Query gi|254780355|ref|YP_003064768.1| type II citrate synthase [Candidatus Liberibacter asiaticus str. psy62] Match_columns 429 No_of_seqs 205 out of 1887 Neff 6.1 Searched_HMMs 39220 Date Sun May 29 15:20:38 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780355.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK05614 gltA type II citrate 100.0 0 0 1157.7 42.7 412 5-417 1-414 (414) 2 cd06114 EcCS_like Escherichia 100.0 0 0 1054.7 41.0 399 17-416 1-400 (400) 3 TIGR01800 cit_synth_II 2-methy 100.0 0 0 1059.3 33.5 376 45-428 2-386 (386) 4 cd06115 AthCS_per_like Arabido 100.0 0 0 1048.4 39.3 398 21-424 2-410 (410) 5 cd06116 CaCS_like Chloroflexus 100.0 0 0 1040.2 40.7 384 38-425 1-384 (384) 6 cd06107 EcCS_AthCS-per_like Es 100.0 0 0 977.6 39.9 375 38-416 1-382 (382) 7 PRK12351 methylcitrate synthas 100.0 0 0 970.1 39.9 371 41-428 7-377 (377) 8 cd06112 citrate_synt_like_1_1 100.0 0 0 940.6 38.8 372 42-425 1-373 (373) 9 COG0372 GltA Citrate synthase 100.0 0 0 942.8 37.0 388 27-428 2-390 (390) 10 PRK12349 citrate synthase 3; P 100.0 0 0 921.5 37.9 360 42-418 4-364 (365) 11 cd06111 DsCS_like Cold-active 100.0 0 0 901.9 38.8 362 44-422 1-362 (362) 12 cd06113 citrate_synt_like_1_2 100.0 0 0 891.7 39.0 370 35-416 7-406 (406) 13 cd06110 BSuCS-II_like Bacillus 100.0 0 0 893.4 37.6 356 44-416 1-356 (356) 14 cd06117 Ec2MCS_like_1 Subgroup 100.0 0 0 891.8 37.9 364 45-425 2-366 (366) 15 cd06103 ScCS-like Saccharomyce 100.0 0 0 891.0 35.7 375 26-416 14-424 (426) 16 TIGR01798 cit_synth_I citrate 100.0 0 0 897.8 30.1 411 12-422 1-413 (413) 17 cd06105 ScCit1-2_like Saccharo 100.0 0 0 887.7 33.7 368 37-420 28-426 (427) 18 cd06108 Ec2MCS_like Escherichi 100.0 0 0 880.3 38.6 361 45-425 2-363 (363) 19 pfam00285 Citrate_synt Citrate 100.0 0 0 878.7 38.2 352 45-410 1-352 (352) 20 cd06118 citrate_synt_like_1 Ci 100.0 0 0 876.5 38.3 358 44-414 1-358 (358) 21 cd06109 BsCS-I_like Bacillus s 100.0 0 0 869.1 35.9 347 44-416 1-349 (349) 22 PRK09569 type I citrate syntha 100.0 0 0 860.8 33.0 359 45-420 41-429 (437) 23 PRK12350 citrate synthase 2; P 100.0 0 0 852.7 30.3 345 42-421 1-350 (352) 24 cd06106 ScCit3_like Saccharomy 100.0 0 0 792.8 36.3 358 45-415 39-425 (428) 25 cd06101 citrate_synt Citrate s 100.0 0 0 698.3 26.7 263 44-414 1-265 (265) 26 cd06102 citrate_synt_like_2 Ci 100.0 0 0 637.6 25.9 266 48-416 17-282 (282) 27 KOG2617 consensus 100.0 0 0 589.0 20.9 394 12-429 39-457 (458) 28 TIGR01793 cit_synth_euk citrat 100.0 0 0 522.7 23.1 348 51-415 50-427 (430) 29 cd06099 CS_ACL-C_CCL Citrate s 100.0 0 0 509.9 20.7 211 192-414 1-213 (213) 30 PRK06224 citrate synthase; Pro 100.0 0 0 438.6 21.7 243 51-422 8-264 (265) 31 cd06100 CCL_ACL-C Citryl-CoA l 100.0 0 0 432.1 18.5 198 190-403 10-214 (227) 32 KOG1254 consensus 99.5 2.2E-14 5.5E-19 119.4 3.6 217 180-409 353-590 (600) 33 cd06100 CCL_ACL-C Citryl-CoA l 97.7 0.0071 1.8E-07 39.8 15.5 43 70-112 1-43 (227) 34 COG3383 Uncharacterized anaero 81.2 1.6 4E-05 23.6 3.0 55 1-62 1-59 (978) 35 KOG2617 consensus 80.1 0.96 2.5E-05 25.1 1.6 25 51-78 71-95 (458) 36 PRK07569 bidirectional hydroge 78.6 2.7 7E-05 21.9 3.6 55 1-64 1-59 (236) 37 TIGR01025 rpsS_arch ribosomal 77.6 1.5 3.9E-05 23.7 2.0 95 66-190 5-101 (136) 38 PRK04038 rps19p 30S ribosomal 76.9 2.8 7.1E-05 21.9 3.2 91 62-186 3-93 (134) 39 TIGR01882 peptidase-T peptidas 75.6 1.6 4E-05 23.6 1.7 90 310-399 292-408 (413) 40 PTZ00096 40S ribosomal protein 73.4 3 7.7E-05 21.6 2.6 90 66-186 16-105 (144) 41 KOG3041 consensus 71.9 3.9 9.9E-05 20.9 2.9 68 14-86 104-184 (225) 42 KOG1182 consensus 71.7 2.8 7.1E-05 21.9 2.1 19 62-80 146-164 (432) 43 PRK08493 NADH dehydrogenase su 71.4 4.2 0.00011 20.6 3.0 52 6-62 2-55 (819) 44 PRK07860 NADH dehydrogenase su 71.0 5.1 0.00013 20.0 3.4 66 3-75 14-83 (809) 45 PRK13866 plasmid partitioning 69.2 3.9 9.9E-05 20.9 2.4 24 382-407 311-334 (336) 46 pfam07249 Cerato-platanin Cera 64.8 6.7 0.00017 19.2 2.9 32 40-72 3-34 (119) 47 TIGR03454 partition_RepB plasm 58.7 6.5 0.00017 19.3 2.0 10 187-196 157-166 (325) 48 PRK09129 NADH dehydrogenase su 54.5 13 0.00034 17.2 3.0 10 261-270 505-514 (777) 49 KOG4183 consensus 53.4 16 0.00042 16.6 8.4 15 61-75 62-76 (413) 50 KOG0416 consensus 53.1 6.4 0.00016 19.4 1.1 18 1-19 17-34 (189) 51 PTZ00295 glucosamine-fructose- 51.3 5.4 0.00014 19.9 0.6 32 45-77 71-112 (691) 52 pfam07583 PSCyt2 Protein of un 50.3 12 0.0003 17.6 2.1 45 75-124 20-64 (200) 53 PRK08166 NADH dehydrogenase su 50.2 10 0.00026 18.0 1.8 18 62-79 258-275 (858) 54 COG1034 NuoG NADH dehydrogenas 50.0 18 0.00045 16.3 3.0 50 6-62 2-55 (693) 55 TIGR01135 glmS glucosamine--fr 49.1 4.4 0.00011 20.5 -0.2 72 210-293 390-465 (628) 56 TIGR01330 bisphos_HAL2 3'(2'), 45.9 9.4 0.00024 18.2 1.1 175 104-281 10-247 (382) 57 PRK07440 hypothetical protein; 44.9 17 0.00044 16.4 2.3 17 1-18 1-17 (70) 58 pfam07587 PSD1 Protein of unkn 44.9 22 0.00056 15.7 3.6 19 172-190 23-41 (258) 59 PRK10528 multifunctional acyl- 43.7 23 0.00058 15.5 7.1 82 280-368 93-175 (191) 60 TIGR00588 ogg 8-oxoguanine DNA 42.7 24 0.0006 15.4 3.6 33 286-332 219-251 (379) 61 TIGR02123 TRAP_fused TRAP tran 42.3 10 0.00025 18.0 0.8 34 235-271 225-265 (681) 62 pfam02332 Phenol_Hydrox Methan 40.2 26 0.00066 15.2 4.7 105 211-343 67-174 (233) 63 pfam00591 Glycos_transf_3 Glyc 39.9 24 0.00062 15.4 2.4 10 221-230 143-152 (254) 64 COG0343 Tgt Queuine/archaeosin 39.8 17 0.00044 16.4 1.6 23 285-307 225-247 (372) 65 KOG0138 consensus 39.3 27 0.00068 15.1 3.4 49 242-292 276-332 (432) 66 PRK00112 tgt queuine tRNA-ribo 37.9 22 0.00056 15.7 1.9 50 258-307 183-252 (366) 67 KOG0205 consensus 37.7 18 0.00046 16.2 1.5 63 2-64 332-421 (942) 68 PRK11780 isoprenoid biosynthes 33.8 7 0.00018 19.1 -1.1 75 69-146 72-146 (217) 69 PRK09130 NADH dehydrogenase su 33.7 32 0.00082 14.5 3.0 17 384-400 660-676 (680) 70 TIGR02335 hydr_PhnA phosphonoa 33.5 30 0.00076 14.7 2.1 44 5-52 15-65 (408) 71 TIGR01495 ETRAMP early transcr 32.7 21 0.00054 15.8 1.2 14 248-261 66-80 (99) 72 KOG0898 consensus 32.0 34 0.00087 14.3 4.3 24 66-90 22-45 (152) 73 TIGR01851 argC_other N-acetyl- 32.0 7.5 0.00019 18.9 -1.2 22 58-83 5-28 (314) 74 PRK10624 L-1,2-propanediol oxi 31.5 35 0.00089 14.3 3.2 48 232-279 243-290 (381) 75 pfam01795 Methyltransf_5 MraW 31.4 35 0.00089 14.3 7.2 55 69-123 131-188 (310) 76 TIGR01245 trpD anthranilate ph 31.1 21 0.00055 15.7 1.0 17 230-246 84-100 (331) 77 pfam01702 TGT Queuine tRNA-rib 30.9 31 0.00078 14.7 1.8 50 258-307 56-125 (238) 78 PRK13222 phosphoglycolate phos 30.8 35 0.00088 14.3 2.0 77 207-293 146-226 (228) 79 TIGR02358 thia_cytX probable h 29.8 37 0.00095 14.1 2.8 15 175-189 164-178 (415) 80 cd03133 GATase1_ES1 Type 1 glu 29.2 8.4 0.00021 18.6 -1.4 75 69-146 69-143 (213) 81 PRK02955 small acid-soluble sp 29.2 26 0.00067 15.1 1.2 27 279-305 16-42 (69) 82 COG0177 Nth Predicted EndoIII- 28.7 39 0.00099 13.9 2.2 16 300-315 179-194 (211) 83 TIGR03092 SASP_sspI small, aci 27.8 29 0.00074 14.8 1.2 27 279-305 13-39 (65) 84 TIGR02365 dha_L_ycgS dihydroxy 27.8 38 0.00097 14.0 1.8 43 251-293 64-109 (200) 85 TIGR02344 chap_CCT_gamma T-com 27.8 40 0.001 13.8 2.4 56 304-362 58-116 (527) 86 TIGR03233 DNA_S_dndB DNA sulfu 27.2 34 0.00087 14.4 1.5 48 68-116 113-162 (355) 87 PRK09860 putative alcohol dehy 27.1 41 0.0011 13.8 6.9 55 232-286 245-299 (383) 88 KOG0962 consensus 26.9 42 0.0011 13.7 3.5 56 37-104 10-65 (1294) 89 KOG0193 consensus 26.7 21 0.00055 15.7 0.4 63 67-129 385-462 (678) 90 TIGR02815 agaS_fam putative su 26.6 24 0.00061 15.4 0.6 19 259-277 223-241 (374) 91 TIGR02044 CueR Cu(I)-responsiv 26.5 42 0.0011 13.7 4.1 50 80-129 58-117 (127) 92 TIGR01148 mtrC tetrahydrometha 26.3 18 0.00046 16.2 -0.1 10 285-294 166-175 (276) 93 cd00529 RuvC_resolvase Hollida 25.7 44 0.0011 13.6 5.8 44 39-87 2-45 (154) 94 TIGR02728 spore_gerQ spore coa 24.9 14 0.00035 17.1 -0.9 18 190-207 4-21 (82) 95 pfam09350 DUF1992 Domain of un 24.6 46 0.0012 13.5 6.3 61 284-345 2-62 (70) 96 TIGR01807 CM_P2 chorismate mut 24.5 36 0.00092 14.2 1.2 26 154-179 8-33 (79) 97 PRK01237 triphosphoribosyl-dep 24.3 46 0.0012 13.4 4.4 49 307-361 221-269 (292) 98 PRK12677 xylose isomerase; Pro 24.0 47 0.0012 13.4 6.0 33 181-215 176-218 (389) 99 pfam00465 Fe-ADH Iron-containi 24.0 47 0.0012 13.4 2.1 11 370-380 277-287 (312) 100 TIGR03293 PhnG_redo phosphonat 23.7 48 0.0012 13.3 2.0 64 303-366 75-139 (144) 101 pfam08235 LNS2 LNS2 (Lipin/Ned 23.4 48 0.0012 13.3 4.8 113 244-378 11-142 (156) 102 PRK13224 consensus 23.1 20 0.00051 15.9 -0.3 80 200-292 132-215 (216) 103 pfam10694 DUF2500 Protein of u 22.5 36 0.00091 14.2 0.8 13 59-71 88-100 (107) 104 TIGR00422 valS valyl-tRNA synt 22.4 6.6 0.00017 19.3 -2.9 22 180-201 658-679 (970) 105 PRK10246 exonuclease subunit S 22.4 36 0.00091 14.2 0.8 14 387-400 1007-1020(1047) 106 PRK01008 queuine tRNA-ribosylt 22.2 51 0.0013 13.2 2.3 22 286-307 246-267 (372) 107 TIGR00713 hemL glutamate-1-sem 22.0 51 0.0013 13.1 3.2 75 307-400 324-416 (434) 108 TIGR01859 fruc_bis_ald_ fructo 21.7 52 0.0013 13.1 3.2 11 251-261 180-190 (339) 109 pfam09370 TIM-br_sig_trns TIM- 21.4 53 0.0013 13.0 2.5 43 236-278 26-75 (268) 110 PRK11552 putative DNA-binding 21.3 53 0.0013 13.0 4.2 35 210-246 10-44 (224) 111 TIGR02111 PQQ_syn_pqqC coenzym 21.3 39 0.00099 14.0 0.8 47 244-293 128-176 (239) 112 KOG1741 consensus 21.1 53 0.0014 13.0 4.7 36 105-140 30-69 (103) 113 PRK10254 hypothetical protein; 20.9 40 0.001 13.9 0.8 20 260-279 50-69 (137) 114 PRK09300 tRNA splicing endonuc 20.9 54 0.0014 13.0 1.5 20 80-99 36-55 (334) 115 TIGR01069 mutS2 MutS2 family p 20.6 35 0.00088 14.3 0.5 26 216-241 383-411 (834) 116 TIGR00987 himA integration hos 20.6 54 0.0014 12.9 1.8 43 272-314 9-59 (96) 117 cd04762 HTH_MerR-trunc Helix-T 20.5 21 0.00054 15.8 -0.7 30 280-312 13-42 (49) 118 pfam05788 Orbi_VP1 Orbivirus R 20.2 47 0.0012 13.4 1.1 62 65-134 622-687 (1301) 119 KOG4448 consensus 20.2 26 0.00066 15.2 -0.3 59 49-113 105-163 (374) 120 pfam01997 Translin Translin fa 20.1 44 0.0011 13.6 0.9 14 250-263 107-120 (186) No 1 >PRK05614 gltA type II citrate synthase; Reviewed Probab=100.00 E-value=0 Score=1157.70 Aligned_cols=412 Identities=66% Similarity=1.122 Sum_probs=402.7 Q ss_pred EEEEEEC-CEEEEEEEECCCCCCCCEEECCCC-CCCEEEECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCH Q ss_conf 6999989-989997523077787510100115-58618988887862387875654334477789899319999750898 Q gi|254780355|r 5 FAKLHLG-HEEIDLPIKEGSLGSSVLDISFLH-KNGIFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDF 82 (429) Q Consensus 5 ~~~l~~~-~~~~~lpi~~~~~~~~~~d~~~l~-~~G~~~~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sF 82 (429) ++||+++ ||+|||||++||+|+++|||++|+ +||++||||||+||++|||+||||||++|+|+||||||||||++++| T Consensus 1 ~a~l~~~~g~~~~~pi~~~t~g~~~idi~~l~~~tG~~t~DpG~~nt~~c~S~It~IDGe~GiL~YRGY~IedLa~~~sF 80 (414) T PRK05614 1 KATLTLEGGKSVELPILKGTLGPDVIDIRKLYGQTGYFTYDPGFTSTASCESKITYIDGDKGILLYRGYPIEQLAEKSDF 80 (414) T ss_pred CCEEEECCCCEEEECEECCCCCCCEEEHHHHHCCCCCEEECCCCCCCCEEEEEEEEEECCCCEEEECCCCHHHHHHCCCH T ss_conf 93699589967980201288898634667653237968878887762147653058736653798899179999853999 Q ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH Q ss_conf 99999998187999899999999886406899899999985124765257899999998752068557678788988899 Q gi|254780355|r 83 LEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSL 162 (429) Q Consensus 83 eEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~ 162 (429) ||||||||||+|||++||++|+.+|++++.+|+++.+++++||+++|||++|+++|++|+++|++..+..++++....++ T Consensus 81 eEvayLLl~G~LPt~~el~~F~~~l~~~~~lpe~v~~~l~~~P~~ahPM~~L~~~vsaL~~~~~~~~d~~~~~~~~~~a~ 160 (414) T PRK05614 81 LEVCYLLLYGELPTAEQKKEFDTTVTRHTMVHEQLKRFFRGFRRDAHPMAVLCGVVGALSAFYHDSLDINDPEHREIAAI 160 (414) T ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH T ss_conf 99999997898999999999999999725585999998851677777489999999998765104578899899999999 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHH Q ss_conf 99999999999999972798534888642468877876428984101479699999875635013678763015555442 Q gi|254780355|r 163 RMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAG 242 (429) Q Consensus 163 rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~va 242 (429) |||||+|+|+|++||++.|+++++||+++||+||||+||+|.+.++++++|..+|+||++|||||||||||||||+|||+ T Consensus 161 rliAk~pti~A~~yr~~~G~~~i~P~~~ls~aeNFL~Ml~g~~~~~~~~~p~~~~ald~~LiLhADHe~NaSTft~Rvva 240 (414) T PRK05614 161 RLIAKMPTLAAMAYKYSIGQPFVYPRNDLSYAENFLHMMFATPCEEYEVNPVLVRALDRIFILHADHEQNASTSTVRLAG 240 (414) T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHEEC T ss_conf 99989999999999995799887899874699999998548985345799899999999999987426771135430000 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHH Q ss_conf 05654246776755421002220352899999862155351279999998214786143027743555540346899999 Q gi|254780355|r 243 SSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETM 322 (429) Q Consensus 243 St~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~ 322 (429) ||+||+||||+|||+||||||||||||+|++||++|++++++++||++++++++++|||||||||||++||||++||+++ T Consensus 241 ST~ad~ysav~aaI~aL~GPLHGGAne~vl~mL~~Ig~~~~v~~~i~~~~~k~~~~rlmGFGHRVYk~~DPRA~ilk~~~ 320 (414) T PRK05614 241 SSGANPFACIAAGIAALWGPAHGGANEAVLKMLEEIGSVDNIPEFIAKAKDKNDGFRLMGFGHRVYKNYDPRAKIMRETC 320 (414) T ss_pred CCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHH T ss_conf 37887899999999965688787868999999999488454899999998523688504778876889992689999999 Q ss_pred HHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 99888608776517999999999996115314579877844788999998499966858999999998999999999707 Q gi|254780355|r 323 YEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVD 402 (429) Q Consensus 323 ~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~pNvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~ 402 (429) ++++++.+. ++|++++|.++|++|++|+||++|+||||||||||++|++||||++||||+||+||++||+|||+||+++ T Consensus 321 ~~l~~~~~~-~~~l~~ia~~lE~~al~d~yf~~r~lypNVDfYsg~vy~~lGiP~~~fT~lFAi~R~~GW~AH~~Eq~~~ 399 (414) T PRK05614 321 HEVLKELGL-DDPLLEVAMELEEIALEDEYFIERKLYPNVDFYSGIILKALGIPTSMFTVIFALARTVGWIAHWNEMHSD 399 (414) T ss_pred HHHHHHHCC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 999998378-8669999999999985112126789888713479999998098867778999999999999999999838 Q ss_pred CCCCCCCCCCCCCCC Q ss_conf 898300456210588 Q gi|254780355|r 403 PSRRIGRPRQLYTGA 417 (429) Q Consensus 403 ~~~ri~RP~~~Y~G~ 417 (429) +.+||+||||+|||. T Consensus 400 ~~~rI~RP~~~Y~G~ 414 (414) T PRK05614 400 PEQKIGRPRQLYTGY 414 (414) T ss_pred CCCCEECCCCCCCCC T ss_conf 788465887524496 No 2 >cd06114 EcCS_like Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some typ Probab=100.00 E-value=0 Score=1054.75 Aligned_cols=399 Identities=63% Similarity=1.080 Sum_probs=390.4 Q ss_pred EEEECCCCCCCCEEECCCC-CCCEEEECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCC Q ss_conf 7523077787510100115-586189888878623878756543344777898993199997508989999999818799 Q gi|254780355|r 17 LPIKEGSLGSSVLDISFLH-KNGIFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELA 95 (429) Q Consensus 17 lpi~~~~~~~~~~d~~~l~-~~G~~~~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLP 95 (429) |||+.||+|+++||+++|+ ++|++||||||.||++|||+||+|||++|+|+||||||+||+++++||||+||||+|+|| T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~g~~~~dPGL~~v~a~eT~Is~iDg~~G~L~YRGy~I~dLa~~~~FEEvayLLl~G~LP 80 (400) T cd06114 1 LPVLEGTEGEKVIDISSLRKKTGVFTYDPGFMNTASCESAITYIDGEKGILRYRGYPIEQLAEKSSFLEVCYLLLYGELP 80 (400) T ss_pred CCCCCCCCCCCEEEHHHHHHHCCCEEECCCCCCCEEEEEECEEEECCCCEEEECCEEHHHHHHCCCHHHHHHHHHCCCCC T ss_conf 98024788997145165586369687788878722687657015077857988991599986169999999999679798 Q ss_pred CHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 98999999998864068998999999851247652578999999987520685576787889888999999999999999 Q gi|254780355|r 96 NVSQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMI 175 (429) Q Consensus 96 t~~el~~F~~~l~~~~~lpe~v~~~i~~~p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~ 175 (429) |++||++|+.+|.+++.+|+.+.++++.+|+++|||++|+++|++|++++++..+..+++...+.++||+|++|+|+|++ T Consensus 81 t~~el~~f~~~L~~~~~lp~~v~~~i~~~P~~~hPM~~L~t~vs~L~~~~~~~~~~~~~~~~~~~a~rLiA~~p~i~A~~ 160 (400) T cd06114 81 TAEQLQEFREEITRHTLVHEQMKRFFNGFPRDAHPMAILSAMVNALSAFYPDSLDVNDPEQRELAAIRLIAKVPTIAAMA 160 (400) T ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999998568999999988513888785999999999988518655688999999999999998999999999 Q ss_pred HHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHH Q ss_conf 99727985348886424688778764289841014796999998756350136787630155554420565424677675 Q gi|254780355|r 176 YKYSIGQPFVYPRSDLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAG 255 (429) Q Consensus 176 yr~~~G~~~i~Pd~~lsyaeNfL~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~ag 255 (429) ||+++|++++.||+++||++|||+||+|.++..++|++..+|+||++||||||||+||||||+|||+||++|+||||+|| T Consensus 161 ~r~~~g~~~~~p~~~ls~a~NfL~Ml~g~~~~~~~p~~~~~~~ld~~LiLhADHe~NaSTFaarvvaSTlsD~ysai~aa 240 (400) T cd06114 161 YRYSIGQPFIYPDNDLSYVENFLHMMFAVPYEPYEVDPVVVKALDTILILHADHEQNASTSTVRMVGSSGANLFASISAG 240 (400) T ss_pred HHHHCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCHHHHHHHH T ss_conf 99875998667998636999999998288764579999999999999988862367623776655424788788999999 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCH Q ss_conf 54210022203528999998621553512799999982147861430277435555403468999999988860877651 Q gi|254780355|r 256 VACLGGRAHGGANEEALNMLMEIGSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDP 335 (429) Q Consensus 256 i~aL~GPlHGGAne~v~~ml~~I~~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~ 335 (429) |+||||||||||||+|++||++|++++++++||++.++++++.|||||||||||.+||||.+||++++++.++.+. +++ T Consensus 241 IgaLkGPLHGGAne~v~~ml~eIg~~~~~~~~i~~~~~~~~~~rimGfGHrVYk~~DPRa~~lk~~~~~l~~~~~~-~~~ 319 (400) T cd06114 241 IAALWGPLHGGANEAVLEMLEEIGSVGNVDKYIAKAKDKNDPFRLMGFGHRVYKNYDPRAKILKKTCDEVLAELGK-DDP 319 (400) T ss_pred HHHCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCC-CCH T ss_conf 9864788777689999999998578651999999998647986302678776888994389999999999988377-537 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC Q ss_conf 79999999999961153145798778447889999984999668589999999989999999997078983004562105 Q gi|254780355|r 336 IAQVAIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYT 415 (429) Q Consensus 336 ~~~~a~~le~~a~~d~~~~~r~l~pNvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~ 415 (429) +++++.++|+++++++||.+|+|+||||||||++|++||||+++|||||++||++||+|||+||+.++.||||||+++|| T Consensus 320 ~~~ia~~ie~~a~~~~~~~~r~l~pNVDfysg~ly~~lGip~dlfT~iFaisR~~GW~AH~~Eq~~~~~nrliRP~~~Yv 399 (400) T cd06114 320 LLEIAMELEEIALKDDYFIERKLYPNVDFYSGIILRALGIPTEMFTVLFALGRTPGWIAQWREMHEDPELKIGRPRQLYT 399 (400) T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCC T ss_conf 99999999999850011367898777035899999981988676369999999999999999998589986548878057 Q ss_pred C Q ss_conf 8 Q gi|254780355|r 416 G 416 (429) Q Consensus 416 G 416 (429) | T Consensus 400 G 400 (400) T cd06114 400 G 400 (400) T ss_pred C T ss_conf 9 No 3 >TIGR01800 cit_synth_II 2-methylcitrate synthase/citrate synthase II; InterPro: IPR011278 Citrate synthase 2.3.3.1 from EC is a member of a small family of enzymes that can directly form a carbon-carbon bond without the presence of metal ion cofactors. It catalyses the first reaction in the Krebs' cycle, namely the conversion of oxaloacetate and acetyl-coenzyme A into citrate and coenzyme A. This reaction is important for energy generation and for carbon assimilation. The reaction proceeds via a non-covalently bound citryl-coenzyme A intermediate in a 2-step process (aldol-Claisen condensation followed by the hydrolysis of citryl-CoA). Citrate synthase enzymes are found in two distinct structural types: type I enzymes (found in eukaryotes, Gram-positive bacteria and archaea) form homodimers and have shorter sequences than type II enzymes, which are found in Gram-negative bacteria and are hexameric in structure. In both types, the monomer is composed of two domains: a large alpha-helical domain consisting of two structural repeats, where the second repeat is interrupted by a small alpha-helical domain. The cleft between these domains forms the active site, where both citrate and acetyl-coenzyme A bind. The enzyme undergoes a conformational change upon binding of the oxaloacetate ligand, whereby the active site cleft closes over in order to form the acetyl-CoA binding site . The energy required for domain closure comes from the interaction of the enzyme with the substrate. Type II enzymes possess an extra N-terminal beta-sheet domain, and some type II enzymes are allosterically inhibited by NADH . This entry represents type I homodimeric citrate synthase enzymes (predominantly from Gram-positive bacteria and archaea), as well as 2-methylcitrate synthase; some enzyme in this entry may be bifunctional citrate synthase/2-methylcitrate synthase enzymes. Members of this family appear as a second citrate synthase isozyme but typically are associated with propionate metabolism and synthesise 2-methylcitrate from propionyl-CoA; citrate synthase activity may be incidental. A number of species, including Thermoplasma acidophilum, Pyrococcus furiosus, and the Antarctic bacterium DS2-3R have a bifunctional member of this family as the only citrate synthase isozyme . 2-methylcitrate (2.3.3.5 from EC) synthase catalyses the conversion of oxaloacetate and propanoyl-CoA into (2R,3S)-2-hydroxybutane-1,2,3-tricarboxylate and coenzyme A. This enzyme is induced during bacterial growth on propionate, while type II hexameric citrate synthase is constitutive . ; GO: 0046912 transferase activity transferring acyl groups acyl groups converted into alkyl on transfer, 0044262 cellular carbohydrate metabolic process, 0005737 cytoplasm. Probab=100.00 E-value=0 Score=1059.30 Aligned_cols=376 Identities=36% Similarity=0.620 Sum_probs=365.4 Q ss_pred CCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCC-HHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHH Q ss_conf 8786238787565433447778989931999975089-899999998187999899999999886406899899999985 Q gi|254780355|r 45 AFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSD-FLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMG 123 (429) Q Consensus 45 G~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~s-FeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~ 123 (429) ||..+.+|+|+||+|||++|+|.||||+|+|||++|+ ||||+||||||+|||++||++|+++|+++|.||++|+.+|+. T Consensus 2 GLegV~~~~T~ls~i~~~~g~L~Y~GY~i~DLa~~a~qFEEv~YLLl~G~LPt~~EL~~fk~~l~~~R~lP~~vi~~~~~ 81 (386) T TIGR01800 2 GLEGVLADETSLSTIDGEEGILTYRGYDIEDLAEKASQFEEVAYLLLHGKLPTKEELEKFKTELAKLRGLPDEVIELLES 81 (386) T ss_pred CCCCCCCCCEEEEEEECCCCEEEECCCCHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHH T ss_conf 76774211100004627887025637658999962264189999998205988889999989999751898989999986 Q ss_pred HCC-CCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC--HHHHHHHHHH Q ss_conf 124-7652578999999987520685576787889888999999999999999997279853488864--2468877876 Q gi|254780355|r 124 FPS-SAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSD--LDYASNFLHM 200 (429) Q Consensus 124 ~p~-~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~--lsyaeNfL~M 200 (429) +|+ ++|||++|||+||+|++++++.....+++..+..+.||+||+|+|+|++||+++|++.|.|+.+ +|||+||||| T Consensus 82 LP~~~~HPM~~LRTAvS~LG~~d~~G~~~~t~~~~r~~a~~l~A~~P~Iva~~~R~~~g~~~v~P~~~s~~s~A~nFL~m 161 (386) T TIGR01800 82 LPAEESHPMAVLRTAVSYLGALDPEGAETRTPEEARDIAKRLLAKLPTIVAAWYRIRNGLEIVAPREDSDLSIAANFLYM 161 (386) T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHH T ss_conf 03025898999999999984358777767898889888788774444999999976436885688435565356778876 Q ss_pred HCCCCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCC Q ss_conf 42898410147969999987563501367876301555544205654246776755421002220352899999862155 Q gi|254780355|r 201 CFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGS 280 (429) Q Consensus 201 l~~~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~ 280 (429) ++|+.+..-+|++..+|+||..||||||||+||||||+||++||+||+||||+||||||+|||||||||.||+||+||++ T Consensus 162 L~GeddGsv~P~~~~~~a~~~aLiLyAeHe~NASTFaarv~aSTLSD~YSaitaAIGALkGPLHGGAnE~vm~~l~ei~~ 241 (386) T TIGR01800 162 LHGEDDGSVEPSKEEEKAMDIALILYAEHELNASTFAARVIASTLSDIYSAITAAIGALKGPLHGGANEAVMKMLDEIGD 241 (386) T ss_pred HCCCCCCCCCCCHHHHHHHCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCC T ss_conf 41787788788979998613001134223885667999999988888999999999970687503189999999975238 Q ss_pred C-CHHHHHHHHHHHC-CCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 3-5127999999821-4786143027743555540346899999998886087765179999999999961153145798 Q gi|254780355|r 281 L-ERIPHYIMRAKDK-NDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKL 358 (429) Q Consensus 281 ~-~~v~~~i~~~~~~-~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l 358 (429) | +++++||.++|++ |+ |||||||||||++|||+++||+++++|.+..|. ..|++++.+||+++. +++.+|+| T Consensus 242 pd~~aE~~~~~~l~~GKE--riMGFGHRVYk~~DPRa~~lk~~a~~L~~~~G~--~K~Yei~~~~E~~~~--~~~g~Kgl 315 (386) T TIGR01800 242 PDDKAEAWIRKKLENGKE--RIMGFGHRVYKTYDPRAKILKEYAKKLSAKKGE--SKWYEISERIEDVME--KALGEKGL 315 (386) T ss_pred HHHHHHHHHHHHHHHCCC--EEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHH--HHHCCCCC T ss_conf 444588999999970896--684057532468996278999999999841688--723688899999999--97214788 Q ss_pred CCCCCHHHHHHHHHCCCCHH--HHHHHHHHHHHHHHHHHHHHHHH-CCCCCCCCCCCCCCCCCCCCCCCHHHC Q ss_conf 77844788999998499966--85899999999899999999970-789830045621058876870685542 Q gi|254780355|r 359 YPNVDFYSGITLRALGFPTN--LFTVLFAVARTAGWVSQWTEMIV-DPSRRIGRPRQLYTGALKRDYVPLEER 428 (429) Q Consensus 359 ~pNvDfysg~i~~~lGip~~--~ft~iFa~~R~~Gw~AH~~Eq~~-~~~~ri~RP~~~Y~G~~~r~y~pi~~R 428 (429) +||||||||.+|+.||||.+ +||||||+||+.||+||++||++ + |||||||+.||||..|+||||++| T Consensus 316 ~PNvDFySa~vY~~lGiP~~nnlFTpiFa~sRvsGW~AH~~Eq~~e~--NRLIRPrA~YvG~~~r~~vPi~~R 386 (386) T TIGR01800 316 YPNVDFYSASVYYSLGIPVDNNLFTPIFAMSRVSGWTAHIIEQYEEN--NRLIRPRAEYVGPEERKYVPIEER 386 (386) T ss_pred CCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 98886145899874688853344405899987777687545413205--631177522467566620670139 No 4 >cd06115 AthCS_per_like Arabidopsis thaliana (Ath) peroxisomal (Per) CS_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains three Arabidopsis peroxisomal CS proteins, CYS1, -2, and -3 which are involved in the glyoxylate cycle. AthCYS1, in addition to a peroxisomal targeting sequence, has a predicted secretory signal peptide; it may be targeted to both the secretory pathway and the peroxisomes and is thought to be located in the extracellular matrix. AthCSY1 is expr Probab=100.00 E-value=0 Score=1048.39 Aligned_cols=398 Identities=47% Similarity=0.823 Sum_probs=379.3 Q ss_pred CCCCCCCCEEECCCC----CCCEEEECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCC Q ss_conf 077787510100115----5861898888786238787565433447778989931999975089899999998187999 Q gi|254780355|r 21 EGSLGSSVLDISFLH----KNGIFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELAN 96 (429) Q Consensus 21 ~~~~~~~~~d~~~l~----~~G~~~~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt 96 (429) ++|+ ++.|++++. ++|++||||||.||++|||+||||||++|+|+||||||+|||++++||||+||||+|+||| T Consensus 2 ~~~~--~~~~~~~i~~~~~~~G~~~~dPGl~~v~~~eS~Is~iDg~~G~L~YRGy~I~dLa~~~~FeEvayLLl~G~LPt 79 (410) T cd06115 2 HGTV--KATDFKKIKAGKDDKGLRLYDPGYLNTAVVRSKISYIDGDKGILRYRGYPIEELAEKSTFLEVAYLLIYGNLPT 79 (410) T ss_pred CCCE--EHHHHHHHCCCCCCCCCEEECCCCCCEEEEEEECEEECCCCCEEEECCEEHHHHHCCCCHHHHHHHHHCCCCCC T ss_conf 9823--05666653246678892765887687016777680062888489889922999845698999999997697959 Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCC-------CCHHHHHHHHHHHHHHHH Q ss_conf 8999999998864068998999999851247652578999999987520685576-------787889888999999999 Q gi|254780355|r 97 VSQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYYSPSGV-------QDLEQCVNVSLRMIAKIS 169 (429) Q Consensus 97 ~~el~~F~~~l~~~~~lpe~v~~~i~~~p~~ahPM~~L~~~vsaL~a~~~~~~~~-------~d~~~~~~~a~rLiA~~p 169 (429) ++|+++|+.+|++++.||+.+.++++.||+++|||++|+++|++|++++++..+. .+.+...+.++||+|++| T Consensus 80 ~~el~~f~~~l~~~~~lp~~v~~~l~~~p~~~hPM~~L~~~vsal~~~~p~~~~~~~~~~~~~~~~~~~~~~irLiAk~p 159 (410) T cd06115 80 KSQLSDWEFAVSQHTAVPTGVLDMIKSFPHDAHPMGMLVSAISALSAFHPEANPALAGQDIYKNKQVRDKQIVRILGKAP 159 (410) T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH T ss_conf 99999999999984579877788875389888957999999999860186545322223334667788899999999999 Q ss_pred HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHH Q ss_conf 99999999727985348886424688778764289841014796999998756350136787630155554420565424 Q gi|254780355|r 170 TIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPF 249 (429) Q Consensus 170 ~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adly 249 (429) +|+|++||++.|++++.|++++||++|||+||++.....++|+|..+|+||++||||||||+||||||+|||+||+||+| T Consensus 160 ~i~A~~yr~~~g~~~~~P~~~ls~a~NfL~Ml~~~~~~~~~p~~~~~~ald~~LILhADHe~NaSTftarvvaST~sD~y 239 (410) T cd06115 160 TIAAAAYRRRAGRPPNLPSQDLSYTENFLYMLDSLGERKYKPNPRLARALDILFILHAEHEMNCSTAAVRHLASSGVDVY 239 (410) T ss_pred HHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHEEHHCCCCCHH T ss_conf 99999999965998888997636998999997078866689898999999999999873157741142112004788889 Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHC Q ss_conf 67767554210022203528999998621553512799999982147861430277435555403468999999988860 Q gi|254780355|r 250 ACIAAGVACLGGRAHGGANEEALNMLMEIGSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVT 329 (429) Q Consensus 250 sai~agi~aL~GPlHGGAne~v~~ml~~I~~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~ 329 (429) |||+|||+||||||||||||+|++||++|++++++++||++++++++ |||||||||||++||||++||++++++.+.. T Consensus 240 saisaaIgaLkGPLHGGAne~v~~ml~ei~s~~~v~~~i~~~l~~~~--rimGfGHrVYk~~DPRa~ilk~~~~~l~~~~ 317 (410) T cd06115 240 TAVAGAVGALYGPLHGGANEAVLRMLAEIGTVENIPAFIEGVKNRKR--KLSGFGHRVYKNYDPRAKIIKKLADEVFEIV 317 (410) T ss_pred HHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHCCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHC T ss_conf 99999998657887777889999999996472237999999871678--7677898768888827799999999999874 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 87765179999999999961153145798778447889999984999668589999999989999999997078983004 Q gi|254780355|r 330 GRFNDPIAQVAIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGR 409 (429) Q Consensus 330 ~~~~~~~~~~a~~le~~a~~d~~~~~r~l~pNvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~R 409 (429) + ++++++++.++|+++++++||.+|+||||||||||++|++||||++|||+||++||++||+|||+||+.+++||||| T Consensus 318 ~--~~~l~~ia~~ie~~~~~~~~~~~k~l~pNVDfysg~v~~~lGip~~~fT~iFa~sR~~GW~AH~~Eq~~~~~~rliR 395 (410) T cd06115 318 G--KDPLIEIAVALEKAALSDEYFVKRKLYPNVDFYSGLIYRAMGFPTDFFPVLFAIPRMAGYLAHWRESLDDPDTKIMR 395 (410) T ss_pred C--CCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEC T ss_conf 9--86179999999999998763556799878236899999980989366689999999999999999998388985768 Q ss_pred CCCCCCCCCCCCCCC Q ss_conf 562105887687068 Q gi|254780355|r 410 PRQLYTGALKRDYVP 424 (429) Q Consensus 410 P~~~Y~G~~~r~y~p 424 (429) |+|+||||.+|+|+| T Consensus 396 P~~~YvG~~~r~y~P 410 (410) T cd06115 396 PQQLYTGVWLRHYVP 410 (410) T ss_pred CCCEEECCCCCCCCC T ss_conf 986003899988898 No 5 >cd06116 CaCS_like Chloroflexus aurantiacus (Ca) citrate synthase (CS)_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). This group is similar to gram-negative Escherichia coli (Ec) CS (type II, gltA) and Arabidopsis thaliana (Ath) peroxisomal (Per) CS. However EcCS and AthPerCS are not found in this group. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers w Probab=100.00 E-value=0 Score=1040.24 Aligned_cols=384 Identities=56% Similarity=0.979 Sum_probs=376.5 Q ss_pred CEEEECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHH Q ss_conf 61898888786238787565433447778989931999975089899999998187999899999999886406899899 Q gi|254780355|r 38 GIFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENM 117 (429) Q Consensus 38 G~~~~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v 117 (429) |++||||||.||++|||+||||||++|+|+||||||+||+++++||||+||||+|+|||++|+++|+.+|++++.+|+.+ T Consensus 1 G~~~~dPGl~~~~~~eT~Is~iDg~~G~L~YRGy~I~dLa~~~sfeEvayLLl~G~LPt~~el~~f~~~l~~~~~l~~~v 80 (384) T cd06116 1 GLMTYDPAYLNTASCKSAITYIDGEKGILRYRGYPIEQLAEQSSYLEVAYLLLHGELPTKERLAQWVYDITRHTMTHENL 80 (384) T ss_pred CCEECCCCCCCCEEEEEECEEEECCCCEEEECCEEHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCHHH T ss_conf 96304787687216876683586898779888835999861499999999997798949999999999999854797789 Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHH Q ss_conf 99998512476525789999999875206855767878898889999999999999999972798534888642468877 Q gi|254780355|r 118 SRFFMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNF 197 (429) Q Consensus 118 ~~~i~~~p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNf 197 (429) .++++.||+++|||++|+++|++|++++++..+..+++.....++||+|++|+|+|++||++.|++++.||+++||++|| T Consensus 81 ~~~i~~~p~~~hPM~~L~~~vsal~~~~~~~~~~~~~~~~~~~~~rliA~~p~i~A~~~r~~~g~~~~~pd~~ls~a~Nf 160 (384) T cd06116 81 KKFMDGFRYDAHPMGILISSVAALSTFYPEAKNIGDEEQRNKQIIRLIGKMPTIAAFAYRHRLGLPYVLPDNDLSYTGNF 160 (384) T ss_pred HHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHH T ss_conf 99983588888947889999999985185444689978889999999999999999999996699977889874789999 Q ss_pred HHHHCCCCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH Q ss_conf 87642898410147969999987563501367876301555544205654246776755421002220352899999862 Q gi|254780355|r 198 LHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLME 277 (429) Q Consensus 198 L~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~ 277 (429) |+||++.....++++|..+|+||++||||||||+||||||+|||+||+||+||||+|||+||||||||||||+|++||++ T Consensus 161 L~Ml~~~~~~~~~p~~~~~~~ld~~LiLhADHe~NaSTftarvvaST~sD~ysai~aaI~aL~GPLHGGAne~v~~ml~e 240 (384) T cd06116 161 LSMLFKMTEPKYEPNPVLAKALDVLFILHADHEQNCSTSAMRSVGSSRADPYTAVAAAVAALYGPLHGGANEAVLRMLQQ 240 (384) T ss_pred HHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH T ss_conf 99970787766789989999999999997147776567888887615888899999999864788777889999999999 Q ss_pred CCCCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 15535127999999821478614302774355554034689999999888608776517999999999996115314579 Q gi|254780355|r 278 IGSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERK 357 (429) Q Consensus 278 I~~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~ 357 (429) |++++++++|+++.+++++ |||||||||||++||||++||+++++++++.+ ++++++++.++|+++++++||++|+ T Consensus 241 I~~~~~v~~~v~~~~~~~~--rimGfGHrVYk~~DPRa~ilk~~~~~l~~~~~--~~~~~~~a~~ie~~~~~~~~~~~k~ 316 (384) T cd06116 241 IGSPKNIPDFIETVKQGKE--RLMGFGHRVYKNYDPRARIIKKIADEVFEATG--RNPLLDIAVELEKIALEDEYFISRK 316 (384) T ss_pred HCCCCCHHHHHHHHHHCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 6794208999999984788--65677887688899268999999999998628--7727899999999998877445689 Q ss_pred CCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCH Q ss_conf 87784478899999849996685899999999899999999970789830045621058876870685 Q gi|254780355|r 358 LYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTGALKRDYVPL 425 (429) Q Consensus 358 l~pNvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~G~~~r~y~pi 425 (429) ||||||||||++|++||||++|||++|++||++||+|||+||++++.+||+||+|+||||.+|+|+|| T Consensus 317 l~pNVDfysg~l~~~lGip~~~fT~iFa~sR~~GW~AH~~E~~~~~~~riiRP~~~Y~G~~~r~y~Pi 384 (384) T cd06116 317 LYPNVDFYSGLIYQALGFPTEAFTVLFAIPRTSGWLAQWIEMLRDPEQKIARPRQVYTGPRDRDYVPI 384 (384) T ss_pred CCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCCCCCC T ss_conf 88781048999999819893666799999999999999999982878864288752139899998889 No 6 >cd06107 EcCS_AthCS-per_like Escherichia coli (Ec) citrate synthase (CS) gltA and Arabidopsis thaliana (Ath) peroxisomal (Per) CS_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of ide Probab=100.00 E-value=0 Score=977.63 Aligned_cols=375 Identities=55% Similarity=0.935 Sum_probs=364.3 Q ss_pred CEEEECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHH Q ss_conf 61898888786238787565433447778989931999975089899999998187999899999999886406899899 Q gi|254780355|r 38 GIFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENM 117 (429) Q Consensus 38 G~~~~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v 117 (429) |+++|||||.||++|||+||+|||++|+|+||||||+||+++++||||+||||||+|||++|+++|+.++.+++.+|+.+ T Consensus 1 g~~~~dpGL~~v~~~es~Is~iDg~~G~L~YRGy~i~dLa~~~~fEeva~LLl~G~lPt~~el~~f~~~l~~~~~lp~~v 80 (382) T cd06107 1 GLRVYDPGYLNTAVCESSITYIDGDKGILLYRGYPIEQLAESSTYEEVAYLLLWGELPTQEQYDEFQRRLSEHMMVPESV 80 (382) T ss_pred CCEEECCCCCCCEEEEEECEEEECCCCEEEECCEEHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCHHH T ss_conf 97643798888437775682365788879889914999850599999999997597979999999999999825898799 Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCC-------CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 9999851247652578999999987520685576-------787889888999999999999999997279853488864 Q gi|254780355|r 118 SRFFMGFPSSAHPMAMLVSAVGALSSFYYSPSGV-------QDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSD 190 (429) Q Consensus 118 ~~~i~~~p~~ahPM~~L~~~vsaL~a~~~~~~~~-------~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~ 190 (429) .++++.+|+++|||++|++++++|++++++..+. .+++...+.++||+|++|+|+|++||++.|+++++|+++ T Consensus 81 ~~~i~~~P~~~hPM~~l~~~vsal~~~~~~~~~~~~~~~~~~~~~~~~~~~~rliA~~p~i~a~~~r~~~g~~~~~p~~~ 160 (382) T cd06107 81 HRLIQTFPRDAHPMGILCAGLSALSAFYPEAIPAHTGDLYQNNPEVRDKQIIRTLAKMPTIAAAAYCHRIGRPFVYPRAN 160 (382) T ss_pred HHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC T ss_conf 99998368878858999999999860395433211233333787789999999998999999999999669998889988 Q ss_pred HHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHH Q ss_conf 24688778764289841014796999998756350136787630155554420565424677675542100222035289 Q gi|254780355|r 191 LDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEE 270 (429) Q Consensus 191 lsyaeNfL~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~ 270 (429) ++|++|||+||++.+...++++|..+++||++||||||||+||||||+|||+||++|+||||+|||+||||||||||||+ T Consensus 161 l~~a~nfl~ml~~~~~~~~~~~~~~~~~ld~~LiLhADHe~NaSTFtarvvaST~aD~ysav~aai~aL~GPlHGGAn~~ 240 (382) T cd06107 161 LSYIENFLYMMGYVDQEPYEPNPRLARALDRLWILHADHEMNCSTSAARHTGSSLADPISCMAAAIAALYGPLHGGANEA 240 (382) T ss_pred CCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCHHHH T ss_conf 57888899987068766678998999999999878612577712455433323788889999999997478887639999 Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 99998621553512799999982147861430277435555403468999999988860877651799999999999611 Q gi|254780355|r 271 ALNMLMEIGSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALED 350 (429) Q Consensus 271 v~~ml~~I~~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d 350 (429) |++||++|++++++++||++.+++++ |||||||||||++||||++|+++++++..+.+ ++++++++.++|++++++ T Consensus 241 v~~ml~ei~~~~~v~~~i~~~l~~~~--ri~GfGHrVYk~~DPRa~~l~~~~~~l~~~~~--~~~~~~~a~~ie~~a~~~ 316 (382) T cd06107 241 ALKMLREIGTPENVPAFIERVKNGKR--RLMGFGHRVYKNYDPRAKVIREILHEVLTEVE--KDPLLKVAMELERIALED 316 (382) T ss_pred HHHHHHHHCCHHHHHHHHHHHHCCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHH T ss_conf 99999984883147999999763678--64577876688899448999999999988648--866999999999999732 Q ss_pred HHCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC Q ss_conf 531457987784478899999849996685899999999899999999970789830045621058 Q gi|254780355|r 351 EYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTG 416 (429) Q Consensus 351 ~~~~~r~l~pNvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~G 416 (429) +||.+|++|||||||||++|++||||++|||+||++||++||+|||+||+.++.+||||||++||| T Consensus 317 ~~~~~k~l~pNVDfysg~l~~~lGip~~~ft~lFa~sR~~GW~AH~~Eq~~~~~~rliRP~~~Y~G 382 (382) T cd06107 317 EYFVSRKLYPNVDFYSGFIYKALGFPPEFFTVLFAVARTSGWMAHWREMMEDPLQRIWRPRQVYTG 382 (382) T ss_pred HHCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCC T ss_conf 433678998680168999999929693677899999999999999999972888857588781569 No 7 >PRK12351 methylcitrate synthase; Provisional Probab=100.00 E-value=0 Score=970.08 Aligned_cols=371 Identities=39% Similarity=0.659 Sum_probs=358.7 Q ss_pred EECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHH Q ss_conf 98888786238787565433447778989931999975089899999998187999899999999886406899899999 Q gi|254780355|r 41 TYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRF 120 (429) Q Consensus 41 ~~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~ 120 (429) .++|||.||++|+|+||+|||++|+|+||||||+||+++++||||+||||+|+|||++|+++|+.++++++.+|+++.++ T Consensus 7 ~~~~GL~gv~v~~S~Is~IDg~~G~L~YRGy~i~dLa~~~~fEEva~LL~~G~LPt~~el~~f~~~l~~~~~lp~~v~~~ 86 (377) T PRK12351 7 KVSKGLEGVVAGNTAISTVGGSGGDLTYRGYDIEDLAENCSFEEVAYLLLHGELPTKAELAAFKEKLRALRGLPAAVKDV 86 (377) T ss_pred CCCCCCCCCEEEEEECCEEECCCCEEEECCEEHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHH T ss_conf 88988899815576581464789889998934999982499999999997797939999999999999727999999999 Q ss_pred HHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH Q ss_conf 98512476525789999999875206855767878898889999999999999999972798534888642468877876 Q gi|254780355|r 121 FMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHM 200 (429) Q Consensus 121 i~~~p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~M 200 (429) ++.||+++|||++|+++|++|++++++..+ .+++...+.++||+|++|+|+|++||+++|++++.|++++||++|||+| T Consensus 87 l~~~p~~~hPM~~L~~~vs~L~~~~~~~~~-~~~~~~~~~a~rliA~~p~i~a~~~r~~~g~~~i~p~~~ls~a~NfL~m 165 (377) T PRK12351 87 LESLPASAHPMDVLRTGVSALGLFDPEAED-HSPEAARDIADRLLAKLPTIVAYWYRYRHGGDPIEPRDDLSIAANFLYM 165 (377) T ss_pred HHHCCCCCCCHHHHHHHHHHHHHHCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHH T ss_conf 985788898078999999998732867566-9989999999999999999999999997799887898520399999998 Q ss_pred HCCCCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCC Q ss_conf 42898410147969999987563501367876301555544205654246776755421002220352899999862155 Q gi|254780355|r 201 CFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGS 280 (429) Q Consensus 201 l~~~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~ 280 (429) |+|. ++++..+|+||++||||||||+||||||+||||||++|||+||+|||+||||||||||||+|++||++|++ T Consensus 166 l~g~-----~p~~~~~~~l~~~LiL~ADHe~NaSTfaaRvvaST~ad~ysav~agi~aL~GPlHGGAn~~v~~ml~eI~~ 240 (377) T PRK12351 166 LHGE-----EPSELWVKAMDVSLILYAEHEFNASTFTARVIASTLSDMYSAITAAIGALKGPLHGGANEAVMEMLEEIGS 240 (377) T ss_pred HCCC-----CCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC T ss_conf 4589-----99989999999999987237888058999999705987899999988863676444667999999999589 Q ss_pred CCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 35127999999821478614302774355554034689999999888608776517999999999996115314579877 Q gi|254780355|r 281 LERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYP 360 (429) Q Consensus 281 ~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~p 360 (429) ++++++||++++++++ |||||||||||++||||++|+++++++.+..+ ++++++++.++|+++.+ .||+|| T Consensus 241 ~~~v~~~i~~~l~~~~--rl~GFGHrvYk~~DPRa~~l~~~~~~l~~~~~--~~~~~~~a~~ie~~~~~-----~~~l~p 311 (377) T PRK12351 241 PEEAEAYLRKRLANKE--KIMGFGHRVYKVSDPRAKILKELAEKLAKEKG--DEKLYDIAERLEKVMWE-----EKGIFP 311 (377) T ss_pred CHHHHHHHHHHHHCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHH-----HCCCCC T ss_conf 2577999999985589--76577876578999368999999999987349--84799999999999997-----379998 Q ss_pred CCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHC Q ss_conf 84478899999849996685899999999899999999970789830045621058876870685542 Q gi|254780355|r 361 NVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTGALKRDYVPLEER 428 (429) Q Consensus 361 NvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~G~~~r~y~pi~~R 428 (429) |||||||++|++||||.+|||+||++||++||+|||+||+++ +|||||||+|||+.+|+|+||++| T Consensus 312 NVDfys~~l~~~lGip~~~ft~iFa~~R~~GW~AH~~Eq~~~--~~liRP~~~YvG~~~r~y~p~~~R 377 (377) T PRK12351 312 NVDFYSGVVYHMMGIPTDLFTPIFAISRVAGWLAHIIEQRED--NRIIRPSANYVGPEDRKYVPIEER 377 (377) T ss_pred CCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 712689999999398866788999999999999999999847--970077640149999888771129 No 8 >cd06112 citrate_synt_like_1_1 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, an Probab=100.00 E-value=0 Score=940.58 Aligned_cols=372 Identities=42% Similarity=0.755 Sum_probs=357.9 Q ss_pred ECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHH Q ss_conf 88887862387875654334477789899319999750898999999981879998999999998864068998999999 Q gi|254780355|r 42 YDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFF 121 (429) Q Consensus 42 ~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i 121 (429) |||||.||++|+|+||+|||++|+|+||||||+||+++++||||+||||+|+|||++|+++|+.+|.+++.+|+.+.+++ T Consensus 1 ~~pGL~gv~v~~T~Is~Idg~~G~L~YRGy~i~dLa~~~~fEeva~LL~~G~LP~~~el~~f~~~l~~~~~l~~~v~~~~ 80 (373) T cd06112 1 YIPGLAGVPAAESSISYIDGKNGILEYRGYDIEELAEYSSFEEVALLLLDGDLPTAAELEEFDKELRQHRRVKYNIRDMM 80 (373) T ss_pred CCCCCCCCCEEEEECEEEECCCCEEEECCEEHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHH T ss_conf 98977898145776817737888798899049998635999999999976989699999999999998456875789998 Q ss_pred HHHCCCCCHHHHHHHHHHHHHHHHCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH Q ss_conf 8512476525789999999875206855-767878898889999999999999999972798534888642468877876 Q gi|254780355|r 122 MGFPSSAHPMAMLVSAVGALSSFYYSPS-GVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHM 200 (429) Q Consensus 122 ~~~p~~ahPM~~L~~~vsaL~a~~~~~~-~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~M 200 (429) +.||+++|||++|++++++|++++++.. +..+++...+.++||+|++|+|+|++||++.|++++.|+++++|++|||+| T Consensus 81 ~~~p~~~hpm~~l~~~vs~l~~~~~~~~~~~~~~~~~~~~~~rliA~~p~i~A~~~r~~~g~~~i~p~~~l~~a~nfl~m 160 (373) T cd06112 81 KCFPETGHPMDMLQATVAALGMFYPKPEVLKPNPDYIDAATVKLIAKMPTLVAMWARIRNGDDPIEPRPDLDYAENFLYM 160 (373) T ss_pred HCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHH T ss_conf 70875479588999999998732865334689999999999999999999999999997699988899630499999999 Q ss_pred HCCCCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCC Q ss_conf 42898410147969999987563501367876301555544205654246776755421002220352899999862155 Q gi|254780355|r 201 CFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGS 280 (429) Q Consensus 201 l~~~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~ 280 (429) ++|. ++++..+++||++||||||||+||||||+|||+||++|+|+||+|||+||||||||||||+|++||++|++ T Consensus 161 l~g~-----~p~~~~~~~ld~~LiL~ADHe~NaSTfa~RvvaST~ad~ysav~aai~aL~GPLHGGAn~~v~~ml~ei~~ 235 (373) T cd06112 161 LFGE-----EPDPATAKILDACLILHAEHTMNASTFSALVTGSTLADPYAVISSAIGTLSGPLHGGANEDVLEMLEEIGS 235 (373) T ss_pred HHCC-----CCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC T ss_conf 7078-----99999999999999687116775789999999658888899999999864687555789999999998499 Q ss_pred CCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 35127999999821478614302774355554034689999999888608776517999999999996115314579877 Q gi|254780355|r 281 LERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYP 360 (429) Q Consensus 281 ~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~p 360 (429) ++++++||++++++|+ |||||||||||++||||++|+++++++.++.+. .+++++++.++|+++ .++|.+||+|| T Consensus 236 ~~~~~~~i~~~l~~~~--~i~GFGHrvYk~~DPRa~~L~~~~~~l~~~~~~-~~~~~~~a~~ie~~~--~e~~~~k~l~p 310 (373) T cd06112 236 PENVKAYLDKKLANKQ--KIWGFGHRVYKTKDPRATILQKLAEDLFAKMGE-LSKLYEIALEVERLC--EELLGHKGVYP 310 (373) T ss_pred HHHHHHHHHHHHHCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHH--HHHHCCCCCCC T ss_conf 8889999999872688--778888765788994289999999999886177-567999999999999--99741479986 Q ss_pred CCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCH Q ss_conf 84478899999849996685899999999899999999970789830045621058876870685 Q gi|254780355|r 361 NVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTGALKRDYVPL 425 (429) Q Consensus 361 NvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~G~~~r~y~pi 425 (429) |||||||++|++||||+++||+||++||++||+|||+||+++ +||||||++||||.+|+|||| T Consensus 311 NVDfys~~l~~~lGip~~~~t~iFa~sR~~GW~AH~~Eq~~~--~~liRP~~~Y~G~~~~~~~p~ 373 (373) T cd06112 311 NVDFYSGIVYKELGIPADLFTPIFAVARVAGWLAHWKEQLGD--NRIFRPTQIYIGEIDRKYVPL 373 (373) T ss_pred CHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCCCCCCCCC T ss_conf 737799999999297957788999999999999999998647--985177660359998898999 No 9 >COG0372 GltA Citrate synthase [Energy production and conversion] Probab=100.00 E-value=0 Score=942.81 Aligned_cols=388 Identities=52% Similarity=0.862 Sum_probs=370.1 Q ss_pred CCEEECCCCCCCEEEECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHH Q ss_conf 51010011558618988887862387875654334477789899319999750898999999981879998999999998 Q gi|254780355|r 27 SVLDISFLHKNGIFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDK 106 (429) Q Consensus 27 ~~~d~~~l~~~G~~~~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~ 106 (429) +.+++++ ..++.++|+||+.+|.+|+|+||+|||++|+|+||||+|+||+++++||||+||||+|+|||.+|+++|..+ T Consensus 2 ~~~~~~~-~~~~~~~~~~Gl~~v~a~~t~is~id~~~g~L~yrGy~i~dla~~~~feev~~LLl~G~lPt~~el~~~~~~ 80 (390) T COG0372 2 DVIDIRT-SDVGRFTYDPGLEGVAACETAISYIDGDGGILRYRGYDIEDLAEKSSFEEVAYLLLYGELPTKAELAAFFAK 80 (390) T ss_pred CCCCCCC-CCCCCCCCCCCCCCCCEEEEEEEEECCCCCEEEECCCCHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHH T ss_conf 8424467-776642147754554246655346658876478888068999750679999999980778971779999999 Q ss_pred HHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 86406899899999985124765257899999998752068557678788988899999999999999999727985348 Q gi|254780355|r 107 ISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVY 186 (429) Q Consensus 107 l~~~~~lpe~v~~~i~~~p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~ 186 (429) +..++.+|+++.+++..+|+++|||++|++++++|++++++..+.++ ..+.+.||+|++|+|+|++||++.|.+++. T Consensus 81 ~~~~~~~~~~~~~~~~~~p~~~hpm~~l~~~vs~l~~~~~~~~~~~~---~~~~a~rlia~~pti~a~~yr~~~g~~~i~ 157 (390) T COG0372 81 LAARRTLPEQVIRLLESLPRDAHPMAVLRTAVSALSAFYPDKLDLND---RREAALRLIAKLPTIAAAVYRYSRGEPPIA 157 (390) T ss_pred HHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCCCCH---HHHHHHHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 99866666889999985777668679999999984012421134423---478888899875589999999753898766 Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCC Q ss_conf 88642468877876428984101479699999875635013678763015555442056542467767554210022203 Q gi|254780355|r 187 PRSDLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGG 266 (429) Q Consensus 187 Pd~~lsyaeNfL~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGG 266 (429) |+++++|++|||+|+++.++++ |..+|+||++||||||||+||||||+||++||++||||||+|||+||||||||| T Consensus 158 p~~~~s~a~nfL~ml~g~~p~~----~~~~~a~d~~LiL~ADHe~NASTftarvvaST~sd~ys~i~agi~aL~GPlHGG 233 (390) T COG0372 158 PDPDLSYAENFLYMLFGEPPSP----PVEARAMDRALILHADHELNASTFTARVVASTGSDLYACIAAGIGALKGPLHGG 233 (390) T ss_pred CCCCCCHHHHHHHHHCCCCCCC----HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCC T ss_conf 8988669999999970889996----799999999998983168871888999998617868999999998757876667 Q ss_pred CCHHHHHHHHHCCCCCH-HHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH Q ss_conf 52899999862155351-27999999821478614302774355554034689999999888608776517999999999 Q gi|254780355|r 267 ANEEALNMLMEIGSLER-IPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELER 345 (429) Q Consensus 267 Ane~v~~ml~~I~~~~~-v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~ 345 (429) |||+|++||+||++..+ +++||+++|++|+ |||||||||||++||||++||++++++.++.| +++++++|.++|+ T Consensus 234 Ane~v~~ml~ei~~~~~~~~~~v~~~l~~~~--~imGFGHRVYk~~DPRa~~lk~~a~~l~~~~g--~~~~~~~a~~~e~ 309 (390) T COG0372 234 ANEAVMKMLEEIGSSGESAEAYVRKALDRKE--RIMGFGHRVYKNYDPRAKVLKELAEKLGKELG--DLKLYEIAEELEE 309 (390) T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC--CCHHHHHHHHHHH T ss_conf 5899999999962132329999999985699--76788977678999559999999999887537--5059999999999 Q ss_pred HHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCH Q ss_conf 99611531457987784478899999849996685899999999899999999970789830045621058876870685 Q gi|254780355|r 346 IALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTGALKRDYVPL 425 (429) Q Consensus 346 ~a~~d~~~~~r~l~pNvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~G~~~r~y~pi 425 (429) +++++.+| +|+||||||||||++|++||||.+|||+||++||++||+|||+||+.++ |||+||||.|+|+.+|+|+|| T Consensus 310 ~~l~~~~~-~k~l~PNvDfysg~v~~~lGiP~~~fT~lFa~aR~~GW~AH~~Eq~~~~-~riiRPr~~Y~G~~~r~~~~~ 387 (390) T COG0372 310 IALEDLGF-EKKLYPNVDFYSGIVYRALGIPTDMFTPLFAIARTVGWIAHWIEQKEDG-NKIIRPRALYTGPEERDYVPI 387 (390) T ss_pred HHHHHHCC-CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCHHHHCCCCCCCCCCC T ss_conf 99973322-4588877414379999981998777310455445789999999999745-884578044258665446576 Q ss_pred HHC Q ss_conf 542 Q gi|254780355|r 426 EER 428 (429) Q Consensus 426 ~~R 428 (429) ++| T Consensus 388 ~~r 390 (390) T COG0372 388 EER 390 (390) T ss_pred CCC T ss_conf 779 No 10 >PRK12349 citrate synthase 3; Provisional Probab=100.00 E-value=0 Score=921.48 Aligned_cols=360 Identities=30% Similarity=0.547 Sum_probs=346.2 Q ss_pred ECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHH Q ss_conf 88887862387875654334477789899319999750898999999981879998999999998864068998999999 Q gi|254780355|r 42 YDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFF 121 (429) Q Consensus 42 ~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i 121 (429) |||||.||++|||+||+|||++|+|+||||||+||+++++||||+||||+|+|||++|+++|+.+|.+++.+|+.+.+++ T Consensus 4 ~~pGL~gv~~~et~Is~iDg~~G~L~YRGy~i~dLa~~~sfeEva~LLl~G~LPt~~el~~f~~~l~~~~~lp~~v~~~i 83 (365) T PRK12349 4 FSPGLDGIVAAETKISFLDTVKGEIVIQGYDLIELSKTKEYLDIVHLLLEGHLPNEDEKATLEKKLKEEYAVPEGVFNIL 83 (365) T ss_pred CCCCCCCCCEEEEECCCEECCCCEEEECCEEHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHH T ss_conf 99976897156887811557998799989259998306999999999987989698999999999998637977899999 Q ss_pred HHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH Q ss_conf 85124765257899999998752068557678788988899999999999999999727985348886424688778764 Q gi|254780355|r 122 MGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMC 201 (429) Q Consensus 122 ~~~p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~Ml 201 (429) +.||+++|||++|+++|++|++++++..+ .+.+...+.++||+|++|+|+|++||+++|++++.|+++++|++|||+|| T Consensus 84 ~~lp~~~hPm~~L~~~vs~l~~~d~~~~~-~~~~~~~~~a~~lia~~p~i~a~~~r~~~g~~~~~p~~~~~~a~nfl~ml 162 (365) T PRK12349 84 KALPKETHPMDGLRTGVSALAGYDNDIED-RSLEVNKSRAYKLLGKVPNIVANSYHILNNEEPIEPLKELSYSANFLYML 162 (365) T ss_pred HHCCCCCCCHHHHHHHHHHHHCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHH T ss_conf 71798998078999999998704976555-89799999999998789999999999976998889984316899988751 Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCC Q ss_conf 28984101479699999875635013678763015555442056542467767554210022203528999998621553 Q gi|254780355|r 202 FSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSL 281 (429) Q Consensus 202 ~~~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~~ 281 (429) +|. +|++..+|+||++||||||||+||||||+|||+||++||||||+|||+||||||||||||+|++||++|+++ T Consensus 163 ~g~-----~p~~~~~~~ld~~LiL~ADHe~naSTfaaRvvaST~ad~ysai~aai~aL~GPLHGGAne~v~~ml~ei~~~ 237 (365) T PRK12349 163 TGK-----KPTELEEKIFDRSLVLYSEHEMPNSTFTARVIASTQSDLYGALTGAVASLKGSLHGGANEAVMYMLLEAGTV 237 (365) T ss_pred CCC-----CCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCH T ss_conf 489-----886699999999999855566753789999997158888999999998667876678789999999982888 Q ss_pred CHHHHHHHHHHHCCCCCEEECCCCCCC-CCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 512799999982147861430277435-5554034689999999888608776517999999999996115314579877 Q gi|254780355|r 282 ERIPHYIMRAKDKNDPFRIMGFGHRVY-RNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYP 360 (429) Q Consensus 282 ~~v~~~i~~~~~~~~~~ri~GfGHrvy-k~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~p 360 (429) +++++||++.+++++ |||||||||| |.+||||++|++++.++.+..+ ++++++++.++|+++.+ +||||| T Consensus 238 ~~~~~~i~~~l~~~~--~i~GFGHrVY~k~~DPRa~~l~~~~~~l~~~~~--~~~l~~~~~~~e~~~~~-----~k~l~p 308 (365) T PRK12349 238 EKFEELLQKKLYNKE--KIMGFGHRVYMKKMDPRALMMKEALKQLCDVKG--DYTLYEMCEAGEKIMEK-----EKGLYP 308 (365) T ss_pred HHHHHHHHHHHHCCC--CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHH-----HCCCCC T ss_conf 779999999871799--611578755578899549999999999976347--61699999999999987-----039996 Q ss_pred CCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC Q ss_conf 8447889999984999668589999999989999999997078983004562105887 Q gi|254780355|r 361 NVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTGAL 418 (429) Q Consensus 361 NvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~G~~ 418 (429) |||||||++|++||||+++||+||++||++||+|||+||+++ +|||||+++||||. T Consensus 309 NvDfys~~l~~~lGip~d~ft~iFa~sR~~Gw~AH~~Eq~~~--~~liRP~~~YvG~~ 364 (365) T PRK12349 309 NLDYYAAPVYWMLGIPIQLYTPIFFSSRTVGLCAHVIEQHAN--NRLFRPRVNYIGER 364 (365) T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCC T ss_conf 758789999998097924668999999999999999999638--97338878306999 No 11 >cd06111 DsCS_like Cold-active citrate synthase (CS) from an Antarctic bacterial strain DS2-3R (Ds)-like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2-methylcitrate synthase (2MCS) catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. DsCS, compared with CS from the hyperthermophile Pyrococcus furiosus (not included in this group), has an increase in the size of surface loops, a higher proline content in the loop regions, a more accessible active site, and a highe Probab=100.00 E-value=0 Score=901.85 Aligned_cols=362 Identities=31% Similarity=0.538 Sum_probs=347.1 Q ss_pred CCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHH Q ss_conf 88786238787565433447778989931999975089899999998187999899999999886406899899999985 Q gi|254780355|r 44 PAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMG 123 (429) Q Consensus 44 pG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~ 123 (429) -|+.++.+|||+||+|||++|+|+||||||+||+++++||||+||||+|+|||++|+++|+.++..++.+|+.+.++++. T Consensus 1 ~GL~gv~~~et~Is~idg~~g~L~YRGy~i~dLa~~~~fEeva~LL~~G~LPt~~el~~f~~~l~~~~~lp~~v~~~l~~ 80 (362) T cd06111 1 KGLAGVVADTTAISKVMPETNSLTYRGYPVQDLAENCSFEEVAYLLWNGELPNAAQLAEFSQRERSYRRLDRNLLSLIAS 80 (362) T ss_pred CCCCCCEEEEEECEEEECCCCEEEECCEEHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHH T ss_conf 99898566133582576899879998932999973499999999996898969999999999999827997999999986 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCC Q ss_conf 12476525789999999875206855767878898889999999999999999972798534888642468877876428 Q gi|254780355|r 124 FPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFS 203 (429) Q Consensus 124 ~p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~Ml~~ 203 (429) ||+++|||++|++++++|++++++..+ .+++...+.++||+|++|+|+|++||++.|++++.|+++++|++|||+||+| T Consensus 81 ~p~~~hpm~~l~~~vs~l~~~d~~~~~-~~~~~~~~~a~~lia~~p~i~a~~~r~~~g~~~~~p~~~ls~a~nfl~ml~g 159 (362) T cd06111 81 LPKNCHPMDVLRTAVSVLGAEDSETDD-SSPDANLAKAIRLLAQLPTVVAADIRRRKGLDPIPPDSDLGIAENFLHMCFG 159 (362) T ss_pred HCCCCCCHHHHHHHHHHHHCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCC T ss_conf 388878377899999998634976121-8979999999986508999999999996699987899407689999998637 Q ss_pred CCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCH Q ss_conf 98410147969999987563501367876301555544205654246776755421002220352899999862155351 Q gi|254780355|r 204 VPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLER 283 (429) Q Consensus 204 ~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~~~~ 283 (429) . +++|..+|+||++||||||||+||||||+|||+||++|+|+||+|||+||||||||||||+|++||++|+++++ T Consensus 160 ~-----~p~~~~~ral~~~LiL~ADHg~NaSTfaaRvvaST~ad~ysav~aal~aL~GPLHGGAn~~v~~ml~ei~~~~~ 234 (362) T cd06111 160 E-----VPSPEVVRAFDVSLILYAEHSFNASTFTARVITSTLSDIYSAITGAIGALKGPLHGGANEAVMHMMLEIDDPEK 234 (362) T ss_pred C-----CCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCHHH T ss_conf 9-----99899999999999997243687389999999658888899999999872788765678999999998378122 Q ss_pred HHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 27999999821478614302774355554034689999999888608776517999999999996115314579877844 Q gi|254780355|r 284 IPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVD 363 (429) Q Consensus 284 v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~pNvD 363 (429) +++||++.+++|+ |||||||||||++||||++|+++++++.+..+ ..++++++.++|+++. ..||+||||| T Consensus 235 ~~~~i~~~l~~~~--~i~GFGHrvYk~~DPRa~~l~~~~~~l~~~~~--~~~~~~~~~~~e~~~~-----~~k~l~pNVD 305 (362) T cd06111 235 AAQWMLDALARKE--KVMGFGHRVYKSGDSRVPTMEKALRRVAAVHD--GQKWLAMYDALEDAMV-----AAKGIKPNLD 305 (362) T ss_pred HHHHHHHHHHCCC--CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHH-----HHCCCCCCCH T ss_conf 6999999984688--77888875577889505999999999876228--7069999999999999-----8479998821 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC Q ss_conf 78899999849996685899999999899999999970789830045621058876870 Q gi|254780355|r 364 FYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTGALKRDY 422 (429) Q Consensus 364 fysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~G~~~r~y 422 (429) ||||++|++||||+++||++|++||++||+|||+||+++ +|||||||+||||.+|+. T Consensus 306 fys~~l~~~lGip~~~~t~lFa~sR~~GW~AH~~Eq~~~--~~liRP~~~YvGp~~r~~ 362 (362) T cd06111 306 FPAGPAYYLMGFDIDFFTPIFVMARITGWTAHIMEQRAD--NALIRPLSEYNGPEQRPV 362 (362) T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCCCCCC T ss_conf 689999999198856778999999999999999999867--985389871429799999 No 12 >cd06113 citrate_synt_like_1_2 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) a carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) h Probab=100.00 E-value=0 Score=891.67 Aligned_cols=370 Identities=33% Similarity=0.527 Sum_probs=331.6 Q ss_pred CCCCEEEECCCCCCEEEEEEEEEEEECCC----CEEEECCEEHHHHHHHCC------HHHHHHHHHCCCCCCHHHHHHHH Q ss_conf 55861898888786238787565433447----778989931999975089------89999999818799989999999 Q gi|254780355|r 35 HKNGIFTYDPAFSSTASCKSKITFIDGNN----GILLYRGYPIEQLSEKSD------FLEVCYLLLHGELANVSQQKDFN 104 (429) Q Consensus 35 ~~~G~~~~dpG~~~ta~ceS~IT~IDG~~----G~L~YRGY~IedLa~~~s------FeEVayLLl~GeLPt~~el~~F~ 104 (429) +.+|++. |.+++ +|-..+++|||++ |+|+||||||+|||++++ ||||+||||||+|||++||++|+ T Consensus 7 ~g~gvia---~~t~i-~~v~g~~~~~ge~~p~~G~L~YRGY~IedLa~~~t~~~~~~FeEvayLLl~G~LPt~~eL~~f~ 82 (406) T cd06113 7 DGTGVLA---GLTNI-SDVVGYKIIDGEKVPCPGKLYYRGYDVEDLVNGAQKENRFGFEETAYLLLFGYLPNKEELEEFC 82 (406) T ss_pred CCCEEEE---CCCEE-EEEEEEEEECCCCCCCCCEEEECCCCHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHH T ss_conf 9997887---44312-2357676246858899873888992199998237767678899999999878798999999999 Q ss_pred HHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH----C Q ss_conf 988640689989999998512476525789999999875206855767878898889999999999999999972----7 Q gi|254780355|r 105 DKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYS----I 180 (429) Q Consensus 105 ~~l~~~~~lpe~v~~~i~~~p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~----~ 180 (429) .+|++++.||+++.+.+..+++++|||++|+++|++|+++++++.+ .+.+...+.++||+|++|+|+|++||.. . T Consensus 83 ~~l~~~r~lp~~~~~~~~~~~p~~~pM~~L~~~vs~L~~~~~~~~~-~~~~~~~~~~irliAk~pti~a~~yr~~~~~~~ 161 (406) T cd06113 83 EILSSYRTLPDNFVEDVILKAPSKDIMNKLQRSVLALYSYDDKPDD-ISLENVLRQSIQLIARLPTIAVYAYQAKRHYYD 161 (406) T ss_pred HHHHHCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 9999817899999999974188877399999999998646877677-999999999999998746999999999850036 Q ss_pred CCC--CCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHEECCC-CCCCHHHHHHHHHCCCCCHHHHHHHHHH Q ss_conf 985--3488864246887787642898410147969999987563501367-8763015555442056542467767554 Q gi|254780355|r 181 GQP--FVYPRSDLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADH-EQNASTSTVRLAGSSGADPFACIAAGVA 257 (429) Q Consensus 181 G~~--~i~Pd~~lsyaeNfL~Ml~~~~~~~~~~~~~~~~ald~~LILhADH-e~NaSTft~R~vaSt~adlysai~agi~ 257 (429) +++ +..||+++||++|||+||++. .+++|..+|+||++||||||| ||||||||+||||||+||+||||+|||+ T Consensus 162 ~~~~~~~~pd~~ls~a~NFL~Ml~~~----~~~~~~~~rald~~LILhADH~~~NaSTftaRvvaST~sD~ysaisaaIg 237 (406) T cd06113 162 GESLYIHHPQPELSTAENILSMLRPD----KKYTELEAKLLDLCLVLHAEHGGGNNSTFTTRVVSSSGTDTYSAIAAAIG 237 (406) T ss_pred CCCCCCCCCCCCCCHHHHHHHHHCCC----CCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHH T ss_conf 88866478986546899999983699----99997999999999999624377760166655553478878999999998 Q ss_pred HHHHHHHCCCCHHHHHHHHHC-------CCCCHHHHHHHHHHHCCC---CCEEECCCCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 210022203528999998621-------553512799999982147---8614302774355554034689999999888 Q gi|254780355|r 258 CLGGRAHGGANEEALNMLMEI-------GSLERIPHYIMRAKDKND---PFRIMGFGHRVYRNHDPRCRIMRETMYEVLE 327 (429) Q Consensus 258 aL~GPlHGGAne~v~~ml~~I-------~~~~~v~~~i~~~~~~~~---~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~ 327 (429) ||||||||||||+|++||++| +++++|++|+++.++++. ..+||||||||||++||||++||+++++|.+ T Consensus 238 aL~GPLHGGAne~vl~ml~eI~~~~~~~~~~~~v~~~i~~~~~k~~~~~~~~imGFGHRVYK~~DPRa~ilk~~a~~l~~ 317 (406) T cd06113 238 SLKGPRHGGANIKVMEMLEDIKENVKDWTDEDEVRAYLRKILNKEAFDKSGLIYGMGHAVYTLSDPRAVVLKKYARSLAK 317 (406) T ss_pred HCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH T ss_conf 64686545848999999999998524789778999999999853302456764257887789999318999999999987 Q ss_pred HCCCCCCHHHHHHHHHHHHH---HHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 60877651799999999999---611531457987784478899999849996685899999999899999999970789 Q gi|254780355|r 328 VTGRFNDPIAQVAIELERIA---LEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPS 404 (429) Q Consensus 328 ~~~~~~~~~~~~a~~le~~a---~~d~~~~~r~l~pNvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~ 404 (429) +.+. +++++++.++|+++ +.++||+.|+||||||||||++|++||||++||||||++||++||+|||+||+.++ T Consensus 318 ~~g~--~~~~~~~~~~e~~a~~~l~~~~~~~r~l~pNVDfYsg~v~~~lGip~~~fT~iFaisR~~GW~AH~~Eq~~~~- 394 (406) T cd06113 318 EKGR--EEEFALYERIERLAPEVIAEERGIGKTVCANVDFYSGFVYKMLGIPQELYTPLFAVARIVGWCAHRIEELLNS- 394 (406) T ss_pred HCCC--CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC- T ss_conf 6188--6279999999999999999874556898878016899999981979245479999999999999999997478- Q ss_pred CCCCCCCCCCCC Q ss_conf 830045621058 Q gi|254780355|r 405 RRIGRPRQLYTG 416 (429) Q Consensus 405 ~ri~RP~~~Y~G 416 (429) ||||||+|+||| T Consensus 395 nriiRP~~~YvG 406 (406) T cd06113 395 GRIIRPAYKYVG 406 (406) T ss_pred CCEECCCCCCCC T ss_conf 974588872679 No 13 >cd06110 BSuCS-II_like Bacillus subtilis (Bs) citrate synthase (CS)-II_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains proteins similar to BsCS-II, the major CS of the gram-positive bacterium Bacillus subtilis. A mutation in the gene which encodes BsCS-II (citZ gene) has been described which resulted in a significant loss of CS activity, partial glutamate auxotrophy, and a sporulation deficiency, a Probab=100.00 E-value=0 Score=893.44 Aligned_cols=356 Identities=37% Similarity=0.624 Sum_probs=342.1 Q ss_pred CCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHH Q ss_conf 88786238787565433447778989931999975089899999998187999899999999886406899899999985 Q gi|254780355|r 44 PAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMG 123 (429) Q Consensus 44 pG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~ 123 (429) -||.||++|+|+||+|||++|+|+||||||+||+++++||||+||||+|+|||++|+++|+.++++++.+|+++.++++. T Consensus 1 ~Gl~gv~~~~s~is~idg~~G~L~YRGy~i~~La~~~~fEeva~LLl~G~lP~~~el~~f~~~l~~~~~lp~~~~~~l~~ 80 (356) T cd06110 1 KGLEGVIAADSKISYIDGDAGILIYRGYDIHDLAENSTFEEVAYLLWNGELPTAEELDAFKAQLAAERELPAEIIDLLKL 80 (356) T ss_pred CCCCCCEEEEEECEEEECCCCEEEECCEEHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHH T ss_conf 99899716578681686898889898923999861699999999997899969999999999998767899989999985 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCC Q ss_conf 12476525789999999875206855767878898889999999999999999972798534888642468877876428 Q gi|254780355|r 124 FPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFS 203 (429) Q Consensus 124 ~p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~Ml~~ 203 (429) +|+++|||++|++++++|++++++..+. +++...+.++||+|++|+|+|++||+++|++++.|+++++|++|||+||++ T Consensus 81 ~p~~~hpm~~l~~~vs~l~~~~~~~~~~-~~~~~~~~a~~lia~~p~i~a~~~r~~~g~~~~~p~~~l~~a~nfl~ml~g 159 (356) T cd06110 81 LPKDAHPMDVLRTAVSALALYDPEADDM-SREANLRKAIRLIAKMPTIVAAFHRIRNGLEPVAPDPDLSHAANFLYMLTG 159 (356) T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCC T ss_conf 7766663679999999987329545446-848999999986609999999999996799988999315499999987438 Q ss_pred CCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCH Q ss_conf 98410147969999987563501367876301555544205654246776755421002220352899999862155351 Q gi|254780355|r 204 VPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLER 283 (429) Q Consensus 204 ~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~~~~ 283 (429) + +|++..+++||++||||||||+||||||+||||||++|||+||+|||+||||||||||||+|++||++|+++++ T Consensus 160 ~-----~p~~~~~~~l~~~LiL~ADHe~NaSTfaaRvvaSt~ad~ysav~agi~aL~GPlHGGAn~~v~~ml~~i~~~~~ 234 (356) T cd06110 160 E-----KPSEEAARAFDVALILHADHELNASTFAARVVASTLSDMYSAVTAAIGALKGPLHGGANERVMKMLLEIGSVDN 234 (356) T ss_pred C-----CCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCHHH T ss_conf 8-----99989999999999997147777066888998468887378999999981687633589999999998488667 Q ss_pred HHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 27999999821478614302774355554034689999999888608776517999999999996115314579877844 Q gi|254780355|r 284 IPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVD 363 (429) Q Consensus 284 v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~pNvD 363 (429) +++||++++++++ |||||||||||++||||++|+++++++.+..+ ++++++++.++|+++.+ +|++||||| T Consensus 235 v~~~i~~~l~~~~--~i~GFGHrvY~~~DPRa~~l~~~~~~l~~~~~--~~~l~~~a~~ie~~~~~-----~k~~~pNVD 305 (356) T cd06110 235 VAAYVKDKLANKE--KIMGFGHRVYKTGDPRAKHLREMSRRLGKETG--EPKWYEMSEAIEQAMRD-----EKGLNPNVD 305 (356) T ss_pred HHHHHHHHHHCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHH-----HHCCCCCHH T ss_conf 9999999983789--88888876688889579999999999976038--85799999999999999-----858997818 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC Q ss_conf 78899999849996685899999999899999999970789830045621058 Q gi|254780355|r 364 FYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTG 416 (429) Q Consensus 364 fysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~G 416 (429) ||||++|++||||++|||++|++||++||+|||+||+++ +|||||||+||| T Consensus 306 fysg~l~~~lGip~~~~t~lFa~~R~~GW~AH~~Eq~~~--~~iiRP~~~YvG 356 (356) T cd06110 306 FYSASVYYMLGIPVDLFTPIFAISRVSGWCAHILEQYFN--NRLIRPRAEYVG 356 (356) T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCC T ss_conf 899999999494945668999999999999999999728--987587770679 No 14 >cd06117 Ec2MCS_like_1 Subgroup of Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and OAA to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). This group contains proteins similar to the E. coli 2MCS, EcPrpC. EcPrpC is one of two CS isozymes in the gram-negative E. coli. EcPrpC is a dimeric (type I ) CS; it is induced during growth on propionate and prefers PrCoA as a substrate, but has a partial CS activity with AcCoA. This group also includes Salmonella typhimurium PrpC and Ralstonia eutropha (Re) 2-MCS1 which are also induced during growth on propionate, prefer PrCoA as substrate, but can also can use AcCoA. Re 2-MCS1 at a low rate can use butyryl-CoA and valeryl-CoA. A second Ralstonia eu Probab=100.00 E-value=0 Score=891.82 Aligned_cols=364 Identities=31% Similarity=0.520 Sum_probs=344.3 Q ss_pred CCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHH Q ss_conf 87862387875654334477789899319999750898999999981879998999999998864068998999999851 Q gi|254780355|r 45 AFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGF 124 (429) Q Consensus 45 G~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~ 124 (429) |+.++.+|||+||+|||++|+|+||||||+|||++++||||+||||+|+|||++|+++|+.+|++++.+|+.+.++++.+ T Consensus 2 GL~gv~~~~t~is~vdg~~g~L~YRGy~i~dLa~~~~fEEva~LLl~G~LP~~~el~~f~~~L~~~~~lp~~v~~~i~~l 81 (366) T cd06117 2 ALSGVAAGNTALCTVGRSGNDLHYRGYDILDLAEKCEFEEVAHLLVHGKLPTKSELAAYKTKLKSLRGLPANVKTALEQL 81 (366) T ss_pred CCCCEEECCCCCCEEECCCCEEEECCEEHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHC T ss_conf 98985651123322508899899998659998614989999999978989599999999999998348989999999836 Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCCCHHHHHHHHHHHCC Q ss_conf 2476525789999999875206855767878898889999999999999999972798-534888642468877876428 Q gi|254780355|r 125 PSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQ-PFVYPRSDLDYASNFLHMCFS 203 (429) Q Consensus 125 p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~-~~i~Pd~~lsyaeNfL~Ml~~ 203 (429) |+++|||++|+++|++|++++++..+. +.+...+.+.||+|++|+|++++|+++.+. ++..|.++++|++|||+|++| T Consensus 82 p~~~hPm~~L~t~vs~l~~~~~~~~~~-~~~~~~~~a~~lia~~~~i~a~~~~~~~~g~~~~~~~~~~~~~~nfl~ml~g 160 (366) T cd06117 82 PAAAHPMDVMRTGVSVLGCVLPEKEDH-PVSGARDIADRLMASLGSILLYWYHYSHNGKRIEVETDDDSIGGHFLHLLHG 160 (366) T ss_pred CCCCCCHHHHHHHHHHHHCCCCCCCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCC T ss_conf 777884889999999985428432349-8489999999999988999999999980898578898643199999998669 Q ss_pred CCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCH Q ss_conf 98410147969999987563501367876301555544205654246776755421002220352899999862155351 Q gi|254780355|r 204 VPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLER 283 (429) Q Consensus 204 ~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~~~~ 283 (429) . ++++..+|+||++||||||||+||||||+|||+||++|+||||+|||+||||||||||||.|++|+++|+++++ T Consensus 161 ~-----~p~~~~~~~ld~~LiL~ADHe~NaSTFaaRvvaSt~adlysai~aai~aL~GPlHGGAne~v~~ml~~i~~~~~ 235 (366) T cd06117 161 E-----KPSESWEKAMHISLILYAEHEFNASTFTARVIAGTGSDMYSAITGAIGALRGPKHGGANEVAFEIQQRYESADE 235 (366) T ss_pred C-----CCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCHHH T ss_conf 9-----99889999999989887205687036889988616888899999999875788766668999999998378776 Q ss_pred HHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 27999999821478614302774355554034689999999888608776517999999999996115314579877844 Q gi|254780355|r 284 IPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVD 363 (429) Q Consensus 284 v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~pNvD 363 (429) +++||++++++|+ +||||||||||++||||++||++++++.++.+ +.++++++.++|+++.+ +|++||||| T Consensus 236 ~~~~i~~~l~~~~--~i~GFGHrvYk~~DPRa~~lk~~~~~l~~~~~--~~~~~~i~~~ie~~~~~-----~k~l~pNvD 306 (366) T cd06117 236 AEADIRRRVENKE--VVIGFGHPVYTIADPRNQVIKEVAKQLSKEGG--DMKMFDIAERLETVMWE-----EKKMFPNLD 306 (366) T ss_pred HHHHHHHHHCCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHH-----HCCCCCCHH T ss_conf 7999999861799--88787877688999368999999999875107--77599999999999998-----469987869 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCH Q ss_conf 78899999849996685899999999899999999970789830045621058876870685 Q gi|254780355|r 364 FYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTGALKRDYVPL 425 (429) Q Consensus 364 fysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~G~~~r~y~pi 425 (429) ||||++|++||||+++||+||++||++||+|||+||+++ +|||||+++||||.+|+|||| T Consensus 307 fys~~l~~~lGip~d~ft~iFa~sR~~GW~AH~~Eq~~~--~~liRP~~~YvGp~~~~y~pi 366 (366) T cd06117 307 WFSAVSYHMMGVPTAMFTPLFVIARTTGWSAHIIEQRQD--GKIIRPSANYTGPEDLKFVPI 366 (366) T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCCCCCCCCC T ss_conf 999999999298856677999999999999999999756--996686550218999998889 No 15 >cd06103 ScCS-like Saccharomyces cerevisiae (Sc) citrate synthase (CS)-like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) with oxaloacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). Some CS proteins function as 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homo Probab=100.00 E-value=0 Score=890.97 Aligned_cols=375 Identities=29% Similarity=0.416 Sum_probs=338.8 Q ss_pred CCCEEECCCCCC---CEEEECC---CCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHH---------CCHHHHHHHHH Q ss_conf 751010011558---6189888---87862387875654334477789899319999750---------89899999998 Q gi|254780355|r 26 SSVLDISFLHKN---GIFTYDP---AFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEK---------SDFLEVCYLLL 90 (429) Q Consensus 26 ~~~~d~~~l~~~---G~~~~dp---G~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~---------~sFeEVayLLl 90 (429) +...++++.+.+ |.+|+|| |+.+|.+|.|.||||||++|+ +||||+|+||+++ ..||||+|||| T Consensus 14 ~~~~~l~~~~g~~~ig~~Tv~~~~gGmrg~~~~~~eis~iD~~~Gi-~yRGy~I~el~e~~~~~~~~~~~~fEevayLLl 92 (426) T cd06103 14 ARIKELRKKYGNTKLGQITVDQVIGGMRGMKGLVYETSVLDPDEGI-RFRGKTIPECQELLPKADGGGEPLPEGLFWLLL 92 (426) T ss_pred HHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCEECEEECCCCCE-EECCCCHHHHHHHCCCCCCCCCCCHHHHHHHHH T ss_conf 9999999985997420166453225314786100007478576533-579964999997563445788885899999998 Q ss_pred CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH------HCCCCC--CCCHHHHHHHHH Q ss_conf 187999899999999886406899899999985124765257899999998752------068557--678788988899 Q gi|254780355|r 91 HGELANVSQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSF------YYSPSG--VQDLEQCVNVSL 162 (429) Q Consensus 91 ~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~p~~ahPM~~L~~~vsaL~a~------~~~~~~--~~d~~~~~~~a~ 162 (429) ||+|||++|+++|+.+|++++.+|+++.+++++||+++|||++|+++|++|+++ |.+... ...++..++.++ T Consensus 93 ~GeLPt~~el~~f~~~l~~~~~lp~~v~~~l~~~P~~aHPM~~L~~~vsaL~~~s~f~~~y~~~~~~~~~~~e~~~~~~~ 172 (426) T cd06103 93 TGEVPTEEQVDELSKEWAKRAEVPSHVVKMIDNLPRNLHPMTQLSAAILALQSESKFAKAYAEGKINKTTYWEYVYEDAM 172 (426) T ss_pred CCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCHHHHCCCCCCCCCHHHHHHHHHHH T ss_conf 08798999999999999982689899999998589879909999999998435530243237434574036788899999 Q ss_pred HHHHHHHHHHHHHHHHH--CCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHEECCCCC-CCHHHHHH Q ss_conf 99999999999999972--7985348886424688778764289841014796999998756350136787-63015555 Q gi|254780355|r 163 RMIAKISTIAAMIYKYS--IGQPFVYPRSDLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQ-NASTSTVR 239 (429) Q Consensus 163 rLiA~~p~i~A~~yr~~--~G~~~i~Pd~~lsyaeNfL~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe~-NaSTft~R 239 (429) |||||+|+|+|++||++ .|.++++||++++|++|||+||+ .+++..+++||++||||||||+ ||||||+| T Consensus 173 ~LiAk~PtIaA~~Yr~~~~~g~~~~~~d~~l~~a~NFl~Ml~-------~~~~~~~~~ld~~liLHADHE~gNaSTft~r 245 (426) T cd06103 173 DLIAKLPVVAAKIYRRKYRKGGEIGAIDSKLDWSANFAHMLG-------YEDEEFTDLMRLYLTLHSDHEGGNVSAHTSH 245 (426) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCC-------CCCHHHHHHHHHHHHHHHHCCCCCCCHHHHH T ss_conf 999998999999999993789987889986559999999808-------9982899999999989643148872057776 Q ss_pred HHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHC----C---CCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCC Q ss_conf 442056542467767554210022203528999998621----5---535127999999821478614302774355554 Q gi|254780355|r 240 LAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEI----G---SLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHD 312 (429) Q Consensus 240 ~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I----~---~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~D 312 (429) +|+||+||||+||+|||+||||||||||||+|++||.+| | +.+++++|+++.+++++ +||||||||||++| T Consensus 246 vv~St~sD~ysaisAai~aL~GPLHGGANe~Vl~ml~~i~~~~g~~~s~e~v~~~v~~~l~~~~--~imGfGHrVYk~~D 323 (426) T cd06103 246 LVGSALSDPYLSFSAALNGLAGPLHGLANQEVLKWLLKMQKELGKDVSDEELEKYIWDTLNSGR--VVPGYGHAVLRKTD 323 (426) T ss_pred HHHCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCC--CCCCCCCCCCCCCC T ss_conf 6634688799999999887158876772899999999999872888888999999999871699--43267876577899 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH--HHHCCCCCCCCCCCHHHHHHHHHCCCC-HHHHHHHHHHHHH Q ss_conf 0346899999998886087765179999999999961--153145798778447889999984999-6685899999999 Q gi|254780355|r 313 PRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALE--DEYFIERKLYPNVDFYSGITLRALGFP-TNLFTVLFAVART 389 (429) Q Consensus 313 PRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~--d~~~~~r~l~pNvDfysg~i~~~lGip-~~~ft~iFa~~R~ 389 (429) |||+++|+++.++++ ++|+++++.++++++.+ +++|+.|+||||||||||++|++|||| ++|||||||+||+ T Consensus 324 PRa~ilk~~a~~~~~-----~d~~~~l~~~l~~i~~~~l~e~~~~k~lyPNVDfySG~iy~~lGipe~~~fT~lFaisR~ 398 (426) T cd06103 324 PRFTCQREFALKHLP-----DDPLFKLVAQCYKIIPGVLKEHGKVKNPYPNVDAHSGVLLQHYGMTEPQYYTVLFGVSRA 398 (426) T ss_pred CHHHHHHHHHHHHCC-----CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHH T ss_conf 469999999998648-----884899999999999999998563479988837578999998499930122699999999 Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCC Q ss_conf 899999999970789830045621058 Q gi|254780355|r 390 AGWVSQWTEMIVDPSRRIGRPRQLYTG 416 (429) Q Consensus 390 ~Gw~AH~~Eq~~~~~~ri~RP~~~Y~G 416 (429) +||+|||+||+... .+|.||||+|+. T Consensus 399 ~GW~Ah~iw~r~~~-~pI~RPrsi~~~ 424 (426) T cd06103 399 LGVLAQLVWSRALG-LPIERPKSMSTE 424 (426) T ss_pred HHHHHHHHHHHHCC-CCCCCCCCCCCC T ss_conf 99999999999669-998899866447 No 16 >TIGR01798 cit_synth_I citrate synthase I; InterPro: IPR010953 Citrate synthase 2.3.3.1 from EC is a member of a small family of enzymes that can directly form a carbon-carbon bond without the presence of metal ion cofactors. It catalyses the first reaction in the Krebs' cycle, namely the conversion of oxaloacetate and acetyl-coenzyme A into citrate and coenzyme A. This reaction is important for energy generation and for carbon assimilation. The reaction proceeds via a non-covalently bound citryl-coenzyme A intermediate in a 2-step process (aldol-Claisen condensation followed by the hydrolysis of citryl-CoA). Citrate synthase enzymes are found in two distinct structural types: type I enzymes (found in eukaryotes, Gram-positive bacteria and archaea) form homodimers and have shorter sequences than type II enzymes, which are found in Gram-negative bacteria and are hexameric in structure. In both types, the monomer is composed of two domains: a large alpha-helical domain consisting of two structural repeats, where the second repeat is interrupted by a small alpha-helical domain. The cleft between these domains forms the active site, where both citrate and acetyl-coenzyme A bind. The enzyme undergoes a conformational change upon binding of the oxaloacetate ligand, whereby the active site cleft closes over in order to form the acetyl-CoA binding site . The energy required for domain closure comes from the interaction of the enzyme with the substrate. Type II enzymes possess an extra N-terminal beta-sheet domain, and some type II enzymes are allosterically inhibited by NADH . This entry represents type II homohexameric citrate synthase enzymes, which are predominantly found in Gram-negative bacteria . These enzymes are allosterically inhibited by NADH in Escherichia coli, Acinetobacter calcoaceticus subsp. anitratus, Azotobacter vinelandii, Pseudomonas aeruginosa, etc . However, other type II enzymes in this entry do not display allosteric regulation. ; GO: 0004108 citrate (Si)-synthase activity, 0044262 cellular carbohydrate metabolic process, 0005737 cytoplasm. Probab=100.00 E-value=0 Score=897.77 Aligned_cols=411 Identities=65% Similarity=1.132 Sum_probs=404.8 Q ss_pred CEEEEEEEECCCCCCCCEEECCCC-CCCEEEECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHH Q ss_conf 989997523077787510100115-5861898888786238787565433447778989931999975089899999998 Q gi|254780355|r 12 HEEIDLPIKEGSLGSSVLDISFLH-KNGIFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLL 90 (429) Q Consensus 12 ~~~~~lpi~~~~~~~~~~d~~~l~-~~G~~~~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl 90 (429) ++++||||.++++|+++||+++|. +.|.++|||||.+|++|+|+||||||++|+|.||||+|++||++++|.||||||+ T Consensus 1 ~~~~~l~~~~~~~G~~v~d~~~l~~~~G~f~~d~Gf~~ta~C~s~it~idG~~G~l~~rGy~i~~la~~~~~le~Cylll 80 (413) T TIGR01798 1 NKEVELPIYSGTLGKDVIDIKKLYKNSGLFTFDPGFTSTASCESKITFIDGDKGILLYRGYPIDQLAEKSDYLEVCYLLL 80 (413) T ss_pred CCCCEEEECCCCCCCHHHHHHHHHHCCCCEEECCCCCEECCCCEEEEEEECCCCEEEECCCCHHHHHHCCCHHHHHHHHH T ss_conf 97510000134346204557778630674332355320022330357864675256544743788850133555556555 Q ss_pred CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 18799989999999988640689989999998512476525789999999875206855767878898889999999999 Q gi|254780355|r 91 HGELANVSQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKIST 170 (429) Q Consensus 91 ~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~ 170 (429) +|++|+++|.++|..++.+|+.+++++..++.+|.+++|||+++...|.+|++||++..++.++.++.-...|||+|+|+ T Consensus 81 ~~~~P~~~~~~~f~~~~~~ht~v~~q~~~~~~~f~~dahPma~~~~~~Gal~afy~~~~~i~~~~~r~~~~~rl~~k~Pt 160 (413) T TIGR01798 81 NGELPTKEQKDEFDDKVKEHTMVHEQLTRFFRGFRRDAHPMAVMVGVVGALSAFYHDALDINDPKHREIAAIRLIAKIPT 160 (413) T ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH T ss_conf 14788556789999999987899999999999731135347889999988998764432012134568999999874368 Q ss_pred HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCC-CCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHH Q ss_conf 999999972798534888642468877876428984101-4796999998756350136787630155554420565424 Q gi|254780355|r 171 IAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFSVPCAEY-QVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPF 249 (429) Q Consensus 171 i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~Ml~~~~~~~~-~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adly 249 (429) ++|..|++..|+|+++|+.+++|++|||+|+|..+.+++ +++|...++||+++|||||||+|+||.|+|+++|++++|+ T Consensus 161 ~~a~~y~y~~G~P~~yP~~~l~y~~nfl~m~f~~~~~~~~~~~P~l~~a~d~i~~lhadheqnast~tvr~aGs~~~nP~ 240 (413) T TIGR01798 161 LAAMSYKYSIGQPFVYPRNDLSYAENFLHMMFATPCEEYYKVNPVLARALDRIFILHADHEQNASTSTVRLAGSSGANPF 240 (413) T ss_pred HHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCEEEECCCCCCCHH T ss_conf 88876632168853152144568889999876033222224561689875455112023111233222453146676437 Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHC Q ss_conf 67767554210022203528999998621553512799999982147861430277435555403468999999988860 Q gi|254780355|r 250 ACIAAGVACLGGRAHGGANEEALNMLMEIGSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVT 329 (429) Q Consensus 250 sai~agi~aL~GPlHGGAne~v~~ml~~I~~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~ 329 (429) +||+|||++||||.||||||++++||++|++.+++.+|+.+++++++.+|||||||||||++||||++|++.|.+++++. T Consensus 241 a~i~aGi~~lWG~ahGGanea~l~ml~~i~~~~~~~~~~~~~k~~~~~~~lmGfGhrvy~n~dPra~~~~~~C~~vl~~~ 320 (413) T TIGR01798 241 ACIAAGIAALWGPAHGGANEAVLKMLEEIGSVEKIAEFIKKVKDKNDEVRLMGFGHRVYKNYDPRAKVMRETCHEVLKEL 320 (413) T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCEEEEEECHHHHCCCCHHHHHHHHHHHHHHHHH T ss_conf 88886577630466774568999999852027789999999740346635553021312047827899999999999972 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 87765179999999999961153145798778447889999984999668589999999989999999997078983004 Q gi|254780355|r 330 GRFNDPIAQVAIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGR 409 (429) Q Consensus 330 ~~~~~~~~~~a~~le~~a~~d~~~~~r~l~pNvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~R 409 (429) |..+++.+++|.+||+++++|+||++|+||||||||||+++.++|||.+|||+||+++|++||++||.|+..++..+|.| T Consensus 321 G~~~~~~~~~a~~le~ial~d~yf~~~klyPnvdfysG~~~~a~G~P~~mft~~fal~r~vGWi~~W~em~~~~~~~~~r 400 (413) T TIGR01798 321 GKEDDPLLKLALELEKIALEDDYFIERKLYPNVDFYSGIILKALGIPTEMFTVIFALARTVGWISHWSEMISDPEQKIGR 400 (413) T ss_pred CCCCCHHHHHHHHHHHHHCCCCHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHCCC T ss_conf 33320578899889876305620100024666114666898861574689999999985444688788863164001025 Q ss_pred CCCCCCCCCCCCC Q ss_conf 5621058876870 Q gi|254780355|r 410 PRQLYTGALKRDY 422 (429) Q Consensus 410 P~~~Y~G~~~r~y 422 (429) |||+|+|...|++ T Consensus 401 Prqly~G~~~r~~ 413 (413) T TIGR01798 401 PRQLYTGEEKRDV 413 (413) T ss_pred CHHHHCCCHHCCC T ss_conf 2455346221169 No 17 >cd06105 ScCit1-2_like Saccharomyces cerevisiae (Sc) citrate synthases Cit1-2_like. Citrate synthases (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) with oxaloacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). Some CS proteins function as 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-neg Probab=100.00 E-value=0 Score=887.74 Aligned_cols=368 Identities=31% Similarity=0.450 Sum_probs=336.6 Q ss_pred CCEEEECCCCCCEEEEEEEEE---EEECCCCEEEECCEEHHHHHHHC---------CHHHHHHHHHCCCCCCHHHHHHHH Q ss_conf 861898888786238787565---43344777898993199997508---------989999999818799989999999 Q gi|254780355|r 37 NGIFTYDPAFSSTASCKSKIT---FIDGNNGILLYRGYPIEQLSEKS---------DFLEVCYLLLHGELANVSQQKDFN 104 (429) Q Consensus 37 ~G~~~~dpG~~~ta~ceS~IT---~IDG~~G~L~YRGY~IedLa~~~---------sFeEVayLLl~GeLPt~~el~~F~ 104 (429) +|.+|+||||.||.+|+|.|| ||||++|| +||||+|+||+++. .+|||+||||||+|||++||++|+ T Consensus 28 ~g~iT~~~~~gg~rg~~~~i~e~S~lD~e~GI-ryRGy~I~el~e~l~~~~~~~~~~~EeV~yLLl~GeLPt~~ql~~f~ 106 (427) T cd06105 28 VGEVTVDMVYGGMRGIKGLVWETSVLDPEEGI-RFRGLSIPECQKLLPKAPGGEEPLPEGLFWLLLTGEVPTKEQVSALS 106 (427) T ss_pred EEEEECCHHHCCCCCCCCCEECCEEECCCCCE-EECCCCHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHH T ss_conf 45465163325666888312247137435484-57897589999875457788888789999999818798999999999 Q ss_pred HHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH------HCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9886406899899999985124765257899999998752------068557-678788988899999999999999999 Q gi|254780355|r 105 DKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSF------YYSPSG-VQDLEQCVNVSLRMIAKISTIAAMIYK 177 (429) Q Consensus 105 ~~l~~~~~lpe~v~~~i~~~p~~ahPM~~L~~~vsaL~a~------~~~~~~-~~d~~~~~~~a~rLiA~~p~i~A~~yr 177 (429) .+|++++.+|+++.++|++||+++|||++|+++|++|++. +.+... ...++..++.++||||++|+|+|++|| T Consensus 107 ~~l~~~~~lp~~v~~~i~~~P~~~HPM~~L~~~vsaL~~~s~f~~~y~~~~~~~~~~e~~~e~~~~LiAk~Pti~A~~yr 186 (427) T cd06105 107 KEWAARAALPSHVVTMLDNFPTNLHPMSQLSAAITALNSESKFAKAYAEGIHKSKYWEYVYEDSMDLIAKLPCVAAKIYR 186 (427) T ss_pred HHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99998458869999999858998886999999999844665213330012552014666789999999999999999999 Q ss_pred HH-CCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHEECCCC-CCCHHHHHHHHHCCCCCHHHHHHHH Q ss_conf 72-798534888642468877876428984101479699999875635013678-7630155554420565424677675 Q gi|254780355|r 178 YS-IGQPFVYPRSDLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHE-QNASTSTVRLAGSSGADPFACIAAG 255 (429) Q Consensus 178 ~~-~G~~~i~Pd~~lsyaeNfL~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe-~NaSTft~R~vaSt~adlysai~ag 255 (429) +. .|.++++||++++|++|||+||+. .+|..+++||.+|||||||| +||||||+|+|+||+||+|+||+|| T Consensus 187 ~~~~g~~~~~pd~~l~~a~NFl~Ml~~-------~~p~~~~~l~~~liLHADHEG~N~ST~t~rvvgStlsd~ysaiaag 259 (427) T cd06105 187 NLYRGGKIIAIDSNLDWSANFANMLGY-------TDPQFTELMRLYLTIHSDHEGGNVSAHTTHLVGSALSDPYLSFAAA 259 (427) T ss_pred HHHCCCCCCCCCCCCCHHHHHHHHCCC-------CCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHHHHH T ss_conf 985699978999887899999998279-------9940999999999997650378700678888862587488999998 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHC----C---CCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 54210022203528999998621----5---5351279999998214786143027743555540346899999998886 Q gi|254780355|r 256 VACLGGRAHGGANEEALNMLMEI----G---SLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEV 328 (429) Q Consensus 256 i~aL~GPlHGGAne~v~~ml~~I----~---~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~ 328 (429) |+||||||||||||+|++||++| | +++++++||++.+++++ |||||||||||++|||++++|+++.+++. T Consensus 260 i~aL~GPLHGGANq~Vl~ml~~i~~~~G~~~s~e~v~~~v~~~l~~~~--~imGfGHrVYk~~DPRa~ilk~~a~~~~~- 336 (427) T cd06105 260 MNGLAGPLHGLANQEVLVWLTKLQKEVGKDVSDEQLREYVWKTLNSGR--VVPGYGHAVLRKTDPRYTCQREFALKHLP- 336 (427) T ss_pred HHHCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHCC- T ss_conf 887068765675899999999999971888878999999998654698--42478866478999548999999998648- Q ss_pred CCCCCCHHHHHHHHHHHHH--HHHHHCCCCCCCCCCCHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 0877651799999999999--61153145798778447889999984999-66858999999998999999999707898 Q gi|254780355|r 329 TGRFNDPIAQVAIELERIA--LEDEYFIERKLYPNVDFYSGITLRALGFP-TNLFTVLFAVARTAGWVSQWTEMIVDPSR 405 (429) Q Consensus 329 ~~~~~~~~~~~a~~le~~a--~~d~~~~~r~l~pNvDfysg~i~~~lGip-~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ 405 (429) +||+++++.++|+++ ..+++|+.|++|||||||||++|+++||| .+||||||++||++||+|||+|++... . T Consensus 337 ----~d~~~~ia~~leeia~~~~~e~~~~k~~yPNVDfySG~iy~~lGipe~~~fT~lFaisR~~Gw~Ah~iw~r~~~-~ 411 (427) T cd06105 337 ----NDPLFKLVSQLYKIVPPVLTEQGKAKNPWPNVDAHSGVLLQYYGLTEMNYYTVLFGVSRALGVLSQLIWDRALG-L 411 (427) T ss_pred ----CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC-C T ss_conf ----88399999999999999999853026998773656899999849997433328999999999999999999648-9 Q ss_pred CCCCCCCCCCCCCCC Q ss_conf 300456210588768 Q gi|254780355|r 406 RIGRPRQLYTGALKR 420 (429) Q Consensus 406 ri~RP~~~Y~G~~~r 420 (429) +|.||||+|||+..| T Consensus 412 pI~RPrsiytg~l~~ 426 (427) T cd06105 412 PLERPKSVSTDGLEK 426 (427) T ss_pred CCCCCCCCCCCHHHC T ss_conf 988988665307534 No 18 >cd06108 Ec2MCS_like Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and OAA to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). This group contains proteins similar to the E. coli 2MCS, EcPrpC. EcPrpC is one of two CS isozymes in the gram-negative E. coli. EcPrpC is a dimeric (type I ) CS; it is induced during growth on propionate and prefers PrCoA as a substrate though it has partial CS activity with AcCoA. This group also includes Salmonella typhimurium PrpC and Ralstonia eutropha (Re) 2-MCS1 which are also induced during growth on propionate and prefer PrCoA as substrate, but can also use AcCoA. Re 2-MCS1 can use butyryl-CoA and valeryl-CoA at a lower rate. A second Ralstonia eutropha 2MC Probab=100.00 E-value=0 Score=880.32 Aligned_cols=361 Identities=31% Similarity=0.536 Sum_probs=342.5 Q ss_pred CCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHH Q ss_conf 87862387875654334477789899319999750898999999981879998999999998864068998999999851 Q gi|254780355|r 45 AFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGF 124 (429) Q Consensus 45 G~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~ 124 (429) ||.||++|||+||+|||++|.|+||||||+||+++++||||+||||+|+|||++|+++|+.+|..++.+|+.+.++++.+ T Consensus 2 Gl~gv~~~et~is~id~~~g~L~YRGy~i~dLa~~~sfEEva~LL~~G~lP~~~el~~f~~~l~~~~~lp~~v~~~~~~~ 81 (363) T cd06108 2 GLAGVVAGQTAISTVGKGGKGLTYRGYDIEDLAENATFEEVAYLLLYGKLPTRKQLDAYKTKLVALRRLPAALKTVLELI 81 (363) T ss_pred CCCCCEEEEEECEEEECCCCEEEECCEEHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHC T ss_conf 98983375767805738999789989119998605999999999976979699999999999998369979999999747 Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCHHHHHHHHHHHCC Q ss_conf 24765257899999998752068557678788988899999999999999999727-98534888642468877876428 Q gi|254780355|r 125 PSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSI-GQPFVYPRSDLDYASNFLHMCFS 203 (429) Q Consensus 125 p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~-G~~~i~Pd~~lsyaeNfL~Ml~~ 203 (429) |+++|||++|++++++|++++++. +++...+.++||+|++|+|++++||++. |.++..|+++++|++|||+|+++ T Consensus 82 p~~~~pm~~l~~~vs~l~~~~~~~----~~~~~~~~a~~lia~~p~i~a~~~~~~~~~~~~~~~~~~~~~a~nfl~ml~g 157 (363) T cd06108 82 PKDSHPMDVMRTGCSMLGCLEPEN----EFSQQYEIAIRLLAIFPSILLYWYHYSHSGKRIETETDEDSIAGHFLHLLHG 157 (363) T ss_pred CCCCCHHHHHHHHHHHHHCCCCCC----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHC T ss_conf 667777999999999972858778----8188999999999998799999999982899888998310389999998508 Q ss_pred CCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCH Q ss_conf 98410147969999987563501367876301555544205654246776755421002220352899999862155351 Q gi|254780355|r 204 VPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLER 283 (429) Q Consensus 204 ~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~~~~ 283 (429) . ++++..+|+||++||||||||+|+||||+||++||++|+|+||+|||+||||||||||||+|++||++|+++++ T Consensus 158 ~-----~p~~~~~~~ld~~LiL~ADHe~NaSTFtaRvvaST~ad~ysav~aai~aL~GPlHGGA~~~v~~~l~ei~~~~~ 232 (363) T cd06108 158 K-----KPGELEIKAMDVSLILYAEHEFNASTFAARVTASTLSDFYSAITGAIGTLRGPLHGGANEAAMELIERFKSPEE 232 (363) T ss_pred C-----CCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCHHH T ss_conf 9-----99789999999999887116787357888988547878899999999874687545757899999997288778 Q ss_pred HHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 27999999821478614302774355554034689999999888608776517999999999996115314579877844 Q gi|254780355|r 284 IPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVD 363 (429) Q Consensus 284 v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~pNvD 363 (429) +++||++++++|+ |||||||||||++||||++|+++++++.+..+ +.++++++.++|+++.+ +|++||||| T Consensus 233 ~~~~i~~~l~~~~--~i~GfGHrvYk~~DPRa~~l~~~~~~l~~~~~--~~~~~~~~~~ie~~~~~-----~k~l~pNVD 303 (363) T cd06108 233 AEQGLLEKLERKE--LIMGFGHRVYKEGDPRSDIIKKWSKKLSEEGG--DPLLYQISERIEEVMWE-----EKKLFPNLD 303 (363) T ss_pred HHHHHHHHHHCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHH-----CCCCCCCHH T ss_conf 9999999984678--77666864367899479999999999986149--84799999999999986-----389996829 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCH Q ss_conf 78899999849996685899999999899999999970789830045621058876870685 Q gi|254780355|r 364 FYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTGALKRDYVPL 425 (429) Q Consensus 364 fysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~G~~~r~y~pi 425 (429) ||||++|++||||.++||+||++||++||+|||+||+++ +||||||++||||.+|+|+|| T Consensus 304 fys~~l~~~lGip~~~~t~iFa~sR~~GW~AH~~Eq~~~--~~liRP~~~YvG~~~r~y~p~ 363 (363) T cd06108 304 FYSASAYHFCGIPTELFTPIFVMSRVTGWAAHIMEQRAN--NRLIRPSADYIGPEPRPFVPI 363 (363) T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCCCCCCCCC T ss_conf 899999999298866788999999999999999999747--985487650359999999989 No 19 >pfam00285 Citrate_synt Citrate synthase. Probab=100.00 E-value=0 Score=878.75 Aligned_cols=352 Identities=46% Similarity=0.767 Sum_probs=340.6 Q ss_pred CCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHH Q ss_conf 87862387875654334477789899319999750898999999981879998999999998864068998999999851 Q gi|254780355|r 45 AFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGF 124 (429) Q Consensus 45 G~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~ 124 (429) ||.||.+|+|+||+|||++|+|+||||+|+||+++++||||+||||+|+|||++|+++|+.++.+++.+|+.+.++++.| T Consensus 1 Gl~gv~~~~s~is~iDg~~G~L~YRGy~i~dLa~~~sfEeva~LL~~G~lP~~~el~~f~~~l~~~~~lp~~~~~~l~~~ 80 (352) T pfam00285 1 GLRGVVACETEISYIDGEKGILRYRGYDIEDLAEKSSFEEVAYLLLYGELPTAEELAEFSSELAARRALPEDVKEVIDAL 80 (352) T ss_pred CCCCCEEEEEECEEEECCCCEEEECCEEHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHC T ss_conf 99998155674826747888798889149998725999999999977989699999999999987147987899999867 Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCC Q ss_conf 24765257899999998752068557678788988899999999999999999727985348886424688778764289 Q gi|254780355|r 125 PSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFSV 204 (429) Q Consensus 125 p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~Ml~~~ 204 (429) |+++|||++|++++++|++++++..+ .+++...+.++||+|++|+|+|++||+++|++++.|+++++|++|||+|+++. T Consensus 81 p~~~hpm~~L~~~vs~l~~~~~~~~~-~~~~~~~~~a~~lia~~p~i~a~~~r~~~g~~~~~p~~~~~~a~nfl~ml~~~ 159 (352) T pfam00285 81 PKDAHPMAVLRAAVSALAAYDPMLYD-ESPEDVLEDAIRLIAKLPTIAAAIYRHRKGLPPIAPDPDLSYAENFLYMLFGE 159 (352) T ss_pred CCCCCHHHHHHHHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCC T ss_conf 88888399999999997601866557-99899999999999888999999999977999889995043999999983688 Q ss_pred CCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHH Q ss_conf 84101479699999875635013678763015555442056542467767554210022203528999998621553512 Q gi|254780355|r 205 PCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLERI 284 (429) Q Consensus 205 ~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~~~~v 284 (429) +++|..+++||++||||||||+||||||+|||+||++|+|+||+|||+||||||||||||+|++||++|++++++ T Consensus 160 -----~~~~~~~~~l~~~LiL~ADHe~NaSTfaaRvvaSt~ad~ys~v~agi~aL~GPlHGGAn~~v~~ml~~i~~~~~~ 234 (352) T pfam00285 160 -----EPDPEEARALDLALILHADHELNASTFTARVVASTLSDLYSAISAAIGALKGPLHGGANEAVLEMLEEIGSPENV 234 (352) T ss_pred -----CCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCHHH T ss_conf -----999899999999999983067880499999998258878999999998634865556689999999995581668 Q ss_pred HHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCH Q ss_conf 79999998214786143027743555540346899999998886087765179999999999961153145798778447 Q gi|254780355|r 285 PHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVDF 364 (429) Q Consensus 285 ~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~pNvDf 364 (429) ++||++++++++ |||||||||||++||||++|+++++++.++.+ ++++++++.++|+++.++ +.+||+|||||| T Consensus 235 ~~~i~~~l~~~~--~i~GFGHrvYk~~DPRa~~l~~~~~~l~~~~~--~~~~~~~a~~~e~~~~~~--~~~~~l~pNvDf 308 (352) T pfam00285 235 EEYIEKALDKGE--RLMGFGHRVYKTYDPRARILKKFARELAAELG--DDPLLEIAEKIEEVALED--LKEKKLYPNVDF 308 (352) T ss_pred HHHHHHHHHCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHH--HHHCCCCCCHHH T ss_conf 999999984689--77678976688899569999999999998559--855999999999999999--985699978288 Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 8899999849996685899999999899999999970789830045 Q gi|254780355|r 365 YSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRP 410 (429) Q Consensus 365 ysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP 410 (429) |+|++|++||||.++||+||++||++||+|||+||+++ +||||| T Consensus 309 ys~~l~~~lGip~~~~t~lFa~sR~~GW~AH~~Eq~~~--~~liRP 352 (352) T pfam00285 309 YSGVLYKALGIPTELFTPLFAVSRVVGWLAHIIEQREN--NKLIRP 352 (352) T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCC T ss_conf 99999998198935557999999999999999999857--988797 No 20 >cd06118 citrate_synt_like_1 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and Probab=100.00 E-value=0 Score=876.48 Aligned_cols=358 Identities=46% Similarity=0.743 Sum_probs=344.8 Q ss_pred CCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHH Q ss_conf 88786238787565433447778989931999975089899999998187999899999999886406899899999985 Q gi|254780355|r 44 PAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMG 123 (429) Q Consensus 44 pG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~ 123 (429) |||.||.+|+|+||+|||++|+|+||||+|+||+++++||||+||||+|+|||++|+++|+.++.+++.+|+.+.++++. T Consensus 1 pGl~gv~~~~t~is~id~~~G~L~YRG~~i~dLa~~~~fEeva~LL~~G~lP~~~el~~f~~~l~~~~~lp~~v~~~l~~ 80 (358) T cd06118 1 PGLEGVKAKETSISYIDGDEGILRYRGYDIEELAEKSSFEEVAYLLLYGKLPTKEELAEFKKKLASHRALPEHVVEILDL 80 (358) T ss_pred CCCCCCCEEEEECEEEECCCCEEEECCEEHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHH T ss_conf 99898733467570686898879888904999860599999999997898979999999999999844675999999996 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCC Q ss_conf 12476525789999999875206855767878898889999999999999999972798534888642468877876428 Q gi|254780355|r 124 FPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFS 203 (429) Q Consensus 124 ~p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~Ml~~ 203 (429) +|+++|||++|++++++|++++++..+ .+++...+.+++|+|++|+|+|++||+++|.+++.|+++++|++|||+||++ T Consensus 81 ~p~~~~pm~~l~~~v~~l~~~~~~~~~-~~~~~~~~~a~~lia~~p~i~a~~~~~~~g~~~~~p~~~~~~a~nfl~ml~g 159 (358) T cd06118 81 LPKNAHPMDVLRTAVSALGSFDPFARD-KSPEARYEKAIRLIAKLPTIAANIYRNREGLEIIAPDPDLSYAENFLYMLFG 159 (358) T ss_pred CCCCCCHHHHHHHHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCC T ss_conf 257865488999999998732865446-9989999999998625889999999995699887889415399999997538 Q ss_pred CCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCH Q ss_conf 98410147969999987563501367876301555544205654246776755421002220352899999862155351 Q gi|254780355|r 204 VPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLER 283 (429) Q Consensus 204 ~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~~~~ 283 (429) . ++++..+++||++||||||||+||||||+||++||++|+|+||+|||+|||||||||||++|++||++|+++++ T Consensus 160 ~-----~~~~~~~~~l~~~LiL~ADHe~NaSTfa~RvvaSt~ad~ysav~agl~aL~GPlHGgAn~~v~~~l~~i~~~~~ 234 (358) T cd06118 160 E-----EPDPEEAKAMDLALILHADHEGNASTFTARVVASTLSDMYSAIAAAIAALKGPLHGGANEAVLKMLLEIGTPEN 234 (358) T ss_pred C-----CCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCHHH T ss_conf 9-----99999999999989786257887059999999823678899999999981686541578999999999688565 Q ss_pred HHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 27999999821478614302774355554034689999999888608776517999999999996115314579877844 Q gi|254780355|r 284 IPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVD 363 (429) Q Consensus 284 v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~pNvD 363 (429) +++||++.+++++ |||||||||||++||||.+|+++++++.++.+ ++++++++.++|+++.+. +..||++|||| T Consensus 235 ~~~~i~~~l~~~~--~i~GFGHrvYk~~DPRa~~l~~~~~~l~~~~~--~~~~~~~~~~ie~~~~~~--~~~r~l~pNvD 308 (358) T cd06118 235 VEAYIWKKLANKR--RIMGFGHRVYKTYDPRAKILKELAEELAEEKG--DDKLFEIAEELEEIALEV--LGEKGIYPNVD 308 (358) T ss_pred HHHHHHHHHCCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHH--HCCCCCCCCHH T ss_conf 8999999740467--77787876578899558999999999875038--876999999999999986--47689987739 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC Q ss_conf 788999998499966858999999998999999999707898300456210 Q gi|254780355|r 364 FYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLY 414 (429) Q Consensus 364 fysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y 414 (429) ||+|++|+++|||+++||++|++||++||+|||+||++++ .||||||++| T Consensus 309 fy~~~l~~~lgip~~~~t~lFa~aR~~Gw~AH~~Eq~~~~-~kiiRP~~~Y 358 (358) T cd06118 309 FYSGVVYKALGFPTELFTPLFAVSRAVGWLAHIIEYRENN-QRLIRPRAEY 358 (358) T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCCCCC T ss_conf 8999999993979566789999999999999999999679-9844888879 No 21 >cd06109 BsCS-I_like Bacillus subtilis (Bs) citrate synthase CS-I_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains proteins similar to BsCS-I, one of two CS isozymes in the gram-positive B. subtilis. The majority of CS activity in B. subtilis is provided by the other isozyme, BsCS-II (not included in this group). BsCS- Probab=100.00 E-value=0 Score=869.15 Aligned_cols=347 Identities=31% Similarity=0.516 Sum_probs=329.8 Q ss_pred CCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHH Q ss_conf 88786238787565433447778989931999975089899999998187999899999999886406899899999985 Q gi|254780355|r 44 PAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMG 123 (429) Q Consensus 44 pG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~ 123 (429) |||.||++|||+||+|||++|+|+||||||+||+++++||||+||||+|+|||++|+++|+..+++++.+|+.+.++++. T Consensus 1 PGl~gv~v~~s~Is~idg~~G~L~YRG~~i~dLa~~~~fEeva~LL~~G~lPt~~el~~f~~~l~~~~~lp~~~~~~~~~ 80 (349) T cd06109 1 PGLEGVVAAETVLSDVDGEAGRLIIRGYSVEDLAGSASFEDVAALLWNGFFPDLPELEEFRAALAAARALPDVVAALLPA 80 (349) T ss_pred CCCCCCEEEEEECEEEECCCCEEEECCEEHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHH T ss_conf 99898505577682563899889898911999972499999999996898979899999999999723674999999974 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCC Q ss_conf 12476525789999999875206855767878898889999999999999999972798534888642468877876428 Q gi|254780355|r 124 FPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFS 203 (429) Q Consensus 124 ~p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~Ml~~ 203 (429) + +..|||+++++++++++. +...+.++||+|++|+|+|++||++.|++++.|+++++|++|||+||++ T Consensus 81 ~-~~~~pm~~l~~~~s~l~~-----------~~~~~~a~~liA~~p~i~a~~~r~~~g~~~~~p~~~~~~a~nfl~ml~g 148 (349) T cd06109 81 L-AGLDPMDALRALLALLPD-----------SPDLATALRLLAAAPVITAALLRLSRGKQPIAPDPSLSHAADYLRMLTG 148 (349) T ss_pred C-CCCCHHHHHHHHHHHCCC-----------CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHCC T ss_conf 6-456869999999885598-----------5428999999989999999999997699988998530489999987238 Q ss_pred CCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCH Q ss_conf 98410147969999987563501367876301555544205654246776755421002220352899999862155351 Q gi|254780355|r 204 VPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLER 283 (429) Q Consensus 204 ~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~~~~ 283 (429) . ++++..+++||++||||||||+||||||+||+|||++|+|+||+|||+||||||||||||+|++||++|+++++ T Consensus 149 ~-----~~~~~~~~~ld~~liL~ADHe~NaSTftarvvAST~ad~ys~v~aai~aL~GPlHGgA~~~v~~~l~ei~~~~~ 223 (349) T cd06109 149 E-----PPSEAHVRALDAYLVTVADHGMNASTFTARVIASTEADLTSAVLGAIGALKGPLHGGAPGPVLDMLDAIGTPEN 223 (349) T ss_pred C-----CCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCHHH T ss_conf 9-----99999999999999998215665057777887515753999999888634788657767999999999588346 Q ss_pred HHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH--HHHCCCCCCCCC Q ss_conf 279999998214786143027743555540346899999998886087765179999999999961--153145798778 Q gi|254780355|r 284 IPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALE--DEYFIERKLYPN 361 (429) Q Consensus 284 v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~--d~~~~~r~l~pN 361 (429) +++||++++++++ |||||||||||++|||+++|+++++++.. ++++++++.++|+++.+ +++|..|+|||| T Consensus 224 ~~~~i~~~l~~~~--~i~GfGHrvY~~~DPRa~~l~~~~~~l~~-----~~~~~~~~~~i~~~a~~~l~~~~~~~~l~pN 296 (349) T cd06109 224 AEAWLREALARGE--RLMGFGHRVYRVRDPRADVLKAAAERLGA-----PDERLEFAEAVEQAALALLREYKPGRPLETN 296 (349) T ss_pred HHHHHHHHHHCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHCC-----CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCC T ss_conf 9999999983578--75378988789999449999999998737-----8728999999999999999984577898748 Q ss_pred CCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC Q ss_conf 4478899999849996685899999999899999999970789830045621058 Q gi|254780355|r 362 VDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTG 416 (429) Q Consensus 362 vDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~G 416 (429) ||||+|++|++||||+++||+||++||++||+|||+||+.+ +||||||++||| T Consensus 297 VDf~s~~l~~~lG~p~~~~t~lFa~~R~~GW~AH~~Eq~~~--~~liRP~~~YvG 349 (349) T cd06109 297 VEFYTALLLEALGLPREAFTPTFAAGRTAGWTAHVLEQART--GRLIRPQSRYVG 349 (349) T ss_pred CHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCC T ss_conf 27889999998198855667999999999999999999867--997588780679 No 22 >PRK09569 type I citrate synthase; Reviewed Probab=100.00 E-value=0 Score=860.78 Aligned_cols=359 Identities=28% Similarity=0.418 Sum_probs=327.7 Q ss_pred CCCCEEEEEEEEEEEECCCCEEEECCEEHHHH---------HHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCH Q ss_conf 87862387875654334477789899319999---------750898999999981879998999999998864068998 Q gi|254780355|r 45 AFSSTASCKSKITFIDGNNGILLYRGYPIEQL---------SEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNE 115 (429) Q Consensus 45 G~~~ta~ceS~IT~IDG~~G~L~YRGY~IedL---------a~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe 115 (429) |+.++.+|-|.||||||++|| +||||+|+|| ++..+||||+||||||+|||++|+++|+.++++++.+|+ T Consensus 41 Gmrg~~~~~~~~S~lD~~~GI-ryRGy~I~el~~~lp~a~~~~~~~fEev~yLLl~GeLPt~~ql~~f~~~l~~~~~lp~ 119 (437) T PRK09569 41 GARDIRSLVTDISYLDPQEGI-RFRGKTIPETFEALPKAPGSEYPTVESFWYFLLTGEVPTPEQVSEVVAEFKTRQNVPQ 119 (437) T ss_pred CCCCCCEEEEECCEECCCCCE-EECCCCHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCH T ss_conf 425887102216147334383-3799428999976557778898879999999984889599999999999998467879 Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHH------HHHCCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCCCC Q ss_conf 999999851247652578999999987------5206855--767878898889999999999999999972-7985348 Q gi|254780355|r 116 NMSRFFMGFPSSAHPMAMLVSAVGALS------SFYYSPS--GVQDLEQCVNVSLRMIAKISTIAAMIYKYS-IGQPFVY 186 (429) Q Consensus 116 ~v~~~i~~~p~~ahPM~~L~~~vsaL~------a~~~~~~--~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~-~G~~~i~ 186 (429) ++.++|++||+++|||++|+++|++|+ .+|++.. ....++..++.++||||++|+|+|++||++ .|.++++ T Consensus 120 ~v~~~i~~~P~~~HPM~~L~~av~al~~~s~~~~~y~~~~~~~~~~~e~~~e~~~~LiAklPtIaA~~yr~~~~g~~~i~ 199 (437) T PRK09569 120 YVIDAIRALPRDSHPMVMLSAGILAMQRDSKFAKFYNSGKFNKMDAWEYMYEDASDLVARIPVIAAFIYNLKYKGDKQIA 199 (437) T ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 99999985899789689999999984245520001563334621014678999999999889999999999846998678 Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHEECCCCC-CCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHC Q ss_conf 886424688778764289841014796999998756350136787-6301555544205654246776755421002220 Q gi|254780355|r 187 PRSDLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQ-NASTSTVRLAGSSGADPFACIAAGVACLGGRAHG 265 (429) Q Consensus 187 Pd~~lsyaeNfL~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe~-NaSTft~R~vaSt~adlysai~agi~aL~GPlHG 265 (429) ||++++|++|||+||++.+ ...++++.+||||||||+ ||||||+|+|+||+||||+||+|||+|||||||| T Consensus 200 ~d~~l~~a~NFl~Ml~~~~--------~~~~~~rl~liLHADHE~gN~STft~rvv~StlsD~y~siaagi~aL~GPLHG 271 (437) T PRK09569 200 SDPQLDLGANFAHMIGQPK--------PYDDVARMYFILHSDHESGNVSAHTTHLVASALSDAYYAYSAGLNGLAGPLHG 271 (437) T ss_pred CCCCCCHHHHHHHHCCCCC--------CHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCC T ss_conf 9999899999999878998--------65999999998972136787117888877515876899999999983587656 Q ss_pred CCCHHHHHHHHHC----C----CCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHH Q ss_conf 3528999998621----5----5351279999998214786143027743555540346899999998886087765179 Q gi|254780355|r 266 GANEEALNMLMEI----G----SLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIA 337 (429) Q Consensus 266 GAne~v~~ml~~I----~----~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~ 337 (429) ||||+|++|+.++ + +.+++++||++.+++++ |||||||||||++|||++++|+++++++. +||++ T Consensus 272 gANq~vl~~l~~~~e~i~~~~~~~e~i~~~i~~~l~~g~--~i~GfGHrVyk~~DPRa~ilk~~a~~~~~-----~d~l~ 344 (437) T PRK09569 272 LANQEVLGWIQQFQEKLNGVEPTKEELTRALWDTLNAGQ--VIPGYGHAVLRKTDPRYTAQREFCLKYLK-----DDPLF 344 (437) T ss_pred CCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHHC-----CCCHH T ss_conf 705899999999999806863559999999997233488--22466864356789368999999999813-----38368 Q ss_pred HHHHHHHHHH--HHHHHCCCCCCCCCCCHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC Q ss_conf 9999999999--61153145798778447889999984999-66858999999998999999999707898300456210 Q gi|254780355|r 338 QVAIELERIA--LEDEYFIERKLYPNVDFYSGITLRALGFP-TNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLY 414 (429) Q Consensus 338 ~~a~~le~~a--~~d~~~~~r~l~pNvDfysg~i~~~lGip-~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y 414 (429) +++.++++++ ..+++|+.|++|||||||||++|+++||| .+||||||++||++||+|||+|++.. +++|.||||+| T Consensus 345 ~l~~~l~eia~~~l~e~~k~k~~yPNVDfySG~iy~~~Gip~~~~fTvlFaisR~~Gw~Ahiiw~r~~-~~pI~RPrsiy 423 (437) T PRK09569 345 KLVAMIFEVAPGVLTEHGKTKNPWPNVDAQSGVIQWYYGVREWDFYTVLFGVGRALGCMANITWDRGL-GYAIERPKSVT 423 (437) T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCHHCCHHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCC T ss_conf 99999999999999985422699888165799999982999041233899999999999999999856-99977988553 Q ss_pred CCCCCC Q ss_conf 588768 Q gi|254780355|r 415 TGALKR 420 (429) Q Consensus 415 ~G~~~r 420 (429) ||..+| T Consensus 424 t~~~~~ 429 (437) T PRK09569 424 TEMLEK 429 (437) T ss_pred CHHHHH T ss_conf 579998 No 23 >PRK12350 citrate synthase 2; Provisional Probab=100.00 E-value=0 Score=852.66 Aligned_cols=345 Identities=28% Similarity=0.445 Sum_probs=305.4 Q ss_pred ECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCC---CCHHHHHHHHHHHHHCCCCCHHHH Q ss_conf 88887862387875654334477789899319999750898999999981879---998999999998864068998999 Q gi|254780355|r 42 YDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGEL---ANVSQQKDFNDKISRHALLNENMS 118 (429) Q Consensus 42 ~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeL---Pt~~el~~F~~~l~~~~~lpe~v~ 118 (429) |||||.||++|||+||+|||++|+|+||||||+|||++++|||||||||+|+| |+.+|...+...+... +.++. T Consensus 1 ~~PGL~gv~~~es~Is~idg~~G~L~YRGy~i~dLa~~~tfEEva~LLl~G~l~~~~~~~e~~~~~~~~~~~---~~~~~ 77 (352) T PRK12350 1 FVPGLEGVVAFETEIAEPDGEGGALRYRGVDIEDLVGRVTFGDVWALLVDGFFGPGLPPAEPFPLPVHLGDA---RVDVQ 77 (352) T ss_pred CCCCCCCCEEEEEECEEEECCCCEEEECCCCHHHHHHCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH---HHHHH T ss_conf 989889961566056017589988998891299986059999999999788778876755666789879999---98677 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHH Q ss_conf 99985124765257899999998752068557678788988899999999999999999727985348886424688778 Q gi|254780355|r 119 RFFMGFPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFL 198 (429) Q Consensus 119 ~~i~~~p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL 198 (429) ..+..+ +||+.+++.+ +.. ..+.+.||++++|+|++++||++.|.+++.|++++||++||| T Consensus 78 ~~~~~l----~~~~~~~~~~-----------~~~----~~~~~~~l~~~~~~i~a~~~r~~~g~~~i~p~~~ls~a~nfl 138 (352) T PRK12350 78 AGLAML----APIWGYRALL-----------DID----DLTARLQLARASVVALSAVAQSARGYQPAVPQREIDHAATVL 138 (352) T ss_pred HHHHHC----CHHHHHCCCC-----------CCC----CHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHH T ss_conf 887742----7275423347-----------866----578999999899999999999976999888998867789999 Q ss_pred HHHCCCCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHC Q ss_conf 76428984101479699999875635013678763015555442056542467767554210022203528999998621 Q gi|254780355|r 199 HMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEI 278 (429) Q Consensus 199 ~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I 278 (429) +||+.. ...+|++..+|+||++||||||||+||||||+||++||++|+||||+|||+||||||||||||+|++||++| T Consensus 139 ~ml~~~--~~~~p~~~~~~ald~~LIL~ADHe~NaSTFaaRvvaST~adlysai~aaI~aL~GPLHGGAne~v~~ml~~i 216 (352) T PRK12350 139 RMFMTR--WGGEPDPRHVEALDAYWVTAAEHGMNASTFTARVIASTGADLAAALSAAIGALSGPLHGGAPGRVLPMLDAI 216 (352) T ss_pred HHHHHC--CCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH T ss_conf 997635--589989999999999999971046781347676554268788999999998626875567799999999984 Q ss_pred CCCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH--HHCCCC Q ss_conf 553512799999982147861430277435555403468999999988860877651799999999999611--531457 Q gi|254780355|r 279 GSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALED--EYFIER 356 (429) Q Consensus 279 ~~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d--~~~~~r 356 (429) ++++++++||++++++|+ |||||||||||++||||++||++++++.+ +.++++.++|+++.+. ++|.+| T Consensus 217 ~~~~~~~~~i~~~l~~~~--rimGFGHrVYk~~DPRa~~lk~~~~~l~~-------~~~~~a~~ie~~~~~~~~~~~~~r 287 (352) T PRK12350 217 ERTGDARGWVKGALDRGE--RLMGFGHRVYRAEDPRARVLRAAAKRLGA-------PRYEVAEAVEQAALAELRERRPDR 287 (352) T ss_pred CCCCCHHHHHHHHHHCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 670028999999985367--65567887788899358999999999744-------248999999999999999856888 Q ss_pred CCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC Q ss_conf 98778447889999984999668589999999989999999997078983004562105887687 Q gi|254780355|r 357 KLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTGALKRD 421 (429) Q Consensus 357 ~l~pNvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~G~~~r~ 421 (429) +||||||||||++|++||||++|||+||++||++||+|||+||+++ ||||||+++||||.+|. T Consensus 288 ~l~~NvDfys~~v~~~lGip~~~ft~iFa~~R~~GW~AH~~Eq~~~--~rliRP~a~YvGp~~R~ 350 (352) T PRK12350 288 PLETNVEFWTAVLLDFAGVPAHMFTAMFTCGRTAGWCAHILEQKRT--GRLVRPSARYVGPGPRA 350 (352) T ss_pred CCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCCCCC T ss_conf 9860703669999999395945567999999999999999998426--98648778046999999 No 24 >cd06106 ScCit3_like Saccharomyces cerevisiae (Sc) 2-methylcitrate synthase Cit3-like. 2-methylcitrate synthase (2MCS) catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxaloacetate (OAA) to form 2-methylcitrate and CoA. Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) with OAA to form citrate and CoA, the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the a Probab=100.00 E-value=0 Score=792.80 Aligned_cols=358 Identities=28% Similarity=0.407 Sum_probs=320.4 Q ss_pred CCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHH---------CCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCH Q ss_conf 87862387875654334477789899319999750---------898999999981879998999999998864068998 Q gi|254780355|r 45 AFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEK---------SDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNE 115 (429) Q Consensus 45 G~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~---------~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe 115 (429) |..++-++-+.+|++|+++|+ +||||+|.||++. ..||||+||||+|+|||++|+++|+++|++++.+|+ T Consensus 39 Gmrg~~~l~~e~S~ld~~~Gi-~yRG~~I~el~~~lp~~~~~~~~lpEev~yLLl~GeLPt~~ql~~f~~~l~~~~~lp~ 117 (428) T cd06106 39 GMRGLKSMLWEGSVLDAEEGI-RFHGKTIPECQKELPKAPIGGEMLPESMLWLLLTGKVPTFEQARGLSKELAERGKLPH 117 (428) T ss_pred CCCCCCEEEECCCEECCCCCE-EECCCCHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCH T ss_conf 426887325417334688784-7889518999987646778898778999999981889799999999999998347729 Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHH------HHCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHH--CCCCCCC Q ss_conf 9999998512476525789999999875------2068557-67878898889999999999999999972--7985348 Q gi|254780355|r 116 NMSRFFMGFPSSAHPMAMLVSAVGALSS------FYYSPSG-VQDLEQCVNVSLRMIAKISTIAAMIYKYS--IGQPFVY 186 (429) Q Consensus 116 ~v~~~i~~~p~~ahPM~~L~~~vsaL~a------~~~~~~~-~~d~~~~~~~a~rLiA~~p~i~A~~yr~~--~G~~~i~ 186 (429) ++.++|++||+++|||++|+++|++|++ .|.+... ...++..++.+++|||++|+|+|++||++ .|.++.. T Consensus 118 ~v~~~l~~lP~~~hPM~~L~~avsaL~~~s~f~~~y~~g~~~~~~we~~~ed~i~LiAklP~I~A~iyr~~~~~g~~~~~ 197 (428) T cd06106 118 YIEKLLDSLPKTLHPMTQLSIGVAALNHDSKFAAAYEKGIKKTEYWEPTLEDSLNLIARLPALAARIYRNVYGEGHGLGK 197 (428) T ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 99999985888668389999999984345420334202677310246789999999999999999999998379988888 Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHEECCCC-CCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHC Q ss_conf 88642468877876428984101479699999875635013678-76301555544205654246776755421002220 Q gi|254780355|r 187 PRSDLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHE-QNASTSTVRLAGSSGADPFACIAAGVACLGGRAHG 265 (429) Q Consensus 187 Pd~~lsyaeNfL~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe-~NaSTft~R~vaSt~adlysai~agi~aL~GPlHG 265 (429) ||++++|++|||+||+. ++++..+++||.+|||||||| +||||||+|+|+||+||||+|++|||+|||||||| T Consensus 198 ~d~~ld~a~Nfl~Mlg~------~~~~~~~~~l~l~liLHADHeG~N~Stft~rvv~StlsD~Yssiaaai~aL~GPLHG 271 (428) T cd06106 198 IDPEVDWSYNFTSMLGY------GDNLDFVDLLRLYIALHGDHEGGNVSAHTTHLVGSALSDPYLSYSAGLMGLAGPLHG 271 (428) T ss_pred CCCCCCHHHHHHHHHCC------CCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCC T ss_conf 99864699999998379------997899999999898862136887317777666347886899999988872687657 Q ss_pred CCCHHHHHHHH----HCCCC---CHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHH Q ss_conf 35289999986----21553---512799999982147861430277435555403468999999988860877651799 Q gi|254780355|r 266 GANEEALNMLM----EIGSL---ERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQ 338 (429) Q Consensus 266 GAne~v~~ml~----~I~~~---~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~ 338 (429) ||||+|++|+. +||++ +++++|+++.+++++ +||||||||||++|||+.++|++++++.+. .+||+++ T Consensus 272 gANq~Vl~~l~~m~~~ig~~~~~e~v~~yv~~~l~~g~--~i~GfGHrVyk~~DPRa~~lk~~a~~~~~~---~~d~~~~ 346 (428) T cd06106 272 LAAQEVLRWILEMQKNIGSKATDQDIRDYLWKTLKSGR--VVPGYGHAVLRKPDPRFTALMEFAQTRPEL---ENDPVVQ 346 (428) T ss_pred CHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCC--EEECCCEECCCCCCCHHHHHHHHHHHHHHC---CCCHHHH T ss_conf 75899999999999980898768999999998544698--632026010357994799999999998731---4882999 Q ss_pred HHHHHHHHH--HHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC Q ss_conf 999999999--61153145798778447889999984999668-589999999989999999997078983004562105 Q gi|254780355|r 339 VAIELERIA--LEDEYFIERKLYPNVDFYSGITLRALGFPTNL-FTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYT 415 (429) Q Consensus 339 ~a~~le~~a--~~d~~~~~r~l~pNvDfysg~i~~~lGip~~~-ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~ 415 (429) ++.++++++ ..+++++.||+|||||||||++|+++|||+++ |||||++||++||+|||+|++..+ .+|.||+|+=+ T Consensus 347 l~~~l~eia~~vl~e~~k~k~~~PNVDfySG~l~~~lGi~~~~fyT~lFavsR~~GwlAhiiw~r~~g-~pI~RPks~~~ 425 (428) T cd06106 347 LVQKLSEIAPGVLTEHGKTKNPFPNVDAASGVLFYHYGIREFLYYTVIFGVSRALGPLTQLVWDRILG-LPIERPKSLSL 425 (428) T ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCHHCCCHHHHHHHHHHHHHHHHHHHHCC-CCCCCCCCCCC T ss_conf 99999999999999856547998881657999999849990103418999999999999999999738-99889885672 No 25 >cd06101 citrate_synt Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the Probab=100.00 E-value=0 Score=698.32 Aligned_cols=263 Identities=51% Similarity=0.825 Sum_probs=251.1 Q ss_pred CCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHH Q ss_conf 88786238787565433447778989931999975089899999998187999899999999886406899899999985 Q gi|254780355|r 44 PAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMG 123 (429) Q Consensus 44 pG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~ 123 (429) |||.||++|||+||+|||++|+|+||||||+||+++++||||+||||+|+|| T Consensus 1 pGl~~~~~~~s~Is~idg~~g~L~yRGy~i~dLa~~~sfeeva~LL~~G~LP---------------------------- 52 (265) T cd06101 1 PGLRGVAALESEISVIDGDEGGLRYRGYPIEELAENSSFEEVAYLLLTGELP---------------------------- 52 (265) T ss_pred CCCCCCCEEEEECEEEECCCCEEEECCEEHHHHHHCCCHHHHHHHHHCCCCC---------------------------- T ss_conf 9988850566456277189998989995899987359999999999479899---------------------------- Q ss_pred HCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCC Q ss_conf 12476525789999999875206855767878898889999999999999999972798534888642468877876428 Q gi|254780355|r 124 FPSSAHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFS 203 (429) Q Consensus 124 ~p~~ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~Ml~~ 203 (429) +|++|||+||++ T Consensus 53 --------------------------------------------------------------------~~a~nfl~ml~g 64 (265) T cd06101 53 --------------------------------------------------------------------SYAENFLYMLGG 64 (265) T ss_pred --------------------------------------------------------------------CCHHHHHHHHCC T ss_conf --------------------------------------------------------------------828789998548 Q ss_pred CCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCC-- Q ss_conf 984101479699999875635013678763015555442056542467767554210022203528999998621553-- Q gi|254780355|r 204 VPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSL-- 281 (429) Q Consensus 204 ~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~~-- 281 (429) . +|+|..+|+||++||||||||+|+||||+|+++||++|+|+||+|||++||||+||||||+|++||++|+++ T Consensus 65 ~-----~p~~~~~~~ld~~Lil~aDH~~n~STfaaRvvaSt~adl~~avaagi~aL~GplHGGA~e~~~~~l~ei~~~~~ 139 (265) T cd06101 65 E-----EPDPEFAKAMDLALILHADHEGNASTFTARVVGSTLSDPYSAIAAAIAALKGPLHGGANEAVLKMLEEIGTPKN 139 (265) T ss_pred C-----CCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCC T ss_conf 9-----99989999999999998315776048887877525987899998778756787777838999999998578654 Q ss_pred CHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 51279999998214786143027743555540346899999998886087765179999999999961153145798778 Q gi|254780355|r 282 ERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPN 361 (429) Q Consensus 282 ~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~pN 361 (429) +++..|+.+.+++++ |||||||||||++||||++|+++++++.++.+ ++++++++.++|+++.++.++ |+|+|| T Consensus 140 ~~a~~~v~~~~~~~~--~i~GFGHrvYk~~DPRa~~L~~~~~~l~~~~~--~~~~~~~a~~~e~~~~~~~~~--k~l~pN 213 (265) T cd06101 140 EPAEAYIRKKLNSKR--VLMGFGHRVYKKYDPRATVLKKFAEKLLKEKG--LDPMFELAAELEKIAPEVLYE--KKLYPN 213 (265) T ss_pred CHHHHHHHHHHHCCC--CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHHHCC--CCCCCC T ss_conf 379999998773488--64467887789999618999999999987518--636999999999998862222--688765 Q ss_pred CCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC Q ss_conf 44788999998499966858999999998999999999707898300456210 Q gi|254780355|r 362 VDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLY 414 (429) Q Consensus 362 vDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y 414 (429) ||||+|++|++||||+++||+||++||++||+|||+||++++ +||+||||+| T Consensus 214 vD~~~a~l~~~lG~p~~~~t~iFaisR~~Gw~AH~~Eq~~~~-~ri~RP~~~Y 265 (265) T cd06101 214 VDFYSGVLYKAMGFPTELFTPLFAVSRAVGWLAHLIEQREDG-QRIIRPRAEY 265 (265) T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCCCCC T ss_conf 799999999990979436779999999999999999999779-9856886769 No 26 >cd06102 citrate_synt_like_2 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and Probab=100.00 E-value=0 Score=637.55 Aligned_cols=266 Identities=31% Similarity=0.434 Sum_probs=232.8 Q ss_pred CEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC Q ss_conf 62387875654334477789899319999750898999999981879998999999998864068998999999851247 Q gi|254780355|r 48 STASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGFPSS 127 (429) Q Consensus 48 ~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~p~~ 127 (429) ...+.+|+||.||+ |.|.||||+|+|||+++||||||||||+|++| T Consensus 17 G~pv~~S~Is~i~~--g~L~YRG~~~~~LAe~asfEevA~LLw~g~~p-------------------------------- 62 (282) T cd06102 17 GEPVLESAITLITE--GRLFYRGRDAVELAETATLEEVAALLWDGDEA-------------------------------- 62 (282) T ss_pred CCEEEECEEEEEEC--CEEEECCCCHHHHHHCCCHHHHHHHHHCCCCH-------------------------------- T ss_conf 78143010059879--98689991399998239899999999779876-------------------------------- Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCC Q ss_conf 65257899999998752068557678788988899999999999999999727985348886424688778764289841 Q gi|254780355|r 128 AHPMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFSVPCA 207 (429) Q Consensus 128 ahPM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~Ml~~~~~~ 207 (429) +++|++.++++....++. .+..+++.++. T Consensus 63 ---~~~lr~~~~~~~~~~~~~------------------------------------------~~~~~~l~~~~------ 91 (282) T cd06102 63 ---ARLLRLLAAALLGAAPSD------------------------------------------APVHRRLARAW------ 91 (282) T ss_pred ---HHHHHHHHHHHCCCCCCC------------------------------------------CHHHHHHHHHC------ T ss_conf ---799999999845789874------------------------------------------56999999981------ Q ss_pred CCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHH Q ss_conf 01479699999875635013678763015555442056542467767554210022203528999998621553512799 Q gi|254780355|r 208 EYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLERIPHY 287 (429) Q Consensus 208 ~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~~~~v~~~ 287 (429) +.+|..+++||++||||||||+||||||+||++||++|+||||+|||+||||||||||||+|++||++|++++++++| T Consensus 92 --~~~~~~~~~l~~aLiL~ADH~~naSTfaaRv~aST~ad~ysav~agi~aL~GPlHGGAne~v~~ml~ei~~~~~~~~~ 169 (282) T cd06102 92 --GLDPAAADLLRRALVLLADHELNASTFAARVAASTGASLYAAVLAGLAALSGPRHGGATARVEALLDEALRAGDAEAA 169 (282) T ss_pred --CCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCHHHH T ss_conf --799507899999897853568756999999999249978999999998766976678799999999985586448999 Q ss_pred HHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHH Q ss_conf 99998214786143027743555540346899999998886087765179999999999961153145798778447889 Q gi|254780355|r 288 IMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVDFYSG 367 (429) Q Consensus 288 i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~pNvDfysg 367 (429) |.+.+++++ +||||||||||++||||++|++.++++.. +.++.+.++++++.+ .++++||||||+| T Consensus 170 i~~~l~~~~--~i~GFGHrvYk~~DPRA~~L~~~~~~l~~-------~~~~~~~~~~~~~~~-----~~~~~pNVDfys~ 235 (282) T cd06102 170 VRERLRRGE--ALPGFGHPLYPDGDPRAAALLAALRPLGP-------AAPPAARALIEAARA-----LTGARPNIDFALA 235 (282) T ss_pred HHHHHHCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHCC-------CHHHHHHHHHHHHHH-----HHCCCCCHHHHHH T ss_conf 999997699--86688887689899439999999998641-------058999999999999-----7589998187899 Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC Q ss_conf 9999849996685899999999899999999970789830045621058 Q gi|254780355|r 368 ITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYTG 416 (429) Q Consensus 368 ~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~G 416 (429) ++|+.||||+++||+||++||++||+|||+||+++ +||||||++||| T Consensus 236 ~l~~~lGip~~~~t~iFai~R~~GW~AH~~Eq~~~--~~liRPr~~YvG 282 (282) T cd06102 236 ALTRALGLPAGAAFALFALGRSAGWIAHALEQRAQ--GKLIRPRARYVG 282 (282) T ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCC T ss_conf 99998499903112699999999999999999857--985588771469 No 27 >KOG2617 consensus Probab=100.00 E-value=0 Score=588.96 Aligned_cols=394 Identities=33% Similarity=0.461 Sum_probs=352.4 Q ss_pred CEEEEEEE-ECCCCCCCCEEECCCC----CCCEEEECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHH Q ss_conf 98999752-3077787510100115----586189888878623878756543344777898993199997508989999 Q gi|254780355|r 12 HEEIDLPI-KEGSLGSSVLDISFLH----KNGIFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVC 86 (429) Q Consensus 12 ~~~~~lpi-~~~~~~~~~~d~~~l~----~~G~~~~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVa 86 (429) +++|.-++ -+|++ +.|++.+.. ..|...+||++.++. +.|.|+|+..++++||+|++++.++. .+|+++ T Consensus 39 ~~~~k~~~~ehG~v--g~v~i~~i~gGmrg~~~~~~e~s~Ld~~---~gI~frg~~i~e~q~~lp~~~~~~e~-lpe~~~ 112 (458) T KOG2617 39 GDEYKKFVSEHGTV--GNVTLKKIYGGMRGKGLLLWETSVLDPE---EGIRFRGGDIPECQKRLPPAEEGAEP-LPEELF 112 (458) T ss_pred HHHHHHHHHHCCCC--CCEEHHHHHCCCCCCCCEEECCCCCCHH---HCEEECCCCHHHHHHHCCCCCCCCCC-CHHHHH T ss_conf 77762228644810--2256888644657777402037643610---07013489779998537887567767-789999 Q ss_pred HHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCC------C-CCCHHHHHH Q ss_conf 999818799989999999988640689989999998512476525789999999875206855------7-678788988 Q gi|254780355|r 87 YLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYYSPS------G-VQDLEQCVN 159 (429) Q Consensus 87 yLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~p~~ahPM~~L~~~vsaL~a~~~~~~------~-~~d~~~~~~ 159 (429) |||++|++||++|+++|+.++++++.+|+.+.++|+++|.+.|||.++.+++++|..+.+... + ...++..++ T Consensus 113 wLL~tG~vPt~~Q~~~~~~~~a~rsavP~~v~~~idsmP~d~HPM~q~~~a~~al~~~s~fa~ay~~G~~k~~yw~~~~e 192 (458) T KOG2617 113 WLLLTGNVPTQSQVAALSFELAQRSAVPQGVLDMIDSMPKDLHPMAQLAAAVLALKIFSPFAKAYLRGIGKYKYWQYTYE 192 (458) T ss_pred HHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHCCCHHHCCCCCHH T ss_conf 99995799978999999999987355638899999718831016999999998626356101466604331101322188 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHEECCCCC-CCHHHHH Q ss_conf 899999999999999999727985348886424688778764289841014796999998756350136787-6301555 Q gi|254780355|r 160 VSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQ-NASTSTV 238 (429) Q Consensus 160 ~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe~-NaSTft~ 238 (429) ++++|||+.|+|+|.+|+..-+.+.+-||++++|++||++|+... +|..++.|+.++++|+|||+ |.|..|. T Consensus 193 d~l~Liak~p~iAa~iY~~~~~dg~~~~~~~~dys~Nf~~mlg~~-------~~~f~~lmrly~~iHadHE~gnVsAh~~ 265 (458) T KOG2617 193 DCLVLIAKLPTIAAAIYRNIYADGIPKPDPNLDYSANFARMLGSR-------QPDFAQLMRLYVGIHADHEGGNVSAHTG 265 (458) T ss_pred HHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHCCC-------CHHHHHHHHHEEEEECCCCCCCHHHHHC T ss_conf 999999743088899999985379888876544567689997358-------7679998777046421034672877741 Q ss_pred HHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHH----HCC---CCCHHHHHHHHHHHCCCCCEEECCCCCCCCCC Q ss_conf 54420565424677675542100222035289999986----215---53512799999982147861430277435555 Q gi|254780355|r 239 RLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLM----EIG---SLERIPHYIMRAKDKNDPFRIMGFGHRVYRNH 311 (429) Q Consensus 239 R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~----~I~---~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~ 311 (429) ++++|.+ |||-+++||+++|.|||||+|||+|++||. ||+ +.+++++||+..+++++ +++||||+|||++ T Consensus 266 HLvGSal-dpYls~aa~~~GLaGPLHGlAnqEvl~~L~~~~~Eig~~~s~e~ikeyiw~~lnsgr--vvpGyGHaVlrkt 342 (458) T KOG2617 266 HLVGSAL-DPYLSFAAGMNGLAGPLHGLANQEVLRFLGKLIEEIGKDLSKENIKEYIWKTLNSGR--VVPGYGHAVLRKT 342 (458) T ss_pred CCCCCCC-CHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCC--CCCCCCCCCCCCC T ss_conf 4434566-526777776325403454676699999999868876344416565465476444575--3347675102068 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH--HHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHH-HHHHHHHH Q ss_conf 403468999999988860877651799999999999--611531457987784478899999849996685-89999999 Q gi|254780355|r 312 DPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIA--LEDEYFIERKLYPNVDFYSGITLRALGFPTNLF-TVLFAVAR 388 (429) Q Consensus 312 DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a--~~d~~~~~r~l~pNvDfysg~i~~~lGip~~~f-t~iFa~~R 388 (429) |||..++++++.+.+ .+||++++..++++++ ..+++++.||+|||||+|||++++++|++...| |++|+++| T Consensus 343 DPR~~~qrefA~kh~-----~~dpl~~lv~~l~kiap~vl~e~gk~kNp~PNVD~hSGvll~~yGl~e~~fyTVLFgVsR 417 (458) T KOG2617 343 DPRYKVQREFALKHL-----PDDPLFLLVSALYKIAPGVLTEHGKVKNPYPNVDAHSGVLLQYYGLPELFFYTVLFGVSR 417 (458) T ss_pred CCHHHHHHHHHHHCC-----CCCCCHHHHHHHHHHCHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 804899999998638-----988404423778764658888874505899765667778998707718988999987766 Q ss_pred HHHHHHH--HHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHCC Q ss_conf 9899999--9999707898300456210588768706855429 Q gi|254780355|r 389 TAGWVSQ--WTEMIVDPSRRIGRPRQLYTGALKRDYVPLEERE 429 (429) Q Consensus 389 ~~Gw~AH--~~Eq~~~~~~ri~RP~~~Y~G~~~r~y~pi~~R~ 429 (429) +.|.++| |.+.+..| |.||.+.|++...+.+.++.+|+ T Consensus 418 a~Gvlsqliw~ralg~p---ieRPks~~t~~~~~~~~~~~~~~ 457 (458) T KOG2617 418 ALGVLSQLIWDRALGLP---IERPKSVSTDWLHRFTNMVRERD 457 (458) T ss_pred HHHHHHHHHHHHHHCCC---CCCCCCCCHHHHHHHHHHHHCCC T ss_conf 67889999999870786---44730033589999998752036 No 28 >TIGR01793 cit_synth_euk citrate (Si)-synthase, eukaryotic; InterPro: IPR010109 Citrate synthase 2.3.3.1 from EC is a member of a small family of enzymes that can directly form a carbon-carbon bond without the presence of metal ion cofactors. It catalyses the first reaction in the Krebs' cycle, namely the conversion of oxaloacetate and acetyl-coenzyme A into citrate and coenzyme A. This reaction is important for energy generation and for carbon assimilation. The reaction proceeds via a non-covalently bound citryl-coenzyme A intermediate in a 2-step process (aldol-Claisen condensation followed by the hydrolysis of citryl-CoA). Citrate synthase enzymes are found in two distinct structural types: type I enzymes (found in eukaryotes, Gram-positive bacteria and archaea) form homodimers and have shorter sequences than type II enzymes, which are found in Gram-negative bacteria and are hexameric in structure. In both types, the monomer is composed of two domains: a large alpha-helical domain consisting of two structural repeats, where the second repeat is interrupted by a small alpha-helical domain. The cleft between these domains forms the active site, where both citrate and acetyl-coenzyme A bind. The enzyme undergoes a conformational change upon binding of the oxaloacetate ligand, whereby the active site cleft closes over in order to form the acetyl-CoA binding site . The energy required for domain closure comes from the interaction of the enzyme with the substrate. Type II enzymes possess an extra N-terminal beta-sheet domain, and some type II enzymes are allosterically inhibited by NADH . This entry includes both mitochondrial and peroxisomal forms of citrate synthase. Peroxisomal forms of the enzyme, recognized by the C-terminal targeting motif SKL, act in the glyoxylate cycle. Eukaryotic homologs include a Tetrahymena thermophila citrate synthase that doubles as a filament protein, a putative citrate synthase from Plasmodium falciparum (no TCA cycle), and a methylcitrate synthase from Aspergillus nidulans (Emericella nidulans).; GO: 0004108 citrate (Si)-synthase activity, 0044262 cellular carbohydrate metabolic process. Probab=100.00 E-value=0 Score=522.71 Aligned_cols=348 Identities=31% Similarity=0.452 Sum_probs=309.8 Q ss_pred EEEEEEEEEECCCCEEEECCEEHHHHH------HH---CCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHH Q ss_conf 878756543344777898993199997------50---898999999981879998999999998864068998999999 Q gi|254780355|r 51 SCKSKITFIDGNNGILLYRGYPIEQLS------EK---SDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFF 121 (429) Q Consensus 51 ~ceS~IT~IDG~~G~L~YRGY~IedLa------~~---~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i 121 (429) +.|| |-+|.|+|| |+|||+|-|=- +. ==-|-..|||++|+.||++|.++++++++.++.||+.|.++| T Consensus 50 vwEt--SvLDpEEGI-RFRGlsIPECQKLLPkAkgGeEPLPEgl~WLLlTG~VPse~Qv~alsaEw~aRadlP~hv~~~i 126 (430) T TIGR01793 50 VWET--SVLDPEEGI-RFRGLSIPECQKLLPKAKGGEEPLPEGLLWLLLTGEVPSEEQVDALSAEWRARADLPKHVVKLI 126 (430) T ss_pred EEEC--CCCCCCCCE-ECCCCCCCHHHHCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 2204--302665460-1278864114410777456579746899999845899808899999999985500278999998 Q ss_pred HHHCCCCCHHHHHHHHHHHHHH---H----HCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH--HHCCCCCCCCCCCHH Q ss_conf 8512476525789999999875---2----068557678788988899999999999999999--727985348886424 Q gi|254780355|r 122 MGFPSSAHPMAMLVSAVGALSS---F----YYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYK--YSIGQPFVYPRSDLD 192 (429) Q Consensus 122 ~~~p~~ahPM~~L~~~vsaL~a---~----~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr--~~~G~~~i~Pd~~ls 192 (429) +.||.+.|||+++.++|.||.. | ...-....-++..+|+++.||||+|+|+|.+|| +++|+..+.-|++++ T Consensus 127 D~~P~tlHPMaQF~~av~AL~~eS~FakAyakGi~K~~YWeytyEDS~dLiAkLPtvAA~IYRn~ykdG~~v~~id~~kD 206 (430) T TIGR01793 127 DALPSTLHPMAQFALAVAALEVESEFAKAYAKGIAKKKYWEYTYEDSMDLIAKLPTVAAKIYRNLYKDGKAVASIDDKKD 206 (430) T ss_pred HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCC T ss_conf 50574357278999999988741045336772554112457304447999984369999999866128805773167654 Q ss_pred HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHEECCCC-CCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHH Q ss_conf 68877876428984101479699999875635013678-76301555544205654246776755421002220352899 Q gi|254780355|r 193 YASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHE-QNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEA 271 (429) Q Consensus 193 yaeNfL~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe-~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v 271 (429) |.+||-+||+- .-+|..++.|+.+|++|.||| +|.|++|.++|||++||||-+.+||++.|.|||||-|||+| T Consensus 207 ysaNfa~~LGy------aD~p~f~ELMRLYltIHsDHEGGNVSAHT~HLVgSALSdPyLSfaAalnGLAGPLHGLANQEV 280 (430) T TIGR01793 207 YSANFASMLGY------ADDPSFAELMRLYLTIHSDHEGGNVSAHTSHLVGSALSDPYLSFAAALNGLAGPLHGLANQEV 280 (430) T ss_pred CHHHHHHHCCC------CCCHHHHHHHHHHHEEEECCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHHHH T ss_conf 01216751575------678758988662300120148886102457888877316568999986311220113688999 Q ss_pred HHHHHHC----C----CCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH Q ss_conf 9998621----5----5351279999998214786143027743555540346899999998886087765179999999 Q gi|254780355|r 272 LNMLMEI----G----SLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIEL 343 (429) Q Consensus 272 ~~ml~~I----~----~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~l 343 (429) +-+|.+| | +.+++.+||++.|+.++ .+|||||.|.|++|||=.+=|++|-+.+ +|||+|++.-.+ T Consensus 281 L~wl~~~v~e~G~~n~t~eqlKdy~WktLnsG~--VVPGYGHaVLRkTDPRY~cQREFALk~L-----PdDplFkLVS~l 353 (430) T TIGR01793 281 LVWLKEVVKEVGEDNLTEEQLKDYVWKTLNSGK--VVPGYGHAVLRKTDPRYICQREFALKHL-----PDDPLFKLVSQL 353 (430) T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCC--EECCCCCCCCCCCCCCCCCHHHHHHHCC-----CCCHHHHHHHHH T ss_conf 999998877517887747678999997605895--4257665202688988431288883317-----896156886410 Q ss_pred HHHH--HHHHHCCCCCCCCCCCHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC Q ss_conf 9999--6115314579877844788999998499-9668589999999989999999997078983004562105 Q gi|254780355|r 344 ERIA--LEDEYFIERKLYPNVDFYSGITLRALGF-PTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLYT 415 (429) Q Consensus 344 e~~a--~~d~~~~~r~l~pNvDfysg~i~~~lGi-p~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y~ 415 (429) -+|+ +-.|..+.||+|||||-.||+++...|+ ...+||++|.+||..|.+.|-+-.|.-+ -.|-||.+.=+ T Consensus 354 yki~PgiLtE~GK~KNPwPNVDaHSGVLLqyyGlTE~~yYTVLFGVSRAlG~lsQLiwdRa~G-lPlERPKS~st 427 (430) T TIGR01793 354 YKIVPGILTELGKVKNPWPNVDAHSGVLLQYYGLTEARYYTVLFGVSRALGVLSQLIWDRALG-LPLERPKSFST 427 (430) T ss_pred HCCCCCCEECCCCCCCCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCCCCCC T ss_conf 101685000478757867787520116764024000021034334668874436899986568-98568866534 No 29 >cd06099 CS_ACL-C_CCL Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) from citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. Some CS proteins function as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. CCL cleaves citryl-CoA (CiCoA) to AcCoA and OAA. ACLs catalyze an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA; they do this in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. The overall CS reaction is thought to proceed through three partial reactions and i Probab=100.00 E-value=0 Score=509.88 Aligned_cols=211 Identities=52% Similarity=0.841 Sum_probs=198.5 Q ss_pred HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHH Q ss_conf 46887787642898410147969999987563501367876301555544205654246776755421002220352899 Q gi|254780355|r 192 DYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEA 271 (429) Q Consensus 192 syaeNfL~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v 271 (429) ||++|||+|++|+ +|+|..+++||++||||||||+|+||||+|+++||++|+|+||+|||++|+||+||||||+| T Consensus 1 S~~~nfl~ml~g~-----~P~~~~~~~ld~~Lvl~aDHg~n~St~aaR~~aSt~ad~~~av~agl~al~GplhGGA~e~~ 75 (213) T cd06099 1 SYAENFLYMLGGE-----EPDPEFARAMDLALILHADHEGNASTFTARVVGSTGSDPYSAIAAAIGALKGPLHGGANEAV 75 (213) T ss_pred CHHHHHHHHHCCC-----CCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCHHHH T ss_conf 9899999996699-----99989999999999998145886059999998535897889999999981586346819999 Q ss_pred HHHHHHCCCC--CHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH Q ss_conf 9998621553--51279999998214786143027743555540346899999998886087765179999999999961 Q gi|254780355|r 272 LNMLMEIGSL--ERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALE 349 (429) Q Consensus 272 ~~ml~~I~~~--~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~ 349 (429) ++||++|+++ +++++||.+.+++++ |||||||||||+.|||+++|+++++++.+..+ ++++++++.++|+++.+ T Consensus 76 ~~~l~ei~~~~~~~~~~~v~~~~~~~~--~ipGFGH~vy~~~DPRa~~L~~~a~~l~~~~~--~~~~~~~~~~~e~~~~~ 151 (213) T cd06099 76 LKMLEEIGTPKNEPAEAYIRKKLESKR--VIMGFGHRVYKKYDPRATVLKKFAEELLKEDG--DDPMFELAAELEKIAEE 151 (213) T ss_pred HHHHHHHCCCCCCHHHHHHHHHHHCCC--CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHH T ss_conf 999998565566539999999884489--65578987789999609999999999987438--87799999999999998 Q ss_pred HHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC Q ss_conf 15314579877844788999998499966858999999998999999999707898300456210 Q gi|254780355|r 350 DEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPSRRIGRPRQLY 414 (429) Q Consensus 350 d~~~~~r~l~pNvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~~ri~RP~~~Y 414 (429) +.+ +|+|+||||||+|++|+.||||+++||++|++||++||+|||+||++++ .||+|||++| T Consensus 152 ~~~--~k~l~~Nvd~~~a~l~~~lG~p~~~~~~lf~i~R~~Gw~AH~~Eq~~~~-~~i~RP~~~Y 213 (213) T cd06099 152 VLY--EKKLYPNVDFYSGVLYKAMGFPTELFTPLFAVARAVGWLAHLIEQLEDN-FKIIRPRSEY 213 (213) T ss_pred HHC--CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCCCCC T ss_conf 644--4799867599999999991988655789999999999999999999779-9876886769 No 30 >PRK06224 citrate synthase; Provisional Probab=100.00 E-value=0 Score=438.61 Aligned_cols=243 Identities=28% Similarity=0.389 Sum_probs=211.3 Q ss_pred EEEEEEEEEECCCCEEEECCEE-HHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCC Q ss_conf 8787565433447778989931-999975089899999998187999899999999886406899899999985124765 Q gi|254780355|r 51 SCKSKITFIDGNNGILLYRGYP-IEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGFPSSAH 129 (429) Q Consensus 51 ~ceS~IT~IDG~~G~L~YRGY~-IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~p~~ah 129 (429) .-+|+|+.+++++ ++||||| ++||..+.+|-|+.||||.|++|+++| T Consensus 8 ~~~T~i~~~~~~~--i~~rG~dl~~dLig~~sf~~~~~ll~~G~~P~~~q------------------------------ 55 (265) T PRK06224 8 WWRTSIGDTTPEE--IYVRGYDLLEDLIGKISFVDMIFLLLRGRLPTPGE------------------------------ 55 (265) T ss_pred HHHCCCCCCCCCE--EEECCCCHHHHHHCCCCHHHHHHHHHHCCCCCHHH------------------------------ T ss_conf 7511000467996--78858640999854789999999998288999999------------------------------ Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCC Q ss_conf 25789999999875206855767878898889999999999999999972798534888642468877876428984101 Q gi|254780355|r 130 PMAMLVSAVGALSSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVYPRSDLDYASNFLHMCFSVPCAEY 209 (429) Q Consensus 130 PM~~L~~~vsaL~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~Pd~~lsyaeNfL~Ml~~~~~~~~ 209 (429) T Consensus 56 -------------------------------------------------------------------------------- 55 (265) T PRK06224 56 -------------------------------------------------------------------------------- 55 (265) T ss_pred -------------------------------------------------------------------------------- T ss_conf -------------------------------------------------------------------------------- Q ss_pred CCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCC------- Q ss_conf 479699999875635013678763015555442056-542467767554210022203528999998621553------- Q gi|254780355|r 210 QVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSG-ADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSL------- 281 (429) Q Consensus 210 ~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~-adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~~------- 281 (429) +|+||++||++||||+|+|||++|+++|++ +++++||+||++++ ||+||||||.|++||+++... T Consensus 56 ------arllda~Lv~~adHG~~pSt~aaR~~as~g~~~~~~avaAgl~~~-G~~hgGA~e~~~~~l~~~~~~~~~~~~~ 128 (265) T PRK06224 56 ------ARMLDAVLVSLVDHGLTPSAAAARMTASGGPESLQAAVAAGLLGA-GSVFGGAGENAAELLQEIAARADDGDDL 128 (265) T ss_pred ------HHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHCC-CCCCCCHHHHHHHHHHHHHHHCCCCCCH T ss_conf ------999999999955779982799999999628504789999999634-6301373589999999997530256559 Q ss_pred -CHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf -5127999999821478614302774355554034689999999888608776517999999999996115314579877 Q gi|254780355|r 282 -ERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYP 360 (429) Q Consensus 282 -~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~p 360 (429) +.+.++|.+.+.+++ |||||||||||+.|||++.|+++++++. ...++++++.++|+.+.+. .+|+|++ T Consensus 129 ~~~a~~~v~~~~~~~~--~ipGfGHrvyk~~DPRa~~L~~la~e~~-----~~g~~~~~a~~ve~~~~~~---~gk~l~~ 198 (265) T PRK06224 129 DAAARALVAEYRAAGR--RVPGFGHPLHKPGDPRAPRLLALARELG-----VAGRHCALAEALEAALDAA---KGKPLPL 198 (265) T ss_pred HHHHHHHHHHHHHCCC--CCCCCCCCCCCCCCCCHHHHHHHHHHHC-----CCCHHHHHHHHHHHHHHHH---CCCCCCC T ss_conf 9999999999997499--8688898888999951799999999837-----6777999999999999984---0899860 Q ss_pred CCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCCCC---CCCCCCCCC Q ss_conf 84478899999849996685899999999899999999970789-830045621---058876870 Q gi|254780355|r 361 NVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDPS-RRIGRPRQL---YTGALKRDY 422 (429) Q Consensus 361 NvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~~-~ri~RP~~~---Y~G~~~r~y 422 (429) |||||+|++|..||||+++|+++|+++|++||+||++||+++|. +|+++|.+. |+|+.+|+. T Consensus 199 Nvdg~~aav~~dlG~p~~~~~~lf~l~R~~G~~AH~~Eq~~~~~~~~~~~~~~~~i~Y~g~~~r~~ 264 (265) T PRK06224 199 NADGAIAAILADMGFPPALARGLAVISRAAGLVAHVLEERQQPIGFRIWDPVEEAIEYDGPPPREL 264 (265) T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCCCCCCCCCCC T ss_conf 679999999998597978873699999999999999999618568777885654531269999999 No 31 >cd06100 CCL_ACL-C Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA). ACL catalyzes an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. ACL may be required for fruiting body maturation in the filamentous fungus Sordaria macrospore. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL; the first enzyme is citryl-CoA synthetase (CC Probab=100.00 E-value=0 Score=432.14 Aligned_cols=198 Identities=26% Similarity=0.360 Sum_probs=180.7 Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHEECCCCC-CCHHHHHHHHHCCCC-CHHHHHHHHHHHHHHHHHCCC Q ss_conf 424688778764289841014796999998756350136787-630155554420565-424677675542100222035 Q gi|254780355|r 190 DLDYASNFLHMCFSVPCAEYQVNPLLARAMNRIFILHADHEQ-NASTSTVRLAGSSGA-DPFACIAAGVACLGGRAHGGA 267 (429) Q Consensus 190 ~lsyaeNfL~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe~-NaSTft~R~vaSt~a-dlysai~agi~aL~GPlHGGA 267 (429) ++||++||++|++|+ +|++..+|+||++||||||||+ |+||||+|+++||++ +++++++||++++ ||+|||| T Consensus 10 ~~s~~e~~~~m~~G~-----~P~~~~~r~ld~~Lvl~adHg~~~~St~aaRv~as~g~~~~~~~vaag~~~~-GplHGGA 83 (227) T cd06100 10 KISFGDVLYLLLKGR-----LPTPYEARLLEALLVALADHGPATPSAHAARLTASAGPEDLQSAVAAGLLGI-GDRFGGA 83 (227) T ss_pred CCCHHHHHHHHHHCC-----CCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHCC-CCCCCCH T ss_conf 188999999998189-----9998999999999999828799864899999999348238999999999655-7743575 Q ss_pred CHHHHHHHHHCC-----CCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH Q ss_conf 289999986215-----535127999999821478614302774355554034689999999888608776517999999 Q gi|254780355|r 268 NEEALNMLMEIG-----SLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIE 342 (429) Q Consensus 268 ne~v~~ml~~I~-----~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~ 342 (429) ||.|++|++++. .++++++|+.+.+++++ |||||||||||++|||+++|+++++++.. ..++++++.+ T Consensus 84 ~e~~~~ml~~~~~~~~~~~~~~~~~v~~~~~~~~--~ipGfGH~vyk~~DPRa~~L~~~a~~~~~-----~~~~~~~a~~ 156 (227) T cd06100 84 GEGAARLFKEAVDSGDALDAAAAEFVAEYRAAKK--RIPGFGHPVHKNPDPRVPRLLELARELGP-----AGPHLDYALA 156 (227) T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCC--CCCCCCCCCCCCCCCHHHHHHHHHHHHCC-----CCHHHHHHHH T ss_conf 6999999999986477628899999999986599--77788988799999459999999998566-----6659999999 Q ss_pred HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 9999961153145798778447889999984999668589999999989999999997078 Q gi|254780355|r 343 LERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFTVLFAVARTAGWVSQWTEMIVDP 403 (429) Q Consensus 343 le~~a~~d~~~~~r~l~pNvDfysg~i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~~~~ 403 (429) +|+++.++ .+|+|+||||||+|++|..||||+++||++|+++|++||+|||+||++++ T Consensus 157 ~e~~~~~~---~~~~l~~NvD~~~a~v~~~lG~p~~~~~~lF~~aR~~Gw~AH~~Eq~~~~ 214 (227) T cd06100 157 VEKALTAA---KGKPLPLNVDGAIAAILLDLGFPPGALRGLFVLGRSPGLIAHALEEKRLG 214 (227) T ss_pred HHHHHHHH---CCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 99999982---38998605498899999984978668989999999999999999999848 No 32 >KOG1254 consensus Probab=99.48 E-value=2.2e-14 Score=119.42 Aligned_cols=217 Identities=22% Similarity=0.314 Sum_probs=152.4 Q ss_pred CCCCCCCCCC--CHHHHHHHH-HHHCCCCCCCCCCCHHHHHHHHHHHHEECCCCCCCHHHH-HHHHHCCCCCHHHHHHHH Q ss_conf 7985348886--424688778-764289841014796999998756350136787630155-554420565424677675 Q gi|254780355|r 180 IGQPFVYPRS--DLDYASNFL-HMCFSVPCAEYQVNPLLARAMNRIFILHADHEQNASTST-VRLAGSSGADPFACIAAG 255 (429) Q Consensus 180 ~G~~~i~Pd~--~lsyaeNfL-~Ml~~~~~~~~~~~~~~~~ald~~LILhADHe~NaSTft-~R~vaSt~adlysai~ag 255 (429) .|.+.+|.+. ++.|++..= +--.+....+.+.-+-..+.+|.++.+.|||+-.+|-.- .-+.+-+++|+++++++| T Consensus 353 rGaeviYA~~p~~~~~a~elG~gg~~Sllw~~~~lp~Ya~kfie~~~m~~aDhgp~Vsga~ntI~~~ra~kdl~sslv~g 432 (600) T KOG1254 353 RGAEVIYADVPISLGYASELGNGGVYSLLWFQRRLPQYARKFIEICTMLTADHGPAVSGAGNTIANFRAGKDLFSSLVRG 432 (600) T ss_pred CCCEEEECCCHHHHHHHHHCCCCCEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEECCCCEEEECCHHHHHHHHHHH T ss_conf 87403655860555567650666057144134411789999999884216898854674167168732589999999998 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHC-CCCCHHHHHHHHHHHCCCCCEEECCCCCCC--CCCCHHHHHHHHHHHHHHHHCCCC Q ss_conf 54210022203528999998621-553512799999982147861430277435--555403468999999988860877 Q gi|254780355|r 256 VACLGGRAHGGANEEALNMLMEI-GSLERIPHYIMRAKDKNDPFRIMGFGHRVY--RNHDPRCRIMRETMYEVLEVTGRF 332 (429) Q Consensus 256 i~aL~GPlHGGAne~v~~ml~~I-~~~~~v~~~i~~~~~~~~~~ri~GfGHrvy--k~~DPRa~~l~~~~~~l~~~~~~~ 332 (429) +... |+.-|||-..+.+++.+- ++.-.+-+++.+.+ +.+.+|||.|||+- -+.|-|..++++++++-+. T Consensus 433 Llti-gdRfggald~aaR~f~~ayd~GL~~m~fv~~~~--k~~~~V~Gighriksi~n~d~rv~~lk~~~~~~fp----- 504 (600) T KOG1254 433 LLTI-GDRFGGALDIAARRFGPAYDKGLAPMRFVGKMR--KVPIEVYGIGHRIKSINNPDKRVEILKAFARKNFP----- 504 (600) T ss_pred HHHH-HHHHCCHHHHHHHHCCHHHHCCCHHHHHHHHHH--CCCCEECCCCCEEECCCCCCCCHHHHHHHHHHHCC----- T ss_conf 8551-012143226998861845434660788776764--78846317865444147855300328999985198----- Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCHHHHH--------------HHHHHHHHHHHHHHHHH Q ss_conf 6517999999999996115314579877844788999998499966858--------------99999999899999999 Q gi|254780355|r 333 NDPIAQVAIELERIALEDEYFIERKLYPNVDFYSGITLRALGFPTNLFT--------------VLFAVARTAGWVSQWTE 398 (429) Q Consensus 333 ~~~~~~~a~~le~~a~~d~~~~~r~l~pNvDfysg~i~~~lGip~~~ft--------------~iFa~~R~~Gw~AH~~E 398 (429) ..|+++.|.++|++... ++-||..|||-.-|++|-.|==-..||| .+|+++|..|++.|+.. T Consensus 505 ~~~~~~yal~ve~~t~~----k~~nlilnvdg~i~~~fvd~l~~~g~ft~~e~~e~i~ig~lng~fvl~rsig~igh~~d 580 (600) T KOG1254 505 ATPLLDYALEVEKITTS----KKPNLILNVDGAIAVLFVDLLRNSGMFTKEEADEYINIGALNGLFVLGRSIGFIGHYLD 580 (600) T ss_pred CCHHHHHHHHHEEEECC----CCCCEEEECCCHHHHHHHHHHHCCCCCCHHHHHHHEECCCCCCEEEEEEECCHHHHHCC T ss_conf 73277866532023215----78877996242278999999844687507765454320230215884201021121213 Q ss_pred HHHCCCCCCCC Q ss_conf 97078983004 Q gi|254780355|r 399 MIVDPSRRIGR 409 (429) Q Consensus 399 q~~~~~~ri~R 409 (429) |..-.+ -|+| T Consensus 581 qkrlkq-~lyr 590 (600) T KOG1254 581 QKRLKQ-GLYR 590 (600) T ss_pred HHHHHC-CCCC T ss_conf 766637-5323 No 33 >cd06100 CCL_ACL-C Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA). ACL catalyzes an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. ACL may be required for fruiting body maturation in the filamentous fungus Sordaria macrospore. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL; the first enzyme is citryl-CoA synthetase (CC Probab=97.65 E-value=0.0071 Score=39.78 Aligned_cols=43 Identities=30% Similarity=0.427 Sum_probs=40.0 Q ss_pred CEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 9319999750898999999981879998999999998864068 Q gi|254780355|r 70 GYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHAL 112 (429) Q Consensus 70 GY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~ 112 (429) ||++.||..+.+|-|+.||||.|++|++.|.+.|..-|.-+.. T Consensus 1 G~~~~elig~~s~~e~~~~m~~G~~P~~~~~r~ld~~Lvl~ad 43 (227) T cd06100 1 GYDLSDLIGKISFGDVLYLLLKGRLPTPYEARLLEALLVALAD 43 (227) T ss_pred CCCHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCC T ss_conf 9978999841889999999981899998999999999999828 No 34 >COG3383 Uncharacterized anaerobic dehydrogenase [General function prediction only] Probab=81.17 E-value=1.6 Score=23.57 Aligned_cols=55 Identities=25% Similarity=0.557 Sum_probs=40.1 Q ss_pred CCCCEEEEEECCEEEEEEEECCCCCCCCEEECCCCCCC----EEEECCCCCCEEEEEEEEEEEECC Q ss_conf 99876999989989997523077787510100115586----189888878623878756543344 Q gi|254780355|r 1 MTDKFAKLHLGHEEIDLPIKEGSLGSSVLDISFLHKNG----IFTYDPAFSSTASCKSKITFIDGN 62 (429) Q Consensus 1 M~~~~~~l~~~~~~~~lpi~~~~~~~~~~d~~~l~~~G----~~~~dpG~~~ta~ceS~IT~IDG~ 62 (429) |+.|..++++||++++-+ + |...++ .+...| -+.|.|++.-..+|.+-+--|||. T Consensus 1 m~~~~i~vtidg~~~~v~--~---G~tiL~--a~~~~gI~iP~iCy~~~l~pi~sCd~ClVEidG~ 59 (978) T COG3383 1 MAEKMITVTIDGRSIEVE--E---GTTILR--AANRNGIEIPHICYHESLGPIGSCDTCLVEIDGK 59 (978) T ss_pred CCCEEEEEEECCEEEECC--C---CHHHHH--HHHHCCCCCCCEECCCCCCCCCCCCEEEEEECCC T ss_conf 973069999878687527--8---708999--9996598555122367878655553689985682 No 35 >KOG2617 consensus Probab=80.13 E-value=0.96 Score=25.06 Aligned_cols=25 Identities=24% Similarity=0.456 Sum_probs=21.0 Q ss_pred EEEEEEEEEECCCCEEEECCEEHHHHHH Q ss_conf 8787565433447778989931999975 Q gi|254780355|r 51 SCKSKITFIDGNNGILLYRGYPIEQLSE 78 (429) Q Consensus 51 ~ceS~IT~IDG~~G~L~YRGY~IedLa~ 78 (429) .||+ |++|.++|| +|||++|.++-. T Consensus 71 ~~e~--s~Ld~~~gI-~frg~~i~e~q~ 95 (458) T KOG2617 71 LWET--SVLDPEEGI-RFRGGDIPECQK 95 (458) T ss_pred EECC--CCCCHHHCE-EECCCCHHHHHH T ss_conf 2037--643610070-134897799985 No 36 >PRK07569 bidirectional hydrogenase complex protein HoxU; Validated Probab=78.60 E-value=2.7 Score=21.91 Aligned_cols=55 Identities=16% Similarity=0.313 Sum_probs=38.4 Q ss_pred CCCCEEEEEECCEEEEEEEECCCCCCCCEEECCCCCCC----EEEECCCCCCEEEEEEEEEEEECCCC Q ss_conf 99876999989989997523077787510100115586----18988887862387875654334477 Q gi|254780355|r 1 MTDKFAKLHLGHEEIDLPIKEGSLGSSVLDISFLHKNG----IFTYDPAFSSTASCKSKITFIDGNNG 64 (429) Q Consensus 1 M~~~~~~l~~~~~~~~lpi~~~~~~~~~~d~~~l~~~G----~~~~dpG~~~ta~ceS~IT~IDG~~G 64 (429) |+- +||+|||++++.| .|...+|... +.| .+-|+|++...++|.-=+--|+|... T Consensus 1 M~m--vtltIdG~~v~v~-----~G~tILeaa~--~~Gi~IP~LCy~~~l~~~G~CR~C~VEveG~~~ 59 (236) T PRK07569 1 MSV--KTLTIDDQLVSAR-----EGETILQAAR--EAGIPIPTLCHLEGVSDVGACRLCLVEVEGSNK 59 (236) T ss_pred CCE--EEEEECCEEEEEC-----CCCHHHHHHH--HCCCCCCEECCCCCCCCCCCCCCCEEEECCCCC T ss_conf 973--8999999999968-----9895999999--859984725468993988866732799899853 No 37 >TIGR01025 rpsS_arch ribosomal protein S19; InterPro: IPR005713 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 represents eukaryotic ribosomal protein S15 and its archaeal equivalent. It excludes bacterial and organellar ribosomal protein S19. The nomenclature for the archaeal members is unresolved and given variously as S19 (after the more distant bacterial homologs) or S15.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit. Probab=77.59 E-value=1.5 Score=23.66 Aligned_cols=95 Identities=17% Similarity=0.277 Sum_probs=50.7 Q ss_pred EEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH Q ss_conf 89899319999750898999999981879998999999998864068998999999851247652578999999987520 Q gi|254780355|r 66 LLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFY 145 (429) Q Consensus 66 L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~p~~ahPM~~L~~~vsaL~a~~ 145 (429) ..||||++|+|. +-+++|++-||= +.|-..+.. -+.++-.+++..+.. +-- T Consensus 5 F~YrG~~Le~L~-~M~~~~l~kL~~------aR~RR~l~R------Gl~~~~~~ll~k~rk----------~k~------ 55 (136) T TIGR01025 5 FRYRGYTLEELL-DMSLEELAKLLP------ARQRRRLKR------GLTPKQKKLLKKLRK----------AKK------ 55 (136) T ss_pred CCCCCCCHHHHH-CCCHHHHHHHCC------CCCCCCCCC------CCCHHHHHHHHHHHH----------HHH------ T ss_conf 100364579874-147888998706------333421102------877447899999999----------887------ Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC--CCCC Q ss_conf 68557678788988899999999999999999727985348--8864 Q gi|254780355|r 146 YSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVY--PRSD 190 (429) Q Consensus 146 ~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~--Pd~~ 190 (429) +.............-+|=+-.+|.+++...-..+|++|+. -.|+ T Consensus 56 -e~~~~g~~P~~~rTH~RdmiilPeMvG~~~~v~NGK~F~~V~i~PE 101 (136) T TIGR01025 56 -EAKPKGEKPEVIRTHCRDMIILPEMVGLTVGVYNGKEFVEVEIKPE 101 (136) T ss_pred -HHHCCCCCCCEEEECCCCEEECCCCCCCEEEEECCCEEEEEEEEEE T ss_conf -4321468886002124421576423360778720865556774200 No 38 >PRK04038 rps19p 30S ribosomal protein S19P; Provisional Probab=76.91 E-value=2.8 Score=21.88 Aligned_cols=91 Identities=16% Similarity=0.255 Sum_probs=50.3 Q ss_pred CCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 47778989931999975089899999998187999899999999886406899899999985124765257899999998 Q gi|254780355|r 62 NNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGAL 141 (429) Q Consensus 62 ~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~p~~ahPM~~L~~~vsaL 141 (429) .+....||||+++||- +-++||.+-|| ++.|-..|. +-+...-..+++.+...- .. T Consensus 3 r~k~FtYRG~~leeL~-~m~~eel~~Ll------paR~RR~l~------RGl~~~~~~Ll~klrkak----------~~- 58 (134) T PRK04038 3 RRKEFTYRGYTLEELQ-EMSLEEFAELL------PARQRRSLK------RGLTPEQRKLLEKIRKAK----------RL- 58 (134) T ss_pred CCCEEEECCCCHHHHH-CCCHHHHHHHC------CHHHHHHHC------CCCCHHHHHHHHHHHHHH----------HC- T ss_conf 6524576586699997-48999998761------467764540------377878999999999866----------43- Q ss_pred HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 752068557678788988899999999999999999727985348 Q gi|254780355|r 142 SSFYYSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVY 186 (429) Q Consensus 142 ~a~~~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~ 186 (429) . ..+..+ ..-+|=+-.+|.+++...-..+|+.++. T Consensus 59 -~--~kp~~i-------kTh~R~~iIlPemvG~~i~VynGk~f~~ 93 (134) T PRK04038 59 -K--NKGRVI-------RTHCRDMIILPEMVGLTIAVYNGKEFVP 93 (134) T ss_pred -C--CCCCCE-------EEECCCCEECHHHCCCEEEEECCCEEEE T ss_conf -5--799862-------6733676868646471898963864788 No 39 >TIGR01882 peptidase-T peptidase T; InterPro: IPR010161 Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This entry represents metallopeptidases belonging to MEROPS peptidase family M20 (clan MH), subfamily M20B. They are tripeptide aminopeptidases commonly known as Peptidase T, which have a substrate preference for hydrophobic peptides.; GO: 0008270 zinc ion binding, 0016285 cytosol alanyl aminopeptidase activity, 0045148 tripeptide aminopeptidase activity, 0006518 peptide metabolic process, 0005737 cytoplasm. Probab=75.63 E-value=1.6 Score=23.55 Aligned_cols=90 Identities=17% Similarity=0.321 Sum_probs=57.9 Q ss_pred CCCHHHHHHHHHHHHHHHHCCCC------CCHHHHHHHHHHHHH----HHHHHCCCCCCCCCCCHHH----HHHHHHCCC Q ss_conf 55403468999999988860877------651799999999999----6115314579877844788----999998499 Q gi|254780355|r 310 NHDPRCRIMRETMYEVLEVTGRF------NDPIAQVAIELERIA----LEDEYFIERKLYPNVDFYS----GITLRALGF 375 (429) Q Consensus 310 ~~DPRa~~l~~~~~~l~~~~~~~------~~~~~~~a~~le~~a----~~d~~~~~r~l~pNvDfys----g~i~~~lGi 375 (429) +..-|-..||+.++++-++.|+. +|-++..|.+||+.+ ++......-+|-||+|=-= |-=+..||+ T Consensus 292 ~f~eRK~l~k~iv~kmn~E~G~~Rikl~~nDQYYNMa~~iek~~~IvdiAk~Amenlgiep~i~PiRGGTDGSqlsyMGL 371 (413) T TIGR01882 292 KFEERKELMKEIVEKMNDEYGQDRIKLDMNDQYYNMAEKIEKDMEIVDIAKKAMENLGIEPKIEPIRGGTDGSQLSYMGL 371 (413) T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHCCCCEEECCCCCCCCCCCCEECCC T ss_conf 52568999999999987651756423352632112587515643024788999985699610045457876121001678 Q ss_pred C-HHHHH------------HHHHHHHHHHHHHHHHHH Q ss_conf 9-66858------------999999998999999999 Q gi|254780355|r 376 P-TNLFT------------VLFAVARTAGWVSQWTEM 399 (429) Q Consensus 376 p-~~~ft------------~iFa~~R~~Gw~AH~~Eq 399 (429) | |++|+ ++=.+-.++-.+-.+++| T Consensus 372 PtPNiFaGgENmHGrfEy~sv~~M~KaVdv~~eia~l 408 (413) T TIGR01882 372 PTPNIFAGGENMHGRFEYVSVESMVKAVDVLVEIAKL 408 (413) T ss_pred CCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHH T ss_conf 7876455886776516888754505589999999998 No 40 >PTZ00096 40S ribosomal protein S15; Provisional Probab=73.39 E-value=3 Score=21.63 Aligned_cols=90 Identities=20% Similarity=0.246 Sum_probs=45.8 Q ss_pred EEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH Q ss_conf 89899319999750898999999981879998999999998864068998999999851247652578999999987520 Q gi|254780355|r 66 LLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFY 145 (429) Q Consensus 66 L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~p~~ahPM~~L~~~vsaL~a~~ 145 (429) ..||||+++||- .-+++|.+-|| .+.|-..|. +-+...-..+++.+.. +-... ... T Consensus 16 FtYRG~~leeL~-~m~~eel~~L~------pAR~RR~l~------RGl~~~~~~Ll~klrk----------ak~~~-~~~ 71 (144) T PTZ00096 16 FTYRGLELEKLL-ALSEEELVELL------RARQRRRIS------RHLKRRAPNLLKKLRK----------AKKEV-KPG 71 (144) T ss_pred EEECCCCHHHHH-CCCHHHHHHHH------HHHHHHHHC------CCCCHHHHHHHHHHHH----------HHHHC-CCC T ss_conf 445267699997-48999998771------245643530------4998899999999999----------77635-456 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 68557678788988899999999999999999727985348 Q gi|254780355|r 146 YSPSGVQDLEQCVNVSLRMIAKISTIAAMIYKYSIGQPFVY 186 (429) Q Consensus 146 ~~~~~~~d~~~~~~~a~rLiA~~p~i~A~~yr~~~G~~~i~ 186 (429) ..+.. ...-+|=+-.+|.+++......+|+.++. T Consensus 72 eKp~~-------ikTh~R~~iIlPemvG~~v~VynGk~f~~ 105 (144) T PTZ00096 72 EKPKP-------VKTHLRNMVIVPEMVGSIVGVYNGRQFNN 105 (144) T ss_pred CCCCC-------EEECCCCCEECCHHCCEEEEEECCCEEEE T ss_conf 78976-------47704777768201360898864851576 No 41 >KOG3041 consensus Probab=71.87 E-value=3.9 Score=20.85 Aligned_cols=68 Identities=26% Similarity=0.427 Sum_probs=34.3 Q ss_pred EEEEEE--ECCCCCCCCEEECCCC-CCC----------EEEECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHC Q ss_conf 999752--3077787510100115-586----------189888878623878756543344777898993199997508 Q gi|254780355|r 14 EIDLPI--KEGSLGSSVLDISFLH-KNG----------IFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKS 80 (429) Q Consensus 14 ~~~lpi--~~~~~~~~~~d~~~l~-~~G----------~~~~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~ 80 (429) .+|||- ++..+....--+|.|. +|| ....||||+|+--|-+... |||+.-. --.|..+|- .- T Consensus 104 ciElPAGLiD~ge~~~~aAiREl~EEtGy~gkv~~~s~~~f~DPGltn~~~~iv~v~-idg~~pE---nqrp~q~le-dg 178 (225) T KOG3041 104 CIELPAGLIDDGEDFEGAAIRELEEETGYKGKVDMVSPTVFLDPGLTNCNLCIVVVD-IDGDVPE---NQRPVQQLE-DG 178 (225) T ss_pred EEECCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEECCCCEECCCCCCCCCEEEEEEE-ECCCCCC---CCCCCCCCC-CC T ss_conf 897235543489766788899888874855314412630772798888715899999-4388710---158665678-88 Q ss_pred CHHHHH Q ss_conf 989999 Q gi|254780355|r 81 DFLEVC 86 (429) Q Consensus 81 sFeEVa 86 (429) .|.||. T Consensus 179 EfIev~ 184 (225) T KOG3041 179 EFIEVF 184 (225) T ss_pred CEEEEE T ss_conf 569999 No 42 >KOG1182 consensus Probab=71.69 E-value=2.8 Score=21.85 Aligned_cols=19 Identities=32% Similarity=0.878 Sum_probs=17.1 Q ss_pred CCCEEEECCEEHHHHHHHC Q ss_conf 4777898993199997508 Q gi|254780355|r 62 NNGILLYRGYPIEQLSEKS 80 (429) Q Consensus 62 ~~G~L~YRGY~IedLa~~~ 80 (429) +.|.|.||||++|+.+++| T Consensus 146 EaGVLlwRgftle~f~~qC 164 (432) T KOG1182 146 EAGVLLWRGFTLEEFMNQC 164 (432) T ss_pred CCCEEEECCCCHHHHHHHH T ss_conf 5736888485299999874 No 43 >PRK08493 NADH dehydrogenase subunit G; Validated Probab=71.38 E-value=4.2 Score=20.63 Aligned_cols=52 Identities=19% Similarity=0.288 Sum_probs=22.4 Q ss_pred EEEEECCEEEEEEEECCCCCCCCEEECCCCC--CCEEEECCCCCCEEEEEEEEEEEECC Q ss_conf 9999899899975230777875101001155--86189888878623878756543344 Q gi|254780355|r 6 AKLHLGHEEIDLPIKEGSLGSSVLDISFLHK--NGIFTYDPAFSSTASCKSKITFIDGN 62 (429) Q Consensus 6 ~~l~~~~~~~~lpi~~~~~~~~~~d~~~l~~--~G~~~~dpG~~~ta~ceS~IT~IDG~ 62 (429) ++++|||++++.| .|...+|.-+-.. -=.+.|+|++.-+++|..=+--|||+ T Consensus 2 v~i~Idg~~~~~~-----~g~til~aa~~~gi~IP~lCy~~~l~p~g~Cr~C~VEv~G~ 55 (819) T PRK08493 2 ITININGKEIECQ-----EGEYILNAARRNGIFIPAICYLSGCSPTLACRLCMVEADGK 55 (819) T ss_pred CEEEECCEEEEEC-----CCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEECCC T ss_conf 1899999999969-----99979999997399856144899929688776638987894 No 44 >PRK07860 NADH dehydrogenase subunit G; Validated Probab=71.03 E-value=5.1 Score=20.03 Aligned_cols=66 Identities=17% Similarity=0.358 Sum_probs=37.8 Q ss_pred CCEEEEEECCEEEEEEEECCCCCCCCEEECCCCCCC----EEEECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHH Q ss_conf 876999989989997523077787510100115586----1898888786238787565433447778989931999 Q gi|254780355|r 3 DKFAKLHLGHEEIDLPIKEGSLGSSVLDISFLHKNG----IFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQ 75 (429) Q Consensus 3 ~~~~~l~~~~~~~~lpi~~~~~~~~~~d~~~l~~~G----~~~~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~Ied 75 (429) .+.+||+||||+++.| + |...++.- .+.| .|.|+|.+...++|.-=+--|+|..+..-=.--++.| T Consensus 14 ~~mv~l~Idg~~v~v~--~---g~til~aa--~~~Gi~IP~fC~h~~L~~~g~CR~ClVev~g~~~~~~sC~tpv~~ 83 (809) T PRK07860 14 PELVTLTIDGVEVSVP--K---GTLVIRAA--ELIGIQIPRFCDHPLLDPVGACRQCLVEVEGQRKPLASCTTTVTD 83 (809) T ss_pred CCCEEEEECCEEEEEC--C---CCHHHHHH--HHCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCC T ss_conf 8806999999999969--9---99899999--974998565679999598886645289989996788061876899 No 45 >PRK13866 plasmid partitioning protein RepB; Provisional Probab=69.23 E-value=3.9 Score=20.87 Aligned_cols=24 Identities=8% Similarity=0.109 Sum_probs=18.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 99999999899999999970789830 Q gi|254780355|r 382 VLFAVARTAGWVSQWTEMIVDPSRRI 407 (429) Q Consensus 382 ~iFa~~R~~Gw~AH~~Eq~~~~~~ri 407 (429) .=|...|...+.+.|.++. ++.++ T Consensus 311 ~~fL~~~L~~Ly~eF~~~~--Gg~~~ 334 (336) T PRK13866 311 GEYVADQLDSLYAQFIETN--GGGKL 334 (336) T ss_pred HHHHHHHHHHHHHHHHHHC--CCCCC T ss_conf 9999988999999999864--89877 No 46 >pfam07249 Cerato-platanin Cerato-platanin. This family contains a number of fungal cerato-platanin phytotoxic proteins approximately 150 residues long. Cerato-platanin contains four cysteine residues that form two disulphide bonds. Probab=64.84 E-value=6.7 Score=19.23 Aligned_cols=32 Identities=28% Similarity=0.717 Sum_probs=23.7 Q ss_pred EEECCCCCCEEEEEEEEEEEECCCCEEEECCEE Q ss_conf 898888786238787565433447778989931 Q gi|254780355|r 40 FTYDPAFSSTASCKSKITFIDGNNGILLYRGYP 72 (429) Q Consensus 40 ~~~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~ 72 (429) ++||++|-+-...-+..+--||.+| |.=|||+ T Consensus 3 vsYD~~YD~~~~sl~~vaCSdG~nG-L~tk~~~ 34 (119) T pfam07249 3 VSYDPGYDDANRSMGSVSCSDGDNG-LMTKYWP 34 (119) T ss_pred EEECCCCCCCCCEEEEEEECCCCCC-CEECCCC T ss_conf 7743876778872425886499875-2416632 No 47 >TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently. Probab=58.70 E-value=6.5 Score=19.30 Aligned_cols=10 Identities=30% Similarity=0.627 Sum_probs=5.3 Q ss_pred CCCCHHHHHH Q ss_conf 8864246887 Q gi|254780355|r 187 PRSDLDYASN 196 (429) Q Consensus 187 Pd~~lsyaeN 196 (429) .+.+|||.|- T Consensus 157 ~R~dLSfIEr 166 (325) T TIGR03454 157 ARRDLSFIER 166 (325) T ss_pred HCCCCCHHHH T ss_conf 2146779999 No 48 >PRK09129 NADH dehydrogenase subunit G; Validated Probab=54.52 E-value=13 Score=17.16 Aligned_cols=10 Identities=30% Similarity=0.205 Sum_probs=5.4 Q ss_pred HHHHCCCCHH Q ss_conf 0222035289 Q gi|254780355|r 261 GRAHGGANEE 270 (429) Q Consensus 261 GPlHGGAne~ 270 (429) |.+.+|+|.. T Consensus 505 g~l~~~~N~~ 514 (777) T PRK09129 505 GFLTEAANSV 514 (777) T ss_pred CCCCCCCHHH T ss_conf 4279854037 No 49 >KOG4183 consensus Probab=53.40 E-value=16 Score=16.55 Aligned_cols=15 Identities=27% Similarity=0.386 Sum_probs=9.0 Q ss_pred CCCCEEEECCEEHHH Q ss_conf 447778989931999 Q gi|254780355|r 61 GNNGILLYRGYPIEQ 75 (429) Q Consensus 61 G~~G~L~YRGY~Ied 75 (429) |+.-+|.|-||.--+ T Consensus 62 geteRleyvg~n~s~ 76 (413) T KOG4183 62 GETERLEYVGNNFST 76 (413) T ss_pred CCCCEEEEEECCCCH T ss_conf 787526887046534 No 50 >KOG0416 consensus Probab=53.10 E-value=6.4 Score=19.39 Aligned_cols=18 Identities=11% Similarity=0.115 Sum_probs=7.0 Q ss_pred CCCCEEEEEECCEEEEEEE Q ss_conf 9987699998998999752 Q gi|254780355|r 1 MTDKFAKLHLGHEEIDLPI 19 (429) Q Consensus 1 M~~~~~~l~~~~~~~~lpi 19 (429) ||+-.++ .+||+.-|+-| T Consensus 17 ~s~yeV~-~ind~m~ef~V 34 (189) T KOG0416 17 MSDYEVT-IINDGMQEFYV 34 (189) T ss_pred HCCCEEE-EECCCCCEEEE T ss_conf 5387688-86586408899 No 51 >PTZ00295 glucosamine-fructose-6-phosphate aminotransferase; Provisional Probab=51.32 E-value=5.4 Score=19.86 Aligned_cols=32 Identities=41% Similarity=0.679 Sum_probs=18.8 Q ss_pred CCCCEEEEEEEEEEEECCC--------C--EEEECCEEHHHHH Q ss_conf 8786238787565433447--------7--7898993199997 Q gi|254780355|r 45 AFSSTASCKSKITFIDGNN--------G--ILLYRGYPIEQLS 77 (429) Q Consensus 45 G~~~ta~ceS~IT~IDG~~--------G--~L~YRGY~IedLa 77 (429) .-.|+|+|.-=|-|+ |.+ | +|.|||||=.=+| T Consensus 71 ~~~~~~~~CGIvGyv-g~~~a~~iLl~GL~rLEYRGYDSAGIA 112 (691) T PTZ00295 71 SVPNKASCCGIIGYV-GNRDASKILLDGIEILQNRGYDSCGMS 112 (691) T ss_pred CCCCCCCCEEEEEEE-ECCCCHHHHHHHHHHHHCCCCCCCEEE T ss_conf 368988731079999-087748999998888611552604489 No 52 >pfam07583 PSCyt2 Protein of unknown function (DUF1549). A family of paralogues in the planctomyces. Probab=50.32 E-value=12 Score=17.56 Aligned_cols=45 Identities=11% Similarity=0.115 Sum_probs=31.8 Q ss_pred HHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHH Q ss_conf 99750898999999981879998999999998864068998999999851 Q gi|254780355|r 75 QLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGF 124 (429) Q Consensus 75 dLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~ 124 (429) ..|...+|.==+||=+.|.+||.+|.++|... .-|+.-.++++.+ T Consensus 20 ~~a~d~~flRRv~LDl~G~iPt~~E~~~Fl~d-----~~~~kr~~lID~L 64 (200) T pfam07583 20 PEADDATLLRRVSLDLTGLPPTPEEVRAFLAD-----QSPDAREKLVDRL 64 (200) T ss_pred CCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCC-----CCHHHHHHHHHHH T ss_conf 88888899999999983889699999988706-----9789999999999 No 53 >PRK08166 NADH dehydrogenase subunit G; Validated Probab=50.15 E-value=10 Score=17.96 Aligned_cols=18 Identities=22% Similarity=-0.068 Sum_probs=11.1 Q ss_pred CCCEEEECCEEHHHHHHH Q ss_conf 477789899319999750 Q gi|254780355|r 62 NNGILLYRGYPIEQLSEK 79 (429) Q Consensus 62 ~~G~L~YRGY~IedLa~~ 79 (429) ++|.|.-||+---|..++ T Consensus 258 N~g~LC~KGrf~~~~v~~ 275 (858) T PRK08166 258 NGYFLCDRGRFGYGYVNL 275 (858) T ss_pred CCCCCCCCCCCHHHHHCC T ss_conf 677657332413655357 No 54 >COG1034 NuoG NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion] Probab=49.97 E-value=18 Score=16.33 Aligned_cols=50 Identities=26% Similarity=0.628 Sum_probs=31.6 Q ss_pred EEEEECCEEEEEEEECCCCCCCCEEECCCCCCC----EEEECCCCCCEEEEEEEEEEEECC Q ss_conf 999989989997523077787510100115586----189888878623878756543344 Q gi|254780355|r 6 AKLHLGHEEIDLPIKEGSLGSSVLDISFLHKNG----IFTYDPAFSSTASCKSKITFIDGN 62 (429) Q Consensus 6 ~~l~~~~~~~~lpi~~~~~~~~~~d~~~l~~~G----~~~~dpG~~~ta~ceS~IT~IDG~ 62 (429) +||++||++++.|= |..++..- ++.| .|.|.|++..++.|.==.-.++|. T Consensus 2 ~tI~IDG~ei~v~~-----g~tvLqAa--~~aGi~IP~fCyh~~ls~~GaCRmClVEveg~ 55 (693) T COG1034 2 VTITIDGKEIEVPE-----GETVLQAA--REAGIDIPTFCYHPRLSIAGACRMCLVEVEGA 55 (693) T ss_pred EEEEECCEEEECCC-----CCHHHHHH--HHCCCCCCCCCCCCCCCCCCCEEEEEEEECCC T ss_conf 39998998986189-----72899999--98599877210357887445325779996688 No 55 >TIGR01135 glmS glucosamine--fructose-6-phosphate aminotransferase, isomerizing; InterPro: IPR005855 Glucosamine:fructose-6-phosphate aminotransferase (2.6.1.16 from EC) catalyses the formation of glucosamine 6-phosphate and is the first and rate-limiting enzyme of the hexosamine biosynthetic pathway. The final product of the hexosamine pathway, UDP-N-acetyl glucosamine, is an active precursor of numerous macromolecules containing amino sugars. This family of sequences belong to the MEROPS peptidase family C44 (clan PB(C)), and are classified as non-peptidase homologs.; GO: 0004360 glutamine-fructose-6-phosphate transaminase (isomerizing) activity, 0016051 carbohydrate biosynthetic process, 0005737 cytoplasm. Probab=49.11 E-value=4.4 Score=20.52 Aligned_cols=72 Identities=21% Similarity=0.250 Sum_probs=40.7 Q ss_pred CCCHHHHHHHHHHHHEECCCC-CCCH--HHHHHHHHCCCCCHHHHHHHHHHHHHHHH-HCCCCHHHHHHHHHCCCCCHHH Q ss_conf 479699999875635013678-7630--15555442056542467767554210022-2035289999986215535127 Q gi|254780355|r 210 QVNPLLARAMNRIFILHADHE-QNAS--TSTVRLAGSSGADPFACIAAGVACLGGRA-HGGANEEALNMLMEIGSLERIP 285 (429) Q Consensus 210 ~~~~~~~~ald~~LILhADHe-~NaS--Tft~R~vaSt~adlysai~agi~aL~GPl-HGGAne~v~~ml~~I~~~~~v~ 285 (429) .+.-...|--|..|-+||==| +=|| |||+-+++ ...++..++-..|-+ +. +.+-+..+.+ ...| T Consensus 390 v~gS~l~Re~D~~L~t~AGpEIGVAsTKaFt~Ql~~------L~~L~~~~a~~~g~~~~~---~~~~~~~~~L---~~lP 457 (628) T TIGR01135 390 VPGSTLTREADHTLYTRAGPEIGVASTKAFTAQLTV------LYLLALALAKARGTLSDA---EEEAELVDAL---RRLP 457 (628) T ss_pred CCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH------HHHHHHHHHHHCCCCCCH---HHHHHHHHHH---HHHH T ss_conf 687533578778776506971114545889999999------999999999853755587---8999999998---7506 Q ss_pred HHHHHHHH Q ss_conf 99999982 Q gi|254780355|r 286 HYIMRAKD 293 (429) Q Consensus 286 ~~i~~~~~ 293 (429) +.+++.+. T Consensus 458 ~~~~~~l~ 465 (628) T TIGR01135 458 ELVEQVLK 465 (628) T ss_pred HHHHHHHH T ss_conf 99999870 No 56 >TIGR01330 bisphos_HAL2 3'(2'),5'-bisphosphate nucleotidase; InterPro: IPR006239 Sulphate is incorporated into 3-phosphoadenylylsulphate, PAPS, for utilization in pathways such as methionine biosynthesis. Transfer of sulphate from PAPS to an acceptor leaves adenosine 3'-5'-bisphosphate, APS. In plants these sequences represent a form of the enzyme, 3'(2'),5'-bisphosphate nucleotidase, which removes the 3'-phosphate from APS to regenerate AMP and help drive the cycle. Sensitivity of this essential enzyme to sodium and other metal ions results is responsible for characterization of this enzyme as a salt tolerance protein . Some members of this family are active also as inositol 1-monophosphatase. ; GO: 0008441 3'(2')5'-bisphosphate nucleotidase activity, 0006790 sulfur metabolic process. Probab=45.91 E-value=9.4 Score=18.23 Aligned_cols=175 Identities=14% Similarity=0.194 Sum_probs=77.7 Q ss_pred HHHHHHCCCCCHHHHHHHHHH--------CCCCCHHHH----HHHHH-HHHHHHHCC-CCCC---CCHHHHHH-HHHHHH Q ss_conf 998864068998999999851--------247652578----99999-998752068-5576---78788988-899999 Q gi|254780355|r 104 NDKISRHALLNENMSRFFMGF--------PSSAHPMAM----LVSAV-GALSSFYYS-PSGV---QDLEQCVN-VSLRMI 165 (429) Q Consensus 104 ~~~l~~~~~lpe~v~~~i~~~--------p~~ahPM~~----L~~~v-saL~a~~~~-~~~~---~d~~~~~~-~a~rLi 165 (429) .+-.+..+.|.+.|.+-+-.- -.|-.|.++ -++.| ..|..-.++ +..+ +|.+...+ .+..++ T Consensus 10 ~~av~~AS~Lt~kvq~~l~~~k~~~~~~sK~D~SPVTvaDyG~QAiv~~~L~~~f~~~~lSiVaEEdS~~L~~~~S~~~~ 89 (382) T TIGR01330 10 VKAVRLASLLTKKVQEKLIKEKDAADVLSKDDKSPVTVADYGAQAIVILVLKEEFPDDPLSIVAEEDSEDLREDDSADTL 89 (382) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHCHHHHHHHH T ss_conf 99999988878999998626555676301368768001003589999999998568997268986165200221356899 Q ss_pred HHHHHHHHHHHHHHC--CC-CCCCCCC---CHHHHHHHHHHHC------CCCCCCCCCCHH-----------HHHHHHHH Q ss_conf 999999999999727--98-5348886---4246887787642------898410147969-----------99998756 Q gi|254780355|r 166 AKISTIAAMIYKYSI--GQ-PFVYPRS---DLDYASNFLHMCF------SVPCAEYQVNPL-----------LARAMNRI 222 (429) Q Consensus 166 A~~p~i~A~~yr~~~--G~-~~i~Pd~---~lsyaeNfL~Ml~------~~~~~~~~~~~~-----------~~~ald~~ 222 (429) ..+--++.-.-.+.. ++ +|...+. -+| ++.+|..+- |.....|..||+ .+=| .+ T Consensus 90 ~~v~~~v~~~~~~~~~Y~~~dflftn~~~~~~S-~~d~l~~Id~G~y~GGr~GR~W~LDPiDGTkGFlRG~QYAva--LA 166 (382) T TIGR01330 90 GRVSELVNETLAEAKNYKKDDFLFTNELVKLKS-AEDLLKIIDRGNYEGGRKGRHWVLDPIDGTKGFLRGDQYAVA--LA 166 (382) T ss_pred HHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCC-HHHHHHHHHCCCCCCCCCCCEEEECCCCCCCCCCCHHHHHHH--HH T ss_conf 999998765788886258865044246667568-899999862578898889875771675676556225689999--87 Q ss_pred HH--------------EECCC--CCCCHHHHHHHHHCCCCCHHHHHHHHH---H-HHHHHHHCC--CCHHHHHHHHHCCC Q ss_conf 35--------------01367--876301555544205654246776755---4-210022203--52899999862155 Q gi|254780355|r 223 FI--------------LHADH--EQNASTSTVRLAGSSGADPFACIAAGV---A-CLGGRAHGG--ANEEALNMLMEIGS 280 (429) Q Consensus 223 LI--------------LhADH--e~NaSTft~R~vaSt~adlysai~agi---~-aL~GPlHGG--Ane~v~~ml~~I~~ 280 (429) || |--+. .+|--.-+.+.=+-++++...||-.|. | |.-=+||-+ +.+.+.=-+.++.+ T Consensus 167 Lie~Gkv~lg~lGCPNlp~~~~~~~~~~nqamktK~~~g~~~~G~i~~A~rg~Gqaf~y~L~~~Gi~~s~~~v~v~~v~d 246 (382) T TIGR01330 167 LIENGKVVLGVLGCPNLPLKSEAAQNEKNQAMKTKAKAGSESKGCIFYAVRGSGQAFMYSLSSEGIKESPVKVHVSSVED 246 (382) T ss_pred HHHCCCEEEEEEECCCCCHHHHCCCCHHHHHHHHHHCCCCCCCCEEEEEEECCCCEEEECCCCCCCCCCCEEEEEEECCC T ss_conf 65279079998606885101102683023455421004677641589866368721520666687046735787741468 Q ss_pred C Q ss_conf 3 Q gi|254780355|r 281 L 281 (429) Q Consensus 281 ~ 281 (429) + T Consensus 247 t 247 (382) T TIGR01330 247 T 247 (382) T ss_pred C T ss_conf 1 No 57 >PRK07440 hypothetical protein; Provisional Probab=44.92 E-value=17 Score=16.40 Aligned_cols=17 Identities=18% Similarity=0.188 Sum_probs=15.2 Q ss_pred CCCCEEEEEECCEEEEEE Q ss_conf 998769999899899975 Q gi|254780355|r 1 MTDKFAKLHLGHEEIDLP 18 (429) Q Consensus 1 M~~~~~~l~~~~~~~~lp 18 (429) ||+ +.++++|||+++++ T Consensus 1 m~~-~i~I~vNGe~~~~~ 17 (70) T PRK07440 1 MSN-PITLQVNGETRTCS 17 (70) T ss_pred CCC-CCEEEECCEEEECC T ss_conf 998-41999999887859 No 58 >pfam07587 PSD1 Protein of unknown function (DUF1553). A family of proteins found in Rhodopirellula baltica. Probab=44.85 E-value=22 Score=15.67 Aligned_cols=19 Identities=16% Similarity=0.280 Sum_probs=7.6 Q ss_pred HHHHHHHHCCCCCCCCCCC Q ss_conf 9999997279853488864 Q gi|254780355|r 172 AAMIYKYSIGQPFVYPRSD 190 (429) Q Consensus 172 ~A~~yr~~~G~~~i~Pd~~ 190 (429) +--++.+.-|..++.|=++ T Consensus 23 vNR~W~~~fG~GlV~pvdd 41 (258) T pfam07587 23 VNRVWQHLFGRGLVDTVDD 41 (258) T ss_pred HHHHHHHHCCCCCCCCHHH T ss_conf 9999999729977388566 No 59 >PRK10528 multifunctional acyl-CoA thioesterase I and protease I and lysophospholipase L1; Provisional Probab=43.68 E-value=23 Score=15.55 Aligned_cols=82 Identities=16% Similarity=0.175 Sum_probs=49.9 Q ss_pred CCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHH-HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 53512799999982147861430277435555403-46899999998886087765179999999999961153145798 Q gi|254780355|r 280 SLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHDPR-CRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKL 358 (429) Q Consensus 280 ~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPR-a~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l 358 (429) ..+|..+-|++.++++-...|+|.- +-.++.+| ......+..+++++.+. +++... ++.++........-++ T Consensus 93 ~~~NL~~ii~~~~~~g~~vlL~g~~--~p~n~g~~y~~~f~~iy~~lA~e~~v---~l~pf~--l~~v~~~~~~~q~Dgi 165 (191) T PRK10528 93 TEQTLRQIIQDVKAANAQPLLMQIR--LPANYGRRYNEAFSAIYPKLAKEFDI---PLLPFF--MEEVYLKPQWMQDDGI 165 (191) T ss_pred HHHHHHHHHHHHHHCCCCEEEEECC--CCCCCCHHHHHHHHHHHHHHHHHHCC---CEEHHH--HHHHCCCHHHCCCCCC T ss_conf 9999999999999889978997065--67551266788899999999998099---741378--8756359755288889 Q ss_pred CCCCCHHHHH Q ss_conf 7784478899 Q gi|254780355|r 359 YPNVDFYSGI 368 (429) Q Consensus 359 ~pNvDfysg~ 368 (429) |||.+-|.-+ T Consensus 166 HPN~~G~~~i 175 (191) T PRK10528 166 HPNRDAQPFI 175 (191) T ss_pred CCCHHHHHHH T ss_conf 9598899999 No 60 >TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg); InterPro: IPR004577 All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. The enzyme incises DNA at 8-oxoG residues, and excises 7,8-dihydro-8-oxoguanine from damaged DNA. It has beta-lyase activity that nicks DNA 3' to the lesion.; GO: 0008534 oxidized purine base lesion DNA N-glycosylase activity, 0006281 DNA repair, 0005634 nucleus. Probab=42.66 E-value=24 Score=15.44 Aligned_cols=33 Identities=33% Similarity=0.516 Sum_probs=23.9 Q ss_pred HHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC Q ss_conf 99999982147861430277435555403468999999988860877 Q gi|254780355|r 286 HYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRF 332 (429) Q Consensus 286 ~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~ 332 (429) +|--+.| |=.|||- ||+.+.+.++.++++.+.. T Consensus 219 dfsfn~L------R~lG~GY--------RA~Yi~~tar~l~ee~~~~ 251 (379) T TIGR00588 219 DFSFNHL------RKLGLGY--------RARYIRETARALLEEQGGR 251 (379) T ss_pred CCCHHHH------HHCCCCC--------CCHHHHHHHHHHHHHCCCC T ss_conf 3462657------5248875--------4068999999988412664 No 61 >TIGR02123 TRAP_fused TRAP transporter, 4TM/12TM fusion protein; InterPro: IPR011853 In some species, the 12-transmembrane spanning and 4-transmembrane spanning components of tripartite ATP-independent periplasmic (TRAP)-type transporters are fused. This entry describes such transporters, found in the archaea and in bacteria.. Probab=42.29 E-value=10 Score=18.03 Aligned_cols=34 Identities=26% Similarity=0.188 Sum_probs=15.4 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHH-------HHHHHHCCCCHHH Q ss_conf 155554420565424677675542-------1002220352899 Q gi|254780355|r 235 TSTVRLAGSSGADPFACIAAGVAC-------LGGRAHGGANEEA 271 (429) Q Consensus 235 Tft~R~vaSt~adlysai~agi~a-------L~GPlHGGAne~v 271 (429) .+-.-+.+|+=|| .|++|.-+ -..|.--||-|++ T Consensus 225 al~G~~sGSsvAN---vVttG~fTIPlMKr~Gy~~~fAgAvEAa 265 (681) T TIGR02123 225 ALMGMISGSSVAN---VVTTGSFTIPLMKRAGYKPEFAGAVEAA 265 (681) T ss_pred HHHHHHHHHHHHH---HHHHHCCHHHHHHHCCCCCCCHHHHHHH T ss_conf 7887789999988---8852000035676377797741666887 No 62 >pfam02332 Phenol_Hydrox Methane/Phenol/Toluene Hydroxylase. Bacterial phenol hydroxylase is a multicomponent enzyme that catabolizes phenol and some of its methylated derivatives. This Pfam family contains both the P1 and P3 polypeptides of phenol hydroxylase and the alpha and beta chain of methane hydroxylase protein A. Probab=40.17 E-value=26 Score=15.19 Aligned_cols=105 Identities=23% Similarity=0.365 Sum_probs=59.6 Q ss_pred CCHHHHHHHHHHH--HEECCCCCC-CHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHH Q ss_conf 7969999987563--501367876-3015555442056542467767554210022203528999998621553512799 Q gi|254780355|r 211 VNPLLARAMNRIF--ILHADHEQN-ASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLERIPHY 287 (429) Q Consensus 211 ~~~~~~~ald~~L--ILhADHe~N-aSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~~~~v~~~ 287 (429) .+|...+.|-..| +-|+||+.+ ++.+.+|..-|+. =.|-.++.+++++.-.. ...+ T Consensus 67 l~~~w~~~l~~~l~~~~~~E~ga~~~~a~~~r~~~~~~--------------------~~n~~~~~a~DelR~~Q-~~~~ 125 (233) T pfam02332 67 LDPGWRETLKRHYGPLRYVEYGANMANAYIARFAPAPT--------------------IRNCATFQALDELRHLQ-RQAY 125 (233) T ss_pred CCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCHH--------------------HHHHHHHHHHHHHHHHH-HHHH T ss_conf 99999999999970121899999998999998658899--------------------99999998879999999-9999 Q ss_pred HHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH Q ss_conf 99998214786143027743555540346899999998886087765179999999 Q gi|254780355|r 288 IMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIEL 343 (429) Q Consensus 288 i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~l 343 (429) ....+.+..+ =++++||-+-..||--..+|+++++++... | +++....+ T Consensus 126 ~~~~l~~~~~--~~~~~~k~~w~~dp~wq~~R~~~E~~~~~~----D-w~E~~va~ 174 (233) T pfam02332 126 FLHELAKADP--DFDWGQRAYWTNDPAWQGLRRLFEDILVTQ----D-WVEAFIAL 174 (233) T ss_pred HHHHHHHCCC--CCCHHHHHHHHHCCHHHHHHHHHHHHHHHC----C-HHHHHHHH T ss_conf 9987752288--868489998861833789999999888607----8-99999999 No 63 >pfam00591 Glycos_transf_3 Glycosyl transferase family, a/b domain. This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate. Probab=39.89 E-value=24 Score=15.35 Aligned_cols=10 Identities=20% Similarity=0.567 Sum_probs=4.1 Q ss_pred HHHHEECCCC Q ss_conf 5635013678 Q gi|254780355|r 221 RIFILHADHE 230 (429) Q Consensus 221 ~~LILhADHe 230 (429) ..||.|-+-| T Consensus 143 ~a~vV~g~dG 152 (254) T pfam00591 143 RALVVHGGDG 152 (254) T ss_pred EEEEEECCCC T ss_conf 5899971799 No 64 >COG0343 Tgt Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis] Probab=39.75 E-value=17 Score=16.40 Aligned_cols=23 Identities=22% Similarity=0.278 Sum_probs=15.0 Q ss_pred HHHHHHHHHCCCCCEEECCCCCC Q ss_conf 79999998214786143027743 Q gi|254780355|r 285 PHYIMRAKDKNDPFRIMGFGHRV 307 (429) Q Consensus 285 ~~~i~~~~~~~~~~ri~GfGHrv 307 (429) -.++...+-.+++..+||.||+. T Consensus 225 l~~~~~~Lp~~kPryLmGvG~P~ 247 (372) T COG0343 225 LEATKPLLPEDKPRYLMGVGHPE 247 (372) T ss_pred HHHHHCCCCCCCCEEEECCCCHH T ss_conf 99864008999987755687989 No 65 >KOG0138 consensus Probab=39.31 E-value=27 Score=15.10 Aligned_cols=49 Identities=24% Similarity=0.311 Sum_probs=33.6 Q ss_pred HCCCCCHHHHHHHH-HHHHHHHHHCCCCHHHHHHHHH-------CCCCCHHHHHHHHHH Q ss_conf 20565424677675-5421002220352899999862-------155351279999998 Q gi|254780355|r 242 GSSGADPFACIAAG-VACLGGRAHGGANEEALNMLME-------IGSLERIPHYIMRAK 292 (429) Q Consensus 242 aSt~adlysai~ag-i~aL~GPlHGGAne~v~~ml~~-------I~~~~~v~~~i~~~~ 292 (429) +++..+|+.|+.-+ ++--|||+ ||.|.|++|-.. .|.|-...+.+.+.+ T Consensus 276 ~~s~qgpf~cLnnaR~giAWg~l--Gase~c~~~arqY~ldRkQFG~PLAanQL~Q~Kl 332 (432) T KOG0138 276 ASSLQGPFGCLNNARYGIAWGAL--GASEFCLHTARQYTLDRKQFGRPLAANQLIQKKL 332 (432) T ss_pred CCCCCCCHHHHHHHHHHEEEHHC--HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH T ss_conf 31137836555333441010002--0678999999999888887587126778999999 No 66 >PRK00112 tgt queuine tRNA-ribosyltransferase; Provisional Probab=37.89 E-value=22 Score=15.67 Aligned_cols=50 Identities=34% Similarity=0.424 Sum_probs=26.6 Q ss_pred HHHHHHHCCCCHHH----HHHHHH-------CC--C---C-C---HHHHHHHHHHHCCCCCEEECCCCCC Q ss_conf 21002220352899----999862-------15--5---3-5---1279999998214786143027743 Q gi|254780355|r 258 CLGGRAHGGANEEA----LNMLME-------IG--S---L-E---RIPHYIMRAKDKNDPFRIMGFGHRV 307 (429) Q Consensus 258 aL~GPlHGGAne~v----~~ml~~-------I~--~---~-~---~v~~~i~~~~~~~~~~ri~GfGHrv 307 (429) +|+|+.+||-.+.. .+-+.+ || + + + ++-+++...+..+++.-|||-||+. T Consensus 183 ~lfgiVQGG~~~dLR~~Sa~~l~~~~f~G~aIGGlsvGe~~~~~~~il~~~~~~LP~~kPryLmGvG~P~ 252 (366) T PRK00112 183 ALFGIVQGGVYEDLREESAKGLVEIDFDGYAIGGLSVGEPKEEMYRILEHTAPLLPEDKPRYLMGVGTPE 252 (366) T ss_pred EEEEEECCCCCHHHHHHHHHHHHHCCCCEEECCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCHH T ss_conf 3887415766799999999999848984885467456778999999999987448877755653589989 No 67 >KOG0205 consensus Probab=37.73 E-value=18 Score=16.24 Aligned_cols=63 Identities=22% Similarity=0.290 Sum_probs=37.1 Q ss_pred CCCEEEEEECCEEEE--EE-EE-C---------------CCCCCCCEEECC---CC--C---CCEEEECCCCCCEEEEEE Q ss_conf 987699998998999--75-23-0---------------777875101001---15--5---861898888786238787 Q gi|254780355|r 2 TDKFAKLHLGHEEID--LP-IK-E---------------GSLGSSVLDISF---LH--K---NGIFTYDPAFSSTASCKS 54 (429) Q Consensus 2 ~~~~~~l~~~~~~~~--lp-i~-~---------------~~~~~~~~d~~~---l~--~---~G~~~~dpG~~~ta~ceS 54 (429) |||+.|||.|.-+.+ || +. + .-+|.++||-.- |. + .|+...+===.|-.+-++ T Consensus 332 SDKTGTLTlNkLSvdknl~ev~v~gv~~D~~~L~A~rAsr~en~DAID~A~v~~L~dPKeara~ikevhF~PFnPV~Krt 411 (942) T KOG0205 332 SDKTGTLTLNKLSVDKNLIEVFVKGVDKDDVLLTAARASRKENQDAIDAAIVGMLADPKEARAGIKEVHFLPFNPVDKRT 411 (942) T ss_pred ECCCCCEEECCEECCCCCCEEEECCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCHHHHHHCCEEEEECCCCCCCCCE T ss_conf 26867156300303767642452678866889999988644272168899998735978886086589513678645305 Q ss_pred EEEEEECCCC Q ss_conf 5654334477 Q gi|254780355|r 55 KITFIDGNNG 64 (429) Q Consensus 55 ~IT~IDG~~G 64 (429) ++||||++-- T Consensus 412 a~ty~d~dG~ 421 (942) T KOG0205 412 ALTYIDPDGN 421 (942) T ss_pred EEEEECCCCC T ss_conf 7999989997 No 68 >PRK11780 isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional Probab=33.78 E-value=7 Score=19.11 Aligned_cols=75 Identities=19% Similarity=0.301 Sum_probs=41.3 Q ss_pred CCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHC Q ss_conf 993199997508989999999818799989999999988640689989999998512476525789999999875206 Q gi|254780355|r 69 RGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYY 146 (429) Q Consensus 69 RGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~p~~ahPM~~L~~~vsaL~a~~~ 146 (429) || +|.+|++ .+-++--.|++=|-.--+.-|.+|..+- ....+.++|.++++.|-...-|+..++.+-..++..++ T Consensus 72 RG-~I~~l~~-~~~~d~DaLI~PGGfGaAKNLs~fA~~G-~~~~V~p~V~~~i~~f~~a~KPiG~iCIaP~l~a~vl~ 146 (217) T PRK11780 72 RG-EIKDLAE-ADAEDFDALIVPGGFGAAKNLSNFAFKG-AECSVDPEVKALARAFHQAGKPIGFICIAPAMLPKILG 146 (217) T ss_pred CC-CCCCHHH-CCHHHCCEEEECCCCHHHHCCCCHHHCC-CCCEECHHHHHHHHHHHHHCCCEEEECHHHHHHHHHCC T ss_conf 15-8667456-9975678799678620443110165349-98648789999999999809998986076899999728 No 69 >PRK09130 NADH dehydrogenase subunit G; Validated Probab=33.75 E-value=32 Score=14.51 Aligned_cols=17 Identities=12% Similarity=0.257 Sum_probs=12.5 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 99999989999999997 Q gi|254780355|r 384 FAVARTAGWVSQWTEMI 400 (429) Q Consensus 384 Fa~~R~~Gw~AH~~Eq~ 400 (429) =.|||..--||.+-... T Consensus 660 ~~Isr~S~tM~~cs~~~ 676 (680) T PRK09130 660 NPIARASATMAECSALA 676 (680) T ss_pred CHHHHCCHHHHHHHHHH T ss_conf 77666029999988554 No 70 >TIGR02335 hydr_PhnA phosphonoacetate hydrolase; InterPro: IPR012710 This family consists of examples of phosphonoacetate hydrolase, an enzyme specific for the cleavage of the C-P bond in phosphonoacetate. Phosphonates are organic compounds with a direct C-P bond that is far less labile than the C-O-P bonds of phosphate attachment sites. Phosphonates may be degraded for phosphorus and energy by broad spectrum C-P lyase encoded by a large operon or by specific enzymes for some of the more common phosphonates in nature. This family represents an enzyme from the latter category. It may be found encoded near genes for phosphonate transport and for other specific phosphonatases .. Probab=33.47 E-value=30 Score=14.74 Aligned_cols=44 Identities=20% Similarity=0.317 Sum_probs=22.3 Q ss_pred EEEEEECCE--EE-EEEEECCCCCCCCEEECCCCCCCEEE----ECCCCCCEEEE Q ss_conf 699998998--99-97523077787510100115586189----88887862387 Q gi|254780355|r 5 FAKLHLGHE--EI-DLPIKEGSLGSSVLDISFLHKNGIFT----YDPAFSSTASC 52 (429) Q Consensus 5 ~~~l~~~~~--~~-~lpi~~~~~~~~~~d~~~l~~~G~~~----~dpG~~~ta~c 52 (429) ++.+|+||. || +=-|-+|.. |. |..|.+.|+.. -=|.|+||=-. T Consensus 15 tvViC~DGcdpEYi~rgIadGv~-P~---ia~l~~~G~v~tadcvvPsfTNpNN~ 65 (408) T TIGR02335 15 TVVICVDGCDPEYIERGIADGVL-PA---IAELTEAGYVATADCVVPSFTNPNNV 65 (408) T ss_pred EEEEEECCCCHHHHHHHHHCCCC-CH---HHHHHCCCCEEEECCCCCCCCCCCCE T ss_conf 79998159887899988750666-15---88875078035540012776688870 No 71 >TIGR01495 ETRAMP early transcribed membrane protein (ETRAMP) family; InterPro: IPR006389 These sequences represent a family of proteins from the malaria parasite Plasmodium falciparum, several of which have been shown to be expressed specifically in the ring stage as well as the rodent parasite Plasmodium yoelii . A homolog from Plasmodium chabaudi was localized to the parasitophorous vacuole membrane . Members have an initial hydrophobic, Phe/Tyr-rich stretch long enough to span the membrane, a highly charged region rich in Lys, a second putative transmembrane region, and a second highly charged, low complexity sequence region. Some members have up to 100 residues of additional C-terminal sequence. These genes have been shown to be found in the sub-telomeric regions of both Plasmodium falciparum and P. yoelii chromosomes.. Probab=32.73 E-value=21 Score=15.75 Aligned_cols=14 Identities=43% Similarity=0.669 Sum_probs=9.7 Q ss_pred HHH-HHHHHHHHHHH Q ss_conf 246-77675542100 Q gi|254780355|r 248 PFA-CIAAGVACLGG 261 (429) Q Consensus 248 lys-ai~agi~aL~G 261 (429) +|| +|++||++|-| T Consensus 66 lySl~~as~lAlL~g 80 (99) T TIGR01495 66 LYSLSIASGLALLVG 80 (99) T ss_pred HHHHHHHHHHHHHHH T ss_conf 998999999999999 No 72 >KOG0898 consensus Probab=32.04 E-value=34 Score=14.33 Aligned_cols=24 Identities=25% Similarity=0.418 Sum_probs=19.9 Q ss_pred EEECCEEHHHHHHHCCHHHHHHHHH Q ss_conf 8989931999975089899999998 Q gi|254780355|r 66 LLYRGYPIEQLSEKSDFLEVCYLLL 90 (429) Q Consensus 66 L~YRGY~IedLa~~~sFeEVayLLl 90 (429) ..|||.+.++|.+ -++|+.+-|.- T Consensus 22 ftyrGVdld~Lld-ms~~~~~~l~~ 45 (152) T KOG0898 22 FTYRGVDLDQLLD-MSTEQLVKLFP 45 (152) T ss_pred CCCCCCCHHHHHC-CCHHHHHHHHH T ss_conf 0125778899864-77999999878 No 73 >TIGR01851 argC_other N-acetyl-gamma-glutamyl-phosphate reductase; InterPro: IPR010136 N -Acetylglutamate (NAG) fulfils distinct biological roles in lower and higher organisms. In prokaryotes, lower eukaryotes and plants it is the first intermediate in the biosynthesis of arginine, whereas in ureotelic (excreting nitrogen mostly in the form of urea) vertebrates, it is an essential allosteric cofactor for carbamyl phosphate synthetase I (CPSI), the first enzyme of the urea cycle. The pathway that leads from glutamate to arginine in lower organisms employs eight steps, starting with the acetylation of glutamate to form NAG. In these species, NAG can be produced by two enzymatic reactions: one catalysed by NAG synthase (NAGS) and the other by ornithine acetyltransferase (OAT). In ureotelic species, NAG is produced exclusively by NAGS. In lower organisms, NAGS is feedback-inhibited by L-arginine, whereas mammalian NAGS activity is significantly enhanced by this amino acid. The NAGS genes of bacteria, fungi and mammals are more diverse than other arginine-biosynthesis and urea-cycle genes. The evolutionary relationship between the distinctly different roles of NAG and its metabolism in lower and higher organisms remains to be determined . The pathway from glutamate to arginine is: NAGS; N-acetylglutamate synthase (2.3.1.1 from EC) (glutamate to N-acetylglutamate) NAGK; N-acetylglutamate kinase (2.7.2.8 from EC) (N-acetylglutamate to N-acetylglutamate-5P) NAGSA; N-acetyl-gamma-glutamyl-phosphate reductase (1.2.1.38 from EC) (N-acetylglutamate-5P to N-acetylglumate semialdehyde) Acetylornithine aminotransferase (2.6.1.11 from EC) (N-acetylglumate semialdehyde to N-acetylornithine) Acetylornithine deacetylase (3.5.1.16 from EC) (N-acetylornithine to ornithine) Arginase (3.5.3.1 from EC) (ornithine to arginine) This entry represents bacterial N-acetyl-gamma-glutamyl-phosphate reductases, an enzyme catalysing the third step of arginine biosynthesis from glutamate.; GO: 0003942 N-acetyl-gamma-glutamyl-phosphate reductase activity, 0006526 arginine biosynthetic process, 0005737 cytoplasm. Probab=31.96 E-value=7.5 Score=18.89 Aligned_cols=22 Identities=45% Similarity=0.685 Sum_probs=16.3 Q ss_pred EEECCCCE--EEECCEEHHHHHHHCCHH Q ss_conf 43344777--898993199997508989 Q gi|254780355|r 58 FIDGNNGI--LLYRGYPIEQLSEKSDFL 83 (429) Q Consensus 58 ~IDG~~G~--L~YRGY~IedLa~~~sFe 83 (429) |||||+|. |+-|-| |+++.+.| T Consensus 5 FiDGeaGTTGLqi~~r----L~~R~Dle 28 (314) T TIGR01851 5 FIDGEAGTTGLQIRER----LSGRDDLE 28 (314) T ss_pred EECCCCCCHHHHHHHH----HCCCCCHH T ss_conf 6417888626789886----24776200 No 74 >PRK10624 L-1,2-propanediol oxidoreductase; Provisional Probab=31.49 E-value=35 Score=14.27 Aligned_cols=48 Identities=17% Similarity=0.057 Sum_probs=34.6 Q ss_pred CCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCC Q ss_conf 630155554420565424677675542100222035289999986215 Q gi|254780355|r 232 NASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIG 279 (429) Q Consensus 232 NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~ 279 (429) ++|+.+.....+++...--+++-+|+++.+--||-++--++--.-+.. T Consensus 243 ~as~lag~a~~~~g~g~~Hal~h~lg~~~~vpHG~~~aillP~v~~~n 290 (381) T PRK10624 243 LGQYVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYN 290 (381) T ss_pred HHHHHHHHHHCCCCCCCHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHH T ss_conf 999999777616452111304465344756770888898779999986 No 75 >pfam01795 Methyltransf_5 MraW methylase family. Members of this family are probably SAM dependent methyltransferases based on Escherichia coli mraW. This family appears to be related to pfam01596. Probab=31.43 E-value=35 Score=14.26 Aligned_cols=55 Identities=5% Similarity=0.035 Sum_probs=36.1 Q ss_pred CCEEHHHHHHHCCHHHHHHHHH-CCCCCCHHHHHHHHHHHHHCCCC--CHHHHHHHHH Q ss_conf 9931999975089899999998-18799989999999988640689--9899999985 Q gi|254780355|r 69 RGYPIEQLSEKSDFLEVCYLLL-HGELANVSQQKDFNDKISRHALL--NENMSRFFMG 123 (429) Q Consensus 69 RGY~IedLa~~~sFeEVayLLl-~GeLPt~~el~~F~~~l~~~~~l--pe~v~~~i~~ 123 (429) .|.++.|+.++.+-+|.+.+|+ |||.+.+...+..--+-++...+ ..++.+++.. T Consensus 131 ~~~tA~~iln~~~e~eL~~il~~yGEe~~a~~IA~~Iv~~R~~~~i~tT~~L~~iI~~ 188 (310) T pfam01795 131 AGLTAAEVLNTYSEEDLARIFKKYGEERFSKRIARAIVERRKKKPIETTKELAEIIKK 188 (310) T ss_pred CCCCHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH T ss_conf 9984999985089999999999857745699999999999986277779999999998 No 76 >TIGR01245 trpD anthranilate phosphoribosyltransferase; InterPro: IPR005940 In many widely different species, including Escherichia coli, Thermotoga maritima, and Archaeoglobus fulgidus, this enzyme is a C-terminal part of a multifunctional protein together with glutamine amidotransferase; the fusion protein is designated anthranilate synthase component II (4.1.3.27 from EC).; GO: 0004048 anthranilate phosphoribosyltransferase activity, 0000162 tryptophan biosynthetic process. Probab=31.12 E-value=21 Score=15.74 Aligned_cols=17 Identities=29% Similarity=0.370 Sum_probs=10.0 Q ss_pred CCCCHHHHHHHHHCCCC Q ss_conf 87630155554420565 Q gi|254780355|r 230 EQNASTSTVRLAGSSGA 246 (429) Q Consensus 230 e~NaSTft~R~vaSt~a 246 (429) -+|.||.++-|+|+.|. T Consensus 84 T~NiST~sAfVaAaaGv 100 (331) T TIGR01245 84 TINISTASAFVAAAAGV 100 (331) T ss_pred CCHHHHHHHHHHHHCCC T ss_conf 11166899999985678 No 77 >pfam01702 TGT Queuine tRNA-ribosyltransferase. This is a family of queuine tRNA-ribosyltransferases EC:2.4.2.29, also known as tRNA-guanine transglycosylase and guanine insertion enzyme. Queuine tRNA-ribosyltransferase modifies tRNAs for asparagine, aspartic acid, histidine and tyrosine with queuine. It catalyses the exchange of guanine-34 at the wobble position with 7-aminomethyl-7-deazaguanine, and the addition of a cyclopentenediol moiety to 7-aminomethyl-7-deazaguanine-34 tRNA; giving a hypermodified base queuine in the wobble position. The aligned region contains a zinc binding motif C-x-C-x2-C-x29-H, and important tRNA and 7-aminomethyl-7deazaguanine binding residues. Probab=30.89 E-value=31 Score=14.67 Aligned_cols=50 Identities=28% Similarity=0.405 Sum_probs=24.0 Q ss_pred HHHHHHHCCCCHH----HHHHHHH-------CCC------CCHH---HHHHHHHHHCCCCCEEECCCCCC Q ss_conf 2100222035289----9999862-------155------3512---79999998214786143027743 Q gi|254780355|r 258 CLGGRAHGGANEE----ALNMLME-------IGS------LERI---PHYIMRAKDKNDPFRIMGFGHRV 307 (429) Q Consensus 258 aL~GPlHGGAne~----v~~ml~~-------I~~------~~~v---~~~i~~~~~~~~~~ri~GfGHrv 307 (429) +|.||.+||-... +.+.+.+ ||. .++. -+++...+..+++.-|||.||+. T Consensus 56 ~lfgivqGG~~~dlR~~s~~~l~~~~~~GyaIgGl~~ge~~~~~~~~l~~~~~~Lp~~kPr~l~G~g~P~ 125 (238) T pfam01702 56 ALFGIVQGGLYEDLREESAEELAELDFDGYAIGGLSVGEEKEEMLELVDAVTPLLPEDKPRYLMGVGTPE 125 (238) T ss_pred EEEEEECCCCCHHHHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCEEECCCCCHH T ss_conf 6996157979899999999997448998798568777889999999999998558877856406999999 No 78 >PRK13222 phosphoglycolate phosphatase; Provisional Probab=30.81 E-value=35 Score=14.30 Aligned_cols=77 Identities=18% Similarity=0.195 Sum_probs=39.1 Q ss_pred CCCCCCHHHH-HHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHH-H--CCCCC Q ss_conf 1014796999-998756350136787630155554420565424677675542100222035289999986-2--15535 Q gi|254780355|r 207 AEYQVNPLLA-RAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLM-E--IGSLE 282 (429) Q Consensus 207 ~~~~~~~~~~-~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~-~--I~~~~ 282 (429) ...+|+|..- ++++++ +.++ .-+-+|+-|..|+-+|-.||+-+. |-..|-.....++... + |.+.. T Consensus 146 ~~~KP~P~~~~~a~~~l-------g~~p--~e~l~VGDs~~Di~aA~~aG~~~i-~v~~G~~~~~~l~~~~ad~vi~~~~ 215 (228) T PRK13222 146 PNKKPDPAPLLLACEKL-------GIDP--EQMLFVGDSRNDIQAAKAAGCPSV-GVTYGYNYGEDIALSEPDVVIDHFA 215 (228) T ss_pred CCCCCCHHHHHHHHHHC-------CCCC--CCEEEEECCHHHHHHHHHCCCEEE-EECCCCCCHHHHHHCCCCEEECCHH T ss_conf 77787869999999981-------9793--434898068889999999699499-9878999977897689999989999 Q ss_pred HHHHHHHHHHH Q ss_conf 12799999982 Q gi|254780355|r 283 RIPHYIMRAKD 293 (429) Q Consensus 283 ~v~~~i~~~~~ 293 (429) +..+++-=++. T Consensus 216 eL~~~Lg~~~~ 226 (228) T PRK13222 216 ELLPALGLALS 226 (228) T ss_pred HHHHHHCHHCC T ss_conf 99998553202 No 79 >TIGR02358 thia_cytX probable hydroxymethylpyrimidine transporter CytX; InterPro: IPR012732 On the basis of a phylogenomic study of thiamine biosynthetic, salvage, and transporter genes and a highly conserved RNA element THI, this protein family has been identified as a probable transporter of hydroxymethylpyrimidine (HMP). ThiD phosphorylates hydroxymethylpyrimidine and when joined (by ThiE) to hydroxyethylthiazole phosphate creates thiamine phosphate.. Probab=29.76 E-value=37 Score=14.07 Aligned_cols=15 Identities=0% Similarity=-0.026 Sum_probs=5.4 Q ss_pred HHHHHCCCCCCCCCC Q ss_conf 999727985348886 Q gi|254780355|r 175 IYKYSIGQPFVYPRS 189 (429) Q Consensus 175 ~yr~~~G~~~i~Pd~ 189 (429) ++.....-+...|+- T Consensus 164 ~F~k~~~~e~~~~~G 178 (415) T TIGR02358 164 VFSKASLSELWNREG 178 (415) T ss_pred HHHCCCCCCEECCCC T ss_conf 983568550004688 No 80 >cd03133 GATase1_ES1 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1. Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1. This group includes, proteins similar to ES1, Escherichia coli enhancing lycopene biosynthesis protein 2, Azospirillum brasilense iaaC and, human HES1. The catalytic triad typical of GATase1domains is not conserved in this GATase1-like domain. However, in common with GATase1domains a reactive cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. Zebrafish ES1 is expressed specifically in adult photoreceptor cells and appears to be a cytoplasmic protein. A. brasilense iaaC is involved in controlling IAA biosynthesis. Probab=29.24 E-value=8.4 Score=18.55 Aligned_cols=75 Identities=19% Similarity=0.289 Sum_probs=36.2 Q ss_pred CCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHC Q ss_conf 993199997508989999999818799989999999988640689989999998512476525789999999875206 Q gi|254780355|r 69 RGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALLNENMSRFFMGFPSSAHPMAMLVSAVGALSSFYY 146 (429) Q Consensus 69 RGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~~~i~~~p~~ahPM~~L~~~vsaL~a~~~ 146 (429) || +|.+|.+ .+-++--.|++=|-.--+.-|.+|..+- ....+.++|.++++.|-...-|+..++.+-..++..++ T Consensus 69 RG-~I~~l~~-~~~~d~DaLiiPGGfGaAKNLs~fA~~g-~~~~v~~~V~~~i~~f~~a~KPiG~iCIAP~l~a~vl~ 143 (213) T cd03133 69 RG-NIKDLAK-LKAADFDALIFPGGFGAAKNLSDFAVKG-ADCTVNPEVERLVREFHQAGKPIGAICIAPALAAKILG 143 (213) T ss_pred CC-CCCCHHH-CCHHHCCEEEECCCHHHHHHHHHHHCCC-CCCEECHHHHHHHHHHHHCCCCEEEECHHHHHHHHHCC T ss_conf 25-8556456-9986789899788514555310021058-87569899999999999849999997578999999818 No 81 >PRK02955 small acid-soluble spore protein SspI; Provisional Probab=29.18 E-value=26 Score=15.12 Aligned_cols=27 Identities=22% Similarity=0.306 Sum_probs=22.4 Q ss_pred CCCCHHHHHHHHHHHCCCCCEEECCCC Q ss_conf 553512799999982147861430277 Q gi|254780355|r 279 GSLERIPHYIMRAKDKNDPFRIMGFGH 305 (429) Q Consensus 279 ~~~~~v~~~i~~~~~~~~~~ri~GfGH 305 (429) .+.+.+++.|..+..+++..-|||.|- T Consensus 16 ~s~~elk~tI~daI~sgEEk~LPGLGV 42 (69) T PRK02955 16 NSQEQLEETIVDAIQSGEEKMLPGLGV 42 (69) T ss_pred CCHHHHHHHHHHHHHCCCHHCCCCCHH T ss_conf 999999999999986463013774067 No 82 >COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair] Probab=28.65 E-value=39 Score=13.94 Aligned_cols=16 Identities=25% Similarity=0.752 Sum_probs=7.0 Q ss_pred EECCCCCCCCCCCHHH Q ss_conf 4302774355554034 Q gi|254780355|r 300 IMGFGHRVYRNHDPRC 315 (429) Q Consensus 300 i~GfGHrvyk~~DPRa 315 (429) +-+||-.+-+...||. T Consensus 179 lI~~GR~iC~ar~P~C 194 (211) T COG0177 179 LILHGRYICKARKPRC 194 (211) T ss_pred HHHHHHHHCCCCCCCC T ss_conf 9996053116899986 No 83 >TIGR03092 SASP_sspI small, acid-soluble spore protein I. This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. It is a minor SASP (small, acid-soluble spore protein) designated SspI. The gene in Bacillus subtilis previously was designated ysfA. Probab=27.83 E-value=29 Score=14.84 Aligned_cols=27 Identities=19% Similarity=0.277 Sum_probs=22.3 Q ss_pred CCCCHHHHHHHHHHHCCCCCEEECCCC Q ss_conf 553512799999982147861430277 Q gi|254780355|r 279 GSLERIPHYIMRAKDKNDPFRIMGFGH 305 (429) Q Consensus 279 ~~~~~v~~~i~~~~~~~~~~ri~GfGH 305 (429) .+.+.+++.|..+..+++..-|||.|- T Consensus 13 ~s~~elk~tI~daI~sgEEk~LPGLGV 39 (65) T TIGR03092 13 NTKEQLEATIVDAIQSGEEKMLPGLGV 39 (65) T ss_pred CCHHHHHHHHHHHHHCCCHHCCCCCHH T ss_conf 999999999999986473003774067 No 84 >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=27.83 E-value=38 Score=14.02 Aligned_cols=43 Identities=19% Similarity=0.166 Sum_probs=26.3 Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHH---CCCCCHHHHHHHHHHH Q ss_conf 776755421002220352899999862---1553512799999982 Q gi|254780355|r 251 CIAAGVACLGGRAHGGANEEALNMLME---IGSLERIPHYIMRAKD 293 (429) Q Consensus 251 ai~agi~aL~GPlHGGAne~v~~ml~~---I~~~~~v~~~i~~~~~ 293 (429) ++.+-+|.-||||-|=|=-++-..+.+ +-++++..+.++.-++ T Consensus 64 ~LiS~VGGASGPLYGT~Fl~as~a~~~~~~~~~~~~l~~~l~~g~~ 109 (200) T TIGR02365 64 ALISKVGGASGPLYGTAFLKASKALKDKEEILDAEDLAEILEAGLE 109 (200) T ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH T ss_conf 8852203201577999999999986230126898899999999999 No 85 >TIGR02344 chap_CCT_gamma T-complex protein 1, gamma subunit; InterPro: IPR012719 The TCP-1 protein , (Tailless Complex Polypeptide 1) was first identified in mice where it is especially abundant in testis but present in all cell types. It has since been found and characterised in many other animal species, as well as in yeast, plants and protists. TCP-1 is a highly conserved protein of about 60 kDa (556 to 560 residues) which participates in a hetero-oligomeric 900 kDa double-torus shaped particle with 6 to 8 other different subunits. These subunits, the chaperonin containing TCP-1 (CCT) subunit beta, gamma, delta, epsilon, zeta and eta are evolutionary related to TCP-1 itself , . The CCT is known to act as a molecular chaperone for tubulin, actin and probably some other proteins. The TCP-1 family of proteins are weakly, but significantly , related to the cpn60/groEL chaperonin family (see IPR001844 from INTERPRO). Proteins in this entry consist exclusively of the CCT gamma chain from animals, plants, fungi, and other eukaryotes.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding. Probab=27.77 E-value=40 Score=13.84 Aligned_cols=56 Identities=23% Similarity=0.319 Sum_probs=24.9 Q ss_pred CCCCCCC---CCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 7743555---5403468999999988860877651799999999999611531457987784 Q gi|254780355|r 304 GHRVYRN---HDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNV 362 (429) Q Consensus 304 GHrvyk~---~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~pNv 362 (429) ||.+.|. .-|=|+-|-++++--=||.|.-.....=+|-|+=.. .+.|.++++||-| T Consensus 58 GnaILREi~v~HPAAKSmiElsR~qDEEVGDGTTSViiLAGE~L~~---A~~f~~~~iHP~i 116 (527) T TIGR02344 58 GNAILREIDVAHPAAKSMIELSRTQDEEVGDGTTSVIILAGEMLSA---AEPFLEQNIHPTI 116 (527) T ss_pred CCEEEEEEECCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH---HHHHHHCCCCCEE T ss_conf 8657755312785245688762145741257502123446899999---9998723899665 No 86 >TIGR03233 DNA_S_dndB DNA sulfur modification protein DndB. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndB is described as a putative ATPase. Probab=27.20 E-value=34 Score=14.36 Aligned_cols=48 Identities=15% Similarity=0.249 Sum_probs=20.0 Q ss_pred ECCEEHHHHHH-HCCH-HHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHH Q ss_conf 89931999975-0898-9999999818799989999999988640689989 Q gi|254780355|r 68 YRGYPIEQLSE-KSDF-LEVCYLLLHGELANVSQQKDFNDKISRHALLNEN 116 (429) Q Consensus 68 YRGY~IedLa~-~~sF-eEVayLLl~GeLPt~~el~~F~~~l~~~~~lpe~ 116 (429) +|-.-||+.-+ +-.. .|..-.+++-+. .=++.+.+-.+|.++..-|.. T Consensus 113 HRraaIe~al~~~p~l~~e~I~Vv~f~d~-gL~r~QQmFaDlN~~a~kPs~ 162 (355) T TIGR03233 113 HRRAAIEEALKEDPELGDETISVVFFHDK-GLERSQQMFADLNRHAVKPSS 162 (355) T ss_pred HHHHHHHHHHHHCCCCCCCCEEEEEEECC-CHHHHHHHHHHHHHCCCCCCH T ss_conf 78999999986296656684459998448-788999999998844688817 No 87 >PRK09860 putative alcohol dehydrogenase; Provisional Probab=27.08 E-value=41 Score=13.76 Aligned_cols=55 Identities=13% Similarity=-0.012 Sum_probs=36.1 Q ss_pred CCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHH Q ss_conf 6301555544205654246776755421002220352899999862155351279 Q gi|254780355|r 232 NASTSTVRLAGSSGADPFACIAAGVACLGGRAHGGANEEALNMLMEIGSLERIPH 286 (429) Q Consensus 232 NaSTft~R~vaSt~adlysai~agi~aL~GPlHGGAne~v~~ml~~I~~~~~v~~ 286 (429) .+|+.+.....+++..+--+++-.|++.++--||-+|--.+--..+.......++ T Consensus 245 ~as~lag~a~~~~~~g~~Hai~h~lg~~~~vpHG~~~aillP~v~~~n~~~~~~r 299 (383) T PRK09860 245 YAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAAR 299 (383) T ss_pred HHHHHHHHHHCCCCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999986689953000323302113087759999999999999834314899 No 88 >KOG0962 consensus Probab=26.86 E-value=42 Score=13.73 Aligned_cols=56 Identities=30% Similarity=0.362 Sum_probs=43.0 Q ss_pred CCEEEECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHH Q ss_conf 86189888878623878756543344777898993199997508989999999818799989999999 Q gi|254780355|r 37 NGIFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFN 104 (429) Q Consensus 37 ~G~~~~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~ 104 (429) .|+++||+-=.+|.---|-.|.|+|.+|- .+-||.|..---.+|+||.-.--..|- T Consensus 10 ~GIRSf~~~d~~~i~F~sPlTLIvG~NG~------------GKTTiIEcLKyatTG~lPpnsk~~~Fi 65 (1294) T KOG0962 10 RGIRSFDDKDRNTIEFFSPLTLIVGANGT------------GKTTIIECLKYATTGELPPNSKGGSFI 65 (1294) T ss_pred HCCCCCCCCCCCEEEECCCEEEEECCCCC------------CCHHHHHHHHHHHCCCCCCCCCCCCCC T ss_conf 21014687665536511770567668887------------716699998888648489987677777 No 89 >KOG0193 consensus Probab=26.72 E-value=21 Score=15.74 Aligned_cols=63 Identities=17% Similarity=0.142 Sum_probs=41.1 Q ss_pred EECCEEHHHHH-----HHCCHHHHHHHHHCC---------CCCCHHHHHHHHHHHHHCCC-CCHHHHHHHHHHCCCCC Q ss_conf 98993199997-----508989999999818---------79998999999998864068-99899999985124765 Q gi|254780355|r 67 LYRGYPIEQLS-----EKSDFLEVCYLLLHG---------ELANVSQQKDFNDKISRHAL-LNENMSRFFMGFPSSAH 129 (429) Q Consensus 67 ~YRGY~IedLa-----~~~sFeEVayLLl~G---------eLPt~~el~~F~~~l~~~~~-lpe~v~~~i~~~p~~ah 129 (429) .|--.+++|+- ..-+|--|--=.||| +-||++|+++|+.+++..+. =|+++.-++..+-...+ T Consensus 385 ~~WeIp~~ev~l~~rIGsGsFGtV~Rg~whGdVAVK~Lnv~~pt~~qlqaFKnEVa~lkkTRH~NIlLFMG~~~~p~~ 462 (678) T KOG0193 385 EEWEIPPEEVLLGERIGSGSFGTVYRGRWHGDVAVKLLNVDDPTPEQLQAFKNEVAVLKKTRHENILLFMGACMNPPL 462 (678) T ss_pred CCCCCCHHHHHCCCEECCCCCCCEEECCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHCCHHHHEEEEHHHCCCCE T ss_conf 121468778510340046654115641040423799981578999999999999998752121120111121148860 No 90 >TIGR02815 agaS_fam putative sugar isomerase, AgaS family; InterPro: IPR014180 Some members of this protein family are found in genic regions associated with N-acetyl-galactosamine and galactosamine utilisation and are suggested to be isomerases.. Probab=26.60 E-value=24 Score=15.40 Aligned_cols=19 Identities=37% Similarity=0.323 Sum_probs=16.8 Q ss_pred HHHHHHCCCCHHHHHHHHH Q ss_conf 1002220352899999862 Q gi|254780355|r 259 LGGRAHGGANEEALNMLME 277 (429) Q Consensus 259 L~GPlHGGAne~v~~ml~~ 277 (429) -||++.|-|-|.++|+|+= T Consensus 223 GSGgl~GlA~EsALK~LEL 241 (374) T TIGR02815 223 GSGGLQGLARESALKVLEL 241 (374) T ss_pred CCCHHHHHHHHHHHHHHHH T ss_conf 8851368998876776643 No 91 >TIGR02044 CueR Cu(I)-responsive transcriptional regulator; InterPro: IPR011789 This entry represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system . 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-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue .; GO: 0003677 DNA binding, 0005507 copper ion binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription. Probab=26.55 E-value=42 Score=13.70 Aligned_cols=50 Identities=14% Similarity=0.191 Sum_probs=22.6 Q ss_pred CCHHHHHHHH--HCCCCC--------CHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCC Q ss_conf 8989999999--818799--------9899999999886406899899999985124765 Q gi|254780355|r 80 SDFLEVCYLL--LHGELA--------NVSQQKDFNDKISRHALLNENMSRFFMGFPSSAH 129 (429) Q Consensus 80 ~sFeEVayLL--l~GeLP--------t~~el~~F~~~l~~~~~lpe~v~~~i~~~p~~ah 129 (429) .|.||+--|| ||..== |-+.+++...+|.+-..+-+++..++++-|.|.. T Consensus 58 FSLeEc~~ll~L~ndp~R~SAdVK~rtl~k~~E~~~kI~eL~~m~~qL~~la~~C~GD~~ 117 (127) T TIGR02044 58 FSLEECKELLSLWNDPNRTSADVKARTLEKVAELERKISELQEMKDQLEELAEACPGDDK 117 (127) T ss_pred CCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 988999999875228889887889999988999999999998899999999985788543 No 92 >TIGR01148 mtrC tetrahydromethanopterin S-methyltransferase, subunit C; InterPro: IPR005865 This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit C in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane. Probab=26.32 E-value=18 Score=16.23 Aligned_cols=10 Identities=10% Similarity=-0.090 Sum_probs=3.6 Q ss_pred HHHHHHHHHC Q ss_conf 7999999821 Q gi|254780355|r 285 PHYIMRAKDK 294 (429) Q Consensus 285 ~~~i~~~~~~ 294 (429) .+++++++++ T Consensus 166 ~~~~~~via~ 175 (276) T TIGR01148 166 QAVISYVIAN 175 (276) T ss_pred HHHHHHHHHH T ss_conf 9999999862 No 93 >cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70. Probab=25.74 E-value=44 Score=13.60 Aligned_cols=44 Identities=18% Similarity=0.196 Sum_probs=27.1 Q ss_pred EEEECCCCCCEEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHH Q ss_conf 1898888786238787565433447778989931999975089899999 Q gi|254780355|r 39 IFTYDPAFSSTASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCY 87 (429) Q Consensus 39 ~~~~dpG~~~ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVay 87 (429) ++-.|||+.+|+-+ .||.+.+.+.+-.|-......+.++.+=.. T Consensus 2 ILGIDPGl~~~G~a-----iie~~~~~~~~l~~g~I~t~~~~~~~~RL~ 45 (154) T cd00529 2 ILGIDPGSRNTGYG-----VIEQEGRKLIYLASGVIRTSSDAPLPSRLK 45 (154) T ss_pred EEEECCCCCCCEEE-----EEEEECCEEEEEEEEEEECCCCCCHHHHHH T ss_conf 69987566871599-----999579978999988896699999899999 No 94 >TIGR02728 spore_gerQ spore coat protein GerQ; InterPro: IPR014099 Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.. Probab=24.87 E-value=14 Score=17.08 Aligned_cols=18 Identities=22% Similarity=0.324 Sum_probs=14.0 Q ss_pred CHHHHHHHHHHHCCCCCC Q ss_conf 424688778764289841 Q gi|254780355|r 190 DLDYASNFLHMCFSVPCA 207 (429) Q Consensus 190 ~lsyaeNfL~Ml~~~~~~ 207 (429) +.||.||+|+|-+|..+. T Consensus 4 ~~SyiENILR~NRG~~aT 21 (82) T TIGR02728 4 EQSYIENILRMNRGKTAT 21 (82) T ss_pred CCCEEEEEEECCCCCEEE T ss_conf 521001000116886157 No 95 >pfam09350 DUF1992 Domain of unknown function (DUF1992). This family of proteins are functionally uncharacterized. Probab=24.60 E-value=46 Score=13.46 Aligned_cols=61 Identities=16% Similarity=0.163 Sum_probs=40.3 Q ss_pred HHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH Q ss_conf 27999999821478614302774355554034689999999888608776517999999999 Q gi|254780355|r 284 IPHYIMRAKDKNDPFRIMGFGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELER 345 (429) Q Consensus 284 v~~~i~~~~~~~~~~ri~GfGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~ 345 (429) |+..|.++.++++..-|+|.|-++=...|+-...-.....++.+..|. --|+++.-.++.+ T Consensus 2 ~e~~I~eA~~~GeFd~LpG~GKPL~~~~~~~~~~~~~~~~~ilk~ag~-lP~~i~l~kEi~~ 62 (70) T pfam09350 2 AERRIREAMERGEFDNLPGAGKPLPLDDDSDPPEELRMGYRILKNAGV-LPPEIELRKEIAE 62 (70) T ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCC-CCHHHHHHHHHHH T ss_conf 789999999849855799999879875556898999999999987699-9879999999999 No 96 >TIGR01807 CM_P2 chorismate mutase; InterPro: IPR010957 This entry primarily represents the chorismate mutase domain of the gamma and beta and epsilonproteobacterial 'P-protein', which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain.; GO: 0004106 chorismate mutase activity, 0009094 L-phenylalanine biosynthetic process, 0005737 cytoplasm. Probab=24.47 E-value=36 Score=14.19 Aligned_cols=26 Identities=8% Similarity=0.192 Sum_probs=13.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 78898889999999999999999972 Q gi|254780355|r 154 LEQCVNVSLRMIAKISTIAAMIYKYS 179 (429) Q Consensus 154 ~~~~~~~a~rLiA~~p~i~A~~yr~~ 179 (429) .+..++..++||..=...+-.+-... T Consensus 8 IDaiD~~ILdLL~eRA~~a~~vGElK 33 (79) T TIGR01807 8 IDAIDDRILDLLSERAKLAQAVGELK 33 (79) T ss_pred HCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 03389999998999999999987652 No 97 >PRK01237 triphosphoribosyl-dephospho-CoA synthase; Validated Probab=24.33 E-value=46 Score=13.42 Aligned_cols=49 Identities=20% Similarity=0.266 Sum_probs=32.5 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 3555540346899999998886087765179999999999961153145798778 Q gi|254780355|r 307 VYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPN 361 (429) Q Consensus 307 vyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~pN 361 (429) ++|.+-+....+++.++++++..|.......+...++ |..|++|||.|- T Consensus 221 l~R~G~~~L~~vq~~A~~~L~~Gg~~~~~g~~~l~~l------d~~~i~rnlSPG 269 (292) T PRK01237 221 LKRAGNPGLEAMQQGAQAVLDLGGSATLAGRRALREL------NQDLLELNASPG 269 (292) T ss_pred HHCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH------HHHHHHCCCCCC T ss_conf 1158999999999999999980798887899999999------999998798963 No 98 >PRK12677 xylose isomerase; Provisional Probab=23.96 E-value=47 Score=13.38 Aligned_cols=33 Identities=18% Similarity=0.119 Sum_probs=14.6 Q ss_pred CCCCCCCCCC----------HHHHHHHHHHHCCCCCCCCCCCHHH Q ss_conf 9853488864----------2468877876428984101479699 Q gi|254780355|r 181 GQPFVYPRSD----------LDYASNFLHMCFSVPCAEYQVNPLL 215 (429) Q Consensus 181 G~~~i~Pd~~----------lsyaeNfL~Ml~~~~~~~~~~~~~~ 215 (429) |+=.|+|.|+ -+++-.||.-.. .....+.+++. T Consensus 176 ~~f~IEPKP~EP~~hqyd~d~~t~laFl~~~~--l~~~~klNiE~ 218 (389) T PRK12677 176 LRFALEPKPNEPRGDILLPTVGHALAFIETLE--HPELVGVNPEV 218 (389) T ss_pred CEEEECCCCCCCCCCCCCCCHHHHHHHHHHHC--CHHHCCCCHHH T ss_conf 51885579979987752751999999999819--84552406016 No 99 >pfam00465 Fe-ADH Iron-containing alcohol dehydrogenase. Probab=23.96 E-value=47 Score=13.38 Aligned_cols=11 Identities=27% Similarity=0.407 Sum_probs=5.9 Q ss_pred HHHCCCCHHHH Q ss_conf 99849996685 Q gi|254780355|r 370 LRALGFPTNLF 380 (429) Q Consensus 370 ~~~lGip~~~f 380 (429) +..+|++.+.+ T Consensus 277 L~~~gv~~~~l 287 (312) T pfam00465 277 LSELGVTEEDL 287 (312) T ss_pred HHHHCCCHHHH T ss_conf 99929899999 No 100 >TIGR03293 PhnG_redo phosphonate C-P lyase system protein PhnG. PhnH is a component of the C-P lyase system (GenProp0232) for the catabolism of phosphonate compounds. The specific function of this component is unknown. This model is based on pfam06754.2, and has been broadened to include sequences missed by that model which are clearly true positive hits based on genome context. Probab=23.69 E-value=48 Score=13.34 Aligned_cols=64 Identities=17% Similarity=0.146 Sum_probs=33.7 Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH-HHHCCCCCCCCCCCHHH Q ss_conf 27743555540346899999998886087765179999999999961-15314579877844788 Q gi|254780355|r 303 FGHRVYRNHDPRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALE-DEYFIERKLYPNVDFYS 366 (429) Q Consensus 303 fGHrvyk~~DPRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~-d~~~~~r~l~pNvDfys 366 (429) .||...-..|++...+-.+++.++........-+-++...++....+ +.....+--..-|||++ T Consensus 75 ~G~~yv~Grd~~~A~~~Av~DAllq~~~~~~~~~~~~i~pl~~~~~~~~~~~~~~~aaTkVdFfT 139 (144) T TIGR03293 75 EGYAYVLGRDKRHAELLAVLDALLQAPLLHDELIADLIAPLAQRLAERRARRQAEAAATRVDFFT 139 (144) T ss_pred EEEEEEECCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEE T ss_conf 36899827899999999999999769962236999998899999999999999998585253660 No 101 >pfam08235 LNS2 LNS2 (Lipin/Ned1/Smp2). This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain (Pfam: PF04571) and phosphatidylinositol transfer proteins. SMP2 (also known as PAH1) is involved in plasmid maintenance and respiration, and has been identified as a Mg2+-dependent phosphatidate phosphatase (EC:3.1.3.4) that contains a haloacid dehalogenase (HAD)-like domain. Lipin proteins are involved in adipose tissue development and insulin resistance. Probab=23.43 E-value=48 Score=13.31 Aligned_cols=113 Identities=22% Similarity=0.349 Sum_probs=59.3 Q ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH-----------CCCCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCC Q ss_conf 5654246776755421002220352899999862-----------15535127999999821478614302774355554 Q gi|254780355|r 244 SGADPFACIAAGVACLGGRAHGGANEEALNMLME-----------IGSLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHD 312 (429) Q Consensus 244 t~adlysai~agi~aL~GPlHGGAne~v~~ml~~-----------I~~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~D 312 (429) |.+|...-+..-+|.= -.|-|+.+..-++-+. |+..+...+|+.+....+. ++|- | +|.-..| T Consensus 11 TkSd~~Ghi~~~~G~D--wth~Gva~ly~~i~~nGY~ilYLTaR~i~qa~~Tr~yL~~~~Q~~~--~LP~-G-Pv~lsp~ 84 (156) T pfam08235 11 TASDALGHILSIMGKD--WVHAGVVDLVRKIQENGYLIIYLTARPDGQADRTRAYLSQHKQDGY--NLPH-G-PVILSPD 84 (156) T ss_pred EHHHHHHCHHHCCCCC--CCCCCHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHHHCCCC--CCCC-C-CEEECCH T ss_conf 7425552334303899--7630199999999978936999834256668999999998351885--3889-9-8897763 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHH--------HHHHHCCCCHH Q ss_conf 0346899999998886087765179999999999961153145798778447889--------99998499966 Q gi|254780355|r 313 PRCRIMRETMYEVLEVTGRFNDPIAQVAIELERIALEDEYFIERKLYPNVDFYSG--------ITLRALGFPTN 378 (429) Q Consensus 313 PRa~~l~~~~~~l~~~~~~~~~~~~~~a~~le~~a~~d~~~~~r~l~pNvDfysg--------~i~~~lGip~~ 378 (429) . .+..+.+|+... +-..|+++. |..+. ..|..++ -||+| +.|.+.|+|++ T Consensus 85 ~---l~~al~rEvi~k----~p~~FKi~~-L~di~---~lfp~~~-----pfyAgFGNr~tD~~aY~~vgip~~ 142 (156) T pfam08235 85 R---LFAALHREVILK----KPLVFKIAC-LRDIR---QLFPNRN-----PFYAGFGNRIKDVIVYRSVGVPPS 142 (156) T ss_pred H---HHHHHHHHHHCC----CCHHHHHHH-HHHHH---HHCCCCC-----CEEECCCCCHHHHHHHHHCCCCHH T ss_conf 3---788756355507----908999999-99999---8768889-----826616896537999997699941 No 102 >PRK13224 consensus Probab=23.10 E-value=20 Score=15.93 Aligned_cols=80 Identities=16% Similarity=0.124 Sum_probs=45.8 Q ss_pred HHCCCCCCCCCCCHHHH-HHHHHHHHEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHH---HHHHHHHHCCCCHHHHHHH Q ss_conf 64289841014796999-9987563501367876301555544205654246776755---4210022203528999998 Q gi|254780355|r 200 MCFSVPCAEYQVNPLLA-RAMNRIFILHADHEQNASTSTVRLAGSSGADPFACIAAGV---ACLGGRAHGGANEEALNML 275 (429) Q Consensus 200 Ml~~~~~~~~~~~~~~~-~ald~~LILhADHe~NaSTft~R~vaSt~adlysai~agi---~aL~GPlHGGAne~v~~ml 275 (429) ...+......+|+|... ++++ .+|++- +-+|+-|-.|+-+|.+||+ +..||--.. .-+.. .-- T Consensus 132 iv~~d~v~~~KP~Pe~~l~a~~---------~l~~~~--~l~VGDs~~D~~aA~~AGi~~i~v~~Gy~~~-~~~~~-~~~ 198 (216) T PRK13224 132 VIGGDSLPQRKPDPAPLRAAFA---------ALGDEP--VLYVGDSEVDAETAENAGVPFLLFTEGYRKA-PVHEL-PHH 198 (216) T ss_pred EECCCCCCCCCCCHHHHHHHHH---------HCCCCC--EEEECCCHHHHHHHHHHCCCEEEECCCCCCC-CHHHC-CCC T ss_conf 6544668999999999999997---------379999--8997598878999999499889977797998-96773-846 Q ss_pred HHCCCCCHHHHHHHHHH Q ss_conf 62155351279999998 Q gi|254780355|r 276 MEIGSLERIPHYIMRAK 292 (429) Q Consensus 276 ~~I~~~~~v~~~i~~~~ 292 (429) --|.+..+.++.|.+.| T Consensus 199 ~~i~~~~el~~~l~~l~ 215 (216) T PRK13224 199 GAFDDHAELPDLVARLL 215 (216) T ss_pred CHHCCHHHHHHHHHHHH T ss_conf 26179998999999984 No 103 >pfam10694 DUF2500 Protein of unknown function (DUF2500). The members of this family are largely confined to the Gammaproteobacteria. The function is not known. Probab=22.54 E-value=36 Score=14.22 Aligned_cols=13 Identities=38% Similarity=0.787 Sum_probs=9.7 Q ss_pred EECCCCEEEECCE Q ss_conf 3344777898993 Q gi|254780355|r 59 IDGNNGILLYRGY 71 (429) Q Consensus 59 IDG~~G~L~YRGY 71 (429) .-|++|.|.|+|- T Consensus 88 ~eGd~G~Lt~QGt 100 (107) T pfam10694 88 NEGDKGKLTYQGT 100 (107) T ss_pred CCCCEEEEEEECC T ss_conf 9996899999046 No 104 >TIGR00422 valS valyl-tRNA synthetase; InterPro: IPR002303 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm. Probab=22.42 E-value=6.6 Score=19.29 Aligned_cols=22 Identities=18% Similarity=0.279 Sum_probs=9.0 Q ss_pred CCCCCCCCCCCHHHHHHHHHHH Q ss_conf 7985348886424688778764 Q gi|254780355|r 180 IGQPFVYPRSDLDYASNFLHMC 201 (429) Q Consensus 180 ~G~~~i~Pd~~lsyaeNfL~Ml 201 (429) .|+++.---.++-++.||++=+ T Consensus 658 ~G~Di~f~~~~v~~~~nF~NKl 679 (970) T TIGR00422 658 PGDDINFDWKRVESARNFANKL 679 (970) T ss_pred CCCCCCCCHHHHHHHHHHHHHH T ss_conf 8986421189887676776788 No 105 >PRK10246 exonuclease subunit SbcC; Provisional Probab=22.41 E-value=36 Score=14.20 Aligned_cols=14 Identities=29% Similarity=0.356 Sum_probs=7.2 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 99989999999997 Q gi|254780355|r 387 ARTAGWVSQWTEMI 400 (429) Q Consensus 387 ~R~~Gw~AH~~Eq~ 400 (429) +|++|.|.|+-|.. T Consensus 1007 gR~VGIISHV~ELk 1020 (1047) T PRK10246 1007 GKTIGVISHVEAMK 1020 (1047) T ss_pred CCEEEEECCHHHHH T ss_conf 89899988878899 No 106 >PRK01008 queuine tRNA-ribosyltransferase; Provisional Probab=22.24 E-value=51 Score=13.15 Aligned_cols=22 Identities=18% Similarity=0.375 Sum_probs=14.9 Q ss_pred HHHHHHHHCCCCCEEECCCCCC Q ss_conf 9999998214786143027743 Q gi|254780355|r 286 HYIMRAKDKNDPFRIMGFGHRV 307 (429) Q Consensus 286 ~~i~~~~~~~~~~ri~GfGHrv 307 (429) +++...+..+++.-|||-||+. T Consensus 246 ~~~~~~LP~~kPRyLmGvG~p~ 267 (372) T PRK01008 246 DITTSNLSKERPVHLLGIGDLP 267 (372) T ss_pred HHHHHHCCCCCCEEEECCCCHH T ss_conf 9998468999875870589879 No 107 >TIGR00713 hemL glutamate-1-semialdehyde-2,1-aminomutase; InterPro: IPR004639 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway . The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin . The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) . This entry represents glutamate-1-semialdehyde (GSA) aminotransferase (5.4.3.8 from EC), which catalyse a transamination reaction to produce 5-aminoaevulinic acid during the first stage of tetrapyrrole biosynthesis by the C5 pathway , . This enzyme has a high degree of similarity to amino acid transaminases, and is classed as a class III aminotransferase.; GO: 0042286 glutamate-1-semialdehyde 21-aminomutase activity, 0033014 tetrapyrrole biosynthetic process. Probab=22.03 E-value=51 Score=13.12 Aligned_cols=75 Identities=25% Similarity=0.321 Sum_probs=39.6 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCCC------------------HHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHH Q ss_conf 3555540346899999998886087765------------------1799999999999611531457987784478899 Q gi|254780355|r 307 VYRNHDPRCRIMRETMYEVLEVTGRFND------------------PIAQVAIELERIALEDEYFIERKLYPNVDFYSGI 368 (429) Q Consensus 307 vyk~~DPRa~~l~~~~~~l~~~~~~~~~------------------~~~~~a~~le~~a~~d~~~~~r~l~pNvDfysg~ 368 (429) +|+.-|--++.|.+-+++++++.+.+.. .-++-|++.+. +.|. .||... T Consensus 324 ~Y~~l~~~~~~L~~g~~e~l~~~gip~~~~~~gSMf~~FFtd~~~V~ny~~A~~SD~-----e~F~--------~Ff~~m 390 (434) T TIGR00713 324 VYTELDELAKRLAEGLSEVLEDKGIPHTVNRVGSMFSLFFTDEEEVTNYADAKKSDT-----ELFA--------KFFHEM 390 (434) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCEEEEEECCCCCCCCHHHHHHHHH-----HHHH--------HHHHHH T ss_conf 348999999999999999998279858995044004566577889878899988618-----9889--------999999 Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99984999668589999999989999999997 Q gi|254780355|r 369 TLRALGFPTNLFTVLFAVARTAGWVSQWTEMI 400 (429) Q Consensus 369 i~~~lGip~~~ft~iFa~~R~~Gw~AH~~Eq~ 400 (429) +-+-.=+|+.-|-+.|.-. ||=-|.. T Consensus 391 L~~GVylpPS~FEa~F~S~------AH~~E~i 416 (434) T TIGR00713 391 LEKGVYLPPSQFEACFISA------AHTEEDI 416 (434) T ss_pred HHCCCCCCCCCHHHHHHCC------CCCHHHH T ss_conf 8588878987211555167------7772117 No 108 >TIGR01859 fruc_bis_ald_ fructose-1,6-bisphosphate aldolase, class II; InterPro: IPR011289 Fructose-1,6-bisphosphate (FBP) aldolases reversibly cleave FBP to two triose phosphates, glycerone phophate and D-glyceraldehyde 3-phosphate. They play a key role in both glycolysis (FBP cleavage) and gluconeogenesis (FBP synthesis). These enzymes can be divide into two classes based on their mode of catalysis. Class I FBP aldolases form a Schiff-base intermediate between glycerone phophate and an active site lysine residue, while the class II enzymes use a divalent cation such as Zn(2+) for catalysis . This entry represents class II FBP aldolases found in Gram-positive bacteria, a variety of Gram-negative baceria, and amitochondriate protists. These enzymes are homotetramers where each momomer forms a TIM barrel fold .; GO: 0004332 fructose-bisphosphate aldolase activity, 0008270 zinc ion binding, 0006096 glycolysis, 0030388 fructose 16-bisphosphate metabolic process. Probab=21.68 E-value=52 Score=13.08 Aligned_cols=11 Identities=27% Similarity=0.419 Sum_probs=4.0 Q ss_pred HHHHHHHHHHH Q ss_conf 77675542100 Q gi|254780355|r 251 CIAAGVACLGG 261 (429) Q Consensus 251 ai~agi~aL~G 261 (429) ++++|||+-.| T Consensus 180 ~LA~aIGt~HG 190 (339) T TIGR01859 180 YLAAAIGTSHG 190 (339) T ss_pred EECCCCCCCCC T ss_conf 54010035023 No 109 >pfam09370 TIM-br_sig_trns TIM-barrel signal transduction protein. This domain is likely to have a TIM barrel fold related to IGPS. Although this family of proteins are functionally uncharacterized this domain is found as an N-terminal domain of sigma 54 -dependent transcriptional activators (enhancer-binding proteins) suggesting a potential role in signal recognition/receiving and signal transduction. Probab=21.35 E-value=53 Score=13.03 Aligned_cols=43 Identities=30% Similarity=0.385 Sum_probs=20.4 Q ss_pred HHHHHHHCCCCCHHHHHHHH------HHHHHHHH-HCCCCHHHHHHHHHC Q ss_conf 55554420565424677675------54210022-203528999998621 Q gi|254780355|r 236 STVRLAGSSGADPFACIAAG------VACLGGRA-HGGANEEALNMLMEI 278 (429) Q Consensus 236 ft~R~vaSt~adlysai~ag------i~aL~GPl-HGGAne~v~~ml~~I 278 (429) .++++.-..|+|+.-...+| .++|.|-+ -|-||+-|++|-.|| T Consensus 26 lsAK~ae~gGaDlIi~ynsGrfRm~G~gSlagllpygdaN~iv~ema~Ev 75 (268) T pfam09370 26 LSAKCEEAGGADLILIYNSGRYRMAGRGSLAGLLPYGNANEIVLEMAREV 75 (268) T ss_pred HHHHHHHHCCCCEEEEECCCHHHHCCCCCHHHHCCCCCHHHHHHHHHHHH T ss_conf 65789985798699861540344358831312013565769999999888 No 110 >PRK11552 putative DNA-binding transcriptional regulator; Provisional Probab=21.34 E-value=53 Score=13.03 Aligned_cols=35 Identities=11% Similarity=0.129 Sum_probs=22.4 Q ss_pred CCCHHHHHHHHHHHHEECCCCCCCHHHHHHHHHCCCC Q ss_conf 4796999998756350136787630155554420565 Q gi|254780355|r 210 QVNPLLARAMNRIFILHADHEQNASTSTVRLAGSSGA 246 (429) Q Consensus 210 ~~~~~~~~ald~~LILhADHe~NaSTft~R~vaSt~a 246 (429) +....-.+.++..+-+-++||+++|| -.++..+|. T Consensus 10 r~e~tr~~ll~aA~~~F~~~G~~att--r~Ia~~Ag~ 44 (224) T PRK11552 10 KGEQAKQQLIAAALAQFGEYGLHATT--RDIAAQAGQ 44 (224) T ss_pred CHHHHHHHHHHHHHHHHHHHCCCHHH--HHHHHHHCC T ss_conf 58999999999999999884914009--999998399 No 111 >TIGR02111 PQQ_syn_pqqC coenzyme PQQ biosynthesis protein C; InterPro: IPR011845 This entry describes the coenzyme PQQ (pyrrolo-quinoline-quinone) biosynthesis protein PqqC. Pyrroloquinoline quinone (PQQ) is the prosthetic group of several bacterial enzymes, including methanol dehydrogenase of methylotrophs and the glucose dehydrogenase of a number of bacteria . PQQC has been found to be required in the synthesis of PQQ but its function is unclear. This entry does not include related proteins likely to be functionally distinct from PqqC, such as homologs found in the Chlamydias.; GO: 0018189 pyrroloquinoline quinone biosynthetic process. Probab=21.34 E-value=39 Score=13.96 Aligned_cols=47 Identities=15% Similarity=0.186 Sum_probs=21.3 Q ss_pred CCCCHHHHHHHHHHHHHHHH-HCCCCHHHHHHHHHCCCCC-HHHHHHHHHHH Q ss_conf 56542467767554210022-2035289999986215535-12799999982 Q gi|254780355|r 244 SGADPFACIAAGVACLGGRA-HGGANEEALNMLMEIGSLE-RIPHYIMRAKD 293 (429) Q Consensus 244 t~adlysai~agi~aL~GPl-HGGAne~v~~ml~~I~~~~-~v~~~i~~~~~ 293 (429) ....+--||+|.|.=|.-|. | .+.+-.|++.-.=.+ +.=+|.+++|. T Consensus 128 r~~sl~EA~aSSLTELFAP~I~---~~R~ag~l~hY~fi~~~~l~YF~~RL~ 176 (239) T TIGR02111 128 REKSLLEAIASSLTELFAPQIH---SERVAGLLQHYDFIDDAALAYFRKRLT 176 (239) T ss_pred HCCCHHHHHHHHHHHHHCCHHH---HHHHHHHHHCCCCCCHHHHHHHHHHHC T ss_conf 3042789998877863060257---887641341366568668999987632 No 112 >KOG1741 consensus Probab=21.09 E-value=53 Score=13.00 Aligned_cols=36 Identities=19% Similarity=0.346 Sum_probs=29.3 Q ss_pred HHHHHCCCCCHHHHH----HHHHHCCCCCHHHHHHHHHHH Q ss_conf 988640689989999----998512476525789999999 Q gi|254780355|r 105 DKISRHALLNENMSR----FFMGFPSSAHPMAMLVSAVGA 140 (429) Q Consensus 105 ~~l~~~~~lpe~v~~----~i~~~p~~ahPM~~L~~~vsa 140 (429) +.+.....||+.+.. -++++|+++||.-+...||.. T Consensus 30 k~i~knp~LP~~~r~ea~~kl~alPrns~ptrI~NRCv~T 69 (103) T KOG1741 30 KEISKNPILPEKLRDEAAEKLQALPRNSAPTRIKNRCVFT 69 (103) T ss_pred HHHHHCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC T ss_conf 9998188612999998999985276565429999888843 No 113 >PRK10254 hypothetical protein; Provisional Probab=20.90 E-value=40 Score=13.88 Aligned_cols=20 Identities=30% Similarity=0.370 Sum_probs=16.0 Q ss_pred HHHHHCCCCHHHHHHHHHCC Q ss_conf 00222035289999986215 Q gi|254780355|r 260 GGRAHGGANEEALNMLMEIG 279 (429) Q Consensus 260 ~GPlHGGAne~v~~ml~~I~ 279 (429) +|-|||||+-+-.+.+-.+. T Consensus 50 ~G~LHGGa~~aLAEt~~s~a 69 (137) T PRK10254 50 FGLLHGGASAALAETLGSMA 69 (137) T ss_pred CCEEECHHHHHHHHHHHHHH T ss_conf 43750013558999998775 No 114 >PRK09300 tRNA splicing endonuclease; Reviewed Probab=20.85 E-value=54 Score=12.96 Aligned_cols=20 Identities=25% Similarity=0.408 Sum_probs=15.9 Q ss_pred CCHHHHHHHHHCCCCCCHHH Q ss_conf 89899999998187999899 Q gi|254780355|r 80 SDFLEVCYLLLHGELANVSQ 99 (429) Q Consensus 80 ~sFeEVayLLl~GeLPt~~e 99 (429) -+.+|++||++.|.++-..+ T Consensus 36 LspvEa~yL~~rg~i~~~d~ 55 (334) T PRK09300 36 LSPVEAAYLLFRGKIEIEDG 55 (334) T ss_pred ECHHHHHHHHCCCCCCCCCC T ss_conf 74899547502486613466 No 115 >TIGR01069 mutS2 MutS2 family protein; InterPro: IPR005747 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication . MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base . MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch . MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level . Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure , and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions . Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts . This entry represents a family of MutS proteins.; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0045005 maintenance of fidelity during DNA-dependent DNA replication. Probab=20.65 E-value=35 Score=14.29 Aligned_cols=26 Identities=31% Similarity=0.303 Sum_probs=18.6 Q ss_pred HHHHHHHHHEECCC---CCCCHHHHHHHH Q ss_conf 99987563501367---876301555544 Q gi|254780355|r 216 ARAMNRIFILHADH---EQNASTSTVRLA 241 (429) Q Consensus 216 ~~ald~~LILhADH---e~NaSTft~R~v 241 (429) ...|+..|+---|= ++|-|||++|++ T Consensus 383 ~p~F~~ifaDIGDEQSi~qnLSTFS~Hm~ 411 (834) T TIGR01069 383 LPLFEEIFADIGDEQSIEQNLSTFSSHMK 411 (834) T ss_pred CHHHHHHCCCCCCCCCHHHHHHHHHHHHH T ss_conf 11012120135884242433778999999 No 116 >TIGR00987 himA integration host factor, alpha subunit; InterPro: IPR005684 Integration host factor (IHF) is a heterodimeric protein consisting of alpha and beta (IPR005685 from INTERPRO) subunits. IHF binds the minor groove of DNA in a sequence-specific manner to induce a large bend. This bending stabilises distinct DNA conformations that are required during several bacterial processes, such as recombination, transposition, replication and transcription .; GO: 0003677 DNA binding, 0005694 chromosome. Probab=20.64 E-value=54 Score=12.93 Aligned_cols=43 Identities=21% Similarity=0.404 Sum_probs=25.7 Q ss_pred HHHHHHCCC-CCH----HH---HHHHHHHHCCCCCEEECCCCCCCCCCCHH Q ss_conf 999862155-351----27---99999982147861430277435555403 Q gi|254780355|r 272 LNMLMEIGS-LER----IP---HYIMRAKDKNDPFRIMGFGHRVYRNHDPR 314 (429) Q Consensus 272 ~~ml~~I~~-~~~----v~---~~i~~~~~~~~~~ri~GfGHrvyk~~DPR 314 (429) -.+++++|= ..+ |+ +-|.++|.+++..+|-|||.=-.++..-| T Consensus 9 E~~f~~~GLs~~ea~~LVE~~~~~~~~AL~~gE~VKlS~FG~F~~RDK~~R 59 (96) T TIGR00987 9 EALFRELGLSKREAKELVELFLEEIRDALERGEQVKLSGFGNFDLRDKTQR 59 (96) T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCC T ss_conf 999998288855778999999999999986388465303655210107778 No 117 >cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles. Probab=20.49 E-value=21 Score=15.79 Aligned_cols=30 Identities=30% Similarity=0.519 Sum_probs=19.7 Q ss_pred CCCHHHHHHHHHHHCCCCCEEECCCCCCCCCCC Q ss_conf 535127999999821478614302774355554 Q gi|254780355|r 280 SLERIPHYIMRAKDKNDPFRIMGFGHRVYRNHD 312 (429) Q Consensus 280 ~~~~v~~~i~~~~~~~~~~ri~GfGHrvyk~~D 312 (429) ++..+..|..+-+-+ +.|.+| |||.|...| T Consensus 13 s~~TlrrW~~~G~i~--~~rt~~-GhRry~~~d 42 (49) T cd04762 13 SPSTLRRWVKEGKLK--AIRTPG-GHRRFPEED 42 (49) T ss_pred CHHHHHHHHHCCCCC--EEECCC-CCEEECHHH T ss_conf 999999999879943--158899-877618999 No 118 >pfam05788 Orbi_VP1 Orbivirus RNA-dependent RNA polymerase (VP1). This family consists of the RNA-dependent RNA polymerase protein VP1 from the Orbiviruses. VP1 may have both enzymatic and structural roles in the virus life cycle. Probab=20.22 E-value=47 Score=13.37 Aligned_cols=62 Identities=26% Similarity=0.387 Sum_probs=39.1 Q ss_pred EEEECCEEHHHHHHHCCHHH--HHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHH--HHHHHHCCCCCHHHHH Q ss_conf 78989931999975089899--9999981879998999999998864068998999--9998512476525789 Q gi|254780355|r 65 ILLYRGYPIEQLSEKSDFLE--VCYLLLHGELANVSQQKDFNDKISRHALLNENMS--RFFMGFPSSAHPMAML 134 (429) Q Consensus 65 ~L~YRGY~IedLa~~~sFeE--VayLLl~GeLPt~~el~~F~~~l~~~~~lpe~v~--~~i~~~p~~ahPM~~L 134 (429) -|+|-||.++||.+ ..|-| |+--||+|+- .-|+..+..+-.|++.-+ .-++ -|+..+|..-+ T Consensus 622 ~lrYeG~t~~elie-fGYGeGRv~~tlWnGkR------~v~k~~~d~Y~~L~~~~r~~g~Fr-~P~GV~pvr~~ 687 (1301) T pfam05788 622 DLRYEGYTLDELIE-FGYGEGRVVNTLWNGKR------RVFKMLFDKYLSLSEEERIQGPFK-SPPGVKPIRNI 687 (1301) T ss_pred HCCCCCCCHHHHHH-HCCCCCHHHHHHHCCCH------HHHHCCCHHHHCCCHHHHCCCCCC-CCCCCEEECHH T ss_conf 15637855999998-51565301231303404------553156044322787660268988-99971341117 No 119 >KOG4448 consensus Probab=20.21 E-value=26 Score=15.17 Aligned_cols=59 Identities=19% Similarity=0.274 Sum_probs=31.1 Q ss_pred EEEEEEEEEEEECCCCEEEECCEEHHHHHHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCC Q ss_conf 23878756543344777898993199997508989999999818799989999999988640689 Q gi|254780355|r 49 TASCKSKITFIDGNNGILLYRGYPIEQLSEKSDFLEVCYLLLHGELANVSQQKDFNDKISRHALL 113 (429) Q Consensus 49 ta~ceS~IT~IDG~~G~L~YRGY~IedLa~~~sFeEVayLLl~GeLPt~~el~~F~~~l~~~~~l 113 (429) --+|-|.|--.--++|+-.|--.+|---...+.|--| |+.+| ..+...|...++.+..| T Consensus 105 Lkv~asglk~~h~qe~l~ly~ahrityc~a~~~~pkv-f~wiy-----rhegk~~~~~lrchaVL 163 (374) T KOG4448 105 LKVEASGLKAFHEQEGLTLYWAHRITYCRAPSGYPKV-FCWIY-----RHEGKQLKSELRCHAVL 163 (374) T ss_pred EEEECCCCEEEECCCCCEEEEEEEEEEEECCCCCCEE-EEEEE-----ECCHHHHHHCCCEEEEE T ss_conf 9971354356513576036663003563068789768-99998-----52224541214211256 No 120 >pfam01997 Translin Translin family. Members of this family include Translin that interacts with DNA and forms a ring around the DNA. This family also includes Translin-associated protein X, which was found to interact with translin with yeast two-hybrid screen. Probab=20.11 E-value=44 Score=13.60 Aligned_cols=14 Identities=21% Similarity=0.128 Sum_probs=8.7 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 67767554210022 Q gi|254780355|r 250 ACIAAGVACLGGRA 263 (429) Q Consensus 250 sai~agi~aL~GPl 263 (429) .....||+-|.|-| T Consensus 107 ~dYL~Gl~DltGEL 120 (186) T pfam01997 107 EDYLLGLFDLTGEL 120 (186) T ss_pred HHHHHHHHHHHHHH T ss_conf 99998999878799 Done!