Query 022299
Match_columns 299
No_of_seqs 187 out of 1726
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 02:27:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022299.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022299hhsearch_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 5.5E-41 1.2E-45 313.4 22.0 194 61-285 3-197 (289)
2 PRK11180 rluD 23S rRNA pseudou 100.0 6.9E-37 1.5E-41 290.2 24.6 195 55-277 2-196 (325)
3 TIGR00005 rluA_subfam pseudour 100.0 3.7E-36 8.1E-41 281.6 22.7 181 67-274 2-182 (299)
4 PRK11025 23S rRNA pseudouridyl 100.0 4.3E-35 9.4E-40 277.1 22.9 183 61-275 10-200 (317)
5 PRK10475 23S rRNA pseudouridin 100.0 2.5E-28 5.4E-33 228.2 16.8 178 68-297 4-194 (290)
6 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 4.2E-28 9.1E-33 222.0 16.2 142 97-273 3-145 (246)
7 PRK10839 16S rRNA pseudouridyl 100.0 4.7E-28 1E-32 219.5 13.4 142 71-261 1-142 (232)
8 PRK10700 23S rRNA pseudouridyl 99.9 1.4E-26 3E-31 216.6 18.8 146 70-261 2-150 (289)
9 KOG1919 RNA pseudouridylate sy 99.9 9E-25 2E-29 209.1 18.8 192 59-286 32-225 (371)
10 PRK10158 23S rRNA/tRNA pseudou 99.9 4E-25 8.7E-30 199.0 15.0 106 136-274 13-119 (219)
11 cd02557 PseudoU_synth_ScRIB2 P 99.9 6.8E-25 1.5E-29 196.7 13.9 109 134-273 13-121 (213)
12 TIGR01621 RluA-like pseudourid 99.9 1.6E-24 3.5E-29 194.9 14.6 106 137-275 2-107 (217)
13 COG1187 RsuA 16S rRNA uridine- 99.9 3.9E-24 8.4E-29 195.0 14.4 178 70-297 2-201 (248)
14 cd02563 PseudoU_synth_TruC tRN 99.9 4.9E-24 1.1E-28 192.3 14.9 106 137-275 1-108 (223)
15 PRK11112 tRNA pseudouridine sy 99.9 1.1E-23 2.3E-28 194.1 13.5 104 137-273 2-107 (257)
16 PF00849 PseudoU_synth_2: RNA 99.8 6.2E-21 1.3E-25 162.6 10.1 101 145-272 1-101 (164)
17 cd02550 PseudoU_synth_Rsu_Rlu_ 99.8 3.2E-20 6.9E-25 158.1 11.1 90 146-270 1-90 (154)
18 cd02869 PseudoU_synth_RluCD_li 99.8 4E-19 8.7E-24 154.1 13.2 100 146-272 1-100 (185)
19 cd02556 PseudoU_synth_RluB Pse 99.8 7.1E-19 1.5E-23 152.1 11.3 82 145-260 1-82 (167)
20 cd02870 PseudoU_synth_RsuA_lik 99.8 4.6E-19 9.9E-24 149.8 8.0 81 146-261 1-81 (146)
21 cd02553 PseudoU_synth_RsuA Pse 99.8 1E-18 2.2E-23 151.2 9.8 83 146-262 2-84 (167)
22 cd02566 PseudoU_synth_RluE Pse 99.7 9.8E-18 2.1E-22 145.1 8.6 79 146-261 1-80 (168)
23 cd02555 PSSA_1 PSSA_1: Pseudou 99.7 1.6E-16 3.5E-21 138.8 9.0 50 211-262 46-95 (177)
24 cd02554 PseudoU_synth_RluF Pse 99.7 4.4E-16 9.5E-21 134.6 10.5 113 146-297 2-127 (164)
25 PRK11394 23S rRNA pseudouridin 99.6 5.4E-16 1.2E-20 139.5 7.8 81 144-261 39-119 (217)
26 cd00165 S4 S4/Hsp/ tRNA synthe 99.3 2.7E-11 5.8E-16 87.2 8.3 70 71-150 1-70 (70)
27 TIGR00093 pseudouridine syntha 99.2 2.8E-11 6.1E-16 100.3 6.9 44 215-260 1-44 (128)
28 cd02868 PseudoU_synth_hTruB2_l 99.2 5.7E-11 1.2E-15 107.6 7.4 75 146-256 2-76 (226)
29 PF01479 S4: S4 domain; Inter 99.0 1.3E-09 2.8E-14 74.9 6.1 48 71-118 1-48 (48)
30 TIGR02988 YaaA_near_RecF S4 do 98.9 2.7E-09 5.8E-14 76.8 6.3 52 67-120 5-58 (59)
31 COG1188 Ribosome-associated he 98.5 2.8E-07 6.1E-12 72.9 5.4 55 68-123 6-60 (100)
32 smart00363 S4 S4 RNA-binding d 98.4 7.9E-07 1.7E-11 61.7 6.4 52 71-122 1-52 (60)
33 PLN00051 RNA-binding S4 domain 98.2 4.6E-06 9.9E-11 77.6 7.1 60 63-123 184-243 (267)
34 PRK10348 ribosome-associated h 98.1 6.9E-06 1.5E-10 68.6 6.9 53 69-122 7-59 (133)
35 TIGR03069 PS_II_S4 photosystem 98.1 5.9E-06 1.3E-10 76.5 6.8 60 63-123 176-235 (257)
36 TIGR01017 rpsD_bact ribosomal 98.1 8.6E-06 1.9E-10 72.7 6.7 54 70-123 89-142 (200)
37 CHL00113 rps4 ribosomal protei 98.0 1E-05 2.2E-10 72.2 6.3 53 71-123 89-141 (201)
38 TIGR00478 tly hemolysin TlyA f 97.9 2.1E-05 4.5E-10 71.6 6.2 52 72-123 1-52 (228)
39 PRK05327 rpsD 30S ribosomal pr 97.9 2.6E-05 5.5E-10 69.8 6.4 53 70-122 92-144 (203)
40 cd02572 PseudoU_synth_hDyskeri 97.7 9.9E-05 2.1E-09 65.0 7.5 70 144-256 2-71 (182)
41 PRK11507 ribosome-associated p 97.7 0.00014 3E-09 54.1 6.7 57 66-122 7-63 (70)
42 COG2302 Uncharacterized conser 97.6 6.4E-05 1.4E-09 68.6 4.8 56 67-123 177-232 (257)
43 COG0522 RpsD Ribosomal protein 97.6 0.00011 2.5E-09 65.7 5.8 54 71-124 94-147 (205)
44 cd00506 PseudoU_synth_TruB_lik 97.5 0.00044 9.5E-09 62.2 7.8 68 146-256 2-69 (210)
45 COG1189 Predicted rRNA methyla 97.5 0.00025 5.4E-09 64.6 6.2 53 70-122 2-54 (245)
46 PRK00989 truB tRNA pseudouridi 97.4 0.00038 8.3E-09 63.3 7.0 71 144-256 9-79 (230)
47 PRK04099 truB tRNA pseudouridi 97.4 0.00049 1.1E-08 64.2 7.4 70 144-256 2-71 (273)
48 PRK00020 truB tRNA pseudouridi 97.3 0.00084 1.8E-08 61.6 8.0 70 144-256 10-79 (244)
49 TIGR00431 TruB tRNA pseudourid 97.3 0.00085 1.8E-08 60.3 7.8 69 145-256 3-71 (209)
50 PF13275 S4_2: S4 domain; PDB: 97.2 5.6E-05 1.2E-09 55.6 -0.4 57 66-122 3-59 (65)
51 PRK00130 truB tRNA pseudouridi 97.2 0.0013 2.8E-08 62.0 8.1 70 144-256 2-71 (290)
52 PRK14124 tRNA pseudouridine sy 97.2 0.0015 3.2E-08 62.0 8.2 70 144-256 3-72 (308)
53 PRK02484 truB tRNA pseudouridi 97.2 0.0012 2.6E-08 62.3 7.5 69 145-256 4-72 (294)
54 PRK03287 truB tRNA pseudouridi 97.2 0.0014 3E-08 62.0 7.8 71 143-256 8-78 (298)
55 PRK14123 tRNA pseudouridine sy 97.1 0.0014 3.1E-08 62.1 7.5 70 144-256 3-72 (305)
56 PRK02755 truB tRNA pseudouridi 97.1 0.0014 3E-08 61.9 7.2 69 144-256 3-71 (295)
57 PRK05389 truB tRNA pseudouridi 97.1 0.0018 3.9E-08 61.4 7.8 70 144-256 13-82 (305)
58 PRK05033 truB tRNA pseudouridi 97.0 0.0023 4.9E-08 60.8 8.0 70 144-256 10-79 (312)
59 PRK04270 H/ACA RNA-protein com 97.0 0.0018 3.9E-08 61.3 7.3 70 144-256 22-91 (300)
60 cd02573 PseudoU_synth_EcTruB P 97.0 0.0023 4.9E-08 60.0 7.8 68 146-256 2-69 (277)
61 PRK01550 truB tRNA pseudouridi 97.0 0.0022 4.7E-08 60.9 7.6 69 145-256 3-71 (304)
62 PRK01851 truB tRNA pseudouridi 97.0 0.0022 4.9E-08 60.7 7.7 70 144-256 16-85 (303)
63 PRK02193 truB tRNA pseudouridi 97.0 0.0025 5.3E-08 59.8 7.7 68 146-256 2-69 (279)
64 PRK04051 rps4p 30S ribosomal p 96.9 0.002 4.4E-08 56.4 6.1 51 71-121 103-155 (177)
65 PRK14846 truB tRNA pseudouridi 96.9 0.0033 7.1E-08 60.2 7.9 70 144-256 3-72 (345)
66 PRK01528 truB tRNA pseudouridi 96.9 0.003 6.5E-08 59.5 7.4 70 144-256 3-72 (292)
67 PRK14122 tRNA pseudouridine sy 96.8 0.0049 1.1E-07 58.6 7.9 69 145-256 2-70 (312)
68 COG2501 S4-like RNA binding pr 96.8 0.0043 9.4E-08 46.5 5.9 58 65-122 6-63 (73)
69 TIGR00425 CBF5 rRNA pseudourid 96.5 0.0067 1.4E-07 58.0 6.9 70 144-256 34-103 (322)
70 PRK04642 truB tRNA pseudouridi 96.4 0.011 2.4E-07 55.9 7.7 70 144-256 10-79 (300)
71 cd02867 PseudoU_synth_TruB_4 P 96.4 0.01 2.2E-07 56.5 7.5 43 210-256 56-98 (312)
72 COG0130 TruB Pseudouridine syn 96.2 0.013 2.8E-07 54.7 6.9 69 145-256 16-84 (271)
73 PLN00189 40S ribosomal protein 96.0 0.0049 1.1E-07 54.7 2.8 55 70-124 100-162 (194)
74 TIGR01018 rpsD_arch ribosomal 95.7 0.018 4E-07 49.8 5.0 50 71-120 104-155 (162)
75 PRK04313 30S ribosomal protein 95.3 0.067 1.5E-06 49.0 7.5 73 68-150 35-108 (237)
76 PTZ00155 40S ribosomal protein 95.3 0.021 4.5E-07 50.3 3.9 53 71-123 107-159 (181)
77 PLN00036 40S ribosomal protein 95.0 0.096 2.1E-06 48.5 7.6 54 69-122 40-94 (261)
78 PTZ00223 40S ribosomal protein 94.8 0.11 2.4E-06 48.4 7.5 55 68-122 36-91 (273)
79 PTZ00118 40S ribosomal protein 94.8 0.11 2.4E-06 48.1 7.5 55 68-122 39-94 (262)
80 PF14451 Ub-Mut7C: Mut7-C ubiq 90.8 0.5 1.1E-05 36.2 4.7 47 67-122 29-75 (81)
81 COG1471 RPS4A Ribosomal protei 90.6 0.62 1.3E-05 42.4 5.9 66 73-151 47-112 (241)
82 PRK01777 hypothetical protein; 89.5 0.6 1.3E-05 36.9 4.3 54 67-123 23-76 (95)
83 PRK13354 tyrosyl-tRNA syntheta 88.8 0.8 1.7E-05 45.3 5.6 48 70-117 342-389 (410)
84 COG4332 Uncharacterized protei 86.9 1.3 2.8E-05 39.0 5.0 62 60-122 127-189 (203)
85 KOG2559 Predicted pseudouridin 86.6 0.7 1.5E-05 42.6 3.4 22 211-232 90-111 (318)
86 cd01291 PseudoU_synth PseudoU_ 86.4 1.1 2.3E-05 34.2 4.0 28 210-256 24-51 (87)
87 PRK05912 tyrosyl-tRNA syntheta 86.0 1.9 4.2E-05 42.6 6.5 45 70-114 342-386 (408)
88 PF06353 DUF1062: Protein of u 85.0 2.1 4.7E-05 36.2 5.4 36 66-102 98-133 (142)
89 PF01509 TruB_N: TruB family p 84.2 1.2 2.5E-05 38.0 3.5 43 210-256 7-49 (149)
90 PRK08364 sulfur carrier protei 81.3 5.3 0.00011 29.3 5.7 43 69-121 22-64 (70)
91 cd00754 MoaD Ubiquitin domain 81.0 4.7 0.0001 29.6 5.4 50 70-121 25-74 (80)
92 TIGR01682 moaD molybdopterin c 70.2 12 0.00025 27.9 5.0 24 97-121 51-74 (80)
93 PLN02799 Molybdopterin synthas 69.4 12 0.00027 27.9 5.1 50 69-121 27-76 (82)
94 PF02597 ThiS: ThiS family; I 69.1 3.1 6.7E-05 30.4 1.6 51 68-121 19-71 (77)
95 PRK05659 sulfur carrier protei 66.5 5.6 0.00012 28.5 2.5 44 69-121 14-60 (66)
96 PRK06437 hypothetical protein; 66.0 6.7 0.00015 28.6 2.9 44 68-121 18-61 (67)
97 cd00565 ThiS ThiaminS ubiquiti 59.8 8.5 0.00018 27.6 2.4 43 69-121 13-59 (65)
98 PRK11130 moaD molybdopterin sy 59.5 7.3 0.00016 29.3 2.1 43 73-121 31-75 (81)
99 COG0162 TyrS Tyrosyl-tRNA synt 55.1 15 0.00032 36.4 4.0 40 73-112 338-377 (401)
100 PF02824 TGS: TGS domain; Int 53.9 14 0.00031 26.2 2.8 23 97-120 36-58 (60)
101 TIGR01687 moaD_arch MoaD famil 53.4 13 0.00028 28.1 2.6 25 96-121 56-82 (88)
102 PRK06944 sulfur carrier protei 52.6 17 0.00036 25.8 3.0 43 69-121 14-59 (65)
103 PRK06083 sulfur carrier protei 51.0 40 0.00086 25.9 5.0 45 68-121 31-78 (84)
104 COG2104 ThiS Sulfur transfer p 50.5 17 0.00037 26.8 2.7 43 70-121 17-62 (68)
105 PRK06488 sulfur carrier protei 48.7 20 0.00043 25.6 2.9 42 71-121 15-59 (65)
106 TIGR01683 thiS thiamine biosyn 47.0 23 0.0005 25.2 3.0 44 69-121 12-58 (64)
107 TIGR00234 tyrS tyrosyl-tRNA sy 45.6 46 0.001 32.6 5.7 40 70-109 329-368 (377)
108 cd01764 Urm1 Urm1-like ubuitin 45.4 43 0.00094 26.1 4.5 25 97-121 61-88 (94)
109 PRK07440 hypothetical protein; 44.9 26 0.00057 25.7 3.0 45 68-121 17-64 (70)
110 PF00498 FHA: FHA domain; Int 42.1 24 0.00052 24.9 2.4 26 95-120 41-67 (68)
111 KOG3301 Ribosomal protein S4 [ 41.4 28 0.0006 30.3 3.0 46 70-115 88-141 (183)
112 PRK08053 sulfur carrier protei 37.5 41 0.0009 24.1 3.1 44 69-121 14-60 (66)
113 KOG2623 Tyrosyl-tRNA synthetas 36.6 55 0.0012 32.5 4.6 40 68-107 396-435 (467)
114 PF14453 ThiS-like: ThiS-like 36.3 36 0.00077 24.4 2.5 23 97-120 31-53 (57)
115 PRK07696 sulfur carrier protei 33.3 44 0.00095 24.2 2.6 42 71-121 17-61 (67)
116 COG4043 Preprotein translocase 30.7 57 0.0012 26.2 3.0 37 86-122 8-44 (111)
117 COG3215 PilZ Tfp pilus assembl 29.9 92 0.002 25.1 4.0 78 91-177 28-105 (117)
118 PRK05449 aspartate alpha-decar 29.6 74 0.0016 26.5 3.6 24 95-122 66-89 (126)
119 PF03658 Ub-RnfH: RnfH family 28.9 23 0.0005 27.3 0.5 29 94-123 45-73 (84)
120 cd01666 TGS_DRG_C TGS_DRG_C: 27.4 44 0.00095 25.1 1.8 47 70-121 24-74 (75)
121 TIGR00223 panD L-aspartate-alp 26.9 89 0.0019 26.0 3.6 24 95-122 66-89 (126)
122 PF04225 OapA: Opacity-associa 26.6 99 0.0021 23.6 3.7 47 69-124 9-55 (85)
123 cd01668 TGS_RelA_SpoT TGS_RelA 26.3 86 0.0019 21.1 3.1 44 69-120 15-58 (60)
124 cd06919 Asp_decarbox Aspartate 25.0 94 0.002 25.3 3.4 24 95-122 65-88 (111)
125 cd01800 SF3a120_C Ubiquitin-li 24.7 58 0.0013 23.9 2.1 66 54-123 4-69 (76)
126 cd01616 TGS The TGS domain, na 24.3 1E+02 0.0022 20.0 3.1 22 98-120 37-58 (60)
127 PF02261 Asp_decarbox: Asparta 24.0 59 0.0013 26.6 2.1 23 95-121 66-88 (116)
128 TIGR01764 excise DNA binding d 23.7 70 0.0015 20.4 2.1 20 79-99 9-28 (49)
129 KOG2529 Pseudouridine synthase 23.4 85 0.0018 31.0 3.4 46 211-260 96-141 (395)
130 PF08068 DKCLD: DKCLD (NUC011) 22.3 39 0.00084 24.4 0.6 16 143-158 41-56 (59)
131 cd01796 DDI1_N DNA damage indu 20.7 94 0.002 22.5 2.5 62 56-120 8-69 (71)
132 KOG4837 Uncharacterized conser 20.1 82 0.0018 28.5 2.3 53 70-123 139-191 (248)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.5e-41 Score=313.35 Aligned_cols=194 Identities=47% Similarity=0.751 Sum_probs=172.3
Q ss_pred EEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeeccccC-CcccccCCCCeeE
Q 022299 61 EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQ-PLRAEAEDIPLDI 139 (299)
Q Consensus 61 ~~~v~~~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~~~~-~~~~~~~~~~~~I 139 (299)
+..|.....++|||+||++.++ +||+.+++++++|.|.|||+++. ++++|..||+|.+...+.. .....+++.+++|
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 4566778899999999999655 99999999999999999999995 9999999999999886544 2344566777999
Q ss_pred EEeCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCC
Q 022299 140 VYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLD 219 (299)
Q Consensus 140 lyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLD 219 (299)
||||+++||||||+||+|||+.++..+|+++++++++.. ...++++|||||
T Consensus 81 lyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~-----------------------------~~~~~~~vHRLD 131 (289)
T COG0564 81 LYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQD-----------------------------GVERPGIVHRLD 131 (289)
T ss_pred EEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhccc-----------------------------cCCceeeeccCC
Confidence 999999999999999999999999999999999988641 035788999999
Q ss_pred CCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCC
Q 022299 220 KGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPG 285 (299)
Q Consensus 220 r~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~~g~I~~pi~~~~~~~~~~~~~~~ 285 (299)
++||||||||||..++..|+++|+++.+.|+|+|+|.|.+..+.++|+.||+++..++.++.+...
T Consensus 132 kdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~~~~~v~~~ 197 (289)
T COG0564 132 KDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNRKKMAVVKE 197 (289)
T ss_pred CCCceEEEEECCHHHHHHHHHHHhcCcCcEEEEEEEECcccCCCCEEeeeeecCCcCCceEEEecc
Confidence 999999999999999999999999999999999999999999889999999999887777766544
No 2
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=6.9e-37 Score=290.24 Aligned_cols=195 Identities=41% Similarity=0.621 Sum_probs=166.1
Q ss_pred CCceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeeccccCCcccccCC
Q 022299 55 YAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAED 134 (299)
Q Consensus 55 ~~~~~~~~~v~~~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~~~~~~~~~~~~ 134 (299)
+.-|++...|+..++|+||++||+..++.+||+.++++|++|.|+|||+++.++++.|.+||.|.+......+....+..
T Consensus 2 ~~~~~~~~~v~~~~~g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~ 81 (325)
T PRK11180 2 AQQVQLTATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQD 81 (325)
T ss_pred CceEEEEEEECcccCCccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEeeccccccCCCCCC
Confidence 34588999999999999999999998888999999999999999999999877899999999999976543222233445
Q ss_pred CCeeEEEeCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccc
Q 022299 135 IPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (299)
Q Consensus 135 ~~~~IlyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~ 214 (299)
.+++|||||+++||+|||+||+|||..++...|+++.+..++.. .. ...++++
T Consensus 82 ~~~~iiyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~~~--~~-------------------------~~~~~~~ 134 (325)
T PRK11180 82 IPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPP--IA-------------------------DVPRAGI 134 (325)
T ss_pred CCCcEEEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHhhh--cc-------------------------CCcccce
Confidence 67899999999999999999999998877778999998876521 10 2245778
Q ss_pred cccCCCCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCC
Q 022299 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNR 277 (299)
Q Consensus 215 VhRLDr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~~g~I~~pi~~~~~~~ 277 (299)
|||||++||||||||||..++..|+++|..+.+.|+|+|+|.|.++ ++++|+.||.++...+
T Consensus 135 vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~Y~A~v~G~~~-~~~~i~~~l~~~~~~~ 196 (325)
T PRK11180 135 VHRLDKDTTGLMVVAKTVPAQTRLVEALQKREITREYEAVAIGHMT-AGGTVDEPISRHPTKR 196 (325)
T ss_pred eccCCCCCceeEEEECCHHHHHHHHHHHHhCCcceEEEEEEecCCC-CCCEEECceecCCCcC
Confidence 9999999999999999999999999999999999999999999986 5689999997654433
No 3
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=100.00 E-value=3.7e-36 Score=281.56 Aligned_cols=181 Identities=39% Similarity=0.697 Sum_probs=153.8
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeeccccCCcccccCCCCeeEEEeCCcE
Q 022299 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNV 146 (299)
Q Consensus 67 ~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~~~~~~~~~~~~~~~~IlyeD~~l 146 (299)
++.++||++||+..++.+||+.++++|++|.|+|||+.+..+++.|++||.|.+...+.......+...+++|+|||++|
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 56789999999998867999999999999999999976557899999999999866432222222344568999999999
Q ss_pred EEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceEE
Q 022299 147 LVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLL 226 (299)
Q Consensus 147 lvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGLl 226 (299)
+|+|||+|++||+.++....|+++.|..++.. .. ....+++|||||++|||||
T Consensus 82 lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~~~--~~-------------------------~~~~~~~vhRLD~~TSGll 134 (299)
T TIGR00005 82 IVINKPSGLVVHPGGGNPFGTVLNALLAHCPP--IA-------------------------GVERVGIVHRLDRDTSGLM 134 (299)
T ss_pred EEEECCCCCeEeCCCCCCcccHHHHHHHhccc--cc-------------------------CCCcCceECCCCCCCceEE
Confidence 99999999999998887778999998876531 00 1245789999999999999
Q ss_pred EEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCC
Q 022299 227 VVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDP 274 (299)
Q Consensus 227 L~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~~g~I~~pi~~~~ 274 (299)
|||+|..+++.|+++|.++.+.|+|+|+|.|.++.+.++|+.||.++.
T Consensus 135 l~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~g~~~~~~~~i~~~l~~~~ 182 (299)
T TIGR00005 135 VVAKTPLALRELQRQLKNRTVTKEYVALVHGQFDSGGGTVDAPLGRVP 182 (299)
T ss_pred EEEcCHHHHHHHHHHHHhCCcceEEEEEEeccccCCCCEEeCceecCC
Confidence 999999999999999999999999999999999888899999997654
No 4
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=4.3e-35 Score=277.12 Aligned_cols=183 Identities=25% Similarity=0.416 Sum_probs=151.5
Q ss_pred EEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeeccccCCcccc--------c
Q 022299 61 EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAE--------A 132 (299)
Q Consensus 61 ~~~v~~~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~~~~~~~~~--------~ 132 (299)
..+|+..++|+||++||+..++.+||+.++++|++|.|+|||+++ ++++.|+.||+|.+........... .
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 457788889999999999888889999999999999999999998 6899999999999864221110000 1
Q ss_pred CCCCeeEEEeCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCc
Q 022299 133 EDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRP 212 (299)
Q Consensus 133 ~~~~~~IlyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~ 212 (299)
...+++|||||++++|||||+|++||+..+.. .++++.+..+.. ....+
T Consensus 89 ~~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~-~~~~~~~~~~~~------------------------------~~~~~ 137 (317)
T PRK11025 89 AALADVILYEDDHILVLNKPSGTAVHGGSGLS-FGVIEGLRALRP------------------------------EARFL 137 (317)
T ss_pred ccCcCCEEEECCCEEEEECCCCCcCcCCCCCC-ccHHHHHHHhcc------------------------------CCCcC
Confidence 12467999999999999999999999977654 356666654311 11235
Q ss_pred cccccCCCCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCC
Q 022299 213 GIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPN 275 (299)
Q Consensus 213 ~~VhRLDr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~~g~I~~pi~~~~~ 275 (299)
++|||||++||||||||||..+++.|+++|+.+.++|+|+|+|.|.+....|+|+.||.++..
T Consensus 138 ~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~v~K~Y~a~v~G~~~~~~~~i~~~i~~~~~ 200 (317)
T PRK11025 138 ELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKVVQAPLLKNIL 200 (317)
T ss_pred ceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCCccEEEEEEEeCcccCCCceEecccccCcc
Confidence 789999999999999999999999999999999999999999999998888999999987753
No 5
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.96 E-value=2.5e-28 Score=228.18 Aligned_cols=178 Identities=23% Similarity=0.339 Sum_probs=136.1
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeeccccCCcccccCCCCeeEEEeCCcEE
Q 022299 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVL 147 (299)
Q Consensus 68 ~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~~~~~~~~~~~~~~~~IlyeD~~ll 147 (299)
.+++||++||++. +.+||+.++++|++|+|+|||+++ .+++.|.+||.|.+......+ . .+||++||
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-TIGDQVKAGDVVKVNGQLIEP-----R------EAEDLVLI 70 (290)
T ss_pred chHHHHHHHHHhC-CCCCHHHHHHHHHCCcEEECCEEc-cCCCCcCCCCEEEECCEEccc-----c------ccCCCeEE
Confidence 4568999999987 578999999999999999999998 689999999999987532111 0 13788999
Q ss_pred EEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceEEE
Q 022299 148 VVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLV 227 (299)
Q Consensus 148 vvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGLlL 227 (299)
|+|||+|++||+.+. ...|+++.|.++ .++++|||||++||||||
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 999999999997765 457888877431 246789999999999999
Q ss_pred EEcCHHHHHHHHHHHhcCccceEEEEEEecccCCC------Cc-----EEEcc--ceeCCCCCeeEEEcCCCCCccccch
Q 022299 228 VAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQS------SG-----RIEVP--ISRDPNNRIRMAAIPGSNKHGQARH 294 (299)
Q Consensus 228 ~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~------~g-----~I~~p--i~~~~~~~~~~~~~~~~~~~~~~r~ 294 (299)
||+|..++..|.. ..+.++|+|+|+|.|.+.++ .| ....| +.......+++++.+|. .+|+|+
T Consensus 116 lT~dg~~~~~L~~--p~~~i~K~Y~v~V~g~~~~~~l~~l~~Gv~l~~~~~~~~~v~~~~~~~~~i~l~eGk--~rqIRr 191 (290)
T PRK10475 116 LTNHGDLVNKILR--AGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRITLVQGL--NRQIRR 191 (290)
T ss_pred EecCHHHHHHhhC--cCCCCCeEEEEEECCCCCHHHHHHHhCCcEECCEEecceEEEecCCcEEEEEEECCc--CHHHHH
Confidence 9999998888855 45679999999999998542 12 12222 12211233567777664 788888
Q ss_pred hhh
Q 022299 295 AAS 297 (299)
Q Consensus 295 ~~~ 297 (299)
|+.
T Consensus 192 m~~ 194 (290)
T PRK10475 192 MCE 194 (290)
T ss_pred HHH
Confidence 775
No 6
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.
Probab=99.96 E-value=4.2e-28 Score=221.99 Aligned_cols=142 Identities=20% Similarity=0.280 Sum_probs=115.8
Q ss_pred cEEECCEEeccccccccCCCEEeeeccccCCcccccCCCCeeEEEeCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhc
Q 022299 97 LVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHC 176 (299)
Q Consensus 97 ~V~vNGk~v~~~~~~l~~GD~I~v~~~~~~~~~~~~~~~~~~IlyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~ 176 (299)
.|..||+++ ++++.|++||.|.+........ +...+++|||||++++|||||+|++||+.+++...|+++.+..++
T Consensus 3 ~~~~ng~~~-~~~~~l~~gd~i~~~~~~~~~~---~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~ 78 (246)
T cd02558 3 VVDADGEPL-DPDSPYRPGTFVWYYRELPDEP---PIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQT 78 (246)
T ss_pred eECCCCcCC-CCCceecCCCEEEEeCCCCCCC---CCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHh
Confidence 344899999 6899999999999875322111 223458999999999999999999999998887788888876543
Q ss_pred CCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 177 SLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 177 ~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
. ...+++|||||++||||||||||..++..++.+|+.+.++|+|+|+|.
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 124578999999999999999999999999999999999999999999
Q ss_pred cccCCCCc-EEEccceeC
Q 022299 257 GVPSQSSG-RIEVPISRD 273 (299)
Q Consensus 257 G~~~~~~g-~I~~pi~~~ 273 (299)
|.+..+.+ .++.+|.++
T Consensus 128 G~~~~~~~~~~~~~i~~~ 145 (246)
T cd02558 128 YVPALTFPLTVRSRIVKG 145 (246)
T ss_pred cCCCCCCCcceecccccc
Confidence 99865444 567676543
No 7
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=99.95 E-value=4.7e-28 Score=219.49 Aligned_cols=142 Identities=21% Similarity=0.324 Sum_probs=113.2
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeeccccCCcccccCCCCeeEEEeCCcEEEEe
Q 022299 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVN 150 (299)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~~~~~~~~~~~~~~~~IlyeD~~llvvn 150 (299)
+||++||++.+ .+||+.++++|++|.|+|||+++.++++.|++||.|.+......+ .+++++||+|
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 48999999887 699999999999999999999986689999999999886421110 1356899999
Q ss_pred CCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceEEEEEc
Q 022299 151 KPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAK 230 (299)
Q Consensus 151 KPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGLlL~Ak 230 (299)
||+||+||+..+. ..|+.+.+... ...++++|||||++|||||||||
T Consensus 67 KP~G~~~~~~~~~-~~tl~~~l~~~--------------------------------~~~~~~~v~RLD~~TSGlll~ak 113 (232)
T PRK10839 67 KPQGYVCSTDDPD-HPTVLYFLDEP--------------------------------VAYKLHAAGRLDIDTTGLVLMTD 113 (232)
T ss_pred CCCCeEecccCCC-CCeEEEecccc--------------------------------cccCceecCCCCCCceeEEEEec
Confidence 9999999987543 34554322110 11356789999999999999999
Q ss_pred CHHHHHHHHHHHhcCccceEEEEEEecccCC
Q 022299 231 DEHSHAHLSEQFKLHTIERVYISLTSGVPSQ 261 (299)
Q Consensus 231 ~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~ 261 (299)
|..++..|.. ..+.++|+|+|++.+.+..
T Consensus 114 ~~~~~~~l~~--~~~~i~K~Y~a~i~~~i~~ 142 (232)
T PRK10839 114 DGQWSHRITS--PRHHCEKTYLVTLESPVAD 142 (232)
T ss_pred CHHHHHHHhC--CCCCCCeEEEEEECCCCCH
Confidence 9998888875 5778999999999998753
No 8
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=99.95 E-value=1.4e-26 Score=216.59 Aligned_cols=146 Identities=21% Similarity=0.190 Sum_probs=118.1
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCC--CEEeeeccccCCcccccCCCCeeEEE-eCCcE
Q 022299 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGG--DMVNCTISELQPLRAEAEDIPLDIVY-EDDNV 146 (299)
Q Consensus 70 g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~G--D~I~v~~~~~~~~~~~~~~~~~~Ily-eD~~l 146 (299)
.+||++||++. +.+||+.++++|++|+|+|||+++ .+++.|.++ |.|.+........ ..+ ||+.|
T Consensus 2 ~~RL~k~La~~-g~~SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g~~~~~~----------~~~~e~~~y 69 (289)
T PRK10700 2 SEKLQKVLARA-GHGSRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRIDGHLISVK----------ESAEQICRV 69 (289)
T ss_pred chhHHHHHHHC-CCCCHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEECCEEeecc----------cccccCCeE
Confidence 37999999986 679999999999999999999988 689999887 5566643211100 011 56789
Q ss_pred EEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceEE
Q 022299 147 LVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLL 226 (299)
Q Consensus 147 lvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGLl 226 (299)
+++|||+|++|++.+.....|+++.|.... ..++++|||||++|||||
T Consensus 70 lvlnKP~G~~~s~~d~~~~~tv~d~l~~~~--------------------------------~~~~~~VgRLD~dTsGLL 117 (289)
T PRK10700 70 LAYYKPEGELCTRNDPEGRPTVFDRLPKLR--------------------------------GARWIAVGRLDVNTCGLL 117 (289)
T ss_pred EEEECCCCCEeecCCCCCCccHHHHhhhhc--------------------------------CCceeEccCCCCCCceEE
Confidence 999999999999987766779998875421 124678999999999999
Q ss_pred EEEcCHHHHHHHHHHHhcCccceEEEEEEecccCC
Q 022299 227 VVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQ 261 (299)
Q Consensus 227 L~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~ 261 (299)
|||+|..++..|.. ..+.++|+|+|+|.|.+.+
T Consensus 118 LlTndg~~~~~L~~--p~~~i~K~Y~v~V~G~~~~ 150 (289)
T PRK10700 118 LFTTDGELANRLMH--PSREVEREYAVRVFGQVDD 150 (289)
T ss_pred EEEcCHHHHHHHhC--ccCCCCeEEEEEEccCCCH
Confidence 99999999999965 6788999999999998753
No 9
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=99.93 E-value=9e-25 Score=209.15 Aligned_cols=192 Identities=29% Similarity=0.383 Sum_probs=160.5
Q ss_pred EEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeeccccCCcccccCCCCee
Q 022299 59 QLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLD 138 (299)
Q Consensus 59 ~~~~~v~~~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~~~~~~~~~~~~~~~~ 138 (299)
.+...+...|.+..+.+++...|...++...+..|+.|.|.+||..+ ..+..++.||.|.......+++.. ..++.
T Consensus 32 ~~~~~~~~rw~~k~~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~-~v~~i~k~~d~l~~~vhrh~p~~~---~~~~~ 107 (371)
T KOG1919|consen 32 TYRTFVKGRWAGKKLVDVFVSEFRLRERAYYESAIKLGRVTVNGEQV-RVSLIVKNGDVLCHTVHRHEPPVA---YLPIR 107 (371)
T ss_pred eeeEEEeeeecccchHHHHHHHHhcCchHhhhhhhhcCceEECcEee-eeEEEeccCCEEEEeeccCCCCcc---ccccc
Confidence 33446678888888999999999889999999999999999999999 589999999999988776666543 36789
Q ss_pred EEEeCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccC
Q 022299 139 IVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRL 218 (299)
Q Consensus 139 IlyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRL 218 (299)
|+|||++|+|||||+|++|||.+....+++...+.... ....+++||||
T Consensus 108 Iv~ed~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~~-------------------------------~~~~~~~~hRL 156 (371)
T KOG1919|consen 108 IVFEDKDYVVVNKPHGIPVHPTGRYRENTITKILAALH-------------------------------KVEGLRPCHRL 156 (371)
T ss_pred eEEecCCEEEEeCCCCCceeccCccccccchHHHHHhc-------------------------------ccccccccccc
Confidence 99999999999999999999988887788877776531 22456789999
Q ss_pred CCCCceEEEEEcCHHHHHHHHHHHhcCccceEE-EEEEecccC-CCCcEEEccceeCCCCCeeEEEcCCC
Q 022299 219 DKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVY-ISLTSGVPS-QSSGRIEVPISRDPNNRIRMAAIPGS 286 (299)
Q Consensus 219 Dr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~Y-lAlV~G~~~-~~~g~I~~pi~~~~~~~~~~~~~~~~ 286 (299)
|+.|||||+||++++++..++.+|+++++.|.| +|.|.|.++ .+..+|..|+..... ..+|.+....
T Consensus 157 Dr~tSGllvlAkt~~~~~~~~~~~r~~~~~k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~-~~~~~l~~~~ 225 (371)
T KOG1919|consen 157 DRLTSGLLVLAKTKEAADKFHEVLRKRTVKKEYVVARVEGPFPVVGEVEIKEPIGEEER-PLRMGLNAVG 225 (371)
T ss_pred CccccceEEEEechhHhHHHHHHHhcccceeEEEEEEEeccCCCCceEEeCCCcccccc-ccceEeeecc
Confidence 999999999999999999999999999999999 799999987 566677778776543 3455555444
No 10
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=99.93 E-value=4e-25 Score=199.00 Aligned_cols=106 Identities=30% Similarity=0.494 Sum_probs=91.8
Q ss_pred CeeEEEeCCcEEEEeCCCCceeecCCC-CCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccc
Q 022299 136 PLDIVYEDDNVLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (299)
Q Consensus 136 ~~~IlyeD~~llvvnKPaGl~v~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~ 214 (299)
+++|||||++++|+|||+|++||+... ....++.+.+..++ ..+++
T Consensus 13 ~~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~---------------------------------~~~~~ 59 (219)
T PRK10158 13 WLVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY---------------------------------PQAES 59 (219)
T ss_pred CCCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC---------------------------------CCCCE
Confidence 478999999999999999999998753 33456777665432 13568
Q ss_pred cccCCCCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCC
Q 022299 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDP 274 (299)
Q Consensus 215 VhRLDr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~~g~I~~pi~~~~ 274 (299)
|||||++||||||||||..+++.|+++|+++.+.|+|+|+|.|.+..+.++|+.||.++.
T Consensus 60 vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~~v~K~Yla~v~G~~~~~~~~i~~~i~~~~ 119 (219)
T PRK10158 60 VHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDW 119 (219)
T ss_pred ECCCCCCCceEEEEECCHHHHHHHHHHHHhCCccEEEEEEEecccCCCCcEEecceecCC
Confidence 999999999999999999999999999999999999999999999888999999997654
No 11
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.
Probab=99.92 E-value=6.8e-25 Score=196.70 Aligned_cols=109 Identities=29% Similarity=0.438 Sum_probs=95.8
Q ss_pred CCCeeEEEeCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCcc
Q 022299 134 DIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPG 213 (299)
Q Consensus 134 ~~~~~IlyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~ 213 (299)
..+++|||||+++||+|||+|++|++.+.....++.+.|..++. ...++
T Consensus 13 ~~~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~-------------------------------~~~~~ 61 (213)
T cd02557 13 NDPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYG-------------------------------LTELR 61 (213)
T ss_pred CCCCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcC-------------------------------CCCcc
Confidence 34679999999999999999999998876666788888876432 12467
Q ss_pred ccccCCCCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeC
Q 022299 214 IVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRD 273 (299)
Q Consensus 214 ~VhRLDr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~~g~I~~pi~~~ 273 (299)
+|||||++||||||||||.++++.|+.+|+++.++|+|+|+|.|.+..+.++|+.||.++
T Consensus 62 ~vhRLD~~TSGllllak~~~~~~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~ 121 (213)
T cd02557 62 PCHRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKEYLARVKGEFPDGEVVVDQPIGLV 121 (213)
T ss_pred CccCCCCCCceEEEEECCHHHHHHHHHHHHcCCccEEEEEEEeCcCCCCCeEEecceecc
Confidence 899999999999999999999999999999999999999999999988889999998654
No 12
>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=99.92 E-value=1.6e-24 Score=194.86 Aligned_cols=106 Identities=29% Similarity=0.477 Sum_probs=90.7
Q ss_pred eeEEEeCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccc
Q 022299 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVH 216 (299)
Q Consensus 137 ~~IlyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~Vh 216 (299)
++|||||++++|||||+||+||+..+. .++.+.+..+. ....+++||
T Consensus 2 ~~ilyed~~~lvvnKP~Gl~v~~~~~~--~~l~~~l~~~~-------------------------------~~~~~~~Vh 48 (217)
T TIGR01621 2 FEILFTHPDFLLINKHPGISVHKDDGE--TGLLQEVATQL-------------------------------GVGQVWLVH 48 (217)
T ss_pred ceEEEeCCCEEEEECCCCCeECCCCCc--ChHHHHHHHhc-------------------------------CCCCccEec
Confidence 479999999999999999999987542 46666665432 113567899
Q ss_pred cCCCCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCC
Q 022299 217 RLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPN 275 (299)
Q Consensus 217 RLDr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~~g~I~~pi~~~~~ 275 (299)
|||++||||||||||..+++.|+++|+++.++|+|+|+|.|.+..++++|+.++.+...
T Consensus 49 RLDr~TSGlll~Ak~~~~~~~L~~~~~~~~v~K~YlAlV~g~~~~~~~~i~~~~~~~~~ 107 (217)
T TIGR01621 49 RLDKMTSGILLLALNAESASELSQGFAKRKIEKTYLALSSKKPKKKQGLICGDMEKSRR 107 (217)
T ss_pred CCCCCCceEEEEEcCHHHHHHHHHHHhcCCccEEEEEEEeccccCCCCEEeCCcccCCC
Confidence 99999999999999999999999999999999999999999998889999999975543
No 13
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=3.9e-24 Score=195.00 Aligned_cols=178 Identities=25% Similarity=0.373 Sum_probs=133.5
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCC-CEEeeeccccCCcccccCCCCeeEEE-eCCcEE
Q 022299 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGG-DMVNCTISELQPLRAEAEDIPLDIVY-EDDNVL 147 (299)
Q Consensus 70 g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~G-D~I~v~~~~~~~~~~~~~~~~~~Ily-eD~~ll 147 (299)
.+||++||++. +.+||++++++|.+|+|+|||++++.....+.++ |.|.+... .+.+ +...|+
T Consensus 2 ~~RL~K~La~~-G~~SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~--------------~~~~~~~~~y~ 66 (248)
T COG1187 2 SMRLNKFLAEA-GVGSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGK--------------RIELKEERVYL 66 (248)
T ss_pred ccchHHHHHHc-CCCCHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCE--------------EeeccccceEE
Confidence 58999999997 7899999999999999999999998888899998 57777553 1233 234499
Q ss_pred EEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceEEE
Q 022299 148 VVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLV 227 (299)
Q Consensus 148 vvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGLlL 227 (299)
++|||.|++|+..++..+.|+.+.|.... + ...++++|+|||+||+||||
T Consensus 67 llnKP~G~v~s~~D~~gr~tv~D~lp~~~--~----------------------------~~~~~~pvGRLD~dTeGLLL 116 (248)
T COG1187 67 LLNKPRGYVSSTEDDEGRPTVFDLLPERL--P----------------------------RKKRLFPVGRLDKDTEGLLL 116 (248)
T ss_pred EEECCCCeEecccCCCCCceeeeeccccc--c----------------------------cccceeeccccCCCCeeEEE
Confidence 99999999999887777778877665320 1 22468899999999999999
Q ss_pred EEcCHHHHHHH-HHHHhcCccceEEEEEEecccCCC------Cc-EEE----cc---c--eeCC---CCCeeEEEcCCCC
Q 022299 228 VAKDEHSHAHL-SEQFKLHTIERVYISLTSGVPSQS------SG-RIE----VP---I--SRDP---NNRIRMAAIPGSN 287 (299)
Q Consensus 228 ~Ak~~~a~~~l-~~~f~~~~v~K~YlAlV~G~~~~~------~g-~I~----~p---i--~~~~---~~~~~~~~~~~~~ 287 (299)
||.|...+..| ++ .+.++|+|+|.|.|.+.++ .| .++ .| . .... ...++++..+|.
T Consensus 117 LTnDG~la~rL~~P---~~~~~K~Y~v~v~g~~~~~~l~~l~~Gv~l~d~~~~~~~~~~l~~~~~~~~s~~~itl~EGr- 192 (248)
T COG1187 117 LTNDGELAHRLMHP---SSEVEKEYLVRVEGPVTEEDLEKLRKGVTLDDGETKPAKPASLEKEPGKNNSWLRITLTEGR- 192 (248)
T ss_pred EeCCHHHHHHhcCC---CCCCCEEEEEEEecCCCHHHHHHHhCCcEecCcccccceeEEEEecCCCCceEEEEEEeCCc-
Confidence 99996555544 44 5779999999999988642 11 222 12 1 1221 224677777664
Q ss_pred Cccccchhhh
Q 022299 288 KHGQARHAAS 297 (299)
Q Consensus 288 ~~~~~r~~~~ 297 (299)
.+|+|+|+.
T Consensus 193 -nrQVRRm~~ 201 (248)
T COG1187 193 -NRQVRRMFE 201 (248)
T ss_pred -CHHHHHHHH
Confidence 889998875
No 14
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.
Probab=99.91 E-value=4.9e-24 Score=192.28 Aligned_cols=106 Identities=30% Similarity=0.548 Sum_probs=87.0
Q ss_pred eeEEEeCCcEEEEeCCCCceeecCCCCCCCc--HHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccc
Q 022299 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGT--LVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (299)
Q Consensus 137 ~~IlyeD~~llvvnKPaGl~v~~~~~~~~~t--l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~ 214 (299)
++|||||+++||||||+|++||+.++....+ ++..+..++ ...+++
T Consensus 1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~ 48 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQL--------------------------------GQHVYP 48 (223)
T ss_pred CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHc--------------------------------CCCccc
Confidence 3699999999999999999999876443332 222232211 124678
Q ss_pred cccCCCCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCC
Q 022299 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPN 275 (299)
Q Consensus 215 VhRLDr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~~g~I~~pi~~~~~ 275 (299)
|||||++||||||||||+.+++.|+.+|+++.++|+|+|+|.|.+.. +++|+.||.++..
T Consensus 49 vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~v~K~Y~alv~G~~~~-~~~i~~~l~~~~~ 108 (223)
T cd02563 49 VHRLDRPTSGVLLFALSSEVARKLGEQFTEHRVHKTYLAVVRGYVPE-SGTIDYPLSEELD 108 (223)
T ss_pred ccCCCCCCeEEEEEEECHHHHHHHHHHHhcCceeEEEEEEEECccCC-CCeEEEeeeeCCC
Confidence 99999999999999999999999999999999999999999999865 7899999977654
No 15
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=99.91 E-value=1.1e-23 Score=194.06 Aligned_cols=104 Identities=28% Similarity=0.461 Sum_probs=85.4
Q ss_pred eeEEEeCCcEEEEeCCCCceeecCCCCCCCcH--HHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccc
Q 022299 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTL--VNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (299)
Q Consensus 137 ~~IlyeD~~llvvnKPaGl~v~~~~~~~~~tl--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~ 214 (299)
++|||||+++||||||+||+||+.......+. ...+..++ ...+++
T Consensus 2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~ 49 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQI--------------------------------GQHVFT 49 (257)
T ss_pred CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHh--------------------------------CCCcee
Confidence 47999999999999999999998754433332 23332211 124668
Q ss_pred cccCCCCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeC
Q 022299 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRD 273 (299)
Q Consensus 215 VhRLDr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~~g~I~~pi~~~ 273 (299)
|||||++||||||||||..+++.|+.+|+++.|.|+|+|+|.|.+. ++++|+.||.++
T Consensus 50 VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~Alv~G~~~-~~~~i~~~l~~~ 107 (257)
T PRK11112 50 AHRLDRPTSGVLLMALSSEVARLLAQQFEQHQIQKTYHAIVRGWLM-EEAVLDYPLKEE 107 (257)
T ss_pred eccCCCCCeeEEEEECCHHHHHHHHHHHHhCCcceEEEEEEEeEeC-CCCeEeeeeeec
Confidence 9999999999999999999999999999999999999999999985 568899998764
No 16
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family. This Prosite family is a subset of the Pfam family.; InterPro: IPR006145 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit). RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [, ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site. RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: RluB modifies uracil-2605. RluC modifies uracil-955, U-2504, and U-2580. RluD modifies uracil-1911, U-1915, and U-1917. RluE modifies uracil-3457. RluF modifies uracil-2604, and to a lesser extent U-2605. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [, ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 2GML_A 3DH3_B 1VIO_A 2I82_B 1XPI_B 1V9K_B 1PRZ_A 1V9F_A 2IST_A 1QYU_A ....
Probab=99.84 E-value=6.2e-21 Score=162.64 Aligned_cols=101 Identities=38% Similarity=0.588 Sum_probs=77.0
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 022299 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (299)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (299)
+|||||||+||+|++.++................ ......+++|||||++|||
T Consensus 1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~~v~RLD~~TsG 53 (164)
T PF00849_consen 1 NLIVVNKPAGVPVHPSDGNESKSVKELPALSLKR---------------------------GDDPPELYPVHRLDRDTSG 53 (164)
T ss_dssp SEEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHHH---------------------------CTTSGGGEESS---TT-EE
T ss_pred CEEEEECCCCCeEecCCCCCcccccchhhhhhhh---------------------------ccCCCceEECCCCCccccC
Confidence 5899999999999998854433333332222110 0134678999999999999
Q ss_pred EEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEcccee
Q 022299 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISR 272 (299)
Q Consensus 225 LlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~~g~I~~pi~~ 272 (299)
|||||+|.++++.|+.+|..+.++|+|+|+|.|.+..+.+.|+.+|..
T Consensus 54 lll~a~~~~~~~~l~~~f~~~~~~K~Y~a~v~~~~~~~~~~~~~~~~~ 101 (164)
T PF00849_consen 54 LLLFAKDKEAAAKLSKQFPKRKVEKTYLALVEGGPVEEEGKINSPLGK 101 (164)
T ss_dssp EEEEESSHHHHHHHHHHHHTTCSEEEEEEEECSSSSTTCEEEESHEEE
T ss_pred CeeccCCcccccccccccccCCCcEEEEEeEcccccccceeeeccccc
Confidence 999999999999999999999999999999998877889999999977
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=99.83 E-value=3.2e-20 Score=158.14 Aligned_cols=90 Identities=31% Similarity=0.455 Sum_probs=74.2
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceE
Q 022299 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (299)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (299)
|+|+|||+|++||+.++....++.+.+... ...++++|||||++||||
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~--------------------------------~~~~~~~vhRLD~~TSGl 48 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKL--------------------------------HGPRVHAAGRLDKDTSGL 48 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhhcc--------------------------------cCCceeEeccCCCCCeeE
Confidence 589999999999998877667777755321 123577899999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccc
Q 022299 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPI 270 (299)
Q Consensus 226 lL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~~g~I~~pi 270 (299)
||||+|.++++.|+.+ ++.++|+|+|+|.|.+++ ++.+..|+
T Consensus 49 ll~ak~~~~~~~l~~~--~~~v~K~Y~a~v~g~~~~-~~~~~~~~ 90 (154)
T cd02550 49 LLLTNDGRLQRRLTEP--RREIEKEYLVTVRGELDE-EGIEDLAT 90 (154)
T ss_pred EEEEcCHHHHHHHhhh--hccCcEEEEEEEEeecCc-chheeccc
Confidence 9999999999999998 788999999999999864 45555553
No 18
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=99.80 E-value=4e-19 Score=154.14 Aligned_cols=100 Identities=52% Similarity=0.887 Sum_probs=83.8
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceE
Q 022299 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (299)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (299)
++|+|||+|++|++.......++.+.+..+.... .....+++|||||++||||
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~v~RLD~~tsGl 53 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLL---------------------------GEEFRPGLVHRLDKDTSGL 53 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhc---------------------------CCCCcCceecccCCCCceE
Confidence 5899999999999988777778877653322100 0234678999999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEcccee
Q 022299 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISR 272 (299)
Q Consensus 226 lL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~~g~I~~pi~~ 272 (299)
||||++.++++.|..+|+++.+.|+|+|+|.|.+....+.++.|+..
T Consensus 54 ll~ak~~~~~~~l~~~~~~~~~~K~Y~a~v~g~~~~~~~~~~~~~~~ 100 (185)
T cd02869 54 LLVAKNKKAAAKLSKQFKERKVKKTYLALVDGKPPEDEGTIDAPLGR 100 (185)
T ss_pred EEEEcCHHHHHHHHHHHhcCceeEEEEEEEeCCCCCCccEEeccccc
Confidence 99999999999999999999999999999999998888888877753
No 19
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.
Probab=99.79 E-value=7.1e-19 Score=152.14 Aligned_cols=82 Identities=26% Similarity=0.261 Sum_probs=69.7
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 022299 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (299)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (299)
.++|+|||+|++||+.+.....|+.+.+..+. ..++++|||||++|||
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 37999999999999876666678888776531 1356789999999999
Q ss_pred EEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccC
Q 022299 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPS 260 (299)
Q Consensus 225 LlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~ 260 (299)
|||||+|..++..|.. .++.++|+|+|+|.|.++
T Consensus 49 Lll~ak~~~~~~~L~~--~~~~i~K~Y~a~V~g~~~ 82 (167)
T cd02556 49 LLLFTNDGELANRLMH--PSNEIEREYAVRVFGQVT 82 (167)
T ss_pred EEEEECCHHHHHHHhC--CcCCCCeEEEEEECccCC
Confidence 9999999999999965 678899999999999875
No 20
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.
Probab=99.78 E-value=4.6e-19 Score=149.84 Aligned_cols=81 Identities=28% Similarity=0.374 Sum_probs=66.1
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceE
Q 022299 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (299)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (299)
|+|+|||+|++||+.++....++.+.+.. ...++++|||||++||||
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~---------------------------------~~~~~~~vhRLD~~TsGl 47 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKD---------------------------------VGERLFPVGRLDYDTEGL 47 (146)
T ss_pred CEEEECCCCcEecccCCCCCCEEeeeccc---------------------------------cCCCEEECCCCCCCCeeE
Confidence 58999999999998776555666543321 123568999999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCC
Q 022299 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQ 261 (299)
Q Consensus 226 lL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~ 261 (299)
||||+|..++..|.. .++.++|+|+|+|.|.+..
T Consensus 48 ll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~ 81 (146)
T cd02870 48 LLLTNDGELANRLTH--PRYGVEKTYLVKVRGVPSE 81 (146)
T ss_pred EEEeCCHHHHHHhhC--ccCCCCeEEEEEECCCCCH
Confidence 999999999999976 4678999999999998853
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=99.77 E-value=1e-18 Score=151.19 Aligned_cols=83 Identities=24% Similarity=0.290 Sum_probs=67.8
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceE
Q 022299 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (299)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (299)
|+|+|||+|++||+.+ ....|+.+.+..++. ..++++|||||++||||
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 456788888765431 13567899999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCC
Q 022299 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQS 262 (299)
Q Consensus 226 lL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~ 262 (299)
||||+|..++..+.. +.+.++|+|+|+|.|.+..+
T Consensus 50 ll~ak~~~~~~~l~~--~~~~i~K~Y~a~V~G~~~~~ 84 (167)
T cd02553 50 LLLTNDGQLAHRLTS--PKKHVPKTYEVTLAGPLTED 84 (167)
T ss_pred EEEEeCHHHHHHhhC--CcCCCceEEEEEEccCCCHH
Confidence 999999987777765 46789999999999998643
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=99.73 E-value=9.8e-18 Score=145.14 Aligned_cols=79 Identities=22% Similarity=0.331 Sum_probs=63.2
Q ss_pred EEEEeCCCCceeecCCC-CCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 022299 146 VLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (299)
Q Consensus 146 llvvnKPaGl~v~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (299)
++|+|||+|++||+.++ ....++.+.+.. .++++|||||++|||
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 344566664420 245689999999999
Q ss_pred EEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCC
Q 022299 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQ 261 (299)
Q Consensus 225 LlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~ 261 (299)
|||||+|..+++.|... .+.++|+|+|+|.|.+..
T Consensus 46 lll~a~d~~~~~~l~~~--~~~v~K~Y~a~v~g~~~~ 80 (168)
T cd02566 46 LLLLTDDGRLQHRITDP--SFKHPKTYYVQVEGVPTE 80 (168)
T ss_pred EEEEEeCHHHHHHHHCC--CCCCCEEEEEEECCcCCH
Confidence 99999999887777664 456999999999999854
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=99.67 E-value=1.6e-16 Score=138.83 Aligned_cols=50 Identities=28% Similarity=0.372 Sum_probs=45.2
Q ss_pred CccccccCCCCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCC
Q 022299 211 RPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQS 262 (299)
Q Consensus 211 ~~~~VhRLDr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~ 262 (299)
++++|||||++||||||||+|..+++.|... .+.++|+|+|+|.|.+.++
T Consensus 46 ~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~~--~~~i~K~Y~v~v~g~~~~~ 95 (177)
T cd02555 46 RLAPIGPLDKDASGLLVFSQDGRVLRKLIGD--ASRLEQEYLVEVRGELTAG 95 (177)
T ss_pred ceeEecCCCCCCeeEEEEECCHHHHHHHhCh--hcCCCEEEEEEEcccCCHH
Confidence 6779999999999999999999999999885 4789999999999998643
No 24
>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=99.66 E-value=4.4e-16 Score=134.57 Aligned_cols=113 Identities=18% Similarity=0.270 Sum_probs=80.6
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceE
Q 022299 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (299)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (299)
|+++|||+|++|++.+. ...|+.+.+.. ..++++|||||++||||
T Consensus 2 y~~lnKP~G~l~s~~~~-~~~tv~~~l~~----------------------------------~~~~~~vgRLD~~tsGl 46 (164)
T cd02554 2 YIAYNKPVGIDCTLERA-DEDNIIDFVNP----------------------------------PPRIFPIGRLDKDSEGL 46 (164)
T ss_pred EEEEECCCCcEeecCCC-CCCcHHHHhcC----------------------------------cCCEEEccCCCCCCeeE
Confidence 78999999999998754 34677766531 13578999999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCCC------Cc-----EEEccc--eeCCCCCeeEEEcCCCCCcccc
Q 022299 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQS------SG-----RIEVPI--SRDPNNRIRMAAIPGSNKHGQA 292 (299)
Q Consensus 226 lL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~~------~g-----~I~~pi--~~~~~~~~~~~~~~~~~~~~~~ 292 (299)
||||+|..++..|.. ..+.++|+|+|.|.|.+.++ .| ....|. .......+++...+| ..+|+
T Consensus 47 ll~t~dg~~~~~L~~--p~~~~~K~Y~V~v~~~l~~~~l~~l~~G~~~~~~~~~~~~v~~~~~~~l~i~l~eG--r~~qI 122 (164)
T cd02554 47 ILLTNDGDLVNKILH--ADNNHEKEYLVTVNKPITDEFIEGMSNGVVILGTVTKPCKVERLAKDKFRIVLTQG--LNRQI 122 (164)
T ss_pred EEEEcCHHHHHHHhh--hhcCCCeEEEEEECCCCCHHHHHHHhCCCEECCeEEcceEEEECCCCEEEEEEECC--cCHHH
Confidence 999999999999955 45678999999999988642 11 112222 221122356666665 37777
Q ss_pred chhhh
Q 022299 293 RHAAS 297 (299)
Q Consensus 293 r~~~~ 297 (299)
|+|++
T Consensus 123 Rrm~~ 127 (164)
T cd02554 123 RRMCE 127 (164)
T ss_pred HHHHH
Confidence 76654
No 25
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.63 E-value=5.4e-16 Score=139.46 Aligned_cols=81 Identities=25% Similarity=0.347 Sum_probs=68.2
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
..|+++|||+|++|+..+.....++.+.+. ..++++|||||++||
T Consensus 39 ~~ylllnKP~G~l~~~~d~~~~~tl~d~l~-----------------------------------~~~~~~vgRLD~~Ts 83 (217)
T PRK11394 39 TRVILFNKPYDVLPQFTDEAGRKTLKEFIP-----------------------------------VQGVYAAGRLDRDSE 83 (217)
T ss_pred CEEEEEECCCCCEEeeCCccCCcchHHhcc-----------------------------------cCCeEEecCCCCCCe
Confidence 469999999999999766555667766542 125678999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccCC
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQ 261 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~~ 261 (299)
||||||+|..++..|... ++.+.|+|+|+|.|.+..
T Consensus 84 GllLlt~d~~~~~~L~~~--~~~i~K~Y~~~v~g~~~~ 119 (217)
T PRK11394 84 GLLVLTNNGALQARLTQP--GKRTGKIYYVQVEGIPTQ 119 (217)
T ss_pred eEEEEECCHHHHHHHhCc--ccCCCEEEEEEECCCCCH
Confidence 999999999999999885 678999999999999754
No 26
>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=2.7e-11 Score=87.24 Aligned_cols=70 Identities=41% Similarity=0.550 Sum_probs=60.6
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeeccccCCcccccCCCCeeEEEeCCcEEEEe
Q 022299 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVN 150 (299)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~~~~~~~~~~~~~~~~IlyeD~~llvvn 150 (299)
+||++||.+.++..||+.++++|++|.|+|||+.++.+++.+.+||.|.+...+ .+..|+|||++++|+|
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 489999998866789999999999999999999997789999999999886421 1128999999999987
No 27
>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=99.21 E-value=2.8e-11 Score=100.25 Aligned_cols=44 Identities=27% Similarity=0.463 Sum_probs=41.2
Q ss_pred cccCCCCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccC
Q 022299 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPS 260 (299)
Q Consensus 215 VhRLDr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~ 260 (299)
|||||++||||||||+|.++++.|.. .++.++|+|+|+|.|.++
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~--~~~~i~K~Y~a~v~g~~~ 44 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTH--PGHHCEKTYLVTVEGPVT 44 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhC--CCCCCCeEEEEEECCCCC
Confidence 79999999999999999999999987 678899999999999875
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=99.17 E-value=5.7e-11 Score=107.63 Aligned_cols=75 Identities=24% Similarity=0.244 Sum_probs=55.6
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceE
Q 022299 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (299)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (299)
+||||||+||.++... .++...|...+. .....++|||||++||||
T Consensus 2 ilvvnKP~Gi~s~~~~----~~~~~~l~~~~~------------------------------~~k~~~~vhrLD~~aSGv 47 (226)
T cd02868 2 LFAVYKPPGVHWKHVR----DTIESNLLKYFP------------------------------EDKVLVGVHRLDAFSSGV 47 (226)
T ss_pred EEEEEcCCCCChhHHH----HHHHHHHHHHcc------------------------------ccceeeEccccCCCCceE
Confidence 7999999999775421 233333333321 112356789999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 226 lL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|+||+++.+ +|.++|.++.+.|+|+|...
T Consensus 48 l~~a~~~~t--kl~~~~~~~~~~K~Y~~~~~ 76 (226)
T cd02868 48 LVLGVNHGN--KLLSHLYSNHPTRVYTIRGL 76 (226)
T ss_pred EEEEeChhH--hHHHHHHhcCCCeEEEEEEE
Confidence 999999876 69999999999999996643
No 29
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=98.98 E-value=1.3e-09 Score=74.91 Aligned_cols=48 Identities=38% Similarity=0.511 Sum_probs=44.8
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEE
Q 022299 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMV 118 (299)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I 118 (299)
+|||+||.+.....||++++++|++|.|+|||+.++++++.|++||+|
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 689999998766778999999999999999999998899999999987
No 30
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=98.93 E-value=2.7e-09 Score=76.75 Aligned_cols=52 Identities=17% Similarity=0.298 Sum_probs=47.4
Q ss_pred CCccchHHHHHHhccCCC--CHHHHHHHHHCCcEEECCEEeccccccccCCCEEee
Q 022299 67 KAGKLRLDAWISSRIDGI--SRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNC 120 (299)
Q Consensus 67 ~~~g~RLdk~L~~~~~~~--Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v 120 (299)
..+++|||+||+.. .+ ||+.++++|+.|.|+|||+++++++++|++||.|.+
T Consensus 5 ~~~~~rLd~~L~~~--~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 5 FTEYITLGQLLKEL--GIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEI 58 (59)
T ss_pred cchHHHHHHHHHHc--CCccCHHHHHHHHHcCCEEECCEEccCCCCCCCCCCEEEe
Confidence 34779999999997 46 999999999999999999999788999999999986
No 31
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=98.46 E-value=2.8e-07 Score=72.85 Aligned_cols=55 Identities=33% Similarity=0.468 Sum_probs=49.0
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeecc
Q 022299 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (299)
Q Consensus 68 ~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~ 123 (299)
...+|||+||.-.--.-+|+.+++++..|+|.+||+++ +++..|+.||+|.+.+.
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 56799999998653356999999999999999999999 89999999999999774
No 32
>smart00363 S4 S4 RNA-binding domain.
Probab=98.42 E-value=7.9e-07 Score=61.73 Aligned_cols=52 Identities=33% Similarity=0.392 Sum_probs=46.5
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeec
Q 022299 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
++|+.||.+.+...|++.+++++..|.|+|||+.++.++..+..||.|.+..
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 4799999987556899999999999999999999967899999999998865
No 33
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=98.16 E-value=4.6e-06 Score=77.56 Aligned_cols=60 Identities=32% Similarity=0.412 Sum_probs=53.9
Q ss_pred EEcCCCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeecc
Q 022299 63 TVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (299)
Q Consensus 63 ~v~~~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~ 123 (299)
.+....+++|||.+++..+ ++||+.++++|++|.|+|||+.++++++.|++||.|.+...
T Consensus 184 e~~~~vas~RLD~vla~~~-~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiRG~ 243 (267)
T PLN00051 184 SFKSVEASLRLDALASAGF-RMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVSGK 243 (267)
T ss_pred EccCCcCcccHHHHHHHHh-ccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEeeC
Confidence 3445567899999999987 89999999999999999999999899999999999999753
No 34
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=98.13 E-value=6.9e-06 Score=68.61 Aligned_cols=53 Identities=30% Similarity=0.288 Sum_probs=48.0
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeec
Q 022299 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 69 ~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
+.+|||+||....-.-||+.++++|..|.|.|||++ .+++..|.+||.|.|..
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 458999999987556799999999999999999999 59999999999999865
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=98.12 E-value=5.9e-06 Score=76.46 Aligned_cols=60 Identities=28% Similarity=0.438 Sum_probs=53.2
Q ss_pred EEcCCCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeecc
Q 022299 63 TVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (299)
Q Consensus 63 ~v~~~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~ 123 (299)
.+....+++|||.+++..+ ++||+.++++|++|+|+|||+.++++++.|++||.|.+...
T Consensus 176 ~~~~~v~s~RLD~lls~~~-~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~IsvrG~ 235 (257)
T TIGR03069 176 ELTTVEASLRIDAIASAGF-GLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRGK 235 (257)
T ss_pred EecCCCccccHHHHHHhhh-hhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEcCC
Confidence 3455668899999999886 78999999999999999999999889999999999999753
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=98.07 E-value=8.6e-06 Score=72.70 Aligned_cols=54 Identities=22% Similarity=0.257 Sum_probs=48.6
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeecc
Q 022299 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (299)
Q Consensus 70 g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~ 123 (299)
.+|||.+|.......||+.++++|..|.|.|||+.++.+++.|++||.|.+...
T Consensus 89 e~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD~I~V~~~ 142 (200)
T TIGR01017 89 ESRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEK 142 (200)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCCEEEEeeC
Confidence 379999997765467999999999999999999999889999999999998754
No 37
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=98.03 E-value=1e-05 Score=72.21 Aligned_cols=53 Identities=19% Similarity=0.226 Sum_probs=48.4
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeecc
Q 022299 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (299)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~ 123 (299)
+|||+||.......||+.++++|..|.|.|||+.++.+++.|++||+|.+...
T Consensus 89 ~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~~~ 141 (201)
T CHL00113 89 MRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDK 141 (201)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEccc
Confidence 79999999876567999999999999999999999889999999999998653
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=97.91 E-value=2.1e-05 Score=71.64 Aligned_cols=52 Identities=29% Similarity=0.238 Sum_probs=47.4
Q ss_pred hHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeecc
Q 022299 72 RLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (299)
Q Consensus 72 RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~ 123 (299)
|||+||.+.....||+.++++|++|+|+|||++++++++.|.+||.|.+...
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 7999999885567899999999999999999999999999999999998653
No 39
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=97.89 E-value=2.6e-05 Score=69.83 Aligned_cols=53 Identities=25% Similarity=0.288 Sum_probs=47.5
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeec
Q 022299 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 70 g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
.+|||.+|.......||+.++++|.+|.|.|||+.++.+++.|++||.|.+..
T Consensus 92 E~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~I~v~~ 144 (203)
T PRK05327 92 ESRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVRE 144 (203)
T ss_pred HHHHHHHHHHcCccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCEEEECC
Confidence 37999999766446899999999999999999999988999999999999865
No 40
>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=97.74 E-value=9.9e-05 Score=64.98 Aligned_cols=70 Identities=21% Similarity=0.256 Sum_probs=52.5
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.+|++|||.|+-+| .+++.+...+. ..+.+..+-||...|
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 369999999998866 46677766543 236778999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+ +.++...+.. -.|+|.|.+.
T Consensus 43 GvLiv~~g~--~Tk~~~~~~~--~~K~Y~a~v~ 71 (182)
T cd02572 43 GCLPVCIDR--ATRLVKSQQE--AGKEYVCVMR 71 (182)
T ss_pred eEEEEEECH--HhhhhHHHhC--CCCEEEEEEE
Confidence 999999987 2344444443 3599999876
No 41
>PRK11507 ribosome-associated protein; Provisional
Probab=97.71 E-value=0.00014 Score=54.12 Aligned_cols=57 Identities=19% Similarity=0.195 Sum_probs=49.7
Q ss_pred CCCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeec
Q 022299 66 TKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 66 ~~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
..++-.+|++||.-.--.-|=.+++.+|..|.|+|||...+.-..+|.+||+|.+..
T Consensus 7 ~~~e~I~L~QlLK~~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~V~~~g 63 (70)
T PRK11507 7 GKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAG 63 (70)
T ss_pred CCCCeEEHHHHHhhhCcccChHHHHHHHHcCceEECCEEecccCCCCCCCCEEEECC
Confidence 456778999999976334589999999999999999999989999999999999854
No 42
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=97.63 E-value=6.4e-05 Score=68.60 Aligned_cols=56 Identities=39% Similarity=0.515 Sum_probs=51.3
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeecc
Q 022299 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (299)
Q Consensus 67 ~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~ 123 (299)
.-+.+|||..++..| ++||..++.+|.+|.|+||.+.++++++.|+.||.|.+.+.
T Consensus 177 ~vsSlRLD~vis~~~-~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG~ 232 (257)
T COG2302 177 TVSSLRLDVVISEGF-GLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRGF 232 (257)
T ss_pred eeehhhHHHHHHHHH-hhhHHHHHHHHHcCceEEeeEEeccccceeccCCEEEEecc
Confidence 345689999999987 69999999999999999999999999999999999998764
No 43
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=97.59 E-value=0.00011 Score=65.70 Aligned_cols=54 Identities=22% Similarity=0.216 Sum_probs=45.8
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeeccc
Q 022299 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (299)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~~ 124 (299)
.|||..+-...-..|+.+++++|..|+|.|||++|+.|++.|++||+|.|....
T Consensus 94 rRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~ 147 (205)
T COG0522 94 RRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKS 147 (205)
T ss_pred HHHHHHHHHhcccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEeeecc
Confidence 456666655534579999999999999999999999999999999999997654
No 44
>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=97.46 E-value=0.00044 Score=62.22 Aligned_cols=68 Identities=22% Similarity=0.289 Sum_probs=52.5
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceE
Q 022299 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (299)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (299)
+|++|||.|+-+| .+++.+++.+. ..+.+..+.||...|||
T Consensus 2 il~i~KP~g~tS~--------~vv~~ik~~~~-------------------------------~kKvGH~GTLDP~AsGv 42 (210)
T cd00506 2 LFAVDKPQGPSSH--------DVVDTIRRIFL-------------------------------AEKVGHGGTLDPFATGV 42 (210)
T ss_pred EEEEEcCCCCCHH--------HHHHHHHHHhC-------------------------------ccccCCCCcCCCcCeeE
Confidence 7999999998765 46777776653 23667899999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 226 lL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|+++-++. .++...|.+ ..|+|.|.+.
T Consensus 43 Liv~vG~a--Tkl~~~~~~--~~K~Y~~~~~ 69 (210)
T cd00506 43 LVVGIGKA--TKLLKHLLA--ATKDYTAIGR 69 (210)
T ss_pred EEEEECHH--HhhhHHHhc--CCceEEEEEE
Confidence 99999873 344444443 7999999976
No 45
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=97.46 E-value=0.00025 Score=64.65 Aligned_cols=53 Identities=34% Similarity=0.319 Sum_probs=49.1
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeec
Q 022299 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 70 g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
.+|||.+|.++...-||+.++.+|.+|.|+|||.+++++++.|..++.|++..
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 58999999998545799999999999999999999999999999999999975
No 46
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.43 E-value=0.00038 Score=63.33 Aligned_cols=71 Identities=18% Similarity=0.343 Sum_probs=53.7
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.+|+||||.|+-+| .+++.+.+.+. ..+.+..+.||...|
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 479999999998766 46777776543 236778999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+. +.+|.+.+.+ ..|+|+|.+.
T Consensus 50 GvLiv~vG~~-aTkl~~~~~~--~~K~Y~~~~~ 79 (230)
T PRK00989 50 GVMVMLIGRK-FTRLSDILLF--EDKEYAAVAH 79 (230)
T ss_pred eEEEEEECCc-hhhhHHHhcC--CCcEEEEEEE
Confidence 9999998763 3444444443 7899999986
No 47
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=97.40 E-value=0.00049 Score=64.18 Aligned_cols=70 Identities=23% Similarity=0.319 Sum_probs=53.8
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.++++|||+|+-+| .+++.+++.+. ..+.+..+.||...|
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 368999999998866 46777777653 235678999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+. .+|.+.+.. -.|+|.|.+.
T Consensus 43 GvLiv~iG~a--TKl~~~l~~--~~K~Y~a~~~ 71 (273)
T PRK04099 43 GVLIVAFGQY--TKLFRFLKK--TPKTYRATLW 71 (273)
T ss_pred eEEEEEEChH--hhhHHHhcc--CCceEEEEEE
Confidence 9999999874 335555543 3899999975
No 48
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=97.33 E-value=0.00084 Score=61.60 Aligned_cols=70 Identities=20% Similarity=0.327 Sum_probs=52.8
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.+|++|||.|+-+| .+++.+++.+. ..+.+..+-||...|
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 469999999998866 46777776543 236778999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+ +.+|...+.+ ..|+|.|.+.
T Consensus 51 GvLiv~iG~--aTKl~~~l~~--~~K~Y~a~~~ 79 (244)
T PRK00020 51 GLLVCCMGR--ATKISGRMLE--ADKTYQATLQ 79 (244)
T ss_pred eEEEEEECH--HhhhhHHhcc--CCcEEEEEEE
Confidence 999999987 2334444433 4699999976
No 49
>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=97.32 E-value=0.00085 Score=60.31 Aligned_cols=69 Identities=19% Similarity=0.284 Sum_probs=53.4
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 022299 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (299)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (299)
.+|+||||.|+-+| .+++.+...+. ..+.+..+.||...||
T Consensus 3 G~l~v~KP~g~tS~--------~vv~~vkk~~~-------------------------------~kKvGH~GTLDP~AsG 43 (209)
T TIGR00431 3 GVLLLDKPQGMTSF--------DALAKVRRLLN-------------------------------VKKVGHTGTLDPFATG 43 (209)
T ss_pred eEEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------CCcCCCCCCCCCcCce
Confidence 68999999998765 46777776553 2356789999999999
Q ss_pred EEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 225 LlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
||+++-.+.. +|...+. ...|+|.|.+.
T Consensus 44 vLiv~vG~~T--kl~~~~~--~~~K~Y~~~~~ 71 (209)
T TIGR00431 44 VLPILVGKAT--KLSPYLT--DLDKEYRAEIR 71 (209)
T ss_pred EEEEEEChHh--hhhHHHc--CCCCeEEEEEE
Confidence 9999999743 4555443 47999999976
No 50
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=97.25 E-value=5.6e-05 Score=55.55 Aligned_cols=57 Identities=19% Similarity=0.243 Sum_probs=36.8
Q ss_pred CCCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeec
Q 022299 66 TKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 66 ~~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
...+-.+|++||...--.-|-.+++.+|.+|.|+|||...+.-+.+|.+||.|.+..
T Consensus 3 I~~e~I~L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~~~ 59 (65)
T PF13275_consen 3 INTEYITLGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEIDG 59 (65)
T ss_dssp ---S---HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEETT
T ss_pred CCCCcEEHHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEECC
Confidence 345678999999976323488899999999999999999989999999999999843
No 51
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=97.21 E-value=0.0013 Score=62.00 Aligned_cols=70 Identities=21% Similarity=0.248 Sum_probs=53.4
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.+|++|||+|+-+| .+++.+++.+. ..+.+..+-||...|
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 368999999998866 46777776553 236678999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+. .++.+.+.. -.|+|.|.+.
T Consensus 43 GvL~v~vG~a--Tkl~~~l~~--~~K~Y~a~~~ 71 (290)
T PRK00130 43 GVLPVCLGKA--TKIVDYLME--GKKTYRAEIK 71 (290)
T ss_pred eEEEEEEChh--hhhHHHhcc--CCcEEEEEEE
Confidence 9999999873 334444443 4899999976
No 52
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=97.18 E-value=0.0015 Score=62.02 Aligned_cols=70 Identities=24% Similarity=0.330 Sum_probs=53.3
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.++++|||+|+-+| .+++.+.+.+. ..+.+..+-||...|
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 368999999998876 46777776553 235678999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+. .++.+.+.. -.|+|.|.+.
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 9999999873 334454443 3899999975
No 53
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=97.18 E-value=0.0012 Score=62.32 Aligned_cols=69 Identities=22% Similarity=0.238 Sum_probs=52.5
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 022299 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (299)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (299)
.+|++|||+|+-+| .+++.+++.+. ..+.+..+.||...||
T Consensus 4 Gil~i~KP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~AtG 44 (294)
T PRK02484 4 GIINLKKEAGMTSH--------DAVFKLRKILQ-------------------------------TKKIGHGGTLDPDVVG 44 (294)
T ss_pred eEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccccCCCCCCCCee
Confidence 69999999998876 46777776553 2367789999999999
Q ss_pred EEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 225 LlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
||+++-.+. .++.+.+.. -.|+|.|.+.
T Consensus 45 vL~i~vG~a--Tkl~~~l~~--~~K~Y~a~~~ 72 (294)
T PRK02484 45 VLPIAVGKA--TRLIEYMTE--AGKVYEGEIT 72 (294)
T ss_pred EEEEEEChh--hhhhHHhcc--CCcEEEEEEE
Confidence 999999873 334444443 4599999976
No 54
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=97.16 E-value=0.0014 Score=61.97 Aligned_cols=71 Identities=24% Similarity=0.384 Sum_probs=53.7
Q ss_pred CCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCC
Q 022299 143 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 222 (299)
Q Consensus 143 D~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~T 222 (299)
-+.+|+||||.|+-+| .+++.+++.+. ..+.+..+-||...
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 3579999999998866 46777776553 23667899999999
Q ss_pred ceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 223 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 223 SGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
||||+++-.+ +.++.+.+.+ -.|+|.|.+.
T Consensus 49 tGvL~i~vG~--aTKl~~~l~~--~~K~Y~a~~~ 78 (298)
T PRK03287 49 TGVLVLGVER--ATKLLGHLTL--TDKSYTATIR 78 (298)
T ss_pred eeEEEEEeCh--hhhhhHHHhc--CCcEEEEEEE
Confidence 9999999986 2334444443 4899999975
No 55
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=97.12 E-value=0.0014 Score=62.11 Aligned_cols=70 Identities=20% Similarity=0.257 Sum_probs=53.7
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.+|+||||+|+-+| .+++.+++.+. ..+.+..+.||...|
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 369999999998866 46777776553 236778999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+.. ++.+.+.. ..|+|.|.+.
T Consensus 44 GvL~v~vG~aT--kl~~~l~~--~~K~Y~~~~~ 72 (305)
T PRK14123 44 GVLPVCIGNAT--RVSDYVMD--MGKAYEATVS 72 (305)
T ss_pred eEEEEEEChhh--hhHHHhcC--CCcEEEEEEE
Confidence 99999998743 44444443 6899999975
No 56
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=97.11 E-value=0.0014 Score=61.90 Aligned_cols=69 Identities=23% Similarity=0.268 Sum_probs=53.8
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.+|++|||.|+-+| .+++.+++.+. ..+.+..+-||...|
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 369999999998866 46777776553 236778999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+.. ++.+.+. . .|+|.|.+.
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 99999998843 4556665 2 799999975
No 57
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=97.09 E-value=0.0018 Score=61.43 Aligned_cols=70 Identities=21% Similarity=0.204 Sum_probs=53.3
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||...|
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 479999999998866 46777776543 235678999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+ +.++...+.. -.|+|.|.+.
T Consensus 54 GvL~v~vG~--aTkl~~~l~~--~~K~Y~a~~~ 82 (305)
T PRK05389 54 GVLPIALGE--ATKTVPYVMD--GTKRYRFTVA 82 (305)
T ss_pred eEEEEEECh--hhhhhHHhcc--CCcEEEEEEE
Confidence 999999987 3344444433 4899999975
No 58
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=97.04 E-value=0.0023 Score=60.84 Aligned_cols=70 Identities=19% Similarity=0.289 Sum_probs=53.9
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.+|+||||+|+-+| .+++.+++.+. ..+.+..+-||...|
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 479999999998876 36777776543 236678999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+. .+|...+.. -.|+|.|.+.
T Consensus 51 GvL~v~vG~a--Tkl~~~~~~--~~K~Y~a~~~ 79 (312)
T PRK05033 51 GMLPICLGEA--TKFSQYLLD--SDKRYRVTAR 79 (312)
T ss_pred eEEEEEECHH--hhhhHHhcC--CCcEEEEEEE
Confidence 9999999874 335555543 4899999976
No 59
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=97.03 E-value=0.0018 Score=61.27 Aligned_cols=70 Identities=17% Similarity=0.209 Sum_probs=52.7
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||...|
T Consensus 22 ~g~l~i~Kp~g~tS~--------~~v~~~r~~~~-------------------------------~kkvGH~GTLDp~A~ 62 (300)
T PRK04270 22 FGVVNLDKPPGPTSH--------EVAAWVRDILG-------------------------------VEKAGHGGTLDPKVT 62 (300)
T ss_pred CCEEEEECCCCCCHH--------HHHHHHHHHhc-------------------------------cccccCCCCCCCcCe
Confidence 579999999998766 46777776543 235678999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+. .+|.+.+.+ -.|+|.|.+.
T Consensus 63 GvL~v~~g~a--tk~~~~~~~--~~K~Y~~~~~ 91 (300)
T PRK04270 63 GVLPVALGKA--TKVVQALLE--SGKEYVCVMH 91 (300)
T ss_pred EEEEEEEChH--hhhhHHhcc--CCcEEEEEEE
Confidence 9999999873 344444443 4699999875
No 60
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Probab=97.03 E-value=0.0023 Score=59.99 Aligned_cols=68 Identities=24% Similarity=0.366 Sum_probs=52.6
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceE
Q 022299 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (299)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (299)
+|++|||.|+-+| .+++.+++.+. ..+.+..+-||...|||
T Consensus 2 il~i~KP~G~tS~--------~vv~~vr~~~~-------------------------------~kKvGH~GTLDP~AtGv 42 (277)
T cd02573 2 ILLLDKPAGLTSH--------DVVQKVRRLLG-------------------------------TKKVGHTGTLDPLATGV 42 (277)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------cCccCCCCCCCCcCeEE
Confidence 7999999998876 46777776543 23567899999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 226 lL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|+++-.+. .+|...+.+ ..|+|.|.+.
T Consensus 43 L~v~vG~a--Tkl~~~l~~--~~K~Y~~~~~ 69 (277)
T cd02573 43 LPIALGEA--TKLSQYLLD--ADKTYRATVR 69 (277)
T ss_pred EEEEEChH--HhhHHHhcC--CCcEEEEEEE
Confidence 99999873 335555543 5999999976
No 61
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=97.02 E-value=0.0022 Score=60.85 Aligned_cols=69 Identities=22% Similarity=0.287 Sum_probs=52.8
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 022299 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (299)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (299)
.+|++|||.||-+| .+++.+++.+. ..+.+..+-||...||
T Consensus 3 Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~AtG 43 (304)
T PRK01550 3 GVLLLHKPRGMTSH--------DCVFKLRKILR-------------------------------TKKVGHTGTLDPEVSG 43 (304)
T ss_pred eEEEEECCCCCCHH--------HHHHHHHHHcC-------------------------------CCCcccCCCCCCcCee
Confidence 68999999998876 46777776553 2356789999999999
Q ss_pred EEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 225 LlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
||+++-.+. .+|...+.. -.|+|.|.+.
T Consensus 44 vL~i~vG~a--Tkl~~~l~~--~~K~Y~a~~~ 71 (304)
T PRK01550 44 VLPICVGRA--TKIAEYLTD--EGKTYEGEVT 71 (304)
T ss_pred EEEEEEChh--hhhhHHhcC--CCcEEEEEEE
Confidence 999999873 334444443 4899999976
No 62
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=97.01 E-value=0.0022 Score=60.66 Aligned_cols=70 Identities=20% Similarity=0.288 Sum_probs=53.3
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.+|++|||.|+-+| .+++.+++.+. ..+.+..+-||...|
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 479999999998866 46777777653 235678999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+. .++.+.+.. -.|+|.|.+.
T Consensus 57 GvL~v~vG~a--Tkl~~~l~~--~~K~Y~~~~~ 85 (303)
T PRK01851 57 GLLPLCFGEA--TKFSQDLLD--ADKTYEATLR 85 (303)
T ss_pred eEEEEEECHH--HhhhHHhcc--cCeEEEEEEE
Confidence 9999999873 334444443 4599999976
No 63
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=97.00 E-value=0.0025 Score=59.75 Aligned_cols=68 Identities=24% Similarity=0.369 Sum_probs=51.4
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCceE
Q 022299 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (299)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (299)
++++|||.|+-+| .+++.+.+.+. ..+.+..+.||-..|||
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 7899999998876 35677766543 23677899999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 226 lL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|+++-.+. .++.+.+ ....|+|.|.+.
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 99999873 3344444 236899999976
No 64
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=96.92 E-value=0.002 Score=56.43 Aligned_cols=51 Identities=18% Similarity=0.210 Sum_probs=44.1
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCC--EEeee
Q 022299 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGD--MVNCT 121 (299)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD--~I~v~ 121 (299)
.|||.+|.+..-.-|+..++++|..|.|.|||++|+++++.|..++ .|.+.
T Consensus 103 rRLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~ 155 (177)
T PRK04051 103 RRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYY 155 (177)
T ss_pred hHHHHHHHHccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEe
Confidence 5888888877556799999999999999999999999999999995 55543
No 65
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=96.91 E-value=0.0033 Score=60.22 Aligned_cols=70 Identities=21% Similarity=0.237 Sum_probs=52.3
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.+|++|||.|+-+| .+++.+++.+. ..+.+..+.||...|
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 469999999998866 46777776543 236778999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+. .++.+.+. .-.|+|.|.+.
T Consensus 44 GVL~i~vG~a--TKl~~~l~--~~~K~Y~a~~~ 72 (345)
T PRK14846 44 GILPFAVGEA--TKLIHLLI--DARKTYIFTVK 72 (345)
T ss_pred eEEEEEEChh--hhhhHHHh--cCCceEEEEEE
Confidence 9999998863 33333333 25899999976
No 66
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=96.90 E-value=0.003 Score=59.54 Aligned_cols=70 Identities=21% Similarity=0.253 Sum_probs=52.3
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.+|++|||+|+-+| .+++.+++.+. ..+.+..+-||...|
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 479999999998866 46777776543 236678999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+. .++...+.+ -.|+|.|.+.
T Consensus 44 GvL~v~vG~a--TKl~~~l~~--~~K~Y~~~~~ 72 (292)
T PRK01528 44 GVLPLAVGEA--TKLVQLLID--AKKTYIFTVK 72 (292)
T ss_pred eEEEEEEChH--hhhhHHHhc--CCceEEEEEE
Confidence 9999999873 333333332 5799999975
No 67
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=96.78 E-value=0.0049 Score=58.58 Aligned_cols=69 Identities=26% Similarity=0.399 Sum_probs=52.7
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 022299 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (299)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (299)
.+|+||||.|+-+| .+++.+++.+. ..+.+..+-||...||
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 48999999998866 46777776543 2366789999999999
Q ss_pred EEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 225 LlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
||+++-.+.. +|.+.+ ....|+|.|.+.
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 9999998732 255544 336899999985
No 68
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=96.76 E-value=0.0043 Score=46.52 Aligned_cols=58 Identities=21% Similarity=0.211 Sum_probs=48.9
Q ss_pred cCCCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeec
Q 022299 65 DTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 65 ~~~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
....+-..|.+||...--.-|-.+++.+|..|.|+|||++-++-..+|..||.|.+..
T Consensus 6 ~i~~e~I~L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~ 63 (73)
T COG2501 6 LIKTEFITLGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPG 63 (73)
T ss_pred EeccceEEHHHHHHHhCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECC
Confidence 3455667899999976323488999999999999999999988999999999999854
No 69
>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=96.52 E-value=0.0067 Score=58.02 Aligned_cols=70 Identities=20% Similarity=0.291 Sum_probs=52.9
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||-..+
T Consensus 34 ~G~l~i~KP~g~tS~--------~~v~~vr~~~~-------------------------------~kkvGH~GTLDP~A~ 74 (322)
T TIGR00425 34 YGVVNLDKPSGPSSH--------EVVAWVRRILN-------------------------------VEKTGHGGTLDPKVT 74 (322)
T ss_pred CCEEEEeCCCCCCHH--------HHHHHHHHHhc-------------------------------ccccCCCCCCCCCCc
Confidence 479999999998876 46777776553 235678999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+. .+|.+.+. .-.|+|.|.+.
T Consensus 75 GvL~v~~G~a--Tkl~~~~~--~~~K~Y~~~v~ 103 (322)
T TIGR00425 75 GVLPVCIERA--TRLVKSLQ--EAPKEYVCLMR 103 (322)
T ss_pred eEEEEEEChH--hhccHHhc--cCCCEEEEEEE
Confidence 9999999873 33444433 26899999875
No 70
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=96.44 E-value=0.011 Score=55.95 Aligned_cols=70 Identities=19% Similarity=0.259 Sum_probs=53.2
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCc
Q 022299 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (299)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TS 223 (299)
+.+|++|||.|+-+| .+++.+++.+. ..+.+..+-||-..|
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 479999999998876 46777777653 235678999999999
Q ss_pred eEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 224 GLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
|||+++-.+. .+|.+.+. .-.|+|.|.+.
T Consensus 51 GvL~v~~G~a--Tkl~~~l~--~~~K~Y~a~~~ 79 (300)
T PRK04642 51 GLLPLCFGEA--TKIAGLLL--GSAKAYDAEIV 79 (300)
T ss_pred eeEEEEEChh--hhhhHHhc--CCCcEEEEEEE
Confidence 9999998863 34444443 25899999985
No 71
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=96.43 E-value=0.01 Score=56.50 Aligned_cols=43 Identities=21% Similarity=0.282 Sum_probs=33.9
Q ss_pred CCccccccCCCCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 210 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 210 ~~~~~VhRLDr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
.+.+..+-||-..||||+++-... .+.++..+. ..|+|.|.+.
T Consensus 56 ~KiGH~GTLDPlAsGVLvvgvG~a-TK~l~~~l~---~~K~Y~~~~~ 98 (312)
T cd02867 56 LKIGHGGTLDPLATGVLVVGVGAG-TKQLQDYLS---CSKTYEATGL 98 (312)
T ss_pred cccccccccCCccceeEEEEECcH-HHHHHHHhc---CCceEEEEEE
Confidence 477889999999999999999863 444444333 7999999975
No 72
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=96.23 E-value=0.013 Score=54.74 Aligned_cols=69 Identities=16% Similarity=0.238 Sum_probs=52.1
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccccCCCCCce
Q 022299 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (299)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (299)
.+|++|||.|+-+| .++..++..+. ..+.+..+-||-..||
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 79999999998766 45666666553 2456779999999999
Q ss_pred EEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 225 LlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
+|+++-. ++.+.+.-+.. -.|+|.|.+.
T Consensus 57 vLpi~ig-~aTKl~~~l~~---~~K~Y~a~~~ 84 (271)
T COG0130 57 VLPICLG-EATKLVQYLLD---ADKEYVATVR 84 (271)
T ss_pred eEEEEec-hhHhHHHHHhh---CCcEEEEEEE
Confidence 9999998 44444443322 6899999986
No 73
>PLN00189 40S ribosomal protein S9; Provisional
Probab=96.01 E-value=0.0049 Score=54.68 Aligned_cols=55 Identities=18% Similarity=0.231 Sum_probs=44.3
Q ss_pred cchHHHHHHhccC--------CCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeeccc
Q 022299 70 KLRLDAWISSRID--------GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (299)
Q Consensus 70 g~RLdk~L~~~~~--------~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~~ 124 (299)
+..+..||..++. .-|...++++|..|.|.|||++|+.|++.|..|+++.|.+..
T Consensus 100 ~Ltvs~~leRRL~~vv~r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~~ 162 (194)
T PLN00189 100 ALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSL 162 (194)
T ss_pred hccHHHHHHhhhceeeeecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEEec
Confidence 3445555554442 348999999999999999999999999999999999887753
No 74
>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=95.69 E-value=0.018 Score=49.75 Aligned_cols=50 Identities=16% Similarity=0.188 Sum_probs=40.1
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCC--CEEee
Q 022299 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGG--DMVNC 120 (299)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~G--D~I~v 120 (299)
.||+-.+-+.--.-|..+++++|.+|.|.|||++|+.|++.|..+ |.|.+
T Consensus 104 RRL~~vv~r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~ 155 (162)
T TIGR01018 104 RRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDF 155 (162)
T ss_pred HhHhhHhhhccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeee
Confidence 455555555433569999999999999999999999999999999 55544
No 75
>PRK04313 30S ribosomal protein S4e; Validated
Probab=95.32 E-value=0.067 Score=48.96 Aligned_cols=73 Identities=14% Similarity=0.151 Sum_probs=53.7
Q ss_pred CccchHHHHHHhccC-CCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeeccccCCcccccCCCCeeEEEeCCcE
Q 022299 68 AGKLRLDAWISSRID-GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNV 146 (299)
Q Consensus 68 ~~g~RLdk~L~~~~~-~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~~~~~~~~~~~~~~~~IlyeD~~l 146 (299)
.+++.|--+|+..|. ..+.+++++.|.+|.|+|||++.+...+.+-.-|+|.+... +...+|||.....
T Consensus 35 ~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~~~----------~e~yRvl~d~kgr 104 (237)
T PRK04313 35 EESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIPET----------GEYYRVLPDEKGR 104 (237)
T ss_pred ccccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEccC----------CCeEEEEECCCCc
Confidence 345668888888775 36999999999999999999999877777777799998432 2234556655554
Q ss_pred EEEe
Q 022299 147 LVVN 150 (299)
Q Consensus 147 lvvn 150 (299)
++++
T Consensus 105 ~~l~ 108 (237)
T PRK04313 105 LVLI 108 (237)
T ss_pred EEEE
Confidence 4443
No 76
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=95.26 E-value=0.021 Score=50.30 Aligned_cols=53 Identities=17% Similarity=0.058 Sum_probs=41.3
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeecc
Q 022299 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (299)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~ 123 (299)
.||+..+.+.--.-|...++++|..|.|.|||++|+.|++.|..|++=.|.+.
T Consensus 107 RRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I~~~ 159 (181)
T PTZ00155 107 RRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFA 159 (181)
T ss_pred HhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceEeccCccCceeee
Confidence 34555554442345899999999999999999999999999999966655553
No 77
>PLN00036 40S ribosomal protein S4; Provisional
Probab=94.98 E-value=0.096 Score=48.55 Aligned_cols=54 Identities=17% Similarity=0.182 Sum_probs=44.7
Q ss_pred ccchHHHHHHhccC-CCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeec
Q 022299 69 GKLRLDAWISSRID-GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 69 ~g~RLdk~L~~~~~-~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
++..|--||+..|. ..+.+++++.+.+|.|+|||++.+...+.+-.-|+|.+..
T Consensus 40 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~k 94 (261)
T PLN00036 40 ECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPK 94 (261)
T ss_pred cccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcC
Confidence 45668888888775 3588999999999999999999987777777779999854
No 78
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=94.79 E-value=0.11 Score=48.44 Aligned_cols=55 Identities=22% Similarity=0.217 Sum_probs=45.1
Q ss_pred CccchHHHHHHhccC-CCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeec
Q 022299 68 AGKLRLDAWISSRID-GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 68 ~~g~RLdk~L~~~~~-~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
.+++.|--||+..|. ..+.+++++.+.+|.|+|||++.+...+.+-.-|+|.+..
T Consensus 36 ~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~k 91 (273)
T PTZ00223 36 RECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPK 91 (273)
T ss_pred ccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcC
Confidence 345668888888775 3588999999999999999999987777777779999844
No 79
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=94.78 E-value=0.11 Score=48.13 Aligned_cols=55 Identities=20% Similarity=0.235 Sum_probs=45.2
Q ss_pred CccchHHHHHHhccC-CCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeec
Q 022299 68 AGKLRLDAWISSRID-GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 68 ~~g~RLdk~L~~~~~-~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
.+++.|--||+..|. ..+.+++++.|.+|.|+|||++.+...+.+-.-|+|.+..
T Consensus 39 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~k 94 (262)
T PTZ00118 39 RECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTK 94 (262)
T ss_pred ccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEcC
Confidence 345668888888775 3588999999999999999999987777777779999853
No 80
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=90.79 E-value=0.5 Score=36.18 Aligned_cols=47 Identities=30% Similarity=0.426 Sum_probs=38.8
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeec
Q 022299 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 67 ~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
-+.+.+|.+.+... +++..++ |.|.|||+.+ ..++.++.||.|.+.-
T Consensus 29 ~~~~~tvkd~IEsL--GVP~tEV------~~i~vNG~~v-~~~~~~~~Gd~v~V~P 75 (81)
T PF14451_consen 29 FDGGATVKDVIESL--GVPHTEV------GLILVNGRPV-DFDYRLKDGDRVAVYP 75 (81)
T ss_pred cCCCCcHHHHHHHc--CCChHHe------EEEEECCEEC-CCcccCCCCCEEEEEe
Confidence 44556788888764 6898877 8999999999 6899999999999864
No 81
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=90.65 E-value=0.62 Score=42.43 Aligned_cols=66 Identities=12% Similarity=0.195 Sum_probs=45.4
Q ss_pred HHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeeccccCCcccccCCCCeeEEEeCCcEEEEeC
Q 022299 73 LDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNK 151 (299)
Q Consensus 73 Ldk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~~~~~~~~~~~~~~~~IlyeD~~llvvnK 151 (299)
|-++|.-. -.-+++++.|.+|.|+|||++.+...+.|-.-|+|.+.. .....+|||.....+++++
T Consensus 47 iRd~LkyA---d~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~----------tgE~yRvl~d~~grl~l~~ 112 (241)
T COG1471 47 IRDYLKYA---DNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPK----------TGEHYRVLPDEKGRLVLHP 112 (241)
T ss_pred ehhHHHhc---cchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECC----------CCceEEEEecCCccEEEEe
Confidence 34555533 466799999999999999999865555555559998853 1223577777776666654
No 82
>PRK01777 hypothetical protein; Validated
Probab=89.52 E-value=0.6 Score=36.86 Aligned_cols=54 Identities=17% Similarity=0.225 Sum_probs=40.6
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeecc
Q 022299 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (299)
Q Consensus 67 ~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~ 123 (299)
-.+|.++.+.|... ++....-.--+..+.|-|||+.+ ..++.|+.||+|+++.+
T Consensus 23 vp~GtTv~dal~~s--gi~~~~pei~~~~~~vgI~Gk~v-~~d~~L~dGDRVeIyrP 76 (95)
T PRK01777 23 LQEGATVEEAIRAS--GLLELRTDIDLAKNKVGIYSRPA-KLTDVLRDGDRVEIYRP 76 (95)
T ss_pred cCCCCcHHHHHHHc--CCCccCcccccccceEEEeCeEC-CCCCcCCCCCEEEEecC
Confidence 44677899999875 45555222234568999999999 69999999999999764
No 83
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=88.78 E-value=0.8 Score=45.31 Aligned_cols=48 Identities=21% Similarity=0.219 Sum_probs=39.8
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCE
Q 022299 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDM 117 (299)
Q Consensus 70 g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~ 117 (299)
+..|.++|.+.--.-|+++++++|.+|.|+|||.+++..+..+.+++.
T Consensus 342 ~~~~~~~l~~~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~~ 389 (410)
T PRK13354 342 TKNLVDLLVDLGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPEDA 389 (410)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhhh
Confidence 577888888764457999999999999999999999777777776653
No 84
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.93 E-value=1.3 Score=38.98 Aligned_cols=62 Identities=21% Similarity=0.393 Sum_probs=47.5
Q ss_pred EEEEEc-CCCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeec
Q 022299 60 LEETVD-TKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 60 ~~~~v~-~~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
.|..+. ......||+.+|++.+ ++|+++++++|..|.|..+-........+++.|-.|.++.
T Consensus 127 vel~l~~~~p~qlrl~~Ll~seL-~LSrS~lq~lie~g~Irgdtd~~~l~rkrlr~~~~i~Id~ 189 (203)
T COG4332 127 VELSLRISRPFQLRLDRLLASEL-GLSRSELQRLIETGQIRGDTDKMLLLRKRLRAGYDIQIDV 189 (203)
T ss_pred EEEEEcccCcchhHHHHHHHHHh-CcCHHHHHHHHHcCceeecchHHHHhhhhhhcCcEEEEEc
Confidence 555554 3445679999999997 7999999999999999987654333456678887777765
No 85
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=86.59 E-value=0.7 Score=42.55 Aligned_cols=22 Identities=32% Similarity=0.416 Sum_probs=19.0
Q ss_pred CccccccCCCCCceEEEEEcCH
Q 022299 211 RPGIVHRLDKGTSGLLVVAKDE 232 (299)
Q Consensus 211 ~~~~VhRLDr~TSGLlL~Ak~~ 232 (299)
...++||||..|||++||.-..
T Consensus 90 ~V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559|consen 90 DVQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred ceeeEEeecccccceEEEecCc
Confidence 3678999999999999998763
No 86
>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=86.44 E-value=1.1 Score=34.15 Aligned_cols=28 Identities=21% Similarity=0.181 Sum_probs=25.3
Q ss_pred CCccccccCCCCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 210 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 210 ~~~~~VhRLDr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
...+.++++|+.++|+++++ ++|..++.
T Consensus 24 ~~i~~aG~kDk~a~t~q~v~-------------------n~f~i~~r 51 (87)
T cd01291 24 KRVGYAGRKDKRAVTTQLVS-------------------NRFTITLR 51 (87)
T ss_pred heEEECccCCCCeeEEEEEc-------------------ccEEEEEE
Confidence 46778999999999999999 88999888
No 87
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=86.04 E-value=1.9 Score=42.56 Aligned_cols=45 Identities=24% Similarity=0.194 Sum_probs=36.8
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccC
Q 022299 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKG 114 (299)
Q Consensus 70 g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~ 114 (299)
+..|.++|.+.--.-|+++++++|++|.|+|||+++...+..+..
T Consensus 342 ~~~~~~~l~~~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~ 386 (408)
T PRK05912 342 GIDLLALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTA 386 (408)
T ss_pred CCcHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEecCccccccc
Confidence 567888888763357999999999999999999999666666655
No 88
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=85.03 E-value=2.1 Score=36.22 Aligned_cols=36 Identities=31% Similarity=0.514 Sum_probs=32.0
Q ss_pred CCCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECC
Q 022299 66 TKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSING 102 (299)
Q Consensus 66 ~~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNG 102 (299)
......||+.+|++.+ ++||+++++++..|.|..+.
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 89
>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=84.23 E-value=1.2 Score=38.03 Aligned_cols=43 Identities=23% Similarity=0.282 Sum_probs=31.2
Q ss_pred CCccccccCCCCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEe
Q 022299 210 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (299)
Q Consensus 210 ~~~~~VhRLDr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~ 256 (299)
.+.+..+.||...||||+++-++ +.+|.+.|.. ..|+|.|.+.
T Consensus 7 ~KvGH~GTLDP~AsGvL~v~vg~--~Tkl~~~l~~--~~K~Y~~~~~ 49 (149)
T PF01509_consen 7 KKVGHGGTLDPFASGVLVVGVGK--ATKLLSYLQN--SDKEYVATIR 49 (149)
T ss_dssp SSEEESS-SSTT-EEEEEEEEGG--GGGGHHHHTT--SEEEEEEEEE
T ss_pred ceeccccccCCcceEEEEEEECC--cchHHHHhhc--cCCEEEEEEE
Confidence 46788999999999999999986 2234445543 4599999875
No 90
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=81.31 E-value=5.3 Score=29.31 Aligned_cols=43 Identities=23% Similarity=0.426 Sum_probs=33.3
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeee
Q 022299 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCT 121 (299)
Q Consensus 69 ~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~ 121 (299)
++.++.++|.+. .++. +.-.|.+||+.+ ..++.|+.||+|++.
T Consensus 22 ~~~tv~~ll~~l--~~~~-------~~v~v~vNg~iv-~~~~~l~~gD~Veii 64 (70)
T PRK08364 22 KGMKVADILRAV--GFNT-------ESAIAKVNGKVA-LEDDPVKDGDYVEVI 64 (70)
T ss_pred CCCcHHHHHHHc--CCCC-------ccEEEEECCEEC-CCCcCcCCCCEEEEE
Confidence 457899999865 3443 335788999999 479999999999874
No 91
>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=81.03 E-value=4.7 Score=29.63 Aligned_cols=50 Identities=14% Similarity=0.201 Sum_probs=32.5
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeee
Q 022299 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCT 121 (299)
Q Consensus 70 g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~ 121 (299)
+.++.++|.......+. ........-.|.|||+.+. .+..|+.||+|.+.
T Consensus 25 ~~tv~~ll~~l~~~~~~-~~~~~~~~~~v~vNg~~v~-~~~~l~~gD~v~i~ 74 (80)
T cd00754 25 GATVGELLDALEARYPG-LLEELLARVRIAVNGEYVR-LDTPLKDGDEVAII 74 (80)
T ss_pred CCcHHHHHHHHHHHCch-HHHhhhhcEEEEECCeEcC-CCcccCCCCEEEEe
Confidence 55677666543211221 1223334457899999994 89999999999874
No 92
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=70.25 E-value=12 Score=27.93 Aligned_cols=24 Identities=25% Similarity=0.356 Sum_probs=21.0
Q ss_pred cEEECCEEeccccccccCCCEEeee
Q 022299 97 LVSINGQVVSKVSHNVKGGDMVNCT 121 (299)
Q Consensus 97 ~V~vNGk~v~~~~~~l~~GD~I~v~ 121 (299)
.|.||++.+. .+..|+.||+|.+.
T Consensus 51 ~v~vn~~~v~-~~~~l~dgDevai~ 74 (80)
T TIGR01682 51 MVAVNEEYVT-DDALLNEGDEVAFI 74 (80)
T ss_pred EEEECCEEcC-CCcCcCCCCEEEEe
Confidence 5889999984 78999999999884
No 93
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=69.36 E-value=12 Score=27.86 Aligned_cols=50 Identities=10% Similarity=0.147 Sum_probs=32.2
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeee
Q 022299 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCT 121 (299)
Q Consensus 69 ~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~ 121 (299)
++.++.+++.......+ .+.+....=.|.|||+.+ ..++.|+.||+|.+.
T Consensus 27 ~~~tv~~L~~~l~~~~p--~l~~~~~~~~vavN~~~v-~~~~~l~dgDeVai~ 76 (82)
T PLN02799 27 AGSTTADCLAELVAKFP--SLEEVRSCCVLALNEEYT-TESAALKDGDELAII 76 (82)
T ss_pred CCCcHHHHHHHHHHHCh--hHHHHhhCcEEEECCEEc-CCCcCcCCCCEEEEe
Confidence 35566666654321111 233433333688999998 588999999999884
No 94
>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=69.09 E-value=3.1 Score=30.35 Aligned_cols=51 Identities=16% Similarity=0.208 Sum_probs=32.5
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEecc--ccccccCCCEEeee
Q 022299 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK--VSHNVKGGDMVNCT 121 (299)
Q Consensus 68 ~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~--~~~~l~~GD~I~v~ 121 (299)
.++.++.++|.......+.-. ....=.|.|||+.+.. .+..|+.||+|.+.
T Consensus 19 ~~~~tv~~ll~~l~~~~p~~~---~~~~~~v~vN~~~v~~~~~~~~l~~gD~V~i~ 71 (77)
T PF02597_consen 19 PEGSTVRDLLEALAERYPELA---LRDRVAVAVNGEIVPDDGLDTPLKDGDEVAIL 71 (77)
T ss_dssp SSTSBHHHHHHHHCHHTGGGH---TTTTEEEEETTEEEGGGTTTSBEETTEEEEEE
T ss_pred CCCCcHHHHHHHHHhhccccc---cCccEEEEECCEEcCCccCCcCcCCCCEEEEE
Confidence 345567777665421122211 3344578899999943 28899999999884
No 95
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=66.48 E-value=5.6 Score=28.45 Aligned_cols=44 Identities=27% Similarity=0.508 Sum_probs=31.1
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEec---cccccccCCCEEeee
Q 022299 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVS---KVSHNVKGGDMVNCT 121 (299)
Q Consensus 69 ~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~---~~~~~l~~GD~I~v~ 121 (299)
++.+|.++|... ++....+ .|.+||..+. ..++.|+.||+|++.
T Consensus 14 ~~~tl~~lL~~l--~~~~~~v-------av~vNg~iv~r~~~~~~~l~~gD~vei~ 60 (66)
T PRK05659 14 DGESVAALLARE--GLAGRRV-------AVEVNGEIVPRSQHASTALREGDVVEIV 60 (66)
T ss_pred CCCCHHHHHHhc--CCCCCeE-------EEEECCeEeCHHHcCcccCCCCCEEEEE
Confidence 467899999864 3333322 3889997763 267889999999884
No 96
>PRK06437 hypothetical protein; Provisional
Probab=66.01 E-value=6.7 Score=28.61 Aligned_cols=44 Identities=30% Similarity=0.354 Sum_probs=33.4
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeee
Q 022299 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCT 121 (299)
Q Consensus 68 ~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~ 121 (299)
.++.++.++|.+. +++...+ .|.+||..+ ..++.|+.||.|++.
T Consensus 18 ~~~~tv~dLL~~L--gi~~~~v-------aV~vNg~iv-~~~~~L~dgD~Veiv 61 (67)
T PRK06437 18 DHELTVNDIIKDL--GLDEEEY-------VVIVNGSPV-LEDHNVKKEDDVLIL 61 (67)
T ss_pred CCCCcHHHHHHHc--CCCCccE-------EEEECCEEC-CCceEcCCCCEEEEE
Confidence 3557899999875 3553222 567999999 589999999999884
No 97
>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=59.85 E-value=8.5 Score=27.56 Aligned_cols=43 Identities=21% Similarity=0.412 Sum_probs=30.4
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEecccc----ccccCCCEEeee
Q 022299 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVS----HNVKGGDMVNCT 121 (299)
Q Consensus 69 ~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~----~~l~~GD~I~v~ 121 (299)
++.++.++|... .++. +.+ .|.+||+.+. .+ +.|+.||+|.+.
T Consensus 13 ~~~tv~~ll~~l--~~~~----~~i---~V~vNg~~v~-~~~~~~~~L~~gD~V~ii 59 (65)
T cd00565 13 EGATLAELLEEL--GLDP----RGV---AVALNGEIVP-RSEWASTPLQDGDRIEIV 59 (65)
T ss_pred CCCCHHHHHHHc--CCCC----CcE---EEEECCEEcC-HHHcCceecCCCCEEEEE
Confidence 456799899865 2442 111 5678999984 45 789999999874
No 98
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=59.53 E-value=7.3 Score=29.25 Aligned_cols=43 Identities=23% Similarity=0.385 Sum_probs=28.4
Q ss_pred HHHHHHhccCCCCHHHHHHHHHCC--cEEECCEEeccccccccCCCEEeee
Q 022299 73 LDAWISSRIDGISRARVQSSIRSG--LVSINGQVVSKVSHNVKGGDMVNCT 121 (299)
Q Consensus 73 Ldk~L~~~~~~~Sr~~~~~lI~~G--~V~vNGk~v~~~~~~l~~GD~I~v~ 121 (299)
|-++|.+.++.+ ...+..+ ++.||+.-+ ..++.|+.||+|.+.
T Consensus 31 l~~~L~~~~~~~-----~~~~~~~~~~~aVN~~~~-~~~~~l~dgDeVai~ 75 (81)
T PRK11130 31 LRQHLAQKGDRW-----ALALEDGKLLAAVNQTLV-SFDHPLTDGDEVAFF 75 (81)
T ss_pred HHHHHHHhCccH-----HhhhcCCCEEEEECCEEc-CCCCCCCCCCEEEEe
Confidence 444555444332 2333455 477999887 578899999999884
No 99
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=55.12 E-value=15 Score=36.39 Aligned_cols=40 Identities=25% Similarity=0.212 Sum_probs=29.7
Q ss_pred HHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccc
Q 022299 73 LDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNV 112 (299)
Q Consensus 73 Ldk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l 112 (299)
+-..|....-.-||++++++|.+|.|++||.++...+..+
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 3333433323579999999999999999999987665444
No 100
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=53.86 E-value=14 Score=26.17 Aligned_cols=23 Identities=35% Similarity=0.689 Sum_probs=19.4
Q ss_pred cEEECCEEeccccccccCCCEEee
Q 022299 97 LVSINGQVVSKVSHNVKGGDMVNC 120 (299)
Q Consensus 97 ~V~vNGk~v~~~~~~l~~GD~I~v 120 (299)
...|||+.+ ..++.|+.||.|++
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 456999998 69999999999987
No 101
>TIGR01687 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.
Probab=53.40 E-value=13 Score=28.10 Aligned_cols=25 Identities=28% Similarity=0.425 Sum_probs=19.8
Q ss_pred CcEEECCEEeccccc--cccCCCEEeee
Q 022299 96 GLVSINGQVVSKVSH--NVKGGDMVNCT 121 (299)
Q Consensus 96 G~V~vNGk~v~~~~~--~l~~GD~I~v~ 121 (299)
=.|.|||+.+. .+. .|+.||+|.+.
T Consensus 56 ~~v~vN~~~v~-~~~~~~l~dgdev~i~ 82 (88)
T TIGR01687 56 VIILVNGRNVD-WGLGTELKDGDVVAIF 82 (88)
T ss_pred EEEEECCEecC-ccCCCCCCCCCEEEEe
Confidence 35789999984 455 89999999874
No 102
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=52.61 E-value=17 Score=25.78 Aligned_cols=43 Identities=14% Similarity=0.251 Sum_probs=30.8
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccc---cccccCCCEEeee
Q 022299 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKV---SHNVKGGDMVNCT 121 (299)
Q Consensus 69 ~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~---~~~l~~GD~I~v~ 121 (299)
++.+|.++|... . +.. .-.|.+||..+.+. +..|+.||+|++.
T Consensus 14 ~~~tl~~ll~~l-~-~~~--------~~~v~vN~~~v~~~~~~~~~L~~gD~vei~ 59 (65)
T PRK06944 14 DGATVADALAAY-G-ARP--------PFAVAVNGDFVARTQHAARALAAGDRLDLV 59 (65)
T ss_pred CCCcHHHHHHhh-C-CCC--------CeEEEECCEEcCchhcccccCCCCCEEEEE
Confidence 456799999864 2 321 12688999988433 6789999999985
No 103
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=50.95 E-value=40 Score=25.87 Aligned_cols=45 Identities=22% Similarity=0.259 Sum_probs=31.2
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEecc---ccccccCCCEEeee
Q 022299 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (299)
Q Consensus 68 ~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~---~~~~l~~GD~I~v~ 121 (299)
.++..|.++|... .++.+.+ .|-+||..+.+ .+..|+.||.|++.
T Consensus 31 ~~~~tl~~LL~~l--~~~~~~v-------AVevNg~iVpr~~w~~t~L~egD~IEIv 78 (84)
T PRK06083 31 DISSSLAQIIAQL--SLPELGC-------VFAINNQVVPRSEWQSTVLSSGDAISLF 78 (84)
T ss_pred CCCCcHHHHHHHc--CCCCceE-------EEEECCEEeCHHHcCcccCCCCCEEEEE
Confidence 4567899999864 3432221 56799998843 46679999999874
No 104
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=50.48 E-value=17 Score=26.81 Aligned_cols=43 Identities=16% Similarity=0.339 Sum_probs=31.7
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEecc---ccccccCCCEEeee
Q 022299 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (299)
Q Consensus 70 g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~---~~~~l~~GD~I~v~ 121 (299)
+.++.++|++. . ++- +.=.|.+||..+.+ .+..|+.||+|++.
T Consensus 17 ~~tv~dLL~~l-~-~~~-------~~vav~vNg~iVpr~~~~~~~l~~gD~ievv 62 (68)
T COG2104 17 GTTVADLLAQL-G-LNP-------EGVAVAVNGEIVPRSQWADTILKEGDRIEVV 62 (68)
T ss_pred CCcHHHHHHHh-C-CCC-------ceEEEEECCEEccchhhhhccccCCCEEEEE
Confidence 37899999986 3 333 11256789999843 78899999999874
No 105
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=48.74 E-value=20 Score=25.61 Aligned_cols=42 Identities=17% Similarity=0.229 Sum_probs=29.4
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEecc---ccccccCCCEEeee
Q 022299 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (299)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~---~~~~l~~GD~I~v~ 121 (299)
.+|.++|... .+..+. =.|-+|++.+.+ .++.|+.||+|++.
T Consensus 15 ~tl~~Ll~~l--~~~~~~-------vavavN~~iv~~~~~~~~~L~dgD~Ieiv 59 (65)
T PRK06488 15 TTLALLLAEL--DYEGNW-------LATAVNGELVHKEARAQFVLHEGDRIEIL 59 (65)
T ss_pred CcHHHHHHHc--CCCCCe-------EEEEECCEEcCHHHcCccccCCCCEEEEE
Confidence 5788888764 232211 147899999853 37789999999984
No 106
>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=46.96 E-value=23 Score=25.19 Aligned_cols=44 Identities=27% Similarity=0.412 Sum_probs=31.0
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEecc---ccccccCCCEEeee
Q 022299 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (299)
Q Consensus 69 ~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~---~~~~l~~GD~I~v~ 121 (299)
++.+|.++|... . +.. ..-.|.+||+.+.+ .++.|+.||+|++.
T Consensus 12 ~~~tv~~ll~~l-~-~~~-------~~v~v~vN~~iv~~~~~~~~~L~~gD~veii 58 (64)
T TIGR01683 12 DGLTLAALLESL-G-LDP-------RRVAVAVNGEIVPRSEWDDTILKEGDRIEIV 58 (64)
T ss_pred CCCcHHHHHHHc-C-CCC-------CeEEEEECCEEcCHHHcCceecCCCCEEEEE
Confidence 356799999864 3 332 23367799998843 34689999999874
No 107
>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=45.62 E-value=46 Score=32.56 Aligned_cols=40 Identities=23% Similarity=0.249 Sum_probs=33.0
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEecccc
Q 022299 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVS 109 (299)
Q Consensus 70 g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~ 109 (299)
+..+.+++...--..|++.++++|++|.|+|||..+...+
T Consensus 329 ~~~~~~~~~~~~~~~S~~~arr~ik~g~v~vn~~~i~~~~ 368 (377)
T TIGR00234 329 DITLADLLVLSGLFPSKSEARRDIKQGGVYINGEKVTDLE 368 (377)
T ss_pred CcCHHHHHHHcCCCcChHHHHHHHHhCCEEECCEeccCch
Confidence 4788888887644579999999999999999999885433
No 108
>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=45.41 E-value=43 Score=26.08 Aligned_cols=25 Identities=24% Similarity=0.194 Sum_probs=20.1
Q ss_pred cEEECCEEec---cccccccCCCEEeee
Q 022299 97 LVSINGQVVS---KVSHNVKGGDMVNCT 121 (299)
Q Consensus 97 ~V~vNGk~v~---~~~~~l~~GD~I~v~ 121 (299)
.|.|||..+. ..++.|+.||+|.+.
T Consensus 61 ~VlvN~~di~~l~g~~t~L~dgD~v~i~ 88 (94)
T cd01764 61 IVLINDTDWELLGEEDYILEDGDHVVFI 88 (94)
T ss_pred EEEECCccccccCCcccCCCCcCEEEEE
Confidence 6779998763 357899999999874
No 109
>PRK07440 hypothetical protein; Provisional
Probab=44.85 E-value=26 Score=25.71 Aligned_cols=45 Identities=16% Similarity=0.236 Sum_probs=31.3
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEecc---ccccccCCCEEeee
Q 022299 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (299)
Q Consensus 68 ~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~---~~~~l~~GD~I~v~ 121 (299)
.++.+|.++|.+. . ++.+. =.|-+||..+.+ .++.|+.||.|++.
T Consensus 17 ~~~~tl~~lL~~l-~-~~~~~-------vav~~N~~iv~r~~w~~~~L~~gD~IEIv 64 (70)
T PRK07440 17 SSGTSLPDLLQQL-G-FNPRL-------VAVEYNGEILHRQFWEQTQVQPGDRLEIV 64 (70)
T ss_pred CCCCCHHHHHHHc-C-CCCCe-------EEEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 3567899999864 2 32211 156789998832 57789999999874
No 110
>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=42.06 E-value=24 Score=24.85 Aligned_cols=26 Identities=23% Similarity=0.355 Sum_probs=17.9
Q ss_pred CCcEEECCEEecc-ccccccCCCEEee
Q 022299 95 SGLVSINGQVVSK-VSHNVKGGDMVNC 120 (299)
Q Consensus 95 ~G~V~vNGk~v~~-~~~~l~~GD~I~v 120 (299)
...++|||+++.. ....|+.||+|.+
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 4678899998842 2567889999875
No 111
>KOG3301 consensus Ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=41.37 E-value=28 Score=30.26 Aligned_cols=46 Identities=20% Similarity=0.272 Sum_probs=34.8
Q ss_pred cchHHHHHHhcc-------C-CCCHHHHHHHHHCCcEEECCEEeccccccccCC
Q 022299 70 KLRLDAWISSRI-------D-GISRARVQSSIRSGLVSINGQVVSKVSHNVKGG 115 (299)
Q Consensus 70 g~RLdk~L~~~~-------~-~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~G 115 (299)
+.+|.+||...+ + ..|-..++.+|.++.|.|+++.|+-+++.|+..
T Consensus 88 ~l~ie~fLErRLqt~vFklGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrld 141 (183)
T KOG3301|consen 88 ALTVEDFLERRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRLD 141 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHhcCccEEecCeEeeccceeEeec
Confidence 355666665443 1 347778999999999999999998888888753
No 112
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=37.51 E-value=41 Score=24.10 Aligned_cols=44 Identities=16% Similarity=0.269 Sum_probs=29.5
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEecc---ccccccCCCEEeee
Q 022299 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (299)
Q Consensus 69 ~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~---~~~~l~~GD~I~v~ 121 (299)
++.+|.++|... . ..... =.|-+|++.+.+ .++.|+.||.|++.
T Consensus 14 ~~~tl~~ll~~l-~-~~~~~-------vaVavN~~iv~r~~w~~~~L~~gD~Ieii 60 (66)
T PRK08053 14 AGQTVHELLEQL-N-QLQPG-------AALAINQQIIPREQWAQHIVQDGDQILLF 60 (66)
T ss_pred CCCCHHHHHHHc-C-CCCCc-------EEEEECCEEeChHHcCccccCCCCEEEEE
Confidence 456788888764 3 22211 146789998842 45679999999874
No 113
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=36.65 E-value=55 Score=32.48 Aligned_cols=40 Identities=18% Similarity=0.106 Sum_probs=33.3
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEecc
Q 022299 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK 107 (299)
Q Consensus 68 ~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~ 107 (299)
+.++.+.+.++++-..-|+..+.++|.+|.|++|++++..
T Consensus 396 ~~~~s~~~l~~ka~~~~s~~~a~r~i~qG~vslnh~~v~~ 435 (467)
T KOG2623|consen 396 EPGVSILDLLRKASRFPSGKEARRMIQQGGVSLNHEKVRD 435 (467)
T ss_pred CCCCcHHHHHHHhhcCCCcHHHHHHHHccceeecCccccC
Confidence 3688889999887444577799999999999999999853
No 114
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=36.33 E-value=36 Score=24.37 Aligned_cols=23 Identities=35% Similarity=0.378 Sum_probs=16.0
Q ss_pred cEEECCEEeccccccccCCCEEee
Q 022299 97 LVSINGQVVSKVSHNVKGGDMVNC 120 (299)
Q Consensus 97 ~V~vNGk~v~~~~~~l~~GD~I~v 120 (299)
-+-+||-++ +.+..|+.||.|.+
T Consensus 31 I~I~NGF~~-~~d~~L~e~D~v~~ 53 (57)
T PF14453_consen 31 IVILNGFPT-KEDIELKEGDEVFL 53 (57)
T ss_pred EEEEcCccc-CCccccCCCCEEEE
Confidence 344677776 57777888887765
No 115
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=33.32 E-value=44 Score=24.23 Aligned_cols=42 Identities=17% Similarity=0.270 Sum_probs=28.2
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccc---cccccCCCEEeee
Q 022299 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKV---SHNVKGGDMVNCT 121 (299)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~---~~~l~~GD~I~v~ 121 (299)
.+|.++|... . +..+.+ .|-+||..+.+. ++.|+.||.|++.
T Consensus 17 ~tv~~lL~~l-~-~~~~~v-------av~vN~~iv~r~~w~~~~L~~gD~iEIv 61 (67)
T PRK07696 17 KTVAELLTHL-E-LDNKIV-------VVERNKDILQKDDHTDTSVFDGDQIEIV 61 (67)
T ss_pred ccHHHHHHHc-C-CCCCeE-------EEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 4688888764 2 322111 577999988432 4779999999874
No 116
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.68 E-value=57 Score=26.16 Aligned_cols=37 Identities=19% Similarity=0.232 Sum_probs=29.5
Q ss_pred HHHHHHHHHCCcEEECCEEeccccccccCCCEEeeec
Q 022299 86 RARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 86 r~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
+...-++|.+|.=+|.++....--..+++||.|.+..
T Consensus 8 ~eeylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~~ 44 (111)
T COG4043 8 REEYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFNG 44 (111)
T ss_pred HHHHHHHHHcccceEEEEecCHhhcCCCCCCEEEEcC
Confidence 5566789999999998877654556799999998864
No 117
>COG3215 PilZ Tfp pilus assembly protein PilZ [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=29.88 E-value=92 Score=25.12 Aligned_cols=78 Identities=13% Similarity=0.045 Sum_probs=46.0
Q ss_pred HHHHCCcEEECCEEeccccccccCCCEEeeeccccCCcccccCCCCeeEEEeCCcEEEEeCCCCceeecCCCCCCCcHHH
Q 022299 91 SSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVN 170 (299)
Q Consensus 91 ~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~~~~~~~~~~~~~~~~IlyeD~~llvvnKPaGl~v~~~~~~~~~tl~~ 170 (299)
-.+++|.++|-- +.....||+|.+...-...++..+ .+=+|+|-..-= .-|||+|+-+|-.++....++-+
T Consensus 28 pfl~nGglFVpT------nk~y~iG~evfl~l~lld~pekl~--vagkVaWitP~g-t~sr~~GiGv~f~d~e~g~~vr~ 98 (117)
T COG3215 28 PFLENGGLFVPT------NKVYSIGEEVFLLLELLDFPEKLP--VAGKVAWITPVG-TQSRPAGIGVQFTDGENGLKVRN 98 (117)
T ss_pred HHHhcCcEEccc------CCccccchhhhhhhhhcCchhhcc--ccceEEEEccCC-CCCCCCceeeeccCCCchhhHHH
Confidence 358899998743 334667888876543222221111 112455544321 22999999999877666556767
Q ss_pred HHHhhcC
Q 022299 171 GILHHCS 177 (299)
Q Consensus 171 ~l~~~~~ 177 (299)
.+..++.
T Consensus 99 ~IE~~Lg 105 (117)
T COG3215 99 QIETLLG 105 (117)
T ss_pred HHHHHHH
Confidence 6665543
No 118
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=29.60 E-value=74 Score=26.45 Aligned_cols=24 Identities=33% Similarity=0.565 Sum_probs=18.0
Q ss_pred CCcEEECCEEeccccccccCCCEEeeec
Q 022299 95 SGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 95 ~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
.|.|.+||-. -..+++||.|.+--
T Consensus 66 Sg~I~lNGAA----Ar~~~~GD~vII~a 89 (126)
T PRK05449 66 SGVICLNGAA----ARLVQVGDLVIIAA 89 (126)
T ss_pred CCEEEeCCHH----HhcCCCCCEEEEEE
Confidence 4778999944 45689999988743
No 119
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=28.91 E-value=23 Score=27.32 Aligned_cols=29 Identities=28% Similarity=0.384 Sum_probs=17.7
Q ss_pred HCCcEEECCEEeccccccccCCCEEeeecc
Q 022299 94 RSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (299)
Q Consensus 94 ~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~ 123 (299)
....|=|=|+.+ +.++.|+.||+|+|+.+
T Consensus 45 ~~~~vGIfGk~~-~~d~~L~~GDRVEIYRP 73 (84)
T PF03658_consen 45 EKNKVGIFGKLV-KLDTVLRDGDRVEIYRP 73 (84)
T ss_dssp TTSEEEEEE-S---TT-B--TT-EEEEE-S
T ss_pred ccceeeeeeeEc-CCCCcCCCCCEEEEecc
Confidence 566777889988 69999999999999874
No 120
>cd01666 TGS_DRG_C TGS_DRG_C: DRG (developmentally regulated GTP-binding protein) represents a family of GTP-binding proteins that includes two members, DRG1 and DRG2. DRG1 and DRG2 have a C-terminal TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) with a predominantly beta-sheet structure. The function of TGS is unknown but its presence in two types of regulatory proteins (the DRG GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=27.35 E-value=44 Score=25.06 Aligned_cols=47 Identities=17% Similarity=0.151 Sum_probs=30.4
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHC---C-cEEECCEEeccccccccCCCEEeee
Q 022299 70 KLRLDAWISSRIDGISRARVQSSIRS---G-LVSINGQVVSKVSHNVKGGDMVNCT 121 (299)
Q Consensus 70 g~RLdk~L~~~~~~~Sr~~~~~lI~~---G-~V~vNGk~v~~~~~~l~~GD~I~v~ 121 (299)
|-++.+|.... .++......-. | .+.++|+++ ..++.|+-||+|++.
T Consensus 24 GaTV~D~a~~i----H~di~~~f~~A~v~g~s~~~~gq~V-gl~~~L~d~DvVeI~ 74 (75)
T cd01666 24 GSTVEDVCNKI----HKDLVKQFKYALVWGSSVKHSPQRV-GLDHVLEDEDVVQIV 74 (75)
T ss_pred CCCHHHHHHHH----HHHHHHhCCeeEEeccCCcCCCeEC-CCCCEecCCCEEEEe
Confidence 56677777643 23333332211 1 334699999 689999999999874
No 121
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=26.87 E-value=89 Score=25.97 Aligned_cols=24 Identities=29% Similarity=0.457 Sum_probs=18.0
Q ss_pred CCcEEECCEEeccccccccCCCEEeeec
Q 022299 95 SGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 95 ~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
.|.|.+||-. -..+++||.|.+--
T Consensus 66 Sg~I~lNGAA----Arl~~~GD~VII~s 89 (126)
T TIGR00223 66 SRIICVNGAA----ARCVSVGDIVIIAS 89 (126)
T ss_pred CCEEEeCCHH----HhcCCCCCEEEEEE
Confidence 4789999944 35689999988743
No 122
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=26.60 E-value=99 Score=23.59 Aligned_cols=47 Identities=13% Similarity=0.232 Sum_probs=28.8
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeeccc
Q 022299 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (299)
Q Consensus 69 ~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~~ 124 (299)
.|.+|...+.+. ++|.+.+.+++.... +++.. .+|+|||.|.+...+
T Consensus 9 ~GDtLs~iF~~~--gls~~dl~~v~~~~~---~~k~L----~~L~pGq~l~f~~d~ 55 (85)
T PF04225_consen 9 SGDTLSTIFRRA--GLSASDLYAVLEADG---EAKPL----TRLKPGQTLEFQLDE 55 (85)
T ss_dssp TT--HHHHHHHT--T--HHHHHHHHHHGG---GT--G----GG--TT-EEEEEE-T
T ss_pred CCCcHHHHHHHc--CCCHHHHHHHHhccC---ccchH----hhCCCCCEEEEEECC
Confidence 455699999876 799999999998753 33333 469999999997753
No 123
>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=26.34 E-value=86 Score=21.10 Aligned_cols=44 Identities=23% Similarity=0.284 Sum_probs=27.6
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEee
Q 022299 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNC 120 (299)
Q Consensus 69 ~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v 120 (299)
.+..+.+++......+++ ..-.+.+||+.+ ..+..+..||.|++
T Consensus 15 ~~~t~~~~~~~~~~~~~~-------~~va~~vng~~v-dl~~~l~~~~~ve~ 58 (60)
T cd01668 15 AGATVLDFAYAIHTEIGN-------RCVGAKVNGKLV-PLSTVLKDGDIVEI 58 (60)
T ss_pred CCCCHHHHHHHHChHhhh-------heEEEEECCEEC-CCCCCCCCCCEEEE
Confidence 455566666543211111 112466999998 57888999998875
No 124
>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=25.05 E-value=94 Score=25.29 Aligned_cols=24 Identities=29% Similarity=0.416 Sum_probs=18.2
Q ss_pred CCcEEECCEEeccccccccCCCEEeeec
Q 022299 95 SGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (299)
Q Consensus 95 ~G~V~vNGk~v~~~~~~l~~GD~I~v~~ 122 (299)
.|.|.+||-. -..+++||.|.+--
T Consensus 65 Sg~I~lNGAA----Ar~~~~GD~vII~s 88 (111)
T cd06919 65 SGVICLNGAA----ARLGQPGDRVIIMA 88 (111)
T ss_pred CCEEEeCCHH----HhcCCCCCEEEEEE
Confidence 4788999944 45689999988743
No 125
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=24.74 E-value=58 Score=23.86 Aligned_cols=66 Identities=15% Similarity=0.215 Sum_probs=44.9
Q ss_pred CCCceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeecc
Q 022299 54 NYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (299)
Q Consensus 54 ~~~~~~~~~~v~~~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~ 123 (299)
+..|-++...++..+.-..|..-|.... +++-+. ++++-.|.+.-|++.+ .++.|..|+.|.+...
T Consensus 4 ~l~g~~~~l~v~~~~TV~~lK~~i~~~~-gip~~~-q~L~~~G~~L~d~~tL--~~~~i~~g~~l~v~~~ 69 (76)
T cd01800 4 KLNGQMLNFTLQLSDPVSVLKVKIHEET-GMPAGK-QKLQYEGIFIKDSNSL--AYYNLANGTIIHLQLK 69 (76)
T ss_pred ccCCeEEEEEECCCCcHHHHHHHHHHHH-CCCHHH-EEEEECCEEcCCCCcH--HHcCCCCCCEEEEEEe
Confidence 3456678888877666666777776653 465543 6777777766666554 4778999999987653
No 126
>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=24.27 E-value=1e+02 Score=20.03 Aligned_cols=22 Identities=36% Similarity=0.599 Sum_probs=18.1
Q ss_pred EEECCEEeccccccccCCCEEee
Q 022299 98 VSINGQVVSKVSHNVKGGDMVNC 120 (299)
Q Consensus 98 V~vNGk~v~~~~~~l~~GD~I~v 120 (299)
+.+||+.+ ..++.|..||.|++
T Consensus 37 ~~vn~~~~-~l~~~l~~~~~i~~ 58 (60)
T cd01616 37 ALVNGQLV-DLSYTLQDGDTVSI 58 (60)
T ss_pred EEECCEEC-CCCcCcCCCCEEEE
Confidence 45899988 58888999998875
No 127
>PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1PYU_C 1AW8_A 1PYQ_B 3TM7_C 1PT1_A 1PQH_A 1PPY_B 1PT0_B 1PQF_A 1PQE_A ....
Probab=24.00 E-value=59 Score=26.63 Aligned_cols=23 Identities=35% Similarity=0.518 Sum_probs=14.8
Q ss_pred CCcEEECCEEeccccccccCCCEEeee
Q 022299 95 SGLVSINGQVVSKVSHNVKGGDMVNCT 121 (299)
Q Consensus 95 ~G~V~vNGk~v~~~~~~l~~GD~I~v~ 121 (299)
.|.|.+||- +...+++||.|.+-
T Consensus 66 Sg~I~lNGa----AArl~~~GD~vII~ 88 (116)
T PF02261_consen 66 SGVICLNGA----AARLVQVGDRVIIM 88 (116)
T ss_dssp TT-EEEEGG----GGGCS-TT-EEEEE
T ss_pred CcEEEECCH----HHhccCCCCEEEEE
Confidence 378888883 45678999998874
No 128
>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=23.65 E-value=70 Score=20.40 Aligned_cols=20 Identities=25% Similarity=0.426 Sum_probs=16.4
Q ss_pred hccCCCCHHHHHHHHHCCcEE
Q 022299 79 SRIDGISRARVQSSIRSGLVS 99 (299)
Q Consensus 79 ~~~~~~Sr~~~~~lI~~G~V~ 99 (299)
+.+ ++|++.+++++++|.+.
T Consensus 9 ~~l-gis~~ti~~~~~~g~i~ 28 (49)
T TIGR01764 9 EYL-GVSKDTVYRLIHEGELP 28 (49)
T ss_pred HHH-CCCHHHHHHHHHcCCCC
Confidence 444 69999999999999754
No 129
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=23.43 E-value=85 Score=31.04 Aligned_cols=46 Identities=22% Similarity=0.370 Sum_probs=34.0
Q ss_pred CccccccCCCCCceEEEEEcCHHHHHHHHHHHhcCccceEEEEEEecccC
Q 022299 211 RPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPS 260 (299)
Q Consensus 211 ~~~~VhRLDr~TSGLlL~Ak~~~a~~~l~~~f~~~~v~K~YlAlV~G~~~ 260 (299)
..+..+-||-+.+|+++..-+.......+- ....|+|.+++...+.
T Consensus 96 k~Gh~gTlDP~vtg~l~v~~~~~tr~~~s~----~s~gk~yvg~~~lt~~ 141 (395)
T KOG2529|consen 96 KTGHSGTLDPEVTGCLIVCIDRATRLLKSQ----QSAGKEYVGIGKLTPE 141 (395)
T ss_pred HhCCCCCCCccccceEEEEeecccccccch----hccCcEEEEEEecCcc
Confidence 345588899999999999988644333322 4579999999887754
No 130
>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=22.32 E-value=39 Score=24.38 Aligned_cols=16 Identities=25% Similarity=0.401 Sum_probs=11.3
Q ss_pred CCcEEEEeCCCCceee
Q 022299 143 DDNVLVVNKPAHMVVH 158 (299)
Q Consensus 143 D~~llvvnKPaGl~v~ 158 (299)
...+|.+|||+|--+|
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 3579999999996655
No 131
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=20.73 E-value=94 Score=22.47 Aligned_cols=62 Identities=21% Similarity=0.237 Sum_probs=40.1
Q ss_pred CceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEee
Q 022299 56 AGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNC 120 (299)
Q Consensus 56 ~~~~~~~~v~~~~~g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v 120 (299)
.|-++...|.....=..|...++... +++-.. ++++-+|++.-|+... -.++.++.||.|.+
T Consensus 8 ~g~~~~l~v~~~~TV~~lK~~I~~~~-gip~~~-q~Li~~Gk~L~D~~~~-L~~~gi~~~~~l~l 69 (71)
T cd01796 8 SETTFSLDVDPDLELENFKALCEAES-GIPASQ-QQLIYNGRELVDNKRL-LALYGVKDGDLVVL 69 (71)
T ss_pred CCCEEEEEECCcCCHHHHHHHHHHHh-CCCHHH-eEEEECCeEccCCccc-HHHcCCCCCCEEEE
Confidence 34456666666555556777787764 566543 6777777777666332 14677889998876
No 132
>KOG4837 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.11 E-value=82 Score=28.55 Aligned_cols=53 Identities=23% Similarity=0.297 Sum_probs=45.5
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHCCcEEECCEEeccccccccCCCEEeeecc
Q 022299 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (299)
Q Consensus 70 g~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~vNGk~v~~~~~~l~~GD~I~v~~~ 123 (299)
..|.|-+|..-+ ++.|..+.-+.-++.+++|+....+.+.+|+.||.+-+.+.
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 457787787664 68999999999999999999988889999999999887654
Done!