Query psy4127 Match_columns 75 No_of_seqs 100 out of 337 Neff 5.0 Searched_HMMs 46136 Date Fri Aug 16 17:38:10 2013 Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4127.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4127hhsearch_cdd -cpu 12 -v 0 No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PF02005 TRM: N2,N2-dimethylgu 100.0 4.9E-35 1.1E-39 222.2 2.0 73 2-75 114-186 (377) 2 COG1867 TRM1 N2,N2-dimethylgua 100.0 1.1E-33 2.5E-38 216.3 5.3 73 2-75 114-186 (380) 3 KOG1253|consensus 100.0 8.1E-34 1.8E-38 223.2 3.4 74 2-75 173-248 (525) 4 TIGR00308 TRM1 tRNA(guanine-26 99.9 2.6E-28 5.7E-33 185.4 5.4 67 9-75 113-179 (374) 5 PRK04338 N(2),N(2)-dimethylgua 99.9 1.3E-22 2.8E-27 154.3 5.5 68 8-75 123-190 (382) 6 PRK04457 spermidine synthase; 89.5 0.73 1.6E-05 33.4 4.4 37 8-44 134-178 (262) 7 PRK14901 16S rRNA methyltransf 88.2 0.84 1.8E-05 35.2 4.1 36 9-44 324-386 (434) 8 TIGR00640 acid_CoA_mut_C methy 85.3 1.1 2.4E-05 29.7 3.0 39 9-49 29-67 (132) 9 PLN02366 spermidine synthase 85.2 1.4 3.1E-05 33.0 3.9 37 8-44 163-207 (308) 10 PRK00811 spermidine synthase; 84.7 1.9 4.1E-05 31.5 4.3 37 8-44 148-192 (283) 11 PRK00121 trmB tRNA (guanine-N( 84.2 2.4 5.3E-05 29.2 4.5 36 8-43 109-156 (202) 12 TIGR02469 CbiT precorrin-6Y C5 84.0 2.6 5.7E-05 25.4 4.1 35 9-43 87-122 (124) 13 PF02475 Met_10: Met-10+ like- 83.2 1.3 2.7E-05 31.5 2.7 33 8-40 167-199 (200) 14 PF01564 Spermine_synth: Sperm 83.0 1.1 2.4E-05 32.3 2.4 34 10-43 150-191 (246) 15 PRK00536 speE spermidine synth 82.5 2.4 5.2E-05 31.4 4.1 35 8-44 137-172 (262) 16 TIGR00446 nop2p NOL1/NOP2/sun 82.5 2.9 6.3E-05 30.1 4.4 36 9-44 139-201 (264) 17 PRK03612 spermidine synthase; 81.1 2.7 5.8E-05 33.5 4.2 36 8-43 371-415 (521) 18 PLN02823 spermine synthase 80.9 3.7 8.1E-05 31.2 4.7 39 8-46 174-223 (336) 19 PRK11524 putative methyltransf 79.8 2.8 6.1E-05 30.5 3.7 36 7-42 24-79 (284) 20 PRK00107 gidB 16S rRNA methylt 78.7 3.7 8.1E-05 28.5 3.8 35 8-42 110-144 (187) 21 TIGR00417 speE spermidine synt 78.1 4.4 9.5E-05 29.2 4.2 36 8-43 143-186 (270) 22 PLN02781 Probable caffeoyl-CoA 77.9 3.4 7.3E-05 29.4 3.5 38 9-46 143-181 (234) 23 PF03537 Glyco_hydro_114: Glyc 77.6 2.8 6.1E-05 25.2 2.6 31 9-43 25-55 (74) 24 cd02440 AdoMet_MTases S-adenos 77.5 5.8 0.00012 21.8 3.8 34 9-42 65-103 (107) 25 PRK01581 speE spermidine synth 75.6 5.2 0.00011 31.4 4.2 37 8-44 224-269 (374) 26 PF13659 Methyltransf_26: Meth 75.5 4.1 8.9E-05 24.6 3.0 36 7-42 67-114 (117) 27 TIGR03065 srtB_sig_QVPTGV sort 74.9 0.68 1.5E-05 24.5 -0.6 22 20-43 8-29 (32) 28 PLN02589 caffeoyl-CoA O-methyl 73.4 4.8 0.0001 29.4 3.4 41 9-52 155-196 (247) 29 TIGR01177 conserved hypothetic 71.5 9.4 0.0002 28.2 4.6 38 8-45 246-296 (329) 30 TIGR00479 rumA 23S rRNA (uraci 71.0 7.5 0.00016 29.7 4.1 35 9-44 361-397 (431) 31 PLN02476 O-methyltransferase 70.9 6 0.00013 29.6 3.5 35 9-43 193-228 (278) 32 TIGR00138 gidB 16S rRNA methyl 70.3 7 0.00015 26.7 3.5 35 8-42 107-141 (181) 33 cd01202 FRS2 Fibroblast growth 69.9 5.9 0.00013 26.1 2.8 46 8-64 5-55 (102) 34 PRK10901 16S rRNA methyltransf 67.5 11 0.00024 29.0 4.4 34 9-42 312-371 (427) 35 COG0144 Sun tRNA and rRNA cyto 67.4 4.9 0.00011 30.5 2.4 24 24-47 269-293 (355) 36 PRK05134 bifunctional 3-demeth 67.2 8 0.00017 26.5 3.3 35 9-43 113-151 (233) 37 KOG0408|consensus 67.0 6.2 0.00013 28.4 2.7 30 24-53 152-181 (190) 38 PRK15128 23S rRNA m(5)C1962 me 64.6 15 0.00033 28.4 4.7 36 8-43 291-339 (396) 39 PF03602 Cons_hypoth95: Conser 64.5 6.7 0.00014 27.1 2.4 35 8-43 112-153 (183) 40 PRK08317 hypothetical protein; 64.2 17 0.00037 24.1 4.3 39 9-47 86-128 (241) 41 PRK11783 rlmL 23S rRNA m(2)G24 63.2 14 0.00031 30.5 4.5 35 8-42 606-655 (702) 42 PRK14967 putative methyltransf 62.7 17 0.00037 25.1 4.3 22 25-46 141-162 (223) 43 COG1092 Predicted SAM-dependen 62.2 14 0.00031 29.0 4.1 37 7-43 287-336 (393) 44 TIGR00438 rrmJ cell division p 61.6 21 0.00045 23.9 4.4 35 8-42 96-145 (188) 45 PRK11630 hypothetical protein; 61.5 13 0.00028 26.2 3.5 34 13-47 4-37 (206) 46 COG4976 Predicted methyltransf 61.1 6.2 0.00014 30.1 1.9 44 6-49 184-231 (287) 47 PF08241 Methyltransf_11: Meth 60.2 6.4 0.00014 22.3 1.5 22 20-41 74-95 (95) 48 TIGR01983 UbiG ubiquinone bios 60.0 11 0.00024 25.5 2.8 36 9-44 111-150 (224) 49 KOG1663|consensus 59.4 12 0.00025 28.0 3.0 36 8-43 147-183 (237) 50 PF13847 Methyltransf_31: Meth 59.3 7.3 0.00016 25.1 1.8 37 9-45 72-112 (152) 51 PF05430 Methyltransf_30: S-ad 59.1 7.4 0.00016 25.7 1.8 54 9-68 49-109 (124) 52 PRK09489 rsmC 16S ribosomal RN 59.0 10 0.00022 28.7 2.8 52 8-63 259-319 (342) 53 TIGR02752 MenG_heptapren 2-hep 58.7 22 0.00048 24.2 4.2 36 8-43 112-151 (231) 54 COG4122 Predicted O-methyltran 58.6 16 0.00034 26.5 3.6 41 8-51 130-171 (219) 55 PF06962 rRNA_methylase: Putat 57.1 8.2 0.00018 26.3 1.8 21 23-43 72-92 (140) 56 TIGR01934 MenG_MenH_UbiE ubiqu 56.7 22 0.00047 23.6 3.8 35 9-43 105-143 (223) 57 PRK08287 cobalt-precorrin-6Y C 56.1 27 0.00058 23.3 4.2 35 9-43 96-131 (187) 58 TIGR01202 bchC 2-desacetyl-2-h 56.0 17 0.00037 26.1 3.4 32 10-43 200-231 (308) 59 PF02083 Urotensin_II: Urotens 55.9 4.9 0.00011 17.1 0.4 9 54-62 3-11 (12) 60 TIGR02072 BioC biotin biosynth 55.9 21 0.00046 23.8 3.7 35 9-43 97-135 (240) 61 TIGR00106 uncharacterized prot 55.2 11 0.00024 24.0 2.0 38 16-53 7-48 (97) 62 COG5526 Lysozyme family protei 54.6 6.1 0.00013 28.3 0.9 31 16-48 94-125 (191) 63 COG4215 ArtQ ABC-type arginine 54.0 4.5 9.7E-05 30.0 0.1 30 9-38 87-128 (230) 64 smart00828 PKS_MT Methyltransf 53.9 21 0.00045 24.2 3.4 35 10-44 67-105 (224) 65 PRK09975 DNA-binding transcrip 53.3 6.1 0.00013 26.4 0.7 40 24-63 15-54 (213) 66 PRK11036 putative S-adenosyl-L 53.3 25 0.00055 24.7 3.9 35 9-43 111-149 (255) 67 PRK11873 arsM arsenite S-adeno 53.3 27 0.00059 24.6 4.0 35 9-43 145-183 (272) 68 COG1041 Predicted DNA modifica 53.3 25 0.00055 27.4 4.1 36 9-44 263-311 (347) 69 PRK00767 transcriptional regul 52.8 7.1 0.00015 25.6 0.9 40 24-63 13-52 (197) 70 PRK09880 L-idonate 5-dehydroge 52.7 19 0.00041 26.1 3.2 33 10-44 235-267 (343) 71 PF12847 Methyltransf_18: Meth 51.9 13 0.00028 22.1 2.0 36 8-43 68-111 (112) 72 PRK07402 precorrin-6B methylas 51.7 34 0.00073 23.0 4.2 38 10-47 109-146 (196) 73 TIGR00563 rsmB ribosomal RNA s 51.2 33 0.00071 26.4 4.4 56 9-64 308-390 (426) 74 PRK00377 cbiT cobalt-precorrin 51.1 40 0.00086 22.8 4.5 37 9-45 110-147 (198) 75 PF01910 DUF77: Domain of unkn 50.9 8.1 0.00018 24.2 0.9 37 21-58 14-50 (92) 76 PF10672 Methyltrans_SAM: S-ad 50.8 15 0.00032 27.6 2.5 41 7-48 192-242 (286) 77 COG1854 LuxS LuxS protein invo 50.5 8 0.00017 27.3 0.9 24 2-25 63-86 (161) 78 PLN02396 hexaprenyldihydroxybe 50.3 19 0.00041 27.2 3.0 36 9-44 197-236 (322) 79 PF01596 Methyltransf_3: O-met 49.6 14 0.00031 26.1 2.1 39 9-47 120-159 (205) 80 cd02067 B12-binding B12 bindin 49.1 33 0.00072 21.2 3.6 39 9-49 26-64 (119) 81 PRK14902 16S rRNA methyltransf 49.0 32 0.00069 26.5 4.1 18 24-41 360-377 (444) 82 TIGR02807 cas6_var CRISPR-asso 48.9 15 0.00032 26.5 2.1 27 12-38 109-135 (190) 83 cd03423 SirA SirA (also known 47.3 43 0.00093 19.3 3.7 36 14-49 2-39 (69) 84 PF13578 Methyltransf_24: Meth 46.7 4.7 0.0001 24.4 -0.6 33 9-41 68-103 (106) 85 PRK14968 putative methyltransf 46.4 61 0.0013 20.9 4.6 23 24-46 129-151 (188) 86 PRK15008 HTH-type transcriptio 45.7 8.5 0.00018 26.2 0.5 41 23-63 21-61 (212) 87 PF00440 TetR_N: Bacterial reg 45.6 1.2 2.5E-05 24.1 -3.2 38 26-63 2-39 (47) 88 PRK14904 16S rRNA methyltransf 45.1 46 0.001 25.8 4.5 18 24-41 358-375 (445) 89 TIGR03534 RF_mod_PrmC protein- 44.4 47 0.001 22.6 4.0 20 24-43 198-217 (251) 90 cd03422 YedF YedF is a bacteri 44.0 43 0.00094 19.4 3.3 37 14-50 2-40 (69) 91 PRK11933 yebU rRNA (cytosine-C 43.7 19 0.00041 28.8 2.2 36 9-44 182-244 (470) 92 PRK00312 pcm protein-L-isoaspa 43.5 48 0.001 22.5 3.9 34 9-44 143-176 (212) 93 TIGR00080 pimt protein-L-isoas 43.3 37 0.00081 23.3 3.4 32 9-42 145-176 (215) 94 PRK10258 biotin biosynthesis p 43.2 46 0.001 23.1 3.9 35 9-43 102-140 (251) 95 TIGR03384 betaine_BetI transcr 42.8 12 0.00026 24.3 0.8 41 23-63 11-51 (189) 96 PRK00299 sulfur transfer prote 42.8 44 0.00095 20.1 3.3 37 13-49 11-49 (81) 97 PRK14903 16S rRNA methyltransf 42.2 47 0.001 25.8 4.1 20 25-44 348-368 (431) 98 PF13489 Methyltransf_23: Meth 42.0 18 0.0004 22.5 1.6 25 22-46 94-118 (161) 99 PRK11014 transcriptional repre 41.2 26 0.00057 22.8 2.3 26 18-43 34-59 (141) 100 COG2520 Predicted methyltransf 40.8 38 0.00082 26.2 3.4 33 9-41 255-287 (341) 101 cd08230 glucose_DH Glucose deh 40.2 35 0.00077 24.7 3.0 32 10-43 238-269 (355) 102 COG2185 Sbm Methylmalonyl-CoA 39.8 54 0.0012 22.6 3.7 53 9-63 39-92 (143) 103 TIGR00477 tehB tellurite resis 39.8 59 0.0013 22.1 3.9 37 9-45 93-136 (195) 104 PTZ00098 phosphoethanolamine N 39.7 34 0.00074 24.5 2.8 35 9-43 116-156 (263) 105 PRK14103 trans-aconitate 2-met 39.5 57 0.0012 22.9 3.9 35 9-43 88-126 (255) 106 TIGR03613 RutR pyrimidine util 39.5 13 0.00027 24.7 0.5 40 24-63 12-51 (202) 107 COG2227 UbiG 2-polyprenyl-3-me 39.3 30 0.00065 25.8 2.5 34 9-42 123-160 (243) 108 TIGR00496 frr ribosome recycli 39.0 18 0.00039 25.3 1.2 42 8-49 25-66 (176) 109 TIGR02822 adh_fam_2 zinc-bindi 39.0 51 0.0011 23.9 3.7 32 10-44 223-255 (329) 110 PRK00216 ubiE ubiquinone/menaq 39.0 59 0.0013 21.7 3.8 35 9-43 120-158 (239) 111 cd02072 Glm_B12_BD B12 binding 38.7 53 0.0011 21.9 3.5 33 9-43 26-58 (128) 112 PRK00311 panB 3-methyl-2-oxobu 38.5 30 0.00065 25.7 2.4 35 11-46 78-116 (264) 113 PLN02336 phosphoethanolamine N 38.5 50 0.0011 25.3 3.7 35 9-43 331-369 (475) 114 PLN02233 ubiquinone biosynthes 38.4 60 0.0013 23.3 3.9 34 9-42 144-181 (261) 115 PRK13168 rumA 23S rRNA m(5)U19 38.3 62 0.0014 25.0 4.2 34 9-43 366-400 (443) 116 KOG0181|consensus 37.7 26 0.00056 26.0 1.9 43 10-53 7-50 (233) 117 TIGR02819 fdhA_non_GSH formald 37.5 53 0.0011 24.8 3.7 34 10-44 254-300 (393) 118 PRK01747 mnmC bifunctional tRN 37.2 77 0.0017 25.7 4.7 53 9-68 165-225 (662) 119 TIGR01501 MthylAspMutase methy 37.0 59 0.0013 21.8 3.5 34 8-43 27-60 (134) 120 TIGR01370 cysRS possible cyste 36.9 29 0.00062 26.5 2.2 36 9-44 63-101 (315) 121 KOG1122|consensus 36.9 22 0.00048 28.9 1.6 21 24-44 352-373 (460) 122 COG0421 SpeE Spermidine syntha 36.5 84 0.0018 23.5 4.5 37 9-45 148-192 (282) 123 PF01189 Nol1_Nop2_Fmu: NOL1/N 36.4 22 0.00047 26.1 1.4 21 24-44 196-221 (283) 124 TIGR00406 prmA ribosomal prote 36.1 52 0.0011 23.9 3.3 36 8-43 223-259 (288) 125 COG0284 PyrF Orotidine-5'-phos 36.0 60 0.0013 23.8 3.6 33 10-43 89-123 (240) 126 COG0742 N6-adenine-specific me 35.6 58 0.0013 23.2 3.4 30 10-41 114-152 (187) 127 COG1192 Soj ATPases involved i 35.2 19 0.00042 25.1 1.0 19 9-27 33-51 (259) 128 PLN02244 tocopherol O-methyltr 34.9 73 0.0016 23.8 4.0 35 9-43 185-223 (340) 129 PRK14996 TetR family transcrip 34.9 16 0.00034 24.2 0.4 40 24-63 12-51 (192) 130 PRK11188 rrmJ 23S rRNA methylt 34.7 83 0.0018 21.8 4.1 35 8-42 115-164 (209) 131 cd08239 THR_DH_like L-threonin 34.3 67 0.0015 22.8 3.6 33 10-44 231-263 (339) 132 cd08293 PTGR2 Prostaglandin re 34.2 58 0.0013 23.1 3.3 29 10-41 224-252 (345) 133 PF10354 DUF2431: Domain of un 34.0 54 0.0012 22.4 3.0 25 24-48 106-130 (166) 134 PF05175 MTS: Methyltransferas 33.8 48 0.001 22.0 2.7 34 8-41 96-138 (170) 135 cd00223 TOPRIM_TopoIIB_SPO TOP 33.1 16 0.00035 24.4 0.3 11 10-20 54-64 (160) 136 cd08264 Zn_ADH_like2 Alcohol d 33.0 72 0.0016 22.4 3.6 32 10-44 223-254 (325) 137 TIGR02825 B4_12hDH leukotriene 32.6 60 0.0013 23.0 3.2 31 10-43 207-237 (325) 138 PRK10668 DNA-binding transcrip 32.3 18 0.00038 24.3 0.3 40 24-63 15-54 (215) 139 PF01206 TusA: Sulfurtransfera 32.1 99 0.0022 17.4 4.1 36 14-49 3-40 (70) 140 TIGR00091 tRNA (guanine-N(7)-) 31.8 55 0.0012 22.2 2.8 26 23-49 112-137 (194) 141 COG0233 Frr Ribosome recycling 31.8 35 0.00076 24.6 1.8 58 9-66 37-94 (187) 142 cd08265 Zn_ADH3 Alcohol dehydr 31.5 87 0.0019 23.1 3.9 33 9-42 274-306 (384) 143 TIGR03704 PrmC_rel_meth putati 31.3 93 0.002 22.3 4.0 19 24-42 197-215 (251) 144 TIGR00537 hemK_rel_arch HemK-r 31.3 1.1E+02 0.0025 20.1 4.2 20 24-43 121-140 (179) 145 PRK15062 hydrogenase isoenzyme 31.2 54 0.0012 25.8 2.9 33 21-53 67-99 (364) 146 PF06971 Put_DNA-bind_N: Putat 30.9 13 0.00028 21.2 -0.4 32 28-59 16-47 (50) 147 TIGR03451 mycoS_dep_FDH mycoth 30.9 91 0.002 22.6 3.9 33 10-44 245-277 (358) 148 PF00107 ADH_zinc_N: Zinc-bind 30.7 37 0.0008 20.7 1.6 35 10-46 58-92 (130) 149 cd03420 SirA_RHOD_Pry_redox Si 30.4 94 0.002 17.9 3.3 31 19-49 7-39 (69) 150 PF05883 Baculo_RING: Baculovi 30.4 37 0.0008 23.2 1.7 37 35-71 39-75 (134) 151 PF04182 B-block_TFIIIC: B-blo 30.2 25 0.00055 20.8 0.8 32 29-60 7-38 (75) 152 cd03752 proteasome_alpha_type_ 30.2 50 0.0011 22.8 2.3 36 17-53 11-47 (213) 153 PRK11018 hypothetical protein; 30.1 1.3E+02 0.0027 17.9 4.1 39 12-50 9-49 (78) 154 PRK13699 putative methylase; P 30.0 88 0.0019 22.2 3.6 40 3-42 13-71 (227) 155 PLN03075 nicotianamine synthas 29.8 78 0.0017 24.0 3.5 35 9-43 194-233 (296) 156 PRK13942 protein-L-isoaspartat 29.5 99 0.0021 21.4 3.7 33 9-43 144-176 (212) 157 TIGR00057 Sua5/YciO/YrdC/YwlC 29.5 69 0.0015 22.3 3.0 26 23-49 8-33 (201) 158 PF03269 DUF268: Caenorhabditi 28.6 63 0.0014 23.2 2.6 27 16-43 85-111 (177) 159 cd08295 double_bond_reductase_ 28.4 77 0.0017 22.7 3.1 29 10-41 221-249 (338) 160 TIGR00452 methyltransferase, p 28.4 66 0.0014 24.3 2.9 34 10-43 188-225 (314) 161 cd03749 proteasome_alpha_type_ 27.9 57 0.0012 22.6 2.3 36 17-53 9-45 (211) 162 PRK00050 16S rRNA m(4)C1402 me 27.7 55 0.0012 24.7 2.3 22 22-43 215-236 (296) 163 KOG1562|consensus 27.4 99 0.0021 24.3 3.7 40 3-43 188-236 (337) 164 TIGR03633 arc_protsome_A prote 26.9 61 0.0013 22.5 2.3 37 16-53 10-47 (224) 165 PRK04266 fibrillarin; Provisio 26.6 1.4E+02 0.0031 21.2 4.2 33 9-42 140-175 (226) 166 TIGR00740 methyltransferase, p 26.2 67 0.0015 22.2 2.4 21 23-43 141-161 (239) 167 cd03754 proteasome_alpha_type_ 26.2 62 0.0013 22.5 2.3 35 16-51 9-45 (215) 168 cd03751 proteasome_alpha_type_ 26.1 66 0.0014 22.4 2.4 36 17-53 12-48 (212) 169 TIGR00006 S-adenosyl-methyltra 26.0 61 0.0013 24.6 2.3 22 22-43 219-240 (305) 170 COG1309 AcrR Transcriptional r 25.7 22 0.00047 21.5 -0.1 40 24-63 16-55 (201) 171 PF05869 Dam: DNA N-6-adenine- 25.7 57 0.0012 22.9 2.0 31 18-48 72-105 (181) 172 TIGR01712 phage_N6A_met phage 25.6 93 0.002 21.9 3.0 29 18-46 70-100 (166) 173 cd08237 ribitol-5-phosphate_DH 25.4 1.1E+02 0.0023 22.3 3.5 32 11-43 223-256 (341) 174 PRK10909 rsmD 16S rRNA m(2)G96 24.8 62 0.0013 22.7 2.0 35 9-45 120-161 (199) 175 PF02878 PGM_PMM_I: Phosphoglu 24.7 58 0.0012 20.9 1.8 34 9-44 67-100 (137) 176 cd05805 MPG1_transferase GTP-m 24.6 1.1E+02 0.0025 23.4 3.6 34 9-44 61-94 (441) 177 cd02071 MM_CoA_mut_B12_BD meth 24.4 1.1E+02 0.0025 19.2 3.1 39 8-48 25-63 (122) 178 COG0275 Predicted S-adenosylme 24.4 68 0.0015 24.9 2.3 25 19-43 220-244 (314) 179 KOG1271|consensus 24.4 88 0.0019 23.2 2.8 35 10-44 145-182 (227) 180 PRK10857 DNA-binding transcrip 24.0 87 0.0019 21.4 2.6 25 18-42 34-58 (164) 181 PRK11202 DNA-binding transcrip 23.8 35 0.00077 23.1 0.6 40 24-63 15-55 (203) 182 cd00824 PTBI IRS-like phosphot 23.4 30 0.00066 22.4 0.2 31 35-65 21-58 (104) 183 PLN02232 ubiquinone biosynthes 23.3 88 0.0019 20.6 2.5 35 9-44 43-82 (160) 184 TIGR03366 HpnZ_proposed putati 23.3 1.4E+02 0.0031 20.9 3.7 32 10-43 187-218 (280) 185 PRK10634 tRNA(ANN) t(6)A37 thr 23.0 73 0.0016 22.1 2.1 39 23-62 7-48 (190) 186 cd05799 PGM2 This CD includes 22.5 1.3E+02 0.0028 23.4 3.6 34 9-44 72-106 (487) 187 PF06080 DUF938: Protein of un 22.4 35 0.00076 24.6 0.4 29 13-41 111-139 (204) 188 PRK00517 prmA ribosomal protei 22.4 1.3E+02 0.0029 21.2 3.4 34 10-43 179-213 (250) 189 TIGR02266 gmx_TIGR02266 Myxoco 22.2 1E+02 0.0022 18.0 2.4 27 20-46 11-37 (96) 190 PF05225 HTH_psq: helix-turn-h 22.1 50 0.0011 17.9 0.9 12 26-37 5-16 (45) 191 PF15540 Toxin_62: Putative to 22.1 51 0.0011 22.0 1.1 29 11-39 8-36 (113) 192 PF02384 N6_Mtase: N-6 DNA Met 22.0 76 0.0016 22.8 2.1 37 24-61 164-200 (311) 193 PHA03356 tegument protein UL11 21.9 48 0.001 21.4 0.9 10 9-18 31-40 (93) 194 PF08242 Methyltransf_12: Meth 21.7 50 0.0011 19.3 1.0 19 21-39 81-99 (99) 195 PRK09480 slmA division inhibit 21.6 42 0.00091 21.8 0.7 40 24-64 14-54 (194) 196 smart00138 MeTrc Methyltransfe 21.5 1E+02 0.0022 22.3 2.7 25 24-48 223-247 (264) 197 PF08704 GCD14: tRNA methyltra 21.5 1E+02 0.0022 22.6 2.7 33 9-42 112-145 (247) 198 PF13602 ADH_zinc_N_2: Zinc-bi 21.5 18 0.00038 22.1 -1.1 31 8-40 17-48 (127) 199 cd08242 MDR_like Medium chain 21.3 1.7E+02 0.0038 20.4 3.8 30 10-41 214-243 (319) 200 PRK00014 ribB 3,4-dihydroxy-2- 21.2 1E+02 0.0022 22.8 2.7 19 26-44 21-39 (230) 201 PRK13944 protein-L-isoaspartat 21.2 1.9E+02 0.0042 19.7 3.9 34 9-44 141-174 (205) 202 PF01555 N6_N4_Mtase: DNA meth 20.9 87 0.0019 20.5 2.1 26 23-48 36-61 (231) 203 KOG2795|consensus 20.5 48 0.001 26.3 0.8 39 11-49 249-297 (372) 204 PRK01683 trans-aconitate 2-met 20.4 1.1E+02 0.0023 21.3 2.5 35 9-43 92-130 (258) 205 PRK02260 S-ribosylhomocysteina 20.4 68 0.0015 22.5 1.5 23 3-25 64-86 (158) 206 COG4798 Predicted methyltransf 20.2 93 0.002 23.2 2.3 23 20-42 143-165 (238) 207 PF05219 DREV: DREV methyltran 20.0 1.1E+02 0.0025 23.1 2.7 22 21-42 166-187 (265) No 1 >PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA:S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A. Probab=100.00 E-value=4.9e-35 Score=222.24 Aligned_cols=73 Identities=59% Similarity=1.018 Sum_probs=58.7 Q ss_pred ccccccCCCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcCcccCCCCccCCC Q psy4127 2 QLEKIRGRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNAVSLKTAACHEMP 75 (75) Q Consensus 2 ~m~~~~~~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~~~~~~~~~~E~~ 75 (75) +|+. .+++||+|||||||||+||||+|+|++++||+|+|||||+++|||++|++|+||||++|++++++||++ T Consensus 114 ll~~-~~~~fD~IDlDPfGSp~pfldsA~~~v~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~~~~~~~~~~E~g 186 (377) T PF02005_consen 114 LLYS-RQERFDVIDLDPFGSPAPFLDSALQAVKDGGLLCVTATDTAVLCGSYPEKCFRKYGAVPRKTPYCHEMG 186 (377) T ss_dssp HHCH-STT-EEEEEE--SS--HHHHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHHHHHSSB---STTHHHHH T ss_pred Hhhh-ccccCCEEEeCCCCCccHhHHHHHHHhhcCCEEEEeccccccccCCChhHHHHhcCCcccCCCcccHHH Confidence 4542 467899999999999999999999999999999999999999999999999999999999999999974 No 2 >COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=1.1e-33 Score=216.27 Aligned_cols=73 Identities=58% Similarity=0.983 Sum_probs=69.0 Q ss_pred ccccccCCCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcCcccCCCCccCCC Q psy4127 2 QLEKIRGRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNAVSLKTAACHEMP 75 (75) Q Consensus 2 ~m~~~~~~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~~~~~~~~~~E~~ 75 (75) +|+++. ..||+|||||||||+||||+|++++++||+|||||||+++|||++|++|+|||++.+++++++||++ T Consensus 114 lm~~~~-~~fd~IDiDPFGSPaPFlDaA~~s~~~~G~l~vTATD~a~L~G~~p~~c~rkY~a~~~~~~~~hE~g 186 (380) T COG1867 114 LLHELH-RAFDVIDIDPFGSPAPFLDAALRSVRRGGLLCVTATDTAPLCGSYPRKCRRKYGAVPLKTEFCHEVG 186 (380) T ss_pred HHHhcC-CCccEEecCCCCCCchHHHHHHHHhhcCCEEEEEecccccccCCChHHHHHHhccccCCCcchhHHH Confidence 566643 6899999999999999999999999999999999999999999999999999999999999999974 No 3 >KOG1253|consensus Probab=99.98 E-value=8.1e-34 Score=223.17 Aligned_cols=74 Identities=58% Similarity=1.044 Sum_probs=70.0 Q ss_pred cccccc--CCCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcCcccCCCCccCCC Q psy4127 2 QLEKIR--GRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNAVSLKTAACHEMP 75 (75) Q Consensus 2 ~m~~~~--~~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~~~~~~~~~~E~~ 75 (75) +|++|+ .++||+|||||||||++|||+|+|+|++||||||||||+++|||+.|++||+|||++++++++||||| T Consensus 173 lM~~~~~~~~~FDvIDLDPyGs~s~FLDsAvqav~~gGLL~vT~TD~aVL~gn~pe~C~~kYG~~~lr~~~chE~a 248 (525) T KOG1253|consen 173 LMYEHPMVAKFFDVIDLDPYGSPSPFLDSAVQAVRDGGLLCVTCTDMAVLAGNAPEKCYSKYGASILRMKYCHEMA 248 (525) T ss_pred HHHhccccccccceEecCCCCCccHHHHHHHHHhhcCCEEEEEecchHhhccCChhhHHHhcCcccccchhhhHHH Confidence 567653 47899999999999999999999999999999999999999999999999999999999999999986 No 4 >TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes. Probab=99.95 E-value=2.6e-28 Score=185.36 Aligned_cols=67 Identities=51% Similarity=0.972 Sum_probs=65.4 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcCcccCCCCccCCC Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNAVSLKTAACHEMP 75 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~~~~~~~~~~E~~ 75 (75) ++||+||+||||+|++|||+|++++++||+|+|||||+++|||++|++|+||||+++++++++||++ T Consensus 113 ~~fDvIdlDPfGs~~~fld~al~~~~~~glL~vTaTD~~~L~G~~~~~~~rkYga~~~~~~~~~E~g 179 (374) T TIGR00308 113 RKFHVIDIDPFGTPAPFVDSAIQASAERGLLLVTATDTSALCGNYPKSCLRKYGANPVKTESCHESA 179 (374) T ss_pred CCCCEEEeCCCCCcHHHHHHHHHhcccCCEEEEEecccHHhcCCChHHHHHHhCCcccCCcchHHHH Confidence 5799999999999999999999999999999999999999999999999999999999999999985 No 5 >PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional Probab=99.87 E-value=1.3e-22 Score=154.27 Aligned_cols=68 Identities=56% Similarity=0.976 Sum_probs=65.6 Q ss_pred CCCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcCcccCCCCccCCC Q psy4127 8 GRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNAVSLKTAACHEMP 75 (75) Q Consensus 8 ~~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~~~~~~~~~~E~~ 75 (75) +++||+||+||||+|.+||++|++++++||+|+|||||+++|||+++.+|+++||.+|.+++++||++ T Consensus 123 ~~~fD~V~lDP~Gs~~~~l~~al~~~~~~gilyvSAtD~~~L~g~y~~~~~~~yd~fP~~~~~~~E~g 190 (382) T PRK04338 123 ERKFDVVDIDPFGSPAPFLDSAIRSVKRGGLLCVTATDTAPLCGAYPKSCLRKYGAVPLKTEFYHEMG 190 (382) T ss_pred cCCCCEEEECCCCCcHHHHHHHHHHhcCCCEEEEEecCchhhcCCChHHHHHHhcCcccCCcchhHHH Confidence 35699999999999999999999999999999999999999999999999999999999999999975 No 6 >PRK04457 spermidine synthase; Provisional Probab=89.55 E-value=0.73 Score=33.43 Aligned_cols=37 Identities=24% Similarity=0.392 Sum_probs=31.3 Q ss_pred CCCCceeeeCCCCCc--------hhhHHHHHHhcccCcEEEEEec Q psy4127 8 GRHFDAIDLDPFGNP--------TRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 8 ~~~fD~IDlDPfGSp--------~pfldsA~~av~~gGll~vTaT 44 (75) ++.||+|=+|.|.+. ..|+..+.+.+++||++.+... T Consensus 134 ~~~yD~I~~D~~~~~~~~~~l~t~efl~~~~~~L~pgGvlvin~~ 178 (262) T PRK04457 134 RHSTDVILVDGFDGEGIIDALCTQPFFDDCRNALSSDGIFVVNLW 178 (262) T ss_pred CCCCCEEEEeCCCCCCCccccCcHHHHHHHHHhcCCCcEEEEEcC Confidence 357999999998654 5899999999999999999643 No 7 >PRK14901 16S rRNA methyltransferase B; Provisional Probab=88.16 E-value=0.84 Score=35.20 Aligned_cols=36 Identities=36% Similarity=0.551 Sum_probs=27.9 Q ss_pred CCCceeeeCCC--CCc------------------------hhhHHHHHHhcccCcE-EEEEec Q psy4127 9 RHFDAIDLDPF--GNP------------------------TRFLDAAVSSLRDGGL-LLVTCT 44 (75) Q Consensus 9 ~~fD~IDlDPf--GSp------------------------~pfldsA~~av~~gGl-l~vTaT 44 (75) +.||.|=+||= |+- ...|+.|.+.+|+||. ++.||| T Consensus 324 ~~fD~Vl~DaPCSg~G~~~r~p~~~~~~~~~~~~~l~~~Q~~iL~~a~~~lkpgG~lvystcs 386 (434) T PRK14901 324 GYFDRILLDAPCSGLGTLHRHPDARWRQTPEKIQELAPLQAELLESLAPLLKPGGTLVYATCT 386 (434) T ss_pred ccCCEEEEeCCCCcccccccCcchhhhCCHHHHHHHHHHHHHHHHHHHHhcCCCCEEEEEeCC Confidence 46999999973 321 3569999999999994 677777 No 8 >TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2. Probab=85.33 E-value=1.1 Score=29.75 Aligned_cols=39 Identities=23% Similarity=0.143 Sum_probs=32.7 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEecCcccc Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVL 49 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~a~L 49 (75) .-|++||+-.|=||..|+++|.+. +-=+++++++++..+ T Consensus 29 ~GfeVi~lg~~~s~e~~v~aa~e~--~adii~iSsl~~~~~ 67 (132) T TIGR00640 29 LGFDVDVGPLFQTPEEIARQAVEA--DVHVVGVSSLAGGHL 67 (132) T ss_pred CCcEEEECCCCCCHHHHHHHHHHc--CCCEEEEcCchhhhH Confidence 469999999999999999999876 444999999886544 No 9 >PLN02366 spermidine synthase Probab=85.16 E-value=1.4 Score=33.02 Aligned_cols=37 Identities=27% Similarity=0.542 Sum_probs=28.1 Q ss_pred CCCCceeeeCC---CCCc-----hhhHHHHHHhcccCcEEEEEec Q psy4127 8 GRHFDAIDLDP---FGNP-----TRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 8 ~~~fD~IDlDP---fGSp-----~pfldsA~~av~~gGll~vTaT 44 (75) +++||+|=+|. .|-+ ..|++.+.+++++||++.+.++ T Consensus 163 ~~~yDvIi~D~~dp~~~~~~L~t~ef~~~~~~~L~pgGvlv~q~~ 207 (308) T PLN02366 163 EGTYDAIIVDSSDPVGPAQELFEKPFFESVARALRPGGVVCTQAE 207 (308) T ss_pred CCCCCEEEEcCCCCCCchhhhhHHHHHHHHHHhcCCCcEEEECcC Confidence 45799998874 4422 2589999999999999977654 No 10 >PRK00811 spermidine synthase; Provisional Probab=84.71 E-value=1.9 Score=31.53 Aligned_cols=37 Identities=24% Similarity=0.567 Sum_probs=28.2 Q ss_pred CCCCceeeeC---CCCCc-----hhhHHHHHHhcccCcEEEEEec Q psy4127 8 GRHFDAIDLD---PFGNP-----TRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 8 ~~~fD~IDlD---PfGSp-----~pfldsA~~av~~gGll~vTaT 44 (75) +++||+|=+| |+|.+ ..|+..+-+.+++||++.+.+. T Consensus 148 ~~~yDvIi~D~~dp~~~~~~l~t~ef~~~~~~~L~~gGvlv~~~~ 192 (283) T PRK00811 148 ENSFDVIIVDSTDPVGPAEGLFTKEFYENCKRALKEDGIFVAQSG 192 (283) T ss_pred CCcccEEEECCCCCCCchhhhhHHHHHHHHHHhcCCCcEEEEeCC Confidence 4579998775 66644 4678888899999999987543 No 11 >PRK00121 trmB tRNA (guanine-N(7)-)-methyltransferase; Reviewed Probab=84.24 E-value=2.4 Score=29.20 Aligned_cols=36 Identities=28% Similarity=0.468 Sum_probs=28.5 Q ss_pred CCCCceeee---CCCCC---------chhhHHHHHHhcccCcEEEEEe Q psy4127 8 GRHFDAIDL---DPFGN---------PTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 8 ~~~fD~IDl---DPfGS---------p~pfldsA~~av~~gGll~vTa 43 (75) ++.||.|.+ ||+-. -..||..+.+.+++||.+.++. T Consensus 109 ~~~~D~V~~~~~~p~~~~~~~~~~~~~~~~l~~i~~~LkpgG~l~i~~ 156 (202) T PRK00121 109 DGSLDRIYLNFPDPWPKKRHHKRRLVQPEFLALYARKLKPGGEIHFAT 156 (202) T ss_pred ccccceEEEECCCCCCCccccccccCCHHHHHHHHHHcCCCCEEEEEc Confidence 456999988 66643 2468999999999999999864 No 12 >TIGR02469 CbiT precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit. This model recognizes the CbiT methylase which is responsible, in part (along with CbiE), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiE subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin biosynthesis pathway, is called CobL. Probab=84.03 E-value=2.6 Score=25.37 Aligned_cols=35 Identities=23% Similarity=0.277 Sum_probs=27.3 Q ss_pred CCCceeeeCC-CCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDLDP-FGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDlDP-fGSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=++. ......+++.+.+.+++||.+.++. T Consensus 87 ~~~D~v~~~~~~~~~~~~l~~~~~~Lk~gG~li~~~ 122 (124) T TIGR02469 87 PEPDRVFIGGSGGLLQEILEAIWRRLRPGGRIVLNA 122 (124) T ss_pred CCCCEEEECCcchhHHHHHHHHHHHcCCCCEEEEEe Confidence 4799998763 2233568999999999999999874 No 13 >PF02475 Met_10: Met-10+ like-protein; InterPro: IPR003402 This entry represents the Trm5 family. Trm5 specifically methylates the N1 position of guanosine-37 in various tRNAs [, , ]. Another members of this family, tRNA wybutosine-synthesizing protein 2 (Tyw2) and its homologues, are S-adenosyl-L-methionine-dependent transferases that act as a component of the wybutosine biosynthesis pathway [, ]. tRNA wybutosine-synthesizing protein 2 was originally thought to be a methyltransferase [].; GO: 0016740 transferase activity; PDB: 3A27_A 2ZZN_B 2YX1_A 2ZZM_A 3AY0_B 3K6R_A 3A26_A 3A25_A. Probab=83.18 E-value=1.3 Score=31.55 Aligned_cols=33 Identities=33% Similarity=0.570 Sum_probs=26.7 Q ss_pred CCCCceeeeCCCCCchhhHHHHHHhcccCcEEE Q psy4127 8 GRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLL 40 (75) Q Consensus 8 ~~~fD~IDlDPfGSp~pfldsA~~av~~gGll~ 40 (75) ++.+|.|=.+...+...||++|++++++||+++ T Consensus 167 ~~~~drvim~lp~~~~~fl~~~~~~~~~~g~ih 199 (200) T PF02475_consen 167 EGKFDRVIMNLPESSLEFLDAALSLLKEGGIIH 199 (200) T ss_dssp TT-EEEEEE--TSSGGGGHHHHHHHEEEEEEEE T ss_pred ccccCEEEECChHHHHHHHHHHHHHhcCCcEEE Confidence 456888888888888899999999999999986 No 14 >PF01564 Spermine_synth: Spermine/spermidine synthase; InterPro: IPR001045 Synonym(s): Spermidine aminopropyltransferase A group of polyamine biosynthetic enzymes involved in the fifth (last) step in the biosynthesis of spermidine from arginine and methionine which includes; spermidine synthase (2.5.1.16 from EC), spermine synthase (2.5.1.22 from EC) and putrescine N-methyltransferase (2.1.1.53 from EC) []. The Thermotoga maritima spermidine synthase monomer consists of two domains: an N-terminal domain composed of six beta-strands, and a Rossmann-like C- terminal domain []. The larger C-terminal catalytic core domain consists of a seven-stranded beta-sheet flanked by nine alpha helices. This domain resembles a topology observed in a number of nucleotide and dinucleotide-binding enzymes, and in S-adenosyl-L-methionine (AdoMet)- dependent methyltransferase (MTases) [].; GO: 0003824 catalytic activity; PDB: 2E5W_C 2ZSU_E 2O0L_B 2O05_B 2O06_B 2O07_B 3RW9_B 2PWP_A 2HTE_B 3RIE_B .... Probab=82.98 E-value=1.1 Score=32.29 Aligned_cols=34 Identities=21% Similarity=0.394 Sum_probs=28.5 Q ss_pred CCceeeeCCCC---Cc-----hhhHHHHHHhcccCcEEEEEe Q psy4127 10 HFDAIDLDPFG---NP-----TRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 10 ~fD~IDlDPfG---Sp-----~pfldsA~~av~~gGll~vTa 43 (75) +||+|=+|.+- .+ .+|++.+-++++++|++.+.+ T Consensus 150 ~yDvIi~D~~dp~~~~~~l~t~ef~~~~~~~L~~~Gv~v~~~ 191 (246) T PF01564_consen 150 KYDVIIVDLTDPDGPAPNLFTREFYQLCKRRLKPDGVLVLQA 191 (246) T ss_dssp -EEEEEEESSSTTSCGGGGSSHHHHHHHHHHEEEEEEEEEEE T ss_pred cccEEEEeCCCCCCCcccccCHHHHHHHHhhcCCCcEEEEEc Confidence 89999988775 22 389999999999999999988 No 15 >PRK00536 speE spermidine synthase; Provisional Probab=82.51 E-value=2.4 Score=31.40 Aligned_cols=35 Identities=14% Similarity=0.196 Sum_probs=29.7 Q ss_pred CCCCceeeeC-CCCCchhhHHHHHHhcccCcEEEEEec Q psy4127 8 GRHFDAIDLD-PFGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 8 ~~~fD~IDlD-PfGSp~pfldsA~~av~~gGll~vTaT 44 (75) .++||+|=+| .|. ..|....-+++++||++.+.++ T Consensus 137 ~~~fDVIIvDs~~~--~~fy~~~~~~L~~~Gi~v~Qs~ 172 (262) T PRK00536 137 IKKYDLIICLQEPD--IHKIDGLKRMLKEDGVFISVAK 172 (262) T ss_pred CCcCCEEEEcCCCC--hHHHHHHHHhcCCCcEEEECCC Confidence 4689999999 443 5888999999999999998876 No 16 >TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase. Probab=82.46 E-value=2.9 Score=30.10 Aligned_cols=36 Identities=42% Similarity=0.746 Sum_probs=26.8 Q ss_pred CCCceeeeCC--CCCc------------------------hhhHHHHHHhcccCcEE-EEEec Q psy4127 9 RHFDAIDLDP--FGNP------------------------TRFLDAAVSSLRDGGLL-LVTCT 44 (75) Q Consensus 9 ~~fD~IDlDP--fGSp------------------------~pfldsA~~av~~gGll-~vTaT 44 (75) +.||.|=+|| +|+- ...|+.|++.+|+||.| +.||| T Consensus 139 ~~fD~Vl~D~Pcsg~G~~~~~p~~~~~~~~~~~~~l~~~q~~iL~~a~~~lkpgG~lvYstcs 201 (264) T TIGR00446 139 PKFDAILLDAPCSGEGVIRKDPSRKKNWSEEDIQEISALQKELIDSAFDALKPGGVLVYSTCS 201 (264) T ss_pred cCCCEEEEcCCCCCCcccccChhhhhcCCHHHHHHHHHHHHHHHHHHHHhcCCCCEEEEEeCC Confidence 3599999997 4431 24899999999999965 55566 No 17 >PRK03612 spermidine synthase; Provisional Probab=81.14 E-value=2.7 Score=33.47 Aligned_cols=36 Identities=31% Similarity=0.427 Sum_probs=28.6 Q ss_pred CCCCceeeeCCCCC--c-------hhhHHHHHHhcccCcEEEEEe Q psy4127 8 GRHFDAIDLDPFGN--P-------TRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 8 ~~~fD~IDlDPfGS--p-------~pfldsA~~av~~gGll~vTa 43 (75) +++||+|=+|+.-. | ..|++.+.+.+++||++.+++ T Consensus 371 ~~~fDvIi~D~~~~~~~~~~~L~t~ef~~~~~~~L~pgG~lv~~~ 415 (521) T PRK03612 371 AEKFDVIIVDLPDPSNPALGKLYSVEFYRLLKRRLAPDGLLVVQS 415 (521) T ss_pred CCCCCEEEEeCCCCCCcchhccchHHHHHHHHHhcCCCeEEEEec Confidence 46899999996531 1 148899999999999999875 No 18 >PLN02823 spermine synthase Probab=80.86 E-value=3.7 Score=31.25 Aligned_cols=39 Identities=26% Similarity=0.452 Sum_probs=29.1 Q ss_pred CCCCceeeeC---CC--CCc-----hhhHH-HHHHhcccCcEEEEEecCc Q psy4127 8 GRHFDAIDLD---PF--GNP-----TRFLD-AAVSSLRDGGLLLVTCTDM 46 (75) Q Consensus 8 ~~~fD~IDlD---Pf--GSp-----~pfld-sA~~av~~gGll~vTaTD~ 46 (75) +++||+|=+| |. |.| ..|++ .+.+.++.||++.+.+... T Consensus 174 ~~~yDvIi~D~~dp~~~~~~~~Lyt~eF~~~~~~~~L~p~Gvlv~q~~s~ 223 (336) T PLN02823 174 DEKFDVIIGDLADPVEGGPCYQLYTKSFYERIVKPKLNPGGIFVTQAGPA 223 (336) T ss_pred CCCccEEEecCCCccccCcchhhccHHHHHHHHHHhcCCCcEEEEeccCc Confidence 4679999999 43 212 24887 7889999999998876643 No 19 >PRK11524 putative methyltransferase; Provisional Probab=79.85 E-value=2.8 Score=30.47 Aligned_cols=36 Identities=19% Similarity=0.360 Sum_probs=29.0 Q ss_pred cCCCCceeeeC-CCCCc-------------------hhhHHHHHHhcccCcEEEEE Q psy4127 7 RGRHFDAIDLD-PFGNP-------------------TRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 7 ~~~~fD~IDlD-PfGSp-------------------~pfldsA~~av~~gGll~vT 42 (75) ..+.||.|=+| ||+.. ..++..+.+.+|+||.+++- T Consensus 24 ~~~siDlIitDPPY~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~rvLK~~G~i~i~ 79 (284) T PRK11524 24 PSESVDLIFADPPYNIGKNFDGLIEAWKEDLFIDWLYEWIDECHRVLKKQGTMYIM 79 (284) T ss_pred ccCcccEEEECCCcccccccccccccccHHHHHHHHHHHHHHHHHHhCCCcEEEEE Confidence 45679999999 78741 25778888999999999985 No 20 >PRK00107 gidB 16S rRNA methyltransferase GidB; Reviewed Probab=78.68 E-value=3.7 Score=28.50 Aligned_cols=35 Identities=17% Similarity=0.393 Sum_probs=31.4 Q ss_pred CCCCceeeeCCCCCchhhHHHHHHhcccCcEEEEE Q psy4127 8 GRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 8 ~~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vT 42 (75) .+.||+|=.+.++.+..|+..+.+.+++||.+.+- T Consensus 110 ~~~fDlV~~~~~~~~~~~l~~~~~~LkpGG~lv~~ 144 (187) T PRK00107 110 EEKFDVVTSRAVASLSDLVELCLPLLKPGGRFLAL 144 (187) T ss_pred CCCccEEEEccccCHHHHHHHHHHhcCCCeEEEEE Confidence 34799999999998899999999999999999875 No 21 >TIGR00417 speE spermidine synthase. the SpeE subunit of spermidine synthase catalysesthe reaction (putrescine + S-adenosylmethioninamine = spermidine + 5'-methylthioadenosine) and is involved in polyamine biosynthesis and in the biosynthesis of spermidine from arganine. The region between residues 77 and 120 of the seed alignment is thought to be involved in binding to decarboxylated SAM. Probab=78.10 E-value=4.4 Score=29.20 Aligned_cols=36 Identities=22% Similarity=0.461 Sum_probs=28.6 Q ss_pred CCCCceeeeCCC---CCc-----hhhHHHHHHhcccCcEEEEEe Q psy4127 8 GRHFDAIDLDPF---GNP-----TRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 8 ~~~fD~IDlDPf---GSp-----~pfldsA~~av~~gGll~vTa 43 (75) ++.||+|=+|++ |.+ ..|++.+.+.+++||++.+.+ T Consensus 143 ~~~yDvIi~D~~~~~~~~~~l~~~ef~~~~~~~L~pgG~lv~~~ 186 (270) T TIGR00417 143 ENTFDVIIVDSTDPVGPAETLFTKEFYELLKKALNEDGIFVAQS 186 (270) T ss_pred CCCccEEEEeCCCCCCcccchhHHHHHHHHHHHhCCCcEEEEcC Confidence 467999999886 322 367888999999999999874 No 22 >PLN02781 Probable caffeoyl-CoA O-methyltransferase Probab=77.92 E-value=3.4 Score=29.42 Aligned_cols=38 Identities=21% Similarity=0.237 Sum_probs=29.6 Q ss_pred CCCceeeeCCC-CCchhhHHHHHHhcccCcEEEEEecCc Q psy4127 9 RHFDAIDLDPF-GNPTRFLDAAVSSLRDGGLLLVTCTDM 46 (75) Q Consensus 9 ~~fD~IDlDPf-GSp~pfldsA~~av~~gGll~vTaTD~ 46 (75) +.||+|=+|.- .....|++.+++.++.||+|.+.-+.. T Consensus 143 ~~fD~VfiDa~k~~y~~~~~~~~~ll~~GG~ii~dn~l~ 181 (234) T PLN02781 143 PEFDFAFVDADKPNYVHFHEQLLKLVKVGGIIAFDNTLW 181 (234) T ss_pred CCCCEEEECCCHHHHHHHHHHHHHhcCCCeEEEEEcCCc Confidence 57999988843 223578999999999999999866543 No 23 >PF03537 Glyco_hydro_114: Glycoside-hydrolase family GH114; InterPro: IPR004352 Eighty-one archaeal-like genes, ranging in size from 4-20kb, are clustered in 15 regions of the Thermotoga maritima genome []. Conservation of gene order between T. maritima and Archaea in many of these regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea []. One of the T. maritima sequences (hypothetical protein TM1410) shares similarity with Methanocaldococcus jannaschii (Methanococcus jannaschii) hypothetical protein MJ1477 and with hypothetical protein DR0705 from Deinococcus radiodurans. The sequences are characterised by relatively variable N- and C-terminal domains, and a more conserved central domain. They share no similarity with any other known, functionally or structurally characterised proteins. ; PDB: 2AAM_F. Probab=77.63 E-value=2.8 Score=25.22 Aligned_cols=31 Identities=16% Similarity=0.328 Sum_probs=18.6 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTa 43 (75) ..+|++|||+|-.+ .+-|+.++..|..-|.. T Consensus 25 ~~~~v~~iD~~~~~----~~~I~~L~~~G~~vicY 55 (74) T PF03537_consen 25 PDVDVVVIDLFDFS----KEEIARLKAQGKKVICY 55 (74) T ss_dssp SS-SEEEE-SBS------HHHHHHHHHTT-EEEEE T ss_pred CCCCEEEECCccCC----HHHHHHHHHCCCEEEEE Confidence 46999999999854 44566677777655543 No 24 >cd02440 AdoMet_MTases S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.). Probab=77.47 E-value=5.8 Score=21.83 Aligned_cols=34 Identities=41% Similarity=0.613 Sum_probs=27.8 Q ss_pred CCCceeeeCCCCCc-----hhhHHHHHHhcccCcEEEEE Q psy4127 9 RHFDAIDLDPFGNP-----TRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 9 ~~fD~IDlDPfGSp-----~pfldsA~~av~~gGll~vT 42 (75) ..||+|=.++.-.. ..++..+.+.++.||.+.++ T Consensus 65 ~~~d~i~~~~~~~~~~~~~~~~l~~~~~~l~~~g~~~~~ 103 (107) T cd02440 65 ESFDVIISDPPLHHLVEDLARFLEEARRLLKPGGVLVLT 103 (107) T ss_pred CceEEEEEccceeehhhHHHHHHHHHHHHcCCCCEEEEE Confidence 45888877776544 88888899999999999887 No 25 >PRK01581 speE spermidine synthase; Validated Probab=75.56 E-value=5.2 Score=31.39 Aligned_cols=37 Identities=14% Similarity=0.223 Sum_probs=28.4 Q ss_pred CCCCceeeeCCCCC---c------hhhHHHHHHhcccCcEEEEEec Q psy4127 8 GRHFDAIDLDPFGN---P------TRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 8 ~~~fD~IDlDPfGS---p------~pfldsA~~av~~gGll~vTaT 44 (75) +++||+|=+|..-. + ..|+..+.+.++.||++.+.+. T Consensus 224 ~~~YDVIIvDl~DP~~~~~~~LyT~EFy~~~~~~LkPgGV~V~Qs~ 269 (374) T PRK01581 224 SSLYDVIIIDFPDPATELLSTLYTSELFARIATFLTEDGAFVCQSN 269 (374) T ss_pred CCCccEEEEcCCCccccchhhhhHHHHHHHHHHhcCCCcEEEEecC Confidence 45799999996431 1 3489999999999999877743 No 26 >PF13659 Methyltransf_26: Methyltransferase domain; PDB: 3GJY_A 3LPM_B 2NP6_D 1AQI_B 2ADM_B 2IH2_A 2JG3_A 2IBS_D 2NP7_A 2IBT_A .... Probab=75.53 E-value=4.1 Score=24.62 Aligned_cols=36 Identities=39% Similarity=0.719 Sum_probs=27.0 Q ss_pred cCCCCceeeeC-CCCCc-----------hhhHHHHHHhcccCcEEEEE Q psy4127 7 RGRHFDAIDLD-PFGNP-----------TRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 7 ~~~~fD~IDlD-PfGSp-----------~pfldsA~~av~~gGll~vT 42 (75) ..++||+|=.| ||+.. ..|++.+.+.+++||.+.+. T Consensus 67 ~~~~~D~Iv~npP~~~~~~~~~~~~~~~~~~~~~~~~~L~~gG~~~~~ 114 (117) T PF13659_consen 67 PDGKFDLIVTNPPYGPRSGDKAALRRLYSRFLEAAARLLKPGGVLVFI 114 (117) T ss_dssp TTT-EEEEEE--STTSBTT----GGCHHHHHHHHHHHHEEEEEEEEEE T ss_pred cCceeEEEEECCCCccccccchhhHHHHHHHHHHHHHHcCCCeEEEEE Confidence 34679999888 56632 47899999999999999875 No 27 >TIGR03065 srtB_sig_QVPTGV sortase B signal domain, QVPTGV class. This model represents a boutique (unusual) sorting signal, recognized by a member of the sortase SrtB family rather than by the housekeeping sortase, SrtA. Probab=74.87 E-value=0.68 Score=24.54 Aligned_cols=22 Identities=27% Similarity=0.382 Sum_probs=17.4 Q ss_pred CCchhhHHHHHHhcccCcEEEEEe Q psy4127 20 GNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 20 GSp~pfldsA~~av~~gGll~vTa 43 (75) |+-+||+ |+..|.-||.|++|- T Consensus 8 gtlapf~--al~iva~gg~~y~tk 29 (32) T TIGR03065 8 GTLAPFA--ALGIVAIGGAIYFTK 29 (32) T ss_pred eeeccce--eEEEEEeccEEEEEE Confidence 5567776 777789999999983 No 28 >PLN02589 caffeoyl-CoA O-methyltransferase Probab=73.36 E-value=4.8 Score=29.39 Aligned_cols=41 Identities=20% Similarity=0.284 Sum_probs=30.5 Q ss_pred CCCceeeeCCCCC-chhhHHHHHHhcccCcEEEEEecCcccccCC Q psy4127 9 RHFDAIDLDPFGN-PTRFLDAAVSSLRDGGLLLVTCTDMAVLCGN 52 (75) Q Consensus 9 ~~fD~IDlDPfGS-p~pfldsA~~av~~gGll~vTaTD~a~L~G~ 52 (75) +.||+|=||---. -..|++.+++.++.||+|.+ |-....|. T Consensus 155 ~~fD~iFiDadK~~Y~~y~~~~l~ll~~GGviv~---DNvl~~G~ 196 (247) T PLN02589 155 GTFDFIFVDADKDNYINYHKRLIDLVKVGGVIGY---DNTLWNGS 196 (247) T ss_pred CcccEEEecCCHHHhHHHHHHHHHhcCCCeEEEE---cCCCCCCc Confidence 4799887775532 36788999999999999987 55555553 No 29 >TIGR01177 conserved hypothetical protein TIGR01177. This family is found exclusively in the Archaea. Probab=71.53 E-value=9.4 Score=28.21 Aligned_cols=38 Identities=26% Similarity=0.482 Sum_probs=29.1 Q ss_pred CCCCceeeeC-CCCCc------------hhhHHHHHHhcccCcEEEEEecC Q psy4127 8 GRHFDAIDLD-PFGNP------------TRFLDAAVSSLRDGGLLLVTCTD 45 (75) Q Consensus 8 ~~~fD~IDlD-PfGSp------------~pfldsA~~av~~gGll~vTaTD 45 (75) .+.||.|=.| |||.. ..+++.+.+.+++||.+.+..++ T Consensus 246 ~~~~D~Iv~dPPyg~~~~~~~~~~~~l~~~~l~~~~r~Lk~gG~lv~~~~~ 296 (329) T TIGR01177 246 SESVDAIATDPPYGRSTTAAGDGLESLYERSLEEFHEVLKSEGWIVYAVPT 296 (329) T ss_pred cCCCCEEEECCCCcCcccccCCchHHHHHHHHHHHHHHccCCcEEEEEEcC Confidence 3579999998 58752 45788888999999988766554 No 30 >TIGR00479 rumA 23S rRNA (uracil-5-)-methyltransferase RumA. This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. Probab=70.99 E-value=7.5 Score=29.68 Aligned_cols=35 Identities=26% Similarity=0.475 Sum_probs=27.6 Q ss_pred CCCceeeeCC--CCCchhhHHHHHHhcccCcEEEEEec Q psy4127 9 RHFDAIDLDP--FGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 9 ~~fD~IDlDP--fGSp~pfldsA~~av~~gGll~vTaT 44 (75) +.||+|-+|| .|-...+++ ++..++.+++++|++. T Consensus 361 ~~~D~vi~dPPr~G~~~~~l~-~l~~l~~~~ivyvsc~ 397 (431) T TIGR00479 361 QIPDVLLLDPPRKGCAAEVLR-TIIELKPERIVYVSCN 397 (431) T ss_pred CCCCEEEECcCCCCCCHHHHH-HHHhcCCCEEEEEcCC Confidence 3599999999 565577776 4666889999999864 No 31 >PLN02476 O-methyltransferase Probab=70.93 E-value=6 Score=29.56 Aligned_cols=35 Identities=14% Similarity=0.289 Sum_probs=28.6 Q ss_pred CCCceeeeCCCCC-chhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDLDPFGN-PTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDlDPfGS-p~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=||+--. -..|++.+++.+++||+|.+-- T Consensus 193 ~~FD~VFIDa~K~~Y~~y~e~~l~lL~~GGvIV~DN 228 (278) T PLN02476 193 SSYDFAFVDADKRMYQDYFELLLQLVRVGGVIVMDN 228 (278) T ss_pred CCCCEEEECCCHHHHHHHHHHHHHhcCCCcEEEEec Confidence 4799999988642 3688999999999999998743 No 32 >TIGR00138 gidB 16S rRNA methyltransferase GidB. GidB (glucose-inhibited division protein B) appears to be present and in a single copy in nearly all complete eubacterial genomes. It is missing only from some obligate intracellular species of various lineages (Chlamydiae, Ehrlichia, Wolbachia, Anaplasma, Buchnera, etc.). GidB shows a methytransferase fold in its the crystal structure, and acts as a 7-methylguanosine (m(7)G) methyltransferase, apparently specific to 16S rRNA. Probab=70.27 E-value=7 Score=26.73 Aligned_cols=35 Identities=23% Similarity=0.420 Sum_probs=30.3 Q ss_pred CCCCceeeeCCCCCchhhHHHHHHhcccCcEEEEE Q psy4127 8 GRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 8 ~~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vT 42 (75) .+.||+|=.+.++....+++.+.+.++.||.+.+- T Consensus 107 ~~~fD~I~s~~~~~~~~~~~~~~~~LkpgG~lvi~ 141 (181) T TIGR00138 107 EEQFDVITSRALASLNVLLELTLNLLKVGGYFLAY 141 (181) T ss_pred cCCccEEEehhhhCHHHHHHHHHHhcCCCCEEEEE Confidence 35799999998887788888889999999999975 No 33 >cd01202 FRS2 Fibroblast growth factor receptor substrate 2 (FRS2/SNT1) Phosphotyrosine-binding domain. Fibroblast growth factor receptor substrate 2 (FRS2/SNT1) Phosphotyrosine-binding domain (IRS1-like). FRS2 mediates signaling downstream of the FGF receptor. It has an N-terminal PTBi domain, which has a PH-like fold and is similiar to the PTB domain that is found in insulin receptor substrate molecules. This PTBi domain is shorter than the PTB domain which is found in SHC, Numb and other proteins. The PTBi domain binds to phosphotyrosines which are in NPXpY motifs. Probab=69.88 E-value=5.9 Score=26.07 Aligned_cols=46 Identities=30% Similarity=0.491 Sum_probs=34.1 Q ss_pred CCCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEecCccccc-CC----ChhHHHHHhcCc Q psy4127 8 GRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLC-GN----TPETCYVKYNAV 64 (75) Q Consensus 8 ~~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~a~L~-G~----~~~~~~r~Yg~~ 64 (75) ++.|-+|.+||=|. .+ ..|+|-||.+++-... ++ =|-.++|+||.. T Consensus 5 ~~~F~V~~~~~~~~---~~--------g~g~L~vt~~~L~l~~~~~~~~~WPl~~LRRYG~d 55 (102) T cd01202 5 SNSFRVINVDDDGN---EL--------GSGWLELTRTELTLYISGKEPVVWPLLCLRRYGYN 55 (102) T ss_pred CcEEEEEEECCCCC---ee--------eeEEEEecceEEEEEcCCCCEEEccHHHhHhhccC Confidence 46799999999774 11 3579999999887543 22 277899999975 No 34 >PRK10901 16S rRNA methyltransferase B; Provisional Probab=67.46 E-value=11 Score=29.02 Aligned_cols=34 Identities=41% Similarity=0.610 Sum_probs=25.9 Q ss_pred CCCceeeeCC-C-CC--------------c----------hhhHHHHHHhcccCcEEEEE Q psy4127 9 RHFDAIDLDP-F-GN--------------P----------TRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 9 ~~fD~IDlDP-f-GS--------------p----------~pfldsA~~av~~gGll~vT 42 (75) +.||.|=+|| + |+ + ..+|+.|.+.+++||.|..+ T Consensus 312 ~~fD~Vl~D~Pcs~~G~~~~~p~~~~~~~~~~l~~l~~~q~~iL~~a~~~LkpGG~lvys 371 (427) T PRK10901 312 QPFDRILLDAPCSATGVIRRHPDIKWLRRPEDIAALAALQSEILDALWPLLKPGGTLLYA 371 (427) T ss_pred CCCCEEEECCCCCcccccccCccccccCCHHHHHHHHHHHHHHHHHHHHhcCCCCEEEEE Confidence 4699999998 2 32 1 15899999999999987643 No 35 >COG0144 Sun tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis] Probab=67.39 E-value=4.9 Score=30.54 Aligned_cols=24 Identities=33% Similarity=0.594 Sum_probs=19.0 Q ss_pred hhHHHHHHhcccCcE-EEEEecCcc Q psy4127 24 RFLDAAVSSLRDGGL-LLVTCTDMA 47 (75) Q Consensus 24 pfldsA~~av~~gGl-l~vTaTD~a 47 (75) ..|++|++.||+||. +|-|||=.. T Consensus 269 ~iL~~a~~~lk~GG~LVYSTCS~~~ 293 (355) T COG0144 269 EILAAALKLLKPGGVLVYSTCSLTP 293 (355) T ss_pred HHHHHHHHhcCCCCEEEEEccCCch Confidence 468999999999995 577887543 No 36 >PRK05134 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional Probab=67.20 E-value=8 Score=26.51 Aligned_cols=35 Identities=26% Similarity=0.618 Sum_probs=27.8 Q ss_pred CCCceee----eCCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAID----LDPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~ID----lDPfGSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|= +.-.+.+..+|..+.+.+++||.+.++. T Consensus 113 ~~fD~Ii~~~~l~~~~~~~~~l~~~~~~L~~gG~l~v~~ 151 (233) T PRK05134 113 GQFDVVTCMEMLEHVPDPASFVRACAKLVKPGGLVFFST 151 (233) T ss_pred CCccEEEEhhHhhccCCHHHHHHHHHHHcCCCcEEEEEe Confidence 5688883 3445567888999999999999999873 No 37 >KOG0408|consensus Probab=67.04 E-value=6.2 Score=28.43 Aligned_cols=30 Identities=37% Similarity=0.355 Sum_probs=26.1 Q ss_pred hhHHHHHHhcccCcEEEEEecCcccccCCC Q psy4127 24 RFLDAAVSSLRDGGLLLVTCTDMAVLCGNT 53 (75) Q Consensus 24 pfldsA~~av~~gGll~vTaTD~a~L~G~~ 53 (75) |==++|++.+.-|||+-++-||-.+++=+. T Consensus 152 pGRmsa~kgl~m~Gl~vvsItD~Tp~~~ng 181 (190) T KOG0408|consen 152 PGRMSALKGLRMGGLLVVSITDNTPMPHNG 181 (190) T ss_pred ccHHHHHhhhhhcceEEEEeecCCcCCCCC Confidence 445789999999999999999999998553 No 38 >PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional Probab=64.64 E-value=15 Score=28.42 Aligned_cols=36 Identities=33% Similarity=0.441 Sum_probs=25.4 Q ss_pred CCCCceeeeCC-CCCch------------hhHHHHHHhcccCcEEEEEe Q psy4127 8 GRHFDAIDLDP-FGNPT------------RFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 8 ~~~fD~IDlDP-fGSp~------------pfldsA~~av~~gGll~vTa 43 (75) .+.||+|=+|| |-++. .++..|++.+++||+|.+.+ T Consensus 291 ~~~fDlVilDPP~f~~~k~~l~~~~~~y~~l~~~a~~lLk~gG~lv~~s 339 (396) T PRK15128 291 GEKFDVIVMDPPKFVENKSQLMGACRGYKDINMLAIQLLNPGGILLTFS 339 (396) T ss_pred CCCCCEEEECCCCCCCChHHHHHHHHHHHHHHHHHHHHcCCCeEEEEEe Confidence 35799999994 43332 23446889999999887644 No 39 >PF03602 Cons_hypoth95: Conserved hypothetical protein 95; InterPro: IPR004398 This entry contains Ribosomal RNA small subunit methyltransferase D as well as the putative rRNA methyltransferase YlbH. They methylate the guanosine in position 966 of 16S rRNA in the assembled 30S particle [].; GO: 0008168 methyltransferase activity, 0031167 rRNA methylation; PDB: 3P9N_A 2ESR_B 2IFT_A 1WS6_A 2FPO_B 2FHP_A. Probab=64.51 E-value=6.7 Score=27.15 Aligned_cols=35 Identities=29% Similarity=0.595 Sum_probs=20.3 Q ss_pred CCCCceeeeCC-CCCchhhHHHHHH------hcccCcEEEEEe Q psy4127 8 GRHFDAIDLDP-FGNPTRFLDAAVS------SLRDGGLLLVTC 43 (75) Q Consensus 8 ~~~fD~IDlDP-fGSp~pfldsA~~------av~~gGll~vTa 43 (75) .+.||+|=+|| |..... ++..++ .++++|+|.+=. T Consensus 112 ~~~fDiIflDPPY~~~~~-~~~~l~~l~~~~~l~~~~~ii~E~ 153 (183) T PF03602_consen 112 GEKFDIIFLDPPYAKGLY-YEELLELLAENNLLNEDGLIIIEH 153 (183) T ss_dssp TS-EEEEEE--STTSCHH-HHHHHHHHHHTTSEEEEEEEEEEE T ss_pred CCCceEEEECCCcccchH-HHHHHHHHHHCCCCCCCEEEEEEe Confidence 56899999998 887642 334443 455667766644 No 40 >PRK08317 hypothetical protein; Provisional Probab=64.16 E-value=17 Score=24.14 Aligned_cols=39 Identities=36% Similarity=0.517 Sum_probs=28.7 Q ss_pred CCCceeeeC----CCCCchhhHHHHHHhcccCcEEEEEecCcc Q psy4127 9 RHFDAIDLD----PFGNPTRFLDAAVSSLRDGGLLLVTCTDMA 47 (75) Q Consensus 9 ~~fD~IDlD----PfGSp~pfldsA~~av~~gGll~vTaTD~a 47 (75) +.||+|=.. -...+..++....+.++.||.+.+...|.. T Consensus 86 ~~~D~v~~~~~~~~~~~~~~~l~~~~~~L~~gG~l~~~~~~~~ 128 (241) T PRK08317 86 GSFDAVRSDRVLQHLEDPARALAEIARVLRPGGRVVVLDTDWD 128 (241) T ss_pred CCceEEEEechhhccCCHHHHHHHHHHHhcCCcEEEEEecCCC Confidence 356665442 224577899999999999999999887643 No 41 >PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional Probab=63.18 E-value=14 Score=30.49 Aligned_cols=35 Identities=37% Similarity=0.625 Sum_probs=26.1 Q ss_pred CCCCceeeeCC--CCCc-------------hhhHHHHHHhcccCcEEEEE Q psy4127 8 GRHFDAIDLDP--FGNP-------------TRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 8 ~~~fD~IDlDP--fGSp-------------~pfldsA~~av~~gGll~vT 42 (75) ++.||+|=+|| |+.. ...+..|++.+++||+|.++ T Consensus 606 ~~~fDlIilDPP~f~~~~~~~~~~~~~~~y~~l~~~a~~lL~~gG~l~~~ 655 (702) T PRK11783 606 REQFDLIFIDPPTFSNSKRMEDSFDVQRDHVALIKDAKRLLRPGGTLYFS 655 (702) T ss_pred CCCcCEEEECCCCCCCCCccchhhhHHHHHHHHHHHHHHHcCCCCEEEEE Confidence 35799999997 3321 23678889999999999664 No 42 >PRK14967 putative methyltransferase; Provisional Probab=62.71 E-value=17 Score=25.10 Aligned_cols=22 Identities=36% Similarity=0.537 Sum_probs=17.6 Q ss_pred hHHHHHHhcccCcEEEEEecCc Q psy4127 25 FLDAAVSSLRDGGLLLVTCTDM 46 (75) Q Consensus 25 fldsA~~av~~gGll~vTaTD~ 46 (75) |++.|.+.+++||.+.+...+. T Consensus 141 ~l~~a~~~Lk~gG~l~~~~~~~ 162 (223) T PRK14967 141 LCDAAPALLAPGGSLLLVQSEL 162 (223) T ss_pred HHHHHHHhcCCCcEEEEEEecc Confidence 6788999999999999754443 No 43 >COG1092 Predicted SAM-dependent methyltransferases [General function prediction only] Probab=62.19 E-value=14 Score=28.97 Aligned_cols=37 Identities=41% Similarity=0.664 Sum_probs=27.1 Q ss_pred cCCCCceeeeCC--CCCc-----------hhhHHHHHHhcccCcEEEEEe Q psy4127 7 RGRHFDAIDLDP--FGNP-----------TRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 7 ~~~~fD~IDlDP--fGSp-----------~pfldsA~~av~~gGll~vTa 43 (75) ..++||+|=+|| |+-- -.-++.|++.+++||+|.+.+ T Consensus 287 ~g~~fDlIilDPPsF~r~k~~~~~~~rdy~~l~~~~~~iL~pgG~l~~~s 336 (393) T COG1092 287 RGEKFDLIILDPPSFARSKKQEFSAQRDYKDLNDLALRLLAPGGTLVTSS 336 (393) T ss_pred cCCcccEEEECCcccccCcccchhHHHHHHHHHHHHHHHcCCCCEEEEEe Confidence 446899999999 3211 134678899999999987654 No 44 >TIGR00438 rrmJ cell division protein FtsJ. Probab=61.63 E-value=21 Score=23.90 Aligned_cols=35 Identities=26% Similarity=0.237 Sum_probs=26.9 Q ss_pred CCCCceeeeCC----CCCc-----------hhhHHHHHHhcccCcEEEEE Q psy4127 8 GRHFDAIDLDP----FGNP-----------TRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 8 ~~~fD~IDlDP----fGSp-----------~pfldsA~~av~~gGll~vT 42 (75) .+.||+|=.|+ +|.+ -.+|..+.+.+++||.+.+. T Consensus 96 ~~~~D~V~~~~~~~~~g~~~~~~~~~~~~~~~~l~~~~~~LkpgG~lvi~ 145 (188) T TIGR00438 96 DDKVDVVMSDAAPNISGYWDIDHLRSIDLVELALDIAKEVLKPKGNFVVK 145 (188) T ss_pred CCCccEEEcCCCCCCCCCccccHHHHHHHHHHHHHHHHHHccCCCEEEEE Confidence 34699998874 3432 25788889999999999996 No 45 >PRK11630 hypothetical protein; Provisional Probab=61.53 E-value=13 Score=26.20 Aligned_cols=34 Identities=26% Similarity=0.482 Sum_probs=24.6 Q ss_pred eeeeCCCCCchhhHHHHHHhcccCcEEEEEecCcc Q psy4127 13 AIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMA 47 (75) Q Consensus 13 ~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~a 47 (75) ++++++...-...++.|++++++||++++= ||+- T Consensus 4 ~~~~~~~~~~~~~i~~a~~~L~~G~vi~~P-TdTv 37 (206) T PRK11630 4 FFYIHPDNPQQRLINQAVEIVRKGGVIVYP-TDSG 37 (206) T ss_pred eEecCCCCCCHHHHHHHHHHHHCCCEEEEe-CCCh Confidence 355676654344689999999999999873 5653 No 46 >COG4976 Predicted methyltransferase (contains TPR repeat) [General function prediction only] Probab=61.07 E-value=6.2 Score=30.05 Aligned_cols=44 Identities=25% Similarity=0.445 Sum_probs=35.8 Q ss_pred ccCCCCcee---eeCCC-CCchhhHHHHHHhcccCcEEEEEecCcccc Q psy4127 6 IRGRHFDAI---DLDPF-GNPTRFLDAAVSSLRDGGLLLVTCTDMAVL 49 (75) Q Consensus 6 ~~~~~fD~I---DlDPf-GSp~pfldsA~~av~~gGll~vTaTD~a~L 49 (75) +.+++||.| |+=|| |+--+++-.|...++.||++.+|.-+...- T Consensus 184 ~~~er~DLi~AaDVl~YlG~Le~~~~~aa~~L~~gGlfaFSvE~l~~~ 231 (287) T COG4976 184 LTQERFDLIVAADVLPYLGALEGLFAGAAGLLAPGGLFAFSVETLPDD 231 (287) T ss_pred ccCCcccchhhhhHHHhhcchhhHHHHHHHhcCCCceEEEEecccCCC Confidence 456789987 67676 777788888999999999999998776554 No 47 >PF08241 Methyltransf_11: Methyltransferase domain; InterPro: IPR013216 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Arsenite methyltransferase (2.1.1.137 from EC) which converts arsenical compounds to their methylated forms [] Biotin synthesis protein bioC, which is involved in the early stages of biotin biosyntheis [] Arginine N-methyltransferase 1, an arginine-methylating enzyme which acts on residues present in a glycine and argine-rich domain and can methylate histones [] Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Sterol 24-C-methyltransferase (2.1.1.41 from EC), shown to participate in ergosterol biosynthesis [] 3-demethylubiquinone-9 3-methyltransferase (2.1.1.64 from EC) involved in ubiquinone biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ]. ; GO: 0008168 methyltransferase activity, 0008152 metabolic process; PDB: 3CGG_B 3CCF_B 3BKW_B 2PXX_A 3I9F_A 2YQZ_B 2YR0_A 3BUS_A 3EGE_A 3G5L_B .... Probab=60.18 E-value=6.4 Score=22.26 Aligned_cols=22 Identities=27% Similarity=0.493 Sum_probs=18.5 Q ss_pred CCchhhHHHHHHhcccCcEEEE Q psy4127 20 GNPTRFLDAAVSSLRDGGLLLV 41 (75) Q Consensus 20 GSp~pfldsA~~av~~gGll~v 41 (75) -.+..++..+.+.+|+||.+.+ T Consensus 74 ~~~~~~l~e~~rvLk~gG~l~~ 95 (95) T PF08241_consen 74 EDPEAALREIYRVLKPGGRLVI 95 (95) T ss_dssp SHHHHHHHHHHHHEEEEEEEEE T ss_pred cCHHHHHHHHHHHcCcCeEEeC Confidence 3567888999999999999875 No 48 >TIGR01983 UbiG ubiquinone biosynthesis O-methyltransferase. This model represents an O-methyltransferase believed to act at two points in the ubiquinone biosynthetic pathway in bacteria (UbiG) and fungi (COQ3). A separate methylase (MenG/UbiE) catalyzes the single C-methylation step. The most commonly used names for genes in this family do not indicate whether this gene is an O-methyl, or C-methyl transferase. Probab=59.97 E-value=11 Score=25.46 Aligned_cols=36 Identities=25% Similarity=0.596 Sum_probs=27.9 Q ss_pred CCCceeee----CCCCCchhhHHHHHHhcccCcEEEEEec Q psy4127 9 RHFDAIDL----DPFGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 9 ~~fD~IDl----DPfGSp~pfldsA~~av~~gGll~vTaT 44 (75) +.||+|=. .-...+..+|+.+.+.++.||.+.++.. T Consensus 111 ~~~D~i~~~~~l~~~~~~~~~l~~~~~~L~~gG~l~i~~~ 150 (224) T TIGR01983 111 KSFDVVTCMEVLEHVPDPQAFIRACAQLLKPGGILFFSTI 150 (224) T ss_pred CCccEEEehhHHHhCCCHHHHHHHHHHhcCCCcEEEEEec Confidence 46888733 3456788899999999999999988753 No 49 >KOG1663|consensus Probab=59.45 E-value=12 Score=27.96 Aligned_cols=36 Identities=22% Similarity=0.372 Sum_probs=29.8 Q ss_pred CCCCceeeeCCCCCc-hhhHHHHHHhcccCcEEEEEe Q psy4127 8 GRHFDAIDLDPFGNP-TRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 8 ~~~fD~IDlDPfGSp-~pfldsA~~av~~gGll~vTa 43 (75) .+-||++=||.+=.- +.|.+-+++.||.||+|.+-- T Consensus 147 ~~tfDfaFvDadK~nY~~y~e~~l~Llr~GGvi~~DN 183 (237) T KOG1663|consen 147 SGTFDFAFVDADKDNYSNYYERLLRLLRVGGVIVVDN 183 (237) T ss_pred CCceeEEEEccchHHHHHHHHHHHhhcccccEEEEec Confidence 456999988887643 688999999999999998854 No 50 >PF13847 Methyltransf_31: Methyltransferase domain; PDB: 3T0I_B 3SVZ_B 3SXJ_A 3F4K_A 3GU3_B 2GH1_A 1R8Y_E 1R8X_B 2B3T_A 1T43_A .... Probab=59.25 E-value=7.3 Score=25.08 Aligned_cols=37 Identities=27% Similarity=0.588 Sum_probs=30.6 Q ss_pred CCCceeeeCC----CCCchhhHHHHHHhcccCcEEEEEecC Q psy4127 9 RHFDAIDLDP----FGNPTRFLDAAVSSLRDGGLLLVTCTD 45 (75) Q Consensus 9 ~~fD~IDlDP----fGSp~pfldsA~~av~~gGll~vTaTD 45 (75) +.||+|=..+ +..+-.++..+.+.++++|.+.++.-. T Consensus 72 ~~~D~I~~~~~l~~~~~~~~~l~~~~~~lk~~G~~i~~~~~ 112 (152) T PF13847_consen 72 EKFDIIISNGVLHHFPDPEKVLKNIIRLLKPGGILIISDPN 112 (152) T ss_dssp TTEEEEEEESTGGGTSHHHHHHHHHHHHEEEEEEEEEEEEE T ss_pred CCeeEEEEcCchhhccCHHHHHHHHHHHcCCCcEEEEEECC Confidence 5799887764 666777899999999999999987765 No 51 >PF05430 Methyltransf_30: S-adenosyl-L-methionine-dependent methyltransferase; InterPro: IPR008471 This entry contains several uncharacterised bacterial proteins with no known function.; GO: 0016645 oxidoreductase activity, acting on the CH-NH group of donors, 0055114 oxidation-reduction process; PDB: 2E58_D 3SGL_A 3PVC_A 3AWI_D 3PS9_A 2QY6_A. Probab=59.05 E-value=7.4 Score=25.67 Aligned_cols=54 Identities=22% Similarity=0.217 Sum_probs=34.2 Q ss_pred CCCceeeeCCCCCc-------hhhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcCcccCC Q psy4127 9 RHFDAIDLDPFGNP-------TRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNAVSLKT 68 (75) Q Consensus 9 ~~fD~IDlDPfGSp-------~pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~~~~~~ 68 (75) .++|+|=+|+|... .+++..-.+..+.||.++.=+..+.+ +..+...|-...+. T Consensus 49 ~~~Da~ylDgFsP~~nPelWs~e~~~~l~~~~~~~~~l~Tys~a~~V------r~~L~~aGF~v~~~ 109 (124) T PF05430_consen 49 ARFDAWYLDGFSPAKNPELWSEELFKKLARLSKPGGTLATYSSAGAV------RRALQQAGFEVEKV 109 (124) T ss_dssp T-EEEEEE-SS-TTTSGGGSSHHHHHHHHHHEEEEEEEEES--BHHH------HHHHHHCTEEEEEE T ss_pred ccCCEEEecCCCCcCCcccCCHHHHHHHHHHhCCCcEEEEeechHHH------HHHHHHcCCEEEEc Confidence 57999999999831 46888777888888887765554443 66666666655443 No 52 >PRK09489 rsmC 16S ribosomal RNA m2G1207 methyltransferase; Provisional Probab=59.05 E-value=10 Score=28.71 Aligned_cols=52 Identities=23% Similarity=0.393 Sum_probs=36.9 Q ss_pred CCCCceeeeCC-CC--------CchhhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcC Q psy4127 8 GRHFDAIDLDP-FG--------NPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNA 63 (75) Q Consensus 8 ~~~fD~IDlDP-fG--------Sp~pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~ 63 (75) +++||+|=.+| |- ....||..|.+.+++||.|.+.+-..- .+++.--+.+|. T Consensus 259 ~~~fDlIvsNPPFH~g~~~~~~~~~~~i~~a~~~LkpgG~L~iVan~~l----~y~~~l~~~Fg~ 319 (342) T PRK09489 259 KGRFDMIISNPPFHDGIQTSLDAAQTLIRGAVRHLNSGGELRIVANAFL----PYPDLLDETFGS 319 (342) T ss_pred CCCccEEEECCCccCCccccHHHHHHHHHHHHHhcCcCCEEEEEEeCCC----ChHHHHHHHcCC Confidence 45799999886 43 246889999999999999999876432 345544444544 No 53 >TIGR02752 MenG_heptapren 2-heptaprenyl-1,4-naphthoquinone methyltransferase. MenG is a generic term for a methyltransferase that catalyzes the last step in menaquinone biosynthesis; the exact enzymatic activity differs for different MenG because the menaquinone differ in their prenoid side chains in different species. Members of this MenG protein family are 2-heptaprenyl-1,4-naphthoquinone methyltransferase, and are found together in operons with the two subunits of the heptaprenyl diphosphate synthase in Bacillus subtilis and related species. Probab=58.74 E-value=22 Score=24.20 Aligned_cols=36 Identities=14% Similarity=0.264 Sum_probs=26.4 Q ss_pred CCCCceeeeC----CCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 8 GRHFDAIDLD----PFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 8 ~~~fD~IDlD----PfGSp~pfldsA~~av~~gGll~vTa 43 (75) .+.||+|=+. -+..+..+|..+.+.+++||++.+.. T Consensus 112 ~~~fD~V~~~~~l~~~~~~~~~l~~~~~~Lk~gG~l~~~~ 151 (231) T TIGR02752 112 DNSFDYVTIGFGLRNVPDYMQVLREMYRVVKPGGKVVCLE 151 (231) T ss_pred CCCccEEEEecccccCCCHHHHHHHHHHHcCcCeEEEEEE Confidence 3568888653 23445678888899999999998754 No 54 >COG4122 Predicted O-methyltransferase [General function prediction only] Probab=58.59 E-value=16 Score=26.55 Aligned_cols=41 Identities=29% Similarity=0.524 Sum_probs=30.3 Q ss_pred CCCCceeeeCCCCCc-hhhHHHHHHhcccCcEEEEEecCcccccC Q psy4127 8 GRHFDAIDLDPFGNP-TRFLDAAVSSLRDGGLLLVTCTDMAVLCG 51 (75) Q Consensus 8 ~~~fD~IDlDPfGSp-~pfldsA~~av~~gGll~vTaTD~a~L~G 51 (75) .+.||+|=||.==+. -+|++.+++.++.||+|.+ |-....| T Consensus 130 ~~~fDliFIDadK~~yp~~le~~~~lLr~GGliv~---DNvl~~G 171 (219) T COG4122 130 DGSFDLVFIDADKADYPEYLERALPLLRPGGLIVA---DNVLFGG 171 (219) T ss_pred CCCccEEEEeCChhhCHHHHHHHHHHhCCCcEEEE---eecccCC Confidence 356887766653322 4899999999999999975 6666666 No 55 >PF06962 rRNA_methylase: Putative rRNA methylase; InterPro: IPR010719 This family contains a number of putative rRNA methylases.; PDB: 3EEY_H 3LBY_A 3MTI_A. Probab=57.06 E-value=8.2 Score=26.33 Aligned_cols=21 Identities=29% Similarity=0.589 Sum_probs=18.2 Q ss_pred hhhHHHHHHhcccCcEEEEEe Q psy4127 23 TRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 23 ~pfldsA~~av~~gGll~vTa 43 (75) ..=|++|++.++.||+|.|.+ T Consensus 72 l~Al~~al~lL~~gG~i~iv~ 92 (140) T PF06962_consen 72 LKALEAALELLKPGGIITIVV 92 (140) T ss_dssp HHHHHHHHHHEEEEEEEEEEE T ss_pred HHHHHHHHHhhccCCEEEEEE Confidence 356889999999999999975 No 56 >TIGR01934 MenG_MenH_UbiE ubiquinone/menaquinone biosynthesis methyltransferases. Note that a number of non-orthologous genes which are members of pfam03737 have been erroneously annotated as MenG methyltransferases. Probab=56.67 E-value=22 Score=23.57 Aligned_cols=35 Identities=23% Similarity=0.384 Sum_probs=25.9 Q ss_pred CCCceeee----CCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDL----DPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDl----DPfGSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=. -.+..+..+++.+.+.++.||.+.+.. T Consensus 105 ~~~D~i~~~~~~~~~~~~~~~l~~~~~~L~~gG~l~~~~ 143 (223) T TIGR01934 105 NSFDAVTIAFGLRNVTDIQKALREMYRVLKPGGRLVILE 143 (223) T ss_pred CcEEEEEEeeeeCCcccHHHHHHHHHHHcCCCcEEEEEE Confidence 35777632 234457788999999999999998754 No 57 >PRK08287 cobalt-precorrin-6Y C(15)-methyltransferase; Validated Probab=56.12 E-value=27 Score=23.28 Aligned_cols=35 Identities=34% Similarity=0.432 Sum_probs=27.3 Q ss_pred CCCceeeeCCC-CCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDLDPF-GNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDlDPf-GSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=++.- +....+++.+.+.++.||.+.+.. T Consensus 96 ~~~D~v~~~~~~~~~~~~l~~~~~~Lk~gG~lv~~~ 131 (187) T PRK08287 96 GKADAIFIGGSGGNLTAIIDWSLAHLHPGGRLVLTF 131 (187) T ss_pred cCCCEEEECCCccCHHHHHHHHHHhcCCCeEEEEEE Confidence 46898876642 445678999999999999998854 No 58 >TIGR01202 bchC 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase. Probab=55.99 E-value=17 Score=26.05 Aligned_cols=32 Identities=31% Similarity=0.638 Sum_probs=25.6 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTa 43 (75) .+|+| +|.-|++ ..++.+++.++++|.+.+-. T Consensus 200 g~Dvv-id~~G~~-~~~~~~~~~l~~~G~iv~~G 231 (308) T TIGR01202 200 DYRAI-YDASGDP-SLIDTLVRRLAKGGEIVLAG 231 (308) T ss_pred CCCEE-EECCCCH-HHHHHHHHhhhcCcEEEEEe Confidence 46765 7889975 36789999999999998654 No 59 >PF02083 Urotensin_II: Urotensin II; InterPro: IPR001483 Urotensin II, a small peptide that contains a disulphide bridge, was originally isolated from the caudal portion of the spinal cord of teleost and elasmobranch fish []. The peptide has also been found in the brain of frogs []. Urotensin II seems to be involved in smooth muscle stimulation.; GO: 0005179 hormone activity, 0005576 extracellular region Probab=55.95 E-value=4.9 Score=17.10 Aligned_cols=9 Identities=33% Similarity=0.840 Sum_probs=6.9 Q ss_pred hhHHHHHhc Q psy4127 54 PETCYVKYN 62 (75) Q Consensus 54 ~~~~~r~Yg 62 (75) ...||+||- T Consensus 3 ~~~CFWKYC 11 (12) T PF02083_consen 3 KSECFWKYC 11 (12) T ss_pred ccchhhhhc Confidence 467999984 No 60 >TIGR02072 BioC biotin biosynthesis protein BioC. This enzyme, which is found in biotin biosynthetic gene clusters in proteobacteria, firmicutes, green-sulfur bacteria, fusobacterium and bacteroides, is believed to carry out an enzymatic step prior to the formation of pimeloyl-CoA (although attribution of this annotation is not traceable). The enzyme appears related to methyltransferases by homology. Probab=55.87 E-value=21 Score=23.78 Aligned_cols=35 Identities=26% Similarity=0.365 Sum_probs=26.4 Q ss_pred CCCceeeeCC----CCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDLDP----FGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDlDP----fGSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=..- +..+..+|+...+.++.||.+.++. T Consensus 97 ~~fD~vi~~~~l~~~~~~~~~l~~~~~~L~~~G~l~~~~ 135 (240) T TIGR02072 97 SSFDLIVSNLALQWCDDLSQALSELARVLKPGGLLAFST 135 (240) T ss_pred CceeEEEEhhhhhhccCHHHHHHHHHHHcCCCcEEEEEe Confidence 4577775432 2356789999999999999999874 No 61 >TIGR00106 uncharacterized protein, MTH1187 family. This protein has been crystallized in both Methanobacterium thermoautotrophicum and yeast, but its function remains unknown. Both crystal structures showed sulfate ions bound at the interface of two dimers to form a tetramer. Probab=55.19 E-value=11 Score=23.96 Aligned_cols=38 Identities=21% Similarity=0.399 Sum_probs=31.3 Q ss_pred eCCCC----CchhhHHHHHHhcccCcEEEEEecCcccccCCC Q psy4127 16 LDPFG----NPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNT 53 (75) Q Consensus 16 lDPfG----Sp~pfldsA~~av~~gGll~vTaTD~a~L~G~~ 53 (75) +=|.| |.++|++.+++.+++.||=+-..-=.+++.|.. T Consensus 7 v~P~g~~~~s~s~yVa~~i~~l~~sGl~y~~~pm~T~IEGe~ 48 (97) T TIGR00106 7 IIPIGTVGASVSSYVAAAIEVLKESGLKYELHPMGTLIEGDL 48 (97) T ss_pred EeecCCCCCcHHHHHHHHHHHHHHcCCCeEecCCccEEecCH Confidence 44666 679999999999999999887777777778863 No 62 >COG5526 Lysozyme family protein [General function prediction only] Probab=54.63 E-value=6.1 Score=28.34 Aligned_cols=31 Identities=29% Similarity=0.542 Sum_probs=25.2 Q ss_pred eCCCCCch-hhHHHHHHhcccCcEEEEEecCccc Q psy4127 16 LDPFGNPT-RFLDAAVSSLRDGGLLLVTCTDMAV 48 (75) Q Consensus 16 lDPfGSp~-pfldsA~~av~~gGll~vTaTD~a~ 48 (75) --|||+|- .|.|+|+.|++..|+.. +.|.+. T Consensus 94 Rp~~~~Pp~~we~sAlDAL~~~~f~g--a~DWsi 125 (191) T COG5526 94 RPPFTGPPYAWEDSALDALRLEGFVG--ASDWSI 125 (191) T ss_pred CCCCCCCCchhhhhHHHHHHHhcccc--cccccc Confidence 35898886 89999999999999865 457655 No 63 >COG4215 ArtQ ABC-type arginine transport system, permease component [Amino acid transport and metabolism] Probab=54.04 E-value=4.5 Score=30.05 Aligned_cols=30 Identities=27% Similarity=0.401 Sum_probs=22.6 Q ss_pred CCCceeeeCCCCC------------chhhHHHHHHhcccCcE Q psy4127 9 RHFDAIDLDPFGN------------PTRFLDAAVSSLRDGGL 38 (75) Q Consensus 9 ~~fD~IDlDPfGS------------p~pfldsA~~av~~gGl 38 (75) ..+|+||++||-+ .+.-+.+|++||.+|-+ T Consensus 87 ~g~~~idi~~FvaGviaL~~i~gAYatEt~RGA~~AVp~GQ~ 128 (230) T COG4215 87 LGVGFIDISPFVAGVIALGLIFGAYATETLRGAFKAVPKGQI 128 (230) T ss_pred cCCCccccChHHHHHHHHHHHHHHHHHHHHHHHHHcCCcchH Confidence 3468999999864 24667889999988743 No 64 >smart00828 PKS_MT Methyltransferase in polyketide synthase (PKS) enzymes. Probab=53.91 E-value=21 Score=24.23 Aligned_cols=35 Identities=17% Similarity=0.286 Sum_probs=25.8 Q ss_pred CCceeee----CCCCCchhhHHHHHHhcccCcEEEEEec Q psy4127 10 HFDAIDL----DPFGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 10 ~fD~IDl----DPfGSp~pfldsA~~av~~gGll~vTaT 44 (75) .||+|=. -..+.+..++..+.+.+++||.+.++.. T Consensus 67 ~fD~I~~~~~l~~~~~~~~~l~~~~~~LkpgG~l~i~~~ 105 (224) T smart00828 67 TYDLVFGFEVIHHIKDKMDLFSNISRHLKDGGHLVLADF 105 (224) T ss_pred CCCEeehHHHHHhCCCHHHHHHHHHHHcCCCCEEEEEEc Confidence 4676642 1134567899999999999999999754 No 65 >PRK09975 DNA-binding transcriptional regulator EnvR; Provisional Probab=53.32 E-value=6.1 Score=26.44 Aligned_cols=40 Identities=18% Similarity=0.272 Sum_probs=37.1 Q ss_pred hhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcC Q psy4127 24 RFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNA 63 (75) Q Consensus 24 pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~ 63 (75) .-+++|++.....|+=.+|=.|.+--+|-++..-|+.|++ T Consensus 15 ~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~~F~s 54 (213) T PRK09975 15 ELIETAIAQFALRGVSNTTLNDIADAANVTRGAIYWHFEN 54 (213) T ss_pred HHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHHHcCC Confidence 4689999999999999999999999999999999998876 No 66 >PRK11036 putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional Probab=53.30 E-value=25 Score=24.71 Aligned_cols=35 Identities=29% Similarity=0.388 Sum_probs=26.3 Q ss_pred CCCceeeeCC----CCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDLDP----FGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDlDP----fGSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=... ...|..+|..+.+.+|+||.|.++. T Consensus 111 ~~fD~V~~~~vl~~~~~~~~~l~~~~~~LkpgG~l~i~~ 149 (255) T PRK11036 111 TPVDLILFHAVLEWVADPKSVLQTLWSVLRPGGALSLMF 149 (255) T ss_pred CCCCEEEehhHHHhhCCHHHHHHHHHHHcCCCeEEEEEE Confidence 4677775432 2356788999999999999998864 No 67 >PRK11873 arsM arsenite S-adenosylmethyltransferase; Reviewed Probab=53.29 E-value=27 Score=24.62 Aligned_cols=35 Identities=20% Similarity=0.260 Sum_probs=26.0 Q ss_pred CCCceeeeCC----CCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDLDP----FGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDlDP----fGSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=... ...+...++.+.+.+|+||.+.++. T Consensus 145 ~~fD~Vi~~~v~~~~~d~~~~l~~~~r~LkpGG~l~i~~ 183 (272) T PRK11873 145 NSVDVIISNCVINLSPDKERVFKEAFRVLKPGGRFAISD 183 (272) T ss_pred CceeEEEEcCcccCCCCHHHHHHHHHHHcCCCcEEEEEE Confidence 4688775442 2345678999999999999999963 No 68 >COG1041 Predicted DNA modification methylase [DNA replication, recombination, and repair] Probab=53.25 E-value=25 Score=27.43 Aligned_cols=36 Identities=33% Similarity=0.614 Sum_probs=30.1 Q ss_pred CCCceeeeCC-CCCch------------hhHHHHHHhcccCcEEEEEec Q psy4127 9 RHFDAIDLDP-FGNPT------------RFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 9 ~~fD~IDlDP-fGSp~------------pfldsA~~av~~gGll~vTaT 44 (75) +.+|-|=.|| ||-.+ .+|+++-..++.||.+.+.+- T Consensus 263 ~~vdaIatDPPYGrst~~~~~~l~~Ly~~~le~~~evLk~gG~~vf~~p 311 (347) T COG1041 263 NSVDAIATDPPYGRSTKIKGEGLDELYEEALESASEVLKPGGRIVFAAP 311 (347) T ss_pred CccceEEecCCCCcccccccccHHHHHHHHHHHHHHHhhcCcEEEEecC Confidence 3589998995 88776 589999999999999998776 No 69 >PRK00767 transcriptional regulator BetI; Validated Probab=52.83 E-value=7.1 Score=25.58 Aligned_cols=40 Identities=20% Similarity=0.303 Sum_probs=36.8 Q ss_pred hhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcC Q psy4127 24 RFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNA 63 (75) Q Consensus 24 pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~ 63 (75) .-|++|++.....|+=.+|-.|.+--+|-.+..-|+.|+. T Consensus 13 ~Il~aA~~lf~~~G~~~~s~~~Ia~~aGvs~gslY~~F~~ 52 (197) T PRK00767 13 QLIDATLRAIGEVGLLDATIAQIARRAGVSTGIISHYFGG 52 (197) T ss_pred HHHHHHHHHHHHcCcccCCHHHHHHHhCCCHHHHHHHhCC Confidence 4689999999999999999999999999999998888875 No 70 >PRK09880 L-idonate 5-dehydrogenase; Provisional Probab=52.70 E-value=19 Score=26.07 Aligned_cols=33 Identities=18% Similarity=0.405 Sum_probs=26.3 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCcEEEEEec Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaT 44 (75) .+|+| +|.-|++. .++.++++++.||.+.+-.. T Consensus 235 ~~D~v-id~~G~~~-~~~~~~~~l~~~G~iv~~G~ 267 (343) T PRK09880 235 YFDVS-FEVSGHPS-SINTCLEVTRAKGVMVQVGM 267 (343) T ss_pred CCCEE-EECCCCHH-HHHHHHHHhhcCCEEEEEcc Confidence 37877 89999764 57889999999998876643 No 71 >PF12847 Methyltransf_18: Methyltransferase domain; PDB: 3G2Q_A 3G2O_A 3G2M_B 3G2P_B 3D2L_B 1IM8_B 3NJR_A 3E05_H 3EVZ_A 3HM2_A .... Probab=51.94 E-value=13 Score=22.09 Aligned_cols=36 Identities=25% Similarity=0.318 Sum_probs=26.6 Q ss_pred CCCCceeeeCCCCC--c------hhhHHHHHHhcccCcEEEEEe Q psy4127 8 GRHFDAIDLDPFGN--P------TRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 8 ~~~fD~IDlDPfGS--p------~pfldsA~~av~~gGll~vTa 43 (75) .++||+|=++-|.. - ..+|+...+.+++||.+.|+. T Consensus 68 ~~~~D~v~~~~~~~~~~~~~~~~~~~l~~~~~~L~pgG~lvi~~ 111 (112) T PF12847_consen 68 LEPFDLVICSGFTLHFLLPLDERRRVLERIRRLLKPGGRLVINT 111 (112) T ss_dssp SSCEEEEEECSGSGGGCCHHHHHHHHHHHHHHHEEEEEEEEEEE T ss_pred CCCCCEEEECCCccccccchhHHHHHHHHHHHhcCCCcEEEEEE Confidence 34699888877321 1 235888999999999999874 No 72 >PRK07402 precorrin-6B methylase; Provisional Probab=51.68 E-value=34 Score=23.03 Aligned_cols=38 Identities=21% Similarity=0.255 Sum_probs=28.4 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCcEEEEEecCcc Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMA 47 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~a 47 (75) .+|.|-+|.......+++.+.+.+++||.+.+...... T Consensus 109 ~~d~v~~~~~~~~~~~l~~~~~~LkpgG~li~~~~~~~ 146 (196) T PRK07402 109 APDRVCIEGGRPIKEILQAVWQYLKPGGRLVATASSLE 146 (196) T ss_pred CCCEEEEECCcCHHHHHHHHHHhcCCCeEEEEEeecHH Confidence 35777777544346889999999999999988876543 No 73 >TIGR00563 rsmB ribosomal RNA small subunit methyltransferase RsmB. The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles. Probab=51.20 E-value=33 Score=26.40 Aligned_cols=56 Identities=27% Similarity=0.373 Sum_probs=34.6 Q ss_pred CCCceeeeCC----CCC----------------------chhhHHHHHHhcccCcEEE-EEecCcccccCCChhHHHHHh Q psy4127 9 RHFDAIDLDP----FGN----------------------PTRFLDAAVSSLRDGGLLL-VTCTDMAVLCGNTPETCYVKY 61 (75) Q Consensus 9 ~~fD~IDlDP----fGS----------------------p~pfldsA~~av~~gGll~-vTaTD~a~L~G~~~~~~~r~Y 61 (75) +.||.|=+|| +|. -...|+.|.+.+|.||.|. .|||=..-=.-..-+..+.+| T Consensus 308 ~~fD~VllDaPcSg~G~~~~~p~~~~~~~~~~~~~l~~lQ~~lL~~a~~~LkpgG~lvystcs~~~~Ene~~v~~~l~~~ 387 (426) T TIGR00563 308 EQFDRILLDAPCSATGVIRRHPDIKWLRKPRDIAELAELQSEILDAIWPLLKTGGTLVYATCSVLPEENSEQIKAFLQEH 387 (426) T ss_pred cccCEEEEcCCCCCCcccccCcchhhcCCHHHHHHHHHHHHHHHHHHHHhcCCCcEEEEEeCCCChhhCHHHHHHHHHhC Confidence 4699999996 332 1358999999999999765 456643222211223445555 Q ss_pred cCc Q psy4127 62 NAV 64 (75) Q Consensus 62 g~~ 64 (75) ..+ T Consensus 388 ~~~ 390 (426) T TIGR00563 388 PDF 390 (426) T ss_pred CCC Confidence 443 No 74 >PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional Probab=51.12 E-value=40 Score=22.83 Aligned_cols=37 Identities=16% Similarity=0.273 Sum_probs=27.4 Q ss_pred CCCceeeeCCC-CCchhhHHHHHHhcccCcEEEEEecC Q psy4127 9 RHFDAIDLDPF-GNPTRFLDAAVSSLRDGGLLLVTCTD 45 (75) Q Consensus 9 ~~fD~IDlDPf-GSp~pfldsA~~av~~gGll~vTaTD 45 (75) +.||.|=+... ..+..+++.+.+.++.||.+.+...+ T Consensus 110 ~~~D~V~~~~~~~~~~~~l~~~~~~LkpgG~lv~~~~~ 147 (198) T PRK00377 110 EKFDRIFIGGGSEKLKEIISASWEIIKKGGRIVIDAIL 147 (198) T ss_pred CCCCEEEECCCcccHHHHHHHHHHHcCCCcEEEEEeec Confidence 46888877541 23567899999999999999875443 No 75 >PF01910 DUF77: Domain of unknown function DUF77; InterPro: IPR002767 This entry contains several hypothetical proteins of unknown function found in archaebacteria, eukaryotes and eubacteria. The structures of YBL001c from Saccharomyces cerevisiae and its homologue MTH1187 from the archaea Methanobacterium thermoautotrophicum have been determined []. These proteins have a ferredoxin-like alpha/beta sandwich structure with anti-parallel beta-sheets. Generally, they have two domains that form a single beta-sheet dimer, where two dimers pack sheet-to-sheet into a tetramer, some proteins having an extra C-terminal helix. ; PDB: 1LXJ_A 1YQH_A 2EKY_G 2EPI_A 1VK8_D 2IBO_C 1LXN_B. Probab=50.85 E-value=8.1 Score=24.24 Aligned_cols=37 Identities=11% Similarity=0.237 Sum_probs=30.9 Q ss_pred CchhhHHHHHHhcccCcEEEEEecCcccccCCChhHHH Q psy4127 21 NPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCY 58 (75) Q Consensus 21 Sp~pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~ 58 (75) |.++|++.|++.++.-||=+-...=.+++.|. -+.++ T Consensus 14 s~~~~V~~~i~~i~~sgl~y~v~pm~T~iEGe-~dev~ 50 (92) T PF01910_consen 14 SVSAYVAEAIEVIKESGLKYEVGPMGTTIEGE-LDEVM 50 (92) T ss_dssp HHHHHHHHHHHHHHTSSSEEEEETTEEEEEEE-HHHHH T ss_pred CHHHHHHHHHHHHHHcCCceEEcCCccEEEec-HHHHH Confidence 57899999999999999999888888888887 44444 No 76 >PF10672 Methyltrans_SAM: S-adenosylmethionine-dependent methyltransferase; InterPro: IPR019614 Members of this entry are S-adenosylmethionine-dependent methyltransferases from gamma-proteobacterial species. The diversity in the roles of methylation is matched by the almost bewildering number of methyltransferase enzymes that catalyse the methylation reaction. Although several classes of methyltransferase enzymes are known, the great majority of methylation reactions are catalysed by the S-adenosylmethionine-dependent methyltransferases. SAM (S-adenosylmethionine, also known as AdoMet) is well known as the methyl donor for the majority of methyltransferases that modify DNA, RNA, histones and other proteins, dictating replicational, transcriptional and translational fidelity, mismatch repair, chromatin modelling, epigenetic modifications and imprinting [].; GO: 0008168 methyltransferase activity; PDB: 2IGT_B 1WXX_A 1WXW_D 2CWW_B 2AS0_B 3V8V_B 3V97_A 3C0K_A 2B78_A 3LDF_A. Probab=50.82 E-value=15 Score=27.55 Aligned_cols=41 Identities=44% Similarity=0.724 Sum_probs=24.0 Q ss_pred cCCCCceeeeCC--CC-----Cc---hhhHHHHHHhcccCcEEEEEecCccc Q psy4127 7 RGRHFDAIDLDP--FG-----NP---TRFLDAAVSSLRDGGLLLVTCTDMAV 48 (75) Q Consensus 7 ~~~~fD~IDlDP--fG-----Sp---~pfldsA~~av~~gGll~vTaTD~a~ 48 (75) .+++||+|=+|| |. -. ..-+..|++.+++||+|. ++|-... T Consensus 192 ~~~~fD~IIlDPPsF~k~~~~~~~~y~~L~~~a~~ll~~gG~l~-~~scs~~ 242 (286) T PF10672_consen 192 KGGRFDLIILDPPSFAKSKFDLERDYKKLLRRAMKLLKPGGLLL-TCSCSHH 242 (286) T ss_dssp HTT-EEEEEE--SSEESSTCEHHHHHHHHHHHHHHTEEEEEEEE-EEE--TT T ss_pred cCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHhcCCCCEEE-EEcCCcc Confidence 346899999998 21 11 124667899999999985 4444333 No 77 >COG1854 LuxS LuxS protein involved in autoinducer AI2 synthesis [Signal transduction mechanisms] Probab=50.46 E-value=8 Score=27.34 Aligned_cols=24 Identities=25% Similarity=0.462 Sum_probs=16.9 Q ss_pred ccccccCCCCceeeeCCCCCchhh Q psy4127 2 QLEKIRGRHFDAIDLDPFGNPTRF 25 (75) Q Consensus 2 ~m~~~~~~~fD~IDlDPfGSp~pf 25 (75) +|++|....+++||+-|+|+-+-| T Consensus 63 ~iRnh~~g~~~iID~SPMGCrTGF 86 (161) T COG1854 63 FIRNHLNGNVEIIDISPMGCRTGF 86 (161) T ss_pred HHHhcccCceeEEEecCcccccce Confidence 355554445789999999976544 No 78 >PLN02396 hexaprenyldihydroxybenzoate methyltransferase Probab=50.33 E-value=19 Score=27.19 Aligned_cols=36 Identities=22% Similarity=0.362 Sum_probs=27.6 Q ss_pred CCCceeee----CCCCCchhhHHHHHHhcccCcEEEEEec Q psy4127 9 RHFDAIDL----DPFGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 9 ~~fD~IDl----DPfGSp~pfldsA~~av~~gGll~vTaT 44 (75) +.||+|=. --...|..||....+.+|.||.+.++.- T Consensus 197 ~~FD~Vi~~~vLeHv~d~~~~L~~l~r~LkPGG~liist~ 236 (322) T PLN02396 197 RKFDAVLSLEVIEHVANPAEFCKSLSALTIPNGATVLSTI 236 (322) T ss_pred CCCCEEEEhhHHHhcCCHHHHHHHHHHHcCCCcEEEEEEC Confidence 46888742 2234578999999999999999999853 No 79 >PF01596 Methyltransf_3: O-methyltransferase; InterPro: IPR002935 Members of this family are O-methyltransferases. The family includes also bacterial O-methyltransferases that may be involved in antibiotic production [].; GO: 0008171 O-methyltransferase activity; PDB: 1SUI_C 1SUS_D 3CBG_A 2GPY_B 3TR6_A 2AVD_A 3DUL_B 3DUW_B 2ZTH_A 1VID_A .... Probab=49.63 E-value=14 Score=26.10 Aligned_cols=39 Identities=23% Similarity=0.372 Sum_probs=29.8 Q ss_pred CCCceeeeCCCC-CchhhHHHHHHhcccCcEEEEEecCcc Q psy4127 9 RHFDAIDLDPFG-NPTRFLDAAVSSLRDGGLLLVTCTDMA 47 (75) Q Consensus 9 ~~fD~IDlDPfG-Sp~pfldsA~~av~~gGll~vTaTD~a 47 (75) ..||+|=||--= .-..|++.+++.++.||+|.+--+... T Consensus 120 ~~fD~VFiDa~K~~y~~y~~~~~~ll~~ggvii~DN~l~~ 159 (205) T PF01596_consen 120 GQFDFVFIDADKRNYLEYFEKALPLLRPGGVIIADNVLWR 159 (205) T ss_dssp TSEEEEEEESTGGGHHHHHHHHHHHEEEEEEEEEETTTGG T ss_pred CceeEEEEcccccchhhHHHHHhhhccCCeEEEEcccccc Confidence 469987777532 246789999999999999998776643 No 80 >cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins. Probab=49.06 E-value=33 Score=21.24 Aligned_cols=39 Identities=18% Similarity=0.152 Sum_probs=27.7 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEecCcccc Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVL 49 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~a~L 49 (75) .-|++|++++.=++..+++.+.+ .+. -++++|+|++..+ T Consensus 26 ~G~~V~~lg~~~~~~~l~~~~~~-~~p-dvV~iS~~~~~~~ 64 (119) T cd02067 26 AGFEVIDLGVDVPPEEIVEAAKE-EDA-DAIGLSGLLTTHM 64 (119) T ss_pred CCCEEEECCCCCCHHHHHHHHHH-cCC-CEEEEeccccccH Confidence 46999999998666666765544 344 4999999865544 No 81 >PRK14902 16S rRNA methyltransferase B; Provisional Probab=49.01 E-value=32 Score=26.53 Aligned_cols=18 Identities=28% Similarity=0.659 Sum_probs=15.5 Q ss_pred hhHHHHHHhcccCcEEEE Q psy4127 24 RFLDAAVSSLRDGGLLLV 41 (75) Q Consensus 24 pfldsA~~av~~gGll~v 41 (75) .+|+.|.+.+|+||.|.. T Consensus 360 ~iL~~a~~~LkpGG~lvy 377 (444) T PRK14902 360 EILESVAQYLKKGGILVY 377 (444) T ss_pred HHHHHHHHHcCCCCEEEE Confidence 479999999999998764 No 82 >TIGR02807 cas6_var CRISPR-associated protein, Cas6-related. Members of this protein family resemble the Cas6 proteins described by TIGR01877 in having a C-terminal motif GXGXXXXXGXG, where the single X of each GXG is hydrophobic and the spacer XXXXX has at least one Lys or Arg. Examples are found in cas gene operons of CRISPR regions in Anabaena variabilis ATCC 29413, Leptospira interrogans, Gemmata obscuriglobus UQM 2246, and twice in Myxococcus xanthus DK 1622. Oddly, an orphan member is found in Thiobacillus denitrificans ATCC 25259, whose genome does not seem to contain other evidence of CRISPR repeats or cas genes. Probab=48.86 E-value=15 Score=26.48 Aligned_cols=27 Identities=22% Similarity=0.361 Sum_probs=23.3 Q ss_pred ceeeeCCCCCchhhHHHHHHhcccCcE Q psy4127 12 DAIDLDPFGNPTRFLDAAVSSLRDGGL 38 (75) Q Consensus 12 D~IDlDPfGSp~pfldsA~~av~~gGl 38 (75) -+|.++++-+|..||++|-+.+..=|+ T Consensus 109 r~V~~~~~~ee~~FLeaa~rqL~~l~i 135 (190) T TIGR02807 109 RIVTFKHAEEPAAFLAVARRQLEALGI 135 (190) T ss_pred EEEecCCCCCHHHHHHHHHHHHHHcCC Confidence 589999999999999999988876443 No 83 >cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding. Probab=47.30 E-value=43 Score=19.32 Aligned_cols=36 Identities=25% Similarity=0.352 Sum_probs=27.2 Q ss_pred eeeCCCCCchhhHH--HHHHhcccCcEEEEEecCcccc Q psy4127 14 IDLDPFGNPTRFLD--AAVSSLRDGGLLLVTCTDMAVL 49 (75) Q Consensus 14 IDlDPfGSp~pfld--sA~~av~~gGll~vTaTD~a~L 49 (75) ||+=-.-+|.|+|. .|++.+..|..|.|.++|..+. T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~~G~~l~V~~dd~~s~ 39 (69) T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMKPGDTLLVLATDPSTT 39 (69) T ss_pred ccccCCcCCHHHHHHHHHHHcCCCCCEEEEEeCCCchH Confidence 44445567888765 4677788999999999998764 No 84 >PF13578 Methyltransf_24: Methyltransferase domain; PDB: 3SSO_A 3SSN_C 3SSM_D. Probab=46.73 E-value=4.7 Score=24.39 Aligned_cols=33 Identities=27% Similarity=0.426 Sum_probs=23.9 Q ss_pred CCCceeeeCC---CCCchhhHHHHHHhcccCcEEEE Q psy4127 9 RHFDAIDLDP---FGNPTRFLDAAVSSLRDGGLLLV 41 (75) Q Consensus 9 ~~fD~IDlDP---fGSp~pfldsA~~av~~gGll~v 41 (75) +++|+|=||- |-.....+..+...+++||+|.+ T Consensus 68 ~~~dli~iDg~H~~~~~~~dl~~~~~~l~~ggviv~ 103 (106) T PF13578_consen 68 GPIDLIFIDGDHSYEAVLRDLENALPRLAPGGVIVF 103 (106) T ss_dssp --EEEEEEES---HHHHHHHHHHHGGGEEEEEEEEE T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHcCCCeEEEE Confidence 4688888884 44456677778888999999875 No 85 >PRK14968 putative methyltransferase; Provisional Probab=46.36 E-value=61 Score=20.91 Aligned_cols=23 Identities=35% Similarity=0.606 Sum_probs=18.9 Q ss_pred hhHHHHHHhcccCcEEEEEecCc Q psy4127 24 RFLDAAVSSLRDGGLLLVTCTDM 46 (75) Q Consensus 24 pfldsA~~av~~gGll~vTaTD~ 46 (75) .|+..+.+.++.||.+.+...+. T Consensus 129 ~~i~~~~~~Lk~gG~~~~~~~~~ 151 (188) T PRK14968 129 RFLDEVGRYLKPGGRILLLQSSL 151 (188) T ss_pred HHHHHHHHhcCCCeEEEEEEccc Confidence 47899999999999988876543 No 86 >PRK15008 HTH-type transcriptional regulator RutR; Provisional Probab=45.67 E-value=8.5 Score=26.19 Aligned_cols=41 Identities=17% Similarity=0.216 Sum_probs=37.7 Q ss_pred hhhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcC Q psy4127 23 TRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNA 63 (75) Q Consensus 23 ~pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~ 63 (75) ..-|++|++.....|+=.+|-.|.+--+|-.+..-|+.|+. T Consensus 21 ~~IL~AA~~lf~e~Gy~~~s~~dIA~~aGvs~gtiY~hF~s 61 (212) T PRK15008 21 KAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPS 61 (212) T ss_pred HHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHHHHHHCCC Confidence 45689999999999999999999999999999999988876 No 87 >PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A .... Probab=45.57 E-value=1.2 Score=24.14 Aligned_cols=38 Identities=24% Similarity=0.358 Sum_probs=33.9 Q ss_pred HHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcC Q psy4127 26 LDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNA 63 (75) Q Consensus 26 ldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~ 63 (75) |++|++.+...|+=.+|-.|.+--.|-.+..-++.|+. T Consensus 2 l~aa~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~~ 39 (47) T PF00440_consen 2 LEAALELFAEKGYEAVSIRDIARRAGVSKGSFYRYFPS 39 (47) T ss_dssp HHHHHHHHHHHHTTTSSHHHHHHHHTSCHHHHHHHCSS T ss_pred HHHHHHHHHHhCHHhCCHHHHHHHHccchhhHHHHcCC Confidence 68899999999999999999999999998888887765 No 88 >PRK14904 16S rRNA methyltransferase B; Provisional Probab=45.07 E-value=46 Score=25.76 Aligned_cols=18 Identities=44% Similarity=0.715 Sum_probs=16.0 Q ss_pred hhHHHHHHhcccCcEEEE Q psy4127 24 RFLDAAVSSLRDGGLLLV 41 (75) Q Consensus 24 pfldsA~~av~~gGll~v 41 (75) ..|+.|.+.|+.||.|.. T Consensus 358 ~iL~~a~~~lkpgG~lvy 375 (445) T PRK14904 358 ELLDHAASLLKPGGVLVY 375 (445) T ss_pred HHHHHHHHhcCCCcEEEE Confidence 479999999999998876 No 89 >TIGR03534 RF_mod_PrmC protein-(glutamine-N5) methyltransferase, release factor-specific. Members of this protein family are HemK (PrmC), a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. SIMBAL analysis (manuscript in prep.) shows the motif [LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers specificity for the release factors rather than for ribosomal protein L3. Probab=44.41 E-value=47 Score=22.63 Aligned_cols=20 Identities=35% Similarity=0.557 Sum_probs=17.2 Q ss_pred hhHHHHHHhcccCcEEEEEe Q psy4127 24 RFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 24 pfldsA~~av~~gGll~vTa 43 (75) .|+..+.+.+++||.+.+.. T Consensus 198 ~~i~~~~~~L~~gG~~~~~~ 217 (251) T TIGR03534 198 RIIAQAPRLLKPGGWLLLEI 217 (251) T ss_pred HHHHHHHHhcccCCEEEEEE Confidence 56788889999999999864 No 90 >cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding. Probab=44.04 E-value=43 Score=19.41 Aligned_cols=37 Identities=24% Similarity=0.250 Sum_probs=27.9 Q ss_pred eeeCCCCCchhhHHH--HHHhcccCcEEEEEecCccccc Q psy4127 14 IDLDPFGNPTRFLDA--AVSSLRDGGLLLVTCTDMAVLC 50 (75) Q Consensus 14 IDlDPfGSp~pflds--A~~av~~gGll~vTaTD~a~L~ 50 (75) ||+=-.=+|.|++.. |++.+..|..|-|-++|..+.. T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~~G~~l~V~~d~~~s~~ 40 (69) T cd03422 2 LDLRGEPCPYPAIATLEALPSLKPGEILEVISDCPQSIN 40 (69) T ss_pred cccCCCcCCHHHHHHHHHHHcCCCCCEEEEEecCchHHH Confidence 344444578888864 6788899999999999987753 No 91 >PRK11933 yebU rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed Probab=43.67 E-value=19 Score=28.75 Aligned_cols=36 Identities=42% Similarity=0.699 Sum_probs=28.0 Q ss_pred CCCceeeeCCCCC--------c------------------hhhHHHHHHhcccCcEE-EEEec Q psy4127 9 RHFDAIDLDPFGN--------P------------------TRFLDAAVSSLRDGGLL-LVTCT 44 (75) Q Consensus 9 ~~fD~IDlDPfGS--------p------------------~pfldsA~~av~~gGll-~vTaT 44 (75) +.||.|=||+==| | ...|++|++.||.||.| |-||| T Consensus 182 ~~fD~ILvDaPCSG~G~~rk~p~~~~~~s~~~v~~l~~lQ~~iL~~A~~~LkpGG~LVYSTCT 244 (470) T PRK11933 182 ETFDAILLDAPCSGEGTVRKDPDALKNWSPESNLEIAATQRELIESAFHALKPGGTLVYSTCT 244 (470) T ss_pred hhcCeEEEcCCCCCCcccccCHHHhhhCCHHHHHHHHHHHHHHHHHHHHHcCCCcEEEEECCC Confidence 4689999998544 1 45789999999999965 66777 No 92 >PRK00312 pcm protein-L-isoaspartate O-methyltransferase; Reviewed Probab=43.47 E-value=48 Score=22.53 Aligned_cols=34 Identities=24% Similarity=0.433 Sum_probs=25.9 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEec Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaT 44 (75) +.||.|=++. +.....+...+.++.||.|.+... T Consensus 143 ~~fD~I~~~~--~~~~~~~~l~~~L~~gG~lv~~~~ 176 (212) T PRK00312 143 APFDRILVTA--AAPEIPRALLEQLKEGGILVAPVG 176 (212) T ss_pred CCcCEEEEcc--CchhhhHHHHHhcCCCcEEEEEEc Confidence 4699988875 334556777789999999988765 No 93 >TIGR00080 pimt protein-L-isoaspartate(D-aspartate) O-methyltransferase. Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt. Probab=43.30 E-value=37 Score=23.27 Aligned_cols=32 Identities=22% Similarity=0.511 Sum_probs=24.1 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEEE Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vT 42 (75) +.||+|=+++- +....+...+.++.||.|.+. T Consensus 145 ~~fD~Ii~~~~--~~~~~~~~~~~L~~gG~lv~~ 176 (215) T TIGR00080 145 APYDRIYVTAA--GPKIPEALIDQLKEGGILVMP 176 (215) T ss_pred CCCCEEEEcCC--cccccHHHHHhcCcCcEEEEE Confidence 46999988853 334456777999999998875 No 94 >PRK10258 biotin biosynthesis protein BioC; Provisional Probab=43.18 E-value=46 Score=23.10 Aligned_cols=35 Identities=26% Similarity=0.301 Sum_probs=25.0 Q ss_pred CCCceeeeCC----CCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDLDP----FGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDlDP----fGSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=... ...+..+|..+.+.+++||.+.++. T Consensus 102 ~~fD~V~s~~~l~~~~d~~~~l~~~~~~Lk~gG~l~~~~ 140 (251) T PRK10258 102 ATFDLAWSNLAVQWCGNLSTALRELYRVVRPGGVVAFTT 140 (251) T ss_pred CcEEEEEECchhhhcCCHHHHHHHHHHHcCCCeEEEEEe Confidence 3577763321 2345678888999999999999974 No 95 >TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme. Probab=42.80 E-value=12 Score=24.29 Aligned_cols=41 Identities=22% Similarity=0.313 Sum_probs=36.9 Q ss_pred hhhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcC Q psy4127 23 TRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNA 63 (75) Q Consensus 23 ~pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~ 63 (75) ..-|++|.+.....|+=.+|-.|.+--+|-....-|+.|+. T Consensus 11 ~~Il~aA~~lf~~~G~~~~s~~~IA~~agvsk~~ly~~F~s 51 (189) T TIGR03384 11 AELIDATIESIGERGSLDVTIAQIARRAGVSSGIISHYFGG 51 (189) T ss_pred HHHHHHHHHHHHhcCcccCCHHHHHHHhCCCHHHHHHHcCC Confidence 35689999999999999999999999999998888888765 No 96 >PRK00299 sulfur transfer protein SirA; Reviewed Probab=42.75 E-value=44 Score=20.14 Aligned_cols=37 Identities=22% Similarity=0.306 Sum_probs=28.0 Q ss_pred eeeeCCCCCchhhHH--HHHHhcccCcEEEEEecCcccc Q psy4127 13 AIDLDPFGNPTRFLD--AAVSSLRDGGLLLVTCTDMAVL 49 (75) Q Consensus 13 ~IDlDPfGSp~pfld--sA~~av~~gGll~vTaTD~a~L 49 (75) .||+=-.-+|.|.|. .|++.++.|+.|-|-++|-++. T Consensus 11 ~lD~~Gl~CP~Pll~~kk~l~~l~~G~~l~V~~dd~~~~ 49 (81) T PRK00299 11 TLDALGLRCPEPVMMVRKTVRNMQPGETLLIIADDPATT 49 (81) T ss_pred EEecCCCCCCHHHHHHHHHHHcCCCCCEEEEEeCCccHH Confidence 355555557777654 5788899999999999998763 No 97 >PRK14903 16S rRNA methyltransferase B; Provisional Probab=42.18 E-value=47 Score=25.82 Aligned_cols=20 Identities=45% Similarity=0.755 Sum_probs=15.8 Q ss_pred hHHHHHHhcccCcEEE-EEec Q psy4127 25 FLDAAVSSLRDGGLLL-VTCT 44 (75) Q Consensus 25 fldsA~~av~~gGll~-vTaT 44 (75) .|+.|.+.|++||.|. .||| T Consensus 348 iL~~a~~~LkpGG~LvYsTCs 368 (431) T PRK14903 348 IVSQAWKLLEKGGILLYSTCT 368 (431) T ss_pred HHHHHHHhcCCCCEEEEEECC Confidence 4889999999998664 4666 No 98 >PF13489 Methyltransf_23: Methyltransferase domain; PDB: 3JWJ_A 3JWH_B 2AOV_B 2AOT_A 1JQD_B 2AOX_A 1JQE_A 2AOU_B 2AOW_A 3DLI_C .... Probab=42.02 E-value=18 Score=22.52 Aligned_cols=25 Identities=28% Similarity=0.559 Sum_probs=21.9 Q ss_pred chhhHHHHHHhcccCcEEEEEecCc Q psy4127 22 PTRFLDAAVSSLRDGGLLLVTCTDM 46 (75) Q Consensus 22 p~pfldsA~~av~~gGll~vTaTD~ 46 (75) |..+|+...+.+|.||++.++--.. T Consensus 94 ~~~~l~~l~~~LkpgG~l~~~~~~~ 118 (161) T PF13489_consen 94 PEEFLKELSRLLKPGGYLVISDPNR 118 (161) T ss_dssp HHHHHHHHHHCEEEEEEEEEEEEBT T ss_pred HHHHHHHHHHhcCCCCEEEEEEcCC Confidence 7889999999999999999987654 No 99 >PRK11014 transcriptional repressor NsrR; Provisional Probab=41.21 E-value=26 Score=22.81 Aligned_cols=26 Identities=12% Similarity=0.258 Sum_probs=22.9 Q ss_pred CCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 18 PFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 18 PfGSp~pfldsA~~av~~gGll~vTa 43 (75) -+|-|-+|+.-+++.+++.|++..+- T Consensus 34 ~~~is~~~vrk~l~~L~~~Glv~s~~ 59 (141) T PRK11014 34 VYGVSRNHMVKIINQLSRAGYVTAVR 59 (141) T ss_pred HHCcCHHHHHHHHHHHHhCCEEEEec Confidence 47889999999999999999986654 No 100 >COG2520 Predicted methyltransferase [General function prediction only] Probab=40.84 E-value=38 Score=26.21 Aligned_cols=33 Identities=27% Similarity=0.351 Sum_probs=28.8 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEE Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLV 41 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~v 41 (75) ..+|.|=.-=+++.-.|++.|+++++.||+|-. T Consensus 255 ~~aDrIim~~p~~a~~fl~~A~~~~k~~g~iHy 287 (341) T COG2520 255 GVADRIIMGLPKSAHEFLPLALELLKDGGIIHY 287 (341) T ss_pred ccCCEEEeCCCCcchhhHHHHHHHhhcCcEEEE Confidence 458888888888888999999999999999864 No 101 >cd08230 glucose_DH Glucose dehydrogenase. Glucose dehydrogenase (GlcDH), a member of the medium chain dehydrogenase/zinc-dependent alcohol dehydrogenase-like family, catalyzes the NADP(+)-dependent oxidation of glucose to gluconate, the first step in the Entner-Doudoroff pathway, an alternative to or substitute for glycolysis or the pentose phosphate pathway. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossman fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contai Probab=40.24 E-value=35 Score=24.71 Aligned_cols=32 Identities=25% Similarity=0.483 Sum_probs=24.4 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTa 43 (75) .+|+| +|.-|++. .++.+++.++++|.+.+-. T Consensus 238 ~~d~v-id~~g~~~-~~~~~~~~l~~~G~~v~~G 269 (355) T cd08230 238 EFDLI-IEATGVPP-LAFEALPALAPNGVVILFG 269 (355) T ss_pred CCCEE-EECcCCHH-HHHHHHHHccCCcEEEEEe Confidence 35655 78888654 7889999999999886543 No 102 >COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism] Probab=39.80 E-value=54 Score=22.57 Aligned_cols=53 Identities=23% Similarity=0.215 Sum_probs=37.7 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEecCcccccC-CChhHHHHHhcC Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLCG-NTPETCYVKYNA 63 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~a~L~G-~~~~~~~r~Yg~ 63 (75) --||+|.+=-+=||..++++|++. +-..+.|+++|..=+.- ..-...+|++|. T Consensus 39 ~GfeVi~~g~~~tp~e~v~aA~~~--dv~vIgvSsl~g~h~~l~~~lve~lre~G~ 92 (143) T COG2185 39 AGFEVINLGLFQTPEEAVRAAVEE--DVDVIGVSSLDGGHLTLVPGLVEALREAGV 92 (143) T ss_pred CCceEEecCCcCCHHHHHHHHHhc--CCCEEEEEeccchHHHHHHHHHHHHHHhCC Confidence 359999999999999999999876 55689999888764321 222334455554 No 103 >TIGR00477 tehB tellurite resistance protein TehB. Part of a tellurite-reducing operon tehA and tehB Probab=39.77 E-value=59 Score=22.10 Aligned_cols=37 Identities=24% Similarity=0.354 Sum_probs=24.0 Q ss_pred CCCcee-eeCCCCC-----chhhHHHHHHhcccCcE-EEEEecC Q psy4127 9 RHFDAI-DLDPFGN-----PTRFLDAAVSSLRDGGL-LLVTCTD 45 (75) Q Consensus 9 ~~fD~I-DlDPfGS-----p~pfldsA~~av~~gGl-l~vTaTD 45 (75) +.||+| ....|.. ...+++.+.+.++.||+ +.++..+ T Consensus 93 ~~fD~I~~~~~~~~~~~~~~~~~l~~~~~~LkpgG~lli~~~~~ 136 (195) T TIGR00477 93 EDYDFIFSTVVFMFLQAGRVPEIIANMQAHTRPGGYNLIVAAMD 136 (195) T ss_pred CCCCEEEEecccccCCHHHHHHHHHHHHHHhCCCcEEEEEEecc Confidence 458865 3344432 24688888899999997 5555433 No 104 >PTZ00098 phosphoethanolamine N-methyltransferase; Provisional Probab=39.66 E-value=34 Score=24.54 Aligned_cols=35 Identities=26% Similarity=0.474 Sum_probs=25.6 Q ss_pred CCCceeee-CCC-----CCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDL-DPF-----GNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDl-DPf-----GSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=. +.+ ..+..+|..+.+.+|+||.+.++- T Consensus 116 ~~FD~V~s~~~l~h~~~~d~~~~l~~i~r~LkPGG~lvi~d 156 (263) T PTZ00098 116 NTFDMIYSRDAILHLSYADKKKLFEKCYKWLKPNGILLITD 156 (263) T ss_pred CCeEEEEEhhhHHhCCHHHHHHHHHHHHHHcCCCcEEEEEE Confidence 45787754 321 135678888999999999999964 No 105 >PRK14103 trans-aconitate 2-methyltransferase; Provisional Probab=39.55 E-value=57 Score=22.86 Aligned_cols=35 Identities=17% Similarity=0.176 Sum_probs=26.1 Q ss_pred CCCceeeeCC----CCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDLDP----FGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDlDP----fGSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=... .-.+..++..+.+.+|.||.+.++. T Consensus 88 ~~fD~v~~~~~l~~~~d~~~~l~~~~~~LkpgG~l~~~~ 126 (255) T PRK14103 88 PDTDVVVSNAALQWVPEHADLLVRWVDELAPGSWIAVQV 126 (255) T ss_pred CCceEEEEehhhhhCCCHHHHHHHHHHhCCCCcEEEEEc Confidence 4577776533 2345778888899999999999974 No 106 >TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region). Probab=39.51 E-value=13 Score=24.70 Aligned_cols=40 Identities=18% Similarity=0.224 Sum_probs=36.6 Q ss_pred hhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcC Q psy4127 24 RFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNA 63 (75) Q Consensus 24 pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~ 63 (75) .-|++|++.....|+=.+|-.|.+--+|-.+..-|+.|++ T Consensus 12 ~Il~aA~~lf~e~G~~~~s~~~IA~~agvs~~~lY~hF~s 51 (202) T TIGR03613 12 AILSAALDTFSRFGFHGTSLEQIAELAGVSKTNLLYYFPS 51 (202) T ss_pred HHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHcCC Confidence 4689999999999999999999999999999998888875 No 107 >COG2227 UbiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme metabolism] Probab=39.29 E-value=30 Score=25.81 Aligned_cols=34 Identities=29% Similarity=0.682 Sum_probs=27.3 Q ss_pred CCCceee----eCCCCCchhhHHHHHHhcccCcEEEEE Q psy4127 9 RHFDAID----LDPFGNPTRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 9 ~~fD~ID----lDPfGSp~pfldsA~~av~~gGll~vT 42 (75) ++||+|= |-=+=-|..|+.++.+.||+||++.++ T Consensus 123 ~~FDvV~cmEVlEHv~dp~~~~~~c~~lvkP~G~lf~S 160 (243) T COG2227 123 GQFDVVTCMEVLEHVPDPESFLRACAKLVKPGGILFLS 160 (243) T ss_pred CCccEEEEhhHHHccCCHHHHHHHHHHHcCCCcEEEEe Confidence 5788885 233445788999999999999999886 No 108 >TIGR00496 frr ribosome recycling factor. This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis, it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD|53116|YHR038W is part of the frr superfamily. Probab=39.03 E-value=18 Score=25.29 Aligned_cols=42 Identities=21% Similarity=0.305 Sum_probs=34.3 Q ss_pred CCCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEecCcccc Q psy4127 8 GRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVL 49 (75) Q Consensus 8 ~~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~a~L 49 (75) ++-+|-|-++-||++.|+-+=|-=.++.+-.|.||.-|-..+ T Consensus 25 p~ild~I~V~~yg~~~pL~~lA~vsv~~~~~l~I~p~D~~~~ 66 (176) T TIGR00496 25 PSLLDRILVEYYGAPTPLRQLASVTVPDARTLVIQPFDKSNI 66 (176) T ss_pred HHHhCCeEEEeCCCcccHHHceeeecCCCCEEEEecCChhhH Confidence 356899999999999998776666677888999999995443 No 109 >TIGR02822 adh_fam_2 zinc-binding alcohol dehydrogenase family protein. Members of this model form a distinct subset of the larger family of oxidoreductases that includes zinc-binding alcohol dehydrogenases and NADPH:quinone reductases (pfam00107). The gene neighborhood of members of this family is not conserved and it appears that no members are characterized. The sequence of the family includes 6 invariant cysteine residues and one invariant histidine. It appears that no member is characterized. Probab=38.99 E-value=51 Score=23.88 Aligned_cols=32 Identities=34% Similarity=0.543 Sum_probs=24.4 Q ss_pred CCc-eeeeCCCCCchhhHHHHHHhcccCcEEEEEec Q psy4127 10 HFD-AIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 10 ~fD-~IDlDPfGSp~pfldsA~~av~~gGll~vTaT 44 (75) .+| +||.|.-| ..++.++++++.||.+.+... T Consensus 223 ~~d~~i~~~~~~---~~~~~~~~~l~~~G~~v~~G~ 255 (329) T TIGR02822 223 PLDAAILFAPAG---GLVPPALEALDRGGVLAVAGI 255 (329) T ss_pred cceEEEECCCcH---HHHHHHHHhhCCCcEEEEEec Confidence 466 47777665 368889999999999987653 No 110 >PRK00216 ubiE ubiquinone/menaquinone biosynthesis methyltransferase; Reviewed Probab=38.97 E-value=59 Score=21.70 Aligned_cols=35 Identities=23% Similarity=0.379 Sum_probs=25.7 Q ss_pred CCCceeee----CCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDL----DPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDl----DPfGSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=. ..+..+..+|+.+.+.++.||.+.+.. T Consensus 120 ~~~D~I~~~~~l~~~~~~~~~l~~~~~~L~~gG~li~~~ 158 (239) T PRK00216 120 NSFDAVTIAFGLRNVPDIDKALREMYRVLKPGGRLVILE 158 (239) T ss_pred CCccEEEEecccccCCCHHHHHHHHHHhccCCcEEEEEE Confidence 45777743 233457789999999999999887643 No 111 >cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains. Probab=38.66 E-value=53 Score=21.93 Aligned_cols=33 Identities=27% Similarity=0.571 Sum_probs=27.2 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTa 43 (75) .-|++||+=..=+|..|+++|.+- +=-++++|+ T Consensus 26 ~GfeVidLG~~v~~e~~v~aa~~~--~adiVglS~ 58 (128) T cd02072 26 AGFNVVNLGVLSPQEEFIDAAIET--DADAILVSS 58 (128) T ss_pred CCCEEEECCCCCCHHHHHHHHHHc--CCCEEEEec Confidence 469999999999999999999876 223777776 No 112 >PRK00311 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase; Reviewed Probab=38.51 E-value=30 Score=25.69 Aligned_cols=35 Identities=23% Similarity=0.322 Sum_probs=27.7 Q ss_pred CceeeeCCCCCc----hhhHHHHHHhcccCcEEEEEecCc Q psy4127 11 FDAIDLDPFGNP----TRFLDAAVSSLRDGGLLLVTCTDM 46 (75) Q Consensus 11 fD~IDlDPfGSp----~pfldsA~~av~~gGll~vTaTD~ 46 (75) +=++|+ |||+. ..-+..|++.+++-|.-+|--=|. T Consensus 78 ~vvaD~-pfg~y~~~~~~av~~a~r~~~~aGa~aVkiEdg 116 (264) T PRK00311 78 LVVADM-PFGSYQASPEQALRNAGRLMKEAGAHAVKLEGG 116 (264) T ss_pred cEEEeC-CCCCccCCHHHHHHHHHHHHHHhCCeEEEEcCc Confidence 556788 98877 556788899999888888877775 No 113 >PLN02336 phosphoethanolamine N-methyltransferase Probab=38.48 E-value=50 Score=25.34 Aligned_cols=35 Identities=20% Similarity=0.294 Sum_probs=27.0 Q ss_pred CCCceeee----CCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDL----DPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDl----DPfGSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=. --+..|..++..+.+.+++||.|.++- T Consensus 331 ~~fD~I~s~~~l~h~~d~~~~l~~~~r~LkpgG~l~i~~ 369 (475) T PLN02336 331 NSFDVIYSRDTILHIQDKPALFRSFFKWLKPGGKVLISD 369 (475) T ss_pred CCEEEEEECCcccccCCHHHHHHHHHHHcCCCeEEEEEE Confidence 45777653 334457789999999999999999874 No 114 >PLN02233 ubiquinone biosynthesis methyltransferase Probab=38.45 E-value=60 Score=23.26 Aligned_cols=34 Identities=18% Similarity=0.256 Sum_probs=25.6 Q ss_pred CCCceeeeC----CCCCchhhHHHHHHhcccCcEEEEE Q psy4127 9 RHFDAIDLD----PFGNPTRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 9 ~~fD~IDlD----PfGSp~pfldsA~~av~~gGll~vT 42 (75) +.||.|=+- -+-.+..+|....+.+|+||.+.++ T Consensus 144 ~sfD~V~~~~~l~~~~d~~~~l~ei~rvLkpGG~l~i~ 181 (261) T PLN02233 144 CYFDAITMGYGLRNVVDRLKAMQEMYRVLKPGSRVSIL 181 (261) T ss_pred CCEeEEEEecccccCCCHHHHHHHHHHHcCcCcEEEEE Confidence 457877431 2235678899999999999999887 No 115 >PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed Probab=38.29 E-value=62 Score=24.99 Aligned_cols=34 Identities=26% Similarity=0.516 Sum_probs=25.7 Q ss_pred CCCceeeeCC-CCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDLDP-FGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDlDP-fGSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=+|| +-.....+ .++..++.+++++|+| T Consensus 366 ~~fD~Vi~dPPr~g~~~~~-~~l~~~~~~~ivyvSC 400 (443) T PRK13168 366 GGFDKVLLDPPRAGAAEVM-QALAKLGPKRIVYVSC 400 (443) T ss_pred CCCCEEEECcCCcChHHHH-HHHHhcCCCeEEEEEe Confidence 4699999995 43345666 4666678899999997 No 116 >KOG0181|consensus Probab=37.67 E-value=26 Score=25.98 Aligned_cols=43 Identities=16% Similarity=0.304 Sum_probs=33.0 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCcE-EEEEecCcccccCCC Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGGL-LLVTCTDMAVLCGNT 53 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gGl-l~vTaTD~a~L~G~~ 53 (75) .|-+--.-|-|- --=++-|++||++|-. +.+.|+|+.+|.--. T Consensus 7 ~fslTtFSpsGK-L~QieyAL~Av~~G~~SvGi~A~nGvVlatek 50 (233) T KOG0181|consen 7 SFSLTTFSPSGK-LVQIEYALTAVVNGQTSVGIKAANGVVLATEK 50 (233) T ss_pred ceeeEEEcCCCc-eehHHHHHHHHhCCCCceeeeecCceEEEecc Confidence 366666677774 4568999999999865 789999999988644 No 117 >TIGR02819 fdhA_non_GSH formaldehyde dehydrogenase, glutathione-independent. Members of this family represent a distinct clade within the larger family of zinc-dependent dehydrogenases of medium chain alcohols, a family that also includes the so-called glutathione-dependent formaldehyde dehydrogenase. Members of this protein family have a tightly bound NAD that can act as a true cofactor, rather than a cosubstrate in dehydrogenase reactions, in dismutase reactions for some aldehydes. The name given to this family, however, is formaldehyde dehydrogenase, glutathione-independent. Probab=37.53 E-value=53 Score=24.82 Aligned_cols=34 Identities=21% Similarity=0.292 Sum_probs=27.5 Q ss_pred CCceeeeCCCCCch-------------hhHHHHHHhcccCcEEEEEec Q psy4127 10 HFDAIDLDPFGNPT-------------RFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 10 ~fD~IDlDPfGSp~-------------pfldsA~~av~~gGll~vTaT 44 (75) .+|+| +|.-|++. .-++.|++.+++||-+.+-.. T Consensus 254 g~Dvv-id~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~i~~~G~ 300 (393) T TIGR02819 254 EVDCA-VDCVGFEARGHGHDGKKEAPATVLNSLMEVTRVGGAIGIPGL 300 (393) T ss_pred CCcEE-EECCCCccccccccccccchHHHHHHHHHHhhCCCEEEEeee Confidence 47777 88999874 468999999999999987543 No 118 >PRK01747 mnmC bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed Probab=37.16 E-value=77 Score=25.66 Aligned_cols=53 Identities=21% Similarity=0.143 Sum_probs=34.9 Q ss_pred CCCceeeeCCCCCc--------hhhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcCcccCC Q psy4127 9 RHFDAIDLDPFGNP--------TRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNAVSLKT 68 (75) Q Consensus 9 ~~fD~IDlDPfGSp--------~pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~~~~~~ 68 (75) .++|.|=+|+|. | ..|+..--+..++||.+..=+...+ -++.+...|....+. T Consensus 165 ~~~d~~~lD~Fs-P~~np~~W~~~~~~~l~~~~~~~~~~~t~t~a~~------vr~~l~~~GF~v~~~ 225 (662) T PRK01747 165 ARADAWFLDGFA-PAKNPDMWSPNLFNALARLARPGATLATFTSAGF------VRRGLQEAGFTVRKV 225 (662) T ss_pred ccccEEEeCCCC-CccChhhccHHHHHHHHHHhCCCCEEEEeehHHH------HHHHHHHcCCeeeec Confidence 359999999998 6 5777766677788777763332222 355666666655443 No 119 >TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation. Probab=36.96 E-value=59 Score=21.80 Aligned_cols=34 Identities=21% Similarity=0.476 Sum_probs=26.6 Q ss_pred CCCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 8 GRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 8 ~~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTa 43 (75) ..-|++||+=..=+|..|+++|.+- +=-++++|+ T Consensus 27 ~~GfeVi~LG~~v~~e~~v~aa~~~--~adiVglS~ 60 (134) T TIGR01501 27 NAGFNVVNLGVLSPQEEFIKAAIET--KADAILVSS 60 (134) T ss_pred HCCCEEEECCCCCCHHHHHHHHHHc--CCCEEEEec Confidence 3469999999999999999999875 222666665 No 120 >TIGR01370 cysRS possible cysteinyl-tRNA synthetase, Methanococcus type. Assignment of this protein family as cysteinyl-tRNA synthetase is controversial, supported by PubMed:11333988 but challenged by PubMed:14679218. Members of this family from Deinococcus radiodurans (bacterial) and Methanococcus jannaschii (archaeal), species lacking a conventional cysteinyl-tRNA synthetase (Cys--tRNA ligase), have been indicated to be a novel form of that enzyme, perhaps distantly related to class I tRNA ligases. The member from Thermotoga maritima is presumed to be a second isozyme of cysteinyl-tRNA synthetase. A number of homologous but more distantly related proteins are annotated as alpha-1,4 polygalactosaminidases. Probab=36.93 E-value=29 Score=26.50 Aligned_cols=36 Identities=11% Similarity=0.199 Sum_probs=23.1 Q ss_pred CCCceeeeCCC--CCch-hhHHHHHHhcccCcEEEEEec Q psy4127 9 RHFDAIDLDPF--GNPT-RFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 9 ~~fD~IDlDPf--GSp~-pfldsA~~av~~gGll~vTaT 44 (75) ..||.++|||+ |+.. .|-.+-++.++..|-.-+..- T Consensus 63 ~~~d~vVID~~~~g~~~~~fs~~~i~~Lk~~g~~viaYl 101 (315) T TIGR01370 63 SPFELVVIDYSKDGTEDGTYSPEEIVRAAAAGRWPIAYL 101 (315) T ss_pred cCCCEEEEccccccCcccCCCHHHHHHHHhCCcEEEEEE Confidence 36999999999 3322 233455777777776555443 No 121 >KOG1122|consensus Probab=36.85 E-value=22 Score=28.86 Aligned_cols=21 Identities=33% Similarity=0.716 Sum_probs=16.8 Q ss_pred hhHHHHHHhcccCcEE-EEEec Q psy4127 24 RFLDAAVSSLRDGGLL-LVTCT 44 (75) Q Consensus 24 pfldsA~~av~~gGll-~vTaT 44 (75) .-|++|++.|+.||+| |=||| T Consensus 352 ~LllsAi~lv~~GGvLVYSTCS 373 (460) T KOG1122|consen 352 ELLLSAIDLVKAGGVLVYSTCS 373 (460) T ss_pred HHHHHHHhhccCCcEEEEEeee Confidence 4688999999999976 45555 No 122 >COG0421 SpeE Spermidine synthase [Amino acid transport and metabolism] Probab=36.54 E-value=84 Score=23.48 Aligned_cols=37 Identities=22% Similarity=0.515 Sum_probs=29.5 Q ss_pred CCCceeeeCCCCC--c------hhhHHHHHHhcccCcEEEEEecC Q psy4127 9 RHFDAIDLDPFGN--P------TRFLDAAVSSLRDGGLLLVTCTD 45 (75) Q Consensus 9 ~~fD~IDlDPfGS--p------~pfldsA~~av~~gGll~vTaTD 45 (75) +.||+|=+|.+=- | ..|.+..-++++.+|++-+-+-+ T Consensus 148 ~~fDvIi~D~tdp~gp~~~Lft~eFy~~~~~~L~~~Gi~v~q~~~ 192 (282) T COG0421 148 EKFDVIIVDSTDPVGPAEALFTEEFYEGCRRALKEDGIFVAQAGS 192 (282) T ss_pred CcCCEEEEcCCCCCCcccccCCHHHHHHHHHhcCCCcEEEEecCC Confidence 4799997765432 4 78999999999999999888555 No 123 >PF01189 Nol1_Nop2_Fmu: NOL1/NOP2/sun family; InterPro: IPR001678 This domain is found in archaeal, bacterial and eukaryotic proteins. In the archaea and bacteria, they are annotated as putative nucleolar protein, Sun (Fmu) family protein or tRNA/rRNA cytosine-C5-methylase. The majority have the S-adenosyl methionine (SAM) binding domain and are related to Escherichia coli Fmu (Sun) protein (16S rRNA m5C 967 methyltransferase) whose structure has been determined []. In the eukaryota, the majority are annotated as being 'hypothetical protein', nucleolar protein or the Nop2/Sun (Fmu) family. Unlike their bacterial homologues, few of the eukaryotic members in this family have a the SAM binding signature. Despite this, Saccharomyces cerevisiae (Baker's yeast) Nop2p is a probable RNA m5C methyltransferase []. It is essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis []; localized to the nucleolus and is essential for viability []. Reduced Nop2p expression limits yeast growth and decreases levels of mature 60S ribosomal subunits while altering rRNA processing []. There is substantial identity between Nop2p and Homo sapiens (Human) p120 (NOL1), which is also called the proliferation-associated nucleolar antigen [, ].; PDB: 3M4X_A 2FRX_B 2YXL_A 1IXK_A 1SQG_A 1SQF_A 3M6U_B 3M6V_B 3M6W_A 3M6X_A .... Probab=36.37 E-value=22 Score=26.15 Aligned_cols=21 Identities=38% Similarity=0.692 Sum_probs=16.4 Q ss_pred hhHHHHHHhc----ccCcE-EEEEec Q psy4127 24 RFLDAAVSSL----RDGGL-LLVTCT 44 (75) Q Consensus 24 pfldsA~~av----~~gGl-l~vTaT 44 (75) .-|+.|++.+ |.||. +|.||| T Consensus 196 ~iL~~a~~~~~~~~k~gG~lvYsTCS 221 (283) T PF01189_consen 196 EILDNAAKLLNIDFKPGGRLVYSTCS 221 (283) T ss_dssp HHHHHHHHCEHHHBEEEEEEEEEESH T ss_pred HHHHHHHHhhcccccCCCeEEEEecc Confidence 3578999999 88885 677776 No 124 >TIGR00406 prmA ribosomal protein L11 methyltransferase. Ribosomal protein L11 methyltransferase is an S-adenosyl-L-methionine-dependent methyltransferase required for the modification of ribosomal protein L11. This protein is found in bacteria and (with a probable transit peptide) in Arabidopsis. Probab=36.09 E-value=52 Score=23.91 Aligned_cols=36 Identities=14% Similarity=0.213 Sum_probs=26.2 Q ss_pred CCCCceeeeCCCCCc-hhhHHHHHHhcccCcEEEEEe Q psy4127 8 GRHFDAIDLDPFGNP-TRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 8 ~~~fD~IDlDPfGSp-~pfldsA~~av~~gGll~vTa 43 (75) ++.||+|=.+....+ ..++..+.+.+++||.+.++. T Consensus 223 ~~~fDlVvan~~~~~l~~ll~~~~~~LkpgG~li~sg 259 (288) T TIGR00406 223 EGKADVIVANILAEVIKELYPQFSRLVKPGGWLILSG 259 (288) T ss_pred CCCceEEEEecCHHHHHHHHHHHHHHcCCCcEEEEEe Confidence 346888866654433 256777889999999998864 No 125 >COG0284 PyrF Orotidine-5'-phosphate decarboxylase [Nucleotide transport and metabolism] Probab=36.04 E-value=60 Score=23.78 Aligned_cols=33 Identities=39% Similarity=0.571 Sum_probs=28.3 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCc--EEEEEe Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGG--LLLVTC 43 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gG--ll~vTa 43 (75) -.|.|.+-||+-. .-++++.++...+| +|++|+ T Consensus 89 g~d~vtvH~~~G~-~~~~~~~e~~~~~~~~vl~vT~ 123 (240) T COG0284 89 GADAVTVHAFGGF-DMLRAAKEALEAGGPFVLAVTS 123 (240) T ss_pred CCcEEEEeCcCCH-HHHHHHHHHHhhcCceEEEEEe Confidence 4799999999964 58999999999887 888876 No 126 >COG0742 N6-adenine-specific methylase [DNA replication, recombination, and repair] Probab=35.59 E-value=58 Score=23.23 Aligned_cols=30 Identities=37% Similarity=0.685 Sum_probs=19.7 Q ss_pred CCceeeeCC-CCCchhhH--HHHHHh------cccCcEEEE Q psy4127 10 HFDAIDLDP-FGNPTRFL--DAAVSS------LRDGGLLLV 41 (75) Q Consensus 10 ~fD~IDlDP-fGSp~pfl--dsA~~a------v~~gGll~v 41 (75) .||+|=+|| |. ...+ ..++.+ ++++|++.+ T Consensus 114 ~FDlVflDPPy~--~~l~~~~~~~~~~~~~~~L~~~~~iv~ 152 (187) T COG0742 114 PFDLVFLDPPYA--KGLLDKELALLLLEENGWLKPGALIVV 152 (187) T ss_pred cccEEEeCCCCc--cchhhHHHHHHHHHhcCCcCCCcEEEE Confidence 499999996 66 3444 445555 566666655 No 127 >COG1192 Soj ATPases involved in chromosome partitioning [Cell division and chromosome partitioning] Probab=35.19 E-value=19 Score=25.06 Aligned_cols=19 Identities=42% Similarity=0.629 Sum_probs=15.3 Q ss_pred CCCceeeeCCCCCchhhHH Q psy4127 9 RHFDAIDLDPFGNPTRFLD 27 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfld 27 (75) .+.=+||+||-||.+-++. T Consensus 33 ~kVLliDlDpQ~s~t~~~~ 51 (259) T COG1192 33 KKVLLIDLDPQGSLTSWLG 51 (259) T ss_pred CcEEEEeCCCcchhhHhcC Confidence 4677899999999877664 No 128 >PLN02244 tocopherol O-methyltransferase Probab=34.94 E-value=73 Score=23.76 Aligned_cols=35 Identities=14% Similarity=0.347 Sum_probs=26.3 Q ss_pred CCCceeee----CCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDL----DPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDl----DPfGSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=. .-+..+..++....+.+|.||.+.++. T Consensus 185 ~~FD~V~s~~~~~h~~d~~~~l~e~~rvLkpGG~lvi~~ 223 (340) T PLN02244 185 GQFDLVWSMESGEHMPDKRKFVQELARVAAPGGRIIIVT 223 (340) T ss_pred CCccEEEECCchhccCCHHHHHHHHHHHcCCCcEEEEEE Confidence 46888743 123445679999999999999999874 No 129 >PRK14996 TetR family transcriptional regulator; Provisional Probab=34.86 E-value=16 Score=24.23 Aligned_cols=40 Identities=15% Similarity=0.139 Sum_probs=36.5 Q ss_pred hhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcC Q psy4127 24 RFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNA 63 (75) Q Consensus 24 pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~ 63 (75) .-|++|++.....|+-.+|=-|.+--.|-.+..-|+.+++ T Consensus 12 ~Il~aA~~lf~e~G~~~tSi~~Ia~~aGvsk~~lY~~F~s 51 (192) T PRK14996 12 VILQAAMRVALAEGFAAMTVRRIASEAQVAAGQVHHHFSS 51 (192) T ss_pred HHHHHHHHHHHhcChhhccHHHHHHHhCCCcHHHHHHcCC Confidence 4589999999999999999999999999999999988876 No 130 >PRK11188 rrmJ 23S rRNA methyltransferase J; Provisional Probab=34.66 E-value=83 Score=21.84 Aligned_cols=35 Identities=26% Similarity=0.354 Sum_probs=25.6 Q ss_pred CCCCceeeeCC----CCCch-----------hhHHHHHHhcccCcEEEEE Q psy4127 8 GRHFDAIDLDP----FGNPT-----------RFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 8 ~~~fD~IDlDP----fGSp~-----------pfldsA~~av~~gGll~vT 42 (75) .+.||+|=-|+ .|.|. ..|+.+.+.+++||.+.+. T Consensus 115 ~~~~D~V~S~~~~~~~g~~~~d~~~~~~~~~~~L~~~~~~LkpGG~~vi~ 164 (209) T PRK11188 115 DSKVQVVMSDMAPNMSGTPAVDIPRAMYLVELALDMCRDVLAPGGSFVVK 164 (209) T ss_pred CCCCCEEecCCCCccCCChHHHHHHHHHHHHHHHHHHHHHcCCCCEEEEE Confidence 45689887664 35542 3677888999999999983 No 131 >cd08239 THR_DH_like L-threonine dehydrogenase (TDH)-like. MDR/AHD-like proteins, including a protein annotated as a threonine dehydrogenase. L-threonine dehydrogenase (TDH) catalyzes the zinc-dependent formation of 2-amino-3-ketobutyrate from L-threonine via NAD(H)-dependent oxidation. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Zinc-dependent ADHs are medium chain dehydrogenase/reductase type proteins (MDRs) and have a NAD(P)(H)-binding domain in a Rossmann fold of an beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. In addition to alcohol dehydrogenases, this group includes quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc at Probab=34.33 E-value=67 Score=22.85 Aligned_cols=33 Identities=21% Similarity=0.226 Sum_probs=25.8 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCcEEEEEec Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaT 44 (75) .+|+| +|.-|++. .++.+++.++.+|-+.+-.+ T Consensus 231 ~~d~v-id~~g~~~-~~~~~~~~l~~~G~~v~~g~ 263 (339) T cd08239 231 GADVA-IECSGNTA-ARRLALEAVRPWGRLVLVGE 263 (339) T ss_pred CCCEE-EECCCCHH-HHHHHHHHhhcCCEEEEEcC Confidence 57877 78888764 56789999999998876544 No 132 >cd08293 PTGR2 Prostaglandin reductase. Prostaglandins and related eicosanoids are metabolized by the oxidation of the 15(S)-hydroxyl group of the NAD+-dependent (type I 15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH) followed by reduction by NADPH/NADH-dependent (type II 15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to 15-keto-13,14,-dihydroprostaglandins. 13-PGR is a bifunctional enzyme, since it also has leukotriene B(4) 12-hydroxydehydrogenase activity. These 15-PGDH and related enzymes are members of the medium chain dehydrogenase/reductase family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acid Probab=34.17 E-value=58 Score=23.13 Aligned_cols=29 Identities=17% Similarity=0.409 Sum_probs=23.1 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCcEEEE Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLV 41 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gGll~v 41 (75) .+|+| +|.-|++. ++.++++++.+|-+.. T Consensus 224 gvd~v-id~~g~~~--~~~~~~~l~~~G~iv~ 252 (345) T cd08293 224 GVDVY-FDNVGGEI--SDTVISQMNENSHIIL 252 (345) T ss_pred CceEE-EECCCcHH--HHHHHHHhccCCEEEE Confidence 47877 68888753 5889999999997764 No 133 >PF10354 DUF2431: Domain of unknown function (DUF2431); InterPro: IPR019446 This entry represents the N-terminal domain of a family of proteins whose function is not known. Probab=34.03 E-value=54 Score=22.38 Aligned_cols=25 Identities=28% Similarity=0.316 Sum_probs=23.1 Q ss_pred hhHHHHHHhcccCcEEEEEecCccc Q psy4127 24 RFLDAAVSSLRDGGLLLVTCTDMAV 48 (75) Q Consensus 24 pfldsA~~av~~gGll~vTaTD~a~ 48 (75) .|+.+|-+.++.+|.+.||--++.+ T Consensus 106 ~Ff~Sa~~~L~~~G~IhVTl~~~~p 130 (166) T PF10354_consen 106 GFFKSASQLLKPDGEIHVTLKDGQP 130 (166) T ss_pred HHHHHHHHhcCCCCEEEEEeCCCCC Confidence 5899999999999999999988877 No 134 >PF05175 MTS: Methyltransferase small domain; InterPro: IPR007848 This domain is found in ribosomal RNA small subunit methyltransferase C and in other methyltransferases.; GO: 0008168 methyltransferase activity; PDB: 1WY7_A 1DUS_A 2OZV_A 2PJD_A 1VQ1_A 1NV9_A 1SG9_C 1NV8_A 3Q87_B 3DMF_A .... Probab=33.82 E-value=48 Score=21.99 Aligned_cols=34 Identities=35% Similarity=0.643 Sum_probs=25.0 Q ss_pred CCCCceeeeCC-C--CC------chhhHHHHHHhcccCcEEEE Q psy4127 8 GRHFDAIDLDP-F--GN------PTRFLDAAVSSLRDGGLLLV 41 (75) Q Consensus 8 ~~~fD~IDlDP-f--GS------p~pfldsA~~av~~gGll~v 41 (75) .++||+|=.+| | |. -..|+..|-+.+++||.+.+ T Consensus 96 ~~~fD~Iv~NPP~~~~~~~~~~~~~~~i~~a~~~Lk~~G~l~l 138 (170) T PF05175_consen 96 DGKFDLIVSNPPFHAGGDDGLDLLRDFIEQARRYLKPGGRLFL 138 (170) T ss_dssp TTCEEEEEE---SBTTSHCHHHHHHHHHHHHHHHEEEEEEEEE T ss_pred ccceeEEEEccchhcccccchhhHHHHHHHHHHhccCCCEEEE Confidence 46899999987 2 32 25789999999999998854 No 135 >cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart Probab=33.06 E-value=16 Score=24.36 Aligned_cols=11 Identities=36% Similarity=0.773 Sum_probs=9.7 Q ss_pred CCceeeeCCCC Q psy4127 10 HFDAIDLDPFG 20 (75) Q Consensus 10 ~fD~IDlDPfG 20 (75) .|-..|.||+| T Consensus 54 ~~~l~D~DP~G 64 (160) T cd00223 54 VYILVDGDPYG 64 (160) T ss_pred EEEEECCCcch Confidence 46789999999 No 136 >cd08264 Zn_ADH_like2 Alcohol dehydrogenases of the MDR family. This group resembles the zinc-dependent alcohol dehydrogenases of the medium chain dehydrogenase family. However, this subgroup does not contain the characteristic catalytic zinc site. Also, it contains an atypical structural zinc-binding pattern: DxxCxxCxxxxxxxC. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the clo Probab=32.96 E-value=72 Score=22.38 Aligned_cols=32 Identities=31% Similarity=0.529 Sum_probs=25.5 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCcEEEEEec Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaT 44 (75) .+|+| +|..|+ +.++.++++++.+|-+..... T Consensus 223 ~~d~v-l~~~g~--~~~~~~~~~l~~~g~~v~~g~ 254 (325) T cd08264 223 MADVV-INSLGS--SFWDLSLSVLGRGGRLVTFGT 254 (325) T ss_pred CCCEE-EECCCH--HHHHHHHHhhccCCEEEEEec Confidence 47776 688885 689999999999998876543 No 137 >TIGR02825 B4_12hDH leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase. Leukotriene B4 12-hydroxydehydrogenase is an NADP-dependent enzyme of arachidonic acid metabolism, responsible for converting leukotriene B4 to the much less active metabolite 12-oxo-leukotriene B4. The BRENDA database lists leukotriene B4 12-hydroxydehydrogenase as one of the synonyms of 2-alkenal reductase (EC 1.3.1.74), while 1.3.1.48 is 15-oxoprostaglandin 13-reductase. Probab=32.58 E-value=60 Score=23.01 Aligned_cols=31 Identities=16% Similarity=0.426 Sum_probs=24.1 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTa 43 (75) .+|+| +|..|.+ .++.++++++.+|-+..-. T Consensus 207 gvdvv-~d~~G~~--~~~~~~~~l~~~G~iv~~G 237 (325) T TIGR02825 207 GYDCY-FDNVGGE--FSNTVIGQMKKFGRIAICG 237 (325) T ss_pred CeEEE-EECCCHH--HHHHHHHHhCcCcEEEEec Confidence 47777 6899964 4688999999999887543 No 138 >PRK10668 DNA-binding transcriptional repressor AcrR; Provisional Probab=32.27 E-value=18 Score=24.30 Aligned_cols=40 Identities=25% Similarity=0.379 Sum_probs=36.8 Q ss_pred hhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcC Q psy4127 24 RFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNA 63 (75) Q Consensus 24 pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~ 63 (75) ..+++|++.....|+-.+|=.|.+--.|-.+..-|+.|++ T Consensus 15 ~Il~AA~~lf~e~G~~~~t~~~Ia~~agvs~~tlY~~F~s 54 (215) T PRK10668 15 HILDAALRLFSQQGVSATSLADIAKAAGVTRGAIYWHFKN 54 (215) T ss_pred HHHHHHHHHHHHcCcccCCHHHHHHHhCCChHHHHHHCCC Confidence 4789999999999999999999999999999988888875 No 139 >PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A. Probab=32.08 E-value=99 Score=17.39 Aligned_cols=36 Identities=31% Similarity=0.434 Sum_probs=26.9 Q ss_pred eeeCCCCCchhhHH--HHHHhcccCcEEEEEecCcccc Q psy4127 14 IDLDPFGNPTRFLD--AAVSSLRDGGLLLVTCTDMAVL 49 (75) Q Consensus 14 IDlDPfGSp~pfld--sA~~av~~gGll~vTaTD~a~L 49 (75) ||+=-..+|.|.+. .|++.+..|..|-|.++|-.+. T Consensus 3 lD~rg~~CP~Pll~~~~~l~~l~~G~~l~v~~d~~~~~ 40 (70) T PF01206_consen 3 LDLRGLSCPMPLLKAKKALKELPPGEVLEVLVDDPAAV 40 (70) T ss_dssp EECSS-STTHHHHHHHHHHHTSGTT-EEEEEESSTTHH T ss_pred EeCCCCCCCHHHHHHHHHHHhcCCCCEEEEEECCccHH Confidence 56666778999865 4677788899999999998765 No 140 >TIGR00091 tRNA (guanine-N(7)-)-methyltransferase. In E. coli, this protein flanks the DNA repair protein MutY, also called micA. Probab=31.82 E-value=55 Score=22.16 Aligned_cols=26 Identities=31% Similarity=0.483 Sum_probs=20.6 Q ss_pred hhhHHHHHHhcccCcEEEEEecCcccc Q psy4127 23 TRFLDAAVSSLRDGGLLLVTCTDMAVL 49 (75) Q Consensus 23 ~pfldsA~~av~~gGll~vTaTD~a~L 49 (75) ..|+..+.+.+|+||.|.+ +||...+ T Consensus 112 ~~~l~~~~r~LkpgG~l~~-~td~~~~ 137 (194) T TIGR00091 112 PHFLKEYANVLKKGGVIHF-KTDNEPL 137 (194) T ss_pred HHHHHHHHHHhCCCCEEEE-EeCCHHH Confidence 3689999999999999976 4566553 No 141 >COG0233 Frr Ribosome recycling factor [Translation, ribosomal structure and biogenesis] Probab=31.81 E-value=35 Score=24.58 Aligned_cols=58 Identities=16% Similarity=0.169 Sum_probs=40.3 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcCccc Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNAVSL 66 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~~~~ 66 (75) ..+|-|-+|-||+++|+-+=|==.|..--.|.|+==|-..+.-....---..+|..|. T Consensus 37 ~lld~i~VeyYG~~tPl~qvAsIsvpe~r~l~I~p~Dks~~~~IekaI~~snLglnP~ 94 (187) T COG0233 37 SLLDRITVEYYGSPTPLNQLASISVPEARTLVIKPFDKSMVKAIEKAILASNLGLNPN 94 (187) T ss_pred HHhcceeeeecCCCCcHHHHhhccCCCcceEEeecCccchHHHHHHHHHHcCCCCCcC Confidence 4588899999999999887776677888888888888655443332223344555443 No 142 >cd08265 Zn_ADH3 Alcohol dehydrogenases of the MDR family. This group resembles the zinc-dependent alcohol dehydrogenase and has the catalytic and structural zinc-binding sites characteristic of this group. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanedi Probab=31.53 E-value=87 Score=23.11 Aligned_cols=33 Identities=15% Similarity=0.186 Sum_probs=25.7 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEEE Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vT 42 (75) +.+|+| +|..|.+...++.+++.++.+|-+..- T Consensus 274 ~gvDvv-ld~~g~~~~~~~~~~~~l~~~G~~v~~ 306 (384) T cd08265 274 WGADIQ-VEAAGAPPATIPQMEKSIAINGKIVYI 306 (384) T ss_pred CCCCEE-EECCCCcHHHHHHHHHHHHcCCEEEEE Confidence 358877 688897666788899999988877643 No 143 >TIGR03704 PrmC_rel_meth putative protein-(glutamine-N5) methyltransferase, unknown substrate-specific. This protein family is closely related to two different families of protein-(glutamine-N5) methyltransferase. The first is PrmB, which modifies ribosomal protein L3 in some bacteria. The second is PrmC (HemK), which modifies peptide chain release factors 1 and 2 in most bacteria and also in eukaryotes. The glutamine side chain-binding motif NPPY shared by PrmB and PrmC is N[VAT]PY in this family. The protein substrate is unknown. Probab=31.33 E-value=93 Score=22.25 Aligned_cols=19 Identities=42% Similarity=0.473 Sum_probs=16.5 Q ss_pred hhHHHHHHhcccCcEEEEE Q psy4127 24 RFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 24 pfldsA~~av~~gGll~vT 42 (75) .+++.|.+.+++||.+.+- T Consensus 197 ~i~~~a~~~L~~gG~l~l~ 215 (251) T TIGR03704 197 RVAAGAPDWLAPGGHLLVE 215 (251) T ss_pred HHHHHHHHhcCCCCEEEEE Confidence 6788888999999999875 No 144 >TIGR00537 hemK_rel_arch HemK-related putative methylase. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. This model represents an archaeal and eukaryotic protein family that lacks an N-terminal domain found in HemK and its eubacterial homologs. It is found in a single copy in the first six completed archaeal and eukaryotic genomes. Probab=31.32 E-value=1.1e+02 Score=20.05 Aligned_cols=20 Identities=35% Similarity=0.587 Sum_probs=16.7 Q ss_pred hhHHHHHHhcccCcEEEEEe Q psy4127 24 RFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 24 pfldsA~~av~~gGll~vTa 43 (75) .||+.+.+.+++||.+.+.. T Consensus 121 ~~l~~~~~~Lk~gG~~~~~~ 140 (179) T TIGR00537 121 RFLDELPEILKEGGRVQLIQ 140 (179) T ss_pred HHHHhHHHhhCCCCEEEEEE Confidence 47888899999999887754 No 145 >PRK15062 hydrogenase isoenzymes formation protein HypD; Provisional Probab=31.17 E-value=54 Score=25.84 Aligned_cols=33 Identities=30% Similarity=0.419 Sum_probs=29.3 Q ss_pred CchhhHHHHHHhcccCcEEEEEecCcccccCCC Q psy4127 21 NPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNT 53 (75) Q Consensus 21 Sp~pfldsA~~av~~gGll~vTaTD~a~L~G~~ 53 (75) +|...||.|+...+..|++-.|.=||-=.-|+. T Consensus 67 tp~~~ID~ai~La~~~~vi~~TfGDmlRVPGs~ 99 (364) T PRK15062 67 TPMGRIDAAIELASRPGVILCTFGDMLRVPGSK 99 (364) T ss_pred CcHHHHHHHHHHhCCCCeEEEeccccccCCCCc Confidence 467899999999999999999999998888874 No 146 >PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A .... Probab=30.93 E-value=13 Score=21.17 Aligned_cols=32 Identities=22% Similarity=0.315 Sum_probs=24.2 Q ss_pred HHHHhcccCcEEEEEecCcccccCCChhHHHH Q psy4127 28 AAVSSLRDGGLLLVTCTDMAVLCGNTPETCYV 59 (75) Q Consensus 28 sA~~av~~gGll~vTaTD~a~L~G~~~~~~~r 59 (75) ..++.++..|.-.|++++++-.+|..|....+ T Consensus 16 r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRK 47 (50) T PF06971_consen 16 RYLEQLKEEGVERVSSQELAEALGITPAQVRK 47 (50) T ss_dssp HHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHH T ss_pred HHHHHHHHcCCeeECHHHHHHHHCCCHHHhcc Confidence 37788889999999999999999998765543 No 147 >TIGR03451 mycoS_dep_FDH mycothiol-dependent formaldehyde dehydrogenase. Members of this protein family are mycothiol-dependent formaldehyde dehydrogenase (EC 1.2.1.66). This protein is found, so far, only in the Actinobacteria (Mycobacterium sp., Streptomyces sp., Corynebacterium sp., and related species), where mycothione replaces glutathione. Probab=30.91 E-value=91 Score=22.64 Aligned_cols=33 Identities=18% Similarity=0.294 Sum_probs=25.7 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCcEEEEEec Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaT 44 (75) .+|+| +|.-|++. -++.++++++.+|.+.+... T Consensus 245 g~d~v-id~~g~~~-~~~~~~~~~~~~G~iv~~G~ 277 (358) T TIGR03451 245 GADVV-IDAVGRPE-TYKQAFYARDLAGTVVLVGV 277 (358) T ss_pred CCCEE-EECCCCHH-HHHHHHHHhccCCEEEEECC Confidence 47877 68889764 56779999999998887653 No 148 >PF00107 ADH_zinc_N: Zinc-binding dehydrogenase; InterPro: IPR013149 Alcohol dehydrogenase (1.1.1.1 from EC) (ADH) catalyzes the reversible oxidation of alcohols to their corresponding acetaldehyde or ketone with the concomitant reduction of NAD:alcohol + NAD = aldehyde or ketone + NADH Currently three structurally and catalytically different types of alcohol dehydrogenases are known: Zinc-containing 'long-chain' alcohol dehydrogenases. Insect-type, or 'short-chain' alcohol dehydrogenases. Iron-containing alcohol dehydrogenases. Zinc-containing ADH's [, ] are dimeric or tetrameric enzymes that bind two atoms of zinc per subunit. One of the zinc atom is essential for catalytic activity while the other is not. Both zinc atoms are coordinated by either cysteine or histidine residues; the catalytic zinc is coordinated by two cysteines and one histidine. Zinc-containing ADH's are found in bacteria, mammals, plants, and in fungi. In many species there is more than one isozyme (for example, humans have at least six isozymes, yeast have three, etc.). A number of other zinc-dependent dehydrogenases are closely related to zinc ADH [] and are included in this family. Sorbitol dehydrogenase (1.1.1.14 from EC) L-threonine 3-dehydrogenase (1.1.1.103 from EC) Glutathione-dependent formaldehyde dehydrogenase (1.1.1.284 from EC) Mannitol dehydrogenase (1.1.1.255 from EC) In addition, this family includes NADP-dependent quinone oxidoreductase (1.6.5.5 from EC), an enzyme found in bacteria (gene qor), in yeast and in mammals where, in some species such as rodents, it has been recruited as an eye lens protein and is known as zeta-crystallin []. The sequence of quinone oxidoreductase is distantly related to that other zinc-containing alcohol dehydrogenases and it lacks the zinc-ligand residues. The torpedo fish and mammalian synaptic vesicle membrane protein vat-1 is related to qor. This entry represents the cofactor-binding domain of these enzymes, which is normally found towards the C terminus. Structural studies indicate that it forms a classical Rossman fold that reversibly binds NAD(H) [, , ].; GO: 0008270 zinc ion binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3PI7_A 3COS_D 1VJ1_A 2ZB3_A 1PIW_B 1Q1N_A 1PS0_A 2EER_B 3KRT_A 1ZSY_A .... Probab=30.72 E-value=37 Score=20.69 Aligned_cols=35 Identities=29% Similarity=0.397 Sum_probs=27.6 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCcEEEEEecCc Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDM 46 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~ 46 (75) .+|+| +|.-|++ .-++.++++++++|-+.+-+--. T Consensus 58 ~~d~v-id~~g~~-~~~~~~~~~l~~~G~~v~vg~~~ 92 (130) T PF00107_consen 58 GVDVV-IDCVGSG-DTLQEAIKLLRPGGRIVVVGVYG 92 (130) T ss_dssp SEEEE-EESSSSH-HHHHHHHHHEEEEEEEEEESSTS T ss_pred cceEE-EEecCcH-HHHHHHHHHhccCCEEEEEEccC Confidence 46665 6788875 67889999999999998876554 No 149 >cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3. Probab=30.42 E-value=94 Score=17.89 Aligned_cols=31 Identities=26% Similarity=0.393 Sum_probs=24.0 Q ss_pred CCCchhhHH--HHHHhcccCcEEEEEecCcccc Q psy4127 19 FGNPTRFLD--AAVSSLRDGGLLLVTCTDMAVL 49 (75) Q Consensus 19 fGSp~pfld--sA~~av~~gGll~vTaTD~a~L 49 (75) .=+|.|.+. .|++-++.|..|-|-++|-++. T Consensus 7 ~~CP~Pvl~~kkal~~l~~G~~l~V~~d~~~a~ 39 (69) T cd03420 7 LQCPGPILKLKKEIDKLQDGEQLEVKASDPGFA 39 (69) T ss_pred CcCCHHHHHHHHHHHcCCCCCEEEEEECCccHH Confidence 336777764 5677788999999999998774 No 150 >PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison. Probab=30.39 E-value=37 Score=23.25 Aligned_cols=37 Identities=14% Similarity=0.091 Sum_probs=28.0 Q ss_pred cCcEEEEEecCcccccCCChhHHHHHhcCcccCCCCc Q psy4127 35 DGGLLLVTCTDMAVLCGNTPETCYVKYNAVSLKTAAC 71 (75) Q Consensus 35 ~gGll~vTaTD~a~L~G~~~~~~~r~Yg~~~~~~~~~ 71 (75) ++|+++||+.=++-|.---...|..|+-..-.+-||. T Consensus 39 ~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rDPfn 75 (134) T PF05883_consen 39 NDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRDPFN 75 (134) T ss_pred CCCEEEEecCCeehHHHHHHHHHHHHHHhhccCCCcc Confidence 5999999999998888777889999984333344443 No 151 >PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms. Probab=30.19 E-value=25 Score=20.80 Aligned_cols=32 Identities=16% Similarity=0.288 Sum_probs=27.2 Q ss_pred HHHhcccCcEEEEEecCcccccCCChhHHHHH Q psy4127 29 AVSSLRDGGLLLVTCTDMAVLCGNTPETCYVK 60 (75) Q Consensus 29 A~~av~~gGll~vTaTD~a~L~G~~~~~~~r~ 60 (75) .++.+...+.-+++..|.+.+.|..|+.++.. T Consensus 7 ~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~ 38 (75) T PF04182_consen 7 LLERIARSRYNGITQSDLSKLLGIDPRSIFYR 38 (75) T ss_pred HHHHHHhcCCCCEehhHHHHHhCCCchHHHHH Confidence 66777777888889999999999999988764 No 152 >cd03752 proteasome_alpha_type_4 proteasome_alpha_type_4. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Probab=30.16 E-value=50 Score=22.82 Aligned_cols=36 Identities=22% Similarity=0.311 Sum_probs=27.9 Q ss_pred CCCCCchhhHHHHHHhcccCc-EEEEEecCcccccCCC Q psy4127 17 DPFGNPTRFLDAAVSSLRDGG-LLLVTCTDMAVLCGNT 53 (75) Q Consensus 17 DPfGSp~pfldsA~~av~~gG-ll~vTaTD~a~L~G~~ 53 (75) .|-|. .-=++-|++++++|+ +|++.+-|+-+|.... T Consensus 11 sp~Gr-l~Qveya~~a~~~G~t~igi~~~dgVvla~d~ 47 (213) T cd03752 11 SPEGR-LYQVEYAMEAISHAGTCLGILAKDGIVLAAEK 47 (213) T ss_pred CCCCE-EhHHHhHHHHHhcCCCEEEEEeCCEEEEEEEe Confidence 45553 344888999999999 8899999988887644 No 153 >PRK11018 hypothetical protein; Provisional Probab=30.07 E-value=1.3e+02 Score=17.94 Aligned_cols=39 Identities=18% Similarity=0.166 Sum_probs=30.6 Q ss_pred ceeeeCCCCCchhhHHH--HHHhcccCcEEEEEecCccccc Q psy4127 12 DAIDLDPFGNPTRFLDA--AVSSLRDGGLLLVTCTDMAVLC 50 (75) Q Consensus 12 D~IDlDPfGSp~pflds--A~~av~~gGll~vTaTD~a~L~ 50 (75) ..||+=-.=+|.|+|.. |++.++.|..|-|-++|.++.. T Consensus 9 ~~lD~rG~~CP~Pvl~~kk~l~~l~~G~~L~V~~d~~~a~~ 49 (78) T PRK11018 9 YRLDMVGEPCPYPAVATLEALPQLKKGEILEVVSDCPQSIN 49 (78) T ss_pred eeEECCCCcCCHHHHHHHHHHHhCCCCCEEEEEeCCccHHH Confidence 35677777789999875 5677889999999999877643 No 154 >PRK13699 putative methylase; Provisional Probab=30.01 E-value=88 Score=22.23 Aligned_cols=40 Identities=15% Similarity=0.210 Sum_probs=27.0 Q ss_pred cccccCCCCceeeeC-CCCC--------c----------hhhHHHHHHhcccCcEEEEE Q psy4127 3 LEKIRGRHFDAIDLD-PFGN--------P----------TRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 3 m~~~~~~~fD~IDlD-PfGS--------p----------~pfldsA~~av~~gGll~vT 42 (75) |.+...+.+|.|=.| ||+. . ..++..+.+.+|+||.+.+- T Consensus 13 l~~lpd~SVDLIiTDPPY~i~~~~~~~~~~~~~~~~ew~~~~l~E~~RVLKpgg~l~if 71 (227) T PRK13699 13 MARFPDNAVDFILTDPPYLVGFRDRQGRTIAGDKTDEWLQPACNEMYRVLKKDALMVSF 71 (227) T ss_pred HHhCCccccceEEeCCCcccccccCCCcccccccHHHHHHHHHHHHHHHcCCCCEEEEE Confidence 334455678888888 4652 1 14556667889999998863 No 155 >PLN03075 nicotianamine synthase; Provisional Probab=29.76 E-value=78 Score=23.97 Aligned_cols=35 Identities=14% Similarity=0.393 Sum_probs=29.5 Q ss_pred CCCceeeeCCC-----CCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDLDPF-----GNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDlDPf-----GSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=++-- ..+...|+...+.++.||++.+-+ T Consensus 194 ~~FDlVF~~ALi~~dk~~k~~vL~~l~~~LkPGG~Lvlr~ 233 (296) T PLN03075 194 KEYDVVFLAALVGMDKEEKVKVIEHLGKHMAPGALLMLRS 233 (296) T ss_pred CCcCEEEEecccccccccHHHHHHHHHHhcCCCcEEEEec Confidence 57999988841 578889999999999999999875 No 156 >PRK13942 protein-L-isoaspartate O-methyltransferase; Provisional Probab=29.47 E-value=99 Score=21.36 Aligned_cols=33 Identities=21% Similarity=0.525 Sum_probs=24.5 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTa 43 (75) ..||.|=++-.- .......++.++.||.|.+.- T Consensus 144 ~~fD~I~~~~~~--~~~~~~l~~~LkpgG~lvi~~ 176 (212) T PRK13942 144 APYDRIYVTAAG--PDIPKPLIEQLKDGGIMVIPV 176 (212) T ss_pred CCcCEEEECCCc--ccchHHHHHhhCCCcEEEEEE Confidence 469999887433 344567778899999998864 No 157 >TIGR00057 Sua5/YciO/YrdC/YwlC family protein. partial match to sua5, which is involved in regulation of translation initiation. 3' end of sua5 has matches to sua5, BS3690, and weakly to AF0781 and BB0734. Probab=29.47 E-value=69 Score=22.31 Aligned_cols=26 Identities=35% Similarity=0.446 Sum_probs=19.6 Q ss_pred hhhHHHHHHhcccCcEEEEEecCcccc Q psy4127 23 TRFLDAAVSSLRDGGLLLVTCTDMAVL 49 (75) Q Consensus 23 ~pfldsA~~av~~gGll~vTaTD~a~L 49 (75) ..-++.|++.+++||++.+ =||+--- T Consensus 8 ~~~i~~a~~~L~~G~ii~~-PTdTvYg 33 (201) T TIGR00057 8 QRGIEQAVKILRKGGIVVY-PTDTVYG 33 (201) T ss_pred HHHHHHHHHHHHCCCEEEE-eCCCHHH Confidence 3468899999999998876 4776543 No 158 >PF03269 DUF268: Caenorhabditis protein of unknown function, DUF268; InterPro: IPR004951 This family consists of proteins of unknown function found in Caenorhabditis species. Probab=28.59 E-value=63 Score=23.19 Aligned_cols=27 Identities=30% Similarity=0.608 Sum_probs=17.6 Q ss_pred eCCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 16 LDPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 16 lDPfGSp~pfldsA~~av~~gGll~vTa 43 (75) +||.|-.-.... .-..+|+||+|.++- T Consensus 85 idp~Gdl~~m~~-i~~vLK~GG~L~l~v 111 (177) T PF03269_consen 85 IDPIGDLRAMAK-IKCVLKPGGLLFLGV 111 (177) T ss_pred CCccccHHHHHH-HHHhhccCCeEEEEe Confidence 357775544332 335589999999863 No 159 >cd08295 double_bond_reductase_like Arabidopsis alkenal double bond reductase and leukotriene B4 12-hydroxydehydrogenase. This group includes proteins identified as the Arabidopsis alkenal double bond reductase and leukotriene B4 12-hydroxydehydrogenase. The Arabidopsis enzyme, a member of the medium chain dehydrogenase/reductase family, catalyzes the reduction of 7-8-double bond of phenylpropanal substrates as a plant defense mechanism. Prostaglandins and related eicosanoids (lipid mediators involved in host defense and inflamation) are metabolized by the oxidation of the 15(S)-hydroxyl group of the NAD+-dependent (type I 15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH) followed by reduction by NADPH/NADH-dependent (type II 15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to 15-keto-13,14,-dihydroprostaglandins. 13-PGR is a bifunctional enzyme, since it also has leukotriene B(4) 12-hydroxydehydrogenase activity. Leukotriene B4 (LTB4) can be metabolized by LTB4 20-hydroxylase in Probab=28.42 E-value=77 Score=22.66 Aligned_cols=29 Identities=24% Similarity=0.410 Sum_probs=23.1 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCcEEEE Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLV 41 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gGll~v 41 (75) .+|+| +|..|+ ..+..++++++++|-+.. T Consensus 221 gvd~v-~d~~g~--~~~~~~~~~l~~~G~iv~ 249 (338) T cd08295 221 GIDIY-FDNVGG--KMLDAVLLNMNLHGRIAA 249 (338) T ss_pred CcEEE-EECCCH--HHHHHHHHHhccCcEEEE Confidence 46776 688885 557889999999998875 No 160 >TIGR00452 methyltransferase, putative. Known examples to date are restricted to the proteobacteria. Probab=28.39 E-value=66 Score=24.25 Aligned_cols=34 Identities=21% Similarity=0.165 Sum_probs=26.2 Q ss_pred CCceeee----CCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 10 HFDAIDL----DPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 10 ~fD~IDl----DPfGSp~pfldsA~~av~~gGll~vTa 43 (75) .||+|=. -=..+|..+|....++++.||.|.++. T Consensus 188 ~FD~V~s~gvL~H~~dp~~~L~el~r~LkpGG~Lvlet 225 (314) T TIGR00452 188 AFDTVFSMGVLYHRKSPLEHLKQLKHQLVIKGELVLET 225 (314) T ss_pred CcCEEEEcchhhccCCHHHHHHHHHHhcCCCCEEEEEE Confidence 5777632 123578889999999999999999874 No 161 >cd03749 proteasome_alpha_type_1 proteasome_alpha_type_1. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Probab=27.86 E-value=57 Score=22.58 Aligned_cols=36 Identities=19% Similarity=0.265 Sum_probs=27.9 Q ss_pred CCCCCchhhHHHHHHhcccCc-EEEEEecCcccccCCC Q psy4127 17 DPFGNPTRFLDAAVSSLRDGG-LLLVTCTDMAVLCGNT 53 (75) Q Consensus 17 DPfGSp~pfldsA~~av~~gG-ll~vTaTD~a~L~G~~ 53 (75) .|.| -.==++-|++++++|+ +|+|...|+.+|.... T Consensus 9 sp~G-rl~Qveya~~av~~G~t~IgIk~~dgVvlaad~ 45 (211) T cd03749 9 SPQG-RLFQVEYAMEAVKQGSATVGLKSKTHAVLVALK 45 (211) T ss_pred CCCC-eEeHHHHHHHHHhcCCCEEEEEeCCEEEEEEec Confidence 4666 3445889999999986 8899999998887543 No 162 >PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional Probab=27.73 E-value=55 Score=24.67 Aligned_cols=22 Identities=41% Similarity=0.522 Sum_probs=18.2 Q ss_pred chhhHHHHHHhcccCcEEEEEe Q psy4127 22 PTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 22 p~pfldsA~~av~~gGll~vTa 43 (75) -..+|.+|.+.++.||.|+|=+ T Consensus 215 L~~~L~~~~~~L~~gGrl~vis 236 (296) T PRK00050 215 LERALEAALDLLKPGGRLAVIS 236 (296) T ss_pred HHHHHHHHHHHhcCCCEEEEEe Confidence 3468999999999999998743 No 163 >KOG1562|consensus Probab=27.35 E-value=99 Score=24.27 Aligned_cols=40 Identities=28% Similarity=0.601 Sum_probs=29.8 Q ss_pred cccccCCCCceeee---CCCCCch------hhHHHHHHhcccCcEEEEEe Q psy4127 3 LEKIRGRHFDAIDL---DPFGNPT------RFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 3 m~~~~~~~fD~IDl---DPfGSp~------pfldsA~~av~~gGll~vTa 43 (75) |....++.||+|=+ ||-| |+ +|...-.+|+|.+|++|+-+ T Consensus 188 l~~~~~~~~dVii~dssdpvg-pa~~lf~~~~~~~v~~aLk~dgv~~~q~ 236 (337) T KOG1562|consen 188 LEDLKENPFDVIITDSSDPVG-PACALFQKPYFGLVLDALKGDGVVCTQG 236 (337) T ss_pred HHHhccCCceEEEEecCCccc-hHHHHHHHHHHHHHHHhhCCCcEEEEec Confidence 33444678998866 4667 43 57777889999999999877 No 164 >TIGR03633 arc_protsome_A proteasome endopeptidase complex, archaeal, alpha subunit. This protein family describes the archaeal proteasome alpha subunit, homologous to both the beta subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated. Probab=26.88 E-value=61 Score=22.51 Aligned_cols=37 Identities=19% Similarity=0.251 Sum_probs=27.6 Q ss_pred eCCCCCchhhHHHHHHhcccCc-EEEEEecCcccccCCC Q psy4127 16 LDPFGNPTRFLDAAVSSLRDGG-LLLVTCTDMAVLCGNT 53 (75) Q Consensus 16 lDPfGSp~pfldsA~~av~~gG-ll~vTaTD~a~L~G~~ 53 (75) -+|-|. .-=|+-|.+++++|+ +|++...|+.++..-. T Consensus 10 f~p~Gr-l~Qieya~~av~~G~tvigi~~~dgvvlaad~ 47 (224) T TIGR03633 10 FSPDGR-LYQVEYAREAVKRGTTAVGIKTKDGVVLAVDK 47 (224) T ss_pred ECCCCe-EeHHHHHHHHHHcCCCEEEEEECCEEEEEEec Confidence 456663 455888999999988 7888888887776543 No 165 >PRK04266 fibrillarin; Provisional Probab=26.56 E-value=1.4e+02 Score=21.20 Aligned_cols=33 Identities=36% Similarity=0.501 Sum_probs=22.9 Q ss_pred CCCceeeeCCCCCc---hhhHHHHHHhcccCcEEEEE Q psy4127 9 RHFDAIDLDPFGNP---TRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 9 ~~fD~IDlDPfGSp---~pfldsA~~av~~gGll~vT 42 (75) +.||+|=.|- ..| ..+|..+.+.+|+||.+.|+ T Consensus 140 ~~~D~i~~d~-~~p~~~~~~L~~~~r~LKpGG~lvI~ 175 (226) T PRK04266 140 EKVDVIYQDV-AQPNQAEIAIDNAEFFLKDGGYLLLA 175 (226) T ss_pred ccCCEEEECC-CChhHHHHHHHHHHHhcCCCcEEEEE Confidence 4588875541 112 12477888899999999996 No 166 >TIGR00740 methyltransferase, putative. A simple BLAST search finds all members of this family and weaker hits to a large number of known and predicted methyltransferases. A single iteration with PSI-BLAST, keeping only clear members of the family, leads to a large number of highly significant hits to a set of known and predicted methyltransferases with a large repertoire of different specifities. This model is restricted to a subfamily found so far only in the Proteobacteria, sharing consistent length, full-length homology, and on average better than 35 % identity. It is reasonable to predict equivalent function within this subfamily. Probab=26.22 E-value=67 Score=22.21 Aligned_cols=21 Identities=19% Similarity=0.344 Sum_probs=18.4 Q ss_pred hhhHHHHHHhcccCcEEEEEe Q psy4127 23 TRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 23 ~pfldsA~~av~~gGll~vTa 43 (75) ..++....+.++.||.+.++- T Consensus 141 ~~~l~~i~~~LkpgG~l~i~d 161 (239) T TIGR00740 141 IALLTKIYEGLNPNGVLVLSE 161 (239) T ss_pred HHHHHHHHHhcCCCeEEEEee Confidence 567888899999999999984 No 167 >cd03754 proteasome_alpha_type_6 proteasome_alpha_type_6. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Probab=26.21 E-value=62 Score=22.53 Aligned_cols=35 Identities=23% Similarity=0.347 Sum_probs=25.6 Q ss_pred eCCCCCchhhHHHHHHhcccCc--EEEEEecCcccccC Q psy4127 16 LDPFGNPTRFLDAAVSSLRDGG--LLLVTCTDMAVLCG 51 (75) Q Consensus 16 lDPfGSp~pfldsA~~av~~gG--ll~vTaTD~a~L~G 51 (75) -+|=|-- -=++-|++|++++| .+++.+-|.-+|.. T Consensus 9 fsp~Grl-~Qveya~~a~~~~g~t~igi~~~d~Vvlaa 45 (215) T cd03754 9 FSPEGRL-YQVEYAFKAVKNAGLTSVAVRGKDCAVVVT 45 (215) T ss_pred ECCCCeE-eHHHhHHHHHhcCCccEEEEEeCCEEEEEE Confidence 3455632 33788999998755 79999888888765 No 168 >cd03751 proteasome_alpha_type_3 proteasome_alpha_type_3. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Probab=26.06 E-value=66 Score=22.43 Aligned_cols=36 Identities=22% Similarity=0.357 Sum_probs=26.3 Q ss_pred CCCCCchhhHHHHHHhcccCc-EEEEEecCcccccCCC Q psy4127 17 DPFGNPTRFLDAAVSSLRDGG-LLLVTCTDMAVLCGNT 53 (75) Q Consensus 17 DPfGSp~pfldsA~~av~~gG-ll~vTaTD~a~L~G~~ 53 (75) +|=|. .-=++-|++|+++|| +|+|...|+-+|..-. T Consensus 12 sp~Gr-l~Qveya~~a~~~G~tvIgik~kdgVvla~d~ 48 (212) T cd03751 12 SPDGR-VFQVEYANKAVENSGTAIGIRCKDGVVLAVEK 48 (212) T ss_pred CCCCc-chHHHHHHHHHhcCCCEEEEEeCCEEEEEEEc Confidence 34442 334888999999987 7888888888876543 No 169 >TIGR00006 S-adenosyl-methyltransferase MraW. Genetics paper in 1972 links mra cluster to peptidoglycan biosynthesis in E. coli. Seems to be common in proteobacteria.wn. Probab=25.97 E-value=61 Score=24.61 Aligned_cols=22 Identities=27% Similarity=0.243 Sum_probs=18.4 Q ss_pred chhhHHHHHHhcccCcEEEEEe Q psy4127 22 PTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 22 p~pfldsA~~av~~gGll~vTa 43 (75) -..+|++|.+.++.||.|+|=+ T Consensus 219 L~~~L~~~~~~L~~gGrl~VIS 240 (305) T TIGR00006 219 LEEALQFAPNLLAPGGRLSIIS 240 (305) T ss_pred HHHHHHHHHHHhcCCCEEEEEe Confidence 3468999999999999998743 No 170 >COG1309 AcrR Transcriptional regulator [Transcription] Probab=25.73 E-value=22 Score=21.46 Aligned_cols=40 Identities=28% Similarity=0.424 Sum_probs=35.6 Q ss_pred hhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHhcC Q psy4127 24 RFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNA 63 (75) Q Consensus 24 pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~ 63 (75) .-+++|+......|+-.+|-.|.+--.|-.+..-|+.|+. T Consensus 16 ~ii~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~Y~~f~~ 55 (201) T COG1309 16 RILDAALRLFAEKGYAATTVDEIAKAAGVSKGTLYRHFPS 55 (201) T ss_pred HHHHHHHHHHHHcCcCCCCHHHHHHHhCCCcchhHHHcCC Confidence 4688899988889999999999999999998888888775 No 171 >PF05869 Dam: DNA N-6-adenine-methyltransferase (Dam); InterPro: IPR008593 This family consists of several bacterial and phage DNA N-6-adenine-methyltransferase (Dam) like sequences [].; GO: 0003677 DNA binding, 0009007 site-specific DNA-methyltransferase (adenine-specific) activity, 0032775 DNA methylation on adenine Probab=25.69 E-value=57 Score=22.88 Aligned_cols=31 Identities=16% Similarity=0.413 Sum_probs=22.6 Q ss_pred CCCC-chhhHHHHHHhcccCcE--EEEEecCccc Q psy4127 18 PFGN-PTRFLDAAVSSLRDGGL--LLVTCTDMAV 48 (75) Q Consensus 18 PfGS-p~pfldsA~~av~~gGl--l~vTaTD~a~ 48 (75) |||. +.+||+-|++.-.+|+. +.|-+.|..+ T Consensus 72 PYs~~i~~wv~Ka~~e~~~g~~~VvLL~~~~~st 105 (181) T PF05869_consen 72 PYSRGIGPWVEKAIEEYERGNQTVVLLPPADTST 105 (181) T ss_pred chhhhHHHHHHHHHHHHHhCCcEEEEEeccCCCc Confidence 8999 99999999987766654 3555555443 No 172 >TIGR01712 phage_N6A_met phage N-6-adenine-methyltransferase. This is a model for a phage-borne DNA N-6-adenine-methyltransferase. Probab=25.55 E-value=93 Score=21.86 Aligned_cols=29 Identities=14% Similarity=0.331 Sum_probs=18.7 Q ss_pred CCCCchhhHHHHHHhcccCc--EEEEEecCc Q psy4127 18 PFGNPTRFLDAAVSSLRDGG--LLLVTCTDM 46 (75) Q Consensus 18 PfGSp~pfldsA~~av~~gG--ll~vTaTD~ 46 (75) ||+-|.+||..|....+..| .+++--.|+ T Consensus 70 PYS~~~~~v~kaae~~~~~g~~~VmLlpa~t 100 (166) T TIGR01712 70 PYSRPDIFVNKTAWFTEARQAAEVILIEADL 100 (166) T ss_pred CCCcHHHHHHHHHHHHHhhCCeEEEEEecCC Confidence 89999999999875433333 444444444 No 173 >cd08237 ribitol-5-phosphate_DH ribitol-5-phosphate dehydrogenase. NAD-linked ribitol-5-phosphate dehydrogenase, a member of the MDR/zinc-dependent alcohol dehydrogenase-like family, oxidizes the phosphate ester of ribitol-5-phosphate to xylulose-5-phosphate of the pentose phosphate pathway. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase ( Probab=25.43 E-value=1.1e+02 Score=22.26 Aligned_cols=32 Identities=13% Similarity=0.240 Sum_probs=24.2 Q ss_pred CceeeeCCCCCc--hhhHHHHHHhcccCcEEEEEe Q psy4127 11 FDAIDLDPFGNP--TRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 11 fD~IDlDPfGSp--~pfldsA~~av~~gGll~vTa 43 (75) +|+| +|--|.+ ..-++.+++.++.+|.+.+-. T Consensus 223 ~d~v-iD~~G~~~~~~~~~~~~~~l~~~G~iv~~G 256 (341) T cd08237 223 VDHA-FECVGGRGSQSAINQIIDYIRPQGTIGLMG 256 (341) T ss_pred CcEE-EECCCCCccHHHHHHHHHhCcCCcEEEEEe Confidence 6665 6888843 246788999999999987654 No 174 >PRK10909 rsmD 16S rRNA m(2)G966-methyltransferase; Provisional Probab=24.79 E-value=62 Score=22.69 Aligned_cols=35 Identities=23% Similarity=0.435 Sum_probs=24.0 Q ss_pred CCCceeeeCC-CCCchhhHHHHHHhc------ccCcEEEEEecC Q psy4127 9 RHFDAIDLDP-FGNPTRFLDAAVSSL------RDGGLLLVTCTD 45 (75) Q Consensus 9 ~~fD~IDlDP-fGSp~pfldsA~~av------~~gGll~vTaTD 45 (75) +.||+|=+|| |-. .+...+++.+ +.+++++|...- T Consensus 120 ~~fDlV~~DPPy~~--g~~~~~l~~l~~~~~l~~~~iv~ve~~~ 161 (199) T PRK10909 120 TPHNVVFVDPPFRK--GLLEETINLLEDNGWLADEALIYVESEV 161 (199) T ss_pred CCceEEEECCCCCC--ChHHHHHHHHHHCCCcCCCcEEEEEecC Confidence 3599999995 543 4555666655 557888888643 No 175 >PF02878 PGM_PMM_I: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I; InterPro: IPR005844 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain I found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 3I3W_B 1WQA_C 1KFQ_B 1KFI_A 2Z0F_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X .... Probab=24.75 E-value=58 Score=20.91 Aligned_cols=34 Identities=29% Similarity=0.422 Sum_probs=26.4 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEec Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaT 44 (75) ..++++|+. -.|+|-+.-+++.....|=+.||+. T Consensus 67 ~G~~V~~~g--~~~tP~~~~~~~~~~~~ggi~iTaS 100 (137) T PF02878_consen 67 NGVDVIDIG--LVPTPALSFAIRQLNADGGIMITAS 100 (137) T ss_dssp TTEEEEEEE--EB-HHHHHHHHHHHTESEEEEE--T T ss_pred ccccccccc--ccCcHHhhhhccccccceeeEEEec Confidence 357999999 6789999999998888888999985 No 176 >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=24.63 E-value=1.1e+02 Score=23.38 Aligned_cols=34 Identities=21% Similarity=0.190 Sum_probs=27.9 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEec Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaT 44 (75) ...|++|++. .|+|-+.-|++..+-.|=+.|||. T Consensus 61 ~G~~V~~~g~--~pTP~~~~av~~~~~~gGi~ITaS 94 (441) T cd05805 61 TGVNVRDLGA--LPLPVARYAIRFLGASGGIHVRTS 94 (441) T ss_pred CCCeEEecCC--cCchHHHHHHHhcCCCeeEEEEeC Confidence 3589999985 799999989988876666788986 No 177 >cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation. Probab=24.43 E-value=1.1e+02 Score=19.22 Aligned_cols=39 Identities=15% Similarity=0.198 Sum_probs=29.1 Q ss_pred CCCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEecCccc Q psy4127 8 GRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAV 48 (75) Q Consensus 8 ~~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaTD~a~ 48 (75) ..-|++|++=++=++..++++|.+. +--++++++++... T Consensus 25 ~~G~~vi~lG~~vp~e~~~~~a~~~--~~d~V~iS~~~~~~ 63 (122) T cd02071 25 DAGFEVIYTGLRQTPEEIVEAAIQE--DVDVIGLSSLSGGH 63 (122) T ss_pred HCCCEEEECCCCCCHHHHHHHHHHc--CCCEEEEcccchhh Confidence 3469999999997777788777755 33488898887543 No 178 >COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane] Probab=24.37 E-value=68 Score=24.88 Aligned_cols=25 Identities=32% Similarity=0.430 Sum_probs=20.2 Q ss_pred CCCchhhHHHHHHhcccCcEEEEEe Q psy4127 19 FGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 19 fGSp~pfldsA~~av~~gGll~vTa 43 (75) -|+--.+|.+|+..++.||-|+|=+ T Consensus 220 L~~L~~~L~~a~~~L~~gGRl~VIs 244 (314) T COG0275 220 LEELEEALEAALDLLKPGGRLAVIS 244 (314) T ss_pred HHHHHHHHHHHHHhhCCCcEEEEEE Confidence 3444578999999999999998753 No 179 >KOG1271|consensus Probab=24.35 E-value=88 Score=23.21 Aligned_cols=35 Identities=34% Similarity=0.641 Sum_probs=27.6 Q ss_pred CCceeeeCC---CCCchhhHHHHHHhcccCcEEEEEec Q psy4127 10 HFDAIDLDP---FGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 10 ~fD~IDlDP---fGSp~pfldsA~~av~~gGll~vTaT 44 (75) -+|.|-|-| =|-++.|+|..=+.++.||++-||+- T Consensus 145 T~DAisLs~d~~~~r~~~Y~d~v~~ll~~~gifvItSC 182 (227) T KOG1271|consen 145 TLDAISLSPDGPVGRLVVYLDSVEKLLSPGGIFVITSC 182 (227) T ss_pred ceeeeecCCCCcccceeeehhhHhhccCCCcEEEEEec Confidence 355666653 45668899999999999999999984 No 180 >PRK10857 DNA-binding transcriptional regulator IscR; Provisional Probab=24.02 E-value=87 Score=21.39 Aligned_cols=25 Identities=28% Similarity=0.409 Sum_probs=22.2 Q ss_pred CCCCchhhHHHHHHhcccCcEEEEE Q psy4127 18 PFGNPTRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 18 PfGSp~pfldsA~~av~~gGll~vT 42 (75) -.|-|.+||..-++.+++.|||-.+ T Consensus 34 ~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164) T PRK10857 34 RQGISLSYLEQLFSRLRKNGLVSSV 58 (164) T ss_pred HHCcCHHHHHHHHHHHHHCCCEEeC Confidence 4678999999999999999999864 No 181 >PRK11202 DNA-binding transcriptional repressor FabR; Provisional Probab=23.80 E-value=35 Score=23.06 Aligned_cols=40 Identities=20% Similarity=0.328 Sum_probs=35.6 Q ss_pred hhHHHHHH-hcccCcEEEEEecCcccccCCChhHHHHHhcC Q psy4127 24 RFLDAAVS-SLRDGGLLLVTCTDMAVLCGNTPETCYVKYNA 63 (75) Q Consensus 24 pfldsA~~-av~~gGll~vTaTD~a~L~G~~~~~~~r~Yg~ 63 (75) ..|++|++ .....|+-.+|=.|.+--.|-.+..-|+.|++ T Consensus 15 ~Il~aA~~~l~~~~G~~~~si~~IA~~Agvs~~t~Y~hF~s 55 (203) T PRK11202 15 ALIDAAFSQLSAERSFSSLSLREVAREAGIAPTSFYRHFRD 55 (203) T ss_pred HHHHHHHHHHHhcCCcccCCHHHHHHHhCCCcchHHHHCCC Confidence 56899997 45899999999999999999999999998875 No 182 >cd00824 PTBI IRS-like phosphotyrosine-binding domain. IRS-like phosphotyrosine-binding domain (PTBi); This domain has a PH-like fold and is found in insulin receptor substrate molecules and in other eukaryotic signaling molecules such as FRS2 and Dok. IRS and Dok molecules have an N-terminal PH domain, which is followed by an IRS-like PTB domain. FRS2 just has an N-terminal PTBi domain. This PTBi domain is shorter than the PTB domain which is found in SHC, Numb and other proteins. The PTBi domain binds to phosphotyrosines which are in NPXpY motifs. Probab=23.44 E-value=30 Score=22.39 Aligned_cols=31 Identities=16% Similarity=0.111 Sum_probs=22.8 Q ss_pred cCcEEEEEecCcccccCC-------ChhHHHHHhcCcc Q psy4127 35 DGGLLLVTCTDMAVLCGN-------TPETCYVKYNAVS 65 (75) Q Consensus 35 ~gGll~vTaTD~a~L~G~-------~~~~~~r~Yg~~~ 65 (75) -.++|++|++.+..+... =|-.++|+||... T Consensus 21 G~y~L~lt~~~l~L~~~~~~~~~~~wpl~~lRRyG~~~ 58 (104) T cd00824 21 GSYRLCLTSKELTLVKLGSRVALVVWPLMFLRRYGYDS 58 (104) T ss_pred eeEEEEECCCEEEEEecCCCceEEEeehHHeeecccCC Confidence 356889998887766655 3667999999753 No 183 >PLN02232 ubiquinone biosynthesis methyltransferase Probab=23.31 E-value=88 Score=20.58 Aligned_cols=35 Identities=20% Similarity=0.362 Sum_probs=24.9 Q ss_pred CCCceeeeCCCC-----CchhhHHHHHHhcccCcEEEEEec Q psy4127 9 RHFDAIDLDPFG-----NPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 9 ~~fD~IDlDPfG-----Sp~pfldsA~~av~~gGll~vTaT 44 (75) +.||.|=. .|+ .+..+|....+.+|+||.+.+.-. T Consensus 43 ~~fD~v~~-~~~l~~~~d~~~~l~ei~rvLkpGG~l~i~d~ 82 (160) T PLN02232 43 CEFDAVTM-GYGLRNVVDRLRAMKEMYRVLKPGSRVSILDF 82 (160) T ss_pred CCeeEEEe-cchhhcCCCHHHHHHHHHHHcCcCeEEEEEEC Confidence 35777744 233 345678888899999999998633 No 184 >TIGR03366 HpnZ_proposed putative phosphonate catabolism associated alcohol dehydrogenase. This clade of zinc-binding alcohol dehydrogenases (members of pfam00107) are repeatedly associated with genes proposed to be involved with the catabolism of phosphonate compounds. Probab=23.29 E-value=1.4e+02 Score=20.87 Aligned_cols=32 Identities=25% Similarity=0.312 Sum_probs=25.2 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCcEEEEEe Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTa 43 (75) .+|+| +|.-|++. -++.++++++.+|-+.+-. T Consensus 187 g~d~v-id~~G~~~-~~~~~~~~l~~~G~iv~~G 218 (280) T TIGR03366 187 GVDVA-LEFSGATA-AVRACLESLDVGGTAVLAG 218 (280) T ss_pred CCCEE-EECCCChH-HHHHHHHHhcCCCEEEEec Confidence 47877 78888764 4667899999999887655 No 185 >PRK10634 tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; Provisional Probab=23.03 E-value=73 Score=22.11 Aligned_cols=39 Identities=13% Similarity=0.111 Sum_probs=24.7 Q ss_pred hhhHHHHHHhcccCcEEEEEecCccccc-C--CChhHHHHHhc Q psy4127 23 TRFLDAAVSSLRDGGLLLVTCTDMAVLC-G--NTPETCYVKYN 62 (75) Q Consensus 23 ~pfldsA~~av~~gGll~vTaTD~a~L~-G--~~~~~~~r~Yg 62 (75) ..=++.|++++++||++++= ||+---. + .++++.-+-|- T Consensus 7 ~~~i~~a~~~L~~G~vv~~P-TdTvYgL~~~~~n~~Av~ri~~ 48 (190) T PRK10634 7 GDAIAAAVDVLNEERVIAYP-TEAVFGVGCDPDSETAVMRLLE 48 (190) T ss_pred HHHHHHHHHHHHCCCEEEEe-CCchhhhhcCCCCHHHHHHHHH Confidence 44678899999999999874 6664322 2 24454444443 No 186 >cd05799 PGM2 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and deoxyribose-1-phosphate to the corresponding 5-phosphopentoses. PGM2L1 is thought to catalyze the 1,3-bisphosphoglycerate-dependent synthesis of glucose 1,6-bisphosphate and other aldose-bisphosphates that serve as cofactors for several sugar phosphomutases and possibly also as regulators of glycolytic enzymes. PGM2 and PGM2L1 belong to the alpha-D-phosphohexomutase superfamily which includes 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/ph Probab=22.52 E-value=1.3e+02 Score=23.39 Aligned_cols=34 Identities=24% Similarity=0.309 Sum_probs=27.3 Q ss_pred CCCceeeeC-CCCCchhhHHHHHHhcccCcEEEEEec Q psy4127 9 RHFDAIDLD-PFGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 9 ~~fD~IDlD-PfGSp~pfldsA~~av~~gGll~vTaT 44 (75) ...+++|+. + .|+|.+.-|++..+-.|=+.||+. T Consensus 72 ~Gi~V~~~g~~--~ptP~~~~~i~~~~~~gGI~iTaS 106 (487) T cd05799 72 NGIKVYLFDDL--RPTPLLSFAVRHLGADAGIMITAS 106 (487) T ss_pred CCCEEEEeCCC--CCCcHHHHHHHHhCCCeeEEEEee Confidence 458999998 5 588889999988876677788874 No 187 >PF06080 DUF938: Protein of unknown function (DUF938); InterPro: IPR010342 This family consists of several hypothetical proteins from both prokaryotes and eukaryotes. The function of this family is unknown. Probab=22.39 E-value=35 Score=24.63 Aligned_cols=29 Identities=24% Similarity=0.571 Sum_probs=24.3 Q ss_pred eeeeCCCCCchhhHHHHHHhcccCcEEEE Q psy4127 13 AIDLDPFGNPTRFLDAAVSSLRDGGLLLV 41 (75) Q Consensus 13 ~IDlDPfGSp~pfldsA~~av~~gGll~v 41 (75) .+.|=|+-...-++..|-+.++.||+|++ T Consensus 111 ~lHI~p~~~~~~lf~~a~~~L~~gG~L~~ 139 (204) T PF06080_consen 111 MLHISPWSAVEGLFAGAARLLKPGGLLFL 139 (204) T ss_pred HHHhcCHHHHHHHHHHHHHhCCCCCEEEE Confidence 34677787777889999999999999986 No 188 >PRK00517 prmA ribosomal protein L11 methyltransferase; Reviewed Probab=22.35 E-value=1.3e+02 Score=21.17 Aligned_cols=34 Identities=24% Similarity=0.365 Sum_probs=24.4 Q ss_pred CCceeeeCCCCCc-hhhHHHHHHhcccCcEEEEEe Q psy4127 10 HFDAIDLDPFGNP-TRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 10 ~fD~IDlDPfGSp-~pfldsA~~av~~gGll~vTa 43 (75) .||+|=.+....+ ..++..+.+.+++||.+.++. T Consensus 179 ~fD~Vvani~~~~~~~l~~~~~~~LkpgG~lilsg 213 (250) T PRK00517 179 KADVIVANILANPLLELAPDLARLLKPGGRLILSG 213 (250) T ss_pred CcCEEEEcCcHHHHHHHHHHHHHhcCCCcEEEEEE Confidence 4888854443322 356778889999999999974 No 189 >TIGR02266 gmx_TIGR02266 Myxococcus xanthus paralogous domain TIGR02266. This domain is related to Type IV pilus assembly protein PilZ (Pfam model pfam07238). It is found in at least 12 copies in Myxococcus xanthus DK 1622. Probab=22.16 E-value=1e+02 Score=18.03 Aligned_cols=27 Identities=26% Similarity=0.418 Sum_probs=20.8 Q ss_pred CCchhhHHHHHHhcccCcEEEEEecCc Q psy4127 20 GNPTRFLDAAVSSLRDGGLLLVTCTDM 46 (75) Q Consensus 20 GSp~pfldsA~~av~~gGll~vTaTD~ 46 (75) .+...+..+-+..++.||+...|..+. T Consensus 11 ~~~~~~~~~~~~diS~gG~~~~~~~~~ 37 (96) T TIGR02266 11 RTDSEFLRDYSINLSKGGLFIRTRKPL 37 (96) T ss_pred CChhhHHHHHhhhcCCceEEEecCCCc Confidence 445567788888899999998876554 No 190 >PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A. Probab=22.15 E-value=50 Score=17.95 Aligned_cols=12 Identities=25% Similarity=0.653 Sum_probs=10.1 Q ss_pred HHHHHHhcccCc Q psy4127 26 LDAAVSSLRDGG 37 (75) Q Consensus 26 ldsA~~av~~gG 37 (75) |..||++|++|+ T Consensus 5 l~~Ai~~v~~g~ 16 (45) T PF05225_consen 5 LQKAIEAVKNGK 16 (45) T ss_dssp HHHHHHHHHTTS T ss_pred HHHHHHHHHhCC Confidence 678999999877 No 191 >PF15540 Toxin_62: Putative toxin 62 Probab=22.07 E-value=51 Score=22.04 Aligned_cols=29 Identities=31% Similarity=0.424 Sum_probs=22.3 Q ss_pred CceeeeCCCCCchhhHHHHHHhcccCcEE Q psy4127 11 FDAIDLDPFGNPTRFLDAAVSSLRDGGLL 39 (75) Q Consensus 11 fD~IDlDPfGSp~pfldsA~~av~~gGll 39 (75) --.+|||+.|.-+-+=|+-..|-++-|+- T Consensus 8 n~~~diD~rgtg~~y~~aldeAfrRTg~p 36 (113) T PF15540_consen 8 NPARDIDPRGTGKSYRDALDEAFRRTGVP 36 (113) T ss_pred CcccccccccccchhhHHHHHHHHhhCCC Confidence 46799999999988887766776665553 No 192 >PF02384 N6_Mtase: N-6 DNA Methylase; InterPro: IPR003356 This domain is fpound in N-6 adenine-specific DNA methylase (2.1.1.72 from EC) from Type I and Type IC restriction systems. These enzymes are responsible for the methylation of specific DNA sequences in order to prevent the host from digesting its own genome via its restriction enzymes. These methylases have the same sequence specificity as their corresponding restriction enzymes. The type I restriction and modification system is composed of three polypeptides R, M and S. The M and S subunits together form a methyltransferase that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. In the presence of the R subunit, the complex can also act as an endonuclease, binding to the same target sequence but cutting the DNA some distance from this site. Whether the DNA is cut or modified depends on the methylation state of the target sequence. When the target site is unmodified, the DNA is cut. When the target site is hemimethylated, the complex acts as a maintenance methyltransferase, modifying the DNA so that both strands become methylated.; GO: 0003677 DNA binding, 0008170 N-methyltransferase activity, 0006306 DNA methylation; PDB: 2F8L_A 2Y7C_C 2Y7H_C 2AR0_B 3KHK_A 3LKD_A 2OKC_B. Probab=22.04 E-value=76 Score=22.80 Aligned_cols=37 Identities=24% Similarity=0.392 Sum_probs=26.3 Q ss_pred hhHHHHHHhcccCcEEEEEecCcccccCCChhHHHHHh Q psy4127 24 RFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKY 61 (75) Q Consensus 24 pfldsA~~av~~gGll~vTaTD~a~L~G~~~~~~~r~Y 61 (75) .||.-+++.++.||.+++=-.+..... ...+.-+|+| T Consensus 164 ~Fi~~~l~~Lk~~G~~~~Ilp~~~L~~-~~~~~~iR~~ 200 (311) T PF02384_consen 164 AFIEHALSLLKPGGRAAIILPNGFLFS-SSSEKKIRKY 200 (311) T ss_dssp HHHHHHHHTEEEEEEEEEEEEHHHHHG-STHHHHHHHH T ss_pred hhHHHHHhhcccccceeEEecchhhhc-cchHHHHHHH Confidence 699999999999998877666554433 3344556655 No 193 >PHA03356 tegument protein UL11; Provisional Probab=21.85 E-value=48 Score=21.40 Aligned_cols=10 Identities=50% Similarity=0.999 Sum_probs=8.4 Q ss_pred CCCceeeeCC Q psy4127 9 RHFDAIDLDP 18 (75) Q Consensus 9 ~~fD~IDlDP 18 (75) +.||.||||+ T Consensus 31 ~~fD~vdles 40 (93) T PHA03356 31 HEFDAVDLES 40 (93) T ss_pred cccceEeecc Confidence 4699999995 No 194 >PF08242 Methyltransf_12: Methyltransferase domain; InterPro: IPR013217 Methyl transfer from the ubiquitous donor S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents a methyltransferase domain found in a large variety of SAM-dependent methyltransferases including, but not limited to: Hexaprenyldihydroxybenzoate methyltransferase (2.1.1.114 from EC), a mitochodrial enzyme involved in ubiquinone biosynthesis [] Fatty acid synthase (2.3.1.85 from EC), a biosynthetic enzyme catalysing the formation of long-chain fatty acids Glycine N-methyltransferase (2.1.1.20 from EC) which catalyses the SAM-dependent methylation of glycine to form sarcosine and may play a role in regulating the methylation potential of the cell [] Enniatin synthetase, involved in non-ribosomal biosynthesis of cyclohexadepsipeptidase, enniatin [] Histamine N-methyltransferase (2.1.1.8 from EC), a SAM-dependent histamine-inactivating enzyme [] A probable cobalt-precorrin-6Y C(15)-methyltransferase thought to be involved in adenosylcobalamin biosynthesis [] Structural studies show that this domain forms the Rossman-like alpha-beta fold typical of SAM-dependent methyltransferases [, , ].; PDB: 2VZ8_A 2VZ9_A. Probab=21.70 E-value=50 Score=19.32 Aligned_cols=19 Identities=26% Similarity=0.426 Sum_probs=12.6 Q ss_pred CchhhHHHHHHhcccCcEE Q psy4127 21 NPTRFLDAAVSSLRDGGLL 39 (75) Q Consensus 21 Sp~pfldsA~~av~~gGll 39 (75) .+..+|....+.+++||.| T Consensus 81 ~~~~~l~~~~~~L~pgG~l 99 (99) T PF08242_consen 81 DIEAVLRNIYRLLKPGGIL 99 (99) T ss_dssp -HHHHHHHHTTT-TSS-EE T ss_pred hHHHHHHHHHHHcCCCCCC Confidence 4567778778889999976 No 195 >PRK09480 slmA division inhibitor protein; Provisional Probab=21.62 E-value=42 Score=21.79 Aligned_cols=40 Identities=20% Similarity=0.303 Sum_probs=34.1 Q ss_pred hhHHHHHHhccc-CcEEEEEecCcccccCCChhHHHHHhcCc Q psy4127 24 RFLDAAVSSLRD-GGLLLVTCTDMAVLCGNTPETCYVKYNAV 64 (75) Q Consensus 24 pfldsA~~av~~-gGll~vTaTD~a~L~G~~~~~~~r~Yg~~ 64 (75) .-+++|++.+.. +| =.+|=.|.+--+|-.+.+-|+.|+.. T Consensus 14 ~Il~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K 54 (194) T PRK09480 14 QILQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSK 54 (194) T ss_pred HHHHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCH Confidence 457888988754 58 99999999999999999999988863 No 196 >smart00138 MeTrc Methyltransferase, chemotaxis proteins. Methylates methyl-accepting chemotaxis proteins to form gamma-glutamyl methyl ester residues. Probab=21.55 E-value=1e+02 Score=22.26 Aligned_cols=25 Identities=20% Similarity=0.452 Sum_probs=20.6 Q ss_pred hhHHHHHHhcccCcEEEEEecCccc Q psy4127 24 RFLDAAVSSLRDGGLLLVTCTDMAV 48 (75) Q Consensus 24 pfldsA~~av~~gGll~vTaTD~a~ 48 (75) ..+....+.+++||+|.+..++.-. T Consensus 223 ~~l~~l~~~L~pGG~L~lg~~E~~~ 247 (264) T smart00138 223 KLLNRFAEALKPGGYLFLGHSESLP 247 (264) T ss_pred HHHHHHHHHhCCCeEEEEECcccCC Confidence 3666667899999999999998754 No 197 >PF08704 GCD14: tRNA methyltransferase complex GCD14 subunit; InterPro: IPR014816 GCD14 is a subunit of the tRNA methyltransferase complex and is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA []. ; GO: 0016429 tRNA (adenine-N1-)-methyltransferase activity, 0030488 tRNA methylation; PDB: 2YVL_C 1YB2_A 2B25_B 1O54_A 2PWY_B 1I9G_A 3LGA_B 3LHD_C 3MB5_A. Probab=21.54 E-value=1e+02 Score=22.59 Aligned_cols=33 Identities=30% Similarity=0.416 Sum_probs=26.4 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhc-ccCcEEEEE Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSL-RDGGLLLVT 42 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av-~~gGll~vT 42 (75) +.+|.|=||= ..|...|+.|.+++ +.||.||+= T Consensus 112 ~~~DavfLDl-p~Pw~~i~~~~~~L~~~gG~i~~f 145 (247) T PF08704_consen 112 SDFDAVFLDL-PDPWEAIPHAKRALKKPGGRICCF 145 (247) T ss_dssp TSEEEEEEES-SSGGGGHHHHHHHE-EEEEEEEEE T ss_pred CcccEEEEeC-CCHHHHHHHHHHHHhcCCceEEEE Confidence 3478887774 45888899999999 899999863 No 198 >PF13602 ADH_zinc_N_2: Zinc-binding dehydrogenase; PDB: 3TQH_A 2VN8_A 3GOH_A 4A27_A. Probab=21.49 E-value=18 Score=22.13 Aligned_cols=31 Identities=29% Similarity=0.494 Sum_probs=19.0 Q ss_pred CCCCceeeeCCCCCch-hhHHHHHHhcccCcEEE Q psy4127 8 GRHFDAIDLDPFGNPT-RFLDAAVSSLRDGGLLL 40 (75) Q Consensus 8 ~~~fD~IDlDPfGSp~-pfldsA~~av~~gGll~ 40 (75) .+.||+| +|..|.+. .+++.+.+++ .+|-+. T Consensus 17 ~~~~D~V-iD~~g~~~~~~~~~~~~~l-~~G~~v 48 (127) T PF13602_consen 17 PGGVDVV-IDTVGQTGESLLDASRKLL-PGGRVV 48 (127) T ss_dssp TS-EEEE-EESS-CCHHHCGGGCCCTE-EEEEEE T ss_pred CCCceEE-EECCCCccHHHHHHHHHHC-CCCEEE Confidence 4568876 78888333 4557777888 767653 No 199 >cd08242 MDR_like Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. This group contains members identified as related to zinc-dependent alcohol dehydrogenase and other members of the MDR family, including threonine dehydrogenase. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group includes various activities, including the founding alcohol dehydrogenase (ADH), quinone reducta Probab=21.28 E-value=1.7e+02 Score=20.41 Aligned_cols=30 Identities=23% Similarity=0.459 Sum_probs=23.2 Q ss_pred CCceeeeCCCCCchhhHHHHHHhcccCcEEEE Q psy4127 10 HFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLV 41 (75) Q Consensus 10 ~fD~IDlDPfGSp~pfldsA~~av~~gGll~v 41 (75) .+|+| +|..|. ...++.++++++++|-+.+ T Consensus 214 ~~d~v-id~~g~-~~~~~~~~~~l~~~g~~v~ 243 (319) T cd08242 214 GFDVV-VEATGS-PSGLELALRLVRPRGTVVL 243 (319) T ss_pred CCCEE-EECCCC-hHHHHHHHHHhhcCCEEEE Confidence 47766 678885 4567889999999997765 No 200 >PRK00014 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional Probab=21.22 E-value=1e+02 Score=22.76 Aligned_cols=19 Identities=26% Similarity=0.371 Sum_probs=17.0 Q ss_pred HHHHHHhcccCcEEEEEec Q psy4127 26 LDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 26 ldsA~~av~~gGll~vTaT 44 (75) ++.|+++++.|..+-|+=- T Consensus 21 i~~ai~al~~Gk~Viv~Dd 39 (230) T PRK00014 21 LERALQHLRIGRPVILMDD 39 (230) T ss_pred HHHHHHHHHCCCeEEEEEC Confidence 9999999999999999853 No 201 >PRK13944 protein-L-isoaspartate O-methyltransferase; Provisional Probab=21.16 E-value=1.9e+02 Score=19.66 Aligned_cols=34 Identities=32% Similarity=0.523 Sum_probs=23.7 Q ss_pred CCCceeeeCCCCCchhhHHHHHHhcccCcEEEEEec Q psy4127 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCT 44 (75) Q Consensus 9 ~~fD~IDlDPfGSp~pfldsA~~av~~gGll~vTaT 44 (75) ..||.|=++.-. .-+.+..++.+++||.|.+.-. T Consensus 141 ~~fD~Ii~~~~~--~~~~~~l~~~L~~gG~lvi~~~ 174 (205) T PRK13944 141 APFDAIIVTAAA--STIPSALVRQLKDGGVLVIPVE 174 (205) T ss_pred CCccEEEEccCc--chhhHHHHHhcCcCcEEEEEEc Confidence 468998777322 2344666788999999988643 No 202 >PF01555 N6_N4_Mtase: DNA methylase; InterPro: IPR002941 This domain is found in DNA methylases. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. This family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases. N-4 cytosine-specific DNA methylases (2.1.1.113 from EC) [] are enzymes that specifically methylate the amino group at the C-4 position of cytosines in DNA. Such enzymes are found as components of type II restriction-modification systems in prokaryotes. Such enzymes recognise a specific sequence in DNA and methylate a cytosine in that sequence. By this action they protect DNA from cleavage by type II restriction enzymes that recognise the same sequence. N-6 adenine-specific DNA methylases (2.1.1.72 from EC) (A-Mtase) are enzymes that specifically methylate the amino group at the C-6 position of adenines in DNA. Such enzymes are found in the three existing types of bacterial restriction-modification systems (in type I system the A-Mtase is the product of the hsdM gene, and in type III it is the product of the mod gene). All of these enzymes recognise a specific sequence in DNA and methylate an adenine in that sequence.; GO: 0003677 DNA binding, 0008170 N-methyltransferase activity, 0006306 DNA methylation; PDB: 2ZIF_A 2ZIE_A 2ZIG_A 1NW6_A 1NW8_A 1NW7_A 1NW5_A 1EG2_A 1BOO_A 1G60_B .... Probab=20.86 E-value=87 Score=20.52 Aligned_cols=26 Identities=19% Similarity=0.442 Sum_probs=20.2 Q ss_pred hhhHHHHHHhcccCcEEEEEecCccc Q psy4127 23 TRFLDAAVSSLRDGGLLLVTCTDMAV 48 (75) Q Consensus 23 ~pfldsA~~av~~gGll~vTaTD~a~ 48 (75) ..++..+.+.++++|.++|-.-|... T Consensus 36 ~~~~~~~~rvLk~~g~~~i~~~~~~~ 61 (231) T PF01555_consen 36 EEWLKECYRVLKPGGSIFIFIDDREI 61 (231) T ss_dssp HHHHHHHHHHEEEEEEEEEEE-CCEE T ss_pred HHHHHHHHhhcCCCeeEEEEecchhh Confidence 35677788999999999999888554 No 203 >KOG2795|consensus Probab=20.55 E-value=48 Score=26.30 Aligned_cols=39 Identities=15% Similarity=0.273 Sum_probs=27.3 Q ss_pred CceeeeCCCC----------CchhhHHHHHHhcccCcEEEEEecCcccc Q psy4127 11 FDAIDLDPFG----------NPTRFLDAAVSSLRDGGLLLVTCTDMAVL 49 (75) Q Consensus 11 fD~IDlDPfG----------Sp~pfldsA~~av~~gGll~vTaTD~a~L 49 (75) |=.+|-|||| |-..+.++.-..+..--+|++=.+|.-.. T Consensus 249 ~~LvDaDP~Gi~I~~~Yk~GS~~ms~e~~~~~~p~I~wiGl~psD~~~~ 297 (372) T KOG2795|consen 249 YGLVDADPYGIEILLTYKYGSKSMSYESHGLTVPTIRWIGLLPSDLEVK 297 (372) T ss_pred EEEeecCCcceEEEEEeeeCccccccccccccCCcceEEeechhhhhhc Confidence 5689999976 55666666666666667777766666543 No 204 >PRK01683 trans-aconitate 2-methyltransferase; Provisional Probab=20.37 E-value=1.1e+02 Score=21.27 Aligned_cols=35 Identities=26% Similarity=0.340 Sum_probs=24.9 Q ss_pred CCCceeeeCC----CCCchhhHHHHHHhcccCcEEEEEe Q psy4127 9 RHFDAIDLDP----FGNPTRFLDAAVSSLRDGGLLLVTC 43 (75) Q Consensus 9 ~~fD~IDlDP----fGSp~pfldsA~~av~~gGll~vTa 43 (75) +.||+|=... ...+..++....+.+++||.+.++. T Consensus 92 ~~fD~v~~~~~l~~~~d~~~~l~~~~~~LkpgG~~~~~~ 130 (258) T PRK01683 92 QALDLIFANASLQWLPDHLELFPRLVSLLAPGGVLAVQM 130 (258) T ss_pred CCccEEEEccChhhCCCHHHHHHHHHHhcCCCcEEEEEC Confidence 3577764331 1235678888999999999999974 No 205 >PRK02260 S-ribosylhomocysteinase; Provisional Probab=20.36 E-value=68 Score=22.46 Aligned_cols=23 Identities=30% Similarity=0.495 Sum_probs=16.2 Q ss_pred cccccCCCCceeeeCCCCCchhh Q psy4127 3 LEKIRGRHFDAIDLDPFGNPTRF 25 (75) Q Consensus 3 m~~~~~~~fD~IDlDPfGSp~pf 25 (75) |.+|.+...++||+=|.|+=+-| T Consensus 64 lRn~~~~~~~iI~~sPMGCrTGF 86 (158) T PRK02260 64 LRNHLDGGVEIIDISPMGCRTGF 86 (158) T ss_pred HhhCccCCceEEEECCCcccccc Confidence 44454456789999999975544 No 206 >COG4798 Predicted methyltransferase [General function prediction only] Probab=20.19 E-value=93 Score=23.24 Aligned_cols=23 Identities=26% Similarity=0.486 Sum_probs=18.9 Q ss_pred CCchhhHHHHHHhcccCcEEEEE Q psy4127 20 GNPTRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 20 GSp~pfldsA~~av~~gGll~vT 42 (75) |....+-.+.++++|.||++.|- T Consensus 143 ~~A~~vna~vf~~LKPGGv~~V~ 165 (238) T COG4798 143 ATAAKVNAAVFKALKPGGVYLVE 165 (238) T ss_pred chHHHHHHHHHHhcCCCcEEEEE Confidence 45567777888999999999874 No 207 >PF05219 DREV: DREV methyltransferase; InterPro: IPR007884 This family contains DREV protein homologues from several eukaryotes. The function of this protein is unknown []. However, these proteins appear to be related to other methyltransferases. Probab=20.03 E-value=1.1e+02 Score=23.06 Aligned_cols=22 Identities=23% Similarity=0.454 Sum_probs=18.6 Q ss_pred CchhhHHHHHHhcccCcEEEEE Q psy4127 21 NPTRFLDAAVSSLRDGGLLLVT 42 (75) Q Consensus 21 Sp~pfldsA~~av~~gGll~vT 42 (75) .|...|...-++++.+|.|-+. T Consensus 166 ~P~~LL~~i~~~l~p~G~lilA 187 (265) T PF05219_consen 166 RPLTLLRDIRRALKPNGRLILA 187 (265) T ss_pred CHHHHHHHHHHHhCCCCEEEEE Confidence 6777888888999999998764 Done!