Query 026355
Match_columns 240
No_of_seqs 167 out of 1682
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 06:58:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026355.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026355hhsearch_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 1E-33 2.3E-38 253.5 12.9 146 61-237 3-149 (289)
2 PRK11180 rluD 23S rRNA pseudou 100.0 2.5E-31 5.5E-36 241.7 15.0 155 56-237 3-157 (325)
3 TIGR00005 rluA_subfam pseudour 100.0 2.4E-30 5.2E-35 232.3 13.0 145 67-238 2-146 (299)
4 PRK11025 23S rRNA pseudouridyl 100.0 5.5E-29 1.2E-33 225.8 13.2 146 61-238 10-163 (317)
5 PRK10475 23S rRNA pseudouridin 99.9 3.2E-25 6.9E-30 198.8 10.6 123 68-238 4-126 (290)
6 PRK10839 16S rRNA pseudouridyl 99.9 3E-25 6.5E-30 192.9 8.1 119 71-236 1-119 (232)
7 PRK10700 23S rRNA pseudouridyl 99.9 7.2E-24 1.6E-28 190.1 11.9 125 70-238 2-129 (289)
8 cd02558 PSRA_1 PSRA_1: Pseudou 99.9 5.9E-23 1.3E-27 180.3 7.4 106 97-237 3-108 (246)
9 COG1187 RsuA 16S rRNA uridine- 99.9 2.4E-22 5.3E-27 175.8 9.4 123 70-237 2-126 (248)
10 KOG1919 RNA pseudouridylate sy 99.9 7E-22 1.5E-26 181.6 11.8 144 61-239 34-177 (371)
11 cd02557 PseudoU_synth_ScRIB2 P 99.7 1.1E-18 2.4E-23 150.1 5.9 73 135-238 14-86 (213)
12 PRK10158 23S rRNA/tRNA pseudou 99.7 3.7E-18 8E-23 147.5 5.7 69 136-237 13-82 (219)
13 TIGR01621 RluA-like pseudourid 99.7 1.2E-17 2.6E-22 144.1 5.6 69 137-238 2-70 (217)
14 cd02563 PseudoU_synth_TruC tRN 99.7 1.8E-17 3.9E-22 143.4 5.3 70 137-238 1-72 (223)
15 PRK11112 tRNA pseudouridine sy 99.7 1.7E-17 3.8E-22 146.5 4.2 70 137-238 2-73 (257)
16 cd02550 PseudoU_synth_Rsu_Rlu_ 99.6 9.9E-16 2.1E-20 125.2 3.9 61 146-238 1-61 (154)
17 cd02556 PseudoU_synth_RluB Pse 99.6 2.8E-15 6E-20 124.4 4.6 62 145-238 1-62 (167)
18 cd02870 PseudoU_synth_RsuA_lik 99.5 1.1E-15 2.4E-20 123.9 1.7 60 146-238 1-60 (146)
19 cd02553 PseudoU_synth_RsuA Pse 99.5 1.5E-14 3.2E-19 120.1 4.8 60 146-237 2-61 (167)
20 cd02566 PseudoU_synth_RluE Pse 99.4 4.9E-14 1.1E-18 117.0 3.4 57 146-237 1-58 (168)
21 PF00849 PseudoU_synth_2: RNA 99.4 3.2E-14 7E-19 116.3 1.8 66 145-237 1-66 (164)
22 cd02869 PseudoU_synth_RluCD_li 99.4 3.2E-13 7E-18 112.3 5.0 65 146-237 1-65 (185)
23 cd00165 S4 S4/Hsp/ tRNA synthe 99.4 3.5E-12 7.6E-17 88.3 7.9 70 71-150 1-70 (70)
24 cd02554 PseudoU_synth_RluF Pse 99.3 6.6E-13 1.4E-17 110.1 3.9 58 146-238 2-59 (164)
25 PRK11394 23S rRNA pseudouridin 99.3 1E-12 2.2E-17 113.5 4.4 59 144-237 39-97 (217)
26 cd02555 PSSA_1 PSSA_1: Pseudou 99.3 1.1E-12 2.3E-17 110.1 3.9 62 144-238 4-73 (177)
27 PF01479 S4: S4 domain; Inter 99.1 1.1E-10 2.5E-15 77.0 5.9 48 71-118 1-48 (48)
28 TIGR02988 YaaA_near_RecF S4 do 99.1 2.9E-10 6.3E-15 78.5 6.0 54 67-120 5-58 (59)
29 COG1188 Ribosome-associated he 98.8 1.5E-08 3.2E-13 76.8 5.4 55 68-123 6-60 (100)
30 cd02868 PseudoU_synth_hTruB2_l 98.6 1.8E-08 3.9E-13 87.6 3.4 55 146-234 2-56 (226)
31 smart00363 S4 S4 RNA-binding d 98.6 1.5E-07 3.2E-12 62.9 6.4 52 71-122 1-52 (60)
32 PLN00051 RNA-binding S4 domain 98.5 2E-07 4.3E-12 83.0 6.8 59 64-123 185-243 (267)
33 PRK10348 ribosome-associated h 98.5 3E-07 6.4E-12 73.6 6.9 54 69-123 7-60 (133)
34 TIGR03069 PS_II_S4 photosystem 98.4 3.7E-07 8E-12 80.9 6.4 59 64-123 177-235 (257)
35 TIGR01017 rpsD_bact ribosomal 98.4 5.4E-07 1.2E-11 77.0 6.6 55 70-124 89-143 (200)
36 CHL00113 rps4 ribosomal protei 98.4 6.9E-07 1.5E-11 76.4 6.2 54 70-123 88-141 (201)
37 TIGR00478 tly hemolysin TlyA f 98.2 1.9E-06 4E-11 75.2 5.7 52 72-123 1-52 (228)
38 PRK05327 rpsD 30S ribosomal pr 98.2 2.5E-06 5.4E-11 73.1 6.2 54 70-123 92-145 (203)
39 COG2302 Uncharacterized conser 98.2 2.1E-06 4.5E-11 75.0 5.0 55 68-123 178-232 (257)
40 COG0522 RpsD Ribosomal protein 98.1 5.1E-06 1.1E-10 71.3 6.0 54 71-124 94-147 (205)
41 PRK11507 ribosome-associated p 98.1 1.3E-05 2.9E-10 57.1 6.4 57 66-122 7-63 (70)
42 COG1189 Predicted rRNA methyla 98.0 1.6E-05 3.5E-10 69.4 6.0 54 70-123 2-55 (245)
43 PF13275 S4_2: S4 domain; PDB: 97.8 5.8E-06 1.2E-10 58.3 -0.0 56 67-122 4-59 (65)
44 PRK04051 rps4p 30S ribosomal p 97.7 0.00011 2.4E-09 61.7 6.1 54 70-123 102-155 (177)
45 COG2501 S4-like RNA binding pr 97.3 0.00078 1.7E-08 48.4 6.2 57 66-122 7-63 (73)
46 PLN00189 40S ribosomal protein 97.2 0.00032 6.9E-09 59.6 3.3 54 71-124 109-162 (194)
47 TIGR01018 rpsD_arch ribosomal 97.1 0.0011 2.3E-08 55.0 5.2 53 70-122 103-155 (162)
48 PTZ00155 40S ribosomal protein 96.9 0.0011 2.4E-08 55.8 4.0 53 71-123 107-159 (181)
49 PRK04313 30S ribosomal protein 96.0 0.02 4.4E-07 50.1 6.8 55 68-122 35-90 (237)
50 PRK00989 truB tRNA pseudouridi 95.9 0.012 2.7E-07 51.3 4.7 50 144-232 9-58 (230)
51 PLN00036 40S ribosomal protein 95.6 0.04 8.6E-07 48.9 6.7 55 68-122 39-94 (261)
52 PTZ00223 40S ribosomal protein 95.6 0.039 8.4E-07 49.3 6.7 55 68-122 36-91 (273)
53 PRK02484 truB tRNA pseudouridi 95.5 0.019 4.1E-07 52.0 4.7 49 145-232 4-52 (294)
54 PTZ00118 40S ribosomal protein 95.5 0.042 9.1E-07 48.8 6.6 55 68-122 39-94 (262)
55 PRK00020 truB tRNA pseudouridi 95.5 0.021 4.6E-07 50.3 4.6 50 144-232 10-59 (244)
56 PRK14123 tRNA pseudouridine sy 95.4 0.022 4.7E-07 51.9 4.6 49 145-232 4-52 (305)
57 PRK03287 truB tRNA pseudouridi 95.2 0.027 5.8E-07 51.1 4.6 50 144-232 9-58 (298)
58 PRK14846 truB tRNA pseudouridi 95.2 0.029 6.2E-07 51.7 4.7 50 144-232 3-52 (345)
59 PRK14124 tRNA pseudouridine sy 95.0 0.035 7.6E-07 50.6 4.8 49 145-232 4-52 (308)
60 PRK05033 truB tRNA pseudouridi 95.0 0.035 7.6E-07 50.6 4.7 50 144-232 10-59 (312)
61 PRK05389 truB tRNA pseudouridi 94.9 0.037 8.1E-07 50.4 4.5 50 144-232 13-62 (305)
62 PRK02755 truB tRNA pseudouridi 94.9 0.039 8.4E-07 50.0 4.6 49 145-232 4-52 (295)
63 PRK01851 truB tRNA pseudouridi 94.8 0.04 8.7E-07 50.1 4.7 50 144-232 16-65 (303)
64 PRK01528 truB tRNA pseudouridi 94.8 0.044 9.6E-07 49.5 4.9 50 144-232 3-52 (292)
65 PRK04270 H/ACA RNA-protein com 94.5 0.056 1.2E-06 49.1 4.7 50 144-232 22-71 (300)
66 COG1471 RPS4A Ribosomal protei 93.1 0.25 5.5E-06 43.1 5.9 66 73-151 47-112 (241)
67 PRK04642 truB tRNA pseudouridi 92.9 0.15 3.2E-06 46.3 4.5 50 144-232 10-59 (300)
68 TIGR00425 CBF5 rRNA pseudourid 92.7 0.18 3.8E-06 46.3 4.7 50 144-232 34-83 (322)
69 cd02867 PseudoU_synth_TruB_4 P 91.6 0.26 5.6E-06 45.1 4.4 74 146-231 2-77 (312)
70 PRK13354 tyrosyl-tRNA syntheta 91.5 0.34 7.4E-06 45.9 5.3 47 70-116 342-388 (410)
71 PF14451 Ub-Mut7C: Mut7-C ubiq 90.8 0.25 5.3E-06 36.3 2.9 47 68-123 30-76 (81)
72 KOG2559 Predicted pseudouridin 90.6 0.26 5.6E-06 43.5 3.3 19 212-230 91-109 (318)
73 PRK01777 hypothetical protein; 90.6 0.3 6.5E-06 36.9 3.2 54 67-123 23-76 (95)
74 COG0130 TruB Pseudouridine syn 90.6 0.33 7.1E-06 43.5 4.0 48 145-231 16-63 (271)
75 COG4332 Uncharacterized protei 90.4 0.54 1.2E-05 39.6 4.8 56 67-123 135-190 (203)
76 PRK05912 tyrosyl-tRNA syntheta 90.2 0.84 1.8E-05 43.2 6.7 45 70-114 342-386 (408)
77 PF06353 DUF1062: Protein of u 89.7 0.81 1.7E-05 37.2 5.3 38 66-104 98-135 (142)
78 PRK08364 sulfur carrier protei 84.4 3.2 6.9E-05 29.2 5.3 44 69-122 22-65 (70)
79 cd00754 MoaD Ubiquitin domain 84.4 3.1 6.7E-05 29.3 5.4 51 70-122 25-75 (80)
80 PRK06437 hypothetical protein; 83.5 1.3 2.9E-05 31.0 3.0 45 68-122 18-62 (67)
81 KOG3301 Ribosomal protein S4 [ 77.6 2.6 5.5E-05 35.0 3.2 38 83-120 109-146 (183)
82 PRK05659 sulfur carrier protei 72.9 3.4 7.4E-05 28.3 2.4 45 69-122 14-61 (66)
83 PF02597 ThiS: ThiS family; I 72.1 4.8 0.0001 28.0 3.1 52 68-122 19-72 (77)
84 TIGR01682 moaD molybdopterin c 71.8 10 0.00022 27.0 4.8 25 97-122 51-75 (80)
85 PLN02799 Molybdopterin synthas 69.0 12 0.00027 26.6 4.8 51 69-122 27-77 (82)
86 cd00565 ThiS ThiaminS ubiquiti 68.9 4.9 0.00011 27.6 2.5 44 69-122 13-60 (65)
87 cd01291 PseudoU_synth PseudoU_ 67.1 3.5 7.6E-05 29.9 1.5 20 210-229 24-43 (87)
88 PRK11130 moaD molybdopterin sy 64.5 5.1 0.00011 28.8 1.9 45 72-122 30-76 (81)
89 COG0162 TyrS Tyrosyl-tRNA synt 62.7 9.1 0.0002 36.3 3.8 40 73-112 338-377 (401)
90 TIGR01687 moaD_arch MoaD famil 62.7 10 0.00022 27.4 3.3 26 96-122 56-83 (88)
91 TIGR00234 tyrS tyrosyl-tRNA sy 62.4 18 0.00039 33.9 5.7 39 70-108 329-367 (377)
92 PF02824 TGS: TGS domain; Int 61.8 10 0.00022 25.8 3.0 24 97-121 36-59 (60)
93 COG4043 Preprotein translocase 61.7 8.8 0.00019 29.4 2.8 38 86-123 8-45 (111)
94 COG2104 ThiS Sulfur transfer p 60.8 9.8 0.00021 26.9 2.8 43 70-121 17-62 (68)
95 PRK06944 sulfur carrier protei 60.5 10 0.00022 25.7 2.9 44 69-122 14-60 (65)
96 TIGR01683 thiS thiamine biosyn 59.1 12 0.00026 25.5 3.0 45 69-122 12-59 (64)
97 PRK06488 sulfur carrier protei 58.6 11 0.00024 25.8 2.8 43 71-122 15-60 (65)
98 PF00498 FHA: FHA domain; Int 55.4 13 0.00029 25.1 2.7 26 95-120 41-67 (68)
99 PRK07440 hypothetical protein; 54.9 16 0.00035 25.7 3.1 46 68-122 17-65 (70)
100 cd01764 Urm1 Urm1-like ubuitin 51.5 29 0.00064 25.8 4.2 26 97-122 61-89 (94)
101 PRK08053 sulfur carrier protei 49.1 21 0.00047 24.5 3.0 45 69-122 14-61 (66)
102 PRK07696 sulfur carrier protei 46.5 22 0.00048 24.7 2.7 43 71-122 17-62 (67)
103 cd01790 Herp_N Homocysteine-re 42.3 13 0.00028 27.1 1.0 62 59-120 13-76 (79)
104 PRK06083 sulfur carrier protei 41.0 31 0.00066 25.3 2.9 46 68-122 31-79 (84)
105 KOG4837 Uncharacterized conser 39.7 30 0.00065 30.0 2.9 54 69-123 138-191 (248)
106 KOG2623 Tyrosyl-tRNA synthetas 39.4 46 0.001 31.7 4.3 39 69-107 397-435 (467)
107 PF00240 ubiquitin: Ubiquitin 37.9 8.7 0.00019 26.2 -0.5 63 56-122 4-66 (69)
108 PF03658 Ub-RnfH: RnfH family 37.9 14 0.0003 27.3 0.6 52 69-123 22-73 (84)
109 cd02572 PseudoU_synth_hDyskeri 37.3 16 0.00035 30.7 1.0 25 145-177 3-27 (182)
110 cd01666 TGS_DRG_C TGS_DRG_C: 37.1 31 0.00066 24.8 2.3 47 70-121 24-74 (75)
111 cd01791 Ubl5 UBL5 ubiquitin-li 35.6 20 0.00044 25.3 1.2 62 57-122 11-72 (73)
112 cd01668 TGS_RelA_SpoT TGS_RelA 33.8 53 0.0011 21.2 2.9 44 69-120 15-58 (60)
113 TIGR02194 GlrX_NrdH Glutaredox 33.0 14 0.0003 25.5 -0.1 15 1-15 1-15 (72)
114 PF14478 DUF4430: Domain of un 32.8 44 0.00096 23.0 2.5 23 98-120 43-67 (68)
115 PF14453 ThiS-like: ThiS-like 32.5 46 0.00099 22.8 2.4 21 99-120 33-53 (57)
116 cd00506 PseudoU_synth_TruB_lik 32.4 21 0.00046 30.8 0.9 24 146-177 2-25 (210)
117 cd01807 GDX_N ubiquitin-like d 32.2 33 0.00073 23.8 1.8 62 57-122 10-71 (74)
118 cd06919 Asp_decarbox Aspartate 32.0 61 0.0013 25.2 3.3 23 95-121 65-87 (111)
119 PRK04099 truB tRNA pseudouridi 31.8 23 0.00049 31.9 1.1 25 145-177 3-27 (273)
120 PRK02193 truB tRNA pseudouridi 31.7 22 0.00048 32.1 1.0 24 146-177 2-25 (279)
121 cd01800 SF3a120_C Ubiquitin-li 31.5 41 0.00089 23.6 2.2 66 54-123 4-69 (76)
122 TIGR00431 TruB tRNA pseudourid 31.4 23 0.00049 30.6 1.0 25 145-177 3-27 (209)
123 cd01616 TGS The TGS domain, na 31.4 62 0.0013 20.1 2.9 22 98-120 37-58 (60)
124 PF04225 OapA: Opacity-associa 30.5 68 0.0015 23.4 3.3 47 69-124 9-55 (85)
125 PRK01550 truB tRNA pseudouridi 30.2 24 0.00053 32.2 1.0 25 145-177 3-27 (304)
126 cd01806 Nedd8 Nebb8-like ubiq 29.3 39 0.00085 23.1 1.8 62 57-122 10-71 (76)
127 PRK05449 aspartate alpha-decar 29.2 80 0.0017 25.1 3.6 23 95-121 66-88 (126)
128 PRK02253 deoxyuridine 5'-triph 28.8 1.8E+02 0.004 23.8 6.0 39 83-121 2-46 (167)
129 PRK00130 truB tRNA pseudouridi 28.5 27 0.00058 31.7 1.0 25 145-177 3-27 (290)
130 PRK11092 bifunctional (p)ppGpp 27.3 50 0.0011 33.6 2.7 25 99-124 425-449 (702)
131 cd01796 DDI1_N DNA damage indu 26.1 67 0.0015 22.2 2.5 62 56-121 8-70 (71)
132 cd02573 PseudoU_synth_EcTruB P 25.9 32 0.00069 31.0 1.0 24 146-177 2-25 (277)
133 TIGR00223 panD L-aspartate-alp 25.8 1E+02 0.0022 24.6 3.6 23 95-121 66-88 (126)
134 PRK14122 tRNA pseudouridine sy 25.3 33 0.00073 31.4 1.0 24 146-177 3-26 (312)
135 PF08068 DKCLD: DKCLD (NUC011) 25.1 32 0.00069 23.7 0.6 16 143-158 41-56 (59)
136 COG0317 SpoT Guanosine polypho 25.1 66 0.0014 32.8 3.0 25 98-123 425-449 (701)
137 cd01810 ISG15_repeat2 ISG15 ub 24.8 45 0.00098 23.2 1.4 62 57-122 8-69 (74)
138 COG2440 FixX Ferredoxin-like p 23.6 38 0.00083 25.8 0.8 23 8-30 69-93 (99)
139 PF01957 NfeD: NfeD-like C-ter 23.5 1E+02 0.0023 23.7 3.4 28 95-123 104-133 (144)
140 PHA03050 glutaredoxin; Provisi 23.5 22 0.00049 27.1 -0.4 14 2-15 16-29 (108)
141 PRK05863 sulfur carrier protei 23.2 54 0.0012 22.4 1.5 45 69-122 14-60 (65)
142 PRK11200 grxA glutaredoxin 1; 22.8 24 0.00052 25.1 -0.4 15 1-15 3-17 (85)
143 TIGR00601 rad23 UV excision re 22.7 53 0.0011 30.9 1.8 65 56-123 9-75 (378)
144 PF02261 Asp_decarbox: Asparta 22.1 65 0.0014 25.3 1.9 22 95-120 66-87 (116)
145 cd00570 GST_N_family Glutathio 22.0 35 0.00075 21.8 0.3 15 1-15 1-15 (71)
146 PF11112 PyocinActivator: Pyoc 21.8 1.1E+02 0.0023 22.1 2.9 33 68-100 12-44 (76)
147 cd03029 GRX_hybridPRX5 Glutare 21.5 25 0.00054 24.0 -0.5 15 1-15 3-17 (72)
148 PRK02268 hypothetical protein; 21.5 1.3E+02 0.0028 24.4 3.6 40 83-123 8-47 (141)
149 cd01813 UBP_N UBP ubiquitin pr 21.5 79 0.0017 22.2 2.1 62 56-121 8-72 (74)
150 PTZ00044 ubiquitin; Provisiona 21.4 76 0.0016 21.8 2.0 62 57-122 10-71 (76)
151 PF11969 DcpS_C: Scavenger mRN 21.3 63 0.0014 24.8 1.7 26 136-161 13-43 (116)
152 cd01812 BAG1_N Ubiquitin-like 21.2 93 0.002 20.9 2.4 61 57-121 9-69 (71)
153 cd01669 TGS_Ygr210_C TGS_Ygr21 20.9 1E+02 0.0022 22.1 2.6 20 101-121 56-75 (76)
154 cd01798 parkin_N amino-termina 20.4 65 0.0014 22.0 1.5 62 56-121 7-68 (70)
155 TIGR01764 excise DNA binding d 20.3 1.4E+02 0.0031 18.0 3.0 21 78-99 8-28 (49)
156 PHA02096 hypothetical protein 20.1 46 0.00099 24.5 0.6 18 140-157 63-80 (103)
157 cd01805 RAD23_N Ubiquitin-like 20.1 68 0.0015 22.1 1.5 61 57-121 10-72 (77)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1e-33 Score=253.54 Aligned_cols=146 Identities=49% Similarity=0.710 Sum_probs=128.5
Q ss_pred EEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEeccCC-cccccccCCCcee
Q 026355 61 EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQ-PLRAEAEDIPLDI 139 (240)
Q Consensus 61 ~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~~~-~~~~~p~~~~l~I 139 (240)
++.|....+++|||+||++.++ +||+.+++++++|+|.|||+++. ++++|+.||+|.+...+.. .....+++++++|
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 4567778899999999999655 99999999999999999999996 9999999999999887644 3445667778999
Q ss_pred eecCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCC
Q 026355 140 VYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLD 219 (240)
Q Consensus 140 lyed~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLD 219 (240)
||||++++|||||+||+|||++++..+|++++|+.++... ..++++|||||
T Consensus 81 lyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~-----------------------------~~~~~~vHRLD 131 (289)
T COG0564 81 LYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDG-----------------------------VERPGIVHRLD 131 (289)
T ss_pred EEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhcccc-----------------------------CCceeeeccCC
Confidence 9999999999999999999999999999999999986310 26788999999
Q ss_pred CCCceEEEeecCCccccC
Q 026355 220 KGTSGLLVVAKVIFSPFG 237 (240)
Q Consensus 220 r~TSGLLl~ak~~~aa~~ 237 (240)
|+||||||+||+..++..
T Consensus 132 kdTSGlll~AK~~~a~~~ 149 (289)
T COG0564 132 KDTSGLLLVAKNREAARE 149 (289)
T ss_pred CCCceEEEEECCHHHHHH
Confidence 999999999999987754
No 2
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=99.97 E-value=2.5e-31 Score=241.75 Aligned_cols=155 Identities=43% Similarity=0.613 Sum_probs=130.6
Q ss_pred CceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEeccCCcccccccCC
Q 026355 56 AGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDI 135 (240)
Q Consensus 56 ~~~~~~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~~~~~~~~p~~~ 135 (240)
.-|.+++.|+..++|+|||+||++.++.+||+.++++|++|+|+|||+++.++++.|.+||+|++......+....+...
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 34778889999999999999999988788999999999999999999998778999999999999875433222334556
Q ss_pred CceeeecCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCcccc
Q 026355 136 PLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIV 215 (240)
Q Consensus 136 ~l~Ilyed~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V 215 (240)
+++|||||++++|+|||+||+|||++++..+|+.+.|..++... ....++++|
T Consensus 83 ~~~iiyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~~~~---------------------------~~~~~~~~v 135 (325)
T PRK11180 83 PLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPI---------------------------ADVPRAGIV 135 (325)
T ss_pred CCcEEEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHhhhc---------------------------cCCccccee
Confidence 78999999999999999999999998887789999998875210 011456789
Q ss_pred CcCCCCCceEEEeecCCccccC
Q 026355 216 HRLDKGTSGLLVVAKVIFSPFG 237 (240)
Q Consensus 216 hRLDr~TSGLLl~ak~~~aa~~ 237 (240)
||||++|||||||||+..++..
T Consensus 136 hRLD~~TSGlll~Ak~~~~~~~ 157 (325)
T PRK11180 136 HRLDKDTTGLMVVAKTVPAQTR 157 (325)
T ss_pred ccCCCCCceeEEEECCHHHHHH
Confidence 9999999999999999887764
No 3
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=99.97 E-value=2.4e-30 Score=232.33 Aligned_cols=145 Identities=41% Similarity=0.685 Sum_probs=119.0
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEeccCCcccccccCCCceeeecCCcE
Q 026355 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNV 146 (240)
Q Consensus 67 ~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~~~~~~~~p~~~~l~Ilyed~~~ 146 (240)
+++++||++||+..++.+||+.++++|++|+|+|||+.+.++++.|++||+|.+.+.+.......+...+++|+|||+++
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 57899999999999766999999999999999999976657899999999999976532222233344568899999999
Q ss_pred EEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCceEE
Q 026355 147 LVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLL 226 (240)
Q Consensus 147 lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSGLL 226 (240)
+|||||+||+|||.+++..+|+.+.|..++... ....++++|||||++|||||
T Consensus 82 lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~~~~---------------------------~~~~~~~~vhRLD~~TSGll 134 (299)
T TIGR00005 82 IVINKPSGLVVHPGGGNPFGTVLNALLAHCPPI---------------------------AGVERVGIVHRLDRDTSGLM 134 (299)
T ss_pred EEEECCCCCeEeCCCCCCcccHHHHHHHhcccc---------------------------cCCCcCceECCCCCCCceEE
Confidence 999999999999998888889999998775210 01145778999999999999
Q ss_pred EeecCCccccCC
Q 026355 227 VVAKVIFSPFGN 238 (240)
Q Consensus 227 l~ak~~~aa~~~ 238 (240)
|||||+++++.+
T Consensus 135 l~ak~~~~~~~l 146 (299)
T TIGR00005 135 VVAKTPLALREL 146 (299)
T ss_pred EEEcCHHHHHHH
Confidence 999999876543
No 4
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=99.96 E-value=5.5e-29 Score=225.80 Aligned_cols=146 Identities=27% Similarity=0.401 Sum_probs=115.9
Q ss_pred EEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEeccCCccccc--------c
Q 026355 61 EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAE--------A 132 (240)
Q Consensus 61 ~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~~~~~~~~--------p 132 (240)
.+.|+..++|+|||+||+..++.+||+.++++|++|+|+|||+++ +++++|+.||+|++........... .
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 467888889999999999887788999999999999999999999 5899999999999864321111111 1
Q ss_pred cCCCceeeecCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCc
Q 026355 133 EDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRP 212 (240)
Q Consensus 133 ~~~~l~Ilyed~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 212 (240)
...+++|+|||++++|||||+|++|||+.+.. .++.+.+..+.. ....+
T Consensus 89 ~~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~-~~~~~~~~~~~~------------------------------~~~~~ 137 (317)
T PRK11025 89 AALADVILYEDDHILVLNKPSGTAVHGGSGLS-FGVIEGLRALRP------------------------------EARFL 137 (317)
T ss_pred ccCcCCEEEECCCEEEEECCCCCcCcCCCCCC-ccHHHHHHHhcc------------------------------CCCcC
Confidence 23467999999999999999999999987654 456676655321 01235
Q ss_pred cccCcCCCCCceEEEeecCCccccCC
Q 026355 213 GIVHRLDKGTSGLLVVAKVIFSPFGN 238 (240)
Q Consensus 213 ~~VhRLDr~TSGLLl~ak~~~aa~~~ 238 (240)
++|||||++||||||||||..+++.+
T Consensus 138 ~~vhRLD~~TSGlll~Ak~~~a~~~l 163 (317)
T PRK11025 138 ELVHRLDRDTSGVLLVAKKRSALRSL 163 (317)
T ss_pred ceeCCCCCCCceEEEEEcCHHHHHHH
Confidence 67999999999999999999887654
No 5
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.92 E-value=3.2e-25 Score=198.76 Aligned_cols=123 Identities=27% Similarity=0.316 Sum_probs=101.9
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEeccCCcccccccCCCceeeecCCcEE
Q 026355 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVL 147 (240)
Q Consensus 68 ~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~~~~~~~~p~~~~l~Ilyed~~~l 147 (240)
.+++||++||++. ..+||++++++|++|+|+|||+++ .++++|.+||+|.|++.... +. .+||++||
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-TIGDQVKAGDVVKVNGQLIE-----PR------EAEDLVLI 70 (290)
T ss_pred chHHHHHHHHHhC-CCCCHHHHHHHHHCCcEEECCEEc-cCCCCcCCCCEEEECCEEcc-----cc------ccCCCeEE
Confidence 4568999999987 478999999999999999999998 58999999999999763211 10 24788999
Q ss_pred EEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCceEEE
Q 026355 148 VVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLV 227 (240)
Q Consensus 148 vvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSGLLl 227 (240)
|+|||+||+||+.+. ...|+++.|..+ .++++|||||++||||||
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 457888877532 346679999999999999
Q ss_pred eecCCccccCC
Q 026355 228 VAKVIFSPFGN 238 (240)
Q Consensus 228 ~ak~~~aa~~~ 238 (240)
||+|+++++.+
T Consensus 116 lT~dg~~~~~L 126 (290)
T PRK10475 116 LTNHGDLVNKI 126 (290)
T ss_pred EecCHHHHHHh
Confidence 99999887643
No 6
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=99.92 E-value=3e-25 Score=192.88 Aligned_cols=119 Identities=22% Similarity=0.289 Sum_probs=94.3
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEeccCCcccccccCCCceeeecCCcEEEEe
Q 026355 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVN 150 (240)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~~~~~~~~p~~~~l~Ilyed~~~lvvn 150 (240)
+|||+||++.+ .+||+.++++|+.|+|+|||+++.+++++|++||+|.+...... ..++++++|+|
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 68999999999999999999999668999999999988642111 12357899999
Q ss_pred CCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCceEEEeec
Q 026355 151 KPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAK 230 (240)
Q Consensus 151 KPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSGLLl~ak 230 (240)
||+||+|||++... .|+.+.+... ...++++|||||++|||||||||
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 99999999985543 5665332211 11356789999999999999999
Q ss_pred CCcccc
Q 026355 231 VIFSPF 236 (240)
Q Consensus 231 ~~~aa~ 236 (240)
|+.++.
T Consensus 114 ~~~~~~ 119 (232)
T PRK10839 114 DGQWSH 119 (232)
T ss_pred CHHHHH
Confidence 998665
No 7
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=99.90 E-value=7.2e-24 Score=190.12 Aligned_cols=125 Identities=19% Similarity=0.127 Sum_probs=99.7
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCC--CEEEEEeccCCcccccccCCCceeee-cCCcE
Q 026355 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGG--DMVNCTISELQPLRAEAEDIPLDIVY-EDDNV 146 (240)
Q Consensus 70 g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~G--D~I~v~~~~~~~~~~~p~~~~l~Ily-ed~~~ 146 (240)
.+||++||++. +.+||++++++|++|+|+|||+++ .++++|.++ |.|.+....... ...+ ||++|
T Consensus 2 ~~RL~k~La~~-g~~SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g~~~~~----------~~~~~e~~~y 69 (289)
T PRK10700 2 SEKLQKVLARA-GHGSRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRIDGHLISV----------KESAEQICRV 69 (289)
T ss_pred chhHHHHHHHC-CCCCHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEECCEEeec----------ccccccCCeE
Confidence 38999999987 579999999999999999999998 689999887 456665421110 0011 56789
Q ss_pred EEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCceEE
Q 026355 147 LVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLL 226 (240)
Q Consensus 147 lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSGLL 226 (240)
+++|||+|++||+.+.....|+++.|.... ..++++|||||++|||||
T Consensus 70 lvlnKP~G~~~s~~d~~~~~tv~d~l~~~~--------------------------------~~~~~~VgRLD~dTsGLL 117 (289)
T PRK10700 70 LAYYKPEGELCTRNDPEGRPTVFDRLPKLR--------------------------------GARWIAVGRLDVNTCGLL 117 (289)
T ss_pred EEEECCCCCEeecCCCCCCccHHHHhhhhc--------------------------------CCceeEccCCCCCCceEE
Confidence 999999999999998777789999886421 134568999999999999
Q ss_pred EeecCCccccCC
Q 026355 227 VVAKVIFSPFGN 238 (240)
Q Consensus 227 l~ak~~~aa~~~ 238 (240)
|||+|+++++.+
T Consensus 118 LlTndg~~~~~L 129 (289)
T PRK10700 118 LFTTDGELANRL 129 (289)
T ss_pred EEEcCHHHHHHH
Confidence 999999887643
No 8
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.
Probab=99.88 E-value=5.9e-23 Score=180.30 Aligned_cols=106 Identities=22% Similarity=0.233 Sum_probs=85.2
Q ss_pred ceEECCEEeeeccceecCCCEEEEEeccCCcccccccCCCceeeecCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhc
Q 026355 97 LVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHC 176 (240)
Q Consensus 97 ~V~VNG~~v~~~~~~L~~GD~I~v~~~~~~~~~~~p~~~~l~Ilyed~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~ 176 (240)
.|..||+++ +++++|+.||+|.+.....+. .+...+++|||||++++|||||+|++|||++++..+|+.+.|..++
T Consensus 3 ~~~~ng~~~-~~~~~l~~gd~i~~~~~~~~~---~~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~ 78 (246)
T cd02558 3 VVDADGEPL-DPDSPYRPGTFVWYYRELPDE---PPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQT 78 (246)
T ss_pred eECCCCcCC-CCCceecCCCEEEEeCCCCCC---CCCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHh
Confidence 345899999 589999999999987532211 1223458999999999999999999999998888889998887654
Q ss_pred CCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCceEEEeecCCccccC
Q 026355 177 SLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKVIFSPFG 237 (240)
Q Consensus 177 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSGLLl~ak~~~aa~~ 237 (240)
.. ..+++|||||++|||||||||+++++..
T Consensus 79 ~~-------------------------------~~~~~vhRLD~~TSGlll~Ak~~~~~~~ 108 (246)
T cd02558 79 GN-------------------------------PDLTPAHRLDRLTAGLVLFSKRPETRGA 108 (246)
T ss_pred CC-------------------------------CcccccccCCCCceeEEEEEcCHHHHHH
Confidence 21 2456799999999999999999988743
No 9
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=99.87 E-value=2.4e-22 Score=175.75 Aligned_cols=123 Identities=25% Similarity=0.274 Sum_probs=102.5
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCC-CEEEEEeccCCcccccccCCCceeee-cCCcEE
Q 026355 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGG-DMVNCTISELQPLRAEAEDIPLDIVY-EDDNVL 147 (240)
Q Consensus 70 g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~G-D~I~v~~~~~~~~~~~p~~~~l~Ily-ed~~~l 147 (240)
.+||+|||++. +.+||++++++|.+|+|+|||++++.....+.++ |.|.+.+.. +.+ +...|+
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 5899999999999999999999999899999999 578876642 233 334499
Q ss_pred EEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCceEEE
Q 026355 148 VVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLV 227 (240)
Q Consensus 148 vvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSGLLl 227 (240)
++|||.|++|+..++..+.|+++.|..... ...++++|+|||+||+||||
T Consensus 67 llnKP~G~v~s~~D~~gr~tv~D~lp~~~~------------------------------~~~~~~pvGRLD~dTeGLLL 116 (248)
T COG1187 67 LLNKPRGYVSSTEDDEGRPTVFDLLPERLP------------------------------RKKRLFPVGRLDKDTEGLLL 116 (248)
T ss_pred EEECCCCeEecccCCCCCceeeeecccccc------------------------------cccceeeccccCCCCeeEEE
Confidence 999999999999988888899886653210 12568899999999999999
Q ss_pred eecCCccccC
Q 026355 228 VAKVIFSPFG 237 (240)
Q Consensus 228 ~ak~~~aa~~ 237 (240)
||.|++.|+.
T Consensus 117 LTnDG~la~r 126 (248)
T COG1187 117 LTNDGELAHR 126 (248)
T ss_pred EeCCHHHHHH
Confidence 9999988764
No 10
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=99.87 E-value=7e-22 Score=181.55 Aligned_cols=144 Identities=33% Similarity=0.372 Sum_probs=122.9
Q ss_pred EEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEeccCCcccccccCCCceee
Q 026355 61 EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIV 140 (240)
Q Consensus 61 ~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~~~~~~~~p~~~~l~Il 140 (240)
...+...|.+..+.+++.+.|....+.+.+..|+.|.|++||..+. .++.++.+|.|....+.+++.. ...++.|+
T Consensus 34 ~~~~~~rw~~k~~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~~-v~~i~k~~d~l~~~vhrh~p~~---~~~~~~Iv 109 (371)
T KOG1919|consen 34 RTFVKGRWAGKKLVDVFVSEFRLRERAYYESAIKLGRVTVNGEQVR-VSLIVKNGDVLCHTVHRHEPPV---AYLPIRIV 109 (371)
T ss_pred eEEEeeeecccchHHHHHHHHhcCchHhhhhhhhcCceEECcEeee-eEEEeccCCEEEEeeccCCCCc---cccccceE
Confidence 3356788999999999999988888999999999999999999995 8999999999998877666544 23678999
Q ss_pred ecCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCC
Q 026355 141 YEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDK 220 (240)
Q Consensus 141 yed~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr 220 (240)
|||++|+|||||+|++|||.+.+..+|+...|..... ...+.+|||||+
T Consensus 110 ~ed~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~~~-------------------------------~~~~~~~hRLDr 158 (371)
T KOG1919|consen 110 FEDKDYVVVNKPHGIPVHPTGRYRENTITKILAALHK-------------------------------VEGLRPCHRLDR 158 (371)
T ss_pred EecCCEEEEeCCCCCceeccCccccccchHHHHHhcc-------------------------------ccccccccccCc
Confidence 9999999999999999999999999999888876421 134567999999
Q ss_pred CCceEEEeecCCccccCCC
Q 026355 221 GTSGLLVVAKVIFSPFGNH 239 (240)
Q Consensus 221 ~TSGLLl~ak~~~aa~~~~ 239 (240)
.|||||+|||+.++|-.+|
T Consensus 159 ~tSGllvlAkt~~~~~~~~ 177 (371)
T KOG1919|consen 159 LTSGLLVLAKTKEAADKFH 177 (371)
T ss_pred cccceEEEEechhHhHHHH
Confidence 9999999999998876543
No 11
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.
Probab=99.75 E-value=1.1e-18 Score=150.09 Aligned_cols=73 Identities=37% Similarity=0.455 Sum_probs=62.1
Q ss_pred CCceeeecCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccc
Q 026355 135 IPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (240)
Q Consensus 135 ~~l~Ilyed~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 (240)
.+++|||||++++|+|||+||+||+++.....|+.+.|..++.. ..+++
T Consensus 14 ~~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~~-------------------------------~~~~~ 62 (213)
T cd02557 14 DPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGL-------------------------------TELRP 62 (213)
T ss_pred CCCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcCC-------------------------------CCccC
Confidence 46789999999999999999999998877778999988775420 24567
Q ss_pred cCcCCCCCceEEEeecCCccccCC
Q 026355 215 VHRLDKGTSGLLVVAKVIFSPFGN 238 (240)
Q Consensus 215 VhRLDr~TSGLLl~ak~~~aa~~~ 238 (240)
|||||++||||||||||+++++.+
T Consensus 63 vhRLD~~TSGllllak~~~~~~~l 86 (213)
T cd02557 63 CHRLDRLTSGLLLFAKTSQTASRL 86 (213)
T ss_pred ccCCCCCCceEEEEECCHHHHHHH
Confidence 999999999999999999987653
No 12
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=99.73 E-value=3.7e-18 Score=147.48 Aligned_cols=69 Identities=32% Similarity=0.449 Sum_probs=57.2
Q ss_pred CceeeecCCcEEEEeCCCCceeecCCC-CCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccc
Q 026355 136 PLDIVYEDDNVLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (240)
Q Consensus 136 ~l~Ilyed~~~lvvnKPaGl~v~p~~~-~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 (240)
++.|||||++++|||||+|++|||+.. ....++.+.|..++ .++++
T Consensus 13 ~~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~---------------------------------~~~~~ 59 (219)
T PRK10158 13 WLVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY---------------------------------PQAES 59 (219)
T ss_pred CCCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC---------------------------------CCCCE
Confidence 478999999999999999999999763 44567888776543 23567
Q ss_pred cCcCCCCCceEEEeecCCccccC
Q 026355 215 VHRLDKGTSGLLVVAKVIFSPFG 237 (240)
Q Consensus 215 VhRLDr~TSGLLl~ak~~~aa~~ 237 (240)
|||||++|||||||||+.+++..
T Consensus 60 vhRLDr~TSGlll~Akt~~~~~~ 82 (219)
T PRK10158 60 VHRLDMATSGVIVVALTKAAERE 82 (219)
T ss_pred ECCCCCCCceEEEEECCHHHHHH
Confidence 99999999999999999988743
No 13
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621. This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.
Probab=99.70 E-value=1.2e-17 Score=144.12 Aligned_cols=69 Identities=29% Similarity=0.381 Sum_probs=55.9
Q ss_pred ceeeecCCcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccC
Q 026355 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVH 216 (240)
Q Consensus 137 l~Ilyed~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Vh 216 (240)
++|||||++|+|||||+||+||++.. ..++.+.+..+.. ..++++||
T Consensus 2 ~~ilyed~~~lvvnKP~Gl~v~~~~~--~~~l~~~l~~~~~-------------------------------~~~~~~Vh 48 (217)
T TIGR01621 2 FEILFTHPDFLLINKHPGISVHKDDG--ETGLLQEVATQLG-------------------------------VGQVWLVH 48 (217)
T ss_pred ceEEEeCCCEEEEECCCCCeECCCCC--cChHHHHHHHhcC-------------------------------CCCccEec
Confidence 47999999999999999999999764 3567776665421 13467899
Q ss_pred cCCCCCceEEEeecCCccccCC
Q 026355 217 RLDKGTSGLLVVAKVIFSPFGN 238 (240)
Q Consensus 217 RLDr~TSGLLl~ak~~~aa~~~ 238 (240)
|||++||||||||||.++++.+
T Consensus 49 RLDr~TSGlll~Ak~~~~~~~L 70 (217)
T TIGR01621 49 RLDKMTSGILLLALNAESASEL 70 (217)
T ss_pred CCCCCCceEEEEEcCHHHHHHH
Confidence 9999999999999999987653
No 14
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.
Probab=99.69 E-value=1.8e-17 Score=143.40 Aligned_cols=70 Identities=29% Similarity=0.402 Sum_probs=53.3
Q ss_pred ceeeecCCcEEEEeCCCCceeecCCCCCCCc--HHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccc
Q 026355 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGT--LVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (240)
Q Consensus 137 l~Ilyed~~~lvvnKPaGl~v~p~~~~~~~T--l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 (240)
++|||||++++|+|||+|++|||.++....+ +...|..++ ..++++
T Consensus 1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~ 48 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQL--------------------------------GQHVYP 48 (223)
T ss_pred CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHc--------------------------------CCCccc
Confidence 3689999999999999999999987544333 222333221 124667
Q ss_pred cCcCCCCCceEEEeecCCccccCC
Q 026355 215 VHRLDKGTSGLLVVAKVIFSPFGN 238 (240)
Q Consensus 215 VhRLDr~TSGLLl~ak~~~aa~~~ 238 (240)
|||||++||||||||||+++++.+
T Consensus 49 vhRLD~~TSGlll~Ak~~~~~~~l 72 (223)
T cd02563 49 VHRLDRPTSGVLLFALSSEVARKL 72 (223)
T ss_pred ccCCCCCCeEEEEEEECHHHHHHH
Confidence 999999999999999999987654
No 15
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=99.68 E-value=1.7e-17 Score=146.52 Aligned_cols=70 Identities=30% Similarity=0.343 Sum_probs=53.5
Q ss_pred ceeeecCCcEEEEeCCCCceeecCCCCCCCcH--HHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccc
Q 026355 137 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTL--VNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 214 (240)
Q Consensus 137 l~Ilyed~~~lvvnKPaGl~v~p~~~~~~~Tl--~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 (240)
++|||||++|||||||+||+||++......++ ...|..++ ..++++
T Consensus 2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~ 49 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQI--------------------------------GQHVFT 49 (257)
T ss_pred CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHh--------------------------------CCCcee
Confidence 47999999999999999999999864444433 23332221 124568
Q ss_pred cCcCCCCCceEEEeecCCccccCC
Q 026355 215 VHRLDKGTSGLLVVAKVIFSPFGN 238 (240)
Q Consensus 215 VhRLDr~TSGLLl~ak~~~aa~~~ 238 (240)
|||||++||||||||||.++++.+
T Consensus 50 VHRLDr~TSGlll~Ak~~~~~~~L 73 (257)
T PRK11112 50 AHRLDRPTSGVLLMALSSEVARLL 73 (257)
T ss_pred eccCCCCCeeEEEEECCHHHHHHH
Confidence 999999999999999999988654
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=99.58 E-value=9.9e-16 Score=125.17 Aligned_cols=61 Identities=33% Similarity=0.352 Sum_probs=50.2
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCceE
Q 026355 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (240)
Q Consensus 146 ~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (240)
++|+|||+|++||++++....|+.+.+.... ..++++|||||++||||
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~vhRLD~~TSGl 48 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLH--------------------------------GPRVHAAGRLDKDTSGL 48 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhhccc--------------------------------CCceeEeccCCCCCeeE
Confidence 5899999999999998877788887654321 14567899999999999
Q ss_pred EEeecCCccccCC
Q 026355 226 LVVAKVIFSPFGN 238 (240)
Q Consensus 226 Ll~ak~~~aa~~~ 238 (240)
||||||+++++.+
T Consensus 49 ll~ak~~~~~~~l 61 (154)
T cd02550 49 LLLTNDGRLQRRL 61 (154)
T ss_pred EEEEcCHHHHHHH
Confidence 9999999987654
No 17
>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=99.55 E-value=2.8e-15 Score=124.39 Aligned_cols=62 Identities=23% Similarity=0.133 Sum_probs=51.6
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCce
Q 026355 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (240)
Q Consensus 145 ~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (240)
.++|+|||+|++||+.+.....|+.+.|..+. ..++++|||||++|||
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 37999999999999977666789998886642 1356789999999999
Q ss_pred EEEeecCCccccCC
Q 026355 225 LLVVAKVIFSPFGN 238 (240)
Q Consensus 225 LLl~ak~~~aa~~~ 238 (240)
|||||+|+++++.+
T Consensus 49 Lll~ak~~~~~~~L 62 (167)
T cd02556 49 LLLFTNDGELANRL 62 (167)
T ss_pred EEEEECCHHHHHHH
Confidence 99999999987654
No 18
>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=99.55 E-value=1.1e-15 Score=123.94 Aligned_cols=60 Identities=25% Similarity=0.160 Sum_probs=48.1
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCceE
Q 026355 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (240)
Q Consensus 146 ~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (240)
|+|+|||+||+||+.+.....|+.+.+..+ ..++.+|||||++||||
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~~---------------------------------~~~~~~vhRLD~~TsGl 47 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDV---------------------------------GERLFPVGRLDYDTEGL 47 (146)
T ss_pred CEEEECCCCcEecccCCCCCCEEeeecccc---------------------------------CCCEEECCCCCCCCeeE
Confidence 689999999999998877677777544321 13467899999999999
Q ss_pred EEeecCCccccCC
Q 026355 226 LVVAKVIFSPFGN 238 (240)
Q Consensus 226 Ll~ak~~~aa~~~ 238 (240)
||||||+++++.+
T Consensus 48 ll~ak~~~~~~~l 60 (146)
T cd02870 48 LLLTNDGELANRL 60 (146)
T ss_pred EEEeCCHHHHHHh
Confidence 9999999887644
No 19
>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=99.50 E-value=1.5e-14 Score=120.08 Aligned_cols=60 Identities=27% Similarity=0.221 Sum_probs=48.7
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCceE
Q 026355 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (240)
Q Consensus 146 ~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (240)
++|+|||+||+||+++ ....|+.+.|..++. ..++++|||||++||||
T Consensus 2 ~ivvnKP~G~~~~~~~-~~~~tl~~~l~~~~~-------------------------------~~~~~~vhRLD~~TSGl 49 (167)
T cd02553 2 YLMLNKPAGVVCATKD-PHHPTVIDLLPEPDR-------------------------------RRDLFPVGRLDKDTTGL 49 (167)
T ss_pred EEEEECCCCCEeCCCC-CCCCcHHHHhhhhcc-------------------------------cCCeEEcccCCCCCEEE
Confidence 7999999999999654 456889988876531 13567899999999999
Q ss_pred EEeecCCccccC
Q 026355 226 LVVAKVIFSPFG 237 (240)
Q Consensus 226 Ll~ak~~~aa~~ 237 (240)
||||||.++++.
T Consensus 50 ll~ak~~~~~~~ 61 (167)
T cd02553 50 LLLTNDGQLAHR 61 (167)
T ss_pred EEEEeCHHHHHH
Confidence 999999976653
No 20
>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=99.44 E-value=4.9e-14 Score=117.03 Aligned_cols=57 Identities=21% Similarity=0.181 Sum_probs=45.4
Q ss_pred EEEEeCCCCceeecCCC-CCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCce
Q 026355 146 VLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (240)
Q Consensus 146 ~lvvnKPaGl~v~p~~~-~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (240)
++|+|||+|++||+.++ ....|+.+.|.. .++++|||||++|||
T Consensus 1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l~~-----------------------------------~~~~~v~RLD~~TsG 45 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYIDD-----------------------------------PGVYAAGRLDRDSEG 45 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCccHHHHcCc-----------------------------------CCeEEccCCCCCCeE
Confidence 58999999999999876 455677765421 234679999999999
Q ss_pred EEEeecCCccccC
Q 026355 225 LLVVAKVIFSPFG 237 (240)
Q Consensus 225 LLl~ak~~~aa~~ 237 (240)
|||||+|+++++.
T Consensus 46 lll~a~d~~~~~~ 58 (168)
T cd02566 46 LLLLTDDGRLQHR 58 (168)
T ss_pred EEEEEeCHHHHHH
Confidence 9999999987653
No 21
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family. This Prosite family is a subset of the Pfam family.; InterPro: IPR006145 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit). RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [, ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site. RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: RluB modifies uracil-2605. RluC modifies uracil-955, U-2504, and U-2580. RluD modifies uracil-1911, U-1915, and U-1917. RluE modifies uracil-3457. RluF modifies uracil-2604, and to a lesser extent U-2605. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [, ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 2GML_A 3DH3_B 1VIO_A 2I82_B 1XPI_B 1V9K_B 1PRZ_A 1V9F_A 2IST_A 1QYU_A ....
Probab=99.43 E-value=3.2e-14 Score=116.25 Aligned_cols=66 Identities=36% Similarity=0.397 Sum_probs=44.1
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCce
Q 026355 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (240)
Q Consensus 145 ~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (240)
||||||||+||+||+.+.............+... ......+++|||||++|||
T Consensus 1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~~v~RLD~~TsG 53 (164)
T PF00849_consen 1 NLIVVNKPAGVPVHPSDGNESKSVKELPALSLKR---------------------------GDDPPELYPVHRLDRDTSG 53 (164)
T ss_dssp SEEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHHH---------------------------CTTSGGGEESS---TT-EE
T ss_pred CEEEEECCCCCeEecCCCCCcccccchhhhhhhh---------------------------ccCCCceEECCCCCccccC
Confidence 6899999999999999865444444444333210 0133567889999999999
Q ss_pred EEEeecCCccccC
Q 026355 225 LLVVAKVIFSPFG 237 (240)
Q Consensus 225 LLl~ak~~~aa~~ 237 (240)
|||||+|++++..
T Consensus 54 lll~a~~~~~~~~ 66 (164)
T PF00849_consen 54 LLLFAKDKEAAAK 66 (164)
T ss_dssp EEEEESSHHHHHH
T ss_pred CeeccCCcccccc
Confidence 9999999988753
No 22
>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=99.39 E-value=3.2e-13 Score=112.28 Aligned_cols=65 Identities=58% Similarity=0.840 Sum_probs=50.9
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCceE
Q 026355 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (240)
Q Consensus 146 ~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (240)
++|+|||+|++|++.+.....++.+.+..+.... ....++++|||||++||||
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~v~RLD~~tsGl 53 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLL---------------------------GEEFRPGLVHRLDKDTSGL 53 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhc---------------------------CCCCcCceecccCCCCceE
Confidence 5899999999999998888888888763322100 1225678899999999999
Q ss_pred EEeecCCccccC
Q 026355 226 LVVAKVIFSPFG 237 (240)
Q Consensus 226 Ll~ak~~~aa~~ 237 (240)
||||+++++++.
T Consensus 54 ll~ak~~~~~~~ 65 (185)
T cd02869 54 LLVAKNKKAAAK 65 (185)
T ss_pred EEEEcCHHHHHH
Confidence 999999988764
No 23
>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=99.36 E-value=3.5e-12 Score=88.29 Aligned_cols=70 Identities=41% Similarity=0.550 Sum_probs=60.6
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEeccCCcccccccCCCceeeecCCcEEEEe
Q 026355 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVN 150 (240)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~~~~~~~~p~~~~l~Ilyed~~~lvvn 150 (240)
+||++||.+.++..||+.++++|++|.|+|||+.++.++..+.+||+|.+.... .+..|+|||++++|+|
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 589999998866789999999999999999999997789999999999886521 1128999999999986
No 24
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.
Probab=99.34 E-value=6.6e-13 Score=110.08 Aligned_cols=58 Identities=17% Similarity=0.120 Sum_probs=47.7
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCceE
Q 026355 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (240)
Q Consensus 146 ~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (240)
|+++|||+|++|++.+. ...|+.+.|.. ..++++|||||++||||
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 78999999999998865 34788776532 14578899999999999
Q ss_pred EEeecCCccccCC
Q 026355 226 LVVAKVIFSPFGN 238 (240)
Q Consensus 226 Ll~ak~~~aa~~~ 238 (240)
||||+|+++++.+
T Consensus 47 ll~t~dg~~~~~L 59 (164)
T cd02554 47 ILLTNDGDLVNKI 59 (164)
T ss_pred EEEEcCHHHHHHH
Confidence 9999999988754
No 25
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.33 E-value=1e-12 Score=113.49 Aligned_cols=59 Identities=24% Similarity=0.183 Sum_probs=48.8
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCc
Q 026355 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (240)
Q Consensus 144 ~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TS 223 (240)
..|+++|||+|++||+.+.....|+.+.+.. .++++|||||++||
T Consensus 39 ~~ylllnKP~G~l~~~~d~~~~~tl~d~l~~-----------------------------------~~~~~vgRLD~~Ts 83 (217)
T PRK11394 39 TRVILFNKPYDVLPQFTDEAGRKTLKEFIPV-----------------------------------QGVYAAGRLDRDSE 83 (217)
T ss_pred CEEEEEECCCCCEEeeCCccCCcchHHhccc-----------------------------------CCeEEecCCCCCCe
Confidence 4599999999999998777667788776531 34678999999999
Q ss_pred eEEEeecCCccccC
Q 026355 224 GLLVVAKVIFSPFG 237 (240)
Q Consensus 224 GLLl~ak~~~aa~~ 237 (240)
||||||+|+++++.
T Consensus 84 GllLlt~d~~~~~~ 97 (217)
T PRK11394 84 GLLVLTNNGALQAR 97 (217)
T ss_pred eEEEEECCHHHHHH
Confidence 99999999988754
No 26
>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=99.32 E-value=1.1e-12 Score=110.09 Aligned_cols=62 Identities=29% Similarity=0.198 Sum_probs=44.3
Q ss_pred CcEEEEeCCCCceeecCCCC--------CCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCcccc
Q 026355 144 DNVLVVNKPAHMVVHPAPGN--------ATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIV 215 (240)
Q Consensus 144 ~~~lvvnKPaGl~v~p~~~~--------~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V 215 (240)
..++++|||+|++|+..+.. ...++.+.|..++ .++++|
T Consensus 4 ~~y~llnKP~G~l~s~~d~~~~~g~~~~~~~~~~~~l~~~~---------------------------------~~l~~V 50 (177)
T cd02555 4 PVTLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGHF---------------------------------ARLAPI 50 (177)
T ss_pred cEEEEEECCCceEecCCCcccccccccccccchhhhhhhcC---------------------------------CceeEe
Confidence 45799999999999776522 1123323332211 356789
Q ss_pred CcCCCCCceEEEeecCCccccCC
Q 026355 216 HRLDKGTSGLLVVAKVIFSPFGN 238 (240)
Q Consensus 216 hRLDr~TSGLLl~ak~~~aa~~~ 238 (240)
||||++||||||||+|+++++.+
T Consensus 51 gRLD~dTsGLLl~t~d~~~~~~L 73 (177)
T cd02555 51 GPLDKDASGLLVFSQDGRVLRKL 73 (177)
T ss_pred cCCCCCCeeEEEEECCHHHHHHH
Confidence 99999999999999999987653
No 27
>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=99.14 E-value=1.1e-10 Score=76.99 Aligned_cols=48 Identities=38% Similarity=0.511 Sum_probs=45.0
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEE
Q 026355 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMV 118 (240)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I 118 (240)
+|||+||++.....||++++++|++|.|+|||++++++++.|++||+|
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 699999998876779999999999999999999998899999999986
No 28
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=99.08 E-value=2.9e-10 Score=78.53 Aligned_cols=54 Identities=13% Similarity=0.119 Sum_probs=47.7
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEE
Q 026355 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNC 120 (240)
Q Consensus 67 ~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v 120 (240)
..+++|||+||++.....||+.++++|..|.|+|||+++++++++|++||+|.|
T Consensus 5 ~~~~~rLd~~L~~~~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 5 FTEYITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEI 58 (59)
T ss_pred cchHHHHHHHHHHcCCccCHHHHHHHHHcCCEEECCEEccCCCCCCCCCCEEEe
Confidence 346799999999982123999999999999999999999888999999999986
No 29
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=98.75 E-value=1.5e-08 Score=76.82 Aligned_cols=55 Identities=33% Similarity=0.468 Sum_probs=49.8
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 68 ~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
...+|||+||.-.-...+|..+++++..|+|.|||+++ +++..|+.||+|+|...
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 56799999999764468999999999999999999999 89999999999999765
No 30
>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=98.64 E-value=1.8e-08 Score=87.60 Aligned_cols=55 Identities=25% Similarity=0.219 Sum_probs=38.1
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCceE
Q 026355 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 225 (240)
Q Consensus 146 ~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSGL 225 (240)
+||||||+||.++... +++...|...+. .....++|||||++||||
T Consensus 2 ilvvnKP~Gi~s~~~~----~~~~~~l~~~~~------------------------------~~k~~~~vhrLD~~aSGv 47 (226)
T cd02868 2 LFAVYKPPGVHWKHVR----DTIESNLLKYFP------------------------------EDKVLVGVHRLDAFSSGV 47 (226)
T ss_pred EEEEEcCCCCChhHHH----HHHHHHHHHHcc------------------------------ccceeeEccccCCCCceE
Confidence 7999999999775532 334443433331 012355789999999999
Q ss_pred EEeecCCcc
Q 026355 226 LVVAKVIFS 234 (240)
Q Consensus 226 Ll~ak~~~a 234 (240)
|+||++..+
T Consensus 48 l~~a~~~~t 56 (226)
T cd02868 48 LVLGVNHGN 56 (226)
T ss_pred EEEEeChhH
Confidence 999998764
No 31
>smart00363 S4 S4 RNA-binding domain.
Probab=98.61 E-value=1.5e-07 Score=62.92 Aligned_cols=52 Identities=33% Similarity=0.392 Sum_probs=46.7
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
+|||.||.+.+...|++.+++++..|.|+|||++++.++..+..||.|.+..
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 4799999987556899999999999999999999966899999999998865
No 32
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=98.52 E-value=2e-07 Score=82.99 Aligned_cols=59 Identities=32% Similarity=0.411 Sum_probs=54.2
Q ss_pred EcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 64 VDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 64 V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
+....+++|||++++..+ ++||+.++++|++|+|+|||+.++++++.|++||+|+|.+.
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 455667899999999997 79999999999999999999999999999999999999864
No 33
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=98.52 E-value=3e-07 Score=73.61 Aligned_cols=54 Identities=30% Similarity=0.286 Sum_probs=49.0
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 69 ~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
+.+|||+||.......||+.++++|..|+|+|||++ .+++..|+.||+|.|...
T Consensus 7 ~~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~ 60 (133)
T PRK10348 7 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQG 60 (133)
T ss_pred ccccHHHHHHHcCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEEC
Confidence 458999999998667899999999999999999999 589999999999998654
No 34
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=98.44 E-value=3.7e-07 Score=80.91 Aligned_cols=59 Identities=29% Similarity=0.446 Sum_probs=53.4
Q ss_pred EcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 64 VDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 64 V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
+....+++|||.+++..+ .+||+.++++|++|+|+|||+.+++++++|++||.|+|.+.
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 455668899999999886 78999999999999999999999889999999999999764
No 35
>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=98.42 E-value=5.4e-07 Score=77.05 Aligned_cols=55 Identities=22% Similarity=0.254 Sum_probs=49.7
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEecc
Q 026355 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (240)
Q Consensus 70 g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~ 124 (240)
.+|||++|.+.....||+.++++|..|+|.|||++++.+++.|++||+|+|....
T Consensus 89 e~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD~I~V~~~~ 143 (200)
T TIGR01017 89 ESRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKS 143 (200)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCCEEEEeeCc
Confidence 3899999987755679999999999999999999999999999999999998653
No 36
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=98.38 E-value=6.9e-07 Score=76.42 Aligned_cols=54 Identities=19% Similarity=0.229 Sum_probs=49.3
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 70 g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
.+|||+||.+.....||..++++|..|+|+|||++++.+++.|++||+|+|...
T Consensus 88 E~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~~~ 141 (201)
T CHL00113 88 EMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDK 141 (201)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEccc
Confidence 379999999886567999999999999999999999999999999999999754
No 37
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=98.23 E-value=1.9e-06 Score=75.19 Aligned_cols=52 Identities=29% Similarity=0.238 Sum_probs=47.8
Q ss_pred hHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 72 RLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 72 RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
|||+||.+.....||+.++++|++|+|+|||+++++++++|.+||.|++...
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 7999999986566999999999999999999999999999999999998754
No 38
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=98.22 E-value=2.5e-06 Score=73.14 Aligned_cols=54 Identities=24% Similarity=0.283 Sum_probs=48.5
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 70 g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
.+|||.+|.+.....||..++++|..|+|+|||+.++.+++.|.+||+|+|...
T Consensus 92 E~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~I~v~~~ 145 (203)
T PRK05327 92 ESRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVREK 145 (203)
T ss_pred HHHHHHHHHHcCccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCEEEECCc
Confidence 379999998765567999999999999999999999889999999999998753
No 39
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=98.19 E-value=2.1e-06 Score=75.04 Aligned_cols=55 Identities=40% Similarity=0.523 Sum_probs=51.5
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 68 ~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
-..+|||.+++..| .+||+.++++|.+|+|+||++.++++++.|+.||.|++.+.
T Consensus 178 vsSlRLD~vis~~~-~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG~ 232 (257)
T COG2302 178 VSSLRLDVVISEGF-GLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRGF 232 (257)
T ss_pred eehhhHHHHHHHHH-hhhHHHHHHHHHcCceEEeeEEeccccceeccCCEEEEecc
Confidence 44699999999997 79999999999999999999999999999999999999875
No 40
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=98.12 E-value=5.1e-06 Score=71.27 Aligned_cols=54 Identities=22% Similarity=0.216 Sum_probs=49.0
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEecc
Q 026355 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (240)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~ 124 (240)
.|||.++.+.....|+.+|+++|..|+|.|||++|+.|++.|.+||+|.|....
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 588888888766779999999999999999999999999999999999997653
No 41
>PRK11507 ribosome-associated protein; Provisional
Probab=98.07 E-value=1.3e-05 Score=57.11 Aligned_cols=57 Identities=19% Similarity=0.195 Sum_probs=50.2
Q ss_pred CCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 66 TKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 66 ~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
...+-.+|++||+-.--.-|-.+++.+|..|.|+|||++.+.-..+|.+||+|++..
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 345679999999987434588999999999999999999999999999999999865
No 42
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=97.95 E-value=1.6e-05 Score=69.36 Aligned_cols=54 Identities=33% Similarity=0.314 Sum_probs=50.0
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 70 g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
.+|||.+|.++...-||+.++.+|.+|.|+|||.++++|++.|..++.|+|...
T Consensus 2 k~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~~ 55 (245)
T COG1189 2 KMRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKGE 55 (245)
T ss_pred cchHHHHHHHccchhhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEccc
Confidence 589999999986567999999999999999999999999999999999999753
No 43
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=97.76 E-value=5.8e-06 Score=58.28 Aligned_cols=56 Identities=20% Similarity=0.251 Sum_probs=37.4
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 67 ~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
..+..+|++||+..--.-|-.+++.+|.+|.|+|||++.+.-+.+|.+||+|++..
T Consensus 4 ~~e~I~L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~~~ 59 (65)
T PF13275_consen 4 NTEYITLGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEIDG 59 (65)
T ss_dssp --S---HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEETT
T ss_pred CCCcEEHHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEECC
Confidence 45678999999987434588899999999999999999999999999999999843
No 44
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=97.65 E-value=0.00011 Score=61.68 Aligned_cols=54 Identities=17% Similarity=0.100 Sum_probs=46.9
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 70 g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
-.|||.+|.+....-|+.+++++|..|+|.|||++|++|++.|..++.-.|.+.
T Consensus 102 erRLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~ 155 (177)
T PRK04051 102 ERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYY 155 (177)
T ss_pred HhHHHHHHHHccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEe
Confidence 469999999886677999999999999999999999999999999965555443
No 45
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=97.34 E-value=0.00078 Score=48.41 Aligned_cols=57 Identities=21% Similarity=0.238 Sum_probs=49.4
Q ss_pred CCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 66 TKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 66 ~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
...+-..|.+||+..--.-|-.+++.+|..|.|+|||++-+.-..+|..||+|++..
T Consensus 7 i~~e~I~L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~ 63 (73)
T COG2501 7 IKTEFITLGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPG 63 (73)
T ss_pred eccceEEHHHHHHHhCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECC
Confidence 345668899999987434588999999999999999999998999999999999855
No 46
>PLN00189 40S ribosomal protein S9; Provisional
Probab=97.18 E-value=0.00032 Score=59.56 Aligned_cols=54 Identities=19% Similarity=0.098 Sum_probs=44.6
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEecc
Q 026355 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (240)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~ 124 (240)
.||+.++.+....-|...++++|..|+|.|||++|+.|++.|..|+++.|++..
T Consensus 109 RRL~~vv~r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~~ 162 (194)
T PLN00189 109 RRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSL 162 (194)
T ss_pred hhhceeeeecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEEec
Confidence 455555554433569999999999999999999999999999999999998753
No 47
>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=97.05 E-value=0.0011 Score=55.00 Aligned_cols=53 Identities=15% Similarity=0.161 Sum_probs=44.5
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 70 g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
..|||.++.+....-|..+++++|..|+|.|||++|+.|++.|..+++-.|++
T Consensus 103 eRRL~~vv~r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~ 155 (162)
T TIGR01018 103 ERRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDF 155 (162)
T ss_pred HHhHhhHhhhccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeee
Confidence 36788877776556799999999999999999999999999999995544444
No 48
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=96.89 E-value=0.0011 Score=55.82 Aligned_cols=53 Identities=17% Similarity=0.058 Sum_probs=45.1
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
.|||.++.+....-|...++++|..|+|.|||++|+.|++.|..|++-.|++.
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 57777777664456999999999999999999999999999999977766664
No 49
>PRK04313 30S ribosomal protein S4e; Validated
Probab=96.04 E-value=0.02 Score=50.14 Aligned_cols=55 Identities=15% Similarity=0.125 Sum_probs=45.5
Q ss_pred CccchHHHHHHhccCC-CCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 68 AGKLRLDAWISSRIDG-ISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 68 ~~g~RLdk~L~~~~~~-~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
.+.+.|--+|...+.. .+.+++++.+.+|.|+|||++.+...+.+---|+|+|..
T Consensus 35 ~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~~ 90 (237)
T PRK04313 35 EESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIPE 90 (237)
T ss_pred ccccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEcc
Confidence 3457788888887653 599999999999999999999987777776779999844
No 50
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=95.86 E-value=0.012 Score=51.32 Aligned_cols=50 Identities=20% Similarity=0.294 Sum_probs=40.0
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCc
Q 026355 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (240)
Q Consensus 144 ~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TS 223 (240)
+-++++|||.|+-+|. +++.+.+.+. ..+++..|.||-..|
T Consensus 9 ~G~l~i~KP~g~TS~d--------vv~~ikk~~~-------------------------------~kKvGH~GTLDP~At 49 (230)
T PRK00989 9 EGILLVDKPQGRTSFS--------LIRSLTKLIG-------------------------------VKKIGHAGTLDPFAT 49 (230)
T ss_pred CEEEEEeCCCCCCHHH--------HHHHHHHHhC-------------------------------CCcCCcCccCCCCCe
Confidence 4599999999987643 6777777653 146788999999999
Q ss_pred eEEEeecCC
Q 026355 224 GLLVVAKVI 232 (240)
Q Consensus 224 GLLl~ak~~ 232 (240)
|||+++-..
T Consensus 50 GvLiv~vG~ 58 (230)
T PRK00989 50 GVMVMLIGR 58 (230)
T ss_pred eEEEEEECC
Confidence 999998654
No 51
>PLN00036 40S ribosomal protein S4; Provisional
Probab=95.56 E-value=0.04 Score=48.94 Aligned_cols=55 Identities=16% Similarity=0.147 Sum_probs=44.9
Q ss_pred CccchHHHHHHhccCC-CCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 68 AGKLRLDAWISSRIDG-ISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 68 ~~g~RLdk~L~~~~~~-~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
.+.+.|--+|...+.. .+.+++++.+.+|.|+|||++.+...+.+---|+|+|..
T Consensus 39 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~k 94 (261)
T PLN00036 39 RECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPK 94 (261)
T ss_pred ccccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcC
Confidence 3456788888887653 588999999999999999999987777776669999854
No 52
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=95.56 E-value=0.039 Score=49.29 Aligned_cols=55 Identities=22% Similarity=0.190 Sum_probs=45.1
Q ss_pred CccchHHHHHHhccCC-CCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 68 AGKLRLDAWISSRIDG-ISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 68 ~~g~RLdk~L~~~~~~-~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
.+.+.|--+|...+.. .+.+++++.+.+|.|.|||++.+...+.+---|+|+|..
T Consensus 36 ~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~k 91 (273)
T PTZ00223 36 RECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPK 91 (273)
T ss_pred ccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcC
Confidence 3457788888887653 588999999999999999999987777776669999854
No 53
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=95.52 E-value=0.019 Score=51.98 Aligned_cols=49 Identities=22% Similarity=0.205 Sum_probs=39.4
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCce
Q 026355 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (240)
Q Consensus 145 ~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (240)
-++++|||+||-+|- +++.+.+.+. ..+++..|.||-..||
T Consensus 4 Gil~i~KP~G~TS~d--------vv~~vrr~l~-------------------------------~kKvGH~GTLDP~AtG 44 (294)
T PRK02484 4 GIINLKKEAGMTSHD--------AVFKLRKILQ-------------------------------TKKIGHGGTLDPDVVG 44 (294)
T ss_pred eEEEEeCCCCCCHHH--------HHHHHHHHhC-------------------------------CCccccCCCCCCCCee
Confidence 589999999987643 7778877653 1467889999999999
Q ss_pred EEEeecCC
Q 026355 225 LLVVAKVI 232 (240)
Q Consensus 225 LLl~ak~~ 232 (240)
||+++-..
T Consensus 45 vL~i~vG~ 52 (294)
T PRK02484 45 VLPIAVGK 52 (294)
T ss_pred EEEEEECh
Confidence 99998654
No 54
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=95.48 E-value=0.042 Score=48.81 Aligned_cols=55 Identities=20% Similarity=0.208 Sum_probs=45.1
Q ss_pred CccchHHHHHHhccCC-CCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 68 AGKLRLDAWISSRIDG-ISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 68 ~~g~RLdk~L~~~~~~-~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
.+.+.|--||...+.. .+.+++++.+.+|.|.|||++.+...+.+---|+|+|..
T Consensus 39 ~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~k 94 (262)
T PTZ00118 39 RECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTK 94 (262)
T ss_pred ccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEcC
Confidence 3457788888887653 588999999999999999999987777776669999854
No 55
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=95.46 E-value=0.021 Score=50.28 Aligned_cols=50 Identities=24% Similarity=0.331 Sum_probs=39.7
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCc
Q 026355 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (240)
Q Consensus 144 ~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TS 223 (240)
+-++++|||.|+-+|. +++.+.+.+. ..+++..+-||-..|
T Consensus 10 ~Gil~vdKP~G~TS~d--------vv~~vkr~~~-------------------------------~kKvGH~GTLDP~At 50 (244)
T PRK00020 10 DGVLLLDKPVGLSSNH--------ALQRAKRTVD-------------------------------AAKAGHTGTLDPFAT 50 (244)
T ss_pred CeEEEEecCCCCCHHH--------HHHHHHHHhC-------------------------------CCCCCcCCcCCCcCe
Confidence 3599999999987643 6777777653 146788999999999
Q ss_pred eEEEeecCC
Q 026355 224 GLLVVAKVI 232 (240)
Q Consensus 224 GLLl~ak~~ 232 (240)
|||+++-..
T Consensus 51 GvLiv~iG~ 59 (244)
T PRK00020 51 GLLVCCMGR 59 (244)
T ss_pred eEEEEEECH
Confidence 999998653
No 56
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=95.40 E-value=0.022 Score=51.86 Aligned_cols=49 Identities=22% Similarity=0.213 Sum_probs=39.4
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCce
Q 026355 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (240)
Q Consensus 145 ~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (240)
-+|++|||+||-+|- +++.+.+.+. ..+++..|-||-..||
T Consensus 4 Gil~i~KP~G~TS~d--------vv~~vrr~~~-------------------------------~kKvGH~GTLDP~AtG 44 (305)
T PRK14123 4 GILPVYKERGLTSHD--------VVFKLRKILK-------------------------------TKKIGHTGTLDPEVAG 44 (305)
T ss_pred eEEEEeCCCCCCHHH--------HHHHHHHHhC-------------------------------CCccccCcCCCCcCee
Confidence 589999999987643 7778877653 1467889999999999
Q ss_pred EEEeecCC
Q 026355 225 LLVVAKVI 232 (240)
Q Consensus 225 LLl~ak~~ 232 (240)
||+++-..
T Consensus 45 vL~v~vG~ 52 (305)
T PRK14123 45 VLPVCIGN 52 (305)
T ss_pred EEEEEECh
Confidence 99998654
No 57
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=95.22 E-value=0.027 Score=51.11 Aligned_cols=50 Identities=28% Similarity=0.365 Sum_probs=40.0
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCc
Q 026355 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (240)
Q Consensus 144 ~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TS 223 (240)
+-++++|||.|+-+|- +++.+.+.+. ..+++..+-||-..|
T Consensus 9 ~Gil~i~KP~G~TS~d--------vv~~vrr~~~-------------------------------~kKvGH~GTLDP~At 49 (298)
T PRK03287 9 SGLVVVDKPAGMTSHD--------VVARCRRLFG-------------------------------TRKVGHAGTLDPMAT 49 (298)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhC-------------------------------CCCCCcCccCCCcce
Confidence 4699999999987643 7777877653 146778999999999
Q ss_pred eEEEeecCC
Q 026355 224 GLLVVAKVI 232 (240)
Q Consensus 224 GLLl~ak~~ 232 (240)
|||+++-..
T Consensus 50 GvL~i~vG~ 58 (298)
T PRK03287 50 GVLVLGVER 58 (298)
T ss_pred eEEEEEeCh
Confidence 999998654
No 58
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=95.16 E-value=0.029 Score=51.66 Aligned_cols=50 Identities=22% Similarity=0.189 Sum_probs=39.6
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCc
Q 026355 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (240)
Q Consensus 144 ~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TS 223 (240)
+-++++|||.||-+|. +++.+.+.+. ..+++..|.||-..|
T Consensus 3 nGiL~idKP~G~TS~d--------vv~~vrk~l~-------------------------------~kKVGH~GTLDP~At 43 (345)
T PRK14846 3 NYWLNIYKPRGISSAQ--------LVSIVKKILG-------------------------------KTKIGHAGTLDVEAE 43 (345)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhC-------------------------------CCcCCcCccCCCcCc
Confidence 3599999999987643 7777877653 146788999999999
Q ss_pred eEEEeecCC
Q 026355 224 GLLVVAKVI 232 (240)
Q Consensus 224 GLLl~ak~~ 232 (240)
|||+++-..
T Consensus 44 GVL~i~vG~ 52 (345)
T PRK14846 44 GILPFAVGE 52 (345)
T ss_pred eEEEEEECh
Confidence 999987553
No 59
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=95.02 E-value=0.035 Score=50.58 Aligned_cols=49 Identities=24% Similarity=0.315 Sum_probs=39.2
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCce
Q 026355 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (240)
Q Consensus 145 ~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (240)
-++++|||+|+-+|- +++.+.+.+. ..+++..|-||-..||
T Consensus 4 Gil~i~KP~G~TS~d--------vv~~vrr~l~-------------------------------~kKvGH~GTLDP~AtG 44 (308)
T PRK14124 4 GFLVAYKPKGPTSHD--------VVDEVRKKLK-------------------------------TRKVGHAGTLDPFATG 44 (308)
T ss_pred eEEEEECCCCCCHHH--------HHHHHHHHcC-------------------------------CCccCcCcCCCCCCcE
Confidence 589999999987643 7777877653 1467789999999999
Q ss_pred EEEeecCC
Q 026355 225 LLVVAKVI 232 (240)
Q Consensus 225 LLl~ak~~ 232 (240)
||+++-..
T Consensus 45 vL~v~vG~ 52 (308)
T PRK14124 45 VLIVGVNK 52 (308)
T ss_pred EEEEEECh
Confidence 99998654
No 60
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=95.00 E-value=0.035 Score=50.65 Aligned_cols=50 Identities=20% Similarity=0.298 Sum_probs=39.7
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCc
Q 026355 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (240)
Q Consensus 144 ~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TS 223 (240)
+-++++|||.||-+|- +++.+.+.+. ..+++..+-||-..|
T Consensus 10 ~Gil~i~KP~G~TS~d--------vv~~vrr~l~-------------------------------~kKvGH~GTLDP~At 50 (312)
T PRK05033 10 NGVLLLDKPQGMSSND--------ALQKVKRLFN-------------------------------ANKAGHTGALDPLAT 50 (312)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhC-------------------------------CCCCCCCCcCCCcCe
Confidence 4699999999987654 6777777653 146778999999999
Q ss_pred eEEEeecCC
Q 026355 224 GLLVVAKVI 232 (240)
Q Consensus 224 GLLl~ak~~ 232 (240)
|||+++-..
T Consensus 51 GvL~v~vG~ 59 (312)
T PRK05033 51 GMLPICLGE 59 (312)
T ss_pred eEEEEEECH
Confidence 999998643
No 61
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=94.88 E-value=0.037 Score=50.35 Aligned_cols=50 Identities=26% Similarity=0.290 Sum_probs=39.8
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCc
Q 026355 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (240)
Q Consensus 144 ~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TS 223 (240)
+-++++|||.|+-+|- +++.+.+.+. ..+++..+-||-..|
T Consensus 13 ~Gil~i~KP~G~TS~d--------vv~~vrk~~~-------------------------------~kKvGH~GTLDP~At 53 (305)
T PRK05389 13 SGWLILDKPAGMTSTE--------AVSKVKWLFD-------------------------------AQKAGHAGTLDPLAS 53 (305)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhc-------------------------------ccccCCcccCCCCCc
Confidence 4699999999987643 7777877653 146778999999999
Q ss_pred eEEEeecCC
Q 026355 224 GLLVVAKVI 232 (240)
Q Consensus 224 GLLl~ak~~ 232 (240)
|||+++-..
T Consensus 54 GvL~v~vG~ 62 (305)
T PRK05389 54 GVLPIALGE 62 (305)
T ss_pred eEEEEEECh
Confidence 999998653
No 62
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=94.86 E-value=0.039 Score=50.00 Aligned_cols=49 Identities=29% Similarity=0.321 Sum_probs=39.3
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCce
Q 026355 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (240)
Q Consensus 145 ~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (240)
-++++|||.||-+|- +++.+.+.+.. .+++..+-||-..||
T Consensus 4 Gil~i~KP~G~TS~d--------vv~~vrr~~~~-------------------------------kKvGH~GTLDP~AtG 44 (295)
T PRK02755 4 GFLNLDKPAGLTSHD--------CVARLRRLLRL-------------------------------KRVGHGGTLDPAATG 44 (295)
T ss_pred eEEEEeCCCCCCHHH--------HHHHHHHHhCC-------------------------------CccccCCCCCCcCee
Confidence 589999999987643 77788776531 467889999999999
Q ss_pred EEEeecCC
Q 026355 225 LLVVAKVI 232 (240)
Q Consensus 225 LLl~ak~~ 232 (240)
||+++-..
T Consensus 45 vL~i~vG~ 52 (295)
T PRK02755 45 VLPIALGK 52 (295)
T ss_pred EEEEEECh
Confidence 99997654
No 63
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=94.84 E-value=0.04 Score=50.07 Aligned_cols=50 Identities=22% Similarity=0.259 Sum_probs=40.0
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCc
Q 026355 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (240)
Q Consensus 144 ~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TS 223 (240)
+-++++|||.||-+|- +++.+.+.+. ..+++..+-||-..|
T Consensus 16 ~Gil~i~KP~G~TS~d--------vv~~vrr~l~-------------------------------~kKvGH~GTLDP~At 56 (303)
T PRK01851 16 DGVLLLDKPLGLSSND--------ALQRAKRLLR-------------------------------AKKAGHTGTLDPLAT 56 (303)
T ss_pred CeEEEEeCCCCCCHHH--------HHHHHHHHhC-------------------------------cccCCCCCCCCCCCc
Confidence 4699999999987643 7788887663 146778999999999
Q ss_pred eEEEeecCC
Q 026355 224 GLLVVAKVI 232 (240)
Q Consensus 224 GLLl~ak~~ 232 (240)
|||+++-..
T Consensus 57 GvL~v~vG~ 65 (303)
T PRK01851 57 GLLPLCFGE 65 (303)
T ss_pred eEEEEEECH
Confidence 999998643
No 64
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=94.83 E-value=0.044 Score=49.55 Aligned_cols=50 Identities=22% Similarity=0.215 Sum_probs=39.6
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCc
Q 026355 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (240)
Q Consensus 144 ~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TS 223 (240)
+-+|++|||.||-+|- +++.+.+.+. ..+++..|-||-..|
T Consensus 3 ~GiL~i~KP~G~TS~d--------vv~~vrk~~~-------------------------------~kKvGH~GTLDP~At 43 (292)
T PRK01528 3 NYWLNIYKPRGISSAK--------LVSIVKKILG-------------------------------KVKIGHAGTLDVEAE 43 (292)
T ss_pred CEEEEEeCCCCCCHHH--------HHHHHHHHcC-------------------------------CCccCcCccCCCcCc
Confidence 4699999999987643 7777877653 146778999999999
Q ss_pred eEEEeecCC
Q 026355 224 GLLVVAKVI 232 (240)
Q Consensus 224 GLLl~ak~~ 232 (240)
|||+++-..
T Consensus 44 GvL~v~vG~ 52 (292)
T PRK01528 44 GVLPLAVGE 52 (292)
T ss_pred eEEEEEECh
Confidence 999987653
No 65
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=94.47 E-value=0.056 Score=49.07 Aligned_cols=50 Identities=22% Similarity=0.179 Sum_probs=39.5
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCc
Q 026355 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (240)
Q Consensus 144 ~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TS 223 (240)
+-++++|||.|+-+|. +++.+.+.+. ..+.+..+-||-..|
T Consensus 22 ~g~l~i~Kp~g~tS~~--------~v~~~r~~~~-------------------------------~kkvGH~GTLDp~A~ 62 (300)
T PRK04270 22 FGVVNLDKPPGPTSHE--------VAAWVRDILG-------------------------------VEKAGHGGTLDPKVT 62 (300)
T ss_pred CCEEEEECCCCCCHHH--------HHHHHHHHhc-------------------------------cccccCCCCCCCcCe
Confidence 4699999999987643 6777777653 146778999999999
Q ss_pred eEEEeecCC
Q 026355 224 GLLVVAKVI 232 (240)
Q Consensus 224 GLLl~ak~~ 232 (240)
|||+++-..
T Consensus 63 GvL~v~~g~ 71 (300)
T PRK04270 63 GVLPVALGK 71 (300)
T ss_pred EEEEEEECh
Confidence 999998643
No 66
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=93.07 E-value=0.25 Score=43.07 Aligned_cols=66 Identities=12% Similarity=0.203 Sum_probs=43.5
Q ss_pred HHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEeccCCcccccccCCCceeeecCCcEEEEeC
Q 026355 73 LDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNK 151 (240)
Q Consensus 73 Ldk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~~~~~~~~p~~~~l~Ilyed~~~lvvnK 151 (240)
+.++|.-. -.-+++++.|.+|.|+|||++.+...+.|---|+|+|..- ....+++|.....+++++
T Consensus 47 iRd~LkyA---d~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~t----------gE~yRvl~d~~grl~l~~ 112 (241)
T COG1471 47 IRDYLKYA---DNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPKT----------GEHYRVLPDEKGRLVLHP 112 (241)
T ss_pred ehhHHHhc---cchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECCC----------CceEEEEecCCccEEEEe
Confidence 34455433 4678999999999999999999755555544499988532 112355665555555544
No 67
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=92.91 E-value=0.15 Score=46.34 Aligned_cols=50 Identities=22% Similarity=0.257 Sum_probs=39.8
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCc
Q 026355 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (240)
Q Consensus 144 ~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TS 223 (240)
+-++++|||.||-+|- +++.+.+.+.. .+++..+=||-..|
T Consensus 10 ~Gil~i~KP~G~TS~d--------vv~~vrr~~~~-------------------------------kKvGH~GTLDP~At 50 (300)
T PRK04642 10 DGILLLDKPAGLSSNN--------ALQAARRLLRA-------------------------------EKGGHTGSLDPLAT 50 (300)
T ss_pred CeEEEEecCCCCCHHH--------HHHHHHHHhCC-------------------------------CcccCCCccCCcCe
Confidence 4699999999987643 77888876631 46778999999999
Q ss_pred eEEEeecCC
Q 026355 224 GLLVVAKVI 232 (240)
Q Consensus 224 GLLl~ak~~ 232 (240)
|||+++-..
T Consensus 51 GvL~v~~G~ 59 (300)
T PRK04642 51 GLLPLCFGE 59 (300)
T ss_pred eeEEEEECh
Confidence 999998643
No 68
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=92.65 E-value=0.18 Score=46.32 Aligned_cols=50 Identities=22% Similarity=0.208 Sum_probs=39.8
Q ss_pred CcEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCc
Q 026355 144 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 223 (240)
Q Consensus 144 ~~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TS 223 (240)
+-+|++|||.|+-+|- +++.+.+.+. ..+++..+=||-..+
T Consensus 34 ~G~l~i~KP~g~tS~~--------~v~~vr~~~~-------------------------------~kkvGH~GTLDP~A~ 74 (322)
T TIGR00425 34 YGVVNLDKPSGPSSHE--------VVAWVRRILN-------------------------------VEKTGHGGTLDPKVT 74 (322)
T ss_pred CCEEEEeCCCCCCHHH--------HHHHHHHHhc-------------------------------ccccCCCCCCCCCCc
Confidence 4699999999988654 7777877653 146778999999999
Q ss_pred eEEEeecCC
Q 026355 224 GLLVVAKVI 232 (240)
Q Consensus 224 GLLl~ak~~ 232 (240)
|||+++-..
T Consensus 75 GvL~v~~G~ 83 (322)
T TIGR00425 75 GVLPVCIER 83 (322)
T ss_pred eEEEEEECh
Confidence 999998643
No 69
>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=91.61 E-value=0.26 Score=45.06 Aligned_cols=74 Identities=19% Similarity=0.221 Sum_probs=40.6
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccc--cccccCCCCCCccccCcCCCCCc
Q 026355 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEE--FSSSISGASIRPGIVHRLDKGTS 223 (240)
Q Consensus 146 ~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~VhRLDr~TS 223 (240)
+++||||.|+-+| .+++.|.+.+...... ... ...+.... .+. ..........+++..+-||-..|
T Consensus 2 il~i~KP~G~TS~--------~vv~~lk~~l~~s~~~-~~~--~~~~~~~~-~~~~~~~~~~~~~~~KiGH~GTLDPlAs 69 (312)
T cd02867 2 VFAINKPSGITSA--------QVLNDLKPLFLNSALF-KDK--IQRAVAKR-GKKARRRKGRKRSKLKIGHGGTLDPLAT 69 (312)
T ss_pred eEEEeCCCCCCHH--------HHHHHHHHHhcccccc-cch--hhhhhhhh-hhhhhhhccccccccccccccccCCccc
Confidence 7899999998764 3778888776421000 000 00000000 000 00001112357889999999999
Q ss_pred eEEEeecC
Q 026355 224 GLLVVAKV 231 (240)
Q Consensus 224 GLLl~ak~ 231 (240)
|||+++-.
T Consensus 70 GVLvvgvG 77 (312)
T cd02867 70 GVLVVGVG 77 (312)
T ss_pred eeEEEEEC
Confidence 99999854
No 70
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=91.45 E-value=0.34 Score=45.86 Aligned_cols=47 Identities=21% Similarity=0.228 Sum_probs=39.5
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCC
Q 026355 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGD 116 (240)
Q Consensus 70 g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD 116 (240)
+..|-++|.......|+++++++|.+|.|+|||++++.+...+.+++
T Consensus 342 ~~~~~~~l~~~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~ 388 (410)
T PRK13354 342 TKNLVDLLVDLGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPED 388 (410)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhh
Confidence 67788888876556799999999999999999999977767776665
No 71
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=90.83 E-value=0.25 Score=36.28 Aligned_cols=47 Identities=30% Similarity=0.442 Sum_probs=36.6
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 68 ~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
+.+.++...+-.. +++..++ |.|.|||+.+ ..++.++.||.|.|...
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 3456677766554 5787775 6899999999 58999999999999753
No 72
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=90.60 E-value=0.26 Score=43.52 Aligned_cols=19 Identities=37% Similarity=0.478 Sum_probs=17.2
Q ss_pred ccccCcCCCCCceEEEeec
Q 026355 212 PGIVHRLDKGTSGLLVVAK 230 (240)
Q Consensus 212 ~~~VhRLDr~TSGLLl~ak 230 (240)
++.+||||..|||+++|+-
T Consensus 91 V~v~h~l~~~~sgvl~~gV 109 (318)
T KOG2559|consen 91 VQVVHVLPLATSGVLLFGV 109 (318)
T ss_pred eeeEEeecccccceEEEec
Confidence 6789999999999999874
No 73
>PRK01777 hypothetical protein; Validated
Probab=90.57 E-value=0.3 Score=36.91 Aligned_cols=54 Identities=17% Similarity=0.225 Sum_probs=40.0
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 67 ~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
-.+|.++.+.|... ++....-+--+..+.|-|||+.+ ..++.|+.||+|+|+.+
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 34578888888876 45444211124568899999999 58999999999999764
No 74
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=90.55 E-value=0.33 Score=43.53 Aligned_cols=48 Identities=21% Similarity=0.230 Sum_probs=38.6
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcCCCccccccccccccccccCcccccccccCCCCCCccccCcCCCCCce
Q 026355 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 224 (240)
Q Consensus 145 ~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VhRLDr~TSG 224 (240)
-++++|||.|+-+|. ++..+.+.+. ..+.+..+-||-..||
T Consensus 16 Gil~ldKP~G~tS~~--------~v~~vkkil~-------------------------------~~K~GH~GTLDP~atG 56 (271)
T COG0130 16 GVINLDKPPGPTSHE--------VVAWVKRILG-------------------------------VEKAGHGGTLDPLATG 56 (271)
T ss_pred ceEEeeCCCCCCHHH--------HHHHHHHHhC-------------------------------ccccccccccCCcccc
Confidence 699999999987644 6677777663 2567779999999999
Q ss_pred EEEeecC
Q 026355 225 LLVVAKV 231 (240)
Q Consensus 225 LLl~ak~ 231 (240)
+|+++-.
T Consensus 57 vLpi~ig 63 (271)
T COG0130 57 VLPICLG 63 (271)
T ss_pred eEEEEec
Confidence 9999865
No 75
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.35 E-value=0.54 Score=39.56 Aligned_cols=56 Identities=21% Similarity=0.394 Sum_probs=44.9
Q ss_pred CCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 67 KAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 67 ~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
.....|||..|++++ ++||+.+|++|..|.|..+-........++..|-.|.++..
T Consensus 135 ~p~qlrl~~Ll~seL-~LSrS~lq~lie~g~Irgdtd~~~l~rkrlr~~~~i~Id~~ 190 (203)
T COG4332 135 RPFQLRLDRLLASEL-GLSRSELQRLIETGQIRGDTDKMLLLRKRLRAGYDIQIDVE 190 (203)
T ss_pred CcchhHHHHHHHHHh-CcCHHHHHHHHHcCceeecchHHHHhhhhhhcCcEEEEEcC
Confidence 445689999999997 79999999999999999887765444566778877777653
No 76
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=90.23 E-value=0.84 Score=43.22 Aligned_cols=45 Identities=24% Similarity=0.194 Sum_probs=37.0
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecC
Q 026355 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKG 114 (240)
Q Consensus 70 g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~ 114 (240)
+..+-++|.......|+++++++|.+|.|+|||++++.....+..
T Consensus 342 ~~~~~~~l~~~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~ 386 (408)
T PRK05912 342 GIDLLALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTA 386 (408)
T ss_pred CCcHHHHHHHhCCCCCHHHHHHHHHcCCEEECCEEecCccccccc
Confidence 567888888764467999999999999999999999766655554
No 77
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=89.72 E-value=0.81 Score=37.15 Aligned_cols=38 Identities=29% Similarity=0.480 Sum_probs=32.6
Q ss_pred CCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEE
Q 026355 66 TKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQV 104 (240)
Q Consensus 66 ~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~ 104 (240)
+..-..|+|.+|++.+ ++||+++++++..|.|..+...
T Consensus 98 ~~~~~~Rld~lLa~~L-~lSrs~l~~l~~~G~I~~~~~~ 135 (142)
T PF06353_consen 98 PFPFPLRLDRLLARQL-GLSRSRLKRLIEQGLIRSDPDK 135 (142)
T ss_pred CCCCCccHHHHHHHHh-CcCHHHHHHHHHCCCEEecCcc
Confidence 3456799999999997 7999999999999999976433
No 78
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=84.42 E-value=3.2 Score=29.16 Aligned_cols=44 Identities=23% Similarity=0.397 Sum_probs=33.5
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 69 ~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
++.++.++|.+. .++. +.-.|.+||+.+. .++.|+.||+|.+-.
T Consensus 22 ~~~tv~~ll~~l--~~~~-------~~v~v~vNg~iv~-~~~~l~~gD~Veii~ 65 (70)
T PRK08364 22 KGMKVADILRAV--GFNT-------ESAIAKVNGKVAL-EDDPVKDGDYVEVIP 65 (70)
T ss_pred CCCcHHHHHHHc--CCCC-------ccEEEEECCEECC-CCcCcCCCCEEEEEc
Confidence 467899988875 3443 3356889999994 789999999998853
No 79
>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=84.39 E-value=3.1 Score=29.32 Aligned_cols=51 Identities=14% Similarity=0.187 Sum_probs=32.9
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 70 g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
+.++..+|.......+.. .......-.|.|||+.+. .+..|+.||+|.+-.
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 666776665432111211 223344556899999995 789999999998853
No 80
>PRK06437 hypothetical protein; Provisional
Probab=83.45 E-value=1.3 Score=30.96 Aligned_cols=45 Identities=29% Similarity=0.327 Sum_probs=34.0
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 68 ~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
.++.++.++|.+. +++...+ .|.+||..+. .++.|+.||.|++..
T Consensus 18 ~~~~tv~dLL~~L--gi~~~~v-------aV~vNg~iv~-~~~~L~dgD~Veiv~ 62 (67)
T PRK06437 18 DHELTVNDIIKDL--GLDEEEY-------VVIVNGSPVL-EDHNVKKEDDVLILE 62 (67)
T ss_pred CCCCcHHHHHHHc--CCCCccE-------EEEECCEECC-CceEcCCCCEEEEEe
Confidence 3467899999875 3443332 4779999995 899999999998853
No 81
>KOG3301 consensus Ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=77.60 E-value=2.6 Score=35.00 Aligned_cols=38 Identities=18% Similarity=0.121 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEE
Q 026355 83 GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNC 120 (240)
Q Consensus 83 ~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v 120 (240)
..|-..++.+|..+.|.|+++.|+.|++.|+...+=.+
T Consensus 109 AkSIhhARvLi~~rhI~V~~qiV~IPsf~vrldsqk~i 146 (183)
T KOG3301|consen 109 AKSIHHARVLIRQRHIRVGKQIVNIPSFMVRLDSQKHI 146 (183)
T ss_pred hhhhHHHHHHhcCccEEecCeEeeccceeEeechhhhc
Confidence 45888899999999999999999999999884433333
No 82
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=72.92 E-value=3.4 Score=28.33 Aligned_cols=45 Identities=27% Similarity=0.480 Sum_probs=31.8
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEee---eccceecCCCEEEEEe
Q 026355 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVS---KVSHNVKGGDMVNCTI 122 (240)
Q Consensus 69 ~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~---~~~~~L~~GD~I~v~~ 122 (240)
++.++.++|... .+....+ .|.+||..+. ..+..|+.||+|+|..
T Consensus 14 ~~~tl~~lL~~l--~~~~~~v-------av~vNg~iv~r~~~~~~~l~~gD~vei~~ 61 (66)
T PRK05659 14 DGESVAALLARE--GLAGRRV-------AVEVNGEIVPRSQHASTALREGDVVEIVH 61 (66)
T ss_pred CCCCHHHHHHhc--CCCCCeE-------EEEECCeEeCHHHcCcccCCCCCEEEEEE
Confidence 467899888865 3333222 2889998873 2678899999999854
No 83
>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=72.15 E-value=4.8 Score=28.03 Aligned_cols=52 Identities=15% Similarity=0.187 Sum_probs=32.9
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeee--ccceecCCCEEEEEe
Q 026355 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK--VSHNVKGGDMVNCTI 122 (240)
Q Consensus 68 ~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~--~~~~L~~GD~I~v~~ 122 (240)
.++.++..+|.......+... ....-.|.|||+.+.. .+..|+.||+|.+-.
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 345667666665421111111 3345568899999953 289999999998854
No 84
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=71.83 E-value=10 Score=27.04 Aligned_cols=25 Identities=24% Similarity=0.307 Sum_probs=21.4
Q ss_pred ceEECCEEeeeccceecCCCEEEEEe
Q 026355 97 LVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 97 ~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
.|.||++.+. .+..|+.||+|.+-.
T Consensus 51 ~v~vn~~~v~-~~~~l~dgDevai~P 75 (80)
T TIGR01682 51 MVAVNEEYVT-DDALLNEGDEVAFIP 75 (80)
T ss_pred EEEECCEEcC-CCcCcCCCCEEEEeC
Confidence 5889999995 689999999998853
No 85
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=69.01 E-value=12 Score=26.64 Aligned_cols=51 Identities=10% Similarity=0.128 Sum_probs=31.6
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 69 ~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
++.++..++.......+ .+.+....=.|.|||+.+ ..+..|+.||+|.+-.
T Consensus 27 ~~~tv~~L~~~l~~~~p--~l~~~~~~~~vavN~~~v-~~~~~l~dgDeVai~P 77 (82)
T PLN02799 27 AGSTTADCLAELVAKFP--SLEEVRSCCVLALNEEYT-TESAALKDGDELAIIP 77 (82)
T ss_pred CCCcHHHHHHHHHHHCh--hHHHHhhCcEEEECCEEc-CCCcCcCCCCEEEEeC
Confidence 35666665554321111 223333333588999998 4789999999998853
No 86
>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=68.87 E-value=4.9 Score=27.58 Aligned_cols=44 Identities=20% Similarity=0.347 Sum_probs=31.0
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeecc----ceecCCCEEEEEe
Q 026355 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVS----HNVKGGDMVNCTI 122 (240)
Q Consensus 69 ~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~----~~L~~GD~I~v~~ 122 (240)
++.++..+|... ..+.. .=.|.|||+.+. .+ ..|+.||+|.+-.
T Consensus 13 ~~~tv~~ll~~l--~~~~~-------~i~V~vNg~~v~-~~~~~~~~L~~gD~V~ii~ 60 (65)
T cd00565 13 EGATLAELLEEL--GLDPR-------GVAVALNGEIVP-RSEWASTPLQDGDRIEIVT 60 (65)
T ss_pred CCCCHHHHHHHc--CCCCC-------cEEEEECCEEcC-HHHcCceecCCCCEEEEEE
Confidence 367888888875 33321 114778999995 44 7899999998854
No 87
>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=67.14 E-value=3.5 Score=29.93 Aligned_cols=20 Identities=30% Similarity=0.282 Sum_probs=17.9
Q ss_pred CCccccCcCCCCCceEEEee
Q 026355 210 IRPGIVHRLDKGTSGLLVVA 229 (240)
Q Consensus 210 ~~~~~VhRLDr~TSGLLl~a 229 (240)
.+.+.+|++|+.++|+++++
T Consensus 24 ~~i~~aG~kDk~a~t~q~v~ 43 (87)
T cd01291 24 KRVGYAGRKDKRAVTTQLVS 43 (87)
T ss_pred heEEECccCCCCeeEEEEEc
Confidence 45677999999999999998
No 88
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=64.46 E-value=5.1 Score=28.85 Aligned_cols=45 Identities=20% Similarity=0.299 Sum_probs=29.1
Q ss_pred hHHHHHHhccCCCCHHHHHHHHHcCc--eEECCEEeeeccceecCCCEEEEEe
Q 026355 72 RLDAWISSRIDGISRARVQSSIRSGL--VSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 72 RLdk~L~~~~~~~SR~~~~klI~~G~--V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
.|-++|.+.++.+ ......+. +.||+..+ ..+..|+.||+|.+..
T Consensus 30 ~l~~~L~~~~~~~-----~~~~~~~~~~~aVN~~~~-~~~~~l~dgDeVai~P 76 (81)
T PRK11130 30 ALRQHLAQKGDRW-----ALALEDGKLLAAVNQTLV-SFDHPLTDGDEVAFFP 76 (81)
T ss_pred HHHHHHHHhCccH-----HhhhcCCCEEEEECCEEc-CCCCCCCCCCEEEEeC
Confidence 3445555554332 22333443 77899888 4788999999999854
No 89
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=62.75 E-value=9.1 Score=36.28 Aligned_cols=40 Identities=25% Similarity=0.212 Sum_probs=29.6
Q ss_pred HHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeecccee
Q 026355 73 LDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNV 112 (240)
Q Consensus 73 Ldk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L 112 (240)
+-..|......-||++++++|..|.|++||.++...+..+
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 3333444333679999999999999999999997655433
No 90
>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=62.66 E-value=10 Score=27.41 Aligned_cols=26 Identities=27% Similarity=0.376 Sum_probs=20.2
Q ss_pred CceEECCEEeeeccc--eecCCCEEEEEe
Q 026355 96 GLVSINGQVVSKVSH--NVKGGDMVNCTI 122 (240)
Q Consensus 96 G~V~VNG~~v~~~~~--~L~~GD~I~v~~ 122 (240)
-.|.|||+.+. ... .|+.||+|.+-.
T Consensus 56 ~~v~vN~~~v~-~~~~~~l~dgdev~i~P 83 (88)
T TIGR01687 56 VIILVNGRNVD-WGLGTELKDGDVVAIFP 83 (88)
T ss_pred EEEEECCEecC-ccCCCCCCCCCEEEEeC
Confidence 35789999995 344 899999998753
No 91
>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=62.36 E-value=18 Score=33.86 Aligned_cols=39 Identities=23% Similarity=0.254 Sum_probs=33.3
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeec
Q 026355 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKV 108 (240)
Q Consensus 70 g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~ 108 (240)
+.++.+++.......|++.++++|+.|.|+||+..++..
T Consensus 329 ~~~~~~~~~~~~~~~S~~~arr~ik~g~v~vn~~~i~~~ 367 (377)
T TIGR00234 329 DITLADLLVLSGLFPSKSEARRDIKQGGVYINGEKVTDL 367 (377)
T ss_pred CcCHHHHHHHcCCCcChHHHHHHHHhCCEEECCEeccCc
Confidence 478888888765567999999999999999999998643
No 92
>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=61.83 E-value=10 Score=25.78 Aligned_cols=24 Identities=33% Similarity=0.652 Sum_probs=19.5
Q ss_pred ceEECCEEeeeccceecCCCEEEEE
Q 026355 97 LVSINGQVVSKVSHNVKGGDMVNCT 121 (240)
Q Consensus 97 ~V~VNG~~v~~~~~~L~~GD~I~v~ 121 (240)
...|||+.+ ..++.|..||+|+|.
T Consensus 36 ~A~Vng~~v-dl~~~L~~~d~v~ii 59 (60)
T PF02824_consen 36 AAKVNGQLV-DLDHPLEDGDVVEII 59 (60)
T ss_dssp EEEETTEEE-ETTSBB-SSEEEEEE
T ss_pred EEEEcCEEC-CCCCCcCCCCEEEEE
Confidence 357999999 589999999999873
No 93
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=61.68 E-value=8.8 Score=29.40 Aligned_cols=38 Identities=18% Similarity=0.231 Sum_probs=31.7
Q ss_pred HHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 86 RARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 86 R~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
+...-.+|.+|+=+|.++..+.--.++++||.|.+++.
T Consensus 8 ~eeylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~~~ 45 (111)
T COG4043 8 REEYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFNGD 45 (111)
T ss_pred HHHHHHHHHcccceEEEEecCHhhcCCCCCCEEEEcCC
Confidence 45667899999999999888766778999999998753
No 94
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=60.80 E-value=9.8 Score=26.89 Aligned_cols=43 Identities=19% Similarity=0.390 Sum_probs=31.9
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeee---ccceecCCCEEEEE
Q 026355 70 KLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCT 121 (240)
Q Consensus 70 g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~---~~~~L~~GD~I~v~ 121 (240)
+.++..+|++. .++- +.=.|.+||..+-+ ..+.|+.||+|+|-
T Consensus 17 ~~tv~dLL~~l--~~~~-------~~vav~vNg~iVpr~~~~~~~l~~gD~ievv 62 (68)
T COG2104 17 GTTVADLLAQL--GLNP-------EGVAVAVNGEIVPRSQWADTILKEGDRIEVV 62 (68)
T ss_pred CCcHHHHHHHh--CCCC-------ceEEEEECCEEccchhhhhccccCCCEEEEE
Confidence 38899999986 2332 22247789999943 78899999999884
No 95
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=60.53 E-value=10 Score=25.72 Aligned_cols=44 Identities=16% Similarity=0.280 Sum_probs=31.2
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeec---cceecCCCEEEEEe
Q 026355 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKV---SHNVKGGDMVNCTI 122 (240)
Q Consensus 69 ~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~---~~~L~~GD~I~v~~ 122 (240)
++.++..+|... .... .-.|.+||..+.+. ...|+.||+|+|..
T Consensus 14 ~~~tl~~ll~~l--~~~~--------~~~v~vN~~~v~~~~~~~~~L~~gD~vei~~ 60 (65)
T PRK06944 14 DGATVADALAAY--GARP--------PFAVAVNGDFVARTQHAARALAAGDRLDLVQ 60 (65)
T ss_pred CCCcHHHHHHhh--CCCC--------CeEEEECCEEcCchhcccccCCCCCEEEEEe
Confidence 467888888865 2221 12588999998532 67899999999854
No 96
>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=59.09 E-value=12 Score=25.55 Aligned_cols=45 Identities=29% Similarity=0.446 Sum_probs=31.7
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeee---ccceecCCCEEEEEe
Q 026355 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCTI 122 (240)
Q Consensus 69 ~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~---~~~~L~~GD~I~v~~ 122 (240)
++.++.++|... .+.. ..-.|.+||+.+.+ ..+.|+.||+|.+-.
T Consensus 12 ~~~tv~~ll~~l--~~~~-------~~v~v~vN~~iv~~~~~~~~~L~~gD~veii~ 59 (64)
T TIGR01683 12 DGLTLAALLESL--GLDP-------RRVAVAVNGEIVPRSEWDDTILKEGDRIEIVT 59 (64)
T ss_pred CCCcHHHHHHHc--CCCC-------CeEEEEECCEEcCHHHcCceecCCCCEEEEEE
Confidence 357899988875 2332 33357899999953 346899999998854
No 97
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=58.64 E-value=11 Score=25.77 Aligned_cols=43 Identities=16% Similarity=0.210 Sum_probs=29.9
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeee---ccceecCCCEEEEEe
Q 026355 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCTI 122 (240)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~---~~~~L~~GD~I~v~~ 122 (240)
.++..+|... .+.... =.|-+|++.+.+ .+..|+.||+|++-.
T Consensus 15 ~tl~~Ll~~l--~~~~~~-------vavavN~~iv~~~~~~~~~L~dgD~Ieiv~ 60 (65)
T PRK06488 15 TTLALLLAEL--DYEGNW-------LATAVNGELVHKEARAQFVLHEGDRIEILS 60 (65)
T ss_pred CcHHHHHHHc--CCCCCe-------EEEEECCEEcCHHHcCccccCCCCEEEEEE
Confidence 5788888765 222211 138899999954 377899999999854
No 98
>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=55.37 E-value=13 Score=25.07 Aligned_cols=26 Identities=23% Similarity=0.355 Sum_probs=18.2
Q ss_pred cCceEECCEEeee-ccceecCCCEEEE
Q 026355 95 SGLVSINGQVVSK-VSHNVKGGDMVNC 120 (240)
Q Consensus 95 ~G~V~VNG~~v~~-~~~~L~~GD~I~v 120 (240)
...++|||+++.. ....|+.||+|.+
T Consensus 41 ~ngt~vng~~l~~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 41 TNGTFVNGQRLGPGEPVPLKDGDIIRF 67 (68)
T ss_dssp SS-EEETTEEESSTSEEEE-TTEEEEE
T ss_pred CCcEEECCEEcCCCCEEECCCCCEEEc
Confidence 4568899999853 2577889998875
No 99
>PRK07440 hypothetical protein; Provisional
Probab=54.94 E-value=16 Score=25.67 Aligned_cols=46 Identities=17% Similarity=0.274 Sum_probs=32.2
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeee---ccceecCCCEEEEEe
Q 026355 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCTI 122 (240)
Q Consensus 68 ~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~---~~~~L~~GD~I~v~~ 122 (240)
.++++|.++|.+. .+..+ .=.|-+||+.+.+ .+..|+.||.|+|-.
T Consensus 17 ~~~~tl~~lL~~l--~~~~~-------~vav~~N~~iv~r~~w~~~~L~~gD~IEIv~ 65 (70)
T PRK07440 17 SSGTSLPDLLQQL--GFNPR-------LVAVEYNGEILHRQFWEQTQVQPGDRLEIVT 65 (70)
T ss_pred CCCCCHHHHHHHc--CCCCC-------eEEEEECCEEeCHHHcCceecCCCCEEEEEE
Confidence 3468899998865 23222 1247789999942 678899999998853
No 100
>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=51.53 E-value=29 Score=25.84 Aligned_cols=26 Identities=23% Similarity=0.164 Sum_probs=20.7
Q ss_pred ceEECCEEee---eccceecCCCEEEEEe
Q 026355 97 LVSINGQVVS---KVSHNVKGGDMVNCTI 122 (240)
Q Consensus 97 ~V~VNG~~v~---~~~~~L~~GD~I~v~~ 122 (240)
.|.|||..+. ..++.|+.||+|.+..
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 5788998874 3578999999998854
No 101
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=49.08 E-value=21 Score=24.49 Aligned_cols=45 Identities=16% Similarity=0.259 Sum_probs=30.3
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeee---ccceecCCCEEEEEe
Q 026355 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCTI 122 (240)
Q Consensus 69 ~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~---~~~~L~~GD~I~v~~ 122 (240)
++.+|..+|... . .... .=.|-+|++.+.+ ....|+.||.|++-.
T Consensus 14 ~~~tl~~ll~~l-~-~~~~-------~vaVavN~~iv~r~~w~~~~L~~gD~Ieii~ 61 (66)
T PRK08053 14 AGQTVHELLEQL-N-QLQP-------GAALAINQQIIPREQWAQHIVQDGDQILLFQ 61 (66)
T ss_pred CCCCHHHHHHHc-C-CCCC-------cEEEEECCEEeChHHcCccccCCCCEEEEEE
Confidence 357788888764 2 2211 1247789999852 456799999998853
No 102
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=46.47 E-value=22 Score=24.66 Aligned_cols=43 Identities=14% Similarity=0.203 Sum_probs=29.0
Q ss_pred chHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeee---ccceecCCCEEEEEe
Q 026355 71 LRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCTI 122 (240)
Q Consensus 71 ~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~---~~~~L~~GD~I~v~~ 122 (240)
.++.++|... .+.... =.|-+||+.+.+ ....|+.||.|+|-.
T Consensus 17 ~tv~~lL~~l--~~~~~~-------vav~vN~~iv~r~~w~~~~L~~gD~iEIv~ 62 (67)
T PRK07696 17 KTVAELLTHL--ELDNKI-------VVVERNKDILQKDDHTDTSVFDGDQIEIVT 62 (67)
T ss_pred ccHHHHHHHc--CCCCCe-------EEEEECCEEeCHHHcCceecCCCCEEEEEE
Confidence 4688888764 232111 147889999943 347899999998743
No 103
>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=42.34 E-value=13 Score=27.11 Aligned_cols=62 Identities=18% Similarity=0.013 Sum_probs=40.9
Q ss_pred EEEEEE--cCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEE
Q 026355 59 QLEETV--DTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNC 120 (240)
Q Consensus 59 ~~~~~V--~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v 120 (240)
++.+.+ +..+.=..|.+-+++.++...-..-+++|-+|+|.-|...+......+..|..|.+
T Consensus 13 ~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GKiLkD~~tL~~~~~~~~~~~tiHL 76 (79)
T cd01790 13 YEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGKLLPDHLKLRDVLRKQDEYHMVHL 76 (79)
T ss_pred eEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCeeccchhhHHHHhhcccCCceEEE
Confidence 444445 55555556777777765433445668999999999888877544334666666654
No 104
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=41.04 E-value=31 Score=25.32 Aligned_cols=46 Identities=22% Similarity=0.240 Sum_probs=31.9
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeee---ccceecCCCEEEEEe
Q 026355 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK---VSHNVKGGDMVNCTI 122 (240)
Q Consensus 68 ~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~---~~~~L~~GD~I~v~~ 122 (240)
.++..|..+|... .+....+ .|-+||..+.+ .+..|+.||+|+|-.
T Consensus 31 ~~~~tl~~LL~~l--~~~~~~v-------AVevNg~iVpr~~w~~t~L~egD~IEIv~ 79 (84)
T PRK06083 31 DISSSLAQIIAQL--SLPELGC-------VFAINNQVVPRSEWQSTVLSSGDAISLFQ 79 (84)
T ss_pred CCCCcHHHHHHHc--CCCCceE-------EEEECCEEeCHHHcCcccCCCCCEEEEEE
Confidence 3467899988864 3332221 47899999843 567799999998843
No 105
>KOG4837 consensus Uncharacterized conserved protein [Function unknown]
Probab=39.73 E-value=30 Score=30.00 Aligned_cols=54 Identities=22% Similarity=0.271 Sum_probs=46.4
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 69 ~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
...|.|.+|..-+ ++.|+.+.-+.-++.+++|+....+.+.+|..||.+-+..-
T Consensus 138 ~sfr~d~llK~Gl-gv~rnKVel~fye~e~R~N~~Kl~kkS~~i~vgds~d~~ig 191 (248)
T KOG4837|consen 138 VSFRVDALLKVGL-GVTRNKVELLFYEYEPRTNSFKLVKKSLRIDVGDSADFKIG 191 (248)
T ss_pred HHHHHHHHHHhcc-ccccchhhHhhhhcccccCcccccccceeeecccccceeee
Confidence 4568888888764 78999999999999999999988889999999998876543
No 106
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=39.43 E-value=46 Score=31.67 Aligned_cols=39 Identities=18% Similarity=0.109 Sum_probs=32.3
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeee
Q 026355 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSK 107 (240)
Q Consensus 69 ~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~ 107 (240)
.++.+-+.+...-..-|+.++.++|.+|.|+||+++++.
T Consensus 397 ~~~s~~~l~~ka~~~~s~~~a~r~i~qG~vslnh~~v~~ 435 (467)
T KOG2623|consen 397 PGVSILDLLRKASRFPSGKEARRMIQQGGVSLNHEKVRD 435 (467)
T ss_pred CCCcHHHHHHHhhcCCCcHHHHHHHHccceeecCccccC
Confidence 577788888876444588899999999999999999964
No 107
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=37.91 E-value=8.7 Score=26.16 Aligned_cols=63 Identities=21% Similarity=0.265 Sum_probs=42.9
Q ss_pred CceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 56 AGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 56 ~~~~~~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
.|..+...+...+.-..|.+.++... +++... ++++-+|++.-|...+ ..+.|+.|++|.+..
T Consensus 4 ~g~~~~~~v~~~~tV~~lK~~i~~~~-~~~~~~-~~L~~~G~~L~d~~tL--~~~~i~~~~~I~l~~ 66 (69)
T PF00240_consen 4 SGKTFTLEVDPDDTVADLKQKIAEET-GIPPEQ-QRLIYNGKELDDDKTL--SDYGIKDGSTIHLVI 66 (69)
T ss_dssp TSEEEEEEEETTSBHHHHHHHHHHHH-TSTGGG-EEEEETTEEESTTSBT--GGGTTSTTEEEEEEE
T ss_pred CCcEEEEEECCCCCHHHhhhhccccc-cccccc-ceeeeeeecccCcCcH--HHcCCCCCCEEEEEE
Confidence 35678888888888788888888875 344433 4455556555444444 467888999887754
No 108
>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=27.31 Aligned_cols=52 Identities=21% Similarity=0.256 Sum_probs=25.3
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 69 ~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
+|.++.+.+... ++-...=.--+...+|=|=|+.+ +.++.|+.||+|+|+.+
T Consensus 22 ~GtTv~~Ai~~S--gi~~~~p~idl~~~~vGIfGk~~-~~d~~L~~GDRVEIYRP 73 (84)
T PF03658_consen 22 EGTTVAQAIEAS--GILEQFPEIDLEKNKVGIFGKLV-KLDTVLRDGDRVEIYRP 73 (84)
T ss_dssp TT-BHHHHHHHH--THHHH-TT--TTTSEEEEEE-S---TT-B--TT-EEEEE-S
T ss_pred CcCcHHHHHHHc--CchhhCcccCcccceeeeeeeEc-CCCCcCCCCCEEEEecc
Confidence 456666666543 12111111123456677779999 58999999999999874
No 109
>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=37.28 E-value=16 Score=30.72 Aligned_cols=25 Identities=24% Similarity=0.270 Sum_probs=18.6
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcC
Q 026355 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177 (240)
Q Consensus 145 ~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~ 177 (240)
-++++|||.||-+|. +++.+.+.+.
T Consensus 3 g~l~i~Kp~g~tS~~--------~v~~~k~~~~ 27 (182)
T cd02572 3 GVINLDKPSGPSSHE--------VVAWIKRILG 27 (182)
T ss_pred eEEEEecCCCCCHHH--------HHHHHHHHhC
Confidence 589999999988653 5666666554
No 110
>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=37.08 E-value=31 Score=24.77 Aligned_cols=47 Identities=17% Similarity=0.151 Sum_probs=30.2
Q ss_pred cchHHHHHHhccCCCCHHHHHHHHHc---C-ceEECCEEeeeccceecCCCEEEEE
Q 026355 70 KLRLDAWISSRIDGISRARVQSSIRS---G-LVSINGQVVSKVSHNVKGGDMVNCT 121 (240)
Q Consensus 70 g~RLdk~L~~~~~~~SR~~~~klI~~---G-~V~VNG~~v~~~~~~L~~GD~I~v~ 121 (240)
|.++.++.... .+.....+.-+ | .+..+|+.+ ..++.|+.||+|+|.
T Consensus 24 GaTV~D~a~~i----H~di~~~f~~A~v~g~s~~~~gq~V-gl~~~L~d~DvVeI~ 74 (75)
T cd01666 24 GSTVEDVCNKI----HKDLVKQFKYALVWGSSVKHSPQRV-GLDHVLEDEDVVQIV 74 (75)
T ss_pred CCCHHHHHHHH----HHHHHHhCCeeEEeccCCcCCCeEC-CCCCEecCCCEEEEe
Confidence 66777766643 23333332221 2 234699999 589999999999874
No 111
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=35.64 E-value=20 Score=25.34 Aligned_cols=62 Identities=8% Similarity=0.024 Sum_probs=42.5
Q ss_pred ceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 57 GVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 57 ~~~~~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
|..+...+.+...=.-|.+.+++.+ .++... +++|..|++.-|+..+ .++.|+.|+.|.++.
T Consensus 11 Gk~~~~~v~~~~TV~~LK~~I~~~~-~~~~~~-qrLi~~Gk~L~D~~tL--~~ygi~~~stv~l~~ 72 (73)
T cd01791 11 GKKVRVKCNPDDTIGDLKKLIAAQT-GTRPEK-IVLKKWYTIFKDHISL--GDYEIHDGMNLELYY 72 (73)
T ss_pred CCEEEEEeCCCCcHHHHHHHHHHHh-CCChHH-EEEEeCCcCCCCCCCH--HHcCCCCCCEEEEEe
Confidence 4456666666555566777777765 455554 5777788887777655 467899999988764
No 112
>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=33.75 E-value=53 Score=21.21 Aligned_cols=44 Identities=23% Similarity=0.292 Sum_probs=27.5
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEE
Q 026355 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNC 120 (240)
Q Consensus 69 ~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v 120 (240)
.+..+.++++.....+++ ..-.+.+||+.+. .++.+..||.|.+
T Consensus 15 ~~~t~~~~~~~~~~~~~~-------~~va~~vng~~vd-l~~~l~~~~~ve~ 58 (60)
T cd01668 15 AGATVLDFAYAIHTEIGN-------RCVGAKVNGKLVP-LSTVLKDGDIVEI 58 (60)
T ss_pred CCCCHHHHHHHHChHhhh-------heEEEEECCEECC-CCCCCCCCCEEEE
Confidence 455666666543211111 1123669999994 7788999998875
No 113
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase.
Probab=32.97 E-value=14 Score=25.50 Aligned_cols=15 Identities=20% Similarity=0.160 Sum_probs=12.1
Q ss_pred Cceeccccccccccc
Q 026355 1 MTMLSLNSASWGSAS 15 (240)
Q Consensus 1 ~~~~~~~~~~~~~~~ 15 (240)
++|.+..+|++|+.-
T Consensus 1 v~ly~~~~Cp~C~~a 15 (72)
T TIGR02194 1 ITVYSKNNCVQCKMT 15 (72)
T ss_pred CEEEeCCCCHHHHHH
Confidence 577888899999864
No 114
>PF14478 DUF4430: Domain of unknown function (DUF4430); PDB: 3U7Z_B 2BB5_A.
Probab=32.81 E-value=44 Score=23.02 Aligned_cols=23 Identities=26% Similarity=0.372 Sum_probs=13.7
Q ss_pred eEECCEEeee--ccceecCCCEEEE
Q 026355 98 VSINGQVVSK--VSHNVKGGDMVNC 120 (240)
Q Consensus 98 V~VNG~~v~~--~~~~L~~GD~I~v 120 (240)
..|||+.++. ..++|+.||.|.+
T Consensus 43 ~~vNG~~~~~ga~~~~l~~GD~i~~ 67 (68)
T PF14478_consen 43 YYVNGESANVGAGSYKLKDGDKITW 67 (68)
T ss_dssp EEETTEE-SS-CCC-B--TTEEEEE
T ss_pred EEECCEEhhcCcceeEeCCCCEEEe
Confidence 5678887643 4677888898875
No 115
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=32.45 E-value=46 Score=22.76 Aligned_cols=21 Identities=33% Similarity=0.316 Sum_probs=13.7
Q ss_pred EECCEEeeeccceecCCCEEEE
Q 026355 99 SINGQVVSKVSHNVKGGDMVNC 120 (240)
Q Consensus 99 ~VNG~~v~~~~~~L~~GD~I~v 120 (240)
-+||=++ +.+..|++||.|.+
T Consensus 33 I~NGF~~-~~d~~L~e~D~v~~ 53 (57)
T PF14453_consen 33 ILNGFPT-KEDIELKEGDEVFL 53 (57)
T ss_pred EEcCccc-CCccccCCCCEEEE
Confidence 3577666 45677777776655
No 116
>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=32.37 E-value=21 Score=30.76 Aligned_cols=24 Identities=25% Similarity=0.324 Sum_probs=17.8
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcC
Q 026355 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177 (240)
Q Consensus 146 ~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~ 177 (240)
++++|||.|+-+|. +++.+.+.+.
T Consensus 2 il~i~KP~g~tS~~--------vv~~ik~~~~ 25 (210)
T cd00506 2 LFAVDKPQGPSSHD--------VVDTIRRIFL 25 (210)
T ss_pred EEEEEcCCCCCHHH--------HHHHHHHHhC
Confidence 78999999988653 5666666553
No 117
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=32.18 E-value=33 Score=23.81 Aligned_cols=62 Identities=13% Similarity=0.183 Sum_probs=43.5
Q ss_pred ceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 57 GVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 57 ~~~~~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
|..+...|...+.-.-|.+.+++.. +++-.. ++++-+|++.-|+..+ .++.|++|+.|.+..
T Consensus 10 G~~~~l~v~~~~tV~~lK~~i~~~~-gi~~~~-q~L~~~G~~L~d~~~L--~~~~i~~~~~l~l~~ 71 (74)
T cd01807 10 GRECSLQVSEKESVSTLKKLVSEHL-NVPEEQ-QRLLFKGKALADDKRL--SDYSIGPNAKLNLVV 71 (74)
T ss_pred CCEEEEEECCCCcHHHHHHHHHHHH-CCCHHH-eEEEECCEECCCCCCH--HHCCCCCCCEEEEEE
Confidence 4456666776666566777777664 455544 7778888888888766 468899999887754
No 118
>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=31.97 E-value=61 Score=25.20 Aligned_cols=23 Identities=30% Similarity=0.446 Sum_probs=16.7
Q ss_pred cCceEECCEEeeeccceecCCCEEEEE
Q 026355 95 SGLVSINGQVVSKVSHNVKGGDMVNCT 121 (240)
Q Consensus 95 ~G~V~VNG~~v~~~~~~L~~GD~I~v~ 121 (240)
.|.|.+||.. .+.+++||+|.|-
T Consensus 65 Sg~I~lNGAA----Ar~~~~GD~vII~ 87 (111)
T cd06919 65 SGVICLNGAA----ARLGQPGDRVIIM 87 (111)
T ss_pred CCEEEeCCHH----HhcCCCCCEEEEE
Confidence 4677888844 4668899988774
No 119
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=31.76 E-value=23 Score=31.87 Aligned_cols=25 Identities=24% Similarity=0.434 Sum_probs=18.6
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcC
Q 026355 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177 (240)
Q Consensus 145 ~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~ 177 (240)
-++++|||+||-+|. +++.+.+.+.
T Consensus 3 gil~vdKP~g~tS~~--------vv~~ikk~~~ 27 (273)
T PRK04099 3 RLFVANKPAGMSSNA--------FLSRLKRKYG 27 (273)
T ss_pred eEEEEeCCCCCCHHH--------HHHHHHHHhC
Confidence 589999999988653 5666666553
No 120
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=31.75 E-value=22 Score=32.05 Aligned_cols=24 Identities=8% Similarity=0.245 Sum_probs=17.4
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcC
Q 026355 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177 (240)
Q Consensus 146 ~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~ 177 (240)
++++|||.|+-+|. +++.+.+.+.
T Consensus 2 il~i~KP~G~tS~d--------vv~~vrr~~~ 25 (279)
T PRK02193 2 IKLLYKPKGISSFK--------FIKNFAKTNN 25 (279)
T ss_pred EEEEECCCCCCHHH--------HHHHHHHHcC
Confidence 78999999988653 5556665553
No 121
>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=31.47 E-value=41 Score=23.59 Aligned_cols=66 Identities=15% Similarity=0.215 Sum_probs=44.4
Q ss_pred CCCceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 54 NYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 54 ~~~~~~~~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
+..|..+...++..+.-..|..-|.... +++-.. ++++-.|++.-|.+.+ ..+.|..|+.|.+...
T Consensus 4 ~l~g~~~~l~v~~~~TV~~lK~~i~~~~-gip~~~-q~L~~~G~~L~d~~tL--~~~~i~~g~~l~v~~~ 69 (76)
T cd01800 4 KLNGQMLNFTLQLSDPVSVLKVKIHEET-GMPAGK-QKLQYEGIFIKDSNSL--AYYNLANGTIIHLQLK 69 (76)
T ss_pred ccCCeEEEEEECCCCcHHHHHHHHHHHH-CCCHHH-EEEEECCEEcCCCCcH--HHcCCCCCCEEEEEEe
Confidence 3456778888877666666666666653 455544 6677777766666555 4688999999887653
No 122
>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=31.45 E-value=23 Score=30.58 Aligned_cols=25 Identities=20% Similarity=0.315 Sum_probs=18.0
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcC
Q 026355 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177 (240)
Q Consensus 145 ~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~ 177 (240)
-++++|||.|+-+|. +++.+.+.+.
T Consensus 3 G~l~v~KP~g~tS~~--------vv~~vkk~~~ 27 (209)
T TIGR00431 3 GVLLLDKPQGMTSFD--------ALAKVRRLLN 27 (209)
T ss_pred eEEEEECCCCCCHHH--------HHHHHHHHhC
Confidence 489999999988642 5666666553
No 123
>cd01616 TGS The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=31.44 E-value=62 Score=20.14 Aligned_cols=22 Identities=36% Similarity=0.599 Sum_probs=18.0
Q ss_pred eEECCEEeeeccceecCCCEEEE
Q 026355 98 VSINGQVVSKVSHNVKGGDMVNC 120 (240)
Q Consensus 98 V~VNG~~v~~~~~~L~~GD~I~v 120 (240)
+.+||+.+. .++.|..||.|++
T Consensus 37 ~~vn~~~~~-l~~~l~~~~~i~~ 58 (60)
T cd01616 37 ALVNGQLVD-LSYTLQDGDTVSI 58 (60)
T ss_pred EEECCEECC-CCcCcCCCCEEEE
Confidence 468999984 7888999998875
No 124
>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=30.52 E-value=68 Score=23.41 Aligned_cols=47 Identities=13% Similarity=0.204 Sum_probs=28.7
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEecc
Q 026355 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISE 124 (240)
Q Consensus 69 ~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~~ 124 (240)
.|.+|..++.+. ++|.+.+.+++.... +++ .-.+|+|||.|.+....
T Consensus 9 ~GDtLs~iF~~~--gls~~dl~~v~~~~~---~~k----~L~~L~pGq~l~f~~d~ 55 (85)
T PF04225_consen 9 SGDTLSTIFRRA--GLSASDLYAVLEADG---EAK----PLTRLKPGQTLEFQLDE 55 (85)
T ss_dssp TT--HHHHHHHT--T--HHHHHHHHHHGG---GT------GGG--TT-EEEEEE-T
T ss_pred CCCcHHHHHHHc--CCCHHHHHHHHhccC---ccc----hHhhCCCCCEEEEEECC
Confidence 467799888886 799999999998653 233 33569999999997754
No 125
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=30.22 E-value=24 Score=32.17 Aligned_cols=25 Identities=28% Similarity=0.335 Sum_probs=18.4
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcC
Q 026355 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177 (240)
Q Consensus 145 ~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~ 177 (240)
-++++|||.||-+|- +++.+.+.+.
T Consensus 3 Gil~i~KP~G~TS~d--------vv~~vrr~~~ 27 (304)
T PRK01550 3 GVLLLHKPRGMTSHD--------CVFKLRKILR 27 (304)
T ss_pred eEEEEECCCCCCHHH--------HHHHHHHHcC
Confidence 489999999988653 5666666554
No 126
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=29.26 E-value=39 Score=23.11 Aligned_cols=62 Identities=18% Similarity=0.329 Sum_probs=39.4
Q ss_pred ceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 57 GVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 57 ~~~~~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
|..++..++....-..|.+.+.+.. +++-.. ++++-.|++.-|...+ ..+.+..|+.|.+..
T Consensus 10 g~~~~~~v~~~~tv~~lK~~i~~~~-g~~~~~-qrL~~~g~~L~d~~tl--~~~~i~~g~~i~l~~ 71 (76)
T cd01806 10 GKEIEIDIEPTDKVERIKERVEEKE-GIPPQQ-QRLIYSGKQMNDDKTA--ADYKLEGGSVLHLVL 71 (76)
T ss_pred CCEEEEEECCCCCHHHHHHHHhHhh-CCChhh-EEEEECCeEccCCCCH--HHcCCCCCCEEEEEE
Confidence 4456667776666666777776664 444443 4555566665555544 467888899888755
No 127
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=29.18 E-value=80 Score=25.13 Aligned_cols=23 Identities=35% Similarity=0.601 Sum_probs=16.7
Q ss_pred cCceEECCEEeeeccceecCCCEEEEE
Q 026355 95 SGLVSINGQVVSKVSHNVKGGDMVNCT 121 (240)
Q Consensus 95 ~G~V~VNG~~v~~~~~~L~~GD~I~v~ 121 (240)
.|.|.+||.. .+.+++||+|.|-
T Consensus 66 Sg~I~lNGAA----Ar~~~~GD~vII~ 88 (126)
T PRK05449 66 SGVICLNGAA----ARLVQVGDLVIIA 88 (126)
T ss_pred CCEEEeCCHH----HhcCCCCCEEEEE
Confidence 4668888844 4668899988774
No 128
>PRK02253 deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional
Probab=28.82 E-value=1.8e+02 Score=23.77 Aligned_cols=39 Identities=18% Similarity=0.206 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHcCceEECC------EEeeeccceecCCCEEEEE
Q 026355 83 GISRARVQSSIRSGLVSING------QVVSKVSHNVKGGDMVNCT 121 (240)
Q Consensus 83 ~~SR~~~~klI~~G~V~VNG------~~v~~~~~~L~~GD~I~v~ 121 (240)
.+|.++++++|.+|.+.++. ..+...+.-|+.|+...+.
T Consensus 2 iLs~~~I~~~i~~g~i~i~p~~~~~~~qiqp~svDlrlg~~~~~~ 46 (167)
T PRK02253 2 LLSKEELRKLIRSGKFVAEHVVDLEDDQVQPNGVDLTLGEVEEQE 46 (167)
T ss_pred cCCHHHHHHHHHcCCeEeecCCCCChhhCCCcEEEEECCcEEEEe
Confidence 36899999999999999852 3454567778888877664
No 129
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=28.50 E-value=27 Score=31.65 Aligned_cols=25 Identities=24% Similarity=0.305 Sum_probs=18.4
Q ss_pred cEEEEeCCCCceeecCCCCCCCcHHHHHHhhcC
Q 026355 145 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177 (240)
Q Consensus 145 ~~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~ 177 (240)
-++++|||.|+-+|- +++.+.+.+.
T Consensus 3 Gil~i~KP~G~tS~d--------vv~~vrr~~~ 27 (290)
T PRK00130 3 GILNILKPPGMTSFD--------VVRKIRKIAK 27 (290)
T ss_pred eEEEEeCCCCCCHHH--------HHHHHHHHhC
Confidence 589999999988653 5666666554
No 130
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=27.27 E-value=50 Score=33.64 Aligned_cols=25 Identities=16% Similarity=0.260 Sum_probs=20.3
Q ss_pred EECCEEeeeccceecCCCEEEEEecc
Q 026355 99 SINGQVVSKVSHNVKGGDMVNCTISE 124 (240)
Q Consensus 99 ~VNG~~v~~~~~~L~~GD~I~v~~~~ 124 (240)
+|||+.+ ..+++|+.||+|+|-...
T Consensus 425 kVNg~~v-pL~~~L~~Gd~VeIiT~~ 449 (702)
T PRK11092 425 RVDRQPY-PLSQPLTSGQTVEIITAP 449 (702)
T ss_pred EECCEEC-CCCccCCCCCEEEEEeCC
Confidence 4488888 589999999999997543
No 131
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=26.09 E-value=67 Score=22.21 Aligned_cols=62 Identities=21% Similarity=0.267 Sum_probs=40.3
Q ss_pred CceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCE-EeeeccceecCCCEEEEE
Q 026355 56 AGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQ-VVSKVSHNVKGGDMVNCT 121 (240)
Q Consensus 56 ~~~~~~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~-~v~~~~~~L~~GD~I~v~ 121 (240)
.|.++...+.....=..|...+++.. +++-.. ++++-.|++.-|+. .+ ..+.++.|+.|.+.
T Consensus 8 ~g~~~~l~v~~~~TV~~lK~~I~~~~-gip~~~-q~Li~~Gk~L~D~~~~L--~~~gi~~~~~l~l~ 70 (71)
T cd01796 8 SETTFSLDVDPDLELENFKALCEAES-GIPASQ-QQLIYNGRELVDNKRLL--ALYGVKDGDLVVLR 70 (71)
T ss_pred CCCEEEEEECCcCCHHHHHHHHHHHh-CCCHHH-eEEEECCeEccCCcccH--HHcCCCCCCEEEEe
Confidence 34556666766555556777777764 455544 67777777776653 33 35778899988763
No 132
>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=25.90 E-value=32 Score=30.95 Aligned_cols=24 Identities=25% Similarity=0.488 Sum_probs=17.4
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcC
Q 026355 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177 (240)
Q Consensus 146 ~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~ 177 (240)
++++|||.||-+|- +++.+.+.+.
T Consensus 2 il~i~KP~G~tS~~--------vv~~vr~~~~ 25 (277)
T cd02573 2 ILLLDKPAGLTSHD--------VVQKVRRLLG 25 (277)
T ss_pred EEEEECCCCCCHHH--------HHHHHHHHhC
Confidence 78999999988653 5566665553
No 133
>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=25.83 E-value=1e+02 Score=24.58 Aligned_cols=23 Identities=30% Similarity=0.502 Sum_probs=16.8
Q ss_pred cCceEECCEEeeeccceecCCCEEEEE
Q 026355 95 SGLVSINGQVVSKVSHNVKGGDMVNCT 121 (240)
Q Consensus 95 ~G~V~VNG~~v~~~~~~L~~GD~I~v~ 121 (240)
.|.|.+||.. .+.+++||+|.|-
T Consensus 66 Sg~I~lNGAA----Arl~~~GD~VII~ 88 (126)
T TIGR00223 66 SRIICVNGAA----ARCVSVGDIVIIA 88 (126)
T ss_pred CCEEEeCCHH----HhcCCCCCEEEEE
Confidence 4668888844 4668899988774
No 134
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=25.27 E-value=33 Score=31.41 Aligned_cols=24 Identities=29% Similarity=0.391 Sum_probs=17.8
Q ss_pred EEEEeCCCCceeecCCCCCCCcHHHHHHhhcC
Q 026355 146 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177 (240)
Q Consensus 146 ~lvvnKPaGl~v~p~~~~~~~Tl~~~L~~~~~ 177 (240)
++++|||.|+-+|- +++.+.+.+.
T Consensus 3 il~idKP~G~TS~d--------vv~~vrr~l~ 26 (312)
T PRK14122 3 VYAVDKPLGLTSHD--------VVNRARRALG 26 (312)
T ss_pred EEEEECCCCCCHHH--------HHHHHHHHhC
Confidence 79999999988653 5666666554
No 135
>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=25.10 E-value=32 Score=23.72 Aligned_cols=16 Identities=25% Similarity=0.401 Sum_probs=10.9
Q ss_pred CCcEEEEeCCCCceee
Q 026355 143 DDNVLVVNKPAHMVVH 158 (240)
Q Consensus 143 d~~~lvvnKPaGl~v~ 158 (240)
..-+|.+|||+|=-+|
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 3569999999995554
No 136
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=25.09 E-value=66 Score=32.82 Aligned_cols=25 Identities=28% Similarity=0.555 Sum_probs=21.1
Q ss_pred eEECCEEeeeccceecCCCEEEEEec
Q 026355 98 VSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 98 V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
.+|||+.+ ..+++|+.||+|+|...
T Consensus 425 AkVnG~iv-pl~~~Lk~Gd~VEIit~ 449 (701)
T COG0317 425 AKVNGRIV-PLTTKLQTGDQVEIITS 449 (701)
T ss_pred EEECCEEe-ccceecCCCCEEEEEeC
Confidence 56799888 68999999999998654
No 137
>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=24.78 E-value=45 Score=23.16 Aligned_cols=62 Identities=15% Similarity=0.023 Sum_probs=41.7
Q ss_pred ceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 57 GVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 57 ~~~~~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
|.++...|.....-..|.+-+.... +++... ++++.+|++.-|++.+. ++.++.|+.|.+..
T Consensus 8 g~~~~l~v~~~~tV~~lK~~I~~~~-gi~~~~-q~L~~~G~~L~D~~tL~--~~~i~~~~tl~l~~ 69 (74)
T cd01810 8 GRSSIYEVQLTQTVATLKQQVSQRE-RVQADQ-FWLSFEGRPMEDEHPLG--EYGLKPGCTVFMNL 69 (74)
T ss_pred CCEEEEEECCcChHHHHHHHHHHHh-CCCHHH-eEEEECCEECCCCCCHH--HcCCCCCCEEEEEE
Confidence 4456666766555455666666553 454443 57778888888887773 58899999888765
No 138
>COG2440 FixX Ferredoxin-like protein [Energy production and conversion]
Probab=23.61 E-value=38 Score=25.77 Aligned_cols=23 Identities=17% Similarity=0.252 Sum_probs=17.1
Q ss_pred ccccccccccc--cccCCCCCCCCc
Q 026355 8 SASWGSASCTK--GLQFSPTKIPFG 30 (240)
Q Consensus 8 ~~~~~~~~~~~--~~~~~~~~~~~~ 30 (240)
-||.||+-|.. ..||..|....+
T Consensus 69 ECGTCRvlc~~~~~i~W~YPrgg~G 93 (99)
T COG2440 69 ECGTCRVLCPHSGLIQWRYPRGGFG 93 (99)
T ss_pred eccceeEecCCCcceEEecCCCCcC
Confidence 48999999875 567877765544
No 139
>PF01957 NfeD: NfeD-like C-terminal, partner-binding; InterPro: IPR002810 The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of Rhizobium meliloti (Sinorhizobium meliloti) (Rhizobium meliloti) on alfalfa roots []. The specific function of this family is unknown although it is unlikely that NfeD is specifically involved in nodulation as the family contains several different archaeal and bacterial species most of which are not symbionts. This entry describes archaeal and bacterial proteins which are variously described, examples are: nodulation protein, nodulation efficiency protein D (nfeD), hypothetical protein and membrane-bound serine protease (ClpP class). A number of these proteins are classified in MEROPS peptidase family S49 as non-peptidase homologues or as unassigned peptidases. ; PDB: 2K5H_A 3CP0_A 2EXD_A.
Probab=23.51 E-value=1e+02 Score=23.65 Aligned_cols=28 Identities=25% Similarity=0.325 Sum_probs=16.1
Q ss_pred cCceEECCEEe--eeccceecCCCEEEEEec
Q 026355 95 SGLVSINGQVV--SKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 95 ~G~V~VNG~~v--~~~~~~L~~GD~I~v~~~ 123 (240)
.|+|+++|..- ...+. +++||.|.|...
T Consensus 104 ~G~V~~~G~~w~A~s~~~-i~~G~~V~Vv~v 133 (144)
T PF01957_consen 104 SGRVKVDGERWRARSEDE-IPKGDRVRVVGV 133 (144)
T ss_dssp -EEEEETTEEEEEEESST-B-TT-EEEEEEE
T ss_pred cEEEEECCeEEEEEeCCC-CCCCCEEEEEEE
Confidence 35788888643 22333 999998887653
No 140
>PHA03050 glutaredoxin; Provisional
Probab=23.46 E-value=22 Score=27.08 Aligned_cols=14 Identities=7% Similarity=0.131 Sum_probs=11.2
Q ss_pred ceeccccccccccc
Q 026355 2 TMLSLNSASWGSAS 15 (240)
Q Consensus 2 ~~~~~~~~~~~~~~ 15 (240)
+|.+..+|+||..-
T Consensus 16 ~vys~~~CPyC~~a 29 (108)
T PHA03050 16 TIFVKFTCPFCRNA 29 (108)
T ss_pred EEEECCCChHHHHH
Confidence 57788899999753
No 141
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=23.18 E-value=54 Score=22.43 Aligned_cols=45 Identities=13% Similarity=0.276 Sum_probs=29.6
Q ss_pred ccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEee--eccceecCCCEEEEEe
Q 026355 69 GKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVS--KVSHNVKGGDMVNCTI 122 (240)
Q Consensus 69 ~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~--~~~~~L~~GD~I~v~~ 122 (240)
++.+|..+|... .+....+ .|.+|+..+. ..+..|+.||+|+|-.
T Consensus 14 ~~~tl~~ll~~l--~~~~~~v-------av~~N~~iv~r~~~~~~L~~gD~ieIv~ 60 (65)
T PRK05863 14 EQTTVAALLDSL--GFPEKGI-------AVAVDWSVLPRSDWATKLRDGARLEVVT 60 (65)
T ss_pred CCCcHHHHHHHc--CCCCCcE-------EEEECCcCcChhHhhhhcCCCCEEEEEe
Confidence 367888888875 3433332 4778998653 2334599999998853
No 142
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=22.84 E-value=24 Score=25.09 Aligned_cols=15 Identities=0% Similarity=0.142 Sum_probs=11.2
Q ss_pred Cceeccccccccccc
Q 026355 1 MTMLSLNSASWGSAS 15 (240)
Q Consensus 1 ~~~~~~~~~~~~~~~ 15 (240)
++|.+..+|++|..-
T Consensus 3 v~iy~~~~C~~C~~a 17 (85)
T PRK11200 3 VVIFGRPGCPYCVRA 17 (85)
T ss_pred EEEEeCCCChhHHHH
Confidence 367788899999753
No 143
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.66 E-value=53 Score=30.91 Aligned_cols=65 Identities=18% Similarity=0.187 Sum_probs=46.5
Q ss_pred CceEEEEEEcCCCccchHHHHHHhccC--CCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 56 AGVQLEETVDTKAGKLRLDAWISSRID--GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 56 ~~~~~~~~V~~~~~g~RLdk~L~~~~~--~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
.|.++...|+..+.-..|.+.|....+ .++-.. +++|-+|+|.-|++.+ .++.|+.||.|.+-..
T Consensus 9 ~g~~~~IeV~~~~TV~dLK~kI~~~~g~~~ip~~~-QkLIy~GkiL~Dd~tL--~dy~I~e~~~Ivvmv~ 75 (378)
T TIGR00601 9 QQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQ-QKLIYSGKILSDDKTV--REYKIKEKDFVVVMVS 75 (378)
T ss_pred CCCEEEEEeCCcChHHHHHHHHHHhhCCCCCChhH-eEEEECCEECCCCCcH--HHcCCCCCCEEEEEec
Confidence 355677777777766777777877642 144433 7889999999888877 3688999998876543
No 144
>PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1PYU_C 1AW8_A 1PYQ_B 3TM7_C 1PT1_A 1PQH_A 1PPY_B 1PT0_B 1PQF_A 1PQE_A ....
Probab=22.13 E-value=65 Score=25.27 Aligned_cols=22 Identities=36% Similarity=0.548 Sum_probs=12.9
Q ss_pred cCceEECCEEeeeccceecCCCEEEE
Q 026355 95 SGLVSINGQVVSKVSHNVKGGDMVNC 120 (240)
Q Consensus 95 ~G~V~VNG~~v~~~~~~L~~GD~I~v 120 (240)
.|.|.+|| -..+.+++||.|.|
T Consensus 66 Sg~I~lNG----aAArl~~~GD~vII 87 (116)
T PF02261_consen 66 SGVICLNG----AAARLVQVGDRVII 87 (116)
T ss_dssp TT-EEEEG----GGGGCS-TT-EEEE
T ss_pred CcEEEECC----HHHhccCCCCEEEE
Confidence 35677777 34567889998776
No 145
>cd00570 GST_N_family Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK subfamily, a member of the DsbA family). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction and isomerization of certain compounds. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical doma
Probab=21.99 E-value=35 Score=21.79 Aligned_cols=15 Identities=0% Similarity=0.045 Sum_probs=11.2
Q ss_pred Cceeccccccccccc
Q 026355 1 MTMLSLNSASWGSAS 15 (240)
Q Consensus 1 ~~~~~~~~~~~~~~~ 15 (240)
|++...+.|++|++-
T Consensus 1 ~~ly~~~~~~~~~~~ 15 (71)
T cd00570 1 LKLYYFPGSPRSLRV 15 (71)
T ss_pred CEEEeCCCCccHHHH
Confidence 567777888888754
No 146
>PF11112 PyocinActivator: Pyocin activator protein PrtN
Probab=21.83 E-value=1.1e+02 Score=22.10 Aligned_cols=33 Identities=6% Similarity=0.131 Sum_probs=28.6
Q ss_pred CccchHHHHHHhccCCCCHHHHHHHHHcCceEE
Q 026355 68 AGKLRLDAWISSRIDGISRARVQSSIRSGLVSI 100 (240)
Q Consensus 68 ~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~V 100 (240)
..-..|+++..+.|+++|...+.+.+.+|++-+
T Consensus 12 ~~~IpL~~v~~~yf~~lt~~~a~rk~~~g~lpl 44 (76)
T PF11112_consen 12 DPVIPLEEVCEDYFPHLTPKTAKRKANAGELPL 44 (76)
T ss_pred CCCCcHHHHHHHHHccCCHHHHHHHHHCCCCCC
Confidence 344679999999988999999999999999865
No 147
>cd03029 GRX_hybridPRX5 Glutaredoxin (GRX) family, PRX5 hybrid subfamily; composed of hybrid proteins containing peroxiredoxin (PRX) and GRX domains, which is found in some pathogenic bacteria and cyanobacteria. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins. PRX-GRX hybrid proteins from Haemophilus influenza and Neisseria meningitis exhibit GSH-dependent peroxidase activity. The flow of reducing equivalents in the catalytic cycle of the hybrid protein goes from NADPH - GSH reductase - GSH - GRX domain of hybrid - PRX domain of hybrid - peroxide substrate.
Probab=21.53 E-value=25 Score=24.02 Aligned_cols=15 Identities=0% Similarity=0.244 Sum_probs=11.7
Q ss_pred Cceeccccccccccc
Q 026355 1 MTMLSLNSASWGSAS 15 (240)
Q Consensus 1 ~~~~~~~~~~~~~~~ 15 (240)
++|.+..+|.+|.+.
T Consensus 3 v~lys~~~Cp~C~~a 17 (72)
T cd03029 3 VSLFTKPGCPFCARA 17 (72)
T ss_pred EEEEECCCCHHHHHH
Confidence 367788899999865
No 148
>PRK02268 hypothetical protein; Provisional
Probab=21.48 E-value=1.3e+02 Score=24.37 Aligned_cols=40 Identities=15% Similarity=0.213 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEec
Q 026355 83 GISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTIS 123 (240)
Q Consensus 83 ~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~~ 123 (240)
..|+..++.-...|-.-|+.... .+-.++++||.|.++-+
T Consensus 8 v~s~~hv~~g~~~gf~qv~hgK~-apl~RmkpGD~ivyYsp 47 (141)
T PRK02268 8 VVSAEHVRRGVEGGFMQVCHGKA-APLRRMKPGDWIIYYSP 47 (141)
T ss_pred EccHHHHHHHHhCCEEEeCCCcc-chhhcCCCCCEEEEEec
Confidence 46899999888888888885555 36688999999988654
No 149
>cd01813 UBP_N UBP ubiquitin processing protease. The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.
Probab=21.47 E-value=79 Score=22.23 Aligned_cols=62 Identities=16% Similarity=0.197 Sum_probs=43.2
Q ss_pred CceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHH---cCceEECCEEeeeccceecCCCEEEEE
Q 026355 56 AGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIR---SGLVSINGQVVSKVSHNVKGGDMVNCT 121 (240)
Q Consensus 56 ~~~~~~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~---~G~V~VNG~~v~~~~~~L~~GD~I~v~ 121 (240)
.|.++...|...+.-..|.+.|.+.. +++-.. |+++- .|++.-|+..+ .++.+++|+.|.+-
T Consensus 8 ~g~~~~v~v~~~~Tv~~lK~~i~~~t-gvp~~~-QKLi~~~~~Gk~l~D~~~L--~~~~i~~g~~i~lm 72 (74)
T cd01813 8 GGQEYSVTTLSEDTVLDLKQFIKTLT-GVLPER-QKLLGLKVKGKPAEDDVKI--SALKLKPNTKIMMM 72 (74)
T ss_pred CCEEEEEEECCCCCHHHHHHHHHHHH-CCCHHH-EEEEeecccCCcCCCCcCH--HHcCCCCCCEEEEE
Confidence 45677777777666667788888764 455554 66663 68777777776 35778899988764
No 150
>PTZ00044 ubiquitin; Provisional
Probab=21.42 E-value=76 Score=21.85 Aligned_cols=62 Identities=13% Similarity=0.136 Sum_probs=42.2
Q ss_pred ceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEEe
Q 026355 57 GVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTI 122 (240)
Q Consensus 57 ~~~~~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~~ 122 (240)
|..+...+...+.-..|...+.+.. +++... ++++-+|++.-|+..+ .++.++.|+.|.+..
T Consensus 10 G~~~~l~v~~~~tv~~lK~~i~~~~-gi~~~~-q~L~~~g~~L~d~~~l--~~~~i~~~~~i~l~~ 71 (76)
T PTZ00044 10 GKKQSFNFEPDNTVQQVKMALQEKE-GIDVKQ-IRLIYSGKQMSDDLKL--SDYKVVPGSTIHMVL 71 (76)
T ss_pred CCEEEEEECCCCcHHHHHHHHHHHH-CCCHHH-eEEEECCEEccCCCcH--HHcCCCCCCEEEEEE
Confidence 4456667776666566777777664 455544 6666777777777666 467888899888754
No 151
>PF11969 DcpS_C: Scavenger mRNA decapping enzyme C-term binding; PDB: 1VLR_B 1XMM_D 1XML_B 1ST0_A 3BLA_B 3BL9_B 3BL7_B 1ST4_B 1XQU_B.
Probab=21.27 E-value=63 Score=24.79 Aligned_cols=26 Identities=35% Similarity=0.708 Sum_probs=18.0
Q ss_pred CceeeecCCcEEEEe--CCCC---ceeecCC
Q 026355 136 PLDIVYEDDNVLVVN--KPAH---MVVHPAP 161 (240)
Q Consensus 136 ~l~Ilyed~~~lvvn--KPaG---l~v~p~~ 161 (240)
+-+|+|||++++|++ +|.. +++-|..
T Consensus 13 ~~~vly~d~~~v~~~D~~P~a~~H~LviPk~ 43 (116)
T PF11969_consen 13 PERVLYEDDDFVVFKDIYPKAPVHLLVIPKD 43 (116)
T ss_dssp GGGESEEETSEEEEE-TT-SCCEEEEEEESS
T ss_pred CCcEEEEeCCEEEeeCCCCCcCcEEEEEeec
Confidence 568899999998886 4433 4466765
No 152
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=21.17 E-value=93 Score=20.92 Aligned_cols=61 Identities=18% Similarity=0.168 Sum_probs=34.8
Q ss_pred ceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEE
Q 026355 57 GVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCT 121 (240)
Q Consensus 57 ~~~~~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~ 121 (240)
|..++..++..+.-..|.+-+.+.. +++... ++++-.|+..-+...+ .++.++.|+.|.+.
T Consensus 9 g~~~~i~v~~~~tv~~lK~~i~~~~-gi~~~~-q~L~~~g~~l~d~~~L--~~~~i~~g~~l~v~ 69 (71)
T cd01812 9 GESHDLSISSQATFGDLKKMLAPVT-GVEPRD-QKLIFKGKERDDAETL--DMSGVKDGSKVMLL 69 (71)
T ss_pred CEEEEEEECCCCcHHHHHHHHHHhh-CCChHH-eEEeeCCcccCccCcH--HHcCCCCCCEEEEe
Confidence 4556666766555455555565553 444443 4555556555444444 35667888888764
No 153
>cd01669 TGS_Ygr210_C TGS_Ygr210_C: The C-terminal TGS domain of Ygr210 GTP-binding protein which is a member of Obg-like family of GTPases, and present in archaea. Several Obg-like family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. 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=20.88 E-value=1e+02 Score=22.07 Aligned_cols=20 Identities=20% Similarity=0.300 Sum_probs=17.3
Q ss_pred CCEEeeeccceecCCCEEEEE
Q 026355 101 NGQVVSKVSHNVKGGDMVNCT 121 (240)
Q Consensus 101 NG~~v~~~~~~L~~GD~I~v~ 121 (240)
||+.+ ..++.|+.||+|+|.
T Consensus 56 ~~~~v-g~~~~L~dgDvV~Ii 75 (76)
T cd01669 56 TGRRV-GEDYELKHRDVIKIV 75 (76)
T ss_pred CCEEe-CCCcEecCCCEEEEe
Confidence 89888 579999999999873
No 154
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=20.39 E-value=65 Score=22.00 Aligned_cols=62 Identities=15% Similarity=0.209 Sum_probs=42.5
Q ss_pred CceEEEEEEcCCCccchHHHHHHhccCCCCHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEE
Q 026355 56 AGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCT 121 (240)
Q Consensus 56 ~~~~~~~~V~~~~~g~RLdk~L~~~~~~~SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~ 121 (240)
.|..+...+.....-..|.+.+++.. +++-.. ++++-+|++.-|+..+ .++.++.|..|.+.
T Consensus 7 ~g~~~~~~v~~~~tV~~lK~~i~~~~-gi~~~~-q~Li~~G~~L~d~~~l--~~~~i~~~stl~l~ 68 (70)
T cd01798 7 TGHTFPVEVDPDTDIKQLKEVVAKRQ-GVPPDQ-LRVIFAGKELRNTTTI--QECDLGQQSILHAV 68 (70)
T ss_pred CCCEEEEEECCCChHHHHHHHHHHHH-CCCHHH-eEEEECCeECCCCCcH--HHcCCCCCCEEEEE
Confidence 34566667776666567777777764 455544 6777788887777666 35788888888663
No 155
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=20.32 E-value=1.4e+02 Score=17.96 Aligned_cols=21 Identities=24% Similarity=0.423 Sum_probs=16.7
Q ss_pred HhccCCCCHHHHHHHHHcCceE
Q 026355 78 SSRIDGISRARVQSSIRSGLVS 99 (240)
Q Consensus 78 ~~~~~~~SR~~~~klI~~G~V~ 99 (240)
++.+ ++|++.+.++++.|.+.
T Consensus 8 a~~l-gis~~ti~~~~~~g~i~ 28 (49)
T TIGR01764 8 AEYL-GVSKDTVYRLIHEGELP 28 (49)
T ss_pred HHHH-CCCHHHHHHHHHcCCCC
Confidence 3444 69999999999999754
No 156
>PHA02096 hypothetical protein
Probab=20.07 E-value=46 Score=24.53 Aligned_cols=18 Identities=22% Similarity=0.508 Sum_probs=14.1
Q ss_pred eecCCcEEEEeCCCCcee
Q 026355 140 VYEDDNVLVVNKPAHMVV 157 (240)
Q Consensus 140 lyed~~~lvvnKPaGl~v 157 (240)
+|--+.++.+|||+|.+.
T Consensus 63 lfg~ptiv~inkps~~la 80 (103)
T PHA02096 63 LFGPPTIVSVNKPSGHLA 80 (103)
T ss_pred hcCCCeEEEecCchHHHH
Confidence 455677999999999763
No 157
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=20.05 E-value=68 Score=22.13 Aligned_cols=61 Identities=18% Similarity=0.146 Sum_probs=32.2
Q ss_pred ceEEEEEEcCCCccchHHHHHHhccCCC--CHHHHHHHHHcCceEECCEEeeeccceecCCCEEEEE
Q 026355 57 GVQLEETVDTKAGKLRLDAWISSRIDGI--SRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCT 121 (240)
Q Consensus 57 ~~~~~~~V~~~~~g~RLdk~L~~~~~~~--SR~~~~klI~~G~V~VNG~~v~~~~~~L~~GD~I~v~ 121 (240)
|..+...+.....-..|.+.+.+.. ++ +.. -++++-+|++.-|+..+ .++.++.|+.|.+.
T Consensus 10 g~~~~l~v~~~~TV~~lK~~i~~~~-~i~~~~~-~q~L~~~G~~L~d~~~L--~~~~i~~~~~i~~~ 72 (77)
T cd01805 10 QQTFPIEVDPDDTVAELKEKIEEEK-GCDYPPE-QQKLIYSGKILKDDTTL--EEYKIDEKDFVVVM 72 (77)
T ss_pred CCEEEEEECCCCcHHHHHHHHHHhh-CCCCChh-HeEEEECCEEccCCCCH--HHcCCCCCCEEEEE
Confidence 4456666666555556666666653 33 322 23444444444444333 34667777776554
Done!