Query gi|254780608|ref|YP_003065021.1| ribosomal large subunit pseudouridine synthase C [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 346
No_of_seqs 165 out of 5456
Neff 7.1
Searched_HMMs 39220
Date Sun May 29 21:40:37 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780608.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11025 23S rRNA pseudouridyl 100.0 0 0 585.7 21.1 308 4-323 5-314 (317)
2 PRK11180 rluD 23S rRNA pseudou 100.0 0 0 571.9 19.7 298 9-328 8-318 (325)
3 TIGR00005 rluA_subfam pseudour 100.0 0 0 564.6 16.8 297 14-322 1-336 (337)
4 COG0564 RluA Pseudouridylate s 100.0 0 0 526.5 19.1 285 8-313 2-289 (289)
5 PRK11112 tRNA pseudouridine sy 100.0 0 0 461.4 13.0 232 99-334 2-246 (257)
6 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 0 0 445.4 14.4 239 46-312 4-245 (246)
7 PRK10158 23S rRNA/tRNA pseudou 100.0 0 0 415.6 11.9 208 95-312 10-218 (219)
8 cd02563 PseudoU_synth_TruC tRN 100.0 0 0 409.4 11.3 210 99-312 1-223 (223)
9 cd02557 PseudoU_synth_ScRIB2 P 100.0 0 0 388.0 9.2 195 97-313 14-210 (213)
10 KOG1919 consensus 100.0 0 0 323.2 17.1 296 11-327 36-357 (371)
11 cd02869 PseudoU_synth_RluCD_li 100.0 0 0 325.0 8.8 182 108-297 1-185 (185)
12 TIGR01621 RluA-like pseudourid 100.0 0 0 309.5 6.3 198 99-313 2-199 (222)
13 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 2.1E-38 5.3E-43 262.2 6.4 151 108-272 1-152 (154)
14 pfam00849 PseudoU_synth_2 RNA 100.0 3.2E-38 8.2E-43 261.0 5.9 149 108-261 1-151 (151)
15 cd02870 PseudoU_synth_RsuA_lik 100.0 9.7E-32 2.5E-36 220.2 7.1 142 108-271 1-143 (146)
16 COG1187 RsuA 16S rRNA uridine- 99.9 4.7E-25 1.2E-29 178.0 13.5 208 17-272 1-213 (248)
17 PRK10475 23S rRNA pseudouridin 99.9 8.4E-25 2.1E-29 176.4 12.7 201 16-270 4-204 (290)
18 PRK10700 23S rRNA pseudouridyl 99.9 5.6E-24 1.4E-28 171.3 12.3 208 18-271 2-212 (291)
19 PRK10839 16S rRNA pseudouridyl 99.9 9.6E-24 2.4E-28 169.8 12.0 201 19-271 1-202 (231)
20 cd02566 PseudoU_synth_RluE Pse 99.8 2E-19 5E-24 142.6 6.8 153 108-272 1-158 (168)
21 PRK11394 23S rRNA pseudouridin 99.6 1E-15 2.6E-20 119.2 7.0 153 107-271 30-186 (207)
22 cd02553 PseudoU_synth_RsuA Pse 99.6 1.5E-15 3.8E-20 118.2 6.9 140 108-271 2-142 (167)
23 TIGR00093 TIGR00093 conserved 99.6 1.1E-15 2.7E-20 119.1 5.9 155 112-272 1-160 (185)
24 cd02556 PseudoU_synth_RluB Pse 99.6 4.7E-15 1.2E-19 115.0 8.1 143 108-271 2-145 (167)
25 cd02555 PSSA_1 PSSA_1: Pseudou 99.5 1.9E-14 4.8E-19 111.2 6.8 142 108-271 6-152 (177)
26 cd02554 PseudoU_synth_RluF Pse 99.5 1E-13 2.6E-18 106.6 6.8 137 108-271 2-138 (164)
27 cd00165 S4 S4/Hsp/ tRNA synthe 99.0 2.4E-09 6.1E-14 79.0 8.1 69 19-112 1-70 (70)
28 smart00363 S4 S4 RNA-binding d 98.5 2.9E-07 7.4E-12 65.9 6.1 51 19-69 1-52 (60)
29 pfam01479 S4 S4 domain. The S4 98.4 3.6E-07 9.1E-12 65.3 4.7 47 19-65 1-48 (48)
30 COG1188 Ribosome-associated he 98.3 1.1E-06 2.9E-11 62.2 4.9 55 16-71 6-61 (100)
31 PRK10348 ribosome-associated h 98.3 1.1E-06 2.8E-11 62.3 4.6 55 14-69 4-59 (133)
32 TIGR03069 PS_II_S4 photosystem 98.1 5.6E-06 1.4E-10 57.7 5.9 54 16-70 181-235 (257)
33 COG2302 Uncharacterized conser 97.9 1.8E-05 4.6E-10 54.6 5.4 54 15-69 177-231 (257)
34 TIGR01017 rpsD_bact ribosomal 97.8 1.3E-05 3.3E-10 55.5 2.9 51 19-70 100-152 (217)
35 PRK12565 30S ribosomal protein 97.6 8.2E-05 2.1E-09 50.4 4.8 52 19-70 88-140 (197)
36 CHL00113 rps4 ribosomal protei 97.6 5.9E-05 1.5E-09 51.3 3.1 52 19-70 89-141 (201)
37 COG1189 Predicted rRNA methyla 97.5 0.00028 7.1E-09 47.1 5.5 51 18-68 2-53 (245)
38 COG0522 RpsD Ribosomal protein 97.4 0.00026 6.7E-09 47.2 5.1 51 19-69 94-145 (205)
39 PRK05327 rpsD 30S ribosomal pr 97.3 0.00024 6E-09 47.5 3.4 52 19-70 92-144 (201)
40 TIGR00478 tly hemolysin A; Int 97.1 0.00057 1.4E-08 45.1 4.2 51 20-70 1-52 (240)
41 cd02868 PseudoU_synth_hTruB2_l 96.8 0.00036 9.2E-09 46.4 0.7 75 107-190 1-79 (226)
42 PRK00989 truB tRNA pseudouridi 96.4 0.0022 5.7E-08 41.4 2.7 71 106-188 9-79 (235)
43 cd00506 PseudoU_synth_TruB_lik 96.4 0.002 5.2E-08 41.6 2.5 69 107-188 1-69 (210)
44 cd01291 PseudoU_synth PseudoU_ 96.4 0.0019 4.9E-08 41.7 2.3 86 111-263 1-87 (87)
45 PRK01851 truB tRNA pseudouridi 96.2 0.0034 8.6E-08 40.2 2.6 70 106-188 17-86 (310)
46 PRK00020 truB tRNA pseudouridi 96.1 0.0027 6.9E-08 40.8 1.8 72 106-190 10-82 (244)
47 PRK02484 truB tRNA pseudouridi 96.0 0.0031 8E-08 40.4 1.8 71 106-189 3-74 (293)
48 PRK00130 truB tRNA pseudouridi 96.0 0.0036 9.2E-08 40.0 1.9 72 106-190 2-74 (289)
49 PRK04099 truB tRNA pseudouridi 96.0 0.0039 9.9E-08 39.8 2.1 72 106-190 2-74 (272)
50 PRK02755 truB tRNA pseudouridi 95.9 0.0061 1.6E-07 38.6 2.7 71 106-190 2-73 (291)
51 PRK02193 truB tRNA pseudouridi 95.8 0.005 1.3E-07 39.1 1.9 68 108-188 2-69 (279)
52 PRK05389 truB tRNA pseudouridi 95.7 0.0054 1.4E-07 38.9 1.9 70 106-188 13-82 (305)
53 PRK01550 truB tRNA pseudouridi 95.6 0.0075 1.9E-07 38.0 2.4 70 106-188 2-71 (307)
54 cd02572 PseudoU_synth_hDyskeri 95.5 0.0065 1.7E-07 38.4 1.7 69 107-188 3-71 (182)
55 PRK03287 truB tRNA pseudouridi 95.5 0.0098 2.5E-07 37.3 2.6 70 106-188 9-78 (298)
56 PRK01528 truB tRNA pseudouridi 95.4 0.012 2.9E-07 36.9 2.8 72 106-190 3-75 (293)
57 PRK04642 truB tRNA pseudouridi 95.4 0.011 2.9E-07 36.9 2.6 70 106-188 10-79 (300)
58 COG0130 TruB Pseudouridine syn 95.3 0.0084 2.1E-07 37.7 1.8 81 107-200 16-97 (271)
59 TIGR02988 YaaA_near_RecF S4 do 95.3 0.032 8.1E-07 34.1 4.7 49 19-68 9-59 (60)
60 cd02573 PseudoU_synth_EcTruB P 95.3 0.0087 2.2E-07 37.6 1.8 69 107-188 1-69 (277)
61 PRK05033 truB tRNA pseudouridi 95.3 0.013 3.3E-07 36.5 2.7 70 106-188 12-81 (314)
62 PRK04270 H/ACA RNA-protein com 95.3 0.012 3E-07 36.8 2.3 72 104-188 20-91 (300)
63 COG2501 S4-like RNA binding pr 94.5 0.099 2.5E-06 31.0 5.4 51 19-69 12-63 (73)
64 cd02867 PseudoU_synth_TruB_4 P 94.3 0.02 5.2E-07 35.3 1.5 41 144-188 58-98 (312)
65 TIGR00431 TruB tRNA pseudourid 93.7 0.014 3.5E-07 36.4 -0.3 70 106-188 2-72 (236)
66 COG4332 Uncharacterized protei 93.5 0.086 2.2E-06 31.3 3.5 17 242-258 126-142 (203)
67 PRK04313 30S ribosomal protein 93.3 0.37 9.3E-06 27.4 6.5 57 16-72 35-93 (237)
68 PRK11507 hypothetical protein; 93.2 0.18 4.5E-06 29.4 4.7 51 17-67 10-61 (70)
69 TIGR01687 moaD_arch MoaD famil 93.1 0.17 4.3E-06 29.5 4.4 54 17-71 24-90 (93)
70 KOG2559 consensus 92.6 0.067 1.7E-06 32.0 1.9 23 142-164 89-111 (318)
71 PTZ00223 40S ribosomal protein 92.5 0.6 1.5E-05 26.0 6.6 57 16-72 36-94 (273)
72 PRK13354 tyrosyl-tRNA syntheta 92.4 0.53 1.4E-05 26.4 6.2 23 230-254 173-195 (405)
73 PTZ00118 40S ribosomal protein 92.3 0.62 1.6E-05 26.0 6.5 57 16-72 39-97 (262)
74 pfam06353 DUF1062 Protein of u 91.9 0.38 9.7E-06 27.3 5.1 41 8-49 92-132 (142)
75 PRK04051 rps4p 30S ribosomal p 91.3 0.47 1.2E-05 26.7 5.0 51 17-67 101-154 (177)
76 TIGR01018 rpsD_arch ribosomal 87.6 0.25 6.4E-06 28.4 1.3 44 19-64 112-158 (170)
77 cd00754 MoaD MoaD family. Memb 86.1 1.4 3.6E-05 23.7 4.4 50 18-71 25-77 (80)
78 PTZ00155 40S ribosomal protein 83.3 1.4 3.5E-05 23.8 3.3 47 18-64 106-153 (188)
79 COG1471 RPS4A Ribosomal protei 81.6 3.6 9.2E-05 21.1 5.0 56 18-73 40-97 (241)
80 PRK11130 moaD molybdopterin sy 77.8 5.2 0.00013 20.1 4.8 55 10-71 19-78 (81)
81 cd01668 TGS_RelA_SpoT TGS_RelA 74.7 2.8 7.1E-05 21.9 2.7 23 45-67 36-58 (60)
82 TIGR00425 CBF5 rRNA pseudourid 70.5 4 0.0001 20.8 2.7 144 105-265 33-181 (326)
83 cd01616 TGS The TGS domain, na 68.8 4.6 0.00012 20.5 2.7 23 45-67 36-58 (60)
84 pfam02824 TGS TGS domain. The 68.3 4.6 0.00012 20.5 2.6 23 45-67 36-58 (60)
85 TIGR01344 malate_syn_A malate 64.6 4 0.0001 20.8 1.8 11 254-264 248-258 (522)
86 PRK11092 bifunctional (p)ppGpp 64.5 6 0.00015 19.7 2.6 22 46-67 424-445 (702)
87 pfam02597 ThiS ThiS family. Th 64.5 7.5 0.00019 19.1 3.1 47 16-71 18-67 (70)
88 COG0162 TyrS Tyrosyl-tRNA synt 62.9 8.8 0.00022 18.7 3.2 12 147-159 152-163 (401)
89 PRK10872 relA GDP/GTP pyrophos 61.5 7.3 0.00019 19.2 2.6 23 46-68 442-464 (743)
90 KOG0062 consensus 56.4 4.6 0.00012 20.5 0.9 18 101-118 212-229 (582)
91 COG0317 SpoT Guanosine polypho 56.1 11 0.00028 18.1 2.7 24 45-68 424-447 (701)
92 pfam01509 TruB_N TruB family p 55.4 6.5 0.00016 19.5 1.5 44 143-190 8-52 (149)
93 TIGR00670 asp_carb_tr aspartat 53.4 12 0.0003 17.9 2.5 54 260-328 173-231 (336)
94 KOG2529 consensus 48.8 11 0.00027 18.2 1.7 75 106-193 68-142 (395)
95 TIGR00691 spoT_relA RelA/SpoT 47.5 21 0.00053 16.3 3.1 55 5-69 387-442 (741)
96 PRK06083 sulfur carrier protei 43.6 25 0.00063 15.9 3.0 44 16-68 16-63 (69)
97 KOG3301 consensus 41.2 24 0.00061 16.0 2.6 18 36-53 114-131 (183)
98 PRK01777 hypothetical protein; 40.9 18 0.00046 16.7 1.9 29 43-71 49-77 (95)
99 TIGR01764 excise DNA binding d 40.1 24 0.00062 15.9 2.5 22 25-47 7-28 (49)
100 PRK11054 helD DNA helicase IV; 39.9 13 0.00033 17.7 1.0 72 100-188 204-280 (684)
101 pfam03658 UPF0125 Uncharacteri 39.4 19 0.0005 16.5 1.9 28 43-70 46-73 (83)
102 COG2104 ThiS Sulfur transfer p 39.3 27 0.00068 15.7 2.6 43 17-68 16-62 (68)
103 pfam04669 DUF579 Protein of un 38.7 8.9 0.00023 18.7 0.0 54 101-155 107-164 (187)
104 pfam00498 FHA FHA domain. The 38.5 30 0.00075 15.4 2.9 22 46-67 44-66 (67)
105 PRK10687 purine nucleoside pho 38.3 22 0.00057 16.1 2.0 16 98-113 16-31 (119)
106 PRK06488 sulfur carrier protei 37.6 29 0.00074 15.4 2.5 42 19-69 15-60 (65)
107 cd01278 aprataxin_related apra 37.2 22 0.00056 16.2 1.9 14 100-113 17-30 (104)
108 PRK11891 aspartate carbamoyltr 36.8 31 0.0008 15.2 3.9 61 255-329 229-300 (430)
109 pfam01230 HIT HIT domain. 36.1 26 0.00067 15.7 2.1 15 98-112 5-19 (98)
110 cd01669 TGS_Ygr210_C TGS_Ygr21 35.3 22 0.00057 16.1 1.6 20 48-67 55-74 (76)
111 cd01276 PKCI_related Protein K 33.0 32 0.0008 15.2 2.1 15 100-114 15-29 (104)
112 cd01277 HINT_subgroup HINT (hi 33.0 32 0.0008 15.2 2.1 16 98-113 13-28 (103)
113 pfam11969 DcpS_C Scavenger mRN 31.8 34 0.00087 15.0 2.1 18 98-115 13-30 (113)
114 TIGR00515 accD acetyl-CoA carb 31.0 22 0.00055 16.2 1.0 46 264-317 204-256 (292)
115 TIGR02477 PFKA_PPi diphosphate 30.8 3.6 9.1E-05 21.1 -3.0 98 156-272 171-280 (566)
116 PRK07440 hypothetical protein; 30.6 40 0.001 14.6 3.7 43 16-67 17-63 (70)
117 PRK06944 sulfur carrier protei 30.1 40 0.001 14.5 2.3 42 17-68 14-59 (65)
118 pfam09014 Sushi_2 Beta-2-glyco 29.9 32 0.0008 15.2 1.7 29 41-69 8-40 (85)
119 TIGR00223 panD aspartate 1-dec 29.2 42 0.0011 14.4 2.5 54 3-70 38-91 (127)
120 TIGR02538 type_IV_pilB type IV 28.7 18 0.00046 16.7 0.3 21 108-128 319-340 (577)
121 PRK08364 sulfur carrier protei 27.4 45 0.0011 14.2 2.6 45 16-69 18-62 (67)
122 PRK02268 hypothetical protein; 26.1 47 0.0012 14.1 3.6 44 31-74 8-51 (141)
123 PRK05659 sulfur carrier protei 25.5 49 0.0012 14.0 2.4 43 17-68 14-60 (66)
124 TIGR01969 minD_arch cell divis 24.7 33 0.00083 15.1 1.0 52 101-159 105-168 (258)
125 TIGR02211 LolD_lipo_ex lipopro 24.0 37 0.00095 14.7 1.2 39 144-184 48-90 (221)
126 COG1977 MoaD Molybdopterin con 23.8 52 0.0013 13.8 2.6 23 49-71 59-81 (84)
127 PRK07570 succinate dehydrogena 23.2 42 0.0011 14.4 1.3 64 5-69 17-101 (247)
128 COG5037 TOS9 Gluconate transpo 22.4 29 0.00073 15.5 0.3 35 1-35 1-35 (248)
129 KOG4476 consensus 22.4 29 0.00073 15.5 0.3 35 1-35 1-35 (248)
130 COG2914 Uncharacterized protei 22.4 55 0.0014 13.7 1.8 29 43-71 49-77 (99)
131 PRK00943 selenophosphate synth 22.2 28 0.00072 15.5 0.3 11 32-42 21-31 (347)
132 COG2514 Predicted ring-cleavag 22.1 56 0.0014 13.6 3.5 32 238-269 165-197 (265)
133 TIGR01249 pro_imino_pep_1 prol 22.1 47 0.0012 14.1 1.4 15 113-127 24-41 (310)
134 cd06919 Asp_decarbox Aspartate 21.6 58 0.0015 13.5 2.6 25 43-70 65-89 (111)
135 TIGR01683 thiS thiamine biosyn 20.9 60 0.0015 13.4 2.5 44 17-68 12-59 (65)
136 TIGR02812 fadR_gamma fatty aci 20.5 50 0.0013 13.9 1.2 34 23-57 34-72 (275)
No 1
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=0 Score=585.73 Aligned_cols=308 Identities=33% Similarity=0.514 Sum_probs=256.2
Q ss_pred CCCEEEEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCC
Q ss_conf 68304999841136866899999876788989999999849903887884511211799889993565542223322223
Q gi|254780608|r 4 MTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKI 83 (346)
Q Consensus 4 M~~~~~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~~~~~~~~~~~~~ 83 (346)
.+.|++++|+++++|+|||+||+..|+++||+.++++|++|.|+|||++++++++|+.||+|+|++.........+.
T Consensus 5 ~~~v~~i~V~~~~~G~RLD~fL~~~l~~~srs~i~klir~g~V~VNg~~vk~~~~l~~GD~I~i~~~~~~~~~~~p~--- 81 (317)
T PRK11025 5 TPSVKIVAISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVRIPPVRVAEREEEAV--- 81 (317)
T ss_pred CCCCEEEEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCCCCCCCEEEECCCCCCCCCCCCC---
T ss_conf 99627999893007975999999756626999999999869989999995710465799999988866564445778---
Q ss_pred CCCCCCCCCCCCCCCCEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECC
Q ss_conf 45543343222345430786178568841765311223578533233201101111100133354453422240462123
Q gi|254780608|r 84 LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163 (346)
Q Consensus 84 ~~~~~~~~~~~~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~ 163 (346)
.+ ... ....++..||||||+|+|||||+||+||||++...++.+.+..+.. ....+++||||||+||||||||||
T Consensus 82 -~~--~~~-~~~~l~~~IlyED~~llvvnKPaGl~vhp~~~~~~~~~~~l~~~~~-~~~~~~iVHRLDr~TSGllv~AK~ 156 (317)
T PRK11025 82 -SP--HLQ-KVAALADVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRP-EARFLELVHRLDRDTSGVLLVAKK 156 (317)
T ss_pred -CC--CCC-CCCCCCCEEEEECCCEEEEECCCCCEECCCCCCHHHHHHHHHHHCC-CCCCCCCEECCCCCCCEEEEEECC
T ss_conf -85--511-0024556079947988999774356226888731689999997588-887678131269987426887168
Q ss_pred CCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEE
Q ss_conf 10122210233332211120001345654100000001223465543211133555555530343010134320244204
Q gi|254780608|r 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL 243 (346)
Q Consensus 164 ~~a~~~l~~~f~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv 243 (346)
..+++.|++||+++.|.|+|+|+|+|.+....++|+.++.++.......+. .....|+.|.|+|+++++++ .+|||
T Consensus 157 ~~a~~~l~~~f~~r~v~K~Y~Alv~G~~~~~~~~i~~pl~~~~~~~~~~~~---~~~~~gk~a~T~~~v~~~~~-~~sLv 232 (317)
T PRK11025 157 RSALRSLHEQLREKGMQKDYLALVRGQWQSHVKVVQAPLLKNILQSGERIV---RVSQEGKPSETRFKVEERYA-FATLV 232 (317)
T ss_pred HHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCEEEEEECCCCCCCCCEEE---ECCCCCCCCHHHHHHHHHCC-CCCCE
T ss_conf 999999999997372575599998276367788796100046676764566---22777776410144676527-86400
Q ss_pred EEEECHHHHHHHHHHHHHCCCCEECCCCCCCCCC-CHHCCCCCCCHHHHHHHHEEECCCCC-EEEEECCCCHHHHHHHHH
Q ss_conf 5786123789999999963980004644466522-10001344624131100043758896-499983997899999998
Q gi|254780608|r 244 EMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFK-GNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKTWDS 321 (346)
Q Consensus 244 ~~~l~TGR~HQIRvhl~~~g~PivGD~~Yg~~~~-~~~~~~~~~r~~LHa~~l~f~hp~~~-~~~~~aplP~~f~~~l~~ 321 (346)
+|+|+|||||||||||+++||||+||.+||+... .........||+|||++|+|.||.++ .++|+||||+||+++|+.
T Consensus 233 ~~~~~TGRtHQIRvHla~~G~PI~GD~~YG~~~~~~~~~~~~~~R~~LHA~~L~F~HP~t~~~~~f~aplP~d~~~~l~~ 312 (317)
T PRK11025 233 RASPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTGTGLNRLFLHAAALKFTHPGTGEVMRIEAPLDNQLKRCLQK 312 (317)
T ss_pred EEECCCCCHHHHHHHHHHCCCCEECCCCCCCCCCCHHHHCCCCCCHHHHCCCCEEECCCCCCEEEEECCCHHHHHHHHHH
T ss_conf 57558075899999998779968385202874212023036885543521865718889998699982684999999999
Q ss_pred HC
Q ss_conf 08
Q gi|254780608|r 322 LG 323 (346)
Q Consensus 322 l~ 323 (346)
|.
T Consensus 313 Lr 314 (317)
T PRK11025 313 LR 314 (317)
T ss_pred HH
T ss_conf 86
No 2
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=0 Score=571.88 Aligned_cols=298 Identities=25% Similarity=0.409 Sum_probs=244.9
Q ss_pred EEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCC
Q ss_conf 999841136866899999876788989999999849903887884-5112117998899935655422233222234554
Q gi|254780608|r 9 YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87 (346)
Q Consensus 9 ~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~ 87 (346)
+++|+++++|+|||+||++.||++||+.++++|++|.|+|||+++ +++++|..||+|.+........
T Consensus 8 T~tV~~~~aG~RLD~fL~~~~~~~srs~i~k~ir~g~I~VNgk~v~k~~~~v~~GD~I~i~~~~~~~~------------ 75 (325)
T PRK11180 8 TATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEA------------ 75 (325)
T ss_pred EEEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCCCCCCCCEEEECCCCCCCC------------
T ss_conf 99999100797399999975788899999999986988999999478212788999999816877634------------
Q ss_pred CCCCCCCCCCCCEEEEECCCEEEECCCCCCEEECCCCCCCC-CCCCHHHCCCC--CCCCCCCCCCCCCCCCCEEEEECCC
Q ss_conf 33432223454307861785688417653112235785332-33201101111--1001333544534222404621231
Q gi|254780608|r 88 VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDS--KGQKPRLTHRLDQETSGILVVARTR 164 (346)
Q Consensus 88 ~~~~~~~~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~-~~~~l~~~~~~--~~~~~~lVHRLDr~TSGlll~AK~~ 164 (346)
...+..+++.|||||+++||||||+||+|||+++.... +.+.+..+... ...++++||||||+||||||||||.
T Consensus 76 ---~~~p~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~r~~iVHRLDr~TSGlll~AK~~ 152 (325)
T PRK11180 76 ---RFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTV 152 (325)
T ss_pred ---CCCCCCCCCCEEEECCCEEEEECCCCCEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCEEECCCCCCCEEEEECCCH
T ss_conf ---47722388518998388999988999447679898887799999875321047876766642799974146641759
Q ss_pred CHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEE
Q ss_conf 01222102333322111200013456541000000012234655432111335555555303430101343202442045
Q gi|254780608|r 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244 (346)
Q Consensus 165 ~a~~~l~~~f~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~ 244 (346)
.+++.|+++|+++.|.|+|+|+|+|.++ ..|+|+.++.+.... +..+ ...+.||+|+|+|++++.++ .+|||+
T Consensus 153 ~a~~~l~~~f~~~~v~K~Y~Alv~G~~~-~~g~i~~pl~~~~~~-~~~~----~~~~~gk~A~T~~~vl~~~~-~~slv~ 225 (325)
T PRK11180 153 PAQTRLVEALQKREITREYEAVAIGHMT-AGGTVDEPISRHPTK-RTHM----AVHPMGKPAVTHYRIMEHFR-VHTRLR 225 (325)
T ss_pred HHHHHHHHHHHHCCCCEEEEEEEEEEEC-CCCEEECCCCCCCCC-CEEE----EECCCCEEECCHHHHHHHCC-CCEEEE
T ss_conf 9999999999738896599999810437-996585420137766-6289----97677702022101444358-845799
Q ss_pred EEECHHHHHHHHHHHHHCCCCEECCCCCCCCCCC------HHC--CCCCCCHHHHHHHHEEECCCCC-EEEEECCCCHHH
Q ss_conf 7861237899999999639800046444665221------000--1344624131100043758896-499983997899
Q gi|254780608|r 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFT--SPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315 (346)
Q Consensus 245 ~~l~TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~------~~~--~~~~~r~~LHa~~l~f~hp~~~-~~~~~aplP~~f 315 (346)
|+|+||||||||+||+++||||+||.+||+.... .+. ..+.+||+|||++|+|.||.++ ++.|+||||+||
T Consensus 226 ~~l~TGRtHQIRvHla~~G~PIvGD~~YG~~~~~~k~~~~~~~~~~~~~~R~~LHA~~L~f~HP~t~~~~~~~aplP~d~ 305 (325)
T PRK11180 226 LRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPIPQDM 305 (325)
T ss_pred EEECCCCCHHHHHHHHHCCCCEECCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHCCCCCCCCCCCCCEEEEECCCCHHH
T ss_conf 98275882899999998799563752468866555443477888761897664631845775789998799980690999
Q ss_pred HHHHHHHCCCCCC
Q ss_conf 9999980898752
Q gi|254780608|r 316 VKTWDSLGFKYDR 328 (346)
Q Consensus 316 ~~~l~~l~~~~d~ 328 (346)
+++|+.|.+.+.+
T Consensus 306 ~~~l~~Lr~d~~~ 318 (325)
T PRK11180 306 VELIEALRADFEE 318 (325)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999998668976
No 3
>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=100.00 E-value=0 Score=564.61 Aligned_cols=297 Identities=31% Similarity=0.464 Sum_probs=244.3
Q ss_pred HHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC--CCCCCCCCCEEE-EECCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 11368668999998767889899999998499038878845--112117998899-935655422233222234554334
Q gi|254780608|r 14 NDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK--FNNRIQSGQVVR-IPPVINALNHIIKEQKILDSSVNL 90 (346)
Q Consensus 14 ~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk--~~~~v~~GD~I~-i~~~~~~~~~~~~~~~~~~~~~~~ 90 (346)
+++.|+|||.||++.|+.+||++++++|++|.|.||++.+. ++++|+.||.|. |...... .......
T Consensus 1 ~~~~g~Rld~~L~~~l~~~sr~~~~~~i~~G~V~vN~~~~~~~~~~~~~~g~~~~~v~~~~~~----------~~~~~~~ 70 (337)
T TIGR00005 1 EEQAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNKGKVTANPKLKIKDGDRITPVRVPEEQ----------EELEVPV 70 (337)
T ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCCEEECCCCCCCCCCEEECCCCEEECEECCCCC----------CCCCCCC
T ss_conf 974302699999998367888899999874968963764256743052387466010014643----------3235766
Q ss_pred CCCCCCCCCEEEEECCCEEEECCCCCCEEECCCCCCCC-CCC-CHHHCCCCC-----CCCCCCCCCCCCCCCCEEEEECC
Q ss_conf 32223454307861785688417653112235785332-332-011011111-----00133354453422240462123
Q gi|254780608|r 91 TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDG-FLKSWVDSK-----GQKPRLTHRLDQETSGILVVART 163 (346)
Q Consensus 91 ~~~~~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~-~~~-~l~~~~~~~-----~~~~~lVHRLDr~TSGlll~AK~ 163 (346)
...+..+++.||||||++||||||+||+|||+++...+ +.+ ++.++.... -.++++||||||+|||+|++||+
T Consensus 71 ~~~p~~l~l~IlfEDe~i~vinKP~G~~vHP~~~~~~~Tv~~~L~~~~~~~~~gig~~~~~~~vHRLD~dTSGl~~vAK~ 150 (337)
T TIGR00005 71 QDIPADLKLDILFEDEDILVINKPSGLVVHPGGGNSFGTVLNALLAHCPERLSGIGGVFRVGIVHRLDRDTSGLMVVAKT 150 (337)
T ss_pred CCCCCCCCCEEEEECCCEEEEECCCCEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEEC
T ss_conf 56734221137875083899978987564488888735489999986476643457612361355247787258999708
Q ss_pred CCHHHHHCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHH--HHCCC
Q ss_conf 10122210233332211120001345654-1000000012234655432111335555555303430101343--20244
Q gi|254780608|r 164 RAAAQHLTESFRMRRIQKIYWSLVWGIPK-NKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDC--FAQKF 240 (346)
Q Consensus 164 ~~a~~~l~~~f~~~~v~K~Y~Aiv~G~~~-~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~--~~~~~ 240 (346)
..|+..|++||++|.++|.|+|+|.|.+. ...++|+.|+.+.......+ .+...+.++||.|+|+|+++++ +++ +
T Consensus 151 ~~A~~~L~~ql~~~~~~k~Y~A~V~G~~~~~~~~~~~~P~~r~~~~~~~~-~v~~~~~~~GK~A~T~f~~~~~~A~~~-~ 228 (337)
T TIGR00005 151 RLALRELQRQLKERTVTKEYVALVHGEFDLSKKGTVDAPLGRVPNNRGKM-AVAPSSEKEGKPAVTHFKVLERIADGN-A 228 (337)
T ss_pred HHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCCEEEECCCCCCCCCCEEE-EEEECCCCCCCEEEEEEEEEHHHCCCC-C
T ss_conf 68999999999838611789999831768876447806532368860268-997678888961234212100110445-2
Q ss_pred CEEEEEECHHHHHHHHHHHHHCCCCEECCCCCCCCCCC-H----HCCCCCCCHHHHHHHHEEECCCC---------CE-E
Q ss_conf 20457861237899999999639800046444665221-0----00134462413110004375889---------64-9
Q gi|254780608|r 241 CWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG-N----FTSPIQNKLYLHARYMDLPHPEG---------GR-L 305 (346)
Q Consensus 241 slv~~~l~TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~-~----~~~~~~~r~~LHa~~l~f~hp~~---------~~-~ 305 (346)
|||+|+|+|||||||||||+++||||+||++||+.... + .......||+|||++|.|.||.+ ++ |
T Consensus 229 sl~~~~L~TGRTHQIRVHl~~~ghPl~gD~~YG~~~~~~~~~g~~~~~~~~~q~LHA~~l~f~HP~~~~W~~~~~~ge~~ 308 (337)
T TIGR00005 229 SLVECELETGRTHQIRVHLQYLGHPLAGDPLYGNKPKKGNNLGLEGLLNFDRQALHAYELGFIHPATSSWYHNETKGELL 308 (337)
T ss_pred CEEEEEECCCCCHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEHHHHHCCCCCCCCCCCCCCCCCEE
T ss_conf 18999853489738999999716853143256888878321451003675402311455310378886621447787143
Q ss_pred E-----------EECCCCHHHHHHHHHH
Q ss_conf 9-----------9839978999999980
Q gi|254780608|r 306 Q-----------ITAPLPAHMVKTWDSL 322 (346)
Q Consensus 306 ~-----------~~aplP~~f~~~l~~l 322 (346)
+ |+||+|+||..+|+.|
T Consensus 309 ~~~~C~~Ce~~~~~AP~p~~~~~~l~~L 336 (337)
T TIGR00005 309 EGKKCSECETELFEAPLPADLKELLEAL 336 (337)
T ss_pred CCCCCCCCCCCHHHCCCCHHHHHHHHHC
T ss_conf 2650532476211058807999999960
No 4
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=526.47 Aligned_cols=285 Identities=35% Similarity=0.583 Sum_probs=234.9
Q ss_pred EEEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCC
Q ss_conf 49998411368668999998767889899999998499038878845112117998899935655422233222234554
Q gi|254780608|r 8 QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87 (346)
Q Consensus 8 ~~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~ 87 (346)
..++|+++.+|+|||+||+..++ +||+++++++++|.|+|||++++++++|..||+|+++....... .
T Consensus 2 ~~~~i~~~~~g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vNg~~v~~~~~l~~gd~i~~~~~~~~~~-----~------ 69 (289)
T COG0564 2 LEFEVPEEEAGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVKPSYKLKPGDVVRIPLPEEPEE-----E------ 69 (289)
T ss_pred CEEEECCHHCCCCHHHHHHHHCC-CCHHHHHHHHHCCCEEECCEECCCCEEECCCCEEEEECCCCCCC-----C------
T ss_conf 44883611135479999987257-47999999988898899999835871608999999535655433-----3------
Q ss_pred CCCCCCCCCCCCEEEEECCCEEEECCCCCCEEECCCCCCCC--CCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf 33432223454307861785688417653112235785332--3320110111110013335445342224046212310
Q gi|254780608|r 88 VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165 (346)
Q Consensus 88 ~~~~~~~~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~--~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~ 165 (346)
...+...++.|||||++++|||||+||+|||+++.... ++.++..+... ..++++||||||+|||+||+|||..
T Consensus 70 ---~~~~~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~-~~~~~~vHRLDkdTSGlll~AK~~~ 145 (289)
T COG0564 70 ---KLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDG-VERPGIVHRLDKDTSGLLLVAKNRE 145 (289)
T ss_pred ---CCCCCCCCCCEEEECCCEEEEECCCCCEECCCCCCCCHHHHHHHHHHCCCC-CCCEEEECCCCCCCCEEEEEECCHH
T ss_conf ---456547787779976999999889997167798875267999998752334-7864351488999856999995999
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEE
Q ss_conf 12221023333221112000134565410000000122346554321113355555553034301013432024420457
Q gi|254780608|r 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245 (346)
Q Consensus 166 a~~~l~~~f~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~ 245 (346)
|++.|++||+++.+.|+|+|+|+|.+....++|+.++.+.......+... .. .+|+.|+|+|++++++++.+||++|
T Consensus 146 a~~~l~~~f~~r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~~~~~v~-~~--~~gk~A~T~~~~~~~~~~~~tlv~~ 222 (289)
T COG0564 146 AARELSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNRKKMAVV-KE--GSGKPAITHYEVLERFGDNYTLVEL 222 (289)
T ss_pred HHHHHHHHHHCCCCCEEEEEEEECCCCCCCCEEECCCCCCCCCCCCEEEE-CC--CCCCCEEEEEEEEEECCCCCEEEEE
T ss_conf 99999999851866179999996855666878835410676776216997-16--8898337999972063876289999
Q ss_pred EECHHHHHHHHHHHHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCE-EEEECCCCH
Q ss_conf 86123789999999963980004644466522100013446241311000437588964-999839978
Q gi|254780608|r 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313 (346)
Q Consensus 246 ~l~TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~-~~~~aplP~ 313 (346)
+|+|||||||||||+++||||+||++||+.. ........||+|||++|+|.||.+++ +.|+||+|.
T Consensus 223 ~~~TGRTHQIRvHl~~lghPI~GD~~Yg~~~--~~~~~~~~r~~LHA~~l~f~hp~t~~~~~~~a~~p~ 289 (289)
T COG0564 223 KPETGRTHQIRVHLAHLGHPIVGDPLYGGKD--KSAGAGLKRQALHAYKLSFTHPLTGEELEFEAPLPE 289 (289)
T ss_pred EECCCCHHHHHHHHHHCCCCEECCCCCCCCC--CCCCCCCCHHHHHHHHHCCCCCCCCCEEEEECCCCC
T ss_conf 9688985199999998799743874678742--112356214788753517788999977999568899
No 5
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=100.00 E-value=0 Score=461.38 Aligned_cols=232 Identities=28% Similarity=0.362 Sum_probs=184.7
Q ss_pred CEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCC
Q ss_conf 30786178568841765311223578533233201101111100133354453422240462123101222102333322
Q gi|254780608|r 99 SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178 (346)
Q Consensus 99 ~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~ 178 (346)
++|||||++|||||||+||+|||+.........++..+.+..+..+++||||||+||||||||||..+++.|++||+++.
T Consensus 2 L~IlyED~~llVVnKPaGl~vh~~~~~~~~~~~~~~~l~~~~~~~~~~VHRLDr~TSGllv~AK~~~a~~~L~~~f~~~~ 81 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQIGQHVFTAHRLDRPTSGVLLMALSSEAARLLAQQFEQHQ 81 (257)
T ss_pred EEEEEECCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHHHCC
T ss_conf 57999669899999999986479988878519999999875277653205778987517999689999999999987576
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH----------HCCCCEEEEEEC
Q ss_conf 1112000134565410000000122346554321113355555553034301013432----------024420457861
Q gi|254780608|r 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248 (346)
Q Consensus 179 v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~----------~~~~slv~~~l~ 248 (346)
|+|+|+|+|.|.+. ..++|+.++.+...... ........+++.|+|+|++++.. ...+|||+|+|+
T Consensus 82 v~K~Y~Alv~G~~~-~~~~i~~~l~~~~~~~~---~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~~~~~~~sLv~~~p~ 157 (257)
T PRK11112 82 IQKTYHAIVRGWLM-EEAVLDYPLKEELDKIA---DKFAREDKEPQPAVTHYRGLATVEMPVATGRYPTTRYSLVELEPK 157 (257)
T ss_pred CCEEEEEEEEEECC-CCCEEEEECCCCCCCCC---CEEECCCCCCEEEEEEEEEEEEEEEECCCCCCCCCCEEEEEEECC
T ss_conf 86399999964538-99768524344666556---313022898636345411102687510123246785799999648
Q ss_pred HHHHHHHHHHHHHCCCCEECCCCCCCCCCCH--HCCCCCCCHHHHHHHHEEECCCCCE-EEEECCCCHHHHHHHHHHCCC
Q ss_conf 2378999999996398000464446652210--0013446241311000437588964-999839978999999980898
Q gi|254780608|r 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK 325 (346)
Q Consensus 249 TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~~--~~~~~~~r~~LHa~~l~f~hp~~~~-~~~~aplP~~f~~~l~~l~~~ 325 (346)
|||||||||||+++||||+||.+||+...+. ......+||||||++|+|+||.|++ |+|+||||+||+++|+.|||+
T Consensus 158 TGRtHQIRvHla~lGhPIvGD~~YG~~~~~~~~~~~~~~~R~~LHA~~L~F~HP~tge~~~~~AplP~d~~~ll~~~g~~ 237 (257)
T PRK11112 158 TGRKHQLRRHMAHLRHPIIGDSKHGDLRQNRSFAEHFGCSRLMLHASELSLTHPFTGEPLTITAGLDETWQQLLSQFGWR 237 (257)
T ss_pred CCCHHHHHHHHHHCCCCEECCCCCCCCCCCCHHHHCCCCCCHHHCCCCCEEECCCCCCEEEEECCCHHHHHHHHHHCCCC
T ss_conf 68529999999987996757725587544601454239963655018347578599986999816859999999976998
Q ss_pred CCCCHHHHC
Q ss_conf 752001100
Q gi|254780608|r 326 YDRNLYIKR 334 (346)
Q Consensus 326 ~d~~~~~~~ 334 (346)
-......+.
T Consensus 238 ~~~~~~~~~ 246 (257)
T PRK11112 238 GLLPENERV 246 (257)
T ss_pred CCCCHHCCC
T ss_conf 889311062
No 6
>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=100.00 E-value=0 Score=445.42 Aligned_cols=239 Identities=20% Similarity=0.305 Sum_probs=181.7
Q ss_pred CEECCEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCEEEECCCCCCEEECCCCC
Q ss_conf 03887884511211799889993565542223322223455433432223454307861785688417653112235785
Q gi|254780608|r 46 VRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI 125 (346)
Q Consensus 46 V~VNG~~vk~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiyED~~livinKPaGl~vhp~~g~ 125 (346)
|+|||++++++++|+.||+|.+......+ ++ ..++++||||||+|||||||+||+|||+++.
T Consensus 4 v~~~G~~v~~~~~l~~Gd~v~~~~~~~~e-----------~p-------~p~~l~IlyEDd~llVVnKPaGl~vhP~~~~ 65 (246)
T cd02558 4 VDADGEPLDPDSPYRPGTFVWYYRELPDE-----------PP-------IPFEETILHQDEHLLVADKPHFLPVTPRGRY 65 (246)
T ss_pred ECCCCEECCCCCEECCCCEEEEEECCCCC-----------CC-------CCCCCCEEEECCCEEEEECCCCCCEEECCCC
T ss_conf 88099797999872799999998058999-----------99-------9998998997899999999999857618997
Q ss_pred CCCCCCCHHHCCCCCC-CCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCC
Q ss_conf 3323320110111110-01333544534222404621231012221023333221112000134565410000-000122
Q gi|254780608|r 126 AYHIDGFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKEC-IANWLL 203 (346)
Q Consensus 126 ~~~~~~~l~~~~~~~~-~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Aiv~G~~~~~~~~-i~~~~~ 203 (346)
.. +.++..+....+ ..+.+||||||+||||||||||+.+++.|++||+++.|+|+|+|+|.|.+....+. +...+.
T Consensus 66 ~~--~tl~~~l~~~~~~~~~~~VHRLDr~TSGllv~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~~~~~~~~~~~~~~~~~ 143 (246)
T cd02558 66 VT--ETLLVRLRRQTGNPDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYEAVAPYVPALTFPLTVRSRIV 143 (246)
T ss_pred CC--CHHHHHHHHHCCCCCCCEECCCCCCCCEEEEEECCHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCEEECCCCC
T ss_conf 20--1799999884099865473467998746999988999999999986468452799999983377678636636557
Q ss_pred CCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHCCCCEECCCCCCCCCCCHHCCC
Q ss_conf 34655432111335555555303430101343202442045786123789999999963980004644466522100013
Q gi|254780608|r 204 KKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSP 283 (346)
Q Consensus 204 ~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~~~~~~ 283 (346)
+.. ... .....++++.|.|+|++++..+ .+||++|+|+||||||||+||+++||||+||.+||+..... ...
T Consensus 144 ~~~----~~~--~~~~~~g~~~A~T~~~~l~~~~-~~slv~~~~~TGRtHQIRvHla~iGhPIvGD~~Yg~~~~~~-~~~ 215 (246)
T cd02558 144 KGR----GFF--QAREVEGEPNAETRIELLARRG-GWGLYRLSPHTGKTHQLRVHMAALGVPILNDPFYPVLLDKD-PDD 215 (246)
T ss_pred CCC----CCE--EEECCCCCCCEEEEEEEEEECC-CEEEEEEEECCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCC-CCC
T ss_conf 887----644--8980589987699999999839-85899999687862999999998799350783777644344-334
Q ss_pred CCCCHHHHHHHHEEECCCCCE-EEEECCCC
Q ss_conf 446241311000437588964-99983997
Q gi|254780608|r 284 IQNKLYLHARYMDLPHPEGGR-LQITAPLP 312 (346)
Q Consensus 284 ~~~r~~LHa~~l~f~hp~~~~-~~~~aplP 312 (346)
...+++|||++|+|.||.|++ |+|+||+|
T Consensus 216 ~~~~l~LHA~~L~F~HP~T~e~m~F~aP~~ 245 (246)
T cd02558 216 FSRPLQLLAKELEFTDPLTGRPRRFESGRS 245 (246)
T ss_pred CCCCCHHHHCEEEEECCCCCCEEEEECCCC
T ss_conf 463302520784878929989889968998
No 7
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=100.00 E-value=0 Score=415.64 Aligned_cols=208 Identities=31% Similarity=0.461 Sum_probs=169.6
Q ss_pred CCCCCEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCC
Q ss_conf 34543078617856884176531122357853323320110111110013335445342224046212310122210233
Q gi|254780608|r 95 DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174 (346)
Q Consensus 95 ~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f 174 (346)
+...+.||||||+|||||||+||++|||... .+...++..... ....+.+||||||+||||||||||+++++.|+++|
T Consensus 10 ~~~~l~IlyED~~llvvnKP~gl~~~pg~~~-~~~~~~~~~~~~-~~~~~~~vHRLDr~TSGlll~AK~~~a~~~l~~~f 87 (219)
T PRK10158 10 QEPWLVILYQDDHIMVVNKPSGLLSVPGRLE-EHKDSVMTRIQR-DYPQAESVHRLDMATSGVIVVALTKAAERELKRQF 87 (219)
T ss_pred CCCCCCEEEECCCEEEEECCCCCCCCCCCCC-CCCHHHHHHHHH-CCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
T ss_conf 9999568997999999999999820799764-562069998774-07866634778999753699978999999998878
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHH
Q ss_conf 33221112000134565410000000122346554321113355555553034301013432024420457861237899
Q gi|254780608|r 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254 (346)
Q Consensus 175 ~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQ 254 (346)
++++|+|+|+|+|+|.+....|+|+.++..+....... . ...++|+.|.|+|++++..++.+++|+|+|+||||||
T Consensus 88 ~~r~v~K~YlA~v~G~~~~~~g~i~~~l~~~~~~~~~~-~---~~~~~gk~a~t~~~~l~~~~~~~~lv~l~p~TGRtHQ 163 (219)
T PRK10158 88 REREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQ-K---VCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQ 163 (219)
T ss_pred HHCCCCCEEEEEEECCCCCCCCCCCCCEEECCCCCCCE-E---EECCCCCCCCEEEEEEEECCCCEEEEEEEECCCCHHH
T ss_conf 73746737999983686643561124525047777616-9---9724674121589999973898599999866685189
Q ss_pred HHHHHHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCE-EEEECCCC
Q ss_conf 99999963980004644466522100013446241311000437588964-99983997
Q gi|254780608|r 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312 (346)
Q Consensus 255 IRvhl~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~-~~~~aplP 312 (346)
||+||+++||||+||.+||..... ....|++|||++|+|.||.|++ ++|+||.|
T Consensus 164 IRvhla~lG~PIvGD~~Yg~~~~~----~~~~rl~LHA~~L~f~HP~t~~~~~~~aP~~ 218 (219)
T PRK10158 164 LRVHMLALGHPILGDRFYASPEAR----AMAPRLLLHAEMLTITHPAYGNSMTFKAPAD 218 (219)
T ss_pred HHHHHHHCCCCEECCCCCCCCCCC----CCCCCHHHHCCEEEEECCCCCCEEEEECCCC
T ss_conf 999999879927478777884324----6775830410875858829999899967999
No 8
>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=100.00 E-value=0 Score=409.40 Aligned_cols=210 Identities=30% Similarity=0.457 Sum_probs=162.2
Q ss_pred CEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCC
Q ss_conf 30786178568841765311223578533233201101111100133354453422240462123101222102333322
Q gi|254780608|r 99 SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178 (346)
Q Consensus 99 ~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~ 178 (346)
++||||||+|||||||+||+|||+.+........+....+..+..+.+||||||+||||||||||+++++.|+++|+++.
T Consensus 1 l~IvyED~~ilvvnKP~Gl~~hp~~~~~~~~~~~~~~~~~~~~~~~~~vHRLDr~TSGllv~Ak~~~a~~~l~~~f~~~~ 80 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLGQHVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTEHR 80 (223)
T ss_pred CEEEEECCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCEECCCCCCCCCEEEEECCHHHHHHHHHHHHHCC
T ss_conf 97999679999999999982658999988369999998875378753404778987635999845899999999987551
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH----------HCCCCEEEEEEC
Q ss_conf 1112000134565410000000122346554321113355555553034301013432----------024420457861
Q gi|254780608|r 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH 248 (346)
Q Consensus 179 v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~----------~~~~slv~~~l~ 248 (346)
|.|+|+|+|+|.++ ..+.++.++.......... .......++.+.|.++++... ...+|||+|+|+
T Consensus 81 v~K~Y~Alv~G~~~-~~~~i~~~l~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~ 156 (223)
T cd02563 81 VHKTYLAVVRGYVP-ESGTIDYPLSEELDKLADK---FASDDKAPQAATTHYRLLAVEELPVVVGKYPTSRYSLVELTPH 156 (223)
T ss_pred CCCEEEEEEEEECC-CCCEEEEECCCCCCCCCCE---EEECCCCCCCEEEEEEEEEEEECCEEECCCCCCCEEEEEEEEC
T ss_conf 12269999984079-9987986545467755636---8742788763488988765532000101147774799999967
Q ss_pred HHHHHHHHHHHHHCCCCEECCCCCCCCCCCHH--CCCCCCCHHHHHHHHEEECCCCCE-EEEECCCC
Q ss_conf 23789999999963980004644466522100--013446241311000437588964-99983997
Q gi|254780608|r 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP 312 (346)
Q Consensus 249 TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~~~--~~~~~~r~~LHa~~l~f~hp~~~~-~~~~aplP 312 (346)
||||||||+||+++||||+||.+||+...... ......||+|||++|+|.||.|++ +.|+|||-
T Consensus 157 TGRtHQIRvHla~lG~PIvGD~~YG~~~~~~~~~~~~~~~rl~LHA~~L~F~HP~tge~i~~eaPl~ 223 (223)
T cd02563 157 TGRKHQLRRHLAHIRHPIIGDTTHGDGRHNRFFREHFGCHRLLLAATRLEFTHPVTGERLLIEAPLD 223 (223)
T ss_pred CCCHHHHHHHHHHCCCCEECCCCCCCCCCCHHHHHCCCCCCHHHHCCEEEEECCCCCCEEEEECCCC
T ss_conf 6870899999998799782772568754350235304996864740874838859998899983699
No 9
>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=100.00 E-value=0 Score=387.99 Aligned_cols=195 Identities=29% Similarity=0.351 Sum_probs=161.1
Q ss_pred CCCEEEEECCCEEEECCCCCCEEECCCCC-CCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCC
Q ss_conf 54307861785688417653112235785-33233201101111100133354453422240462123101222102333
Q gi|254780608|r 97 LKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175 (346)
Q Consensus 97 ~~~~IiyED~~livinKPaGl~vhp~~g~-~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~ 175 (346)
.+++|||||++|||||||+||+|||+++. ...+..++..... ...+++|||||++||||||||||+.+++.|+++|+
T Consensus 14 ~~l~IlyED~~iiVVnKP~Gl~~~p~~~~~~~~l~~~l~~~~~--~~~~~~vHRLDr~TSGllv~Ak~~~a~~~l~~~f~ 91 (213)
T cd02557 14 DPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYG--LTELRPCHRLDRLTSGLLLFAKTSQTASRLQQQIR 91 (213)
T ss_pred CCCEEEEECCCEEEEECCCCCCEECCCCCCCCHHHHHHHHHCC--CCCCCEEECCCCCCCCEEEEECCHHHHHHHHHHHH
T ss_conf 9988999689999999999986803899872479999997679--98762640568887652899745789999999972
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH-CCCCEEEEEECHHHHHH
Q ss_conf 32211120001345654100000001223465543211133555555530343010134320-24420457861237899
Q gi|254780608|r 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQ 254 (346)
Q Consensus 176 ~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~-~~~slv~~~l~TGR~HQ 254 (346)
++.|.|+|+|+|+|.++...+.++.++...... ........++++.|+|.|++++..+ ..+||++|+|+||||||
T Consensus 92 ~~~v~K~Y~Alv~G~~~~~~~~i~~~i~~~~~~----~~~~~~~~~~~k~a~T~~~~l~~~~~~~~sll~~~~~TGRtHQ 167 (213)
T cd02557 92 SREVKKEYLARVKGEFPDGEVVVDQPIGLVSPK----GGLRNDVDEKGKDARTIFKRLSYNGDLNTSVVLCKPITGRTHQ 167 (213)
T ss_pred CCCCCEEEEEEEEEECCCCEEEEECCCCEECCC----CCEEEEECCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCHHH
T ss_conf 475635999999726588838995321000776----7258851488864316999999838899899999958788899
Q ss_pred HHHHHHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCEEEEECCCCH
Q ss_conf 99999963980004644466522100013446241311000437588964999839978
Q gi|254780608|r 255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313 (346)
Q Consensus 255 IRvhl~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~~~~~aplP~ 313 (346)
||+||+++||||+||.+||+ .+++|||++|.|+. ++|+||||+
T Consensus 168 IRvhla~lG~PIvGD~~YG~-----------~~l~LHA~~~~~~~-----~~f~~~~p~ 210 (213)
T cd02557 168 IRVHLQYLGHPIVNDPIYNN-----------LGIYLHALRYEGPD-----WSYETELPD 210 (213)
T ss_pred HHHHHHHCCCCEECCCCCCC-----------CCEEEEEEEECCCC-----EEEECCCCC
T ss_conf 99999987995718513298-----------56676863541898-----799768997
No 10
>KOG1919 consensus
Probab=100.00 E-value=0 Score=323.17 Aligned_cols=296 Identities=26% Similarity=0.317 Sum_probs=212.8
Q ss_pred EECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 98411368668999998767889899999998499038878845112117998899935655422233222234554334
Q gi|254780608|r 11 VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL 90 (346)
Q Consensus 11 ~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~~~~ 90 (346)
.+...+.+.-+..++...|...++.+.+..|+.|.|++||..+..++.++.||.+........
T Consensus 36 ~~~~rw~~k~~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~~v~~i~k~~d~l~~~vhrh~----------------- 98 (371)
T KOG1919 36 FVKGRWAGKKLVDVFVSEFRLRERAYYESAIKLGRVTVNGEQVRVSLIVKNGDVLCHTVHRHE----------------- 98 (371)
T ss_pred EEEEEECCCCHHHHHHHHHHCCCHHHHHHHHHCCCEEECCEEEEEEEEECCCCEEEEEECCCC-----------------
T ss_conf 885124462077999898753715766656536865888586004787125888877640478-----------------
Q ss_pred CCCCCCCCCEEEEECCCEEEECCCCCCEEECCCCC-CCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHH
Q ss_conf 32223454307861785688417653112235785-33233201101111100133354453422240462123101222
Q gi|254780608|r 91 TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGI-AYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQH 169 (346)
Q Consensus 91 ~~~~~~~~~~IiyED~~livinKPaGl~vhp~~g~-~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~ 169 (346)
.........|+|||++++|||||+|++|||++.. .+.+...+... .....+++|||||+.|||+|+|||++.++..
T Consensus 99 -p~~~~~~~~Iv~ed~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~--~~~~~~~~~hRLDr~tSGllvlAkt~~~~~~ 175 (371)
T KOG1919 99 -PPVAYLPIRIVFEDKDYVVVNKPHGIPVHPTGRYRENTITKILAAL--HKVEGLRPCHRLDRLTSGLLVLAKTKEAADK 175 (371)
T ss_pred -CCCCCCCCCEEEECCCEEEEECCCCCCEECCCCCCCCCCHHHHHHH--CCCCCCCCCCCCCCCCCCEEEEEECHHHHHH
T ss_conf -8754434415885399899958998754016854436536888874--1455662322467665644899856557689
Q ss_pred HCCCCCCCCCCCCC-CCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCEEEEECCHHHHHHCCCCEEEEE
Q ss_conf 10233332211120-001345654-10000000122346554321113-3555555530343010134320244204578
Q gi|254780608|r 170 LTESFRMRRIQKIY-WSLVWGIPK-NKKECIANWLLKKSHIGGDYVHV-VKQNEKGANYAISHFKVIDCFAQKFCWLEMQ 246 (346)
Q Consensus 170 l~~~f~~~~v~K~Y-~Aiv~G~~~-~~~~~i~~~~~~~~~~~~~~~~~-~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~ 246 (346)
|+++|+++.+.|.| +|-|.|..+ ...-.+..++......-+..... ...+...++.|+|.|+++... ...++|+|+
T Consensus 176 ~~~~~r~~~~~k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~~~~~~l~~~~~~~~~~~k~a~T~~~~~~~~-~~ss~V~~~ 254 (371)
T KOG1919 176 FHEVLRKRTVKKEYVVARVEGPFPVVGEVEIKEPIGEEERPLRMGLNAVGVRDEVAAKDAKTLFKVLSYD-GGSSLVECR 254 (371)
T ss_pred HHHHHHCCCCEEEEEEEEEECCCCCCCEEEECCCCCCCCCCCCEEEEECCCCCCCCCCCCEEEEEECCCC-CCEEEEEEE
T ss_conf 9999743541037999997245787762771787553456651576401224444565644688872348-966999963
Q ss_pred ECHHHHHHHHHHHHHCCCCEECCCCCCCCCCCH---------------HCCCCCCCHHHHHHHHEE-ECCCCC----EEE
Q ss_conf 612378999999996398000464446652210---------------001344624131100043-758896----499
Q gi|254780608|r 247 PHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN---------------FTSPIQNKLYLHARYMDL-PHPEGG----RLQ 306 (346)
Q Consensus 247 l~TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~~---------------~~~~~~~r~~LHa~~l~f-~hp~~~----~~~ 306 (346)
|+||||||||+||+++|+||+||.+|++..... ..........+|-.+..+ .||.++ .+.
T Consensus 255 PlTGRtHQIRvHlq~lG~PI~gD~~Y~~~~~~~~~P~~g~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 (371)
T KOG1919 255 PLTGRTHQIRVHLQYLGHPIAGDPKYGNHIVWAGLPFTGREGTAKKKSLEEEIQRLIDVHLLENWLGFHPRTGPLIEELC 334 (371)
T ss_pred CCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHH
T ss_conf 26796799999999719985788556664444558878988876666831001455422213434565666563145555
Q ss_pred EECCCC--HHHHHHHHHHCCCCC
Q ss_conf 983997--899999998089875
Q gi|254780608|r 307 ITAPLP--AHMVKTWDSLGFKYD 327 (346)
Q Consensus 307 ~~aplP--~~f~~~l~~l~~~~d 327 (346)
.+++.| .||..++-.+-.+..
T Consensus 335 ~~C~~~~~~Dl~~~lha~~y~~~ 357 (371)
T KOG1919 335 QECKVPIDNDLELFLHALKYEMK 357 (371)
T ss_pred HHCCCCCCCHHHHHHHHCCCCCC
T ss_conf 21799987327676421662467
No 11
>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=100.00 E-value=0 Score=325.03 Aligned_cols=182 Identities=36% Similarity=0.557 Sum_probs=148.6
Q ss_pred EEEECCCCCCEEECCCCCCCC-CCCCHH--HCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCC
Q ss_conf 688417653112235785332-332011--01111100133354453422240462123101222102333322111200
Q gi|254780608|r 108 IYVFNKPAGISVQGGSGIAYH-IDGFLK--SWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184 (346)
Q Consensus 108 livinKPaGl~vhp~~g~~~~-~~~~l~--~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~ 184 (346)
++|||||+|++|||+.+.... +...+. .........+++|||||++|||||++|||+++++.|+.+|+++.+.|+|+
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 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHCCC
Q ss_conf 01345654100000001223465543211133555555530343010134320244204578612378999999996398
Q gi|254780608|r 185 SLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGC 264 (346)
Q Consensus 185 Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~g~ 264 (346)
|+|.|.+....+.+..++....... .......++++.|+|+|++++..+ .+||++|+|.||||||||+||+++||
T Consensus 81 a~~~g~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~k~a~t~~~~l~~~~-~~slv~~~~~TGR~HQIR~hla~lg~ 155 (185)
T cd02869 81 ALVDGKPPEDEGTIDAPLGRKKRKK----RARVVVSEDGKPAITHYKVLERFG-NVTLVELQLETGRTHQIRVHLASIGH 155 (185)
T ss_pred EEECCCCCCCCCEEECCEEECCCCC----CEEEEECCCCCEEEEEHHHHHHCC-CEEEEEEECCCCCHHHHHHHHHHCCC
T ss_conf 9966765657656822144156667----138985699847620013455379-86999988165877999999998799
Q ss_pred CEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEE
Q ss_conf 000464446652210001344624131100043
Q gi|254780608|r 265 PIVGDHKYCANFKGNFTSPIQNKLYLHARYMDL 297 (346)
Q Consensus 265 PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f 297 (346)
||+||.+||+..... ....|++||||+|.|
T Consensus 156 PIvGD~~Yg~~~~~~---~~~~r~~LHA~~l~f 185 (185)
T cd02869 156 PIVGDPKYGGKASDS---PGLKRLALHAYRLSF 185 (185)
T ss_pred CEECCCCCCCCCCCC---CCCCCHHHCCCCCCC
T ss_conf 674863569853347---899667334787879
No 12
>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=100.00 E-value=0 Score=309.49 Aligned_cols=198 Identities=30% Similarity=0.409 Sum_probs=162.1
Q ss_pred CEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCC
Q ss_conf 30786178568841765311223578533233201101111100133354453422240462123101222102333322
Q gi|254780608|r 99 SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR 178 (346)
Q Consensus 99 ~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~ 178 (346)
++|||.-.|||+||||.|+.||-.+|..- +...++.. ....+..+||||||-|||+||+|+|.++|+.|+.+|..++
T Consensus 2 ~eilf~H~DF~~INK~~giSVHkD~getg-L~~~vA~Q--lgv~~vwLvHRLDK~TSGiLllAlNaesAselS~~Fa~~k 78 (222)
T TIGR01621 2 LEILFRHSDFVLINKSEGISVHKDDGETG-LLREVAKQ--LGVEKVWLVHRLDKVTSGILLLALNAESASELSRLFAKKK 78 (222)
T ss_pred CEEEEECCCEEEEECCCCEEEEECCCCHH-HHHHHHHH--HCCCCEEEEEECCHHHHHHHHHHHCHHHHHHHHHHHHCCE
T ss_conf 05775368678986799832772571113-89999998--1898089987000344689998604789999987652170
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHH
Q ss_conf 11120001345654100000001223465543211133555555530343010134320244204578612378999999
Q gi|254780608|r 179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVH 258 (346)
Q Consensus 179 v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvh 258 (346)
|+|+|+||-.-.|+...|.|.+.+.+. |.-+|....+. -.+|+|+|.-+.... +.=|--|+|+||+||||||-
T Consensus 79 i~KtYLAls~~KPkKKQGlI~GdMeks----R~g~WKL~~~~--eNpAiTrF~S~s~a~-~lRLFilkPhTGKTHQlRVA 151 (222)
T TIGR01621 79 IKKTYLALSDKKPKKKQGLIIGDMEKS----RRGAWKLVRSK--ENPAITRFESVSIAE-KLRLFILKPHTGKTHQLRVA 151 (222)
T ss_pred EEEEEEECCCCCCCCCCCEEECCHHHH----HCCCCHHCCCC--CCCEECCEEEEEECC-CCCEEEECCCCCCHHHHHHH
T ss_conf 666776313689874442025571242----00010002789--896011124565238-88637556899963788788
Q ss_pred HHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCEEEEECCCCH
Q ss_conf 9963980004644466522100013446241311000437588964999839978
Q gi|254780608|r 259 ALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA 313 (346)
Q Consensus 259 l~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~~~~~aplP~ 313 (346)
|.++|.|||||.+||.+... ..|++|||+.|+|.+ .++-+.+.|++-.
T Consensus 152 mKSlGSpIlGD~lYg~n~~e------sdr~yLhA~~l~FdY-~n~~i~~~c~p~q 199 (222)
T TIGR01621 152 MKSLGSPILGDSLYGKNADE------SDRTYLHAFKLRFDY-QNEVIEVVCDPKQ 199 (222)
T ss_pred HHHCCCCCCCCCCCCCCCCH------HHHHHHHHHHHHHHC-CCCEEEEEECCCC
T ss_conf 87727630056767886421------332422222100100-4758899865424
No 13
>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=100.00 E-value=2.1e-38 Score=262.24 Aligned_cols=151 Identities=26% Similarity=0.374 Sum_probs=118.3
Q ss_pred EEEECCCCCCEEECCCCCCCC-CCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 688417653112235785332-3320110111110013335445342224046212310122210233332211120001
Q gi|254780608|r 108 IYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186 (346)
Q Consensus 108 livinKPaGl~vhp~~g~~~~-~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Ai 186 (346)
|||||||+|++|||+.+.... +.+++. ...+.++++|||||++||||||||||.++++.|+++ .+.+.|+|+|+
T Consensus 1 iivvnKP~G~~~~~~~~~~~~~~~~~l~---~~~~~~l~~vhRLDr~TSGlll~ak~~~~~~~l~~~--~~~v~K~Y~a~ 75 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLD---KLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEP--RREIEKEYLVT 75 (154)
T ss_pred CEEEECCCCCEEECCCCCCCCCHHHHHH---HHCCCCEEEECCCCCCCCCCEEECCCHHHHHHHHHH--HCCCCEEEEEE
T ss_conf 9999999997185899999970999987---517986137126899997856773798999999850--05650579999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHCCCCE
Q ss_conf 34565410000000122346554321113355555553034301013432024420457861237899999999639800
Q gi|254780608|r 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266 (346)
Q Consensus 187 v~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~g~Pi 266 (346)
|.|.++.. +.......... .......++++.|.|.|++++..+ .+|+++|+|.||||||||+||+++||||
T Consensus 76 v~g~~~~~-~~~~~~~~~~~-------~~~~~~~~~~~~~~t~~~~~~~~~-~~slv~~~l~TGR~HQIR~hl~~~G~PI 146 (154)
T cd02550 76 VRGELDEE-GIEDLATVRRG-------RLSGLVDEGVPLAVTKVRVIGEHG-GTGRLRLTLKTGRTHQIRRHCAAVGFPV 146 (154)
T ss_pred EEEECCHH-HHEECCCCCCC-------CCEEEECCCCEECCCEEEEECCCC-CCEEEEEEECCCCCHHHHHHHHHCCCEE
T ss_conf 98727858-82444456424-------551266599620432889931479-9489999979886699999999869939
Q ss_pred ECCCCC
Q ss_conf 046444
Q gi|254780608|r 267 VGDHKY 272 (346)
Q Consensus 267 vGD~~Y 272 (346)
+||.+|
T Consensus 147 l~l~R~ 152 (154)
T cd02550 147 LRLHRV 152 (154)
T ss_pred EEEEEE
T ss_conf 568998
No 14
>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=100.00 E-value=3.2e-38 Score=261.04 Aligned_cols=149 Identities=28% Similarity=0.343 Sum_probs=116.7
Q ss_pred EEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf 68841765311223578533233201101111100133354453422240462123101222102333322111200013
Q gi|254780608|r 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187 (346)
Q Consensus 108 livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Aiv 187 (346)
|||||||+|++|||+.+..................++++|||||++||||||||||.++++.|+++|+++.|.|+|+|+|
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 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH--CCCCEEEEEECHHHHHHHHHHHHH
Q ss_conf 45654100000001223465543211133555555530343010134320--244204578612378999999996
Q gi|254780608|r 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA--QKFCWLEMQPHTGRTHQLRVHALH 261 (346)
Q Consensus 188 ~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~--~~~slv~~~l~TGR~HQIRvhl~~ 261 (346)
.|.+ ...+.+..++........ .......+++.|.|.|++++... ..+|||+|+|.||||||||+|||+
T Consensus 81 ~g~~-~~~~~~~~~~~~~~~~~~----~~~~~~~~~k~a~t~~~~l~~~~~~~~~slv~~~l~TGR~HQIRvhlas 151 (151)
T pfam00849 81 DGPE-EEEGTIKAPIKKDKNKVP----RRKKEELDGKKAVTHLRVLRSGSKIEDVSLVELELVTGRKHQIRAHLAA 151 (151)
T ss_pred ECCC-CCCCEEEEECCCCCCCCE----EEEEECCCCCCCCEEEEEEEECCCCCCEEEEEEEECCCHHHHHHHHHCC
T ss_conf 6777-877089810113677772----7987569984242599998872568996999999672837999998669
No 15
>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=99.97 E-value=9.7e-32 Score=220.19 Aligned_cols=142 Identities=24% Similarity=0.319 Sum_probs=109.4
Q ss_pred EEEECCCCCCEEECCCCCC-CCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 6884176531122357853-323320110111110013335445342224046212310122210233332211120001
Q gi|254780608|r 108 IYVFNKPAGISVQGGSGIA-YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186 (346)
Q Consensus 108 livinKPaGl~vhp~~g~~-~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Ai 186 (346)
++++|||+|+.|+++.+.. .++.+++. ....+.++|||||++||||||||++.+.+..|.. ..+.++|+|+|+
T Consensus 1 yi~lnKP~G~~~~~~~~~~~~tv~~ll~----~~~~~l~~V~RLD~~TsGLll~t~d~~~~~~l~~--~~~~i~K~Y~a~ 74 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLK----DVGERLFPVGRLDYDTEGLLLLTNDGELANRLTH--PRYGVEKTYLVK 74 (146)
T ss_pred CEEEECCCCCEECCCCCCCCCCHHHHHH----HCCCCEEECCCCCCCCCCEEEEECCHHHHHHHHC--CCCCCCEEEEEE
T ss_conf 9899999982861669989985789543----0578672266689778765999579899998754--035424699999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHCCCCE
Q ss_conf 34565410000000122346554321113355555553034301013432024420457861237899999999639800
Q gi|254780608|r 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266 (346)
Q Consensus 187 v~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~g~Pi 266 (346)
|.|.+.+... ... + . ....++++.+.+++++++..+ ..|++++.|.|||+||||+||+++||||
T Consensus 75 v~g~~~~~~~--~~~--~---------~--g~~~~~~~~~~~~~~~~~~~~-~~s~l~v~l~tGR~hQIR~h~~~lg~pI 138 (146)
T cd02870 75 VRGVPSEEEL--RRL--R---------A--GVELDDGKTAPAKVKVLSRDP-KNTLLEVTLHEGRNRQVRRMFEAVGHPV 138 (146)
T ss_pred EECCCCHHHH--HHH--H---------C--CEECCCCEEEEEEEEEECCCC-CCEEEEEEECCCCHHHHHHHHHHCCCEE
T ss_conf 9026999999--998--6---------6--645589887214899823789-9599999978994399999999849979
Q ss_pred ECCCC
Q ss_conf 04644
Q gi|254780608|r 267 VGDHK 271 (346)
Q Consensus 267 vGD~~ 271 (346)
+....
T Consensus 139 ~~L~R 143 (146)
T cd02870 139 LRLKR 143 (146)
T ss_pred EEEEE
T ss_conf 67999
No 16
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=4.7e-25 Score=178.02 Aligned_cols=208 Identities=18% Similarity=0.236 Sum_probs=140.9
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCC-EEEEECCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 68668999998767889899999998499038878845-112117998-8999356554222332222345543343222
Q gi|254780608|r 17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQ-VVRIPPVINALNHIIKEQKILDSSVNLTKHS 94 (346)
Q Consensus 17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD-~I~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (346)
..|||++||++. +..||+.++++|++|+|+|||+.++ ....+..++ .|.+...
T Consensus 1 ~~~RL~K~La~~-G~~SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~------------------------ 55 (248)
T COG1187 1 DSMRLNKFLAEA-GVGSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGK------------------------ 55 (248)
T ss_pred CCCCHHHHHHHC-CCCCHHHHHHHHHCCCEEECCEEECCCCEEECCCCCEEEECCE------------------------
T ss_conf 952068999874-7778899999997398788999922477672798768998998------------------------
Q ss_pred CCCCCEEEE-ECCCEEEECCCCCCEEECC-CCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCC
Q ss_conf 345430786-1785688417653112235-78533233201101111100133354453422240462123101222102
Q gi|254780608|r 95 DFLKSILLY-EDSKIYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTE 172 (346)
Q Consensus 95 ~~~~~~Iiy-ED~~livinKPaGl~vhp~-~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~ 172 (346)
.+.+ +..-++++|||.|+.|.-. +....++.+++... -....+..+|.|||++|||+||+.-+...+..|..
T Consensus 56 -----~~~~~~~~~y~llnKP~G~v~s~~D~~gr~tv~D~lp~~-~~~~~~~~pvGRLD~dTeGLLLLTnDG~la~rL~~ 129 (248)
T COG1187 56 -----RIELKEERVYLLLNKPRGYVSSTEDDEGRPTVFDLLPER-LPRKKRLFPVGRLDKDTEGLLLLTNDGELAHRLMH 129 (248)
T ss_pred -----EEECCCCCEEEEEECCCCEEECCCCCCCCCEEEEECCCC-CCCCCCEEECCCCCCCCEEEEEEECCHHHHHHHCC
T ss_conf -----811266646999989987692666889981600025543-46666333426657777127999578789887528
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHC-CCCEEEEEECHHH
Q ss_conf 333322111200013456541000000012234655432111335555555303430101343202-4420457861237
Q gi|254780608|r 173 SFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQ-KFCWLEMQPHTGR 251 (346)
Q Consensus 173 ~f~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~-~~slv~~~l~TGR 251 (346)
-...+.|+|+|-|.|.+.+.. ++..- . .+.-.....+.|.- .. +..... ..|.+++.+..||
T Consensus 130 --P~~~~~K~Y~v~v~g~~~~~~--l~~l~-~----------Gv~l~d~~~~~~~~-~~-l~~~~~~~~s~~~itl~EGr 192 (248)
T COG1187 130 --PSSEVEKEYLVRVEGPVTEED--LEKLR-K----------GVTLDDGETKPAKP-AS-LEKEPGKNNSWLRITLTEGR 192 (248)
T ss_pred --CCCCCCEEEEEEEECCCCHHH--HHHHH-C----------CCEECCCCCCCCEE-EE-EEECCCCCCEEEEEEEECCC
T ss_conf --888997799999925899899--99985-7----------83866735660104-78-98317887469999995784
Q ss_pred HHHHHHHHHHCCCCEECCCCC
Q ss_conf 899999999639800046444
Q gi|254780608|r 252 THQLRVHALHMGCPIVGDHKY 272 (346)
Q Consensus 252 ~HQIRvhl~~~g~PivGD~~Y 272 (346)
.||||.++++.|+|++.=..+
T Consensus 193 nrQVRRm~~a~G~~V~~L~R~ 213 (248)
T COG1187 193 NRQVRRMFEAVGLEVLRLKRI 213 (248)
T ss_pred CHHHHHHHHHCCCEEEEEEEE
T ss_conf 789999999849967489999
No 17
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.93 E-value=8.4e-25 Score=176.44 Aligned_cols=201 Identities=17% Similarity=0.220 Sum_probs=140.4
Q ss_pred HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 36866899999876788989999999849903887884511211799889993565542223322223455433432223
Q gi|254780608|r 16 EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95 (346)
Q Consensus 16 ~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 95 (346)
+.+.||++||++. ...||+.+.+||++|+|+|||+.++..+.|..+|.|.+..... .+.
T Consensus 4 ~~~~RL~K~LA~~-G~~SRReAe~lI~~GrV~VNGk~v~~g~~V~~~D~V~vdg~~i------------~~~-------- 62 (290)
T PRK10475 4 DSSTRLNKYISES-GICSRREADRYIEQGNVFINGKRATIGDQVKPGDVVKVNGQLI------------EPR-------- 62 (290)
T ss_pred CCCCHHHHHHHHC-CCCHHHHHHHHHHCCCEEECCEECCCCCCCCCCCEEEECCEEC------------CCC--------
T ss_conf 8861499999877-7835999999998597898999957988869999899999891------------233--------
Q ss_pred CCCCEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCC
Q ss_conf 45430786178568841765311223578533233201101111100133354453422240462123101222102333
Q gi|254780608|r 96 FLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR 175 (346)
Q Consensus 96 ~~~~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~ 175 (346)
-.++--+|++|||.|+.|....+....+.+++.. ..+..+|.|||++|+|||||.-+...+..|.. -
T Consensus 63 ------~~~~~~yi~lnKP~G~v~t~~d~~r~ti~d~l~~-----~~rl~pVGRLD~dSeGLLlLTNDG~l~~~l~h--P 129 (290)
T PRK10475 63 ------EAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNH-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILR--A 129 (290)
T ss_pred ------CCCCEEEEEEECCCCCCCCCCCCCCCCEEECCCC-----CCCEEECCCCCCCCCCEEEECCCHHHHHHHHC--C
T ss_conf ------6676399999589870677766789864641477-----56350504668777675998598799998735--7
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHH
Q ss_conf 32211120001345654100000001223465543211133555555530343010134320244204578612378999
Q gi|254780608|r 176 MRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQL 255 (346)
Q Consensus 176 ~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQI 255 (346)
...+.|+|++.|.|.+.+.. +.. +..- -. -.++......+ ...+ -+.+++.+..||.|||
T Consensus 130 ~~~i~K~Y~V~v~g~i~~~~--l~~-l~~G-----v~-------i~g~~~~~~~v---~~~~--~~~~~i~L~EGknRqI 189 (290)
T PRK10475 130 GNDHEKEYLVTVDKPITDEF--IRG-MGAG-----VP-------ILGTVTKKCKV---KKEA--PFVFRITLVQGLNRQI 189 (290)
T ss_pred CCCCCEEEEEEECCCCCHHH--HHH-HHCC-----CE-------ECCEECCEEEE---EECC--CCEEEEEEECCCCHHH
T ss_conf 67895599999898589999--999-8589-----65-------68886011499---9648--9789999986804999
Q ss_pred HHHHHHCCCCEECCC
Q ss_conf 999996398000464
Q gi|254780608|r 256 RVHALHMGCPIVGDH 270 (346)
Q Consensus 256 Rvhl~~~g~PivGD~ 270 (346)
|.+|+++|++++-=.
T Consensus 190 RRm~~~~g~~V~~L~ 204 (290)
T PRK10475 190 RRMCEHFGYEVTKLE 204 (290)
T ss_pred HHHHHHCCCEEEEEE
T ss_conf 999998599781789
No 18
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=99.91 E-value=5.6e-24 Score=171.26 Aligned_cols=208 Identities=19% Similarity=0.283 Sum_probs=135.7
Q ss_pred CCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCC--CCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 8668999998767889899999998499038878845112117--99889993565542223322223455433432223
Q gi|254780608|r 18 NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQ--SGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSD 95 (346)
Q Consensus 18 g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~--~GD~I~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 95 (346)
.+||++||+.. ...||+.++++|++|+|+|||+.++..+++. .+|.|.+....... ....
T Consensus 2 ~eRL~K~LA~~-G~~SRReae~lI~~GrV~VNG~v~~lg~~v~~~~~~~V~vDG~~i~~----------------~~~~- 63 (291)
T PRK10700 2 SEKLQKVLARA-GHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISV----------------KESA- 63 (291)
T ss_pred HHHHHHHHHHC-CCCHHHHHHHHHHCCEEEECCEECCCCCEECCCCCCEEEECCEEEEC----------------CCCC-
T ss_conf 17999999987-89439999999986949989999556882658999889999999432----------------4554-
Q ss_pred CCCCEEEEECCCEEEECCCCCCEEECCC-CCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCC
Q ss_conf 4543078617856884176531122357-853323320110111110013335445342224046212310122210233
Q gi|254780608|r 96 FLKSILLYEDSKIYVFNKPAGISVQGGS-GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF 174 (346)
Q Consensus 96 ~~~~~IiyED~~livinKPaGl~vhp~~-g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f 174 (346)
..+| .++++|||.|..|.... ....++.+++.. ..+.+..+|.|||++|||||||.-+.+.+..|..
T Consensus 64 ----~~~~---~~l~l~KP~G~v~T~~D~~~r~tV~dllp~---~~~~rl~~VGRLD~dT~GLLLlTNDG~La~rL~h-- 131 (291)
T PRK10700 64 ----EQIC---RVLAYYKPEGELCTRNDPEGRPTVFDRLPK---LRGARWIAVGRLDVNTCGLLLFTTDGELANRLMH-- 131 (291)
T ss_pred ----CCCE---EEEEEECCCEEECCCCCCCCCCCHHHHCCC---CCCCCEEEECCCCCCCCCCEEECCCHHHHHHHCC--
T ss_conf ----4301---468998785775466775579837784632---2366455630578888772898387799986248--
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHH
Q ss_conf 33221112000134565410000000122346554321113355555553034301013432024420457861237899
Q gi|254780608|r 175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ 254 (346)
Q Consensus 175 ~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQ 254 (346)
-...+.|+|.+.|.|.+.... +... .+ + +. -.++............ ....+.+++.+..||.||
T Consensus 132 P~~~v~K~Y~V~v~g~i~~~~--l~~l-~~-----G--v~-----ledg~~~~~~i~~~~~-~~~~~~~~i~L~EGrnrq 195 (291)
T PRK10700 132 PSREVEREYAVRVFGQVDDAK--LRDL-SR-----G--VQ-----LEDGPAAFKTIKFSGG-EGINQWYNVTLTEGRNRE 195 (291)
T ss_pred CCCCCCEEEEEEECCCCCHHH--HHHH-HC-----C--CE-----ECCCEEEEEEEEEECC-CCCCEEEEEEEEECCCHH
T ss_conf 867987799999888799999--9999-76-----9--77-----6780146799988447-788579999999696889
Q ss_pred HHHHHHHCCCCEECCCC
Q ss_conf 99999963980004644
Q gi|254780608|r 255 LRVHALHMGCPIVGDHK 271 (346)
Q Consensus 255 IRvhl~~~g~PivGD~~ 271 (346)
||.+|+++|++++.=..
T Consensus 196 IRRMf~~~G~~V~~LkR 212 (291)
T PRK10700 196 VRRLWEAVGVQVSRLIR 212 (291)
T ss_pred HHHHHHHCCCEEEEEEE
T ss_conf 99999985997918899
No 19
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=99.91 E-value=9.6e-24 Score=169.77 Aligned_cols=201 Identities=19% Similarity=0.266 Sum_probs=134.5
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 668999998767889899999998499038878845-1121179988999356554222332222345543343222345
Q gi|254780608|r 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97 (346)
Q Consensus 19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 97 (346)
|||++||++.- ..||+.+.++|++|+|+|||+.++ ++++|..+|.|.+..... .
T Consensus 1 mRL~K~La~~g-~~SRR~ae~lI~~GrV~VNg~~v~~~~~~V~~~~~v~vdg~~i------------~------------ 55 (231)
T PRK10839 1 MRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVKNAAFKLLPEHDVAYDGNPL------------A------------ 55 (231)
T ss_pred CCHHHHHHHCC-CCCHHHHHHHHHCCEEEECCEEECCCCEECCCCCEEEECCCEE------------C------------
T ss_conf 93789998878-9569999999987979999999145880849998699919586------------1------------
Q ss_pred CCEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCC
Q ss_conf 43078617856884176531122357853323320110111110013335445342224046212310122210233332
Q gi|254780608|r 98 KSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR 177 (346)
Q Consensus 98 ~~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~ 177 (346)
-.+..-++++|||.|..|.........+..++. .....+..+|.|||++|+|++|++-+...+..|.. ...
T Consensus 56 ----~~~~~~y~~lnKP~G~v~s~~d~~~~~~~~~l~---~~~~~~l~~vGRLD~ds~GLlllTnDg~l~~~l~~--P~~ 126 (231)
T PRK10839 56 ----QQHGPRYFMLNKPQGYVCSTDDPDHPTVLYFLD---EPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITS--PRH 126 (231)
T ss_pred ----CCCCCEEEEEECCCCCCCCCCCCCCCCEEEECC---CCCCCCEEEEECCCCCCCCEEEECCCHHHHHHCCC--CCC
T ss_conf ----466868999989987534788999972698637---65556357700468898776997688899953518--768
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHH
Q ss_conf 21112000134565410000000122346554321113355555553034301013432024420457861237899999
Q gi|254780608|r 178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV 257 (346)
Q Consensus 178 ~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRv 257 (346)
.+.|+|++.+.|.+.+.. +.... + + +.. .....-.+.|. ++.+ . . +.+++.+..||.||||.
T Consensus 127 ~i~k~Y~V~v~~~i~~~~--l~~l~-~-----G--v~i-~~~~~~~~~~~--v~~~---~-~-~~~~i~l~eGk~rqIRr 188 (231)
T PRK10839 127 HCEKTYLVTLESPVADDT--AEQFA-K-----G--VQL-HNEKDLTKPAV--LEVI---T-P-TQVRLTISEGRYHQVKR 188 (231)
T ss_pred CCCEEEEEEECCCCCHHH--HHHHH-C-----C--CEE-CCEECCEEEEE--EEEC---C-C-CEEEEEEECCCCHHHHH
T ss_conf 997899999898799999--99996-7-----9--698-78231160369--9984---8-9-69999996687679999
Q ss_pred HHHHCCCCEECCCC
Q ss_conf 99963980004644
Q gi|254780608|r 258 HALHMGCPIVGDHK 271 (346)
Q Consensus 258 hl~~~g~PivGD~~ 271 (346)
+|+++|++++-=.+
T Consensus 189 mf~~~g~~V~~L~R 202 (231)
T PRK10839 189 MFAAVGNRVVELHR 202 (231)
T ss_pred HHHHCCCEEEEEEE
T ss_conf 99985998989999
No 20
>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=99.79 E-value=2e-19 Score=142.60 Aligned_cols=153 Identities=18% Similarity=0.291 Sum_probs=93.8
Q ss_pred EEEECCCCCCEEECCC--CCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 6884176531122357--85332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 108 IYVFNKPAGISVQGGS--GIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 108 livinKPaGl~vhp~~--g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
+|++|||.|..|.... .....+.+++. ..+.++|+|||++|||+|||+.+.+.+..|.. ....+.|+|+|
T Consensus 1 ~i~lnKP~G~v~t~~d~~~~~~~v~d~~~------~~~l~~VGRLD~ds~GLLLlTnDG~l~~~L~h--P~~~i~K~Y~v 72 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYID------DPGVYAAGRLDRDSEGLLLLTDDGRLQHRITD--PSFKHPKTYYV 72 (168)
T ss_pred CEEEECCCCEEECCCCCCCCCCEEHHHCC------CCCEEECCCCCCCCCCEEEEECCHHHHHHHHC--CCCCCCEEEEE
T ss_conf 98998999979796688899978244078------88817842667898875998296999998737--76799779999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHC
Q ss_conf 1345654100000001223465543211133---5555555303430101343202442045786123789999999963
Q gi|254780608|r 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVV---KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262 (346)
Q Consensus 186 iv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~---~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~ 262 (346)
.|.|.+.+.. +.. +.+--...+...... ..+..............+. ....|++++.+.+||+||||.+|+++
T Consensus 73 ~v~g~~~~~~--l~~-l~~Gv~i~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~-~~~~s~~~i~l~eGknrqIRrm~~~~ 148 (168)
T cd02566 73 QVEGVPTEDA--LEQ-LRNGVELGDGLTLPAKVEKVDEPPWLWEREPPIRFRK-NIPTSWIEITICEGKNRQVRRMTAAV 148 (168)
T ss_pred EECCCCCHHH--HHH-HHCCCEECCEEEEEEEEEEECCCCCCCCCCCCCEEEC-CCCCEEEEEEEEECCHHHHHHHHHHC
T ss_conf 9866799999--999-8779697987864459999426544321256613201-47834899999617219999999985
Q ss_pred CCCEECCCCC
Q ss_conf 9800046444
Q gi|254780608|r 263 GCPIVGDHKY 272 (346)
Q Consensus 263 g~PivGD~~Y 272 (346)
|+|+..=.+.
T Consensus 149 g~~V~~L~Rv 158 (168)
T cd02566 149 GFPTLRLIRV 158 (168)
T ss_pred CCEEEEEEEE
T ss_conf 9969589999
No 21
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.62 E-value=1e-15 Score=119.18 Aligned_cols=153 Identities=22% Similarity=0.290 Sum_probs=92.6
Q ss_pred CEEEECCCCCCEEECCCC-CCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 568841765311223578-5332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 107 KIYVFNKPAGISVQGGSG-IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 107 ~livinKPaGl~vhp~~g-~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
-++++|||.|..|..... ...++.+++. ..+.++|.|||++|+|+||+.-+.+.+..|.. -...+.|+|.+
T Consensus 30 r~illnKP~G~i~T~~D~~gR~tV~dllp------~~~l~pVGRLD~dSeGLLLlTNDG~la~~L~h--P~~~i~K~Y~V 101 (207)
T PRK11394 30 RVILFNKPYDVLPQFTDEAGRKTLKEFIP------VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQ--PGKRTGKIYYV 101 (207)
T ss_pred EEEEEECCCCEEECCCCCCCCCCHHHHCC------CCCCEECCCCCCCCCCEEEECCCHHHHHHHHC--CCCCCCEEEEE
T ss_conf 89999899985868889999976789688------56745777767898772998087899987525--65797789999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE---EECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHC
Q ss_conf 134565410000000122346554321113355555553034---30101343202442045786123789999999963
Q gi|254780608|r 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAI---SHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262 (346)
Q Consensus 186 iv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~---T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~ 262 (346)
.|.|.+.... +... ..--..+..........- -...+. ..-.+.+.-....|++++.+..||.||||..|+++
T Consensus 102 ~v~g~~~~~~--l~~l-~~Gv~i~dg~~~p~~~~~-v~~~~~~~~~~~~~~~~~~~~~s~l~i~L~EGKnRqIRRmf~~~ 177 (207)
T PRK11394 102 QVEGIPTQDA--LEAL-RNGVTLNDGPTLPAGAEL-VDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHV 177 (207)
T ss_pred EECCCCCHHH--HHHH-HCCCEECCEEEEEEEEEE-ECCCCCCCCCCCCHHHCCCCCCCEEEEEEEECCCHHHHHHHHHC
T ss_conf 9916899999--9999-779785984764548999-44742123457641110257865799999746359999999986
Q ss_pred CCCEECCCC
Q ss_conf 980004644
Q gi|254780608|r 263 GCPIVGDHK 271 (346)
Q Consensus 263 g~PivGD~~ 271 (346)
|++++-=..
T Consensus 178 G~~V~~L~R 186 (207)
T PRK11394 178 GFPTLRLIR 186 (207)
T ss_pred CCEEEEEEE
T ss_conf 997938999
No 22
>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=99.61 E-value=1.5e-15 Score=118.16 Aligned_cols=140 Identities=19% Similarity=0.263 Sum_probs=91.5
Q ss_pred EEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf 68841765311223578533233201101111100133354453422240462123101222102333322111200013
Q gi|254780608|r 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187 (346)
Q Consensus 108 livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Aiv 187 (346)
++++|||.|..|.-......++.+++.... ...+..+|+|||++|||++||+-+.+.+..|.. ....+.|+|++.+
T Consensus 2 YillnKP~G~v~t~~d~~~ktv~dll~~~~--~~~~l~~vGRLD~~s~GLLLlTNDG~l~~~l~h--P~~~i~K~Y~V~v 77 (167)
T cd02553 2 YLMLNKPAGVVCATKDPHHPTVIDLLPEPD--RRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTS--PKKHVPKTYEVTL 77 (167)
T ss_pred EEEEECCCCEEECCCCCCCCCHHHHCCCCC--CCCCEEECCCCCCCCCCEEEECCCHHHHHHHHC--CCCCCCEEEEEEE
T ss_conf 999988999796988999997744335500--367556744568997622999188889976414--4478888999987
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHCCCCE
Q ss_conf 456541000000012234655432111335555555-3034301013432024420457861237899999999639800
Q gi|254780608|r 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA-NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266 (346)
Q Consensus 188 ~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~g~Pi 266 (346)
.|.+.+.. +... .+ . +. -.++ ..+....+.+ ++ +.+++.+..||.||||.+++++|+++
T Consensus 78 ~~~i~~~~--l~~l-~~-G------v~-----i~dg~~~~~~~v~~~---~~--~~~~i~l~eGknrqIRrm~~~~g~~V 137 (167)
T cd02553 78 AGPLTEDD--IEAF-AE-G------VL-----LHDGYPTKPAKLEIL---SP--TTVRLTITEGKYHQVKRMFAAVGNKV 137 (167)
T ss_pred CCCCCHHH--HHHH-HC-C------CE-----ECCCCEEEEEEEEEE---CC--CEEEEEEECCCCHHHHHHHHHCCCEE
T ss_conf 67899999--9999-76-9------89-----649859751799992---58--68999998884629999999869888
Q ss_pred ECCCC
Q ss_conf 04644
Q gi|254780608|r 267 VGDHK 271 (346)
Q Consensus 267 vGD~~ 271 (346)
..=.+
T Consensus 138 ~~L~R 142 (167)
T cd02553 138 VALHR 142 (167)
T ss_pred EEEEE
T ss_conf 58999
No 23
>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=99.60 E-value=1.1e-15 Score=119.08 Aligned_cols=155 Identities=19% Similarity=0.260 Sum_probs=97.3
Q ss_pred CCCCCCEEECCCCCCCC-CCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf 17653112235785332-33201101111100133354453422240462123101222102333322111200013456
Q gi|254780608|r 112 NKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190 (346)
Q Consensus 112 nKPaGl~vhp~~g~~~~-~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Aiv~G~ 190 (346)
|||.|++|.-..+.... +.+.+.... ..+.+.++|.|||++|+|+||++-+.+-+..|.. ..+.++|+|++-|+|.
T Consensus 1 nKP~g~l~~~~Dp~~r~~~~~~l~~~~-~~~~~~~a~GRLD~ds~GLlLLT~~G~L~~RL~~--p~~~~eK~Y~V~v~g~ 77 (185)
T TIGR00093 1 NKPQGVLCTTDDPEGRKTVKDLLPKKL-IRGKRLHAVGRLDRDSEGLLLLTNDGELQHRLTH--PKFHHEKTYLVTVEGP 77 (185)
T ss_pred CCCCCEEECCCCCCCCCEEEECCCHHH-HCCCCEEEEECCCCCCCCEEEECCCHHHHHHHHC--CCCCCCCEEEEEECCC
T ss_conf 998504435849887723500452023-1057467740267456203899069799998717--6435896699995598
Q ss_pred CCCCCC--CCCCCCCCCCCCC--CCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHCCCCE
Q ss_conf 541000--0000122346554--321113355555553034301013432024420457861237899999999639800
Q gi|254780608|r 191 PKNKKE--CIANWLLKKSHIG--GDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266 (346)
Q Consensus 191 ~~~~~~--~i~~~~~~~~~~~--~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~g~Pi 266 (346)
|.++.- .-.+-...+.... ...+..+.+... - .-..-+...+. .-.+|.+++.|..||.||||.++|++|+++
T Consensus 78 v~~~~~~~~~~Gv~L~~~~~~tk~a~~~~~~~~~~-~-~pr~ppir~r~-~i~~S~l~~tl~EGRNRqvRRm~a~~G~~V 154 (185)
T TIGR00093 78 VTDEDLEALRKGVQLEDGKTLTKPAKLKVISEPED-L-WPRNPPIRERK-SIPTSWLRVTLTEGRNRQVRRMFAAVGFPV 154 (185)
T ss_pred CCHHHHHHHHCCCEECCCCCCCCCEEEEEECCCCC-C-CCCCCCEEECC-CCCCCEEEEEEEECCCHHHHHHHHHHCCEE
T ss_conf 58889989871760058735644237787067131-3-56787312003-688225899996087068878889838903
Q ss_pred ECCCCC
Q ss_conf 046444
Q gi|254780608|r 267 VGDHKY 272 (346)
Q Consensus 267 vGD~~Y 272 (346)
+.=..+
T Consensus 155 ~~L~R~ 160 (185)
T TIGR00093 155 LRLHRV 160 (185)
T ss_pred EEEEEE
T ss_conf 478988
No 24
>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=99.59 E-value=4.7e-15 Score=114.99 Aligned_cols=143 Identities=17% Similarity=0.229 Sum_probs=94.8
Q ss_pred EEEECCCCCCEEECC-CCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 688417653112235-7853323320110111110013335445342224046212310122210233332211120001
Q gi|254780608|r 108 IYVFNKPAGISVQGG-SGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186 (346)
Q Consensus 108 livinKPaGl~vhp~-~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Ai 186 (346)
++++|||.|..|.-. +....++.+++.. ....+..+|.|||++|||+||+.-+...+..|.. ....+.|+|++.
T Consensus 2 ~illnKP~G~v~s~~d~~~r~tv~dll~~---~~~~rl~~vGRLD~ds~GLLLlTnDG~l~~~l~h--P~~~i~k~Y~V~ 76 (167)
T cd02556 2 VLIYHKPEGLICTRKDPKGRPTVFDLLPK---LGIPRWISVGRLDLNTEGLLLFTNDGELANRLMH--PSNEIEREYAVR 76 (167)
T ss_pred EEEEECCCCEEECCCCCCCCCCHHHHCCC---CCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHCC--CCCCCCEEEEEE
T ss_conf 89998999989786299889757896553---3555723641389576785999278367576409--877885799999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHCCCCE
Q ss_conf 34565410000000122346554321113355555553034301013432024420457861237899999999639800
Q gi|254780608|r 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI 266 (346)
Q Consensus 187 v~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~g~Pi 266 (346)
+.|.+.... +.. +.+ . + .. .++.........+... ...+.+++.+..||.||||..++++|++|
T Consensus 77 v~~~~~~~~--l~~-l~~-G------v---~i--~~~~~~~~~v~~~~~~-~~~~~~~i~l~eGk~rqIRrmf~~~g~~V 140 (167)
T cd02556 77 VFGQVTDEQ--LKS-LKK-G------V---EL--EDGFAGFKSIQLEGGE-GKNSWYRVTLREGRNREVRRLWEAFGLQV 140 (167)
T ss_pred ECCCCCHHH--HHH-HHC-C------C---EE--CCEEEEEEEEEEECCC-CCCEEEEEEEECCCHHHHHHHHHHCCCEE
T ss_conf 758999999--999-877-9------7---87--9988400699996267-99679999997694689999999869989
Q ss_pred ECCCC
Q ss_conf 04644
Q gi|254780608|r 267 VGDHK 271 (346)
Q Consensus 267 vGD~~ 271 (346)
+.=.+
T Consensus 141 ~~L~R 145 (167)
T cd02556 141 SRLIR 145 (167)
T ss_pred EEEEE
T ss_conf 58999
No 25
>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=99.53 E-value=1.9e-14 Score=111.17 Aligned_cols=142 Identities=16% Similarity=0.148 Sum_probs=87.7
Q ss_pred EEEECCCCCCEEECCCC-----CCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCC
Q ss_conf 68841765311223578-----5332332011011111001333544534222404621231012221023333221112
Q gi|254780608|r 108 IYVFNKPAGISVQGGSG-----IAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI 182 (346)
Q Consensus 108 livinKPaGl~vhp~~g-----~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~ 182 (346)
++++|||+|..|.-... ..................+..+|.|||++|||+||+.-+...+..|.. -...+.|+
T Consensus 6 yllLnKP~G~v~t~~d~~~~~~~~~~~~~~~~~~l~~~~~rl~pVGRLD~~s~GLLllTNDG~l~~~l~~--P~~~i~k~ 83 (177)
T cd02555 6 TLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGHFARLAPIGPLDKDASGLLVFSQDGRVLRKLIG--DASRLEQE 83 (177)
T ss_pred EEEEECCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCEEEEEECCHHHHHHHCC--CCCCCCEE
T ss_conf 9999899848707757667875013334541000102236621604789998118999188899987549--86689789
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHC
Q ss_conf 00013456541000000012234655432111335555555303430101343202442045786123789999999963
Q gi|254780608|r 183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM 262 (346)
Q Consensus 183 Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~ 262 (346)
|++.|.|.+.... +.. +.+- + ..+....+.+. .... + -+.+++.+..||.||||..|+++
T Consensus 84 Y~V~v~~~~~~~~--l~~-l~~G-------v---~l~g~~~~~~~--v~~~---~--~~~~~i~l~eGknrqIRrm~~~~ 143 (177)
T cd02555 84 YLVEVRGELTAGG--LER-LNHG-------L---TYDGRELPPAK--VSWQ---N--EQRLRFALKEPQPGQIRRMCESV 143 (177)
T ss_pred EEEEECCCCCHHH--HHH-HHCC-------E---EECCEEECCEE--EEEE---C--CCEEEEEEECCCCHHHHHHHHHC
T ss_conf 9999898799999--987-5287-------6---78998967869--9995---7--99599999918416999999987
Q ss_pred CCCEECCCC
Q ss_conf 980004644
Q gi|254780608|r 263 GCPIVGDHK 271 (346)
Q Consensus 263 g~PivGD~~ 271 (346)
|+++..=..
T Consensus 144 g~~V~~L~R 152 (177)
T cd02555 144 GLEVVALRR 152 (177)
T ss_pred CCEEEEEEE
T ss_conf 997989999
No 26
>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=99.47 E-value=1e-13 Score=106.58 Aligned_cols=137 Identities=15% Similarity=0.186 Sum_probs=89.6
Q ss_pred EEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf 68841765311223578533233201101111100133354453422240462123101222102333322111200013
Q gi|254780608|r 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187 (346)
Q Consensus 108 livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Aiv 187 (346)
++++|||.|..|.-.+.....+.+.+. ...+..+|+|||++|+|+||+.-+...+..|.. ....+.|+|++.+
T Consensus 2 YillnKP~G~v~s~~~~~~~~~~~~l~-----~~~rl~~vGRLD~~s~GLLLlTNDg~l~~~L~h--P~~~i~k~Y~V~~ 74 (164)
T cd02554 2 YIAYNKPVGIDCTLERADEDNIIDFVN-----PPPRIFPIGRLDKDSEGLILLTNDGDLVNKILH--ADNNHEKEYLVTV 74 (164)
T ss_pred EEEEECCCCEEECCCCCCCCCEEEECC-----CCCCEEECCCCCCCCCCEEEEECCHHHHHHHCC--CCCCCCCEEEEEE
T ss_conf 999989998283878999996699748-----867778886789998565999578899976219--9888962999999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHCCCCEE
Q ss_conf 45654100000001223465543211133555555530343010134320244204578612378999999996398000
Q gi|254780608|r 188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267 (346)
Q Consensus 188 ~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~g~Piv 267 (346)
.|.+.... +.. +.. . -.. .++.......+.+ .+ ..+++.+..|+.||||..++++|+++.
T Consensus 75 ~~~i~~~~--l~~-l~~-G----i~i-------~~~~~~~~~v~~~---~~--~~~~i~l~eGknrqIRrmf~~~g~~V~ 134 (164)
T cd02554 75 NKPITDEF--IEG-MSN-G----VVI-------LGTVTKPCKVERL---AK--DKFRIVLTQGLNRQIRRMCEALGYRVT 134 (164)
T ss_pred CCCCCHHH--HHH-HHC-C----EEE-------CCEEEECEEEEEE---CC--CEEEEEEEECCCHHHHHHHHHCCCEEE
T ss_conf 56699999--998-747-8----598-------9889802199994---79--849999992674899999998699884
Q ss_pred CCCC
Q ss_conf 4644
Q gi|254780608|r 268 GDHK 271 (346)
Q Consensus 268 GD~~ 271 (346)
-=.+
T Consensus 135 ~L~R 138 (164)
T cd02554 135 DLKR 138 (164)
T ss_pred EEEE
T ss_conf 8999
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=98.99 E-value=2.4e-09 Score=78.98 Aligned_cols=69 Identities=26% Similarity=0.376 Sum_probs=59.7
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 66899999876788989999999849903887884-51121179988999356554222332222345543343222345
Q gi|254780608|r 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97 (346)
Q Consensus 19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 97 (346)
+|||+||.+.....||++++++|+.|.|+|||+++ +++++|..||.|.+.......
T Consensus 1 ~RLd~~l~~~~~~~Sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~gd~i~i~~~~~~~----------------------- 57 (70)
T cd00165 1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEE----------------------- 57 (70)
T ss_pred CCHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCCCCEEEECCCCCCC-----------------------
T ss_conf 948899987487158999999998193898999958888898999999987877886-----------------------
Q ss_pred CCEEEEECCCEEEEC
Q ss_conf 430786178568841
Q gi|254780608|r 98 KSILLYEDSKIYVFN 112 (346)
Q Consensus 98 ~~~IiyED~~livin 112 (346)
.++|||+.++++|
T Consensus 58 --~i~~~~~~~~~i~ 70 (70)
T cd00165 58 --DIVYEDKKLLVVN 70 (70)
T ss_pred --CEEEECCCEEEEC
T ss_conf --7323269899969
No 28
>smart00363 S4 S4 RNA-binding domain.
Probab=98.50 E-value=2.9e-07 Score=65.86 Aligned_cols=51 Identities=24% Similarity=0.389 Sum_probs=46.9
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEEC
Q ss_conf 66899999876788989999999849903887884-5112117998899935
Q gi|254780608|r 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69 (346)
Q Consensus 19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~ 69 (346)
+|||.||++.....||++++++|++|.|+|||+++ ++++.|+.||.|.+..
T Consensus 1 ~RLD~~l~~~~~~~Sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I~~~~ 52 (60)
T smart00363 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred CCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCEEEECC
T ss_conf 9788999983870479999999984917989999478988989999999988
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=98.41 E-value=3.6e-07 Score=65.31 Aligned_cols=47 Identities=32% Similarity=0.469 Sum_probs=43.4
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEE
Q ss_conf 668999998767889899999998499038878845-11211799889
Q gi|254780608|r 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV 65 (346)
Q Consensus 19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I 65 (346)
+|||.||.+.....||++++++|+.|.|+|||++++ +++.|+.||.|
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=98.28 E-value=1.1e-06 Score=62.17 Aligned_cols=55 Identities=22% Similarity=0.446 Sum_probs=46.9
Q ss_pred HCCCCHHHHHH-HHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCC
Q ss_conf 36866899999-876788989999999849903887884511211799889993565
Q gi|254780608|r 16 EENMRLDRWFK-NHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71 (346)
Q Consensus 16 ~~g~RLd~~L~-~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~ 71 (346)
..-||||+||. .+| --+|+..+.++..|+|.+||.++|++..|+.||+|+|....
T Consensus 6 ~~~mRLDKwL~~aR~-~KrRslAk~~~~~GrV~vNG~~aKpS~~VK~GD~l~i~~~~ 61 (100)
T COG1188 6 ADRMRLDKWLWAARF-IKRRSLAKEMIEGGRVKVNGQRAKPSKEVKVGDILTIRFGN 61 (100)
T ss_pred CCCEEHHHHHHHHHH-HHHHHHHHHHHHCCEEEECCEECCCCCCCCCCCEEEEEECC
T ss_conf 651656788878877-42289999998779698999675655614779899999578
No 31
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=98.27 E-value=1.1e-06 Score=62.26 Aligned_cols=55 Identities=15% Similarity=0.352 Sum_probs=47.4
Q ss_pred HHHCCCCHHHHH-HHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEEC
Q ss_conf 113686689999-98767889899999998499038878845112117998899935
Q gi|254780608|r 14 NDEENMRLDRWF-KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69 (346)
Q Consensus 14 ~~~~g~RLd~~L-~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~ 69 (346)
+..+.+|||+|| +-+| .-+|+...++|+.|.|+|||.++|++..|+.||+|.|..
T Consensus 4 ~p~~k~RiDkwLW~aRf-fKTRslA~~a~~~G~V~vnG~~~Kps~~V~~GD~l~i~~ 59 (133)
T PRK10348 4 KPAVEVRLDKWLWAARF-YKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQ 59 (133)
T ss_pred CCCCCEEEHHHHHHHEE-HHHHHHHHHHHHCCCEEECCEECCCCCCCCCCCEEEEEE
T ss_conf 87550540200315201-000999999998798898998868888768999999986
No 32
>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=98.14 E-value=5.6e-06 Score=57.75 Aligned_cols=54 Identities=15% Similarity=0.342 Sum_probs=48.0
Q ss_pred HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEECC
Q ss_conf 36866899999876788989999999849903887884-51121179988999356
Q gi|254780608|r 16 EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70 (346)
Q Consensus 16 ~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~~ 70 (346)
.+.+|||..++..| ++||++++.+|++|.|+||++.+ ++++.|+.||+|.+-..
T Consensus 181 vsSlRLDavvs~~~-~~SRska~~lI~~g~V~vN~~~v~~~s~~v~~gDiiSvRG~ 235 (257)
T TIGR03069 181 EASLRIDAIASAGF-GLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRGK 235 (257)
T ss_pred ECCCCHHHHHHHHH-CCCHHHHHHHHHCCEEEECCEEECCCCCCCCCCCEEEEECC
T ss_conf 21213899999886-65799999998849689899990578756689999999067
No 33
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=97.94 E-value=1.8e-05 Score=54.58 Aligned_cols=54 Identities=22% Similarity=0.398 Sum_probs=48.6
Q ss_pred HHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEEC
Q ss_conf 1368668999998767889899999998499038878845-112117998899935
Q gi|254780608|r 15 DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69 (346)
Q Consensus 15 ~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~~ 69 (346)
..+.+|||...+..| ++||++.+++|.+|.|+||.+.+. +++.|+.||.|.+-.
T Consensus 177 ~vsSlRLD~vis~~~-~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG 231 (257)
T COG2302 177 TVSSLRLDVVISEGF-GLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRG 231 (257)
T ss_pred EEEHHHHHHHHHHHH-HHHHHHHHHHHHCCCEEEEEEEECCCCCEECCCCEEEEEC
T ss_conf 421240799999887-6559999998773732771299126663322498999840
No 34
>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=97.81 E-value=1.3e-05 Score=55.48 Aligned_cols=51 Identities=18% Similarity=0.276 Sum_probs=42.7
Q ss_pred CCHHHHHHHHCC-CCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEECC
Q ss_conf 668999998767-889899999998499038878845-1121179988999356
Q gi|254780608|r 19 MRLDRWFKNHYP-HINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70 (346)
Q Consensus 19 ~RLd~~L~~~~~-~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~~~ 70 (346)
+|||+.+=++ + ..+|..+++|+.+|.|.|||++|. ||+.|++||.|.|-..
T Consensus 100 ~RLDNvVYRl-GfA~Tr~~ARQLVsHGhi~vNGk~VdIPSy~v~~Gd~i~ikEk 152 (217)
T TIGR01017 100 SRLDNVVYRL-GFAPTRRAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEK 152 (217)
T ss_pred CCCCCEEECC-CCHHHHHHHHHHHHCCEEEECCEEECCCEEEECCCCEEEEEEC
T ss_conf 1001010212-7120078763564088078798185224067079988998103
No 35
>PRK12565 30S ribosomal protein S4; Provisional
Probab=97.64 E-value=8.2e-05 Score=50.41 Aligned_cols=52 Identities=15% Similarity=0.219 Sum_probs=43.3
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEECC
Q ss_conf 668999998767889899999998499038878845-1121179988999356
Q gi|254780608|r 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70 (346)
Q Consensus 19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~~~ 70 (346)
+|||..+-+.==..|+.++++++..|.|.|||+++. |++.|+.||+|.+.+.
T Consensus 88 ~RLDnvv~R~gfa~t~~~ARQlV~Hghi~vng~kVdIPSy~vk~GDvI~vkek 140 (197)
T PRK12565 88 CRLDNVVYRIGFASSIRQARQMVNHGHILVNGKKVNIPSYEVKVGDEITLREK 140 (197)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCEEECCCCEEEECHH
T ss_conf 86667711344105799986674078889799895588767069999997332
No 36
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=97.56 E-value=5.9e-05 Score=51.32 Aligned_cols=52 Identities=17% Similarity=0.225 Sum_probs=43.5
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEECC
Q ss_conf 668999998767889899999998499038878845-1121179988999356
Q gi|254780608|r 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70 (346)
Q Consensus 19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~~~ 70 (346)
+|||+.+-+.==..|+.++++++.+|.|.|||+++. |++.|++||+|.|.+.
T Consensus 89 ~RLDnvVyRlGfA~Tr~~ARQlV~HgHi~VNgkkVnIPSy~vk~GDvI~v~~k 141 (201)
T CHL00113 89 MRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPRDIITIKDK 141 (201)
T ss_pred HHHHHHHHHCCCCCCHHHHHHEEECCEEEECCEEECCCCEEEECCCEEEECCC
T ss_conf 99999998705405888761058466299899893378758427998997534
No 37
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=97.46 E-value=0.00028 Score=47.06 Aligned_cols=51 Identities=18% Similarity=0.256 Sum_probs=45.9
Q ss_pred CCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEE
Q ss_conf 866899999876788989999999849903887884-511211799889993
Q gi|254780608|r 18 NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68 (346)
Q Consensus 18 g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~ 68 (346)
.||||.+|.++--.-||++++.+|.+|.|.|||.++ ||++.|..++.|++.
T Consensus 2 k~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~ 53 (245)
T COG1189 2 KMRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVK 53 (245)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCCEEEECCEEECCCCEECCCCCEEEEC
T ss_conf 3238999997353320999999987685788999942765245898637875
No 38
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=97.43 E-value=0.00026 Score=47.22 Aligned_cols=51 Identities=18% Similarity=0.197 Sum_probs=42.3
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEEC
Q ss_conf 668999998767889899999998499038878845-112117998899935
Q gi|254780608|r 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69 (346)
Q Consensus 19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~~ 69 (346)
.|||..+-+.-=..|+.++++++.+|.|.|||++|. |++.|+.||+|.|..
T Consensus 94 rRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~ 145 (205)
T COG0522 94 RRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVRE 145 (205)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCEEECCCCEEEEEC
T ss_conf 8878999984041359999988406628999999526737963777887520
No 39
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=97.28 E-value=0.00024 Score=47.50 Aligned_cols=52 Identities=17% Similarity=0.249 Sum_probs=43.3
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEECC
Q ss_conf 668999998767889899999998499038878845-1121179988999356
Q gi|254780608|r 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV 70 (346)
Q Consensus 19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~~~ 70 (346)
+|||..+-+.-=..|+.+.++++..|.|.|||+++. |++.|+.||+|.+.+.
T Consensus 92 ~RLD~vv~r~g~a~t~~~ARQ~v~Hghi~vNg~~v~ips~~~k~gd~i~vkek 144 (201)
T PRK05327 92 RRLDNVVYRLGFAPTRAQARQLVSHGHILVNGKKVNIPSYQVKPGDVIEVREK 144 (201)
T ss_pred HHHHHHHHHHCCCCCHHHHHHEEEEEEEEECCEEECCCCEECCCCCEEEECCC
T ss_conf 99889998714105888862006440599899983578747389999997700
No 40
>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=97.15 E-value=0.00057 Score=45.11 Aligned_cols=51 Identities=20% Similarity=0.223 Sum_probs=45.8
Q ss_pred CHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEECC
Q ss_conf 6899999876788989999999849903887884-51121179988999356
Q gi|254780608|r 20 RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPV 70 (346)
Q Consensus 20 RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~~ 70 (346)
|||..|.++...-||+.++++|++|.|.||++++ ||+..|...+.|.+-..
T Consensus 1 RLD~lLv~rgl~~sR~~Ak~lI~kG~V~VN~~~v~KP~~~v~~~~~i~l~~~ 52 (240)
T TIGR00478 1 RLDILLVKRGLVESREKAKRLILKGEVLVNKKKVDKPSALVDKDAKIELVQN 52 (240)
T ss_pred CCHHHHHHHCHHHHHHHHHHHHHCCCEEECCEEECCCCCEECCCCCEEEECC
T ss_conf 9036776501145789999998739455557652088604416760344147
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=96.80 E-value=0.00036 Score=46.36 Aligned_cols=75 Identities=20% Similarity=0.318 Sum_probs=46.3
Q ss_pred CEEEECCCCCCEEECCCCCCCCCCCCH-HHCCCCCCCCCCCC--CCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCC
Q ss_conf 568841765311223578533233201-10111110013335--445342224046212310122210233332211120
Q gi|254780608|r 107 KIYVFNKPAGISVQGGSGIAYHIDGFL-KSWVDSKGQKPRLT--HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183 (346)
Q Consensus 107 ~livinKPaGl~vhp~~g~~~~~~~~l-~~~~~~~~~~~~lV--HRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y 183 (346)
.+|+||||+|+.+|. +.+.+ ..+........... +-||-..||+|+++-++.+ .+...+......|+|
T Consensus 1 Gil~v~KP~G~TS~~-------vv~~v~~~l~k~~~~~kk~g~~GTLDP~AtGvLvi~vG~aT--Kl~~~l~~~~~~K~Y 71 (226)
T cd02868 1 GLFAVYKPPGVHWKH-------VRDTIESNLLKYFPEDKVLVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYSNHPTRVY 71 (226)
T ss_pred CEEEEECCCCCCHHH-------HHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCEEEEECHHH--HHHHHHHCCCCCEEE
T ss_conf 989997599998999-------99999999976641774696088889756033899988777--256998668997699
Q ss_pred CCCC-CCC
Q ss_conf 0013-456
Q gi|254780608|r 184 WSLV-WGI 190 (346)
Q Consensus 184 ~Aiv-~G~ 190 (346)
.|-+ .|.
T Consensus 72 ~~~~~lG~ 79 (226)
T cd02868 72 TIRGLLGK 79 (226)
T ss_pred EEEEEECC
T ss_conf 99999756
No 42
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=96.43 E-value=0.0022 Score=41.36 Aligned_cols=71 Identities=20% Similarity=0.244 Sum_probs=47.1
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 85688417653112235785332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
+.|++||||.|+.+|- +...++..... .+.+-..=||-..||+|+++-++.+. .|...|. .-.|+|.|
T Consensus 9 ~GillidKP~G~TS~~-------vv~~vkk~l~~--kKvGH~GTLDP~AtGvLiv~iG~~~T-kl~~~~~--~~~K~Y~a 76 (235)
T PRK00989 9 EGILLVDKPQGRTSFS-------LIRALTKLIGV--KKIGHAGTLDPFATGVMVMLIGRKFT-RLSDILL--FEDKEYAA 76 (235)
T ss_pred CCEEEEECCCCCCHHH-------HHHHHHHHHCC--CCCCCCCCCCCCCCCEEEEECCCCCC-CHHHHHC--CCCCEEEE
T ss_conf 8199997899999899-------99999998587--74687867797443528884074511-2789867--57846999
Q ss_pred CCC
Q ss_conf 134
Q gi|254780608|r 186 LVW 188 (346)
Q Consensus 186 iv~ 188 (346)
.+.
T Consensus 77 ~i~ 79 (235)
T PRK00989 77 IAH 79 (235)
T ss_pred EEE
T ss_conf 999
No 43
>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=96.42 E-value=0.002 Score=41.59 Aligned_cols=69 Identities=22% Similarity=0.282 Sum_probs=46.0
Q ss_pred CEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 56884176531122357853323320110111110013335445342224046212310122210233332211120001
Q gi|254780608|r 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186 (346)
Q Consensus 107 ~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Ai 186 (346)
.|++||||.|+.+|. +...+..... ..+.+-.+.||-..||||+++-++. .+ +...|.. -.|+|.|.
T Consensus 1 Gil~i~KP~G~TS~~-------vv~~vk~~~~--~kKvGH~GTLDP~AtGvL~i~vG~a-TK-~~~~~~~--~~K~Y~~~ 67 (210)
T cd00506 1 GLFAVDKPQGPSSHD-------VVDTIRRIFL--AEKVGHGGTLDPFATGVLVVGIGKA-TK-LLKHLLA--ATKDYTAI 67 (210)
T ss_pred CEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEEECHH-HH-HHHHHCC--CCCEEEEE
T ss_conf 989996799999899-------9999999858--7735768666974524289997788-87-9998755--99778799
Q ss_pred CC
Q ss_conf 34
Q gi|254780608|r 187 VW 188 (346)
Q Consensus 187 v~ 188 (346)
+.
T Consensus 68 ~~ 69 (210)
T cd00506 68 GR 69 (210)
T ss_pred EE
T ss_conf 99
No 44
>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=96.41 E-value=0.0019 Score=41.74 Aligned_cols=86 Identities=13% Similarity=0.112 Sum_probs=52.1
Q ss_pred ECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf 41765311223578533233201101111100133354453422240462123101222102333322111200013456
Q gi|254780608|r 111 FNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGI 190 (346)
Q Consensus 111 inKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Aiv~G~ 190 (346)
++||.+..++. ...+.........+.+.++|+||.++|+.+++ +.|...+.
T Consensus 1 l~K~~~~t~~~--------~~~~~~~~~~~~~~v~~aG~kDk~a~t~Q~~s-------------------n~f~i~lr-- 51 (87)
T cd01291 1 LYKPGGDTMEA--------ARQLAKLLGIPPKRVGYAGRKDKRAVTTQLVS-------------------NRFTITLR-- 51 (87)
T ss_pred CCCCCCCHHHH--------HHHHHHHHCCCHHHEEECCCCCCCEEEEEEEE-------------------EEEEEEEC--
T ss_conf 96568789999--------99999982998777517446666554788764-------------------43589821--
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH-CCCCEEEEEECHHHHHHHHHHHHHCC
Q ss_conf 54100000001223465543211133555555530343010134320-24420457861237899999999639
Q gi|254780608|r 191 PKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFA-QKFCWLEMQPHTGRTHQLRVHALHMG 263 (346)
Q Consensus 191 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~-~~~slv~~~l~TGR~HQIRvhl~~~g 263 (346)
.....+..... .....+++.| |+.||+|.++.+++
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 45
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=96.20 E-value=0.0034 Score=40.22 Aligned_cols=70 Identities=21% Similarity=0.248 Sum_probs=47.8
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 85688417653112235785332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
+.+|+||||.|+.+|- +...+..... ..+.+-..=||-..||+|+++-++. ..+...|.+ -.|+|.|
T Consensus 17 ~G~l~idKP~G~TS~~-------vv~~vk~~~~--~kKvGH~GTLDP~AtGvL~v~~G~a--TK~~~~~~~--~~K~Y~~ 83 (310)
T PRK01851 17 DGVLLLDKPVGLSSND-------ALIRAKRLLL--AKKAGHTGTLDPLASGLLPLCFGEA--TKFSQDLLE--ADKTYEA 83 (310)
T ss_pred CEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHCC--CCCEEEE
T ss_conf 7899970599899899-------9999999858--8845778677973404068997887--733177576--9808999
Q ss_pred CCC
Q ss_conf 134
Q gi|254780608|r 186 LVW 188 (346)
Q Consensus 186 iv~ 188 (346)
.+.
T Consensus 84 ~~~ 86 (310)
T PRK01851 84 TMR 86 (310)
T ss_pred EEE
T ss_conf 999
No 46
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=96.13 E-value=0.0027 Score=40.83 Aligned_cols=72 Identities=26% Similarity=0.331 Sum_probs=48.6
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 85688417653112235785332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
+.|++||||.|+.+|- +...+....+ ..+.+-..-||-..||+|+++-++. ..+...|. ...|+|.|
T Consensus 10 ~G~l~idKP~G~TS~~-------vv~~vkk~l~--~kKvGH~GTLDP~AtGvLiv~vG~a--TKl~~~~~--~~~K~Y~a 76 (244)
T PRK00020 10 DGVLLLDKPVGLSSNH-------ALQRAKRTVD--AAKAGHTGTLDPFATGLLVCCMGRA--TKISGRML--EADKTYQA 76 (244)
T ss_pred CEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHC--CCCCEEEE
T ss_conf 7799971699899899-------9999999829--8715778667975514189996737--67659766--89927999
Q ss_pred CCC-CC
Q ss_conf 134-56
Q gi|254780608|r 186 LVW-GI 190 (346)
Q Consensus 186 iv~-G~ 190 (346)
.+. |.
T Consensus 77 ~i~lG~ 82 (244)
T PRK00020 77 TLQFGE 82 (244)
T ss_pred EEEECC
T ss_conf 999787
No 47
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=96.05 E-value=0.0031 Score=40.42 Aligned_cols=71 Identities=24% Similarity=0.274 Sum_probs=47.2
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 85688417653112235785332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
+.+|+||||.|+.+|- +...++.... ..+.+-..=||-..||+|++|-++ +..|...|.+ -.|+|.|
T Consensus 3 ~G~l~vdKP~G~TS~~-------vv~~ikk~~~--~kKvGH~GTLDP~AtGvL~v~~G~--aTkl~~~~~~--~~K~Y~~ 69 (293)
T PRK02484 3 NGIINLKKEAGMTSHD-------AVFKLRKILQ--TKKIGHGGTLDPDVVGVLPIAVGK--ATRVIEYMTE--AGKVYEG 69 (293)
T ss_pred CEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCEEEEEEEECH--HHHHHHHHCC--CCCEEEE
T ss_conf 6699972699999899-------9999999848--985565836798661268999788--7715187664--8938999
Q ss_pred CC-CC
Q ss_conf 13-45
Q gi|254780608|r 186 LV-WG 189 (346)
Q Consensus 186 iv-~G 189 (346)
.+ .|
T Consensus 70 ~~~lG 74 (293)
T PRK02484 70 EVTLG 74 (293)
T ss_pred EEEEC
T ss_conf 99943
No 48
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=95.99 E-value=0.0036 Score=40.03 Aligned_cols=72 Identities=21% Similarity=0.247 Sum_probs=48.0
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 85688417653112235785332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
+.++.||||.|+.+|- +...+..... ..+.+-..-||-..||+|++|-++. ..+...|. .-.|+|.|
T Consensus 2 ~G~l~i~KP~g~TS~~-------vv~~vkk~l~--~kKvGH~GTLDP~AtGvL~v~~G~a--TK~~~~~~--~~~K~Y~a 68 (289)
T PRK00130 2 NGVINVYKPKGMTSFD-------VVRKIRKIAK--IKKVGHTGTLDPLASGVLPVCLGKA--TKIVDYIM--EGKKVYRV 68 (289)
T ss_pred CEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHC--CCCEEEEE
T ss_conf 7799960899999899-------9999999848--8855778467985604289997877--61436767--99907999
Q ss_pred CCC-CC
Q ss_conf 134-56
Q gi|254780608|r 186 LVW-GI 190 (346)
Q Consensus 186 iv~-G~ 190 (346)
.+. |.
T Consensus 69 ~~~lG~ 74 (289)
T PRK00130 69 ELKLGT 74 (289)
T ss_pred EEEECC
T ss_conf 999787
No 49
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=95.99 E-value=0.0039 Score=39.85 Aligned_cols=72 Identities=26% Similarity=0.373 Sum_probs=47.4
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 85688417653112235785332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
+.+++||||.|+.+|. +...+..... ..+.+-..-||-..||||++|-++.+ + |...+. ...|+|.|
T Consensus 2 ngil~i~KP~G~TS~~-------vv~~vkk~l~--~kKvGH~GTLDP~AtGvLiv~~G~aT-K-l~~~l~--~~~K~Y~a 68 (272)
T PRK04099 2 NRLFVANKPPGLSSNA-------FLSRLKRKYG--VKKAGFSGTLDPFAKGVLIVAFGQYT-K-LFRFLD--KTPKTYKA 68 (272)
T ss_pred CEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEEECHHH-H-HHHHHC--CCCCEEEE
T ss_conf 7399961899899899-------9999999849--98446370569866045999988776-3-117667--78827999
Q ss_pred CC-CCC
Q ss_conf 13-456
Q gi|254780608|r 186 LV-WGI 190 (346)
Q Consensus 186 iv-~G~ 190 (346)
.+ .|.
T Consensus 69 ~i~lG~ 74 (272)
T PRK04099 69 TLWLGA 74 (272)
T ss_pred EEEECC
T ss_conf 999886
No 50
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=95.89 E-value=0.0061 Score=38.60 Aligned_cols=71 Identities=24% Similarity=0.303 Sum_probs=47.4
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 85688417653112235785332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
+.++.||||.|+.+|- +...+..... ..+.+-..-||-..||+|++|-...+ .+...+.+ .|+|.|
T Consensus 2 ~G~l~i~Kp~G~tS~~-------vv~~~k~~~~--~kKvGH~GTLDP~AtGvL~i~~G~aT--k~~~~l~~---~K~Y~~ 67 (291)
T PRK02755 2 QGFLNLNKPAGWTSHD-------CVAKLRRLLR--LKRVGHGGTLDPAATGVLPIAVGKAT--RLLPYLPS---GKAYKA 67 (291)
T ss_pred CEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEEECHHH--EECCCCCC---CCEEEE
T ss_conf 7699983599899899-------9999999858--88367785779755052899976576--64300489---958999
Q ss_pred CCC-CC
Q ss_conf 134-56
Q gi|254780608|r 186 LVW-GI 190 (346)
Q Consensus 186 iv~-G~ 190 (346)
.+. |.
T Consensus 68 ~~~lG~ 73 (291)
T PRK02755 68 TVRFGL 73 (291)
T ss_pred EEEECC
T ss_conf 999897
No 51
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=95.77 E-value=0.005 Score=39.12 Aligned_cols=68 Identities=22% Similarity=0.179 Sum_probs=45.2
Q ss_pred EEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf 68841765311223578533233201101111100133354453422240462123101222102333322111200013
Q gi|254780608|r 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV 187 (346)
Q Consensus 108 livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Aiv 187 (346)
|++||||.|+.+|- +...+..... ..+.+-..-||-..||+|++|-+..+ .+...|.+ -.|+|.|.+
T Consensus 2 illi~KP~G~TS~~-------vv~~vkk~~~--~kKvGH~GTLDP~AtGvL~v~~G~aT--K~~~~~~~--~~K~Y~~~~ 68 (279)
T PRK02193 2 ITLLYKPKKISSFK-------FIRQFSKTNL--IKKIGHAGTLDPLATGLLLVATDEDT--KLLDYLDQ--KTKTYLAKI 68 (279)
T ss_pred EEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCEEEEEEEECHHH--HHCHHHCC--CCCEEEEEE
T ss_conf 89998999899899-------9999999839--99536174679867447999978665--12645545--782699999
Q ss_pred C
Q ss_conf 4
Q gi|254780608|r 188 W 188 (346)
Q Consensus 188 ~ 188 (346)
.
T Consensus 69 ~ 69 (279)
T PRK02193 69 Q 69 (279)
T ss_pred E
T ss_conf 9
No 52
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=95.72 E-value=0.0054 Score=38.92 Aligned_cols=70 Identities=27% Similarity=0.223 Sum_probs=46.6
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 85688417653112235785332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
+.+|+||||.|+.+|- +...+..... ..+.+-..=||-..||||++|-.+ + ..+...+.+ -.|+|.|
T Consensus 13 ~G~l~idKP~G~TS~~-------vv~~vkk~~~--~kKvGH~GTLDP~AtGvL~i~~G~-a-Tk~~~~~~~--~~K~Y~~ 79 (305)
T PRK05389 13 SGWLILDKPAGMTSTE-------AVSKVKWLFD--AQKAGHAGTLDPLASGVLPIALGE-A-TKTVPYVMD--GTKRYRF 79 (305)
T ss_pred CEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEEECH-H-HHHHHHHCC--CCEEEEE
T ss_conf 7799982499999899-------9999999858--885677867798660238899887-7-623367656--8807999
Q ss_pred CCC
Q ss_conf 134
Q gi|254780608|r 186 LVW 188 (346)
Q Consensus 186 iv~ 188 (346)
.+.
T Consensus 80 ~~~ 82 (305)
T PRK05389 80 TVA 82 (305)
T ss_pred EEE
T ss_conf 999
No 53
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=95.64 E-value=0.0075 Score=38.03 Aligned_cols=70 Identities=20% Similarity=0.274 Sum_probs=47.0
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 85688417653112235785332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
+.|++||||.|+.+|. +...++.... ..+.+-..-||-..||+|++|-.+.+ .+...+.+ -.|+|.|
T Consensus 2 ~Gil~idKP~G~TS~~-------vv~~vr~~l~--~kKvGH~GTLDP~AtGvL~i~iG~aT--Kl~~~l~~--~~K~Y~a 68 (307)
T PRK01550 2 EGVVLLHKPKGMTSHD-------CVFKLRKILR--EKRIGHTGTLDPDVTGVLPICVGRAT--KIAQFLTS--ETKTYEG 68 (307)
T ss_pred CEEEEECCCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCEEEEEEEECCCH--HHCHHHCC--CCCEEEE
T ss_conf 7799970699899899-------9999999848--98346474679866216999978000--01344466--7834899
Q ss_pred CCC
Q ss_conf 134
Q gi|254780608|r 186 LVW 188 (346)
Q Consensus 186 iv~ 188 (346)
.+.
T Consensus 69 ~~~ 71 (307)
T PRK01550 69 EVT 71 (307)
T ss_pred EEE
T ss_conf 999
No 54
>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=95.53 E-value=0.0065 Score=38.42 Aligned_cols=69 Identities=25% Similarity=0.344 Sum_probs=46.5
Q ss_pred CEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 56884176531122357853323320110111110013335445342224046212310122210233332211120001
Q gi|254780608|r 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186 (346)
Q Consensus 107 ~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Ai 186 (346)
.+++||||.|+.+|. +...+..... ..+.+-..=||-..||||+++-++.+ .|...|. .-.|+|.|.
T Consensus 3 Gil~idKP~G~TS~~-------vv~~ikk~l~--~kKvGH~GTLDP~AtGvL~v~iG~aT--Kl~~~~~--~~~K~Y~~~ 69 (182)
T cd02572 3 GVINLDKPSGPSSHE-------VVAWIKRILG--VEKTGHSGTLDPKVTGCLPVCIDRAT--RLVKSQQ--EAGKEYVCV 69 (182)
T ss_pred EEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEECCHHH--HHHHHHC--CCCEEEEEE
T ss_conf 899995799999899-------9999999857--66468897779755434776326788--9999867--798089981
Q ss_pred CC
Q ss_conf 34
Q gi|254780608|r 187 VW 188 (346)
Q Consensus 187 v~ 188 (346)
+.
T Consensus 70 ~~ 71 (182)
T cd02572 70 MR 71 (182)
T ss_pred EE
T ss_conf 67
No 55
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=95.52 E-value=0.0098 Score=37.30 Aligned_cols=70 Identities=24% Similarity=0.332 Sum_probs=46.3
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 85688417653112235785332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
..|++||||.|+.+|. +...+..... ..+.+-..=||--.||+|+++-++. ..+...|. .-.|+|.|
T Consensus 9 sGil~idKP~G~TS~~-------vv~~vk~~~~--~kKvGH~GTLDP~AtGvL~v~~G~a--TKl~~~~~--~~~K~Y~a 75 (298)
T PRK03287 9 SGLVVVDKPAGMTSHD-------VVARCRRIFG--TRKVGHAGTLDPMATGVLVLGVERA--TKLLGHLV--ATDKSYTA 75 (298)
T ss_pred CEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEEECHH--HCCCHHHC--CCCCEEEE
T ss_conf 7899994799999899-------9999999848--9833668577974604389997877--62187465--57817999
Q ss_pred CCC
Q ss_conf 134
Q gi|254780608|r 186 LVW 188 (346)
Q Consensus 186 iv~ 188 (346)
.+.
T Consensus 76 ~~~ 78 (298)
T PRK03287 76 TIR 78 (298)
T ss_pred EEE
T ss_conf 999
No 56
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=95.45 E-value=0.012 Score=36.86 Aligned_cols=72 Identities=28% Similarity=0.303 Sum_probs=48.1
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 85688417653112235785332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
+.||+||||.|+.+|. +...+....+ ..+.+-..-||-..||+|++|-+. |.+ +...|. .-.|+|.|
T Consensus 3 ng~l~i~KP~g~TS~~-------vv~~vkk~~~--~~KvGH~GTLDP~AtGvL~i~~g~-aTK-~~~~~~--~~~K~Y~~ 69 (293)
T PRK01528 3 NYWLNIYKPRGISSAK-------LVSIVKKILG--KVKIGHAGTLDVEAEGILPLAVGE-ATK-LIQLLI--DAKKTYIF 69 (293)
T ss_pred CEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEEECH-HHH-HHHHHC--CCCEEEEE
T ss_conf 7589987799999899-------9999999848--980576867887570158999786-650-337865--79806999
Q ss_pred CC-CCC
Q ss_conf 13-456
Q gi|254780608|r 186 LV-WGI 190 (346)
Q Consensus 186 iv-~G~ 190 (346)
.+ .|.
T Consensus 70 ~~~~G~ 75 (293)
T PRK01528 70 TVKFGK 75 (293)
T ss_pred EEEECC
T ss_conf 999788
No 57
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=95.41 E-value=0.011 Score=36.89 Aligned_cols=70 Identities=21% Similarity=0.249 Sum_probs=46.8
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 85688417653112235785332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
+.+++||||+|+.+|. +...+..... ..+.+-..=||-..||||++|-+. +. .+...+. .-.|+|.|
T Consensus 10 ~Gil~idKP~g~TS~~-------vv~~vrr~l~--~~KvGH~GTLDP~AtGvL~i~~g~-aT-K~~~~~~--~~~K~Y~~ 76 (300)
T PRK04642 10 HGILLLDKPAGLSSNN-------ALQAARRLLR--AEKGGHTGSLDPLATGLLPLCFGE-AT-KIAGLLL--GSAKAYDA 76 (300)
T ss_pred CEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEEECH-HH-HHCHHHC--CCCCEEEE
T ss_conf 7799970799899899-------9999999868--984576857798560437899787-65-1366656--13664379
Q ss_pred CCC
Q ss_conf 134
Q gi|254780608|r 186 LVW 188 (346)
Q Consensus 186 iv~ 188 (346)
.+.
T Consensus 77 ~~~ 79 (300)
T PRK04642 77 EIV 79 (300)
T ss_pred EEE
T ss_conf 999
No 58
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=95.34 E-value=0.0084 Score=37.72 Aligned_cols=81 Identities=19% Similarity=0.259 Sum_probs=50.7
Q ss_pred CEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 56884176531122357853323320110111110013335445342224046212310122210233332211120001
Q gi|254780608|r 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186 (346)
Q Consensus 107 ~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Ai 186 (346)
.++++|||.|+.+|- +...+..... ..+.+-..-||-..||+|++|-. ++.+.++-+. .-.|+|.|.
T Consensus 16 Gil~ldKP~G~tS~~-------~v~~vkkil~--~~K~GH~GTLDP~atGvLpi~ig-~aTKl~~~l~---~~~K~Y~a~ 82 (271)
T COG0130 16 GVINLDKPPGPTSHE-------VVAWVKRILG--VEKAGHGGTLDPLATGVLPICLG-EATKLVQYLL---DADKEYVAT 82 (271)
T ss_pred CEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEEEC-HHHHHHHHHH---HCCCEEEEE
T ss_conf 469840799997799-------9999999858--64056463448743441888834-1474898872---089479999
Q ss_pred CC-CCCCCCCCCCCC
Q ss_conf 34-565410000000
Q gi|254780608|r 187 VW-GIPKNKKECIAN 200 (346)
Q Consensus 187 v~-G~~~~~~~~i~~ 200 (346)
+. |.-......+..
T Consensus 83 ~~lG~~t~~~e~i~~ 97 (271)
T COG0130 83 VRLGDQTDSEEEVRA 97 (271)
T ss_pred EEECCCCCCHHHHHH
T ss_conf 996775799999999
No 59
>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=95.33 E-value=0.032 Score=34.07 Aligned_cols=49 Identities=20% Similarity=0.301 Sum_probs=40.7
Q ss_pred CCHHHHHHHHCCCC-CHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEE
Q ss_conf 66899999876788-989999999849903887884-511211799889993
Q gi|254780608|r 19 MRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP 68 (346)
Q Consensus 19 ~RLd~~L~~~~~~~-sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~ 68 (346)
++|+.||+.. .-+ |=.+++..|..+.|.|||+.. +=..+|+.||.|.|+
T Consensus 9 ITLgQlLK~~-~~i~sGG~AK~fL~e~~V~vNGe~e~RRGkKL~~gD~i~i~ 59 (60)
T TIGR02988 9 ITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIP 59 (60)
T ss_pred ECHHHHHHHH-HHHCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEC
T ss_conf 6276786688-56228257889870695554784404588700489668826
No 60
>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=95.31 E-value=0.0087 Score=37.63 Aligned_cols=69 Identities=25% Similarity=0.367 Sum_probs=45.8
Q ss_pred CEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 56884176531122357853323320110111110013335445342224046212310122210233332211120001
Q gi|254780608|r 107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186 (346)
Q Consensus 107 ~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Ai 186 (346)
.+++||||.|+.+|- +...+...... .+.+-..=||-..||+|++|-+. +. .+...|.+ -.|+|.|.
T Consensus 1 G~l~i~Kp~g~tS~~-------~v~~~k~~~~~--kKvGH~GTLDP~AtGvL~i~~g~-aT-Kl~~~~~~--~~K~Y~~~ 67 (277)
T cd02573 1 GILLLDKPAGLTSHD-------VVQKVRRLLGT--KKVGHTGTLDPLATGVLPIALGE-AT-KLSQYLLD--ADKTYRAT 67 (277)
T ss_pred CEEEEECCCCCCHHH-------HHHHHHHHHCC--CCCCCCCCCCCCCCCEEEEEECH-HH-HHHHHHCC--CCCEEEEE
T ss_conf 989996799999899-------99999998588--85563757797660337899888-87-05278678--99179999
Q ss_pred CC
Q ss_conf 34
Q gi|254780608|r 187 VW 188 (346)
Q Consensus 187 v~ 188 (346)
+.
T Consensus 68 ~~ 69 (277)
T cd02573 68 VR 69 (277)
T ss_pred EE
T ss_conf 99
No 61
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=95.30 E-value=0.013 Score=36.51 Aligned_cols=70 Identities=20% Similarity=0.261 Sum_probs=46.5
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 85688417653112235785332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
+.+|+||||.|+.+|- +...+..... ..+.+-..-||--.||+|+++-.+ + ..+...|.+ -.|+|.|
T Consensus 12 ~Gil~idKP~g~TS~~-------~v~~~kk~~~--~kKvGH~GTLDP~AtGvL~i~~G~-a-TK~~~~~~~--~~K~Y~~ 78 (314)
T PRK05033 12 NGVLLLDKPQGMSSND-------ALQKVKRIYN--ANKAGHTGALDPLATGMLPICLGE-A-TKFSQFLLD--SDKRYRV 78 (314)
T ss_pred CEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEEECH-H-HHHHHHHCC--CCCEEEE
T ss_conf 6799981599999899-------9999999858--885687857797560218999888-8-704088668--9917999
Q ss_pred CCC
Q ss_conf 134
Q gi|254780608|r 186 LVW 188 (346)
Q Consensus 186 iv~ 188 (346)
.+.
T Consensus 79 ~~~ 81 (314)
T PRK05033 79 IAK 81 (314)
T ss_pred EEE
T ss_conf 999
No 62
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=95.26 E-value=0.012 Score=36.82 Aligned_cols=72 Identities=18% Similarity=0.302 Sum_probs=48.0
Q ss_pred ECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCC
Q ss_conf 17856884176531122357853323320110111110013335445342224046212310122210233332211120
Q gi|254780608|r 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY 183 (346)
Q Consensus 104 ED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y 183 (346)
-+..+|.+|||.|+.+|- +...+..... ..+.+-..-||-..||||+++-.+. ..+...+.+ -.|+|
T Consensus 20 ~~~Gil~idKP~G~TS~~-------vv~~vrk~l~--~kKvGH~GTLDP~AtGvL~i~~G~a--TK~~~~l~~--~~K~Y 86 (300)
T PRK04270 20 INYGVVNLDKPPGPTSHE-------VAAWVRDILG--VEKAGHGGTLDPKVTGVLPVALGKA--TKVVQALLE--SPKEY 86 (300)
T ss_pred HHCCEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEEECHH--HHHHHHHCC--CCCEE
T ss_conf 729999996898999899-------9999999858--8846878678974623378886798--888698675--89458
Q ss_pred CCCCC
Q ss_conf 00134
Q gi|254780608|r 184 WSLVW 188 (346)
Q Consensus 184 ~Aiv~ 188 (346)
.|.+.
T Consensus 87 ~~~~~ 91 (300)
T PRK04270 87 VCVMH 91 (300)
T ss_pred EEEEE
T ss_conf 77101
No 63
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=94.53 E-value=0.099 Score=30.98 Aligned_cols=51 Identities=20% Similarity=0.282 Sum_probs=41.3
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEEC
Q ss_conf 66899999876788989999999849903887884-5112117998899935
Q gi|254780608|r 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP 69 (346)
Q Consensus 19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~ 69 (346)
..|+.||+..=---|=.+++..|..|.|+|||+.- +-..+++.||+|.++.
T Consensus 12 I~L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~ 63 (73)
T COG2501 12 ITLGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPG 63 (73)
T ss_pred EEHHHHHHHHCCCCCCHHHHHHHHCCEEEECCEEECCCCCEEECCCEEEECC
T ss_conf 8799999874950574788899877918988866301677601698999899
No 64
>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=94.30 E-value=0.02 Score=35.29 Aligned_cols=41 Identities=20% Similarity=0.198 Sum_probs=28.1
Q ss_pred CCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 333544534222404621231012221023333221112000134
Q gi|254780608|r 144 PRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVW 188 (346)
Q Consensus 144 ~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Aiv~ 188 (346)
.+-..-||=-.||+|+++-... .+. ...|.+ ..|+|.|.+.
T Consensus 58 vGH~GTLDP~AtGvL~i~~G~a-TK~-~~~~~~--~~K~Y~a~~~ 98 (312)
T cd02867 58 IGHGGTLDPLATGVLVVGVGAG-TKQ-LQDYLS--CSKTYEATGL 98 (312)
T ss_pred EEECCCCCCCCCCEEEEEECHH-HEE-CHHHCC--CCCEEEEEEE
T ss_conf 4026567874603388998754-404-586667--9917999999
No 65
>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=93.75 E-value=0.014 Score=36.41 Aligned_cols=70 Identities=20% Similarity=0.192 Sum_probs=47.0
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCC-CCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCC
Q ss_conf 8568841765311223578533233201101111-100133354453422240462123101222102333322111200
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDS-KGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~-~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~ 184 (346)
+.++.+|||.|+.+|. ++...... ...+.+-..=||+..||+|+++=-+++-+...-+. .-.|+|.
T Consensus 2 ~GvLll~Kp~G~TSfd----------~~~~v~rLl~~kkvGHtGTLDp~A~G~L~~~vGr~aTkl~~yl~---~~dK~Y~ 68 (236)
T TIGR00431 2 NGVLLLDKPQGMTSFD----------ALAKVRRLLGVKKVGHTGTLDPFATGVLPILVGRKATKLSPYLT---DLDKEYE 68 (236)
T ss_pred CCCCCCCCCCCCCHHH----------HHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC---CCCCEEE
T ss_conf 7204155788878899----------99999998707852206665302410354223001343433312---6476179
Q ss_pred CCCC
Q ss_conf 0134
Q gi|254780608|r 185 SLVW 188 (346)
Q Consensus 185 Aiv~ 188 (346)
|.++
T Consensus 69 A~~~ 72 (236)
T TIGR00431 69 AEIR 72 (236)
T ss_pred EEEE
T ss_conf 9998
No 66
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=93.53 E-value=0.086 Score=31.35 Aligned_cols=17 Identities=29% Similarity=0.417 Sum_probs=8.1
Q ss_pred EEEEEECHHHHHHHHHH
Q ss_conf 04578612378999999
Q gi|254780608|r 242 WLEMQPHTGRTHQLRVH 258 (346)
Q Consensus 242 lv~~~l~TGR~HQIRvh 258 (346)
-||+.+---+.-|+|+-
T Consensus 126 ~vel~l~~~~p~qlrl~ 142 (203)
T COG4332 126 AVELSLRISRPFQLRLD 142 (203)
T ss_pred EEEEEECCCCCCHHHHH
T ss_conf 27899745676065799
No 67
>PRK04313 30S ribosomal protein S4e; Validated
Probab=93.32 E-value=0.37 Score=27.40 Aligned_cols=57 Identities=21% Similarity=0.239 Sum_probs=46.0
Q ss_pred HCCCCHHHHHHHHCCCC-CHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEECCCC
Q ss_conf 36866899999876788-9899999998499038878845-112117998899935655
Q gi|254780608|r 16 EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72 (346)
Q Consensus 16 ~~g~RLd~~L~~~~~~~-sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~~~~~ 72 (346)
..++.|--+|++.+... +...+++++.+|.|.|||++.+ ..+.|-.-|+|+|+...+
T Consensus 35 ~~siPL~v~LRd~L~~a~t~rEak~Il~~~~V~VDG~vr~d~~~pvGlmDVisi~~~~e 93 (237)
T PRK04313 35 ESSLPLLIVLRDVLGYADTAREARKIISEGKVLVDGRVRKDYKFPVGLMDVISIPETGE 93 (237)
T ss_pred CCCCCCHHHHHHHHHHHCCHHHHHHHHHCCEEEECCEEEECCCCCCCEEEEEEECCCCC
T ss_conf 55423389998777250448899998648859989999603788754167998647897
No 68
>PRK11507 hypothetical protein; Provisional
Probab=93.16 E-value=0.18 Score=29.36 Aligned_cols=51 Identities=22% Similarity=0.167 Sum_probs=39.5
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEE
Q ss_conf 6866899999876788989999999849903887884-51121179988999
Q gi|254780608|r 17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRI 67 (346)
Q Consensus 17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i 67 (346)
.-..|+++|+-.==--|=...+.+|..|.|+|||..- +...++.+||+|.+
T Consensus 10 ~yIeL~~lLK~~glv~sGg~AK~~Ia~G~V~VnGevEtRKr~Ki~~GdvV~f 61 (70)
T PRK11507 10 PHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSF 61 (70)
T ss_pred CCEEHHHHHHHCCCCCCCHHHHHHEECCEEEECCEEEEEEEEEEECCCEEEE
T ss_conf 7100888884717204658778654187689999996331025108999999
No 69
>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=93.08 E-value=0.17 Score=29.53 Aligned_cols=54 Identities=15% Similarity=0.328 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHC-C-------CCEECCE-EECC----CCCCCCCCEEEEECCC
Q ss_conf 686689999987678898999999984-9-------9038878-8451----1211799889993565
Q gi|254780608|r 17 ENMRLDRWFKNHYPHINFVNLQKILRS-G-------QVRVDKK-RVKF----NNRIQSGQVVRIPPVI 71 (346)
Q Consensus 17 ~g~RLd~~L~~~~~~~sr~~~~~lir~-G-------~V~VNG~-~vk~----~~~v~~GD~I~i~~~~ 71 (346)
.|.+++..|......+++.. .+++.. | .|.|||+ -+.. ++.|+.||+|.|.|+.
T Consensus 24 ~g~tv~dll~~l~~~Yp~~~-~e~~~et~~~~~~~v~ilvNGran~~~l~GL~~~LkdGD~vai~PPV 90 (93)
T TIGR01687 24 DGKTVGDLLEELSSRYPKEF-SELFKETGLGLVPNVIILVNGRANVDWLEGLETELKDGDVVAIFPPV 90 (93)
T ss_pred CCCCHHHHHHHHHHHCCHHH-HHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCC
T ss_conf 99807998999886156556-66514778876465789851641432203657523278756750699
No 70
>KOG2559 consensus
Probab=92.65 E-value=0.067 Score=32.03 Aligned_cols=23 Identities=26% Similarity=0.403 Sum_probs=19.5
Q ss_pred CCCCCCCCCCCCCCCEEEEECCC
Q ss_conf 01333544534222404621231
Q gi|254780608|r 142 QKPRLTHRLDQETSGILVVARTR 164 (346)
Q Consensus 142 ~~~~lVHRLDr~TSGlll~AK~~ 164 (346)
...+++||||-.|||+++|.-+.
T Consensus 89 ~~V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559 89 EDVQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred CCEEEEEEECCCCCCEEEEECCC
T ss_conf 23136775044225428873175
No 71
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=92.50 E-value=0.6 Score=26.02 Aligned_cols=57 Identities=32% Similarity=0.215 Sum_probs=45.8
Q ss_pred HCCCCHHHHHHHHCCCC-CHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEECCCC
Q ss_conf 36866899999876788-9899999998499038878845-112117998899935655
Q gi|254780608|r 16 EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72 (346)
Q Consensus 16 ~~g~RLd~~L~~~~~~~-sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~~~~~ 72 (346)
.+++.|--||.+.+... +...+++.+.+|.|.|||++.+ ..+.+-.-|+|+|+...+
T Consensus 36 ~eslPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvG~MDVIsI~kt~e 94 (273)
T PTZ00223 36 RECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPKTGD 94 (273)
T ss_pred CCCCCCHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCEEEEEEECCCCC
T ss_conf 44444257876564521657999999877937977999655899885789999857887
No 72
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=92.36 E-value=0.53 Score=26.36 Aligned_cols=23 Identities=13% Similarity=0.351 Sum_probs=8.5
Q ss_pred CCHHHHHHCCCCEEEEEECHHHHHH
Q ss_conf 1013432024420457861237899
Q gi|254780608|r 230 FKVIDCFAQKFCWLEMQPHTGRTHQ 254 (346)
Q Consensus 230 ~~vl~~~~~~~slv~~~l~TGR~HQ 254 (346)
|-+++.+. .+.| .|.+.-|=+-|
T Consensus 173 Y~llQayD-~~~L-~~~iqiGGsDQ 195 (405)
T PRK13354 173 YPLLQAYD-SVHL-DADIELGGTDQ 195 (405)
T ss_pred HHHHHHHH-HHHH-CCCEEEECHHH
T ss_conf 78888864-9986-88379950868
No 73
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=92.29 E-value=0.62 Score=25.96 Aligned_cols=57 Identities=18% Similarity=0.157 Sum_probs=45.8
Q ss_pred HCCCCHHHHHHHHCCCC-CHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEECCCC
Q ss_conf 36866899999876788-9899999998499038878845-112117998899935655
Q gi|254780608|r 16 EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVIN 72 (346)
Q Consensus 16 ~~g~RLd~~L~~~~~~~-sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~~~~~ 72 (346)
..++.|--||.+.+... +...+++++.+|.|.|||++.+ ..+.+-.-|+|+|+...+
T Consensus 39 ~eslPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvG~MDVIsI~kt~e 97 (262)
T PTZ00118 39 RECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTKTNE 97 (262)
T ss_pred CCCCCCHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCEEEEEEECCCCC
T ss_conf 44554335643464522658999999867908889999534899874678999856896
No 74
>pfam06353 DUF1062 Protein of unknown function (DUF1062). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=91.94 E-value=0.38 Score=27.27 Aligned_cols=41 Identities=22% Similarity=0.300 Sum_probs=32.3
Q ss_pred EEEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEEC
Q ss_conf 499984113686689999987678898999999984990388
Q gi|254780608|r 8 QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVD 49 (346)
Q Consensus 8 ~~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VN 49 (346)
..-+.-+.....|+|+.|++.| ++||+.+++++..|.|+-+
T Consensus 92 ~I~i~~~~~~~~Rl~~Lla~~L-~lSrs~l~~l~~~G~i~~~ 132 (142)
T pfam06353 92 EIQLRLEFPFSLRLDRLLAEEL-GLSRSRLQRLIDQGQIRGV 132 (142)
T ss_pred EEEEECCCCCCCCHHHHHHHHH-CCCHHHHHHHHHCCCEECC
T ss_conf 9999627877642999999881-8689999999988987705
No 75
>PRK04051 rps4p 30S ribosomal protein S4; Validated
Probab=91.26 E-value=0.47 Score=26.69 Aligned_cols=51 Identities=12% Similarity=0.111 Sum_probs=35.8
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCC--CEEEE
Q ss_conf 68668999998767889899999998499038878845-11211799--88999
Q gi|254780608|r 17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSG--QVVRI 67 (346)
Q Consensus 17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~G--D~I~i 67 (346)
-.+||+..+.+.-=.-|-.+..++|.+|.|+|||+++. |++.|..+ |.|..
T Consensus 101 l~RRL~~vv~r~~~a~si~~Ar~lI~hgHi~V~~~~v~~Ps~~V~r~~Ed~I~~ 154 (177)
T PRK04051 101 LERRLQTIVYRKGLARTPKQARQLIVHGHIAVNGRRVTSPGYLVSREEEDKIDY 154 (177)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEEECCCCEEEEECCCCCEEE
T ss_conf 996888999880566889999999747828999999536865886556685463
No 76
>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=87.65 E-value=0.25 Score=28.44 Aligned_cols=44 Identities=16% Similarity=0.292 Sum_probs=31.0
Q ss_pred CCHHHHHHHHCCCC--CHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCE
Q ss_conf 66899999876788--9899999998499038878845-1121179988
Q gi|254780608|r 19 MRLDRWFKNHYPHI--NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64 (346)
Q Consensus 19 ~RLd~~L~~~~~~~--sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~ 64 (346)
+||+...-++ |+ |=.+++++|-+|.|.|||++|. |+|.|..+..
T Consensus 112 RRLQT~Vyk~--GLArTi~~ARqLi~hGHI~v~Gr~v~~Psy~V~~e~e 158 (170)
T TIGR01018 112 RRLQTLVYKK--GLARTIKQARQLIVHGHIAVDGRRVTSPSYIVRREEE 158 (170)
T ss_pred HHHHHHHHHH--HHCCCHHHCCEEEEECEEEECCEEEECCCEEEECCCC
T ss_conf 4567899986--3022632343023203388768477358616746554
No 77
>cd00754 MoaD MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=86.11 E-value=1.4 Score=23.70 Aligned_cols=50 Identities=20% Similarity=0.464 Sum_probs=33.3
Q ss_pred CCCHHH---HHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCC
Q ss_conf 866899---999876788989999999849903887884511211799889993565
Q gi|254780608|r 18 NMRLDR---WFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71 (346)
Q Consensus 18 g~RLd~---~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~ 71 (346)
+.++.. +|..++|.. ...+...-.|-||++.+..++.|+.||.|.+.|+.
T Consensus 25 ~~Tv~~L~~~L~~~~~~~----~~~~~~~~~iavN~~~~~~~~~l~~gdEva~~PPv 77 (80)
T cd00754 25 GATVGELLDALEARYPGL----LEELLARVRIAVNGEYVRLDTPLKDGDEVAIIPPV 77 (80)
T ss_pred CCCHHHHHHHHHHHCCHH----HHHHHHCEEEEECCEECCCCCCCCCCCEEEEECCC
T ss_conf 988999999999878176----76431040998887983677156999999997998
No 78
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=83.33 E-value=1.4 Score=23.81 Aligned_cols=47 Identities=15% Similarity=0.090 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCE
Q ss_conf 8668999998767889899999998499038878845-1121179988
Q gi|254780608|r 18 NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV 64 (346)
Q Consensus 18 g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~ 64 (346)
.+||+.++.+.-=.-|-.+...+|.+|.|+|+|+++. |++.|..++.
T Consensus 106 ~RRLqt~v~~~glA~si~~Ar~lI~hgHI~V~~~~V~~Ps~lV~r~~E 153 (188)
T PTZ00155 106 ERRLQTKVFKLGLAKSVHHARVLIRQRHIRVGKQIVDIPSFLVRVDSE 153 (188)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHEECCEEEECCEEECCCCEEEEECCC
T ss_conf 876768999860115889888883446288999895377458860544
No 79
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=81.63 E-value=3.6 Score=21.12 Aligned_cols=56 Identities=25% Similarity=0.251 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHCCCC-CHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEECCCCC
Q ss_conf 866899999876788-9899999998499038878845-1121179988999356554
Q gi|254780608|r 18 NMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPVINA 73 (346)
Q Consensus 18 g~RLd~~L~~~~~~~-sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~~~~~~ 73 (346)
...|--++++.|... .-+.++++|..|.|+|||+..+ ....|-.=|+|+|+...+.
T Consensus 40 slPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~tgE~ 97 (241)
T COG1471 40 SLPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPKTGEH 97 (241)
T ss_pred CCCEEEEEHHHHHHCCCHHHHHHHHHCCCEEECCEEECCCCCCCCEEEEEEECCCCCE
T ss_conf 5528853036877622348899987669579888980135578406899997688965
No 80
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=77.80 E-value=5.2 Score=20.10 Aligned_cols=55 Identities=16% Similarity=0.310 Sum_probs=34.9
Q ss_pred EEECHHHCCCCHH---HHHHHHCCCCCHHHHHHHHHCCCC--EECCEEECCCCCCCCCCEEEEECCC
Q ss_conf 9984113686689---999987678898999999984990--3887884511211799889993565
Q gi|254780608|r 10 VVVENDEENMRLD---RWFKNHYPHINFVNLQKILRSGQV--RVDKKRVKFNNRIQSGQVVRIPPVI 71 (346)
Q Consensus 10 ~~V~~~~~g~RLd---~~L~~~~~~~sr~~~~~lir~G~V--~VNG~~vk~~~~v~~GD~I~i~~~~ 71 (346)
+.++.+ +..++ .+|+.+.+ .++..+..+.+ -||...+..++.|+.||+|.+.|+.
T Consensus 19 ~~l~~~--~~tv~~l~~~L~~~~~-----~~~~~l~~~~~~~AVNq~~~~~d~~l~~gDEVAffPPV 78 (81)
T PRK11130 19 LELAAD--FPTVEALRQHLAQQGD-----RWALALEDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPV 78 (81)
T ss_pred EECCCC--CCCHHHHHHHHHHHCC-----HHHHHHCCCCEEEEECCEECCCCCCCCCCCEEEECCCC
T ss_conf 787899--9889999999998583-----58886246856773313776899766999999980898
No 81
>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=74.65 E-value=2.8 Score=21.85 Aligned_cols=23 Identities=26% Similarity=0.504 Sum_probs=21.0
Q ss_pred CCEECCEEECCCCCCCCCCEEEE
Q ss_conf 90388788451121179988999
Q gi|254780608|r 45 QVRVDKKRVKFNNRIQSGQVVRI 67 (346)
Q Consensus 45 ~V~VNG~~vk~~~~v~~GD~I~i 67 (346)
..+|||+.+..++.|+.||.|+|
T Consensus 36 ~a~vNg~~~~l~~~L~~GD~VeI 58 (60)
T cd01668 36 GAKVNGKLVPLSTVLKDGDIVEI 58 (60)
T ss_pred EEEECCEECCCCCCCCCCCEEEE
T ss_conf 99999999898768289999998
No 82
>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=70.50 E-value=4 Score=20.85 Aligned_cols=144 Identities=17% Similarity=0.235 Sum_probs=74.3
Q ss_pred CCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCC
Q ss_conf 78568841765311223578533233201101111100133354453422240462123101222102333322111200
Q gi|254780608|r 105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW 184 (346)
Q Consensus 105 D~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~ 184 (346)
-..++.+|||.|=.+| -+..++...++-. +.+--.=||==.+|||.++=.+.+ +..+- ...-.|+|.
T Consensus 33 ~~Gvv~lDKP~gPsSH-------eV~~Wvr~iL~ve--KtGH~GTLDPKVTGvLpv~ierAT-r~v~~---~~~a~KEYV 99 (326)
T TIGR00425 33 RKGVVNLDKPSGPSSH-------EVVAWVRRILRVE--KTGHGGTLDPKVTGVLPVCIERAT-RLVKS---LQEAPKEYV 99 (326)
T ss_pred HCCEEEEECCCCCCCC-------EEHHHHHHHHCCC--CCCCCCCCCCCEEEEEEEEEHHHH-HHHHH---HHCCCCCEE
T ss_conf 0650787648418864-------0102212101011--246587578831246212100023-56445---316997459
Q ss_pred CCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCC-CCCCCEEEEEC--CHHHHHHCC-CCEEEEEECHHHHHHHHHHH
Q ss_conf 013456541000-00001223465543211133555-55553034301--013432024-42045786123789999999
Q gi|254780608|r 185 SLVWGIPKNKKE-CIANWLLKKSHIGGDYVHVVKQN-EKGANYAISHF--KVIDCFAQK-FCWLEMQPHTGRTHQLRVHA 259 (346)
Q Consensus 185 Aiv~G~~~~~~~-~i~~~~~~~~~~~~~~~~~~~~~-~~~~k~a~T~~--~vl~~~~~~-~slv~~~l~TGR~HQIRvhl 259 (346)
++++=+-.-++. .|..-+. ...++-++++.-.+ .+..-.-.|-| .+++.-++. .-|-++.-+.|= =||--|
T Consensus 100 ClmRLH~~~~~e~~~~rvl~--~f~G~ifQrPPLksAVKr~LRvR~IYe~~llE~Dg~d~LvlFrv~CeaGT--YiRkLC 175 (326)
T TIGR00425 100 CLMRLHRDAKEEKDIERVLK--EFTGRIFQRPPLKSAVKRQLRVRTIYESELLEVDGKDRLVLFRVSCEAGT--YIRKLC 175 (326)
T ss_pred EEEEECHHHHHHHHHHHHHH--HCCCEEECCCCCHHHHCCCCCEEEEEEEEEEEECCCCCEEEEEEEECCCC--CHHHHH
T ss_conf 97761201212578999988--51830333886256522336501689988772079962689999875786--156878
Q ss_pred HHCCCC
Q ss_conf 963980
Q gi|254780608|r 260 LHMGCP 265 (346)
Q Consensus 260 ~~~g~P 265 (346)
.++|-=
T Consensus 176 ~d~G~~ 181 (326)
T TIGR00425 176 VDIGEL 181 (326)
T ss_pred HHHHHH
T ss_conf 888676
No 83
>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=68.76 E-value=4.6 Score=20.48 Aligned_cols=23 Identities=26% Similarity=0.387 Sum_probs=20.9
Q ss_pred CCEECCEEECCCCCCCCCCEEEE
Q ss_conf 90388788451121179988999
Q gi|254780608|r 45 QVRVDKKRVKFNNRIQSGQVVRI 67 (346)
Q Consensus 45 ~V~VNG~~vk~~~~v~~GD~I~i 67 (346)
..+|||+.+..++.|+.||.|+|
T Consensus 36 ~a~Vng~~~~l~~~L~~gd~V~I 58 (60)
T cd01616 36 GALVNGQLVDLSYTLQDGDTVSI 58 (60)
T ss_pred EEEECCEECCCCCCCCCCCEEEE
T ss_conf 99999999651669999999999
No 84
>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=68.29 E-value=4.6 Score=20.49 Aligned_cols=23 Identities=30% Similarity=0.608 Sum_probs=20.9
Q ss_pred CCEECCEEECCCCCCCCCCEEEE
Q ss_conf 90388788451121179988999
Q gi|254780608|r 45 QVRVDKKRVKFNNRIQSGQVVRI 67 (346)
Q Consensus 45 ~V~VNG~~vk~~~~v~~GD~I~i 67 (346)
..+|||+.+..++.|+.||+|+|
T Consensus 36 ~A~VnG~~v~l~~~L~~gd~V~I 58 (60)
T pfam02824 36 GAKVNGQRVGLDHVLEDGDVVEI 58 (60)
T ss_pred EEEECCEECCCCCCCCCCCEEEE
T ss_conf 78999888762112489999998
No 85
>TIGR01344 malate_syn_A malate synthase A; InterPro: IPR006252 These sequences represent plant malate synthase and one of two bacterial forms, designated malate synthase A. This enzyme and isocitrate lyase are the two characteristic enzymes of the glyoxylate shunt. The shunt enables the cell to use acetyl-CoA to generate increased levels of TCA cycle intermediates for biosynthetic pathways such as gluconeogenesis.; GO: 0004474 malate synthase activity, 0006097 glyoxylate cycle.
Probab=64.60 E-value=4 Score=20.82 Aligned_cols=11 Identities=36% Similarity=0.812 Sum_probs=5.0
Q ss_pred HHHHHHHHCCC
Q ss_conf 99999996398
Q gi|254780608|r 254 QLRVHALHMGC 264 (346)
Q Consensus 254 QIRvhl~~~g~ 264 (346)
|||=|.+-+.|
T Consensus 248 eLrEH~~GLNC 258 (522)
T TIGR01344 248 ELREHSSGLNC 258 (522)
T ss_pred HHHHHHCCCCC
T ss_conf 88763201366
No 86
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=64.52 E-value=6 Score=19.71 Aligned_cols=22 Identities=36% Similarity=0.596 Sum_probs=13.1
Q ss_pred CEECCEEECCCCCCCCCCEEEE
Q ss_conf 0388788451121179988999
Q gi|254780608|r 46 VRVDKKRVKFNNRIQSGQVVRI 67 (346)
Q Consensus 46 V~VNG~~vk~~~~v~~GD~I~i 67 (346)
.+|||+.+..++.|+.||+|+|
T Consensus 424 AkVNG~~vPL~t~LknGD~VEI 445 (702)
T PRK11092 424 ARVDRQPYPLSQPLTSGQTVEI 445 (702)
T ss_pred EEECCEECCCCCCCCCCCEEEE
T ss_conf 9999998899871678988899
No 87
>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=64.49 E-value=7.5 Score=19.12 Aligned_cols=47 Identities=19% Similarity=0.253 Sum_probs=32.1
Q ss_pred HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECC---CCCCCCCCEEEEECCC
Q ss_conf 3686689999987678898999999984990388788451---1211799889993565
Q gi|254780608|r 16 EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF---NNRIQSGQVVRIPPVI 71 (346)
Q Consensus 16 ~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~---~~~v~~GD~I~i~~~~ 71 (346)
..+.++..+|... ..+ .+.=.|-+||..+.. ++.|+.||+|.+.++.
T Consensus 18 ~~~~tv~~ll~~l--~~~-------~~~v~v~vN~~~v~~~~~~~~L~~gD~v~ivppV 67 (70)
T pfam02597 18 PEGATVAELLEAL--GLN-------PERVAVAVNGEIVPRSQADTPLKDGDEVAIIPPV 67 (70)
T ss_pred CCCCCHHHHHHHH--CCC-------CCCEEEEECCEECCCCCCCCCCCCCCEEEEECCC
T ss_conf 9999699999983--888-------8888999999986785677677999999997886
No 88
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=62.90 E-value=8.8 Score=18.68 Aligned_cols=12 Identities=42% Similarity=0.722 Sum_probs=5.1
Q ss_pred CCCCCCCCCCEEE
Q ss_conf 5445342224046
Q gi|254780608|r 147 THRLDQETSGILV 159 (346)
Q Consensus 147 VHRLDr~TSGlll 159 (346)
.-|++++ .|+-+
T Consensus 152 ~~R~~~~-~~is~ 163 (401)
T COG0162 152 KKRLERE-QGISF 163 (401)
T ss_pred HHHHCCC-CCCCH
T ss_conf 8886068-99752
No 89
>PRK10872 relA GDP/GTP pyrophosphokinase; Provisional
Probab=61.46 E-value=7.3 Score=19.19 Aligned_cols=23 Identities=22% Similarity=0.445 Sum_probs=18.4
Q ss_pred CEECCEEECCCCCCCCCCEEEEE
Q ss_conf 03887884511211799889993
Q gi|254780608|r 46 VRVDKKRVKFNNRIQSGQVVRIP 68 (346)
Q Consensus 46 V~VNG~~vk~~~~v~~GD~I~i~ 68 (346)
.+|||+.+..++.|+.||.|+|-
T Consensus 442 AKVNGkivPL~~~L~nGD~VEIi 464 (743)
T PRK10872 442 AKIGGRIVPFTYQLQMGDQIEII 464 (743)
T ss_pred EEECCEECCCCCEECCCCEEEEE
T ss_conf 99999987887452688789995
No 90
>KOG0062 consensus
Probab=56.40 E-value=4.6 Score=20.47 Aligned_cols=18 Identities=11% Similarity=0.438 Sum_probs=15.4
Q ss_pred EEEECCCEEEECCCCCCE
Q ss_conf 786178568841765311
Q gi|254780608|r 101 LLYEDSKIYVFNKPAGIS 118 (346)
Q Consensus 101 IiyED~~livinKPaGl~ 118 (346)
-+|.+.|++.+|-|.++.
T Consensus 212 Alf~~pDlLLLDEPTNhL 229 (582)
T KOG0062 212 ALFAKPDLLLLDEPTNHL 229 (582)
T ss_pred HHHCCCCEEEECCCCCCC
T ss_conf 872499988654875310
No 91
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=56.07 E-value=11 Score=18.09 Aligned_cols=24 Identities=25% Similarity=0.463 Sum_probs=20.5
Q ss_pred CCEECCEEECCCCCCCCCCEEEEE
Q ss_conf 903887884511211799889993
Q gi|254780608|r 45 QVRVDKKRVKFNNRIQSGQVVRIP 68 (346)
Q Consensus 45 ~V~VNG~~vk~~~~v~~GD~I~i~ 68 (346)
..+|||+.+.-+++|+.||+|+|-
T Consensus 424 gAkVnG~ivpl~~~Lk~Gd~VEIi 447 (701)
T COG0317 424 GAKVNGRIVPLTTKLQTGDQVEII 447 (701)
T ss_pred EEEECCEEECCCEECCCCCEEEEE
T ss_conf 778899981465034789989999
No 92
>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=55.42 E-value=6.5 Score=19.54 Aligned_cols=44 Identities=27% Similarity=0.332 Sum_probs=30.7
Q ss_pred CCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCCC-CCC
Q ss_conf 133354453422240462123101222102333322111200013-456
Q gi|254780608|r 143 KPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV-WGI 190 (346)
Q Consensus 143 ~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Aiv-~G~ 190 (346)
+.+-.+.||--.||+|++|-+. + ..+...|.+ -.|+|.|.+ .|.
T Consensus 8 KvGH~GTLDP~AsGlL~i~ig~-~-TK~~~~~~~--~~K~Y~~~~~~G~ 52 (149)
T pfam01509 8 KVGHTGTLDPLATGVLPVCVGK-A-TKLLQYLLD--ADKEYRATIRLGV 52 (149)
T ss_pred CCCCCCCCCCCCEEEEEEEECH-H-HHHHHHHCC--CCCEEEEEEEECC
T ss_conf 0242744698665689999987-8-712188758--9817999998625
No 93
>TIGR00670 asp_carb_tr aspartate carbamoyltransferase; InterPro: IPR002082 Aspartate carbamoyltransferase (ATCase) catalyses the formation of carbamoyl-aspartate in the pyrimidine biosynthesis pathway, by the association of aspartate and carbamoyl-phosphate. This is the commitment step in the Escherichia coli pathway and is regulated by feedback inhibition by CTP, the final product of the pathway. The structural organisation of the ATCase protein varies considerably between different organisms. In bacteria such as E. coli, Salmonella typhimurium and Serratia marcescens, the ATCase is a dodecamer of 2 catalytic (c) trimers and 3 regulatory (r) dimers. The catalytic domains are coded for by the pyrB gene, and the regulatory domains by pyrI. In Gram-positive bacteria such as Bacillus subtilis, ATCase exists as a trimer of catalytic subunits, but unlike in E. coli, it neither contains nor binds to regulatory subunits. In eukaryotes, ATCase is found as a single domain in a multifunctional enzyme that contains activity for glutamine amidotransferase, carbamoylphosphate synthetase, dihydroorotase, and aspartate carbamoyltransferase. ; GO: 0004070 aspartate carbamoyltransferase activity, 0006207 'de novo' pyrimidine base biosynthetic process.
Probab=53.36 E-value=12 Score=17.93 Aligned_cols=54 Identities=20% Similarity=0.353 Sum_probs=36.2
Q ss_pred HHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCC-CEEEEECCC----CHHHHHHHHHHCCCCCC
Q ss_conf 9639800046444665221000134462413110004375889-649998399----78999999980898752
Q gi|254780608|r 260 LHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEG-GRLQITAPL----PAHMVKTWDSLGFKYDR 328 (346)
Q Consensus 260 ~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~-~~~~~~apl----P~~f~~~l~~l~~~~d~ 328 (346)
..+.--++||-|||---... ++.|++ .+ -++-|.||- |+++.+-++.-|.+.-.
T Consensus 173 ~Gl~iA~vGDlkygRtvhS~------------~~~L~~---f~~~~v~l~sP~~LrmP~~~~e~~~~~G~~~~~ 231 (336)
T TIGR00670 173 DGLKIALVGDLKYGRTVHSL------------IKALAL---FGNAEVYLISPEELRMPKEILEDLKAKGVKVRE 231 (336)
T ss_pred CCCEEEEEEECCCCHHHHHH------------HHHHHH---HCCCEEEEECCHHHHCHHHHHHHHHHCCCEEEE
T ss_conf 88579998431202476678------------899865---189569986772430617889998528962899
No 94
>KOG2529 consensus
Probab=48.77 E-value=11 Score=18.15 Aligned_cols=75 Identities=25% Similarity=0.301 Sum_probs=45.9
Q ss_pred CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf 85688417653112235785332332011011111001333544534222404621231012221023333221112000
Q gi|254780608|r 106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185 (346)
Q Consensus 106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~A 185 (346)
..+++++||++ |.+ ..+.+++...+. ....+-..-||=+.||+++..-+... +.+.. .....|+|..
T Consensus 68 sgv~~i~kpa~----pss---~e~~swvk~iL~--~ek~Gh~gTlDP~vtg~l~v~~~~~t-r~~~s---~~s~gk~yvg 134 (395)
T KOG2529 68 SGVINIDKPAN----PSS---HEVVSWVKNILR--VEKTGHSGTLDPEVTGCLIVCIDRAT-RLLKS---QQSAGKEYVG 134 (395)
T ss_pred CCCEECCCCCC----CCH---HHHHHHHHHHHH--HHHHCCCCCCCCCCCCEEEEEEECCC-CCCCC---HHCCCCEEEE
T ss_conf 47463368979----860---788888888766--88707998889652322799960000-24212---0105867999
Q ss_pred CCCCCCCC
Q ss_conf 13456541
Q gi|254780608|r 186 LVWGIPKN 193 (346)
Q Consensus 186 iv~G~~~~ 193 (346)
++.+.+.-
T Consensus 135 ~~~lt~~v 142 (395)
T KOG2529 135 IGKLTPEV 142 (395)
T ss_pred EEECCCCH
T ss_conf 98547523
No 95
>TIGR00691 spoT_relA RelA/SpoT family protein; InterPro: IPR004811 The functions of Escherichia coli RelA and SpoT differ somewhat. RelA (2.7.6.5 from EC) produces pppGpp (or ppGpp) from ATP and GTP (or GDP). SpoT (3.1.7.2 from EC) degrades ppGpp, but may also act as a secondary ppGpp synthetase. The two proteins are strongly similar. In many species, a single homolog to SpoT and RelA appears responsible for both ppGpp synthesis and ppGpp degradation. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species. ; GO: 0015969 guanosine tetraphosphate metabolic process.
Probab=47.48 E-value=21 Score=16.32 Aligned_cols=55 Identities=16% Similarity=0.251 Sum_probs=34.6
Q ss_pred CCEEEEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEEC
Q ss_conf 83049998411368668999998767889899999998499038878845-112117998899935
Q gi|254780608|r 5 TYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPP 69 (346)
Q Consensus 5 ~~~~~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~~ 69 (346)
|..+.+.++.+.. -|| |-=...+.+-- +.-.++|||+.+. -++.|+.||+|+|..
T Consensus 387 P~G~~~~Lp~Gs~--~vD-fAY~vHtd~G~-------~~~ga~~ng~~~~Sl~~~L~nG~vVEi~t 442 (741)
T TIGR00691 387 PKGDVVELPSGST--PVD-FAYAVHTDVGH-------KCTGAKVNGKIVPSLDKELENGDVVEIIT 442 (741)
T ss_pred CCEEEEEECCCCC--HHH-HHHHHCHHHCC-------EEEEEEECCEEECCCCEEECCCCEEEEEE
T ss_conf 8300887468995--667-78763302434-------36746897888034450103786899985
No 96
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=43.59 E-value=25 Score=15.87 Aligned_cols=44 Identities=7% Similarity=0.131 Sum_probs=29.9
Q ss_pred HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC----CCCCCCCCCEEEEE
Q ss_conf 368668999998767889899999998499038878845----11211799889993
Q gi|254780608|r 16 EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK----FNNRIQSGQVVRIP 68 (346)
Q Consensus 16 ~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk----~~~~v~~GD~I~i~ 68 (346)
.++..|..+|... +++.. .=.|-||+..+. .++.|+.||.|.|.
T Consensus 16 ~~~~tl~~Ll~~l--~l~~~-------giAvaiN~~iVPRs~W~~~~l~~gD~Iei~ 63 (69)
T PRK06083 16 PTSSSLAQIIEQL--SLPEL-------GCVFAINNQVVPRSEWQSTVLSEGDAISLF 63 (69)
T ss_pred CCCCCHHHHHHHH--CCCCC-------CEEEEECCEEECHHHCCCCCCCCCCEEEEE
T ss_conf 8998399999973--89988-------689997783843567160458999999999
No 97
>KOG3301 consensus
Probab=41.22 E-value=24 Score=15.96 Aligned_cols=18 Identities=28% Similarity=0.510 Sum_probs=7.8
Q ss_pred HHHHHHHCCCCEECCEEE
Q ss_conf 999999849903887884
Q gi|254780608|r 36 NLQKILRSGQVRVDKKRV 53 (346)
Q Consensus 36 ~~~~lir~G~V~VNG~~v 53 (346)
+...+|+.+.|+|+++.+
T Consensus 114 hARvLi~~rhI~V~~qiV 131 (183)
T KOG3301 114 HARVLIRQRHIRVGKQIV 131 (183)
T ss_pred HHHHHHCCCCEEECCEEE
T ss_conf 889874276076157576
No 98
>PRK01777 hypothetical protein; Validated
Probab=40.87 E-value=18 Score=16.70 Aligned_cols=29 Identities=21% Similarity=0.338 Sum_probs=22.9
Q ss_pred CCCCEECCEEECCCCCCCCCCEEEEECCC
Q ss_conf 49903887884511211799889993565
Q gi|254780608|r 43 SGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71 (346)
Q Consensus 43 ~G~V~VNG~~vk~~~~v~~GD~I~i~~~~ 71 (346)
...|=|=|+.++.++.|+.||+|+|+-+.
T Consensus 49 ~~~vGIfgk~~~ld~~L~~GDRVEIYRPL 77 (95)
T PRK01777 49 KNKVGIFSRPVKLTDVLRDGDRVEIYRPL 77 (95)
T ss_pred CCCEEEECCCCCCCCCCCCCCEEEEECCC
T ss_conf 47450788483887728999999985365
No 99
>TIGR01764 excise DNA binding domain, excisionase family; InterPro: IPR010093 An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This entry represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This entry identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (IPR000551 from INTERPRO).; GO: 0003677 DNA binding.
Probab=40.07 E-value=24 Score=15.89 Aligned_cols=22 Identities=5% Similarity=0.199 Sum_probs=18.2
Q ss_pred HHHHCCCCCHHHHHHHHHCCCCE
Q ss_conf 99876788989999999849903
Q gi|254780608|r 25 FKNHYPHINFVNLQKILRSGQVR 47 (346)
Q Consensus 25 L~~~~~~~sr~~~~~lir~G~V~ 47 (346)
.++.+ ++|+..+++||++|.+.
T Consensus 7 aA~yL-gv~~~t~~~l~~~g~l~ 28 (49)
T TIGR01764 7 AAEYL-GVSKSTVYRLIEEGELP 28 (49)
T ss_pred HHHHC-CCCHHHHHHHHHCCCCC
T ss_conf 99771-99905789999718985
No 100
>PRK11054 helD DNA helicase IV; Provisional
Probab=39.91 E-value=13 Score=17.66 Aligned_cols=72 Identities=25% Similarity=0.370 Sum_probs=41.5
Q ss_pred EEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCC--
Q ss_conf 078617856884176531122357853323320110111110013335445342224046212310122210233332--
Q gi|254780608|r 100 ILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR-- 177 (346)
Q Consensus 100 ~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~-- 177 (346)
-||..|+..+|| || ||+|-...+...+..+.......| +-+|++|-|++||..|.+-++++
T Consensus 204 Avi~~ed~~LVL---AG----AGSGKT~vLt~RiayLI~~g~~~P----------~~ILaLTFT~kAA~EMreRl~~~lg 266 (684)
T PRK11054 204 AVVNGEDSLLVL---AG----AGSGKTSVLVARAGWLLARGQAQP----------EQILLLAFGRKAAEEMDERIRERLG 266 (684)
T ss_pred HEEECCCCEEEE---EC----CCCCCHHHHHHHHHHHHHCCCCCH----------HHEEEEECCHHHHHHHHHHHHHHCC
T ss_conf 727479964898---33----899707799999999997599986----------6778686349999999999997549
Q ss_pred --CC-CCCCCCCCC
Q ss_conf --21-112000134
Q gi|254780608|r 178 --RI-QKIYWSLVW 188 (346)
Q Consensus 178 --~v-~K~Y~Aiv~ 188 (346)
.| -.|+++++-
T Consensus 267 ~~~v~~~TFHSlal 280 (684)
T PRK11054 267 TEDITARTFHALAL 280 (684)
T ss_pred CCCEEEEEHHHHHH
T ss_conf 99837865999999
No 101
>pfam03658 UPF0125 Uncharacterized protein family (UPF0125).
Probab=39.41 E-value=19 Score=16.51 Aligned_cols=28 Identities=21% Similarity=0.338 Sum_probs=22.8
Q ss_pred CCCCEECCEEECCCCCCCCCCEEEEECC
Q ss_conf 4990388788451121179988999356
Q gi|254780608|r 43 SGQVRVDKKRVKFNNRIQSGQVVRIPPV 70 (346)
Q Consensus 43 ~G~V~VNG~~vk~~~~v~~GD~I~i~~~ 70 (346)
+-.|=|=|+.++.++.|+.||+|+|.-+
T Consensus 46 ~~~vGIfgk~v~l~~~L~~GDRVEIYRP 73 (83)
T pfam03658 46 KNKVGIFGKPVKLDDPLKDGDRIEIYRP 73 (83)
T ss_pred CCCEEEECCCCCCCCCCCCCCEEEEECC
T ss_conf 4636468847388770799999999536
No 102
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=39.32 E-value=27 Score=15.65 Aligned_cols=43 Identities=14% Similarity=0.174 Sum_probs=30.6
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC----CCCCCCCCCEEEEE
Q ss_conf 68668999998767889899999998499038878845----11211799889993
Q gi|254780608|r 17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK----FNNRIQSGQVVRIP 68 (346)
Q Consensus 17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk----~~~~v~~GD~I~i~ 68 (346)
+++++-.+|++. +++-. .=.|.+||..+. ..+.++.||+|+|-
T Consensus 16 ~~~tv~dLL~~l--~~~~~-------~vav~vNg~iVpr~~~~~~~l~~gD~ievv 62 (68)
T COG2104 16 EGTTVADLLAQL--GLNPE-------GVAVAVNGEIVPRSQWADTILKEGDRIEVV 62 (68)
T ss_pred CCCCHHHHHHHH--CCCCC-------EEEEEECCEECCCHHHHHCCCCCCCEEEEE
T ss_conf 887399999972--99985-------599998899825046320131589989999
No 103
>pfam04669 DUF579 Protein of unknown function (DUF579). This is a eukaryotic family of uncharacterized proteins.
Probab=38.68 E-value=8.9 Score=18.67 Aligned_cols=54 Identities=17% Similarity=0.198 Sum_probs=26.8
Q ss_pred EEEECCC-EEEECCCCCCEEECCCCCCCC--CCCCHHHCCCCCCCC-CCCCCCCCCCCC
Q ss_conf 7861785-688417653112235785332--332011011111001-333544534222
Q gi|254780608|r 101 LLYEDSK-IYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQK-PRLTHRLDQETS 155 (346)
Q Consensus 101 IiyED~~-livinKPaGl~vhp~~g~~~~--~~~~l~~~~~~~~~~-~~lVHRLDr~TS 155 (346)
.+|+-++ +|+||.|.|..-. .+|-... ..+.+..-....+.. --.||+.||.+.
T Consensus 107 ~vy~~~WDvi~VD~P~G~~~~-~PGRM~aIytAg~laR~r~~~~~t~~VfVHdv~R~vE 164 (187)
T pfam04669 107 EVYKEKWDRIFVDAPEGYVED-APGRMGAIYTAGTLARSRASGEYTTTVFVHDVDRRVE 164 (187)
T ss_pred HHHCCCCCEEEEECCCCCCCC-CCCHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCHHH
T ss_conf 995570668998089998989-9850488999999975337899875089836884899
No 104
>pfam00498 FHA FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif.
Probab=38.48 E-value=30 Score=15.37 Aligned_cols=22 Identities=27% Similarity=0.490 Sum_probs=12.2
Q ss_pred CEECCEEECC-CCCCCCCCEEEE
Q ss_conf 0388788451-121179988999
Q gi|254780608|r 46 VRVDKKRVKF-NNRIQSGQVVRI 67 (346)
Q Consensus 46 V~VNG~~vk~-~~~v~~GD~I~i 67 (346)
..|||+++.. ...|+.||.|.+
T Consensus 44 t~vNg~~i~~~~~~L~~GD~i~i 66 (67)
T pfam00498 44 TFVNGQRLGPEPVRLKDGDVIRL 66 (67)
T ss_pred EEECCEECCCCCEECCCCCEEEE
T ss_conf 59999996788769999999984
No 105
>PRK10687 purine nucleoside phosphoramidase; Provisional
Probab=38.29 E-value=22 Score=16.13 Aligned_cols=16 Identities=25% Similarity=0.497 Sum_probs=12.5
Q ss_pred CCEEEEECCCEEEECC
Q ss_conf 4307861785688417
Q gi|254780608|r 98 KSILLYEDSKIYVFNK 113 (346)
Q Consensus 98 ~~~IiyED~~livinK 113 (346)
+-.++||||+++++-=
T Consensus 16 pa~~VyEdd~~~AFlD 31 (119)
T PRK10687 16 PSDIVYQDELVTAFRD 31 (119)
T ss_pred CCCEEEECCCEEEEEC
T ss_conf 7657974798899867
No 106
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=37.58 E-value=29 Score=15.43 Aligned_cols=42 Identities=12% Similarity=-0.001 Sum_probs=27.3
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC----CCCCCCCCCEEEEEC
Q ss_conf 668999998767889899999998499038878845----112117998899935
Q gi|254780608|r 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK----FNNRIQSGQVVRIPP 69 (346)
Q Consensus 19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk----~~~~v~~GD~I~i~~ 69 (346)
..|+..|.+. ++.-. .=.+-|||..+. .++.|+.||+|+|-.
T Consensus 15 ~tl~~Ll~el--g~~~~-------~vAvAvN~~~Vpr~~~~~~~L~eGDriEIv~ 60 (65)
T PRK06488 15 TTLALLLAEL--GYEGN-------WLATAVNGELVHSEARAQFVLHEGDRIEILS 60 (65)
T ss_pred HHHHHHHHHC--CCCCC-------CEEEEECCEEECHHHHCCCCCCCCCEEEEEC
T ss_conf 6899999972--98888-------0899989998742450545179999999964
No 107
>cd01278 aprataxin_related aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are predominantly eukaryotic in origin.
Probab=37.19 E-value=22 Score=16.17 Aligned_cols=14 Identities=36% Similarity=0.700 Sum_probs=11.7
Q ss_pred EEEEECCCEEEECC
Q ss_conf 07861785688417
Q gi|254780608|r 100 ILLYEDSKIYVFNK 113 (346)
Q Consensus 100 ~IiyED~~livinK 113 (346)
.++||||+++++.=
T Consensus 17 ~ivyEdd~~~af~D 30 (104)
T cd01278 17 DQVYEDDRVVVFKD 30 (104)
T ss_pred CEEEECCCEEEEEC
T ss_conf 67975797999967
No 108
>PRK11891 aspartate carbamoyltransferase; Provisional
Probab=36.76 E-value=31 Score=15.20 Aligned_cols=61 Identities=21% Similarity=0.422 Sum_probs=32.9
Q ss_pred HHHHHHHC-------CCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCEEEEECC----CCHHHHHHHHHHC
Q ss_conf 99999963-------980004644466522100013446241311000437588964999839----9789999999808
Q gi|254780608|r 255 LRVHALHM-------GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP----LPAHMVKTWDSLG 323 (346)
Q Consensus 255 IRvhl~~~-------g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~~~~~ap----lP~~f~~~l~~l~ 323 (346)
||-.+..+ .--++||-+||-.-.. + +.-|+.- .+-++.|.|| +|++..+.+..-|
T Consensus 229 I~~e~g~~~~~idGl~IalvGDLKyGRTVHS---------L---~klLs~y--~~v~~~lVSP~~L~mP~~i~~~l~~~g 294 (430)
T PRK11891 229 IQREFSRLGKIVDGAHIALVGDLKYGRTVHS---------L---VKLLALY--RGLKFTLVSPPTLEMPAYIVDQISTNG 294 (430)
T ss_pred HHHHHCCCCCCCCCCEEEEECCCCCCCCHHH---------H---HHHHHHC--CCCEEEEECCHHHCCCHHHHHHHHHCC
T ss_conf 9987532235557857998645456600989---------9---9999854--694699989213079889999999779
Q ss_pred CCCCCC
Q ss_conf 987520
Q gi|254780608|r 324 FKYDRN 329 (346)
Q Consensus 324 ~~~d~~ 329 (346)
.++.+.
T Consensus 295 ~~~~e~ 300 (430)
T PRK11891 295 HVIEQT 300 (430)
T ss_pred CEEEEE
T ss_conf 869993
No 109
>pfam01230 HIT HIT domain.
Probab=36.13 E-value=26 Score=15.70 Aligned_cols=15 Identities=33% Similarity=0.585 Sum_probs=12.2
Q ss_pred CCEEEEECCCEEEEC
Q ss_conf 430786178568841
Q gi|254780608|r 98 KSILLYEDSKIYVFN 112 (346)
Q Consensus 98 ~~~IiyED~~livin 112 (346)
+..||||||+++|+-
T Consensus 5 p~~ivyed~~~~afl 19 (98)
T pfam01230 5 PSTVVYEDDLVLAFL 19 (98)
T ss_pred CCCEEEECCCEEEEE
T ss_conf 761899789799998
No 110
>cd01669 TGS_Ygr210_C TGS_Ygr210_C: The C-terminal TGS domain of Ygr210 GTP-binding protein which is a member of Obg-like family of GTPases, and present in archaea. Several Obg-like family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. 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=35.27 E-value=22 Score=16.13 Aligned_cols=20 Identities=20% Similarity=0.353 Sum_probs=17.3
Q ss_pred ECCEEECCCCCCCCCCEEEE
Q ss_conf 88788451121179988999
Q gi|254780608|r 48 VDKKRVKFNNRIQSGQVVRI 67 (346)
Q Consensus 48 VNG~~vk~~~~v~~GD~I~i 67 (346)
+||+++..++.|+.||+|+|
T Consensus 55 ~~~r~v~~d~~L~~gDvi~I 74 (76)
T cd01669 55 RTGRRVGEDYELKHRDVIKI 74 (76)
T ss_pred ECCCCCCCCCCCCCCCEEEE
T ss_conf 05878588728479999998
No 111
>cd01276 PKCI_related Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a hydrophobic residue) that is a signature for this family. No enzymatic activity has been reported however, for PKCI and its related members.
Probab=33.01 E-value=32 Score=15.19 Aligned_cols=15 Identities=27% Similarity=0.549 Sum_probs=12.0
Q ss_pred EEEEECCCEEEECCC
Q ss_conf 078617856884176
Q gi|254780608|r 100 ILLYEDSKIYVFNKP 114 (346)
Q Consensus 100 ~IiyED~~livinKP 114 (346)
.++||||+++|+.=-
T Consensus 15 ~ivyede~~~aflD~ 29 (104)
T cd01276 15 KKVYEDDEVLAFHDI 29 (104)
T ss_pred CEEEECCCEEEEECC
T ss_conf 889979979999888
No 112
>cd01277 HINT_subgroup HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life. Although the biochemical function has not been characterised for many of the members of this subgroup, the proteins from Yeast have been shown to be involved in secretion, peroxisome formation and gene expression.
Probab=32.96 E-value=32 Score=15.19 Aligned_cols=16 Identities=31% Similarity=0.532 Sum_probs=12.2
Q ss_pred CCEEEEECCCEEEECC
Q ss_conf 4307861785688417
Q gi|254780608|r 98 KSILLYEDSKIYVFNK 113 (346)
Q Consensus 98 ~~~IiyED~~livinK 113 (346)
+..||||||+++|+.=
T Consensus 13 ~~~iv~E~e~~~af~d 28 (103)
T cd01277 13 PSYKVYEDDHVLAFLD 28 (103)
T ss_pred CCCEEEECCCEEEEEC
T ss_conf 7677997997999977
No 113
>pfam11969 DcpS_C Scavenger mRNA decapping enzyme C-term binding. This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the C-terminal region. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway. The C-terminal domain contains a histidine triad (HIT) sequence with three histidines separated by hydrophobic residues. The central histidine within the DcpS HIT motif is critical for decapping activity and defines the HIT motif as a new mRNA decapping domain, making DcpS the first member of the HIT family of proteins with a defined biological function.
Probab=31.75 E-value=34 Score=14.96 Aligned_cols=18 Identities=22% Similarity=0.420 Sum_probs=13.2
Q ss_pred CCEEEEECCCEEEECCCC
Q ss_conf 430786178568841765
Q gi|254780608|r 98 KSILLYEDSKIYVFNKPA 115 (346)
Q Consensus 98 ~~~IiyED~~livinKPa 115 (346)
+..++||||+++++.=-.
T Consensus 13 p~~ivyedd~~vaf~D~~ 30 (113)
T pfam11969 13 PERIVYEDDGFVAFKDIK 30 (113)
T ss_pred CCCEEEECCCEEEEECCC
T ss_conf 778899799999986899
No 114
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit; InterPro: IPR000438 Fatty acid synthesis involves a set of reactions, commencing with carboxylation of acetyl-CoA to malonyl-CoA. This is an irreversible reaction, catalysed by the acetyl-CoA carboxylase complex (6.4.1.2 from EC); a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase and two non-identical carboxyl transferase subunits (alpha and beta) in a 2:2 association . The reaction involves two steps: Biotin carrier protein + ATP + HCO_3^- = Carboxybiotin carrier protein + ADP + P_i Carboxybiotin carrier protein + Acetyl-CoA = Malonyl-CoA + Biotin carrier protein In the first step, biotin carboxylase catalyses the carboxylation of the carrier protein to form an intermediate. Next, the transcarboxylase complex transfers the carboxyl group from the intermediate to acetyl-CoA forming malonyl-CoA.; GO: 0003989 acetyl-CoA carboxylase activity, 0006633 fatty acid biosynthetic process, 0009317 acetyl-CoA carboxylase complex.
Probab=30.99 E-value=22 Score=16.21 Aligned_cols=46 Identities=15% Similarity=0.148 Sum_probs=28.3
Q ss_pred CCEECCCCCCCCCC-------CHHCCCCCCCHHHHHHHHEEECCCCCEEEEECCCCHHHHH
Q ss_conf 80004644466522-------1000134462413110004375889649998399789999
Q gi|254780608|r 264 CPIVGDHKYCANFK-------GNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHMVK 317 (346)
Q Consensus 264 ~PivGD~~Yg~~~~-------~~~~~~~~~r~~LHa~~l~f~hp~~~~~~~~aplP~~f~~ 317 (346)
-|++-|++|||-.. .++.+|+ .-|.|--|.==+=++-+.||+||+.
T Consensus 204 ISvLTdPT~GGVSASFA~LGDL~iAEPk--------AlIGFAGpRVIeQT~rekLPegFQt 256 (292)
T TIGR00515 204 ISVLTDPTTGGVSASFAMLGDLNIAEPK--------ALIGFAGPRVIEQTIREKLPEGFQT 256 (292)
T ss_pred EEECCCCCCCHHHHHHHHHHHHHHHCCC--------CCCCCCCCEEEEECCCCCCCCCHHH
T ss_conf 4413688972267898764025441564--------2312787502323265658670035
No 115
>TIGR02477 PFKA_PPi diphosphate--fructose-6-phosphate 1-phosphotransferase; InterPro: IPR011183 Diphosphate--fructose-6-phosphate 1-phosphotransferase catalyses the addition of phosphate from diphosphate (PPi) to fructose 6-phosphate to give fructose 1,6-bisphosphate (2.7.1.90 from EC). The enzyme is also known as pyrophosphate-dependent phosphofructokinase. The usage of PPi-dependent enzymes in glycolysis presumably frees up ATP for other processes . IPR012828 from INTERPRO represents the ATP-dependent 6-phosphofructokinase enzyme contained within Phosphofructokinase. This entry contains primarily bacterial, plant alpha, and plant beta sequences. These may be dimeric nonallosteric enzymes (bacteria) or allosteric heterotetramers (plants) . For additional information please see , , , .; GO: 0005524 ATP binding, 0047334 diphosphate-fructose-6-phosphate 1-phosphotransferase activity, 0006096 glycolysis, 0005945 6-phosphofructokinase complex.
Probab=30.75 E-value=3.6 Score=21.15 Aligned_cols=98 Identities=23% Similarity=0.335 Sum_probs=52.8
Q ss_pred CEEEEECC--CCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCC-----CCCCCCCCCCCCCE
Q ss_conf 40462123--1012221023333221112000134565410000000122346---55432-----11133555555530
Q gi|254780608|r 156 GILVVART--RAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKS---HIGGD-----YVHVVKQNEKGANY 225 (346)
Q Consensus 156 Glll~AK~--~~a~~~l~~~f~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~---~~~~~-----~~~~~~~~~~~~k~ 225 (346)
||||+.=+ ...|..|.+-|.++... ..|.|+|+ |||+.+.-.- .-+-+ +-.++-.-..|+..
T Consensus 171 gLVIIGGDdSNTnAA~LAEyF~~~~~~----t~viGVPK----TIDGDLKn~~iEtsFGFDTacK~YSElIGNi~rDA~S 242 (566)
T TIGR02477 171 GLVIIGGDDSNTNAALLAEYFAKKGLK----TQVIGVPK----TIDGDLKNQYIETSFGFDTACKVYSELIGNICRDALS 242 (566)
T ss_pred EEEEECCCCCHHHHHHHHHHHHHCCCC----CEEEEEEC----CCCHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 489974798679999999999973899----22786402----5472110271045876104788998875578887664
Q ss_pred EEEECCHHHHHHCCCCE--EEEEECHHHHHHHHHHHHHCCCCEECCCCC
Q ss_conf 34301013432024420--457861237899999999639800046444
Q gi|254780608|r 226 AISHFKVIDCFAQKFCW--LEMQPHTGRTHQLRVHALHMGCPIVGDHKY 272 (346)
Q Consensus 226 a~T~~~vl~~~~~~~sl--v~~~l~TGR~HQIRvhl~~~g~PivGD~~Y 272 (346)
|.=+|.-++-.|..+|. +||-|.| +=..-|+|...=
T Consensus 243 ~~KYwHFIrLMGRsASHiaLECALqT-----------hPN~ciigEEv~ 280 (566)
T TIGR02477 243 AKKYWHFIRLMGRSASHIALECALQT-----------HPNVCIIGEEVA 280 (566)
T ss_pred CCCCEEEEEECCCCHHHHHHHHHCCC-----------CCCEEEHHHHHH
T ss_conf 28713677743763158999873214-----------797675123355
No 116
>PRK07440 hypothetical protein; Provisional
Probab=30.57 E-value=40 Score=14.57 Aligned_cols=43 Identities=14% Similarity=0.144 Sum_probs=29.4
Q ss_pred HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECC----CCCCCCCCEEEE
Q ss_conf 3686689999987678898999999984990388788451----121179988999
Q gi|254780608|r 16 EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF----NNRIQSGQVVRI 67 (346)
Q Consensus 16 ~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~----~~~v~~GD~I~i 67 (346)
.++..|..+|... ++... .=.|-+||..+.. ++.++.||+|+|
T Consensus 17 ~~~~ti~~LL~~l--~~~~~-------~vaVE~N~~Iv~r~~~~~~~l~~gD~iEI 63 (70)
T PRK07440 17 SPGTTLPDLLQQL--GFNPR-------LVAVEYNGEILHRQFWEQTQVQPGDRLEI 63 (70)
T ss_pred CCCCCHHHHHHHC--CCCCC-------EEEEEECCEEECHHHCCCEECCCCCEEEE
T ss_conf 9999899999876--99987-------69999688670867707106799999999
No 117
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=30.06 E-value=40 Score=14.51 Aligned_cols=42 Identities=12% Similarity=0.120 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC----CCCCCCCCCEEEEE
Q ss_conf 68668999998767889899999998499038878845----11211799889993
Q gi|254780608|r 17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK----FNNRIQSGQVVRIP 68 (346)
Q Consensus 17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk----~~~~v~~GD~I~i~ 68 (346)
+|..+...|+. + +... .=.|-||+..+- ..+.|+.||+|.|-
T Consensus 14 ~g~tvadll~~-l-~~~~--------~~AVavN~~~VPRs~~~~~~L~~GD~ieiv 59 (65)
T PRK06944 14 DGATVADALAA-Y-GARP--------PFAVAVNGNFVARTQHAARALAAGDRLDLV 59 (65)
T ss_pred CCCCHHHHHHH-C-CCCC--------CEEEEECCEEECHHHHHHCCCCCCCEEEEE
T ss_conf 99979999986-2-8689--------779998479803145333127899999999
No 118
>pfam09014 Sushi_2 Beta-2-glycoprotein-1 fifth domain. The fifth domain of beta-2-glycoprotein-1 (b2GP-1) is composed of four well-defined anti-parallel beta-strands and two short alpha-helices, as well as a long highly flexible loop. It plays an important role in the binding of b2GP-1 to negatively charged compounds and subsequent capture for binding of anti-b2GP-1 antibodies.
Probab=29.87 E-value=32 Score=15.19 Aligned_cols=29 Identities=21% Similarity=0.271 Sum_probs=22.7
Q ss_pred HHCCCCEECCEEECC----CCCCCCCCEEEEEC
Q ss_conf 984990388788451----12117998899935
Q gi|254780608|r 41 LRSGQVRVDKKRVKF----NNRIQSGQVVRIPP 69 (346)
Q Consensus 41 ir~G~V~VNG~~vk~----~~~v~~GD~I~i~~ 69 (346)
|++++|..||+++.. ...+..||.|.++-
T Consensus 8 ikka~Vly~G~k~~i~d~~~~~ilHGe~VsffC 40 (85)
T pfam09014 8 IKKATVVYNGVKVKIQDLFKNMVLHGDKVTFFC 40 (85)
T ss_pred EEEEEEEECCEEECHHHCCCCCCEECCEEEEEE
T ss_conf 027899988789600350657602077789997
No 119
>TIGR00223 panD aspartate 1-decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process.
Probab=29.23 E-value=42 Score=14.42 Aligned_cols=54 Identities=19% Similarity=0.178 Sum_probs=32.3
Q ss_pred CCCCEEEEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECC
Q ss_conf 66830499984113686689999987678898999999984990388788451121179988999356
Q gi|254780608|r 3 LMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV 70 (346)
Q Consensus 3 ~M~~~~~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~ 70 (346)
|.+..+.=|| ....|.|+..|.-- +-.|. .|-|.|||.-++ .++.||+|-|-.+
T Consensus 38 ~lenekv~Iv-nvnNG~RfsTY~I~---gkkRG-------s~~IcvNGAAAr---~v~~GD~VII~sy 91 (127)
T TIGR00223 38 LLENEKVDIV-NVNNGKRFSTYVIA---GKKRG-------SRVICVNGAAAR---LVSVGDVVIILSY 91 (127)
T ss_pred CCCCCEEEEE-ECCCCCCEEEEEEC---CCCCC-------CEEEEECHHHHC---EECCCCEEEEEEE
T ss_conf 2899848998-66899712346651---42358-------723770504511---0023889998851
No 120
>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB; InterPro: IPR013374 This model describes a protein involved in type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly, and is closely related to GspE (IPR013369 from INTERPRO) of type II secretion systems (also referred to as the main terminal branch of the general secretion pathway). Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0009297 pilus biogenesis.
Probab=28.74 E-value=18 Score=16.71 Aligned_cols=21 Identities=29% Similarity=0.521 Sum_probs=13.6
Q ss_pred EEEECCCCCC-EEECCCCCCCC
Q ss_conf 6884176531-12235785332
Q gi|254780608|r 108 IYVFNKPAGI-SVQGGSGIAYH 128 (346)
Q Consensus 108 livinKPaGl-~vhp~~g~~~~ 128 (346)
+=+|+||.|| +|.|.+|++.+
T Consensus 319 L~Ai~kPqGMvLVTGPTGSGKT 340 (577)
T TIGR02538 319 LEAIHKPQGMVLVTGPTGSGKT 340 (577)
T ss_pred HHHHHCCCCCEEEECCCCCCHH
T ss_conf 9997079972886266598416
No 121
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=27.41 E-value=45 Score=14.22 Aligned_cols=45 Identities=13% Similarity=0.291 Sum_probs=31.1
Q ss_pred HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEEC
Q ss_conf 368668999998767889899999998499038878845112117998899935
Q gi|254780608|r 16 EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP 69 (346)
Q Consensus 16 ~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~ 69 (346)
..||.+-..|..- ++.-. .+| -+|||+.+-..+.++.||-+++-|
T Consensus 18 ~~gmkv~dvlr~v--gfnte---sai----akvngkvaled~~v~dgdyvevip 62 (67)
T PRK08364 18 RKGMKVADVLRAV--GFNTE---SAI----AKVNGRVALEEEEVKDGDYVEVIP 62 (67)
T ss_pred HCCCCHHHHHHHH--CCCCH---HHH----HEECCEEEECCCCCCCCCEEEEEE
T ss_conf 5088899999984--67607---665----503766873247667897389997
No 122
>PRK02268 hypothetical protein; Provisional
Probab=26.10 E-value=47 Score=14.07 Aligned_cols=44 Identities=9% Similarity=0.126 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCCCCC
Q ss_conf 88989999999849903887884511211799889993565542
Q gi|254780608|r 31 HINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74 (346)
Q Consensus 31 ~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~~~~ 74 (346)
-.|+..+++..+.|=..++..+..+=.++++||.|....+....
T Consensus 8 VaS~~HV~~g~~~GF~QvcHGK~apL~Rm~~GD~ivYYSPk~~~ 51 (141)
T PRK02268 8 VVSAEHVRRGVEGGFMQVCHGKAAPLRRMKPGDWIIYYSPKTTF 51 (141)
T ss_pred EEEHHHHHHHHHCCEEEECCCCCCHHHCCCCCCEEEEECCEEEC
T ss_conf 54099999887487534137840155328999989995784104
No 123
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=25.47 E-value=49 Score=14.00 Aligned_cols=43 Identities=16% Similarity=0.183 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC----CCCCCCCCCEEEEE
Q ss_conf 68668999998767889899999998499038878845----11211799889993
Q gi|254780608|r 17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK----FNNRIQSGQVVRIP 68 (346)
Q Consensus 17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk----~~~~v~~GD~I~i~ 68 (346)
++..|..+|... +++.. .=.|-+|+..+. .++.|+.||.|+|-
T Consensus 14 ~~~tl~~Ll~~l--~~~~~-------~vAVevN~~ivpr~~~~~~~L~egD~iEIv 60 (66)
T PRK05659 14 DGESVAALLARE--GLAGR-------RVAVEVNGEIVPRSQHASTALREGDVVEIV 60 (66)
T ss_pred CCCCHHHHHHHC--CCCCC-------CEEEEECCEECCHHHHCCCCCCCCCEEEEE
T ss_conf 999699999876--99998-------099998998817789572658999999999
No 124
>TIGR01969 minD_arch cell division ATPase MinD; InterPro: IPR010224 Proper placement of the bacterial cell division site requires the site-specific inactivation of other potential division sites. In Escherichia coli, selection of the correct mid-cell site is mediated by the MinC, MinD and MinE proteins. Several members of this family are found in archaeal genomes but their function is uncharacterised. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. This entry represents the archaeal MinD family. The exact roles of the various archaeal MinD homologs are unknown. .
Probab=24.70 E-value=33 Score=15.10 Aligned_cols=52 Identities=13% Similarity=0.315 Sum_probs=30.3
Q ss_pred EEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCC-----------CCCCCCC-CCCCCCCCCCCEEE
Q ss_conf 78617856884176531122357853323320110111-----------1100133-35445342224046
Q gi|254780608|r 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVD-----------SKGQKPR-LTHRLDQETSGILV 159 (346)
Q Consensus 101 IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~-----------~~~~~~~-lVHRLDr~TSGlll 159 (346)
=|.||-|||.||=||||- ...+..++..-.- ....+.. +.-|||-.--|++|
T Consensus 105 ~i~~~~D~lLIDAPAGL~-------~~a~~Al~~a~elLLVvNPEi~SItDaLK~k~va~~lGt~ilG~vl 168 (258)
T TIGR01969 105 EIIDDTDFLLIDAPAGLE-------RDAVTALAAADELLLVVNPEISSITDALKVKIVAEKLGTAILGVVL 168 (258)
T ss_pred HHHCCCCEEEEECCCCCC-------HHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf 872043778874789833-------7899999861866486676544677788999998760883246899
No 125
>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein; InterPro: IPR011924 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry represents LolD, a member of the ABC transporter family. LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on the residue immediately following the modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. Excluded from this entry are homologs from the archaeal genus Methanosarcina .; GO: 0005524 ATP binding, 0006810 transport, 0016020 membrane.
Probab=24.04 E-value=37 Score=14.74 Aligned_cols=39 Identities=26% Similarity=0.370 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCCCEEEEECCCCHHHHHCC----CCCCCCCCCCCC
Q ss_conf 33354453422240462123101222102----333322111200
Q gi|254780608|r 144 PRLTHRLDQETSGILVVARTRAAAQHLTE----SFRMRRIQKIYW 184 (346)
Q Consensus 144 ~~lVHRLDr~TSGlll~AK~~~a~~~l~~----~f~~~~v~K~Y~ 184 (346)
.|+..=||.+|||=|+| +.+..+.|+. .+|++..-=.|.
T Consensus 48 LHlLGGLD~PT~G~v~f--~G~~l~~lS~~~~~~LRN~~LGFiYQ 90 (221)
T TIGR02211 48 LHLLGGLDNPTSGEVLF--NGQSLSKLSSNERAKLRNKKLGFIYQ 90 (221)
T ss_pred HHHHHCCCCCCCCEEEE--CCCCHHHCCHHHHHHHHHHHCCCEEE
T ss_conf 99873068996315897--06323440446788751222584443
No 126
>COG1977 MoaD Molybdopterin converting factor, small subunit [Coenzyme metabolism]
Probab=23.81 E-value=52 Score=13.80 Aligned_cols=23 Identities=17% Similarity=0.339 Sum_probs=17.5
Q ss_pred CCEEECCCCCCCCCCEEEEECCC
Q ss_conf 87884511211799889993565
Q gi|254780608|r 49 DKKRVKFNNRIQSGQVVRIPPVI 71 (346)
Q Consensus 49 NG~~vk~~~~v~~GD~I~i~~~~ 71 (346)
|...+..++.|+.||+|.+.|+.
T Consensus 59 ~~~~~~~~t~L~dGDeVa~~PPV 81 (84)
T COG1977 59 NEFLVGLDTPLKDGDEVAFFPPV 81 (84)
T ss_pred CEEECCCCCCCCCCCEEEEECCC
T ss_conf 34764777526899999994898
No 127
>PRK07570 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated
Probab=23.22 E-value=42 Score=14.38 Aligned_cols=64 Identities=13% Similarity=0.187 Sum_probs=35.3
Q ss_pred CCEEEEEECHHHCCCCHHHHHHH---HCC---CCCHHHHHHHHHCC-----CCEECCEE-------ECCCCC---CCCCC
Q ss_conf 83049998411368668999998---767---88989999999849-----90388788-------451121---17998
Q gi|254780608|r 5 TYVQYVVVENDEENMRLDRWFKN---HYP---HINFVNLQKILRSG-----QVRVDKKR-------VKFNNR---IQSGQ 63 (346)
Q Consensus 5 ~~~~~~~V~~~~~g~RLd~~L~~---~~~---~~sr~~~~~lir~G-----~V~VNG~~-------vk~~~~---v~~GD 63 (346)
++.+.+.|+....||.+...|.. .+. .-| =.++.-.|.| .+.|||++ ..-.+. +..|+
T Consensus 17 p~~q~y~v~~~~~~mtVL~aL~~i~~~~~~~~~~p-LsfR~sCr~giCGSCam~ING~p~~~~~~~LAC~t~v~~~~~g~ 95 (247)
T PRK07570 17 GKFETYEVKDISPDMSFLEMLDVLNEQLILKGEEP-VAFDHDCREGICGMCGLVINGRPHGPDRGTTTCQLHMRSFKDGD 95 (247)
T ss_pred CCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCC-EEEECCCCCCCCCCCEEEECCCCCCCCCCCCCEECHHHHCCCCC
T ss_conf 73288880688998849999999999876526996-47742567776776841688852777656541025123278898
Q ss_pred EEEEEC
Q ss_conf 899935
Q gi|254780608|r 64 VVRIPP 69 (346)
Q Consensus 64 ~I~i~~ 69 (346)
.|.|-|
T Consensus 96 ~I~ieP 101 (247)
T PRK07570 96 TITIEP 101 (247)
T ss_pred CEEECC
T ss_conf 137724
No 128
>COG5037 TOS9 Gluconate transport-inducing protein [Signal transduction mechanisms / Carbohydrate transport and metabolism]
Probab=22.38 E-value=29 Score=15.45 Aligned_cols=35 Identities=11% Similarity=0.087 Sum_probs=17.7
Q ss_pred CCCCCCEEEEEECHHHCCCCHHHHHHHHCCCCCHH
Q ss_conf 97668304999841136866899999876788989
Q gi|254780608|r 1 MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFV 35 (346)
Q Consensus 1 ~~~M~~~~~~~V~~~~~g~RLd~~L~~~~~~~sr~ 35 (346)
|.+|+...=+|=+++++-.-+++.....++.+.|+
T Consensus 1 mdi~pTf~GyI~te~DalLlf~a~r~G~l~~I~RR 35 (248)
T COG5037 1 MDIMPTFYGYIETEEDALLLFQAVRLGYLPRIERR 35 (248)
T ss_pred CCCCCCEEEEECCHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 98664324675776788899999970663212122
No 129
>KOG4476 consensus
Probab=22.38 E-value=29 Score=15.45 Aligned_cols=35 Identities=11% Similarity=0.087 Sum_probs=17.7
Q ss_pred CCCCCCEEEEEECHHHCCCCHHHHHHHHCCCCCHH
Q ss_conf 97668304999841136866899999876788989
Q gi|254780608|r 1 MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFV 35 (346)
Q Consensus 1 ~~~M~~~~~~~V~~~~~g~RLd~~L~~~~~~~sr~ 35 (346)
|.+|+...=+|=+++++-.-+++.....++.+.|+
T Consensus 1 mdi~pTf~GyI~te~DalLlf~a~r~G~l~~I~RR 35 (248)
T KOG4476 1 MDIMPTFYGYIETEEDALLLFQAVRLGYLPRIERR 35 (248)
T ss_pred CCCCCCEEEEECCHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 98664324675776788899999970663212122
No 130
>COG2914 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.36 E-value=55 Score=13.68 Aligned_cols=29 Identities=24% Similarity=0.408 Sum_probs=21.5
Q ss_pred CCCCEECCEEECCCCCCCCCCEEEEECCC
Q ss_conf 49903887884511211799889993565
Q gi|254780608|r 43 SGQVRVDKKRVKFNNRIQSGQVVRIPPVI 71 (346)
Q Consensus 43 ~G~V~VNG~~vk~~~~v~~GD~I~i~~~~ 71 (346)
...+=|=++.++..+.|+.||+|+|.-+.
T Consensus 49 ~n~~GI~~k~~kl~~~l~dgDRVEIyRPL 77 (99)
T COG2914 49 ENKVGIYSKPVKLDDELHDGDRVEIYRPL 77 (99)
T ss_pred CCCEEEECCCCCCCCCCCCCCEEEEECCC
T ss_conf 24034771455764402578778986354
No 131
>PRK00943 selenophosphate synthetase; Provisional
Probab=22.21 E-value=28 Score=15.48 Aligned_cols=11 Identities=36% Similarity=0.416 Sum_probs=5.8
Q ss_pred CCHHHHHHHHH
Q ss_conf 89899999998
Q gi|254780608|r 32 INFVNLQKILR 42 (346)
Q Consensus 32 ~sr~~~~~lir 42 (346)
+|...+.++++
T Consensus 21 v~~~~L~~~L~ 31 (347)
T PRK00943 21 ISPKVLETILK 31 (347)
T ss_pred CCHHHHHHHHH
T ss_conf 69899999997
No 132
>COG2514 Predicted ring-cleavage extradiol dioxygenase [General function prediction only]
Probab=22.14 E-value=56 Score=13.60 Aligned_cols=32 Identities=3% Similarity=-0.045 Sum_probs=23.9
Q ss_pred CCCCEEEEEECHHHHHHHHHHHHH-CCCCEECC
Q ss_conf 244204578612378999999996-39800046
Q gi|254780608|r 238 QKFCWLEMQPHTGRTHQLRVHALH-MGCPIVGD 269 (346)
Q Consensus 238 ~~~slv~~~l~TGR~HQIRvhl~~-~g~PivGD 269 (346)
....+=.+.+.||.--+-+.--.. +|++++.+
T Consensus 165 ~~t~IGHvHL~v~~l~eA~~fY~~~LG~~~~~~ 197 (265)
T COG2514 165 AGTIIGHVHLKVADLEEAEQFYEDVLGLEVTAR 197 (265)
T ss_pred CCCEEEEEEEEECCHHHHHHHHHHHCCCEEEEC
T ss_conf 776886777884788999999997509863302
No 133
>TIGR01249 pro_imino_pep_1 proline iminopeptidase; InterPro: IPR005944 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of serine peptidase belong to MEROPS peptidase family S33 (clan SC). They are proline iminopeptidase (Prolyl aminopeptidase, 3.4.11.5 from EC), which catalyzes the removal of the N-terminal proline from peptides. This family represents one of two related families of proline iminopeptidase containing the alpha/beta fold. The fine specificities of the various members, including both the range of short peptides from which proline can be removed and whether other amino acids such as alanine can be also removed, may vary among members. ; GO: 0016804 prolyl aminopeptidase activity, 0005737 cytoplasm.
Probab=22.13 E-value=47 Score=14.12 Aligned_cols=15 Identities=40% Similarity=0.769 Sum_probs=10.5
Q ss_pred CCCCCEE---ECCCCCCC
Q ss_conf 7653112---23578533
Q gi|254780608|r 113 KPAGISV---QGGSGIAY 127 (346)
Q Consensus 113 KPaGl~v---hp~~g~~~ 127 (346)
||.|-|| |+|+|.+.
T Consensus 24 nP~G~PV~~lHGGPGsGt 41 (310)
T TIGR01249 24 NPDGKPVVFLHGGPGSGT 41 (310)
T ss_pred CCCCCEEEEEECCCCCCC
T ss_conf 989954899756878998
No 134
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=21.63 E-value=58 Score=13.53 Aligned_cols=25 Identities=24% Similarity=0.191 Sum_probs=14.9
Q ss_pred CCCCEECCEEECCCCCCCCCCEEEEECC
Q ss_conf 4990388788451121179988999356
Q gi|254780608|r 43 SGQVRVDKKRVKFNNRIQSGQVVRIPPV 70 (346)
Q Consensus 43 ~G~V~VNG~~vk~~~~v~~GD~I~i~~~ 70 (346)
+|.|.+||..+ .+++.||.|.|-.+
T Consensus 65 Sg~I~lNGaAA---~~~~~GD~vII~sy 89 (111)
T cd06919 65 SGVICLNGAAA---RLGQPGDRVIIMAY 89 (111)
T ss_pred CCEEEECCHHH---HCCCCCCEEEEEEC
T ss_conf 87687466786---21799999999987
No 135
>TIGR01683 thiS thiamine biosynthesis protein ThiS; InterPro: IPR010035 This entry identifies the ThiS family, which are thiamine-biosynthesis proteins related to MoaD (IPR010034 from INTERPRO). MoaD is a molybdenum cofactor biosynthesis protein. Both ThiS and MoaD proteins are involved in sulphur transfer..
Probab=20.88 E-value=60 Score=13.43 Aligned_cols=44 Identities=14% Similarity=0.114 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECC----CCCCCCCCEEEEE
Q ss_conf 686689999987678898999999984990388788451----1211799889993
Q gi|254780608|r 17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF----NNRIQSGQVVRIP 68 (346)
Q Consensus 17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~----~~~v~~GD~I~i~ 68 (346)
.++.+..+|.. +...+... =.|-+|+..+.. ++.|+.||.|.|-
T Consensus 12 ~~~t~~~LL~~-~~~~~~~~-------vave~N~~ivp~~~w~~~~l~~gD~iEiv 59 (65)
T TIGR01683 12 DGTTLAALLES-LGLDPKRR-------VAVEVNGEIVPRSEWEDTILKEGDRIEIV 59 (65)
T ss_pred CCCCHHHHHHH-HCCCCCCE-------EEEEECCEEECCCCCCCEEECCCCEEEEE
T ss_conf 88887898886-07535874-------89986983408345675101589858899
No 136
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR; InterPro: IPR014178 Members of this entry are transcriptional regulators of fatty acid metabolism (FadR), including both biosynthesis and beta-oxidation reactions, which are found exclusively in a subset of Gammaproteobacteria with strictly one copy per genome. Proteins have an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR when expressed in Escherichia coli shows differences in regulatory response and fatty acid binding profiles. All members of this entry are expected to have the same function.; GO: 0000062 acyl-CoA binding, 0003677 DNA binding, 0003700 transcription factor activity, 0019217 regulation of fatty acid metabolic process.
Probab=20.54 E-value=50 Score=13.94 Aligned_cols=34 Identities=26% Similarity=0.344 Sum_probs=22.5
Q ss_pred HHHHHHCCCCCHH----HHHHHHHCCCCEE-CCEEECCCC
Q ss_conf 9999876788989----9999998499038-878845112
Q gi|254780608|r 23 RWFKNHYPHINFV----NLQKILRSGQVRV-DKKRVKFNN 57 (346)
Q Consensus 23 ~~L~~~~~~~sr~----~~~~lir~G~V~V-NG~~vk~~~ 57 (346)
|=|+++. |++|+ -+|||-|.|=.+| .||++|.|+
T Consensus 34 RELsElI-GVTRTTLREVLQRLARDGWLTIQHGKPTKVNn 72 (275)
T TIGR02812 34 RELSELI-GVTRTTLREVLQRLARDGWLTIQHGKPTKVNN 72 (275)
T ss_pred HHHHHHC-CCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf 6575423-76630378999887641134365889986276
Done!