Query gi|254780406|ref|YP_003064819.1| putative ribosomal large subunit pseudouridine synthase B [Candidatus Liberibacter asiaticus str. psy62] Match_columns 354 No_of_seqs 197 out of 4149 Neff 8.4 Searched_HMMs 39220 Date Sun May 29 16:19:50 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780406.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK10700 23S rRNA pseudouridyl 100.0 0 0 520.4 25.5 240 12-252 1-248 (291) 2 PRK10475 23S rRNA pseudouridin 100.0 0 0 514.1 25.6 234 10-250 3-238 (290) 3 COG1187 RsuA 16S rRNA uridine- 100.0 0 0 492.4 24.0 237 12-248 1-245 (248) 4 PRK10839 16S rRNA pseudouridyl 100.0 0 0 474.7 22.2 227 14-244 1-230 (231) 5 PRK11394 23S rRNA pseudouridin 100.0 0 0 360.3 14.7 167 70-238 26-207 (207) 6 cd02556 PseudoU_synth_RluB Pse 100.0 0 0 348.1 14.4 165 74-238 1-167 (167) 7 TIGR00093 TIGR00093 conserved 100.0 0 0 343.0 12.1 160 79-238 1-185 (185) 8 cd02553 PseudoU_synth_RsuA Pse 100.0 0 0 339.3 14.1 163 74-241 1-167 (167) 9 cd02555 PSSA_1 PSSA_1: Pseudou 100.0 0 0 337.3 14.1 165 72-240 3-175 (177) 10 cd02554 PseudoU_synth_RluF Pse 100.0 0 0 332.9 14.9 164 74-243 1-164 (164) 11 cd02566 PseudoU_synth_RluE Pse 100.0 0 0 310.7 13.5 152 75-228 1-168 (168) 12 cd02870 PseudoU_synth_RsuA_lik 100.0 8.7E-39 2.2E-43 264.1 11.2 146 75-220 1-146 (146) 13 TIGR00005 rluA_subfam pseudour 100.0 8.3E-32 2.1E-36 220.2 10.6 212 9-222 1-262 (337) 14 PRK11180 rluD 23S rRNA pseudou 100.0 3.8E-31 9.7E-36 216.0 9.7 215 6-222 10-255 (325) 15 COG0564 RluA Pseudouridylate s 100.0 3.6E-30 9.2E-35 209.8 11.9 216 5-223 4-252 (289) 16 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 8.1E-31 2.1E-35 213.9 8.5 146 75-220 1-154 (154) 17 PRK11025 23S rRNA pseudouridyl 100.0 1E-29 2.6E-34 207.0 8.7 215 6-224 12-265 (317) 18 cd02558 PSRA_1 PSRA_1: Pseudou 99.9 6.6E-24 1.7E-28 170.4 7.5 183 39-224 3-209 (246) 19 pfam00849 PseudoU_synth_2 RNA 99.8 2.2E-20 5.7E-25 148.2 4.5 133 75-207 1-151 (151) 20 cd02557 PseudoU_synth_ScRIB2 P 99.8 3.5E-19 8.9E-24 140.6 5.2 154 69-224 19-189 (213) 21 PRK11112 tRNA pseudouridine sy 99.8 2.7E-19 7E-24 141.3 3.8 155 69-225 5-186 (257) 22 PRK10158 23S rRNA/tRNA pseudou 99.8 1E-18 2.6E-23 137.8 5.7 152 69-222 17-183 (219) 23 KOG1919 consensus 99.7 2.7E-17 7E-22 128.7 10.0 204 16-222 46-282 (371) 24 cd02563 PseudoU_synth_TruC tRN 99.7 2.9E-18 7.4E-23 134.8 4.6 154 69-224 4-184 (223) 25 cd02869 PseudoU_synth_RluCD_li 99.7 3.4E-17 8.7E-22 128.1 4.3 149 75-225 1-168 (185) 26 TIGR01621 RluA-like pseudourid 99.4 2.1E-13 5.2E-18 104.3 2.8 140 70-214 6-161 (222) 27 cd00165 S4 S4/Hsp/ tRNA synthe 99.1 2.8E-10 7.1E-15 84.6 6.2 66 14-79 1-70 (70) 28 smart00363 S4 S4 RNA-binding d 99.0 6.5E-10 1.7E-14 82.3 6.0 55 14-68 1-56 (60) 29 pfam01479 S4 S4 domain. The S4 98.9 2.9E-09 7.4E-14 78.2 4.5 47 14-60 1-48 (48) 30 COG1188 Ribosome-associated he 98.5 2.3E-07 6E-12 66.2 5.3 51 11-62 6-57 (100) 31 TIGR03069 PS_II_S4 photosystem 98.5 3.2E-07 8.1E-12 65.3 5.6 53 12-64 182-234 (257) 32 COG1189 Predicted rRNA methyla 98.5 4.8E-07 1.2E-11 64.2 6.3 55 12-66 1-56 (245) 33 TIGR01017 rpsD_bact ribosomal 98.4 3.3E-07 8.5E-12 65.2 3.6 53 14-66 100-153 (217) 34 COG0522 RpsD Ribosomal protein 98.3 1.7E-06 4.4E-11 60.7 5.9 56 14-69 94-150 (205) 35 COG2302 Uncharacterized conser 98.2 1.7E-06 4.2E-11 60.8 4.7 58 7-64 174-231 (257) 36 PRK04270 H/ACA RNA-protein com 98.2 4.4E-06 1.1E-10 58.1 6.1 152 66-227 15-188 (300) 37 PRK12565 30S ribosomal protein 98.2 4.4E-06 1.1E-10 58.1 5.8 53 14-66 88-141 (197) 38 PRK10348 ribosome-associated h 98.1 3.7E-06 9.4E-11 58.6 5.0 56 8-64 3-59 (133) 39 PRK04099 truB tRNA pseudouridi 98.1 1.5E-05 3.9E-10 54.7 8.1 144 74-227 3-202 (272) 40 CHL00113 rps4 ribosomal protei 98.1 4.5E-06 1.2E-10 58.1 4.6 53 14-66 89-142 (201) 41 cd02868 PseudoU_synth_hTruB2_l 98.1 1.5E-05 3.8E-10 54.8 7.0 156 75-233 2-217 (226) 42 PRK00020 truB tRNA pseudouridi 98.1 8.3E-06 2.1E-10 56.4 5.6 156 73-245 10-224 (244) 43 TIGR00478 tly hemolysin A; Int 98.0 6.4E-06 1.6E-10 57.1 4.4 53 15-67 1-54 (240) 44 PRK00989 truB tRNA pseudouridi 98.0 3.4E-05 8.7E-10 52.5 7.9 146 73-227 9-209 (235) 45 PRK05327 rpsD 30S ribosomal pr 98.0 8.9E-06 2.3E-10 56.2 4.7 53 14-66 92-145 (201) 46 PRK02193 truB tRNA pseudouridi 98.0 3.4E-05 8.6E-10 52.6 7.3 155 75-243 2-215 (279) 47 PRK01851 truB tRNA pseudouridi 98.0 4.3E-05 1.1E-09 51.9 7.7 151 73-233 17-224 (310) 48 cd02572 PseudoU_synth_hDyskeri 97.9 6.3E-05 1.6E-09 50.9 8.3 144 74-227 3-170 (182) 49 PRK05033 truB tRNA pseudouridi 97.9 4.5E-05 1.1E-09 51.8 7.3 145 73-227 12-212 (314) 50 PRK00130 truB tRNA pseudouridi 97.9 5E-05 1.3E-09 51.5 7.4 143 74-227 3-202 (289) 51 PRK04642 truB tRNA pseudouridi 97.9 6.4E-05 1.6E-09 50.8 7.4 146 72-227 9-211 (300) 52 cd02573 PseudoU_synth_EcTruB P 97.9 5.3E-05 1.3E-09 51.3 6.5 143 75-227 2-203 (277) 53 PRK11507 hypothetical protein; 97.8 4.2E-05 1.1E-09 51.9 5.5 62 8-69 6-68 (70) 54 PRK01528 truB tRNA pseudouridi 97.8 7.9E-05 2E-09 50.2 6.7 145 73-227 3-205 (293) 55 PRK03287 truB tRNA pseudouridi 97.8 0.00013 3.3E-09 48.8 7.7 149 71-227 7-214 (298) 56 cd00506 PseudoU_synth_TruB_lik 97.8 9.6E-05 2.5E-09 49.7 6.9 143 75-227 2-203 (210) 57 PRK05389 truB tRNA pseudouridi 97.6 0.00021 5.3E-09 47.6 6.9 151 73-233 13-221 (305) 58 PRK02484 truB tRNA pseudouridi 97.6 0.00027 6.8E-09 46.9 6.7 144 74-227 4-210 (293) 59 PRK01550 truB tRNA pseudouridi 97.6 0.00032 8.2E-09 46.4 6.9 145 74-227 3-210 (307) 60 PRK02755 truB tRNA pseudouridi 97.6 0.00059 1.5E-08 44.7 8.2 144 75-227 4-205 (291) 61 PRK13354 tyrosyl-tRNA syntheta 97.5 0.00047 1.2E-08 45.3 7.5 48 11-58 339-387 (405) 62 COG2501 S4-like RNA binding pr 97.4 0.00049 1.3E-08 45.2 5.8 63 7-69 5-68 (73) 63 PRK05912 tyrosyl-tRNA syntheta 97.4 0.00044 1.1E-08 45.5 5.5 39 16-54 337-376 (402) 64 cd01291 PseudoU_synth PseudoU_ 97.1 0.00036 9.2E-09 46.1 2.4 86 79-209 2-87 (87) 65 PRK04051 rps4p 30S ribosomal p 97.0 0.0018 4.6E-08 41.7 5.9 55 14-68 103-161 (177) 66 TIGR02988 YaaA_near_RecF S4 do 96.9 0.0017 4.5E-08 41.8 5.0 55 10-64 5-60 (60) 67 COG0130 TruB Pseudouridine syn 96.9 0.0011 2.8E-08 43.0 3.8 144 74-227 16-184 (271) 68 cd02867 PseudoU_synth_TruB_4 P 96.8 0.0045 1.2E-07 39.2 6.5 151 75-227 2-234 (312) 69 PTZ00155 40S ribosomal protein 96.7 0.0027 6.8E-08 40.6 4.6 54 14-67 107-164 (188) 70 TIGR00425 CBF5 rRNA pseudourid 96.2 0.036 9.1E-07 33.5 7.8 166 70-245 31-231 (326) 71 PTZ00118 40S ribosomal protein 96.0 0.092 2.3E-06 30.9 9.0 124 12-150 40-165 (262) 72 TIGR01018 rpsD_arch ribosomal 95.7 0.0069 1.8E-07 38.0 2.3 50 14-63 112-164 (170) 73 PRK04313 30S ribosomal protein 94.9 0.062 1.6E-06 32.0 5.2 53 12-64 36-90 (237) 74 PTZ00223 40S ribosomal protein 94.8 0.085 2.2E-06 31.1 5.7 74 12-90 37-112 (273) 75 COG1471 RPS4A Ribosomal protei 93.9 0.24 6.1E-06 28.3 6.3 37 27-63 56-92 (241) 76 KOG2559 consensus 86.8 1.5 3.9E-05 23.2 4.9 37 199-235 220-263 (318) 77 KOG3301 consensus 84.6 1 2.7E-05 24.3 3.2 49 10-58 93-142 (183) 78 KOG2623 consensus 83.6 2.9 7.4E-05 21.5 5.1 20 116-135 152-171 (467) 79 pfam06353 DUF1062 Protein of u 81.7 2.1 5.3E-05 22.4 3.7 49 73-135 8-56 (142) 80 COG4332 Uncharacterized protei 79.3 2.3 5.8E-05 22.1 3.3 120 56-214 31-155 (203) 81 pfam01509 TruB_N TruB family p 77.6 1.6 4.1E-05 23.1 2.1 49 106-156 7-55 (149) 82 TIGR00431 TruB tRNA pseudourid 77.5 0.49 1.2E-05 26.4 -0.6 70 75-151 4-73 (236) 83 pfam05910 DUF868 Plant protein 74.8 3.2 8.2E-05 21.2 3.0 12 209-220 181-192 (272) 84 TIGR02414 pepN_proteo aminopep 70.9 4 0.0001 20.6 2.8 62 39-101 55-128 (898) 85 COG4043 Preprotein translocase 70.5 4.8 0.00012 20.1 3.1 43 26-68 6-48 (111) 86 PRK10590 ATP-dependent RNA hel 67.7 9.4 0.00024 18.3 9.0 13 232-244 345-357 (457) 87 KOG4655 consensus 66.3 3.8 9.8E-05 20.7 1.9 42 27-68 121-165 (181) 88 pfam02824 TGS TGS domain. The 57.1 11 0.00029 17.8 3.0 22 40-62 37-58 (60) 89 cd01668 TGS_RelA_SpoT TGS_RelA 57.0 11 0.00028 17.9 2.9 23 39-62 36-58 (60) 90 PRK08857 para-aminobenzoate sy 55.8 6.6 0.00017 19.2 1.6 99 121-225 2-106 (192) 91 pfam05949 DUF881 Bacterial pro 55.7 15 0.00039 16.9 4.0 31 39-69 61-91 (150) 92 PRK08007 para-aminobenzoate sy 55.1 6.5 0.00017 19.3 1.5 100 121-225 2-106 (187) 93 PRK02491 putative deoxyribonuc 53.7 15 0.00039 16.9 3.2 30 187-216 129-158 (328) 94 pfam06668 ITI_HC_C Inter-alpha 49.0 20 0.0005 16.2 5.0 11 40-50 4-14 (188) 95 cd01616 TGS The TGS domain, na 48.3 17 0.00044 16.6 2.7 22 40-62 37-58 (60) 96 COG4909 PduC Propanediol dehyd 48.1 10 0.00027 18.0 1.6 57 1-68 1-57 (554) 97 cd07973 Spt4 Transcription elo 47.5 21 0.00053 16.1 3.3 49 115-163 44-93 (98) 98 PRK07649 para-aminobenzoate/an 43.4 11 0.00028 17.9 1.1 99 121-224 2-105 (195) 99 PRK05670 anthranilate synthase 42.9 19 0.00047 16.4 2.2 98 121-223 2-104 (192) 100 PRK02967 nickel responsive reg 42.2 24 0.0006 15.7 2.7 34 188-225 95-128 (138) 101 KOG2529 consensus 39.6 19 0.00048 16.3 1.8 157 74-240 69-250 (395) 102 TIGR00601 rad23 UV excision re 39.0 10 0.00027 18.0 0.4 33 203-235 31-66 (453) 103 pfam02597 ThiS ThiS family. Th 38.3 29 0.00073 15.2 3.1 44 11-62 18-63 (70) 104 PRK06774 para-aminobenzoate sy 36.6 15 0.00038 17.0 0.9 100 121-225 2-106 (191) 105 COG2104 ThiS Sulfur transfer p 36.4 31 0.00079 15.0 2.9 42 13-62 17-61 (68) 106 PRK04460 nickel responsive reg 33.6 34 0.00087 14.7 2.6 20 14-33 17-36 (139) 107 PRK00630 nickel responsive reg 32.6 35 0.0009 14.6 2.6 24 14-37 20-44 (143) 108 PRK06065 acetyl-CoA acetyltran 30.7 31 0.0008 15.0 1.8 16 16-32 38-53 (393) 109 PRK11092 bifunctional (p)ppGpp 30.1 39 0.001 14.4 3.0 60 183-246 452-513 (702) 110 TIGR01687 moaD_arch MoaD famil 30.1 37 0.00095 14.5 2.1 26 37-62 57-86 (93) 111 TIGR01278 DPOR_BchB light-inde 29.9 38 0.00098 14.4 2.1 40 171-215 160-199 (562) 112 pfam05597 Phasin Poly(hydroxya 28.7 41 0.0011 14.2 3.2 24 13-36 93-116 (132) 113 cd00986 PDZ_LON_protease PDZ d 27.7 40 0.001 14.3 1.9 17 54-70 25-42 (79) 114 KOG3449 consensus 27.1 44 0.0011 14.0 2.1 17 197-213 19-35 (112) 115 PRK10872 relA GDP/GTP pyrophos 26.5 45 0.0012 14.0 3.3 20 70-89 305-324 (743) 116 pfam11685 DUF3281 Protein of u 26.0 46 0.0012 13.9 1.9 12 110-121 119-130 (269) 117 PRK06059 lipid-transfer protei 25.2 44 0.0011 14.1 1.7 18 16-34 31-48 (399) 118 PRK06488 sulfur carrier protei 25.2 48 0.0012 13.8 3.1 41 14-62 15-58 (65) 119 CHL00101 trpG anthranilate syn 25.2 36 0.00092 14.6 1.3 99 122-225 3-106 (190) 120 KOG2582 consensus 25.0 26 0.00067 15.4 0.6 20 75-94 182-201 (422) 121 PRK01002 nickel responsive reg 24.8 49 0.0012 13.8 2.6 20 14-33 17-36 (141) 122 PRK07855 lipid-transfer protei 24.4 48 0.0012 13.8 1.8 14 201-214 272-285 (386) 123 PRK08313 acetyl-CoA acetyltran 23.2 48 0.0012 13.8 1.6 17 17-34 34-50 (391) 124 PTZ00246 proteasome subunit al 22.6 53 0.0014 13.5 1.8 95 135-252 150-245 (253) 125 TIGR02542 B_forsyth_147 Bacter 22.5 37 0.00094 14.5 0.9 101 128-236 26-127 (154) 126 cd06555 ASCH_PF0470_like ASC-1 22.5 53 0.0014 13.5 1.7 34 31-64 9-42 (109) 127 TIGR01670 YrbI-phosphatas 3-de 21.2 44 0.0011 14.1 1.1 18 117-134 12-29 (154) 128 pfam10574 UPF0552 Uncharacteri 21.0 58 0.0015 13.3 5.2 95 148-245 19-120 (224) 129 KOG2553 consensus 21.0 58 0.0015 13.3 3.0 25 184-208 262-288 (416) 130 KOG0151 consensus 20.9 58 0.0015 13.3 2.9 24 221-244 719-745 (877) 131 pfam12471 GTP_CH_N GTP cyclohy 20.5 57 0.0015 13.3 1.5 15 156-170 137-151 (195) 132 PRK06365 acetyl-CoA acetyltran 20.4 59 0.0015 13.2 1.7 17 15-32 30-46 (415) No 1 >PRK10700 23S rRNA pseudouridylate synthase B; Provisional Probab=100.00 E-value=0 Score=520.41 Aligned_cols=240 Identities=39% Similarity=0.563 Sum_probs=222.1 Q ss_pred CCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECC--CCEEEECCEECCCCCCE----EEEECCCCCEEE Q ss_conf 734478899988687789999999869869999992406878079--99799999892255643----896027875156 Q gi|254780406|r 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS--TDHIEVDGVPLRKAERT----RLWLYHKPIGLV 85 (354) Q Consensus 12 ~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~--~d~v~vdg~~i~~~~~~----~~~~~~KP~g~~ 85 (354) ..||||||||++|+||||+||+||.+|+|+|||++++ ++.+|+. +|.|+|||++|.+.+.. +||+||||.|++ T Consensus 1 m~eRL~K~LA~~G~~SRReae~lI~~GrV~VNG~v~~-lg~~v~~~~~~~V~vDG~~i~~~~~~~~~~~~l~l~KP~G~v 79 (291) T PRK10700 1 MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAK-LGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGEL 79 (291) T ss_pred CHHHHHHHHHHCCCCHHHHHHHHHHCCEEEECCEECC-CCCEECCCCCCEEEECCEEEECCCCCCCCEEEEEEECCCEEE T ss_conf 9179999999878943999999998694998999955-688265899988999999943245544301468998785775 Q ss_pred ECCCCCCCCCCCCEEECCC-CCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHH Q ss_conf 3144333364421011023-432002665543323202223676410001234457404775211245564678887400 Q gi|254780406|r 86 TTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164 (354) Q Consensus 86 ~~~~~~~~~~~~~~~~~~~-~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g 164 (354) ||..|+++++++|+.++.. ..+|++|||||+||||||||||||+|+|+|+||+++++|+|+|+|+++++++.++.|..| T Consensus 80 ~T~~D~~~r~tV~dllp~~~~~rl~~VGRLD~dT~GLLLlTNDG~La~rL~hP~~~v~K~Y~V~v~g~i~~~~l~~l~~G 159 (291) T PRK10700 80 CTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRG 159 (291) T ss_pred CCCCCCCCCCCHHHHCCCCCCCCEEEECCCCCCCCCCEEECCCHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHCC T ss_conf 46677557983778463223664556305788887728983877999862488679877999998887999999999769 Q ss_pred HHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEEC-CCCCCCCEEECCHHHHHH Q ss_conf 0008767503430364026880799999951842899999998398686889758705451-875547488679999987 Q gi|254780406|r 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243 (354) Q Consensus 165 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l-~~L~~G~~r~l~~~e~~~ 243 (354) +.++|+.+.+..+.+....+.++|++|+|+|||||||||||+++|++|++|+||+||+|+| ++||+|+||+||.+||.. T Consensus 160 v~ledg~~~~~~i~~~~~~~~~~~~~i~L~EGrnrqIRRMf~~~G~~V~~LkRi~iG~i~L~~~Lp~G~wR~Lt~~Ev~~ 239 (291) T PRK10700 160 VQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNY 239 (291) T ss_pred CEECCCEEEEEEEEEECCCCCCEEEEEEEEECCCHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCCCEECCHHHHHH T ss_conf 77678014679998844778857999999969688999999985997918899998776358999896771899999999 Q ss_pred HHHHHHHHC Q ss_conf 532100000 Q gi|254780406|r 244 QLGPHLLEE 252 (354) Q Consensus 244 l~~~~~~~~ 252 (354) |..+..... T Consensus 240 Lr~~v~l~~ 248 (291) T PRK10700 240 LRELVELPP 248 (291) T ss_pred HHHHCCCCC T ss_conf 999819991 No 2 >PRK10475 23S rRNA pseudouridine synthase F; Provisional Probab=100.00 E-value=0 Score=514.08 Aligned_cols=234 Identities=26% Similarity=0.394 Sum_probs=216.9 Q ss_pred CCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCC--CCEEEEECCCCCEEEEC Q ss_conf 6773447889998868778999999986986999999240687807999799999892255--64389602787515631 Q gi|254780406|r 10 NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--ERTRLWLYHKPIGLVTT 87 (354) Q Consensus 10 ~~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~--~~~~~~~~~KP~g~~~~ 87 (354) ..+++|||||||++|+||||+||+||.+|+|+|||++|+ ++++|+++|.|.|||+.|.+. +...||+||||.|++|| T Consensus 3 ~~~~~RL~K~LA~~G~~SRReAe~lI~~GrV~VNGk~v~-~g~~V~~~D~V~vdg~~i~~~~~~~~~yi~lnKP~G~v~t 81 (290) T PRK10475 3 PDSSTRLNKYISESGICSRREADRYIEQGNVFINGKRAT-IGDQVKPGDVVKVNGQLIEPREAEDLVLIALNKPVGIVST 81 (290) T ss_pred CCCCCHHHHHHHHCCCCHHHHHHHHHHCCCEEECCEECC-CCCCCCCCCEEEECCEECCCCCCCCEEEEEEECCCCCCCC T ss_conf 988614999998777835999999998597898999957-9888699998999998912336676399999589870677 Q ss_pred CCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHC Q ss_conf 44333364421011023432002665543323202223676410001234457404775211245564678887400000 Q gi|254780406|r 88 HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167 (354) Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~ 167 (354) ..|. .+.+++++++. ..++++|||||+||+|||||||||+|+++|+||+++++|+|+|+|+++++++.++.|..|+.+ T Consensus 82 ~~d~-~r~ti~d~l~~-~~rl~pVGRLD~dSeGLLlLTNDG~l~~~l~hP~~~i~K~Y~V~v~g~i~~~~l~~l~~Gv~i 159 (290) T PRK10475 82 TEDG-ERDNIVDFVNH-SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI 159 (290) T ss_pred CCCC-CCCCEEECCCC-CCCEEECCCCCCCCCCEEEECCCHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHCCCEE T ss_conf 7667-89864641477-563505046687776759985987999987357678955999998985899999998589656 Q ss_pred CCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCEEECCHHHHHHHHHH Q ss_conf 87675034303640268807999999518428999999983986868897587054518755474886799999875321 Q gi|254780406|r 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247 (354) Q Consensus 168 ~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e~~~l~~~ 247 (354) +++.+.+|.+... ..+|++|+|+||+||||||||+++|++|.+|+||+||+|.|++|++|+||+|+++||.+|++. T Consensus 160 ~g~~~~~~~v~~~----~~~~~~i~L~EGknRqIRRm~~~~g~~V~~L~Ri~iG~i~L~~L~~G~wR~Lt~~Ei~~l~~~ 235 (290) T PRK10475 160 LGTVTKKCKVKKE----APFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235 (290) T ss_pred CCEECCEEEEEEC----CCCEEEEEEECCCCHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCCEECCHHHHHHHHHH T ss_conf 8886011499964----897899999868049999999985997817899998887858989987158999999999976 Q ss_pred HHH Q ss_conf 000 Q gi|254780406|r 248 HLL 250 (354) Q Consensus 248 ~~~ 250 (354) ... T Consensus 236 ~~~ 238 (290) T PRK10475 236 IEN 238 (290) T ss_pred HHC T ss_conf 534 No 3 >COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=0 Score=492.41 Aligned_cols=237 Identities=39% Similarity=0.617 Sum_probs=220.6 Q ss_pred CCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCC-CEEEECCEECCCCCCEEEEECCCCCEEEECCCC Q ss_conf 7344788999886877899999998698699999924068780799-979999989225564389602787515631443 Q gi|254780406|r 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSD 90 (354) Q Consensus 12 ~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~-d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~~ 90 (354) .++|||||||++|+||||+|++||++|+|+|||+++++++.+|+++ |.|.|||+++...+...|||||||.|++||..| T Consensus 1 ~~~RL~K~La~~G~~SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~~~~~~~~~y~llnKP~G~v~s~~D 80 (248) T COG1187 1 DSMRLNKFLAEAGVGSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKRIELKEERVYLLLNKPRGYVSSTED 80 (248) T ss_pred CCCCHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEECCCCEEECCCCCEEEECCEEEECCCCCEEEEEECCCCEEECCCC T ss_conf 95206899987477788999999973987889999224776727987689989988112666469999899876926668 Q ss_pred CCCCCCCCEEECC---CCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHC Q ss_conf 3336442101102---3432002665543323202223676410001234457404775211245564678887400000 Q gi|254780406|r 91 PDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167 (354) Q Consensus 91 ~~~~~~~~~~~~~---~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~ 167 (354) +.+++|+++.++. ...++++|||||+||||||||||||+|+|+|+||+++++|+|+|+|.++++++.++.|+.|+.+ T Consensus 81 ~~gr~tv~D~lp~~~~~~~~~~pvGRLD~dTeGLLLLTnDG~la~rL~~P~~~~~K~Y~v~v~g~~~~~~l~~l~~Gv~l 160 (248) T COG1187 81 DEGRPTVFDLLPERLPRKKRLFPVGRLDKDTEGLLLLTNDGELAHRLMHPSSEVEKEYLVRVEGPVTEEDLEKLRKGVTL 160 (248) T ss_pred CCCCCEEEEECCCCCCCCCCEEECCCCCCCCEEEEEEECCHHHHHHHCCCCCCCCEEEEEEEECCCCHHHHHHHHCCCEE T ss_conf 89981600025543466663334266577771279995787898875288889977999999258998999998578386 Q ss_pred CCEEEECCC-EEEEECCC-CEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECCCC--CCCCEEECCHHHHHH Q ss_conf 876750343-03640268-80799999951842899999998398686889758705451875--547488679999987 Q gi|254780406|r 168 QGICYGDMQ-VTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVSKKILRE 243 (354) Q Consensus 168 ~~~~~~~~~-~~~~~~~~-~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~~L--~~G~~r~l~~~e~~~ 243 (354) +|+.+.|+. +.+..... .++|++|+|+|||||||||||+++|++|.+|+|++||+|.|++| ++|+||+|+..|+.. T Consensus 161 ~d~~~~~~~~~~l~~~~~~~~s~~~itl~EGrnrQVRRm~~a~G~~V~~L~R~r~G~l~L~~L~l~~G~~R~L~~~E~~~ 240 (248) T COG1187 161 DDGETKPAKPASLEKEPGKNNSWLRITLTEGRNRQVRRMFEAVGLEVLRLKRIRIGPLSLGDLPLPPGEWRELTLEEIAQ 240 (248) T ss_pred CCCCCCCCEEEEEEECCCCCCEEEEEEEECCCCHHHHHHHHHCCCEEEEEEEEEEEEEECCCCCCCCCEEEECCHHHHHH T ss_conf 67356601047898317887469999995784789999999849967489999870167289888882058998999999 Q ss_pred HHHHH Q ss_conf 53210 Q gi|254780406|r 244 QLGPH 248 (354) Q Consensus 244 l~~~~ 248 (354) |.... T Consensus 241 l~~~~ 245 (248) T COG1187 241 LRKLV 245 (248) T ss_pred HHHHH T ss_conf 99875 No 4 >PRK10839 16S rRNA pseudouridylate synthase A; Provisional Probab=100.00 E-value=0 Score=474.66 Aligned_cols=227 Identities=26% Similarity=0.412 Sum_probs=208.2 Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEEEECCCCCEEEECCCCCCC Q ss_conf 44788999886877899999998698699999924068780799979999989225564389602787515631443333 Q gi|254780406|r 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93 (354) Q Consensus 14 ~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~~~~~ 93 (354) ||||||||++|+||||+|++||.+|+|+|||++|++++++|+++|.|.|||+++.......||++|||+|++||..|+.+ T Consensus 1 mRL~K~La~~g~~SRR~ae~lI~~GrV~VNg~~v~~~~~~V~~~~~v~vdg~~i~~~~~~~y~~lnKP~G~v~s~~d~~~ 80 (231) T PRK10839 1 MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVKNAAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPDH 80 (231) T ss_pred CCHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCEECCCCCEEEECCCEECCCCCCEEEEEECCCCCCCCCCCCCC T ss_conf 93789998878956999999998797999999914588084999869991958614668689999899875347889999 Q ss_pred CCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEE-- Q ss_conf 644210110234320026655433232022236764100012344574047752112455646788874000008767-- Q gi|254780406|r 94 RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-- 171 (354) Q Consensus 94 ~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~-- 171 (354) +++++...+....++++|||||+||||||||||||+|+++|+||+++++|+|+|+|+++++++.+.+|..|+.+++.. T Consensus 81 ~~~~~~l~~~~~~~l~~vGRLD~ds~GLlllTnDg~l~~~l~~P~~~i~k~Y~V~v~~~i~~~~l~~l~~Gv~i~~~~~~ 160 (231) T PRK10839 81 PTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDL 160 (231) T ss_pred CCEEEECCCCCCCCEEEEECCCCCCCCEEEECCCHHHHHHCCCCCCCCCEEEEEEECCCCCHHHHHHHHCCCEECCEECC T ss_conf 72698637655563577004688987769976888999535187689978999998987999999999679698782311 Q ss_pred EECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEEC-CCCCCCCEEECCHHHHHHH Q ss_conf 503430364026880799999951842899999998398686889758705451-8755474886799999875 Q gi|254780406|r 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244 (354) Q Consensus 172 ~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l-~~L~~G~~r~l~~~e~~~l 244 (354) ++|+.+... ..+|++|+|+||+||||||||+++|++|.+|+||+||+|+| ++|++|+||+||++||..| T Consensus 161 ~~~~~v~~~----~~~~~~i~l~eGk~rqIRrmf~~~g~~V~~L~Ri~iG~i~L~~dL~~G~~R~Lt~~Ei~~l 230 (231) T PRK10839 161 TKPAVLEVI----TPTQVRLTISEGRYHQVKRMFAAVGNRVVELHRERIGGITLDADLAPGEYRPLTEEEIASV 230 (231) T ss_pred EEEEEEEEC----CCCEEEEEEECCCCHHHHHHHHHCCCEEEEEEEEEEECEECCCCCCCCCEEECCHHHHHHC T ss_conf 603699984----8969999996687679999999859989899999990552389999975019999999742 No 5 >PRK11394 23S rRNA pseudouridine synthase E; Provisional Probab=100.00 E-value=0 Score=360.31 Aligned_cols=167 Identities=31% Similarity=0.529 Sum_probs=157.3 Q ss_pred CCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEE Q ss_conf 56438960278751563144333364421011023432002665543323202223676410001234457404775211 Q gi|254780406|r 70 AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149 (354) Q Consensus 70 ~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v 149 (354) ..+..||++|||+|++||..|+.+++||+++++. .++++|||||+||+|||||||||+|+++|+||+++++|+|.|+| T Consensus 26 ~~p~r~illnKP~G~i~T~~D~~gR~tV~dllp~--~~l~pVGRLD~dSeGLLLlTNDG~la~~L~hP~~~i~K~Y~V~v 103 (207) T PRK11394 26 NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV--QGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQV 103 (207) T ss_pred CCCCEEEEEECCCCEEECCCCCCCCCCHHHHCCC--CCCEECCCCCCCCCCEEEECCCHHHHHHHHCCCCCCCEEEEEEE T ss_conf 9998899998999858688899999767896885--67457777678987729980878999875256579778999999 Q ss_pred CCCCCHHHHHHHHHHHHCCCEEEECCCEEEEE---------------CCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEE Q ss_conf 24556467888740000087675034303640---------------268807999999518428999999983986868 Q gi|254780406|r 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT---------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214 (354) Q Consensus 150 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~---------------~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~ 214 (354) .+.++.+.+++|.+|+.++|+.+.|+.+.+.. ....++|++|+|+|||||||||||+++|++|.+ T Consensus 104 ~g~~~~~~l~~l~~Gv~i~dg~~~p~~~~~v~~~~~~~~~~~~~~~~~~~~~s~l~i~L~EGKnRqIRRmf~~~G~~V~~ 183 (207) T PRK11394 104 EGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLR 183 (207) T ss_pred CCCCCHHHHHHHHCCCEECCEEEEEEEEEEECCCCCCCCCCCCHHHCCCCCCCEEEEEEEECCCHHHHHHHHHCCCEEEE T ss_conf 16899999999977978598476454899944742123457641110257865799999746359999999986997938 Q ss_pred EEEEEECCEECCCCCCCCEEECCH Q ss_conf 897587054518755474886799 Q gi|254780406|r 215 LIRISYGPFQLGTLLAGSTREVSK 238 (354) Q Consensus 215 L~Rv~~G~~~l~~L~~G~~r~l~~ 238 (354) |+||+||+|.|++|++|+||+||. T Consensus 184 L~Ri~iG~l~L~~L~~G~~ReLTe 207 (207) T PRK11394 184 LIRYAMGDYSLDNLANGEWREATD 207 (207) T ss_pred EEEEEECCEECCCCCCCCCEECCC T ss_conf 999998988739989988377969 No 6 >cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site. Probab=100.00 E-value=0 Score=348.09 Aligned_cols=165 Identities=50% Similarity=0.815 Sum_probs=159.5 Q ss_pred EEEECCCCCEEEECCCCCCCCCCCCEEECC-CCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC Q ss_conf 896027875156314433336442101102-3432002665543323202223676410001234457404775211245 Q gi|254780406|r 74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152 (354) Q Consensus 74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~-~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~ 152 (354) +||++|||.|++||..|+.+++++++.++. ...++++|||||+||||||||||||+|+++|+||+++++|+|.|+++++ T Consensus 1 r~illnKP~G~v~s~~d~~~r~tv~dll~~~~~~rl~~vGRLD~ds~GLLLlTnDG~l~~~l~hP~~~i~k~Y~V~v~~~ 80 (167) T cd02556 1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80 (167) T ss_pred CEEEEECCCCEEECCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHCCCCCCCCEEEEEEECCC T ss_conf 98999899998978629988975789655335557236413895767859992783675764098778857999997589 Q ss_pred CCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEEC-CCCCCC Q ss_conf 5646788874000008767503430364026880799999951842899999998398686889758705451-875547 Q gi|254780406|r 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAG 231 (354) Q Consensus 153 ~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l-~~L~~G 231 (354) ++++.++++..|+.++++.++++.+.+......++|++|+|+||+||||||||+++|++|.+|+||+||+|+| ++|++| T Consensus 81 ~~~~~l~~l~~Gv~i~~~~~~~~~v~~~~~~~~~~~~~i~l~eGk~rqIRrmf~~~g~~V~~L~Ri~iG~l~l~~dL~~G 160 (167) T cd02556 81 VTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRG 160 (167) T ss_pred CCHHHHHHHHCCCEECCEEEEEEEEEEECCCCCCEEEEEEEECCCHHHHHHHHHHCCCEEEEEEEEEECCCCCCCCCCCC T ss_conf 99999999877978799884006999962679967999999769468999999986998958999998885257898997 Q ss_pred CEEECCH Q ss_conf 4886799 Q gi|254780406|r 232 STREVSK 238 (354) Q Consensus 232 ~~r~l~~ 238 (354) +||+||| T Consensus 161 ~~R~LtP 167 (167) T cd02556 161 QWEELPP 167 (167) T ss_pred CEEECCC T ss_conf 4586989 No 7 >TIGR00093 TIGR00093 conserved hypothetical protein; InterPro: IPR000748 Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. Several bacterial proteins from the Rsu family of pseudouridine synthases have been shown to share regions of similarities, including Escherichia coli and Haemophilus influenzae 16S pseudouridylate 516 synthase (gene rsuA); E. coli hypothetical proteins yciL and ymfC and the corresponding H. influenzae proteins HI1199 and HI0694 respectively; Aquifex aeolicus hypothetical proteins AQ_554 and AQ_1464; Bacillus subtilis hypothetical proteins ypuL and ytzF; Borrelia burgdorferi hypothetical protein BB0129; Helicobacter pylori hypothetical protein HP1459; and Synechocystis sp. (strain PCC 6803) hypothetical proteins slr0361 and slr0612. These are proteins of from 25 to 40 kD which contain a number of conserved regions in their central section.; GO: 0003723 RNA binding, 0004730 pseudouridylate synthase activity, 0001522 pseudouridine synthesis. Probab=100.00 E-value=0 Score=342.99 Aligned_cols=160 Identities=36% Similarity=0.605 Sum_probs=153.2 Q ss_pred CCCCEEEECCCCCCCCCCCCEEECCCC---CCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCH Q ss_conf 787515631443333644210110234---32002665543323202223676410001234457404775211245564 Q gi|254780406|r 79 HKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155 (354) Q Consensus 79 ~KP~g~~~~~~~~~~~~~~~~~~~~~~---~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~ 155 (354) |||.|++||..|+.++.++++.++... .+|++|||||+||+|||||||||+|+++|+||.++++|+|.|+|++.+++ T Consensus 1 nKP~g~l~~~~Dp~~r~~~~~~l~~~~~~~~~~~a~GRLD~ds~GLlLLT~~G~L~~RL~~p~~~~eK~Y~V~v~g~v~~ 80 (185) T TIGR00093 1 NKPQGVLCTTDDPEGRKTVKDLLPKKLIRGKRLHAVGRLDRDSEGLLLLTNDGELQHRLTHPKFHHEKTYLVTVEGPVTD 80 (185) T ss_pred CCCCCEEECCCCCCCCCEEEECCCHHHHCCCCEEEEECCCCCCCCEEEECCCHHHHHHHHCCCCCCCCEEEEEECCCCCH T ss_conf 99850443584988772350045202310574677402674562038990697999987176435896699995598588 Q ss_pred HHHHHHHHHHHCCCEEEE--CCCEEEEECCC---------------CEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEE Q ss_conf 678887400000876750--34303640268---------------8079999995184289999999839868688975 Q gi|254780406|r 156 DKLNLLKKGIVIQGICYG--DMQVTLDTQKG---------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218 (354) Q Consensus 156 ~~~~~~~~g~~~~~~~~~--~~~~~~~~~~~---------------~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv 218 (354) +.+..|++||.++|+.+. ++.+.++.+.. ..|||.|||.||||||||||||++|++|.+|+|+ T Consensus 81 ~~~~~~~~Gv~L~~~~~~tk~a~~~~~~~~~~~~pr~ppir~r~~i~~S~l~~tl~EGRNRqvRRm~a~~G~~V~~L~R~ 160 (185) T TIGR00093 81 EDLEALRKGVQLEDGKTLTKPAKLKVISEPEDLWPRNPPIRERKSIPTSWLRVTLTEGRNRQVRRMFAAVGFPVLRLHRV 160 (185) T ss_pred HHHHHHHCCCEECCCCCCCCCEEEEEECCCCCCCCCCCCEEECCCCCCCEEEEEEEECCCHHHHHHHHHHCCEEEEEEEE T ss_conf 89989871760058735644237787067131356787312003688225899996087068878889838903478988 Q ss_pred EECCEEC-CC----CCCCCEEECCH Q ss_conf 8705451-87----55474886799 Q gi|254780406|r 219 SYGPFQL-GT----LLAGSTREVSK 238 (354) Q Consensus 219 ~~G~~~l-~~----L~~G~~r~l~~ 238 (354) +||++.| .+ |+.|+||+||+ T Consensus 161 ~iG~~~L~~~rGkvL~~G~wR~L~~ 185 (185) T TIGR00093 161 RIGDVSLDEGRGKVLPNGEWRELTD 185 (185) T ss_pred EECCEEECCCCCEECCCCCEEECCC T ss_conf 6224342455743538983021889 No 8 >cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms. Probab=100.00 E-value=0 Score=339.32 Aligned_cols=163 Identities=32% Similarity=0.497 Sum_probs=150.7 Q ss_pred EEEECCCCCEEEECCCCCCCCCCCCEEECCCC--CCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC Q ss_conf 89602787515631443333644210110234--3200266554332320222367641000123445740477521124 Q gi|254780406|r 74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151 (354) Q Consensus 74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~--~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~ 151 (354) .|+++|||+|++||..|+.+ +++++.++... .++++|||||+||||||||||||+|+++|+||+++++|+|+|+|++ T Consensus 1 VYillnKP~G~v~t~~d~~~-ktv~dll~~~~~~~~l~~vGRLD~~s~GLLLlTNDG~l~~~l~hP~~~i~K~Y~V~v~~ 79 (167) T cd02553 1 VYLMLNKPAGVVCATKDPHH-PTVIDLLPEPDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAG 79 (167) T ss_pred CEEEEECCCCEEECCCCCCC-CCHHHHCCCCCCCCCEEECCCCCCCCCCEEEECCCHHHHHHHHCCCCCCCEEEEEEECC T ss_conf 99999889997969889999-97744335500367556744568997622999188889976414447888899998767 Q ss_pred CCCHHHHHHHHHHHHCCCE-EEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECC-CCC Q ss_conf 5564678887400000876-75034303640268807999999518428999999983986868897587054518-755 Q gi|254780406|r 152 QVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL 229 (354) Q Consensus 152 ~~~~~~~~~~~~g~~~~~~-~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~-~L~ 229 (354) +++++++++|.+|+.++|+ .+.|+.+.... ++|++|+|+||+||||||||+++|++|.+|+||+||+|+|+ +|+ T Consensus 80 ~i~~~~l~~l~~Gv~i~dg~~~~~~~v~~~~----~~~~~i~l~eGknrqIRrm~~~~g~~V~~L~Rv~iG~l~L~~~L~ 155 (167) T cd02553 80 PLTEDDIEAFAEGVLLHDGYPTKPAKLEILS----PTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDDDLA 155 (167) T ss_pred CCCHHHHHHHHCCCEECCCCEEEEEEEEEEC----CCEEEEEEECCCCHHHHHHHHHCCCEEEEEEEEEECCEECCCCCC T ss_conf 8999999999769896498597517999925----868999998884629999999869888589999981771599999 Q ss_pred CCCEEECCHHHH Q ss_conf 474886799999 Q gi|254780406|r 230 AGSTREVSKKIL 241 (354) Q Consensus 230 ~G~~r~l~~~e~ 241 (354) +|+||+|+++|| T Consensus 156 ~G~~R~Lt~~Ei 167 (167) T cd02553 156 PGEWRPLTEEEL 167 (167) T ss_pred CCCEEECCHHHC T ss_conf 976138987879 No 9 >cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA. Probab=100.00 E-value=0 Score=337.29 Aligned_cols=165 Identities=25% Similarity=0.353 Sum_probs=150.8 Q ss_pred CEEEEECCCCCEEEECCCCCCCCCC--------CCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEE Q ss_conf 4389602787515631443333644--------21011023432002665543323202223676410001234457404 Q gi|254780406|r 72 RTRLWLYHKPIGLVTTHSDPDGRST--------VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143 (354) Q Consensus 72 ~~~~~~~~KP~g~~~~~~~~~~~~~--------~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k 143 (354) ++.|+++|||+|++||..|+...++ ....++.++.+++||||||+||||||||||||+|+++|+||+++++| T Consensus 3 epvyllLnKP~G~v~t~~d~~~~~~~~~~~~~~~~~~l~~~~~rl~pVGRLD~~s~GLLllTNDG~l~~~l~~P~~~i~k 82 (177) T cd02555 3 EPVTLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGHFARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQ 82 (177) T ss_pred CCEEEEEECCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCEEEEEECCHHHHHHHCCCCCCCCE T ss_conf 44999998998487077576678750133345410001022366216047899981189991888999875498668978 Q ss_pred EEEEEECCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCE Q ss_conf 77521124556467888740000087675034303640268807999999518428999999983986868897587054 Q gi|254780406|r 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223 (354) Q Consensus 144 ~Y~v~v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~ 223 (354) +|+|+|+++++++.++.+..|+.+++..++|+.+.... ..+++|+|+||+||||||||+++|++|.+|+||+||+| T Consensus 83 ~Y~V~v~~~~~~~~l~~l~~Gv~l~g~~~~~~~v~~~~----~~~~~i~l~eGknrqIRrm~~~~g~~V~~L~Ri~iG~l 158 (177) T cd02555 83 EYLVEVRGELTAGGLERLNHGLTYDGRELPPAKVSWQN----EQRLRFALKEPQPGQIRRMCESVGLEVVALRRIRIGRV 158 (177) T ss_pred EEEEEECCCCCHHHHHHHHCCEEECCEEECCEEEEEEC----CCEEEEEEECCCCHHHHHHHHHCCCEEEEEEEEEECCE T ss_conf 99999898799999987528767899896786999957----99599999918416999999987997989999999888 Q ss_pred ECCCCCCCCEEECCHHH Q ss_conf 51875547488679999 Q gi|254780406|r 224 QLGTLLAGSTREVSKKI 240 (354) Q Consensus 224 ~l~~L~~G~~r~l~~~e 240 (354) +|++|++|+||+|+++| T Consensus 159 ~L~~L~~G~wR~Lt~~E 175 (177) T cd02555 159 SLGKLPLGQWRYLTTGE 175 (177) T ss_pred ECCCCCCCCCEECCCCC T ss_conf 83889998831992426 No 10 >cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site. Probab=100.00 E-value=0 Score=332.90 Aligned_cols=164 Identities=27% Similarity=0.435 Sum_probs=152.1 Q ss_pred EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCC Q ss_conf 89602787515631443333644210110234320026655433232022236764100012344574047752112455 Q gi|254780406|r 74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153 (354) Q Consensus 74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~ 153 (354) .|+++|||+|++||..+. +++++++.++.. .++++|||||.||||||||||||+|+++|+||+++++|+|.|++++++ T Consensus 1 vYillnKP~G~v~s~~~~-~~~~~~~~l~~~-~rl~~vGRLD~~s~GLLLlTNDg~l~~~L~hP~~~i~k~Y~V~~~~~i 78 (164) T cd02554 1 VYIAYNKPVGIDCTLERA-DEDNIIDFVNPP-PRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPI 78 (164) T ss_pred CEEEEECCCCEEECCCCC-CCCCEEEECCCC-CCEEECCCCCCCCCCEEEEECCHHHHHHHCCCCCCCCCEEEEEECCCC T ss_conf 999998999828387899-999669974886-777888678999856599957889997621998889629999995669 Q ss_pred CHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCE Q ss_conf 64678887400000876750343036402688079999995184289999999839868688975870545187554748 Q gi|254780406|r 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233 (354) Q Consensus 154 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~~L~~G~~ 233 (354) +++.++++.+|+.++++.+.|+.+.... +.|++|+|+||+||||||||+++|++|.+|+||+||+|+|++|++|+| T Consensus 79 ~~~~l~~l~~Gi~i~~~~~~~~~v~~~~----~~~~~i~l~eGknrqIRrmf~~~g~~V~~L~Rv~~G~l~L~~L~~G~~ 154 (164) T cd02554 79 TDEFIEGMSNGVVILGTVTKPCKVERLA----KDKFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIELGDLAPGEW 154 (164) T ss_pred CHHHHHHHHCCEEECCEEEECEEEEEEC----CCEEEEEEEECCCHHHHHHHHHCCCEEEEEEEEEECCEECCCCCCCCC T ss_conf 9999998747859898898021999947----984999999267489999999869988489999988989399899782 Q ss_pred EECCHHHHHH Q ss_conf 8679999987 Q gi|254780406|r 234 REVSKKILRE 243 (354) Q Consensus 234 r~l~~~e~~~ 243 (354) |+|+++||++ T Consensus 155 R~Lt~~Eike 164 (164) T cd02554 155 RPLTDAELFE 164 (164) T ss_pred EECCHHHHCC T ss_conf 6999899088 No 11 >cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved. Probab=100.00 E-value=0 Score=310.68 Aligned_cols=152 Identities=31% Similarity=0.522 Sum_probs=141.0 Q ss_pred EEECCCCCEEEECCCCC-CCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCC Q ss_conf 96027875156314433-33644210110234320026655433232022236764100012344574047752112455 Q gi|254780406|r 75 LWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153 (354) Q Consensus 75 ~~~~~KP~g~~~~~~~~-~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~ 153 (354) +|++|||+|++||..|+ .++++++++++. +++++|||||+||||||||||||+|+++|+||+++++|+|+|+|++.+ T Consensus 1 ~i~lnKP~G~v~t~~d~~~~~~~v~d~~~~--~~l~~VGRLD~ds~GLLLlTnDG~l~~~L~hP~~~i~K~Y~v~v~g~~ 78 (168) T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYIDD--PGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVP 78 (168) T ss_pred CEEEECCCCEEECCCCCCCCCCEEHHHCCC--CCEEECCCCCCCCCCEEEEECCHHHHHHHHCCCCCCCEEEEEEECCCC T ss_conf 989989999797966888999782440788--881784266789887599829699999873776799779999986679 Q ss_pred CHHHHHHHHHHHHCCCEEEECCCEEEEE---------------CCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEE Q ss_conf 6467888740000087675034303640---------------2688079999995184289999999839868688975 Q gi|254780406|r 154 DQDKLNLLKKGIVIQGICYGDMQVTLDT---------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218 (354) Q Consensus 154 ~~~~~~~~~~g~~~~~~~~~~~~~~~~~---------------~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv 218 (354) +++.+..|.+|+.++++.+.|+.+.... ....++|++|+|+|||||||||||+++|++|.+|+|| T Consensus 79 ~~~~l~~l~~Gv~i~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~s~~~i~l~eGknrqIRrm~~~~g~~V~~L~Rv 158 (168) T cd02566 79 TEDALEQLRNGVELGDGLTLPAKVEKVDEPPWLWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIRV 158 (168) T ss_pred CHHHHHHHHCCCEECCEEEEEEEEEEECCCCCCCCCCCCCEEECCCCCEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEE T ss_conf 99999998779697987864459999426544321256613201478348999996172199999999859969589999 Q ss_pred EECCEECCCC Q ss_conf 8705451875 Q gi|254780406|r 219 SYGPFQLGTL 228 (354) Q Consensus 219 ~~G~~~l~~L 228 (354) +||+|.|++| T Consensus 159 ~~G~i~L~~L 168 (168) T cd02566 159 SIGDIGLDNL 168 (168) T ss_pred EECCEECCCC T ss_conf 9887884979 No 12 >cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins. Probab=100.00 E-value=8.7e-39 Score=264.11 Aligned_cols=146 Identities=38% Similarity=0.583 Sum_probs=141.9 Q ss_pred EEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCC Q ss_conf 96027875156314433336442101102343200266554332320222367641000123445740477521124556 Q gi|254780406|r 75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154 (354) Q Consensus 75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~ 154 (354) |+++|||+|++|+..|+.++.++++.++....++++|||||++||||||||||++++++|++|+++++|+|++.|.|.++ T Consensus 1 yi~lnKP~G~~~~~~~~~~~~tv~~ll~~~~~~l~~V~RLD~~TsGLll~t~d~~~~~~l~~~~~~i~K~Y~a~v~g~~~ 80 (146) T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDVGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVPS 80 (146) T ss_pred CEEEECCCCCEECCCCCCCCCCHHHHHHHCCCCEEECCCCCCCCCCEEEEECCHHHHHHHHCCCCCCCEEEEEEEECCCC T ss_conf 98999999828616699899857895430578672266689778765999579899998754035424699999902699 Q ss_pred HHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEE Q ss_conf 467888740000087675034303640268807999999518428999999983986868897587 Q gi|254780406|r 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220 (354) Q Consensus 155 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~ 220 (354) .+.+..+..|+.++++.+.++.+.+.......+|++|+|.|||+||||+||+++|++|.+|+||+| T Consensus 81 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~s~l~v~l~tGR~hQIR~h~~~lg~pI~~L~Ri~i 146 (146) T cd02870 81 EEELRRLRAGVELDDGKTAPAKVKVLSRDPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146 (146) T ss_pred HHHHHHHHCCEECCCCEEEEEEEEEECCCCCCEEEEEEECCCCHHHHHHHHHHCCCEEEEEEEEEC T ss_conf 999999866645589887214899823789959999997899439999999984997967999979 No 13 >TIGR00005 rluA_subfam pseudouridine synthase, RluA family; InterPro: IPR006225 This is the RluD subfamily of pseudouridine synthases. In Escherichia coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917. RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homologue from E. coli outside this family, TruC (Q46918 from SWISSPROT), modifies uracil-65 in transfer RNAs to pseudouridine. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis. Probab=99.97 E-value=8.3e-32 Score=220.15 Aligned_cols=212 Identities=24% Similarity=0.317 Sum_probs=175.8 Q ss_pred CCCCCHHHHHHHHHCCC-CCHHHHHHHHHCCCEEEC-CEECCCCCEEECCCCEEE-EC-------------CEE----CC Q ss_conf 66773447889998868-778999999986986999-999240687807999799-99-------------989----22 Q gi|254780406|r 9 ENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIE-VD-------------GVP----LR 68 (354) Q Consensus 9 ~~~~~~RL~K~la~~g~-~SRr~a~~lI~~G~V~Vn-g~~v~~~~~~v~~~d~v~-vd-------------g~~----i~ 68 (354) +...++||++||+...- .||..++++|++|.|.|| +.+..++.++|..+|.|. |+ .+| ++ T Consensus 1 ~~~~g~Rld~~L~~~l~~~sr~~~~~~i~~G~V~vN~~~~~~~~~~~~~~g~~~~~v~~~~~~~~~~~~~~~~p~~l~l~ 80 (337) T TIGR00005 1 EEQAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNKGKVTANPKLKIKDGDRITPVRVPEEQEELEVPVQDIPADLKLD 80 (337) T ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCCEEECCCCCCCCCCEEECCCCEEECEECCCCCCCCCCCCCCCCCCCCCE T ss_conf 97430269999999836788889999987496896376425674305238746601001464332357665673422113 Q ss_pred -CCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCC----------CEECCCCCCCCCCCEEEECCCCCCCCCCCC- Q ss_conf -55643896027875156314433336442101102343----------200266554332320222367641000123- Q gi|254780406|r 69 -KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVISVGRLDINTEGLLLLTNDGGLARVLEL- 136 (354) Q Consensus 69 -~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~----------~~~~vgRLD~~t~GLlllTndg~l~~~l~~- 136 (354) .+|+..+|++|||+|++|++.......||...|..+.+ ++++|+|||+||||||+++..-.-...|.. T Consensus 81 IlfEDe~i~vinKP~G~~vHP~~~~~~~Tv~~~L~~~~~~~~~gig~~~~~~~vHRLD~dTSGl~~vAK~~~A~~~L~~q 160 (337) T TIGR00005 81 ILFEDEDILVINKPSGLVVHPGGGNSFGTVLNALLAHCPERLSGIGGVFRVGIVHRLDRDTSGLMVVAKTRLALRELQRQ 160 (337) T ss_pred EEEECCCEEEEECCCCEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECHHHHHHHHHH T ss_conf 78750838999789875644888887354899999864766434576123613552477872589997086899999999 Q ss_pred -CCCCCEEEEEEEECCCCC-HHHH-----------HHHHHHHHCCC---EEEECCCEEEEEC--CCCEEEEEEEEEECCH Q ss_conf -445740477521124556-4678-----------88740000087---6750343036402--6880799999951842 Q gi|254780406|r 137 -PSTQWLRVYRVRFHGQVD-QDKL-----------NLLKKGIVIQG---ICYGDMQVTLDTQ--KGSNAWVTVGLREGKN 198 (354) Q Consensus 137 -p~~~~~k~Y~v~v~~~~~-~~~~-----------~~~~~g~~~~~---~~~~~~~~~~~~~--~~~~~~~~v~l~eGr~ 198 (354) ....+.|+|.+.|.|++. .... ......|...+ +.-....+.+... .+..+||++.|.+||+ T Consensus 161 l~~~~~~k~Y~A~V~G~~~~~~~~~~~~P~~r~~~~~~~~~v~~~~~~~GK~A~T~f~~~~~~A~~~~sl~~~~L~TGRT 240 (337) T TIGR00005 161 LKERTVTKEYVALVHGEFDLSKKGTVDAPLGRVPNNRGKMAVAPSSEKEGKPAVTHFKVLERIADGNASLVECELETGRT 240 (337) T ss_pred HHHCCCEEEEEEEEECCCCCCCCEEEECCCCCCCCCCEEEEEEECCCCCCCEEEEEEEEEHHHCCCCCCEEEEEECCCCC T ss_conf 98386117899998317688764478065323688602689976788889612342121001104452189998534897 Q ss_pred HHHHHHHHHCCCEEEEEEEEEECC Q ss_conf 899999998398686889758705 Q gi|254780406|r 199 REIKKVFEFFNWKVNRLIRISYGP 222 (354) Q Consensus 199 ~qIrr~~~~~g~~V~~L~Rv~~G~ 222 (354) ||||.+|+++||++..-. -||+ T Consensus 241 HQIRVHl~~~ghPl~gD~--~YG~ 262 (337) T TIGR00005 241 HQIRVHLQYLGHPLAGDP--LYGN 262 (337) T ss_pred HHHHHHHHHHCCCEECCC--CCCC T ss_conf 389999997168531432--5688 No 14 >PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Probab=99.97 E-value=3.8e-31 Score=215.99 Aligned_cols=215 Identities=20% Similarity=0.222 Sum_probs=165.6 Q ss_pred CCCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCE----------EC---CCCC Q ss_conf 4466677344788999886-87789999999869869999992406878079997999998----------92---2556 Q gi|254780406|r 6 IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----------PL---RKAE 71 (354) Q Consensus 6 ~~~~~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~----------~i---~~~~ 71 (354) -++++..++|||+||+... ..||+.++++|++|.|+|||++++.+.++|..+|.|.++.. .+ ..+| T Consensus 10 tV~~~~aG~RLD~fL~~~~~~~srs~i~k~ir~g~I~VNgk~v~k~~~~v~~GD~I~i~~~~~~~~~~~p~~~~l~IlyE 89 (325) T PRK11180 10 TVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEAQDIPLDIVYE 89 (325) T ss_pred EECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCEEEE T ss_conf 99910079739999997578889999999998698899999947821278899999981687763447722388518998 Q ss_pred CEEEEECCCCCEEEECCCCCCCCCCCCEEECCCC------CCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEE Q ss_conf 4389602787515631443333644210110234------3200266554332320222367641000123--4457404 Q gi|254780406|r 72 RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLR 143 (354) Q Consensus 72 ~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~------~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k 143 (354) +..++++|||.|++|+........++.+.+...+ .+...|+|||++|||||||+.+...+..|.. ....+.| T Consensus 90 D~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~r~~iVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K 169 (325) T PRK11180 90 DDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQKREITR 169 (325) T ss_pred CCCEEEEECCCCCEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCEEECCCCCCCEEEEECCCHHHHHHHHHHHHHCCCCE T ss_conf 38899998899944767989888779999987532104787676664279997414664175999999999997388965 Q ss_pred EEEEEECCCCCHHHHHHH--HH-H-----H-HCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEE Q ss_conf 775211245564678887--40-0-----0-0087675034303640268807999999518428999999983986868 Q gi|254780406|r 144 VYRVRFHGQVDQDKLNLL--KK-G-----I-VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214 (354) Q Consensus 144 ~Y~v~v~~~~~~~~~~~~--~~-g-----~-~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~ 214 (354) +|++.|.|.++....... .. . + ....+......+.++......+++++.|.+||.||||.+|+++|++|.. T Consensus 170 ~Y~Alv~G~~~~~g~i~~pl~~~~~~~~~~~~~~~gk~A~T~~~vl~~~~~~slv~~~l~TGRtHQIRvHla~~G~PIvG 249 (325) T PRK11180 170 EYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVG 249 (325) T ss_pred EEEEEEEEEECCCCEEECCCCCCCCCCEEEEECCCCEEECCHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHCCCCEEC T ss_conf 99999810437996585420137766628997677702022101444358845799982758828999999987995637 Q ss_pred EEEEEECC Q ss_conf 89758705 Q gi|254780406|r 215 LIRISYGP 222 (354) Q Consensus 215 L~Rv~~G~ 222 (354) -..||. T Consensus 250 --D~~YG~ 255 (325) T PRK11180 250 --DQVYGG 255 (325) T ss_pred --CCCCCC T ss_conf --524688 No 15 >COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Probab=99.97 E-value=3.6e-30 Score=209.83 Aligned_cols=216 Identities=24% Similarity=0.291 Sum_probs=163.6 Q ss_pred CCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCE-------------EC-CCC Q ss_conf 3446667734478899988687789999999869869999992406878079997999998-------------92-255 Q gi|254780406|r 5 NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-------------PL-RKA 70 (354) Q Consensus 5 ~~~~~~~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~-------------~i-~~~ 70 (354) ..+.+...++||++||+....+||....++|++|.|.|||+++. ++++|..+|.|.+.-. ++ ..+ T Consensus 4 ~~i~~~~~g~rld~~L~~l~~~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~Ily 82 (289) T COG0564 4 FEVPEEEAGQRLDKFLAKLLPISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILY 82 (289) T ss_pred EEECCHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCEEECCEECC-CCEEECCCCEEEEECCCCCCCCCCCCCCCCCCEEE T ss_conf 88361113547999998725747999999988898899999835-87160899999953565543334565477877799 Q ss_pred CCEEEEECCCCCEEEECCCCCCCCCCCCEEECCC----CCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEEE Q ss_conf 6438960278751563144333364421011023----43200266554332320222367641000123--44574047 Q gi|254780406|r 71 ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI----FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRV 144 (354) Q Consensus 71 ~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~----~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k~ 144 (354) |+..++++|||+|++|+........++...+..+ ..++++|+|||++||||||++.+...+..|.. ....+.|+ T Consensus 83 ED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K~ 162 (289) T COG0564 83 EDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDGVERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKKT 162 (289) T ss_pred ECCCEEEEECCCCCEECCCCCCCCHHHHHHHHHHCCCCCCCEEEECCCCCCCCEEEEEECCHHHHHHHHHHHHCCCCCEE T ss_conf 76999999889997167798875267999998752334786435148899985699999599999999999851866179 Q ss_pred EEEEECCCCCHHH--HHH---------HHHHHHCCC-EEEECCCEEEEECCCC-EEEEEEEEEECCHHHHHHHHHHCCCE Q ss_conf 7521124556467--888---------740000087-6750343036402688-07999999518428999999983986 Q gi|254780406|r 145 YRVRFHGQVDQDK--LNL---------LKKGIVIQG-ICYGDMQVTLDTQKGS-NAWVTVGLREGKNREIKKVFEFFNWK 211 (354) Q Consensus 145 Y~v~v~~~~~~~~--~~~---------~~~g~~~~~-~~~~~~~~~~~~~~~~-~~~~~v~l~eGr~~qIrr~~~~~g~~ 211 (354) |++.|.|.+..+. ++. ...-+...+ +...-..+.+....+. .+++++.+.+||+||||.+|+++|++ T Consensus 163 Y~Alv~G~~~~~~~~i~~pi~r~~~~~~~~~v~~~~~gk~A~T~~~~~~~~~~~~tlv~~~~~TGRTHQIRvHl~~lghP 242 (289) T COG0564 163 YLALVRGHLPEDEGTIDAPIGRDPKNRKKMAVVKEGSGKPAITHYEVLERFGDNYTLVELKPETGRTHQIRVHLAHLGHP 242 (289) T ss_pred EEEEEECCCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCEEEEEEEEEECCCCCEEEEEEECCCCHHHHHHHHHHCCCC T ss_conf 99999685566687883541067677621699716889833799997206387628999996889851999999987997 Q ss_pred EEEEEEEEECCE Q ss_conf 868897587054 Q gi|254780406|r 212 VNRLIRISYGPF 223 (354) Q Consensus 212 V~~L~Rv~~G~~ 223 (354) +.. ---||.. T Consensus 243 I~G--D~~Yg~~ 252 (289) T COG0564 243 IVG--DPLYGGK 252 (289) T ss_pred EEC--CCCCCCC T ss_conf 438--7467874 No 16 >cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli. Probab=99.97 E-value=8.1e-31 Score=213.91 Aligned_cols=146 Identities=32% Similarity=0.469 Sum_probs=128.4 Q ss_pred EEECCCCCEEEECCCCCCCCCCCCEEECCC-CCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCC Q ss_conf 960278751563144333364421011023-4320026655433232022236764100012344574047752112455 Q gi|254780406|r 75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153 (354) Q Consensus 75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~-~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~ 153 (354) ++++|||.|++|++.+.....++++.+... ..++++|||||++||||||||+|+++++.|+++...+.|+|++.|.|.+ T Consensus 1 iivvnKP~G~~~~~~~~~~~~~~~~~l~~~~~~~l~~vhRLDr~TSGlll~ak~~~~~~~l~~~~~~v~K~Y~a~v~g~~ 80 (154) T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80 (154) T ss_pred CEEEECCCCCEEECCCCCCCCCHHHHHHHHCCCCEEEECCCCCCCCCCEEECCCHHHHHHHHHHHCCCCEEEEEEEEEEC T ss_conf 99999999971858999999709999875179861371268999978567737989999998500565057999998727 Q ss_pred CHHHHHHHHHHH-------HCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEE Q ss_conf 646788874000-------0087675034303640268807999999518428999999983986868897587 Q gi|254780406|r 154 DQDKLNLLKKGI-------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220 (354) Q Consensus 154 ~~~~~~~~~~g~-------~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~ 220 (354) ..+.+..+..+. ..+++......+.+.......+|+++.|.|||+||||+||+++|++|++|+||+| T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~slv~~~l~TGR~HQIR~hl~~~G~PIl~l~R~ri 154 (154) T cd02550 81 DEEGIEDLATVRRGRLSGLVDEGVPLAVTKVRVIGEHGGTGRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154 (154) T ss_pred CHHHHEECCCCCCCCCEEEECCCCEECCCEEEEECCCCCCEEEEEEECCCCCHHHHHHHHHCCCEEEEEEEEEC T ss_conf 85882444456424551266599620432889931479948999997988669999999986993956899879 No 17 >PRK11025 23S rRNA pseudouridylate synthase C; Provisional Probab=99.96 E-value=1e-29 Score=207.01 Aligned_cols=215 Identities=16% Similarity=0.198 Sum_probs=158.9 Q ss_pred CCCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC--------EEC--------- Q ss_conf 4466677344788999886-8778999999986986999999240687807999799999--------892--------- Q gi|254780406|r 6 IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--------VPL--------- 67 (354) Q Consensus 6 ~~~~~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg--------~~i--------- 67 (354) .+++++.++||++||+... ..||+.++++|++|.|+|||+.++ ++++|..+|.|++.. .++ T Consensus 12 ~V~~~~~G~RLD~fL~~~l~~~srs~i~klir~g~V~VNg~~vk-~~~~l~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~ 90 (317) T PRK11025 12 AISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIK-PEYKLEAGDEVRIPPVRVAEREEEAVSPHLQKVAA 90 (317) T ss_pred EECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECC-CCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCC T ss_conf 98930079759999997566269999999998699899999957-10465799999988866564445778855110024 Q ss_pred ----CCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCC---CCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CC Q ss_conf ----25564389602787515631443333644210110234---3200266554332320222367641000123--44 Q gi|254780406|r 68 ----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PS 138 (354) Q Consensus 68 ----~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~---~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~ 138 (354) ..+|+..++++|||+|++++........ +.+.+.... ..+..|+|||++||||||++.+...+..|.. .. T Consensus 91 l~~~IlyED~~llvvnKPaGl~vhp~~~~~~~-~~~~l~~~~~~~~~~~iVHRLDr~TSGllv~AK~~~a~~~l~~~f~~ 169 (317) T PRK11025 91 LADVILYEDDHILVLNKPSGTAVHGGSGLSFG-VIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLRE 169 (317) T ss_pred CCCEEEEECCCEEEEECCCCCEECCCCCCHHH-HHHHHHHHCCCCCCCCCEECCCCCCCEEEEEECCHHHHHHHHHHHHH T ss_conf 55607994798899977435622688873168-99999975888876781312699874268871689999999999973 Q ss_pred CCCEEEEEEEECCCCCHHHH--H------HHHHH---HH-CCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHH Q ss_conf 57404775211245564678--8------87400---00-0876750343036402688079999995184289999999 Q gi|254780406|r 139 TQWLRVYRVRFHGQVDQDKL--N------LLKKG---IV-IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206 (354) Q Consensus 139 ~~~~k~Y~v~v~~~~~~~~~--~------~~~~g---~~-~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~ 206 (354) ..|.|+|++.|.|.+....- + .+..+ +. ..++......+.+.......+++++.+.+||.||||.+|+ T Consensus 170 r~v~K~Y~Alv~G~~~~~~~~i~~pl~~~~~~~~~~~~~~~~~gk~a~T~~~v~~~~~~~sLv~~~~~TGRtHQIRvHla 249 (317) T PRK11025 170 KGMQKDYLALVRGQWQSHVKVVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRASPVTGRTHQIRVHTQ 249 (317) T ss_pred CCCCCEEEEEEECCCCCCCCEEEEEECCCCCCCCCEEEECCCCCCCCHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHH T ss_conf 72575599998276367788796100046676764566227777764101446765278640057558075899999998 Q ss_pred HCCCEEEEEEEEEECCEE Q ss_conf 839868688975870545 Q gi|254780406|r 207 FFNWKVNRLIRISYGPFQ 224 (354) Q Consensus 207 ~~g~~V~~L~Rv~~G~~~ 224 (354) ++|++|..- ..||.-. T Consensus 250 ~~G~PI~GD--~~YG~~~ 265 (317) T PRK11025 250 YAGHPIAFD--DRYGDRE 265 (317) T ss_pred HCCCCEECC--CCCCCCC T ss_conf 779968385--2028742 No 18 >cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA. Probab=99.90 E-value=6.6e-24 Score=170.39 Aligned_cols=183 Identities=15% Similarity=0.120 Sum_probs=133.6 Q ss_pred CEEECCEECCCCCEEECCCCEEEE-----CCEECC-----CCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCC--C Q ss_conf 869999992406878079997999-----998922-----5564389602787515631443333644210110234--3 Q gi|254780406|r 39 RVKVNGILLERAAVNVMSTDHIEV-----DGVPLR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--S 106 (354) Q Consensus 39 ~V~Vng~~v~~~~~~v~~~d~v~v-----dg~~i~-----~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~--~ 106 (354) .|+|||+.|+ +.++|.++|.|.+ +..++. .+|+..++++|||+|+++++.......++...+.... . T Consensus 3 ~v~~~G~~v~-~~~~l~~Gd~v~~~~~~~~e~p~p~~l~IlyEDd~llVVnKPaGl~vhP~~~~~~~tl~~~l~~~~~~~ 81 (246) T cd02558 3 VVDADGEPLD-PDSPYRPGTFVWYYRELPDEPPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTGNP 81 (246) T ss_pred EECCCCEECC-CCCEECCCCEEEEEECCCCCCCCCCCCCEEEECCCEEEEECCCCCCEEECCCCCCCHHHHHHHHHCCCC T ss_conf 8880997979-998727999999980589999999989989978999999999998576189972017999998840998 Q ss_pred CEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEEEEEEEECCCCCHHHHHHHHH----H------HHCCCEEEEC Q ss_conf 200266554332320222367641000123--445740477521124556467888740----0------0008767503 Q gi|254780406|r 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKK----G------IVIQGICYGD 174 (354) Q Consensus 107 ~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k~Y~v~v~~~~~~~~~~~~~~----g------~~~~~~~~~~ 174 (354) .+++|+|||++||||||++.+...+..|.. ....+.|+|++.+.+......-..... + ...++..... T Consensus 82 ~~~~VHRLDr~TSGllv~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~A~ 161 (246) T cd02558 82 DLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYEAVAPYVPALTFPLTVRSRIVKGRGFFQAREVEGEPNAE 161 (246) T ss_pred CCCEECCCCCCCCEEEEEECCHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCEEECCCCCCCCCCEEEECCCCCCCEE T ss_conf 65473467998746999988999999999986468452799999983377678636636557887644898058998769 Q ss_pred CCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEE Q ss_conf 43036402688079999995184289999999839868688975870545 Q gi|254780406|r 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224 (354) Q Consensus 175 ~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~ 224 (354) ..+.+.......+.+++.+.+||+||||.+|+++|++|..-. .||+.. T Consensus 162 T~~~~l~~~~~~slv~~~~~TGRtHQIRvHla~iGhPIvGD~--~Yg~~~ 209 (246) T cd02558 162 TRIELLARRGGWGLYRLSPHTGKTHQLRVHMAALGVPILNDP--FYPVLL 209 (246) T ss_pred EEEEEEEECCCEEEEEEEECCCCHHHHHHHHHHCCCCCCCCC--CCCCCC T ss_conf 999999983985899999687862999999998799350783--777644 No 19 >pfam00849 PseudoU_synth_2 RNA pseudouridylate synthase. Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA. Probab=99.80 E-value=2.2e-20 Score=148.17 Aligned_cols=133 Identities=20% Similarity=0.184 Sum_probs=97.1 Q ss_pred EEECCCCCEEEECCCCCCCCCCCCEEEC---CCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEEEEEEEE Q ss_conf 9602787515631443333644210110---2343200266554332320222367641000123--4457404775211 Q gi|254780406|r 75 LWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRF 149 (354) Q Consensus 75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~---~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k~Y~v~v 149 (354) |+++|||+|+.|+..+.....++..... ....++++|||||++|||||||++|.+.++.|.. +...+.|+|++.| T Consensus 1 ~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~f~~~~v~K~Y~a~v 80 (151) T pfam00849 1 YIVVNKPAGVPVHPTDLSDLLSLTELLLVAELGKFRLYPVHRLDRDTSGLLLLAKDGEAANKLNKLFPERKVEKEYLALV 80 (151) T ss_pred CEEEECCCCCEEECCCCCCCCCHHHHHHHHCCCCCCEEEECCCCCCCCCEEEECCCHHHHHHHHHHHHHCCCCEEEEEEE T ss_conf 99999999985821899878628886555515997355851778888544786232688888999866535542899999 Q ss_pred CCCCCHHHHHHHHH----------HHHCCCEEEECCCEEEEEC---CCCEEEEEEEEEECCHHHHHHHHHH Q ss_conf 24556467888740----------0000876750343036402---6880799999951842899999998 Q gi|254780406|r 150 HGQVDQDKLNLLKK----------GIVIQGICYGDMQVTLDTQ---KGSNAWVTVGLREGKNREIKKVFEF 207 (354) Q Consensus 150 ~~~~~~~~~~~~~~----------g~~~~~~~~~~~~~~~~~~---~~~~~~~~v~l~eGr~~qIrr~~~~ 207 (354) .+++..+....... .....++......+.++.. ....+++++.|.+||+||||.||++ T Consensus 81 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~~~slv~~~l~TGR~HQIRvhlas 151 (151) T pfam00849 81 DGPEEEEGTIKAPIKKDKNKVPRRKKEELDGKKAVTHLRVLRSGSKIEDVSLVELELVTGRKHQIRAHLAA 151 (151) T ss_pred ECCCCCCCEEEEECCCCCCCCEEEEEECCCCCCCCEEEEEEEECCCCCCEEEEEEEECCCHHHHHHHHHCC T ss_conf 67778770898101136777727987569984242599998872568996999999672837999998669 No 20 >cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs. Probab=99.77 E-value=3.5e-19 Score=140.63 Aligned_cols=154 Identities=19% Similarity=0.198 Sum_probs=107.3 Q ss_pred CCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCC--CCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEEE Q ss_conf 556438960278751563144333364421011023--43200266554332320222367641000123--44574047 Q gi|254780406|r 69 KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRV 144 (354) Q Consensus 69 ~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~--~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k~ 144 (354) .+|+..++++|||.|+.++........++...+... ...+++|+|||++|||||||+.+.+.+..|.. ....+.|+ T Consensus 19 lyED~~iiVVnKP~Gl~~~p~~~~~~~~l~~~l~~~~~~~~~~~vHRLDr~TSGllv~Ak~~~a~~~l~~~f~~~~v~K~ 98 (213) T cd02557 19 VHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGLTELRPCHRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKE 98 (213) T ss_pred EEECCCEEEEECCCCCCEECCCCCCCCHHHHHHHHHCCCCCCCEEECCCCCCCCEEEEECCHHHHHHHHHHHHCCCCCEE T ss_conf 99689999999999986803899872479999997679987626405688876528997457899999999724756359 Q ss_pred EEEEECCCCCHHHHH--------HHHHHH---HCCCEEEECCCEEEEE--CCCCEEEEEEEEEECCHHHHHHHHHHCCCE Q ss_conf 752112455646788--------874000---0087675034303640--268807999999518428999999983986 Q gi|254780406|r 145 YRVRFHGQVDQDKLN--------LLKKGI---VIQGICYGDMQVTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211 (354) Q Consensus 145 Y~v~v~~~~~~~~~~--------~~~~g~---~~~~~~~~~~~~~~~~--~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~ 211 (354) |++.|.|.+...... ...... ...++......+.+.. .....+++++.+.+||+||||.+|+++|++ T Consensus 99 Y~Alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~sll~~~~~TGRtHQIRvhla~lG~P 178 (213) T cd02557 99 YLARVKGEFPDGEVVVDQPIGLVSPKGGLRNDVDEKGKDARTIFKRLSYNGDLNTSVVLCKPITGRTHQIRVHLQYLGHP 178 (213) T ss_pred EEEEEEEECCCCEEEEECCCCEECCCCCEEEEECCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHCCCC T ss_conf 99999726588838995321000776725885148886431699999983889989999995878889999999987995 Q ss_pred EEEEEEEEECCEE Q ss_conf 8688975870545 Q gi|254780406|r 212 VNRLIRISYGPFQ 224 (354) Q Consensus 212 V~~L~Rv~~G~~~ 224 (354) ++. -..||+.. T Consensus 179 IvG--D~~YG~~~ 189 (213) T cd02557 179 IVN--DPIYNNLG 189 (213) T ss_pred EEC--CCCCCCCC T ss_conf 718--51329856 No 21 >PRK11112 tRNA pseudouridine synthase C; Provisional Probab=99.76 E-value=2.7e-19 Score=141.31 Aligned_cols=155 Identities=16% Similarity=0.183 Sum_probs=103.8 Q ss_pred CCCCEEEEECCCCCEEEECCCCCCCCC--CCCEEECC-CCCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEE Q ss_conf 556438960278751563144333364--42101102-343200266554332320222367641000123--4457404 Q gi|254780406|r 69 KAERTRLWLYHKPIGLVTTHSDPDGRS--TVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLR 143 (354) Q Consensus 69 ~~~~~~~~~~~KP~g~~~~~~~~~~~~--~~~~~~~~-~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k 143 (354) .+|+.+++++|||+|++|+........ .++..+.. ....+++|+|||++||||||++.+...+..|.. ....+.| T Consensus 5 lyED~~llVVnKPaGl~vh~~~~~~~~~~~~~~~l~~~~~~~~~~VHRLDr~TSGllv~AK~~~a~~~L~~~f~~~~v~K 84 (257) T PRK11112 5 LYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQIGQHVFTAHRLDRPTSGVLLMALSSEAARLLAQQFEQHQIQK 84 (257) T ss_pred EEECCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHHHCCCCE T ss_conf 99669899999999986479988878519999999875277653205778987517999689999999999987576863 Q ss_pred EEEEEECCCCCHHHHH---------HHHHHHHCCCEEEECC--CEEEEE-----------CCCCEEEEEEEEEECCHHHH Q ss_conf 7752112455646788---------8740000087675034--303640-----------26880799999951842899 Q gi|254780406|r 144 VYRVRFHGQVDQDKLN---------LLKKGIVIQGICYGDM--QVTLDT-----------QKGSNAWVTVGLREGKNREI 201 (354) Q Consensus 144 ~Y~v~v~~~~~~~~~~---------~~~~g~~~~~~~~~~~--~~~~~~-----------~~~~~~~~~v~l~eGr~~qI 201 (354) +|++.|.|.+...... .+...+...+...+++ .+.... .....+++++.+.+||.||| T Consensus 85 ~Y~Alv~G~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~~~~~~~sLv~~~p~TGRtHQI 164 (257) T PRK11112 85 TYHAIVRGWLMEEAVLDYPLKEELDKIADKFAREDKEPQPAVTHYRGLATVEMPVATGRYPTTRYSLVELEPKTGRKHQL 164 (257) T ss_pred EEEEEEEEECCCCCEEEEECCCCCCCCCCEEECCCCCCEEEEEEEEEEEEEEEECCCCCCCCCCEEEEEEECCCCCHHHH T ss_conf 99999964538997685243446665563130228986363454111026875101232467857999996486852999 Q ss_pred HHHHHHCCCEEEEEEEEEECCEEC Q ss_conf 999998398686889758705451 Q gi|254780406|r 202 KKVFEFFNWKVNRLIRISYGPFQL 225 (354) Q Consensus 202 rr~~~~~g~~V~~L~Rv~~G~~~l 225 (354) |.+|+++|++|+. -..||+... T Consensus 165 RvHla~lGhPIvG--D~~YG~~~~ 186 (257) T PRK11112 165 RRHMAHLRHPIIG--DSKHGDLRQ 186 (257) T ss_pred HHHHHHCCCCEEC--CCCCCCCCC T ss_conf 9999987996757--725587544 No 22 >PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional Probab=99.75 E-value=1e-18 Score=137.76 Aligned_cols=152 Identities=14% Similarity=0.178 Sum_probs=105.9 Q ss_pred CCCCEEEEECCCCCEEEECCCCC-CCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEEEE Q ss_conf 55643896027875156314433-336442101102343200266554332320222367641000123--445740477 Q gi|254780406|r 69 KAERTRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVY 145 (354) Q Consensus 69 ~~~~~~~~~~~KP~g~~~~~~~~-~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k~Y 145 (354) .+|+..++++|||.|++++...- ....++...+....+...+|+|||++|||||||+.+.+.+..|.. ....+.|+| T Consensus 17 lyED~~llvvnKP~gl~~~pg~~~~~~~~~~~~~~~~~~~~~~vHRLDr~TSGlll~AK~~~a~~~l~~~f~~r~v~K~Y 96 (219) T PRK10158 17 LYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQY 96 (219) T ss_pred EEECCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCEE T ss_conf 99799999999999982079976456206999877407866634778999753699978999999998878737467379 Q ss_pred EEEECCCCCHHHHH-H----------HHHHHHCCCEEEECCCEEEEE-CCCCEEEEEEEEEECCHHHHHHHHHHCCCEEE Q ss_conf 52112455646788-8----------740000087675034303640-26880799999951842899999998398686 Q gi|254780406|r 146 RVRFHGQVDQDKLN-L----------LKKGIVIQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213 (354) Q Consensus 146 ~v~v~~~~~~~~~~-~----------~~~g~~~~~~~~~~~~~~~~~-~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~ 213 (354) ++.|.|.+....-. . ....+..+.+......+.+.. .....+++++.+.+||+||||.+|+++|+++. T Consensus 97 lA~v~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~~~lv~l~p~TGRtHQIRvhla~lG~PIv 176 (219) T PRK10158 97 VARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPIL 176 (219) T ss_pred EEEEECCCCCCCCCCCCCEEECCCCCCCEEEECCCCCCCCEEEEEEEECCCCEEEEEEEECCCCHHHHHHHHHHCCCCEE T ss_conf 99983686643561124525047777616997246741215899999738985999998666851899999998799274 Q ss_pred EEEEEEECC Q ss_conf 889758705 Q gi|254780406|r 214 RLIRISYGP 222 (354) Q Consensus 214 ~L~Rv~~G~ 222 (354) .- .-||. T Consensus 177 GD--~~Yg~ 183 (219) T PRK10158 177 GD--RFYAS 183 (219) T ss_pred CC--CCCCC T ss_conf 78--77788 No 23 >KOG1919 consensus Probab=99.73 E-value=2.7e-17 Score=128.71 Aligned_cols=204 Identities=20% Similarity=0.232 Sum_probs=142.1 Q ss_pred HHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEE--C--C-----EECC-CCCCEEEEECCCCCEE Q ss_conf 788999886-87789999999869869999992406878079997999--9--9-----8922-5564389602787515 Q gi|254780406|r 16 VSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--D--G-----VPLR-KAERTRLWLYHKPIGL 84 (354) Q Consensus 16 L~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~v--d--g-----~~i~-~~~~~~~~~~~KP~g~ 84 (354) |..+++... .-.|-..+..|+.|.|+|||+.+. ..+.+..+|.|.. . . .++. ..++..|+++|||.|+ T Consensus 46 ~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~~-v~~i~k~~d~l~~~vhrh~p~~~~~~~~Iv~ed~~~vVvnKP~gi 124 (371) T KOG1919 46 LVDVFVSEFRLRERAYYESAIKLGRVTVNGEQVR-VSLIVKNGDVLCHTVHRHEPPVAYLPIRIVFEDKDYVVVNKPHGI 124 (371) T ss_pred HHHHHHHHHHCCCHHHHHHHHHCCCEEECCEEEE-EEEEECCCCEEEEEECCCCCCCCCCCCCEEEECCCEEEEECCCCC T ss_conf 7799989875371576665653686588858600-478712588887764047887544344158853998999589987 Q ss_pred EECCCCCCCCCCCCEEECCC--CCCEECCCCCCCCCCCEEEECCCCCCCCCCCCC--CCCCEEEE-EEEECCCCCHHHHH Q ss_conf 63144333364421011023--432002665543323202223676410001234--45740477-52112455646788 Q gi|254780406|r 85 VTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVY-RVRFHGQVDQDKLN 159 (354) Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~--~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p--~~~~~k~Y-~v~v~~~~~~~~~~ 159 (354) .+++.......++...+... ...+.+++|||+.|||||+|..+-+-+..+... ...+.|+| .+.|.+.+...... T Consensus 125 pVhp~g~~~~n~i~~~l~~~~~~~~~~~~hRLDr~tSGllvlAkt~~~~~~~~~~~r~~~~~k~Y~v~~v~g~fp~~~~~ 204 (371) T KOG1919 125 PVHPTGRYRENTITKILAALHKVEGLRPCHRLDRLTSGLLVLAKTKEAADKFHEVLRKRTVKKEYVVARVEGPFPVVGEV 204 (371) T ss_pred CEECCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEECHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCCEE T ss_conf 54016854436536888874145566232246766564489985655768999997435410379999972457877627 Q ss_pred HHHH-----------HHHCCC------EEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECC Q ss_conf 8740-----------000087------67503430364026880799999951842899999998398686889758705 Q gi|254780406|r 160 LLKK-----------GIVIQG------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222 (354) Q Consensus 160 ~~~~-----------g~~~~~------~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~ 222 (354) .... ++.-.+ +......+......+..+|+++-+.+||.||||.+|+++|+++. --.-|++ T Consensus 205 ~i~~~~~~~~~~~~~~l~~~~~~~~~~~k~a~T~~~~~~~~~~ss~V~~~PlTGRtHQIRvHlq~lG~PI~--gD~~Y~~ 282 (371) T KOG1919 205 EIKEPIGEEERPLRMGLNAVGVRDEVAAKDAKTLFKVLSYDGGSSLVECRPLTGRTHQIRVHLQYLGHPIA--GDPKYGN 282 (371) T ss_pred EECCCCCCCCCCCCEEEEECCCCCCCCCCCCEEEEEECCCCCCEEEEEEECCCCCHHHHHHHHHHHCCCCC--CCCCCCC T ss_conf 71787553456651576401224444565644688872348966999963267967999999997199857--8855666 No 24 >cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved. Probab=99.73 E-value=2.9e-18 Score=134.84 Aligned_cols=154 Identities=19% Similarity=0.195 Sum_probs=100.3 Q ss_pred CCCCEEEEECCCCCEEEECCCCCCCCCC--CCEEECCC-CCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEE Q ss_conf 5564389602787515631443333644--21011023-43200266554332320222367641000123--4457404 Q gi|254780406|r 69 KAERTRLWLYHKPIGLVTTHSDPDGRST--VFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLR 143 (354) Q Consensus 69 ~~~~~~~~~~~KP~g~~~~~~~~~~~~~--~~~~~~~~-~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k 143 (354) .+|+..++++|||.|+.|+........+ .+..+... ...+++|+|||++|||||||+.+.+.+..|.. ....+.| T Consensus 4 vyED~~ilvvnKP~Gl~~hp~~~~~~~~~~~~~~~~~~~~~~~~~vHRLDr~TSGllv~Ak~~~a~~~l~~~f~~~~v~K 83 (223) T cd02563 4 LYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLGQHVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTEHRVHK 83 (223) T ss_pred EEECCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCEECCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCC T ss_conf 99679999999999982658999988369999998875378753404778987635999845899999999987551122 Q ss_pred EEEEEECCCCCHHHHHH--H-------HHHHHCCCEEEECC--CEEEE-----------ECCCCEEEEEEEEEECCHHHH Q ss_conf 77521124556467888--7-------40000087675034--30364-----------026880799999951842899 Q gi|254780406|r 144 VYRVRFHGQVDQDKLNL--L-------KKGIVIQGICYGDM--QVTLD-----------TQKGSNAWVTVGLREGKNREI 201 (354) Q Consensus 144 ~Y~v~v~~~~~~~~~~~--~-------~~g~~~~~~~~~~~--~~~~~-----------~~~~~~~~~~v~l~eGr~~qI 201 (354) +|++.|.|.+....... + .......+....++ ..... ......+++++.+.+||+||| T Consensus 84 ~Y~Alv~G~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGRtHQI 163 (223) T cd02563 84 TYLAVVRGYVPESGTIDYPLSEELDKLADKFASDDKAPQAATTHYRLLAVEELPVVVGKYPTSRYSLVELTPHTGRKHQL 163 (223) T ss_pred EEEEEEEEECCCCCEEEEECCCCCCCCCCEEEECCCCCCCEEEEEEEEEEEECCEEECCCCCCCEEEEEEEECCCCHHHH T ss_conf 69999984079998798654546775563687427887634889887655320001011477747999999676870899 Q ss_pred HHHHHHCCCEEEEEEEEEECCEE Q ss_conf 99999839868688975870545 Q gi|254780406|r 202 KKVFEFFNWKVNRLIRISYGPFQ 224 (354) Q Consensus 202 rr~~~~~g~~V~~L~Rv~~G~~~ 224 (354) |.+|+++|+++..- .-||.-. T Consensus 164 RvHla~lG~PIvGD--~~YG~~~ 184 (223) T cd02563 164 RRHLAHIRHPIIGD--TTHGDGR 184 (223) T ss_pred HHHHHHCCCCEECC--CCCCCCC T ss_conf 99999879978277--2568754 No 25 >cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli. Probab=99.67 E-value=3.4e-17 Score=128.10 Aligned_cols=149 Identities=20% Similarity=0.191 Sum_probs=110.3 Q ss_pred EEECCCCCEEEECCCCCCCCCCCCEE------ECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCC--CCCCEEEEE Q ss_conf 96027875156314433336442101------1023432002665543323202223676410001234--457404775 Q gi|254780406|r 75 LWLYHKPIGLVTTHSDPDGRSTVFDN------LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146 (354) Q Consensus 75 ~~~~~KP~g~~~~~~~~~~~~~~~~~------~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p--~~~~~k~Y~ 146 (354) ++++|||.|+.++........++... .......+++|+|||++|+||||++.+...+..|... ...+.|.|. T Consensus 1 ~lvvnKP~gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGl~l~Ak~~~~~~~l~~~~~~~~~~K~Y~ 80 (185) T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYL 80 (185) T ss_pred CEEEECCCCCCEECCCCCCCCCHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCEEEECHHHHHHHHHHHHCCCCEEEEEE T ss_conf 99999999983648989988589999999998648998653434789887561888660999999987446564403999 Q ss_pred EEECCCCCHHHHHHHH-----------HHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEE Q ss_conf 2112455646788874-----------00000876750343036402688079999995184289999999839868688 Q gi|254780406|r 147 VRFHGQVDQDKLNLLK-----------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215 (354) Q Consensus 147 v~v~~~~~~~~~~~~~-----------~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L 215 (354) +.+.|.+......... .-....++...-..+.+.......+++++.+.+||.||||.+|+++|+++ + T Consensus 81 a~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~slv~~~~~TGR~HQIR~hla~lg~PI--v 158 (185) T cd02869 81 ALVDGKPPEDEGTIDAPLGRKKRKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASIGHPI--V 158 (185) T ss_pred EEECCCCCCCCCEEECCEEECCCCCCEEEEECCCCCEEEEEHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHCCCCE--E T ss_conf 99667656576568221441566671389856998476200134553798699998816587799999999879967--4 Q ss_pred EEEEECCEEC Q ss_conf 9758705451 Q gi|254780406|r 216 IRISYGPFQL 225 (354) Q Consensus 216 ~Rv~~G~~~l 225 (354) --..||...- T Consensus 159 GD~~Yg~~~~ 168 (185) T cd02869 159 GDPKYGGKAS 168 (185) T ss_pred CCCCCCCCCC T ss_conf 8635698533 No 26 >TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621; InterPro: IPR006508 These sequences represent a clade within the pseudouridine synthase superfamily. The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences in this family are most closely related to RluA ; only Neisseria does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.. Probab=99.37 E-value=2.1e-13 Score=104.30 Aligned_cols=140 Identities=15% Similarity=0.176 Sum_probs=100.0 Q ss_pred CCCEEEEECCCCCEEEECCCCCCCCCCCCEEECC--CCCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEEEE Q ss_conf 5643896027875156314433336442101102--343200266554332320222367641000123--445740477 Q gi|254780406|r 70 AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVY 145 (354) Q Consensus 70 ~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~--~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k~Y 145 (354) +.-..++++|||.|+.+|.++.+ .-+...+.. ..++++.|+|||+.|||||||+-+-+-|..|.. ....|+|+| T Consensus 6 f~H~DF~~INK~~giSVHkD~ge--tgL~~~vA~Qlgv~~vwLvHRLDK~TSGiLllAlNaesAselS~~Fa~~ki~KtY 83 (222) T TIGR01621 6 FRHSDFVLINKSEGISVHKDDGE--TGLLREVAKQLGVEKVWLVHRLDKVTSGILLLALNAESASELSRLFAKKKIKKTY 83 (222) T ss_pred EECCCEEEEECCCCEEEEECCCC--HHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHCHHHHHHHHHHHHCCEEEEEE T ss_conf 53686789867998327725711--1389999998189808998700034468999860478999998765217066677 Q ss_pred EEEECCCCCHH------HHHHHHHHHHC-----C-CEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEE Q ss_conf 52112455646------78887400000-----8-767503430364026880799999951842899999998398686 Q gi|254780406|r 146 RVRFHGQVDQD------KLNLLKKGIVI-----Q-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213 (354) Q Consensus 146 ~v~v~~~~~~~------~~~~~~~g~~~-----~-~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~ 213 (354) ++--+..+... .+++-+.|..= | --.+++..+.+ ...--.|-+..++||+||||.-|.++|.+|+ T Consensus 84 LAls~~KPkKKQGlI~GdMeksR~g~WKL~~~~eNpAiTrF~S~s~---a~~lRLFilkPhTGKTHQlRVAmKSlGSpIl 160 (222) T TIGR01621 84 LALSDKKPKKKQGLIIGDMEKSRRGAWKLVRSKENPAITRFESVSI---AEKLRLFILKPHTGKTHQLRVAMKSLGSPIL 160 (222) T ss_pred EECCCCCCCCCCCEEECCHHHHHCCCCHHCCCCCCCEECCEEEEEE---CCCCCEEEECCCCCCHHHHHHHHHHCCCCCC T ss_conf 6313689874442025571242000100027898960111245652---3888637556899963788788877276300 Q ss_pred E Q ss_conf 8 Q gi|254780406|r 214 R 214 (354) Q Consensus 214 ~ 214 (354) . T Consensus 161 G 161 (222) T TIGR01621 161 G 161 (222) T ss_pred C T ss_conf 5 No 27 >cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes. Probab=99.07 E-value=2.8e-10 Score=84.56 Aligned_cols=66 Identities=32% Similarity=0.478 Sum_probs=55.6 Q ss_pred HHHHHHHHHC-CCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCC---CCCEEEEECC Q ss_conf 4478899988-6877899999998698699999924068780799979999989225---5643896027 Q gi|254780406|r 14 QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---AERTRLWLYH 79 (354) Q Consensus 14 ~RL~K~la~~-g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~---~~~~~~~~~~ 79 (354) +||++||+.+ +.+||++|.++|.+|.|+|||+++++++++|.++|.|+++++.... +++..++++| T Consensus 1 ~RLd~~l~~~~~~~Sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~gd~i~i~~~~~~~~i~~~~~~~~~i~ 70 (70) T cd00165 1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVYEDKKLLVVN 70 (70) T ss_pred CCHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCCCCEEEECCCCCCCCEEEECCCEEEEC T ss_conf 9488999874871589999999981938989999588888989999999878778867323269899969 No 28 >smart00363 S4 S4 RNA-binding domain. Probab=99.01 E-value=6.5e-10 Score=82.27 Aligned_cols=55 Identities=38% Similarity=0.579 Sum_probs=50.2 Q ss_pred HHHHHHHHHCCC-CCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECC Q ss_conf 447889998868-7789999999869869999992406878079997999998922 Q gi|254780406|r 14 QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68 (354) Q Consensus 14 ~RL~K~la~~g~-~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~ 68 (354) .|||+||+..|+ +||++|+++|..|.|+|||++++++++.|.++|.|+++++... T Consensus 1 ~RLD~~l~~~~~~~Sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I~~~~~~~~ 56 (60) T smart00363 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKELK 56 (60) T ss_pred CCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCEEEECCCCCC T ss_conf 97889999838704799999999849179899994789889899999999885003 No 29 >pfam01479 S4 S4 domain. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA. Probab=98.85 E-value=2.9e-09 Score=78.16 Aligned_cols=47 Identities=38% Similarity=0.591 Sum_probs=44.7 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEE Q ss_conf 4478899988687-7899999998698699999924068780799979 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v 60 (354) +||++||+..|+| ||++|.++|.+|.|+|||++++++++.|.++|.| T Consensus 1 ~RLd~~l~~~~~~~Sr~~a~~~I~~G~V~VNg~~v~~~~~~v~~gD~i 48 (48) T pfam01479 1 MRLDKVLARLGLASSRSEARQLIRHGHVRVNGKVVKDPSYRVKPGDVI 48 (48) T ss_pred CCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCCC T ss_conf 966799998676148999999998897798999957898688992999 No 30 >COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis] Probab=98.48 E-value=2.3e-07 Score=66.16 Aligned_cols=51 Identities=29% Similarity=0.314 Sum_probs=47.0 Q ss_pred CCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEE Q ss_conf 77344788999886-87789999999869869999992406878079997999 Q gi|254780406|r 11 FTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 11 ~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) ...+||||||.-+. +-+|.-|+.+|+.|+|.|||+.+ .++..|..+|.|+| T Consensus 6 ~~~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i 57 (100) T COG1188 6 ADRMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTI 57 (100) T ss_pred CCCEEHHHHHHHHHHHHHHHHHHHHHHCCEEEECCEEC-CCCCCCCCCCEEEE T ss_conf 65165678887887742289999998779698999675-65561477989999 No 31 >TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium. Probab=98.46 E-value=3.2e-07 Score=65.31 Aligned_cols=53 Identities=15% Similarity=0.234 Sum_probs=51.2 Q ss_pred CCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC Q ss_conf 73447889998868778999999986986999999240687807999799999 Q gi|254780406|r 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64 (354) Q Consensus 12 ~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg 64 (354) .+.|||.++|....+||.+|..+|++|+|+||+++++++++.|.++|.|.|-| T Consensus 182 sSlRLDavvs~~~~~SRska~~lI~~g~V~vN~~~v~~~s~~v~~gDiiSvRG 234 (257) T TIGR03069 182 ASLRIDAIASAGFGLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRG 234 (257) T ss_pred CCCCHHHHHHHHHCCCHHHHHHHHHCCEEEECCEEECCCCCCCCCCCEEEEEC T ss_conf 12138999998866579999999884968989999057875668999999906 No 32 >COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] Probab=98.45 E-value=4.8e-07 Score=64.21 Aligned_cols=55 Identities=27% Similarity=0.383 Sum_probs=50.3 Q ss_pred CCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE Q ss_conf 734478899988687-7899999998698699999924068780799979999989 Q gi|254780406|r 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66 (354) Q Consensus 12 ~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~ 66 (354) ..+||+.+|.+.|++ ||..|..+|.+|.|.|||..|+.|++.|+.++.|+|.+.. T Consensus 1 ~k~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~~~ 56 (245) T COG1189 1 NKMRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKGEE 56 (245) T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHCCEEEECCEEECCCCEECCCCCEEEECCCC T ss_conf 93238999997353320999999987685788999942765245898637875666 No 33 >TIGR01017 rpsD_bact ribosomal protein S4; InterPro: IPR005709 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This family consists of organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit. Probab=98.36 E-value=3.3e-07 Score=65.18 Aligned_cols=53 Identities=25% Similarity=0.438 Sum_probs=49.4 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE Q ss_conf 4478899988687-7899999998698699999924068780799979999989 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~ 66 (354) .|||-++-++|+| ||+.|.+|+..|-|.|||++|+-|++.|.++|.|.|-.+. T Consensus 100 ~RLDNvVYRlGfA~Tr~~ARQLVsHGhi~vNGk~VdIPSy~v~~Gd~i~ikEk~ 153 (217) T TIGR01017 100 SRLDNVVYRLGFAPTRRAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKS 153 (217) T ss_pred CCCCCEEECCCCHHHHHHHHHHHHCCEEEECCEEECCCEEEECCCCEEEEEECC T ss_conf 100101021271200787635640880787981852240670799889981032 No 34 >COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis] Probab=98.29 E-value=1.7e-06 Score=60.71 Aligned_cols=56 Identities=25% Similarity=0.396 Sum_probs=50.7 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCC Q ss_conf 4478899988687-7899999998698699999924068780799979999989225 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~ 69 (354) -|||-++-.+|++ |+++|.+||..|.|.|||++|+.|++.|.++|.|.|+.+.-.. T Consensus 94 rRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~~s~ 150 (205) T COG0522 94 RRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKSKSP 150 (205) T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCEEECCCCEEEEECCCCCH T ss_conf 887899998404135999998840662899999952673796377788752034542 No 35 >COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown] Probab=98.22 E-value=1.7e-06 Score=60.79 Aligned_cols=58 Identities=26% Similarity=0.370 Sum_probs=53.5 Q ss_pred CCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC Q ss_conf 4666773447889998868778999999986986999999240687807999799999 Q gi|254780406|r 7 VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64 (354) Q Consensus 7 ~~~~~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg 64 (354) ++-.-.+.|||.++|...-.||..|.+||+.|+|+||.++|+++.+.|..+|.|.+-| T Consensus 174 ~~~~vsSlRLD~vis~~~~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG 231 (257) T COG2302 174 LDVTVSSLRLDVVISEGFGLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRG 231 (257) T ss_pred EEEEEEHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCEECCCCEEEEEC T ss_conf 7654212407999998876559999998773732771299126663322498999840 No 36 >PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed Probab=98.18 E-value=4.4e-06 Score=58.12 Aligned_cols=152 Identities=19% Similarity=0.201 Sum_probs=93.3 Q ss_pred ECCCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEE Q ss_conf 92255643896027875156314433336442101102343200266554332320222367641000123445740477 Q gi|254780406|r 66 PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145 (354) Q Consensus 66 ~i~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y 145 (354) +|.-.-..-++++|||.|+.++..=..-+.. + ...+....|-||-..+|+|++.-.. +.++..--....|+| T Consensus 15 ~~~~~~~~Gil~idKP~G~TS~~vv~~vrk~----l--~~kKvGH~GTLDP~AtGvL~i~~G~--aTK~~~~l~~~~K~Y 86 (300) T PRK04270 15 PIEEYINYGVVNLDKPPGPTSHEVAAWVRDI----L--GVEKAGHGGTLDPKVTGVLPVALGK--ATKVVQALLESPKEY 86 (300) T ss_pred CHHHHHHCCEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEECH--HHHHHHHHCCCCCEE T ss_conf 9999972999999689899989999999998----5--8884687867897462337888679--888869867589458 Q ss_pred EEEE--CCCCCHHHHHHHHHHHHCCCEEEECCC--------------EEEEECCCCEEEEEEEEEECCHHHHHHHHHHCC Q ss_conf 5211--245564678887400000876750343--------------036402688079999995184289999999839 Q gi|254780406|r 146 RVRF--HGQVDQDKLNLLKKGIVIQGICYGDMQ--------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209 (354) Q Consensus 146 ~v~v--~~~~~~~~~~~~~~g~~~~~~~~~~~~--------------~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g 209 (354) .+++ ..+++.+.+......+.-.-.+..|.. +.+..-+.....++|.-.-|-| ||-++..+| T Consensus 87 ~~~~~l~~~~~~~~i~~~l~~f~G~i~Q~PP~~SAvKr~~R~~~I~~~~ll~~~~~~~~~~v~cskGTY--IRsL~~DiG 164 (300) T PRK04270 87 VCVMHLHGDVPEEKIREVFKEFTGEIYQKPPLKSAVKRRLRIRTIYELEILEIDGRDVLFRVGCESGTY--IRKLCHDIG 164 (300) T ss_pred EEEEECCCCCCHHHHHHHHHHCCCEEEECCCHHHHHCCCCCCCEEEEEEEEEEECCEEEEEEEECCCCC--HHHHHHHHH T ss_conf 771013999999999999997785352069736640455567469999988860886999999789847--899999999 Q ss_pred ------CEEEEEEEEEECCEECCC Q ss_conf ------868688975870545187 Q gi|254780406|r 210 ------WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 210 ------~~V~~L~Rv~~G~~~l~~ 227 (354) -.+..|.|+++|+|.+.+ T Consensus 165 ~~Lg~~a~m~~LrRt~~G~F~~~~ 188 (300) T PRK04270 165 EALGTGAHMRELRRTRTGPFTEDE 188 (300) T ss_pred HHHCCCEEEEEEEEEEECCCCHHH T ss_conf 984986686353514783717898 No 37 >PRK12565 30S ribosomal protein S4; Provisional Probab=98.16 E-value=4.4e-06 Score=58.13 Aligned_cols=53 Identities=26% Similarity=0.379 Sum_probs=49.2 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE Q ss_conf 4478899988687-7899999998698699999924068780799979999989 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~ 66 (354) .|||-++-++|++ ||.+|.+||..|.|.|||+.|+-|++.|.++|.|+|..+. T Consensus 88 ~RLDnvv~R~gfa~t~~~ARQlV~Hghi~vng~kVdIPSy~vk~GDvI~vkeks 141 (197) T PRK12565 88 CRLDNVVYRIGFASSIRQARQMVNHGHILVNGKKVNIPSYEVKVGDEITLREKS 141 (197) T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCEEECCCCEEEECHHH T ss_conf 866677113441057999866740788897998955887670699999973322 No 38 >PRK10348 ribosome-associated heat shock protein Hsp15; Provisional Probab=98.14 E-value=3.7e-06 Score=58.62 Aligned_cols=56 Identities=18% Similarity=0.148 Sum_probs=49.0 Q ss_pred CCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC Q ss_conf 66677344788999886-8778999999986986999999240687807999799999 Q gi|254780406|r 8 QENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64 (354) Q Consensus 8 ~~~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg 64 (354) ++....+||||||..+= +-||.-|-.+|..|+|+|||+.++ |+..|.++|.|+|-- T Consensus 3 ~~p~~k~RiDkwLW~aRffKTRslA~~a~~~G~V~vnG~~~K-ps~~V~~GD~l~i~~ 59 (133) T PRK10348 3 EKPAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSK-PSKIVELNATLTLRQ 59 (133) T ss_pred CCCCCCEEEHHHHHHHEEHHHHHHHHHHHHCCCEEECCEECC-CCCCCCCCCEEEEEE T ss_conf 887550540200315201000999999998798898998868-888768999999986 No 39 >PRK04099 truB tRNA pseudouridine synthase B; Provisional Probab=98.13 E-value=1.5e-05 Score=54.69 Aligned_cols=144 Identities=19% Similarity=0.181 Sum_probs=88.0 Q ss_pred EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC-- Q ss_conf 896027875156314433336442101102343200266554332320222367641000123445740477521124-- Q gi|254780406|r 74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG-- 151 (354) Q Consensus 74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~-- 151 (354) -++++|||.|+.++..=..-+. .+ ...+....|-||-..+|||++.-. -+.+|..--....|+|.+++.- T Consensus 3 gil~i~KP~G~TS~~vv~~vkk----~l--~~kKvGH~GTLDP~AtGvLiv~~G--~aTKl~~~l~~~~K~Y~a~i~lG~ 74 (272) T PRK04099 3 RLFVANKPPGLSSNAFLSRLKR----KY--GVKKAGFSGTLDPFAKGVLIVAFG--QYTKLFRFLDKTPKTYKATLWLGA 74 (272) T ss_pred EEEEEECCCCCCHHHHHHHHHH----HH--CCCCCCCCCCCCCCCCCEEEEEEC--HHHHHHHHHCCCCCEEEEEEEECC T ss_conf 3999618998998999999999----84--998446370569866045999988--776311766778827999999886 Q ss_pred -----------------CCCHHHHHHHHHHHHCCCEE--------------------------EECCCE-----EEEECC Q ss_conf -----------------55646788874000008767--------------------------503430-----364026 Q gi|254780406|r 152 -----------------QVDQDKLNLLKKGIVIQGIC--------------------------YGDMQV-----TLDTQK 183 (354) Q Consensus 152 -----------------~~~~~~~~~~~~g~~~~~~~--------------------------~~~~~~-----~~~~~~ 183 (354) +++.+.++.....+.-.-.. ..+..+ .+..-. T Consensus 75 ~TdT~D~e~i~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySA~Kv~Gkr~YelAR~G~~ve~~~r~v~I~~i~ll~~~ 154 (272) T PRK04099 75 KSPSLDIENIESIEIIKPFDLADLEKIIKSLQGEISYTPPKFSAKKINGTRAYELARKGEEFELKPIQMEIFECKILSYN 154 (272) T ss_pred CCCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCHHHHHHHCCHHHHHHHHCCCCCCCCCEEEEEEEEEEEEEC T ss_conf 14788745136744689999999999999777018983888996301454399998669730357579999999999612 Q ss_pred CCEEEEEEEEEECCHHHHHHHHHHCCC------EEEEEEEEEECCEECCC Q ss_conf 880799999951842899999998398------68688975870545187 Q gi|254780406|r 184 GSNAWVTVGLREGKNREIKKVFEFFNW------KVNRLIRISYGPFQLGT 227 (354) Q Consensus 184 ~~~~~~~v~l~eGr~~qIrr~~~~~g~------~V~~L~Rv~~G~~~l~~ 227 (354) .....++|....|-| ||-++.-+|. .+..|.|+++|+|.|.+ T Consensus 155 ~p~~~f~v~cSkGTY--IRSLa~Dig~~Lg~~a~l~~L~Rt~~G~F~le~ 202 (272) T PRK04099 155 HPFLTFEITVSEGAY--IRSYAELFAKKLGVNGTLSSLERISEGKFVYEN 202 (272) T ss_pred CCEEEEEEEECCCCC--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH T ss_conf 986999999869595--889999998985991898342821681717787 No 40 >CHL00113 rps4 ribosomal protein S4; Reviewed Probab=98.09 E-value=4.5e-06 Score=58.06 Aligned_cols=53 Identities=17% Similarity=0.359 Sum_probs=49.4 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE Q ss_conf 4478899988687-7899999998698699999924068780799979999989 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~ 66 (354) .|||-++-++|++ ||.+|.+||..|.|.|||+.|+-|++.|.++|+|+|..+. T Consensus 89 ~RLDnvVyRlGfA~Tr~~ARQlV~HgHi~VNgkkVnIPSy~vk~GDvI~v~~ks 142 (201) T CHL00113 89 MRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPRDIITIKDKQ 142 (201) T ss_pred HHHHHHHHHCCCCCCHHHHHHEEECCEEEECCEEECCCCEEEECCCEEEECCCC T ss_conf 999999987054058887610584662998998933787584279989975344 No 41 >cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Probab=98.07 E-value=1.5e-05 Score=54.81 Aligned_cols=156 Identities=22% Similarity=0.236 Sum_probs=84.8 Q ss_pred EEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCC-C-CCCCCCCCCCCCCEEEEEEEECC- Q ss_conf 96027875156314433336442101102343200266554332320222367-6-41000123445740477521124- Q gi|254780406|r 75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND-G-GLARVLELPSTQWLRVYRVRFHG- 151 (354) Q Consensus 75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTnd-g-~l~~~l~~p~~~~~k~Y~v~v~~- 151 (354) ++++|||.|+.++..=..-...+...+.. .......|-||-.++|||++.-. + .+...|+ .....|+|.+++.- T Consensus 2 il~v~KP~G~TS~~vv~~v~~~l~k~~~~-~kk~g~~GTLDP~AtGvLvi~vG~aTKl~~~l~--~~~~~K~Y~~~~~lG 78 (226) T cd02868 2 LFAVYKPPGVHWKHVRDTIESNLLKYFPE-DKVLVGVHRLDAFSSGVLVLGVNHGNKLLSHLY--SNHPTRVYTIRGLLG 78 (226) T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHHCC-CEEEECCCCCCCCCCCCEEEEECHHHHHHHHHH--CCCCCEEEEEEEEEC T ss_conf 89997599998999999999999766417-746960888897560338999887772569986--689976999999975 Q ss_pred -------------------CCCHHHHHHHHHHHHCCCEEEE--------------------------CCC-----EEEEE Q ss_conf -------------------5564678887400000876750--------------------------343-----03640 Q gi|254780406|r 152 -------------------QVDQDKLNLLKKGIVIQGICYG--------------------------DMQ-----VTLDT 181 (354) Q Consensus 152 -------------------~~~~~~~~~~~~g~~~~~~~~~--------------------------~~~-----~~~~~ 181 (354) +++.+.++.....+.-.-.... +-. +.+.. T Consensus 79 ~~TdT~D~~G~v~~~~~~~~i~~~~i~~~l~~~~g~~~q~pP~~SA~k~~GkraYelAR~G~~~~~~~r~v~I~~i~l~~ 158 (226) T cd02868 79 KATENFFHTGRVIEKTTYDHITREKIERLLAVIQSGHQQKAFELCSVDDQSQQAAELAARGLIRPADKSPPIIYGIRLLE 158 (226) T ss_pred CCCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHCCCEEEECCCHHEEEECCHHHHHHHHCCCCCCCCCCCEEEEEEEEEE T ss_conf 65479899708797358987999999999997158705857622357708812899986899766788734999999985 Q ss_pred CCCCEEEEEEEEEECCHHHHHHHHHHCCC------EEEEEEEEEECCEECCC-CCCCCE Q ss_conf 26880799999951842899999998398------68688975870545187-554748 Q gi|254780406|r 182 QKGSNAWVTVGLREGKNREIKKVFEFFNW------KVNRLIRISYGPFQLGT-LLAGST 233 (354) Q Consensus 182 ~~~~~~~~~v~l~eGr~~qIrr~~~~~g~------~V~~L~Rv~~G~~~l~~-L~~G~~ 233 (354) -+.....++|.-.-|.=-.||-+..-+|. .+..|.|+++|+|.+++ |..=+| T Consensus 159 ~~~p~~~~~v~cs~gtGtYIRsLa~DlG~~Lg~~a~l~~LrRt~~G~f~i~~al~~~~~ 217 (226) T cd02868 159 FRPPEFTLEVQCINETQEYLRKLIHEIGLELRSSAVCTQVRRTRDGPFTVDDALLRKQW 217 (226) T ss_pred ECCCEEEEEEEEECCCHHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHHCCCHHHC T ss_conf 06998999999992867618999999998739927997789788967969995397778 No 42 >PRK00020 truB tRNA pseudouridine synthase B; Provisional Probab=98.07 E-value=8.3e-06 Score=56.38 Aligned_cols=156 Identities=22% Similarity=0.254 Sum_probs=92.0 Q ss_pred EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC Q ss_conf 38960278751563144333364421011023432002665543323202223676410001234457404775211245 Q gi|254780406|r 73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152 (354) Q Consensus 73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~ 152 (354) .-++++|||.|+.++..=..-+.. + ...++...|-||-..+|||++.-.. +.++..--.+..|+|.+++.-- T Consensus 10 ~G~l~idKP~G~TS~~vv~~vkk~----l--~~kKvGH~GTLDP~AtGvLiv~vG~--aTKl~~~~~~~~K~Y~a~i~lG 81 (244) T PRK00020 10 DGVLLLDKPVGLSSNHALQRAKRT----V--DAAKAGHTGTLDPFATGLLVCCMGR--ATKISGRMLEADKTYQATLQFG 81 (244) T ss_pred CEEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEECH--HHHHHHHHCCCCCEEEEEEEEC T ss_conf 779997169989989999999998----2--9871577866797551418999673--7676597668992799999978 Q ss_pred ----------------------CCHHHHHHHHHHHH--------------CCCE------------EEECCC-----EEE Q ss_conf ----------------------56467888740000--------------0876------------750343-----036 Q gi|254780406|r 153 ----------------------VDQDKLNLLKKGIV--------------IQGI------------CYGDMQ-----VTL 179 (354) Q Consensus 153 ----------------------~~~~~~~~~~~g~~--------------~~~~------------~~~~~~-----~~~ 179 (354) ++++.+......+. +++. ...+-. +.+ T Consensus 82 ~~TdT~D~eG~v~~~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySA~Kv~GkrlY~lAR~G~~v~~~~R~v~I~~iel 161 (244) T PRK00020 82 EETDSGDLTGHIVARAPDGFAGVEEAALRDVLSRFVGTIEQIPPMYSALKRDGKPLYEYARAGIELDRPPRQVTIRHIEL 161 (244) T ss_pred CCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHCCCEECCCCEEEEEEEEEE T ss_conf 76677676551564146767888999999999971686501498899756235428999977963214754899999999 Q ss_pred EECCCCEEEEEEEEEECCHHHHHHHHHHCCC------EEEEEEEEEECCEECCCCCCCCEEECCHHHHHHHH Q ss_conf 4026880799999951842899999998398------68688975870545187554748867999998753 Q gi|254780406|r 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNW------KVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245 (354) Q Consensus 180 ~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~------~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e~~~l~ 245 (354) ..-......++|.-..|-| ||-++..+|. .+..|.|+++|+|.+++- ++-++|+.+. T Consensus 162 l~~~~~~~~~~v~cSkGTY--IRSLa~Dig~~Lg~~a~l~~L~Rt~~G~f~l~~a-------i~ld~l~~~~ 224 (244) T PRK00020 162 LSFSGMQAQIDVACSKGTY--IRTLAQDIGRALGCHAHLAALRRTHVGPFSLDRA-------VTLEALQAMP 224 (244) T ss_pred EEECCCEEEEEEEECCCEE--EHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHHC-------CCHHHHHHCC T ss_conf 8732886899999769668--1638999999859957986749526747087986-------7899998473 No 43 >TIGR00478 tly hemolysin A; InterPro: IPR004538 Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture. The mechanism of action is not well defined. Hemolysin A is induced by sodium ribonucleate, and is produced by pathogenic bacterial strains. Hemolysin A from Treponema hyodysenteriae causes swine dysentry.; GO: 0003723 RNA binding, 0019836 hemolysis by symbiont of host red blood cells. Probab=98.03 E-value=6.4e-06 Score=57.09 Aligned_cols=53 Identities=26% Similarity=0.421 Sum_probs=48.9 Q ss_pred HHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEEC Q ss_conf 478899988687-78999999986986999999240687807999799999892 Q gi|254780406|r 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67 (354) Q Consensus 15 RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i 67 (354) ||+-.|...|+| ||.+|.++|.+|.|.||++.|+.|+..|+.++.|+|-..+. T Consensus 1 RLD~lLv~rgl~~sR~~Ak~lI~kG~V~VN~~~v~KP~~~v~~~~~i~l~~~~~ 54 (240) T TIGR00478 1 RLDILLVKRGLVESREKAKRLILKGEVLVNKKKVDKPSALVDKDAKIELVQNPL 54 (240) T ss_pred CCHHHHHHHCHHHHHHHHHHHHHCCCEEECCEEECCCCCEECCCCCEEEECCCC T ss_conf 903677650114578999999873945555765208860441676034414777 No 44 >PRK00989 truB tRNA pseudouridine synthase B; Provisional Probab=98.01 E-value=3.4e-05 Score=52.51 Aligned_cols=146 Identities=12% Similarity=0.028 Sum_probs=80.6 Q ss_pred EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC Q ss_conf 38960278751563144333364421011023432002665543323202223676410001234457404775211245 Q gi|254780406|r 73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152 (354) Q Consensus 73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~ 152 (354) .-++++|||+|+.++..=..-+.. + ...++...|-||-..+|||++.-.. -+.+|..--....|+|.+++.-- T Consensus 9 ~GillidKP~G~TS~~vv~~vkk~----l--~~kKvGH~GTLDP~AtGvLiv~iG~-~~Tkl~~~~~~~~K~Y~a~i~lG 81 (235) T PRK00989 9 EGILLVDKPQGRTSFSLIRALTKL----I--GVKKIGHAGTLDPFATGVMVMLIGR-KFTRLSDILLFEDKEYAAIAHLG 81 (235) T ss_pred CCEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEECCC-CCCCHHHHHCCCCCEEEEEEEEC T ss_conf 819999789999989999999998----5--8774687867797443528884074-51127898675784699999989 Q ss_pred -------------------CCHHHHHHHHHHHHCCCEEEEC--------------------------C----CEEEEECC Q ss_conf -------------------5646788874000008767503--------------------------4----30364026 Q gi|254780406|r 153 -------------------VDQDKLNLLKKGIVIQGICYGD--------------------------M----QVTLDTQK 183 (354) Q Consensus 153 -------------------~~~~~~~~~~~g~~~~~~~~~~--------------------------~----~~~~~~~~ 183 (354) ++.+++......+.-.-.+..| . .+.+..-+ T Consensus 82 ~~TdT~D~eG~i~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAiKv~Gkr~Y~lAR~g~~ve~~~r~v~I~~~l~~~~ 161 (235) T PRK00989 82 TTTDSYDCDGKVVGRSKKIPTLEEVLEAASYFQGEIQQVPPMFSAKKVQGKKLYEYARQGLSIERRHSTVQVHLQITKYE 161 (235) T ss_pred CCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHCCCEEECCCCCEEEEECCCCHHHHHHCCCEECCCCEEEEEEEEEEECC T ss_conf 84777666785532148899999999999973387314188620588847068999867860115745899999997425 Q ss_pred CCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC Q ss_conf 88079999995184289999999839------868688975870545187 Q gi|254780406|r 184 GSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 184 ~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~ 227 (354) .....|+|.-..|-| ||-++..+| -.+..|.|+++|+|.+.+ T Consensus 162 ~~~~~~~v~cSkGTY--IRSLa~Dig~~Lg~~a~l~~L~Rt~~G~f~l~~ 209 (235) T PRK00989 162 YPLLHFVVQCSKGTY--IRSIAHELGTMLGCGAYLEELRRLRSGSFSIDQ 209 (235) T ss_pred CCEEEEEEEECCCCC--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH T ss_conf 882899999899356--999999999986984898551864683838899 No 45 >PRK05327 rpsD 30S ribosomal protein S4; Validated Probab=98.00 E-value=8.9e-06 Score=56.20 Aligned_cols=53 Identities=26% Similarity=0.433 Sum_probs=49.0 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEE Q ss_conf 4478899988687-7899999998698699999924068780799979999989 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~ 66 (354) .|||-++-++|++ |+.+|.+||..|.|.|||+.|+.|++.|.++|.|.|..+. T Consensus 92 ~RLD~vv~r~g~a~t~~~ARQ~v~Hghi~vNg~~v~ips~~~k~gd~i~vkeks 145 (201) T PRK05327 92 RRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVKPGDVIEVREKS 145 (201) T ss_pred HHHHHHHHHHCCCCCHHHHHHEEEEEEEEECCEEECCCCEECCCCCEEEECCCC T ss_conf 998899987141058888620064405998999835787473899999977000 No 46 >PRK02193 truB tRNA pseudouridine synthase B; Provisional Probab=97.97 E-value=3.4e-05 Score=52.56 Aligned_cols=155 Identities=16% Similarity=0.135 Sum_probs=89.6 Q ss_pred EEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC--- Q ss_conf 96027875156314433336442101102343200266554332320222367641000123445740477521124--- Q gi|254780406|r 75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG--- 151 (354) Q Consensus 75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~--- 151 (354) ++++|||.|+.++..=..-+. . ....++...|-||-..+|||++.-.. +.++..--....|+|.+++.- T Consensus 2 illi~KP~G~TS~~vv~~vkk----~--~~~kKvGH~GTLDP~AtGvL~v~~G~--aTK~~~~~~~~~K~Y~~~~~lG~~ 73 (279) T PRK02193 2 ITLLYKPKKISSFKFIRQFSK----T--NLIKKIGHAGTLDPLATGLLLVATDE--DTKLLDYLDQKTKTYLAKIQLGFW 73 (279) T ss_pred EEEEECCCCCCHHHHHHHHHH----H--HCCCCCCCCCCCCCCCEEEEEEEECH--HHHHCHHHCCCCCEEEEEEEECCC T ss_conf 899989998998999999999----8--39995361746798674479999786--651264554578269999996775 Q ss_pred -----------------CCCHHHHHHHHHHHHCCCEEE--------------------------ECCCE-----EEEECC Q ss_conf -----------------556467888740000087675--------------------------03430-----364026 Q gi|254780406|r 152 -----------------QVDQDKLNLLKKGIVIQGICY--------------------------GDMQV-----TLDTQK 183 (354) Q Consensus 152 -----------------~~~~~~~~~~~~g~~~~~~~~--------------------------~~~~~-----~~~~~~ 183 (354) .++.+.+......+.-.-.+. .+..+ .+..-+ T Consensus 74 TdT~D~eG~v~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySA~Kv~GkrlY~lAR~g~~ve~~~r~v~I~~~~l~~~~ 153 (279) T PRK02193 74 STTYDSEGQIINVSSNIKVTKDNLEQALNRFSGSQKQVPPVFSAKKVNGKRAYHYARQGKQIELKPIEIKISKIILINFD 153 (279) T ss_pred CCCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHCCCEEECCCEEEEEEEEEEEEEC T ss_conf 77656777456304899999999999999667878982888996231563589898668543056478999999999841 Q ss_pred --CCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCCCCCCCEEECCHHHHHH Q ss_conf --88079999995184289999999839------8686889758705451875547488679999987 Q gi|254780406|r 184 --GSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243 (354) Q Consensus 184 --~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e~~~ 243 (354) .....++|.-.-|-| ||-++..+| -.+..|.|+++|+|.++++.. -|.+.++-+ T Consensus 154 ~~~~~~~~~v~CSkGTY--IRsLa~Dig~~Lg~~a~~~~L~Rt~~G~f~~~~~~~----~l~~~~l~~ 215 (279) T PRK02193 154 EKLQNCVFMWQVSRGTY--IRSLIDDIGKMLKTRAYMDDLERTKIGNLDKNFLNQ----SLKPQDIID 215 (279) T ss_pred CCCCEEEEEEEECCCCC--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHHHHH----HCCHHHHCC T ss_conf 78974999999899768--999999999986984798353977786859668761----089778568 No 47 >PRK01851 truB tRNA pseudouridine synthase B; Provisional Probab=97.97 E-value=4.3e-05 Score=51.91 Aligned_cols=151 Identities=17% Similarity=0.155 Sum_probs=90.2 Q ss_pred EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC- Q ss_conf 3896027875156314433336442101102343200266554332320222367641000123445740477521124- Q gi|254780406|r 73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG- 151 (354) Q Consensus 73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~- 151 (354) .-++++|||.|+.++..=..-+. .+ ...+....|-||-..+|||++.-. -+.++..--....|+|.+++.- T Consensus 17 ~G~l~idKP~G~TS~~vv~~vk~----~~--~~kKvGH~GTLDP~AtGvL~v~~G--~aTK~~~~~~~~~K~Y~~~~~lG 88 (310) T PRK01851 17 DGVLLLDKPVGLSSNDALIRAKR----LL--LAKKAGHTGTLDPLASGLLPLCFG--EATKFSQDLLEADKTYEATMRLG 88 (310) T ss_pred CEEEEEECCCCCCHHHHHHHHHH----HH--CCCCCCCCCCCCCCCCCEEEEEEC--HHHHHHHHHCCCCCEEEEEEEEC T ss_conf 78999705998998999999999----85--888457786779734040689978--87733177576980899999989 Q ss_pred ------------------CCCHHHHHHHHHHHHC--------------CCE--------------EEECCC---EEEEEC Q ss_conf ------------------5564678887400000--------------876--------------750343---036402 Q gi|254780406|r 152 ------------------QVDQDKLNLLKKGIVI--------------QGI--------------CYGDMQ---VTLDTQ 182 (354) Q Consensus 152 ------------------~~~~~~~~~~~~g~~~--------------~~~--------------~~~~~~---~~~~~~ 182 (354) .++.+.++.....+.- ++. ..+.+. +.+..- T Consensus 89 ~~TdT~D~~G~v~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAiKv~GkrlY~lAR~G~~ve~~~R~v~I~~i~l~~~ 168 (310) T PRK01851 89 VRTTTGDAEGEVLDTRPVSCDRAAVEAALARFVGEIVQVPPMYSALKRDGKPLYEYARAGQTVEREGRRVTIRALDLLAC 168 (310) T ss_pred CCCCCCCCCCCEECCCCCCCCHHHHHHHHHHCCCCEEECCCHHHHEEECCHHHHHHHHCCCCEEEEEEEEEEEEEEEEEC T ss_conf 86777787787720367999999999999967751676597068344458878999857886055028999999999723 Q ss_pred CCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC-CCCCCE Q ss_conf 688079999995184289999999839------868688975870545187-554748 Q gi|254780406|r 183 KGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT-LLAGST 233 (354) Q Consensus 183 ~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~-L~~G~~ 233 (354) ......++|.-..|-| ||-++.-+| -.+..|.|+++|+|.+.+ +..-++ T Consensus 169 ~~~~~~~~v~CSkGTY--IRsLa~Dig~~Lg~~a~l~~LrRt~~G~f~~~~a~~Le~l 224 (310) T PRK01851 169 ALPDVTFRVTCSKGTY--VRTLAEDIGEALGCGAHLTMLRRTGVGALTLEHAVTLDAL 224 (310) T ss_pred CCCCEEEEEEECCCEE--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHHCCCHHHH T ss_conf 7982899999889616--6999999999869856982419667877266877089999 No 48 >cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like. This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl r Probab=97.95 E-value=6.3e-05 Score=50.86 Aligned_cols=144 Identities=18% Similarity=0.144 Sum_probs=87.5 Q ss_pred EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC-- Q ss_conf 896027875156314433336442101102343200266554332320222367641000123445740477521124-- Q gi|254780406|r 74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG-- 151 (354) Q Consensus 74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~-- 151 (354) -++++|||.|+.++..=..-+.. + ...++...|-||-..+|||++.-.. +.++..--....|+|.+++.. T Consensus 3 Gil~idKP~G~TS~~vv~~ikk~----l--~~kKvGH~GTLDP~AtGvL~v~iG~--aTKl~~~~~~~~K~Y~~~~~f~~ 74 (182) T cd02572 3 GVINLDKPSGPSSHEVVAWIKRI----L--GVEKTGHSGTLDPKVTGCLPVCIDR--ATRLVKSQQEAGKEYVCVMRLHD 74 (182) T ss_pred EEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEECCH--HHHHHHHHCCCCEEEEEEEEECC T ss_conf 89999579999989999999998----5--7664688977797554347763267--88999986779808998167078 Q ss_pred CCCHHHHHHHHHHHHCCCEEEECC-----------CE---EEEECCC--CEEEEEEEEEECCHHHHHHHHHHCC------ Q ss_conf 556467888740000087675034-----------30---3640268--8079999995184289999999839------ Q gi|254780406|r 152 QVDQDKLNLLKKGIVIQGICYGDM-----------QV---TLDTQKG--SNAWVTVGLREGKNREIKKVFEFFN------ 209 (354) Q Consensus 152 ~~~~~~~~~~~~g~~~~~~~~~~~-----------~~---~~~~~~~--~~~~~~v~l~eGr~~qIrr~~~~~g------ 209 (354) .++.+.+......+.-.-....|. .+ .+..-+. ....++|+-..|-| ||-+..-+| T Consensus 75 ~~~~~~i~~~l~~f~G~i~Q~PP~ySAvK~~~r~~~I~~~~~l~~~~~~~~~~f~v~cskGTY--IRSLa~Dig~~Lg~~ 152 (182) T cd02572 75 DVDEEKVRRVLEEFTGAIFQRPPLISAVKRQLRVRTIYESKLLEYDGERRLVLFRVSCEAGTY--IRTLCVHIGLLLGVG 152 (182) T ss_pred CCCHHHHHHHHHHCCEEEEECCCCHHHCCCCCCCCEEEEEEEEEECCCCCEEEEEEEECCCEE--HHHHHHHHHHHHCCC T ss_conf 899999999999788037233785431214467627999999998188767999999679656--999999999986996 Q ss_pred CEEEEEEEEEECCEECCC Q ss_conf 868688975870545187 Q gi|254780406|r 210 WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 210 ~~V~~L~Rv~~G~~~l~~ 227 (354) -.+..|.|+++|+|.+.+ T Consensus 153 a~l~~L~Rt~~G~f~~ed 170 (182) T cd02572 153 AHMQELRRTRSGPFSEED 170 (182) T ss_pred EEEEEEEEEEEECCCCHH T ss_conf 799787957870887063 No 49 >PRK05033 truB tRNA pseudouridine synthase B; Provisional Probab=97.93 E-value=4.5e-05 Score=51.77 Aligned_cols=145 Identities=14% Similarity=0.133 Sum_probs=85.6 Q ss_pred EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC- Q ss_conf 3896027875156314433336442101102343200266554332320222367641000123445740477521124- Q gi|254780406|r 73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG- 151 (354) Q Consensus 73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~- 151 (354) .-++++|||.|+.++..=..-+.. + ...++...|-||-..+|||++.-. + +.++..--....|+|.+++.- T Consensus 12 ~Gil~idKP~g~TS~~~v~~~kk~----~--~~kKvGH~GTLDP~AtGvL~i~~G-~-aTK~~~~~~~~~K~Y~~~~~lG 83 (314) T PRK05033 12 NGVLLLDKPQGMSSNDALQKVKRI----Y--NANKAGHTGALDPLATGMLPICLG-E-ATKFSQFLLDSDKRYRVIAKLG 83 (314) T ss_pred CEEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEEC-H-HHHHHHHHCCCCCEEEEEEEEC T ss_conf 679998159999989999999998----5--888568785779756021899988-8-8704088668991799999978 Q ss_pred ------------------CCCHHHHHHHHHHHHCCCEEE----------------------------ECC---CEEEEEC Q ss_conf ------------------556467888740000087675----------------------------034---3036402 Q gi|254780406|r 152 ------------------QVDQDKLNLLKKGIVIQGICY----------------------------GDM---QVTLDTQ 182 (354) Q Consensus 152 ------------------~~~~~~~~~~~~g~~~~~~~~----------------------------~~~---~~~~~~~ 182 (354) .++.+.+......+.-.-.+. +++ .+.+..- T Consensus 84 ~~TdT~D~eG~i~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySA~Kv~Gkr~Y~lAR~G~~ve~~~R~v~I~~i~l~~~ 163 (314) T PRK05033 84 QRTDTSDADGQVVEERPVTFSAEQLAAALETFRGDIEQIPSMYSALKYQGKPLYEYARQGIEVPREARPITVYELLFIRH 163 (314) T ss_pred CCCCCCCCCCCEEECCCCCCCHHHHHHHHHHCCCCEEECCCHHHHEEECCHHHHHHHHCCCCEEECCEEEEEEEEEEEEE T ss_conf 86566788887720368999999999999975584524588789542578609999877984142017989989999973 Q ss_pred CCCEEEEEEEEEECCHHHHHHHHHHC------CCEEEEEEEEEECCEECCC Q ss_conf 68807999999518428999999983------9868688975870545187 Q gi|254780406|r 183 KGSNAWVTVGLREGKNREIKKVFEFF------NWKVNRLIRISYGPFQLGT 227 (354) Q Consensus 183 ~~~~~~~~v~l~eGr~~qIrr~~~~~------g~~V~~L~Rv~~G~~~l~~ 227 (354) +.....++|.-.-| ..||-++..+ +-.+..|.|+++|+|.+.+ T Consensus 164 ~~~~~~~~V~CSkG--TYIRSLa~Dig~~Lg~~a~l~~LrRt~vG~f~~~~ 212 (314) T PRK05033 164 EGNELELEVHCSKG--TYIRTIIDDLGEKLGCGAHVTYLRRLAVSKYPVER 212 (314) T ss_pred CCCEEEEEEEECCC--CCHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH T ss_conf 28868999997897--23589999999875983797324853586818798 No 50 >PRK00130 truB tRNA pseudouridine synthase B; Provisional Probab=97.92 E-value=5e-05 Score=51.49 Aligned_cols=143 Identities=17% Similarity=0.167 Sum_probs=86.8 Q ss_pred EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC- Q ss_conf 8960278751563144333364421011023432002665543323202223676410001234457404775211245- Q gi|254780406|r 74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ- 152 (354) Q Consensus 74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~- 152 (354) -++++|||.|+.++..=..-+.. -...++...|-||-..+|||++.-.. +.++..--....|+|.+++.-- T Consensus 3 G~l~i~KP~g~TS~~vv~~vkk~------l~~kKvGH~GTLDP~AtGvL~v~~G~--aTK~~~~~~~~~K~Y~a~~~lG~ 74 (289) T PRK00130 3 GVINVYKPKGMTSFDVVRKIRKI------AKIKKVGHTGTLDPLASGVLPVCLGK--ATKIVDYIMEGKKVYRVELKLGT 74 (289) T ss_pred EEEEEECCCCCCHHHHHHHHHHH------HCCCCCCCCCCCCCCCCCEEEEEECH--HHHHHHHHCCCCEEEEEEEEECC T ss_conf 79996089999989999999998------48885577846798560428999787--76143676799907999999787 Q ss_pred ------------------CCHHHHHHHHHHH-----------------------------HCCCEEEECC---CEEEEEC Q ss_conf ------------------5646788874000-----------------------------0087675034---3036402 Q gi|254780406|r 153 ------------------VDQDKLNLLKKGI-----------------------------VIQGICYGDM---QVTLDTQ 182 (354) Q Consensus 153 ------------------~~~~~~~~~~~g~-----------------------------~~~~~~~~~~---~~~~~~~ 182 (354) ++.+.+......+ .++- ..+++ .+.+..- T Consensus 75 ~TdT~D~~G~i~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~~SA~Kv~GkrlY~lAR~G~~ve~-~~R~v~I~~i~l~~~ 153 (289) T PRK00130 75 TTDTYDREGEVLEEKEVSITEDEVEEAINSFIGEIDQVPPMYSALKINGVRLYELARKGIEVER-EARKITIYDICILSI 153 (289) T ss_pred CCCCCCCCCCEEEECCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHCCCCCCC-CCEEEEEEEEEEECC T ss_conf 5776546797876458998999999999975682625288789624159869999975875566-856999999998407 Q ss_pred CCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC Q ss_conf 688079999995184289999999839------868688975870545187 Q gi|254780406|r 183 KGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 183 ~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~ 227 (354) +.....++|.-..|-| ||-++.-+| -.+..|.|+++|+|.+.+ T Consensus 154 ~~~~~~~~v~CSkGTY--IRsLa~Dig~~Lg~~a~l~~L~Rt~vG~f~~~~ 202 (289) T PRK00130 154 DLPYVIFDVKCSKGTY--IRSLCYDIGEKLNVGATMWNLERLETGPFNIEE 202 (289) T ss_pred CCCEEEEEEEECCCEE--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH T ss_conf 8996999999779557--799999999976984798664965786718899 No 51 >PRK04642 truB tRNA pseudouridine synthase B; Provisional Probab=97.88 E-value=6.4e-05 Score=50.80 Aligned_cols=146 Identities=17% Similarity=0.148 Sum_probs=86.2 Q ss_pred CEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC Q ss_conf 43896027875156314433336442101102343200266554332320222367641000123445740477521124 Q gi|254780406|r 72 RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151 (354) Q Consensus 72 ~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~ 151 (354) -.-++++|||.|+.++..=..-+.. + ...+....|-||-..+|||++.-. -+.++..--....|+|.+++.- T Consensus 9 m~Gil~idKP~g~TS~~vv~~vrr~----l--~~~KvGH~GTLDP~AtGvL~i~~g--~aTK~~~~~~~~~K~Y~~~~~l 80 (300) T PRK04642 9 LHGILLLDKPAGLSSNNALQAARRL----L--RAEKGGHTGSLDPLATGLLPLCFG--EATKIAGLLLGSAKAYDAEIVL 80 (300) T ss_pred CCEEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEEC--HHHHHCHHHCCCCCEEEEEEEE T ss_conf 6779997079989989999999998----6--898457685779856043789978--7651366656136643799998 Q ss_pred --------------------CCCHHHHHHHHHHHH--------------CCCE--------------EEECCC---EEEE Q ss_conf --------------------556467888740000--------------0876--------------750343---0364 Q gi|254780406|r 152 --------------------QVDQDKLNLLKKGIV--------------IQGI--------------CYGDMQ---VTLD 180 (354) Q Consensus 152 --------------------~~~~~~~~~~~~g~~--------------~~~~--------------~~~~~~---~~~~ 180 (354) .++.+.+......+. +++. ..+.+. +.+. T Consensus 81 G~~TdT~D~~G~v~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySA~Kv~GkrlY~lAR~G~~ve~~~R~v~I~~l~ll 160 (300) T PRK04642 81 GVTTDTDDADGQVLRERPVPDLSEAALQAALAPFIGRIQQQAPIYSALKQGGEPLYAKARRGEVIEAPVREVEVHAIEVL 160 (300) T ss_pred CCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHCCCHHHHHHHHCCCEEEECEEEEEEEEEEEE T ss_conf 75136767778676405789889999999999777535652978897242882188887669703202089999999985 Q ss_pred ECCCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC Q ss_conf 02688079999995184289999999839------868688975870545187 Q gi|254780406|r 181 TQKGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 181 ~~~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~ 227 (354) .-......++|.-..| -.||-++..+| -.+..|.|+++|+|.+.+ T Consensus 161 ~~~~~~~~~~v~CskG--TYIRsLa~Dig~~Lg~~a~l~~LrRt~vG~f~~~~ 211 (300) T PRK04642 161 GYAAPRLRLRVTCGSG--TYIRSLARDLGEVLGCGAHIAALRRLWVEPFRAPQ 211 (300) T ss_pred ECCCCEEEEEEEECCC--CHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH T ss_conf 0369859999998870--15999999999985985797021843786808798 No 52 >cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine. Probab=97.85 E-value=5.3e-05 Score=51.34 Aligned_cols=143 Identities=21% Similarity=0.222 Sum_probs=84.6 Q ss_pred EEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC--- Q ss_conf 96027875156314433336442101102343200266554332320222367641000123445740477521124--- Q gi|254780406|r 75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG--- 151 (354) Q Consensus 75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~--- 151 (354) ++++|||.|+.++..=..-+.. + ...++...|-||-..+|||++.-. -+.++..--.+..|+|.+++.- T Consensus 2 ~l~i~Kp~g~tS~~~v~~~k~~----~--~~kKvGH~GTLDP~AtGvL~i~~g--~aTKl~~~~~~~~K~Y~~~~~lG~~ 73 (277) T cd02573 2 ILLLDKPAGLTSHDVVQKVRRL----L--GTKKVGHTGTLDPLATGVLPIALG--EATKLSQYLLDADKTYRATVRLGEA 73 (277) T ss_pred EEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEEC--HHHHHHHHHCCCCCEEEEEEEECCC T ss_conf 8999679999989999999998----5--888556375779766033789988--8870527867899179999998760 Q ss_pred -----------------CCCHHHHHHHHHHHH--------------CCCE--------------EEECCC---EEEEECC Q ss_conf -----------------556467888740000--------------0876--------------750343---0364026 Q gi|254780406|r 152 -----------------QVDQDKLNLLKKGIV--------------IQGI--------------CYGDMQ---VTLDTQK 183 (354) Q Consensus 152 -----------------~~~~~~~~~~~~g~~--------------~~~~--------------~~~~~~---~~~~~~~ 183 (354) .++.+.+......+. +++. ..+.+. +.+..-. T Consensus 74 TdT~D~~G~i~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySA~Kv~GkrlY~lAR~G~~v~~~~r~v~I~~i~ll~~~ 153 (277) T cd02573 74 TDTDDAEGEIIETSPPPRLTEEEIEAALKAFTGEIEQVPPMYSAVKVNGKRLYELARAGEEVERPPRKVTIYSLELLSFD 153 (277) T ss_pred CCCCCCCCCEECCCCCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHCCCCCCCCCEEEEEEEEEEEEEC T ss_conf 47655679871137899999999999999787707871988897464585199998779845568778999999998851 Q ss_pred C--CEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC Q ss_conf 8--8079999995184289999999839------868688975870545187 Q gi|254780406|r 184 G--SNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 184 ~--~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~ 227 (354) . ....++|.-..| -.||-++.-+| -.+..|.|+++|+|.+.+ T Consensus 154 ~~~~~~~~~v~cSkG--TYIRsLa~Dig~~Lg~~a~l~~L~Rt~~G~f~~~~ 203 (277) T cd02573 154 PENPEADFEVECSKG--TYIRSLARDLGKALGCGAHLSALRRTRSGPFTLED 203 (277) T ss_pred CCCCEEEEEEEECCC--EEHHHHHHHHHHHHCCCEEEEEEECCEECCCCHHH T ss_conf 789859999997786--33999999999985991898463820578869799 No 53 >PRK11507 hypothetical protein; Provisional Probab=97.81 E-value=4.2e-05 Score=51.94 Aligned_cols=62 Identities=16% Similarity=0.281 Sum_probs=55.3 Q ss_pred CCCCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCC Q ss_conf 6667734478899988687-7899999998698699999924068780799979999989225 Q gi|254780406|r 8 QENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69 (354) Q Consensus 8 ~~~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~ 69 (354) -+...-+.|.++|--+|+| |=-+|+.+|.+|.|+|||++-+.-..|+..+|.|+++|+.|.. T Consensus 6 L~~~~yIeL~~lLK~~glv~sGg~AK~~Ia~G~V~VnGevEtRKr~Ki~~GdvV~f~g~~i~V 68 (70) T PRK11507 6 LGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQV 68 (70) T ss_pred CCCCCCEEHHHHHHHCCCCCCCHHHHHHEECCEEEECCEEEEEEEEEEECCCEEEECCEEEEE T ss_conf 389871008888847172046587786541876899999963310251089999999999999 No 54 >PRK01528 truB tRNA pseudouridine synthase B; Provisional Probab=97.80 E-value=7.9e-05 Score=50.24 Aligned_cols=145 Identities=18% Similarity=0.108 Sum_probs=83.9 Q ss_pred EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC Q ss_conf 38960278751563144333364421011023432002665543323202223676410001234457404775211245 Q gi|254780406|r 73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152 (354) Q Consensus 73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~ 152 (354) .-++++|||.|+.++..=..-+.. + ...++...|-||-..+|||++.-.. +.++..--....|+|.+++.-- T Consensus 3 ng~l~i~KP~g~TS~~vv~~vkk~----~--~~~KvGH~GTLDP~AtGvL~i~~g~--aTK~~~~~~~~~K~Y~~~~~~G 74 (293) T PRK01528 3 NYWLNIYKPRGISSAKLVSIVKKI----L--GKVKIGHAGTLDVEAEGILPLAVGE--ATKLIQLLIDAKKTYIFTVKFG 74 (293) T ss_pred CEEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEECH--HHHHHHHHCCCCEEEEEEEEEC T ss_conf 758998779999989999999998----4--8980576867887570158999786--6503378657980699999978 Q ss_pred C-------------------CHHHHHHHHHHH--------------HCCCE------------EEECCCE-----EEEEC Q ss_conf 5-------------------646788874000--------------00876------------7503430-----36402 Q gi|254780406|r 153 V-------------------DQDKLNLLKKGI--------------VIQGI------------CYGDMQV-----TLDTQ 182 (354) Q Consensus 153 ~-------------------~~~~~~~~~~g~--------------~~~~~------------~~~~~~~-----~~~~~ 182 (354) . +.+.+......+ .+++. ...+-.+ .+..- T Consensus 75 ~~TdT~D~eG~ii~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~GkraY~lAR~G~~vel~~R~v~I~~l~ll~~ 154 (293) T PRK01528 75 KQTDSGDYAGKVIATKDYIPSQEEAYAVCSKFIGNVTQIPPAFSALKVNGVRAYKLAREGKEVELKPRNITIYDLKCLNF 154 (293) T ss_pred CCCCCCCCCCCEEECCCCCCCHHHHHHHHHHCCCCEEEECCHHHHHCCCCHHHHHHHHCCCEEECCCEEEEEEEEEEEEE T ss_conf 84798886775874157899999999999857782799088899620067609999866972442767999999897640 Q ss_pred CCCE--EEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC Q ss_conf 6880--79999995184289999999839------868688975870545187 Q gi|254780406|r 183 KGSN--AWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 183 ~~~~--~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~ 227 (354) ...+ ..+.|.-.-| -.||-++.-+| -.+..|.|+++|+|.+.+ T Consensus 155 ~~~~~~~~f~v~CskG--TYIRSLa~Dlg~~Lg~~a~~~~LrRt~~G~F~~~~ 205 (293) T PRK01528 155 DEKNATATYYTECSKG--TYIRTLAEDLALSLQSLGFVIELRRTQVGIFKEEN 205 (293) T ss_pred CCCCCEEEEEEEECCC--EEHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH T ss_conf 4778669999997897--05378999999985985687244876773878688 No 55 >PRK03287 truB tRNA pseudouridine synthase B; Provisional Probab=97.79 E-value=0.00013 Score=48.84 Aligned_cols=149 Identities=15% Similarity=0.158 Sum_probs=85.4 Q ss_pred CCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEEC Q ss_conf 64389602787515631443333644210110234320026655433232022236764100012344574047752112 Q gi|254780406|r 71 ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150 (354) Q Consensus 71 ~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~ 150 (354) ...-++++|||.|+.++..=..-+.. + ...++...|-||-..+|||++.-.. +.++..--.+..|+|.+++. T Consensus 7 ~~sGil~idKP~G~TS~~vv~~vk~~----~--~~kKvGH~GTLDP~AtGvL~v~~G~--aTKl~~~~~~~~K~Y~a~~~ 78 (298) T PRK03287 7 TGSGLVVVDKPAGMTSHDVVARCRRI----F--GTRKVGHAGTLDPMATGVLVLGVER--ATKLLGHLVATDKSYTATIR 78 (298) T ss_pred CCCEEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEECH--HHCCCHHHCCCCCEEEEEEE T ss_conf 88789999479999989999999998----4--8983366857797460438999787--76218746557817999999 Q ss_pred C--------------------CCCHHHHHHHHHHHHCCCEEEEC----------------------------CCE---EE Q ss_conf 4--------------------55646788874000008767503----------------------------430---36 Q gi|254780406|r 151 G--------------------QVDQDKLNLLKKGIVIQGICYGD----------------------------MQV---TL 179 (354) Q Consensus 151 ~--------------------~~~~~~~~~~~~g~~~~~~~~~~----------------------------~~~---~~ 179 (354) - .++.+.++.....+.-+-.+..| +.+ .+ T Consensus 79 lG~~TdT~D~eG~v~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySA~Kv~GkrlY~lAR~G~~ve~~~R~v~I~~~~l 158 (298) T PRK03287 79 LGQTTSTDDAEGEVLSSAPASHLTEEAIAAAVAALTGEIMQVPSAVSAIKVDGKRAYARVRAGEEVELPARPVTISRFEV 158 (298) T ss_pred ECCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHCCCCEEEECCCHHEEEECCHHHHHHHHCCCCCCCCCEEEEEEEEEE T ss_conf 89737776677877503679989999999999975762447077213233267989999975984205866899999999 Q ss_pred EECCCCE--EEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC Q ss_conf 4026880--79999995184289999999839------868688975870545187 Q gi|254780406|r 180 DTQKGSN--AWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 180 ~~~~~~~--~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~ 227 (354) ..-.... ..+.+.+.=++=-.||-++..+| -.+..|.|+++|+|.+.+ T Consensus 159 ~~~~~~~~~~~~~~~V~CSkGTYIRSLa~Dlg~~Lg~~a~l~~LrRt~~G~f~~~~ 214 (298) T PRK03287 159 LAVRRDDAFIDLDVEVDCSSGTYIRALARDLGAALGVGGHLTALRRTRVGPFTLDQ 214 (298) T ss_pred EEECCCCCCCEEEEEEEECCCEEHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH T ss_conf 85227777510799999679646799999999976985798554855685809799 No 56 >cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker Probab=97.78 E-value=9.6e-05 Score=49.69 Aligned_cols=143 Identities=17% Similarity=0.112 Sum_probs=81.4 Q ss_pred EEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC-- Q ss_conf 960278751563144333364421011023432002665543323202223676410001234457404775211245-- Q gi|254780406|r 75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-- 152 (354) Q Consensus 75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~-- 152 (354) ++++|||.|+.++..=..-+.. + ...++...|.||-..+|||++--. + +.++..--....|+|.+++.-- T Consensus 2 il~i~KP~G~TS~~vv~~vk~~----~--~~kKvGH~GTLDP~AtGvL~i~vG-~-aTK~~~~~~~~~K~Y~~~~~lG~~ 73 (210) T cd00506 2 LFAVDKPQGPSSHDVVDTIRRI----F--LAEKVGHGGTLDPFATGVLVVGIG-K-ATKLLKHLLAATKDYTAIGRLGQA 73 (210) T ss_pred EEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEEC-H-HHHHHHHHCCCCCEEEEEEEECCE T ss_conf 8999679999989999999998----5--877357686669745242899977-8-887999875599778799998530 Q ss_pred ------------------CCHHHHHHHHHHHHCCCEEEEC--------------------------CC-----EEEEECC Q ss_conf ------------------5646788874000008767503--------------------------43-----0364026 Q gi|254780406|r 153 ------------------VDQDKLNLLKKGIVIQGICYGD--------------------------MQ-----VTLDTQK 183 (354) Q Consensus 153 ------------------~~~~~~~~~~~g~~~~~~~~~~--------------------------~~-----~~~~~~~ 183 (354) ++.+.++.....+.-.-....| -. +.+..-. T Consensus 74 TdT~D~~G~i~~~~~~~~~~~~~i~~~l~~f~G~~~Q~PP~ySA~Kv~Gkr~Y~lAR~g~~v~~~~r~v~I~~~~ll~~~ 153 (210) T cd00506 74 TDTFDATGQVIEETPYDHITHEQLERALETLTGDIQQVPPLYSAVKRQGQRAYELARRGLLVPDEARPPTIYELLCIRFN 153 (210) T ss_pred ECCCCCCCCEECCCCCCCCCHHHHHHHHHHCCCCEEECCCHHHEEEECCCCHHHHHHCCCCCCCCCEEEEEEEEEEEEEC T ss_conf 17999888621336899899999999998665776551855775631783489998668621346403489999999852 Q ss_pred CCE--EEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC Q ss_conf 880--79999995184289999999839------868688975870545187 Q gi|254780406|r 184 GSN--AWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 184 ~~~--~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~ 227 (354) ... ..++|.-..|-| ||.+..-+| -.+..|.|+++|+|.+.+ T Consensus 154 ~~~~~~~~~v~cs~GTY--IRsLa~Dig~~Lg~~a~l~~LrRt~~G~f~~~~ 203 (210) T cd00506 154 PPHFLLEVEVVCETGTY--IRTLIHDLGLELGVGAHVTELRRTRVGPFKVEN 203 (210) T ss_pred CCCCEEEEEEEECCCCC--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH T ss_conf 88878999999669727--999999999986998798378987786777898 No 57 >PRK05389 truB tRNA pseudouridine synthase B; Provisional Probab=97.64 E-value=0.00021 Score=47.60 Aligned_cols=151 Identities=17% Similarity=0.169 Sum_probs=86.7 Q ss_pred EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCC Q ss_conf 38960278751563144333364421011023432002665543323202223676410001234457404775211245 Q gi|254780406|r 73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152 (354) Q Consensus 73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~ 152 (354) .-++++|||.|+.++..=..-+.. + ...++...|-||-..+|||++.-.. +.++..--....|+|.+++.-- T Consensus 13 ~G~l~idKP~G~TS~~vv~~vkk~----~--~~kKvGH~GTLDP~AtGvL~i~~G~--aTk~~~~~~~~~K~Y~~~~~lG 84 (305) T PRK05389 13 SGWLILDKPAGMTSTEAVSKVKWL----F--DAQKAGHAGTLDPLASGVLPIALGE--ATKTVPYVMDGTKRYRFTVAWG 84 (305) T ss_pred CEEEEEECCCCCCHHHHHHHHHHH----H--CCCCCCCCCCCCCCCCCEEEEEECH--HHHHHHHHCCCCEEEEEEEEEC T ss_conf 779998249999989999999998----5--8885677867798660238899887--7623367656880799999984 Q ss_pred -------------------CCHHHHHHHHHHHH--------------CCCE--------------EEECCCE---EEEEC Q ss_conf -------------------56467888740000--------------0876--------------7503430---36402 Q gi|254780406|r 153 -------------------VDQDKLNLLKKGIV--------------IQGI--------------CYGDMQV---TLDTQ 182 (354) Q Consensus 153 -------------------~~~~~~~~~~~g~~--------------~~~~--------------~~~~~~~---~~~~~ 182 (354) ++.+.++.....+. +++. ..+.+.+ .+..- T Consensus 85 ~~TdT~D~~G~v~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAiKv~Gkr~Y~lAR~G~~ve~~~R~v~I~~i~ll~~ 164 (305) T PRK05389 85 EERDTDDLEGEVTATSDKRPTDEEIRALLPAFTGVIMQVPPQFSAIKIDGERAYDLAREGETVELPPRPVEIDRLTLVDR 164 (305) T ss_pred CCCCCCCCCCCEEEECCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHCCCCCCCCCEEEEEEEEEEEEC T ss_conf 31335666885456258997599999999968761787288789644368019999877982135637999999899733 Q ss_pred -CCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC-CCCCCE Q ss_conf -688079999995184289999999839------868688975870545187-554748 Q gi|254780406|r 183 -KGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT-LLAGST 233 (354) Q Consensus 183 -~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~-L~~G~~ 233 (354) ......|+|.-.-|- .||-++.-+| -.+..|.|+++|+|.+.+ +..-++ T Consensus 165 ~~~~~~~f~v~CSkGT--YIRsLa~Dig~~Lg~~a~l~~LrRt~vG~f~~~~a~~le~l 221 (305) T PRK05389 165 PDADHAVFEVECGKGT--YVRSLARDMGRALGCYGHIAALRRTWVGPFTEEDMITLDKL 221 (305) T ss_pred CCCCEEEEEEEECCCE--EHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHHCCCHHHH T ss_conf 7899899999978963--76998999998759847984338446878287996689999 No 58 >PRK02484 truB tRNA pseudouridine synthase B; Provisional Probab=97.58 E-value=0.00027 Score=46.90 Aligned_cols=144 Identities=13% Similarity=0.083 Sum_probs=82.7 Q ss_pred EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC-- Q ss_conf 896027875156314433336442101102343200266554332320222367641000123445740477521124-- Q gi|254780406|r 74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG-- 151 (354) Q Consensus 74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~-- 151 (354) -++++|||.|+.++..=..-+..+ ...++...|-||-..+|||++.-.. +.++..--....|+|.+++.- T Consensus 4 G~l~vdKP~G~TS~~vv~~ikk~~------~~kKvGH~GTLDP~AtGvL~v~~G~--aTkl~~~~~~~~K~Y~~~~~lG~ 75 (293) T PRK02484 4 GIINLKKEAGMTSHDAVFKLRKIL------QTKKIGHGGTLDPDVVGVLPIAVGK--ATRVIEYMTEAGKVYEGEVTLGY 75 (293) T ss_pred EEEEEECCCCCCHHHHHHHHHHHH------CCCCCCCCCCCCCCCEEEEEEEECH--HHHHHHHHCCCCCEEEEEEEECC T ss_conf 699972699999899999999984------8985565836798661268999788--77151876648938999999433 Q ss_pred -------------------CCCHHHHHHHHHHH--------------HCCCE--------------EEECCCEEEE---- Q ss_conf -------------------55646788874000--------------00876--------------7503430364---- Q gi|254780406|r 152 -------------------QVDQDKLNLLKKGI--------------VIQGI--------------CYGDMQVTLD---- 180 (354) Q Consensus 152 -------------------~~~~~~~~~~~~g~--------------~~~~~--------------~~~~~~~~~~---- 180 (354) .++.+.++.....+ .+++. ..+++.+.-. T Consensus 76 ~TdT~D~~G~ii~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAiKv~Gkr~Y~lAR~g~~ve~~~R~v~I~~~~l~~ 155 (293) T PRK02484 76 STTTEDASGEVVARTPVPAVLTEELVDQAMTSFTGKITQIPPMYSAVKVNGRKLYEYARAGEEVERPRRQVTISQFERTS 155 (293) T ss_pred CCCCCCCCCCEEEECCCCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHCCCCCCCCCEEEEEEEEEECC T ss_conf 25666788866763477789999999999986874067659768962215567999987797034687789999988225 Q ss_pred --ECCCC--EEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC Q ss_conf --02688--079999995184289999999839------868688975870545187 Q gi|254780406|r 181 --TQKGS--NAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 181 --~~~~~--~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~ 227 (354) .-+.. ...++|+-..|-| ||-++.-+| -.+..|.|+++|+|.+.+ T Consensus 156 ~~~~~~~~~~~~~~v~CSkGTY--IRsLa~Dlg~~Lg~~a~~~~LrRt~~G~F~~~~ 210 (293) T PRK02484 156 PLNFEDGLCRFSFKVACSKGTY--VRTLAVDLGRKLGYASHMSFLQRTASAGLTLED 210 (293) T ss_pred CCCCCCCCCEEEEEEEECCCEE--HHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH T ss_conf 3335677506999999767447--389999999985993798563976785838798 No 59 >PRK01550 truB tRNA pseudouridine synthase B; Provisional Probab=97.56 E-value=0.00032 Score=46.38 Aligned_cols=145 Identities=17% Similarity=0.196 Sum_probs=82.5 Q ss_pred EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC-- Q ss_conf 896027875156314433336442101102343200266554332320222367641000123445740477521124-- Q gi|254780406|r 74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG-- 151 (354) Q Consensus 74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~-- 151 (354) -++++|||.|+.++..=..-+... ...++...|-||-..+|||++.-.- +.++..--....|+|.+++.- T Consensus 3 Gil~idKP~G~TS~~vv~~vr~~l------~~kKvGH~GTLDP~AtGvL~i~iG~--aTKl~~~l~~~~K~Y~a~~~lG~ 74 (307) T PRK01550 3 GVVLLHKPKGMTSHDCVFKLRKIL------REKRIGHTGTLDPDVTGVLPICVGR--ATKIAQFLTSETKTYEGEVTLGF 74 (307) T ss_pred EEEEECCCCCCCHHHHHHHHHHHH------CCCCCCCCCCCCCCCEEEEEEEECC--CHHHCHHHCCCCCEEEEEEEEEE T ss_conf 799970699899899999999984------8983464746798662169999780--00013444667834899999976 Q ss_pred -------------------CCCHHHHHHHHHHH-----------------------------HCCCEEEECCCEE---EE Q ss_conf -------------------55646788874000-----------------------------0087675034303---64 Q gi|254780406|r 152 -------------------QVDQDKLNLLKKGI-----------------------------VIQGICYGDMQVT---LD 180 (354) Q Consensus 152 -------------------~~~~~~~~~~~~g~-----------------------------~~~~~~~~~~~~~---~~ 180 (354) .++.+.++.....+ .++- ..+++.+. +. T Consensus 75 ~TdT~D~~G~vi~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySA~Kv~GkrlY~lAR~G~~ve~-~~R~v~I~~~~ll 153 (307) T PRK01550 75 STTTEDASGEVVETKHVDRVITRKEVEEVLAELTGTIEQMPPMFSAVKVNGKKLYEYARAGQEVER-PVRTITIHEFVLL 153 (307) T ss_pred ECCCCCCCCCEEEECCCCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHCCHHHHHHHHCCCCCCC-CCEEEEEEEEEEE T ss_conf 468767787766404788899999999999967873635188899754334769999877882346-8668999999961 Q ss_pred E----CCCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC Q ss_conf 0----2688079999995184289999999839------868688975870545187 Q gi|254780406|r 181 T----QKGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 181 ~----~~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~ 227 (354) . -++.+..+.+.+.=++=..||-+..-+| -.+..|.|+++|+|.+.+ T Consensus 154 ~~~~~~~~~~~~~~~~v~CskGTYIRsLa~Dig~~Lg~~a~l~~L~Rt~~G~f~l~~ 210 (307) T PRK01550 154 DDREVFEGENISFRFRVTCSKGTYVRTLAVMIGEKLGFPSHMSHLVRTASGEFLLED 210 (307) T ss_pred CCCCCCCCCCCEEEEEEEECCCEEHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH T ss_conf 452124555633899999889517699999999985983798353865786808798 No 60 >PRK02755 truB tRNA pseudouridine synthase B; Provisional Probab=97.56 E-value=0.00059 Score=44.73 Aligned_cols=144 Identities=18% Similarity=0.161 Sum_probs=78.3 Q ss_pred EEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC--- Q ss_conf 96027875156314433336442101102343200266554332320222367641000123445740477521124--- Q gi|254780406|r 75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG--- 151 (354) Q Consensus 75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~--- 151 (354) ++++|||.|+.++..=..-+. .+ ...+....|-||-..+|||++.-.- +.++..--.. .|+|.+++.- T Consensus 4 ~l~i~Kp~G~tS~~vv~~~k~----~~--~~kKvGH~GTLDP~AtGvL~i~~G~--aTk~~~~l~~-~K~Y~~~~~lG~~ 74 (291) T PRK02755 4 FLNLNKPAGWTSHDCVAKLRR----LL--RLKRVGHGGTLDPAATGVLPIAVGK--ATRLLPYLPS-GKAYKATVRFGLQ 74 (291) T ss_pred EEEEECCCCCCHHHHHHHHHH----HH--CCCCCCCCCCCCCCCCCEEEEEECH--HHEECCCCCC-CCEEEEEEEECCC T ss_conf 999835998998999999999----85--8883677857797550528999765--7664300489-9589999998974 Q ss_pred -----------------CCCHHHHHHHHHHH--------------HCCCEE------------EECCCEEE-----EE-C Q ss_conf -----------------55646788874000--------------008767------------50343036-----40-2 Q gi|254780406|r 152 -----------------QVDQDKLNLLKKGI--------------VIQGIC------------YGDMQVTL-----DT-Q 182 (354) Q Consensus 152 -----------------~~~~~~~~~~~~g~--------------~~~~~~------------~~~~~~~~-----~~-~ 182 (354) .++.+.++.....+ .+++.. ..+-.+.+ .. . T Consensus 75 TdT~D~~G~i~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAiKv~GkrlY~lAR~G~~ve~~~R~v~I~~~~ll~~~ 154 (291) T PRK02755 75 TTTDDLTGEILASQPASHLSLAAVETALPQFLGKIEQIPPQYSAIQVEGKRLYDLARQGEAVEVPPRTVEVFSIDILDWR 154 (291) T ss_pred CCCCCCCCCCEEECCCCCCCHHHHHHHHHHCCCCEEECCCHHHHHHCCCHHHHHHHHCCCCCCCCCEEEEEEEEEEEECC T ss_conf 66566678711336799899999999999736826254897895101572099998669803367789999999987104 Q ss_pred CCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC Q ss_conf 688079999995184289999999839------868688975870545187 Q gi|254780406|r 183 KGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 183 ~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~ 227 (354) ......+.+.+.=++=..||-+++-+| -.+..|.|+++|+|.+.+ T Consensus 155 ~~~~~~~~~~v~CSkGTYIRsLa~Dig~~Lg~~a~l~~L~Rt~~G~f~~~~ 205 (291) T PRK02755 155 SGDFPELDVEIACGSGTYIRAIARDLGAVLGTGGTLAALIRTESSGFALED 205 (291) T ss_pred CCCCCEEEEEEEECCCHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCHHH T ss_conf 677846999999768611999999998976983898574964786708798 No 61 >PRK13354 tyrosyl-tRNA synthetase; Provisional Probab=97.53 E-value=0.00047 Score=45.33 Aligned_cols=48 Identities=25% Similarity=0.442 Sum_probs=31.6 Q ss_pred CCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCC Q ss_conf 7734478899988687-78999999986986999999240687807999 Q gi|254780406|r 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD 58 (354) Q Consensus 11 ~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d 58 (354) ....-|-.+|..+|+| |++||.++|++|-|+|||+.|+++.+.+..++ T Consensus 339 ~~~~~l~dlLv~~gl~~SksEARRlI~qGgV~INgekV~D~~~~l~~~~ 387 (405) T PRK13354 339 KETKNIVDLLVDLGLAPSKREARRLINNGAVKINGEKVTDVGTDVTVEN 387 (405) T ss_pred CCCCCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCC T ss_conf 5788899999983986788999999985998989999328876446899 No 62 >COG2501 S4-like RNA binding protein [Replication, recombination, and repair] Probab=97.37 E-value=0.00049 Score=45.24 Aligned_cols=63 Identities=25% Similarity=0.307 Sum_probs=56.1 Q ss_pred CCCCCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCC Q ss_conf 466677344788999886-877899999998698699999924068780799979999989225 Q gi|254780406|r 7 VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69 (354) Q Consensus 7 ~~~~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~ 69 (354) +..+.+-+-|++||--+| +-|=.+|+.+|.+|.|+|||++.+--+.|+..+|.|+++|..+.. T Consensus 5 ~~i~~e~I~L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~~~~~v 68 (73) T COG2501 5 VLIKTEFITLGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPGQRYQV 68 (73) T ss_pred EEECCCEEEHHHHHHHHCCCCCCHHHHHHHHCCEEEECCEEECCCCCEEECCCEEEECCEEEEE T ss_conf 8721351879999987495057478889987791898886630167760169899989978999 No 63 >PRK05912 tyrosyl-tRNA synthetase; Validated Probab=97.36 E-value=0.00044 Score=45.54 Aligned_cols=39 Identities=28% Similarity=0.457 Sum_probs=13.9 Q ss_pred HHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEE Q ss_conf 78899988687-7899999998698699999924068780 Q gi|254780406|r 16 VSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNV 54 (354) Q Consensus 16 L~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v 54 (354) |-.+|..+|+| |++||.++|++|-|+|||+.|.++.+.+ T Consensus 337 i~dlLv~~gl~~SksEARRlI~qGgV~IN~~kI~D~~~~l 376 (402) T PRK05912 337 LVDLLVEAGLVPSKSEARRLIQQGAVKINGEKVSDPDYVF 376 (402) T ss_pred HHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCC T ss_conf 9999998688678899999998199898999964955422 No 64 >cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA). Probab=97.05 E-value=0.00036 Score=46.08 Aligned_cols=86 Identities=13% Similarity=0.098 Sum_probs=55.6 Q ss_pred CCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHH Q ss_conf 78751563144333364421011023432002665543323202223676410001234457404775211245564678 Q gi|254780406|r 79 HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158 (354) Q Consensus 79 ~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~ 158 (354) +||.+..+........ .+.....++..+|++|+.++|+.+++ ++|.+++. T Consensus 2 ~K~~~~t~~~~~~~~~-----~~~~~~~~v~~aG~kDk~a~t~Q~~s-----------------n~f~i~lr-------- 51 (87) T cd01291 2 YKPGGDTMEAARQLAK-----LLGIPPKRVGYAGRKDKRAVTTQLVS-----------------NRFTITLR-------- 51 (87) T ss_pred CCCCCCHHHHHHHHHH-----HHCCCHHHEEECCCCCCCEEEEEEEE-----------------EEEEEEEC-------- T ss_conf 6568789999999999-----82998777517446666554788764-----------------43589821-------- Q ss_pred HHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCC Q ss_conf 887400000876750343036402688079999995184289999999839 Q gi|254780406|r 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209 (354) Q Consensus 159 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g 209 (354) ..+..+..........++.++| ++.+|++.|+..++ T Consensus 52 -------------~~~~~~~~~~~~~~~~~l~f~L--~~~~yat~~lrel~ 87 (87) T cd01291 52 -------------VKPLNLKWPEERKRALVLEFTL--PRGSYATMLLRELG 87 (87) T ss_pred -------------CCCCCCCCHHHHHHHEEEEEEC--CCCHHHHHHHHHCC T ss_conf -------------6466777678864115789852--67407899898619 No 65 >PRK04051 rps4p 30S ribosomal protein S4; Validated Probab=97.03 E-value=0.0018 Score=41.67 Aligned_cols=55 Identities=24% Similarity=0.450 Sum_probs=46.7 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECC--CCEEEE-CCEECC Q ss_conf 4478899988687-789999999869869999992406878079--997999-998922 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS--TDHIEV-DGVPLR 68 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~--~d~v~v-dg~~i~ 68 (354) -||+-++...|++ |-.+|.+||..|-|.|||++|+.|++.|.. .|.|.+ ++-+|. T Consensus 103 RRL~~vv~r~~~a~si~~Ar~lI~hgHi~V~~~~v~~Ps~~V~r~~Ed~I~~~~~S~i~ 161 (177) T PRK04051 103 RRLQTIVYRKGLARTPKQARQLIVHGHIAVNGRRVTSPGYLVSREEEDKIDYYPTSPLA 161 (177) T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEEECCCCEEEEECCCCCEEECCCCCCC T ss_conf 68889998805668899999997478289999995368658865566854631799777 No 66 >TIGR02988 YaaA_near_RecF S4 domain protein YaaA; InterPro: IPR014330 This small protein has a single S4 domain (IPR002942 from INTERPRO); it is also found in bacterial S4 ribosomal proteins, some pseudouridine synthases and tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members that are not near recF are found instead near dnaA and/or dnaN, the usual neighbours of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.. Probab=96.92 E-value=0.0017 Score=41.76 Aligned_cols=55 Identities=22% Similarity=0.312 Sum_probs=49.7 Q ss_pred CCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC Q ss_conf 677344788999886-8778999999986986999999240687807999799999 Q gi|254780406|r 10 NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64 (354) Q Consensus 10 ~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg 64 (354) +.+-+-|++||=..+ +-|=.+|+.||.++.|.|||+..+-=|-|+.++|.|+|++ T Consensus 5 ~tEyITLgQlLK~~~~i~sGG~AK~fL~e~~V~vNGe~e~RRGkKL~~gD~i~i~~ 60 (60) T TIGR02988 5 KTEYITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIPD 60 (60) T ss_pred CCCEECHHHHHHHHHHHCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEECC T ss_conf 43416276786688562282578898706955547844045887004896688269 No 67 >COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Probab=96.90 E-value=0.0011 Score=43.04 Aligned_cols=144 Identities=13% Similarity=0.036 Sum_probs=88.0 Q ss_pred EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCC Q ss_conf 89602787515631443333644210110234320026655433232022236764100012344574047752112455 Q gi|254780406|r 74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153 (354) Q Consensus 74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~ 153 (354) -+++++||.|..++..-..-+..+ ...+....|-||-..+|+|.+.-+ -+.+|..--..-.|+|.+++.--. T Consensus 16 Gil~ldKP~G~tS~~~v~~vkkil------~~~K~GH~GTLDP~atGvLpi~ig--~aTKl~~~l~~~~K~Y~a~~~lG~ 87 (271) T COG0130 16 GVINLDKPPGPTSHEVVAWVKRIL------GVEKAGHGGTLDPLATGVLPICLG--EATKLVQYLLDADKEYVATVRLGD 87 (271) T ss_pred CEEEEECCCCCCHHHHHHHHHHHH------CCCCCCCCCCCCCCCCCEEEEEEC--HHHHHHHHHHHCCCEEEEEEEECC T ss_conf 469840799997799999999985------864056463448743441888834--147489887208947999999677 Q ss_pred C---HHHHHHHHHHHHCCCEEE-------------ECCCE---EEEECCCCEEEEEEEEEECCHHHHHHHHHHCC----- Q ss_conf 6---467888740000087675-------------03430---36402688079999995184289999999839----- Q gi|254780406|r 154 D---QDKLNLLKKGIVIQGICY-------------GDMQV---TLDTQKGSNAWVTVGLREGKNREIKKVFEFFN----- 209 (354) Q Consensus 154 ~---~~~~~~~~~g~~~~~~~~-------------~~~~~---~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g----- 209 (354) + .+.+......+.-+=.+. +.+.+ .+.........++|.-..| ..||-+|.-+| T Consensus 88 ~t~~~e~i~~~l~~F~G~I~Q~PP~~SAvK~~v~~R~V~i~~l~~~~~~~~~~~~~v~CskG--TYIRtL~~DlG~~LG~ 165 (271) T COG0130 88 QTDSEEEVRAALEAFTGEIYQIPPMFSAVKREVERRKITIYDLLELDFDRNLVTLRVECSKG--TYIRTLARDLGEALGC 165 (271) T ss_pred CCCCHHHHHHHHHHCCEEEEECCCCHHHCCCEEEEEEEEEEEEEECCCCCCEEEEEEEEECC--CCHHHHHHHHHHHHCC T ss_conf 57999999999986651058438703101346866799999866604777648999997068--5768889999998788 Q ss_pred -CEEEEEEEEEECCEECCC Q ss_conf -868688975870545187 Q gi|254780406|r 210 -WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 210 -~~V~~L~Rv~~G~~~l~~ 227 (354) -++..|.|++.|+|.+.+ T Consensus 166 gahm~~LrRt~~g~f~~~~ 184 (271) T COG0130 166 GAHMSELRRTRVGPFSEED 184 (271) T ss_pred CCCHHHHCCCCCCCCCCCC T ss_conf 5105552042246633023 No 68 >cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Probab=96.83 E-value=0.0045 Score=39.17 Aligned_cols=151 Identities=13% Similarity=0.101 Sum_probs=82.4 Q ss_pred EEECCCCCEEEECCCCCCCCCC-----CCEEEC------------------CCCCCEECCCCCCCCCCCEEEECCCCCCC Q ss_conf 9602787515631443333644-----210110------------------23432002665543323202223676410 Q gi|254780406|r 75 LWLYHKPIGLVTTHSDPDGRST-----VFDNLP------------------SIFSRVISVGRLDINTEGLLLLTNDGGLA 131 (354) Q Consensus 75 ~~~~~KP~g~~~~~~~~~~~~~-----~~~~~~------------------~~~~~~~~vgRLD~~t~GLlllTndg~l~ 131 (354) ++++|||.|+.++..=..-+.. +|.... ...-.+...|-||-..+|||++.-.- + T Consensus 2 i~~vdKP~GiTS~~vv~~lk~~f~~s~~f~~~~~~~~~~~~~~~~r~k~~~~~~~KvGH~GTLDP~AtGvL~i~~G~--a 79 (312) T cd02867 2 VFAINKPSGITSAQVLNDLKPLFLNSALFKDKIQRAVAKRGKKARRRKGRKRSKLKIGHGGTLDPLATGVLVVGVGA--G 79 (312) T ss_pred EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCHHCCCCCCCCEEEECCCCCCCCCCEEEEEECH--H T ss_conf 68874799999899999999983411102310222222101100000012457744402656787460338899875--4 Q ss_pred CCCCCCCCCCEEEEEEEECC--------------------CCCHHHHHHHHHHHHC--------------CCEE------ Q ss_conf 00123445740477521124--------------------5564678887400000--------------8767------ Q gi|254780406|r 132 RVLELPSTQWLRVYRVRFHG--------------------QVDQDKLNLLKKGIVI--------------QGIC------ 171 (354) Q Consensus 132 ~~l~~p~~~~~k~Y~v~v~~--------------------~~~~~~~~~~~~g~~~--------------~~~~------ 171 (354) .++...-....|+|.+++.- .++.+.+......+.- ++.. T Consensus 80 TK~~~~~~~~~K~Y~a~~~lG~~TdT~D~eG~v~~~~~~~~~t~~~i~~~l~~F~G~i~Q~PP~ySA~Kv~GkrlYelAR 159 (312) T cd02867 80 TKQLQDYLSCSKTYEATGLFGASTTTYDREGKILKKKPYSHITREDIEEVLAKFRGDIKQVPPLYSALKMDGKRLYEYAR 159 (312) T ss_pred HEECHHHCCCCCEEEEEEEECCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCCEEEECCHHHEEEECCEEHHHHHH T ss_conf 40458666799179999998840578777787775057886889999999997788657648756834379988998986 Q ss_pred ----------EECCCEE---EEECCCCEEEEEEEEEECCHHHHHHHHHHCC------CEEEEEEEEEECCEECCC Q ss_conf ----------5034303---6402688079999995184289999999839------868688975870545187 Q gi|254780406|r 172 ----------YGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFN------WKVNRLIRISYGPFQLGT 227 (354) Q Consensus 172 ----------~~~~~~~---~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g------~~V~~L~Rv~~G~~~l~~ 227 (354) .+.+.+. +.........+.+.+..++--.||.++.-+| -++..|.|++.|++.-.+ T Consensus 160 ~G~~ver~i~~R~V~I~~l~l~~~~~~~~~~~~~v~cskGTYiRsla~dlg~~Lg~~ah~~~LrRt~~G~~~e~~ 234 (312) T cd02867 160 EGKPLPRPIERRQVVVSELLVKDWIEPGPLFTRTVEEEGKQYERSVVKMLGKELKTFAEVTELTATAEGDPVEEV 234 (312) T ss_pred CCCCCCCCCCCEEEEEEEEEEEECCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEEEHEEECCCCCCCCCCC T ss_conf 897135777741699999998741588875999998179753889999986875886460104535458997222 No 69 >PTZ00155 40S ribosomal protein S9; Provisional Probab=96.72 E-value=0.0027 Score=40.62 Aligned_cols=54 Identities=20% Similarity=0.370 Sum_probs=45.8 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECC--CCEEEEC-CEEC Q ss_conf 4478899988687-789999999869869999992406878079--9979999-9892 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS--TDHIEVD-GVPL 67 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~--~d~v~vd-g~~i 67 (354) -||+-++...|++ |-.+|-.||..|-|.|||++|+.|++.|.. .|.|.+. .-|+ T Consensus 107 RRLqt~v~~~glA~si~~Ar~lI~hgHI~V~~~~V~~Ps~lV~r~~Ed~I~~~~~Spl 164 (188) T PTZ00155 107 RRLQTKVFKLGLAKSVHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIAFALTSPF 164 (188) T ss_pred HHHHHHHHHHCCCCCHHHHHHHEECCEEEECCEEECCCCEEEEECCCCCEEEECCCCC T ss_conf 7676899986011588988888344628899989537745886054464454368988 No 70 >TIGR00425 CBF5 rRNA pseudouridine synthase, putative; InterPro: IPR004802 This family contains the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether the archaeal proteins in this family modify tRNA, rRNA, or both. . Probab=96.20 E-value=0.036 Score=33.52 Aligned_cols=166 Identities=20% Similarity=0.194 Sum_probs=107.2 Q ss_pred CCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEE Q ss_conf 56438960278751563144333364421011023432002665543323202223676410001234457404775211 Q gi|254780406|r 70 AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149 (354) Q Consensus 70 ~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v 149 (354) +-..=++.+.||.|-.+|.-.- +-. .+| +..+...-|-||---||.|++.=|-.----=+.....-|..+++++ T Consensus 31 yI~~Gvv~lDKP~gPsSHeV~~-Wvr---~iL--~veKtGH~GTLDPKVTGvLpv~ierATr~v~~~~~a~KEYVClmRL 104 (326) T TIGR00425 31 YIRKGVVNLDKPSGPSSHEVVA-WVR---RIL--RVEKTGHGGTLDPKVTGVLPVCIERATRLVKSLQEAPKEYVCLMRL 104 (326) T ss_pred HHHCCEEEEECCCCCCCCEEHH-HHH---HHH--CCCCCCCCCCCCCCEEEEEEEEEHHHHHHHHHHHCCCCCEEEEEEE T ss_conf 6206507876484188640102-212---101--0112465875788312462121000235644531699745997761 Q ss_pred CCCCCHH-HHHHHHHHHHCCCEEEE--CCC--------------EEEEECCCCE--EEEEEEEEECCHHHHHHHHHHCCC Q ss_conf 2455646-78887400000876750--343--------------0364026880--799999951842899999998398 Q gi|254780406|r 150 HGQVDQD-KLNLLKKGIVIQGICYG--DMQ--------------VTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNW 210 (354) Q Consensus 150 ~~~~~~~-~~~~~~~g~~~~~~~~~--~~~--------------~~~~~~~~~~--~~~~v~l~eGr~~qIrr~~~~~g~ 210 (354) +.++..+ .+.+.-+-+ -|-.|+ |.. +.++.-++.. -.|+|.=.-|=| ||.+|..+|. T Consensus 105 H~~~~~e~~~~rvl~~f--~G~ifQrPPLksAVKr~LRvR~IYe~~llE~Dg~d~LvlFrv~CeaGTY--iRkLC~d~G~ 180 (326) T TIGR00425 105 HRDAKEEKDIERVLKEF--TGRIFQRPPLKSAVKRQLRVRTIYESELLEVDGKDRLVLFRVSCEAGTY--IRKLCVDIGE 180 (326) T ss_pred CHHHHHHHHHHHHHHHC--CCEEECCCCCHHHHCCCCCEEEEEEEEEEEECCCCCEEEEEEEECCCCC--HHHHHHHHHH T ss_conf 20121257899998851--8303338862565223365016899887720799626899998757861--5687888867 Q ss_pred ------EEEEEEEEEECCEE-------CCCCCCCCEEECCH---HHHHHHH Q ss_conf ------68688975870545-------18755474886799---9998753 Q gi|254780406|r 211 ------KVNRLIRISYGPFQ-------LGTLLAGSTREVSK---KILREQL 245 (354) Q Consensus 211 ------~V~~L~Rv~~G~~~-------l~~L~~G~~r~l~~---~e~~~l~ 245 (354) +-.-|.|++-|.|. |-||.=-+|-+-.. .+|+... T Consensus 181 ~LG~GahMqELRRtrsG~f~E~d~~vtLhDllDAy~fw~e~gDE~yLR~~I 231 (326) T TIGR00425 181 LLGTGAHMQELRRTRSGAFGERDDMVTLHDLLDAYVFWKEDGDESYLREVI 231 (326) T ss_pred HHCCCCCCCHHEEEEEECCCCCCCCEEHHHHHEEEEEEECCCCHHHHHHHH T ss_conf 617672120010100102202467060420311102220378725656542 No 71 >PTZ00118 40S ribosomal protein S4; Provisional Probab=95.95 E-value=0.092 Score=30.92 Aligned_cols=124 Identities=15% Similarity=0.143 Sum_probs=68.7 Q ss_pred CCHHHHHHHHHC-C-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEEEECCCCCEEEECCC Q ss_conf 734478899988-6-87789999999869869999992406878079997999998922556438960278751563144 Q gi|254780406|r 12 TPQRVSKVIARA-G-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHS 89 (354) Q Consensus 12 ~~~RL~K~la~~-g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~ 89 (354) +++=|.=||-+. + --+.|||...|.+|.|.|||++.++..+-|---|+|++.. ..+ .|-++|+.-.-+..+.. T Consensus 40 eslPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvG~MDVIsI~k----t~e-~yRvl~d~kGrf~l~~I 114 (262) T PTZ00118 40 ECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTK----TNE-YFRLLYDTKGRFVPHKI 114 (262) T ss_pred CCCCCHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCEEEEEEECC----CCC-EEEEEECCCCEEEEEEC T ss_conf 4554335643464522658999999867908889999534899874678999856----896-59999868970999988 Q ss_pred CCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEEC Q ss_conf 3333644210110234320026655433232022236764100012344574047752112 Q gi|254780406|r 90 DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150 (354) Q Consensus 90 ~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~ 150 (354) +.+.-. +.+.. .....+--|... +++|.||.-. .+..|...+.-+..+.+. T Consensus 115 ~~eEA~--~KLcK-V~K~~i~~g~iq------~~~thDGr~i-~~~d~~ik~~Dtv~i~l~ 165 (262) T PTZ00118 115 TNEEAK--YKLCR-VKKTFLGPKEVS------IAVTHDGRTI-RYVHPDVKVGDSLRLDLE 165 (262) T ss_pred CHHHHC--CEEEE-EEEEEECCCCEE------EEECCCCCEE-ECCCCCCCCCCEEEEECC T ss_conf 967814--38999-999998689537------8872477668-326887666988999889 No 72 >TIGR01018 rpsD_arch ribosomal protein S4; InterPro: IPR005710 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This model finds eukaryotic ribosomal protein S9 as well as eukaryotic and archaeal ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit. Probab=95.66 E-value=0.0069 Score=37.99 Aligned_cols=50 Identities=18% Similarity=0.406 Sum_probs=43.4 Q ss_pred HHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECC--CCEEEEC Q ss_conf 4478899988687-789999999869869999992406878079--9979999 Q gi|254780406|r 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS--TDHIEVD 63 (354) Q Consensus 14 ~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~--~d~v~vd 63 (354) =|||=..-..|++ |=++|-+||-.|-|.|||++|+.|++-|.- .|.|.+. T Consensus 112 RRLQT~Vyk~GLArTi~~ARqLi~hGHI~v~Gr~v~~Psy~V~~e~e~kI~fa 164 (170) T TIGR01018 112 RRLQTLVYKKGLARTIKQARQLIVHGHIAVDGRRVTSPSYIVRREEEDKIDFA 164 (170) T ss_pred HHHHHHHHHHHHCCCHHHCCEEEEECEEEECCEEEECCCEEEECCCCCCCCCC T ss_conf 45678999863022632343023203388768477358616746554421205 No 73 >PRK04313 30S ribosomal protein S4e; Validated Probab=94.94 E-value=0.062 Score=31.99 Aligned_cols=53 Identities=21% Similarity=0.286 Sum_probs=42.5 Q ss_pred CCHHHHHHHHHC-C-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC Q ss_conf 734478899988-6-8778999999986986999999240687807999799999 Q gi|254780406|r 12 TPQRVSKVIARA-G-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64 (354) Q Consensus 12 ~~~RL~K~la~~-g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg 64 (354) +++=|.=+|-+. + .-+.|||...|.+|.|.|||++.++..+-|---|+|++.. T Consensus 36 ~siPL~v~LRd~L~~a~t~rEak~Il~~~~V~VDG~vr~d~~~pvGlmDVisi~~ 90 (237) T PRK04313 36 SSLPLLIVLRDVLGYADTAREARKIISEGKVLVDGRVRKDYKFPVGLMDVISIPE 90 (237) T ss_pred CCCCCHHHHHHHHHHHCCHHHHHHHHHCCEEEECCEEEECCCCCCCEEEEEEECC T ss_conf 5423389998777250448899998648859989999603788754167998647 No 74 >PTZ00223 40S ribosomal protein S4; Provisional Probab=94.84 E-value=0.085 Score=31.12 Aligned_cols=74 Identities=15% Similarity=0.065 Sum_probs=50.4 Q ss_pred CCHHHHHHHHHC-C-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECCCCCCEEEEECCCCCEEEECCC Q ss_conf 734478899988-6-87789999999869869999992406878079997999998922556438960278751563144 Q gi|254780406|r 12 TPQRVSKVIARA-G-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHS 89 (354) Q Consensus 12 ~~~RL~K~la~~-g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~ 89 (354) +++=|.=||-+. + .-+.|||...|.+|.|.|||++.++..+-|---|+|++.. . .+.|-++|+.-.-+..+.. T Consensus 37 eslPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvG~MDVIsI~k----t-~e~yRvl~D~kGr~~l~~I 111 (273) T PTZ00223 37 ECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPK----T-GDRFRILYDVKGRFALVKV 111 (273) T ss_pred CCCCCHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCEEEEEEECC----C-CCEEEEEECCCCEEEEEEC T ss_conf 4444257876564521657999999877937977999655899885789999857----8-8749999868962999984 Q ss_pred C Q ss_conf 3 Q gi|254780406|r 90 D 90 (354) Q Consensus 90 ~ 90 (354) + T Consensus 112 ~ 112 (273) T PTZ00223 112 S 112 (273) T ss_pred C T ss_conf 9 No 75 >COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis] Probab=93.90 E-value=0.24 Score=28.31 Aligned_cols=37 Identities=22% Similarity=0.331 Sum_probs=32.9 Q ss_pred CHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEEC Q ss_conf 7899999998698699999924068780799979999 Q gi|254780406|r 27 SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63 (354) Q Consensus 27 SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vd 63 (354) .-|||...|.+|.|.|||++.++.-.-|---|+|++. T Consensus 56 ~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip 92 (241) T COG1471 56 NAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIP 92 (241) T ss_pred CHHHHHHHHHCCCEEECCEEECCCCCCCCEEEEEEEC T ss_conf 3488999876695798889801355784068999976 No 76 >KOG2559 consensus Probab=86.80 E-value=1.5 Score=23.22 Aligned_cols=37 Identities=19% Similarity=0.329 Sum_probs=29.8 Q ss_pred HHHHHHHHHCCCE------EEEEEEEEECCEECC-CCCCCCEEE Q ss_conf 8999999983986------868897587054518-755474886 Q gi|254780406|r 199 REIKKVFEFFNWK------VNRLIRISYGPFQLG-TLLAGSTRE 235 (354) Q Consensus 199 ~qIrr~~~~~g~~------V~~L~Rv~~G~~~l~-~L~~G~~r~ 235 (354) -.+|.+...+|+. .++|.|+++|+|.++ .|.+-+|-. T Consensus 220 e~Lr~LVh~igl~L~T~a~c~qlrr~r~g~F~~d~aLLr~qw~L 263 (318) T KOG2559 220 EMLRQLVHHIGLNLGTEATCIQLRRQRFGPFGSDNALLRKQWNL 263 (318) T ss_pred HHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCCCHHHHHHHHCC T ss_conf 99999999974312541555242343257877518999986162 No 77 >KOG3301 consensus Probab=84.57 E-value=1 Score=24.29 Aligned_cols=49 Identities=18% Similarity=0.357 Sum_probs=40.6 Q ss_pred CCCCHHHHHHHHHCCCC-CHHHHHHHHHCCCEEECCEECCCCCEEECCCC Q ss_conf 67734478899988687-78999999986986999999240687807999 Q gi|254780406|r 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD 58 (354) Q Consensus 10 ~~~~~RL~K~la~~g~~-SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d 58 (354) +.=..||+-.+...|++ |=-.|..||..+.|.|++++|.-|++.|.... T Consensus 93 ~fLErRLqt~vFklGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrlds 142 (183) T KOG3301 93 DFLERRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRLDS 142 (183) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCEEEECCCEEEEECH T ss_conf 99999999999998665442788987427607615757624654566121 No 78 >KOG2623 consensus Probab=83.59 E-value=2.9 Score=21.47 Aligned_cols=20 Identities=10% Similarity=0.287 Sum_probs=10.4 Q ss_pred CCCCCEEEECCCCCCCCCCC Q ss_conf 33232022236764100012 Q gi|254780406|r 116 INTEGLLLLTNDGGLARVLE 135 (354) Q Consensus 116 ~~t~GLlllTndg~l~~~l~ 135 (354) --+.|=.+.-|+.+|-..+. T Consensus 152 ~~s~g~~~ivnN~dW~~d~~ 171 (467) T KOG2623 152 GSSQGKYIIVNNSDWYKDIK 171 (467) T ss_pred CCCCCCEEEEECHHHHHHCH T ss_conf 75668616750567762456 No 79 >pfam06353 DUF1062 Protein of unknown function (DUF1062). This family consists of several hypothetical bacterial proteins of unknown function. Probab=81.65 E-value=2.1 Score=22.41 Aligned_cols=49 Identities=31% Similarity=0.390 Sum_probs=25.4 Q ss_pred EEEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCC Q ss_conf 389602787515631443333644210110234320026655433232022236764100012 Q gi|254780406|r 73 TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135 (354) Q Consensus 73 ~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~ 135 (354) ..+|++ |-|+.++.-..-++|...... .+.-.-||. |.+||-.+++.+. T Consensus 8 LDvWLI-----YkC~~C~~TwN~ti~eR~~v~---~I~p~ll~~------f~~ND~~la~~~a 56 (142) T pfam06353 8 LDVWLI-----YKCTKCDYTWNITIFERRNVR---SINPELLEA------LHSNDPGLARAYA 56 (142) T ss_pred EEEEEE-----EEECCCCCEECCCEEEECCCC---CCCHHHHHH------HHHCCHHHHHHHH T ss_conf 348889-----871468684050114315812---079999998------9736999999994 No 80 >COG4332 Uncharacterized protein conserved in bacteria [Function unknown] Probab=79.35 E-value=2.3 Score=22.15 Aligned_cols=120 Identities=21% Similarity=0.262 Sum_probs=60.1 Q ss_pred CCCEEEECCEECCCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEECCC--CCCEECCCCCCCCCCCEEEECCCCCCCCC Q ss_conf 9997999998922556438960278751563144333364421011023--43200266554332320222367641000 Q gi|254780406|r 56 STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARV 133 (354) Q Consensus 56 ~~d~v~vdg~~i~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~--~~~~~~vgRLD~~t~GLlllTndg~l~~~ 133 (354) .++.++|+-+- +...+|+++ -|+.+|..+.-++|..++.. .+.++. -|..||.+++++ T Consensus 31 cSg~fRvNAq~----K~LDvWlIY-----kC~~Cd~tWN~~IfeR~~~~~Iep~lle-----------al~~NDa~larr 90 (203) T COG4332 31 CSGKFRVNAQG----KVLDVWLIY-----KCTHCDYTWNISIFERLNVSDIEPDLLE-----------ALMANDAALARR 90 (203) T ss_pred ECCCEEECCCC----CEEEEEEEE-----EEECCCCCCCHHHHHCCCCCCCCHHHHH-----------HHHCCCHHHHHH T ss_conf 35727884788----378899999-----8504677256103101682008989999-----------998189999998 Q ss_pred CCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHH---HHHHCCC Q ss_conf 1234457404775211245564678887400000876750343036402688079999995184289999---9998398 Q gi|254780406|r 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK---VFEFFNW 210 (354) Q Consensus 134 l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr---~~~~~g~ 210 (354) .+... .+.+.-..++++..+ -.++..+..+..+..-+++.|.--+.-|||- +-+.+|+ T Consensus 91 ~afdl-a~lRr~~~r~~g~pd------------------~~i~krilge~~~~~~vel~l~~~~p~qlrl~~Ll~seL~L 151 (203) T COG4332 91 FAFDL-AILRRNNARLSGFPD------------------FHIQKRILGEIASHAAVELSLRISRPFQLRLDRLLASELGL 151 (203) T ss_pred HHHHH-HHHHHCCCCCCCCCC------------------HHHHHHEECCCCCCEEEEEEECCCCCCHHHHHHHHHHHHCC T ss_conf 87319-999720344457875------------------00311100574440027899745676065799999988583 Q ss_pred EEEE Q ss_conf 6868 Q gi|254780406|r 211 KVNR 214 (354) Q Consensus 211 ~V~~ 214 (354) .-.. T Consensus 152 SrS~ 155 (203) T COG4332 152 SRSE 155 (203) T ss_pred CHHH T ss_conf 7999 No 81 >pfam01509 TruB_N TruB family pseudouridylate synthase (N terminal domain). Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA. Probab=77.62 E-value=1.6 Score=23.11 Aligned_cols=49 Identities=24% Similarity=0.164 Sum_probs=34.0 Q ss_pred CCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHH Q ss_conf 320026655433232022236764100012344574047752112455646 Q gi|254780406|r 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156 (354) Q Consensus 106 ~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~ 156 (354) .++...|.||-..+|||++.-+. +.++..--....|+|.+++.--...+ T Consensus 7 kKvGH~GTLDP~AsGlL~i~ig~--~TK~~~~~~~~~K~Y~~~~~~G~~Td 55 (149) T pfam01509 7 KKVGHTGTLDPLATGVLPVCVGK--ATKLLQYLLDADKEYRATIRLGVATD 55 (149) T ss_pred CCCCCCCCCCCCCEEEEEEEECH--HHHHHHHHCCCCCEEEEEEEECCCCC T ss_conf 60242744698665689999987--87121887589817999998625668 No 82 >TIGR00431 TruB tRNA pseudouridine synthase B; InterPro: IPR014780 TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific functions.; GO: 0003723 RNA binding, 0016439 tRNA-pseudouridine synthase activity, 0031119 tRNA pseudouridine synthesis. Probab=77.47 E-value=0.49 Score=26.35 Aligned_cols=70 Identities=24% Similarity=0.215 Sum_probs=48.3 Q ss_pred EEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECC Q ss_conf 96027875156314433336442101102343200266554332320222367641000123445740477521124 Q gi|254780406|r 75 LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151 (354) Q Consensus 75 ~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~ 151 (354) ++++|||.|..++..=.. |-.++ ..+++.+.|-||.-.+|+|++-= |.-+.+|..--..-+|+|.+...- T Consensus 4 vLll~Kp~G~TSfd~~~~----v~rLl--~~kkvGHtGTLDp~A~G~L~~~v-Gr~aTkl~~yl~~~dK~Y~A~~~l 73 (236) T TIGR00431 4 VLLLDKPQGMTSFDALAK----VRRLL--GVKKVGHTGTLDPFATGVLPILV-GRKATKLSPYLTDLDKEYEAEIRL 73 (236) T ss_pred CCCCCCCCCCCHHHHHHH----HHHHH--CCCCCCCCCCCCHHHHHHHHHHH-HHHHHHHHHHHCCCCCEEEEEEEC T ss_conf 041557888788999999----99987--07852206665302410354223-001343433312647617999982 No 83 >pfam05910 DUF868 Plant protein of unknown function (DUF868). This family consists of several hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown. Probab=74.78 E-value=3.2 Score=21.21 Aligned_cols=12 Identities=17% Similarity=0.263 Sum_probs=6.2 Q ss_pred CCEEEEEEEEEE Q ss_conf 986868897587 Q gi|254780406|r 209 NWKVNRLIRISY 220 (354) Q Consensus 209 g~~V~~L~Rv~~ 220 (354) |..|+..+|.++ T Consensus 181 gk~v~~VkrL~W 192 (272) T pfam05910 181 GKVVVQVKRLQW 192 (272) T ss_pred CEEEEEEEEEEE T ss_conf 999999987233 No 84 >TIGR02414 pepN_proteo aminopeptidase N; InterPro: IPR012779 Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. The M1 family of zinc metallopeptidases contains a number of distinct, well-separated clades of proteins with aminopeptidase activity. Several are designated aminopeptidase N, 3.4.11.2 from EC, after the Escherichia coli enzyme, suggesting a similar activity profile (see P04825 from SWISSPROT for a description of catalytic activity). This family of zinc metallopeptidases belong to MEROPS peptidase family M1 (aminopeptidase N, clan MA); the majority are identified as alanyl aminopeptidases (proteobacteria) that are closely related to Escherichia coli PepN and presumed to have a similar (not identical) function. Nearly all are found in proteobacteria, but members are found also in cyanobacteria, plants, and apicomplexan parasites , . This family differs greatly in sequence from the family of aminopeptidases typified by Streptomyces lividans PepN (IPR012778 from INTERPRO) and from the membrane bound aminopeptidase N family in animals.; GO: 0004179 membrane alanyl aminopeptidase activity, 0008270 zinc ion binding. Probab=70.85 E-value=4 Score=20.59 Aligned_cols=62 Identities=19% Similarity=0.222 Sum_probs=46.1 Q ss_pred CEEECCEECCCCCEEECCCCEEEECCEEC------------CCCCCEEEEECCCCCEEEECCCCCCCCCCCCEEE Q ss_conf 86999999240687807999799999892------------2556438960278751563144333364421011 Q gi|254780406|r 39 RVKVNGILLERAAVNVMSTDHIEVDGVPL------------RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101 (354) Q Consensus 39 ~V~Vng~~v~~~~~~v~~~d~v~vdg~~i------------~~~~~~~~~~~~KP~g~~~~~~~~~~~~~~~~~~ 101 (354) .|+|||+....-+|.+++. ..+|.+.|- .|.+.+-+.=++|=.|..||.|..+|-+-|.-++ T Consensus 55 si~idG~~L~~~~Y~~d~~-~LTI~~~P~~~~F~l~~~t~i~P~~Nt~L~GLY~SgG~fcTQCEAEGFRrITYf~ 128 (898) T TIGR02414 55 SIAIDGQPLAADDYQLDDE-SLTIASVPESKEFTLEIETEIKPEENTSLEGLYKSGGNFCTQCEAEGFRRITYFL 128 (898) T ss_pred EEEECCCEECCCCCEECCC-CCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCHHHCCCCEEEECCCCCCCCCCCC T ss_conf 9986585205885367365-2325876898627999999986376772002020288407750577755002247 No 85 >COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport] Probab=70.55 E-value=4.8 Score=20.13 Aligned_cols=43 Identities=21% Similarity=0.260 Sum_probs=35.9 Q ss_pred CCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECC Q ss_conf 7789999999869869999992406878079997999998922 Q gi|254780406|r 26 ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68 (354) Q Consensus 26 ~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~ 68 (354) +-+-+--.+|++|+=+|.+.+...--.++.++|+|.++|..|. T Consensus 6 gL~eeylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~~~~l~ 48 (111) T COG4043 6 GLREEYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFNGDKLK 48 (111) T ss_pred CHHHHHHHHHHCCCCEEEEEECCHHHCCCCCCCEEEECCCEEE T ss_conf 0378899998704436899955776627898998998388467 No 86 >PRK10590 ATP-dependent RNA helicase RhlE; Provisional Probab=67.73 E-value=9.4 Score=18.26 Aligned_cols=13 Identities=8% Similarity=-0.181 Sum_probs=6.9 Q ss_pred CEEECCHHHHHHH Q ss_conf 4886799999875 Q gi|254780406|r 232 STREVSKKILREQ 244 (354) Q Consensus 232 ~~r~l~~~e~~~l 244 (354) .+-.++++|...+ T Consensus 345 ait~v~~~e~~~~ 357 (457) T PRK10590 345 ALSLVCVDEHKLL 357 (457) T ss_pred EEEEECHHHHHHH T ss_conf 9998668999999 No 87 >KOG4655 consensus Probab=66.35 E-value=3.8 Score=20.72 Aligned_cols=42 Identities=26% Similarity=0.396 Sum_probs=33.2 Q ss_pred CHHHHHHHHHCCCEEECCEECCCCCEEECCC--CEEE-ECCEECC Q ss_conf 7899999998698699999924068780799--9799-9998922 Q gi|254780406|r 27 SRREVERMIAQQRVKVNGILLERAAVNVMST--DHIE-VDGVPLR 68 (354) Q Consensus 27 SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~--d~v~-vdg~~i~ 68 (354) |-.+|-++|++|-|.|--++|++|++.|..+ |-|+ ||...|+ T Consensus 121 ~~k~A~~~vEqGHVRvGp~~vtDPa~lvtr~mEDfvtWvd~SKIK 165 (181) T KOG4655 121 SVKEAVRFVEQGHVRVGPKVVTDPAFLVTRSMEDFVTWVDSSKIK 165 (181) T ss_pred HHHHHHHHHHCCCEEECCEECCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 699999999818535178000472577422266564242268899 No 88 >pfam02824 TGS TGS domain. The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role. Probab=57.14 E-value=11 Score=17.77 Aligned_cols=22 Identities=27% Similarity=0.302 Sum_probs=18.9 Q ss_pred EEECCEECCCCCEEECCCCEEEE Q ss_conf 69999992406878079997999 Q gi|254780406|r 40 VKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 40 V~Vng~~v~~~~~~v~~~d~v~v 62 (354) .+|||+.+ .+.+.+..+|+|++ T Consensus 37 A~VnG~~v-~l~~~L~~gd~V~I 58 (60) T pfam02824 37 AKVNGQRV-GLDHVLEDGDVVEI 58 (60) T ss_pred EEECCEEC-CCCCCCCCCCEEEE T ss_conf 89998887-62112489999998 No 89 >cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown. Probab=57.03 E-value=11 Score=17.87 Aligned_cols=23 Identities=30% Similarity=0.417 Sum_probs=18.9 Q ss_pred CEEECCEECCCCCEEECCCCEEEE Q ss_conf 869999992406878079997999 Q gi|254780406|r 39 RVKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 39 ~V~Vng~~v~~~~~~v~~~d~v~v 62 (354) -++|||+.+ .+.+.+..+|+|++ T Consensus 36 ~a~vNg~~~-~l~~~L~~GD~VeI 58 (60) T cd01668 36 GAKVNGKLV-PLSTVLKDGDIVEI 58 (60) T ss_pred EEEECCEEC-CCCCCCCCCCEEEE T ss_conf 999999998-98768289999998 No 90 >PRK08857 para-aminobenzoate synthase component II; Provisional Probab=55.82 E-value=6.6 Score=19.22 Aligned_cols=99 Identities=17% Similarity=0.151 Sum_probs=60.0 Q ss_pred EEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHH-HHHHCCCEEEECCCEEEEEC-----CCCEEEEEEEEE Q ss_conf 022236764100012344574047752112455646788874-00000876750343036402-----688079999995 Q gi|254780406|r 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQ-----KGSNAWVTVGLR 194 (354) Q Consensus 121 LlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~~~~-----~~~~~~~~v~l~ 194 (354) +||+-|-..+.+.|.+--.+..-...|.-...++.+.+..+. .++.+..|+-.|........ ...-- -+-|. T Consensus 2 iLiiDn~DsfT~ni~~~l~~lg~~v~vv~~d~~~~~~i~~~~p~~IilS~GPg~p~~~~~~~~~~~~~~~~iP--ILGIC 79 (192) T PRK08857 2 LLMIDNYDSFTYNLYQYFCELGAEVKVVRNDEIDIAGIEALNPSHLVISPGPCTPNEAGISLQAIEHFAGKLP--ILGVC 79 (192) T ss_pred EEEEECCCCHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHCCCCEEEECCCCCCHHHCCCCHHHHHHHCCCCC--EEEEC T ss_conf 9999799977999999998779928999699899999984297959998999996782861466997357999--89987 Q ss_pred ECCHHHHHHHHHHCCCEEEEEEEEEECCEEC Q ss_conf 1842899999998398686889758705451 Q gi|254780406|r 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225 (354) Q Consensus 195 eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l 225 (354) =| ||+ |+.++|-+|.+++...+|.... T Consensus 80 lG--~Q~--ia~~~Gg~v~~~~~~~hG~~~~ 106 (192) T PRK08857 80 LG--HQA--IAQVFGGDVVRARQVMHGKTSP 106 (192) T ss_pred HH--HHH--HHHHHCCEEEECCCCEEEEEEE T ss_conf 99--999--9998398299888432511579 No 91 >pfam05949 DUF881 Bacterial protein of unknown function (DUF881). This family consists of a series of hypothetical bacterial proteins. One of the family members from Bacillus subtilis is thought to be involved in cell division and sporulation. Probab=55.72 E-value=15 Score=16.91 Aligned_cols=31 Identities=23% Similarity=0.335 Sum_probs=22.0 Q ss_pred CEEECCEECCCCCEEECCCCEEEECCEECCC Q ss_conf 8699999924068780799979999989225 Q gi|254780406|r 39 RVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69 (354) Q Consensus 39 ~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~~ 69 (354) -|.|||+.+.....-...+..|.|||.++.+ T Consensus 61 AIsIng~Ri~~~s~Ir~~g~~i~Vng~~i~~ 91 (150) T pfam05949 61 AISINGQRITATTEIRCAGGTILVDGRPISP 91 (150) T ss_pred EEEECCEEECCEEEEEECCCEEEECCEEECC T ss_conf 9999999972507999729989999999079 No 92 >PRK08007 para-aminobenzoate synthase component II; Provisional Probab=55.14 E-value=6.5 Score=19.28 Aligned_cols=100 Identities=17% Similarity=0.126 Sum_probs=59.8 Q ss_pred EEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHH-HHHHCCCEEEECCCEEEE----ECCCCEEEEEEEEEE Q ss_conf 022236764100012344574047752112455646788874-000008767503430364----026880799999951 Q gi|254780406|r 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLD----TQKGSNAWVTVGLRE 195 (354) Q Consensus 121 LlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~~----~~~~~~~~~~v~l~e 195 (354) +||+-|-..+.+.|.+--.+..-+..|.-..+++.+.++.+. .++.+..|+-.|...... ...... .=-+-|.= T Consensus 2 ILiIDn~DsFT~ni~~~l~~~g~~v~V~~~d~~~~~~i~~~~p~~IvlSpGPg~P~~~~~~~~~i~~~~~~-iPiLGICl 80 (187) T PRK08007 2 ILLIDNYDSFTWNLYQYFCELGADVLVKRNDALTLADIDALKPQKIVISPGPCTPDEAGISLDVIRHYAGR-LPILGVCL 80 (187) T ss_pred EEEEECCCCHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHCCCCEEEECCCCCCHHHCCCCHHHHHHHCCC-CCEEEECH T ss_conf 99996898189999999987799799993898999999842989799999999958908404689975389-98899879 Q ss_pred CCHHHHHHHHHHCCCEEEEEEEEEECCEEC Q ss_conf 842899999998398686889758705451 Q gi|254780406|r 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQL 225 (354) Q Consensus 196 Gr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l 225 (354) | ||+ |+.++|-+|.++....+|.-.+ T Consensus 81 G--~Q~--ia~~~Gg~v~~~~~~~hG~~~~ 106 (187) T PRK08007 81 G--HQA--MAQAFGGKVVRAAKVMHGKTSP 106 (187) T ss_pred H--HHH--HHHHCCCEEEECCCCCCCCCEE T ss_conf 9--999--9998098073478320152069 No 93 >PRK02491 putative deoxyribonucleotide triphosphate pyrophosphatase/unknown domain fusion protein; Reviewed Probab=53.70 E-value=15 Score=16.92 Aligned_cols=30 Identities=30% Similarity=0.494 Sum_probs=25.0 Q ss_pred EEEEEEEEECCHHHHHHHHHHCCCEEEEEE Q ss_conf 799999951842899999998398686889 Q gi|254780406|r 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLI 216 (354) Q Consensus 187 ~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~ 216 (354) +.+--|=.+||-+|.+.||+.+|++|..|. T Consensus 129 tilIAT~N~GK~kEf~~l~~~~g~~V~sL~ 158 (328) T PRK02491 129 TILIATRNEGKTKEFRKLFGKLGYKVENLN 158 (328) T ss_pred EEEEEECCCCHHHHHHHHHHHCCCEEEEHH T ss_conf 799983796569999998875495897887 No 94 >pfam06668 ITI_HC_C Inter-alpha-trypsin inhibitor heavy chain C-terminus. This family represents the C-terminal region of inter-alpha-trypsin inhibitor heavy chains. Inter-alpha-trypsin inhibitors are glycoproteins with a high inhibitory activity against trypsin, built up from different combinations of four polypeptides: bikunin and the three heavy chains that belong to this family (HC1, HC2, HC3). The heavy chains do not have any protease inhibitory properties but have the capacity to interact in vitro and in vivo with hyaluronic acid, which promotes the stability of the extra-cellular matrix. All family members contain the pfam00092 domain. Probab=48.97 E-value=20 Score=16.24 Aligned_cols=11 Identities=45% Similarity=0.619 Sum_probs=7.7 Q ss_pred EEECCEECCCC Q ss_conf 69999992406 Q gi|254780406|r 40 VKVNGILLERA 50 (354) Q Consensus 40 V~Vng~~v~~~ 50 (354) |.|||++|-.+ T Consensus 4 i~VNGqlIgak 14 (188) T pfam06668 4 VTVNGQLIGAK 14 (188) T ss_pred EEEECEEECCC T ss_conf 79806897388 No 95 >cd01616 TGS The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role. Probab=48.28 E-value=17 Score=16.61 Aligned_cols=22 Identities=23% Similarity=0.391 Sum_probs=18.5 Q ss_pred EEECCEECCCCCEEECCCCEEEE Q ss_conf 69999992406878079997999 Q gi|254780406|r 40 VKVNGILLERAAVNVMSTDHIEV 62 (354) Q Consensus 40 V~Vng~~v~~~~~~v~~~d~v~v 62 (354) .+|||+.+ .+.+.+..+|+|++ T Consensus 37 a~Vng~~~-~l~~~L~~gd~V~I 58 (60) T cd01616 37 ALVNGQLV-DLSYTLQDGDTVSI 58 (60) T ss_pred EEECCEEC-CCCCCCCCCCEEEE T ss_conf 99999996-51669999999999 No 96 >COG4909 PduC Propanediol dehydratase, large subunit [Secondary metabolites biosynthesis, transport, and catabolism] Probab=48.07 E-value=10 Score=17.97 Aligned_cols=57 Identities=16% Similarity=0.186 Sum_probs=37.4 Q ss_pred CCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECCEECC Q ss_conf 98653446667734478899988687789999999869869999992406878079997999998922 Q gi|254780406|r 1 MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68 (354) Q Consensus 1 ~~~~~~~~~~~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg~~i~ 68 (354) |+.|.+-+-...|.++++| +.++|++|.+-..-----.|+.++..+-+|++||++.. T Consensus 1 mrskrfe~lakrpvnqdgf-----------vkewieegfiamespndpkpsiki~ng~v~eldgk~~~ 57 (554) T COG4909 1 MRSKRFEDLAKRPVNQDGF-----------VKEWIEEGFIAMESPNDPKPSIKIKNGRVIELDGKLEH 57 (554) T ss_pred CCHHHHHHHHHCCCCCCCH-----------HHHHHHHCCEECCCCCCCCCCCEECCCEEEEECCCCCC T ss_conf 9234678986287541212-----------66626521002238899999610115728863682312 No 97 >cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl Probab=47.53 E-value=21 Score=16.10 Aligned_cols=49 Identities=16% Similarity=0.241 Sum_probs=39.3 Q ss_pred CCCCCCEEEECCC-CCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHH Q ss_conf 4332320222367-641000123445740477521124556467888740 Q gi|254780406|r 115 DINTEGLLLLTND-GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163 (354) Q Consensus 115 D~~t~GLlllTnd-g~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~ 163 (354) -.+.+|++-+.+- -.|+-+.+.-...+.-.|.+.|.|.+.++....|.. T Consensus 44 S~~F~G~Ial~~P~~SWvarw~ri~~~vpG~YAi~V~G~lp~~i~~~le~ 93 (98) T cd07973 44 SPNFEGIIALMDPEKSWVARWQRIDKFVPGIYAISVSGRLPEDIVEELES 93 (98) T ss_pred CCCCCEEEEEECCCCCHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHH T ss_conf 67723278873685148999864467788758888458699899999998 No 98 >PRK07649 para-aminobenzoate/anthranilate synthase glutamine amidotransferase component II; Validated Probab=43.41 E-value=11 Score=17.88 Aligned_cols=99 Identities=14% Similarity=0.109 Sum_probs=51.2 Q ss_pred EEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHH-HHHHCCCEEEECCCEEEE----ECCCCEEEEEEEEEE Q ss_conf 022236764100012344574047752112455646788874-000008767503430364----026880799999951 Q gi|254780406|r 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLD----TQKGSNAWVTVGLRE 195 (354) Q Consensus 121 LlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~~----~~~~~~~~~~v~l~e 195 (354) +||+-|-..+.+.|.+--.+.-.+..|.-...++.+.+..+. .++.+-.|+-.|...... .....+ .=-+-|.= T Consensus 2 ILlIDn~DsFT~ni~~~l~~~g~~~~v~~~d~~~~~~i~~~~pd~IiLSpGPg~p~~~~~~~~~~~~~~~~-iPILGICl 80 (195) T PRK07649 2 ILMIDNYDSFTYNLVQYLGELGQELVVKRNDEVTISDIENMKPDFLMISPGPCSPNEAGISMEVIRYFAGK-IPIFGVCL 80 (195) T ss_pred EEEEECCCCHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHCCCCEEEECCCCCCHHHCCCCHHHHHHHCCC-CCEEEECH T ss_conf 99995898079999999997899799988996899999841989899889999957847614679975289-97843029 Q ss_pred CCHHHHHHHHHHCCCEEEEEEEEEECCEE Q ss_conf 84289999999839868688975870545 Q gi|254780406|r 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQ 224 (354) Q Consensus 196 Gr~~qIrr~~~~~g~~V~~L~Rv~~G~~~ 224 (354) | ||+ |+.++|-+|.++....+|... T Consensus 81 G--~Q~--ia~~~Gg~v~~~~~~~hG~~~ 105 (195) T PRK07649 81 G--HQS--IAQVFGGEVVRAERLMHGKTS 105 (195) T ss_pred H--HHH--HHHHCCCCEEECCCEEECEEE T ss_conf 9--999--998739728337960764065 No 99 >PRK05670 anthranilate synthase component II; Provisional Probab=42.94 E-value=19 Score=16.41 Aligned_cols=98 Identities=17% Similarity=0.099 Sum_probs=53.6 Q ss_pred EEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHH-HHHHCCCEEEECCCEEE----EECCCCEEEEEEEEEE Q ss_conf 022236764100012344574047752112455646788874-00000876750343036----4026880799999951 Q gi|254780406|r 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTL----DTQKGSNAWVTVGLRE 195 (354) Q Consensus 121 LlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~----~~~~~~~~~~~v~l~e 195 (354) +||+.|-+.+.+.+.+.-.+.--...|.-...++.+.+..+. .|+.+-+|+-.|..... ...-..+ .=-+-|.= T Consensus 2 iLiiD~~dsfT~nI~~~lr~~g~~v~V~~~d~~~~~~i~~~~pdgiiLS~GPg~P~~~~~~~~~i~~~~~~-iPiLGICl 80 (192) T PRK05670 2 ILLIDNYDSFTYNLVQYLGELGAEVVVYRNDEITLEEIEALAPDAIVLSPGPGTPAEAGISLELIREFAGK-VPILGVCL 80 (192) T ss_pred EEEEECCCCHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHCCCCEEEECCCCCCHHHCCCHHHHHHHHCCC-CCEEEEEH T ss_conf 99996898689999999986899699998998999999850989899999999936605549999973469-97899847 Q ss_pred CCHHHHHHHHHHCCCEEEEEEEEEECCE Q ss_conf 8428999999983986868897587054 Q gi|254780406|r 196 GKNREIKKVFEFFNWKVNRLIRISYGPF 223 (354) Q Consensus 196 Gr~~qIrr~~~~~g~~V~~L~Rv~~G~~ 223 (354) | ||+ |+.++|-+|.++....+|.. T Consensus 81 G--~Ql--ia~~~Gg~v~~~~~~~hG~~ 104 (192) T PRK05670 81 G--HQA--IGEAFGGKVVRAKEIMHGKT 104 (192) T ss_pred H--HHH--HHHHCCCEEEECCCCCCCEE T ss_conf 7--899--99871973888886363704 No 100 >PRK02967 nickel responsive regulator; Provisional Probab=42.24 E-value=24 Score=15.74 Aligned_cols=34 Identities=12% Similarity=0.130 Sum_probs=19.9 Q ss_pred EEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEEC Q ss_conf 99999951842899999998398686889758705451 Q gi|254780406|r 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225 (354) Q Consensus 188 ~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l 225 (354) .+++.+..|...+|+.+...+. .++=|++|.++| T Consensus 95 CLEvivv~G~~~~i~~la~~l~----~~kGVk~gkL~~ 128 (138) T PRK02967 95 CLEVAVLKGDMGDVQHFADDVI----AERGVRHGHLQC 128 (138) T ss_pred CEEEEEEECCHHHHHHHHHHHH----CCCCEEEEEEEE T ss_conf 2799999557899999999985----058978879999 No 101 >KOG2529 consensus Probab=39.60 E-value=19 Score=16.35 Aligned_cols=157 Identities=15% Similarity=0.020 Sum_probs=74.1 Q ss_pred EEEECCCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCC Q ss_conf 89602787515631443333644210110234320026655433232022236764100012344574047752112455 Q gi|254780406|r 74 RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153 (354) Q Consensus 74 ~~~~~~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~ 153 (354) -++.++||++- +..+-..-+...+. ....+..|-||-..+|-|+.++|-. +++..-+....++|...+..-. T Consensus 69 gv~~i~kpa~p----ss~e~~swvk~iL~--~ek~Gh~gTlDP~vtg~l~v~~~~~--tr~~~s~~s~gk~yvg~~~lt~ 140 (395) T KOG2529 69 GVINIDKPANP----SSHEVVSWVKNILR--VEKTGHSGTLDPEVTGCLIVCIDRA--TRLLKSQQSAGKEYVGIGKLTP 140 (395) T ss_pred CCEECCCCCCC----CHHHHHHHHHHHHH--HHHHCCCCCCCCCCCCEEEEEEECC--CCCCCCHHCCCCEEEEEEECCC T ss_conf 74633689798----60788888888766--8870799888965232279996000--0242120105867999985475 Q ss_pred CHH---HHHHHHHHHHCCCEEEECCCEE-----E---------EECCCCE--EEEEEEEEECCHHHHHHHHHHCC----- Q ss_conf 646---7888740000087675034303-----6---------4026880--79999995184289999999839----- Q gi|254780406|r 154 DQD---KLNLLKKGIVIQGICYGDMQVT-----L---------DTQKGSN--AWVTVGLREGKNREIKKVFEFFN----- 209 (354) Q Consensus 154 ~~~---~~~~~~~g~~~~~~~~~~~~~~-----~---------~~~~~~~--~~~~v~l~eGr~~qIrr~~~~~g----- 209 (354) ..+ .+.+...-.....+...|.... . +...... -.+.+.+.+|- -+|-||-++| T Consensus 141 ~v~~~~k~~~~~e~l~g~l~~~~pl~~~~kr~~~v~~~y~s~~ie~d~~~~l~~f~~~~~~~t--~~rt~~~~lg~ll~~ 218 (395) T KOG2529 141 EVEDALKLHQKLEHLYGALFQRPPLISAVKRVLRVRTLYESKIIEYDRDYPLLRFGVSCEAGT--YKRTMCVHLGLLLGF 218 (395) T ss_pred CHHHHHHHCCCHHHHHHHHCCCCCHHHHCCCEEEEECHHHHHCCCCCCCCHHCCCCCCCCCCC--HHHHHHHHHHHHHHH T ss_conf 234566641213330043236782333114245740013331001130001003652334554--687777766157662 Q ss_pred -CEEEEEEEEEECCEECCCCCCCCEEECCHHH Q ss_conf -8686889758705451875547488679999 Q gi|254780406|r 210 -WKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240 (354) Q Consensus 210 -~~V~~L~Rv~~G~~~l~~L~~G~~r~l~~~e 240 (354) -+-.-++|++-|...=.++..-..-++..+. T Consensus 219 g~k~~E~~r~r~~~~~E~~~~~t~~d~~~~q~ 250 (395) T KOG2529 219 GGKMQELRRVRSGICSEEDDMLTEHDEQDAQF 250 (395) T ss_pred CCHHHHHHHCCCCCCCCCCCCCCCCCCHHHHH T ss_conf 30135332214555446666542000002566 No 102 >TIGR00601 rad23 UV excision repair protein Rad23; InterPro: IPR004806 All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. Rad23 contains a ubiquitin-like domain that interacts with catalytically active proteasomes and two ubiquitin (Ub)-associated (UBA) sequences that bind Ub. Rad23 interacts with ubiquitinated cellular proteins through the synergistic action of its UBA domains. In humans, Rad23 complexes with the XPC protein.; GO: 0006289 nucleotide-excision repair, 0005634 nucleus. Probab=38.98 E-value=10 Score=17.98 Aligned_cols=33 Identities=12% Similarity=-0.006 Sum_probs=21.3 Q ss_pred HHHHHCC---CEEEEEEEEEECCEECCCCCCCCEEE Q ss_conf 9999839---86868897587054518755474886 Q gi|254780406|r 203 KVFEFFN---WKVNRLIRISYGPFQLGTLLAGSTRE 235 (354) Q Consensus 203 r~~~~~g---~~V~~L~Rv~~G~~~l~~L~~G~~r~ 235 (354) ++=...| |+|.+.|=|-=|.|--++-..++|.- T Consensus 31 KI~~~~gkDa~pv~~qKLIY~GKiL~Dd~t~~Ey~I 66 (453) T TIGR00601 31 KIEQEQGKDAYPVAQQKLIYSGKILSDDKTVSEYKI 66 (453) T ss_pred HHHHHCCCCCCCHHCCEEEECCCCCCCCCCHHHCCC T ss_conf 999760873562002021004533167541544266 No 103 >pfam02597 ThiS ThiS family. ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in E. coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS. MoaD, a protein involved sulphur transfer in molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end. Probab=38.28 E-value=29 Score=15.20 Aligned_cols=44 Identities=18% Similarity=0.308 Sum_probs=30.2 Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCC--CEEECCCCEEEE Q ss_conf 7734478899988687789999999869869999992406--878079997999 Q gi|254780406|r 11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA--AVNVMSTDHIEV 62 (354) Q Consensus 11 ~~~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~~--~~~v~~~d~v~v 62 (354) .++.-+..+|...++ ....=.|-|||++|... .+.+.++|.|.+ T Consensus 18 ~~~~tv~~ll~~l~~--------~~~~v~v~vN~~~v~~~~~~~~L~~gD~v~i 63 (70) T pfam02597 18 PEGATVAELLEALGL--------NPERVAVAVNGEIVPRSQADTPLKDGDEVAI 63 (70) T ss_pred CCCCCHHHHHHHHCC--------CCCCEEEEECCEECCCCCCCCCCCCCCEEEE T ss_conf 999969999998388--------8888899999998678567767799999999 No 104 >PRK06774 para-aminobenzoate synthase component II; Provisional Probab=36.57 E-value=15 Score=17.00 Aligned_cols=100 Identities=15% Similarity=0.106 Sum_probs=56.9 Q ss_pred EEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHH-HHHHCCCEEEECCCEEEE----ECCCCEEEEEEEEEE Q ss_conf 022236764100012344574047752112455646788874-000008767503430364----026880799999951 Q gi|254780406|r 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLD----TQKGSNAWVTVGLRE 195 (354) Q Consensus 121 LlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~~----~~~~~~~~~~v~l~e 195 (354) +||+-|-..+.+.|.|--.+..-+..|.-...++.+.+..+. .++.+..|+-.|...... ...... .=-+-|.= T Consensus 2 ILiiDn~DsFT~nl~~~l~~~g~~v~V~~~d~~~~~~i~~~~p~~ivLSpGPG~P~~~~~~~~~i~~~~~~-iPILGICl 80 (191) T PRK06774 2 LLLIDNYDSFTYNLYQYFCELGTEVMVKRNDELQLTDIEQLAPSHVVISPGPCTPNEAGISLAVIRHFADK-LPILGVCL 80 (191) T ss_pred EEEEECCCCHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHCCCCEEEECCCCCCHHHHCCHHHHHHHHCCC-CCEEEEHH T ss_conf 99996999769999999987799599986998899999853999699999998967907306899974469-97886168 Q ss_pred CCHHHHHHHHHHCCCEEEEEEEEEECCEEC Q ss_conf 842899999998398686889758705451 Q gi|254780406|r 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQL 225 (354) Q Consensus 196 Gr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l 225 (354) | ||+ |+.++|-+|.++....+|.... T Consensus 81 G--~Q~--ia~~~Gg~v~~~~~~~hG~~~~ 106 (191) T PRK06774 81 G--HQA--LGQAFGARVVRARQVMHGKTSA 106 (191) T ss_pred H--HHH--HHHHCCCEEEECCCCEECEEEE T ss_conf 7--999--8656098492899747570368 No 105 >COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism] Probab=36.43 E-value=31 Score=15.02 Aligned_cols=42 Identities=31% Similarity=0.437 Sum_probs=27.3 Q ss_pred CHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCC---CCEEECCCCEEEE Q ss_conf 3447889998868778999999986986999999240---6878079997999 Q gi|254780406|r 13 PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER---AAVNVMSTDHIEV 62 (354) Q Consensus 13 ~~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~---~~~~v~~~d~v~v 62 (354) +..+.-+|++.|+-.+.- -|.|||++|-. ..+.++.+|.|+| T Consensus 17 ~~tv~dLL~~l~~~~~~v--------av~vNg~iVpr~~~~~~~l~~gD~iev 61 (68) T COG2104 17 GTTVADLLAQLGLNPEGV--------AVAVNGEIVPRSQWADTILKEGDRIEV 61 (68) T ss_pred CCCHHHHHHHHCCCCCEE--------EEEECCEECCCHHHHHCCCCCCCEEEE T ss_conf 873999999729998559--------999889982504632013158998999 No 106 >PRK04460 nickel responsive regulator; Provisional Probab=33.55 E-value=34 Score=14.73 Aligned_cols=20 Identities=25% Similarity=0.506 Sum_probs=15.2 Q ss_pred HHHHHHHHHCCCCCHHHHHH Q ss_conf 44788999886877899999 Q gi|254780406|r 14 QRVSKVIARAGIASRREVER 33 (354) Q Consensus 14 ~RL~K~la~~g~~SRr~a~~ 33 (354) .+|++++...|+-||++|-+ T Consensus 17 ~~lD~~i~~~Gy~nRSeaIR 36 (139) T PRK04460 17 EKFDRLIEEKGYQNRSEAIR 36 (139) T ss_pred HHHHHHHHHCCCCCHHHHHH T ss_conf 99999999809987889999 No 107 >PRK00630 nickel responsive regulator; Provisional Probab=32.65 E-value=35 Score=14.64 Aligned_cols=24 Identities=29% Similarity=0.526 Sum_probs=15.4 Q ss_pred HHHHHHHHHCCCCCHHHHHH-HHHC Q ss_conf 44788999886877899999-9986 Q gi|254780406|r 14 QRVSKVIARAGIASRREVER-MIAQ 37 (354) Q Consensus 14 ~RL~K~la~~g~~SRr~a~~-lI~~ 37 (354) +.+++++...|+.||++|-+ +|+. T Consensus 20 ~~~D~~i~~~Gy~nRSEaIRdliR~ 44 (143) T PRK00630 20 DELDNRIIKNGYSSRSELVRDLIRE 44 (143) T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 9999999981999788999999999 No 108 >PRK06065 acetyl-CoA acetyltransferase; Provisional Probab=30.71 E-value=31 Score=14.99 Aligned_cols=16 Identities=13% Similarity=0.530 Sum_probs=7.5 Q ss_pred HHHHHHHCCCCCHHHHH Q ss_conf 78899988687789999 Q gi|254780406|r 16 VSKVIARAGIASRREVE 32 (354) Q Consensus 16 L~K~la~~g~~SRr~a~ 32 (354) +.+-|.++|+ +.+++| T Consensus 38 ~~~Al~DAGl-~~~dID 53 (393) T PRK06065 38 ARQALDEAGL-ELKDID 53 (393) T ss_pred HHHHHHHCCC-CHHHCC T ss_conf 9999998499-989989 No 109 >PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional Probab=30.06 E-value=39 Score=14.37 Aligned_cols=60 Identities=15% Similarity=0.309 Sum_probs=30.3 Q ss_pred CCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEEEEEEECCEECC-CCC-CCCEEECCHHHHHHHHH Q ss_conf 68807999999518428999999983986868897587054518-755-47488679999987532 Q gi|254780406|r 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL-AGSTREVSKKILREQLG 246 (354) Q Consensus 183 ~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L~Rv~~G~~~l~-~L~-~G~~r~l~~~e~~~l~~ 246 (354) ..+..|+.++.+.--...||++|......-. +..|.--|. .|. .+....+..+.+..++. T Consensus 452 ~Ps~~WL~fV~T~kARskIr~~lk~~~r~~~----i~~Gk~lL~~~l~~~~~l~~~~~~~l~~~~~ 513 (702) T PRK11092 452 RPNAAWLNFVVSSKARAKIRQLLKNLKRDDS----VSLGRRLLNHALGGSRKLDEIPQENIQRELD 513 (702) T ss_pred CCCHHHHHHHHCHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH T ss_conf 9897899763267889999999987558999----9999999999986256612289899999999 No 110 >TIGR01687 moaD_arch MoaD family protein; InterPro: IPR010038 Members of this family appear to be archaeal and bacterial (proteobacteria and Thermus) versions of MoaD, subunit 1 of molybdopterin converting factor.. Probab=30.05 E-value=37 Score=14.51 Aligned_cols=26 Identities=15% Similarity=0.226 Sum_probs=20.1 Q ss_pred CCCEEECCE-ECCC---CCEEECCCCEEEE Q ss_conf 698699999-9240---6878079997999 Q gi|254780406|r 37 QQRVKVNGI-LLER---AAVNVMSTDHIEV 62 (354) Q Consensus 37 ~G~V~Vng~-~v~~---~~~~v~~~d~v~v 62 (354) .=.|.|||+ =|.. +.++++.+|.|.+ T Consensus 57 ~v~ilvNGran~~~l~GL~~~LkdGD~vai 86 (93) T TIGR01687 57 NVIILVNGRANVDWLEGLETELKDGDVVAI 86 (93) T ss_pred EEEEEECCCCCCCCCCCCCCCCCCCCEEEE T ss_conf 578985164143220365752327875675 No 111 >TIGR01278 DPOR_BchB light-independent protochlorophyllide reductase, B subunit; InterPro: IPR005969 Synonym: dark protochlorophyllide reductase Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite .; GO: 0016730 oxidoreductase activity acting on iron-sulfur proteins as donors, 0015995 chlorophyll biosynthetic process, 0019685 photosynthesis dark reaction. Probab=29.85 E-value=38 Score=14.43 Aligned_cols=40 Identities=18% Similarity=0.136 Sum_probs=23.4 Q ss_pred EEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEEE Q ss_conf 750343036402688079999995184289999999839868688 Q gi|254780406|r 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215 (354) Q Consensus 171 ~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~L 215 (354) .+.+..|-+++- +.|.+-.. --..+||||++.||.+|+-. T Consensus 160 ~T~~psVNllGp----~~LGFH~r-~D~~elrrlL~~LG~evN~v 199 (562) T TIGR01278 160 TTEKPSVNLLGP----ASLGFHHR-HDLIELRRLLKTLGIEVNVV 199 (562) T ss_pred CCCCCEEEECCC----CCCCCCCH-HHHHHHHHHHHHCCEEEEEE T ss_conf 889623761141----13342321-03389999996589479897 No 112 >pfam05597 Phasin Poly(hydroxyalcanoate) granule associated protein (phasin). Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon. Probab=28.73 E-value=41 Score=14.22 Aligned_cols=24 Identities=46% Similarity=0.729 Sum_probs=21.4 Q ss_pred CHHHHHHHHHCCCCCHHHHHHHHH Q ss_conf 344788999886877899999998 Q gi|254780406|r 13 PQRVSKVIARAGIASRREVERMIA 36 (354) Q Consensus 13 ~~RL~K~la~~g~~SRr~a~~lI~ 36 (354) .+|++++|...|+-|+++++.|.+ T Consensus 93 e~rV~~aL~rLGips~~di~~L~~ 116 (132) T pfam05597 93 DERVAKALNRLGVPSRKEVEALSA 116 (132) T ss_pred HHHHHHHHHHCCCCCHHHHHHHHH T ss_conf 999999998569998999999999 No 113 >cd00986 PDZ_LON_protease PDZ domain of ATP-dependent LON serine proteases. Most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this bacterial subfamily of protease-associated PDZ domains a C-terminal beta-strand is thought to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins. Probab=27.72 E-value=40 Score=14.28 Aligned_cols=17 Identities=47% Similarity=0.862 Sum_probs=9.5 Q ss_pred ECCCCE-EEECCEECCCC Q ss_conf 079997-99999892255 Q gi|254780406|r 54 VMSTDH-IEVDGVPLRKA 70 (354) Q Consensus 54 v~~~d~-v~vdg~~i~~~ 70 (354) +..+|. +.|||+++.-. T Consensus 25 Lk~GDvI~~vdGk~v~~~ 42 (79) T cd00986 25 LKAGDHIIAVDGKPFKEA 42 (79) T ss_pred CCCCCEEEEECCEECCCH T ss_conf 778999999999895799 No 114 >KOG3449 consensus Probab=27.15 E-value=44 Score=14.05 Aligned_cols=17 Identities=24% Similarity=0.432 Sum_probs=11.9 Q ss_pred CHHHHHHHHHHCCCEEE Q ss_conf 42899999998398686 Q gi|254780406|r 197 KNREIKKVFEFFNWKVN 213 (354) Q Consensus 197 r~~qIrr~~~~~g~~V~ 213 (354) .+.-|+.+|+++|.++- T Consensus 19 sa~DikkIl~sVG~E~d 35 (112) T KOG3449 19 SASDIKKILESVGAEID 35 (112) T ss_pred CHHHHHHHHHHHCCCCC T ss_conf 78899999987173347 No 115 >PRK10872 relA GDP/GTP pyrophosphokinase; Provisional Probab=26.51 E-value=45 Score=13.97 Aligned_cols=20 Identities=25% Similarity=0.252 Sum_probs=14.5 Q ss_pred CCCEEEEECCCCCEEEECCC Q ss_conf 56438960278751563144 Q gi|254780406|r 70 AERTRLWLYHKPIGLVTTHS 89 (354) Q Consensus 70 ~~~~~~~~~~KP~g~~~~~~ 89 (354) .....||...||.||-+=++ T Consensus 305 ~rfkDYIa~PK~NgYQSLHT 324 (743) T PRK10872 305 DEFDDYVANPKPNGYQSIHT 324 (743) T ss_pred CHHHHHCCCCCCCCCEEEEE T ss_conf 24665421789888306889 No 116 >pfam11685 DUF3281 Protein of unknown function (DUF3281). This family of bacterial proteins has no known function. Probab=26.01 E-value=46 Score=13.93 Aligned_cols=12 Identities=33% Similarity=0.490 Sum_probs=4.8 Q ss_pred CCCCCCCCCCCE Q ss_conf 266554332320 Q gi|254780406|r 110 SVGRLDINTEGL 121 (354) Q Consensus 110 ~vgRLD~~t~GL 121 (354) ++|.=-.-.+|. T Consensus 119 ~~GsNtIsVSGt 130 (269) T pfam11685 119 PVGSNTISVSGT 130 (269) T ss_pred CCCCCEEEEEEE T ss_conf 567736887678 No 117 >PRK06059 lipid-transfer protein; Provisional Probab=25.25 E-value=44 Score=14.06 Aligned_cols=18 Identities=28% Similarity=0.484 Sum_probs=10.6 Q ss_pred HHHHHHHCCCCCHHHHHHH Q ss_conf 7889998868778999999 Q gi|254780406|r 16 VSKVIARAGIASRREVERM 34 (354) Q Consensus 16 L~K~la~~g~~SRr~a~~l 34 (354) +.+-|.++|+ ++.+++-+ T Consensus 31 ~~~AL~DAGl-~~~dVD~v 48 (399) T PRK06059 31 ARAALADAGL-DWRQVQLV 48 (399) T ss_pred HHHHHHHCCC-CHHHCCEE T ss_conf 9999985599-98994688 No 118 >PRK06488 sulfur carrier protein ThiS; Validated Probab=25.25 E-value=48 Score=13.83 Aligned_cols=41 Identities=24% Similarity=0.339 Sum_probs=25.5 Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCC---CCEEECCCCEEEE Q ss_conf 447889998868778999999986986999999240---6878079997999 Q gi|254780406|r 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLER---AAVNVMSTDHIEV 62 (354) Q Consensus 14 ~RL~K~la~~g~~SRr~a~~lI~~G~V~Vng~~v~~---~~~~v~~~d~v~v 62 (354) .-|+-.|+..|+..++-| |-|||++|-. ..+.+.++|.|+| T Consensus 15 ~tl~~Ll~elg~~~~~vA--------vAvN~~~Vpr~~~~~~~L~eGDriEI 58 (65) T PRK06488 15 TTLALLLAELGYEGNWLA--------TAVNGELVHSEARAQFVLHEGDRIEI 58 (65) T ss_pred HHHHHHHHHCCCCCCCEE--------EEECCEEECHHHHCCCCCCCCCEEEE T ss_conf 689999997298888089--------99899987424505451799999999 No 119 >CHL00101 trpG anthranilate synthase component 2 Probab=25.20 E-value=36 Score=14.59 Aligned_cols=99 Identities=14% Similarity=0.086 Sum_probs=51.4 Q ss_pred EEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHH-HHHHCCCEEEECCCEEEEE----CCCCEEEEEEEEEEC Q ss_conf 22236764100012344574047752112455646788874-0000087675034303640----268807999999518 Q gi|254780406|r 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDT----QKGSNAWVTVGLREG 196 (354) Q Consensus 122 lllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~~~----~~~~~~~~~v~l~eG 196 (354) ||+-|-..+.+.|.+.-.+..-...|.-...++.+.+..+. +|+.+-+|+-.|....... .-... .=-+-|.=| T Consensus 3 LiiD~~dsft~~i~r~lrelg~~~~v~~~d~~~~~~i~~~~p~gIILS~GPg~p~~~~~~~~~~~~~~~~-iPILGIClG 81 (190) T CHL00101 3 LIIDNYDSFTYNLVQSLGELNSDLLVCRNDEIDLSKIKNLNPRHIIISPGPGHPRDSGISLDVISSYAPT-IPILGVCLG 81 (190) T ss_pred EEEECCCHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHCCCCEEEECCCCCCHHHCCCCHHHHHHHHCC-CCEEEECHH T ss_conf 9997888089999999986899899986998999999707979899979999957857616899997149-987897398 Q ss_pred CHHHHHHHHHHCCCEEEEEEEEEECCEEC Q ss_conf 42899999998398686889758705451 Q gi|254780406|r 197 KNREIKKVFEFFNWKVNRLIRISYGPFQL 225 (354) Q Consensus 197 r~~qIrr~~~~~g~~V~~L~Rv~~G~~~l 225 (354) ||+ |..++|-+|.++....+|...+ T Consensus 82 --~Q~--ia~~~Gg~v~~~~~~~~G~~~~ 106 (190) T CHL00101 82 --HQS--IGYVYGGKIIKASKPMHGKTSL 106 (190) T ss_pred --HHH--HHHHCCCEEEECCCEEECCEEE T ss_conf --899--9887586499788204362479 No 120 >KOG2582 consensus Probab=25.02 E-value=26 Score=15.44 Aligned_cols=20 Identities=20% Similarity=0.142 Sum_probs=9.2 Q ss_pred EEECCCCCEEEECCCCCCCC Q ss_conf 96027875156314433336 Q gi|254780406|r 75 LWLYHKPIGLVTTHSDPDGR 94 (354) Q Consensus 75 ~~~~~KP~g~~~~~~~~~~~ 94 (354) ++.|--=.|++|.......+ T Consensus 182 fL~Y~yYgg~iciglk~fe~ 201 (422) T KOG2582 182 FLLYLYYGGMICIGLKRFER 201 (422) T ss_pred HHHHHHHCCEEEECCCCHHH T ss_conf 99999732144321263888 No 121 >PRK01002 nickel responsive regulator; Provisional Probab=24.79 E-value=49 Score=13.78 Aligned_cols=20 Identities=35% Similarity=0.494 Sum_probs=15.5 Q ss_pred HHHHHHHHHCCCCCHHHHHH Q ss_conf 44788999886877899999 Q gi|254780406|r 14 QRVSKVIARAGIASRREVER 33 (354) Q Consensus 14 ~RL~K~la~~g~~SRr~a~~ 33 (354) ..|++++...|+-||++|-+ T Consensus 17 ~~lD~~i~~~Gy~nRSeaIR 36 (141) T PRK01002 17 AEFDEIIEERGYASRSEAIR 36 (141) T ss_pred HHHHHHHHHCCCCCHHHHHH T ss_conf 99999999809987889999 No 122 >PRK07855 lipid-transfer protein; Provisional Probab=24.36 E-value=48 Score=13.79 Aligned_cols=14 Identities=0% Similarity=0.003 Sum_probs=7.4 Q ss_pred HHHHHHHCCCEEEE Q ss_conf 99999983986868 Q gi|254780406|r 201 IKKVFEFFNWKVNR 214 (354) Q Consensus 201 Irr~~~~~g~~V~~ 214 (354) .++.|+..|....+ T Consensus 272 a~~ay~~AGi~p~D 285 (386) T PRK07855 272 ARQLWRQSGLGPAD 285 (386) T ss_pred HHHHHHHCCCCHHH T ss_conf 99999984999788 No 123 >PRK08313 acetyl-CoA acetyltransferase; Provisional Probab=23.18 E-value=48 Score=13.83 Aligned_cols=17 Identities=18% Similarity=0.540 Sum_probs=7.1 Q ss_pred HHHHHHCCCCCHHHHHHH Q ss_conf 889998868778999999 Q gi|254780406|r 17 SKVIARAGIASRREVERM 34 (354) Q Consensus 17 ~K~la~~g~~SRr~a~~l 34 (354) ..=|+++|+ +.+++|.+ T Consensus 34 ~~Al~DAGl-~~~dID~~ 50 (391) T PRK08313 34 DRALADAGL-TFDDIDAV 50 (391) T ss_pred HHHHHHCCC-CHHHCCEE T ss_conf 999997499-98998999 No 124 >PTZ00246 proteasome subunit alpha; Provisional Probab=22.64 E-value=53 Score=13.51 Aligned_cols=95 Identities=17% Similarity=0.126 Sum_probs=58.6 Q ss_pred CCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCCCEEEE Q ss_conf 23445740477521124556467888740000087675034303640268807999999518428999999983986868 Q gi|254780406|r 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214 (354) Q Consensus 135 ~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g~~V~~ 214 (354) +.| ......|....-|.=.......|.+... . .+++.|....-|+-+.+.+...+.. T Consensus 150 ~DP-sG~~~~~ka~AiG~gs~~a~~~LEk~y~-------~---------------~ms~eeai~lAi~aL~~~~~~~~~~ 206 (253) T PTZ00246 150 TDP-SGNYSGWKATAIGTNNQTAQSILKQEWK-------E---------------DMTLEQGLLLALKVLTKSMDSTTPK 206 (253) T ss_pred ECC-CCCEEEEEEEEECCCHHHHHHHHHHHCC-------C---------------CCCHHHHHHHHHHHHHHHHHCCCCC T ss_conf 879-8878545799989880899999987466-------9---------------9999999999999999998564798 Q ss_pred EEEEEECCEECCC-CCCCCEEECCHHHHHHHHHHHHHHC Q ss_conf 8975870545187-5547488679999987532100000 Q gi|254780406|r 215 LIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEE 252 (354) Q Consensus 215 L~Rv~~G~~~l~~-L~~G~~r~l~~~e~~~l~~~~~~~~ 252 (354) -.-|.++=++..+ --...+|-|+++||++++.....+. T Consensus 207 ~~~iEvavvt~~~~~~~~~~r~L~~~EI~~~l~~~~~~~ 245 (253) T PTZ00246 207 ADKIEVGYLSKGNGDGEPFQKMLSEKEIAELLKKYTQEY 245 (253) T ss_pred CCCEEEEEEECCCCCCCCCEEECCHHHHHHHHHHHHHHH T ss_conf 883899999826888874158789999999999999887 No 125 >TIGR02542 B_forsyth_147 Bacteroides forsythus 147-residue repeat. Probab=22.52 E-value=37 Score=14.53 Aligned_cols=101 Identities=18% Similarity=0.130 Sum_probs=62.9 Q ss_pred CCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCCCEE-EECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHH Q ss_conf 64100012344574047752112455646788874000008767-50343036402688079999995184289999999 Q gi|254780406|r 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206 (354) Q Consensus 128 g~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~~~~~~g~~~~~~~-~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~ 206 (354) |+..+-++--.+-+...|+..+.|-+..-+ .+||.+..+. .....|.+.+.-+.+ -+.+.-.+=-+.+.|.||. T Consensus 26 GKI~svI~~t~~p~~~~~l~~~~G~lE~~D----g~gi~IGs~~g~~~~sV~i~~TPsGN-~v~F~PYTlTy~~~r~~F~ 100 (154) T TIGR02542 26 GKIQSVITVTQYPMDNDALLRVRGTLEQVD----GNGIRIGSGQGITAASVRIKGTPSGN-NVIFPPYTLTYNELREIFR 100 (154) T ss_pred CCEEEEEEEECCCCCCCCEEEEEEEEEEEC----CCEEEECCCCCCCCCCEEEEECCCCC-CCCCCCCCCCHHHHHHHHC T ss_conf 825789987315535541024542477025----87468717888512513770068988-5321883013567776631 Q ss_pred HCCCEEEEEEEEEECCEECCCCCCCCEEEC Q ss_conf 839868688975870545187554748867 Q gi|254780406|r 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREV 236 (354) Q Consensus 207 ~~g~~V~~L~Rv~~G~~~l~~L~~G~~r~l 236 (354) .--+.-..+-|-.+ .-++||.|.||-= T Consensus 101 E~~~~YQGITReQV---~rdGLP~G~YR~C 127 (154) T TIGR02542 101 EPTMVYQGITREQV---LRDGLPEGSYRLC 127 (154) T ss_pred CCCEEECCCCHHHH---HHCCCCCCCEEEE T ss_conf 67602237236887---5258999974576 No 126 >cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. Probab=22.47 E-value=53 Score=13.53 Aligned_cols=34 Identities=12% Similarity=0.093 Sum_probs=28.0 Q ss_pred HHHHHHCCCEEECCEECCCCCEEECCCCEEEECC Q ss_conf 9999986986999999240687807999799999 Q gi|254780406|r 31 VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64 (354) Q Consensus 31 a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg 64 (354) --.+|++|.=+|-+.+...--.++.++|.|.+.. T Consensus 9 ~F~~Ik~G~KtIE~Rl~d~kr~~ik~GD~I~F~~ 42 (109) T cd06555 9 PFELIKSGKKTIEIRLNDEKRQQIKVGDKILFND 42 (109) T ss_pred HHHHHHCCCCEEEEECCCHHHHHCCCCCEEEEEE T ss_conf 5899876997799982706787189999999998 No 127 >TIGR01670 YrbI-phosphatas 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family; InterPro: IPR010023 This entry is a part of the haloacid dehalogenase (HAD) superfamily of hydrolases from beta, gamma and epsilon proteobacteria, Aquifex, Fusobacterium, Porphyromonas and Methanosarcina. All characterised members of the HAD-superfamily hydrolase, subfamily IIIA and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs , all of which are found conserved in this family. Lipopolysaccharides of Gram-negative bacteria consist of a heteropolysaccharide component (O-antigen) and a hydrophobic component (lipid A). Linking the two portions is 3-Deoxy-D-manno-octulosonate (KDO), an 8-carbon sugar. Biosynthesis of KDO linked to lipid A proceeds via five steps, one of which involves removal of a phosphate from KDO 8-P via the action of KDO 8-P phosphatase (3.1.3.45 from EC; IPR008230 from INTERPRO) . One member of this family, the YrbI protein from Haemophilus influenzae has been cloned, expressed, purified and found to be an active phosphatase. Furthermore, its crystal structure has been determined . The sequence from Methanosarcina acetivorans, Q8TJL6 from SWISSPROT, is distinctive in that it is linked to an N-terminal cytidylyltransferase domain (IPR003329 from INTERPRO) and is annotated as acylneuraminate cytidylyltransferase. This may give some clue as the function of these phosphatases. Several eukaryotic sequences are also closely related to this family; one such sequence is the CMP-N-acetylneuraminic acid synthetase from mouse, but in this case as in the others the phosphatase domain is clearly inactive as many of the active site residues are not conserved.; GO: 0019143 3-deoxy-manno-octulosonate-8-phosphatase activity, 0009103 lipopolysaccharide biosynthetic process. Probab=21.16 E-value=44 Score=14.07 Aligned_cols=18 Identities=22% Similarity=0.410 Sum_probs=14.5 Q ss_pred CCCCEEEECCCCCCCCCC Q ss_conf 323202223676410001 Q gi|254780406|r 117 NTEGLLLLTNDGGLARVL 134 (354) Q Consensus 117 ~t~GLlllTndg~l~~~l 134 (354) -|.|++.+|++||....+ T Consensus 12 LtDGkiyyt~nGE~iK~F 29 (154) T TIGR01670 12 LTDGKIYYTENGEEIKAF 29 (154) T ss_pred EECCEEEECCCCCEEEEE T ss_conf 106706663888443120 No 128 >pfam10574 UPF0552 Uncharacterized protein family UPF0552. This family of proteins has no known function. Probab=21.00 E-value=58 Score=13.30 Aligned_cols=95 Identities=16% Similarity=0.283 Sum_probs=44.5 Q ss_pred EECCCCCHHHHHHHHHHHHCCCEEEECCCEEEEECCCC-EEEEEEEEEECCHHHHHHHHHHCCCEE----EEEEEEEECC Q ss_conf 11245564678887400000876750343036402688-079999995184289999999839868----6889758705 Q gi|254780406|r 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NAWVTVGLREGKNREIKKVFEFFNWKV----NRLIRISYGP 222 (354) Q Consensus 148 ~v~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~-~~~~~v~l~eGr~~qIrr~~~~~g~~V----~~L~Rv~~G~ 222 (354) +..+..+++.. +-..|+.+++....+....+....+. .-++-+.|. -.+-+||-|.+-|++| ++-..|.-|- T Consensus 19 ~~~g~w~P~~~-q~G~GvilEG~l~d~srH~itd~~~~k~Ry~vl~i~--~s~~hrR~Fd~~G~EiepnfS~t~kVntG~ 95 (224) T pfam10574 19 KFSGTWDPEVF-QSGDGVLLEGTLLDVSRHTITDQKNQKERYYVLYIR--PSRIHRRKFDSKGNEIEPNFSDTKKVNTGF 95 (224) T ss_pred CCCCCCCHHHH-CCCCEEEEEEEEEEEEEEEEECCCCCCEEEEEEEEE--CCHHHHHHCCCCCCCCCCCCCCCEEEEEEE T ss_conf 05775074571-478648998798532467886278981579999982--145545322787768798755221542312 Q ss_pred EECC-CC-CCCCEEECCHHHHHHHH Q ss_conf 4518-75-54748867999998753 Q gi|254780406|r 223 FQLG-TL-LAGSTREVSKKILREQL 245 (354) Q Consensus 223 ~~l~-~L-~~G~~r~l~~~e~~~l~ 245 (354) |.-. .. +.|+.-.|++.+|..|+ T Consensus 96 L~SsykVEAkG~tDrls~~~L~~lV 120 (224) T pfam10574 96 LMSSYKVEAKGESDRLSEDQLSVLV 120 (224) T ss_pred EECEEEEEECCCCCCCCHHHHHHHH T ss_conf 3000177742753434899999774 No 129 >KOG2553 consensus Probab=20.98 E-value=58 Score=13.30 Aligned_cols=25 Identities=12% Similarity=0.242 Sum_probs=18.3 Q ss_pred CCEEEEEEEEEECC--HHHHHHHHHHC Q ss_conf 88079999995184--28999999983 Q gi|254780406|r 184 GSNAWVTVGLREGK--NREIKKVFEFF 208 (354) Q Consensus 184 ~~~~~~~v~l~eGr--~~qIrr~~~~~ 208 (354) ...-|+.|.|+.-. .||||+|...+ T Consensus 262 ~~~e~V~i~i~GQSFMLHQIRKMVgla 288 (416) T KOG2553 262 EGVEFVKIKIHGQSFMLHQIRKMVGLA 288 (416) T ss_pred CCCEEEEEEEECCHHHHHHHHHHHHHH T ss_conf 782399999976105999999999999 No 130 >KOG0151 consensus Probab=20.93 E-value=58 Score=13.30 Aligned_cols=24 Identities=17% Similarity=0.158 Sum_probs=13.4 Q ss_pred CCEECC--CCCCCCEEECCHH-HHHHH Q ss_conf 054518--7554748867999-99875 Q gi|254780406|r 221 GPFQLG--TLLAGSTREVSKK-ILREQ 244 (354) Q Consensus 221 G~~~l~--~L~~G~~r~l~~~-e~~~l 244 (354) |-|.-+ +|.+|....+++. +.+.+ T Consensus 719 d~l~sg~~~lk~~~sv~~qpe~~~d~~ 745 (877) T KOG0151 719 DELESGERDLKPGSSVREQPENERDRL 745 (877) T ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHH T ss_conf 555778755788976014804677799 No 131 >pfam12471 GTP_CH_N GTP cyclohydrolase N terminal. This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. This family is the N terminal of GTP cyclohydrolase, the rate limiting enzyme in the synthesis of tetrahydrobiopterin. Probab=20.54 E-value=57 Score=13.34 Aligned_cols=15 Identities=13% Similarity=0.162 Sum_probs=5.5 Q ss_pred HHHHHHHHHHHCCCE Q ss_conf 678887400000876 Q gi|254780406|r 156 DKLNLLKKGIVIQGI 170 (354) Q Consensus 156 ~~~~~~~~g~~~~~~ 170 (354) |..+.+..|-..-|| T Consensus 137 Ei~eAv~~GrL~~DG 151 (195) T pfam12471 137 ELREAVAKGRLVPDG 151 (195) T ss_pred HHHHHHHCCCCCCCC T ss_conf 799999849988887 No 132 >PRK06365 acetyl-CoA acetyltransferase; Provisional Probab=20.41 E-value=59 Score=13.23 Aligned_cols=17 Identities=12% Similarity=0.372 Sum_probs=8.9 Q ss_pred HHHHHHHHCCCCCHHHHH Q ss_conf 478899988687789999 Q gi|254780406|r 15 RVSKVIARAGIASRREVE 32 (354) Q Consensus 15 RL~K~la~~g~~SRr~a~ 32 (354) =+.+=|.++|+ +.+++| T Consensus 30 A~~~AL~DAGl-~~~dID 46 (415) T PRK06365 30 AFDYAMNDAGL-TLADID 46 (415) T ss_pred HHHHHHHHCCC-CHHHCC T ss_conf 99999997599-989969 Done!