Query psy254 Match_columns 187 No_of_seqs 158 out of 1053 Neff 6.9 Searched_HMMs 46136 Date Fri Aug 16 18:46:54 2013 Command hhsearch -i /work/01045/syshi/Psyhhblits/psy254.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/254hhsearch_cdd -cpu 12 -v 0 No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PF00224 PK: Pyruvate kinase, 100.0 2.1E-45 4.5E-50 321.2 17.3 144 34-184 1-144 (348) 2 PRK08187 pyruvate kinase; Vali 100.0 3.9E-44 8.5E-49 323.6 19.6 167 11-185 110-278 (493) 3 PLN02762 pyruvate kinase compl 100.0 2.8E-43 6E-48 318.4 19.6 141 34-185 24-166 (509) 4 PTZ00066 pyruvate kinase; Prov 100.0 3.8E-43 8.3E-48 317.5 19.7 160 17-186 19-180 (513) 5 COG0469 PykF Pyruvate kinase [ 100.0 3.9E-43 8.5E-48 314.6 19.2 144 32-185 2-145 (477) 6 PLN02765 pyruvate kinase 100.0 6.7E-43 1.4E-47 316.4 19.8 159 15-186 10-176 (526) 7 PRK09206 pyruvate kinase; Prov 100.0 7.4E-43 1.6E-47 313.8 19.4 143 34-186 1-143 (470) 8 PLN02623 pyruvate kinase 100.0 9.8E-43 2.1E-47 317.7 19.8 149 26-186 101-249 (581) 9 PRK06247 pyruvate kinase; Prov 100.0 8.3E-43 1.8E-47 313.5 18.9 142 33-186 3-144 (476) 10 cd00288 Pyruvate_Kinase Pyruva 100.0 2.3E-42 4.9E-47 311.9 19.1 143 34-185 1-144 (480) 11 PRK05826 pyruvate kinase; Prov 100.0 3.2E-42 7E-47 309.9 19.4 143 33-186 2-144 (465) 12 PLN02461 Probable pyruvate kin 100.0 7.1E-42 1.5E-46 309.4 19.6 144 28-181 14-157 (511) 13 PRK06354 pyruvate kinase; Prov 100.0 8.2E-42 1.8E-46 314.5 19.4 142 32-185 5-148 (590) 14 PRK14725 pyruvate kinase; Prov 100.0 1.3E-41 2.7E-46 310.7 19.9 169 11-186 116-399 (608) 15 TIGR01064 pyruv_kin pyruvate k 100.0 3.2E-41 7E-46 304.7 18.9 142 35-186 1-142 (473) 16 PRK06739 pyruvate kinase; Vali 100.0 1.5E-40 3.3E-45 289.7 17.4 135 36-186 2-136 (352) 17 KOG2323|consensus 100.0 1.8E-38 4E-43 283.8 15.5 160 17-184 2-162 (501) 18 PTZ00300 pyruvate kinase; Prov 100.0 3.2E-31 6.9E-36 237.8 15.5 116 61-185 1-117 (454) 19 PF00478 IMPDH: IMP dehydrogen 94.1 0.18 4E-06 44.6 7.0 52 35-86 95-146 (352) 20 cd00381 IMPDH IMPDH: The catal 91.5 0.49 1.1E-05 41.3 5.9 48 39-86 85-132 (325) 21 PRK05458 guanosine 5'-monophos 90.6 0.75 1.6E-05 40.4 6.2 46 41-86 90-137 (326) 22 TIGR01302 IMP_dehydrog inosine 90.5 0.62 1.3E-05 42.5 5.8 49 38-86 214-262 (450) 23 PRK05096 guanosine 5'-monophos 90.1 0.79 1.7E-05 40.5 5.9 49 38-86 98-148 (346) 24 TIGR01305 GMP_reduct_1 guanosi 90.0 0.86 1.9E-05 40.2 6.0 49 38-86 97-147 (343) 25 PLN02274 inosine-5'-monophosph 88.5 1.1 2.3E-05 41.7 5.8 49 38-86 238-286 (505) 26 PTZ00314 inosine-5'-monophosph 87.9 0.89 1.9E-05 42.1 4.9 46 41-86 234-279 (495) 27 PRK06843 inosine 5-monophospha 86.7 1.4 3E-05 39.9 5.3 50 37-86 142-191 (404) 28 TIGR01306 GMP_reduct_2 guanosi 85.9 2 4.4E-05 37.7 5.8 49 38-86 84-134 (321) 29 PRK10737 FKBP-type peptidyl-pr 83.0 3.4 7.4E-05 33.7 5.6 60 126-186 52-118 (196) 30 PF01136 Peptidase_U32: Peptid 83.0 3.7 8.1E-05 33.4 5.9 42 49-90 158-199 (233) 31 KOG2550|consensus 79.8 3.9 8.4E-05 37.2 5.2 46 41-86 244-289 (503) 32 TIGR01303 IMP_DH_rel_1 IMP deh 79.0 4.2 9.2E-05 37.5 5.4 48 39-86 216-263 (475) 33 PLN02495 oxidoreductase, actin 78.7 7 0.00015 35.1 6.6 34 36-69 113-149 (385) 34 PF07521 RMMBL: RNA-metabolisi 78.5 1.4 3E-05 26.9 1.5 24 61-84 7-31 (43) 35 PRK05567 inosine 5'-monophosph 78.4 6.8 0.00015 36.0 6.6 51 36-86 216-266 (486) 36 COG4043 Preprotein translocase 78.3 3.5 7.7E-05 30.2 3.7 31 150-181 25-55 (111) 37 PRK07107 inosine 5-monophospha 76.3 5.5 0.00012 37.0 5.4 51 35-86 230-280 (502) 38 PF09370 TIM-br_sig_trns: TIM- 76.0 11 0.00023 32.4 6.5 51 40-91 151-212 (268) 39 PRK07535 methyltetrahydrofolat 75.7 7.1 0.00015 33.0 5.5 60 50-117 28-87 (261) 40 cd00423 Pterin_binding Pterin 74.8 14 0.0003 31.0 7.0 53 51-111 28-88 (258) 41 TIGR01949 AroFGH_arch predicte 73.8 18 0.00039 30.2 7.5 69 35-109 69-148 (258) 42 PRK06806 fructose-bisphosphate 72.9 23 0.0005 30.4 8.0 53 38-91 76-128 (281) 43 PF06953 ArsD: Arsenical resis 72.0 12 0.00025 28.4 5.3 27 51-77 31-57 (123) 44 PRK07807 inosine 5-monophospha 71.4 8.3 0.00018 35.6 5.3 44 43-86 222-265 (479) 45 PRK07315 fructose-bisphosphate 71.0 31 0.00066 29.8 8.4 52 38-91 79-130 (293) 46 PF00677 Lum_binding: Lumazine 69.4 13 0.00028 25.9 4.8 37 147-185 20-57 (85) 47 PRK01712 carbon storage regula 69.0 9.4 0.0002 25.6 3.7 26 159-185 5-30 (64) 48 PRK15452 putative protease; Pr 68.9 13 0.00027 34.1 5.8 42 49-90 270-311 (443) 49 PF02599 CsrA: Global regulato 68.5 7.2 0.00016 25.2 3.0 25 160-185 6-30 (54) 50 PRK08185 hypothetical protein; 67.3 39 0.00084 29.1 8.2 54 37-91 69-122 (283) 51 TIGR01093 aroD 3-dehydroquinat 67.2 28 0.0006 28.5 7.1 55 34-88 116-176 (228) 52 TIGR01496 DHPS dihydropteroate 66.5 17 0.00036 30.7 5.7 54 50-111 26-87 (257) 53 PRK00568 carbon storage regula 66.4 9.9 0.00021 26.4 3.5 25 160-185 6-30 (76) 54 PF01079 Hint: Hint module; I 66.2 13 0.00027 30.8 4.8 65 97-168 49-114 (217) 55 PF00150 Cellulase: Cellulase 65.5 15 0.00033 29.9 5.3 54 48-109 22-85 (281) 56 PF04028 DUF374: Domain of unk 64.4 34 0.00074 23.4 6.0 54 45-109 17-72 (74) 57 PF01487 DHquinase_I: Type I 3 64.2 48 0.001 26.8 8.0 73 34-112 111-190 (224) 58 cd03316 MR_like Mandelate race 64.1 46 0.001 28.8 8.3 64 36-108 126-198 (357) 59 PRK15108 biotin synthase; Prov 63.6 25 0.00054 30.9 6.5 30 37-68 125-154 (345) 60 COG2945 Predicted hydrolase of 62.3 17 0.00036 30.0 4.7 37 50-86 50-98 (210) 61 PRK08195 4-hyroxy-2-oxovalerat 61.6 34 0.00073 30.1 6.9 51 34-84 75-125 (337) 62 PF04055 Radical_SAM: Radical 61.3 60 0.0013 23.5 8.1 39 36-74 76-114 (166) 63 PRK07565 dihydroorotate dehydr 61.0 31 0.00067 30.0 6.6 34 37-70 102-137 (334) 64 COG1047 SlpA FKBP-type peptidy 60.5 28 0.00062 27.9 5.7 62 124-186 51-119 (174) 65 PF04472 DUF552: Protein of un 60.2 49 0.0011 22.2 6.4 44 47-91 9-52 (73) 66 TIGR00693 thiE thiamine-phosph 59.8 46 0.001 26.1 7.0 42 50-91 16-57 (196) 67 COG0051 RpsJ Ribosomal protein 59.7 19 0.00042 26.4 4.3 31 61-91 3-33 (104) 68 PRK07709 fructose-bisphosphate 59.5 65 0.0014 27.8 8.1 53 38-91 79-131 (285) 69 TIGR00202 csrA carbon storage 59.3 19 0.00041 24.5 3.8 26 159-185 5-30 (69) 70 COG2040 MHT1 Homocysteine/sele 59.1 40 0.00086 29.3 6.7 56 50-116 137-193 (300) 71 COG0646 MetH Methionine syntha 59.1 46 0.00099 29.1 7.1 56 35-91 113-186 (311) 72 PF00809 Pterin_bind: Pterin b 59.0 19 0.00041 29.2 4.6 55 51-112 23-85 (210) 73 PRK07226 fructose-bisphosphate 58.2 41 0.0009 28.2 6.7 56 50-111 96-153 (267) 74 cd00564 TMP_TenI Thiamine mono 57.3 56 0.0012 25.0 7.0 42 50-91 15-56 (196) 75 cd03320 OSBS o-Succinylbenzoat 56.9 46 0.001 27.7 6.8 65 35-108 71-136 (263) 76 COG1862 YajC Preprotein transl 56.6 21 0.00046 25.9 4.0 31 153-184 37-67 (97) 77 TIGR00739 yajC preprotein tran 56.5 25 0.00053 24.7 4.2 31 154-185 32-62 (84) 78 TIGR03217 4OH_2_O_val_ald 4-hy 56.2 49 0.0011 29.0 7.0 49 34-82 74-122 (333) 79 PRK00043 thiE thiamine-phospha 55.5 60 0.0013 25.6 7.0 42 50-91 24-65 (212) 80 TIGR01859 fruc_bis_ald_ fructo 55.3 75 0.0016 27.2 7.9 54 37-91 75-128 (282) 81 cd07943 DRE_TIM_HOA 4-hydroxy- 54.9 50 0.0011 27.5 6.7 46 35-80 73-118 (263) 82 PF04551 GcpE: GcpE protein; 54.5 28 0.00061 31.1 5.2 50 49-107 33-82 (359) 83 cd00739 DHPS DHPS subgroup of 54.4 29 0.00063 29.2 5.2 54 50-111 27-88 (257) 84 PLN02389 biotin synthase 54.4 41 0.0009 30.1 6.3 62 38-106 168-237 (379) 85 PRK02412 aroD 3-dehydroquinate 54.3 60 0.0013 27.1 7.0 55 34-88 133-193 (253) 86 PRK02048 4-hydroxy-3-methylbut 54.1 28 0.0006 33.2 5.3 55 49-112 43-98 (611) 87 PRK06342 transcription elongat 53.9 1.1E+02 0.0023 24.1 10.0 96 69-180 55-159 (160) 88 TIGR01858 tag_bisphos_ald clas 53.7 84 0.0018 27.0 7.9 53 38-91 74-126 (282) 89 PF02581 TMP-TENI: Thiamine mo 53.4 70 0.0015 25.0 6.9 43 49-91 14-56 (180) 90 PRK02506 dihydroorotate dehydr 53.4 38 0.00083 29.2 5.8 50 37-86 93-155 (310) 91 PLN03034 phosphoglycerate kina 53.1 15 0.00033 34.0 3.4 100 50-171 121-224 (481) 92 PRK15095 FKBP-type peptidyl-pr 52.6 54 0.0012 25.5 6.1 61 125-185 54-121 (156) 93 PRK09195 gatY tagatose-bisphos 51.7 98 0.0021 26.7 8.0 54 37-91 75-128 (284) 94 PF11213 DUF3006: Protein of u 51.7 39 0.00084 22.7 4.5 42 128-175 8-50 (71) 95 PF00162 PGK: Phosphoglycerate 51.0 3.6 7.9E-05 36.9 -0.9 104 50-171 37-146 (384) 96 cd00958 DhnA Class I fructose- 50.9 63 0.0014 26.2 6.5 42 50-91 79-122 (235) 97 cd00502 DHQase_I Type I 3-dehy 50.9 79 0.0017 25.6 7.1 55 35-89 112-172 (225) 98 PLN02282 phosphoglycerate kina 50.8 18 0.00038 32.8 3.4 99 51-171 47-149 (401) 99 TIGR03096 nitroso_cyanin nitro 50.8 43 0.00094 25.7 5.1 42 122-166 61-102 (135) 100 COG1551 CsrA RNA-binding globa 50.5 26 0.00056 24.1 3.4 24 161-185 7-30 (73) 101 PRK07084 fructose-bisphosphate 49.9 1.1E+02 0.0025 26.8 8.2 53 38-91 87-139 (321) 102 PRK00694 4-hydroxy-3-methylbut 49.4 36 0.00077 32.4 5.2 50 49-107 47-96 (606) 103 TIGR00187 ribE riboflavin synt 49.1 40 0.00088 27.5 5.0 36 147-184 22-58 (200) 104 COG2730 BglC Endoglucanase [Ca 49.0 41 0.00089 30.2 5.5 53 50-110 76-140 (407) 105 PRK07998 gatY putative fructos 49.0 1.2E+02 0.0026 26.2 8.1 53 38-91 76-128 (283) 106 PRK05835 fructose-bisphosphate 48.6 1.3E+02 0.0029 26.2 8.4 54 37-91 75-128 (307) 107 PRK06836 aspartate aminotransf 48.4 61 0.0013 28.4 6.4 52 38-91 331-393 (394) 108 COG1167 ARO8 Transcriptional r 48.3 79 0.0017 28.7 7.3 55 36-90 386-456 (459) 109 cd01311 PDC_hydrolase 2-pyrone 47.6 1.1E+02 0.0025 25.2 7.7 33 38-70 71-103 (263) 110 cd07944 DRE_TIM_HOA_like 4-hyd 47.6 74 0.0016 26.8 6.6 45 36-80 71-115 (266) 111 PRK08610 fructose-bisphosphate 47.6 1.3E+02 0.0027 26.0 8.0 53 38-91 79-131 (286) 112 PRK12738 kbaY tagatose-bisphos 47.6 1.2E+02 0.0025 26.3 7.8 54 37-91 75-128 (286) 113 PRK08207 coproporphyrinogen II 47.4 1.5E+02 0.0032 27.5 9.0 39 38-76 256-295 (488) 114 smart00729 Elp3 Elongator prot 47.3 1.2E+02 0.0027 22.9 9.4 43 45-87 95-146 (216) 115 PTZ00005 phosphoglycerate kina 47.3 23 0.00051 32.2 3.6 106 50-171 45-165 (417) 116 PRK06801 hypothetical protein; 47.3 1.7E+02 0.0036 25.2 8.7 53 38-91 76-128 (286) 117 PRK03512 thiamine-phosphate py 46.8 95 0.0021 25.2 6.9 42 50-91 22-63 (211) 118 COG0352 ThiE Thiamine monophos 46.4 88 0.0019 25.7 6.6 42 50-91 24-65 (211) 119 PRK02714 O-succinylbenzoate sy 46.2 57 0.0012 28.1 5.8 64 36-108 109-172 (320) 120 PRK05585 yajC preprotein trans 45.9 44 0.00094 24.5 4.3 17 155-171 48-64 (106) 121 COG1873 Protein implicated in 45.7 55 0.0012 23.1 4.6 60 105-172 18-80 (87) 122 PRK08999 hypothetical protein; 45.6 99 0.0021 26.2 7.2 42 50-91 147-188 (312) 123 PF03659 Glyco_hydro_71: Glyco 45.4 62 0.0014 29.0 6.1 52 50-108 20-71 (386) 124 PLN02741 riboflavin synthase 45.2 50 0.0011 26.8 5.0 35 148-184 24-58 (194) 125 PRK02901 O-succinylbenzoate sy 44.8 1.4E+02 0.003 26.1 8.0 62 36-108 78-143 (327) 126 KOG0407|consensus 44.7 13 0.00028 27.8 1.3 23 43-67 96-118 (139) 127 PF07745 Glyco_hydro_53: Glyco 44.4 52 0.0011 29.0 5.3 49 50-107 27-79 (332) 128 cd00945 Aldolase_Class_I Class 44.2 83 0.0018 24.0 6.0 55 36-90 48-110 (201) 129 PRK12857 fructose-1,6-bisphosp 44.1 1.5E+02 0.0033 25.5 8.0 53 38-91 76-128 (284) 130 cd00405 PRAI Phosphoribosylant 44.0 42 0.00091 26.7 4.4 53 48-106 7-60 (203) 131 PRK06512 thiamine-phosphate py 43.9 1.8E+02 0.0039 23.8 9.9 42 50-91 29-71 (221) 132 cd00947 TBP_aldolase_IIB Tagat 43.9 1.6E+02 0.0035 25.2 8.1 54 37-91 70-123 (276) 133 cd00453 FTBP_aldolase_II Fruct 43.7 1.3E+02 0.0029 26.6 7.7 54 37-91 86-152 (340) 134 PRK05628 coproporphyrinogen II 43.6 2E+02 0.0042 25.3 8.9 42 38-79 96-137 (375) 135 cd02801 DUS_like_FMN Dihydrour 43.4 73 0.0016 25.5 5.8 52 35-86 53-121 (231) 136 PRK05886 yajC preprotein trans 43.3 47 0.001 24.6 4.1 29 155-184 34-62 (109) 137 PRK14469 ribosomal RNA large s 42.6 1.3E+02 0.0028 26.3 7.5 40 34-78 184-224 (343) 138 PRK11613 folP dihydropteroate 41.7 1.7E+02 0.0036 25.2 7.9 68 36-111 14-102 (282) 139 COG0689 Rph RNase PH [Translat 41.7 56 0.0012 27.4 4.8 38 33-73 38-78 (230) 140 PRK09197 fructose-bisphosphate 41.5 1.6E+02 0.0035 26.3 7.9 54 37-91 93-159 (350) 141 PRK13479 2-aminoethylphosphona 41.3 1.8E+02 0.0038 24.9 8.1 44 48-91 311-365 (368) 142 PF09953 DUF2187: Uncharacteri 40.9 55 0.0012 21.5 3.7 26 159-185 3-28 (57) 143 cd03328 MR_like_3 Mandelate ra 39.6 1.8E+02 0.004 25.3 8.1 63 36-108 125-191 (352) 144 PF00478 IMPDH: IMP dehydrogen 39.6 84 0.0018 28.0 5.9 59 36-105 149-217 (352) 145 PF13606 Ank_3: Ankyrin repeat 39.6 23 0.00049 19.5 1.6 16 48-63 13-28 (30) 146 PLN02925 4-hydroxy-3-methylbut 39.5 63 0.0014 31.5 5.3 53 49-110 112-165 (733) 147 smart00306 HintN Hint (Hedgeho 39.3 54 0.0012 22.3 3.8 42 124-169 58-99 (100) 148 PRK14112 urease accessory prot 39.2 94 0.002 24.2 5.5 25 148-173 46-70 (149) 149 PRK05660 HemN family oxidoredu 39.0 2.3E+02 0.0049 25.0 8.6 40 37-76 94-133 (378) 150 cd06555 ASCH_PF0470_like ASC-1 38.9 55 0.0012 24.2 3.9 24 158-181 30-57 (109) 151 PRK04147 N-acetylneuraminate l 38.9 1E+02 0.0022 26.1 6.2 65 36-107 73-139 (293) 152 COG4464 CapC Capsular polysacc 38.5 21 0.00046 29.9 1.8 46 39-85 8-57 (254) 153 TIGR00300 conserved hypothetic 37.9 74 0.0016 28.8 5.2 51 36-86 201-280 (407) 154 COG0107 HisF Imidazoleglycerol 37.7 1E+02 0.0022 26.2 5.7 62 35-107 71-132 (256) 155 TIGR01211 ELP3 histone acetylt 37.7 2.6E+02 0.0057 26.2 9.1 72 37-109 193-269 (522) 156 PRK12737 gatY tagatose-bisphos 37.5 1.9E+02 0.0042 24.8 7.7 53 38-91 76-128 (284) 157 PRK09057 coproporphyrinogen II 37.4 2E+02 0.0044 25.3 8.1 70 37-111 91-169 (380) 158 TIGR00167 cbbA ketose-bisphosp 37.3 2.2E+02 0.0048 24.5 8.0 53 38-91 79-131 (288) 159 PF02814 UreE_N: UreE urease a 37.2 66 0.0014 21.0 3.8 25 148-173 40-64 (65) 160 PRK00073 pgk phosphoglycerate 36.9 27 0.00059 31.5 2.4 100 50-171 39-142 (389) 161 PRK06256 biotin synthase; Vali 36.9 90 0.0019 26.9 5.6 29 38-68 142-170 (336) 162 PRK09289 riboflavin synthase s 36.8 77 0.0017 25.6 4.9 35 148-184 23-57 (194) 163 COG0826 Collagenase and relate 36.6 96 0.0021 27.5 5.8 44 48-91 230-273 (347) 164 PTZ00314 inosine-5'-monophosph 36.6 1E+02 0.0023 28.5 6.2 53 36-91 282-344 (495) 165 PRK14456 ribosomal RNA large s 36.5 1.1E+02 0.0024 27.3 6.2 35 40-79 215-251 (368) 166 TIGR03424 urea_degr_1 urea car 36.3 1.4E+02 0.0029 24.4 6.2 59 121-179 13-82 (198) 167 PRK14113 urease accessory prot 36.1 1E+02 0.0022 24.1 5.2 25 148-173 40-64 (152) 168 PTZ00413 lipoate synthase; Pro 35.9 1.2E+02 0.0025 27.6 6.2 54 36-89 228-290 (398) 169 PF00701 DHDPS: Dihydrodipicol 35.3 1.2E+02 0.0026 25.5 6.0 63 35-103 69-133 (289) 170 PRK08599 coproporphyrinogen II 34.7 2.9E+02 0.0064 24.1 8.6 40 37-76 87-126 (377) 171 cd04739 DHOD_like Dihydroorota 34.6 1.2E+02 0.0026 26.3 6.0 35 36-70 99-135 (325) 172 TIGR01036 pyrD_sub2 dihydrooro 34.4 3.2E+02 0.0068 23.9 8.7 68 36-107 134-218 (335) 173 cd03327 MR_like_2 Mandelate ra 34.4 1.5E+02 0.0033 25.7 6.7 67 36-108 108-180 (341) 174 PF01116 F_bP_aldolase: Fructo 34.4 1.8E+02 0.004 24.9 7.0 54 37-91 74-127 (287) 175 cd00408 DHDPS-like Dihydrodipi 34.3 1.3E+02 0.0028 25.1 6.0 65 36-107 66-132 (281) 176 PF13378 MR_MLE_C: Enolase C-t 34.1 95 0.0021 21.9 4.6 41 44-84 1-43 (111) 177 PRK05892 nucleoside diphosphat 34.1 2.3E+02 0.0049 22.1 10.2 73 105-182 77-156 (158) 178 cd00740 MeTr MeTr subgroup of 33.9 96 0.0021 26.0 5.1 57 50-117 29-88 (252) 179 cd00331 IGPS Indole-3-glycerol 33.6 1E+02 0.0022 24.7 5.1 51 36-86 10-70 (217) 180 PRK04165 acetyl-CoA decarbonyl 33.6 2.4E+02 0.0052 26.0 7.9 69 31-111 86-167 (450) 181 PRK08433 flagellar motor switc 33.6 1.8E+02 0.0038 21.6 5.9 67 98-181 32-98 (111) 182 PRK00366 ispG 4-hydroxy-3-meth 33.4 1.2E+02 0.0026 27.2 5.8 51 36-91 80-130 (360) 183 PRK01261 aroD 3-dehydroquinate 33.3 1.7E+02 0.0038 24.2 6.5 52 33-85 17-74 (229) 184 COG2450 Uncharacterized conser 33.3 1.4E+02 0.0031 22.6 5.4 58 33-92 38-97 (124) 185 cd02932 OYE_YqiM_FMN Old yello 33.0 1.7E+02 0.0038 25.2 6.8 19 54-72 161-179 (336) 186 PRK12290 thiE thiamine-phospha 32.9 1.5E+02 0.0033 27.2 6.5 43 49-91 219-261 (437) 187 PRK15447 putative protease; Pr 32.9 91 0.002 26.8 4.9 36 50-88 230-265 (301) 188 cd02803 OYE_like_FMN_family Ol 32.5 1.6E+02 0.0035 25.1 6.4 19 54-72 148-166 (327) 189 PRK10377 PTS system glucitol/s 32.5 76 0.0017 23.8 3.9 32 149-182 41-72 (120) 190 PRK06939 2-amino-3-ketobutyrat 32.4 1.2E+02 0.0025 26.1 5.7 44 48-91 337-395 (397) 191 PRK08508 biotin synthase; Prov 32.3 1.4E+02 0.003 25.2 5.9 53 36-91 90-150 (279) 192 PF13742 tRNA_anti_2: OB-fold 32.2 1.8E+02 0.004 20.5 8.3 30 153-182 61-99 (99) 193 PF13473 Cupredoxin_1: Cupredo 32.2 68 0.0015 22.6 3.5 42 122-166 35-76 (104) 194 COG4766 EutQ Ethanolamine util 32.2 53 0.0011 26.0 3.0 29 121-155 143-171 (176) 195 PRK01261 aroD 3-dehydroquinate 32.2 2.4E+02 0.0051 23.4 7.1 56 34-89 117-174 (229) 196 PF03610 EIIA-man: PTS system 32.2 1.7E+02 0.0037 20.9 5.7 65 39-110 3-70 (116) 197 PRK15481 transcriptional regul 32.0 1.6E+02 0.0035 26.1 6.6 48 38-87 368-429 (431) 198 PF03829 PTSIIA_gutA: PTS syst 32.0 49 0.0011 24.7 2.7 32 149-182 41-72 (117) 199 TIGR00048 radical SAM enzyme, 31.9 2E+02 0.0043 25.4 7.0 36 40-79 196-232 (355) 200 PRK08898 coproporphyrinogen II 31.8 2.1E+02 0.0046 25.4 7.3 66 37-110 109-186 (394) 201 TIGR03784 marine_sortase sorta 31.8 81 0.0017 25.1 4.1 24 157-180 106-132 (174) 202 PLN02898 HMP-P kinase/thiamin- 31.7 1.7E+02 0.0037 26.8 6.8 42 50-91 310-351 (502) 203 PF03471 CorC_HlyC: Transporte 31.7 95 0.0021 20.9 4.0 29 158-186 45-73 (81) 204 KOG2792|consensus 31.7 80 0.0017 27.1 4.2 43 61-106 141-186 (280) 205 PF02699 YajC: Preprotein tran 31.6 18 0.00038 25.2 0.3 30 154-184 31-60 (82) 206 PRK14017 galactonate dehydrata 31.5 1.7E+02 0.0037 25.8 6.6 67 36-108 113-186 (382) 207 TIGR00538 hemN oxygen-independ 31.5 3.9E+02 0.0085 24.1 9.3 39 38-76 139-177 (455) 208 PRK02615 thiamine-phosphate py 31.4 2.5E+02 0.0054 24.9 7.5 53 39-91 149-201 (347) 209 cd02810 DHOD_DHPD_FMN Dihydroo 31.3 1.6E+02 0.0035 24.6 6.2 51 36-86 98-160 (289) 210 KOG3303|consensus 31.1 42 0.00091 27.2 2.3 79 51-140 88-173 (192) 211 TIGR01521 FruBisAldo_II_B fruc 30.8 3E+02 0.0065 24.5 7.9 54 37-91 74-134 (347) 212 PRK13020 riboflavin synthase s 30.8 1.2E+02 0.0025 24.9 5.0 35 148-184 23-58 (206) 213 cd01335 Radical_SAM Radical SA 30.6 2.2E+02 0.0048 21.0 9.1 36 44-79 82-117 (204) 214 PRK09196 fructose-1,6-bisphosp 30.5 3E+02 0.0066 24.5 7.9 53 38-91 77-136 (347) 215 PF02662 FlpD: Methyl-viologen 30.4 1.9E+02 0.0041 21.5 5.7 57 32-91 27-90 (124) 216 PRK12271 rps10p 30S ribosomal 30.3 90 0.0019 22.7 3.8 31 61-91 1-31 (102) 217 PRK05096 guanosine 5'-monophos 30.0 1.5E+02 0.0032 26.4 5.8 53 36-91 151-213 (346) 218 PRK00366 ispG 4-hydroxy-3-meth 29.8 98 0.0021 27.7 4.6 45 49-107 44-88 (360) 219 PLN02489 homocysteine S-methyl 29.8 1.7E+02 0.0036 25.7 6.1 78 29-115 125-227 (335) 220 PRK06108 aspartate aminotransf 29.8 1.9E+02 0.0041 24.8 6.5 48 39-87 319-380 (382) 221 PF01729 QRPTase_C: Quinolinat 29.8 2.8E+02 0.006 21.8 7.1 44 37-86 81-124 (169) 222 cd05800 PGM_like2 This PGM-lik 29.7 2.4E+02 0.0051 25.5 7.3 88 16-112 154-249 (461) 223 COG0809 QueA S-adenosylmethion 29.7 66 0.0014 28.6 3.5 28 155-183 97-124 (348) 224 PRK06033 hypothetical protein; 29.4 99 0.0022 21.5 3.8 67 98-181 7-73 (83) 225 TIGR02326 transamin_PhnW 2-ami 29.3 3E+02 0.0065 23.4 7.7 37 50-86 312-359 (363) 226 COG3033 TnaA Tryptophanase [Am 29.2 58 0.0013 29.6 3.1 35 33-68 10-44 (471) 227 cd02966 TlpA_like_family TlpA- 29.2 1.7E+02 0.0038 19.3 6.8 33 51-83 39-75 (116) 228 PRK13347 coproporphyrinogen II 29.0 4.4E+02 0.0095 23.9 9.2 38 37-74 139-176 (453) 229 TIGR00849 gutA PTS system, glu 29.0 97 0.0021 23.3 3.9 31 150-182 42-72 (121) 230 cd06541 ASCH ASC-1 homology or 28.9 1.1E+02 0.0024 21.9 4.2 24 158-181 29-55 (105) 231 cd04738 DHOD_2_like Dihydrooro 28.9 2.8E+02 0.0061 24.0 7.4 54 36-89 128-198 (327) 232 PF12198 Tuberculin: Theoretic 28.7 53 0.0011 19.0 1.8 18 32-49 16-33 (34) 233 PRK03170 dihydrodipicolinate s 28.6 1.6E+02 0.0035 24.8 5.7 65 36-107 70-136 (292) 234 cd04741 DHOD_1A_like Dihydroor 28.3 1.8E+02 0.004 24.7 6.1 50 37-86 92-155 (294) 235 PF13509 S1_2: S1 domain; PDB: 28.2 57 0.0012 21.1 2.3 23 146-168 24-46 (61) 236 TIGR00539 hemN_rel putative ox 28.2 3.9E+02 0.0085 23.2 8.3 40 37-76 87-126 (360) 237 COG1180 PflA Pyruvate-formate 28.1 1.5E+02 0.0032 25.0 5.3 51 50-108 71-121 (260) 238 cd03325 D-galactonate_dehydrat 28.1 3.5E+02 0.0076 23.5 7.9 67 36-108 112-185 (352) 239 PRK06225 aspartate aminotransf 28.0 1.4E+02 0.003 25.8 5.4 42 48-90 322-377 (380) 240 TIGR00824 EIIA-man PTS system, 27.9 2.4E+02 0.0051 20.5 5.8 65 38-109 4-70 (116) 241 PF01180 DHO_dh: Dihydroorotat 27.9 2.1E+02 0.0045 24.2 6.3 35 36-70 96-134 (295) 242 cd05805 MPG1_transferase GTP-m 27.9 1.7E+02 0.0038 26.2 6.1 87 17-111 150-242 (441) 243 PRK09289 riboflavin synthase s 27.9 1.5E+02 0.0033 23.9 5.2 37 146-184 117-154 (194) 244 TIGR00510 lipA lipoate synthas 27.7 1.8E+02 0.0038 25.2 5.8 20 49-68 155-174 (302) 245 PF00128 Alpha-amylase: Alpha 27.6 1.1E+02 0.0023 24.9 4.4 37 51-87 152-189 (316) 246 PRK13962 bifunctional phosphog 27.6 47 0.001 32.0 2.5 100 50-171 42-146 (645) 247 PRK05698 fliN flagellar motor 27.6 1.4E+02 0.0031 23.5 4.7 66 98-180 79-144 (155) 248 TIGR00433 bioB biotin syntheta 27.5 1.3E+02 0.0029 25.1 5.0 38 37-77 112-149 (296) 249 cd05845 Ig2_L1-CAM_like Second 27.3 2.3E+02 0.005 20.1 5.7 54 122-178 11-65 (95) 250 PRK13263 ureE urease accessory 27.2 1.9E+02 0.004 23.9 5.6 33 148-183 46-78 (206) 251 TIGR03471 HpnJ hopanoid biosyn 27.1 4.7E+02 0.01 23.6 8.9 41 38-79 276-316 (472) 252 PRK02610 histidinol-phosphate 27.0 2.3E+02 0.005 24.5 6.6 50 38-89 316-371 (374) 253 PRK06788 flagellar motor switc 26.8 1.4E+02 0.0031 22.4 4.5 69 98-183 34-102 (119) 254 cd05829 Sortase_E Sortase E (S 26.8 1.1E+02 0.0024 23.2 4.0 23 158-180 71-96 (144) 255 cd03329 MR_like_4 Mandelate ra 26.8 2.2E+02 0.0047 25.0 6.4 50 51-108 149-198 (368) 256 PRK05764 aspartate aminotransf 26.6 1E+02 0.0022 26.7 4.3 39 50-89 341-391 (393) 257 PRK06294 coproporphyrinogen II 26.4 4.5E+02 0.0097 23.1 8.4 40 37-76 90-129 (370) 258 COG0502 BioB Biotin synthase a 26.4 89 0.0019 27.7 3.8 31 37-69 133-163 (335) 259 cd00318 Phosphoglycerate_kinas 26.4 42 0.0009 30.4 1.8 106 50-171 36-147 (397) 260 smart00148 PLCXc Phospholipase 26.3 2.8E+02 0.0061 20.7 6.2 53 48-107 29-95 (135) 261 COG4558 ChuT ABC-type hemin tr 26.3 2.5E+02 0.0054 24.5 6.3 44 33-81 97-142 (300) 262 TIGR02539 SepCysS Sep-tRNA:Cys 26.2 1.8E+02 0.0039 25.2 5.8 40 50-89 321-368 (370) 263 TIGR00683 nanA N-acetylneurami 26.1 2.3E+02 0.005 24.0 6.3 37 51-87 25-67 (290) 264 PRK13399 fructose-1,6-bisphosp 25.9 4.2E+02 0.0091 23.6 7.9 53 38-91 77-136 (347) 265 cd03321 mandelate_racemase Man 25.9 1.3E+02 0.0029 26.1 4.8 64 36-108 130-195 (355) 266 cd03326 MR_like_1 Mandelate ra 25.6 2.5E+02 0.0055 25.0 6.6 49 51-108 166-214 (385) 267 PLN02892 isocitrate lyase 25.5 2E+02 0.0043 27.4 6.0 55 37-91 170-242 (570) 268 PF13550 Phage-tail_3: Putativ 25.5 1.5E+02 0.0034 22.0 4.7 25 157-181 137-163 (164) 269 cd03315 MLE_like Muconate lact 25.5 2.8E+02 0.006 22.9 6.5 63 36-108 74-138 (265) 270 COG0126 Pgk 3-phosphoglycerate 25.5 86 0.0019 28.4 3.5 104 50-171 42-149 (395) 271 KOG2733|consensus 25.4 2.2E+02 0.0048 25.9 6.0 55 34-91 81-137 (423) 272 cd06552 ASCH_yqfb_like ASC-1 h 25.4 1.3E+02 0.0028 20.9 3.9 23 159-181 28-53 (100) 273 cd00950 DHDPS Dihydrodipicolin 25.4 1.9E+02 0.0042 24.1 5.6 65 36-107 69-135 (284) 274 PRK07107 inosine 5-monophospha 25.3 2E+02 0.0042 26.9 6.0 20 47-66 292-311 (502) 275 cd04740 DHOD_1B_like Dihydroor 25.1 2.5E+02 0.0055 23.6 6.3 50 37-86 90-152 (296) 276 COG0821 gcpE 1-hydroxy-2-methy 25.1 1.8E+02 0.0039 26.0 5.4 44 49-106 38-81 (361) 277 cd00954 NAL N-Acetylneuraminic 25.0 2.7E+02 0.0059 23.4 6.5 65 36-107 70-137 (288) 278 cd01422 MGS Methylglyoxal synt 25.0 1.7E+02 0.0036 21.4 4.6 61 37-105 48-109 (115) 279 PF10844 DUF2577: Protein of u 24.8 2.3E+02 0.0051 20.1 5.2 13 156-168 73-85 (100) 280 TIGR03249 KdgD 5-dehydro-4-deo 24.8 2E+02 0.0044 24.3 5.7 64 35-104 73-137 (296) 281 PTZ00039 40S ribosomal protein 24.7 1.2E+02 0.0026 22.6 3.7 31 61-91 16-46 (115) 282 COG0309 HypE Hydrogenase matur 24.7 3.3E+02 0.0071 24.2 7.0 26 66-91 96-122 (339) 283 PRK07379 coproporphyrinogen II 24.7 5E+02 0.011 23.1 8.8 40 37-76 102-141 (400) 284 TIGR01302 IMP_dehydrog inosine 24.7 2.2E+02 0.0048 25.9 6.2 31 37-71 266-297 (450) 285 cd06451 AGAT_like Alanine-glyo 24.5 4.2E+02 0.0092 22.3 7.7 46 42-87 297-355 (356) 286 TIGR01305 GMP_reduct_1 guanosi 24.5 1.5E+02 0.0033 26.4 4.8 31 36-69 150-180 (343) 287 cd00006 PTS_IIA_man PTS_IIA, P 24.5 2.1E+02 0.0046 20.7 5.1 63 39-108 4-68 (122) 288 TIGR01346 isocit_lyase isocitr 24.5 2.3E+02 0.0049 26.8 6.2 75 37-117 151-245 (527) 289 cd03318 MLE Muconate Lactonizi 24.4 2.5E+02 0.0054 24.4 6.3 65 36-109 131-198 (365) 290 PRK00278 trpC indole-3-glycero 24.3 2.4E+02 0.0051 23.7 5.9 33 36-68 49-91 (260) 291 COG0825 AccA Acetyl-CoA carbox 24.2 1.5E+02 0.0032 26.0 4.6 41 67-114 127-167 (317) 292 PRK14460 ribosomal RNA large s 24.1 3.1E+02 0.0066 24.3 6.8 35 39-79 195-231 (354) 293 TIGR03537 DapC succinyldiamino 24.0 1.8E+02 0.0039 24.8 5.3 45 39-84 291-348 (350) 294 KOG2550|consensus 23.9 87 0.0019 28.8 3.3 44 48-91 301-354 (503) 295 COG4702 Uncharacterized conser 23.9 1.6E+02 0.0035 23.3 4.4 42 65-112 20-61 (168) 296 PF09926 DUF2158: Uncharacteri 23.8 87 0.0019 20.0 2.4 23 161-183 2-24 (53) 297 TIGR00007 phosphoribosylformim 23.8 2.7E+02 0.0059 22.3 6.1 61 41-113 75-136 (230) 298 cd03319 L-Ala-DL-Glu_epimerase 23.8 2.3E+02 0.0049 24.1 5.8 61 37-108 124-186 (316) 299 PRK14711 ureE urease accessory 23.5 2.6E+02 0.0056 22.7 5.7 31 149-180 50-80 (191) 300 PLN02428 lipoic acid synthase 23.4 2.6E+02 0.0056 24.9 6.2 30 37-67 182-212 (349) 301 PRK06444 prephenate dehydrogen 23.3 1.7E+02 0.0036 23.7 4.6 60 20-87 71-135 (197) 302 TIGR01979 sufS cysteine desulf 23.3 3.2E+02 0.0069 23.6 6.8 29 63-91 374-403 (403) 303 PRK13958 N-(5'-phosphoribosyl) 23.3 1.8E+02 0.0038 23.6 4.8 58 48-111 9-67 (207) 304 PF11964 SpoIIAA-like: SpoIIAA 23.1 1.2E+02 0.0025 21.1 3.3 38 63-107 2-40 (109) 305 TIGR01520 FruBisAldo_II_A fruc 22.9 4.8E+02 0.01 23.4 7.7 55 36-91 99-166 (357) 306 TIGR00649 MG423 conserved hypo 22.7 1.6E+02 0.0035 26.3 4.8 30 55-84 344-375 (422) 307 COG1830 FbaB DhnA-type fructos 22.6 3.9E+02 0.0084 22.9 6.8 57 51-113 101-159 (265) 308 PRK08624 hypothetical protein; 22.6 4.4E+02 0.0095 23.8 7.4 67 37-108 267-337 (373) 309 cd00452 KDPG_aldolase KDPG and 22.5 1.9E+02 0.004 22.8 4.7 34 49-85 18-51 (190) 310 PLN02858 fructose-bisphosphate 22.5 4E+02 0.0088 28.2 8.2 55 36-91 1169-1223(1378) 311 PRK15072 bifunctional D-altron 22.4 3.4E+02 0.0073 24.2 6.8 19 51-69 133-151 (404) 312 COG2108 Uncharacterized conser 22.3 1.3E+02 0.0029 26.7 4.0 42 46-91 120-164 (353) 313 TIGR00612 ispG_gcpE 1-hydroxy- 22.3 1.2E+02 0.0027 26.9 3.8 44 49-106 36-79 (346) 314 PF09347 DUF1989: Domain of un 22.3 2.1E+02 0.0046 22.5 4.9 59 121-179 9-78 (166) 315 COG0106 HisA Phosphoribosylfor 22.2 2.8E+02 0.006 23.5 5.8 63 40-115 77-140 (241) 316 cd00571 UreE UreE urease acces 22.1 3.1E+02 0.0067 20.7 5.7 25 148-173 44-68 (136) 317 PF03325 Herpes_PAP: Herpesvir 22.0 1.8E+02 0.0039 24.7 4.6 91 58-158 23-113 (281) 318 cd00951 KDGDH 5-dehydro-4-deox 22.0 2.9E+02 0.0063 23.3 6.1 63 36-104 69-132 (289) 319 PF00012 HSP70: Hsp70 protein; 21.8 1.2E+02 0.0026 28.1 3.9 67 36-116 135-205 (602) 320 PF13653 GDPD_2: Glycerophosph 21.8 1.2E+02 0.0025 17.1 2.4 17 48-64 8-24 (30) 321 cd03692 mtIF2_IVc mtIF2_IVc: t 21.8 1.9E+02 0.0042 19.6 4.1 11 108-118 19-29 (84) 322 PRK08983 fliN flagellar motor 21.7 2.1E+02 0.0045 21.7 4.5 66 98-180 51-116 (127) 323 cd00377 ICL_PEPM Members of th 21.5 2.5E+02 0.0054 23.3 5.5 52 37-89 70-139 (243) 324 PRK13575 3-dehydroquinate dehy 21.4 4.7E+02 0.01 21.6 8.2 74 35-113 124-203 (238) 325 TIGR01921 DAP-DH diaminopimela 21.3 2.2E+02 0.0049 25.0 5.3 45 44-91 68-112 (324) 326 TIGR02313 HpaI-NOT-DapA 2,4-di 21.3 3.1E+02 0.0068 23.2 6.2 65 36-107 69-136 (294) 327 PRK07259 dihydroorotate dehydr 21.0 2.9E+02 0.0063 23.3 5.9 50 37-86 92-155 (301) 328 PRK03620 5-dehydro-4-deoxygluc 20.9 2.9E+02 0.0062 23.6 5.9 63 36-104 76-139 (303) 329 PF06903 VirK: VirK protein; 20.9 80 0.0017 23.0 2.0 15 98-112 17-31 (100) 330 COG0191 Fba Fructose/tagatose 20.8 3.6E+02 0.0077 23.4 6.3 47 45-91 83-129 (286) 331 PF04203 Sortase: Sortase fami 20.8 1.3E+02 0.0028 21.8 3.3 24 158-181 59-85 (128) 332 PF00682 HMGL-like: HMGL-like 20.8 3.5E+02 0.0075 21.7 6.1 49 53-109 114-162 (237) 333 TIGR03301 PhnW-AepZ 2-aminoeth 20.8 5E+02 0.011 21.6 7.8 37 50-86 307-354 (355) 334 PRK09058 coproporphyrinogen II 20.8 6.4E+02 0.014 22.8 9.3 39 38-76 151-189 (449) 335 PRK09875 putative hydrolase; P 20.7 1.9E+02 0.0041 24.9 4.7 54 45-110 161-214 (292) 336 PRK05286 dihydroorotate dehydr 20.7 3.1E+02 0.0067 23.9 6.1 66 15-88 124-206 (344) 337 PRK13576 3-dehydroquinate dehy 20.6 1.8E+02 0.004 23.9 4.4 35 36-72 2-39 (216) 338 PLN02452 phosphoserine transam 20.5 2.4E+02 0.0052 24.9 5.4 47 39-88 9-62 (365) 339 PF01624 MutS_I: MutS domain I 20.5 88 0.0019 22.5 2.3 48 19-67 37-84 (113) 340 COG0710 AroD 3-dehydroquinate 20.4 3.2E+02 0.007 22.8 5.8 57 50-113 136-193 (231) 341 PRK14484 phosphotransferase ma 20.3 1.8E+02 0.004 21.8 4.0 66 39-113 5-73 (124) 342 KOG1816|consensus 20.2 4.3E+02 0.0094 23.1 6.6 74 98-186 88-174 (308) 343 PRK07428 nicotinate-nucleotide 20.0 3.6E+02 0.0078 23.2 6.2 43 37-85 197-239 (288) 344 PRK08088 4-aminobutyrate amino 20.0 3.1E+02 0.0066 24.4 6.1 40 50-89 374-423 (425) No 1 >PF00224 PK: Pyruvate kinase, barrel domain; InterPro: IPR015793 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP:ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the two barrel domains, the beta/alpha-barrel, and the beta-barrel inserted within it.; GO: 0000287 magnesium ion binding, 0004743 pyruvate kinase activity, 0030955 potassium ion binding, 0006096 glycolysis; PDB: 3HQQ_W 3KTX_A 3E0V_A 3QV6_D 3QV7_D 1PKL_D 3HQP_A 3QV8_D 3HQO_C 3IS4_B .... Probab=100.00 E-value=2.1e-45 Score=321.18 Aligned_cols=144 Identities=49% Similarity=0.781 Sum_probs=130.1 Q ss_pred CCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEe Q psy254 34 VRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRT 113 (187) Q Consensus 34 ~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRt 113 (187) +|+||||||||||+++++.|++|+++||||||||||||++++|+++++++|+++++++ ++++||+||+|||||| T Consensus 1 mRkTKIi~TiGPas~~~e~l~~li~aGm~v~RiN~SHg~~e~~~~~i~~iR~a~~~~~------~~i~IllDl~GPkIRt 74 (348) T PF00224_consen 1 MRKTKIIATIGPASESVEVLRKLIEAGMNVARINFSHGTHEEHKEIIENIREAEKELG------KPIAILLDLKGPKIRT 74 (348) T ss_dssp -SSSEEEEEESTTTCSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHHTT------TS-EEEEEE-TS-EBB T ss_pred CCCCeEEEEECCCCCCHHHHHHHHHhccEEEEEeeecCCHHHHHHHHHHHHHHHhccC------CceEEEeccCCCccee Confidence 6999999999999999999999999999999999999999999999999999999998 7899999999999999 Q ss_pred eecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeCCe Q psy254 114 GLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVKSY 184 (187) Q Consensus 114 G~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~ 184 (187) |.+.++ ..++.|++|++|+|+.+..+...++++.|++||++|+++|++||+||+|||+|.|+|.++.++. T Consensus 75 g~l~~g-~~~i~L~~G~~v~lt~d~~~~~~g~~~~I~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~ 144 (348) T PF00224_consen 75 GRLKDG-KKEIELKKGDTVTLTTDDSYEESGDSNRIPVNYPELFEDVKPGDKILIDDGKIELEVTEVDGDS 144 (348) T ss_dssp -BBTTS-SSSEEE-TTSEEEEESSCTGTTCBBSSEEEBSSTTHHHHS-TTEEEEETTTTEEEEEEEEESTE T ss_pred eeeccc-cccccccCCCEEEEEeccccccccCcccccCCchhhhhhcCCCCEEEEcCCCcEEEEEEEcCCc Confidence 999874 2579999999999999988877778899999999999999999999999999999999999887 No 2 >PRK08187 pyruvate kinase; Validated Probab=100.00 E-value=3.9e-44 Score=323.64 Aligned_cols=167 Identities=22% Similarity=0.317 Sum_probs=148.9 Q ss_pred hhhhhccHHHhhcCCCCCCCCCCCCCceEEEec-CCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHH Q psy254 11 RALAANTFVDHLCGLDIDNKSSYVRLTGIICTI-GPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVEN 89 (187) Q Consensus 11 ~~~~~~~~l~~~~~l~i~~~~~~~r~TkIi~Ti-GPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~ 89 (187) .++.++..|++.+.. ++++++..|+||||||| ||++++++.|++|+++||||||||||||++++|+++|++||+++++ T Consensus 110 ~~~~g~~~l~~~~~~-l~g~~~~~r~tkIv~Tlg~pa~~~~e~i~~Li~aGmdvaRiN~SHg~~e~~~~~i~~vR~a~~~ 188 (493) T PRK08187 110 QFFAGERLLAAHTEE-LFGPRPAARRTRIMVTLPSEAADDPDFVLRLAERGMDCARINCAHDDPAAWQAMIGHLRQAERA 188 (493) T ss_pred hhhhHHHHHHHHHHH-HcCCCcCCCCceEEEECCCCccCCHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHH Confidence 445566777777777 89999999999999999 5999999999999999999999999999999999999999999999 Q ss_pred hCCCCCCcceeEEEeeCCCCeeEeeecCCCCcccEEeeeCCEEEEeeCCCccc-CCCcCEEeeCcchhhhcCCCCCEEEE Q psy254 90 YSKRIGMPHALAIALDTKGPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAFAE-KGSATDLYVDYTNITKVVKPGSRIFV 168 (187) Q Consensus 90 ~~~~~~~~~~v~I~~Dl~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~-~~~~~~i~v~~~~l~~~v~~Gd~Ili 168 (187) ++ ++|+||+||+|||||||.+.++ .+++.|++|+.|+|+.+..... .++...|+|+|+++++++++||+||+ T Consensus 189 ~g------~~i~Il~DL~GPKIRtG~l~~~-~~~~~l~~Gd~i~l~~~~~~~~~~~~~~~i~~~~~~l~~~v~~Gd~Ili 261 (493) T PRK08187 189 TG------RRCKILMDLAGPKIRTGAVAGP-LGKTRLYTGDRLALVAQGPPRRIDEEHFQVTCTLPEILARLAVGARVWI 261 (493) T ss_pred cC------CCeEEEEeCCCCceeecccCCC-CccEEecCCCEEEEeccccccCCCCCccEEEechHHHHHhcCCCCEEEE Confidence 99 8999999999999999999864 2358999999999998754221 12456899999999999999999999 Q ss_pred eCCeEEEEEEEEeCCee Q psy254 169 DDGLISLVVKSIVKSYQ 185 (187) Q Consensus 169 dDG~i~l~V~~v~~~~i 185 (187) |||+|.|+|.+++++.+ T Consensus 262 dDG~I~l~V~~v~~~~v 278 (493) T PRK08187 262 DDGKLGARVERVGPGGA 278 (493) T ss_pred eCCeEEEEEEEEeCCEE Confidence 99999999999988765 No 3 >PLN02762 pyruvate kinase complex alpha subunit Probab=100.00 E-value=2.8e-43 Score=318.42 Aligned_cols=141 Identities=33% Similarity=0.558 Sum_probs=131.0 Q ss_pred CCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEe Q psy254 34 VRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRT 113 (187) Q Consensus 34 ~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRt 113 (187) +|+|||||||||||++++.|++|+++||||||||||||++++|+++++++|+++++++ ++++||+||+|||||| T Consensus 24 ~rrTKIV~TiGPas~~~e~l~~li~aGm~v~RlNfSHg~~e~h~~~i~~iR~~~~~~~------~~vaIl~Dl~GPkIR~ 97 (509) T PLN02762 24 TRRTKLVCTIGPACCGFEQLEALAMGGMNVARLNMCHGTREWHRDVIRRVRRLNEEKG------FAVAVMMDTEGSEIHM 97 (509) T ss_pred CCCceEEEEeCCCCCCHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHcC------CceEEEecCCCCceEE Confidence 7899999999999999999999999999999999999999999999999999999998 8999999999999999 Q ss_pred eecCCCCcccEEeeeCCEEEEeeCCCcccCC--CcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeCCee Q psy254 114 GLLQGGGSAEVELVKGQTIRLTTDAAFAEKG--SATDLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVKSYQ 185 (187) Q Consensus 114 G~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~--~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~i 185 (187) |.+.++ +++.|++|+.|.|+.+. ..+ +.+.++++|++|++++++||.||+|||.|.|+|.+++++.+ T Consensus 98 g~~~~~--~~i~l~~G~~v~lt~~~---~~g~~~~~~i~v~y~~l~~~v~~Gd~IlidDG~i~l~V~~~~~~~v 166 (509) T PLN02762 98 GDLGGA--SSAKAEDGEEWTFTVRK---FDGSRPEFTIQVNYDGFAEDVKVGDELVVDGGMVRFEVIEKIGPDV 166 (509) T ss_pred EecCCC--ccEEecCCCEEEEeCCc---cCCCCCCcEEeechHHHHHhcCCCCEEEEeCCEEEEEEEEEECCEE Confidence 999752 46999999999999763 234 35789999999999999999999999999999999988765 No 4 >PTZ00066 pyruvate kinase; Provisional Probab=100.00 E-value=3.8e-43 Score=317.50 Aligned_cols=160 Identities=39% Similarity=0.595 Sum_probs=142.8 Q ss_pred cHHHhhcCCCC-CCCCCCCCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHh-CCCC Q psy254 17 TFVDHLCGLDI-DNKSSYVRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENY-SKRI 94 (187) Q Consensus 17 ~~l~~~~~l~i-~~~~~~~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~-~~~~ 94 (187) +++.|.+.+++ ...+..+|+|||||||||+|+++++|++|+++||||||||||||++++|+++++++|+++++. + T Consensus 19 ~~~~~~~~~~~~~~~~~~~rktKIi~TiGPas~~~e~l~~mi~aGm~v~RlN~SHg~~e~~~~~i~~vR~~~~~~~~--- 95 (513) T PTZ00066 19 TNISLDKILEPISDNDLRQKKTHIVCTMGPACKNVETLVKLIDAGMNICRFNFSHGDHESHKKTLNNVREAAKARPN--- 95 (513) T ss_pred cccchhhhccccccCcccCCCCeEEEeeCCCcCCHHHHHHHHHcCCCEEEEECCCCCHHHHHHHHHHHHHHHHhcCC--- Confidence 44555566765 344567899999999999999999999999999999999999999999999999999999986 5 Q ss_pred CCcceeEEEeeCCCCeeEeeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEE Q psy254 95 GMPHALAIALDTKGPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLIS 174 (187) Q Consensus 95 ~~~~~v~I~~Dl~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~ 174 (187) ++++||+||+|||||+|.++++ +++.|++|+.|+|+.+.. ..++++.++++|++|++++++||+||+|||+|. T Consensus 96 ---~~iaIl~Dl~GPkiR~g~~~~~--~~i~l~~G~~~~l~~~~~--~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~ 168 (513) T PTZ00066 96 ---ANLGILLDTKGPEIRTGFLKNH--KPITLKEGQTLKITTDYT--FLGDETCISCSYKKLPQSVKVGNIILIADGSLS 168 (513) T ss_pred ---CceEEEeeCCCCceeecccCCC--CeEEeCCCCEEEEecCCc--cCCCCcEEecchHHHHhhccCCCEEEEeCCEEE Confidence 8999999999999999999863 469999999999998743 357778899999999999999999999999999 Q ss_pred EEEEEEeCCeee Q psy254 175 LVVKSIVKSYQL 186 (187) Q Consensus 175 l~V~~v~~~~i~ 186 (187) |+|.+++++.+. T Consensus 169 l~V~~~~~~~v~ 180 (513) T PTZ00066 169 CKVLEVHDDYII 180 (513) T ss_pred EEEEEEECCEEE Confidence 999999887653 No 5 >COG0469 PykF Pyruvate kinase [Carbohydrate transport and metabolism] Probab=100.00 E-value=3.9e-43 Score=314.59 Aligned_cols=144 Identities=47% Similarity=0.745 Sum_probs=134.8 Q ss_pred CCCCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCee Q psy254 32 SYVRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEI 111 (187) Q Consensus 32 ~~~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkI 111 (187) ..+|+||||||||||+++++.|++|++|||||||||||||++++|.++++++|+++++++ +|++||+||||||| T Consensus 2 ~~~~kTKIVaTiGPas~s~e~l~~li~aG~nV~RlNfSHG~~e~h~~~i~~vR~~~~~~~------~~vaIl~DlkGPkI 75 (477) T COG0469 2 RMMRKTKIVATLGPATESEEMLEKLIEAGMNVVRLNFSHGDHEEHKKRIDNVREAAEKLG------RPVAILLDLKGPKI 75 (477) T ss_pred CCCccceEEEEECCCCCCHHHHHHHHHccCcEEEEecCCCChHHHHHHHHHHHHHHHHhC------CceEEEEcCCCCcc Confidence 358999999999999999999999999999999999999999999999999999999999 99999999999999 Q ss_pred EeeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeCCee Q psy254 112 RTGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVKSYQ 185 (187) Q Consensus 112 RtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~i 185 (187) |+|.+.+ +.+.|+.|+.|+|+.+.... .++++.++++|+.|+++|++|++||+|||+|.|+|.+++++.+ T Consensus 76 R~g~~~~---~~~~l~~G~~~~~~~~~~~~-~~~~~~v~v~y~~l~~dV~~G~~iLlDDG~i~l~V~~v~~~~v 145 (477) T COG0469 76 RTGKFKG---GAVELEKGEKFTLTTDDKVG-EGDEERVSVDYKDLAKDVKPGDRILLDDGKIELRVVEVDGDAV 145 (477) T ss_pred eeEecCC---CcEEeecCCEEEEecccccc-CCCCcEEeccHHHHHhhcCCCCEEEEeCCeeEEEEEEeeCCEE Confidence 9999997 36999999999999987642 3457889999999999999999999999999999999998764 No 6 >PLN02765 pyruvate kinase Probab=100.00 E-value=6.7e-43 Score=316.42 Aligned_cols=159 Identities=32% Similarity=0.513 Sum_probs=138.9 Q ss_pred hccHHHhhcCCCCCCCCCCCCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCC Q psy254 15 ANTFVDHLCGLDIDNKSSYVRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRI 94 (187) Q Consensus 15 ~~~~l~~~~~l~i~~~~~~~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~ 94 (187) +...++++ ++........|+|||||||||+|++++.|++|+++||||||||||||++++|.++|++||+++++++ T Consensus 10 ~~~~~~~~--~~~~~~~~~~~~tKIVaTiGPas~~~e~l~~li~aGm~v~RlNfSHg~~e~h~~~i~~vR~~~~~~~--- 84 (526) T PLN02765 10 EPIRLASI--LEPSKPSFFPALTKIVGTLGPKSRSVEVIEACLKAGMSVARFDFSWGDAEYHQETLENLKIAVKNTK--- 84 (526) T ss_pred cccchhhh--cccccccccCCCceEEEEeCCCCCCHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHhC--- Confidence 44566666 4333322233459999999999999999999999999999999999999999999999999999998 Q ss_pred CCcceeEEEeeCCCCeeEeeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCC--- Q psy254 95 GMPHALAIALDTKGPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDG--- 171 (187) Q Consensus 95 ~~~~~v~I~~Dl~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG--- 171 (187) +|++||+||+|||||||.+++ +++.|++|++|+|+.+.. ..++++.++++|++|++++++||+||+||| T Consensus 85 ---~~vaIl~Dl~GPkIR~g~~~~---~~i~l~~G~~~~l~~~~~--~~g~~~~i~v~~~~l~~~v~~Gd~IlidDG~~~ 156 (526) T PLN02765 85 ---KLCAVMLDTVGPELQVINKTE---KPISLKAGNTVTLTPDQS--KEASSEVLPINFPGLAKAVKPGDTIFVGQYLFT 156 (526) T ss_pred ---CCeEEEecCCCCceeeeecCC---CcEecCCCCEEEEecccc--cCCCCCEEeechHHHHhhcCCCCEEEECCcccc Confidence 899999999999999999975 479999999999998643 356778999999999999999999999988 Q ss_pred -----eEEEEEEEEeCCeee Q psy254 172 -----LISLVVKSIVKSYQL 186 (187) Q Consensus 172 -----~i~l~V~~v~~~~i~ 186 (187) +|.|+|.+++++.+. T Consensus 157 g~~dg~i~l~V~~~~~~~v~ 176 (526) T PLN02765 157 GSETTSVWLEVDEVKGDDVV 176 (526) T ss_pred cccCceEEEEEEEEECCEEE Confidence 899999999877653 No 7 >PRK09206 pyruvate kinase; Provisional Probab=100.00 E-value=7.4e-43 Score=313.83 Aligned_cols=143 Identities=45% Similarity=0.730 Sum_probs=133.3 Q ss_pred CCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEe Q psy254 34 VRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRT 113 (187) Q Consensus 34 ~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRt 113 (187) +|+|||||||||+|+++|+|++|+++||||||||||||++++|.++|+++|+++++++ ++++||+||+|||||| T Consensus 1 mr~tKIi~TiGPas~~~e~l~~li~aGm~v~RlN~sHg~~~~~~~~i~~vr~~~~~~~------~~i~Il~Dl~GPkiR~ 74 (470) T PRK09206 1 MKKTKIVCTIGPKTESEEMLTKLLDAGMNVMRLNFSHGDYAEHGQRIKNLRNVMSKTG------KKAAILLDTKGPEIRT 74 (470) T ss_pred CCCceEEEEeCCCCCCHHHHHHHHHcCCCEEEEECCCCCHHHHHHHHHHHHHHHHHhC------CCeEEEeeCCCCceec Confidence 5899999999999999999999999999999999999999999999999999999998 8999999999999999 Q ss_pred eecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeCCeee Q psy254 114 GLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVKSYQL 186 (187) Q Consensus 114 G~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~i~ 186 (187) |.++++ .++.|++|+.|.|+.+.. ..++.+.++++|++|+++++|||+||+|||+|.|+|.+++++.++ T Consensus 75 g~~~~~--~~i~l~~G~~~~l~~~~~--~~~~~~~i~~~~~~~~~~v~~G~~i~idDG~i~l~V~~~~~~~v~ 143 (470) T PRK09206 75 MKLEGG--NDVSLKAGQTFTFTTDKS--VVGNKERVAVTYEGFTADLSVGNTVLVDDGLIGMEVTAITGNEVI 143 (470) T ss_pred cccCCC--CeeeecCCCEEEEEecCc--cCCCCCEEEechHHHHhhcCCCCEEEEeCCEEEEEEEEEeCCEEE Confidence 999863 369999999999998754 246778899999999999999999999999999999999987753 No 8 >PLN02623 pyruvate kinase Probab=100.00 E-value=9.8e-43 Score=317.69 Aligned_cols=149 Identities=36% Similarity=0.541 Sum_probs=138.0 Q ss_pred CCCCCCCCCCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEee Q psy254 26 DIDNKSSYVRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALD 105 (187) Q Consensus 26 ~i~~~~~~~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~D 105 (187) .+++.|..+|+|||||||||+|+++++|++|+++||||||||||||++++|+++|+++|+++++.+. ++++||+| T Consensus 101 ~~~~~~~~~rkTKIV~TiGPas~s~e~l~~li~aGmnv~RlNfSHg~~e~h~~~i~~vr~~~~~~~~-----~~iaIl~D 175 (581) T PLN02623 101 GMWSKPSVRRKTKIVCTIGPSTNTREMIWKLAEAGMNVARLNMSHGDHASHQKVIDLVKEYNAQSKD-----NVIAIMLD 175 (581) T ss_pred hhcCCCCCCCCCeEEEEeCCCcCCHHHHHHHHHcCCCEEEEECCCCCHHHHHHHHHHHHHHHHHcCC-----CceEEEec Confidence 4788899999999999999999999999999999999999999999999999999999999988642 78999999 Q ss_pred CCCCeeEeeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeCCee Q psy254 106 TKGPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVKSYQ 185 (187) Q Consensus 106 l~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~i 185 (187) |+|||||+|.+.+ ++.|++|++|.|+.+.. .++++.++++|++|++++++||.||+|||+|.|+|.+++++.+ T Consensus 176 l~GPkIRig~~~~----~i~l~~G~~v~lt~~~~---~g~~~~i~v~y~~l~~~v~~Gd~IlidDG~i~l~V~~~~~~~v 248 (581) T PLN02623 176 TKGPEVRSGDLPQ----PIMLEEGQEFTFTIKRG---VSTEDCVSVNYDDFVNDVEVGDMLLVDGGMMSLAVKSKTSDSV 248 (581) T ss_pred CCCCceecccCCC----CEEecCCCEEEEecCcc---CCCCCEEeechHHHHhhCCCCCEEEEeCCeEEEEEEEEECCEE Confidence 9999999999974 59999999999998742 5778899999999999999999999999999999999988765 Q ss_pred e Q psy254 186 L 186 (187) Q Consensus 186 ~ 186 (187) . T Consensus 249 ~ 249 (581) T PLN02623 249 K 249 (581) T ss_pred E Confidence 3 No 9 >PRK06247 pyruvate kinase; Provisional Probab=100.00 E-value=8.3e-43 Score=313.46 Aligned_cols=142 Identities=35% Similarity=0.597 Sum_probs=133.3 Q ss_pred CCCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeE Q psy254 33 YVRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIR 112 (187) Q Consensus 33 ~~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIR 112 (187) .+|+|||||||||++++++.|++|+++||||||||||||++++|+++++++|+++++++ ++++||+||+||||| T Consensus 3 ~~r~tKIi~TiGPas~~~e~l~~li~aGm~v~RlN~SHg~~e~~~~~i~~vr~~~~~~~------~~i~Il~Dl~GpkiR 76 (476) T PRK06247 3 RNRRVKILATLGPASSSEDMIRKLVEAGADVFRLNFSHGDHDDHRELYKRIREVEDETG------RPIGILADLQGPKLR 76 (476) T ss_pred CCCCceEEEEECCCcCCHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHcC------CCeeEEEeCCCCcee Confidence 37899999999999999999999999999999999999999999999999999999998 899999999999999 Q ss_pred eeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeCCeee Q psy254 113 TGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVKSYQL 186 (187) Q Consensus 113 tG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~i~ 186 (187) ||.+++ .++.|++|++|.|+.+. ..++++.++++|++|++++++||+||+|||+|.|+|.+++++.+. T Consensus 77 ~g~~~~---~~i~l~~G~~~~l~~~~---~~~~~~~i~v~~~~l~~~v~~G~~I~idDG~i~l~V~~~~~~~i~ 144 (476) T PRK06247 77 LGRFAD---GKVQLANGQTFRLDVDD---APGDHDRVSLPHPEIAAALKPGDRLLVDDGKVRLVVEACDGDDVV 144 (476) T ss_pred ccccCC---CcEeccCCCEEEEEecc---cCCCCCEeecChhHhHhhcCCCCEEEEeCCeEEEEEEEEECCEEE Confidence 999975 36999999999999873 357788999999999999999999999999999999999887653 No 10 >cd00288 Pyruvate_Kinase Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low affinity T state. PK exists as several different isozymes, depending on organism and tissue type. In mammals, there are four PK isozymes: R, found in red blood cells, L, found in liver, M1, found in skeletal muscle, and M2, found in kidney, adipose tissue, and lung. PK forms a homotetramer, with each subunit containing three domains. The T state to R state transition of PK is more complex than in most allosteric enzymes, involving a concerted rotation of all 3 domains of each monomer in the homotetramer. Probab=100.00 E-value=2.3e-42 Score=311.92 Aligned_cols=143 Identities=55% Similarity=0.865 Sum_probs=133.2 Q ss_pred CCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEe Q psy254 34 VRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRT 113 (187) Q Consensus 34 ~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRt 113 (187) +|+|||||||||+|++++.|++|+++||||||||||||++++|+++++++|+++++++ ++++||+||+|||||| T Consensus 1 ~~~tkIi~TiGp~s~~~e~l~~li~aG~~v~RiN~sHg~~~~~~~~i~~vr~~~~~~~------~~i~il~Dl~GpkiR~ 74 (480) T cd00288 1 LRRTKIVCTIGPATDSVENLKKLIKAGMNVARMNFSHGSHEYHQSRIDNVREAAEKTG------GPVAIALDTKGPEIRT 74 (480) T ss_pred CCCCeEEEEeCCCCCCHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHHHHHhC------CCeEEEEecCCCceee Confidence 4899999999999999999999999999999999999999999999999999999998 8999999999999999 Q ss_pred eecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeCC-ee Q psy254 114 GLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVKS-YQ 185 (187) Q Consensus 114 G~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~-~i 185 (187) |.++++ .++.|++|+.|+|+.+.. ...++.+.|+++|++|++.+++||+||+|||+|.|+|.+++++ .+ T Consensus 75 g~~~~~--~~i~l~~G~~~~lt~~~~-~~~~~~~~i~v~~~~l~~~v~~Gd~i~idDG~i~l~V~~~~~~~~i 144 (480) T cd00288 75 GLFKGG--KDISLKAGDKFLVTTDPA-AKKGTKEKIYVDYKNLTKDVSPGNTILVDDGLLSLKVLSKDDDKTL 144 (480) T ss_pred cccCCC--CceecCCCCEEEEEeccc-ccCCCCcEEeechHHhHhhcCCCCEEEEeCCEEEEEEEEEcCCceE Confidence 999863 369999999999998753 2357788999999999999999999999999999999999887 54 No 11 >PRK05826 pyruvate kinase; Provisional Probab=100.00 E-value=3.2e-42 Score=309.94 Aligned_cols=143 Identities=40% Similarity=0.629 Sum_probs=134.1 Q ss_pred CCCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeE Q psy254 33 YVRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIR 112 (187) Q Consensus 33 ~~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIR 112 (187) .+|+|||||||||+|+++|.|++|+++|||+||||||||++++|+++++++|+++++++ +|++|++||+||||| T Consensus 2 ~~~~tkIi~TiGp~s~~~e~l~~li~~G~~v~RiN~sHg~~~~~~~~i~~ir~~~~~~~------~~i~I~~Dl~GpkiR 75 (465) T PRK05826 2 MLRRTKIVATLGPASDSPENLEKLIEAGVNVVRLNFSHGSHEEHGKRAALVREIAAKLG------RPVAILLDLKGPKIR 75 (465) T ss_pred CCCCceEEEeeCCCCCCHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHHHHHhC------CCeEEEEeCCCCcee Confidence 36899999999999999999999999999999999999999999999999999999998 899999999999999 Q ss_pred eeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeCCeee Q psy254 113 TGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVKSYQL 186 (187) Q Consensus 113 tG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~i~ 186 (187) +|.+.+ +++.|++|++|+|+.+.. ..++++.|+++|++|++++++||+||+|||+|.|+|.+++++.+. T Consensus 76 ~g~~~~---~~i~l~~G~~v~l~~~~~--~~~~~~~i~v~~~~l~~~v~~Gd~ilidDG~i~l~V~~~~~~~v~ 144 (465) T PRK05826 76 VGKFKE---GKITLKTGDKFTLDTDQK--EEGDKERVGVDYKGLPKDVKPGDILLLDDGKLQLKVVEVDGDEVE 144 (465) T ss_pred eccccC---CcEEecCCCEEEEEeccc--cCCCCCEEEechHHhHhhcCCCCEEEEeCCeEEEEEEEEeCCEEE Confidence 999975 369999999999998743 357888999999999999999999999999999999999988753 No 12 >PLN02461 Probable pyruvate kinase Probab=100.00 E-value=7.1e-42 Score=309.39 Aligned_cols=144 Identities=49% Similarity=0.724 Sum_probs=133.2 Q ss_pred CCCCCCCCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC Q psy254 28 DNKSSYVRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK 107 (187) Q Consensus 28 ~~~~~~~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~ 107 (187) +.+..++|+|||||||||+|++++.|++|+++|||+||||||||++++|.++++++|+++++++ +|++||+||+ T Consensus 14 ~~~~~~~r~tKIi~TiGPas~~~e~l~~li~aGm~v~RlN~SHg~~e~h~~~i~~vr~~~~~~g------~~i~Il~Dl~ 87 (511) T PLN02461 14 PADGLRRPKTKIVCTLGPASRSVPMLEKLLRAGMNVARFNFSHGSHEYHQETLDNLRQAMANTG------ILCAVMLDTK 87 (511) T ss_pred cCccccCCCCeEEEEeCCCcCCHHHHHHHHHcCCCEEEEECCCCCHHHHHHHHHHHHHHHHHcC------CCeEEEeeCC Confidence 3344578999999999999999999999999999999999999999999999999999999998 8999999999 Q ss_pred CCeeEeeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEe Q psy254 108 GPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIV 181 (187) Q Consensus 108 GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~ 181 (187) |||||||.++++ +++.|++|+.|.|+.+.. ..++++.|+++|++|++++++||+||+|||+|.|+|.+++ T Consensus 88 GPkIR~g~~~~~--~~i~l~~G~~v~lt~~~~--~~~~~~~i~v~~~~~~~~v~~Gd~IlidDG~i~l~V~~~~ 157 (511) T PLN02461 88 GPEIRTGFLKDG--KPVQLKQGQEITITTDYS--IKGDENMIAMSYKKLAVDVKPGSVILCADGTITLTVLSCD 157 (511) T ss_pred CCceeccccCCC--CceecCCCCEEEEecCCc--cCCCCCEEEeccHHHHhhcCCCCEEEEeCCEEEEEEEEEe Confidence 999999999863 469999999999998743 3577789999999999999999999999999999999987 No 13 >PRK06354 pyruvate kinase; Provisional Probab=100.00 E-value=8.2e-42 Score=314.45 Aligned_cols=142 Identities=40% Similarity=0.623 Sum_probs=132.7 Q ss_pred CCCCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCee Q psy254 32 SYVRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEI 111 (187) Q Consensus 32 ~~~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkI 111 (187) ..+|+|||||||||+|+++++|++|+++|||+||||||||++++|.++++++|+++++++ +||+||+||+|||| T Consensus 5 ~~~r~tKIi~TiGPas~~~e~l~~li~aG~~v~RlN~sHg~~e~~~~~i~~ir~~~~~~~------~~i~i~~Dl~Gpki 78 (590) T PRK06354 5 DLMRRTKIVATIGPASESPEKLRQLIEAGATTARLNFSHGDHEEHGARIKNIREASKKLG------KTVGILQDLQGPKI 78 (590) T ss_pred CCCCCceEEEeeCCCCCCHHHHHHHHHcCCCEEEEECCCCCHHHHHHHHHHHHHHHHHhC------CCEEEEeeCCCCce Confidence 347999999999999999999999999999999999999999999999999999999998 89999999999999 Q ss_pred EeeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEe--CCee Q psy254 112 RTGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIV--KSYQ 185 (187) Q Consensus 112 RtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~--~~~i 185 (187) |||.+++ +++.|++|++|.|+.+. ..++++.++++|++|++++++||.||+|||+|.|+|.+++ ++.+ T Consensus 79 R~g~~~~---~~i~l~~G~~~~l~~~~---~~~~~~~i~v~~~~l~~~v~~Gd~i~idDG~i~l~V~~~~~~~~~v 148 (590) T PRK06354 79 RLGRFED---GPIELKTGDEFILTSRE---VLGTQEKFSVTYDGLADEVPVGSRILLDDGLIELEVEEVDKADGEL 148 (590) T ss_pred eccccCC---CcEEecCCCEEEEEecc---cCCCCCEEeechHHHHhhcCCCCEEEEeCCeEEEEEEEEEcCCCEE Confidence 9999975 36999999999999873 3577889999999999999999999999999999999987 6654 No 14 >PRK14725 pyruvate kinase; Provisional Probab=100.00 E-value=1.3e-41 Score=310.71 Aligned_cols=169 Identities=27% Similarity=0.391 Sum_probs=147.2 Q ss_pred hhhhhccHHHhhcCCCCCCCCCCCCCceEEEecC-CCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHH Q psy254 11 RALAANTFVDHLCGLDIDNKSSYVRLTGIICTIG-PASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVEN 89 (187) Q Consensus 11 ~~~~~~~~l~~~~~l~i~~~~~~~r~TkIi~TiG-Pas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~ 89 (187) .++.++..|++.+.. ++++++..|+|||||||| ||+++++.|++|+++||||||||||||++++|++||++||+++++ T Consensus 116 ~~~~g~~lL~~~~~~-l~G~~~~~R~tkImvTlg~~Aa~d~e~i~~Li~aGmdvaRINcAHg~~e~w~~mi~~vR~a~~~ 194 (608) T PRK14725 116 TFEEGDELLDEHAEA-LLGPPPSGRPTRIMVTLPTEAADDPDLVRRLLAAGMDIARINCAHDDPEAWRAMIANVRTAEEE 194 (608) T ss_pred hhhhHHHHHHHHHHH-hcCCCCCCCCceEEEeCCCcccCCHHHHHHHHHcCCCEeeeECCCCCHHHHHHHHHHHHHHHHH Confidence 344455666666666 899999999999999999 699999999999999999999999999999999999999999999 Q ss_pred hCCCCCCcceeEEEeeCCCCeeEeeecCCCCc------------------------------------------------ Q psy254 90 YSKRIGMPHALAIALDTKGPEIRTGLLQGGGS------------------------------------------------ 121 (187) Q Consensus 90 ~~~~~~~~~~v~I~~Dl~GPkIRtG~~~~~~~------------------------------------------------ 121 (187) +| ++|+|+|||+|||||||.+.+++. T Consensus 195 ~g------r~~~I~mDL~GPKiRtG~l~~g~~v~~~~p~rd~~G~v~~pa~~~l~~~~~~~~~~~~~~~~~~v~~~~~~~ 268 (608) T PRK14725 195 LG------RRCRIAMDLAGPKLRTGPIAPGPRVIKLRPTRDALGRVLTPARLWLTASESPPPSPPPGPVGLPVDPEWLAR 268 (608) T ss_pred cC------CCEEEEEeCCCCcceEEecCCCccccccccccccccccccchhheeecccCCCCCCCccccccccChhhhhh Confidence 99 999999999999999999986421 Q ss_pred --------------------------------------------------------------ccEEeeeCCEEEEeeCCC Q psy254 122 --------------------------------------------------------------AEVELVKGQTIRLTTDAA 139 (187) Q Consensus 122 --------------------------------------------------------------~~i~l~~G~~v~lt~~~~ 139 (187) ..+.|+.|+++.|+.+.. T Consensus 269 l~~Gd~i~~~DaRg~~R~l~V~~~~~~~~~~~~~~~~Y~~~G~~l~~~~~~~~~v~~~p~~~~~i~L~~Gd~l~lt~~~~ 348 (608) T PRK14725 269 LEPGDELRFTDARGKKRKLTVTEVDDEGVLAEGSQTAYLANGTLLRLGRHDSTRVGGLPPVEQKLRLKVGDRLVLTRDDA 348 (608) T ss_pred cCCCceeeeeeccccceeeeEEeecCceeEEeecceeeeccCceeeeccccccccccccccCcceEecCCCEEEEecCCc Confidence 158999999999998743 Q ss_pred cc--cCCCcC--EEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeCCeee Q psy254 140 FA--EKGSAT--DLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVKSYQL 186 (187) Q Consensus 140 ~~--~~~~~~--~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~i~ 186 (187) .. ..++.. .|+|+|+++++++++||.||+|||+|.++|.+++++.++ T Consensus 349 ~~~~~~~~~~~~~i~~t~p~l~~~v~~G~~VlidDG~I~l~V~~~~~~~v~ 399 (608) T PRK14725 349 PGDPAQGDAPPARISCTLPEAFRAARVGERVWFDDGKIGAVVVKVEADEVE 399 (608) T ss_pred CCccccCCCCccEEEechHHHHHhcCCCCEEEEeCCeEEEEEEEEECCEEE Confidence 21 113444 899999999999999999999999999999999887653 No 15 >TIGR01064 pyruv_kin pyruvate kinase. This enzyme is a homotetramer. Some forms are active only in the presence of fructose-1,6-bisphosphate or similar phosphorylated sugars. Probab=100.00 E-value=3.2e-41 Score=304.75 Aligned_cols=142 Identities=51% Similarity=0.806 Sum_probs=132.2 Q ss_pred CCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEee Q psy254 35 RLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTG 114 (187) Q Consensus 35 r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG 114 (187) |+|||||||||+|++++.|++|+++|||+||||||||++++|+++|+++|+++++++ ++++||+||+|||||+| T Consensus 1 ~~tkii~Tigp~~~~~e~l~~l~~~G~~~~R~N~shg~~~~~~~~i~~ir~~~~~~~------~~~~i~~Dl~GpkiR~g 74 (473) T TIGR01064 1 RRTKIVCTIGPATNSPEMLKKLLDAGMNVARLNFSHGSHEEHGKRIENVREAAEKLG------RPVAILLDTKGPEIRTG 74 (473) T ss_pred CCceEEEeeCCCCCCHHHHHHHHHcCCCEEEEECCCCCHHHHHHHHHHHHHHHHHhC------CCeEEEEeCCCCceecc Confidence 689999999999999999999999999999999999999999999999999999998 89999999999999999 Q ss_pred ecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeCCeee Q psy254 115 LLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVKSYQL 186 (187) Q Consensus 115 ~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~i~ 186 (187) .+.+ +++.|++|+.|.|+.+..+ ..++++.|+++|++|++++++||.||+|||+|.|+|.+++++.+. T Consensus 75 ~~~~---~~~~l~~g~~v~l~~~~~~-~~~~~~~i~~~~~~~~~~~~~g~~i~iddG~i~l~V~~~~~~~~~ 142 (473) T TIGR01064 75 EIKG---GPVKLKKGDKVIITTDDIK-GEGDEEDVSVDYKGLTKDVSEGDKILVDDGKISLVVVSVEGDKVI 142 (473) T ss_pred ccCC---CceecCCCCEEEEeccccc-CCCCCCEEEechHHHHHhcCCCCEEEEeCCeEEEEEEEEECCEEE Confidence 9975 3699999999999987422 347778999999999999999999999999999999999887753 No 16 >PRK06739 pyruvate kinase; Validated Probab=100.00 E-value=1.5e-40 Score=289.68 Aligned_cols=135 Identities=38% Similarity=0.622 Sum_probs=124.8 Q ss_pred CceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEeee Q psy254 36 LTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTGL 115 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG~ 115 (187) +++|||||||+|++++.|++|+++|||+||||||||++++|.++++++|++.+ +++||+||+|||||||. T Consensus 2 ~~~~V~TiGPas~~~e~l~~Li~aGm~v~RlNfSHGs~e~h~~~i~~vR~~~~----------~vaIl~Dl~GPkIR~G~ 71 (352) T PRK06739 2 TIDRICTIGPASNNKETLAQLINNGMKIVRLNLSHGTHESHKDIIRLVKSLDD----------SIKILGDVQGPKIRLGE 71 (352) T ss_pred CceEEEEeCCCCCCHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHhhh----------hcceeecCCCCcceecc Confidence 68999999999999999999999999999999999999999999999999753 48999999999999999 Q ss_pred cCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeCCeee Q psy254 116 LQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVKSYQL 186 (187) Q Consensus 116 ~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~i~ 186 (187) +++ +++.|++|+.|+|+.+. ..++++.++++|++|++++++||.||+|||+|.|+|.+++++.+. T Consensus 72 ~~~---~~i~l~~G~~v~lt~~~---~~g~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~v~ 136 (352) T PRK06739 72 IKG---EQITLQAGDSFILHTQP---VTGSSTEASVDYEGIANDVKVGSRILMNDGEVELIVEKVSTDKIE 136 (352) T ss_pred cCC---CcEEecCCCEEEEecCc---cCCCCCEEecchHHHHhhcCCCCEEEEeCCEEEEEEEEEeCCEEE Confidence 975 36999999999999874 356778899999999999999999999999999999999887653 No 17 >KOG2323|consensus Probab=100.00 E-value=1.8e-38 Score=283.75 Aligned_cols=160 Identities=53% Similarity=0.812 Sum_probs=148.4 Q ss_pred cHHHhhcCCCC-CCCCCCCCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCC Q psy254 17 TFVDHLCGLDI-DNKSSYVRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIG 95 (187) Q Consensus 17 ~~l~~~~~l~i-~~~~~~~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~ 95 (187) ++++|.|.|+. ...|...|+|+|+||+||++++.|+|+.|+++|||+||+|||||++++|++.++|+|++...++. T Consensus 2 s~~~~~~~L~~~~~~~~~~~~t~ivctigP~s~s~e~l~~m~~aGmniarlNfShGs~~~h~~tidn~~~a~~~~~~--- 78 (501) T KOG2323|consen 2 SFLKHECLLSGSNGAPKKRRKTKIVCTIGPASRSVEMLRKLLKAGMNIARLNFSHGSHEYHQETIDNLRDAISNTGA--- 78 (501) T ss_pred chhhhhhhhcccccccccccceeeEeccCCccchHHHHHHHHHcCCcEEEEEcCCCChHHHHHHHHHHHHHHhhcCC--- Confidence 68899999987 55567789999999999999999999999999999999999999999999999999999999984 Q ss_pred CcceeEEEeeCCCCeeEeeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEE Q psy254 96 MPHALAIALDTKGPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISL 175 (187) Q Consensus 96 ~~~~v~I~~Dl~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l 175 (187) .|++||+|++|||||||.++++ .+++|++|+.++||++..+... +++.+++||+++.++|++|+.||+|||.+.+ T Consensus 79 --~~~ai~LDtkGpEirtg~~~~~--~~i~L~~G~~i~~t~d~~~~~~-~~~~~~vdyk~~~~~V~~G~~i~vddgi~s~ 153 (501) T KOG2323|consen 79 --LPCAIMLDTKGPEIRTGDLKNG--KPIKLKEGQEITITTDYSYEAK-LSETISVDYKKLAKDVKPGDIIYVDDGLISL 153 (501) T ss_pred --cchhhhhccCCCeEeecccCCC--CceeecCCCEEEEEcChhhccc-cceEEEeehHHhhhccccCCEEEECCceeee Confidence 4699999999999999999975 5899999999999999988766 6789999999999999999999999999999 Q ss_pred EEEEEeCCe Q psy254 176 VVKSIVKSY 184 (187) Q Consensus 176 ~V~~v~~~~ 184 (187) .|.++..+. T Consensus 154 ~V~~~~~~~ 162 (501) T KOG2323|consen 154 IVKSVSKDE 162 (501) T ss_pred EEEEeecCc Confidence 999986553 No 18 >PTZ00300 pyruvate kinase; Provisional Probab=99.97 E-value=3.2e-31 Score=237.79 Aligned_cols=116 Identities=53% Similarity=0.876 Sum_probs=106.8 Q ss_pred CcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEeeecCCCCcccEEeeeCCEEEEeeCCCc Q psy254 61 MNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAF 140 (187) Q Consensus 61 m~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~ 140 (187) |||||||||||++++|+++++++|+++++++ ++++||+||+|||||||.++++ ++.|++|++|.|+.+..+ T Consensus 1 ~~v~RlN~sHg~~e~h~~~i~~vr~~~~~~~------~~i~il~Dl~GPkiR~g~~~~~---~~~l~~G~~~~l~~~~~~ 71 (454) T PTZ00300 1 MSVARMNFSHGSHEYHQTTINNVRQAAAELG------VNIAIALDTKGPEIRTGLFVGG---EAVMERGATCYVTTDPAF 71 (454) T ss_pred CCEEEEECCCCCHHHHHHHHHHHHHHHHHhC------CCeEEEEecCCCceeccccCCC---cEEecCCCEEEEEecccc Confidence 8999999999999999999999999999998 8999999999999999999763 699999999999988655 Q ss_pred ccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeC-Cee Q psy254 141 AEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVK-SYQ 185 (187) Q Consensus 141 ~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~-~~i 185 (187) ...++++.++++|++|++.+++||.||+|||+|.|+|.++.+ +.+ T Consensus 72 ~~~~~~~~i~v~~~~l~~~v~~G~~ilidDG~i~l~V~~~~~~~~v 117 (454) T PTZ00300 72 ADKGTKDKFYIDYQNLSKVVRPGGYIYIDDGILILHVQSHEDEQTL 117 (454) T ss_pred ccCCCCCEEEecCcccccccCCCCEEEEeCCeEEEEEEEEcCCceE Confidence 556778899999999999999999999999999999999875 344 No 19 >PF00478 IMPDH: IMP dehydrogenase / GMP reductase domain; InterPro: IPR001093 Synonym(s): Inosine-5'-monophosphate dehydrogenase, Inosinic acid dehydrogenase; Synonym(s): Guanosine 5'-monophosphate oxidoreductase This entry contains two related enzymes IMP dehydrogenase and GMP reducatase. These enzymes adopt a TIM barrel structure. IMP dehydrogenase (1.1.1.205 from EC) (IMPDH) catalyzes the rate-limiting reaction of de novo GTP biosynthesis, the NAD-dependent reduction of IMP into XMP [].Inosine 5-phosphate + NAD+ + H2O = xanthosine 5-phosphate + NADH IMP dehydrogenase is associated with cell proliferation and is a possible target for cancer chemotherapy. Mammalian and bacterial IMPDHs are tetramers of identical chains. There are two IMP dehydrogenase isozymes in humans []. IMP dehydrogenase nearly always contains a long insertion that has two CBS domains within it. GMP reductase (1.7.1.7 from EC) catalyzes the irreversible and NADPH-dependent reductive deamination of GMP into IMP [].NADPH + guanosine 5-phosphate = NADP+ + inosine 5-phosphate + NH3 It converts nucleobase, nucleoside and nucleotide derivatives of G to A nucleotides, and maintains intracellular balance of A and G nucleotides.; GO: 0003824 catalytic activity, 0055114 oxidation-reduction process; PDB: 3FFS_D 1VRD_A 1JCN_B 1EEP_B 3TSB_B 3USB_B 3TSD_A 4FF0_A 4FEZ_A 3KHJ_D .... Probab=94.09 E-value=0.18 Score=44.65 Aligned_cols=52 Identities=19% Similarity=0.320 Sum_probs=43.8 Q ss_pred CCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 35 RLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 35 r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) .+-.+-+.+||..++.+....|+++|+|++=|..+||..+...++++++|+. T Consensus 95 ~~l~V~aavg~~~~~~er~~~L~~agvD~ivID~a~g~s~~~~~~ik~ik~~ 146 (352) T PF00478_consen 95 GRLLVAAAVGTRDDDFERAEALVEAGVDVIVIDSAHGHSEHVIDMIKKIKKK 146 (352) T ss_dssp SCBCEEEEEESSTCHHHHHHHHHHTT-SEEEEE-SSTTSHHHHHHHHHHHHH T ss_pred ccceEEEEecCCHHHHHHHHHHHHcCCCEEEccccCccHHHHHHHHHHHHHh Confidence 3456788899999999999999999999999999999999888888877754 No 20 >cd00381 IMPDH IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine nucleotides. There is often a CBS domain inserted in the middle of this domain, which is proposed to play a regulatory role. IMPDH is a key enzyme in the regulation of cell proliferation and differentiation. It has been identified as an attractive target for developing chemotherapeutic agents. Probab=91.45 E-value=0.49 Score=41.32 Aligned_cols=48 Identities=21% Similarity=0.378 Sum_probs=40.5 Q ss_pred EEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 39 IICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 39 Ii~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) +-+.+|+.....+.+..++++|++++=+|++||..+.+.++|+.+|+. T Consensus 85 v~~~~~~~~~~~~~~~~l~eagv~~I~vd~~~G~~~~~~~~i~~ik~~ 132 (325) T cd00381 85 VGAAVGTREDDKERAEALVEAGVDVIVIDSAHGHSVYVIEMIKFIKKK 132 (325) T ss_pred EEEecCCChhHHHHHHHHHhcCCCEEEEECCCCCcHHHHHHHHHHHHH Confidence 455666655667899999999999999999999998888888888875 No 21 >PRK05458 guanosine 5'-monophosphate oxidoreductase; Provisional Probab=90.61 E-value=0.75 Score=40.39 Aligned_cols=46 Identities=15% Similarity=0.387 Sum_probs=39.1 Q ss_pred EecCCCCCCHHHHHHHHHhcC--cEEEEecCCCCHHHHHHHHHHHHHH Q psy254 41 CTIGPASVAVDMLEKIIETGM--NIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 41 ~TiGPas~~~~~i~~li~aGm--~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) +.+|...++.+.+.+|+++|+ |+.=|..+||..+..+++|+.||+. T Consensus 90 ~~vg~~~~~~~~~~~Lv~ag~~~d~i~iD~a~gh~~~~~e~I~~ir~~ 137 (326) T PRK05458 90 ISVGVKDDEYDFVDQLAAEGLTPEYITIDIAHGHSDSVINMIQHIKKH 137 (326) T ss_pred EEecCCHHHHHHHHHHHhcCCCCCEEEEECCCCchHHHHHHHHHHHhh Confidence 345655677899999999966 9999999999999999999998874 No 22 >TIGR01302 IMP_dehydrog inosine-5'-monophosphate dehydrogenase. This model describes a rather tightly conserved cluster of IMP dehydrogenase sequences, many of which are characterized. The model excludes two related families of proteins proposed also to be IMP dehydrogenases, but without characterized members. These are related families are the subject of separate models. Probab=90.53 E-value=0.62 Score=42.45 Aligned_cols=49 Identities=20% Similarity=0.388 Sum_probs=41.0 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) .+=+.+|....+.+....|+++|++++-++.+||..+.+.++|+.+|+. T Consensus 214 ~V~aav~~~~~~~~r~~~L~~aG~d~I~vd~a~g~~~~~~~~i~~i~~~ 262 (450) T TIGR01302 214 IVGAAVGTREFDKERAEALVKAGVDVIVIDSSHGHSIYVIDSIKEIKKT 262 (450) T ss_pred EEEEEecCchhHHHHHHHHHHhCCCEEEEECCCCcHhHHHHHHHHHHHh Confidence 3445777767778999999999999999999999988888888887763 No 23 >PRK05096 guanosine 5'-monophosphate oxidoreductase; Provisional Probab=90.14 E-value=0.79 Score=40.49 Aligned_cols=49 Identities=16% Similarity=0.320 Sum_probs=43.8 Q ss_pred eEEEecCCCCCCHHHHHHHHHh--cCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 38 GIICTIGPASVAVDMLEKIIET--GMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~a--Gm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) .+.+++|-..++.+.+.+|+++ |+|+.=|..|||..+...++|+.||+. T Consensus 98 ~~~vavG~~~~d~er~~~L~~~~~g~D~iviD~AhGhs~~~i~~ik~ik~~ 148 (346) T PRK05096 98 HVMVSTGTSDADFEKTKQILALSPALNFICIDVANGYSEHFVQFVAKAREA 148 (346) T ss_pred eEEEEecCCHHHHHHHHHHHhcCCCCCEEEEECCCCcHHHHHHHHHHHHHh Confidence 4556888888999999999995 999999999999999999999999874 No 24 >TIGR01305 GMP_reduct_1 guanosine monophosphate reductase, eukaryotic. A deep split separates two families of GMP reductase. This family includes both eukaryotic and some proteobacterial sequences, while the other family contains other bacterial sequences. Probab=90.00 E-value=0.86 Score=40.24 Aligned_cols=49 Identities=18% Similarity=0.327 Sum_probs=44.0 Q ss_pred eEEEecCCCCCCHHHHHHHHHhc--CcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 38 GIICTIGPASVAVDMLEKIIETG--MNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aG--m~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) .+.+++|-..++.+.+++|+++| .|+.=|..|||..+...++|++||+. T Consensus 97 ~~~vsvG~~~~d~er~~~L~~a~~~~d~iviD~AhGhs~~~i~~ik~ir~~ 147 (343) T TIGR01305 97 NVAVSSGSSDNDLEKMTSILEAVPQLKFICLDVANGYSEHFVEFVKLVREA 147 (343) T ss_pred eEEEEeccCHHHHHHHHHHHhcCCCCCEEEEECCCCcHHHHHHHHHHHHhh Confidence 35558899999999999999996 99999999999999999999999974 No 25 >PLN02274 inosine-5'-monophosphate dehydrogenase Probab=88.47 E-value=1.1 Score=41.71 Aligned_cols=49 Identities=24% Similarity=0.414 Sum_probs=42.6 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) .+=|.+|+..+..+..++|+++|+|+.=+..+||...+..++|++||+. T Consensus 238 ~vgaavg~~~~~~~r~~~l~~ag~d~i~iD~~~g~~~~~~~~i~~ik~~ 286 (505) T PLN02274 238 LVGAAIGTRESDKERLEHLVKAGVDVVVLDSSQGDSIYQLEMIKYIKKT 286 (505) T ss_pred EEEEEEcCCccHHHHHHHHHHcCCCEEEEeCCCCCcHHHHHHHHHHHHh Confidence 3455688888889999999999999999999999998888888888864 No 26 >PTZ00314 inosine-5'-monophosphate dehydrogenase; Provisional Probab=87.89 E-value=0.89 Score=42.06 Aligned_cols=46 Identities=20% Similarity=0.383 Sum_probs=39.4 Q ss_pred EecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 41 CTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 41 ~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) +.+|....+.+.++.|+++|+++.=|+.+||......++|+.||+. T Consensus 234 aavg~~~~~~~~~~~l~~ag~d~i~id~a~G~s~~~~~~i~~ik~~ 279 (495) T PTZ00314 234 AAISTRPEDIERAAALIEAGVDVLVVDSSQGNSIYQIDMIKKLKSN 279 (495) T ss_pred EEECCCHHHHHHHHHHHHCCCCEEEEecCCCCchHHHHHHHHHHhh Confidence 4677766778999999999999999999999988877788877764 No 27 >PRK06843 inosine 5-monophosphate dehydrogenase; Validated Probab=86.70 E-value=1.4 Score=39.86 Aligned_cols=50 Identities=12% Similarity=0.232 Sum_probs=42.4 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) -.+-|.+|+..++.+.++.|+++|+++.=|..+||..+...++++++|+. T Consensus 142 l~v~aavg~~~~~~~~v~~lv~aGvDvI~iD~a~g~~~~~~~~v~~ik~~ 191 (404) T PRK06843 142 LRVGAAVSIDIDTIERVEELVKAHVDILVIDSAHGHSTRIIELVKKIKTK 191 (404) T ss_pred eEEEEEEeCCHHHHHHHHHHHhcCCCEEEEECCCCCChhHHHHHHHHHhh Confidence 35677788876678999999999999999999999988888888888763 No 28 >TIGR01306 GMP_reduct_2 guanosine monophosphate reductase, bacterial. A deep split separates two families of GMP reductase. The other (TIGR01305) is found in eukaryotic and some proteobacterial lineages, including E. coli, while this family is found in a variety of bacterial lineages. Probab=85.93 E-value=2 Score=37.66 Aligned_cols=49 Identities=14% Similarity=0.239 Sum_probs=43.5 Q ss_pred eEEEecCCCCCCHHHHHHHHHhc--CcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 38 GIICTIGPASVAVDMLEKIIETG--MNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aG--m~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) -..+++|-..++.+.+..|+++| .++.=+..|||......++++.+|+. T Consensus 84 ~v~~SvG~t~e~~~r~~~lv~a~~~~d~i~~D~ahg~s~~~~~~i~~i~~~ 134 (321) T TIGR01306 84 FASISVGVKACEYEFVTQLAEEALTPEYITIDIAHGHSNSVINMIKHIKTH 134 (321) T ss_pred EEEEEcCCCHHHHHHHHHHHhcCCCCCEEEEeCccCchHHHHHHHHHHHHh Confidence 46777888888899999999999 69999999999999888888888864 No 29 >PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional Probab=83.05 E-value=3.4 Score=33.71 Aligned_cols=60 Identities=12% Similarity=0.197 Sum_probs=41.5 Q ss_pred eeeCCEEEEeeC--CCcccCCCcC-EEeeCcchhh--hcCCCCCEEEE--eCCeEEEEEEEEeCCeee Q psy254 126 LVKGQTIRLTTD--AAFAEKGSAT-DLYVDYTNIT--KVVKPGSRIFV--DDGLISLVVKSIVKSYQL 186 (187) Q Consensus 126 l~~G~~v~lt~~--~~~~~~~~~~-~i~v~~~~l~--~~v~~Gd~Ili--dDG~i~l~V~~v~~~~i~ 186 (187) ++.|+++.++.. ..|.. .+++ ...++-..|. ..+++|++++. ++|.+.++|++++++.|. T Consensus 52 ~~~Gd~~~v~l~peeAyGe-~d~~lV~~vpr~~F~~~~~l~~G~~~~~~~~~G~~~~~V~ev~~d~V~ 118 (196) T PRK10737 52 HEVGDKFDVAVGANDAYGQ-YDENLVQRVPKDVFMGVDELQVGMRFLAETDQGPVPVEITAVEDDHVV 118 (196) T ss_pred CCCCCEEEEEEChHHhcCC-CChHHEEEecHHHCCCccCCCCCCEEEEeCCCCcEEEEEEEEcCCEEE Confidence 457888777654 34432 3333 4556655553 35899999987 488899999999988763 No 30 >PF01136 Peptidase_U32: Peptidase family U32 This is family U32 in the peptidase classification. ; InterPro: IPR001539 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: 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-, N-, 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. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; 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. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This is a group of peptidases belonging to MEROPS peptidase family U32 (clan U-). The type example is collagenase (gene prtC) from Porphyromonas gingivalis (Bacteroides gingivalis) [], which is an enzyme that degrades type I collagen and that seems to require a metal cofactor. The product of PrtC is evolutionary related to a number of uncharacterised proteins with a well conserved region containing two cysteines.; GO: 0008233 peptidase activity, 0006508 proteolysis Probab=82.96 E-value=3.7 Score=33.42 Aligned_cols=42 Identities=26% Similarity=0.393 Sum_probs=38.1 Q ss_pred CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHh Q psy254 49 AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENY 90 (187) Q Consensus 49 ~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~ 90 (187) -.+.|.+|.++|++.+||.+-.-+.++..++++..|++.... T Consensus 158 l~~~l~~L~~~Gv~~~rI~~r~~~~~~~~~iv~~Y~~~l~~~ 199 (233) T PF01136_consen 158 LLDELPELKDAGVDSFRIDGRTESPEYIEEIVKAYREALDNP 199 (233) T ss_pred HHHHHHHHHHcCCCEEEEcCccCCHHHHHHHHHHHHHHHHHH Confidence 467899999999999999999999999999999999987764 No 31 >KOG2550|consensus Probab=79.80 E-value=3.9 Score=37.24 Aligned_cols=46 Identities=24% Similarity=0.450 Sum_probs=42.0 Q ss_pred EecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 41 CTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 41 ~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) |.||-..++.+.+.-|.++|+|+.=|.-|.|+..+..+||.+||+. T Consensus 244 AaiGTre~dK~rl~ll~~aGvdvviLDSSqGnS~~qiemik~iK~~ 289 (503) T KOG2550|consen 244 AAIGTRDDDKERLDLLVQAGVDVVILDSSQGNSIYQLEMIKYIKET 289 (503) T ss_pred eccccccchhHHHHHhhhcCCcEEEEecCCCcchhHHHHHHHHHhh Confidence 4567777889999999999999999999999999999999999974 No 32 >TIGR01303 IMP_DH_rel_1 IMP dehydrogenase family protein. This model represents a family of proteins, often annotated as a putative IMP dehydrogenase, related to IMP dehydrogenase and GMP reductase and restricted to the high GC Gram-positive bacteria. All species in which a member is found so far (Corynebacterium glutamicum, Mycobacterium tuberculosis, Streptomyces coelicolor, etc.) also have IMP dehydrogenase as described by TIGRFAMs entry TIGR01302. Probab=79.01 E-value=4.2 Score=37.47 Aligned_cols=48 Identities=17% Similarity=0.266 Sum_probs=40.2 Q ss_pred EEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 39 IICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 39 Ii~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) +=+-+|.+.+..+.++.|+++|+++.=|..+||..+...++++.||+. T Consensus 216 Vgaav~~~~~~~~ra~~Lv~aGVd~i~~D~a~g~~~~~~~~i~~i~~~ 263 (475) T TIGR01303 216 IGAAVGINGDVGGKAKALLDAGVDVLVIDTAHGHQVKMISAIKAVRAL 263 (475) T ss_pred ehheeeeCccHHHHHHHHHHhCCCEEEEeCCCCCcHHHHHHHHHHHHH Confidence 333456666778999999999999999999999998888888888863 No 33 >PLN02495 oxidoreductase, acting on the CH-CH group of donors Probab=78.73 E-value=7 Score=35.10 Aligned_cols=34 Identities=29% Similarity=0.437 Sum_probs=25.4 Q ss_pred CceEEEec-CCCC-CC-HHHHHHHHHhcCcEEEEecC Q psy254 36 LTGIICTI-GPAS-VA-VDMLEKIIETGMNIARLNFS 69 (187) Q Consensus 36 ~TkIi~Ti-GPas-~~-~~~i~~li~aGm~v~RiN~s 69 (187) .+.+|++| |+.+ .+ .+.++.+-++|++.+=|||| T Consensus 113 ~~pvIaSi~~~~s~~~~~~~a~~~e~~GaD~iELNiS 149 (385) T PLN02495 113 DRILIASIMEEYNKDAWEEIIERVEETGVDALEINFS 149 (385) T ss_pred CCcEEEEccCCCCHHHHHHHHHHHHhcCCCEEEEECC Confidence 45899999 6433 33 35666677889999999999 No 34 >PF07521 RMMBL: RNA-metabolising metallo-beta-lactamase; InterPro: IPR011108 The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in IPR001279 from INTERPRO and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in RNA metabolism [].; PDB: 3ZQ4_D 2I7T_A 2I7V_A 2YCB_B 3BK1_A 3T3N_A 3BK2_A 3T3O_A 3AF5_A 3AF6_A .... Probab=78.53 E-value=1.4 Score=26.91 Aligned_cols=24 Identities=21% Similarity=0.372 Sum_probs=19.3 Q ss_pred CcEEEEecC-CCCHHHHHHHHHHHH Q psy254 61 MNIARLNFS-HGSYEYHGQTIKNIR 84 (187) Q Consensus 61 m~v~RiN~s-Hg~~e~~~~~i~~ir 84 (187) |.|.+++|| |++.++..++++.++ T Consensus 7 a~v~~~~fSgHad~~~L~~~i~~~~ 31 (43) T PF07521_consen 7 ARVEQIDFSGHADREELLEFIEQLN 31 (43) T ss_dssp SEEEESGCSSS-BHHHHHHHHHHHC T ss_pred EEEEEEeecCCCCHHHHHHHHHhcC Confidence 678899998 999998888888773 No 35 >PRK05567 inosine 5'-monophosphate dehydrogenase; Reviewed Probab=78.38 E-value=6.8 Score=36.03 Aligned_cols=51 Identities=16% Similarity=0.283 Sum_probs=41.6 Q ss_pred CceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 36 LTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) +..+=+-+|+.-.+.+.++.|+++|++++-++.+||..+.+.+.++.+|+. T Consensus 216 ~l~V~aai~~~~~~~e~a~~L~~agvdvivvD~a~g~~~~vl~~i~~i~~~ 266 (486) T PRK05567 216 RLRVGAAVGVGADNEERAEALVEAGVDVLVVDTAHGHSEGVLDRVREIKAK 266 (486) T ss_pred CEEEEeecccCcchHHHHHHHHHhCCCEEEEECCCCcchhHHHHHHHHHhh Confidence 445566677555678999999999999999999999998888888877763 No 36 >COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport] Probab=78.30 E-value=3.5 Score=30.23 Aligned_cols=31 Identities=16% Similarity=0.363 Sum_probs=25.2 Q ss_pred eeCcchhhhcCCCCCEEEEeCCeEEEEEEEEe Q psy254 150 YVDYTNITKVVKPGSRIFVDDGLISLVVKSIV 181 (187) Q Consensus 150 ~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~ 181 (187) -+.++. ...++|||+|.+..+++..+|+++. T Consensus 25 Rl~d~k-rr~ik~GD~IiF~~~~l~v~V~~vr 55 (111) T COG4043 25 RLADPK-RRQIKPGDKIIFNGDKLKVEVIDVR 55 (111) T ss_pred EecCHh-hcCCCCCCEEEEcCCeeEEEEEEEe Confidence 344544 3789999999999999999999874 No 37 >PRK07107 inosine 5-monophosphate dehydrogenase; Validated Probab=76.33 E-value=5.5 Score=36.98 Aligned_cols=51 Identities=18% Similarity=0.270 Sum_probs=42.2 Q ss_pred CCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 35 RLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 35 r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) .+-.+.+.+|+. +..+..+.|+++|+++.=+..|||..+...+.|+.+|+. T Consensus 230 grL~V~~av~~~-~~~~ra~~Lv~aGvd~i~vd~a~g~~~~~~~~i~~ir~~ 280 (502) T PRK07107 230 KRYVVGAGINTR-DYAERVPALVEAGADVLCIDSSEGYSEWQKRTLDWIREK 280 (502) T ss_pred cCeeeeeccChh-hHHHHHHHHHHhCCCeEeecCcccccHHHHHHHHHHHHh Confidence 344567788875 567999999999999999999999988888888888864 No 38 >PF09370 TIM-br_sig_trns: TIM-barrel signal transduction protein; InterPro: IPR009215 Members of this family are predicted to have a TIM barrel fold, based on PSI-BLAST analysis (iteration 4) and on SCOP prediction (using SMART). Interestingly, this novel domain also exists as an N-terminal domain of sigma54-dependent transcriptional activators (enhancer-binding proteins). Because sigma54 dependent activators typically have a three-domain structure: the variable N-terminal regulatory (activation) domain involved in signal recognition/receiving, the central AAA-type ATPase domain, and the DNA-binding domain (see PIRSF003187 from PIRSF, PIRSF005263 from PIRSF, PIRSF003184 from PIRSF, PIRSF005263 from PIRSF, IPR014443 from INTERPRO for details), the proteins of the current entry may be predicted to play a role in signal recognition/receiving and signal transduction.; PDB: 2P10_C. Probab=75.97 E-value=11 Score=32.37 Aligned_cols=51 Identities=18% Similarity=0.180 Sum_probs=35.8 Q ss_pred EEecCCCCCCHHHHHHHHHhcCcEEEEec-----------CCCCHHHHHHHHHHHHHHHHHhC Q psy254 40 ICTIGPASVAVDMLEKIIETGMNIARLNF-----------SHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 40 i~TiGPas~~~~~i~~li~aGm~v~RiN~-----------sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) +.|+ |-.-+++.-++|.+||+||.=.++ ..-+.++..+.++.+.+++.+.+ T Consensus 151 l~T~-~yvf~~e~A~~M~~AGaDiiv~H~GlT~gG~~Ga~~~~sl~~a~~~~~~i~~aa~~v~ 212 (268) T PF09370_consen 151 LFTT-AYVFNEEQARAMAEAGADIIVAHMGLTTGGSIGAKTALSLEEAAERIQEIFDAARAVN 212 (268) T ss_dssp -EE---EE-SHHHHHHHHHHT-SEEEEE-SS----------S--HHHHHHHHHHHHHHHHCC- T ss_pred Ceee-eeecCHHHHHHHHHcCCCEEEecCCccCCCCcCccccCCHHHHHHHHHHHHHHHHHhC Confidence 4566 767789999999999999988888 34467788899999999888776 No 39 >PRK07535 methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase; Validated Probab=75.71 E-value=7.1 Score=33.05 Aligned_cols=60 Identities=15% Similarity=0.118 Sum_probs=46.2 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEeeecC Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTGLLQ 117 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG~~~ 117 (187) .+..++|+++|+++.=+|+.-...+++.++..-|+.+.+.++ ++|.+|+.-|++.--.++ T Consensus 28 ~~~A~~~~~~GAdiIDVg~~~~~~eE~~r~~~~v~~l~~~~~--------~plsIDT~~~~v~eaaL~ 87 (261) T PRK07535 28 QKLALKQAEAGADYLDVNAGTAVEEEPETMEWLVETVQEVVD--------VPLCIDSPNPAAIEAGLK 87 (261) T ss_pred HHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHHHHhCC--------CCEEEeCCCHHHHHHHHH Confidence 356677899999999999987667778888888887765543 578999999887654443 No 40 >cd00423 Pterin_binding Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and protein biosynthesis. Prokaryotes (and some lower eukaryotes) must synthesize folate de novo, while higher eukaryotes are able to utilize dietary folate and therefore lack DHPS. Sulfonamide drugs, which are substrate analogs of pABA, target DHPS. Cobalamin-dependent methyltransferases catalyze the transfer of a methyl group via a methyl- cob(III)amide intermediate. These include MeTr, a functional heterodimer, and the folate binding domain of MetH. Probab=74.79 E-value=14 Score=31.01 Aligned_cols=53 Identities=19% Similarity=0.258 Sum_probs=40.3 Q ss_pred HHHHHHHHhcCcEEEEecCCC--------CHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCee Q psy254 51 DMLEKIIETGMNIARLNFSHG--------SYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEI 111 (187) Q Consensus 51 ~~i~~li~aGm~v~RiN~sHg--------~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkI 111 (187) +..++|+++|+++.=+|+.-. ..+++.++...|+.+.+.. .++|.+|+.=|++ T Consensus 28 ~~a~~~~~~GAdiIDvG~~st~p~~~~~~~~~E~~rl~~~v~~l~~~~--------~~piSIDT~~~~v 88 (258) T cd00423 28 EHARRMVEEGADIIDIGGESTRPGAEPVSVEEELERVIPVLRALAGEP--------DVPISVDTFNAEV 88 (258) T ss_pred HHHHHHHHCCCCEEEECCCcCCCCCCcCCHHHHHHHHHHHHHHHHhcC--------CCeEEEeCCcHHH Confidence 566789999999999998665 5677777777777776543 3568889877765 No 41 >TIGR01949 AroFGH_arch predicted phospho-2-dehydro-3-deoxyheptonate aldolase. Together these two genes appear to perform the synthesis of 3-dehydroquinate. It is presumed that the substrates and the chemical transformations involved are identical, but this has not yet been proven experimentally. Probab=73.84 E-value=18 Score=30.18 Aligned_cols=69 Identities=16% Similarity=0.257 Sum_probs=43.1 Q ss_pred CCceEEEec--CCCC-----C--CHHHHHHHHHhcCc--EEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEE Q psy254 35 RLTGIICTI--GPAS-----V--AVDMLEKIIETGMN--IARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIA 103 (187) Q Consensus 35 r~TkIi~Ti--GPas-----~--~~~~i~~li~aGm~--v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~ 103 (187) ..++++.++ |... . -...+++.+++|++ -+|.|....+..+..+.+..+++++.+++ .|+-|+ T Consensus 69 ~~~~~~~~~~~~~~~g~~~~~~~~~~~v~~al~~Ga~~v~~~~~~g~~~~~~~~~~~~~i~~~~~~~g------~~liv~ 142 (258) T TIGR01949 69 KDVGLIIHLSASTSLSPDPNDKRIVTTVEDAIRMGADAVSIHVNVGSDTEWEQIRDLGMIAEICDDWG------VPLLAM 142 (258) T ss_pred CCCcEEEEEcCCCCCCCCCCcceeeeeHHHHHHCCCCEEEEEEecCCchHHHHHHHHHHHHHHHHHcC------CCEEEE Confidence 467788888 4322 1 22558999999998 56666554343445566777777777777 566554 Q ss_pred eeCCCC Q psy254 104 LDTKGP 109 (187) Q Consensus 104 ~Dl~GP 109 (187) +-..|. T Consensus 143 ~~~~Gv 148 (258) T TIGR01949 143 MYPRGP 148 (258) T ss_pred EeccCc Confidence 444443 No 42 >PRK06806 fructose-bisphosphate aldolase; Provisional Probab=72.87 E-value=23 Score=30.36 Aligned_cols=53 Identities=17% Similarity=0.248 Sum_probs=47.0 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+..-+ ..+.+.+.+++.+++|.+.+-|.-||-+.++..+....+++.+..++ T Consensus 76 pv~lHl-DH~~~~e~i~~Al~~G~tsVm~d~s~~~~~eni~~t~~v~~~a~~~g 128 (281) T PRK06806 76 PVAVHF-DHGMTFEKIKEALEIGFTSVMFDGSHLPLEENIQKTKEIVELAKQYG 128 (281) T ss_pred CEEEEC-CCCCCHHHHHHHHHcCCCEEEEcCCCCCHHHHHHHHHHHHHHHHHcC Confidence 455555 66779999999999999999999999999999999999999998887 No 43 >PF06953 ArsD: Arsenical resistance operon trans-acting repressor ArsD; InterPro: IPR010712 This family consists of several bacterial arsenical resistance operon trans-acting repressor ArsD proteins. ArsD is a trans-acting repressor of the arsRDABC operon that confers resistance to arsenicals and antimonials in Escherichia coli. It possesses two-pairs of vicinal cysteine residues, Cys(12)-Cys(13) and Cys(112)-Cys(113), that potentially form separate binding sites for the metalloids that trigger dissociation of ArsD from the operon. However, as a homodimer it has four vicinal cysteine pairs [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent, 0046685 response to arsenic-containing substance; PDB: 3MWH_A 3KGK_A 3KTB_B. Probab=72.03 E-value=12 Score=28.35 Aligned_cols=27 Identities=19% Similarity=0.379 Sum_probs=21.1 Q ss_pred HHHHHHHHhcCcEEEEecCCCCHHHHH Q psy254 51 DMLEKIIETGMNIARLNFSHGSYEYHG 77 (187) Q Consensus 51 ~~i~~li~aGm~v~RiN~sHg~~e~~~ 77 (187) ..+..|-+.|++|.|+|+++....... T Consensus 31 ~~~~~Lk~~gv~v~RyNL~~~P~aF~~ 57 (123) T PF06953_consen 31 ADLDWLKEQGVEVERYNLAQNPQAFVE 57 (123) T ss_dssp HHHHHHHHTT-EEEEEETTT-TTHHHH T ss_pred HHHHHHHhCCceEEEEccccCHHHHHh Confidence 567889999999999999999876543 No 44 >PRK07807 inosine 5-monophosphate dehydrogenase; Validated Probab=71.44 E-value=8.3 Score=35.60 Aligned_cols=44 Identities=16% Similarity=0.342 Sum_probs=36.9 Q ss_pred cCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 43 IGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 43 iGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) +|.+.+..+.++.|+++|+++.=+..+||......++|+.||+. T Consensus 222 v~~~~~~~~~a~~Lv~aGvd~i~~D~a~~~~~~~~~~i~~ik~~ 265 (479) T PRK07807 222 VGINGDVAAKARALLEAGVDVLVVDTAHGHQEKMLEALRAVRAL 265 (479) T ss_pred hccChhHHHHHHHHHHhCCCEEEEeccCCccHHHHHHHHHHHHH Confidence 35555678999999999999999999999988777778777763 No 45 >PRK07315 fructose-bisphosphate aldolase; Provisional Probab=71.04 E-value=31 Score=29.78 Aligned_cols=52 Identities=13% Similarity=0.062 Sum_probs=46.1 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+..-+ ..+ +.+.+++.+++|.+..-|..||-+.++..+....+++.+..++ T Consensus 79 PV~lHL-DH~-~~~~i~~ai~~GftSVm~d~S~l~~eEni~~t~~v~~~a~~~g 130 (293) T PRK07315 79 PVAIHL-DHG-HYEDALECIEVGYTSIMFDGSHLPVEENLKLAKEVVEKAHAKG 130 (293) T ss_pred cEEEEC-CCC-CHHHHHHHHHcCCCEEEEcCCCCCHHHHHHHHHHHHHHHHHcC Confidence 456666 566 7999999999999999999999999999999999999988877 No 46 >PF00677 Lum_binding: Lumazine binding domain; InterPro: IPR001783 The following proteins have been shown [, ] to be structurally and evolutionary related: Riboflavin synthase alpha chain (2.5.1.9 from EC) (RS-alpha) (gene ribC in Escherichia coli, ribB in Bacillus subtilis and Photobacterium leiognathi, RIB5 in yeast. This enzyme synthesises riboflavin from two moles of 6,7- dimethyl-8-(1'-D-ribityl)lumazine (Lum), a pteridine-derivative. Photobacterium phosphoreum lumazine protein (LumP) (gene luxL). LumP is a protein that modulates the colour of the bioluminescence emission of bacterial luciferase. In the presence of LumP, light emission is shifted to higher energy values (shorter wavelength). LumP binds non-covalently to 6,7-dimethyl-8-(1'-D-ribityl)lumazine. Vibrio fischeri yellow fluorescent protein (YFP) (gene luxY). Like LumP, YFP modulates light emission but towards a longer wavelength. YFP binds non-covalently to FMN. These proteins seem to have evolved from the duplication of a domain of about 100 residues. In its C-terminal section, this domain contains a conserved motif [KR]-V-N-[LI]-E which has been proposed to be the binding site for lumazine (Lum) and some of its derivatives. RS-alpha which binds two molecules of Lum has two perfect copies of this motif, while LumP which binds one molecule of Lum, has a Glu instead of Lys/Arg in the first position of the second copy of the motif. Similarly, YFP, which binds to one molecule of FMN, also seems to have a potentially dysfunctional binding site by substitution of Gly for Glu in the last position of the first copy of the motif.; GO: 0004746 riboflavin synthase activity, 0009231 riboflavin biosynthetic process; PDB: 3DDY_A 1KZL_A 3A3G_B 3A35_B 3A3B_B 1I8D_C 1PKV_B 1HZE_B 1I18_B. Probab=69.45 E-value=13 Score=25.94 Aligned_cols=37 Identities=24% Similarity=0.367 Sum_probs=28.6 Q ss_pred CEEeeCcc-hhhhcCCCCCEEEEeCCeEEEEEEEEeCCee Q psy254 147 TDLYVDYT-NITKVVKPGSRIFVDDGLISLVVKSIVKSYQ 185 (187) Q Consensus 147 ~~i~v~~~-~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~i 185 (187) ..+.+..| ..+..+.+|+.|-+|. ++|+|.++.++++ T Consensus 20 ~~~~i~~~~~~~~~~~~g~SIavnG--vcLTV~~~~~~~f 57 (85) T PF00677_consen 20 QRLRIEIPDKILSDLKIGGSIAVNG--VCLTVTDINEDWF 57 (85) T ss_dssp EEEEEEESTGGGGTG-TTSEEEETT--EEEEEEEEETTEE T ss_pred EEEEEEcCHHHHhhCccCcEEEECC--eeeEEEEecCCEE Confidence 34555555 7788999999999986 7999999988764 No 47 >PRK01712 carbon storage regulator; Provisional Probab=68.97 E-value=9.4 Score=25.63 Aligned_cols=26 Identities=19% Similarity=0.258 Sum_probs=21.9 Q ss_pred cCCCCCEEEEeCCeEEEEEEEEeCCee Q psy254 159 VVKPGSRIFVDDGLISLVVKSIVKSYQ 185 (187) Q Consensus 159 ~v~~Gd~IlidDG~i~l~V~~v~~~~i 185 (187) .-++|..|.|+| .|..+|.++.++.+ T Consensus 5 tRk~gE~I~Igd-~I~I~V~~i~~~~V 30 (64) T PRK01712 5 TRKVGESLMIGD-DIEVTVLGVKGNQV 30 (64) T ss_pred EccCCCEEEeCC-CEEEEEEEEeCCEE Confidence 348899999998 69999999988754 No 48 >PRK15452 putative protease; Provisional Probab=68.89 E-value=13 Score=34.08 Aligned_cols=42 Identities=19% Similarity=0.391 Sum_probs=38.4 Q ss_pred CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHh Q psy254 49 AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENY 90 (187) Q Consensus 49 ~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~ 90 (187) -.+.|.+|+++|++.+||.+-.-++++..+++...|++...+ T Consensus 270 ~i~~l~~L~~aGV~s~KIEgR~ks~~yv~~vv~~YR~ald~~ 311 (443) T PRK15452 270 AIQHVERLTKMGVHSLKIEGRTKSFYYVARTAQVYRKAIDDA 311 (443) T ss_pred HHHHHHHHHHcCCCEEEEEeeeCCHHHHHHHHHHHHHHHHHH Confidence 357899999999999999999999999999999999987654 No 49 >PF02599 CsrA: Global regulator protein family; InterPro: IPR003751 The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay []. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [].; GO: 0003723 RNA binding, 0006109 regulation of carbohydrate metabolic process, 0006402 mRNA catabolic process; PDB: 1Y00_B 2JPP_A 1T3O_A 1VPZ_A. Probab=68.54 E-value=7.2 Score=25.22 Aligned_cols=25 Identities=28% Similarity=0.290 Sum_probs=19.6 Q ss_pred CCCCCEEEEeCCeEEEEEEEEeCCee Q psy254 160 VKPGSRIFVDDGLISLVVKSIVKSYQ 185 (187) Q Consensus 160 v~~Gd~IlidDG~i~l~V~~v~~~~i 185 (187) -++|..|.++| .|..+|.++.++.+ T Consensus 6 Rk~gE~I~Ig~-~I~I~Vl~i~~~~V 30 (54) T PF02599_consen 6 RKVGESIVIGD-DIEITVLEISGGQV 30 (54) T ss_dssp EETT-EEEETT-TEEEEEEEEETTEE T ss_pred ccCCCEEEECC-CEEEEEEEEcCCEE Confidence 37889999987 89999999987754 No 50 >PRK08185 hypothetical protein; Provisional Probab=67.30 E-value=39 Score=29.09 Aligned_cols=54 Identities=11% Similarity=0.151 Sum_probs=47.3 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) ..+..-+ ..+.+.+.+++.+++|.+-+.|.-||-+.++..+....+.+.+..+| T Consensus 69 vPV~lHL-DHg~~~e~i~~ai~~Gf~SVM~D~S~l~~eeNi~~t~~vv~~a~~~g 122 (283) T PRK08185 69 VPFVIHL-DHGATIEDVMRAIRCGFTSVMIDGSLLPYEENVALTKEVVELAHKVG 122 (283) T ss_pred CCEEEEC-CCCCCHHHHHHHHHcCCCEEEEeCCCCCHHHHHHHHHHHHHHHHHcC Confidence 3466666 67778999999999999999999999999999999999988888877 No 51 >TIGR01093 aroD 3-dehydroquinate dehydratase, type I. Type II 3-dehydroquinate dehydratase, designated AroQ, is described by TIGR01088. Probab=67.18 E-value=28 Score=28.52 Aligned_cols=55 Identities=24% Similarity=0.197 Sum_probs=42.4 Q ss_pred CCCceEEEec-----CCCCCC-HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHH Q psy254 34 VRLTGIICTI-----GPASVA-VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVE 88 (187) Q Consensus 34 ~r~TkIi~Ti-----GPas~~-~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~ 88 (187) ...+|||++- .|+... .+.+++|...|.|+++|-..--+.++..++++..+++.. T Consensus 116 ~~~~kvI~S~H~f~~tp~~~~l~~~~~~~~~~gaDivKia~~a~~~~D~~~ll~~~~~~~~ 176 (228) T TIGR01093 116 KGGTKIIMSYHDFQKTPSWEEIVERLEKALSYGADIVKIAVMANSKEDVLTLLEITNKVDE 176 (228) T ss_pred HCCCEEEEeccCCCCCCCHHHHHHHHHHHHHhCCCEEEEEeccCCHHHHHHHHHHHHHHHh Confidence 4588999998 233322 367888999999999999988888888888877766643 No 52 >TIGR01496 DHPS dihydropteroate synthase. This model represents dihydropteroate synthase, the enzyme that catalyzes the second to last step in folic acid biosynthesis. The gene is usually designated folP (folic acid biosynthsis) or sul (sulfanilamide resistance). This model represents one branch of the family of pterin-binding enzymes (pfam00809) and of a cluster of dihydropteroate synthase and related enzymes (COG0294). Other members of pfam00809 and COG0294 are represented by TIGR00284. Probab=66.50 E-value=17 Score=30.70 Aligned_cols=54 Identities=24% Similarity=0.293 Sum_probs=37.5 Q ss_pred HHHHHHHHHhcCcEEEEec-CC------CC-HHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCee Q psy254 50 VDMLEKIIETGMNIARLNF-SH------GS-YEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEI 111 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~-sH------g~-~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkI 111 (187) .+..++++++|+++.=+|. |- -+ .+|+.++...|+.+.+..+ +.|.+|+.-|+. T Consensus 26 ~~~a~~~~~~GA~iIDIG~~st~p~~~~i~~~~E~~rl~~~v~~~~~~~~--------~plsiDT~~~~v 87 (257) T TIGR01496 26 VAHAERMLEEGADIIDVGGESTRPGADRVSPEEELNRVVPVIKALRDQPD--------VPISVDTYRAEV 87 (257) T ss_pred HHHHHHHHHCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHhcCC--------CeEEEeCCCHHH Confidence 4677788999999999984 22 12 3356666666666654433 578999998876 No 53 >PRK00568 carbon storage regulator; Provisional Probab=66.42 E-value=9.9 Score=26.41 Aligned_cols=25 Identities=32% Similarity=0.292 Sum_probs=21.6 Q ss_pred CCCCCEEEEeCCeEEEEEEEEeCCee Q psy254 160 VKPGSRIFVDDGLISLVVKSIVKSYQ 185 (187) Q Consensus 160 v~~Gd~IlidDG~i~l~V~~v~~~~i 185 (187) =++|..|.|+| .|..+|.++.++.+ T Consensus 6 RK~gEsI~Igd-~I~I~Vl~i~g~~V 30 (76) T PRK00568 6 RKVNEGIVIDD-NIHIKVISIDRGSV 30 (76) T ss_pred eeCCCeEEeCC-CeEEEEEEEcCCEE Confidence 37899999999 79999999988765 No 54 >PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B .... Probab=66.23 E-value=13 Score=30.82 Aligned_cols=65 Identities=17% Similarity=0.267 Sum_probs=27.8 Q ss_pred cceeEEEeeCCCCeeEeeecCCCCcccEEeeeCCEEEEeeCCCc-ccCCCcCEEeeCcchhhhcCCCCCEEEE Q psy254 97 PHALAIALDTKGPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAF-AEKGSATDLYVDYTNITKVVKPGSRIFV 168 (187) Q Consensus 97 ~~~v~I~~Dl~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~-~~~~~~~~i~v~~~~l~~~v~~Gd~Ili 168 (187) |-||-.++| +.|+.+.-.+ .++.+.|.++.||..--. ...++....+-...-++++|++||.|++ T Consensus 49 yS~V~~flh-r~~~~~~~F~------~i~te~g~~l~LTp~HLI~v~~~~~~~~~~~~~vfA~~V~~Gd~v~~ 114 (217) T PF01079_consen 49 YSPVIMFLH-RDPEQRAEFV------VIETEDGRSLTLTPNHLIFVADCNGSESSNFRAVFASDVRVGDCVLV 114 (217) T ss_dssp EEEEEEEEE-EEEEEEEEEE------EEEETTS-EEEE-TT-EEEEEETTTTEE---EEEEGGG--TT-EEEE T ss_pred EEeEEEEec-cCccccEEEE------EEEcCCCCeEEecCCcEEEEecCCCCcccccceeehhhCCCCCEEEE Confidence 345555555 3343333222 255556777777654210 0111111111112456789999999999 No 55 >PF00150 Cellulase: Cellulase (glycosyl hydrolase family 5); InterPro: IPR001547 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 5 GH5 from CAZY comprises enzymes with several known activities; endoglucanase (3.2.1.4 from EC); beta-mannanase (3.2.1.78 from EC); exo-1,3-glucanase (3.2.1.58 from EC); endo-1,6-glucanase (3.2.1.75 from EC); xylanase (3.2.1.8 from EC); endoglycoceramidase (3.2.1.123 from EC). The microbial degradation of cellulose and xylans requires several types of enzymes. Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family A [] or as the glycosyl hydrolases family 5 []. One of the conserved regions in this family contains a conserved glutamic acid residue which is potentially involved [] in the catalytic mechanism.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3NDY_A 3NDZ_B 1LF1_A 1TVP_B 1TVN_A 3AYR_A 3AYS_A 1QI0_A 1W3K_A 1OCQ_A .... Probab=65.46 E-value=15 Score=29.93 Aligned_cols=54 Identities=17% Similarity=0.329 Sum_probs=36.6 Q ss_pred CCHHHHHHHHHhcCcEEEEecCCCCHH----------HHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCC Q psy254 48 VAVDMLEKIIETGMNIARLNFSHGSYE----------YHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGP 109 (187) Q Consensus 48 ~~~~~i~~li~aGm~v~RiN~sHg~~e----------~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GP 109 (187) ...+.++.|-..|+|..||-+...... ...+.++.+-+++++.| +.|++|+-++ T Consensus 22 ~~~~~~~~~~~~G~n~VRi~v~~~~~~~~~~~~~~~~~~~~~ld~~v~~a~~~g--------i~vild~h~~ 85 (281) T PF00150_consen 22 ITEADFDQLKALGFNTVRIPVGWEAYQEPNPGYNYDETYLARLDRIVDAAQAYG--------IYVILDLHNA 85 (281) T ss_dssp SHHHHHHHHHHTTESEEEEEEESTSTSTTSTTTSBTHHHHHHHHHHHHHHHHTT---------EEEEEEEES T ss_pred CHHHHHHHHHHCCCCEEEeCCCHHHhcCCCCCccccHHHHHHHHHHHHHHHhCC--------CeEEEEeccC Confidence 567899999999999999999963322 23344444444445544 7788898874 No 56 >PF04028 DUF374: Domain of unknown function (DUF374); InterPro: IPR007172 This is a bacterial domain of unknown function. Probab=64.38 E-value=34 Score=23.39 Aligned_cols=54 Identities=19% Similarity=0.320 Sum_probs=42.2 Q ss_pred CCCCCHHHHHH-HHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC-CC Q psy254 45 PASVAVDMLEK-IIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK-GP 109 (187) Q Consensus 45 Pas~~~~~i~~-li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~-GP 109 (187) -.+.+-|.+.. +-..|+.++|-+-++|..+...+++..+++ + ..++|-.|-+ || T Consensus 17 S~s~DGe~ia~~~~~~G~~~iRGSs~rgg~~Alr~~~~~lk~-----G------~~~~itpDGPrGP 72 (74) T PF04028_consen 17 SRSRDGELIARVLERFGFRTIRGSSSRGGARALREMLRALKE-----G------YSIAITPDGPRGP 72 (74) T ss_pred ccCcCHHHHHHHHHHcCCCeEEeCCCCcHHHHHHHHHHHHHC-----C------CeEEEeCCCCCCC Confidence 45777888887 456799999999999999888888877773 3 6788888854 54 No 57 >PF01487 DHquinase_I: Type I 3-dehydroquinase; InterPro: IPR001381 3-dehydroquinate dehydratase (4.2.1.10 from EC), or dehydroquinase, catalyzes the conversion of 3-dehydroquinate into 3-dehydroshikimate. It is the third step in the shikimate pathway for the biosynthesis of aromatic amino acids from chorismate. Two classes of dehydroquinases exist, known as types I and II. The best studied type I enzyme is from Escherichia coli (gene aroD) and related bacteria where it is a homodimeric protein. In fungi, dehydroquinase is part of a multifunctional enzyme which catalyzes five consecutive steps in the shikimate pathway. A histidine [] is involved in the catalytic mechanism.; GO: 0003855 3-dehydroquinate dehydratase activity; PDB: 2O7Q_A 2GPT_A 2O7S_A 1SFL_A 2OCZ_A 2OX1_C 1GQN_A 1QFE_B 1L9W_D 3L9C_A .... Probab=64.23 E-value=48 Score=26.83 Aligned_cols=73 Identities=21% Similarity=0.224 Sum_probs=50.5 Q ss_pred CCCceEEEecC--CCCCC----HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcce-eEEEeeC Q psy254 34 VRLTGIICTIG--PASVA----VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHA-LAIALDT 106 (187) Q Consensus 34 ~r~TkIi~TiG--Pas~~----~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~-v~I~~Dl 106 (187) ..++|||++-= ..+.+ .+.+++|...|.++++|-..-.+.++..++++..+++.+..+ .| +++.|-- T Consensus 111 ~~~~~iI~S~H~f~~tp~~~~l~~~~~~~~~~gadivKia~~~~~~~D~~~l~~~~~~~~~~~~------~p~i~~~MG~ 184 (224) T PF01487_consen 111 KGGTKIILSYHDFEKTPSWEELIELLEEMQELGADIVKIAVMANSPEDVLRLLRFTKEFREEPD------IPVIAISMGE 184 (224) T ss_dssp HTTSEEEEEEEESS---THHHHHHHHHHHHHTT-SEEEEEEE-SSHHHHHHHHHHHHHHHHHTS------SEEEEEEETG T ss_pred hCCCeEEEEeccCCCCCCHHHHHHHHHHHHhcCCCeEEEEeccCCHHHHHHHHHHHHHHhhccC------CcEEEEEcCC Confidence 46889999873 11222 377888999999999999999999999998888888876633 44 4555544 Q ss_pred CCCeeE Q psy254 107 KGPEIR 112 (187) Q Consensus 107 ~GPkIR 112 (187) .|.--| T Consensus 185 ~G~~SR 190 (224) T PF01487_consen 185 LGRISR 190 (224) T ss_dssp GGHHHH T ss_pred CchhHH Confidence 444444 No 58 >cd03316 MR_like Mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. Members of the MR subgroup are mandelate racemase, D-glucarate/L-idarate dehydratase (GlucD), D-altronate/D-mannonate dehydratase , D-galactonate dehydratase (GalD) , D-gluconate dehydratase (GlcD), and L-rhamnonate dehydratase (RhamD). Probab=64.13 E-value=46 Score=28.78 Aligned_cols=64 Identities=11% Similarity=0.222 Sum_probs=42.7 Q ss_pred CceEEEecCCCCCCH----HHHHHHHHhcCcEEEEecCCCC-----HHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeC Q psy254 36 LTGIICTIGPASVAV----DMLEKIIETGMNIARLNFSHGS-----YEYHGQTIKNIRQAVENYSKRIGMPHALAIALDT 106 (187) Q Consensus 36 ~TkIi~TiGPas~~~----~~i~~li~aGm~v~RiN~sHg~-----~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl 106 (187) +....+|+|..+.++ +..+++.++|.+.+.|...|+. .+.-.++++.+|++ .+ ..+.+++|. T Consensus 126 ~v~~~~~~~~~~~~~~~~~~~a~~~~~~Gf~~~Kik~g~~~~~~~~~~~d~~~v~~ir~~---~g------~~~~l~vDa 196 (357) T cd03316 126 RVRVYASGGGYDDSPEELAEEAKRAVAEGFTAVKLKVGGPDSGGEDLREDLARVRAVREA---VG------PDVDLMVDA 196 (357) T ss_pred ceeeEEecCCCCCCHHHHHHHHHHHHHcCCCEEEEcCCCCCcchHHHHHHHHHHHHHHHh---hC------CCCEEEEEC Confidence 345556776553223 4566678899999999999886 56556666666654 44 346788888 Q ss_pred CC Q psy254 107 KG 108 (187) Q Consensus 107 ~G 108 (187) -+ T Consensus 197 N~ 198 (357) T cd03316 197 NG 198 (357) T ss_pred CC Confidence 53 No 59 >PRK15108 biotin synthase; Provisional Probab=63.64 E-value=25 Score=30.88 Aligned_cols=30 Identities=17% Similarity=0.285 Sum_probs=24.1 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEec Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNF 68 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~ 68 (187) ..+++|+|+-+ .+.+++|.+||++.+-+|+ T Consensus 125 i~v~~s~G~ls--~e~l~~LkeAGld~~n~~l 154 (345) T PRK15108 125 LETCMTLGTLS--ESQAQRLANAGLDYYNHNL 154 (345) T ss_pred CEEEEeCCcCC--HHHHHHHHHcCCCEEeecc Confidence 46788888754 8999999999999765544 No 60 >COG2945 Predicted hydrolase of the alpha/beta superfamily [General function prediction only] Probab=62.32 E-value=17 Score=30.00 Aligned_cols=37 Identities=16% Similarity=0.359 Sum_probs=29.5 Q ss_pred HHHHHHHHHhcCcEEEEec------------CCCCHHHHHHHHHHHHHH Q psy254 50 VDMLEKIIETGMNIARLNF------------SHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~------------sHg~~e~~~~~i~~ir~a 86 (187) ...-+.|.+.|+.+.|+|| -+|..++....++++|.. T Consensus 50 ~~la~~l~~~G~atlRfNfRgVG~S~G~fD~GiGE~~Da~aaldW~~~~ 98 (210) T COG2945 50 QTLARALVKRGFATLRFNFRGVGRSQGEFDNGIGELEDAAAALDWLQAR 98 (210) T ss_pred HHHHHHHHhCCceEEeecccccccccCcccCCcchHHHHHHHHHHHHhh Confidence 3556678999999999999 346677888888888864 No 61 >PRK08195 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated Probab=61.59 E-value=34 Score=30.06 Aligned_cols=51 Identities=22% Similarity=0.244 Sum_probs=34.4 Q ss_pred CCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHH Q psy254 34 VRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIR 84 (187) Q Consensus 34 ~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir 84 (187) .+++|+.+-+=|...+.+.++...++|++++|+-+.-...+...+.++.+| T Consensus 75 ~~~~~~~~ll~pg~~~~~dl~~a~~~gvd~iri~~~~~e~~~~~~~i~~ak 125 (337) T PRK08195 75 VKQAKIAALLLPGIGTVDDLKMAYDAGVRVVRVATHCTEADVSEQHIGLAR 125 (337) T ss_pred CCCCEEEEEeccCcccHHHHHHHHHcCCCEEEEEEecchHHHHHHHHHHHH Confidence 356788775546666788999999999999999764333344444444333 No 62 >PF04055 Radical_SAM: Radical SAM superfamily; InterPro: IPR007197 Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. Evidence exists that these proteins generate a radical species by reductive cleavage of S:-adenosylmethionine (SAM) through an unusual Fe-S centre [, ].; GO: 0003824 catalytic activity, 0051536 iron-sulfur cluster binding; PDB: 2A5H_D 3T7V_A 3C8F_A 3CB8_A 2FB2_A 2FB3_A 3CIX_A 3IIX_A 3IIZ_A 3CIW_A .... Probab=61.35 E-value=60 Score=23.52 Aligned_cols=39 Identities=13% Similarity=0.177 Sum_probs=29.9 Q ss_pred CceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHH Q psy254 36 LTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYE 74 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e 74 (187) ..++..+..+...+.+.++.|.++|++.+++++...+.+ T Consensus 76 ~~~i~~~t~~~~~~~~~l~~l~~~~~~~i~~~l~s~~~~ 114 (166) T PF04055_consen 76 GIRISINTNGTLLDEELLDELKKLGVDRIRISLESLDEE 114 (166) T ss_dssp TEEEEEEEESTTHCHHHHHHHHHTTCSEEEEEEBSSSHH T ss_pred ccceeeeccccchhHHHHHHHHhcCccEEecccccCCHH Confidence 334444443333349999999999999999999999998 No 63 >PRK07565 dihydroorotate dehydrogenase 2; Reviewed Probab=61.03 E-value=31 Score=29.98 Aligned_cols=34 Identities=24% Similarity=0.352 Sum_probs=25.8 Q ss_pred ceEEEecCCCCCC--HHHHHHHHHhcCcEEEEecCC Q psy254 37 TGIICTIGPASVA--VDMLEKIIETGMNIARLNFSH 70 (187) Q Consensus 37 TkIi~TiGPas~~--~~~i~~li~aGm~v~RiN~sH 70 (187) ..+++.|+..+.. .+..+.+.++|.+.+=||+|+ T Consensus 102 ~pvi~sI~g~~~~e~~~~a~~~~~agad~ielN~sc 137 (334) T PRK07565 102 IPVIASLNGSSAGGWVDYARQIEQAGADALELNIYY 137 (334) T ss_pred CcEEEEeccCCHHHHHHHHHHHHHcCCCEEEEeCCC Confidence 5789999554432 266677778899999999985 No 64 >COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones] Probab=60.47 E-value=28 Score=27.89 Aligned_cols=62 Identities=15% Similarity=0.154 Sum_probs=42.9 Q ss_pred EEeeeCCEEEEee--CCCcccCCCcCEE-eeCcchhhh--cCCCCCEEEEeC--CeEEEEEEEEeCCeee Q psy254 124 VELVKGQTIRLTT--DAAFAEKGSATDL-YVDYTNITK--VVKPGSRIFVDD--GLISLVVKSIVKSYQL 186 (187) Q Consensus 124 i~l~~G~~v~lt~--~~~~~~~~~~~~i-~v~~~~l~~--~v~~Gd~IlidD--G~i~l~V~~v~~~~i~ 186 (187) .-++.|++..+.. +.+|. ..+++.+ .++-..|.. .+.+|..+.+++ |.+..+|++|+++.+. T Consensus 51 ~g~~~Ge~~~V~IpPE~AfG-e~~~~lvq~vp~~~F~~~~~~~vGm~~~~~~~~~~~~~~V~~V~~~~V~ 119 (174) T COG1047 51 LGKEVGEEFTVEIPPEDAFG-EYDPDLVQRVPRDEFQGVGELEVGMEVEAEGGDGEIPGVVTEVSGDRVT 119 (174) T ss_pred hCCCCCceeEEEeCchHhcC-CCChHHeEEecHHHhCcCCCCCCCcEEEEcCCCceeeEEEEEEcCCEEE Confidence 3456788777765 44443 3344433 456666666 589999999975 5788999999988763 No 65 >PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A. Probab=60.25 E-value=49 Score=22.15 Aligned_cols=44 Identities=14% Similarity=0.101 Sum_probs=35.3 Q ss_pred CCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 47 SVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 47 s~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) -++...+.+.+++| ++.=+||++-+.+..++.++.+..+....+ T Consensus 9 ~~D~~~i~~~l~~g-~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~ 52 (73) T PF04472_consen 9 FEDAREIVDALREG-KIVIVNLENLDDEEAQRILDFLSGAVYALD 52 (73) T ss_dssp GGGHHHHHHHHHTT---EEEE-TTS-HHHHHHHHHHHHHHHHHTT T ss_pred HHHHHHHHHHHHcC-CEEEEECCCCCHHHHHHHHHHHhchheeeC Confidence 35677899999999 666899999999999999999999988776 No 66 >TIGR00693 thiE thiamine-phosphate pyrophosphorylase. This model includes ThiE from Bacillus subtilis but excludes its paralog, the regulatory protein TenI, and neighbors of TenI. Probab=59.85 E-value=46 Score=26.06 Aligned_cols=42 Identities=10% Similarity=0.222 Sum_probs=36.5 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+.+++++++|++.+-+..-+.+..+..+.+..++...+.++ T Consensus 16 ~~~~~~~~~~g~~~v~lR~~~~~~~~~~~~~~~l~~~~~~~~ 57 (196) T TIGR00693 16 LNRVEAALKGGVTLVQLRDKGSNTRERLALAEKLQELCRRYG 57 (196) T ss_pred HHHHHHHHhcCCCEEEEecCCCCHHHHHHHHHHHHHHHHHhC Confidence 567889999999999998888888888899999998887766 No 67 >COG0051 RpsJ Ribosomal protein S10 [Translation, ribosomal structure and biogenesis] Probab=59.72 E-value=19 Score=26.45 Aligned_cols=31 Identities=10% Similarity=0.082 Sum_probs=28.5 Q ss_pred CcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 61 MNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 61 m~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) +..+||-+.-.++....+....|.+.++.+| T Consensus 3 ~~kirI~L~s~d~~~LD~~~~~Ive~akrtg 33 (104) T COG0051 3 KQKIRIRLKSFDHRLLDQVCREIVETAKRTG 33 (104) T ss_pred CceEEEEEecCCHHHHHHHHHHHHHHHHHhC Confidence 3589999999999999999999999999888 No 68 >PRK07709 fructose-bisphosphate aldolase; Provisional Probab=59.47 E-value=65 Score=27.76 Aligned_cols=53 Identities=13% Similarity=0.231 Sum_probs=44.6 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+..-+ ..+.+.+.+.+.+++|.+-..|..||-+.++.-+.-..+-+.+...| T Consensus 79 PV~lHL-DHg~~~e~i~~ai~~GftSVM~DgS~lp~eeNi~~Trevv~~Ah~~g 131 (285) T PRK07709 79 PVAIHL-DHGSSFEKCKEAIDAGFTSVMIDASHHPFEENVETTKKVVEYAHARN 131 (285) T ss_pred cEEEEC-CCCCCHHHHHHHHHcCCCEEEEeCCCCCHHHHHHHHHHHHHHHHHcC Confidence 566666 77788999999999999999999999999887777777777777666 No 69 >TIGR00202 csrA carbon storage regulator (csrA). Modulates the expression of genes in the glycogen biosynthesis and gluconeogenesis pathways by accelerating the 5'-to-3' degradation of these transcripts through selective RNA binding. The N-terminal end of the sequence (AA 11-45) contains the KH motif which is characteristic of a set of RNA-binding proteins. Probab=59.26 E-value=19 Score=24.53 Aligned_cols=26 Identities=23% Similarity=0.124 Sum_probs=21.4 Q ss_pred cCCCCCEEEEeCCeEEEEEEEEeCCee Q psy254 159 VVKPGSRIFVDDGLISLVVKSIVKSYQ 185 (187) Q Consensus 159 ~v~~Gd~IlidDG~i~l~V~~v~~~~i 185 (187) .-++|..|.++| .|..+|.++.++.+ T Consensus 5 tRk~gE~I~Igd-~I~I~Vl~i~g~~V 30 (69) T TIGR00202 5 SRKVNESIQIGD-DIEVKVLSVKGDQV 30 (69) T ss_pred EccCCCEEEeCC-CEEEEEEEEcCCeE Confidence 348899999998 59999999987754 No 70 >COG2040 MHT1 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism] Probab=59.08 E-value=40 Score=29.35 Aligned_cols=56 Identities=18% Similarity=0.208 Sum_probs=38.2 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC-CCeeEeeec Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK-GPEIRTGLL 116 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~-GPkIRtG~~ 116 (187) ...|..+.++|+|+.=+-. =-+..|-+ -|.++.++++ +|++|-+=+. ++.+|.|.. T Consensus 137 ~~rie~l~~ag~Dlla~ET-ip~i~Ea~----Aiv~l~~~~s------~p~wISfT~~d~~~lr~Gt~ 193 (300) T COG2040 137 RPRIEALNEAGADLLACET-LPNITEAE----AIVQLVQEFS------KPAWISFTLNDDTRLRDGTP 193 (300) T ss_pred HHHHHHHHhCCCcEEeecc-cCChHHHH----HHHHHHHHhC------CceEEEEEeCCCCccCCCcc Confidence 4578899999999865422 11222233 3444555556 8999999988 999999964 No 71 >COG0646 MetH Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism] Probab=59.06 E-value=46 Score=29.11 Aligned_cols=56 Identities=14% Similarity=0.268 Sum_probs=44.1 Q ss_pred CCceEEEecCCCCC----C--------------HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 35 RLTGIICTIGPASV----A--------------VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 35 r~TkIi~TiGPas~----~--------------~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) |++-+.+||||-.. + .+.++-|++.|+|++-|-...... +.+..+..+|++-++.+ T Consensus 113 k~rfVaGsiGPt~k~~~~~~~~~v~fd~l~~ay~eq~~~Li~gG~D~iLiET~~D~l-~~KaA~~a~~~~~~~~~ 186 (311) T COG0646 113 KPRFVAGSIGPTNKTLSISPDFAVTFDELVEAYREQVEGLIDGGADLILIETIFDTL-NAKAAVFAAREVFEELG 186 (311) T ss_pred CceEEEEeccCcCCcCCcCCcccccHHHHHHHHHHHHHHHHhCCCcEEEEehhccHH-HHHHHHHHHHHHHHhcC Confidence 67789999999552 1 367888999999999998877665 46777778888887776 No 72 >PF00809 Pterin_bind: Pterin binding enzyme This Prosite entry is a subset of the Pfam family; InterPro: IPR000489 The ~250-residue pterin-binding domain has been shown to adopt a (beta/alpha)8 barrel fold, which has the overall shape of a distorted cylinder. It has eight alpha-helices stacked around the outside of an inner cylinder of parallel beta-strands. The pterin ring binds at the bottom of the (beta/alpha;)8 barrel in a polar cup-like region that is relatively solvent exposed and fairly negatively charged. The pterin ring is partially buried within the (beta/alpha)8 barrel. The pterin binding residues are highly conserved and include aspartate and asparagine residues located at the C terminus of the beta-strands of the barrel, which are predicted to form hydrogen bonds with the nitrogen and oxygen atoms of the pterin ring [, , ]. Some proteins known to contain a pterin-binding domain are listed below: Prokaryotic and eukaryotic B12-dependent methionine synthase (MetH) (2.1.1.13 from EC), a large, modular protein that catalyzes the transfer of a methyl group from methyltetrahydrofolate (CH3-H4folate) to Hcy to form methionine, using cobalamin as an intermediate methyl carrier. Prokaryotic and eukaryotic dihydropteroate synthase (DHPS) (2.5.1.15 from EC). It catalyzes the condensation of para-aminobenzoic acid (pABA) with 7,8- dihydropterin-pyrophosphate (DHPPP), eliminating pyrophosphate to form 7,8- dihydropteroate which is subsequently converted to tetrahydrofolate. Moorella thermoacetica 5-methyltetrahydrofolate corrinoid/iron sulphur protein methyltransferase (MeTr). It transfers the N5-methyl group from CH3-H4folate to a cob(I)amide centre in another protein, the corrinoid iron sulphur protein. ; GO: 0042558 pteridine-containing compound metabolic process; PDB: 2VP8_B 2BMB_A 2Y5S_B 2Y5J_A 3BOF_B 1Q7Q_B 1Q85_B 1Q7Z_A 1Q7M_A 1Q8A_B .... Probab=58.97 E-value=19 Score=29.23 Aligned_cols=55 Identities=16% Similarity=0.265 Sum_probs=39.9 Q ss_pred HHHHHHHHhcCcEEEEecCC--------CCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeE Q psy254 51 DMLEKIIETGMNIARLNFSH--------GSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIR 112 (187) Q Consensus 51 ~~i~~li~aGm~v~RiN~sH--------g~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIR 112 (187) ...++++++|+++.=||.-- ...+++.+++..|+.+.+.. ..+.|.+|+.=|++= T Consensus 23 ~~a~~~~~~GAdiIDIg~~st~p~~~~v~~~eE~~rl~~~l~~i~~~~-------~~~plSIDT~~~~v~ 85 (210) T PF00809_consen 23 KRAREQVEAGADIIDIGAESTRPGATPVSEEEEMERLVPVLQAIREEN-------PDVPLSIDTFNPEVA 85 (210) T ss_dssp HHHHHHHHTT-SEEEEESSTSSTTSSSSHHHHHHHHHHHHHHHHHHHH-------TTSEEEEEESSHHHH T ss_pred HHHHHHHHhcCCEEEecccccCCCCCcCCHHHHHHHHHHHHHHHhccC-------CCeEEEEECCCHHHH Confidence 35788999999999999643 33557777777777776522 347899999888763 No 73 >PRK07226 fructose-bisphosphate aldolase; Provisional Probab=58.20 E-value=41 Score=28.23 Aligned_cols=56 Identities=18% Similarity=0.318 Sum_probs=38.1 Q ss_pred HHHHHHHHHhcCc--EEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCee Q psy254 50 VDMLEKIIETGMN--IARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEI 111 (187) Q Consensus 50 ~~~i~~li~aGm~--v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkI 111 (187) ...+++.++.|++ -+|+|+.-...++..+.+..+++++.+++ .|+-++....|+.+ T Consensus 96 ~~~ve~A~~~Gad~v~~~~~~g~~~~~~~~~~~~~v~~~~~~~g------~pl~vi~~~~g~~~ 153 (267) T PRK07226 96 VGTVEEAIKLGADAVSVHVNVGSETEAEMLEDLGEVAEECEEWG------MPLLAMMYPRGPGI 153 (267) T ss_pred eecHHHHHHcCCCEEEEEEecCChhHHHHHHHHHHHHHHHHHcC------CcEEEEEecCCCcc Confidence 4568899999998 56666654445556666666777777777 67766655556655 No 74 >cd00564 TMP_TenI Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl) thiazole phosphate to yield thiamine phosphate. TenI is a enzymatically inactive regulatory protein involved in the regulation of several extracellular enzymes. This superfamily also contains other enzymatically inactive proteins with unknown functions. Probab=57.29 E-value=56 Score=25.03 Aligned_cols=42 Identities=14% Similarity=0.268 Sum_probs=35.3 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+.+++++++|++.+-+..-.++..+..+.++.+++....++ T Consensus 15 ~~~l~~l~~~g~~~i~lr~~~~~~~~~~~~~~~i~~~~~~~~ 56 (196) T cd00564 15 LEVVEAALKGGVTLVQLREKDLSARELLELARALRELCRKYG 56 (196) T ss_pred HHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHHHHhC Confidence 578999999999998888888888888888888887766554 No 75 >cd03320 OSBS o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway. Menaquinone is an essential cofactor for anaerobic growth in eubacteria and some archaea. OSBS belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Probab=56.91 E-value=46 Score=27.69 Aligned_cols=65 Identities=14% Similarity=0.224 Sum_probs=43.0 Q ss_pred CCceEEEecCCCC-CCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 35 RLTGIICTIGPAS-VAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 35 r~TkIi~TiGPas-~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) .+..+-+|+|..+ ...+.++.+.+.|-+.+.+-+...+.+.-.++++.+|+ .++ ..+.+++|--+ T Consensus 71 ~~v~~~~~~~~~~~~~~~~~~~~~~~Gf~~~KiKvg~~~~~~d~~~v~~vr~---~~g------~~~~l~vDaN~ 136 (263) T cd03320 71 NRIPVNALLPAGDAAALGEAKAAYGGGYRTVKLKVGATSFEEDLARLRALRE---ALP------ADAKLRLDANG 136 (263) T ss_pred cCcceeEEecCCCHHHHHHHHHHHhCCCCEEEEEECCCChHHHHHHHHHHHH---HcC------CCCeEEEeCCC Confidence 3445667776543 23356777888999999999876565555555555554 445 34788999765 No 76 >COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion] Probab=56.63 E-value=21 Score=25.86 Aligned_cols=31 Identities=16% Similarity=0.207 Sum_probs=24.3 Q ss_pred cchhhhcCCCCCEEEEeCCeEEEEEEEEeCCe Q psy254 153 YTNITKVVKPGSRIFVDDGLISLVVKSIVKSY 184 (187) Q Consensus 153 ~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~ 184 (187) +.++.+.+++||+|..-.| |.-+|.+++++. T Consensus 37 ~~~ml~sL~kGD~VvT~gG-i~G~V~~v~d~~ 67 (97) T COG1862 37 HQELLNSLKKGDEVVTIGG-IVGTVTKVGDDT 67 (97) T ss_pred HHHHHHhccCCCEEEEcCC-eEEEEEEEecCc Confidence 4578889999999998876 456778887765 No 77 >TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas. Probab=56.52 E-value=25 Score=24.66 Aligned_cols=31 Identities=19% Similarity=0.366 Sum_probs=20.8 Q ss_pred chhhhcCCCCCEEEEeCCeEEEEEEEEeCCee Q psy254 154 TNITKVVKPGSRIFVDDGLISLVVKSIVKSYQ 185 (187) Q Consensus 154 ~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~i 185 (187) .++.+.+++||+|..-.|-. -+|.+++++.+ T Consensus 32 ~~m~~~L~~Gd~VvT~gGi~-G~V~~i~d~~v 62 (84) T TIGR00739 32 KKLIESLKKGDKVLTIGGII-GTVTKIAENTI 62 (84) T ss_pred HHHHHhCCCCCEEEECCCeE-EEEEEEeCCEE Confidence 46777888888888776644 45556666553 No 78 >TIGR03217 4OH_2_O_val_ald 4-hydroxy-2-oxovalerate aldolase. Members of this protein family are 4-hydroxy-2-oxovalerate aldolase, also called 4-hydroxy-2-ketovalerate aldolase and 2-oxo-4-hydroxypentanoate aldolase. This enzyme, part of the pathway for the meta-cleavage of catechol, produces pyruvate and acetaldehyde. Acetaldehyde is then converted by acetaldehyde dehydrogenase (acylating) (DmpF; EC 1.2.1.10) to acetyl-CoA. The two enzymes are tightly associated. Probab=56.20 E-value=49 Score=29.01 Aligned_cols=49 Identities=16% Similarity=0.156 Sum_probs=32.8 Q ss_pred CCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHH Q psy254 34 VRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKN 82 (187) Q Consensus 34 ~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ 82 (187) .+++|+.+-+=|...+.+.++...++|++++|+-++-...+...+.++. T Consensus 74 ~~~~~~~~ll~pg~~~~~dl~~a~~~gvd~iri~~~~~e~d~~~~~i~~ 122 (333) T TIGR03217 74 VKRAKVAVLLLPGIGTVHDLKAAYDAGARTVRVATHCTEADVSEQHIGM 122 (333) T ss_pred CCCCEEEEEeccCccCHHHHHHHHHCCCCEEEEEeccchHHHHHHHHHH Confidence 3457776555565567889999999999999996643333333333333 No 79 >PRK00043 thiE thiamine-phosphate pyrophosphorylase; Reviewed Probab=55.50 E-value=60 Score=25.56 Aligned_cols=42 Identities=12% Similarity=0.262 Sum_probs=33.8 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+.+++++++|++.+-+.....+..+..+.+..+++....++ T Consensus 24 ~~~~~~~~~~gv~~v~lr~~~~~~~~~~~~~~~~~~~~~~~~ 65 (212) T PRK00043 24 LEVVEAALEGGVTLVQLREKGLDTRERLELARALKELCRRYG 65 (212) T ss_pred HHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHHHHhC Confidence 467899999999999998888777777777777777666555 No 80 >TIGR01859 fruc_bis_ald_ fructose-1,6-bisphosphate aldolase, class II, various bacterial and amitochondriate protist. This model represents of one of several subtypes of the class II fructose-1,6-bisphosphate aldolase, an enzyme of glycolysis. The subtypes are split into several models to allow separation of a family of tagatose bisphosphate aldolases. This form is found in Gram-positive bacteria, a variety of Gram-negative, and in amitochondriate protists. The class II enzymes share homology with tagatose bisphosphate aldolase but not with class I aldolase. Probab=55.33 E-value=75 Score=27.16 Aligned_cols=54 Identities=13% Similarity=0.124 Sum_probs=46.1 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) ..+..-+ ..+.+.+.+++.+++|.+...|..||-+.++..+....+++.+..++ T Consensus 75 vpv~lhl-DH~~~~e~i~~ai~~Gf~sVmid~s~l~~~eni~~t~~v~~~a~~~g 128 (282) T TIGR01859 75 VPVALHL-DHGSSYESCIKAIKAGFSSVMIDGSHLPFEENLALTKKVVEIAHAKG 128 (282) T ss_pred CeEEEEC-CCCCCHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHHHHHHHcC Confidence 3455544 55668999999999999999999999999999999999998888877 No 81 >cd07943 DRE_TIM_HOA 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain. 4-hydroxy 2-ketovalerate aldolase (Also known as 4-hydroxy-2-ketovalerate aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA)) converts 4-hydroxy-2-oxopentanoate to acetaldehyde and pyruvate, the penultimate step in the meta-cleavage pathway for the degradation of phenols, cresols and catechol. This family includes the Escherichia coli MhpE aldolase, the Pseudomonas DmpG aldolase, and the Burkholderia xenovorans BphI pyruvate aldolase. In Pseudomonas, the DmpG aldolase tightly associates with a dehydrogenase (DmpF ) and is inactive without it. HOA has a canonical TIM-barrel fold with a C-terminal extension that forms a funnel leading to the active site. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate Probab=54.92 E-value=50 Score=27.54 Aligned_cols=46 Identities=17% Similarity=0.207 Sum_probs=31.3 Q ss_pred CCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHH Q psy254 35 RLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTI 80 (187) Q Consensus 35 r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i 80 (187) ..+|+.+-+=|.....+.++...++|++.+|+-++-...+...+.+ T Consensus 73 ~~~~~~~~~~~~~~~~~~i~~a~~~g~~~iri~~~~s~~~~~~~~i 118 (263) T cd07943 73 KQAKLGVLLLPGIGTVDDLKMAADLGVDVVRVATHCTEADVSEQHI 118 (263) T ss_pred cCCEEEEEecCCccCHHHHHHHHHcCCCEEEEEechhhHHHHHHHH Confidence 3577765543545567889999999999999977655544333333 No 82 >PF04551 GcpE: GcpE protein; InterPro: IPR004588 This protein previously of unknown biochemical function is essential in Escherichia coli. It has now been characterised as 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, which converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4CPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in the sixth step of nonmevalonate terpenoid biosynthesis. The family is largely restricted to bacteria, where it is widely but not universally distributed. No homology can be detected between this family and other proteins.; GO: 0046429 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity, 0016114 terpenoid biosynthetic process, 0055114 oxidation-reduction process; PDB: 2Y0F_C 3NOY_A. Probab=54.53 E-value=28 Score=31.05 Aligned_cols=50 Identities=16% Similarity=0.369 Sum_probs=35.9 Q ss_pred CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC Q psy254 49 AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK 107 (187) Q Consensus 49 ~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~ 107 (187) +.+.|.+|.++|.++.|+-.-. .+..+.+..|++...+.+ .+++++.|+. T Consensus 33 tv~QI~~L~~aGceivRvavp~---~~~a~al~~I~~~l~~~g------~~iPlVADIH 82 (359) T PF04551_consen 33 TVAQIKRLEEAGCEIVRVAVPD---MEAAEALKEIKKRLRALG------SPIPLVADIH 82 (359) T ss_dssp HHHHHHHHHHCT-SEEEEEE-S---HHHHHHHHHHHHHHHCTT-------SS-EEEEES T ss_pred HHHHHHHHHHcCCCEEEEcCCC---HHHHHHHHHHHHhhccCC------CCCCeeeecC Confidence 4688999999999999986643 445667777777666666 7899999986 No 83 >cd00739 DHPS DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and protein biosynthesis. Prokaryotes (and some lower eukaryotes) must synthesize folate de novo, while higher eukaryotes are able to utilize dietary folate and therefore lack DHPS. Sulfonamide drugs, which are substrate analogs of pABA, target DHPS. Probab=54.40 E-value=29 Score=29.22 Aligned_cols=54 Identities=22% Similarity=0.232 Sum_probs=36.7 Q ss_pred HHHHHHHHHhcCcEEEEecC-C-------CCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCee Q psy254 50 VDMLEKIIETGMNIARLNFS-H-------GSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEI 111 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~s-H-------g~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkI 111 (187) .+..++|+++|+++.=+|+. - ...+++.++...|+.+.+.. .+.|.+|+.=|++ T Consensus 27 ~~~a~~~~~~GAdiIDIG~~st~p~~~~i~~~~E~~rl~~~v~~i~~~~--------~~plSIDT~~~~v 88 (257) T cd00739 27 VAHAEKMIAEGADIIDIGGESTRPGADPVSVEEELERVIPVLEALRGEL--------DVLISVDTFRAEV 88 (257) T ss_pred HHHHHHHHHCCCCEEEECCCcCCCCCCCCCHHHHHHHHHHHHHHHHhcC--------CCcEEEeCCCHHH Confidence 35678899999999999852 2 22456666655566554432 3568889887775 No 84 >PLN02389 biotin synthase Probab=54.39 E-value=41 Score=30.05 Aligned_cols=62 Identities=10% Similarity=0.198 Sum_probs=40.2 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCC-----C---CHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSH-----G---SYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDT 106 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sH-----g---~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl 106 (187) .|.+|.|+ .+.+.++.|.+||++.+-+|+-= . +...|.++++.++.+. +.| ......+++-+ T Consensus 168 ~i~~s~G~--l~~E~l~~LkeAGld~~~~~LeTs~~~y~~i~~~~s~e~rl~ti~~a~-~~G----i~v~sg~IiGl 237 (379) T PLN02389 168 EVCCTLGM--LEKEQAAQLKEAGLTAYNHNLDTSREYYPNVITTRSYDDRLETLEAVR-EAG----ISVCSGGIIGL 237 (379) T ss_pred EEEECCCC--CCHHHHHHHHHcCCCEEEeeecCChHHhCCcCCCCCHHHHHHHHHHHH-HcC----CeEeEEEEECC Confidence 46778887 46899999999999988777761 0 1124566666666663 334 12334666666 No 85 >PRK02412 aroD 3-dehydroquinate dehydratase; Provisional Probab=54.30 E-value=60 Score=27.13 Aligned_cols=55 Identities=16% Similarity=0.180 Sum_probs=42.4 Q ss_pred CCCceEEEec-----CCCCCC-HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHH Q psy254 34 VRLTGIICTI-----GPASVA-VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVE 88 (187) Q Consensus 34 ~r~TkIi~Ti-----GPas~~-~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~ 88 (187) ...+|||++- .|+.++ .+.+++|...|.|+++|-..--+.++..+++...+++.. T Consensus 133 ~~~~kvI~S~H~f~~tP~~~~l~~~~~~~~~~gaDivKia~~a~~~~D~~~ll~~~~~~~~ 193 (253) T PRK02412 133 EHGVKVVLSYHDFEKTPPKEEIVERLRKMESLGADIVKIAVMPQSEQDVLTLLNATREMKE 193 (253) T ss_pred HcCCEEEEeeCCCCCCcCHHHHHHHHHHHHHhCCCEEEEEecCCCHHHHHHHHHHHHHHHh Confidence 3578999988 333222 367888999999999999988888888888877777644 No 86 >PRK02048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional Probab=54.13 E-value=28 Score=33.24 Aligned_cols=55 Identities=18% Similarity=0.307 Sum_probs=41.9 Q ss_pred CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC-CCeeE Q psy254 49 AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK-GPEIR 112 (187) Q Consensus 49 ~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~-GPkIR 112 (187) +.+.+.+|.+||.++.|+-.- -.+..+.+.+|++.....| .++++..|+. -|++- T Consensus 43 tv~Qi~~l~~aGceiVRvtv~---~~~~a~~l~~I~~~l~~~G------~~iPLVADIHF~~~~A 98 (611) T PRK02048 43 CVAQAKRIIDAGGEYVRLTTQ---GVREAENLMNINIGLRSQG------YMVPLVADVHFNPKVA 98 (611) T ss_pred HHHHHHHHHHcCCCEEEEcCC---CHHHHHhHHHHHHHHhhcC------CCCCEEEecCCCcHHH Confidence 478999999999999997442 2345677778887776667 7899999987 55543 No 87 >PRK06342 transcription elongation factor regulatory protein; Validated Probab=53.89 E-value=1.1e+02 Score=24.08 Aligned_cols=96 Identities=10% Similarity=0.011 Sum_probs=52.0 Q ss_pred CCCCHHHH---HHHH-HHHHHHHHHhCCCCCCcceeEEEeeCCCC--eeEeeecCCCCcccEEeeeCCEEEEe-eCCCcc Q psy254 69 SHGSYEYH---GQTI-KNIRQAVENYSKRIGMPHALAIALDTKGP--EIRTGLLQGGGSAEVELVKGQTIRLT-TDAAFA 141 (187) Q Consensus 69 sHg~~e~~---~~~i-~~ir~a~~~~~~~~~~~~~v~I~~Dl~GP--kIRtG~~~~~~~~~i~l~~G~~v~lt-~~~~~~ 141 (187) +||+..+- +..+ ..||+..+.+. -+-.+|-..| .++.|... .+....|+..+++ .... . T Consensus 55 ~~GDlsEak~~~~~~e~rI~~L~~~L~--------~A~Ii~~~~~~d~V~~Gs~V-----~l~~~~~~~~~~~IVg~~-E 120 (160) T PRK06342 55 AIEDVNERRRQMARPLRDLRYLAARRR--------TAQLMPDPASTDVVAFGSTV-----TFSRDDGRVQTYRIVGED-E 120 (160) T ss_pred HCCChhHHHHHHHHHHHHHHHHHHHHc--------cCEEECCCCCCCEEEeCcEE-----EEEECCCCEEEEEEEChH-H Confidence 78886663 3334 44666666654 2444564433 45554432 1323345555544 2211 1 Q ss_pred cCCCcCEEeeCcc--hhhhcCCCCCEEEEeCCeEEEEEEEE Q psy254 142 EKGSATDLYVDYT--NITKVVKPGSRIFVDDGLISLVVKSI 180 (187) Q Consensus 142 ~~~~~~~i~v~~~--~l~~~v~~Gd~IlidDG~i~l~V~~v 180 (187) .......|++..| .-+-.-++||.|-+ |...++|.++ T Consensus 121 ad~~~g~IS~~SPlG~ALlGk~vGD~V~v--~~~~~eI~~I 159 (160) T PRK06342 121 ADPKAGSISYVSPVARALMGKAVGDVVSV--GGQELEIIAI 159 (160) T ss_pred hCcCCCcccccCHHHHHHcCCCCCCEEEE--CCEEEEEEEe Confidence 1223345777544 22345689999999 5788888776 No 88 >TIGR01858 tag_bisphos_ald class II aldolase, tagatose bisphosphate family. This model describes tagatose-1,6-bisphosphate aldolases, and perhaps other closely related class II aldolases. This tetrameric, Zn2+-dependent enzyme is related to the class II fructose bisphosphate aldolase; fructose 1,6-bisphosphate and tagatose 1,6 bisphosphate differ only in chirality at C4. Probab=53.65 E-value=84 Score=27.03 Aligned_cols=53 Identities=11% Similarity=0.175 Sum_probs=44.8 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+..-+ ..+.+.+.+.+-+++|.+-..+..||-+.++.-+.-..+.+.+...| T Consensus 74 PValHL-DHg~~~e~i~~ai~~GFtSVM~DgS~lp~eeNi~~T~~vv~~Ah~~g 126 (282) T TIGR01858 74 PLALHL-DHHESLDDIRQKVHAGVRSAMIDGSHFPFAQNVKLVKEVVDFCHRQD 126 (282) T ss_pred CEEEEC-CCCCCHHHHHHHHHcCCCEEeecCCCCCHHHHHHHHHHHHHHHHHcC Confidence 455555 66778999999999999999999999999988888888877777766 No 89 >PF02581 TMP-TENI: Thiamine monophosphate synthase/TENI; InterPro: IPR003733 Thiamine monophosphate synthase (TMP) (2.5.1.3 from EC) catalyzes the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to yield thiamine phosphate in the thiamine biosynthesis pathway []. TENI, a protein from Bacillus subtilis that regulates the production of several extracellular enzymes by reducing alkaline protease production belongs to this group [].; GO: 0004789 thiamine-phosphate diphosphorylase activity, 0009228 thiamine biosynthetic process; PDB: 3NL5_A 3NL2_A 3NM1_A 3NM3_C 3NL6_B 3NL3_A 3CEU_A 3O63_B 3QH2_C 1YAD_D .... Probab=53.39 E-value=70 Score=24.99 Aligned_cols=43 Identities=16% Similarity=0.252 Sum_probs=35.9 Q ss_pred CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 49 AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 49 ~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) -.+.+.+++++|++.+-+..-..+.++..+.++.+++..++++ T Consensus 14 ~~~~l~~~~~~gv~~v~lR~k~~~~~~~~~~a~~l~~~~~~~~ 56 (180) T PF02581_consen 14 FLEQLEAALAAGVDLVQLREKDLSDEELLELARRLAELCQKYG 56 (180) T ss_dssp HHHHHHHHHHTT-SEEEEE-SSS-HHHHHHHHHHHHHHHHHTT T ss_pred HHHHHHHHHHCCCcEEEEcCCCCCccHHHHHHHHHHHHhhcce Confidence 3578999999999999999999999999999999999988876 No 90 >PRK02506 dihydroorotate dehydrogenase 1A; Reviewed Probab=53.38 E-value=38 Score=29.21 Aligned_cols=50 Identities=18% Similarity=0.263 Sum_probs=30.5 Q ss_pred ceEEEec-CCCCCC-HHHHHHHHHhc-CcEEEEecC--CC--------CHHHHHHHHHHHHHH Q psy254 37 TGIICTI-GPASVA-VDMLEKIIETG-MNIARLNFS--HG--------SYEYHGQTIKNIRQA 86 (187) Q Consensus 37 TkIi~Ti-GPas~~-~~~i~~li~aG-m~v~RiN~s--Hg--------~~e~~~~~i~~ir~a 86 (187) +.+|++| |-+..+ .+..+.+-.+| ++.+=||+| |. +++...++++.+|++ T Consensus 93 ~pvI~Si~G~~~~~~~~~a~~~~~~g~ad~iElN~ScPn~~~~~~~g~d~~~~~~i~~~v~~~ 155 (310) T PRK02506 93 KPHFLSVVGLSPEETHTILKKIQASDFNGLVELNLSCPNVPGKPQIAYDFETTEQILEEVFTY 155 (310) T ss_pred CCEEEEEEeCcHHHHHHHHHHHhhcCCCCEEEEECCCCCCCCccccccCHHHHHHHHHHHHHh Confidence 5677776 543322 34444455578 999999999 32 345555556555554 No 91 >PLN03034 phosphoglycerate kinase; Provisional Probab=53.12 E-value=15 Score=33.96 Aligned_cols=100 Identities=17% Similarity=0.197 Sum_probs=64.0 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHH----HHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEeeecCCCCcccEE Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYE----YHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTGLLQGGGSAEVE 125 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e----~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG~~~~~~~~~i~ 125 (187) ..+|+.|++.|..|.= +||-..- ....+-......++.++ ++|...=|.-||+++- ..-. T Consensus 121 lpTI~~L~~~gakvVl--~SHlGRPkg~~~~~SL~pva~~Ls~lL~------~~V~fv~d~~G~~~~~--------~i~~ 184 (481) T PLN03034 121 IPTIKYLISNGAKVIL--SSHLGRPKGVTPKFSLAPLVPRLSELLG------IQVVKADDCIGPEVEK--------LVAS 184 (481) T ss_pred HHHHHHHHHCCCeEEE--EEecCCCCCCCcccCHHHHHHHHHHHhC------CCeEECCCCCCHHHHH--------HHhc Confidence 3699999999998766 5886532 22333334455566666 7888888899998762 1224 Q ss_pred eeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCC Q psy254 126 LVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDG 171 (187) Q Consensus 126 l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG 171 (187) |+.|+.+.|-.-.-|..+. -+.++|.+.+.+--.||++|. T Consensus 185 l~~GeVlLLENvRF~~eE~------~nd~~fa~~LA~l~DiyVNDA 224 (481) T PLN03034 185 LPEGGVLLLENVRFYKEEE------KNEPEFAKKLASLADLYVNDA 224 (481) T ss_pred CCCCcEEEEeccCcCcccc------cCcHHHHHHHHhhCCEEEecc Confidence 6667666654322222111 144678888888777999984 No 92 >PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional Probab=52.62 E-value=54 Score=25.47 Aligned_cols=61 Identities=16% Similarity=0.218 Sum_probs=40.4 Q ss_pred EeeeCCEEEEeeCC--CcccCCCcCEEeeCcchhhh--cCCCCCEEEEe--CC-eEEEEEEEEeCCee Q psy254 125 ELVKGQTIRLTTDA--AFAEKGSATDLYVDYTNITK--VVKPGSRIFVD--DG-LISLVVKSIVKSYQ 185 (187) Q Consensus 125 ~l~~G~~v~lt~~~--~~~~~~~~~~i~v~~~~l~~--~v~~Gd~Ilid--DG-~i~l~V~~v~~~~i 185 (187) -++.|+++.++... .|..........++-..|.. .+++|..+.+. +| .+..+|.+++++.+ T Consensus 54 gm~~Ge~~~v~ipp~~ayG~~d~~~v~~vp~~~f~~~~~~~~G~~~~~~~~~G~~~~~~V~~i~~~~v 121 (156) T PRK15095 54 GLKVGDKKTFSLEPEAAFGVPSPDLIQYFSRRDFMDAGEPEIGAIMLFTAMDGSEMPGVIREINGDSI 121 (156) T ss_pred CCCCCCEEEEEEChHHhcCCCChHHEEEecHHHCCcccCCCCCCEEEEECCCCCEEEEEEEEEcCCEE Confidence 35789988887653 34322223345566666653 58899998875 56 46788999988875 No 93 >PRK09195 gatY tagatose-bisphosphate aldolase; Reviewed Probab=51.70 E-value=98 Score=26.65 Aligned_cols=54 Identities=9% Similarity=0.171 Sum_probs=44.5 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) ..+..-+ ..+.+.+.+++.+++|.+-..+.-||-+.++..+.-..+-+.+..+| T Consensus 75 VPV~lHL-DHg~~~e~i~~Ai~~GftSVM~DgS~l~~eeNi~~T~~vv~~Ah~~g 128 (284) T PRK09195 75 HPLALHL-DHHEKFDDIAQKVRSGVRSVMIDGSHLPFAQNISLVKEVVDFCHRFD 128 (284) T ss_pred CCEEEEC-CCCCCHHHHHHHHHcCCCEEEeCCCCCCHHHHHHHHHHHHHHHHHcC Confidence 3455555 67778999999999999999999999999988777777777777665 No 94 >PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function. Probab=51.66 E-value=39 Score=22.68 Aligned_cols=42 Identities=19% Similarity=0.355 Sum_probs=29.0 Q ss_pred eCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEE-eCCeEEE Q psy254 128 KGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFV-DDGLISL 175 (187) Q Consensus 128 ~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~Ili-dDG~i~l 175 (187) +|+...|-.+.. ...+.++-..|+..++.||.+.+ ++|.+.+ T Consensus 8 E~~~AVl~~~~~------~~~~~vp~~~LP~~~keGDvl~i~~~~~~~~ 50 (71) T PF11213_consen 8 EGDYAVLELEDG------EKEIDVPRSRLPEGAKEGDVLEIGEDGSIEI 50 (71) T ss_pred eCCEEEEEECCC------eEEEEEEHHHCCCCCCcccEEEECCCceEEE Confidence 355555554321 13577777889999999999999 7776643 No 95 >PF00162 PGK: Phosphoglycerate kinase; InterPro: IPR001576 Phosphoglycerate kinase (2.7.2.3 from EC) (PGK) is an enzyme that catalyses the formation of ATP to ADP and vice versa. In the second step of the second phase in glycolysis, 1,3-diphosphoglycerate is converted to 3-phosphoglycerate, forming one molecule of ATP. If the reverse were to occur, one molecule of ADP would be formed. This reaction is essential in most cells for the generation of ATP in aerobes, for fermentation in anaerobes and for carbon fixation in plants. PGK is found in all living organisms and its sequence has been highly conserved throughout evolution. The enzyme exists as a monomer containing two nearly equal-sized domains that correspond to the N- and C-termini of the protein (the last 15 C-terminal residues loop back into the N-terminal domain). 3-phosphoglycerate (3-PG) binds to the N-terminal, while the nucleotide substrates, MgATP or MgADP, bind to the C-terminal domain of the enzyme. This extended two-domain structure is associated with large-scale 'hinge-bending' conformational changes, similar to those found in hexokinase []. At the core of each domain is a 6-stranded parallel beta-sheet surrounded by alpha helices. Domain 1 has a parallel beta-sheet of six strands with an order of 342156, while domain 2 has a parallel beta-sheet of six strands with an order of 321456. Analysis of the reversible unfolding of yeast phosphoglycerate kinase leads to the conclusion that the two lobes are capable of folding independently, consistent with the presence of intermediates on the folding pathway with a single domain folded []. Phosphoglycerate kinase (PGK) deficiency is associated with haemolytic anaemia and mental disorders in man []. This group represents a phosphoglycerate kinase.; GO: 0004618 phosphoglycerate kinase activity, 0006096 glycolysis; PDB: 1PHP_A 1V6S_A 2IE8_A 1ZMR_A 16PK_A 13PK_B 2P9Q_A 2P9T_A 2PAA_B 3OZA_A .... Probab=50.98 E-value=3.6 Score=36.94 Aligned_cols=104 Identities=13% Similarity=0.163 Sum_probs=64.2 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHH------HHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEeeecCCCCccc Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYE------YHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTGLLQGGGSAE 123 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e------~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG~~~~~~~~~ 123 (187) ..+|+.|++.|..|.= +||-..- ....+-...+..++.++ ++|...-|.-||+.+- .+ T Consensus 37 lpTI~~l~~~gakvVl--~sH~GRPk~~~~~~~~SL~~va~~L~~~L~------~~V~f~~d~~g~~~~~-~i------- 100 (384) T PF00162_consen 37 LPTIKYLLEKGAKVVL--MSHLGRPKGKGYDDFFSLEPVAERLSKLLG------KPVKFVDDCIGEEAEE-AI------- 100 (384) T ss_dssp HHHHHHHHHTTEEEEE--E---SSTTTSSSTGGG-SHHHHHHHHHHHT------SEEEEESTSSSHHHHH-HH------- T ss_pred HHHHHHHHhcCCeEEE--EeccCCcccCCCCcccChHHHHHHHHHHhC------CCeeeccccCCHHHHH-HH------- Confidence 4799999999988765 7886543 23333333455666667 8899999998988873 12 Q ss_pred EEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCC Q psy254 124 VELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDG 171 (187) Q Consensus 124 i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG 171 (187) -.|++|+.+.|-.-.-|..+.. .-.-+.+.|.+.+.+..-||++|. T Consensus 101 ~~l~~G~IllLENlRf~~eE~~--~~~~~~~~f~~~LA~l~DvyVNDA 146 (384) T PF00162_consen 101 ESLKPGEILLLENLRFYPEEEG--KKEKNDTEFARKLASLADVYVNDA 146 (384) T ss_dssp HTSSTTEEEEESSGGGSTTTTS--EEHHTHHHHHHHHHTT-SEEEEES T ss_pred hccCCCCEEEEeeecccccccc--ccccccHHHHHHHHHhCCEEEEcC Confidence 2366777666543222222211 125577888888888888999884 No 96 >cd00958 DhnA Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs) found in bacteria and archaea. Catalysis of the enzymes proceeds via a Schiff-base mechanism like other class I aldolases, although this subfamily is clearly divergent based on sequence similarity to other class I and class II (metal dependent) aldolase subfamilies. Probab=50.89 E-value=63 Score=26.22 Aligned_cols=42 Identities=10% Similarity=0.174 Sum_probs=32.5 Q ss_pred HHHHHHHHHhcCcEE--EEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 50 VDMLEKIIETGMNIA--RLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 50 ~~~i~~li~aGm~v~--RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) ...+++.+++|++.. -+|+.....++..+.+..+++++..++ T Consensus 79 ~~~v~~a~~~Ga~~v~~~~~~~~~~~~~~~~~i~~v~~~~~~~g 122 (235) T cd00958 79 VASVEDAVRLGADAVGVTVYVGSEEEREMLEELARVAAEAHKYG 122 (235) T ss_pred hcCHHHHHHCCCCEEEEEEecCCchHHHHHHHHHHHHHHHHHcC Confidence 345889999999966 777777667777778888888777766 No 97 >cd00502 DHQase_I Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase.) Catalyzes the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate to produce dehydroshikimate. Dehydroquinase is the third enzyme in the shikimate pathway, which is involved in the biosynthesis of aromatic amino acids. Type I DHQase exists as a homodimer. Type II 3-dehydroquinase also catalyzes the same overall reaction, but is unrelated in terms of sequence and structure, and utilizes a completely different reaction mechanism. Probab=50.88 E-value=79 Score=25.64 Aligned_cols=55 Identities=27% Similarity=0.271 Sum_probs=41.8 Q ss_pred CCceEEEecC-----CCCCC-HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHH Q psy254 35 RLTGIICTIG-----PASVA-VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVEN 89 (187) Q Consensus 35 r~TkIi~TiG-----Pas~~-~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~ 89 (187) .++|||++.= |+... .+.+.+|...|.+++++-..--+.++..++++..+++... T Consensus 112 ~~~kiI~S~H~f~~tp~~~~l~~~~~~~~~~gadivKla~~~~~~~D~~~ll~~~~~~~~~ 172 (225) T cd00502 112 GNTKIIGSYHDFSGTPSDEELVSRLEKMAALGADIVKIAVMANSIEDNLRLLKFTRQVKNL 172 (225) T ss_pred CCCEEEEEeccCCCCcCHHHHHHHHHHHHHhCCCEEEEEecCCCHHHHHHHHHHHHHHHhc Confidence 5899999982 21111 2578889999999999999888888888888777776543 No 98 >PLN02282 phosphoglycerate kinase Probab=50.84 E-value=18 Score=32.83 Aligned_cols=99 Identities=16% Similarity=0.187 Sum_probs=62.3 Q ss_pred HHHHHHHHhcCcEEEEecCCCCHH----HHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEeeecCCCCcccEEe Q psy254 51 DMLEKIIETGMNIARLNFSHGSYE----YHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTGLLQGGGSAEVEL 126 (187) Q Consensus 51 ~~i~~li~aGm~v~RiN~sHg~~e----~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG~~~~~~~~~i~l 126 (187) .+|+.|++.|..+.= +||-..- ....+-...+..++.++ ++|...-|.-||+++- ..-.| T Consensus 47 pTI~~l~~~gakvVl--~SHlGRP~g~~~~~SL~~va~~Ls~lL~------~~V~fv~d~~g~~~~~--------~i~~l 110 (401) T PLN02282 47 PTIKYLMGHGARVIL--CSHLGRPKGVTPKYSLKPLVPRLSELLG------VEVVMANDCIGEEVEK--------LVAEL 110 (401) T ss_pred HHHHHHHHCCCeEEE--EecCCCCCCCCcccCHHHHHHHHHHHHC------CCeEECCCCCCHHHHH--------HHhcC Confidence 699999999998765 5886633 12233333345556666 7888888999998761 12246 Q ss_pred eeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCC Q psy254 127 VKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDG 171 (187) Q Consensus 127 ~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG 171 (187) +.|+.+.|-.-.=|..+. -+.++|.+.+.+---||+.|. T Consensus 111 ~~G~ilLLEN~RF~~~E~------~~~~~~a~~LA~l~DvyVNDA 149 (401) T PLN02282 111 PEGGVLLLENVRFYKEEE------KNDPEFAKKLASLADVYVNDA 149 (401) T ss_pred CCCCEEEEeccccCcccc------cCHHHHHHHHHHhCcEeeech Confidence 667666554322221111 144578888887777999884 No 99 >TIGR03096 nitroso_cyanin nitrosocyanin. Nitrosocyanin, as described from the obligate chemolithoautotroph Nitrosomonas europaea, is a red copper protein of unknown function with sequence similarity to a number of blue copper redox proteins. Probab=50.83 E-value=43 Score=25.72 Aligned_cols=42 Identities=19% Similarity=0.347 Sum_probs=26.9 Q ss_pred ccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEE Q psy254 122 AEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRI 166 (187) Q Consensus 122 ~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~I 166 (187) ..+.+++|+.|+++..+. ..+ ++.+.++..++-..+.||+.. T Consensus 61 ~~I~VkaGD~Vtl~vtN~--d~~-~H~f~i~~~gis~~I~pGet~ 102 (135) T TIGR03096 61 EALVVKKGTPVKVTVENK--SPI-SEGFSIDAYGISEVIKAGETK 102 (135) T ss_pred CEEEECCCCEEEEEEEeC--CCC-ccceEECCCCcceEECCCCeE Confidence 578999999998864432 122 333444444566677888764 No 100 >COG1551 CsrA RNA-binding global regulator CsrA [Signal transduction mechanisms] Probab=50.52 E-value=26 Score=24.05 Aligned_cols=24 Identities=33% Similarity=0.375 Sum_probs=20.8 Q ss_pred CCCCEEEEeCCeEEEEEEEEeCCee Q psy254 161 KPGSRIFVDDGLISLVVKSIVKSYQ 185 (187) Q Consensus 161 ~~Gd~IlidDG~i~l~V~~v~~~~i 185 (187) ++|..|+|+| .|..+|.++.++.+ T Consensus 7 k~~Esi~Igd-dI~itVl~i~gnqV 30 (73) T COG1551 7 KVGESIMIGD-DIEITVLSIKGNQV 30 (73) T ss_pred ecCceEEecC-CeEEEEEEEcCCeE Confidence 6889999999 68999999988865 No 101 >PRK07084 fructose-bisphosphate aldolase; Provisional Probab=49.87 E-value=1.1e+02 Score=26.84 Aligned_cols=53 Identities=15% Similarity=0.266 Sum_probs=44.5 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+..-+ ..+.+.+.+++-+++|.+-+.|..||-+.++..+.-..+-+.+..+| T Consensus 87 PV~lHL-DHg~~~e~i~~ai~~GftSVMiD~S~lp~eeNI~~T~evv~~Ah~~G 139 (321) T PRK07084 87 PIVLHL-DHGDSFELCKDCIDSGFSSVMIDGSHLPYEENVALTKKVVEYAHQFD 139 (321) T ss_pred cEEEEC-CCCCCHHHHHHHHHcCCCEEEeeCCCCCHHHHHHHHHHHHHHHHHcC Confidence 344444 77789999999999999999999999999988888877777777766 No 102 >PRK00694 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated Probab=49.44 E-value=36 Score=32.38 Aligned_cols=50 Identities=16% Similarity=0.226 Sum_probs=38.8 Q ss_pred CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC Q psy254 49 AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK 107 (187) Q Consensus 49 ~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~ 107 (187) +.+.+.+|.++|.++.|+-.- -.+..+.+.+|++.....| .++++..|+. T Consensus 47 tv~Qi~~L~~aGceiVRvtvp---~~~~A~al~~I~~~L~~~g------~~iPLVADIH 96 (606) T PRK00694 47 TVRQICALQEWGCDIVRVTVQ---GLKEAQACEHIKERLIQQG------ISIPLVADIH 96 (606) T ss_pred HHHHHHHHHHcCCCEEEEcCC---CHHHHHhHHHHHHHHhccC------CCCCEEeecC Confidence 468999999999999997442 2345667777877766666 7899999985 No 103 >TIGR00187 ribE riboflavin synthase, alpha subunit. The name ribE was selected, from among alternatives including ribB and ribC, to match the usage in EcoCyc. Probab=49.05 E-value=40 Score=27.49 Aligned_cols=36 Identities=25% Similarity=0.359 Sum_probs=29.3 Q ss_pred CEEeeCcc-hhhhcCCCCCEEEEeCCeEEEEEEEEeCCe Q psy254 147 TDLYVDYT-NITKVVKPGSRIFVDDGLISLVVKSIVKSY 184 (187) Q Consensus 147 ~~i~v~~~-~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~ 184 (187) ..+.+..| .+++.+++||.|-+|. ++|+|.++.++. T Consensus 22 ~~l~i~~~~~~~~~l~~G~SIAvnG--vCLTV~~i~~~~ 58 (200) T TIGR00187 22 ISLVVNLADHMLDDLELGDSIAVNG--VCLTVTEINKNH 58 (200) T ss_pred EEEEEEeChHHhcccccCCEEEECc--EEEEEEEEcCCE Confidence 34666666 7788999999999986 799999997765 No 104 >COG2730 BglC Endoglucanase [Carbohydrate transport and metabolism] Probab=49.02 E-value=41 Score=30.16 Aligned_cols=53 Identities=11% Similarity=0.164 Sum_probs=37.0 Q ss_pred HHHHHHHHHhcCcEEEEecCCCC--------HHH----HHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCe Q psy254 50 VDMLEKIIETGMNIARLNFSHGS--------YEY----HGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPE 110 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~--------~e~----~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPk 110 (187) .+.+..+-.+|+|..||.+.+-. +.. ..+.+..+=+.+++.| +.|++|+-|+. T Consensus 76 ~~~~~~ik~~G~n~VRiPi~~~~~~~~~~~~p~~~~~~~~~~ld~~I~~a~~~g--------i~V~iD~H~~~ 140 (407) T COG2730 76 EEDFDQIKSAGFNAVRIPIGYWALQATDGDNPYLIGLTQLKILDEAINWAKKLG--------IYVLIDLHGYP 140 (407) T ss_pred hhHHHHHHHcCCcEEEcccchhhhhccCCCCCCeecchHHHHHHHHHHHHHhcC--------eeEEEEecccC Confidence 79999999999999999988433 211 1224444434444444 89999998876 No 105 >PRK07998 gatY putative fructose-1,6-bisphosphate aldolase; Reviewed Probab=49.00 E-value=1.2e+02 Score=26.17 Aligned_cols=53 Identities=8% Similarity=0.112 Sum_probs=43.4 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+..-+ ..+.+.+.+++-+++|.+-..+..||-+.++..+.-..+.+.+..+| T Consensus 76 PV~lHL-DH~~~~e~i~~Ai~~GftSVM~DgS~l~~eeNi~~T~~vve~Ah~~g 128 (283) T PRK07998 76 PVSLHL-DHGKTFEDVKQAVRAGFTSVMIDGAALPFEENIAFTKEAVDFAKSYG 128 (283) T ss_pred CEEEEC-cCCCCHHHHHHHHHcCCCEEEEeCCCCCHHHHHHHHHHHHHHHHHcC Confidence 344444 46678999999999999999999999999888888877777777777 No 106 >PRK05835 fructose-bisphosphate aldolase; Provisional Probab=48.62 E-value=1.3e+02 Score=26.21 Aligned_cols=54 Identities=13% Similarity=0.219 Sum_probs=45.5 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) ..+..-+ ..+.+.+.+++-+++|.+-..+.-||-+.++..+.-..+-+.+...| T Consensus 75 VPValHL-DHg~~~e~i~~ai~~GftSVM~DgS~l~~eeNi~~T~~vve~Ah~~g 128 (307) T PRK05835 75 IPVALHL-DHGTTFESCEKAVKAGFTSVMIDASHHAFEENLELTSKVVKMAHNAG 128 (307) T ss_pred CeEEEEC-CCCCCHHHHHHHHHcCCCEEEEeCCCCCHHHHHHHHHHHHHHHHHcC Confidence 4567767 67778999999999999999999999999988777777777777666 No 107 >PRK06836 aspartate aminotransferase; Provisional Probab=48.45 E-value=61 Score=28.38 Aligned_cols=52 Identities=15% Similarity=0.226 Sum_probs=37.2 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcC-----------cEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 38 GIICTIGPASVAVDMLEKIIETGM-----------NIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm-----------~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) -+.+++ |.-+..+..+.|.+.|+ ..+||+|++ +.+...+.+..++++.++|. T Consensus 331 ~~~~~~-~~~~~~~~~~~l~~~gv~v~~g~~f~~~~~iRi~~~~-~~~~~~~~i~~l~~~l~~~~ 393 (394) T PRK06836 331 YLFPKS-PEEDDVAFCEKAKKHNLLLVPGSGFGCPGYFRLSYCV-DTETIERSLPAFEKLAKEYK 393 (394) T ss_pred EEEEeC-CCCCHHHHHHHHHhCCEEEECchhcCCCCeEEEEecC-CHHHHHHHHHHHHHHHHHhc Confidence 345555 33234556667777786 679999995 78888899999998877663 No 108 >COG1167 ARO8 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism] Probab=48.33 E-value=79 Score=28.74 Aligned_cols=55 Identities=24% Similarity=0.188 Sum_probs=44.9 Q ss_pred CceEEEecCCCCCCHHHHHHHHHhcC----------------cEEEEecCCCCHHHHHHHHHHHHHHHHHh Q psy254 36 LTGIICTIGPASVAVDMLEKIIETGM----------------NIARLNFSHGSYEYHGQTIKNIRQAVENY 90 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~aGm----------------~v~RiN~sHg~~e~~~~~i~~ir~a~~~~ 90 (187) ---|.+++.+..++.+.++...+.|+ +.+|||||+-+.++..+-+..+.++.++. T Consensus 386 G~flwl~l~~~~~~~~l~~~a~~~gv~i~~~g~~f~~~~~~~~~~Rl~~s~~~~e~i~~gi~~l~~~~~~~ 456 (459) T COG1167 386 GLFLWLELPEGIDARELLAAALEKGVVVTPLGSAFSADGDPRNGLRLSFSSPSEEEIEEGIKRLAALLREA 456 (459) T ss_pred eEEEEEEcCCCCCHHHHHHHHHHCCCEEEcCCccccCCCCCCCeEEEEcCCCCHHHHHHHHHHHHHHHHHH Confidence 34788899666777888888888764 36999999999999999999988877654 No 109 >cd01311 PDC_hydrolase 2-pyrone-4,6-dicarboxylic acid (PDC) hydrolase hydrolyzes PDC to yield 4-oxalomesaconic acid (OMA) or its tautomer, 4-carboxy-2-hydroxymuconic acid (CHM). This reaction is part of the protocatechuate (PCA) 4,5-cleavage pathway. PCA is one of the most important intermediate metabolites in the bacterial pathways for various phenolic compounds, including lignin, which is the most abundant aromatic material in nature. Probab=47.64 E-value=1.1e+02 Score=25.21 Aligned_cols=33 Identities=21% Similarity=0.300 Sum_probs=26.1 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSH 70 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sH 70 (187) .-+|++-|.....+.|+++...|+..+|+|... T Consensus 71 ~g~~~~~p~~~~~~~l~~~~~~g~rGvRl~~~~ 103 (263) T cd01311 71 RGGATVDPRTTTDAELKEMHDAGVRGVRFNFLF 103 (263) T ss_pred EEEEEECCCCCCHHHHHHHHHCCCeEEEEeccc Confidence 344556565556799999999999999999874 No 110 >cd07944 DRE_TIM_HOA_like 4-hydroxy-2-oxovalerate aldolase-like, N-terminal catalytic TIM barrel domain. This family of bacterial enzymes is sequence-similar to 4-hydroxy-2-oxovalerate aldolase (HOA) but its exact function is unknown. This family includes the Bacteroides vulgatus Bvu_2661 protein and belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues t Probab=47.64 E-value=74 Score=26.79 Aligned_cols=45 Identities=18% Similarity=0.239 Sum_probs=32.2 Q ss_pred CceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHH Q psy254 36 LTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTI 80 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i 80 (187) ++++.+-+-|...+.+.+......|++.+|+.+.-...+...+.+ T Consensus 71 ~~~~~~~~~~~~~~~~~l~~a~~~gv~~iri~~~~~~~~~~~~~i 115 (266) T cd07944 71 NTKIAVMVDYGNDDIDLLEPASGSVVDMIRVAFHKHEFDEALPLI 115 (266) T ss_pred CCEEEEEECCCCCCHHHHHHHhcCCcCEEEEecccccHHHHHHHH Confidence 678888775655678889999999999999987544443333333 No 111 >PRK08610 fructose-bisphosphate aldolase; Reviewed Probab=47.63 E-value=1.3e+02 Score=26.04 Aligned_cols=53 Identities=13% Similarity=0.233 Sum_probs=44.3 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+..-+ ..+.+.+.+++-+++|.+-..|..||-+.++..+.-..+-+.+..+| T Consensus 79 PV~lHL-DHg~~~e~i~~ai~~GftSVM~DgS~l~~eeNi~~T~~vve~Ah~~g 131 (286) T PRK08610 79 PVAIHL-DHGSSFEKCKEAIDAGFTSVMIDASHSPFEENVATTKKVVEYAHEKG 131 (286) T ss_pred CEEEEC-CCCCCHHHHHHHHHcCCCEEEEeCCCCCHHHHHHHHHHHHHHHHHcC Confidence 355555 67778999999999999999999999999988887777777777666 No 112 >PRK12738 kbaY tagatose-bisphosphate aldolase; Reviewed Probab=47.59 E-value=1.2e+02 Score=26.26 Aligned_cols=54 Identities=11% Similarity=0.173 Sum_probs=45.1 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) ..+..-+ ..+.+.+.+++-+++|.+-..|..||-+.++.-+.-..+-+.+..+| T Consensus 75 VPValHL-DHg~~~e~i~~ai~~GFtSVM~DgS~lp~eeNi~~T~evv~~Ah~~g 128 (286) T PRK12738 75 MPLALHL-DHHESLDDIRRKVHAGVRSAMIDGSHFPFAENVKLVKSVVDFCHSQD 128 (286) T ss_pred CCEEEEC-CCCCCHHHHHHHHHcCCCeEeecCCCCCHHHHHHHHHHHHHHHHHcC Confidence 4555555 67779999999999999999999999999988877777777777666 No 113 >PRK08207 coproporphyrinogen III oxidase; Provisional Probab=47.41 E-value=1.5e+02 Score=27.45 Aligned_cols=39 Identities=15% Similarity=0.169 Sum_probs=29.3 Q ss_pred eEEEec-CCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHH Q psy254 38 GIICTI-GPASVAVDMLEKIIETGMNIARLNFSHGSYEYH 76 (187) Q Consensus 38 kIi~Ti-GPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~ 76 (187) -+.++. -|.+-+.+.++.|-++|++.+-||.=.++.+.. T Consensus 256 EiTvE~grPd~it~e~L~~Lk~~Gv~RISIGvQS~~d~vL 295 (488) T PRK08207 256 EFTVEAGRPDTITEEKLEVLKKYGVDRISINPQTMNDETL 295 (488) T ss_pred EEEEEcCCCCCCCHHHHHHHHhcCCCeEEEcCCcCCHHHH Confidence 455555 488899999999999999976666666665543 No 114 >smart00729 Elp3 Elongator protein 3, MiaB family, Radical SAM. This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases. Probab=47.34 E-value=1.2e+02 Score=22.87 Aligned_cols=43 Identities=23% Similarity=0.417 Sum_probs=33.3 Q ss_pred CCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHH---------HHHHHHHHHH Q psy254 45 PASVAVDMLEKIIETGMNIARLNFSHGSYEYHG---------QTIKNIRQAV 87 (187) Q Consensus 45 Pas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~---------~~i~~ir~a~ 87 (187) +...+.+.++.|.++|.+.+.|++-+++.+.+. ++++.++.+. T Consensus 95 ~~~~~~~~~~~l~~~~~~~i~isl~~~~~~~~~~~~~~~~~~~~~~~i~~~~ 146 (216) T smart00729 95 PGTLTEELLEALKEAGVNRVSLGVQSGSDEVLKAINRGHTVEDVLEAVEKLR 146 (216) T ss_pred cccCCHHHHHHHHHcCCCeEEEecccCCHHHHHHhcCCCCHHHHHHHHHHHH Confidence 456688999999999999999999998877654 4555555554 No 115 >PTZ00005 phosphoglycerate kinase; Provisional Probab=47.30 E-value=23 Score=32.19 Aligned_cols=106 Identities=17% Similarity=0.169 Sum_probs=59.2 Q ss_pred HHHHHHHHHhcCc-EEEEecCCCCH-----HHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEeeecCCCCccc Q psy254 50 VDMLEKIIETGMN-IARLNFSHGSY-----EYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTGLLQGGGSAE 123 (187) Q Consensus 50 ~~~i~~li~aGm~-v~RiN~sHg~~-----e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG~~~~~~~~~ 123 (187) ..+|+.|++.|.. |.= +||-.. +....+-......++.++ ++|...-|.-||+.+- .. T Consensus 45 lpTI~~L~~~gak~vvl--~SHlGRP~g~~~~~~SL~~va~~L~~lL~------~~V~fv~d~~g~~~~~--------~i 108 (417) T PTZ00005 45 LPTIKYLLEQGAKSVVL--MSHLGRPDGRRVEKYSLKPVVPKLEELLG------KKVTFLNDCVGPEVEE--------AC 108 (417) T ss_pred HHHHHHHHHCCCCEEEE--EecCCCCCCCcCcccCHHHHHHHHHHHHC------CCeEECCCCCCHHHHH--------HH Confidence 4799999999996 544 789322 112233333445556666 7888888999998651 12 Q ss_pred EEeeeCCEEEEeeCCCcccCCCc----CEEe-eCc----chhhhcCCCCCEEEEeCC Q psy254 124 VELVKGQTIRLTTDAAFAEKGSA----TDLY-VDY----TNITKVVKPGSRIFVDDG 171 (187) Q Consensus 124 i~l~~G~~v~lt~~~~~~~~~~~----~~i~-v~~----~~l~~~v~~Gd~IlidDG 171 (187) -.|++|+.+.|-.=.=|..+... +-.. -+. ..|.+.+.+---||++|. T Consensus 109 ~~l~~GeVlLLENvRF~~~Ee~~~~~~~~~~~~~d~~~~~~fa~~LA~l~DiyVNDA 165 (417) T PTZ00005 109 ANAKNGSVILLENLRFHIEEEGKGVDANGNKVKADKEEVKKFRKSLTKLGDIYVNDA 165 (417) T ss_pred HcCCCCCEEEEeccccccccccccccccccccCCCHHHHHHHHHHHHhhCCEEEecc Confidence 34666666555322211111100 0000 111 237777777667999884 No 116 >PRK06801 hypothetical protein; Provisional Probab=47.26 E-value=1.7e+02 Score=25.24 Aligned_cols=53 Identities=8% Similarity=0.171 Sum_probs=45.2 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+..-+ ..+.+.+.+.+-+++|.+.+-+.-||-+.++..+....+++.+..++ T Consensus 76 pV~lHl-DH~~~~e~i~~Ai~~GftSVm~D~S~l~~eeNi~~t~~v~~~a~~~g 128 (286) T PRK06801 76 PVVLNL-DHGLHFEAVVRALRLGFSSVMFDGSTLEYEENVRQTREVVKMCHAVG 128 (286) T ss_pred CEEEEC-CCCCCHHHHHHHHHhCCcEEEEcCCCCCHHHHHHHHHHHHHHHHHcC Confidence 344444 66778999999999999999999999999988888888888888877 No 117 >PRK03512 thiamine-phosphate pyrophosphorylase; Provisional Probab=46.79 E-value=95 Score=25.23 Aligned_cols=42 Identities=14% Similarity=0.249 Sum_probs=37.9 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+.+++++++|+..+.|-.-+.+.+++.+....+++..++++ T Consensus 22 ~~~l~~~l~~G~~~vqLR~k~~~~~~~~~la~~l~~~~~~~~ 63 (211) T PRK03512 22 VQWIERLLDAGVRTLQLRIKDRRDEEVEADVVAAIALGRRYQ 63 (211) T ss_pred HHHHHHHHhCCCCEEEEcCCCCCHHHHHHHHHHHHHHHHHhC Confidence 467999999999999999999999999999999988888776 No 118 >COG0352 ThiE Thiamine monophosphate synthase [Coenzyme metabolism] Probab=46.44 E-value=88 Score=25.73 Aligned_cols=42 Identities=17% Similarity=0.215 Sum_probs=38.6 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+.+++.++.|++++=|--=..+.+++++....+|.++++++ T Consensus 24 ~~~ve~al~~Gv~~vQlR~K~~~~~~~~~~a~~~~~lc~~~~ 65 (211) T COG0352 24 LEWVEAALKGGVTAVQLREKDLSDEEYLALAEKLRALCQKYG 65 (211) T ss_pred HHHHHHHHhCCCeEEEEecCCCChHHHHHHHHHHHHHHHHhC Confidence 789999999999999888888888888999999999999987 No 119 >PRK02714 O-succinylbenzoate synthase; Provisional Probab=46.21 E-value=57 Score=28.14 Aligned_cols=64 Identities=9% Similarity=0.163 Sum_probs=44.6 Q ss_pred CceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 36 LTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) .+.+-.+|+......+.++++.+.|-+.+.+.....+.++-.++++.+|++ ++ ..+.+++|--+ T Consensus 109 ~~~~~~~i~~~~~~~~~a~~~~~~G~~~~KvKvG~~~~~~d~~~v~air~~---~g------~~~~l~vDaN~ 172 (320) T PRK02714 109 PLSYSALLPAGEAALQQWQTLWQQGYRTFKWKIGVDPLEQELKIFEQLLER---LP------AGAKLRLDANG 172 (320) T ss_pred CCceeeecCCCHHHHHHHHHHHHcCCCEEEEEECCCChHHHHHHHHHHHHh---cC------CCCEEEEECCC Confidence 366667775544445677888899999999998766666556666666654 44 34688888755 No 120 >PRK05585 yajC preprotein translocase subunit YajC; Validated Probab=45.93 E-value=44 Score=24.50 Aligned_cols=17 Identities=12% Similarity=0.423 Sum_probs=7.7 Q ss_pred hhhhcCCCCCEEEEeCC Q psy254 155 NITKVVKPGSRIFVDDG 171 (187) Q Consensus 155 ~l~~~v~~Gd~IlidDG 171 (187) ++.+.+++||+|..-.| T Consensus 48 ~~~~~Lk~Gd~VvT~gG 64 (106) T PRK05585 48 KMLSSLAKGDEVVTNGG 64 (106) T ss_pred HHHHhcCCCCEEEECCC Confidence 34444444444444433 No 121 >COG1873 Protein implicated in RNA metabolism, contains PRC-barrel domain [General function prediction only] Probab=45.73 E-value=55 Score=23.09 Aligned_cols=60 Identities=17% Similarity=0.277 Sum_probs=36.7 Q ss_pred eCCCCeeEeeecCCCCcccEEeeeCCEEEEeeCC---CcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCe Q psy254 105 DTKGPEIRTGLLQGGGSAEVELVKGQTIRLTTDA---AFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGL 172 (187) Q Consensus 105 Dl~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~---~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~ 172 (187) +..|- +.|.+.+ -.+.+++|....|-... .+...+..+.+-++|..+- ++||.|++++.. T Consensus 18 ~~~G~--~vG~V~d---v~ld~~~g~i~~l~v~~~~~~l~~~~k~~~v~IP~~~V~---aIGd~III~~~~ 80 (87) T COG1873 18 TNDGK--YVGTVSD---VVLDIKEGKITGLLVIPTNKGLFLFGKGKEVIVPYEYVK---AIGDIIIIKDVP 80 (87) T ss_pred cCCCe--EEEEEEe---EEEEccCCcEEEEEEecCCccccccCCCcEEEEehhHeE---EecCEEEEechH Confidence 44443 5677765 35778888655443321 2222233357888887653 899999999753 No 122 >PRK08999 hypothetical protein; Provisional Probab=45.57 E-value=99 Score=26.19 Aligned_cols=42 Identities=10% Similarity=0.086 Sum_probs=37.7 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+.+++++.+|+..+-+-.-+.+.++..+.+..+++..+.++ T Consensus 147 ~~~~~~~l~~g~~~vqlR~k~~~~~~~~~~~~~l~~~~~~~~ 188 (312) T PRK08999 147 LARLERALAAGIRLIQLRAPQLPPAAYRALARAALGLCRRAG 188 (312) T ss_pred HHHHHHHHHCCCcEEEEeCCCCCHHHHHHHHHHHHHHHHHhC Confidence 367889999999999999999999999999999999888876 No 123 >PF03659 Glyco_hydro_71: Glycosyl hydrolase family 71 ; InterPro: IPR005197 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This is a family of alpha-1,3-glucanases belonging to glycoside hydrolase family 71 (GH71 from CAZY). Probab=45.45 E-value=62 Score=29.02 Aligned_cols=52 Identities=15% Similarity=0.212 Sum_probs=41.4 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) ...|+.-..+|.|.|=+|+.-.+ ....+.+..+=+|++..+ +.+.+.+|..+ T Consensus 20 ~~di~~A~~~GIDgFaLNig~~d-~~~~~~l~~a~~AA~~~g------FKlf~SfD~~~ 71 (386) T PF03659_consen 20 EADIRLAQAAGIDGFALNIGSSD-SWQPDQLADAYQAAEAVG------FKLFFSFDMNS 71 (386) T ss_pred HHHHHHHHHcCCCEEEEecccCC-cccHHHHHHHHHHHHhcC------CEEEEEecccC Confidence 36788888999999999998444 455577777778888887 88999999963 No 124 >PLN02741 riboflavin synthase Probab=45.17 E-value=50 Score=26.80 Aligned_cols=35 Identities=26% Similarity=0.304 Sum_probs=28.2 Q ss_pred EEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeCCe Q psy254 148 DLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVKSY 184 (187) Q Consensus 148 ~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~ 184 (187) .+.+..+.+++.+++|+.|-+|. ++|+|.++.+++ T Consensus 24 ~l~i~~~~~~~~l~~G~SIAvnG--vCLTV~~~~~~~ 58 (194) T PLN02741 24 DLKIEASTVLDGVKLGDSIAVNG--TCLTVTEFDGDE 58 (194) T ss_pred EEEEEcchhhcccccCCEEEECc--EEEEEEEECCCE Confidence 45555556788999999999986 799999998775 No 125 >PRK02901 O-succinylbenzoate synthase; Provisional Probab=44.85 E-value=1.4e+02 Score=26.08 Aligned_cols=62 Identities=13% Similarity=0.269 Sum_probs=42.1 Q ss_pred CceEEEecCCCCCCHHHHHHHHHh--cCcEEEEecCCC--CHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 36 LTGIICTIGPASVAVDMLEKIIET--GMNIARLNFSHG--SYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~a--Gm~v~RiN~sHg--~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) +..+-+|+ |.. +++.+.++++. |.+.+.+..+.. +.++-.+++..+|+ .+| ..+.|++|--| T Consensus 78 ~vp~~~tv-~~~-~~e~~~~~~~~~~G~~~~KvKVg~~~~~~~~Di~rv~avRe---~lG------pd~~LrvDAN~ 143 (327) T PRK02901 78 RVPVNATV-PAV-DAAQVPEVLARFPGCRTAKVKVAEPGQTLADDVARVNAVRD---ALG------PDGRVRVDANG 143 (327) T ss_pred eEEeeEEe-CCC-CHHHHHHHHHHhCCCCEEEEEECCCCCCHHHHHHHHHHHHH---hcC------CCCEEEEECCC Confidence 44566666 543 46778888887 999999998743 45555555655554 445 34688888765 No 126 >KOG0407|consensus Probab=44.72 E-value=13 Score=27.75 Aligned_cols=23 Identities=30% Similarity=0.631 Sum_probs=18.3 Q ss_pred cCCCCCCHHHHHHHHHhcCcEEEEe Q psy254 43 IGPASVAVDMLEKIIETGMNIARLN 67 (187) Q Consensus 43 iGPas~~~~~i~~li~aGm~v~RiN 67 (187) .||-. ...|+.|.++||.+-||. T Consensus 96 pgpga--qsalralar~gmrigrie 118 (139) T KOG0407|consen 96 PGPGA--QSALRALARSGMRIGRIE 118 (139) T ss_pred CCccH--HHHHHHHHHhcceeeeec Confidence 45543 468999999999999984 No 127 >PF07745 Glyco_hydro_53: Glycosyl hydrolase family 53; InterPro: IPR011683 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This domain is found in family 53 of the glycosyl hydrolase classification []. These enzymes are endo-1,4- beta-galactanases (3.2.1.89 from EC). The structure of this domain is known [] and has a TIM barrel fold.; GO: 0015926 glucosidase activity; PDB: 1HJQ_A 1HJS_A 1HJU_B 1FHL_A 1FOB_A 2GFT_A 1UR4_B 1UR0_A 1R8L_B 2CCR_A .... Probab=44.45 E-value=52 Score=28.98 Aligned_cols=49 Identities=20% Similarity=0.304 Sum_probs=31.2 Q ss_pred HHHHHHHHHhcCcEEEEecCCCC----HHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC Q psy254 50 VDMLEKIIETGMNIARLNFSHGS----YEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK 107 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~----~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~ 107 (187) .+.++=|-.+|+|.+||-.-+.. .......++..|+|. +.| ..+|+|+- T Consensus 27 ~d~~~ilk~~G~N~vRlRvwv~P~~~g~~~~~~~~~~akrak-~~G--------m~vlldfH 79 (332) T PF07745_consen 27 KDLFQILKDHGVNAVRLRVWVNPYDGGYNDLEDVIALAKRAK-AAG--------MKVLLDFH 79 (332) T ss_dssp --HHHHHHHTT--EEEEEE-SS-TTTTTTSHHHHHHHHHHHH-HTT---------EEEEEE- T ss_pred CCHHHHHHhcCCCeEEEEeccCCcccccCCHHHHHHHHHHHH-HCC--------CeEEEeec Confidence 46788888899999999987663 335667777777764 445 68888863 No 128 >cd00945 Aldolase_Class_I Class I aldolases. The class I aldolases use an active-site lysine which stablilzes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin. Probab=44.19 E-value=83 Score=24.04 Aligned_cols=55 Identities=22% Similarity=0.294 Sum_probs=35.2 Q ss_pred CceEEEecCCCC------CCHHHHHHHHHhcCcEEEEecCCCCHHH--HHHHHHHHHHHHHHh Q psy254 36 LTGIICTIGPAS------VAVDMLEKIIETGMNIARLNFSHGSYEY--HGQTIKNIRQAVENY 90 (187) Q Consensus 36 ~TkIi~TiGPas------~~~~~i~~li~aGm~v~RiN~sHg~~e~--~~~~i~~ir~a~~~~ 90 (187) +..+++.+|..+ ...+..+...++|++.+=+-..++.... ...+++.+++..+.. T Consensus 48 ~~~v~~~v~~~~~~~~~~~~~~~a~~a~~~Gad~i~v~~~~~~~~~~~~~~~~~~~~~i~~~~ 110 (201) T cd00945 48 DVPVIVVVGFPTGLTTTEVKVAEVEEAIDLGADEIDVVINIGSLKEGDWEEVLEEIAAVVEAA 110 (201) T ss_pred CCeEEEEecCCCCCCcHHHHHHHHHHHHHcCCCEEEEeccHHHHhCCCHHHHHHHHHHHHHHh Confidence 466777776644 3567888999999998877444432222 455666666665553 No 129 >PRK12857 fructose-1,6-bisphosphate aldolase; Reviewed Probab=44.08 E-value=1.5e+02 Score=25.47 Aligned_cols=53 Identities=11% Similarity=0.089 Sum_probs=43.7 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+..-+ ..+.+.+.+.+-+++|.+-..|.-||-+.++..+.-..+-+.+...| T Consensus 76 PValHL-DH~~~~e~i~~ai~~GftSVM~DgS~lp~eeNi~~T~~vv~~Ah~~g 128 (284) T PRK12857 76 PVALHL-DHGTDFEQVMKCIRNGFTSVMIDGSKLPLEENIALTKKVVEIAHAVG 128 (284) T ss_pred CEEEEC-CCCCCHHHHHHHHHcCCCeEEEeCCCCCHHHHHHHHHHHHHHHHHcC Confidence 344444 67789999999999999999999999999888887777777777665 No 130 >cd00405 PRAI Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric, monofunctional and thermolabile, but in some thermophile organisms PRAI is dimeric for reasons of stability and in others it is fused to other components of the tryptophan biosynthesis pathway to form multifunctional enzymes. Probab=44.03 E-value=42 Score=26.74 Aligned_cols=53 Identities=13% Similarity=0.221 Sum_probs=39.0 Q ss_pred CCHHHHHHHHHhcCcEEEEecCCCCHHHH-HHHHHHHHHHHHHhCCCCCCcceeEEEeeC Q psy254 48 VAVDMLEKIIETGMNIARLNFSHGSYEYH-GQTIKNIRQAVENYSKRIGMPHALAIALDT 106 (187) Q Consensus 48 ~~~~~i~~li~aGm~v~RiN~sHg~~e~~-~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl 106 (187) .+.+.++..+++|++.+=+.|...++.+. .+....+++...... .+|+++++- T Consensus 7 ~~~ed~~~a~~~Gvd~ig~i~~~~s~R~v~~~~a~~l~~~~~~~~------~~V~v~vn~ 60 (203) T cd00405 7 TTLEDALAAAEAGADAIGFIFAPKSPRYVSPEQAREIVAALPPFV------KRVGVFVNE 60 (203) T ss_pred CCHHHHHHHHHcCCCEEEEecCCCCCCCCCHHHHHHHHHhCCCCC------cEEEEEeCC Confidence 56889999999999999888887777766 666666666544321 457777654 No 131 >PRK06512 thiamine-phosphate pyrophosphorylase; Provisional Probab=43.94 E-value=1.8e+02 Score=23.83 Aligned_cols=42 Identities=7% Similarity=0.071 Sum_probs=38.2 Q ss_pred HHHHHHHHHhc-CcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 50 VDMLEKIIETG-MNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 50 ~~~i~~li~aG-m~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+.+++.+.+| ++++-+-.-+-+.++..+....+++..+.++ T Consensus 29 ~~~l~~al~~G~v~~vQlR~K~l~~~~~~~~a~~l~~l~~~~g 71 (221) T PRK06512 29 AKLLRAALQGGDVASVILPQYGLDEATFQKQAEKLVPVIQEAG 71 (221) T ss_pred HHHHHHHHcCCCccEEEEeCCCCCHHHHHHHHHHHHHHHHHhC Confidence 47899999999 7999998999999999999999999998877 No 132 >cd00947 TBP_aldolase_IIB Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1,6-bisphosphate. There is an absolute requirement for a divalent metal ion, usually zinc, and in addition the enzymes are activated by monovalent cations such as Na+. The type A and type B Class II FBPA's differ in the presence and absence of distinct indels in the sequence that result in differing loop lengths in the structures. Probab=43.89 E-value=1.6e+02 Score=25.20 Aligned_cols=54 Identities=13% Similarity=0.274 Sum_probs=44.3 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) ..+..-+ ..+.+++.+.+-+++|-+-..|..||-+.++..+.-..+.+.+...| T Consensus 70 VPV~lHL-DH~~~~~~i~~ai~~GftSVMiD~S~l~~eeNi~~t~~vv~~ah~~g 123 (276) T cd00947 70 VPVALHL-DHGSSFELIKRAIRAGFSSVMIDGSHLPFEENVAKTKEVVELAHAYG 123 (276) T ss_pred CCEEEEC-CCCCCHHHHHHHHHhCCCEEEeCCCCCCHHHHHHHHHHHHHHHHHcC Confidence 3455555 66778999999999999999999999999888777777777777665 No 133 >cd00453 FTBP_aldolase_II Fructose/tagarose-bisphosphate aldolase class II. This family includes fructose-1,6-bisphosphate (FBP) and tagarose 1,6-bisphosphate (TBP) aldolases. FBP-aldolase is homodimeric and used in gluconeogenesis and glycolysis; the enzyme controls the condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to yield fructose-1,6-bisphosphate. TBP-aldolase is tetrameric and produces tagarose-1,6-bisphosphate. There is an absolute requirement for a divalent metal ion, usually zinc, and in addition the enzymes are activated by monovalent cations such as Na+. Although structurally similar, the class I aldolases use a different mechanism and are believed to have an independent evolutionary origin. Probab=43.71 E-value=1.3e+02 Score=26.63 Aligned_cols=54 Identities=7% Similarity=0.168 Sum_probs=43.3 Q ss_pred ceEEEecCCCCC--CHHHHHHHHHhc-----------CcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 37 TGIICTIGPASV--AVDMLEKIIETG-----------MNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 37 TkIi~TiGPas~--~~~~i~~li~aG-----------m~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) ..|..-+ ..+. +.+.++.++++| .+-..|..||-+.++..+.-..+-+.+...+ T Consensus 86 VPV~lHL-DH~~~~~~e~i~~ai~~G~~~~~~~~~~~FsSVMiDgS~l~~eeNi~~T~~vve~Ah~~g 152 (340) T cd00453 86 VPVILHT-DHCAKKLLPWIDGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIG 152 (340) T ss_pred CCEEEEc-CCCCCCCHHHHHHHHHcCCccccccCCCCceeEEecCCCCCHHHHHHHHHHHHHHHHHcC Confidence 4566666 5566 899999999999 9999999999999987777777666666554 No 134 >PRK05628 coproporphyrinogen III oxidase; Validated Probab=43.56 E-value=2e+02 Score=25.26 Aligned_cols=42 Identities=10% Similarity=0.181 Sum_probs=33.0 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHH Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQT 79 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~ 79 (187) .+-+..-|.+-+.+.++.|.++|++-+-|..=.++.+....+ T Consensus 96 e~t~e~~p~~i~~e~l~~l~~~G~~rvslGvQS~~~~~L~~l 137 (375) T PRK05628 96 EVTTEANPESTSPEFFAALRAAGFTRVSLGMQSAAPHVLAVL 137 (375) T ss_pred EEEEEeCCCCCCHHHHHHHHHcCCCEEEEecccCCHHHHHHc Confidence 455555799999999999999999988887777777655433 No 135 >cd02801 DUS_like_FMN Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present. Probab=43.43 E-value=73 Score=25.50 Aligned_cols=52 Identities=17% Similarity=0.266 Sum_probs=32.8 Q ss_pred CCceEEEecCCCC-CC-HHHHHHHHHhcCcEEEEecCC---------------CCHHHHHHHHHHHHHH Q psy254 35 RLTGIICTIGPAS-VA-VDMLEKIIETGMNIARLNFSH---------------GSYEYHGQTIKNIRQA 86 (187) Q Consensus 35 r~TkIi~TiGPas-~~-~~~i~~li~aGm~v~RiN~sH---------------g~~e~~~~~i~~ir~a 86 (187) -...+++.|+=.+ ++ .+..+.+.++|.+.+=||++| ...+...++++.+|++ T Consensus 53 ~~~p~~~qi~g~~~~~~~~aa~~~~~aG~d~ieln~g~p~~~~~~~~~G~~l~~~~~~~~eii~~v~~~ 121 (231) T cd02801 53 EERPLIVQLGGSDPETLAEAAKIVEELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREA 121 (231) T ss_pred cCCCEEEEEcCCCHHHHHHHHHHHHhcCCCEEEEeCCCCHHHHhCCCeeehhcCCHHHHHHHHHHHHHh Confidence 3457888885221 22 234455666799999999999 2444555666666543 No 136 >PRK05886 yajC preprotein translocase subunit YajC; Validated Probab=43.34 E-value=47 Score=24.57 Aligned_cols=29 Identities=21% Similarity=0.501 Sum_probs=15.6 Q ss_pred hhhhcCCCCCEEEEeCCeEEEEEEEEeCCe Q psy254 155 NITKVVKPGSRIFVDDGLISLVVKSIVKSY 184 (187) Q Consensus 155 ~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~ 184 (187) ++...|++||+|..-.|.. -+|.+++++. T Consensus 34 ~m~~~Lk~GD~VvT~gGi~-G~V~~I~d~~ 62 (109) T PRK05886 34 DLHESLQPGDRVHTTSGLQ-ATIVGITDDT 62 (109) T ss_pred HHHHhcCCCCEEEECCCeE-EEEEEEeCCE Confidence 4556666666666655433 3344454443 No 137 >PRK14469 ribosomal RNA large subunit methyltransferase N; Provisional Probab=42.59 E-value=1.3e+02 Score=26.32 Aligned_cols=40 Identities=20% Similarity=0.326 Sum_probs=25.4 Q ss_pred CCCceEEEecCCCCCCHHHHHHHHHhcCcE-EEEecCCCCHHHHHH Q psy254 34 VRLTGIICTIGPASVAVDMLEKIIETGMNI-ARLNFSHGSYEYHGQ 78 (187) Q Consensus 34 ~r~TkIi~TiGPas~~~~~i~~li~aGm~v-~RiN~sHg~~e~~~~ 78 (187) .|++.| .|.|- ++.+++|.++|.++ .-+.+-..+.+.+.+ T Consensus 184 ~~~iti-sTnG~----~~~i~~L~~~~l~~~LaiSL~a~~~e~r~~ 224 (343) T PRK14469 184 IRRITI-STVGI----PEKIIQLAEEGLDVKLALSLHAPTNFKRDQ 224 (343) T ss_pred CCeEEE-ECCCC----hHHHHHHHhhCCCcEEEEEeCCCCHHHHHh Confidence 345555 77774 67899999999994 444444444443443 No 138 >PRK11613 folP dihydropteroate synthase; Provisional Probab=41.67 E-value=1.7e+02 Score=25.21 Aligned_cols=68 Identities=21% Similarity=0.339 Sum_probs=46.7 Q ss_pred CceEEEec--CCCCC-------C----HHHHHHHHHhcCcEEEEecCC---CC-----HHHHHHHHHHHHHHHHHhCCCC Q psy254 36 LTGIICTI--GPASV-------A----VDMLEKIIETGMNIARLNFSH---GS-----YEYHGQTIKNIRQAVENYSKRI 94 (187) Q Consensus 36 ~TkIi~Ti--GPas~-------~----~~~i~~li~aGm~v~RiN~sH---g~-----~e~~~~~i~~ir~a~~~~~~~~ 94 (187) +|.||+-| -|-|- + .+...+|+++|+++.=|+.-- |. .+++.+++.-|+.+.+.. T Consensus 14 ~~~imGIlNvTpDSFsdgg~~~~~~~a~~~a~~~~~~GAdIIDIGgeSTrPg~~~v~~eeE~~Rv~pvI~~l~~~~---- 89 (282) T PRK11613 14 HPHVMGILNVTPDSFSDGGTHNSLIDAVKHANLMINAGATIIDVGGESTRPGAAEVSVEEELDRVIPVVEAIAQRF---- 89 (282) T ss_pred CceEEEEEcCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCcEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHhcC---- Confidence 68899887 45331 1 467788999999999999422 22 356777776676665443 Q ss_pred CCcceeEEEeeCCCCee Q psy254 95 GMPHALAIALDTKGPEI 111 (187) Q Consensus 95 ~~~~~v~I~~Dl~GPkI 111 (187) .+.|-+|+-=|++ T Consensus 90 ----~~~ISIDT~~~~v 102 (282) T PRK11613 90 ----EVWISVDTSKPEV 102 (282) T ss_pred ----CCeEEEECCCHHH Confidence 3568889987775 No 139 >COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis] Probab=41.65 E-value=56 Score=27.39 Aligned_cols=38 Identities=24% Similarity=0.265 Sum_probs=25.5 Q ss_pred CCCCceEEEec-CCCCCCHHHHHHHHH--hcCcEEEEecCCCCH Q psy254 33 YVRLTGIICTI-GPASVAVDMLEKIIE--TGMNIARLNFSHGSY 73 (187) Q Consensus 33 ~~r~TkIi~Ti-GPas~~~~~i~~li~--aGm~v~RiN~sHg~~ 73 (187) .+-+||++||. ||... .-+.|.. .|.-.+|.||.--+- T Consensus 38 ~~G~tkVic~vsGp~e~---~p~~l~~~~~g~~t~ey~m~p~sT 78 (230) T COG0689 38 EFGNTKVICTVSGPREP---VPRFLRGTGKGWLTAEYGMLPRST 78 (230) T ss_pred EeCCeEEEEEEecCCCC---CChhhcCCCceEEEEEEecccccc Confidence 56799999999 68632 2233333 478888888875443 No 140 >PRK09197 fructose-bisphosphate aldolase; Provisional Probab=41.53 E-value=1.6e+02 Score=26.26 Aligned_cols=54 Identities=7% Similarity=0.163 Sum_probs=43.4 Q ss_pred ceEEEecCCCCCC--HHHHHHHHHhc-----------CcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 37 TGIICTIGPASVA--VDMLEKIIETG-----------MNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 37 TkIi~TiGPas~~--~~~i~~li~aG-----------m~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) ..+..-+ ..+.+ .+.++..+++| .+-..|..||-+.++..+.-..+-+.+..++ T Consensus 93 VPValHL-DHg~~~~~~~i~~ai~~g~~~v~~a~~~gftSVMiDgS~lpfEeNI~~TkevVe~Ah~~G 159 (350) T PRK09197 93 VPVILHT-DHCAKKLLPWIDGLLDAGEKHFAAGGKPLFSSHMIDLSEEPLEENIEICSKYLERMAKAG 159 (350) T ss_pred CCEEEEC-CCCCCcchHHHHHHHHhhHHHHHhcCCCCceeEEeeCCCCCHHHHHHHHHHHHHHHHHcC Confidence 3455555 55666 78899999988 9999999999999988888888877777766 No 141 >PRK13479 2-aminoethylphosphonate--pyruvate transaminase; Provisional Probab=41.26 E-value=1.8e+02 Score=24.92 Aligned_cols=44 Identities=16% Similarity=0.155 Sum_probs=34.9 Q ss_pred CCHHHHHHHHHhcCcE----------EEEe-cCCCCHHHHHHHHHHHHHHHHHhC Q psy254 48 VAVDMLEKIIETGMNI----------ARLN-FSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 48 ~~~~~i~~li~aGm~v----------~RiN-~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) +..+..+.|.+.|+-| +|++ +.+-+.++..+.++.++++.++.+ T Consensus 311 ~~~~l~~~L~~~gi~v~~g~~~~~~~iRis~~~~~t~edi~~~l~~L~~~l~~~~ 365 (368) T PRK13479 311 DFKEFYERLKEQGFVIYPGKLTQVDTFRIGCIGDVDAADIRRLVAAIAEALYWMG 365 (368) T ss_pred CHHHHHHHHHHCCEEEecCCCCCCCEEEEecCCCCCHHHHHHHHHHHHHHHHHcC Confidence 3456777888888766 6885 477799999999999999887765 No 142 >PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis. Probab=40.91 E-value=55 Score=21.46 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=20.9 Q ss_pred cCCCCCEEEEeCCeEEEEEEEEeCCee Q psy254 159 VVKPGSRIFVDDGLISLVVKSIVKSYQ 185 (187) Q Consensus 159 ~v~~Gd~IlidDG~i~l~V~~v~~~~i 185 (187) ..++||.|.+-+| +.-+|..+.++++ T Consensus 3 ~a~vGdiIefk~g-~~G~V~kv~eNSV 28 (57) T PF09953_consen 3 KAKVGDIIEFKDG-FTGIVEKVYENSV 28 (57) T ss_pred ccccCcEEEEcCC-cEEEEEEEecCcE Confidence 3578999999888 7888888877664 No 143 >cd03328 MR_like_3 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 3. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. This subgroup's function is unknown. Probab=39.65 E-value=1.8e+02 Score=25.32 Aligned_cols=63 Identities=11% Similarity=0.140 Sum_probs=39.5 Q ss_pred CceEEEecCCCCCCH----HHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 36 LTGIICTIGPASVAV----DMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 36 ~TkIi~TiGPas~~~----~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) +...-+|+|..+.++ +..+++++.|.+.+.+-+. .+++ +-++.+|.+.+..| .-+.+++|--+ T Consensus 125 ~v~~y~s~~~~~~~~e~~~~~a~~~~~~Gf~~~Kikvg-~~~~---~d~~~v~~vRe~~G------~~~~l~vDaN~ 191 (352) T cd03328 125 SVPVYGSGGFTSYDDDRLREQLSGWVAQGIPRVKMKIG-RDPR---RDPDRVAAARRAIG------PDAELFVDANG 191 (352) T ss_pred CeEEEEecCCCCCCHHHHHHHHHHHHHCCCCEEEeecC-CCHH---HHHHHHHHHHHHcC------CCCeEEEECCC Confidence 455556765433333 4556678899999999874 2333 44555555555566 34788999765 No 144 >PF00478 IMPDH: IMP dehydrogenase / GMP reductase domain; InterPro: IPR001093 Synonym(s): Inosine-5'-monophosphate dehydrogenase, Inosinic acid dehydrogenase; Synonym(s): Guanosine 5'-monophosphate oxidoreductase This entry contains two related enzymes IMP dehydrogenase and GMP reducatase. These enzymes adopt a TIM barrel structure. IMP dehydrogenase (1.1.1.205 from EC) (IMPDH) catalyzes the rate-limiting reaction of de novo GTP biosynthesis, the NAD-dependent reduction of IMP into XMP [].Inosine 5-phosphate + NAD+ + H2O = xanthosine 5-phosphate + NADH IMP dehydrogenase is associated with cell proliferation and is a possible target for cancer chemotherapy. Mammalian and bacterial IMPDHs are tetramers of identical chains. There are two IMP dehydrogenase isozymes in humans []. IMP dehydrogenase nearly always contains a long insertion that has two CBS domains within it. GMP reductase (1.7.1.7 from EC) catalyzes the irreversible and NADPH-dependent reductive deamination of GMP into IMP [].NADPH + guanosine 5-phosphate = NADP+ + inosine 5-phosphate + NH3 It converts nucleobase, nucleoside and nucleotide derivatives of G to A nucleotides, and maintains intracellular balance of A and G nucleotides.; GO: 0003824 catalytic activity, 0055114 oxidation-reduction process; PDB: 3FFS_D 1VRD_A 1JCN_B 1EEP_B 3TSB_B 3USB_B 3TSD_A 4FF0_A 4FEZ_A 3KHJ_D .... Probab=39.63 E-value=84 Score=27.98 Aligned_cols=59 Identities=19% Similarity=0.321 Sum_probs=41.6 Q ss_pred CceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHH----------HHHHHHHHHHHHHHhCCCCCCcceeEEEee Q psy254 36 LTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEY----------HGQTIKNIRQAVENYSKRIGMPHALAIALD 105 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~----------~~~~i~~ir~a~~~~~~~~~~~~~v~I~~D 105 (187) ++.||+ |. ..+.+..++|+++|++..|+-+--|+... ....|..+.+++.+++ +.|+.| T Consensus 149 ~~~via--GN-V~T~e~a~~L~~aGad~vkVGiGpGsiCtTr~v~GvG~PQ~tAv~~~a~~a~~~~--------v~iIAD 217 (352) T PF00478_consen 149 DVPVIA--GN-VVTYEGAKDLIDAGADAVKVGIGPGSICTTREVTGVGVPQLTAVYECAEAARDYG--------VPIIAD 217 (352) T ss_dssp TSEEEE--EE-E-SHHHHHHHHHTT-SEEEESSSSSTTBHHHHHHSBSCTHHHHHHHHHHHHHCTT--------SEEEEE T ss_pred CceEEe--cc-cCCHHHHHHHHHcCCCEEEEeccCCcccccccccccCCcHHHHHHHHHHHhhhcc--------Cceeec Confidence 556776 44 46789999999999999999999888664 3345555666666544 677777 No 145 >PF13606 Ank_3: Ankyrin repeat Probab=39.58 E-value=23 Score=19.52 Aligned_cols=16 Identities=13% Similarity=0.536 Sum_probs=14.0 Q ss_pred CCHHHHHHHHHhcCcE Q psy254 48 VAVDMLEKIIETGMNI 63 (187) Q Consensus 48 ~~~~~i~~li~aGm~v 63 (187) .+.+.++.|++.|+|+ T Consensus 13 g~~e~v~~Ll~~gadv 28 (30) T PF13606_consen 13 GNIEIVKYLLEHGADV 28 (30) T ss_pred CCHHHHHHHHHcCCCC Confidence 4689999999999886 No 146 >PLN02925 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase Probab=39.48 E-value=63 Score=31.51 Aligned_cols=53 Identities=17% Similarity=0.334 Sum_probs=38.8 Q ss_pred CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC-CCe Q psy254 49 AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK-GPE 110 (187) Q Consensus 49 ~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~-GPk 110 (187) +.+.+.+|.++|.++.|+-.- -....+.+.+||+.....+ .++++..|+. -|+ T Consensus 112 tv~Qi~~l~~aGceiVRvtv~---~~~~A~al~~I~~~L~~~g------~~iPLVADIHF~~~ 165 (733) T PLN02925 112 TVDQVMRIADKGADIVRITVQ---GKKEADACFEIKNTLVQKG------YNIPLVADIHFAPS 165 (733) T ss_pred HHHHHHHHHHcCCCEEEEcCC---CHHHHHhHHHHHHHHhhcC------CCCCEEEecCCCHH Confidence 478999999999999998542 2345566777776555555 7789999986 443 No 147 >smart00306 HintN Hint (Hedgehog/Intein) domain N-terminal region. Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases. Probab=39.33 E-value=54 Score=22.26 Aligned_cols=42 Identities=21% Similarity=0.405 Sum_probs=21.6 Q ss_pred EEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEe Q psy254 124 VELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVD 169 (187) Q Consensus 124 i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~Ilid 169 (187) +.+..|..+..|.+-.+.........+ -.+.+|++||.|++- T Consensus 58 i~~~~g~~i~~T~~H~~~~~~~~~~~w----~~a~~l~~gd~v~~~ 99 (100) T smart00306 58 IKTENGREITLTPDHLLLVRDGGKLVW----VFASELKPGDYVLVP 99 (100) T ss_pred EEECCCCEEEECCCCEEEEecCCcEEE----EEHHHCCCCCEEEec Confidence 334456666666554321111111112 235788999999863 No 148 >PRK14112 urease accessory protein UreE; Provisional Probab=39.20 E-value=94 Score=24.19 Aligned_cols=25 Identities=16% Similarity=0.275 Sum_probs=19.3 Q ss_pred EEeeCcchhhhcCCCCCEEEEeCCeE Q psy254 148 DLYVDYTNITKVVKPGSRIFVDDGLI 173 (187) Q Consensus 148 ~i~v~~~~l~~~v~~Gd~IlidDG~i 173 (187) .+.+..+. ...|..||.++.|||.+ T Consensus 46 ei~l~L~r-~~~L~dGDvL~~ddg~~ 70 (149) T PRK14112 46 EYGIRLEE-DKKLMDGDILYKDDYKL 70 (149) T ss_pred EEEEECCC-CCccCCCCEEEeCCCCE Confidence 35555555 34799999999999976 No 149 >PRK05660 HemN family oxidoreductase; Provisional Probab=38.96 E-value=2.3e+02 Score=25.03 Aligned_cols=40 Identities=20% Similarity=0.178 Sum_probs=30.6 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHH Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYH 76 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~ 76 (187) +.|-+...|.+-+.+.++.|.++|++.+-|..=-.+.+.+ T Consensus 94 ~eit~e~np~~l~~e~l~~Lk~~Gv~risiGvqS~~~~~L 133 (378) T PRK05660 94 AEITMEANPGTVEADRFVGYQRAGVNRISIGVQSFSEEKL 133 (378) T ss_pred cEEEEEeCcCcCCHHHHHHHHHcCCCEEEeccCcCCHHHH Confidence 4676777899999999999999999966555555555543 No 150 >cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. Probab=38.89 E-value=55 Score=24.17 Aligned_cols=24 Identities=25% Similarity=0.367 Sum_probs=18.0 Q ss_pred hcCCCCCEEEEeCC----eEEEEEEEEe Q psy254 158 KVVKPGSRIFVDDG----LISLVVKSIV 181 (187) Q Consensus 158 ~~v~~Gd~IlidDG----~i~l~V~~v~ 181 (187) +.+++||.|.+.+. .+..+|+.+. T Consensus 30 ~~ikvGD~I~f~~~~~~~~l~v~V~~i~ 57 (109) T cd06555 30 QQIKVGDKILFNDLDTGQQLLVKVVDIR 57 (109) T ss_pred hcCCCCCEEEEEEcCCCcEEEEEEEEEE Confidence 56788888888663 5778888774 No 151 >PRK04147 N-acetylneuraminate lyase; Provisional Probab=38.87 E-value=1e+02 Score=26.08 Aligned_cols=65 Identities=9% Similarity=0.098 Sum_probs=45.1 Q ss_pred CceEEEecCCCC--CCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC Q psy254 36 LTGIICTIGPAS--VAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK 107 (187) Q Consensus 36 ~TkIi~TiGPas--~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~ 107 (187) +..||+.+|..+ +..+..+...++|++.+-+-.-+-..-....+++..++..+..+ .||-++ +.+ T Consensus 73 ~~~viagvg~~~t~~ai~~a~~a~~~Gad~v~v~~P~y~~~~~~~l~~~f~~va~a~~------lPv~iY-n~P 139 (293) T PRK04147 73 KVKLIAQVGSVNTAEAQELAKYATELGYDAISAVTPFYYPFSFEEICDYYREIIDSAD------NPMIVY-NIP 139 (293) T ss_pred CCCEEecCCCCCHHHHHHHHHHHHHcCCCEEEEeCCcCCCCCHHHHHHHHHHHHHhCC------CCEEEE-eCc Confidence 467888887644 34567788899999988887766544344677777888777655 566665 443 No 152 >COG4464 CapC Capsular polysaccharide biosynthesis protein [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane] Probab=38.50 E-value=21 Score=29.94 Aligned_cols=46 Identities=24% Similarity=0.387 Sum_probs=28.1 Q ss_pred EEEec--CCCC--CCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHH Q psy254 39 IICTI--GPAS--VAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQ 85 (187) Q Consensus 39 Ii~Ti--GPas--~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~ 85 (187) |+--| ||.| .+.+++++-.++|++-. +-.||--+.....-++.|++ T Consensus 8 Ilp~iDDGp~s~eesl~ml~~A~~qGvt~i-VaTsHh~~g~y~n~~~~v~~ 57 (254) T COG4464 8 ILPDIDDGPKSLEESLAMLREAVRQGVTKI-VATSHHLHGRYENPIEKVKE 57 (254) T ss_pred ccCCCCCCCCcHHHHHHHHHHHHHcCceEE-eecccccCCccCChHHHHHH Confidence 44444 7766 35688899999999853 34677655444444444443 No 153 >TIGR00300 conserved hypothetical protein TIGR00300. All members of the family come from genome projects. A partial length search brings in two plant lysine-ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzymes hitting the N-terminal region of the family. Probab=37.91 E-value=74 Score=28.84 Aligned_cols=51 Identities=29% Similarity=0.336 Sum_probs=41.3 Q ss_pred CceEEEecCCC---CCCHHHHHHHHHh--------------------------cCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 36 LTGIICTIGPA---SVAVDMLEKIIET--------------------------GMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 36 ~TkIi~TiGPa---s~~~~~i~~li~a--------------------------Gm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) .=||+...||| +...+-+.+|+++ ||++.+=.-..+.|..|.+.|..||++ T Consensus 201 gG~Iv~V~GPAvvhtga~~ala~Lir~GYV~~LlaGNAlAtHDiE~al~GTsLG~di~~~~~v~~GH~~Hl~~IN~irra 280 (407) T TIGR00300 201 GGKIGVVAGPAVIHTGAAQALAHLIREGYVDALLAGNALAVHDIEQALYGTSLGVDIQRGIPVPGGHRHHLKAINSVRRA 280 (407) T ss_pred CCCEEEEecCeEEecCcHHHHHHHHHcCcccEEecchHHHHhhhhHhhhCccccccccccccCCCchHHHHHHHHHHHHc Confidence 55899999997 4567888888876 466777666678889999999999985 No 154 >COG0107 HisF Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism] Probab=37.74 E-value=1e+02 Score=26.21 Aligned_cols=62 Identities=19% Similarity=0.281 Sum_probs=48.7 Q ss_pred CCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC Q psy254 35 RLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK 107 (187) Q Consensus 35 r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~ 107 (187) ...-|=-|+|---.+.+.+++++.+|+|=.-||.+--.. -+.|+++++.+|.+ +|-+.+|-+ T Consensus 71 ~~vfiPltVGGGI~s~eD~~~ll~aGADKVSINsaAv~~------p~lI~~~a~~FGsQ-----ciVvaIDak 132 (256) T COG0107 71 EQVFIPLTVGGGIRSVEDARKLLRAGADKVSINSAAVKD------PELITEAADRFGSQ-----CIVVAIDAK 132 (256) T ss_pred hhceeeeEecCCcCCHHHHHHHHHcCCCeeeeChhHhcC------hHHHHHHHHHhCCc-----eEEEEEEee Confidence 344666788888899999999999999999999874432 34789999999974 467777754 No 155 >TIGR01211 ELP3 histone acetyltransferase, ELP3 family. The Saccharomyces cerevisiae member YPL086C has been characterized in vitro as an N-terminal acetyltransferase for all four core histones. It is a component of the RNA polymerase II holoenzyme, designated Elp3p for Elongator Protein 3. Members of this family are found in eukaryotes and archaea. These proteins are part of the larger set of GNAT acetyltransferases. Probab=37.73 E-value=2.6e+02 Score=26.19 Aligned_cols=72 Identities=13% Similarity=0.232 Sum_probs=45.6 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHH-----HHHHHHHHHHhCCCCCCcceeEEEeeCCCC Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQT-----IKNIRQAVENYSKRIGMPHALAIALDTKGP 109 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~-----i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GP 109 (187) ..|-+-.-|-+-+.+.|+.|.++|++.+=|..=.++.+....+ .+.+.++.+... +.|+...+-+|..|+|- T Consensus 193 vgitiEtRPD~i~~e~L~~L~~~G~~rVslGVQS~~d~VL~~inRght~~~v~~Ai~~lr-~~G~~v~~~LM~GLPgq 269 (522) T TIGR01211 193 VGLTIETRPDYCREEHIDRMLKLGATRVELGVQTIYNDILERTKRGHTVRDVVEATRLLR-DAGLKVVYHIMPGLPGS 269 (522) T ss_pred EEEEEEEcCCcCCHHHHHHHHHcCCCEEEEECccCCHHHHHHhCCCCCHHHHHHHHHHHH-HcCCeEEEEeecCCCCC Confidence 3443334798999999999999999988888878777654332 222333322211 12233556788888873 No 156 >PRK12737 gatY tagatose-bisphosphate aldolase; Reviewed Probab=37.52 E-value=1.9e+02 Score=24.80 Aligned_cols=53 Identities=17% Similarity=0.257 Sum_probs=43.8 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+..-+ ..+.+.+.+.+-+++|.+-..|..||-+.++.-+.-..+-+.+..+| T Consensus 76 PValHL-DH~~~~e~i~~ai~~GftSVMiDgS~lp~eeNi~~T~~vv~~Ah~~g 128 (284) T PRK12737 76 PLALHL-DHHEDLDDIKKKVRAGIRSVMIDGSHLSFEENIAIVKEVVEFCHRYD 128 (284) T ss_pred CEEEEC-CCCCCHHHHHHHHHcCCCeEEecCCCCCHHHHHHHHHHHHHHHHHcC Confidence 344444 67778999999999999999999999999988887777777777766 No 157 >PRK09057 coproporphyrinogen III oxidase; Provisional Probab=37.44 E-value=2e+02 Score=25.34 Aligned_cols=70 Identities=16% Similarity=0.121 Sum_probs=44.4 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHH---------HHHHHHHHHHHHhCCCCCCcceeEEEeeCC Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHG---------QTIKNIRQAVENYSKRIGMPHALAIALDTK 107 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~---------~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~ 107 (187) +.|-+-..|.+-+.+.++.|.++|+|-+-|..=.++.+..+ +.++.++.+.+. . ....+-+|..++ T Consensus 91 ~eit~E~~P~~i~~e~L~~l~~~GvnrislGvQS~~d~vL~~l~R~~~~~~~~~ai~~~~~~-~----~~v~~dli~GlP 165 (380) T PRK09057 91 IEITLEANPTSVEAGRFRGYRAAGVNRVSLGVQALNDADLRFLGRLHSVAEALAAIDLAREI-F----PRVSFDLIYARP 165 (380) T ss_pred ccEEEEECcCcCCHHHHHHHHHcCCCEEEEecccCCHHHHHHcCCCCCHHHHHHHHHHHHHh-C----ccEEEEeecCCC Confidence 34555557999999999999999999777766666655432 222222222222 2 125566688888 Q ss_pred CCee Q psy254 108 GPEI 111 (187) Q Consensus 108 GPkI 111 (187) |-.. T Consensus 166 gqt~ 169 (380) T PRK09057 166 GQTL 169 (380) T ss_pred CCCH Confidence 8764 No 158 >TIGR00167 cbbA ketose-bisphosphate aldolases. fructose-bisphosphate and tagatose-bisphosphate aldolase. Probab=37.27 E-value=2.2e+02 Score=24.46 Aligned_cols=53 Identities=9% Similarity=0.173 Sum_probs=42.8 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+..-+ ..+.+.+.+++-+++|-+-..|..||-+.++..+.-..+-+.+...| T Consensus 79 PV~lHL-DHg~~~e~i~~ai~~GftSVMiDgS~lp~eeNi~~T~~vv~~Ah~~g 131 (288) T TIGR00167 79 PVALHL-DHGASEEDCAQAVKAGFSSVMIDGSHEPFEENIELTKKVVERAHKMG 131 (288) T ss_pred cEEEEC-CCCCCHHHHHHHHHcCCCEEEecCCCCCHHHHHHHHHHHHHHHHHcC Confidence 455554 77789999999999999999999999998877777777766666655 No 159 >PF02814 UreE_N: UreE urease accessory protein, N-terminal domain; InterPro: IPR004029 Urease and other nickel metalloenzymes are synthesised as precursors devoid of the metalloenzyme active site. These precursors then undergo a complex post-translational maturation process that requires a number of accessory proteins. Members of this group are nickel-binding proteins required for urease metallocentre assembly []. They are believed to function as metallochaperones to deliver nickel to urease apoprotein [, ]. It has been shown by yeast two-hybrid analysis that UreE forms a dimeric complex with UreG in Helicobacter pylori []. The UreDFG-apoenzyme complex has also been shown to exist [, ] and is believed to be, with the addition of UreE, the assembly system for active urease []. The complexes, rather than the individual proteins, presumably bind to UreB via UreE/H recognition sites. The structure of Klebsiella aerogenes UreE reveals a unique two-domain architecture.The N-terminal domain is structurally related to a heat shock protein, while the C-terminal domain shows homology to the Atx1 copper metallochaperone [, ]. Significantly, the metal-binding sites in UreE and Atx1 are distinct in location and types of residues despite the relationship between these proteins and the mechanism for UreE activation of urease is proposed to be different from the thiol ligand exchange mechanism used by the copper metallochaperones. The N-terminal domain is termed the peptide-binding domain. Deletion of this domain does not eliminate enzymatic activity, and the truncated protein can still activate urease [].; GO: 0016151 nickel ion binding, 0006461 protein complex assembly, 0019627 urea metabolic process; PDB: 3NXZ_B 3TJA_B 3LA0_B 3TJ9_B 3NY0_A 3L9Z_A 3TJ8_A 1EAR_A 1EB0_A 1GMU_B .... Probab=37.18 E-value=66 Score=21.02 Aligned_cols=25 Identities=24% Similarity=0.586 Sum_probs=16.2 Q ss_pred EEeeCcchhhhcCCCCCEEEEeCCeE Q psy254 148 DLYVDYTNITKVVKPGSRIFVDDGLI 173 (187) Q Consensus 148 ~i~v~~~~l~~~v~~Gd~IlidDG~i 173 (187) .+.+..|.= ..|+.||.++.|||.+ T Consensus 40 ei~i~L~r~-~~L~~GDvL~~d~g~~ 64 (65) T PF02814_consen 40 EIGIDLPRG-TVLRDGDVLYLDDGRL 64 (65) T ss_dssp EEEEE-SST-TT--TTEEEEECTSEE T ss_pred EEEEECCCC-cccCCCCEEEeCCCCC Confidence 355544443 5599999999999987 No 160 >PRK00073 pgk phosphoglycerate kinase; Provisional Probab=36.93 E-value=27 Score=31.47 Aligned_cols=100 Identities=17% Similarity=0.191 Sum_probs=61.2 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHH----HHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEeeecCCCCcccEE Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYE----YHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTGLLQGGGSAEVE 125 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e----~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG~~~~~~~~~i~ 125 (187) ..+|+.|++.|..|.= +||-..- ....+-......++.++ ++|...-|.-||+.+- ..-. T Consensus 39 lpTI~~l~~~gakvvl--~sH~gRP~g~~~~~SL~~va~~L~~lL~------~~V~fv~d~~g~~~~~--------~i~~ 102 (389) T PRK00073 39 LPTIKYLLEKGAKVIL--LSHLGRPKGEDPEFSLAPVAKRLSELLG------KEVKFVDDCIGEEARE--------AIAA 102 (389) T ss_pred HHHHHHHHHCCCeEEE--EEecCCCCCCCCCcCHHHHHHHHHHHhC------CCeEECCCCCCHHHHH--------HHhc Confidence 4799999999998765 5886632 11222222334455555 7788888888887662 1234 Q ss_pred eeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCC Q psy254 126 LVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDG 171 (187) Q Consensus 126 l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG 171 (187) |++|+.+.|-.=.-|..+.. +.+.|.+.+.+---||++|. T Consensus 103 l~~G~ilLLEN~Rf~~~E~~------~d~~~a~~LA~l~DiyVNDA 142 (389) T PRK00073 103 LKDGEVLLLENVRFNKGEEK------NDPELAKKLASLGDVFVNDA 142 (389) T ss_pred CCCCcEEEEeccCcCccccc------CHHHHHHHHHHhCCEEEECc Confidence 66777666543222211111 34678888888777999884 No 161 >PRK06256 biotin synthase; Validated Probab=36.88 E-value=90 Score=26.85 Aligned_cols=29 Identities=21% Similarity=0.362 Sum_probs=22.4 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEec Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNF 68 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~ 68 (187) ++.+++|. -+.+.++.|.++|++..=+|+ T Consensus 142 ~~~~~~g~--l~~e~l~~LkeaG~~~v~~~l 170 (336) T PRK06256 142 EICACLGL--LTEEQAERLKEAGVDRYNHNL 170 (336) T ss_pred cEEecCCc--CCHHHHHHHHHhCCCEEecCC Confidence 56677775 678999999999998665544 No 162 >PRK09289 riboflavin synthase subunit alpha; Provisional Probab=36.80 E-value=77 Score=25.62 Aligned_cols=35 Identities=23% Similarity=0.290 Sum_probs=27.0 Q ss_pred EEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeCCe Q psy254 148 DLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVKSY 184 (187) Q Consensus 148 ~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~ 184 (187) .+.+..|..+..+++|+.|-+|. ++|+|.++++++ T Consensus 23 ~~~i~~~~~~~~l~~g~SIAvnG--vcLTV~~~~~~~ 57 (194) T PRK09289 23 RLTIEAGKLLSDLKLGDSIAVNG--VCLTVTEIDGDS 57 (194) T ss_pred EEEEEcCccccccccCCEEEEcc--EEEEEEEEcCCE Confidence 45555555566699999999986 799999997765 No 163 >COG0826 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones] Probab=36.63 E-value=96 Score=27.47 Aligned_cols=44 Identities=25% Similarity=0.397 Sum_probs=39.0 Q ss_pred CCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 48 VAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 48 ~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .-.+.|.+|+++|++.++|.=---+.++..+..+-.|++..... T Consensus 230 ~~~~~l~~L~~~GV~s~KIeGR~k~~~yv~~v~~~yr~aid~~~ 273 (347) T COG0826 230 NLLEELPELIEAGVDSLKIEGRMKSIEYVARVVKAYRQAIDAAE 273 (347) T ss_pred hhHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHHHHHHHHh Confidence 34689999999999999999999999999999999999887543 No 164 >PTZ00314 inosine-5'-monophosphate dehydrogenase; Provisional Probab=36.55 E-value=1e+02 Score=28.51 Aligned_cols=53 Identities=19% Similarity=0.339 Sum_probs=34.9 Q ss_pred CceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHH----------HHHHHHHHHHHHHHhC Q psy254 36 LTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEY----------HGQTIKNIRQAVENYS 91 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~----------~~~~i~~ir~a~~~~~ 91 (187) ...|+| | .-.+.+..+.++++|++.+++-...|+... ....+..++++.++++ T Consensus 282 ~~~v~a--G-~V~t~~~a~~~~~aGad~I~vg~g~Gs~~~t~~~~~~g~p~~~ai~~~~~~~~~~~ 344 (495) T PTZ00314 282 HVDIIA--G-NVVTADQAKNLIDAGADGLRIGMGSGSICITQEVCAVGRPQASAVYHVARYARERG 344 (495) T ss_pred CceEEE--C-CcCCHHHHHHHHHcCCCEEEECCcCCcccccchhccCCCChHHHHHHHHHHHhhcC Confidence 357777 3 346789999999999999988665553211 1234556666666544 No 165 >PRK14456 ribosomal RNA large subunit methyltransferase N; Provisional Probab=36.54 E-value=1.1e+02 Score=27.29 Aligned_cols=35 Identities=23% Similarity=0.466 Sum_probs=22.3 Q ss_pred EEecCCCCCCHHHHHHHHHhcCcEEEEecC-CC-CHHHHHHH Q psy254 40 ICTIGPASVAVDMLEKIIETGMNIARLNFS-HG-SYEYHGQT 79 (187) Q Consensus 40 i~TiGPas~~~~~i~~li~aGm~v~RiN~s-Hg-~~e~~~~~ 79 (187) +.|.|. .+.+++|.++|.+ .+||+| |+ +.+.+.++ T Consensus 215 isT~Gl----~~~i~~L~~~gl~-~~LaiSL~a~~~e~r~~i 251 (368) T PRK14456 215 ISTVGI----TPEIDRLATSGLK-TKLAVSLHSADQEKRERL 251 (368) T ss_pred EECCCC----hHHHHHHHHcCCC-ceEEEEecCCCHHHHHHh Confidence 667773 3568999999987 456666 55 34443333 No 166 >TIGR03424 urea_degr_1 urea carboxylase-associated protein 1. A number of bacteria degrade urea as a nitrogen source by the urea carboxylase/allophanate hydrolase pathway, which uses biotin and consumes ATP, rather than my means of the nickel-dependent enzyme urease. This model represents one of a pair of homologous, tandem uncharacterized genes found together with the urea carboxylase and allophanate hydrolase genes. Probab=36.31 E-value=1.4e+02 Score=24.41 Aligned_cols=59 Identities=15% Similarity=0.165 Sum_probs=34.7 Q ss_pred cccEEeeeCCEEEEeeCCCccc-------CCC-cCEEeeCc--chh-hhcCCCCCEEEEeCCeEEEEEEE Q psy254 121 SAEVELVKGQTIRLTTDAAFAE-------KGS-ATDLYVDY--TNI-TKVVKPGSRIFVDDGLISLVVKS 179 (187) Q Consensus 121 ~~~i~l~~G~~v~lt~~~~~~~-------~~~-~~~i~v~~--~~l-~~~v~~Gd~IlidDG~i~l~V~~ 179 (187) .....|++|+.++|+.-+..+. ..+ .+..+... +.. -..+.+|+.++=+.|+.-++|.+ T Consensus 13 ~~a~~v~~Gq~lri~d~~G~q~~d~~~~na~d~~Er~~~~~T~~~~~~~~l~~G~~l~S~~~rpm~tIve 82 (198) T TIGR03424 13 PWSAVVKAGQTLRIVDLEGNQAVDTLFYNAHDTAERYSAQDTIRAQGNIYLTTGSVLYSNEGNPMLTIVA 82 (198) T ss_pred ceEEEECCCCEEEEEeCCCCeEEEEEEecCCCCccccCHHHHHHHhCcccccCCCEEEeCCCCeeEEEEc Confidence 4567889999999875322100 011 11121110 011 12578999999999999888865 No 167 >PRK14113 urease accessory protein UreE; Provisional Probab=36.09 E-value=1e+02 Score=24.06 Aligned_cols=25 Identities=16% Similarity=0.110 Sum_probs=18.8 Q ss_pred EEeeCcchhhhcCCCCCEEEEeCCeE Q psy254 148 DLYVDYTNITKVVKPGSRIFVDDGLI 173 (187) Q Consensus 148 ~i~v~~~~l~~~v~~Gd~IlidDG~i 173 (187) .+.+..+. -..|..||.++.|||.+ T Consensus 40 e~~l~L~r-~~~L~dGD~L~~ddg~~ 64 (152) T PRK14113 40 EIGVFLER-GHPLLVGEILKTECGKI 64 (152) T ss_pred EEEEECCC-CcccCCCCEEEcCCCCE Confidence 35555555 34799999999999976 No 168 >PTZ00413 lipoate synthase; Provisional Probab=35.89 E-value=1.2e+02 Score=27.60 Aligned_cols=54 Identities=13% Similarity=0.081 Sum_probs=35.6 Q ss_pred CceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCC---------CHHHHHHHHHHHHHHHHH Q psy254 36 LTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHG---------SYEYHGQTIKNIRQAVEN 89 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg---------~~e~~~~~i~~ir~a~~~ 89 (187) .++|=|.+|.-.-+.+.++.|.+||++++=.|+--. +...|.+.++.|+.+.+. T Consensus 228 ~~~IevligDf~g~~e~l~~L~eAG~dvynHNLETv~rLyp~VRt~~atYe~sLe~Lr~AKe~ 290 (398) T PTZ00413 228 ELLLEALVGDFHGDLKSVEKLANSPLSVYAHNIECVERITPYVRDRRASYRQSLKVLEHVKEF 290 (398) T ss_pred CCeEEEcCCccccCHHHHHHHHhcCCCEEecccccCHhHHHHHccCcCCHHHHHHHHHHHHHH Confidence 456777777555578999999999999988884221 112455555566655443 No 169 >PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A .... Probab=35.33 E-value=1.2e+02 Score=25.51 Aligned_cols=63 Identities=13% Similarity=0.120 Sum_probs=42.7 Q ss_pred CCceEEEecCCCC--CCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEE Q psy254 35 RLTGIICTIGPAS--VAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIA 103 (187) Q Consensus 35 r~TkIi~TiGPas--~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~ 103 (187) .++.+|+.+|..+ +..+..+..-++|++.+-+-.-+-..-...++++..++.++..+ .|+-++ T Consensus 69 ~~~~vi~gv~~~st~~~i~~a~~a~~~Gad~v~v~~P~~~~~s~~~l~~y~~~ia~~~~------~pi~iY 133 (289) T PF00701_consen 69 GRVPVIAGVGANSTEEAIELARHAQDAGADAVLVIPPYYFKPSQEELIDYFRAIADATD------LPIIIY 133 (289) T ss_dssp TSSEEEEEEESSSHHHHHHHHHHHHHTT-SEEEEEESTSSSCCHHHHHHHHHHHHHHSS------SEEEEE T ss_pred CceEEEecCcchhHHHHHHHHHHHhhcCceEEEEeccccccchhhHHHHHHHHHHhhcC------CCEEEE Confidence 4577888887644 45688888999999988766444333345567888888877665 566654 No 170 >PRK08599 coproporphyrinogen III oxidase; Provisional Probab=34.74 E-value=2.9e+02 Score=24.12 Aligned_cols=40 Identities=15% Similarity=0.213 Sum_probs=31.3 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHH Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYH 76 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~ 76 (187) +.|-+..-|.+-+.+.++.|.++|++.+-|..=.++.+.. T Consensus 87 ~eit~e~~p~~l~~e~l~~l~~~G~~rvsiGvqS~~~~~l 126 (377) T PRK08599 87 EEFTFEANPGDLTKEKLQVLKDSGVNRISLGVQTFNDELL 126 (377) T ss_pred CEEEEEeCCCCCCHHHHHHHHHcCCCEEEEecccCCHHHH Confidence 4677777898889999999999999866666666665544 No 171 >cd04739 DHOD_like Dihydroorotate dehydrogenase (DHOD) like proteins. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. This subgroup has the conserved FMN binding site, but lacks some catalytic residues and may therefore be inactive. Probab=34.56 E-value=1.2e+02 Score=26.28 Aligned_cols=35 Identities=26% Similarity=0.344 Sum_probs=24.7 Q ss_pred CceEEEecCCCCCC--HHHHHHHHHhcCcEEEEecCC Q psy254 36 LTGIICTIGPASVA--VDMLEKIIETGMNIARLNFSH 70 (187) Q Consensus 36 ~TkIi~TiGPas~~--~~~i~~li~aGm~v~RiN~sH 70 (187) .+.+++.|.-.+.+ .+..+.+-++|.+.+=||+|| T Consensus 99 ~~pvi~si~g~~~~~~~~~a~~~~~~gad~iElN~s~ 135 (325) T cd04739 99 SIPVIASLNGVSAGGWVDYARQIEEAGADALELNIYA 135 (325) T ss_pred CCeEEEEeCCCCHHHHHHHHHHHHhcCCCEEEEeCCC Confidence 35689999433322 255566667899999999996 No 172 >TIGR01036 pyrD_sub2 dihydroorotate dehydrogenase, subfamily 2. The subfamilies 1 and 2 share extensive homology, particularly toward the C-terminus. This subfamily has a longer N-terminal region. Probab=34.43 E-value=3.2e+02 Score=23.89 Aligned_cols=68 Identities=15% Similarity=0.141 Sum_probs=39.8 Q ss_pred CceEEEecCCCC-----CC-HHHHHHHHHhc--CcEEEEecC--CC-------CHHHHHHHHHHHHHHHHHhCCCCCCcc Q psy254 36 LTGIICTIGPAS-----VA-VDMLEKIIETG--MNIARLNFS--HG-------SYEYHGQTIKNIRQAVENYSKRIGMPH 98 (187) Q Consensus 36 ~TkIi~TiGPas-----~~-~~~i~~li~aG--m~v~RiN~s--Hg-------~~e~~~~~i~~ir~a~~~~~~~~~~~~ 98 (187) .+.|++++|-.. .+ .+..+.+-+++ ++.+=||+| |. ..+...++++.+|++....... . T Consensus 134 ~~~i~vsi~~~~~~~~~~~~~dy~~~~~~~~~~ad~iElNlScPn~~~~~~~~~~~~~~~i~~~V~~~~~~~~~~----~ 209 (335) T TIGR01036 134 KGPIGINIGKNKDTPSEDAKEDYAACLRKLGPLADYLVVNVSSPNTPGLRDLQYKAELRDLLTAVKQEQDGLRRV----H 209 (335) T ss_pred CCcEEEEEeCCCCCCcccCHHHHHHHHHHHhhhCCEEEEEccCCCCCCcccccCHHHHHHHHHHHHHHHHhhhhc----c Confidence 457889886432 11 23333333344 999999998 22 4567778888888776532211 1 Q ss_pred eeEEEeeCC Q psy254 99 ALAIALDTK 107 (187) Q Consensus 99 ~v~I~~Dl~ 107 (187) .++|++-|. T Consensus 210 ~~Pv~vKLs 218 (335) T TIGR01036 210 RVPVLVKIA 218 (335) T ss_pred CCceEEEeC Confidence 256666654 No 173 >cd03327 MR_like_2 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 2. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. This subgroup's function is unknown. Probab=34.42 E-value=1.5e+02 Score=25.66 Aligned_cols=67 Identities=12% Similarity=0.062 Sum_probs=40.9 Q ss_pred CceEEEecCCCCCC---HHHHHHHHHhcCcEEEEecCCCC---HHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 36 LTGIICTIGPASVA---VDMLEKIIETGMNIARLNFSHGS---YEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 36 ~TkIi~TiGPas~~---~~~i~~li~aGm~v~RiN~sHg~---~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) +....+|.+..... .+..+++++.|-+.+.+.+.++. .+...+-++.++.+.+..| .-+.+++|--+ T Consensus 108 ~i~~y~~~~~~~~~~~~~~~a~~~~~~Gf~~~Kikvg~~~~~~~~~~~~d~~~v~avr~~~g------~~~~l~vDan~ 180 (341) T cd03327 108 KIPAYASGLYPTDLDELPDEAKEYLKEGYRGMKMRFGYGPSDGHAGLRKNVELVRAIREAVG------YDVDLMLDCYM 180 (341) T ss_pred ceEEEEECCCCCCHHHHHHHHHHHHHcCCCEEEECCCCCCCcchHHHHHHHHHHHHHHHHhC------CCCcEEEECCC Confidence 44555564322211 24566788899999999875432 2334455666666656666 44789999765 No 174 >PF01116 F_bP_aldolase: Fructose-bisphosphate aldolase class-II; InterPro: IPR000771 Fructose-bisphosphate aldolase [, ] is a glycolytic enzyme that catalyses the reversible aldol cleavage or condensation of fructose-1,6-bisphosphate into dihydroxyacetone-phosphate and glyceraldehyde 3-phosphate. There are two classes of fructose-bisphosphate aldolases with different catalytic mechanisms. Class-II aldolases [], mainly found in prokaryotes and fungi, are homodimeric enzymes, which require a divalent metal ion, generally zinc, for their activity. This family also includes the Escherichia coli galactitol operon protein, gatY, which catalyses the transformation of tagatose 1,6-bisphosphate into glycerone phosphate and D-glyceraldehyde 3-phosphate; and E. coli N-acetyl galactosamine operon protein, agaY, which catalyses the same reaction. There are two histidine residues in the first half of the sequence of these enzymes that have been shown to be involved in binding a zinc ion [].; GO: 0008270 zinc ion binding, 0016832 aldehyde-lyase activity, 0005975 carbohydrate metabolic process; PDB: 3Q94_A 1RVG_B 1RV8_C 3C4U_A 3C56_B 3C52_A 2FJK_A 3N9R_P 3N9S_A 1GVF_B .... Probab=34.40 E-value=1.8e+02 Score=24.92 Aligned_cols=54 Identities=9% Similarity=0.175 Sum_probs=41.6 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) +.|..-+ ..+.+.+.+++-+++|.+-..|.-||-+.++.-+.-..+-+.+..+| T Consensus 74 vPValHL-DH~~~~e~i~~ai~~GftSVM~DgS~l~~eeNi~~T~~vv~~ah~~g 127 (287) T PF01116_consen 74 VPVALHL-DHGKDFEDIKRAIDAGFTSVMIDGSALPFEENIAITREVVEYAHAYG 127 (287) T ss_dssp SEEEEEE-EEE-SHHHHHHHHHHTSSEEEEE-TTS-HHHHHHHHHHHHHHHHHTT T ss_pred CCEEeec-ccCCCHHHHHHHHHhCcccccccCCcCCHHHHHHHHHHHHHhhhhhC Confidence 4566655 66678999999999999999999999999987777777777777666 No 175 >cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family. Probab=34.32 E-value=1.3e+02 Score=25.06 Aligned_cols=65 Identities=9% Similarity=0.117 Sum_probs=44.1 Q ss_pred CceEEEecCCCCC--CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC Q psy254 36 LTGIICTIGPASV--AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK 107 (187) Q Consensus 36 ~TkIi~TiGPas~--~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~ 107 (187) +..||+.+|..+. ..+..+..-++|++.+-+-.-+-.......+++..++..+..+ .|+-|+ +.+ T Consensus 66 ~~~vi~gv~~~~~~~~i~~a~~a~~~Gad~v~v~pP~y~~~~~~~~~~~~~~ia~~~~------~pi~iY-n~P 132 (281) T cd00408 66 RVPVIAGVGANSTREAIELARHAEEAGADGVLVVPPYYNKPSQEGIVAHFKAVADASD------LPVILY-NIP 132 (281) T ss_pred CCeEEEecCCccHHHHHHHHHHHHHcCCCEEEECCCcCCCCCHHHHHHHHHHHHhcCC------CCEEEE-ECc Confidence 5678888877543 4566777888899988876654444345677777777777655 566554 444 No 176 >PF13378 MR_MLE_C: Enolase C-terminal domain-like; PDB: 3FCP_B 3P0W_D 3VFC_A 3VDG_A 3FJ4_B 3CT2_B 3DGB_A 3V3W_A 3V4B_A 3NO1_E .... Probab=34.15 E-value=95 Score=21.91 Aligned_cols=41 Identities=15% Similarity=0.290 Sum_probs=31.9 Q ss_pred CCCCCCHHHHHHHHHhc-CcEEEEecCC-CCHHHHHHHHHHHH Q psy254 44 GPASVAVDMLEKIIETG-MNIARLNFSH-GSYEYHGQTIKNIR 84 (187) Q Consensus 44 GPas~~~~~i~~li~aG-m~v~RiN~sH-g~~e~~~~~i~~ir 84 (187) |.+..+...+++|+++| ++++++..++ |...+..++++..+ T Consensus 1 gE~~~~~~~~~~li~~~a~d~~~~~~~~~GGit~~~~i~~~A~ 43 (111) T PF13378_consen 1 GESLFSLHDFRRLIEAGAVDIVQIDPTRCGGITEALRIAALAE 43 (111) T ss_dssp STTSSSHHHHHHHHHTTSCSEEEEBHHHHTSHHHHHHHHHHHH T ss_pred CCCCCCHHHHHHHHHcCCCCEEEeCchhcCCHHHHHHHHHHHH Confidence 44567888999999998 7999999887 67877776665443 No 177 >PRK05892 nucleoside diphosphate kinase regulator; Provisional Probab=34.08 E-value=2.3e+02 Score=22.11 Aligned_cols=73 Identities=11% Similarity=0.102 Sum_probs=42.8 Q ss_pred eCCCCeeEeeecCCCCcccEEeeeCCEEEEeeCCCcccC---CCcCEEeeCcc--hhhhcCCCCCEEEEe--CCeEEEEE Q psy254 105 DTKGPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAFAEK---GSATDLYVDYT--NITKVVKPGSRIFVD--DGLISLVV 177 (187) Q Consensus 105 Dl~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~---~~~~~i~v~~~--~l~~~v~~Gd~Ilid--DG~i~l~V 177 (187) +....+++.|..- .+....|+..+++.-...... .+...|++..| .-+-.-++||.|-+. +|...++| T Consensus 77 ~~~~~~V~~Gs~V-----tl~~~~g~~~~~~IVg~~e~d~~~~~~~~IS~~SPlG~ALlGk~vGD~v~v~~p~g~~~~eI 151 (158) T PRK05892 77 WSGSETLPGGTEV-----TLRFPDGEVETMHVISVVEETPVGREAETLTADSPLGQALAGHQAGDTVTYSTPQGPAQVEL 151 (158) T ss_pred cCCCCEEEcCcEE-----EEEECCCCEEEEEEeCchhcCcccccCCEEccCCHHHHHHhCCCCCCEEEEEcCCCcEEEEE Confidence 5566678877653 233344565544322111011 12446776654 223466999999885 78899999 Q ss_pred EEEeC Q psy254 178 KSIVK 182 (187) Q Consensus 178 ~~v~~ 182 (187) .+|.. T Consensus 152 ~~I~~ 156 (158) T PRK05892 152 LAVKL 156 (158) T ss_pred EEEEc Confidence 98864 No 178 >cd00740 MeTr MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent methyltransferases catalyze the transfer of a methyl group via a methyl- cob(III)amide intermediate. These include MeTr, a functional heterodimer, and the folate binding domain of MetH. Probab=33.87 E-value=96 Score=26.04 Aligned_cols=57 Identities=19% Similarity=0.276 Sum_probs=37.0 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHH---HHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEeeecC Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYE---YHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTGLLQ 117 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e---~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG~~~ 117 (187) .+..++|+++|+++.=+|+.-+..+ ++.+++..+++. ..++|.+|+.=|++.--.++ T Consensus 29 ~~~A~~~~~~GAdiIDIG~~~~~~~~~ee~~r~v~~i~~~-----------~~~piSIDT~~~~v~e~aL~ 88 (252) T cd00740 29 LDVARQQVEGGAQILDLNVDYGGLDGVSAMKWLLNLLATE-----------PTVPLMLDSTNWEVIEAGLK 88 (252) T ss_pred HHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHHHh-----------cCCcEEeeCCcHHHHHHHHh Confidence 3667788999999999999655433 333333333322 24678999988887654443 No 179 >cd00331 IGPS Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the release of carbon dioxide and water. IGPS is active as a separate monomer in most organisms, but is also found fused to other enzymes as part of a bifunctional or multifunctional enzyme involved in tryptophan biosynthesis. Probab=33.60 E-value=1e+02 Score=24.70 Aligned_cols=51 Identities=16% Similarity=0.221 Sum_probs=36.1 Q ss_pred CceEEEecCCCCCC----------HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 36 LTGIICTIGPASVA----------VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 36 ~TkIi~TiGPas~~----------~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) +..||+-+=++|-+ .+.-+.+.++|.+..|++.-.+......+.+..||+. T Consensus 10 ~~~vIae~k~~sp~~~~~~~~~~~~~~A~~~~~~GA~~l~v~~~~~~~~g~~~~~~~i~~~ 70 (217) T cd00331 10 GLGVIAEVKRASPSKGLIREDFDPVEIAKAYEKAGAAAISVLTEPKYFQGSLEDLRAVREA 70 (217) T ss_pred CceEEEEecCCCCCCCcCCCCCCHHHHHHHHHHcCCCEEEEEeCccccCCCHHHHHHHHHh Confidence 46788888665543 3777889999999999996655555455566666654 No 180 >PRK04165 acetyl-CoA decarbonylase/synthase complex subunit gamma; Provisional Probab=33.58 E-value=2.4e+02 Score=26.03 Aligned_cols=69 Identities=19% Similarity=0.404 Sum_probs=47.2 Q ss_pred CCCCCCceEEEecCCCCCCHHHH----HHH-----HHhc----CcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCc Q psy254 31 SSYVRLTGIICTIGPASVAVDML----EKI-----IETG----MNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMP 97 (187) Q Consensus 31 ~~~~r~TkIi~TiGPas~~~~~i----~~l-----i~aG----m~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~ 97 (187) ..+..+++|.+.|-+. -+.+.+ +.+ .+.| +|++-|.+.-++++.....++.++++ .+ T Consensus 86 ~tf~np~~Ia~eI~D~-l~~e~i~~r~~~~~~~~~~rvG~~~~AD~IaL~~~s~dp~~v~~~Vk~V~~~---~d------ 155 (450) T PRK04165 86 KTFFNPTGIAVDVSDT-MDDEEIDARLKKINNFQFERVGEILKLDMVALRNASGDPEKFAKAVKKVAET---TD------ 155 (450) T ss_pred cCCCCCCEEEEEEeCC-CChHHHHHHHHHhhcchHhhhcccccCCEEEEeCCCCCHHHHHHHHHHHHHh---cC------ Confidence 3456788999999443 233333 333 5678 99999999888888777777666643 23 Q ss_pred ceeEEEeeCCCCee Q psy254 98 HALAIALDTKGPEI 111 (187) Q Consensus 98 ~~v~I~~Dl~GPkI 111 (187) +++.+|+.-|++ T Consensus 156 --vPLSIDT~dpev 167 (450) T PRK04165 156 --LPLILCSEDPAV 167 (450) T ss_pred --CCEEEeCCCHHH Confidence 567889876665 No 181 >PRK08433 flagellar motor switch protein; Validated Probab=33.56 E-value=1.8e+02 Score=21.56 Aligned_cols=67 Identities=18% Similarity=0.325 Sum_probs=44.9 Q ss_pred ceeEEEeeCCCCeeEeeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEE Q psy254 98 HALAIALDTKGPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVV 177 (187) Q Consensus 98 ~~v~I~~Dl~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V 177 (187) .||.+-+-|.-.++.+..+ +.|+.||.+.|... ..++-.++++-..++. ..+-.-+|+..++| T Consensus 32 v~VeV~v~LG~t~itl~dl-------L~Lq~GDVI~Ld~~-----~~e~v~v~V~g~~~f~-----G~~G~~~~k~AVrI 94 (111) T PRK08433 32 IEVDFSAELGTTQISLLEI-------LKFEKGSVIDLEKP-----AGESVELYINGRIIGK-----GEVMVYEKNLAIRI 94 (111) T ss_pred ceeEEEEEEecccccHHHH-------hCCCCCCEEEeCCC-----CCCCEEEEECCEEEEE-----EEEEEECCEEEEEE Confidence 6778877777777777666 56999999988543 2233346776444443 33444578999998 Q ss_pred EEEe Q psy254 178 KSIV 181 (187) Q Consensus 178 ~~v~ 181 (187) .++- T Consensus 95 ~e~i 98 (111) T PRK08433 95 NEIL 98 (111) T ss_pred EEec Confidence 8863 No 182 >PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed Probab=33.38 E-value=1.2e+02 Score=27.17 Aligned_cols=51 Identities=14% Similarity=0.259 Sum_probs=36.3 Q ss_pred CceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 36 LTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) ...+||-| .-++...-+-+++|++..|||=-.- ..+.+.+..+=+++++.+ T Consensus 80 ~iPlvADI---HFd~~lAl~a~~~G~~~iRINPGNi--g~~~~~v~~vv~~ak~~~ 130 (360) T PRK00366 80 PVPLVADI---HFDYRLALAAAEAGADALRINPGNI--GKRDERVREVVEAAKDYG 130 (360) T ss_pred CCCEEEec---CCCHHHHHHHHHhCCCEEEECCCCC--CchHHHHHHHHHHHHHCC Confidence 34567765 5678888899999999999996544 444455566666667765 No 183 >PRK01261 aroD 3-dehydroquinate dehydratase; Provisional Probab=33.34 E-value=1.7e+02 Score=24.21 Aligned_cols=52 Identities=17% Similarity=0.144 Sum_probs=32.9 Q ss_pred CCCCceEEEecCCCCCCHHHHH---HHHHhcCcE--EEEecCCC-CHHHHHHHHHHHHH Q psy254 33 YVRLTGIICTIGPASVAVDMLE---KIIETGMNI--ARLNFSHG-SYEYHGQTIKNIRQ 85 (187) Q Consensus 33 ~~r~TkIi~TiGPas~~~~~i~---~li~aGm~v--~RiN~sHg-~~e~~~~~i~~ir~ 85 (187) ...+++|++.| ++..-.+.+. .+...|+|+ +|+.+-+. +.+...+.+..+|+ T Consensus 17 g~~~p~Icvpi-~~~~~ee~~~~~~~~~~~~aDivE~RlD~l~~~~~~~~~~~~~~l~~ 74 (229) T PRK01261 17 GNMQPIVVESI-FFKDIKEMKERFKTKVLSDKNLYEIRFDLFHDHSIESEPEIISALNE 74 (229) T ss_pred CCCCcEEEEEe-CCCCHHHHHHHHHHhhcCCCCEEEEEeeccCCCChHHHHHHHHHHhh Confidence 34568999999 3333344443 455578999 89998866 34445555555543 No 184 >COG2450 Uncharacterized conserved protein [Function unknown] Probab=33.31 E-value=1.4e+02 Score=22.62 Aligned_cols=58 Identities=14% Similarity=0.184 Sum_probs=43.0 Q ss_pred CCCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCC--CHHHHHHHHHHHHHHHHHhCC Q psy254 33 YVRLTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHG--SYEYHGQTIKNIRQAVENYSK 92 (187) Q Consensus 33 ~~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg--~~e~~~~~i~~ir~a~~~~~~ 92 (187) ....+-++|.+ -.-.+...+.+.+-+| |+.-...+-- ..+.+.++++.+|+.++++|. T Consensus 38 ~~~~~Ikvaei-~~~~Dl~~~~~eiy~G-NIvIaDit~l~~d~~~~~~V~e~lr~~a~~~gg 97 (124) T COG2450 38 EAKVYIKVAEI-SSYEDLEEAKREIYAG-NIVIADITPLERDDDLFERVIEELRDTAEEVGG 97 (124) T ss_pred CCeEEEEEEEe-CCHHHHHHHHHHHhcC-CEEEEEcCCcccChhHHHHHHHHHHHHHHHhCc Confidence 34455677887 2334567778888899 8776655532 688899999999999999883 No 185 >cd02932 OYE_YqiM_FMN Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent. The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs. Probab=32.96 E-value=1.7e+02 Score=25.22 Aligned_cols=19 Identities=21% Similarity=0.635 Sum_probs=15.7 Q ss_pred HHHHHhcCcEEEEecCCCC Q psy254 54 EKIIETGMNIARLNFSHGS 72 (187) Q Consensus 54 ~~li~aGm~v~RiN~sHg~ 72 (187) +...++|.|.+=||++||. T Consensus 161 ~~a~~aGfDgVei~~~~gy 179 (336) T cd02932 161 RRAVEAGFDVIEIHAAHGY 179 (336) T ss_pred HHHHHcCCCEEEEcccccc Confidence 4556799999999999963 No 186 >PRK12290 thiE thiamine-phosphate pyrophosphorylase; Reviewed Probab=32.94 E-value=1.5e+02 Score=27.21 Aligned_cols=43 Identities=19% Similarity=0.279 Sum_probs=39.0 Q ss_pred CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 49 AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 49 ~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) +.+.+++++++|++++-+..-+.+.++..+.+..++++.+.++ T Consensus 219 ~~~~ve~aL~aGv~~VQLReK~ls~~el~~la~~l~~l~~~~g 261 (437) T PRK12290 219 DVEWIERLLPLGINTVQLRIKDPQQADLEQQIIRAIALGREYN 261 (437) T ss_pred CHHHHHHHHhCCCCEEEEeCCCCCHHHHHHHHHHHHHHHHHhC Confidence 3578999999999999999999999999999999999988876 No 187 >PRK15447 putative protease; Provisional Probab=32.89 E-value=91 Score=26.78 Aligned_cols=36 Identities=14% Similarity=0.227 Sum_probs=27.4 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHH Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVE 88 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~ 88 (187) .+.+.+|+++|++.+||.+.. ++..+++...|++.. T Consensus 230 l~~l~eL~~~Gv~~~RIe~~~---~~v~~vv~~Yr~~ld 265 (301) T PRK15447 230 LNELPSMQALGVDVVRLSPQS---TDMVAVADAFRAVLN 265 (301) T ss_pred HHHHHHHHHhCCCEEEEcCCc---chHHHHHHHHHHHHc Confidence 478999999999999999863 355666666666543 No 188 >cd02803 OYE_like_FMN_family Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase. Probab=32.55 E-value=1.6e+02 Score=25.06 Aligned_cols=19 Identities=21% Similarity=0.377 Sum_probs=15.5 Q ss_pred HHHHHhcCcEEEEecCCCC Q psy254 54 EKIIETGMNIARLNFSHGS 72 (187) Q Consensus 54 ~~li~aGm~v~RiN~sHg~ 72 (187) +.+.++|.|.+=||++||. T Consensus 148 ~~a~~aGfDgveih~~~gy 166 (327) T cd02803 148 RRAKEAGFDGVEIHGAHGY 166 (327) T ss_pred HHHHHcCCCEEEEcchhhh Confidence 3456789999999999974 No 189 >PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional Probab=32.50 E-value=76 Score=23.79 Aligned_cols=32 Identities=9% Similarity=0.143 Sum_probs=24.2 Q ss_pred EeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeC Q psy254 149 LYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVK 182 (187) Q Consensus 149 i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~ 182 (187) +..+..++...+++||.+.||+= ...|+.|++ T Consensus 41 vih~~~~~~~~i~~Gd~l~i~~~--~Y~ItaVG~ 72 (120) T PRK10377 41 FIHCHGELKGALQPGLQFELGQH--RYPVTAVGS 72 (120) T ss_pred EEEEcCcccCccCCCCEEEECCE--EEEEEEEhH Confidence 33455688889999999999884 677777753 No 190 >PRK06939 2-amino-3-ketobutyrate coenzyme A ligase; Provisional Probab=32.42 E-value=1.2e+02 Score=26.08 Aligned_cols=44 Identities=16% Similarity=0.286 Sum_probs=34.2 Q ss_pred CCHHHHHHHHHhcCc--------------EEEEecCC-CCHHHHHHHHHHHHHHHHHhC Q psy254 48 VAVDMLEKIIETGMN--------------IARLNFSH-GSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 48 ~~~~~i~~li~aGm~--------------v~RiN~sH-g~~e~~~~~i~~ir~a~~~~~ 91 (187) .+.+..+.|.+.|+- .+||.|++ -+.++..+.++.++++.++.+ T Consensus 337 ~~~~~~~~L~~~gI~v~~~~~~~~~~~~~~iRi~~~~~~~~~~i~~~l~~L~~~~~~~~ 395 (397) T PRK06939 337 LAQEFADRLLEEGVYVIGFSFPVVPKGQARIRTQMSAAHTKEQLDRAIDAFEKVGKELG 395 (397) T ss_pred HHHHHHHHHHHCCceEeeeCCCCCCCCCceEEEEECCCCCHHHHHHHHHHHHHHHHHhC Confidence 345677888888864 36888876 678899999999998887765 No 191 >PRK08508 biotin synthase; Provisional Probab=32.33 E-value=1.4e+02 Score=25.23 Aligned_cols=53 Identities=15% Similarity=0.184 Sum_probs=36.0 Q ss_pred CceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCC--------CCHHHHHHHHHHHHHHHHHhC Q psy254 36 LTGIICTIGPASVAVDMLEKIIETGMNIARLNFSH--------GSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sH--------g~~e~~~~~i~~ir~a~~~~~ 91 (187) ...+.++.|.. +.+.+++|.+||++.+-+|+-= .+...|.++++.++.+ ++.| T Consensus 90 ~l~i~~s~G~~--~~e~l~~Lk~aGld~~~~~lEt~~~~~~~i~~~~~~~~~l~~i~~a-~~~G 150 (279) T PRK08508 90 GLHLIACNGTA--SVEQLKELKKAGIFSYNHNLETSKEFFPKICTTHTWEERFQTCENA-KEAG 150 (279) T ss_pred CcEEEecCCCC--CHHHHHHHHHcCCCEEcccccchHHHhcCCCCCCCHHHHHHHHHHH-HHcC Confidence 34667787876 4899999999999887765221 1124567777777776 3444 No 192 >PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain Probab=32.24 E-value=1.8e+02 Score=20.52 Aligned_cols=30 Identities=30% Similarity=0.442 Sum_probs=23.5 Q ss_pred cchhh-hcCCCCCEEEEe--------CCeEEEEEEEEeC Q psy254 153 YTNIT-KVVKPGSRIFVD--------DGLISLVVKSIVK 182 (187) Q Consensus 153 ~~~l~-~~v~~Gd~Ilid--------DG~i~l~V~~v~~ 182 (187) +..+. ..++.|++|++- .|.++|.|.++++ T Consensus 61 ~~~i~~~~l~~G~~V~v~g~~~~y~~~G~~sl~v~~i~P 99 (99) T PF13742_consen 61 ARRIRGFDLKDGDKVLVRGRVSFYEPRGSLSLIVEDIDP 99 (99) T ss_pred HhhCCCCCCCCCCEEEEEEEEEEECCCcEEEEEEEEeEC Confidence 34444 678999999884 8999999998864 No 193 >PF13473 Cupredoxin_1: Cupredoxin-like domain; PDB: 1IBZ_D 1IC0_E 1IBY_D. Probab=32.23 E-value=68 Score=22.62 Aligned_cols=42 Identities=21% Similarity=0.393 Sum_probs=24.1 Q ss_pred ccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEE Q psy254 122 AEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRI 166 (187) Q Consensus 122 ~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~I 166 (187) ..+.+++|+.|+|+..+. ....+.+.++.-++-..+.+|+.. T Consensus 35 ~~i~v~~G~~v~l~~~N~---~~~~h~~~i~~~~~~~~l~~g~~~ 76 (104) T PF13473_consen 35 STITVKAGQPVTLTFTNN---DSRPHEFVIPDLGISKVLPPGETA 76 (104) T ss_dssp -EEEEETTCEEEEEEEE----SSS-EEEEEGGGTEEEEE-TT-EE T ss_pred CEEEEcCCCeEEEEEEEC---CCCcEEEEECCCceEEEECCCCEE Confidence 479999999777665432 112245666555555677888753 No 194 >COG4766 EutQ Ethanolamine utilization protein [Amino acid transport and metabolism] Probab=32.23 E-value=53 Score=26.04 Aligned_cols=29 Identities=34% Similarity=0.551 Sum_probs=20.6 Q ss_pred cccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcch Q psy254 121 SAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTN 155 (187) Q Consensus 121 ~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~ 155 (187) +..+.+-+|+.|.|++. +....+||.||. T Consensus 143 GDvifiPKgssIefst~------gea~flyvtyPa 171 (176) T COG4766 143 GDVIFIPKGSSIEFSTT------GEAKFLYVTYPA 171 (176) T ss_pred CcEEEecCCCeEEEecc------ceEEEEEEEccc Confidence 34566777888888764 335679999986 No 195 >PRK01261 aroD 3-dehydroquinate dehydratase; Provisional Probab=32.17 E-value=2.4e+02 Score=23.43 Aligned_cols=56 Identities=11% Similarity=0.080 Sum_probs=38.0 Q ss_pred CCCceEEEec-CCCCCC-HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHH Q psy254 34 VRLTGIICTI-GPASVA-VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVEN 89 (187) Q Consensus 34 ~r~TkIi~Ti-GPas~~-~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~ 89 (187) ...+|+|.+- -|+.++ .+.+.+|.+.|.|++-|-..-.+.++....+..+.+...+ T Consensus 117 ~~~~kvIvS~Htp~~eeL~~~l~~m~~~gaDI~KiAvmp~~~~Dvl~~l~~~~~~~~~ 174 (229) T PRK01261 117 PRNTMLMVSYHTNNSDNMPAILDIMNEKNPDYVKVACNYNDNKKFVDDLQYILMKKDE 174 (229) T ss_pred cCCCeEEEEeCCCCHHHHHHHHHHHHHhCCCEEEEEeCCCChHHHHHHHHHHHHHHhc Confidence 3578888876 553322 2677888999999999998777766655555555444333 No 196 >PF03610 EIIA-man: PTS system fructose IIA component; InterPro: IPR004701 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for IIA and IIB components.; GO: 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane; PDB: 3GDW_B 2JZN_A 1VSQ_A 2JZO_B 1VRC_A 1PDO_A 3GX1_A 3B48_B 3BED_B 3IPR_C .... Probab=32.17 E-value=1.7e+02 Score=20.95 Aligned_cols=65 Identities=20% Similarity=0.232 Sum_probs=38.2 Q ss_pred EEEecCCCCCCHHHHHHHHHhcC--cEEEEecCCC-CHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCe Q psy254 39 IICTIGPASVAVDMLEKIIETGM--NIARLNFSHG-SYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPE 110 (187) Q Consensus 39 Ii~TiGPas~~~~~i~~li~aGm--~v~RiN~sHg-~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPk 110 (187) |++|-|+-+.....--+|+..-. ++.=+.|..+ +.++. .+.++++.++.... -.+-|+.|+.|-- T Consensus 3 ii~sHG~~A~g~~~~~~~i~G~~~~~i~~~~~~~~~~~~~~---~~~l~~~i~~~~~~----~~vlil~Dl~ggs 70 (116) T PF03610_consen 3 IIASHGSLAEGLLESAEMILGEDQDNIEAVDLYPDESIEDF---EEKLEEAIEELDEG----DGVLILTDLGGGS 70 (116) T ss_dssp EEEEETTHHHHHHHHHHHHHTSTCSSEEEEEETTTSCHHHH---HHHHHHHHHHCCTT----SEEEEEESSTTSH T ss_pred EEEECcHHHHHHHHHHHHHcCCCcccEEEEECcCCCCHHHH---HHHHHHHHHhccCC----CcEEEEeeCCCCc Confidence 67888865544444444554443 6777887754 44443 34444444444311 5799999998853 No 197 >PRK15481 transcriptional regulatory protein PtsJ; Provisional Probab=32.02 E-value=1.6e+02 Score=26.06 Aligned_cols=48 Identities=10% Similarity=0.095 Sum_probs=34.2 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcC--------------cEEEEecCCCCHHHHHHHHHHHHHHH Q psy254 38 GIICTIGPASVAVDMLEKIIETGM--------------NIARLNFSHGSYEYHGQTIKNIRQAV 87 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm--------------~v~RiN~sHg~~e~~~~~i~~ir~a~ 87 (187) -+.+.+.+ .+.+..+.|.+.|+ +.+||+|++-+.++..+.++.++++. T Consensus 368 f~~~~l~~--~~~~~~~~l~~~gV~v~pg~~f~~~~~~~~iRis~~~~~~~~i~~~~~~l~~~~ 429 (431) T PRK15481 368 NLWLPLDT--DSQATALTLAKSGWLVREGEAFGVSAPSHGLRITLSTLNDAEINRLAADLHQAL 429 (431) T ss_pred EEEEECCC--CHHHHHHHHHHCCcEEecCCccccCCCCCeEEEEcCCCChHHHHHHHHHHHHHh Confidence 45555532 34566666766653 46899999999999999999888763 No 198 >PF03829 PTSIIA_gutA: PTS system glucitol/sorbitol-specific IIA component; InterPro: IPR004716 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The Man family is unique in several respects among PTS permease families: It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria. The system in Escherichia coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 2F9H_A. Probab=31.98 E-value=49 Score=24.68 Aligned_cols=32 Identities=9% Similarity=0.374 Sum_probs=18.5 Q ss_pred EeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeC Q psy254 149 LYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVK 182 (187) Q Consensus 149 i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~ 182 (187) +..+..++...+++||++.||+= ..+|+.|++ T Consensus 41 vih~~~~~~~~i~~Gd~l~i~~~--~y~ItaVG~ 72 (117) T PF03829_consen 41 VIHTFNELKGDIKPGDTLIIGGQ--EYTITAVGS 72 (117) T ss_dssp EEEE-TGGG----TT-EEEETTE--EEEEEEE-T T ss_pred EEEecCcccCCcCCCCEEEECCe--EEEEEEEhH Confidence 33444578899999999999874 677777764 No 199 >TIGR00048 radical SAM enzyme, Cfr family. A Staphylococcus sciuri plasmid-borne member of this family, Cfr, has been identified as essential to transferrable resistance to chloramphenicol and florfenicol by an unknown mechanism. A 14-15 residue cluster with four perfectly conserved Cys residues suggests this protein may be an enzyme with an iron-sulfur cluster. The Cys cluster is part of the radical SAM domain, suggested to provide a general mechanism by which the Fe-S center cleaves S-adenosylmethionine to initiate radical-based catalysis. Members of this family lack apparent transmembrane domains. Probab=31.89 E-value=2e+02 Score=25.43 Aligned_cols=36 Identities=14% Similarity=0.234 Sum_probs=25.8 Q ss_pred EEecCCCCCCHHHHHHHHHhcCcE-EEEecCCCCHHHHHHH Q psy254 40 ICTIGPASVAVDMLEKIIETGMNI-ARLNFSHGSYEYHGQT 79 (187) Q Consensus 40 i~TiGPas~~~~~i~~li~aGm~v-~RiN~sHg~~e~~~~~ 79 (187) |.|.|. ...+++|.++++++ ..+.+-+.+.+.+.++ T Consensus 196 isT~G~----~~~i~~l~~~~l~~~LaiSL~a~~~e~r~~l 232 (355) T TIGR00048 196 ISTSGV----VPKIDILADKMLQVALAISLHAPNDELRSSL 232 (355) T ss_pred EECCCc----hHHHHHHHHhCCCcEEEEEeCCCCHHHHHHh Confidence 666664 36899999999985 3567777777777554 No 200 >PRK08898 coproporphyrinogen III oxidase; Provisional Probab=31.82 E-value=2.1e+02 Score=25.41 Aligned_cols=66 Identities=11% Similarity=0.108 Sum_probs=44.7 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHH------------HHHHHHHHHHHHhCCCCCCcceeEEEe Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHG------------QTIKNIRQAVENYSKRIGMPHALAIAL 104 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~------------~~i~~ir~a~~~~~~~~~~~~~v~I~~ 104 (187) +.|-+-..|.+-+.+.++.|.++|+|.+-|..=-++.+... +.++.+|++ . ....+-+|. T Consensus 109 ~eit~E~~p~~~~~e~L~~l~~~GvnrisiGvQS~~~~~L~~l~R~~~~~~~~~~i~~~~~~----~----~~v~~dlI~ 180 (394) T PRK08898 109 AEITLEANPGTFEAEKFAQFRASGVNRLSIGIQSFNDAHLKALGRIHDGAEARAAIEIAAKH----F----DNFNLDLMY 180 (394) T ss_pred CeEEEEECCCCCCHHHHHHHHHcCCCeEEEecccCCHHHHHHhCCCCCHHHHHHHHHHHHHh----C----CceEEEEEc Confidence 45666668988899999999999999887776666655443 233333332 1 125677888 Q ss_pred eCCCCe Q psy254 105 DTKGPE 110 (187) Q Consensus 105 Dl~GPk 110 (187) .++|-. T Consensus 181 GlPgqt 186 (394) T PRK08898 181 ALPGQT 186 (394) T ss_pred CCCCCC Confidence 888754 No 201 >TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004). Probab=31.80 E-value=81 Score=25.06 Aligned_cols=24 Identities=29% Similarity=0.439 Sum_probs=19.1 Q ss_pred hhcCCCCCEEEEe--CCe-EEEEEEEE Q psy254 157 TKVVKPGSRIFVD--DGL-ISLVVKSI 180 (187) Q Consensus 157 ~~~v~~Gd~Ilid--DG~-i~l~V~~v 180 (187) +..|++||.|.+. ||. ..-+|.++ T Consensus 106 L~~L~~GD~I~v~~~~g~~~~Y~V~~~ 132 (174) T TIGR03784 106 LQELRPGDVIRLQTPDGQWQSYQVTAT 132 (174) T ss_pred hhhCCCCCEEEEEECCCeEEEEEEeEE Confidence 5789999999997 676 46788775 No 202 >PLN02898 HMP-P kinase/thiamin-monophosphate pyrophosphorylase Probab=31.73 E-value=1.7e+02 Score=26.85 Aligned_cols=42 Identities=21% Similarity=0.229 Sum_probs=36.8 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .+.+++++.+|+.++-|-.-+.+.++..+.+..+++..++++ T Consensus 310 ~~~l~~~l~~Gv~~vqlR~k~~~~~~~~~~a~~l~~~~~~~~ 351 (502) T PLN02898 310 VDAVRAAIEGGATIVQLREKEAETREFIEEAKACLAICRSYG 351 (502) T ss_pred HHHHHHHHHcCCCEEEEccCCCCHHHHHHHHHHHHHHHHHhC Confidence 468999999999999999888888888889989888887765 No 203 >PF03471 CorC_HlyC: Transporter associated domain; InterPro: IPR005170 This small domain is found in a family of proteins with the CBS IPR002550 from INTERPRO domain and two CBS domains with this domain found at the C terminus of the proteins, the domain is also found at the C terminus of some Na+/H+ antiporters. This domain is also found in CorC that is involved in Magnesium and cobalt efflux. The function of this domain is uncertain but might be involved in modulating transport of ion substrates.; PDB: 3DED_F 2PLI_C 2R2Z_A 2P4P_A 2O3G_A 2P3H_A 3LLB_A 3LAE_A 2P13_B 2NQW_A .... Probab=31.72 E-value=95 Score=20.91 Aligned_cols=29 Identities=10% Similarity=0.067 Sum_probs=22.7 Q ss_pred hcCCCCCEEEEeCCeEEEEEEEEeCCeee Q psy254 158 KVVKPGSRIFVDDGLISLVVKSIVKSYQL 186 (187) Q Consensus 158 ~~v~~Gd~IlidDG~i~l~V~~v~~~~i~ 186 (187) ..-++|+.+-++.+...++|.++++..+. T Consensus 45 ~iP~~Ge~~~i~~~~~~~~V~~~~~~rI~ 73 (81) T PF03471_consen 45 RIPEVGERVEIELENYEFEVLEMDGRRIR 73 (81) T ss_dssp SS--TTSEEEEEETTEEEEEEEEETTEEE T ss_pred CCCCCCeEEEEEcCCEEEEEEEeeCCEEE Confidence 44467999999988899999999988764 No 204 >KOG2792|consensus Probab=31.68 E-value=80 Score=27.15 Aligned_cols=43 Identities=12% Similarity=0.096 Sum_probs=35.7 Q ss_pred CcEEEEecCCCC---HHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeC Q psy254 61 MNIARLNFSHGS---YEYHGQTIKNIRQAVENYSKRIGMPHALAIALDT 106 (187) Q Consensus 61 m~v~RiN~sHg~---~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl 106 (187) ..+.=|-|+|.. ++|..+|...|.+.+.+.+-+. .|+.|.+|= T Consensus 141 w~LiYFGFThCPDICPdELeKm~~~Vd~i~~~~~~~~---~PlFIsvDP 186 (280) T KOG2792|consen 141 WSLIYFGFTHCPDICPDELEKMSAVVDEIEAKPGLPP---VPLFISVDP 186 (280) T ss_pred eEEEEecccCCCCcChHHHHHHHHHHHHHhccCCCCc---cceEEEeCc Confidence 567778999998 9999999999999988877443 578898884 No 205 >PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B. Probab=31.64 E-value=18 Score=25.18 Aligned_cols=30 Identities=20% Similarity=0.298 Sum_probs=2.6 Q ss_pred chhhhcCCCCCEEEEeCCeEEEEEEEEeCCe Q psy254 154 TNITKVVKPGSRIFVDDGLISLVVKSIVKSY 184 (187) Q Consensus 154 ~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~ 184 (187) .++.+.+++||+|..-.|-. -+|.++++|. T Consensus 31 ~~m~~~Lk~Gd~VvT~gGi~-G~V~~i~~~~ 60 (82) T PF02699_consen 31 QEMLASLKPGDEVVTIGGIY-GTVVEIDDDT 60 (82) T ss_dssp TTGGG-------------------------- T ss_pred HHHHHcCCCCCEEEECCcEE-EEEEEEeCCE Confidence 34556667777766665533 3344444443 No 206 >PRK14017 galactonate dehydratase; Provisional Probab=31.53 E-value=1.7e+02 Score=25.81 Aligned_cols=67 Identities=15% Similarity=0.194 Sum_probs=42.0 Q ss_pred CceEEEecCCCCC--CHHHHHHHHHhcCcEEEEecC-----CCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 36 LTGIICTIGPASV--AVDMLEKIIETGMNIARLNFS-----HGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 36 ~TkIi~TiGPas~--~~~~i~~li~aGm~v~RiN~s-----Hg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) +....+|+|..+. -.+.++++.+.|.+.+.+... .+.+....+-++.|+.+.+.++ .-+.+++|--+ T Consensus 113 ~i~~~~~~~~~~~~~~~~~a~~~~~~Gf~~~KiKv~~~~~~~~~~~~~~~d~~~i~avr~~~g------~~~~l~vDaN~ 186 (382) T PRK14017 113 RIRVYSWIGGDRPADVAEAARARVERGFTAVKMNGTEELQYIDSPRKVDAAVARVAAVREAVG------PEIGIGVDFHG 186 (382) T ss_pred eeeEeEeCCCCCHHHHHHHHHHHHHcCCCEEEEcCcCCccccccHHHHHHHHHHHHHHHHHhC------CCCeEEEECCC Confidence 3455566653221 125667788899999999762 1223445556667777667766 34688888765 No 207 >TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase. This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein. Probab=31.51 E-value=3.9e+02 Score=24.12 Aligned_cols=39 Identities=18% Similarity=0.296 Sum_probs=29.1 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHH Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYH 76 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~ 76 (187) .+-+..-|.+-+.+.++.|.++|++.+-|.+=..+.+.+ T Consensus 139 eitie~np~~l~~e~l~~lk~~G~~risiGvqS~~~~~l 177 (455) T TIGR00538 139 EISIEIDPRYITKDVIDALRDEGFNRLSFGVQDFNKEVQ 177 (455) T ss_pred eEEEEeccCcCCHHHHHHHHHcCCCEEEEcCCCCCHHHH Confidence 455556788889999999999999977666555555433 No 208 >PRK02615 thiamine-phosphate pyrophosphorylase; Provisional Probab=31.38 E-value=2.5e+02 Score=24.89 Aligned_cols=53 Identities=9% Similarity=0.253 Sum_probs=42.5 Q ss_pred EEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 39 IICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 39 Ii~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) +..-..|...-.+.+.+++.+|+..+-+..-+.+..+..+....+++..+.++ T Consensus 149 LylIT~~~~~ll~~l~~al~~Gv~~VQLR~K~~~~~~~~~~a~~L~~l~~~~~ 201 (347) T PRK02615 149 LYLITSPSENLLEVVEAALKGGVTLVQYRDKTADDRQRLEEAKKLKELCHRYG 201 (347) T ss_pred EEEEECCchhHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHHHHHHHhC Confidence 44433453223578999999999999999999999999999999999988876 No 209 >cd02810 DHOD_DHPD_FMN Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of Probab=31.35 E-value=1.6e+02 Score=24.57 Aligned_cols=51 Identities=25% Similarity=0.311 Sum_probs=34.3 Q ss_pred CceEEEecCCCC--CCHHHHHHHHHhcCcEEEEecCCC----------CHHHHHHHHHHHHHH Q psy254 36 LTGIICTIGPAS--VAVDMLEKIIETGMNIARLNFSHG----------SYEYHGQTIKNIRQA 86 (187) Q Consensus 36 ~TkIi~TiGPas--~~~~~i~~li~aGm~v~RiN~sHg----------~~e~~~~~i~~ir~a 86 (187) ...+++.|+-++ +-.+..+.+.++|.+.+=||++.- .++...++++.+|++ T Consensus 98 ~~pvi~si~g~~~~~~~~~a~~~~~~G~d~ielN~~cP~~~~~~~~~~~~~~~~eiv~~vr~~ 160 (289) T cd02810 98 GQPLIASVGGSSKEDYVELARKIERAGAKALELNLSCPNVGGGRQLGQDPEAVANLLKAVKAA 160 (289) T ss_pred CCeEEEEeccCCHHHHHHHHHHHHHhCCCEEEEEcCCCCCCCCcccccCHHHHHHHHHHHHHc Confidence 356899895542 223556677788999999999842 344556667666654 No 210 >KOG3303|consensus Probab=31.12 E-value=42 Score=27.24 Aligned_cols=79 Identities=23% Similarity=0.320 Sum_probs=52.2 Q ss_pred HHHHHH-HHhc---CcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCe---eEeeecCCCCccc Q psy254 51 DMLEKI-IETG---MNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPE---IRTGLLQGGGSAE 123 (187) Q Consensus 51 ~~i~~l-i~aG---m~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPk---IRtG~~~~~~~~~ 123 (187) +.|++| ...| +++.|+.+||-..|+..+.-..+++.....+ +-+..|+..|| |-+-.+++ .++ T Consensus 88 ~~lr~~~W~~g~~lps~i~~sls~~E~eyf~~Ys~~La~y~~~~g--------idl~~~~vPPk~lfI~VR~LkD--~Ge 157 (192) T KOG3303|consen 88 ARLRDLAWSYGLDLPSSIRFSLSHEEEEYFKNYSNLLAEYMGPLG--------IDLTGDMVPPKDLFIQVRVLKD--YGE 157 (192) T ss_pred HHHHHHHHhcCCCccHHHHHhhhHHHHHHHHHHHHHHHHHhcCcc--------chhccCcCCCccceEEEEEecc--cCc Confidence 344443 3556 8899999999999888888877777655433 55666777775 22333554 245 Q ss_pred EEeeeCCEEEEeeCCCc Q psy254 124 VELVKGQTIRLTTDAAF 140 (187) Q Consensus 124 i~l~~G~~v~lt~~~~~ 140 (187) ++..-| +|.|+.++.+ T Consensus 158 ~ete~g-~inL~KdS~h 173 (192) T KOG3303|consen 158 FETEDG-TINLKKDSQH 173 (192) T ss_pred eeecCC-eEEeeccchh Confidence 666667 8888776543 No 211 >TIGR01521 FruBisAldo_II_B fructose-bisphosphate aldolase, class II, Calvin cycle subtype. Members of this family are class II examples of the enzyme fructose-bisphosphate aldolase, an enzyme both of glycolysis and (in the opposite direction) of the Calvin cycle of CO2 fixation. A deep split separates the tightly conserved yeast/E. coli/Mycobacterium subtype (all species lacking the Calvin cycle) represented by model TIGR01520 from a broader group of aldolases that includes both tagatose- and fructose-bisphosphate aldolases. This model represents a distinct, elongated, very well conserved subtype within the latter group. Most species with this aldolase subtype have the Calvin cycle. Probab=30.83 E-value=3e+02 Score=24.50 Aligned_cols=54 Identities=9% Similarity=0.145 Sum_probs=42.5 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCC-------CHHHHHHHHHHHHHHHHHhC Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHG-------SYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg-------~~e~~~~~i~~ir~a~~~~~ 91 (187) ..|..-+ ..+.+.+.+++-+++|.+-+.|..||- +.++.-+.-..+-+.+...| T Consensus 74 VPValHL-DHg~~~e~i~~Ai~~GFtSVMiDgS~l~~~~~~~p~eENI~~Tkevve~Ah~~G 134 (347) T TIGR01521 74 IPVVMHQ-DHGNSPATCQRAIQLGFTSVMMDGSLREDAKTPADYDYNVRVTAEVVAFAHAVG 134 (347) T ss_pred CcEEEEC-CCCCCHHHHHHHHHcCCCEEeecCcCCcccCCCCCHHHHHHHHHHHHHHHHHcC Confidence 3466666 677899999999999999999999997 67776666666666666655 No 212 >PRK13020 riboflavin synthase subunit alpha; Provisional Probab=30.78 E-value=1.2e+02 Score=24.91 Aligned_cols=35 Identities=17% Similarity=0.330 Sum_probs=27.4 Q ss_pred EEeeCcc-hhhhcCCCCCEEEEeCCeEEEEEEEEeCCe Q psy254 148 DLYVDYT-NITKVVKPGSRIFVDDGLISLVVKSIVKSY 184 (187) Q Consensus 148 ~i~v~~~-~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~ 184 (187) .+.+..| .+.+.+.+|+.|-+|. ++|+|.++.++. T Consensus 23 ~l~i~~~~~~~~~l~~g~SIavnG--VcLTV~~v~~~~ 58 (206) T PRK13020 23 TLEIAFPPELLEGLEIGASVAVNG--VCLTVTKIEGDR 58 (206) T ss_pred EEEEEeChhHhccCCCCCEEEECC--EEEEEEEECCCE Confidence 3555444 4678999999999986 799999998774 No 213 >cd01335 Radical_SAM Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme o Probab=30.58 E-value=2.2e+02 Score=20.97 Aligned_cols=36 Identities=14% Similarity=0.289 Sum_probs=28.2 Q ss_pred CCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHH Q psy254 44 GPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQT 79 (187) Q Consensus 44 GPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~ 79 (187) .+...+.+.++.|.++|+....+++-..+......+ T Consensus 82 ~~~~~~~~~~~~l~~~g~~~i~i~le~~~~~~~~~~ 117 (204) T cd01335 82 NGTLLTEELLKELKELGLDGVGVSLDSGDEEVADKI 117 (204) T ss_pred CcccCCHHHHHHHHhCCCceEEEEcccCCHHHHHHH Confidence 344447899999999999999999888887755543 No 214 >PRK09196 fructose-1,6-bisphosphate aldolase; Reviewed Probab=30.51 E-value=3e+02 Score=24.45 Aligned_cols=53 Identities=13% Similarity=0.208 Sum_probs=41.5 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCC-------CHHHHHHHHHHHHHHHHHhC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHG-------SYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg-------~~e~~~~~i~~ir~a~~~~~ 91 (187) .+..-+ ..+.+.+.+++-+++|-+-+.|.-||- +.++.-+.-..+-+.+..+| T Consensus 77 PValHL-DHg~~~e~i~~ai~~GftSVMiDgS~l~~~~~~~p~eENI~~Tkevve~Ah~~G 136 (347) T PRK09196 77 PVVMHQ-DHGNSPATCQRAIQLGFTSVMMDGSLKADGKTPASYEYNVDVTRKVVEMAHACG 136 (347) T ss_pred cEEEEC-CCCCCHHHHHHHHHcCCCEEEecCCCCcccCCCCCHHHHHHHHHHHHHHHHHcC Confidence 355555 667789999999999999999999998 67776666666666666655 No 215 >PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process Probab=30.39 E-value=1.9e+02 Score=21.50 Aligned_cols=57 Identities=12% Similarity=0.275 Sum_probs=40.8 Q ss_pred CCCCCceEEEecCCCCCCHHHHHHHHHhcCcEEEE------ecCCCC-HHHHHHHHHHHHHHHHHhC Q psy254 32 SYVRLTGIICTIGPASVAVDMLEKIIETGMNIARL------NFSHGS-YEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 32 ~~~r~TkIi~TiGPas~~~~~i~~li~aGm~v~Ri------N~sHg~-~e~~~~~i~~ir~a~~~~~ 91 (187) ...|-.++.|| ..-+++.|-.-++.|+|..-+ +|.|.. ...-.++++.+|+..++.| T Consensus 27 ~~vriIrvpC~---Grv~~~~il~Af~~GADGV~V~gC~~g~Ch~~~Gn~~a~~Rv~~~k~~L~~~G 90 (124) T PF02662_consen 27 PNVRIIRVPCS---GRVDPEFILRAFEKGADGVLVAGCHPGDCHYREGNYRAEKRVERLKKLLEELG 90 (124) T ss_pred CCeEEEEccCC---CccCHHHHHHHHHcCCCEEEEeCCCCCCCCcchhhHHHHHHHHHHHHHHHHcC Confidence 33555555553 367889999999999998888 444432 3456688888888888877 No 216 >PRK12271 rps10p 30S ribosomal protein S10P; Reviewed Probab=30.26 E-value=90 Score=22.70 Aligned_cols=31 Identities=23% Similarity=0.273 Sum_probs=27.5 Q ss_pred CcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 61 MNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 61 m~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) |.-+||-+.-.++....+....|.+.++..| T Consensus 1 ~~~irI~L~S~d~~~Ld~~~~~I~~~~k~~g 31 (102) T PRK12271 1 MQKARIRLSSTNPEDLDEVCDQIKEIAEKTG 31 (102) T ss_pred CceEEEEEEeCCHHHHHHHHHHHHHHHHHcC Confidence 4568999999999999999999999988877 No 217 >PRK05096 guanosine 5'-monophosphate oxidoreductase; Provisional Probab=30.02 E-value=1.5e+02 Score=26.43 Aligned_cols=53 Identities=21% Similarity=0.288 Sum_probs=35.1 Q ss_pred CceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHH----------HHHHHHHHHHHHHHhC Q psy254 36 LTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEY----------HGQTIKNIRQAVENYS 91 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~----------~~~~i~~ir~a~~~~~ 91 (187) .+-||| |. -.+.+..++|+++|+|+.|+-.--|+... ....+....+++.+++ T Consensus 151 ~~~vIa--GN-V~T~e~a~~Li~aGAD~vKVGIGpGSiCtTr~vtGvG~PQltAV~~~a~~a~~~g 213 (346) T PRK05096 151 DKTICA--GN-VVTGEMVEELILSGADIVKVGIGPGSVCTTRVKTGVGYPQLSAVIECADAAHGLG 213 (346) T ss_pred CCcEEE--ec-ccCHHHHHHHHHcCCCEEEEcccCCccccCccccccChhHHHHHHHHHHHHHHcC Confidence 345666 33 45689999999999999998877766542 3344445555555444 No 218 >PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed Probab=29.81 E-value=98 Score=27.68 Aligned_cols=45 Identities=13% Similarity=0.324 Sum_probs=32.3 Q ss_pred CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC Q psy254 49 AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK 107 (187) Q Consensus 49 ~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~ 107 (187) +.+.|.+|.+||.++.|+-.-. .+..+.+..|++. .|++++.|+. T Consensus 44 tv~Qi~~L~~aGceiVRvav~~---~~~a~al~~I~~~-----------~~iPlvADIH 88 (360) T PRK00366 44 TVAQIKRLARAGCEIVRVAVPD---MEAAAALPEIKKQ-----------LPVPLVADIH 88 (360) T ss_pred HHHHHHHHHHcCCCEEEEccCC---HHHHHhHHHHHHc-----------CCCCEEEecC Confidence 4689999999999999986543 2344555555543 4688888875 No 219 >PLN02489 homocysteine S-methyltransferase Probab=29.79 E-value=1.7e+02 Score=25.68 Aligned_cols=78 Identities=13% Similarity=0.172 Sum_probs=0.0 Q ss_pred CCCCCCCCceEEEecCCCCC----------CHHH--------------HHHHHHhcCcEEEEecCCCCHHHHHHHHHHHH Q psy254 29 NKSSYVRLTGIICTIGPASV----------AVDM--------------LEKIIETGMNIARLNFSHGSYEYHGQTIKNIR 84 (187) Q Consensus 29 ~~~~~~r~TkIi~TiGPas~----------~~~~--------------i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir 84 (187) ......+...|.++|||.-. ++.. ++.|+++|+|++-+-.--.-.|.. .+++.+| T Consensus 125 ~~~~~~~~~~VaGsiGP~g~~l~~g~ey~g~y~~~~~~~e~~~~~~~qi~~l~~~gvD~i~~ET~~~l~E~~-a~~~~~~ 203 (335) T PLN02489 125 GRELSYRPILVAASIGSYGAYLADGSEYSGDYGPSVTLEKLKDFHRRRLQVLAEAGPDLIAFETIPNKLEAQ-AYVELLE 203 (335) T ss_pred ccccCCCCcEEEEEcCCccccccCCcccCCCCccCCCHHHHHHHHHHHHHHHHhCCCCEEEEeccCChHHHH-HHHHHHH Q ss_pred HHHHHhCCCCCCcceeEEEeeC-CCCeeEeee Q psy254 85 QAVENYSKRIGMPHALAIALDT-KGPEIRTGL 115 (187) Q Consensus 85 ~a~~~~~~~~~~~~~v~I~~Dl-~GPkIRtG~ 115 (187) +.... .|+.|-+.. .|.+++.|. T Consensus 204 ~~~~~--------~p~~iS~t~~~~~~l~~G~ 227 (335) T PLN02489 204 EENIK--------IPAWISFNSKDGVNVVSGD 227 (335) T ss_pred HcCCC--------CeEEEEEEeCCCCccCCCC No 220 >PRK06108 aspartate aminotransferase; Provisional Probab=29.78 E-value=1.9e+02 Score=24.79 Aligned_cols=48 Identities=10% Similarity=0.319 Sum_probs=32.1 Q ss_pred EEEecCCCCCCHHHHHHHHH-hcC-------------cEEEEecCCCCHHHHHHHHHHHHHHH Q psy254 39 IICTIGPASVAVDMLEKIIE-TGM-------------NIARLNFSHGSYEYHGQTIKNIRQAV 87 (187) Q Consensus 39 Ii~TiGPas~~~~~i~~li~-aGm-------------~v~RiN~sHg~~e~~~~~i~~ir~a~ 87 (187) +.+.+.+...+.+..+.|++ .|+ +.+||+|+. +.++..+.++.++++. T Consensus 319 ~~~~l~~~~~~~~~~~~ll~~~gV~v~pg~~f~~~~~~~~Ris~~~-~~~~l~~~l~~l~~~l 380 (382) T PRK06108 319 AFFRIPGVTDSLALAKRLVDEAGLGLAPGTAFGPGGEGFLRWCFAR-DPARLDEAVERLRRFL 380 (382) T ss_pred EEEeCCCCCCHHHHHHHHHHhCCEEEeCchhhCCCCCCEEEEEecC-CHHHHHHHHHHHHHHH Confidence 44555333344556666654 454 358999999 8888888888887653 No 221 >PF01729 QRPTase_C: Quinolinate phosphoribosyl transferase, C-terminal domain; InterPro: IPR002638 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0004514 nicotinate-nucleotide diphosphorylase (carboxylating) activity, 0009435 NAD biosynthetic process; PDB: 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 1QPN_E 1QPO_A 1QPQ_F 1QPR_E 2I14_D .... Probab=29.78 E-value=2.8e+02 Score=21.82 Aligned_cols=44 Identities=20% Similarity=0.267 Sum_probs=31.7 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHH Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a 86 (187) .||.+-. ++.+.+.+.+++|+++.||.= .++++.++.++.+|.. T Consensus 81 ~~I~VEv----~~~ee~~ea~~~g~d~I~lD~--~~~~~~~~~v~~l~~~ 124 (169) T PF01729_consen 81 KKIEVEV----ENLEEAEEALEAGADIIMLDN--MSPEDLKEAVEELREL 124 (169) T ss_dssp SEEEEEE----SSHHHHHHHHHTT-SEEEEES---CHHHHHHHHHHHHHH T ss_pred ceEEEEc----CCHHHHHHHHHhCCCEEEecC--cCHHHHHHHHHHHhhc Confidence 3477765 678999999999999999743 3777777777766543 No 222 >cd05800 PGM_like2 This PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily and is found in both archaea and bacteria. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four structural domains (subdomains) with a centrally located active site formed by four loops, one from each subdomain. All four subdomains are included in this alignment model. Probab=29.75 E-value=2.4e+02 Score=25.48 Aligned_cols=88 Identities=14% Similarity=0.199 Sum_probs=50.8 Q ss_pred ccHHHhhcCCCCCCCCCCCCCceEEEecCCCCCCHHHHHHHH-HhcCcEEEEecC-------CCCHHHHHHHHHHHHHHH Q psy254 16 NTFVDHLCGLDIDNKSSYVRLTGIICTIGPASVAVDMLEKII-ETGMNIARLNFS-------HGSYEYHGQTIKNIRQAV 87 (187) Q Consensus 16 ~~~l~~~~~l~i~~~~~~~r~TkIi~TiGPas~~~~~i~~li-~aGm~v~RiN~s-------Hg~~e~~~~~i~~ir~a~ 87 (187) ..+++++... +..++...+.-||+...+-.+. ...+.+++ +.|+++.-+|.. |..... .+.++.++++. T Consensus 154 ~~Y~~~l~~~-~~~~~i~~~~~kivvd~~~G~~-~~~~~~il~~lg~~v~~~~~~~dg~F~~~~p~p~-~~~l~~l~~~v 230 (461) T cd05800 154 PDYLEALRSL-VDLEAIREAGLKVVVDPMYGAG-AGYLEELLRGAGVDVEEIRAERDPLFGGIPPEPI-EKNLGELAEAV 230 (461) T ss_pred HHHHHHHHHH-hChhhhhcCCceEEEeCCCCCc-HHHHHHHHHHcCCCEEEeeCCcCCCCCCCCCCCC-HHHHHHHHHHH Confidence 3455555443 2222223456799998743332 23444433 449999999855 222222 45666677777 Q ss_pred HHhCCCCCCcceeEEEeeCCCCeeE Q psy254 88 ENYSKRIGMPHALAIALDTKGPEIR 112 (187) Q Consensus 88 ~~~~~~~~~~~~v~I~~Dl~GPkIR 112 (187) ++.+ ..+++.+|=-|=.+. T Consensus 231 ~~~~------ad~Gia~D~DgDR~~ 249 (461) T cd05800 231 KEGG------ADLGLATDGDADRIG 249 (461) T ss_pred HhcC------CCEEEEECCCCCeEE Confidence 7666 568888887666554 No 223 >COG0809 QueA S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) [Translation, ribosomal structure and biogenesis] Probab=29.67 E-value=66 Score=28.55 Aligned_cols=28 Identities=25% Similarity=0.452 Sum_probs=23.2 Q ss_pred hhhhcCCCCCEEEEeCCeEEEEEEEEeCC Q psy254 155 NITKVVKPGSRIFVDDGLISLVVKSIVKS 183 (187) Q Consensus 155 ~l~~~v~~Gd~IlidDG~i~l~V~~v~~~ 183 (187) ...+.+++|++|++++| +..+|.+..++ T Consensus 97 ~~~kr~k~G~~i~f~~~-l~a~v~e~~~~ 124 (348) T COG0809 97 KPSKRLKAGDEIYFGDG-LKATVLERLEH 124 (348) T ss_pred ccccCCCCCCEEEeCCC-ceEEEEEecCC Confidence 34578999999999999 88888887655 No 224 >PRK06033 hypothetical protein; Validated Probab=29.39 E-value=99 Score=21.50 Aligned_cols=67 Identities=10% Similarity=0.218 Sum_probs=44.2 Q ss_pred ceeEEEeeCCCCeeEeeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEE Q psy254 98 HALAIALDTKGPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVV 177 (187) Q Consensus 98 ~~v~I~~Dl~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V 177 (187) .|+.+-+-|...++....+ ..|++|+.+.|... ..++=.++++-...+. ..+-..+|+..++| T Consensus 7 v~V~l~v~Lg~~~i~l~dl-------L~L~~GDVI~L~~~-----~~~~v~v~V~~~~~f~-----g~~G~~~~~~AV~I 69 (83) T PRK06033 7 VSVELMVVLGRSSMPIHQV-------LRMGRGAVIPLDAT-----EADEVWILANNHPIAR-----GEVLIDRNRIAVEV 69 (83) T ss_pred ceEEEEEEEecccccHHHH-------hCCCCCCEEEeCCC-----CCCcEEEEECCEEEEE-----EEEEEECCEEEEEE Confidence 5677777777777777655 56899999988542 1223346776544443 23335788999998 Q ss_pred EEEe Q psy254 178 KSIV 181 (187) Q Consensus 178 ~~v~ 181 (187) +++. T Consensus 70 ~~~~ 73 (83) T PRK06033 70 TRAA 73 (83) T ss_pred EEhH Confidence 8764 No 225 >TIGR02326 transamin_PhnW 2-aminoethylphosphonate--pyruvate transaminase. Members of this family are 2-aminoethylphosphonate--pyruvate transaminase. This enzyme acts on the most common type of naturally occurring phosphonate. It interconverts 2-aminoethylphosphonate plus pyruvate with 2-phosphonoacetaldehyde plus alanine. The enzyme phosphonoacetaldehyde hydrolase (EC 3.11.1.1), usually encoded by an adjacent gene, then cleaves the C-P bond of phosphonoacetaldehyde, adding water to yield acetaldehyde plus inorganic phosphate. Species with this pathway generally have an identified phosphonate ABC transporter but do not also have the multisubunit C-P lysase complex as found in Escherichia coli. Probab=29.30 E-value=3e+02 Score=23.45 Aligned_cols=37 Identities=16% Similarity=0.276 Sum_probs=27.6 Q ss_pred HHHHHHHHHhcC----------cEEEEe-cCCCCHHHHHHHHHHHHHH Q psy254 50 VDMLEKIIETGM----------NIARLN-FSHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 50 ~~~i~~li~aGm----------~v~RiN-~sHg~~e~~~~~i~~ir~a 86 (187) .+..+.|.+.|+ +++||+ +.|-+.++..+.++.++++ T Consensus 312 ~~v~~~L~~~gi~v~~g~~~~~~~iRi~~~~~~~~edv~~~l~~l~~~ 359 (363) T TIGR02326 312 ADFYQRLKEQGFVIYPGKVSQVDCFRIGNIGEVDAADITRLLTAIGKA 359 (363) T ss_pred HHHHHHHHHCCEEEECCcCCCCCEEEEecCCCCCHHHHHHHHHHHHHH Confidence 455566776664 458997 5888999999988888765 No 226 >COG3033 TnaA Tryptophanase [Amino acid transport and metabolism] Probab=29.23 E-value=58 Score=29.56 Aligned_cols=35 Identities=14% Similarity=-0.012 Sum_probs=25.9 Q ss_pred CCCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEec Q psy254 33 YVRLTGIICTIGPASVAVDMLEKIIETGMNIARLNF 68 (187) Q Consensus 33 ~~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~ 68 (187) ...+-+.+=.| +-+.-..--+.|.++|||.|+||- T Consensus 10 ePfrir~vepi-~~ttre~RE~al~~ag~N~F~l~S 44 (471) T COG3033 10 EPFRIRVVEPI-KRTTREYREEALKKAGYNPFLLDS 44 (471) T ss_pred Cceeeeeeccc-cccCHHHHHHHHHHcCCCeeeccc Confidence 34455566666 555556777889999999999984 No 227 >cd02966 TlpA_like_family TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases. Probab=29.16 E-value=1.7e+02 Score=19.31 Aligned_cols=33 Identities=15% Similarity=0.219 Sum_probs=22.3 Q ss_pred HHHHHHHH----hcCcEEEEecCCCCHHHHHHHHHHH Q psy254 51 DMLEKIIE----TGMNIARLNFSHGSYEYHGQTIKNI 83 (187) Q Consensus 51 ~~i~~li~----aGm~v~RiN~sHg~~e~~~~~i~~i 83 (187) ..+.++.+ .++.++.+++...+.+++++.++.. T Consensus 39 ~~l~~~~~~~~~~~~~~~~v~~d~~~~~~~~~~~~~~ 75 (116) T cd02966 39 PELEALAKEYKDDGVEVVGVNVDDDDPAAVKAFLKKY 75 (116) T ss_pred HHHHHHHHHhCCCCeEEEEEECCCCCHHHHHHHHHHc Confidence 44444443 3789999998766677777776664 No 228 >PRK13347 coproporphyrinogen III oxidase; Provisional Probab=29.04 E-value=4.4e+02 Score=23.87 Aligned_cols=38 Identities=24% Similarity=0.364 Sum_probs=28.5 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHH Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYE 74 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e 74 (187) +.|-+..-|.+-+.+.++.|.++|++.+-|..=..+.+ T Consensus 139 ~e~tie~~p~~lt~e~l~~L~~~G~~rvsiGvQS~~~~ 176 (453) T PRK13347 139 AEIAVEIDPRTVTAEMLQALAALGFNRASFGVQDFDPQ 176 (453) T ss_pred ceEEEEeccccCCHHHHHHHHHcCCCEEEECCCCCCHH Confidence 46667778988999999999999988555554444443 No 229 >TIGR00849 gutA PTS system, glucitol/sorbitol-specific IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria.The system in E.Coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component. Probab=29.02 E-value=97 Score=23.27 Aligned_cols=31 Identities=13% Similarity=0.269 Sum_probs=23.1 Q ss_pred eeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeC Q psy254 150 YVDYTNITKVVKPGSRIFVDDGLISLVVKSIVK 182 (187) Q Consensus 150 ~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~ 182 (187) ..+..++-..+++||.+.||+= ...|+.|++ T Consensus 42 ih~~~~~~~~i~~Gd~l~i~~~--~Y~ItaVG~ 72 (121) T TIGR00849 42 IHNIKEVKGTLKPGQVFMIGGI--AYPVTAVGD 72 (121) T ss_pred EEEcCcccCCcCCCCEEEECCE--EEEEEEEhH Confidence 3445667778999999999884 667777753 No 230 >cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery. Probab=28.93 E-value=1.1e+02 Score=21.86 Aligned_cols=24 Identities=25% Similarity=0.360 Sum_probs=17.5 Q ss_pred hcCCCCCEEEEeCC---eEEEEEEEEe Q psy254 158 KVVKPGSRIFVDDG---LISLVVKSIV 181 (187) Q Consensus 158 ~~v~~Gd~IlidDG---~i~l~V~~v~ 181 (187) ...++||.+.+-|| .+..+|++|. T Consensus 29 ~~~k~Gd~~i~~~~~~~~~~i~v~~V~ 55 (105) T cd06541 29 QLPKAGDYLIILDGQQPLAIAEVVKVE 55 (105) T ss_pred cCCCCCCEEEEecCCCcEEEEEEEEEE Confidence 56789999999988 5556666653 No 231 >cd04738 DHOD_2_like Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences, their cellular location and their natural electron acceptor used to reoxidize the flavin group. Members of class 1 are cytosolic enzymes and multimers, while class 2 enzymes are membrane associated, monomeric and use respiratory quinones as their physiological electron acceptors. Probab=28.93 E-value=2.8e+02 Score=23.95 Aligned_cols=54 Identities=13% Similarity=0.102 Sum_probs=32.7 Q ss_pred CceEEEecCCCCCC-----H-HHHH--HHHHhcCcEEEEecCCCC---------HHHHHHHHHHHHHHHHH Q psy254 36 LTGIICTIGPASVA-----V-DMLE--KIIETGMNIARLNFSHGS---------YEYHGQTIKNIRQAVEN 89 (187) Q Consensus 36 ~TkIi~TiGPas~~-----~-~~i~--~li~aGm~v~RiN~sHg~---------~e~~~~~i~~ir~a~~~ 89 (187) .+.++++|+-...+ . +..+ +.+..+.+.+=||||.=. ++...++++.+|++... T Consensus 128 ~~plivsi~g~~~~~~~~~~~d~~~~~~~~~~~ad~ielN~scP~~~g~~~~~~~~~~~~iv~av~~~~~~ 198 (327) T cd04738 128 GGPLGVNIGKNKDTPLEDAVEDYVIGVRKLGPYADYLVVNVSSPNTPGLRDLQGKEALRELLTAVKEERNK 198 (327) T ss_pred CCeEEEEEeCCCCCcccccHHHHHHHHHHHHhhCCEEEEECCCCCCCccccccCHHHHHHHHHHHHHHHhh Confidence 46799999554311 2 2222 223345899999997332 35667777777776543 No 232 >PF12198 Tuberculin: Theoretical tuberculin protein; InterPro: IPR022015 This domain family is found in bacteria, and is approximately 30 amino acids in length. This protein is a theoretical model of the tuberculin protein from Mycobacterium tuberculosis. Probab=28.66 E-value=53 Score=18.98 Aligned_cols=18 Identities=22% Similarity=0.303 Sum_probs=13.9 Q ss_pred CCCCCceEEEecCCCCCC Q psy254 32 SYVRLTGIICTIGPASVA 49 (187) Q Consensus 32 ~~~r~TkIi~TiGPas~~ 49 (187) .+....+.||-+||++.+ T Consensus 16 rNG~Q~R~iA~~GP~SsT 33 (34) T PF12198_consen 16 RNGNQMRFIAPMGPESST 33 (34) T ss_pred cCCceeEEeeccCccccc Confidence 345677899999998854 No 233 >PRK03170 dihydrodipicolinate synthase; Provisional Probab=28.64 E-value=1.6e+02 Score=24.77 Aligned_cols=65 Identities=11% Similarity=0.075 Sum_probs=42.1 Q ss_pred CceEEEecCCCC--CCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC Q psy254 36 LTGIICTIGPAS--VAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK 107 (187) Q Consensus 36 ~TkIi~TiGPas--~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~ 107 (187) ++.|++.+|..+ +..+..+..-++|++.+-+=.-+-..-...++++..++.++..+ .|+-++ +.+ T Consensus 70 ~~~vi~gv~~~~~~~~i~~a~~a~~~G~d~v~~~pP~~~~~~~~~i~~~~~~ia~~~~------~pv~lY-n~P 136 (292) T PRK03170 70 RVPVIAGTGSNSTAEAIELTKFAEKAGADGALVVTPYYNKPTQEGLYQHFKAIAEATD------LPIILY-NVP 136 (292) T ss_pred CCcEEeecCCchHHHHHHHHHHHHHcCCCEEEECCCcCCCCCHHHHHHHHHHHHhcCC------CCEEEE-ECc Confidence 457888887643 34577778888999987774333222234677777777776655 566655 543 No 234 >cd04741 DHOD_1A_like Dihydroorotate dehydrogenase (DHOD) class 1A FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. Probab=28.34 E-value=1.8e+02 Score=24.70 Aligned_cols=50 Identities=14% Similarity=0.153 Sum_probs=30.5 Q ss_pred ceEEEecCCCCCC-HHHHHHHHHh---cCcEEEEecC--CC--------CHHHHHHHHHHHHHH Q psy254 37 TGIICTIGPASVA-VDMLEKIIET---GMNIARLNFS--HG--------SYEYHGQTIKNIRQA 86 (187) Q Consensus 37 TkIi~TiGPas~~-~~~i~~li~a---Gm~v~RiN~s--Hg--------~~e~~~~~i~~ir~a 86 (187) ..++++|+-..++ .+..+.+.++ |.+.+=||+| |. +++...++++.+|++ T Consensus 92 ~pvivsi~g~~~~~~~~~~~~~~~~~~~ad~ielN~sCPn~~~~~~~~~~~~~~~~i~~~v~~~ 155 (294) T cd04741 92 KPFFISVTGSAEDIAAMYKKIAAHQKQFPLAMELNLSCPNVPGKPPPAYDFDATLEYLTAVKAA 155 (294) T ss_pred CeEEEECCCCHHHHHHHHHHHHhhccccccEEEEECCCCCCCCcccccCCHHHHHHHHHHHHHh Confidence 4688999543222 2334445554 6999999999 32 355555666666554 No 235 >PF13509 S1_2: S1 domain; PDB: 3GO5_A. Probab=28.18 E-value=57 Score=21.05 Aligned_cols=23 Identities=13% Similarity=0.326 Sum_probs=12.1 Q ss_pred cCEEeeCcchhhhcCCCCCEEEE Q psy254 146 ATDLYVDYTNITKVVKPGSRIFV 168 (187) Q Consensus 146 ~~~i~v~~~~l~~~v~~Gd~Ili 168 (187) ...+.++..+..+.+++||.|.+ T Consensus 24 ~~~vlLp~~e~~~~~~~Gd~v~V 46 (61) T PF13509_consen 24 GKEVLLPKSEVPEPLKVGDEVEV 46 (61) T ss_dssp -EEEEEEGGG------TTSEEEE T ss_pred CCEEEechHHcCCCCCCCCEEEE Confidence 35688888888889999997543 No 236 >TIGR00539 hemN_rel putative oxygen-independent coproporphyrinogen III oxidase. Experimentally determined examples of oxygen-independent coproporphyrinogen III oxidase, an enzyme that replaces HemF function under anaerobic conditions, belong to a family of proteins described by the model hemN. This model, hemN_rel, models a closely related protein, shorter at the amino end and lacking the region containing the motif PYRT[SC]YP found in members of the hemN family. Several species, including E. coli, Helicobacter pylori, Aquifex aeolicus, and Chlamydia trachomatis, have members of both this family and the E. coli hemN family. The member of this family from Bacillus subtilis was shown to complement an hemF/hemN double mutant of Salmonella typimurium and to prevent accumulation of coproporphyrinogen III under anaerobic conditions, but the exact role of this protein is still uncertain. It is found in a number of species that do not synthesize heme de novo. Probab=28.17 E-value=3.9e+02 Score=23.21 Aligned_cols=40 Identities=13% Similarity=0.130 Sum_probs=30.4 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHH Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYH 76 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~ 76 (187) ..|-+..-|.+-+.+.++.|.++|++.+-|.+=..+.+.+ T Consensus 87 ~eitie~np~~lt~e~l~~l~~~Gv~risiGvqS~~~~~l 126 (360) T TIGR00539 87 CEITTEANPELITAEWCKGLKGAGINRLSLGVQSFRDDKL 126 (360) T ss_pred CEEEEEeCCCCCCHHHHHHHHHcCCCEEEEecccCChHHH Confidence 3466656799999999999999999977666666655544 No 237 >COG1180 PflA Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones] Probab=28.15 E-value=1.5e+02 Score=24.97 Aligned_cols=51 Identities=22% Similarity=0.247 Sum_probs=34.4 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) ++.+.+.....-.+=-+-||-|.+--|.+.+..+-+++++.| +.+.+||.| T Consensus 71 ~e~l~~~~~~~~~~~gvt~SGGEP~~q~e~~~~~~~~ake~G--------l~~~l~TnG 121 (260) T COG1180 71 PEVLVDKAFYSESGGGVTFSGGEPTLQAEFALDLLRAAKERG--------LHVALDTNG 121 (260) T ss_pred HHHHHHHhhhcCCCCEEEEECCcchhhHHHHHHHHHHHHHCC--------CcEEEEcCC Confidence 566666665555666688999998777777777766667655 455555554 No 238 >cd03325 D-galactonate_dehydratase D-galactonate dehydratase catalyses the dehydration of galactonate to 2-keto-3-deoxygalactnate (KDGal), as part of the D-galactonate nonphosphorolytic catabolic Entner-Doudoroff pathway. D-galactonate dehydratase belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Probab=28.13 E-value=3.5e+02 Score=23.47 Aligned_cols=67 Identities=13% Similarity=0.199 Sum_probs=41.8 Q ss_pred CceEEEecCCCCC--CHHHHHHHHHhcCcEEEEecCCC-----CHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 36 LTGIICTIGPASV--AVDMLEKIIETGMNIARLNFSHG-----SYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 36 ~TkIi~TiGPas~--~~~~i~~li~aGm~v~RiN~sHg-----~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) +..+-+|+|..+. -.+.++++.+.|.+.+.+..... ......+-++.||.+.+.++ .-+.|++|--+ T Consensus 112 ~i~~~~~~~~~~~~~~~~~~~~~~~~Gf~~~KiKvg~~~~~~~~~~~~~~D~~~i~avr~~~g------~~~~l~vDaN~ 185 (352) T cd03325 112 RVRVYSWIGGDRPSDVAEAARARREAGFTAVKMNATEELQWIDTSKKVDAAVERVAALREAVG------PDIDIGVDFHG 185 (352) T ss_pred eeEEEEeCCCCCHHHHHHHHHHHHHcCCCEEEecCCCCcccCCCHHHHHHHHHHHHHHHHhhC------CCCEEEEECCC Confidence 4456667754321 13456667788999999987521 12344555666666666666 34788998765 No 239 >PRK06225 aspartate aminotransferase; Provisional Probab=28.02 E-value=1.4e+02 Score=25.81 Aligned_cols=42 Identities=21% Similarity=0.241 Sum_probs=32.0 Q ss_pred CCHHHHHHHHHhcCc--------------EEEEecCCCCHHHHHHHHHHHHHHHHHh Q psy254 48 VAVDMLEKIIETGMN--------------IARLNFSHGSYEYHGQTIKNIRQAVENY 90 (187) Q Consensus 48 ~~~~~i~~li~aGm~--------------v~RiN~sHg~~e~~~~~i~~ir~a~~~~ 90 (187) +..+..+.|.+.|+- .+|++|++ +.++..+.++.++++.++. T Consensus 322 ~~~~l~~~l~~~gi~v~~g~~~~~~~~~~~iR~s~~~-~~e~l~~~~~~l~~~~~~~ 377 (380) T PRK06225 322 DPEDLVEYLLERKIFVRQGTYTSKRFGDRYIRVSFSI-PREQVEVFCEEFPDVVETL 377 (380) T ss_pred CHHHHHHHHHHCCEEEcCCcccCcCCCCceEEEEeCC-CHHHHHHHHHHHHHHHHHh Confidence 345666668777764 59999997 6789999999998877643 No 240 >TIGR00824 EIIA-man PTS system, mannose/fructose/sorbose family, IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIA components. Probab=27.93 E-value=2.4e+02 Score=20.52 Aligned_cols=65 Identities=20% Similarity=0.227 Sum_probs=39.3 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCc-EEEEecCCCC-HHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMN-IARLNFSHGS-YEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGP 109 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~-v~RiN~sHg~-~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GP 109 (187) =+++|-|.-+.....--+|+-...+ +.=++|..+. .++..+.+ +++.++...+ ..+-|+.|+.|- T Consensus 4 ili~sHG~~A~gl~~s~~~i~G~~~~i~~i~~~~~~~~~~~~~~l---~~~i~~~~~~----~~vivltDl~GG 70 (116) T TIGR00824 4 IIISGHGQAAIALLKSAEMIFGEQNNVGAVPFVPGENAETLQEKY---NAALADLDTE----EEVLFLVDIFGG 70 (116) T ss_pred EEEEecHHHHHHHHHHHHHHcCCcCCeEEEEcCCCcCHHHHHHHH---HHHHHhcCCC----CCEEEEEeCCCC Confidence 3678888866555444555543333 8888888755 45444443 4444444321 468999999763 No 241 >PF01180 DHO_dh: Dihydroorotate dehydrogenase; InterPro: IPR012135 Dihydroorotate dehydrogenase (DHOD), also known as dihydroorotate oxidase, catalyses the fourth step in de novo pyrimidine biosynthesis, the stereospecific oxidation of (S)-dihydroorotate to orotate, which is the only redox reaction in this pathway. DHODs can be divided into two mains classes: class 1 cytosolic enzymes found primarily in Gram-positive bacteria, and class 2 membrane-associated enzymes found primarily in eukaryotic mitochondria and Gram-negative bacteria []. The class 1 DHODs can be further divided into subclasses 1A and 1B, which differ in their structural organisation and use of electron acceptors. The 1A enzyme is a homodimer of two PyrD subunits where each subunit forms a TIM barrel fold with a bound FMN cofactor located near the top of the barrel []. Fumarate is the natural electron acceptor for this enzyme. The 1B enzyme, in contrast is a heterotetramer composed of a central, FMN-containing, PyrD homodimer resembling the 1A homodimer, and two additional PyrK subunits which contain FAD and a 2Fe-2S cluster []. These additional groups allow the enzyme to use NAD(+) as its natural electron acceptor. The class 2 membrane-associated enzymes are monomers which have the FMN-containing TIM barrel domain found in the class 1 PyrD subunit, and an additional N-terminal alpha helical domain [, ]. These enzymes use respiratory quinones as the physiological electron acceptor. This entry represents the FMN-binding subunit common to all classes of dihydroorotate dehydrogenase.; GO: 0004152 dihydroorotate dehydrogenase activity, 0006222 UMP biosynthetic process, 0055114 oxidation-reduction process; PDB: 3GYE_A 3GZ3_A 3MHU_B 3MJY_A 3TQ0_A 2B4G_C 1EP3_A 1EP2_A 1EP1_A 3I6R_A .... Probab=27.89 E-value=2.1e+02 Score=24.16 Aligned_cols=35 Identities=29% Similarity=0.283 Sum_probs=24.5 Q ss_pred CceEEEecCCCC----CCHHHHHHHHHhcCcEEEEecCC Q psy254 36 LTGIICTIGPAS----VAVDMLEKIIETGMNIARLNFSH 70 (187) Q Consensus 36 ~TkIi~TiGPas----~~~~~i~~li~aGm~v~RiN~sH 70 (187) ...+++++.-.+ .+...+-+.+++|++.+=||+|. T Consensus 96 ~~pvi~Si~~~~~~~~~d~~~~a~~~~~~ad~lElN~Sc 134 (295) T PF01180_consen 96 DIPVIASINGDSEEEIEDWAELAKRLEAGADALELNLSC 134 (295) T ss_dssp CEEEEEEE-TSSSGHHHHHHHHHHHHHHHCSEEEEESTS T ss_pred ceeEEEEeecCCchhHHHHHHHHHHhcCcCCceEEEeec Confidence 568899985544 34444444556999999999995 No 242 >cd05805 MPG1_transferase GTP-mannose-1-phosphate guanyltransferase (MPG1 transferase), also known as GDP-mannose pyrophosphorylase, is a bifunctional enzyme with both phosphomannose isomerase (PMI) activity and GDP-mannose phosphorylase (GMP) activity. The protein contains an N-terminal NTP transferase domain, an L-beta-H domain, and a C-terminal PGM-like domain that belongs to the alpha-D-phosphohexomutase superfamily. This subfamily is limited to bacteria and archaea. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this group appear to lack conserved residues necessary for metal binding and catalytic activity. Other members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional Probab=27.88 E-value=1.7e+02 Score=26.21 Aligned_cols=87 Identities=10% Similarity=0.193 Sum_probs=49.6 Q ss_pred cHHHhhcCCCCCCCCCCCCCceEEEecCCCCCCHHHHHHHH-HhcCcEEEEecC-----CCCHHHHHHHHHHHHHHHHHh Q psy254 17 TFVDHLCGLDIDNKSSYVRLTGIICTIGPASVAVDMLEKII-ETGMNIARLNFS-----HGSYEYHGQTIKNIRQAVENY 90 (187) Q Consensus 17 ~~l~~~~~l~i~~~~~~~r~TkIi~TiGPas~~~~~i~~li-~aGm~v~RiN~s-----Hg~~e~~~~~i~~ir~a~~~~ 90 (187) .+++++... +..++...+.-||+.+-+-.+.. ..+.+++ +.|+++.-+|.. |.++....+.++.++++.++. T Consensus 150 ~Y~~~l~~~-i~~~~i~~~~lkIvvd~~~G~~~-~~~~~ll~~lG~~v~~i~~~~d~~~~~~~~~~~~~l~~l~~~v~~~ 227 (441) T cd05805 150 YYIRGLLRA-LDTSGLKKSGLKVVIDYAYGVAG-IVLPGLLSRLGCDVVILNARLDEDAPRTDTERQRSLDRLGRIVKAL 227 (441) T ss_pred HHHHHHHHH-hCHHHHhhcCCeEEEECCCchHH-HHHHHHHHHcCCEEEEEecccCCccCCCCccchhHHHHHHHHHHhC Confidence 355555422 22222234567898876332221 3333333 348999988877 333332356777788877777 Q ss_pred CCCCCCcceeEEEeeCCCCee Q psy254 91 SKRIGMPHALAIALDTKGPEI 111 (187) Q Consensus 91 ~~~~~~~~~v~I~~Dl~GPkI 111 (187) + ..++|..|=-|=.+ T Consensus 228 ~------adlgia~DgDaDR~ 242 (441) T cd05805 228 G------ADFGVIIDPNGERL 242 (441) T ss_pred C------CCEEEEEcCCCCEE Confidence 6 56777777655544 No 243 >PRK09289 riboflavin synthase subunit alpha; Provisional Probab=27.87 E-value=1.5e+02 Score=23.90 Aligned_cols=37 Identities=19% Similarity=0.275 Sum_probs=29.1 Q ss_pred cCEEeeCcc-hhhhcCCCCCEEEEeCCeEEEEEEEEeCCe Q psy254 146 ATDLYVDYT-NITKVVKPGSRIFVDDGLISLVVKSIVKSY 184 (187) Q Consensus 146 ~~~i~v~~~-~l~~~v~~Gd~IlidDG~i~l~V~~v~~~~ 184 (187) ...+.+.+| .+.+.+.+|+.|-+|. ++|+|.++.++. T Consensus 117 ~~~~~i~~~~~~~~~l~~kgSIavdG--vsLTV~~~~~~~ 154 (194) T PRK09289 117 SVEFRFKAPAELAKYIVEKGSIAVDG--VSLTVNEVDGDR 154 (194) T ss_pred cEEEEEECChHHhcccccCCEEEEcc--EEEEEEEEcCCE Confidence 345666665 5678999999999986 799999997765 No 244 >TIGR00510 lipA lipoate synthase. The family shows strong sequence conservation. Probab=27.70 E-value=1.8e+02 Score=25.23 Aligned_cols=20 Identities=10% Similarity=0.311 Sum_probs=17.0 Q ss_pred CHHHHHHHHHhcCcEEEEec Q psy254 49 AVDMLEKIIETGMNIARLNF 68 (187) Q Consensus 49 ~~~~i~~li~aGm~v~RiN~ 68 (187) +.+.++.|.++|.+++-.|+ T Consensus 155 ~~e~l~~l~~aG~dv~~hnl 174 (302) T TIGR00510 155 NIAALDILLDAPPDVYNHNL 174 (302) T ss_pred CHHHHHHHHHcCchhhcccc Confidence 67899999999999877663 No 245 >PF00128 Alpha-amylase: Alpha amylase, catalytic domain; InterPro: IPR006047 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Enzymes containing this domain, such as alpha-amylase, belong to family 13 (GH13 from CAZY) of the glycosyl hydrolases. The maltogenic alpha-amylase is an enzyme which catalyses hydrolysis of (1-4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive alpha-maltose residues from the non-reducing ends of the chains in the conversion of starch to maltose. Other enzymes include neopullulanase, which hydrolyses pullulan to panose, and cyclomaltodextrinase, which hydrolyses cyclodextrins. This entry represents the catalytic domain found in several protein members of this family. It has a structure consisting of an 8 stranded alpha/beta barrel that contains the active site, interrupted by a ~70 amino acid calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain []. More information about this protein can be found at Protein of the Month: alpha-Amylase [].; GO: 0003824 catalytic activity, 0043169 cation binding, 0005975 carbohydrate metabolic process; PDB: 3FAX_A 3FAW_A 2DH3_B 2DH2_A 1CIU_A 1A47_A 3BMW_A 3BMV_A 2FH8_A 2FH6_A .... Probab=27.60 E-value=1.1e+02 Score=24.95 Aligned_cols=37 Identities=22% Similarity=0.332 Sum_probs=26.0 Q ss_pred HHHHHHHHhcCcEEEEecCCC-CHHHHHHHHHHHHHHH Q psy254 51 DMLEKIIETGMNIARLNFSHG-SYEYHGQTIKNIRQAV 87 (187) Q Consensus 51 ~~i~~li~aGm~v~RiN~sHg-~~e~~~~~i~~ir~a~ 87 (187) +.++-.++.|++.|||..++. ..+.+++....+++.. T Consensus 152 ~~~~~w~~~giDGfR~D~~~~~~~~~~~~~~~~~~~~~ 189 (316) T PF00128_consen 152 DVLKFWIEEGIDGFRLDAAKHIPKEFWKEFRDEVKEEK 189 (316) T ss_dssp HHHHHHHHTTESEEEETTGGGSSHHHHHHHHHHHHHHH T ss_pred ccccchhhceEeEEEEccccccchhhHHHHhhhhhhhc Confidence 466777889999999987754 4555666666665543 No 246 >PRK13962 bifunctional phosphoglycerate kinase/triosephosphate isomerase; Provisional Probab=27.57 E-value=47 Score=31.97 Aligned_cols=100 Identities=16% Similarity=0.203 Sum_probs=61.6 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHH-H----HHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEeeecCCCCcccE Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYE-Y----HGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTGLLQGGGSAEV 124 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e-~----~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG~~~~~~~~~i 124 (187) ..+|+.|++.|..+.= +||-..- . ...+-......++.++ ++|...=|.-||+.+- ..- T Consensus 42 lpTI~~l~~~gakvvl--~SH~gRP~~~~~~~~SL~~va~~L~~~L~------~~V~f~~d~~g~~~~~--------~i~ 105 (645) T PRK13962 42 LPTIKYLLDHGAKVIL--VSHLGRPKGEFDPKFSMAPVAKRLSELLG------KEVIFAKDVIGDDAKK--------AVA 105 (645) T ss_pred HHHHHHHHhCCCeEEE--EEecCCCCCCcCccCCHHHHHHHHHHHHC------CCeEECCCCCCHHHHH--------HHh Confidence 3699999999998765 6887542 1 1122222334555566 7888888998988761 122 Q ss_pred EeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCC Q psy254 125 ELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDG 171 (187) Q Consensus 125 ~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG 171 (187) .|+.|+.+.|-.=.-|..+. -+.++|.+.+.+---||++|. T Consensus 106 ~l~~GeilLLEN~Rf~~~E~------~~d~~~~~~LA~l~DvyVNDA 146 (645) T PRK13962 106 QLKEGDVLLLENVRFHKEET------KNDPEFAKELASLADIYVNDA 146 (645) T ss_pred cCCCCcEEEEeccCcCcccc------cCHHHHHHHHHHhCCEEEech Confidence 46666666554322221111 144678888888777899884 No 247 >PRK05698 fliN flagellar motor switch protein; Validated Probab=27.56 E-value=1.4e+02 Score=23.46 Aligned_cols=66 Identities=20% Similarity=0.329 Sum_probs=46.4 Q ss_pred ceeEEEeeCCCCeeEeeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEE Q psy254 98 HALAIALDTKGPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVV 177 (187) Q Consensus 98 ~~v~I~~Dl~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V 177 (187) .||.|-+-|.-.++.++.+ +.|++|+.|.|... .+++-.++|+-.-++. ..+-+-++++.++| T Consensus 79 vpV~lsveLG~t~itlrdL-------L~L~~GDVI~Ldk~-----~~epv~V~VnG~~~f~-----Ge~Gvvn~k~AVrI 141 (155) T PRK05698 79 IPVSISMEVGSTDINIRNL-------LQLNQGSVIELDRL-----AGEPLDVLVNGTLIAH-----GEVVVVNEKFGIRL 141 (155) T ss_pred ceeEEEEEEecCcccHHHH-------hCCCCCCEEEeCCC-----CCCCEEEEECCEEEEE-----EEEEEECCEEEEEE Confidence 6788888888888887766 56999999998542 2334457777555544 23445567999998 Q ss_pred EEE Q psy254 178 KSI 180 (187) Q Consensus 178 ~~v 180 (187) +++ T Consensus 142 tei 144 (155) T PRK05698 142 TDV 144 (155) T ss_pred EEe Confidence 876 No 248 >TIGR00433 bioB biotin synthetase. Catalyzes the last step of the biotin biosynthesis pathway. Probab=27.48 E-value=1.3e+02 Score=25.08 Aligned_cols=38 Identities=16% Similarity=0.298 Sum_probs=28.6 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHH Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHG 77 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~ 77 (187) .++.++.|. -+.+.++.|-+||++.+-+++- ++++.+. T Consensus 112 i~~~~~~g~--~~~e~l~~Lk~aG~~~v~i~~E-~~~~~~~ 149 (296) T TIGR00433 112 LKTCATLGL--LDPEQAKRLKDAGLDYYNHNLD-TSQEFYS 149 (296) T ss_pred CeEEecCCC--CCHHHHHHHHHcCCCEEEEccc-CCHHHHh Confidence 355666664 4589999999999999888887 6655433 No 249 >cd05845 Ig2_L1-CAM_like Second immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM) and similar proteins. Ig2_L1-CAM_like: domain similar to the second immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains, five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, or spastic paraplegia type 1, that involves abnormalities of axonal growth. Probab=27.34 E-value=2.3e+02 Score=20.09 Aligned_cols=54 Identities=11% Similarity=0.171 Sum_probs=33.9 Q ss_pred ccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEe-CCeEEEEEE Q psy254 122 AEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVD-DGLISLVVK 178 (187) Q Consensus 122 ~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~Ilid-DG~i~l~V~ 178 (187) +.+.+.+|+.+.|.+.... ........|++.. ...+....+|.++ +|.|.+.=. T Consensus 11 ~~v~V~eG~~~~L~C~pP~-g~P~P~i~W~~~~--~~~i~~~~Ri~~~~~GnL~fs~v 65 (95) T cd05845 11 RPVEVEEGDSVVLPCNPPK-SAVPLRIYWMNSD--LLHITQDERVSMGQNGNLYFANV 65 (95) T ss_pred ceeEEecCCCEEEEecCCC-CCCCCEEEEECCC--CccccccccEEECCCceEEEEEE Confidence 4688999999999987431 1122345666432 2334457788885 688866533 No 250 >PRK13263 ureE urease accessory protein UreE; Provisional Probab=27.20 E-value=1.9e+02 Score=23.87 Aligned_cols=33 Identities=18% Similarity=0.333 Sum_probs=21.7 Q ss_pred EEeeCcchhhhcCCCCCEEEEeCCeEEEEEEEEeCC Q psy254 148 DLYVDYTNITKVVKPGSRIFVDDGLISLVVKSIVKS 183 (187) Q Consensus 148 ~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v~~~ 183 (187) .+.+..+. -..|..||.++.|||.+ .|....++ T Consensus 46 evgl~LpR-g~~L~dGDvL~~ddg~~--IvV~aapE 78 (206) T PRK13263 46 EVAVVLPR-GTVLRDGDVLVAEDGAL--VRVAAAPE 78 (206) T ss_pred EEEEECCC-CCccCCCCEEEeCCCCE--EEEEeCCC Confidence 35555554 34789999999999974 33444443 No 251 >TIGR03471 HpnJ hopanoid biosynthesis associated radical SAM protein HpnJ. One of the well-described hopanoid intermediates is bacteriohopanetetrol. In the conversion from hopene several reactions must occur in the side chain for which a radical mechanism might be reasonable. These include the four (presumably anaerobic) hydroxylations and a methyl shift. Probab=27.11 E-value=4.7e+02 Score=23.64 Aligned_cols=41 Identities=17% Similarity=0.334 Sum_probs=30.8 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHH Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQT 79 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~ 79 (187) +..|.. .+.-+.+.++.|-++|++.+-+.+-.++.+....+ T Consensus 276 ~~~~~~-~~~~~~e~l~~l~~aG~~~v~iGiES~s~~~L~~~ 316 (472) T TIGR03471 276 TWSCNA-RANVDYETLKVMKENGLRLLLVGYESGDQQILKNI 316 (472) T ss_pred eEEEEe-cCCCCHHHHHHHHHcCCCEEEEcCCCCCHHHHHHh Confidence 344443 34568999999999999988888888887765543 No 252 >PRK02610 histidinol-phosphate aminotransferase; Provisional Probab=27.02 E-value=2.3e+02 Score=24.49 Aligned_cols=50 Identities=10% Similarity=0.173 Sum_probs=34.4 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcC------cEEEEecCCCCHHHHHHHHHHHHHHHHH Q psy254 38 GIICTIGPASVAVDMLEKIIETGM------NIARLNFSHGSYEYHGQTIKNIRQAVEN 89 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm------~v~RiN~sHg~~e~~~~~i~~ir~a~~~ 89 (187) -+.+.+-+..++.+..+.|.+.|+ +.+||+|+. .++..+.++.++++..+ T Consensus 316 f~~~~l~~~~~~~~~~~~l~~~gi~v~~~~~~lRls~~~--~~~~~~~l~~l~~~l~~ 371 (374) T PRK02610 316 FLYLRLSQDAALAALHQALKAQGTLVRHTGGGLRITIGT--PEENQRTLERLQAALTQ 371 (374) T ss_pred EEEEeCCCCCCHHHHHHHHHHCCEEEEeCCCeEEEeCCC--HHHHHHHHHHHHHHHhh Confidence 477777333345667777888886 458998874 56678888888776543 No 253 >PRK06788 flagellar motor switch protein; Validated Probab=26.84 E-value=1.4e+02 Score=22.36 Aligned_cols=69 Identities=14% Similarity=0.300 Sum_probs=47.4 Q ss_pred ceeEEEeeCCCCeeEeeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEE Q psy254 98 HALAIALDTKGPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVV 177 (187) Q Consensus 98 ~~v~I~~Dl~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V 177 (187) .+|.+-+.|.--++.++.+ +.|+.|+.|.|... ..++-.++++-..++. ..+-+.+|+...+| T Consensus 34 v~V~v~aeLG~t~ltl~Dl-------L~L~vGDVI~Ldk~-----~~dpv~v~Vng~~~f~-----G~~Gv~~~~~AVrI 96 (119) T PRK06788 34 ISIELGVKLGKASITLGDV-------KQLKVGDVLEVEKN-----LGHKVDVYLSNMKVGI-----GEAIVMDEKFGIII 96 (119) T ss_pred CceEEEEEEecceecHHHH-------hCCCCCCEEEeCCc-----CCCCEEEEECCEEEEE-----EEEEEECCEEEEEE Confidence 5677777777777776655 56999999998532 2334457777555544 45556688999999 Q ss_pred EEEeCC Q psy254 178 KSIVKS 183 (187) Q Consensus 178 ~~v~~~ 183 (187) +++.++ T Consensus 97 tei~~~ 102 (119) T PRK06788 97 SEIEAD 102 (119) T ss_pred EEecCh Confidence 988653 No 254 >cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices. Probab=26.78 E-value=1.1e+02 Score=23.21 Aligned_cols=23 Identities=17% Similarity=0.361 Sum_probs=18.0 Q ss_pred hcCCCCCEEEEeC--C-eEEEEEEEE Q psy254 158 KVVKPGSRIFVDD--G-LISLVVKSI 180 (187) Q Consensus 158 ~~v~~Gd~IlidD--G-~i~l~V~~v 180 (187) ..|++||.|++.+ | ....+|.++ T Consensus 71 ~~l~~GD~I~v~~~~g~~~~Y~V~~~ 96 (144) T cd05829 71 GDLRKGDKVEVTRADGQTATFRVDRV 96 (144) T ss_pred hcCCCCCEEEEEECCCCEEEEEEeEE Confidence 6889999999987 3 477777764 No 255 >cd03329 MR_like_4 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 4. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. This subgroup's function is unknown. Probab=26.76 E-value=2.2e+02 Score=24.96 Aligned_cols=50 Identities=14% Similarity=0.075 Sum_probs=31.9 Q ss_pred HHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 51 DMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 51 ~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) +..+++.+.|.+.+.|-.. ......+-++.++.+.+.+| ..+.|++|--+ T Consensus 149 ~~a~~~~~~Gf~~~Kik~~--~~~~~~~di~~i~~vR~~~G------~~~~l~vDan~ 198 (368) T cd03329 149 DFAEECKALGYRAIKLHPW--GPGVVRRDLKACLAVREAVG------PDMRLMHDGAH 198 (368) T ss_pred HHHHHHHHcCCCEEEEecC--CchhHHHHHHHHHHHHHHhC------CCCeEEEECCC Confidence 4566677889999998422 11123455666666656666 44688899864 No 256 >PRK05764 aspartate aminotransferase; Provisional Probab=26.64 E-value=1e+02 Score=26.65 Aligned_cols=39 Identities=23% Similarity=0.478 Sum_probs=28.9 Q ss_pred HHHHHHHHH-hcCc-----------EEEEecCCCCHHHHHHHHHHHHHHHHH Q psy254 50 VDMLEKIIE-TGMN-----------IARLNFSHGSYEYHGQTIKNIRQAVEN 89 (187) Q Consensus 50 ~~~i~~li~-aGm~-----------v~RiN~sHg~~e~~~~~i~~ir~a~~~ 89 (187) .+....|++ .|+. .+||+|+| +.++..+.++.++++.++ T Consensus 341 ~~~~~~l~~~~gi~v~~g~~f~~~~~vRis~~~-~~~~~~~~i~~l~~~~~~ 391 (393) T PRK05764 341 LEFAEALLEEAGVAVVPGIAFGAPGYVRLSYAT-SLEDLEEGLERIERFLES 391 (393) T ss_pred HHHHHHHHHhCCEEEccccccCCCCEEEEEecC-CHHHHHHHHHHHHHHHHh Confidence 455666665 4644 47999998 688888889988887654 No 257 >PRK06294 coproporphyrinogen III oxidase; Provisional Probab=26.39 E-value=4.5e+02 Score=23.10 Aligned_cols=40 Identities=15% Similarity=0.170 Sum_probs=30.7 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHH Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYH 76 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~ 76 (187) +.|-....|.+-+.+.++.|-++|+|-+-|..=..+.+.. T Consensus 90 ~eit~E~~P~~~~~~~l~~l~~~G~nrislGvQS~~~~~L 129 (370) T PRK06294 90 TEITLEANPENLSESYIRALALTGINRISIGVQTFDDPLL 129 (370) T ss_pred CeEEEEeCCCCCCHHHHHHHHHCCCCEEEEccccCCHHHH Confidence 4566677899999999999999999966666556655543 No 258 >COG0502 BioB Biotin synthase and related enzymes [Coenzyme metabolism] Probab=26.38 E-value=89 Score=27.68 Aligned_cols=31 Identities=16% Similarity=0.358 Sum_probs=25.1 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecC Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFS 69 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~s 69 (187) -++.||+| ..+.+..++|.+||++..=.|+- T Consensus 133 le~c~slG--~l~~eq~~~L~~aGvd~ynhNLe 163 (335) T COG0502 133 LEVCASLG--MLTEEQAEKLADAGVDRYNHNLE 163 (335) T ss_pred cHHhhccC--CCCHHHHHHHHHcChhheecccc Confidence 46889999 67789999999999987655543 No 259 >cd00318 Phosphoglycerate_kinase Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level phosphorylation events in the glycolytic pathway. Substrate-level phosphorylation is defined as production of ATP by a process, which is catalyzed by water-soluble enzymes in the cytosol; not involving membranes and ion gradients. Probab=26.35 E-value=42 Score=30.40 Aligned_cols=106 Identities=18% Similarity=0.212 Sum_probs=61.3 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHH-----HHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEeeecCCCCcccE Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYE-----YHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTGLLQGGGSAEV 124 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e-----~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG~~~~~~~~~i 124 (187) ..+|+.|++.|..|.= +||-..- ....+-......++.++ ++|...-|.-||+.+- ..- T Consensus 36 lpTI~~l~~~gakvvl--~SHlGRP~g~~~~~~SL~~va~~L~~lL~------~~V~f~~d~~g~~~~~--------~i~ 99 (397) T cd00318 36 LPTIKYLLEQGAKVVL--LSHLGRPKGEPNEKYSLAPVAKALSELLG------QPVTFANDCVGPEAEE--------AVE 99 (397) T ss_pred HHHHHHHHHCCCeEEE--EEecCCCCCCCCCCCCHHHHHHHHHHHHC------CCcEECCCCCCHHHHH--------HHh Confidence 4799999999998766 5886632 11222222334555556 7888888899987662 122 Q ss_pred EeeeCCEEEEeeCCCcccCC-CcCEEeeCcchhhhcCCCCCEEEEeCC Q psy254 125 ELVKGQTIRLTTDAAFAEKG-SATDLYVDYTNITKVVKPGSRIFVDDG 171 (187) Q Consensus 125 ~l~~G~~v~lt~~~~~~~~~-~~~~i~v~~~~l~~~v~~Gd~IlidDG 171 (187) .|+.|+.+.|-.=.-|..+. +.+.-..+.+.|.+.+.+---||++|. T Consensus 100 ~l~~GeIlLLEN~RF~~~E~~~~~~e~~~~~~~a~~LA~l~DiyVNDA 147 (397) T cd00318 100 ALKPGDVLLLENVRFYPEEEGKRDDDKEADEEFAKKLASLGDVYVNDA 147 (397) T ss_pred cCCCCcEEEEeccCccccccccCCcchhhHHHHHHHHHHhCCEEEEcc Confidence 46666666553222111110 000011124577888877777899884 No 260 >smart00148 PLCXc Phospholipase C, catalytic domain (part); domain X. Phosphoinositide-specific phospholipases C. These enzymes contain 2 regions (X and Y) which together form a TIM barrel-like structure containing the active site residues. Phospholipase C enzymes (PI-PLC) act as signal transducers that generate two second messengers, inositol-1,4,5-trisphosphate and diacylglycerol. The bacterial enzyme [6] appears to be a homologue of the mammalian PLCs. Probab=26.32 E-value=2.8e+02 Score=20.73 Aligned_cols=53 Identities=13% Similarity=0.147 Sum_probs=38.1 Q ss_pred CCHHHHHHHHHhcCcEEEEecCCCCH--------------HHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC Q psy254 48 VAVDMLEKIIETGMNIARLNFSHGSY--------------EYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK 107 (187) Q Consensus 48 ~~~~~i~~li~aGm~v~RiN~sHg~~--------------e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~ 107 (187) .+...+++-+..|++++=|.+.++.. -...+.++.|++-..+..+ =.|+|+++ T Consensus 29 ~q~~~i~~qL~~GvR~~dirv~~~~~~~~~v~Hg~~~~~~~~~~dvL~~i~~fl~~~p~-------e~VIl~l~ 95 (135) T smart00148 29 SSVEGYIQALDHGCRCVELDCWDGPDGEPVIYHGHTFTLPIKLSEVLEAIKDFAFVTSP-------YPVILSLE 95 (135) T ss_pred ccHHHHHHHHHhCCCEEEEEcccCCCCCEEEEECCcccccEEHHHHHHHHHHHHHhCCC-------CcEEEeeh Confidence 56788989999999998776555421 3567888888887776543 35777775 No 261 >COG4558 ChuT ABC-type hemin transport system, periplasmic component [Inorganic ion transport and metabolism] Probab=26.27 E-value=2.5e+02 Score=24.53 Aligned_cols=44 Identities=18% Similarity=0.377 Sum_probs=34.4 Q ss_pred CCCCceEEEec--CCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHH Q psy254 33 YVRLTGIICTI--GPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIK 81 (187) Q Consensus 33 ~~r~TkIi~Ti--GPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~ 81 (187) ..+.|-||.+= ||+ +.+.+|-.+|+++.=++ .+.+++.....|+ T Consensus 97 slkPdlvi~~~~aGP~----~vl~qLraagV~vv~v~-~~~~~~~i~~~Ir 142 (300) T COG4558 97 SLKPDLVIGSEGAGPA----TVLDQLRAAGVPVVTVP-EQPTLDGIGTKIR 142 (300) T ss_pred ecCCCEEEeecccCcH----HHHHHHHHcCCcEEEcC-CCCCHHHHHHHHH Confidence 46788888875 675 69999999999999998 8888775444443 No 262 >TIGR02539 SepCysS Sep-tRNA:Cys-tRNA synthase. Aminoacylation of tRNA(Cys) with Cys, and cysteine biosynthesis in the process, happens in Methanocaldococcus jannaschii and several other archaea by misacylation of tRNA(Cys) with O-phosphoserine (Sep), followed by modification of the phosphoserine to cysteine. In some species, direct tRNA-cys aminoacylation also occurs but this pathway is required for Cys biosynthesis. Members of this protein catalyze the second step in this two step pathway, using pyridoxal phosphate and a sulfur donor to synthesize Cys from Sep while attached to the tRNA. Probab=26.17 E-value=1.8e+02 Score=25.15 Aligned_cols=40 Identities=15% Similarity=0.189 Sum_probs=30.2 Q ss_pred HHHHHHHHHhcCc--------EEEEecCCCCHHHHHHHHHHHHHHHHH Q psy254 50 VDMLEKIIETGMN--------IARLNFSHGSYEYHGQTIKNIRQAVEN 89 (187) Q Consensus 50 ~~~i~~li~aGm~--------v~RiN~sHg~~e~~~~~i~~ir~a~~~ 89 (187) ....+.|.+.|+- .+|+...+++.++..+.++.+++..++ T Consensus 321 ~~~~~~L~e~GI~~ir~~~~~~iRis~~~~t~e~i~~l~~~L~~~~~~ 368 (370) T TIGR02539 321 YFLYEELKKRGIHGIRSGQTKYFKLSVYGLTKEQVEYVVDSFEEIVEE 368 (370) T ss_pred HHHHHHHHhCCCccccCCcceEEEEEecCCCHHHHHHHHHHHHHHHHh Confidence 4577778888874 566664447999999999999887654 No 263 >TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate. Probab=26.14 E-value=2.3e+02 Score=24.03 Aligned_cols=37 Identities=8% Similarity=0.004 Sum_probs=28.8 Q ss_pred HHHHHHHHhc-CcEEEEe-----cCCCCHHHHHHHHHHHHHHH Q psy254 51 DMLEKIIETG-MNIARLN-----FSHGSYEYHGQTIKNIRQAV 87 (187) Q Consensus 51 ~~i~~li~aG-m~v~RiN-----~sHg~~e~~~~~i~~ir~a~ 87 (187) ..++.++.+| ++..=+| +.+-+.+|+.++++.+++.. T Consensus 25 ~~i~~~i~~G~v~gi~~~GstGE~~~Lt~eEr~~~~~~~~~~~ 67 (290) T TIGR00683 25 QIIRHNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEA 67 (290) T ss_pred HHHHHHHhCCCcCEEEECCcccccccCCHHHHHHHHHHHHHHh Confidence 5666778889 9998888 66677888888887777654 No 264 >PRK13399 fructose-1,6-bisphosphate aldolase; Provisional Probab=25.93 E-value=4.2e+02 Score=23.57 Aligned_cols=53 Identities=11% Similarity=0.147 Sum_probs=39.2 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCC-------HHHHHHHHHHHHHHHHHhC Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGS-------YEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~-------~e~~~~~i~~ir~a~~~~~ 91 (187) .+..-+ ..+.+.+.+++-+++|-+-+.|..||-+ .++.-+.-..+-+.+..+| T Consensus 77 PVaLHL-DHg~~~e~i~~Ai~~GFtSVMiDgS~l~~~~~~~~~eeNI~~Trevve~Ah~~G 136 (347) T PRK13399 77 PICLHQ-DHGNSPATCQSAIRSGFTSVMMDGSLLADGKTPASYDYNVDVTRRVTEMAHAVG 136 (347) T ss_pred cEEEEC-CCCCCHHHHHHHHhcCCCEEEEeCCCCCCCCCccCHHHHHHHHHHHHHHHHHcC Confidence 455555 6777999999999999999999999986 5655555555555555544 No 265 >cd03321 mandelate_racemase Mandelate racemase (MR) catalyzes the Mg2+-dependent 1,1-proton transfer reaction that interconverts the enantiomers of mandelic acid. MR is the first enzyme in the bacterial pathway that converts mandelic acid to benzoic acid and allows this pathway to utilize either enantiomer of mandelate. MR belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Probab=25.87 E-value=1.3e+02 Score=26.15 Aligned_cols=64 Identities=13% Similarity=0.159 Sum_probs=42.1 Q ss_pred CceEEEecCCCC--CCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 36 LTGIICTIGPAS--VAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 36 ~TkIi~TiGPas--~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) ....-+|+|-.+ ...+..+++++.|-+.+.+-....+.+.-.++++.+|+ .+| ..+.|++|--+ T Consensus 130 ~v~~y~s~~~~~~~~~~~~a~~~~~~Gf~~~KiKvg~~~~~~d~~~v~air~---~~g------~~~~l~vDaN~ 195 (355) T cd03321 130 PVQAYDSHGLDGAKLATERAVTAAEEGFHAVKTKIGYPTADEDLAVVRSIRQ---AVG------DGVGLMVDYNQ 195 (355) T ss_pred CeeEEEeCCCChHHHHHHHHHHHHHhhhHHHhhhcCCCChHhHHHHHHHHHH---hhC------CCCEEEEeCCC Confidence 445666765332 22456777889999999998765555555566666664 455 34788999765 No 266 >cd03326 MR_like_1 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 1. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. This subgroup's function is unknown. Probab=25.57 E-value=2.5e+02 Score=24.97 Aligned_cols=49 Identities=12% Similarity=0.325 Sum_probs=34.1 Q ss_pred HHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 51 DMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 51 ~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) +..+++++.|.+.+.+.....+.++-.++++.+|+ ..| .-+.+++|--+ T Consensus 166 ~~a~~~~~~Gf~~~Kikvg~~~~~~di~~v~avRe---~~G------~~~~l~vDaN~ 214 (385) T cd03326 166 DEMRRYLDRGYTVVKIKIGGAPLDEDLRRIEAALD---VLG------DGARLAVDANG 214 (385) T ss_pred HHHHHHHHCCCCEEEEeCCCCCHHHHHHHHHHHHH---hcC------CCCeEEEECCC Confidence 45667788899999998866555555555555554 455 34688999765 No 267 >PLN02892 isocitrate lyase Probab=25.55 E-value=2e+02 Score=27.40 Aligned_cols=55 Identities=16% Similarity=0.196 Sum_probs=39.7 Q ss_pred ceEEEec----CCCCCCHHHHHHHHHhcCcEEEE--------ecCCC------CHHHHHHHHHHHHHHHHHhC Q psy254 37 TGIICTI----GPASVAVDMLEKIIETGMNIARL--------NFSHG------SYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 37 TkIi~Ti----GPas~~~~~i~~li~aGm~v~Ri--------N~sHg------~~e~~~~~i~~ir~a~~~~~ 91 (187) ..|++-+ |-.....+.++.|+++|+..+-| +|.|. +.+++.+.|..+|.+....| T Consensus 170 ~PIiADaEtGyG~~~~~~~~vk~~ieaGAaGIhIEDQ~~~~KkCGh~~gk~Lvp~~e~v~RI~AAR~aad~~G 242 (570) T PLN02892 170 KPIIADGDTGFGGTTATVKLCKLFVERGAAGVHIEDQSSVTKKCGHMGGKVLVATSEHINRLVAARLQFDVMG 242 (570) T ss_pred cceeeecCCCCCccHHHHHHHHHHHHcCCeEEEEECCCCcccccCCCCCCcccCHHHHHHHHHHHHHHHHhcC Confidence 3677766 33444567899999999988777 24564 45678888888888777666 No 268 >PF13550 Phage-tail_3: Putative phage tail protein Probab=25.54 E-value=1.5e+02 Score=22.00 Aligned_cols=25 Identities=16% Similarity=0.262 Sum_probs=19.6 Q ss_pred hhcCCCCCEEEEe--CCeEEEEEEEEe Q psy254 157 TKVVKPGSRIFVD--DGLISLVVKSIV 181 (187) Q Consensus 157 ~~~v~~Gd~Ilid--DG~i~l~V~~v~ 181 (187) .-.++|||.|.+. .....++|.+++ T Consensus 137 ~~~l~pGDvi~l~~~~~~~~~RI~~i~ 163 (164) T PF13550_consen 137 GLALEPGDVIALSDDGRDMRFRITEIE 163 (164) T ss_pred hccCCCCCEEEEEeCCCceEEEEEEEe Confidence 3568999999998 457778888775 No 269 >cd03315 MLE_like Muconate lactonizing enzyme (MLE) like subgroup of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and residues that can function as general acid/base catalysts, a Lys-X-Lys motif and another conserved lysine. Despite these conserved residues, the members of the MLE subgroup, like muconate lactonizing enzyme, o-succinylbenzoate synthase (OSBS) and N-acylamino acid racemase (NAAAR), catalyze different reactions. Probab=25.52 E-value=2.8e+02 Score=22.88 Aligned_cols=63 Identities=10% Similarity=0.200 Sum_probs=39.4 Q ss_pred CceEEEecCCCC--CCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 36 LTGIICTIGPAS--VAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 36 ~TkIi~TiGPas--~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) +..+-+|+|..+ .-.+.++++.+.|-+.+.+++.. +.++-.++++.||+ ..+ ..+.+++|-.+ T Consensus 74 ~i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~KiKvg~-~~~~d~~~v~~vr~---~~g------~~~~l~vDan~ 138 (265) T cd03315 74 RVRVAHMLGLGEPAEVAEEARRALEAGFRTFKLKVGR-DPARDVAVVAALRE---AVG------DDAELRVDANR 138 (265) T ss_pred ceEEEEEecCCCHHHHHHHHHHHHHCCCCEEEEecCC-CHHHHHHHHHHHHH---hcC------CCCEEEEeCCC Confidence 345666775432 12346667888999999999864 33444555555554 444 34688888754 No 270 >COG0126 Pgk 3-phosphoglycerate kinase [Carbohydrate transport and metabolism] Probab=25.50 E-value=86 Score=28.41 Aligned_cols=104 Identities=20% Similarity=0.254 Sum_probs=59.4 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHH----HHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEeeecCCCCcccEE Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYE----YHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTGLLQGGGSAEVE 125 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e----~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG~~~~~~~~~i~ 125 (187) ..+|+.|++.|..|.= +||-..- +...+-...+...+-.+ ++|...-|.-||+.|. .... T Consensus 42 lpTIk~l~~~ga~Vvl--~SHlGRPk~~~~~~SL~pva~~Ls~ll~------~~V~f~~d~~g~~a~~--------~v~~ 105 (395) T COG0126 42 LPTIKYLLEKGAKVVL--LSHLGRPKEYSDKTSLEPVAKRLSELLG------KEVKFVDDCVGPEARQ--------AVAE 105 (395) T ss_pred hHHHHHHHhCCCeEEE--EecCCCCCCCCCcccHHHHHHHHHHhcC------CceEecccccCHHHHH--------HHhc Confidence 3699999999988654 8996533 12222222233333334 7788888988988773 2345 Q ss_pred eeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCC Q psy254 126 LVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDG 171 (187) Q Consensus 126 l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG 171 (187) |+.|+.+.|-.-+=|..+..+ =.-+-++|.+.+.+---||++|. T Consensus 106 l~~GevlLLEN~RF~~~E~~~--d~~~~~~l~k~la~l~DvfVnDA 149 (395) T COG0126 106 LKDGEVLLLENVRFYSEEEKN--DEEARTELVKKLASLGDVFVNDA 149 (395) T ss_pred cCCCcEEEEeeccccccccCc--chhhHHHHHHHHHhhcCEEEech Confidence 777777766433222111111 01112346666666555888884 No 271 >KOG2733|consensus Probab=25.45 E-value=2.2e+02 Score=25.86 Aligned_cols=55 Identities=13% Similarity=0.247 Sum_probs=44.0 Q ss_pred CCCceEEE-ecCCC-CCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 34 VRLTGIIC-TIGPA-SVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 34 ~r~TkIi~-TiGPa-s~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) .++|++|. ++||- ---+..++.-+++|.+..=| -|.+++.++|..+..+.+++.| T Consensus 81 ak~~~vivN~vGPyR~hGE~VVkacienG~~~vDI---SGEP~f~E~mq~kYhd~A~ekG 137 (423) T KOG2733|consen 81 AKQARVIVNCVGPYRFHGEPVVKACIENGTHHVDI---SGEPQFMERMQLKYHDLAKEKG 137 (423) T ss_pred HhhhEEEEeccccceecCcHHHHHHHHcCCceecc---CCCHHHHHHHHHHHHHHHHhcC Confidence 46777665 67994 34467899999999877665 4899999999999999888876 No 272 >cd06552 ASCH_yqfb_like ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. Probab=25.45 E-value=1.3e+02 Score=20.92 Aligned_cols=23 Identities=26% Similarity=0.385 Sum_probs=15.7 Q ss_pred cCCCCCEEEEeCC---eEEEEEEEEe Q psy254 159 VVKPGSRIFVDDG---LISLVVKSIV 181 (187) Q Consensus 159 ~v~~Gd~IlidDG---~i~l~V~~v~ 181 (187) .++|||.+++.++ ...++|.+|. T Consensus 28 ~~~~Gd~~~~~~~~~~~~~~~v~~V~ 53 (100) T cd06552 28 HLKPGDVVEVHTGERIFGEAEITSVE 53 (100) T ss_pred CCCCCCEEEEEECCEEEEEEEEEEEE Confidence 4788888888876 4455666553 No 273 >cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways. Probab=25.41 E-value=1.9e+02 Score=24.12 Aligned_cols=65 Identities=9% Similarity=0.103 Sum_probs=41.7 Q ss_pred CceEEEecCCCC--CCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC Q psy254 36 LTGIICTIGPAS--VAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK 107 (187) Q Consensus 36 ~TkIi~TiGPas--~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~ 107 (187) ++.|++.+|..+ +..+..+...++|++.+-+=.-+-..-.-.++++..++..+..+ .|+-++ +.+ T Consensus 69 ~~~vi~gv~~~~~~~~~~~a~~a~~~G~d~v~~~~P~~~~~~~~~l~~~~~~ia~~~~------~pi~lY-n~P 135 (284) T cd00950 69 RVPVIAGTGSNNTAEAIELTKRAEKAGADAALVVTPYYNKPSQEGLYAHFKAIAEATD------LPVILY-NVP 135 (284) T ss_pred CCcEEeccCCccHHHHHHHHHHHHHcCCCEEEEcccccCCCCHHHHHHHHHHHHhcCC------CCEEEE-ECh Confidence 567888887643 45677788899999966654332222223667788888777655 566644 554 No 274 >PRK07107 inosine 5-monophosphate dehydrogenase; Validated Probab=25.26 E-value=2e+02 Score=26.85 Aligned_cols=20 Identities=15% Similarity=0.326 Sum_probs=17.4 Q ss_pred CCCHHHHHHHHHhcCcEEEE Q psy254 47 SVAVDMLEKIIETGMNIARL 66 (187) Q Consensus 47 s~~~~~i~~li~aGm~v~Ri 66 (187) ..+.+..+.|+++|++..++ T Consensus 292 V~t~e~a~~li~aGAd~I~v 311 (502) T PRK07107 292 VVDREGFRYLAEAGADFVKV 311 (502) T ss_pred ccCHHHHHHHHHcCCCEEEE Confidence 36789999999999999966 No 275 >cd04740 DHOD_1B_like Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. Probab=25.11 E-value=2.5e+02 Score=23.55 Aligned_cols=50 Identities=26% Similarity=0.413 Sum_probs=33.0 Q ss_pred ceEEEecCCCC-CC-HHHHHHHHHhcCcEEEEecCC-----------CCHHHHHHHHHHHHHH Q psy254 37 TGIICTIGPAS-VA-VDMLEKIIETGMNIARLNFSH-----------GSYEYHGQTIKNIRQA 86 (187) Q Consensus 37 TkIi~TiGPas-~~-~~~i~~li~aGm~v~RiN~sH-----------g~~e~~~~~i~~ir~a 86 (187) ..+++.|+-.+ ++ .+..+.+.++|.+.+=|||+. ++++...++++.+|++ T Consensus 90 ~p~ivsi~g~~~~~~~~~a~~~~~~G~d~iElN~~cP~~~~~g~~~~~~~~~~~eiv~~vr~~ 152 (296) T cd04740 90 TPVIASIAGSTVEEFVEVAEKLADAGADAIELNISCPNVKGGGMAFGTDPEAVAEIVKAVKKA 152 (296) T ss_pred CcEEEEEecCCHHHHHHHHHHHHHcCCCEEEEECCCCCCCCCcccccCCHHHHHHHHHHHHhc Confidence 46899995432 22 344555667899999999983 3445556666666654 No 276 >COG0821 gcpE 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism] Probab=25.08 E-value=1.8e+02 Score=25.97 Aligned_cols=44 Identities=18% Similarity=0.350 Sum_probs=0.0 Q ss_pred CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeC Q psy254 49 AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDT 106 (187) Q Consensus 49 ~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl 106 (187) +.+.|++|-++|.++.|+-+.. .+..+.+..|++- .++++..|. T Consensus 38 Tv~QI~~L~~aG~dIVRvtv~~---~e~A~A~~~Ik~~-----------~~vPLVaDi 81 (361) T COG0821 38 TVAQIKALERAGCDIVRVTVPD---MEAAEALKEIKQR-----------LNVPLVADI 81 (361) T ss_pred HHHHHHHHHHcCCCEEEEecCC---HHHHHHHHHHHHh-----------CCCCEEEEe No 277 >cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases. Probab=25.03 E-value=2.7e+02 Score=23.44 Aligned_cols=65 Identities=11% Similarity=0.052 Sum_probs=41.6 Q ss_pred CceEEEecCCCC--CCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHh-CCCCCCcceeEEEeeCC Q psy254 36 LTGIICTIGPAS--VAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENY-SKRIGMPHALAIALDTK 107 (187) Q Consensus 36 ~TkIi~TiGPas--~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~-~~~~~~~~~v~I~~Dl~ 107 (187) +..||+.+|..+ +..+..+...++|++.+-+---+-..-...++++..++..+.. + .|+-++ +.+ T Consensus 70 ~~~viagv~~~~~~~ai~~a~~a~~~Gad~v~~~~P~y~~~~~~~i~~~~~~v~~a~~~------lpi~iY-n~P 137 (288) T cd00954 70 KVTLIAHVGSLNLKESQELAKHAEELGYDAISAITPFYYKFSFEEIKDYYREIIAAAAS------LPMIIY-HIP 137 (288) T ss_pred CCeEEeccCCCCHHHHHHHHHHHHHcCCCEEEEeCCCCCCCCHHHHHHHHHHHHHhcCC------CCEEEE-eCc Confidence 467888776533 3356777889999998876544443323456777777777665 4 566553 543 No 278 >cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria. Probab=25.02 E-value=1.7e+02 Score=21.37 Aligned_cols=61 Identities=18% Similarity=0.228 Sum_probs=38.4 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCC-CHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEee Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHG-SYEYHGQTIKNIRQAVENYSKRIGMPHALAIALD 105 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg-~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~D 105 (187) ++.+ .+||...+ ..+.++++.|==-+=||+..- ..+.+..-...||+++-+++ .|+.--+| T Consensus 48 v~~v-k~~~~~g~-~~i~~~i~~g~i~~VInt~~~~~~~~~~~dg~~iRr~a~~~~------Ip~~Ttl~ 109 (115) T cd01422 48 VNRM-KSGPLGGD-QQIGALIAEGEIDAVIFFRDPLTAQPHEPDVKALLRLCDVYN------IPLATNRS 109 (115) T ss_pred EEEE-ecCCCCch-hHHHHHHHcCceeEEEEcCCCCCCCcccccHHHHHHHHHHcC------CCEEEcHH Confidence 3445 77776544 568888888832333788652 33333555778899888887 66655444 No 279 >PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function Probab=24.84 E-value=2.3e+02 Score=20.13 Aligned_cols=13 Identities=23% Similarity=0.529 Sum_probs=10.5 Q ss_pred hhhcCCCCCEEEE Q psy254 156 ITKVVKPGSRIFV 168 (187) Q Consensus 156 l~~~v~~Gd~Ili 168 (187) +...|++||+|++ T Consensus 73 ~~~~Lk~GD~V~l 85 (100) T PF10844_consen 73 FTDGLKVGDKVLL 85 (100) T ss_pred EecCCcCCCEEEE Confidence 4468899999887 No 280 >TIGR03249 KdgD 5-dehydro-4-deoxyglucarate dehydratase. 5-dehydro-4-deoxyglucarate dehydratase not only catalyzes the dehydration of the substrate (diol to ketone + water), but causes the decarboxylation of the intermediate product to yield 2-oxoglutarate semialdehyde (2,5-dioxopentanoate). The gene for the enzyme is usually observed in the vicinity of transporters and dehydratases handling D-galactarate and D-gluconate as well as aldehyde dehydrogenases which convert the product to alpha-ketoglutarate. Probab=24.78 E-value=2e+02 Score=24.33 Aligned_cols=64 Identities=8% Similarity=-0.020 Sum_probs=41.3 Q ss_pred CCceEEEecCCCC-CCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEe Q psy254 35 RLTGIICTIGPAS-VAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIAL 104 (187) Q Consensus 35 r~TkIi~TiGPas-~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~ 104 (187) .++.||+.+|.++ +..+..+...++|++.+-+---+-.+-..+.+++..++..+... .|+-++= T Consensus 73 g~~pvi~gv~~~t~~ai~~a~~a~~~Gadav~~~pP~y~~~s~~~i~~~f~~v~~a~~------~pvilYn 137 (296) T TIGR03249 73 GKVPVYTGVGGNTSDAIEIARLAEKAGADGYLLLPPYLINGEQEGLYAHVEAVCESTD------LGVIVYQ 137 (296) T ss_pred CCCcEEEecCccHHHHHHHHHHHHHhCCCEEEECCCCCCCCCHHHHHHHHHHHHhccC------CCEEEEe Confidence 3567888888532 23456677888999988764443333234667777777766654 6776663 No 281 >PTZ00039 40S ribosomal protein S20; Provisional Probab=24.71 E-value=1.2e+02 Score=22.64 Aligned_cols=31 Identities=6% Similarity=0.150 Sum_probs=28.4 Q ss_pred CcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 61 MNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 61 m~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) |.-+||.+.-.++....+..+.|.+.++..| T Consensus 16 ~~kirI~L~S~d~~~Ld~~~~~Ii~~ak~~g 46 (115) T PTZ00039 16 LHKIRITLTSKNLKSIEKVCADIITGAKEKN 46 (115) T ss_pred eeEEEEEEEECCHHHHHHHHHHHHHHHHHcC Confidence 6788999999999999999999999988877 No 282 >COG0309 HypE Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones] Probab=24.70 E-value=3.3e+02 Score=24.23 Aligned_cols=26 Identities=23% Similarity=0.282 Sum_probs=19.9 Q ss_pred EecCCCC-HHHHHHHHHHHHHHHHHhC Q psy254 66 LNFSHGS-YEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 66 iN~sHg~-~e~~~~~i~~ir~a~~~~~ 91 (187) ||+.-|. .|+..++++.++++++++| T Consensus 96 lil~eg~~~e~l~~i~~si~e~a~~~G 122 (339) T COG0309 96 LILPEGLPIEDLERILKSIDEEAEEAG 122 (339) T ss_pred EecCCCCCHHHHHHHHHHHHHHHHHcC Confidence 5666665 4567788899999999877 No 283 >PRK07379 coproporphyrinogen III oxidase; Provisional Probab=24.69 E-value=5e+02 Score=23.09 Aligned_cols=40 Identities=20% Similarity=0.211 Sum_probs=31.2 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHH Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYH 76 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~ 76 (187) +.|-+...|.+-+.+.++.|-++|+|-+-|..=.++.+.. T Consensus 102 ~eit~E~~P~~lt~e~l~~l~~~GvnrislGvQS~~d~~L 141 (400) T PRK07379 102 AEISLEIDPGTFDLEQLQGYRSLGVNRVSLGVQAFQDELL 141 (400) T ss_pred CEEEEEeCCCcCCHHHHHHHHHCCCCEEEEEcccCCHHHH Confidence 4566666898999999999999999977776666665543 No 284 >TIGR01302 IMP_dehydrog inosine-5'-monophosphate dehydrogenase. This model describes a rather tightly conserved cluster of IMP dehydrogenase sequences, many of which are characterized. The model excludes two related families of proteins proposed also to be IMP dehydrogenases, but without characterized members. These are related families are the subject of separate models. Probab=24.65 E-value=2.2e+02 Score=25.87 Aligned_cols=31 Identities=19% Similarity=0.424 Sum_probs=23.7 Q ss_pred ceEEE-ecCCCCCCHHHHHHHHHhcCcEEEEecCCC Q psy254 37 TGIIC-TIGPASVAVDMLEKIIETGMNIARLNFSHG 71 (187) Q Consensus 37 TkIi~-TiGPas~~~~~i~~li~aGm~v~RiN~sHg 71 (187) ..||| ++ .+.+..+.++++|++.+++-..-| T Consensus 266 ~~vi~G~v----~t~~~a~~l~~aGad~i~vg~g~G 297 (450) T TIGR01302 266 LDIIAGNV----ATAEQAKALIDAGADGLRVGIGPG 297 (450) T ss_pred CCEEEEeC----CCHHHHHHHHHhCCCEEEECCCCC Confidence 34555 44 678999999999999998865444 No 285 >cd06451 AGAT_like Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT), serine-glyoxylate aminotransferase (SGAT), and 3-hydroxykynurenine transaminase (HKT). AGAT is a homodimeric protein, which catalyses the transamination of glyoxylate to glycine, and SGAT converts serine and glyoxylate to hydroxypyruvate and glycine. HKT catalyzes the PLP-dependent transamination of 3-hydroxykynurenine, a potentially toxic metabolite of the kynurenine pathway. Probab=24.54 E-value=4.2e+02 Score=22.31 Aligned_cols=46 Identities=7% Similarity=0.168 Sum_probs=31.0 Q ss_pred ecCCCCCCHHHHHHHHHh-cC-----------cEEEEecCCC-CHHHHHHHHHHHHHHH Q psy254 42 TIGPASVAVDMLEKIIET-GM-----------NIARLNFSHG-SYEYHGQTIKNIRQAV 87 (187) Q Consensus 42 TiGPas~~~~~i~~li~a-Gm-----------~v~RiN~sHg-~~e~~~~~i~~ir~a~ 87 (187) .+.+.....+..+.|.+. |+ +++|+.+++. +.++..+.++.++++. T Consensus 297 ~~~~~~~~~~~~~~L~~~~gI~~~~g~~~~~~~~iRis~~~~~~~e~v~~~~~~l~~~~ 355 (356) T cd06451 297 LVPEGVDGDEVVRRLMKRYNIEIAGGLGPTAGKVFRIGHMGEATREDVLGVLSALEEAL 355 (356) T ss_pred ECCCCCCHHHHHHHHHHhCCEEEecccccccCCEEEEecCCCCCHHHHHHHHHHHHHHh Confidence 333333445666778887 85 3589999754 6788888888887653 No 286 >TIGR01305 GMP_reduct_1 guanosine monophosphate reductase, eukaryotic. A deep split separates two families of GMP reductase. This family includes both eukaryotic and some proteobacterial sequences, while the other family contains other bacterial sequences. Probab=24.52 E-value=1.5e+02 Score=26.36 Aligned_cols=31 Identities=23% Similarity=0.411 Sum_probs=23.5 Q ss_pred CceEEEecCCCCCCHHHHHHHHHhcCcEEEEecC Q psy254 36 LTGIICTIGPASVAVDMLEKIIETGMNIARLNFS 69 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~s 69 (187) ..-||+- . -.+++..++|+++|+|..++.+- T Consensus 150 ~~~viaG--N-V~T~e~a~~Li~aGAD~ikVgiG 180 (343) T TIGR01305 150 EHTIMAG--N-VVTGEMVEELILSGADIVKVGIG 180 (343) T ss_pred CCeEEEe--c-ccCHHHHHHHHHcCCCEEEEccc Confidence 3456663 2 25689999999999999998754 No 287 >cd00006 PTS_IIA_man PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. IIA subunits receive phosphoryl groups from HPr and transfer them to IIB subunits, which in turn phosphorylate the substrate. Probab=24.48 E-value=2.1e+02 Score=20.69 Aligned_cols=63 Identities=24% Similarity=0.254 Sum_probs=36.3 Q ss_pred EEEecCCCCCCHHHHHHHHHhcC-cEEEEecCCC-CHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 39 IICTIGPASVAVDMLEKIIETGM-NIARLNFSHG-SYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 39 Ii~TiGPas~~~~~i~~li~aGm-~v~RiN~sHg-~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) +++|-|+-+......-+|+.... ++.=++|..+ +.++..+.++. +.++.... ..+-|+.|+.| T Consensus 4 li~sHG~~A~gi~~~~~~i~G~~~~i~~~~~~~~~~~~~~~~~i~~---~i~~~~~~----~~viil~Dl~G 68 (122) T cd00006 4 IIATHGGFASGLLNSAEMILGEQENVEAIDFPPGESPDDLLEKIKA---ALAELDSG----EGVLILTDLFG 68 (122) T ss_pred EEEcCHHHHHHHHHHHHHhcCCCCCeEEEEeCCCCCHHHHHHHHHH---HHHHhCCC----CcEEEEEeCCC Confidence 57778865544444444553334 6777787754 56655554443 33333211 46899999943 No 288 >TIGR01346 isocit_lyase isocitrate lyase. Isocitrate lyase and malate synthase are the enzymes of the glyoxylate shunt, a pathway associated with the TCA cycle. Probab=24.45 E-value=2.3e+02 Score=26.77 Aligned_cols=75 Identities=16% Similarity=0.179 Sum_probs=49.2 Q ss_pred ceEEEec----CCCCCCHHHHHHHHHhcCcEEEE--------ecCCC------CHHHHHHHHHHHHHHHHHhCCCCCCcc Q psy254 37 TGIICTI----GPASVAVDMLEKIIETGMNIARL--------NFSHG------SYEYHGQTIKNIRQAVENYSKRIGMPH 98 (187) Q Consensus 37 TkIi~Ti----GPas~~~~~i~~li~aGm~v~Ri--------N~sHg------~~e~~~~~i~~ir~a~~~~~~~~~~~~ 98 (187) ..|++-+ |....-.+.++.|+++|+..+-| +|.|. +.+++.+.|..+|.+....+ . T Consensus 151 iPIiaD~DtGyG~~~~v~~~vk~~ieaGAaGI~IEDq~~~~KkcGh~~gk~Lvp~~e~v~RI~AAr~Aad~~g------~ 224 (527) T TIGR01346 151 VPIVADGDAGFGGATAVFKLQKAFIERGAAGVHWEDQLSSEKKCGHMAGKVLIPVQEHVNRLVAARLAADIMG------V 224 (527) T ss_pred cceEEECCCCCCCcHHHHHHHHHHHHcCCeEEEEEcCCCcccccCCCCCCcccCHHHHHHHHHHHHHHHHhcC------C Confidence 4577766 44444567899999999988777 45664 45677788888887777766 4 Q ss_pred eeEEEe--eCCCCeeEeeecC Q psy254 99 ALAIAL--DTKGPEIRTGLLQ 117 (187) Q Consensus 99 ~v~I~~--Dl~GPkIRtG~~~ 117 (187) ++-|.. |..+-++=+..+. T Consensus 225 d~vI~ARTDA~~A~LitS~iD 245 (527) T TIGR01346 225 PTLVVARTDAEAATLITSDVD 245 (527) T ss_pred CEEEEEecCccccccccccCC Confidence 444443 4445555454443 No 289 >cd03318 MLE Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived aromatics, catechol and protocatechuate, to citric acid cycle intermediates. Some bacterial species are also capable of dehalogenating chloroaromatic compounds by the action of chloromuconate lactonizing enzymes (Cl-MLEs). MLEs are members of the enolase superfamily characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and that is stabilized by coordination to the essential Mg2+ ion. Probab=24.36 E-value=2.5e+02 Score=24.41 Aligned_cols=65 Identities=11% Similarity=0.162 Sum_probs=40.5 Q ss_pred CceEEEecCCCC--CCHHHHHHHHHhc-CcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCC Q psy254 36 LTGIICTIGPAS--VAVDMLEKIIETG-MNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGP 109 (187) Q Consensus 36 ~TkIi~TiGPas--~~~~~i~~li~aG-m~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GP 109 (187) +..+-+|++..+ ...+..+++++.| -+.+.+-....+.++-.++++.+| +.++ .-+.|++|--+. T Consensus 131 ~v~~~~~~~~~~~~~~~~~~~~~~~~G~f~~~KiKvg~~~~~~d~~~v~avr---~~~g------~~~~l~iDaN~~ 198 (365) T cd03318 131 SLPVAWTLASGDTERDIAEAEEMLEAGRHRRFKLKMGARPPADDLAHVEAIA---KALG------DRASVRVDVNQA 198 (365) T ss_pred ceEEEEEEeCCCHHHHHHHHHHHHhCCCceEEEEEeCCCChHHHHHHHHHHH---HHcC------CCcEEEEECCCC Confidence 456666763322 2234567788899 999999886444444445555555 4455 346888997653 No 290 >PRK00278 trpC indole-3-glycerol-phosphate synthase; Reviewed Probab=24.27 E-value=2.4e+02 Score=23.67 Aligned_cols=33 Identities=15% Similarity=0.151 Sum_probs=24.7 Q ss_pred CceEEEecCCCCCC----------HHHHHHHHHhcCcEEEEec Q psy254 36 LTGIICTIGPASVA----------VDMLEKIIETGMNIARLNF 68 (187) Q Consensus 36 ~TkIi~TiGPas~~----------~~~i~~li~aGm~v~RiN~ 68 (187) +..|||.+=++|-+ .+.-+.+.++|++..|+.. T Consensus 49 ~~~vIaeik~~sps~g~i~~~~~~~~~A~~~~~~GA~aisvlt 91 (260) T PRK00278 49 KPAVIAEVKKASPSKGVIREDFDPVEIAKAYEAGGAACLSVLT 91 (260) T ss_pred CCeEEEEeeCCCCCCCccCCCCCHHHHHHHHHhCCCeEEEEec Confidence 47899999443333 5777788899999999944 No 291 >COG0825 AccA Acetyl-CoA carboxylase alpha subunit [Lipid metabolism] Probab=24.19 E-value=1.5e+02 Score=26.04 Aligned_cols=41 Identities=20% Similarity=0.245 Sum_probs=33.7 Q ss_pred ecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEee Q psy254 67 NFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTG 114 (187) Q Consensus 67 N~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG 114 (187) ||---.+|..++-+.....|+ +++ .||-.++||+|+--=+| T Consensus 127 NFGm~~PeGyRKAlRlm~~Ae-kF~------lPiitfIDT~GAypG~~ 167 (317) T COG0825 127 NFGMPRPEGYRKALRLMKLAE-KFG------LPIITFIDTPGAYPGIG 167 (317) T ss_pred cCCCCCchHHHHHHHHHHHHH-HhC------CCEEEEecCCCCCCCcc Confidence 899899999999988887775 456 89999999999865443 No 292 >PRK14460 ribosomal RNA large subunit methyltransferase N; Provisional Probab=24.09 E-value=3.1e+02 Score=24.25 Aligned_cols=35 Identities=26% Similarity=0.266 Sum_probs=24.0 Q ss_pred EEEecCCCCCCHHHHHHHHHhcCcEEEEecC--CCCHHHHHHH Q psy254 39 IICTIGPASVAVDMLEKIIETGMNIARLNFS--HGSYEYHGQT 79 (187) Q Consensus 39 Ii~TiGPas~~~~~i~~li~aGm~v~RiN~s--Hg~~e~~~~~ 79 (187) -|-|.|- .+.++.|..+|. +++++| +.+.+.+.++ T Consensus 195 tvsT~G~----~~~i~~L~~~~l--~~L~iSLha~~~e~r~~i 231 (354) T PRK14460 195 TVSTCGI----EKGLRELGESGL--AFLAVSLHAPNQELRERI 231 (354) T ss_pred EEECCCC----hHHHHHHHhCCC--cEEEEeCCCCCHHHHHHh Confidence 3456664 568889998887 678877 5666655554 No 293 >TIGR03537 DapC succinyldiaminopimelate transaminase. Note: the detailed information included in the EC:2.6.1.17 record includes the assertions that the enzyme uses the pyridoxal pyrophosphate cofactor, which is consistent with the pfam00155 family, and the assertion that the amino group donor is L-glutamate, which is undetermined for the sequences in this clade. Probab=23.96 E-value=1.8e+02 Score=24.83 Aligned_cols=45 Identities=13% Similarity=0.237 Sum_probs=28.6 Q ss_pred EEEecCCCCCCHHHHHHHHHhcCcE-------------EEEecCCCCHHHHHHHHHHHH Q psy254 39 IICTIGPASVAVDMLEKIIETGMNI-------------ARLNFSHGSYEYHGQTIKNIR 84 (187) Q Consensus 39 Ii~TiGPas~~~~~i~~li~aGm~v-------------~RiN~sHg~~e~~~~~i~~ir 84 (187) +.+.+.+.-.+.+..+.|.++|+-| +||+++ .+.++.++-++.++ T Consensus 291 ~~~~~~~~~~~~~l~~~L~~~gv~v~~g~~f~~~~~~~~Ri~~~-~~~~~~~~~l~~~~ 348 (350) T TIGR03537 291 LWVKVPSGIDAKDYALRLLENGIVVAPGENFGSGEEGYVRVALV-PTLEECEEALRLWE 348 (350) T ss_pred EEEECCCCCCHHHHHHHHHHCCEEEcCchhhCCCCCCEEEEEec-CCHHHHHHHHHHHh Confidence 4566643334567777787777543 788887 66666666665554 No 294 >KOG2550|consensus Probab=23.94 E-value=87 Score=28.82 Aligned_cols=44 Identities=14% Similarity=0.280 Sum_probs=32.3 Q ss_pred CCHHHHHHHHHhcCcEEEEecCCCCHHHHH----------HHHHHHHHHHHHhC Q psy254 48 VAVDMLEKIIETGMNIARLNFSHGSYEYHG----------QTIKNIRQAVENYS 91 (187) Q Consensus 48 ~~~~~i~~li~aGm~v~RiN~sHg~~e~~~----------~~i~~ir~a~~~~~ 91 (187) -+.+.-++||.||+|..|+-|--|+..--+ ..+.++-+.+..+| T Consensus 301 VT~~qa~nLI~aGaDgLrVGMGsGSiCiTqevma~GrpQ~TAVy~va~~A~q~g 354 (503) T KOG2550|consen 301 VTKEQAANLIAAGADGLRVGMGSGSICITQKVMACGRPQGTAVYKVAEFANQFG 354 (503) T ss_pred eeHHHHHHHHHccCceeEeccccCceeeeceeeeccCCcccchhhHHHHHHhcC Confidence 456899999999999999999999876544 23445555555544 No 295 >COG4702 Uncharacterized conserved protein [Function unknown] Probab=23.88 E-value=1.6e+02 Score=23.32 Aligned_cols=42 Identities=26% Similarity=0.284 Sum_probs=33.4 Q ss_pred EEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeE Q psy254 65 RLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIR 112 (187) Q Consensus 65 RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIR 112 (187) |+-|+|-+.+..-+.=..||+++++.+ .||+|=+-|.|..+- T Consensus 20 ~l~f~~fd~~dAf~LG~~IR~~a~k~~------~piaIDItL~g~~lF 61 (168) T COG4702 20 RLQFSSFDYADAFSLGTYIRRAAKKNK------LPIAIDITLNGHQLF 61 (168) T ss_pred hhccccCcHHHHHHHHHHHHHHHHhcC------CCEEEEEEECCceEE Confidence 456999999999999999999888876 677776666666553 No 296 >PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function. Probab=23.84 E-value=87 Score=20.04 Aligned_cols=23 Identities=17% Similarity=0.219 Sum_probs=17.8 Q ss_pred CCCCEEEEeCCeEEEEEEEEeCC Q psy254 161 KPGSRIFVDDGLISLVVKSIVKS 183 (187) Q Consensus 161 ~~Gd~IlidDG~i~l~V~~v~~~ 183 (187) ++||.|.+--|-=.|+|.++.+. T Consensus 2 ~~GDvV~LKSGGp~MTV~~v~~~ 24 (53) T PF09926_consen 2 KIGDVVQLKSGGPRMTVTEVGPN 24 (53) T ss_pred CCCCEEEEccCCCCeEEEEcccc Confidence 67888888888888888877543 No 297 >TIGR00007 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase. Examples of this enzyme in Actinobacteria have been found to be bifunctional, also possessing phosphoribosylanthranilate isomerase activity ; the trusted cutoff here has now been raised to 275.0 to exclude the bifunctional group, now represented by model TIGR01919. HisA from Lactococcus lactis was reported to be inactive (MEDLINE:93322317). Probab=23.83 E-value=2.7e+02 Score=22.31 Aligned_cols=61 Identities=15% Similarity=0.390 Sum_probs=41.1 Q ss_pred EecCCCCCCHHHHHHHHHhcCcEEEEecC-CCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEe Q psy254 41 CTIGPASVAVDMLEKIIETGMNIARLNFS-HGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRT 113 (187) Q Consensus 41 ~TiGPas~~~~~i~~li~aGm~v~RiN~s-Hg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRt 113 (187) ..+|---.+.+.++.++++|++..=++.+ +.++ +.++++.++++. .++.+.+|.++.++-+ T Consensus 75 i~~ggGI~~~ed~~~~~~~Ga~~vvlgs~~l~d~-------~~~~~~~~~~g~-----~~i~~sid~~~~~v~~ 136 (230) T TIGR00007 75 VQVGGGIRSLEDVEKLLDLGVDRVIIGTAAVENP-------DLVKELLKEYGP-----ERIVVSLDARGGEVAV 136 (230) T ss_pred EEEeCCcCCHHHHHHHHHcCCCEEEEChHHhhCH-------HHHHHHHHHhCC-----CcEEEEEEEECCEEEE Confidence 33445557799999999999997766533 4333 345666667653 3467888998877643 No 298 >cd03319 L-Ala-DL-Glu_epimerase L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of the murein peptide of peptidoglycan, of which L-Ala-D-Glu is a component. L-Ala-D/L-Glu epimerase is a member of the enolase-superfamily, which is characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Probab=23.78 E-value=2.3e+02 Score=24.10 Aligned_cols=61 Identities=16% Similarity=0.202 Sum_probs=37.2 Q ss_pred ceEEEecCCCCC--CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 37 TGIICTIGPASV--AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 37 TkIi~TiGPas~--~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) -...++++..+. -.+.++++.+.|-+.+.||+... .+.-.++++.+|++ ++ + +.|++|..+ T Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~~~~Gf~~iKik~g~~-~~~d~~~v~~lr~~---~g-~------~~l~vD~n~ 186 (316) T cd03319 124 LETDYTISIDTPEAMAAAAKKAAKRGFPLLKIKLGGD-LEDDIERIRAIREA---AP-D------ARLRVDANQ 186 (316) T ss_pred ceeEEEEeCCCHHHHHHHHHHHHHcCCCEEEEEeCCC-hhhHHHHHHHHHHh---CC-C------CeEEEeCCC Confidence 345566644221 12456778888999999999543 34445555555544 33 1 478889865 No 299 >PRK14711 ureE urease accessory protein UreE; Provisional Probab=23.47 E-value=2.6e+02 Score=22.72 Aligned_cols=31 Identities=16% Similarity=0.273 Sum_probs=21.0 Q ss_pred EeeCcchhhhcCCCCCEEEEeCCeEEEEEEEE Q psy254 149 LYVDYTNITKVVKPGSRIFVDDGLISLVVKSI 180 (187) Q Consensus 149 i~v~~~~l~~~v~~Gd~IlidDG~i~l~V~~v 180 (187) +.+..+. -..|..||.++.+||...+.|.++ T Consensus 50 igI~L~r-~~~L~dGDVL~~~dg~~v~Vvv~~ 80 (191) T PRK14711 50 LALSLDR-NTHLHDGDILLWNEGDKCAVVARV 80 (191) T ss_pred EEEECCC-CCcCCCCCEEEecCCCEEEEEEEe Confidence 4554444 346899999999999765444454 No 300 >PLN02428 lipoic acid synthase Probab=23.41 E-value=2.6e+02 Score=24.87 Aligned_cols=30 Identities=13% Similarity=0.243 Sum_probs=21.1 Q ss_pred ceEEEecCCCCC-CHHHHHHHHHhcCcEEEEe Q psy254 37 TGIICTIGPASV-AVDMLEKIIETGMNIARLN 67 (187) Q Consensus 37 TkIi~TiGPas~-~~~~i~~li~aGm~v~RiN 67 (187) ++|-+ +-|.-. +.+.|+.|.++|.+++=.| T Consensus 182 i~Ie~-L~pdf~~d~elL~~L~eAG~d~i~hn 212 (349) T PLN02428 182 ILVEA-LVPDFRGDLGAVETVATSGLDVFAHN 212 (349) T ss_pred cEEEE-eCccccCCHHHHHHHHHcCCCEEccC Confidence 34444 446432 7899999999999985544 No 301 >PRK06444 prephenate dehydrogenase; Provisional Probab=23.35 E-value=1.7e+02 Score=23.68 Aligned_cols=60 Identities=13% Similarity=0.127 Sum_probs=37.2 Q ss_pred HhhcCCCCCCCCCCCC---CceEEEecCCCCC--CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHH Q psy254 20 DHLCGLDIDNKSSYVR---LTGIICTIGPASV--AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAV 87 (187) Q Consensus 20 ~~~~~l~i~~~~~~~r---~TkIi~TiGPas~--~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~ 87 (187) +.++...++++..... +.-|++ .|.+. ..+.+++|++ |+.+.++ ++++|.+.+..+-... T Consensus 71 ~~vg~HPMfGp~~a~~~lf~~~iv~--~~~~~~~~~~~~~~l~~-G~~~~~~-----t~eeHD~~~A~ishLp 135 (197) T PRK06444 71 KIVSIHPLFGPMSYNDGVHRTVIFI--NDISRDNYLNEINEMFR-GYHFVEM-----TADEHDLLMSEIMVKP 135 (197) T ss_pred CEEecCCCCCCCcCcccccceEEEE--CCCCCHHHHHHHHHHHc-CCEEEEe-----CHHHHHHHHHHHHHHH Confidence 4566777888544221 444554 34332 2356888887 8877764 6788887777775543 No 302 >TIGR01979 sufS cysteine desulfurases, SufS subfamily. This model represents a subfamily of NifS-related cysteine desulfurases involved in FeS cluster formation needed for nitrogen fixation among other vital functions. Many cysteine desulfurases are also active as selenocysteine lyase and/or cysteine sulfinate desulfinase. This subfamily is associated with the six-gene SUF system described in E. coli and Erwinia as an FeS cluster formation system during oxidative stress. The active site Cys is this subfamily resembles GHHC with one or both His conserved. Probab=23.31 E-value=3.2e+02 Score=23.63 Aligned_cols=29 Identities=10% Similarity=0.189 Sum_probs=21.8 Q ss_pred EEEEecCC-CCHHHHHHHHHHHHHHHHHhC Q psy254 63 IARLNFSH-GSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 63 v~RiN~sH-g~~e~~~~~i~~ir~a~~~~~ 91 (187) ..||.+.+ -+.++..+.++.++++.+.+| T Consensus 374 ~iRiS~~~~~t~~di~~l~~~l~~~~~~~~ 403 (403) T TIGR01979 374 TCRASFYIYNTEEDIDALVEALKKVRKFFG 403 (403) T ss_pred EEEEEeccCCCHHHHHHHHHHHHHHHHHhC Confidence 47887764 367888899999988776653 No 303 >PRK13958 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional Probab=23.29 E-value=1.8e+02 Score=23.59 Aligned_cols=58 Identities=9% Similarity=0.076 Sum_probs=36.5 Q ss_pred CCHHHHHHHHHhcCcEEEEecCCCCHHHH-HHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCee Q psy254 48 VAVDMLEKIIETGMNIARLNFSHGSYEYH-GQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEI 111 (187) Q Consensus 48 ~~~~~i~~li~aGm~v~RiN~sHg~~e~~-~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkI 111 (187) .+.+.++...++|+|..=|.|...++.+. .+....|.+. .... ..+|+++.+..--+| T Consensus 9 t~~eda~~~~~~GaD~iGfIf~~~SpR~V~~~~a~~i~~~---~~~~---~~~VgVf~~~~~~~i 67 (207) T PRK13958 9 TTIKDVTAASQLPIDAIGFIHYEKSKRHQTITQIKKLASA---VPNH---IDKVCVVVNPDLTTI 67 (207) T ss_pred CcHHHHHHHHHcCCCEEEEecCCCCcccCCHHHHHHHHHh---CCCC---CCEEEEEeCCCHHHH Confidence 67889999999999999999988776543 2333333322 2211 146777776543333 No 304 >PF11964 SpoIIAA-like: SpoIIAA-like; InterPro: IPR021866 This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 120 to 132 amino acids in length. This protein has a single completely conserved residue A that may be functionally important. ; PDB: 2Q3L_B 2OOK_A 3BL4_A. Probab=23.12 E-value=1.2e+02 Score=21.08 Aligned_cols=38 Identities=8% Similarity=0.145 Sum_probs=25.9 Q ss_pred EEEEec-CCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCC Q psy254 63 IARLNF-SHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTK 107 (187) Q Consensus 63 v~RiN~-sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~ 107 (187) |+++.+ .+-+.++.++++..+.+..+.. .++.+++|+. T Consensus 2 il~v~~~g~~t~ed~~~~~~~~~~~~~~~-------~~~~ll~d~~ 40 (109) T PF11964_consen 2 ILAVRVSGKLTEEDYKELLPALEELIADH-------GKIRLLVDLR 40 (109) T ss_dssp -EEEEEEEEE-HHHHHHHHHHHHHHHTTS-------SSEEEEEEEC T ss_pred EEEEEEeeeeCHHHHHHHHHHHHHHHhcC-------CceEEEEEec Confidence 344444 4667888888888888876543 4689999987 No 305 >TIGR01520 FruBisAldo_II_A fructose-bisphosphate aldolase, class II, yeast/E. coli subtype. This model represents one of two deeply split, architecturally distinct clades of the family that includes class II fructose-bisphosphate aldolases, tagatose-bisphosphate aldolases, and related uncharacterized proteins. This family is well-conserved and includes characterized FBA from Saccharomyces cerevisiae, Escherichia coli, and Corynebacterium glutamicum. Proteins outside the scope of this model may also be designated as class II fructose-bisphosphate aldolases, but are well separated in an alignment-based phylogenetic tree. Probab=22.95 E-value=4.8e+02 Score=23.38 Aligned_cols=55 Identities=7% Similarity=0.097 Sum_probs=42.1 Q ss_pred CceEEEecCCCCCCH--HHHHHHHHhc-----------CcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 36 LTGIICTIGPASVAV--DMLEKIIETG-----------MNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 36 ~TkIi~TiGPas~~~--~~i~~li~aG-----------m~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) +..+..-+ ..+.+. +.++..+++| .+-..|..||-+.++.-+.-..+-+.+...| T Consensus 99 ~VPValHL-DHg~~~~~~~i~~ai~ag~~~~~~~g~~gftSVMiDgS~lpfeENI~~TrevVe~Ah~~G 166 (357) T TIGR01520 99 GVPVVLHT-DHCAKKLLPWVDGLLEAGEKYFSAHGKPLFSSHMIDLSEEPIEENIEICVKYLKRMAKIK 166 (357) T ss_pred CCCEEEEC-CCCCCcchHHHHHHHHhhhhhhhhcCCCCCceEEeeCCCCCHHHHHHHHHHHHHHHHHcC Confidence 34566666 556666 7799999987 8999999999999887777777766666655 No 306 >TIGR00649 MG423 conserved hypothetical protein. Contains an ATP-binding domain at the N-terminal end of the protein. Possibly part of a superfamily of beta-lactmases Probab=22.69 E-value=1.6e+02 Score=26.27 Aligned_cols=30 Identities=27% Similarity=0.485 Sum_probs=24.5 Q ss_pred HHHHhcCcEE-EEecC-CCCHHHHHHHHHHHH Q psy254 55 KIIETGMNIA-RLNFS-HGSYEYHGQTIKNIR 84 (187) Q Consensus 55 ~li~aGm~v~-RiN~s-Hg~~e~~~~~i~~ir 84 (187) .+.+.|+++. ++.+| |++.+++.++++.+| T Consensus 344 ~~~~~~~~~~~~~h~SgHa~~~dl~~~i~~~~ 375 (422) T TIGR00649 344 RLNEVGARVIKRIHVSGHASQEDHKLLLRLLK 375 (422) T ss_pred HHHhcCCEEEeceEecCCCCHHHHHHHHHHhC Confidence 4778999874 46777 999999999998775 No 307 >COG1830 FbaB DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes [Carbohydrate transport and metabolism] Probab=22.60 E-value=3.9e+02 Score=22.92 Aligned_cols=57 Identities=16% Similarity=0.197 Sum_probs=43.4 Q ss_pred HHHHHHHHhcCc--EEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEe Q psy254 51 DMLEKIIETGMN--IARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRT 113 (187) Q Consensus 51 ~~i~~li~aGm~--v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRt 113 (187) ...++.++.|++ .+-+|+--.+..+..+.+..++..+.++| .|+-+++=..||.+.- T Consensus 101 ~~ve~ai~lgadAV~~~Vy~Gse~e~~~i~~~~~v~~~a~~~G------mp~v~~~YpRg~~~~~ 159 (265) T COG1830 101 ATVEDAIRLGADAVGATVYVGSETEREMIENISQVVEDAHELG------MPLVAWAYPRGPAIKD 159 (265) T ss_pred eeHHHHHhCCCcEEEEEEecCCcchHHHHHHHHHHHHHHHHcC------CceEEEEeccCCcccc Confidence 356777899998 56677766666666677777777788888 8888888888998854 No 308 >PRK08624 hypothetical protein; Provisional Probab=22.57 E-value=4.4e+02 Score=23.77 Aligned_cols=67 Identities=16% Similarity=0.253 Sum_probs=40.8 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCC----CHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHG----SYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg----~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) +-.|||+| ++-+.+.++-|.+.+.+-.-|-|--. ..++..+.+..|++.++.+.. +..+.++.|..| T Consensus 267 ~naVA~lG-TalT~~q~~lL~r~~~~~Vil~~Dgd~~d~~~~~~~~~~~ki~k~~~~~~~----~~~~~~~~d~~g 337 (373) T PRK08624 267 NFVVAICG-SNISEVQAEKLLRLGVEEVTIALDKEYMDVTEEEVYEYIKKLMKPVKTFAP----YVNIYILKDEAG 337 (373) T ss_pred CcEEECCh-hhCCHHHHHHHHhcCCCcEEEEecCCccccchHHHHHHHHHHHHHHHhcCc----ceEEEEEecchh Confidence 45899998 66778999999988874333333321 123455666666666666542 245566666543 No 309 >cd00452 KDPG_aldolase KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate (KHG) aldolase, which has enzymatic specificity toward glyoxylate, forming KHG in the presence of pyruvate, and is capable of regulating glyoxylate levels in the glyoxylate bypass, an alternate pathway when bacteria are grown on acetate carbon sources. Probab=22.51 E-value=1.9e+02 Score=22.78 Aligned_cols=34 Identities=21% Similarity=0.416 Sum_probs=24.9 Q ss_pred CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHH Q psy254 49 AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQ 85 (187) Q Consensus 49 ~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~ 85 (187) -.+.++.++++|++++.+.++... +.+.++.+++ T Consensus 18 ~~~~~~~l~~~G~~~vev~~~~~~---~~~~i~~l~~ 51 (190) T cd00452 18 ALALAEALIEGGIRAIEITLRTPG---ALEAIRALRK 51 (190) T ss_pred HHHHHHHHHHCCCCEEEEeCCChh---HHHHHHHHHH Confidence 357888999999999999988554 4445554443 No 310 >PLN02858 fructose-bisphosphate aldolase Probab=22.46 E-value=4e+02 Score=28.15 Aligned_cols=55 Identities=16% Similarity=0.117 Sum_probs=45.7 Q ss_pred CceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 36 LTGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) ...+..-+ ..+.+.+.+.+-+++|.+-..|..||-+.|+.-+.-..+-+.+..++ T Consensus 1169 ~vpV~lHL-DHg~~~~~i~~ai~~Gf~SVM~DgS~l~~eeNi~~t~~vv~~Ah~~g 1223 (1378) T PLN02858 1169 SVPITVHF-DHGTSKHELLEALELGFDSVMVDGSHLSFTENISYTKSISSLAHSKG 1223 (1378) T ss_pred CCCEEEEC-CCCCCHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHHHHHHHcC Confidence 34566666 67789999999999999999999999999888777777777777665 No 311 >PRK15072 bifunctional D-altronate/D-mannonate dehydratase; Provisional Probab=22.44 E-value=3.4e+02 Score=24.20 Aligned_cols=19 Identities=21% Similarity=0.378 Sum_probs=15.0 Q ss_pred HHHHHHHHhcCcEEEEecC Q psy254 51 DMLEKIIETGMNIARLNFS 69 (187) Q Consensus 51 ~~i~~li~aGm~v~RiN~s 69 (187) +..+++++.|.+.+.+.+. T Consensus 133 ~~a~~~~~~Gf~~~KiKvg 151 (404) T PRK15072 133 DDVARHLELGYKAIRVQCG 151 (404) T ss_pred HHHHHHHHcCCCEEEEecC Confidence 5556677889999999864 No 312 >COG2108 Uncharacterized conserved protein related to pyruvate formate-lyase activating enzyme [General function prediction only] Probab=22.31 E-value=1.3e+02 Score=26.69 Aligned_cols=42 Identities=24% Similarity=0.389 Sum_probs=28.6 Q ss_pred CCCCHHHHHHHHHhcCcEEEEec---CCCCHHHHHHHHHHHHHHHHHhC Q psy254 46 ASVAVDMLEKIIETGMNIARLNF---SHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 46 as~~~~~i~~li~aGm~v~RiN~---sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) ..-+.+.++.|.+||.|=.||+- .-...+ +.+++++.| +.++ T Consensus 120 ~~~~~e~l~~L~eAGLDEIRfHp~~~~~~~~e---~~i~~l~~A-~~~g 164 (353) T COG2108 120 ILATEEALKALAEAGLDEIRFHPPRPGSKSSE---KYIENLKIA-KKYG 164 (353) T ss_pred ccCCHHHHHHHHhCCCCeEEecCCCccccccH---HHHHHHHHH-HHhC Confidence 34568999999999999999988 333344 445555433 2445 No 313 >TIGR00612 ispG_gcpE 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase. Chlamydial members of the family have a long insert. The family is largely restricted to Bacteria, where it is widely but not universally distributed. No homology can be detected between the GcpE family and other proteins. Probab=22.26 E-value=1.2e+02 Score=26.92 Aligned_cols=44 Identities=18% Similarity=0.281 Sum_probs=0.0 Q ss_pred CHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeC Q psy254 49 AVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDT 106 (187) Q Consensus 49 ~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl 106 (187) +.+.|.+|.++|.++.|+-.---...+....|.. + .++++..|+ T Consensus 36 tv~QI~~L~~aGceiVRvavp~~~~A~al~~I~~--------~------~~iPlVADI 79 (346) T TIGR00612 36 TVAQIRALEEAGCDIVRVTVPDRESAAAFEAIKE--------G------TNVPLVADI 79 (346) T ss_pred HHHHHHHHHHcCCCEEEEcCCCHHHHHhHHHHHh--------C------CCCCEEEee No 314 >PF09347 DUF1989: Domain of unknown function (DUF1989); InterPro: IPR018959 This entry represents proteins that are functionally uncharacterised. ; PDB: 3ORU_A 3SIY_C 3DI4_A. Probab=22.25 E-value=2.1e+02 Score=22.51 Aligned_cols=59 Identities=17% Similarity=0.212 Sum_probs=30.1 Q ss_pred cccEEeeeCCEEEEeeCCCccc-------CCC-cCEEeeCcc--h-hhhcCCCCCEEEEeCCeEEEEEEE Q psy254 121 SAEVELVKGQTIRLTTDAAFAE-------KGS-ATDLYVDYT--N-ITKVVKPGSRIFVDDGLISLVVKS 179 (187) Q Consensus 121 ~~~i~l~~G~~v~lt~~~~~~~-------~~~-~~~i~v~~~--~-l~~~v~~Gd~IlidDG~i~l~V~~ 179 (187) .....|++|+.++|+.-+.-+. ..+ .+.++.... . --..+++|+.++=+.|+.-++|++ T Consensus 9 ~~a~~v~rG~~lri~d~~G~q~~d~~~~~a~d~~Er~s~~~T~~~~~~~~l~~G~~L~S~~~rpm~tIv~ 78 (166) T PF09347_consen 9 GWAFRVKRGQVLRITDPEGNQVVDLLAYNADDPSERLSMGDTRKAQHTIYLTTGDVLYSNMGRPMLTIVE 78 (166) T ss_dssp EEEEEE-TT-EEEEEESSSS--EEEEEEETTEEEEEB-HHHHHHHHCBSC--TT-EEEBTTTSEEEEEEE T ss_pred ceEEEECCCCEEEEEeCCCCceeEEEEEecCCCcEEeCHHHHHHhhcccccCCCCEEEcCCCCeEEEEEc Confidence 3457889999999875432110 000 011111100 0 113578999999999999998876 No 315 >COG0106 HisA Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism] Probab=22.22 E-value=2.8e+02 Score=23.47 Aligned_cols=63 Identities=13% Similarity=0.285 Sum_probs=45.4 Q ss_pred EEecCCCCCCHHHHHHHHHhcCcEEEEe-cCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEeee Q psy254 40 ICTIGPASVAVDMLEKIIETGMNIARLN-FSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTGL 115 (187) Q Consensus 40 i~TiGPas~~~~~i~~li~aGm~v~RiN-~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG~ 115 (187) =+=+|=--++.+.+..|+.+|++..=+- +++-++ +.++++.++++ -.+.+-+|.++-+..+.. T Consensus 77 ~vQvGGGIRs~~~v~~ll~~G~~rViiGt~av~~p-------~~v~~~~~~~g------~rivv~lD~r~g~vav~G 140 (241) T COG0106 77 PVQVGGGIRSLEDVEALLDAGVARVIIGTAAVKNP-------DLVKELCEEYG------DRIVVALDARDGKVAVSG 140 (241) T ss_pred CEEeeCCcCCHHHHHHHHHCCCCEEEEecceecCH-------HHHHHHHHHcC------CcEEEEEEccCCcccccc Confidence 3444556689999999999998855543 333333 45677888888 468999999998887643 No 316 >cd00571 UreE UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The C-terminal region of UreE contains a histidine rich nickel binding site. Probab=22.12 E-value=3.1e+02 Score=20.66 Aligned_cols=25 Identities=28% Similarity=0.624 Sum_probs=19.0 Q ss_pred EEeeCcchhhhcCCCCCEEEEeCCeE Q psy254 148 DLYVDYTNITKVVKPGSRIFVDDGLI 173 (187) Q Consensus 148 ~i~v~~~~l~~~v~~Gd~IlidDG~i 173 (187) .+.+..+. -..|+.||.++.|||.+ T Consensus 44 ei~i~L~r-~~~L~dGdvL~~d~~~~ 68 (136) T cd00571 44 ELGIRLPR-GQVLRDGDVLFLDDGRL 68 (136) T ss_pred EEEEECCC-CCcCCCCCEEEeCCCCE Confidence 35565555 35799999999999976 No 317 >PF03325 Herpes_PAP: Herpesvirus polymerase accessory protein; InterPro: IPR004997 This is an accessory subunit of Herpesvirus DNA polymerase that acts to increase the processivity of polymerisation.; GO: 0030337 DNA polymerase processivity factor activity, 0019079 viral genome replication; PDB: 1YYP_A 1T6L_A. Probab=22.03 E-value=1.8e+02 Score=24.74 Aligned_cols=91 Identities=19% Similarity=0.232 Sum_probs=43.8 Q ss_pred HhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEeeecCCCCcccEEeeeCCEEEEeeC Q psy254 58 ETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRTGLLQGGGSAEVELVKGQTIRLTTD 137 (187) Q Consensus 58 ~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~ 137 (187) +.|=+.+|+.|.|+.-.+..++|.=.-++.....+...-.-.+-|++--.-|-|.--...+ .++++..+.+|.|..- T Consensus 23 Esg~SavrvDlD~svV~eliKWiaP~tr~KR~~Kk~~~p~~tvQIlVhanPPtiKfil~~~---nELEFta~nrV~FH~V 99 (281) T PF03325_consen 23 ESGNSAVRVDLDHSVVSELIKWIAPHTRVKRNVKKQPCPAGTVQILVHANPPTIKFILTSG---NELEFTANNRVSFHDV 99 (281) T ss_dssp --STTSEEEEE-HHHHHHHHHHH-----------------SEEEEEEETTTTEEEEEETTS----EEEEESCTTEEECC- T ss_pred ccCCcceEEecchHHHHHHHHHhCccccccccccCCCCCcceEEEEEecCCCceEEEecCC---ceEEEecCCeEEEeec Confidence 4677889999999998888777765544433322221111346788887777776422222 3455555555544321 Q ss_pred CCcccCCCcCEEeeCcchhhh Q psy254 138 AAFAEKGSATDLYVDYTNITK 158 (187) Q Consensus 138 ~~~~~~~~~~~i~v~~~~l~~ 158 (187) . .-.+.|..++|.. T Consensus 100 K-------nmR~~vq~KNl~q 113 (281) T PF03325_consen 100 K-------NMRLNVQLKNLYQ 113 (281) T ss_dssp --------SEEEEEEHHHHHH T ss_pred c-------eeEEEEehhHHHH Confidence 1 1236666666553 No 318 >cd00951 KDGDH 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH), which is member of dihydrodipicolinate synthase (DHDPS) family that comprises several pyruvate-dependent class I aldolases. The enzyme is involved in glucarate metabolism, and its mechanism presumbly involves a Schiff-base intermediate similar to members of DHDPS family. While in the case of Pseudomonas sp. 5-dehydro-4-deoxy-D-glucarate is degraded by KDGDH to 2,5-dioxopentanoate, in certain species of Enterobacteriaceae it is degraded instead to pyruvate and glycerate. Probab=21.99 E-value=2.9e+02 Score=23.34 Aligned_cols=63 Identities=6% Similarity=-0.015 Sum_probs=41.0 Q ss_pred CceEEEecCCCC-CCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEe Q psy254 36 LTGIICTIGPAS-VAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIAL 104 (187) Q Consensus 36 ~TkIi~TiGPas-~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~ 104 (187) +..+|+.+|.++ +..+..+..-++|++.+-+=--+-.+-....+++..++..+..+ .|+-++= T Consensus 69 ~~pvi~gv~~~t~~~i~~a~~a~~~Gad~v~~~pP~y~~~~~~~i~~~f~~v~~~~~------~pi~lYn 132 (289) T cd00951 69 RVPVLAGAGYGTATAIAYAQAAEKAGADGILLLPPYLTEAPQEGLYAHVEAVCKSTD------LGVIVYN 132 (289) T ss_pred CCCEEEecCCCHHHHHHHHHHHHHhCCCEEEECCCCCCCCCHHHHHHHHHHHHhcCC------CCEEEEe Confidence 567888887532 23566777889999987765333332234667777777776655 6776663 No 319 >PF00012 HSP70: Hsp70 protein; InterPro: IPR013126 Heat shock proteins, Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region []. Hsp70 proteins have an average molecular weight of 70 kDa [, , ]. In most species,there are many proteins that belong to the hsp70 family. Some of these are only expressed under stress conditions (strictly inducible), while some are present in cells under normal growth conditions and are not heat-inducible (constitutive or cognate) [, ]. Hsp70 proteins can be found in different cellular compartments(nuclear, cytosolic, mitochondrial, endoplasmic reticulum, for example).; PDB: 2P32_D 3D2F_A 2QXL_A 3D2E_C 3C7N_A 3FE1_C 4ANI_C 2V7Y_A 2KHO_A 3DPQ_B .... Probab=21.84 E-value=1.2e+02 Score=28.08 Aligned_cols=67 Identities=19% Similarity=0.262 Sum_probs=35.3 Q ss_pred CceEEEecCCCCCCHHHHHHH----HHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCee Q psy254 36 LTGIICTIGPASVAVDMLEKI----IETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEI 111 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~l----i~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkI 111 (187) -++++.|+ |+.++....+.| -.||+++.||= .|- -.|+-.++.........-+.+|+-|--+ T Consensus 135 ~~~~vitV-Pa~~~~~qr~~~~~Aa~~agl~~~~li-----~Ep--------~Aaa~~y~~~~~~~~~~vlv~D~Gggt~ 200 (602) T PF00012_consen 135 VTDVVITV-PAYFTDEQRQALRDAAELAGLNVLRLI-----NEP--------TAAALAYGLERSDKGKTVLVVDFGGGTF 200 (602) T ss_dssp EEEEEEEE--TT--HHHHHHHHHHHHHTT-EEEEEE-----EHH--------HHHHHHTTTTSSSSEEEEEEEEEESSEE T ss_pred cccceeee-chhhhhhhhhcccccccccccccceee-----ccc--------ccccccccccccccccceeccccccceE Confidence 46899999 999887655444 45899998871 111 1222223211111133567789888766 Q ss_pred Eeeec Q psy254 112 RTGLL 116 (187) Q Consensus 112 RtG~~ 116 (187) -+..+ T Consensus 201 dvs~~ 205 (602) T PF00012_consen 201 DVSVV 205 (602) T ss_dssp EEEEE T ss_pred eeeeh Confidence 55443 No 320 >PF13653 GDPD_2: Glycerophosphoryl diester phosphodiesterase family; PDB: 3RLG_A 2F9R_B 1XX1_A 3RLH_A. Probab=21.84 E-value=1.2e+02 Score=17.14 Aligned_cols=17 Identities=6% Similarity=0.124 Sum_probs=13.2 Q ss_pred CCHHHHHHHHHhcCcEE Q psy254 48 VAVDMLEKIIETGMNIA 64 (187) Q Consensus 48 ~~~~~i~~li~aGm~v~ 64 (187) +.++.+++++.+|++-. T Consensus 8 d~~~~~~~~l~~GVDgI 24 (30) T PF13653_consen 8 DKPASWRELLDLGVDGI 24 (30) T ss_dssp -SHHHHHHHHHHT-SEE T ss_pred CCHHHHHHHHHcCCCEe Confidence 56889999999999964 No 321 >cd03692 mtIF2_IVc mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits. Probab=21.75 E-value=1.9e+02 Score=19.62 Aligned_cols=11 Identities=18% Similarity=0.350 Sum_probs=5.5 Q ss_pred CCeeEeeecCC Q psy254 108 GPEIRTGLLQG 118 (187) Q Consensus 108 GPkIRtG~~~~ 118 (187) |-++..|.+.. T Consensus 19 g~kV~~G~l~~ 29 (84) T cd03692 19 GCYVTDGKIKR 29 (84) T ss_pred EEEEEECEEeC Confidence 44555555543 No 322 >PRK08983 fliN flagellar motor switch protein; Validated Probab=21.70 E-value=2.1e+02 Score=21.68 Aligned_cols=66 Identities=20% Similarity=0.304 Sum_probs=45.3 Q ss_pred ceeEEEeeCCCCeeEeeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcchhhhcCCCCCEEEEeCCeEEEEE Q psy254 98 HALAIALDTKGPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYTNITKVVKPGSRIFVDDGLISLVV 177 (187) Q Consensus 98 ~~v~I~~Dl~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~~l~~~v~~Gd~IlidDG~i~l~V 177 (187) .||.+-+-|...++.++.+ +.|+.|+.|.|.... .++=.++|+-..++. ..+-.-+|+..++| T Consensus 51 v~V~v~v~LG~t~ltl~dl-------L~L~~GDVI~Ld~~~-----ddpv~v~Vng~~~f~-----G~~G~~~~k~AVrI 113 (127) T PRK08983 51 IPVTISMEVGRSFISIRNL-------LQLNQGSVVELDRVA-----GEPLDVMVNGTLIAH-----GEVVVVNDKFGIRL 113 (127) T ss_pred CeeEEEEEEecCcccHHHH-------hCCCCCCEEEeCCCC-----CCCEEEEECCEEEEE-----EEEEEECCEEEEEE Confidence 6788888888888888766 569999999885431 223347776544443 33444567888888 Q ss_pred EEE Q psy254 178 KSI 180 (187) Q Consensus 178 ~~v 180 (187) .++ T Consensus 114 ~~i 116 (127) T PRK08983 114 TDV 116 (127) T ss_pred EEc Confidence 875 No 323 >cd00377 ICL_PEPM Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate lyase (ICL), and 2-methylisocitrate lyase (MICL). Isocitrate lyase (ICL) catalyzes the conversion of isocitrate to succinate and glyoxylate, the first committed step in the glyoxylate pathway. This carbon-conserving pathway is present in most prokaryotes, lower eukaryotes and plants, but has not been observed in vertebrates. PEP mutase (PEPM) turns phosphoenolpyruvate (PEP) into phosphonopyruvate (P-pyr), an important intermediate in the formation of organophosphonates, which function as antibiotics or play a role in pathogenesis or signaling. P-pyr can be hydrolyzed by phosphonopyruvate hydrolase (PPH) to from pyruvate and phosphate. Oxaloacetate acetylhydrolase (OAH) catalyzes the hydrolytic cleavage of oxaloacetate to Probab=21.47 E-value=2.5e+02 Score=23.27 Aligned_cols=52 Identities=19% Similarity=0.211 Sum_probs=34.8 Q ss_pred ceEEEecCCC---C--CCHHHHHHHHHhcCcEEEE--------ecCCC-----CHHHHHHHHHHHHHHHHH Q psy254 37 TGIICTIGPA---S--VAVDMLEKIIETGMNIARL--------NFSHG-----SYEYHGQTIKNIRQAVEN 89 (187) Q Consensus 37 TkIi~TiGPa---s--~~~~~i~~li~aGm~v~Ri--------N~sHg-----~~e~~~~~i~~ir~a~~~ 89 (187) +.+++-+ |. . .-...++.++++|++..-| |..++ +.+++.+.|+.++++.+. T Consensus 70 ~Pv~~D~-~~G~g~~~~~~~~v~~~~~~G~~gv~iED~~~~k~~g~~~~~~~~~~ee~~~ki~aa~~a~~~ 139 (243) T cd00377 70 LPVIADA-DTGYGNALNVARTVRELEEAGAAGIHIEDQVGPKKCGHHGGKVLVPIEEFVAKIKAARDARDD 139 (243) T ss_pred CCEEEEc-CCCCCCHHHHHHHHHHHHHcCCEEEEEecCCCCccccCCCCCeecCHHHHHHHHHHHHHHHhc Confidence 4466655 32 1 2345688899999999999 55444 567777777777776654 No 324 >PRK13575 3-dehydroquinate dehydratase; Provisional Probab=21.43 E-value=4.7e+02 Score=21.64 Aligned_cols=74 Identities=9% Similarity=0.041 Sum_probs=51.7 Q ss_pred CCceEEEecC-----CCCCC-HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCC Q psy254 35 RLTGIICTIG-----PASVA-VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKG 108 (187) Q Consensus 35 r~TkIi~TiG-----Pas~~-~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~G 108 (187) ..+|+|++-= |+.+. .+.+.+|.+.|.|++.|-+.--+.++..++++..+++.+..+. .-+++.|--.| T Consensus 124 ~~~~vI~S~H~F~~TP~~~~l~~~~~~m~~~gaDi~KiAv~~~~~~Dvl~Ll~~~~~~~~~~~~-----p~i~i~MG~~G 198 (238) T PRK13575 124 YNKEVVISHHNFESTPPLDELKFIFFKMQKFNPEYVKLAVMPHNKNDVLNLLQAMSTFSDTMDC-----KVVGISMSKLG 198 (238) T ss_pred cCCEEEEecCCCCCCCCHHHHHHHHHHHHHhCCCEEEEEecCCCHHHHHHHHHHHHHHHhccCC-----CEEEEeCCCCC Confidence 4689999872 22211 2577788899999999999988899999998877776554431 23567766666 Q ss_pred CeeEe Q psy254 109 PEIRT 113 (187) Q Consensus 109 PkIRt 113 (187) ---|+ T Consensus 199 ~iSRi 203 (238) T PRK13575 199 LISRT 203 (238) T ss_pred chhhc Confidence 55554 No 325 >TIGR01921 DAP-DH diaminopimelate dehydrogenase. This model represents the diaminopimelate dehydrogenase enzyme which provides an alternate (shortcut) route of lysine buiosynthesis in Corynebacterium, Bacterioides, Porphyromonas and scattered other species. The enzyme from Corynebacterium glutamicum has been crystallized and characterized. Probab=21.34 E-value=2.2e+02 Score=24.98 Aligned_cols=45 Identities=7% Similarity=-0.074 Sum_probs=31.3 Q ss_pred CCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 44 GPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 44 GPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) +|+....+.+..++++|.||.=--.-|.... +..+.+.+++++.+ T Consensus 68 tPs~th~~~~~~~L~aG~NVV~s~~~h~~~p---~~~~~ld~AAk~~g 112 (324) T TIGR01921 68 MGSATDIPEQAPYFAQFANTVDSFDNHRDIP---RHRQVMDAAAKAAG 112 (324) T ss_pred CCCccCHHHHHHHHHcCCCEEECCCcccCCH---HHHHHHHHHHHHcC Confidence 6888889999999999999876533344443 34455556777643 No 326 >TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism. Probab=21.28 E-value=3.1e+02 Score=23.24 Aligned_cols=65 Identities=8% Similarity=0.044 Sum_probs=43.6 Q ss_pred CceEEEecCCCC--CCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHh-CCCCCCcceeEEEeeCC Q psy254 36 LTGIICTIGPAS--VAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENY-SKRIGMPHALAIALDTK 107 (187) Q Consensus 36 ~TkIi~TiGPas--~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~-~~~~~~~~~v~I~~Dl~ 107 (187) ++.||+-+|..+ +..+..+..-+.|++.+-+=--+-.+-...++++..+..++.. + .|+-++ +.+ T Consensus 69 ~~pvi~gv~~~~t~~ai~~a~~A~~~Gad~v~v~pP~y~~~~~~~l~~~f~~ia~a~~~------lpv~iY-n~P 136 (294) T TIGR02313 69 RIPFAPGTGALNHDETLELTKFAEEAGADAAMVIVPYYNKPNQEALYDHFAEVADAVPD------FPIIIY-NIP 136 (294) T ss_pred CCcEEEECCcchHHHHHHHHHHHHHcCCCEEEEcCccCCCCCHHHHHHHHHHHHHhccC------CCEEEE-eCc Confidence 567888887644 3456777788889998877655444434477788888877766 4 566555 443 No 327 >PRK07259 dihydroorotate dehydrogenase 1B; Reviewed Probab=20.96 E-value=2.9e+02 Score=23.31 Aligned_cols=50 Identities=24% Similarity=0.403 Sum_probs=30.6 Q ss_pred ceEEEecCCC-CCC-HHHHHHHHHhc-CcEEEEecC-----CC------CHHHHHHHHHHHHHH Q psy254 37 TGIICTIGPA-SVA-VDMLEKIIETG-MNIARLNFS-----HG------SYEYHGQTIKNIRQA 86 (187) Q Consensus 37 TkIi~TiGPa-s~~-~~~i~~li~aG-m~v~RiN~s-----Hg------~~e~~~~~i~~ir~a 86 (187) ..+++.|+-. .++ .+..+.+-++| .+.+=||+| || +++...++++.+|++ T Consensus 92 ~p~i~si~g~~~~~~~~~a~~~~~aG~~D~iElN~~cP~~~~gg~~~~~~~~~~~eiv~~vr~~ 155 (301) T PRK07259 92 TPIIANVAGSTEEEYAEVAEKLSKAPNVDAIELNISCPNVKHGGMAFGTDPELAYEVVKAVKEV 155 (301) T ss_pred CcEEEEeccCCHHHHHHHHHHHhccCCcCEEEEECCCCCCCCCccccccCHHHHHHHHHHHHHh Confidence 4689999432 222 23344455678 999999884 42 234556666666665 No 328 >PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional Probab=20.94 E-value=2.9e+02 Score=23.59 Aligned_cols=63 Identities=8% Similarity=0.003 Sum_probs=41.3 Q ss_pred CceEEEecCCCC-CCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEe Q psy254 36 LTGIICTIGPAS-VAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIAL 104 (187) Q Consensus 36 ~TkIi~TiGPas-~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~ 104 (187) +..+|+.+|.++ +..+..+..-++|++.+-+---+-..-..+.+++..+..++..+ .||-|+= T Consensus 76 ~~pvi~gv~~~t~~~i~~~~~a~~~Gadav~~~pP~y~~~~~~~i~~~f~~va~~~~------lpi~lYn 139 (303) T PRK03620 76 RVPVIAGAGGGTAQAIEYAQAAERAGADGILLLPPYLTEAPQEGLAAHVEAVCKSTD------LGVIVYN 139 (303) T ss_pred CCcEEEecCCCHHHHHHHHHHHHHhCCCEEEECCCCCCCCCHHHHHHHHHHHHHhCC------CCEEEEc Confidence 467888888532 34566777888999988765444332234667777777777665 6776663 No 329 >PF06903 VirK: VirK protein; InterPro: IPR010694 This family consists of several bacterial VirK proteins of around 145 residues in length. The function of this family is unknown []. Probab=20.89 E-value=80 Score=23.04 Aligned_cols=15 Identities=7% Similarity=0.131 Sum_probs=12.3 Q ss_pred ceeEEEeeCCCCeeE Q psy254 98 HALAIALDTKGPEIR 112 (187) Q Consensus 98 ~~v~I~~Dl~GPkIR 112 (187) ++|.+.+||.=++-. T Consensus 17 k~V~v~iDls~Ct~~ 31 (100) T PF06903_consen 17 KNVTVVIDLSQCTPE 31 (100) T ss_pred CeEEEEEEHHHCccC Confidence 899999999866655 No 330 >COG0191 Fba Fructose/tagatose bisphosphate aldolase [Carbohydrate transport and metabolism] Probab=20.82 E-value=3.6e+02 Score=23.41 Aligned_cols=47 Identities=15% Similarity=0.210 Sum_probs=40.2 Q ss_pred CCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhC Q psy254 45 PASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYS 91 (187) Q Consensus 45 Pas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~ 91 (187) ....+.+...+-+++|.+-..|.-||-+.||.-+.-+.+-+.+..++ T Consensus 83 DHg~~~~~~~~ai~~GFsSvMiDgS~~~~eENi~~tkevv~~ah~~g 129 (286) T COG0191 83 DHGASFEDCKQAIRAGFSSVMIDGSHLPFEENIAITKEVVEFAHAYG 129 (286) T ss_pred CCCCCHHHHHHHHhcCCceEEecCCcCCHHHHHHHHHHHHHHHHHcC Confidence 55568999999999999999999999999988777777777777666 No 331 >PF04203 Sortase: Sortase family; InterPro: IPR005754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: 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-, N-, 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. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; 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. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C60 (clan C-) and include the members of both subfamilies of sortases. The Staphylococcus aureus sortase is a transpeptidase that attaches surface proteins to the cell wall; it cleaves between the Gly and Thr of the LPXTG motif and catalyses the formation of an amide bond between the carboxyl-group of threonine and the amino-group of the cell-wall peptidoglycan []. Sortase homologues are found in almost all Gram-positives, a single Gram-negative (Shewanella putrefaciens) and an archaean (Methanobacterium thermoautotrophicum), where cell wall LPXTG-mediated decoration has not been reported [, ]. Surface proteins not only promote interaction between the invading pathogen and animal tissues, but also provide ingenious strategies for bacterial escape from the host's immune response. In the case of S. aureus protein A, immunoglobulins are captured on the microbial surface and camouflage bacteria during the invasion of host tissues. S. aureus mutants lacking the srtA gene fail to anchor and display some surface proteins and are impaired in the ability to cause animal infections. Sortase acts on surface proteins that are initiated into the secretion (Sec) pathway and have their signal peptide removed by signal peptidase. The S. aureus genome encodes two sets of sortase and secretion genes. It is conceivable that S. aureus has evolved more than one pathway for the transport of 20 surface proteins to the cell wall envelope. ; PDB: 2W1K_A 2OQZ_A 1RZ2_A 2OQW_A 1T2W_A 1IJA_A 1T2P_A 1T2O_C 2KID_A 3RCC_N .... Probab=20.77 E-value=1.3e+02 Score=21.76 Aligned_cols=24 Identities=25% Similarity=0.433 Sum_probs=17.8 Q ss_pred hcCCCCCEEEEeC--CeE-EEEEEEEe Q psy254 158 KVVKPGSRIFVDD--GLI-SLVVKSIV 181 (187) Q Consensus 158 ~~v~~Gd~IlidD--G~i-~l~V~~v~ 181 (187) ..+++||.|++.+ |.. +.+|.++. T Consensus 59 ~~~~~gd~i~~~~~~g~~~~Y~V~~~~ 85 (128) T PF04203_consen 59 NKLKKGDEIYLTTPDGKTYEYRVTSVK 85 (128) T ss_dssp GGGHTT-EEEEEETSSEEEEEEEEEEE T ss_pred cccCCCCEEEEEEecCEEEEEEEEEEE Confidence 4569999999986 777 88887753 No 332 >PF00682 HMGL-like: HMGL-like of this family is not conserved in other members. are a sub-families of this Pfam.; InterPro: IPR000891 Pyruvate carboxylase (6.4.1.1 from EC) (PC), a member of the biotin-dependent enzyme family, is involved in the gluconeogenesis by mediating the carboxylation of pyruvate to oxaloacetate. Biotin-dependent carboxylase enzymes perform a two step reaction. Enzyme-bound biotin is first carboxylated by bicarbonate and ATP and the carboxyl group temporarily bound to biotin is subsequently transferred to an acceptor substrate such as pyruvate []. PC has three functional domains: a biotin carboxylase (BC) domain, a carboxyltransferase (CT) domain which perform the second part of the reaction and a biotinyl domain [, ]. The mechanism by which the carboxyl group is transferred from the carboxybiotin to the pyruvate is not well understood. The pyruvate carboxyltransferase domain is also found in other pyruvate binding enzymes and acetyl-CoA dependent enzymes suggesting that this domain can be associated with different enzymatic activities. This domain is found towards the N-terminal region of various aldolase enzymes. This N-terminal TIM barrel domain [] interacts with the C-terminal domain. The C-terminal DmpG_comm domain (IPR012425 from INTERPRO) is thought to promote heterodimerisation with members of IPR003361 from INTERPRO to form a bifunctional aldolase-dehydrogenase []. ; GO: 0003824 catalytic activity; PDB: 3MP5_E 3MP3_E 2CW6_E 3MP4_D 3HBL_A 3HB9_C 3HO8_A 3BG5_C 1YDN_B 3RMJ_A .... Probab=20.77 E-value=3.5e+02 Score=21.74 Aligned_cols=49 Identities=14% Similarity=0.132 Sum_probs=29.9 Q ss_pred HHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCC Q psy254 53 LEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGP 109 (187) Q Consensus 53 i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GP 109 (187) ++..-+.|..+ ++|+-+.+.-....+.+.++++.+. + ...-.+.|+-|- T Consensus 114 v~~ak~~g~~v-~~~~~~~~~~~~~~~~~~~~~~~~~-g------~~~i~l~Dt~G~ 162 (237) T PF00682_consen 114 VKYAKELGYEV-AFGCEDASRTDPEELLELAEALAEA-G------ADIIYLADTVGI 162 (237) T ss_dssp HHHHHHTTSEE-EEEETTTGGSSHHHHHHHHHHHHHH-T-------SEEEEEETTS- T ss_pred HHHHHhcCCce-EeCccccccccHHHHHHHHHHHHHc-C------CeEEEeeCccCC Confidence 33444677777 8888877766666666666665433 4 334566777663 No 333 >TIGR03301 PhnW-AepZ 2-aminoethylphosphonate aminotransferase. This family includes a number of 2-aminoethylphosphonate aminotransferases, some of which are indicated to operate in the catabolism of 2-aminoethylphosphonate (AEP) and others which are involved in the biosynthesis of the same compound. The catabolic enzyme (PhnW, ) is known to use pyruvate:alanine as the transfer partner and is modeled by the equivalog-level alignment (TIGR02326). The PhnW family is apparently a branch of a larger tree including genes (AepZ) adjacent to others responsible for the biosynthesis of phosphonoacetaldehyde. The identity of the transfer partner is unknown for these enzymes and considering the reversed flux compared to PhnW, it may very well be different. Probab=20.77 E-value=5e+02 Score=21.62 Aligned_cols=37 Identities=19% Similarity=0.241 Sum_probs=28.2 Q ss_pred HHHHHHHHHhcCcE----------EEEec-CCCCHHHHHHHHHHHHHH Q psy254 50 VDMLEKIIETGMNI----------ARLNF-SHGSYEYHGQTIKNIRQA 86 (187) Q Consensus 50 ~~~i~~li~aGm~v----------~RiN~-sHg~~e~~~~~i~~ir~a 86 (187) .+..+.|.+.|+-+ +||++ .+-+.++..+.++.++++ T Consensus 307 ~~~~~~l~~~gi~i~~~~~~~~~~iRis~~~~~~~~~i~~~~~~l~~~ 354 (355) T TIGR03301 307 DDFYQELKERGFVIYPGKLTLADTFRIGTIGEIDAADIERLLEAIKDA 354 (355) T ss_pred HHHHHHHHHCCEEEECCccccccEEEEecCCCCCHHHHHHHHHHHHhh Confidence 46777888888764 78876 566888888888888753 No 334 >PRK09058 coproporphyrinogen III oxidase; Provisional Probab=20.76 E-value=6.4e+02 Score=22.84 Aligned_cols=39 Identities=8% Similarity=0.008 Sum_probs=28.8 Q ss_pred eEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHH Q psy254 38 GIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYH 76 (187) Q Consensus 38 kIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~ 76 (187) .|-+-.-|.+-+.+.++.|.++|+|.+-|-.=..+.+.. T Consensus 151 eitiE~~p~~~t~e~l~~l~~aGvnRiSiGVQSf~d~vL 189 (449) T PRK09058 151 EITLEGRINGFDDEKADAALDAGANRFSIGVQSFNTQVR 189 (449) T ss_pred EEEEEeCcCcCCHHHHHHHHHcCCCEEEecCCcCCHHHH Confidence 444444688889999999999999987766655554433 No 335 >PRK09875 putative hydrolase; Provisional Probab=20.68 E-value=1.9e+02 Score=24.88 Aligned_cols=54 Identities=17% Similarity=0.401 Sum_probs=36.0 Q ss_pred CCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCe Q psy254 45 PASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPE 110 (187) Q Consensus 45 Pas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPk 110 (187) +...-.+.++-|.++|++--|+-++|-+.. .-.+.++++. +.| +.|-+|+-|.. T Consensus 161 ~~~~g~e~l~il~e~Gvd~~rvvi~H~d~~---~d~~~~~~l~-~~G--------~~l~fD~~g~~ 214 (292) T PRK09875 161 FSTMGLEQLALLQAHGVDLSRVTVGHCDLK---DNLDNILKMI-DLG--------AYVQFDTIGKN 214 (292) T ss_pred CccchHHHHHHHHHcCcCcceEEEeCCCCC---CCHHHHHHHH-HcC--------CEEEeccCCCc Confidence 333556788889999999999999999522 1222333333 234 78888987765 No 336 >PRK05286 dihydroorotate dehydrogenase 2; Reviewed Probab=20.66 E-value=3.1e+02 Score=23.93 Aligned_cols=66 Identities=14% Similarity=0.045 Sum_probs=37.9 Q ss_pred hccHHHhhcCCCCCCCCCCCCCceEEEecCCC--C------CCHHHHHHHHHhcCcEEEEecCCC---------CHHHHH Q psy254 15 ANTFVDHLCGLDIDNKSSYVRLTGIICTIGPA--S------VAVDMLEKIIETGMNIARLNFSHG---------SYEYHG 77 (187) Q Consensus 15 ~~~~l~~~~~l~i~~~~~~~r~TkIi~TiGPa--s------~~~~~i~~li~aGm~v~RiN~sHg---------~~e~~~ 77 (187) .+.+++++.... ..+.++++|+-. + .++..+-+.+..+++.+=+|||.= ..+... T Consensus 124 ~~~~~~~l~~~~--------~~~pvivsI~~~~~~~~~~~~~d~~~~~~~~~~~ad~lelN~scP~~~g~~~~~~~~~~~ 195 (344) T PRK05286 124 ADALAERLKKAY--------RGIPLGINIGKNKDTPLEDAVDDYLICLEKLYPYADYFTVNISSPNTPGLRDLQYGEALD 195 (344) T ss_pred HHHHHHHHHHhc--------CCCcEEEEEecCCCCCcccCHHHHHHHHHHHHhhCCEEEEEccCCCCCCcccccCHHHHH Confidence 345566665432 245699999642 1 122333333344599999999842 234556 Q ss_pred HHHHHHHHHHH Q psy254 78 QTIKNIRQAVE 88 (187) Q Consensus 78 ~~i~~ir~a~~ 88 (187) ++++.+|++.. T Consensus 196 eiv~aVr~~~~ 206 (344) T PRK05286 196 ELLAALKEAQA 206 (344) T ss_pred HHHHHHHHHHh Confidence 66677776643 No 337 >PRK13576 3-dehydroquinate dehydratase; Provisional Probab=20.58 E-value=1.8e+02 Score=23.86 Aligned_cols=35 Identities=17% Similarity=0.321 Sum_probs=24.6 Q ss_pred CceEEEecCCCCCCHHHHHHHHHh-cCcE--EEEecCCCC Q psy254 36 LTGIICTIGPASVAVDMLEKIIET-GMNI--ARLNFSHGS 72 (187) Q Consensus 36 ~TkIi~TiGPas~~~~~i~~li~a-Gm~v--~RiN~sHg~ 72 (187) ++||++.| +.. +.+.+..-.+. |+|+ +|+.+-+.. T Consensus 2 ~p~i~vpi-~~~-~~e~i~~~~~~~~aD~vE~RlD~l~~~ 39 (216) T PRK13576 2 RPLIVASL-PIK-KIEDLKLIGNFLDADLIELRLDYLKDR 39 (216) T ss_pred CCEEEEEe-CCC-CHHHHHHHHhcCCCCEEEEEecccccc Confidence 56999988 333 34555555666 9999 899888664 No 338 >PLN02452 phosphoserine transaminase Probab=20.54 E-value=2.4e+02 Score=24.89 Aligned_cols=47 Identities=23% Similarity=0.471 Sum_probs=33.5 Q ss_pred EEEecCCCCCCHHHHHHHHHh-------cCcEEEEecCCCCHHHHHHHHHHHHHHHH Q psy254 39 IICTIGPASVAVDMLEKIIET-------GMNIARLNFSHGSYEYHGQTIKNIRQAVE 88 (187) Q Consensus 39 Ii~TiGPas~~~~~i~~li~a-------Gm~v~RiN~sHg~~e~~~~~i~~ir~a~~ 88 (187) +.=|=||+.-..+++++|.+. ||.+ +-+||-+.+.. ++++.+++-.+ T Consensus 9 ~~f~pGP~~lp~~Vl~~~~~~~~~~~~~g~s~--~~~sHRs~~f~-~i~~~~~~~L~ 62 (365) T PLN02452 9 FNFSAGPATLPANVLAKAQAELYNWEGSGMSV--MEMSHRGKEFL-SIIQKAEADLR 62 (365) T ss_pred EeeeCCCCCCCHHHHHHHHHHHhcccccCccc--cccCCCchHHH-HHHHHHHHHHH Confidence 445669999999999998866 6766 45899998763 55555554333 No 339 >PF01624 MutS_I: MutS domain I C-terminus.; InterPro: IPR007695 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. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. 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. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].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 the N-terminal domain of proteins in the MutS family of DNA mismatch repair proteins, as well as closely related proteins. The N-terminal domain of MutS is responsible for mismatch recognition and forms a 6-stranded mixed beta-sheet surrounded by three alpha-helices, which is similar to the structure of tRNA endonuclease. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 3THY_B 3THZ_B 3THW_B 3THX_B 2WTU_A 1OH7_A .... Probab=20.50 E-value=88 Score=22.54 Aligned_cols=48 Identities=21% Similarity=0.317 Sum_probs=30.3 Q ss_pred HHhhcCCCCCCCCCCCCCceEEEecCCCCCCHHHHHHHHHhcCcEEEEe Q psy254 19 VDHLCGLDIDNKSSYVRLTGIICTIGPASVAVDMLEKIIETGMNIARLN 67 (187) Q Consensus 19 l~~~~~l~i~~~~~~~r~TkIi~TiGPas~~~~~i~~li~aGm~v~RiN 67 (187) +...+++.+........++.=+|++ |.+.-...++.|+.+|.+|+... T Consensus 37 ~a~~l~~~~~~~~~~~~~~~~~~gf-p~~~l~~~l~~Ll~~G~~V~i~~ 84 (113) T PF01624_consen 37 VAEILGLKLSKRKTGGGKSVPMAGF-PKSQLDKYLKKLLEAGYRVAIYE 84 (113) T ss_dssp HHHHHTSSSEEEECSSSECEEEEEE-EGGGHHHHHHHHHHTT-EEEEEE T ss_pred HHHhccceeeeccccccccccEecc-cHHHHHHHHHHHHHcCCEEEEEE Confidence 4455555443221112222568888 87777889999999999998864 No 340 >COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism] Probab=20.43 E-value=3.2e+02 Score=22.83 Aligned_cols=57 Identities=19% Similarity=0.274 Sum_probs=44.3 Q ss_pred HHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHHHHHHhCCCCCCcce-eEEEeeCCCCeeEe Q psy254 50 VDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQAVENYSKRIGMPHA-LAIALDTKGPEIRT 113 (187) Q Consensus 50 ~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~a~~~~~~~~~~~~~-v~I~~Dl~GPkIRt 113 (187) .+.+.+|...|.++.-|-..-.+.++....++..|+... .+ .| +++.|--.|---|+ T Consensus 136 ~~~l~km~~~~aDivKiAvm~~~~~DvL~ll~~~~~~~~-~~------~p~i~i~MG~~G~~SRv 193 (231) T COG0710 136 IERLDKMESLGADIVKIAVMPQSKEDVLDLLEATREFKE-AE------KPVITISMGKTGKISRV 193 (231) T ss_pred HHHHHHHHhhCCCeEEEEecCCCHHHHHHHHHHHHhccc-cC------CCEEEEecCCCCchhhh Confidence 378889999999999999999999999999999887644 44 34 46666555555553 No 341 >PRK14484 phosphotransferase mannnose-specific family component IIA; Provisional Probab=20.31 E-value=1.8e+02 Score=21.82 Aligned_cols=66 Identities=15% Similarity=0.255 Sum_probs=36.8 Q ss_pred EEEecCC--CCCCHHHHHHHHHhcCcEEEEecCCC-CHHHHHHHHHHHHHHHHHhCCCCCCcceeEEEeeCCCCeeEe Q psy254 39 IICTIGP--ASVAVDMLEKIIETGMNIARLNFSHG-SYEYHGQTIKNIRQAVENYSKRIGMPHALAIALDTKGPEIRT 113 (187) Q Consensus 39 Ii~TiGP--as~~~~~i~~li~aGm~v~RiN~sHg-~~e~~~~~i~~ir~a~~~~~~~~~~~~~v~I~~Dl~GPkIRt 113 (187) |++|-|+ |..=.+.++.|. .-+++.-+.+..+ +.+ ...++|+++.+++.. --|-|+.||-|-...+ T Consensus 5 VlVSHs~~lA~gl~~~~~~i~-~~~~i~~~gg~~d~~~g---t~~~~i~~ai~~~~~-----dGVlVltDLGssp~n~ 73 (124) T PRK14484 5 VIVSHSKKIAEGVKDLIKQMA-PDVPIIYAGGTEDGRIG---TSFDQIQEAIEKNES-----DGVLIFFDLGSAEMNA 73 (124) T ss_pred EEEeCcHHHHHHHHHHHHHhh-CCCCEEEecCCCCCCcc---chHHHHHHHHHhcCc-----CCeEEEEeCCChHHHH Confidence 5666663 222345555565 6677877777653 333 333444454444421 1389999995555444 No 342 >KOG1816|consensus Probab=20.23 E-value=4.3e+02 Score=23.09 Aligned_cols=74 Identities=16% Similarity=0.202 Sum_probs=43.9 Q ss_pred ceeEEEeeC---CCCeeEeeecCCCCcccEEeeeCCEEEEeeCCCcccCCCcCEEeeCcc-hh-------hhcCCCCCEE Q psy254 98 HALAIALDT---KGPEIRTGLLQGGGSAEVELVKGQTIRLTTDAAFAEKGSATDLYVDYT-NI-------TKVVKPGSRI 166 (187) Q Consensus 98 ~~v~I~~Dl---~GPkIRtG~~~~~~~~~i~l~~G~~v~lt~~~~~~~~~~~~~i~v~~~-~l-------~~~v~~Gd~I 166 (187) .|.|-|.-| .|+.+|+- .+.|-+|.-+.|-... .+.+-++.| .+ +..|..||.| T Consensus 88 LP~WMmq~L~le~gdlv~i~--------~v~lpkgtyvKLqP~s-------~dFLDItNpKAvLE~~LRn~acLT~gDvi 152 (308) T KOG1816|consen 88 LPYWMMQNLLLEEGDLVRIR--------SVTLPKGTYVKLQPHS-------VDFLDITNPKAVLENALRNYACLTTGDVI 152 (308) T ss_pred eehHhhhhccCCCCCeEEEE--------EeeccccceeeeccCC-------CCccccCChHHHHHHHHhhccccccCCEE Confidence 444444333 27777763 3456677777775543 233333322 22 2578899999 Q ss_pred EEeCCeE--EEEEEEEeCCeee Q psy254 167 FVDDGLI--SLVVKSIVKSYQL 186 (187) Q Consensus 167 lidDG~i--~l~V~~v~~~~i~ 186 (187) .+..+.. +++|.++.+...+ T Consensus 153 ~i~Yn~k~y~i~V~e~kPa~aV 174 (308) T KOG1816|consen 153 LINYNEKTYELKVVETKPANAV 174 (308) T ss_pred EEecCCeEEEEEEEEecCCcee Confidence 9987655 5777777765544 No 343 >PRK07428 nicotinate-nucleotide pyrophosphorylase; Provisional Probab=20.04 E-value=3.6e+02 Score=23.21 Aligned_cols=43 Identities=21% Similarity=0.298 Sum_probs=34.6 Q ss_pred ceEEEecCCCCCCHHHHHHHHHhcCcEEEEecCCCCHHHHHHHHHHHHH Q psy254 37 TGIICTIGPASVAVDMLEKIIETGMNIARLNFSHGSYEYHGQTIKNIRQ 85 (187) Q Consensus 37 TkIi~TiGPas~~~~~i~~li~aGm~v~RiN~sHg~~e~~~~~i~~ir~ 85 (187) .||-... ++.+.+.+.+++|+|+..+. +.++++.++.++.+|+ T Consensus 197 ~~I~VEv----~tleea~eA~~~GaD~I~LD--n~~~e~l~~av~~~~~ 239 (288) T PRK07428 197 LTIEVET----ETLEQVQEALEYGADIIMLD--NMPVDLMQQAVQLIRQ 239 (288) T ss_pred CEEEEEC----CCHHHHHHHHHcCCCEEEEC--CCCHHHHHHHHHHHHh Confidence 4566654 78999999999999998854 8888888888877654 No 344 >PRK08088 4-aminobutyrate aminotransferase; Validated Probab=20.03 E-value=3.1e+02 Score=24.38 Aligned_cols=40 Identities=15% Similarity=0.239 Sum_probs=31.7 Q ss_pred HHHHHHHHHhcC---------cEEEEecC-CCCHHHHHHHHHHHHHHHHH Q psy254 50 VDMLEKIIETGM---------NIARLNFS-HGSYEYHGQTIKNIRQAVEN 89 (187) Q Consensus 50 ~~~i~~li~aGm---------~v~RiN~s-Hg~~e~~~~~i~~ir~a~~~ 89 (187) .+..+++.+.|+ +++||+++ .-+.++..+.++.++++..+ T Consensus 374 ~~l~~~~~~~Gv~~~~~~~~~~~iRl~~~~~~t~~ei~~~i~~l~~~l~~ 423 (425) T PRK08088 374 AQIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIIAQCFDE 423 (425) T ss_pred HHHHHHHHhCCCEEecCCCCCCEEEEECCCCcCHHHHHHHHHHHHHHHHh Confidence 456677888884 77899999 56788999999998887653 Done!