Query 015203
Match_columns 411
No_of_seqs 418 out of 1964
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 04:05:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015203.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015203hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0564 RluA Pseudouridylate s 100.0 4.2E-57 9.1E-62 441.4 28.5 264 73-343 6-278 (289)
2 TIGR00005 rluA_subfam pseudour 100.0 1.3E-53 2.9E-58 420.1 29.6 263 75-343 1-278 (299)
3 PRK11025 23S rRNA pseudouridyl 100.0 1.4E-53 3E-58 423.1 28.5 264 72-343 12-293 (317)
4 PRK11180 rluD 23S rRNA pseudou 100.0 2.8E-53 6E-58 422.4 30.4 268 67-343 5-292 (325)
5 KOG1919 RNA pseudouridylate sy 100.0 2.8E-53 6.2E-58 422.5 27.3 333 50-393 14-358 (371)
6 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 4.8E-48 1E-52 370.6 21.9 229 106-343 3-235 (246)
7 cd02557 PseudoU_synth_ScRIB2 P 100.0 1.2E-46 2.6E-51 353.7 20.7 195 128-333 2-198 (213)
8 TIGR01621 RluA-like pseudourid 100.0 2.9E-44 6.3E-49 338.4 20.8 185 142-340 2-186 (217)
9 PRK10158 23S rRNA/tRNA pseudou 100.0 8.5E-44 1.8E-48 335.7 20.5 193 142-343 14-208 (219)
10 cd02563 PseudoU_synth_TruC tRN 100.0 8.8E-43 1.9E-47 329.7 22.0 193 143-343 2-213 (223)
11 PRK11112 tRNA pseudouridine sy 100.0 1.3E-42 2.9E-47 335.0 19.9 194 142-343 2-214 (257)
12 PRK10839 16S rRNA pseudouridyl 100.0 4.4E-41 9.6E-46 319.8 16.3 201 80-315 1-202 (232)
13 cd02869 PseudoU_synth_RluCD_li 100.0 9E-39 1.9E-43 292.1 19.9 175 151-332 1-183 (185)
14 PRK10700 23S rRNA pseudouridyl 100.0 4.4E-38 9.5E-43 307.8 20.9 204 80-312 3-209 (289)
15 COG1187 RsuA 16S rRNA uridine- 100.0 3.7E-37 8.1E-42 292.2 18.2 203 79-313 2-210 (248)
16 PRK10475 23S rRNA pseudouridin 100.0 5.6E-37 1.2E-41 299.5 18.6 198 78-312 5-202 (290)
17 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 9.9E-35 2.1E-39 259.5 16.2 148 151-312 1-148 (154)
18 cd02556 PseudoU_synth_RluB Pse 100.0 1.6E-33 3.5E-38 255.1 13.5 141 151-312 2-142 (167)
19 cd02870 PseudoU_synth_RsuA_lik 100.0 6.6E-34 1.4E-38 252.0 9.9 140 151-312 1-140 (146)
20 cd02553 PseudoU_synth_RsuA Pse 100.0 2E-32 4.3E-37 248.0 12.3 144 151-319 2-146 (167)
21 PF00849 PseudoU_synth_2: RNA 100.0 2.5E-31 5.4E-36 238.6 15.6 149 150-305 1-164 (164)
22 cd02566 PseudoU_synth_RluE Pse 100.0 1.9E-30 4.2E-35 235.2 12.2 154 151-316 1-158 (168)
23 PRK11394 23S rRNA pseudouridin 100.0 8.6E-30 1.9E-34 238.5 12.4 148 148-320 38-201 (217)
24 cd02555 PSSA_1 PSSA_1: Pseudou 100.0 4.5E-29 9.7E-34 227.9 11.4 142 149-317 4-154 (177)
25 cd02554 PseudoU_synth_RluF Pse 99.9 5.2E-27 1.1E-31 211.5 12.6 135 151-313 2-136 (164)
26 TIGR00093 pseudouridine syntha 99.9 2.3E-27 4.9E-32 205.8 9.2 111 189-319 1-111 (128)
27 cd02868 PseudoU_synth_hTruB2_l 99.0 3E-10 6.5E-15 107.5 6.9 74 151-230 2-76 (226)
28 cd00165 S4 S4/Hsp/ tRNA synthe 99.0 8.9E-10 1.9E-14 83.2 8.0 69 80-155 1-70 (70)
29 PF01479 S4: S4 domain; Inter 98.7 2.5E-08 5.4E-13 71.4 6.0 47 80-126 1-48 (48)
30 TIGR02988 YaaA_near_RecF S4 do 98.6 1.2E-07 2.7E-12 70.9 5.9 51 78-128 7-58 (59)
31 COG1188 Ribosome-associated he 98.1 3.6E-06 7.7E-11 69.1 5.4 55 77-132 6-61 (100)
32 smart00363 S4 S4 RNA-binding d 98.1 1.2E-05 2.6E-10 58.5 6.7 51 80-130 1-52 (60)
33 cd02572 PseudoU_synth_hDyskeri 97.8 7.4E-05 1.6E-09 68.7 7.3 71 149-231 2-72 (182)
34 PRK10348 ribosome-associated h 97.7 8.6E-05 1.9E-09 64.6 7.0 53 78-130 7-59 (133)
35 PLN00051 RNA-binding S4 domain 97.6 9.1E-05 2E-09 72.1 6.3 54 75-129 187-241 (267)
36 TIGR01017 rpsD_bact ribosomal 97.6 0.00011 2.4E-09 68.6 6.6 51 79-129 89-140 (200)
37 CHL00113 rps4 ribosomal protei 97.6 0.00012 2.5E-09 68.4 6.3 51 79-129 88-139 (201)
38 TIGR03069 PS_II_S4 photosystem 97.6 0.00011 2.3E-09 71.3 6.4 55 74-129 178-233 (257)
39 cd01291 PseudoU_synth PseudoU_ 97.6 0.00027 5.8E-09 56.9 7.5 63 183-307 23-87 (87)
40 PRK00989 truB tRNA pseudouridi 97.5 0.00027 5.8E-09 67.1 6.7 71 149-230 9-79 (230)
41 cd00506 PseudoU_synth_TruB_lik 97.4 0.00036 7.8E-09 65.6 7.0 68 151-230 2-69 (210)
42 PRK04099 truB tRNA pseudouridi 97.4 0.0004 8.7E-09 67.6 7.3 70 149-230 2-71 (273)
43 PRK05327 rpsD 30S ribosomal pr 97.4 0.00038 8.3E-09 65.1 6.3 51 79-129 92-143 (203)
44 PRK00020 truB tRNA pseudouridi 97.3 0.0006 1.3E-08 65.2 7.4 70 149-230 10-79 (244)
45 TIGR00431 TruB tRNA pseudourid 97.3 0.00053 1.1E-08 64.3 6.9 69 150-230 3-71 (209)
46 TIGR00478 tly hemolysin TlyA f 97.3 0.00036 7.9E-09 66.4 5.7 49 81-129 1-50 (228)
47 PRK02484 truB tRNA pseudouridi 97.2 0.00089 1.9E-08 66.0 7.4 69 150-230 4-72 (294)
48 PRK14124 tRNA pseudouridine sy 97.2 0.001 2.2E-08 65.9 7.6 70 149-230 3-72 (308)
49 PRK03287 truB tRNA pseudouridi 97.2 0.001 2.2E-08 65.7 7.3 71 148-230 8-78 (298)
50 PRK00130 truB tRNA pseudouridi 97.2 0.0011 2.4E-08 65.2 7.5 70 149-230 2-71 (290)
51 PRK05389 truB tRNA pseudouridi 97.1 0.0012 2.6E-08 65.4 7.3 70 149-230 13-82 (305)
52 PRK14123 tRNA pseudouridine sy 97.1 0.0012 2.7E-08 65.3 7.3 70 149-230 3-72 (305)
53 PRK02755 truB tRNA pseudouridi 97.1 0.0012 2.7E-08 65.0 7.2 69 149-230 3-71 (295)
54 COG2302 Uncharacterized conser 97.1 0.00072 1.6E-08 64.3 5.3 51 78-129 179-230 (257)
55 PRK02193 truB tRNA pseudouridi 97.1 0.0013 2.8E-08 64.3 7.1 68 151-230 2-69 (279)
56 COG0522 RpsD Ribosomal protein 97.1 0.0012 2.5E-08 61.8 6.5 40 92-131 106-146 (205)
57 PRK01851 truB tRNA pseudouridi 97.1 0.0015 3.3E-08 64.5 7.6 70 149-230 16-85 (303)
58 PRK01550 truB tRNA pseudouridi 97.1 0.0015 3.3E-08 64.6 7.5 70 149-230 2-71 (304)
59 PRK14846 truB tRNA pseudouridi 97.1 0.0015 3.2E-08 65.2 7.4 70 149-230 3-72 (345)
60 PRK05033 truB tRNA pseudouridi 97.1 0.0016 3.4E-08 64.7 7.5 70 149-230 10-79 (312)
61 cd02573 PseudoU_synth_EcTruB P 97.1 0.0015 3.2E-08 64.0 7.2 68 151-230 2-69 (277)
62 PRK04270 H/ACA RNA-protein com 97.0 0.0015 3.3E-08 64.7 7.2 72 147-230 20-91 (300)
63 PRK01528 truB tRNA pseudouridi 97.0 0.0021 4.5E-08 63.3 7.3 70 149-230 3-72 (292)
64 PRK11507 ribosome-associated p 96.9 0.0034 7.3E-08 48.5 6.6 54 76-129 8-62 (70)
65 PRK14122 tRNA pseudouridine sy 96.8 0.003 6.5E-08 62.7 7.1 68 151-230 3-70 (312)
66 COG1189 Predicted rRNA methyla 96.7 0.003 6.4E-08 60.1 6.0 51 79-129 2-53 (245)
67 PRK04642 truB tRNA pseudouridi 96.7 0.0046 1E-07 61.0 7.0 70 149-230 10-79 (300)
68 TIGR00425 CBF5 rRNA pseudourid 96.6 0.004 8.7E-08 62.3 6.6 71 148-230 33-103 (322)
69 COG0130 TruB Pseudouridine syn 96.3 0.0089 1.9E-07 58.3 6.6 69 150-230 16-84 (271)
70 PRK04051 rps4p 30S ribosomal p 96.2 0.013 2.9E-07 53.5 6.8 50 79-128 102-152 (177)
71 cd02867 PseudoU_synth_TruB_4 P 96.2 0.013 2.8E-07 58.3 7.0 42 185-230 57-98 (312)
72 PF13275 S4_2: S4 domain; PDB: 95.9 0.0018 4E-08 49.4 -0.1 51 78-129 6-58 (65)
73 COG2501 S4-like RNA binding pr 95.6 0.042 9.1E-07 42.8 6.2 51 78-129 10-62 (73)
74 PLN00189 40S ribosomal protein 94.5 0.04 8.7E-07 51.0 3.8 40 92-131 121-161 (194)
75 TIGR01018 rpsD_arch ribosomal 94.3 0.1 2.2E-06 47.1 5.8 46 80-125 104-150 (162)
76 PRK04313 30S ribosomal protein 93.3 0.28 6.2E-06 46.8 7.2 73 77-156 35-109 (237)
77 PTZ00155 40S ribosomal protein 93.1 0.13 2.9E-06 47.2 4.6 50 80-129 107-157 (181)
78 PLN00036 40S ribosomal protein 92.3 0.45 9.7E-06 46.1 7.2 73 77-156 39-113 (261)
79 PTZ00223 40S ribosomal protein 92.2 0.46 9.9E-06 46.3 7.1 73 77-156 36-110 (273)
80 PTZ00118 40S ribosomal protein 91.9 0.5 1.1E-05 45.8 7.0 72 77-155 39-112 (262)
81 PF14451 Ub-Mut7C: Mut7-C ubiq 89.8 0.32 6.9E-06 38.8 3.0 43 79-129 32-74 (81)
82 PRK01777 hypothetical protein; 89.3 0.38 8.2E-06 39.6 3.2 52 77-130 24-75 (95)
83 COG1471 RPS4A Ribosomal protei 89.1 0.78 1.7E-05 43.5 5.5 55 95-156 57-112 (241)
84 KOG2559 Predicted pseudouridin 85.1 1 2.2E-05 43.1 3.7 22 185-206 90-111 (318)
85 PRK13354 tyrosyl-tRNA syntheta 81.8 2.1 4.5E-05 44.4 4.9 48 78-125 341-389 (410)
86 PF01509 TruB_N: TruB family p 80.7 2.1 4.6E-05 38.1 3.9 43 184-230 7-49 (149)
87 PRK05912 tyrosyl-tRNA syntheta 78.5 5.2 0.00011 41.5 6.5 44 79-122 342-386 (408)
88 cd00754 MoaD Ubiquitin domain 78.2 4.6 9.9E-05 31.2 4.7 50 79-129 25-74 (80)
89 COG2104 ThiS Sulfur transfer p 73.7 3.6 7.9E-05 31.7 3.0 42 79-129 17-62 (68)
90 PRK08364 sulfur carrier protei 72.2 8.1 0.00018 29.6 4.6 43 78-129 22-64 (70)
91 COG4332 Uncharacterized protei 71.3 5.6 0.00012 36.4 4.0 53 76-129 135-188 (203)
92 PF13453 zf-TFIIB: Transcripti 70.0 0.91 2E-05 31.2 -1.0 13 378-390 24-36 (41)
93 PRK11130 moaD molybdopterin sy 69.9 3.5 7.7E-05 32.5 2.2 44 81-129 30-75 (81)
94 PRK05659 sulfur carrier protei 69.2 5.6 0.00012 29.8 3.1 43 78-129 14-60 (66)
95 PRK06437 hypothetical protein; 68.9 6.6 0.00014 29.9 3.5 43 78-129 19-61 (67)
96 PF06353 DUF1062: Protein of u 67.9 9 0.0002 33.9 4.6 35 76-111 99-133 (142)
97 TIGR01682 moaD molybdopterin c 63.2 13 0.00028 29.0 4.3 24 106-129 51-74 (80)
98 cd00565 ThiS ThiaminS ubiquiti 62.6 8.1 0.00018 29.0 2.9 42 79-129 14-59 (65)
99 PLN02799 Molybdopterin synthas 60.6 22 0.00048 27.7 5.2 24 106-129 53-76 (82)
100 PF02824 TGS: TGS domain; Int 60.0 9.4 0.0002 28.3 2.7 24 106-129 36-59 (60)
101 PF02597 ThiS: ThiS family; I 59.1 10 0.00022 28.9 3.0 50 77-129 19-71 (77)
102 cd01764 Urm1 Urm1-like ubuitin 54.3 25 0.00055 28.7 4.6 24 106-129 61-88 (94)
103 TIGR01687 moaD_arch MoaD famil 53.7 12 0.00026 29.6 2.6 24 106-129 57-82 (88)
104 PRK06488 sulfur carrier protei 50.5 18 0.00039 27.0 3.0 42 79-129 14-59 (65)
105 PRK07440 hypothetical protein; 45.9 29 0.00063 26.6 3.5 43 78-129 18-64 (70)
106 COG4043 Preprotein translocase 42.1 25 0.00055 29.2 2.8 35 95-129 8-43 (111)
107 COG3531 Predicted protein-disu 41.9 8.6 0.00019 35.8 0.0 17 355-371 6-22 (212)
108 COG0162 TyrS Tyrosyl-tRNA synt 40.7 33 0.00073 35.5 4.1 39 82-120 338-377 (401)
109 PF00498 FHA: FHA domain; Int 38.7 35 0.00076 25.2 3.0 25 104-128 41-67 (68)
110 TIGR01683 thiS thiamine biosyn 38.5 42 0.00092 24.9 3.4 42 79-129 13-58 (64)
111 KOG2529 Pseudouridine synthase 38.3 31 0.00066 35.5 3.3 77 147-235 66-142 (395)
112 PRK07696 sulfur carrier protei 38.2 33 0.00073 26.0 2.8 41 80-129 17-61 (67)
113 PRK06944 sulfur carrier protei 35.8 43 0.00094 24.7 3.1 42 78-129 14-59 (65)
114 PRK08053 sulfur carrier protei 34.6 52 0.0011 24.7 3.3 42 79-129 15-60 (66)
115 KOG3301 Ribosomal protein S4 [ 34.4 48 0.001 30.0 3.5 30 93-122 110-140 (183)
116 COG0317 SpoT Guanosine polypho 32.7 41 0.00089 37.3 3.4 28 106-133 424-451 (701)
117 cd01666 TGS_DRG_C TGS_DRG_C: 32.7 38 0.00083 26.5 2.4 47 79-129 24-74 (75)
118 TIGR00234 tyrS tyrosyl-tRNA sy 32.2 90 0.002 32.0 5.6 37 79-115 329-365 (377)
119 PRK11092 bifunctional (p)ppGpp 31.2 44 0.00095 37.3 3.3 27 106-132 423-449 (702)
120 cd01616 TGS The TGS domain, na 31.0 58 0.0013 22.4 3.0 22 107-128 37-58 (60)
121 cd01668 TGS_RelA_SpoT TGS_RelA 30.5 59 0.0013 23.1 3.0 44 78-128 15-58 (60)
122 PF03658 Ub-RnfH: RnfH family 30.4 22 0.00048 28.5 0.7 51 78-130 22-72 (84)
123 KOG0921 Dosage compensation co 24.3 1.1E+02 0.0023 35.3 4.6 31 7-37 1173-1203(1282)
124 PF14453 ThiS-like: ThiS-like 22.3 87 0.0019 23.3 2.5 22 107-128 32-53 (57)
125 PRK06083 sulfur carrier protei 22.3 96 0.0021 24.8 3.0 42 78-129 32-78 (84)
126 PF14478 DUF4430: Domain of un 22.1 87 0.0019 23.6 2.6 22 107-128 43-67 (68)
127 KOG2623 Tyrosyl-tRNA synthetas 21.9 1.4E+02 0.003 31.0 4.6 38 78-115 397-434 (467)
128 PF08068 DKCLD: DKCLD (NUC011) 21.8 41 0.00089 25.2 0.7 18 146-163 39-56 (59)
129 PRK00364 groES co-chaperonin G 20.5 1.6E+02 0.0035 24.0 4.0 29 119-155 58-86 (95)
130 TIGR00691 spoT_relA (p)ppGpp s 20.5 85 0.0018 34.9 3.1 25 107-131 398-422 (683)
131 PRK10872 relA (p)ppGpp synthet 20.3 97 0.0021 34.8 3.5 27 107-133 442-468 (743)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.2e-57 Score=441.42 Aligned_cols=264 Identities=30% Similarity=0.388 Sum_probs=222.8
Q ss_pred ecCCCcCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecCCceecCCCEEEEeeecCCC--CCcCC--CceEeeeC
Q 015203 73 VKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHRHEP--PVMAW--DVSILQKE 148 (411)
Q Consensus 73 v~~~~~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~~~~~e~--~~~~~--~~~IlyEd 148 (411)
+...+.|+||++||++.++ +||+.+.++|++|.|+|||+++..+++|+.||.|.+....... ...+. .+.|||||
T Consensus 6 v~~~~~g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vNg~~v~~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED 84 (289)
T COG0564 6 VPEEEAGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVKPSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILYED 84 (289)
T ss_pred eChhhcCCCHHHHHHHccC-cCHHHHHHHHHCCCEEECCEEccCCeeeCCCCEEEEecccccccccccccCCCccEEEec
Confidence 4457789999999999555 9999999999999999999999999999999999988755322 12222 36799999
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccC--CCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHD--LAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYI 226 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~--~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~Yl 226 (411)
+++||||||+||+|||++.+...|++..+..... ...+++||||||+||||||||||..++..|+++|+++.+.|+|+
T Consensus 85 ~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~ 164 (289)
T COG0564 85 EDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDGVERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKKTYL 164 (289)
T ss_pred CCEEEEECCCCCcCcCCCCCccHhHHHHHHHhccccCCceeeeccCCCCCceEEEEECCHHHHHHHHHHHhcCcCcEEEE
Confidence 9999999999999999988888899988776432 35689999999999999999999999999999999999999999
Q ss_pred EEEecccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCC-eEEEEEEeccCcccHHHHHHhh
Q 015203 227 ARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGT-HSIVLCEPITGRTHQIRVHLQY 305 (411)
Q Consensus 227 A~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~-~slv~~~l~TGRtHQIRvhla~ 305 (411)
|+|.|.++.+.++|+.||.++............ .+|+.|+|+|++++..+. .|+|+|+|+||||||||+||++
T Consensus 165 Alv~G~~~~~~~~i~~pi~r~~~~~~~~~v~~~------~~gk~A~T~~~~l~~~~~~~tlv~~~~~TGRTHQIRVHl~~ 238 (289)
T COG0564 165 ALVRGHLPEDEGTIDAPIGRDPKNRKKMAVVKE------GSGKPAITHYEVLERFGDNYTLVELKPETGRTHQIRVHLAH 238 (289)
T ss_pred EEEECcccCCCCEEeeeeecCCcCCceEEEecc------CCCCceEEEEEehhccCCceEEEEEEeCCCCHhHHHHHHHH
Confidence 999999999989999999987665544433321 238999999999999887 5999999999999999999999
Q ss_pred cCCCeeecCCCCccc--cCCccCccccceeeeeecCCCCC
Q 015203 306 TGYPIANDMLYLCEH--VTHREGMSADRAAAYSHHSPPPV 343 (411)
Q Consensus 306 lG~PIvGD~~Yg~~~--~~~~~~~~a~~~~~~~~~lp~~~ 343 (411)
|||||+||++||... ........+++++.+.|.+|...
T Consensus 239 lghPI~GD~~Yg~~~~~~~~~~~r~~LHA~~l~f~hp~t~ 278 (289)
T COG0564 239 LGHPIVGDPLYGGKDKSAGAGLKRQALHAYKLSFTHPLTG 278 (289)
T ss_pred CCCCeeCCcccCCchhhcccCcchhhhhhceeEccCCCCC
Confidence 999999999999852 11113344555667888888764
No 2
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=100.00 E-value=1.3e-53 Score=420.05 Aligned_cols=263 Identities=30% Similarity=0.401 Sum_probs=216.8
Q ss_pred CCCcCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEeeec-CCC--CCcCCCceEeeeCCc
Q 015203 75 NRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHR-HEP--PVMAWDVSILQKEPD 150 (411)
Q Consensus 75 ~~~~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~-~e~--~~~~~~~~IlyEd~~ 150 (411)
++|.|+||++||+..|+.+||+.++++|++|.|+|||+.+ .+++.|+.||.|.+.... .++ +.....+.|+|||++
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 899999999999986543 121 112224679999999
Q ss_pred EEEEeCCCCceeecCCCCCCchHHHHHhhccCC----CCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEE
Q 015203 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDL----APLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYI 226 (411)
Q Consensus 151 ~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~----~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~Yl 226 (411)
|+|||||+|++||+++....+|++++|...... ..+++|||||++||||||||+|+++++.|+++|+++.|.|+|+
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 999999999999999887778999998764321 4589999999999999999999999999999999999999999
Q ss_pred EEEecccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCCeEEEEEEeccCcccHHHHHHhhc
Q 015203 227 ARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYT 306 (411)
Q Consensus 227 A~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slv~~~l~TGRtHQIRvhla~l 306 (411)
|+|.|.++.+.+.|+.+|..+........ +.. ..+++.|.|+|+++....+.|+|+|+|+|||+||||+||+++
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 99999999888899999976543222111 111 135899999999998877899999999999999999999999
Q ss_pred CCCeeecCCCCccccC-------CccCccccceeeeeecCCCCC
Q 015203 307 GYPIANDMLYLCEHVT-------HREGMSADRAAAYSHHSPPPV 343 (411)
Q Consensus 307 G~PIvGD~~Yg~~~~~-------~~~~~~a~~~~~~~~~lp~~~ 343 (411)
||||+||.+||+...+ ......+++++.+.|.+|...
T Consensus 235 G~pI~gD~~Yg~~~~~~~~~~~~~~~~r~~Lha~~l~f~~p~~~ 278 (299)
T TIGR00005 235 GHPLAGDPLYGNKPVPGNNLNGLLNFDRQALHAYELGFIHPATG 278 (299)
T ss_pred CCcEeCccccCCccccccccccccCCcchhhccCeeeccCCCCC
Confidence 9999999999975431 112235566667888888663
No 3
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=1.4e-53 Score=423.12 Aligned_cols=264 Identities=27% Similarity=0.348 Sum_probs=214.1
Q ss_pred eecCCCcCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecCCceecCCCEEEEeeec----CCCCCc-------CC
Q 015203 72 HVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHR----HEPPVM-------AW 140 (411)
Q Consensus 72 ~v~~~~~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~~~~----~e~~~~-------~~ 140 (411)
.+...++|+||++||+..++..||+.++++|++|.|+|||+++.++++|+.||.|.+.... .++|.. ..
T Consensus 12 ~v~~~~~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v~~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~~ 91 (317)
T PRK11025 12 TISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKVAAL 91 (317)
T ss_pred EECcccCCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEcCcccccCCCCEEEeCCCCccccccccccccccccccC
Confidence 3667788999999999988889999999999999999999999999999999999875321 111221 12
Q ss_pred CceEeeeCCcEEEEeCCCCceeecCCCCCCchHHHHHhhcc-CCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcC
Q 015203 141 DVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEH-DLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAG 219 (411)
Q Consensus 141 ~~~IlyEd~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~-~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~ 219 (411)
.+.|+|||++|+|||||+|++||+++... .++.+.+.... ....+++|||||++||||||||+|..+++.|+++|.++
T Consensus 92 ~~~Ilyed~~~lvvnKP~gl~~~~~~~~~-~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~ 170 (317)
T PRK11025 92 ADVILYEDDHILVLNKPSGTAVHGGSGLS-FGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREK 170 (317)
T ss_pred cCCEEEECCCEEEEECCCCCcCcCCCCCC-ccHHHHHHHhccCCCcCceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhC
Confidence 46899999999999999999999976654 34555554322 22346789999999999999999999999999999999
Q ss_pred eecEEEEEEEecccCCCCceEeeeeecccCCC-cceeeeCCCCCCCCCCCceeeeEEEEeeeCCCeEEEEEEeccCcccH
Q 015203 220 KVIKRYIARVNGVFPEGEQVVDVNINYNASAG-RSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQ 298 (411)
Q Consensus 220 ~v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~-~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slv~~~l~TGRtHQ 298 (411)
.|.|+|+|+|.|.++...+.|+.+|..+.... ...+.+ ..+|+.|.|+|++++..++.|||+|+|+||||||
T Consensus 171 ~v~K~Y~a~v~G~~~~~~~~i~~~i~~~~~~~~~~~~~~-------~~~gk~a~T~~~~l~~~~~~sLv~~~~~TGRtHQ 243 (317)
T PRK11025 171 GMQKDYLALVRGQWQSHVKVVQAPLLKNILQSGERIVRV-------SQEGKPSETRFKVEERYAFATLVRASPVTGRTHQ 243 (317)
T ss_pred CccEEEEEEEeCcccCCCceEecccccCcccCCceEEec-------CCCCccceEEEEEeEEcCCcEEEEEEeCCCCHHH
Confidence 99999999999999888889999997654322 212111 2478999999999998888999999999999999
Q ss_pred HHHHHhhcCCCeeecCCCCccccCC-----ccCccccceeeeeecCCCCC
Q 015203 299 IRVHLQYTGYPIANDMLYLCEHVTH-----REGMSADRAAAYSHHSPPPV 343 (411)
Q Consensus 299 IRvhla~lG~PIvGD~~Yg~~~~~~-----~~~~~a~~~~~~~~~lp~~~ 343 (411)
||+||+++||||+||.+||...... .....+++++.+.|.+|...
T Consensus 244 IRvhla~lG~PIlGD~~Yg~~~~~~~~~~~~~~r~~LHa~~l~f~~P~~~ 293 (317)
T PRK11025 244 IRVHTQYAGHPIAFDDRYGDREFDQQLTGTGLNRLFLHAAALKFTHPGTG 293 (317)
T ss_pred HHHHHHHCCCCEECCcccCCcccchhhhccCCcchhhhcCcceeeCCCCC
Confidence 9999999999999999999643211 12234666777889888764
No 4
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=2.8e-53 Score=422.39 Aligned_cols=268 Identities=21% Similarity=0.243 Sum_probs=220.2
Q ss_pred eEEEeeecCCCcCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEeeecCCCC---CcCCCc
Q 015203 67 FEFISHVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPP---VMAWDV 142 (411)
Q Consensus 67 ~~~~~~v~~~~~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~~---~~~~~~ 142 (411)
..+...++.+|.|+||+++|++.|+.+||+.++++|++|.|+|||+++ .+++.|+.||.|.+.....++. ....++
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 356667889999999999999998889999999999999999999998 6899999999999876433221 112357
Q ss_pred eEeeeCCcEEEEeCCCCceeecCCCCCCchHHHHHhhccC----CCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhc
Q 015203 143 SILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHD----LAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEA 218 (411)
Q Consensus 143 ~IlyEd~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~----~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~ 218 (411)
.|+|||++|||||||+||+|||++.....|+.+.+..... ...+++|||||++||||||||+|..++..|+++|.+
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 8999999999999999999999887767788887765321 234679999999999999999999999999999999
Q ss_pred CeecEEEEEEEecccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCCeEEEEEEeccCcccH
Q 015203 219 GKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQ 298 (411)
Q Consensus 219 ~~v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slv~~~l~TGRtHQ 298 (411)
+.|.|+|+|+|.|.++. ++.|+.+|....... ..+.+ ...++.|.|+|+++....+.|+|+|+|+||||||
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 578899887543221 11111 1468999999999988888999999999999999
Q ss_pred HHHHHhhcCCCeeecCCCCccccCC------------ccCccccceeeeeecCCCCC
Q 015203 299 IRVHLQYTGYPIANDMLYLCEHVTH------------REGMSADRAAAYSHHSPPPV 343 (411)
Q Consensus 299 IRvhla~lG~PIvGD~~Yg~~~~~~------------~~~~~a~~~~~~~~~lp~~~ 343 (411)
||+||+++||||+||.+||+..... .....+++++.+.|.+|...
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 9999999999999999999653210 01234566777888888664
No 5
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=100.00 E-value=2.8e-53 Score=422.50 Aligned_cols=333 Identities=38% Similarity=0.571 Sum_probs=270.6
Q ss_pred CCCeeeeCCeeeccceeeEEEeeecCCCcCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecCCceecCCCEEEEe
Q 015203 50 KEDYIFRDGRRNVKPYYFEFISHVKNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHF 129 (411)
Q Consensus 50 ~~~y~~~~~~r~v~P~~~~~~~~v~~~~~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~ 129 (411)
..+|.++++.|++.||+|+|.++++.+|.++.+.++|+.+|...++.+++..|+.|.|++||+.+...+.++.+|.|.+.
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 35678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecCCCCCcCCCceEeeeCCcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHH
Q 015203 130 LHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKA 209 (411)
Q Consensus 130 ~~~~e~~~~~~~~~IlyEd~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a 209 (411)
+|+++|++....+.|+|||++|+|||||+|++|||++.+..+++..++........+++|||||+.|||||+||++.+.+
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 99999999988899999999999999999999999999999999999988655567899999999999999999999999
Q ss_pred HHHHHhhhcCeecEEE-EEEEecccC-CCCceEeeeeecccC-CCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCCeEE
Q 015203 210 DLFRQQIEAGKVIKRY-IARVNGVFP-EGEQVVDVNINYNAS-AGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSI 286 (411)
Q Consensus 210 ~~L~~~~~~~~v~K~Y-lA~V~G~~~-~~~~~i~~~i~~~~~-~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~sl 286 (411)
..+.++|+++.+.|.| +|.|.|.++ ....+|..++..... .+..+..+. ..+...++.|+|.|++++.++..|+
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 566677777764432 111111111 1111358999999999999999999
Q ss_pred EEEEeccCcccHHHHHHhhcCCCeeecCCCCccccCCc-----cCccccce-eeeeec---CCCCCCCCCCCCCCccccc
Q 015203 287 VLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTHR-----EGMSADRA-AAYSHH---SPPPVSSDKSESSSEDFSI 357 (411)
Q Consensus 287 v~~~l~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~~~~-----~~~~a~~~-~~~~~~---lp~~~~~~~~~~~~~~~~~ 357 (411)
|+|.|+||||||||+||+++|+||+||.+|++...++. ....+... ....+. -....+.|..........+
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 99999999999999999999999999999987666652 11111100 000010 1111122332334444778
Q ss_pred CCCCCCCCCCCCCccchhhhhccceeeeeeccCCCc
Q 015203 358 DPMCTNCPNLAPKDTKDMKRACGYIVFDTLDLDGHM 393 (411)
Q Consensus 358 ~~~c~~c~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ 393 (411)
+++|.+|..-.+ .=..+||||+...+..
T Consensus 331 ~~~~~~C~~~~~--------~Dl~~~lha~~y~~~~ 358 (371)
T KOG1919|consen 331 EELCQECKVPID--------NDLELFLHALKYEMKG 358 (371)
T ss_pred hhhhhhCCCCCC--------chHhHhhhhcccccCC
Confidence 899999997622 1234799999876653
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=4.8e-48 Score=370.64 Aligned_cols=229 Identities=23% Similarity=0.291 Sum_probs=181.5
Q ss_pred cEEECCEEecCCceecCCCEEEEeeecCCCCCcCCCceEeeeCCcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCC
Q 015203 106 RIQVDEEMVPVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAP 185 (411)
Q Consensus 106 ~V~VNGk~v~~~~~v~~gD~I~~~~~~~e~~~~~~~~~IlyEd~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~ 185 (411)
.|..||+++..+++|+.||.|.+.....+.+..+.++.|||||++|+|||||+|++||+++....+|++..+........
T Consensus 3 ~~~~ng~~~~~~~~l~~gd~i~~~~~~~~~~~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~~~~~ 82 (246)
T cd02558 3 VVDADGEPLDPDSPYRPGTFVWYYRELPDEPPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTGNPD 82 (246)
T ss_pred eECCCCcCCCCCceecCCCEEEEeCCCCCCCCCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHhCCCc
Confidence 45689999999999999999988643222222234578999999999999999999999988888899988876544456
Q ss_pred cccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEecccCCCCc-eEeeeeecccCCCcceeeeCCCCCCC
Q 015203 186 LFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQ-VVDVNINYNASAGRSTAESGDSLGDT 264 (411)
Q Consensus 186 l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~G~~~~~~~-~i~~~i~~~~~~~~~~~~~~~~~~~~ 264 (411)
+++|||||++||||||||||.++++.|+.+|+++.++|+|+|+|.|.++.+.. .++.+|...... .....
T Consensus 83 ~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~YlA~v~G~~~~~~~~~~~~~i~~~~~~--~~~~~------- 153 (246)
T cd02558 83 LTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYEAVAPYVPALTFPLTVRSRIVKGRGF--FQARE------- 153 (246)
T ss_pred ccccccCCCCceeEEEEEcCHHHHHHHHHHHHcCCccEEEEEEEecCCCCCCCcceeccccccCCc--ceeec-------
Confidence 88999999999999999999999999999999999999999999998874433 456555443211 11111
Q ss_pred CCCCceeeeEEEEeeeCCCeEEEEEEeccCcccHHHHHHhhcCCCeeecCCCCccccC---CccCccccceeeeeecCCC
Q 015203 265 PLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVT---HREGMSADRAAAYSHHSPP 341 (411)
Q Consensus 265 ~~~gk~a~t~~~~l~~~~~~slv~~~l~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~~---~~~~~~a~~~~~~~~~lp~ 341 (411)
.++++.|.|+|++++...+.|+|+|+|+|||+||||+||+++||||+||.+||..... ......+++++.+.|.+|.
T Consensus 154 ~~~~~~a~T~~~~l~~~~~~slv~~~l~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~Lha~~l~f~hP~ 233 (246)
T cd02558 154 VEGEPNAETRIELLARRGGWGLYRLSPHTGKTHQLRVHMAALGVPILNDPFYPVLLDKDPDDFSRPLQLLAKELEFTDPL 233 (246)
T ss_pred cCCCCCceEEEEEEEecCCeEEEEEEeCCCCHHHHHHHHHHCCCcccCCccCCCCCcccccccccCchhhhcccCccCCC
Confidence 1345789999999988778999999999999999999999999999999999964211 1111235667778888886
Q ss_pred CC
Q 015203 342 PV 343 (411)
Q Consensus 342 ~~ 343 (411)
..
T Consensus 234 t~ 235 (246)
T cd02558 234 TG 235 (246)
T ss_pred CC
Confidence 64
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=1.2e-46 Score=353.73 Aligned_cols=195 Identities=50% Similarity=0.770 Sum_probs=167.2
Q ss_pred EeeecCCCCCcCCCceEeeeCCcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChH
Q 015203 128 HFLHRHEPPVMAWDVSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNAS 207 (411)
Q Consensus 128 ~~~~~~e~~~~~~~~~IlyEd~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~ 207 (411)
+..+++|+|+....++|+|||++|+|||||+|++|++++.....|+.++|........+++|||||++||||||||+|++
T Consensus 2 ~~~~~~~~~~~~~~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~~~~~~~vhRLD~~TSGllllak~~~ 81 (213)
T cd02557 2 HTVHRHEPPVTNDPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGLTELRPCHRLDRLTSGLLLFAKTSQ 81 (213)
T ss_pred ccccccCCCCCCCCCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcCCCCccCccCCCCCCceEEEEECCHH
Confidence 34678899998888999999999999999999999998877778999999875543468899999999999999999999
Q ss_pred HHHHHHHhhhcCeecEEEEEEEecccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCC--CeE
Q 015203 208 KADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNG--THS 285 (411)
Q Consensus 208 ~a~~L~~~~~~~~v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~--~~s 285 (411)
++++|+++|.++.++|+|+|+|.|.++.+.+.++.+|............ ....++.|.|+|+++...+ +.|
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 9999999999999999999999999998888999998765332211110 1246789999999998766 789
Q ss_pred EEEEEeccCcccHHHHHHhhcCCCeeecCCCCccccCCccCcccccee
Q 015203 286 IVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTHREGMSADRAA 333 (411)
Q Consensus 286 lv~~~l~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~a~~~~ 333 (411)
+|+|+|+|||+||||+||+++||||+||.+||. .++.|||.+..
T Consensus 155 lv~v~~~TGR~HQIR~hla~lG~PIlGD~~Yg~----~~l~Lha~~l~ 198 (213)
T cd02557 155 VVLCKPITGRTHQIRVHLQYLGHPIVNDPIYNN----LGIYLHALRYE 198 (213)
T ss_pred EEEEEeCCCCHHHHHHHHHHCCCCCcCccccCC----cChhhhhccCc
Confidence 999999999999999999999999999999997 45677776433
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=2.9e-44 Score=338.36 Aligned_cols=185 Identities=26% Similarity=0.362 Sum_probs=153.1
Q ss_pred ceEeeeCCcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCee
Q 015203 142 VSILQKEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKV 221 (411)
Q Consensus 142 ~~IlyEd~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v 221 (411)
++|||||++|+|||||+|++||++.. ..++.+.+........+++|||||++||||||||+|.++++.|+++|+++.|
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 46999999999999999999998754 3567777765433356899999999999999999999999999999999999
Q ss_pred cEEEEEEEecccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCCeEEEEEEeccCcccHHHH
Q 015203 222 IKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRV 301 (411)
Q Consensus 222 ~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slv~~~l~TGRtHQIRv 301 (411)
.|+|+|+|.|.++.+++.|+.++..... +... +. ...++.|.|+|+++....+.|+|+|+|+||||||||+
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 9999999999999888889888864432 2221 11 1367899999999988888999999999999999999
Q ss_pred HHhhcCCCeeecCCCCccccCCccCccccceeeeeecCC
Q 015203 302 HLQYTGYPIANDMLYLCEHVTHREGMSADRAAAYSHHSP 340 (411)
Q Consensus 302 hla~lG~PIvGD~~Yg~~~~~~~~~~~a~~~~~~~~~lp 340 (411)
||+++||||+||.+||......+..|| +..+.|.++
T Consensus 151 hla~lG~PIlGD~~Yg~~~~~~~~~Lh---a~~l~f~~~ 186 (217)
T TIGR01621 151 AMKSLGSPILGDPLYGTTDESDRGYLH---AFALRFDYQ 186 (217)
T ss_pred HHHHCCCceeCCcccCCCCCccCceee---eeEeEEEEC
Confidence 999999999999999975434445444 445556553
No 9
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=100.00 E-value=8.5e-44 Score=335.69 Aligned_cols=193 Identities=25% Similarity=0.336 Sum_probs=157.5
Q ss_pred ceEeeeCCcEEEEeCCCCceeecCCC-CCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCe
Q 015203 142 VSILQKEPDVLTVCKPPSVPVHPCGQ-YRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGK 220 (411)
Q Consensus 142 ~~IlyEd~~~ivvnKP~Gl~v~~~~~-~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~ 220 (411)
+.|||||++|+|||||+|++||+... ....++.+.+.... ..+++|||||++||||||||+|.+++..|+++|.++.
T Consensus 14 ~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~--~~~~~vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~~ 91 (219)
T PRK10158 14 LVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY--PQAESVHRLDMATSGVIVVALTKAAERELKRQFRERE 91 (219)
T ss_pred CCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC--CCCCEECCCCCCCceEEEEECCHHHHHHHHHHHHhCC
Confidence 67999999999999999999998653 34567888876543 3578999999999999999999999999999999999
Q ss_pred ecEEEEEEEecccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCC-eEEEEEEeccCcccHH
Q 015203 221 VIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGT-HSIVLCEPITGRTHQI 299 (411)
Q Consensus 221 v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~-~slv~~~l~TGRtHQI 299 (411)
|.|+|+|+|.|.++.++++++.+|..+....... .+. .++++.|.|+|++++.... .++|+|+|+|||||||
T Consensus 92 v~K~Yla~v~G~~~~~~~~i~~~i~~~~~~~~~~-~~~------~~~gk~a~t~~~~l~~~~~~~sll~~~~~TGRtHQI 164 (219)
T PRK10158 92 PKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQ-KVC------YETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQL 164 (219)
T ss_pred ccEEEEEEEecccCCCCcEEecceecCCCCCceE-Eec------CCCCceeeEEEEEEEEcCCCCEEEEEEeCCCCHHHH
Confidence 9999999999999988899999987654322211 111 1468999999999987654 4899999999999999
Q ss_pred HHHHhhcCCCeeecCCCCccccCCccCccccceeeeeecCCCCC
Q 015203 300 RVHLQYTGYPIANDMLYLCEHVTHREGMSADRAAAYSHHSPPPV 343 (411)
Q Consensus 300 Rvhla~lG~PIvGD~~Yg~~~~~~~~~~~a~~~~~~~~~lp~~~ 343 (411)
|+||+++||||+||.+||...........++++..+.|.+|...
T Consensus 165 R~hla~lG~PIvGD~~Yg~~~~~~~~~r~~Lha~~l~f~~P~~~ 208 (219)
T PRK10158 165 RVHMLALGHPILGDRFYASPEARAMAPRLLLHAEMLTITHPAYG 208 (219)
T ss_pred HHHHHHCCCcEECCcccCCccccccccchhhhhCccCccCCCCC
Confidence 99999999999999999975432112234555666788888654
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=8.8e-43 Score=329.68 Aligned_cols=193 Identities=26% Similarity=0.323 Sum_probs=151.6
Q ss_pred eEeeeCCcEEEEeCCCCceeecCCCCCC--chHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCe
Q 015203 143 SILQKEPDVLTVCKPPSVPVHPCGQYRK--NTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGK 220 (411)
Q Consensus 143 ~IlyEd~~~ivvnKP~Gl~v~~~~~~~~--~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~ 220 (411)
+|||||++|+|||||+|++||+++.... .+++..+..... ..+++|||||++||||||||+|.++++.|+++|+++.
T Consensus 2 ~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~ 80 (223)
T cd02563 2 EILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLG-QHVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTEHR 80 (223)
T ss_pred cEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHcC-CCcccccCCCCCCeEEEEEEECHHHHHHHHHHHhcCc
Confidence 6999999999999999999998764333 234445544332 4588999999999999999999999999999999999
Q ss_pred ecEEEEEEEecccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeC-----------CCeEEEEE
Q 015203 221 VIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTN-----------GTHSIVLC 289 (411)
Q Consensus 221 v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~-----------~~~slv~~ 289 (411)
|.|+|+|+|.|.++. ++.|+.++..+.......... ....++.|.|.|++++.. ...|+|+|
T Consensus 81 v~K~Y~alv~G~~~~-~~~i~~~l~~~~~~~~~~~~~------~~~~~~~a~t~~~~l~~~~~~~~~~~~~~~~~slv~~ 153 (223)
T cd02563 81 VHKTYLAVVRGYVPE-SGTIDYPLSEELDKLADKFAS------DDKAPQAATTHYRLLAVEELPVVVGKYPTSRYSLVEL 153 (223)
T ss_pred eeEEEEEEEECccCC-CCeEEEeeeeCCCccceEEee------cCCCCceeEEEEEEeeecccccccccCCCCCeEEEEE
Confidence 999999999999876 678999987654432222111 124678999999999742 24899999
Q ss_pred EeccCcccHHHHHHhhcCCCeeecCCCCccccCC------ccCccccceeeeeecCCCCC
Q 015203 290 EPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTH------REGMSADRAAAYSHHSPPPV 343 (411)
Q Consensus 290 ~l~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~~~------~~~~~a~~~~~~~~~lp~~~ 343 (411)
+|+||||||||+||+++||||+||.+||...... .....++++..+.|.+|...
T Consensus 154 ~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~rl~Lha~~L~F~hP~t~ 213 (223)
T cd02563 154 TPHTGRKHQLRRHLAHIRHPIIGDTTHGDGRHNRFFREHFGCHRLLLAATRLEFTHPVTG 213 (223)
T ss_pred EeCCCCHHHHHHHHHHcCCCeeCCcccCCcccChhHHhhcCCccceeecCeeEeeCCCCC
Confidence 9999999999999999999999999999653211 11234555667788888664
No 11
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=100.00 E-value=1.3e-42 Score=334.99 Aligned_cols=194 Identities=27% Similarity=0.287 Sum_probs=151.0
Q ss_pred ceEeeeCCcEEEEeCCCCceeecCCCCCCc--hHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcC
Q 015203 142 VSILQKEPDVLTVCKPPSVPVHPCGQYRKN--TVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAG 219 (411)
Q Consensus 142 ~~IlyEd~~~ivvnKP~Gl~v~~~~~~~~~--tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~ 219 (411)
++|||||++|||||||+|++||++.....+ ++...+..... ..+++|||||++||||||||+|.++++.|+++|+++
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 469999999999999999999987533333 34455544332 357899999999999999999999999999999999
Q ss_pred eecEEEEEEEecccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeC-----------CCeEEEE
Q 015203 220 KVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTN-----------GTHSIVL 288 (411)
Q Consensus 220 ~v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~-----------~~~slv~ 288 (411)
.|.|+|+|+|.|.++. ++.++.++............. ...+++.|.|.|++++.. .+.|+|+
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 577888887543221111100 124689999999999752 3479999
Q ss_pred EEeccCcccHHHHHHhhcCCCeeecCCCCccccCC------ccCccccceeeeeecCCCCC
Q 015203 289 CEPITGRTHQIRVHLQYTGYPIANDMLYLCEHVTH------REGMSADRAAAYSHHSPPPV 343 (411)
Q Consensus 289 ~~l~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~~~------~~~~~a~~~~~~~~~lp~~~ 343 (411)
|+|.||||||||+||+++||||+||.+||...... .....+++++.+.|.+|...
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 01234566677888888664
No 12
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=100.00 E-value=4.4e-41 Score=319.83 Aligned_cols=201 Identities=15% Similarity=0.176 Sum_probs=161.0
Q ss_pred chHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEeeecCCCCCcCCCceEeeeCCcEEEEeCCC
Q 015203 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKPP 158 (411)
Q Consensus 80 ~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~~~~~~~~~IlyEd~~~ivvnKP~ 158 (411)
+||++||++.+ .+||+.++++|++|.|+|||+++ .++++|+.||.|.+.....+ ..++++++|+|||+
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 48999999986 79999999999999999999999 48999999999987632111 12456899999999
Q ss_pred CceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEecccCCCCc
Q 015203 159 SVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQ 238 (411)
Q Consensus 159 Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~G~~~~~~~ 238 (411)
||+||+++... .|+.+++.... ...+++|||||++||||||||||+.+++.|.. +++.+.|+|+|++++.+..+..
T Consensus 70 G~~~~~~~~~~-~tl~~~l~~~~-~~~~~~v~RLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~i~~~i~~~~~ 145 (232)
T PRK10839 70 GYVCSTDDPDH-PTVLYFLDEPV-AYKLHAAGRLDIDTTGLVLMTDDGQWSHRITS--PRHHCEKTYLVTLESPVADDTA 145 (232)
T ss_pred CeEecccCCCC-CeEEEeccccc-ccCceecCCCCCCceeEEEEecCHHHHHHHhC--CCCCCCeEEEEEECCCCCHHHH
Confidence 99999885543 67776664322 23578999999999999999999999999994 7889999999998887754321
Q ss_pred eEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCCeEEEEEEeccCcccHHHHHHhhcCCCeeecCC
Q 015203 239 VVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDML 315 (411)
Q Consensus 239 ~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slv~~~l~TGRtHQIRvhla~lG~PIvGD~~ 315 (411)
.....+. ..+|+.|.|+|.+++... .|+|+|+|+||||||||+||+++||||+|=..
T Consensus 146 -------~~~~~~~------------~~~g~~a~t~~~~~~~~~-~sll~~~l~tGRtHQIR~h~~~~G~pi~gl~R 202 (232)
T PRK10839 146 -------EQFAKGV------------QLHNEKDLTKPAVLEVIT-PTQVRLTISEGRYHQVKRMFAAVGNHVVELHR 202 (232)
T ss_pred -------HHHHCCe------------EECCCcccccccEEEEec-CCEEEEEEEcCcCHHHHHHHHHcCCeEeeEEE
Confidence 0001111 125778899999998755 48999999999999999999999999998544
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=9e-39 Score=292.14 Aligned_cols=175 Identities=35% Similarity=0.434 Sum_probs=144.2
Q ss_pred EEEEeCCCCceeecCCCCCCchHHHHH----hhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEE
Q 015203 151 VLTVCKPPSVPVHPCGQYRKNTVVGIL----QAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYI 226 (411)
Q Consensus 151 ~ivvnKP~Gl~v~~~~~~~~~tv~~~l----~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~Yl 226 (411)
|+|+|||+|++|++.+.....++.+++ ........+++|||||++||||||||+|+++++.|+++|+++.+.|+|+
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 589999999999998887778888775 2222335688999999999999999999999999999999999999999
Q ss_pred EEEecccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCCeEEEEEEeccCcccHHHHHHhhc
Q 015203 227 ARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYT 306 (411)
Q Consensus 227 A~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slv~~~l~TGRtHQIRvhla~l 306 (411)
|+|.|.++.+.+.++.++..+......... ..++++.+.|+|++++...+.|+|+|+|+|||+||||+||+++
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 999999998888887777543111111111 1246789999999998877899999999999999999999999
Q ss_pred CCCeeecCCCCccccC----CccCccccce
Q 015203 307 GYPIANDMLYLCEHVT----HREGMSADRA 332 (411)
Q Consensus 307 G~PIvGD~~Yg~~~~~----~~~~~~a~~~ 332 (411)
||||+||.+||....+ .+..|||.+.
T Consensus 154 G~pIvGD~~Yg~~~~~~~~~~~~~Lha~~l 183 (185)
T cd02869 154 GHPIVGDPKYGGKASDSPGLKRLALHAYRL 183 (185)
T ss_pred CCCEeCccccCCccccccCCcchhhcccEe
Confidence 9999999999987653 4566666643
No 14
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=100.00 E-value=4.4e-38 Score=307.84 Aligned_cols=204 Identities=20% Similarity=0.195 Sum_probs=157.7
Q ss_pred chHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecCCceecCC--CEEEEeeecCCCCCcCCCceEee-eCCcEEEEeC
Q 015203 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSS--QKISHFLHRHEPPVMAWDVSILQ-KEPDVLTVCK 156 (411)
Q Consensus 80 ~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~g--D~I~~~~~~~e~~~~~~~~~Ily-Ed~~~ivvnK 156 (411)
+||++||++. +.|||++++++|++|+|+|||+++.++++|..+ |.|.++...... ...+ ||+.|+++||
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-GHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISV-------KESAEQICRVLAYYK 74 (289)
T ss_pred hhHHHHHHHC-CCCCHHHHHHHHHcCCEEECCEeccCCCEeCCCCCeEEEECCEEeec-------ccccccCCeEEEEEC
Confidence 8999999986 889999999999999999999999999999877 446554211110 0111 5578999999
Q ss_pred CCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEecccCCC
Q 015203 157 PPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEG 236 (411)
Q Consensus 157 P~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~G~~~~~ 236 (411)
|+|++||+++.....||++++.... ...+++|||||++||||||||+|+++++.|+ .+++.|.|+|+|+|.|.++++
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 9999999988777789999986522 2458899999999999999999999999998 489999999999999998765
Q ss_pred CceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCCeEEEEEEeccCcccHHHHHHhhcCCCeee
Q 015203 237 EQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIAN 312 (411)
Q Consensus 237 ~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slv~~~l~TGRtHQIRvhla~lG~PIvG 312 (411)
.+. ....|..+ .++......++.+......++++|+|+|||+||||+||+++||||+.
T Consensus 152 ~l~-------~l~~Gv~l-----------~~~~~~~~~v~~~~~~~~~s~l~v~L~EGk~hQIRrm~~~lG~~V~~ 209 (289)
T PRK10700 152 KLR-------QLSRGVQL-----------EDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSR 209 (289)
T ss_pred HHH-------HHHcCCEe-----------CCceeeeEEEEeccCCCCceEEEEEEeCCccHHHHHHHHHcCCEEeE
Confidence 431 11222221 12322233333332222357899999999999999999999999975
No 15
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.7e-37 Score=292.17 Aligned_cols=203 Identities=21% Similarity=0.245 Sum_probs=163.7
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCC-EEEEeeecCCCCCcCCCceEee-eCCcEEEEe
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQ-KISHFLHRHEPPVMAWDVSILQ-KEPDVLTVC 155 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD-~I~~~~~~~e~~~~~~~~~Ily-Ed~~~ivvn 155 (411)
.+||+|+|++. +.+||++++++|++|+|+|||+++ ..+..+.+++ .|.+. +..+.+ +...|+++|
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-GVGSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVD-----------GKRIELKEERVYLLLN 69 (248)
T ss_pred ccchHHHHHHc-CCCCHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEEC-----------CEEeeccccceEEEEE
Confidence 58999999998 999999999999999999999998 6788888884 66665 444555 345599999
Q ss_pred CCCCceeecCCCCCCchHHHHHhhc-cCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEecccC
Q 015203 156 KPPSVPVHPCGQYRKNTVVGILQAE-HDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFP 234 (411)
Q Consensus 156 KP~Gl~v~~~~~~~~~tv~~~l~~~-~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~G~~~ 234 (411)
||.|++|+..++..+.||.++|... ....+++||+|||+||+||||||+|++++++|. +|+.++.|+|+|.|.|.++
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 9999999998888899999999853 112459999999999999999999999999999 6999999999999999887
Q ss_pred CCCceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEe-eeCC-CeEEEEEEeccCcccHHHHHHhhcCCCeee
Q 015203 235 EGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRI-STNG-THSIVLCEPITGRTHQIRVHLQYTGYPIAN 312 (411)
Q Consensus 235 ~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l-~~~~-~~slv~~~l~TGRtHQIRvhla~lG~PIvG 312 (411)
++.. ...+.|..+ .++....+....+ ...+ ..|++++.|.+||+||||+||+++|+||+.
T Consensus 148 ~~~l-------~~l~~Gv~l-----------~d~~~~~~~~~~l~~~~~~~~s~~~itl~EGrnrQVRRm~~a~G~~V~~ 209 (248)
T COG1187 148 EEDL-------EKLRKGVTL-----------DDGETKPAKPASLEKEPGKNNSWLRITLTEGRNRQVRRMFEAVGLEVLR 209 (248)
T ss_pred HHHH-------HHHhCCcEe-----------cCcccccceeEEEEecCCCCceEEEEEEeCCcCHHHHHHHHHcCCEEeE
Confidence 6543 222333322 2433334342222 2233 589999999999999999999999999975
Q ss_pred c
Q 015203 313 D 313 (411)
Q Consensus 313 D 313 (411)
=
T Consensus 210 L 210 (248)
T COG1187 210 L 210 (248)
T ss_pred E
Confidence 3
No 16
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=100.00 E-value=5.6e-37 Score=299.55 Aligned_cols=198 Identities=15% Similarity=0.205 Sum_probs=156.7
Q ss_pred cCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecCCceecCCCEEEEeeecCCCCCcCCCceEeeeCCcEEEEeCC
Q 015203 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCKP 157 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~~~~~e~~~~~~~~~IlyEd~~~ivvnKP 157 (411)
.++||++||++. +.|||++++++|++|+|+|||+++.++++|.+||.|.++...-++ ..+||++|||+|||
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 468999999987 789999999999999999999999999999999999886421111 11478899999999
Q ss_pred CCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEecccCCCC
Q 015203 158 PSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGE 237 (411)
Q Consensus 158 ~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~G~~~~~~ 237 (411)
+|++||+.+. ...||+++|... ..++||||||++||||||||+|++++++|+. +.+.+.|+|+|+|.|.++++.
T Consensus 76 ~G~~~~~~~~-~~~tv~~~l~~~---~~l~~VgRLDrdTsGLLLlT~dg~~~~~L~~--p~~~i~K~Y~v~V~g~~~~~~ 149 (290)
T PRK10475 76 VGIVSTTEDG-ERDNIVDFVNHS---KRVFPIGRLDKDSQGLIFLTNHGDLVNKILR--AGNDHEKEYLVTVDKPITDEF 149 (290)
T ss_pred CCCCcCCCCC-CCCcHHHHhhcc---ccccccccCCCCCcceEEEecCHHHHHHhhC--cCCCCCeEEEEEECCCCCHHH
Confidence 9999997765 457899998642 4589999999999999999999999999984 777899999999999987653
Q ss_pred ceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCCeEEEEEEeccCcccHHHHHHhhcCCCeee
Q 015203 238 QVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIAN 312 (411)
Q Consensus 238 ~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slv~~~l~TGRtHQIRvhla~lG~PIvG 312 (411)
+ .....|..+ +++......++.+ +.++++|+|.+||+||||+||+++|+||+-
T Consensus 150 l-------~~l~~Gv~l-----------~~~~~~~~~v~~~----~~~~~~i~l~eGk~rqIRrm~~~~G~~V~~ 202 (290)
T PRK10475 150 I-------RGMGAGVPI-----------LGTVTKKCKVKKE----APFVFRITLVQGLNRQIRRMCEHFGYEVTK 202 (290)
T ss_pred H-------HHHhCCcEE-----------CCEEecceEEEec----CCcEEEEEEECCcCHHHHHHHHHcCCEEeE
Confidence 3 111222221 1111112223322 245799999999999999999999999975
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=9.9e-35 Score=259.50 Aligned_cols=148 Identities=29% Similarity=0.385 Sum_probs=121.6
Q ss_pred EEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEe
Q 015203 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (411)
Q Consensus 151 ~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (411)
|+|+|||+|++||+++.....++.+.+.... ...+++|||||++||||||||+|+++++.|+++ ++.+.|+|+|+|.
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 5899999999999988777788888876532 256899999999999999999999999999986 7889999999999
Q ss_pred cccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCCeEEEEEEeccCcccHHHHHHhhcCCCe
Q 015203 231 GVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPI 310 (411)
Q Consensus 231 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slv~~~l~TGRtHQIRvhla~lG~PI 310 (411)
|.++++ ..+..++... +..... ..++++.+.|+|++++..++.|+|+|+|.|||+||||+||+++||||
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 4455554331 111111 12467889999999987777899999999999999999999999999
Q ss_pred ee
Q 015203 311 AN 312 (411)
Q Consensus 311 vG 312 (411)
.-
T Consensus 147 ~~ 148 (154)
T cd02550 147 LR 148 (154)
T ss_pred Ee
Confidence 73
No 18
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.
Probab=100.00 E-value=1.6e-33 Score=255.07 Aligned_cols=141 Identities=20% Similarity=0.243 Sum_probs=117.3
Q ss_pred EEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEe
Q 015203 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (411)
Q Consensus 151 ~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (411)
++|+|||+|++||+.+.....|+.+++.... ...+++|||||++||||||||+|++++++|+ .+++.+.|+|+|+|.
T Consensus 2 ~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~-~~~~~~V~RLD~~TsGLll~ak~~~~~~~L~--~~~~~i~K~Y~a~V~ 78 (167)
T cd02556 2 VLIYHKPEGLICTRKDPKGRPTVFDLLPKLG-IPRWISVGRLDLNTEGLLLFTNDGELANRLM--HPSNEIEREYAVRVF 78 (167)
T ss_pred EEEEECCCCcEECccCCCCCccHHHhhhhhc-cCceEEcCcCCCCCeeEEEEECCHHHHHHHh--CCcCCCCeEEEEEEC
Confidence 7899999999999877666789999886532 2457899999999999999999999999998 488999999999999
Q ss_pred cccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCCeEEEEEEeccCcccHHHHHHhhcCCCe
Q 015203 231 GVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPI 310 (411)
Q Consensus 231 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slv~~~l~TGRtHQIRvhla~lG~PI 310 (411)
|.++.+.. .....+.. ..+++.+.|+|+++....+.|+|+|+|+|||+||||+||+++||||
T Consensus 79 g~~~~~~~-------~~~~~gv~-----------~~~~~~~~~~~~~~~~~~~~sll~v~l~tGR~HQIR~~~a~~G~pV 140 (167)
T cd02556 79 GQVTDEQL-------KSLKKGVE-----------LEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQV 140 (167)
T ss_pred ccCCHHHH-------HHHHcCCE-----------ECCCcCcceEEEEEecCCCcEEEEEEEEeCCCHHHHHHHHHcCCeE
Confidence 99876542 11111111 1357788899999976666799999999999999999999999999
Q ss_pred ee
Q 015203 311 AN 312 (411)
Q Consensus 311 vG 312 (411)
+-
T Consensus 141 ~~ 142 (167)
T cd02556 141 SR 142 (167)
T ss_pred eE
Confidence 85
No 19
>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=6.6e-34 Score=252.03 Aligned_cols=140 Identities=29% Similarity=0.355 Sum_probs=116.4
Q ss_pred EEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEe
Q 015203 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (411)
Q Consensus 151 ~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (411)
|+|+|||+|++||+.+.....++.+++... ...+++|||||++||||||||+|+++++.|.. +++.+.|+|+|+|.
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~~--~~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~ 76 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDV--GERLFPVGRLDYDTEGLLLLTNDGELANRLTH--PRYGVEKTYLVKVR 76 (146)
T ss_pred CEEEECCCCcEecccCCCCCCEEeeecccc--CCCEEECCCCCCCCeeEEEEeCCHHHHHHhhC--ccCCCCeEEEEEEC
Confidence 589999999999998877677888777642 24689999999999999999999999999985 67889999999999
Q ss_pred cccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCCeEEEEEEeccCcccHHHHHHhhcCCCe
Q 015203 231 GVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPI 310 (411)
Q Consensus 231 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slv~~~l~TGRtHQIRvhla~lG~PI 310 (411)
|.++.+.+ .....+.. ..+++.+.|+|++++..++.|+|+|+|+|||+||||+||+++||||
T Consensus 77 g~~~~~~~-------~~~~~~~~-----------~~~~~~~~t~~~~l~~~~~~sll~~~l~tGR~HQIR~hla~~G~pI 138 (146)
T cd02870 77 GVPSEEEL-------RRLRAGVE-----------LDDGKTAPAKVKVLSRDPKNTLLEVTLHEGRNRQVRRMFEAVGHPV 138 (146)
T ss_pred CCCCHHHH-------HHHHCCeE-----------eCCceEcceEEEEeccCCCCcEEEEEEEeCCcHHHHHHHHHcCCcC
Confidence 99876542 01111111 1357889999999987777899999999999999999999999999
Q ss_pred ee
Q 015203 311 AN 312 (411)
Q Consensus 311 vG 312 (411)
+.
T Consensus 139 ~~ 140 (146)
T cd02870 139 LR 140 (146)
T ss_pred Ce
Confidence 74
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=99.98 E-value=2e-32 Score=247.96 Aligned_cols=144 Identities=23% Similarity=0.276 Sum_probs=112.9
Q ss_pred EEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEe
Q 015203 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (411)
Q Consensus 151 ~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (411)
|+|+|||+|++||++ .....|+.+++........+++|||||++||||||||+|.++++.|.. +++.++|+|+|+|.
T Consensus 2 ~ivvnKP~G~~~~~~-~~~~~tl~~~l~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~V~ 78 (167)
T cd02553 2 YLMLNKPAGVVCATK-DPHHPTVIDLLPEPDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTS--PKKHVPKTYEVTLA 78 (167)
T ss_pred EEEEECCCCCEeCCC-CCCCCcHHHHhhhhcccCCeEEcccCCCCCEEEEEEEeCHHHHHHhhC--CcCCCceEEEEEEc
Confidence 799999999999964 445689999887654335689999999999999999999999999885 67889999999999
Q ss_pred cccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCC-ceeeeEEEEeeeCCCeEEEEEEeccCcccHHHHHHhhcCCC
Q 015203 231 GVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKG-KAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYP 309 (411)
Q Consensus 231 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~g-k~a~t~~~~l~~~~~~slv~~~l~TGRtHQIRvhla~lG~P 309 (411)
|.++.+++. ....+.. . .++ +...+.+++++ .++|+|+|+|||+||||+||+++|||
T Consensus 79 G~~~~~~~~-------~~~~~~~---~--------~~~~~~~~~~~~~~~----~sll~v~l~tGR~HQIR~hla~lG~p 136 (167)
T cd02553 79 GPLTEDDIE-------AFAEGVL---L--------HDGYPTKPAKLEILS----PTTVRLTITEGKYHQVKRMFAAVGNK 136 (167)
T ss_pred cCCCHHHHH-------HHHCCeE---E--------cCCCEeeeeEEEEeC----CcEEEEEEEeCCCHHHHHHHHHcCCe
Confidence 998765421 0111110 1 122 23445666663 38999999999999999999999999
Q ss_pred eeecCCCCcc
Q 015203 310 IANDMLYLCE 319 (411)
Q Consensus 310 IvGD~~Yg~~ 319 (411)
|++|..++-.
T Consensus 137 I~~~~R~~~g 146 (167)
T cd02553 137 VVALHRIRIG 146 (167)
T ss_pred EEEEEEEEEC
Confidence 9999887643
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=99.97 E-value=2.5e-31 Score=238.55 Aligned_cols=149 Identities=37% Similarity=0.549 Sum_probs=113.2
Q ss_pred cEEEEeCCCCceeecCCCCCCchHHH----HHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEE
Q 015203 150 DVLTVCKPPSVPVHPCGQYRKNTVVG----ILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRY 225 (411)
Q Consensus 150 ~~ivvnKP~Gl~v~~~~~~~~~tv~~----~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~Y 225 (411)
+|||||||+||+|++.+......+.. ..........+++|||||++||||||||+|++++++|+++|+++.++|+|
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 58999999999999988433333322 22223344678999999999999999999999999999999999999999
Q ss_pred EEEEecccCCCCceEeeeeeccc--CCCcceeeeCCCCCCCCCCCceeeeEEEEeeeC---------CCeEEEEEEeccC
Q 015203 226 IARVNGVFPEGEQVVDVNINYNA--SAGRSTAESGDSLGDTPLKGKAACTKFTRISTN---------GTHSIVLCEPITG 294 (411)
Q Consensus 226 lA~V~G~~~~~~~~i~~~i~~~~--~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~---------~~~slv~~~l~TG 294 (411)
+|+|.|.+..+++.++.++..+. ......... ..+++.+.|.|+++... ...++|+|+|.||
T Consensus 81 ~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~t~~~~l~~~~~~~~~~~~~~~s~v~~~l~tG 153 (164)
T PF00849_consen 81 LALVEGGPVEEEGKINSPLGKDVGKNKSSNKDPP-------GRDGKPAITRYRVLRSGSRTPSKDENAGCSLVECELITG 153 (164)
T ss_dssp EEEECSSSSTTCEEEESHEEE-EECSSCTCCEEE-------TTTSBTSEEEEEEEEEETT---EECCSSEEEEEEEESS-
T ss_pred EEeEcccccccceeeeccccccccccccceeeee-------cccccccceeeeeeccccccccccccCCCEEEEEEECcC
Confidence 99999777777888988887621 111111111 25788999999999986 6799999999999
Q ss_pred cccHHHHHHhh
Q 015203 295 RTHQIRVHLQY 305 (411)
Q Consensus 295 RtHQIRvhla~ 305 (411)
|+||||+|||+
T Consensus 154 r~HQIR~hla~ 164 (164)
T PF00849_consen 154 RTHQIRVHLAH 164 (164)
T ss_dssp STTHHHHHHHH
T ss_pred CCHHHHHHhcC
Confidence 99999999986
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=99.97 E-value=1.9e-30 Score=235.18 Aligned_cols=154 Identities=18% Similarity=0.182 Sum_probs=109.8
Q ss_pred EEEEeCCCCceeecCCC-CCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEE
Q 015203 151 VLTVCKPPSVPVHPCGQ-YRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARV 229 (411)
Q Consensus 151 ~ivvnKP~Gl~v~~~~~-~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V 229 (411)
|+|+|||+|++||+++. ....|+.+++.. ..+++|||||++||||||||+|+++++.|++ +++.++|+|+|+|
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----PGVYAAGRLDRDSEGLLLLTDDGRLQHRITD--PSFKHPKTYYVQV 74 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCccHHHHcCc----CCeEEccCCCCCCeEEEEEEeCHHHHHHHHC--CCCCCCEEEEEEE
Confidence 58999999999998765 456788888852 4578999999999999999999999999985 5677999999999
Q ss_pred ecccCCCCce-EeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeee--CCCeEEEEEEeccCcccHHHHHHhhc
Q 015203 230 NGVFPEGEQV-VDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRIST--NGTHSIVLCEPITGRTHQIRVHLQYT 306 (411)
Q Consensus 230 ~G~~~~~~~~-i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~--~~~~slv~~~l~TGRtHQIRvhla~l 306 (411)
.|.++.+... +..++...... .....+.. ...+....+.|.++.. ..+.|+|+|+|+|||+||||+||+++
T Consensus 75 ~g~~~~~~~~~l~~g~~~~~~~-~~~~~v~~-----~~~~~~~~~~~~~~~~~~~~~~sll~v~l~tGR~HQIR~~la~l 148 (168)
T cd02566 75 EGVPTEDALEQLRNGVELGDGL-TLPAKVEK-----VDEPPWLWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAV 148 (168)
T ss_pred CCcCCHHHHHHHhCCcEECCeE-ecceEEEE-----ecccccccccccccccccCCCccEEEEEEecCccHHHHHHHHHc
Confidence 9998764321 11122111000 00001100 0111233344555543 33568999999999999999999999
Q ss_pred CCCeeecCCC
Q 015203 307 GYPIANDMLY 316 (411)
Q Consensus 307 G~PIvGD~~Y 316 (411)
||||+.....
T Consensus 149 G~pV~~L~R~ 158 (168)
T cd02566 149 GFPTLRLIRV 158 (168)
T ss_pred CCeEeEEEEE
Confidence 9999987654
No 23
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.96 E-value=8.6e-30 Score=238.52 Aligned_cols=148 Identities=20% Similarity=0.247 Sum_probs=114.0
Q ss_pred CCcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEE
Q 015203 148 EPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIA 227 (411)
Q Consensus 148 d~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA 227 (411)
...|+++|||+|++||+.+.....++.+++.. .++++|||||++||||||||+|++++++|+. +++.+.|+|+|
T Consensus 38 ~~~ylllnKP~G~l~~~~d~~~~~tl~d~l~~----~~~~~vgRLD~~TsGllLlt~d~~~~~~L~~--~~~~i~K~Y~~ 111 (217)
T PRK11394 38 PTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV----QGVYAAGRLDRDSEGLLVLTNNGALQARLTQ--PGKRTGKIYYV 111 (217)
T ss_pred CCEEEEEECCCCCEEeeCCccCCcchHHhccc----CCeEEecCCCCCCeeEEEEECCHHHHHHHhC--cccCCCEEEEE
Confidence 34689999999999998777777899999852 4689999999999999999999999999996 58899999999
Q ss_pred EEecccCCCCceE-eeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEee---------------eCCCeEEEEEEe
Q 015203 228 RVNGVFPEGEQVV-DVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRIS---------------TNGTHSIVLCEP 291 (411)
Q Consensus 228 ~V~G~~~~~~~~i-~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~---------------~~~~~slv~~~l 291 (411)
+|.|.++.+.+.. ..++... ++......++.+. ...+.|+|+|+|
T Consensus 112 ~v~g~~~~~~l~~l~~Gv~i~-------------------~~~~~p~~~~~i~~~~~~~~~~~~~~~~~~~~~s~l~I~L 172 (217)
T PRK11394 112 QVEGIPTQDALEALRNGVTLN-------------------DGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITL 172 (217)
T ss_pred EECCCCCHHHHHHHhCCeEEC-------------------CccccccEEEEecccccccccccccccccCCCceEEEEEE
Confidence 9999987654422 2222111 0110011111111 122478999999
Q ss_pred ccCcccHHHHHHhhcCCCeeecCCCCccc
Q 015203 292 ITGRTHQIRVHLQYTGYPIANDMLYLCEH 320 (411)
Q Consensus 292 ~TGRtHQIRvhla~lG~PIvGD~~Yg~~~ 320 (411)
.|||+||||+||+++||||+||.+|+-..
T Consensus 173 ~eGR~hQIRrm~a~lG~pVl~L~Ry~iG~ 201 (217)
T PRK11394 173 YEGRNRQVRRMTAHVGFPTLRLIRYAMGD 201 (217)
T ss_pred eCCCCHHHHHHHHHcCCeEeeeEEEEECC
Confidence 99999999999999999999999998544
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=99.96 E-value=4.5e-29 Score=227.93 Aligned_cols=142 Identities=18% Similarity=0.239 Sum_probs=105.4
Q ss_pred CcEEEEeCCCCceeecCCCC--------CCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCe
Q 015203 149 PDVLTVCKPPSVPVHPCGQY--------RKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGK 220 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~--------~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~ 220 (411)
..|+++|||+|++|+..++. ...++.+++.... .++++|||||++||||||||+|+++++.|+. +.+.
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 35799999999999876532 2245556665432 4689999999999999999999999999996 5688
Q ss_pred ecEEEEEEEecccCCCCc-eEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCCeEEEEEEeccCcccHH
Q 015203 221 VIKRYIARVNGVFPEGEQ-VVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQI 299 (411)
Q Consensus 221 v~K~YlA~V~G~~~~~~~-~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slv~~~l~TGRtHQI 299 (411)
|.|+|+|+|.|.++++.. .+..++..+ + ...+.+.+.+ .+.++|+|+|.|||+|||
T Consensus 80 i~K~Y~v~v~g~~~~~~l~~l~~g~~~~---~--------------~~~~~~~~~~------~~~~~l~i~l~tGr~hQI 136 (177)
T cd02555 80 LEQEYLVEVRGELTAGGLERLNHGLTYD---G--------------RELPPAKVSW------QNEQRLRFALKEPQPGQI 136 (177)
T ss_pred CCEEEEEEEcccCCHHHHHHHhcCcccC---C--------------eecceEEEEE------cCCCEEEEEEECCcChHH
Confidence 999999999999876432 122111100 0 0112232222 135789999999999999
Q ss_pred HHHHhhcCCCeeecCCCC
Q 015203 300 RVHLQYTGYPIANDMLYL 317 (411)
Q Consensus 300 Rvhla~lG~PIvGD~~Yg 317 (411)
|+||+++||||+|+....
T Consensus 137 R~~~~~~G~pV~~L~R~~ 154 (177)
T cd02555 137 RRMCESVGLEVVALRRIR 154 (177)
T ss_pred HHHHHHcCCeEEEEEEEE
Confidence 999999999999998764
No 25
>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=99.94 E-value=5.2e-27 Score=211.50 Aligned_cols=135 Identities=19% Similarity=0.255 Sum_probs=104.5
Q ss_pred EEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEe
Q 015203 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (411)
Q Consensus 151 ~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (411)
|+++|||+|++|++.+. ...|+.+++.. ...++||||||++||||||||+|++++++|+ ++.+.+.|+|+|.|.
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-DEDNIIDFVNP---PPRIFPIGRLDKDSEGLILLTNDGDLVNKIL--HADNNHEKEYLVTVN 75 (164)
T ss_pred EEEEECCCCcEeecCCC-CCCcHHHHhcC---cCCEEEccCCCCCCeeEEEEEcCHHHHHHHh--hhhcCCCeEEEEEEC
Confidence 78999999999998765 45899999865 2569999999999999999999999999998 588899999999999
Q ss_pred cccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCCceeeeEEEEeeeCCCeEEEEEEeccCcccHHHHHHhhcCCCe
Q 015203 231 GVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKGKAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPI 310 (411)
Q Consensus 231 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~gk~a~t~~~~l~~~~~~slv~~~l~TGRtHQIRvhla~lG~PI 310 (411)
|.+.++.. .....|... .++......++.+ .. +.++|.|++||+||||+||+++||||
T Consensus 76 ~~l~~~~l-------~~l~~G~~~-----------~~~~~~~~~v~~~---~~-~~l~i~l~eGr~~qIRrm~~~~G~~V 133 (164)
T cd02554 76 KPITDEFI-------EGMSNGVVI-----------LGTVTKPCKVERL---AK-DKFRIVLTQGLNRQIRRMCEALGYRV 133 (164)
T ss_pred CCCCHHHH-------HHHhCCCEE-----------CCeEEcceEEEEC---CC-CEEEEEEECCcCHHHHHHHHHcCCEE
Confidence 99876532 111222211 1222222333333 22 34999999999999999999999999
Q ss_pred eec
Q 015203 311 AND 313 (411)
Q Consensus 311 vGD 313 (411)
+-=
T Consensus 134 ~~L 136 (164)
T cd02554 134 TDL 136 (164)
T ss_pred EEE
Confidence 853
No 26
>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=99.94 E-value=2.3e-27 Score=205.82 Aligned_cols=111 Identities=21% Similarity=0.302 Sum_probs=91.9
Q ss_pred ccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEecccCCCCceEeeeeecccCCCcceeeeCCCCCCCCCCC
Q 015203 189 VHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLGDTPLKG 268 (411)
Q Consensus 189 VhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~g 268 (411)
|||||++||||||||+|+++++.|+. +++.|.|+|+|+|.|.++++.. + ++ ..+.. . .++
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~--~~~~i~K~Y~a~v~g~~~~~~~--~-~~----~~g~~---~--------~~~ 60 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTH--PGHHCEKTYLVTVEGPVTDEDL--E-AL----RKGVQ---L--------EDG 60 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhC--CCCCCCeEEEEEECCCCCHHHH--H-HH----hCCeE---E--------CCc
Confidence 79999999999999999999999995 7889999999999999876532 1 11 11111 1 245
Q ss_pred ceeeeEEEEeeeCCCeEEEEEEeccCcccHHHHHHhhcCCCeeecCCCCcc
Q 015203 269 KAACTKFTRISTNGTHSIVLCEPITGRTHQIRVHLQYTGYPIANDMLYLCE 319 (411)
Q Consensus 269 k~a~t~~~~l~~~~~~slv~~~l~TGRtHQIRvhla~lG~PIvGD~~Yg~~ 319 (411)
+.+.+.|++++.....++|+|+|.|||+||||+||+++||||+||..+.-.
T Consensus 61 ~~~~~~~~~l~~~~~~~~l~~~l~tGR~HQIR~~~~~lG~pI~g~~R~~~g 111 (128)
T TIGR00093 61 PTKPAKLEVITEPGFPTWLRITLSEGRNRQVRRMFAAVGFPVLRLHRVRIG 111 (128)
T ss_pred EEeeeEEEEEccCCCceEEEEEEeCCCCHHHHHHHHHcCCeEeEEEEEEEC
Confidence 667888999876666889999999999999999999999999999998644
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=99.05 E-value=3e-10 Score=107.52 Aligned_cols=74 Identities=27% Similarity=0.343 Sum_probs=56.0
Q ss_pred EEEEeCCCCceeecCCCCCCchHHHHHhhccCCC-CcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEE
Q 015203 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLA-PLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARV 229 (411)
Q Consensus 151 ~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~-~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V 229 (411)
+||||||+|+.++... +++...+....+.. ..++|||||++|||||+||.+... +|.++|.++.+.|+|+|..
T Consensus 2 ilvvnKP~Gi~s~~~~----~~~~~~l~~~~~~~k~~~~vhrLD~~aSGvl~~a~~~~t--kl~~~~~~~~~~K~Y~~~~ 75 (226)
T cd02868 2 LFAVYKPPGVHWKHVR----DTIESNLLKYFPEDKVLVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYSNHPTRVYTIRG 75 (226)
T ss_pred EEEEEcCCCCChhHHH----HHHHHHHHHHccccceeeEccccCCCCceEEEEEeChhH--hHHHHHHhcCCCeEEEEEE
Confidence 7999999999776532 44444443322222 256889999999999999999986 6888899888999999654
Q ss_pred e
Q 015203 230 N 230 (411)
Q Consensus 230 ~ 230 (411)
.
T Consensus 76 ~ 76 (226)
T cd02868 76 L 76 (226)
T ss_pred E
Confidence 3
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=99.04 E-value=8.9e-10 Score=83.19 Aligned_cols=69 Identities=19% Similarity=0.167 Sum_probs=59.7
Q ss_pred chHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEeeecCCCCCcCCCceEeeeCCcEEEEe
Q 015203 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVC 155 (411)
Q Consensus 80 ~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~~~~~~~~~IlyEd~~~ivvn 155 (411)
+||+++|.+.+...||+.++++|++|.|+|||+.+ .+++.+.+||.|.+... ++ ...|+|||++++++|
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 58999999886678999999999999999999999 89999999999887632 11 238999999999987
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=98.74 E-value=2.5e-08 Score=71.39 Aligned_cols=47 Identities=21% Similarity=0.240 Sum_probs=42.7
Q ss_pred chHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEE
Q 015203 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKI 126 (411)
Q Consensus 80 ~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I 126 (411)
|||++||++.....||++++++|++|.|+|||+++ ++++.|++||+|
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 69999999875556799999999999999999999 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=98.57 E-value=1.2e-07 Score=70.95 Aligned_cols=51 Identities=12% Similarity=-0.092 Sum_probs=45.5
Q ss_pred cCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEE
Q 015203 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISH 128 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~ 128 (411)
+++||++||+......||+.++++|+.|.|+|||+++ .++++|+.||.|.+
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 5799999999972223999999999999999999999 78999999999976
No 31
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=98.15 E-value=3.6e-06 Score=69.10 Aligned_cols=55 Identities=13% Similarity=0.096 Sum_probs=48.3
Q ss_pred CcCchHHHHHHHh-cCCCCHHHHHHHHHcCcEEECCEEecCCceecCCCEEEEeeec
Q 015203 77 WAGKTIVDLFAEE-FKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFLHR 132 (411)
Q Consensus 77 ~~g~rL~k~L~~~-~~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~~~~ 132 (411)
...|||++||.-. | .-+|+.++++++.|+|.|||+.++++..|+.||+|++.+..
T Consensus 6 ~~~mRLDKwL~~aR~-~KrRslAk~~~~~GrV~vNG~~aKpS~~VK~GD~l~i~~~~ 61 (100)
T COG1188 6 ADRMRLDKWLWAARF-IKRRSLAKEMIEGGRVKVNGQRAKPSKEVKVGDILTIRFGN 61 (100)
T ss_pred ccceehHHHHHHHHH-hhhHHHHHHHHHCCeEEECCEEcccccccCCCCEEEEEeCC
Confidence 3469999999765 4 57899999999999999999999999999999999987644
No 32
>smart00363 S4 S4 RNA-binding domain.
Probab=98.09 E-value=1.2e-05 Score=58.47 Aligned_cols=51 Identities=22% Similarity=0.180 Sum_probs=45.4
Q ss_pred chHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEee
Q 015203 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFL 130 (411)
Q Consensus 80 ~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~ 130 (411)
++|+.+|...+...|++.++++|..|.|+|||+++ .+++.+..||.|.+..
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 47889998764568999999999999999999999 8999999999998763
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=97.76 E-value=7.4e-05 Score=68.72 Aligned_cols=71 Identities=18% Similarity=0.181 Sum_probs=54.2
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.+++||||.|+-+| .++..++...+..++...|-||...||||+++-+.. -++.+.+.. -.|+|.|.
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 YGVINLDKPSGPSSH--------EVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRA--TRLVKSQQE--AGKEYVCV 69 (182)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhCCCccCcCCCCCCcCeeEEEEEECHH--hhhhHHHhC--CCCEEEEE
Confidence 468999999999776 456677765666678889999999999999998863 344443443 45999998
Q ss_pred Eec
Q 015203 229 VNG 231 (411)
Q Consensus 229 V~G 231 (411)
+.=
T Consensus 70 v~~ 72 (182)
T cd02572 70 MRL 72 (182)
T ss_pred EEE
Confidence 763
No 34
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=97.74 E-value=8.6e-05 Score=64.58 Aligned_cols=53 Identities=6% Similarity=-0.034 Sum_probs=47.3
Q ss_pred cCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecCCceecCCCEEEEee
Q 015203 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFL 130 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~~ 130 (411)
+.+||++||...--.-||+.+..+|..|.|.|||++++++..|+.||.|.+..
T Consensus 7 ~~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~~Kps~~V~~gd~l~v~~ 59 (133)
T PRK10348 7 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQ 59 (133)
T ss_pred ccccHHHHHHHcCccccHHHHHHHHHCCCEEECCEECCCCCccCCCCEEEEEE
Confidence 35899999988734679999999999999999999999999999999998753
No 35
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=97.64 E-value=9.1e-05 Score=72.07 Aligned_cols=54 Identities=19% Similarity=0.143 Sum_probs=49.6
Q ss_pred CCCcCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEe
Q 015203 75 NRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (411)
Q Consensus 75 ~~~~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (411)
..-.++||+.+++..| ..||+.+..+|++|.|+|||+.+ ++++.|++||.|++.
T Consensus 187 ~~vas~RLD~vla~~~-~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiR 241 (267)
T PLN00051 187 SVEASLRLDALASAGF-RMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVS 241 (267)
T ss_pred CCcCcccHHHHHHHHh-ccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEe
Confidence 3456799999999997 89999999999999999999998 899999999999986
No 36
>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=97.64 E-value=0.00011 Score=68.64 Aligned_cols=51 Identities=20% Similarity=0.053 Sum_probs=45.6
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEe
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (411)
.+||+++|.......||+.++++|..|.|.|||+++ .+++.|++||.|.+.
T Consensus 89 e~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD~I~V~ 140 (200)
T TIGR01017 89 ESRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIK 140 (200)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCCEEEEe
Confidence 489999998763356899999999999999999999 789999999999876
No 37
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=97.61 E-value=0.00012 Score=68.41 Aligned_cols=51 Identities=18% Similarity=0.105 Sum_probs=45.9
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEe
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (411)
.+||+++|.+.....||+.++++|..|.|+|||+++ .+++.|++||.|.+.
T Consensus 88 E~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~ 139 (201)
T CHL00113 88 EMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVK 139 (201)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEc
Confidence 479999998874356999999999999999999999 789999999999875
No 38
>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=97.61 E-value=0.00011 Score=71.28 Aligned_cols=55 Identities=20% Similarity=0.233 Sum_probs=49.3
Q ss_pred cCCCcCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEe
Q 015203 74 KNRWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (411)
Q Consensus 74 ~~~~~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (411)
.....++||+.+++..| ..||+.++++|++|+|+|||+++ ++++.|++||.|++.
T Consensus 178 ~~~v~s~RLD~lls~~~-~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~Isvr 233 (257)
T TIGR03069 178 TTVEASLRIDAIASAGF-GLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLR 233 (257)
T ss_pred cCCCccccHHHHHHhhh-hhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEc
Confidence 34567899998888876 68999999999999999999999 899999999999986
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=97.60 E-value=0.00027 Score=56.90 Aligned_cols=63 Identities=10% Similarity=0.028 Sum_probs=46.0
Q ss_pred CCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEecccCCCCceEeeeeecccCCCcceeeeCCCCC
Q 015203 183 LAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVNGVFPEGEQVVDVNINYNASAGRSTAESGDSLG 262 (411)
Q Consensus 183 ~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~ 262 (411)
...+..+|++|+.++|+++++ ++|.+++. +..
T Consensus 23 ~~~i~~aG~kDk~a~t~q~v~-------------------n~f~i~~r--~~~--------------------------- 54 (87)
T cd01291 23 PKRVGYAGRKDKRAVTTQLVS-------------------NRFTITLR--VKP--------------------------- 54 (87)
T ss_pred hheEEECccCCCCeeEEEEEc-------------------ccEEEEEE--Eec---------------------------
Confidence 356889999999999999999 78988887 000
Q ss_pred CCCCCCceeeeEEEEeeeC--CCeEEEEEEeccCcccHHHHHHhhcC
Q 015203 263 DTPLKGKAACTKFTRISTN--GTHSIVLCEPITGRTHQIRVHLQYTG 307 (411)
Q Consensus 263 ~~~~~gk~a~t~~~~l~~~--~~~slv~~~l~TGRtHQIRvhla~lG 307 (411)
....... .....+++.| |+.||+|.+++.++
T Consensus 55 ------------~~~~~~~~~~~~~~l~f~l--~~~~yat~~l~el~ 87 (87)
T cd01291 55 ------------LNLKWPEERKRALVLEFTL--PRGSYATMLLRELG 87 (87)
T ss_pred ------------ceeEEcccccceEEEEEEc--CCcchHHHHHHHhC
Confidence 0000011 1355678888 99999999999875
No 40
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.46 E-value=0.00027 Score=67.10 Aligned_cols=71 Identities=15% Similarity=0.171 Sum_probs=54.8
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.+++||||.|+-+| .++..++...+..++...|.||-..||||+++-... +.+|.+.+. ...|+|.|.
T Consensus 9 ~G~l~i~KP~g~TS~--------dvv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~vG~~-aTkl~~~~~--~~~K~Y~~~ 77 (230)
T PRK00989 9 EGILLVDKPQGRTSF--------SLIRSLTKLIGVKKIGHAGTLDPFATGVMVMLIGRK-FTRLSDILL--FEDKEYAAV 77 (230)
T ss_pred CEEEEEeCCCCCCHH--------HHHHHHHHHhCCCcCCcCccCCCCCeeEEEEEECCc-hhhhHHHhc--CCCcEEEEE
Confidence 368999999999776 466677766666778899999999999999997753 344444343 278999998
Q ss_pred Ee
Q 015203 229 VN 230 (411)
Q Consensus 229 V~ 230 (411)
+.
T Consensus 78 ~~ 79 (230)
T PRK00989 78 AH 79 (230)
T ss_pred EE
Confidence 76
No 41
>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=97.42 E-value=0.00036 Score=65.59 Aligned_cols=68 Identities=21% Similarity=0.239 Sum_probs=53.0
Q ss_pred EEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEe
Q 015203 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (411)
Q Consensus 151 ~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (411)
+++||||.|+-+| .++..++...+..++...|-||-..||||+++-+.. .++...+.+ ..|+|.|.+.
T Consensus 2 il~i~KP~g~tS~--------~vv~~ik~~~~~kKvGH~GTLDP~AsGvLiv~vG~a--Tkl~~~~~~--~~K~Y~~~~~ 69 (210)
T cd00506 2 LFAVDKPQGPSSH--------DVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKA--TKLLKHLLA--ATKDYTAIGR 69 (210)
T ss_pred EEEEEcCCCCCHH--------HHHHHHHHHhCccccCCCCcCCCcCeeEEEEEECHH--HhhhHHHhc--CCceEEEEEE
Confidence 7899999999776 466667666666678889999999999999998863 333333443 7999999876
No 42
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=97.41 E-value=0.0004 Score=67.57 Aligned_cols=70 Identities=17% Similarity=0.184 Sum_probs=55.1
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.++++|||+|+.+| .++..++...+..++...|-||-..||||+++-... .+|.+.+.+ ..|+|.|.
T Consensus 2 ngil~vdKP~g~tS~--------~vv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~--~~K~Y~a~ 69 (273)
T PRK04099 2 NRLFVANKPAGMSSN--------AFLSRLKRKYGVKKAGFSGTLDPFAKGVLIVAFGQY--TKLFRFLKK--TPKTYRAT 69 (273)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCCCccccCccCCCCCeeEEEEEEChH--hhhHHHhcc--CCceEEEE
Confidence 368999999999776 567777776666778889999999999999998864 334444443 48999998
Q ss_pred Ee
Q 015203 229 VN 230 (411)
Q Consensus 229 V~ 230 (411)
+.
T Consensus 70 ~~ 71 (273)
T PRK04099 70 LW 71 (273)
T ss_pred EE
Confidence 76
No 43
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=97.35 E-value=0.00038 Score=65.14 Aligned_cols=51 Identities=20% Similarity=0.077 Sum_probs=44.9
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEe
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (411)
.+||+.+|.+.....||+.++++|..|.|+|||+++ .+++.|++||.|.+.
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 479999997763357999999999999999999999 599999999999875
No 44
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=97.33 E-value=0.0006 Score=65.24 Aligned_cols=70 Identities=20% Similarity=0.217 Sum_probs=54.1
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.+++||||.|+-+| .++..++...+..++...|-||-..||||+++-... -+|...+. ...|+|.|.
T Consensus 10 ~Gil~vdKP~G~TS~--------dvv~~vkr~~~~kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~--~~~K~Y~a~ 77 (244)
T PRK00020 10 DGVLLLDKPVGLSSN--------HALQRAKRTVDAAKAGHTGTLDPFATGLLVCCMGRA--TKISGRML--EADKTYQAT 77 (244)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhCCCCCCcCCcCCCcCeeEEEEEECHH--hhhhHHhc--cCCcEEEEE
Confidence 468999999999776 466777776666778889999999999999998863 33443343 345999998
Q ss_pred Ee
Q 015203 229 VN 230 (411)
Q Consensus 229 V~ 230 (411)
+.
T Consensus 78 ~~ 79 (244)
T PRK00020 78 LQ 79 (244)
T ss_pred EE
Confidence 75
No 45
>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=97.33 E-value=0.00053 Score=64.33 Aligned_cols=69 Identities=16% Similarity=0.233 Sum_probs=54.7
Q ss_pred cEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEE
Q 015203 150 DVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARV 229 (411)
Q Consensus 150 ~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V 229 (411)
.+++||||.|+-+| .++..++...+..++...|-||-..||||+++-+... +|.+.+. ...|+|.|.+
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 58999999999765 5677777766667788899999999999999988753 4544443 5789999987
Q ss_pred e
Q 015203 230 N 230 (411)
Q Consensus 230 ~ 230 (411)
.
T Consensus 71 ~ 71 (209)
T TIGR00431 71 R 71 (209)
T ss_pred E
Confidence 5
No 46
>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=97.31 E-value=0.00036 Score=66.44 Aligned_cols=49 Identities=16% Similarity=0.009 Sum_probs=43.8
Q ss_pred hHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEe
Q 015203 81 TIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (411)
Q Consensus 81 rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (411)
||+++|.+.....||+.++++|++|+|+|||+++ ++++.|..+|.|.+.
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 7899999984345899999999999999999999 899999999988765
No 47
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=97.21 E-value=0.00089 Score=66.00 Aligned_cols=69 Identities=17% Similarity=0.148 Sum_probs=53.8
Q ss_pred cEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEE
Q 015203 150 DVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARV 229 (411)
Q Consensus 150 ~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V 229 (411)
.+++||||+|+-+| .++..++...+..++...|.||-..||||+++-... .++.+.+. ...|+|.|.+
T Consensus 4 Gil~i~KP~G~TS~--------dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~--~~~K~Y~a~~ 71 (294)
T PRK02484 4 GIINLKKEAGMTSH--------DAVFKLRKILQTKKIGHGGTLDPDVVGVLPIAVGKA--TRLIEYMT--EAGKVYEGEI 71 (294)
T ss_pred eEEEEeCCCCCCHH--------HHHHHHHHHhCCCccccCCCCCCCCeeEEEEEEChh--hhhhHHhc--cCCcEEEEEE
Confidence 68999999999776 466777766666778899999999999999998764 33444343 3459999987
Q ss_pred e
Q 015203 230 N 230 (411)
Q Consensus 230 ~ 230 (411)
.
T Consensus 72 ~ 72 (294)
T PRK02484 72 T 72 (294)
T ss_pred E
Confidence 6
No 48
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=97.19 E-value=0.001 Score=65.88 Aligned_cols=70 Identities=20% Similarity=0.277 Sum_probs=54.4
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.+++||||+|+-+| .++..++...+..++...|-||-..||||+++-... .+|.+.+.. -.|+|.|.
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~--~~K~Y~a~ 70 (308)
T PRK14124 3 HGFLVAYKPKGPTSH--------DVVDEVRKKLKTRKVGHAGTLDPFATGVLIVGVNKA--TRLLEYLKN--EKKVYYVK 70 (308)
T ss_pred ceEEEEECCCCCCHH--------HHHHHHHHHcCCCccCcCcCCCCCCcEEEEEEEChH--HhhhHHHhc--CCceEEEE
Confidence 368999999999776 467777776666778889999999999999998864 334443443 38999998
Q ss_pred Ee
Q 015203 229 VN 230 (411)
Q Consensus 229 V~ 230 (411)
+.
T Consensus 71 ~~ 72 (308)
T PRK14124 71 MR 72 (308)
T ss_pred EE
Confidence 75
No 49
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=97.17 E-value=0.001 Score=65.67 Aligned_cols=71 Identities=20% Similarity=0.272 Sum_probs=54.5
Q ss_pred CCcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEE
Q 015203 148 EPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIA 227 (411)
Q Consensus 148 d~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA 227 (411)
-+.+++||||.|+-+| .++..++...+..++...|-||-..||||+++-... .++.+.+.+ ..|+|.|
T Consensus 8 ~~Gil~i~KP~G~TS~--------dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~a--TKl~~~l~~--~~K~Y~a 75 (298)
T PRK03287 8 GSGLVVVDKPAGMTSH--------DVVARCRRLFGTRKVGHAGTLDPMATGVLVLGVERA--TKLLGHLTL--TDKSYTA 75 (298)
T ss_pred cCeEEEEeCCCCCCHH--------HHHHHHHHHhCCCCCCcCccCCCcceeEEEEEeChh--hhhhHHHhc--CCcEEEE
Confidence 3478999999999776 466777766666678889999999999999998853 333333432 4899999
Q ss_pred EEe
Q 015203 228 RVN 230 (411)
Q Consensus 228 ~V~ 230 (411)
.+.
T Consensus 76 ~~~ 78 (298)
T PRK03287 76 TIR 78 (298)
T ss_pred EEE
Confidence 875
No 50
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=97.17 E-value=0.0011 Score=65.24 Aligned_cols=70 Identities=21% Similarity=0.287 Sum_probs=54.5
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.+++||||+|+-+| .++..++...+..++...|-||-..||||+++-... -+|.+.+.. -.|+|.|.
T Consensus 2 ~Gil~i~KP~G~tS~--------dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~--~~K~Y~a~ 69 (290)
T PRK00130 2 DGILNILKPPGMTSF--------DVVRKIRKIAKIKKVGHTGTLDPLASGVLPVCLGKA--TKIVDYLME--GKKTYRAE 69 (290)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCCCccCcCCCCCCCCeeEEEEEEChh--hhhHHHhcc--CCcEEEEE
Confidence 368999999999776 466777766666678889999999999999998863 334444442 48999998
Q ss_pred Ee
Q 015203 229 VN 230 (411)
Q Consensus 229 V~ 230 (411)
+.
T Consensus 70 ~~ 71 (290)
T PRK00130 70 IK 71 (290)
T ss_pred EE
Confidence 76
No 51
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=97.13 E-value=0.0012 Score=65.44 Aligned_cols=70 Identities=23% Similarity=0.172 Sum_probs=54.1
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.+++||||.|+-+| .++..++...+..++...|-||-..||||+++-... -+|.+.+. .-.|+|.|.
T Consensus 13 ~Gil~i~KP~G~TS~--------dvv~~vrk~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~--~~~K~Y~a~ 80 (305)
T PRK05389 13 SGWLILDKPAGMTST--------EAVSKVKWLFDAQKAGHAGTLDPLASGVLPIALGEA--TKTVPYVM--DGTKRYRFT 80 (305)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhcccccCCcccCCCCCceEEEEEEChh--hhhhHHhc--cCCcEEEEE
Confidence 478999999999776 466777766665678889999999999999998763 34444343 248999998
Q ss_pred Ee
Q 015203 229 VN 230 (411)
Q Consensus 229 V~ 230 (411)
+.
T Consensus 81 ~~ 82 (305)
T PRK05389 81 VA 82 (305)
T ss_pred EE
Confidence 75
No 52
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=97.11 E-value=0.0012 Score=65.35 Aligned_cols=70 Identities=23% Similarity=0.200 Sum_probs=54.7
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.+|+||||+|+-+| .++..++...+..++...|-||-..||||+++-... .+|.+.+. ...|+|.|.
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~--~~~K~Y~~~ 70 (305)
T PRK14123 3 NGILPVYKERGLTSH--------DVVFKLRKILKTKKIGHTGTLDPEVAGVLPVCIGNA--TRVSDYVM--DMGKAYEAT 70 (305)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhCCCccccCcCCCCcCeeEEEEEEChh--hhhHHHhc--CCCcEEEEE
Confidence 368999999999776 466777766666678889999999999999998864 24444443 368999998
Q ss_pred Ee
Q 015203 229 VN 230 (411)
Q Consensus 229 V~ 230 (411)
+.
T Consensus 71 ~~ 72 (305)
T PRK14123 71 VS 72 (305)
T ss_pred EE
Confidence 75
No 53
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=97.11 E-value=0.0012 Score=65.02 Aligned_cols=69 Identities=20% Similarity=0.200 Sum_probs=54.8
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.+++||||.|+.+| .++..++...+..++...|-||-..||||+++-.... +|.+.+. . .|+|.|.
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~aT--kl~~~l~--~-~K~Y~a~ 69 (295)
T PRK02755 3 FGFLNLDKPAGLTSH--------DCVARLRRLLRLKRVGHGGTLDPAATGVLPIALGKAT--RLLPYLP--G-EKTYRGT 69 (295)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhCCCccccCCCCCCcCeeEEEEEEChhh--hhHHHhC--C-CcEEEEE
Confidence 368999999999776 5677777766667788999999999999999988743 4555454 3 7999998
Q ss_pred Ee
Q 015203 229 VN 230 (411)
Q Consensus 229 V~ 230 (411)
+.
T Consensus 70 ~~ 71 (295)
T PRK02755 70 IR 71 (295)
T ss_pred EE
Confidence 76
No 54
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=97.10 E-value=0.00072 Score=64.29 Aligned_cols=51 Identities=22% Similarity=0.284 Sum_probs=47.4
Q ss_pred cCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEe
Q 015203 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (411)
..+||+.++++-| ..||..+.++|.+|+|+||.++| ++++.|+.||.|.+.
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 3589999999986 79999999999999999999999 699999999999985
No 55
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=97.09 E-value=0.0013 Score=64.30 Aligned_cols=68 Identities=21% Similarity=0.356 Sum_probs=52.9
Q ss_pred EEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEe
Q 015203 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (411)
Q Consensus 151 ~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (411)
++++|||.|+.+| .++..++...+..++...|.||-..||||+++-... .++.+.+ ....|+|.|.+.
T Consensus 2 il~i~KP~G~tS~--------dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l--~~~~K~Y~a~~~ 69 (279)
T PRK02193 2 IKLLYKPKGISSF--------KFIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDED--TKLIDYL--DQKDKTYIAKIK 69 (279)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHcCCCccccCccCCCcCeeEEEEEEChh--hhhhHHh--ccCCcEEEEEEE
Confidence 6899999999776 456667765666678889999999999999998863 3344434 246899999876
No 56
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=97.08 E-value=0.0012 Score=61.81 Aligned_cols=40 Identities=25% Similarity=0.196 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEeee
Q 015203 92 GRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLH 131 (411)
Q Consensus 92 ~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~ 131 (411)
..|+++|+++|..|.|.|||++| .++|.|++||+|.|...
T Consensus 106 A~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k 146 (205)
T COG0522 106 AKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREK 146 (205)
T ss_pred cccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEeeec
Confidence 57999999999999999999999 79999999999998743
No 57
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=97.08 E-value=0.0015 Score=64.51 Aligned_cols=70 Identities=23% Similarity=0.207 Sum_probs=54.3
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.+++||||.|+-+| .++..++...+..++...+-||-..||||+++-... -+|.+.+. ...|+|.|.
T Consensus 16 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~--~~~K~Y~~~ 83 (303)
T PRK01851 16 DGVLLLDKPLGLSSN--------DALQRAKRLLRAKKAGHTGTLDPLATGLLPLCFGEA--TKFSQDLL--DADKTYEAT 83 (303)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCcccCCCCCCCCCCCceEEEEEECHH--HhhhHHhc--ccCeEEEEE
Confidence 479999999999776 467777766566678889999999999999998864 33444344 345999998
Q ss_pred Ee
Q 015203 229 VN 230 (411)
Q Consensus 229 V~ 230 (411)
+.
T Consensus 84 ~~ 85 (303)
T PRK01851 84 LR 85 (303)
T ss_pred EE
Confidence 76
No 58
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=97.07 E-value=0.0015 Score=64.63 Aligned_cols=70 Identities=23% Similarity=0.199 Sum_probs=54.4
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.+++||||+|+-+| .++..++...+..++...+-||-..||||+++-... .+|.+.+. .-.|+|.|.
T Consensus 2 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~--~~~K~Y~a~ 69 (304)
T PRK01550 2 NGVLLLHKPRGMTSH--------DCVFKLRKILRTKKVGHTGTLDPEVSGVLPICVGRA--TKIAEYLT--DEGKTYEGE 69 (304)
T ss_pred CeEEEEECCCCCCHH--------HHHHHHHHHcCCCCcccCCCCCCcCeeEEEEEEChh--hhhhHHhc--CCCcEEEEE
Confidence 368999999999776 466777776666778889999999999999998764 33444444 348999998
Q ss_pred Ee
Q 015203 229 VN 230 (411)
Q Consensus 229 V~ 230 (411)
+.
T Consensus 70 ~~ 71 (304)
T PRK01550 70 VT 71 (304)
T ss_pred EE
Confidence 76
No 59
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=97.07 E-value=0.0015 Score=65.20 Aligned_cols=70 Identities=20% Similarity=0.214 Sum_probs=53.9
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.+++||||.|+-+| .++..++...+..++...|.||-..||||+++-... .++.+.+. ...|+|.|.
T Consensus 3 nGiL~idKP~G~TS~--------dvv~~vrk~l~~kKVGH~GTLDP~AtGVL~i~vG~a--TKl~~~l~--~~~K~Y~a~ 70 (345)
T PRK14846 3 NYWLNIYKPRGISSA--------QLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEA--TKLIHLLI--DARKTYIFT 70 (345)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCCCcCCcCccCCCcCceEEEEEEChh--hhhhHHHh--cCCceEEEE
Confidence 468999999999776 466777766666778899999999999999998763 33333333 467899998
Q ss_pred Ee
Q 015203 229 VN 230 (411)
Q Consensus 229 V~ 230 (411)
+.
T Consensus 71 ~~ 72 (345)
T PRK14846 71 VK 72 (345)
T ss_pred EE
Confidence 76
No 60
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=97.07 E-value=0.0016 Score=64.67 Aligned_cols=70 Identities=20% Similarity=0.227 Sum_probs=54.6
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.+++||||.|+-+| .++..++...+..++...|-||-..||||+++-... -+|.+.+.. -.|+|.|.
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~~~~--~~K~Y~a~ 77 (312)
T PRK05033 10 NGVLLLDKPQGMSSN--------DALQKVKRLFNANKAGHTGALDPLATGMLPICLGEA--TKFSQYLLD--SDKRYRVT 77 (312)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCCCCCCCCCcCCCcCeeEEEEEECHH--hhhhHHhcC--CCcEEEEE
Confidence 478999999999876 466677765566678889999999999999998864 334444443 48999998
Q ss_pred Ee
Q 015203 229 VN 230 (411)
Q Consensus 229 V~ 230 (411)
+.
T Consensus 78 ~~ 79 (312)
T PRK05033 78 AR 79 (312)
T ss_pred EE
Confidence 76
No 61
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Probab=97.06 E-value=0.0015 Score=63.99 Aligned_cols=68 Identities=25% Similarity=0.271 Sum_probs=53.5
Q ss_pred EEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEe
Q 015203 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (411)
Q Consensus 151 ~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (411)
+++||||+|+-+| .++..++...+..++...|-||-..||||+++-+.. .+|.+.+.+ ..|+|.|.+.
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 ILLLDKPAGLTSH--------DVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEA--TKLSQYLLD--ADKTYRATVR 69 (277)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHhCcCccCCCCCCCCcCeEEEEEEEChH--HhhHHHhcC--CCcEEEEEEE
Confidence 7899999999776 466677766666678889999999999999998864 334444443 5899999876
No 62
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=97.04 E-value=0.0015 Score=64.69 Aligned_cols=72 Identities=21% Similarity=0.209 Sum_probs=54.9
Q ss_pred eCCcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEE
Q 015203 147 KEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYI 226 (411)
Q Consensus 147 Ed~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~Yl 226 (411)
-.+.+++||||.|+.+| .++..++...+..++...|-||-..||||+++-... .+|.+.+. ...|+|.
T Consensus 20 ~~~g~l~i~Kp~g~tS~--------~~v~~~r~~~~~kkvGH~GTLDp~A~GvL~v~~g~a--tk~~~~~~--~~~K~Y~ 87 (300)
T PRK04270 20 IKFGVVNLDKPPGPTSH--------EVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKA--TKVVQALL--ESGKEYV 87 (300)
T ss_pred cCCCEEEEECCCCCCHH--------HHHHHHHHHhccccccCCCCCCCcCeEEEEEEEChH--hhhhHHhc--cCCcEEE
Confidence 34679999999999776 456667665555678889999999999999998763 44444343 3459999
Q ss_pred EEEe
Q 015203 227 ARVN 230 (411)
Q Consensus 227 A~V~ 230 (411)
|.+.
T Consensus 88 ~~~~ 91 (300)
T PRK04270 88 CVMH 91 (300)
T ss_pred EEEE
Confidence 9875
No 63
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=96.97 E-value=0.0021 Score=63.31 Aligned_cols=70 Identities=23% Similarity=0.227 Sum_probs=53.6
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.+|+||||+|+-+| .++..++...+..++...|-||-..||||+++-... .++.+.+. ...|+|.|.
T Consensus 3 ~GiL~i~KP~G~TS~--------dvv~~vrk~~~~kKvGH~GTLDP~AtGvL~v~vG~a--TKl~~~l~--~~~K~Y~~~ 70 (292)
T PRK01528 3 NYWLNIYKPRGISSA--------KLVSIVKKILGKVKIGHAGTLDVEAEGVLPLAVGEA--TKLVQLLI--DAKKTYIFT 70 (292)
T ss_pred CEEEEEeCCCCCCHH--------HHHHHHHHHcCCCccCcCccCCCcCceEEEEEEChH--hhhhHHHh--cCCceEEEE
Confidence 468999999999776 466777765555678889999999999999998763 33333333 357999998
Q ss_pred Ee
Q 015203 229 VN 230 (411)
Q Consensus 229 V~ 230 (411)
+.
T Consensus 71 ~~ 72 (292)
T PRK01528 71 VK 72 (292)
T ss_pred EE
Confidence 76
No 64
>PRK11507 ribosome-associated protein; Provisional
Probab=96.93 E-value=0.0034 Score=48.54 Aligned_cols=54 Identities=17% Similarity=0.131 Sum_probs=45.2
Q ss_pred CCcCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEe
Q 015203 76 RWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (411)
Q Consensus 76 ~~~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (411)
..+-++|.++|.-.=-.-|=-+++.+|.+|.|+|||++. .-+.+|.+||.|.+.
T Consensus 8 ~~e~I~L~QlLK~~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~V~~~ 62 (70)
T PRK11507 8 KHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFA 62 (70)
T ss_pred CCCeEEHHHHHhhhCcccChHHHHHHHHcCceEECCEEecccCCCCCCCCEEEEC
Confidence 334589999998762235678899999999999999998 779999999999975
No 65
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=96.82 E-value=0.003 Score=62.65 Aligned_cols=68 Identities=26% Similarity=0.308 Sum_probs=53.4
Q ss_pred EEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEe
Q 015203 151 VLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (411)
Q Consensus 151 ~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (411)
+++||||.|+-+| .++..++...+..++...+-||-..||||+++-... -+|.+.+ ....|+|.|.+.
T Consensus 3 il~idKP~G~TS~--------dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~iG~a--TKl~~~l--~~~~K~Y~a~~~ 70 (312)
T PRK14122 3 VYAVDKPLGLTSH--------DVVNRARRALGTRRVGHTGTLDPLATGVLVLCTDDS--TKLVPFL--SAEDKEYLAWVS 70 (312)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHhCCCCCCCCCCCCCcCeeeEEEEEChh--hhhhHHh--cCCCceEEEEEE
Confidence 6899999999776 466777766666778889999999999999998864 3344444 257899999875
No 66
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=96.72 E-value=0.003 Score=60.09 Aligned_cols=51 Identities=18% Similarity=0.067 Sum_probs=45.9
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEe
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (411)
-|||+.+|.+.--.-||..|+.+|.+|.|.|||+.+ ++++.|..++.|.+.
T Consensus 2 k~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~ 53 (245)
T COG1189 2 KMRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVK 53 (245)
T ss_pred cchHHHHHHHccchhhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEc
Confidence 389999999984457999999999999999999999 899999999998875
No 67
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=96.66 E-value=0.0046 Score=61.04 Aligned_cols=70 Identities=19% Similarity=0.146 Sum_probs=54.6
Q ss_pred CcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEE
Q 015203 149 PDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIAR 228 (411)
Q Consensus 149 ~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~ 228 (411)
+.+++||||.|+-+| .++..++...+..++...+-||-..||||+++-... -+|.+.+. .-.|+|.|.
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~~G~a--Tkl~~~l~--~~~K~Y~a~ 77 (300)
T PRK04642 10 DGILLLDKPAGLSSN--------NALQAARRLLRAEKGGHTGSLDPLATGLLPLCFGEA--TKIAGLLL--GSAKAYDAE 77 (300)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhCCCcccCCCccCCcCeeeEEEEEChh--hhhhHHhc--CCCcEEEEE
Confidence 479999999999776 467777776666778889999999999999988763 34444333 467999998
Q ss_pred Ee
Q 015203 229 VN 230 (411)
Q Consensus 229 V~ 230 (411)
+.
T Consensus 78 ~~ 79 (300)
T PRK04642 78 IV 79 (300)
T ss_pred EE
Confidence 84
No 68
>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=96.64 E-value=0.004 Score=62.27 Aligned_cols=71 Identities=18% Similarity=0.237 Sum_probs=54.8
Q ss_pred CCcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEE
Q 015203 148 EPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIA 227 (411)
Q Consensus 148 d~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA 227 (411)
.+.+|+||||.|+-+| .++..++...+..++...+-||-..||||+++-... .+|.+.+. ...|+|.|
T Consensus 33 ~~G~l~i~KP~g~tS~--------~~v~~vr~~~~~kkvGH~GTLDP~A~GvL~v~~G~a--Tkl~~~~~--~~~K~Y~~ 100 (322)
T TIGR00425 33 SYGVVNLDKPSGPSSH--------EVVAWVRRILNVEKTGHGGTLDPKVTGVLPVCIERA--TRLVKSLQ--EAPKEYVC 100 (322)
T ss_pred CCCEEEEeCCCCCCHH--------HHHHHHHHHhcccccCCCCCCCCCCceEEEEEEChH--hhccHHhc--cCCCEEEE
Confidence 3579999999999776 466677766666678889999999999999998763 34443333 46899999
Q ss_pred EEe
Q 015203 228 RVN 230 (411)
Q Consensus 228 ~V~ 230 (411)
.+.
T Consensus 101 ~v~ 103 (322)
T TIGR00425 101 LMR 103 (322)
T ss_pred EEE
Confidence 875
No 69
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=96.32 E-value=0.0089 Score=58.29 Aligned_cols=69 Identities=25% Similarity=0.323 Sum_probs=53.7
Q ss_pred cEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEE
Q 015203 150 DVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARV 229 (411)
Q Consensus 150 ~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V 229 (411)
.++++|||.|+.+| .++..++...+..+....+-||-..||+|.++-. ++.+.+.- +. .-.|+|.|.+
T Consensus 16 Gil~ldKP~G~tS~--------~~v~~vkkil~~~K~GH~GTLDP~atGvLpi~ig-~aTKl~~~-l~--~~~K~Y~a~~ 83 (271)
T COG0130 16 GVINLDKPPGPTSH--------EVVAWVKRILGVEKAGHGGTLDPLATGVLPICLG-EATKLVQY-LL--DADKEYVATV 83 (271)
T ss_pred ceEEeeCCCCCCHH--------HHHHHHHHHhCccccccccccCCcccceEEEEec-hhHhHHHH-Hh--hCCcEEEEEE
Confidence 78999999999776 4666666666667788899999999999999988 44443332 32 3689999998
Q ss_pred e
Q 015203 230 N 230 (411)
Q Consensus 230 ~ 230 (411)
.
T Consensus 84 ~ 84 (271)
T COG0130 84 R 84 (271)
T ss_pred E
Confidence 6
No 70
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=96.21 E-value=0.013 Score=53.53 Aligned_cols=50 Identities=16% Similarity=0.106 Sum_probs=41.3
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEE
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISH 128 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~ 128 (411)
.+||+.+|.+.--.-|+..|+++|..|.|.|||++| .+++.|..+++-.|
T Consensus 102 erRLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I 152 (177)
T PRK04051 102 ERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLI 152 (177)
T ss_pred HhHHHHHHHHccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceE
Confidence 468888887763357999999999999999999999 89999998854333
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=96.18 E-value=0.013 Score=58.28 Aligned_cols=42 Identities=21% Similarity=0.217 Sum_probs=32.2
Q ss_pred CcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEe
Q 015203 185 PLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (411)
Q Consensus 185 ~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (411)
++...|-||-..||||+++-... .+.++. +.. ..|+|.|.+.
T Consensus 57 KiGH~GTLDPlAsGVLvvgvG~a-TK~l~~-~l~--~~K~Y~~~~~ 98 (312)
T cd02867 57 KIGHGGTLDPLATGVLVVGVGAG-TKQLQD-YLS--CSKTYEATGL 98 (312)
T ss_pred ccccccccCCccceeEEEEECcH-HHHHHH-Hhc--CCceEEEEEE
Confidence 56678999999999999998763 444443 332 8999999875
No 72
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=95.94 E-value=0.0018 Score=49.39 Aligned_cols=51 Identities=10% Similarity=0.013 Sum_probs=34.7
Q ss_pred cCchHHHHHHHhcCC-CCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEe
Q 015203 78 AGKTIVDLFAEEFKG-RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~-~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (411)
+-++|.++|... +. -|=.+|+.+|.+|.|+|||++. .-+.+|.+||.|.+.
T Consensus 6 e~I~L~qlLK~~-glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~~ 58 (65)
T PF13275_consen 6 EYITLGQLLKLA-GLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEID 58 (65)
T ss_dssp S---HHHHHHHH-TS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEET
T ss_pred CcEEHHHHHhHc-CCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEEC
Confidence 458999999877 44 3556889999999999999998 789999999999874
No 73
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=95.63 E-value=0.042 Score=42.78 Aligned_cols=51 Identities=10% Similarity=0.001 Sum_probs=43.8
Q ss_pred cCchHHHHHHHhcCC-CCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEe
Q 015203 78 AGKTIVDLFAEEFKG-RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~-~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (411)
+-++|.++|... +. -|=..|+.+|..|.|+|||++- .-+.+|..||.|.+.
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 348999999886 43 4667899999999999999988 789999999999875
No 74
>PLN00189 40S ribosomal protein S9; Provisional
Probab=94.46 E-value=0.04 Score=50.97 Aligned_cols=40 Identities=13% Similarity=0.158 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEeee
Q 015203 92 GRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLH 131 (411)
Q Consensus 92 ~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~ 131 (411)
.-|...|.++|..|.|.|||++| .|++.|..++++.|.+.
T Consensus 121 a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~ 161 (194)
T PLN00189 121 AKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFS 161 (194)
T ss_pred cCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEEe
Confidence 35788999999999999999999 89999999998887654
No 75
>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=94.26 E-value=0.1 Score=47.11 Aligned_cols=46 Identities=20% Similarity=0.224 Sum_probs=35.8
Q ss_pred chHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCE
Q 015203 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQK 125 (411)
Q Consensus 80 ~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~ 125 (411)
+||+-++-+.--.-|..+|.++|..|.|.|||++| .+++.|..+++
T Consensus 104 RRL~~vv~r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~E 150 (162)
T TIGR01018 104 RRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEE 150 (162)
T ss_pred HhHhhHhhhccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCC
Confidence 45544444431246889999999999999999999 89999998844
No 76
>PRK04313 30S ribosomal protein S4e; Validated
Probab=93.25 E-value=0.28 Score=46.83 Aligned_cols=73 Identities=12% Similarity=0.042 Sum_probs=53.7
Q ss_pred CcCchHHHHHHHhcCC-CCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEeeecCCCCCcCCCceEeeeCCcEEEE
Q 015203 77 WAGKTIVDLFAEEFKG-RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTV 154 (411)
Q Consensus 77 ~~g~rL~k~L~~~~~~-~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~~~~~~~~~IlyEd~~~ivv 154 (411)
.+.+.|.=+|.+.|+. .+.+++++.+.+|.|.|||++. +..+.|---|+|++.- .....+++|.....+++
T Consensus 35 ~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~~-------~~e~yRvl~d~kgr~~l 107 (237)
T PRK04313 35 EESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIPE-------TGEYYRVLPDEKGRLVL 107 (237)
T ss_pred ccccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEcc-------CCCeEEEEECCCCcEEE
Confidence 3457777777776554 5789999999999999999998 7888888889998741 12235677666655555
Q ss_pred eC
Q 015203 155 CK 156 (411)
Q Consensus 155 nK 156 (411)
.+
T Consensus 108 ~~ 109 (237)
T PRK04313 108 IP 109 (237)
T ss_pred EE
Confidence 43
No 77
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=93.10 E-value=0.13 Score=47.15 Aligned_cols=50 Identities=10% Similarity=0.040 Sum_probs=37.7
Q ss_pred chHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEe
Q 015203 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (411)
Q Consensus 80 ~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (411)
+||+-++.+.--.-|...|.++|..|.|.|||++| .+++.|+.+++-.|.
T Consensus 107 RRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I~ 157 (181)
T PTZ00155 107 RRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHID 157 (181)
T ss_pred HhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceEeccCccCcee
Confidence 45544444431235788999999999999999999 899999998764443
No 78
>PLN00036 40S ribosomal protein S4; Provisional
Probab=92.31 E-value=0.45 Score=46.10 Aligned_cols=73 Identities=11% Similarity=0.077 Sum_probs=54.1
Q ss_pred CcCchHHHHHHHhcCC-CCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEeeecCCCCCcCCCceEeeeCCcEEEE
Q 015203 77 WAGKTIVDLFAEEFKG-RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTV 154 (411)
Q Consensus 77 ~~g~rL~k~L~~~~~~-~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~~~~~~~~~IlyEd~~~ivv 154 (411)
.+.+.|.=+|.+.|+. .+.+++++.+.+|.|.|||++. +..+.+---|+|++.- .....+++|.....+++
T Consensus 39 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~k-------t~e~yRvl~D~kGrf~l 111 (261)
T PLN00036 39 RECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPK-------TNENFRLLYDTKGRFRL 111 (261)
T ss_pred ccccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcC-------CCCeEEEEECCCceEEE
Confidence 3457777777776654 5788999999999999999998 7788887889998741 12246677766665555
Q ss_pred eC
Q 015203 155 CK 156 (411)
Q Consensus 155 nK 156 (411)
++
T Consensus 112 ~~ 113 (261)
T PLN00036 112 HR 113 (261)
T ss_pred EE
Confidence 43
No 79
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=92.20 E-value=0.46 Score=46.29 Aligned_cols=73 Identities=11% Similarity=-0.018 Sum_probs=53.7
Q ss_pred CcCchHHHHHHHhcCC-CCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEeeecCCCCCcCCCceEeeeCCcEEEE
Q 015203 77 WAGKTIVDLFAEEFKG-RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTV 154 (411)
Q Consensus 77 ~~g~rL~k~L~~~~~~-~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~~~~~~~~~IlyEd~~~ivv 154 (411)
.+.+.|.=+|.+.|+. .+.+++++.+.+|.|.|||++. +..+.|---|+|++.- .....+++|.....+++
T Consensus 36 ~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~k-------t~e~yRvl~D~kGrf~l 108 (273)
T PTZ00223 36 RECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPK-------TGDRFRILYDVKGRFAL 108 (273)
T ss_pred ccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcC-------CCCeEEEEECCCCcEEE
Confidence 3457777777776654 5788999999999999999998 7888888889998741 12246677766665555
Q ss_pred eC
Q 015203 155 CK 156 (411)
Q Consensus 155 nK 156 (411)
.+
T Consensus 109 ~~ 110 (273)
T PTZ00223 109 VK 110 (273)
T ss_pred EE
Confidence 43
No 80
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=91.92 E-value=0.5 Score=45.76 Aligned_cols=72 Identities=17% Similarity=0.066 Sum_probs=52.6
Q ss_pred CcCchHHHHHHHhcCC-CCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEeeecCCCCCcCCCceEeeeCCcEEEE
Q 015203 77 WAGKTIVDLFAEEFKG-RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTV 154 (411)
Q Consensus 77 ~~g~rL~k~L~~~~~~-~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~~~~~~~~~IlyEd~~~ivv 154 (411)
.+.+.|.=+|.+.|+. .+.+++++.+.+|.|.|||++. +..+.|---|+|++.- .....+++|.....+++
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 3457777777776654 5789999999999999999998 7788888889998741 11235666666555554
Q ss_pred e
Q 015203 155 C 155 (411)
Q Consensus 155 n 155 (411)
.
T Consensus 112 ~ 112 (262)
T PTZ00118 112 H 112 (262)
T ss_pred E
Confidence 4
No 81
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=89.84 E-value=0.32 Score=38.83 Aligned_cols=43 Identities=26% Similarity=0.500 Sum_probs=34.4
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecCCceecCCCEEEEe
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHF 129 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~ 129 (411)
+-++.+.+.. + +.+..+ =|.|.|||+.+..+++++.||.|.++
T Consensus 32 ~~tvkd~IEs-L-GVP~tE------V~~i~vNG~~v~~~~~~~~Gd~v~V~ 74 (81)
T PF14451_consen 32 GATVKDVIES-L-GVPHTE------VGLILVNGRPVDFDYRLKDGDRVAVY 74 (81)
T ss_pred CCcHHHHHHH-c-CCChHH------eEEEEECCEECCCcccCCCCCEEEEE
Confidence 4566565554 4 577664 57899999999999999999999987
No 82
>PRK01777 hypothetical protein; Validated
Probab=89.35 E-value=0.38 Score=39.58 Aligned_cols=52 Identities=4% Similarity=0.011 Sum_probs=39.7
Q ss_pred CcCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecCCceecCCCEEEEee
Q 015203 77 WAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFL 130 (411)
Q Consensus 77 ~~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~~ 130 (411)
.+|.++.+.+... +. ...+-+--+..+.|-|||+.+..++.|+.||+|.++.
T Consensus 24 p~GtTv~dal~~s-gi-~~~~pei~~~~~~vgI~Gk~v~~d~~L~dGDRVeIyr 75 (95)
T PRK01777 24 QEGATVEEAIRAS-GL-LELRTDIDLAKNKVGIYSRPAKLTDVLRDGDRVEIYR 75 (95)
T ss_pred CCCCcHHHHHHHc-CC-CccCcccccccceEEEeCeECCCCCcCCCCCEEEEec
Confidence 4578999999886 43 3332122345689999999999999999999999983
No 83
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=89.13 E-value=0.78 Score=43.48 Aligned_cols=55 Identities=16% Similarity=0.092 Sum_probs=41.9
Q ss_pred HHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEeeecCCCCCcCCCceEeeeCCcEEEEeC
Q 015203 95 YDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVCK 156 (411)
Q Consensus 95 r~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~~~~~e~~~~~~~~~IlyEd~~~ivvnK 156 (411)
-|++++.|.+|.|+|||++. +..+.|---|+|++. ...+..+|+|.....+++++
T Consensus 57 ~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip-------~tgE~yRvl~d~~grl~l~~ 112 (241)
T COG1471 57 AREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIP-------KTGEHYRVLPDEKGRLVLHP 112 (241)
T ss_pred hHHHHHHHhcCcEEECCEEeccccCCcceEEEEEEC-------CCCceEEEEecCCccEEEEe
Confidence 47899999999999999988 666666666988874 12224678888877777765
No 84
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=85.08 E-value=1 Score=43.10 Aligned_cols=22 Identities=27% Similarity=0.327 Sum_probs=18.8
Q ss_pred CcccccCCCCCCceEEEEEcCh
Q 015203 185 PLFPVHRLDRLVSGLLILARNA 206 (411)
Q Consensus 185 ~l~pVhRLDr~TSGLLL~Akd~ 206 (411)
.+..+||||-.|||++||.-..
T Consensus 90 ~V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559|consen 90 DVQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred ceeeEEeecccccceEEEecCc
Confidence 3667999999999999998653
No 85
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=81.77 E-value=2.1 Score=44.45 Aligned_cols=48 Identities=19% Similarity=0.210 Sum_probs=39.2
Q ss_pred cCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCE
Q 015203 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQK 125 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~ 125 (411)
.+..|.++|.+.--..|+++++++|.+|.|+|||+++ +..+.+.+.+.
T Consensus 341 ~~~~~~~~l~~~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~~ 389 (410)
T PRK13354 341 ETKNLVDLLVDLGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPEDA 389 (410)
T ss_pred CCCCHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhhh
Confidence 3688999998763357899999999999999999998 66777766553
No 86
>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=80.68 E-value=2.1 Score=38.11 Aligned_cols=43 Identities=19% Similarity=0.267 Sum_probs=30.1
Q ss_pred CCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEEEEEe
Q 015203 184 APLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYIARVN 230 (411)
Q Consensus 184 ~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~YlA~V~ 230 (411)
.++...|.||-..||||+++-+.. -+|.+.+.. ..|+|.|...
T Consensus 7 ~KvGH~GTLDP~AsGvL~v~vg~~--Tkl~~~l~~--~~K~Y~~~~~ 49 (149)
T PF01509_consen 7 KKVGHGGTLDPFASGVLVVGVGKA--TKLLSYLQN--SDKEYVATIR 49 (149)
T ss_dssp SSEEESS-SSTT-EEEEEEEEGGG--GGGHHHHTT--SEEEEEEEEE
T ss_pred ceeccccccCCcceEEEEEEECCc--chHHHHhhc--cCCEEEEEEE
Confidence 457779999999999999998653 334444543 4599999765
No 87
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=78.50 E-value=5.2 Score=41.53 Aligned_cols=44 Identities=18% Similarity=0.235 Sum_probs=36.1
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecC
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKS 122 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~ 122 (411)
+..|.++|.+.--..|+++++++|++|.|+|||++| +..+.+..
T Consensus 342 ~~~~~~~l~~~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~ 386 (408)
T PRK05912 342 GIDLLALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTA 386 (408)
T ss_pred CCcHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEecCccccccc
Confidence 578999998762347999999999999999999998 55655554
No 88
>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=78.17 E-value=4.6 Score=31.20 Aligned_cols=50 Identities=20% Similarity=0.204 Sum_probs=32.7
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecCCceecCCCEEEEe
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHF 129 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~ 129 (411)
+.++.+++.......+.- .......-.|.|||+.+..++.|+.||+|.+.
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 567766655431112210 22233344689999999999999999999986
No 89
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=73.70 E-value=3.6 Score=31.67 Aligned_cols=42 Identities=29% Similarity=0.453 Sum_probs=32.8
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEec----CCceecCCCEEEEe
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVP----VSYTVKSSQKISHF 129 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~----~~~~v~~gD~I~~~ 129 (411)
+.++.++|++. +.-++.. .|.+||+++. .+..++.||+|++.
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 38999999886 5444322 4678999997 89999999999874
No 90
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=72.19 E-value=8.1 Score=29.58 Aligned_cols=43 Identities=12% Similarity=0.142 Sum_probs=33.2
Q ss_pred cCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecCCceecCCCEEEEe
Q 015203 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHF 129 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~ 129 (411)
.+.++.++|... + .+. +.-.|.+||+.+..++.|+.||+|.+.
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 357888888764 3 332 234678999999999999999999875
No 91
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.27 E-value=5.6 Score=36.36 Aligned_cols=53 Identities=17% Similarity=0.170 Sum_probs=42.0
Q ss_pred CCcCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEe
Q 015203 76 RWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (411)
Q Consensus 76 ~~~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (411)
.....+|+.+|++++ ++||+.++++|+.|.|..+-... ....+++.|-.|.++
T Consensus 135 ~p~qlrl~~Ll~seL-~LSrS~lq~lie~g~Irgdtd~~~l~rkrlr~~~~i~Id 188 (203)
T COG4332 135 RPFQLRLDRLLASEL-GLSRSELQRLIETGQIRGDTDKMLLLRKRLRAGYDIQID 188 (203)
T ss_pred CcchhHHHHHHHHHh-CcCHHHHHHHHHcCceeecchHHHHhhhhhhcCcEEEEE
Confidence 344689999999996 79999999999999999887654 345566677666665
No 92
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=70.04 E-value=0.91 Score=31.15 Aligned_cols=13 Identities=46% Similarity=0.869 Sum_probs=10.7
Q ss_pred hccceeeeeeccC
Q 015203 378 ACGYIVFDTLDLD 390 (411)
Q Consensus 378 ~~~~i~~~~~~~~ 390 (411)
.|++|||++-|++
T Consensus 24 ~C~G~W~d~~el~ 36 (41)
T PF13453_consen 24 SCGGIWFDAGELE 36 (41)
T ss_pred CCCeEEccHHHHH
Confidence 6899999987754
No 93
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=69.86 E-value=3.5 Score=32.46 Aligned_cols=44 Identities=14% Similarity=0.283 Sum_probs=30.9
Q ss_pred hHHHHHHHhcCCCCHHHHHHHHHcCc--EEECCEEecCCceecCCCEEEEe
Q 015203 81 TIVDLFAEEFKGRPYDYYVSAVKCGR--IQVDEEMVPVSYTVKSSQKISHF 129 (411)
Q Consensus 81 rL~k~L~~~~~~~Sr~~~~~~I~~G~--V~VNGk~v~~~~~v~~gD~I~~~ 129 (411)
.|.+.|...++.. ......|. +.||+..+..++.|+.||+|.+.
T Consensus 30 ~l~~~L~~~~~~~-----~~~~~~~~~~~aVN~~~~~~~~~l~dgDeVai~ 75 (81)
T PRK11130 30 ALRQHLAQKGDRW-----ALALEDGKLLAAVNQTLVSFDHPLTDGDEVAFF 75 (81)
T ss_pred HHHHHHHHhCccH-----HhhhcCCCEEEEECCEEcCCCCCCCCCCEEEEe
Confidence 4555666654332 22334554 67899998889999999999987
No 94
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=69.22 E-value=5.6 Score=29.78 Aligned_cols=43 Identities=21% Similarity=0.358 Sum_probs=31.4
Q ss_pred cCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEec----CCceecCCCEEEEe
Q 015203 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVP----VSYTVKSSQKISHF 129 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~----~~~~v~~gD~I~~~ 129 (411)
++.+|.++|... +.-+..- .|.+||+.+. ..+.|+.||+|.+.
T Consensus 14 ~~~tl~~lL~~l-~~~~~~v--------av~vNg~iv~r~~~~~~~l~~gD~vei~ 60 (66)
T PRK05659 14 DGESVAALLARE-GLAGRRV--------AVEVNGEIVPRSQHASTALREGDVVEIV 60 (66)
T ss_pred CCCCHHHHHHhc-CCCCCeE--------EEEECCeEeCHHHcCcccCCCCCEEEEE
Confidence 467898888774 4322211 3789999886 68899999999875
No 95
>PRK06437 hypothetical protein; Provisional
Probab=68.92 E-value=6.6 Score=29.93 Aligned_cols=43 Identities=14% Similarity=0.071 Sum_probs=32.8
Q ss_pred cCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecCCceecCCCEEEEe
Q 015203 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHF 129 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~ 129 (411)
++.++.++|... + ++... + .|.+||+++..++.|+.||.|.+.
T Consensus 19 ~~~tv~dLL~~L-g-i~~~~----v---aV~vNg~iv~~~~~L~dgD~Veiv 61 (67)
T PRK06437 19 HELTVNDIIKDL-G-LDEEE----Y---VVIVNGSPVLEDHNVKKEDDVLIL 61 (67)
T ss_pred CCCcHHHHHHHc-C-CCCcc----E---EEEECCEECCCceEcCCCCEEEEE
Confidence 457898988774 4 33221 1 467999999999999999999875
No 96
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=67.92 E-value=9 Score=33.87 Aligned_cols=35 Identities=17% Similarity=0.110 Sum_probs=30.7
Q ss_pred CCcCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECC
Q 015203 76 RWAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDE 111 (411)
Q Consensus 76 ~~~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNG 111 (411)
.....||+.+|++.| .+||+.+++++.+|.|..+-
T Consensus 99 ~~~~~Rld~lLa~~L-~lSrs~l~~l~~~G~I~~~~ 133 (142)
T PF06353_consen 99 FPFPLRLDRLLARQL-GLSRSRLKRLIEQGLIRSDP 133 (142)
T ss_pred CCCCccHHHHHHHHh-CcCHHHHHHHHHCCCEEecC
Confidence 344689999999997 79999999999999998763
No 97
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=63.22 E-value=13 Score=28.95 Aligned_cols=24 Identities=17% Similarity=0.304 Sum_probs=22.0
Q ss_pred cEEECCEEecCCceecCCCEEEEe
Q 015203 106 RIQVDEEMVPVSYTVKSSQKISHF 129 (411)
Q Consensus 106 ~V~VNGk~v~~~~~v~~gD~I~~~ 129 (411)
.|.||++.+..+..|+.||+|.+.
T Consensus 51 ~v~vn~~~v~~~~~l~dgDevai~ 74 (80)
T TIGR01682 51 MVAVNEEYVTDDALLNEGDEVAFI 74 (80)
T ss_pred EEEECCEEcCCCcCcCCCCEEEEe
Confidence 588999999889999999999986
No 98
>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=62.62 E-value=8.1 Score=28.96 Aligned_cols=42 Identities=24% Similarity=0.387 Sum_probs=30.6
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecCC----ceecCCCEEEEe
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVS----YTVKSSQKISHF 129 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~~----~~v~~gD~I~~~ 129 (411)
+.++.++|... + .+. +.+ .|.|||+.+..+ +.|+.||+|.+.
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 57888888774 3 332 111 467899999766 899999999875
No 99
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=60.64 E-value=22 Score=27.73 Aligned_cols=24 Identities=17% Similarity=0.295 Sum_probs=22.0
Q ss_pred cEEECCEEecCCceecCCCEEEEe
Q 015203 106 RIQVDEEMVPVSYTVKSSQKISHF 129 (411)
Q Consensus 106 ~V~VNGk~v~~~~~v~~gD~I~~~ 129 (411)
.|.|||+.+..++.|+.||+|.+.
T Consensus 53 ~vavN~~~v~~~~~l~dgDeVai~ 76 (82)
T PLN02799 53 VLALNEEYTTESAALKDGDELAII 76 (82)
T ss_pred EEEECCEEcCCCcCcCCCCEEEEe
Confidence 578999999999999999999986
No 100
>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=60.00 E-value=9.4 Score=28.35 Aligned_cols=24 Identities=8% Similarity=0.245 Sum_probs=20.2
Q ss_pred cEEECCEEecCCceecCCCEEEEe
Q 015203 106 RIQVDEEMVPVSYTVKSSQKISHF 129 (411)
Q Consensus 106 ~V~VNGk~v~~~~~v~~gD~I~~~ 129 (411)
...|||+.+.+++.|+.||.|++.
T Consensus 36 ~A~Vng~~vdl~~~L~~~d~v~ii 59 (60)
T PF02824_consen 36 AAKVNGQLVDLDHPLEDGDVVEII 59 (60)
T ss_dssp EEEETTEEEETTSBB-SSEEEEEE
T ss_pred EEEEcCEECCCCCCcCCCCEEEEE
Confidence 457999999999999999999863
No 101
>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=59.10 E-value=10 Score=28.88 Aligned_cols=50 Identities=20% Similarity=0.214 Sum_probs=32.7
Q ss_pred CcCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecC---CceecCCCEEEEe
Q 015203 77 WAGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPV---SYTVKSSQKISHF 129 (411)
Q Consensus 77 ~~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~---~~~v~~gD~I~~~ 129 (411)
.++.+|.++|.......+.-. ....=.|.|||+.+.. ++.|+.||+|.+.
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 346777776665411111111 2233467899999987 9999999999986
No 102
>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=54.30 E-value=25 Score=28.65 Aligned_cols=24 Identities=4% Similarity=0.212 Sum_probs=20.5
Q ss_pred cEEECCEEec----CCceecCCCEEEEe
Q 015203 106 RIQVDEEMVP----VSYTVKSSQKISHF 129 (411)
Q Consensus 106 ~V~VNGk~v~----~~~~v~~gD~I~~~ 129 (411)
.|.|||..+. .++.|+.||+|.+.
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 57999999999987
No 103
>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=53.71 E-value=12 Score=29.61 Aligned_cols=24 Identities=21% Similarity=0.245 Sum_probs=20.0
Q ss_pred cEEECCEEecCCc--eecCCCEEEEe
Q 015203 106 RIQVDEEMVPVSY--TVKSSQKISHF 129 (411)
Q Consensus 106 ~V~VNGk~v~~~~--~v~~gD~I~~~ 129 (411)
.|.|||+.+..+. .|+.||+|.+.
T Consensus 57 ~v~vN~~~v~~~~~~~l~dgdev~i~ 82 (88)
T TIGR01687 57 IILVNGRNVDWGLGTELKDGDVVAIF 82 (88)
T ss_pred EEEECCEecCccCCCCCCCCCEEEEe
Confidence 5789999996554 89999999986
No 104
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=50.45 E-value=18 Score=27.04 Aligned_cols=42 Identities=19% Similarity=0.237 Sum_probs=29.4
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecC----CceecCCCEEEEe
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPV----SYTVKSSQKISHF 129 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~----~~~v~~gD~I~~~ 129 (411)
..+|.++|... +.-+. .+ .|-||++.+.. ++.|+.||+|.+.
T Consensus 14 ~~tl~~Ll~~l-~~~~~-----~v---avavN~~iv~~~~~~~~~L~dgD~Ieiv 59 (65)
T PRK06488 14 ATTLALLLAEL-DYEGN-----WL---ATAVNGELVHKEARAQFVLHEGDRIEIL 59 (65)
T ss_pred cCcHHHHHHHc-CCCCC-----eE---EEEECCEEcCHHHcCccccCCCCEEEEE
Confidence 35788887663 32221 11 37899999964 7889999999976
No 105
>PRK07440 hypothetical protein; Provisional
Probab=45.88 E-value=29 Score=26.61 Aligned_cols=43 Identities=14% Similarity=0.235 Sum_probs=31.1
Q ss_pred cCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEec----CCceecCCCEEEEe
Q 015203 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVP----VSYTVKSSQKISHF 129 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~----~~~~v~~gD~I~~~ 129 (411)
++.+|.++|... +.-++. =.|-+||+.+. ..+.|+.||.|.+.
T Consensus 18 ~~~tl~~lL~~l-~~~~~~--------vav~~N~~iv~r~~w~~~~L~~gD~IEIv 64 (70)
T PRK07440 18 SGTSLPDLLQQL-GFNPRL--------VAVEYNGEILHRQFWEQTQVQPGDRLEIV 64 (70)
T ss_pred CCCCHHHHHHHc-CCCCCe--------EEEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 368899988764 332211 14678999997 68899999999874
No 106
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=42.13 E-value=25 Score=29.16 Aligned_cols=35 Identities=20% Similarity=0.416 Sum_probs=29.0
Q ss_pred HHHHHHHHHcCcEEECCEEe-cCCceecCCCEEEEe
Q 015203 95 YDYYVSAVKCGRIQVDEEMV-PVSYTVKSSQKISHF 129 (411)
Q Consensus 95 r~~~~~~I~~G~V~VNGk~v-~~~~~v~~gD~I~~~ 129 (411)
+.++-.+|++|+=+|.++.. .....+++||.|.+.
T Consensus 8 ~eeylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~ 43 (111)
T COG4043 8 REEYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFN 43 (111)
T ss_pred HHHHHHHHHcccceEEEEecCHhhcCCCCCCEEEEc
Confidence 56778899999999999888 456779999998765
No 107
>COG3531 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=41.92 E-value=8.6 Score=35.84 Aligned_cols=17 Identities=41% Similarity=0.769 Sum_probs=14.2
Q ss_pred cccCCCCCCCCCCCCCc
Q 015203 355 FSIDPMCTNCPNLAPKD 371 (411)
Q Consensus 355 ~~~~~~c~~c~~~~~~~ 371 (411)
+..||||-||+...|.-
T Consensus 6 YifDPmCgWCyGa~Pll 22 (212)
T COG3531 6 YIFDPMCGWCYGAAPLL 22 (212)
T ss_pred EecCcchhhhhCccHHH
Confidence 56799999999988754
No 108
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=40.71 E-value=33 Score=35.53 Aligned_cols=39 Identities=18% Similarity=0.285 Sum_probs=30.2
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEe-cCCcee
Q 015203 82 IVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMV-PVSYTV 120 (411)
Q Consensus 82 L~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v 120 (411)
+.+.|....-..||+++++.|..|.|++||+++ +.++.+
T Consensus 338 ~~~~lv~~~L~psr~earr~i~~g~v~in~~~v~d~~~~~ 377 (401)
T COG0162 338 LVDLLVDAGLAPSRSEARRLIQQGGVKINGEKVEDENYVL 377 (401)
T ss_pred HHHHHHHhCCcccHHHHHhhcccCCEEECCEeccccccch
Confidence 555566653467899999999999999999988 555444
No 109
>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=38.71 E-value=35 Score=25.17 Aligned_cols=25 Identities=12% Similarity=0.092 Sum_probs=18.6
Q ss_pred cCcEEECCEEecC--CceecCCCEEEE
Q 015203 104 CGRIQVDEEMVPV--SYTVKSSQKISH 128 (411)
Q Consensus 104 ~G~V~VNGk~v~~--~~~v~~gD~I~~ 128 (411)
..-++|||+++.. .+.|+.||.|.+
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 4568999999966 678899999875
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=38.51 E-value=42 Score=24.91 Aligned_cols=42 Identities=24% Similarity=0.340 Sum_probs=30.0
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEec----CCceecCCCEEEEe
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVP----VSYTVKSSQKISHF 129 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~----~~~~v~~gD~I~~~ 129 (411)
+.+|.++|... +.-+ ..-.|.+||+.+. ..+.|+.||+|.+.
T Consensus 13 ~~tv~~ll~~l-~~~~--------~~v~v~vN~~iv~~~~~~~~~L~~gD~veii 58 (64)
T TIGR01683 13 GLTLAALLESL-GLDP--------RRVAVAVNGEIVPRSEWDDTILKEGDRIEIV 58 (64)
T ss_pred CCcHHHHHHHc-CCCC--------CeEEEEECCEEcCHHHcCceecCCCCEEEEE
Confidence 57888888764 3322 2235789999984 24689999999875
No 111
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=38.30 E-value=31 Score=35.53 Aligned_cols=77 Identities=19% Similarity=0.172 Sum_probs=50.9
Q ss_pred eCCcEEEEeCCCCceeecCCCCCCchHHHHHhhccCCCCcccccCCCCCCceEEEEEcChHHHHHHHHhhhcCeecEEEE
Q 015203 147 KEPDVLTVCKPPSVPVHPCGQYRKNTVVGILQAEHDLAPLFPVHRLDRLVSGLLILARNASKADLFRQQIEAGKVIKRYI 226 (411)
Q Consensus 147 Ed~~~ivvnKP~Gl~v~~~~~~~~~tv~~~l~~~~~~~~l~pVhRLDr~TSGLLL~Akd~~~a~~L~~~~~~~~v~K~Yl 226 (411)
-.-.+++++||+ +|+.. .++..+.+........-.+-||=+.||+++...+.......+ .....|+|.
T Consensus 66 ~~sgv~~i~kpa----~pss~----e~~swvk~iL~~ek~Gh~gTlDP~vtg~l~v~~~~~tr~~~s----~~s~gk~yv 133 (395)
T KOG2529|consen 66 SRSGVINIDKPA----NPSSH----EVVSWVKNILRVEKTGHSGTLDPEVTGCLIVCIDRATRLLKS----QQSAGKEYV 133 (395)
T ss_pred hhcCceeccCCC----CCchH----HHHHHHHHHhhHHHhCCCCCCCccccceEEEEeecccccccc----hhccCcEEE
Confidence 334578999999 44433 344444433222445678999999999999999866433332 236889999
Q ss_pred EEEecccCC
Q 015203 227 ARVNGVFPE 235 (411)
Q Consensus 227 A~V~G~~~~ 235 (411)
+++....+-
T Consensus 134 g~~~lt~~v 142 (395)
T KOG2529|consen 134 GIGKLTPEV 142 (395)
T ss_pred EEEecCcch
Confidence 888876543
No 112
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=38.22 E-value=33 Score=25.97 Aligned_cols=41 Identities=12% Similarity=0.141 Sum_probs=28.4
Q ss_pred chHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecC----CceecCCCEEEEe
Q 015203 80 KTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPV----SYTVKSSQKISHF 129 (411)
Q Consensus 80 ~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~----~~~v~~gD~I~~~ 129 (411)
.+|.++|... +.-+.. =.|.+||+.+.. .+.|+.||.|.+.
T Consensus 17 ~tv~~lL~~l-~~~~~~--------vav~vN~~iv~r~~w~~~~L~~gD~iEIv 61 (67)
T PRK07696 17 KTVAELLTHL-ELDNKI--------VVVERNKDILQKDDHTDTSVFDGDQIEIV 61 (67)
T ss_pred ccHHHHHHHc-CCCCCe--------EEEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 4688888763 432221 147889999964 4889999999864
No 113
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=35.83 E-value=43 Score=24.72 Aligned_cols=42 Identities=19% Similarity=0.328 Sum_probs=30.4
Q ss_pred cCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecC----CceecCCCEEEEe
Q 015203 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPV----SYTVKSSQKISHF 129 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~----~~~v~~gD~I~~~ 129 (411)
++.+|.++|... +..+ .=.|.|||+.+.. ...|+.||+|.+.
T Consensus 14 ~~~tl~~ll~~l-~~~~---------~~~v~vN~~~v~~~~~~~~~L~~gD~vei~ 59 (65)
T PRK06944 14 DGATVADALAAY-GARP---------PFAVAVNGDFVARTQHAARALAAGDRLDLV 59 (65)
T ss_pred CCCcHHHHHHhh-CCCC---------CeEEEECCEEcCchhcccccCCCCCEEEEE
Confidence 357888888764 3321 1257899999843 6789999999976
No 114
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=34.65 E-value=52 Score=24.68 Aligned_cols=42 Identities=17% Similarity=0.404 Sum_probs=28.8
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEec----CCceecCCCEEEEe
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVP----VSYTVKSSQKISHF 129 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~----~~~~v~~gD~I~~~ 129 (411)
+.+|.++|... +.-.+. =.|-||++.+. ..+.|+.||.|.+.
T Consensus 15 ~~tl~~ll~~l-~~~~~~--------vaVavN~~iv~r~~w~~~~L~~gD~Ieii 60 (66)
T PRK08053 15 GQTVHELLEQL-NQLQPG--------AALAINQQIIPREQWAQHIVQDGDQILLF 60 (66)
T ss_pred CCCHHHHHHHc-CCCCCc--------EEEEECCEEeChHHcCccccCCCCEEEEE
Confidence 57888888763 322111 14678999995 45689999999875
No 115
>KOG3301 consensus Ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=34.39 E-value=48 Score=29.95 Aligned_cols=30 Identities=17% Similarity=0.238 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHcCcEEECCEEe-cCCceecC
Q 015203 93 RPYDYYVSAVKCGRIQVDEEMV-PVSYTVKS 122 (411)
Q Consensus 93 ~Sr~~~~~~I~~G~V~VNGk~v-~~~~~v~~ 122 (411)
.|--.+..+|..+.|.|++++| -++++|+.
T Consensus 110 kSIhhARvLi~~rhI~V~~qiV~IPsf~vrl 140 (183)
T KOG3301|consen 110 KSIHHARVLIRQRHIRVGKQIVNIPSFMVRL 140 (183)
T ss_pred hhhHHHHHHhcCccEEecCeEeeccceeEee
Confidence 5667788999999999999999 68998884
No 116
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=32.74 E-value=41 Score=37.35 Aligned_cols=28 Identities=14% Similarity=0.439 Sum_probs=23.9
Q ss_pred cEEECCEEecCCceecCCCEEEEeeecC
Q 015203 106 RIQVDEEMVPVSYTVKSSQKISHFLHRH 133 (411)
Q Consensus 106 ~V~VNGk~v~~~~~v~~gD~I~~~~~~~ 133 (411)
-.+|||+.+..++.|+.||.|.|....+
T Consensus 424 gAkVnG~ivpl~~~Lk~Gd~VEIit~k~ 451 (701)
T COG0317 424 GAKVNGRIVPLTTKLQTGDQVEIITSKH 451 (701)
T ss_pred EEEECCEEeccceecCCCCEEEEEeCCC
Confidence 3688999999999999999999875544
No 117
>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=32.72 E-value=38 Score=26.47 Aligned_cols=47 Identities=13% Similarity=0.169 Sum_probs=30.2
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHc---C-cEEECCEEecCCceecCCCEEEEe
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKC---G-RIQVDEEMVPVSYTVKSSQKISHF 129 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~---G-~V~VNGk~v~~~~~v~~gD~I~~~ 129 (411)
|-++.++..... ++.++.+.-+ | .+.++|+.|..++.|+.||+|++.
T Consensus 24 GaTV~D~a~~iH----~di~~~f~~A~v~g~s~~~~gq~Vgl~~~L~d~DvVeI~ 74 (75)
T cd01666 24 GSTVEDVCNKIH----KDLVKQFKYALVWGSSVKHSPQRVGLDHVLEDEDVVQIV 74 (75)
T ss_pred CCCHHHHHHHHH----HHHHHhCCeeEEeccCCcCCCeECCCCCEecCCCEEEEe
Confidence 667777665531 2222222211 1 233699999999999999999874
No 118
>TIGR00234 tyrS tyrosyl-tRNA synthetase. This tyrosyl-tRNA synthetase model starts picking up tryptophanyl-tRNA synthetases at scores of 0 and below. The proteins found by this model have a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples.
Probab=32.19 E-value=90 Score=32.04 Aligned_cols=37 Identities=19% Similarity=0.099 Sum_probs=31.8
Q ss_pred CchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEec
Q 015203 79 GKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVP 115 (411)
Q Consensus 79 g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~ 115 (411)
+.++.+++...--..|++++.+.|++|.|+|||..+.
T Consensus 329 ~~~~~~~~~~~~~~~S~~~arr~ik~g~v~vn~~~i~ 365 (377)
T TIGR00234 329 DITLADLLVLSGLFPSKSEARRDIKQGGVYINGEKVT 365 (377)
T ss_pred CcCHHHHHHHcCCCcChHHHHHHHHhCCEEECCEecc
Confidence 4889998887633578999999999999999999884
No 119
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=31.18 E-value=44 Score=37.29 Aligned_cols=27 Identities=22% Similarity=0.283 Sum_probs=22.9
Q ss_pred cEEECCEEecCCceecCCCEEEEeeec
Q 015203 106 RIQVDEEMVPVSYTVKSSQKISHFLHR 132 (411)
Q Consensus 106 ~V~VNGk~v~~~~~v~~gD~I~~~~~~ 132 (411)
..+|||+.|.+++.|+.||.|+|-...
T Consensus 423 gAkVNg~~vpL~~~L~~Gd~VeIiT~~ 449 (702)
T PRK11092 423 GARVDRQPYPLSQPLTSGQTVEIITAP 449 (702)
T ss_pred EEEECCEECCCCccCCCCCEEEEEeCC
Confidence 358899999999999999999976433
No 120
>cd01616 TGS The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=30.97 E-value=58 Score=22.37 Aligned_cols=22 Identities=27% Similarity=0.489 Sum_probs=19.2
Q ss_pred EEECCEEecCCceecCCCEEEE
Q 015203 107 IQVDEEMVPVSYTVKSSQKISH 128 (411)
Q Consensus 107 V~VNGk~v~~~~~v~~gD~I~~ 128 (411)
+.+||+.+...+.|..+|.|.+
T Consensus 37 ~~vn~~~~~l~~~l~~~~~i~~ 58 (60)
T cd01616 37 ALVNGQLVDLSYTLQDGDTVSI 58 (60)
T ss_pred EEECCEECCCCcCcCCCCEEEE
Confidence 4689999999999999998875
No 121
>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=30.54 E-value=59 Score=23.09 Aligned_cols=44 Identities=23% Similarity=0.362 Sum_probs=29.0
Q ss_pred cCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecCCceecCCCEEEE
Q 015203 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISH 128 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~ 128 (411)
.+.++.+++.......++ ..-.+.+||+.++.++.+..||.|.+
T Consensus 15 ~~~t~~~~~~~~~~~~~~-------~~va~~vng~~vdl~~~l~~~~~ve~ 58 (60)
T cd01668 15 AGATVLDFAYAIHTEIGN-------RCVGAKVNGKLVPLSTVLKDGDIVEI 58 (60)
T ss_pred CCCCHHHHHHHHChHhhh-------heEEEEECCEECCCCCCCCCCCEEEE
Confidence 467777766553211111 11235689999999999999998875
No 122
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=30.44 E-value=22 Score=28.55 Aligned_cols=51 Identities=6% Similarity=0.166 Sum_probs=27.2
Q ss_pred cCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEecCCceecCCCEEEEee
Q 015203 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVPVSYTVKSSQKISHFL 130 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~~~~~v~~gD~I~~~~ 130 (411)
+|-++.+.+..+ |.. ..+-+--+....|=|=|+.+.+++.|+.||+|+++-
T Consensus 22 ~GtTv~~Ai~~S-gi~-~~~p~idl~~~~vGIfGk~~~~d~~L~~GDRVEIYR 72 (84)
T PF03658_consen 22 EGTTVAQAIEAS-GIL-EQFPEIDLEKNKVGIFGKLVKLDTVLRDGDRVEIYR 72 (84)
T ss_dssp TT-BHHHHHHHH-THH-HH-TT--TTTSEEEEEE-S--TT-B--TT-EEEEE-
T ss_pred CcCcHHHHHHHc-Cch-hhCcccCcccceeeeeeeEcCCCCcCCCCCEEEEec
Confidence 477888877765 321 111111235677888999999999999999999873
No 123
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=24.31 E-value=1.1e+02 Score=35.28 Aligned_cols=31 Identities=26% Similarity=0.414 Sum_probs=13.7
Q ss_pred hhcccCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 015203 7 EEKSKANDSNSNGNGNGNGNGNGNGNSSNNM 37 (411)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 (411)
+..+..+++-.+|+++..|+|-|++.+++|.
T Consensus 1173 nG~~~n~SgyRRGgssysgGGYGggys~gGy 1203 (1282)
T KOG0921|consen 1173 NGPSNNNSGYRRGGSSYSGGGYGGGYSGGGY 1203 (1282)
T ss_pred CCCccCccccccCCCCCCCCCcCCCCCCCCc
Confidence 3334444444444444444444444444443
No 124
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=22.32 E-value=87 Score=23.30 Aligned_cols=22 Identities=5% Similarity=0.024 Sum_probs=17.6
Q ss_pred EEECCEEecCCceecCCCEEEE
Q 015203 107 IQVDEEMVPVSYTVKSSQKISH 128 (411)
Q Consensus 107 V~VNGk~v~~~~~v~~gD~I~~ 128 (411)
+-+||=+++.+..|+.||.|.+
T Consensus 32 ~I~NGF~~~~d~~L~e~D~v~~ 53 (57)
T PF14453_consen 32 VILNGFPTKEDIELKEGDEVFL 53 (57)
T ss_pred EEEcCcccCCccccCCCCEEEE
Confidence 4468888888888999988764
No 125
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=22.31 E-value=96 Score=24.79 Aligned_cols=42 Identities=24% Similarity=0.400 Sum_probs=29.5
Q ss_pred cCchHHHHHHHhcCCCCHHHHHHHHHcC-cEEECCEEec----CCceecCCCEEEEe
Q 015203 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCG-RIQVDEEMVP----VSYTVKSSQKISHF 129 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~~Sr~~~~~~I~~G-~V~VNGk~v~----~~~~v~~gD~I~~~ 129 (411)
++.+|.++|... +. +. ++ .|-+||+.+. ..+.|+.||.|.+.
T Consensus 32 ~~~tl~~LL~~l-~~-~~--------~~vAVevNg~iVpr~~w~~t~L~egD~IEIv 78 (84)
T PRK06083 32 ISSSLAQIIAQL-SL-PE--------LGCVFAINNQVVPRSEWQSTVLSSGDAISLF 78 (84)
T ss_pred CCCcHHHHHHHc-CC-CC--------ceEEEEECCEEeCHHHcCcccCCCCCEEEEE
Confidence 357888888763 32 21 11 4689999994 36789999999875
No 126
>PF14478 DUF4430: Domain of unknown function (DUF4430); PDB: 3U7Z_B 2BB5_A.
Probab=22.07 E-value=87 Score=23.58 Aligned_cols=22 Identities=36% Similarity=0.486 Sum_probs=14.2
Q ss_pred EEECCEEecC---CceecCCCEEEE
Q 015203 107 IQVDEEMVPV---SYTVKSSQKISH 128 (411)
Q Consensus 107 V~VNGk~v~~---~~~v~~gD~I~~ 128 (411)
..|||+.... .++|+.||.|.+
T Consensus 43 ~~vNG~~~~~ga~~~~l~~GD~i~~ 67 (68)
T PF14478_consen 43 YYVNGESANVGAGSYKLKDGDKITW 67 (68)
T ss_dssp EEETTEE-SS-CCC-B--TTEEEEE
T ss_pred EEECCEEhhcCcceeEeCCCCEEEe
Confidence 5789998753 688999999875
No 127
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=21.93 E-value=1.4e+02 Score=31.05 Aligned_cols=38 Identities=18% Similarity=0.238 Sum_probs=31.5
Q ss_pred cCchHHHHHHHhcCCCCHHHHHHHHHcCcEEECCEEec
Q 015203 78 AGKTIVDLFAEEFKGRPYDYYVSAVKCGRIQVDEEMVP 115 (411)
Q Consensus 78 ~g~rL~k~L~~~~~~~Sr~~~~~~I~~G~V~VNGk~v~ 115 (411)
.|+.+.+.+++.-..-|+.++.++|.+|.|+||++++.
T Consensus 397 ~~~s~~~l~~ka~~~~s~~~a~r~i~qG~vslnh~~v~ 434 (467)
T KOG2623|consen 397 PGVSILDLLRKASRFPSGKEARRMIQQGGVSLNHEKVR 434 (467)
T ss_pred CCCcHHHHHHHhhcCCCcHHHHHHHHccceeecCcccc
Confidence 58999999988733345669999999999999999884
No 128
>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=21.79 E-value=41 Score=25.19 Aligned_cols=18 Identities=22% Similarity=0.272 Sum_probs=12.6
Q ss_pred eeCCcEEEEeCCCCceee
Q 015203 146 QKEPDVLTVCKPPSVPVH 163 (411)
Q Consensus 146 yEd~~~ivvnKP~Gl~v~ 163 (411)
|-...+|.+|||+|-.+|
T Consensus 39 ~i~~GvinlDKP~gPtSH 56 (59)
T PF08068_consen 39 YIKYGVINLDKPSGPTSH 56 (59)
T ss_dssp HHHTEEEEEEE-SSS-HH
T ss_pred HHhCCcEEeeCCCCCCcc
Confidence 345689999999997766
No 129
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=20.47 E-value=1.6e+02 Score=23.99 Aligned_cols=29 Identities=14% Similarity=0.015 Sum_probs=17.3
Q ss_pred eecCCCEEEEeeecCCCCCcCCCceEeeeCCcEEEEe
Q 015203 119 TVKSSQKISHFLHRHEPPVMAWDVSILQKEPDVLTVC 155 (411)
Q Consensus 119 ~v~~gD~I~~~~~~~e~~~~~~~~~IlyEd~~~ivvn 155 (411)
.|+.||.|.+.- ..+..|-++++.|+++.
T Consensus 58 ~vk~GD~Vlf~~--------~~g~ev~~~~~~y~iv~ 86 (95)
T PRK00364 58 DVKVGDKVLFGK--------YAGTEVKIDGEEYLILR 86 (95)
T ss_pred ccCCCCEEEEcC--------CCCeEEEECCEEEEEEE
Confidence 488899887641 11345666666666553
No 130
>TIGR00691 spoT_relA (p)ppGpp synthetase, RelA/SpoT family. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species.
Probab=20.45 E-value=85 Score=34.90 Aligned_cols=25 Identities=12% Similarity=0.311 Sum_probs=21.9
Q ss_pred EEECCEEecCCceecCCCEEEEeee
Q 015203 107 IQVDEEMVPVSYTVKSSQKISHFLH 131 (411)
Q Consensus 107 V~VNGk~v~~~~~v~~gD~I~~~~~ 131 (411)
.+|||+.|..++.|+.||.|.+...
T Consensus 398 a~vng~~v~l~~~l~~gd~vei~t~ 422 (683)
T TIGR00691 398 AKVNGKIVPLDKELENGDVVEIITG 422 (683)
T ss_pred EEECCEECCCCccCCCCCEEEEEeC
Confidence 3799999999999999999987643
No 131
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=20.33 E-value=97 Score=34.81 Aligned_cols=27 Identities=15% Similarity=0.469 Sum_probs=23.2
Q ss_pred EEECCEEecCCceecCCCEEEEeeecC
Q 015203 107 IQVDEEMVPVSYTVKSSQKISHFLHRH 133 (411)
Q Consensus 107 V~VNGk~v~~~~~v~~gD~I~~~~~~~ 133 (411)
.+|||+.|..++.|+.||.|+|.....
T Consensus 442 Akvng~~v~l~~~L~~GD~VeIits~~ 468 (743)
T PRK10872 442 AKIGGRIVPFTYQLQMGDQIEIITQKQ 468 (743)
T ss_pred EEECCEECCCCcCCCCCCEEEEEeCCC
Confidence 389999999999999999999865443
Done!