98.00 E-value=8.8e-05 Score=47.76 Aligned_cols=130 Identities=16% Similarity=0.186 Sum_probs=77.2 Q ss_pred CCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CCCCCCCCEEEECCCCCCCCCCCCCCC Q ss_conf 9874788312615489999999999999999998798898478210568----985445412410247886783200002 Q gi|254781066|r 5 PSQPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GNETHIRAFSTELIIQDHIRKPLYLQT 80 (355) Q Consensus 5 p~~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g~~~~~~f~t~~~~~~~~~~~~yL~~ 80 (355) |-.++|+|. =.++|..+...+|+-..++||.||-||.+.... +| |.+-+.-..+...--++.+.|.. T Consensus 264 pG~~fwlP~-------G~~i~~~le~~~r~~~~~~GY~eV~TP~i~~~~Lw~~SG--H~~~Y~e~Mf~~~~d~~~~~lKP 334 (639) T PRK12444 264 PGMPFYLPK-------GQIIRNELEAFLREIQKEYNYQEVRTPFMMNQELWERSG--HWGHYKDNMYFSEVDNKSFALKP 334 (639) T ss_pred CCCEEEECC-------HHHHHHHHHHHHHHHHHHCCCEEECCCEEEHHHHHHHCC--HHHHHHHCCCCCCCCCCEEECCC T ss_conf 974478467-------869999999999999998398782286662156876166--04333302755454540331267 Q ss_pred -----CHHHHHHHHHHHHHH---HHHHHHHHHCCCCCCCC----CCCCEEEECEEECCCCHHHHHHHHHHHHHHHHH Q ss_conf -----858999989874468---89998864245677754----484300200011577657877755788877666 Q gi|254781066|r 81 -----SPEFSCKKLLAAGEE---KIFCFAHAWRNGEQGCL----HQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAE 145 (355) Q Consensus 81 -----SPql~lK~ll~~G~~---rvyqig~~FRaE~~~~r----HlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~ 145 (355) --+.|. .-.-|.-+ |++++|.|||+|-++.. -.-.|||=|.. .|.+.+++-+.+.+++..+.. T Consensus 335 MNCP~H~~if~-~~~rSYRdLPlR~aEfg~vhR~E~SG~L~GL~RVR~FtqDDAH-IFct~dQi~~Ei~~~~~~~~~ 409 (639) T PRK12444 335 MNCPGHMLMFK-NKLHSYRELPIRMCEFGQVHRHEFSGALNGLLRVRTFCQDDAH-LFVTPEQIEDEIKSVMAQIDY 409 (639) T ss_pred CCCHHHHHHHH-CCCCCHHHCCHHHHHCCCEECCCCCCCCCCCCCCCCCCCCCCE-EECCHHHHHHHHHHHHHHHHH T ss_conf 68588999986-0562144365222433646337787664576778899879824-653889999999999999999 No 66 >COG0442 ProS Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] Probab=97.92 E-value=2.8e-05 Score=50.68 Aligned_cols=123 Identities=20% Similarity=0.237 Sum_probs=82.6 Q ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCEECCC---CCCCCCCCEEEECCC-CCCCCCCCCCCCCHHHHH----HHHHHHH Q ss_conf 99999999999999998798898478210568---985445412410247-886783200002858999----9898744 Q gi|254781066|r 22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSP---GNETHIRAFSTELII-QDHIRKPLYLQTSPEFSC----KKLLAAG 93 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~---~g~~~~~~f~t~~~~-~~~~~~~~yL~~SPql~l----K~ll~~G 93 (355) ++.+.+|.+-||+.|++-|..||-=|+|+++- +.+ +.+-|.-+++. .+-.+.++.|+...|--+ +.-+-|. T Consensus 47 ~rv~~kI~~iir~em~~~G~~Evl~P~L~p~eLwkEs~-r~~~f~~El~~v~drg~~~l~L~PTsEe~it~~~~~~i~SY 125 (500) T COG0442 47 LRVLEKIENIIREEMDKIGAQEVLFPTLIPAELWKESG-RWEGFGPELFRVKDRGDRPLALRPTSEEVITDMFRKWIRSY 125 (500) T ss_pred HHHHHHHHHHHHHHHHHCCCEEEECHHCCHHHHHHHHC-HHHCCCHHHEEEECCCCCEEEECCCCHHHHHHHHHHHHHHH T ss_conf 99999999999999986085088311058789998748-56303644489971699634357886899999999986556 Q ss_pred HH---HHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHH Q ss_conf 68---8999886424567775---4484300200011577657877755788877666 Q gi|254781066|r 94 EE---KIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAE 145 (355) Q Consensus 94 ~~---rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~ 145 (355) -+ ++|||+..||+|-.-| --.-||+|=|.|.+++|.+++.+..+.|...-.+ T Consensus 126 kdLPl~lYQi~~kfRdE~rpr~gllR~REF~mkdaySfh~~~e~a~~~y~~~~~~Y~~ 183 (500) T COG0442 126 KDLPLKLYQIQSKFRDEKRPRFGLLRGREFLMKDAYSFHADEEDAEETYEKMLDAYSR 183 (500) T ss_pred HHCCCCEEEEEEEEECCCCCCCCCCCHHEEEECCCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 5188121013458843346887730002033011121028989999999999999999 No 67 >TIGR00469 pheS_mito phenylalanyl-tRNA synthetase; InterPro: IPR004530 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases . This family describes the mitochondrial phenylalanyl-tRNA synthetases. Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases.; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=97.88 E-value=7.3e-05 Score=48.27 Aligned_cols=129 Identities=16% Similarity=0.197 Sum_probs=67.0 Q ss_pred CCCHHHCCCH-HHHHHHHHHHHHHHHHHHH-HCCCE-----EEECCCEECCCCCCCCCCCEEEECCCCC----------C Q ss_conf 7883126154-8999999999999999999-87988-----9847821056898544541241024788----------6 Q gi|254781066|r 9 WWNRDFHYRR-RPFLLKRNMIQSSLREYFV-ENQFI-----EIDSMSLQYSPGNETHIRAFSTELIIQD----------H 71 (355) Q Consensus 9 ~~~~~~~~r~-R~~l~~Rs~i~~~iR~ff~-~~gF~-----EV~TPiL~~~~~g~~~~~~f~t~~~~~~----------~ 71 (355) +-+++.||+. .|+=++|..|...+-.--. .+|== .=--|+.+.... .+.. .++.+ | T Consensus 31 ~~~~~~HL~~~HP~~I~R~~I~~~l~~~~~nqrGnP~F~~y~~~~PVVT~~~N----FD~L---~~P~DH~~R~KSD~YY 103 (460) T TIGR00469 31 LVDASKHLKEDHPLSILRDLIVKKLYSVDRNQRGNPLFKVYDNFKPVVTVQEN----FDSL---LIPKDHVSRSKSDTYY 103 (460) T ss_pred HHCCHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEHCCCCCCEEEECCC----CCCC---CCCCCCCCCCCCCEEE T ss_conf 62100011235764677889998763221035688511110057974732013----3112---7888778875454133 Q ss_pred CCCCCCCC---CCHHHHHHHHHHHHHHH-------HHHHHHHHCCCCCCCCCCCCEEEECEEECC-CCHHHH-------H Q ss_conf 78320000---28589999898744688-------999886424567775448430020001157-765787-------7 Q gi|254781066|r 72 IRKPLYLQ---TSPEFSCKKLLAAGEEK-------IFCFAHAWRNGEQGCLHQPEFTMLEWYRAH-ESYEQL-------M 133 (355) Q Consensus 72 ~~~~~yL~---~SPql~lK~ll~~G~~r-------vyqig~~FRaE~~~~rHlpEFtmLE~e~af-~d~~dl-------m 133 (355) .++.--|+ ++.|+- |+.+|.+. --=.|-+||-.++|.+|=|=|-|+|--..+ .+-.++ + T Consensus 104 IN~~HLLR~HT~AH~~E---~~~~~~~~sdniksGFL~~~~VYRRDEID~THYPVFHQ~~Ga~~~~~TK~~~~~~~P~y~ 180 (460) T TIGR00469 104 INETHLLRAHTSAHELE---LISKILDDSDNIKSGFLVVADVYRRDEIDKTHYPVFHQADGAAVRKVTKDDLFVKEPGYL 180 (460) T ss_pred ECCCHHHHHCCCHHHHH---HHHCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEECCCCCEEHHHHHHHHCCCCCCHH T ss_conf 03300333302134545---442223532111212068743441234568788701426762121002344304687401 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 75578887766641 Q gi|254781066|r 134 KDCMNIIRCAAEVA 147 (355) Q Consensus 134 ~~~E~li~~~~~~~ 147 (355) +.+++-++.+.... T Consensus 181 E~~~E~~~~~~~~~ 194 (460) T TIGR00469 181 EKIREDIRQVLALL 194 (460) T ss_pred HHHHHHHHHHHHCC T ss_conf 24566678885100 No 68 >PRK03991 threonyl-tRNA synthetase; Validated Probab=97.84 E-value=3.8e-05 Score=49.94 Aligned_cols=123 Identities=13% Similarity=0.167 Sum_probs=75.2 Q ss_pred HHHHHHHHHHHHHHHHCCCEEEECCCEECC--CCCCCCCCCEEEECCCCCCCCCCCCCCCC--H---HHHHHHHHHHHHH Q ss_conf 999999999999999879889847821056--89854454124102478867832000028--5---8999989874468 Q gi|254781066|r 23 LKRNMIQSSLREYFVENQFIEIDSMSLQYS--PGNETHIRAFSTELIIQDHIRKPLYLQTS--P---EFSCKKLLAAGEE 95 (355) Q Consensus 23 ~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~--~~g~~~~~~f~t~~~~~~~~~~~~yL~~S--P---ql~lK~ll~~G~~ 95 (355) ..|+.+.+.+|+-..+.|+.||.||+|-.. ..-..|++-|.-..+....-++.+.|+-. | +.|+ .-+.|.-+ T Consensus 228 ~i~~lle~Yv~~~~~~~G~~eV~TP~m~d~~~~~~sgH~~~f~e~my~~~~d~~~~~LrpmnCpgh~~i~~-~~~~SYRd 306 (613) T PRK03991 228 LMKDLLEDYVYNLVKELGAMPVETPNMYDLSHPAIREHADKFGERQYRVKSDKKDLMLRFAACFGQFAMLK-DMTISYKN 306 (613) T ss_pred HHHHHHHHHHHHHHHHCCCEEEECCCEEECCCCHHHHHHHHHCCCCEEEECCCHHHCCCCCCCCCCEEEEC-CCCCCHHH T ss_conf 99999999999999863966845761640554025568876111342563276332304457863123510-24457432 Q ss_pred ---HHHHHHHH-HCCCCCCC----CCCCCEEEECEEECCC-CHHHHHHHHHHHHHHHHHHH Q ss_conf ---89998864-24567775----4484300200011577-65787775578887766641 Q gi|254781066|r 96 ---KIFCFAHA-WRNGEQGC----LHQPEFTMLEWYRAHE-SYEQLMKDCMNIIRCAAEVA 147 (355) Q Consensus 96 ---rvyqig~~-FRaE~~~~----rHlpEFtmLE~e~af~-d~~dlm~~~E~li~~~~~~~ 147 (355) |+|++|.| ||+|.++. .-+-.|||=|.= .|+ +.+++++.+.+++..+.+.. T Consensus 307 LPlRl~E~g~~syR~E~SG~L~GL~RVR~FTqdDaH-IFC~~~dQi~~E~~~~~~li~~v~ 366 (613) T PRK03991 307 LPLKMYELSDYSFRLEQRGELVGLKRLRAFTMPDMH-TLCKDMDEAMEEFEKQHKLILETG 366 (613) T ss_pred CCHHHHHHCCCEEECCCCCCEECEEEEECCCCCCCE-ECCCCHHHHHHHHHHHHHHHHHHH T ss_conf 646776522420212567744440133235668611-316877899999999999999999 No 69 >COG0441 ThrS Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] Probab=97.78 E-value=7.2e-05 Score=48.27 Aligned_cols=114 Identities=18% Similarity=0.240 Sum_probs=72.5 Q ss_pred HHHHHHHHHHHHHHHHCCCEEEECCCEECCCC--CCCCCCCEEEECCCCCCCCCCCCCCCCH--HHHHHHHHHHH----- Q ss_conf 99999999999999987988984782105689--8544541241024788678320000285--89999898744----- Q gi|254781066|r 23 LKRNMIQSSLREYFVENQFIEIDSMSLQYSPG--NETHIRAFSTELIIQDHIRKPLYLQTSP--EFSCKKLLAAG----- 93 (355) Q Consensus 23 ~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~--g~~~~~~f~t~~~~~~~~~~~~yL~~SP--ql~lK~ll~~G----- 93 (355) +.|+.+.+.+|.-..+.||-||.||+|....- ...|.+ .+...+|+..|. ++.+|.+=+-| T Consensus 221 ~ir~~le~y~~~~~~~~Gy~~V~TP~~~~~~l~~~SGH~~----------~y~e~mf~~~~~~~~~~lKpmNCpgh~~if 290 (589) T COG0441 221 TIRNLLEDYVRTKLRSYGYQEVKTPVLADLELWELSGHWD----------NYKEDMFLTESDDREYALKPMNCPGHILIF 290 (589) T ss_pred CHHHHHHHHHHHHHHHCCCEEECCCEEEECCCCHHCCCHH----------HCCCCCEEECCCCHHHEEEECCCHHHHHHH T ss_conf 6999999999989875585271287363000010112045----------513660662137723306410787689998 Q ss_pred ------H----HHHHHHHHHHCCCCCCC----CCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf ------6----88999886424567775----448430020001157765787775578887766641 Q gi|254781066|r 94 ------E----EKIFCFAHAWRNGEQGC----LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA 147 (355) Q Consensus 94 ------~----~rvyqig~~FRaE~~~~----rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~ 147 (355) + -|++++|.|+|.|.++- +-+-+|||=|. --|...+++.+.+.+.+..+.... T Consensus 291 k~~~~SYR~LP~r~~E~g~v~R~E~SGal~GL~RvR~ftqdD~-Hifc~~dQi~~E~~~~~~~i~~v~ 357 (589) T COG0441 291 KSGLRSYRELPLRLAEFGYVYRYEKSGALHGLMRVRGFTQDDA-HIFCTPDQIKDEFKGILELILEVY 357 (589) T ss_pred HCCCCCEECCCHHHHHCCEEECCCCCCHHHCCCCCCCEEECCC-CEECCHHHHHHHHHHHHHHHHHHH T ss_conf 5378611004404331442211567642222400113224562-014046788999999999999999 No 70 >PRK08661 prolyl-tRNA synthetase; Provisional Probab=97.71 E-value=0.0002 Score=45.65 Aligned_cols=122 Identities=20% Similarity=0.150 Sum_probs=83.1 Q ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCEECCC--CCCC-CCCC-----EEEECCCCCCCCCCCCCCCCHHHHH----HHH Q ss_conf 99999999999999998798898478210568--9854-4541-----2410247886783200002858999----989 Q gi|254781066|r 22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSP--GNET-HIRA-----FSTELIIQDHIRKPLYLQTSPEFSC----KKL 89 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~-~~~~-----f~t~~~~~~~~~~~~yL~~SPql~l----K~l 89 (355) +.+.-+|.+.+|+-|++.|--|+-=|+|++.. .-+. |.+- |.|.-.....++.++.|+...|--+ +.- T Consensus 45 ~~iw~~i~~~~~~~~~~~g~~~~~fP~liP~~~l~kE~~hvegF~pE~~~VT~~G~~~l~~~l~lrPTsEt~i~~~~~~w 124 (478) T PRK08661 45 YAIWENIQKILDEMFKETGHENVYFPLLIPESLLQKEAEHIEGFAPEVAWVTHGGGEKLEEPLALRPTSETIIYPMFKKW 124 (478) T ss_pred HHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHH T ss_conf 99999999999999986398087302406689998666566156740489954787555676310888799999999998 Q ss_pred HHHHHH---HHHHHHHHHCCCCCCC--CCCCCEEEECEEECCCCHHHHHHHHHHHHHHH Q ss_conf 874468---8999886424567775--44843002000115776578777557888776 Q gi|254781066|r 90 LAAGEE---KIFCFAHAWRNGEQGC--LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCA 143 (355) Q Consensus 90 l~~G~~---rvyqig~~FRaE~~~~--rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~ 143 (355) +-|.-+ ++||++-+||+|-..| --..||.|=|.|.+++|.++..+.+..|+..- T Consensus 125 I~SyrdLPl~l~Qw~~v~R~E~r~r~flR~rEFl~qe~ht~h~t~eea~~~~~~~~~~Y 183 (478) T PRK08661 125 IQSYRDLPLLYNQWVNVVRWEKKTRPFLRTREFLWQEGHTAHATEEEAEEETLEMLEIY 183 (478) T ss_pred HHHHHHCCCEEEEEEEEEECCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH T ss_conf 52365269000200445865788963143426354212011399999999999999999 No 71 >KOG2784 consensus Probab=97.69 E-value=5.7e-05 Score=48.91 Aligned_cols=59 Identities=22% Similarity=0.246 Sum_probs=43.1 Q ss_pred HHHHHHHHHHHHH--HHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCHHHHHHHHHHHHHHH Q ss_conf 8999989874468--8999886424567775448430020001157--76578777557888776 Q gi|254781066|r 83 EFSCKKLLAAGEE--KIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESYEQLMKDCMNIIRCA 143 (355) Q Consensus 83 ql~lK~ll~~G~~--rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~~dlm~~~E~li~~~ 143 (355) .|| +|--.||. |+|.|-++||||-+|..|++||-|+|--.+. .++-++|.+.++++..+ T Consensus 322 mLy--~LAk~~f~p~K~FSIDrVFRNEtvDaTHLAEFHQVEGviad~gltLgdLig~l~~ff~~l 384 (483) T KOG2784 322 MLY--RLAKKGFKPAKYFSIDRVFRNETVDATHLAEFHQVEGVIADKGLTLGDLIGILMEFFTKL 384 (483) T ss_pred HHH--HHHHCCCCCCCCCCHHHHHHCCCCCHHHHHHHHHHCEEEECCCCCHHHHHHHHHHHHHCC T ss_conf 999--997479985110104134403432057787776320365137876999999999997326 No 72 >PRK04173 glycyl-tRNA synthetase; Provisional Probab=97.64 E-value=0.00018 Score=45.98 Aligned_cols=33 Identities=18% Similarity=0.096 Sum_probs=24.2 Q ss_pred HHHHHHHHCCCCCCCCC----CCCEEEECEEECCCCHHH Q ss_conf 99988642456777544----843002000115776578 Q gi|254781066|r 97 IFCFAHAWRNGEQGCLH----QPEFTMLEWYRAHESYEQ 131 (355) Q Consensus 97 vyqig~~FRaE~~~~rH----lpEFtmLE~e~af~d~~d 131 (355) |-|||++|||| +++|+ +-||+|+|+|. |.+-++ T Consensus 192 iaQIGKaFRNE-IsPr~~lfR~REFeQmEiE~-F~~P~~ 228 (460) T PRK04173 192 IAQIGKSFRNE-ITPRNFIFRTREFEQMELEF-FVKPGT 228 (460) T ss_pred EEECCCCCCCC-CCCCCCCHHHHHHHHHHHHH-HCCCCC T ss_conf 31004001243-06554512234555524331-058674 No 73 >COG2502 AsnA Asparagine synthetase A [Amino acid transport and metabolism] Probab=97.61 E-value=0.002 Score=39.79 Aligned_cols=106 Identities=15% Similarity=0.172 Sum_probs=55.5 Q ss_pred HHHHHHHHHHHHHHH-----HHCCCEEEECCCEECCCCCCC-C----CCCEEEECCCCCCCCCCCC-CCCCHHHHHHHHH Q ss_conf 999999999999999-----987988984782105689854-4----5412410247886783200-0028589999898 Q gi|254781066|r 22 LLKRNMIQSSLREYF-----VENQFIEIDSMSLQYSPGNET-H----IRAFSTELIIQDHIRKPLY-LQTSPEFSCKKLL 90 (355) Q Consensus 22 l~~Rs~i~~~iR~ff-----~~~gF~EV~TPiL~~~~~g~~-~----~~~f~t~~~~~~~~~~~~y-L~~SPql~lK~ll 90 (355) ++...+-++.+.++| ++.|.+||..|+|+....|-- + -++..+.... .+...| ...|---++...| T Consensus 5 fI~qq~~IsfvKn~Ft~~l~~~L~lieVq~Pils~vg~G~qDnLsg~ekaVsv~vk~---~p~a~fEvVhSLAKWKR~tL 81 (330) T COG2502 5 FILQQQAISFVKNTFTQHLEERLGLIEVQAPILSRVGDGLQDNLSGTEKAVSVKVKK---LPDATFEVVHSLAKWKRHTL 81 (330) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCEEEEECCEEECCCCCCCCCCCCCCCCEEEEEEE---CCCCHHHHHHHHHHHHHHHH T ss_conf 777888899999999999998649688614517505775445555751435888753---68734467688899988889 Q ss_pred H-HHH---HHHHHHHHHHCCC-C-CCCCCCCCEEEECEEECCCCHH Q ss_conf 7-446---8899988642456-7-7754484300200011577657 Q gi|254781066|r 91 A-AGE---EKIFCFAHAWRNG-E-QGCLHQPEFTMLEWYRAHESYE 130 (355) Q Consensus 91 ~-~G~---~rvyqig~~FRaE-~-~~~rHlpEFtmLE~e~af~d~~ 130 (355) + -|| +-+|+=-++.|.. + .|..|+-=--|-|||..-.+.+ T Consensus 82 ~r~~f~~~eGlythM~AlRpDeD~ld~~HSvYVDQWDWEkvi~~g~ 127 (330) T COG2502 82 ARYGFSAGEGLYTHMKALRPDEDRLDPIHSVYVDQWDWEKVIPDGD 127 (330) T ss_pred HHCCCCCCCCEEEECCCCCCCCCCCCCHHEEEECCCCHHHHCCCCC T ss_conf 8638767872465211037873344530227852113644258754 No 74 >TIGR00418 thrS threonyl-tRNA synthetase; InterPro: IPR002320 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Threonyl-tRNA synthetase (6.1.1.3 from EC) exists as a monomer and belongs to class IIa. The enzyme from Escherichia coli represses the translation of its own mRNA. The crystal structure of the complex between tRNA(Thr) and ThrRS show structural features that reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination . The zinc ion may act to ensure that only amino acids that possess a hydroxyl group attached to the beta-position are activated .; GO: 0004829 threonine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006435 threonyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=97.54 E-value=0.00012 Score=46.88 Aligned_cols=133 Identities=16% Similarity=0.164 Sum_probs=81.3 Q ss_pred CCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC--CCCCCCCCEEEECCCCCCCC-CCCCCCCCH- Q ss_conf 74788312615489999999999999999998798898478210568--98544541241024788678-320000285- Q gi|254781066|r 7 QPWWNRDFHYRRRPFLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP--GNETHIRAFSTELIIQDHIR-KPLYLQTSP- 82 (355) Q Consensus 7 ~~~~~~~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~~~~~f~t~~~~~~~~~-~~~yL~~SP- 82 (355) .++|.|.= -++|..|-..+|.-..+.||-+|.||+|.... ....|.+-|.=..+.....+ +.++|+-.- T Consensus 204 ~~~WlPkG-------~~ir~~ledf~~~~~~~~Gy~~V~TP~m~~~~l~~~sGH~~~Y~e~Mf~~~~~~~~~~~LkPMnC 276 (595) T TIGR00418 204 LPFWLPKG-------ALIRNLLEDFVREKQIKRGYEEVETPIMYDSELWEISGHWDHYKERMFPFTEEDNQEFMLKPMNC 276 (595) T ss_pred CEEECCCH-------HHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHCCCCCCCCEEECCCCCCCCCCCC T ss_conf 41465764-------67899999999999987588641574121565424530545034235401010353033456775 Q ss_pred ----HHHHHHHHHHHHH---HHHHHH-HHHCCCCCCC----CCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf ----8999989874468---899988-6424567775----448430020001157765787775578887766641 Q gi|254781066|r 83 ----EFSCKKLLAAGEE---KIFCFA-HAWRNGEQGC----LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA 147 (355) Q Consensus 83 ----ql~lK~ll~~G~~---rvyqig-~~FRaE~~~~----rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~ 147 (355) +.|+ .-+-|--+ |+|++| -|||.|-+|. +=+=.|||.|.=.--.|.+++.+.+.+.++-+.+.. T Consensus 277 pgH~~i~k-~~~~SYR~LP~R~aE~g~~~hR~E~sG~L~GL~RvR~FT~dDaHifc~d~dQi~~E~~~~~~l~~~v~ 352 (595) T TIGR00418 277 PGHILIFK-SSLRSYRDLPLRIAELGTTVHRYEKSGALHGLKRVRGFTQDDAHIFCTDEDQIKSEIKNQFRLIQKVY 352 (595) T ss_pred HHHHHHHC-CCCCCHHHCCCHHHHCCCEEEEEECCCCCCHHHHHHHCCCCCCCEEECCHHHHHHHHHHHHHHHHHHH T ss_conf 44533001-77777323350343318604788425421010164430699852453786779999999999999998 No 75 >COG0423 GRS1 Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis] Probab=97.44 E-value=0.00017 Score=46.12 Aligned_cols=31 Identities=26% Similarity=0.372 Sum_probs=25.0 Q ss_pred HHHHHHHHHHHHHHHHH--CCCEEEECCCEECC Q ss_conf 99999999999999998--79889847821056 Q gi|254781066|r 22 LLKRNMIQSSLREYFVE--NQFIEIDSMSLQYS 52 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~~--~gF~EV~TPiL~~~ 52 (355) ...+..|.++-|++|-. .+++|||||+|.+. T Consensus 40 ~~LK~nI~~~Wrk~fV~~~e~~~eIdtpii~p~ 72 (558) T COG0423 40 VELKNNIKEAWRKSFVTEREDVVEIDTPIILPE 72 (558) T ss_pred HHHHHHHHHHHHHHHEECCCCEEEECCCCCCCH T ss_conf 899999999999986624687678425544868 No 76 >PRK09194 prolyl-tRNA synthetase; Provisional Probab=97.38 E-value=0.00085 Score=41.96 Aligned_cols=123 Identities=15% Similarity=0.127 Sum_probs=76.4 Q ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----CC--CC-CCCCEEEECCCCCCCCCCCCCCCCH-HHHH---HHHH Q ss_conf 99999999999999998798898478210568----98--54-4541241024788678320000285-8999---9898 Q gi|254781066|r 22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----GN--ET-HIRAFSTELIIQDHIRKPLYLQTSP-EFSC---KKLL 90 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~g--~~-~~~~f~t~~~~~~~~~~~~yL~~SP-ql~l---K~ll 90 (355) +|...+|.+-||+-|++-|..||..|+|++.. .| +. +-+-|+.. |-.+.++.|.... |..- +..+ T Consensus 47 ~rvl~Kie~IIr~em~~iGa~Ev~mp~l~p~elW~~sgR~~~~g~el~r~k----DR~~~~~~L~PThEE~it~lv~~~i 122 (570) T PRK09194 47 LRVLRKIENIVREEMNKIGAQEVLMPALQPAELWQESGRWEKYGPELLRLK----DRHGRDFVLGPTHEEVITDLVRNEI 122 (570) T ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCHHHCCHHHEEEE----CCCCCEEEECCCCHHHHHHHHHHHH T ss_conf 999999999999999864987985356797789876188212361346985----2789856537873899999999851 Q ss_pred HHHH---HHHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHHHH---HHHHHHC Q ss_conf 7446---88999886424567775---448430020001157765787775578887---7666418 Q gi|254781066|r 91 AAGE---EKIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIR---CAAEVAN 148 (355) Q Consensus 91 ~~G~---~rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~---~~~~~~~ 148 (355) .|.- =++|||+.-||||-.-| --.-||+|-|.|--..|.+++.+.-+.+.. .+++.++ T Consensus 123 ~SYkqLP~~lYQIqtKfRDE~RPR~GllR~REF~MKDaYSFd~~~e~l~~tY~~~~~AY~~IF~rlg 189 (570) T PRK09194 123 KSYKQLPLNLYQIQTKFRDEIRPRFGLMRGREFIMKDAYSFHADEESLDETYDAMYQAYSRIFTRLG 189 (570) T ss_pred CCHHHCCHHEECCCCEECCCCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 1376468020013233347788767623456534512456669989999999999999999999809 No 77 >PRK05431 seryl-tRNA synthetase; Provisional Probab=97.27 E-value=0.00059 Score=42.88 Aligned_cols=122 Identities=15% Similarity=0.183 Sum_probs=66.8 Q ss_pred HHHHHHHHHHHHHHHHCCCEEEECCCEECC-C-CCCCCCCCEEEECCCCCCCCCCCCCCCCHHH-----HHHHHHHH-HH Q ss_conf 999999999999999879889847821056-8-9854454124102478867832000028589-----99989874-46 Q gi|254781066|r 23 LKRNMIQSSLREYFVENQFIEIDSMSLQYS-P-GNETHIRAFSTELIIQDHIRKPLYLQTSPEF-----SCKKLLAA-GE 94 (355) Q Consensus 23 ~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~-~-~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql-----~lK~ll~~-G~ 94 (355) +.--.+++.+-+++.++||.+|.||.|... . .|...+--|....+... +.++||.-..|. |....+-. -+ T Consensus 171 ~LerALi~f~ld~~~~~Gy~~v~~P~lv~~~~~~gtGqlPkfe~~~Y~i~--~~dl~Li~TAEvpL~~~~~~eil~~~~L 248 (422) T PRK05431 171 RLERALIQFMLDLHTEEGYTEVIPPYLVNEESMYGTGQLPKFEEDLFKIE--DDDLYLIPTAEVPLTNLHRDEILDEEEL 248 (422) T ss_pred HHHHHHHHHHHHHHHHCCCEEEECHHHHHHHHHHHHCCCCCCHHHHHHHC--CCCEEEECCCCCCHHHHHHCCCCCHHHC T ss_conf 99999999999999987997996737636788744537974487754105--8871760565321233440113365439 Q ss_pred -HHHHHHHHHHCCC-CC---CCC---CCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf -8899988642456-77---754---48430020001157765787775578887766641 Q gi|254781066|r 95 -EKIFCFAHAWRNG-EQ---GCL---HQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA 147 (355) Q Consensus 95 -~rvyqig~~FRaE-~~---~~r---HlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~ 147 (355) =||.-++||||.| ++ |+| ..-+|+=+|.. +++.-++..+.-|.|+..+.+.+ T Consensus 249 Pik~~~~S~CFR~EAGs~GkdtrGl~RvHQF~KVE~f-~~~~pe~S~~~~e~~~~~~e~i~ 308 (422) T PRK05431 249 PIKYTAYSPCFRSEAGSAGRDTRGLIRQHQFDKVELV-KFTKPEDSYAELEELTGNAEEIL 308 (422) T ss_pred CHHHEEECCHHHHCCCCCCCCCCCCEEEEEECEEEEE-EECCHHHHHHHHHHHHHHHHHHH T ss_conf 8445278836530313367556761244300003433-53586779999999999999999 No 78 >KOG2324 consensus Probab=97.12 E-value=0.0018 Score=40.05 Aligned_cols=125 Identities=15% Similarity=0.100 Sum_probs=80.7 Q ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCCEECCC---CCC----CCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHH Q ss_conf 99999999999999998798898478210568---985----44541241024788678320000285899998987446 Q gi|254781066|r 22 LLKRNMIQSSLREYFVENQFIEIDSMSLQYSP---GNE----THIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGE 94 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~---~g~----~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~ 94 (355) +|.-.++.+.|+.-|++-|=.+|.-|+|++.. .++ .+-+-|..+ +--++.+.|...-|=-.-.||+.-. T Consensus 52 ~R~~~K~~~~l~~~mqs~Ga~kIslp~ls~~~LWekTgRw~~~gsEl~rl~----Dr~gkq~cL~pThEE~iT~lmat~~ 127 (457) T KOG2324 52 LRVLNKLCRLLDNEMQSGGAQKISLPILSSKELWEKTGRWDAMGSELFRLH----DRKGKQMCLTPTHEEDITALMATYI 127 (457) T ss_pred HHHHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHCCCCCCCCHHHEEEE----CCCCCEECCCCCHHHHHHHHHHHCC T ss_conf 799999999999998723670574044686899876185112460453751----0478773057754899999998627 Q ss_pred H--------HHHHHHHHHCCCCCCC---CCCCCEEEECEEECCCCHHHHHHHHHHH---HHHHHHHHCCC Q ss_conf 8--------8999886424567775---4484300200011577657877755788---87766641883 Q gi|254781066|r 95 E--------KIFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHESYEQLMKDCMNI---IRCAAEVANQK 150 (355) Q Consensus 95 ~--------rvyqig~~FRaE~~~~---rHlpEFtmLE~e~af~d~~dlm~~~E~l---i~~~~~~~~~~ 150 (355) . +|||||+-||||-..| -.--||.|=|+|.-..|-++.|+.-+.+ ...+++.++.. T Consensus 128 ~lsykqlPi~vYQigrKfRDElrpRfGLlRgREFlMKDmYsFd~~~etA~qTy~~v~~aY~~iFkqL~~p 197 (457) T KOG2324 128 PLSYKQLPIRVYQIGRKFRDELRPRFGLLRGREFLMKDMYSFDSDEETAQQTYQLVDQAYDRIFKQLGLP 197 (457) T ss_pred CCCCCCCCEEEEEECHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 4322028677665054544134754230124788876533025888899999999999999999973997 No 79 >COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis] Probab=96.78 E-value=0.0016 Score=40.38 Aligned_cols=113 Identities=14% Similarity=0.170 Sum_probs=58.1 Q ss_pred HHHHHHHHHHCCCEEEECCCEECCC--CCCCCCCCEEEECCCCCCCCCCCCCCCCHH-----HHHHHHHHHH--HHHHHH Q ss_conf 9999999998798898478210568--985445412410247886783200002858-----9999898744--688999 Q gi|254781066|r 29 QSSLREYFVENQFIEIDSMSLQYSP--GNETHIRAFSTELIIQDHIRKPLYLQTSPE-----FSCKKLLAAG--EEKIFC 99 (355) Q Consensus 29 ~~~iR~ff~~~gF~EV~TPiL~~~~--~g~~~~~~f~t~~~~~~~~~~~~yL~~SPq-----l~lK~ll~~G--~~rvyq 99 (355) ++.+=++..++||.||.+|.|.... -|...+.-|.-..+... +...||.-.-| +|-++.+... =-++.- T Consensus 181 ~~f~ld~~~~~Gf~e~~~P~lv~~e~m~gtgqlpkf~e~~y~v~--~~~~~LipTaEvpl~~l~~~Eil~~~~LP~k~~~ 258 (429) T COG0172 181 IQFMLDLHTKHGFTEVLPPYLVNLESMFGTGQLPKFEEDLYKVE--DPDLYLIPTAEVPLTNLHRDEILDEEDLPIKYTA 258 (429) T ss_pred HHHHHHHHHHCCCEEEECCEEECHHHHHCCCCCCCCCCCCEEEC--CCCEEEEECCHHHHHHHHCCCCCCCCCCCEEEEE T ss_conf 99999999876965865760605988622378988801215845--8987997020215678651620152127802678 Q ss_pred HHHHHCCC-CC---CCC---CCCCEEEECEEECCCCHHHHHHHHHHHHHHHH Q ss_conf 88642456-77---754---48430020001157765787775578887766 Q gi|254781066|r 100 FAHAWRNG-EQ---GCL---HQPEFTMLEWYRAHESYEQLMKDCMNIIRCAA 144 (355) Q Consensus 100 ig~~FRaE-~~---~~r---HlpEFtmLE~e~af~d~~dlm~~~E~li~~~~ 144 (355) .+||||.| ++ |+| -.-+|..+|.- +++.-++..+.-|.|+.+.- T Consensus 259 ~S~cFR~EAGs~GrdtrGliRvHQF~KVE~v-~~~~Pe~S~~~~E~m~~~ae 309 (429) T COG0172 259 YSPCFRSEAGSAGKDTRGLIRVHQFDKVELV-VITKPEESEEELEEMLGNAE 309 (429) T ss_pred ECHHHHCCCCCCCCCCCCEEEEEEEEEEEEE-EEECCCHHHHHHHHHHHHHH T ss_conf 7725421456566435530146643558999-97070116999999999999 No 80 >TIGR00442 hisS histidyl-tRNA synthetase; InterPro: IPR015807 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Histidyl-tRNA synthetase (6.1.1.21 from EC) is an alpha2 dimer that belongs to class IIa. Every completed genome includes a histidyl-tRNA synthetase. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and not demonstrated to act as histidyl-tRNA synthetases (see IPR004517 from INTERPRO). The regulatory protein kinase GCN2 of Saccharomyces cerevisiae (YDR283c), and related proteins from other species designated eIF-2 alpha kinase, have a domain closely related to histidyl-tRNA synthetase that may serve to detect and respond to uncharged tRNA(his), an indicator of amino acid starvation, but these regulatory proteins are not orthologous.; GO: 0000166 nucleotide binding, 0004821 histidine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006427 histidyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=96.25 E-value=0.0081 Score=36.14 Aligned_cols=128 Identities=14% Similarity=0.149 Sum_probs=73.8 Q ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC-----CCCCCCCCEEEE-CCCCCCCCCCCCCC---CCH--HHHHHHH Q ss_conf 999999999999999998798898478210568-----985445412410-24788678320000---285--8999989 Q gi|254781066|r 21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP-----GNETHIRAFSTE-LIIQDHIRKPLYLQ---TSP--EFSCKKL 89 (355) Q Consensus 21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~-----~g~~~~~~f~t~-~~~~~~~~~~~yL~---~SP--ql~lK~l 89 (355) -...|..+...+|+.+.+-||.||.||++..+. .|+. .+..... +...+..++..-|+ ++| .++.... T Consensus 17 ~~~~~~~~~~~~~~~~~~~g~~~~~~P~~e~~~~~~~~~~~~-~~~~~~~~y~f~d~~~~~~~lrp~~t~~~~r~~~~~~ 95 (446) T TIGR00442 17 ELVYRQWIEAKLRSVLESYGYSEIRTPIFEYTELFARGIGKS-GDEVEKELYTFKDKGGRDLALRPELTAPVVRLVAENK 95 (446) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCC-HHHHHHHHEEEECCCCCEEEECCCHHHHHHHHHHHHH T ss_conf 578999999999999975177200121144456665302530-1334444301212788414422200368999998754 Q ss_pred H-H--HHHHHHHHHHHHHCCCCCC-CCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHCC Q ss_conf 8-7--4468899988642456777-544843002000115776578777557888776664188 Q gi|254781066|r 90 L-A--AGEEKIFCFAHAWRNGEQG-CLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVANQ 149 (355) Q Consensus 90 l-~--~G~~rvyqig~~FRaE~~~-~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~~ 149 (355) + . ..--|.|.+|+|||-|... .-..-|||++.++..+..-...-..+-.+....++.++- T Consensus 96 ~~~~~~~p~~~~~~g~~~r~e~p~~~gr~r~f~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~g~ 159 (446) T TIGR00442 96 LLLPANKPLRLYYIGPVFRYERPQLKGRYREFWQFGCEVIGSESPLADAEVLSLAVEGLKALGL 159 (446) T ss_pred HHCCCCCCEEEEEEECHHHCCCHHHHCCHHHHHHCCEEEECCCCCHHHHHHHHHHHHHHHHHCC T ss_conf 3104676424323201010224123010113321150464366520368999999998986076 No 81 >TIGR00389 glyS_dimeric glycyl-tRNA synthetase; InterPro: IPR002315 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . In eubacteria, glycyl-tRNA synthetase (6.1.1.14 from EC) is an alpha2/beta2 tetramer composed of 2 different subunits , , . In some eubacteria, in archaea and eukaryota, glycyl-tRNA synthetase is an alpha2 dimer, this family. It belongs to class IIc and is one of the most complex synthetases. What is most interesting is the lack of similarity between the two types: divergence at the sequence level is so great that it is impossible to infer descent from common genes. The alpha (see IPR002310 from INTERPRO) and beta subunits (see IPR002311 from INTERPRO) also lack significant sequence similarity. However, they are translated from a single mRNA , and a single chain glycyl-tRNA synthetase from Chlamydia trachomatis has been found to have significant similarity with both domains, suggesting divergence from a single polypeptide chain . The sequence and crystal structure of the homodimeric glycyl-tRNA synthetase from Thermus thermophilus, shows that each monomer consists of an active site strongly resembling that of the aspartyl and seryl enzymes, a C-terminal anticodon recognition domain of 100 residues and a third domain unusually inserted between motifs 1 and 2 almost certainly interacting with the acceptor arm of tRNA(Gly). The C-terminal domain has a novel five-stranded parallel-antiparallel beta-sheet structure with three surrounding helices. The active site residues most probably responsible for substrate recognition, in particular in the Gly binding pocket, can be identified by inference from aspartyl-tRNA synthetase due to the conserved nature of the class II active site , .; GO: 0000166 nucleotide binding, 0004820 glycine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006426 glycyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=95.69 E-value=0.0013 Score=40.84 Aligned_cols=30 Identities=27% Similarity=0.497 Sum_probs=24.7 Q ss_pred HHHHHHHHHHHHHHHH-CC-CEEEECCCEECC Q ss_conf 9999999999999998-79-889847821056 Q gi|254781066|r 23 LKRNMIQSSLREYFVE-NQ-FIEIDSMSLQYS 52 (355) Q Consensus 23 ~~Rs~i~~~iR~ff~~-~g-F~EV~TPiL~~~ 52 (355) ..+.+|+++-|+||-- ++ ++|||||++++. T Consensus 38 ~Lk~~I~~~wr~~fi~~e~d~~~id~P~i~~~ 69 (606) T TIGR00389 38 VLKNNIKNAWRKFFIINERDVLEIDSPIITPE 69 (606) T ss_pred HHHHHHHHHHHHHHCCCCCCEEEECCCCCCCH T ss_conf 89999999888751110365346424533725 No 82 >KOG1035 consensus Probab=95.31 E-value=0.073 Score=30.49 Aligned_cols=110 Identities=15% Similarity=0.178 Sum_probs=59.6 Q ss_pred HHHHHHHHHHHHHHHCCCEEEECCCEEC-C--CCCCCCCCCEEEECCCCC----CCCCCC--CCCCCHHHHHHHHHHHHH Q ss_conf 9999999999999987988984782105-6--898544541241024788----678320--000285899998987446 Q gi|254781066|r 24 KRNMIQSSLREYFVENQFIEIDSMSLQY-S--PGNETHIRAFSTELIIQD----HIRKPL--YLQTSPEFSCKKLLAAGE 94 (355) Q Consensus 24 ~Rs~i~~~iR~ff~~~gF~EV~TPiL~~-~--~~g~~~~~~f~t~~~~~~----~~~~~~--yL~~SPql~lK~ll~~G~ 94 (355) .|..+.--+-+-|..+|++|++||.|.. . +-+-+.+..+.++.+..- .+..+| |+.--+=+ . T Consensus 934 l~~~v~e~~~~ifr~Hga~~l~tpp~~~~~~~~~~~~~~v~~ld~sG~~v~Lp~DLr~pfar~vs~N~~~---------~ 1004 (1351) T KOG1035 934 LREYVVEEVVKIFRKHGAIELETPPLSLRNACAYFSRKAVELLDHSGDVVELPYDLRLPFARYVSRNSVL---------S 1004 (1351) T ss_pred HHHHHHHHHHHHHHHHCCEECCCCCCCCCCCCCHHCCCEEEEECCCCCEEEEECCCCCHHHHHHHHCHHH---------H T ss_conf 9999999999999982430216786553345420015403544279978996300124677886605288---------8 Q ss_pred HHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCC----HHHHHHHHHHHHHHHH Q ss_conf 8899988642456777544843002000115776----5787775578887766 Q gi|254781066|r 95 EKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHES----YEQLMKDCMNIIRCAA 144 (355) Q Consensus 95 ~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d----~~dlm~~~E~li~~~~ 144 (355) -|=|+|+++||-+. .+ |=-|++.+++-...-+ --+++.++-+++..++ T Consensus 1005 ~Kry~i~rVyr~~~-~~-hP~~~~ec~fDii~~t~sl~~AE~L~vi~Ei~~~~l 1056 (1351) T KOG1035 1005 FKRYCISRVYRPAI-HN-HPKECLECDFDIIGPTTSLTEAELLKVIVEITTEIL 1056 (1351) T ss_pred HHHHHHHEEECCCC-CC-CCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHH T ss_conf 77762320344634-58-984010015667558777407899999999999986 No 83 >COG3705 HisZ ATP phosphoribosyltransferase involved in histidine biosynthesis [Amino acid transport and metabolism] Probab=95.25 E-value=0.02 Score=33.82 Aligned_cols=100 Identities=16% Similarity=0.178 Sum_probs=62.8 Q ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCC----C-CCC-CCCCEEEECCCCCCCCCCCCCCC--CHHHHHHHHH-- Q ss_conf 999999999999999998798898478210568----9-854-45412410247886783200002--8589999898-- Q gi|254781066|r 21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSP----G-NET-HIRAFSTELIIQDHIRKPLYLQT--SPEFSCKKLL-- 90 (355) Q Consensus 21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~----~-g~~-~~~~f~t~~~~~~~~~~~~yL~~--SPql~lK~ll-- 90 (355) -......|.+.+++.|...||-.|+||+|.... + |+- -.+-|++. +..++.+-|+- .++.. ++. T Consensus 16 e~~~~~~i~~~l~~~f~~~Gy~~v~tP~lE~~d~~l~~~g~~l~~~~f~l~----d~~g~~l~LRpD~T~pVa--R~~~~ 89 (390) T COG3705 16 EARRKEEIRDQLLALFRAWGYERVETPTLEPADPLLDGAGEDLRRRLFKLE----DETGGRLGLRPDFTIPVA--RIHAT 89 (390) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCHHHHHHHEEEE----CCCCCEEEECCCCCHHHH--HHHHH T ss_conf 776479999999999998087404663134026654022255552206876----578976883543308999--99998 Q ss_pred --HHHHHHHHHHHHHHCCC-CCCCCCCCCEEEECEEECCC Q ss_conf --74468899988642456-77754484300200011577 Q gi|254781066|r 91 --AAGEEKIFCFAHAWRNG-EQGCLHQPEFTMLEWYRAHE 127 (355) Q Consensus 91 --~~G~~rvyqig~~FRaE-~~~~rHlpEFtmLE~e~af~ 127 (355) .++-.|++..|++||+. +.+.+ ..||+|+=+|.-+. T Consensus 90 ~~~~~P~Rl~Y~G~Vfr~~~~~~g~-~~Ef~QaGiEllG~ 128 (390) T COG3705 90 LLAGTPLRLSYAGKVFRAREGRHGR-RAEFLQAGIELLGD 128 (390) T ss_pred HCCCCCCEEEECCHHHHCCHHCCCC-CCCHHHHHHHHHCC T ss_conf 2378871466401454020102676-42045533677378 No 84 >cd00673 AlaRS_core Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its predicted structure and the presence of three characteristic sequence motifs. Probab=94.56 E-value=0.34 Score=26.52 Aligned_cols=95 Identities=17% Similarity=0.220 Sum_probs=55.7 Q ss_pred HHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCH-HHHHHHHHH----HHHHHHHHHH Q ss_conf 99999999999879889847821056898544541241024788678320000285-899998987----4468899988 Q gi|254781066|r 27 MIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSP-EFSCKKLLA----AGEEKIFCFA 101 (355) Q Consensus 27 ~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SP-ql~lK~ll~----~G~~rvyqig 101 (355) +|-+..=+||.++|-..|..--|. |..++ .++++.|. +.+ |..+. ....|+-... T Consensus 3 eiR~~Fl~fF~~~gH~~vpssslv--p~~Dp-----------------tllFtnAGM~~F-kp~flG~~~p~~~r~~~~Q 62 (232) T cd00673 3 EIRETFLSFFEKKGHTRVPSSPVV--PRDDP-----------------TLLFTNAGMNQF-KPIFLGEVPPPANRLVNSQ 62 (232) T ss_pred HHHHHHHHHHHHCCCEECCCCCCC--CCCCC-----------------CEEEEECCHHHH-HHHHCCCCCCCCCCCEEEE T ss_conf 899999999987898882787722--38999-----------------501441146888-9986778899987510000 Q ss_pred HHHCCCCC-----CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 64245677-----75448430020001157765787775578887766641 Q gi|254781066|r 102 HAWRNGEQ-----GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVA 147 (355) Q Consensus 102 ~~FRaE~~-----~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~ 147 (355) ||.|..+. |.||++=|-||-= .||.||- -++.|..+.+.+ T Consensus 63 kCiR~~di~nvG~t~rH~TfFEMLGn-fSFGdYf-----K~eaI~~awe~l 107 (232) T cd00673 63 KCIRAGDIDNVGKTGRHHTFFEMLGN-FSFGDYF-----KEEAIAFAWELL 107 (232) T ss_pred ECCCCCCCCCCCCCCCCCHHHHCCCC-CCHHHHH-----HHHHHHHHHHHH T ss_conf 12365783246777764023330444-2031458-----999999999987 No 85 >TIGR00468 pheS phenylalanyl-tRNA synthetase, alpha subunit; InterPro: IPR004529 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases . This family describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this family. ; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=94.31 E-value=0.018 Score=34.12 Aligned_cols=119 Identities=17% Similarity=0.180 Sum_probs=66.8 Q ss_pred HHHHHHHHHHHHHHCCCEEEECCC-EECCC-CCCCC-------C----CCEEEEC------------------------- Q ss_conf 999999999999987988984782-10568-98544-------5----4124102------------------------- Q gi|254781066|r 25 RNMIQSSLREYFVENQFIEIDSMS-LQYSP-GNETH-------I----RAFSTEL------------------------- 66 (355) Q Consensus 25 Rs~i~~~iR~ff~~~gF~EV~TPi-L~~~~-~g~~~-------~----~~f~t~~------------------------- 66 (355) -.+++..++++|...||.+..-|. +...- .-++- + +.|-... T Consensus 83 ~~~~~~~~~~~~~~~g~~~~~g~~~~~~~~~~f~~l~~p~~hp~r~~~d~f~~~~p~~~~~~~~~~~~~~~~~~~~~~~g 162 (362) T TIGR00468 83 LTRVIDEIRDIFLGLGFTEEKGPEYVETDFWNFDALNLPQDHPARDLQDTFYLKDPLTGDLPPELVSDVKDAHETGGATG 162 (362) T ss_pred HHHHHHHHHHHHHHHCCEEECCCCEECCCCCCCHHHCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHCCCCC T ss_conf 78999999998765033010473101111001011127754543112330331374200032246776777665202122 Q ss_pred -CCCCC-C----CCCCCC--CCCH----HHHHHHHHH---HHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECC--CCH Q ss_conf -47886-7----832000--0285----899998987---44688999886424567775448430020001157--765 Q gi|254781066|r 67 -IIQDH-I----RKPLYL--QTSP----EFSCKKLLA---AGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAH--ESY 129 (355) Q Consensus 67 -~~~~~-~----~~~~yL--~~SP----ql~lK~ll~---~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af--~d~ 129 (355) ....+ . .+..-| ++++ ++.-....- ..--|++.++++||++..|..|+++|.++|.-... .++ T Consensus 163 ~~gw~~~~~~~~~~~~~lrt~~~~~~~~~~~~~~~~~~~~~pp~~~~~~~~~~r~~~~d~~h~~~f~~~~g~~~~~~~~~ 242 (362) T TIGR00468 163 SRGWRYEWDEDLARRLLLRTHTTASSAVQLRTLEENPKAKNPPIRIFCPGRVFRRDTVDATHLPEFHQLEGLVVDKNVSF 242 (362) T ss_pred CCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHHHCCCCCCCCCCCHHHHEEEEEEECCCCH T ss_conf 32445444555665555431132135666666654101378862576410111023333101410221002354156646 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 78777557888776 Q gi|254781066|r 130 EQLMKDCMNIIRCA 143 (355) Q Consensus 130 ~dlm~~~E~li~~~ 143 (355) .++...++++++.+ T Consensus 243 ~~l~g~~~~~~~~~ 256 (362) T TIGR00468 243 TNLKGLLEEFLKKL 256 (362) T ss_pred HHHHHHHHHHHHHH T ss_conf 78899999999974 No 86 >KOG1936 consensus Probab=94.16 E-value=0.018 Score=34.05 Aligned_cols=108 Identities=19% Similarity=0.198 Sum_probs=63.2 Q ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCEE--CC---CCCCCCCCCEEEECCCCCCCCCCC---C-CCCCHHHHHHHHHH Q ss_conf 999999999999999998798898478210--56---898544541241024788678320---0-00285899998987 Q gi|254781066|r 21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQ--YS---PGNETHIRAFSTELIIQDHIRKPL---Y-LQTSPEFSCKKLLA 91 (355) Q Consensus 21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~--~~---~~g~~~~~~f~t~~~~~~~~~~~~---y-L~~SPql~lK~ll~ 91 (355) -+..|.++++.|.+-|..+|...|+||++- .+ .-|+- .+ .-+...+..++-. | |+++= -|.+| T Consensus 73 qm~lRe~if~~i~~vFkrhGa~~iDTPVFElkeiL~gKYGEd-sk---LiYdlkDQGGEl~SLRYDLTVPf----ARylA 144 (518) T KOG1936 73 QMALREKIFSTIKEVFKRHGAETIDTPVFELKEILTGKYGED-SK---LIYDLKDQGGELCSLRYDLTVPF----ARYLA 144 (518) T ss_pred HHHHHHHHHHHHHHHHHHCCCEECCCCCHHHHHHHHHHCCCC-CC---EEEEHHHCCCCEEEEECCCCCHH----HHHHH T ss_conf 889999999999999997197444660045999986640553-23---06752324885887413566479----99998 Q ss_pred HH---HHHHHHHHHHHCCCC-C-CCCCCCCEEEECEEECCCCHHHHHHHHH Q ss_conf 44---688999886424567-7-7544843002000115776578777557 Q gi|254781066|r 92 AG---EEKIFCFAHAWRNGE-Q-GCLHQPEFTMLEWYRAHESYEQLMKDCM 137 (355) Q Consensus 92 ~G---~~rvyqig~~FRaE~-~-~~rHlpEFtmLE~e~af~d~~dlm~~~E 137 (355) .. .=+-|+||+++|-+. . ++=..-||.|+|+-.|+ +++.++-..| T Consensus 145 mNki~sikRy~iAkVyRRd~P~mtrGR~REFYQcDFDIAG-~~d~M~pdaE 194 (518) T KOG1936 145 MNKITSIKRYHIAKVYRRDQPAMTRGRYREFYQCDFDIAG-QFDPMIPDAE 194 (518) T ss_pred HCCCCCCEEEEEEEEEECCCCHHHCHHHHHHHCCCCCCCC-CCCCCCCHHH T ss_conf 7145521104678787506814423024556506752126-6777786099 No 87 >PRK00252 alaS alanyl-tRNA synthetase; Reviewed Probab=94.11 E-value=0.43 Score=25.95 Aligned_cols=99 Identities=20% Similarity=0.198 Sum_probs=51.8 Q ss_pred HHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 99999999999987988984782105689854454124102478867832000028589999898744688999886424 Q gi|254781066|r 26 NMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWR 105 (355) Q Consensus 26 s~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FR 105 (355) ++|-+..-+||.++|=..|..--|. |-.++-+ .| |.-. .+.| ++.||-+.+-- ..|+-...||.| T Consensus 5 ~eiR~~fl~fF~~k~H~~v~s~~lv--p~~Dptl-lf-tnAG-m~~f-k~~f~G~~~p~---------~~r~~~~QkCiR 69 (864) T PRK00252 5 AEIRQAFLDFFESKGHTVVPSSSLV--PKNDPTL-LF-TNAG-MVQF-KDYFLGLEKPP---------YPRATTSQKCIR 69 (864) T ss_pred HHHHHHHHHHHHHCCCEEECCCCCC--CCCCCCE-EE-EECC-CCCC-HHHHCCCCCCC---------CCCCCCCCCCEE T ss_conf 9999999999987898880787725--5899804-67-5036-4016-22325887899---------997345403400 Q ss_pred CCCC-----CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHH Q ss_conf 5677-----754484300200011577657877755788877666 Q gi|254781066|r 106 NGEQ-----GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAE 145 (355) Q Consensus 106 aE~~-----~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~ 145 (355) +.|+ |.||.+=|-||-= +||.||- =++-|.+.++ T Consensus 70 ~nDld~VG~t~rH~TfFEMlGN-~SfGdYf-----K~eai~~awe 108 (864) T PRK00252 70 TNDLENVGYTARHHTFFEMLGN-FSFGDYF-----KKEAIEFAWE 108 (864) T ss_pred CCCHHHCCCCCCCCHHHHCCCC-CCCCCCH-----HHHHHHHHHH T ss_conf 3648763888775254423765-6655105-----8899999999 No 88 >KOG2783 consensus Probab=93.94 E-value=0.031 Score=32.68 Aligned_cols=98 Identities=16% Similarity=0.218 Sum_probs=53.3 Q ss_pred HHHHHHHHHHHCCC-----EEEECCCEECCCCCCCCCCCE--EEECCCC-CCCCCCCCC--CCCHHHHHHHHHHHHHHHH Q ss_conf 99999999998798-----898478210568985445412--4102478-867832000--0285899998987446889 Q gi|254781066|r 28 IQSSLREYFVENQF-----IEIDSMSLQYSPGNETHIRAF--STELIIQ-DHIRKPLYL--QTSPEFSCKKLLAAGEEKI 97 (355) Q Consensus 28 i~~~iR~ff~~~gF-----~EV~TPiL~~~~~g~~~~~~f--~t~~~~~-~~~~~~~yL--~~SPql~lK~ll~~G~~rv 97 (355) +-+.|-++|...+- .+..+|+.+....=+..+-|= ...+... .|.+...-| ++|--. -.++..|.+.- T Consensus 77 lr~~i~~~f~~~~~~~fs~~~~~spvvt~~qnfdsl~~p~dh~sr~ksdtyy~n~~~~lr~htsahq--~e~~~~~~~~f 154 (436) T KOG2783 77 LRQRIEDYFYKTYRNLFSIFENESPVVTTYQNFDSLLFPADHVSRSKSDTYYVNHTHCLRAHTSAHQ--HELFQKGLDGF 154 (436) T ss_pred HHHHHHHHHHHHHCCCCHHCCCCCCEEEHHHHCCCCCCCCCCCCCCCCCCEEECCEEEEHHCCHHHH--HHHHHHCCCCC T ss_conf 9998777898862353100467886023554144445742355567677414212332111350537--99997315466 Q ss_pred HHHHHHHCCCCCCCCCCCCEEEECEEECCC Q ss_conf 998864245677754484300200011577 Q gi|254781066|r 98 FCFAHAWRNGEQGCLHQPEFTMLEWYRAHE 127 (355) Q Consensus 98 yqig~~FRaE~~~~rHlpEFtmLE~e~af~ 127 (355) -..|-++|-.++|+.|-|=|-++|--..+. T Consensus 155 lv~~DVyrrdeidsthypvfhq~eg~~~~s 184 (436) T KOG2783 155 LVTGDVYRRDEIDSTHYPVFHQMEGVRLWS 184 (436) T ss_pred CEEEEEEEECCCCCCCCCEECCCCCEEEEE T ss_conf 234334530000230251003553305773 No 89 >KOG2509 consensus Probab=93.92 E-value=0.038 Score=32.20 Aligned_cols=122 Identities=11% Similarity=0.123 Sum_probs=64.2 Q ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCC--CCCEEEE-CCCCCCCCCCCCCCCCHHHH-----HHHHHHH Q ss_conf 99999999999999999879889847821056898544--5412410-24788678320000285899-----9989874 Q gi|254781066|r 21 FLLKRNMIQSSLREYFVENQFIEIDSMSLQYSPGNETH--IRAFSTE-LIIQDHIRKPLYLQTSPEFS-----CKKLLAA 92 (355) Q Consensus 21 ~l~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~--~~~f~t~-~~~~~~~~~~~yL~~SPql~-----lK~ll~~ 92 (355) ....-..+++..-+|+.++||+-+.||.+......+.. ..-|.-+ +...+.. .+.||.-..|.. +...+.. T Consensus 184 ~a~LeqALi~yal~~l~~kGy~pl~~P~i~rkeVm~~cg~~~~~d~~~~y~ld~~-~~~~LiaTaE~plAa~~~~e~~~~ 262 (455) T KOG2509 184 GAFLEQALINYALDFLNAKGYTPLTTPDILRKEVMQKCGQLPRFDEEQYYVLDGG-DEKYLIATAEQPLAAYHRDEWLEE 262 (455) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCCCEEEEECCC-CCCEEEEECCCHHHHHHCCCCCCC T ss_conf 9999999999999999976982466814536999998565767883217860688-642267621110666503640361 Q ss_pred H-H-HHHHHHHHHHCCC-CC---CCC---CCCCEEEECE------EECCCCHHHHHHHHHHHHHHH Q ss_conf 4-6-8899988642456-77---754---4843002000------115776578777557888776 Q gi|254781066|r 93 G-E-EKIFCFAHAWRNG-EQ---GCL---HQPEFTMLEW------YRAHESYEQLMKDCMNIIRCA 143 (355) Q Consensus 93 G-~-~rvyqig~~FRaE-~~---~~r---HlpEFtmLE~------e~af~d~~dlm~~~E~li~~~ 143 (355) + + -||--.++|||+| ++ +++ -.-+|+-+|. +.|+.-++++++..|++++.+ T Consensus 263 ~~lPiK~vg~S~CfR~EaGs~G~d~~GlyRVHqF~KVE~Fvit~Pe~S~~~~eEmi~~~eef~qsL 328 (455) T KOG2509 263 DQLPIKYVGVSRCFRAEAGSHGKDTKGLYRVHQFEKVEQFVITGPEDSWEMLEEMINNQEEFYQSL 328 (455) T ss_pred CCCCEEEEEHHHHHHHHHHHCCCCCCCCEEEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 127601343037888776004654555146652002578886585356999999999999999980 No 90 >PRK13902 alaS lanyl-tRNA synthetase; Provisional Probab=93.76 E-value=0.033 Score=32.53 Aligned_cols=32 Identities=16% Similarity=0.140 Sum_probs=22.9 Q ss_pred HHHHHHHHHCCCCC-----CCCCCCCEEEECEEECCCC Q ss_conf 89998864245677-----7544843002000115776 Q gi|254781066|r 96 KIFCFAHAWRNGEQ-----GCLHQPEFTMLEWYRAHES 128 (355) Q Consensus 96 rvyqig~~FRaE~~-----~~rHlpEFtmLE~e~af~d 128 (355) ++=...||.|+.|+ +.||.+=|-||== .||.| T Consensus 117 ~~~~sQkCiR~nDlenVG~t~rHhTfFEMlGn-~SFg~ 153 (898) T PRK13902 117 PLVISQPCIRLNDIDNVGRTGRHLTSFEMMAH-HAFNY 153 (898) T ss_pred CCCCCCCCEECCCHHHCCCCCCCCHHHHCCCC-CCCCC T ss_conf 72565223004767543888774354523765-41489 No 91 >cd00769 PheRS_beta_core Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer. While the alpha chain contains a catalytic core domain, the beta chain has a non-catalytic core domain. Probab=93.55 E-value=0.08 Score=30.28 Aligned_cols=81 Identities=17% Similarity=0.144 Sum_probs=45.0 Q ss_pred HHHHHHHHHHHHHHCCCEEEECCCEECCCCC----CCCCCCEEEECCCCCCCCCC-CCCCCCHHHHHHHHHHH----HH- Q ss_conf 9999999999999879889847821056898----54454124102478867832-00002858999989874----46- Q gi|254781066|r 25 RNMIQSSLREYFVENQFIEIDSMSLQYSPGN----ETHIRAFSTELIIQDHIRKP-LYLQTSPEFSCKKLLAA----GE- 94 (355) Q Consensus 25 Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g----~~~~~~f~t~~~~~~~~~~~-~yL~~SPql~lK~ll~~----G~- 94 (355) +.++.+.||++|-+.||.||-|-.+++...- ....++..+ .|-...+ -+||+|-=--+=..++. |. T Consensus 2 ~~~l~~~ir~~L~~~Gf~Ev~t~s~~~~~~~~~~~~~~~~~i~l----~NPls~e~~~lR~sLlp~LL~~~~~N~~r~~~ 77 (198) T cd00769 2 LQKLERKLRRLLAGLGFQEVITYSLTSPEEAELFDGGLDEAVEL----SNPLSEEYSVLRTSLLPGLLDALARNLNRKNK 77 (198) T ss_pred HHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHCCCCCCEEEE----ECCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 67999999999997897141306768989998724887873897----08865668898887799999999865056777 Q ss_pred -HHHHHHHHHHCCCCC Q ss_conf -889998864245677 Q gi|254781066|r 95 -EKIFCFAHAWRNGEQ 109 (355) Q Consensus 95 -~rvyqig~~FRaE~~ 109 (355) -++|+||+||..++. T Consensus 78 ~~~lFEiG~vy~~~~~ 93 (198) T cd00769 78 PLRLFEIGRVFLKDED 93 (198) T ss_pred CCEEEEEEEEEECCCC T ss_conf 7328997638966888 No 92 >PRK09348 glyQ glycyl-tRNA synthetase subunit alpha; Validated Probab=93.41 E-value=0.058 Score=31.09 Aligned_cols=20 Identities=15% Similarity=0.346 Sum_probs=15.7 Q ss_pred HHHHHHHHHHHHHCCCEEEE Q ss_conf 99999999999987988984 Q gi|254781066|r 26 NMIQSSLREYFVENQFIEID 45 (355) Q Consensus 26 s~i~~~iR~ff~~~gF~EV~ 45 (355) ..|+..+.+|..++|-+=++ T Consensus 5 q~~I~~Lq~~W~~~GC~i~q 24 (291) T PRK09348 5 QDIILTLQDYWADQGCAILQ 24 (291) T ss_pred HHHHHHHHHHHHHCCCEEEC T ss_conf 99999999999767978865 No 93 >TIGR00408 proS_fam_I prolyl-tRNA synthetase; InterPro: IPR004499 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by IPR002314 from INTERPRO, which recognises tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi (Lyme desease spirochete). The other family, IPR004500 from INTERPRO, includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis sp. (strain PCC6803), and one of the two prolyl-tRNA synthetases of Saccharomyces cerevisiae (Baker's yeast).; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=93.31 E-value=0.11 Score=29.34 Aligned_cols=214 Identities=20% Similarity=0.179 Sum_probs=119.4 Q ss_pred HHHHHHHHHHHHHHHHHC-------------------CCEEEECCCEECCCCC---CCCCCCEE-----EECCCCCCCCC Q ss_conf 999999999999999987-------------------9889847821056898---54454124-----10247886783 Q gi|254781066|r 22 LLKRNMIQSSLREYFVEN-------------------QFIEIDSMSLQYSPGN---ETHIRAFS-----TELIIQDHIRK 74 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~~~-------------------gF~EV~TPiL~~~~~g---~~~~~~f~-----t~~~~~~~~~~ 74 (355) +.+|+.|.+.+|+-+++. |.-||-=|+|.+...- ..|++=|. +.-.....+.. T Consensus 39 ~~iw~~iq~~~~~~~~~~~~~~~~~L~~F~P~~~~~Y~h~~v~fP~L~p~~~L~KEk~HikGF~pEv~wi~~~G~~~L~~ 118 (533) T TIGR00408 39 FKIWENIQKILRDKLDEIKLKDKVILKKFIPIESLPYGHEEVYFPMLIPESELEKEKDHIKGFEPEVYWITHGGLKKLDE 118 (533) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHEECCCCCCHHHHHHHCCCCCCCCCHHHHEECCCCCCCCC T ss_conf 78999999999999987643546766405677777777001005644525578632135688584002101037772467 Q ss_pred CCCCCCCHHH-----HHHHHHHHHHH---HHHHHHHHHCCCC-CCC--CCCCCEE-EECEEECCCCHHHHHHHHHHHH-- Q ss_conf 2000028589-----99989874468---8999886424567-775--4484300-2000115776578777557888-- Q gi|254781066|r 75 PLYLQTSPEF-----SCKKLLAAGEE---KIFCFAHAWRNGE-QGC--LHQPEFT-MLEWYRAHESYEQLMKDCMNII-- 140 (355) Q Consensus 75 ~~yL~~SPql-----~lK~ll~~G~~---rvyqig~~FRaE~-~~~--rHlpEFt-mLE~e~af~d~~dlm~~~E~li-- 140 (355) |+-||-..|. |.|..- +.-| ||||+.-+||.|- ++| --+.||+ ==|.=-+|.|.++--+.+...+ T Consensus 119 pLaLRPTSEt~~y~m~~kWv~-sy~DLPlk~nQw~~vfR~E~kHTRPflR~rEf~twqE~HT~H~t~~eAee~v~~~~~~ 197 (533) T TIGR00408 119 PLALRPTSETAMYNMYKKWVK-SYRDLPLKINQWVNVFRYEKKHTRPFLRTREFLTWQEAHTAHATAEEAEEEVLKALDL 197 (533) T ss_pred CCEECCCCHHHHHHHHHHHHH-HCCCCCEEEEEEEEEEECCCCCCCCCHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH T ss_conf 501258617888765787851-2158876898435889802178786102333210100013143777889999999998 Q ss_pred -HHHHH-HHCCCEECCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHH Q ss_conf -77666-4188300022343324677320788886566608765323455562327999999997688778765347898 Q gi|254781066|r 141 -RCAAE-VANQKIFSFQNVNCNPFSEPEYITVAEAFARYANIDLGTTLDNPDQPDRHLLYLQAQQAGIRVAHDDTWSDIF 218 (355) Q Consensus 141 -~~~~~-~~~~~~~~~~~~~~~~~~~~~~i~~~e~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 218 (355) +.+++ .++-+.+--. -.+| .+++|.+...+.+.. -+|. -.++.+.-.-..|+-| T Consensus 198 Yk~f~~~~LaIP~~~g~------k~E~---------eKFaGA~~T~~~e~i-mPDg--------G~~LQ~ATsH~LGqnF 253 (533) T TIGR00408 198 YKEFIENLLAIPYFVGR------KSEK---------EKFAGAEYTWTFETI-MPDG--------GRTLQIATSHDLGQNF 253 (533) T ss_pred HHHHHHHCCCCCEEEEC------CCCC---------CCCCCCCCCEEEEEE-CCCC--------CEEHHHHHHHHHHCCC T ss_conf 89997502886468714------8875---------547887622356752-4776--------5001221211330354 Q ss_pred HHHHHCEECCCCCCCC-CCCCCC--CCHH---HHHHCCCCCCCCCCCC Q ss_conf 7664300362237675-443257--6888---8641367877836330 Q gi|254781066|r 219 SRILIEKIEPNLGINC-CTILDR--YPAP---ESALANIYPADPRFTK 260 (355) Q Consensus 219 ~~l~~~~ie~~l~~~~-pvfi~~--yP~~---~~plak~~~~~~~va~ 260 (355) .+-|+=..+...|++. =.|.+. |=.+ ++++=+.|-||.|++. T Consensus 254 ~K~F~i~fe~p~Gs~~~~~~ayq~s~G~StR~igali~~HsD~~GLVL 301 (533) T TIGR00408 254 AKTFDIKFENPTGSDMDKVYAYQTSYGISTRVIGALILIHSDEKGLVL 301 (533) T ss_pred EEEEEEEEECCCCCCCCCCCCEECCCCHHHHHHHHEEEEECCCCCCCC T ss_conf 020367887788897641010010133578875450001226777516 No 94 >PRK09616 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed Probab=93.29 E-value=0.29 Score=27.00 Aligned_cols=13 Identities=8% Similarity=0.013 Sum_probs=6.2 Q ss_pred EECCCCHHHHHHH Q ss_conf 1157765787775 Q gi|254781066|r 123 YRAHESYEQLMKD 135 (355) Q Consensus 123 e~af~d~~dlm~~ 135 (355) |.|+.|...+... T Consensus 228 EsAg~Dp~~v~~a 240 (546) T PRK09616 228 DVTGTDLEAVLLA 240 (546) T ss_pred EEECCCHHHHHHH T ss_conf 8515898999999 No 95 >COG0013 AlaS Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] Probab=92.87 E-value=0.7 Score=24.71 Aligned_cols=45 Identities=20% Similarity=0.138 Sum_probs=29.8 Q ss_pred HHHHHHHHHCCCCC-----CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHH Q ss_conf 89998864245677-----7544843002000115776578777557888776664 Q gi|254781066|r 96 KIFCFAHAWRNGEQ-----GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEV 146 (355) Q Consensus 96 rvyqig~~FRaE~~-----~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~ 146 (355) |+-...||-|+.|+ +.||++=|-||== .||.||- -|+-|.++++. T Consensus 64 r~~~sQkcIR~NDieNVG~T~RHhTfFEMLGN-fSFGdYF-----KeeAI~~AwEf 113 (879) T COG0013 64 RAVTSQKCIRTNDIDNVGYTARHHTFFEMLGN-FSFGDYF-----KEEAIEFAWEF 113 (879) T ss_pred CEECCCCCCCCCCHHHCCCCCCCHHHHHHHHC-CCHHHHH-----HHHHHHHHHHH T ss_conf 70010212014766543766541067776505-7066778-----89999999999 No 96 >COG0752 GlyQ Glycyl-tRNA synthetase, alpha subunit [Translation, ribosomal structure and biogenesis] Probab=90.25 E-value=0.24 Score=27.44 Aligned_cols=20 Identities=15% Similarity=0.306 Sum_probs=16.1 Q ss_pred HHHHHHHHHHHHHCCCEEEE Q ss_conf 99999999999987988984 Q gi|254781066|r 26 NMIQSSLREYFVENQFIEID 45 (355) Q Consensus 26 s~i~~~iR~ff~~~gF~EV~ 45 (355) +.+|..+.+|..++|-+=++ T Consensus 8 Q~~IltLq~yW~~qGC~i~Q 27 (298) T COG0752 8 QGLILTLQNYWAEQGCTILQ 27 (298) T ss_pred HHHHHHHHHHHHHCCCEEEC T ss_conf 99999999999876978614 No 97 >TIGR00389 glyS_dimeric glycyl-tRNA synthetase; InterPro: IPR002315 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . In eubacteria, glycyl-tRNA synthetase (6.1.1.14 from EC) is an alpha2/beta2 tetramer composed of 2 different subunits , , . In some eubacteria, in archaea and eukaryota, glycyl-tRNA synthetase is an alpha2 dimer, this family. It belongs to class IIc and is one of the most complex synthetases. What is most interesting is the lack of similarity between the two types: divergence at the sequence level is so great that it is impossible to infer descent from common genes. The alpha (see IPR002310 from INTERPRO) and beta subunits (see IPR002311 from INTERPRO) also lack significant sequence similarity. However, they are translated from a single mRNA , and a single chain glycyl-tRNA synthetase from Chlamydia trachomatis has been found to have significant similarity with both domains, suggesting divergence from a single polypeptide chain . The sequence and crystal structure of the homodimeric glycyl-tRNA synthetase from Thermus thermophilus, shows that each monomer consists of an active site strongly resembling that of the aspartyl and seryl enzymes, a C-terminal anticodon recognition domain of 100 residues and a third domain unusually inserted between motifs 1 and 2 almost certainly interacting with the acceptor arm of tRNA(Gly). The C-terminal domain has a novel five-stranded parallel-antiparallel beta-sheet structure with three surrounding helices. The active site residues most probably responsible for substrate recognition, in particular in the Gly binding pocket, can be identified by inference from aspartyl-tRNA synthetase due to the conserved nature of the class II active site , .; GO: 0000166 nucleotide binding, 0004820 glycine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006426 glycyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=89.95 E-value=0.28 Score=27.04 Aligned_cols=64 Identities=25% Similarity=0.260 Sum_probs=43.2 Q ss_pred EEEECCCCCCCCCCCCCCCCHHH-------HHHHHHHHHHHH----HHHHHHHHCCCCCCC---CCCCCEEEECEEECCC Q ss_conf 24102478867832000028589-------999898744688----999886424567775---4484300200011577 Q gi|254781066|r 62 FSTELIIQDHIRKPLYLQTSPEF-------SCKKLLAAGEEK----IFCFAHAWRNGEQGC---LHQPEFTMLEWYRAHE 127 (355) Q Consensus 62 f~t~~~~~~~~~~~~yL~~SPql-------~lK~ll~~G~~r----vyqig~~FRaE~~~~---rHlpEFtmLE~e~af~ 127 (355) |.|+.+..+.-.+..||| ||. | |+||-.--.| |=||||+||||=+-+ --+-||+|.|+|. |+ T Consensus 171 F~T~IG~~~~~~~~gYLR--PETAQG~FinF-k~LL~~~r~klPFgvAQiGKSfRNEIsPr~gl~R~REF~QaE~E~-FV 246 (606) T TIGR00389 171 FQTEIGVVGDSKRKGYLR--PETAQGIFINF-KRLLQFFRNKLPFGVAQIGKSFRNEISPRQGLIRLREFEQAEIEF-FV 246 (606) T ss_pred CEEEECCCCCCCCEEECC--CHHCCCCCHHH-HHHHHHHCCCCCEEEEEECCEEECCCCCCCCEEEECHHHHHHHHH-CC T ss_conf 110211334776224147--60104751216-899997458996489974413604003898757103154466874-25 Q ss_pred CH Q ss_conf 65 Q gi|254781066|r 128 SY 129 (355) Q Consensus 128 d~ 129 (355) |- T Consensus 247 ~P 248 (606) T TIGR00389 247 DP 248 (606) T ss_pred CC T ss_conf 96 No 98 >TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase; InterPro: IPR005246 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . All known phenylalanyl-tRNA synthetases, excepting a monomeric mitochondrial form, have an alpha 2 beta 2 heterotetrameric structure. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains but is longer and of unknown function; more generally, it resembles class 2 aminoacyl tRNA ligases. . Probab=89.77 E-value=0.14 Score=28.77 Aligned_cols=33 Identities=18% Similarity=0.522 Sum_probs=27.3 Q ss_pred CCCC-CCCEEECCHHHHHHHHHCCCCHHHHCCCCC Q ss_conf 1889-632453159999899815597131115856 Q gi|254781066|r 314 TEMP-QSSGIAMGFDRLVMLVTGANNINEVIWTPF 347 (355) Q Consensus 314 ~G~P-PhgG~glGidRLvm~l~g~~~Irdvi~FP~ 347 (355) ||.| |-=-.|+|+|||.|+|-|.+.+|+-+ +|. T Consensus 329 Y~Id~pVMNLGlGVERlAMIlygy~DVR~MV-YPQ 362 (558) T TIGR00470 329 YDIDVPVMNLGLGVERLAMILYGYEDVRKMV-YPQ 362 (558) T ss_pred CCCCCCEEECCCHHHHHHHHHHCHHHHHHCC-CCC T ss_conf 6849652225631876787781403343226-884 No 99 >COG2024 Phenylalanyl-tRNA synthetase alpha subunit (archaeal type) [Translation, ribosomal structure and biogenesis] Probab=89.23 E-value=0.26 Score=27.26 Aligned_cols=32 Identities=22% Similarity=0.596 Sum_probs=26.5 Q ss_pred CCCC-CCCEEECCHHHHHHHHHCCCCHHHHCCCC Q ss_conf 1889-63245315999989981559713111585 Q gi|254781066|r 314 TEMP-QSSGIAMGFDRLVMLVTGANNINEVIWTP 346 (355) Q Consensus 314 ~G~P-PhgG~glGidRLvm~l~g~~~Irdvi~FP 346 (355) ||.| |---.|+|+|||+|+|-|.+.+|..+ +| T Consensus 319 Y~Id~pVMNLGlGVERlaMIl~g~~DVR~mv-Yp 351 (536) T COG2024 319 YGIDYPVMNLGLGVERLAMILHGADDVRSMV-YP 351 (536) T ss_pred CCCCCCEEECCHHHHHHHHHHHCCHHHHHHH-CC T ss_conf 2999701203220899999981744776651-34 No 100 >KOG0188 consensus Probab=86.85 E-value=2.3 Score=21.65 Aligned_cols=102 Identities=17% Similarity=0.250 Sum_probs=54.2 Q ss_pred HHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 99999999999987988984782105689854454124102478867832000028589999898744688999886424 Q gi|254781066|r 26 NMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWR 105 (355) Q Consensus 26 s~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FR 105 (355) |.+-++.=+||.++.-.-|+.--. .|-.++-+ .|. .-..|.| +|.||-+ .+.+.|+.-..+|-| T Consensus 5 ~evR~tFldfF~~k~H~~V~SSsV--iP~dDpTL-LFa--NAGMNQF-KpifLgt----------~a~lkRa~NsQKCIR 68 (895) T KOG0188 5 SEVRKTFLDFFKSKHHKIVHSSSV--IPFDDPTL-LFA--NAGMNQF-KPIFLGT----------MAKLKRAANSQKCIR 68 (895) T ss_pred HHHHHHHHHHHHHCCCEEECCCCC--CCCCCCEE-EEE--CCCHHHC-CHHHHHC----------HHHHHHHHHHHHHHH T ss_conf 899999999998548468446874--45899804-773--2654432-1365422----------145676650466776 Q ss_pred CCCC---------CCCCCCCEEEECEEECCCCHH--HHHHHHHHHHHHHH Q ss_conf 5677---------754484300200011577657--87775578887766 Q gi|254781066|r 106 NGEQ---------GCLHQPEFTMLEWYRAHESYE--QLMKDCMNIIRCAA 144 (355) Q Consensus 106 aE~~---------~~rHlpEFtmLE~e~af~d~~--dlm~~~E~li~~~~ 144 (355) |.+. |.-|-+=|-||-= |||.||- +.+...=+++..+. T Consensus 69 AGGKHNDLdDVGkD~yHHTfFEMLGN-WSFGdYFKeEac~~AwElLt~vy 117 (895) T KOG0188 69 AGGKHNDLDDVGKDFYHHTFFEMLGN-WSFGDYFKEEACAWAWELLTFVY 117 (895) T ss_pred CCCCCCCHHHCCCCCHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHH T ss_conf 26876766662665215679998637-63887889999999999987763 No 101 >pfam02091 tRNA-synt_2e Glycyl-tRNA synthetase alpha subunit. Probab=86.76 E-value=0.42 Score=25.99 Aligned_cols=21 Identities=14% Similarity=0.370 Sum_probs=16.5 Q ss_pred HHHHHHHHHHHHHCCCEEEEC Q ss_conf 999999999999879889847 Q gi|254781066|r 26 NMIQSSLREYFVENQFIEIDS 46 (355) Q Consensus 26 s~i~~~iR~ff~~~gF~EV~T 46 (355) ..|+..+.+|..++|.+=+++ T Consensus 2 q~ii~~L~~fW~~~GC~i~qp 22 (284) T pfam02091 2 QSMILTLQEYWASQGCVIMQP 22 (284) T ss_pred HHHHHHHHHHHHHCCCEEECC T ss_conf 589999999998779688777 No 102 >KOG2298 consensus Probab=85.85 E-value=0.2 Score=27.90 Aligned_cols=30 Identities=30% Similarity=0.463 Sum_probs=24.0 Q ss_pred HHHHHHHHHHHHH-HHCCCEEEECCCEECCC Q ss_conf 9999999999999-98798898478210568 Q gi|254781066|r 24 KRNMIQSSLREYF-VENQFIEIDSMSLQYSP 53 (355) Q Consensus 24 ~Rs~i~~~iR~ff-~~~gF~EV~TPiL~~~~ 53 (355) ..+-|++.-|+.| .+++.+||++|+|++.+ T Consensus 48 lk~Nil~~WRkhFilEE~MlEvdct~ltP~~ 78 (599) T KOG2298 48 LKSNILSLWRKHFILEEDMLEVDCTMLTPEP 78 (599) T ss_pred HHHHHHHHHHHHHHHHHCCEEECCCCCCCHH T ss_conf 6776999999987413020440167578088 No 103 >cd00733 GlyRS_alpha_core Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. This alignment contains only sequences from the GlyRS form which heterotetramerizes. The homodimer form of GlyRS is in a different family of class II aaRS. Class II assignment is based upon structure and the presence of three characteristic sequence motifs. Probab=85.04 E-value=0.55 Score=25.32 Aligned_cols=29 Identities=31% Similarity=0.756 Sum_probs=22.1 Q ss_pred CCCCCEEECCHHHHHHHHHCCCCHHHHCC Q ss_conf 89632453159999899815597131115 Q gi|254781066|r 316 MPQSSGIAMGFDRLVMLVTGANNINEVIW 344 (355) Q Consensus 316 ~PPhgG~glGidRLvm~l~g~~~Irdvi~ 344 (355) .|..+-+.-|+|||.|++-|.+||-|++. T Consensus 150 ~pv~~EiTYGLERiaMylQ~vd~v~dl~w 178 (279) T cd00733 150 KPISVEITYGLERIAMYLQGVDNVYDIEW 178 (279) T ss_pred CCCCEEEEHHHHHHHHHHHCCCHHEEEEC T ss_conf 45323310119999999857542314123 No 104 >CHL00192 syfB phenylalanyl-tRNA synthetase beta chain; Provisional Probab=83.34 E-value=3.1 Score=20.84 Aligned_cols=113 Identities=12% Similarity=0.041 Sum_probs=53.9 Q ss_pred HHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCC-CCCCCCCHHHHHHHHHHH----HHH--HH Q ss_conf 99999999999998798898478210568985445412410247886783-200002858999989874----468--89 Q gi|254781066|r 25 RNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRK-PLYLQTSPEFSCKKLLAA----GEE--KI 97 (355) Q Consensus 25 Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~-~~yL~~SPql~lK~ll~~----G~~--rv 97 (355) ..++.+.+|++|.+.||.|+-|=.+++....+. ... . ..|-... --+|++|-=--|=..++- |.. ++ T Consensus 396 ~~~~~~~lr~~L~~~Gf~E~itysf~s~~~~~~--~~v--~--l~NPis~e~s~LR~sLlpgLL~~~~~N~~r~~~~i~l 469 (702) T CHL00192 396 LRNFIDKIRSLLRNLGLTELVHYSLVKSYTYYK--GEI--K--LYNPLLQDYSTLRSSLLPGLILAQQYNLKQSNQTIEG 469 (702) T ss_pred HHHHHHHHHHHHHHCCCCEEEEECCCCHHHCCC--CCE--E--ECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEE T ss_conf 899999999999968983477531468444567--728--9--7087524378888877999999998615359977428 Q ss_pred HHHHHHHCCCCCC---CCCCCCEEE------ECEEEC--CCCHHHHHHHHHHHHHHH Q ss_conf 9988642456777---544843002------000115--776578777557888776 Q gi|254781066|r 98 FCFAHAWRNGEQG---CLHQPEFTM------LEWYRA--HESYEQLMKDCMNIIRCA 143 (355) Q Consensus 98 yqig~~FRaE~~~---~rHlpEFtm------LE~e~a--f~d~~dlm~~~E~li~~~ 143 (355) |+||++|...... ..|+.=..+ -.|-.. -.|+.++-..+|.++..+ T Consensus 470 FEiG~vf~~~~~~~~e~~~l~~~~~~g~~~~~~w~~~~~~~dFfd~Kg~ve~ll~~l 526 (702) T CHL00192 470 FEIGHVFRDNTEKIFETLHLAGGIGGGLDIRSSWSEKAQSLNWYEAKGIVEEFFQRL 526 (702) T ss_pred EEEECCCCCCCCCCCCHHEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH T ss_conf 976455268878862112299999818866544456677678999999999999981 No 105 >TIGR00468 pheS phenylalanyl-tRNA synthetase, alpha subunit; InterPro: IPR004529 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases . This family describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this family. ; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=81.85 E-value=0.58 Score=25.17 Aligned_cols=27 Identities=22% Similarity=0.449 Sum_probs=24.1 Q ss_pred CCCEEECCHHHHHHHHHCCCCHHHHCC Q ss_conf 632453159999899815597131115 Q gi|254781066|r 318 QSSGIAMGFDRLVMLVTGANNINEVIW 344 (355) Q Consensus 318 PhgG~glGidRLvm~l~g~~~Irdvi~ 344 (355) +--+||+|++|+.|+-.|.++||+..- T Consensus 323 ~~~~~g~g~~r~~~~~~~~~d~r~~~~ 349 (362) T TIGR00468 323 PGLAWGLGIERLAMLKYGLDDLRDLYE 349 (362) T ss_pred EEEEECCCHHHHHHHHHCHHHHHHHHC T ss_conf 134321240124454513356888640 No 106 >TIGR00669 asnA aspartate--ammonia ligase; InterPro: IPR004618 Aspartate--ammonia ligase (asparagine synthetase) 6.3.1.1 from EC catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia. This family represents one of two non-homologous forms of aspartate--ammonia ligase found in Escherichia coli. This type is also found in Haemophilus influenzae, Treponema pallidum and Lactobacillus delbrueckii, but appears to have a very limited distribution. The fact that the protein from the H. influenzae is more than 70 0dentical to that from the spirochete T. pallidum, but less than 65 0dentical to that from the closely related E. coli, strongly suggests lateral transfer.; GO: 0004071 aspartate-ammonia ligase activity, 0006529 asparagine biosynthetic process, 0005737 cytoplasm. Probab=77.12 E-value=3.3 Score=20.70 Aligned_cols=47 Identities=26% Similarity=0.311 Sum_probs=34.2 Q ss_pred CCCCCCCHHHHHHHHHHCC-CCCCCEEECCHHHHHHHHHCCCCHHHHCC Q ss_conf 2888530101899998618-89632453159999899815597131115 Q gi|254781066|r 297 KIYNETYPIDEDFLACLTE-MPQSSGIAMGFDRLVMLVTGANNINEVIW 344 (355) Q Consensus 297 ~~~~e~~~~D~~fl~al~G-~PPhgG~glGidRLvm~l~g~~~Irdvi~ 344 (355) .|+.....+++ .-+-+.| +|-+-|-|+|--||.|+|+..+.|-+|-. T Consensus 268 tGded~l~~~W-hq~l~~G~lP~~iGGGiGqsrl~mlll~~~hiG~vq~ 315 (330) T TIGR00669 268 TGDEDRLELEW-HQDLLNGKLPQTIGGGIGQSRLAMLLLQKKHIGEVQA 315 (330) T ss_pred CCCCCHHHHHH-HHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHC T ss_conf 47610123477-8997448776201565307899999862001452000 No 107 >COG2160 AraA L-arabinose isomerase [Carbohydrate transport and metabolism] Probab=71.64 E-value=7.5 Score=18.60 Aligned_cols=53 Identities=8% Similarity=-0.039 Sum_probs=22.9 Q ss_pred HHHHHHHHHHHCCCC---CCC--CCCCCEEEECEEECCCCHHHHHHH-HHHHHHHHHHHH Q ss_conf 688999886424567---775--448430020001157765787775-578887766641 Q gi|254781066|r 94 EEKIFCFAHAWRNGE---QGC--LHQPEFTMLEWYRAHESYEQLMKD-CMNIIRCAAEVA 147 (355) Q Consensus 94 ~~rvyqig~~FRaE~---~~~--rHlpEFtmLE~e~af~d~~dlm~~-~E~li~~~~~~~ 147 (355) .-||=-+|...|.=- .|. .+-.==|.++.+-. .|+-.+|+. +|+=|..+.+.. T Consensus 175 h~kvarfGdnmr~vavtegDkv~aqiqFGwsv~~~gI-gdLv~~~~~vse~eV~~l~eey 233 (497) T COG2160 175 HLKVARFGDNMREVAVTEGDKVAAQIQFGWSVNTWGI-GDLVEVVNEVSEGEVEALLEEY 233 (497) T ss_pred HHHHHHHCCHHHHHCCCCCHHHHHHHHHCCEEEEEEH-HHHHHHHHHCCHHHHHHHHHHH T ss_conf 2014122201331201022788998863625767744-6899999751687899999998 No 108 >cd00768 class_II_aaRS-like_core Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial ATP phosphoribosyltransferase regulatory subunit HisZ. Probab=69.72 E-value=0.32 Score=26.69 Aligned_cols=52 Identities=25% Similarity=0.328 Sum_probs=29.4 Q ss_pred CCCCCEEEEC-----CEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH-H-CCCCCCCEEECCHHHH Q ss_conf 3302202236-----712256402106999999999999999972888530101899998-6-1889632453159999 Q gi|254781066|r 258 FTKRFELYAC-----NIELCNACDELLDPIEQRHRFEKEMQEKKKIYNETYPIDEDFLAC-L-TEMPQSSGIAMGFDRL 329 (355) Q Consensus 258 va~rfdl~i~-----G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e~~~~D~~fl~a-l-~G~PPhgG~glGidRL 329 (355) .+..||+.+. +.|+++++.-. ..|..||.. .|.+. - ...|++.|+|||++|| T Consensus 153 a~~~~Die~~~p~~~~~Ev~s~~~~~---d~qsr~~~i-----------------~y~~~dg~~~~~~~~~~gl~v~Rl 211 (211) T cd00768 153 AGPGFEIEVDHPEGRGLEIGSGGYRQ---DEQARAADL-----------------YFLDEALEYRYPPTIGFGLGLERL 211 (211) T ss_pred CEEEEEEEEECCCCCEEEEECEECCC---CHHHHHCCC-----------------EEECCCCCEEEEEEEECEECCCCC T ss_conf 23545578983789799993546167---787884698-----------------999999999875563032413669 No 109 >pfam10026 DUF2268 Predicted Zn-dependent protease (DUF2268). This domain, found in various hypothetical bacterial proteins, as well as predicted zinc dependent proteases, has no known function. Probab=68.71 E-value=3 Score=20.91 Aligned_cols=88 Identities=15% Similarity=0.166 Sum_probs=41.2 Q ss_pred CCCCCCEEEECCEECCCCCHHCCCHHHHHHHHHHHHHHHHCCCCC-CCHHHHHH-HHHHCCCCCCCEEECCHHHHHHHHH Q ss_conf 633022022367122564021069999999999999999728885-30101899-9986188963245315999989981 Q gi|254781066|r 257 RFTKRFELYACNIELCNACDELLDPIEQRHRFEKEMQEKKKIYNE-TYPIDEDF-LACLTEMPQSSGIAMGFDRLVMLVT 334 (355) Q Consensus 257 ~va~rfdl~i~G~El~ng~~El~d~~~q~~rf~~q~~~k~~~~~e-~~~~D~~f-l~al~G~PPhgG~glGidRLvm~l~ 334 (355) |+|+.|.--+.|.+...-+..-.|....++...+ . .+...+.. ....+..+ .+...++|+.+|.++|..=+--+|. T Consensus 99 GLAe~f~~e~~G~~~~~pw~~~~~~~~l~~~~~~-~-~~~~l~~~~~~~~~~~l~G~~~~~~P~~~GYa~Gy~iV~~yL~ 176 (195) T pfam10026 99 GLAEHFVAELYGEEYLGPWTTPYDEEQLEHLWKQ-V-IKPNLDLKGFSEHDPYLYGDDIGRLPKWAGYAVGYYIVKKYLE 176 (195) T ss_pred HHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHH-H-HHHHCCCCCCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHH T ss_conf 2399999998198778773324899999999999-9-8764146663221405557876789860037989999999999 Q ss_pred C-CCCHHHHCCCC Q ss_conf 5-59713111585 Q gi|254781066|r 335 G-ANNINEVIWTP 346 (355) Q Consensus 335 g-~~~Irdvi~FP 346 (355) . -.+|.+...-| T Consensus 177 ~~~~s~~e~t~~~ 189 (195) T pfam10026 177 KNGKSIAEATLLP 189 (195) T ss_pred HCCCCHHHHHCCC T ss_conf 8799889986399 No 110 >PRK02929 L-arabinose isomerase; Provisional Probab=68.50 E-value=8.8 Score=18.20 Aligned_cols=14 Identities=21% Similarity=0.458 Sum_probs=10.0 Q ss_pred CCCCEEEECCEECC Q ss_conf 30220223671225 Q gi|254781066|r 259 TKRFELYACNIELC 272 (355) Q Consensus 259 a~rfdl~i~G~El~ 272 (355) ..||-|++|-++.+ T Consensus 399 G~rFRli~n~V~~v 412 (499) T PRK02929 399 GDRFRLLVNEVDTV 412 (499) T ss_pred CCCEEEEEEEEEEE T ss_conf 77568997567776 No 111 >pfam02610 Arabinose_Isome L-arabinose isomerase. This is a family of L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyse the reaction: L-arabinose <= L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme. Probab=66.54 E-value=9.6 Score=17.96 Aligned_cols=50 Identities=10% Similarity=0.060 Sum_probs=26.0 Q ss_pred CCCCCCCCCCCH--HHCCCHHHHHHHHHHHHHHHHHHHHHCCCEE---EECCCEE Q ss_conf 998898747883--1261548999999999999999999879889---8478210 Q gi|254781066|r 1 MHQIPSQPWWNR--DFHYRRRPFLLKRNMIQSSLREYFVENQFIE---IDSMSLQ 50 (355) Q Consensus 1 ~~~~p~~~~~~~--~~~~r~R~~l~~Rs~i~~~iR~ff~~~gF~E---V~TPiL~ 50 (355) |..++...+|+- |.||=--+.|..=++=.+.|-+.|++.+-+- |--|+++ T Consensus 1 M~~~~~~e~WFvtGSQ~LYG~e~L~qVa~~s~~i~~~Ln~s~~lp~~iv~Kpv~~ 55 (359) T pfam02610 1 MLDFKQYEFWFVTGSQHLYGEETLKQVAAHSQEIVEGLNASGKLPVKIVLKPVVT 55 (359) T ss_pred CCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCC T ss_conf 9878883599994786556889999999999999998700689854899704437 No 112 >PRK00629 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed Probab=64.46 E-value=7.5 Score=18.58 Aligned_cols=115 Identities=14% Similarity=0.115 Sum_probs=58.3 Q ss_pred HHHHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEE---ECCCCCCCCCC-CCCCCCHHHHHHHHHH----HHHH- Q ss_conf 9999999999999879889847821056898544541241---02478867832-0000285899998987----4468- Q gi|254781066|r 25 RNMIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFST---ELIIQDHIRKP-LYLQTSPEFSCKKLLA----AGEE- 95 (355) Q Consensus 25 Rs~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t---~~~~~~~~~~~-~yL~~SPql~lK~ll~----~G~~- 95 (355) ..+..+.+|++|.+.||.||-|=.+++.. .++.|.. .....|-...+ -+||+|-=.-|=..+. -|.. T Consensus 486 ~~~~~~~ir~~L~~~Gf~EvitySf~s~~----~~~~~~~~~~~v~l~NPls~e~s~lR~SLlp~LL~~~~~N~~r~~~~ 561 (786) T PRK00629 486 AQKRRRRVRRALAARGYQEAITYSFVSPE----VADLFGLGEDALKLLNPISSELSVMRTSLLPGLLEALAYNQNRKNKD 561 (786) T ss_pred HHHHHHHHHHHHHHCCCEEEECCCCCCHH----HHHHHCCCCCCEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 99999999999997898424136667979----99862788775685375421268888877999999899886279987 Q ss_pred -HHHHHHHHHCCCCCCCCCCCCEE-----EECEEE--CCCCHHHHHHHHHHHHHHH Q ss_conf -89998864245677754484300-----200011--5776578777557888776 Q gi|254781066|r 96 -KIFCFAHAWRNGEQGCLHQPEFT-----MLEWYR--AHESYEQLMKDCMNIIRCA 143 (355) Q Consensus 96 -rvyqig~~FRaE~~~~rHlpEFt-----mLE~e~--af~d~~dlm~~~E~li~~~ 143 (355) ++|+||++|.....-..|+.=-. .-.|.. .-.|+.++-..+|.++..+ T Consensus 562 i~lFEiG~vf~~~~~E~~~La~~~~G~~~~~~w~~~~~~~dffdlKg~ve~ll~~l 617 (786) T PRK00629 562 VALFEIGLVFLPGPREPLHLAGVLTGLRLNESWGGKGRPVDFFDAKGDLEALLGAL 617 (786) T ss_pred EEEEEEEEEECCCCCHHEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC T ss_conf 67998754389998446599999989877666566676468999999999999973 No 113 >PRK01584 alanyl-tRNA synthetase; Provisional Probab=63.55 E-value=4.6 Score=19.88 Aligned_cols=101 Identities=17% Similarity=0.217 Sum_probs=55.5 Q ss_pred HHHHHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 99999999999879889847821056898544541241024788678320000285899998987446889998864245 Q gi|254781066|r 27 MIQSSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAGEEKIFCFAHAWRN 106 (355) Q Consensus 27 ~i~~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G~~rvyqig~~FRa 106 (355) .|-+..-+||.++|-..|..--|.+ -+++-+ -| |... .+.| ++.||-+.+-- ..|+=...||.|+ T Consensus 5 eiR~~Fl~fF~~kgH~~v~ssslvp--~~dptl-lf-tnAG-m~~F-k~~f~G~~~p~---------~~r~~~~QkCiR~ 69 (593) T PRK01584 5 ELRKKYIDFFKSKGHVEIAGKSLVP--ENDPTV-LF-NTAG-MQPL-VPYLLGEPHPS---------GDMLVNVQKCLRT 69 (593) T ss_pred HHHHHHHHHHHHCCCEECCCCCCCC--CCCCCE-EE-EECC-CCCC-CHHHCCCCCCC---------CCCCCCCCCEEEC T ss_conf 9999999999878988837877177--999983-57-4045-1017-12325888999---------9974567531333 Q ss_pred CCC----CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHHHHHC Q ss_conf 677----754484300200011577657877755788877666418 Q gi|254781066|r 107 GEQ----GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAAEVAN 148 (355) Q Consensus 107 E~~----~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~~~~~ 148 (355) .++ +++|.+=|-||== .||.||- -++-|.++++.+. T Consensus 70 ~DldnVG~~~H~TfFEMLGn-~SFgdYf-----K~eaI~~awe~lt 109 (593) T PRK01584 70 GDIDEVGDLSHLTFFEMLGN-WSLGAYF-----KEESVKYSFEFLT 109 (593) T ss_pred CCHHHCCCCCCCHHHHHCCC-CCCCCHH-----HHHHHHHHHHHHC T ss_conf 75633688875277750544-5233114-----8999999999806 No 114 >PRK07080 hypothetical protein; Validated Probab=62.88 E-value=5.9 Score=19.21 Aligned_cols=42 Identities=19% Similarity=0.178 Sum_probs=29.2 Q ss_pred HHHHCCCCC-CCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHH Q ss_conf 864245677-7544843002000115776578777557888776 Q gi|254781066|r 101 AHAWRNGEQ-GCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCA 143 (355) Q Consensus 101 g~~FRaE~~-~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~ 143 (355) +-|||.|.+ |+.-+.+|.|-|+=.. .+-+++++.-|..+.-. T Consensus 160 ~yCFRhEPS~dp~Rmq~FRMrEyV~i-Gt~e~v~a~R~~W~~r~ 202 (318) T PRK07080 160 SYCFRHEPSLDPARMQLFRMREYVRI-GTPEQILAFRQRWIERG 202 (318) T ss_pred EEHHCCCCCCCHHHHHHHHCEEEEEE-CCHHHHHHHHHHHHHHH T ss_conf 42101789888588886440445771-79999999999999999 No 115 >KOG0903 consensus Probab=60.93 E-value=5 Score=19.64 Aligned_cols=14 Identities=14% Similarity=0.057 Sum_probs=5.3 Q ss_pred HHCCCEEEECCCEE Q ss_conf 98798898478210 Q gi|254781066|r 37 VENQFIEIDSMSLQ 50 (355) Q Consensus 37 ~~~gF~EV~TPiL~ 50 (355) .+.++-+++.|.+. T Consensus 312 ~n~~la~~~i~~~~ 325 (847) T KOG0903 312 RNCDLAEAEITLLI 325 (847) T ss_pred HCCCHHHHEECCCC T ss_conf 50334551200145 No 116 >pfam01411 tRNA-synt_2c tRNA synthetases class II (A). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only alanyl-tRNA synthetases. Probab=58.16 E-value=8.7 Score=18.23 Aligned_cols=91 Identities=14% Similarity=0.223 Sum_probs=48.1 Q ss_pred HHHHHHHHHCCCEEEECCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHH-----HHHHHHHHHHH Q ss_conf 9999999987988984782105689854454124102478867832000028589999898744-----68899988642 Q gi|254781066|r 30 SSLREYFVENQFIEIDSMSLQYSPGNETHIRAFSTELIIQDHIRKPLYLQTSPEFSCKKLLAAG-----EEKIFCFAHAW 104 (355) Q Consensus 30 ~~iR~ff~~~gF~EV~TPiL~~~~~g~~~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~ll~~G-----~~rvyqig~~F 104 (355) +..-+||.++|-..|..--|.+ -.+. +.++..|.=.-.|....+| ..|+=...||+ T Consensus 4 ~~fl~fF~~~gH~~i~s~~lvp--~~d~-----------------~llft~Agm~~fkp~~~g~~~~pp~~~l~~~Q~Ci 64 (545) T pfam01411 4 QTFLDFFEKKGHTRVPSSPVVP--RNDP-----------------TLLFTNAGMNQFKPIFLGGEDKPPYNRAVNSQKCI 64 (545) T ss_pred HHHHHHHHHCCCEEECCCCCCC--CCCC-----------------CEEEECCCCHHCHHHHCCCCCCCCCCCCCCCCCCE T ss_conf 9999999878988807867067--9999-----------------81464046011737654987589988724433324 Q ss_pred CCCCC-----CCCCCCCEEEECEEECCCCHH--HHHHHHHHHH Q ss_conf 45677-----754484300200011577657--8777557888 Q gi|254781066|r 105 RNGEQ-----GCLHQPEFTMLEWYRAHESYE--QLMKDCMNII 140 (355) Q Consensus 105 RaE~~-----~~rHlpEFtmLE~e~af~d~~--dlm~~~E~li 140 (355) |..++ |.||++=|-||-= .||.||- +.++.+-+++ T Consensus 65 R~~DidnVG~t~rH~T~FEMlGn-~SFg~YfK~eai~~a~e~l 106 (545) T pfam01411 65 RAGDLDNVGRTARHHTFFEMLGN-FSFGDYFKEEAIEFAWELL 106 (545) T ss_pred ECCCHHHCCCCCCCCHHHHCCCC-CCCCCCHHHHHHHHHHHHH T ss_conf 43765433677775323220334-5156243789999999997 No 117 >PRK13384 delta-aminolevulinic acid dehydratase; Provisional Probab=44.88 E-value=11 Score=17.56 Aligned_cols=15 Identities=27% Similarity=0.454 Sum_probs=7.1 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 989874468899988 Q gi|254781066|r 87 KKLLAAGEEKIFCFA 101 (355) Q Consensus 87 K~ll~~G~~rvyqig 101 (355) +.++..|...|.=+| T Consensus 69 e~~~~lGI~av~LFg 83 (323) T PRK13384 69 ERLYALGIRYVMPFG 83 (323) T ss_pred HHHHHCCCCEEEECC T ss_conf 999978996898369 No 118 >TIGR02151 IPP_isom_2 isopentenyl-diphosphate delta-isomerase, type 2; InterPro: IPR011179 This group represents the bacterial and archaeal isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP isomerase catalyses the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), and is a key enzyme in the biosynthesis of isoprenoids via the mevalonate pathway. The bacterial and archaeal IPP isomerase (type 2 enzyme) differs from that found in eukaryotes (type 1 enzyme), and requires NADPH, magnesium, and FMN for activity , .; GO: 0004452 isopentenyl-diphosphate delta-isomerase activity, 0010181 FMN binding, 0008299 isoprenoid biosynthetic process, 0005737 cytoplasm. Probab=44.61 E-value=12 Score=17.36 Aligned_cols=19 Identities=42% Similarity=0.719 Sum_probs=15.3 Q ss_pred HHHHHHHCCCCHHHHCCCC Q ss_conf 9989981559713111585 Q gi|254781066|r 328 RLVMLVTGANNINEVIWTP 346 (355) Q Consensus 328 RLvm~l~g~~~Irdvi~FP 346 (355) |.+|+++|+.||+|.--=| T Consensus 326 k~~mfl~G~~~i~EL~~~~ 344 (349) T TIGR02151 326 KVAMFLTGAKNIKELKKVP 344 (349) T ss_pred HHHHHHHCCCCHHHHCCCC T ss_conf 9999871798879861787 No 119 >PRK09283 delta-aminolevulinic acid dehydratase; Validated Probab=37.83 E-value=23 Score=15.71 Aligned_cols=11 Identities=9% Similarity=0.232 Sum_probs=5.4 Q ss_pred HHHHHHHHHHH Q ss_conf 98987446889 Q gi|254781066|r 87 KKLLAAGEEKI 97 (355) Q Consensus 87 K~ll~~G~~rv 97 (355) ++++..|...| T Consensus 66 e~~~~lGI~av 76 (321) T PRK09283 66 EEAVDLGIPAV 76 (321) T ss_pred HHHHHCCCCEE T ss_conf 99998799989 No 120 >pfam05830 NodZ Nodulation protein Z (NodZ). The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal. Probab=37.50 E-value=11 Score=17.70 Aligned_cols=21 Identities=19% Similarity=0.270 Sum_probs=11.9 Q ss_pred HHHHHHHHHHC---CCCCCCEEEC Q ss_conf 10189999861---8896324531 Q gi|254781066|r 304 PIDEDFLACLT---EMPQSSGIAM 324 (355) Q Consensus 304 ~~D~~fl~al~---G~PPhgG~gl 324 (355) -+|-+.|..+. ..||++-|+. T Consensus 267 LidM~lLarCD~lIrf~~~SaFsr 290 (322) T pfam05830 267 LVEMYLLARCDTVIRFPPTSAFTR 290 (322) T ss_pred HHHHHHHHHCCEEEECCCCCHHHH T ss_conf 999999873754353488426778 No 121 >cd04823 ALAD_PBGS_aspartate_rich Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. All of PBGS_aspartate_rich contain an aspartate rich metal binding site with the general sequence DXALDX(Y/F)X3G(H/Q)DG. They also contain an allosteric magnesiu Probab=36.95 E-value=21 Score=15.98 Aligned_cols=11 Identities=9% Similarity=0.232 Sum_probs=4.8 Q ss_pred HHHHHHHHHHH Q ss_conf 98987446889 Q gi|254781066|r 87 KKLLAAGEEKI 97 (355) Q Consensus 87 K~ll~~G~~rv 97 (355) ++++..|...| T Consensus 61 ~~~~~lGI~av 71 (320) T cd04823 61 EEAVDLGIPAV 71 (320) T ss_pred HHHHHCCCCEE T ss_conf 99998899789 No 122 >pfam03590 AsnA Aspartate-ammonia ligase. Probab=35.52 E-value=32 Score=14.90 Aligned_cols=120 Identities=16% Similarity=0.156 Sum_probs=66.9 Q ss_pred HHHHHHHHHHHHHHHHH-----CCCEEEECCCEECC-CC-CCC---CCCCEEEECCCCCCCCCCCCCCCCHHHHHHHH-H Q ss_conf 99999999999999998-----79889847821056-89-854---45412410247886783200002858999989-8 Q gi|254781066|r 22 LLKRNMIQSSLREYFVE-----NQFIEIDSMSLQYS-PG-NET---HIRAFSTELIIQDHIRKPLYLQTSPEFSCKKL-L 90 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~~-----~gF~EV~TPiL~~~-~~-g~~---~~~~f~t~~~~~~~~~~~~yL~~SPql~lK~l-l 90 (355) ++.+.+.|+.|+++|.. -+.+.|..|+++.. .| .+- .-+|...+.. +.-+..+=-.+|--=+ ||+ | T Consensus 3 ~i~~Q~AI~~iK~~F~~~L~~~LnL~rVsAPLfv~~~sGlND~LnG~ErpV~F~ik--~~~~~~~EIVhSLAKW-KR~aL 79 (244) T pfam03590 3 FILQQQEISFVKNTFTQKLAEHLGLIEVQGPILSQVGDGIQDNLSGAEKAVSVKVK--QIPDATFEVVHSLAKW-KRHTL 79 (244) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCEEECCCEEEECCCCCCCCCCCEEEEEEEECC--CCCCCCEEEEEEHHHH-HHHHH T ss_conf 88999999999999999999973917966662871798877687873611386457--8899716997214888-99999 Q ss_pred H-HHH---HHHHHHHHHHC-CCC-CCCCCCCCEEEECEEECCCCHHHHHHHHHHHHHHHH Q ss_conf 7-446---88999886424-567-775448430020001157765787775578887766 Q gi|254781066|r 91 A-AGE---EKIFCFAHAWR-NGE-QGCLHQPEFTMLEWYRAHESYEQLMKDCMNIIRCAA 144 (355) Q Consensus 91 ~-~G~---~rvyqig~~FR-aE~-~~~rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~~ 144 (355) . -|| +-+|+=-.+-| +|+ +|..|+-=.-|-|||..-...+-.++...+.++.+. T Consensus 80 ~~Y~f~~geGlyTdMnAIR~DEe~Ldn~HSiYVDQWDWEkvI~~~dR~~~~LK~tV~~Iy 139 (244) T pfam03590 80 ARFGFSEGEGLFVHMKALRPDEDSLDPTHSVYVDQWDWEKVIPNGDRNLAYLKSTVNKIY 139 (244) T ss_pred HHCCCCCCCEEEECCCCCCCCCCCCCCCCEEEECCCCHHHHCCCCCCCHHHHHHHHHHHH T ss_conf 965998995455245600167545787600898510221226801167899999999999 No 123 >TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family; InterPro: IPR004589 The ATP-dependent DNA helicase RecQ (3.6.1 from EC) is involved in genome maintenance . All homologues tested to date unwind paired DNA, translocating in a 3' to 5' direction and several have a preference for forked or 4-way DNA structures (e.g. Holliday junctions) or for G-quartet DNA. The yeast protein, Sgs1, is present in numerous foci that coincide with sites of de novo synthesis DNA, such as the replication fork, and protein levels peak during S-phase. A model has been proposed for Sgs1p action in the S-phase checkpoint response, both as a 'sensor' for damage during replication and a 'resolvase' for structures that arise at paused forks, such as the four-way 'chickenfoot' structure. The action of Sgs1p may serve to maintain the proper amount and integrity of ss DNA that is necessary for the binding of RPA (replication protein A, the eukaryotic ss DNA-binding protein)DNA pol complexes. Sgs1p would thus function by detecting (or resolving) aberrant DNA structures, and would thus contribute to the full activation of the DNA-dependent protein kinase, Mec1p and the effector kinase, Rad53p. Its ability to bind both the large subunit of RPA and the RecA-like protein Rad51p, place it in a unique position to resolve inappropriate fork structures that can occur when either the leading or lagging strand synthesis is stalled. Thus, RecQ helicases integrate checkpoint activation and checkpoint response. ; GO: 0008026 ATP-dependent helicase activity, 0006310 DNA recombination. Probab=34.81 E-value=12 Score=17.30 Aligned_cols=20 Identities=30% Similarity=0.323 Sum_probs=8.0 Q ss_pred CCHHHHHHH-HHHHHHHHHHH Q ss_conf 285899998-98744688999 Q gi|254781066|r 80 TSPEFSCKK-LLAAGEEKIFC 99 (355) Q Consensus 80 ~SPql~lK~-ll~~G~~rvyq 99 (355) ++||.=++- -+.+-+++.|+ T Consensus 110 vtPE~~~~~~~ll~~Le~~Y~ 130 (497) T TIGR00614 110 VTPEKISKSKSLLQTLEKLYE 130 (497) T ss_pred ECHHHHHCCHHHHHHHHHHHH T ss_conf 163465346478999999886 No 124 >TIGR00409 proS_fam_II prolyl-tRNA synthetase; InterPro: IPR004500 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Prolyl-tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form, is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa. This family includes the enzyme from Escherichia coli that contains all three of the conserved consensus motifs characteristic of class II aminoacyl-tRNA synthetases and the enzyme from the spirochete Borrelia burgdorferi.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=34.62 E-value=33 Score=14.81 Aligned_cols=123 Identities=15% Similarity=0.162 Sum_probs=75.6 Q ss_pred HHHHHHHHHHHHHHHHHCC-CEEEECCCEEC-CC---CCCC---C----CCCEEEECCCCCCCCCCCCCCCCHH-----H Q ss_conf 9999999999999999879-88984782105-68---9854---4----5412410247886783200002858-----9 Q gi|254781066|r 22 LLKRNMIQSSLREYFVENQ-FIEIDSMSLQY-SP---GNET---H----IRAFSTELIIQDHIRKPLYLQTSPE-----F 84 (355) Q Consensus 22 l~~Rs~i~~~iR~ff~~~g-F~EV~TPiL~~-~~---~g~~---~----~~~f~t~~~~~~~~~~~~yL~~SPq-----l 84 (355) +|.=.+|-+.||+-|++.| =+||-=|.+++ +. ..++ | -.-|.- .|-.+++|-|.-.-| | T Consensus 48 ~rVL~Kv~~ivreeM~~~GGA~E~~lp~~~~la~LW~~SGRW~~YG~seGELl~l----kDR~~r~f~LgpT~EEvIT~l 123 (620) T TIGR00409 48 LRVLKKVENIVREEMNKDGGAIEVLLPALQPLAELWQESGRWDTYGPSEGELLRL----KDRKGREFVLGPTHEEVITDL 123 (620) T ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEE----EECCCCCCCCCCCCHHHHHHH T ss_conf 9999988999998622678533466766778999875407532468654336676----526888735678665568999 Q ss_pred HHHHHHHHHHH---HHHHHHHHHCCCC--C-CC-CCCCCEEEECEEECCCCHHHHHHHHHHH---HHHHHHHHCCC Q ss_conf 99989874468---8999886424567--7-75-4484300200011577657877755788---87766641883 Q gi|254781066|r 85 SCKKLLAAGEE---KIFCFAHAWRNGE--Q-GC-LHQPEFTMLEWYRAHESYEQLMKDCMNI---IRCAAEVANQK 150 (355) Q Consensus 85 ~lK~ll~~G~~---rvyqig~~FRaE~--~-~~-rHlpEFtmLE~e~af~d~~dlm~~~E~l---i~~~~~~~~~~ 150 (355) - |..+.|.-. ..|||..=||||= . += | .=||.|=|.|-=..|.+++-+.=..| .+.++..++-. T Consensus 124 ~-~~~i~SYKqLP~~lYQI~tKFRDEiRPRFGl~R-gREFiMKDAYSFH~~~ESL~~ty~~m~~aY~~IF~rlGld 197 (620) T TIGR00409 124 V-RNEIKSYKQLPLNLYQIQTKFRDEIRPRFGLLR-GREFIMKDAYSFHSDEESLDATYQKMDQAYSNIFSRLGLD 197 (620) T ss_pred H-HHHHHHHHHCCCCEECCCCCCCCCCCCCCCCCC-CHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 9-998754530683010045121442048876000-1232302425544787679999889999999999865898 No 125 >TIGR00414 serS seryl-tRNA synthetase; InterPro: IPR002317 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa .; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm. Probab=33.97 E-value=34 Score=14.75 Aligned_cols=119 Identities=14% Similarity=0.207 Sum_probs=60.1 Q ss_pred HHHHHHHHHHHHH-HHCCCEEEECCCEECC---CCCC--CCCCCEEEECCCCCCCCCC-CCCCCCHHH-----HHHHHHH Q ss_conf 9999999999999-9879889847821056---8985--4454124102478867832-000028589-----9998987 Q gi|254781066|r 24 KRNMIQSSLREYF-VENQFIEIDSMSLQYS---PGNE--THIRAFSTELIIQDHIRKP-LYLQTSPEF-----SCKKLLA 91 (355) Q Consensus 24 ~Rs~i~~~iR~ff-~~~gF~EV~TPiL~~~---~~g~--~~~~~f~t~~~~~~~~~~~-~yL~~SPql-----~lK~ll~ 91 (355) ....++...-++. .++||.++.+|.+... .|.+ .....|.-..+.....+.+ .||....|. +....+. T Consensus 204 ~~~al~~~~l~~~~~~~g~~~~~~p~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~l~~t~e~~~~~~~~~~~~~ 283 (460) T TIGR00414 204 LERALINFMLDLLREKNGYSELYPPYLVNEELLDGTGFNPQLPKFEEDLFKLEDTDDEKLYLIPTAEVPLTNLHRDEILD 283 (460) T ss_pred HHHHHHHHHHHHHHHHCCCCEECCCHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCEEEEEECCHHHHHHHHHHHHCC T ss_conf 99999999998644322640101403542344310245655653023443212677750465201000122222000102 Q ss_pred H--H-H-HHHHHHHHHHCCC-CC---CC---CCCCCEEEECEEECCCCHHHHHHHHHHHHHHH Q ss_conf 4--4-6-8899988642456-77---75---44843002000115776578777557888776 Q gi|254781066|r 92 A--G-E-EKIFCFAHAWRNG-EQ---GC---LHQPEFTMLEWYRAHESYEQLMKDCMNIIRCA 143 (355) Q Consensus 92 ~--G-~-~rvyqig~~FRaE-~~---~~---rHlpEFtmLE~e~af~d~~dlm~~~E~li~~~ 143 (355) . + + -++--.++|||.| ++ ++ -..-+|..+|.. .+..-++.....|.++... T Consensus 284 ~~~~~lp~~~~~~~~cfr~eag~~g~~~~g~~r~h~f~k~e~~-~~~~p~~~~~~~~~~~~~~ 345 (460) T TIGR00414 284 LPSEELPIKYTGYSPCFRSEAGSYGKDTKGLIRVHQFNKVELV-KFCKPEESWEELEELLSDA 345 (460) T ss_pred CCCCCCCEEHCCCCHHHHHHCCCCCCCCHHHHHHHHCCCEEEE-EEECCHHHHHHHHHHHHHH T ss_conf 6521034000002202333213455410001211100310245-6635401489999998789 No 126 >cd00384 ALAD_PBGS Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. They either contain a cysteine-rich zinc binding site (consensus DXCXCX(Y/F)X3G(H/Q)CG) or an aspartate-rich magnesium binding site (consensus DXALDX(Y/F)X3G(H/Q)DG). The cyste Probab=33.75 E-value=24 Score=15.64 Aligned_cols=11 Identities=18% Similarity=0.326 Sum_probs=5.0 Q ss_pred HHHHHHHHHHH Q ss_conf 98987446889 Q gi|254781066|r 87 KKLLAAGEEKI 97 (355) Q Consensus 87 K~ll~~G~~rv 97 (355) +.++..|...| T Consensus 58 ~~~~~lGI~av 68 (314) T cd00384 58 EELADLGIRAV 68 (314) T ss_pred HHHHHCCCCEE T ss_conf 99998799889 No 127 >TIGR01226 phe_am_lyase phenylalanine ammonia-lyase; InterPro: IPR005922 The ubiquitous higher plant enzyme phenylalanine ammonia-lyase (PAL; 4.3.1.5 from EC) is a key biosynthetic catalyst in phenylpropanoid assembly. PAL catalyses the non-oxidative deamination of L-phenylalanine to trans-cinnamic acid. PAL contains a catalytic Ala-Ser-Gly triad that is post-translationally cyclised. PAL is structurally similar to the mechanistically related histidine ammonia lyase (HAL; 4.3.1.3 from EC), with PAL having an additional approximately 160 residues extending from the common fold . Catalysis in PAL may be governed by the dipole moments of seven alpha helices associated with the PAL active site. The cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) resides atop the positive poles of three helices, for increasing its electrophilicity. Plant and fungal PAL enzymes contain aa approximately 100-residue long C-terminal multi-helix domain, which might play a role in the rapid response of PAL in the regulation of phenylpropanoid biosynthesis by destabilising the enzyme . ; GO: 0016841 ammonia-lyase activity, 0006559 L-phenylalanine catabolic process, 0005737 cytoplasm. Probab=33.18 E-value=14 Score=17.08 Aligned_cols=14 Identities=36% Similarity=0.655 Sum_probs=8.4 Q ss_pred CCCCCC-CCCCHHHH Q ss_conf 783200-00285899 Q gi|254781066|r 72 IRKPLY-LQTSPEFS 85 (355) Q Consensus 72 ~~~~~y-L~~SPql~ 85 (355) ..|+.| ||+|||.- T Consensus 340 ~kQDRY~LRtSPQwL 354 (714) T TIGR01226 340 PKQDRYALRTSPQWL 354 (714) T ss_pred CCCCCCCCCCCCCCC T ss_conf 675644235775212 No 128 >COG4302 EutC Ethanolamine ammonia-lyase, small subunit [Amino acid transport and metabolism] Probab=32.24 E-value=36 Score=14.58 Aligned_cols=13 Identities=15% Similarity=0.217 Sum_probs=5.9 Q ss_pred HHHHHHHHHHHCC Q ss_conf 9999999999879 Q gi|254781066|r 28 IQSSLREYFVENQ 40 (355) Q Consensus 28 i~~~iR~ff~~~g 40 (355) +-.-||.-+.+-+ T Consensus 6 ~~eii~~v~~~m~ 18 (294) T COG4302 6 IEEIVRSVMASMG 18 (294) T ss_pred HHHHHHHHHHHHC T ss_conf 9999999999954 No 129 >pfam00490 ALAD Delta-aminolevulinic acid dehydratase. Probab=30.61 E-value=31 Score=14.92 Aligned_cols=10 Identities=30% Similarity=0.428 Sum_probs=4.3 Q ss_pred HHHHHHHHHC Q ss_conf 9999999987 Q gi|254781066|r 30 SSLREYFVEN 39 (355) Q Consensus 30 ~~iR~ff~~~ 39 (355) ..+|+...++ T Consensus 13 ~~iR~lv~Et 22 (322) T pfam00490 13 PALRRLVRET 22 (322) T ss_pred HHHHHHHHCC T ss_conf 7899998527 No 130 >KOG1637 consensus Probab=29.91 E-value=39 Score=14.34 Aligned_cols=120 Identities=16% Similarity=0.161 Sum_probs=58.7 Q ss_pred HHHHHHHHHHHHHHHHCCCEEEECCCEECC----CCCCC--CC-CCEEEECCCCCCCCCCCC-----C--CCCHHHHHHH Q ss_conf 999999999999999879889847821056----89854--45-412410247886783200-----0--0285899998 Q gi|254781066|r 23 LKRNMIQSSLREYFVENQFIEIDSMSLQYS----PGNET--HI-RAFSTELIIQDHIRKPLY-----L--QTSPEFSCKK 88 (355) Q Consensus 23 ~~Rs~i~~~iR~ff~~~gF~EV~TPiL~~~----~~g~~--~~-~~f~t~~~~~~~~~~~~y-----L--~~SPql~lK~ 88 (355) ++=.+++..||.-...+||.||-||-+-.. .+|-- |. +-|.++.....+.-+|+- | ..-+--| +. T Consensus 193 ~iyN~Lv~fir~ey~~rGf~EVitPniy~~~LWe~SGHwqnY~enmF~~e~eke~~~LKPMNCPgHcLmf~~r~rS~-re 271 (560) T KOG1637 193 RIYNTLVDFIRAEYRKRGFTEVITPNIYNKKLWETSGHWQNYSENMFKFEVEKEEFALKPMNCPGHCLMFAHRDRSY-RE 271 (560) T ss_pred HHHHHHHHHHHHHHHHCCCCEECCCCHHHHHHHHHCCCHHHHHHHCEEEEECHHHHCCCCCCCCCCCCCCCCCCCCH-HH T ss_conf 27889999999998753874322722121566653252555443101231010332258668975301336677427-44 Q ss_pred HHHHHHHHHHHHHHHHCCCCCC----CCCCCCEEEECEEECCCCHHH---HHHHHHHHHHHHHHHHC Q ss_conf 9874468899988642456777----544843002000115776578---77755788877666418 Q gi|254781066|r 89 LLAAGEEKIFCFAHAWRNGEQG----CLHQPEFTMLEWYRAHESYEQ---LMKDCMNIIRCAAEVAN 148 (355) Q Consensus 89 ll~~G~~rvyqig~~FRaE~~~----~rHlpEFtmLE~e~af~d~~d---lm~~~E~li~~~~~~~~ 148 (355) |= =|.=.+|..-|||-|+ -.|+-+|.|=|.-. |.+.++ -++-+-++++++...++ T Consensus 272 LP----lR~aDFg~LHRnE~SGaLsGLTRvRrFqQDDaHI-FCt~~Qi~~Eik~~l~fl~~vY~~fg 333 (560) T KOG1637 272 LP----LRFADFGVLHRNEASGALSGLTRVRRFQQDDAHI-FCTPDQVKEEIKGCLDFLDYVYGVFG 333 (560) T ss_pred CC----CCCCCCCEEEECCCCCCCCCCCEEEEECCCCCEE-EECCCCHHHHHHHHHHHHHHHHHHCC T ss_conf 78----4226752253054564232210110110157158-85576379999879999999986125 No 131 >TIGR02400 trehalose_OtsA alpha,alpha-trehalose-phosphate synthase [UDP-forming]; InterPro: IPR012766 This enzyme catalyzes the key, penultimate step in biosynthesis of trehalose, a compatible solute made as an osmoprotectant in some species in all three domains of life. The gene symbol OtsA stands for osmotically regulated trehalose synthesis A. Trehalose helps protect against both osmotic and thermal stresses, and is made from two glucose subunits. This entry excludes glucosylglycerol-phosphate synthase, an enzyme of an analogous osmoprotectant system in many cyanobacterial strains. This entry does not identify archaeal examples, as they are more divergent than glucosylglycerol-phosphate synthase. Sequences that score in the gray zone between the trusted and noise cut offs include a number of yeast multidomain proteins in which the N-terminal domain may be functionally equivalent to this family. The gray zone also includes the OtsA of Cornyebacterium glutamicum (and related species), shown to be responsible for synthesis of only trace amounts of trehalose while the majority is synthesized by the TreYZ pathway; the significance of OtsA in this species is unclear (see ).; GO: 0003825 alphaalpha-trehalose-phosphate synthase (UDP-forming) activity, 0005992 trehalose biosynthetic process. Probab=29.38 E-value=40 Score=14.29 Aligned_cols=23 Identities=0% Similarity=0.004 Sum_probs=18.7 Q ss_pred CEEEECEEECCCCHHHHHHHHHH Q ss_conf 30020001157765787775578 Q gi|254781066|r 116 EFTMLEWYRAHESYEQLMKDCMN 138 (355) Q Consensus 116 EFtmLE~e~af~d~~dlm~~~E~ 138 (355) =.+.++.|=-++|-+...+.+.+ T Consensus 239 R~~~v~aFPIGID~~~f~~~a~~ 261 (476) T TIGR02400 239 RTVRVGAFPIGIDVDRFAEQAKK 261 (476) T ss_pred CEEEEEEEEECCCHHHHHHHHHC T ss_conf 36999887420077999987314 No 132 >TIGR02764 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB; InterPro: IPR014132 This entry describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reduced sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterised polysaccharide deacetylase; the exact function this protein family is unknown.. Probab=28.74 E-value=13 Score=17.10 Aligned_cols=10 Identities=10% Similarity=0.056 Sum_probs=4.0 Q ss_pred EEECCEECCC Q ss_conf 2236712256 Q gi|254781066|r 264 LYACNIELCN 273 (355) Q Consensus 264 l~i~G~El~n 273 (355) ++=+|-||+| T Consensus 58 I~~~GHEIGs 67 (198) T TIGR02764 58 IVKDGHEIGS 67 (198) T ss_pred HHHCCCCCCC T ss_conf 9844843033 No 133 >cd03557 L-arabinose_isomerase L-Arabinose isomerase (AI) catalyzes the isomerization of L-arabinose to L-ribulose, the first reaction in its conversion into D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway, which allows L-arabinose to be used as a carbon source. AI can also convert D-galactose to D-tagatose at elevated temperatures in the presence of divalent metal ions. D-tagatose, rarely found in nature, is of commercial interest as a low-calorie sugar substitute. Probab=28.73 E-value=41 Score=14.22 Aligned_cols=16 Identities=19% Similarity=0.412 Sum_probs=11.1 Q ss_pred CCCCEEEECCEECCCC Q ss_conf 3022022367122564 Q gi|254781066|r 259 TKRFELYACNIELCNA 274 (355) Q Consensus 259 a~rfdl~i~G~El~ng 274 (355) .+||-|+++-.|.+.. T Consensus 393 G~rFRLivneve~v~p 408 (484) T cd03557 393 GNRFRLVVNEVDAVEP 408 (484) T ss_pred CCCEEEEEEEEEEECC T ss_conf 8847999975777468 No 134 >pfam09743 DUF2042 Uncharacterized conserved protein (DUF2042). This entry is the conserved N-terminal 300 residues of a group of proteins found from protozoa to Humans. The function is unknown. Probab=28.54 E-value=29 Score=15.11 Aligned_cols=17 Identities=29% Similarity=0.407 Sum_probs=8.3 Q ss_pred HHHH-HHHHHHHHHHHHH Q ss_conf 8987-4468899988642 Q gi|254781066|r 88 KLLA-AGEEKIFCFAHAW 104 (355) Q Consensus 88 ~ll~-~G~~rvyqig~~F 104 (355) +|.+ +|-=.+.++++.- T Consensus 63 El~~~gGRinl~dL~~~L 80 (272) T pfam09743 63 ELLANGGRINVVDLAKIL 80 (272) T ss_pred HHHHCCCCEEHHHHHHHC T ss_conf 999829955699988761 No 135 >TIGR01184 ntrCD nitrate ABC transporter, ATP-binding proteins C and D; InterPro: IPR005890 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This model describes the ATP binding subunits of nitrate transport in bacteria and archaea. This protein belongs to the ATP-binding cassette (ABC) superfamily. It is thought that the two subunits encoded by ntrC and ntrD form the binding surface for interaction with ATP. This model is restricted in identifying ATP binding subunit associated with the nitrate transport. Nitrate assimilation is aided by other proteins derived from the operon which among others include products of ntrA - a regulatory protein; ntrB - a hydropbobic transmembrane permease and narB - a reductase. ; GO: 0015112 nitrate transmembrane transporter activity, 0015706 nitrate transport, 0016020 membrane. Probab=28.51 E-value=17 Score=16.48 Aligned_cols=38 Identities=37% Similarity=0.656 Sum_probs=26.2 Q ss_pred CCHHHHHHHHHHCCCCCCCEEECCHHHHHHHHHC-CCCHHHHCCCCCCCCCCC Q ss_conf 3010189999861889632453159999899815-597131115856487433 Q gi|254781066|r 302 TYPIDEDFLACLTEMPQSSGIAMGFDRLVMLVTG-ANNINEVIWTPFSQSNQE 353 (355) Q Consensus 302 ~~~~D~~fl~al~G~PPhgG~glGidRLvm~l~g-~~~Irdvi~FP~~r~~~~ 353 (355) ++-+||.++=| ||+||+-.| ..+|=+++--|+.||++- T Consensus 172 THDvDEAllLs--------------DR~VMlTnGP~a~IG~il~v~~~RPR~R 210 (230) T TIGR01184 172 THDVDEALLLS--------------DRVVMLTNGPAAKIGQILEVPFPRPRDR 210 (230) T ss_pred ECCHHHHHHHH--------------CCEEEEECCCCCCCCCEEEECCCCCHHH T ss_conf 52445788873--------------5102430777422575776278886007 No 136 >TIGR01733 AA-adenyl-dom amino acid adenylation domain; InterPro: IPR010071 This entry represents a domain responsible for the specific recognition of amino acids and activation as adenylyl amino acids. The reaction catalysed is aa + ATP to aa-AMP + PPi. These domains are usually found as components of multi-domain non-ribosomal peptide synthetases and are usually called 'A-domains' in that context (for a review, see ). A-domains are almost invariably followed by 'T-domains' (thiolation domains, IPR006163 from INTERPRO) to which the amino acid adenylate is transferred as a thiol-ester to a bound pantetheine cofactor with the release of AMP (these are also called peptide carrier proteins, or PCPs. When the A-domain does not represent the first module (corresponding to the first amino acid in the product molecule) it is usually preceded by a 'C-domain' (condensation domain, IPR001242 from INTERPRO) which catalyses the ligation of two amino acid thiol-esters from neighbouring modules. This domain is a subset of the AMP-binding domain, which also hits substrate--CoA ligases and luciferases.; GO: 0016874 ligase activity. Probab=27.96 E-value=33 Score=14.78 Aligned_cols=26 Identities=27% Similarity=0.309 Sum_probs=21.9 Q ss_pred EEEECCEECCCCCHHCCCHHHHHHHHHH Q ss_conf 0223671225640210699999999999 Q gi|254781066|r 263 ELYACNIELCNACDELLDPIEQRHRFEK 290 (355) Q Consensus 263 dl~i~G~El~ng~~El~d~~~q~~rf~~ 290 (355) ||||.|.=+|-|| +|+|+.=.+||-. T Consensus 357 ELyi~G~gvArGY--lnrp~lTaerFv~ 382 (452) T TIGR01733 357 ELYIGGPGVARGY--LNRPELTAERFVP 382 (452) T ss_pred EEEECCCCEECCC--CCCHHHHHHHCCC T ss_conf 2786165010245--7875331654157 No 137 >PRK05776 DNA topoisomerase III; Provisional Probab=25.73 E-value=47 Score=13.89 Aligned_cols=23 Identities=17% Similarity=0.231 Sum_probs=10.9 Q ss_pred HHCCCHHHHHHHHHHHHHHHHCCC Q ss_conf 210699999999999999997288 Q gi|254781066|r 276 DELLDPIEQRHRFEKEMQEKKKIY 299 (355) Q Consensus 276 ~El~d~~~q~~rf~~q~~~k~~~~ 299 (355) .++.+|+. ...+|+++..-+.|. T Consensus 538 ~~l~~p~~-Ta~~E~~L~~I~~Gk 560 (675) T PRK05776 538 PDLTSVEL-TRRFEEKLEKIRSGK 560 (675) T ss_pred HHHCCHHH-HHHHHHHHHHHHCCC T ss_conf 65259148-999999989998799 No 138 >TIGR02676 cas_provis_2 CRISPR-associated large protein (provisional); InterPro: IPR013492 Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognizable features . This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins.. Probab=25.43 E-value=47 Score=13.86 Aligned_cols=93 Identities=16% Similarity=0.143 Sum_probs=48.7 Q ss_pred HHHHHHHHHHHCCCEEEECCC----EECCCCC--CCCCCCEEEECCCCCCCCCCCCCCCCH-------HHHHHHHHHHHH Q ss_conf 999999999987988984782----1056898--544541241024788678320000285-------899998987446 Q gi|254781066|r 28 IQSSLREYFVENQFIEIDSMS----LQYSPGN--ETHIRAFSTELIIQDHIRKPLYLQTSP-------EFSCKKLLAAGE 94 (355) Q Consensus 28 i~~~iR~ff~~~gF~EV~TPi----L~~~~~g--~~~~~~f~t~~~~~~~~~~~~yL~~SP-------ql~lK~ll~~G~ 94 (355) --++|+-+|++|||+.|++-. |.-.|+- +.-.+-|. ++...+ +.+-||.-+. |.| -.||-.-+ T Consensus 87 ~~~ai~~lfN~RGyty~~~~ldteylnivPeqvkailmdifd-dynGed--dldsylklateqeskiseiy-nklmqkil 162 (1104) T TIGR02676 87 EEQAISFLFNKRGYTYVDDDLDTEYLNIVPEQVKAILMDIFD-DYNGED--DLDSYLKLATEQESKISEIY-NKLMQKIL 162 (1104) T ss_pred HHHHHHHHHHCCCCCEECCCCCHHHHHHCHHHHHHHHHHHHH-CCCCCC--HHHHHHHHHHHHHHHHHHHH-HHHHHHHH T ss_conf 037999987178752332775514665036889999988764-037741--16788876532124689999-99999999 Q ss_pred H-HHHHHHHHHCCCCCCCCCCCCEEEECEEE Q ss_conf 8-89998864245677754484300200011 Q gi|254781066|r 95 E-KIFCFAHAWRNGEQGCLHQPEFTMLEWYR 124 (355) Q Consensus 95 ~-rvyqig~~FRaE~~~~rHlpEFtmLE~e~ 124 (355) + +.=.++-=......++.-|-||+.-|.+. T Consensus 163 efklrklCte~kkD~~~~~tLKE~ls~e~e~ 193 (1104) T TIGR02676 163 EFKLRKLCTEIKKDKVETDTLKELLSEELEL 193 (1104) T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH T ss_conf 8888886101220102366775420367764 No 139 >COG1304 idi Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism] Probab=21.75 E-value=52 Score=13.61 Aligned_cols=20 Identities=40% Similarity=0.714 Sum_probs=17.0 Q ss_pred HHHHHHHCCCCHHHHCCCCC Q ss_conf 99899815597131115856 Q gi|254781066|r 328 RLVMLVTGANNINEVIWTPF 347 (355) Q Consensus 328 RLvm~l~g~~~Irdvi~FP~ 347 (355) +..|.|||+.||.|+-..|. T Consensus 329 ~~~M~L~G~~~i~el~~~~l 348 (360) T COG1304 329 KIAMALTGAKNIEELKRVPL 348 (360) T ss_pred HHHHHHCCCCCHHHHCCCCE T ss_conf 99997428881999655736 No 140 >TIGR02708 L_lactate_ox L-lactate oxidase; InterPro: IPR014080 Members of this entry oxidize L-lactate to pyruvate, reducing molecular oxygen to hydrogen peroxide. The enzyme is known in Aerococcus viridans, Streptococcus iniae, and some strains of Streptococcus pyogenes where it appears to contribute to virulence.. Probab=21.11 E-value=46 Score=13.93 Aligned_cols=21 Identities=29% Similarity=0.382 Sum_probs=17.2 Q ss_pred HHHHHHHCCCCHHHHCCCCCC Q ss_conf 998998155971311158564 Q gi|254781066|r 328 RLVMLVTGANNINEVIWTPFS 348 (355) Q Consensus 328 RLvm~l~g~~~Irdvi~FP~~ 348 (355) ..||-|+|++||.||=.|-+- T Consensus 340 ~~VMQL~G~Q~i~D~K~~~L~ 360 (368) T TIGR02708 340 KRVMQLTGTQTIEDVKGLDLR 360 (368) T ss_pred HHHHHHCCCCCHHHHHCCCCC T ss_conf 777641387515653214133 No 141 >TIGR02653 Lon_rel_chp conserved hypothetical protein; InterPro: IPR013473 This entry describes a protein family of unknown function, about 690 residues in length, in which some members show C-terminal sequence similarity to IPR008269 from INTERPRO, which is the Lon protease C-terminal proteolytic domain, from MEROPS family S16. However, the annotated catalytic sites of Escherichia coli Lon protease are not conserved in members of this family. Members have a motif GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif GxxGxGK[ST].. Probab=21.08 E-value=50 Score=13.73 Aligned_cols=17 Identities=29% Similarity=0.481 Sum_probs=8.4 Q ss_pred CCCCCCCCEEEECCEEC Q ss_conf 83633022022367122 Q gi|254781066|r 255 DPRFTKRFELYACNIEL 271 (355) Q Consensus 255 ~~~va~rfdl~i~G~El 271 (355) |.-+-+|+--|+.|+|| T Consensus 344 DtAFfDR~H~YiPGWEI 360 (677) T TIGR02653 344 DTAFFDRIHYYIPGWEI 360 (677) T ss_pred HHHHHHHHHCCCCCCCC T ss_conf 02567556305888768 No 142 >pfam12109 CXCR4_N CXCR4 Chemokine receptor N terminal. CXCR4 and its ligand stromal cell-derived factor-1 (a.k.a. CXCL12) are essential for proper fetal development. CXCR4 is also the major coreceptor for T-tropic strains of human immunodeficiency virus 1 (HIV-1), and SDF-1 inhibits HIV-1 infection. Additionally, SDF-1 and CXCR4 mediate cancer cell migration and metastasis. The N terminal domain of most chemokine receptors is the ligand binding domain and so the N terminal domain of CXCR4 is the binding site for SDF-1. Probab=20.96 E-value=31 Score=14.99 Aligned_cols=10 Identities=10% Similarity=0.298 Sum_probs=6.3 Q ss_pred HHHHCCCCCC Q ss_conf 8642456777 Q gi|254781066|r 101 AHAWRNGEQG 110 (355) Q Consensus 101 g~~FRaE~~~ 110 (355) -||||.|+.+ T Consensus 21 EPCf~~eNa~ 30 (33) T pfam12109 21 EPCFRHENAD 30 (33) T ss_pred CCCCCCCCCC T ss_conf 7410113454 No 143 >COG0113 HemB Delta-aminolevulinic acid dehydratase [Coenzyme metabolism] Probab=20.43 E-value=60 Score=13.26 Aligned_cols=15 Identities=7% Similarity=0.224 Sum_probs=5.8 Q ss_pred CHHHHHHHHHHHHHH Q ss_conf 657877755788877 Q gi|254781066|r 128 SYEQLMKDCMNIIRC 142 (355) Q Consensus 128 d~~dlm~~~E~li~~ 142 (355) |-+.+..-+-..||. T Consensus 98 ~~~givqravr~ik~ 112 (330) T COG0113 98 DPDGIVQRAVRAIKE 112 (330) T ss_pred CCCCHHHHHHHHHHH T ss_conf 877809999999998 No 144 >COG3919 Predicted ATP-grasp enzyme [General function prediction only] Probab=20.07 E-value=61 Score=13.22 Aligned_cols=40 Identities=18% Similarity=0.223 Sum_probs=17.4 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECEEECCCCHHHHHHHHHH Q ss_conf 98744688999886424567775448430020001157765787775578 Q gi|254781066|r 89 LLAAGEEKIFCFAHAWRNGEQGCLHQPEFTMLEWYRAHESYEQLMKDCMN 138 (355) Q Consensus 89 ll~~G~~rvyqig~~FRaE~~~~rHlpEFtmLE~e~af~d~~dlm~~~E~ 138 (355) ||+++-+-.-++.-..|.| +++| ++....++..+--++|+ T Consensus 76 LLva~GDgev~lvSq~ree------LSa~----f~v~lp~w~~l~wlceK 115 (415) T COG3919 76 LLVACGDGEVLLVSQYREE------LSAF----FEVPLPDWALLRWLCEK 115 (415) T ss_pred EEEECCCCEEEEHHHHHHH------HHHH----HCCCCCCHHHHHHHHHC T ss_conf 9996388306625756999------9887----65778738999998608 Done!