Query 019431
Match_columns 341
No_of_seqs 175 out of 1830
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 09:25:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019431.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019431hhsearch_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 1.3E-57 2.9E-62 429.3 27.6 244 61-341 3-248 (289)
2 PRK11180 rluD 23S rRNA pseudou 100.0 6.4E-53 1.4E-57 405.2 31.3 250 56-341 3-252 (325)
3 PRK11025 23S rRNA pseudouridyl 100.0 6.6E-52 1.4E-56 396.8 29.3 243 61-341 10-260 (317)
4 TIGR00005 rluA_subfam pseudour 100.0 1.3E-51 2.7E-56 392.1 29.8 242 67-341 2-243 (299)
5 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 4E-44 8.6E-49 331.6 22.4 201 97-341 3-204 (246)
6 PRK10158 23S rRNA/tRNA pseudou 100.0 1.1E-41 2.4E-46 310.2 21.5 167 136-341 13-180 (219)
7 cd02557 PseudoU_synth_ScRIB2 P 100.0 1.8E-41 4E-46 307.5 22.0 172 134-341 13-184 (213)
8 PRK10839 16S rRNA pseudouridyl 100.0 1.5E-42 3.2E-47 318.6 14.1 199 71-338 1-199 (232)
9 TIGR01621 RluA-like pseudourid 100.0 7.7E-41 1.7E-45 304.2 21.2 163 137-341 2-164 (217)
10 cd02563 PseudoU_synth_TruC tRN 100.0 1.2E-40 2.7E-45 304.1 21.7 168 137-341 1-179 (223)
11 PRK11112 tRNA pseudouridine sy 100.0 3.6E-40 7.8E-45 307.0 20.5 168 137-341 2-180 (257)
12 KOG1919 RNA pseudouridylate sy 100.0 9.8E-39 2.1E-43 307.1 23.9 241 63-341 36-279 (371)
13 PRK10700 23S rRNA pseudouridyl 100.0 1.7E-38 3.6E-43 299.9 18.3 205 70-338 2-209 (289)
14 PRK10475 23S rRNA pseudouridin 100.0 6.4E-38 1.4E-42 295.4 16.6 198 68-337 4-201 (290)
15 COG1187 RsuA 16S rRNA uridine- 100.0 7.7E-38 1.7E-42 286.3 15.3 206 70-337 2-208 (248)
16 cd02869 PseudoU_synth_RluCD_li 100.0 7E-36 1.5E-40 263.9 19.5 162 146-341 1-162 (185)
17 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 2E-34 4.4E-39 248.6 16.3 147 146-337 1-147 (154)
18 cd02556 PseudoU_synth_RluB Pse 100.0 2E-33 4.3E-38 245.7 11.6 141 145-337 1-141 (167)
19 cd02870 PseudoU_synth_RsuA_lik 100.0 1E-33 2.3E-38 242.1 7.9 140 146-338 1-140 (146)
20 PF00849 PseudoU_synth_2: RNA 100.0 3.2E-32 7E-37 236.1 15.4 155 145-331 1-164 (164)
21 cd02553 PseudoU_synth_RsuA Pse 100.0 8.4E-32 1.8E-36 235.4 10.6 139 146-340 2-141 (167)
22 cd02566 PseudoU_synth_RluE Pse 100.0 1.5E-30 3.2E-35 227.8 10.3 152 146-338 1-154 (168)
23 cd02555 PSSA_1 PSSA_1: Pseudou 100.0 3E-29 6.5E-34 221.0 10.3 107 210-340 45-151 (177)
24 PRK11394 23S rRNA pseudouridin 100.0 6.7E-29 1.5E-33 224.3 10.8 144 144-340 39-195 (217)
25 cd02554 PseudoU_synth_RluF Pse 99.9 1E-26 2.3E-31 202.1 10.0 133 146-337 2-134 (164)
26 TIGR00093 pseudouridine syntha 99.9 5.8E-27 1.3E-31 196.2 7.8 106 215-340 1-106 (128)
27 cd00165 S4 S4/Hsp/ tRNA synthe 99.3 2.6E-11 5.6E-16 88.7 8.1 70 71-150 1-70 (70)
28 cd02868 PseudoU_synth_hTruB2_l 99.1 1.5E-10 3.2E-15 105.6 6.9 76 145-256 1-76 (226)
29 PF01479 S4: S4 domain; Inter 99.1 2.6E-10 5.7E-15 78.8 5.8 48 71-118 1-48 (48)
30 TIGR02988 YaaA_near_RecF S4 do 99.0 5.7E-10 1.2E-14 80.6 6.2 55 67-121 5-59 (59)
31 COG1188 Ribosome-associated he 98.6 6.8E-08 1.5E-12 76.2 5.3 55 68-123 6-60 (100)
32 smart00363 S4 S4 RNA-binding d 98.4 6.3E-07 1.4E-11 63.1 6.3 52 71-122 1-52 (60)
33 PRK10348 ribosome-associated h 98.4 9.4E-07 2E-11 73.9 6.4 53 69-122 7-59 (133)
34 PLN00051 RNA-binding S4 domain 98.3 1.2E-06 2.7E-11 82.0 7.0 59 64-123 185-243 (267)
35 TIGR03069 PS_II_S4 photosystem 98.2 2.1E-06 4.5E-11 80.2 6.7 59 64-123 177-235 (257)
36 TIGR01017 rpsD_bact ribosomal 98.2 2.5E-06 5.3E-11 76.8 6.8 54 71-124 90-143 (200)
37 CHL00113 rps4 ribosomal protei 98.2 2.8E-06 6E-11 76.3 6.3 54 71-124 89-142 (201)
38 TIGR00478 tly hemolysin TlyA f 98.1 6.4E-06 1.4E-10 75.6 6.1 52 72-123 1-52 (228)
39 PRK05327 rpsD 30S ribosomal pr 98.0 9.5E-06 2.1E-10 73.1 6.3 53 71-123 93-145 (203)
40 PRK11507 ribosome-associated p 98.0 2.3E-05 4.9E-10 58.2 6.2 56 67-122 8-63 (70)
41 COG2302 Uncharacterized conser 97.9 1.6E-05 3.6E-10 72.5 4.6 54 69-123 179-232 (257)
42 cd02572 PseudoU_synth_hDyskeri 97.8 5.4E-05 1.2E-09 67.1 7.6 70 144-256 2-71 (182)
43 COG1189 Predicted rRNA methyla 97.8 4.5E-05 9.8E-10 69.6 6.1 53 70-122 2-54 (245)
44 COG0522 RpsD Ribosomal protein 97.8 4.5E-05 9.7E-10 68.6 5.7 55 71-125 94-148 (205)
45 PF13275 S4_2: S4 domain; PDB: 97.7 9.1E-06 2E-10 59.6 -0.3 56 67-122 4-59 (65)
46 cd01291 PseudoU_synth PseudoU_ 97.6 0.00038 8.3E-09 54.0 8.0 64 210-333 24-87 (87)
47 cd00506 PseudoU_synth_TruB_lik 97.6 0.00021 4.7E-09 64.6 7.2 69 145-256 1-69 (210)
48 PRK00989 truB tRNA pseudouridi 97.5 0.00021 4.6E-09 65.3 6.5 71 144-256 9-79 (230)
49 PRK04099 truB tRNA pseudouridi 97.5 0.0003 6.5E-09 65.9 7.4 70 144-256 2-71 (273)
50 TIGR00431 TruB tRNA pseudourid 97.4 0.00039 8.5E-09 62.8 7.3 70 144-256 2-71 (209)
51 PRK00020 truB tRNA pseudouridi 97.4 0.0004 8.7E-09 64.0 7.5 70 144-256 10-79 (244)
52 PRK02484 truB tRNA pseudouridi 97.4 0.0005 1.1E-08 65.3 7.4 70 144-256 3-72 (294)
53 PRK14124 tRNA pseudouridine sy 97.4 0.00062 1.3E-08 65.0 7.8 70 144-256 3-72 (308)
54 PRK00130 truB tRNA pseudouridi 97.3 0.00064 1.4E-08 64.5 7.6 70 144-256 2-71 (290)
55 COG2501 S4-like RNA binding pr 97.3 0.00063 1.4E-08 50.8 5.8 57 66-122 7-63 (73)
56 PRK03287 truB tRNA pseudouridi 97.3 0.00063 1.4E-08 64.7 7.3 71 143-256 8-78 (298)
57 PRK14123 tRNA pseudouridine sy 97.3 0.00071 1.5E-08 64.6 7.4 70 144-256 3-72 (305)
58 PRK05389 truB tRNA pseudouridi 97.3 0.00071 1.5E-08 64.6 7.3 70 144-256 13-82 (305)
59 PRK02755 truB tRNA pseudouridi 97.3 0.00075 1.6E-08 64.1 7.1 69 144-256 3-71 (295)
60 PRK04270 H/ACA RNA-protein com 97.3 0.00078 1.7E-08 64.4 7.3 71 143-256 21-91 (300)
61 PRK01851 truB tRNA pseudouridi 97.3 0.0009 2E-08 63.7 7.6 70 144-256 16-85 (303)
62 PRK01550 truB tRNA pseudouridi 97.2 0.00094 2E-08 63.7 7.6 70 144-256 2-71 (304)
63 PRK04051 rps4p 30S ribosomal p 97.2 0.00068 1.5E-08 59.6 6.1 52 71-122 103-156 (177)
64 PRK05033 truB tRNA pseudouridi 97.2 0.001 2.2E-08 63.7 7.6 70 144-256 10-79 (312)
65 PRK02193 truB tRNA pseudouridi 97.2 0.00094 2E-08 62.9 7.3 68 146-256 2-69 (279)
66 cd02573 PseudoU_synth_EcTruB P 97.2 0.0011 2.3E-08 62.6 7.5 69 145-256 1-69 (277)
67 PRK14846 truB tRNA pseudouridi 97.2 0.0011 2.4E-08 63.7 7.4 70 144-256 3-72 (345)
68 PRK01528 truB tRNA pseudouridi 97.1 0.0014 3E-08 62.2 7.3 70 144-256 3-72 (292)
69 PRK14122 tRNA pseudouridine sy 97.0 0.0021 4.6E-08 61.4 7.4 69 145-256 2-70 (312)
70 PRK04642 truB tRNA pseudouridi 96.9 0.0026 5.7E-08 60.5 7.3 70 144-256 10-79 (300)
71 TIGR00425 CBF5 rRNA pseudourid 96.9 0.0023 4.9E-08 61.8 6.9 71 143-256 33-103 (322)
72 cd02867 PseudoU_synth_TruB_4 P 96.6 0.0061 1.3E-07 58.3 7.0 93 145-256 1-98 (312)
73 PRK04313 30S ribosomal protein 96.5 0.013 2.8E-07 53.8 8.4 71 71-151 38-109 (237)
74 COG0130 TruB Pseudouridine syn 96.5 0.007 1.5E-07 56.8 6.8 69 145-256 16-84 (271)
75 PLN00189 40S ribosomal protein 96.5 0.0021 4.6E-08 57.1 2.9 42 83-124 121-162 (194)
76 PTZ00223 40S ribosomal protein 96.3 0.019 4.1E-07 53.6 8.2 71 71-151 39-110 (273)
77 PLN00036 40S ribosomal protein 96.3 0.022 4.8E-07 52.9 8.5 71 71-151 42-113 (261)
78 TIGR01018 rpsD_arch ribosomal 96.2 0.0078 1.7E-07 52.2 5.0 51 71-121 104-156 (162)
79 PTZ00118 40S ribosomal protein 96.2 0.023 5E-07 52.9 8.3 70 71-150 42-112 (262)
80 PTZ00155 40S ribosomal protein 95.7 0.011 2.3E-07 52.2 3.9 52 71-122 107-158 (181)
81 COG1471 RPS4A Ribosomal protei 93.9 0.13 2.8E-06 46.8 5.7 59 84-152 55-113 (241)
82 PF14451 Ub-Mut7C: Mut7-C ubiq 89.9 0.3 6.6E-06 37.4 2.8 46 69-123 31-76 (81)
83 PRK13354 tyrosyl-tRNA syntheta 89.7 0.6 1.3E-05 46.6 5.6 47 70-116 342-388 (410)
84 PRK01777 hypothetical protein; 88.7 0.49 1.1E-05 37.4 3.3 54 68-124 24-77 (95)
85 COG4332 Uncharacterized protei 88.6 0.48 1E-05 41.5 3.4 63 58-122 127-189 (203)
86 PF01509 TruB_N: TruB family p 87.5 0.56 1.2E-05 40.2 3.2 43 210-256 7-49 (149)
87 PRK05912 tyrosyl-tRNA syntheta 86.0 1.8 3.8E-05 43.3 6.3 45 70-114 342-386 (408)
88 KOG2559 Predicted pseudouridin 85.0 0.85 1.8E-05 42.0 3.1 23 210-232 89-111 (318)
89 PF06353 DUF1062: Protein of u 84.0 2.1 4.5E-05 36.4 4.9 36 66-102 98-133 (142)
90 cd00754 MoaD Ubiquitin domain 79.6 5.7 0.00012 29.5 5.5 51 70-122 25-75 (80)
91 PRK08364 sulfur carrier protei 75.5 5.1 0.00011 29.5 4.1 44 69-122 22-65 (70)
92 TIGR01682 moaD molybdopterin c 72.4 9.9 0.00021 28.5 5.1 25 97-122 51-75 (80)
93 PLN02799 Molybdopterin synthas 67.9 14 0.0003 27.8 5.1 50 70-122 28-77 (82)
94 PRK05659 sulfur carrier protei 66.9 6.3 0.00014 28.3 2.9 45 69-122 14-61 (66)
95 PRK06437 hypothetical protein; 65.5 6.8 0.00015 28.7 2.8 45 68-122 18-62 (67)
96 KOG3301 Ribosomal protein S4 [ 63.3 7.1 0.00015 33.8 2.9 33 83-115 109-141 (183)
97 PF02597 ThiS: ThiS family; I 60.7 5.8 0.00013 29.1 1.7 52 68-122 19-72 (77)
98 cd00565 ThiS ThiaminS ubiquiti 60.6 8.2 0.00018 27.8 2.5 44 69-122 13-60 (65)
99 PRK11130 moaD molybdopterin sy 59.2 7.1 0.00015 29.5 2.0 29 93-122 46-76 (81)
100 COG2104 ThiS Sulfur transfer p 55.4 12 0.00027 27.6 2.7 43 70-121 17-62 (68)
101 COG0162 TyrS Tyrosyl-tRNA synt 53.8 16 0.00035 36.5 4.0 40 73-112 338-377 (401)
102 TIGR00234 tyrS tyrosyl-tRNA sy 52.6 29 0.00064 34.3 5.7 41 69-109 328-368 (377)
103 PRK06944 sulfur carrier protei 49.5 19 0.00042 25.6 2.9 44 69-122 14-60 (65)
104 PF02824 TGS: TGS domain; Int 48.0 18 0.0004 25.7 2.5 23 97-120 36-58 (60)
105 cd01764 Urm1 Urm1-like ubuitin 46.9 49 0.0011 25.9 5.1 26 97-122 61-89 (94)
106 KOG2529 Pseudouridine synthase 46.2 17 0.00038 35.9 2.8 47 210-260 95-141 (395)
107 PRK06488 sulfur carrier protei 45.0 23 0.0005 25.4 2.7 43 71-122 15-60 (65)
108 PRK07440 hypothetical protein; 44.9 25 0.00055 25.9 3.0 44 69-121 18-64 (70)
109 TIGR01687 moaD_arch MoaD famil 44.8 26 0.00056 26.6 3.1 26 96-122 56-83 (88)
110 TIGR01683 thiS thiamine biosyn 44.2 26 0.00057 25.0 2.9 44 70-122 13-59 (64)
111 COG4043 Preprotein translocase 42.5 29 0.00064 27.7 3.1 38 85-122 7-44 (111)
112 PF03658 Ub-RnfH: RnfH family 39.0 13 0.00029 28.6 0.7 30 94-124 45-74 (84)
113 PRK07696 sulfur carrier protei 37.2 34 0.00073 24.9 2.6 42 71-121 17-61 (67)
114 KOG2623 Tyrosyl-tRNA synthetas 37.1 45 0.00097 33.2 4.0 41 67-107 395-435 (467)
115 PF00498 FHA: FHA domain; Int 36.3 31 0.00068 24.4 2.3 26 95-120 41-67 (68)
116 PRK08053 sulfur carrier protei 36.0 44 0.00096 24.1 3.0 44 69-121 14-60 (66)
117 PF08068 DKCLD: DKCLD (NUC011) 31.9 21 0.00046 25.6 0.7 16 143-158 41-56 (59)
118 cd01666 TGS_DRG_C TGS_DRG_C: 29.0 42 0.0009 25.2 1.9 22 99-121 53-74 (75)
119 TIGR02194 GlrX_NrdH Glutaredox 27.3 22 0.00048 25.8 0.2 15 1-15 1-15 (72)
120 cd01668 TGS_RelA_SpoT TGS_RelA 25.8 86 0.0019 21.3 3.0 23 97-120 36-58 (60)
121 PRK06083 sulfur carrier protei 23.9 85 0.0018 24.1 2.9 45 68-121 31-78 (84)
122 cd06919 Asp_decarbox Aspartate 23.4 76 0.0017 25.8 2.6 25 95-123 65-89 (111)
123 PRK02253 deoxyuridine 5'-triph 22.7 2.4E+02 0.0052 24.4 5.8 39 83-121 2-46 (167)
124 cd01616 TGS The TGS domain, na 22.5 1.1E+02 0.0023 20.1 3.0 22 98-120 37-58 (60)
125 KOG4655 U3 small nucleolar rib 22.0 56 0.0012 28.5 1.6 36 85-120 121-158 (181)
126 PRK11092 bifunctional (p)ppGpp 21.3 74 0.0016 34.2 2.8 23 100-123 426-448 (702)
127 COG2440 FixX Ferredoxin-like p 20.6 60 0.0013 25.8 1.4 23 8-30 69-93 (99)
128 KOG4837 Uncharacterized conser 20.1 81 0.0018 28.6 2.3 53 70-123 139-191 (248)
129 TIGR01764 excise DNA binding d 20.0 95 0.0021 19.9 2.2 25 73-99 4-28 (49)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-57 Score=429.34 Aligned_cols=244 Identities=44% Similarity=0.694 Sum_probs=218.1
Q ss_pred EEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccccC-CccccCCCCCeeE
Q 019431 61 EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQ-PLRAEAEDIPLDI 139 (341)
Q Consensus 61 ~~~v~~~~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~-~~~~~~~~~~~~I 139 (341)
+..|+.+.+++|||+||++.++ +||+.++++|++|.|.|||+++. ++++|..||+|++...... .....+++.+++|
T Consensus 3 ~~~v~~~~~g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~I 80 (289)
T COG0564 3 EFEVPEEEAGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDI 80 (289)
T ss_pred eEEeChhhcCCCHHHHHHHccC-cCHHHHHHHHHCCCEEECCEEcc-CCeeeCCCCEEEEecccccccccccccCCCccE
Confidence 3456678889999999999655 99999999999999999999995 9999999999999886543 2334556777999
Q ss_pred EeeCCcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCC
Q 019431 140 VYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLD 219 (341)
Q Consensus 140 lyed~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD 219 (341)
||||+++||||||+||+|||+.++..+|++++++.++... ..++++|||||
T Consensus 81 lyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~-----------------------------~~~~~~vHRLD 131 (289)
T COG0564 81 LYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDG-----------------------------VERPGIVHRLD 131 (289)
T ss_pred EEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhcccc-----------------------------CCceeeeccCC
Confidence 9999999999999999999999988899999999876311 26789999999
Q ss_pred CCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCceeEEEE
Q 019431 220 KGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRY 299 (341)
Q Consensus 220 ~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~t~~ 299 (341)
++|||||||||+..+++.|+.+|+++.+.|+|+|+|.|.+.++++.|+.||+++..++..+.+... ..++.|.|+|
T Consensus 132 kdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~~~~~v~~~----~~gk~A~T~~ 207 (289)
T COG0564 132 KDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNRKKMAVVKE----GSGKPAITHY 207 (289)
T ss_pred CCCceEEEEECCHHHHHHHHHHHhcCcCcEEEEEEEECcccCCCCEEeeeeecCCcCCceEEEecc----CCCCceEEEE
Confidence 999999999999999999999999999999999999999999999999999999988888877654 1389999999
Q ss_pred EEEEEecCCC-EEEEEEEeCCCchhHHHHHHHhCCCceecccC
Q 019431 300 KVIEILAGGG-SALVEWRLETGRTHQVLMLYKLFYIPRMIKVF 341 (341)
Q Consensus 300 ~~l~~~~~~~-~slv~~~l~TGR~HQIR~hla~lG~PIvGD~~ 341 (341)
++++.. +. .||++|+|.||||||||+||+++||||+||.+
T Consensus 208 ~~l~~~--~~~~tlv~~~~~TGRTHQIRVHl~~lghPI~GD~~ 248 (289)
T COG0564 208 EVLERF--GDNYTLVELKPETGRTHQIRVHLAHLGHPIVGDPL 248 (289)
T ss_pred Eehhcc--CCceEEEEEEeCCCCHhHHHHHHHHCCCCeeCCcc
Confidence 999986 34 69999999999999999999999999999975
No 2
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=6.4e-53 Score=405.22 Aligned_cols=250 Identities=38% Similarity=0.574 Sum_probs=213.2
Q ss_pred CceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccccCCccccCCCC
Q 019431 56 AGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDI 135 (341)
Q Consensus 56 ~~~~~~~~v~~~~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~ 135 (341)
+.|.+..+|+.+++++|||+||++.++.+||+.++++|++|.|+|||+++.++++.|.+||.|++...........+...
T Consensus 3 ~~~~~~~~v~~~~~g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~ 82 (325)
T PRK11180 3 QQVQLTATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQDI 82 (325)
T ss_pred ceEEEEEEECcccCCccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEeeccccccCCCCCCC
Confidence 45778888998899999999999988889999999999999999999998778999999999999875433222234456
Q ss_pred CeeEEeeCCcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCcccc
Q 019431 136 PLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIV 215 (341)
Q Consensus 136 ~~~Ilyed~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v 215 (341)
+++|||||+++||+|||+||+|||..+...+|+.+.|..++.. . ....++++|
T Consensus 83 ~~~iiyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~~~--~-------------------------~~~~~~~~v 135 (325)
T PRK11180 83 PLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPP--I-------------------------ADVPRAGIV 135 (325)
T ss_pred CCcEEEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHhhh--c-------------------------cCCccccee
Confidence 7899999999999999999999998877778999998876521 0 011457889
Q ss_pred ccCCCCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCcee
Q 019431 216 HRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHA 295 (341)
Q Consensus 216 hRLD~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a 295 (341)
||||++||||||||+|..+++.|+.+|.++.+.|+|+|+|.|.++ +++.|+.||.+...++..+.+.. .++.|
T Consensus 136 hRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~Y~A~v~G~~~-~~~~i~~~l~~~~~~~~~~~~~~------~gk~a 208 (325)
T PRK11180 136 HRLDKDTTGLMVVAKTVPAQTRLVEALQKREITREYEAVAIGHMT-AGGTVDEPISRHPTKRTHMAVHP------MGKPA 208 (325)
T ss_pred ccCCCCCceeEEEECCHHHHHHHHHHHHhCCcceEEEEEEecCCC-CCCEEECceecCCCcCcEEEeCC------CCcEE
Confidence 999999999999999999999999999999999999999999986 56889999987655544443322 58899
Q ss_pred EEEEEEEEEecCCCEEEEEEEeCCCchhHHHHHHHhCCCceecccC
Q 019431 296 ASRYKVIEILAGGGSALVEWRLETGRTHQVLMLYKLFYIPRMIKVF 341 (341)
Q Consensus 296 ~t~~~~l~~~~~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~~ 341 (341)
.|+|+++... .+.+||+|+|.|||+||||+||+++||||+||.+
T Consensus 209 ~T~~~~l~~~--~~~slv~~~~~TGRtHQIRvhla~lG~PI~GD~~ 252 (325)
T PRK11180 209 VTHYRIMEHF--RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQV 252 (325)
T ss_pred eEEEEEeEEc--CCeEEEEEEeCCCCHHHHHHHHHhCCCCEeCccc
Confidence 9999999874 5689999999999999999999999999999974
No 3
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=6.6e-52 Score=396.85 Aligned_cols=243 Identities=24% Similarity=0.346 Sum_probs=199.5
Q ss_pred EEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccccCCcccc--------C
Q 019431 61 EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAE--------A 132 (341)
Q Consensus 61 ~~~v~~~~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~--------~ 132 (341)
.++|+.+++++||++||+..++..||+.++++|++|.|+|||+++ +++++|+.||+|++........... .
T Consensus 10 ~~~v~~~~~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v-~~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~ 88 (317)
T PRK11025 10 IVTISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKV 88 (317)
T ss_pred EEEECcccCCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEc-CcccccCCCCEEEeCCCCcccccccccccccccc
Confidence 457888889999999999887889999999999999999999998 6899999999999864322110000 1
Q ss_pred CCCCeeEEeeCCcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCc
Q 019431 133 EDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRP 212 (341)
Q Consensus 133 ~~~~~~Ilyed~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 212 (341)
...+++|||||++++|+|||+|++||+..+.. .++.+.+..+.. ....+
T Consensus 89 ~~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~-~~~~~~~~~~~~------------------------------~~~~~ 137 (317)
T PRK11025 89 AALADVILYEDDHILVLNKPSGTAVHGGSGLS-FGVIEGLRALRP------------------------------EARFL 137 (317)
T ss_pred ccCcCCEEEECCCEEEEECCCCCcCcCCCCCC-ccHHHHHHHhcc------------------------------CCCcC
Confidence 12467999999999999999999999986554 356666654221 01235
Q ss_pred cccccCCCCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCC
Q 019431 213 GIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQA 292 (341)
Q Consensus 213 ~~vhRLD~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~ 292 (341)
++|||||++||||||||+|+.+++.|+.+|+++.++|+|+|+|.|.+..+.+.|+.||.++........+.. ...+
T Consensus 138 ~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~v~K~Y~a~v~G~~~~~~~~i~~~i~~~~~~~~~~~~~~----~~~g 213 (317)
T PRK11025 138 ELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKVVQAPLLKNILQSGERIVRV----SQEG 213 (317)
T ss_pred ceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCCccEEEEEEEeCcccCCCceEecccccCcccCCceEEec----CCCC
Confidence 789999999999999999999999999999999999999999999998888999999987653322222211 1268
Q ss_pred ceeEEEEEEEEEecCCCEEEEEEEeCCCchhHHHHHHHhCCCceecccC
Q 019431 293 RHAASRYKVIEILAGGGSALVEWRLETGRTHQVLMLYKLFYIPRMIKVF 341 (341)
Q Consensus 293 k~a~t~~~~l~~~~~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~~ 341 (341)
+.|.|+|++++.. +++|||+|+|.|||+||||+||+++||||+||.+
T Consensus 214 k~a~T~~~~l~~~--~~~sLv~~~~~TGRtHQIRvhla~lG~PIlGD~~ 260 (317)
T PRK11025 214 KPSETRFKVEERY--AFATLVRASPVTGRTHQIRVHTQYAGHPIAFDDR 260 (317)
T ss_pred ccceEEEEEeEEc--CCcEEEEEEeCCCCHHHHHHHHHHCCCCEECCcc
Confidence 9999999999874 5789999999999999999999999999999975
No 4
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=100.00 E-value=1.3e-51 Score=392.06 Aligned_cols=242 Identities=38% Similarity=0.642 Sum_probs=203.9
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccccCCccccCCCCCeeEEeeCCcE
Q 019431 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNV 146 (341)
Q Consensus 67 ~~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~Ilyed~~l 146 (341)
+++++||++||++.++.+||+.++++|++|.|+|||+++.++++.|++||.|.++..........+...+++|+|||++|
T Consensus 2 ~~~g~rLd~~L~~~~~~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~I~i~~~~~~~~~~~~~~~~~~i~~ed~~~ 81 (299)
T TIGR00005 2 EQAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDEDI 81 (299)
T ss_pred CccchhHHHHHHHhcccCCHHHHHHHHHCCcEEECCEeccCcccCCCCCCEEEEecCCcccccCCccCCCccEEEeCCCE
Confidence 46789999999998766999999999999999999976557899999999999976532211222334468899999999
Q ss_pred EEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceeE
Q 019431 147 LVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLL 226 (341)
Q Consensus 147 lvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGLl 226 (341)
+|+|||+|++||+.++...+|+.+.|..++... ....++++|||||++|||||
T Consensus 82 lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~~~~---------------------------~~~~~~~~vhRLD~~TSGll 134 (299)
T TIGR00005 82 IVINKPSGLVVHPGGGNPFGTVLNALLAHCPPI---------------------------AGVERVGIVHRLDRDTSGLM 134 (299)
T ss_pred EEEECCCCCeEeCCCCCCcccHHHHHHHhcccc---------------------------cCCCcCceECCCCCCCceEE
Confidence 999999999999998877789999988765310 01145789999999999999
Q ss_pred EeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCceeEEEEEEEEEec
Q 019431 227 VVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILA 306 (341)
Q Consensus 227 l~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~ 306 (341)
|||+|+.+++.|+++|+++.++|+|+|+|.|.++++++.|+.||.++..+...+.+... .+++.|.|+|+++...
T Consensus 135 l~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~g~~~~~~~~i~~~l~~~~~~~~~~~~~~~----~~~k~a~t~~~~l~~~- 209 (299)
T TIGR00005 135 VVAKTPLALRELQRQLKNRTVTKEYVALVHGQFDSGGGTVDAPLGRVPNNRGLMAVHPS----SEGKPAVTHFRVLERF- 209 (299)
T ss_pred EEEcCHHHHHHHHHHHHhCCcceEEEEEEeccccCCCCEEeCceecCCCCCceEEEecC----CCCCeeeEEEEEeEEc-
Confidence 99999999999999999999999999999999988899999999887555444444322 2588999999999863
Q ss_pred CCCEEEEEEEeCCCchhHHHHHHHhCCCceecccC
Q 019431 307 GGGSALVEWRLETGRTHQVLMLYKLFYIPRMIKVF 341 (341)
Q Consensus 307 ~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~~ 341 (341)
.+.|+++|+|.|||+||||+||+++||||+||.+
T Consensus 210 -~~~slv~~~l~tGR~HQIR~hla~lG~pI~gD~~ 243 (299)
T TIGR00005 210 -GNASLVECELETGRTHQIRVHLQYLGHPLAGDPL 243 (299)
T ss_pred -CCeEEEEEEeCCCChHHHHHHHHHCCCcEeCccc
Confidence 5689999999999999999999999999999974
No 5
>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=4e-44 Score=331.58 Aligned_cols=201 Identities=20% Similarity=0.280 Sum_probs=162.9
Q ss_pred ceEECCEEeccccccccCCCEEeeeccccCCccccCCCCCeeEEeeCCcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhc
Q 019431 97 LVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHC 176 (341)
Q Consensus 97 ~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~Ilyed~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~ 176 (341)
.|..||+++ +++++|++||+|.+....... .+...+++|||||++++|+|||+|++||+.++...+|+.+.+..++
T Consensus 3 ~~~~ng~~~-~~~~~l~~gd~i~~~~~~~~~---~~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~ 78 (246)
T cd02558 3 VVDADGEPL-DPDSPYRPGTFVWYYRELPDE---PPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQT 78 (246)
T ss_pred eECCCCcCC-CCCceecCCCEEEEeCCCCCC---CCCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHh
Confidence 344899999 689999999999987532211 1223458999999999999999999999998887788888886543
Q ss_pred CCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 177 SLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 177 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
. ...+++|||||++||||||||||+++++.++.+|++++++|+|+|+|.
T Consensus 79 ~-------------------------------~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~YlA~v~ 127 (246)
T cd02558 79 G-------------------------------NPDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYEAVAP 127 (246)
T ss_pred C-------------------------------CCcccccccCCCCceeEEEEEcCHHHHHHHHHHHHcCCccEEEEEEEe
Confidence 2 134678999999999999999999999999999999999999999999
Q ss_pred ccCCCCCc-EEEecceeCCCCCeeEEecCCCCCCCCCceeEEEEEEEEEecCCCEEEEEEEeCCCchhHHHHHHHhCCCc
Q 019431 257 GVPSQSSG-RIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQVLMLYKLFYIP 335 (341)
Q Consensus 257 G~~~~~~~-~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~~slv~~~l~TGR~HQIR~hla~lG~P 335 (341)
|.+..+.+ .+..+|.+.... .. ....+ +++.|.|+|++++.. .++++++|+|.|||+||||+||+++|||
T Consensus 128 G~~~~~~~~~~~~~i~~~~~~-~~-~~~~~-----~~~~a~T~~~~l~~~--~~~slv~~~l~TGRtHQIRvhla~lG~P 198 (246)
T cd02558 128 YVPALTFPLTVRSRIVKGRGF-FQ-AREVE-----GEPNAETRIELLARR--GGWGLYRLSPHTGKTHQLRVHMAALGVP 198 (246)
T ss_pred cCCCCCCCcceeccccccCCc-ce-eeccC-----CCCCceEEEEEEEec--CCeEEEEEEeCCCCHHHHHHHHHHCCCc
Confidence 99864443 566677654321 11 11111 467899999999874 5789999999999999999999999999
Q ss_pred eecccC
Q 019431 336 RMIKVF 341 (341)
Q Consensus 336 IvGD~~ 341 (341)
|+||.+
T Consensus 199 IvGD~~ 204 (246)
T cd02558 199 ILNDPF 204 (246)
T ss_pred ccCCcc
Confidence 999975
No 6
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=100.00 E-value=1.1e-41 Score=310.19 Aligned_cols=167 Identities=29% Similarity=0.419 Sum_probs=143.4
Q ss_pred CeeEEeeCCcEEEEeCCCCCeeecCCC-CCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccc
Q 019431 136 PLDIVYEDDNVLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (341)
Q Consensus 136 ~~~Ilyed~~llvvnKP~Gl~~~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 (341)
+++|||||++++|+|||+|++||+... ....++.+.+..++ .++++
T Consensus 13 ~~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~---------------------------------~~~~~ 59 (219)
T PRK10158 13 WLVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY---------------------------------PQAES 59 (219)
T ss_pred CCCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC---------------------------------CCCCE
Confidence 478999999999999999999998753 33457777775433 23578
Q ss_pred cccCCCCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCce
Q 019431 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH 294 (341)
Q Consensus 215 vhRLD~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~ 294 (341)
|||||++||||||||++.++++.|+++|.++.|.|+|+|+|.|.+..+++.++.||..+..++..+.+... +++.
T Consensus 60 vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~~v~K~Yla~v~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~-----~gk~ 134 (219)
T PRK10158 60 VHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYE-----TGKP 134 (219)
T ss_pred ECCCCCCCceEEEEECCHHHHHHHHHHHHhCCccEEEEEEEecccCCCCcEEecceecCCCCCceEEecCC-----CCce
Confidence 99999999999999999999999999999999999999999999998999999999877655555555432 6789
Q ss_pred eEEEEEEEEEecCCCEEEEEEEeCCCchhHHHHHHHhCCCceecccC
Q 019431 295 AASRYKVIEILAGGGSALVEWRLETGRTHQVLMLYKLFYIPRMIKVF 341 (341)
Q Consensus 295 a~t~~~~l~~~~~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~~ 341 (341)
+.|+|++++... ...++++|+|+|||+||||+||+++||||+||.+
T Consensus 135 a~t~~~~l~~~~-~~~sll~~~~~TGRtHQIR~hla~lG~PIvGD~~ 180 (219)
T PRK10158 135 AQTEYEVVEYAA-DNTARVVLKPITGRSHQLRVHMLALGHPILGDRF 180 (219)
T ss_pred eeEEEEEEEEcC-CCCEEEEEEeCCCCHHHHHHHHHHCCCcEECCcc
Confidence 999999998752 3358999999999999999999999999999974
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=1.8e-41 Score=307.52 Aligned_cols=172 Identities=24% Similarity=0.336 Sum_probs=145.7
Q ss_pred CCCeeEEeeCCcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCcc
Q 019431 134 DIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPG 213 (341)
Q Consensus 134 ~~~~~Ilyed~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 213 (341)
..+++|||||+++||+|||+|++|++.+.....++.+.|..++. ...++
T Consensus 13 ~~~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~-------------------------------~~~~~ 61 (213)
T cd02557 13 NDPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYG-------------------------------LTELR 61 (213)
T ss_pred CCCCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcC-------------------------------CCCcc
Confidence 34689999999999999999999999877667789988876432 12467
Q ss_pred ccccCCCCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCc
Q 019431 214 IVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQAR 293 (341)
Q Consensus 214 ~vhRLD~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k 293 (341)
+|||||++||||||||+|+++++.|+++|.+++++|+|+|+|.|.++++.+.++.||.+...+....... ...++
T Consensus 62 ~vhRLD~~TSGllllak~~~~~~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~-----~~~~~ 136 (213)
T cd02557 62 PCHRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKEYLARVKGEFPDGEVVVDQPIGLVSPKGGLRNDV-----DEKGK 136 (213)
T ss_pred CccCCCCCCceEEEEECCHHHHHHHHHHHHcCCccEEEEEEEeCcCCCCCeEEecceeccCcCCceeecc-----CCCCc
Confidence 8999999999999999999999999999999999999999999999888999999997754322111111 23678
Q ss_pred eeEEEEEEEEEecCCCEEEEEEEeCCCchhHHHHHHHhCCCceecccC
Q 019431 294 HAASRYKVIEILAGGGSALVEWRLETGRTHQVLMLYKLFYIPRMIKVF 341 (341)
Q Consensus 294 ~a~t~~~~l~~~~~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~~ 341 (341)
.|.|+|+++......+.+|++|+|.|||+||||+||+++||||+||.+
T Consensus 137 ~a~t~~~~~~~~~~~~~slv~v~~~TGR~HQIR~hla~lG~PIlGD~~ 184 (213)
T cd02557 137 DARTIFKRLSYNGDLNTSVVLCKPITGRTHQIRVHLQYLGHPIVNDPI 184 (213)
T ss_pred eeeEEEEEEEEcCCCCeEEEEEEeCCCCHHHHHHHHHHCCCCCcCccc
Confidence 999999999875434789999999999999999999999999999974
No 8
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=100.00 E-value=1.5e-42 Score=318.63 Aligned_cols=199 Identities=19% Similarity=0.291 Sum_probs=157.4
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccccCCccccCCCCCeeEEeeCCcEEEEe
Q 019431 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVN 150 (341)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~Ilyed~~llvvn 150 (341)
+|||+||++.+ .+||+.++++|++|.|+|||+++.+++++|++||.|++......+ .+++++||+|
T Consensus 1 ~rld~~L~~~~-~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~I~l~~~~~~~-------------~~~~~~lvvn 66 (232)
T PRK10839 1 MRLDKFISQQL-GVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDGNPLAQ-------------QHGPRYFMLN 66 (232)
T ss_pred CcHHHHHHHcC-CCCHHHHHHHHHcCeEEECCEEeccCCcCcCCCCEEEECCEEccc-------------CCCCEEEEEE
Confidence 48999999886 799999999999999999999986689999999999987522111 1357899999
Q ss_pred CCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceeEEeec
Q 019431 151 KPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAK 230 (341)
Q Consensus 151 KP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGLll~ak 230 (341)
||+||+||+.++.. .|+.+.+... ...++++|||||++||||||||+
T Consensus 67 KP~G~~~~~~~~~~-~tl~~~l~~~--------------------------------~~~~~~~v~RLD~~TSGlll~ak 113 (232)
T PRK10839 67 KPQGYVCSTDDPDH-PTVLYFLDEP--------------------------------VAYKLHAAGRLDIDTTGLVLMTD 113 (232)
T ss_pred CCCCeEecccCCCC-CeEEEecccc--------------------------------cccCceecCCCCCCceeEEEEec
Confidence 99999999875533 4554322110 01356789999999999999999
Q ss_pred CHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCceeEEEEEEEEEecCCCE
Q 019431 231 DEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGS 310 (341)
Q Consensus 231 ~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~~ 310 (341)
|+.++..|.. +.+.++|+|+|++.+.+..+.. +..+.++.. .++.|.|+|.+++... .
T Consensus 114 ~~~~~~~l~~--~~~~i~K~Y~a~i~~~i~~~~~-----------~~~~~~~~~------~g~~a~t~~~~~~~~~---~ 171 (232)
T PRK10839 114 DGQWSHRITS--PRHHCEKTYLVTLESPVADDTA-----------EQFAKGVQL------HNEKDLTKPAVLEVIT---P 171 (232)
T ss_pred CHHHHHHHhC--CCCCCCeEEEEEECCCCCHHHH-----------HHHHCCeEE------CCCcccccccEEEEec---C
Confidence 9999999986 6789999999988877653321 122223322 4677889999998753 3
Q ss_pred EEEEEEeCCCchhHHHHHHHhCCCceec
Q 019431 311 ALVEWRLETGRTHQVLMLYKLFYIPRMI 338 (341)
Q Consensus 311 slv~~~l~TGR~HQIR~hla~lG~PIvG 338 (341)
++++|+|.|||+||||+||+++||||+|
T Consensus 172 sll~~~l~tGRtHQIR~h~~~~G~pi~g 199 (232)
T PRK10839 172 TQVRLTISEGRYHQVKRMFAAVGNHVVE 199 (232)
T ss_pred CEEEEEEEcCcCHHHHHHHHHcCCeEee
Confidence 8999999999999999999999999998
No 9
>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=7.7e-41 Score=304.16 Aligned_cols=163 Identities=26% Similarity=0.389 Sum_probs=138.1
Q ss_pred eeEEeeCCcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccc
Q 019431 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVH 216 (341)
Q Consensus 137 ~~Ilyed~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vh 216 (341)
++|||||++++|+|||+|++||+..+ ..++.+.+..+.. ..++++||
T Consensus 2 ~~ilyed~~~lvvnKP~Gl~v~~~~~--~~~l~~~l~~~~~-------------------------------~~~~~~Vh 48 (217)
T TIGR01621 2 FEILFTHPDFLLINKHPGISVHKDDG--ETGLLQEVATQLG-------------------------------VGQVWLVH 48 (217)
T ss_pred ceEEEeCCCEEEEECCCCCeECCCCC--cChHHHHHHHhcC-------------------------------CCCccEec
Confidence 57999999999999999999998754 3466666654321 13578899
Q ss_pred cCCCCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCceeE
Q 019431 217 RLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAA 296 (341)
Q Consensus 217 RLD~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~ 296 (341)
|||++||||||||+|+++++.|+++|+++.++|+|+|+|.|.+..+++.|+.++.+...+... +... .++.|.
T Consensus 49 RLDr~TSGlll~Ak~~~~~~~L~~~~~~~~v~K~YlAlV~g~~~~~~~~i~~~~~~~~~~~~~--~~~~-----~~k~a~ 121 (217)
T TIGR01621 49 RLDKMTSGILLLALNAESASELSQGFAKRKIEKTYLALSSKKPKKKQGLICGDMEKSRRGSWK--LVNS-----QENPAI 121 (217)
T ss_pred CCCCCCceEEEEEcCHHHHHHHHHHHhcCCccEEEEEEEeccccCCCCEEeCCcccCCCCCEE--EeCC-----CCCcee
Confidence 999999999999999999999999999999999999999999998999999999765443322 2221 578899
Q ss_pred EEEEEEEEecCCCEEEEEEEeCCCchhHHHHHHHhCCCceecccC
Q 019431 297 SRYKVIEILAGGGSALVEWRLETGRTHQVLMLYKLFYIPRMIKVF 341 (341)
Q Consensus 297 t~~~~l~~~~~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~~ 341 (341)
|+|+++... .+.++++|+|.|||+||||+||+++||||+||.+
T Consensus 122 t~~~~~~~~--~~~slv~~~~~TGR~HQIRvhla~lG~PIlGD~~ 164 (217)
T TIGR01621 122 TRFFSASAA--TGLRLFILKPHTGKTHQLRVAMKSLGSPILGDPL 164 (217)
T ss_pred EEEEEEEEc--CCeEEEEEEeCCCCHHHHHHHHHHCCCceeCCcc
Confidence 999999874 5689999999999999999999999999999974
No 10
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.
Probab=100.00 E-value=1.2e-40 Score=304.13 Aligned_cols=168 Identities=26% Similarity=0.416 Sum_probs=136.3
Q ss_pred eeEEeeCCcEEEEeCCCCCeeecCCCCCCCc--HHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccc
Q 019431 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGT--LVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (341)
Q Consensus 137 ~~Ilyed~~llvvnKP~Gl~~~~~~~~~~~t--l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 (341)
++|||||+++||+|||+|++||+.+.....+ +...|..++ ..++++
T Consensus 1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~ 48 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQL--------------------------------GQHVYP 48 (223)
T ss_pred CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHc--------------------------------CCCccc
Confidence 3699999999999999999999876443332 222332221 135678
Q ss_pred cccCCCCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCce
Q 019431 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH 294 (341)
Q Consensus 215 vhRLD~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~ 294 (341)
|||||++||||||||+|+.+++.|+++|+++.++|+|+|+|.|.+++ ++.|+.|+.++........+.. ...++.
T Consensus 49 vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~v~K~Y~alv~G~~~~-~~~i~~~l~~~~~~~~~~~~~~----~~~~~~ 123 (223)
T cd02563 49 VHRLDRPTSGVLLFALSSEVARKLGEQFTEHRVHKTYLAVVRGYVPE-SGTIDYPLSEELDKLADKFASD----DKAPQA 123 (223)
T ss_pred ccCCCCCCeEEEEEEECHHHHHHHHHHHhcCceeEEEEEEEECccCC-CCeEEEeeeeCCCccceEEeec----CCCCce
Confidence 99999999999999999999999999999999999999999999865 7899999988765544333322 226789
Q ss_pred eEEEEEEEEEe---------cCCCEEEEEEEeCCCchhHHHHHHHhCCCceecccC
Q 019431 295 AASRYKVIEIL---------AGGGSALVEWRLETGRTHQVLMLYKLFYIPRMIKVF 341 (341)
Q Consensus 295 a~t~~~~l~~~---------~~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~~ 341 (341)
|.|.|+++... ...+.+||+|+|.|||+||||+||+++||||+||.+
T Consensus 124 a~t~~~~l~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~ 179 (223)
T cd02563 124 ATTHYRLLAVEELPVVVGKYPTSRYSLVELTPHTGRKHQLRRHLAHIRHPIIGDTT 179 (223)
T ss_pred eEEEEEEeeecccccccccCCCCCeEEEEEEeCCCCHHHHHHHHHHcCCCeeCCcc
Confidence 99999999752 123589999999999999999999999999999974
No 11
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=100.00 E-value=3.6e-40 Score=307.00 Aligned_cols=168 Identities=24% Similarity=0.343 Sum_probs=134.4
Q ss_pred eeEEeeCCcEEEEeCCCCCeeecCCCCCCCcH--HHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccc
Q 019431 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTL--VNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (341)
Q Consensus 137 ~~Ilyed~~llvvnKP~Gl~~~~~~~~~~~tl--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 (341)
++|||||+++||+|||+|++||+.+.....+. ...+..++ ..++++
T Consensus 2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~ 49 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQI--------------------------------GQHVFT 49 (257)
T ss_pred CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHh--------------------------------CCCcee
Confidence 57999999999999999999999754443332 23332221 134678
Q ss_pred cccCCCCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCce
Q 019431 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH 294 (341)
Q Consensus 215 vhRLD~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~ 294 (341)
|||||++||||||||+|+++++.|+++|+++.|.|+|+|+|.|.+. +++.++.|+.+...+........ ...++.
T Consensus 50 VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~Alv~G~~~-~~~~i~~~l~~~~~~~~~~~~~~----~~~~k~ 124 (257)
T PRK11112 50 AHRLDRPTSGVLLMALSSEVARLLAQQFEQHQIQKTYHAIVRGWLM-EEAVLDYPLKEELDKIADKFARE----DKAPQP 124 (257)
T ss_pred eccCCCCCeeEEEEECCHHHHHHHHHHHHhCCcceEEEEEEEeEeC-CCCeEeeeeeecccccceeeccc----CCCCeE
Confidence 9999999999999999999999999999999999999999999885 56789999987543322111111 236899
Q ss_pred eEEEEEEEEEec---------CCCEEEEEEEeCCCchhHHHHHHHhCCCceecccC
Q 019431 295 AASRYKVIEILA---------GGGSALVEWRLETGRTHQVLMLYKLFYIPRMIKVF 341 (341)
Q Consensus 295 a~t~~~~l~~~~---------~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~~ 341 (341)
|.|.|++++... ..+.+|++|+|.|||+||||+||+++||||+||.+
T Consensus 125 a~T~~~~l~~~~~~~~~~~~~~~~~slv~i~~~TGRtHQIRvhla~lG~PIvGD~~ 180 (257)
T PRK11112 125 AVTHYRGLATVEMPVATGRYPTTRYSLVELEPKTGRKHQLRRHMAHLRHPIIGDTK 180 (257)
T ss_pred eEEEEEEEEEecccccccccCCCCeEEEEEEcCCCChHHHHHHHHHcCCCEeCCcc
Confidence 999999997641 24589999999999999999999999999999974
No 12
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=100.00 E-value=9.8e-39 Score=307.13 Aligned_cols=241 Identities=30% Similarity=0.380 Sum_probs=199.0
Q ss_pred EEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccccCCccccCCCCCeeEEee
Q 019431 63 TVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYE 142 (341)
Q Consensus 63 ~v~~~~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~Ilye 142 (341)
.+.....+..+.+++++.|-..++...+..|+.|.|++||+.+ ..++.++.||.|....+..++.. ...++.|+||
T Consensus 36 ~~~~rw~~k~~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~-~v~~i~k~~d~l~~~vhrh~p~~---~~~~~~Iv~e 111 (371)
T KOG1919|consen 36 FVKGRWAGKKLVDVFVSEFRLRERAYYESAIKLGRVTVNGEQV-RVSLIVKNGDVLCHTVHRHEPPV---AYLPIRIVFE 111 (371)
T ss_pred EEeeeecccchHHHHHHHHhcCchHhhhhhhhcCceEECcEee-eeEEEeccCCEEEEeeccCCCCc---cccccceEEe
Confidence 3445566667788888888888889999999999999999999 58999999999998777666554 2367899999
Q ss_pred CCcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCC
Q 019431 143 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 222 (341)
Q Consensus 143 d~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T 222 (341)
|++|+|||||+|++|||.+....+++...+..... ...+.+|||||+.|
T Consensus 112 d~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~~~-------------------------------~~~~~~~hRLDr~t 160 (371)
T KOG1919|consen 112 DKDYVVVNKPHGIPVHPTGRYRENTITKILAALHK-------------------------------VEGLRPCHRLDRLT 160 (371)
T ss_pred cCCEEEEeCCCCCceeccCccccccchHHHHHhcc-------------------------------ccccccccccCccc
Confidence 99999999999999999888888888777765311 24567899999999
Q ss_pred ceeEEeecCHHHHHHHHHHhhcCccceEE-EEEEeccCC-CCCcEEEecceeCCCCCeeEEecCCCC-CCCCCceeEEEE
Q 019431 223 SGLLVVAKDEHSHAHLSEQFKLHTIERVY-ISLTSGVPS-QSSGRIEVPISRDPNNRIRMAAIPGSN-KHGQARHAASRY 299 (341)
Q Consensus 223 SGLll~ak~~~~a~~l~~~f~~~~v~K~Y-~a~v~G~~~-~~~~~i~~~l~~~~~~~~~~~~~~~~~-~~~~~k~a~t~~ 299 (341)
||||+||++...+..++.+|+++.+.|.| +|.|.|.++ .+...|..|+..... -.+|.+..... ....++.|.|.|
T Consensus 161 SGllvlAkt~~~~~~~~~~~r~~~~~k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~-~~~~~l~~~~~~~~~~~k~a~T~~ 239 (371)
T KOG1919|consen 161 SGLLVLAKTKEAADKFHEVLRKRTVKKEYVVARVEGPFPVVGEVEIKEPIGEEER-PLRMGLNAVGVRDEVAAKDAKTLF 239 (371)
T ss_pred cceEEEEechhHhHHHHHHHhcccceeEEEEEEEeccCCCCceEEeCCCcccccc-ccceEeeecccccccccccceeEE
Confidence 99999999999999999999999999999 799999997 566667667665432 13344332211 112489999999
Q ss_pred EEEEEecCCCEEEEEEEeCCCchhHHHHHHHhCCCceecccC
Q 019431 300 KVIEILAGGGSALVEWRLETGRTHQVLMLYKLFYIPRMIKVF 341 (341)
Q Consensus 300 ~~l~~~~~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~~ 341 (341)
+++..+ +..++|+|.|+|||+||||+||+++|+||+||..
T Consensus 240 ~~~~~~--~~ss~V~~~PlTGRtHQIRvHlq~lG~PI~gD~~ 279 (371)
T KOG1919|consen 240 KVLSYD--GGSSLVECRPLTGRTHQIRVHLQYLGHPIAGDPK 279 (371)
T ss_pred EEcccC--CceEEEEeeccCCcHHHHHHHHHHhCCCcCCCcc
Confidence 999986 7899999999999999999999999999999974
No 13
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=100.00 E-value=1.7e-38 Score=299.94 Aligned_cols=205 Identities=19% Similarity=0.193 Sum_probs=157.3
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCC--CEEeeeccccCCccccCCCCCeeEEeeCCcEE
Q 019431 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGG--DMVNCTISELQPLRAEAEDIPLDIVYEDDNVL 147 (341)
Q Consensus 70 ~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~g--D~I~v~~~~~~~~~~~~~~~~~~Ilyed~~ll 147 (341)
.+||++||++. +.+||+.++++|++|+|+|||+++ .++++|.++ |.|.++........ + .-|++.|+
T Consensus 2 ~~RL~k~La~~-g~~SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g~~~~~~~--~-------~~e~~~yl 70 (289)
T PRK10700 2 SEKLQKVLARA-GHGSRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRIDGHLISVKE--S-------AEQICRVL 70 (289)
T ss_pred chhHHHHHHHC-CCCCHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEECCEEeeccc--c-------cccCCeEE
Confidence 37999999986 789999999999999999999998 689999887 56777653221100 0 01557899
Q ss_pred EEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceeEE
Q 019431 148 VVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLV 227 (341)
Q Consensus 148 vvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGLll 227 (341)
++|||+|++|++.+.....|+++.+.... ..++++|||||++||||||
T Consensus 71 vlnKP~G~~~s~~d~~~~~tv~d~l~~~~--------------------------------~~~~~~VgRLD~dTsGLLL 118 (289)
T PRK10700 71 AYYKPEGELCTRNDPEGRPTVFDRLPKLR--------------------------------GARWIAVGRLDVNTCGLLL 118 (289)
T ss_pred EEECCCCCEeecCCCCCCccHHHHhhhhc--------------------------------CCceeEccCCCCCCceEEE
Confidence 99999999999988777789998885311 1356789999999999999
Q ss_pred eecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCceeEEEEEEEEEec-
Q 019431 228 VAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILA- 306 (341)
Q Consensus 228 ~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~- 306 (341)
||+|++++..|.. +++.|+|+|+|+|.|.++++... .+..++..+ ++. +.+..+....
T Consensus 119 lTndg~~~~~L~~--p~~~i~K~Y~v~V~G~~~~~~l~-----------~l~~Gv~l~-----~~~---~~~~~v~~~~~ 177 (289)
T PRK10700 119 FTTDGELANRLMH--PSREVEREYAVRVFGQVDDAKLR-----------QLSRGVQLE-----DGP---AAFKTIKFSGG 177 (289)
T ss_pred EEcCHHHHHHHhC--ccCCCCeEEEEEEccCCCHHHHH-----------HHHcCCEeC-----Cce---eeeEEEEeccC
Confidence 9999999999987 78899999999999998765432 122222221 222 2233333221
Q ss_pred CCCEEEEEEEeCCCchhHHHHHHHhCCCceec
Q 019431 307 GGGSALVEWRLETGRTHQVLMLYKLFYIPRMI 338 (341)
Q Consensus 307 ~~~~slv~~~l~TGR~HQIR~hla~lG~PIvG 338 (341)
....++++++|.|||+||||+||+++|+||+.
T Consensus 178 ~~~~s~l~v~L~EGk~hQIRrm~~~lG~~V~~ 209 (289)
T PRK10700 178 EGINQWYNVTLTEGRNREVRRLWEAVGVQVSR 209 (289)
T ss_pred CCCceEEEEEEeCCccHHHHHHHHHcCCEEeE
Confidence 13458999999999999999999999999973
No 14
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=100.00 E-value=6.4e-38 Score=295.39 Aligned_cols=198 Identities=21% Similarity=0.235 Sum_probs=154.8
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccccCCccccCCCCCeeEEeeCCcEE
Q 019431 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVL 147 (341)
Q Consensus 68 ~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~Ilyed~~ll 147 (341)
.+++||++||++. +.+||+.++++|++|+|+|||+++ .++++|.+||.|.|+.....+. .+||++||
T Consensus 4 ~~~~RL~k~La~~-g~~SRr~a~~lI~~G~V~VNGk~v-~~~~~V~~gD~V~v~g~~i~~~-----------~~ed~~~l 70 (290)
T PRK10475 4 DSSTRLNKYISES-GICSRREADRYIEQGNVFINGKRA-TIGDQVKAGDVVKVNGQLIEPR-----------EAEDLVLI 70 (290)
T ss_pred chHHHHHHHHHhC-CCCCHHHHHHHHHCCcEEECCEEc-cCCCCcCCCCEEEECCEEcccc-----------ccCCCeEE
Confidence 4568999999987 789999999999999999999998 6899999999999986422211 13788999
Q ss_pred EEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceeEE
Q 019431 148 VVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLV 227 (341)
Q Consensus 148 vvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGLll 227 (341)
++|||+|++||+.+. ...++++.|..+ .++++|||||++||||||
T Consensus 71 vlnKP~G~~~~~~~~-~~~tv~~~l~~~----------------------------------~~l~~VgRLDrdTsGLLL 115 (290)
T PRK10475 71 ALNKPVGIVSTTEDG-ERDNIVDFVNHS----------------------------------KRVFPIGRLDKDSQGLIF 115 (290)
T ss_pred EEECCCCCCcCCCCC-CCCcHHHHhhcc----------------------------------ccccccccCCCCCcceEE
Confidence 999999999998765 457888877421 356789999999999999
Q ss_pred eecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCceeEEEEEEEEEecC
Q 019431 228 VAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAG 307 (341)
Q Consensus 228 ~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~ 307 (341)
||+|++++..|.. +.+.++|+|+|+|.|.++++... .+..++... +.......+..+
T Consensus 116 lT~dg~~~~~L~~--p~~~i~K~Y~v~V~g~~~~~~l~-----------~l~~Gv~l~-----~~~~~~~~v~~~----- 172 (290)
T PRK10475 116 LTNHGDLVNKILR--AGNDHEKEYLVTVDKPITDEFIR-----------GMGAGVPIL-----GTVTKKCKVKKE----- 172 (290)
T ss_pred EecCHHHHHHhhC--cCCCCCeEEEEEECCCCCHHHHH-----------HHhCCcEEC-----CEEecceEEEec-----
Confidence 9999999999987 56789999999999998765432 222222221 111111122211
Q ss_pred CCEEEEEEEeCCCchhHHHHHHHhCCCcee
Q 019431 308 GGSALVEWRLETGRTHQVLMLYKLFYIPRM 337 (341)
Q Consensus 308 ~~~slv~~~l~TGR~HQIR~hla~lG~PIv 337 (341)
+.++++++|.+||+||||+||+++|++|+
T Consensus 173 -~~~~~~i~l~eGk~rqIRrm~~~~G~~V~ 201 (290)
T PRK10475 173 -APFVFRITLVQGLNRQIRRMCEHFGYEVT 201 (290)
T ss_pred -CCcEEEEEEECCcCHHHHHHHHHcCCEEe
Confidence 23579999999999999999999999986
No 15
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.7e-38 Score=286.31 Aligned_cols=206 Identities=21% Similarity=0.295 Sum_probs=165.5
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCC-CEEeeeccccCCccccCCCCCeeEEeeCCcEEE
Q 019431 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGG-DMVNCTISELQPLRAEAEDIPLDIVYEDDNVLV 148 (341)
Q Consensus 70 ~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~g-D~I~v~~~~~~~~~~~~~~~~~~Ilyed~~llv 148 (341)
.+||+|||++. +.+||++++++|++|+|+|||++++..+..+.++ |.|.+++...... +...|++
T Consensus 2 ~~RL~K~La~~-G~~SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~~~~~-------------~~~~y~l 67 (248)
T COG1187 2 SMRLNKFLAEA-GVGSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKRIELK-------------EERVYLL 67 (248)
T ss_pred ccchHHHHHHc-CCCCHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCEEeecc-------------ccceEEE
Confidence 58999999998 8999999999999999999999998889999998 5788877432211 2344999
Q ss_pred EeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceeEEe
Q 019431 149 VNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVV 228 (341)
Q Consensus 149 vnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGLll~ 228 (341)
+|||.|++|+..++..+.|+.+.|.... + ...++++|+|||+||||||||
T Consensus 68 lnKP~G~v~s~~D~~gr~tv~D~lp~~~--~----------------------------~~~~~~pvGRLD~dTeGLLLL 117 (248)
T COG1187 68 LNKPRGYVSSTEDDEGRPTVFDLLPERL--P----------------------------RKKRLFPVGRLDKDTEGLLLL 117 (248)
T ss_pred EECCCCeEecccCCCCCceeeeeccccc--c----------------------------cccceeeccccCCCCeeEEEE
Confidence 9999999999998888889888775321 0 135789999999999999999
Q ss_pred ecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCceeEEEEEEEEEecCC
Q 019431 229 AKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGG 308 (341)
Q Consensus 229 ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~ 308 (341)
|+|++++.+|.. +.+.++|+|+|.|.|.++++... .++.++... ++....+....+......
T Consensus 118 TnDG~la~rL~~--P~~~~~K~Y~v~v~g~~~~~~l~-----------~l~~Gv~l~-----d~~~~~~~~~~l~~~~~~ 179 (248)
T COG1187 118 TNDGELAHRLMH--PSSEVEKEYLVRVEGPVTEEDLE-----------KLRKGVTLD-----DGETKPAKPASLEKEPGK 179 (248)
T ss_pred eCCHHHHHHhcC--CCCCCCEEEEEEEecCCCHHHHH-----------HHhCCcEec-----CcccccceeEEEEecCCC
Confidence 999999999988 89999999999999998766544 455555543 333334442223222122
Q ss_pred CEEEEEEEeCCCchhHHHHHHHhCCCcee
Q 019431 309 GSALVEWRLETGRTHQVLMLYKLFYIPRM 337 (341)
Q Consensus 309 ~~slv~~~l~TGR~HQIR~hla~lG~PIv 337 (341)
+.+|++++|.+||+||||+||+++|+|++
T Consensus 180 ~~s~~~itl~EGrnrQVRRm~~a~G~~V~ 208 (248)
T COG1187 180 NNSWLRITLTEGRNRQVRRMFEAVGLEVL 208 (248)
T ss_pred CceEEEEEEeCCcCHHHHHHHHHcCCEEe
Confidence 68999999999999999999999999986
No 16
>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=7e-36 Score=263.90 Aligned_cols=162 Identities=43% Similarity=0.693 Sum_probs=133.6
Q ss_pred EEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCcee
Q 019431 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (341)
Q Consensus 146 llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (341)
++|+|||+|++|++.+.....++.+.+....... ....++++|||||++||||
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~v~RLD~~tsGl 53 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLL---------------------------GEEFRPGLVHRLDKDTSGL 53 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhc---------------------------CCCCcCceecccCCCCceE
Confidence 5899999999999998877778877653222100 1125678999999999999
Q ss_pred EEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCceeEEEEEEEEEe
Q 019431 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL 305 (341)
Q Consensus 226 ll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~ 305 (341)
||||+|+++++.|..+|+.+.++|+|+|+|.|.+..+.+.+..++..+........... .+++.+.|+|+++...
T Consensus 54 ll~ak~~~~~~~l~~~~~~~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~t~~~~l~~~ 128 (185)
T cd02869 54 LLVAKNKKAAAKLSKQFKERKVKKTYLALVDGKPPEDEGTIDAPLGRKKRKKRARVVVS-----EDGKPAITHYKVLERF 128 (185)
T ss_pred EEEEcCHHHHHHHHHHHhcCceeEEEEEEEeCCCCCCccEEecccccCCccCceEEEEC-----CCCeEEEEEEEEEEEc
Confidence 99999999999999999999999999999999999999998888876422222222222 2678999999999863
Q ss_pred cCCCEEEEEEEeCCCchhHHHHHHHhCCCceecccC
Q 019431 306 AGGGSALVEWRLETGRTHQVLMLYKLFYIPRMIKVF 341 (341)
Q Consensus 306 ~~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~~ 341 (341)
.++++++|+|.|||+||||+||+++|+||+||.+
T Consensus 129 --~~~s~~~~~l~tGR~HQIR~hl~~~G~pIvGD~~ 162 (185)
T cd02869 129 --GNVTLVELQLETGRTHQIRVHLASIGHPIVGDPK 162 (185)
T ss_pred --CCcEEEEEEeCcCCccHHHHHHHHCCCCEeCccc
Confidence 4789999999999999999999999999999974
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=2e-34 Score=248.64 Aligned_cols=147 Identities=29% Similarity=0.422 Sum_probs=119.0
Q ss_pred EEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCcee
Q 019431 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (341)
Q Consensus 146 llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (341)
++|+|||+|++||+.++....++.+.+.... ..++++|||||++||||
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~vhRLD~~TSGl 48 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLH--------------------------------GPRVHAAGRLDKDTSGL 48 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhhccc--------------------------------CCceeEeccCCCCCeeE
Confidence 5899999999999988777778877553211 14578899999999999
Q ss_pred EEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCceeEEEEEEEEEe
Q 019431 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL 305 (341)
Q Consensus 226 ll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~ 305 (341)
||||+|+++++.|+.+ ++.++|+|+|+|.|.+++ ++.+..++.+. ++.. ++... +++.+.|+|+++...
T Consensus 49 ll~ak~~~~~~~l~~~--~~~v~K~Y~a~v~g~~~~-~~~~~~~~~~~--~~~~-~~~~~-----~~~~~~t~~~~l~~~ 117 (154)
T cd02550 49 LLLTNDGRLQRRLTEP--RREIEKEYLVTVRGELDE-EGIEDLATVRR--GRLS-GLVDE-----GVPLAVTKVRVIGEH 117 (154)
T ss_pred EEEEcCHHHHHHHhhh--hccCcEEEEEEEEeecCc-chheecccccc--Ccce-eEEcC-----CCcccceEEEEEEec
Confidence 9999999999999997 788999999999999864 44556666541 1222 22222 578899999999753
Q ss_pred cCCCEEEEEEEeCCCchhHHHHHHHhCCCcee
Q 019431 306 AGGGSALVEWRLETGRTHQVLMLYKLFYIPRM 337 (341)
Q Consensus 306 ~~~~~slv~~~l~TGR~HQIR~hla~lG~PIv 337 (341)
.+.++++++|.|||+||||+||+++||||.
T Consensus 118 --~~~sll~~~l~tGR~HQIR~hla~~G~pI~ 147 (154)
T cd02550 118 --GGTGRLRLTLKTGRTHQIRRHCAAVGFPVL 147 (154)
T ss_pred --CCcEEEEEEEcCCCcHHHHHHHHHcCCcEE
Confidence 467999999999999999999999999996
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=2e-33 Score=245.70 Aligned_cols=141 Identities=20% Similarity=0.193 Sum_probs=114.7
Q ss_pred cEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 019431 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (341)
Q Consensus 145 ~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (341)
.++|+|||+|++|++.++....++.+.+..+. ..++++|||||++|||
T Consensus 1 ~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~--------------------------------~~~~~~V~RLD~~TsG 48 (167)
T cd02556 1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLG--------------------------------IPRWISVGRLDLNTEG 48 (167)
T ss_pred CEEEEECCCCcEECccCCCCCccHHHhhhhhc--------------------------------cCceEEcCcCCCCCee
Confidence 37999999999999877666778888876431 1356789999999999
Q ss_pred eEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCceeEEEEEEEEE
Q 019431 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEI 304 (341)
Q Consensus 225 Lll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~ 304 (341)
|||||+|+++++.|.. +++.++|+|+|+|.|.++++... .+..++..+ +++.+.++|+++..
T Consensus 49 Lll~ak~~~~~~~L~~--~~~~i~K~Y~a~V~g~~~~~~~~-----------~~~~gv~~~-----~~~~~~~~~~~~~~ 110 (167)
T cd02556 49 LLLFTNDGELANRLMH--PSNEIEREYAVRVFGQVTDEQLK-----------SLKKGVELE-----DGFAGFKSIQLEGG 110 (167)
T ss_pred EEEEECCHHHHHHHhC--CcCCCCeEEEEEECccCCHHHHH-----------HHHcCCEEC-----CCcCcceEEEEEec
Confidence 9999999999999986 78899999999999998765421 111122222 56788899999865
Q ss_pred ecCCCEEEEEEEeCCCchhHHHHHHHhCCCcee
Q 019431 305 LAGGGSALVEWRLETGRTHQVLMLYKLFYIPRM 337 (341)
Q Consensus 305 ~~~~~~slv~~~l~TGR~HQIR~hla~lG~PIv 337 (341)
. .++++++|+|.|||+||||+||+++||||+
T Consensus 111 ~--~~~sll~v~l~tGR~HQIR~~~a~~G~pV~ 141 (167)
T cd02556 111 E--GKNSWYRVTLREGRNREVRRLWEAFGLQVS 141 (167)
T ss_pred C--CCcEEEEEEEEeCCCHHHHHHHHHcCCeEe
Confidence 3 457999999999999999999999999996
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=1e-33 Score=242.15 Aligned_cols=140 Identities=26% Similarity=0.337 Sum_probs=111.7
Q ss_pred EEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCcee
Q 019431 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (341)
Q Consensus 146 llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (341)
|+|+|||+|++|++.++...+++.+.+... ..++++|||||++||||
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~~---------------------------------~~~~~~vhRLD~~TsGl 47 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDV---------------------------------GERLFPVGRLDYDTEGL 47 (146)
T ss_pred CEEEECCCCcEecccCCCCCCEEeeecccc---------------------------------CCCEEECCCCCCCCeeE
Confidence 589999999999998766666765443210 14578999999999999
Q ss_pred EEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCceeEEEEEEEEEe
Q 019431 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL 305 (341)
Q Consensus 226 ll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~ 305 (341)
||||+|+++++.|.. +++.++|+|+|+|.|.+.++.+. ....++... +++.+.|+|+++...
T Consensus 48 ll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~~~~~-----------~~~~~~~~~-----~~~~~~t~~~~l~~~ 109 (146)
T cd02870 48 LLLTNDGELANRLTH--PRYGVEKTYLVKVRGVPSEEELR-----------RLRAGVELD-----DGKTAPAKVKVLSRD 109 (146)
T ss_pred EEEeCCHHHHHHhhC--ccCCCCeEEEEEECCCCCHHHHH-----------HHHCCeEeC-----CceEcceEEEEeccC
Confidence 999999999999986 67889999999999998755431 111112221 577899999999763
Q ss_pred cCCCEEEEEEEeCCCchhHHHHHHHhCCCceec
Q 019431 306 AGGGSALVEWRLETGRTHQVLMLYKLFYIPRMI 338 (341)
Q Consensus 306 ~~~~~slv~~~l~TGR~HQIR~hla~lG~PIvG 338 (341)
.+.++++|+|.|||+||||+||+++|+||+-
T Consensus 110 --~~~sll~~~l~tGR~HQIR~hla~~G~pI~~ 140 (146)
T cd02870 110 --PKNTLLEVTLHEGRNRQVRRMFEAVGHPVLR 140 (146)
T ss_pred --CCCcEEEEEEEeCCcHHHHHHHHHcCCcCCe
Confidence 4579999999999999999999999999973
No 20
>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=100.00 E-value=3.2e-32 Score=236.13 Aligned_cols=155 Identities=35% Similarity=0.525 Sum_probs=116.2
Q ss_pred cEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 019431 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (341)
Q Consensus 145 ~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (341)
+|||+|||+||+|++.++............... ......++++|||||++|||
T Consensus 1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~~~v~RLD~~TsG 53 (164)
T PF00849_consen 1 NLIVVNKPAGVPVHPSDGNESKSVKELPALSLK---------------------------RGDDPPELYPVHRLDRDTSG 53 (164)
T ss_dssp SEEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHH---------------------------HCTTSGGGEESS---TT-EE
T ss_pred CEEEEECCCCCeEecCCCCCcccccchhhhhhh---------------------------hccCCCceEECCCCCccccC
Confidence 589999999999999885333333222222111 01234678999999999999
Q ss_pred eEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeC--CCCCeeEEecCCCCCCCCCceeEEEEEEE
Q 019431 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRD--PNNRIRMAAIPGSNKHGQARHAASRYKVI 302 (341)
Q Consensus 225 Lll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~--~~~~~~~~~~~~~~~~~~~k~a~t~~~~l 302 (341)
|||||+|+++++.|+++|+.+.++|+|+|+|.|.+.++++.++.++..+ .......... ...++.+.|.|+++
T Consensus 54 lll~a~~~~~~~~l~~~f~~~~~~K~Y~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~t~~~~l 128 (164)
T PF00849_consen 54 LLLFAKDKEAAAKLSKQFPKRKVEKTYLALVEGGPVEEEGKINSPLGKDVGKNKSSNKDPP-----GRDGKPAITRYRVL 128 (164)
T ss_dssp EEEEESSHHHHHHHHHHHHTTCSEEEEEEEECSSSSTTCEEEESHEEE-EECSSCTCCEEE-----TTTSBTSEEEEEEE
T ss_pred CeeccCCcccccccccccccCCCcEEEEEeEcccccccceeeeccccccccccccceeeee-----cccccccceeeeee
Confidence 9999999999999999999999999999999988888899999999772 1111112222 23788999999999
Q ss_pred EEe-------cCCCEEEEEEEeCCCchhHHHHHHHh
Q 019431 303 EIL-------AGGGSALVEWRLETGRTHQVLMLYKL 331 (341)
Q Consensus 303 ~~~-------~~~~~slv~~~l~TGR~HQIR~hla~ 331 (341)
... ....+++++|+|.|||+||||+||++
T Consensus 129 ~~~~~~~~~~~~~~~s~v~~~l~tGr~HQIR~hla~ 164 (164)
T PF00849_consen 129 RSGSRTPSKDENAGCSLVECELITGRTHQIRVHLAH 164 (164)
T ss_dssp EEETT---EECCSSEEEEEEEESS-STTHHHHHHHH
T ss_pred ccccccccccccCCCEEEEEEECcCCCHHHHHHhcC
Confidence 986 56789999999999999999999986
No 21
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.
Probab=99.97 E-value=8.4e-32 Score=235.41 Aligned_cols=139 Identities=18% Similarity=0.221 Sum_probs=106.2
Q ss_pred EEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCcee
Q 019431 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (341)
Q Consensus 146 llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (341)
++|+|||+|++|++.+ ....++.+.+..++. ..++++|||||++||||
T Consensus 2 ~ivvnKP~G~~~~~~~-~~~~tl~~~l~~~~~-------------------------------~~~~~~vhRLD~~TSGl 49 (167)
T cd02553 2 YLMLNKPAGVVCATKD-PHHPTVIDLLPEPDR-------------------------------RRDLFPVGRLDKDTTGL 49 (167)
T ss_pred EEEEECCCCCEeCCCC-CCCCcHHHHhhhhcc-------------------------------cCCeEEcccCCCCCEEE
Confidence 7999999999999654 446788888865431 13578899999999999
Q ss_pred EEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCC-ceeEEEEEEEEE
Q 019431 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQA-RHAASRYKVIEI 304 (341)
Q Consensus 226 ll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~-k~a~t~~~~l~~ 304 (341)
||||+|..+++.+.. +.+.++|+|+|+|.|.++++.+. ....++... ++ +...+.++++.
T Consensus 50 ll~ak~~~~~~~l~~--~~~~i~K~Y~a~V~G~~~~~~~~-----------~~~~~~~~~-----~~~~~~~~~~~~~~- 110 (167)
T cd02553 50 LLLTNDGQLAHRLTS--PKKHVPKTYEVTLAGPLTEDDIE-----------AFAEGVLLH-----DGYPTKPAKLEILS- 110 (167)
T ss_pred EEEEeCHHHHHHhhC--CcCCCceEEEEEEccCCCHHHHH-----------HHHCCeEEc-----CCCEeeeeEEEEeC-
Confidence 999999998888876 57889999999999998755431 011111111 12 23445555552
Q ss_pred ecCCCEEEEEEEeCCCchhHHHHHHHhCCCceeccc
Q 019431 305 LAGGGSALVEWRLETGRTHQVLMLYKLFYIPRMIKV 340 (341)
Q Consensus 305 ~~~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~ 340 (341)
.++++|+|.|||+||||+||+++||||++|.
T Consensus 111 -----~sll~v~l~tGR~HQIR~hla~lG~pI~~~~ 141 (167)
T cd02553 111 -----PTTVRLTITEGKYHQVKRMFAAVGNKVVALH 141 (167)
T ss_pred -----CcEEEEEEEeCCCHHHHHHHHHcCCeEEEEE
Confidence 2899999999999999999999999999983
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=1.5e-30 Score=227.80 Aligned_cols=152 Identities=16% Similarity=0.183 Sum_probs=104.3
Q ss_pred EEEEeCCCCCeeecCCC-CCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 019431 146 VLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (341)
Q Consensus 146 llvvnKP~Gl~~~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (341)
++++|||+|++||+.++ ....++.+.+.. .++++|||||++|||
T Consensus 1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l~~-----------------------------------~~~~~v~RLD~~TsG 45 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYIDD-----------------------------------PGVYAAGRLDRDSEG 45 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCccHHHHcCc-----------------------------------CCeEEccCCCCCCeE
Confidence 58999999999998765 445677665521 245789999999999
Q ss_pred eEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcE-EEecceeCCCCCeeEEecCCCCCCCCCceeEEEEEEEE
Q 019431 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGR-IEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIE 303 (341)
Q Consensus 225 Lll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~-i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~ 303 (341)
|||||+|+++++.|.+ +.+.++|+|+|+|.|.++++... +...+...........+... .......+.|+++.
T Consensus 46 lll~a~d~~~~~~l~~--~~~~v~K~Y~a~v~g~~~~~~~~~l~~g~~~~~~~~~~~~v~~~----~~~~~~~~~~~~~~ 119 (168)
T cd02566 46 LLLLTDDGRLQHRITD--PSFKHPKTYYVQVEGVPTEDALEQLRNGVELGDGLTLPAKVEKV----DEPPWLWEREPPIR 119 (168)
T ss_pred EEEEEeCHHHHHHHHC--CCCCCCEEEEEEECCcCCHHHHHHHhCCcEECCeEecceEEEEe----cccccccccccccc
Confidence 9999999999888887 45679999999999998654321 00111111000011111110 01223334444454
Q ss_pred EecCCCEEEEEEEeCCCchhHHHHHHHhCCCceec
Q 019431 304 ILAGGGSALVEWRLETGRTHQVLMLYKLFYIPRMI 338 (341)
Q Consensus 304 ~~~~~~~slv~~~l~TGR~HQIR~hla~lG~PIvG 338 (341)
.....+.++++|+|.|||+||||+||+++||||+.
T Consensus 120 ~~~~~~~sll~v~l~tGR~HQIR~~la~lG~pV~~ 154 (168)
T cd02566 120 FRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLR 154 (168)
T ss_pred cccCCCccEEEEEEecCccHHHHHHHHHcCCeEeE
Confidence 32234568999999999999999999999999975
No 23
>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=3e-29 Score=221.02 Aligned_cols=107 Identities=17% Similarity=0.178 Sum_probs=80.5
Q ss_pred CCccccccCCCCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCC
Q 019431 210 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKH 289 (341)
Q Consensus 210 ~~~~~vhRLD~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~ 289 (341)
.++++|||||++||||||||+|+.+++.|.. +.+.|+|+|+|+|.|.++++... .+..++..+ .
T Consensus 45 ~~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~--~~~~i~K~Y~v~v~g~~~~~~l~-----------~l~~g~~~~---~ 108 (177)
T cd02555 45 ARLAPIGPLDKDASGLLVFSQDGRVLRKLIG--DASRLEQEYLVEVRGELTAGGLE-----------RLNHGLTYD---G 108 (177)
T ss_pred CceeEecCCCCCCeeEEEEECCHHHHHHHhC--hhcCCCEEEEEEEcccCCHHHHH-----------HHhcCcccC---C
Confidence 3678999999999999999999999999998 45889999999999998754321 111111111 0
Q ss_pred CCCceeEEEEEEEEEecCCCEEEEEEEeCCCchhHHHHHHHhCCCceeccc
Q 019431 290 GQARHAASRYKVIEILAGGGSALVEWRLETGRTHQVLMLYKLFYIPRMIKV 340 (341)
Q Consensus 290 ~~~k~a~t~~~~l~~~~~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~ 340 (341)
...+.+.+.+ .+.++++++|.|||+||||+||+++||||+|+.
T Consensus 109 ~~~~~~~~~~--------~~~~~l~i~l~tGr~hQIR~~~~~~G~pV~~L~ 151 (177)
T cd02555 109 RELPPAKVSW--------QNEQRLRFALKEPQPGQIRRMCESVGLEVVALR 151 (177)
T ss_pred eecceEEEEE--------cCCCEEEEEEECCcChHHHHHHHHcCCeEEEEE
Confidence 0112222222 135789999999999999999999999999973
No 24
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.96 E-value=6.7e-29 Score=224.26 Aligned_cols=144 Identities=19% Similarity=0.236 Sum_probs=106.4
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
..|+++|||+|++|+..+.....++.+.+.. .++++|||||++||
T Consensus 39 ~~ylllnKP~G~l~~~~d~~~~~tl~d~l~~-----------------------------------~~~~~vgRLD~~Ts 83 (217)
T PRK11394 39 TRVILFNKPYDVLPQFTDEAGRKTLKEFIPV-----------------------------------QGVYAAGRLDRDSE 83 (217)
T ss_pred CEEEEEECCCCCEEeeCCccCCcchHHhccc-----------------------------------CCeEEecCCCCCCe
Confidence 5699999999999997766666788776530 35678999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCceeEEEEEEEE
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIE 303 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~ 303 (341)
||||||+|+++++.|.. +++.++|+|+|+|.|.+.++.+.. +..++... ++......++.+.
T Consensus 84 GllLlt~d~~~~~~L~~--~~~~i~K~Y~~~v~g~~~~~~l~~-----------l~~Gv~i~-----~~~~~p~~~~~i~ 145 (217)
T PRK11394 84 GLLVLTNNGALQARLTQ--PGKRTGKIYYVQVEGIPTQDALEA-----------LRNGVTLN-----DGPTLPAGAELVD 145 (217)
T ss_pred eEEEEECCHHHHHHHhC--cccCCCEEEEEEECCCCCHHHHHH-----------HhCCeEEC-----CccccccEEEEec
Confidence 99999999999999999 478899999999999987655431 11111110 0110011111111
Q ss_pred -------------EecCCCEEEEEEEeCCCchhHHHHHHHhCCCceeccc
Q 019431 304 -------------ILAGGGSALVEWRLETGRTHQVLMLYKLFYIPRMIKV 340 (341)
Q Consensus 304 -------------~~~~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~ 340 (341)
.....+.++++++|.|||+||||+||+++|+||+||.
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~s~l~I~L~eGR~hQIRrm~a~lG~pVl~L~ 195 (217)
T PRK11394 146 EPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLI 195 (217)
T ss_pred ccccccccccccccccCCCceEEEEEEeCCCCHHHHHHHHHcCCeEeeeE
Confidence 1112357899999999999999999999999999985
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=1e-26 Score=202.13 Aligned_cols=133 Identities=14% Similarity=0.127 Sum_probs=100.5
Q ss_pred EEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCcee
Q 019431 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (341)
Q Consensus 146 llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (341)
|+++|||+|++|++.+.. ..++.+.+.. ..++++|||||++||||
T Consensus 2 y~~lnKP~G~l~s~~~~~-~~tv~~~l~~----------------------------------~~~~~~vgRLD~~tsGl 46 (164)
T cd02554 2 YIAYNKPVGIDCTLERAD-EDNIIDFVNP----------------------------------PPRIFPIGRLDKDSEGL 46 (164)
T ss_pred EEEEECCCCcEeecCCCC-CCcHHHHhcC----------------------------------cCCEEEccCCCCCCeeE
Confidence 789999999999988653 4678776632 14678999999999999
Q ss_pred EEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCceeEEEEEEEEEe
Q 019431 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL 305 (341)
Q Consensus 226 ll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~ 305 (341)
||||+|+.+++.|.. +.+.++|+|+|.|.|.+.++... .+..++..+ ++ .+....++..
T Consensus 47 ll~t~dg~~~~~L~~--p~~~~~K~Y~V~v~~~l~~~~l~-----------~l~~G~~~~-----~~---~~~~~~v~~~ 105 (164)
T cd02554 47 ILLTNDGDLVNKILH--ADNNHEKEYLVTVNKPITDEFIE-----------GMSNGVVIL-----GT---VTKPCKVERL 105 (164)
T ss_pred EEEEcCHHHHHHHhh--hhcCCCeEEEEEECCCCCHHHHH-----------HHhCCCEEC-----Ce---EEcceEEEEC
Confidence 999999999999976 67889999999999998765422 222222211 22 2333333332
Q ss_pred cCCCEEEEEEEeCCCchhHHHHHHHhCCCcee
Q 019431 306 AGGGSALVEWRLETGRTHQVLMLYKLFYIPRM 337 (341)
Q Consensus 306 ~~~~~slv~~~l~TGR~HQIR~hla~lG~PIv 337 (341)
. . ++++|.|.|||+||||+||+++|+||+
T Consensus 106 ~--~-~~l~i~l~eGr~~qIRrm~~~~G~~V~ 134 (164)
T cd02554 106 A--K-DKFRIVLTQGLNRQIRRMCEALGYRVT 134 (164)
T ss_pred C--C-CEEEEEEECCcCHHHHHHHHHcCCEEE
Confidence 1 1 359999999999999999999999996
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=5.8e-27 Score=196.18 Aligned_cols=106 Identities=21% Similarity=0.297 Sum_probs=86.6
Q ss_pred cccCCCCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCCCCCce
Q 019431 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH 294 (341)
Q Consensus 215 vhRLD~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~k~ 294 (341)
|||||++||||||||+|+++++.|.. +++.|+|+|+|+|.|.++++... ++ ..++... +++.
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~--~~~~i~K~Y~a~v~g~~~~~~~~---~~--------~~g~~~~-----~~~~ 62 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTH--PGHHCEKTYLVTVEGPVTDEDLE---AL--------RKGVQLE-----DGPT 62 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhC--CCCCCCeEEEEEECCCCCHHHHH---HH--------hCCeEEC-----CcEE
Confidence 79999999999999999999999998 78899999999999998655421 12 1111111 3566
Q ss_pred eEEEEEEEEEecCCCEEEEEEEeCCCchhHHHHHHHhCCCceeccc
Q 019431 295 AASRYKVIEILAGGGSALVEWRLETGRTHQVLMLYKLFYIPRMIKV 340 (341)
Q Consensus 295 a~t~~~~l~~~~~~~~slv~~~l~TGR~HQIR~hla~lG~PIvGD~ 340 (341)
+.+.|+++... .+.++++|+|.|||+||||+||+++||||+||.
T Consensus 63 ~~~~~~~l~~~--~~~~~l~~~l~tGR~HQIR~~~~~lG~pI~g~~ 106 (128)
T TIGR00093 63 KPAKLEVITEP--GFPTWLRITLSEGRNRQVRRMFAAVGFPVLRLH 106 (128)
T ss_pred eeeEEEEEccC--CCceEEEEEEeCCCCHHHHHHHHHcCCeEeEEE
Confidence 77888888653 446899999999999999999999999999984
No 27
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=99.26 E-value=2.6e-11 Score=88.68 Aligned_cols=70 Identities=41% Similarity=0.550 Sum_probs=60.8
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccccCCccccCCCCCeeEEeeCCcEEEEe
Q 019431 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVN 150 (341)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~Ilyed~~llvvn 150 (341)
+||++||.+.++..||+.++++|++|.|+|||+.++.+++.+.+||.|.+.... .+..|+|||++++++|
T Consensus 1 ~rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~~~~----------~~~~i~~ed~~~lvv~ 70 (70)
T cd00165 1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKS----------IEEDIVYEDKKLLVVN 70 (70)
T ss_pred CcHHHHHHHhccccCHHHHHHHHHcCCEEECCEEccCCccCcCCCCEEEEcCCC----------cccceeeccCCEEEeC
Confidence 489999998866789999999999999999999987789999999999887521 1128999999999987
No 28
>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=99.10 E-value=1.5e-10 Score=105.64 Aligned_cols=76 Identities=24% Similarity=0.243 Sum_probs=55.9
Q ss_pred cEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 019431 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (341)
Q Consensus 145 ~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (341)
.+|++|||+||.++... +.+...++..+. .....+.|||||.+|||
T Consensus 1 GilvvnKP~Gi~s~~~~----~~~~~~l~~~~~------------------------------~~k~~~~vhrLD~~aSG 46 (226)
T cd02868 1 GLFAVYKPPGVHWKHVR----DTIESNLLKYFP------------------------------EDKVLVGVHRLDAFSSG 46 (226)
T ss_pred CEEEEEcCCCCChhHHH----HHHHHHHHHHcc------------------------------ccceeeEccccCCCCce
Confidence 47999999999875432 233333333221 01235678999999999
Q ss_pred eEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 225 Lll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
||+||+++.+ +|..+|.++.+.|+|+|...
T Consensus 47 vl~~a~~~~t--kl~~~~~~~~~~K~Y~~~~~ 76 (226)
T cd02868 47 VLVLGVNHGN--KLLSHLYSNHPTRVYTIRGL 76 (226)
T ss_pred EEEEEeChhH--hHHHHHHhcCCCeEEEEEEE
Confidence 9999999876 69999999999999997653
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=99.08 E-value=2.6e-10 Score=78.77 Aligned_cols=48 Identities=38% Similarity=0.511 Sum_probs=44.5
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEE
Q 019431 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMV 118 (341)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I 118 (341)
||||+||++.....||++++++|++|.|+|||++++++++.|++||+|
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 699999998766678999999999999999999998899999999986
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=99.03 E-value=5.7e-10 Score=80.64 Aligned_cols=55 Identities=13% Similarity=0.118 Sum_probs=48.1
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeee
Q 019431 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCT 121 (341)
Q Consensus 67 ~~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~ 121 (341)
+.+++|||+||+......||+.++.+|++|.|+|||+++++++++|++||.|.|+
T Consensus 5 ~~~~~rLd~~L~~~~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~Gd~v~i~ 59 (59)
T TIGR02988 5 FTEYITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIP 59 (59)
T ss_pred cchHHHHHHHHHHcCCccCHHHHHHHHHcCCEEECCEEccCCCCCCCCCCEEEeC
Confidence 4467999999999722239999999999999999999998889999999999874
No 31
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=98.60 E-value=6.8e-08 Score=76.17 Aligned_cols=55 Identities=33% Similarity=0.468 Sum_probs=49.3
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeecc
Q 019431 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (341)
Q Consensus 68 ~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~ 123 (341)
...||||+||.-.--.-+|+.+++++..|+|+|||.++ +++..|+.||+|+|...
T Consensus 6 ~~~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~ 60 (100)
T COG1188 6 ADRMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTIRFG 60 (100)
T ss_pred ccceehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEEc-ccccccCCCCEEEEEeC
Confidence 56799999998663368999999999999999999999 89999999999999764
No 32
>smart00363 S4 S4 RNA-binding domain.
Probab=98.43 E-value=6.3e-07 Score=63.12 Aligned_cols=52 Identities=33% Similarity=0.392 Sum_probs=46.7
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeec
Q 019431 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
+||+.||.+.+...||+.++++|++|.|+|||+.++.+++.+..||.|.+..
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 4799999887456899999999999999999999867899999999998865
No 33
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=98.36 E-value=9.4e-07 Score=73.91 Aligned_cols=53 Identities=30% Similarity=0.288 Sum_probs=48.4
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeec
Q 019431 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 69 ~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
+.+|||+||...--.-||+.++++|..|.|+|||++ .+++..|.+||.|.|..
T Consensus 7 ~~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~ 59 (133)
T PRK10348 7 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQ 59 (133)
T ss_pred ccccHHHHHHHcCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEE
Confidence 458999999988667899999999999999999999 59999999999999965
No 34
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=98.32 E-value=1.2e-06 Score=81.95 Aligned_cols=59 Identities=32% Similarity=0.411 Sum_probs=53.6
Q ss_pred EcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeecc
Q 019431 64 VDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (341)
Q Consensus 64 v~~~~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~ 123 (341)
+....+++|||++++..+ ++||+.++++|++|.|+|||+.+.++++.|++||.|+|.+.
T Consensus 185 ~~~~vas~RLD~vla~~~-~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiRG~ 243 (267)
T PLN00051 185 FKSVEASLRLDALASAGF-RMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVSGK 243 (267)
T ss_pred ccCCcCcccHHHHHHHHh-ccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEeeC
Confidence 345567899999999987 89999999999999999999999899999999999999764
No 35
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=98.24 E-value=2.1e-06 Score=80.15 Aligned_cols=59 Identities=29% Similarity=0.446 Sum_probs=52.5
Q ss_pred EcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeecc
Q 019431 64 VDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (341)
Q Consensus 64 v~~~~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~ 123 (341)
+....+++|||.+++..+ ..||+.++++|++|.|+|||+.++++++.|++||.|++.+.
T Consensus 177 ~~~~v~s~RLD~lls~~~-~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~IsvrG~ 235 (257)
T TIGR03069 177 LTTVEASLRIDAIASAGF-GLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRGK 235 (257)
T ss_pred ecCCCccccHHHHHHhhh-hhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEcCC
Confidence 344567899999998876 68999999999999999999999889999999999999763
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=98.23 E-value=2.5e-06 Score=76.77 Aligned_cols=54 Identities=22% Similarity=0.251 Sum_probs=48.8
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccc
Q 019431 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (341)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~ 124 (341)
+|||++|.......||+.++++|..|.|+|||++++.+++.|++||+|+|....
T Consensus 90 ~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD~I~V~~~~ 143 (200)
T TIGR01017 90 SRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKS 143 (200)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCCEEEEeeCc
Confidence 799999987644569999999999999999999998999999999999998654
No 37
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=98.20 E-value=2.8e-06 Score=76.29 Aligned_cols=54 Identities=19% Similarity=0.232 Sum_probs=49.0
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccc
Q 019431 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (341)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~ 124 (341)
+|||+||.+.....||+.++++|..|.|+|||++++.+++.|++||+|+|....
T Consensus 89 ~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~~~~ 142 (201)
T CHL00113 89 MRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQ 142 (201)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEcccc
Confidence 799999998754579999999999999999999998999999999999997643
No 38
>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=98.07 E-value=6.4e-06 Score=75.57 Aligned_cols=52 Identities=29% Similarity=0.238 Sum_probs=47.4
Q ss_pred hHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeecc
Q 019431 72 RLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (341)
Q Consensus 72 RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~ 123 (341)
|||+||.+.....||+.++++|++|+|+|||++++++++.|.+||.|++...
T Consensus 1 RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~d~I~v~~~ 52 (228)
T TIGR00478 1 RLDILLVRRGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFDAKIELLQN 52 (228)
T ss_pred CHHHHHHHcCCccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCCCEEeccCc
Confidence 7999999884456899999999999999999999999999999999999764
No 39
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=98.03 E-value=9.5e-06 Score=73.15 Aligned_cols=53 Identities=25% Similarity=0.281 Sum_probs=47.8
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeecc
Q 019431 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (341)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~ 123 (341)
+|||.+|.+.....||+.++++|..|.|+|||+.++.+++.|.+||.|++...
T Consensus 93 ~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~I~v~~~ 145 (203)
T PRK05327 93 SRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVREK 145 (203)
T ss_pred HHHHHHHHHcCccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCEEEECCc
Confidence 79999997764467999999999999999999999889999999999999764
No 40
>PRK11507 ribosome-associated protein; Provisional
Probab=97.97 E-value=2.3e-05 Score=58.16 Aligned_cols=56 Identities=20% Similarity=0.205 Sum_probs=49.7
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeec
Q 019431 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 67 ~~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
+++-++|++||.-.--.-|=.+++.+|.+|.|+|||.+.+.-+.+|++||.|++..
T Consensus 8 ~~e~I~L~QlLK~~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~V~~~g 63 (70)
T PRK11507 8 KHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAG 63 (70)
T ss_pred CCCeEEHHHHHhhhCcccChHHHHHHHHcCceEECCEEecccCCCCCCCCEEEECC
Confidence 45678999999876445689999999999999999999999999999999999965
No 41
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=97.86 E-value=1.6e-05 Score=72.54 Aligned_cols=54 Identities=41% Similarity=0.532 Sum_probs=50.6
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeecc
Q 019431 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (341)
Q Consensus 69 ~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~ 123 (341)
+.+|||..+++.+ ..||..+..+|.+|.|+||++.++++++.|..||.|.+.+.
T Consensus 179 sSlRLD~vis~~~-~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG~ 232 (257)
T COG2302 179 SSLRLDVVISEGF-GLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRGF 232 (257)
T ss_pred ehhhHHHHHHHHH-hhhHHHHHHHHHcCceEEeeEEeccccceeccCCEEEEecc
Confidence 4689999999986 79999999999999999999999999999999999999765
No 42
>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=97.84 E-value=5.4e-05 Score=67.09 Aligned_cols=70 Identities=21% Similarity=0.269 Sum_probs=53.1
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.+|++|||.||-++ .+++.++..+. ..+.+..|-||...|
T Consensus 2 ~g~l~i~Kp~g~tS~--------~~v~~~k~~~~-------------------------------~kkvGH~GTLDp~A~ 42 (182)
T cd02572 2 YGVINLDKPSGPSSH--------EVVAWIKRILG-------------------------------VEKTGHSGTLDPKVT 42 (182)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhC-------------------------------CCccCcCCCCCCcCe
Confidence 479999999999875 46777776543 146789999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-+.. -++.+.|. .-.|+|.|.+.
T Consensus 43 GvLiv~~g~~--Tk~~~~~~--~~~K~Y~a~v~ 71 (182)
T cd02572 43 GCLPVCIDRA--TRLVKSQQ--EAGKEYVCVMR 71 (182)
T ss_pred eEEEEEECHH--hhhhHHHh--CCCCEEEEEEE
Confidence 9999999873 33444443 34599999875
No 43
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=97.78 E-value=4.5e-05 Score=69.63 Aligned_cols=53 Identities=34% Similarity=0.319 Sum_probs=49.5
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeec
Q 019431 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 70 ~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
.||||.+|.++...-||..|+++|.+|.|.|||.++++|++.|..++.|++..
T Consensus 2 k~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~ 54 (245)
T COG1189 2 KMRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKG 54 (245)
T ss_pred cchHHHHHHHccchhhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEcc
Confidence 58999999998556799999999999999999999999999999999999975
No 44
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=97.75 E-value=4.5e-05 Score=68.64 Aligned_cols=55 Identities=22% Similarity=0.199 Sum_probs=47.1
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeecccc
Q 019431 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISEL 125 (341)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~ 125 (341)
.|||.++-+..-..|+++|+++|..|.|.|||++|+.|++.|++||+|.|.....
T Consensus 94 rRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~~ 148 (205)
T COG0522 94 RRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKSK 148 (205)
T ss_pred HHHHHHHHHhcccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEeeeccc
Confidence 4677766665346799999999999999999999999999999999999976543
No 45
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=97.65 E-value=9.1e-06 Score=59.61 Aligned_cols=56 Identities=20% Similarity=0.251 Sum_probs=37.3
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeec
Q 019431 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 67 ~~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
..+.++|++||...--..|-.+++.+|.+|.|+|||.+.+..+.++++||.|++..
T Consensus 4 ~~e~I~L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~~~ 59 (65)
T PF13275_consen 4 NTEYITLGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEIDG 59 (65)
T ss_dssp --S---HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEETT
T ss_pred CCCcEEHHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEECC
Confidence 45678999999877334588899999999999999999999999999999999954
No 46
>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=97.59 E-value=0.00038 Score=53.96 Aligned_cols=64 Identities=19% Similarity=0.154 Sum_probs=45.3
Q ss_pred CCccccccCCCCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCCCCCcEEEecceeCCCCCeeEEecCCCCCC
Q 019431 210 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKH 289 (341)
Q Consensus 210 ~~~~~vhRLD~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~ 289 (341)
.+++.+|++|+.++|+++++ ++|.+++. +.+. ......
T Consensus 24 ~~i~~aG~kDk~a~t~q~v~-------------------n~f~i~~r--~~~~----------------~~~~~~----- 61 (87)
T cd01291 24 KRVGYAGRKDKRAVTTQLVS-------------------NRFTITLR--VKPL----------------NLKWPE----- 61 (87)
T ss_pred heEEECccCCCCeeEEEEEc-------------------ccEEEEEE--Eecc----------------eeEEcc-----
Confidence 56788999999999999999 78888888 0000 000000
Q ss_pred CCCceeEEEEEEEEEecCCCEEEEEEEeCCCchhHHHHHHHhCC
Q 019431 290 GQARHAASRYKVIEILAGGGSALVEWRLETGRTHQVLMLYKLFY 333 (341)
Q Consensus 290 ~~~k~a~t~~~~l~~~~~~~~slv~~~l~TGR~HQIR~hla~lG 333 (341)
.. ....++++.| |+.||+|.+++.+|
T Consensus 62 --~~--------------~~~~~l~f~l--~~~~yat~~l~el~ 87 (87)
T cd01291 62 --ER--------------KRALVLEFTL--PRGSYATMLLRELG 87 (87)
T ss_pred --cc--------------cceEEEEEEc--CCcchHHHHHHHhC
Confidence 00 1345688888 99999999999875
No 47
>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=97.57 E-value=0.00021 Score=64.63 Aligned_cols=69 Identities=22% Similarity=0.296 Sum_probs=53.3
Q ss_pred cEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 019431 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (341)
Q Consensus 145 ~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (341)
.++++|||.|+-+| .+++.++..+. ..+.+..|.||...||
T Consensus 1 Gil~i~KP~g~tS~--------~vv~~ik~~~~-------------------------------~kKvGH~GTLDP~AsG 41 (210)
T cd00506 1 GLFAVDKPQGPSSH--------DVVDTIRRIFL-------------------------------AEKVGHGGTLDPFATG 41 (210)
T ss_pred CEEEEEcCCCCCHH--------HHHHHHHHHhC-------------------------------ccccCCCCcCCCcCee
Confidence 37999999999875 46777776553 1577889999999999
Q ss_pred eEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 225 Lll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
||+++-+.. .++...|. ...|+|.|...
T Consensus 42 vLiv~vG~a--Tkl~~~~~--~~~K~Y~~~~~ 69 (210)
T cd00506 42 VLVVGIGKA--TKLLKHLL--AATKDYTAIGR 69 (210)
T ss_pred EEEEEECHH--HhhhHHHh--cCCceEEEEEE
Confidence 999999863 33444443 38999999875
No 48
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.52 E-value=0.00021 Score=65.29 Aligned_cols=71 Identities=18% Similarity=0.323 Sum_probs=54.7
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.+|++|||.|+-+| .+++.++..+. ..+++..|.||...|
T Consensus 9 ~G~l~i~KP~g~TS~--------dvv~~ikk~~~-------------------------------~kKvGH~GTLDP~At 49 (230)
T PRK00989 9 EGILLVDKPQGRTSF--------SLIRSLTKLIG-------------------------------VKKIGHAGTLDPFAT 49 (230)
T ss_pred CEEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCcCCcCccCCCCCe
Confidence 689999999999875 46777776553 256789999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-.+. +.+|.+.+. ...|+|+|.+.
T Consensus 50 GvLiv~vG~~-aTkl~~~~~--~~~K~Y~~~~~ 79 (230)
T PRK00989 50 GVMVMLIGRK-FTRLSDILL--FEDKEYAAVAH 79 (230)
T ss_pred eEEEEEECCc-hhhhHHHhc--CCCcEEEEEEE
Confidence 9999998763 344555442 37899999875
No 49
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=97.49 E-value=0.0003 Score=65.94 Aligned_cols=70 Identities=23% Similarity=0.329 Sum_probs=54.2
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.++++|||+||-|| .+++.++..+. ..+.+..|-||...|
T Consensus 2 ngil~vdKP~g~tS~--------~vv~~ikk~~~-------------------------------~kKvGH~GTLDP~At 42 (273)
T PRK04099 2 NRLFVANKPAGMSSN--------AFLSRLKRKYG-------------------------------VKKAGFSGTLDPFAK 42 (273)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccccCccCCCCCe
Confidence 479999999999875 47777876653 256788999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-... -+|.+.+. .-.|+|.|.+.
T Consensus 43 GvLiv~iG~a--TKl~~~l~--~~~K~Y~a~~~ 71 (273)
T PRK04099 43 GVLIVAFGQY--TKLFRFLK--KTPKTYRATLW 71 (273)
T ss_pred eEEEEEEChH--hhhHHHhc--cCCceEEEEEE
Confidence 9999999874 33554443 34899999874
No 50
>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=97.45 E-value=0.00039 Score=62.83 Aligned_cols=70 Identities=19% Similarity=0.289 Sum_probs=54.8
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.++++|||.|+-++ .+++.++..+. ..+.+..|-||...|
T Consensus 2 ~G~l~v~KP~g~tS~--------~vv~~vkk~~~-------------------------------~kKvGH~GTLDP~As 42 (209)
T TIGR00431 2 NGVLLLDKPQGMTSF--------DALAKVRRLLN-------------------------------VKKVGHTGTLDPFAT 42 (209)
T ss_pred CeEEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------CCcCCCCCCCCCcCc
Confidence 469999999999865 46777776553 146788999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-...+ +|...+ ..-.|+|.|.+.
T Consensus 43 GvLiv~vG~~T--kl~~~~--~~~~K~Y~~~~~ 71 (209)
T TIGR00431 43 GVLPILVGKAT--KLSPYL--TDLDKEYRAEIR 71 (209)
T ss_pred eEEEEEEChHh--hhhHHH--cCCCCeEEEEEE
Confidence 99999999753 455544 367999999874
No 51
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=97.45 E-value=0.0004 Score=64.01 Aligned_cols=70 Identities=20% Similarity=0.340 Sum_probs=53.7
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.+|++|||.|+-+| .+++.++..+. ..+++..|-||...|
T Consensus 10 ~Gil~vdKP~G~TS~--------dvv~~vkr~~~-------------------------------~kKvGH~GTLDP~At 50 (244)
T PRK00020 10 DGVLLLDKPVGLSSN--------HALQRAKRTVD-------------------------------AAKAGHTGTLDPFAT 50 (244)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhC-------------------------------CCCCCcCCcCCCcCe
Confidence 579999999999875 46777776553 257788999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-... -+|...|. ...|+|.|.+.
T Consensus 51 GvLiv~iG~a--TKl~~~l~--~~~K~Y~a~~~ 79 (244)
T PRK00020 51 GLLVCCMGRA--TKISGRML--EADKTYQATLQ 79 (244)
T ss_pred eEEEEEECHH--hhhhHHhc--cCCcEEEEEEE
Confidence 9999999873 34444442 44599999864
No 52
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=97.38 E-value=0.0005 Score=65.31 Aligned_cols=70 Identities=21% Similarity=0.257 Sum_probs=54.1
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.+|++|||.||-|| .+++.++..+. ..+.+..|.||...|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~At 43 (294)
T PRK02484 3 NGIINLKKEAGMTSH--------DAVFKLRKILQ-------------------------------TKKIGHGGTLDPDVV 43 (294)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccccCCCCCCCCe
Confidence 479999999999875 47777776553 257789999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-.+. .++.+.+. .-.|+|.|.+.
T Consensus 44 GvL~i~vG~a--Tkl~~~l~--~~~K~Y~a~~~ 72 (294)
T PRK02484 44 GVLPIAVGKA--TRLIEYMT--EAGKVYEGEIT 72 (294)
T ss_pred eEEEEEEChh--hhhhHHhc--cCCcEEEEEEE
Confidence 9999999874 33444443 34599999875
No 53
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=97.35 E-value=0.00062 Score=64.99 Aligned_cols=70 Identities=24% Similarity=0.330 Sum_probs=54.1
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.++++|||.|+-+| .+++.++..+. ..+.+..|-||...|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~At 43 (308)
T PRK14124 3 HGFLVAYKPKGPTSH--------DVVDEVRKKLK-------------------------------TRKVGHAGTLDPFAT 43 (308)
T ss_pred ceEEEEECCCCCCHH--------HHHHHHHHHcC-------------------------------CCccCcCcCCCCCCc
Confidence 479999999999875 47777776553 156788999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-... .++.+.+.. -.|+|.|.+.
T Consensus 44 GvL~v~vG~a--Tkl~~~l~~--~~K~Y~a~~~ 72 (308)
T PRK14124 44 GVLIVGVNKA--TRLLEYLKN--EKKVYYVKMR 72 (308)
T ss_pred EEEEEEEChH--HhhhHHHhc--CCceEEEEEE
Confidence 9999999864 334454433 3899999875
No 54
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=97.33 E-value=0.00064 Score=64.50 Aligned_cols=70 Identities=21% Similarity=0.261 Sum_probs=54.3
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.+|++|||.|+-|| .+++.++..+. ..+.+..|-||...|
T Consensus 2 ~Gil~i~KP~G~tS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At 42 (290)
T PRK00130 2 DGILNILKPPGMTSF--------DVVRKIRKIAK-------------------------------IKKVGHTGTLDPLAS 42 (290)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccCcCCCCCCCCe
Confidence 479999999999875 47777776553 146788999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-.+. -++.+.+. .-.|+|.|.+.
T Consensus 43 GvL~v~vG~a--Tkl~~~l~--~~~K~Y~a~~~ 71 (290)
T PRK00130 43 GVLPVCLGKA--TKIVDYLM--EGKKTYRAEIK 71 (290)
T ss_pred eEEEEEEChh--hhhHHHhc--cCCcEEEEEEE
Confidence 9999999873 33555443 34899999875
No 55
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=97.32 E-value=0.00063 Score=50.80 Aligned_cols=57 Identities=21% Similarity=0.238 Sum_probs=49.4
Q ss_pred CCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeec
Q 019431 66 TKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 66 ~~~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
...+-+.|.+||...--.-|=.+++.+|..|.|+|||++.+.-+.+|+.||.|++..
T Consensus 7 i~~e~I~L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~ 63 (73)
T COG2501 7 IKTEFITLGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPG 63 (73)
T ss_pred eccceEEHHHHHHHhCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECC
Confidence 345667899999876335688999999999999999999999999999999999954
No 56
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=97.32 E-value=0.00063 Score=64.68 Aligned_cols=71 Identities=23% Similarity=0.359 Sum_probs=54.3
Q ss_pred CCcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCC
Q 019431 143 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 222 (341)
Q Consensus 143 d~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T 222 (341)
-+.+|++|||.|+-|| .+++.++..+. ..+.+..|-||...
T Consensus 8 ~~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~A 48 (298)
T PRK03287 8 GSGLVVVDKPAGMTSH--------DVVARCRRLFG-------------------------------TRKVGHAGTLDPMA 48 (298)
T ss_pred cCeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCCCCcCccCCCcc
Confidence 4689999999999875 47777776553 15678899999999
Q ss_pred ceeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 223 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 223 SGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
||||+++-... -++.+.+. .-.|+|.|.+.
T Consensus 49 tGvL~i~vG~a--TKl~~~l~--~~~K~Y~a~~~ 78 (298)
T PRK03287 49 TGVLVLGVERA--TKLLGHLT--LTDKSYTATIR 78 (298)
T ss_pred eeEEEEEeChh--hhhhHHHh--cCCcEEEEEEE
Confidence 99999999862 33444443 34899999874
No 57
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=97.29 E-value=0.00071 Score=64.61 Aligned_cols=70 Identities=20% Similarity=0.276 Sum_probs=54.7
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.+|++|||.|+-+| .+++.++..+. ..+.+..|.||...|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At 43 (305)
T PRK14123 3 NGILPVYKERGLTSH--------DVVFKLRKILK-------------------------------TKKIGHTGTLDPEVA 43 (305)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccccCcCCCCcCe
Confidence 479999999999875 47777776553 256789999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-.+.+ ++.+.+. ...|+|.|.+.
T Consensus 44 GvL~v~vG~aT--kl~~~l~--~~~K~Y~~~~~ 72 (305)
T PRK14123 44 GVLPVCIGNAT--RVSDYVM--DMGKAYEATVS 72 (305)
T ss_pred eEEEEEEChhh--hhHHHhc--CCCcEEEEEEE
Confidence 99999998753 4555442 37899999874
No 58
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=97.28 E-value=0.00071 Score=64.56 Aligned_cols=70 Identities=21% Similarity=0.223 Sum_probs=54.2
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.+|++|||.|+-+| .+++.++..+. ..+.+..|-||...|
T Consensus 13 ~Gil~i~KP~G~TS~--------dvv~~vrk~~~-------------------------------~kKvGH~GTLDP~At 53 (305)
T PRK05389 13 SGWLILDKPAGMTST--------EAVSKVKWLFD-------------------------------AQKAGHAGTLDPLAS 53 (305)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhc-------------------------------ccccCCcccCCCCCc
Confidence 689999999999875 47777776553 156788999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-... -++.+.+. .-.|+|.|.+.
T Consensus 54 GvL~v~vG~a--Tkl~~~l~--~~~K~Y~a~~~ 82 (305)
T PRK05389 54 GVLPIALGEA--TKTVPYVM--DGTKRYRFTVA 82 (305)
T ss_pred eEEEEEEChh--hhhhHHhc--cCCcEEEEEEE
Confidence 9999999863 34444442 34899999874
No 59
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=97.26 E-value=0.00075 Score=64.11 Aligned_cols=69 Identities=23% Similarity=0.268 Sum_probs=54.6
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.+|++|||.||-|| .+++.++..+. ..+.+..|-||...|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At 43 (295)
T PRK02755 3 FGFLNLDKPAGLTSH--------DCVARLRRLLR-------------------------------LKRVGHGGTLDPAAT 43 (295)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccccCCCCCCcCe
Confidence 479999999999875 47777776553 156788999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-.+.+ +|.+.+. . .|+|.|.+.
T Consensus 44 GvL~i~vG~aT--kl~~~l~--~-~K~Y~a~~~ 71 (295)
T PRK02755 44 GVLPIALGKAT--RLLPYLP--G-EKTYRGTIR 71 (295)
T ss_pred eEEEEEEChhh--hhHHHhC--C-CcEEEEEEE
Confidence 99999998754 4556554 3 799999874
No 60
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=97.26 E-value=0.00078 Score=64.38 Aligned_cols=71 Identities=17% Similarity=0.221 Sum_probs=54.2
Q ss_pred CCcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCC
Q 019431 143 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 222 (341)
Q Consensus 143 d~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T 222 (341)
.+.+|++|||.|+-+| .+++.++..+. ..+.+..|-||...
T Consensus 21 ~~g~l~i~Kp~g~tS~--------~~v~~~r~~~~-------------------------------~kkvGH~GTLDp~A 61 (300)
T PRK04270 21 KFGVVNLDKPPGPTSH--------EVAAWVRDILG-------------------------------VEKAGHGGTLDPKV 61 (300)
T ss_pred CCCEEEEECCCCCCHH--------HHHHHHHHHhc-------------------------------cccccCCCCCCCcC
Confidence 4689999999999875 46777776553 14678899999999
Q ss_pred ceeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 223 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 223 SGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
||||+++-.+. -+|.+.+. .-.|+|.|.+.
T Consensus 62 ~GvL~v~~g~a--tk~~~~~~--~~~K~Y~~~~~ 91 (300)
T PRK04270 62 TGVLPVALGKA--TKVVQALL--ESGKEYVCVMH 91 (300)
T ss_pred eEEEEEEEChH--hhhhHHhc--cCCcEEEEEEE
Confidence 99999999863 34444443 34599998764
No 61
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=97.25 E-value=0.0009 Score=63.72 Aligned_cols=70 Identities=20% Similarity=0.307 Sum_probs=54.2
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.+|++|||.||-|| .+++.++..+. ..+.+..+-||...|
T Consensus 16 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~At 56 (303)
T PRK01851 16 DGVLLLDKPLGLSSN--------DALQRAKRLLR-------------------------------AKKAGHTGTLDPLAT 56 (303)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------cccCCCCCCCCCCCc
Confidence 689999999999875 47777776653 146788999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-.+. -++.+.+. .-.|+|.|.+.
T Consensus 57 GvL~v~vG~a--Tkl~~~l~--~~~K~Y~~~~~ 85 (303)
T PRK01851 57 GLLPLCFGEA--TKFSQDLL--DADKTYEATLR 85 (303)
T ss_pred eEEEEEECHH--HhhhHHhc--ccCeEEEEEEE
Confidence 9999999874 33444443 34599999874
No 62
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=97.23 E-value=0.00094 Score=63.75 Aligned_cols=70 Identities=21% Similarity=0.312 Sum_probs=54.1
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.+|++|||.||-|| .+++.++..+. ..+.+..+-||...|
T Consensus 2 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At 42 (304)
T PRK01550 2 NGVLLLHKPRGMTSH--------DCVFKLRKILR-------------------------------TKKVGHTGTLDPEVS 42 (304)
T ss_pred CeEEEEECCCCCCHH--------HHHHHHHHHcC-------------------------------CCCcccCCCCCCcCe
Confidence 479999999999875 47777776553 256788999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-.+. -+|.+.+. .-.|+|.|.+.
T Consensus 43 GvL~i~vG~a--Tkl~~~l~--~~~K~Y~a~~~ 71 (304)
T PRK01550 43 GVLPICVGRA--TKIAEYLT--DEGKTYEGEVT 71 (304)
T ss_pred eEEEEEEChh--hhhhHHhc--CCCcEEEEEEE
Confidence 9999999864 33555443 34899999875
No 63
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=97.23 E-value=0.00068 Score=59.62 Aligned_cols=52 Identities=19% Similarity=0.203 Sum_probs=45.3
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCC--CEEeeec
Q 019431 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGG--DMVNCTI 122 (341)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~g--D~I~v~~ 122 (341)
.|||.+|.+..-.-|+.+++++|..|.|+|||+++++|++.|..+ |.|.+..
T Consensus 103 rRLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~ 156 (177)
T PRK04051 103 RRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYP 156 (177)
T ss_pred hHHHHHHHHccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEeC
Confidence 589999888755679999999999999999999999999999998 5666543
No 64
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=97.22 E-value=0.001 Score=63.66 Aligned_cols=70 Identities=19% Similarity=0.308 Sum_probs=54.5
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.+|++|||.||-|| .+++.++..+. ..+++..|-||...|
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~At 50 (312)
T PRK05033 10 NGVLLLDKPQGMSSN--------DALQKVKRLFN-------------------------------ANKAGHTGALDPLAT 50 (312)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCCCCCCCcCCCcCe
Confidence 689999999999876 46777776553 256788999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-.+. -+|.+.+. .-.|+|.|.+.
T Consensus 51 GvL~v~vG~a--Tkl~~~~~--~~~K~Y~a~~~ 79 (312)
T PRK05033 51 GMLPICLGEA--TKFSQYLL--DSDKRYRVTAR 79 (312)
T ss_pred eEEEEEECHH--hhhhHHhc--CCCcEEEEEEE
Confidence 9999999874 33555443 34899999875
No 65
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=97.22 E-value=0.00094 Score=62.91 Aligned_cols=68 Identities=24% Similarity=0.369 Sum_probs=52.5
Q ss_pred EEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCcee
Q 019431 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (341)
Q Consensus 146 llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (341)
++++|||.|+-|| .+++.++..+. ..+.+..|.||...|||
T Consensus 2 il~i~KP~G~tS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~AtGv 42 (279)
T PRK02193 2 IKLLYKPKGISSF--------KFIKNFAKTNN-------------------------------IKKIGHTGTLDPLASGL 42 (279)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHcC-------------------------------CCccccCccCCCcCeeE
Confidence 6899999999875 46777776543 25788999999999999
Q ss_pred EEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 226 ll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|+++-.+. .++.+.+ ....|+|.|.+.
T Consensus 43 L~v~vG~a--Tkl~~~l--~~~~K~Y~a~~~ 69 (279)
T PRK02193 43 LLVATDED--TKLIDYL--DQKDKTYIAKIK 69 (279)
T ss_pred EEEEEChh--hhhhHHh--ccCCcEEEEEEE
Confidence 99999863 3344444 457899999874
No 66
>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=97.21 E-value=0.0011 Score=62.60 Aligned_cols=69 Identities=23% Similarity=0.382 Sum_probs=53.5
Q ss_pred cEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 019431 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (341)
Q Consensus 145 ~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (341)
.+|++|||.|+-+| .+++.++..+. ..+.+..|-||...||
T Consensus 1 Gil~i~KP~G~tS~--------~vv~~vr~~~~-------------------------------~kKvGH~GTLDP~AtG 41 (277)
T cd02573 1 GILLLDKPAGLTSH--------DVVQKVRRLLG-------------------------------TKKVGHTGTLDPLATG 41 (277)
T ss_pred CEEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------cCccCCCCCCCCcCeE
Confidence 47999999999875 46777776553 1467889999999999
Q ss_pred eEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 225 Lll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
||+++-... -+|...+. .-.|+|.|.+.
T Consensus 42 vL~v~vG~a--Tkl~~~l~--~~~K~Y~~~~~ 69 (277)
T cd02573 42 VLPIALGEA--TKLSQYLL--DADKTYRATVR 69 (277)
T ss_pred EEEEEEChH--HhhHHHhc--CCCcEEEEEEE
Confidence 999999874 33555443 36999999875
No 67
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=97.17 E-value=0.0011 Score=63.71 Aligned_cols=70 Identities=21% Similarity=0.236 Sum_probs=53.5
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.+|++|||.||-+| .+++.++..+. ..+++..|.||...|
T Consensus 3 nGiL~idKP~G~TS~--------dvv~~vrk~l~-------------------------------~kKVGH~GTLDP~At 43 (345)
T PRK14846 3 NYWLNIYKPRGISSA--------QLVSIVKKILG-------------------------------KTKIGHAGTLDVEAE 43 (345)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCcCCcCccCCCcCc
Confidence 579999999999875 47777776553 257889999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-... -++.+.+ ..-.|+|.|.+.
T Consensus 44 GVL~i~vG~a--TKl~~~l--~~~~K~Y~a~~~ 72 (345)
T PRK14846 44 GILPFAVGEA--TKLIHLL--IDARKTYIFTVK 72 (345)
T ss_pred eEEEEEEChh--hhhhHHH--hcCCceEEEEEE
Confidence 9999998863 3334333 256889999874
No 68
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=97.11 E-value=0.0014 Score=62.20 Aligned_cols=70 Identities=21% Similarity=0.272 Sum_probs=53.4
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.+|++|||.||-+| .+++.++..+. ..+.+..|-||...|
T Consensus 3 ~GiL~i~KP~G~TS~--------dvv~~vrk~~~-------------------------------~kKvGH~GTLDP~At 43 (292)
T PRK01528 3 NYWLNIYKPRGISSA--------KLVSIVKKILG-------------------------------KVKIGHAGTLDVEAE 43 (292)
T ss_pred CEEEEEeCCCCCCHH--------HHHHHHHHHcC-------------------------------CCccCcCccCCCcCc
Confidence 589999999999875 47777776553 157788999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-.+. -++.+.+. .-.|+|.|.+.
T Consensus 44 GvL~v~vG~a--TKl~~~l~--~~~K~Y~~~~~ 72 (292)
T PRK01528 44 GVLPLAVGEA--TKLVQLLI--DAKKTYIFTVK 72 (292)
T ss_pred eEEEEEEChH--hhhhHHHh--cCCceEEEEEE
Confidence 9999998863 33343332 45799999874
No 69
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=96.99 E-value=0.0021 Score=61.40 Aligned_cols=69 Identities=26% Similarity=0.399 Sum_probs=53.9
Q ss_pred cEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 019431 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (341)
Q Consensus 145 ~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (341)
.+|++|||.|+-|| .+++.++..+. ..+.+..+-||...||
T Consensus 2 ~il~idKP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~AtG 42 (312)
T PRK14122 2 PVYAVDKPLGLTSH--------DVVNRARRALG-------------------------------TRRVGHTGTLDPLATG 42 (312)
T ss_pred cEEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------CCCCCCCCCCCCcCee
Confidence 37999999999875 47777776553 2577889999999999
Q ss_pred eEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 225 Lll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
||+++-...+ +|.+.+ ....|+|.|.+.
T Consensus 43 vL~i~iG~aT--Kl~~~l--~~~~K~Y~a~~~ 70 (312)
T PRK14122 43 VLVLCTDDST--KLVPFL--SAEDKEYLAWVS 70 (312)
T ss_pred eEEEEEChhh--hhhHHh--cCCCceEEEEEE
Confidence 9999998743 355544 467899999874
No 70
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=96.92 E-value=0.0026 Score=60.46 Aligned_cols=70 Identities=19% Similarity=0.260 Sum_probs=54.6
Q ss_pred CcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 019431 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (341)
Q Consensus 144 ~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (341)
+.+|++|||.||-|| .+++.++..+. ..+.+..+-||...|
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At 50 (300)
T PRK04642 10 DGILLLDKPAGLSSN--------NALQAARRLLR-------------------------------AEKGGHTGSLDPLAT 50 (300)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhC-------------------------------CCcccCCCccCCcCe
Confidence 689999999999875 47788876653 146788999999999
Q ss_pred eeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 224 GLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
|||+++-.+. -+|.+.+ ..-.|+|.|.+.
T Consensus 51 GvL~v~~G~a--Tkl~~~l--~~~~K~Y~a~~~ 79 (300)
T PRK04642 51 GLLPLCFGEA--TKIAGLL--LGSAKAYDAEIV 79 (300)
T ss_pred eeEEEEEChh--hhhhHHh--cCCCcEEEEEEE
Confidence 9999998863 3444444 256899999873
No 71
>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=96.91 E-value=0.0023 Score=61.75 Aligned_cols=71 Identities=20% Similarity=0.287 Sum_probs=54.8
Q ss_pred CCcEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCC
Q 019431 143 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 222 (341)
Q Consensus 143 d~~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T 222 (341)
.+.+|++|||.|+-+| .+++.++..+. ..+.+..+-||...
T Consensus 33 ~~G~l~i~KP~g~tS~--------~~v~~vr~~~~-------------------------------~kkvGH~GTLDP~A 73 (322)
T TIGR00425 33 SYGVVNLDKPSGPSSH--------EVVAWVRRILN-------------------------------VEKTGHGGTLDPKV 73 (322)
T ss_pred CCCEEEEeCCCCCCHH--------HHHHHHHHHhc-------------------------------ccccCCCCCCCCCC
Confidence 4689999999999876 47777776553 15678899999999
Q ss_pred ceeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 223 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 223 SGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
||||+++-.+. -+|.+.+ ..-.|+|.|.+.
T Consensus 74 ~GvL~v~~G~a--Tkl~~~~--~~~~K~Y~~~v~ 103 (322)
T TIGR00425 74 TGVLPVCIERA--TRLVKSL--QEAPKEYVCLMR 103 (322)
T ss_pred ceEEEEEEChH--hhccHHh--ccCCCEEEEEEE
Confidence 99999998863 3344444 357899998774
No 72
>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=96.57 E-value=0.0061 Score=58.31 Aligned_cols=93 Identities=16% Similarity=0.204 Sum_probs=55.1
Q ss_pred cEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCcc-cc-c---cccccccccccCcccccccccCCCCCCccccccCC
Q 019431 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTL-AS-S---NQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLD 219 (341)
Q Consensus 145 ~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~-~~-~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD 219 (341)
.+++||||.|+-++ .+++.|+..+....+ .. + .++. +.... ..........+.+..|-||
T Consensus 1 Gil~i~KP~G~TS~--------~vv~~lk~~l~~s~~~~~~~~~~~~~~------~~~~~-~~~~~~~~~~KiGH~GTLD 65 (312)
T cd02867 1 GVFAINKPSGITSA--------QVLNDLKPLFLNSALFKDKIQRAVAKR------GKKAR-RRKGRKRSKLKIGHGGTLD 65 (312)
T ss_pred CeEEEeCCCCCCHH--------HHHHHHHHHhcccccccchhhhhhhhh------hhhhh-hhccccccccccccccccC
Confidence 47999999999875 477777776642110 00 0 0000 00000 0000001125789999999
Q ss_pred CCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 220 KGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 220 ~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
-..||||+++-... .+.++. |. ...|+|.+...
T Consensus 66 PlAsGVLvvgvG~a-TK~l~~-~l--~~~K~Y~~~~~ 98 (312)
T cd02867 66 PLATGVLVVGVGAG-TKQLQD-YL--SCSKTYEATGL 98 (312)
T ss_pred CccceeEEEEECcH-HHHHHH-Hh--cCCceEEEEEE
Confidence 99999999998863 334443 32 28999999864
No 73
>PRK04313 30S ribosomal protein S4e; Validated
Probab=96.50 E-value=0.013 Score=53.85 Aligned_cols=71 Identities=14% Similarity=0.156 Sum_probs=53.7
Q ss_pred chHHHHHHhccC-CCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccccCCccccCCCCCeeEEeeCCcEEEE
Q 019431 71 LRLDAWISSRID-GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVV 149 (341)
Q Consensus 71 ~RLdk~L~~~~~-~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~Ilyed~~llvv 149 (341)
+-|.=+|...++ ..+.+++++.+.+|.|.|||++.+...+.|---|+|++... +...+|+|.....+++
T Consensus 38 iPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~~~----------~e~yRvl~d~kgr~~l 107 (237)
T PRK04313 38 IPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIPET----------GEYYRVLPDEKGRLVL 107 (237)
T ss_pred cccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEccC----------CCeEEEEECCCCcEEE
Confidence 347777887765 46999999999999999999999888888888899999542 2235566666555554
Q ss_pred eC
Q 019431 150 NK 151 (341)
Q Consensus 150 nK 151 (341)
++
T Consensus 108 ~~ 109 (237)
T PRK04313 108 IP 109 (237)
T ss_pred EE
Confidence 43
No 74
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=96.50 E-value=0.007 Score=56.85 Aligned_cols=69 Identities=16% Similarity=0.234 Sum_probs=52.7
Q ss_pred cEEEEeCCCCCeeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 019431 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (341)
Q Consensus 145 ~llvvnKP~Gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (341)
.+|++|||.|+-+| .++..++..+. ..+.+..+-||...||
T Consensus 16 Gil~ldKP~G~tS~--------~~v~~vkkil~-------------------------------~~K~GH~GTLDP~atG 56 (271)
T COG0130 16 GVINLDKPPGPTSH--------EVVAWVKRILG-------------------------------VEKAGHGGTLDPLATG 56 (271)
T ss_pred ceEEeeCCCCCCHH--------HHHHHHHHHhC-------------------------------ccccccccccCCcccc
Confidence 89999999999875 46677766553 2567889999999999
Q ss_pred eEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 225 Lll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
+|+++-. ++.+.++- + ..-.|+|.|.+.
T Consensus 57 vLpi~ig-~aTKl~~~-l--~~~~K~Y~a~~~ 84 (271)
T COG0130 57 VLPICLG-EATKLVQY-L--LDADKEYVATVR 84 (271)
T ss_pred eEEEEec-hhHhHHHH-H--hhCCcEEEEEEE
Confidence 9999998 33333332 2 246899999875
No 75
>PLN00189 40S ribosomal protein S9; Provisional
Probab=96.45 E-value=0.0021 Score=57.14 Aligned_cols=42 Identities=19% Similarity=0.125 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccc
Q 019431 83 GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (341)
Q Consensus 83 ~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~ 124 (341)
.-|..++.++|..|.|.|||++|+.|++.|+.|+++.|.+..
T Consensus 121 a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~~ 162 (194)
T PLN00189 121 AKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSL 162 (194)
T ss_pred cCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEEec
Confidence 458999999999999999999999999999999988887654
No 76
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=96.27 E-value=0.019 Score=53.65 Aligned_cols=71 Identities=21% Similarity=0.262 Sum_probs=54.3
Q ss_pred chHHHHHHhccC-CCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccccCCccccCCCCCeeEEeeCCcEEEE
Q 019431 71 LRLDAWISSRID-GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVV 149 (341)
Q Consensus 71 ~RLdk~L~~~~~-~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~Ilyed~~llvv 149 (341)
+.|.=||...++ ..+.++++..+.+|.|.|||++.+...+.|---|+|+|... +...+|+|.....+++
T Consensus 39 iPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~kt----------~e~yRvl~D~kGrf~l 108 (273)
T PTZ00223 39 LPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPKT----------GDRFRILYDVKGRFAL 108 (273)
T ss_pred cccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcCC----------CCeEEEEECCCCcEEE
Confidence 347778887765 35899999999999999999999888888887899999542 2335667666665555
Q ss_pred eC
Q 019431 150 NK 151 (341)
Q Consensus 150 nK 151 (341)
++
T Consensus 109 ~~ 110 (273)
T PTZ00223 109 VK 110 (273)
T ss_pred EE
Confidence 43
No 77
>PLN00036 40S ribosomal protein S4; Provisional
Probab=96.25 E-value=0.022 Score=52.92 Aligned_cols=71 Identities=14% Similarity=0.256 Sum_probs=54.4
Q ss_pred chHHHHHHhccC-CCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccccCCccccCCCCCeeEEeeCCcEEEE
Q 019431 71 LRLDAWISSRID-GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVV 149 (341)
Q Consensus 71 ~RLdk~L~~~~~-~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~Ilyed~~llvv 149 (341)
+-|.=||...+. ..+.+++++.+.+|.|.|||++.+...+.+---|+|++... +...+|+|.....+++
T Consensus 42 lPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt----------~e~yRvl~D~kGrf~l 111 (261)
T PLN00036 42 LPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPKT----------NENFRLLYDTKGRFRL 111 (261)
T ss_pred cccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcCC----------CCeEEEEECCCceEEE
Confidence 347778888765 35889999999999999999999888888877899999642 2335667766666555
Q ss_pred eC
Q 019431 150 NK 151 (341)
Q Consensus 150 nK 151 (341)
++
T Consensus 112 ~~ 113 (261)
T PLN00036 112 HR 113 (261)
T ss_pred EE
Confidence 43
No 78
>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=96.20 E-value=0.0078 Score=52.19 Aligned_cols=51 Identities=16% Similarity=0.188 Sum_probs=42.0
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCC--CEEeee
Q 019431 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGG--DMVNCT 121 (341)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~g--D~I~v~ 121 (341)
.||+-++.+.--.-|..+|.++|..|.|.|||++|+.|++.|+.+ |.|.+.
T Consensus 104 RRL~~vv~r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~ 156 (162)
T TIGR01018 104 RRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFA 156 (162)
T ss_pred HhHhhHhhhccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeee
Confidence 466666666533569999999999999999999999999999999 566654
No 79
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=96.19 E-value=0.023 Score=52.85 Aligned_cols=70 Identities=19% Similarity=0.292 Sum_probs=53.0
Q ss_pred chHHHHHHhccC-CCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccccCCccccCCCCCeeEEeeCCcEEEE
Q 019431 71 LRLDAWISSRID-GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVV 149 (341)
Q Consensus 71 ~RLdk~L~~~~~-~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~Ilyed~~llvv 149 (341)
+-|.=||...+. ..+.++++..+.+|.|.|||++.+...+.|---|+|++... +...+++|.....+++
T Consensus 42 lPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt----------~e~yRvl~D~kGr~~l 111 (262)
T PTZ00118 42 LPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTKT----------NEYFRLLYDTKGRFVP 111 (262)
T ss_pred cccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEcCC----------CCeEEEEECCCccEEE
Confidence 347778887765 35899999999999999999999888888888899999542 2235566665555554
Q ss_pred e
Q 019431 150 N 150 (341)
Q Consensus 150 n 150 (341)
+
T Consensus 112 ~ 112 (262)
T PTZ00118 112 H 112 (262)
T ss_pred E
Confidence 4
No 80
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=95.75 E-value=0.011 Score=52.24 Aligned_cols=52 Identities=17% Similarity=0.052 Sum_probs=41.0
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeec
Q 019431 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
.||+.++.+.--.-|..+|.++|..|.|.|||++|+.|++.|+.+++=.|++
T Consensus 107 RRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I~~ 158 (181)
T PTZ00155 107 RRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDF 158 (181)
T ss_pred HhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceEeccCccCceee
Confidence 4566665554234689999999999999999999999999999995544443
No 81
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=93.88 E-value=0.13 Score=46.85 Aligned_cols=59 Identities=14% Similarity=0.166 Sum_probs=46.7
Q ss_pred CCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccccCCccccCCCCCeeEEeeCCcEEEEeCC
Q 019431 84 ISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKP 152 (341)
Q Consensus 84 ~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~Ilyed~~llvvnKP 152 (341)
..-+++++.|.+|.|+|||++.....+.|---|+|++.. .+...+|+|.....+++++=
T Consensus 55 d~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~----------tgE~yRvl~d~~grl~l~~i 113 (241)
T COG1471 55 DNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPK----------TGEHYRVLPDEKGRLVLHPI 113 (241)
T ss_pred cchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECC----------CCceEEEEecCCccEEEEec
Confidence 467899999999999999999877667776669999954 23346788888888777653
No 82
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=89.93 E-value=0.3 Score=37.44 Aligned_cols=46 Identities=30% Similarity=0.490 Sum_probs=35.6
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeecc
Q 019431 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (341)
Q Consensus 69 ~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~ 123 (341)
.+..+...+.. + +.+..++ |.|.|||+.+ ..+++++.||.|.|++.
T Consensus 31 ~~~tvkd~IEs-L-GVP~tEV------~~i~vNG~~v-~~~~~~~~Gd~v~V~P~ 76 (81)
T PF14451_consen 31 GGATVKDVIES-L-GVPHTEV------GLILVNGRPV-DFDYRLKDGDRVAVYPV 76 (81)
T ss_pred CCCcHHHHHHH-c-CCChHHe------EEEEECCEEC-CCcccCCCCCEEEEEec
Confidence 34567766544 3 4676665 7899999999 68999999999999864
No 83
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=89.73 E-value=0.6 Score=46.64 Aligned_cols=47 Identities=21% Similarity=0.228 Sum_probs=39.7
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCC
Q 019431 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGD 116 (341)
Q Consensus 70 ~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD 116 (341)
++.|.++|...--..|+++++++|++|.|+|||++++.+.+.+.+++
T Consensus 342 ~~~~~~~l~~~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~ 388 (410)
T PRK13354 342 TKNLVDLLVDLGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPED 388 (410)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhh
Confidence 57788888876446799999999999999999999977777777665
No 84
>PRK01777 hypothetical protein; Validated
Probab=88.74 E-value=0.49 Score=37.44 Aligned_cols=54 Identities=15% Similarity=0.181 Sum_probs=39.0
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeeccc
Q 019431 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (341)
Q Consensus 68 ~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~ 124 (341)
.+|.++.+.|... + +....-+=-+..+.|-|||+.+ ..++.|+.||+|+|+.+.
T Consensus 24 p~GtTv~dal~~s-g-i~~~~pei~~~~~~vgI~Gk~v-~~d~~L~dGDRVeIyrPL 77 (95)
T PRK01777 24 QEGATVEEAIRAS-G-LLELRTDIDLAKNKVGIYSRPA-KLTDVLRDGDRVEIYRPL 77 (95)
T ss_pred CCCCcHHHHHHHc-C-CCccCcccccccceEEEeCeEC-CCCCcCCCCCEEEEecCC
Confidence 4466788888764 3 3433111134568999999999 689999999999998753
No 85
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=88.57 E-value=0.48 Score=41.51 Aligned_cols=63 Identities=22% Similarity=0.402 Sum_probs=47.7
Q ss_pred eEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeec
Q 019431 58 VQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 58 ~~~~~~v~~~~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
+++..+++ -....||+..|++++ +.||+.++++|+.|.|..+-........+++.|-.|.++.
T Consensus 127 vel~l~~~-~p~qlrl~~Ll~seL-~LSrS~lq~lie~g~Irgdtd~~~l~rkrlr~~~~i~Id~ 189 (203)
T COG4332 127 VELSLRIS-RPFQLRLDRLLASEL-GLSRSELQRLIETGQIRGDTDKMLLLRKRLRAGYDIQIDV 189 (203)
T ss_pred EEEEEccc-CcchhHHHHHHHHHh-CcCHHHHHHHHHcCceeecchHHHHhhhhhhcCcEEEEEc
Confidence 55554443 234579999999997 7999999999999999987665434456777887777765
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=87.55 E-value=0.56 Score=40.24 Aligned_cols=43 Identities=23% Similarity=0.309 Sum_probs=31.1
Q ss_pred CCccccccCCCCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEe
Q 019431 210 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (341)
Q Consensus 210 ~~~~~vhRLD~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~ 256 (341)
.+.+..|.||..+||||+++-+.. -+|...|. ...|+|.|...
T Consensus 7 ~KvGH~GTLDP~AsGvL~v~vg~~--Tkl~~~l~--~~~K~Y~~~~~ 49 (149)
T PF01509_consen 7 KKVGHGGTLDPFASGVLVVGVGKA--TKLLSYLQ--NSDKEYVATIR 49 (149)
T ss_dssp SSEEESS-SSTT-EEEEEEEEGGG--GGGHHHHT--TSEEEEEEEEE
T ss_pred ceeccccccCCcceEEEEEEECCc--chHHHHhh--ccCCEEEEEEE
Confidence 578899999999999999999763 23444443 44599999864
No 87
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=86.03 E-value=1.8 Score=43.32 Aligned_cols=45 Identities=24% Similarity=0.194 Sum_probs=37.1
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccC
Q 019431 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKG 114 (341)
Q Consensus 70 ~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~ 114 (341)
+..|.++|.+.--..|+++++++|++|.|+|||+++...+..+..
T Consensus 342 ~~~~~~~l~~~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~ 386 (408)
T PRK05912 342 GIDLLALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTA 386 (408)
T ss_pred CCcHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEecCccccccc
Confidence 567888888763457999999999999999999998766666655
No 88
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=85.01 E-value=0.85 Score=41.99 Aligned_cols=23 Identities=30% Similarity=0.359 Sum_probs=19.6
Q ss_pred CCccccccCCCCCceeEEeecCH
Q 019431 210 IRPGIVHRLDKGTSGLLVVAKDE 232 (341)
Q Consensus 210 ~~~~~vhRLD~~TSGLll~ak~~ 232 (341)
..+..+||||-.|||++||.-..
T Consensus 89 ~~V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559|consen 89 EDVQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred cceeeEEeecccccceEEEecCc
Confidence 34688999999999999998764
No 89
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=84.04 E-value=2.1 Score=36.45 Aligned_cols=36 Identities=31% Similarity=0.514 Sum_probs=31.6
Q ss_pred CCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECC
Q 019431 66 TKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSING 102 (341)
Q Consensus 66 ~~~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG 102 (341)
+..-..||+.+|++.+ ++||+++++++.+|.|..+.
T Consensus 98 ~~~~~~Rld~lLa~~L-~lSrs~l~~l~~~G~I~~~~ 133 (142)
T PF06353_consen 98 PFPFPLRLDRLLARQL-GLSRSRLKRLIEQGLIRSDP 133 (142)
T ss_pred CCCCCccHHHHHHHHh-CcCHHHHHHHHHCCCEEecC
Confidence 4556789999999997 69999999999999999764
No 90
>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=79.59 E-value=5.7 Score=29.47 Aligned_cols=51 Identities=14% Similarity=0.187 Sum_probs=32.8
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeec
Q 019431 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 70 ~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
+.++.+++.......+.- .......-.|.|||+.+. .++.|+.||+|.+-.
T Consensus 25 ~~tv~~ll~~l~~~~~~~-~~~~~~~~~v~vNg~~v~-~~~~l~~gD~v~i~p 75 (80)
T cd00754 25 GATVGELLDALEARYPGL-LEELLARVRIAVNGEYVR-LDTPLKDGDEVAIIP 75 (80)
T ss_pred CCcHHHHHHHHHHHCchH-HHhhhhcEEEEECCeEcC-CCcccCCCCEEEEeC
Confidence 556776655432112211 233344557889999994 889999999999854
No 91
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=75.46 E-value=5.1 Score=29.53 Aligned_cols=44 Identities=20% Similarity=0.348 Sum_probs=33.4
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeec
Q 019431 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 69 ~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
++..+.++|.+. + .+. +.-.|.+||+.+ ..++.|+.||+|++-.
T Consensus 22 ~~~tv~~ll~~l-~-~~~-------~~v~v~vNg~iv-~~~~~l~~gD~Veii~ 65 (70)
T PRK08364 22 KGMKVADILRAV-G-FNT-------ESAIAKVNGKVA-LEDDPVKDGDYVEVIP 65 (70)
T ss_pred CCCcHHHHHHHc-C-CCC-------ccEEEEECCEEC-CCCcCcCCCCEEEEEc
Confidence 356899988764 3 332 345788999999 5789999999999843
No 92
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=72.41 E-value=9.9 Score=28.49 Aligned_cols=25 Identities=24% Similarity=0.288 Sum_probs=21.7
Q ss_pred ceEECCEEeccccccccCCCEEeeec
Q 019431 97 LVSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 97 ~V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
.|.|||+.+ ..+..|+.||+|.+-+
T Consensus 51 ~v~vn~~~v-~~~~~l~dgDevai~P 75 (80)
T TIGR01682 51 MVAVNEEYV-TDDALLNEGDEVAFIP 75 (80)
T ss_pred EEEECCEEc-CCCcCcCCCCEEEEeC
Confidence 588999998 4689999999999854
No 93
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=67.93 E-value=14 Score=27.79 Aligned_cols=50 Identities=10% Similarity=0.126 Sum_probs=32.2
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeec
Q 019431 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 70 ~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
+..+.+++....... ..+.++...=.|.|||+.+ ..++.|+.||+|.+-+
T Consensus 28 ~~tv~~L~~~l~~~~--p~l~~~~~~~~vavN~~~v-~~~~~l~dgDeVai~P 77 (82)
T PLN02799 28 GSTTADCLAELVAKF--PSLEEVRSCCVLALNEEYT-TESAALKDGDELAIIP 77 (82)
T ss_pred CCcHHHHHHHHHHHC--hhHHHHhhCcEEEECCEEc-CCCcCcCCCCEEEEeC
Confidence 556666655432111 1233333333578999998 5889999999999854
No 94
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=66.93 E-value=6.3 Score=28.34 Aligned_cols=45 Identities=24% Similarity=0.379 Sum_probs=30.9
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEec---cccccccCCCEEeeec
Q 019431 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVS---KVSHNVKGGDMVNCTI 122 (341)
Q Consensus 69 ~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~---~~~~~v~~gD~I~v~~ 122 (341)
++..|.++|... +. ....+ .|.+||+.+. -.++.|+.||+|++..
T Consensus 14 ~~~tl~~lL~~l-~~-~~~~v-------av~vNg~iv~r~~~~~~~l~~gD~vei~~ 61 (66)
T PRK05659 14 DGESVAALLARE-GL-AGRRV-------AVEVNGEIVPRSQHASTALREGDVVEIVH 61 (66)
T ss_pred CCCCHHHHHHhc-CC-CCCeE-------EEEECCeEeCHHHcCcccCCCCCEEEEEE
Confidence 356788888764 33 22221 3889998773 2678999999999853
No 95
>PRK06437 hypothetical protein; Provisional
Probab=65.55 E-value=6.8 Score=28.68 Aligned_cols=45 Identities=27% Similarity=0.282 Sum_probs=33.1
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeec
Q 019431 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 68 ~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
+++.++.++|.+. + ++... + .|.+||+.+ ..++.|+.||+|++-.
T Consensus 18 ~~~~tv~dLL~~L-g-i~~~~----v---aV~vNg~iv-~~~~~L~dgD~Veiv~ 62 (67)
T PRK06437 18 DHELTVNDIIKDL-G-LDEEE----Y---VVIVNGSPV-LEDHNVKKEDDVLILE 62 (67)
T ss_pred CCCCcHHHHHHHc-C-CCCcc----E---EEEECCEEC-CCceEcCCCCEEEEEe
Confidence 3457899988774 4 34322 1 577999999 5899999999999843
No 96
>KOG3301 consensus Ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=63.30 E-value=7.1 Score=33.79 Aligned_cols=33 Identities=21% Similarity=0.161 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHcCceEECCEEeccccccccCC
Q 019431 83 GISRARVQSSIRSGLVSINGQVVSKVSHNVKGG 115 (341)
Q Consensus 83 ~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~g 115 (341)
..|-..+.-+|.++.|.|+++.|+-|++.|+..
T Consensus 109 AkSIhhARvLi~~rhI~V~~qiV~IPsf~vrld 141 (183)
T KOG3301|consen 109 AKSIHHARVLIRQRHIRVGKQIVNIPSFMVRLD 141 (183)
T ss_pred hhhhHHHHHHhcCccEEecCeEeeccceeEeec
Confidence 458888999999999999999998899998843
No 97
>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=60.72 E-value=5.8 Score=29.13 Aligned_cols=52 Identities=15% Similarity=0.187 Sum_probs=32.8
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc--ccccccCCCEEeeec
Q 019431 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK--VSHNVKGGDMVNCTI 122 (341)
Q Consensus 68 ~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~--~~~~v~~gD~I~v~~ 122 (341)
.++..+.++|.......+... ....=.|.|||+.+.. .++.|+.||+|.+-+
T Consensus 19 ~~~~tv~~ll~~l~~~~p~~~---~~~~~~v~vN~~~v~~~~~~~~l~~gD~V~i~p 72 (77)
T PF02597_consen 19 PEGSTVRDLLEALAERYPELA---LRDRVAVAVNGEIVPDDGLDTPLKDGDEVAILP 72 (77)
T ss_dssp SSTSBHHHHHHHHCHHTGGGH---TTTTEEEEETTEEEGGGTTTSBEETTEEEEEEE
T ss_pred CCCCcHHHHHHHHHhhccccc---cCccEEEEECCEEcCCccCCcCcCCCCEEEEEC
Confidence 345567777665421111111 3355567799999943 289999999999854
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=60.61 E-value=8.2 Score=27.79 Aligned_cols=44 Identities=18% Similarity=0.349 Sum_probs=30.4
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecccc----ccccCCCEEeeec
Q 019431 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVS----HNVKGGDMVNCTI 122 (341)
Q Consensus 69 ~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~----~~v~~gD~I~v~~ 122 (341)
+++.+.++|... . .+. +.+ .|.|||+.+. .+ +.|+.||+|++-.
T Consensus 13 ~~~tv~~ll~~l-~-~~~----~~i---~V~vNg~~v~-~~~~~~~~L~~gD~V~ii~ 60 (65)
T cd00565 13 EGATLAELLEEL-G-LDP----RGV---AVALNGEIVP-RSEWASTPLQDGDRIEIVT 60 (65)
T ss_pred CCCCHHHHHHHc-C-CCC----CcE---EEEECCEEcC-HHHcCceecCCCCEEEEEE
Confidence 356788888764 3 332 111 4679999984 45 8999999999843
No 99
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=59.25 E-value=7.1 Score=29.52 Aligned_cols=29 Identities=24% Similarity=0.405 Sum_probs=23.0
Q ss_pred HHcCc--eEECCEEeccccccccCCCEEeeec
Q 019431 93 IRSGL--VSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 93 I~~G~--V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
...|. +.||+..+ ..++.|+.||+|.+.+
T Consensus 46 ~~~~~~~~aVN~~~~-~~~~~l~dgDeVai~P 76 (81)
T PRK11130 46 LEDGKLLAAVNQTLV-SFDHPLTDGDEVAFFP 76 (81)
T ss_pred hcCCCEEEEECCEEc-CCCCCCCCCCEEEEeC
Confidence 34554 67999887 5789999999999865
No 100
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=55.35 E-value=12 Score=27.55 Aligned_cols=43 Identities=16% Similarity=0.276 Sum_probs=32.3
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc---ccccccCCCEEeee
Q 019431 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (341)
Q Consensus 70 ~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~---~~~~v~~gD~I~v~ 121 (341)
++++.++|++. +.-.+.. .|.+||..+.+ .++.++.||+|+|-
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 37899999885 4433222 57799999833 78999999999984
No 101
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=53.79 E-value=16 Score=36.46 Aligned_cols=40 Identities=25% Similarity=0.212 Sum_probs=30.4
Q ss_pred HHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccc
Q 019431 73 LDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNV 112 (341)
Q Consensus 73 Ldk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v 112 (341)
+.+.|....-.-||++++++|.+|.|++||.++...+..+
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 4444444434679999999999999999999986665444
No 102
>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=52.65 E-value=29 Score=34.26 Aligned_cols=41 Identities=24% Similarity=0.297 Sum_probs=33.7
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecccc
Q 019431 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVS 109 (341)
Q Consensus 69 ~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~ 109 (341)
++..+.+++...--..|++.++++|++|.|+|||.++...+
T Consensus 328 ~~~~~~~~~~~~~~~~S~~~arr~ik~g~v~vn~~~i~~~~ 368 (377)
T TIGR00234 328 GDITLADLLVLSGLFPSKSEARRDIKQGGVYINGEKVTDLE 368 (377)
T ss_pred CCcCHHHHHHHcCCCcChHHHHHHHHhCCEEECCEeccCch
Confidence 34788888887644689999999999999999999985443
No 103
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=49.50 E-value=19 Score=25.61 Aligned_cols=44 Identities=14% Similarity=0.241 Sum_probs=31.0
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccc---cccccCCCEEeeec
Q 019431 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKV---SHNVKGGDMVNCTI 122 (341)
Q Consensus 69 ~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~---~~~v~~gD~I~v~~ 122 (341)
++..|.++|... +. .. .-.|-+||..+.+. ++.|+.||+|+|-.
T Consensus 14 ~~~tl~~ll~~l-~~-~~--------~~~v~vN~~~v~~~~~~~~~L~~gD~vei~~ 60 (65)
T PRK06944 14 DGATVADALAAY-GA-RP--------PFAVAVNGDFVARTQHAARALAAGDRLDLVQ 60 (65)
T ss_pred CCCcHHHHHHhh-CC-CC--------CeEEEECCEEcCchhcccccCCCCCEEEEEe
Confidence 356788888764 33 21 13688999988432 67899999999854
No 104
>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=47.97 E-value=18 Score=25.68 Aligned_cols=23 Identities=35% Similarity=0.689 Sum_probs=19.2
Q ss_pred ceEECCEEeccccccccCCCEEee
Q 019431 97 LVSINGQVVSKVSHNVKGGDMVNC 120 (341)
Q Consensus 97 ~V~VNG~~v~~~~~~v~~gD~I~v 120 (341)
...|||+.+ ..++.|+.||.|++
T Consensus 36 ~A~Vng~~v-dl~~~L~~~d~v~i 58 (60)
T PF02824_consen 36 AAKVNGQLV-DLDHPLEDGDVVEI 58 (60)
T ss_dssp EEEETTEEE-ETTSBB-SSEEEEE
T ss_pred EEEEcCEEC-CCCCCcCCCCEEEE
Confidence 456999999 79999999999987
No 105
>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=46.93 E-value=49 Score=25.86 Aligned_cols=26 Identities=23% Similarity=0.164 Sum_probs=20.9
Q ss_pred ceEECCEEec---cccccccCCCEEeeec
Q 019431 97 LVSINGQVVS---KVSHNVKGGDMVNCTI 122 (341)
Q Consensus 97 ~V~VNG~~v~---~~~~~v~~gD~I~v~~ 122 (341)
.|.|||..+. ..++.|+.||+|.+-+
T Consensus 61 ~VlvN~~di~~l~g~~t~L~dgD~v~i~P 89 (94)
T cd01764 61 IVLINDTDWELLGEEDYILEDGDHVVFIS 89 (94)
T ss_pred EEEECCccccccCCcccCCCCcCEEEEEC
Confidence 5779998763 4679999999999865
No 106
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=46.16 E-value=17 Score=35.92 Aligned_cols=47 Identities=21% Similarity=0.343 Sum_probs=35.9
Q ss_pred CCccccccCCCCCceeEEeecCHHHHHHHHHHhhcCccceEEEEEEeccCC
Q 019431 210 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPS 260 (341)
Q Consensus 210 ~~~~~vhRLD~~TSGLll~ak~~~~a~~l~~~f~~~~v~K~Y~a~v~G~~~ 260 (341)
...+..+-||-+.||.++...+......... ....|+|.+++.....
T Consensus 95 ek~Gh~gTlDP~vtg~l~v~~~~~tr~~~s~----~s~gk~yvg~~~lt~~ 141 (395)
T KOG2529|consen 95 EKTGHSGTLDPEVTGCLIVCIDRATRLLKSQ----QSAGKEYVGIGKLTPE 141 (395)
T ss_pred HHhCCCCCCCccccceEEEEeecccccccch----hccCcEEEEEEecCcc
Confidence 3457789999999999999998665443333 4689999988877654
No 107
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=44.97 E-value=23 Score=25.40 Aligned_cols=43 Identities=19% Similarity=0.251 Sum_probs=29.5
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc---ccccccCCCEEeeec
Q 019431 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCTI 122 (341)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~---~~~~v~~gD~I~v~~ 122 (341)
..|.++|... ..-. . .+ .|-+|++.+.+ .++.|+.||+|++-.
T Consensus 15 ~tl~~Ll~~l-~~~~-~----~v---avavN~~iv~~~~~~~~~L~dgD~Ieiv~ 60 (65)
T PRK06488 15 TTLALLLAEL-DYEG-N----WL---ATAVNGELVHKEARAQFVLHEGDRIEILS 60 (65)
T ss_pred CcHHHHHHHc-CCCC-C----eE---EEEECCEEcCHHHcCccccCCCCEEEEEE
Confidence 4788888764 3211 1 11 37899999843 378999999999843
No 108
>PRK07440 hypothetical protein; Provisional
Probab=44.88 E-value=25 Score=25.88 Aligned_cols=44 Identities=18% Similarity=0.209 Sum_probs=30.8
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc---ccccccCCCEEeee
Q 019431 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (341)
Q Consensus 69 ~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~---~~~~v~~gD~I~v~ 121 (341)
+++.|.++|.+. ..-.+ .=.|-+||+.+.+ .++.|+.||.|+|-
T Consensus 18 ~~~tl~~lL~~l-~~~~~--------~vav~~N~~iv~r~~w~~~~L~~gD~IEIv 64 (70)
T PRK07440 18 SGTSLPDLLQQL-GFNPR--------LVAVEYNGEILHRQFWEQTQVQPGDRLEIV 64 (70)
T ss_pred CCCCHHHHHHHc-CCCCC--------eEEEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 467799988764 33221 1257799999832 67889999999874
No 109
>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=44.76 E-value=26 Score=26.60 Aligned_cols=26 Identities=27% Similarity=0.376 Sum_probs=20.3
Q ss_pred CceEECCEEeccccc--cccCCCEEeeec
Q 019431 96 GLVSINGQVVSKVSH--NVKGGDMVNCTI 122 (341)
Q Consensus 96 G~V~VNG~~v~~~~~--~v~~gD~I~v~~ 122 (341)
=.|.|||+.+. .+. .|+.||+|.+-+
T Consensus 56 ~~v~vN~~~v~-~~~~~~l~dgdev~i~P 83 (88)
T TIGR01687 56 VIILVNGRNVD-WGLGTELKDGDVVAIFP 83 (88)
T ss_pred EEEEECCEecC-ccCCCCCCCCCEEEEeC
Confidence 35789999984 444 899999999854
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=44.19 E-value=26 Score=25.02 Aligned_cols=44 Identities=27% Similarity=0.407 Sum_probs=30.8
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc---ccccccCCCEEeeec
Q 019431 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCTI 122 (341)
Q Consensus 70 ~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~---~~~~v~~gD~I~v~~ 122 (341)
++.|.++|... + ... ..-.|.+||+.+.+ ..+.|+.||+|++-.
T Consensus 13 ~~tv~~ll~~l-~-~~~-------~~v~v~vN~~iv~~~~~~~~~L~~gD~veii~ 59 (64)
T TIGR01683 13 GLTLAALLESL-G-LDP-------RRVAVAVNGEIVPRSEWDDTILKEGDRIEIVT 59 (64)
T ss_pred CCcHHHHHHHc-C-CCC-------CeEEEEECCEEcCHHHcCceecCCCCEEEEEE
Confidence 56789988764 3 221 33467799999853 346899999999853
No 111
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=42.55 E-value=29 Score=27.67 Aligned_cols=38 Identities=18% Similarity=0.208 Sum_probs=31.8
Q ss_pred CHHHHHHHHHcCceEECCEEeccccccccCCCEEeeec
Q 019431 85 SRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (341)
Q Consensus 85 SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~ 122 (341)
=+...-++|.+|.=+|-+++....-..+++||.|.+.+
T Consensus 7 L~eeylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~~ 44 (111)
T COG4043 7 LREEYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFNG 44 (111)
T ss_pred hHHHHHHHHHcccceEEEEecCHhhcCCCCCCEEEEcC
Confidence 35566789999999999999866668899999998865
No 112
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=39.02 E-value=13 Score=28.63 Aligned_cols=30 Identities=27% Similarity=0.340 Sum_probs=17.7
Q ss_pred HcCceEECCEEeccccccccCCCEEeeeccc
Q 019431 94 RSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (341)
Q Consensus 94 ~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~ 124 (341)
....|=|=|+.+ +.++.++.||+|+|+.+.
T Consensus 45 ~~~~vGIfGk~~-~~d~~L~~GDRVEIYRPL 74 (84)
T PF03658_consen 45 EKNKVGIFGKLV-KLDTVLRDGDRVEIYRPL 74 (84)
T ss_dssp TTSEEEEEE-S---TT-B--TT-EEEEE-S-
T ss_pred ccceeeeeeeEc-CCCCcCCCCCEEEEeccC
Confidence 566777889998 699999999999999753
No 113
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=37.18 E-value=34 Score=24.90 Aligned_cols=42 Identities=14% Similarity=0.191 Sum_probs=28.0
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc---ccccccCCCEEeee
Q 019431 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (341)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~---~~~~v~~gD~I~v~ 121 (341)
..|.++|... +.-... =.|-+||+.+.+ ..+.|+.||+|++-
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 4588888764 332111 157899999843 23889999999873
No 114
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=37.05 E-value=45 Score=33.17 Aligned_cols=41 Identities=17% Similarity=0.108 Sum_probs=33.3
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc
Q 019431 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK 107 (341)
Q Consensus 67 ~~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~ 107 (341)
.+.++.+.+.+.++-..-|+.++.++|.+|.|.+|++++..
T Consensus 395 ~~~~~s~~~l~~ka~~~~s~~~a~r~i~qG~vslnh~~v~~ 435 (467)
T KOG2623|consen 395 DEPGVSILDLLRKASRFPSGKEARRMIQQGGVSLNHEKVRD 435 (467)
T ss_pred cCCCCcHHHHHHHhhcCCCcHHHHHHHHccceeecCccccC
Confidence 34577888888877445678899999999999999999854
No 115
>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=36.32 E-value=31 Score=24.44 Aligned_cols=26 Identities=23% Similarity=0.355 Sum_probs=17.8
Q ss_pred cCceEECCEEecc-ccccccCCCEEee
Q 019431 95 SGLVSINGQVVSK-VSHNVKGGDMVNC 120 (341)
Q Consensus 95 ~G~V~VNG~~v~~-~~~~v~~gD~I~v 120 (341)
..-++|||+++.. ..+.|..||+|.+
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 4568899988842 2577889998875
No 116
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=36.01 E-value=44 Score=24.06 Aligned_cols=44 Identities=16% Similarity=0.305 Sum_probs=29.4
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc---ccccccCCCEEeee
Q 019431 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (341)
Q Consensus 69 ~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~---~~~~v~~gD~I~v~ 121 (341)
+++.|.++|... +.-.+ .=.|-+|++.+.+ ..+.|+.||.|++-
T Consensus 14 ~~~tl~~ll~~l-~~~~~--------~vaVavN~~iv~r~~w~~~~L~~gD~Ieii 60 (66)
T PRK08053 14 AGQTVHELLEQL-NQLQP--------GAALAINQQIIPREQWAQHIVQDGDQILLF 60 (66)
T ss_pred CCCCHHHHHHHc-CCCCC--------cEEEEECCEEeChHHcCccccCCCCEEEEE
Confidence 356788888764 32111 1246799999842 45689999999884
No 117
>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=31.93 E-value=21 Score=25.61 Aligned_cols=16 Identities=25% Similarity=0.401 Sum_probs=11.9
Q ss_pred CCcEEEEeCCCCCeee
Q 019431 143 DDNVLVVNKPAHMVVH 158 (341)
Q Consensus 143 d~~llvvnKP~Gl~~~ 158 (341)
...+|.+|||+|-.+|
T Consensus 41 ~~GvinlDKP~gPtSH 56 (59)
T PF08068_consen 41 KYGVINLDKPSGPTSH 56 (59)
T ss_dssp HTEEEEEEE-SSS-HH
T ss_pred hCCcEEeeCCCCCCcc
Confidence 4789999999997765
No 118
>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=28.96 E-value=42 Score=25.22 Aligned_cols=22 Identities=23% Similarity=0.273 Sum_probs=19.2
Q ss_pred EECCEEeccccccccCCCEEeee
Q 019431 99 SINGQVVSKVSHNVKGGDMVNCT 121 (341)
Q Consensus 99 ~VNG~~v~~~~~~v~~gD~I~v~ 121 (341)
.++|+++ ..++.|+-||+|+|.
T Consensus 53 ~~~gq~V-gl~~~L~d~DvVeI~ 74 (75)
T cd01666 53 KHSPQRV-GLDHVLEDEDVVQIV 74 (75)
T ss_pred cCCCeEC-CCCCEecCCCEEEEe
Confidence 3699998 789999999999984
No 119
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase.
Probab=27.27 E-value=22 Score=25.77 Aligned_cols=15 Identities=20% Similarity=0.160 Sum_probs=12.1
Q ss_pred CceeccccCcccccc
Q 019431 1 MTMLSLNSASWGSAS 15 (341)
Q Consensus 1 ~~~~~~~~~~~~~~~ 15 (341)
++|.+..+|++|+.-
T Consensus 1 v~ly~~~~Cp~C~~a 15 (72)
T TIGR02194 1 ITVYSKNNCVQCKMT 15 (72)
T ss_pred CEEEeCCCCHHHHHH
Confidence 578888899999864
No 120
>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=25.80 E-value=86 Score=21.29 Aligned_cols=23 Identities=35% Similarity=0.566 Sum_probs=19.0
Q ss_pred ceEECCEEeccccccccCCCEEee
Q 019431 97 LVSINGQVVSKVSHNVKGGDMVNC 120 (341)
Q Consensus 97 ~V~VNG~~v~~~~~~v~~gD~I~v 120 (341)
.+.+||+.+ ..++.+..||.|++
T Consensus 36 a~~vng~~v-dl~~~l~~~~~ve~ 58 (60)
T cd01668 36 GAKVNGKLV-PLSTVLKDGDIVEI 58 (60)
T ss_pred EEEECCEEC-CCCCCCCCCCEEEE
Confidence 456999998 57888999998876
No 121
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=23.92 E-value=85 Score=24.08 Aligned_cols=45 Identities=22% Similarity=0.260 Sum_probs=30.3
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc---ccccccCCCEEeee
Q 019431 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (341)
Q Consensus 68 ~~~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~---~~~~v~~gD~I~v~ 121 (341)
.++..|.++|... . .....+ .|-+||..+.+ .++.|+.||+|+|-
T Consensus 31 ~~~~tl~~LL~~l-~-~~~~~v-------AVevNg~iVpr~~w~~t~L~egD~IEIv 78 (84)
T PRK06083 31 DISSSLAQIIAQL-S-LPELGC-------VFAINNQVVPRSEWQSTVLSSGDAISLF 78 (84)
T ss_pred CCCCcHHHHHHHc-C-CCCceE-------EEEECCEEeCHHHcCcccCCCCCEEEEE
Confidence 3456788888764 3 222111 56799998743 45779999999873
No 122
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=23.39 E-value=76 Score=25.79 Aligned_cols=25 Identities=28% Similarity=0.361 Sum_probs=18.4
Q ss_pred cCceEECCEEeccccccccCCCEEeeecc
Q 019431 95 SGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (341)
Q Consensus 95 ~G~V~VNG~~v~~~~~~v~~gD~I~v~~~ 123 (341)
+|.|.+||--+ +.+.+||+|.|---
T Consensus 65 Sg~I~lNGAAA----r~~~~GD~vII~sy 89 (111)
T cd06919 65 SGVICLNGAAA----RLGQPGDRVIIMAY 89 (111)
T ss_pred CCEEEeCCHHH----hcCCCCCEEEEEEC
Confidence 47788888654 56788999887543
No 123
>PRK02253 deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional
Probab=22.68 E-value=2.4e+02 Score=24.37 Aligned_cols=39 Identities=18% Similarity=0.206 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHcCceEECC------EEeccccccccCCCEEeee
Q 019431 83 GISRARVQSSIRSGLVSING------QVVSKVSHNVKGGDMVNCT 121 (341)
Q Consensus 83 ~~SR~~~~~lI~~G~V~VNG------~~v~~~~~~v~~gD~I~v~ 121 (341)
.+|.++++++|++|.+.++. ..+...+.-++.|+.+.+.
T Consensus 2 iLs~~~I~~~i~~g~i~i~p~~~~~~~qiqp~svDlrlg~~~~~~ 46 (167)
T PRK02253 2 LLSKEELRKLIRSGKFVAEHVVDLEDDQVQPNGVDLTLGEVEEQE 46 (167)
T ss_pred cCCHHHHHHHHHcCCeEeecCCCCChhhCCCcEEEEECCcEEEEe
Confidence 36899999999999999852 2444567777888777664
No 124
>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=22.51 E-value=1.1e+02 Score=20.08 Aligned_cols=22 Identities=36% Similarity=0.599 Sum_probs=18.1
Q ss_pred eEECCEEeccccccccCCCEEee
Q 019431 98 VSINGQVVSKVSHNVKGGDMVNC 120 (341)
Q Consensus 98 V~VNG~~v~~~~~~v~~gD~I~v 120 (341)
+.+||+.+ ..++.+..||.|++
T Consensus 37 ~~vn~~~~-~l~~~l~~~~~i~~ 58 (60)
T cd01616 37 ALVNGQLV-DLSYTLQDGDTVSI 58 (60)
T ss_pred EEECCEEC-CCCcCcCCCCEEEE
Confidence 45899988 57889999998875
No 125
>KOG4655 consensus U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification]
Probab=21.96 E-value=56 Score=28.49 Aligned_cols=36 Identities=22% Similarity=0.260 Sum_probs=30.7
Q ss_pred CHHHHHHHHHcCceEECCEEeccccccccCC--CEEee
Q 019431 85 SRARVQSSIRSGLVSINGQVVSKVSHNVKGG--DMVNC 120 (341)
Q Consensus 85 SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~g--D~I~v 120 (341)
|-..+-++|++|.|+|.-++++.|.+.|... |.|+.
T Consensus 121 ~~k~A~~~vEqGHVRvGp~~vtDPa~lvtr~mEDfvtW 158 (181)
T KOG4655|consen 121 SVKEAVRFVEQGHVRVGPKVVTDPAFLVTRSMEDFVTW 158 (181)
T ss_pred hHHHHHHHHHcCceeeCCeeccCchHHhhhhhhhhhhh
Confidence 5667889999999999999999999998865 66654
No 126
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=21.31 E-value=74 Score=34.22 Aligned_cols=23 Identities=17% Similarity=0.293 Sum_probs=19.8
Q ss_pred ECCEEeccccccccCCCEEeeecc
Q 019431 100 INGQVVSKVSHNVKGGDMVNCTIS 123 (341)
Q Consensus 100 VNG~~v~~~~~~v~~gD~I~v~~~ 123 (341)
|||+.+ ..++.|+.||+|+|--.
T Consensus 426 VNg~~v-pL~~~L~~Gd~VeIiT~ 448 (702)
T PRK11092 426 VDRQPY-PLSQPLTSGQTVEIITA 448 (702)
T ss_pred ECCEEC-CCCccCCCCCEEEEEeC
Confidence 488888 79999999999998644
No 127
>COG2440 FixX Ferredoxin-like protein [Energy production and conversion]
Probab=20.58 E-value=60 Score=25.81 Aligned_cols=23 Identities=17% Similarity=0.252 Sum_probs=17.3
Q ss_pred cCcccccccCc--eeeeccCCCCcc
Q 019431 8 SASWGSASCTK--GLQFSPTKIPFG 30 (341)
Q Consensus 8 ~~~~~~~~~~~--~~~~~~~~~~~~ 30 (341)
-||.||+-|+. .-||..|...++
T Consensus 69 ECGTCRvlc~~~~~i~W~YPrgg~G 93 (99)
T COG2440 69 ECGTCRVLCPHSGLIQWRYPRGGFG 93 (99)
T ss_pred eccceeEecCCCcceEEecCCCCcC
Confidence 48999999875 567877765554
No 128
>KOG4837 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.07 E-value=81 Score=28.57 Aligned_cols=53 Identities=23% Similarity=0.297 Sum_probs=43.4
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccccccccCCCEEeeecc
Q 019431 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (341)
Q Consensus 70 ~~RLdk~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~ 123 (341)
.-|.|..|..-+ ++.|+.++-+.-++.+++|+....+.+.+|..||.+-+-..
T Consensus 139 sfr~d~llK~Gl-gv~rnKVel~fye~e~R~N~~Kl~kkS~~i~vgds~d~~ig 191 (248)
T KOG4837|consen 139 SFRVDALLKVGL-GVTRNKVELLFYEYEPRTNSFKLVKKSLRIDVGDSADFKIG 191 (248)
T ss_pred HHHHHHHHHhcc-ccccchhhHhhhhcccccCcccccccceeeecccccceeee
Confidence 456677666543 68999999999999999999887789999999998776543
No 129
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=20.03 E-value=95 Score=19.88 Aligned_cols=25 Identities=20% Similarity=0.368 Sum_probs=18.7
Q ss_pred HHHHHHhccCCCCHHHHHHHHHcCceE
Q 019431 73 LDAWISSRIDGISRARVQSSIRSGLVS 99 (341)
Q Consensus 73 Ldk~L~~~~~~~SR~~~~~lI~~G~V~ 99 (341)
+.+. ++.+ ++|++.+.+++++|.+.
T Consensus 4 ~~e~-a~~l-gis~~ti~~~~~~g~i~ 28 (49)
T TIGR01764 4 VEEA-AEYL-GVSKDTVYRLIHEGELP 28 (49)
T ss_pred HHHH-HHHH-CCCHHHHHHHHHcCCCC
Confidence 4443 4554 68999999999999754
Done!