Query 015839
Match_columns 399
No_of_seqs 429 out of 1954
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 01:22:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015839.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015839hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1919 RNA pseudouridylate sy 100.0 1.8E-59 3.9E-64 463.9 11.3 333 50-394 14-358 (371)
2 COG0564 RluA Pseudouridylate s 100.0 8.4E-58 1.8E-62 443.6 4.2 263 74-343 7-278 (289)
3 TIGR00005 rluA_subfam pseudour 100.0 3.4E-54 7.5E-59 421.8 4.5 262 75-342 1-277 (299)
4 PRK11025 23S rRNA pseudouridyl 100.0 4.1E-54 8.9E-59 424.4 4.2 263 73-343 13-293 (317)
5 PRK11180 rluD 23S rRNA pseudou 100.0 7.6E-54 1.6E-58 423.9 4.3 268 67-343 5-292 (325)
6 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 4.2E-49 9.1E-54 375.7 5.7 229 105-343 2-235 (246)
7 cd02557 PseudoU_synth_ScRIB2 P 100.0 1.1E-46 2.4E-51 351.8 5.1 184 128-318 2-187 (213)
8 TIGR01621 RluA-like pseudourid 100.0 3.1E-45 6.6E-50 342.9 0.5 185 142-340 2-186 (217)
9 PRK10158 23S rRNA/tRNA pseudou 100.0 1.4E-44 3.1E-49 339.0 4.3 194 141-343 13-208 (219)
10 cd02563 PseudoU_synth_TruC tRN 100.0 1.8E-43 3.8E-48 332.5 4.5 194 142-343 1-213 (223)
11 PRK11112 tRNA pseudouridine sy 100.0 3.9E-43 8.4E-48 336.7 4.1 194 142-343 2-214 (257)
12 PRK10839 16S rRNA pseudouridyl 100.0 7.9E-42 1.7E-46 323.1 -0.2 202 80-317 1-204 (232)
13 cd02869 PseudoU_synth_RluCD_li 100.0 1.2E-38 2.7E-43 289.6 3.1 165 151-322 1-169 (185)
14 PRK10700 23S rRNA pseudouridyl 100.0 9.2E-39 2E-43 310.7 -2.3 205 80-314 3-211 (289)
15 COG1187 RsuA 16S rRNA uridine- 100.0 1E-37 2.3E-42 294.0 1.5 205 79-316 2-213 (248)
16 PRK10475 23S rRNA pseudouridin 100.0 9.5E-38 2.1E-42 303.1 -3.2 199 78-314 5-204 (290)
17 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 4.2E-35 9.1E-40 260.3 1.9 148 151-312 1-148 (154)
18 cd02870 PseudoU_synth_RsuA_lik 100.0 1E-34 2.2E-39 255.7 0.6 140 151-312 1-140 (146)
19 cd02556 PseudoU_synth_RluB Pse 100.0 3.4E-34 7.3E-39 258.0 -1.5 144 150-314 1-144 (167)
20 cd02553 PseudoU_synth_RsuA Pse 100.0 3.3E-33 7.2E-38 251.5 -2.7 144 151-320 2-147 (167)
21 PF00849 PseudoU_synth_2: RNA 100.0 7.3E-32 1.6E-36 240.7 0.3 151 150-305 1-164 (164)
22 cd02566 PseudoU_synth_RluE Pse 100.0 2.4E-31 5.1E-36 239.7 -2.6 155 151-317 1-159 (168)
23 PRK11394 23S rRNA pseudouridin 100.0 1.2E-30 2.6E-35 242.7 -0.5 160 148-320 38-201 (217)
24 cd02555 PSSA_1 PSSA_1: Pseudou 100.0 3.3E-30 7.1E-35 233.9 -2.2 144 149-319 4-156 (177)
25 TIGR00093 pseudouridine syntha 99.9 6.3E-28 1.4E-32 208.0 -2.1 112 189-320 1-112 (128)
26 cd02554 PseudoU_synth_RluF Pse 99.9 7E-28 1.5E-32 215.8 -2.2 137 151-316 2-139 (164)
27 cd02868 PseudoU_synth_hTruB2_l 98.9 1.7E-10 3.6E-15 108.5 -0.7 74 150-229 1-75 (226)
28 cd00165 S4 S4/Hsp/ tRNA synthe 98.8 8.7E-10 1.9E-14 82.8 0.7 69 80-155 1-70 (70)
29 PF01479 S4: S4 domain; Inter 98.4 3.1E-08 6.8E-13 70.4 -2.1 47 80-126 1-48 (48)
30 TIGR02988 YaaA_near_RecF S4 do 98.2 1.9E-07 4.2E-12 69.4 -1.7 51 78-128 7-58 (59)
31 COG1188 Ribosome-associated he 97.7 3.9E-06 8.4E-11 68.4 -1.1 54 78-132 7-61 (100)
32 smart00363 S4 S4 RNA-binding d 97.6 1.5E-05 3.3E-10 57.5 -0.3 51 80-130 1-52 (60)
33 cd02572 PseudoU_synth_hDyskeri 97.5 2.8E-05 6.2E-10 71.0 0.0 70 149-230 2-71 (182)
34 PRK00989 truB tRNA pseudouridi 97.1 9.6E-05 2.1E-09 69.6 -0.4 71 149-230 9-79 (230)
35 PLN00051 RNA-binding S4 domain 97.1 7.7E-05 1.7E-09 72.1 -1.2 53 76-129 188-241 (267)
36 TIGR03069 PS_II_S4 photosystem 97.1 9.7E-05 2.1E-09 71.1 -0.8 54 75-129 179-233 (257)
37 cd00506 PseudoU_synth_TruB_lik 97.1 0.00013 2.7E-09 68.2 -0.2 68 151-230 2-69 (210)
38 PRK10348 ribosome-associated h 97.0 8.6E-05 1.9E-09 64.1 -1.3 51 79-129 8-58 (133)
39 cd01291 PseudoU_synth PseudoU_ 97.0 6.4E-05 1.4E-09 60.1 -2.4 62 184-307 24-87 (87)
40 PRK04099 truB tRNA pseudouridi 97.0 0.00016 3.5E-09 69.8 -0.3 70 149-230 2-71 (273)
41 CHL00113 rps4 ribosomal protei 96.9 0.00014 2.9E-09 67.5 -1.1 52 78-129 87-139 (201)
42 TIGR01017 rpsD_bact ribosomal 96.9 0.00013 2.7E-09 67.8 -1.4 52 78-129 88-140 (200)
43 TIGR00431 TruB tRNA pseudourid 96.9 0.0002 4.3E-09 66.7 -0.5 69 150-230 3-71 (209)
44 PRK00020 truB tRNA pseudouridi 96.9 0.00022 4.8E-09 67.7 -0.2 70 149-230 10-79 (244)
45 PRK02484 truB tRNA pseudouridi 96.7 0.00034 7.4E-09 68.4 -0.2 69 150-230 4-72 (294)
46 PRK14124 tRNA pseudouridine sy 96.7 0.00039 8.5E-09 68.4 0.1 70 149-230 3-72 (308)
47 PRK03287 truB tRNA pseudouridi 96.7 0.00041 8.9E-09 67.9 0.1 71 148-230 8-78 (298)
48 PRK00130 truB tRNA pseudouridi 96.6 0.00045 9.7E-09 67.5 -0.2 70 149-230 2-71 (290)
49 PRK02193 truB tRNA pseudouridi 96.6 0.00047 1E-08 67.0 -0.3 68 151-230 2-69 (279)
50 PRK14123 tRNA pseudouridine sy 96.6 0.00047 1E-08 67.8 -0.3 70 149-230 3-72 (305)
51 PRK05389 truB tRNA pseudouridi 96.6 0.00047 1E-08 67.8 -0.4 70 149-230 13-82 (305)
52 PRK02755 truB tRNA pseudouridi 96.6 0.00047 1E-08 67.5 -0.4 69 149-230 3-71 (295)
53 cd02573 PseudoU_synth_EcTruB P 96.5 0.00053 1.1E-08 66.6 -0.4 68 151-230 2-69 (277)
54 PRK01851 truB tRNA pseudouridi 96.5 0.00061 1.3E-08 66.8 -0.1 70 149-230 16-85 (303)
55 PRK14846 truB tRNA pseudouridi 96.5 0.00064 1.4E-08 67.3 -0.1 70 149-230 3-72 (345)
56 PRK01550 truB tRNA pseudouridi 96.5 0.00063 1.4E-08 66.9 -0.1 70 149-230 2-71 (304)
57 PRK04270 H/ACA RNA-protein com 96.5 0.00066 1.4E-08 66.9 -0.1 72 147-230 20-91 (300)
58 TIGR00478 tly hemolysin TlyA f 96.5 0.0004 8.8E-09 65.7 -1.5 49 81-129 1-50 (228)
59 PRK05033 truB tRNA pseudouridi 96.5 0.00065 1.4E-08 66.9 -0.2 70 149-230 10-79 (312)
60 PRK05327 rpsD 30S ribosomal pr 96.5 0.00043 9.2E-09 64.4 -1.5 51 79-129 92-143 (203)
61 COG2302 Uncharacterized conser 96.5 0.00055 1.2E-08 64.6 -0.8 51 78-129 179-230 (257)
62 PRK01528 truB tRNA pseudouridi 96.3 0.00096 2.1E-08 65.2 0.0 70 149-230 3-72 (292)
63 PRK14122 tRNA pseudouridine sy 96.2 0.0011 2.4E-08 65.3 -0.2 68 151-230 3-70 (312)
64 COG0522 RpsD Ribosomal protein 96.1 0.0018 3.8E-08 60.2 0.5 52 80-131 94-146 (205)
65 PRK04642 truB tRNA pseudouridi 95.8 0.002 4.4E-08 63.1 -0.3 70 149-230 10-79 (300)
66 TIGR00425 CBF5 rRNA pseudourid 95.8 0.0019 4.1E-08 64.2 -0.6 71 148-230 33-103 (322)
67 PF13275 S4_2: S4 domain; PDB: 95.5 0.0016 3.4E-08 49.4 -2.0 50 78-128 6-57 (65)
68 PRK11507 ribosome-associated p 95.4 0.0031 6.6E-08 48.4 -0.7 52 78-129 10-62 (70)
69 COG0130 TruB Pseudouridine syn 95.4 0.0041 8.9E-08 60.2 -0.1 69 150-230 16-84 (271)
70 COG1189 Predicted rRNA methyla 95.3 0.0041 8.9E-08 58.7 -0.4 52 79-130 2-54 (245)
71 cd02867 PseudoU_synth_TruB_4 P 95.3 0.0049 1.1E-07 60.8 0.0 42 185-230 57-98 (312)
72 PRK04051 rps4p 30S ribosomal p 93.8 0.016 3.5E-07 52.6 -0.2 49 79-127 102-151 (177)
73 COG2501 S4-like RNA binding pr 93.4 0.026 5.6E-07 43.6 0.3 51 78-129 10-62 (73)
74 PLN00189 40S ribosomal protein 92.8 0.049 1.1E-06 50.1 1.3 39 93-131 122-161 (194)
75 PTZ00155 40S ribosomal protein 90.5 0.19 4.1E-06 45.8 2.5 49 80-129 107-157 (181)
76 TIGR01018 rpsD_arch ribosomal 90.1 0.13 2.9E-06 46.0 1.1 47 80-126 104-151 (162)
77 PRK01777 hypothetical protein; 86.8 0.39 8.4E-06 39.2 1.7 51 78-130 25-75 (95)
78 PRK04313 30S ribosomal protein 86.7 0.27 5.9E-06 46.6 0.9 72 78-156 36-109 (237)
79 PF14451 Ub-Mut7C: Mut7-C ubiq 85.8 0.41 8.9E-06 37.9 1.3 43 79-129 32-74 (81)
80 PTZ00223 40S ribosomal protein 83.3 0.44 9.6E-06 46.1 0.6 72 78-156 37-110 (273)
81 PLN00036 40S ribosomal protein 83.3 0.44 9.5E-06 45.8 0.6 72 78-156 40-113 (261)
82 PTZ00118 40S ribosomal protein 82.2 0.48 1E-05 45.6 0.4 73 77-156 39-113 (262)
83 KOG2559 Predicted pseudouridin 78.7 1.1 2.5E-05 42.4 1.6 21 186-206 91-111 (318)
84 PF01509 TruB_N: TruB family p 75.7 1.4 3E-05 39.0 1.2 44 183-230 6-49 (149)
85 COG1471 RPS4A Ribosomal protei 75.1 0.98 2.1E-05 42.5 0.1 70 80-156 41-112 (241)
86 PRK05659 sulfur carrier protei 67.1 5.6 0.00012 29.6 2.7 43 78-129 14-60 (66)
87 COG2104 ThiS Sulfur transfer p 65.4 6.5 0.00014 30.0 2.8 42 79-129 17-62 (68)
88 PRK11130 moaD molybdopterin sy 60.2 4.3 9.3E-05 31.7 1.0 24 106-129 52-75 (81)
89 PRK08364 sulfur carrier protei 56.9 8.7 0.00019 29.2 2.2 43 78-129 22-64 (70)
90 PRK13354 tyrosyl-tRNA syntheta 55.1 3 6.6E-05 43.0 -0.8 47 79-125 342-389 (410)
91 PRK06437 hypothetical protein; 54.9 7.4 0.00016 29.4 1.5 43 78-129 19-61 (67)
92 cd00754 MoaD Ubiquitin domain 51.7 7.7 0.00017 29.7 1.2 50 79-129 25-74 (80)
93 cd00565 ThiS ThiaminS ubiquiti 50.4 8.8 0.00019 28.5 1.2 42 79-129 14-59 (65)
94 PF02824 TGS: TGS domain; Int 45.3 9.9 0.00022 28.0 0.8 22 107-128 37-58 (60)
95 PF02597 ThiS: ThiS family; I 45.0 11 0.00024 28.5 1.0 50 77-129 19-71 (77)
96 PRK05912 tyrosyl-tRNA syntheta 43.4 6.5 0.00014 40.5 -0.6 44 79-122 342-386 (408)
97 cd01764 Urm1 Urm1-like ubuitin 39.4 15 0.00032 29.8 1.0 24 106-129 61-88 (94)
98 TIGR01682 moaD molybdopterin c 38.5 16 0.00035 28.2 1.1 24 106-129 51-74 (80)
99 PF06353 DUF1062: Protein of u 37.0 6.9 0.00015 34.4 -1.4 33 78-111 101-133 (142)
100 TIGR01687 moaD_arch MoaD famil 36.6 14 0.0003 29.1 0.4 25 105-129 56-82 (88)
101 PRK06488 sulfur carrier protei 36.0 18 0.0004 26.8 1.0 42 79-129 14-59 (65)
102 PRK07440 hypothetical protein; 33.3 28 0.0006 26.5 1.6 43 78-129 18-64 (70)
103 PLN02799 Molybdopterin synthas 33.2 22 0.00047 27.6 1.1 24 106-129 53-76 (82)
104 PF00498 FHA: FHA domain; Int 32.2 37 0.0008 24.9 2.2 25 104-128 41-67 (68)
105 PRK07696 sulfur carrier protei 27.8 34 0.00074 25.7 1.3 41 80-129 17-61 (67)
106 cd01666 TGS_DRG_C TGS_DRG_C: 27.7 27 0.00059 27.1 0.7 24 106-129 51-74 (75)
107 COG0317 SpoT Guanosine polypho 27.6 34 0.00074 37.7 1.7 28 106-133 424-451 (701)
108 COG4332 Uncharacterized protei 27.6 7 0.00015 35.5 -2.9 49 78-127 137-186 (203)
109 PF08068 DKCLD: DKCLD (NUC011) 26.5 32 0.0007 25.5 0.9 17 147-163 40-56 (59)
110 TIGR01683 thiS thiamine biosyn 25.2 44 0.00094 24.7 1.4 42 79-129 13-58 (64)
111 PRK11092 bifunctional (p)ppGpp 24.6 33 0.00072 38.0 1.0 26 106-131 423-448 (702)
112 PF06170 DUF983: Protein of un 24.3 52 0.0011 26.3 1.8 23 356-378 6-28 (86)
113 cd01668 TGS_RelA_SpoT TGS_RelA 23.9 59 0.0013 22.9 1.9 44 78-128 15-58 (60)
114 PRK08053 sulfur carrier protei 21.7 54 0.0012 24.4 1.4 42 79-129 15-60 (66)
115 PRK06944 sulfur carrier protei 21.6 46 0.001 24.4 1.0 41 79-129 15-59 (65)
No 1
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=100.00 E-value=1.8e-59 Score=463.90 Aligned_cols=333 Identities=38% Similarity=0.567 Sum_probs=271.6
Q ss_pred CCCceeeCCeecccceeeeeehhccccccCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeeeeEEEecccccccc
Q 015839 50 KEDYIFRDGRRNVKPYYFEFISHVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHF 129 (399)
Q Consensus 50 ~~~~~~~~~~r~v~P~~~~~~~~v~~~~~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~ 129 (399)
..+|++++|+|++.|||++|.++++.+|.++.+.++|+.+|...++.+++..|+.|.|++||+.+...+.++.+|.|.+.
T Consensus 14 ~~~~~~~~~~~~v~pyy~~~~~~~~~rw~~k~~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~~v~~i~k~~d~l~~~ 93 (371)
T KOG1919|consen 14 EISVYIDGGLRKVAPYYFTYRTFVKGRWAGKKLVDVFVSEFRLRERAYYESAIKLGRVTVNGEQVRVSLIVKNGDVLCHT 93 (371)
T ss_pred ccceeecCCcceeeeEEEeeeEEEeeeecccchHHHHHHHHhcCchHhhhhhhhcCceEECcEeeeeEEEeccCCEEEEe
Confidence 45788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCeeeccceeeccCCCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchh
Q 015839 130 LHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKA 209 (399)
Q Consensus 130 ~~~~e~pv~~~~~~IlyEd~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a 209 (399)
+|+|+|++....+.|+|||++|+|||||+|++|||++.+..|++..++........+++|||||+.|||||+||++.+.+
T Consensus 94 vhrh~p~~~~~~~~Iv~ed~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~~~~~~~~~~hRLDr~tSGllvlAkt~~~~ 173 (371)
T KOG1919|consen 94 VHRHEPPVAYLPIRIVFEDKDYVVVNKPHGIPVHPTGRYRENTITKILAALHKVEGLRPCHRLDRLTSGLLVLAKTKEAA 173 (371)
T ss_pred eccCCCCccccccceEEecCCEEEEeCCCCCceeccCccccccchHHHHHhccccccccccccCccccceEEEEechhHh
Confidence 99999999888999999999999999999999999999999999999887655567899999999999999999999999
Q ss_pred HHHHHHHhhchhhhhh-heeeccccC-CCceEEeeeeeeccc-CCccccccCCCCCCCCCCCcccccceEEeecCCeeeE
Q 015839 210 DLFRQQIEAGKVIKRY-IARVNGVFP-EGEQVVDVNINYNAS-AGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSI 286 (399)
Q Consensus 210 ~~L~~~~~~~~v~K~Y-lA~V~G~~~-~~~~~i~~~i~~~~~-~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~sl 286 (399)
..+.++|+++.+.|.| +|.|.|.|+ .+...+..++..... .+.....+. ..+...++.|+|.|+++.+++..++
T Consensus 174 ~~~~~~~r~~~~~k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~~~~~~l~~~~---~~~~~~~k~a~T~~~~~~~~~~ss~ 250 (371)
T KOG1919|consen 174 DKFHEVLRKRTVKKEYVVARVEGPFPVVGEVEIKEPIGEEERPLRMGLNAVG---VRDEVAAKDAKTLFKVLSYDGGSSL 250 (371)
T ss_pred HHHHHHHhcccceeEEEEEEEeccCCCCceEEeCCCccccccccceEeeecc---cccccccccceeEEEEcccCCceEE
Confidence 9999999999999999 799999999 555577776654322 011111111 1111358999999999999998999
Q ss_pred EEeecccCceeEEEEEeeeeCcccccCceeecccccc--ccCCCccccccccc-------cCCCCCCCCCcCCCCCcccc
Q 015839 287 VLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTH--REGMSADRAAAYSH-------HSPPPVSSDKSESSSEDFSI 357 (399)
Q Consensus 287 V~~~l~TGRtHQIR~hla~lG~PIvGD~~Yg~~~~~~--~~~~~~~~~~~~~~-------~lp~~~~~~~~~~~~~~~~~ 357 (399)
|+|.|+||||||||+||+++|+||+||.+|++...|+ +.-.........+. .-....+.|..........+
T Consensus 251 V~~~PlTGRtHQIRvHlq~lG~PI~gD~~Y~~~~~~~~~P~~g~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (371)
T KOG1919|consen 251 VECRPLTGRTHQIRVHLQYLGHPIAGDPKYGNHIVWAGLPFTGREGTAKKKSLEEEIQRLIDVHLLENWLGFHPRTGPLI 330 (371)
T ss_pred EEeeccCCcHHHHHHHHHHhCCCcCCCcccccccccccCCCCCCCCCccccCccccccccchhhccccccccccccccch
Confidence 9999999999999999999999999999998877776 21111111110110 00001111221222333667
Q ss_pred CccCcCCCCCCcccccccccCchhhhhhhhhhceeee
Q 015839 358 DPMCTNCPNLAPKGKRLLSSNSLEDLCYGHMRQYQTS 394 (399)
Q Consensus 358 ~~~C~~c~~~~~~~~~~~~~~~~~~l~lha~~y~~~~ 394 (399)
+++|.+|..+ ..+ ++.+|||||+|....
T Consensus 331 ~~~~~~C~~~--------~~~-Dl~~~lha~~y~~~~ 358 (371)
T KOG1919|consen 331 EELCQECKVP--------IDN-DLELFLHALKYEMKG 358 (371)
T ss_pred hhhhhhCCCC--------CCc-hHhHhhhhcccccCC
Confidence 8899999975 122 789999999998764
No 2
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.4e-58 Score=443.59 Aligned_cols=263 Identities=30% Similarity=0.385 Sum_probs=223.3
Q ss_pred cccccCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeeeeEEEecccccccccccCCC--Ceeec--cceeeccCC
Q 015839 74 KNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHRHEP--PVMAW--DVSILQKEP 149 (399)
Q Consensus 74 ~~~~~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~~~~~e~--pv~~~--~~~IlyEd~ 149 (399)
...+.|+||++||+..++ +||+.+.++|++|.|+|||+++..+++|+.||+|.+....+.. ...+. ++.|||||+
T Consensus 7 ~~~~~g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vNg~~v~~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED~ 85 (289)
T COG0564 7 PEEEAGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVKPSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDE 85 (289)
T ss_pred ChhhcCCCHHHHHHHccC-cCHHHHHHHHHCCCEEECCEEccCCeeeCCCCEEEEecccccccccccccCCCccEEEecC
Confidence 346789999999999555 9999999999999999999999999999999999987754322 12222 367999999
Q ss_pred CeEEeecCCCcccccCcccccceEEEEeecccC--CCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhe
Q 015839 150 DVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHD--LAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIA 227 (399)
Q Consensus 150 ~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~--~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA 227 (399)
++||||||+||+|||++.+...|++..|..... ..++++||||||+||||||||||..++..|+++|+++.+.|+|+|
T Consensus 86 ~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~A 165 (289)
T COG0564 86 DLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDGVERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKKTYLA 165 (289)
T ss_pred CEEEEECCCCCcCcCCCCCccHhHHHHHHHhccccCCceeeeccCCCCCceEEEEECCHHHHHHHHHHHhcCcCcEEEEE
Confidence 999999999999999988888888877665432 356899999999999999999999999999999999999999999
Q ss_pred eeccccCCCceEEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCe-eeEEEeecccCceeEEEEEeeee
Q 015839 228 RVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGT-HSIVLCEPITGRTHQIRVHLQYT 306 (399)
Q Consensus 228 ~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~-~slV~~~l~TGRtHQIR~hla~l 306 (399)
+|.|.++.+.++|+.+|..+............ .+|+.|+|.|++++..++ .|||+|+|+||||||||+||++|
T Consensus 166 lv~G~~~~~~~~i~~pi~r~~~~~~~~~v~~~------~~gk~A~T~~~~l~~~~~~~tlv~~~~~TGRTHQIRVHl~~l 239 (289)
T COG0564 166 LVRGHLPEDEGTIDAPIGRDPKNRKKMAVVKE------GSGKPAITHYEVLERFGDNYTLVELKPETGRTHQIRVHLAHL 239 (289)
T ss_pred EEECcccCCCCEEeeeeecCCcCCceEEEecc------CCCCceEEEEEehhccCCceEEEEEEeCCCCHhHHHHHHHHC
Confidence 99999999889999999987655444333221 138999999999999887 59999999999999999999999
Q ss_pred CcccccCceeeccc--cccccCCCccccccccccCCCCC
Q 015839 307 GYPIANDMLYLCEH--VTHREGMSADRAAAYSHHSPPPV 343 (399)
Q Consensus 307 G~PIvGD~~Yg~~~--~~~~~~~~~~~~~~~~~~lp~~~ 343 (399)
||||+||++||... ........++++..+.|.+|.+-
T Consensus 240 ghPI~GD~~Yg~~~~~~~~~~~r~~LHA~~l~f~hp~t~ 278 (289)
T COG0564 240 GHPIVGDPLYGGKDKSAGAGLKRQALHAYKLSFTHPLTG 278 (289)
T ss_pred CCCeeCCcccCCchhhcccCcchhhhhhceeEccCCCCC
Confidence 99999999999852 22225567788889999998873
No 3
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=100.00 E-value=3.4e-54 Score=421.79 Aligned_cols=262 Identities=30% Similarity=0.407 Sum_probs=215.8
Q ss_pred ccccCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEeccccccccccc-CCC--CeeeccceeeccCCC
Q 015839 75 NRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHR-HEP--PVMAWDVSILQKEPD 150 (399)
Q Consensus 75 ~~~~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~-~e~--pv~~~~~~IlyEd~~ 150 (399)
++|.|+||++||+..|+.+||+.++++|++|.|+|||+.+ ++++.|+.||.|.+.... +++ +.....++|+|||++
T Consensus 1 ~~~~g~rLd~~L~~~~~~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~I~i~~~~~~~~~~~~~~~~~~i~~ed~~ 80 (299)
T TIGR00005 1 EEQAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDED 80 (299)
T ss_pred CCccchhHHHHHHHhcccCCHHHHHHHHHCCcEEECCEeccCcccCCCCCCEEEEecCCcccccCCccCCCccEEEeCCC
Confidence 3788999999999998679999999999999999999654 789999999999985542 222 121224679999999
Q ss_pred eEEeecCCCcccccCcccccceEEEEeecccCC----CCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhh
Q 015839 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDL----APLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYI 226 (399)
Q Consensus 151 ~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~----~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~Yl 226 (399)
|||||||+|++||+++....+|++++|...... ..+++|||||++||||||||+|+++++.|+++|+++.|.|+|+
T Consensus 81 ~lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~ 160 (299)
T TIGR00005 81 IIVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYV 160 (299)
T ss_pred EEEEECCCCCeEeCCCCCCcccHHHHHHHhcccccCCCcCceECCCCCCCceEEEEEcCHHHHHHHHHHHHhCCcceEEE
Confidence 999999999999998887778888877654321 4589999999999999999999999999999999999999999
Q ss_pred eeeccccCCCceEEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeEEEEEeeee
Q 015839 227 ARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYT 306 (399)
Q Consensus 227 A~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR~hla~l 306 (399)
|+|.|.++.+.++|+.+|..+........ +.. ..++++|.|+|+++....+.|+|+|+|+|||+||||+||+++
T Consensus 161 a~v~g~~~~~~~~i~~~l~~~~~~~~~~~-~~~-----~~~~k~a~t~~~~l~~~~~~slv~~~l~tGR~HQIR~hla~l 234 (299)
T TIGR00005 161 ALVHGQFDSGGGTVDAPLGRVPNNRGLMA-VHP-----SSEGKPAVTHFRVLERFGNASLVECELETGRTHQIRVHLQYL 234 (299)
T ss_pred EEEeccccCCCCEEeCceecCCCCCceEE-Eec-----CCCCCeeeEEEEEeEEcCCeEEEEEEeCCCChHHHHHHHHHC
Confidence 99999999888889988876433221111 110 125889999999998777789999999999999999999999
Q ss_pred CcccccCceeeccccc-------cccCCCccccccccccCCCC
Q 015839 307 GYPIANDMLYLCEHVT-------HREGMSADRAAAYSHHSPPP 342 (399)
Q Consensus 307 G~PIvGD~~Yg~~~~~-------~~~~~~~~~~~~~~~~lp~~ 342 (399)
||||+||.+||+...+ ......++++..+.|.+|.+
T Consensus 235 G~pI~gD~~Yg~~~~~~~~~~~~~~~~r~~Lha~~l~f~~p~~ 277 (299)
T TIGR00005 235 GHPLAGDPLYGNKPVPGNNLNGLLNFDRQALHAYELGFIHPAT 277 (299)
T ss_pred CCcEeCccccCCccccccccccccCCcchhhccCeeeccCCCC
Confidence 9999999999975432 11235678888899988866
No 4
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=4.1e-54 Score=424.39 Aligned_cols=263 Identities=27% Similarity=0.346 Sum_probs=212.0
Q ss_pred ccccccCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeeeeEEEeccccccccccc----CCCCee-------ecc
Q 015839 73 VKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHR----HEPPVM-------AWD 141 (399)
Q Consensus 73 v~~~~~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~~~~----~e~pv~-------~~~ 141 (399)
+...++|+||++||+..|+..||+.++++|++|.|+|||+++.++++|+.||.|.+.... .++|+. ...
T Consensus 13 v~~~~~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v~~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~~~ 92 (317)
T PRK11025 13 ISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKVAALA 92 (317)
T ss_pred ECcccCCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEcCcccccCCCCEEEeCCCCccccccccccccccccccCc
Confidence 556778999999999888889999999999999999999999999999999999875321 112221 134
Q ss_pred ceeeccCCCeEEeecCCCcccccCcccccceEEEEeecc-cCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhch
Q 015839 142 VSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAE-HDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGK 220 (399)
Q Consensus 142 ~~IlyEd~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~-~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~ 220 (399)
+.|+|||++|||||||+|++|||++.... ++.+.+... .....+++|||||++||||||||+|..+++.|+++|.++.
T Consensus 93 ~~Ilyed~~~lvvnKP~gl~~~~~~~~~~-~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~ 171 (317)
T PRK11025 93 DVILYEDDHILVLNKPSGTAVHGGSGLSF-GVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKG 171 (317)
T ss_pred CCEEEECCCEEEEECCCCCcCcCCCCCCc-cHHHHHHHhccCCCcCceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCC
Confidence 68999999999999999999999765433 344433321 1123367899999999999999999999999999999999
Q ss_pred hhhhhheeeccccCCCceEEeeeeeecccCCc-cccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeEE
Q 015839 221 VIKRYIARVNGVFPEGEQVVDVNINYNASAGR-STAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQI 299 (399)
Q Consensus 221 v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~-~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQI 299 (399)
|.|+|+|+|.|.++...+.|+.+|..+..... ..+.+ .++|+.|.|+|++++...+.|||+|+|+|||||||
T Consensus 172 v~K~Y~a~v~G~~~~~~~~i~~~i~~~~~~~~~~~~~~-------~~~gk~a~T~~~~l~~~~~~sLv~~~~~TGRtHQI 244 (317)
T PRK11025 172 MQKDYLALVRGQWQSHVKVVQAPLLKNILQSGERIVRV-------SQEGKPSETRFKVEERYAFATLVRASPVTGRTHQI 244 (317)
T ss_pred ccEEEEEEEeCcccCCCceEecccccCcccCCceEEec-------CCCCccceEEEEEeEEcCCcEEEEEEeCCCCHHHH
Confidence 99999999999998877889999876532221 11111 24789999999999988889999999999999999
Q ss_pred EEEeeeeCcccccCceeecccccc-----ccCCCccccccccccCCCCC
Q 015839 300 RVHLQYTGYPIANDMLYLCEHVTH-----REGMSADRAAAYSHHSPPPV 343 (399)
Q Consensus 300 R~hla~lG~PIvGD~~Yg~~~~~~-----~~~~~~~~~~~~~~~lp~~~ 343 (399)
|+||+++||||+||.+||...... .....++++..+.|.+|.+-
T Consensus 245 Rvhla~lG~PIlGD~~Yg~~~~~~~~~~~~~~r~~LHa~~l~f~~P~~~ 293 (317)
T PRK11025 245 RVHTQYAGHPIAFDDRYGDREFDQQLTGTGLNRLFLHAAALKFTHPGTG 293 (317)
T ss_pred HHHHHHCCCCEECCcccCCcccchhhhccCCcchhhhcCcceeeCCCCC
Confidence 999999999999999999643211 12346788889999998763
No 5
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=7.6e-54 Score=423.95 Aligned_cols=268 Identities=21% Similarity=0.250 Sum_probs=217.8
Q ss_pred eeeehhccccccCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEecccccccccccCCCC---eeeccc
Q 015839 67 FEFISHVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPP---VMAWDV 142 (399)
Q Consensus 67 ~~~~~~v~~~~~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~p---v~~~~~ 142 (399)
..+...++.+|.|+||+++|++.|+.+||+.++++|++|.|+|||+.+ .+++.|+.||.|.+.....++. ....++
T Consensus 5 ~~~~~~v~~~~~g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~ 84 (325)
T PRK11180 5 VQLTATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQDIPL 84 (325)
T ss_pred EEEEEEECcccCCccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEeeccccccCCCCCCCCC
Confidence 345556788999999999999998889999999999999999999998 6899999999999875432211 112357
Q ss_pred eeeccCCCeEEeecCCCcccccCcccccceEEEEeeccc----CCCCcccchhhhhhhhheeeeecccchhHHHHHHHhh
Q 015839 143 SILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEH----DLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEA 218 (399)
Q Consensus 143 ~IlyEd~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~----~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~ 218 (399)
.|||||++|||||||+|++|||++.....|+.+.|.... ....+++|||||++||||||||||.+++..|+++|.+
T Consensus 85 ~iiyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~ 164 (325)
T PRK11180 85 DIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQK 164 (325)
T ss_pred cEEEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHhhhccCCcccceeccCCCCCceeEEEECCHHHHHHHHHHHHh
Confidence 899999999999999999999987766677776554322 1235779999999999999999999999999999999
Q ss_pred chhhhhhheeeccccCCCceEEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeE
Q 015839 219 GKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQ 298 (399)
Q Consensus 219 ~~v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQ 298 (399)
+.|.|+|+|+|.|.++. ++.|+.+|....... ..+.+ ...++.|.|.|+++....+.|+|+|+|+||||||
T Consensus 165 ~~v~K~Y~A~v~G~~~~-~~~i~~~l~~~~~~~-~~~~~-------~~~gk~a~T~~~~l~~~~~~slv~~~~~TGRtHQ 235 (325)
T PRK11180 165 REITREYEAVAIGHMTA-GGTVDEPISRHPTKR-THMAV-------HPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQ 235 (325)
T ss_pred CCcceEEEEEEecCCCC-CCEEECceecCCCcC-cEEEe-------CCCCcEEeEEEEEeEEcCCeEEEEEEeCCCCHHH
Confidence 99999999999999875 567888886533221 11111 1468899999999988777999999999999999
Q ss_pred EEEEeeeeCcccccCceeecccccc------------ccCCCccccccccccCCCCC
Q 015839 299 IRVHLQYTGYPIANDMLYLCEHVTH------------REGMSADRAAAYSHHSPPPV 343 (399)
Q Consensus 299 IR~hla~lG~PIvGD~~Yg~~~~~~------------~~~~~~~~~~~~~~~lp~~~ 343 (399)
||+||+++||||+||.+||+..... .....++++..++|.+|.+-
T Consensus 236 IRvhla~lG~PI~GD~~Yg~~~~~~~~~~~~~~~~~~~~~r~~Lha~~l~f~hP~~~ 292 (325)
T PRK11180 236 IRVHMAHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITG 292 (325)
T ss_pred HHHHHHhCCCCEeCccccCCCcccccccchhhhhhccccchhhhhcceeEeeCCCCC
Confidence 9999999999999999999753210 01346788888998888763
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=4.2e-49 Score=375.68 Aligned_cols=229 Identities=24% Similarity=0.304 Sum_probs=182.0
Q ss_pred eeeEecCeeeeeeEEEeccccccccccc-CCCCeeeccceeeccCCCeEEeecCCCcccccCcccccceEEEEeecccCC
Q 015839 105 GRIQVDEEMVPVSYTVKSSQKISHFLHR-HEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDL 183 (399)
Q Consensus 105 G~V~VNGk~v~~~~~v~~gD~I~~~~~~-~e~pv~~~~~~IlyEd~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~ 183 (399)
+.|.+||+.++.+++|+.||.|.+.... +++++ +.++.|||||++|+|||||+|++|||++....+|++..+......
T Consensus 2 ~~~~~ng~~~~~~~~l~~gd~i~~~~~~~~~~~~-~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~~~ 80 (246)
T cd02558 2 LVVDADGEPLDPDSPYRPGTFVWYYRELPDEPPI-PFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTGN 80 (246)
T ss_pred eeECCCCcCCCCCceecCCCEEEEeCCCCCCCCC-CCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHhCC
Confidence 3456899999999999999999876432 23332 345889999999999999999999999888788888777654444
Q ss_pred CCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeeccccCCCce-EEeeeeeecccCCccccccCCCCC
Q 015839 184 APLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQ-VVDVNINYNASAGRSTAESGDSLG 262 (399)
Q Consensus 184 ~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~G~~~~~~~-~i~~~i~~~~~~~~~~~~~~~~~~ 262 (399)
..+++|||||++||||||||||.++++.|+.+|+++.+.|+|+|+|.|.++.+.. .++.+|...... .....
T Consensus 81 ~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~YlA~v~G~~~~~~~~~~~~~i~~~~~~--~~~~~----- 153 (246)
T cd02558 81 PDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYEAVAPYVPALTFPLTVRSRIVKGRGF--FQARE----- 153 (246)
T ss_pred CcccccccCCCCceeEEEEEcCHHHHHHHHHHHHcCCccEEEEEEEecCCCCCCCcceeccccccCCc--ceeec-----
Confidence 5688999999999999999999999999999999999999999999999864433 455555433211 11100
Q ss_pred CCCCCCcccccceEEeecCCeeeEEEeecccCceeEEEEEeeeeCcccccCceeecccccc---ccCCCccccccccccC
Q 015839 263 DTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTH---REGMSADRAAAYSHHS 339 (399)
Q Consensus 263 ~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR~hla~lG~PIvGD~~Yg~~~~~~---~~~~~~~~~~~~~~~l 339 (399)
.++++.|.|+|++++...+.|+|+|+|+||||||||+||+++||||+||.+||...... .....++++..+.|.+
T Consensus 154 --~~~~~~a~T~~~~l~~~~~~slv~~~l~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~Lha~~l~f~h 231 (246)
T cd02558 154 --VEGEPNAETRIELLARRGGWGLYRLSPHTGKTHQLRVHMAALGVPILNDPFYPVLLDKDPDDFSRPLQLLAKELEFTD 231 (246)
T ss_pred --cCCCCCceEEEEEEEecCCeEEEEEEeCCCCHHHHHHHHHHCCCcccCCccCCCCCcccccccccCchhhhcccCccC
Confidence 13567899999999877779999999999999999999999999999999999742111 1123578888899999
Q ss_pred CCCC
Q 015839 340 PPPV 343 (399)
Q Consensus 340 p~~~ 343 (399)
|.+.
T Consensus 232 P~t~ 235 (246)
T cd02558 232 PLTG 235 (246)
T ss_pred CCCC
Confidence 8764
No 7
>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=1.1e-46 Score=351.82 Aligned_cols=184 Identities=52% Similarity=0.827 Sum_probs=159.6
Q ss_pred cccccCCCCeeeccceeeccCCCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccc
Q 015839 128 HFLHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNAS 207 (399)
Q Consensus 128 ~~~~~~e~pv~~~~~~IlyEd~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~ 207 (399)
+.+|.+|||+....++|+|||++|||||||+|++|++++.....|+.++|........+++|||||++||||||||||++
T Consensus 2 ~~~~~~~~~~~~~~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~~~~~~~vhRLD~~TSGllllak~~~ 81 (213)
T cd02557 2 HTVHRHEPPVTNDPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGLTELRPCHRLDRLTSGLLLFAKTSQ 81 (213)
T ss_pred ccccccCCCCCCCCCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcCCCCccCccCCCCCCceEEEEECCHH
Confidence 45788999998888999999999999999999999998877778888888765443468899999999999999999999
Q ss_pred hhHHHHHHHhhchhhhhhheeeccccCCCceEEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCC--eee
Q 015839 208 KADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNG--THS 285 (399)
Q Consensus 208 ~a~~L~~~~~~~~v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~--~~s 285 (399)
++++|+++|.++.+.|+|+|+|.|.++.+.+.++.++..+......... ....++.|.|.|+++.... +.|
T Consensus 82 ~~~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~-------~~~~~~~a~t~~~~~~~~~~~~~s 154 (213)
T cd02557 82 TASRLQQQIRSREVKKEYLARVKGEFPDGEVVVDQPIGLVSPKGGLRND-------VDEKGKDARTIFKRLSYNGDLNTS 154 (213)
T ss_pred HHHHHHHHHHcCCccEEEEEEEeCcCCCCCeEEecceeccCcCCceeec-------cCCCCceeeEEEEEEEEcCCCCeE
Confidence 9999999999999999999999999988888898888754322111110 1246789999999998765 789
Q ss_pred EEEeecccCceeEEEEEeeeeCcccccCceeec
Q 015839 286 IVLCEPITGRTHQIRVHLQYTGYPIANDMLYLC 318 (399)
Q Consensus 286 lV~~~l~TGRtHQIR~hla~lG~PIvGD~~Yg~ 318 (399)
+|+|+|+|||+||||+||+++||||+||.+||.
T Consensus 155 lv~v~~~TGR~HQIR~hla~lG~PIlGD~~Yg~ 187 (213)
T cd02557 155 VVLCKPITGRTHQIRVHLQYLGHPIVNDPIYNN 187 (213)
T ss_pred EEEEEeCCCCHHHHHHHHHHCCCCCcCccccCC
Confidence 999999999999999999999999999999997
No 8
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621. This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, 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=3.1e-45 Score=342.95 Aligned_cols=185 Identities=26% Similarity=0.345 Sum_probs=151.1
Q ss_pred ceeeccCCCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchh
Q 015839 142 VSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKV 221 (399)
Q Consensus 142 ~~IlyEd~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v 221 (399)
++|||||++|+|||||+|++||++.. ..++.+.+........+++|||||++||||||||+|.++++.|+++|+++.+
T Consensus 2 ~~ilyed~~~lvvnKP~Gl~v~~~~~--~~~l~~~l~~~~~~~~~~~VhRLDr~TSGlll~Ak~~~~~~~L~~~~~~~~v 79 (217)
T TIGR01621 2 FEILFTHPDFLLINKHPGISVHKDDG--ETGLLQEVATQLGVGQVWLVHRLDKMTSGILLLALNAESASELSQGFAKRKI 79 (217)
T ss_pred ceEEEeCCCEEEEECCCCCeECCCCC--cChHHHHHHHhcCCCCccEecCCCCCCceEEEEEcCHHHHHHHHHHHhcCCc
Confidence 46999999999999999999998753 2345544443333346889999999999999999999999999999999999
Q ss_pred hhhhheeeccccCCCceEEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeEEEE
Q 015839 222 IKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRV 301 (399)
Q Consensus 222 ~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR~ 301 (399)
.|+|+|+|.|.++.+++.|+.++..... +... +. ...++.|.|+|+++....+.|+|+|+|+||||||||+
T Consensus 80 ~K~YlAlV~g~~~~~~~~i~~~~~~~~~-~~~~--~~------~~~~k~a~t~~~~~~~~~~~slv~~~~~TGR~HQIRv 150 (217)
T TIGR01621 80 EKTYLALSSKKPKKKQGLICGDMEKSRR-GSWK--LV------NSQENPAITRFFSASAATGLRLFILKPHTGKTHQLRV 150 (217)
T ss_pred cEEEEEEEeccccCCCCEEeCCcccCCC-CCEE--Ee------CCCCCceeEEEEEEEEcCCeEEEEEEeCCCCHHHHHH
Confidence 9999999999998888888887754322 2111 11 1357889999999988778999999999999999999
Q ss_pred EeeeeCcccccCceeeccccccccCCCccccccccccCC
Q 015839 302 HLQYTGYPIANDMLYLCEHVTHREGMSADRAAAYSHHSP 340 (399)
Q Consensus 302 hla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~lp 340 (399)
||+++||||+||.+||..... ...++++..+.|.++
T Consensus 151 hla~lG~PIlGD~~Yg~~~~~---~~~~Lha~~l~f~~~ 186 (217)
T TIGR01621 151 AMKSLGSPILGDPLYGTTDES---DRGYLHAFALRFDYQ 186 (217)
T ss_pred HHHHCCCceeCCcccCCCCCc---cCceeeeeEeEEEEC
Confidence 999999999999999975322 345677777877764
No 9
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=100.00 E-value=1.4e-44 Score=338.96 Aligned_cols=194 Identities=25% Similarity=0.325 Sum_probs=158.1
Q ss_pred cceeeccCCCeEEeecCCCcccccCcc-cccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhc
Q 015839 141 DVSILQKEPDVLTVCKPPSVPVHPCGQ-YRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAG 219 (399)
Q Consensus 141 ~~~IlyEd~~~ivvnKP~Gl~v~p~~~-~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~ 219 (399)
.++|||||++|+|||||+|++||+... ....++.+.+.... ..+++|||||++||||||||+|.++++.|+++|.++
T Consensus 13 ~~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~--~~~~~vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~ 90 (219)
T PRK10158 13 WLVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY--PQAESVHRLDMATSGVIVVALTKAAERELKRQFRER 90 (219)
T ss_pred CCCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC--CCCCEECCCCCCCceEEEEECCHHHHHHHHHHHHhC
Confidence 367999999999999999999998653 33456666665433 357899999999999999999999999999999999
Q ss_pred hhhhhhheeeccccCCCceEEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCe-eeEEEeecccCceeE
Q 015839 220 KVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGT-HSIVLCEPITGRTHQ 298 (399)
Q Consensus 220 ~v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~-~slV~~~l~TGRtHQ 298 (399)
.|.|+|+|+|.|.++.++++++.+|..+....... .+. .++++.|.|+|++++...+ .++|+|+|+||||||
T Consensus 91 ~v~K~Yla~v~G~~~~~~~~i~~~i~~~~~~~~~~-~~~------~~~gk~a~t~~~~l~~~~~~~sll~~~~~TGRtHQ 163 (219)
T PRK10158 91 EPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQ-KVC------YETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQ 163 (219)
T ss_pred CccEEEEEEEecccCCCCcEEecceecCCCCCceE-Eec------CCCCceeeEEEEEEEEcCCCCEEEEEEeCCCCHHH
Confidence 99999999999999888889998887653322111 111 1468899999999987654 489999999999999
Q ss_pred EEEEeeeeCcccccCceeeccccccccCCCccccccccccCCCCC
Q 015839 299 IRVHLQYTGYPIANDMLYLCEHVTHREGMSADRAAAYSHHSPPPV 343 (399)
Q Consensus 299 IR~hla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~lp~~~ 343 (399)
||+||+++||||+||.+||...........++++..+.|.+|.+.
T Consensus 164 IR~hla~lG~PIvGD~~Yg~~~~~~~~~r~~Lha~~l~f~~P~~~ 208 (219)
T PRK10158 164 LRVHMLALGHPILGDRFYASPEARAMAPRLLLHAEMLTITHPAYG 208 (219)
T ss_pred HHHHHHHCCCcEECCcccCCccccccccchhhhhCccCccCCCCC
Confidence 999999999999999999975432223356788888999988663
No 10
>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=1.8e-43 Score=332.46 Aligned_cols=194 Identities=26% Similarity=0.333 Sum_probs=151.5
Q ss_pred ceeeccCCCeEEeecCCCcccccCcccccce--EEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhc
Q 015839 142 VSILQKEPDVLTVCKPPSVPVHPCGQYRKNT--VVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAG 219 (399)
Q Consensus 142 ~~IlyEd~~~ivvnKP~Gl~v~p~~~~~~~t--v~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~ 219 (399)
++|||||++|||||||+|++|||++....++ ++..|....+ ..+++|||||++||||||||+|.++++.|+++|+++
T Consensus 1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~ 79 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLG-QHVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTEH 79 (223)
T ss_pred CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHcC-CCcccccCCCCCCeEEEEEEECHHHHHHHHHHHhcC
Confidence 3699999999999999999999876433222 2233333222 457899999999999999999999999999999999
Q ss_pred hhhhhhheeeccccCCCceEEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecC-----------CeeeEEE
Q 015839 220 KVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTN-----------GTHSIVL 288 (399)
Q Consensus 220 ~v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~-----------~~~slV~ 288 (399)
.+.|+|+|+|.|.++. ++.|+.++..+.......... ....++.|.|.|+++... .+.|||+
T Consensus 80 ~v~K~Y~alv~G~~~~-~~~i~~~l~~~~~~~~~~~~~------~~~~~~~a~t~~~~l~~~~~~~~~~~~~~~~~slv~ 152 (223)
T cd02563 80 RVHKTYLAVVRGYVPE-SGTIDYPLSEELDKLADKFAS------DDKAPQAATTHYRLLAVEELPVVVGKYPTSRYSLVE 152 (223)
T ss_pred ceeEEEEEEEECccCC-CCeEEEeeeeCCCccceEEee------cCCCCceeEEEEEEeeecccccccccCCCCCeEEEE
Confidence 9999999999999876 678888887654332211111 123578999999998641 2489999
Q ss_pred eecccCceeEEEEEeeeeCcccccCceeecccccc------ccCCCccccccccccCCCCC
Q 015839 289 CEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTH------REGMSADRAAAYSHHSPPPV 343 (399)
Q Consensus 289 ~~l~TGRtHQIR~hla~lG~PIvGD~~Yg~~~~~~------~~~~~~~~~~~~~~~lp~~~ 343 (399)
|+|+||||||||+||+++||||+||.+||...... .....++++..+.|.+|.+-
T Consensus 153 ~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~rl~Lha~~L~F~hP~t~ 213 (223)
T cd02563 153 LTPHTGRKHQLRRHLAHIRHPIIGDTTHGDGRHNRFFREHFGCHRLLLAATRLEFTHPVTG 213 (223)
T ss_pred EEeCCCCHHHHHHHHHHcCCCeeCCcccCCcccChhHHhhcCCccceeecCeeEeeCCCCC
Confidence 99999999999999999999999999999753211 12345778888889888764
No 11
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=100.00 E-value=3.9e-43 Score=336.69 Aligned_cols=194 Identities=28% Similarity=0.295 Sum_probs=150.6
Q ss_pred ceeeccCCCeEEeecCCCcccccCcccccce--EEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhc
Q 015839 142 VSILQKEPDVLTVCKPPSVPVHPCGQYRKNT--VVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAG 219 (399)
Q Consensus 142 ~~IlyEd~~~ivvnKP~Gl~v~p~~~~~~~t--v~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~ 219 (399)
++|||||++|||||||+|++||++.....++ +...|..... ..+++|||||++||||||||||.++++.|+++|+++
T Consensus 2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~~ 80 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQIG-QHVFTAHRLDRPTSGVLLMALSSEVARLLAQQFEQH 80 (257)
T ss_pred CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHhC-CCceeeccCCCCCeeEEEEECCHHHHHHHHHHHHhC
Confidence 4699999999999999999999875333332 3334432222 357899999999999999999999999999999999
Q ss_pred hhhhhhheeeccccCCCceEEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecC-----------CeeeEEE
Q 015839 220 KVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTN-----------GTHSIVL 288 (399)
Q Consensus 220 ~v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~-----------~~~slV~ 288 (399)
.|.|+|+|+|.|.++. ++.++.++..........+.. ....++.|.|.|++++.. .+.|||+
T Consensus 81 ~v~K~Y~Alv~G~~~~-~~~i~~~l~~~~~~~~~~~~~------~~~~~k~a~T~~~~l~~~~~~~~~~~~~~~~~slv~ 153 (257)
T PRK11112 81 QIQKTYHAIVRGWLME-EAVLDYPLKEELDKIADKFAR------EDKAPQPAVTHYRGLATVEMPVATGRYPTTRYSLVE 153 (257)
T ss_pred CcceEEEEEEEeEeCC-CCeEeeeeeecccccceeecc------cCCCCeEeEEEEEEEEEecccccccccCCCCeEEEE
Confidence 9999999999999864 467888886542211111100 124688999999999652 3479999
Q ss_pred eecccCceeEEEEEeeeeCcccccCceeecccccc------ccCCCccccccccccCCCCC
Q 015839 289 CEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTH------REGMSADRAAAYSHHSPPPV 343 (399)
Q Consensus 289 ~~l~TGRtHQIR~hla~lG~PIvGD~~Yg~~~~~~------~~~~~~~~~~~~~~~lp~~~ 343 (399)
|+|+||||||||+||+++||||+||.+||...... .....++++..+.|.+|.+-
T Consensus 154 i~~~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~rl~LHA~~L~F~hP~t~ 214 (257)
T PRK11112 154 LEPKTGRKHQLRRHMAHLRHPIIGDTKHGDLRQNRSLAEHFGCSRLMLHASELSLTHPFTG 214 (257)
T ss_pred EEcCCCChHHHHHHHHHcCCCEeCCcccCCcccchhhhhccCCcchhHhhCccCccCCCCC
Confidence 99999999999999999999999999999743211 12346788888999888663
No 12
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=100.00 E-value=7.9e-42 Score=323.07 Aligned_cols=202 Identities=15% Similarity=0.163 Sum_probs=162.4
Q ss_pred cchhhhhhhhhcCCccceeeeeEEeeeeEecCeeee-eeEEEecccccccccccCCCCeeeccceeeccCCCeEEeecCC
Q 015839 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVP-VSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKPP 158 (399)
Q Consensus 80 ~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~-~~~~v~~gD~I~~~~~~~e~pv~~~~~~IlyEd~~~ivvnKP~ 158 (399)
+||++||++.+ .+||+.++++|++|.|+|||+++. ++++|+.||.|.+.....+ ..++++|||+|||+
T Consensus 1 ~rld~~L~~~~-~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~I~l~~~~~~----------~~~~~~~lvvnKP~ 69 (232)
T PRK10839 1 MRLDKFISQQL-GVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDGNPLA----------QQHGPRYFMLNKPQ 69 (232)
T ss_pred CcHHHHHHHcC-CCCHHHHHHHHHcCeEEECCEEeccCCcCcCCCCEEEECCEEcc----------cCCCCEEEEEECCC
Confidence 47899999886 799999999999999999999994 8999999999986531100 12457899999999
Q ss_pred CcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeeccccCCCce
Q 015839 159 SVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQ 238 (399)
Q Consensus 159 Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~G~~~~~~~ 238 (399)
||+|||++.. ..|+.+++.... ...+++|||||++||||||||||+++++.|. .+++.+.|+|+|++++.+..+..
T Consensus 70 G~~~~~~~~~-~~tl~~~l~~~~-~~~~~~v~RLD~~TSGlll~ak~~~~~~~l~--~~~~~i~K~Y~a~i~~~i~~~~~ 145 (232)
T PRK10839 70 GYVCSTDDPD-HPTVLYFLDEPV-AYKLHAAGRLDIDTTGLVLMTDDGQWSHRIT--SPRHHCEKTYLVTLESPVADDTA 145 (232)
T ss_pred CeEecccCCC-CCeEEEeccccc-ccCceecCCCCCCceeEEEEecCHHHHHHHh--CCCCCCCeEEEEEECCCCCHHHH
Confidence 9999987554 478887775432 2357899999999999999999999999999 47889999999998887754321
Q ss_pred -EEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeEEEEEeeeeCcccccCceee
Q 015839 239 -VVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLYL 317 (399)
Q Consensus 239 -~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR~hla~lG~PIvGD~~Yg 317 (399)
.+..++ ..+|+.|.|+|.+++... .|+|+|+|+||||||||+||+++||||+|=....
T Consensus 146 ~~~~~~~--------------------~~~g~~a~t~~~~~~~~~-~sll~~~l~tGRtHQIR~h~~~~G~pi~gl~R~~ 204 (232)
T PRK10839 146 EQFAKGV--------------------QLHNEKDLTKPAVLEVIT-PTQVRLTISEGRYHQVKRMFAAVGNHVVELHRER 204 (232)
T ss_pred HHHHCCe--------------------EECCCcccccccEEEEec-CCEEEEEEEcCcCHHHHHHHHHcCCeEeeEEEEE
Confidence 111111 125778889999997754 4999999999999999999999999999965543
No 13
>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=1.2e-38 Score=289.62 Aligned_cols=165 Identities=35% Similarity=0.443 Sum_probs=135.9
Q ss_pred eEEeecCCCcccccCcccccceEEEEe----ecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhh
Q 015839 151 VLTVCKPPSVPVHPCGQYRKNTVVGIL----QAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYI 226 (399)
Q Consensus 151 ~ivvnKP~Gl~v~p~~~~~~~tv~~~L----~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~Yl 226 (399)
|+|+|||+|++|++.+.....++.+++ ........+++|||||++||||||||+|+++++.|+++|+++.+.|+|+
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~tsGlll~ak~~~~~~~l~~~~~~~~~~K~Y~ 80 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYL 80 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhcCCCCcCceecccCCCCceEEEEEcCHHHHHHHHHHHhcCceeEEEE
Confidence 689999999999998877777777653 2122235688999999999999999999999999999999999999999
Q ss_pred eeeccccCCCceEEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeEEEEEeeee
Q 015839 227 ARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYT 306 (399)
Q Consensus 227 A~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR~hla~l 306 (399)
|+|.|.++.+.+.++.++..+......... ..++++.+.|.|+++....+.|+|+|+|+|||+||||+||+++
T Consensus 81 a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~t~~~~l~~~~~~s~~~~~l~tGR~HQIR~hl~~~ 153 (185)
T cd02869 81 ALVDGKPPEDEGTIDAPLGRKKRKKRARVV-------VSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLASI 153 (185)
T ss_pred EEEeCCCCCCccEEecccccCCccCceEEE-------ECCCCeEEEEEEEEEEEcCCcEEEEEEeCcCCccHHHHHHHHC
Confidence 999999998877777766543111111100 1246789999999998777789999999999999999999999
Q ss_pred CcccccCceeeccccc
Q 015839 307 GYPIANDMLYLCEHVT 322 (399)
Q Consensus 307 G~PIvGD~~Yg~~~~~ 322 (399)
||||+||.+||....+
T Consensus 154 G~pIvGD~~Yg~~~~~ 169 (185)
T cd02869 154 GHPIVGDPKYGGKASD 169 (185)
T ss_pred CCCEeCccccCCcccc
Confidence 9999999999986654
No 14
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=100.00 E-value=9.2e-39 Score=310.72 Aligned_cols=205 Identities=20% Similarity=0.209 Sum_probs=157.6
Q ss_pred cchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeeeeEEEeccc--ccccccccCCCCeeeccceeec-cCCCeEEeec
Q 015839 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQ--KISHFLHRHEPPVMAWDVSILQ-KEPDVLTVCK 156 (399)
Q Consensus 80 ~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD--~I~~~~~~~e~pv~~~~~~Ily-Ed~~~ivvnK 156 (399)
+||++||++. +.+||+.++++|++|+|+|||+++.++++|..+| .|.+...... ....+ ||+.|+++||
T Consensus 3 ~RL~k~La~~-g~~SRr~a~~lI~~G~V~VNG~~~~~g~~V~~~~~d~I~v~g~~~~-------~~~~~~e~~~ylvlnK 74 (289)
T PRK10700 3 EKLQKVLARA-GHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLIS-------VKESAEQICRVLAYYK 74 (289)
T ss_pred hhHHHHHHHC-CCCCHHHHHHHHHcCCEEECCEeccCCCEeCCCCCeEEEECCEEee-------cccccccCCeEEEEEC
Confidence 7999999986 8899999999999999999999989999998874 4554311100 00112 5578999999
Q ss_pred CCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeeccccCCC
Q 015839 157 PPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEG 236 (399)
Q Consensus 157 P~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~G~~~~~ 236 (399)
|+|++||+++.....||+++|.... ...++||||||++||||||||||++++++|+ ++++.+.|+|+|+|.|.++++
T Consensus 75 P~G~~~s~~d~~~~~tv~d~l~~~~-~~~~~~VgRLD~dTsGLLLlTndg~~~~~L~--~p~~~i~K~Y~v~V~G~~~~~ 151 (289)
T PRK10700 75 PEGELCTRNDPEGRPTVFDRLPKLR-GARWIAVGRLDVNTCGLLLFTTDGELANRLM--HPSREVEREYAVRVFGQVDDA 151 (289)
T ss_pred CCCCEeecCCCCCCccHHHHhhhhc-CCceeEccCCCCCCceEEEEEcCHHHHHHHh--CccCCCCeEEEEEEccCCCHH
Confidence 9999999988777789998886421 2457899999999999999999999999998 689999999999999998765
Q ss_pred ce-EEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeEEEEEeeeeCcccccCc
Q 015839 237 EQ-VVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDM 314 (399)
Q Consensus 237 ~~-~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR~hla~lG~PIvGD~ 314 (399)
.+ .+..++.++ ++......++.+......++++|+|++||+||||+||+++||||+.=.
T Consensus 152 ~l~~l~~Gv~l~-------------------~~~~~~~~v~~~~~~~~~s~l~v~L~EGk~hQIRrm~~~lG~~V~~L~ 211 (289)
T PRK10700 152 KLRQLSRGVQLE-------------------DGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLI 211 (289)
T ss_pred HHHHHHcCCEeC-------------------CceeeeEEEEeccCCCCceEEEEEEeCCccHHHHHHHHHcCCEEeEEE
Confidence 44 233343331 222222222322222235789999999999999999999999997643
No 15
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1e-37 Score=294.02 Aligned_cols=205 Identities=20% Similarity=0.241 Sum_probs=165.9
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEeccc-ccccccccCCCCeeeccceeec-cCCCeEEee
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQ-KISHFLHRHEPPVMAWDVSILQ-KEPDVLTVC 155 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD-~I~~~~~~~e~pv~~~~~~Ily-Ed~~~ivvn 155 (399)
.+||+|||++. +.+||++++++|++|+|+|||+++ ..+..+.+++ .|. .++..+.+ +...|+++|
T Consensus 2 ~~RL~K~La~~-G~~SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~-----------v~g~~~~~~~~~~y~lln 69 (248)
T COG1187 2 SMRLNKFLAEA-GVGSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVE-----------VDGKRIELKEERVYLLLN 69 (248)
T ss_pred ccchHHHHHHc-CCCCHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEE-----------ECCEEeeccccceEEEEE
Confidence 58999999998 999999999999999999999999 6788888885 555 33444555 345599999
Q ss_pred cCCCcccccCcccccceEEEEeecc-cCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeeccccC
Q 015839 156 KPPSVPVHPCGQYRKNTVVGILQAE-HDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFP 234 (399)
Q Consensus 156 KP~Gl~v~p~~~~~~~tv~~~L~~~-~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~G~~~ 234 (399)
||.|++|+..++..+.||.++|... ....+++||+|||+||+||||||+|++++++|. +|++++.|+|+|.|.|.++
T Consensus 70 KP~G~v~s~~D~~gr~tv~D~lp~~~~~~~~~~pvGRLD~dTeGLLLLTnDG~la~rL~--~P~~~~~K~Y~v~v~g~~~ 147 (248)
T COG1187 70 KPRGYVSSTEDDEGRPTVFDLLPERLPRKKRLFPVGRLDKDTEGLLLLTNDGELAHRLM--HPSSEVEKEYLVRVEGPVT 147 (248)
T ss_pred CCCCeEecccCCCCCceeeeecccccccccceeeccccCCCCeeEEEEeCCHHHHHHhc--CCCCCCCEEEEEEEecCCC
Confidence 9999999988888899999999853 112459999999999999999999999999999 9999999999999999887
Q ss_pred CCce-EEeeeeeecccCCccccccCCCCCCCCCCCcccccc-eEEeecCC-eeeEEEeecccCceeEEEEEeeeeCcccc
Q 015839 235 EGEQ-VVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTK-FTRISTNG-THSIVLCEPITGRTHQIRVHLQYTGYPIA 311 (399)
Q Consensus 235 ~~~~-~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~-~~~l~~~~-~~slV~~~l~TGRtHQIR~hla~lG~PIv 311 (399)
++.+ .+..++.++ ++....+. ..+....+ +.|++++.|.+||+||||+||+++|+||+
T Consensus 148 ~~~l~~l~~Gv~l~-------------------d~~~~~~~~~~l~~~~~~~~s~~~itl~EGrnrQVRRm~~a~G~~V~ 208 (248)
T COG1187 148 EEDLEKLRKGVTLD-------------------DGETKPAKPASLEKEPGKNNSWLRITLTEGRNRQVRRMFEAVGLEVL 208 (248)
T ss_pred HHHHHHHhCCcEec-------------------CcccccceeEEEEecCCCCceEEEEEEeCCcCHHHHHHHHHcCCEEe
Confidence 7654 555566553 32222223 22222222 58999999999999999999999999997
Q ss_pred cCcee
Q 015839 312 NDMLY 316 (399)
Q Consensus 312 GD~~Y 316 (399)
.=..+
T Consensus 209 ~L~R~ 213 (248)
T COG1187 209 RLKRI 213 (248)
T ss_pred EEEEE
Confidence 65443
No 16
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=100.00 E-value=9.5e-38 Score=303.06 Aligned_cols=199 Identities=14% Similarity=0.168 Sum_probs=157.3
Q ss_pred cCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeeeeEEEecccccccccccCCCCeeeccceeeccCCCeEEeecC
Q 015839 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKP 157 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~~~~~e~pv~~~~~~IlyEd~~~ivvnKP 157 (399)
.++||++||++. +.+||+.++++|++|+|+|||+++.++++|.+||.|.+....-++ ..+||++|||+|||
T Consensus 5 ~~~RL~k~La~~-g~~SRr~a~~lI~~G~V~VNGk~v~~~~~V~~gD~V~v~g~~i~~--------~~~ed~~~lvlnKP 75 (290)
T PRK10475 5 SSTRLNKYISES-GICSRREADRYIEQGNVFINGKRATIGDQVKAGDVVKVNGQLIEP--------REAEDLVLIALNKP 75 (290)
T ss_pred hHHHHHHHHHhC-CCCCHHHHHHHHHCCcEEECCEEccCCCCcCCCCEEEECCEEccc--------cccCCCeEEEEECC
Confidence 458999999986 789999999999999999999999889999999999875321111 12478899999999
Q ss_pred CCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeeccccCCCc
Q 015839 158 PSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGE 237 (399)
Q Consensus 158 ~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~G~~~~~~ 237 (399)
+|++||+.+. ...||+++|... ..++||||||++||||||||+|++++++|. .+.+.+.|+|+|+|.|.++++.
T Consensus 76 ~G~~~~~~~~-~~~tv~~~l~~~---~~l~~VgRLDrdTsGLLLlT~dg~~~~~L~--~p~~~i~K~Y~v~V~g~~~~~~ 149 (290)
T PRK10475 76 VGIVSTTEDG-ERDNIVDFVNHS---KRVFPIGRLDKDSQGLIFLTNHGDLVNKIL--RAGNDHEKEYLVTVDKPITDEF 149 (290)
T ss_pred CCCCcCCCCC-CCCcHHHHhhcc---ccccccccCCCCCcceEEEecCHHHHHHhh--CcCCCCCeEEEEEECCCCCHHH
Confidence 9999997765 457888887542 468999999999999999999999999998 6778899999999999997654
Q ss_pred e-EEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeEEEEEeeeeCcccccCc
Q 015839 238 Q-VVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDM 314 (399)
Q Consensus 238 ~-~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR~hla~lG~PIvGD~ 314 (399)
+ .+..++.++ ++......+..+ +.++++|.|.+||+||||+||+++||||+-=.
T Consensus 150 l~~l~~Gv~l~-------------------~~~~~~~~v~~~----~~~~~~i~l~eGk~rqIRrm~~~~G~~V~~L~ 204 (290)
T PRK10475 150 IRGMGAGVPIL-------------------GTVTKKCKVKKE----APFVFRITLVQGLNRQIRRMCEHFGYEVTKLE 204 (290)
T ss_pred HHHHhCCcEEC-------------------CEEecceEEEec----CCcEEEEEEECCcCHHHHHHHHHcCCEEeEEE
Confidence 4 334444332 111111122222 24579999999999999999999999997533
No 17
>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=4.2e-35 Score=260.34 Aligned_cols=148 Identities=29% Similarity=0.385 Sum_probs=119.4
Q ss_pred eEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeec
Q 015839 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (399)
Q Consensus 151 ~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (399)
|||+|||+|++||+++.....++.+.+.... ...+++|||||++||||||||+|++++++|+++ ++.+.|+|+|+|.
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~~-~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~v~K~Y~a~v~ 77 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLH-GPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEP--RREIEKEYLVTVR 77 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhhccc-CCceeEeccCCCCCeeEEEEEcCHHHHHHHhhh--hccCcEEEEEEEE
Confidence 6899999999999988777778887765432 256889999999999999999999999999976 7889999999999
Q ss_pred cccCCCceEEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeEEEEEeeeeCccc
Q 015839 231 GVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPI 310 (399)
Q Consensus 231 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR~hla~lG~PI 310 (399)
|.++++ ..+..++... +..... ..++++.+.|.|+++....+.|+|+|+|+|||+||||+||+++||||
T Consensus 78 g~~~~~-~~~~~~~~~~---~~~~~~-------~~~~~~~~~t~~~~l~~~~~~sll~~~l~tGR~HQIR~hla~~G~pI 146 (154)
T cd02550 78 GELDEE-GIEDLATVRR---GRLSGL-------VDEGVPLAVTKVRVIGEHGGTGRLRLTLKTGRTHQIRRHCAAVGFPV 146 (154)
T ss_pred eecCcc-hheecccccc---CcceeE-------EcCCCcccceEEEEEEecCCcEEEEEEEcCCCcHHHHHHHHHcCCcE
Confidence 998754 3344443321 110000 12467889999999987667899999999999999999999999999
Q ss_pred cc
Q 015839 311 AN 312 (399)
Q Consensus 311 vG 312 (399)
..
T Consensus 147 ~~ 148 (154)
T cd02550 147 LR 148 (154)
T ss_pred Ee
Confidence 63
No 18
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.
Probab=100.00 E-value=1e-34 Score=255.68 Aligned_cols=140 Identities=29% Similarity=0.346 Sum_probs=116.5
Q ss_pred eEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeec
Q 015839 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (399)
Q Consensus 151 ~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (399)
|+|+|||+|++||+.+....+++.+++... ...+++|||||++||||||||||+++++.|. .+++.+.|+|+|+|.
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~~--~~~~~~vhRLD~~TsGlll~ak~~~~~~~l~--~~~~~i~K~Y~a~v~ 76 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDV--GERLFPVGRLDYDTEGLLLLTNDGELANRLT--HPRYGVEKTYLVKVR 76 (146)
T ss_pred CEEEECCCCcEecccCCCCCCEEeeecccc--CCCEEECCCCCCCCeeEEEEeCCHHHHHHhh--CccCCCCeEEEEEEC
Confidence 689999999999998877778998887653 2468999999999999999999999999998 467889999999999
Q ss_pred cccCCCceEEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeEEEEEeeeeCccc
Q 015839 231 GVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPI 310 (399)
Q Consensus 231 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR~hla~lG~PI 310 (399)
|.++.+.+. ....+. ...+++.+.|+|+++....+.++|+|+|+|||+||||+||+++||||
T Consensus 77 g~~~~~~~~-------~~~~~~-----------~~~~~~~~~t~~~~l~~~~~~sll~~~l~tGR~HQIR~hla~~G~pI 138 (146)
T cd02870 77 GVPSEEELR-------RLRAGV-----------ELDDGKTAPAKVKVLSRDPKNTLLEVTLHEGRNRQVRRMFEAVGHPV 138 (146)
T ss_pred CCCCHHHHH-------HHHCCe-----------EeCCceEcceEEEEeccCCCCcEEEEEEEeCCcHHHHHHHHHcCCcC
Confidence 998765420 000110 01357789999999987767899999999999999999999999999
Q ss_pred cc
Q 015839 311 AN 312 (399)
Q Consensus 311 vG 312 (399)
+.
T Consensus 139 ~~ 140 (146)
T cd02870 139 LR 140 (146)
T ss_pred Ce
Confidence 74
No 19
>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=99.97 E-value=3.4e-34 Score=257.98 Aligned_cols=144 Identities=19% Similarity=0.239 Sum_probs=117.3
Q ss_pred CeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheee
Q 015839 150 DVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARV 229 (399)
Q Consensus 150 ~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V 229 (399)
.|+|+|||+|++||+.+....+|+.++|.... ...+++|||||++||||||||||++++++|+ ++++.+.|+|+|+|
T Consensus 1 ~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~-~~~~~~V~RLD~~TsGLll~ak~~~~~~~L~--~~~~~i~K~Y~a~V 77 (167)
T cd02556 1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLG-IPRWISVGRLDLNTEGLLLFTNDGELANRLM--HPSNEIEREYAVRV 77 (167)
T ss_pred CEEEEECCCCcEECccCCCCCccHHHhhhhhc-cCceEEcCcCCCCCeeEEEEECCHHHHHHHh--CCcCCCCeEEEEEE
Confidence 37899999999999877666788888876432 2457899999999999999999999999998 68899999999999
Q ss_pred ccccCCCceEEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeEEEEEeeeeCcc
Q 015839 230 NGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYP 309 (399)
Q Consensus 230 ~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR~hla~lG~P 309 (399)
.|.++.+.. . ....+. ...+++.+.++|+++....+.|+|+|+|+|||+||||+||+++|||
T Consensus 78 ~g~~~~~~~--~-----~~~~gv-----------~~~~~~~~~~~~~~~~~~~~~sll~v~l~tGR~HQIR~~~a~~G~p 139 (167)
T cd02556 78 FGQVTDEQL--K-----SLKKGV-----------ELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQ 139 (167)
T ss_pred CccCCHHHH--H-----HHHcCC-----------EECCCcCcceEEEEEecCCCcEEEEEEEEeCCCHHHHHHHHHcCCe
Confidence 999876542 1 001110 0135778889999987666679999999999999999999999999
Q ss_pred cccCc
Q 015839 310 IANDM 314 (399)
Q Consensus 310 IvGD~ 314 (399)
|+-=.
T Consensus 140 V~~L~ 144 (167)
T cd02556 140 VSRLI 144 (167)
T ss_pred EeEEE
Confidence 98643
No 20
>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=99.97 E-value=3.3e-33 Score=251.53 Aligned_cols=144 Identities=22% Similarity=0.271 Sum_probs=112.2
Q ss_pred eEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeec
Q 015839 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (399)
Q Consensus 151 ~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (399)
|+|+|||+|++||++ .....|+.+++........+++|||||++||||||||||.+++++|. .+++.+.|+|+|+|.
T Consensus 2 ~ivvnKP~G~~~~~~-~~~~~tl~~~l~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~--~~~~~i~K~Y~a~V~ 78 (167)
T cd02553 2 YLMLNKPAGVVCATK-DPHHPTVIDLLPEPDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLT--SPKKHVPKTYEVTLA 78 (167)
T ss_pred EEEEECCCCCEeCCC-CCCCCcHHHHhhhhcccCCeEEcccCCCCCEEEEEEEeCHHHHHHhh--CCcCCCceEEEEEEc
Confidence 799999999999964 44567888877664333568899999999999999999999999998 467889999999999
Q ss_pred cccCCCce-EEeeeeeecccCCccccccCCCCCCCCCCC-cccccceEEeecCCeeeEEEeecccCceeEEEEEeeeeCc
Q 015839 231 GVFPEGEQ-VVDVNINYNASAGRSTAESGDSLGDTPLKG-KAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGY 308 (399)
Q Consensus 231 G~~~~~~~-~i~~~i~~~~~~~~~~~~~~~~~~~~~~~g-k~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR~hla~lG~ 308 (399)
|.++.+++ .+..++.. .++ +...+.+++++ .++|+|+|+|||+||||+||+++||
T Consensus 79 G~~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~----~sll~v~l~tGR~HQIR~hla~lG~ 135 (167)
T cd02553 79 GPLTEDDIEAFAEGVLL-------------------HDGYPTKPAKLEILS----PTTVRLTITEGKYHQVKRMFAAVGN 135 (167)
T ss_pred cCCCHHHHHHHHCCeEE-------------------cCCCEeeeeEEEEeC----CcEEEEEEEeCCCHHHHHHHHHcCC
Confidence 99876543 11111111 122 23344566663 3999999999999999999999999
Q ss_pred ccccCceeeccc
Q 015839 309 PIANDMLYLCEH 320 (399)
Q Consensus 309 PIvGD~~Yg~~~ 320 (399)
||++|..++-..
T Consensus 136 pI~~~~R~~~g~ 147 (167)
T cd02553 136 KVVALHRIRIGG 147 (167)
T ss_pred eEEEEEEEEECC
Confidence 999998887543
No 21
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family. This Prosite family is a subset of the Pfam family.; InterPro: IPR006145 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit). RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [, ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site. RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: RluB modifies uracil-2605. RluC modifies uracil-955, U-2504, and U-2580. RluD modifies uracil-1911, U-1915, and U-1917. RluE modifies uracil-3457. RluF modifies uracil-2604, and to a lesser extent U-2605. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [, ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 2GML_A 3DH3_B 1VIO_A 2I82_B 1XPI_B 1V9K_B 1PRZ_A 1V9F_A 2IST_A 1QYU_A ....
Probab=99.96 E-value=7.3e-32 Score=240.71 Aligned_cols=151 Identities=37% Similarity=0.566 Sum_probs=111.2
Q ss_pred CeEEeecCCCcccccCcccccceEEEE----eecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhh
Q 015839 150 DVLTVCKPPSVPVHPCGQYRKNTVVGI----LQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRY 225 (399)
Q Consensus 150 ~~ivvnKP~Gl~v~p~~~~~~~tv~~~----L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~Y 225 (399)
+|||||||+|++|++.+......+... +........+++|||||++||||||||+|.+++++|+++|+++.++|+|
T Consensus 1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~TsGlll~a~~~~~~~~l~~~f~~~~~~K~Y 80 (164)
T PF00849_consen 1 NLIVVNKPAGVPVHPSDGNESKSVKELPALSLKRGDDPPELYPVHRLDRDTSGLLLFAKDKEAAAKLSKQFPKRKVEKTY 80 (164)
T ss_dssp SEEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHHHCTTSGGGEESS---TT-EEEEEEESSHHHHHHHHHHHHTTCSEEEE
T ss_pred CEEEEECCCCCeEecCCCCCcccccchhhhhhhhccCCCceEECCCCCccccCCeeccCCcccccccccccccCCCcEEE
Confidence 689999999999999874222222211 1112334678999999999999999999999999999999999999999
Q ss_pred heeeccccCCCceEEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecC---------CeeeEEEeecccCce
Q 015839 226 IARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTN---------GTHSIVLCEPITGRT 296 (399)
Q Consensus 226 lA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~---------~~~slV~~~l~TGRt 296 (399)
+|+|.|.+..+++.++.++..+.......... ....+++.+.|.|+++... ...++|+|+|.|||+
T Consensus 81 ~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~t~~~~l~~~~~~~~~~~~~~~s~v~~~l~tGr~ 155 (164)
T PF00849_consen 81 LALVEGGPVEEEGKINSPLGKDVGKNKSSNKD-----PPGRDGKPAITRYRVLRSGSRTPSKDENAGCSLVECELITGRT 155 (164)
T ss_dssp EEEECSSSSTTCEEEESHEEE-EECSSCTCCE-----EETTTSBTSEEEEEEEEEETT---EECCSSEEEEEEEESS-ST
T ss_pred EEeEcccccccceeeeccccccccccccceee-----eecccccccceeeeeeccccccccccccCCCEEEEEEECcCCC
Confidence 99999777777888888886621111111000 0125788999999999876 679999999999999
Q ss_pred eEEEEEeee
Q 015839 297 HQIRVHLQY 305 (399)
Q Consensus 297 HQIR~hla~ 305 (399)
||||+|||+
T Consensus 156 HQIR~hla~ 164 (164)
T PF00849_consen 156 HQIRVHLAH 164 (164)
T ss_dssp THHHHHHHH
T ss_pred HHHHHHhcC
Confidence 999999985
No 22
>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=99.96 E-value=2.4e-31 Score=239.70 Aligned_cols=155 Identities=18% Similarity=0.165 Sum_probs=111.6
Q ss_pred eEEeecCCCcccccCcc-cccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheee
Q 015839 151 VLTVCKPPSVPVHPCGQ-YRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARV 229 (399)
Q Consensus 151 ~ivvnKP~Gl~v~p~~~-~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V 229 (399)
|+|+|||+|++||+++. ....|+.+++.. ..+++|||||++||||||||+|+++++.|+ .+++.++|+|+|+|
T Consensus 1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l~~----~~~~~v~RLD~~TsGlll~a~d~~~~~~l~--~~~~~v~K~Y~a~v 74 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYIDD----PGVYAAGRLDRDSEGLLLLTDDGRLQHRIT--DPSFKHPKTYYVQV 74 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCccHHHHcCc----CCeEEccCCCCCCeEEEEEEeCHHHHHHHH--CCCCCCCEEEEEEE
Confidence 58999999999998765 455788777752 357899999999999999999999999998 55677999999999
Q ss_pred ccccCCCce-EEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeec--CCeeeEEEeecccCceeEEEEEeeee
Q 015839 230 NGVFPEGEQ-VVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRIST--NGTHSIVLCEPITGRTHQIRVHLQYT 306 (399)
Q Consensus 230 ~G~~~~~~~-~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~--~~~~slV~~~l~TGRtHQIR~hla~l 306 (399)
.|.++.+.. .+..++..+.... ....+.. ...+....+.|.++.. ..+.|+|+|+|+|||+||||+||+++
T Consensus 75 ~g~~~~~~~~~l~~g~~~~~~~~-~~~~v~~-----~~~~~~~~~~~~~~~~~~~~~~sll~v~l~tGR~HQIR~~la~l 148 (168)
T cd02566 75 EGVPTEDALEQLRNGVELGDGLT-LPAKVEK-----VDEPPWLWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAV 148 (168)
T ss_pred CCcCCHHHHHHHhCCcEECCeEe-cceEEEE-----ecccccccccccccccccCCCccEEEEEEecCccHHHHHHHHHc
Confidence 999976542 1222332211100 0000100 0112234455555553 33468999999999999999999999
Q ss_pred CcccccCceee
Q 015839 307 GYPIANDMLYL 317 (399)
Q Consensus 307 G~PIvGD~~Yg 317 (399)
||||+......
T Consensus 149 G~pV~~L~R~~ 159 (168)
T cd02566 149 GFPTLRLIRVS 159 (168)
T ss_pred CCeEeEEEEEE
Confidence 99999876654
No 23
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.96 E-value=1.2e-30 Score=242.66 Aligned_cols=160 Identities=19% Similarity=0.217 Sum_probs=115.5
Q ss_pred CCCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhe
Q 015839 148 EPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIA 227 (399)
Q Consensus 148 d~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA 227 (399)
...|+++|||+|++||+.+.....++.+++.. .+++||||||++||||||||+|++++++|. .+++.+.|+|+|
T Consensus 38 ~~~ylllnKP~G~l~~~~d~~~~~tl~d~l~~----~~~~~vgRLD~~TsGllLlt~d~~~~~~L~--~~~~~i~K~Y~~ 111 (217)
T PRK11394 38 PTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV----QGVYAAGRLDRDSEGLLVLTNNGALQARLT--QPGKRTGKIYYV 111 (217)
T ss_pred CCEEEEEECCCCCEEeeCCccCCcchHHhccc----CCeEEecCCCCCCeeEEEEECCHHHHHHHh--CcccCCCEEEEE
Confidence 34699999999999997777667899888852 468999999999999999999999999999 468899999999
Q ss_pred eeccccCCCceE-EeeeeeecccCCc-cccccCCCCCCCCCCCcccccceEEee--cCCeeeEEEeecccCceeEEEEEe
Q 015839 228 RVNGVFPEGEQV-VDVNINYNASAGR-STAESGDSLGDTPLKGKAACTKFTRIS--TNGTHSIVLCEPITGRTHQIRVHL 303 (399)
Q Consensus 228 ~V~G~~~~~~~~-i~~~i~~~~~~~~-~~~~~~~~~~~~~~~gk~a~t~~~~l~--~~~~~slV~~~l~TGRtHQIR~hl 303 (399)
+|.|.++.+.+. +..++.++...-. ..+.... ........+..+. ...+.++|+|.|+|||+||||+||
T Consensus 112 ~v~g~~~~~~l~~l~~Gv~i~~~~~~p~~~~~i~-------~~~~~~~~~~~~~~~~~~~~s~l~I~L~eGR~hQIRrm~ 184 (217)
T PRK11394 112 QVEGIPTQDALEALRNGVTLNDGPTLPAGAELVD-------EPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMT 184 (217)
T ss_pred EECCCCCHHHHHHHhCCeEECCccccccEEEEec-------ccccccccccccccccCCCceEEEEEEeCCCCHHHHHHH
Confidence 999999776543 2444443211000 0000000 0000000011111 122478999999999999999999
Q ss_pred eeeCcccccCceeeccc
Q 015839 304 QYTGYPIANDMLYLCEH 320 (399)
Q Consensus 304 a~lG~PIvGD~~Yg~~~ 320 (399)
+++||||+||..|+-..
T Consensus 185 a~lG~pVl~L~Ry~iG~ 201 (217)
T PRK11394 185 AHVGFPTLRLIRYAMGD 201 (217)
T ss_pred HHcCCeEeeeEEEEECC
Confidence 99999999999998554
No 24
>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=99.95 E-value=3.3e-30 Score=233.94 Aligned_cols=144 Identities=17% Similarity=0.217 Sum_probs=106.2
Q ss_pred CCeEEeecCCCcccccCccc--------ccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhch
Q 015839 149 PDVLTVCKPPSVPVHPCGQY--------RKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGK 220 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~--------~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~ 220 (399)
..|+++|||+|++|+..++. ...++.++|.... .++++|||||++||||||||||+++++.|+. +.+.
T Consensus 4 ~~y~llnKP~G~l~s~~d~~~~~g~~~~~~~~~~~~l~~~~--~~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~--~~~~ 79 (177)
T cd02555 4 PVTLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGHF--ARLAPIGPLDKDASGLLVFSQDGRVLRKLIG--DASR 79 (177)
T ss_pred cEEEEEECCCceEecCCCcccccccccccccchhhhhhhcC--CceeEecCCCCCCeeEEEEECCHHHHHHHhC--hhcC
Confidence 35799999999999866532 2233444554332 4688999999999999999999999999994 6788
Q ss_pred hhhhhheeeccccCCCce-EEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeEE
Q 015839 221 VIKRYIARVNGVFPEGEQ-VVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQI 299 (399)
Q Consensus 221 v~K~YlA~V~G~~~~~~~-~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQI 299 (399)
+.|+|+|+|.|.++++.. .+..++.. +++. .+.+++.. . +.++|+|+|.|||+|||
T Consensus 80 i~K~Y~v~v~g~~~~~~l~~l~~g~~~--------------------~~~~-~~~~~~~~-~-~~~~l~i~l~tGr~hQI 136 (177)
T cd02555 80 LEQEYLVEVRGELTAGGLERLNHGLTY--------------------DGRE-LPPAKVSW-Q-NEQRLRFALKEPQPGQI 136 (177)
T ss_pred CCEEEEEEEcccCCHHHHHHHhcCccc--------------------CCee-cceEEEEE-c-CCCEEEEEEECCcChHH
Confidence 999999999999876432 23333321 1111 11222211 1 35899999999999999
Q ss_pred EEEeeeeCcccccCceeecc
Q 015839 300 RVHLQYTGYPIANDMLYLCE 319 (399)
Q Consensus 300 R~hla~lG~PIvGD~~Yg~~ 319 (399)
|+||+++||||+|+....-.
T Consensus 137 R~~~~~~G~pV~~L~R~~ig 156 (177)
T cd02555 137 RRMCESVGLEVVALRRIRIG 156 (177)
T ss_pred HHHHHHcCCeEEEEEEEEEC
Confidence 99999999999999887643
No 25
>TIGR00093 pseudouridine synthase. This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc.
Probab=99.93 E-value=6.3e-28 Score=207.98 Aligned_cols=112 Identities=21% Similarity=0.277 Sum_probs=91.4
Q ss_pred chhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeeccccCCCceEEeeeeeecccCCccccccCCCCCCCCCCC
Q 015839 189 VHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKG 268 (399)
Q Consensus 189 VhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~g 268 (399)
|||||++||||||||||+++++.|. .+++.+.|+|+|+|.|.++.+... .+ ..+.. ..++
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~--~~~~~i~K~Y~a~v~g~~~~~~~~---~~----~~g~~-----------~~~~ 60 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLT--HPGHHCEKTYLVTVEGPVTDEDLE---AL----RKGVQ-----------LEDG 60 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHh--CCCCCCCeEEEEEECCCCCHHHHH---HH----hCCeE-----------ECCc
Confidence 7999999999999999999999999 478899999999999998765421 01 00100 0235
Q ss_pred cccccceEEeecCCeeeEEEeecccCceeEEEEEeeeeCcccccCceeeccc
Q 015839 269 KAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEH 320 (399)
Q Consensus 269 k~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR~hla~lG~PIvGD~~Yg~~~ 320 (399)
+.+.+.|+++....+.++|+|+|.|||+||||+||+++||||+||..+.-..
T Consensus 61 ~~~~~~~~~l~~~~~~~~l~~~l~tGR~HQIR~~~~~lG~pI~g~~R~~~g~ 112 (128)
T TIGR00093 61 PTKPAKLEVITEPGFPTWLRITLSEGRNRQVRRMFAAVGFPVLRLHRVRIGD 112 (128)
T ss_pred EEeeeEEEEEccCCCceEEEEEEeCCCCHHHHHHHHHcCCeEeEEEEEEECC
Confidence 5677789988766667899999999999999999999999999999987543
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=99.93 E-value=7e-28 Score=215.77 Aligned_cols=137 Identities=16% Similarity=0.217 Sum_probs=106.1
Q ss_pred eEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeec
Q 015839 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (399)
Q Consensus 151 ~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (399)
|+++|||+|++|++.+. ...|+.+++... .+++||||||++||||||||+|++++++|+ ++.+.+.|+|+|.|.
T Consensus 2 y~~lnKP~G~l~s~~~~-~~~tv~~~l~~~---~~~~~vgRLD~~tsGlll~t~dg~~~~~L~--~p~~~~~K~Y~V~v~ 75 (164)
T cd02554 2 YIAYNKPVGIDCTLERA-DEDNIIDFVNPP---PRIFPIGRLDKDSEGLILLTNDGDLVNKIL--HADNNHEKEYLVTVN 75 (164)
T ss_pred EEEEECCCCcEeecCCC-CCCcHHHHhcCc---CCEEEccCCCCCCeeEEEEEcCHHHHHHHh--hhhcCCCeEEEEEEC
Confidence 78999999999998765 458899888642 568999999999999999999999999998 788899999999999
Q ss_pred cccCCCce-EEeeeeeecccCCccccccCCCCCCCCCCCcccccceEEeecCCeeeEEEeecccCceeEEEEEeeeeCcc
Q 015839 231 GVFPEGEQ-VVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYP 309 (399)
Q Consensus 231 G~~~~~~~-~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slV~~~l~TGRtHQIR~hla~lG~P 309 (399)
|.+.++.. .+..++..+ ++......++.+ . .+.++|.|++||+||||+||+++|||
T Consensus 76 ~~l~~~~l~~l~~G~~~~-------------------~~~~~~~~v~~~---~-~~~l~i~l~eGr~~qIRrm~~~~G~~ 132 (164)
T cd02554 76 KPITDEFIEGMSNGVVIL-------------------GTVTKPCKVERL---A-KDKFRIVLTQGLNRQIRRMCEALGYR 132 (164)
T ss_pred CCCCHHHHHHHhCCCEEC-------------------CeEEcceEEEEC---C-CCEEEEEEECCcCHHHHHHHHHcCCE
Confidence 99876543 223333221 222122223333 1 23599999999999999999999999
Q ss_pred cccCcee
Q 015839 310 IANDMLY 316 (399)
Q Consensus 310 IvGD~~Y 316 (399)
|+-=..+
T Consensus 133 V~~L~Ri 139 (164)
T cd02554 133 VTDLKRV 139 (164)
T ss_pred EEEEEEE
Confidence 9864443
No 27
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=98.91 E-value=1.7e-10 Score=108.51 Aligned_cols=74 Identities=27% Similarity=0.357 Sum_probs=54.4
Q ss_pred CeEEeecCCCcccccCcccccceEEEEeecccCC-CCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 150 DVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDL-APLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 150 ~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~-~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
.+||||||+||.++... +++...|....+. ...++|||||++|||||+||++..+ +|..++.++.+.|+|+|.
T Consensus 1 GilvvnKP~Gi~s~~~~----~~~~~~l~~~~~~~k~~~~vhrLD~~aSGvl~~a~~~~t--kl~~~~~~~~~~K~Y~~~ 74 (226)
T cd02868 1 GLFAVYKPPGVHWKHVR----DTIESNLLKYFPEDKVLVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYSNHPTRVYTIR 74 (226)
T ss_pred CEEEEEcCCCCChhHHH----HHHHHHHHHHccccceeeEccccCCCCceEEEEEeChhH--hHHHHHHhcCCCeEEEEE
Confidence 37999999999887532 2332222211211 2256889999999999999999976 688889988899999965
Q ss_pred e
Q 015839 229 V 229 (399)
Q Consensus 229 V 229 (399)
.
T Consensus 75 ~ 75 (226)
T cd02868 75 G 75 (226)
T ss_pred E
Confidence 4
No 28
>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=98.82 E-value=8.7e-10 Score=82.78 Aligned_cols=69 Identities=19% Similarity=0.167 Sum_probs=58.9
Q ss_pred cchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEecccccccccccCCCCeeeccceeeccCCCeEEee
Q 015839 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVC 155 (399)
Q Consensus 80 ~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~pv~~~~~~IlyEd~~~ivvn 155 (399)
+||+++|.+.+...||+.++++|++|.|+|||+.+ .+++++.+||.|.+... ++ ...|+|||++++|+|
T Consensus 1 ~rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~~~--~~-----~~~i~~ed~~~lvv~ 70 (70)
T cd00165 1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGK--SI-----EEDIVYEDKKLLVVN 70 (70)
T ss_pred CcHHHHHHHhccccCHHHHHHHHHcCCEEECCEEccCCccCcCCCCEEEEcCC--Cc-----ccceeeccCCEEEeC
Confidence 47899999875678999999999999999999999 89999999999886532 11 128999999999987
No 29
>PF01479 S4: S4 domain; InterPro: IPR002942 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 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 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 uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=98.36 E-value=3.1e-08 Score=70.37 Aligned_cols=47 Identities=21% Similarity=0.240 Sum_probs=42.4
Q ss_pred cchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEeccccc
Q 015839 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKI 126 (399)
Q Consensus 80 ~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I 126 (399)
+||++||++.....||++++++|++|.|+|||+++ ++++.|++||+|
T Consensus 1 ~RLd~~L~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 1 MRLDKFLSRLGLASSRSEARRLIKQGRVKVNGKVVKDPSYIVKPGDVI 48 (48)
T ss_dssp EBHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEESSTTSBESTTEEE
T ss_pred CCHHHHHHHcCCcCCHHHHHHhcCCCEEEECCEEEcCCCCCCCCcCCC
Confidence 68999999775456799999999999999999999 599999999986
No 30
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family 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 of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=98.16 E-value=1.9e-07 Score=69.40 Aligned_cols=51 Identities=12% Similarity=-0.092 Sum_probs=44.9
Q ss_pred cCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEeccccccc
Q 015839 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISH 128 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~ 128 (399)
+++||++||+......||+.++++|++|.|+|||+++ .++++|+.||.|.+
T Consensus 7 ~~~rLd~~L~~~~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 7 EYITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEI 58 (59)
T ss_pred hHHHHHHHHHHcCCccCHHHHHHHHHcCCEEECCEEccCCCCCCCCCCEEEe
Confidence 5699999999972123999999999999999999999 78999999999874
No 31
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=97.75 E-value=3.9e-06 Score=68.37 Aligned_cols=54 Identities=13% Similarity=0.120 Sum_probs=47.5
Q ss_pred cCcchhhhhhhh-hcCCccceeeeeEEeeeeEecCeeeeeeEEEeccccccccccc
Q 015839 78 AGKTIVDLFAEE-FKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHR 132 (399)
Q Consensus 78 ~g~rL~k~L~~~-f~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~~~~ 132 (399)
..|||++||--. | .-+|..+++++..|+|.|||+.++++..|+.||+|++.+..
T Consensus 7 ~~mRLDKwL~~aR~-~KrRslAk~~~~~GrV~vNG~~aKpS~~VK~GD~l~i~~~~ 61 (100)
T COG1188 7 DRMRLDKWLWAARF-IKRRSLAKEMIEGGRVKVNGQRAKPSKEVKVGDILTIRFGN 61 (100)
T ss_pred cceehHHHHHHHHH-hhhHHHHHHHHHCCeEEECCEEcccccccCCCCEEEEEeCC
Confidence 469999999654 4 56899999999999999999999999999999999987654
No 32
>smart00363 S4 S4 RNA-binding domain.
Probab=97.55 E-value=1.5e-05 Score=57.51 Aligned_cols=51 Identities=22% Similarity=0.180 Sum_probs=44.3
Q ss_pred cchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEeccccccccc
Q 015839 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFL 130 (399)
Q Consensus 80 ~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~ 130 (399)
++|+.+|...+...|++.+.++|..|.|+|||+.+ .+++.|..||.|.+..
T Consensus 1 ~rl~~~l~~~~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred CcHHHHHHHcCcccCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 47888888764468999999999999999999999 8999999999987653
No 33
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like. This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl r
Probab=97.45 E-value=2.8e-05 Score=70.99 Aligned_cols=70 Identities=20% Similarity=0.209 Sum_probs=51.4
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.+|+||||.|+.+|. ++..++...+..++-.+|-||...||||+++-+. +.++.+.+.. -.|+|.|.
T Consensus 2 ~g~l~i~Kp~g~tS~~--------~v~~~k~~~~~kkvGH~GTLDp~A~GvLiv~~g~--~Tk~~~~~~~--~~K~Y~a~ 69 (182)
T cd02572 2 YGVINLDKPSGPSSHE--------VVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDR--ATRLVKSQQE--AGKEYVCV 69 (182)
T ss_pred CeEEEEecCCCCCHHH--------HHHHHHHHhCCCccCcCCCCCCcCeeEEEEEECH--HhhhhHHHhC--CCCEEEEE
Confidence 4689999999998873 3344444445567888999999999999998876 3444444443 35999998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 70 v~ 71 (182)
T cd02572 70 MR 71 (182)
T ss_pred EE
Confidence 75
No 34
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.12 E-value=9.6e-05 Score=69.63 Aligned_cols=71 Identities=17% Similarity=0.185 Sum_probs=52.5
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.+|+||||.|+.+|- ++..++...+..++...|.||...||||+++-.. .+.+|.+.+.+ ..|+|.|.
T Consensus 9 ~G~l~i~KP~g~TS~d--------vv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~vG~-~aTkl~~~~~~--~~K~Y~~~ 77 (230)
T PRK00989 9 EGILLVDKPQGRTSFS--------LIRSLTKLIGVKKIGHAGTLDPFATGVMVMLIGR-KFTRLSDILLF--EDKEYAAV 77 (230)
T ss_pred CEEEEEeCCCCCCHHH--------HHHHHHHHhCCCcCCcCccCCCCCeeEEEEEECC-chhhhHHHhcC--CCcEEEEE
Confidence 3689999999998873 3344444445567889999999999999999765 33445544432 68999998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 78 ~~ 79 (230)
T PRK00989 78 AH 79 (230)
T ss_pred EE
Confidence 75
No 35
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=97.11 E-value=7.7e-05 Score=72.09 Aligned_cols=53 Identities=19% Similarity=0.140 Sum_probs=48.9
Q ss_pred cccCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEecccccccc
Q 015839 76 RWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (399)
Q Consensus 76 ~~~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (399)
...+.||+.+++..| .+||+.++++|++|.|+|||+.+ ++++.|++||.|++.
T Consensus 188 ~vas~RLD~vla~~~-~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiR 241 (267)
T PLN00051 188 VEASLRLDALASAGF-RMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVS 241 (267)
T ss_pred CcCcccHHHHHHHHh-ccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEe
Confidence 346799999999987 89999999999999999999998 899999999999875
No 36
>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=97.08 E-value=9.7e-05 Score=71.14 Aligned_cols=54 Identities=20% Similarity=0.236 Sum_probs=48.3
Q ss_pred ccccCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEecccccccc
Q 015839 75 NRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (399)
Q Consensus 75 ~~~~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (399)
....++||+.+++..| ..||+.++++|++|+|+|||+++ ++++.|++||.|++.
T Consensus 179 ~~v~s~RLD~lls~~~-~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~Isvr 233 (257)
T TIGR03069 179 TVEASLRIDAIASAGF-GLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLR 233 (257)
T ss_pred CCCccccHHHHHHhhh-hhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEc
Confidence 3557899998888876 67999999999999999999999 899999999999865
No 37
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker
Probab=97.07 E-value=0.00013 Score=68.18 Aligned_cols=68 Identities=21% Similarity=0.236 Sum_probs=50.4
Q ss_pred eEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeec
Q 015839 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (399)
Q Consensus 151 ~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (399)
+++||||.|+-+|- ++..++...+..++-.+|-||-..||||+++-+.. .+|...+.+ ..|+|.|.+.
T Consensus 2 il~i~KP~g~tS~~--------vv~~ik~~~~~kKvGH~GTLDP~AsGvLiv~vG~a--Tkl~~~~~~--~~K~Y~~~~~ 69 (210)
T cd00506 2 LFAVDKPQGPSSHD--------VVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKA--TKLLKHLLA--ATKDYTAIGR 69 (210)
T ss_pred EEEEEcCCCCCHHH--------HHHHHHHHhCccccCCCCcCCCcCeeEEEEEECHH--HhhhHHHhc--CCceEEEEEE
Confidence 78999999998873 33344444444678889999999999999988862 344433433 7999999875
No 38
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=97.05 E-value=8.6e-05 Score=64.11 Aligned_cols=51 Identities=6% Similarity=-0.025 Sum_probs=45.6
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeeeeEEEecccccccc
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHF 129 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~ 129 (399)
.+||+++|...--.-||..+.++|..|.|+|||++++++..|+.||.|.+.
T Consensus 8 ~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~~Kps~~V~~gd~l~v~ 58 (133)
T PRK10348 8 EVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLR 58 (133)
T ss_pred cccHHHHHHHcCccccHHHHHHHHHCCCEEECCEECCCCCccCCCCEEEEE
Confidence 489999998763367999999999999999999999999999999999864
No 39
>cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).
Probab=97.01 E-value=6.4e-05 Score=60.14 Aligned_cols=62 Identities=10% Similarity=0.043 Sum_probs=44.8
Q ss_pred CCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeeccccCCCceEEeeeeeecccCCccccccCCCCCC
Q 015839 184 APLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGD 263 (399)
Q Consensus 184 ~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~ 263 (399)
..+..+|++|+.++|+++++ ++|.+++. +. +.
T Consensus 24 ~~i~~aG~kDk~a~t~q~v~-------------------n~f~i~~r--~~--------~~------------------- 55 (87)
T cd01291 24 KRVGYAGRKDKRAVTTQLVS-------------------NRFTITLR--VK--------PL------------------- 55 (87)
T ss_pred heEEECccCCCCeeEEEEEc-------------------ccEEEEEE--Ee--------cc-------------------
Confidence 56788999999999999999 78888776 00 00
Q ss_pred CCCCCcccccceEEeecC--CeeeEEEeecccCceeEEEEEeeeeC
Q 015839 264 TPLKGKAACTKFTRISTN--GTHSIVLCEPITGRTHQIRVHLQYTG 307 (399)
Q Consensus 264 ~~~~gk~a~t~~~~l~~~--~~~slV~~~l~TGRtHQIR~hla~lG 307 (399)
...... .....+++.| |+.||+|.+|+.+|
T Consensus 56 ------------~~~~~~~~~~~~~l~f~l--~~~~yat~~l~el~ 87 (87)
T cd01291 56 ------------NLKWPEERKRALVLEFTL--PRGSYATMLLRELG 87 (87)
T ss_pred ------------eeEEcccccceEEEEEEc--CCcchHHHHHHHhC
Confidence 000000 1356688888 99999999998775
No 40
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=96.98 E-value=0.00016 Score=69.78 Aligned_cols=70 Identities=17% Similarity=0.182 Sum_probs=52.4
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.++++|||+|+.+|. ++..++...+..++...|-||-..||||+++-... .+|.+.+.+ ..|+|.|.
T Consensus 2 ngil~vdKP~g~tS~~--------vv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~--~~K~Y~a~ 69 (273)
T PRK04099 2 NRLFVANKPAGMSSNA--------FLSRLKRKYGVKKAGFSGTLDPFAKGVLIVAFGQY--TKLFRFLKK--TPKTYRAT 69 (273)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhCCCccccCccCCCCCeeEEEEEEChH--hhhHHHhcc--CCceEEEE
Confidence 3589999999998873 34445554555678889999999999999998863 345544433 38999998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 70 ~~ 71 (273)
T PRK04099 70 LW 71 (273)
T ss_pred EE
Confidence 75
No 41
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=96.94 E-value=0.00014 Score=67.48 Aligned_cols=52 Identities=17% Similarity=0.096 Sum_probs=45.7
Q ss_pred cCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEecccccccc
Q 015839 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (399)
-.+||+++|.+.....||+.++++|..|.|+|||+++ .+++.|++||.|.+.
T Consensus 87 LE~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~ 139 (201)
T CHL00113 87 LEMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVK 139 (201)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEc
Confidence 3589999998873356889999999999999999999 789999999999865
No 42
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=96.94 E-value=0.00013 Score=67.77 Aligned_cols=52 Identities=19% Similarity=0.045 Sum_probs=45.4
Q ss_pred cCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEecccccccc
Q 015839 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (399)
..+||+.+|.......||+.++++|..|.|+|||+++ .+++.|++||.|++.
T Consensus 88 le~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD~I~V~ 140 (200)
T TIGR01017 88 LESRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIK 140 (200)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCCEEEEe
Confidence 3589999997763356899999999999999999999 789999999999865
No 43
>TIGR00431 TruB tRNA pseudouridine 55 synthase. TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) 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
Probab=96.89 E-value=0.0002 Score=66.71 Aligned_cols=69 Identities=16% Similarity=0.233 Sum_probs=52.1
Q ss_pred CeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheee
Q 015839 150 DVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARV 229 (399)
Q Consensus 150 ~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V 229 (399)
.+++||||.|+-+| .++..++...+..++-..|-||-..||||+++-+... +|...+. ...|+|.|.+
T Consensus 3 G~l~v~KP~g~tS~--------~vv~~vkk~~~~kKvGH~GTLDP~AsGvLiv~vG~~T--kl~~~~~--~~~K~Y~~~~ 70 (209)
T TIGR00431 3 GVLLLDKPQGMTSF--------DALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKAT--KLSPYLT--DLDKEYRAEI 70 (209)
T ss_pred eEEEEECCCCCCHH--------HHHHHHHHHhCCCcCCCCCCCCCcCceEEEEEEChHh--hhhHHHc--CCCCeEEEEE
Confidence 58999999999876 3344444444556788899999999999999988743 4554443 5689999987
Q ss_pred c
Q 015839 230 N 230 (399)
Q Consensus 230 ~ 230 (399)
.
T Consensus 71 ~ 71 (209)
T TIGR00431 71 R 71 (209)
T ss_pred E
Confidence 5
No 44
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=96.89 E-value=0.00022 Score=67.70 Aligned_cols=70 Identities=21% Similarity=0.219 Sum_probs=51.6
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.+|+||||.|+.+|- ++..++...+..++...|-||...||||+++-.. +-+|...+. ...|+|.|.
T Consensus 10 ~Gil~vdKP~G~TS~d--------vv~~vkr~~~~kKvGH~GTLDP~AtGvLiv~iG~--aTKl~~~l~--~~~K~Y~a~ 77 (244)
T PRK00020 10 DGVLLLDKPVGLSSNH--------ALQRAKRTVDAAKAGHTGTLDPFATGLLVCCMGR--ATKISGRML--EADKTYQAT 77 (244)
T ss_pred CeEEEEecCCCCCHHH--------HHHHHHHHhCCCCCCcCCcCCCcCeeEEEEEECH--HhhhhHHhc--cCCcEEEEE
Confidence 4689999999998873 3344444455567888999999999999998876 344443343 345999998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 78 ~~ 79 (244)
T PRK00020 78 LQ 79 (244)
T ss_pred EE
Confidence 75
No 45
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=96.74 E-value=0.00034 Score=68.44 Aligned_cols=69 Identities=17% Similarity=0.145 Sum_probs=51.2
Q ss_pred CeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheee
Q 015839 150 DVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARV 229 (399)
Q Consensus 150 ~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V 229 (399)
.+|+||||+|+.+|- ++..++...+..++...|.||-..||||+++-... .+|.+.+. ...|+|.|.+
T Consensus 4 Gil~i~KP~G~TS~d--------vv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~--~~~K~Y~a~~ 71 (294)
T PRK02484 4 GIINLKKEAGMTSHD--------AVFKLRKILQTKKIGHGGTLDPDVVGVLPIAVGKA--TRLIEYMT--EAGKVYEGEI 71 (294)
T ss_pred eEEEEeCCCCCCHHH--------HHHHHHHHhCCCccccCCCCCCCCeeEEEEEEChh--hhhhHHhc--cCCcEEEEEE
Confidence 589999999998873 33444444455678889999999999999988763 33444443 3459999987
Q ss_pred c
Q 015839 230 N 230 (399)
Q Consensus 230 ~ 230 (399)
.
T Consensus 72 ~ 72 (294)
T PRK02484 72 T 72 (294)
T ss_pred E
Confidence 5
No 46
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=96.73 E-value=0.00039 Score=68.37 Aligned_cols=70 Identities=20% Similarity=0.274 Sum_probs=51.7
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.+++||||+|+.+|- ++..++...+..++...|-||-..||||+++-... .+|.+.+.. -.|+|.|.
T Consensus 3 ~Gil~i~KP~G~TS~d--------vv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~--~~K~Y~a~ 70 (308)
T PRK14124 3 HGFLVAYKPKGPTSHD--------VVDEVRKKLKTRKVGHAGTLDPFATGVLIVGVNKA--TRLLEYLKN--EKKVYYVK 70 (308)
T ss_pred ceEEEEECCCCCCHHH--------HHHHHHHHcCCCccCcCcCCCCCCcEEEEEEEChH--HhhhHHHhc--CCceEEEE
Confidence 3689999999998873 33444444455678889999999999999988763 334444443 38999998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 71 ~~ 72 (308)
T PRK14124 71 MR 72 (308)
T ss_pred EE
Confidence 75
No 47
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=96.71 E-value=0.00041 Score=67.93 Aligned_cols=71 Identities=21% Similarity=0.275 Sum_probs=52.1
Q ss_pred CCCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhe
Q 015839 148 EPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIA 227 (399)
Q Consensus 148 d~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA 227 (399)
-+.+|+||||.|+.+|- ++..++...+..++...|-||-.+||||+++-.. +.+|.+.+.+ ..|+|.|
T Consensus 8 ~~Gil~i~KP~G~TS~d--------vv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~--aTKl~~~l~~--~~K~Y~a 75 (298)
T PRK03287 8 GSGLVVVDKPAGMTSHD--------VVARCRRLFGTRKVGHAGTLDPMATGVLVLGVER--ATKLLGHLTL--TDKSYTA 75 (298)
T ss_pred cCeEEEEeCCCCCCHHH--------HHHHHHHHhCCCCCCcCccCCCcceeEEEEEeCh--hhhhhHHHhc--CCcEEEE
Confidence 35799999999998873 3444444445567888999999999999998885 3344433432 4899999
Q ss_pred eec
Q 015839 228 RVN 230 (399)
Q Consensus 228 ~V~ 230 (399)
.+.
T Consensus 76 ~~~ 78 (298)
T PRK03287 76 TIR 78 (298)
T ss_pred EEE
Confidence 875
No 48
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=96.63 E-value=0.00045 Score=67.53 Aligned_cols=70 Identities=23% Similarity=0.296 Sum_probs=51.8
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.+|+||||.|+.+|- ++..++...+..++...|-||-..||||+++-.. +.+|.+.+. ...|+|.|.
T Consensus 2 ~Gil~i~KP~G~tS~d--------vv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~--aTkl~~~l~--~~~K~Y~a~ 69 (290)
T PRK00130 2 DGILNILKPPGMTSFD--------VVRKIRKIAKIKKVGHTGTLDPLASGVLPVCLGK--ATKIVDYLM--EGKKTYRAE 69 (290)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhCCCccCcCCCCCCCCeeEEEEEECh--hhhhHHHhc--cCCcEEEEE
Confidence 3689999999998873 3344444445567888999999999999998886 334544444 338999998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 70 ~~ 71 (290)
T PRK00130 70 IK 71 (290)
T ss_pred EE
Confidence 75
No 49
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=96.60 E-value=0.00047 Score=66.95 Aligned_cols=68 Identities=21% Similarity=0.353 Sum_probs=50.4
Q ss_pred eEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeec
Q 015839 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (399)
Q Consensus 151 ~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (399)
++++|||.|+.+|- ++..++...+..++...|.||-..||||+++-... .+|...+ ....|+|.|.+.
T Consensus 2 il~i~KP~G~tS~d--------vv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l--~~~~K~Y~a~~~ 69 (279)
T PRK02193 2 IKLLYKPKGISSFK--------FIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDED--TKLIDYL--DQKDKTYIAKIK 69 (279)
T ss_pred EEEEECCCCCCHHH--------HHHHHHHHcCCCccccCccCCCcCeeEEEEEEChh--hhhhHHh--ccCCcEEEEEEE
Confidence 68999999998873 33344444455678889999999999999988762 3444444 356899999875
No 50
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=96.60 E-value=0.00047 Score=67.81 Aligned_cols=70 Identities=23% Similarity=0.197 Sum_probs=52.0
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.+|+||||+|+.+|- ++..++...+..++...|-||-..||||+++-... .+|.+.+. ...|+|.|.
T Consensus 3 ~Gil~i~KP~G~TS~d--------vv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~--~~~K~Y~~~ 70 (305)
T PRK14123 3 NGILPVYKERGLTSHD--------VVFKLRKILKTKKIGHTGTLDPEVAGVLPVCIGNA--TRVSDYVM--DMGKAYEAT 70 (305)
T ss_pred ceEEEEeCCCCCCHHH--------HHHHHHHHhCCCccccCcCCCCcCeeEEEEEEChh--hhhHHHhc--CCCcEEEEE
Confidence 3689999999998873 34444444455678889999999999999988864 34544443 368999998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 71 ~~ 72 (305)
T PRK14123 71 VS 72 (305)
T ss_pred EE
Confidence 75
No 51
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=96.59 E-value=0.00047 Score=67.76 Aligned_cols=70 Identities=24% Similarity=0.177 Sum_probs=51.5
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.+|+||||.|+.+|- ++..++...+..++...|-||...||||+++-.. +-+|.+.+. ...|+|.|.
T Consensus 13 ~Gil~i~KP~G~TS~d--------vv~~vrk~~~~kKvGH~GTLDP~AtGvL~v~vG~--aTkl~~~l~--~~~K~Y~a~ 80 (305)
T PRK05389 13 SGWLILDKPAGMTSTE--------AVSKVKWLFDAQKAGHAGTLDPLASGVLPIALGE--ATKTVPYVM--DGTKRYRFT 80 (305)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhcccccCCcccCCCCCceEEEEEECh--hhhhhHHhc--cCCcEEEEE
Confidence 4699999999998873 3344444444456888999999999999998876 334444443 248999998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 81 ~~ 82 (305)
T PRK05389 81 VA 82 (305)
T ss_pred EE
Confidence 75
No 52
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=96.58 E-value=0.00047 Score=67.46 Aligned_cols=69 Identities=20% Similarity=0.197 Sum_probs=52.2
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.+|+||||.|+.+|- ++..++...+..++...|-||-..||||+++-.... +|.+.+. . .|+|.|.
T Consensus 3 ~Gil~i~KP~G~TS~d--------vv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~aT--kl~~~l~--~-~K~Y~a~ 69 (295)
T PRK02755 3 FGFLNLDKPAGLTSHD--------CVARLRRLLRLKRVGHGGTLDPAATGVLPIALGKAT--RLLPYLP--G-EKTYRGT 69 (295)
T ss_pred ceEEEEeCCCCCCHHH--------HHHHHHHHhCCCccccCCCCCCcCeeEEEEEEChhh--hhHHHhC--C-CcEEEEE
Confidence 3689999999998873 344455545556788899999999999999888643 4555554 3 7999998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 70 ~~ 71 (295)
T PRK02755 70 IR 71 (295)
T ss_pred EE
Confidence 75
No 53
>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=96.54 E-value=0.00053 Score=66.65 Aligned_cols=68 Identities=25% Similarity=0.267 Sum_probs=50.9
Q ss_pred eEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeec
Q 015839 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (399)
Q Consensus 151 ~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (399)
+|+||||+|+.+|- ++..++...+..++...|-||-..||||+++-+.. .+|...+.+ ..|+|.|.+.
T Consensus 2 il~i~KP~G~tS~~--------vv~~vr~~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~--~~K~Y~~~~~ 69 (277)
T cd02573 2 ILLLDKPAGLTSHD--------VVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEA--TKLSQYLLD--ADKTYRATVR 69 (277)
T ss_pred EEEEECCCCCCHHH--------HHHHHHHHhCcCccCCCCCCCCcCeEEEEEEEChH--HhhHHHhcC--CCcEEEEEEE
Confidence 78999999998873 33344444444678889999999999999988863 345544443 5899999875
No 54
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=96.51 E-value=0.00061 Score=66.85 Aligned_cols=70 Identities=23% Similarity=0.203 Sum_probs=51.7
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.+|+||||.|+.+|- ++..++...+..++...+-||-..||||+++-... -+|.+.+. ...|+|.|.
T Consensus 16 ~Gil~i~KP~G~TS~d--------vv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~--~~~K~Y~~~ 83 (303)
T PRK01851 16 DGVLLLDKPLGLSSND--------ALQRAKRLLRAKKAGHTGTLDPLATGLLPLCFGEA--TKFSQDLL--DADKTYEAT 83 (303)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhCcccCCCCCCCCCCCceEEEEEECHH--HhhhHHhc--ccCeEEEEE
Confidence 4799999999998873 34444444445678889999999999999988763 33444443 345999998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 84 ~~ 85 (303)
T PRK01851 84 LR 85 (303)
T ss_pred EE
Confidence 75
No 55
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=96.50 E-value=0.00064 Score=67.31 Aligned_cols=70 Identities=20% Similarity=0.213 Sum_probs=51.2
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.+|+||||.|+.+|- ++..++...+..++...|.||...||||+++-... .+|...+. ...|+|.|.
T Consensus 3 nGiL~idKP~G~TS~d--------vv~~vrk~l~~kKVGH~GTLDP~AtGVL~i~vG~a--TKl~~~l~--~~~K~Y~a~ 70 (345)
T PRK14846 3 NYWLNIYKPRGISSAQ--------LVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEA--TKLIHLLI--DARKTYIFT 70 (345)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhCCCcCCcCccCCCcCceEEEEEEChh--hhhhHHHh--cCCceEEEE
Confidence 4689999999998873 34444444455678899999999999999988752 33443332 457899998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 71 ~~ 72 (345)
T PRK14846 71 VK 72 (345)
T ss_pred EE
Confidence 75
No 56
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=96.50 E-value=0.00063 Score=66.88 Aligned_cols=70 Identities=23% Similarity=0.195 Sum_probs=51.5
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.+|+||||.|+.+|- ++..++...+..++-..+-||-..||||+++-... .+|.+.+. ...|+|.|.
T Consensus 2 ~Gil~i~KP~G~TS~d--------vv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~--~~~K~Y~a~ 69 (304)
T PRK01550 2 NGVLLLHKPRGMTSHD--------CVFKLRKILRTKKVGHTGTLDPEVSGVLPICVGRA--TKIAEYLT--DEGKTYEGE 69 (304)
T ss_pred CeEEEEECCCCCCHHH--------HHHHHHHHcCCCCcccCCCCCCcCeeEEEEEEChh--hhhhHHhc--CCCcEEEEE
Confidence 3589999999998873 33444444455678889999999999999988763 33444443 348999998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 70 ~~ 71 (304)
T PRK01550 70 VT 71 (304)
T ss_pred EE
Confidence 75
No 57
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=96.50 E-value=0.00066 Score=66.87 Aligned_cols=72 Identities=22% Similarity=0.213 Sum_probs=52.2
Q ss_pred cCCCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhh
Q 015839 147 KEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYI 226 (399)
Q Consensus 147 Ed~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~Yl 226 (399)
-.+.+|+||||.|+.+|- ++..++...+..++...|-||...||||+++-.. +.+|.+.+. ...|+|.
T Consensus 20 ~~~g~l~i~Kp~g~tS~~--------~v~~~r~~~~~kkvGH~GTLDp~A~GvL~v~~g~--atk~~~~~~--~~~K~Y~ 87 (300)
T PRK04270 20 IKFGVVNLDKPPGPTSHE--------VAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGK--ATKVVQALL--ESGKEYV 87 (300)
T ss_pred cCCCEEEEECCCCCCHHH--------HHHHHHHHhccccccCCCCCCCcCeEEEEEEECh--HhhhhHHhc--cCCcEEE
Confidence 345799999999998873 3334444444457888999999999999998876 344444443 3469999
Q ss_pred eeec
Q 015839 227 ARVN 230 (399)
Q Consensus 227 A~V~ 230 (399)
|.+.
T Consensus 88 ~~~~ 91 (300)
T PRK04270 88 CVMH 91 (300)
T ss_pred EEEE
Confidence 9874
No 58
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=96.49 E-value=0.0004 Score=65.70 Aligned_cols=49 Identities=16% Similarity=0.009 Sum_probs=43.2
Q ss_pred chhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEecccccccc
Q 015839 81 TIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (399)
Q Consensus 81 rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (399)
||+++|++.....||+.++++|++|+|+|||+++ ++++.|..+|.|++.
T Consensus 1 RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~d~I~v~ 50 (228)
T TIGR00478 1 RLDILLVRRGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFDAKIELL 50 (228)
T ss_pred CHHHHHHHcCCccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCCCEEecc
Confidence 7899999873345899999999999999999999 899999999988764
No 59
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=96.48 E-value=0.00065 Score=66.93 Aligned_cols=70 Identities=20% Similarity=0.227 Sum_probs=51.9
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.+|+||||.|+.+|- ++..++...+..++...|-||-..||||+++-... -+|.+.+. ...|+|.|.
T Consensus 10 ~Gil~i~KP~G~TS~d--------vv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~~~--~~~K~Y~a~ 77 (312)
T PRK05033 10 NGVLLLDKPQGMSSND--------ALQKVKRLFNANKAGHTGALDPLATGMLPICLGEA--TKFSQYLL--DSDKRYRVT 77 (312)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhCCCCCCCCCcCCCcCeeEEEEEECHH--hhhhHHhc--CCCcEEEEE
Confidence 4799999999998873 33444444444678889999999999999988763 33554444 348999998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 78 ~~ 79 (312)
T PRK05033 78 AR 79 (312)
T ss_pred EE
Confidence 75
No 60
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=96.47 E-value=0.00043 Score=64.41 Aligned_cols=51 Identities=20% Similarity=0.077 Sum_probs=44.4
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEecccccccc
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (399)
.+||+.+|.+.....||..++++|..|.|+|||+++ .+++.|++||.|++.
T Consensus 92 E~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~I~v~ 143 (203)
T PRK05327 92 ESRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVR 143 (203)
T ss_pred HHHHHHHHHHcCccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCEEEEC
Confidence 479999997652357999999999999999999999 589999999999865
No 61
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=96.45 E-value=0.00055 Score=64.62 Aligned_cols=51 Identities=22% Similarity=0.284 Sum_probs=47.2
Q ss_pred cCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEecccccccc
Q 015839 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (399)
..+||+.++++-| ..||..+.++|.+|+|+||.+++ ++++.|+.||.|.+.
T Consensus 179 sSlRLD~vis~~~-~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSir 230 (257)
T COG2302 179 SSLRLDVVISEGF-GLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIR 230 (257)
T ss_pred ehhhHHHHHHHHH-hhhHHHHHHHHHcCceEEeeEEeccccceeccCCEEEEe
Confidence 4689999999987 78999999999999999999999 699999999999975
No 62
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=96.33 E-value=0.00096 Score=65.20 Aligned_cols=70 Identities=23% Similarity=0.224 Sum_probs=50.8
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.+|+||||.|+.+|- ++..++...+..++...|-||-..||||+++-... .+|.+.+. ...|+|.|.
T Consensus 3 ~GiL~i~KP~G~TS~d--------vv~~vrk~~~~kKvGH~GTLDP~AtGvL~v~vG~a--TKl~~~l~--~~~K~Y~~~ 70 (292)
T PRK01528 3 NYWLNIYKPRGISSAK--------LVSIVKKILGKVKIGHAGTLDVEAEGVLPLAVGEA--TKLVQLLI--DAKKTYIFT 70 (292)
T ss_pred CEEEEEeCCCCCCHHH--------HHHHHHHHcCCCccCcCccCCCcCceEEEEEEChH--hhhhHHHh--cCCceEEEE
Confidence 4689999999998873 33344444444578889999999999999988762 33443333 357999998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 71 ~~ 72 (292)
T PRK01528 71 VK 72 (292)
T ss_pred EE
Confidence 75
No 63
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=96.23 E-value=0.0011 Score=65.31 Aligned_cols=68 Identities=26% Similarity=0.305 Sum_probs=50.9
Q ss_pred eEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeec
Q 015839 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (399)
Q Consensus 151 ~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (399)
+|+||||.|+.+|- ++..++...+..++-..+-||-..||||+++-... -+|...+ ....|+|.|.+.
T Consensus 3 il~idKP~G~TS~d--------vv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~iG~a--TKl~~~l--~~~~K~Y~a~~~ 70 (312)
T PRK14122 3 VYAVDKPLGLTSHD--------VVNRARRALGTRRVGHTGTLDPLATGVLVLCTDDS--TKLVPFL--SAEDKEYLAWVS 70 (312)
T ss_pred EEEEECCCCCCHHH--------HHHHHHHHhCCCCCCCCCCCCCcCeeeEEEEEChh--hhhhHHh--cCCCceEEEEEE
Confidence 78999999998873 33344444455678889999999999999988763 3355444 356899999875
No 64
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=96.10 E-value=0.0018 Score=60.20 Aligned_cols=52 Identities=19% Similarity=0.109 Sum_probs=40.7
Q ss_pred cchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEecccccccccc
Q 015839 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLH 131 (399)
Q Consensus 80 ~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~ 131 (399)
+||+-++-+.--..|+++|.++|..|.|.|||++| .+++.|++||+|.|...
T Consensus 94 rRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k 146 (205)
T COG0522 94 RRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREK 146 (205)
T ss_pred HHHHHHHHHhcccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEeeec
Confidence 34444433321147899999999999999999999 79999999999997643
No 65
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=95.84 E-value=0.002 Score=63.08 Aligned_cols=70 Identities=20% Similarity=0.145 Sum_probs=51.8
Q ss_pred CCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhee
Q 015839 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (399)
Q Consensus 149 ~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (399)
+.+|+||||.|+.+|- ++..++...+..++-..+-||-..||||+++-.. |-+|.+.+. ...|+|.|.
T Consensus 10 ~Gil~i~KP~G~TS~d--------vv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~~G~--aTkl~~~l~--~~~K~Y~a~ 77 (300)
T PRK04642 10 DGILLLDKPAGLSSNN--------ALQAARRLLRAEKGGHTGSLDPLATGLLPLCFGE--ATKIAGLLL--GSAKAYDAE 77 (300)
T ss_pred CeEEEEecCCCCCHHH--------HHHHHHHHhCCCcccCCCccCCcCeeeEEEEECh--hhhhhHHhc--CCCcEEEEE
Confidence 4699999999998873 3444444445567888999999999999998776 244443333 457999998
Q ss_pred ec
Q 015839 229 VN 230 (399)
Q Consensus 229 V~ 230 (399)
+.
T Consensus 78 ~~ 79 (300)
T PRK04642 78 IV 79 (300)
T ss_pred EE
Confidence 74
No 66
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes 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 archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=95.84 E-value=0.0019 Score=64.19 Aligned_cols=71 Identities=20% Similarity=0.242 Sum_probs=52.0
Q ss_pred CCCeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhhe
Q 015839 148 EPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIA 227 (399)
Q Consensus 148 d~~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA 227 (399)
.+.+|+||||.|+.+|- ++..++...+..++...+-||-..||||+++-.. |.+|.+.+. ...|+|.|
T Consensus 33 ~~G~l~i~KP~g~tS~~--------~v~~vr~~~~~kkvGH~GTLDP~A~GvL~v~~G~--aTkl~~~~~--~~~K~Y~~ 100 (322)
T TIGR00425 33 SYGVVNLDKPSGPSSHE--------VVAWVRRILNVEKTGHGGTLDPKVTGVLPVCIER--ATRLVKSLQ--EAPKEYVC 100 (322)
T ss_pred CCCEEEEeCCCCCCHHH--------HHHHHHHHhcccccCCCCCCCCCCceEEEEEECh--HhhccHHhc--cCCCEEEE
Confidence 45799999999998873 3333444444467888999999999999998876 334443333 45899999
Q ss_pred eec
Q 015839 228 RVN 230 (399)
Q Consensus 228 ~V~ 230 (399)
.+.
T Consensus 101 ~v~ 103 (322)
T TIGR00425 101 LMR 103 (322)
T ss_pred EEE
Confidence 874
No 67
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=95.50 E-value=0.0016 Score=49.38 Aligned_cols=50 Identities=10% Similarity=0.043 Sum_probs=34.1
Q ss_pred cCcchhhhhhhhhcC-CccceeeeeEEeeeeEecCeee-eeeEEEeccccccc
Q 015839 78 AGKTIVDLFAEEFKG-RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISH 128 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~-~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~ 128 (399)
+-++|.++|... +. -|=.+++.+|.+|.|+|||++. .-+.++++||.|.+
T Consensus 6 e~I~L~qlLK~~-glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~ 57 (65)
T PF13275_consen 6 EYITLGQLLKLA-GLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEI 57 (65)
T ss_dssp S---HHHHHHHH-TS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEE
T ss_pred CcEEHHHHHhHc-CCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEE
Confidence 458999999876 43 4667889999999999999998 78999999999985
No 68
>PRK11507 ribosome-associated protein; Provisional
Probab=95.39 E-value=0.0031 Score=48.38 Aligned_cols=52 Identities=17% Similarity=0.124 Sum_probs=42.6
Q ss_pred cCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEecccccccc
Q 015839 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (399)
+-++|.++|.-.=-.-|=-+++.+|.+|.|+|||++. .-+.+|.+||.|.+.
T Consensus 10 e~I~L~QlLK~~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~V~~~ 62 (70)
T PRK11507 10 PHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFA 62 (70)
T ss_pred CeEEHHHHHhhhCcccChHHHHHHHHcCceEECCEEecccCCCCCCCCEEEEC
Confidence 4489999997651234667788999999999999998 679999999999853
No 69
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=95.39 E-value=0.0041 Score=60.22 Aligned_cols=69 Identities=25% Similarity=0.321 Sum_probs=51.1
Q ss_pred CeEEeecCCCcccccCcccccceEEEEeecccCCCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheee
Q 015839 150 DVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARV 229 (399)
Q Consensus 150 ~~ivvnKP~Gl~v~p~~~~~~~tv~~~L~~~~~~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V 229 (399)
.+|++|||.|+.+|- ++..++...+..+....+-||-..||+|.++-. ++.+.+. .+. .-.|+|.|.+
T Consensus 16 Gil~ldKP~G~tS~~--------~v~~vkkil~~~K~GH~GTLDP~atGvLpi~ig-~aTKl~~-~l~--~~~K~Y~a~~ 83 (271)
T COG0130 16 GVINLDKPPGPTSHE--------VVAWVKRILGVEKAGHGGTLDPLATGVLPICLG-EATKLVQ-YLL--DADKEYVATV 83 (271)
T ss_pred ceEEeeCCCCCCHHH--------HHHHHHHHhCccccccccccCCcccceEEEEec-hhHhHHH-HHh--hCCcEEEEEE
Confidence 799999999998873 333344444556677899999999999999998 4444333 332 4589999988
Q ss_pred c
Q 015839 230 N 230 (399)
Q Consensus 230 ~ 230 (399)
.
T Consensus 84 ~ 84 (271)
T COG0130 84 R 84 (271)
T ss_pred E
Confidence 5
No 70
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=95.28 E-value=0.0041 Score=58.74 Aligned_cols=52 Identities=17% Similarity=0.038 Sum_probs=45.8
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEeccccccccc
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFL 130 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~ 130 (399)
-+||+.+|.+.--.-||+.|+.+|.+|.|.|||+.+ ++++.|...+.|++..
T Consensus 2 k~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~ 54 (245)
T COG1189 2 KMRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKG 54 (245)
T ss_pred cchHHHHHHHccchhhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEcc
Confidence 389999999873357999999999999999999999 8999999999988753
No 71
>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=95.27 E-value=0.0049 Score=60.76 Aligned_cols=42 Identities=21% Similarity=0.205 Sum_probs=32.0
Q ss_pred CcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeec
Q 015839 185 PLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (399)
Q Consensus 185 ~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (399)
++-..|-||-..||||+++-.. +.+.|+. +.. ..|+|.|.+.
T Consensus 57 KiGH~GTLDPlAsGVLvvgvG~-aTK~l~~-~l~--~~K~Y~~~~~ 98 (312)
T cd02867 57 KIGHGGTLDPLATGVLVVGVGA-GTKQLQD-YLS--CSKTYEATGL 98 (312)
T ss_pred ccccccccCCccceeEEEEECc-HHHHHHH-Hhc--CCceEEEEEE
Confidence 5677999999999999998876 3444443 332 7999999865
No 72
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=93.76 E-value=0.016 Score=52.58 Aligned_cols=49 Identities=16% Similarity=0.123 Sum_probs=40.2
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEecccccc
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKIS 127 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~ 127 (399)
.+||+.+|.+.--.-|+..|.++|..|.|+|||++| .+++.|..+++-.
T Consensus 102 erRLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~ 151 (177)
T PRK04051 102 ERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDL 151 (177)
T ss_pred HhHHHHHHHHccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcce
Confidence 468877777662356899999999999999999999 8999999885433
No 73
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=93.38 E-value=0.026 Score=43.62 Aligned_cols=51 Identities=10% Similarity=0.001 Sum_probs=42.4
Q ss_pred cCcchhhhhhhhhcC-CccceeeeeEEeeeeEecCeee-eeeEEEecccccccc
Q 015839 78 AGKTIVDLFAEEFKG-RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~-~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (399)
+-++|.++|... +. -|=..++.+|..|.|+|||++- +-+.+|+.||.|.+.
T Consensus 10 e~I~L~qlLK~~-g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~ 62 (73)
T COG2501 10 EFITLGQLLKLA-GLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIP 62 (73)
T ss_pred ceEEHHHHHHHh-CcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEEC
Confidence 347899998775 43 4667788999999999999998 779999999999853
No 74
>PLN00189 40S ribosomal protein S9; Provisional
Probab=92.80 E-value=0.049 Score=50.08 Aligned_cols=39 Identities=13% Similarity=0.158 Sum_probs=34.4
Q ss_pred CccceeeeeEEeeeeEecCeee-eeeEEEecccccccccc
Q 015839 93 RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLH 131 (399)
Q Consensus 93 ~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~ 131 (399)
-|...|.++|..|.|.|||++| .|++.|..++++.|.+.
T Consensus 122 ~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~ 161 (194)
T PLN00189 122 KSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFS 161 (194)
T ss_pred CCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEEe
Confidence 4778899999999999999999 79999999988876543
No 75
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=90.50 E-value=0.19 Score=45.84 Aligned_cols=49 Identities=10% Similarity=0.083 Sum_probs=37.3
Q ss_pred cchhhhhhhhhc-CCccceeeeeEEeeeeEecCeee-eeeEEEecccccccc
Q 015839 80 KTIVDLFAEEFK-GRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (399)
Q Consensus 80 ~rL~k~L~~~f~-~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (399)
+||+-++.+. + .-|...|.++|..|.|.|||++| .+++.|..+++=.|.
T Consensus 107 RRL~~iv~r~-g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I~ 157 (181)
T PTZ00155 107 RRLQTKVFKL-GLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHID 157 (181)
T ss_pred HhhhhHHHhc-cCcCCHHHhhhheeCCCEEECCEEeccCceEeccCccCcee
Confidence 4554444443 3 35778899999999999999999 799999998765443
No 76
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=90.11 E-value=0.13 Score=46.02 Aligned_cols=47 Identities=19% Similarity=0.205 Sum_probs=35.5
Q ss_pred cchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEeccccc
Q 015839 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKI 126 (399)
Q Consensus 80 ~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I 126 (399)
+||+-++.+.--.-|...|.++|..|.|+|||++| .|++.|..+++-
T Consensus 104 RRL~~vv~r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed 151 (162)
T TIGR01018 104 RRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEK 151 (162)
T ss_pred HhHhhHhhhccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCC
Confidence 45544444331135788899999999999999999 799999988543
No 77
>PRK01777 hypothetical protein; Validated
Probab=86.79 E-value=0.39 Score=39.23 Aligned_cols=51 Identities=4% Similarity=0.044 Sum_probs=39.1
Q ss_pred cCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeeeeEEEeccccccccc
Q 015839 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFL 130 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~~ 130 (399)
.|.++.+.|... + +...+-+--+..+.|-|||+.+..++.|+.||.|+++.
T Consensus 25 ~GtTv~dal~~s-g-i~~~~pei~~~~~~vgI~Gk~v~~d~~L~dGDRVeIyr 75 (95)
T PRK01777 25 EGATVEEAIRAS-G-LLELRTDIDLAKNKVGIYSRPAKLTDVLRDGDRVEIYR 75 (95)
T ss_pred CCCcHHHHHHHc-C-CCccCcccccccceEEEeCeECCCCCcCCCCCEEEEec
Confidence 578898988875 4 33332222345688999999999999999999999874
No 78
>PRK04313 30S ribosomal protein S4e; Validated
Probab=86.66 E-value=0.27 Score=46.61 Aligned_cols=72 Identities=13% Similarity=0.063 Sum_probs=53.0
Q ss_pred cCcchhhhhhhhhcC-CccceeeeeEEeeeeEecCeee-eeeEEEecccccccccccCCCCeeeccceeeccCCCeEEee
Q 015839 78 AGKTIVDLFAEEFKG-RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVC 155 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~-~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~pv~~~~~~IlyEd~~~ivvn 155 (399)
+.+.|.=+|.+.|+. .+.+++++.+.+|.|.|||++. +..+.|-.-|+|++.- .....+++|.....+++.
T Consensus 36 ~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~~-------~~e~yRvl~d~kgr~~l~ 108 (237)
T PRK04313 36 ESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIPE-------TGEYYRVLPDEKGRLVLI 108 (237)
T ss_pred cccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEcc-------CCCeEEEEECCCCcEEEE
Confidence 467777777776653 5788999999999999999998 7788887779998631 123466777666655555
Q ss_pred c
Q 015839 156 K 156 (399)
Q Consensus 156 K 156 (399)
+
T Consensus 109 ~ 109 (237)
T PRK04313 109 P 109 (237)
T ss_pred E
Confidence 4
No 79
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=85.83 E-value=0.41 Score=37.91 Aligned_cols=43 Identities=26% Similarity=0.492 Sum_probs=33.8
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeeeeEEEecccccccc
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHF 129 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~ 129 (399)
+-++.+.+.. + +.+..++ |.|.|||+.+..+++++.||.|.++
T Consensus 32 ~~tvkd~IEs-L-GVP~tEV------~~i~vNG~~v~~~~~~~~Gd~v~V~ 74 (81)
T PF14451_consen 32 GATVKDVIES-L-GVPHTEV------GLILVNGRPVDFDYRLKDGDRVAVY 74 (81)
T ss_pred CCcHHHHHHH-c-CCChHHe------EEEEECCEECCCcccCCCCCEEEEE
Confidence 4566555554 4 5677654 6789999999999999999999976
No 80
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=83.34 E-value=0.44 Score=46.06 Aligned_cols=72 Identities=11% Similarity=-0.011 Sum_probs=52.6
Q ss_pred cCcchhhhhhhhhcC-CccceeeeeEEeeeeEecCeee-eeeEEEecccccccccccCCCCeeeccceeeccCCCeEEee
Q 015839 78 AGKTIVDLFAEEFKG-RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVC 155 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~-~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~pv~~~~~~IlyEd~~~ivvn 155 (399)
+.+.|.=+|.+.|+. .+.+++++.+.+|.|.|||++. +..+.|---|+|++.- ....++++|.....+++.
T Consensus 37 esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~k-------t~e~yRvl~D~kGrf~l~ 109 (273)
T PTZ00223 37 ECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPK-------TGDRFRILYDVKGRFALV 109 (273)
T ss_pred cccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcC-------CCCeEEEEECCCCcEEEE
Confidence 467777777776654 4778899999999999999998 7777777779998631 123467777766666555
Q ss_pred c
Q 015839 156 K 156 (399)
Q Consensus 156 K 156 (399)
+
T Consensus 110 ~ 110 (273)
T PTZ00223 110 K 110 (273)
T ss_pred E
Confidence 4
No 81
>PLN00036 40S ribosomal protein S4; Provisional
Probab=83.33 E-value=0.44 Score=45.82 Aligned_cols=72 Identities=11% Similarity=0.086 Sum_probs=52.9
Q ss_pred cCcchhhhhhhhhcC-CccceeeeeEEeeeeEecCeee-eeeEEEecccccccccccCCCCeeeccceeeccCCCeEEee
Q 015839 78 AGKTIVDLFAEEFKG-RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVC 155 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~-~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~pv~~~~~~IlyEd~~~ivvn 155 (399)
+.+.|.=+|.+.|+. .+.+++++.+.+|.|.|||++. +..+.|=--|+|++.- ....++++|.....+++.
T Consensus 40 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~k-------t~e~yRvl~D~kGrf~l~ 112 (261)
T PLN00036 40 ECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPK-------TNENFRLLYDTKGRFRLH 112 (261)
T ss_pred cccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcC-------CCCeEEEEECCCceEEEE
Confidence 467777777776654 4678899999999999999998 7777777779998631 123467777776666655
Q ss_pred c
Q 015839 156 K 156 (399)
Q Consensus 156 K 156 (399)
+
T Consensus 113 ~ 113 (261)
T PLN00036 113 R 113 (261)
T ss_pred E
Confidence 4
No 82
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=82.20 E-value=0.48 Score=45.59 Aligned_cols=73 Identities=18% Similarity=0.079 Sum_probs=52.3
Q ss_pred ccCcchhhhhhhhhcC-CccceeeeeEEeeeeEecCeee-eeeEEEecccccccccccCCCCeeeccceeeccCCCeEEe
Q 015839 77 WAGKTIVDLFAEEFKG-RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTV 154 (399)
Q Consensus 77 ~~g~rL~k~L~~~f~~-~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~pv~~~~~~IlyEd~~~ivv 154 (399)
.+.+.|.=+|.+.|+. .+.+++++.+.+|.|.|||++. +..+.|---|+|++.- ....++++|.....+++
T Consensus 39 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~k-------t~e~yRvl~D~kGr~~l 111 (262)
T PTZ00118 39 RECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTK-------TNEYFRLLYDTKGRFVP 111 (262)
T ss_pred ccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEcC-------CCCeEEEEECCCccEEE
Confidence 3467777777776653 5778899999999999999998 7777777779998531 12345677666665555
Q ss_pred ec
Q 015839 155 CK 156 (399)
Q Consensus 155 nK 156 (399)
.+
T Consensus 112 ~~ 113 (262)
T PTZ00118 112 HK 113 (262)
T ss_pred EE
Confidence 43
No 83
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=78.67 E-value=1.1 Score=42.43 Aligned_cols=21 Identities=29% Similarity=0.354 Sum_probs=18.1
Q ss_pred cccchhhhhhhhheeeeeccc
Q 015839 186 LFPVHRLDRLVSGLLILARNA 206 (399)
Q Consensus 186 l~pVhRLDr~TSGLLL~akd~ 206 (399)
+..+||||-.|||++||.-..
T Consensus 91 V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559|consen 91 VQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred eeeEEeecccccceEEEecCc
Confidence 567999999999999997654
No 84
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. This entry represents pseudouridine synthase TruB, as well as Cbf5p that modifies rRNA [].; GO: 0006396 RNA processing; PDB: 1SGV_B 2AUS_C 3UAI_A 3U28_A 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=75.67 E-value=1.4 Score=39.02 Aligned_cols=44 Identities=20% Similarity=0.301 Sum_probs=30.6
Q ss_pred CCCcccchhhhhhhhheeeeecccchhHHHHHHHhhchhhhhhheeec
Q 015839 183 LAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (399)
Q Consensus 183 ~~~l~pVhRLDr~TSGLLL~akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (399)
..++-..|.||-.+||||+++-+. +-+|...+. ...|+|.|.+.
T Consensus 6 ~~KvGH~GTLDP~AsGvL~v~vg~--~Tkl~~~l~--~~~K~Y~~~~~ 49 (149)
T PF01509_consen 6 IKKVGHGGTLDPFASGVLVVGVGK--ATKLLSYLQ--NSDKEYVATIR 49 (149)
T ss_dssp BSSEEESS-SSTT-EEEEEEEEGG--GGGGHHHHT--TSEEEEEEEEE
T ss_pred cceeccccccCCcceEEEEEEECC--cchHHHHhh--ccCCEEEEEEE
Confidence 345678999999999999999876 333554454 34599999764
No 85
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=75.07 E-value=0.98 Score=42.52 Aligned_cols=70 Identities=14% Similarity=0.087 Sum_probs=46.9
Q ss_pred cchhhhhhhhhcC-CccceeeeeEEeeeeEecCeee-eeeEEEecccccccccccCCCCeeeccceeeccCCCeEEeec
Q 015839 80 KTIVDLFAEEFKG-RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCK 156 (399)
Q Consensus 80 ~rL~k~L~~~f~~-~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~pv~~~~~~IlyEd~~~ivvnK 156 (399)
..|.=++.+-+.. -.-+++++.|.+|.|+|||++. +..+.|---|+|++. ...+..+|+|.....+++.+
T Consensus 41 lPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip-------~tgE~yRvl~d~~grl~l~~ 112 (241)
T COG1471 41 LPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIP-------KTGEHYRVLPDEKGRLVLHP 112 (241)
T ss_pred ccEEeeehhHHHhccchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEEC-------CCCceEEEEecCCccEEEEe
Confidence 4444444433322 2346788999999999999998 666666556998863 11334788888888877765
No 86
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=67.14 E-value=5.6 Score=29.57 Aligned_cols=43 Identities=21% Similarity=0.346 Sum_probs=30.5
Q ss_pred cCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeee----eeEEEecccccccc
Q 015839 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVP----VSYTVKSSQKISHF 129 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~----~~~~v~~gD~I~~~ 129 (399)
++.+|.++|... +. +...+ .|.+||+++. ..+.|+.||.|++.
T Consensus 14 ~~~tl~~lL~~l-~~-~~~~v-------av~vNg~iv~r~~~~~~~l~~gD~vei~ 60 (66)
T PRK05659 14 DGESVAALLARE-GL-AGRRV-------AVEVNGEIVPRSQHASTALREGDVVEIV 60 (66)
T ss_pred CCCCHHHHHHhc-CC-CCCeE-------EEEECCeEeCHHHcCcccCCCCCEEEEE
Confidence 467888888763 43 32222 2778998885 67899999999864
No 87
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=65.43 E-value=6.5 Score=30.03 Aligned_cols=42 Identities=29% Similarity=0.453 Sum_probs=32.1
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeee----eeEEEecccccccc
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVP----VSYTVKSSQKISHF 129 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~----~~~~v~~gD~I~~~ 129 (399)
+.++.++|++. +.-++.. .|.+||+++. .+..++.||.|++.
T Consensus 17 ~~tv~dLL~~l-~~~~~~v--------av~vNg~iVpr~~~~~~~l~~gD~ievv 62 (68)
T COG2104 17 GTTVADLLAQL-GLNPEGV--------AVAVNGEIVPRSQWADTILKEGDRIEVV 62 (68)
T ss_pred CCcHHHHHHHh-CCCCceE--------EEEECCEEccchhhhhccccCCCEEEEE
Confidence 38999999885 5444433 3678999996 78999999999853
No 88
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=60.20 E-value=4.3 Score=31.74 Aligned_cols=24 Identities=13% Similarity=0.350 Sum_probs=20.9
Q ss_pred eeEecCeeeeeeEEEecccccccc
Q 015839 106 RIQVDEEMVPVSYTVKSSQKISHF 129 (399)
Q Consensus 106 ~V~VNGk~v~~~~~v~~gD~I~~~ 129 (399)
.+.||+..+..++.|+.||+|.++
T Consensus 52 ~~aVN~~~~~~~~~l~dgDeVai~ 75 (81)
T PRK11130 52 LAAVNQTLVSFDHPLTDGDEVAFF 75 (81)
T ss_pred EEEECCEEcCCCCCCCCCCEEEEe
Confidence 377899988888999999999875
No 89
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=56.94 E-value=8.7 Score=29.20 Aligned_cols=43 Identities=12% Similarity=0.142 Sum_probs=31.9
Q ss_pred cCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeeeeEEEecccccccc
Q 015839 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHF 129 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~ 129 (399)
.+.++.++|... + .+. +.-.|.+||+.+..++.|+.||.|.+.
T Consensus 22 ~~~tv~~ll~~l-~-~~~-------~~v~v~vNg~iv~~~~~l~~gD~Veii 64 (70)
T PRK08364 22 KGMKVADILRAV-G-FNT-------ESAIAKVNGKVALEDDPVKDGDYVEVI 64 (70)
T ss_pred CCCcHHHHHHHc-C-CCC-------ccEEEEECCEECCCCcCcCCCCEEEEE
Confidence 357888888663 3 332 234678999999889999999999864
No 90
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=55.12 E-value=3 Score=42.97 Aligned_cols=47 Identities=19% Similarity=0.215 Sum_probs=37.6
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEecccc
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQK 125 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~ 125 (399)
+..|.++|.+.--..|+++++++|.+|.|+|||+.+ +..+.+.+.+.
T Consensus 342 ~~~~~~~l~~~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~~ 389 (410)
T PRK13354 342 TKNLVDLLVDLGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPEDA 389 (410)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhhh
Confidence 678889888752246899999999999999999998 66666665553
No 91
>PRK06437 hypothetical protein; Provisional
Probab=54.91 E-value=7.4 Score=29.43 Aligned_cols=43 Identities=16% Similarity=0.139 Sum_probs=31.8
Q ss_pred cCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeeeeEEEecccccccc
Q 015839 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHF 129 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~ 129 (399)
.+.++.++|... + ++...+ .|.+||+++..++.|+.||.|.+.
T Consensus 19 ~~~tv~dLL~~L-g-i~~~~v-------aV~vNg~iv~~~~~L~dgD~Veiv 61 (67)
T PRK06437 19 HELTVNDIIKDL-G-LDEEEY-------VVIVNGSPVLEDHNVKKEDDVLIL 61 (67)
T ss_pred CCCcHHHHHHHc-C-CCCccE-------EEEECCEECCCceEcCCCCEEEEE
Confidence 457888888763 4 443322 355899999999999999999864
No 92
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. 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=51.69 E-value=7.7 Score=29.66 Aligned_cols=50 Identities=20% Similarity=0.204 Sum_probs=31.3
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeeeeEEEecccccccc
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHF 129 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~ 129 (399)
+.++.+++.......+.- .......-.|.|||+.+..++.|+.||+|.+.
T Consensus 25 ~~tv~~ll~~l~~~~~~~-~~~~~~~~~v~vNg~~v~~~~~l~~gD~v~i~ 74 (80)
T cd00754 25 GATVGELLDALEARYPGL-LEELLARVRIAVNGEYVRLDTPLKDGDEVAII 74 (80)
T ss_pred CCcHHHHHHHHHHHCchH-HHhhhhcEEEEECCeEcCCCcccCCCCEEEEe
Confidence 567776665432111210 11112233688999999989999999999865
No 93
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=50.36 E-value=8.8 Score=28.55 Aligned_cols=42 Identities=24% Similarity=0.387 Sum_probs=30.1
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeeee----EEEecccccccc
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVS----YTVKSSQKISHF 129 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~~----~~v~~gD~I~~~ 129 (399)
+.++.++|... + .+. +.+ .|.|||+.+... +.|+.||.|.+.
T Consensus 14 ~~tv~~ll~~l-~-~~~----~~i---~V~vNg~~v~~~~~~~~~L~~gD~V~ii 59 (65)
T cd00565 14 GATLAELLEEL-G-LDP----RGV---AVALNGEIVPRSEWASTPLQDGDRIEIV 59 (65)
T ss_pred CCCHHHHHHHc-C-CCC----CcE---EEEECCEEcCHHHcCceecCCCCEEEEE
Confidence 57888888763 3 332 222 367999999766 899999999864
No 94
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present 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 []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=45.27 E-value=9.9 Score=27.98 Aligned_cols=22 Identities=9% Similarity=0.261 Sum_probs=18.7
Q ss_pred eEecCeeeeeeEEEeccccccc
Q 015839 107 IQVDEEMVPVSYTVKSSQKISH 128 (399)
Q Consensus 107 V~VNGk~v~~~~~v~~gD~I~~ 128 (399)
..|||+.+.+++.|+.||.|++
T Consensus 37 A~Vng~~vdl~~~L~~~d~v~i 58 (60)
T PF02824_consen 37 AKVNGQLVDLDHPLEDGDVVEI 58 (60)
T ss_dssp EEETTEEEETTSBB-SSEEEEE
T ss_pred EEEcCEECCCCCCcCCCCEEEE
Confidence 3589999999999999999875
No 95
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia 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 in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=45.01 E-value=11 Score=28.52 Aligned_cols=50 Identities=20% Similarity=0.214 Sum_probs=32.2
Q ss_pred ccCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeee---eEEEecccccccc
Q 015839 77 WAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPV---SYTVKSSQKISHF 129 (399)
Q Consensus 77 ~~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~---~~~v~~gD~I~~~ 129 (399)
..+.++.++|.......+.-. ....=.|.|||+.+.. ++.|+.||+|.+.
T Consensus 19 ~~~~tv~~ll~~l~~~~p~~~---~~~~~~v~vN~~~v~~~~~~~~l~~gD~V~i~ 71 (77)
T PF02597_consen 19 PEGSTVRDLLEALAERYPELA---LRDRVAVAVNGEIVPDDGLDTPLKDGDEVAIL 71 (77)
T ss_dssp SSTSBHHHHHHHHCHHTGGGH---TTTTEEEEETTEEEGGGTTTSBEETTEEEEEE
T ss_pred CCCCcHHHHHHHHHhhccccc---cCccEEEEECCEEcCCccCCcCcCCCCEEEEE
Confidence 346777776665311122111 2233468899999987 8999999999864
No 96
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=43.44 E-value=6.5 Score=40.51 Aligned_cols=44 Identities=18% Similarity=0.235 Sum_probs=34.7
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEec
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKS 122 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~ 122 (399)
+..|.++|.+.--..|+++++++|++|.|+|||+.+ +....+..
T Consensus 342 ~~~~~~~l~~~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~ 386 (408)
T PRK05912 342 GIDLLALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTA 386 (408)
T ss_pred CCcHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEecCccccccc
Confidence 578889888652246999999999999999999998 55555543
No 97
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=39.40 E-value=15 Score=29.82 Aligned_cols=24 Identities=4% Similarity=0.212 Sum_probs=20.1
Q ss_pred eeEecCeeee----eeEEEecccccccc
Q 015839 106 RIQVDEEMVP----VSYTVKSSQKISHF 129 (399)
Q Consensus 106 ~V~VNGk~v~----~~~~v~~gD~I~~~ 129 (399)
.|.|||..++ .++.|+.||+|.+.
T Consensus 61 ~VlvN~~di~~l~g~~t~L~dgD~v~i~ 88 (94)
T cd01764 61 IVLINDTDWELLGEEDYILEDGDHVVFI 88 (94)
T ss_pred EEEECCccccccCCcccCCCCcCEEEEE
Confidence 5789999873 47999999999875
No 98
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=38.48 E-value=16 Score=28.24 Aligned_cols=24 Identities=17% Similarity=0.304 Sum_probs=21.3
Q ss_pred eeEecCeeeeeeEEEecccccccc
Q 015839 106 RIQVDEEMVPVSYTVKSSQKISHF 129 (399)
Q Consensus 106 ~V~VNGk~v~~~~~v~~gD~I~~~ 129 (399)
.|.||++.+..+..|+.||+|.+.
T Consensus 51 ~v~vn~~~v~~~~~l~dgDevai~ 74 (80)
T TIGR01682 51 MVAVNEEYVTDDALLNEGDEVAFI 74 (80)
T ss_pred EEEECCEEcCCCcCcCCCCEEEEe
Confidence 488999999889999999999865
No 99
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=36.98 E-value=6.9 Score=34.37 Aligned_cols=33 Identities=18% Similarity=0.199 Sum_probs=29.5
Q ss_pred cCcchhhhhhhhhcCCccceeeeeEEeeeeEecC
Q 015839 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDE 111 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNG 111 (399)
...||+.+|+++| .+||+.+++++.+|.|..+-
T Consensus 101 ~~~Rld~lLa~~L-~lSrs~l~~l~~~G~I~~~~ 133 (142)
T PF06353_consen 101 FPLRLDRLLARQL-GLSRSRLKRLIEQGLIRSDP 133 (142)
T ss_pred CCccHHHHHHHHh-CcCHHHHHHHHHCCCEEecC
Confidence 4689999999997 79999999999999998753
No 100
>TIGR01687 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.
Probab=36.55 E-value=14 Score=29.08 Aligned_cols=25 Identities=20% Similarity=0.191 Sum_probs=19.9
Q ss_pred eeeEecCeeeeeeE--EEecccccccc
Q 015839 105 GRIQVDEEMVPVSY--TVKSSQKISHF 129 (399)
Q Consensus 105 G~V~VNGk~v~~~~--~v~~gD~I~~~ 129 (399)
=.|.|||+.+.... .|+.||+|.+.
T Consensus 56 ~~v~vN~~~v~~~~~~~l~dgdev~i~ 82 (88)
T TIGR01687 56 VIILVNGRNVDWGLGTELKDGDVVAIF 82 (88)
T ss_pred EEEEECCEecCccCCCCCCCCCEEEEe
Confidence 35889999986554 89999999865
No 101
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=36.01 E-value=18 Score=26.77 Aligned_cols=42 Identities=19% Similarity=0.229 Sum_probs=28.9
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeee----eEEEecccccccc
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPV----SYTVKSSQKISHF 129 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~----~~~v~~gD~I~~~ 129 (399)
..+|.++|... .. .. +.+ .|-||++.+.. ++.|+.||+|.+.
T Consensus 14 ~~tl~~Ll~~l-~~-~~----~~v---avavN~~iv~~~~~~~~~L~dgD~Ieiv 59 (65)
T PRK06488 14 ATTLALLLAEL-DY-EG----NWL---ATAVNGELVHKEARAQFVLHEGDRIEIL 59 (65)
T ss_pred cCcHHHHHHHc-CC-CC----CeE---EEEECCEEcCHHHcCccccCCCCEEEEE
Confidence 35777777653 32 21 112 38899999964 7889999999864
No 102
>PRK07440 hypothetical protein; Provisional
Probab=33.33 E-value=28 Score=26.52 Aligned_cols=43 Identities=14% Similarity=0.252 Sum_probs=30.5
Q ss_pred cCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeee----eeEEEecccccccc
Q 015839 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVP----VSYTVKSSQKISHF 129 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~----~~~~v~~gD~I~~~ 129 (399)
.+.+|.++|... +.-++.. .|-+||+++. ..+.|+.||.|++.
T Consensus 18 ~~~tl~~lL~~l-~~~~~~v--------av~~N~~iv~r~~w~~~~L~~gD~IEIv 64 (70)
T PRK07440 18 SGTSLPDLLQQL-GFNPRLV--------AVEYNGEILHRQFWEQTQVQPGDRLEIV 64 (70)
T ss_pred CCCCHHHHHHHc-CCCCCeE--------EEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 467888888753 3322211 4678999996 67899999999853
No 103
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=33.22 E-value=22 Score=27.59 Aligned_cols=24 Identities=17% Similarity=0.295 Sum_probs=21.0
Q ss_pred eeEecCeeeeeeEEEecccccccc
Q 015839 106 RIQVDEEMVPVSYTVKSSQKISHF 129 (399)
Q Consensus 106 ~V~VNGk~v~~~~~v~~gD~I~~~ 129 (399)
.|.|||+.+..++.|+.||+|.+.
T Consensus 53 ~vavN~~~v~~~~~l~dgDeVai~ 76 (82)
T PLN02799 53 VLALNEEYTTESAALKDGDELAII 76 (82)
T ss_pred EEEECCEEcCCCcCcCCCCEEEEe
Confidence 477899999889999999999865
No 104
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=32.24 E-value=37 Score=24.87 Aligned_cols=25 Identities=12% Similarity=0.092 Sum_probs=17.5
Q ss_pred eeeeEecCeeeee--eEEEeccccccc
Q 015839 104 CGRIQVDEEMVPV--SYTVKSSQKISH 128 (399)
Q Consensus 104 ~G~V~VNGk~v~~--~~~v~~gD~I~~ 128 (399)
...++|||+.+.. .+.|+.||.|.+
T Consensus 41 ~ngt~vng~~l~~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 41 TNGTFVNGQRLGPGEPVPLKDGDIIRF 67 (68)
T ss_dssp SS-EEETTEEESSTSEEEE-TTEEEEE
T ss_pred CCcEEECCEEcCCCCEEECCCCCEEEc
Confidence 3457789988855 788889998863
No 105
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=27.79 E-value=34 Score=25.74 Aligned_cols=41 Identities=15% Similarity=0.195 Sum_probs=27.8
Q ss_pred cchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeee----eEEEecccccccc
Q 015839 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPV----SYTVKSSQKISHF 129 (399)
Q Consensus 80 ~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~----~~~v~~gD~I~~~ 129 (399)
.+|.++|... +.-+.. + .|-+||+++.. .+.|+.||.|++.
T Consensus 17 ~tv~~lL~~l-~~~~~~-----v---av~vN~~iv~r~~w~~~~L~~gD~iEIv 61 (67)
T PRK07696 17 KTVAELLTHL-ELDNKI-----V---VVERNKDILQKDDHTDTSVFDGDQIEIV 61 (67)
T ss_pred ccHHHHHHHc-CCCCCe-----E---EEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 4677887653 332221 1 37789999964 4889999999853
No 106
>cd01666 TGS_DRG_C TGS_DRG_C: DRG (developmentally regulated GTP-binding protein) represents a family of GTP-binding proteins that includes two members, DRG1 and DRG2. DRG1 and DRG2 have a C-terminal TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) with a predominantly beta-sheet structure. The function of TGS is unknown but its presence in two types of regulatory proteins (the DRG GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=27.74 E-value=27 Score=27.11 Aligned_cols=24 Identities=4% Similarity=0.119 Sum_probs=20.7
Q ss_pred eeEecCeeeeeeEEEecccccccc
Q 015839 106 RIQVDEEMVPVSYTVKSSQKISHF 129 (399)
Q Consensus 106 ~V~VNGk~v~~~~~v~~gD~I~~~ 129 (399)
.+.++|+.+..++.|+.||+|++.
T Consensus 51 s~~~~gq~Vgl~~~L~d~DvVeI~ 74 (75)
T cd01666 51 SVKHSPQRVGLDHVLEDEDVVQIV 74 (75)
T ss_pred CCcCCCeECCCCCEecCCCEEEEe
Confidence 455799999999999999999863
No 107
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=27.60 E-value=34 Score=37.68 Aligned_cols=28 Identities=14% Similarity=0.439 Sum_probs=23.8
Q ss_pred eeEecCeeeeeeEEEecccccccccccC
Q 015839 106 RIQVDEEMVPVSYTVKSSQKISHFLHRH 133 (399)
Q Consensus 106 ~V~VNGk~v~~~~~v~~gD~I~~~~~~~ 133 (399)
..+|||+.+..++.|+.||.|+|....+
T Consensus 424 gAkVnG~ivpl~~~Lk~Gd~VEIit~k~ 451 (701)
T COG0317 424 GAKVNGRIVPLTTKLQTGDQVEIITSKH 451 (701)
T ss_pred EEEECCEEeccceecCCCCEEEEEeCCC
Confidence 3689999999999999999999765544
No 108
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.55 E-value=7 Score=35.51 Aligned_cols=49 Identities=16% Similarity=0.231 Sum_probs=36.0
Q ss_pred cCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeee-eeeEEEecccccc
Q 015839 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKIS 127 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~ 127 (399)
...+|+..|++++ ++||+.++++|+.|.|..+-... ....+++.|-.|.
T Consensus 137 ~qlrl~~Ll~seL-~LSrS~lq~lie~g~Irgdtd~~~l~rkrlr~~~~i~ 186 (203)
T COG4332 137 FQLRLDRLLASEL-GLSRSELQRLIETGQIRGDTDKMLLLRKRLRAGYDIQ 186 (203)
T ss_pred chhHHHHHHHHHh-CcCHHHHHHHHHcCceeecchHHHHhhhhhhcCcEEE
Confidence 4579999999997 79999999999999999876543 2233344444443
No 109
>PF08068 DKCLD: DKCLD (NUC011) domain; InterPro: IPR012960 This is an N-terminal domain of dyskerin-like proteins, which is often associated with the TruB N-terminal(IPR002501 from INTERPRO) and PUA(IPR002478 from INTERPRO) domains [].; PDB: 3ZV0_D 3UAI_A 3U28_A 2AUS_C 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=26.49 E-value=32 Score=25.53 Aligned_cols=17 Identities=24% Similarity=0.321 Sum_probs=12.0
Q ss_pred cCCCeEEeecCCCcccc
Q 015839 147 KEPDVLTVCKPPSVPVH 163 (399)
Q Consensus 147 Ed~~~ivvnKP~Gl~v~ 163 (399)
-...+|.+|||+|=.+|
T Consensus 40 i~~GvinlDKP~gPtSH 56 (59)
T PF08068_consen 40 IKYGVINLDKPSGPTSH 56 (59)
T ss_dssp HHTEEEEEEE-SSS-HH
T ss_pred HhCCcEEeeCCCCCCcc
Confidence 34678999999997766
No 110
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=25.19 E-value=44 Score=24.66 Aligned_cols=42 Identities=21% Similarity=0.252 Sum_probs=29.0
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeee----eeEEEecccccccc
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVP----VSYTVKSSQKISHF 129 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~----~~~~v~~gD~I~~~ 129 (399)
+.+|.++|... +. .. ..-.|.+||+.+. ..+.|+.||.|.+.
T Consensus 13 ~~tv~~ll~~l-~~-~~-------~~v~v~vN~~iv~~~~~~~~~L~~gD~veii 58 (64)
T TIGR01683 13 GLTLAALLESL-GL-DP-------RRVAVAVNGEIVPRSEWDDTILKEGDRIEIV 58 (64)
T ss_pred CCcHHHHHHHc-CC-CC-------CeEEEEECCEEcCHHHcCceecCCCCEEEEE
Confidence 56788888763 32 22 2225789999984 24689999999864
No 111
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=24.57 E-value=33 Score=37.95 Aligned_cols=26 Identities=23% Similarity=0.305 Sum_probs=22.3
Q ss_pred eeEecCeeeeeeEEEecccccccccc
Q 015839 106 RIQVDEEMVPVSYTVKSSQKISHFLH 131 (399)
Q Consensus 106 ~V~VNGk~v~~~~~v~~gD~I~~~~~ 131 (399)
..+|||+.|.+++.|+.||+|+|...
T Consensus 423 gAkVNg~~vpL~~~L~~Gd~VeIiT~ 448 (702)
T PRK11092 423 GARVDRQPYPLSQPLTSGQTVEIITA 448 (702)
T ss_pred EEEECCEECCCCccCCCCCEEEEEeC
Confidence 35799999999999999999986543
No 112
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=24.31 E-value=52 Score=26.29 Aligned_cols=23 Identities=13% Similarity=0.268 Sum_probs=17.3
Q ss_pred ccCccCcCCCCCCcccccccccC
Q 015839 356 SIDPMCTNCPNLAPKGKRLLSSN 378 (399)
Q Consensus 356 ~~~~~C~~c~~~~~~~~~~~~~~ 378 (399)
...+.|+.|+..+-....++||.
T Consensus 6 k~~~~C~~CG~d~~~~~adDgPA 28 (86)
T PF06170_consen 6 KVAPRCPHCGLDYSHARADDGPA 28 (86)
T ss_pred cCCCcccccCCccccCCcCccch
Confidence 45678999998876666677665
No 113
>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=23.90 E-value=59 Score=22.92 Aligned_cols=44 Identities=23% Similarity=0.307 Sum_probs=27.5
Q ss_pred cCcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeeeeEEEeccccccc
Q 015839 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISH 128 (399)
Q Consensus 78 ~g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~ 128 (399)
.+.++.+++.......++. .+ .+.+||+.++.++.+..||.|.+
T Consensus 15 ~~~t~~~~~~~~~~~~~~~----~v---a~~vng~~vdl~~~l~~~~~ve~ 58 (60)
T cd01668 15 AGATVLDFAYAIHTEIGNR----CV---GAKVNGKLVPLSTVLKDGDIVEI 58 (60)
T ss_pred CCCCHHHHHHHHChHhhhh----eE---EEEECCEECCCCCCCCCCCEEEE
Confidence 4667777665432222221 11 24589999988888988888763
No 114
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=21.74 E-value=54 Score=24.37 Aligned_cols=42 Identities=17% Similarity=0.404 Sum_probs=28.1
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeee----eeEEEecccccccc
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVP----VSYTVKSSQKISHF 129 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~----~~~~v~~gD~I~~~ 129 (399)
+.+|.++|... +.-.+ .+ .|-||++++. ..+.|+.||.|.+.
T Consensus 15 ~~tl~~ll~~l-~~~~~-----~v---aVavN~~iv~r~~w~~~~L~~gD~Ieii 60 (66)
T PRK08053 15 GQTVHELLEQL-NQLQP-----GA---ALAINQQIIPREQWAQHIVQDGDQILLF 60 (66)
T ss_pred CCCHHHHHHHc-CCCCC-----cE---EEEECCEEeChHHcCccccCCCCEEEEE
Confidence 57888888653 32111 12 3778999995 35689999999864
No 115
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=21.56 E-value=46 Score=24.37 Aligned_cols=41 Identities=17% Similarity=0.272 Sum_probs=28.7
Q ss_pred CcchhhhhhhhhcCCccceeeeeEEeeeeEecCeeeee----eEEEecccccccc
Q 015839 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPV----SYTVKSSQKISHF 129 (399)
Q Consensus 79 g~rL~k~L~~~f~~~Sr~~~~~~I~~G~V~VNGk~v~~----~~~v~~gD~I~~~ 129 (399)
+.+|.++|... +.. .. -.|.+||+.+.. .+.|+.||+|.+.
T Consensus 15 ~~tl~~ll~~l-~~~-~~--------~~v~vN~~~v~~~~~~~~~L~~gD~vei~ 59 (65)
T PRK06944 15 GATVADALAAY-GAR-PP--------FAVAVNGDFVARTQHAARALAAGDRLDLV 59 (65)
T ss_pred CCcHHHHHHhh-CCC-CC--------eEEEECCEEcCchhcccccCCCCCEEEEE
Confidence 56788888753 332 11 147899999843 6789999999864
Done!