Query 022339
Match_columns 298
No_of_seqs 188 out of 1775
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 02:47:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022339.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022339hhsearch_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 3.4E-41 7.4E-46 314.2 21.1 195 61-286 3-198 (289)
2 PRK11180 rluD 23S rRNA pseudou 100.0 1E-36 2.2E-41 288.7 23.9 198 56-281 3-200 (325)
3 TIGR00005 rluA_subfam pseudour 100.0 2.9E-36 6.2E-41 282.0 22.0 183 67-276 2-184 (299)
4 PRK11025 23S rRNA pseudouridyl 100.0 2.2E-35 4.7E-40 278.7 22.0 184 60-275 9-200 (317)
5 PRK10475 23S rRNA pseudouridin 100.0 1.9E-29 4E-34 235.3 16.7 178 68-297 4-194 (290)
6 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 4E-28 8.6E-33 221.8 15.1 142 97-273 3-145 (246)
7 PRK10700 23S rRNA pseudouridyl 100.0 8E-28 1.7E-32 224.5 17.4 179 71-297 3-201 (289)
8 PRK10839 16S rRNA pseudouridyl 100.0 3.3E-28 7.2E-33 220.1 12.5 142 71-261 1-142 (232)
9 COG1187 RsuA 16S rRNA uridine- 99.9 5.5E-26 1.2E-30 206.6 13.9 179 70-297 2-201 (248)
10 KOG1919 RNA pseudouridylate sy 99.9 1E-24 2.2E-29 208.3 17.7 192 59-286 32-225 (371)
11 PRK10158 23S rRNA/tRNA pseudou 99.9 1.2E-24 2.7E-29 195.5 14.5 109 136-277 13-122 (219)
12 cd02557 PseudoU_synth_ScRIB2 P 99.9 1E-24 2.2E-29 195.3 13.5 108 135-273 14-121 (213)
13 TIGR01621 RluA-like pseudourid 99.9 2.1E-24 4.6E-29 193.7 14.3 107 137-276 2-108 (217)
14 cd02563 PseudoU_synth_TruC tRN 99.9 1E-23 2.2E-28 189.9 14.5 107 137-276 1-109 (223)
15 PRK11112 tRNA pseudouridine sy 99.9 2.6E-23 5.7E-28 191.1 13.5 104 137-273 2-107 (257)
16 PF00849 PseudoU_synth_2: RNA 99.8 3.5E-21 7.6E-26 164.0 10.0 101 145-272 1-101 (164)
17 cd02550 PseudoU_synth_Rsu_Rlu_ 99.8 5E-20 1.1E-24 156.7 11.4 90 146-270 1-90 (154)
18 cd02869 PseudoU_synth_RluCD_li 99.8 9.3E-19 2E-23 151.7 13.2 100 146-272 1-100 (185)
19 cd02556 PseudoU_synth_RluB Pse 99.8 6.4E-19 1.4E-23 152.1 11.1 83 145-261 1-83 (167)
20 cd02553 PseudoU_synth_RsuA Pse 99.8 1.2E-18 2.6E-23 150.5 9.3 83 146-262 2-84 (167)
21 cd02870 PseudoU_synth_RsuA_lik 99.8 7.9E-19 1.7E-23 148.1 7.5 81 146-261 1-81 (146)
22 cd02554 PseudoU_synth_RluF Pse 99.7 1E-16 2.2E-21 138.3 10.2 113 146-297 2-127 (164)
23 cd02555 PSSA_1 PSSA_1: Pseudou 99.7 8.3E-17 1.8E-21 140.4 9.1 51 210-262 45-95 (177)
24 cd02566 PseudoU_synth_RluE Pse 99.7 7.1E-17 1.5E-21 139.5 7.7 79 146-261 1-80 (168)
25 PRK11394 23S rRNA pseudouridin 99.7 1.2E-16 2.7E-21 143.3 7.9 82 143-261 38-119 (217)
26 cd00165 S4 S4/Hsp/ tRNA synthe 99.3 1.2E-11 2.6E-16 88.9 8.0 70 71-150 1-70 (70)
27 TIGR00093 pseudouridine syntha 99.2 1.8E-11 3.9E-16 101.2 5.8 45 215-261 1-45 (128)
28 cd02868 PseudoU_synth_hTruB2_l 99.1 8.6E-11 1.9E-15 106.2 7.6 75 146-256 2-76 (226)
29 PF01479 S4: S4 domain; Inter 99.0 5.2E-10 1.1E-14 76.7 5.9 48 71-118 1-48 (48)
30 TIGR02988 YaaA_near_RecF S4 do 99.0 8.8E-10 1.9E-14 79.1 6.3 52 67-120 5-58 (59)
31 smart00363 S4 S4 RNA-binding d 98.5 3.4E-07 7.4E-12 63.5 6.3 52 71-122 1-52 (60)
32 COG1188 Ribosome-associated he 98.5 1.8E-07 3.8E-12 73.7 5.1 55 68-123 6-60 (100)
33 PLN00051 RNA-binding S4 domain 98.3 1.6E-06 3.5E-11 80.4 6.9 59 64-123 185-243 (267)
34 TIGR03069 PS_II_S4 photosystem 98.2 2.7E-06 5.9E-11 78.5 6.8 59 64-123 177-235 (257)
35 PRK10348 ribosome-associated h 98.2 3.4E-06 7.3E-11 70.3 6.6 54 69-123 7-60 (133)
36 TIGR01017 rpsD_bact ribosomal 98.2 3.2E-06 6.9E-11 75.3 6.5 54 70-123 89-142 (200)
37 CHL00113 rps4 ribosomal protei 98.2 3.8E-06 8.3E-11 74.8 6.3 54 70-123 88-141 (201)
38 TIGR00478 tly hemolysin TlyA f 98.1 7.5E-06 1.6E-10 74.3 6.1 52 72-123 1-52 (228)
39 PRK05327 rpsD 30S ribosomal pr 98.0 1E-05 2.3E-10 72.2 6.4 54 70-123 92-145 (203)
40 COG2302 Uncharacterized conser 97.8 2.4E-05 5.2E-10 71.2 4.6 56 67-123 177-232 (257)
41 COG0522 RpsD Ribosomal protein 97.8 4.1E-05 8.9E-10 68.4 5.4 54 71-124 94-147 (205)
42 cd02572 PseudoU_synth_hDyskeri 97.7 0.00014 2.9E-09 64.0 7.6 70 144-256 2-71 (182)
43 PRK11507 ribosome-associated p 97.7 0.00014 3.1E-09 53.9 6.3 57 66-122 7-63 (70)
44 COG1189 Predicted rRNA methyla 97.6 0.00014 3.1E-09 66.0 6.2 53 70-122 2-54 (245)
45 cd00506 PseudoU_synth_TruB_lik 97.5 0.00044 9.6E-09 62.1 7.7 68 146-256 2-69 (210)
46 PRK00989 truB tRNA pseudouridi 97.4 0.00052 1.1E-08 62.3 7.0 71 144-256 9-79 (230)
47 TIGR00431 TruB tRNA pseudourid 97.3 0.00077 1.7E-08 60.4 7.7 69 145-256 3-71 (209)
48 PRK04099 truB tRNA pseudouridi 97.3 0.00068 1.5E-08 63.1 7.4 72 144-258 2-74 (273)
49 PRK00020 truB tRNA pseudouridi 97.3 0.0011 2.3E-08 60.8 8.0 70 144-256 10-79 (244)
50 PF13275 S4_2: S4 domain; PDB: 97.3 5.2E-05 1.1E-09 55.6 -0.4 56 67-122 4-59 (65)
51 PRK00130 truB tRNA pseudouridi 97.2 0.0015 3.1E-08 61.5 8.1 69 145-256 3-71 (290)
52 PRK04051 rps4p 30S ribosomal p 97.1 0.0009 2E-08 58.5 5.9 52 70-121 102-155 (177)
53 PRK14124 tRNA pseudouridine sy 97.1 0.0018 3.8E-08 61.4 8.2 70 144-256 3-72 (308)
54 PRK03287 truB tRNA pseudouridi 97.1 0.0016 3.4E-08 61.4 7.7 71 143-256 8-78 (298)
55 PRK02484 truB tRNA pseudouridi 97.1 0.0015 3.2E-08 61.5 7.4 69 145-256 4-72 (294)
56 PRK14123 tRNA pseudouridine sy 97.1 0.0015 3.1E-08 61.9 7.3 70 144-256 3-72 (305)
57 PRK02755 truB tRNA pseudouridi 97.1 0.0015 3.2E-08 61.6 7.2 71 144-258 3-74 (295)
58 PRK05389 truB tRNA pseudouridi 97.1 0.002 4.3E-08 61.0 7.8 72 144-258 13-85 (305)
59 PRK02193 truB tRNA pseudouridi 97.0 0.002 4.3E-08 60.2 7.5 68 146-256 2-69 (279)
60 cd02573 PseudoU_synth_EcTruB P 97.0 0.0021 4.6E-08 60.0 7.7 70 146-258 2-72 (277)
61 PRK04270 H/ACA RNA-protein com 97.0 0.0022 4.7E-08 60.7 7.3 71 143-256 21-91 (300)
62 PRK05033 truB tRNA pseudouridi 97.0 0.0028 6E-08 60.1 8.0 70 144-256 10-79 (312)
63 PRK14846 truB tRNA pseudouridi 97.0 0.0029 6.2E-08 60.5 8.0 70 144-256 3-72 (345)
64 PRK01550 truB tRNA pseudouridi 97.0 0.0026 5.6E-08 60.2 7.6 69 145-256 3-71 (304)
65 PRK01528 truB tRNA pseudouridi 96.9 0.0026 5.7E-08 59.8 7.5 70 144-256 3-72 (292)
66 COG2501 S4-like RNA binding pr 96.9 0.0026 5.6E-08 47.5 5.8 57 66-122 7-63 (73)
67 PRK01851 truB tRNA pseudouridi 96.9 0.0034 7.4E-08 59.3 7.9 70 144-256 16-85 (303)
68 PRK14122 tRNA pseudouridine sy 96.8 0.0038 8.1E-08 59.2 7.6 69 145-256 2-70 (312)
69 TIGR00425 CBF5 rRNA pseudourid 96.6 0.0058 1.3E-07 58.3 6.8 71 143-256 33-103 (322)
70 PRK04642 truB tRNA pseudouridi 96.5 0.0092 2E-07 56.3 7.6 70 144-256 10-79 (300)
71 TIGR01018 rpsD_arch ribosomal 96.5 0.0048 1E-07 53.2 5.1 51 71-121 104-156 (162)
72 cd02867 PseudoU_synth_TruB_4 P 96.4 0.0089 1.9E-07 56.7 7.1 43 210-256 56-98 (312)
73 PLN00189 40S ribosomal protein 96.4 0.0021 4.6E-08 56.8 2.7 53 72-124 110-162 (194)
74 COG0130 TruB Pseudouridine syn 96.1 0.015 3.2E-07 54.2 6.8 72 145-259 16-88 (271)
75 PRK04313 30S ribosomal protein 96.0 0.024 5.2E-07 51.7 7.2 74 68-151 35-109 (237)
76 PTZ00155 40S ribosomal protein 95.8 0.0098 2.1E-07 52.2 3.7 52 71-122 107-158 (181)
77 PLN00036 40S ribosomal protein 95.7 0.035 7.7E-07 51.3 7.2 74 68-151 39-113 (261)
78 PTZ00223 40S ribosomal protein 95.6 0.039 8.4E-07 51.3 7.1 74 68-151 36-110 (273)
79 PTZ00118 40S ribosomal protein 95.6 0.042 9.1E-07 50.8 7.2 73 68-150 39-112 (262)
80 COG1471 RPS4A Ribosomal protei 92.7 0.25 5.4E-06 44.8 5.6 71 72-152 42-113 (241)
81 PRK01777 hypothetical protein; 91.1 0.24 5.2E-06 39.0 3.2 54 67-123 23-76 (95)
82 PRK13354 tyrosyl-tRNA syntheta 89.7 0.61 1.3E-05 46.0 5.5 47 70-116 342-388 (410)
83 PF14451 Ub-Mut7C: Mut7-C ubiq 89.5 0.33 7.2E-06 37.1 2.7 47 67-122 29-75 (81)
84 COG4332 Uncharacterized protei 88.4 0.82 1.8E-05 40.0 4.7 64 58-123 127-190 (203)
85 PRK05912 tyrosyl-tRNA syntheta 88.2 1.1 2.4E-05 44.1 6.2 45 70-114 342-386 (408)
86 cd01291 PseudoU_synth PseudoU_ 87.6 0.98 2.1E-05 34.3 4.3 28 210-256 24-51 (87)
87 PF06353 DUF1062: Protein of u 85.7 1.2 2.6E-05 37.6 4.2 36 66-102 98-133 (142)
88 PF01509 TruB_N: TruB family p 85.2 1.1 2.4E-05 38.1 3.8 43 210-256 7-49 (149)
89 PRK08364 sulfur carrier protei 84.4 3.5 7.6E-05 30.2 5.7 45 68-122 21-65 (70)
90 cd00754 MoaD Ubiquitin domain 82.2 4 8.7E-05 30.0 5.4 51 70-122 25-75 (80)
91 PLN02799 Molybdopterin synthas 70.2 11 0.00023 28.1 4.9 51 69-122 27-77 (82)
92 PF02597 ThiS: ThiS family; I 70.1 4.9 0.00011 29.2 2.9 52 68-122 19-72 (77)
93 PRK06437 hypothetical protein; 69.9 4.9 0.00011 29.3 2.8 45 68-122 18-62 (67)
94 PRK05659 sulfur carrier protei 69.0 5.4 0.00012 28.5 2.9 46 68-122 13-61 (66)
95 cd00565 ThiS ThiaminS ubiquiti 65.2 6.1 0.00013 28.3 2.5 44 69-122 13-60 (65)
96 TIGR01682 moaD molybdopterin c 65.1 16 0.00034 27.1 4.8 25 97-122 51-75 (80)
97 PRK11130 moaD molybdopterin sy 63.0 18 0.00039 27.0 4.8 45 72-122 30-76 (81)
98 COG0162 TyrS Tyrosyl-tRNA synt 62.0 9.6 0.00021 37.6 3.9 40 73-112 338-377 (401)
99 PRK06083 sulfur carrier protei 61.7 20 0.00044 27.4 4.9 57 56-121 15-78 (84)
100 KOG3301 Ribosomal protein S4 [ 61.6 8.4 0.00018 33.3 3.0 33 83-115 109-141 (183)
101 COG2104 ThiS Sulfur transfer p 59.0 10 0.00022 27.9 2.7 44 69-121 16-62 (68)
102 PRK06944 sulfur carrier protei 57.3 12 0.00027 26.4 2.9 44 69-122 14-60 (65)
103 PRK06488 sulfur carrier protei 56.3 12 0.00027 26.6 2.8 43 71-122 15-60 (65)
104 PF02824 TGS: TGS domain; Int 55.7 12 0.00026 26.5 2.6 23 97-120 36-58 (60)
105 TIGR01683 thiS thiamine biosyn 53.8 15 0.00033 26.1 2.9 45 69-122 12-59 (64)
106 TIGR01687 moaD_arch MoaD famil 53.7 24 0.00052 26.5 4.2 26 96-122 56-83 (88)
107 KOG2559 Predicted pseudouridin 53.2 7.8 0.00017 35.8 1.5 23 210-232 89-111 (318)
108 PRK07440 hypothetical protein; 52.3 17 0.00036 26.7 3.0 45 68-121 17-64 (70)
109 TIGR00234 tyrS tyrosyl-tRNA sy 50.9 33 0.00073 33.5 5.7 41 70-110 329-369 (377)
110 PF00498 FHA: FHA domain; Int 49.5 15 0.00033 25.9 2.3 26 95-120 41-67 (68)
111 PRK08053 sulfur carrier protei 44.5 28 0.0006 25.0 3.1 44 69-121 14-60 (66)
112 KOG2623 Tyrosyl-tRNA synthetas 43.7 36 0.00077 33.7 4.5 40 68-107 396-435 (467)
113 COG4043 Preprotein translocase 42.9 28 0.0006 27.8 3.0 38 85-122 7-44 (111)
114 PRK07696 sulfur carrier protei 41.8 26 0.00057 25.4 2.6 42 71-121 17-61 (67)
115 PF03658 Ub-RnfH: RnfH family 38.5 12 0.00026 28.8 0.4 30 93-123 44-73 (84)
116 cd01666 TGS_DRG_C TGS_DRG_C: 32.7 31 0.00066 25.8 1.7 47 70-121 24-74 (75)
117 PF04225 OapA: Opacity-associa 32.5 64 0.0014 24.6 3.5 47 69-124 9-55 (85)
118 PF14453 ThiS-like: ThiS-like 31.8 45 0.00098 23.8 2.4 22 98-120 32-53 (57)
119 cd01764 Urm1 Urm1-like ubuitin 31.8 42 0.00091 26.1 2.5 26 97-122 61-89 (94)
120 KOG4837 Uncharacterized conser 31.6 37 0.0008 30.6 2.3 55 68-123 137-191 (248)
121 cd01668 TGS_RelA_SpoT TGS_RelA 28.9 70 0.0015 21.5 3.0 23 97-120 36-58 (60)
122 TIGR02194 GlrX_NrdH Glutaredox 27.4 21 0.00046 25.6 0.1 15 1-15 1-15 (72)
123 cd01616 TGS The TGS domain, na 26.0 86 0.0019 20.3 3.0 22 98-120 37-58 (60)
124 TIGR01764 excise DNA binding d 25.9 59 0.0013 20.7 2.1 20 79-99 9-28 (49)
125 PF14478 DUF4430: Domain of un 25.1 69 0.0015 23.0 2.5 23 98-120 43-67 (68)
126 PF08068 DKCLD: DKCLD (NUC011) 24.1 33 0.00072 24.6 0.6 16 143-158 41-56 (59)
127 cd06919 Asp_decarbox Aspartate 23.3 85 0.0018 25.5 2.8 23 95-121 65-87 (111)
128 cd01800 SF3a120_C Ubiquitin-li 23.0 63 0.0014 23.6 1.9 66 54-123 4-69 (76)
129 PRK02253 deoxyuridine 5'-triph 21.8 2.5E+02 0.0053 24.0 5.7 39 83-121 2-46 (167)
130 PRK05449 aspartate alpha-decar 21.5 1.2E+02 0.0026 25.2 3.4 23 95-121 66-88 (126)
131 PRK05863 sulfur carrier protei 20.9 64 0.0014 23.0 1.6 44 69-121 14-59 (65)
132 cd01790 Herp_N Homocysteine-re 20.6 52 0.0011 24.9 1.0 56 65-120 21-76 (79)
133 PRK11092 bifunctional (p)ppGpp 20.1 81 0.0018 33.5 2.7 25 99-124 425-449 (702)
134 PF12728 HTH_17: Helix-turn-he 20.1 87 0.0019 20.7 2.0 20 79-99 9-28 (51)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.4e-41 Score=314.17 Aligned_cols=195 Identities=47% Similarity=0.748 Sum_probs=172.9
Q ss_pred EEEEcCCCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccc-cccccCCCCeee
Q 022339 61 EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQP-LRAEAEDIPLDI 139 (298)
Q Consensus 61 ~~~v~~~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~-~~~~~~~~~~~I 139 (298)
++.|..+.+++|||+||++.++ +||+.++++|++|.|.|||+++. ++++|..||+|++...+... ....+++.+++|
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 4566778899999999999666 99999999999999999999996 99999999999998865442 334456777999
Q ss_pred eecCCcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCC
Q 022339 140 VYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLD 219 (298)
Q Consensus 140 lyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD 219 (298)
||||+++||||||+||+|||++++..+|++++++.++.. ...++++|||||
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 999999999999999999999999999999999987631 135788999999
Q ss_pred CCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEccceeCCCCCeEEEEcCCC
Q 022339 220 KGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGS 286 (298)
Q Consensus 220 ~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl~~~~~~~~~~~~~~~~ 286 (298)
++||||||+|||..++..|+++|+++.+.|+|+|+|.|.+..++++|+.||+++..++.++.+....
T Consensus 132 kdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~~~~~v~~~~ 198 (289)
T COG0564 132 KDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNRKKMAVVKEG 198 (289)
T ss_pred CCCceEEEEECCHHHHHHHHHHHhcCcCcEEEEEEEECcccCCCCEEeeeeecCCcCCceEEEeccC
Confidence 9999999999999999999999999999999999999999998999999999998887777665443
No 2
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=1e-36 Score=288.69 Aligned_cols=198 Identities=41% Similarity=0.627 Sum_probs=166.8
Q ss_pred CceEEEEEEcCCCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccccccccCCC
Q 022339 56 AGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDI 135 (298)
Q Consensus 56 ~~~~~~~~v~~~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~~~~~~~~~ 135 (298)
.-+.++..|+..++|+|||+||++.++.+||+.++++|++|.|+|||+++.++++.|.+||+|++......+....+...
T Consensus 3 ~~~~~~~~v~~~~~g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~ 82 (325)
T PRK11180 3 QQVQLTATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQDI 82 (325)
T ss_pred ceEEEEEEECcccCCccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEeeccccccCCCCCCC
Confidence 45788889999999999999999998889999999999999999999998778999999999999765432222234456
Q ss_pred CeeeeecCCcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceec
Q 022339 136 PLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIV 215 (298)
Q Consensus 136 ~~~IlyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~v 215 (298)
+++|||||+++||||||+||+||++.+....|+.+.+..++.. .. ...++++|
T Consensus 83 ~~~iiyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~~~--~~-------------------------~~~~~~~v 135 (325)
T PRK11180 83 PLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPP--IA-------------------------DVPRAGIV 135 (325)
T ss_pred CCcEEEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHhhh--cc-------------------------CCccccee
Confidence 7899999999999999999999998877778999998876521 00 22457789
Q ss_pred ccCCCCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEccceeCCCCCeEEE
Q 022339 216 HRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMA 281 (298)
Q Consensus 216 hRLD~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl~~~~~~~~~~~ 281 (298)
||||++||||||||||..++..|+++|+.+.+.|+|+|+|.|.++ ++++|+.||.+....+.++.
T Consensus 136 hRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~Y~A~v~G~~~-~~~~i~~~l~~~~~~~~~~~ 200 (325)
T PRK11180 136 HRLDKDTTGLMVVAKTVPAQTRLVEALQKREITREYEAVAIGHMT-AGGTVDEPISRHPTKRTHMA 200 (325)
T ss_pred ccCCCCCceeEEEECCHHHHHHHHHHHHhCCcceEEEEEEecCCC-CCCEEECceecCCCcCcEEE
Confidence 999999999999999999999999999999999999999999985 56899999977554444433
No 3
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=100.00 E-value=2.9e-36 Score=281.95 Aligned_cols=183 Identities=39% Similarity=0.690 Sum_probs=154.4
Q ss_pred CCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccccccccCCCCeeeeecCCcE
Q 022339 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNV 146 (298)
Q Consensus 67 ~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~~~~~~~~~~~~IlyeD~~l 146 (298)
+++++||++||+..++.+||+.++++|++|.|+|||+++.++++.|++||+|.+...+.......+...+++|+|||+++
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 56789999999999867999999999999999999976557899999999999966432222222334468899999999
Q ss_pred EEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCceeE
Q 022339 147 LVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLL 226 (298)
Q Consensus 147 lvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGLl 226 (298)
+|||||+|++||+.++....|+++.|..++.... ...++++|||||++|||||
T Consensus 82 lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~~~~~---------------------------~~~~~~~vhRLD~~TSGll 134 (299)
T TIGR00005 82 IVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIA---------------------------GVERVGIVHRLDRDTSGLM 134 (299)
T ss_pred EEEECCCCCeEeCCCCCCcccHHHHHHHhccccc---------------------------CCCcCceECCCCCCCceEE
Confidence 9999999999999888777899999887653100 1245789999999999999
Q ss_pred EEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEccceeCCCC
Q 022339 227 VVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNN 276 (298)
Q Consensus 227 L~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl~~~~~~ 276 (298)
|||+|..+++.|+++|+++.+.|+|+|+|.|.+..++++|+.||.++..+
T Consensus 135 l~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~g~~~~~~~~i~~~l~~~~~~ 184 (299)
T TIGR00005 135 VVAKTPLALRELQRQLKNRTVTKEYVALVHGQFDSGGGTVDAPLGRVPNN 184 (299)
T ss_pred EEEcCHHHHHHHHHHHHhCCcceEEEEEEeccccCCCCEEeCceecCCCC
Confidence 99999999999999999999999999999999988899999999775433
No 4
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=2.2e-35 Score=278.72 Aligned_cols=184 Identities=25% Similarity=0.410 Sum_probs=152.3
Q ss_pred EEEEEcCCCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccccccc--------
Q 022339 60 LEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAE-------- 131 (298)
Q Consensus 60 ~~~~v~~~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~~~~~-------- 131 (298)
..++|..+++|+||++||+..++.+||+.++++|++|.|+|||+++ ++++.|+.||+|.+...........
T Consensus 9 ~~~~v~~~~~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v-~~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~ 87 (317)
T PRK11025 9 KIVTISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAGDEVRIPPVRVAEREEEAVSPKLQK 87 (317)
T ss_pred EEEEECcccCCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEc-CcccccCCCCEEEeCCCCccccccccccccccc
Confidence 3457888899999999999888889999999999999999999998 6899999999999864321110000
Q ss_pred cCCCCeeeeecCCcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCC
Q 022339 132 AEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIR 211 (298)
Q Consensus 132 ~~~~~~~IlyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~ 211 (298)
....+++|||||+++||||||+|++||++.+.. .++++.+..+.. ....
T Consensus 88 ~~~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~-~~~~~~~~~~~~------------------------------~~~~ 136 (317)
T PRK11025 88 VAALADVILYEDDHILVLNKPSGTAVHGGSGLS-FGVIEGLRALRP------------------------------EARF 136 (317)
T ss_pred cccCcCCEEEECCCEEEEECCCCCcCcCCCCCC-ccHHHHHHHhcc------------------------------CCCc
Confidence 112467999999999999999999999976654 356666654311 1123
Q ss_pred ceecccCCCCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEccceeCCC
Q 022339 212 PGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPN 275 (298)
Q Consensus 212 ~~~vhRLD~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl~~~~~ 275 (298)
+++|||||++||||||||||..+++.|+++|+.+.++|+|+|+|.|.+....++|+.||.++..
T Consensus 137 ~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~v~K~Y~a~v~G~~~~~~~~i~~~i~~~~~ 200 (317)
T PRK11025 137 LELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKVVQAPLLKNIL 200 (317)
T ss_pred CceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCCccEEEEEEEeCcccCCCceEecccccCcc
Confidence 5789999999999999999999999999999999999999999999998888999999988754
No 5
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.96 E-value=1.9e-29 Score=235.31 Aligned_cols=178 Identities=23% Similarity=0.331 Sum_probs=138.3
Q ss_pred CccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccccccccCCCCeeeeecCCcEE
Q 022339 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVL 147 (298)
Q Consensus 68 ~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~~~~~~~~~~~~IlyeD~~ll 147 (298)
.+++||++||++. +.+||++++++|++|+|+|||+++ .++..|.+||.|.|+.....+ . .+||++||
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 689999999999999999999998 689999999999997632111 0 14788999
Q ss_pred EEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCceeEE
Q 022339 148 VVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLV 227 (298)
Q Consensus 148 vvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGLlL 227 (298)
|+|||+|++||+.+. ...|+++.|..+ .++++|||||++||||||
T Consensus 71 vlnKP~G~~~~~~~~-~~~tv~~~l~~~----------------------------------~~l~~VgRLDrdTsGLLL 115 (290)
T PRK10475 71 ALNKPVGIVSTTEDG-ERDNIVDFVNHS----------------------------------KRVFPIGRLDKDSQGLIF 115 (290)
T ss_pred EEECCCCCCcCCCCC-CCCcHHHHhhcc----------------------------------ccccccccCCCCCcceEE
Confidence 999999999998765 456888776531 245689999999999999
Q ss_pred EEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCC------Cc-----EEEccc--eeCCCCCeEEEEcCCCCCchhhhh
Q 022339 228 VAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQS------SG-----RIEVPI--SRDPNNRIRMAAIPGSNKHGQARH 294 (298)
Q Consensus 228 ~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~------~g-----~I~~pl--~~~~~~~~~~~~~~~~~~~~~~r~ 294 (298)
||+|..++..|.. ..+.++|+|+|+|.|.+.++ .| ....|. .......+++.+.+|. .+++|+
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 9999999988855 55679999999999998543 12 122221 2212234577777776 899999
Q ss_pred hhc
Q 022339 295 AAS 297 (298)
Q Consensus 295 ~~~ 297 (298)
||.
T Consensus 192 m~~ 194 (290)
T PRK10475 192 MCE 194 (290)
T ss_pred HHH
Confidence 985
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=4e-28 Score=221.75 Aligned_cols=142 Identities=20% Similarity=0.280 Sum_probs=115.8
Q ss_pred ceEECCEEeccccccccCCCEEeeccccccccccccCCCCeeeeecCCcEEEEeCCCCceeecCCCCCCccHHHHHHhhc
Q 022339 97 LVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHC 176 (298)
Q Consensus 97 ~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~~~~~~~~~~~~IlyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~ 176 (298)
.|..||+++ +++++|++||+|.+........ +...+++|||||++++|||||+|++||++++....|+++.+..++
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 345999999 6899999999999875321111 123458999999999999999999999998887788888877553
Q ss_pred CCCccccccccccccccccccccccccccCCCCCCceecccCCCCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 177 SLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 177 ~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
. ...+++|||||++||||||||||..++..++.+|+.+.++|+|+|+|.
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 124568999999999999999999999999999999999999999999
Q ss_pred eecCCCCc-EEEccceeC
Q 022339 257 GVPSQSSG-RIEVPISRD 273 (298)
Q Consensus 257 G~~~~~~g-~I~~pl~~~ 273 (298)
|.+..+.+ .++.+|.++
T Consensus 128 G~~~~~~~~~~~~~i~~~ 145 (246)
T cd02558 128 YVPALTFPLTVRSRIVKG 145 (246)
T ss_pred cCCCCCCCcceecccccc
Confidence 98865444 567676554
No 7
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=99.96 E-value=8e-28 Score=224.48 Aligned_cols=179 Identities=20% Similarity=0.194 Sum_probs=135.3
Q ss_pred chHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCC--CEEeeccccccccccccCCCCeeeee-cCCcEE
Q 022339 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGG--DMVNCTISELQPLRAEAEDIPLDIVY-EDDNVL 147 (298)
Q Consensus 71 ~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~g--D~I~i~~~~~~~~~~~~~~~~~~Ily-eD~~ll 147 (298)
+||++||++. +.+||++++++|++|+|+|||+++ .++..|.++ |.|++........ ..+ ||++||
T Consensus 3 ~RL~k~La~~-g~~SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g~~~~~~----------~~~~e~~~yl 70 (289)
T PRK10700 3 EKLQKVLARA-GHGSRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRIDGHLISVK----------ESAEQICRVL 70 (289)
T ss_pred hhHHHHHHHC-CCCCHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEECCEEeecc----------cccccCCeEE
Confidence 7999999986 779999999999999999999998 689999887 5576653211100 011 567899
Q ss_pred EEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCceeEE
Q 022339 148 VVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLV 227 (298)
Q Consensus 148 vvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGLlL 227 (298)
++|||+|++|++.+.....|+++.+... ...++++|||||++||||||
T Consensus 71 vlnKP~G~~~s~~d~~~~~tv~d~l~~~--------------------------------~~~~~~~VgRLD~dTsGLLL 118 (289)
T PRK10700 71 AYYKPEGELCTRNDPEGRPTVFDRLPKL--------------------------------RGARWIAVGRLDVNTCGLLL 118 (289)
T ss_pred EEECCCCCEeecCCCCCCccHHHHhhhh--------------------------------cCCceeEccCCCCCCceEEE
Confidence 9999999999998776667998887642 11246789999999999999
Q ss_pred EEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCC------Cc-EEE----cc--ceeCC--C--CCeEEEEcCCCCCch
Q 022339 228 VAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQS------SG-RIE----VP--ISRDP--N--NRIRMAAIPGSNKHG 290 (298)
Q Consensus 228 ~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~------~g-~I~----~p--l~~~~--~--~~~~~~~~~~~~~~~ 290 (298)
||+|.+++..|.. ..+.++|+|+|+|.|.+.++ .| .|+ .| +.... . ..+++.+.+|. .+
T Consensus 119 lTndg~~~~~L~~--p~~~i~K~Y~v~V~G~~~~~~l~~l~~Gv~l~~~~~~~~~v~~~~~~~~~s~l~v~L~EGk--~h 194 (289)
T PRK10700 119 FTTDGELANRLMH--PSREVEREYAVRVFGQVDDAKLRQLSRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGR--NR 194 (289)
T ss_pred EEcCHHHHHHHhC--ccCCCCeEEEEEEccCCCHHHHHHHHcCCEeCCceeeeEEEEeccCCCCceEEEEEEeCCc--cH
Confidence 9999999999965 67889999999999987542 12 221 11 11111 1 12566666666 89
Q ss_pred hhhhhhc
Q 022339 291 QARHAAS 297 (298)
Q Consensus 291 ~~r~~~~ 297 (298)
+||+||+
T Consensus 195 QIRrm~~ 201 (289)
T PRK10700 195 EVRRLWE 201 (289)
T ss_pred HHHHHHH
Confidence 9999985
No 8
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=99.95 E-value=3.3e-28 Score=220.10 Aligned_cols=142 Identities=21% Similarity=0.321 Sum_probs=113.7
Q ss_pred chHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccccccccCCCCeeeeecCCcEEEEe
Q 022339 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVN 150 (298)
Q Consensus 71 ~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~~~~~~~~~~~~IlyeD~~llvvn 150 (298)
+|||+||++.+ .+||+.++++|++|.|+|||+++.+++++|++||.|++...... ..+++++||+|
T Consensus 1 ~rld~~L~~~~-~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~I~l~~~~~~-------------~~~~~~~lvvn 66 (232)
T PRK10839 1 MRLDKFISQQL-GVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDGNPLA-------------QQHGPRYFMLN 66 (232)
T ss_pred CcHHHHHHHcC-CCCHHHHHHHHHcCeEEECCEEeccCCcCcCCCCEEEECCEEcc-------------cCCCCEEEEEE
Confidence 48999999986 69999999999999999999998668999999999998652111 01357899999
Q ss_pred CCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCceeEEEEc
Q 022339 151 KPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAK 230 (298)
Q Consensus 151 KPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGLlL~Ak 230 (298)
||+||+||++.+. ..|+.+.+... ...++++|||||++||||||||+
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 34543322110 11356789999999999999999
Q ss_pred CHHHHHHHHHHHhcCeeceEEEEEEeeecCC
Q 022339 231 DEHSHAHLSEQFKLHTIERVYISLTSGVPSQ 261 (298)
Q Consensus 231 ~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~ 261 (298)
|..++..|.. +.+.++|+|+|++.+.+..
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 6778999999999998753
No 9
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=5.5e-26 Score=206.63 Aligned_cols=179 Identities=25% Similarity=0.354 Sum_probs=137.6
Q ss_pred cchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCC-CEEeeccccccccccccCCCCeeeee-cCCcEE
Q 022339 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGG-DMVNCTISELQPLRAEAEDIPLDIVY-EDDNVL 147 (298)
Q Consensus 70 g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~g-D~I~i~~~~~~~~~~~~~~~~~~Ily-eD~~ll 147 (298)
.+||+|||++. +.+||++++++|.+|+|+|||++++.+...+.++ |.|.+.... +.+ +...|+
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-GVGSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKR--------------IELKEERVYL 66 (248)
T ss_pred ccchHHHHHHc-CCCCHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCEE--------------eeccccceEE
Confidence 57999999998 7999999999999999999999998899999988 577776532 222 334499
Q ss_pred EEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCceeEE
Q 022339 148 VVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLV 227 (298)
Q Consensus 148 vvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGLlL 227 (298)
++|||.|++|+..++..+.|+.+.|.... + ...++++|+|||+||+||||
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 99999999999887777778777654320 0 23468899999999999999
Q ss_pred EEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCC------Cc-EEE----cc---c--eeC---CCCCeEEEEcCCCCC
Q 022339 228 VAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQS------SG-RIE----VP---I--SRD---PNNRIRMAAIPGSNK 288 (298)
Q Consensus 228 ~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~------~g-~I~----~p---l--~~~---~~~~~~~~~~~~~~~ 288 (298)
||+|.+.+..| ....+.++|+|+|.|.|.+..+ .| .++ .| . ... +...+++++.+|.
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 LTNDGELAHRL--MHPSSEVEKEYLVRVEGPVTEEDLEKLRKGVTLDDGETKPAKPASLEKEPGKNNSWLRITLTEGR-- 192 (248)
T ss_pred EeCCHHHHHHh--cCCCCCCCEEEEEEEecCCCHHHHHHHhCCcEecCcccccceeEEEEecCCCCceEEEEEEeCCc--
Confidence 99998777777 4467889999999999988643 11 121 12 1 222 2235677777777
Q ss_pred chhhhhhhc
Q 022339 289 HGQARHAAS 297 (298)
Q Consensus 289 ~~~~r~~~~ 297 (298)
.+++|+||.
T Consensus 193 nrQVRRm~~ 201 (248)
T COG1187 193 NRQVRRMFE 201 (248)
T ss_pred CHHHHHHHH
Confidence 899999985
No 10
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=99.93 E-value=1e-24 Score=208.34 Aligned_cols=192 Identities=29% Similarity=0.378 Sum_probs=158.4
Q ss_pred EEEEEEcCCCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccccccccCCCCee
Q 022339 59 QLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLD 138 (298)
Q Consensus 59 ~~~~~v~~~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~~~~~~~~~~~~ 138 (298)
.+...+...+.+..+.+++.+.|...++...+..|+.|.|.+||..+ ..++.++.||.|.......+++. ...++.
T Consensus 32 ~~~~~~~~rw~~k~~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~-~v~~i~k~~d~l~~~vhrh~p~~---~~~~~~ 107 (371)
T KOG1919|consen 32 TYRTFVKGRWAGKKLVDVFVSEFRLRERAYYESAIKLGRVTVNGEQV-RVSLIVKNGDVLCHTVHRHEPPV---AYLPIR 107 (371)
T ss_pred eeeEEEeeeecccchHHHHHHHHhcCchHhhhhhhhcCceEECcEee-eeEEEeccCCEEEEeeccCCCCc---cccccc
Confidence 33446678889998999999999889999999999999999999999 58999999999998766555433 235789
Q ss_pred eeecCCcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccC
Q 022339 139 IVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRL 218 (298)
Q Consensus 139 IlyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRL 218 (298)
|+|||++|+|||||+|++|||.+....+++...+.... ....+.+||||
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 99999999999999999999988887778777776531 22346789999
Q ss_pred CCCCceeEEEEcCHHHHHHHHHHHhcCeeceEE-EEEEeeecC-CCCcEEEccceeCCCCCeEEEEcCCC
Q 022339 219 DKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVY-ISLTSGVPS-QSSGRIEVPISRDPNNRIRMAAIPGS 286 (298)
Q Consensus 219 D~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~Y-lAlv~G~~~-~~~g~I~~pl~~~~~~~~~~~~~~~~ 286 (298)
|+.|||||+||++++++..++.+|+++++.|.| +|.|.|.++ ....+|..|+..... ..+|.+....
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 799999986 556677777766533 3455555444
No 11
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=99.92 E-value=1.2e-24 Score=195.52 Aligned_cols=109 Identities=31% Similarity=0.503 Sum_probs=93.0
Q ss_pred CeeeeecCCcEEEEeCCCCceeecCCC-CCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCcee
Q 022339 136 PLDIVYEDDNVLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (298)
Q Consensus 136 ~~~IlyeD~~llvvnKPaGl~v~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~ 214 (298)
+++|||||++++|+|||+|++||++.+ ....++.+.+..++ ..+++
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 cccCCCCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEccceeCCCCC
Q 022339 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNR 277 (298)
Q Consensus 215 vhRLD~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl~~~~~~~ 277 (298)
|||||++||||||||+|..+++.|+++|+++.+.|+|+|+|.|.+..++++|+.||.++...+
T Consensus 60 vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~~v~K~Yla~v~G~~~~~~~~i~~~i~~~~~~~ 122 (219)
T PRK10158 60 VHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNR 122 (219)
T ss_pred ECCCCCCCceEEEEECCHHHHHHHHHHHHhCCccEEEEEEEecccCCCCcEEecceecCCCCC
Confidence 999999999999999999999999999999999999999999999889999999997654333
No 12
>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=1e-24 Score=195.26 Aligned_cols=108 Identities=30% Similarity=0.435 Sum_probs=95.5
Q ss_pred CCeeeeecCCcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCcee
Q 022339 135 IPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (298)
Q Consensus 135 ~~~~IlyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~ 214 (298)
.+++|||||+++||+|||+|++|++++.....|+.+.|..++. ...+++
T Consensus 14 ~~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~-------------------------------~~~~~~ 62 (213)
T cd02557 14 DPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYG-------------------------------LTELRP 62 (213)
T ss_pred CCCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcC-------------------------------CCCccC
Confidence 4678999999999999999999999877666788888876432 124678
Q ss_pred cccCCCCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEccceeC
Q 022339 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRD 273 (298)
Q Consensus 215 vhRLD~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl~~~ 273 (298)
|||||++||||||||||.++++.|+++|+++.++|+|+|+|.|.+..+.++|+.||.++
T Consensus 63 vhRLD~~TSGllllak~~~~~~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~ 121 (213)
T cd02557 63 CHRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKEYLARVKGEFPDGEVVVDQPIGLV 121 (213)
T ss_pred ccCCCCCCceEEEEECCHHHHHHHHHHHHcCCccEEEEEEEeCcCCCCCeEEecceecc
Confidence 99999999999999999999999999999999999999999999988899999998654
No 13
>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=2.1e-24 Score=193.74 Aligned_cols=107 Identities=29% Similarity=0.471 Sum_probs=91.5
Q ss_pred eeeeecCCcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecc
Q 022339 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVH 216 (298)
Q Consensus 137 ~~IlyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vh 216 (298)
++|||||++++|||||+|++||++.+ ..++.+.+..+. ....+++||
T Consensus 2 ~~ilyed~~~lvvnKP~Gl~v~~~~~--~~~l~~~l~~~~-------------------------------~~~~~~~Vh 48 (217)
T TIGR01621 2 FEILFTHPDFLLINKHPGISVHKDDG--ETGLLQEVATQL-------------------------------GVGQVWLVH 48 (217)
T ss_pred ceEEEeCCCEEEEECCCCCeECCCCC--cChHHHHHHHhc-------------------------------CCCCccEec
Confidence 47999999999999999999998754 245666665432 113567899
Q ss_pred cCCCCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEccceeCCCC
Q 022339 217 RLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNN 276 (298)
Q Consensus 217 RLD~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl~~~~~~ 276 (298)
|||++||||||||||.++++.|+++|+++.++|+|+|+|.|.+..++++|+.++.+....
T Consensus 49 RLDr~TSGlll~Ak~~~~~~~L~~~~~~~~v~K~YlAlV~g~~~~~~~~i~~~~~~~~~~ 108 (217)
T TIGR01621 49 RLDKMTSGILLLALNAESASELSQGFAKRKIEKTYLALSSKKPKKKQGLICGDMEKSRRG 108 (217)
T ss_pred CCCCCCceEEEEEcCHHHHHHHHHHHhcCCccEEEEEEEeccccCCCCEEeCCcccCCCC
Confidence 999999999999999999999999999999999999999999988899999999765443
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=1e-23 Score=189.85 Aligned_cols=107 Identities=30% Similarity=0.545 Sum_probs=87.5
Q ss_pred eeeeecCCcEEEEeCCCCceeecCCCCCCcc--HHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCcee
Q 022339 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGT--LVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (298)
Q Consensus 137 ~~IlyeD~~llvvnKPaGl~v~~~~~~~~~t--l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~ 214 (298)
++|||||+++||||||+|++||+..+....+ ++..+..++ ..++++
T Consensus 1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~ 48 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQL--------------------------------GQHVYP 48 (223)
T ss_pred CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHc--------------------------------CCCccc
Confidence 3689999999999999999999976443332 222232211 124678
Q ss_pred cccCCCCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEccceeCCCC
Q 022339 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNN 276 (298)
Q Consensus 215 vhRLD~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl~~~~~~ 276 (298)
|||||++||||||||||+.+++.|+.+|+++.++|+|+|+|.|.+.. +++|+.||.++...
T Consensus 49 vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~v~K~Y~alv~G~~~~-~~~i~~~l~~~~~~ 109 (223)
T cd02563 49 VHRLDRPTSGVLLFALSSEVARKLGEQFTEHRVHKTYLAVVRGYVPE-SGTIDYPLSEELDK 109 (223)
T ss_pred ccCCCCCCeEEEEEEECHHHHHHHHHHHhcCceeEEEEEEEECccCC-CCeEEEeeeeCCCc
Confidence 99999999999999999999999999999999999999999999865 78999999776543
No 15
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=99.90 E-value=2.6e-23 Score=191.14 Aligned_cols=104 Identities=28% Similarity=0.461 Sum_probs=85.4
Q ss_pred eeeeecCCcEEEEeCCCCceeecCCCCCCccH--HHHHHhhcCCCccccccccccccccccccccccccccCCCCCCcee
Q 022339 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTL--VNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (298)
Q Consensus 137 ~~IlyeD~~llvvnKPaGl~v~~~~~~~~~tl--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~ 214 (298)
++|||||+++||||||+|++||+.......+. ...+..++ ..++++
T Consensus 2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~ 49 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQI--------------------------------GQHVFT 49 (257)
T ss_pred CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHh--------------------------------CCCcee
Confidence 47999999999999999999998754433332 23332221 124568
Q ss_pred cccCCCCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEccceeC
Q 022339 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRD 273 (298)
Q Consensus 215 vhRLD~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl~~~ 273 (298)
|||||++||||||||||..+++.|+.+|+++.|+|+|+|+|.|.+. .+++|+.|+.++
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 568899998765
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=99.85 E-value=3.5e-21 Score=163.97 Aligned_cols=101 Identities=38% Similarity=0.588 Sum_probs=76.5
Q ss_pred cEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCce
Q 022339 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (298)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (298)
++||||||+|++|++.++................ ......+++|||||++|||
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 6899999999999998854333333322222110 0144678999999999999
Q ss_pred eEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEcccee
Q 022339 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISR 272 (298)
Q Consensus 225 LlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl~~ 272 (298)
|||||+|.++++.|+.+|+.+.++|+|+|+|.|.+..+++.|+.++..
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 999999999999999999999999999999998777889999998876
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=99.82 E-value=5e-20 Score=156.71 Aligned_cols=90 Identities=31% Similarity=0.455 Sum_probs=74.2
Q ss_pred EEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCcee
Q 022339 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (298)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (298)
++|+|||+|++||++++....++.+.+... ...++++|||||++||||
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~--------------------------------~~~~~~~vhRLD~~TSGl 48 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKL--------------------------------HGPRVHAAGRLDKDTSGL 48 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhhcc--------------------------------cCCceeEeccCCCCCeeE
Confidence 589999999999998877667777655421 124578899999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEccc
Q 022339 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPI 270 (298)
Q Consensus 226 lL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl 270 (298)
||||+|.++++.|+.+ ++.++|+|+|+|.|.++. ++.+..|+
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 9999999999999987 788999999999999864 45566554
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=99.79 E-value=9.3e-19 Score=151.68 Aligned_cols=100 Identities=52% Similarity=0.887 Sum_probs=83.5
Q ss_pred EEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCcee
Q 022339 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (298)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (298)
++|+|||+|++|++.......++.+.+..+.... .....+++|||||++||||
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~v~RLD~~tsGl 53 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLL---------------------------GEEFRPGLVHRLDKDTSGL 53 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhc---------------------------CCCCcCceecccCCCCceE
Confidence 5899999999999988777777777653222100 0234678999999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEcccee
Q 022339 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISR 272 (298)
Q Consensus 226 lL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl~~ 272 (298)
||||++.++++.|..+|+++.+.|+|+|+|.|.+....+.++.|+..
T Consensus 54 ll~ak~~~~~~~l~~~~~~~~~~K~Y~a~v~g~~~~~~~~~~~~~~~ 100 (185)
T cd02869 54 LLVAKNKKAAAKLSKQFKERKVKKTYLALVDGKPPEDEGTIDAPLGR 100 (185)
T ss_pred EEEEcCHHHHHHHHHHHhcCceeEEEEEEEeCCCCCCccEEeccccc
Confidence 99999999999999999999999999999999998888888877754
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=6.4e-19 Score=152.13 Aligned_cols=83 Identities=25% Similarity=0.262 Sum_probs=70.0
Q ss_pred cEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCce
Q 022339 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (298)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (298)
.++|+|||+|++||+.+.....|+.+.+..+. ..++++|||||++|||
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 eEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCC
Q 022339 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQ 261 (298)
Q Consensus 225 LlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~ 261 (298)
|||||+|..+++.|.. +++.++|+|+|+|.|.++.
T Consensus 49 Lll~ak~~~~~~~L~~--~~~~i~K~Y~a~V~g~~~~ 83 (167)
T cd02556 49 LLLFTNDGELANRLMH--PSNEIEREYAVRVFGQVTD 83 (167)
T ss_pred EEEEECCHHHHHHHhC--CcCCCCeEEEEEECccCCH
Confidence 9999999999999964 7889999999999998753
No 20
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.
Probab=99.77 E-value=1.2e-18 Score=150.54 Aligned_cols=83 Identities=24% Similarity=0.290 Sum_probs=68.1
Q ss_pred EEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCcee
Q 022339 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (298)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (298)
++|+|||+|++||+++ ....|+.+.+..++. ..++++|||||++||||
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 456788888775431 13567899999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCC
Q 022339 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQS 262 (298)
Q Consensus 226 lL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~ 262 (298)
||||+|..++..+.. +.+.++|+|+|+|.|.+..+
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 999999988777765 56789999999999998644
No 21
>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=99.76 E-value=7.9e-19 Score=148.12 Aligned_cols=81 Identities=28% Similarity=0.374 Sum_probs=66.2
Q ss_pred EEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCcee
Q 022339 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (298)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (298)
|+|+|||+|++||+.++....++.+.+.. ...++.+|||||++||||
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 123578999999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCC
Q 022339 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQ 261 (298)
Q Consensus 226 lL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~ 261 (298)
||||+|.+++..|+. +++.++|+|+|+|.|.+..
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 999999999999975 5678999999999998853
No 22
>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=99.69 E-value=1e-16 Score=138.27 Aligned_cols=113 Identities=18% Similarity=0.259 Sum_probs=82.9
Q ss_pred EEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCcee
Q 022339 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (298)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (298)
|+++|||+|++|++.+. ...|+.+.+.. ..++++|||||++||||
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 34677665431 13578999999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCC------c-----EEEccc--eeCCCCCeEEEEcCCCCCchhh
Q 022339 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSS------G-----RIEVPI--SRDPNNRIRMAAIPGSNKHGQA 292 (298)
Q Consensus 226 lL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~------g-----~I~~pl--~~~~~~~~~~~~~~~~~~~~~~ 292 (298)
||||+|..++..|.. ..+.++|+|+|.|.|.+.++. | ....|. .......+++.+.+|. .+++
T Consensus 47 ll~t~dg~~~~~L~~--p~~~~~K~Y~V~v~~~l~~~~l~~l~~G~~~~~~~~~~~~v~~~~~~~l~i~l~eGr--~~qI 122 (164)
T cd02554 47 ILLTNDGDLVNKILH--ADNNHEKEYLVTVNKPITDEFIEGMSNGVVILGTVTKPCKVERLAKDKFRIVLTQGL--NRQI 122 (164)
T ss_pred EEEEcCHHHHHHHhh--hhcCCCeEEEEEECCCCCHHHHHHHhCCCEECCeEEcceEEEECCCCEEEEEEECCc--CHHH
Confidence 999999999999954 566789999999999886431 1 112222 2211223566666665 8999
Q ss_pred hhhhc
Q 022339 293 RHAAS 297 (298)
Q Consensus 293 r~~~~ 297 (298)
|+||+
T Consensus 123 Rrm~~ 127 (164)
T cd02554 123 RRMCE 127 (164)
T ss_pred HHHHH
Confidence 99985
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=99.69 E-value=8.3e-17 Score=140.42 Aligned_cols=51 Identities=27% Similarity=0.360 Sum_probs=45.5
Q ss_pred CCceecccCCCCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCC
Q 022339 210 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQS 262 (298)
Q Consensus 210 ~~~~~vhRLD~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~ 262 (298)
.++++|||||++||||||||+|..+++.|... .+.++|+|+|+|.|.++++
T Consensus 45 ~~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~~--~~~i~K~Y~v~v~g~~~~~ 95 (177)
T cd02555 45 ARLAPIGPLDKDASGLLVFSQDGRVLRKLIGD--ASRLEQEYLVEVRGELTAG 95 (177)
T ss_pred CceeEecCCCCCCeeEEEEECCHHHHHHHhCh--hcCCCEEEEEEEcccCCHH
Confidence 36789999999999999999999999999884 4679999999999998643
No 24
>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=99.68 E-value=7.1e-17 Score=139.52 Aligned_cols=79 Identities=22% Similarity=0.331 Sum_probs=63.4
Q ss_pred EEEEeCCCCceeecCCC-CCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCce
Q 022339 146 VLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (298)
Q Consensus 146 llvvnKPaGl~v~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (298)
++|+|||+|++||+.++ ....|+.+.+.. .++++|||||++|||
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 344566654420 245789999999999
Q ss_pred eEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCC
Q 022339 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQ 261 (298)
Q Consensus 225 LlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~ 261 (298)
|||||+|..+++.|... .+.++|+|+|+|.|.+..
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 99999999888888663 456999999999999854
No 25
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.67 E-value=1.2e-16 Score=143.26 Aligned_cols=82 Identities=24% Similarity=0.340 Sum_probs=68.4
Q ss_pred CCcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCC
Q 022339 143 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 222 (298)
Q Consensus 143 D~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~T 222 (298)
...|+++|||+|++|+..+.....++.+.+. ..++++|||||++|
T Consensus 38 ~~~ylllnKP~G~l~~~~d~~~~~tl~d~l~-----------------------------------~~~~~~vgRLD~~T 82 (217)
T PRK11394 38 PTRVILFNKPYDVLPQFTDEAGRKTLKEFIP-----------------------------------VQGVYAAGRLDRDS 82 (217)
T ss_pred CCEEEEEECCCCCEEeeCCccCCcchHHhcc-----------------------------------cCCeEEecCCCCCC
Confidence 3579999999999999766555567766542 12467899999999
Q ss_pred ceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCC
Q 022339 223 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQ 261 (298)
Q Consensus 223 SGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~ 261 (298)
|||||||+|..++..|... ++.++|+|+|+|.|.+..
T Consensus 83 sGllLlt~d~~~~~~L~~~--~~~i~K~Y~~~v~g~~~~ 119 (217)
T PRK11394 83 EGLLVLTNNGALQARLTQP--GKRTGKIYYVQVEGIPTQ 119 (217)
T ss_pred eeEEEEECCHHHHHHHhCc--ccCCCEEEEEEECCCCCH
Confidence 9999999999999999884 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=99.30 E-value=1.2e-11 Score=88.94 Aligned_cols=70 Identities=41% Similarity=0.550 Sum_probs=60.8
Q ss_pred chHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccccccccCCCCeeeeecCCcEEEEe
Q 022339 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVN 150 (298)
Q Consensus 71 ~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~~~~~~~~~~~~IlyeD~~llvvn 150 (298)
+||++||.+.++..||+.++++|++|.|+|||+.++.++..+.+||.|.+...+ .+.+|+|||++++++|
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 489999998866789999999999999999999997799999999999886521 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=1.8e-11 Score=101.20 Aligned_cols=45 Identities=27% Similarity=0.460 Sum_probs=41.6
Q ss_pred cccCCCCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCC
Q 022339 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQ 261 (298)
Q Consensus 215 vhRLD~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~ 261 (298)
|||||++||||||||+|.++++.|.. +++.++|+|+|+|.|.++.
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~--~~~~i~K~Y~a~v~g~~~~ 45 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTH--PGHHCEKTYLVTVEGPVTD 45 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhC--CCCCCCeEEEEEECCCCCH
Confidence 79999999999999999999999986 6788999999999998753
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=99.15 E-value=8.6e-11 Score=106.21 Aligned_cols=75 Identities=24% Similarity=0.244 Sum_probs=55.6
Q ss_pred EEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCcee
Q 022339 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (298)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (298)
+||||||+|+.++... .++...+...+. .....++|||||++||||
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 333343433321 112256789999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 226 lL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
|+||+++.+ +|.++|..+.+.|+|+|...
T Consensus 48 l~~a~~~~t--kl~~~~~~~~~~K~Y~~~~~ 76 (226)
T cd02868 48 LVLGVNHGN--KLLSHLYSNHPTRVYTIRGL 76 (226)
T ss_pred EEEEeChhH--hHHHHHHhcCCCeEEEEEEE
Confidence 999999976 69999999899999996654
No 29
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=99.04 E-value=5.2e-10 Score=76.74 Aligned_cols=48 Identities=38% Similarity=0.511 Sum_probs=44.7
Q ss_pred chHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEE
Q 022339 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMV 118 (298)
Q Consensus 71 ~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I 118 (298)
+|||+||.+.....||++++++|++|.|+|||++++++++.|.+||+|
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 589999998866678999999999999999999998899999999987
No 30
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=99.00 E-value=8.8e-10 Score=79.10 Aligned_cols=52 Identities=17% Similarity=0.298 Sum_probs=47.7
Q ss_pred CCccchHHHHHHhccCCc--CHHHHHHHHHCCceEECCEEeccccccccCCCEEee
Q 022339 67 KAGKLRLDAWISSRIDGI--SRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNC 120 (298)
Q Consensus 67 ~~~g~rLdk~L~~~~~~~--Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i 120 (298)
..++.|||+||+.. .+ ||+.++++|..|.|+|||+++++++++|.+||.|+|
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 34779999999998 45 999999999999999999999888999999999986
No 31
>smart00363 S4 S4 RNA-binding domain.
Probab=98.50 E-value=3.4e-07 Score=63.52 Aligned_cols=52 Identities=33% Similarity=0.392 Sum_probs=46.7
Q ss_pred chHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeecc
Q 022339 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (298)
Q Consensus 71 ~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~ 122 (298)
++|+.||.+.+...|+++++++|+.|.|+|||++++.++..|..||.|.+..
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 32
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=98.50 E-value=1.8e-07 Score=73.75 Aligned_cols=55 Identities=33% Similarity=0.468 Sum_probs=49.1
Q ss_pred CccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccc
Q 022339 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (298)
Q Consensus 68 ~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~ 123 (298)
...+|||+||...--.-+|+.+++++..|+|.|||+++ +++..|+.||+|+|.+.
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 56789999998763356999999999999999999999 89999999999999774
No 33
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=98.28 E-value=1.6e-06 Score=80.37 Aligned_cols=59 Identities=32% Similarity=0.411 Sum_probs=53.8
Q ss_pred EcCCCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccc
Q 022339 64 VDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (298)
Q Consensus 64 v~~~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~ 123 (298)
+....+++|||.+++..+ .+||+.++++|++|.|+|||+.++++++.|++||.|.|...
T Consensus 185 ~~~~vas~RLD~vla~~~-~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiRG~ 243 (267)
T PLN00051 185 FKSVEASLRLDALASAGF-RMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVSGK 243 (267)
T ss_pred ccCCcCcccHHHHHHHHh-ccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEeeC
Confidence 345668899999999997 79999999999999999999999899999999999999753
No 34
>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=98.21 E-value=2.7e-06 Score=78.54 Aligned_cols=59 Identities=29% Similarity=0.446 Sum_probs=53.1
Q ss_pred EcCCCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccc
Q 022339 64 VDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (298)
Q Consensus 64 v~~~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~ 123 (298)
+....+++|||.+++..+ .+||+.++++|++|.|.|||+.++++++.|++||.|.+...
T Consensus 177 ~~~~v~s~RLD~lls~~~-~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~IsvrG~ 235 (257)
T TIGR03069 177 LTTVEASLRIDAIASAGF-GLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRGK 235 (257)
T ss_pred ecCCCccccHHHHHHhhh-hhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEcCC
Confidence 445668899999999886 68999999999999999999999889999999999999753
No 35
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=98.21 E-value=3.4e-06 Score=70.25 Aligned_cols=54 Identities=30% Similarity=0.286 Sum_probs=48.4
Q ss_pred ccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccc
Q 022339 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (298)
Q Consensus 69 ~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~ 123 (298)
+.+|||+||-..--.-||+.++++|..|.|.|||++ .+++..|.+||+|.|...
T Consensus 7 ~~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~ 60 (133)
T PRK10348 7 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQG 60 (133)
T ss_pred ccccHHHHHHHcCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEEC
Confidence 457999999988556799999999999999999999 599999999999998653
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=98.19 E-value=3.2e-06 Score=75.32 Aligned_cols=54 Identities=22% Similarity=0.257 Sum_probs=48.7
Q ss_pred cchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccc
Q 022339 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (298)
Q Consensus 70 g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~ 123 (298)
.+|||++|.......||+.++++|..|.|.|||++++.+++.|++||+|+|...
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 379999997775457999999999999999999999899999999999999764
No 37
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=98.16 E-value=3.8e-06 Score=74.79 Aligned_cols=54 Identities=19% Similarity=0.229 Sum_probs=48.9
Q ss_pred cchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccc
Q 022339 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (298)
Q Consensus 70 g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~ 123 (298)
.+|||+||.+.....||+.++++|..|.|.|||+.++.+++.|.+||+|+|...
T Consensus 88 E~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~~~ 141 (201)
T CHL00113 88 EMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDK 141 (201)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEccc
Confidence 369999999885567999999999999999999999999999999999998653
No 38
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=98.05 E-value=7.5e-06 Score=74.32 Aligned_cols=52 Identities=29% Similarity=0.238 Sum_probs=47.5
Q ss_pred hHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccc
Q 022339 72 RLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (298)
Q Consensus 72 rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~ 123 (298)
|||+||.+.....||+.++++|++|+|+|||++++++++.|.+||.|++...
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 7999999985456899999999999999999999999999999999998754
No 39
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=98.02 E-value=1e-05 Score=72.16 Aligned_cols=54 Identities=24% Similarity=0.283 Sum_probs=48.1
Q ss_pred cchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccc
Q 022339 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (298)
Q Consensus 70 g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~ 123 (298)
.+|||.+|.+.....||+.++++|..|.|.|||+.++.+++.|.+||.|+|...
T Consensus 92 E~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~I~v~~~ 145 (203)
T PRK05327 92 ESRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVREK 145 (203)
T ss_pred HHHHHHHHHHcCccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCEEEECCc
Confidence 379999997764468999999999999999999999889999999999998653
No 40
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=97.80 E-value=2.4e-05 Score=71.18 Aligned_cols=56 Identities=39% Similarity=0.515 Sum_probs=51.6
Q ss_pred CCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccc
Q 022339 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (298)
Q Consensus 67 ~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~ 123 (298)
.-+.+|||..+++.| .+||..+.++|.+|.|+||.+.++++++.|+.||.|.+...
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 356789999999997 69999999999999999999999999999999999999764
No 41
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=97.76 E-value=4.1e-05 Score=68.35 Aligned_cols=54 Identities=22% Similarity=0.216 Sum_probs=46.8
Q ss_pred chHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeecccc
Q 022339 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (298)
Q Consensus 71 ~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~ 124 (298)
.|||..+-+..-..|+.+++++|..|.|.|||++|+.|++.|++||+|.|....
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 467776666644679999999999999999999999999999999999997643
No 42
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like. This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl r
Probab=97.69 E-value=0.00014 Score=63.97 Aligned_cols=70 Identities=21% Similarity=0.256 Sum_probs=52.6
Q ss_pred CcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCc
Q 022339 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (298)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TS 223 (298)
+.+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||...|
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 368999999998765 36777776543 246778999999999
Q ss_pred eeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 224 GLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
|||+++-++. .++.+.+.. -.|+|.|.+.
T Consensus 43 GvLiv~~g~~--Tk~~~~~~~--~~K~Y~a~v~ 71 (182)
T cd02572 43 GCLPVCIDRA--TRLVKSQQE--AGKEYVCVMR 71 (182)
T ss_pred eEEEEEECHH--hhhhHHHhC--CCCEEEEEEE
Confidence 9999999873 334444443 3599999886
No 43
>PRK11507 ribosome-associated protein; Provisional
Probab=97.67 E-value=0.00014 Score=53.93 Aligned_cols=57 Identities=19% Similarity=0.195 Sum_probs=49.5
Q ss_pred CCCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeecc
Q 022339 66 TKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (298)
Q Consensus 66 ~~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~ 122 (298)
...+-.+|++||.-.--.-|=.+++.+|..|.|+|||++.+.-..+|.+||+|++..
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 346778999999877334588999999999999999999999999999999999865
No 44
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=97.57 E-value=0.00014 Score=66.00 Aligned_cols=53 Identities=34% Similarity=0.319 Sum_probs=49.2
Q ss_pred cchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeecc
Q 022339 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (298)
Q Consensus 70 g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~ 122 (298)
.+|||.+|.++...-||+.++.+|.+|.|+|||.++++|+..|..++.|++..
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 57999999999545799999999999999999999999999999999999975
No 45
>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=62.05 Aligned_cols=68 Identities=22% Similarity=0.289 Sum_probs=52.7
Q ss_pred EEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCcee
Q 022339 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (298)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (298)
+|++|||.|+-+| .+++.+++.+. ..+.+..+.||-..|||
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 7899999998765 46777777653 24677899999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 226 lL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
|+++-++. .++...|.+ ..|+|.|.+.
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 99999973 334444443 7999999986
No 46
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.36 E-value=0.00052 Score=62.32 Aligned_cols=71 Identities=18% Similarity=0.343 Sum_probs=54.1
Q ss_pred CcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCc
Q 022339 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (298)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TS 223 (298)
+.+|+||||.|+-+| .+++.+.+.+. ..+.+..|.||...|
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 479999999998765 36777776653 246778999999999
Q ss_pred eeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 224 GLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
|+|+++-.+. +.+|.+.+.+ ..|+|+|.+.
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 6899999986
No 47
>TIGR00431 TruB tRNA pseudouridine 55 synthase. TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific
Probab=97.33 E-value=0.00077 Score=60.44 Aligned_cols=69 Identities=19% Similarity=0.284 Sum_probs=53.8
Q ss_pred cEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCce
Q 022339 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (298)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (298)
.+|+||||.|+-+| -+++.+.+.+. ..+.+..+.||-..||
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 68999999998755 36777777653 2356789999999999
Q ss_pred eEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 225 LlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
||+++-...+ +|...+. .-.|+|.|.+.
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 9999999853 4545444 47999999986
No 48
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=97.32 E-value=0.00068 Score=63.08 Aligned_cols=72 Identities=24% Similarity=0.341 Sum_probs=54.9
Q ss_pred CcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCc
Q 022339 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (298)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TS 223 (298)
+.++++|||+|+-+| .+++.+.+.+. ..+.+..+-||-..|
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 368999999998765 46787877653 246678999999999
Q ss_pred eeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe-ee
Q 022339 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS-GV 258 (298)
Q Consensus 224 GLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~-G~ 258 (298)
|+|+++-.+. .+|.+.+.. -.|+|.|.+. |.
T Consensus 43 GvLiv~iG~a--TKl~~~l~~--~~K~Y~a~~~lG~ 74 (273)
T PRK04099 43 GVLIVAFGQY--TKLFRFLKK--TPKTYRATLWLGA 74 (273)
T ss_pred eEEEEEEChH--hhhHHHhcc--CCceEEEEEEECC
Confidence 9999999874 335444444 4899999986 44
No 49
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=97.27 E-value=0.0011 Score=60.80 Aligned_cols=70 Identities=20% Similarity=0.327 Sum_probs=53.0
Q ss_pred CcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCc
Q 022339 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (298)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TS 223 (298)
+.+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||...|
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 469999999998765 36777776553 246778999999999
Q ss_pred eeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 224 GLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
|||+++-.+. .+|.+.+.+ ..|+|+|.+.
T Consensus 51 GvLiv~iG~a--TKl~~~l~~--~~K~Y~a~~~ 79 (244)
T PRK00020 51 GLLVCCMGRA--TKISGRMLE--ADKTYQATLQ 79 (244)
T ss_pred eEEEEEECHH--hhhhHHhcc--CCcEEEEEEE
Confidence 9999999873 333344433 4699999986
No 50
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=97.27 E-value=5.2e-05 Score=55.56 Aligned_cols=56 Identities=20% Similarity=0.251 Sum_probs=36.8
Q ss_pred CCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeecc
Q 022339 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (298)
Q Consensus 67 ~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~ 122 (298)
..+..+|++||...--.-|=.+++.+|.+|.|+|||+..+..+.+|++||+|++..
T Consensus 4 ~~e~I~L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~~~ 59 (65)
T PF13275_consen 4 NTEYITLGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEIDG 59 (65)
T ss_dssp --S---HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEETT
T ss_pred CCCcEEHHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEECC
Confidence 45677899999877323477899999999999999999999999999999999844
No 51
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=97.18 E-value=0.0015 Score=61.50 Aligned_cols=69 Identities=20% Similarity=0.229 Sum_probs=53.2
Q ss_pred cEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCce
Q 022339 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (298)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (298)
.+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||-..||
T Consensus 3 Gil~i~KP~G~tS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~AtG 43 (290)
T PRK00130 3 GILNILKPPGMTSF--------DVVRKIRKIAK-------------------------------IKKVGHTGTLDPLASG 43 (290)
T ss_pred eEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccCcCCCCCCCCee
Confidence 68999999998765 46777776653 2367789999999999
Q ss_pred eEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 225 LlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
+|+++-.+. .++.+.+.. -.|+|.|.+.
T Consensus 44 vL~v~vG~a--Tkl~~~l~~--~~K~Y~a~~~ 71 (290)
T PRK00130 44 VLPVCLGKA--TKIVDYLME--GKKTYRAEIK 71 (290)
T ss_pred EEEEEEChh--hhhHHHhcc--CCcEEEEEEE
Confidence 999999873 334444443 4899999986
No 52
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=97.14 E-value=0.0009 Score=58.48 Aligned_cols=52 Identities=17% Similarity=0.214 Sum_probs=45.3
Q ss_pred cchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCC--EEeec
Q 022339 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGD--MVNCT 121 (298)
Q Consensus 70 g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD--~I~i~ 121 (298)
..|||.+|.+..-.-|+.+++++|..|.|.|||+++++|++.|..++ .|.+.
T Consensus 102 erRLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~ 155 (177)
T PRK04051 102 ERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYY 155 (177)
T ss_pred HhHHHHHHHHccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEe
Confidence 45999999888556799999999999999999999999999999984 56554
No 53
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=97.13 E-value=0.0018 Score=61.37 Aligned_cols=70 Identities=24% Similarity=0.330 Sum_probs=53.6
Q ss_pred CcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCc
Q 022339 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (298)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TS 223 (298)
+.+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||...|
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 368999999998766 36777777653 236678999999999
Q ss_pred eeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 224 GLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
|+|+++-.+. .+|.+.+.. -.|+|.|.+.
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 9999999874 334444444 3899999986
No 54
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=97.12 E-value=0.0016 Score=61.44 Aligned_cols=71 Identities=24% Similarity=0.384 Sum_probs=53.8
Q ss_pred CCcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCC
Q 022339 143 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 222 (298)
Q Consensus 143 D~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~T 222 (298)
-+.+|+||||.|+-+| .+++.+.+.+. ..+.+..+-||-..
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 3579999999998765 36777777653 23677899999999
Q ss_pred ceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 223 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 223 SGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
||||+++-.+. .++.+.+.+ -.|+|.|.+.
T Consensus 49 tGvL~i~vG~a--TKl~~~l~~--~~K~Y~a~~~ 78 (298)
T PRK03287 49 TGVLVLGVERA--TKLLGHLTL--TDKSYTATIR 78 (298)
T ss_pred eeEEEEEeChh--hhhhHHHhc--CCcEEEEEEE
Confidence 99999999862 333344443 4899999986
No 55
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=97.11 E-value=0.0015 Score=61.52 Aligned_cols=69 Identities=22% Similarity=0.233 Sum_probs=52.7
Q ss_pred cEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCce
Q 022339 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (298)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (298)
.+|++|||+|+-+| .+++.+.+.+. ..+.+..+.||-..||
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 68999999998766 36777776653 2467789999999999
Q ss_pred eEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 225 LlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
+|+++-.+. . ++.+.+.. -.|+|.|.+.
T Consensus 45 vL~i~vG~a-T-kl~~~l~~--~~K~Y~a~~~ 72 (294)
T PRK02484 45 VLPIAVGKA-T-RLIEYMTE--AGKVYEGEIT 72 (294)
T ss_pred EEEEEEChh-h-hhhHHhcc--CCcEEEEEEE
Confidence 999999874 2 34444443 4699999986
No 56
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=97.10 E-value=0.0015 Score=61.90 Aligned_cols=70 Identities=20% Similarity=0.257 Sum_probs=54.0
Q ss_pred CcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCc
Q 022339 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (298)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TS 223 (298)
+.+|+||||.|+-+| .+++.+.+.+. ..+.+..+.||-..|
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 368999999998765 36777776653 246778999999999
Q ss_pred eeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 224 GLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
|+|+++-.+.+ ++.+.+.. ..|+|.|.+.
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 99999999753 34444443 6899999985
No 57
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=97.09 E-value=0.0015 Score=61.59 Aligned_cols=71 Identities=25% Similarity=0.307 Sum_probs=54.7
Q ss_pred CcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCc
Q 022339 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (298)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TS 223 (298)
+.+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||-..|
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 368999999998765 36777776653 246778999999999
Q ss_pred eeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe-ee
Q 022339 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS-GV 258 (298)
Q Consensus 224 GLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~-G~ 258 (298)
|+|+++-.+.+ +|.+.+. . .|+|.|.+. |.
T Consensus 44 GvL~i~vG~aT--kl~~~l~--~-~K~Y~a~~~lG~ 74 (295)
T PRK02755 44 GVLPIALGKAT--RLLPYLP--G-EKTYRGTIRFGV 74 (295)
T ss_pred eEEEEEEChhh--hhHHHhC--C-CcEEEEEEEECC
Confidence 99999999854 4555554 2 799999986 44
No 58
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=97.07 E-value=0.002 Score=61.00 Aligned_cols=72 Identities=22% Similarity=0.220 Sum_probs=54.3
Q ss_pred CcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCc
Q 022339 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (298)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TS 223 (298)
+.+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||...|
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 479999999998766 36777776653 246778999999999
Q ss_pred eeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe-ee
Q 022339 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS-GV 258 (298)
Q Consensus 224 GLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~-G~ 258 (298)
|||+++-.+. .++.+.+.. -.|+|.|.+. |.
T Consensus 54 GvL~v~vG~a--Tkl~~~l~~--~~K~Y~a~~~lG~ 85 (305)
T PRK05389 54 GVLPIALGEA--TKTVPYVMD--GTKRYRFTVAWGE 85 (305)
T ss_pred eEEEEEEChh--hhhhHHhcc--CCcEEEEEEEECC
Confidence 9999999873 334444433 4899999986 43
No 59
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=97.04 E-value=0.002 Score=60.22 Aligned_cols=68 Identities=24% Similarity=0.370 Sum_probs=51.6
Q ss_pred EEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCcee
Q 022339 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (298)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (298)
+|++|||.|+-+| .+++.+.+.+. ..+.+..+.||-..||+
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 6899999998776 35777776543 24677899999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 226 lL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
|+++-.+. .++.+.+. ...|+|.|.+.
T Consensus 43 L~v~vG~a--Tkl~~~l~--~~~K~Y~a~~~ 69 (279)
T PRK02193 43 LLVATDED--TKLIDYLD--QKDKTYIAKIK 69 (279)
T ss_pred EEEEEChh--hhhhHHhc--cCCcEEEEEEE
Confidence 99999873 33444442 36899999986
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=0.0021 Score=60.00 Aligned_cols=70 Identities=24% Similarity=0.378 Sum_probs=53.6
Q ss_pred EEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCcee
Q 022339 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (298)
Q Consensus 146 llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (298)
+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||-..|||
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 7899999998766 36777776653 23567899999999999
Q ss_pred EEEEcCHHHHHHHHHHHhcCeeceEEEEEEe-ee
Q 022339 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTS-GV 258 (298)
Q Consensus 226 lL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~-G~ 258 (298)
|+++-.+. .+|.+.+.. ..|+|.|.+. |.
T Consensus 43 L~v~vG~a--Tkl~~~l~~--~~K~Y~~~~~~G~ 72 (277)
T cd02573 43 LPIALGEA--TKLSQYLLD--ADKTYRATVRLGE 72 (277)
T ss_pred EEEEEChH--HhhHHHhcC--CCcEEEEEEEECC
Confidence 99999974 335455444 5999999986 43
No 61
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=96.98 E-value=0.0022 Score=60.66 Aligned_cols=71 Identities=17% Similarity=0.209 Sum_probs=53.3
Q ss_pred CCcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCC
Q 022339 143 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 222 (298)
Q Consensus 143 D~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~T 222 (298)
.+.+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||...
T Consensus 21 ~~g~l~i~Kp~g~tS~--------~~v~~~r~~~~-------------------------------~kkvGH~GTLDp~A 61 (300)
T PRK04270 21 KFGVVNLDKPPGPTSH--------EVAAWVRDILG-------------------------------VEKAGHGGTLDPKV 61 (300)
T ss_pred CCCEEEEECCCCCCHH--------HHHHHHHHHhc-------------------------------cccccCCCCCCCcC
Confidence 3579999999998765 36777776553 23567899999999
Q ss_pred ceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 223 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 223 SGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
||+|+++-.+. .+|.+.+.+ -.|+|.|.+.
T Consensus 62 ~GvL~v~~g~a--tk~~~~~~~--~~K~Y~~~~~ 91 (300)
T PRK04270 62 TGVLPVALGKA--TKVVQALLE--SGKEYVCVMH 91 (300)
T ss_pred eEEEEEEEChH--hhhhHHhcc--CCcEEEEEEE
Confidence 99999999873 344444443 4699999875
No 62
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=96.98 E-value=0.0028 Score=60.11 Aligned_cols=70 Identities=19% Similarity=0.289 Sum_probs=54.0
Q ss_pred CcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCc
Q 022339 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (298)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TS 223 (298)
+.+|+||||.|+-+| .+++.+.+.+. ..+.+..+-||-..|
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 479999999998776 36777776553 246678999999999
Q ss_pred eeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 224 GLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
|||+++-.+. .+|.+.+.. -.|+|.|.+.
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 235555444 4899999986
No 63
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=96.97 E-value=0.0029 Score=60.48 Aligned_cols=70 Identities=21% Similarity=0.218 Sum_probs=52.7
Q ss_pred CcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCc
Q 022339 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (298)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TS 223 (298)
+.+|++|||.|+-+| .+++.+.+.+. ..+.+..+.||...|
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 479999999998765 36777776553 246778999999999
Q ss_pred eeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 224 GLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
|+|+++-.+. .++.+.+.+ -.|+|.|.+.
T Consensus 44 GVL~i~vG~a--TKl~~~l~~--~~K~Y~a~~~ 72 (345)
T PRK14846 44 GILPFAVGEA--TKLIHLLID--ARKTYIFTVK 72 (345)
T ss_pred eEEEEEEChh--hhhhHHHhc--CCceEEEEEE
Confidence 9999999873 333333332 5899999986
No 64
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=96.96 E-value=0.0026 Score=60.19 Aligned_cols=69 Identities=22% Similarity=0.287 Sum_probs=53.0
Q ss_pred cEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCce
Q 022339 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (298)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (298)
.+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||-..||
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 68999999998766 36777777653 2356789999999999
Q ss_pred eEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 225 LlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
+|+++-.+. .+|.+.+.. -.|+|.|.+.
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 999999874 234444443 4899999986
No 65
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=96.95 E-value=0.0026 Score=59.78 Aligned_cols=70 Identities=21% Similarity=0.248 Sum_probs=52.7
Q ss_pred CcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCc
Q 022339 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (298)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TS 223 (298)
+.+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||-..|
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 479999999998765 46777776653 246778999999999
Q ss_pred eeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 224 GLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
|+|+++-.+. . ++.+.+.+ -.|+|.|.+.
T Consensus 44 GvL~v~vG~a-T-Kl~~~l~~--~~K~Y~~~~~ 72 (292)
T PRK01528 44 GVLPLAVGEA-T-KLVQLLID--AKKTYIFTVK 72 (292)
T ss_pred eEEEEEEChH-h-hhhHHHhc--CCceEEEEEE
Confidence 9999999873 3 33333332 5799999986
No 66
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=96.93 E-value=0.0026 Score=47.54 Aligned_cols=57 Identities=21% Similarity=0.238 Sum_probs=48.5
Q ss_pred CCCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeecc
Q 022339 66 TKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (298)
Q Consensus 66 ~~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~ 122 (298)
...+-..|.+||...--.-|=.+++.+|..|.|+|||++-++-..+|..||.|++..
T Consensus 7 i~~e~I~L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~ 63 (73)
T COG2501 7 IKTEFITLGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPG 63 (73)
T ss_pred eccceEEHHHHHHHhCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECC
Confidence 445667899999876323488899999999999999999988999999999999854
No 67
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=96.90 E-value=0.0034 Score=59.31 Aligned_cols=70 Identities=20% Similarity=0.288 Sum_probs=53.5
Q ss_pred CcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCc
Q 022339 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (298)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TS 223 (298)
+.+|+||||.|+-+| .+++.+.+.+. ..+.+..+-||-..|
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 579999999998765 36777777653 235677999999999
Q ss_pred eeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 224 GLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
|+|+++-.+. .+|.+.+.. -.|+|.|.+.
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 9999999874 234444443 4699999986
No 68
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=96.84 E-value=0.0038 Score=59.22 Aligned_cols=69 Identities=26% Similarity=0.400 Sum_probs=52.9
Q ss_pred cEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCce
Q 022339 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (298)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (298)
.+|+||||.|+-+| .+++.+.+.+. ..+.+..+-||-..||
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 47999999998765 36777776653 2366789999999999
Q ss_pred eEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 225 LlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
+|+++-.+.+ +|.+.+. ...|+|.|.+.
T Consensus 43 vL~i~iG~aT--Kl~~~l~--~~~K~Y~a~~~ 70 (312)
T PRK14122 43 VLVLCTDDST--KLVPFLS--AEDKEYLAWVS 70 (312)
T ss_pred eEEEEEChhh--hhhHHhc--CCCceEEEEEE
Confidence 9999998743 2544443 36899999986
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=96.55 E-value=0.0058 Score=58.30 Aligned_cols=71 Identities=20% Similarity=0.276 Sum_probs=53.5
Q ss_pred CCcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCC
Q 022339 143 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 222 (298)
Q Consensus 143 D~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~T 222 (298)
.+.+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||-..
T Consensus 33 ~~G~l~i~KP~g~tS~--------~~v~~vr~~~~-------------------------------~kkvGH~GTLDP~A 73 (322)
T TIGR00425 33 SYGVVNLDKPSGPSSH--------EVVAWVRRILN-------------------------------VEKTGHGGTLDPKV 73 (322)
T ss_pred CCCEEEEeCCCCCCHH--------HHHHHHHHHhc-------------------------------ccccCCCCCCCCCC
Confidence 3479999999998776 36777776653 23567799999999
Q ss_pred ceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 223 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 223 SGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
||+|+++-.+. .+|.+.+.. -.|+|.|.+.
T Consensus 74 ~GvL~v~~G~a--Tkl~~~~~~--~~K~Y~~~v~ 103 (322)
T TIGR00425 74 TGVLPVCIERA--TRLVKSLQE--APKEYVCLMR 103 (322)
T ss_pred ceEEEEEEChH--hhccHHhcc--CCCEEEEEEE
Confidence 99999999873 334343332 6899999885
No 70
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=96.50 E-value=0.0092 Score=56.33 Aligned_cols=70 Identities=19% Similarity=0.244 Sum_probs=53.3
Q ss_pred CcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCc
Q 022339 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (298)
Q Consensus 144 ~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TS 223 (298)
+.+|++|||.|+-+| .+++.+.+.+. ..+.+..+-||-..|
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 479999999998766 36777777653 235677999999999
Q ss_pred eeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 224 GLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
|+|+++-.+. .+|.+.+.. -.|+|.|.+.
T Consensus 51 GvL~v~~G~a--Tkl~~~l~~--~~K~Y~a~~~ 79 (300)
T PRK04642 51 GLLPLCFGEA--TKIAGLLLG--SAKAYDAEIV 79 (300)
T ss_pred eeEEEEEChh--hhhhHHhcC--CCcEEEEEEE
Confidence 9999998873 334444332 5899999985
No 71
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=96.47 E-value=0.0048 Score=53.18 Aligned_cols=51 Identities=16% Similarity=0.188 Sum_probs=42.3
Q ss_pred chHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCC--CEEeec
Q 022339 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGG--DMVNCT 121 (298)
Q Consensus 71 ~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~g--D~I~i~ 121 (298)
.||+-.+.+.--.-|..+++++|..|.|.|||++|+.|++.|..| |.|.+.
T Consensus 104 RRL~~vv~r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~ 156 (162)
T TIGR01018 104 RRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFA 156 (162)
T ss_pred HhHhhHhhhccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeee
Confidence 577777766644569999999999999999999999999999998 556553
No 72
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=96.43 E-value=0.0089 Score=56.72 Aligned_cols=43 Identities=21% Similarity=0.234 Sum_probs=34.0
Q ss_pred CCceecccCCCCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 210 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 210 ~~~~~vhRLD~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
.+.+..+-||-..||||+++-... .+.++.. .. ..|+|.|.+.
T Consensus 56 ~KiGH~GTLDPlAsGVLvvgvG~a-TK~l~~~-l~--~~K~Y~~~~~ 98 (312)
T cd02867 56 LKIGHGGTLDPLATGVLVVGVGAG-TKQLQDY-LS--CSKTYEATGL 98 (312)
T ss_pred cccccccccCCccceeEEEEECcH-HHHHHHH-hc--CCceEEEEEE
Confidence 578899999999999999999864 4444443 32 7999999876
No 73
>PLN00189 40S ribosomal protein S9; Provisional
Probab=96.42 E-value=0.0021 Score=56.78 Aligned_cols=53 Identities=19% Similarity=0.114 Sum_probs=42.1
Q ss_pred hHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeecccc
Q 022339 72 RLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (298)
Q Consensus 72 rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~ 124 (298)
||+..+.+.--.-|..+++++|..|.|.|||++|+.|++.|..|+++.|.+.+
T Consensus 110 RL~~vv~r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~~ 162 (194)
T PLN00189 110 RLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSL 162 (194)
T ss_pred hhceeeeecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEEec
Confidence 44444433322459999999999999999999999999999999988887643
No 74
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=96.14 E-value=0.015 Score=54.24 Aligned_cols=72 Identities=17% Similarity=0.244 Sum_probs=53.7
Q ss_pred cEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCCCCCce
Q 022339 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (298)
Q Consensus 145 ~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (298)
.+|++|||.|+-+| .++..+.+.+. ..+.+..+-||-..||
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 89999999998766 36677776653 2456779999999999
Q ss_pred eEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe-eec
Q 022339 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS-GVP 259 (298)
Q Consensus 225 LlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~-G~~ 259 (298)
+|.++-. ++.+.+.-+.. -.|+|.|.+. |.-
T Consensus 57 vLpi~ig-~aTKl~~~l~~---~~K~Y~a~~~lG~~ 88 (271)
T COG0130 57 VLPICLG-EATKLVQYLLD---ADKEYVATVRLGDQ 88 (271)
T ss_pred eEEEEec-hhHhHHHHHhh---CCcEEEEEEEeCCc
Confidence 9999998 44444443322 5899999986 543
No 75
>PRK04313 30S ribosomal protein S4e; Validated
Probab=95.99 E-value=0.024 Score=51.73 Aligned_cols=74 Identities=14% Similarity=0.126 Sum_probs=56.6
Q ss_pred CccchHHHHHHhccCC-cCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccccccccCCCCeeeeecCCcE
Q 022339 68 AGKLRLDAWISSRIDG-ISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNV 146 (298)
Q Consensus 68 ~~g~rLdk~L~~~~~~-~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~~~~~~~~~~~~IlyeD~~l 146 (298)
.+...|.-+|+..|+. .+.+++++.|.+|.|.|||++.+...+.+-.-|+|+|... +...+|||.....
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 4556788899988764 5999999999999999999999877777777799999542 2235666666665
Q ss_pred EEEeC
Q 022339 147 LVVNK 151 (298)
Q Consensus 147 lvvnK 151 (298)
+++.+
T Consensus 105 ~~l~~ 109 (237)
T PRK04313 105 LVLIP 109 (237)
T ss_pred EEEEE
Confidence 55544
No 76
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=95.79 E-value=0.0098 Score=52.17 Aligned_cols=52 Identities=17% Similarity=0.052 Sum_probs=41.9
Q ss_pred chHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeecc
Q 022339 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (298)
Q Consensus 71 ~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~ 122 (298)
.||+..+.+.--.-|..+++++|..|.|.|||++|+.|++.|..|++=.|.+
T Consensus 107 RRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I~~ 158 (181)
T PTZ00155 107 RRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDF 158 (181)
T ss_pred HhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceEeccCccCceee
Confidence 4666666655334699999999999999999999999999999986554444
No 77
>PLN00036 40S ribosomal protein S4; Provisional
Probab=95.72 E-value=0.035 Score=51.26 Aligned_cols=74 Identities=14% Similarity=0.207 Sum_probs=56.0
Q ss_pred CccchHHHHHHhccCC-cCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccccccccCCCCeeeeecCCcE
Q 022339 68 AGKLRLDAWISSRIDG-ISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNV 146 (298)
Q Consensus 68 ~~g~rLdk~L~~~~~~-~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~~~~~~~~~~~~IlyeD~~l 146 (298)
.+...|.-||+..|+. .+.+++++.+.+|.|.|||++.+...+.+-.-|+|+|... +...+|||.....
T Consensus 39 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt----------~e~yRvl~D~kGr 108 (261)
T PLN00036 39 RECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPKT----------NENFRLLYDTKGR 108 (261)
T ss_pred ccccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcCC----------CCeEEEEECCCce
Confidence 3556788899998764 5889999999999999999999877777766699999542 2235666666665
Q ss_pred EEEeC
Q 022339 147 LVVNK 151 (298)
Q Consensus 147 lvvnK 151 (298)
+++++
T Consensus 109 f~l~~ 113 (261)
T PLN00036 109 FRLHR 113 (261)
T ss_pred EEEEE
Confidence 55544
No 78
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=95.62 E-value=0.039 Score=51.29 Aligned_cols=74 Identities=20% Similarity=0.213 Sum_probs=55.8
Q ss_pred CccchHHHHHHhccCC-cCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccccccccCCCCeeeeecCCcE
Q 022339 68 AGKLRLDAWISSRIDG-ISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNV 146 (298)
Q Consensus 68 ~~g~rLdk~L~~~~~~-~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~~~~~~~~~~~~IlyeD~~l 146 (298)
.+...|.-||+..|+. .+.+++++.+.+|.|.|||++.+...+.|-.-|+|+|... +...+|||.....
T Consensus 36 ~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~kt----------~e~yRvl~D~kGr 105 (273)
T PTZ00223 36 RECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPKT----------GDRFRILYDVKGR 105 (273)
T ss_pred ccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcCC----------CCeEEEEECCCCc
Confidence 4556788899988764 5899999999999999999999877777766699998542 2235666666665
Q ss_pred EEEeC
Q 022339 147 LVVNK 151 (298)
Q Consensus 147 lvvnK 151 (298)
+++++
T Consensus 106 f~l~~ 110 (273)
T PTZ00223 106 FALVK 110 (273)
T ss_pred EEEEE
Confidence 55543
No 79
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=95.57 E-value=0.042 Score=50.79 Aligned_cols=73 Identities=18% Similarity=0.241 Sum_probs=54.9
Q ss_pred CccchHHHHHHhccCC-cCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccccccccCCCCeeeeecCCcE
Q 022339 68 AGKLRLDAWISSRIDG-ISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNV 146 (298)
Q Consensus 68 ~~g~rLdk~L~~~~~~-~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~~~~~~~~~~~~IlyeD~~l 146 (298)
.+...|.-||+..++. .+.+++++.|.+|.|.|||++.+...+.+-.-|+|+|... +...+|||.....
T Consensus 39 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt----------~e~yRvl~D~kGr 108 (262)
T PTZ00118 39 RECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTKT----------NEYFRLLYDTKGR 108 (262)
T ss_pred ccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEcCC----------CCeEEEEECCCcc
Confidence 4556788899988864 5899999999999999999999877777766799998542 2234566655555
Q ss_pred EEEe
Q 022339 147 LVVN 150 (298)
Q Consensus 147 lvvn 150 (298)
++++
T Consensus 109 ~~l~ 112 (262)
T PTZ00118 109 FVPH 112 (262)
T ss_pred EEEE
Confidence 5444
No 80
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=92.72 E-value=0.25 Score=44.82 Aligned_cols=71 Identities=14% Similarity=0.163 Sum_probs=48.6
Q ss_pred hHHHHHHhccC-CcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccccccccCCCCeeeeecCCcEEEEe
Q 022339 72 RLDAWISSRID-GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVN 150 (298)
Q Consensus 72 rLdk~L~~~~~-~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~~~~~~~~~~~~IlyeD~~llvvn 150 (298)
.|.-+++..+. .-.-+++++.|.+|.|+|||++.+...+.|---|+|+|... ....+|||.....++++
T Consensus 42 PL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~t----------gE~yRvl~d~~grl~l~ 111 (241)
T COG1471 42 PLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPKT----------GEHYRVLPDEKGRLVLH 111 (241)
T ss_pred cEEeeehhHHHhccchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECCC----------CceEEEEecCCccEEEE
Confidence 34434444433 24678999999999999999998655555544499998542 23467888887777776
Q ss_pred CC
Q 022339 151 KP 152 (298)
Q Consensus 151 KP 152 (298)
+=
T Consensus 112 ~i 113 (241)
T COG1471 112 PI 113 (241)
T ss_pred ec
Confidence 53
No 81
>PRK01777 hypothetical protein; Validated
Probab=91.08 E-value=0.24 Score=39.00 Aligned_cols=54 Identities=17% Similarity=0.225 Sum_probs=40.8
Q ss_pred CCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccc
Q 022339 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (298)
Q Consensus 67 ~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~ 123 (298)
-.+|.++.+.|... ++....-+--+..+.|-|||+.+ ..++.|+.||+|+|+.+
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 45677888888876 45554222234568999999999 69999999999999874
No 82
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=89.68 E-value=0.61 Score=46.05 Aligned_cols=47 Identities=21% Similarity=0.228 Sum_probs=39.1
Q ss_pred cchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCC
Q 022339 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGD 116 (298)
Q Consensus 70 g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD 116 (298)
+..|.++|...--.-|+++++++|.+|.|+|||++++.++..+.+++
T Consensus 342 ~~~~~~~l~~~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~ 388 (410)
T PRK13354 342 TKNLVDLLVDLGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPED 388 (410)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhh
Confidence 56788888876445699999999999999999999977777776665
No 83
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=89.46 E-value=0.33 Score=37.06 Aligned_cols=47 Identities=30% Similarity=0.426 Sum_probs=38.8
Q ss_pred CCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeecc
Q 022339 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (298)
Q Consensus 67 ~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~ 122 (298)
-+.+..+...+... +++..++ |.|.|||+.+ ..++.++.||.|.|+.
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 34566788888665 5888877 8999999999 6999999999999975
No 84
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=88.39 E-value=0.82 Score=40.01 Aligned_cols=64 Identities=22% Similarity=0.402 Sum_probs=47.6
Q ss_pred eEEEEEEcCCCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccc
Q 022339 58 VQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (298)
Q Consensus 58 ~~~~~~v~~~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~ 123 (298)
+.+...+ ......||+.+|++.+ ++||++++++|..|.|..+-........+++.|-.|.|+..
T Consensus 127 vel~l~~-~~p~qlrl~~Ll~seL-~LSrS~lq~lie~g~Irgdtd~~~l~rkrlr~~~~i~Id~~ 190 (203)
T COG4332 127 VELSLRI-SRPFQLRLDRLLASEL-GLSRSELQRLIETGQIRGDTDKMLLLRKRLRAGYDIQIDVE 190 (203)
T ss_pred EEEEEcc-cCcchhHHHHHHHHHh-CcCHHHHHHHHHcCceeecchHHHHhhhhhhcCcEEEEEcC
Confidence 4444333 3567789999999997 69999999999999999876543334566778877777653
No 85
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=88.24 E-value=1.1 Score=44.12 Aligned_cols=45 Identities=24% Similarity=0.194 Sum_probs=36.7
Q ss_pred cchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccC
Q 022339 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKG 114 (298)
Q Consensus 70 g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~ 114 (298)
+..|.++|.+.--.-|+++++++|++|.|+|||++++..+..+..
T Consensus 342 ~~~~~~~l~~~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~ 386 (408)
T PRK05912 342 GIDLLALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTA 386 (408)
T ss_pred CCcHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEecCccccccc
Confidence 567888888763356999999999999999999999766666655
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=87.62 E-value=0.98 Score=34.29 Aligned_cols=28 Identities=21% Similarity=0.181 Sum_probs=25.5
Q ss_pred CCceecccCCCCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 210 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 210 ~~~~~vhRLD~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
.+++.++++|+.++|+++++ ++|..++.
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 46788999999999999999 88999888
No 87
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=85.66 E-value=1.2 Score=37.63 Aligned_cols=36 Identities=31% Similarity=0.514 Sum_probs=32.3
Q ss_pred CCCccchHHHHHHhccCCcCHHHHHHHHHCCceEECC
Q 022339 66 TKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSING 102 (298)
Q Consensus 66 ~~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNG 102 (298)
+.....||+.+|++.+ ++||+++++++.+|.|..+-
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 5667889999999997 69999999999999999764
No 88
>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=85.24 E-value=1.1 Score=38.08 Aligned_cols=43 Identities=23% Similarity=0.282 Sum_probs=31.6
Q ss_pred CCceecccCCCCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEe
Q 022339 210 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (298)
Q Consensus 210 ~~~~~vhRLD~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~ 256 (298)
.+.+..+.||-..||||+++-+.. .+|.+.+.. ..|+|.|...
T Consensus 7 ~KvGH~GTLDP~AsGvL~v~vg~~--Tkl~~~l~~--~~K~Y~~~~~ 49 (149)
T PF01509_consen 7 KKVGHGGTLDPFASGVLVVGVGKA--TKLLSYLQN--SDKEYVATIR 49 (149)
T ss_dssp SSEEESS-SSTT-EEEEEEEEGGG--GGGHHHHTT--SEEEEEEEEE
T ss_pred ceeccccccCCcceEEEEEEECCc--chHHHHhhc--cCCEEEEEEE
Confidence 577889999999999999999873 234445554 4599999875
No 89
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=84.42 E-value=3.5 Score=30.19 Aligned_cols=45 Identities=20% Similarity=0.336 Sum_probs=34.1
Q ss_pred CccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeecc
Q 022339 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (298)
Q Consensus 68 ~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~ 122 (298)
.++.++.++|... . ++. +.-.|.+||+.+ ..+..|+.||+|++..
T Consensus 21 ~~~~tv~~ll~~l-~-~~~-------~~v~v~vNg~iv-~~~~~l~~gD~Veii~ 65 (70)
T PRK08364 21 RKGMKVADILRAV-G-FNT-------ESAIAKVNGKVA-LEDDPVKDGDYVEVIP 65 (70)
T ss_pred CCCCcHHHHHHHc-C-CCC-------ccEEEEECCEEC-CCCcCcCCCCEEEEEc
Confidence 3457899999876 3 443 335788999999 5799999999998843
No 90
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=82.22 E-value=4 Score=29.97 Aligned_cols=51 Identities=14% Similarity=0.180 Sum_probs=32.5
Q ss_pred cchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeecc
Q 022339 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (298)
Q Consensus 70 g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~ 122 (298)
+.++..+|.......+. ........-.|.|||+.+. .+..|+.||+|.+..
T Consensus 25 ~~tv~~ll~~l~~~~~~-~~~~~~~~~~v~vNg~~v~-~~~~l~~gD~v~i~p 75 (80)
T cd00754 25 GATVGELLDALEARYPG-LLEELLARVRIAVNGEYVR-LDTPLKDGDEVAIIP 75 (80)
T ss_pred CCcHHHHHHHHHHHCch-HHHhhhhcEEEEECCeEcC-CCcccCCCCEEEEeC
Confidence 55666555543211221 1223334457899999995 889999999999854
No 91
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=70.16 E-value=11 Score=28.12 Aligned_cols=51 Identities=10% Similarity=0.127 Sum_probs=32.3
Q ss_pred ccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeecc
Q 022339 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (298)
Q Consensus 69 ~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~ 122 (298)
++.++..++....... ..+.++...=.|.|||+.+ ..+..|+.||+|.+..
T Consensus 27 ~~~tv~~L~~~l~~~~--p~l~~~~~~~~vavN~~~v-~~~~~l~dgDeVai~P 77 (82)
T PLN02799 27 AGSTTADCLAELVAKF--PSLEEVRSCCVLALNEEYT-TESAALKDGDELAIIP 77 (82)
T ss_pred CCCcHHHHHHHHHHHC--hhHHHHhhCcEEEECCEEc-CCCcCcCCCCEEEEeC
Confidence 3555666655442111 1233433333688999998 5889999999999853
No 92
>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=70.07 E-value=4.9 Score=29.20 Aligned_cols=52 Identities=15% Similarity=0.187 Sum_probs=32.3
Q ss_pred CccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEecc--ccccccCCCEEeecc
Q 022339 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK--VSHNVKGGDMVNCTI 122 (298)
Q Consensus 68 ~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~--~~~~v~~gD~I~i~~ 122 (298)
.++.++..+|.......+.-. ....=.|.|||+.+.. .+..|+.||+|.+..
T Consensus 19 ~~~~tv~~ll~~l~~~~p~~~---~~~~~~v~vN~~~v~~~~~~~~l~~gD~V~i~p 72 (77)
T PF02597_consen 19 PEGSTVRDLLEALAERYPELA---LRDRVAVAVNGEIVPDDGLDTPLKDGDEVAILP 72 (77)
T ss_dssp SSTSBHHHHHHHHCHHTGGGH---TTTTEEEEETTEEEGGGTTTSBEETTEEEEEEE
T ss_pred CCCCcHHHHHHHHHhhccccc---cCccEEEEECCEEcCCccCCcCcCCCCEEEEEC
Confidence 344556666655421122111 3345578899999953 289999999998843
No 93
>PRK06437 hypothetical protein; Provisional
Probab=69.91 E-value=4.9 Score=29.27 Aligned_cols=45 Identities=27% Similarity=0.279 Sum_probs=33.8
Q ss_pred CccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeecc
Q 022339 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (298)
Q Consensus 68 ~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~ 122 (298)
+++.++.++|.++ + ++...+ .|.+||+.+ ..++.|+.||.|++..
T Consensus 18 ~~~~tv~dLL~~L-g-i~~~~v-------aV~vNg~iv-~~~~~L~dgD~Veiv~ 62 (67)
T PRK06437 18 DHELTVNDIIKDL-G-LDEEEY-------VVIVNGSPV-LEDHNVKKEDDVLILE 62 (67)
T ss_pred CCCCcHHHHHHHc-C-CCCccE-------EEEECCEEC-CCceEcCCCCEEEEEe
Confidence 4557899999875 3 543222 577999999 4899999999999853
No 94
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=69.00 E-value=5.4 Score=28.48 Aligned_cols=46 Identities=24% Similarity=0.425 Sum_probs=31.9
Q ss_pred CccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEec---cccccccCCCEEeecc
Q 022339 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVS---KVSHNVKGGDMVNCTI 122 (298)
Q Consensus 68 ~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~---~~~~~v~~gD~I~i~~ 122 (298)
.++.+|..+|... + +....+ .|.+||+.+. ..+..|+.||+|+|..
T Consensus 13 ~~~~tl~~lL~~l-~-~~~~~v-------av~vNg~iv~r~~~~~~~l~~gD~vei~~ 61 (66)
T PRK05659 13 PDGESVAALLARE-G-LAGRRV-------AVEVNGEIVPRSQHASTALREGDVVEIVH 61 (66)
T ss_pred CCCCCHHHHHHhc-C-CCCCeE-------EEEECCeEeCHHHcCcccCCCCCEEEEEE
Confidence 3467788888765 3 333222 3889998773 2678899999999853
No 95
>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=65.19 E-value=6.1 Score=28.27 Aligned_cols=44 Identities=18% Similarity=0.349 Sum_probs=30.7
Q ss_pred ccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEecccc----ccccCCCEEeecc
Q 022339 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVS----HNVKGGDMVNCTI 122 (298)
Q Consensus 69 ~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~----~~v~~gD~I~i~~ 122 (298)
++.++..+|... . ++. +.+ .|.|||+.+. .+ ..|+.||+|++..
T Consensus 13 ~~~tv~~ll~~l-~-~~~----~~i---~V~vNg~~v~-~~~~~~~~L~~gD~V~ii~ 60 (65)
T cd00565 13 EGATLAELLEEL-G-LDP----RGV---AVALNGEIVP-RSEWASTPLQDGDRIEIVT 60 (65)
T ss_pred CCCCHHHHHHHc-C-CCC----CcE---EEEECCEEcC-HHHcCceecCCCCEEEEEE
Confidence 356788888765 3 332 111 4679999984 45 7899999998843
No 96
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=65.09 E-value=16 Score=27.11 Aligned_cols=25 Identities=24% Similarity=0.307 Sum_probs=21.5
Q ss_pred ceEECCEEeccccccccCCCEEeecc
Q 022339 97 LVSINGQVVSKVSHNVKGGDMVNCTI 122 (298)
Q Consensus 97 ~V~VNGk~v~~~~~~v~~gD~I~i~~ 122 (298)
.|.|||+.+. .+..|+.||+|.+..
T Consensus 51 ~v~vn~~~v~-~~~~l~dgDevai~P 75 (80)
T TIGR01682 51 MVAVNEEYVT-DDALLNEGDEVAFIP 75 (80)
T ss_pred EEEECCEEcC-CCcCcCCCCEEEEeC
Confidence 5889999985 689999999998853
No 97
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=63.05 E-value=18 Score=27.03 Aligned_cols=45 Identities=22% Similarity=0.344 Sum_probs=29.7
Q ss_pred hHHHHHHhccCCcCHHHHHHHHHCC--ceEECCEEeccccccccCCCEEeecc
Q 022339 72 RLDAWISSRIDGISRARVQSSIRSG--LVSINGQVVSKVSHNVKGGDMVNCTI 122 (298)
Q Consensus 72 rLdk~L~~~~~~~Sr~~~~~lI~~G--~V~VNGk~v~~~~~~v~~gD~I~i~~ 122 (298)
.|-++|.+.++.+ ...+..| .+.||+.-+ ..+..|+.||+|.+..
T Consensus 30 ~l~~~L~~~~~~~-----~~~~~~~~~~~aVN~~~~-~~~~~l~dgDeVai~P 76 (81)
T PRK11130 30 ALRQHLAQKGDRW-----ALALEDGKLLAAVNQTLV-SFDHPLTDGDEVAFFP 76 (81)
T ss_pred HHHHHHHHhCccH-----HhhhcCCCEEEEECCEEc-CCCCCCCCCCEEEEeC
Confidence 3555555554332 2333455 477999887 4788999999999854
No 98
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=62.04 E-value=9.6 Score=37.63 Aligned_cols=40 Identities=25% Similarity=0.212 Sum_probs=29.6
Q ss_pred HHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccc
Q 022339 73 LDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNV 112 (298)
Q Consensus 73 Ldk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v 112 (298)
+-..|....-.-||++++++|.+|.|++||.++...+..+
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 3333333323579999999999999999999987665444
No 99
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=61.68 E-value=20 Score=27.38 Aligned_cols=57 Identities=21% Similarity=0.258 Sum_probs=36.4
Q ss_pred CceEEEEEEcCC----CccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEecc---ccccccCCCEEeec
Q 022339 56 AGVQLEETVDTK----AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (298)
Q Consensus 56 ~~~~~~~~v~~~----~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~---~~~~v~~gD~I~i~ 121 (298)
.+..++.+|... .++..|..+|... . +..+.+ .|.+||..+.+ .+..|+.||.|+|.
T Consensus 15 ~~~~m~I~VNG~~~~~~~~~tl~~LL~~l-~-~~~~~v-------AVevNg~iVpr~~w~~t~L~egD~IEIv 78 (84)
T PRK06083 15 AMVLITISINDQSIQVDISSSLAQIIAQL-S-LPELGC-------VFAINNQVVPRSEWQSTVLSSGDAISLF 78 (84)
T ss_pred CCceEEEEECCeEEEcCCCCcHHHHHHHc-C-CCCceE-------EEEECCEEeCHHHcCcccCCCCCEEEEE
Confidence 344555555422 3567799888864 3 332111 56799998843 55779999999874
No 100
>KOG3301 consensus Ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=61.57 E-value=8.4 Score=33.29 Aligned_cols=33 Identities=21% Similarity=0.161 Sum_probs=29.2
Q ss_pred CcCHHHHHHHHHCCceEECCEEeccccccccCC
Q 022339 83 GISRARVQSSIRSGLVSINGQVVSKVSHNVKGG 115 (298)
Q Consensus 83 ~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~g 115 (298)
..|-..++.+|.++.|.|+++.|+.|++.|+..
T Consensus 109 AkSIhhARvLi~~rhI~V~~qiV~IPsf~vrld 141 (183)
T KOG3301|consen 109 AKSIHHARVLIRQRHIRVGKQIVNIPSFMVRLD 141 (183)
T ss_pred hhhhHHHHHHhcCccEEecCeEeeccceeEeec
Confidence 358888999999999999999999999998843
No 101
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=58.99 E-value=10 Score=27.94 Aligned_cols=44 Identities=16% Similarity=0.326 Sum_probs=32.4
Q ss_pred ccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEecc---ccccccCCCEEeec
Q 022339 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (298)
Q Consensus 69 ~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~---~~~~v~~gD~I~i~ 121 (298)
++.++..+|++. + ++- +.=.|.+||..+.+ .++.|+.||+|+|.
T Consensus 16 ~~~tv~dLL~~l-~-~~~-------~~vav~vNg~iVpr~~~~~~~l~~gD~ievv 62 (68)
T COG2104 16 EGTTVADLLAQL-G-LNP-------EGVAVAVNGEIVPRSQWADTILKEGDRIEVV 62 (68)
T ss_pred CCCcHHHHHHHh-C-CCC-------ceEEEEECCEEccchhhhhccccCCCEEEEE
Confidence 347899999987 3 332 12256799999843 78999999999984
No 102
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=57.27 E-value=12 Score=26.43 Aligned_cols=44 Identities=14% Similarity=0.231 Sum_probs=31.3
Q ss_pred ccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccc---cccccCCCEEeecc
Q 022339 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKV---SHNVKGGDMVNCTI 122 (298)
Q Consensus 69 ~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~---~~~v~~gD~I~i~~ 122 (298)
++.+|..+|... . +.. .-.|.+||..+.+. +..|+.||+|+|..
T Consensus 14 ~~~tl~~ll~~l-~-~~~--------~~~v~vN~~~v~~~~~~~~~L~~gD~vei~~ 60 (65)
T PRK06944 14 DGATVADALAAY-G-ARP--------PFAVAVNGDFVARTQHAARALAAGDRLDLVQ 60 (65)
T ss_pred CCCcHHHHHHhh-C-CCC--------CeEEEECCEEcCchhcccccCCCCCEEEEEe
Confidence 456789898865 3 221 13688999988433 67899999999854
No 103
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=56.30 E-value=12 Score=26.63 Aligned_cols=43 Identities=19% Similarity=0.288 Sum_probs=29.8
Q ss_pred chHHHHHHhccCCcCHHHHHHHHHCCceEECCEEecc---ccccccCCCEEeecc
Q 022339 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCTI 122 (298)
Q Consensus 71 ~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~---~~~~v~~gD~I~i~~ 122 (298)
.+|..+|... . +... .+ .|-+|++.+.+ .+..|+.||+|+|..
T Consensus 15 ~tl~~Ll~~l-~-~~~~----~v---avavN~~iv~~~~~~~~~L~dgD~Ieiv~ 60 (65)
T PRK06488 15 TTLALLLAEL-D-YEGN----WL---ATAVNGELVHKEARAQFVLHEGDRIEILS 60 (65)
T ss_pred CcHHHHHHHc-C-CCCC----eE---EEEECCEEcCHHHcCccccCCCCEEEEEE
Confidence 4788888765 2 3221 11 38899999853 377899999999853
No 104
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=55.68 E-value=12 Score=26.47 Aligned_cols=23 Identities=35% Similarity=0.689 Sum_probs=19.3
Q ss_pred ceEECCEEeccccccccCCCEEee
Q 022339 97 LVSINGQVVSKVSHNVKGGDMVNC 120 (298)
Q Consensus 97 ~V~VNGk~v~~~~~~v~~gD~I~i 120 (298)
...|||+.+ ..++.|+.||+|+|
T Consensus 36 ~A~Vng~~v-dl~~~L~~~d~v~i 58 (60)
T PF02824_consen 36 AAKVNGQLV-DLDHPLEDGDVVEI 58 (60)
T ss_dssp EEEETTEEE-ETTSBB-SSEEEEE
T ss_pred EEEEcCEEC-CCCCCcCCCCEEEE
Confidence 456999999 69999999999987
No 105
>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=53.82 E-value=15 Score=26.10 Aligned_cols=45 Identities=27% Similarity=0.398 Sum_probs=31.4
Q ss_pred ccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEecc---ccccccCCCEEeecc
Q 022339 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCTI 122 (298)
Q Consensus 69 ~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~---~~~~v~~gD~I~i~~ 122 (298)
++.+|..+|... . +.. ..-.|.+||+.+.+ .++.|+.||+|++..
T Consensus 12 ~~~tv~~ll~~l-~-~~~-------~~v~v~vN~~iv~~~~~~~~~L~~gD~veii~ 59 (64)
T TIGR01683 12 DGLTLAALLESL-G-LDP-------RRVAVAVNGEIVPRSEWDDTILKEGDRIEIVT 59 (64)
T ss_pred CCCcHHHHHHHc-C-CCC-------CeEEEEECCEEcCHHHcCceecCCCCEEEEEE
Confidence 356788899865 3 332 33367899999853 346899999999843
No 106
>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=53.66 E-value=24 Score=26.50 Aligned_cols=26 Identities=27% Similarity=0.376 Sum_probs=20.2
Q ss_pred CceEECCEEeccccc--cccCCCEEeecc
Q 022339 96 GLVSINGQVVSKVSH--NVKGGDMVNCTI 122 (298)
Q Consensus 96 G~V~VNGk~v~~~~~--~v~~gD~I~i~~ 122 (298)
=.|.|||+.+. .+. .|+.||+|.+..
T Consensus 56 ~~v~vN~~~v~-~~~~~~l~dgdev~i~P 83 (88)
T TIGR01687 56 VIILVNGRNVD-WGLGTELKDGDVVAIFP 83 (88)
T ss_pred EEEEECCEecC-ccCCCCCCCCCEEEEeC
Confidence 35789999984 444 899999998753
No 107
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=53.16 E-value=7.8 Score=35.76 Aligned_cols=23 Identities=30% Similarity=0.359 Sum_probs=20.0
Q ss_pred CCceecccCCCCCceeEEEEcCH
Q 022339 210 IRPGIVHRLDKGTSGLLVVAKDE 232 (298)
Q Consensus 210 ~~~~~vhRLD~~TSGLlL~Ak~~ 232 (298)
...+.+||||..|||++||.-..
T Consensus 89 ~~V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559|consen 89 EDVQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred cceeeEEeecccccceEEEecCc
Confidence 34688999999999999998775
No 108
>PRK07440 hypothetical protein; Provisional
Probab=52.33 E-value=17 Score=26.70 Aligned_cols=45 Identities=16% Similarity=0.237 Sum_probs=31.4
Q ss_pred CccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEecc---ccccccCCCEEeec
Q 022339 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (298)
Q Consensus 68 ~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~---~~~~v~~gD~I~i~ 121 (298)
.++..|..+|... . ++.+ .=.|.+||..+.+ .+..|+.||.|+|.
T Consensus 17 ~~~~tl~~lL~~l-~-~~~~-------~vav~~N~~iv~r~~w~~~~L~~gD~IEIv 64 (70)
T PRK07440 17 SSGTSLPDLLQQL-G-FNPR-------LVAVEYNGEILHRQFWEQTQVQPGDRLEIV 64 (70)
T ss_pred CCCCCHHHHHHHc-C-CCCC-------eEEEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 3567899999765 3 3221 1157799998832 67889999999874
No 109
>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=50.87 E-value=33 Score=33.46 Aligned_cols=41 Identities=22% Similarity=0.234 Sum_probs=33.4
Q ss_pred cchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccc
Q 022339 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSH 110 (298)
Q Consensus 70 g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~ 110 (298)
+..+.+++...--..|+++++++|++|.|+|||.+++..+.
T Consensus 329 ~~~~~~~~~~~~~~~S~~~arr~ik~g~v~vn~~~i~~~~~ 369 (377)
T TIGR00234 329 DITLADLLVLSGLFPSKSEARRDIKQGGVYINGEKVTDLEP 369 (377)
T ss_pred CcCHHHHHHHcCCCcChHHHHHHHHhCCEEECCEeccCchh
Confidence 47888888876445799999999999999999999864443
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=49.48 E-value=15 Score=25.86 Aligned_cols=26 Identities=23% Similarity=0.355 Sum_probs=18.3
Q ss_pred CCceEECCEEecc-ccccccCCCEEee
Q 022339 95 SGLVSINGQVVSK-VSHNVKGGDMVNC 120 (298)
Q Consensus 95 ~G~V~VNGk~v~~-~~~~v~~gD~I~i 120 (298)
...++|||+++.. ....|..||+|.+
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 4678899999842 2577888998875
No 111
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=44.48 E-value=28 Score=24.95 Aligned_cols=44 Identities=16% Similarity=0.280 Sum_probs=29.5
Q ss_pred ccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEecc---ccccccCCCEEeec
Q 022339 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (298)
Q Consensus 69 ~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~---~~~~v~~gD~I~i~ 121 (298)
++..|..+|... . .... .=.|.+|++.+.+ .+..|+.||.|+|-
T Consensus 14 ~~~tl~~ll~~l-~-~~~~-------~vaVavN~~iv~r~~w~~~~L~~gD~Ieii 60 (66)
T PRK08053 14 AGQTVHELLEQL-N-QLQP-------GAALAINQQIIPREQWAQHIVQDGDQILLF 60 (66)
T ss_pred CCCCHHHHHHHc-C-CCCC-------cEEEEECCEEeChHHcCccccCCCCEEEEE
Confidence 456788888764 3 2211 1246799998842 45679999999874
No 112
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=43.72 E-value=36 Score=33.67 Aligned_cols=40 Identities=18% Similarity=0.106 Sum_probs=33.0
Q ss_pred CccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEecc
Q 022339 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK 107 (298)
Q Consensus 68 ~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~ 107 (298)
+.++.+.+.+++.-..-|+.++.++|.+|.|+||++++..
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 4678888888887434577799999999999999999854
No 113
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=42.90 E-value=28 Score=27.81 Aligned_cols=38 Identities=18% Similarity=0.208 Sum_probs=31.3
Q ss_pred CHHHHHHHHHCCceEECCEEeccccccccCCCEEeecc
Q 022339 85 SRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (298)
Q Consensus 85 Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~ 122 (298)
=+...-++|++|.=+|.++........+++||.|.+..
T Consensus 7 L~eeylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~~ 44 (111)
T COG4043 7 LREEYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFNG 44 (111)
T ss_pred hHHHHHHHHHcccceEEEEecCHhhcCCCCCCEEEEcC
Confidence 35667789999999999988766667799999998875
No 114
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=41.84 E-value=26 Score=25.35 Aligned_cols=42 Identities=14% Similarity=0.240 Sum_probs=28.2
Q ss_pred chHHHHHHhccCCcCHHHHHHHHHCCceEECCEEecc---ccccccCCCEEeec
Q 022339 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (298)
Q Consensus 71 ~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~---~~~~v~~gD~I~i~ 121 (298)
..|.++|... + +..+. =.|.+||+.+.+ .+..|+.||.|+|.
T Consensus 17 ~tv~~lL~~l-~-~~~~~-------vav~vN~~iv~r~~w~~~~L~~gD~iEIv 61 (67)
T PRK07696 17 KTVAELLTHL-E-LDNKI-------VVVERNKDILQKDDHTDTSVFDGDQIEIV 61 (67)
T ss_pred ccHHHHHHHc-C-CCCCe-------EEEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 4588888764 3 32111 157899998843 23779999999874
No 115
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=38.50 E-value=12 Score=28.76 Aligned_cols=30 Identities=27% Similarity=0.402 Sum_probs=18.2
Q ss_pred HHCCceEECCEEeccccccccCCCEEeeccc
Q 022339 93 IRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (298)
Q Consensus 93 I~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~ 123 (298)
+....|=|=|+.+ +.++.|+.||+|+|+.+
T Consensus 44 l~~~~vGIfGk~~-~~d~~L~~GDRVEIYRP 73 (84)
T PF03658_consen 44 LEKNKVGIFGKLV-KLDTVLRDGDRVEIYRP 73 (84)
T ss_dssp TTTSEEEEEE-S---TT-B--TT-EEEEE-S
T ss_pred cccceeeeeeeEc-CCCCcCCCCCEEEEecc
Confidence 3566777889998 69999999999999874
No 116
>cd01666 TGS_DRG_C TGS_DRG_C: DRG (developmentally regulated GTP-binding protein) represents a family of GTP-binding proteins that includes two members, DRG1 and DRG2. DRG1 and DRG2 have a C-terminal TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) with a predominantly beta-sheet structure. The function of TGS is unknown but its presence in two types of regulatory proteins (the DRG GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=32.74 E-value=31 Score=25.83 Aligned_cols=47 Identities=17% Similarity=0.151 Sum_probs=29.5
Q ss_pred cchHHHHHHhccCCcCHHHHHHHHHC---C-ceEECCEEeccccccccCCCEEeec
Q 022339 70 KLRLDAWISSRIDGISRARVQSSIRS---G-LVSINGQVVSKVSHNVKGGDMVNCT 121 (298)
Q Consensus 70 g~rLdk~L~~~~~~~Sr~~~~~lI~~---G-~V~VNGk~v~~~~~~v~~gD~I~i~ 121 (298)
|-++..+.... .+..+...... | .+.++|+++ -.++.|+-||+|+|.
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 55566666543 23333332211 1 334699999 589999999999984
No 117
>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=32.52 E-value=64 Score=24.57 Aligned_cols=47 Identities=13% Similarity=0.232 Sum_probs=28.9
Q ss_pred ccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeecccc
Q 022339 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (298)
Q Consensus 69 ~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~ 124 (298)
.|-.|...+.+. ++|.+.+.+++.... +++.. .+|+|||.|.+...+
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 455699999886 699999999999754 33344 469999999997754
No 118
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=31.84 E-value=45 Score=23.75 Aligned_cols=22 Identities=36% Similarity=0.353 Sum_probs=14.0
Q ss_pred eEECCEEeccccccccCCCEEee
Q 022339 98 VSINGQVVSKVSHNVKGGDMVNC 120 (298)
Q Consensus 98 V~VNGk~v~~~~~~v~~gD~I~i 120 (298)
+-+||=++ +.+..|++||.|.+
T Consensus 32 ~I~NGF~~-~~d~~L~e~D~v~~ 53 (57)
T PF14453_consen 32 VILNGFPT-KEDIELKEGDEVFL 53 (57)
T ss_pred EEEcCccc-CCccccCCCCEEEE
Confidence 34677665 56777777776654
No 119
>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=31.80 E-value=42 Score=26.08 Aligned_cols=26 Identities=23% Similarity=0.164 Sum_probs=20.8
Q ss_pred ceEECCEEec---cccccccCCCEEeecc
Q 022339 97 LVSINGQVVS---KVSHNVKGGDMVNCTI 122 (298)
Q Consensus 97 ~V~VNGk~v~---~~~~~v~~gD~I~i~~ 122 (298)
.|.|||..+. ..++.|+.||+|.+..
T Consensus 61 ~VlvN~~di~~l~g~~t~L~dgD~v~i~P 89 (94)
T cd01764 61 IVLINDTDWELLGEEDYILEDGDHVVFIS 89 (94)
T ss_pred EEEECCccccccCCcccCCCCcCEEEEEC
Confidence 6789998863 3578999999998854
No 120
>KOG4837 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.58 E-value=37 Score=30.63 Aligned_cols=55 Identities=22% Similarity=0.267 Sum_probs=46.3
Q ss_pred CccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccc
Q 022339 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (298)
Q Consensus 68 ~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~ 123 (298)
-...|.|-+|..-+ ++.|..++-+.-++.+++|+....+.+.+|..||.+-+.+.
T Consensus 137 v~sfr~d~llK~Gl-gv~rnKVel~fye~e~R~N~~Kl~kkS~~i~vgds~d~~ig 191 (248)
T KOG4837|consen 137 VVSFRVDALLKVGL-GVTRNKVELLFYEYEPRTNSFKLVKKSLRIDVGDSADFKIG 191 (248)
T ss_pred HHHHHHHHHHHhcc-ccccchhhHhhhhcccccCcccccccceeeecccccceeee
Confidence 34568888887764 68999999999999999999988889999999998876543
No 121
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown.
Probab=28.93 E-value=70 Score=21.51 Aligned_cols=23 Identities=35% Similarity=0.566 Sum_probs=18.8
Q ss_pred ceEECCEEeccccccccCCCEEee
Q 022339 97 LVSINGQVVSKVSHNVKGGDMVNC 120 (298)
Q Consensus 97 ~V~VNGk~v~~~~~~v~~gD~I~i 120 (298)
.+.+||+.+ ..+..+..||.|++
T Consensus 36 a~~vng~~v-dl~~~l~~~~~ve~ 58 (60)
T cd01668 36 GAKVNGKLV-PLSTVLKDGDIVEI 58 (60)
T ss_pred EEEECCEEC-CCCCCCCCCCEEEE
Confidence 456999998 47888999998876
No 122
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase.
Probab=27.36 E-value=21 Score=25.60 Aligned_cols=15 Identities=20% Similarity=0.160 Sum_probs=11.9
Q ss_pred CceeccccCcccccc
Q 022339 1 MTMLSLNSASWGSAS 15 (298)
Q Consensus 1 ~~~~~~~~~~~~~~~ 15 (298)
++|.+..+|++|+.-
T Consensus 1 v~ly~~~~Cp~C~~a 15 (72)
T TIGR02194 1 ITVYSKNNCVQCKMT 15 (72)
T ss_pred CEEEeCCCCHHHHHH
Confidence 577888899999864
No 123
>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=26.01 E-value=86 Score=20.33 Aligned_cols=22 Identities=36% Similarity=0.599 Sum_probs=18.0
Q ss_pred eEECCEEeccccccccCCCEEee
Q 022339 98 VSINGQVVSKVSHNVKGGDMVNC 120 (298)
Q Consensus 98 V~VNGk~v~~~~~~v~~gD~I~i 120 (298)
+.+||+.+ ..++.|..||.|++
T Consensus 37 ~~vn~~~~-~l~~~l~~~~~i~~ 58 (60)
T cd01616 37 ALVNGQLV-DLSYTLQDGDTVSI 58 (60)
T ss_pred EEECCEEC-CCCcCcCCCCEEEE
Confidence 45999988 47888999998876
No 124
>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=25.93 E-value=59 Score=20.73 Aligned_cols=20 Identities=25% Similarity=0.426 Sum_probs=16.4
Q ss_pred hccCCcCHHHHHHHHHCCceE
Q 022339 79 SRIDGISRARVQSSIRSGLVS 99 (298)
Q Consensus 79 ~~~~~~Sr~~~~~lI~~G~V~ 99 (298)
+.+ ++|++.+.+++++|.+.
T Consensus 9 ~~l-gis~~ti~~~~~~g~i~ 28 (49)
T TIGR01764 9 EYL-GVSKDTVYRLIHEGELP 28 (49)
T ss_pred HHH-CCCHHHHHHHHHcCCCC
Confidence 444 59999999999999754
No 125
>PF14478 DUF4430: Domain of unknown function (DUF4430); PDB: 3U7Z_B 2BB5_A.
Probab=25.15 E-value=69 Score=22.99 Aligned_cols=23 Identities=26% Similarity=0.391 Sum_probs=13.4
Q ss_pred eEECCEEec--cccccccCCCEEee
Q 022339 98 VSINGQVVS--KVSHNVKGGDMVNC 120 (298)
Q Consensus 98 V~VNGk~v~--~~~~~v~~gD~I~i 120 (298)
..|||+... -..+.|+.||.|++
T Consensus 43 ~~vNG~~~~~ga~~~~l~~GD~i~~ 67 (68)
T PF14478_consen 43 YYVNGESANVGAGSYKLKDGDKITW 67 (68)
T ss_dssp EEETTEE-SS-CCC-B--TTEEEEE
T ss_pred EEECCEEhhcCcceeEeCCCCEEEe
Confidence 458888753 25677888888875
No 126
>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=24.05 E-value=33 Score=24.64 Aligned_cols=16 Identities=25% Similarity=0.401 Sum_probs=11.5
Q ss_pred CCcEEEEeCCCCceee
Q 022339 143 DDNVLVVNKPAHMVVH 158 (298)
Q Consensus 143 D~~llvvnKPaGl~v~ 158 (298)
...+|.+|||+|-.+|
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 4689999999996655
No 127
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=23.27 E-value=85 Score=25.45 Aligned_cols=23 Identities=30% Similarity=0.446 Sum_probs=17.4
Q ss_pred CCceEECCEEeccccccccCCCEEeec
Q 022339 95 SGLVSINGQVVSKVSHNVKGGDMVNCT 121 (298)
Q Consensus 95 ~G~V~VNGk~v~~~~~~v~~gD~I~i~ 121 (298)
.|.|.+||-- .+.+++||.|.|-
T Consensus 65 Sg~I~lNGAA----Ar~~~~GD~vII~ 87 (111)
T cd06919 65 SGVICLNGAA----ARLGQPGDRVIIM 87 (111)
T ss_pred CCEEEeCCHH----HhcCCCCCEEEEE
Confidence 4788899944 4568899988774
No 128
>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=22.99 E-value=63 Score=23.62 Aligned_cols=66 Identities=15% Similarity=0.193 Sum_probs=45.8
Q ss_pred CCCceEEEEEEcCCCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccc
Q 022339 54 NYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (298)
Q Consensus 54 ~~~~~~~~~~v~~~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~ 123 (298)
+..|..+...|+..+.-..|-.-|.... +++-. -++++-.|.+.-|++.+ .++.|..|+.|.+...
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-GMPAG-KQKLQYEGIFIKDSNSL--AYYNLANGTIIHLQLK 69 (76)
T ss_pred ccCCeEEEEEECCCCcHHHHHHHHHHHH-CCCHH-HEEEEECCEEcCCCCcH--HHcCCCCCCEEEEEEe
Confidence 3456677888887777677777777764 46553 36777777776666555 4678889998887653
No 129
>PRK02253 deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional
Probab=21.83 E-value=2.5e+02 Score=24.02 Aligned_cols=39 Identities=18% Similarity=0.206 Sum_probs=27.6
Q ss_pred CcCHHHHHHHHHCCceEECC------EEeccccccccCCCEEeec
Q 022339 83 GISRARVQSSIRSGLVSING------QVVSKVSHNVKGGDMVNCT 121 (298)
Q Consensus 83 ~~Sr~~~~~lI~~G~V~VNG------k~v~~~~~~v~~gD~I~i~ 121 (298)
.+|.++++++|++|.+.++. ..+...+.-|+.|+...+.
T Consensus 2 iLs~~~I~~~i~~g~i~i~p~~~~~~~qiqp~svDlrlg~~~~~~ 46 (167)
T PRK02253 2 LLSKEELRKLIRSGKFVAEHVVDLEDDQVQPNGVDLTLGEVEEQE 46 (167)
T ss_pred cCCHHHHHHHHHcCCeEeecCCCCChhhCCCcEEEEECCcEEEEe
Confidence 36899999999999999853 2333345556677766654
No 130
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=21.54 E-value=1.2e+02 Score=25.20 Aligned_cols=23 Identities=35% Similarity=0.601 Sum_probs=17.2
Q ss_pred CCceEECCEEeccccccccCCCEEeec
Q 022339 95 SGLVSINGQVVSKVSHNVKGGDMVNCT 121 (298)
Q Consensus 95 ~G~V~VNGk~v~~~~~~v~~gD~I~i~ 121 (298)
.|.|.+||-- .+.+++||.|.|-
T Consensus 66 Sg~I~lNGAA----Ar~~~~GD~vII~ 88 (126)
T PRK05449 66 SGVICLNGAA----ARLVQVGDLVIIA 88 (126)
T ss_pred CCEEEeCCHH----HhcCCCCCEEEEE
Confidence 4778899944 4568899988773
No 131
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=20.92 E-value=64 Score=23.02 Aligned_cols=44 Identities=11% Similarity=0.237 Sum_probs=28.8
Q ss_pred ccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEec--cccccccCCCEEeec
Q 022339 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVS--KVSHNVKGGDMVNCT 121 (298)
Q Consensus 69 ~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~--~~~~~v~~gD~I~i~ 121 (298)
++.+|..+|... . ++...+ .|.+||..+. ..+..|+.||+|+|.
T Consensus 14 ~~~tl~~ll~~l-~-~~~~~v-------av~~N~~iv~r~~~~~~L~~gD~ieIv 59 (65)
T PRK05863 14 EQTTVAALLDSL-G-FPEKGI-------AVAVDWSVLPRSDWATKLRDGARLEVV 59 (65)
T ss_pred CCCcHHHHHHHc-C-CCCCcE-------EEEECCcCcChhHhhhhcCCCCEEEEE
Confidence 456788888865 3 433222 5778998552 234459999999874
No 132
>cd01790 Herp_N Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein. Herp (Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein) , is an integral membrane protein that is induced by the endoplasmic reticulum (ER) stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. Herp has an N-terminal ubiquitin-like domain that is involved in Herp degradation, but is not necessary for its enhancement of amyloid beta-protein generation.
Probab=20.58 E-value=52 Score=24.93 Aligned_cols=56 Identities=16% Similarity=-0.021 Sum_probs=37.0
Q ss_pred cCCCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEee
Q 022339 65 DTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNC 120 (298)
Q Consensus 65 ~~~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i 120 (298)
+..+.=..|-+-+++.++...-..-+++|-+|+|.-|.+.+......+..|..|.+
T Consensus 21 ~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHL 76 (79)
T cd01790 21 FLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHL 76 (79)
T ss_pred CCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccchhhHHHHhhcccCCceEEE
Confidence 45555556777787775544556778999999999888766433223555555543
No 133
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=20.12 E-value=81 Score=33.52 Aligned_cols=25 Identities=16% Similarity=0.260 Sum_probs=20.7
Q ss_pred EECCEEeccccccccCCCEEeecccc
Q 022339 99 SINGQVVSKVSHNVKGGDMVNCTISE 124 (298)
Q Consensus 99 ~VNGk~v~~~~~~v~~gD~I~i~~~~ 124 (298)
+|||+.+ ..++.|+.||+|+|-...
T Consensus 425 kVNg~~v-pL~~~L~~Gd~VeIiT~~ 449 (702)
T PRK11092 425 RVDRQPY-PLSQPLTSGQTVEIITAP 449 (702)
T ss_pred EECCEEC-CCCccCCCCCEEEEEeCC
Confidence 3589888 589999999999987543
No 134
>PF12728 HTH_17: Helix-turn-helix domain
Probab=20.10 E-value=87 Score=20.71 Aligned_cols=20 Identities=40% Similarity=0.572 Sum_probs=16.3
Q ss_pred hccCCcCHHHHHHHHHCCceE
Q 022339 79 SRIDGISRARVQSSIRSGLVS 99 (298)
Q Consensus 79 ~~~~~~Sr~~~~~lI~~G~V~ 99 (298)
+.+ ++|++.+++++++|.+.
T Consensus 9 ~~l-~is~~tv~~~~~~g~i~ 28 (51)
T PF12728_consen 9 ELL-GISRSTVYRWIRQGKIP 28 (51)
T ss_pred HHH-CcCHHHHHHHHHcCCCC
Confidence 444 58999999999999763
Done!