Query gi|254780979|ref|YP_003065392.1| aspartyl/glutamyl-tRNA amidotransferase subunit B [Candidatus Liberibacter asiaticus str. psy62] Match_columns 500 No_of_seqs 209 out of 1752 Neff 6.3 Searched_HMMs 39220 Date Mon May 30 02:51:55 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780979.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK05477 gatB aspartyl/glutamy 100.0 0 0 1383.7 47.7 474 19-497 2-478 (479) 2 COG0064 GatB Asp-tRNAAsn/Glu-t 100.0 0 0 1327.4 46.7 475 19-498 3-482 (483) 3 PRK04028 glutamyl-tRNA(Gln) am 100.0 0 0 1152.6 42.3 447 19-498 2-628 (631) 4 KOG2438 consensus 100.0 0 0 1148.9 35.6 480 16-498 17-505 (505) 5 pfam02934 GatB_N GatB/GatE cat 100.0 0 0 961.2 26.7 286 23-314 1-287 (287) 6 TIGR00133 gatB glutamyl-tRNA(G 100.0 0 0 823.7 34.4 477 20-497 2-523 (523) 7 COG2511 GatE Archaeal Glu-tRNA 100.0 0 0 712.2 38.1 444 21-497 5-626 (631) 8 TIGR00134 gatE_arch glutamyl-t 100.0 0 0 423.0 25.3 446 21-498 3-629 (631) 9 pfam02637 GatB_Yqey GatB domai 100.0 1.2E-34 3.1E-39 275.6 16.6 146 351-496 1-148 (148) 10 smart00845 GatB_Yqey GatB doma 100.0 4.1E-34 1E-38 271.7 16.0 145 352-496 1-147 (147) 11 pfam01162 consensus 99.8 1.6E-21 4E-26 179.0 5.6 69 281-349 1-69 (69) 12 pfam09424 YqeY Yqey-like prote 97.8 0.00025 6.4E-09 52.3 9.4 113 365-496 22-143 (143) 13 pfam04558 tRNA_synt_1c_R1 Glut 97.3 0.027 6.8E-07 37.4 13.7 152 323-486 4-164 (164) 14 KOG1148 consensus 96.8 0.066 1.7E-06 34.5 14.1 19 188-206 294-312 (764) 15 COG1610 Uncharacterized conser 96.0 0.024 6.1E-07 37.8 6.3 97 387-497 43-148 (148) 16 TIGR00838 argH argininosuccina 88.1 1.3 3.3E-05 25.0 5.1 119 359-481 158-311 (469) 17 COG3937 Uncharacterized conser 75.4 6.8 0.00017 19.7 5.6 64 386-449 18-94 (108) 18 cd07363 45_DOPA_Dioxygenase Th 71.5 4.5 0.00012 21.0 3.2 43 256-308 85-129 (253) 19 TIGR02407 ectoine_ectB diamino 69.0 9.3 0.00024 18.7 4.7 68 408-493 300-368 (413) 20 TIGR01398 FlhA flagellar biosy 68.1 7.1 0.00018 19.5 3.6 59 363-421 472-531 (713) 21 PRK10628 hypothetical protein; 65.7 4.1 0.00011 21.3 2.0 41 258-308 77-118 (246) 22 pfam06576 DUF1133 Protein of u 65.3 11 0.00028 18.1 6.6 61 399-459 48-120 (176) 23 TIGR02653 Lon_rel_chp conserve 64.7 7.4 0.00019 19.4 3.1 123 294-434 333-458 (677) 24 pfam12570 DUF3750 Protein of u 64.0 5.1 0.00013 20.6 2.2 29 289-323 90-118 (129) 25 PRK00116 ruvA Holliday junctio 63.9 12 0.0003 18.0 10.7 105 324-428 70-187 (198) 26 COG3384 Aromatic ring-opening 63.5 8.2 0.00021 19.1 3.2 100 188-308 26-140 (268) 27 PRK11913 phhA phenylalanine 4- 63.4 5.8 0.00015 20.2 2.4 45 279-335 104-148 (272) 28 PHA01082 putative transcriptio 62.7 3 7.7E-05 22.3 0.8 56 138-201 78-133 (133) 29 cd03346 eu_TrpOH Eukaryotic tr 61.8 11 0.00029 18.1 3.6 111 185-335 80-190 (287) 30 cd03348 pro_PheOH Prokaryotic 59.7 7.9 0.0002 19.2 2.5 45 279-335 92-136 (228) 31 TIGR01011 rpsB_bact ribosomal 58.6 5.2 0.00013 20.5 1.4 122 258-416 5-136 (227) 32 KOG2305 consensus 58.5 11 0.00028 18.2 3.1 37 186-224 35-71 (313) 33 pfam11212 DUF2999 Protein of u 50.0 19 0.00049 16.4 5.3 18 469-492 47-64 (82) 34 pfam11867 DUF3387 Domain of un 49.8 19 0.00049 16.3 6.3 18 391-408 198-215 (333) 35 cd00361 arom_aa_hydroxylase Bi 49.6 14 0.00036 17.4 2.4 45 279-335 86-130 (221) 36 cd04775 HTH_Cfa-like Helix-Tur 48.0 5.4 0.00014 20.4 0.1 59 269-350 15-73 (102) 37 COG4901 Ribosomal protein S25 47.6 21 0.00053 16.1 3.2 42 304-345 40-81 (107) 38 pfam04262 Glu_cys_ligase Gluta 46.7 16 0.0004 17.0 2.3 50 166-220 56-105 (377) 39 pfam06519 TolA TolA C-terminal 43.9 23 0.00059 15.8 2.8 48 186-235 9-56 (96) 40 COG1490 Dtd D-Tyr-tRNAtyr deac 43.6 24 0.0006 15.7 3.7 47 180-229 89-138 (145) 41 pfam05606 DUF777 Borrelia burg 43.1 9.2 0.00023 18.7 0.7 23 89-112 88-113 (180) 42 KOG1795 consensus 41.5 25 0.00065 15.5 4.8 10 255-264 783-792 (2321) 43 COG0105 Ndk Nucleoside diphosp 40.5 13 0.00034 17.6 1.1 77 139-226 32-112 (135) 44 KOG2181 consensus 40.2 16 0.0004 17.0 1.5 128 194-342 119-255 (415) 45 cd03345 eu_TyrOH Eukaryotic ty 39.9 21 0.00053 16.1 2.1 46 279-336 145-190 (298) 46 PRK02107 glutamate--cysteine l 39.5 26 0.00066 15.4 2.5 33 393-427 430-462 (523) 47 TIGR01083 nth endonuclease III 38.7 28 0.00071 15.2 6.7 24 428-451 142-165 (192) 48 KOG2243 consensus 38.5 24 0.00062 15.6 2.2 27 235-261 1824-1855(5019) 49 PRK09849 putative oxidoreducta 38.3 12 0.00032 17.7 0.7 14 67-80 210-224 (702) 50 PRK13979 DNA topoisomerase IV 37.2 29 0.00075 15.0 7.5 37 307-345 402-438 (959) 51 cd04789 HTH_Cfa Helix-Turn-Hel 37.1 9.9 0.00025 18.5 0.1 55 269-346 15-69 (102) 52 cd04770 HTH_HMRTR Helix-Turn-H 37.0 15 0.00038 17.1 1.0 50 272-345 18-68 (123) 53 PRK09514 zntR zinc-responsive 36.7 14 0.00035 17.4 0.7 54 269-345 15-69 (140) 54 CHL00139 rpl18 ribosomal prote 35.4 31 0.00079 14.8 2.9 62 29-103 26-92 (109) 55 TIGR01059 gyrB DNA gyrase, B s 35.3 26 0.00067 15.3 2.0 29 439-467 729-761 (818) 56 cd04766 HTH_HspR Helix-Turn-He 35.3 10 0.00027 18.3 -0.0 53 271-346 18-70 (91) 57 TIGR03575 selen_PSTK_euk L-ser 35.1 29 0.00073 15.1 2.2 14 468-481 262-275 (340) 58 PRK05560 DNA gyrase subunit A; 35.1 32 0.0008 14.8 7.3 76 304-381 387-480 (822) 59 COG2326 Uncharacterized conser 35.0 32 0.00081 14.8 3.2 30 255-284 122-151 (270) 60 TIGR00676 fadh2 5,10-methylene 34.9 24 0.00062 15.6 1.8 18 200-221 96-113 (302) 61 pfam11181 YflT Heat induced st 34.9 32 0.00081 14.7 5.0 45 300-345 47-92 (103) 62 cd01110 HTH_SoxR Helix-Turn-He 34.4 9.7 0.00025 18.5 -0.3 56 267-345 13-68 (139) 63 COG4050 Uncharacterized protei 34.3 32 0.00083 14.7 3.7 38 166-206 112-149 (152) 64 pfam11950 DUF3467 Protein of u 34.2 32 0.00083 14.7 4.3 58 145-203 15-80 (90) 65 cd03347 eu_PheOH Eukaryotic ph 32.8 33 0.00084 14.6 2.2 109 187-335 82-190 (306) 66 KOG4168 consensus 32.5 34 0.00088 14.5 4.4 80 369-452 50-129 (149) 67 COG5418 Predicted secreted pro 32.4 18 0.00045 16.6 0.8 16 102-117 38-53 (164) 68 cd05298 GH4_GlvA_pagL_like Gly 32.3 34 0.00086 14.6 2.2 86 369-462 351-437 (437) 69 COG3495 Uncharacterized protei 32.0 17 0.00043 16.8 0.6 29 100-128 113-141 (166) 70 TIGR00034 aroFGH phospho-2-deh 31.8 35 0.0009 14.4 3.2 72 178-250 54-155 (348) 71 cd01199 INT_Tn1545_C Tn1545-re 31.6 36 0.00091 14.4 2.3 40 207-246 46-85 (205) 72 PRK11814 cysteine desulfurase 31.0 35 0.00088 14.5 2.0 38 317-355 425-462 (484) 73 PRK06740 histidinol-phosphatas 30.8 34 0.00086 14.5 2.0 47 308-357 155-208 (338) 74 TIGR02614 ftsW cell division p 30.3 15 0.00038 17.2 0.1 32 99-130 214-252 (370) 75 KOG2050 consensus 30.1 38 0.00096 14.2 11.7 13 292-304 275-287 (652) 76 CHL00085 ycf24 putative ABC tr 30.1 23 0.00058 15.8 1.0 36 317-357 426-461 (485) 77 KOG0823 consensus 30.0 12 0.0003 17.9 -0.5 46 19-64 45-94 (230) 78 KOG3591 consensus 29.6 38 0.00098 14.1 3.4 24 105-128 123-146 (173) 79 PRK02471 bifunctional glutamat 29.3 39 0.00099 14.1 2.3 41 363-407 349-389 (753) 80 pfam07028 DUF1319 Protein of u 28.9 33 0.00084 14.6 1.6 20 440-460 84-103 (119) 81 cd04767 HTH_HspR-like_MBC Heli 28.6 12 0.0003 17.9 -0.7 57 267-346 13-69 (120) 82 TIGR00954 3a01203 Peroxysomal 28.5 40 0.001 14.0 3.2 73 278-354 592-664 (788) 83 TIGR01204 bioW 6-carboxyhexano 28.4 40 0.001 14.0 2.4 49 141-207 38-86 (238) 84 KOG3666 consensus 28.4 40 0.001 14.0 6.2 46 295-341 790-835 (1141) 85 pfam00351 Biopterin_H Biopteri 28.3 40 0.001 14.0 2.0 111 185-335 80-190 (309) 86 KOG1261 consensus 27.5 41 0.0011 13.9 3.0 78 141-224 175-261 (552) 87 KOG2599 consensus 27.3 42 0.0011 13.9 2.1 108 140-305 30-137 (308) 88 pfam09043 Lys-AminoMut_A D-Lys 26.8 43 0.0011 13.8 8.4 52 401-462 414-465 (509) 89 PRK13335 superantigen-like pro 26.6 43 0.0011 13.8 2.2 70 256-336 239-308 (356) 90 cd04790 HTH_Cfa-like_unk Helix 26.5 18 0.00047 16.5 -0.0 56 270-347 16-71 (172) 91 PRK12559 transcriptional regul 26.5 43 0.0011 13.8 3.6 85 360-470 11-105 (131) 92 PRK05561 DNA topoisomerase IV 26.5 43 0.0011 13.8 6.7 34 307-345 396-429 (745) 93 TIGR00577 fpg formamidopyrimid 26.5 43 0.0011 13.8 2.0 57 366-433 184-243 (292) 94 pfam12224 Amidoligase_2 Putati 26.3 43 0.0011 13.7 5.0 69 166-251 65-135 (250) 95 TIGR01801 CM_A chorismate muta 26.3 22 0.00055 16.0 0.3 33 393-426 56-88 (104) 96 TIGR01846 type_I_sec_HlyB type 26.2 40 0.001 14.0 1.7 52 294-346 91-145 (703) 97 COG1978 Uncharacterized protei 26.1 27 0.00068 15.3 0.7 70 323-396 73-143 (152) 98 PRK06108 aspartate aminotransf 25.6 45 0.0011 13.6 2.2 42 231-275 78-119 (382) 99 smart00422 HTH_MERR helix_turn 25.4 22 0.00056 15.9 0.2 50 272-345 18-68 (70) 100 PRK13901 ruvA Holliday junctio 25.3 45 0.0012 13.6 10.8 115 324-452 69-192 (196) 101 cd01018 ZntC Metal binding pro 25.2 34 0.00087 14.5 1.2 47 387-438 199-245 (266) 102 PRK07531 bifunctional 3-hydrox 24.7 46 0.0012 13.5 1.8 29 173-206 144-172 (489) 103 PRK01966 ddl D-alanyl-alanine 24.4 47 0.0012 13.5 2.7 37 168-210 112-149 (344) 104 TIGR00707 argD acetylornithine 24.4 42 0.0011 13.8 1.5 282 146-477 12-349 (402) 105 KOG2164 consensus 24.1 36 0.00093 14.3 1.1 45 16-66 147-198 (513) 106 TIGR02698 CopY_TcrY copper tra 23.5 49 0.0012 13.4 2.3 41 408-449 74-116 (130) 107 cd02977 ArsC_family Arsenate R 23.4 49 0.0012 13.4 4.0 77 376-470 18-105 (105) 108 pfam11829 DUF3349 Protein of u 23.0 50 0.0013 13.3 6.4 84 370-470 5-90 (97) 109 cd04779 HTH_MerR-like_sg4 Heli 23.0 19 0.00047 16.5 -0.5 54 270-346 15-68 (134) 110 COG3608 Predicted deacylase [G 22.8 50 0.0013 13.3 5.2 55 168-223 198-255 (331) 111 PRK13344 spxA transcriptional 22.8 50 0.0013 13.3 1.8 91 360-470 11-105 (132) 112 PRK09261 phospho-2-dehydro-3-d 22.6 50 0.0013 13.3 3.3 26 178-203 56-82 (351) 113 TIGR02051 MerR Hg(II)-responsi 22.6 48 0.0012 13.4 1.5 62 261-345 5-67 (126) 114 TIGR01267 Phe4hydrox_mono phen 22.5 45 0.0012 13.6 1.4 62 280-353 93-154 (251) 115 COG2905 Predicted signal-trans 22.3 36 0.00092 14.3 0.8 48 141-190 160-207 (610) 116 cd04165 GTPBP1_like GTPBP1-lik 22.3 51 0.0013 13.2 4.3 40 169-208 135-174 (224) 117 pfam08777 RRM_3 RNA binding mo 22.0 52 0.0013 13.2 2.1 40 178-219 6-45 (102) 118 pfam02885 Glycos_trans_3N Glyc 21.9 52 0.0013 13.2 5.6 42 388-429 14-55 (66) 119 KOG1280 consensus 21.7 29 0.00074 15.0 0.2 56 263-327 247-302 (381) 120 PRK13752 putative transcriptio 21.7 50 0.0013 13.3 1.5 56 267-345 19-75 (144) 121 pfam10228 DUF2228 Uncharacteri 21.7 53 0.0013 13.1 6.1 21 279-300 150-170 (253) 122 TIGR00591 phr2 deoxyribodipyri 21.6 49 0.0013 13.3 1.4 31 142-181 90-121 (471) 123 pfam11202 DUF2983 Protein of u 21.6 38 0.00096 14.2 0.8 17 159-175 79-95 (353) 124 PRK13515 carboxylate-amine lig 21.6 53 0.0013 13.1 3.7 29 175-204 52-80 (381) 125 PRK08136 glycosyl transferase 21.5 53 0.0013 13.1 4.6 11 78-88 44-54 (316) 126 TIGR02333 2met_isocit_dHY 2-me 21.5 53 0.0014 13.1 1.8 90 189-287 250-350 (864) 127 KOG0979 consensus 21.4 53 0.0014 13.1 1.6 47 25-71 22-74 (1072) 128 cd04782 HTH_BltR Helix-Turn-He 21.3 53 0.0014 13.1 2.3 59 271-352 17-75 (97) 129 PRK01372 ddl D-alanine--D-alan 21.3 53 0.0014 13.1 2.5 13 198-210 103-115 (304) 130 PRK04182 cytidylate kinase; Pr 21.2 54 0.0014 13.1 4.7 72 321-405 100-173 (178) 131 pfam07830 PP2C_C Protein serin 20.9 54 0.0014 13.0 1.6 10 443-452 28-37 (81) 132 KOG1147 consensus 20.8 47 0.0012 13.5 1.2 28 289-318 370-397 (712) 133 TIGR02365 dha_L_ycgS dihydroxy 20.6 33 0.00084 14.6 0.4 99 308-420 2-109 (200) 134 PRK09071 hypothetical protein; 20.3 56 0.0014 12.9 6.6 69 168-248 128-206 (323) 135 KOG0479 consensus 20.0 47 0.0012 13.5 1.1 53 363-415 578-639 (818) 136 COG2160 AraA L-arabinose isome 20.0 57 0.0014 12.9 2.9 33 230-262 201-234 (497) No 1 >PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated Probab=100.00 E-value=0 Score=1383.66 Aligned_cols=474 Identities=58% Similarity=0.944 Sum_probs=462.5 Q ss_pred CCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCEECCCCEEECC Q ss_conf 47803389899978886898655588424689876520613026898887378999999999877829762442013113 Q gi|254780979|r 19 TGDWEVVIGIEVHAQLSVVSKLFSGASVNFGAEPNTQVSFFDAAMPGMLPILNGRCVQQAVMTGLGLNAHINKYSVFARK 98 (500) Q Consensus 19 ~~~~e~vIGLEiH~qL~t~tKlFc~c~~~~~~~pNt~v~~~~~g~PG~lP~lN~~av~~ai~~~~al~~~i~~~~~fdRK 98 (500) ..||++||||||||||+|+|||||+|+++|+++|||+|||||+|+|||||++|++||++|+++|+||||+|+++++|||| T Consensus 2 ~~~~~~viGlEiH~qL~t~tKlF~~~~~~~~~~pNt~v~~v~~~~PG~lP~lN~~av~~ai~~a~al~~~i~~~~~f~RK 81 (479) T PRK05477 2 MMNFEVVIGLEVHVQLNTKSKIFSGCSTEFGAEPNTNVCPVCLGLPGALPVLNKEAVEKAIKAGLALNCEIAKRSVFDRK 81 (479) T ss_pred CCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEECCC T ss_conf 87653168899987707996857899987899976663842006898877669999999999999839864633155023 Q ss_pred CEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEE Q ss_conf 21237678882014454420153389997067777741037984236665202310011567871488661578612576 Q gi|254780979|r 99 NYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRTIEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEI 178 (500) Q Consensus 99 ~YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~~~~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEI 178 (500) ||||||||||||||||+.|||.||+|++...++. .++|+|+||||||||||++|+..+++|||||||||+||||| T Consensus 82 ~YfYpDlp~gyQiTq~~~Pi~~~G~l~~~~~~g~-----~k~i~I~~i~lEeD~gk~~h~~~~~~~~vD~NRaG~PLiEI 156 (479) T PRK05477 82 NYFYPDLPKGYQISQYDEPIVENGYLEIEVEDGE-----EKRIGIERIHLEEDAGKSVHDGGAGYSLVDYNRAGVPLIEI 156 (479) T ss_pred CCCCCCCCCCCCCCCCCCCEECCCEEEEEECCCC-----EEEEEEEEEEECCCHHHHCCCCCCCCEEEECCCCCCCEEEE T ss_conf 4668989877521667556306618999807896-----45762278886001001024679982476224579733788 Q ss_pred EECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 30365277899999999999998642045676432201125754321376-66788622235402465999999999999 Q gi|254780979|r 179 VTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPG-EAWGTRCEVKNVNSIRFLGLAIEYEARRQ 257 (500) Q Consensus 179 VT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~-~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ 257 (500) ||+|||+||+||++|+++||+||||+|+|||+||+||||||||||||+.| ..|||||||||||||++|++||+||+.|| T Consensus 157 vT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~me~GslR~DvNVSi~~~g~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ 236 (479) T PRK05477 157 VSEPDMRSPEEAVAYLKKLRSILRYLGISDGNMEEGSLRCDANVSVRPKGQEEFGTRVEIKNLNSFRFVEKAIEYEIQRQ 236 (479) T ss_pred ECCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHH T ss_conf 54799899999999999999999861878666334512056624424788655563588627787889999999999999 Q ss_pred HHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCH Q ss_conf 99731398003443233755433665303566777783327787731269999999885302483689886432026889 Q gi|254780979|r 258 IAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISL 337 (500) Q Consensus 258 ~~ll~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~ 337 (500) +++|++|++|.||||+||+.+|+|++||+||+++||||||||||||+.|+++||++++.+|||||+++++||+++||||+ T Consensus 237 ~~ll~~G~~v~qETR~~d~~~g~T~~mR~Ke~a~DYRyfPEpDLppi~i~~e~i~~ik~~lPelP~~~~~rl~~~ygLs~ 316 (479) T PRK05477 237 IEILESGGEVVQETRLFDEDKGETRSMRSKEEAHDYRYFPEPDLPPLEISDEWIEEIRATLPELPDAKRARFVEEYGLSE 316 (479) T ss_pred HHHHHCCCCCCCCEEEECCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCH T ss_conf 99997599823321215378996754445777656440678887773589999999997489989999999998619999 Q ss_pred HHHHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHH Q ss_conf 998887641136789886402-4302457777654578876433874000648989999999888638731478999999 Q gi|254780979|r 338 YDASVLVSDKSIADYFEKLAV-NRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFN 416 (500) Q Consensus 338 ~dA~~L~~~~~la~~FE~v~~-~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~ 416 (500) ++|++|++++.+++|||.++. ..+||.+||||+++++++||+.+.++++++++|++|++|+.|+++|+||.++||+||+ T Consensus 317 ~~a~~L~~~~~l~~~Fe~v~~~~~~pk~aanwi~~el~~~Ln~~~~~i~~~~i~~~~laeLi~li~~g~Is~~~AK~il~ 396 (479) T PRK05477 317 YDARVLTSDKELADYFEAVVAGGADAKLAANWLMGELLGRLNKEGLEIEESPVTPEQLAELIKLIDDGTISGKIAKKVFE 396 (479) T ss_pred HHHHHHHHCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHH T ss_conf 99999984679999999999857887775457666789987452798663788999999999999859856899999999 Q ss_pred HHHHCCCCHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHH-CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 9981799988999963987618988999999999983999899752-721322658999999728977889999999997 Q gi|254780979|r 417 ILWEKGGTPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIA-TKPNLVSWFVGQVMKNTGGKANPSIVQKMLKEK 495 (500) Q Consensus 417 ~l~~~~~~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~k-gk~ka~gfLvGqVMK~tkGkAdpk~v~~lL~e~ 495 (500) .|+.++++|+++|+++||.++||+++|+++|++||++||++|++|+ ||++++|||||||||+|||||||+.|+++|+++ T Consensus 397 ~m~~~~~sp~~ii~~~gL~~isD~~eLe~ii~eVI~~np~~Ve~yk~Gk~ka~gfLmGqVMK~tkGkAdPk~v~elL~e~ 476 (479) T PRK05477 397 EMLEGGGDPDEIVEEKGLKQISDEGALEAIVDEVLAANPKAVEDYKAGKEKALGFLVGQVMKATKGKANPKLVNELLKEK 476 (479) T ss_pred HHHHCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH T ss_conf 99966999999999739824489999999999999979999999976438778789999999857997999999999998 Q ss_pred HC Q ss_conf 07 Q gi|254780979|r 496 LG 497 (500) Q Consensus 496 L~ 497 (500) || T Consensus 477 L~ 478 (479) T PRK05477 477 LG 478 (479) T ss_pred HC T ss_conf 67 No 2 >COG0064 GatB Asp-tRNAAsn/Glu-tRNAGln amidotransferase B subunit (PET112 homolog) [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=0 Score=1327.39 Aligned_cols=475 Identities=56% Similarity=0.914 Sum_probs=459.5 Q ss_pred CCCCCEEEEEEEEEEECCCCCCCCCCCCCCC-CCCCCCCCHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCEECCCCEEEC Q ss_conf 4780338989997888689865558842468-987652061302689888737899999999987782976244201311 Q gi|254780979|r 19 TGDWEVVIGIEVHAQLSVVSKLFSGASVNFG-AEPNTQVSFFDAAMPGMLPILNGRCVQQAVMTGLGLNAHINKYSVFAR 97 (500) Q Consensus 19 ~~~~e~vIGLEiH~qL~t~tKlFc~c~~~~~-~~pNt~v~~~~~g~PG~lP~lN~~av~~ai~~~~al~~~i~~~~~fdR 97 (500) ..+|++|||||||+||+|+|||||+|+++|+ ++|||||||||+||||+||+||++||+.|+++|+||||+|+..++||| T Consensus 3 ~~~~e~vIGLEvHvqL~T~tKlFs~~~~~f~~a~PNtnv~pv~lglPGaLPvlN~~av~~ai~~~lAL~~~i~~~~~FdR 82 (483) T COG0064 3 MMNFEVVIGLEVHVQLNTKTKLFSGCSTDFGGAEPNTNVCPVCLGLPGALPVLNKEAVEKAIKAGLALNCEINEKSVFDR 82 (483) T ss_pred CCCCEEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEECCCEECCC T ss_conf 65520576557877861576646788521267899777885002689876656899999999964531656256503166 Q ss_pred CCEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEE Q ss_conf 32123767888201445442015338999706777774103798423666520231001156787148866157861257 Q gi|254780979|r 98 KNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRTIEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALME 177 (500) Q Consensus 98 K~YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~~~~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiE 177 (500) |||||||||||||||||+.|||.||++++...++ ..++|+|+|+||||||||++|.+++++|+|||||||||||| T Consensus 83 K~YFYPDlPkgyQIsQ~d~Pi~~~G~i~i~~~~~-----~~k~i~I~r~HlEEDaGK~~h~~~~~~s~vD~NRaGvPLiE 157 (483) T COG0064 83 KNYFYPDLPKGYQISQFDKPIAENGYLEIELEDG-----EEKRIGIERIHLEEDAGKLTHEGSAGYSLVDYNRAGVPLIE 157 (483) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCC-----CCEEECCCEEECCCCCCCCCCCCCCCCEEEECCCCCCCEEE T ss_conf 7889998888865013556656685799864788-----60253452343023687650058998404541326874046 Q ss_pred EEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 630365277899999999999998642045676432201125754321376-6678862223540246599999999999 Q gi|254780979|r 178 IVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPG-EAWGTRCEVKNVNSIRFLGLAIEYEARR 256 (500) Q Consensus 178 IVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~-~~~GtRvEIKNlnS~~~i~~AI~yEi~R 256 (500) |||+||||||+||++|+.+||.|+||+|||||+||+||||||||||||+.| .+|||||||||+|||++|++||+||+.| T Consensus 158 IVtePdirs~~eA~ayl~~Lr~ilrylgisd~~meeGsmR~DaNvSvr~~g~~~~GtrvEiKNiNS~~~v~kAi~yE~~R 237 (483) T COG0064 158 IVTEPDIRSPEEARAYLKKLRSILRYLGISDGNMEEGSMRCDANVSVRPKGQEEFGTRVEIKNLNSFRNVEKAIEYEIQR 237 (483) T ss_pred EECCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHH T ss_conf 54146789999999999999999998088988756675676410330246654557635452586499999999999999 Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCC Q ss_conf 99973139800344323375543366530356677778332778773126999999988530248368988643202688 Q gi|254780979|r 257 QIAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGIS 336 (500) Q Consensus 257 Q~~ll~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs 336 (500) |.+++++|+.|.||||+||+.+|.|++||+||++.||||||||||||+.||++|+++++..|||||+++++||+.+|||| T Consensus 238 Q~~~l~~g~~i~qeTR~~d~~~g~T~~mR~KE~a~DYRYfpePDl~p~~is~~~i~~~~~~lPelP~~~~~r~~~~~gls 317 (483) T COG0064 238 QIELLESGGEIEQETRRFDEATGKTVSMRSKEEAEDYRYFPEPDLPPLEISDEWIEEVRATLPELPDEKRERYIKEYGLS 317 (483) T ss_pred HHHHHHCCCCEEEHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHCCCC T ss_conf 99999738966502005056788076410346644456579998487237999999999757789899999999974999 Q ss_pred HHHHHHHHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHH- Q ss_conf 999888764113678988640-243024577776545788764338740006489899999998886387314789999- Q gi|254780979|r 337 LYDASVLVSDKSIADYFEKLA-VNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDI- 414 (500) Q Consensus 337 ~~dA~~L~~~~~la~~FE~v~-~~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~i- 414 (500) ++||++|++++.+++|||+++ .+.+||.+|||+++||++.||+.++++.+++++|++|++|++++++|+||+++||++ T Consensus 318 ~~dA~~L~~d~~la~~fe~~~~~~~~~k~~anW~~~el~~~Ln~~~~~i~~~~~~p~~la~Li~li~~g~IS~k~AK~~v 397 (483) T COG0064 318 EYDARVLTSDKELADYFEEAVKAGADAKLAANWLTNELLGLLNKAGITLEESPLTPEQLAELIKLIDEGTISGKIAKELV 397 (483) T ss_pred HHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHH T ss_conf 88999997689999999999745888899888999999999986599755358998999999999970873199999999 Q ss_pred HHHHHHCCCCHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHH-CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHH Q ss_conf 999981799988999963987618988999999999983999899752-7213226589999997289778899999999 Q gi|254780979|r 415 FNILWEKGGTPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIA-TKPNLVSWFVGQVMKNTGGKANPSIVQKMLK 493 (500) Q Consensus 415 l~~l~~~~~~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~k-gk~ka~gfLvGqVMK~tkGkAdpk~v~~lL~ 493 (500) +..|+..+++|.+||+++||.|++|+++|+++|++||++||++|++|+ ||++++|||||||||+|+|||||+.|+++|+ T Consensus 398 ~~~~~~~~~~p~~iie~~gL~qisD~~~l~~~V~evia~Np~~ve~yk~GK~~~~~f~vGQVMk~T~GkAnP~~v~~ll~ 477 (483) T COG0064 398 FEILANGGKDPEEIIEEKGLVQISDEGELEKIVDEVLAENPKAVEDYKSGKEKALGFLVGQVMKATKGKANPQQVNELLK 477 (483) T ss_pred HHHHHCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH T ss_conf 99997379998999986496324899999999999999798999998646898988899999998469999899999999 Q ss_pred HHHCC Q ss_conf 97078 Q gi|254780979|r 494 EKLGI 498 (500) Q Consensus 494 e~L~~ 498 (500) ++|+. T Consensus 478 ~~L~~ 482 (483) T COG0064 478 EKLGK 482 (483) T ss_pred HHHCC T ss_conf 98624 No 3 >PRK04028 glutamyl-tRNA(Gln) amidotransferase subunit E; Validated Probab=100.00 E-value=0 Score=1152.57 Aligned_cols=447 Identities=32% Similarity=0.497 Sum_probs=409.0 Q ss_pred CCCCCEE---EEEEEEEEECCCCCCCCCCCCCCCC-C-------------------------------------CCCCCC Q ss_conf 4780338---9899978886898655588424689-8-------------------------------------765206 Q gi|254780979|r 19 TGDWEVV---IGIEVHAQLSVVSKLFSGASVNFGA-E-------------------------------------PNTQVS 57 (500) Q Consensus 19 ~~~~e~v---IGLEiH~qL~t~tKlFc~c~~~~~~-~-------------------------------------pNt~v~ 57 (500) +-|||.+ ||||||+||+|+|||||+|+++|++ + ||+++| T Consensus 2 ~~~~e~~gl~IGLEiH~QL~T~tKlFc~c~t~~~~~~pn~~~~~~~~~~~~~lg~~d~aa~~e~~~~~~f~y~~~~~~~C 81 (631) T PRK04028 2 KMDYEELGLKVGLEIHQQLDTKRKLFCRCPTELRDDEPHFEFERYLRPTQSELGEIDPAALEESKKGRKFIYEAYRDTTC 81 (631) T ss_pred CCCHHHHCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCC T ss_conf 98859969876689987748998737899986567886531000245431111323265554321133334458899857 Q ss_pred HH-HCCCCCCCCCCCHHHHHHHHHHHHHHCCEECCCCEEECCCEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCC Q ss_conf 13-02689888737899999999987782976244201311321237678882014454420153389997067777741 Q gi|254780979|r 58 FF-DAAMPGMLPILNGRCVQQAVMTGLGLNAHINKYSVFARKNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQF 136 (500) Q Consensus 58 ~~-~~g~PG~lP~lN~~av~~ai~~~~al~~~i~~~~~fdRK~YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~ 136 (500) || |.|+||++| |++||++|+++|+||||+|+++++|||||||||||||||||||+ ||.||+|+++ T Consensus 82 ~v~~~~~Pp~~~--N~~av~~ai~~~~alnc~I~~~~~f~RK~yfypd~pkgyQiTq~---i~~~G~le~~--------- 147 (631) T PRK04028 82 LVELDEEPPHEL--NEEALEIALAVAKLLNMKPVDEIHVMRKIVIDGSNTSGFQRTAL---VALGGYIETS--------- 147 (631) T ss_pred CCCCCCCCCCCC--CHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE---ECCCCEEECC--------- T ss_conf 223678998777--99999999999998498136465003666668876631345635---5389679656--------- Q ss_pred EEEEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEE Q ss_conf 03798423666520231001156787148866157861257630365277899999999999998642045676432201 Q gi|254780979|r 137 RTIEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSM 216 (500) Q Consensus 137 ~~~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGsl 216 (500) .++|+|+||||||||||++|+. ++++.+||||||||||||||+|||+||+||++|+++|++||||+|.|+++ +||| T Consensus 148 -~~~V~I~rihLEEDagK~i~~~-~~~~~ydlNRaGvPLiEIVTePDi~s~eeA~~~~~~l~~ilr~~g~~~~~--~Gsl 223 (631) T PRK04028 148 -GGKVGIETICLEEDAARKIEEK-GDYVVYSLDRLGIPLIEISTEPDIHSPEQAKEVALRIGMILRSTGKVKRG--LGTI 223 (631) T ss_pred -CCEEEEEEEEECCCCCCCCCCC-CCCEEEECCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC--CCCE T ss_conf -8434037998512457643468-98337744557985388843788899999999999999999986412456--7754 Q ss_pred ECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH---------------------------------- Q ss_conf 1257543213766678862223540246599999999999999731---------------------------------- Q gi|254780979|r 217 RADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILE---------------------------------- 262 (500) Q Consensus 217 R~DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~---------------------------------- 262 (500) ||||||||| +||||||||||||++|++||+||+.||+++|+ T Consensus 224 R~DvNVSvr-----~GtRvEIKNlnS~~~i~~AieyEi~RQ~~ll~~~~ei~~~g~~~~~~~~~~~d~t~~~~~t~s~ii 298 (631) T PRK04028 224 RQDVNVSIA-----GGARVEIKGVQDLDLIPKVVEYEVQRQLNLLKIRDELRRRGASREEVVDEIVDVTELFKNTKSKVI 298 (631) T ss_pred EEEEEEEEC-----CCCEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCHHH T ss_conf 566676414-----785256407754889999999999999999875777753144311134320013555313530788 Q ss_pred -----CCCC----------------------------------------------------------------------- Q ss_conf -----3980----------------------------------------------------------------------- Q gi|254780979|r 263 -----DGGH----------------------------------------------------------------------- 266 (500) Q Consensus 263 -----~G~~----------------------------------------------------------------------- 266 (500) .||. T Consensus 299 ~~~l~~gg~v~a~~~~~~~g~lg~e~q~~rR~g~E~~d~~k~~g~~Gi~HsDElp~Ygi~~~e~~~~~~~l~~~~~Da~~ 378 (631) T PRK04028 299 KRALKKGGKVLAVKLPGFKGLLGREIQPGRRLGTELADYAKWAGVGGIFHSDELPGYGITEEEVEALRDALGAGENDAVI 378 (631) T ss_pred HHHHHCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCEE T ss_conf 76550487378775156344336566754200056766765415565334543434465266778888752467554135 Q ss_pred --------------------------CCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCC Q ss_conf --------------------------034432337554336653035667777833277877312699999998853024 Q gi|254780979|r 267 --------------------------IRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPE 320 (500) Q Consensus 267 --------------------------v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPe 320 (500) |.||||+|+++ |.|.+||+||+++ ||||||||||+.|+++||++++++||| T Consensus 379 l~~~~~~~~~~~~~~v~~R~~~~~~~vp~EtR~~~~d-g~T~~mR~k~ga~--RyfPEPDLPPi~Is~e~Ie~Ik~~LPE 455 (631) T PRK04028 379 LVADEEEKAKKALEAVIERAKEALEGVPEETRKALPD-GTTRYLRPLPGAA--RMYPETDIPPIRITEELLEKIKKNLPE 455 (631) T ss_pred EECCCHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCCC-CCEEECCCCCCCC--CCCCCCCCCCEECCHHHHHHHHHHCCC T ss_conf 5327377788899999999987540685554156778-9874235567532--207798877464699999999971899 Q ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHH Q ss_conf 836898864320268899988876411367898864-0243024577776545788764338740006489899999998 Q gi|254780979|r 321 LPDAKRERFIGEFGISLYDASVLVSDKSIADYFEKL-AVNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELID 399 (500) Q Consensus 321 lP~~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v-~~~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~ 399 (500) ||+++++||+++||||++||.+|++++.+ +|||++ ..+.+|+.+|||+++.+ +.||+.+.++. .++|++|++|+. T Consensus 456 LP~~kr~Rl~~eygLs~~dA~~L~~~~~l-~~FE~~v~~~~~pk~~An~l~~~l-~~L~~~~~~i~--~I~pe~La~Li~ 531 (631) T PRK04028 456 LPEEKLERLVKEYGLSEELAEQLANSERL-DLFEELVKKGVKPTLIARTLVNTL-KELKREGVDIE--NITDEHIEEVFD 531 (631) T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHH-HHHHHHHHCCCCHHHHHHHHHHHH-HHHHHCCCCCC--CCCHHHHHHHHH T ss_conf 99999999999709899999999747389-999999971699999999999999-99997689813--399999999999 Q ss_pred HHHCCCCCHHHHHHHHHHHHHC-CCCHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHHHHHHH Q ss_conf 8863873147899999999817-999889999639876189889999999999839998997527213226589999997 Q gi|254780979|r 400 LIIDGTISGKIAKDIFNILWEK-GGTPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIATKPNLVSWFVGQVMKN 478 (500) Q Consensus 400 li~~g~Is~~~aK~il~~l~~~-~~~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~kgk~ka~gfLvGqVMK~ 478 (500) |+++|+||.++||+||+.|+.+ +.+|++||++.||.|+||+ +|+++|++||++||++|++ ||++++|||||||||+ T Consensus 532 Li~~G~IS~~~aK~V~~~m~~~~g~~p~~Iiee~gL~qisd~-eLe~iV~eVI~eN~~~Vk~--gK~kaigfLvGQVMK~ 608 (631) T PRK04028 532 LVSEGKIAKEAIEEILKALAENPGKSVEEAAEELGLTRLSEE-EVEKIIEEIVEENIDFVKE--KGMGAFGPLMGEVMAE 608 (631) T ss_pred HHHCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHH-HHHHHHHHHHHHCHHHHHH--CCCCCCHHHHHHHHHH T ss_conf 998698538999999999985799899999997699768999-9999999999978999985--4423201099999998 Q ss_pred HCCCCCHHHHHHHHHHHHCC Q ss_conf 28977889999999997078 Q gi|254780979|r 479 TGGKANPSIVQKMLKEKLGI 498 (500) Q Consensus 479 tkGkAdpk~v~~lL~e~L~~ 498 (500) |||||||+.|+++|+++|.. T Consensus 609 tkGKAnPk~VnelLkekLke 628 (631) T PRK04028 609 LRGKADGKIVSEILREKLKE 628 (631) T ss_pred HCCCCCHHHHHHHHHHHHHH T ss_conf 57997999999999999999 No 4 >KOG2438 consensus Probab=100.00 E-value=0 Score=1148.93 Aligned_cols=480 Identities=43% Similarity=0.742 Sum_probs=462.0 Q ss_pred CCCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCEECCCCEE Q ss_conf 24547803389899978886898655588424689876520613026898887378999999999877829762442013 Q gi|254780979|r 16 SGTTGDWEVVIGIEVHAQLSVVSKLFSGASVNFGAEPNTQVSFFDAAMPGMLPILNGRCVQQAVMTGLGLNAHINKYSVF 95 (500) Q Consensus 16 ~~~~~~~e~vIGLEiH~qL~t~tKlFc~c~~~~~~~pNt~v~~~~~g~PG~lP~lN~~av~~ai~~~~al~~~i~~~~~f 95 (500) ..-..+|.+|||||||+||+|.+||||+|.++|++.|||+||+||+++||||||||++||++|++.||||||+++..|.| T Consensus 17 ~~~~r~waaviGlEiH~Ql~t~~KlFs~s~~~~~a~pNt~v~yfd~slPGtlPVLN~~~vefavk~~LALnc~vn~~s~F 96 (505) T KOG2438 17 GMPFRKWAAVIGLEIHAQLATVSKLFSGSKVNFGAPPNTSVSYFDASLPGTLPVLNREAVEFAVKLSLALNCEVNNVSKF 96 (505) T ss_pred CCCHHHHHHHHCCEEHHHHHHHHHHHCCCCCCCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHC T ss_conf 87256566631111014576656551566787788997620255235887644357999999988776434611033320 Q ss_pred ECCCEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCE Q ss_conf 11321237678882014454420153389997067777741037984236665202310011567871488661578612 Q gi|254780979|r 96 ARKNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRTIEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVAL 175 (500) Q Consensus 96 dRK~YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~~~~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPL 175 (500) |||||||||||+||||||++.||+.||.+.+..+.+. ...++|+|.|||||||||||+|+....+|||||||||+|| T Consensus 97 DRKhYFY~DlP~GYQitQ~~~pia~~G~~~l~~~~~~---v~~k~~~i~qiqlEqDtgKst~~d~~~~sLvDlNRAGvpL 173 (505) T KOG2438 97 DRKHYFYPDLPAGYQITQQRIPIARNGFIPLSAGLDN---VPDKTIGILQIQLEQDTGKSTHDDAPSRSLVDLNRAGVPL 173 (505) T ss_pred CCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCC---CCCCEECEEEEEEECCCCCCCCCCCCCCEEEECCCCCCCE T ss_conf 2100446788887344432223035885335656678---8763102389986123564531258873366213369852 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 57630365277899999999999998642045676432201125754321376667886222354024659999999999 Q gi|254780979|r 176 MEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEAR 255 (500) Q Consensus 176 iEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~ 255 (500) +||||+|||++.+||.+|+.+||.|+|++|+|+|+||+|+|||||||||+++|++||||||||||||+|+|.+||+|||. T Consensus 174 lEiVt~Pdf~~~~eaa~fv~elqlIlr~lgis~g~meeG~lRvDvNiSI~~~g~~lG~RvElKNLnsirsI~~AI~yEi~ 253 (505) T KOG2438 174 LEIVTKPDFSDGIEAAAFVKELQLILRHLGISSGNMEEGALRVDVNISIAPDGSELGTRVELKNLNSIRSISNAIDYEIQ 253 (505) T ss_pred EEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHCCCEEEEEEEEECCCCCCCEEEEEECCCHHHHHHHHHHHHHHH T ss_conf 78762766212899999999999999996436442203845775446766777623234553155138899998879999 Q ss_pred HHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC Q ss_conf 99997313980034432337554336653035667777833277877312699999998853024836898864320268 Q gi|254780979|r 256 RQIAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI 335 (500) Q Consensus 256 RQ~~ll~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL 335 (500) ||+++++.|+.|..|||+||...|.|++||.||+.+||||||||||||+.++.+||+.++.+||+||++.+++|.++||+ T Consensus 254 RQvel~~nGg~i~nETR~wd~~~~rTvsmRdKEt~~DYRfmPEPnLPpl~L~~~~v~~Vre~LPeLP~~~~~~L~e~~gl 333 (505) T KOG2438 254 RQVELLNNGGAIQNETRGWDSEGGRTVSMRDKETLQDYRFMPEPNLPPLILHGKYVDSVREELPELPDATREKLVEQYGL 333 (505) T ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCCCCEECCCCCCCCCEEECHHHHHHHHHHCCCCCHHHHHHHHHHHCC T ss_conf 99999965882555244543567725861354431011016899998766448899999975523768899999886266 Q ss_pred CHHHHHHHHHHHHHHHHH-HHH-H----CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHH Q ss_conf 899988876411367898-864-0----2430245777765457887643387400064898999999988863873147 Q gi|254780979|r 336 SLYDASVLVSDKSIADYF-EKL-A----VNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGK 409 (500) Q Consensus 336 s~~dA~~L~~~~~la~~F-E~v-~----~~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~ 409 (500) +.++|.+|+++.++.+|| +.+ . ....||.+++||+++++++++.......++.++|.+||+|+.++++++||.. T Consensus 334 ~~k~a~~L~~~~~~~~~~~d~v~i~k~~ae~~~k~~~~Wi~~~~~g~lrq~~ls~~~~~~~p~~la~ll~ll~~~~Is~~ 413 (505) T KOG2438 334 SAKDAVTLANEVELLEFYKDSVRIIKYKAETTPKLITYWIKEEFLGYLRQIALSPNQSIVTPRQLADLLKLLSEETISAL 413 (505) T ss_pred CHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 54553455435568888765466653025455321178999999888751467865343686999999998534012577 Q ss_pred HHHHHHHHHHHCCC--CHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHH-CCCCCHHHHHHHHHHHHCCCCCHH Q ss_conf 89999999981799--988999963987618988999999999983999899752-721322658999999728977889 Q gi|254780979|r 410 IAKDIFNILWEKGG--TPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIA-TKPNLVSWFVGQVMKNTGGKANPS 486 (500) Q Consensus 410 ~aK~il~~l~~~~~--~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~k-gk~ka~gfLvGqVMK~tkGkAdpk 486 (500) +||++|.+++++++ ++..+|+++.|++|.|.+||+++|.+||++|||.|++++ ||.|+++||+|+|||.|+|+|||+ T Consensus 414 ~ak~ll~~l~~~~~~~~~s~LIeek~l~~I~dp~eIe~lv~~vm~~h~k~ve~~rsGk~k~~~~l~G~vmk~s~g~a~p~ 493 (505) T KOG2438 414 SAKQLLRHLLKNPGVMTVSILIEEKRLWQIRDPAEIEELVRSVMEKHPKQVEQLRSGKTKSIKRLIGLVMKSSQGRANPK 493 (505) T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCHH T ss_conf 89999999984878688899976643541179999999999999877899999875568899999999999751679989 Q ss_pred HHHHHHHHHHCC Q ss_conf 999999997078 Q gi|254780979|r 487 IVQKMLKEKLGI 498 (500) Q Consensus 487 ~v~~lL~e~L~~ 498 (500) .+.+.|+++|+. T Consensus 494 ~le~~l~~~L~~ 505 (505) T KOG2438 494 DLEKILEELLNR 505 (505) T ss_pred HHHHHHHHHHCC T ss_conf 999999987369 No 5 >pfam02934 GatB_N GatB/GatE catalytic domain. This domain is found in the GatB and GatE proteins. Probab=100.00 E-value=0 Score=961.25 Aligned_cols=286 Identities=57% Similarity=0.924 Sum_probs=278.2 Q ss_pred CEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCEECCCCEEECCCEEC Q ss_conf 33898999788868986555884246898765206130268988873789999999998778297624420131132123 Q gi|254780979|r 23 EVVIGIEVHAQLSVVSKLFSGASVNFGAEPNTQVSFFDAAMPGMLPILNGRCVQQAVMTGLGLNAHINKYSVFARKNYFY 102 (500) Q Consensus 23 e~vIGLEiH~qL~t~tKlFc~c~~~~~~~pNt~v~~~~~g~PG~lP~lN~~av~~ai~~~~al~~~i~~~~~fdRK~YfY 102 (500) |+|||||||+||+|+|||||+|+++|+++|||+|||+|+|+||+||++|++||++|+++|+||||+|++.++|||||||| T Consensus 1 e~vIGLEiH~qL~T~tKlFc~c~~~~~~~PNt~v~p~~lg~PG~LPvlN~~av~~Ai~~~laL~c~I~~~s~fdRK~YfY 80 (287) T pfam02934 1 ELVIGLEIHVQLNTKTKLFCGCPTEFGAEPNTNVCPVCLGLPGALPVLNKEAVELAIKAGLALNCEINDESRFDRKNYFY 80 (287) T ss_pred CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEECCEEEEC T ss_conf 98899999988179977668999867899756578043069878764699999999999998298636221761202676 Q ss_pred CCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECC Q ss_conf 76788820144544201533899970677777410379842366652023100115678714886615786125763036 Q gi|254780979|r 103 PDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRTIEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKP 182 (500) Q Consensus 103 pDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~~~~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~P 182 (500) |||||||||||++.|||.||++++..++ ..++|+|+||||||||||++|+..+++|+|||||||+|||||||+| T Consensus 81 pDlPkgYQITQ~~~Pi~~~G~l~i~~~~------~~k~i~I~rihlEEDagK~~h~~~~~~slvD~NRaGvPLiEIVTeP 154 (287) T pfam02934 81 PDLPKGYQITQYDLPIATNGYLEIEVDG------EEKRIGIERIHLEEDAGKLIHEGGGDYSLVDLNRAGVPLIEIVTEP 154 (287) T ss_pred CCCCCCCCEECCCCCEECCCEEEEECCC------CCEEEEEEEEEECCCCCCCCCCCCCCEEEEECCCCCCCEEEEEECC T ss_conf 9888564300564677301389860289------6205714798870023424546899736884045798248998358 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 5277899999999999998642045676432201125754321376-667886222354024659999999999999973 Q gi|254780979|r 183 DMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPG-EAWGTRCEVKNVNSIRFLGLAIEYEARRQIAIL 261 (500) Q Consensus 183 d~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~-~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll 261 (500) ||+||+||++|+++|++||||+|+|||+||+|+||||||||||+.| ..||+||||||||||++|++||+||+.||+++| T Consensus 155 d~~s~eeA~~~~~~L~~il~~lgisd~~me~GslR~DvNVSv~~~g~~~~g~rvEIKNlNS~~~v~~Ai~~Ei~RQ~~~l 234 (287) T pfam02934 155 DIRSPEEARAYLKKLRQILRYLGVSDGNMEEGSLRCDANVSVRPKGSEEFGTRVEIKNLNSFRFVEKAIEYEIERQIELL 234 (287) T ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHH T ss_conf 88999999999999999999747555674556345420377535788765315886347679999999999999999999 Q ss_pred HCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHH Q ss_conf 13980034432337554336653035667777833277877312699999998 Q gi|254780979|r 262 EDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAI 314 (500) Q Consensus 262 ~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i 314 (500) ++|+.|.||||+||+.+++|++||+||+|+||||||||||||+.|+++||++| T Consensus 235 ~~G~~v~qETR~~d~~~~~T~~mR~Ke~a~DYRyfPePDLppi~i~~~~i~~i 287 (287) T pfam02934 235 EEGGKVPQETRLWDEDKGETVSMRSKEGAADYRYFPEPDLPPIVISDEWIEEI 287 (287) T ss_pred HCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCEECCHHHHHHC T ss_conf 85998432116797898958106268863365757899978767699999349 No 6 >TIGR00133 gatB glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, B subunit; InterPro: IPR004413 In many species, Gln-tRNA ligase is missing. tRNA(Gln) is misacylated with Glu after which a heterotrimeric amidotransferase converts Glu to Gln. This group represents the chain of the heterotrimer, encoded by the gatB gene called glutamyl-tRNA(Gln) amidotransferase, B subunit 6.3.5 from EC. This enzyme functions as an alternative to a direct Gln-tRNA synthetase (Gln-tRNA ligase) in mitochondria, chloroplasts, Gram-positive bacteria, cyanobacteria, and the archaea. The archaea have an Asp-tRNA(Asn) amidotransferase instead of an Asp-tRNA ligase. In the archaea a paralog of gatB is found, here designated gatB_rel, that is a candidate B subunit of the Asp-tRNA(Asn) amidotransferase. The gatA-encoded subunit may be shared by gatB and gatB_rel. ; GO: 0016884 carbon-nitrogen ligase activity with glutamine as amido-N-donor, 0006412 translation. Probab=100.00 E-value=0 Score=823.72 Aligned_cols=477 Identities=48% Similarity=0.806 Sum_probs=454.8 Q ss_pred CCCCEEEEEEEEEEECCCCCCCCCCCCCCCC-CC--CCCCCHHHCCCCCCCCC-CCHHHHHHHHHHHHHHCCE-EC-CCC Q ss_conf 7803389899978886898655588424689-87--65206130268988873-7899999999987782976-24-420 Q gi|254780979|r 20 GDWEVVIGIEVHAQLSVVSKLFSGASVNFGA-EP--NTQVSFFDAAMPGMLPI-LNGRCVQQAVMTGLGLNAH-IN-KYS 93 (500) Q Consensus 20 ~~~e~vIGLEiH~qL~t~tKlFc~c~~~~~~-~p--Nt~v~~~~~g~PG~lP~-lN~~av~~ai~~~~al~~~-i~-~~~ 93 (500) -+|+.+||||+|+||+|++|+||+|+++|+. .| |+++||+|+|+||++|+ +|.+++..|++++.|++|+ +. +.+ T Consensus 2 ~~~~~~~gle~h~~l~~~~k~f~~~~~~~~~~~p~pn~~~~p~~lg~pg~~p~p~n~~~~~~~~~~~~~~~~~~~~~~~~ 81 (523) T TIGR00133 2 IEYEAVIGLEVHVQLNTKTKLFCSCPNDFGSAPPAPNTNVCPVCLGLPGALPVPLNKEAVKKALKLGLALNAKIVSPPVS 81 (523) T ss_pred CCCCEEEEEEEEEEECCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCHH T ss_conf 75200211235555323201100475333456778765445000157876566644889999998877631200254112 Q ss_pred EEECCCEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEEEECCCCCCCCCC--CCCEEEEECCC Q ss_conf 1311321237678882014454420153389997067777741037984236665202310011567--87148866157 Q gi|254780979|r 94 VFARKNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRTIEVGIERIHLEQDAGKSIHDQY--SAVSCIDLNRS 171 (500) Q Consensus 94 ~fdRK~YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~~~~~v~I~~i~lEED~gk~~h~~~--~~~slvD~NRa 171 (500) .||||||||||+|+|||+||++.|++.+|++.+....+..... .+.|+|.++|+|||+||+.|... +.++++||||+ T Consensus 82 ~f~~k~y~y~d~p~g~~~~~~~~p~~~~g~~~~~~~~~~~~~~-~~~~~~~~~~~e~d~g~~~~~~~~~~~~~~~d~n~~ 160 (523) T TIGR00133 82 VFDRKHYFYPDLPKGYQITQFDRPIAEGGKLEIELDGGETDES-AKRIGIERLHLEEDPGKLQHKGSDKPSQSLVDFNRS 160 (523) T ss_pred HHHHHHCCCCCCCCCCEECCCCCCEECCCEEEEEECCCHHHHH-HHHHHHEEEEECCCCCHHHHCCCCCCCEEEEECCCC T ss_conf 2211003466676543000024540016526884065302344-444311002101132101102355432034422445 Q ss_pred CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHHH Q ss_conf 861257630365277899999999999998642045676432201125754321376-6678862223540246599999 Q gi|254780979|r 172 GVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPG-EAWGTRCEVKNVNSIRFLGLAI 250 (500) Q Consensus 172 GvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~-~~~GtRvEIKNlnS~~~i~~AI 250 (500) |+||+||||+||++++++|++|+++++.+++|+|+++|+|++|++|||+|||++..| ..+|+|+||||+|||+++.+|+ T Consensus 161 g~pl~e~~~~p~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~g~~~~d~n~~~~~~g~~~~~~~~e~kn~~~~~~~~~~~ 240 (523) T TIGR00133 161 GAPLLEIVTKPDLNSPKEARAFLKKLRQLLRYLGISDGNLEEGSLRCDVNVSIRPKGQEEGGTRVEIKNLNSFKGVEKAI 240 (523) T ss_pred CCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEECEEEEEECCCCCCCCEEEEECCCCHHHHHHHH T ss_conf 76332110144557778999999999999987311235534464121000235541432244314541253046788888 Q ss_pred HHHHHHHHHHHHCC---CCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHH-HHHHCCCCHHHHH Q ss_conf 99999999973139---8003443233755433665303566777783327787731269999999-8853024836898 Q gi|254780979|r 251 EYEARRQIAILEDG---GHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRA-IKKQIPELPDAKR 326 (500) Q Consensus 251 ~yEi~RQ~~ll~~G---~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~-i~~~lPelP~~~~ 326 (500) +||+.||.+++..| ..+.++||+|++..+.|++||.||++.||||||||||||+.+++.++.. +...+|++|..++ T Consensus 241 ~~e~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~dy~y~~~p~~~~~~~~~~~~~~~~~~~~~~~p~~~~ 320 (523) T TIGR00133 241 EYEIERQKKLLIRGKYDEEVLQETRLFDESSGITVSLRSKETSSDYRYFPEPDLPPINIDEELVKGPVAGKLPELPSAKR 320 (523) T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHCCHHHHH T ss_conf 88888889998602100123443321001244123320222200000025776430002466753234442002336888 Q ss_pred HHHHHHCCCCHHHHHHHHHHHH------------HHHHHHHHHC-CCCH---HHHHHHHHHHHHHHHHHCCCCCCCC--C Q ss_conf 8643202688999888764113------------6789886402-4302---4577776545788764338740006--4 Q gi|254780979|r 327 ERFIGEFGISLYDASVLVSDKS------------IADYFEKLAV-NRDK---KIVANWVINDLLGVLNRSGKSIEDT--P 388 (500) Q Consensus 327 ~rl~~~yGLs~~dA~~L~~~~~------------la~~FE~v~~-~~~p---k~~Anwi~~el~~~ln~~~~~~~~~--~ 388 (500) .|+..+||++++++.+|+.+.. +++||+++.. ..+| +.+++|++.++.+.++..+..+..+ . T Consensus 321 ~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~W~~~~~~~~l~~~~~~~~~~~~~ 400 (523) T TIGR00133 321 IRLKKEYGLSEEDAKLLTSDLDQNDLYNHEALRYLADYFEEVVKLGGPPSNAKLAANWLCDELLGELNKLKISLAECWEG 400 (523) T ss_pred HHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH T ss_conf 87766406763342332103310100246899999999999986125400246788999999998864215634565420 Q ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHC--------CCCHHHHHHH--CCCEECCCHHHHHHHHHHHHHHCHHHH Q ss_conf 898999999988863873147899999999817--------9998899996--398761898899999999998399989 Q gi|254780979|r 389 ISPNQLGELIDLIIDGTISGKIAKDIFNILWEK--------GGTPKEIVEE--LGLRQVTDLSAIEKVVDEVINSNPNNV 458 (500) Q Consensus 389 i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~--------~~~p~~iie~--~gL~~isD~~eL~~iv~eVI~~np~~V 458 (500) +.|.++++++.++..|+|+.+.+|+++..++.. +++|..++++ .|+.++.|..++..+|.+++.+||+.+ T Consensus 401 ~~p~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~d~~~~~~~~~~~~~~~l~~~~d~~~~~~~~~~~~~~~~~~~ 480 (523) T TIGR00133 401 LKPSDLAELLKLIKEGKISGKSAKELLDELLENFGQNCQDLGGDPDKLIEEFELGLEQISDPDELVKIIEEVIKENPKEV 480 (523) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCHHHH T ss_conf 26478999999875432114678899998875202212331455889999975001015777899999999973173457 Q ss_pred HHHH---C-CCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHC Q ss_conf 9752---7-2132265899999972897788999999999707 Q gi|254780979|r 459 ARIA---T-KPNLVSWFVGQVMKNTGGKANPSIVQKMLKEKLG 497 (500) Q Consensus 459 ~~~k---g-k~ka~gfLvGqVMK~tkGkAdpk~v~~lL~e~L~ 497 (500) .+|. + +..+++|++||+|+.++|+|+|..+.+++++.|+ T Consensus 481 ~~~~~~~~g~~~~~~~~~g~~~~~~~g~~~p~~~~~~~~~~l~ 523 (523) T TIGR00133 481 EDYLLVTSGKERALKFLVGQVMKKTRGRANPKLVNELLKELLS 523 (523) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCC T ss_conf 7776542015678888887777651354457899999987419 No 7 >COG2511 GatE Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=0 Score=712.19 Aligned_cols=444 Identities=33% Similarity=0.532 Sum_probs=397.2 Q ss_pred CCC---EEEEEEEEEEECCCCCCCCCCCCCCCC-C-------------------------------------CCCCCCHH Q ss_conf 803---389899978886898655588424689-8-------------------------------------76520613 Q gi|254780979|r 21 DWE---VVIGIEVHAQLSVVSKLFSGASVNFGA-E-------------------------------------PNTQVSFF 59 (500) Q Consensus 21 ~~e---~vIGLEiH~qL~t~tKlFc~c~~~~~~-~-------------------------------------pNt~v~~~ 59 (500) ||+ +.+|||||+||+|++||||+||+...+ + ++.++|.| T Consensus 5 dy~~lgLKvGLEIHqQLdT~~KLFC~Cpt~~~~~E~~~~f~R~Lrpt~SElGevD~AA~~E~~r~R~f~Y~~~~d~tCLV 84 (631) T COG2511 5 DYEELGLKVGLEIHQQLDTKRKLFCRCPTELRDGEPDFEFERYLRPTRSELGEVDPAALEESKRGRKFIYEAYYDTTCLV 84 (631) T ss_pred CHHHHCCEECEEEHHHHCCCCCEECCCCCCCCCCCCCCEEEEEECCCHHHHCCCCHHHHHHHHHCCEEEEEECCCCCEEE T ss_conf 76774640000201001677643336986445687674167763453666355478889998756668998137863565 Q ss_pred HCC-CCCCCCCCCHHHHHHHHHHHHHHCCEECCCCEEECCCEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEE Q ss_conf 026-8988873789999999998778297624420131132123767888201445442015338999706777774103 Q gi|254780979|r 60 DAA-MPGMLPILNGRCVQQAVMTGLGLNAHINKYSVFARKNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRT 138 (500) Q Consensus 60 ~~g-~PG~lP~lN~~av~~ai~~~~al~~~i~~~~~fdRK~YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~~~ 138 (500) -+- .|- .-+|++|+..|+.+|++|||+|.++++.|||.+.+++|+.|||+|.. |+.||+++++.| T Consensus 85 E~DEEPP--h~~neeAl~iAl~Va~lln~~iVDei~vMRKiVIDGSNTsGFQRTai---va~~G~iets~g--------- 150 (631) T COG2511 85 EADEEPP--HEPNEEALAIALAVAKLLNMDIVDEIHVMRKIVIDGSNTSGFQRTAI---VAIGGYIETSEG--------- 150 (631) T ss_pred ECCCCCC--CCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCCCCCEEEEE---EEECCEEECCCC--------- T ss_conf 5478999--99898999999999998389740104677788861687755112578---851765535888--------- Q ss_pred EEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEC Q ss_conf 79842366652023100115678714886615786125763036527789999999999999864204567643220112 Q gi|254780979|r 139 IEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRA 218 (500) Q Consensus 139 ~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~ 218 (500) +|+|..+|||||||+.+.+.++.. .+.++|+|+|||||.|+||++||++|++.++.|+.+||.+|.+..++ |++|| T Consensus 151 -~V~I~tlclEEDAARKIee~~~~V-vYsLDRLGIPLiEIsT~PdI~sp~~A~evA~~IG~~lrsTGkvKrgl--gTIRQ 226 (631) T COG2511 151 -PVGIETLCLEEDAARKIEEKGDTV-VYSLDRLGIPLIEISTEPDIRSPEQAREVAERIGYILRSTGKVKRGL--GTIRQ 226 (631) T ss_pred -CCCCEEEEECHHHHHHHHCCCCEE-EEEECCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC--CCEEE T ss_conf -756413662377766654058738-99721368744884268888997999999999879999835512367--64000 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH------------------------------------ Q ss_conf 57543213766678862223540246599999999999999731------------------------------------ Q gi|254780979|r 219 DVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILE------------------------------------ 262 (500) Q Consensus 219 DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~------------------------------------ 262 (500) |||||| .+|+|||||+++++..|++.|+||+.||.+||+ T Consensus 227 DvNvSI-----~~GarvEIKGVq~LdlI~~vv~yEv~RQ~nLlkirdeL~~RG~~~~~~~~~DVTdlF~~TkSkiI~~~l 301 (631) T COG2511 227 DVNVSI-----KGGARVEIKGVQDLDLIPDVVEYEVERQLNLLKIRDELKERGGADVSEEVFDVTDLFANTKSKIIRSGL 301 (631) T ss_pred EEEEEE-----CCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHCCCCHHHHHHHH T ss_conf 002553-----387168862740566678999999999988999999999735530014445289886557318888754 Q ss_pred -CCC---------------------------------------------------------------------------- Q ss_conf -398---------------------------------------------------------------------------- Q gi|254780979|r 263 -DGG---------------------------------------------------------------------------- 265 (500) Q Consensus 263 -~G~---------------------------------------------------------------------------- 265 (500) +|| T Consensus 302 ~~gG~V~A~~l~~f~GlvG~EiqpGrRlGtE~AD~ar~~GvgGlfHsDELP~YGITeeEV~~v~~~lga~~~Davvlva~ 381 (631) T COG2511 302 KKGGKVYAVLLPGFAGLVGREIQPGRRLGTEFADYARAYGVGGLFHSDELPGYGITEEEVEAVRDALGAGEEDAVVLVAG 381 (631) T ss_pred CCCCEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEEC T ss_conf 24876999974775652230025774103578999998277751005667567879999999999847997774899707 Q ss_pred ---------------------CCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHH Q ss_conf ---------------------00344323375543366530356677778332778773126999999988530248368 Q gi|254780979|r 266 ---------------------HIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDA 324 (500) Q Consensus 266 ---------------------~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~ 324 (500) -|..|||+-.++ |+|.+||+.++++ ||||||||||+.|++++++.++..+||+|++ T Consensus 382 ~~~~~~~a~~~V~~Ra~~ai~gvpeETR~a~~D-GtT~yLRPlPGaa--RMYPETDIPpi~i~~~~l~~~~~~~Pe~~~e 458 (631) T COG2511 382 EEERAKRALEAVIERAKEAIEGVPEETRGALPD-GTTVYLRPLPGAA--RMYPETDIPPIRIDEELLEKIKENLPELPEE 458 (631) T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCHHHCCCCCC-CCCEEECCCCCCC--CCCCCCCCCCEECCHHHHHHHHHHCCCCHHH T ss_conf 788999999999999999871797766357889-8703515799854--5687678997205889987766437878799 Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHC Q ss_conf 9886432026889998887641136789886402-430245777765457887643387400064898999999988863 Q gi|254780979|r 325 KRERFIGEFGISLYDASVLVSDKSIADYFEKLAV-NRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIID 403 (500) Q Consensus 325 ~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v~~-~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~ 403 (500) +.+||+.+||||.+.|++++++..+ +.||++.. +.+|+.+|..+++.+. .|.+.+..++ +++-+|+.+++.++.+ T Consensus 459 k~~r~~~eygLs~~LA~~~~~~~~~-~~FEel~e~~v~p~~~A~~L~~~~~-~L~reg~~i~--~l~~~~i~~~~~~~~~ 534 (631) T COG2511 459 KVERYVKEYGLSKELAEQLASDPRV-DLFEELVEKGVDPTLIASTLVNTLP-ELRREGVEID--NLDDEHIEELLRLVSE 534 (631) T ss_pred HHHHHHHHHCCCHHHHHHHHHCHHH-HHHHHHHHCCCCHHHHHHHHHHHHH-HHHHCCCCCC--CCCHHHHHHHHHHHHC T ss_conf 9999999849779999999742048-9999999747877899999998779-9985687466--6667999999999862 Q ss_pred CCCCHHHHHHHHHHHHHC-CCCHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHHHHHHHHCCC Q ss_conf 873147899999999817-9998899996398761898899999999998399989975272132265899999972897 Q gi|254780979|r 404 GTISGKIAKDIFNILWEK-GGTPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIATKPNLVSWFVGQVMKNTGGK 482 (500) Q Consensus 404 g~Is~~~aK~il~~l~~~-~~~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~kgk~ka~gfLvGqVMK~tkGk 482 (500) |+|+..++.++|..|..+ +.++.+++++.||...+ .+|++.+|++++..|-+.+.+.+ ++++|++||+||++++|+ T Consensus 535 g~iake~iee~l~~l~~~p~~~~~~~~~~~gL~~ls-~eEve~iI~eii~~~~d~i~~rg--~~a~g~lmg~~M~~~rg~ 611 (631) T COG2511 535 GKIAKEAIEEILKALAENPGKDAAEIAEKLGLKELS-EEEVEKIIDEIIESNLDVIKERG--MGAMGLLMGRVMAKLRGR 611 (631) T ss_pred CCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHHHHHHHHC--HHHHHHHHHHHHHHHHCC T ss_conf 520099999999999848898999999872633279-99999999999974378998712--226899999999986065 Q ss_pred CCHHHHHHHHHHHHC Q ss_conf 788999999999707 Q gi|254780979|r 483 ANPSIVQKMLKEKLG 497 (500) Q Consensus 483 Adpk~v~~lL~e~L~ 497 (500) |||++|+++|+++|. T Consensus 612 aDgk~v~e~l~~~i~ 626 (631) T COG2511 612 ADGKLVSEILREKLQ 626 (631) T ss_pred CCCHHHHHHHHHHHH T ss_conf 780899999999999 No 8 >TIGR00134 gatE_arch glutamyl-tRNA(Gln) amidotransferase, subunit E; InterPro: IPR004414 The aspartyl-tRNA(Asn) amidotransferase, B subunit or designated here gatB_rel, is found only in the archaea. It is paralogous to the gatB-encoded subunit of Glu-tRNA(Gln) amidotransferase. The GatABC system operates in many bacteria to convert Glu-tRNA(Gln) into Gln-tRNA(Gln). However, the homologous system in archaea instead converts Asp-tRNA(Asn) to Asn-tRNA(Asn). Glu-tRNA(Gln) is converted to Gln-tRNA(Gln) by a heterodimeric amidotransferase of GatE (this protein) and GatD. The Archaea have an Asp-tRNA(Asn) amidotransferase instead of an Asp--tRNA ligase, but the genes have not been identified. It is likely that this protein replaces gatB in Asp-tRNA(Asn) amidotransferase but that both enzymes share gatA . ; GO: 0016884 carbon-nitrogen ligase activity with glutamine as amido-N-donor, 0006412 translation. Probab=100.00 E-value=0 Score=422.98 Aligned_cols=446 Identities=28% Similarity=0.418 Sum_probs=384.2 Q ss_pred CCCEE---EEEEEEEEECCCCCCCCCCCCCC-CCCC-CC-------------------------------------CCCH Q ss_conf 80338---98999788868986555884246-8987-65-------------------------------------2061 Q gi|254780979|r 21 DWEVV---IGIEVHAQLSVVSKLFSGASVNF-GAEP-NT-------------------------------------QVSF 58 (500) Q Consensus 21 ~~e~v---IGLEiH~qL~t~tKlFc~c~~~~-~~~p-Nt-------------------------------------~v~~ 58 (500) +|+.+ +|+|||.||+|++|+||.|++.. ..+| |. .+|. T Consensus 3 ~~~~~gl~~g~~~~~~l~~~~~l~c~c~~~~~~~~~~~~~~~~~l~~~~~~~g~~d~~~~~~~~~~~~~~~~~~~~~~cl 82 (631) T TIGR00134 3 DYEKVGLKVGLEIHQQLDTKHKLFCPCPTLLRDDEPSDGEIVRYLRPSLSELGEFDRAALEEAERGKKFIYEFYNDTTCL 82 (631) T ss_pred CHHHHCHHHCHHHHHHHCCCCHHEECCCHHHCCCCCCCCHHHHHHCHHHHHHCHHHHHHHHHHHHHHHHHHHCCCCCEEE T ss_conf 50221102011344330311000001302212455444300101000034401134678888774212221002542024 Q ss_pred HHCCCCCCCCCCCHHHHHHHHHHHHHHCCEECCCCEEECCCEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEE Q ss_conf 30268988873789999999998778297624420131132123767888201445442015338999706777774103 Q gi|254780979|r 59 FDAAMPGMLPILNGRCVQQAVMTGLGLNAHINKYSVFARKNYFYPDLPQGYQISQHDKPIVGEGKVSVSIGPDKSGQFRT 138 (500) Q Consensus 59 ~~~g~PG~lP~lN~~av~~ai~~~~al~~~i~~~~~fdRK~YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~~~~~~~~~~~ 138 (500) +.+...-.. -+|++|+..|+.+++.+|+++.+..+.+||..+.++++.|||.|.+ ++.+|++++.. T Consensus 83 ~~~d~~pp~-~~~~~~l~~~~~~~~~~~~~~~d~~~~~~~~~~dg~~~~g~~~~~~---~~~~g~~~~~~---------- 148 (631) T TIGR00134 83 VEADEEPPH-PPNPEALLIALEVALLLNMEVVDEAHTMRKIVIDGSNTGGFQRTGL---VAFDGYLETPG---------- 148 (631) T ss_pred EECCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHEEE---EEECCEEECCC---------- T ss_conf 432556888-7666788899999988512456667665543112666543100021---23065222476---------- Q ss_pred EEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEC Q ss_conf 79842366652023100115678714886615786125763036527789999999999999864204567643220112 Q gi|254780979|r 139 IEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRA 218 (500) Q Consensus 139 ~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~ 218 (500) .+++|..+|||||+++.+.+. ++...+.++|.|+||+||.|+|++.+|+.++..+..++.++|.+|....++ |++|+ T Consensus 149 ~~~~~~~lcl~~~~~~~~~~~-~~~~~~~ld~lg~pl~~~~~~p~~~~p~~~~~~~~~~g~~l~~~g~~~~gl--g~~~~ 225 (631) T TIGR00134 149 GKVGIASLCLEEDAARKIEDG-GDGVVYNLDRLGIPLVEIGTDPDIDDPELAKEVAARLGEILRSTGKVKRGL--GTIRQ 225 (631) T ss_pred CCEEHHHHHHHHHHHHHHHCC-CCEEEEEECCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHH T ss_conf 520012222203555432025-770466400016530220467776666789999998878876310123200--01222 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC--------------------------------- Q ss_conf 57543213766678862223540246599999999999999731398--------------------------------- Q gi|254780979|r 219 DVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILEDGG--------------------------------- 265 (500) Q Consensus 219 DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~~G~--------------------------------- 265 (500) |+|+|++. |.|+|+|+++.+..+.+.+++|+.||.++++... T Consensus 226 d~~~~~~d-----g~~~~~~g~~~ld~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~ 300 (631) T TIGR00134 226 DLNISIRD-----GARVEVKGVQDLDLLPKIVENEVLRQLNLLKIRDELKERGAEVEEKIFDVTEVFADTKSKIIRNALK 300 (631) T ss_pred CCCEEECC-----CCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 02201126-----7513322530234567887778876666778778887415413455543577753235666643332 Q ss_pred -------------------------------------------------------------------------------- Q ss_conf -------------------------------------------------------------------------------- Q gi|254780979|r 266 -------------------------------------------------------------------------------- 265 (500) Q Consensus 266 -------------------------------------------------------------------------------- 265 (500) T Consensus 301 ~~~g~~~~~~l~g~~g~~g~~~~pg~~lg~~~~d~~~~~~g~~g~~~~d~lp~~g~~~~~~~~l~~~~~~~~~d~~~~~~ 380 (631) T TIGR00134 301 KKNGKVKAVLLRGFGGLVGKEIQPGRRLGTEFADYAKTYAGVGGLFHTDELPAYGITEEEVKGLRDAVGAEEGDAVVLVA 380 (631) T ss_pred HCCCCEEEEEECCCCCCCCCCCCCCCHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEC T ss_conf 01453212211022320133126630101035555555420243111222443467678887777750666676268851 Q ss_pred ----------------------CCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHH Q ss_conf ----------------------0034432337554336653035667777833277877312699999998853024836 Q gi|254780979|r 266 ----------------------HIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPD 323 (500) Q Consensus 266 ----------------------~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~ 323 (500) .+..+||... ..|.|..+|+-+++. |+|||+|+||+.+.+++++.++.++|++|. T Consensus 381 ~~~~~~~~~l~~~~~~~~~~~~g~p~~~~~~~-~dg~~~~l~plp~~~--~~~~~~d~p~~~~~~~~~~~~~~~~p~l~~ 457 (631) T TIGR00134 381 GEEVKVERALREVIERAKEALVGVPEETRKAL-EDGNTAYLRPLPGAA--RMYPETDIPPVVIEEELLEGIRANLPELPE 457 (631) T ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCHHHHHCC-CCCCCHHHCCCCCCH--HHCCCCCCCCEEEHHHHHHHHHHHCCCCHH T ss_conf 50345778999999876676505852454215-576510102476300--002123666202107787677642010036 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCC---CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH Q ss_conf 898864320268899988876411367898864024---30245777765457887643387400064898999999988 Q gi|254780979|r 324 AKRERFIGEFGISLYDASVLVSDKSIADYFEKLAVN---RDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDL 400 (500) Q Consensus 324 ~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v~~~---~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~l 400 (500) ++.+|+..+|+++.+.+..++. ..+.+.|+.++.. .+|..++..+... +..+++.+.+++. +...++...+.+ T Consensus 458 ~~~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~g~~~~~--l~~~~~~~~~~~ 533 (631) T TIGR00134 458 EKAERFKKEYGLPDDLAWELVD-SPYVDLFEDLCEKFKNVDPTVIATLLEGT-LKELRREGYDIDG--LEDRHLRDALKL 533 (631) T ss_pred HHHHHHHHHHCCCHHHHHHHHH-HHHHHHHHHHHHHHHCCCHHHHHHHHHHH-HHHHHHCCCCCCC--CCHHHHHHHHHH T ss_conf 7888888761473567888875-46788899998874044336778888876-8987531552000--214678999988 Q ss_pred HHCCCCCHHHHHHHHHHHHHCCCCH-HHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 8638731478999999998179998-899996398761898899999999998399989975272132265899999972 Q gi|254780979|r 401 IIDGTISGKIAKDIFNILWEKGGTP-KEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIATKPNLVSWFVGQVMKNT 479 (500) Q Consensus 401 i~~g~Is~~~aK~il~~l~~~~~~p-~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~kgk~ka~gfLvGqVMK~t 479 (500) +..|+|+...+.+++..+...+... ....+-.|+...+ .++++.++.+++.++.+.+.+.+ .+++|++||++|+.. T Consensus 534 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~-~~~~~~~~~~~~~~~~~~~~~~g--~~~~~~l~g~~~~~~ 610 (631) T TIGR00134 534 LLEGKIAKEGLEEVLKGLCEEPDKAEDAAGELKGLKLLA-EEEIEGIIEGLIEENLDLIAERG--EGAFGPLMGLAMGKL 610 (631) T ss_pred HHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHC--CHHHHHHHHHHHHHH T ss_conf 862011256799999986216613567777643233100-56788999998654555655403--202467888888874 Q ss_pred CCCCCHHHHHHHHHHHHCC Q ss_conf 8977889999999997078 Q gi|254780979|r 480 GGKANPSIVQKMLKEKLGI 498 (500) Q Consensus 480 kGkAdpk~v~~lL~e~L~~ 498 (500) +|++|++.++++|+++|.. T Consensus 611 ~g~~dg~~~~~~l~~~~~~ 629 (631) T TIGR00134 611 RGKADGKVVNDILRKKLKE 629 (631) T ss_pred HCCCCHHHHHHHHHHHHHH T ss_conf 0211046889999998762 No 9 >pfam02637 GatB_Yqey GatB domain. This domain is found in GatB. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB, which transamidates Glu-tRNA to Gln-tRNA. Probab=100.00 E-value=1.2e-34 Score=275.62 Aligned_cols=146 Identities=50% Similarity=0.853 Sum_probs=141.2 Q ss_pred HHHHHHH-CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHH Q ss_conf 8988640-243024577776545788764338740006489899999998886387314789999999981799988999 Q gi|254780979|r 351 DYFEKLA-VNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIV 429 (500) Q Consensus 351 ~~FE~v~-~~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~ii 429 (500) +|||+++ ...+|+.+|||+++|++++||+.+.++++++++|++|++|+.++++|+||.++||+||+.|+.++++|.+++ T Consensus 1 d~FE~~~~~~~~~k~aanwi~~el~~~l~~~~~~~~~~~i~~~~la~li~lv~~g~Is~~~ak~vl~~~~~~~~~~~~ii 80 (148) T pfam02637 1 DFFEEAVKAGADPKLAANWLLGELLGYLNKEGLDIDESPLTPEHLAELIKLIDEGTISGKIAKEVLEELLENGKSPEEIV 80 (148) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHH T ss_conf 97899988079899999999999999997779986637989999999999998699768999999999987699879999 Q ss_pred HHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHH-CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 963987618988999999999983999899752-7213226589999997289778899999999970 Q gi|254780979|r 430 EELGLRQVTDLSAIEKVVDEVINSNPNNVARIA-TKPNLVSWFVGQVMKNTGGKANPSIVQKMLKEKL 496 (500) Q Consensus 430 e~~gL~~isD~~eL~~iv~eVI~~np~~V~~~k-gk~ka~gfLvGqVMK~tkGkAdpk~v~~lL~e~L 496 (500) +++||.+++|+++|+.+|++||++||++|++|+ ||++++|||||||||+|||||||+.|+++|+++| T Consensus 81 ~~~gl~~i~d~~~l~~iv~~vi~~np~~v~~yk~Gk~k~~~~lvGqvMK~tkGkadp~~v~~~l~e~L 148 (148) T pfam02637 81 EEKGLVQISDEEELEKIVDEVIAENPKAVEDYKSGKEKALGFLVGQVMKKTRGKADPKLVNELLKEKL 148 (148) T ss_pred HHCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHC T ss_conf 88197646888999999999999899999999837677899999999998579989999999999659 No 10 >smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism. Probab=100.00 E-value=4.1e-34 Score=271.72 Aligned_cols=145 Identities=51% Similarity=0.866 Sum_probs=139.9 Q ss_pred HHHHHH-CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHH Q ss_conf 988640-2430245777765457887643387400064898999999988863873147899999999817999889999 Q gi|254780979|r 352 YFEKLA-VNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVE 430 (500) Q Consensus 352 ~FE~v~-~~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie 430 (500) |||+++ .+.+|+.+|||+++|++++||+.+.++++++++|++|++|+.++++|+||.++||+||..|+.++++|.++++ T Consensus 1 ~Fe~~~~~~~~~k~~anwi~~el~~~ln~~~~~i~~~~i~~~~la~li~lv~~g~Is~~~ak~il~~~~~~~~~~~~ii~ 80 (147) T smart00845 1 YFEEVVKAGADPKLAANWLLGELLGELNKEGLEIEESPITPEHLAELLKLIEDGTISGKIAKEVLEELLESGKSPEEIVE 80 (147) T ss_pred CHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHH T ss_conf 96889770799999999999999999847799856378799999999999986997589899999999873688899998 Q ss_pred HCCCEECCCHHHHHHHHHHHHHHCHHHHHHHH-CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 63987618988999999999983999899752-7213226589999997289778899999999970 Q gi|254780979|r 431 ELGLRQVTDLSAIEKVVDEVINSNPNNVARIA-TKPNLVSWFVGQVMKNTGGKANPSIVQKMLKEKL 496 (500) Q Consensus 431 ~~gL~~isD~~eL~~iv~eVI~~np~~V~~~k-gk~ka~gfLvGqVMK~tkGkAdpk~v~~lL~e~L 496 (500) ++||.++||+++|+.+|++||++||++|++|+ ||++++|||||||||+|||||||+.|+++|+++| T Consensus 81 ~~gl~~isd~~~l~~lv~~ii~~n~~~v~~~~~Gk~k~~~~lvGqvMK~tkGkadp~~v~~ll~e~L 147 (147) T smart00845 81 EKGLKQISDEGELEAIVDEVIAENPKAVEDYRAGKKKALGFLVGQVMKATRGKADPKLVNELLKEKL 147 (147) T ss_pred HCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHC T ss_conf 8297546883899999999999899999999877488899999999998679989999999999659 No 11 >pfam01162 consensus Probab=99.84 E-value=1.6e-21 Score=179.01 Aligned_cols=69 Identities=55% Similarity=0.935 Sum_probs=66.9 Q ss_pred EEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 665303566777783327787731269999999885302483689886432026889998887641136 Q gi|254780979|r 281 TRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDKSI 349 (500) Q Consensus 281 T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~~l 349 (500) |++||+||+++||||||||||||+.|+++||+.++.+|||||+++++||+++|||+.++|.+|++++.+ T Consensus 1 T~~mR~KE~a~DYRyfPePDLppi~i~~~~i~~ik~~lPElP~~~~~r~~~~ygL~~~dA~~L~~~~~l 69 (69) T pfam01162 1 TVIMRAKEEAEDYRYFPEPDLPPLNITDELIEEIRATLPELPDEKRERLVKEYGLSEEDAQTLVSDKEL 69 (69) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCC T ss_conf 976656576446580789987886689999999999489999999999999939699999999726669 No 12 >pfam09424 YqeY Yqey-like protein. The function of this domain found in the YqeY protein is uncertain. Probab=97.81 E-value=0.00025 Score=52.34 Aligned_cols=113 Identities=19% Similarity=0.219 Sum_probs=73.6 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHH-HHHHCCCCCHHHHHHHHHHHHHCCC--------CHHHHHHHCCCE Q ss_conf 7777654578876433874000648989999999-8886387314789999999981799--------988999963987 Q gi|254780979|r 365 VANWVINDLLGVLNRSGKSIEDTPISPNQLGELI-DLIIDGTISGKIAKDIFNILWEKGG--------TPKEIVEELGLR 435 (500) Q Consensus 365 ~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi-~li~~g~Is~~~aK~il~~l~~~~~--------~p~~iie~~gL~ 435 (500) +...+.+++...-...+ ..++.+.+..+| .++.+. ++-++.+-..|- .=-+|+++.=.. T Consensus 22 ~lR~i~saik~~ei~~~-----~~l~D~~v~~ii~k~vKqr-------kes~e~y~~agR~dlae~e~~Ei~il~~yLP~ 89 (143) T pfam09424 22 TLRMLKAAIKQEEVDER-----IELSDEEVLTVLAKEVKQR-------RESIEQFEKAGRQDLAEKEKAEIAILEEYLPQ 89 (143) T ss_pred HHHHHHHHHHHHHHHCC-----CCCCHHHHHHHHHHHHHHH-------HHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 99999999989986579-----9999999999999999978-------99999998869866899999999999974633 Q ss_pred ECCCHHHHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 6189889999999999839998997527213226589999997289778899999999970 Q gi|254780979|r 436 QVTDLSAIEKVVDEVINSNPNNVARIATKPNLVSWFVGQVMKNTGGKANPSIVQKMLKEKL 496 (500) Q Consensus 436 ~isD~~eL~~iv~eVI~~np~~V~~~kgk~ka~gfLvGqVMK~tkGkAdpk~v~~lL~e~L 496 (500) |+| +++++.+|.++|+++.- ...+-+|..||.+|+..+|+||++.|++++++.| T Consensus 90 qls-eeEl~~~i~~~i~e~ga------~~~kdmGkVM~~l~~~~~G~~Dg~~vs~iVk~~L 143 (143) T pfam09424 90 QLS-DEEIEALVDEAIAEVGA------TSMKDMGKVMGALMPKVAGRADGKLVSALVKELL 143 (143) T ss_pred CCC-HHHHHHHHHHHHHHHCC------CCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHC T ss_conf 699-99999999999998389------9858899999999987588687799999998629 No 13 >pfam04558 tRNA_synt_1c_R1 Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1. This is a region found N terminal to the catalytic domain of glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes but not in Escherichia coli. This region is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function. Probab=97.25 E-value=0.027 Score=37.38 Aligned_cols=152 Identities=16% Similarity=0.187 Sum_probs=97.8 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCC-----CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHH Q ss_conf 6898864320268899988876411367898864024-----30245777765457887643387400064898999999 Q gi|254780979|r 323 DAKRERFIGEFGISLYDASVLVSDKSIADYFEKLAVN-----RDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGEL 397 (500) Q Consensus 323 ~~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v~~~-----~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeL 397 (500) ++..+.| .+.||++.-|.-++.++.++.-+..+... .-++...+.+ ..+...++. -...+..-| T Consensus 4 eel~~lF-~~iGL~e~kAketlKN~k~t~~L~~ii~ea~~~~~~dk~~g~LL-y~lAtk~k~---------~~~~~~~~i 72 (164) T pfam04558 4 EELLKLF-SKIGLDEKKAKETLKNKKVSASLLAIIAEAGATSGCDKKTGALL-YNLATKLKG---------NEVPHRPLI 72 (164) T ss_pred HHHHHHH-HHCCCCHHHHHHHHHCHHHHHHHHHHHHHCCCCCCCCHHHHHHH-HHHHHHCCC---------CCCHHHHHH T ss_conf 9999999-98598714599998389999999999997565567887899999-999986565---------321207999 Q ss_pred HHHHHCCCCCH-HHHHHHHHHHHHCCC---CHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHH Q ss_conf 98886387314-789999999981799---98899996398761898899999999998399989975272132265899 Q gi|254780979|r 398 IDLIIDGTISG-KIAKDIFNILWEKGG---TPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIATKPNLVSWFVG 473 (500) Q Consensus 398 i~li~~g~Is~-~~aK~il~~l~~~~~---~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~kgk~ka~gfLvG 473 (500) +..|-+|+|.. .+.-..|.-+...+. +..++-++.|-..+-..++++..|+++|++|.+.+..-|-+.=-+|.++| T Consensus 73 v~yI~~~kikT~~Qv~aA~~Yl~~~~~~~id~~~fe~~cGVGV~VT~eqI~~~V~~~i~~~k~~i~~~RY~~~n~g~~~~ 152 (164) T pfam04558 73 VSYIVDGKLKTTLQVDAALKYLKSNGSEAFDVAEFEEACGVGVVVTPEDVERAVADYIEENKEEILEKRYKLFNVGLLLV 152 (164) T ss_pred HHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCEEECHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH T ss_conf 99998566897999999999999779988888999997799868889999999999999969999986223565167888 Q ss_pred HHHHHHCCCCCHH Q ss_conf 9999728977889 Q gi|254780979|r 474 QVMKNTGGKANPS 486 (500) Q Consensus 474 qVMK~tkGkAdpk 486 (500) ++....|= |||+ T Consensus 153 ~~r~~LkW-Ad~k 164 (164) T pfam04558 153 KARPELKW-ADPK 164 (164) T ss_pred HHHCCCCC-CCCC T ss_conf 76115899-8989 No 14 >KOG1148 consensus Probab=96.79 E-value=0.066 Score=34.48 Aligned_cols=19 Identities=16% Similarity=0.557 Sum_probs=12.3 Q ss_pred HHHHHHHHHHHHHHHHHCC Q ss_conf 9999999999999864204 Q gi|254780979|r 188 LEAKAFLTKLRSILRYLGT 206 (500) Q Consensus 188 ~ea~~~~~~l~~ilr~~gi 206 (500) .|...|...|..++..+|- T Consensus 294 kEee~yf~sI~e~V~WLG~ 312 (764) T KOG1148 294 KEEEEYFESIKEMVAWLGF 312 (764) T ss_pred HHHHHHHHHHHHHHHHHCC T ss_conf 3368999999999987187 No 15 >COG1610 Uncharacterized conserved protein [Function unknown] Probab=96.05 E-value=0.024 Score=37.75 Aligned_cols=97 Identities=19% Similarity=0.217 Sum_probs=64.0 Q ss_pred CCCCHHHHHHHH-HHHHCCCCCHHHHHHHHHHHHHCCC-C-------HHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHH Q ss_conf 648989999999-8886387314789999999981799-9-------889999639876189889999999999839998 Q gi|254780979|r 387 TPISPNQLGELI-DLIIDGTISGKIAKDIFNILWEKGG-T-------PKEIVEELGLRQVTDLSAIEKVVDEVINSNPNN 457 (500) Q Consensus 387 ~~i~p~~laeLi-~li~~g~Is~~~aK~il~~l~~~~~-~-------p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~ 457 (500) .+++.+.+-.++ +++.+ -++.+..+-+.+- + --.|+++.-..|.+ +++|..+|+++|++--. T Consensus 43 ~~l~d~~il~vl~k~iKQ-------RrdS~~~y~~agR~dLa~kE~~Ei~Ii~~ylP~qLs-d~e~~~~v~~aIae~Ga- 113 (148) T COG1610 43 DELDDEEILKVLAKEIKQ-------RRDSAEEYEKAGRQDLAAKERAEIAIIEEYLPQQLS-EDELRALVDAAIAEVGA- 113 (148) T ss_pred CCCCHHHHHHHHHHHHHH-------HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHHH- T ss_conf 889869999999999998-------789999998768487999999499999986764689-89999999999999877- Q ss_pred HHHHHCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHC Q ss_conf 9975272132265899999972897788999999999707 Q gi|254780979|r 458 VARIATKPNLVSWFVGQVMKNTGGKANPSIVQKMLKEKLG 497 (500) Q Consensus 458 V~~~kgk~ka~gfLvGqVMK~tkGkAdpk~v~~lL~e~L~ 497 (500) ...+-+|..||..|-..+|+||++.|+.++++.|. T Consensus 114 -----s~~~dMGkvM~al~~k~~GkaD~~~vs~~VK~~L~ 148 (148) T COG1610 114 -----SSMKDMGKVMKALKPKVAGKADGGRVSKLVKELLS 148 (148) T ss_pred -----HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHC T ss_conf -----21888999999881885266838899999998729 No 16 >TIGR00838 argH argininosuccinate lyase; InterPro: IPR009049 This entry represents argininosuccinate lyase, but may include examples of avian delta crystallins, in which argininosuccinate lyase activity may or may not be present and the biological role is to provide the optically clear cellular protein of the eye lens. ; GO: 0004056 argininosuccinate lyase activity, 0042450 arginine biosynthetic process via ornithine. Probab=88.09 E-value=1.3 Score=25.00 Aligned_cols=119 Identities=15% Similarity=0.235 Sum_probs=77.1 Q ss_pred CCCHHHHHHHHHHHHHHHH----------HHCCC--------CCCCCCCCHHHHHHHHH--HHHCCCCCHHHHHH-HHHH Q ss_conf 4302457777654578876----------43387--------40006489899999998--88638731478999-9999 Q gi|254780979|r 359 NRDKKIVANWVINDLLGVL----------NRSGK--------SIEDTPISPNQLGELID--LIIDGTISGKIAKD-IFNI 417 (500) Q Consensus 359 ~~~pk~~Anwi~~el~~~l----------n~~~~--------~~~~~~i~p~~laeLi~--li~~g~Is~~~aK~-il~~ 417 (500) .+.|-..|.|++...--+. ++-+. .-...+|..+.+|+++. .+-++.+-+.++++ |++. T Consensus 158 rAQPi~lAHhLLAY~~~l~RD~~RL~d~~kR~n~SPLGsGAlAGt~f~iDR~~~A~lLGF~~~~~NSlDaVSdRDFi~E~ 237 (469) T TIGR00838 158 RAQPITLAHHLLAYAEMLERDYERLQDALKRVNVSPLGSGALAGTSFPIDREYTAELLGFDAVTENSLDAVSDRDFIIEL 237 (469) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCCCHHHHHHHCCHHHHHHCCHHHHHHHHHHHHH T ss_conf 50105699999999989998899999999885048865503206898768888976318678875204665207899999 Q ss_pred HHHC---CCCH----HHHH----HHCCCEECCCHHHHHHHHHHHH--HHCHHHHHHHHCCC-CCHHHHHHHHHHHHCC Q ss_conf 9817---9998----8999----9639876189889999999999--83999899752721-3226589999997289 Q gi|254780979|r 418 LWEK---GGTP----KEIV----EELGLRQVTDLSAIEKVVDEVI--NSNPNNVARIATKP-NLVSWFVGQVMKNTGG 481 (500) Q Consensus 418 l~~~---~~~p----~~ii----e~~gL~~isD~~eL~~iv~eVI--~~np~~V~~~kgk~-ka~gfLvGqVMK~tkG 481 (500) |+.. ..+. +++| .|.|+..++|+=. -=-+++ .+|||..|-+|||. +++|=|+|..| -.|| T Consensus 238 l~~~a~~m~hLSR~aEelIlw~s~EFgfieL~D~~s---tGSSiMPQKKNPD~aELiRGK~Grv~G~L~g~L~-~lKa 311 (469) T TIGR00838 238 LFVAALIMVHLSRLAEELILWSSQEFGFIELPDEFS---TGSSIMPQKKNPDVAELIRGKTGRVIGNLTGLLT-ILKA 311 (469) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCEE---ECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH-HHHH T ss_conf 999999974176898999998446876067457320---0576888877720799998755268999999999-9711 No 17 >COG3937 Uncharacterized conserved protein [Function unknown] Probab=75.37 E-value=6.8 Score=19.66 Aligned_cols=64 Identities=19% Similarity=0.406 Sum_probs=43.3 Q ss_pred CCCCCHHHHHHHHH-HHHCCCCCHHHHHHHHHHHHHCCCC---------H---HHHHHHCCCEECCCHHHHHHHHHH Q ss_conf 06489899999998-8863873147899999999817999---------8---899996398761898899999999 Q gi|254780979|r 386 DTPISPNQLGELID-LIIDGTISGKIAKDIFNILWEKGGT---------P---KEIVEELGLRQVTDLSAIEKVVDE 449 (500) Q Consensus 386 ~~~i~p~~laeLi~-li~~g~Is~~~aK~il~~l~~~~~~---------p---~~iie~~gL~~isD~~eL~~iv~e 449 (500) ....+.+++.+|++ ||..|+||...||.++..++...+. | ..++.+.++.+-|+-.++..=|+. T Consensus 18 ~~a~~~ek~~klvDelVkkGeln~eEak~~vddl~~q~k~~~~e~e~K~~r~i~~ml~~~~~~r~~~~~~l~~rvd~ 94 (108) T COG3937 18 LAAETAEKVQKLVDELVKKGELNAEEAKRFVDDLLRQAKEAQGELEEKIPRKIEEMLSDLEVARQSEMDELTERVDA 94 (108) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH T ss_conf 89999999999999999827878999999999999998987602777636899999845020000248888989999 No 18 >cd07363 45_DOPA_Dioxygenase The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine. This subfamily is composed of plant 4,5-DOPA Dioxygenase, the uncharacterized Escherichia coli protein Jw3007, and similar proteins. 4,5-DOPA Dioxygenase catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine (4,5-DOPA). The reaction results in the opening of the cyclic ring between carbons 4 and 5 and producing an unstable seco-DOPA that rearranges to betalamic acid. 4,5-DOPA Dioxygenase is a key enzyme in the biosynthetic pathway of the plant pigment betalain. Homologs of DODA are present not only in betalain-producing plants but also in bacteria and archaea. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated ca Probab=71.50 E-value=4.5 Score=20.96 Aligned_cols=43 Identities=19% Similarity=0.280 Sum_probs=30.1 Q ss_pred HHHHHHHC-CCCCCC-CCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCH Q ss_conf 99997313-980034-432337554336653035667777833277877312699 Q gi|254780979|r 256 RQIAILED-GGHIRQ-ETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDE 308 (500) Q Consensus 256 RQ~~ll~~-G~~v~q-ETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~ 308 (500) |=.++|.. |-.+.. .+|+|| -|..++|+ .||||.|+|-|.||- T Consensus 85 ~i~~~L~~~gi~~~~d~~rGlD--HG~wvpL~--------~m~P~adiPVvqlSl 129 (253) T cd07363 85 RVAELLKAAGIPARLDPERGLD--HGAWVPLK--------LMYPDADIPVVQLSL 129 (253) T ss_pred HHHHHHHHCCCCEEECCCCCCC--CCCEEEEE--------EECCCCCCCEEEEEC T ss_conf 9999998649871305766766--55225788--------627899997799755 No 19 >TIGR02407 ectoine_ectB diaminobutyrate--2-oxoglutarate aminotransferase; InterPro: IPR012773 Members of this family of class III pyridoxal-phosphate-dependent aminotransferases are diaminobutyrate--2-oxoglutarate aminotransferase (2.6.1.76 from EC) that catalyze the first step in ectoine biosynthesis from L-aspartate beta-semialdehyde. This family is readily separated phylogenetically from enzymes with the same substrate and product but involved in other process such as siderophore (Q9Z3R2 from SWISSPROT) or 1,3-diaminopropane (P44951 from SWISSPROT) biosynthesis. Ectoine is a compatible solute particularly effective in conferring salt tolerance.; GO: 0030170 pyridoxal phosphate binding, 0047307 diaminobutyrate-pyruvate transaminase activity, 0019491 ectoine biosynthetic process. Probab=68.98 E-value=9.3 Score=18.65 Aligned_cols=68 Identities=15% Similarity=0.262 Sum_probs=47.9 Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHH-HHHHCCCCCHHHHHHHHHHHHCCCCCHH Q ss_conf 478999999998179998899996398761898899999999998399989-9752721322658999999728977889 Q gi|254780979|r 408 GKIAKDIFNILWEKGGTPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNV-ARIATKPNLVSWFVGQVMKNTGGKANPS 486 (500) Q Consensus 408 ~~~aK~il~~l~~~~~~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V-~~~kgk~ka~gfLvGqVMK~tkGkAdpk 486 (500) --+|++.|+.+|. +.+.++-|+++ ...|++..++++++||+.. .+.||+ ||+.|-.+ .++. T Consensus 300 FVtA~aAL~~yW~-Dd~f~~~v~~~-------s~~~~~~l~~~~~~~~~~~~~~~RGR----Glm~Gl~~------~~~~ 361 (413) T TIGR02407 300 FVTATAALEYYWS-DDAFEKAVQRK-------SEIIQERLDEIVAEFPELIEKSVRGR----GLMQGLEC------GDGD 361 (413) T ss_pred HHHHHHHHHHHCC-CHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHCCCCCCCC----CEEEECCC------CCHH T ss_conf 9999999998489-62689999999-------99999999999987455213110452----01420004------7724 Q ss_pred HHHHHHH Q ss_conf 9999999 Q gi|254780979|r 487 IVQKMLK 493 (500) Q Consensus 487 ~v~~lL~ 493 (500) .+.++.+ T Consensus 362 ~A~~i~~ 368 (413) T TIGR02407 362 LAGKIAK 368 (413) T ss_pred HHHHHHH T ss_conf 6899999 No 20 >TIGR01398 FlhA flagellar biosynthesis protein FlhA; InterPro: IPR006301 These sequences describe the flagellar biosynthesis protein FlhA, one of a large number of genes associated with the biosynthesis of functional bacterial flagella. Homologs of many such proteins, including FlhA, function in type III protein secretion systems. ; GO: 0015031 protein transport, 0016021 integral to membrane, 0019861 flagellum. Probab=68.06 E-value=7.1 Score=19.52 Aligned_cols=59 Identities=15% Similarity=0.269 Sum_probs=35.3 Q ss_pred HHHHHHHHHHHHHHHHHCCCCC-CCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHC Q ss_conf 4577776545788764338740-0064898999999988863873147899999999817 Q gi|254780979|r 363 KIVANWVINDLLGVLNRSGKSI-EDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEK 421 (500) Q Consensus 363 k~~Anwi~~el~~~ln~~~~~~-~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~ 421 (500) ..-|-||.....-.....|-++ +...+=+-||.|+|+--...-+|.+.++.+|+.+-++ T Consensus 472 Gl~A~WI~e~~~e~A~~~GYTVVDp~tVlaTHL~E~ik~na~~LL~r~ev~~LLd~l~~~ 531 (713) T TIGR01398 472 GLPAYWIEEKNKEEAERLGYTVVDPATVLATHLSEVIKNNAAELLTRQEVQNLLDRLKEE 531 (713) T ss_pred CCCCEECCHHHHHHHHHCCCEEECCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHH T ss_conf 986121381348999864985870179999999999999898851589999999860132 No 21 >PRK10628 hypothetical protein; Provisional Probab=65.73 E-value=4.1 Score=21.27 Aligned_cols=41 Identities=15% Similarity=0.271 Sum_probs=27.8 Q ss_pred HHHHHCCC-CCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCH Q ss_conf 99731398-0034432337554336653035667777833277877312699 Q gi|254780979|r 258 IAILEDGG-HIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDE 308 (500) Q Consensus 258 ~~ll~~G~-~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~ 308 (500) .++|...+ ....+.|+|| -|..++|+ +||||.|+|-|.+|= T Consensus 77 ~~lL~~~~~~~~~~~~GlD--HG~W~pL~--------~myP~AdiPVVqlSl 118 (246) T PRK10628 77 VELLAPVPVTLDKEAWGFD--HGSWGVLI--------KMYPDADIPMVQLSI 118 (246) T ss_pred HHHHHCCCCCCCCCCCCCC--CCCCHHHH--------HHCCCCCCCEEEEEC T ss_conf 9985146865576556877--54216678--------638899997799756 No 22 >pfam06576 DUF1133 Protein of unknown function (DUF1133). This family consists of a number of hypothetical proteins from Escherichia coli O157:H7 and Salmonella typhi. The function of this family is unknown. Probab=65.28 E-value=11 Score=18.14 Aligned_cols=61 Identities=20% Similarity=0.338 Sum_probs=44.5 Q ss_pred HHHHCCCCCHHHHHHHHHHHHHCCCCH---HHHHHH-------CCCEECCCHHH--HHHHHHHHHHHCHHHHH Q ss_conf 888638731478999999998179998---899996-------39876189889--99999999983999899 Q gi|254780979|r 399 DLIIDGTISGKIAKDIFNILWEKGGTP---KEIVEE-------LGLRQVTDLSA--IEKVVDEVINSNPNNVA 459 (500) Q Consensus 399 ~li~~g~Is~~~aK~il~~l~~~~~~p---~~iie~-------~gL~~isD~~e--L~~iv~eVI~~np~~V~ 459 (500) .|+.+++||.+..+++|..|-++|-+- +++..+ -+|.--+|.+. ++.+|-+|++++|..+. T Consensus 48 ~LLas~klTKtAinealrrmKksGl~k~eLeaflrem~n~K~kS~La~CtD~E~l~iD~VI~~vl~~~pgL~~ 120 (176) T pfam06576 48 QLLASKKLTKTAVNEALRRMKKSGIEKPELEAFFREMLNGKQKSWLAHCTDTEALKIDRVISEVLGEYPGLIS 120 (176) T ss_pred HHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHHHHHHHCCCHHH T ss_conf 9984043139999999999998379808999999998574321364021451567889999999985830999 No 23 >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=64.68 E-value=7.4 Score=19.38 Aligned_cols=123 Identities=21% Similarity=0.384 Sum_probs=78.2 Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHCC--CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 83327787731269999999885302--4836898864320268899988876411367898864024302457777654 Q gi|254780979|r 294 RYFSEPDLLPLEIDEDFIRAIKKQIP--ELPDAKRERFIGEFGISLYDASVLVSDKSIADYFEKLAVNRDKKIVANWVIN 371 (500) Q Consensus 294 RyfPEPDLPpi~is~e~i~~i~~~lP--elP~~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v~~~~~pk~~Anwi~~ 371 (500) -+.|=|++ +..+-.|++.+..-+| |.|-=|-+-|...||+=- ..||+||-++-...-+..+-+++ T Consensus 333 Lf~PfP~a--~~~DtAFfDR~H~YiPGWEIPKmRpEyFT~~YGfiv---------DYlAE~~REmRkrsf~d~idrfF-- 399 (677) T TIGR02653 333 LFAPFPEA--MREDTAFFDRIHYYIPGWEIPKMRPEYFTNRYGFIV---------DYLAEYLREMRKRSFADAIDRFF-- 399 (677) T ss_pred HCCCCHHH--HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHH---------HHHHHHHHHHHCCCHHHHHHHHH-- T ss_conf 30440688--741025675563058887688876442017776035---------67899999852011124555666-- Q ss_pred HHHHHHHHCCCCCCCCCCCHHHHHHHHHHHH-CCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCC Q ss_conf 5788764338740006489899999998886-38731478999999998179998899996398 Q gi|254780979|r 372 DLLGVLNRSGKSIEDTPISPNQLGELIDLII-DGTISGKIAKDIFNILWEKGGTPKEIVEELGL 434 (500) Q Consensus 372 el~~~ln~~~~~~~~~~i~p~~laeLi~li~-~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL 434 (500) .|-..||.++.-- + -.-++-|++|+. ++.+|+..++++|+.-+++--.++|=.++.|- T Consensus 400 klGnnLNqRDViA----V-rkTvSGL~KLlyP~~~~tk~~~~~~l~yalegRRRVKEQLKK~Gg 458 (677) T TIGR02653 400 KLGNNLNQRDVIA----V-RKTVSGLLKLLYPDGEYTKDDVREILDYALEGRRRVKEQLKKLGG 458 (677) T ss_pred HHCCCCCCCCHHH----H-HHHHCEEEEEECCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHCC T ss_conf 5123233231321----2-110010000126885568799999988762356203666643067 No 24 >pfam12570 DUF3750 Protein of unknown function (DUF3750). This family of proteins is found in bacteria. Proteins in this family are typically between 175 and 265 amino acids in length. Probab=63.98 E-value=5.1 Score=20.58 Aligned_cols=29 Identities=28% Similarity=0.550 Sum_probs=24.5 Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHH Q ss_conf 67777833277877312699999998853024836 Q gi|254780979|r 289 DALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPD 323 (500) Q Consensus 289 ~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~ 323 (500) -..+||+||-|| |+.|++-|-...|||-- T Consensus 90 ~~~~Yr~wPGPN------SNTFvawv~r~vpel~~ 118 (129) T pfam12570 90 YPNEYRAWPGPN------SNTFVAWVLRQVPELDL 118 (129) T ss_pred CCCCCEECCCCC------HHHHHHHHHHHCHHCCC T ss_conf 889721778997------07799999865810146 No 25 >PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Probab=63.87 E-value=12 Score=17.96 Aligned_cols=105 Identities=15% Similarity=0.136 Sum_probs=56.8 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCC---------HHHHHHHHHHHHHHHHHHCCCC----CCCCCCC Q ss_conf 89886432026889998887641136789886402430---------2457777654578876433874----0006489 Q gi|254780979|r 324 AKRERFIGEFGISLYDASVLVSDKSIADYFEKLAVNRD---------KKIVANWVINDLLGVLNRSGKS----IEDTPIS 390 (500) Q Consensus 324 ~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v~~~~~---------pk~~Anwi~~el~~~ln~~~~~----~~~~~i~ 390 (500) +.+..|++--|+-+..|-.+++.....++.+++..+.. .+..|.-|+.||.+-+.+.... ....... T Consensus 70 ~~F~~Li~V~GIGpK~AL~ILs~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~ 149 (198) T PRK00116 70 ELFRLLISVSGVGPKLALAILSGLSPEELAQAIANGDIKALTKVPGVGKKTAERIVLELKDKLAALADAGAAAAAAASAA 149 (198) T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC T ss_conf 99999856688578999988702999999999985899997068897889999999999988874212455454566777 Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHH Q ss_conf 89999999888638731478999999998179998899 Q gi|254780979|r 391 PNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEI 428 (500) Q Consensus 391 p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~i 428 (500) ...+.+++..+.+=-.+...++.++..+...+.+.+++ T Consensus 150 ~~~~~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~eel 187 (198) T PRK00116 150 NDALEEAVSALVALGYKPKEAQKAVAAILKEGASVEEL 187 (198) T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHH T ss_conf 52599999999985999999999999864369999999 No 26 >COG3384 Aromatic ring-opening dioxygenase, catalytic LigB subunit related enzyme [Amino acid transport and metabolism] Probab=63.46 E-value=8.2 Score=19.06 Aligned_cols=100 Identities=17% Similarity=0.168 Sum_probs=55.3 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCC-CC----CCCCCCCHHHHHHH---HHHHH------ Q ss_conf 999999999999986420456764322011257543213766678-86----22235402465999---99999------ Q gi|254780979|r 188 LEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWG-TR----CEVKNVNSIRFLGL---AIEYE------ 253 (500) Q Consensus 188 ~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~G-tR----vEIKNlnS~~~i~~---AI~yE------ 253 (500) ..+....++|++-++- +|.|+=|=+..+=...| +. -.-+.+..|-..+. ++.|. T Consensus 26 n~~~~~l~~lG~~~~e------------~rp~tIiV~SaHw~t~~~~~v~~~e~~~~i~DfygFP~~ly~~~Y~a~G~pe 93 (268) T COG3384 26 NAATRGLRELGRELPE------------LRPDTIIVFSAHWETRGAYHVTASEHPETIHDFYGFPDELYDVKYPAPGSPE 93 (268) T ss_pred CHHHHHHHHHHHHHHH------------CCCCEEEEEECEEEECCCEEEECCCCCCEEECCCCCCHHHHHCCCCCCCCHH T ss_conf 0789999999776566------------0898799983507862743687066766122158898899843379999989 Q ss_pred H-HHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCH Q ss_conf 9-999997313980034432337554336653035667777833277877312699 Q gi|254780979|r 254 A-RRQIAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDE 308 (500) Q Consensus 254 i-~RQ~~ll~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~ 308 (500) . +|=++++...+-..| +-.|.-+-|+.++|| -||||-|+|-|.||- T Consensus 94 La~~i~~~l~~~~v~a~-~~~~gLDHGtwvpL~--------~M~PdadipVV~iSi 140 (268) T COG3384 94 LAQRIVELLAKLGVPAD-APSWGLDHGTWVPLR--------YMFPDADIPVVQISI 140 (268) T ss_pred HHHHHHHHHCCCCCCCC-CCCCCCCCCCEEEEH--------HHCCCCCCCEEEEEC T ss_conf 99999997412586666-876687764333303--------227756896799963 No 27 >PRK11913 phhA phenylalanine 4-monooxygenase; Reviewed Probab=63.38 E-value=5.8 Score=20.20 Aligned_cols=45 Identities=24% Similarity=0.466 Sum_probs=35.7 Q ss_pred CEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC Q ss_conf 336653035667777833277877312699999998853024836898864320268 Q gi|254780979|r 279 NETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI 335 (500) Q Consensus 279 ~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL 335 (500) -.|..+|+.+.-. |-||||+ +-++---.|.|-+.....|...||. T Consensus 104 p~t~~iR~~~~~~---YtpEPDi---------fHe~fGHvP~L~~p~fA~f~~~~G~ 148 (272) T PRK11913 104 PVATFIRTPEELD---YLQEPDI---------FHDVFGHVPLLTNPVFADFMQAYGQ 148 (272) T ss_pred CEEEEECCCCCCC---CCCCCHH---------HHHHHCCCCCCCCHHHHHHHHHHHH T ss_conf 2253435776556---6888437---------8876256742079889999999999 No 28 >PHA01082 putative transcription regulator Probab=62.66 E-value=3 Score=22.26 Aligned_cols=56 Identities=18% Similarity=0.256 Sum_probs=37.2 Q ss_pred EEEEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHH Q ss_conf 3798423666520231001156787148866157861257630365277899999999999998 Q gi|254780979|r 138 TIEVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSIL 201 (500) Q Consensus 138 ~~~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~il 201 (500) +...++..=.||=-+|.++- +...+ .|+.|+||-.++|+......-.|++.|..++ T Consensus 78 W~~f~m~~~rLelPTG~lVt---pQqIL-----tGiALLEIGAe~D~~~~~kiLKyAR~L~~~~ 133 (133) T PHA01082 78 WENFVMRHDRLELPTGDLVT---AQQVL-----IGVALLELGASNDIKVAHQILKYARALKRFI 133 (133) T ss_pred HHHHEEECCEEECCCCCCCC---HHHHH-----HHHHHHCCCCCCCHHHHHHHHHHHHHHHHHC T ss_conf 45452157768768877136---99998-----7766520167610789999999999998639 No 29 >cd03346 eu_TrpOH Eukaryotic tryptophan hydroxylase (TrpOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH) and eukaryotic tyrosine hydroxylase (TyrOH). TrpOH oxidizes L-tryptophan to 5-hydroxy-L-tryptophan, the rate-limiting step in the biosynthesis of serotonin (5-hydroxytryptamine), a widely distributed hormone and neurotransmitter. Probab=61.75 E-value=11 Score=18.07 Aligned_cols=111 Identities=22% Similarity=0.320 Sum_probs=62.9 Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 77899999999999998642045676432201125754321376667886222354024659999999999999973139 Q gi|254780979|r 185 RSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILEDG 264 (500) Q Consensus 185 ~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~~G 264 (500) ....-+++|+.-+..+-+++|...-++ =+++ |||-=+++. +.|. -+-+-++=|.|.--..+.+ T Consensus 80 ~~~~AC~eyl~~~~~L~~~~g~~~d~I--PQl~-dvs~~L~~~-TGf~-l~pV~Gll~~r~F~~~LA~------------ 142 (287) T cd03346 80 YPTHACREYLKNLPLLEKHCGYREDNI--PQLE-DVSRFLKER-TGFT-IRPVAGYLSPRDFLAGLAF------------ 142 (287) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCC--CCHH-HHHHHHHHH-CCCE-EEECCCCCCHHHHHHHHHH------------ T ss_conf 530638999999999998449997789--9779-999999874-1988-9854665788899998731------------ Q ss_pred CCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC Q ss_conf 80034432337554336653035667777833277877312699999998853024836898864320268 Q gi|254780979|r 265 GHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI 335 (500) Q Consensus 265 ~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL 335 (500) |.| -.|..+|..+.- -|-||||+ +-++---+|.|-+.....|..++|+ T Consensus 143 -------r~F----~~TqyIRh~~~p---~YtpEPDi---------~HEl~GHvPlLadp~fA~f~q~iG~ 190 (287) T cd03346 143 -------RVF----HCTQYVRHSSDP---FYTPEPDT---------CHELLGHVPLLADPSFAQFSQEIGL 190 (287) T ss_pred -------CCC----CCEEEECCCCCC---CCCCCCCH---------HHHHHCCCCCCCCHHHHHHHHHHHH T ss_conf -------637----621345258887---77899962---------6566445633379889999999999 No 30 >cd03348 pro_PheOH Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH), tyrosine hydroxylase (TyrOH) and tryptophan hydroxylase (TrpOH). PheOH catalyzes the hydroxylation of L-Phe to L-tyrosine (L-Tyr). It uses (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) as the physiological electron donor. Probab=59.74 E-value=7.9 Score=19.19 Aligned_cols=45 Identities=27% Similarity=0.475 Sum_probs=36.2 Q ss_pred CEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC Q ss_conf 336653035667777833277877312699999998853024836898864320268 Q gi|254780979|r 279 NETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI 335 (500) Q Consensus 279 ~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL 335 (500) -.|..+|+.+.-. |-||||+ +-++---+|.|-+.....|...||. T Consensus 92 p~t~~iR~~~~~~---YtpEPDi---------fHe~~GH~P~L~np~fA~f~q~~G~ 136 (228) T cd03348 92 PVTNFIRRPEELD---YLQEPDI---------FHDIFGHVPMLTNPVFADFMQAYGK 136 (228) T ss_pred CEEEEECCCCCCC---CCCCCCH---------HHHHHCCCCCCCCHHHHHHHHHHHH T ss_conf 3352445865356---6889428---------9998365620088899999999999 No 31 >TIGR01011 rpsB_bact ribosomal protein S2; InterPro: IPR005706 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . This family describes the bacterial, mitochondrial and chloroplast forms of ribosomal protein S2.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit. Probab=58.58 E-value=5.2 Score=20.55 Aligned_cols=122 Identities=19% Similarity=0.256 Sum_probs=60.2 Q ss_pred HHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCC-C-CCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHC-- Q ss_conf 997313980034432337554336653035667777833277-8-773126999999988530248368988643202-- Q gi|254780979|r 258 IAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEP-D-LLPLEIDEDFIRAIKKQIPELPDAKRERFIGEF-- 333 (500) Q Consensus 258 ~~ll~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEP-D-LPpi~is~e~i~~i~~~lPelP~~~~~rl~~~y-- 333 (500) .+|||+|-..--+||+|||..+.=. |+|- | +=-+.|. ..+..++..+.. ..+.+++- T Consensus 5 k~LleaGvHFGHqtRRWNPkMk~fI-------------f~eRKngihIIDL~-kT~~~~~~Ay~~-----v~~~~~~gg~ 65 (227) T TIGR01011 5 KDLLEAGVHFGHQTRRWNPKMKPFI-------------FGERKNGIHIIDLQ-KTLQLLEEAYNF-----VREVVANGGK 65 (227) T ss_pred HHHHHCCCCCCCEECCCCCCCCCCC-------------CCCCCCCCEEECHH-HHHHHHHHHHHH-----HHHHHHCCCE T ss_conf 7686388543754223688898855-------------32012785122578-999999999999-----9999981995 Q ss_pred ----CCCH-HHHHHHHHHHHHHHHHHHHHCCCCHHHHH-HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCC Q ss_conf ----6889-99888764113678988640243024577-77654578876433874000648989999999888638731 Q gi|254780979|r 334 ----GISL-YDASVLVSDKSIADYFEKLAVNRDKKIVA-NWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTIS 407 (500) Q Consensus 334 ----GLs~-~dA~~L~~~~~la~~FE~v~~~~~pk~~A-nwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is 407 (500) | +. .+|+.++. +.+..++.-.+. .||=|-|. +|....-+-+.|-+|-.+.++|... T Consensus 66 iLFVG-TKNkQA~~~i~---------~~A~r~g~~YVn~RWLGGMLT--------Nf~TirkSi~kL~~lE~~~~~g~~~ 127 (227) T TIGR01011 66 ILFVG-TKNKQAKEIIK---------EEAERCGMFYVNQRWLGGMLT--------NFKTIRKSIKKLKKLEKMEEDGTFD 127 (227) T ss_pred EEEEE-CHHHHHHHHHH---------HHHHHCCCCEECCCCCCCCCH--------HHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 88851-65889999999---------999874896211333464002--------4799999999999999877613312 Q ss_pred HHHHHHHHH Q ss_conf 478999999 Q gi|254780979|r 408 GKIAKDIFN 416 (500) Q Consensus 408 ~~~aK~il~ 416 (500) .-+=||++. T Consensus 128 ~LtKKE~~~ 136 (227) T TIGR01011 128 VLTKKEILM 136 (227) T ss_pred CCCCCCHHH T ss_conf 477000776 No 32 >KOG2305 consensus Probab=58.51 E-value=11 Score=18.18 Aligned_cols=37 Identities=19% Similarity=0.276 Sum_probs=20.0 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCC Q ss_conf 789999999999999864204567643220112575432 Q gi|254780979|r 186 SSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSV 224 (500) Q Consensus 186 s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi 224 (500) .+++....++.++.=|+-+.- .+.-.|++++|--.+. T Consensus 35 ~e~Ql~~ALen~~Kel~~Lee--~g~lrGnlsa~eqla~ 71 (313) T KOG2305 35 LEKQLQTALENVEKELRKLEE--HGLLRGNLSADEQLAL 71 (313) T ss_pred CHHHHHHHHHHHHHHHHHHHH--HHHHCCCCCHHHHHHH T ss_conf 599999999999999999997--2101267648888888 No 33 >pfam11212 DUF2999 Protein of unknown function (DUF2999). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. Probab=50.00 E-value=19 Score=16.36 Aligned_cols=18 Identities=22% Similarity=0.477 Sum_probs=7.8 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHH Q ss_conf 658999999728977889999999 Q gi|254780979|r 469 SWFVGQVMKNTGGKANPSIVQKML 492 (500) Q Consensus 469 gfLvGqVMK~tkGkAdpk~v~~lL 492 (500) ..|||+|| .||..+++-. T Consensus 47 Q~lm~~VM------~nP~LIkeAv 64 (82) T pfam11212 47 QQLMMLVM------QNPALIKEAV 64 (82) T ss_pred HHHHHHHH------CCHHHHHHHH T ss_conf 99999997------1928899999 No 34 >pfam11867 DUF3387 Domain of unknown function (DUF3387). This domain is functionally uncharacterized. This domain is found in bacteria and archaea. This presumed domain is typically between 255 to 340 amino acids in length. This domain is found associated with pfam04851, pfam04313. Probab=49.75 E-value=19 Score=16.34 Aligned_cols=18 Identities=22% Similarity=0.294 Sum_probs=9.0 Q ss_pred HHHHHHHHHHHHCCCCCH Q ss_conf 899999998886387314 Q gi|254780979|r 391 PNQLGELIDLIIDGTISG 408 (500) Q Consensus 391 p~~laeLi~li~~g~Is~ 408 (500) .+.|.++++-..++.|+. T Consensus 198 sE~Le~~i~~Y~nr~it~ 215 (333) T pfam11867 198 SERLEEAINKYHNRAITT 215 (333) T ss_pred HHHHHHHHHHHHCCCCCH T ss_conf 999999999998077749 No 35 >cd00361 arom_aa_hydroxylase Biopterin-dependent aromatic amino acid hydroxylase; a family of non-heme, iron(II)-dependent enzymes that includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan hydroxylase (TrpOH). PheOH converts L-phenylalanine to L-tyrosine, an important step in phenylalanine catabolism and neurotransmitter biosynthesis, and is linked to a severe variant of phenylketonuria in humans. TyrOH and TrpOH are involved in the biosynthesis of catecholamine and serotonin, respectively. The eukaryotic enzymes are all homotetramers. Probab=49.56 E-value=14 Score=17.37 Aligned_cols=45 Identities=29% Similarity=0.523 Sum_probs=35.0 Q ss_pred CEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC Q ss_conf 336653035667777833277877312699999998853024836898864320268 Q gi|254780979|r 279 NETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI 335 (500) Q Consensus 279 ~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL 335 (500) -.|..+|..+.-. |-||||+ +-++---+|.|-+.....|...||. T Consensus 86 p~t~~iR~~~~~~---YtpEPDi---------fHe~~GH~P~L~~p~fA~f~q~~G~ 130 (221) T cd00361 86 PVTQYIRHPEEPD---YTPEPDI---------FHELFGHVPLLADPSFADFSQEYGL 130 (221) T ss_pred CEEEEECCCCCCC---CCCCCCH---------HHHHHCCCCCCCCHHHHHHHHHHHH T ss_conf 3253445787677---7899943---------8776167731179889999999999 No 36 >cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil Probab=47.98 E-value=5.4 Score=20.43 Aligned_cols=59 Identities=27% Similarity=0.312 Sum_probs=35.6 Q ss_pred CCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHH Q ss_conf 44323375543366530356677778332778773126999999988530248368988643202688999888764113 Q gi|254780979|r 269 QETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDKS 348 (500) Q Consensus 269 qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~~ 348 (500) ..|-+|=+..|.-.+.| ++..||+|.+.|+.-+. ...++ .+.|+|.+++..+++.+. T Consensus 15 ~~tlRyYe~~GLl~~~r---~~~gyR~Y~~~~i~~l~-------------------~I~~l-r~~G~sL~eIk~lL~~~~ 71 (102) T cd04775 15 RSTLLYYESIGLIPSAR---SEANYRLYSEADLSRLE-------------------KIVFL-QAGGLPLEEIAGCLAQPH 71 (102) T ss_pred HHHHHHHHHCCCCCCCC---CCCCCEECCHHHHHHHH-------------------HHHHH-HHCCCCHHHHHHHHCCCC T ss_conf 99999999879999873---99999637899999999-------------------99999-996999999999985995 Q ss_pred HH Q ss_conf 67 Q gi|254780979|r 349 IA 350 (500) Q Consensus 349 la 350 (500) .. T Consensus 72 ~~ 73 (102) T cd04775 72 VQ 73 (102) T ss_pred HH T ss_conf 79 No 37 >COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis] Probab=47.58 E-value=21 Score=16.10 Aligned_cols=42 Identities=19% Similarity=0.388 Sum_probs=32.2 Q ss_pred CCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 126999999988530248368988643202688999888764 Q gi|254780979|r 304 LEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS 345 (500) Q Consensus 304 i~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~ 345 (500) +.++++.++.|++++|-.-....--+.+.||++-..|...+. T Consensus 40 v~vdee~~~ki~KEV~~~r~VTpy~la~r~gI~~SvAr~vLR 81 (107) T COG4901 40 VTVDEELLDKIRKEVPRERVVTPYVLASRYGINGSVARIVLR 81 (107) T ss_pred HHCCHHHHHHHHHHCCCCEEECHHHHHHHHCCCHHHHHHHHH T ss_conf 120599999999862545155499988885552589999999 No 38 >pfam04262 Glu_cys_ligase Glutamate-cysteine ligase. Family of bacterial f glutamate-cysteine ligases (EC:6.3.2.2) that carry out the first step of the glutathione biosynthesis pathway. Probab=46.71 E-value=16 Score=16.97 Aligned_cols=50 Identities=20% Similarity=0.271 Sum_probs=33.7 Q ss_pred EEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCC Q ss_conf 8661578612576303652778999999999999986420456764322011257 Q gi|254780979|r 166 IDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADV 220 (500) Q Consensus 166 vD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~Dv 220 (500) -||-- .|+|+|| |...++++|..|+..|+.++...= -|--+=-.||=|-. T Consensus 56 TDFSE---sqlE~IT-P~~~s~~~~~~~L~~lh~~v~~~l-~dE~LWP~SMP~~l 105 (377) T pfam04262 56 TDFAE---SLLEFIT-PPSKDIEDTLAFLSDIHRFVQSKL-KGEYLWPLSMPCRL 105 (377) T ss_pred CCCCH---HHHHHCC-CCCCCHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCCC T ss_conf 75578---8766178-998999999999999999999618-98643567788889 No 39 >pfam06519 TolA TolA C-terminal. This family consists of several bacterial TolA proteins as well as two eukaryotic proteins of unknown function. Tol proteins are involved in the translocation of group A colicins. Colicins are bacterial protein toxins, which are active against Escherichia coli and other related species (See pfam01024). TolA is anchored to the cytoplasmic membrane by a single membrane spanning segment near the N-terminus, leaving most of the protein exposed to the periplasm. Probab=43.85 E-value=23 Score=15.77 Aligned_cols=48 Identities=13% Similarity=0.230 Sum_probs=33.6 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCC Q ss_conf 78999999999999986420456764322011257543213766678862 Q gi|254780979|r 186 SSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRC 235 (500) Q Consensus 186 s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRv 235 (500) +..|+-.|...+++.++.-=.-+..| .|- .|.++|.+.+.|.-.+.++ T Consensus 9 ~~sev~~Y~a~I~~~Iq~~~~~~~~~-~GK-~C~v~I~LapdG~v~~v~~ 56 (96) T pfam06519 9 SGAEVDRYAGQIKQAIQSRFLDDDSF-AGK-TCRVRIKLAPDGTLISVKV 56 (96) T ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCC-CCC-EEEEEEEECCCCEEEEEEE T ss_conf 47689999999999999844886134-999-7899999869956987440 No 40 >COG1490 Dtd D-Tyr-tRNAtyr deacylase [Translation, ribosomal structure and biogenesis] Probab=43.60 E-value=24 Score=15.68 Aligned_cols=47 Identities=28% Similarity=0.483 Sum_probs=38.5 Q ss_pred ECCCCCC---HHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCC Q ss_conf 0365277---8999999999999986420456764322011257543213766 Q gi|254780979|r 180 TKPDMRS---SLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGE 229 (500) Q Consensus 180 T~Pd~~s---~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~ 229 (500) +.|.++. |++|.+.-+++-..+|-.|+ .-|.|-+..|-+||+-..|. T Consensus 89 ~RPsFs~aa~p~~A~~lYe~f~~~lr~~~~---~V~tG~FgA~M~V~LvNdGP 138 (145) T COG1490 89 RRPSFSKAAKPDQAEELYEYFVELLRELGI---KVETGRFGADMQVSLVNDGP 138 (145) T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHCCC---CEEEEEEECEEEEEEECCCC T ss_conf 998866658857889999999999986288---40210220000789861897 No 41 >pfam05606 DUF777 Borrelia burgdorferi protein of unknown function (DUF777). This family consists of several hypothetical proteins of unknown function from Borrelia burgdorferi (Lyme disease spirochete). Probab=43.09 E-value=9.2 Score=18.71 Aligned_cols=23 Identities=35% Similarity=0.456 Sum_probs=14.3 Q ss_pred ECCCCEEECCCEECCC---CCCCCCCC Q ss_conf 2442013113212376---78882014 Q gi|254780979|r 89 INKYSVFARKNYFYPD---LPQGYQIS 112 (500) Q Consensus 89 i~~~~~fdRK~YfYpD---lpkgyQiT 112 (500) .++..+|| |||||-= .||.--|- T Consensus 88 ~nDnnhFD-K~yFYILs~i~pk~l~i~ 113 (180) T pfam05606 88 ESDNNHFD-KNYFYILSVLNPKKIGII 113 (180) T ss_pred CCCCCCCC-CCEEEEEECCCCCEEEEE T ss_conf 46665544-426899972585300058 No 42 >KOG1795 consensus Probab=41.52 E-value=25 Score=15.46 Aligned_cols=10 Identities=50% Similarity=0.704 Sum_probs=3.2 Q ss_pred HHHHHHHHCC Q ss_conf 9999973139 Q gi|254780979|r 255 RRQIAILEDG 264 (500) Q Consensus 255 ~RQ~~ll~~G 264 (500) .||.+.+..| T Consensus 783 Erq~n~~k~G 792 (2321) T KOG1795 783 ERQHNYLKDG 792 (2321) T ss_pred HHHHHHHHCC T ss_conf 8876566228 No 43 >COG0105 Ndk Nucleoside diphosphate kinase [Nucleotide transport and metabolism] Probab=40.50 E-value=13 Score=17.56 Aligned_cols=77 Identities=16% Similarity=0.303 Sum_probs=50.1 Q ss_pred EEEEEEEEEEEECCCCCCCCCCCCC----EEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 7984236665202310011567871----488661578612576303652778999999999999986420456764322 Q gi|254780979|r 139 IEVGIERIHLEQDAGKSIHDQYSAV----SCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEG 214 (500) Q Consensus 139 ~~v~I~~i~lEED~gk~~h~~~~~~----slvD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeG 214 (500) +-+..+.+|+.++.+..-+....+. .||+| |++.|.+----|-...+...|.++-.+.-.++ +.| T Consensus 32 kiva~K~~~~~~e~Ae~~Y~~h~~kpFf~~Lv~f---------itSgPvv~~VleGe~ai~~~R~l~GaTnp~~A--~pG 100 (135) T COG0105 32 KIVALKMVQLSRELAENHYAEHKGKPFFGELVEF---------ITSGPVVAMVLEGENAISVVRKLMGATNPANA--APG 100 (135) T ss_pred EEEEEEEECCCHHHHHHHHHHHCCCCCCHHHHHH---------EECCCEEEEEEECHHHHHHHHHHHCCCCCCCC--CCC T ss_conf 8876440204799997778987678752877862---------31265899998527699999999779981217--998 Q ss_pred EEECCCCCCCCC Q ss_conf 011257543213 Q gi|254780979|r 215 SMRADVNVSVCR 226 (500) Q Consensus 215 slR~DvNVSi~~ 226 (500) +||.|-++|+.. T Consensus 101 TIRgdfa~~~~~ 112 (135) T COG0105 101 TIRGDFALSVGE 112 (135) T ss_pred EEEEEHHCCCCC T ss_conf 276232014676 No 44 >KOG2181 consensus Probab=40.20 E-value=16 Score=17.00 Aligned_cols=128 Identities=16% Similarity=0.186 Sum_probs=61.8 Q ss_pred HHHHHHHHHHHCCCCCCCCCCE--EECCCCCCCCCCCCCCCCC--CCCCCCCHH--HHH--HHHHHHHHHHHHHHHHCCC Q ss_conf 9999999864204567643220--1125754321376667886--222354024--659--9999999999999731398 Q gi|254780979|r 194 LTKLRSILRYLGTCDGNMEEGS--MRADVNVSVCRPGEAWGTR--CEVKNVNSI--RFL--GLAIEYEARRQIAILEDGG 265 (500) Q Consensus 194 ~~~l~~ilr~~gisd~~meeGs--lR~DvNVSi~~~~~~~GtR--vEIKNlnS~--~~i--~~AI~yEi~RQ~~ll~~G~ 265 (500) +.+|+-+|++- .+....|| +-||--.-|-.+|..+=|+ +|-|=+=.| ..+ -|+-.+||+|..+++-+ T Consensus 119 ~~eLyyvLkh~---ket~hn~s~~~dcdq~~~iTqhgkp~ft~VctegrL~lEF~fDd~MRIK~Wh~~ik~~rElvpr-- 193 (415) T KOG2181 119 MRELYYVLKHP---KETLHNGSQAYDCDQVLQITQHGKPSFTEVCTEGRLYLEFAFDDVMRIKAWHLEIKRSRELVPR-- 193 (415) T ss_pred HHHHHHHHCCC---HHHHCCCCEEEECCCEEEEEECCCCCCEEEECCCEEEEEEEHHHHHHHHHEEEEEECCCCCCCH-- T ss_conf 24316555185---5553277356513533577534874013561365388874112455121103662201001404-- Q ss_pred CCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCH-HHHHHHHHHHCCCCHHHHHH Q ss_conf 003443233755433665303566777783327787731269999999885302483-68988643202688999888 Q gi|254780979|r 266 HIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELP-DAKRERFIGEFGISLYDASV 342 (500) Q Consensus 266 ~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP-~~~~~rl~~~yGLs~~dA~~ 342 (500) .|.|-|--||+.--- -+ --+++-.-++...++-++-..---| .+...|- +.|.||+.|.-. T Consensus 194 sil~~~a~~dp~~ld------q~---------~kNitR~G~~nsTlNylrlcvILePMQelMSrh-KayalsPRdclK 255 (415) T KOG2181 194 SILQNTADYDPEALD------QE---------QKNITRMGFFNSTLNYLRLCVILEPMQELMSRH-KAYALSPRDCLK 255 (415) T ss_pred HHHHCCCCCCHHHHC------HH---------HCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCHHHHHH T ss_conf 565304798845637------45---------506632101110488999999875899998753-566788899999 No 45 >cd03345 eu_TyrOH Eukaryotic tyrosine hydroxylase (TyrOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH) and eukaryotic tryptophan hydroxylase (TrpOH). TyrOH catalyzes the conversion of tyrosine to L-dihydroxyphenylalanine (L-DOPA), the rate-limiting step in the biosynthesis of the catecholamines dopamine, noradrenaline, and adrenaline. Probab=39.92 E-value=21 Score=16.06 Aligned_cols=46 Identities=22% Similarity=0.369 Sum_probs=34.1 Q ss_pred CEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCC Q ss_conf 3366530356677778332778773126999999988530248368988643202688 Q gi|254780979|r 279 NETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGIS 336 (500) Q Consensus 279 ~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs 336 (500) -.|..+|..+.- -|-||||+ +-++---+|.|-+.....|..++|+. T Consensus 145 ~~TqyIRh~~~p---~YtpEPDi---------~Hel~GH~Plladp~fA~f~q~iG~a 190 (298) T cd03345 145 QCTQYIRHASSP---MHSPEPDC---------CHELLGHVPMLADPTFAQFSQDIGLA 190 (298) T ss_pred CCEEEECCCCCC---CCCCCCCH---------HHHHHCCCCCCCCHHHHHHHHHHHHH T ss_conf 530024267777---77899953---------66664456122798999999999998 No 46 >PRK02107 glutamate--cysteine ligase; Provisional Probab=39.49 E-value=26 Score=15.38 Aligned_cols=33 Identities=12% Similarity=0.108 Sum_probs=14.6 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHH Q ss_conf 99999988863873147899999999817999889 Q gi|254780979|r 393 QLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKE 427 (500) Q Consensus 393 ~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~ 427 (500) .+......+.+-..|-+ -.+|.+|.+.+.+-.+ T Consensus 430 Al~~~~~ki~dp~lTPS--ariL~em~~~g~sf~e 462 (523) T PRK02107 430 ACDALRAKFDDPELTPS--ARVLRSMRENGQSFGG 462 (523) T ss_pred HHHHHHHHHCCCCCCHH--HHHHHHHHHCCCCHHH T ss_conf 99999998449888948--9999999873998999 No 47 >TIGR01083 nth endonuclease III; InterPro: IPR005759 The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases. Among these modified bases, 7,8-dihydro-8-oxoguanine (8-oxoG) is an important mutagenic lesion. Base excision repair is a critical mechanism for preventing mutations by removing the oxidative lesion from the DNA. Escherichia coli Nth protein (endonuclease III) has an 8-oxoG DNA glycosylase/AP lyase activity which removes 8-oxoG preferentially from 8-oxoG/G mispairs. Human hNTH1 protein, a homolog of E. coli Nth protein, has similar DNA glycosylase/AP lyase activity that removes 8-oxoG from 8-oxoG/G mispairs . ; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0006284 base-excision repair, 0005622 intracellular. Probab=38.68 E-value=28 Score=15.16 Aligned_cols=24 Identities=25% Similarity=0.410 Sum_probs=8.6 Q ss_pred HHHHCCCEECCCHHHHHHHHHHHH Q ss_conf 999639876189889999999999 Q gi|254780979|r 428 IVEELGLRQVTDLSAIEKVVDEVI 451 (500) Q Consensus 428 iie~~gL~~isD~~eL~~iv~eVI 451 (500) +.++.||..-.|..++|+-..+++ T Consensus 142 v~~Rlgl~~~~dp~~vE~~L~~l~ 165 (192) T TIGR01083 142 VSNRLGLSKGKDPDKVEEELLKLI 165 (192) T ss_pred HHHHHCCCCCCCHHHHHHHHHHHC T ss_conf 543313577789899999998744 No 48 >KOG2243 consensus Probab=38.49 E-value=24 Score=15.62 Aligned_cols=27 Identities=22% Similarity=0.349 Sum_probs=11.9 Q ss_pred CCCCCCCHHHHHHH-----HHHHHHHHHHHHH Q ss_conf 22235402465999-----9999999999973 Q gi|254780979|r 235 CEVKNVNSIRFLGL-----AIEYEARRQIAIL 261 (500) Q Consensus 235 vEIKNlnS~~~i~~-----AI~yEi~RQ~~ll 261 (500) +|.-=+.-++.+.. ...-+-.||+-+| T Consensus 1824 ~ef~fvp~ikl~~tllimgif~~dd~k~il~l 1855 (5019) T KOG2243 1824 TEFLFVPLIKLFGTLLIMGIFDDDDLKHILLL 1855 (5019) T ss_pred EEEEEEHHHHHHHHHHHEEECCCHHHHHHHHH T ss_conf 47863049999988872310251668889996 No 49 >PRK09849 putative oxidoreductase; Provisional Probab=38.34 E-value=12 Score=17.75 Aligned_cols=14 Identities=7% Similarity=0.040 Sum_probs=8.1 Q ss_pred CCCC-CHHHHHHHHH Q ss_conf 8737-8999999999 Q gi|254780979|r 67 LPIL-NGRCVQQAVM 80 (500) Q Consensus 67 lP~l-N~~av~~ai~ 80 (500) +|+. +++.++...+ T Consensus 210 v~va~d~e~~~~~~~ 224 (702) T PRK09849 210 VNIAGDRQEMKRLND 224 (702) T ss_pred CCCCCCHHHHHHHHH T ss_conf 767789999999999 No 50 >PRK13979 DNA topoisomerase IV subunit A; Provisional,Validated Probab=37.22 E-value=29 Score=15.00 Aligned_cols=37 Identities=19% Similarity=0.392 Sum_probs=31.4 Q ss_pred CHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 999999988530248368988643202688999888764 Q gi|254780979|r 307 DEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS 345 (500) Q Consensus 307 s~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~ 345 (500) =++.|+-||++ ..|.+-+++|++.|+||+.+|+.++. T Consensus 402 IDevI~iIR~S--~~~~~Ak~~L~~~f~lse~QA~AILd 438 (959) T PRK13979 402 MDEIIKTIRAS--KSKKDASENLIEKFGFTDEQAEAILE 438 (959) T ss_pred HHHHHHHHHCC--CCHHHHHHHHHHHCCCCHHHHHHHHH T ss_conf 99999999818--98379999898761999999999999 No 51 >cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. Probab=37.06 E-value=9.9 Score=18.46 Aligned_cols=55 Identities=22% Similarity=0.273 Sum_probs=34.4 Q ss_pred CCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 443233755433665303566777783327787731269999999885302483689886432026889998887641 Q gi|254780979|r 269 QETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSD 346 (500) Q Consensus 269 qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~ 346 (500) ..|-+|=+..|.-.+.|+ +.-||+|++-|+--+. ...++ ..+|+|..++..+++. T Consensus 15 ~~TlRyYe~~GLl~~~R~---~ngyR~Y~~~~l~~l~-------------------~I~~l-r~~G~sL~eI~~~l~~ 69 (102) T cd04789 15 RSTLLYYEKLGLITGTRN---ANGYRLYPDSDLQRLL-------------------LIQQL-QAGGLSLKECLACLQG 69 (102) T ss_pred HHHHHHHHHCCCCCCCCC---CCCCCCCCHHHHHHHH-------------------HHHHH-HHCCCCHHHHHHHHCC T ss_conf 999999998699898819---9999506999999999-------------------99999-9979989999999859 No 52 >cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. Probab=36.98 E-value=15 Score=17.15 Aligned_cols=50 Identities=28% Similarity=0.389 Sum_probs=26.2 Q ss_pred CCCCCCCCEE-EEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 2337554336-6530356677778332778773126999999988530248368988643202688999888764 Q gi|254780979|r 272 RLFDPSKNET-RSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS 345 (500) Q Consensus 272 R~~d~~~~~T-~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~ 345 (500) |.|+ ..|.- .+-| ++..||||.+-|+.-+. - ..++ .+.|+|..++..++. T Consensus 18 R~Ye-~~GLl~~~~R---~~~gyR~Y~~~~l~~l~-------~------------I~~l-r~~G~sL~eI~~ll~ 68 (123) T cd04770 18 RYYE-RIGLLPPPQR---SENGYRLYGEADLARLR-------F------------IRRA-QALGFSLAEIRELLS 68 (123) T ss_pred HHHH-HCCCCCCCEE---CCCCCEEEHHHHHHHHH-------H------------HHHH-HHCCCCHHHHHHHHH T ss_conf 9999-8189875146---79995621377878899-------9------------9999-986999999999985 No 53 >PRK09514 zntR zinc-responsive transcriptional regulator; Provisional Probab=36.66 E-value=14 Score=17.45 Aligned_cols=54 Identities=30% Similarity=0.399 Sum_probs=32.5 Q ss_pred CCCCCCCCCCCEEE-EEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 44323375543366-530356677778332778773126999999988530248368988643202688999888764 Q gi|254780979|r 269 QETRLFDPSKNETR-SLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS 345 (500) Q Consensus 269 qETR~~d~~~~~T~-~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~ 345 (500) .+|-+|=+..|.-. +.| ++..||+|++.|+.-+. -| .++ .++|+|..++..|+. T Consensus 15 ~~tiRyYE~~GLl~~~~R---~~~gyR~Y~~~~v~rL~-------fI------------~~~-r~lGfsL~eI~~ll~ 69 (140) T PRK09514 15 PDTLRFYEKQGLMDPSVR---TESGYRLYTEQDLQRLR-------FI------------LRA-KQLGFTLEEIRELLS 69 (140) T ss_pred HHHHHHHHHCCCCCCCCC---CCCCEECCCCCHHHHHH-------HH------------HHH-HHCCCCHHHHHHHHH T ss_conf 999999998699986511---89980206710999999-------99------------999-993999999999981 No 54 >CHL00139 rpl18 ribosomal protein L18; Validated Probab=35.39 E-value=31 Score=14.80 Aligned_cols=62 Identities=19% Similarity=0.134 Sum_probs=32.7 Q ss_pred EEEEEE--CCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCC-CCHH-HHHHH-HHHHHHHCCEECCCCEEECCCEECC Q ss_conf 997888--68986555884246898765206130268988873-7899-99999-9987782976244201311321237 Q gi|254780979|r 29 EVHAQL--SVVSKLFSGASVNFGAEPNTQVSFFDAAMPGMLPI-LNGR-CVQQA-VMTGLGLNAHINKYSVFARKNYFYP 103 (500) Q Consensus 29 EiH~qL--~t~tKlFc~c~~~~~~~pNt~v~~~~~g~PG~lP~-lN~~-av~~a-i~~~~al~~~i~~~~~fdRK~YfYp 103 (500) -|++|+ ++..+-.|+++|---+-. ..+.. -|.+ |-..+ +.+-.|+...|. ...|||--|-|. T Consensus 26 hiyaQiIDD~~g~tl~saST~~k~~~------------~~~~~~~n~e~A~~vG~~ia~~a~~~gI~-~VvFDRggy~YH 92 (109) T CHL00139 26 HIYAQIIDDTNGKTLVSCSTLDPDVK------------SNLSIGSTCDASKLVGQKLAKKSLKKGIT-KVVFDRGGKLYH 92 (109) T ss_pred EEEEEEEECCCCCEEEEEECCHHHHH------------HHHCCCCHHHHHHHHHHHHHHHHHHCCCC-EEEECCCCCCCH T ss_conf 18999998799989999623367776------------55147866999999999999999987999-999858998422 No 55 >TIGR01059 gyrB DNA gyrase, B subunit; InterPro: IPR011557 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively. This entry represents the B subunit (gyrB) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrB has two functional domains: an N-terminal ATPase and a C-terminal responsible for subunit interactions, the latter differing between subunit B and single polypeptide topoisomerase II . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome. Probab=35.31 E-value=26 Score=15.33 Aligned_cols=29 Identities=14% Similarity=0.393 Sum_probs=20.0 Q ss_pred CHHHHHHHHHHHHHHCHHHH--HHHH--CCCCC Q ss_conf 98899999999998399989--9752--72132 Q gi|254780979|r 439 DLSAIEKVVDEVINSNPNNV--ARIA--TKPNL 467 (500) Q Consensus 439 D~~eL~~iv~eVI~~np~~V--~~~k--gk~ka 467 (500) +...++++++..+..+++.+ .+|| |.+.+ T Consensus 729 ~~~~~~~~~~~l~~~~~~g~~iQRYKGLGEMna 761 (818) T TIGR01059 729 EINSLEEALDKLVELGRKGIEIQRYKGLGEMNA 761 (818) T ss_pred CCCCHHHHHHHHHHCCCCCCEEEEECCCCCCCH T ss_conf 002589999999840789860454316666782 No 56 >cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Probab=35.28 E-value=10 Score=18.29 Aligned_cols=53 Identities=25% Similarity=0.351 Sum_probs=34.3 Q ss_pred CCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 3233755433665303566777783327787731269999999885302483689886432026889998887641 Q gi|254780979|r 271 TRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSD 346 (500) Q Consensus 271 TR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~ 346 (500) -|.|+ ..|.-.|.|+ ..-||+|.+-||.-+ + ...+|..+.|+|..++..++.. T Consensus 18 LR~yE-~~GLl~P~R~---~~g~R~Ys~~di~~l----------~---------~I~~L~~~~G~sl~~I~~~L~l 70 (91) T cd04766 18 LRLYE-RLGLLSPSRT---DGGTRRYSERDIERL----------R---------RIQRLTQELGVNLAGVKRILEL 70 (91) T ss_pred HHHHH-HCCCCCCCCC---CCCCEECCHHHHHHH----------H---------HHHHHHHHCCCCHHHHHHHHHH T ss_conf 99999-8599798839---999974479999999----------9---------9999999869989999999980 No 57 >TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic. Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity. Probab=35.08 E-value=29 Score=15.06 Aligned_cols=14 Identities=14% Similarity=0.352 Sum_probs=5.9 Q ss_pred HHHHHHHHHHHHCC Q ss_conf 26589999997289 Q gi|254780979|r 468 VSWFVGQVMKNTGG 481 (500) Q Consensus 468 ~gfLvGqVMK~tkG 481 (500) +--+|+|.||+.|| T Consensus 262 ~Rr~is~tmk~ak~ 275 (340) T TIGR03575 262 LRRIISQTMREAKD 275 (340) T ss_pred HHHHHHHHHHHHHH T ss_conf 99999999999850 No 58 >PRK05560 DNA gyrase subunit A; Validated Probab=35.06 E-value=32 Score=14.76 Aligned_cols=76 Identities=16% Similarity=0.341 Sum_probs=46.4 Q ss_pred CCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHH--HHHHH--------HHHHH--------CCCCHHHH Q ss_conf 12699999998853024836898864320268899988876411--36789--------88640--------24302457 Q gi|254780979|r 304 LEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDK--SIADY--------FEKLA--------VNRDKKIV 365 (500) Q Consensus 304 i~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~--~la~~--------FE~v~--------~~~~pk~~ 365 (500) +..-++.|+-||++ .-|.+-++.|++.|+||+.+|+.++.=+ .|..+ ++++. .-.+.+.. T Consensus 387 ~~~iDeVI~iIR~S--~~~~~Ak~~L~~~f~lse~QA~AIL~mrL~rLt~Le~~kl~~E~~eL~~~I~~l~~IL~s~~~l 464 (822) T PRK05560 387 LDNIDEVIALIRAS--PTPAEAREGLMERYGLSEIQAQAILDMRLQRLTGLEREKIEDEYKELLAEIADLLDILASPERL 464 (822) T ss_pred HHCHHHHHHHHHCC--CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH T ss_conf 95879999999718--9878999989887588999999999989999876789999999999999999999886599999 Q ss_pred HHHHHHHHHHHHHHCC Q ss_conf 7776545788764338 Q gi|254780979|r 366 ANWVINDLLGVLNRSG 381 (500) Q Consensus 366 Anwi~~el~~~ln~~~ 381 (500) .+.|..||....++-+ T Consensus 465 ~~iI~~EL~eik~kyg 480 (822) T PRK05560 465 MEIIREELEEIKEKFG 480 (822) T ss_pred HHHHHHHHHHHHHHHC T ss_conf 9999999999999829 No 59 >COG2326 Uncharacterized conserved protein [Function unknown] Probab=34.98 E-value=32 Score=14.75 Aligned_cols=30 Identities=23% Similarity=0.241 Sum_probs=15.8 Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCEEEEE Q ss_conf 999997313980034432337554336653 Q gi|254780979|r 255 RRQIAILEDGGHIRQETRLFDPSKNETRSL 284 (500) Q Consensus 255 ~RQ~~ll~~G~~v~qETR~~d~~~~~T~~m 284 (500) .|=+.-+-.+|+|.==-|.|=..-|++..| T Consensus 122 qRy~~~lPa~GeiviFdRSwYnr~gVeRVm 151 (270) T COG2326 122 QRYVAHLPAAGEIVIFDRSWYNRAGVERVM 151 (270) T ss_pred HHHHHHCCCCCEEEEECHHHCCCCCEEECC T ss_conf 999986788873898651221332714402 No 60 >TIGR00676 fadh2 5,10-methylenetetrahydrofolate reductase; InterPro: IPR004620 The enzyme activities methylenetetrahydrofolate reductase (1.5.1.20 from EC) and 5,10-methylenetetrahydrofolate reductase (FADH) (1.7.99.5 from EC) differ in that the former (assigned in many eukaryotes) is defined to use NADP+ as an acceptor, while the latter (assigned in many bacteria) is flexible with respect to the acceptor. Both convert 5-methyltetrahydrofolate to 5,10-methylenetetrahydrofolate. From a larger set of proteins assigned as one or the other, this family describes the subset of proteins found in bacteria, and currently designated 5,10-methylenetetrahydrofolate reductase. This protein is an FAD-containing flavoprotein.; GO: 0009086 methionine biosynthetic process. Probab=34.95 E-value=24 Score=15.59 Aligned_cols=18 Identities=28% Similarity=0.348 Sum_probs=7.5 Q ss_pred HHHHHCCCCCCCCCCEEECCCC Q ss_conf 9864204567643220112575 Q gi|254780979|r 200 ILRYLGTCDGNMEEGSMRADVN 221 (500) Q Consensus 200 ilr~~gisd~~meeGslR~DvN 221 (500) -++.+||.+= | .||-|.- T Consensus 96 ~y~~~Gi~~i-l---ALRGD~p 113 (302) T TIGR00676 96 EYRELGIRNI-L---ALRGDPP 113 (302) T ss_pred HHHHCCCCEE-E---EECCCCC T ss_conf 9987488679-8---7437688 No 61 >pfam11181 YflT Heat induced stress protein YflT. YflT is a heat induced protein. Probab=34.92 E-value=32 Score=14.75 Aligned_cols=45 Identities=16% Similarity=0.208 Sum_probs=31.6 Q ss_pred CCCCCCCC-HHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 87731269-99999988530248368988643202688999888764 Q gi|254780979|r 300 DLLPLEID-EDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS 345 (500) Q Consensus 300 DLPpi~is-~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~ 345 (500) |--++.++ ..|++.++.....--++.+.++ .+|||+++.|..+-. T Consensus 47 ~~~~~~~~e~g~~~~v~n~F~~~gDElr~~l-~~lGl~~~ea~~ye~ 92 (103) T pfam11181 47 DTNTIGAKEQGLGDSVMNTFRKKGDELRNKM-SELGLSDDEAEQYEE 92 (103) T ss_pred CCCCCCCCCCCHHHHHHHHHCCCCHHHHHHH-HHCCCCHHHHHHHHH T ss_conf 8763455447589999998655758889999-985999999999999 No 62 >cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center. Probab=34.38 E-value=9.7 Score=18.52 Aligned_cols=56 Identities=18% Similarity=0.151 Sum_probs=34.5 Q ss_pred CCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 0344323375543366530356677778332778773126999999988530248368988643202688999888764 Q gi|254780979|r 267 IRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS 345 (500) Q Consensus 267 v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~ 345 (500) |.-.|-+|=+..|.-.+.|+ ..-||+|++.||--+. - ..++ .+.|+|.+++..|+. T Consensus 13 vs~~tiRyYE~~GLl~p~R~---~~gyR~Y~~~~l~rl~-------~------------I~~~-r~lGfsL~eI~~lL~ 68 (139) T cd01110 13 VAVSALHFYEQKGLIASWRN---AGNQRRYPRDVLRRIA-------F------------IKVA-QRLGLSLAEIAEALA 68 (139) T ss_pred CCHHHHHHHHHCCCCCCCCC---CCCCCEECHHHHHHHH-------H------------HHHH-HHCCCCHHHHHHHHH T ss_conf 78899999998788466678---9887704989999999-------9------------9999-985998999999998 No 63 >COG4050 Uncharacterized protein conserved in archaea [Function unknown] Probab=34.29 E-value=32 Score=14.68 Aligned_cols=38 Identities=32% Similarity=0.538 Sum_probs=30.5 Q ss_pred EEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 86615786125763036527789999999999999864204 Q gi|254780979|r 166 IDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGT 206 (500) Q Consensus 166 vD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gi 206 (500) +-.-|-|+|.+|.-- | +|-|||+.|+.++...|..+-. T Consensus 112 ylvR~k~iPiLelkY-P--~s~Eea~~~VnkI~~FL~sLe~ 149 (152) T COG4050 112 YLVRRKGIPILELKY-P--RSEEEAIDFVNKIANFLKSLEA 149 (152) T ss_pred HHHHHCCCCEEEEEC-C--CCHHHHHHHHHHHHHHHHHHHH T ss_conf 876426984388757-8--8679999999999999986666 No 64 >pfam11950 DUF3467 Protein of unknown function (DUF3467). This family of proteins are functionally uncharacterized. This protein is found in bacteria, archaea and viruses. Proteins in this family are typically between 101 to 118 amino acids in length. Probab=34.20 E-value=32 Score=14.67 Aligned_cols=58 Identities=17% Similarity=0.208 Sum_probs=38.6 Q ss_pred EEEEEECCCCCCCC------CCCCCEEEEECCC--CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 66652023100115------6787148866157--86125763036527789999999999999864 Q gi|254780979|r 145 RIHLEQDAGKSIHD------QYSAVSCIDLNRS--GVALMEIVTKPDMRSSLEAKAFLTKLRSILRY 203 (500) Q Consensus 145 ~i~lEED~gk~~h~------~~~~~slvD~NRa--GvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~ 203 (500) +|.+.+|.++.++. .+...-.+||.+. |+|=..+. .-.+.||..|+.++..|+.-+.- T Consensus 15 ~iel~~~~~~g~YsN~~~v~~S~~Ef~idF~~~~pg~~~~~v~-sRVilsP~hAKrL~~aL~~ni~~ 80 (90) T pfam11950 15 NIELDEDNARGTYSNLAQVSHSPEEFILDFLWLMPGEPEAKVK-SRVILSPQHAKRLLAALQNNIKK 80 (90) T ss_pred EEECCHHHHEEEEEEEEEECCCCHHEEEEEEECCCCCCCCCEE-EEEEECHHHHHHHHHHHHHHHHH T ss_conf 7880856701564216896268216468713027999866269-99982999999999999999999 No 65 >cd03347 eu_PheOH Eukaryotic phenylalanine-4-hydroxylase (eu_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic phenylalanine-4-hydroxylase (pro_PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan hydroxylase (TrpOH). PheOH catalyzes the first and rate-limiting step in the metabolism of the amino acid L-phenylalanine (L-Phe), the hydroxylation of L-Phe to L-tyrosine (L-Tyr). It uses (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) as the physiological electron donor. The catalytic activity of the tetrameric enzyme is tightly regulated by the binding of L-Phe and BH4 as well as by phosphorylation. Mutations in the human enzyme are linked to a severe variant of phenylketonuria. Probab=32.84 E-value=33 Score=14.60 Aligned_cols=109 Identities=19% Similarity=0.285 Sum_probs=56.7 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 89999999999999864204567643220112575432137666788622235402465999999999999997313980 Q gi|254780979|r 187 SLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILEDGGH 266 (500) Q Consensus 187 ~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~~G~~ 266 (500) -.-+++|+..+..+-+++|...-++ -+++ |||-=+++. +.|-- .-+-++=|.|.--.. |. T Consensus 82 ~~Ac~ey~~~~~~l~~~~g~~~d~I--PQl~-dvs~~L~~~-TGf~l-~pv~Glls~rdF~~~-----------LA---- 141 (306) T cd03347 82 THACYEYNHVFPLLEKNCGFSEDNI--PQLE-DVSNFLQTC-TGFRL-RPVAGLLSSRDFLAG-----------LA---- 141 (306) T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCC--CCHH-HHHHHHHHH-HCCEE-EECCCCCCHHHHHHH-----------HH---- T ss_conf 7778999999999999549998889--9769-999998862-09889-743664788999999-----------74---- Q ss_pred CCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC Q ss_conf 034432337554336653035667777833277877312699999998853024836898864320268 Q gi|254780979|r 267 IRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI 335 (500) Q Consensus 267 v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL 335 (500) -|.| -.|..+|..+.- -|-||||+ +-++---+|.|-+.....|..++|+ T Consensus 142 ----~rvF----~~TqyiRh~~~p---~YtpEPDi---------~He~~GH~p~ladp~fA~f~q~iG~ 190 (306) T cd03347 142 ----FRVF----HSTQYIRHPSKP---MYTPEPDI---------CHELLGHVPLFADPSFAQFSQEIGL 190 (306) T ss_pred ----CCCC----CCEEEECCCCCC---CCCCCCCH---------HHHHHCCCCCCCCHHHHHHHHHHHH T ss_conf ----1835----410134267777---77899962---------6566445744478889999999999 No 66 >KOG4168 consensus Probab=32.48 E-value=34 Score=14.47 Aligned_cols=80 Identities=18% Similarity=0.176 Sum_probs=46.4 Q ss_pred HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCEECCCHHHHHHHHH Q ss_conf 65457887643387400064898999999988863873147899999999817999889999639876189889999999 Q gi|254780979|r 369 VINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVEELGLRQVTDLSAIEKVVD 448 (500) Q Consensus 369 i~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL~~isD~~eL~~iv~ 448 (500) +.-++..+|+...- -+..+.+.|.+++.....++++..-+++++..--.+-....-+|++-.= ...|++.|+++|. T Consensus 50 i~~et~kYls~~~n---~~~qt~E~i~el~~k~~~fkLtKAE~LqiiN~rPss~vel~~~iE~~ee-Rf~~ee~i~elv~ 125 (149) T KOG4168 50 ITYETLKYLSDNKN---ASTQTNESIIELITKLKSFKLTKAEILQIINLRPSSSVELYLIIEEVEE-RFQDEEDIEELVE 125 (149) T ss_pred HHHHHHHHHHCCCC---CCCCCHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHH-HCCCHHCHHHHHH T ss_conf 69999999844733---2313688999999986232203899998850286148999999988887-3003105999987 Q ss_pred HHHH Q ss_conf 9998 Q gi|254780979|r 449 EVIN 452 (500) Q Consensus 449 eVI~ 452 (500) .|-. T Consensus 126 ~i~~ 129 (149) T KOG4168 126 TISK 129 (149) T ss_pred HCCC T ss_conf 6015 No 67 >COG5418 Predicted secreted protein [Function unknown] Probab=32.42 E-value=18 Score=16.59 Aligned_cols=16 Identities=31% Similarity=0.546 Sum_probs=9.8 Q ss_pred CCCCCCCCCCCCCCCC Q ss_conf 3767888201445442 Q gi|254780979|r 102 YPDLPQGYQISQHDKP 117 (500) Q Consensus 102 YpDlpkgyQiTQ~~~P 117 (500) -|.|||||||-|+--| T Consensus 38 l~~npk~~~IiqlPCP 53 (164) T COG5418 38 LPSNPKDWNIIQLPCP 53 (164) T ss_pred HCCCCCCCCEEECCCC T ss_conf 4059777855762583 No 68 >cd05298 GH4_GlvA_pagL_like Glycoside Hydrolases Family 4; GlvA- and pagL-like glycosidases. Bacillus subtilis GlvA and Clostridium acetobutylicum pagL are 6-phospho-alpha-glucosidase, catalyzing the hydrolysis of alpha-glucopyranoside bonds to release glucose from oligosaccharides. The substrate specificities of other members of this subgroup are unknown. Some bacteria simultaneously translocate and phosphorylate disaccharides via the phosphoenolpyruvate-dependent phosphotransferase system (PEP_PTS). After translocation, these phospho-disaccharides may be hydrolyzed by the GH4 glycoside hydrolases, which include 6-phospho-beta-glucosidases, 6-phospho-alpha-glucosidases, alpha-glucosidases/alpha-glucuronidases (only from Thermotoga), and alpha-galactosidases. Members of this subfamily are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductas Probab=32.31 E-value=34 Score=14.56 Aligned_cols=86 Identities=15% Similarity=0.231 Sum_probs=47.1 Q ss_pred HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCC-EECCCHHHHHHHH Q ss_conf 654578876433874000648989999999888638731478999999998179998899996398-7618988999999 Q gi|254780979|r 369 VINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVEELGL-RQVTDLSAIEKVV 447 (500) Q Consensus 369 i~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL-~~isD~~eL~~iv 447 (500) .+.|+...+++.|.......--|.+++.|+.....- -+-.++..++ +|.+.+....-+ -.+.+.+..++++ T Consensus 351 ~vVEvp~~Vd~~Gi~P~~vg~lP~~~~~L~~~~~~~------e~LtveAal~--g~~~~a~~Al~~dPlv~s~~~a~~l~ 422 (437) T cd05298 351 AMVEVPAYIGSNGPEPLVVGKIPTFYKGLMEQQVAY------EKLLVEAYLE--GSYQKALQAFTLNRTVPSAKVAKEVL 422 (437) T ss_pred CEEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHH------HHHHHHHHHH--CCHHHHHHHHHHCCCCCCHHHHHHHH T ss_conf 679988897699853141698998999999999999------9999999996--89999999997298999989999999 Q ss_pred HHHHHHCHHHHHHHH Q ss_conf 999983999899752 Q gi|254780979|r 448 DEVINSNPNNVARIA 462 (500) Q Consensus 448 ~eVI~~np~~V~~~k 462 (500) ++.|++|.+-.-+|| T Consensus 423 deml~a~~~~LP~fk 437 (437) T cd05298 423 DDLIEANKGYWPELK 437 (437) T ss_pred HHHHHHHHHHCCCCC T ss_conf 999999787665669 No 69 >COG3495 Uncharacterized protein conserved in bacteria [Function unknown] Probab=32.05 E-value=17 Score=16.76 Aligned_cols=29 Identities=21% Similarity=0.374 Sum_probs=24.3 Q ss_pred EECCCCCCCCCCCCCCCCCCCCEEEEEEC Q ss_conf 12376788820144544201533899970 Q gi|254780979|r 100 YFYPDLPQGYQISQHDKPIVGEGKVSVSI 128 (500) Q Consensus 100 YfYpDlpkgyQiTQ~~~Pi~~~G~l~~~~ 128 (500) -.|---|||||+++.+.|+...|.+.++. T Consensus 113 IV~Vk~~kg~km~elyqp~wV~GtlK~e~ 141 (166) T COG3495 113 IVLVKPAKGYKMSELYQPVWVTGTLKPEI 141 (166) T ss_pred EEEEECCCCCCHHHHHCEEEEEEEECHHH T ss_conf 89985698861767302147863202102 No 70 >TIGR00034 aroFGH phospho-2-dehydro-3-deoxyheptonate aldolase; InterPro: IPR006219 Members of this group catalyze the first enzymatic reaction of the shikimate pathway. The common (shikimate) pathway links metabolism of carbohydrates to biosynthesis of aromatic amino acids phenylalanine, tyrosine, tryptophan, and derivatives in microorganisms and in plants. In a sequence of seven enzymatic reactions, D-erythrose 4-phosphate (E4P), an intermediate of the pentose phosphate pathway, and phosphoenol pyruvate (PEP), a glycolytic intermediate, are converted to chorismate. The pathway begins with the stereospecific condensation of E4P and PEP to yield 7-phospho 2-dehydro 3-deoxy-D-arabino-heptulosonate (DAHP), catalyzed by 3-deoxy-7-phosphoheptulonate synthase (DAHPS) (EC 2.5.1.54, formerly EC 4.1.2.15). The divalent metal cation requirement of this enzyme can be satisfied by a broad range of metals . A Cys residue in a Cys-X-X-His motif has been identified as part of a metal binding site . In Escherichia coli, the enzyme exists in three isoforms, each specifically inhibited by one of the three aromatic amino acids. DAHP synthetases fall into two classes, class I (represented by this entry) and class II (represented by PIRSF015573 from PIRSF). Class I was believed to be limited to microorganisms and class II to plants. However, a more recent study showed that class II also contains enzymes from a microbial eukaryote and several bacteria . Brick and Woodard proposed that the difference between the two classes lies in their metal ion requirement for activity. Whereas class I requires no metal cation, class II is dependent on a metal cation for activity. However, recently a class I DAHP synthase from Thermotoga maritima has been purified, characterised, and shown to be a metalloenzyme . The three-dimentional structures of DAHP synthases have been determined , , , , . The DAHPS(Phe) monomer is a (beta/alpha)8 barrel with an additional N-terminal beta strand and helices and an extra beta sheet near the C terminus . The active site is located in a cleft at the carboxyl end of the barrel . The allosteric feedback inhibition binding site of DAHPS(Phe) is composed of residues from two adjacent subunits of a tight dimer and is at least 20 angstroms away from the closest active site . The absence of the shikimate pathway in animals makes it an attractive target for nontoxic herbicidal, antimicrobial, and antifungal agents. The nontoxic herbicide glyphosphate competitively inhibits 3-phosphoshikimate 1-carboxyvinyltransferase, the sixth enzymatic reaction of the pathway.; GO: 0003849 3-deoxy-7-phosphoheptulonate synthase activity, 0009073 aromatic amino acid family biosynthetic process. Probab=31.80 E-value=35 Score=14.40 Aligned_cols=72 Identities=21% Similarity=0.330 Sum_probs=38.0 Q ss_pred EEECCC-CCCHHHHHHHHHHHHHHHHHH----------------------C-CCCCCCCCCEEECCCCCCCCCC-----C Q ss_conf 630365-277899999999999998642----------------------0-4567643220112575432137-----6 Q gi|254780979|r 178 IVTKPD-MRSSLEAKAFLTKLRSILRYL----------------------G-TCDGNMEEGSMRADVNVSVCRP-----G 228 (500) Q Consensus 178 IVT~Pd-~~s~~ea~~~~~~l~~ilr~~----------------------g-isd~~meeGslR~DvNVSi~~~-----~ 228 (500) +|-.|| +|+|+-|.+|+..|..|-.-+ | |+|..| .||+|..-=.-|.++ . T Consensus 54 VViGPCSiHDP~AA~eYA~RL~~L~~~l~~~L~IvMRvYfEKPRTtVGWKGLINDP~l-n~sf~in~GL~iARkLL~~~~ 132 (348) T TIGR00034 54 VVIGPCSIHDPEAAIEYATRLKKLREKLKDDLEIVMRVYFEKPRTTVGWKGLINDPDL-NGSFRINKGLRIARKLLLDLN 132 (348) T ss_pred EEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCCCC-CCCCCHHHHHHHHHHHHHHHH T ss_conf 9975888574689999999999999875037607876431698701034444588888-885220256899999998886 Q ss_pred -CCCCCCCCCCCCCHHHHHHHHH Q ss_conf -6678862223540246599999 Q gi|254780979|r 229 -EAWGTRCEVKNVNSIRFLGLAI 250 (500) Q Consensus 229 -~~~GtRvEIKNlnS~~~i~~AI 250 (500) -.+-.-+|.=-++|=-++.+.+ T Consensus 133 ~~GlP~a~EfLD~~sPQylADl~ 155 (348) T TIGR00034 133 NLGLPIAGEFLDMISPQYLADLV 155 (348) T ss_pred HCCCCCCCCCCCCCCHHHHHHHH T ss_conf 31576344312466637899999 No 71 >cd01199 INT_Tn1545_C Tn1545-related conjugative transposon integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes bacterial (gram positive) and phage integrases, including those similar to Tn1545, Tn5252, and Tn5276 conjugative transposon integrases and Lactobacillus phage phi adh integrase. Probab=31.63 E-value=36 Score=14.38 Aligned_cols=40 Identities=23% Similarity=0.170 Sum_probs=17.8 Q ss_pred CCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHH Q ss_conf 5676432201125754321376667886222354024659 Q gi|254780979|r 207 CDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFL 246 (500) Q Consensus 207 sd~~meeGslR~DvNVSi~~~~~~~GtRvEIKNlnS~~~i 246 (500) +|-+++++.++++-++.-.......+.+...|+-+|.|.| T Consensus 46 ~did~~~~~i~i~~~~~~~~~~~~~~~~~~~Kt~~~~R~v 85 (205) T cd01199 46 KDIDFENKLINIDGTLDSHTGKEENGYKDTPKTKSSIRTI 85 (205) T ss_pred HHCCCCCCEEEEEEEEEEECCCCCCCEECCCCCCCCEEEE T ss_conf 8806558989997788641256666243457788863686 No 72 >PRK11814 cysteine desulfurase activator complex subunit SufB; Provisional Probab=31.03 E-value=35 Score=14.46 Aligned_cols=38 Identities=18% Similarity=0.181 Sum_probs=22.4 Q ss_pred HCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 302483689886432026889998887641136789886 Q gi|254780979|r 317 QIPELPDAKRERFIGEFGISLYDASVLVSDKSIADYFEK 355 (500) Q Consensus 317 ~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~ 355 (500) +...+-.+..--|++ =||++++|..|+-..-+...+++ T Consensus 425 tvg~I~eeqlfYLmS-RGl~e~eA~~lIV~GF~~~v~~~ 462 (484) T PRK11814 425 TTSKISEDQLFYCRQ-RGISEEDAVSMIVNGFCKDVFQE 462 (484) T ss_pred ECCCCCHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHH T ss_conf 445679899999986-79999999999999978999876 No 73 >PRK06740 histidinol-phosphatase; Validated Probab=30.78 E-value=34 Score=14.53 Aligned_cols=47 Identities=11% Similarity=0.188 Sum_probs=25.8 Q ss_pred HHHHHHHHHHCCCCHHHHH---HHHHHHCCCCHHHHHHHHHHHH----HHHHHHHHH Q ss_conf 9999998853024836898---8643202688999888764113----678988640 Q gi|254780979|r 308 EDFIRAIKKQIPELPDAKR---ERFIGEFGISLYDASVLVSDKS----IADYFEKLA 357 (500) Q Consensus 308 ~e~i~~i~~~lPelP~~~~---~rl~~~yGLs~~dA~~L~~~~~----la~~FE~v~ 357 (500) ++.+.++-+. -|++.. --|+..||+.......--.... ..+||+.+. T Consensus 155 E~~l~~lL~~---YpfDYvIGSVHFl~gWgFDnPe~~~~~~~~Dl~~iy~~YF~~ve 208 (338) T PRK06740 155 EQELQSLLAL---GDFDYVIGSVHFLNGWGFDNPDTKEYFEEHDLYALYDTFFKTVE 208 (338) T ss_pred HHHHHHHHHC---CCCCEEEEEEEEECCCCCCCHHHHHHHHHCCHHHHHHHHHHHHH T ss_conf 9999999744---99755998888607878889789988850899999999999999 No 74 >TIGR02614 ftsW cell division protein FtsW; InterPro: IPR013437 FtsW is an integral membrane protein with ten transmembrane segments . In general, it is one of two paralogs involved in peptidoglycan biosynthesis, the other being RodA, and is essential for cell division. The FtsW designation is not used in endospore-forming bacteria (e.g. Bacillus subtilis), where these proteins are designated SpoVE, and three or more RodA/FtsW/SpoVE family paralogs are present. SpoVE acts in spore cortex formation and is dispensable for growth. Biological roles for FtsW in cell division include recruitment of penicillin-binding protein 3 to the division site.; GO: 0009252 peptidoglycan biosynthetic process, 0051301 cell division, 0016021 integral to membrane. Probab=30.28 E-value=15 Score=17.15 Aligned_cols=32 Identities=25% Similarity=0.398 Sum_probs=25.9 Q ss_pred CEECCCC-------CCCCCCCCCCCCCCCCEEEEEECCC Q ss_conf 2123767-------8882014454420153389997067 Q gi|254780979|r 99 NYFYPDL-------PQGYQISQHDKPIVGEGKVSVSIGP 130 (500) Q Consensus 99 ~YfYpDl-------pkgyQiTQ~~~Pi~~~G~l~~~~~~ 130 (500) .|..|+. -+|||+||--..++++|..=...|. T Consensus 214 ~Fl~P~~Dp~~~~~g~gyQl~qsl~A~g~GG~~G~GLG~ 252 (370) T TIGR02614 214 SFLDPWADPFLADQGSGYQLTQSLIALGRGGLFGVGLGN 252 (370) T ss_pred HHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEECCCC T ss_conf 873777664010478960499999998679856741687 No 75 >KOG2050 consensus Probab=30.09 E-value=38 Score=14.20 Aligned_cols=13 Identities=15% Similarity=0.506 Sum_probs=6.4 Q ss_pred CCCCCCCCCCCCC Q ss_conf 7783327787731 Q gi|254780979|r 292 DYRYFSEPDLLPL 304 (500) Q Consensus 292 DYRyfPEPDLPpi 304 (500) .|+-|-|.|.+.+ T Consensus 275 efqlfK~sn~~Tl 287 (652) T KOG2050 275 EFQLFKDSNDKTL 287 (652) T ss_pred HHHHHHCCCCCCH T ss_conf 9898761685519 No 76 >CHL00085 ycf24 putative ABC transporter Probab=30.08 E-value=23 Score=15.81 Aligned_cols=36 Identities=17% Similarity=0.265 Sum_probs=22.0 Q ss_pred HCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 30248368988643202688999888764113678988640 Q gi|254780979|r 317 QIPELPDAKRERFIGEFGISLYDASVLVSDKSIADYFEKLA 357 (500) Q Consensus 317 ~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v~ 357 (500) +...+-.+..--|++ =||++++|..|+-.. |++.+. T Consensus 426 tvgkI~eeqlfYLmS-RGl~e~eA~~lIV~G----F~~~v~ 461 (485) T CHL00085 426 STSKIGEEQIFYFLQ-RGINLEEAISLMISG----FCQDVF 461 (485) T ss_pred ECCCCCHHHHHHHHH-CCCCHHHHHHHHHHH----HHHHHH T ss_conf 435679999999986-699999999999998----479888 No 77 >KOG0823 consensus Probab=29.99 E-value=12 Score=17.95 Aligned_cols=46 Identities=15% Similarity=0.239 Sum_probs=28.1 Q ss_pred CCCCCEEEEEEEEEE-ECCC-CCCCC-CCCCCC-CCCCCCCCCHHHCCCC Q ss_conf 478033898999788-8689-86555-884246-8987652061302689 Q gi|254780979|r 19 TGDWEVVIGIEVHAQ-LSVV-SKLFS-GASVNF-GAEPNTQVSFFDAAMP 64 (500) Q Consensus 19 ~~~~e~vIGLEiH~q-L~t~-tKlFc-~c~~~~-~~~pNt~v~~~~~g~P 64 (500) -++|+-=|-||.-.. .-|- --||| +|-..+ ..-+|+..||||-+-- T Consensus 45 ~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~V 94 (230) T KOG0823 45 GGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEV 94 (230) T ss_pred CCCEEEEEECCCCCCCEEEECCCCEEHHHHHHHHHHCCCCEECCCCCCCC T ss_conf 88222365312357877741454303488888776347870488624323 No 78 >KOG3591 consensus Probab=29.55 E-value=38 Score=14.13 Aligned_cols=24 Identities=13% Similarity=0.364 Sum_probs=17.3 Q ss_pred CCCCCCCCCCCCCCCCCEEEEEEC Q ss_conf 788820144544201533899970 Q gi|254780979|r 105 LPQGYQISQHDKPIVGEGKVSVSI 128 (500) Q Consensus 105 lpkgyQiTQ~~~Pi~~~G~l~~~~ 128 (500) ||+||-.++-.--+..+|.|.|.. T Consensus 123 LP~~vdp~~V~S~LS~dGvLtI~a 146 (173) T KOG3591 123 LPEDVDPTSVTSTLSSDGVLTIEA 146 (173) T ss_pred CCCCCCHHHEEEEECCCCEEEEEC T ss_conf 999989506278637994089973 No 79 >PRK02471 bifunctional glutamate--cysteine ligase/glutathione synthetase; Provisional Probab=29.31 E-value=39 Score=14.11 Aligned_cols=41 Identities=10% Similarity=0.170 Sum_probs=21.5 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCC Q ss_conf 457777654578876433874000648989999999888638731 Q gi|254780979|r 363 KIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTIS 407 (500) Q Consensus 363 k~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is 407 (500) +..|.+++.++...++.-+.+-. -.+-+.++...+.+-+.| T Consensus 349 ~~~a~~il~~l~~~~~~l~l~~~----y~~~~~~~~~~v~~P~~T 389 (753) T PRK02471 349 AAEGELILDAMEDFVQHLGLPDE----FQDLIEQLKEQVTDPKKT 389 (753) T ss_pred HHHHHHHHHHHHHHHHHHCCCHH----HHHHHHHHHHHHHCCCCC T ss_conf 78999999999999997199889----999999999987391139 No 80 >pfam07028 DUF1319 Protein of unknown function (DUF1319). This family contains a number of viral proteins of unknown function approximately 200 residues long. Family members seem to be restricted to badnaviruses. Probab=28.87 E-value=33 Score=14.63 Aligned_cols=20 Identities=20% Similarity=0.406 Sum_probs=12.1 Q ss_pred HHHHHHHHHHHHHHCHHHHHH Q ss_conf 889999999999839998997 Q gi|254780979|r 440 LSAIEKVVDEVINSNPNNVAR 460 (500) Q Consensus 440 ~~eL~~iv~eVI~~np~~V~~ 460 (500) ..+++++|.+ |++.|+.|++ T Consensus 84 k~dV~eLV~~-IseQPK~IEq 103 (119) T pfam07028 84 KEDVEELVLR-ISEQPKLIEK 103 (119) T ss_pred HHHHHHHHHH-HHHCCHHHHH T ss_conf 8999999999-9868588999 No 81 >cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe Probab=28.63 E-value=12 Score=17.88 Aligned_cols=57 Identities=21% Similarity=0.278 Sum_probs=38.5 Q ss_pred CCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 03443233755433665303566777783327787731269999999885302483689886432026889998887641 Q gi|254780979|r 267 IRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSD 346 (500) Q Consensus 267 v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~ 346 (500) |...|-+|=+..|.-.+-|. .-||+|.+-|+ +.++ ..+||+++.|++...+..|++= T Consensus 13 v~~~TLR~YEr~GLi~P~R~----~G~RlYs~~Di----------~rLr---------fIkrL~~e~G~nlagI~~iLsl 69 (120) T cd04767 13 IHPETLRIWERHGLIKPARR----NGQRLYSNNDL----------KRLR---------FIKKLINEKGLNIAGVKQILSM 69 (120) T ss_pred CCHHHHHHHHHCCCCCCCCC----CCCCCCCHHHH----------HHHH---------HHHHHHHHCCCCHHHHHHHHHC T ss_conf 68899999998589688888----98227799999----------9999---------9999999759689999999806 No 82 >TIGR00954 3a01203 Peroxysomal long chain fatty acyl transporter; InterPro: IPR005283 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). The members of this family are integral membrane proteins and they are involved in the import of activated long-chain fatty acids from the cytosol to the peroxisomal matrix. ; GO: 0005524 ATP binding, 0006810 transport, 0016021 integral to membrane. Probab=28.51 E-value=40 Score=14.01 Aligned_cols=73 Identities=15% Similarity=0.252 Sum_probs=46.4 Q ss_pred CCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 43366530356677778332778773126999999988530248368988643202688999888764113678988 Q gi|254780979|r 278 KNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDKSIADYFE 354 (500) Q Consensus 278 ~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE 354 (500) .......++|+... ++|==|==|-+-.-..+=+.|= =|..+++..+||-++||+++.|=..++..-.|.+..+ T Consensus 592 sklimG~Lt~P~~~--~lFY~PQRPYM~~G~TLRDQiI--YPDs~~d~~~ryhndyG~sD~dL~~iL~~V~L~~iL~ 664 (788) T TIGR00954 592 SKLIMGRLTKPAKG--KLFYVPQRPYMTLGSTLRDQII--YPDSSEDMKRRYHNDYGLSDKDLEQILDNVQLEHILE 664 (788) T ss_pred CEEECCEECCCCCC--CEEECCCCCCCCCCCCCCCCCC--CCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCHHHHHH T ss_conf 20344410558888--7641357764588885334103--5889799998630258998899999975413223422 No 83 >TIGR01204 bioW 6-carboxyhexanoate--CoA ligase; InterPro: IPR005499 This family contains the enzyme 6-carboxyhexanoate--CoA ligase 6.2.1.14 from EC. This enzyme is involved in the first step of biotin synthesis, where it converts pimelate into pimeloyl-CoA . The enzyme requires magnesium as a cofactor and forms a homodimer .; GO: 0009102 biotin biosynthetic process. Probab=28.41 E-value=40 Score=14.00 Aligned_cols=49 Identities=20% Similarity=0.321 Sum_probs=26.8 Q ss_pred EEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCC Q ss_conf 8423666520231001156787148866157861257630365277899999999999998642045 Q gi|254780979|r 141 VGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTC 207 (500) Q Consensus 141 v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gis 207 (500) ..-.+|++|+=.+-+| +-+ |=++|.|- ++.|||+|..++. .+|..-||| T Consensus 38 ~DF~qi~vEkv~~~~i---------~~~-----~PL~i~T~-~~~spEea~k~Ar---~~Lt~eGv~ 86 (238) T TIGR01204 38 ADFMQIKVEKVKDEEI---------VKI-----NPLKISTI-EVSSPEEARKLAR---KLLTKEGVS 86 (238) T ss_pred CCEEEEEEEEEECCEE---------EEE-----CCCEEEEE-ECCCHHHHHHHHH---HHHHHCCCH T ss_conf 6535678998707566---------752-----48612331-0158467899999---876514742 No 84 >KOG3666 consensus Probab=28.37 E-value=40 Score=13.99 Aligned_cols=46 Identities=24% Similarity=0.366 Sum_probs=18.9 Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHH Q ss_conf 33277877312699999998853024836898864320268899988 Q gi|254780979|r 295 YFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDAS 341 (500) Q Consensus 295 yfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~ 341 (500) ..|=|+.||+..|..+|.++-.++-...+-+..+|.. ...+=+|.+ T Consensus 790 ~ipip~f~p~d~s~~fIgrL~~eilriTdPK~t~F~d-~~~tWyd~K 835 (1141) T KOG3666 790 HIPIPKFTPVDESVTFIGRLCREILRITDPKMTCFID-QLNTWYDMK 835 (1141) T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHH-HHHHHHHHH T ss_conf 5678889998815679999999888238823678887-441488787 No 85 >pfam00351 Biopterin_H Biopterin-dependent aromatic amino acid hydroxylase. This family includes phenylalanine-4-hydroxylase, the phenylketonuria disease protein. Probab=28.30 E-value=40 Score=14.02 Aligned_cols=111 Identities=22% Similarity=0.334 Sum_probs=57.1 Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 77899999999999998642045676432201125754321376667886222354024659999999999999973139 Q gi|254780979|r 185 RSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILEDG 264 (500) Q Consensus 185 ~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~~G 264 (500) ..-.-+++|+..+..+-+++|...-++ -+++ |||-=+++. +.|.- .=+-++=|.|.--.. |. T Consensus 80 ~~~~AC~eyl~~~~~L~~~~g~~~d~I--PQL~-dvs~~L~~~-TGf~l-rpv~Glls~rdFl~~-----------LA-- 141 (309) T pfam00351 80 YPTHACREYLHAFPLLEKYCGFREDNI--PQLE-DVSNFLKER-TGFSL-RPVAGLLSARDFLAG-----------LA-- 141 (309) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCC--CCHH-HHHHHHHHC-CCCEE-EECCCCCCHHHHHHH-----------HH-- T ss_conf 776758999999999998459998888--9769-999988750-39878-632553688999999-----------74-- Q ss_pred CCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC Q ss_conf 80034432337554336653035667777833277877312699999998853024836898864320268 Q gi|254780979|r 265 GHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI 335 (500) Q Consensus 265 ~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL 335 (500) -|.| -.|-.+|.-+.- -|-||||+ +-++---+|.|-+.....|..++|+ T Consensus 142 ------~rvF----~~TqyIRh~s~p---~YtpEPD~---------~Hel~GH~p~l~dp~fA~f~q~~G~ 190 (309) T pfam00351 142 ------FRVF----HCTQYIRHASSP---MYTPEPDC---------CHELLGHVPLLADPSFAQFSQEIGL 190 (309) T ss_pred ------HCCC----CCCCEECCCCCC---CCCCCCCH---------HHHHHCCCCCCCCHHHHHHHHHHHH T ss_conf ------1836----521114158887---77899962---------6566445734378789999999999 No 86 >KOG1261 consensus Probab=27.53 E-value=41 Score=13.89 Aligned_cols=78 Identities=23% Similarity=0.231 Sum_probs=51.5 Q ss_pred EEEEEEEEEECCCCCCCCCCCCCEEEEEC----CCCCCEEEEEECC-----CCCCHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 84236665202310011567871488661----5786125763036-----52778999999999999986420456764 Q gi|254780979|r 141 VGIERIHLEQDAGKSIHDQYSAVSCIDLN----RSGVALMEIVTKP-----DMRSSLEAKAFLTKLRSILRYLGTCDGNM 211 (500) Q Consensus 141 v~I~~i~lEED~gk~~h~~~~~~slvD~N----RaGvPLiEIVT~P-----d~~s~~ea~~~~~~l~~ilr~~gisd~~m 211 (500) ||=.--||-|--- .+|+...+-|++||- ----.||-+.+.| -|.+.+||+-+-.-+...-.++|+.. T Consensus 175 VRPRGWHl~EkH~-~Id~eP~sgslfDFGLyffHNAK~li~~GsGPyFYLPKmeh~~EaklWndvF~~aed~~Gi~R--- 250 (552) T KOG1261 175 VRPRGWHLPEKHL-LIDDEPISGSLFDFGLYFFHNAKELIKQGSGPYFYLPKMEHHEEAKLWNDVFCVAEDKIGIPR--- 250 (552) T ss_pred ECCCCCCCCHHEE-EECCCCCCCEEEEEEEEEEECHHHHHHCCCCCEEECCCCCCHHHHHHHHHHHHHHHHHCCCCC--- T ss_conf 7167656750026-652874541366434567712799985489873656321106788888989998888608876--- Q ss_pred CCCEEECCCCCCC Q ss_conf 3220112575432 Q gi|254780979|r 212 EEGSMRADVNVSV 224 (500) Q Consensus 212 eeGslR~DvNVSi 224 (500) |++||-|=|-- T Consensus 251 --GtIraTVLIEt 261 (552) T KOG1261 251 --GTIRATVLIET 261 (552) T ss_pred --CCEEEEEEHHH T ss_conf --73578874863 No 87 >KOG2599 consensus Probab=27.28 E-value=42 Score=13.86 Aligned_cols=108 Identities=15% Similarity=0.200 Sum_probs=49.4 Q ss_pred EEEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECC Q ss_conf 98423666520231001156787148866157861257630365277899999999999998642045676432201125 Q gi|254780979|r 140 EVGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRAD 219 (500) Q Consensus 140 ~v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~D 219 (500) ....+-.--|=|+--+++= =|-+| -..++.+. .+++|.....+. ....++ .--| T Consensus 30 tFPLQllGwdVD~insVqF---------SNHtG---Y~~~kG~~-~~~~eL~dL~eg---------l~~nn~----~~Y~ 83 (308) T KOG2599 30 TFPLQLLGWDVDVINSVQF---------SNHTG---YAHVKGQV-LNEEELEDLYEG---------LLLNNL----NKYD 83 (308) T ss_pred CCCHHHHCCCCCCCCCEEE---------CCCCC---CCCCCCCC-CCHHHHHHHHHH---------HHHCCC----CCCC T ss_conf 3421220632343441564---------26668---74111631-689999999998---------764366----3322 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCC Q ss_conf 75432137666788622235402465999999999999997313980034432337554336653035667777833277 Q gi|254780979|r 220 VNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEP 299 (500) Q Consensus 220 vNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEP 299 (500) +=.+ ==+-|.++++.|...+. + +-+.... -+-..|+..|- ++ |||-+. T Consensus 84 ~vLT-----------GY~~n~~~l~~i~~iv~-----~--lk~~np~---~~wv~DPVmGD-------nG----~lYV~e 131 (308) T KOG2599 84 AVLT-----------GYLPNVSFLQKIADIVK-----K--LKKKNPN---LTWVCDPVMGD-------NG----RLYVPE 131 (308) T ss_pred EEEE-----------ECCCCHHHHHHHHHHHH-----H--HHHCCCC---EEEEECCCCCC-------CC----CEECCH T ss_conf 4553-----------05688269999999999-----9--9842998---49996763467-------85----174458 Q ss_pred CCCCCC Q ss_conf 877312 Q gi|254780979|r 300 DLLPLE 305 (500) Q Consensus 300 DLPpi~ 305 (500) |+-|+. T Consensus 132 elipvY 137 (308) T KOG2599 132 ELIPVY 137 (308) T ss_pred HHHHHH T ss_conf 777999 No 88 >pfam09043 Lys-AminoMut_A D-Lysine 5,6-aminomutase alpha subunit. Members of his family are involved in the 1,2 rearrangement of the terminal amino group of DL-lysine and of L-beta-lysine, using adenosylcobalamin (AdoCbl) and pyridoxal-5'-phosphate as cofactors. The structure is predominantly a PLP-binding TIM barrel domain, with several additional alpha-helices and beta-strands at the N and C termini. These helices and strands form an intertwined accessory clamp structure that wraps around the sides of the TIM barrel and extends up toward the Ado ligand of the Cbl cofactor, providing most of the interactions observed between the protein and the Ado ligand of the Cbl, suggesting that its role is mainly in stabilising AdoCbl in the precatalytic resting state. Probab=26.75 E-value=43 Score=13.79 Aligned_cols=52 Identities=25% Similarity=0.321 Sum_probs=26.6 Q ss_pred HHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCEECCCHHHHHHHHHHHHHHCHHHHHHHH Q ss_conf 86387314789999999981799988999963987618988999999999983999899752 Q gi|254780979|r 401 IIDGTISGKIAKDIFNILWEKGGTPKEIVEELGLRQVTDLSAIEKVVDEVINSNPNNVARIA 462 (500) Q Consensus 401 i~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL~~isD~~eL~~iv~eVI~~np~~V~~~k 462 (500) +.+.-++-..||-||..+-.-+ ++. .....+-++.-..+|+.+--+..+++. T Consensus 414 l~DR~laiena~Yifn~~~~l~-------~ei---~fk~~G~i~~RA~eVL~~a~~LLe~i~ 465 (509) T pfam09043 414 MSDRALAIENAKYIFNNMKDIG-------EEI---EFKEGGIIQSRAQEVLEKALALLEEIE 465 (509) T ss_pred HHHHHHHHHHHHHHHHHHHHCC-------CCE---EECCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 4457888634699998776425-------323---368987289999999999999999998 No 89 >PRK13335 superantigen-like protein; Reviewed Probab=26.63 E-value=43 Score=13.78 Aligned_cols=70 Identities=16% Similarity=0.227 Sum_probs=38.0 Q ss_pred HHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC Q ss_conf 99997313980034432337554336653035667777833277877312699999998853024836898864320268 Q gi|254780979|r 256 RQIAILEDGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGI 335 (500) Q Consensus 256 RQ~~ll~~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGL 335 (500) ||..-+.-||--.---..+|..-+..+.--.+++.. ++|.-++.|..|.| +|-||-...|++|+++||| T Consensus 239 ~q~~kYSIGGITKtNsk~vd~~~~~~i~k~d~~g~~------~~d~s~y~I~KEeI-----SLKELDFKLRK~LIe~~gL 307 (356) T PRK13335 239 YQLKKYSVGGITKTNSKKVDHKVELSITKKDNQGMI------SRDVSEYMITKEEI-----SLKELDFKLRKQLIEKHNL 307 (356) T ss_pred CCCCEEEECCEECCCCHHHHEECCCEEEEECCCCCC------CCCCCCEEECHHHC-----CHHHHHHHHHHHHHHHCCC T ss_conf 333200125673157300100046404662247740------45554113115234-----3766426999999986064 Q ss_pred C Q ss_conf 8 Q gi|254780979|r 336 S 336 (500) Q Consensus 336 s 336 (500) = T Consensus 308 Y 308 (356) T PRK13335 308 Y 308 (356) T ss_pred C T ss_conf 2 No 90 >cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain Probab=26.54 E-value=18 Score=16.50 Aligned_cols=56 Identities=25% Similarity=0.310 Sum_probs=33.7 Q ss_pred CCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 432337554336653035667777833277877312699999998853024836898864320268899988876411 Q gi|254780979|r 270 ETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDK 347 (500) Q Consensus 270 ETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~ 347 (500) .|-+|=+..|.-.+-+ -+..-||||.+-|+.-+. ....| .++|+|..++..++.++ T Consensus 16 ~TLRyYe~~GLl~P~~--r~~nGYR~Ys~~dl~rL~-------------------~I~~l-r~lG~sL~eIk~~L~~~ 71 (172) T cd04790 16 STLLYYERIGLLSPSA--RSESNYRLYGERDLERLE-------------------QICAY-RSAGVSLEDIRSLLQQP 71 (172) T ss_pred HHHHHHHHCCCCCCCC--CCCCCCCCCCHHHHHHHH-------------------HHHHH-HHCCCCHHHHHHHHCCC T ss_conf 8999999887989988--499987077999999999-------------------99999-98799999999998399 No 91 >PRK12559 transcriptional regulator Spx; Provisional Probab=26.51 E-value=43 Score=13.77 Aligned_cols=85 Identities=15% Similarity=0.354 Sum_probs=46.4 Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCC-----CCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCC Q ss_conf 302457777654578876433874-----000648989999999888638731478999999998179998899996398 Q gi|254780979|r 360 RDKKIVANWVINDLLGVLNRSGKS-----IEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVEELGL 434 (500) Q Consensus 360 ~~pk~~Anwi~~el~~~ln~~~~~-----~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL 434 (500) ...+.|-.|+- +.+++ +.+.+++.+.|..++.+.+.|. .+++. ..+.... +.++ T Consensus 11 stcRKA~~wL~--------~~~I~y~~~d~~~~~~t~~el~~ll~~~~~g~------~~lin---trs~~~k----~L~~ 69 (131) T PRK12559 11 ASCRKAKAWLE--------ENQIDYTEKNIVSNSMTVDELKSILRLTEEGA------TEIIS---TRSKTFQ----DLNI 69 (131) T ss_pred HHHHHHHHHHH--------HCCCCCEEECCCCCCCCHHHHHHHHHHHCCCH------HHHHH---CCCHHHH----HCCC T ss_conf 77999999999--------87998187210028989999999999836789------99873---4436688----7489 Q ss_pred --EECCCHHHHHHHHHHHHHHCHHHHHH-H--HCCCCCHHH Q ss_conf --76189889999999999839998997-5--272132265 Q gi|254780979|r 435 --RQVTDLSAIEKVVDEVINSNPNNVAR-I--ATKPNLVSW 470 (500) Q Consensus 435 --~~isD~~eL~~iv~eVI~~np~~V~~-~--kgk~ka~gf 470 (500) ...+ ..+++ ++|.+||..+++ + .++.-.+|| T Consensus 70 ~~~~ls----~~e~i-~ll~~~P~LiKRPIl~~~~~~~vGf 105 (131) T PRK12559 70 NIEELS----LNEFY-KLIIEHPLMLRRPIMLDEKRLQIGF 105 (131) T ss_pred CCHHCC----HHHHH-HHHHHCHHHEECCEEEECCEEEECC T ss_conf 710189----99999-9999594351285696299888579 No 92 >PRK05561 DNA topoisomerase IV subunit A; Validated Probab=26.49 E-value=43 Score=13.76 Aligned_cols=34 Identities=18% Similarity=0.478 Sum_probs=27.0 Q ss_pred CHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 999999988530248368988643202688999888764 Q gi|254780979|r 307 DEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS 345 (500) Q Consensus 307 s~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~ 345 (500) -++.|+-||++ ++-++.|++.|+||+.+|+.++. T Consensus 396 iD~VI~iIR~S-----~dak~~L~~~f~lse~QA~AIL~ 429 (745) T PRK05561 396 IDEVIEIIRES-----DEPKANLMARFGLTEIQAEAILE 429 (745) T ss_pred HHHHHHHHHCC-----CHHHHHHHHHHCCCHHHHHHHHH T ss_conf 68999999706-----32667775550879999999999 No 93 >TIGR00577 fpg formamidopyrimidine-DNA glycosylase; InterPro: IPR000191 Formamidopyrimidine-DNA glycosylase (3.2.2.23 from EC) (Fapy-DNA glycosylase) (gene fpg) is a bacterial enzyme involved in DNA repair and which excise oxidized purine bases to release 2,6-diamino-4-hydroxy-5N-methylformamido- pyrimidine (Fapy) and 7,8-dihydro-8-oxoguanine (8-OxoG) residues. In addition to its glycosylase activity, FPG can also nick DNA at apurinic/apyrimidinic sites (AP sites). FPG is a monomeric protein of about 32 Kd which binds and require zinc for its activity. The C-terminal region is the zinc binding site in the enzyme where four conserved and essential cysteines are located .. Probab=26.47 E-value=43 Score=13.76 Aligned_cols=57 Identities=21% Similarity=0.255 Sum_probs=35.2 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC-CCHHH--HHHHCC Q ss_conf 777654578876433874000648989999999888638731478999999998179-99889--999639 Q gi|254780979|r 366 ANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKG-GTPKE--IVEELG 433 (500) Q Consensus 366 Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~-~~p~~--iie~~g 433 (500) =||.+.|.+=. ++|.|++.|.=+..-+=..| ...+++||++-++.| .+..+ +....| T Consensus 184 GNIYADE~LF~----------A~ihP~~~A~~L~~~~~~~L-~~~i~~vL~~Aie~GGtt~~~q~f~~~~G 243 (292) T TIGR00577 184 GNIYADEVLFR----------AGIHPERLANQLSKEECELL-HKAIKEVLRKAIEAGGTTIRDQLFVQSDG 243 (292) T ss_pred HHHHHHHHHHH----------HCCCCCHHHHCCCHHHHHHH-HHHHHHHHHHHHHCCCCCCCCEEEEECCC T ss_conf 01066689987----------36881010001588899999-99999999999864897000200230478 No 94 >pfam12224 Amidoligase_2 Putative amidoligase enzyme. This family of proteins are likely to act as amidoligase enzymes Protein in this family are found in conserved gene neighborhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes). Probab=26.27 E-value=43 Score=13.74 Aligned_cols=69 Identities=30% Similarity=0.299 Sum_probs=39.6 Q ss_pred EEECCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCC--CCHH Q ss_conf 86615786125763036527789999999999999864204567643220112575432137666788622235--4024 Q gi|254780979|r 166 IDLNRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKN--VNSI 243 (500) Q Consensus 166 vD~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRvEIKN--lnS~ 243 (500) -|+..+++| +||||-|.--+ +...-++++-..||..|..-.+- | |..-|-|. .|.-+ .+++ T Consensus 65 ~~~~~~~~p-~EiVSPpl~~~--~~l~~l~~l~~~Lr~~ga~~tn~---s--cG~hVHin---------~~~~~~~~~~l 127 (250) T pfam12224 65 RDLADADVP-VEIVSPPLPYS--EDLEQLQELVRALRRAGAKGTNA---S--CGFHVHIN---------AEPPDLTAQTL 127 (250) T ss_pred HHHHCCCCC-EEEECCCCCCH--HHHHHHHHHHHHHHHCCCCCCCC---C--EEEEEECC---------CCCCCCCHHHH T ss_conf 231025787-46888986770--67899999999999828834677---5--47778715---------75678898999 Q ss_pred HHHHHHHH Q ss_conf 65999999 Q gi|254780979|r 244 RFLGLAIE 251 (500) Q Consensus 244 ~~i~~AI~ 251 (500) +.+-+|+- T Consensus 128 ~~~~~~~~ 135 (250) T pfam12224 128 RNLLQAYA 135 (250) T ss_pred HHHHHHHH T ss_conf 99999999 No 95 >TIGR01801 CM_A chorismate mutase; InterPro: IPR010954 This entry represents chorismate mutase (CM) domains N-terminally fused to the first enzyme in the chorismate pathway, 2-dehydro-3-deoxyphosphoheptanoate aldolase (DAHP synthetase, AroA) which are found in some Gram-positive species and Deinococcus. Only in Deinococcus, where this domain is the sole CM domain in the genome can a trusted assignment of function be made. In the other species there is at least one other CM domain present. The similarity between the Deinococcus gene and the others in this clade is sufficiently strong (~44 0dentity), that the whole clade can be trusted to be functional. The possibility exists, however, that in the Gram-positive species the fusion to the first enzyme in the pathway has evolved a separate, regulatory role.. Probab=26.27 E-value=22 Score=15.96 Aligned_cols=33 Identities=27% Similarity=0.400 Sum_probs=20.7 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHH Q ss_conf 9999998886387314789999999981799988 Q gi|254780979|r 393 QLGELIDLIIDGTISGKIAKDIFNILWEKGGTPK 426 (500) Q Consensus 393 ~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~ 426 (500) .|-+|++ ...|-...++.|.||.++|.-+.+.+ T Consensus 56 ~L~~li~-~N~GPF~~~Tik~iFKEIFkAsl~L~ 88 (104) T TIGR01801 56 MLNELIE-SNDGPFEDATIKQIFKEIFKASLELQ 88 (104) T ss_pred HHHHHHH-CCCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 9999986-07876884047788899987504543 No 96 >TIGR01846 type_I_sec_HlyB type I secretion system ATPase; InterPro: IPR010132 Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This entry contains one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane. Probab=26.18 E-value=40 Score=13.98 Aligned_cols=52 Identities=23% Similarity=0.272 Sum_probs=26.9 Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHH---HHHCCCCHHHHHHHHHH Q ss_conf 833277877312699999998853024836898864---32026889998887641 Q gi|254780979|r 294 RYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERF---IGEFGISLYDASVLVSD 346 (500) Q Consensus 294 RyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl---~~~yGLs~~dA~~L~~~ 346 (500) =|+|+.|= |-.++.+-+++.-..-=-|-..|-+-. ..++|+|=--+.++=+- T Consensus 91 ~~d~~~~~-p~~~~~e~~~~lw~g~viL~A~r~~~~~~k~~kFgfsWFiP~~~ryR 145 (703) T TIGR01846 91 IYDPEEDK-PRVLDREVLEALWSGKVILLATRSEVLGVKKLKFGFSWFIPAVIRYR 145 (703) T ss_pred EEECCCCC-CCCCCHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHH T ss_conf 98078788-65127788998748827999826877343001467512689999879 No 97 >COG1978 Uncharacterized protein conserved in bacteria [Function unknown] Probab=26.10 E-value=27 Score=15.31 Aligned_cols=70 Identities=21% Similarity=0.321 Sum_probs=45.9 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHH Q ss_conf 689886432026889998887641136789886-40243024577776545788764338740006489899999 Q gi|254780979|r 323 DAKRERFIGEFGISLYDASVLVSDKSIADYFEK-LAVNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGE 396 (500) Q Consensus 323 ~~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~-v~~~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~lae 396 (500) ...|+|+..+-.+|.+.|..+..--... -||- +..+.|.+-+..-+++|..|++.-.|.... |.|+.+|. T Consensus 73 ~slrqrI~~Eta~Sle~A~~v~ha~d~~-~feVHlDIg~~~kglTk~Lv~e~tGyvtg~G~~~q---IKPdSyaA 143 (152) T COG1978 73 NSLRQRIMEETARSLEHALMVMHAVDGR-HFEVHLDIGPDEKGLTKDLVKEATGYVTGQGYTYQ---IKPDSYAA 143 (152) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCC-CEEEEEECCCCCCCCHHHHHHHHHHHEECCCCCCE---ECCCHHHH T ss_conf 4699999999998999999999986357-63899833777454417889987530414765411---27407888 No 98 >PRK06108 aspartate aminotransferase; Provisional Probab=25.58 E-value=45 Score=13.65 Aligned_cols=42 Identities=14% Similarity=0.101 Sum_probs=19.9 Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC Q ss_conf 788622235402465999999999999997313980034432337 Q gi|254780979|r 231 WGTRCEVKNVNSIRFLGLAIEYEARRQIAILEDGGHIRQETRLFD 275 (500) Q Consensus 231 ~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~~G~~v~qETR~~d 275 (500) +|..++-.|+--......|+..=+ ..+++.|..|.-+|=.|. T Consensus 78 ~g~~v~~d~I~it~G~~~al~~~~---~~~~~pGD~Vlv~~P~Y~ 119 (382) T PRK06108 78 HGATTPPERIAVTSSGVQALMLAA---QALVGPGDEVVAVTPAWP 119 (382) T ss_pred HCCCCCHHHEEECCCHHHHHHHHH---HHHCCCCCEEEECCCCCC T ss_conf 788986684998078999999999---996699998998168786 No 99 >smart00422 HTH_MERR helix_turn_helix, mercury resistance. Probab=25.37 E-value=22 Score=15.92 Aligned_cols=50 Identities=28% Similarity=0.435 Sum_probs=28.1 Q ss_pred CCCCCCCCEEEE-EECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 233755433665-30356677778332778773126999999988530248368988643202688999888764 Q gi|254780979|r 272 RLFDPSKNETRS-LRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS 345 (500) Q Consensus 272 R~~d~~~~~T~~-mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~ 345 (500) |.|+.. |.-.+ -| ++..||||.+-|+.-+. . ...| .+.|+|..++..++. T Consensus 18 R~ye~~-Gll~p~~r---~~~g~R~Y~~~di~~l~-------~------------I~~l-r~~G~~l~~Ik~~l~ 68 (70) T smart00422 18 RYYERI-GLLPPPIR---TEGGYRLYSDEDLERLR-------F------------IKRL-KELGFSLEEIKELLE 68 (70) T ss_pred HHHHHC-CCCCCCCC---CCCCCEECCHHHHHHHH-------H------------HHHH-HHCCCCHHHHHHHHH T ss_conf 999985-89899844---89997443999999999-------9------------9999-997899999999996 No 100 >PRK13901 ruvA Holliday junction DNA helicase motor protein; Provisional Probab=25.25 E-value=45 Score=13.61 Aligned_cols=115 Identities=17% Similarity=0.145 Sum_probs=61.2 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCC---------HHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHH Q ss_conf 89886432026889998887641136789886402430---------245777765457887643387400064898999 Q gi|254780979|r 324 AKRERFIGEFGISLYDASVLVSDKSIADYFEKLAVNRD---------KKIVANWVINDLLGVLNRSGKSIEDTPISPNQL 394 (500) Q Consensus 324 ~~~~rl~~~yGLs~~dA~~L~~~~~la~~FE~v~~~~~---------pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~l 394 (500) +.++.|++--|+-+..|-.+++.-...++.+++..+.. .+..|.-|+.||.+-+.+.... . -....+ T Consensus 69 ~~F~~LisVsGIGpk~Al~iLs~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~ELk~Kl~~~~~~-~---~~~~~~ 144 (196) T PRK13901 69 EVFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRGKLVKNDEL-E---SSLFKF 144 (196) T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCC-C---CCCCCH T ss_conf 999998765882689999997579999999999928999983199958999999999997653156655-6---553448 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCEECCCHHHHHHHHHHHHH Q ss_conf 9999888638731478999999998179998899996398761898899999999998 Q gi|254780979|r 395 GELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVEELGLRQVTDLSAIEKVVDEVIN 452 (500) Q Consensus 395 aeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL~~isD~~eL~~iv~eVI~ 452 (500) .++...+..=-.+.+.++.++.++.. ......+.|.+..+.+|++++. T Consensus 145 ~e~~~AL~~LGy~~~~a~~al~~i~~----------~~~~~~~~~~~~~e~likeaLK 192 (196) T PRK13901 145 KELEQSIVNMGFDRKLVNSAIKEIML----------LDEFLNLKDSEQEQFLFKEVLK 192 (196) T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHH----------HCCCCCCCCCHHHHHHHHHHHH T ss_conf 99999999849998999999999985----------0845677850428999999999 No 101 >cd01018 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence). Probab=25.18 E-value=34 Score=14.52 Aligned_cols=47 Identities=28% Similarity=0.331 Sum_probs=32.6 Q ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCEECC Q ss_conf 6489899999998886387314789999999981799988999963987618 Q gi|254780979|r 387 TPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVEELGLRQVT 438 (500) Q Consensus 387 ~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL~~is 438 (500) ...+|.++++|++.+.+..|. -||.+--.+.+..+.|+++.|...+. T Consensus 199 ~eps~~~l~~l~~~ik~~~v~-----~If~E~~~~~k~~~~ia~etg~kv~~ 245 (266) T cd01018 199 KEPSPADLKRLIDLAKEKGVR-----VVFVQPQFSTKSAEAIAREIGAKVVT 245 (266) T ss_pred CCCCHHHHHHHHHHHHHCCCC-----EEEEECCCCCHHHHHHHHHHCCCEEE T ss_conf 898999999999999983998-----99970899909999999970993799 No 102 >PRK07531 bifunctional 3-hydroxyacyl-CoA dehydrogenase/thioesterase; Validated Probab=24.72 E-value=46 Score=13.55 Aligned_cols=29 Identities=28% Similarity=0.429 Sum_probs=16.4 Q ss_pred CCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 6125763036527789999999999999864204 Q gi|254780979|r 173 VALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGT 206 (500) Q Consensus 173 vPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gi 206 (500) +||+|||-.|.- .. +.+.....+++.+|. T Consensus 144 ~PLVEvV~g~~T--~~---~~v~~a~~~~~~iG~ 172 (489) T PRK07531 144 LPLVELVGGGKT--SP---ETIERAKEILREIGM 172 (489) T ss_pred CCEEEEECCCCC--CH---HHHHHHHHHHHHCCC T ss_conf 762798168888--99---999999999998298 No 103 >PRK01966 ddl D-alanyl-alanine synthetase A; Reviewed Probab=24.42 E-value=47 Score=13.50 Aligned_cols=37 Identities=16% Similarity=0.120 Sum_probs=18.9 Q ss_pred ECCCCCCEEEEEECCCCCCHHHHHHHHHHH-HHHHHHHCCCCCC Q ss_conf 615786125763036527789999999999-9998642045676 Q gi|254780979|r 168 LNRSGVALMEIVTKPDMRSSLEAKAFLTKL-RSILRYLGTCDGN 210 (500) Q Consensus 168 ~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l-~~ilr~~gisd~~ 210 (500) |+-+|+|- |.++..+. |.++=+.+ ..+++..|+...+ T Consensus 112 Le~l~IPY----tGs~~~as--al~mDK~~tK~i~~~~gI~tp~ 149 (344) T PRK01966 112 LELLNIPY----VGCGVLAS--AVSMDKILTKRLLAAAGIPQAP 149 (344) T ss_pred HHHCCCCC----CCCCHHHH--HHHHHHHHHHHHHHHCCCCCCC T ss_conf 99759993----68848999--9876699999999987999898 No 104 >TIGR00707 argD acetylornithine and succinylornithine aminotransferases; InterPro: IPR004636 This family of proteins, for which ornithine aminotransferases form an outgroup, consists mostly of proteins designated acetylornithine aminotransferase. However, the two very closely related members from Escherichia coli are assigned different enzymatic activities. One is acetylornithine aminotransferase (2.6.1.11 from EC), ArgD, an enzyme of arginine biosynthesis, while another is succinylornithine aminotransferase, an enzyme of the arginine succinyltransferase pathway, an ammonia-generating pathway of arginine catabolism . Members of this family may also act on ornithine, like ornithine aminotransferase (2.6.1.13 from EC) and on succinyldiaminopimelate, like N-succinyldiaminopmelate-aminotransferase (2.6.1.17 from EC, DapC, an enzyme of lysine biosynthesis) . ; GO: 0008483 transaminase activity, 0006525 arginine metabolic process. Probab=24.39 E-value=42 Score=13.82 Aligned_cols=282 Identities=20% Similarity=0.237 Sum_probs=136.0 Q ss_pred EEEEECCCCCCCCCCCCCEEEEECCCCCC----------EEEEEEC---------CCCCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 66520231001156787148866157861----------2576303---------6527789999999999999864204 Q gi|254780979|r 146 IHLEQDAGKSIHDQYSAVSCIDLNRSGVA----------LMEIVTK---------PDMRSSLEAKAFLTKLRSILRYLGT 206 (500) Q Consensus 146 i~lEED~gk~~h~~~~~~slvD~NRaGvP----------LiEIVT~---------Pd~~s~~ea~~~~~~l~~ilr~~gi 206 (500) |.+..=-|-.++|+.++.+|||| =+||. |+|.|++ +-..++ +-.+.++||-.+.-. T Consensus 12 ~~i~rG~G~~v~Dd~~GK~YlDf-~aGIAV~~LGH~hP~l~Ea~~~Q~~kL~H~SNlY~~~-~~~~LA~kLv~~~~~--- 86 (402) T TIGR00707 12 IVIVRGKGAYVYDDVNGKEYLDF-VAGIAVNALGHAHPKLVEALKEQLEKLVHVSNLYYTE-PQEELAEKLVEHSGA--- 86 (402) T ss_pred EEEECCCCCEEEECCCCCEEEEE-CCCHHHHCCCCCCHHHHHHHHHHHHHHEEECCCCCCC-HHHHHHHHHHHHHHC--- T ss_conf 01631664089876789465201-0022440113578899999998662406607765580-899999999999704--- Q ss_pred CCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEC Q ss_conf 56764322011257543213766678862223540246599999999999999731398003443233755433665303 Q gi|254780979|r 207 CDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQIAILEDGGHIRQETRLFDPSKNETRSLRT 286 (500) Q Consensus 207 sd~~meeGslR~DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ~~ll~~G~~v~qETR~~d~~~~~T~~mR~ 286 (500) |+ |+ .--+||=.=| .---++|-|+.+=.+--..--....+|+-=+-.|+-.|--|.+.=. T Consensus 87 -dg----Gq--------------hd~~rvFFCN-SGaEAnEAAlKlARk~~~~~g~~k~~ivaf~naFHGRT~g~LsaTg 146 (402) T TIGR00707 87 -DG----GQ--------------HDASRVFFCN-SGAEANEAALKLARKYTGDKGKEKKKIVAFENAFHGRTMGALSATG 146 (402) T ss_pred -CC----CC--------------CCCCEEEEEC-CHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHCCC T ss_conf -68----83--------------0232667514-7478999999998986402278865388887077630045430047 Q ss_pred CCCCCCCCCCCCCCCCCCC-CCHHH-HHHHHHHCCCC-----HHHHH-HHHHHHCCCCHHHHHHHHHHHHHHHH------ Q ss_conf 5667777833277877312-69999-99988530248-----36898-86432026889998887641136789------ Q gi|254780979|r 287 KEDALDYRYFSEPDLLPLE-IDEDF-IRAIKKQIPEL-----PDAKR-ERFIGEFGISLYDASVLVSDKSIADY------ 352 (500) Q Consensus 287 KE~a~DYRyfPEPDLPpi~-is~e~-i~~i~~~lPel-----P~~~~-~rl~~~yGLs~~dA~~L~~~~~la~~------ 352 (500) |+ =||=.-+|=+|++. +.=.- |+++++.+-+. -.+.. +=.+.|=|+.+-+.+.|..=+++.+= T Consensus 147 qp---Ky~~~F~PLvpgf~y~~yNDe~~~l~~~i~~~~eg~rtAAvivEpiQGEgGV~pa~~~fL~a~r~lc~~~~~LLI 223 (402) T TIGR00707 147 QP---KYQKPFEPLVPGFKYVPYNDEIEALKEAIDDEKEGDRTAAVIVEPIQGEGGVVPADKEFLKALRELCEDKDALLI 223 (402) T ss_pred CC---CCCCCCCCCCCCCEEECCCCCHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHCCEEEE T ss_conf 76---456857884238124448897899999850257787188999853217865334877899999999864891899 Q ss_pred HHHHHC--CCCHHHHHHHHHHHHHHHHHHCCCCCCCCC--CCHHHHHHHHHHHHCC-CCCHHHHHHHHHHHHHC------ Q ss_conf 886402--430245777765457887643387400064--8989999999888638-73147899999999817------ Q gi|254780979|r 353 FEKLAV--NRDKKIVANWVINDLLGVLNRSGKSIEDTP--ISPNQLGELIDLIIDG-TISGKIAKDIFNILWEK------ 421 (500) Q Consensus 353 FE~v~~--~~~pk~~Anwi~~el~~~ln~~~~~~~~~~--i~p~~laeLi~li~~g-~Is~~~aK~il~~l~~~------ 421 (500) |++|=. +...|..|. +-.. ++|+ +..+-+-+-.| =|-...+|+=+...+.- T Consensus 224 ~DEVQtG~GRTG~~fA~-----------------~Hygse~~PD-i~T~AKgLGgG~PiGA~~~~e~~a~~~~~G~HGsT 285 (402) T TIGR00707 224 FDEVQTGLGRTGKLFAY-----------------EHYGSEVEPD-IITLAKGLGGGVPIGAVLAKEEVAEALTPGDHGST 285 (402) T ss_pred EEEEEECCCCCHHHHHH-----------------HCCCCCCCCH-HHHHHHHHHCCCHHHHHEEHHHHHHHCCCCCCCCC T ss_conf 94475287743322331-----------------2068845523-87540555278202232023678731589898666 Q ss_pred -CCCHH---------HHHHHCCCE-ECCCHH-HHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHHHHHH Q ss_conf -99988---------999963987-618988-999999999983999899752721322658999999 Q gi|254780979|r 422 -GGTPK---------EIVEELGLR-QVTDLS-AIEKVVDEVINSNPNNVARIATKPNLVSWFVGQVMK 477 (500) Q Consensus 422 -~~~p~---------~iie~~gL~-~isD~~-eL~~iv~eVI~~np~~V~~~kgk~ka~gfLvGqVMK 477 (500) |++|- ++|++..|. ++++.+ -+.+-.++.+....+.+.++||+ |-++|-+.. T Consensus 286 FGGNPLAc~Aa~~vl~~i~~~~~l~~v~~~G~~f~~~L~~~~~~~~~l~k~VRG~----GLmlG~e~~ 349 (402) T TIGR00707 286 FGGNPLACAAALAVLEVIEKERLLEKVKEKGDYFKERLEELIKKYIDLIKEVRGK----GLMLGIELE 349 (402) T ss_pred CCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECC----EEEEEEEEC T ss_conf 7873899999877666550510478999988999999998617766740153231----234655642 No 105 >KOG2164 consensus Probab=24.15 E-value=36 Score=14.30 Aligned_cols=45 Identities=9% Similarity=0.104 Sum_probs=29.1 Q ss_pred CCCCCCCCEEEEEEEEEEECCC-C------CCCCCCCCCCCCCCCCCCCHHHCCCCCC Q ss_conf 2454780338989997888689-8------6555884246898765206130268988 Q gi|254780979|r 16 SGTTGDWEVVIGIEVHAQLSVV-S------KLFSGASVNFGAEPNTQVSFFDAAMPGM 66 (500) Q Consensus 16 ~~~~~~~e~vIGLEiH~qL~t~-t------KlFc~c~~~~~~~pNt~v~~~~~g~PG~ 66 (500) ..-..||..||-.+=|++.++. . ++||- +++. ...||||++.|-+ T Consensus 147 ~f~~any~fvv~~gd~~~qn~dpD~p~~~e~i~qv----~~~t--~~~CPICL~~~~~ 198 (513) T KOG2164 147 TFLNANYRFVVDEGDYVLQNTDPDAPVDWEDIFQV----YGST--DMQCPICLEPPSV 198 (513) T ss_pred HHHCCCCEEEECCCCHHHHCCCCCCCCCHHHHHHH----HCCC--CCCCCCCCCCCCC T ss_conf 20102200122233102330697643067877664----0476--7768700478885 No 106 >TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family; InterPro: IPR014071 This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferable copper resistance) of an Enterococcus faecium (Streptococcus faecium) plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this entry are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.. Probab=23.48 E-value=49 Score=13.37 Aligned_cols=41 Identities=32% Similarity=0.559 Sum_probs=27.4 Q ss_pred HHHHHHHHHHHHHC--CCCHHHHHHHCCCEECCCHHHHHHHHHH Q ss_conf 47899999999817--9998899996398761898899999999 Q gi|254780979|r 408 GKIAKDIFNILWEK--GGTPKEIVEELGLRQVTDLSAIEKVVDE 449 (500) Q Consensus 408 ~~~aK~il~~l~~~--~~~p~~iie~~gL~~isD~~eL~~iv~e 449 (500) ...|+++|+++... |.-...||++.-|.+ +|-+.|++++.+ T Consensus 74 ~~~~~~lf~~~C~~k~g~~i~~Liee~~ls~-~Di~~L~~~L~~ 116 (130) T TIGR02698 74 ENAAEDLFSRICSKKVGNVIADLIEESTLSQ-DDIEKLEKLLSE 116 (130) T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHCCCCCH-HHHHHHHHHHHH T ss_conf 9999999987602138999999884066787-689999999987 No 107 >cd02977 ArsC_family Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. Spx is a general regulator that exerts negative and positive control over transcription initiation by binding to the C-terminal domain of the alpha subunit of RNA polymerase. Probab=23.42 E-value=49 Score=13.37 Aligned_cols=77 Identities=27% Similarity=0.439 Sum_probs=38.4 Q ss_pred HHHHCCCCCC-----CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCE---ECCCHHHHHHHH Q ss_conf 7643387400-----06489899999998886387314789999999981799988999963987---618988999999 Q gi|254780979|r 376 VLNRSGKSIE-----DTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVEELGLR---QVTDLSAIEKVV 447 (500) Q Consensus 376 ~ln~~~~~~~-----~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL~---~isD~~eL~~iv 447 (500) +|++.+++++ ..+++.+.|.+++.....+ ..+ ++...+ ..-++.++. ..++ ++ + T Consensus 18 ~L~~~~i~~~~~d~~k~~~s~~eL~~~l~~~~~~------~~~----li~~~~---~~~k~l~~~~~~~ls~-~e----~ 79 (105) T cd02977 18 WLEEHGIEYEFIDYLKEPPTKEELKELLAKLGLG------VED----LFNTRG---TPYRKLGLADKDELSD-EE----A 79 (105) T ss_pred HHHHCCCCCEEEHHHHCCCCHHHHHHHHHHCCCC------HHH----HHHHCC---HHHHHCCCCCCCCCCH-HH----H T ss_conf 9985799738860432269999999999975998------999----986332---4598849834013999-99----9 Q ss_pred HHHHHHCHHHHHH-H--HCCCCCHHH Q ss_conf 9999839998997-5--272132265 Q gi|254780979|r 448 DEVINSNPNNVAR-I--ATKPNLVSW 470 (500) Q Consensus 448 ~eVI~~np~~V~~-~--kgk~ka~gf 470 (500) -+.|.+||..+++ + .|+.-.+|| T Consensus 80 ~~ll~~~P~LlkRPIi~~~~~~~iGf 105 (105) T cd02977 80 LELMAEHPKLIKRPIVVDGDRLLVGF 105 (105) T ss_pred HHHHHHCHHHHCCCEEEECCEEEECC T ss_conf 99999696783397698699888259 No 108 >pfam11829 DUF3349 Protein of unknown function (DUF3349). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. Probab=23.04 E-value=50 Score=13.31 Aligned_cols=84 Identities=15% Similarity=0.326 Sum_probs=55.2 Q ss_pred HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCEECCCHHHHHHHHHH Q ss_conf 54578876433874000648989999999888638731478999999998179998899996398761898899999999 Q gi|254780979|r 370 INDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIVEELGLRQVTDLSAIEKVVDE 449 (500) Q Consensus 370 ~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~iie~~gL~~isD~~eL~~iv~e 449 (500) +..++++|+. |- ...+++.+..-|+.|+.. .+|....++|...+...+..+ + |..+|...|.+ T Consensus 5 l~~iv~WLRa-GY---P~GvP~~Dy~pLLALL~r-~Ltddev~~Va~~L~~~~~~~-----------i-~~~dI~~~I~~ 67 (97) T pfam11829 5 LASIVAWLRA-GY---PEGVPGPDYVPLLALLRR-RLTDDEVAEVAAELTRRGEPA-----------I-DDDDIGVLITA 67 (97) T ss_pred HHHHHHHHHC-CC---CCCCCCCCCHHHHHHHHC-CCCHHHHHHHHHHHHHCCCCC-----------C-CHHHHHHHHHH T ss_conf 9999999986-89---999898870899999814-288999999999998647899-----------9-99999999999 Q ss_pred HHHH--CHHHHHHHHCCCCCHHH Q ss_conf 9983--99989975272132265 Q gi|254780979|r 450 VINS--NPNNVARIATKPNLVSW 470 (500) Q Consensus 450 VI~~--np~~V~~~kgk~ka~gf 470 (500) |..+ .|+.|++...+-.+-|| T Consensus 68 vt~~~P~p~di~RV~arLaa~Gw 90 (97) T pfam11829 68 VTDELPSPEDVERVRARLAAHGW 90 (97) T ss_pred HHCCCCCHHHHHHHHHHHHHCCC T ss_conf 87479898999999999986799 No 109 >cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. Probab=22.97 E-value=19 Score=16.45 Aligned_cols=54 Identities=20% Similarity=0.222 Sum_probs=33.6 Q ss_pred CCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHH Q ss_conf 43233755433665303566777783327787731269999999885302483689886432026889998887641 Q gi|254780979|r 270 ETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSD 346 (500) Q Consensus 270 ETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~ 346 (500) .|-+|=+..|.-.+.| ....||||.+.|+.-+. ...++ .++|+|..++..++.. T Consensus 15 ~TlRyYe~~GLl~p~R---~~~gyR~Y~~~~~~rL~-------------------~I~~l-r~lg~sL~eIk~lL~~ 68 (134) T cd04779 15 RTIDYYTNLGLLTPER---SDSNYRYYDETALDRLQ-------------------LIEHL-KGQRLSLAEIKDQLEE 68 (134) T ss_pred HHHHHHHHCCCCCCCC---CCCCCCCCCHHHHHHHH-------------------HHHHH-HHCCCCHHHHHHHHHC T ss_conf 9999999779979996---99998206999999999-------------------99999-9979989999999847 No 110 >COG3608 Predicted deacylase [General function prediction only] Probab=22.83 E-value=50 Score=13.28 Aligned_cols=55 Identities=16% Similarity=0.228 Sum_probs=34.9 Q ss_pred ECCCCCCEE--EEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEE-CCCCCC Q ss_conf 615786125--76303652778999999999999986420456764322011-257543 Q gi|254780979|r 168 LNRSGVALM--EIVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMR-ADVNVS 223 (500) Q Consensus 168 ~NRaGvPLi--EIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR-~DvNVS 223 (500) .+|+|+|-+ |+... -=-+|+.+..++..+...|++.|+..+.++..-.+ .+.+-| T Consensus 198 ~~~~gi~~iT~E~gg~-g~v~~~~i~~~~~gi~n~L~~~Gil~g~~~~~p~~~~~~~~~ 255 (331) T COG3608 198 AERAGIPVITVELGGA-GDVDAESIEIAAEGILNFLRHRGILAGEVEKTPTKGLALPSS 255 (331) T ss_pred HHHCCCCEEEEEECCC-CCCCHHHHHHHHHHHHHHHHHHCEECCCCCCCCCCEEECCCC T ss_conf 8873996797651686-434788888899999999997184448867888523540365 No 111 >PRK13344 spxA transcriptional regulator Spx; Reviewed Probab=22.81 E-value=50 Score=13.28 Aligned_cols=91 Identities=14% Similarity=0.280 Sum_probs=50.0 Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHC-CCCHHHHHHHCCCEECC Q ss_conf 30245777765457887643387400064898999999988863873147899999999817-99988999963987618 Q gi|254780979|r 360 RDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELIDLIIDGTISGKIAKDIFNILWEK-GGTPKEIVEELGLRQVT 438 (500) Q Consensus 360 ~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~-~~~p~~iie~~gL~~is 438 (500) ...+.|-.|+-.- -+.....++.+.+++.+.|..++.+.+.|. + .++.+ +.+..++-. .+..+| T Consensus 11 ~TcrKA~kWL~~~---~I~y~~~di~k~p~s~~el~~~L~~~~~g~------~----~lintrs~~~r~L~~--~~~~ls 75 (132) T PRK13344 11 TSCKKAKTWLNAH---QLAYKEQNLGKEPLTKEEILAILSKTENGV------E----SIVSSKNRYAKALDC--DIEELS 75 (132) T ss_pred HHHHHHHHHHHHC---CCCEEEEEEECCCCCHHHHHHHHHHCCCCH------H----HHEECCCCHHHHCCC--CHHHCC T ss_conf 6789999999987---996388541227969999999999815589------9----913788821664275--644399 Q ss_pred CHHHHHHHHHHHHHHCHHHHHH-H--HCCCCCHHH Q ss_conf 9889999999999839998997-5--272132265 Q gi|254780979|r 439 DLSAIEKVVDEVINSNPNNVAR-I--ATKPNLVSW 470 (500) Q Consensus 439 D~~eL~~iv~eVI~~np~~V~~-~--kgk~ka~gf 470 (500) .. +++ ++|.+||..+.+ + .|+.-.+|| T Consensus 76 ~~----E~i-~ll~~~p~LiKRPil~~~~~~~vGF 105 (132) T PRK13344 76 VS----EVI-DLIQENPRILKSPILIDDKRLQVGY 105 (132) T ss_pred HH----HHH-HHHHHCCCCEECCEEEECCEEEECC T ss_conf 99----999-9999590103274795199889625 No 112 >PRK09261 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated Probab=22.61 E-value=50 Score=13.26 Aligned_cols=26 Identities=15% Similarity=0.261 Sum_probs=17.5 Q ss_pred EEECCC-CCCHHHHHHHHHHHHHHHHH Q ss_conf 630365-27789999999999999864 Q gi|254780979|r 178 IVTKPD-MRSSLEAKAFLTKLRSILRY 203 (500) Q Consensus 178 IVT~Pd-~~s~~ea~~~~~~l~~ilr~ 203 (500) +|..|| +|+|+.|.+|+++|..+-.- T Consensus 56 vivGPCSiHD~~aaleYA~rL~~l~~~ 82 (351) T PRK09261 56 VVVGPCSIHDPKAALEYARRLAKLREE 82 (351) T ss_pred EEECCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 997178668989999999999999998 No 113 >TIGR02051 MerR Hg(II)-responsive transcriptional regulator; InterPro: IPR011794 This entry represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix .; GO: 0003677 DNA binding, 0045340 mercury ion binding, 0045449 regulation of transcription, 0046689 response to mercury ion. Probab=22.59 E-value=48 Score=13.44 Aligned_cols=62 Identities=21% Similarity=0.247 Sum_probs=36.7 Q ss_pred HHCCCCCCCCCCCCCCCCCEE-EEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHH Q ss_conf 313980034432337554336-6530356677778332778773126999999988530248368988643202688999 Q gi|254780979|r 261 LEDGGHIRQETRLFDPSKNET-RSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYD 339 (500) Q Consensus 261 l~~G~~v~qETR~~d~~~~~T-~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~d 339 (500) |.+--.|-.||=+|=+.+|-- -|-| ...-||.||+.|+-=|+ .- +| +.++|+|.+. T Consensus 5 LA~~~GVNvETiRyYeRkGLl~eP~k---~~~GyR~Y~~~~v~R~r-----------------FI--KR-~QeLGFsL~E 61 (126) T TIGR02051 5 LAKAAGVNVETIRYYERKGLLPEPDK---PEGGYRRYPEETVKRVR-----------------FI--KR-AQELGFSLEE 61 (126) T ss_pred HHHHCCCCEEEEEHHHHCCCCCCCCC---CCCCCCCCCHHHHHHHH-----------------HH--HH-HHHCCCCHHH T ss_conf 36666897012210010077888899---88771407865443645-----------------54--42-0003797889 Q ss_pred HHHHHH Q ss_conf 888764 Q gi|254780979|r 340 ASVLVS 345 (500) Q Consensus 340 A~~L~~ 345 (500) +..|+. T Consensus 62 I~~LL~ 67 (126) T TIGR02051 62 IGKLLG 67 (126) T ss_pred HHHHCC T ss_conf 998706 No 114 >TIGR01267 Phe4hydrox_mono phenylalanine-4-hydroxylase; InterPro: IPR005960 This entry represents the small, monomeric form of phenylalanine-4-hydroxylase (PAH; 1.14.16.1 from EC), as found in a certain Gram-negative bacteria. The enzyme is biopterin and metal dependent, and acts to irreversibly convert phenylalanine to tyrosine, the rate-limiting step in phenylalanine catabolism in some systems:L-phenylalanine + tetrahydrobiopterin + O2 = L-tyrosine + dihydrobiopterin + H2O The structure of PAH from Colwellia psychrerythraea (strain 34H / ATCC BAA-681), which binds tetrahydrobiopterin (BH4) as cofactor, is a cold-active form of the enzyme that has increased stability and flexibility around the active site . More information about these proteins can be found at Protein of the Month: Phenylalanine Hydroxylase .; GO: 0004505 phenylalanine 4-monooxygenase activity, 0006559 L-phenylalanine catabolic process. Probab=22.46 E-value=45 Score=13.59 Aligned_cols=62 Identities=26% Similarity=0.398 Sum_probs=47.3 Q ss_pred EEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH Q ss_conf 36653035667777833277877312699999998853024836898864320268899988876411367898 Q gi|254780979|r 280 ETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDKSIADYF 353 (500) Q Consensus 280 ~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~~la~~F 353 (500) +|..+|+.++-+ |.-|||+- -++=--.|-|-.-....|+..||=.--+|..+=.+..++.+| T Consensus 93 Vt~wlRtp~eLD---Yl~EPD~F---------Hd~FGHvPlL~nPvFAdf~~~YGK~g~ka~alg~~e~laRLY 154 (251) T TIGR01267 93 VTTWLRTPEELD---YLQEPDVF---------HDLFGHVPLLTNPVFADFLEAYGKKGVKAKALGAAEFLARLY 154 (251) T ss_pred CCCCCCCHHHCC---CCCCCCCC---------CCCCCCCCCCCCCCHHHHHHHHCCCCCCHHHHCCHHHHHHHH T ss_conf 422136720056---14387421---------000376653457404688875164200001111125677777 No 115 >COG2905 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms] Probab=22.31 E-value=36 Score=14.33 Aligned_cols=48 Identities=35% Similarity=0.456 Sum_probs=34.7 Q ss_pred EEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCHHHH Q ss_conf 84236665202310011567871488661578612576303652778999 Q gi|254780979|r 141 VGIERIHLEQDAGKSIHDQYSAVSCIDLNRSGVALMEIVTKPDMRSSLEA 190 (500) Q Consensus 141 v~I~~i~lEED~gk~~h~~~~~~slvD~NRaGvPLiEIVT~Pd~~s~~ea 190 (500) +.+.-...=+|+++.+-+.+.+ |++-++++| |+.-|||+-||++.--| T Consensus 160 ~~v~~~~~i~~aa~km~~~gv~-s~v~l~~~~-~~~GIvT~~dl~~~v~~ 207 (610) T COG2905 160 VTVSPQASIQDAARKMKDEGVS-SLVVLDDSG-PLLGIVTRKDLRSRVIA 207 (610) T ss_pred CCCCCCCCHHHHHHHHHHCCCC-EEEEECCCC-CCCCEEEHHHHHHHHHH T ss_conf 5268657679999999960887-289983798-74332422777899986 No 116 >cd04165 GTPBP1_like GTPBP1-like. Mammalian GTP binding protein 1 (GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1 are GTPases whose specific functions remain unknown. In mouse, GTPBP1 is expressed in macrophages, in smooth muscle cells of various tissues and in some neurons of the cerebral cortex; GTPBP2 tissue distribution appears to overlap that of GTPBP1. In human leukemia and macrophage cell lines, expression of both GTPBP1 and GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The chromosomal location of both genes has been identified in humans, with GTPBP1 located in chromosome 22q12-13.1 and GTPBP2 located in chromosome 6p21-12. Human glioblastoma multiforme (GBM), a highly-malignant astrocytic glioma and the most common cancer in the central nervous system, has been linked to chromosomal deletions and a translocation on chromosome 6. The GBM translocation results in a fusion of GTPBP2 and PTPRZ1, a protein involved in oligodendrocyte differentiation, recovery, and Probab=22.29 E-value=51 Score=13.21 Aligned_cols=40 Identities=23% Similarity=0.279 Sum_probs=32.3 Q ss_pred CCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 1578612576303652778999999999999986420456 Q gi|254780979|r 169 NRSGVALMEIVTKPDMRSSLEAKAFLTKLRSILRYLGTCD 208 (500) Q Consensus 169 NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd 208 (500) ...|+|.+=+||.=|+.+++.....+.+|..+++..|+.. T Consensus 135 ~~l~ip~~vvitKiDl~~~~~l~~~~~~i~~~lk~p~~~k 174 (224) T cd04165 135 LALNIPVFVVVTKIDLAPANILQETLKDLKRILKVPGVRK 174 (224) T ss_pred HHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCC T ss_conf 9839998999989776898999999999999970447556 No 117 >pfam08777 RRM_3 RNA binding motif. This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif. Probab=21.99 E-value=52 Score=13.17 Aligned_cols=40 Identities=18% Similarity=0.264 Sum_probs=17.2 Q ss_pred EEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECC Q ss_conf 630365277899999999999998642045676432201125 Q gi|254780979|r 178 IVTKPDMRSSLEAKAFLTKLRSILRYLGTCDGNMEEGSMRAD 219 (500) Q Consensus 178 IVT~Pd~~s~~ea~~~~~~l~~ilr~~gisd~~meeGslR~D 219 (500) +..-+...|-++.++.+.++.. +.|++.+.|.. +|.+|++ T Consensus 6 ~~~~~~~~sRediK~~f~~~g~-V~yVD~~~Gd~-eg~vRf~ 45 (102) T pfam08777 6 FSGLNKPTSREDIKEAFSQHGE-VKYVDFLEGDK-EGYVRFK 45 (102) T ss_pred EECCCCCCCHHHHHHHHHHCCC-EEEEEECCCCC-EEEEEEC T ss_conf 9568988899999999983597-56898427883-6999967 No 118 >pfam02885 Glycos_trans_3N Glycosyl transferase family, helical bundle domain. This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate. Probab=21.90 E-value=52 Score=13.16 Aligned_cols=42 Identities=31% Similarity=0.421 Sum_probs=26.6 Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHH Q ss_conf 489899999998886387314789999999981799988999 Q gi|254780979|r 388 PISPNQLGELIDLIIDGTISGKIAKDIFNILWEKGGTPKEIV 429 (500) Q Consensus 388 ~i~p~~laeLi~li~~g~Is~~~aK~il~~l~~~~~~p~~ii 429 (500) .++.++...++..+-+|+++..+.-..|-.+...|.++++++ T Consensus 14 ~Ls~~e~~~~~~~i~~g~~s~~qi~afL~al~~kget~~Ei~ 55 (66) T pfam02885 14 DLSREEAEALMDAIMSGEASDAQIAAFLMALRIKGETPEEIA 55 (66) T ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHH T ss_conf 979999999999998699999999999999998399999999 No 119 >KOG1280 consensus Probab=21.75 E-value=29 Score=15.03 Aligned_cols=56 Identities=13% Similarity=0.105 Sum_probs=36.8 Q ss_pred CCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH Q ss_conf 39800344323375543366530356677778332778773126999999988530248368988 Q gi|254780979|r 263 DGGHIRQETRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRE 327 (500) Q Consensus 263 ~G~~v~qETR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~ 327 (500) .+..-...|+.-+...-.|..+ +++-+++|-+..-|...|..-+..+|.+|+.+.. T Consensus 247 ~~~t~~naa~~~~T~~~~~~~~---------ef~~t~~i~~tess~~~l~~t~~~~~~~~~~~~~ 302 (381) T KOG1280 247 QLETPRNAAPRTNTSDVTTTIT---------EFTATTNIANTESSQQTLQNTQFLLTRLNDPKMS 302 (381) T ss_pred HCCCCCCCCCCCCCCCCHHHHH---------HHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 2137544678765672012324---------3331105556767899999877643037875446 No 120 >PRK13752 putative transcriptional regulator MerR; Provisional Probab=21.69 E-value=50 Score=13.25 Aligned_cols=56 Identities=21% Similarity=0.237 Sum_probs=32.9 Q ss_pred CCCCCCCCCCCCCEE-EEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 034432337554336-6530356677778332778773126999999988530248368988643202688999888764 Q gi|254780979|r 267 IRQETRLFDPSKNET-RSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS 345 (500) Q Consensus 267 v~qETR~~d~~~~~T-~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~ 345 (500) |--+|-+|=+..|.- .+.| .+..||+|++.|+--+. -| + + ..++|+|.+++..|+. T Consensus 19 vs~~tIRyYE~~GLl~~~~R---~~~gyR~Y~~~~v~rL~-------fI----------~--~-~r~lGfsL~eI~~LL~ 75 (144) T PRK13752 19 VNVETIRFYQRKGLLPEPDK---PYGSIRRYGEADVTRVR-------FV----------K--S-AQRLGFSLDEIAELLR 75 (144) T ss_pred CCHHHHHHHHHCCCCCCCCC---CCCCCCCCCHHHHHHHH-------HH----------H--H-HHHCCCCHHHHHHHHC T ss_conf 98456679872599798777---99998247999999999-------99----------9--9-9987998999999977 No 121 >pfam10228 DUF2228 Uncharacterized conserved protein (DUF2228). This is a family of conserved proteins of approximately 700 residues found from worms to humans. Probab=21.66 E-value=53 Score=13.12 Aligned_cols=21 Identities=24% Similarity=0.377 Sum_probs=9.2 Q ss_pred CEEEEEECCCCCCCCCCCCCCC Q ss_conf 3366530356677778332778 Q gi|254780979|r 279 NETRSLRTKEDALDYRYFSEPD 300 (500) Q Consensus 279 ~~T~~mR~KE~a~DYRyfPEPD 300 (500) |..++- .+.+..-||=-|+.| T Consensus 150 GiVVP~-d~k~~vGYR~L~~sd 170 (253) T pfam10228 150 GLVVPV-DNKTDVGYRPLSESD 170 (253) T ss_pred EEEEEC-CCCCCCCCCCCCCCH T ss_conf 489711-687875551078573 No 122 >TIGR00591 phr2 deoxyribodipyrimidine photolyase; InterPro: IPR008148 Deoxyribodipyrimidine photolyase (DNA photolyase) is a DNA repair enzyme. It binds to UV-damaged DNA containing pyrimidine dimers and, upon absorbing a near-UV photon (300 to 500 nm), breaks the cyclobutane ring joining the two pyrimidines of the dimer. DNA photolyase is an enzyme that requires two choromophore-cofactors for its activity: a reduced FADH2 and either 5,10-methenyltetrahydrofolate (5,10-MTFH) or an oxidized 8-hydroxy-5- deazaflavin (8-HDF) derivative (F420). The folate or deazaflavin chromophore appears to function as an antenna, while the FADH2 chromophore is thought to be responsible for electron transfer. On the basis of sequence similarities DNA photolyases can be grouped into two classes. The second class contains enzymes from Myxococcus xanthus, methanogenic archaebacteria, insects, fish and marsupial mammals. It is not yet known what second cofactor is bound to class 2 enzymes. There are a number of conserved sequence regions in all known class 2 DNA photolyases, especially in the C-terminal part. ; GO: 0003904 deoxyribodipyrimidine photo-lyase activity, 0006281 DNA repair. Probab=21.64 E-value=49 Score=13.33 Aligned_cols=31 Identities=19% Similarity=0.190 Sum_probs=17.5 Q ss_pred EEEEEEEEEC-CCCCCCCCCCCCEEEEECCCCCCEEEEEEC Q ss_conf 4236665202-310011567871488661578612576303 Q gi|254780979|r 142 GIERIHLEQD-AGKSIHDQYSAVSCIDLNRSGVALMEIVTK 181 (500) Q Consensus 142 ~I~~i~lEED-~gk~~h~~~~~~slvD~NRaGvPLiEIVT~ 181 (500) +=.+-|||.+ +++.+-. .+++--++|. |||+ T Consensus 90 l~Ipf~Ll~gr~~~~~lP-----~f~~~~~~~a----~VtD 121 (471) T TIGR00591 90 LGIPFHLLLGRSAKEVLP-----KFVQERDAGA----VVTD 121 (471) T ss_pred CCCCEEEECCCCCHHHHH-----HHHHHCCCCE----EECC T ss_conf 489879757898666558-----8885417752----6536 No 123 >pfam11202 DUF2983 Protein of unknown function (DUF2983). This bacterial family of proteins has no known function. Probab=21.62 E-value=38 Score=14.18 Aligned_cols=17 Identities=18% Similarity=0.421 Sum_probs=14.0 Q ss_pred CCCCCEEEEECCCCCCE Q ss_conf 67871488661578612 Q gi|254780979|r 159 QYSAVSCIDLNRSGVAL 175 (500) Q Consensus 159 ~~~~~slvD~NRaGvPL 175 (500) .+...+||.+-|||+|+ T Consensus 79 ~~~~ivLVSLaRAGtPi 95 (353) T pfam11202 79 RGEPIVLVSLARAGTPI 95 (353) T ss_pred CCCCCEEEEEECCCCCH T ss_conf 18996799853258738 No 124 >PRK13515 carboxylate-amine ligase; Provisional Probab=21.60 E-value=53 Score=13.11 Aligned_cols=29 Identities=31% Similarity=0.250 Sum_probs=19.1 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 257630365277899999999999998642 Q gi|254780979|r 175 LMEIVTKPDMRSSLEAKAFLTKLRSILRYL 204 (500) Q Consensus 175 LiEIVT~Pd~~s~~ea~~~~~~l~~ilr~~ 204 (500) -|||+|. ..++..|+++.+..++..+... T Consensus 52 qiEi~T~-v~~~~~e~~~~L~~~r~~l~~a 80 (381) T PRK13515 52 QIEVGTP-VCATLAEAREELGRLRQRLAEL 80 (381) T ss_pred EEEECCC-CCCCHHHHHHHHHHHHHHHHHH T ss_conf 7994687-7799999999999999999999 No 125 >PRK08136 glycosyl transferase family protein; Provisional Probab=21.51 E-value=53 Score=13.10 Aligned_cols=11 Identities=18% Similarity=0.477 Sum_probs=3.9 Q ss_pred HHHHHHHHCCE Q ss_conf 99987782976 Q gi|254780979|r 78 AVMTGLGLNAH 88 (500) Q Consensus 78 ai~~~~al~~~ 88 (500) |+.+++....+ T Consensus 44 afL~alr~KGE 54 (316) T PRK08136 44 AILIALRIKGE 54 (316) T ss_pred HHHHHHHCCCC T ss_conf 99999972289 No 126 >TIGR02333 2met_isocit_dHY 2-methylisocitrate dehydratase, Fe/S-dependent; InterPro: IPR012708 This entry represents Fe/S-dependent 2-methylisocitrate dehydratase (AcnD; 4.2.1.99 from EC), which is part of the 2-methylcitrate (2-MC) cycle that occurs in certain fungi and bacteria. The 2-MC cycle is involved in the degradation of propionyl-CoA via 2-methylcitrate, with AcnD functioning after PrpD and before PrpB. AcnD acts to catalyse the dehydration of 2-methylcitrate and citrate to 2-methyl-cis-aconitate and cis-aconitate, respectively, as well as to catalyse the hydration of cis-aconitate. However, 2-methylisocitrate and isocitrate were not substrates for AcnD, indicating that AcnD only catalyses the first half of the aconitase-like dehydration reactions . The enzyme from the fungus Yarrowia lipolytica (Candida lipolytica) does not act on isocitrate. AcnD is homologous to aconitases A and B. In Escherichia coli, which lacks a member of this family, 2-methylisocitrate dehydratase activity was traced to aconitase B (IPR004406 from INTERPRO) . Information about related proteins can be found at Protein of the Month: Aconitase .. Probab=21.46 E-value=53 Score=13.09 Aligned_cols=90 Identities=18% Similarity=0.195 Sum_probs=40.9 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH-HHHHHCCCCC Q ss_conf 999999999999864204567643220112575432137666788622235402465999999999999-9973139800 Q gi|254780979|r 189 EAKAFLTKLRSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEVKNVNSIRFLGLAIEYEARRQ-IAILEDGGHI 267 (500) Q Consensus 189 ea~~~~~~l~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRvEIKNlnS~~~i~~AI~yEi~RQ-~~ll~~G~~v 267 (500) .|...+..|-..||.-.+..+-+|- -..---++ ..|.|.-|.||.- .+=..|--|-|..| ++.|.--|.- T Consensus 250 tatd~vlalteflr~~~vv~~y~ef---~GeGa~~l-----~~Gdratisnm~P-e~Gata~mf~id~qt~~yl~ltGr~ 320 (864) T TIGR02333 250 TATDIVLALTEFLRKEKVVSAYLEF---FGEGARAL-----TLGDRATISNMTP-EYGATAAMFAIDEQTIDYLKLTGRE 320 (864) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH---HCCCCCEE-----ECCCCHHHHCCCC-CCCHHHHHHHHHHHHHHHHHHCCCC T ss_conf 2788999999987642466555665---05651012-----1143001101574-2001466777667778777523885 Q ss_pred ----------CCCCCCCCCCCCEEEEEECC Q ss_conf ----------34432337554336653035 Q gi|254780979|r 268 ----------RQETRLFDPSKNETRSLRTK 287 (500) Q Consensus 268 ----------~qETR~~d~~~~~T~~mR~K 287 (500) -+.+-.|.+.-.....-|.- T Consensus 321 ~~qv~lve~yak~~GlW~d~l~~a~y~r~l 350 (864) T TIGR02333 321 EEQVKLVETYAKAAGLWADSLKQAVYERVL 350 (864) T ss_pred HHHHHHHHHHHHHHCCCHHHHCCHHHHHHE T ss_conf 688888877765402105544000000110 No 127 >KOG0979 consensus Probab=21.36 E-value=53 Score=13.08 Aligned_cols=47 Identities=23% Similarity=0.277 Sum_probs=31.2 Q ss_pred EEEEEEEEEECCCCCCCCCCCC-CCCCCCC-----CCCCHHHCCCCCCCCCCC Q ss_conf 8989997888689865558842-4689876-----520613026898887378 Q gi|254780979|r 25 VIGIEVHAQLSVVSKLFSGASV-NFGAEPN-----TQVSFFDAAMPGMLPILN 71 (500) Q Consensus 25 vIGLEiH~qL~t~tKlFc~c~~-~~~~~pN-----t~v~~~~~g~PG~lP~lN 71 (500) +|-+|.|-=+.-+.=-|.+||. ++-.-|| |-||.+|+|+-|..-++- T Consensus 22 IvrI~l~NF~Ty~~~e~~pgpsLNmIiGpNGSGKSSiVcAIcLglgG~Pk~lG 74 (1072) T KOG0979 22 IVRIELHNFLTYDHTEFLPGPSLNMIIGPNGSGKSSIVCAICLGLGGKPKLLG 74 (1072) T ss_pred EEEEEEEEEEEEEEEEECCCCCEEEEECCCCCCCHHHHHHHHHHCCCCHHHCC T ss_conf 69999740044433344378861268778989704889999997279744314 No 128 >cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Probab=21.30 E-value=53 Score=13.07 Aligned_cols=59 Identities=15% Similarity=0.215 Sum_probs=34.0 Q ss_pred CCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHH Q ss_conf 32337554336653035667777833277877312699999998853024836898864320268899988876411367 Q gi|254780979|r 271 TRLFDPSKNETRSLRTKEDALDYRYFSEPDLLPLEIDEDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVSDKSIA 350 (500) Q Consensus 271 TR~~d~~~~~T~~mR~KE~a~DYRyfPEPDLPpi~is~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~~~~la 350 (500) -|.|+ ..|.-.|-+. +..-||||-+-|+. .+. ....| ..+|+|..++..++++.... T Consensus 17 LRyYe-~~GLl~p~~~--~~ngYR~Y~~~~~~----------~l~---------~I~~~-r~lG~sL~eI~~~~~~~~~~ 73 (97) T cd04782 17 LFHYD-KIGLFKPEIV--KENGYRYYTLEQFE----------QLD---------IILLL-KELGISLKEIKDYLDNRNPD 73 (97) T ss_pred HHHHH-HCCCCCCCCC--CCCCCCCCCHHHHH----------HHH---------HHHHH-HHCCCCHHHHHHHHHCCCHH T ss_conf 99999-6699898613--99998427999999----------999---------99999-99699999999998279989 Q ss_pred HH Q ss_conf 89 Q gi|254780979|r 351 DY 352 (500) Q Consensus 351 ~~ 352 (500) ++ T Consensus 74 ~~ 75 (97) T cd04782 74 EL 75 (97) T ss_pred HH T ss_conf 99 No 129 >PRK01372 ddl D-alanine--D-alanine ligase; Reviewed Probab=21.29 E-value=53 Score=13.07 Aligned_cols=13 Identities=8% Similarity=0.077 Sum_probs=8.2 Q ss_pred HHHHHHHCCCCCC Q ss_conf 9998642045676 Q gi|254780979|r 198 RSILRYLGTCDGN 210 (500) Q Consensus 198 ~~ilr~~gisd~~ 210 (500) .++++..|+.... T Consensus 103 K~i~~~~gI~tp~ 115 (304) T PRK01372 103 KLVWQAAGLPTAP 115 (304) T ss_pred HHHHHHCCCCCCC T ss_conf 9999986999898 No 130 >PRK04182 cytidylate kinase; Provisional Probab=21.16 E-value=54 Score=13.05 Aligned_cols=72 Identities=21% Similarity=0.153 Sum_probs=40.0 Q ss_pred CHHHHHHHHHHHCCCCHHHHHHHHH--HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHH Q ss_conf 8368988643202688999888764--11367898864024302457777654578876433874000648989999999 Q gi|254780979|r 321 LPDAKRERFIGEFGISLYDASVLVS--DKSIADYFEKLAVNRDKKIVANWVINDLLGVLNRSGKSIEDTPISPNQLGELI 398 (500) Q Consensus 321 lP~~~~~rl~~~yGLs~~dA~~L~~--~~~la~~FE~v~~~~~pk~~Anwi~~el~~~ln~~~~~~~~~~i~p~~laeLi 398 (500) .++.|.+|.+..++++..+|...+. +..-..+|...- +.++... ...++-++.+.++++..+++| T Consensus 100 ~~e~R~~Ri~~r~~~~~~~a~~~i~~rd~~~~~r~~~~y-~~~~~d~------------~~ydl~Idts~l~~d~vv~~I 166 (178) T PRK04182 100 PLEVRAKRIAEREGISVEEALEETIEREESEAKRYLEYY-GIDIDDL------------SIYDLVINTSKWSPEEVFEII 166 (178) T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCC------------CCCCEEEECCCCCHHHHHHHH T ss_conf 999999999973299999999999998999999999860-8997753------------107489989999999999999 Q ss_pred HHHHCCC Q ss_conf 8886387 Q gi|254780979|r 399 DLIIDGT 405 (500) Q Consensus 399 ~li~~g~ 405 (500) .-.-+.. T Consensus 167 ~~~i~k~ 173 (178) T PRK04182 167 LAAIDKL 173 (178) T ss_pred HHHHHHH T ss_conf 9999999 No 131 >pfam07830 PP2C_C Protein serine/threonine phosphatase 2C, C-terminal domain. Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain. Probab=20.87 E-value=54 Score=13.01 Aligned_cols=10 Identities=40% Similarity=0.787 Sum_probs=3.8 Q ss_pred HHHHHHHHHH Q ss_conf 9999999998 Q gi|254780979|r 443 IEKVVDEVIN 452 (500) Q Consensus 443 L~~iv~eVI~ 452 (500) |+..|+++++ T Consensus 28 le~~v~Eii~ 37 (81) T pfam07830 28 LEQRVEEIIE 37 (81) T ss_pred HHHHHHHHHH T ss_conf 9999999999 No 132 >KOG1147 consensus Probab=20.82 E-value=47 Score=13.48 Aligned_cols=28 Identities=11% Similarity=0.290 Sum_probs=14.2 Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHC Q ss_conf 677778332778773126999999988530 Q gi|254780979|r 289 DALDYRYFSEPDLLPLEIDEDFIRAIKKQI 318 (500) Q Consensus 289 ~a~DYRyfPEPDLPpi~is~e~i~~i~~~l 318 (500) +..-|+-||-=|...=.++. |+.+...| T Consensus 370 TG~KYkvYPTYDFaCPIVDs--lEGVThaL 397 (712) T KOG1147 370 TGDKYKVYPTYDFACPIVDS--LEGVTHAL 397 (712) T ss_pred CCCCEEEECCCCCCCCCCHH--HHHHHHHH T ss_conf 78730330454424522002--43245665 No 133 >TIGR02365 dha_L_ycgS dihydroxyacetone kinase, L subunit; InterPro: IPR012737 Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated 2.7.1.29 from EC. By contract, Escherichia coli and many other bacterial species have a multisubunit form (2.7.1 from EC) with a phosphoprotein donor related to PTS transport proteins. The sequences in this entry represent the subunit homologous to the E. coli YcgS subunit.. Probab=20.60 E-value=33 Score=14.60 Aligned_cols=99 Identities=14% Similarity=0.173 Sum_probs=37.5 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHH-HHHHHHHHHHHHCC--CCH----HHHHHHHHHHHHHHHHHC Q ss_conf 99999988530248368988643202688999888764-11367898864024--302----457777654578876433 Q gi|254780979|r 308 EDFIRAIKKQIPELPDAKRERFIGEFGISLYDASVLVS-DKSIADYFEKLAVN--RDK----KIVANWVINDLLGVLNRS 380 (500) Q Consensus 308 ~e~i~~i~~~lPelP~~~~~rl~~~yGLs~~dA~~L~~-~~~la~~FE~v~~~--~~p----k~~Anwi~~el~~~ln~~ 380 (500) .+||..+...+ .+-+++| .++.-.--|+..=++ ++-+..+-+.+... .++ |.++-.|++.+-| T Consensus 2 ~~wl~~~~~~~----~~~~~yL-TeLD~aIGDgDHG~Nm~RGF~~v~~kL~~~~~~~~~~~LK~~gM~LiS~VGG----- 71 (200) T TIGR02365 2 LEWLKNLGDLV----IENKEYL-TELDRAIGDGDHGINMARGFSEVKEKLDDFKDKTIQEILKKTGMALISKVGG----- 71 (200) T ss_pred HHHHHHHHHHH----HHHHHHH-HHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCC----- T ss_conf 67899999999----8623420-0105433565455147888999999974258999878999988888522032----- Q ss_pred CCCCCCCCCCHHHHHHHHHHHHC-CCC-CHHHHHHHHHHHHH Q ss_conf 87400064898999999988863-873-14789999999981 Q gi|254780979|r 381 GKSIEDTPISPNQLGELIDLIID-GTI-SGKIAKDIFNILWE 420 (500) Q Consensus 381 ~~~~~~~~i~p~~laeLi~li~~-g~I-s~~~aK~il~~l~~ 420 (500) -+=||==-.|.+.=..+.+ ..+ +.....++|+.+++ T Consensus 72 ----ASGPLYGT~Fl~as~a~~~~~~~~~~~~l~~~l~~g~~ 109 (200) T TIGR02365 72 ----ASGPLYGTAFLKASKALKDKEEILDAEDLAEILEAGLE 109 (200) T ss_pred ----HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH T ss_conf ----01577999999999986230126898899999999999 No 134 >PRK09071 hypothetical protein; Validated Probab=20.30 E-value=56 Score=12.93 Aligned_cols=69 Identities=17% Similarity=0.238 Sum_probs=33.0 Q ss_pred ECCCCCCEEEEEECCCCCCHHHHHHHHHHH----------HHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCC Q ss_conf 615786125763036527789999999999----------9998642045676432201125754321376667886222 Q gi|254780979|r 168 LNRSGVALMEIVTKPDMRSSLEAKAFLTKL----------RSILRYLGTCDGNMEEGSMRADVNVSVCRPGEAWGTRCEV 237 (500) Q Consensus 168 ~NRaGvPLiEIVT~Pd~~s~~ea~~~~~~l----------~~ilr~~gisd~~meeGslR~DvNVSi~~~~~~~GtRvEI 237 (500) +..+|+|+ -.+|+++...+.+. .--++++.-.+..| .+|-=.|+-- |--.+.+.+.-+ T Consensus 128 LeaLGi~i--------~~~~~~~~~~l~~~gi~Fl~ap~fhP~~~~v~~~R~~L---G~rTifN~lg-pL~NPa~~~~ql 195 (323) T PRK09071 128 LEALGIPI--------ARSWAEAEQALEEHGIAYLPLEDFAPQLQRMIDLRNTL---GLRSPINTLA-RLLNPLNAKASL 195 (323) T ss_pred HHHCCCCC--------CCCHHHHHHHHHHCCCEEEEHHHHCHHHHHHHHHHHHH---CCCCHHHHHH-HHCCCCCCCCEE T ss_conf 99769976--------68999999999971955723778699999999999995---8897999888-612877887649 Q ss_pred CCCCHHHHHHH Q ss_conf 35402465999 Q gi|254780979|r 238 KNVNSIRFLGL 248 (500) Q Consensus 238 KNlnS~~~i~~ 248 (500) =++-+-..+.. T Consensus 196 ~GV~~~~~~~~ 206 (323) T PRK09071 196 QGIFHPGYQQL 206 (323) T ss_pred EEEECHHHHHH T ss_conf 97758889999 No 135 >KOG0479 consensus Probab=20.05 E-value=47 Score=13.46 Aligned_cols=53 Identities=17% Similarity=0.280 Sum_probs=32.2 Q ss_pred HHHHHHHHHHHHHHHHHCCC--CCCCCCCCHHHHHHHHHHHHC-------CCCCHHHHHHHH Q ss_conf 45777765457887643387--400064898999999988863-------873147899999 Q gi|254780979|r 363 KIVANWVINDLLGVLNRSGK--SIEDTPISPNQLGELIDLIID-------GTISGKIAKDIF 415 (500) Q Consensus 363 k~~Anwi~~el~~~ln~~~~--~~~~~~i~p~~laeLi~li~~-------g~Is~~~aK~il 415 (500) ..++.+|..+..++-|.... .-..+||++..|-.||.|--. ..++...|+..+ T Consensus 578 ~ea~e~Ia~~Y~~LR~~d~~~d~~rt~PiTARtLETlIRLaTAhAKaRlSk~V~~~DAe~A~ 639 (818) T KOG0479 578 QEAAEYIAEEYTDLRNDDSRKDQERTSPITARTLETLIRLATAHAKARLSKVVEKDDAEAAV 639 (818) T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHH T ss_conf 99999999997643023443333454677189999999998877776631412454189999 No 136 >COG2160 AraA L-arabinose isomerase [Carbohydrate transport and metabolism] Probab=20.04 E-value=57 Score=12.89 Aligned_cols=33 Identities=9% Similarity=0.059 Sum_probs=16.8 Q ss_pred CCCCCCCCCCCCHHHHHHHHH-HHHHHHHHHHHH Q ss_conf 678862223540246599999-999999999731 Q gi|254780979|r 230 AWGTRCEVKNVNSIRFLGLAI-EYEARRQIAILE 262 (500) Q Consensus 230 ~~GtRvEIKNlnS~~~i~~AI-~yEi~RQ~~ll~ 262 (500) .||+-|++=.+..+-.+.+++ +-|+.+-.+-++ T Consensus 201 qFGwsv~~~gIgdLv~~~~~vse~eV~~l~eey~ 234 (497) T COG2160 201 QFGWSVNTWGIGDLVEVVNEVSEGEVEALLEEYR 234 (497) T ss_pred HHCCEEEEEEHHHHHHHHHHCCHHHHHHHHHHHH T ss_conf 6362576774468999997516878999999988 Done!