Query 020570
Match_columns 324
No_of_seqs 197 out of 1614
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 03:27:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020570.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020570hhsearch_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 8.4E-50 1.8E-54 373.5 24.1 228 61-324 3-231 (289)
2 PRK11180 rluD 23S rRNA pseudou 100.0 2.8E-45 6E-50 349.5 27.1 233 56-324 3-235 (325)
3 PRK11025 23S rRNA pseudouridyl 100.0 7.2E-45 1.6E-49 345.5 24.9 226 61-324 10-243 (317)
4 TIGR00005 rluA_subfam pseudour 100.0 4.4E-44 9.5E-49 337.5 25.5 225 67-324 2-226 (299)
5 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 2.5E-36 5.3E-41 277.4 18.1 183 98-324 4-187 (246)
6 PRK10839 16S rRNA pseudouridyl 100.0 7.3E-35 1.6E-39 265.5 10.7 185 71-324 1-185 (232)
7 cd02557 PseudoU_synth_ScRIB2 P 100.0 2.3E-33 5.1E-38 252.5 18.0 155 134-324 13-167 (213)
8 KOG1919 RNA pseudouridylate sy 100.0 6.6E-33 1.4E-37 264.9 21.7 226 61-324 34-262 (371)
9 PRK10158 23S rRNA/tRNA pseudou 100.0 2.7E-33 5.9E-38 253.0 17.4 150 136-324 13-163 (219)
10 TIGR01621 RluA-like pseudourid 100.0 1.2E-32 2.5E-37 248.6 17.1 146 137-324 2-147 (217)
11 cd02563 PseudoU_synth_TruC tRN 100.0 3E-32 6.5E-37 246.9 17.6 151 137-324 1-162 (223)
12 PRK11112 tRNA pseudouridine sy 100.0 7.2E-32 1.6E-36 249.3 17.1 151 137-324 2-163 (257)
13 PRK10700 23S rRNA pseudouridyl 100.0 5.4E-30 1.2E-34 240.2 16.7 189 71-324 3-195 (289)
14 PRK10475 23S rRNA pseudouridin 100.0 2.2E-29 4.8E-34 235.7 13.8 145 68-262 4-148 (290)
15 PF00849 PseudoU_synth_2: RNA 100.0 1.1E-28 2.4E-33 212.2 13.8 148 145-324 1-157 (164)
16 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 2.4E-28 5.3E-33 209.1 14.0 134 146-324 1-134 (154)
17 cd02869 PseudoU_synth_RluCD_li 100.0 3.5E-27 7.5E-32 206.6 17.3 145 146-324 1-145 (185)
18 COG1187 RsuA 16S rRNA uridine- 100.0 1.3E-27 2.7E-32 217.6 14.7 192 70-324 2-195 (248)
19 cd02556 PseudoU_synth_RluB Pse 99.9 8.1E-26 1.8E-30 196.1 8.6 128 145-324 1-128 (167)
20 cd02870 PseudoU_synth_RsuA_lik 99.9 3.2E-26 7E-31 194.3 5.5 126 146-324 1-126 (146)
21 cd02566 PseudoU_synth_RluE Pse 99.9 1.6E-23 3.4E-28 182.0 9.5 136 146-324 1-140 (168)
22 cd02553 PseudoU_synth_RsuA Pse 99.9 1.3E-23 2.9E-28 182.2 8.7 124 146-324 2-125 (167)
23 cd02555 PSSA_1 PSSA_1: Pseudou 99.8 1.3E-20 2.9E-25 164.8 8.3 89 211-324 46-135 (177)
24 PRK11394 23S rRNA pseudouridin 99.8 2.5E-20 5.5E-25 167.3 9.4 83 144-263 39-121 (217)
25 cd02554 PseudoU_synth_RluF Pse 99.7 3.8E-18 8.3E-23 147.4 9.4 80 146-262 2-81 (164)
26 TIGR00093 pseudouridine syntha 99.7 8.1E-18 1.7E-22 139.8 6.1 90 215-324 1-90 (128)
27 cd00165 S4 S4/Hsp/ tRNA synthe 99.2 4.4E-11 9.6E-16 86.7 7.5 70 71-150 1-70 (70)
28 cd02868 PseudoU_synth_hTruB2_l 99.1 1.1E-10 2.4E-15 105.7 7.0 43 212-256 34-76 (226)
29 PF01479 S4: S4 domain; Inter 99.0 7.3E-10 1.6E-14 76.0 5.5 48 71-118 1-48 (48)
30 TIGR02988 YaaA_near_RecF S4 do 98.9 1.9E-09 4.2E-14 77.3 5.6 51 68-120 6-58 (59)
31 COG1188 Ribosome-associated he 98.5 2.1E-07 4.5E-12 73.0 5.1 55 68-123 6-60 (100)
32 smart00363 S4 S4 RNA-binding d 98.4 8.1E-07 1.8E-11 62.1 6.3 52 71-122 1-52 (60)
33 PLN00051 RNA-binding S4 domain 98.2 2.8E-06 6E-11 79.0 6.6 59 64-123 185-243 (267)
34 PRK10348 ribosome-associated h 98.2 3.4E-06 7.4E-11 70.1 6.3 53 69-122 7-59 (133)
35 TIGR03069 PS_II_S4 photosystem 98.1 5.1E-06 1.1E-10 77.0 6.2 59 64-123 177-235 (257)
36 TIGR01017 rpsD_bact ribosomal 98.1 7.3E-06 1.6E-10 73.2 6.1 53 71-123 90-142 (200)
37 CHL00113 rps4 ribosomal protei 98.0 7.3E-06 1.6E-10 73.1 5.8 53 71-123 89-141 (201)
38 TIGR00478 tly hemolysin TlyA f 97.9 1.4E-05 3.1E-10 72.8 5.4 52 72-123 1-52 (228)
39 PRK05327 rpsD 30S ribosomal pr 97.9 2.2E-05 4.8E-10 70.3 5.8 52 71-122 93-144 (203)
40 cd02572 PseudoU_synth_hDyskeri 97.7 8.8E-05 1.9E-09 65.3 7.3 70 144-256 2-71 (182)
41 COG2302 Uncharacterized conser 97.7 4.4E-05 9.6E-10 69.3 4.8 54 69-123 179-232 (257)
42 PRK11507 ribosome-associated p 97.7 0.00013 2.9E-09 53.7 6.1 57 66-122 7-63 (70)
43 COG0522 RpsD Ribosomal protein 97.5 0.00015 3.3E-09 64.8 5.8 54 71-124 94-147 (205)
44 COG1189 Predicted rRNA methyla 97.5 0.00016 3.4E-09 65.7 5.7 53 70-122 2-54 (245)
45 cd00506 PseudoU_synth_TruB_lik 97.5 0.00038 8.2E-09 62.6 7.5 68 146-256 2-69 (210)
46 PRK04099 truB tRNA pseudouridi 97.4 0.00038 8.2E-09 64.8 7.0 70 144-256 2-71 (273)
47 TIGR00431 TruB tRNA pseudourid 97.4 0.00048 1E-08 61.8 7.4 70 144-256 2-71 (209)
48 PRK00989 truB tRNA pseudouridi 97.4 0.00043 9.3E-09 62.9 6.5 71 144-256 9-79 (230)
49 PRK00020 truB tRNA pseudouridi 97.3 0.00074 1.6E-08 61.8 7.6 70 144-256 10-79 (244)
50 PF13275 S4_2: S4 domain; PDB: 97.3 5E-05 1.1E-09 55.4 -0.2 55 67-121 4-58 (65)
51 PRK14124 tRNA pseudouridine sy 97.2 0.0011 2.3E-08 63.0 7.9 70 144-256 3-72 (308)
52 PRK00130 truB tRNA pseudouridi 97.2 0.0011 2.4E-08 62.5 7.7 70 144-256 2-71 (290)
53 PRK02484 truB tRNA pseudouridi 97.2 0.00092 2E-08 63.1 7.1 70 144-256 3-72 (294)
54 PRK03287 truB tRNA pseudouridi 97.2 0.0011 2.5E-08 62.5 7.6 71 143-256 8-78 (298)
55 PRK14123 tRNA pseudouridine sy 97.2 0.00093 2E-08 63.3 7.0 70 144-256 3-72 (305)
56 PRK02755 truB tRNA pseudouridi 97.2 0.0009 1.9E-08 63.1 6.8 69 144-256 3-71 (295)
57 PRK05389 truB tRNA pseudouridi 97.1 0.0014 3.1E-08 62.1 7.5 70 144-256 13-82 (305)
58 PRK05033 truB tRNA pseudouridi 97.1 0.0016 3.4E-08 61.9 7.7 70 144-256 10-79 (312)
59 PRK02193 truB tRNA pseudouridi 97.1 0.0014 3.1E-08 61.2 7.2 68 146-256 2-69 (279)
60 PRK14846 truB tRNA pseudouridi 97.1 0.0017 3.6E-08 62.1 7.7 70 144-256 3-72 (345)
61 PRK01550 truB tRNA pseudouridi 97.1 0.0015 3.3E-08 61.8 7.2 70 144-256 2-71 (304)
62 PRK04270 H/ACA RNA-protein com 97.1 0.0015 3.2E-08 62.0 7.1 71 143-256 21-91 (300)
63 PRK01528 truB tRNA pseudouridi 97.0 0.0017 3.7E-08 61.1 7.2 70 144-256 3-72 (292)
64 PRK04051 rps4p 30S ribosomal p 97.0 0.0014 3E-08 57.3 6.0 52 71-122 103-154 (177)
65 cd02573 PseudoU_synth_EcTruB P 97.0 0.002 4.3E-08 60.4 7.5 68 146-256 2-69 (277)
66 PRK01851 truB tRNA pseudouridi 97.0 0.0025 5.5E-08 60.3 7.8 70 144-256 16-85 (303)
67 PRK14122 tRNA pseudouridine sy 97.0 0.0022 4.8E-08 60.8 7.4 69 145-256 2-70 (312)
68 COG2501 S4-like RNA binding pr 97.0 0.0033 7.1E-08 46.7 6.5 56 67-122 8-63 (73)
69 TIGR00425 CBF5 rRNA pseudourid 96.8 0.0032 6.9E-08 60.3 6.7 71 143-256 33-103 (322)
70 PRK04642 truB tRNA pseudouridi 96.7 0.0054 1.2E-07 57.9 7.3 70 144-256 10-79 (300)
71 COG0130 TruB Pseudouridine syn 96.4 0.0077 1.7E-07 56.2 6.6 69 145-256 16-84 (271)
72 cd02867 PseudoU_synth_TruB_4 P 96.3 0.011 2.3E-07 56.2 7.1 43 210-256 56-98 (312)
73 PLN00189 40S ribosomal protein 96.2 0.0047 1E-07 54.6 3.4 54 71-124 101-162 (194)
74 TIGR01018 rpsD_arch ribosomal 95.8 0.017 3.7E-07 49.8 5.4 50 71-120 104-153 (162)
75 PRK04313 30S ribosomal protein 95.6 0.032 6.8E-07 50.9 6.4 54 68-121 35-89 (237)
76 PTZ00155 40S ribosomal protein 95.5 0.017 3.7E-07 50.7 4.2 53 71-123 107-159 (181)
77 PLN00036 40S ribosomal protein 95.3 0.047 1E-06 50.5 6.4 73 68-150 39-112 (261)
78 PTZ00223 40S ribosomal protein 95.2 0.05 1.1E-06 50.5 6.3 73 68-150 36-109 (273)
79 PTZ00118 40S ribosomal protein 95.1 0.055 1.2E-06 50.0 6.3 54 68-121 39-93 (262)
80 COG1471 RPS4A Ribosomal protei 92.3 0.24 5.2E-06 44.8 5.0 58 84-151 55-112 (241)
81 COG4332 Uncharacterized protei 91.9 0.28 6E-06 42.7 4.7 64 58-123 127-190 (203)
82 cd01291 PseudoU_synth PseudoU_ 91.0 0.85 1.8E-05 34.7 6.2 28 210-256 24-51 (87)
83 PF14451 Ub-Mut7C: Mut7-C ubiq 90.1 0.28 6.1E-06 37.4 2.8 47 68-123 30-76 (81)
84 PRK01777 hypothetical protein; 89.4 0.35 7.7E-06 38.0 2.9 54 67-123 23-76 (95)
85 PRK13354 tyrosyl-tRNA syntheta 87.5 0.97 2.1E-05 44.8 5.3 47 70-116 342-388 (410)
86 KOG2559 Predicted pseudouridin 87.3 0.65 1.4E-05 42.5 3.6 23 210-232 89-111 (318)
87 PF06353 DUF1062: Protein of u 87.0 1.7 3.6E-05 36.8 5.7 43 58-102 91-133 (142)
88 PF01509 TruB_N: TruB family p 86.2 0.77 1.7E-05 39.1 3.3 43 210-256 7-49 (149)
89 PRK05912 tyrosyl-tRNA syntheta 85.7 1.8 3.9E-05 42.9 6.1 45 70-114 342-386 (408)
90 cd00754 MoaD Ubiquitin domain 80.0 4.1 8.9E-05 30.0 4.8 51 70-122 25-75 (80)
91 PRK08364 sulfur carrier protei 75.3 4.3 9.4E-05 29.7 3.6 43 69-121 22-64 (70)
92 PF02597 ThiS: ThiS family; I 68.9 5.2 0.00011 29.2 2.8 52 68-122 19-72 (77)
93 PLN02799 Molybdopterin synthas 68.6 11 0.00023 28.2 4.6 50 70-122 28-77 (82)
94 TIGR01682 moaD molybdopterin c 67.9 13 0.00027 27.7 4.8 25 97-122 51-75 (80)
95 PRK06437 hypothetical protein; 66.7 6.1 0.00013 28.7 2.8 44 68-121 18-61 (67)
96 cd00565 ThiS ThiaminS ubiquiti 60.8 8.1 0.00018 27.6 2.5 42 70-121 14-59 (65)
97 PRK05659 sulfur carrier protei 60.7 8.6 0.00019 27.4 2.6 44 69-121 14-60 (66)
98 COG0162 TyrS Tyrosyl-tRNA synt 57.2 12 0.00026 37.1 3.7 40 73-112 338-377 (401)
99 KOG3301 Ribosomal protein S4 [ 55.7 14 0.00031 31.8 3.4 45 70-114 88-140 (183)
100 PRK11130 moaD molybdopterin sy 55.1 7.6 0.00016 29.1 1.6 30 92-122 45-76 (81)
101 PF02824 TGS: TGS domain; Int 53.3 13 0.00028 26.3 2.4 23 97-120 36-58 (60)
102 PF00498 FHA: FHA domain; Int 52.2 18 0.00039 25.6 3.1 27 94-120 40-67 (68)
103 TIGR00234 tyrS tyrosyl-tRNA sy 50.2 33 0.00073 33.6 5.6 41 69-109 328-368 (377)
104 COG2104 ThiS Sulfur transfer p 50.1 16 0.00035 26.8 2.5 43 70-121 17-62 (68)
105 TIGR01683 thiS thiamine biosyn 49.1 16 0.00035 26.0 2.4 43 70-121 13-58 (64)
106 PRK06944 sulfur carrier protei 48.9 17 0.00037 25.7 2.5 44 69-122 14-60 (65)
107 PRK06083 sulfur carrier protei 47.9 41 0.00088 25.7 4.6 45 68-121 31-78 (84)
108 PRK06488 sulfur carrier protei 47.9 18 0.0004 25.7 2.5 42 71-121 15-59 (65)
109 COG4043 Preprotein translocase 46.9 21 0.00046 28.3 2.8 37 86-122 8-44 (111)
110 TIGR01687 moaD_arch MoaD famil 43.7 23 0.00049 26.7 2.7 25 97-122 57-83 (88)
111 PRK07440 hypothetical protein; 42.7 28 0.0006 25.5 2.9 45 68-121 17-64 (70)
112 KOG2623 Tyrosyl-tRNA synthetas 38.3 40 0.00086 33.3 3.9 40 68-107 396-435 (467)
113 PF03658 Ub-RnfH: RnfH family 37.9 14 0.0003 28.4 0.6 30 93-123 44-73 (84)
114 KOG2529 Pseudouridine synthase 37.1 35 0.00076 33.6 3.3 47 211-261 96-142 (395)
115 cd01666 TGS_DRG_C TGS_DRG_C: 35.6 27 0.00059 26.1 1.9 22 99-121 53-74 (75)
116 PRK07696 sulfur carrier protei 35.2 39 0.00084 24.4 2.6 42 71-121 17-61 (67)
117 PRK08053 sulfur carrier protei 32.1 49 0.0011 23.6 2.7 44 69-121 14-60 (66)
118 cd01764 Urm1 Urm1-like ubuitin 31.8 36 0.00077 26.5 2.0 26 97-122 61-89 (94)
119 PF04225 OapA: Opacity-associa 31.4 76 0.0017 24.1 3.8 51 62-124 5-55 (85)
120 PRK05449 aspartate alpha-decar 27.9 65 0.0014 26.6 3.0 24 95-122 66-89 (126)
121 KOG4837 Uncharacterized conser 27.1 55 0.0012 29.4 2.6 53 70-123 139-191 (248)
122 PF11112 PyocinActivator: Pyoc 26.3 94 0.002 23.3 3.4 34 67-100 11-44 (76)
123 cd01790 Herp_N Homocysteine-re 25.8 29 0.00063 26.2 0.6 56 65-120 21-76 (79)
124 cd06919 Asp_decarbox Aspartate 24.7 77 0.0017 25.6 2.8 24 95-122 65-88 (111)
125 TIGR00223 panD L-aspartate-alp 23.8 87 0.0019 25.9 3.0 24 95-122 66-89 (126)
126 cd01668 TGS_RelA_SpoT TGS_RelA 23.5 81 0.0017 21.3 2.5 23 97-120 36-58 (60)
127 PRK02268 hypothetical protein; 23.2 84 0.0018 26.5 2.9 42 82-124 7-48 (141)
128 KOG0062 ATPase component of AB 23.0 80 0.0017 32.4 3.2 67 74-156 447-513 (582)
129 PF08068 DKCLD: DKCLD (NUC011) 22.1 32 0.00069 24.6 0.2 16 143-158 41-56 (59)
130 cd01800 SF3a120_C Ubiquitin-li 21.0 68 0.0015 23.5 1.8 65 54-122 4-68 (76)
131 PF14453 ThiS-like: ThiS-like 20.5 86 0.0019 22.2 2.1 20 100-120 34-53 (57)
132 PRK02253 deoxyuridine 5'-triph 20.3 3.6E+02 0.0078 23.0 6.4 38 84-121 3-46 (167)
133 cd01616 TGS The TGS domain, na 20.2 1.1E+02 0.0023 19.9 2.5 22 98-120 37-58 (60)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.4e-50 Score=373.54 Aligned_cols=228 Identities=46% Similarity=0.742 Sum_probs=201.0
Q ss_pred EEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccccCc-ccccccCCCcee
Q 020570 61 EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQP-LRAEAEDIPLDI 139 (324)
Q Consensus 61 ~~~v~~~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~~~~-~~~~~~~~~~~I 139 (324)
++.|+.+.+++|||+||++.++ +||+.++++|++|.|.|||+++. ++++|..||+|.+...+... ....+++++++|
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 4567778899999999999656 99999999999999999999995 99999999999998866442 344556777999
Q ss_pred eccCCcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCC
Q 020570 140 VYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLD 219 (324)
Q Consensus 140 lyed~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD 219 (324)
||||++++|||||+||+|||+.++..++++++++.++.. ...++++|||||
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 999999999999999999999888889999999887631 035788999999
Q ss_pred CCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCeeeEEEE
Q 020570 220 KGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRY 299 (324)
Q Consensus 220 ~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~a~T~~ 299 (324)
++||||||||||..+++.|+++|+++.+.|+|+|+|.|.++.++|.|+.||.+......++.+... .+|+.|.|+|
T Consensus 132 kdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~~~~~v~~~----~~gk~A~T~~ 207 (289)
T COG0564 132 KDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNRKKMAVVKE----GSGKPAITHY 207 (289)
T ss_pred CCCceEEEEECCHHHHHHHHHHHhcCcCcEEEEEEEECcccCCCCEEeeeeecCCcCCceEEEecc----CCCCceEEEE
Confidence 999999999999999999999999999999999999999999889999999998877777766542 1389999999
Q ss_pred EEEEEeCCCCEEEEEEEcCCCCCCC
Q 020570 300 KVIEILAGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 300 ~vl~~~~~~~~slv~~~l~TGRtHQ 324 (324)
++++++... +||++|+|+||||||
T Consensus 208 ~~l~~~~~~-~tlv~~~~~TGRTHQ 231 (289)
T COG0564 208 EVLERFGDN-YTLVELKPETGRTHQ 231 (289)
T ss_pred EehhccCCc-eEEEEEEeCCCCHhH
Confidence 999986322 799999999999999
No 2
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=2.8e-45 Score=349.52 Aligned_cols=233 Identities=41% Similarity=0.627 Sum_probs=196.8
Q ss_pred CceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccccCcccccccCC
Q 020570 56 AGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDI 135 (324)
Q Consensus 56 ~~~~~~~~v~~~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~~~~~~~~~~~~ 135 (324)
+.|.+...|+.+++++|||+||++.++.+||+.++++|++|.|+|||+++.+++..|.+||+|.+......+....+...
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 45788889999999999999999988889999999999999999999998778999999999999765433222334456
Q ss_pred CceeeccCCcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCcccc
Q 020570 136 PLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIV 215 (324)
Q Consensus 136 ~~~Ilyed~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v 215 (324)
+++|||||++++|+|||+||+|||.++...+++.+.+..++. ... ...++++|
T Consensus 83 ~~~iiyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~~--~~~-------------------------~~~~~~~v 135 (325)
T PRK11180 83 PLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYP--PIA-------------------------DVPRAGIV 135 (325)
T ss_pred CCcEEEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHhh--hcc-------------------------CCccccee
Confidence 789999999999999999999999887777789888876642 100 12457789
Q ss_pred CCCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCeee
Q 020570 216 HRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHA 295 (324)
Q Consensus 216 hRLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~a 295 (324)
||||++||||||||+|..++..|+++|.++.|+|+|+|+|.|.++ .+|.|+.||.+.......+.+.+ .++.|
T Consensus 136 hRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~Y~A~v~G~~~-~~~~i~~~l~~~~~~~~~~~~~~------~gk~a 208 (325)
T PRK11180 136 HRLDKDTTGLMVVAKTVPAQTRLVEALQKREITREYEAVAIGHMT-AGGTVDEPISRHPTKRTHMAVHP------MGKPA 208 (325)
T ss_pred ccCCCCCceeEEEECCHHHHHHHHHHHHhCCcceEEEEEEecCCC-CCCEEECceecCCCcCcEEEeCC------CCcEE
Confidence 999999999999999999999999999999999999999999986 46899999987654444433322 68999
Q ss_pred EEEEEEEEEeCCCCEEEEEEEcCCCCCCC
Q 020570 296 ASRYKVIEILAGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 296 ~T~~~vl~~~~~~~~slv~~~l~TGRtHQ 324 (324)
.|+|+++... .++|||+|+|+||||||
T Consensus 209 ~T~~~~l~~~--~~~slv~~~~~TGRtHQ 235 (325)
T PRK11180 209 VTHYRIMEHF--RVHTRLRLRLETGRTHQ 235 (325)
T ss_pred eEEEEEeEEc--CCeEEEEEEeCCCCHHH
Confidence 9999999874 46899999999999999
No 3
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=7.2e-45 Score=345.49 Aligned_cols=226 Identities=26% Similarity=0.384 Sum_probs=182.6
Q ss_pred EEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccccCccccc--------c
Q 020570 61 EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAE--------A 132 (324)
Q Consensus 61 ~~~v~~~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~~~~~~~~--------~ 132 (324)
+++|+.+++|+|||+||+..++.+||+.++++|++|.|+|||+++ +++..|+.||+|.+........... .
T Consensus 10 ~~~v~~~~~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v-~~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~ 88 (317)
T PRK11025 10 IVTISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKV 88 (317)
T ss_pred EEEECcccCCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEc-CcccccCCCCEEEeCCCCcccccccccccccccc
Confidence 457888899999999999888889999999999999999999998 6899999999999864221110100 1
Q ss_pred cCCCceeeccCCcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCc
Q 020570 133 EDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRP 212 (324)
Q Consensus 133 ~~~~~~Ilyed~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 212 (324)
...+++|||||++++|+|||+|++|||..+.. .++++.+..+.. ....+
T Consensus 89 ~~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~-~~~~~~~~~~~~------------------------------~~~~~ 137 (317)
T PRK11025 89 AALADVILYEDDHILVLNKPSGTAVHGGSGLS-FGVIEGLRALRP------------------------------EARFL 137 (317)
T ss_pred ccCcCCEEEECCCEEEEECCCCCcCcCCCCCC-ccHHHHHHHhcc------------------------------CCCcC
Confidence 12457999999999999999999999976553 345665543210 11235
Q ss_pred cccCCCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCC
Q 020570 213 GIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQA 292 (324)
Q Consensus 213 ~~vhRLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~ 292 (324)
++|||||++||||||||+|..+++.|+++|+++.++|+|+|+|.|.+...+|.|+.||.++........+.. ...|
T Consensus 138 ~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~v~K~Y~a~v~G~~~~~~~~i~~~i~~~~~~~~~~~~~~----~~~g 213 (317)
T PRK11025 138 ELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKVVQAPLLKNILQSGERIVRV----SQEG 213 (317)
T ss_pred ceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCCccEEEEEEEeCcccCCCceEecccccCcccCCceEEec----CCCC
Confidence 789999999999999999999999999999999999999999999998888999999987643222222211 1268
Q ss_pred eeeEEEEEEEEEeCCCCEEEEEEEcCCCCCCC
Q 020570 293 RHAASRYKVIEILAGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 293 k~a~T~~~vl~~~~~~~~slv~~~l~TGRtHQ 324 (324)
+.|.|+|++++.. +++|||+|+|+||||||
T Consensus 214 k~a~T~~~~l~~~--~~~sLv~~~~~TGRtHQ 243 (317)
T PRK11025 214 KPSETRFKVEERY--AFATLVRASPVTGRTHQ 243 (317)
T ss_pred ccceEEEEEeEEc--CCcEEEEEEeCCCCHHH
Confidence 9999999999875 56899999999999999
No 4
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=100.00 E-value=4.4e-44 Score=337.50 Aligned_cols=225 Identities=40% Similarity=0.700 Sum_probs=186.8
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccccCcccccccCCCceeeccCCcE
Q 020570 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNV 146 (324)
Q Consensus 67 ~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~~~~~~~~~~~~~~~Ilyed~~~ 146 (324)
+++++||++||++.++.+||+.++++|++|.|+|||+.+.+++..|++||+|.+...........+...+++|+|||++|
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 56789999999998877999999999999999999975557899999999999976532222222334467899999999
Q ss_pred EEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCceEE
Q 020570 147 LVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLL 226 (324)
Q Consensus 147 lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGLL 226 (324)
+|+|||+|++||+.++...+++.+.+..++.. . ....++++|||||++|||||
T Consensus 82 lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~~~--~-------------------------~~~~~~~~vhRLD~~TSGll 134 (299)
T TIGR00005 82 IVINKPSGLVVHPGGGNPFGTVLNALLAHCPP--I-------------------------AGVERVGIVHRLDRDTSGLM 134 (299)
T ss_pred EEEECCCCCeEeCCCCCCcccHHHHHHHhccc--c-------------------------cCCCcCceECCCCCCCceEE
Confidence 99999999999999887778899888766421 0 01245789999999999999
Q ss_pred EeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCeeeEEEEEEEEEeC
Q 020570 227 VVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILA 306 (324)
Q Consensus 227 l~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~ 306 (324)
|||+|..+++.|+++|+++.|+|+|+|+|.|.++.+++.|+.||.+...+...+.+... .+++.|.|.|+++...
T Consensus 135 l~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~g~~~~~~~~i~~~l~~~~~~~~~~~~~~~----~~~k~a~t~~~~l~~~- 209 (299)
T TIGR00005 135 VVAKTPLALRELQRQLKNRTVTKEYVALVHGQFDSGGGTVDAPLGRVPNNRGLMAVHPS----SEGKPAVTHFRVLERF- 209 (299)
T ss_pred EEEcCHHHHHHHHHHHHhCCcceEEEEEEeccccCCCCEEeCceecCCCCCceEEEecC----CCCCeeeEEEEEeEEc-
Confidence 99999999999999999999999999999999988899999999876544444443331 2589999999999864
Q ss_pred CCCEEEEEEEcCCCCCCC
Q 020570 307 GGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 307 ~~~~slv~~~l~TGRtHQ 324 (324)
.++|||+|+|+|||+||
T Consensus 210 -~~~slv~~~l~tGR~HQ 226 (299)
T TIGR00005 210 -GNASLVECELETGRTHQ 226 (299)
T ss_pred -CCeEEEEEEeCCCChHH
Confidence 47899999999999999
No 5
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.
Probab=100.00 E-value=2.5e-36 Score=277.40 Aligned_cols=183 Identities=21% Similarity=0.291 Sum_probs=145.7
Q ss_pred eEECCEEeccceeeeecCCEEeeeccccCcccccccCCCceeeccCCcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcC
Q 020570 98 VSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177 (324)
Q Consensus 98 V~VNg~~v~~~~~~l~~GD~V~v~~~~~~~~~~~~~~~~~~Ilyed~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~ 177 (324)
|..||+++ +++.+|++||+|.+.....+.. +...+++|||||++++|+|||+|++|||.++...+++++.+..++.
T Consensus 4 ~~~ng~~~-~~~~~l~~gd~i~~~~~~~~~~---~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~~ 79 (246)
T cd02558 4 VDADGEPL-DPDSPYRPGTFVWYYRELPDEP---PIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTG 79 (246)
T ss_pred ECCCCcCC-CCCceecCCCEEEEeCCCCCCC---CCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHhC
Confidence 44899999 6899999999999875322111 2234589999999999999999999999988777788887765431
Q ss_pred CCccccccccccccccccccccccccccCCCCCCccccCCCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEec
Q 020570 178 LPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSG 257 (324)
Q Consensus 178 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G 257 (324)
...+++|||||++||||||||||+.+++.++.+|++++++|+|+|+|.|
T Consensus 80 -------------------------------~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~YlA~v~G 128 (246)
T cd02558 80 -------------------------------NPDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYEAVAPY 128 (246)
T ss_pred -------------------------------CCcccccccCCCCceeEEEEEcCHHHHHHHHHHHHcCCccEEEEEEEec
Confidence 1245789999999999999999999999999999999999999999999
Q ss_pred ccCCCCc-EEEccceeCCCCCeeEEEcCCCCCCCCCeeeEEEEEEEEEeCCCCEEEEEEEcCCCCCCC
Q 020570 258 VPSQSSG-RIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 258 ~~~~~~g-~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGRtHQ 324 (324)
.++.+.+ .+..++.+.... ..+... .+++.|.|+|++++.. .++|+|+|+|+||||||
T Consensus 129 ~~~~~~~~~~~~~i~~~~~~-~~~~~~------~~~~~a~T~~~~l~~~--~~~slv~~~l~TGRtHQ 187 (246)
T cd02558 129 VPALTFPLTVRSRIVKGRGF-FQAREV------EGEPNAETRIELLARR--GGWGLYRLSPHTGKTHQ 187 (246)
T ss_pred CCCCCCCcceeccccccCCc-ceeecc------CCCCCceEEEEEEEec--CCeEEEEEEeCCCCHHH
Confidence 9865444 567677654321 222221 1467899999999864 47899999999999999
No 6
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=100.00 E-value=7.3e-35 Score=265.46 Aligned_cols=185 Identities=20% Similarity=0.318 Sum_probs=140.5
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccccCcccccccCCCceeeccCCcEEEEe
Q 020570 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVN 150 (324)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~~~~~~~~~~~~~~~Ilyed~~~lvvn 150 (324)
+|||+||++.+ .+||+.++++|+.|.|+|||+++.+++.+|++||.|.+...... ..++++++|+|
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 69999999999999999999998668899999999988642111 01356899999
Q ss_pred CCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCceEEEeec
Q 020570 151 KPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAK 230 (324)
Q Consensus 151 KPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGLLl~ak 230 (324)
||+||+||++++.. .++.+.+... ...++++|||||++||||||||+
T Consensus 67 KP~G~~~~~~~~~~-~tl~~~l~~~--------------------------------~~~~~~~v~RLD~~TSGlll~ak 113 (232)
T PRK10839 67 KPQGYVCSTDDPDH-PTVLYFLDEP--------------------------------VAYKLHAAGRLDIDTTGLVLMTD 113 (232)
T ss_pred CCCCeEecccCCCC-CeEEEecccc--------------------------------cccCceecCCCCCCceeEEEEec
Confidence 99999999875432 4443221100 11356789999999999999999
Q ss_pred CHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCeeeEEEEEEEEEeCCCCE
Q 020570 231 DEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGS 310 (324)
Q Consensus 231 ~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~ 310 (324)
|..++..|.. +++.++|+|+|++.+.+..+. + ...+..+.. .|+.|.|+|.+++... .
T Consensus 114 ~~~~~~~l~~--~~~~i~K~Y~a~i~~~i~~~~------~-----~~~~~~~~~------~g~~a~t~~~~~~~~~---~ 171 (232)
T PRK10839 114 DGQWSHRITS--PRHHCEKTYLVTLESPVADDT------A-----EQFAKGVQL------HNEKDLTKPAVLEVIT---P 171 (232)
T ss_pred CHHHHHHHhC--CCCCCCeEEEEEECCCCCHHH------H-----HHHHCCeEE------CCCcccccccEEEEec---C
Confidence 9998888885 678899999998877664211 1 111111111 4677899999998753 3
Q ss_pred EEEEEEcCCCCCCC
Q 020570 311 ALVEWRLETGRTHQ 324 (324)
Q Consensus 311 slv~~~l~TGRtHQ 324 (324)
++++|+|+||||||
T Consensus 172 sll~~~l~tGRtHQ 185 (232)
T PRK10839 172 TQVRLTISEGRYHQ 185 (232)
T ss_pred CEEEEEEEcCcCHH
Confidence 89999999999999
No 7
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.
Probab=100.00 E-value=2.3e-33 Score=252.48 Aligned_cols=155 Identities=26% Similarity=0.364 Sum_probs=129.0
Q ss_pred CCCceeeccCCcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCcc
Q 020570 134 DIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPG 213 (324)
Q Consensus 134 ~~~~~Ilyed~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 213 (324)
..+++|||||++++|+|||+|++|++.+.....++.+.+..++. ...+.
T Consensus 13 ~~~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~-------------------------------~~~~~ 61 (213)
T cd02557 13 NDPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYG-------------------------------LTELR 61 (213)
T ss_pred CCCCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcC-------------------------------CCCcc
Confidence 34678999999999999999999999877666788887765431 12467
Q ss_pred ccCCCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCe
Q 020570 214 IVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQAR 293 (324)
Q Consensus 214 ~vhRLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k 293 (324)
+|||||++||||||||+|..++++|+++|++++++|+|+|+|.|.++.+++.++.||.+...... ..... ...++
T Consensus 62 ~vhRLD~~TSGllllak~~~~~~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~-~~~~~----~~~~~ 136 (213)
T cd02557 62 PCHRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKEYLARVKGEFPDGEVVVDQPIGLVSPKGG-LRNDV----DEKGK 136 (213)
T ss_pred CccCCCCCCceEEEEECCHHHHHHHHHHHHcCCccEEEEEEEeCcCCCCCeEEecceeccCcCCc-eeecc----CCCCc
Confidence 89999999999999999999999999999999999999999999998889999999976543221 11111 23678
Q ss_pred eeEEEEEEEEEeCCCCEEEEEEEcCCCCCCC
Q 020570 294 HAASRYKVIEILAGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 294 ~a~T~~~vl~~~~~~~~slv~~~l~TGRtHQ 324 (324)
.|.|.|+++......+++||+|+|.|||+||
T Consensus 137 ~a~t~~~~~~~~~~~~~slv~v~~~TGR~HQ 167 (213)
T cd02557 137 DARTIFKRLSYNGDLNTSVVLCKPITGRTHQ 167 (213)
T ss_pred eeeEEEEEEEEcCCCCeEEEEEEeCCCCHHH
Confidence 9999999998764447899999999999999
No 8
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=100.00 E-value=6.6e-33 Score=264.95 Aligned_cols=226 Identities=32% Similarity=0.420 Sum_probs=185.1
Q ss_pred EEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccccCcccccccCCCceee
Q 020570 61 EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIV 140 (324)
Q Consensus 61 ~~~v~~~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~~~~~~~~~~~~~~~Il 140 (324)
...+...+.+..+.+++...|...++...++.|+.|.|++||+.+ ..+..++.||.|.+..+.++++.+ ..++.|+
T Consensus 34 ~~~~~~rw~~k~~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~-~v~~i~k~~d~l~~~vhrh~p~~~---~~~~~Iv 109 (371)
T KOG1919|consen 34 RTFVKGRWAGKKLVDVFVSEFRLRERAYYESAIKLGRVTVNGEQV-RVSLIVKNGDVLCHTVHRHEPPVA---YLPIRIV 109 (371)
T ss_pred eEEEeeeecccchHHHHHHHHhcCchHhhhhhhhcCceEECcEee-eeEEEeccCCEEEEeeccCCCCcc---ccccceE
Confidence 335567788888899999888889999999999999999999999 589999999999998877666543 3578999
Q ss_pred ccCCcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCC
Q 020570 141 YEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDK 220 (324)
Q Consensus 141 yed~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~ 220 (324)
|||++|+|||||+|++|||.+....+++...+.... ....+.+|||||+
T Consensus 110 ~ed~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~~-------------------------------~~~~~~~~hRLDr 158 (371)
T KOG1919|consen 110 FEDKDYVVVNKPHGIPVHPTGRYRENTITKILAALH-------------------------------KVEGLRPCHRLDR 158 (371)
T ss_pred EecCCEEEEeCCCCCceeccCccccccchHHHHHhc-------------------------------cccccccccccCc
Confidence 999999999999999999988888788777665431 2245678999999
Q ss_pred CCceEEEeecCHHHHHHHHHHHhcCccceEE-EEEEecccC-CCCcEEEccceeCCCCCeeEEEcCC-CCCCCCCeeeEE
Q 020570 221 GTSGLLVVAKDEHSHAHLSEQFKLHTIERVY-ISLTSGVPS-QSSGRIEVPISRDPNNRIRMAAIPG-SNKHGQARHAAS 297 (324)
Q Consensus 221 ~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y-~A~v~G~~~-~~~g~i~~pl~~~~~~~~~~~~~~~-~~~~~~~k~a~T 297 (324)
.|||||+||+++.++..++.+|+++++.|.| +|.|.|.++ .+...|..|+..... ..+|.+... ......++.|.|
T Consensus 159 ~tSGllvlAkt~~~~~~~~~~~r~~~~~k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~-~~~~~l~~~~~~~~~~~k~a~T 237 (371)
T KOG1919|consen 159 LTSGLLVLAKTKEAADKFHEVLRKRTVKKEYVVARVEGPFPVVGEVEIKEPIGEEER-PLRMGLNAVGVRDEVAAKDAKT 237 (371)
T ss_pred cccceEEEEechhHhHHHHHHHhcccceeEEEEEEEeccCCCCceEEeCCCcccccc-ccceEeeeccccccccccccee
Confidence 9999999999999999999999999999999 799999987 445556566654432 133333221 112245899999
Q ss_pred EEEEEEEeCCCCEEEEEEEcCCCCCCC
Q 020570 298 RYKVIEILAGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 298 ~~~vl~~~~~~~~slv~~~l~TGRtHQ 324 (324)
.|+++.++ +..++|+|+|+||||||
T Consensus 238 ~~~~~~~~--~~ss~V~~~PlTGRtHQ 262 (371)
T KOG1919|consen 238 LFKVLSYD--GGSSLVECRPLTGRTHQ 262 (371)
T ss_pred EEEEcccC--CceEEEEeeccCCcHHH
Confidence 99999986 78999999999999999
No 9
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=100.00 E-value=2.7e-33 Score=253.05 Aligned_cols=150 Identities=31% Similarity=0.465 Sum_probs=124.5
Q ss_pred CceeeccCCcEEEEeCCCceEEecCCC-CCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccc
Q 020570 136 PLDIVYEDDNVLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (324)
Q Consensus 136 ~~~Ilyed~~~lvvnKPaGl~~~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 (324)
+++|||||++++|+|||+|++||+... ....++.+.+..++ ..+.+
T Consensus 13 ~~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~---------------------------------~~~~~ 59 (219)
T PRK10158 13 WLVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY---------------------------------PQAES 59 (219)
T ss_pred CCCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC---------------------------------CCCCE
Confidence 368999999999999999999998753 33456666654332 13568
Q ss_pred cCCCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCee
Q 020570 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH 294 (324)
Q Consensus 215 vhRLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~ 294 (324)
|||||++||||||||++..+++.|+++|+++.|.|+|+|+|.|.++.+++.++.||..+......+.+.. .+++.
T Consensus 60 vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~~v~K~Yla~v~G~~~~~~~~i~~~i~~~~~~~~~~~~~~-----~~gk~ 134 (219)
T PRK10158 60 VHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCY-----ETGKP 134 (219)
T ss_pred ECCCCCCCceEEEEECCHHHHHHHHHHHHhCCccEEEEEEEecccCCCCcEEecceecCCCCCceEEecC-----CCCce
Confidence 9999999999999999999999999999999999999999999998889999999987654444444432 26789
Q ss_pred eEEEEEEEEEeCCCCEEEEEEEcCCCCCCC
Q 020570 295 AASRYKVIEILAGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 295 a~T~~~vl~~~~~~~~slv~~~l~TGRtHQ 324 (324)
|.|.|++++... ...++|+|+|+||||||
T Consensus 135 a~t~~~~l~~~~-~~~sll~~~~~TGRtHQ 163 (219)
T PRK10158 135 AQTEYEVVEYAA-DNTARVVLKPITGRSHQ 163 (219)
T ss_pred eeEEEEEEEEcC-CCCEEEEEEeCCCCHHH
Confidence 999999998753 33589999999999999
No 10
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621. This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.
Probab=100.00 E-value=1.2e-32 Score=248.56 Aligned_cols=146 Identities=28% Similarity=0.440 Sum_probs=121.2
Q ss_pred ceeeccCCcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccC
Q 020570 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVH 216 (324)
Q Consensus 137 ~~Ilyed~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vh 216 (324)
++|||||++|+|+|||+|++||+..+ ..++.+.+..+. ....+++||
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 47999999999999999999998753 245655554321 113567899
Q ss_pred CCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCeeeE
Q 020570 217 RLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAA 296 (324)
Q Consensus 217 RLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~a~ 296 (324)
|||++||||||||+|..+++.|+++|+++.++|+|+|+|.|.++.++|.|+.++.+...+...+ .. ..++.|.
T Consensus 49 RLDr~TSGlll~Ak~~~~~~~L~~~~~~~~v~K~YlAlV~g~~~~~~~~i~~~~~~~~~~~~~~--~~-----~~~k~a~ 121 (217)
T TIGR01621 49 RLDKMTSGILLLALNAESASELSQGFAKRKIEKTYLALSSKKPKKKQGLICGDMEKSRRGSWKL--VN-----SQENPAI 121 (217)
T ss_pred CCCCCCceEEEEEcCHHHHHHHHHHHhcCCccEEEEEEEeccccCCCCEEeCCcccCCCCCEEE--eC-----CCCCcee
Confidence 9999999999999999999999999999999999999999999888999999997654443322 21 1578899
Q ss_pred EEEEEEEEeCCCCEEEEEEEcCCCCCCC
Q 020570 297 SRYKVIEILAGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 297 T~~~vl~~~~~~~~slv~~~l~TGRtHQ 324 (324)
|.|+++... +++++|+|+|+||||||
T Consensus 122 t~~~~~~~~--~~~slv~~~~~TGR~HQ 147 (217)
T TIGR01621 122 TRFFSASAA--TGLRLFILKPHTGKTHQ 147 (217)
T ss_pred EEEEEEEEc--CCeEEEEEEeCCCCHHH
Confidence 999999875 46899999999999999
No 11
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.
Probab=100.00 E-value=3e-32 Score=246.92 Aligned_cols=151 Identities=28% Similarity=0.478 Sum_probs=118.8
Q ss_pred ceeeccCCcEEEEeCCCceEEecCCCCCCCcH--HHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccc
Q 020570 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTL--VNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (324)
Q Consensus 137 ~~Ilyed~~~lvvnKPaGl~~~~~~~~~~~tl--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 (324)
++|||||++++|+|||+|++||+.++....+. ...+..++ ..++++
T Consensus 1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~ 48 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQL--------------------------------GQHVYP 48 (223)
T ss_pred CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHc--------------------------------CCCccc
Confidence 36999999999999999999998764433322 22221111 124678
Q ss_pred cCCCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCee
Q 020570 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH 294 (324)
Q Consensus 215 vhRLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~ 294 (324)
|||||++||||||||+|+.+++.|+.+|+++.++|+|+|+|.|.++. ++.|+.|+.+.........+.. ...++.
T Consensus 49 vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~v~K~Y~alv~G~~~~-~~~i~~~l~~~~~~~~~~~~~~----~~~~~~ 123 (223)
T cd02563 49 VHRLDRPTSGVLLFALSSEVARKLGEQFTEHRVHKTYLAVVRGYVPE-SGTIDYPLSEELDKLADKFASD----DKAPQA 123 (223)
T ss_pred ccCCCCCCeEEEEEEECHHHHHHHHHHHhcCceeEEEEEEEECccCC-CCeEEEeeeeCCCccceEEeec----CCCCce
Confidence 99999999999999999999999999999999999999999999865 7899999987654433333322 236789
Q ss_pred eEEEEEEEEEe---------CCCCEEEEEEEcCCCCCCC
Q 020570 295 AASRYKVIEIL---------AGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 295 a~T~~~vl~~~---------~~~~~slv~~~l~TGRtHQ 324 (324)
|.|.|+++... ...++|||+|+|+||||||
T Consensus 124 a~t~~~~l~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQ 162 (223)
T cd02563 124 ATTHYRLLAVEELPVVVGKYPTSRYSLVELTPHTGRKHQ 162 (223)
T ss_pred eEEEEEEeeecccccccccCCCCCeEEEEEEeCCCCHHH
Confidence 99999999752 1235899999999999999
No 12
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=99.98 E-value=7.2e-32 Score=249.30 Aligned_cols=151 Identities=26% Similarity=0.399 Sum_probs=117.7
Q ss_pred ceeeccCCcEEEEeCCCceEEecCCCCCCCcH--HHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccc
Q 020570 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTL--VNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (324)
Q Consensus 137 ~~Ilyed~~~lvvnKPaGl~~~~~~~~~~~tl--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 (324)
++|||||++++|||||+|++||+.......+. ...+...+ ..++++
T Consensus 2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~ 49 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQI--------------------------------GQHVFT 49 (257)
T ss_pred CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHh--------------------------------CCCcee
Confidence 47999999999999999999998754443332 22221111 124668
Q ss_pred cCCCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCee
Q 020570 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH 294 (324)
Q Consensus 215 vhRLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~ 294 (324)
|||||++||||||||+|..+++.|+++|+++.|+|+|+|+|.|.++ .++.++.|+.+............ ...++.
T Consensus 50 VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~Alv~G~~~-~~~~i~~~l~~~~~~~~~~~~~~----~~~~k~ 124 (257)
T PRK11112 50 AHRLDRPTSGVLLMALSSEVARLLAQQFEQHQIQKTYHAIVRGWLM-EEAVLDYPLKEELDKIADKFARE----DKAPQP 124 (257)
T ss_pred eccCCCCCeeEEEEECCHHHHHHHHHHHHhCCcceEEEEEEEeEeC-CCCeEeeeeeecccccceeeccc----CCCCeE
Confidence 9999999999999999999999999999999999999999999985 56899999986533222222111 236899
Q ss_pred eEEEEEEEEEeC---------CCCEEEEEEEcCCCCCCC
Q 020570 295 AASRYKVIEILA---------GGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 295 a~T~~~vl~~~~---------~~~~slv~~~l~TGRtHQ 324 (324)
|.|.|++++... ..++|||+|+|.||||||
T Consensus 125 a~T~~~~l~~~~~~~~~~~~~~~~~slv~i~~~TGRtHQ 163 (257)
T PRK11112 125 AVTHYRGLATVEMPVATGRYPTTRYSLVELEPKTGRKHQ 163 (257)
T ss_pred eEEEEEEEEEecccccccccCCCCeEEEEEEcCCCChHH
Confidence 999999997642 246899999999999999
No 13
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=99.97 E-value=5.4e-30 Score=240.20 Aligned_cols=189 Identities=20% Similarity=0.198 Sum_probs=138.5
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecC--CEEeeeccccCcccccccCCCceeec-cCCcEE
Q 020570 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGG--DMVNCTISELQPLRAEAEDIPLDIVY-EDDNVL 147 (324)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~G--D~V~v~~~~~~~~~~~~~~~~~~Ily-ed~~~l 147 (324)
+||++||++. +.+||++++++|++|+|+|||+++ .++.+|.++ |.|.++....... ..+ ||+.|+
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 789999999999999999999988 689999887 4566643211100 111 557899
Q ss_pred EEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCceEEE
Q 020570 148 VVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLV 227 (324)
Q Consensus 148 vvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGLLl 227 (324)
++|||+|++|++.+.....|+++.+... ...++++|||||++||||||
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 9999999999998776667888877431 11246789999999999999
Q ss_pred eecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCeeeEEEEEEEEEeC-
Q 020570 228 VAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILA- 306 (324)
Q Consensus 228 ~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~- 306 (324)
||+|..++..|.. ..+.|+|+|+|+|.|.++++.. .. +. . .+.+. ++. +.+..+....
T Consensus 119 lTndg~~~~~L~~--p~~~i~K~Y~v~V~G~~~~~~l--~~-l~---~---Gv~l~-------~~~---~~~~~v~~~~~ 177 (289)
T PRK10700 119 FTTDGELANRLMH--PSREVEREYAVRVFGQVDDAKL--RQ-LS---R---GVQLE-------DGP---AAFKTIKFSGG 177 (289)
T ss_pred EEcCHHHHHHHhC--ccCCCCeEEEEEEccCCCHHHH--HH-HH---c---CCEeC-------Cce---eeeEEEEeccC
Confidence 9999999999976 6888999999999998865432 11 10 0 01111 111 2233333221
Q ss_pred CCCEEEEEEEcCCCCCCC
Q 020570 307 GGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 307 ~~~~slv~~~l~TGRtHQ 324 (324)
....+++++.|.+||+||
T Consensus 178 ~~~~s~l~v~L~EGk~hQ 195 (289)
T PRK10700 178 EGINQWYNVTLTEGRNRE 195 (289)
T ss_pred CCCceEEEEEEeCCccHH
Confidence 124588999999999998
No 14
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.96 E-value=2.2e-29 Score=235.66 Aligned_cols=145 Identities=25% Similarity=0.333 Sum_probs=119.4
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccccCcccccccCCCceeeccCCcEE
Q 020570 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVL 147 (324)
Q Consensus 68 ~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~~~~~~~~~~~~~~~Ilyed~~~l 147 (324)
.+++||++||++. +.+||++++++|++|+|+|||+++ .++..|.+||.|.++.....+ ..+||++|+
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-----------REAEDLVLI 70 (290)
T ss_pred chHHHHHHHHHhC-CCCCHHHHHHHHHCCcEEECCEEc-cCCCCcCCCCEEEECCEEccc-----------cccCCCeEE
Confidence 4568999999987 689999999999999999999998 689999999999997532111 013788999
Q ss_pred EEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCceEEE
Q 020570 148 VVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLV 227 (324)
Q Consensus 148 vvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGLLl 227 (324)
|+|||+|++||+.+. ...++++.+..+ .++++|||||++||||||
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 456777766321 246789999999999999
Q ss_pred eecCHHHHHHHHHHHhcCccceEEEEEEecccCCC
Q 020570 228 VAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQS 262 (324)
Q Consensus 228 ~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~ 262 (324)
||+|..++..|.. ..+.++|+|+|+|.|.++++
T Consensus 116 lT~dg~~~~~L~~--p~~~i~K~Y~v~V~g~~~~~ 148 (290)
T PRK10475 116 LTNHGDLVNKILR--AGNDHEKEYLVTVDKPITDE 148 (290)
T ss_pred EecCHHHHHHhhC--cCCCCCeEEEEEECCCCCHH
Confidence 9999998888866 45679999999999988653
No 15
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family. This Prosite family is a subset of the Pfam family.; InterPro: IPR006145 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit). RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [, ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site. RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: RluB modifies uracil-2605. RluC modifies uracil-955, U-2504, and U-2580. RluD modifies uracil-1911, U-1915, and U-1917. RluE modifies uracil-3457. RluF modifies uracil-2604, and to a lesser extent U-2605. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [, ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 2GML_A 3DH3_B 1VIO_A 2I82_B 1XPI_B 1V9K_B 1PRZ_A 1V9F_A 2IST_A 1QYU_A ....
Probab=99.96 E-value=1.1e-28 Score=212.20 Aligned_cols=148 Identities=37% Similarity=0.554 Sum_probs=109.5
Q ss_pred cEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCce
Q 020570 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (324)
Q Consensus 145 ~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (324)
+|+|+|||+|++|++.++............... .......+++|||||++|||
T Consensus 1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~~~v~RLD~~TsG 53 (164)
T PF00849_consen 1 NLIVVNKPAGVPVHPSDGNESKSVKELPALSLK---------------------------RGDDPPELYPVHRLDRDTSG 53 (164)
T ss_dssp SEEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHH---------------------------HCTTSGGGEESS---TT-EE
T ss_pred CEEEEECCCCCeEecCCCCCcccccchhhhhhh---------------------------hccCCCceEECCCCCccccC
Confidence 689999999999999875333333322222110 00134678899999999999
Q ss_pred EEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeC--CCCCeeEEEcCCCCCCCCCeeeEEEEEEE
Q 020570 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRD--PNNRIRMAAIPGSNKHGQARHAASRYKVI 302 (324)
Q Consensus 225 LLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~--~~~~~~~~~~~~~~~~~~~k~a~T~~~vl 302 (324)
|||||+|..+++.|+.+|+.+.++|+|+|+|.|.+.++++.++.++... .......... ..+++.+.|.|+++
T Consensus 54 lll~a~~~~~~~~l~~~f~~~~~~K~Y~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~t~~~~l 128 (164)
T PF00849_consen 54 LLLFAKDKEAAAKLSKQFPKRKVEKTYLALVEGGPVEEEGKINSPLGKDVGKNKSSNKDPP-----GRDGKPAITRYRVL 128 (164)
T ss_dssp EEEEESSHHHHHHHHHHHHTTCSEEEEEEEECSSSSTTCEEEESHEEE-EECSSCTCCEEE-----TTTSBTSEEEEEEE
T ss_pred CeeccCCcccccccccccccCCCcEEEEEeEcccccccceeeeccccccccccccceeeee-----cccccccceeeeee
Confidence 9999999999999999999999999999999988878899999999772 1111111111 23789999999999
Q ss_pred EEe-------CCCCEEEEEEEcCCCCCCC
Q 020570 303 EIL-------AGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 303 ~~~-------~~~~~slv~~~l~TGRtHQ 324 (324)
+.. ...++++++|+|.|||+||
T Consensus 129 ~~~~~~~~~~~~~~~s~v~~~l~tGr~HQ 157 (164)
T PF00849_consen 129 RSGSRTPSKDENAGCSLVECELITGRTHQ 157 (164)
T ss_dssp EEETT---EECCSSEEEEEEEESS-STTH
T ss_pred ccccccccccccCCCEEEEEEECcCCCHH
Confidence 987 5678999999999999999
No 16
>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=99.96 E-value=2.4e-28 Score=209.09 Aligned_cols=134 Identities=31% Similarity=0.438 Sum_probs=106.1
Q ss_pred EEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCceE
Q 020570 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (324)
Q Consensus 146 ~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (324)
|+|+|||+|++||+.++....++.+.+... ...++++|||||++||||
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~--------------------------------~~~~~~~vhRLD~~TSGl 48 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKL--------------------------------HGPRVHAAGRLDKDTSGL 48 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhhcc--------------------------------cCCceeEeccCCCCCeeE
Confidence 589999999999998877667776644221 123577899999999999
Q ss_pred EEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCeeeEEEEEEEEEe
Q 020570 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL 305 (324)
Q Consensus 226 Ll~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~ 305 (324)
||||+|.++++.|+.+ +++++|+|+|+|.|.+++ ++.+..++.+. +....... .+++.+.|.|+++...
T Consensus 49 ll~ak~~~~~~~l~~~--~~~v~K~Y~a~v~g~~~~-~~~~~~~~~~~--~~~~~~~~------~~~~~~~t~~~~l~~~ 117 (154)
T cd02550 49 LLLTNDGRLQRRLTEP--RREIEKEYLVTVRGELDE-EGIEDLATVRR--GRLSGLVD------EGVPLAVTKVRVIGEH 117 (154)
T ss_pred EEEEcCHHHHHHHhhh--hccCcEEEEEEEEeecCc-chheecccccc--CcceeEEc------CCCcccceEEEEEEec
Confidence 9999999999999997 788999999999999864 56677776542 22222222 2578899999999753
Q ss_pred CCCCEEEEEEEcCCCCCCC
Q 020570 306 AGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 306 ~~~~~slv~~~l~TGRtHQ 324 (324)
.++++++|+|.|||+||
T Consensus 118 --~~~sll~~~l~tGR~HQ 134 (154)
T cd02550 118 --GGTGRLRLTLKTGRTHQ 134 (154)
T ss_pred --CCcEEEEEEEcCCCcHH
Confidence 46899999999999999
No 17
>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=99.95 E-value=3.5e-27 Score=206.59 Aligned_cols=145 Identities=48% Similarity=0.794 Sum_probs=116.3
Q ss_pred EEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCceE
Q 020570 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (324)
Q Consensus 146 ~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (324)
++|+|||+|++|++.+.....++.+.+..+.... .....+.+|||||++||||
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~v~RLD~~tsGl 53 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLL---------------------------GEEFRPGLVHRLDKDTSGL 53 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhc---------------------------CCCCcCceecccCCCCceE
Confidence 5899999999999988777777776653221100 0234678999999999999
Q ss_pred EEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCeeeEEEEEEEEEe
Q 020570 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL 305 (324)
Q Consensus 226 Ll~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~ 305 (324)
||||+|.++++.|..+|+++.++|+|+|+|.|.++...+.++.|+............. ..+++.+.|.|+++...
T Consensus 54 ll~ak~~~~~~~l~~~~~~~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~t~~~~l~~~ 128 (185)
T cd02869 54 LLVAKNKKAAAKLSKQFKERKVKKTYLALVDGKPPEDEGTIDAPLGRKKRKKRARVVV-----SEDGKPAITHYKVLERF 128 (185)
T ss_pred EEEEcCHHHHHHHHHHHhcCceeEEEEEEEeCCCCCCccEEecccccCCccCceEEEE-----CCCCeEEEEEEEEEEEc
Confidence 9999999999999999999999999999999999988999998887642222222222 12679999999999864
Q ss_pred CCCCEEEEEEEcCCCCCCC
Q 020570 306 AGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 306 ~~~~~slv~~~l~TGRtHQ 324 (324)
.++|+++|+|+|||+||
T Consensus 129 --~~~s~~~~~l~tGR~HQ 145 (185)
T cd02869 129 --GNVTLVELQLETGRTHQ 145 (185)
T ss_pred --CCcEEEEEEeCcCCccH
Confidence 47899999999999999
No 18
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=1.3e-27 Score=217.58 Aligned_cols=192 Identities=22% Similarity=0.300 Sum_probs=137.8
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecC-CEEeeeccccCcccccccCCCceeec-cCCcEE
Q 020570 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGG-DMVNCTISELQPLRAEAEDIPLDIVY-EDDNVL 147 (324)
Q Consensus 70 ~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~G-D~V~v~~~~~~~~~~~~~~~~~~Ily-ed~~~l 147 (324)
.+||+|||++. +.+||++++++|.+|+|+|||++++..+..+.++ |.|.+.... +.+ +...|+
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 58999999998 8999999999999999999999998888899998 467775531 222 234499
Q ss_pred EEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCceEEE
Q 020570 148 VVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLV 227 (324)
Q Consensus 148 vvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGLLl 227 (324)
++|||.|++|+..++..+.|+.+.+.... + ...++++|+|||++|+||||
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 99999999999887777778766553210 0 22468899999999999999
Q ss_pred eecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCeeeEEEEEEEEEeCC
Q 020570 228 VAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAG 307 (324)
Q Consensus 228 ~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~ 307 (324)
||+|.+.+..|.. ....++|+|+|.|.|.+.++. +..-.. .+... ++....+....+.....
T Consensus 117 LTnDG~la~rL~~--P~~~~~K~Y~v~v~g~~~~~~------l~~l~~---Gv~l~-------d~~~~~~~~~~l~~~~~ 178 (248)
T COG1187 117 LTNDGELAHRLMH--PSSEVEKEYLVRVEGPVTEED------LEKLRK---GVTLD-------DGETKPAKPASLEKEPG 178 (248)
T ss_pred EeCCHHHHHHhcC--CCCCCCEEEEEEEecCCCHHH------HHHHhC---CcEec-------CcccccceeEEEEecCC
Confidence 9999776666654 677899999999999875432 111100 01111 11112222112222111
Q ss_pred CCEEEEEEEcCCCCCCC
Q 020570 308 GGSALVEWRLETGRTHQ 324 (324)
Q Consensus 308 ~~~slv~~~l~TGRtHQ 324 (324)
.+.|++++.|..||.||
T Consensus 179 ~~~s~~~itl~EGrnrQ 195 (248)
T COG1187 179 KNNSWLRITLTEGRNRQ 195 (248)
T ss_pred CCceEEEEEEeCCcCHH
Confidence 15789999999999998
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=99.92 E-value=8.1e-26 Score=196.13 Aligned_cols=128 Identities=20% Similarity=0.188 Sum_probs=99.2
Q ss_pred cEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCce
Q 020570 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (324)
Q Consensus 145 ~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (324)
.++|+|||+|++||+.+.....++.+.+..+. ..++++|||||++|||
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 37999999999999876665678877764321 1356789999999999
Q ss_pred EEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCeeeEEEEEEEEE
Q 020570 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEI 304 (324)
Q Consensus 225 LLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~ 304 (324)
|||||+|..+++.|.. +++.++|+|+|+|.|.++++. + ..... .+.. .+++.+.|.|+++..
T Consensus 49 Lll~ak~~~~~~~L~~--~~~~i~K~Y~a~V~g~~~~~~--~----~~~~~---gv~~-------~~~~~~~~~~~~~~~ 110 (167)
T cd02556 49 LLLFTNDGELANRLMH--PSNEIEREYAVRVFGQVTDEQ--L----KSLKK---GVEL-------EDGFAGFKSIQLEGG 110 (167)
T ss_pred EEEEECCHHHHHHHhC--CcCCCCeEEEEEECccCCHHH--H----HHHHc---CCEE-------CCCcCcceEEEEEec
Confidence 9999999999999975 788999999999999986543 1 11000 1111 146788899999865
Q ss_pred eCCCCEEEEEEEcCCCCCCC
Q 020570 305 LAGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 305 ~~~~~~slv~~~l~TGRtHQ 324 (324)
. .++|+++|+|+|||+||
T Consensus 111 ~--~~~sll~v~l~tGR~HQ 128 (167)
T cd02556 111 E--GKNSWYRVTLREGRNRE 128 (167)
T ss_pred C--CCcEEEEEEEEeCCCHH
Confidence 3 35799999999999999
No 20
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.
Probab=99.92 E-value=3.2e-26 Score=194.33 Aligned_cols=126 Identities=25% Similarity=0.334 Sum_probs=96.0
Q ss_pred EEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCceE
Q 020570 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (324)
Q Consensus 146 ~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (324)
|+|+|||+|++|++.++....++.+.+.. ...++.+|||||++||||
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~---------------------------------~~~~~~~vhRLD~~TsGl 47 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKD---------------------------------VGERLFPVGRLDYDTEGL 47 (146)
T ss_pred CEEEECCCCcEecccCCCCCCEEeeeccc---------------------------------cCCCEEECCCCCCCCeeE
Confidence 58999999999998876555565543211 113568899999999999
Q ss_pred EEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCeeeEEEEEEEEEe
Q 020570 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL 305 (324)
Q Consensus 226 Ll~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~ 305 (324)
||||+|..+++.|.. +++.++|+|+|+|.|.+..+.+ .. + . . . ... .+++.+.|+|+++...
T Consensus 48 ll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~~~~--~~-~---~-~--~-~~~------~~~~~~~t~~~~l~~~ 109 (146)
T cd02870 48 LLLTNDGELANRLTH--PRYGVEKTYLVKVRGVPSEEEL--RR-L---R-A--G-VEL------DDGKTAPAKVKVLSRD 109 (146)
T ss_pred EEEeCCHHHHHHhhC--ccCCCCeEEEEEECCCCCHHHH--HH-H---H-C--C-eEe------CCceEcceEEEEeccC
Confidence 999999999999976 5778999999999999865432 11 1 0 0 1 111 1568899999999754
Q ss_pred CCCCEEEEEEEcCCCCCCC
Q 020570 306 AGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 306 ~~~~~slv~~~l~TGRtHQ 324 (324)
.+.++++|+|.|||+||
T Consensus 110 --~~~sll~~~l~tGR~HQ 126 (146)
T cd02870 110 --PKNTLLEVTLHEGRNRQ 126 (146)
T ss_pred --CCCcEEEEEEEeCCcHH
Confidence 46799999999999999
No 21
>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=99.89 E-value=1.6e-23 Score=181.99 Aligned_cols=136 Identities=17% Similarity=0.225 Sum_probs=91.0
Q ss_pred EEEEeCCCceEEecCCC-CCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCce
Q 020570 146 VLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (324)
Q Consensus 146 ~lvvnKPaGl~~~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (324)
++|+|||+|++||+.++ ....++.+.+. ..++.+|||||++|||
T Consensus 1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l~-----------------------------------~~~~~~v~RLD~~TsG 45 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYID-----------------------------------DPGVYAAGRLDRDSEG 45 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCccHHHHcC-----------------------------------cCCeEEccCCCCCCeE
Confidence 58999999999998765 34456655431 0245689999999999
Q ss_pred EEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcE-EEccce-eCCC-CCeeEEEcCCCCCCCCCeeeEEEEEE
Q 020570 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGR-IEVPIS-RDPN-NRIRMAAIPGSNKHGQARHAASRYKV 301 (324)
Q Consensus 225 LLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~-i~~pl~-~~~~-~~~~~~~~~~~~~~~~~k~a~T~~~v 301 (324)
|||||+|..+++.|... .+.++|+|+|+|.|.++.+... +...+. .+.. ....+...+ .+....+.|++
T Consensus 46 lll~a~d~~~~~~l~~~--~~~v~K~Y~a~v~g~~~~~~~~~l~~g~~~~~~~~~~~~v~~~~------~~~~~~~~~~~ 117 (168)
T cd02566 46 LLLLTDDGRLQHRITDP--SFKHPKTYYVQVEGVPTEDALEQLRNGVELGDGLTLPAKVEKVD------EPPWLWEREPP 117 (168)
T ss_pred EEEEEeCHHHHHHHHCC--CCCCCEEEEEEECCcCCHHHHHHHhCCcEECCeEecceEEEEec------ccccccccccc
Confidence 99999999888887763 4569999999999998653210 001111 1111 111111111 12244566666
Q ss_pred EEEeCCCCEEEEEEEcCCCCCCC
Q 020570 302 IEILAGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 302 l~~~~~~~~slv~~~l~TGRtHQ 324 (324)
+......+.|+++|+|.|||+||
T Consensus 118 ~~~~~~~~~sll~v~l~tGR~HQ 140 (168)
T cd02566 118 IRFRKNIPTSWIEITICEGKNRQ 140 (168)
T ss_pred cccccCCCccEEEEEEecCccHH
Confidence 76543456789999999999999
No 22
>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=99.89 E-value=1.3e-23 Score=182.24 Aligned_cols=124 Identities=20% Similarity=0.245 Sum_probs=88.9
Q ss_pred EEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCceE
Q 020570 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (324)
Q Consensus 146 ~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (324)
|+|+|||+|++|++.+ ....++.+.+..++ ...++.+|||||++||||
T Consensus 2 ~ivvnKP~G~~~~~~~-~~~~tl~~~l~~~~-------------------------------~~~~~~~vhRLD~~TSGl 49 (167)
T cd02553 2 YLMLNKPAGVVCATKD-PHHPTVIDLLPEPD-------------------------------RRRDLFPVGRLDKDTTGL 49 (167)
T ss_pred EEEEECCCCCEeCCCC-CCCCcHHHHhhhhc-------------------------------ccCCeEEcccCCCCCEEE
Confidence 7999999999999654 44678877765432 113567899999999999
Q ss_pred EEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCeeeEEEEEEEEEe
Q 020570 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL 305 (324)
Q Consensus 226 Ll~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~ 305 (324)
||||+|..+++.+.. +.+.++|+|+|+|.|.++.+++ .... . .+.... +.+...+.++++.
T Consensus 50 ll~ak~~~~~~~l~~--~~~~i~K~Y~a~V~G~~~~~~~--~~~~----~---~~~~~~------~~~~~~~~~~~~~-- 110 (167)
T cd02553 50 LLLTNDGQLAHRLTS--PKKHVPKTYEVTLAGPLTEDDI--EAFA----E---GVLLHD------GYPTKPAKLEILS-- 110 (167)
T ss_pred EEEEeCHHHHHHhhC--CcCCCceEEEEEEccCCCHHHH--HHHH----C---CeEEcC------CCEeeeeEEEEeC--
Confidence 999999987777765 5788999999999999865432 1110 0 111111 1123445566552
Q ss_pred CCCCEEEEEEEcCCCCCCC
Q 020570 306 AGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 306 ~~~~~slv~~~l~TGRtHQ 324 (324)
.++++|+|.|||+||
T Consensus 111 ----~sll~v~l~tGR~HQ 125 (167)
T cd02553 111 ----PTTVRLTITEGKYHQ 125 (167)
T ss_pred ----CcEEEEEEEeCCCHH
Confidence 299999999999998
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=99.83 E-value=1.3e-20 Score=164.81 Aligned_cols=89 Identities=20% Similarity=0.274 Sum_probs=63.5
Q ss_pred CccccCCCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcE-EEccceeCCCCCeeEEEcCCCCCC
Q 020570 211 RPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGR-IEVPISRDPNNRIRMAAIPGSNKH 289 (324)
Q Consensus 211 ~~~~vhRLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~-i~~pl~~~~~~~~~~~~~~~~~~~ 289 (324)
++.+|||||++||||||||+|..+++.|... .+.|+|+|+|+|.|.++++... +..++. .++
T Consensus 46 ~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~~--~~~i~K~Y~v~v~g~~~~~~l~~l~~g~~-----------~~~---- 108 (177)
T cd02555 46 RLAPIGPLDKDASGLLVFSQDGRVLRKLIGD--ASRLEQEYLVEVRGELTAGGLERLNHGLT-----------YDG---- 108 (177)
T ss_pred ceeEecCCCCCCeeEEEEECCHHHHHHHhCh--hcCCCEEEEEEEcccCCHHHHHHHhcCcc-----------cCC----
Confidence 5778999999999999999999999999984 4779999999999998653210 111110 010
Q ss_pred CCCeeeEEEEEEEEEeCCCCEEEEEEEcCCCCCCC
Q 020570 290 GQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 290 ~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGRtHQ 324 (324)
...+++.+.+ .+.+++++.|.|||+||
T Consensus 109 ~~~~~~~~~~--------~~~~~l~i~l~tGr~hQ 135 (177)
T cd02555 109 RELPPAKVSW--------QNEQRLRFALKEPQPGQ 135 (177)
T ss_pred eecceEEEEE--------cCCCEEEEEEECCcChH
Confidence 0112233322 12479999999999998
No 24
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.82 E-value=2.5e-20 Score=167.33 Aligned_cols=83 Identities=24% Similarity=0.345 Sum_probs=69.3
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
..|+++|||+|++|+..++....++.+.+. ..++++|||||++||
T Consensus 39 ~~ylllnKP~G~l~~~~d~~~~~tl~d~l~-----------------------------------~~~~~~vgRLD~~Ts 83 (217)
T PRK11394 39 TRVILFNKPYDVLPQFTDEAGRKTLKEFIP-----------------------------------VQGVYAAGRLDRDSE 83 (217)
T ss_pred CEEEEEECCCCCEEeeCCccCCcchHHhcc-----------------------------------cCCeEEecCCCCCCe
Confidence 579999999999999766665667766542 124678999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCC
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSS 263 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~ 263 (324)
||||||+|..+++.|... ++.++|+|+|+|.|.+..+.
T Consensus 84 GllLlt~d~~~~~~L~~~--~~~i~K~Y~~~v~g~~~~~~ 121 (217)
T PRK11394 84 GLLVLTNNGALQARLTQP--GKRTGKIYYVQVEGIPTQDA 121 (217)
T ss_pred eEEEEECCHHHHHHHhCc--ccCCCEEEEEEECCCCCHHH
Confidence 999999999999999984 67899999999999986543
No 25
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.
Probab=99.75 E-value=3.8e-18 Score=147.40 Aligned_cols=80 Identities=16% Similarity=0.213 Sum_probs=65.5
Q ss_pred EEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCceE
Q 020570 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (324)
Q Consensus 146 ~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (324)
|+++|||+|++|++.+. ...++.+.+.. ..++++|||||++||||
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 78999999999998764 34666655421 13578899999999999
Q ss_pred EEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCC
Q 020570 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQS 262 (324)
Q Consensus 226 Ll~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~ 262 (324)
||||+|..+++.|.. ..+.++|+|+|.|.|.+.++
T Consensus 47 ll~t~dg~~~~~L~~--p~~~~~K~Y~V~v~~~l~~~ 81 (164)
T cd02554 47 ILLTNDGDLVNKILH--ADNNHEKEYLVTVNKPITDE 81 (164)
T ss_pred EEEEcCHHHHHHHhh--hhcCCCeEEEEEECCCCCHH
Confidence 999999999999965 55678999999999988653
No 26
>TIGR00093 pseudouridine synthase. This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc.
Probab=99.71 E-value=8.1e-18 Score=139.79 Aligned_cols=90 Identities=22% Similarity=0.371 Sum_probs=70.4
Q ss_pred cCCCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCCCCcEEEccceeCCCCCeeEEEcCCCCCCCCCee
Q 020570 215 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH 294 (324)
Q Consensus 215 vhRLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~~~g~i~~pl~~~~~~~~~~~~~~~~~~~~~~k~ 294 (324)
|||||++||||||||+|..+++.|.. +++.|+|+|+|+|.|.++++. +. ++. . .+.. . +++.
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~--~~~~i~K~Y~a~v~g~~~~~~--~~-~~~---~---g~~~-~------~~~~ 62 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTH--PGHHCEKTYLVTVEGPVTDED--LE-ALR---K---GVQL-E------DGPT 62 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhC--CCCCCCeEEEEEECCCCCHHH--HH-HHh---C---CeEE-C------CcEE
Confidence 79999999999999999999999987 678899999999999986543 11 221 0 1111 1 3566
Q ss_pred eEEEEEEEEEeCCCCEEEEEEEcCCCCCCC
Q 020570 295 AASRYKVIEILAGGGSALVEWRLETGRTHQ 324 (324)
Q Consensus 295 a~T~~~vl~~~~~~~~slv~~~l~TGRtHQ 324 (324)
+.+.|+++... .+.++++|+|.|||+||
T Consensus 63 ~~~~~~~l~~~--~~~~~l~~~l~tGR~HQ 90 (128)
T TIGR00093 63 KPAKLEVITEP--GFPTWLRITLSEGRNRQ 90 (128)
T ss_pred eeeEEEEEccC--CCceEEEEEEeCCCCHH
Confidence 78889988653 34789999999999999
No 27
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=99.22 E-value=4.4e-11 Score=86.73 Aligned_cols=70 Identities=41% Similarity=0.550 Sum_probs=60.5
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccccCcccccccCCCceeeccCCcEEEEe
Q 020570 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVN 150 (324)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~~~~~~~~~~~~~~~Ilyed~~~lvvn 150 (324)
+||++||.+.++..||+.++++|++|.|+|||+.++.++..+.+||.|.+.... .+..|+|||++++|+|
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 489999998866789999999999999999999987789999999999886421 1128999999999987
No 28
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=99.12 E-value=1.1e-10 Score=105.67 Aligned_cols=43 Identities=30% Similarity=0.291 Sum_probs=38.2
Q ss_pred ccccCCCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 212 PGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 212 ~~~vhRLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
.+.|||||.+|||||+||+++.+ ++.++|.++.+.|+|+|...
T Consensus 34 ~~~vhrLD~~aSGvl~~a~~~~t--kl~~~~~~~~~~K~Y~~~~~ 76 (226)
T cd02868 34 LVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYSNHPTRVYTIRGL 76 (226)
T ss_pred eeEccccCCCCceEEEEEeChhH--hHHHHHHhcCCCeEEEEEEE
Confidence 56789999999999999999876 59999999999999997653
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=99.00 E-value=7.3e-10 Score=76.02 Aligned_cols=48 Identities=38% Similarity=0.511 Sum_probs=44.6
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEE
Q 020570 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMV 118 (324)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V 118 (324)
+|||+||.+.....||++++++|.+|.|+|||++++++++.|.+||+|
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 589999998766678999999999999999999998899999999987
No 30
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=98.93 E-value=1.9e-09 Score=77.32 Aligned_cols=51 Identities=18% Similarity=0.325 Sum_probs=46.9
Q ss_pred CccchHHHHHHhccCCC--CHHHHHHHHHcCceEECCEEeccceeeeecCCEEee
Q 020570 68 AGKLRLDAWISSRIDGI--SRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNC 120 (324)
Q Consensus 68 ~~~~RLdk~L~~~~~~~--Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v 120 (324)
.+++|||+||+.. .. ||+.++++|..|.|+|||+++++++++|++||+|.+
T Consensus 6 ~~~~rLd~~L~~~--~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 6 TEYITLGQLLKEL--GIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEI 58 (59)
T ss_pred chHHHHHHHHHHc--CCccCHHHHHHHHHcCCEEECCEEccCCCCCCCCCCEEEe
Confidence 3679999999997 45 999999999999999999999778999999999986
No 31
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=98.48 E-value=2.1e-07 Score=73.00 Aligned_cols=55 Identities=33% Similarity=0.468 Sum_probs=48.6
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeecc
Q 020570 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (324)
Q Consensus 68 ~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~ 123 (324)
...+|||+||.-.--.-+|+.++++|..|+|.|||.++ +++..|+.||+|.+.+.
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 45699999998642257999999999999999999999 89999999999999774
No 32
>smart00363 S4 S4 RNA-binding domain.
Probab=98.41 E-value=8.1e-07 Score=62.06 Aligned_cols=52 Identities=33% Similarity=0.392 Sum_probs=46.4
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeec
Q 020570 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
+||+.||.+.+...|++.++++|..|.|+|||++++.++..+..||.|.+..
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 4799999987556899999999999999999999866899999999998854
No 33
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=98.20 E-value=2.8e-06 Score=79.02 Aligned_cols=59 Identities=32% Similarity=0.411 Sum_probs=53.4
Q ss_pred EcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeecc
Q 020570 64 VDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (324)
Q Consensus 64 v~~~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~ 123 (324)
++...+++|||.+++..+ ++||+.++++|.+|.|+|||+.+.++++.|++||+|.+...
T Consensus 185 ~~~~vas~RLD~vla~~~-~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiRG~ 243 (267)
T PLN00051 185 FKSVEASLRLDALASAGF-RMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVSGK 243 (267)
T ss_pred ccCCcCcccHHHHHHHHh-ccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEeeC
Confidence 345567899999999987 89999999999999999999999889999999999999653
No 34
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=98.20 E-value=3.4e-06 Score=70.11 Aligned_cols=53 Identities=30% Similarity=0.288 Sum_probs=47.8
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeec
Q 020570 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 69 ~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
+.+|||+||...--.-||+.++++|..|.|+|||++ .+++..|.+||+|.|..
T Consensus 7 ~~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~ 59 (133)
T PRK10348 7 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQ 59 (133)
T ss_pred ccccHHHHHHHcCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEE
Confidence 458999999987556799999999999999999999 58999999999999855
No 35
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=98.11 E-value=5.1e-06 Score=77.01 Aligned_cols=59 Identities=29% Similarity=0.446 Sum_probs=52.3
Q ss_pred EcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeecc
Q 020570 64 VDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (324)
Q Consensus 64 v~~~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~ 123 (324)
+....+++|||.+++..+ .+||+.++++|++|+|+|||++++++++.|++||.|.+...
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 344567899999999886 68999999999999999999999889999999999999653
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=98.06 E-value=7.3e-06 Score=73.18 Aligned_cols=53 Identities=23% Similarity=0.254 Sum_probs=47.9
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeecc
Q 020570 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (324)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~ 123 (324)
+|||++|.+..-..||+.++++|..|.|.|||++++.+++.|.+||+|.+...
T Consensus 90 ~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD~I~V~~~ 142 (200)
T TIGR01017 90 SRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEK 142 (200)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCCEEEEeeC
Confidence 89999998764456999999999999999999999889999999999999754
No 37
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=98.05 E-value=7.3e-06 Score=73.09 Aligned_cols=53 Identities=19% Similarity=0.226 Sum_probs=48.1
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeecc
Q 020570 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (324)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~ 123 (324)
+|||+||.+.....||+.++++|..|+|+|||++++.+++.|.+||+|.+...
T Consensus 89 ~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~~~ 141 (201)
T CHL00113 89 MRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDK 141 (201)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEccc
Confidence 79999999875457999999999999999999999889999999999998653
No 38
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=97.92 E-value=1.4e-05 Score=72.78 Aligned_cols=52 Identities=29% Similarity=0.238 Sum_probs=47.1
Q ss_pred hHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeecc
Q 020570 72 RLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (324)
Q Consensus 72 RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~ 123 (324)
|||+||.+.....||+.++++|.+|+|+|||+++++++..|.+||.|.+...
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 7999999985456899999999999999999999999999999999998653
No 39
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=97.88 E-value=2.2e-05 Score=70.29 Aligned_cols=52 Identities=25% Similarity=0.286 Sum_probs=46.9
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeec
Q 020570 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
+|||.+|.+.....||+.++++|..|.|.|||+.++.+++.|.+||.|.+..
T Consensus 93 ~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~I~v~~ 144 (203)
T PRK05327 93 SRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVRE 144 (203)
T ss_pred HHHHHHHHHcCccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCEEEECC
Confidence 7999999776446799999999999999999999988999999999999864
No 40
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like. This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl r
Probab=97.74 E-value=8.8e-05 Score=65.27 Aligned_cols=70 Identities=21% Similarity=0.256 Sum_probs=52.5
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-++ .+++.+...+ ...+.+..|-||...|
T Consensus 2 ~g~l~i~Kp~g~tS~--------~~v~~~k~~~-------------------------------~~kkvGH~GTLDp~A~ 42 (182)
T cd02572 2 YGVINLDKPSGPSSH--------EVVAWIKRIL-------------------------------GVEKTGHSGTLDPKVT 42 (182)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHh-------------------------------CCCccCcCCCCCCcCe
Confidence 479999999999775 3566665543 2246888999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-++. -++.+.+.. -.|+|.|.+.
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 9999999973 334444443 4699999885
No 41
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=97.70 E-value=4.4e-05 Score=69.33 Aligned_cols=54 Identities=41% Similarity=0.532 Sum_probs=50.2
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeecc
Q 020570 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (324)
Q Consensus 69 ~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~ 123 (324)
..+|||.++++.| .+||+.++.+|.+|.|.||.+.++++++.|+.||.|.+...
T Consensus 179 sSlRLD~vis~~~-~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG~ 232 (257)
T COG2302 179 SSLRLDVVISEGF-GLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRGF 232 (257)
T ss_pred ehhhHHHHHHHHH-hhhHHHHHHHHHcCceEEeeEEeccccceeccCCEEEEecc
Confidence 3489999999987 69999999999999999999999999999999999999664
No 42
>PRK11507 ribosome-associated protein; Provisional
Probab=97.67 E-value=0.00013 Score=53.74 Aligned_cols=57 Identities=19% Similarity=0.195 Sum_probs=49.2
Q ss_pred CCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeec
Q 020570 66 TKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 66 ~~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
.+.+-++|++||+-.--.-|=.+++.+|..|.|+|||++.+.-+.+|.+||+|.+..
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 345668999999976334688899999999999999999988899999999999954
No 43
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=97.54 E-value=0.00015 Score=64.75 Aligned_cols=54 Identities=22% Similarity=0.216 Sum_probs=45.4
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccc
Q 020570 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (324)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~ 124 (324)
.|||.++-+..=..|+.+++++|..|+|.|||++|+.|++.|.+||+|.|....
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 456666555433579999999999999999999999999999999999997643
No 44
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=97.52 E-value=0.00016 Score=65.73 Aligned_cols=53 Identities=34% Similarity=0.319 Sum_probs=49.4
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeec
Q 020570 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 70 ~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
.+|||.+|.++...-||+.++.+|.+|.|+|||.++++|+..|..++.|.+..
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 58999999998556899999999999999999999999999999999999975
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=97.47 E-value=0.00038 Score=62.58 Aligned_cols=68 Identities=22% Similarity=0.294 Sum_probs=52.2
Q ss_pred EEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCceE
Q 020570 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (324)
Q Consensus 146 ~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (324)
++++|||.|+-++ .+++.+...+ ...+.+..|.||-..|||
T Consensus 2 il~i~KP~g~tS~--------~vv~~ik~~~-------------------------------~~kKvGH~GTLDP~AsGv 42 (210)
T cd00506 2 LFAVDKPQGPSSH--------DVVDTIRRIF-------------------------------LAEKVGHGGTLDPFATGV 42 (210)
T ss_pred EEEEEcCCCCCHH--------HHHHHHHHHh-------------------------------CccccCCCCcCCCcCeeE
Confidence 7899999999775 3666666544 224678899999999999
Q ss_pred EEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 226 Ll~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|+++-++. .++...|.. ..|+|.|.+.
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 99999974 334444443 7999999985
No 46
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=97.42 E-value=0.00038 Score=64.82 Aligned_cols=70 Identities=23% Similarity=0.323 Sum_probs=53.7
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||+|+-+| .+++.+...+ ...+.+..+-||-..|
T Consensus 2 ngil~vdKP~g~tS~--------~vv~~ikk~~-------------------------------~~kKvGH~GTLDP~At 42 (273)
T PRK04099 2 NRLFVANKPAGMSSN--------AFLSRLKRKY-------------------------------GVKKAGFSGTLDPFAK 42 (273)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHh-------------------------------CCCccccCccCCCCCe
Confidence 468999999999875 3677776554 2246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+.+ +|.+.+.. -.|+|.|.+.
T Consensus 43 GvLiv~iG~aT--Kl~~~l~~--~~K~Y~a~~~ 71 (273)
T PRK04099 43 GVLIVAFGQYT--KLFRFLKK--TPKTYRATLW 71 (273)
T ss_pred eEEEEEEChHh--hhHHHhcc--CCceEEEEEE
Confidence 99999999753 34454443 4999999885
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=97.41 E-value=0.00048 Score=61.80 Aligned_cols=70 Identities=19% Similarity=0.291 Sum_probs=54.0
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-++ .+++.+...+. ..+.+..|.||-..|
T Consensus 2 ~G~l~v~KP~g~tS~--------~vv~~vkk~~~-------------------------------~kKvGH~GTLDP~As 42 (209)
T TIGR00431 2 NGVLLLDKPQGMTSF--------DALAKVRRLLN-------------------------------VKKVGHTGTLDPFAT 42 (209)
T ss_pred CeEEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------CCcCCCCCCCCCcCc
Confidence 368999999999765 36666665542 246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-+... ++...+. .-.|+|.|.+.
T Consensus 43 GvLiv~vG~~T--kl~~~~~--~~~K~Y~~~~~ 71 (209)
T TIGR00431 43 GVLPILVGKAT--KLSPYLT--DLDKEYRAEIR 71 (209)
T ss_pred eEEEEEEChHh--hhhHHHc--CCCCeEEEEEE
Confidence 99999999754 4555553 47999999885
No 48
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.36 E-value=0.00043 Score=62.87 Aligned_cols=71 Identities=18% Similarity=0.344 Sum_probs=53.9
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-+| .+++.+...+ ...+.+..|.||...|
T Consensus 9 ~G~l~i~KP~g~TS~--------dvv~~ikk~~-------------------------------~~kKvGH~GTLDP~At 49 (230)
T PRK00989 9 EGILLVDKPQGRTSF--------SLIRSLTKLI-------------------------------GVKKIGHAGTLDPFAT 49 (230)
T ss_pred CEEEEEeCCCCCCHH--------HHHHHHHHHh-------------------------------CCCcCCcCccCCCCCe
Confidence 579999999999775 3566666544 2347888999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+. +.+|.+.+.. ..|+|.|.+.
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 3345454433 7899999985
No 49
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=97.32 E-value=0.00074 Score=61.82 Aligned_cols=70 Identities=20% Similarity=0.323 Sum_probs=52.9
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-+| .+++.+...+ ...+.+..+-||...|
T Consensus 10 ~Gil~vdKP~G~TS~--------dvv~~vkr~~-------------------------------~~kKvGH~GTLDP~At 50 (244)
T PRK00020 10 DGVLLLDKPVGLSSN--------HALQRAKRTV-------------------------------DAAKAGHTGTLDPFAT 50 (244)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHh-------------------------------CCCCCCcCCcCCCcCe
Confidence 579999999999875 3666666544 2357888999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+. -++...+.+ ..|+|.|.+.
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 334444433 5699999885
No 50
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=97.30 E-value=5e-05 Score=55.37 Aligned_cols=55 Identities=20% Similarity=0.282 Sum_probs=36.2
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeee
Q 020570 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCT 121 (324)
Q Consensus 67 ~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~ 121 (324)
..+.++|++||...--.-|=.+++.+|..|.|+|||+..+..+.+|++||+|.+.
T Consensus 4 ~~e~I~L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~~ 58 (65)
T PF13275_consen 4 NTEYITLGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEID 58 (65)
T ss_dssp --S---HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEET
T ss_pred CCCcEEHHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEEC
Confidence 3466899999998633457789999999999999999998889999999999984
No 51
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=97.24 E-value=0.0011 Score=62.98 Aligned_cols=70 Identities=24% Similarity=0.332 Sum_probs=53.6
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-+| .+++.+...+ ...+.+..+-||-..|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l-------------------------------~~kKvGH~GTLDP~At 43 (308)
T PRK14124 3 HGFLVAYKPKGPTSH--------DVVDEVRKKL-------------------------------KTRKVGHAGTLDPFAT 43 (308)
T ss_pred ceEEEEECCCCCCHH--------HHHHHHHHHc-------------------------------CCCccCcCcCCCCCCc
Confidence 479999999999875 3666666544 2346788999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+.+ ++.+.+.. -.|+|.|.+.
T Consensus 44 GvL~v~vG~aT--kl~~~l~~--~~K~Y~a~~~ 72 (308)
T PRK14124 44 GVLIVGVNKAT--RLLEYLKN--EKKVYYVKMR 72 (308)
T ss_pred EEEEEEEChHH--hhhHHHhc--CCceEEEEEE
Confidence 99999999753 34455543 3899999985
No 52
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=97.22 E-value=0.0011 Score=62.48 Aligned_cols=70 Identities=21% Similarity=0.250 Sum_probs=53.6
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-+| .+++.+...+ ...+.+..+-||-..|
T Consensus 2 ~Gil~i~KP~G~tS~--------dvv~~vrr~~-------------------------------~~kKvGH~GTLDP~At 42 (290)
T PRK00130 2 DGILNILKPPGMTSF--------DVVRKIRKIA-------------------------------KIKKVGHTGTLDPLAS 42 (290)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHh-------------------------------CCCccCcCCCCCCCCe
Confidence 479999999999875 3666666544 2246888999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+.+ ++.+.+.. -.|+|.|.+.
T Consensus 43 GvL~v~vG~aT--kl~~~l~~--~~K~Y~a~~~ 71 (290)
T PRK00130 43 GVLPVCLGKAT--KIVDYLME--GKKTYRAEIK 71 (290)
T ss_pred eEEEEEEChhh--hhHHHhcc--CCcEEEEEEE
Confidence 99999999743 35555543 4899999985
No 53
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=97.21 E-value=0.00092 Score=63.05 Aligned_cols=70 Identities=21% Similarity=0.247 Sum_probs=53.3
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-+| .+++.+...+ ...+.+..|.||-..|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l-------------------------------~~kKvGH~GTLDP~At 43 (294)
T PRK02484 3 NGIINLKKEAGMTSH--------DAVFKLRKIL-------------------------------QTKKIGHGGTLDPDVV 43 (294)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHh-------------------------------CCCccccCCCCCCCCe
Confidence 479999999999875 3666666544 2357888999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+.+ ++.+.+.. -.|+|.|.+.
T Consensus 44 GvL~i~vG~aT--kl~~~l~~--~~K~Y~a~~~ 72 (294)
T PRK02484 44 GVLPIAVGKAT--RLIEYMTE--AGKVYEGEIT 72 (294)
T ss_pred eEEEEEEChhh--hhhHHhcc--CCcEEEEEEE
Confidence 99999998743 24444443 4699999985
No 54
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=97.20 E-value=0.0011 Score=62.48 Aligned_cols=71 Identities=24% Similarity=0.384 Sum_probs=53.8
Q ss_pred CCcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCC
Q 020570 143 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 222 (324)
Q Consensus 143 d~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T 222 (324)
-+.++++|||.|+-+| .+++.+...+ ...+.+..+-||-..
T Consensus 8 ~~Gil~i~KP~G~TS~--------dvv~~vrr~~-------------------------------~~kKvGH~GTLDP~A 48 (298)
T PRK03287 8 GSGLVVVDKPAGMTSH--------DVVARCRRLF-------------------------------GTRKVGHAGTLDPMA 48 (298)
T ss_pred cCeEEEEeCCCCCCHH--------HHHHHHHHHh-------------------------------CCCCCCcCccCCCcc
Confidence 3689999999999875 3666666544 224678899999999
Q ss_pred ceEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 223 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 223 SGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
||||+++-.+. -++.+.+.+ -.|+|.|.+.
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 99999999863 334444443 4899999885
No 55
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=97.19 E-value=0.00093 Score=63.33 Aligned_cols=70 Identities=20% Similarity=0.255 Sum_probs=54.0
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-+| .+++.+...+ ...+.+..|.||-..|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~-------------------------------~~kKvGH~GTLDP~At 43 (305)
T PRK14123 3 NGILPVYKERGLTSH--------DVVFKLRKIL-------------------------------KTKKIGHTGTLDPEVA 43 (305)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHh-------------------------------CCCccccCcCCCCcCe
Confidence 479999999999875 3666666544 2346888999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+.+ ++.+.+.. ..|+|.|.+.
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 99999999754 34554443 6899999885
No 56
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=97.19 E-value=0.0009 Score=63.12 Aligned_cols=69 Identities=23% Similarity=0.266 Sum_probs=53.9
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-+| .+++.+...+ ...+.+..+-||-..|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~-------------------------------~~kKvGH~GTLDP~At 43 (295)
T PRK02755 3 FGFLNLDKPAGLTSH--------DCVARLRRLL-------------------------------RLKRVGHGGTLDPAAT 43 (295)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHh-------------------------------CCCccccCCCCCCcCe
Confidence 479999999999875 3666666544 2246888999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+.+ ++.+.+. . .|+|.|.+.
T Consensus 44 GvL~i~vG~aT--kl~~~l~--~-~K~Y~a~~~ 71 (295)
T PRK02755 44 GVLPIALGKAT--RLLPYLP--G-EKTYRGTIR 71 (295)
T ss_pred eEEEEEEChhh--hhHHHhC--C-CcEEEEEEE
Confidence 99999999854 4556554 2 799999885
No 57
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=97.12 E-value=0.0014 Score=62.05 Aligned_cols=70 Identities=21% Similarity=0.200 Sum_probs=53.5
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-+| .+++.+...+ ...+.+..+-||...|
T Consensus 13 ~Gil~i~KP~G~TS~--------dvv~~vrk~~-------------------------------~~kKvGH~GTLDP~At 53 (305)
T PRK05389 13 SGWLILDKPAGMTST--------EAVSKVKWLF-------------------------------DAQKAGHAGTLDPLAS 53 (305)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHh-------------------------------cccccCCcccCCCCCc
Confidence 589999999999875 3666666544 2246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+. -++.+.+.. -.|+|.|.+.
T Consensus 54 GvL~v~vG~a--Tkl~~~l~~--~~K~Y~a~~~ 82 (305)
T PRK05389 54 GVLPIALGEA--TKTVPYVMD--GTKRYRFTVA 82 (305)
T ss_pred eEEEEEEChh--hhhhHHhcc--CCcEEEEEEE
Confidence 9999999873 334444433 4899999885
No 58
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=97.11 E-value=0.0016 Score=61.89 Aligned_cols=70 Identities=19% Similarity=0.288 Sum_probs=54.2
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-+| .+++.+...+ ...+.+..+-||-..|
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~l-------------------------------~~kKvGH~GTLDP~At 50 (312)
T PRK05033 10 NGVLLLDKPQGMSSN--------DALQKVKRLF-------------------------------NANKAGHTGALDPLAT 50 (312)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHh-------------------------------CCCCCCCCCcCCCcCe
Confidence 589999999999875 3566666543 2246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+.+. |.+.+.. -.|+|.|.+.
T Consensus 51 GvL~v~vG~aTk--l~~~~~~--~~K~Y~a~~~ 79 (312)
T PRK05033 51 GMLPICLGEATK--FSQYLLD--SDKRYRVTAR 79 (312)
T ss_pred eEEEEEECHHhh--hhHHhcC--CCcEEEEEEE
Confidence 999999997533 5555543 4999999885
No 59
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=97.11 E-value=0.0014 Score=61.25 Aligned_cols=68 Identities=24% Similarity=0.364 Sum_probs=51.3
Q ss_pred EEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCceE
Q 020570 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (324)
Q Consensus 146 ~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (324)
++++|||.|+-+| .+++.+...+ ...+.+..|.||-..|||
T Consensus 2 il~i~KP~G~tS~--------dvv~~vrr~~-------------------------------~~kKvGH~GTLDP~AtGv 42 (279)
T PRK02193 2 IKLLYKPKGISSF--------KFIKNFAKTN-------------------------------NIKKIGHTGTLDPLASGL 42 (279)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHc-------------------------------CCCccccCccCCCcCeeE
Confidence 6899999999875 3566665543 224688899999999999
Q ss_pred EEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 226 Ll~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|+++-.+. -++.+.+. ...|+|.|.+.
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 99999874 23444442 36899999885
No 60
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=97.10 E-value=0.0017 Score=62.09 Aligned_cols=70 Identities=21% Similarity=0.218 Sum_probs=52.7
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-+| .+++.+...+ ...+.+..|.||...|
T Consensus 3 nGiL~idKP~G~TS~--------dvv~~vrk~l-------------------------------~~kKVGH~GTLDP~At 43 (345)
T PRK14846 3 NYWLNIYKPRGISSA--------QLVSIVKKIL-------------------------------GKTKIGHAGTLDVEAE 43 (345)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHh-------------------------------CCCcCCcCccCCCcCc
Confidence 579999999999875 3666666544 2357888999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+. -++.+.+.+ ..|+|.|.+.
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 9999999874 233333332 6899999885
No 61
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=97.07 E-value=0.0015 Score=61.84 Aligned_cols=70 Identities=21% Similarity=0.295 Sum_probs=53.5
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-+| .+++.+...+ ...+.+..+-||-..|
T Consensus 2 ~Gil~i~KP~G~TS~--------dvv~~vrr~~-------------------------------~~kKvGH~GTLDP~At 42 (304)
T PRK01550 2 NGVLLLHKPRGMTSH--------DCVFKLRKIL-------------------------------RTKKVGHTGTLDPEVS 42 (304)
T ss_pred CeEEEEECCCCCCHH--------HHHHHHHHHc-------------------------------CCCCcccCCCCCCcCe
Confidence 469999999999875 3666666544 2246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+.+. |.+.+.. -.|+|.|.+.
T Consensus 43 GvL~i~vG~aTk--l~~~l~~--~~K~Y~a~~~ 71 (304)
T PRK01550 43 GVLPICVGRATK--IAEYLTD--EGKTYEGEVT 71 (304)
T ss_pred eEEEEEEChhhh--hhHHhcC--CCcEEEEEEE
Confidence 999999987532 5555543 4899999885
No 62
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=97.07 E-value=0.0015 Score=61.97 Aligned_cols=71 Identities=17% Similarity=0.209 Sum_probs=53.5
Q ss_pred CCcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCC
Q 020570 143 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 222 (324)
Q Consensus 143 d~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T 222 (324)
.+.++++|||.|+-+| .+++.+...+ ...+.+..+-||...
T Consensus 21 ~~g~l~i~Kp~g~tS~--------~~v~~~r~~~-------------------------------~~kkvGH~GTLDp~A 61 (300)
T PRK04270 21 KFGVVNLDKPPGPTSH--------EVAAWVRDIL-------------------------------GVEKAGHGGTLDPKV 61 (300)
T ss_pred CCCEEEEECCCCCCHH--------HHHHHHHHHh-------------------------------ccccccCCCCCCCcC
Confidence 3689999999999875 3566666543 224678899999999
Q ss_pred ceEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 223 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 223 SGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
||||+++-.+. -++.+.+.+ -.|+|.|.+.
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 99999999874 334444443 4699999874
No 63
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=97.05 E-value=0.0017 Score=61.10 Aligned_cols=70 Identities=21% Similarity=0.249 Sum_probs=52.5
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.+|++|||.|+-+| .+++.+...+ ...+.+..+-||-..|
T Consensus 3 ~GiL~i~KP~G~TS~--------dvv~~vrk~~-------------------------------~~kKvGH~GTLDP~At 43 (292)
T PRK01528 3 NYWLNIYKPRGISSA--------KLVSIVKKIL-------------------------------GKVKIGHAGTLDVEAE 43 (292)
T ss_pred CEEEEEeCCCCCCHH--------HHHHHHHHHc-------------------------------CCCccCcCccCCCcCc
Confidence 579999999999875 3666666544 2247788999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+. . ++.+.+.+ -.|+|.|.+.
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 9999999874 2 33333332 5799999885
No 64
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=97.04 E-value=0.0014 Score=57.33 Aligned_cols=52 Identities=17% Similarity=0.108 Sum_probs=44.4
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeec
Q 020570 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
.|||.+|.+..-.-|+.+++++|..|.|+|||++|+++++.|.+++.-.|.+
T Consensus 103 rRLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~ 154 (177)
T PRK04051 103 RRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDY 154 (177)
T ss_pred hHHHHHHHHccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEE
Confidence 6899988887556799999999999999999999999999999995444433
No 65
>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=97.04 E-value=0.002 Score=60.37 Aligned_cols=68 Identities=24% Similarity=0.371 Sum_probs=52.5
Q ss_pred EEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCceE
Q 020570 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (324)
Q Consensus 146 ~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGL 225 (324)
++++|||.|+-+| .+++.+...+ ...+.+..+-||-..|||
T Consensus 2 il~i~KP~G~tS~--------~vv~~vr~~~-------------------------------~~kKvGH~GTLDP~AtGv 42 (277)
T cd02573 2 ILLLDKPAGLTSH--------DVVQKVRRLL-------------------------------GTKKVGHTGTLDPLATGV 42 (277)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHh-------------------------------CcCccCCCCCCCCcCeEE
Confidence 7899999999875 3666666544 224678899999999999
Q ss_pred EEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 226 LVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 226 Ll~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|+++-.+.+ +|.+.+.. ..|+|.|.+.
T Consensus 43 L~v~vG~aT--kl~~~l~~--~~K~Y~~~~~ 69 (277)
T cd02573 43 LPIALGEAT--KLSQYLLD--ADKTYRATVR 69 (277)
T ss_pred EEEEEChHH--hhHHHhcC--CCcEEEEEEE
Confidence 999999753 35555543 5999999985
No 66
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=96.99 E-value=0.0025 Score=60.25 Aligned_cols=70 Identities=20% Similarity=0.292 Sum_probs=53.6
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-+| .+++.+...+. ..+.+..+-||-..|
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 589999999999875 36666665542 246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+.+ ++.+.+.. -.|+|.|.+.
T Consensus 57 GvL~v~vG~aT--kl~~~l~~--~~K~Y~~~~~ 85 (303)
T PRK01851 57 GLLPLCFGEAT--KFSQDLLD--ADKTYEATLR 85 (303)
T ss_pred eEEEEEECHHH--hhhHHhcc--cCeEEEEEEE
Confidence 99999999753 24444443 4699999985
No 67
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=96.99 E-value=0.0022 Score=60.84 Aligned_cols=69 Identities=26% Similarity=0.401 Sum_probs=53.0
Q ss_pred cEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCce
Q 020570 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (324)
Q Consensus 145 ~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (324)
.++++|||.|+-+| .+++.+...+ ...+.+..+-||-..||
T Consensus 2 ~il~idKP~G~TS~--------dvv~~vrr~l-------------------------------~~kKvGH~GTLDP~AtG 42 (312)
T PRK14122 2 PVYAVDKPLGLTSH--------DVVNRARRAL-------------------------------GTRRVGHTGTLDPLATG 42 (312)
T ss_pred cEEEEECCCCCCHH--------HHHHHHHHHh-------------------------------CCCCCCCCCCCCCcCee
Confidence 37999999999875 3666666544 23477889999999999
Q ss_pred EEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 225 LLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
||+++-.+.+. |.+.+. ...|+|.|.+.
T Consensus 43 vL~i~iG~aTK--l~~~l~--~~~K~Y~a~~~ 70 (312)
T PRK14122 43 VLVLCTDDSTK--LVPFLS--AEDKEYLAWVS 70 (312)
T ss_pred eEEEEEChhhh--hhHHhc--CCCceEEEEEE
Confidence 99999997543 555553 36899999984
No 68
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=96.96 E-value=0.0033 Score=46.75 Aligned_cols=56 Identities=21% Similarity=0.246 Sum_probs=47.6
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeec
Q 020570 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 67 ~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
..+-..|.+||...--.-|=.+++.+|..|.|+|||++-++-+.+|+.||+|.+..
T Consensus 8 ~~e~I~L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~ 63 (73)
T COG2501 8 KTEFITLGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPG 63 (73)
T ss_pred ccceEEHHHHHHHhCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECC
Confidence 44557899999986334578899999999999999999988899999999999843
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=96.77 E-value=0.0032 Score=60.25 Aligned_cols=71 Identities=20% Similarity=0.271 Sum_probs=53.8
Q ss_pred CCcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCC
Q 020570 143 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 222 (324)
Q Consensus 143 d~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T 222 (324)
.+.++++|||.|+-+| .+++.+...+ ...+.+..+-||-..
T Consensus 33 ~~G~l~i~KP~g~tS~--------~~v~~vr~~~-------------------------------~~kkvGH~GTLDP~A 73 (322)
T TIGR00425 33 SYGVVNLDKPSGPSSH--------EVVAWVRRIL-------------------------------NVEKTGHGGTLDPKV 73 (322)
T ss_pred CCCEEEEeCCCCCCHH--------HHHHHHHHHh-------------------------------cccccCCCCCCCCCC
Confidence 3589999999999875 3666666554 224678899999999
Q ss_pred ceEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 223 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 223 SGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
||||+++-.+. -+|.+.+.. -.|+|.|.+.
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 99999999874 334444432 6999999874
No 70
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=96.66 E-value=0.0054 Score=57.93 Aligned_cols=70 Identities=19% Similarity=0.244 Sum_probs=53.6
Q ss_pred CcEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCc
Q 020570 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (324)
Q Consensus 144 ~~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 223 (324)
+.++++|||.|+-+| .+++.+...+. ..+.+..+-||-..|
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 589999999999875 36777765542 246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 224 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 224 GLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
|||+++-.+. -++.+.+.. -.|+|.|.+.
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 9999999874 334444432 6899999984
No 71
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=96.43 E-value=0.0077 Score=56.17 Aligned_cols=69 Identities=16% Similarity=0.238 Sum_probs=51.7
Q ss_pred cEEEEeCCCceEEecCCCCCCCcHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCccccCCCCCCCce
Q 020570 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (324)
Q Consensus 145 ~~lvvnKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 224 (324)
.++++|||.|+-+| .++..+...+ ...+.+..+-||-..||
T Consensus 16 Gil~ldKP~G~tS~--------~~v~~vkkil-------------------------------~~~K~GH~GTLDP~atG 56 (271)
T COG0130 16 GVINLDKPPGPTSH--------EVVAWVKRIL-------------------------------GVEKAGHGGTLDPLATG 56 (271)
T ss_pred ceEEeeCCCCCCHH--------HHHHHHHHHh-------------------------------CccccccccccCCcccc
Confidence 89999999999875 3566665544 23567889999999999
Q ss_pred EEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 225 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 225 LLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
+|+++-. .+-+.+.-+.. -.|+|.|.+.
T Consensus 57 vLpi~ig-~aTKl~~~l~~---~~K~Y~a~~~ 84 (271)
T COG0130 57 VLPICLG-EATKLVQYLLD---ADKEYVATVR 84 (271)
T ss_pred eEEEEec-hhHhHHHHHhh---CCcEEEEEEE
Confidence 9999999 33333333322 6899999985
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=96.34 E-value=0.011 Score=56.25 Aligned_cols=43 Identities=21% Similarity=0.234 Sum_probs=33.9
Q ss_pred CCccccCCCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 210 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 210 ~~~~~vhRLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
.+.+..+-||-..||||+++-... .+.++.. .. ..|+|.|.+.
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 3344433 32 7999999875
No 73
>PLN00189 40S ribosomal protein S9; Provisional
Probab=96.16 E-value=0.0047 Score=54.59 Aligned_cols=54 Identities=19% Similarity=0.238 Sum_probs=44.2
Q ss_pred chHHHHHHhccC--------CCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccc
Q 020570 71 LRLDAWISSRID--------GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (324)
Q Consensus 71 ~RLdk~L~~~~~--------~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~ 124 (324)
..+..||.+++. .-|..+++++|..|.|.|||++|+.|++.|..|+++.|.+..
T Consensus 101 Ltvs~~leRRL~~vv~r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~~ 162 (194)
T PLN00189 101 LTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSL 162 (194)
T ss_pred ccHHHHHHhhhceeeeecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEEec
Confidence 445555555442 358999999999999999999999999999999999887754
No 74
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=95.85 E-value=0.017 Score=49.80 Aligned_cols=50 Identities=16% Similarity=0.155 Sum_probs=39.7
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEee
Q 020570 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNC 120 (324)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v 120 (324)
.||+-++-+.--.-|..+++++|..|.|.|||++|+.|++.|..|++=.|
T Consensus 104 RRL~~vv~r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I 153 (162)
T TIGR01018 104 RRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKI 153 (162)
T ss_pred HhHhhHhhhccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCee
Confidence 45555555542356999999999999999999999999999999944333
No 75
>PRK04313 30S ribosomal protein S4e; Validated
Probab=95.61 E-value=0.032 Score=50.94 Aligned_cols=54 Identities=15% Similarity=0.143 Sum_probs=45.8
Q ss_pred CccchHHHHHHhccCC-CCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeee
Q 020570 68 AGKLRLDAWISSRIDG-ISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCT 121 (324)
Q Consensus 68 ~~~~RLdk~L~~~~~~-~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~ 121 (324)
.+.+.|--+|+..+.. .+.+++++.|.+|.|.|||++.++..+.+---|+|++.
T Consensus 35 ~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~ 89 (237)
T PRK04313 35 EESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIP 89 (237)
T ss_pred ccccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEc
Confidence 3456788899987753 69999999999999999999998777877777999993
No 76
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=95.52 E-value=0.017 Score=50.66 Aligned_cols=53 Identities=17% Similarity=0.058 Sum_probs=41.6
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeecc
Q 020570 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (324)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~ 123 (324)
.||+-++.+.--.-|..+++++|..|.|.|||++|+.|++.|..|++=.|.+.
T Consensus 107 RRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I~~~ 159 (181)
T PTZ00155 107 RRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDFA 159 (181)
T ss_pred HhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceEeccCccCceeee
Confidence 45555555442246899999999999999999999999999999976666553
No 77
>PLN00036 40S ribosomal protein S4; Provisional
Probab=95.26 E-value=0.047 Score=50.46 Aligned_cols=73 Identities=14% Similarity=0.190 Sum_probs=54.4
Q ss_pred CccchHHHHHHhccCC-CCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccccCcccccccCCCceeeccCCcE
Q 020570 68 AGKLRLDAWISSRIDG-ISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNV 146 (324)
Q Consensus 68 ~~~~RLdk~L~~~~~~-~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~~~~~~~~~~~~~~~Ilyed~~~ 146 (324)
.+.+.|--||+..+.. .+.+++++.|.+|.|.|||++.++..+.+---|+|++.. .+...+|+|.....
T Consensus 39 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~k----------t~e~yRvl~D~kGr 108 (261)
T PLN00036 39 RECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPK----------TNENFRLLYDTKGR 108 (261)
T ss_pred ccccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcC----------CCCeEEEEECCCce
Confidence 3456788999987753 588999999999999999999987777777779999943 12234666665555
Q ss_pred EEEe
Q 020570 147 LVVN 150 (324)
Q Consensus 147 lvvn 150 (324)
++++
T Consensus 109 f~l~ 112 (261)
T PLN00036 109 FRLH 112 (261)
T ss_pred EEEE
Confidence 5544
No 78
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=95.17 E-value=0.05 Score=50.53 Aligned_cols=73 Identities=19% Similarity=0.194 Sum_probs=54.4
Q ss_pred CccchHHHHHHhccCC-CCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccccCcccccccCCCceeeccCCcE
Q 020570 68 AGKLRLDAWISSRIDG-ISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNV 146 (324)
Q Consensus 68 ~~~~RLdk~L~~~~~~-~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~~~~~~~~~~~~~~~Ilyed~~~ 146 (324)
.+.+.|--||+..+.. .+.+++++.|.+|.|.|||++.++..+.+---|+|.+.. .+...+|||.....
T Consensus 36 ~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~k----------t~e~yRvl~D~kGr 105 (273)
T PTZ00223 36 RECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPK----------TGDRFRILYDVKGR 105 (273)
T ss_pred ccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcC----------CCCeEEEEECCCCc
Confidence 3457788999987753 588999999999999999999987777777779999943 12234666665555
Q ss_pred EEEe
Q 020570 147 LVVN 150 (324)
Q Consensus 147 lvvn 150 (324)
++++
T Consensus 106 f~l~ 109 (273)
T PTZ00223 106 FALV 109 (273)
T ss_pred EEEE
Confidence 5544
No 79
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=95.08 E-value=0.055 Score=50.02 Aligned_cols=54 Identities=20% Similarity=0.225 Sum_probs=45.4
Q ss_pred CccchHHHHHHhccCC-CCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeee
Q 020570 68 AGKLRLDAWISSRIDG-ISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCT 121 (324)
Q Consensus 68 ~~~~RLdk~L~~~~~~-~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~ 121 (324)
.+.+.|--||+..+.. .+.+++++.|.+|.|.|||++.++..+.+---|+|++.
T Consensus 39 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~ 93 (262)
T PTZ00118 39 RECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLT 93 (262)
T ss_pred ccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEc
Confidence 3456788899987753 68899999999999999999998777777777999994
No 80
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=92.32 E-value=0.24 Score=44.82 Aligned_cols=58 Identities=14% Similarity=0.184 Sum_probs=43.8
Q ss_pred CCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccccCcccccccCCCceeeccCCcEEEEeC
Q 020570 84 ISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNK 151 (324)
Q Consensus 84 ~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~~~~~~~~~~~~~~~Ilyed~~~lvvnK 151 (324)
-.-+++++.|.+|.|+|||++.++..+.+---|+|++.. .....+|||.....+++++
T Consensus 55 d~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~----------tgE~yRvl~d~~grl~l~~ 112 (241)
T COG1471 55 DNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPK----------TGEHYRVLPDEKGRLVLHP 112 (241)
T ss_pred cchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECC----------CCceEEEEecCCccEEEEe
Confidence 467899999999999999999865556555559999842 2334678888877777665
No 81
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=91.90 E-value=0.28 Score=42.73 Aligned_cols=64 Identities=22% Similarity=0.397 Sum_probs=49.2
Q ss_pred eEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeecc
Q 020570 58 VQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (324)
Q Consensus 58 ~~~~~~v~~~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~ 123 (324)
+++...++ -....||+..|++.+ ++||+.++++|..|.|+.+-........+++.|-.|.++..
T Consensus 127 vel~l~~~-~p~qlrl~~Ll~seL-~LSrS~lq~lie~g~Irgdtd~~~l~rkrlr~~~~i~Id~~ 190 (203)
T COG4332 127 VELSLRIS-RPFQLRLDRLLASEL-GLSRSELQRLIETGQIRGDTDKMLLLRKRLRAGYDIQIDVE 190 (203)
T ss_pred EEEEEccc-CcchhHHHHHHHHHh-CcCHHHHHHHHHcCceeecchHHHHhhhhhhcCcEEEEEcC
Confidence 66665554 334489999999997 69999999999999999887653334567888888888653
No 82
>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=90.99 E-value=0.85 Score=34.73 Aligned_cols=28 Identities=21% Similarity=0.181 Sum_probs=25.2
Q ss_pred CCccccCCCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 210 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 210 ~~~~~vhRLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
.+.+.+|++|+.++|+++++ ++|...+.
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 56788999999999999999 88888887
No 83
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=90.09 E-value=0.28 Score=37.37 Aligned_cols=47 Identities=30% Similarity=0.442 Sum_probs=36.7
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeecc
Q 020570 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (324)
Q Consensus 68 ~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~ 123 (324)
+.+.++...+... +++..++ |.|.|||+.+ ..++.+++||+|.++..
T Consensus 30 ~~~~tvkd~IEsL--GVP~tEV------~~i~vNG~~v-~~~~~~~~Gd~v~V~P~ 76 (81)
T PF14451_consen 30 DGGATVKDVIESL--GVPHTEV------GLILVNGRPV-DFDYRLKDGDRVAVYPV 76 (81)
T ss_pred CCCCcHHHHHHHc--CCChHHe------EEEEECCEEC-CCcccCCCCCEEEEEec
Confidence 3446677776553 4777765 7899999999 68999999999999753
No 84
>PRK01777 hypothetical protein; Validated
Probab=89.37 E-value=0.35 Score=37.97 Aligned_cols=54 Identities=17% Similarity=0.225 Sum_probs=39.7
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeecc
Q 020570 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (324)
Q Consensus 67 ~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~ 123 (324)
-.+|.++...|... ++....-+=-+..+.|-|||+.+ ..++.|+.||+|.++.+
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 34567888888875 45444212134568999999999 68999999999999763
No 85
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=87.50 E-value=0.97 Score=44.82 Aligned_cols=47 Identities=21% Similarity=0.228 Sum_probs=39.0
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCC
Q 020570 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGD 116 (324)
Q Consensus 70 ~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD 116 (324)
+..|-++|...--.-|+++++++|.+|.|+|||+++..++..+.+++
T Consensus 342 ~~~~~~~l~~~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~ 388 (410)
T PRK13354 342 TKNLVDLLVDLGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPED 388 (410)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhh
Confidence 57788888876446799999999999999999999977777666655
No 86
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=87.30 E-value=0.65 Score=42.47 Aligned_cols=23 Identities=30% Similarity=0.359 Sum_probs=19.9
Q ss_pred CCccccCCCCCCCceEEEeecCH
Q 020570 210 IRPGIVHRLDKGTSGLLVVAKDE 232 (324)
Q Consensus 210 ~~~~~vhRLD~~TSGLLl~ak~~ 232 (324)
...+++||||..|||++||.-..
T Consensus 89 ~~V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559|consen 89 EDVQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred cceeeEEeecccccceEEEecCc
Confidence 34688999999999999998874
No 87
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=86.95 E-value=1.7 Score=36.76 Aligned_cols=43 Identities=28% Similarity=0.488 Sum_probs=34.2
Q ss_pred eEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECC
Q 020570 58 VQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSING 102 (324)
Q Consensus 58 ~~~~~~v~~~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg 102 (324)
++++..+ +..-..||+.+|++.+ ++||+++++++..|.|..+.
T Consensus 91 ~~v~i~~-~~~~~~Rld~lLa~~L-~lSrs~l~~l~~~G~I~~~~ 133 (142)
T PF06353_consen 91 IEVEIRF-PFPFPLRLDRLLARQL-GLSRSRLKRLIEQGLIRSDP 133 (142)
T ss_pred eEEEEEe-CCCCCccHHHHHHHHh-CcCHHHHHHHHHCCCEEecC
Confidence 4444333 3455699999999997 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=86.20 E-value=0.77 Score=39.09 Aligned_cols=43 Identities=23% Similarity=0.289 Sum_probs=31.7
Q ss_pred CCccccCCCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEe
Q 020570 210 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 256 (324)
Q Consensus 210 ~~~~~vhRLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~ 256 (324)
.+.+..+.||-..||||+++-++... |.+.+.. ..|+|.|...
T Consensus 7 ~KvGH~GTLDP~AsGvL~v~vg~~Tk--l~~~l~~--~~K~Y~~~~~ 49 (149)
T PF01509_consen 7 KKVGHGGTLDPFASGVLVVGVGKATK--LLSYLQN--SDKEYVATIR 49 (149)
T ss_dssp SSEEESS-SSTT-EEEEEEEEGGGGG--GHHHHTT--SEEEEEEEEE
T ss_pred ceeccccccCCcceEEEEEEECCcch--HHHHhhc--cCCEEEEEEE
Confidence 57889999999999999999986332 4445543 5699999874
No 89
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=85.67 E-value=1.8 Score=42.91 Aligned_cols=45 Identities=24% Similarity=0.194 Sum_probs=36.6
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeec
Q 020570 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKG 114 (324)
Q Consensus 70 ~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~ 114 (324)
+..|-++|...--.-|+++++++|.+|.|+|||+++...+..+..
T Consensus 342 ~~~~~~~l~~~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~ 386 (408)
T PRK05912 342 GIDLLALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTA 386 (408)
T ss_pred CCcHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEecCccccccc
Confidence 467888888753457999999999999999999999766665554
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=80.00 E-value=4.1 Score=30.01 Aligned_cols=51 Identities=14% Similarity=0.187 Sum_probs=32.9
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeec
Q 020570 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 70 ~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
+.++..++.......+.- .......-.|.|||+.+. .+..|+.||+|.+..
T Consensus 25 ~~tv~~ll~~l~~~~~~~-~~~~~~~~~v~vNg~~v~-~~~~l~~gD~v~i~p 75 (80)
T cd00754 25 GATVGELLDALEARYPGL-LEELLARVRIAVNGEYVR-LDTPLKDGDEVAIIP 75 (80)
T ss_pred CCcHHHHHHHHHHHCchH-HHhhhhcEEEEECCeEcC-CCcccCCCCEEEEeC
Confidence 566776665432112211 223334447889999995 789999999999853
No 91
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=75.26 E-value=4.3 Score=29.68 Aligned_cols=43 Identities=21% Similarity=0.376 Sum_probs=32.8
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeee
Q 020570 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCT 121 (324)
Q Consensus 69 ~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~ 121 (324)
++.++..+|.+. . ++. +.-.|.+||+.+ ..+..|+.||+|.+.
T Consensus 22 ~~~tv~~ll~~l-~-~~~-------~~v~v~vNg~iv-~~~~~l~~gD~Veii 64 (70)
T PRK08364 22 KGMKVADILRAV-G-FNT-------ESAIAKVNGKVA-LEDDPVKDGDYVEVI 64 (70)
T ss_pred CCCcHHHHHHHc-C-CCC-------ccEEEEECCEEC-CCCcCcCCCCEEEEE
Confidence 357899999775 3 433 335778999999 478999999999884
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=68.94 E-value=5.2 Score=29.18 Aligned_cols=52 Identities=15% Similarity=0.187 Sum_probs=32.5
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc--ceeeeecCCEEeeec
Q 020570 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK--VSHNVKGGDMVNCTI 122 (324)
Q Consensus 68 ~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~--~~~~l~~GD~V~v~~ 122 (324)
.++.++..+|.......+.-. ....=.|.|||+.+.. .+..|+.||+|.+..
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 344567776665421122111 3344477899999943 289999999998843
No 93
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=68.63 E-value=11 Score=28.20 Aligned_cols=50 Identities=10% Similarity=0.126 Sum_probs=32.2
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeec
Q 020570 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 70 ~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
+.++..++....... ..+.+....=.|.|||+.+ ..+..|+.||+|.+..
T Consensus 28 ~~tv~~L~~~l~~~~--p~l~~~~~~~~vavN~~~v-~~~~~l~dgDeVai~P 77 (82)
T PLN02799 28 GSTTADCLAELVAKF--PSLEEVRSCCVLALNEEYT-TESAALKDGDELAIIP 77 (82)
T ss_pred CCcHHHHHHHHHHHC--hhHHHHhhCcEEEECCEEc-CCCcCcCCCCEEEEeC
Confidence 556666665432111 1233433333688999998 5789999999999843
No 94
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=67.86 E-value=13 Score=27.70 Aligned_cols=25 Identities=24% Similarity=0.307 Sum_probs=21.4
Q ss_pred ceEECCEEeccceeeeecCCEEeeec
Q 020570 97 LVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 97 ~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
.|.||++.+. .+..|+.||+|.+..
T Consensus 51 ~v~vn~~~v~-~~~~l~dgDevai~P 75 (80)
T TIGR01682 51 MVAVNEEYVT-DDALLNEGDEVAFIP 75 (80)
T ss_pred EEEECCEEcC-CCcCcCCCCEEEEeC
Confidence 5889999984 689999999999853
No 95
>PRK06437 hypothetical protein; Provisional
Probab=66.68 E-value=6.1 Score=28.71 Aligned_cols=44 Identities=27% Similarity=0.308 Sum_probs=32.5
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeee
Q 020570 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCT 121 (324)
Q Consensus 68 ~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~ 121 (324)
+++.++.++|.+. + ++... + .|.+||+.+ ..++.|+.||+|.+.
T Consensus 18 ~~~~tv~dLL~~L-g-i~~~~----v---aV~vNg~iv-~~~~~L~dgD~Veiv 61 (67)
T PRK06437 18 DHELTVNDIIKDL-G-LDEEE----Y---VVIVNGSPV-LEDHNVKKEDDVLIL 61 (67)
T ss_pred CCCCcHHHHHHHc-C-CCCcc----E---EEEECCEEC-CCceEcCCCCEEEEE
Confidence 3457899999875 3 44322 1 566999999 589999999999984
No 96
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=60.82 E-value=8.1 Score=27.62 Aligned_cols=42 Identities=19% Similarity=0.377 Sum_probs=29.5
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccce----eeeecCCEEeee
Q 020570 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVS----HNVKGGDMVNCT 121 (324)
Q Consensus 70 ~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~----~~l~~GD~V~v~ 121 (324)
+.++..+|... . ++. +.+ .|.|||+.+. .+ ..|+.||+|.+.
T Consensus 14 ~~tv~~ll~~l-~-~~~----~~i---~V~vNg~~v~-~~~~~~~~L~~gD~V~ii 59 (65)
T cd00565 14 GATLAELLEEL-G-LDP----RGV---AVALNGEIVP-RSEWASTPLQDGDRIEIV 59 (65)
T ss_pred CCCHHHHHHHc-C-CCC----CcE---EEEECCEEcC-HHHcCceecCCCCEEEEE
Confidence 56788888775 3 332 111 4668999984 44 889999999884
No 97
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=60.72 E-value=8.6 Score=27.43 Aligned_cols=44 Identities=25% Similarity=0.459 Sum_probs=30.3
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEec---cceeeeecCCEEeee
Q 020570 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVS---KVSHNVKGGDMVNCT 121 (324)
Q Consensus 69 ~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~---~~~~~l~~GD~V~v~ 121 (324)
++.+|..+|... + +....+ .|.+||+.+. -.+..|+.||+|.+.
T Consensus 14 ~~~tl~~lL~~l-~-~~~~~v-------av~vNg~iv~r~~~~~~~l~~gD~vei~ 60 (66)
T PRK05659 14 DGESVAALLARE-G-LAGRRV-------AVEVNGEIVPRSQHASTALREGDVVEIV 60 (66)
T ss_pred CCCCHHHHHHhc-C-CCCCeE-------EEEECCeEeCHHHcCcccCCCCCEEEEE
Confidence 457788888764 3 322222 3779997763 267889999999984
No 98
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=57.16 E-value=12 Score=37.09 Aligned_cols=40 Identities=25% Similarity=0.212 Sum_probs=29.9
Q ss_pred HHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeee
Q 020570 73 LDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNV 112 (324)
Q Consensus 73 Ldk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l 112 (324)
+-..|....-.-||+++++.|..|.|++||.++.+.+..+
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 3333333333679999999999999999999987665444
No 99
>KOG3301 consensus Ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=55.68 E-value=14 Score=31.80 Aligned_cols=45 Identities=20% Similarity=0.247 Sum_probs=35.1
Q ss_pred cchHHHHHHhcc--------CCCCHHHHHHHHHcCceEECCEEeccceeeeec
Q 020570 70 KLRLDAWISSRI--------DGISRARVQSSIRSGLVSINGQVVSKVSHNVKG 114 (324)
Q Consensus 70 ~~RLdk~L~~~~--------~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~ 114 (324)
++.+..||-.++ -..|-..++-+|..+.|+|+++.|+-|++.|+.
T Consensus 88 ~l~ie~fLErRLqt~vFklGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrl 140 (183)
T KOG3301|consen 88 ALTVEDFLERRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRL 140 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHhcCccEEecCeEeeccceeEee
Confidence 355566665544 246888999999999999999999888888874
No 100
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=55.05 E-value=7.6 Score=29.13 Aligned_cols=30 Identities=27% Similarity=0.471 Sum_probs=22.9
Q ss_pred HHHcC--ceEECCEEeccceeeeecCCEEeeec
Q 020570 92 SIRSG--LVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 92 lI~~G--~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
++..| ++.||++-+ ..+..|+.||+|.+..
T Consensus 45 ~~~~~~~~~aVN~~~~-~~~~~l~dgDeVai~P 76 (81)
T PRK11130 45 ALEDGKLLAAVNQTLV-SFDHPLTDGDEVAFFP 76 (81)
T ss_pred hhcCCCEEEEECCEEc-CCCCCCCCCCEEEEeC
Confidence 33455 467999887 5788999999999854
No 101
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=53.26 E-value=13 Score=26.30 Aligned_cols=23 Identities=35% Similarity=0.689 Sum_probs=19.1
Q ss_pred ceEECCEEeccceeeeecCCEEee
Q 020570 97 LVSINGQVVSKVSHNVKGGDMVNC 120 (324)
Q Consensus 97 ~V~VNg~~v~~~~~~l~~GD~V~v 120 (324)
...|||+.+ ..++.|+.||+|++
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 446999998 68999999999987
No 102
>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=52.22 E-value=18 Score=25.55 Aligned_cols=27 Identities=22% Similarity=0.340 Sum_probs=19.1
Q ss_pred HcCceEECCEEecc-ceeeeecCCEEee
Q 020570 94 RSGLVSINGQVVSK-VSHNVKGGDMVNC 120 (324)
Q Consensus 94 ~~G~V~VNg~~v~~-~~~~l~~GD~V~v 120 (324)
....++|||+++.. ....|..||+|.+
T Consensus 40 s~ngt~vng~~l~~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 40 STNGTFVNGQRLGPGEPVPLKDGDIIRF 67 (68)
T ss_dssp SSS-EEETTEEESSTSEEEE-TTEEEEE
T ss_pred CCCcEEECCEEcCCCCEEECCCCCEEEc
Confidence 35678899999843 2678999999875
No 103
>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=50.20 E-value=33 Score=33.61 Aligned_cols=41 Identities=24% Similarity=0.297 Sum_probs=33.8
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccce
Q 020570 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVS 109 (324)
Q Consensus 69 ~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~ 109 (324)
++.++..++...--..|++.++++|.+|.|+|||..+...+
T Consensus 328 ~~~~~~~~~~~~~~~~S~~~arr~ik~g~v~vn~~~i~~~~ 368 (377)
T TIGR00234 328 GDITLADLLVLSGLFPSKSEARRDIKQGGVYINGEKVTDLE 368 (377)
T ss_pred CCcCHHHHHHHcCCCcChHHHHHHHHhCCEEECCEeccCch
Confidence 34789888887644679999999999999999999885443
No 104
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=50.14 E-value=16 Score=26.79 Aligned_cols=43 Identities=16% Similarity=0.339 Sum_probs=31.1
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc---ceeeeecCCEEeee
Q 020570 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (324)
Q Consensus 70 ~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~---~~~~l~~GD~V~v~ 121 (324)
++++..+|.+. + ++- +.=.|.+||..+-+ .+..++.||+|++.
T Consensus 17 ~~tv~dLL~~l-~-~~~-------~~vav~vNg~iVpr~~~~~~~l~~gD~ievv 62 (68)
T COG2104 17 GTTVADLLAQL-G-LNP-------EGVAVAVNGEIVPRSQWADTILKEGDRIEVV 62 (68)
T ss_pred CCcHHHHHHHh-C-CCC-------ceEEEEECCEEccchhhhhccccCCCEEEEE
Confidence 37899999885 3 222 12256689999843 78899999999873
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=49.11 E-value=16 Score=25.97 Aligned_cols=43 Identities=28% Similarity=0.421 Sum_probs=30.3
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc---ceeeeecCCEEeee
Q 020570 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (324)
Q Consensus 70 ~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~---~~~~l~~GD~V~v~ 121 (324)
+.+|..+|... . +.. ..-.|.+||+.+.+ .++.|+.||+|.+.
T Consensus 13 ~~tv~~ll~~l-~-~~~-------~~v~v~vN~~iv~~~~~~~~~L~~gD~veii 58 (64)
T TIGR01683 13 GLTLAALLESL-G-LDP-------RRVAVAVNGEIVPRSEWDDTILKEGDRIEIV 58 (64)
T ss_pred CCcHHHHHHHc-C-CCC-------CeEEEEECCEEcCHHHcCceecCCCCEEEEE
Confidence 46789988874 3 321 33367799998853 24689999999884
No 106
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=48.85 E-value=17 Score=25.69 Aligned_cols=44 Identities=14% Similarity=0.231 Sum_probs=30.7
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccc---eeeeecCCEEeeec
Q 020570 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKV---SHNVKGGDMVNCTI 122 (324)
Q Consensus 69 ~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~---~~~l~~GD~V~v~~ 122 (324)
++.+|..+|... . ... .-.|.+||+.+.+. +..|+.||+|.+..
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 356788888764 3 221 12578999988433 67899999999853
No 107
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=47.95 E-value=41 Score=25.68 Aligned_cols=45 Identities=22% Similarity=0.260 Sum_probs=30.4
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc---ceeeeecCCEEeee
Q 020570 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (324)
Q Consensus 68 ~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~---~~~~l~~GD~V~v~ 121 (324)
.++..|..+|... . +....+ .|-+||+.+.+ .+..|+.||+|.+.
T Consensus 31 ~~~~tl~~LL~~l-~-~~~~~v-------AVevNg~iVpr~~w~~t~L~egD~IEIv 78 (84)
T PRK06083 31 DISSSLAQIIAQL-S-LPELGC-------VFAINNQVVPRSEWQSTVLSSGDAISLF 78 (84)
T ss_pred CCCCcHHHHHHHc-C-CCCceE-------EEEECCEEeCHHHcCcccCCCCCEEEEE
Confidence 4467889888764 2 322111 56799998843 46679999999874
No 108
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=47.91 E-value=18 Score=25.74 Aligned_cols=42 Identities=19% Similarity=0.309 Sum_probs=29.1
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc---ceeeeecCCEEeee
Q 020570 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (324)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~---~~~~l~~GD~V~v~ 121 (324)
.+|..+|... . +... .+ .|-+|++.+.+ .+..|+.||+|.+.
T Consensus 15 ~tl~~Ll~~l-~-~~~~----~v---avavN~~iv~~~~~~~~~L~dgD~Ieiv 59 (65)
T PRK06488 15 TTLALLLAEL-D-YEGN----WL---ATAVNGELVHKEARAQFVLHEGDRIEIL 59 (65)
T ss_pred CcHHHHHHHc-C-CCCC----eE---EEEECCEEcCHHHcCccccCCCCEEEEE
Confidence 4788888764 2 2211 01 37899999854 37789999999984
No 109
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=46.92 E-value=21 Score=28.31 Aligned_cols=37 Identities=19% Similarity=0.232 Sum_probs=30.0
Q ss_pred HHHHHHHHHcCceEECCEEeccceeeeecCCEEeeec
Q 020570 86 RARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 86 r~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
+...-.+|.+|+=+|.++.....-..+++||.|.+..
T Consensus 8 ~eeylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~~ 44 (111)
T COG4043 8 REEYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFNG 44 (111)
T ss_pred HHHHHHHHHcccceEEEEecCHhhcCCCCCCEEEEcC
Confidence 5667789999999999887754556799999998864
No 110
>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=43.70 E-value=23 Score=26.68 Aligned_cols=25 Identities=28% Similarity=0.434 Sum_probs=19.7
Q ss_pred ceEECCEEecccee--eeecCCEEeeec
Q 020570 97 LVSINGQVVSKVSH--NVKGGDMVNCTI 122 (324)
Q Consensus 97 ~V~VNg~~v~~~~~--~l~~GD~V~v~~ 122 (324)
.|.|||+.+. .+. .|+.||+|.+..
T Consensus 57 ~v~vN~~~v~-~~~~~~l~dgdev~i~P 83 (88)
T TIGR01687 57 IILVNGRNVD-WGLGTELKDGDVVAIFP 83 (88)
T ss_pred EEEECCEecC-ccCCCCCCCCCEEEEeC
Confidence 5789999984 444 899999998843
No 111
>PRK07440 hypothetical protein; Provisional
Probab=42.74 E-value=28 Score=25.46 Aligned_cols=45 Identities=16% Similarity=0.237 Sum_probs=30.7
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc---ceeeeecCCEEeee
Q 020570 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (324)
Q Consensus 68 ~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~---~~~~l~~GD~V~v~ 121 (324)
.++.+|..+|... . ++.. .=.|-+||+.+.+ .+..|+.||+|.+.
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 3457899988764 3 2211 1156689998832 57889999999874
No 112
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=38.34 E-value=40 Score=33.32 Aligned_cols=40 Identities=18% Similarity=0.106 Sum_probs=32.7
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc
Q 020570 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK 107 (324)
Q Consensus 68 ~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~ 107 (324)
+.++.+-+.+++.-..-|+.++.++|.+|.|++|++++..
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 3678888888886434577799999999999999999854
No 113
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=37.85 E-value=14 Score=28.40 Aligned_cols=30 Identities=27% Similarity=0.402 Sum_probs=17.9
Q ss_pred HHcCceEECCEEeccceeeeecCCEEeeecc
Q 020570 93 IRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (324)
Q Consensus 93 I~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~ 123 (324)
+....|=|=|+.+ +.++.|+.||+|+|+.+
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 68999999999999874
No 114
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=37.09 E-value=35 Score=33.59 Aligned_cols=47 Identities=21% Similarity=0.352 Sum_probs=35.2
Q ss_pred CccccCCCCCCCceEEEeecCHHHHHHHHHHHhcCccceEEEEEEecccCC
Q 020570 211 RPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQ 261 (324)
Q Consensus 211 ~~~~vhRLD~~TSGLLl~ak~~~~~~~l~~~f~~~~i~K~Y~A~v~G~~~~ 261 (324)
..+..+-||-+.||.++...+.......+. ....|+|++++.+..+-
T Consensus 96 k~Gh~gTlDP~vtg~l~v~~~~~tr~~~s~----~s~gk~yvg~~~lt~~v 142 (395)
T KOG2529|consen 96 KTGHSGTLDPEVTGCLIVCIDRATRLLKSQ----QSAGKEYVGIGKLTPEV 142 (395)
T ss_pred HhCCCCCCCccccceEEEEeecccccccch----hccCcEEEEEEecCcch
Confidence 456688999999999999998764443333 23799999998776543
No 115
>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=35.61 E-value=27 Score=26.05 Aligned_cols=22 Identities=23% Similarity=0.273 Sum_probs=19.1
Q ss_pred EECCEEeccceeeeecCCEEeee
Q 020570 99 SINGQVVSKVSHNVKGGDMVNCT 121 (324)
Q Consensus 99 ~VNg~~v~~~~~~l~~GD~V~v~ 121 (324)
.++|+++ ..++.|+.||+|+|.
T Consensus 53 ~~~gq~V-gl~~~L~d~DvVeI~ 74 (75)
T cd01666 53 KHSPQRV-GLDHVLEDEDVVQIV 74 (75)
T ss_pred cCCCeEC-CCCCEecCCCEEEEe
Confidence 3699999 689999999999884
No 116
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=35.19 E-value=39 Score=24.42 Aligned_cols=42 Identities=14% Similarity=0.245 Sum_probs=27.7
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc---ceeeeecCCEEeee
Q 020570 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (324)
Q Consensus 71 ~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~---~~~~l~~GD~V~v~ 121 (324)
..|..+|... . +... .=.|-+||+.+.+ ....|+.||+|.+.
T Consensus 17 ~tv~~lL~~l-~-~~~~-------~vav~vN~~iv~r~~w~~~~L~~gD~iEIv 61 (67)
T PRK07696 17 KTVAELLTHL-E-LDNK-------IVVVERNKDILQKDDHTDTSVFDGDQIEIV 61 (67)
T ss_pred ccHHHHHHHc-C-CCCC-------eEEEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 4588888764 3 2211 1147789998843 24789999999874
No 117
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=32.05 E-value=49 Score=23.63 Aligned_cols=44 Identities=16% Similarity=0.286 Sum_probs=29.1
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEecc---ceeeeecCCEEeee
Q 020570 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (324)
Q Consensus 69 ~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~---~~~~l~~GD~V~v~ 121 (324)
++.+|..+|... .. ... .=.|-+|++.+.+ ....|+.||.|.+.
T Consensus 14 ~~~tl~~ll~~l-~~-~~~-------~vaVavN~~iv~r~~w~~~~L~~gD~Ieii 60 (66)
T PRK08053 14 AGQTVHELLEQL-NQ-LQP-------GAALAINQQIIPREQWAQHIVQDGDQILLF 60 (66)
T ss_pred CCCCHHHHHHHc-CC-CCC-------cEEEEECCEEeChHHcCccccCCCCEEEEE
Confidence 346788888764 32 111 1146789998842 45579999999874
No 118
>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=31.77 E-value=36 Score=26.48 Aligned_cols=26 Identities=23% Similarity=0.164 Sum_probs=20.6
Q ss_pred ceEECCEEec---cceeeeecCCEEeeec
Q 020570 97 LVSINGQVVS---KVSHNVKGGDMVNCTI 122 (324)
Q Consensus 97 ~V~VNg~~v~---~~~~~l~~GD~V~v~~ 122 (324)
.|.|||..+. ..++.|+.||+|.+..
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 6779998763 3578999999998853
No 119
>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=31.36 E-value=76 Score=24.13 Aligned_cols=51 Identities=16% Similarity=0.219 Sum_probs=29.4
Q ss_pred EEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccc
Q 020570 62 ETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (324)
Q Consensus 62 ~~v~~~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~ 124 (324)
++|.. |..|..++.+. ++|.+.+.+++.... +++. =.+|+|||.|.+....
T Consensus 5 ~~V~~---GDtLs~iF~~~--gls~~dl~~v~~~~~---~~k~----L~~L~pGq~l~f~~d~ 55 (85)
T PF04225_consen 5 YTVKS---GDTLSTIFRRA--GLSASDLYAVLEADG---EAKP----LTRLKPGQTLEFQLDE 55 (85)
T ss_dssp EE--T---T--HHHHHHHT--T--HHHHHHHHHHGG---GT------GGG--TT-EEEEEE-T
T ss_pred EEECC---CCcHHHHHHHc--CCCHHHHHHHHhccC---ccch----HhhCCCCCEEEEEECC
Confidence 44544 45699999886 799999999999743 2233 3459999999997753
No 120
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=27.95 E-value=65 Score=26.60 Aligned_cols=24 Identities=33% Similarity=0.565 Sum_probs=18.1
Q ss_pred cCceEECCEEeccceeeeecCCEEeeec
Q 020570 95 SGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 95 ~G~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
.|.|.+||- +...+++||+|.+.-
T Consensus 66 Sg~I~lNGA----AAr~~~~GD~vII~a 89 (126)
T PRK05449 66 SGVICLNGA----AARLVQVGDLVIIAA 89 (126)
T ss_pred CCEEEeCCH----HHhcCCCCCEEEEEE
Confidence 477889993 456789999988743
No 121
>KOG4837 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.10 E-value=55 Score=29.44 Aligned_cols=53 Identities=23% Similarity=0.297 Sum_probs=44.7
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeecc
Q 020570 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (324)
Q Consensus 70 ~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~ 123 (324)
.-|.|.+|.--+ ++.|+.++-+.-.+.+++|+....+.+.+|..||.+-+.+.
T Consensus 139 sfr~d~llK~Gl-gv~rnKVel~fye~e~R~N~~Kl~kkS~~i~vgds~d~~ig 191 (248)
T KOG4837|consen 139 SFRVDALLKVGL-GVTRNKVELLFYEYEPRTNSFKLVKKSLRIDVGDSADFKIG 191 (248)
T ss_pred HHHHHHHHHhcc-ccccchhhHhhhhcccccCcccccccceeeecccccceeee
Confidence 367777777654 68999999999999999999888789999999998876553
No 122
>PF11112 PyocinActivator: Pyocin activator protein PrtN
Probab=26.25 E-value=94 Score=23.27 Aligned_cols=34 Identities=6% Similarity=0.117 Sum_probs=29.5
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEE
Q 020570 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSI 100 (324)
Q Consensus 67 ~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~V 100 (324)
++.-..|+++....|++++.+.+.+.+++|.+-+
T Consensus 11 ~~~~IpL~~v~~~yf~~lt~~~a~rk~~~g~lpl 44 (76)
T PF11112_consen 11 GDPVIPLEEVCEDYFPHLTPKTAKRKANAGELPL 44 (76)
T ss_pred CCCCCcHHHHHHHHHccCCHHHHHHHHHCCCCCC
Confidence 3455789999999999999999999999999854
No 123
>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=25.80 E-value=29 Score=26.21 Aligned_cols=56 Identities=16% Similarity=-0.021 Sum_probs=36.3
Q ss_pred cCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEee
Q 020570 65 DTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNC 120 (324)
Q Consensus 65 ~~~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v 120 (324)
+.++-=.-|-+-++..++...-..-+++|-+|+|.-|...+......+..|..|.+
T Consensus 21 ~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHL 76 (79)
T cd01790 21 FLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHL 76 (79)
T ss_pred CCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccchhhHHHHhhcccCCceEEE
Confidence 44444445566666655444556778999999999888777544334666666654
No 124
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=24.70 E-value=77 Score=25.61 Aligned_cols=24 Identities=29% Similarity=0.416 Sum_probs=18.3
Q ss_pred cCceEECCEEeccceeeeecCCEEeeec
Q 020570 95 SGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 95 ~G~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
.|.|.+||- +...+++||+|.|.-
T Consensus 65 Sg~I~lNGA----AAr~~~~GD~vII~s 88 (111)
T cd06919 65 SGVICLNGA----AARLGQPGDRVIIMA 88 (111)
T ss_pred CCEEEeCCH----HHhcCCCCCEEEEEE
Confidence 578889993 456789999988743
No 125
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=23.83 E-value=87 Score=25.86 Aligned_cols=24 Identities=29% Similarity=0.457 Sum_probs=18.2
Q ss_pred cCceEECCEEeccceeeeecCCEEeeec
Q 020570 95 SGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 95 ~G~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
.|.|.+||- +...+++||+|.+.-
T Consensus 66 Sg~I~lNGA----AArl~~~GD~VII~s 89 (126)
T TIGR00223 66 SRIICVNGA----AARCVSVGDIVIIAS 89 (126)
T ss_pred CCEEEeCCH----HHhcCCCCCEEEEEE
Confidence 477889993 446789999988743
No 126
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown.
Probab=23.52 E-value=81 Score=21.26 Aligned_cols=23 Identities=35% Similarity=0.566 Sum_probs=18.6
Q ss_pred ceEECCEEeccceeeeecCCEEee
Q 020570 97 LVSINGQVVSKVSHNVKGGDMVNC 120 (324)
Q Consensus 97 ~V~VNg~~v~~~~~~l~~GD~V~v 120 (324)
.+.+||+.+ ..+..+..||+|.+
T Consensus 36 a~~vng~~v-dl~~~l~~~~~ve~ 58 (60)
T cd01668 36 GAKVNGKLV-PLSTVLKDGDIVEI 58 (60)
T ss_pred EEEECCEEC-CCCCCCCCCCEEEE
Confidence 356999998 57888999998876
No 127
>PRK02268 hypothetical protein; Provisional
Probab=23.18 E-value=84 Score=26.49 Aligned_cols=42 Identities=14% Similarity=0.213 Sum_probs=32.6
Q ss_pred CCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccc
Q 020570 82 DGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (324)
Q Consensus 82 ~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~ 124 (324)
...|+..++.-.+.|-..|+.... .+=.++++||.|.++.+.
T Consensus 7 ~v~s~~hv~~g~~~gf~qv~hgK~-apl~RmkpGD~ivyYsp~ 48 (141)
T PRK02268 7 GVVSAEHVRRGVEGGFMQVCHGKA-APLRRMKPGDWIIYYSPK 48 (141)
T ss_pred EEccHHHHHHHHhCCEEEeCCCcc-chhhcCCCCCEEEEEece
Confidence 457999999988888888885443 355789999999987643
No 128
>KOG0062 consensus ATPase component of ABC transporters with duplicated ATPase domains/Translation elongation factor EF-3b [Amino acid transport and metabolism; Translation, ribosomal structure and biogenesis]
Probab=23.00 E-value=80 Score=32.45 Aligned_cols=67 Identities=12% Similarity=0.382 Sum_probs=45.7
Q ss_pred HHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeeccccCcccccccCCCceeeccCCcEEEEeCCC
Q 020570 74 DAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPA 153 (324)
Q Consensus 74 dk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~~~~~~~~~~~~~~~~~Ilyed~~~lvvnKPa 153 (324)
-.|+.+.+|+.+++++++.+.. +=+.|.-+...=..|.-|+.+++.+. .+-+..++++|+|-|.
T Consensus 447 vd~~~~~~pG~~~ee~r~hl~~--~Gl~g~la~~si~~LSGGQKsrvafA--------------~~~~~~PhlLVLDEPT 510 (582)
T KOG0062|consen 447 VDFMEKSFPGKTEEEIRRHLGS--FGLSGELALQSIASLSGGQKSRVAFA--------------ACTWNNPHLLVLDEPT 510 (582)
T ss_pred HHHHHHhCCCCCHHHHHHHHHh--cCCCchhhhccccccCCcchhHHHHH--------------HHhcCCCcEEEecCCC
Confidence 3456667788899999888765 33445444332234777888887653 2345678999999999
Q ss_pred ceE
Q 020570 154 HMV 156 (324)
Q Consensus 154 Gl~ 156 (324)
+.+
T Consensus 511 NhL 513 (582)
T KOG0062|consen 511 NHL 513 (582)
T ss_pred ccc
Confidence 876
No 129
>PF08068 DKCLD: DKCLD (NUC011) domain; InterPro: IPR012960 This is an N-terminal domain of dyskerin-like proteins, which is often associated with the TruB N-terminal(IPR002501 from INTERPRO) and PUA(IPR002478 from INTERPRO) domains [].; PDB: 3ZV0_D 3UAI_A 3U28_A 2AUS_C 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=22.08 E-value=32 Score=24.56 Aligned_cols=16 Identities=25% Similarity=0.401 Sum_probs=11.6
Q ss_pred CCcEEEEeCCCceEEe
Q 020570 143 DDNVLVVNKPAHMVVH 158 (324)
Q Consensus 143 d~~~lvvnKPaGl~~~ 158 (324)
...+|.+|||+|--+|
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 3689999999997655
No 130
>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=20.98 E-value=68 Score=23.46 Aligned_cols=65 Identities=15% Similarity=0.195 Sum_probs=42.1
Q ss_pred CCCceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeccceeeeecCCEEeeec
Q 020570 54 NYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (324)
Q Consensus 54 ~~~~~~~~~~v~~~~~~~RLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~l~~GD~V~v~~ 122 (324)
+..|-.+...++..+.-..|-.-|.... +++-+ -++++-.|.+.-|++.+ .++.|.+|+.|.+..
T Consensus 4 ~l~g~~~~l~v~~~~TV~~lK~~i~~~~-gip~~-~q~L~~~G~~L~d~~tL--~~~~i~~g~~l~v~~ 68 (76)
T cd01800 4 KLNGQMLNFTLQLSDPVSVLKVKIHEET-GMPAG-KQKLQYEGIFIKDSNSL--AYYNLANGTIIHLQL 68 (76)
T ss_pred ccCCeEEEEEECCCCcHHHHHHHHHHHH-CCCHH-HEEEEECCEEcCCCCcH--HHcCCCCCCEEEEEE
Confidence 4556677777776666555666665553 45443 35777777766666555 367788999888755
No 131
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=20.53 E-value=86 Score=22.21 Aligned_cols=20 Identities=35% Similarity=0.361 Sum_probs=13.2
Q ss_pred ECCEEeccceeeeecCCEEee
Q 020570 100 INGQVVSKVSHNVKGGDMVNC 120 (324)
Q Consensus 100 VNg~~v~~~~~~l~~GD~V~v 120 (324)
+||=++ +.+..|+.||.|.+
T Consensus 34 ~NGF~~-~~d~~L~e~D~v~~ 53 (57)
T PF14453_consen 34 LNGFPT-KEDIELKEGDEVFL 53 (57)
T ss_pred EcCccc-CCccccCCCCEEEE
Confidence 577665 46677777777655
No 132
>PRK02253 deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional
Probab=20.31 E-value=3.6e+02 Score=23.04 Aligned_cols=38 Identities=18% Similarity=0.250 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHcCceEECC------EEeccceeeeecCCEEeee
Q 020570 84 ISRARVQSSIRSGLVSING------QVVSKVSHNVKGGDMVNCT 121 (324)
Q Consensus 84 ~Sr~~~~~lI~~G~V~VNg------~~v~~~~~~l~~GD~V~v~ 121 (324)
+|.++++++|.+|.+.++. ..+...+.-|+-|+...+.
T Consensus 3 Ls~~~I~~~i~~g~i~i~p~~~~~~~qiqp~svDlrlg~~~~~~ 46 (167)
T PRK02253 3 LSKEELRKLIRSGKFVAEHVVDLEDDQVQPNGVDLTLGEVEEQE 46 (167)
T ss_pred CCHHHHHHHHHcCCeEeecCCCCChhhCCCcEEEEECCcEEEEe
Confidence 6889999999999999853 2344456778888777664
No 133
>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=20.21 E-value=1.1e+02 Score=19.94 Aligned_cols=22 Identities=36% Similarity=0.599 Sum_probs=17.8
Q ss_pred eEECCEEeccceeeeecCCEEee
Q 020570 98 VSINGQVVSKVSHNVKGGDMVNC 120 (324)
Q Consensus 98 V~VNg~~v~~~~~~l~~GD~V~v 120 (324)
+.+||+.+ ..+..+..||.|.+
T Consensus 37 ~~vn~~~~-~l~~~l~~~~~i~~ 58 (60)
T cd01616 37 ALVNGQLV-DLSYTLQDGDTVSI 58 (60)
T ss_pred EEECCEEC-CCCcCcCCCCEEEE
Confidence 45899887 57888999998875
Done!