Query 026204
Match_columns 241
No_of_seqs 153 out of 1580
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 05:00:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026204.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026204hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0564 RluA Pseudouridylate s 100.0 1.5E-46 3.3E-51 328.9 21.0 193 15-241 38-231 (289)
2 PRK11180 rluD 23S rRNA pseudou 100.0 4.4E-40 9.6E-45 293.5 23.1 191 15-241 44-235 (325)
3 PRK11025 23S rRNA pseudouridyl 100.0 2.8E-40 6.1E-45 293.8 21.1 190 15-241 46-243 (317)
4 TIGR00005 rluA_subfam pseudour 100.0 7.3E-40 1.6E-44 289.0 22.7 194 15-241 32-226 (299)
5 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 1.2E-39 2.6E-44 280.2 19.4 183 16-241 4-187 (246)
6 PRK10158 23S rRNA/tRNA pseudou 100.0 2.5E-36 5.5E-41 255.4 18.2 150 53-241 13-163 (219)
7 cd02557 PseudoU_synth_ScRIB2 P 100.0 3.3E-36 7.2E-41 253.7 18.8 153 53-241 15-167 (213)
8 cd02563 PseudoU_synth_TruC tRN 100.0 1.9E-35 4.1E-40 250.8 18.8 151 54-241 1-162 (223)
9 TIGR01621 RluA-like pseudourid 100.0 1.5E-35 3.3E-40 250.3 17.9 146 54-241 2-147 (217)
10 PRK11112 tRNA pseudouridine sy 100.0 6E-35 1.3E-39 252.6 17.4 151 54-241 2-163 (257)
11 KOG1919 RNA pseudouridylate sy 100.0 5.7E-33 1.2E-37 248.3 17.6 204 1-241 47-262 (371)
12 PF00849 PseudoU_synth_2: RNA 100.0 1.4E-31 3.1E-36 215.9 15.2 148 62-241 1-157 (164)
13 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 4.1E-31 9E-36 212.0 13.9 134 63-241 1-134 (154)
14 cd02869 PseudoU_synth_RluCD_li 100.0 7.2E-30 1.6E-34 209.7 17.4 145 63-241 1-145 (185)
15 PRK10839 16S rRNA pseudouridyl 100.0 2.2E-31 4.7E-36 227.2 6.8 159 15-241 26-185 (232)
16 cd02870 PseudoU_synth_RsuA_lik 100.0 7.2E-29 1.6E-33 197.4 5.5 126 63-241 1-126 (146)
17 cd02556 PseudoU_synth_RluB Pse 99.9 4.3E-28 9.4E-33 197.1 9.0 128 62-241 1-128 (167)
18 PRK10700 23S rRNA pseudouridyl 99.9 1E-25 2.2E-30 197.7 12.9 165 15-241 28-195 (289)
19 cd02553 PseudoU_synth_RsuA Pse 99.9 8.3E-26 1.8E-30 183.6 8.7 124 63-241 2-125 (167)
20 cd02566 PseudoU_synth_RluE Pse 99.9 1.3E-25 2.7E-30 182.7 9.2 136 63-241 1-140 (168)
21 PRK10475 23S rRNA pseudouridin 99.9 2.7E-25 5.9E-30 194.7 10.3 116 15-178 32-147 (290)
22 cd02555 PSSA_1 PSSA_1: Pseudou 99.9 1.4E-22 3.1E-27 165.9 8.0 89 128-241 46-135 (177)
23 PRK11394 23S rRNA pseudouridin 99.9 6.1E-22 1.3E-26 166.3 9.0 83 61-180 39-121 (217)
24 COG1187 RsuA 16S rRNA uridine- 99.8 1.2E-20 2.5E-25 161.0 10.2 164 15-241 28-195 (248)
25 cd02554 PseudoU_synth_RluF Pse 99.8 4.3E-20 9.3E-25 149.3 8.0 120 63-241 2-121 (164)
26 TIGR00093 pseudouridine syntha 99.8 1.2E-19 2.7E-24 141.2 5.9 90 132-241 1-90 (128)
27 cd02868 PseudoU_synth_hTruB2_l 99.3 7E-12 1.5E-16 106.2 6.7 76 62-173 1-76 (226)
28 cd02572 PseudoU_synth_hDyskeri 98.0 1.7E-05 3.6E-10 65.3 7.0 70 61-173 2-71 (182)
29 cd00165 S4 S4/Hsp/ tRNA synthe 97.8 3.8E-05 8.2E-10 51.7 4.5 43 15-67 27-70 (70)
30 PRK00989 truB tRNA pseudouridi 97.8 5.8E-05 1.2E-09 64.1 6.2 71 61-173 9-79 (230)
31 cd00506 PseudoU_synth_TruB_lik 97.8 7.9E-05 1.7E-09 62.6 6.9 69 62-173 1-69 (210)
32 PRK04099 truB tRNA pseudouridi 97.7 8.7E-05 1.9E-09 64.6 7.0 70 61-173 2-71 (273)
33 TIGR00431 TruB tRNA pseudourid 97.7 9.2E-05 2E-09 62.1 6.7 70 61-173 2-71 (209)
34 PRK00020 truB tRNA pseudouridi 97.7 0.00013 2.7E-09 62.5 7.0 70 61-173 10-79 (244)
35 PRK02484 truB tRNA pseudouridi 97.6 0.00018 3.9E-09 63.4 7.0 70 61-173 3-72 (294)
36 PRK14124 tRNA pseudouridine sy 97.6 0.00025 5.4E-09 62.8 7.5 70 61-173 3-72 (308)
37 PRK14123 tRNA pseudouridine sy 97.5 0.00023 5E-09 63.1 7.0 70 61-173 3-72 (305)
38 PRK03287 truB tRNA pseudouridi 97.5 0.00023 5E-09 62.8 6.7 71 60-173 8-78 (298)
39 PRK02193 truB tRNA pseudouridi 97.5 0.00024 5.2E-09 62.1 6.8 68 63-173 2-69 (279)
40 PRK00130 truB tRNA pseudouridi 97.5 0.00027 5.9E-09 62.2 7.1 70 61-173 2-71 (290)
41 PRK14846 truB tRNA pseudouridi 97.5 0.00031 6.6E-09 62.7 7.2 70 61-173 3-72 (345)
42 cd02573 PseudoU_synth_EcTruB P 97.5 0.0003 6.6E-09 61.5 7.0 69 62-173 1-69 (277)
43 PRK05389 truB tRNA pseudouridi 97.5 0.00029 6.2E-09 62.4 6.9 70 61-173 13-82 (305)
44 PRK02755 truB tRNA pseudouridi 97.5 0.00031 6.7E-09 62.0 6.9 69 61-173 3-71 (295)
45 PRK04270 H/ACA RNA-protein com 97.5 0.00033 7.1E-09 62.1 7.0 71 60-173 21-91 (300)
46 PRK01528 truB tRNA pseudouridi 97.5 0.00038 8.3E-09 61.2 7.1 70 61-173 3-72 (292)
47 PRK05033 truB tRNA pseudouridi 97.4 0.00039 8.5E-09 61.7 7.1 70 61-173 10-79 (312)
48 PRK01851 truB tRNA pseudouridi 97.4 0.00043 9.3E-09 61.2 7.3 70 61-173 16-85 (303)
49 PRK01550 truB tRNA pseudouridi 97.4 0.00041 9E-09 61.4 7.1 70 61-173 2-71 (304)
50 PRK14122 tRNA pseudouridine sy 97.3 0.00074 1.6E-08 59.9 6.8 69 62-173 2-70 (312)
51 TIGR00425 CBF5 rRNA pseudourid 97.2 0.00073 1.6E-08 60.5 6.5 71 60-173 33-103 (322)
52 PRK04642 truB tRNA pseudouridi 97.2 0.00096 2.1E-08 58.9 6.8 70 61-173 10-79 (300)
53 COG0130 TruB Pseudouridine syn 97.0 0.002 4.4E-08 56.1 6.5 69 62-173 16-84 (271)
54 cd02867 PseudoU_synth_TruB_4 P 96.8 0.0035 7.5E-08 55.7 6.7 93 62-173 1-98 (312)
55 cd01291 PseudoU_synth PseudoU_ 94.2 0.19 4.2E-06 35.8 6.1 29 126-173 23-51 (87)
56 TIGR02988 YaaA_near_RecF S4 do 93.9 0.056 1.2E-06 35.8 2.6 23 15-37 35-58 (59)
57 PF14451 Ub-Mut7C: Mut7-C ubiq 93.5 0.13 2.8E-06 36.6 4.0 28 13-40 49-76 (81)
58 COG1188 Ribosome-associated he 93.3 0.1 2.3E-06 38.5 3.4 27 15-41 35-61 (100)
59 PF01479 S4: S4 domain; Inter 92.6 0.1 2.2E-06 32.8 2.2 21 15-35 27-48 (48)
60 KOG2559 Predicted pseudouridin 92.0 0.11 2.5E-06 44.3 2.4 22 128-149 90-111 (318)
61 PRK01777 hypothetical protein; 91.3 0.25 5.4E-06 36.3 3.3 28 14-41 50-77 (95)
62 smart00363 S4 S4 RNA-binding d 91.1 0.25 5.5E-06 31.4 2.9 26 14-39 26-52 (60)
63 PF01509 TruB_N: TruB family p 89.3 0.46 1E-05 37.8 3.6 43 127-173 7-49 (149)
64 PRK06437 hypothetical protein; 86.9 0.92 2E-05 30.9 3.4 25 15-39 38-62 (67)
65 COG0522 RpsD Ribosomal protein 86.2 0.82 1.8E-05 38.3 3.4 27 15-41 120-147 (205)
66 cd00754 MoaD Ubiquitin domain 82.8 1.6 3.4E-05 30.2 3.2 28 11-38 47-74 (80)
67 PRK10348 ribosome-associated h 82.4 1.5 3.3E-05 34.2 3.2 25 15-39 35-59 (133)
68 PRK11507 ribosome-associated p 81.6 1.6 3.4E-05 30.2 2.7 24 15-38 38-62 (70)
69 cd00565 ThiS ThiaminS ubiquiti 81.1 1.6 3.5E-05 29.3 2.6 26 14-39 31-60 (65)
70 PRK08364 sulfur carrier protei 81.0 2 4.3E-05 29.4 3.0 25 14-38 40-64 (70)
71 TIGR01682 moaD molybdopterin c 80.3 2.2 4.8E-05 29.8 3.2 29 10-38 46-74 (80)
72 PF03658 Ub-RnfH: RnfH family 78.0 2.1 4.5E-05 30.7 2.4 30 12-41 45-74 (84)
73 PRK05659 sulfur carrier protei 75.8 3.8 8.2E-05 27.4 3.2 26 13-38 31-60 (66)
74 PF02824 TGS: TGS domain; Int 75.7 3.2 7E-05 27.5 2.8 26 12-37 33-58 (60)
75 COG2104 ThiS Sulfur transfer p 75.4 3.3 7.2E-05 28.4 2.8 30 8-38 29-62 (68)
76 PF13275 S4_2: S4 domain; PDB: 75.3 1.5 3.2E-05 29.8 1.0 23 15-37 34-57 (65)
77 PRK06488 sulfur carrier protei 75.2 3.2 7E-05 27.7 2.7 27 12-38 29-59 (65)
78 PF02597 ThiS: ThiS family; I 74.7 3.8 8.2E-05 27.9 3.1 28 12-39 42-72 (77)
79 COG2501 S4-like RNA binding pr 72.1 4.9 0.00011 28.0 3.0 24 15-38 38-62 (73)
80 TIGR01017 rpsD_bact ribosomal 72.1 3.9 8.5E-05 34.1 3.0 26 15-40 116-142 (200)
81 PRK07440 hypothetical protein; 71.9 5.2 0.00011 27.4 3.1 26 13-38 35-64 (70)
82 TIGR01687 moaD_arch MoaD famil 70.4 6.1 0.00013 27.9 3.4 26 13-38 55-82 (88)
83 CHL00113 rps4 ribosomal protei 70.1 4.1 8.8E-05 34.1 2.7 25 15-39 115-140 (201)
84 PLN02799 Molybdopterin synthas 69.7 6.2 0.00013 27.5 3.2 24 15-38 53-76 (82)
85 PF00498 FHA: FHA domain; Int 68.6 4.4 9.5E-05 26.9 2.2 26 12-37 40-67 (68)
86 PRK05327 rpsD 30S ribosomal pr 68.5 4.6 0.0001 33.8 2.7 25 15-39 119-144 (203)
87 PRK07696 sulfur carrier protei 68.0 5.7 0.00012 26.9 2.6 26 13-38 32-61 (67)
88 PRK06944 sulfur carrier protei 65.9 7.4 0.00016 25.8 2.9 27 13-39 30-60 (65)
89 KOG2529 Pseudouridine synthase 62.1 8.9 0.00019 35.2 3.4 47 128-178 96-142 (395)
90 PRK08053 sulfur carrier protei 62.1 10 0.00022 25.4 3.0 27 12-38 30-60 (66)
91 COG2914 Uncharacterized protei 61.8 9.2 0.0002 28.0 2.8 34 8-41 42-77 (99)
92 cd01666 TGS_DRG_C TGS_DRG_C: 61.5 8.6 0.00019 26.8 2.6 21 18-38 54-74 (75)
93 TIGR03069 PS_II_S4 photosystem 60.9 8.2 0.00018 33.5 2.9 25 15-39 209-234 (257)
94 PRK11130 moaD molybdopterin sy 60.4 11 0.00024 26.4 3.0 24 15-38 52-75 (81)
95 TIGR01683 thiS thiamine biosyn 58.8 13 0.00029 24.6 3.1 27 12-38 28-58 (64)
96 cd01764 Urm1 Urm1-like ubuitin 58.2 12 0.00027 27.1 3.1 29 11-39 57-89 (94)
97 cd01668 TGS_RelA_SpoT TGS_RelA 58.0 15 0.00033 23.3 3.3 26 12-37 33-58 (60)
98 PF14478 DUF4430: Domain of un 54.9 12 0.00027 25.2 2.5 23 15-37 42-67 (68)
99 PLN00189 40S ribosomal protein 54.9 16 0.00035 30.3 3.6 27 16-42 136-163 (194)
100 cd01616 TGS The TGS domain, na 52.4 21 0.00045 22.0 3.2 26 12-37 33-58 (60)
101 PLN00051 RNA-binding S4 domain 51.8 15 0.00032 32.1 3.0 26 15-40 217-243 (267)
102 PRK06083 sulfur carrier protei 48.3 22 0.00048 25.3 3.0 23 15-37 51-77 (84)
103 PF14453 ThiS-like: ThiS-like 48.0 21 0.00045 23.6 2.5 19 19-37 35-53 (57)
104 PF08068 DKCLD: DKCLD (NUC011) 45.0 9.2 0.0002 25.4 0.5 16 60-75 41-56 (59)
105 PRK05863 sulfur carrier protei 44.7 21 0.00045 23.9 2.3 27 12-38 30-59 (65)
106 cd01669 TGS_Ygr210_C TGS_Ygr21 44.4 23 0.00049 24.7 2.5 20 19-38 56-75 (76)
107 TIGR00478 tly hemolysin TlyA f 41.6 22 0.00047 30.3 2.4 25 15-39 26-51 (228)
108 TIGR00008 infA translation ini 35.8 78 0.0017 21.7 4.0 25 17-41 33-57 (68)
109 cd00060 FHA Forkhead associate 33.6 44 0.00096 23.3 2.7 29 10-38 62-92 (102)
110 PRK11092 bifunctional (p)ppGpp 33.0 41 0.0009 33.5 3.2 30 12-41 420-449 (702)
111 PF13021 DUF3885: Domain of un 30.7 75 0.0016 19.1 2.9 24 138-161 5-28 (38)
112 COG2302 Uncharacterized conser 30.6 49 0.0011 28.6 2.8 27 15-41 206-233 (257)
113 COG0317 SpoT Guanosine polypho 30.2 68 0.0015 32.0 4.1 29 13-41 422-450 (701)
114 TIGR00691 spoT_relA (p)ppGpp s 29.6 72 0.0016 31.7 4.2 30 13-42 395-424 (683)
115 PRK12442 translation initiatio 29.1 1.2E+02 0.0026 21.9 4.1 38 17-61 35-72 (87)
116 PRK04313 30S ribosomal protein 28.9 84 0.0018 27.0 4.0 44 15-68 65-109 (237)
117 COG0361 InfA Translation initi 28.8 1.1E+02 0.0024 21.4 3.9 34 19-59 37-70 (75)
118 PTZ00155 40S ribosomal protein 27.7 57 0.0012 26.8 2.7 27 16-42 134-161 (181)
119 PTZ00223 40S ribosomal protein 25.7 95 0.0021 27.2 3.8 44 15-68 66-110 (273)
120 PLN00036 40S ribosomal protein 25.4 1E+02 0.0022 26.9 3.8 44 15-68 69-113 (261)
121 PRK10872 relA (p)ppGpp synthet 24.6 93 0.002 31.3 4.0 29 13-41 439-467 (743)
122 PRK11840 bifunctional sulfur c 23.7 80 0.0017 28.4 3.0 27 13-39 31-61 (326)
123 PF07732 Cu-oxidase_3: Multico 23.4 75 0.0016 23.8 2.5 33 8-40 9-41 (117)
124 PRK04051 rps4p 30S ribosomal p 22.7 91 0.002 25.5 3.0 27 15-41 129-156 (177)
125 PTZ00118 40S ribosomal protein 22.4 1.2E+02 0.0025 26.5 3.7 44 15-68 69-113 (262)
126 PRK14533 groES co-chaperonin G 21.6 1.4E+02 0.003 21.6 3.4 10 28-37 53-62 (91)
127 PF11969 DcpS_C: Scavenger mRN 21.0 70 0.0015 23.9 1.9 15 53-67 13-27 (116)
128 PRK03427 cell division protein 20.9 1.3E+02 0.0028 27.2 3.7 17 130-146 231-248 (333)
129 COG1977 MoaD Molybdopterin con 20.1 1.3E+02 0.0029 21.0 3.1 21 18-38 58-78 (84)
130 cd01667 TGS_ThrRS_N TGS _ThrRS 20.0 1.5E+02 0.0033 18.0 3.1 26 12-37 33-58 (61)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-46 Score=328.95 Aligned_cols=193 Identities=47% Similarity=0.747 Sum_probs=169.7
Q ss_pred eEEecCeecCCCceecCCCEEEEEecCCCC-ccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhc
Q 026204 15 ALFLSMDKLSVSHNVKGGDMVNCTISELQP-LRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHC 93 (241)
Q Consensus 15 ~v~vng~~~~~~~~l~~GD~i~~~~~~~~~-~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~ 93 (241)
+|.|||++++++++|..||+|.+...+... ....+++.+++|||||++++|||||+||+|||++++..+|+++.++.++
T Consensus 38 ~v~vNg~~v~~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~ 117 (289)
T COG0564 38 RVRVNGKKVKPSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHC 117 (289)
T ss_pred CEEECCEEccCCeeeCCCCEEEEecccccccccccccCCCccEEEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhc
Confidence 699999999999999999999998866332 3334455568899999999999999999999998888899999999886
Q ss_pred CCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 94 SLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
... ..++++|||||++||||||+|||..+++.|+++|+.+.+.|+|+|+|.
T Consensus 118 ~~~-----------------------------~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~ 168 (289)
T COG0564 118 QDG-----------------------------VERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVR 168 (289)
T ss_pred ccc-----------------------------CCceeeeccCCCCCceEEEEECCHHHHHHHHHHHhcCcCcEEEEEEEE
Confidence 310 367899999999999999999999999999999999999999999999
Q ss_pred cccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204 174 GVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 174 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ 241 (241)
|.++.+.+.|+.||.++...+..+.+... ..++.|.|+|++++++.. .+||++|+|+||||||
T Consensus 169 G~~~~~~~~i~~pi~r~~~~~~~~~v~~~----~~gk~A~T~~~~l~~~~~-~~tlv~~~~~TGRTHQ 231 (289)
T COG0564 169 GHLPEDEGTIDAPIGRDPKNRKKMAVVKE----GSGKPAITHYEVLERFGD-NYTLVELKPETGRTHQ 231 (289)
T ss_pred CcccCCCCEEeeeeecCCcCCceEEEecc----CCCCceEEEEEehhccCC-ceEEEEEEeCCCCHhH
Confidence 99999999999999999888777777653 138999999999999632 2799999999999999
No 2
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=4.4e-40 Score=293.52 Aligned_cols=191 Identities=40% Similarity=0.651 Sum_probs=157.4
Q ss_pred eEEecCeec-CCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhc
Q 026204 15 ALFLSMDKL-SVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHC 93 (241)
Q Consensus 15 ~v~vng~~~-~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~ 93 (241)
.|.|||+++ ++++.|.+||.|.+...........+...+++|||||++++|+|||+||+|||+.+....|+.+.+..++
T Consensus 44 ~V~VNg~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~iiyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~ 123 (325)
T PRK11180 44 RVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYY 123 (325)
T ss_pred CEEECCEEccCCCcCcCCCCEEEEeeccccccCCCCCCCCCcEEEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHh
Confidence 489999987 5899999999999986543222222344568999999999999999999999988777779999888765
Q ss_pred CCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 94 SLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
... ....++++|||||++||||||||||..++..|+++|+.+.++|+|+|+|.
T Consensus 124 ~~~---------------------------~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~Y~A~v~ 176 (325)
T PRK11180 124 PPI---------------------------ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQKREITREYEAVAI 176 (325)
T ss_pred hhc---------------------------cCCcccceeccCCCCCceeEEEECCHHHHHHHHHHHHhCCcceEEEEEEe
Confidence 210 11245789999999999999999999999999999999999999999999
Q ss_pred cccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204 174 GVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 174 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ 241 (241)
|.++ ..+.|+.||.+.......+.... .++.|.|+|+++... .++||++|+|+||||||
T Consensus 177 G~~~-~~~~i~~~l~~~~~~~~~~~~~~------~gk~a~T~~~~l~~~--~~~slv~~~~~TGRtHQ 235 (325)
T PRK11180 177 GHMT-AGGTVDEPISRHPTKRTHMAVHP------MGKPAVTHYRIMEHF--RVHTRLRLRLETGRTHQ 235 (325)
T ss_pred cCCC-CCCEEECceecCCCcCcEEEeCC------CCcEEeEEEEEeEEc--CCeEEEEEEeCCCCHHH
Confidence 9986 46899999987654444443333 678999999999874 57899999999999999
No 3
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=2.8e-40 Score=293.80 Aligned_cols=190 Identities=26% Similarity=0.357 Sum_probs=150.2
Q ss_pred eEEecCeecCCCceecCCCEEEEEecCCCCccCC--------CCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHH
Q 026204 15 ALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAE--------AEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLV 86 (241)
Q Consensus 15 ~v~vng~~~~~~~~l~~GD~i~~~~~~~~~~~~~--------~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~ 86 (241)
.|.|||+++++++.|+.||.|.+........... ....+++|||||++++|||||+|++|||+.+.. .++.
T Consensus 46 ~V~VNg~~v~~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~-~~~~ 124 (317)
T PRK11025 46 EVRVNKKRIKPEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKVAALADVILYEDDHILVLNKPSGTAVHGGSGLS-FGVI 124 (317)
T ss_pred CEEECCEEcCcccccCCCCEEEeCCCCccccccccccccccccccCcCCEEEECCCEEEEECCCCCcCcCCCCCC-ccHH
Confidence 4899999999999999999999864221110000 112457899999999999999999999986554 3566
Q ss_pred HHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeE
Q 026204 87 NGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIER 166 (241)
Q Consensus 87 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K 166 (241)
+.+..... ....+++|||||++||||||||||+.+++.|+++|+.+.++|
T Consensus 125 ~~~~~~~~------------------------------~~~~~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~v~K 174 (317)
T PRK11025 125 EGLRALRP------------------------------EARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQK 174 (317)
T ss_pred HHHHHhcc------------------------------CCCcCceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCCccE
Confidence 66554311 113367899999999999999999999999999999999999
Q ss_pred EEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204 167 VYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 167 ~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ 241 (241)
+|+|+|.|.++...++|+.||.++........+.. ...|+.|.|+|++++.. .++||++|+|+||||||
T Consensus 175 ~Y~a~v~G~~~~~~~~i~~~i~~~~~~~~~~~~~~----~~~gk~a~T~~~~l~~~--~~~sLv~~~~~TGRtHQ 243 (317)
T PRK11025 175 DYLALVRGQWQSHVKVVQAPLLKNILQSGERIVRV----SQEGKPSETRFKVEERY--AFATLVRASPVTGRTHQ 243 (317)
T ss_pred EEEEEEeCcccCCCceEecccccCcccCCceEEec----CCCCccceEEEEEeEEc--CCcEEEEEEeCCCCHHH
Confidence 99999999998888999999987753322222211 12689999999999984 57899999999999999
No 4
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=100.00 E-value=7.3e-40 Score=289.04 Aligned_cols=194 Identities=40% Similarity=0.658 Sum_probs=159.0
Q ss_pred eEEecCe-ecCCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhc
Q 026204 15 ALFLSMD-KLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHC 93 (241)
Q Consensus 15 ~v~vng~-~~~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~ 93 (241)
.|+|||+ ..++++.|++||.|.+...........+...+++|+|||++|+|+|||+|++||+..+...+|+.+.+..++
T Consensus 32 ~V~VNg~~~~~~~~~v~~gd~I~i~~~~~~~~~~~~~~~~~~i~~ed~~~lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~ 111 (299)
T TIGR00005 32 QVKVNGKVTANPKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDEDIIVINKPSGLVVHPGGGNPFGTVLNALLAHC 111 (299)
T ss_pred cEEECCEeccCcccCCCCCCEEEEecCCcccccCCccCCCccEEEeCCCEEEEECCCCCeEeCCCCCCcccHHHHHHHhc
Confidence 5899996 467999999999999976432222222333457899999999999999999999998777788999888765
Q ss_pred CCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 94 SLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
... ....++++|||||++||||||||+|..+++.|+++|+++.+.|+|+|+|.
T Consensus 112 ~~~---------------------------~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~ 164 (299)
T TIGR00005 112 PPI---------------------------AGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYVALVH 164 (299)
T ss_pred ccc---------------------------cCCCcCceECCCCCCCceEEEEEcCHHHHHHHHHHHHhCCcceEEEEEEe
Confidence 310 01245789999999999999999999999999999999999999999999
Q ss_pred cccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204 174 GVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 174 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ 241 (241)
|.++.+.++|+.||.++..+...+.+... .++++|.|+|+++.. ..++||++|+|+|||+||
T Consensus 165 g~~~~~~~~i~~~l~~~~~~~~~~~~~~~----~~~k~a~t~~~~l~~--~~~~slv~~~l~tGR~HQ 226 (299)
T TIGR00005 165 GQFDSGGGTVDAPLGRVPNNRGLMAVHPS----SEGKPAVTHFRVLER--FGNASLVECELETGRTHQ 226 (299)
T ss_pred ccccCCCCEEeCceecCCCCCceEEEecC----CCCCeeeEEEEEeEE--cCCeEEEEEEeCCCChHH
Confidence 99988899999999886554444444331 258999999999987 357899999999999999
No 5
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.
Probab=100.00 E-value=1.2e-39 Score=280.15 Aligned_cols=183 Identities=20% Similarity=0.268 Sum_probs=147.6
Q ss_pred EEecCeecCCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCC
Q 026204 16 LFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSL 95 (241)
Q Consensus 16 v~vng~~~~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~ 95 (241)
+..||++++++++|+.||+|.++...... .+...+++|||||++|+|||||+|++|||+++...+|+.+.+...+.
T Consensus 4 ~~~ng~~~~~~~~l~~gd~i~~~~~~~~~---~~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~~- 79 (246)
T cd02558 4 VDADGEPLDPDSPYRPGTFVWYYRELPDE---PPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTG- 79 (246)
T ss_pred ECCCCcCCCCCceecCCCEEEEeCCCCCC---CCCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHhC-
Confidence 34699999999999999999997532211 12223588999999999999999999999987777888888765532
Q ss_pred CccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecc
Q 026204 96 PTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGV 175 (241)
Q Consensus 96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~ 175 (241)
...+++|||||++||||||||||+++++.|+.+|+.+.++|+|+|+|.|.
T Consensus 80 ------------------------------~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~YlA~v~G~ 129 (246)
T cd02558 80 ------------------------------NPDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYEAVAPYV 129 (246)
T ss_pred ------------------------------CCcccccccCCCCceeEEEEEcCHHHHHHHHHHHHcCCccEEEEEEEecC
Confidence 13467899999999999999999999999999999999999999999999
Q ss_pred cCCCcc-EEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204 176 PSQSSG-RIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 176 ~~~~~~-~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ 241 (241)
++...+ .++.+|.++... ..+... .+++.|.|+|++++.. .++|+++|+|+|||+||
T Consensus 130 ~~~~~~~~~~~~i~~~~~~-~~~~~~------~~~~~a~T~~~~l~~~--~~~slv~~~l~TGRtHQ 187 (246)
T cd02558 130 PALTFPLTVRSRIVKGRGF-FQAREV------EGEPNAETRIELLARR--GGWGLYRLSPHTGKTHQ 187 (246)
T ss_pred CCCCCCcceeccccccCCc-ceeecc------CCCCCceEEEEEEEec--CCeEEEEEEeCCCCHHH
Confidence 864444 577777665432 122222 2567899999999873 57999999999999999
No 6
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=100.00 E-value=2.5e-36 Score=255.45 Aligned_cols=150 Identities=31% Similarity=0.465 Sum_probs=126.4
Q ss_pred CccEEEecCcEEEEECCCCceeecCCC-CCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccc
Q 026204 53 PLDIVYEDDNVLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 131 (241)
Q Consensus 53 ~~~Ilyed~~llVinKPaGl~~~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 131 (241)
.++|||||++++|+|||+|++||++.. ....++.+.+...+ ..+++
T Consensus 13 ~~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~---------------------------------~~~~~ 59 (219)
T PRK10158 13 WLVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY---------------------------------PQAES 59 (219)
T ss_pred CCCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC---------------------------------CCCCE
Confidence 467999999999999999999998753 33456777665442 23678
Q ss_pred cccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcc
Q 026204 132 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH 211 (241)
Q Consensus 132 vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~ 211 (241)
|||||++||||||+|+|.++++.|+++|+.+.+.|+|+|+|.|.++...++|+.||.++......+.+.. ++++.
T Consensus 60 vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~~v~K~Yla~v~G~~~~~~~~i~~~i~~~~~~~~~~~~~~-----~~gk~ 134 (219)
T PRK10158 60 VHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCY-----ETGKP 134 (219)
T ss_pred ECCCCCCCceEEEEECCHHHHHHHHHHHHhCCccEEEEEEEecccCCCCcEEecceecCCCCCceEEecC-----CCCce
Confidence 9999999999999999999999999999999999999999999998889999999987755544444432 26789
Q ss_pred eEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204 212 AASRYKVIEILAGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 212 a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ 241 (241)
|.|+|++++... .+.++++|+|+||||||
T Consensus 135 a~t~~~~l~~~~-~~~sll~~~~~TGRtHQ 163 (219)
T PRK10158 135 AQTEYEVVEYAA-DNTARVVLKPITGRSHQ 163 (219)
T ss_pred eeEEEEEEEEcC-CCCEEEEEEeCCCCHHH
Confidence 999999998742 34589999999999999
No 7
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.
Probab=100.00 E-value=3.3e-36 Score=253.71 Aligned_cols=153 Identities=27% Similarity=0.377 Sum_probs=129.2
Q ss_pred CccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCcccc
Q 026204 53 PLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIV 132 (241)
Q Consensus 53 ~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v 132 (241)
+++|||||++++|+|||+|++|++++.....++.+.|...+. ...+++|
T Consensus 15 ~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~-------------------------------~~~~~~v 63 (213)
T cd02557 15 PIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYG-------------------------------LTELRPC 63 (213)
T ss_pred CCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcC-------------------------------CCCccCc
Confidence 578999999999999999999999876666788888876542 1346789
Q ss_pred ccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcce
Q 026204 133 HRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHA 212 (241)
Q Consensus 133 hRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a 212 (241)
||||++||||||||+|++++++|+++|+++.++|+|+|+|.|.++.+.+.|+.||.++.......... ...++.|
T Consensus 64 hRLD~~TSGllllak~~~~~~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~-----~~~~~~a 138 (213)
T cd02557 64 HRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKEYLARVKGEFPDGEVVVDQPIGLVSPKGGLRNDV-----DEKGKDA 138 (213)
T ss_pred cCCCCCCceEEEEECCHHHHHHHHHHHHcCCccEEEEEEEeCcCCCCCeEEecceeccCcCCceeecc-----CCCCcee
Confidence 99999999999999999999999999999999999999999999888999999998764322111111 1367899
Q ss_pred EEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204 213 ASRYKVIEILAGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 213 ~T~~~vl~~~~~~~~slv~~~l~TGR~HQ 241 (241)
.|+|+++......++||++|+|.|||+||
T Consensus 139 ~t~~~~~~~~~~~~~slv~v~~~TGR~HQ 167 (213)
T cd02557 139 RTIFKRLSYNGDLNTSVVLCKPITGRTHQ 167 (213)
T ss_pred eEEEEEEEEcCCCCeEEEEEEeCCCCHHH
Confidence 99999999854348999999999999999
No 8
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.
Probab=100.00 E-value=1.9e-35 Score=250.76 Aligned_cols=151 Identities=28% Similarity=0.480 Sum_probs=120.0
Q ss_pred ccEEEecCcEEEEECCCCceeecCCCCCCCC--HHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccc
Q 026204 54 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGT--LVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 131 (241)
Q Consensus 54 ~~Ilyed~~llVinKPaGl~~~~~~~~~~~t--l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 131 (241)
++|||||++++|||||+|++|||.......+ +...+...+ ...+++
T Consensus 1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~ 48 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQL--------------------------------GQHVYP 48 (223)
T ss_pred CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHc--------------------------------CCCccc
Confidence 3599999999999999999999976443333 222222221 134678
Q ss_pred cccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcc
Q 026204 132 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH 211 (241)
Q Consensus 132 vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~ 211 (241)
|||||++||||||||||+++++.|+++|+.+.++|+|+|+|.|.++. +++|+.||.++........+.. ...++.
T Consensus 49 vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~v~K~Y~alv~G~~~~-~~~i~~~l~~~~~~~~~~~~~~----~~~~~~ 123 (223)
T cd02563 49 VHRLDRPTSGVLLFALSSEVARKLGEQFTEHRVHKTYLAVVRGYVPE-SGTIDYPLSEELDKLADKFASD----DKAPQA 123 (223)
T ss_pred ccCCCCCCeEEEEEEECHHHHHHHHHHHhcCceeEEEEEEEECccCC-CCeEEEeeeeCCCccceEEeec----CCCCce
Confidence 99999999999999999999999999999999999999999999875 7899999988765433333322 136789
Q ss_pred eEEEEEEEEEe---------cCCCEEEEEEEcCCCCCCC
Q 026204 212 AASRYKVIEIL---------AGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 212 a~T~~~vl~~~---------~~~~~slv~~~l~TGR~HQ 241 (241)
|.|+|+++... ...++||++|+|+||||||
T Consensus 124 a~t~~~~l~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQ 162 (223)
T cd02563 124 ATTHYRLLAVEELPVVVGKYPTSRYSLVELTPHTGRKHQ 162 (223)
T ss_pred eEEEEEEeeecccccccccCCCCCeEEEEEEeCCCCHHH
Confidence 99999999752 1236899999999999999
No 9
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621. This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.
Probab=100.00 E-value=1.5e-35 Score=250.31 Aligned_cols=146 Identities=28% Similarity=0.433 Sum_probs=122.6
Q ss_pred ccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccc
Q 026204 54 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVH 133 (241)
Q Consensus 54 ~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vh 133 (241)
++|||||++++|||||+||+||++.+. .++.+.+..+.. ...+++||
T Consensus 2 ~~ilyed~~~lvvnKP~Gl~v~~~~~~--~~l~~~l~~~~~-------------------------------~~~~~~Vh 48 (217)
T TIGR01621 2 FEILFTHPDFLLINKHPGISVHKDDGE--TGLLQEVATQLG-------------------------------VGQVWLVH 48 (217)
T ss_pred ceEEEeCCCEEEEECCCCCeECCCCCc--ChHHHHHHHhcC-------------------------------CCCccEec
Confidence 469999999999999999999987532 456666654321 13578899
Q ss_pred cCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceE
Q 026204 134 RLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAA 213 (241)
Q Consensus 134 RLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~ 213 (241)
|||++||||||||+|+++++.|+++|+++.++|+|+|+|.|.++..+++|+.++.+...+... +.. ..++.|.
T Consensus 49 RLDr~TSGlll~Ak~~~~~~~L~~~~~~~~v~K~YlAlV~g~~~~~~~~i~~~~~~~~~~~~~--~~~-----~~~k~a~ 121 (217)
T TIGR01621 49 RLDKMTSGILLLALNAESASELSQGFAKRKIEKTYLALSSKKPKKKQGLICGDMEKSRRGSWK--LVN-----SQENPAI 121 (217)
T ss_pred CCCCCCceEEEEEcCHHHHHHHHHHHhcCCccEEEEEEEeccccCCCCEEeCCcccCCCCCEE--EeC-----CCCCcee
Confidence 999999999999999999999999999999999999999999998999999999765443322 222 2568899
Q ss_pred EEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204 214 SRYKVIEILAGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 214 T~~~vl~~~~~~~~slv~~~l~TGR~HQ 241 (241)
|+|+++... .++|+++|+|.||||||
T Consensus 122 t~~~~~~~~--~~~slv~~~~~TGR~HQ 147 (217)
T TIGR01621 122 TRFFSASAA--TGLRLFILKPHTGKTHQ 147 (217)
T ss_pred EEEEEEEEc--CCeEEEEEEeCCCCHHH
Confidence 999999874 57999999999999999
No 10
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=100.00 E-value=6e-35 Score=252.56 Aligned_cols=151 Identities=26% Similarity=0.399 Sum_probs=118.8
Q ss_pred ccEEEecCcEEEEECCCCceeecCCCCCCCCH--HHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccc
Q 026204 54 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTL--VNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI 131 (241)
Q Consensus 54 ~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 131 (241)
++|||||++|+|||||+||+||+.......+. ...+...+ ...+++
T Consensus 2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~ 49 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQI--------------------------------GQHVFT 49 (257)
T ss_pred CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHh--------------------------------CCCcee
Confidence 46999999999999999999999754444332 22222221 124678
Q ss_pred cccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcc
Q 026204 132 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH 211 (241)
Q Consensus 132 vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~ 211 (241)
|||||++||||||||||+++++.|+++|+.+.++|+|+|+|.|.++ .+++|+.|+.++........... ..++++
T Consensus 50 VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~Alv~G~~~-~~~~i~~~l~~~~~~~~~~~~~~----~~~~k~ 124 (257)
T PRK11112 50 AHRLDRPTSGVLLMALSSEVARLLAQQFEQHQIQKTYHAIVRGWLM-EEAVLDYPLKEELDKIADKFARE----DKAPQP 124 (257)
T ss_pred eccCCCCCeeEEEEECCHHHHHHHHHHHHhCCcceEEEEEEEeEeC-CCCeEeeeeeecccccceeeccc----CCCCeE
Confidence 9999999999999999999999999999999999999999999885 56889999987643322222211 236899
Q ss_pred eEEEEEEEEEec---------CCCEEEEEEEcCCCCCCC
Q 026204 212 AASRYKVIEILA---------GGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 212 a~T~~~vl~~~~---------~~~~slv~~~l~TGR~HQ 241 (241)
|.|+|+++.... +.++||++|+|.||||||
T Consensus 125 a~T~~~~l~~~~~~~~~~~~~~~~~slv~i~~~TGRtHQ 163 (257)
T PRK11112 125 AVTHYRGLATVEMPVATGRYPTTRYSLVELEPKTGRKHQ 163 (257)
T ss_pred eEEEEEEEEEecccccccccCCCCeEEEEEEcCCCChHH
Confidence 999999998641 246899999999999999
No 11
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=100.00 E-value=5.7e-33 Score=248.25 Aligned_cols=204 Identities=31% Similarity=0.434 Sum_probs=164.7
Q ss_pred Ccceecccccee---------eeeEEecCeecCCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCC
Q 026204 1 MELVELEFNQVS---------VLALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAH 71 (241)
Q Consensus 1 ~~~~~~~~~~~~---------~~~v~vng~~~~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaG 71 (241)
+|++..||+.++ ...+.+||+.+..++.++.||.|.+..+...++. ...++.|+|||++|+|||||+|
T Consensus 47 ~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~~v~~i~k~~d~l~~~vhrh~p~~---~~~~~~Iv~ed~~~vVvnKP~g 123 (371)
T KOG1919|consen 47 VDVFVSEFRLRERAYYESAIKLGRVTVNGEQVRVSLIVKNGDVLCHTVHRHEPPV---AYLPIRIVFEDKDYVVVNKPHG 123 (371)
T ss_pred HHHHHHHHhcCchHhhhhhhhcCceEECcEeeeeEEEeccCCEEEEeeccCCCCc---cccccceEEecCCEEEEeCCCC
Confidence 466777777776 3348999999999999999999999877654433 2247889999999999999999
Q ss_pred ceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHH
Q 026204 72 MVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHS 151 (241)
Q Consensus 72 l~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~ 151 (241)
++|||.+....+++...+..... ...++++||||+.|||||+||+++.+
T Consensus 124 ipVhp~g~~~~n~i~~~l~~~~~-------------------------------~~~~~~~hRLDr~tSGllvlAkt~~~ 172 (371)
T KOG1919|consen 124 IPVHPTGRYRENTITKILAALHK-------------------------------VEGLRPCHRLDRLTSGLLVLAKTKEA 172 (371)
T ss_pred CceeccCccccccchHHHHHhcc-------------------------------ccccccccccCccccceEEEEechhH
Confidence 99999888888888777776421 24467899999999999999999999
Q ss_pred HHHHHHHhhcCeeeEEE-EEEEecccC-CCccEEEcceeeCCCCCeeEEEec-CCCCCCCCcceEEEEEEEEEecCCCEE
Q 026204 152 HAHLSEQFKLHTIERVY-ISLTSGVPS-QSSGRIEVPISRDPNNRIRMAAIP-GSNKHGQARHAASRYKVIEILAGGGSA 228 (241)
Q Consensus 152 ~~~L~~~f~~~~v~K~Y-~AlV~G~~~-~~~~~i~~~i~~~~~~~~~~~~~~-~~~~~~~~k~a~T~~~vl~~~~~~~~s 228 (241)
+..+++.|+++++.|.| +|-|.|.++ .+...|..++..... ..+|.+.. .+.+...++.|.|.|+++.++ ++.+
T Consensus 173 ~~~~~~~~r~~~~~k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~-~~~~~l~~~~~~~~~~~k~a~T~~~~~~~~--~~ss 249 (371)
T KOG1919|consen 173 ADKFHEVLRKRTVKKEYVVARVEGPFPVVGEVEIKEPIGEEER-PLRMGLNAVGVRDEVAAKDAKTLFKVLSYD--GGSS 249 (371)
T ss_pred hHHHHHHHhcccceeEEEEEEEeccCCCCceEEeCCCcccccc-ccceEeeecccccccccccceeEEEEcccC--CceE
Confidence 99999999999999999 799999987 556677777765442 23333322 111223589999999999984 8999
Q ss_pred EEEEEcCCCCCCC
Q 026204 229 LVEWRLETGRTHQ 241 (241)
Q Consensus 229 lv~~~l~TGR~HQ 241 (241)
+|+|+|+||||||
T Consensus 250 ~V~~~PlTGRtHQ 262 (371)
T KOG1919|consen 250 LVECRPLTGRTHQ 262 (371)
T ss_pred EEEeeccCCcHHH
Confidence 9999999999999
No 12
>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=99.98 E-value=1.4e-31 Score=215.91 Aligned_cols=148 Identities=37% Similarity=0.554 Sum_probs=111.5
Q ss_pred cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204 62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 141 (241)
Q Consensus 62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 141 (241)
+|+|||||+||+|++................... ......+++|||||++|||
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 6899999999999998754443333333322210 0234678999999999999
Q ss_pred EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeC--CCCCeeEEEecCCCCCCCCcceEEEEEEE
Q 026204 142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRD--PNNRIRMAAIPGSNKHGQARHAASRYKVI 219 (241)
Q Consensus 142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~--~~~~~~~~~~~~~~~~~~~k~a~T~~~vl 219 (241)
|||||+|.++++.|+++|+.+.++|+|+|+|.|.+....+.++.++..+ ........... .+++.+.|.|+++
T Consensus 54 lll~a~~~~~~~~l~~~f~~~~~~K~Y~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~t~~~~l 128 (164)
T PF00849_consen 54 LLLFAKDKEAAAKLSKQFPKRKVEKTYLALVEGGPVEEEGKINSPLGKDVGKNKSSNKDPPG-----RDGKPAITRYRVL 128 (164)
T ss_dssp EEEEESSHHHHHHHHHHHHTTCSEEEEEEEECSSSSTTCEEEESHEEE-EECSSCTCCEEET-----TTSBTSEEEEEEE
T ss_pred CeeccCCcccccccccccccCCCcEEEEEeEcccccccceeeeccccccccccccceeeeec-----ccccccceeeeee
Confidence 9999999999999999999999999999999988888899999999872 22222222222 3789999999999
Q ss_pred EEe-------cCCCEEEEEEEcCCCCCCC
Q 026204 220 EIL-------AGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 220 ~~~-------~~~~~slv~~~l~TGR~HQ 241 (241)
... .+.++++++|+|.|||+||
T Consensus 129 ~~~~~~~~~~~~~~~s~v~~~l~tGr~HQ 157 (164)
T PF00849_consen 129 RSGSRTPSKDENAGCSLVECELITGRTHQ 157 (164)
T ss_dssp EEETT---EECCSSEEEEEEEESS-STTH
T ss_pred ccccccccccccCCCEEEEEEECcCCCHH
Confidence 986 5678999999999999999
No 13
>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=99.97 E-value=4.1e-31 Score=212.02 Aligned_cols=134 Identities=31% Similarity=0.438 Sum_probs=107.4
Q ss_pred EEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceE
Q 026204 63 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 142 (241)
Q Consensus 63 llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGl 142 (241)
|+|+|||+|++||++.+....++.+.+.... ..++++|||||++||||
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~vhRLD~~TSGl 48 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLH--------------------------------GPRVHAAGRLDKDTSGL 48 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhhccc--------------------------------CCceeEeccCCCCCeeE
Confidence 5899999999999988776677777554321 24578899999999999
Q ss_pred EEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEe
Q 026204 143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL 222 (241)
Q Consensus 143 ll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~ 222 (241)
||||+|+++++.|+++ .+.+.|+|+|+|.|.++. ++.+..++.+. ........ .+++.+.|+|+++..
T Consensus 49 ll~ak~~~~~~~l~~~--~~~v~K~Y~a~v~g~~~~-~~~~~~~~~~~--~~~~~~~~------~~~~~~~t~~~~l~~- 116 (154)
T cd02550 49 LLLTNDGRLQRRLTEP--RREIEKEYLVTVRGELDE-EGIEDLATVRR--GRLSGLVD------EGVPLAVTKVRVIGE- 116 (154)
T ss_pred EEEEcCHHHHHHHhhh--hccCcEEEEEEEEeecCc-chheecccccc--CcceeEEc------CCCcccceEEEEEEe-
Confidence 9999999999999997 788999999999999864 45677776552 22222222 267889999999976
Q ss_pred cCCCEEEEEEEcCCCCCCC
Q 026204 223 AGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 223 ~~~~~slv~~~l~TGR~HQ 241 (241)
..++|+++|+|.|||+||
T Consensus 117 -~~~~sll~~~l~tGR~HQ 134 (154)
T cd02550 117 -HGGTGRLRLTLKTGRTHQ 134 (154)
T ss_pred -cCCcEEEEEEEcCCCcHH
Confidence 357899999999999999
No 14
>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=99.97 E-value=7.2e-30 Score=209.68 Aligned_cols=145 Identities=48% Similarity=0.796 Sum_probs=118.3
Q ss_pred EEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceE
Q 026204 63 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 142 (241)
Q Consensus 63 llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGl 142 (241)
++|+|||+|++|++.......++...+....... .....+++|||||++||||
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~v~RLD~~tsGl 53 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLL---------------------------GEEFRPGLVHRLDKDTSGL 53 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhc---------------------------CCCCcCceecccCCCCceE
Confidence 5899999999999998877778877753222100 1235678999999999999
Q ss_pred EEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEe
Q 026204 143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL 222 (241)
Q Consensus 143 ll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~ 222 (241)
||+|+|+++++.|++.|+.+.+.|+|+|+|.|.++...+.+..|+..+........... .+++.+.|+|+++...
T Consensus 54 ll~ak~~~~~~~l~~~~~~~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~t~~~~l~~~ 128 (185)
T cd02869 54 LLVAKNKKAAAKLSKQFKERKVKKTYLALVDGKPPEDEGTIDAPLGRKKRKKRARVVVS-----EDGKPAITHYKVLERF 128 (185)
T ss_pred EEEEcCHHHHHHHHHHHhcCceeEEEEEEEeCCCCCCccEEecccccCCccCceEEEEC-----CCCeEEEEEEEEEEEc
Confidence 99999999999999999999999999999999999889999999876522222222222 3678999999999873
Q ss_pred cCCCEEEEEEEcCCCCCCC
Q 026204 223 AGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 223 ~~~~~slv~~~l~TGR~HQ 241 (241)
.++|+++|+|.|||+||
T Consensus 129 --~~~s~~~~~l~tGR~HQ 145 (185)
T cd02869 129 --GNVTLVELQLETGRTHQ 145 (185)
T ss_pred --CCcEEEEEEeCcCCccH
Confidence 58899999999999999
No 15
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=99.97 E-value=2.2e-31 Score=227.17 Aligned_cols=159 Identities=16% Similarity=0.216 Sum_probs=117.1
Q ss_pred eEEecCeecC-CCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhc
Q 026204 15 ALFLSMDKLS-VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHC 93 (241)
Q Consensus 15 ~v~vng~~~~-~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~ 93 (241)
.|.|||+++. ++++|+.||.|.+...... + .++++++|+|||+||+|||+... ..|+...+...
T Consensus 26 ~V~VNg~~~~~~~~~l~~gd~I~l~~~~~~-----~--------~~~~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~~- 90 (232)
T PRK10839 26 RVTVDGEIVKNGAFKLLPEHDVAYDGNPLA-----Q--------QHGPRYFMLNKPQGYVCSTDDPD-HPTVLYFLDEP- 90 (232)
T ss_pred eEEECCEEeccCCcCcCCCCEEEECCEEcc-----c--------CCCCEEEEEECCCCeEecccCCC-CCeEEEecccc-
Confidence 5899999986 8999999999988531100 0 13568999999999999987443 24543322110
Q ss_pred CCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 94 SLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
...++++|||||++||||||||+|..+++.|.. +.+.++|+|+|.+.
T Consensus 91 -------------------------------~~~~~~~v~RLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~i~ 137 (232)
T PRK10839 91 -------------------------------VAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITS--PRHHCEKTYLVTLE 137 (232)
T ss_pred -------------------------------cccCceecCCCCCCceeEEEEecCHHHHHHHhC--CCCCCCeEEEEEEC
Confidence 113567899999999999999999999999986 78889999999877
Q ss_pred cccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204 174 GVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 174 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ 241 (241)
+.+.. +........+.. +++.|.|+|.+++... .|+++|+|.||||||
T Consensus 138 ~~i~~-----------~~~~~~~~~~~~------~g~~a~t~~~~~~~~~---~sll~~~l~tGRtHQ 185 (232)
T PRK10839 138 SPVAD-----------DTAEQFAKGVQL------HNEKDLTKPAVLEVIT---PTQVRLTISEGRYHQ 185 (232)
T ss_pred CCCCH-----------HHHHHHHCCeEE------CCCcccccccEEEEec---CCEEEEEEEcCcCHH
Confidence 65532 211111112222 4677899999998853 399999999999999
No 16
>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=99.95 E-value=7.2e-29 Score=197.37 Aligned_cols=126 Identities=25% Similarity=0.323 Sum_probs=97.5
Q ss_pred EEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceE
Q 026204 63 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 142 (241)
Q Consensus 63 llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGl 142 (241)
|+|+|||+|++|++.......++.+.+... ..++.+|||||++||||
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~~---------------------------------~~~~~~vhRLD~~TsGl 47 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDV---------------------------------GERLFPVGRLDYDTEGL 47 (146)
T ss_pred CEEEECCCCcEecccCCCCCCEEeeecccc---------------------------------CCCEEECCCCCCCCeeE
Confidence 589999999999988765556665543211 23578999999999999
Q ss_pred EEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEe
Q 026204 143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL 222 (241)
Q Consensus 143 ll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~ 222 (241)
||||+|+++++.|+. +.+.++|+|+|+|.|.++.+.+ .. +. ..... .+++.+.|+|++++..
T Consensus 48 ll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~~~~--~~-~~-------~~~~~------~~~~~~~t~~~~l~~~ 109 (146)
T cd02870 48 LLLTNDGELANRLTH--PRYGVEKTYLVKVRGVPSEEEL--RR-LR-------AGVEL------DDGKTAPAKVKVLSRD 109 (146)
T ss_pred EEEeCCHHHHHHhhC--ccCCCCeEEEEEECCCCCHHHH--HH-HH-------CCeEe------CCceEcceEEEEeccC
Confidence 999999999999986 6778999999999999864432 11 10 00111 2567899999999763
Q ss_pred cCCCEEEEEEEcCCCCCCC
Q 026204 223 AGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 223 ~~~~~slv~~~l~TGR~HQ 241 (241)
.++++++|+|.|||+||
T Consensus 110 --~~~sll~~~l~tGR~HQ 126 (146)
T cd02870 110 --PKNTLLEVTLHEGRNRQ 126 (146)
T ss_pred --CCCcEEEEEEEeCCcHH
Confidence 46799999999999999
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=99.95 E-value=4.3e-28 Score=197.05 Aligned_cols=128 Identities=20% Similarity=0.206 Sum_probs=100.4
Q ss_pred cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204 62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 141 (241)
Q Consensus 62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 141 (241)
.++|+|||+|++||+.......++.+.+..+. ..++++|||||++|||
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 37899999999999876555678888775431 1356789999999999
Q ss_pred EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEE
Q 026204 142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEI 221 (241)
Q Consensus 142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~ 221 (241)
|||||+|.++++.|+. +++.+.|+|+|+|.|.++.+. +. .+ . . .+.. .+++.+.|+|+++..
T Consensus 49 Lll~ak~~~~~~~L~~--~~~~i~K~Y~a~V~g~~~~~~--~~-~~---~-~----gv~~-----~~~~~~~~~~~~~~~ 110 (167)
T cd02556 49 LLLFTNDGELANRLMH--PSNEIEREYAVRVFGQVTDEQ--LK-SL---K-K----GVEL-----EDGFAGFKSIQLEGG 110 (167)
T ss_pred EEEEECCHHHHHHHhC--CcCCCCeEEEEEECccCCHHH--HH-HH---H-c----CCEE-----CCCcCcceEEEEEec
Confidence 9999999999999976 888999999999999986543 11 00 0 0 1111 156778899999975
Q ss_pred ecCCCEEEEEEEcCCCCCCC
Q 026204 222 LAGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 222 ~~~~~~slv~~~l~TGR~HQ 241 (241)
..++|+++|+|.|||+||
T Consensus 111 --~~~~sll~v~l~tGR~HQ 128 (167)
T cd02556 111 --EGKNSWYRVTLREGRNRE 128 (167)
T ss_pred --CCCcEEEEEEEEeCCCHH
Confidence 346799999999999999
No 18
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=99.93 E-value=1e-25 Score=197.73 Aligned_cols=165 Identities=18% Similarity=0.153 Sum_probs=115.2
Q ss_pred eEEecCeecCCCceecCCC--EEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHh
Q 026204 15 ALFLSMDKLSVSHNVKGGD--MVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHH 92 (241)
Q Consensus 15 ~v~vng~~~~~~~~l~~GD--~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~ 92 (241)
.|.|||+++.+++.|..+| .|.+....... . . ..-||+.|+++|||+|++|++.......|+.+.+...
T Consensus 28 ~V~VNG~~~~~g~~V~~~~~d~I~v~g~~~~~---~-~-----~~~e~~~ylvlnKP~G~~~s~~d~~~~~tv~d~l~~~ 98 (289)
T PRK10700 28 RVSVDGKIATLGDRVEVTPGLKIRIDGHLISV---K-E-----SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKL 98 (289)
T ss_pred CEEECCEeccCCCEeCCCCCeEEEECCEEeec---c-c-----ccccCCeEEEEECCCCCEeecCCCCCCccHHHHhhhh
Confidence 4899999999999998874 46553211100 0 0 0015578999999999999988766667898887642
Q ss_pred cCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEE
Q 026204 93 CSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLT 172 (241)
Q Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV 172 (241)
. ..++++|||||++||||||||+|.++++.|.+ +.+.++|+|+|+|
T Consensus 99 ~--------------------------------~~~~~~VgRLD~dTsGLLLlTndg~~~~~L~~--p~~~i~K~Y~v~V 144 (289)
T PRK10700 99 R--------------------------------GARWIAVGRLDVNTCGLLLFTTDGELANRLMH--PSREVEREYAVRV 144 (289)
T ss_pred c--------------------------------CCceeEccCCCCCCceEEEEEcCHHHHHHHhC--ccCCCCeEEEEEE
Confidence 1 13467899999999999999999999999987 8889999999999
Q ss_pred ecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEec-CCCEEEEEEEcCCCCCCC
Q 026204 173 SGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILA-GGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 173 ~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~-~~~~slv~~~l~TGR~HQ 241 (241)
.|.+++... . .+. . .+.+. ++. |.+..+.... ....+++++.|.+||+||
T Consensus 145 ~G~~~~~~l--~-~l~-~-----Gv~l~-------~~~---~~~~~v~~~~~~~~~s~l~v~L~EGk~hQ 195 (289)
T PRK10700 145 FGQVDDAKL--R-QLS-R-----GVQLE-------DGP---AAFKTIKFSGGEGINQWYNVTLTEGRNRE 195 (289)
T ss_pred ccCCCHHHH--H-HHH-c-----CCEeC-------Cce---eeeEEEEeccCCCCceEEEEEEeCCccHH
Confidence 998864332 1 110 0 01111 121 2233333321 234589999999999998
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=99.93 E-value=8.3e-26 Score=183.64 Aligned_cols=124 Identities=20% Similarity=0.246 Sum_probs=90.7
Q ss_pred EEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceE
Q 026204 63 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 142 (241)
Q Consensus 63 llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGl 142 (241)
|+|+|||+|++||++. ....++.+.+..++. ..++++|||||++||||
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 7899999999999654 445788888766531 13578899999999999
Q ss_pred EEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEe
Q 026204 143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL 222 (241)
Q Consensus 143 ll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~ 222 (241)
||||+|.++++.|.+ +.+.++|+|+|+|.|.++.+.. .... . .+.... +.+...+.+++++
T Consensus 50 ll~ak~~~~~~~l~~--~~~~i~K~Y~a~V~G~~~~~~~--~~~~----~---~~~~~~------~~~~~~~~~~~~~-- 110 (167)
T cd02553 50 LLLTNDGQLAHRLTS--PKKHVPKTYEVTLAGPLTEDDI--EAFA----E---GVLLHD------GYPTKPAKLEILS-- 110 (167)
T ss_pred EEEEeCHHHHHHhhC--CcCCCceEEEEEEccCCCHHHH--HHHH----C---CeEEcC------CCEeeeeEEEEeC--
Confidence 999999999988877 6788999999999999865432 1110 0 011111 1123445565553
Q ss_pred cCCCEEEEEEEcCCCCCCC
Q 026204 223 AGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 223 ~~~~~slv~~~l~TGR~HQ 241 (241)
.++++|+|.|||+||
T Consensus 111 ----~sll~v~l~tGR~HQ 125 (167)
T cd02553 111 ----PTTVRLTITEGKYHQ 125 (167)
T ss_pred ----CcEEEEEEEeCCCHH
Confidence 299999999999999
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=99.92 E-value=1.3e-25 Score=182.74 Aligned_cols=136 Identities=17% Similarity=0.224 Sum_probs=93.0
Q ss_pred EEEEECCCCceeecCCC-CCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204 63 VLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 141 (241)
Q Consensus 63 llVinKPaGl~~~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 141 (241)
++|+|||+|++||+... ....++.+.+.. .++++|||||++|||
T Consensus 1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l~~-----------------------------------~~~~~v~RLD~~TsG 45 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYIDD-----------------------------------PGVYAAGRLDRDSEG 45 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCccHHHHcCc-----------------------------------CCeEEccCCCCCCeE
Confidence 58999999999998765 444566655421 235789999999999
Q ss_pred EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccE-EEccee-eCCC-CCeeEEEecCCCCCCCCcceEEEEEE
Q 026204 142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGR-IEVPIS-RDPN-NRIRMAAIPGSNKHGQARHAASRYKV 218 (241)
Q Consensus 142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~-i~~~i~-~~~~-~~~~~~~~~~~~~~~~~k~a~T~~~v 218 (241)
|||||+|+++++.|.+ +.+.++|+|+|+|.|.++.+... +...+. .+.. ......... .+....|.|++
T Consensus 46 lll~a~d~~~~~~l~~--~~~~v~K~Y~a~v~g~~~~~~~~~l~~g~~~~~~~~~~~~v~~~~------~~~~~~~~~~~ 117 (168)
T cd02566 46 LLLLTDDGRLQHRITD--PSFKHPKTYYVQVEGVPTEDALEQLRNGVELGDGLTLPAKVEKVD------EPPWLWEREPP 117 (168)
T ss_pred EEEEEeCHHHHHHHHC--CCCCCCEEEEEEECCcCCHHHHHHHhCCcEECCeEecceEEEEec------ccccccccccc
Confidence 9999999999888877 45679999999999998643210 011111 1111 111111111 22345566666
Q ss_pred EEEecCCCEEEEEEEcCCCCCCC
Q 026204 219 IEILAGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 219 l~~~~~~~~slv~~~l~TGR~HQ 241 (241)
+....+.+.|+++|+|.|||+||
T Consensus 118 ~~~~~~~~~sll~v~l~tGR~HQ 140 (168)
T cd02566 118 IRFRKNIPTSWIEITICEGKNRQ 140 (168)
T ss_pred cccccCCCccEEEEEEecCccHH
Confidence 76543456789999999999999
No 21
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=99.92 E-value=2.7e-25 Score=194.69 Aligned_cols=116 Identities=22% Similarity=0.312 Sum_probs=94.9
Q ss_pred eEEecCeecCCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcC
Q 026204 15 ALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 94 (241)
Q Consensus 15 ~v~vng~~~~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~ 94 (241)
.|.|||+++.+++.|.+||.|.+..... .+ ..+||++|+|+|||+|++||+... ...|+.+.+...
T Consensus 32 ~V~VNGk~v~~~~~V~~gD~V~v~g~~i-----~~------~~~ed~~~lvlnKP~G~~~~~~~~-~~~tv~~~l~~~-- 97 (290)
T PRK10475 32 NVFINGKRATIGDQVKAGDVVKVNGQLI-----EP------REAEDLVLIALNKPVGIVSTTEDG-ERDNIVDFVNHS-- 97 (290)
T ss_pred cEEECCEEccCCCCcCCCCEEEECCEEc-----cc------cccCCCeEEEEECCCCCCcCCCCC-CCCcHHHHhhcc--
Confidence 4899999999999999999999864211 11 013788999999999999997765 356887776532
Q ss_pred CCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEec
Q 026204 95 LPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSG 174 (241)
Q Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G 174 (241)
.++++|||||++||||||||+|.++++.|.+ +.+.++|+|+|+|.|
T Consensus 98 --------------------------------~~l~~VgRLDrdTsGLLLlT~dg~~~~~L~~--p~~~i~K~Y~v~V~g 143 (290)
T PRK10475 98 --------------------------------KRVFPIGRLDKDSQGLIFLTNHGDLVNKILR--AGNDHEKEYLVTVDK 143 (290)
T ss_pred --------------------------------ccccccccCCCCCcceEEEecCHHHHHHhhC--cCCCCCeEEEEEECC
Confidence 2467899999999999999999999999977 667899999999999
Q ss_pred ccCC
Q 026204 175 VPSQ 178 (241)
Q Consensus 175 ~~~~ 178 (241)
.+++
T Consensus 144 ~~~~ 147 (290)
T PRK10475 144 PITD 147 (290)
T ss_pred CCCH
Confidence 8854
No 22
>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=99.87 E-value=1.4e-22 Score=165.93 Aligned_cols=89 Identities=21% Similarity=0.274 Sum_probs=64.4
Q ss_pred CccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCcc-EEEcceeeCCCCCeeEEEecCCCCC
Q 026204 128 RPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSG-RIEVPISRDPNNRIRMAAIPGSNKH 206 (241)
Q Consensus 128 ~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~-~i~~~i~~~~~~~~~~~~~~~~~~~ 206 (241)
++++|||||++||||||||+|..+++.|++ +.+.+.|+|+|+|.|.++.+.. .+..++..+.
T Consensus 46 ~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~--~~~~i~K~Y~v~v~g~~~~~~l~~l~~g~~~~~--------------- 108 (177)
T cd02555 46 RLAPIGPLDKDASGLLVFSQDGRVLRKLIG--DASRLEQEYLVEVRGELTAGGLERLNHGLTYDG--------------- 108 (177)
T ss_pred ceeEecCCCCCCeeEEEEECCHHHHHHHhC--hhcCCCEEEEEEEcccCCHHHHHHHhcCcccCC---------------
Confidence 577899999999999999999999999999 5678999999999999865321 1222221110
Q ss_pred CCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204 207 GQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 207 ~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ 241 (241)
...+++.+.+ .+.+++++.|.|||+||
T Consensus 109 ~~~~~~~~~~--------~~~~~l~i~l~tGr~hQ 135 (177)
T cd02555 109 RELPPAKVSW--------QNEQRLRFALKEPQPGQ 135 (177)
T ss_pred eecceEEEEE--------cCCCEEEEEEECCcChH
Confidence 0011223222 13589999999999998
No 23
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.86 E-value=6.1e-22 Score=166.35 Aligned_cols=83 Identities=24% Similarity=0.340 Sum_probs=69.5
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
..|+++|||+|++|++.......++.+.+.. .++++|||||++||
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 3599999999999997655555677766531 24678999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCc
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSS 180 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~ 180 (241)
||||+|+|.++++.|.+ +++.+.|+|+|+|.|.++.+.
T Consensus 84 GllLlt~d~~~~~~L~~--~~~~i~K~Y~~~v~g~~~~~~ 121 (217)
T PRK11394 84 GLLVLTNNGALQARLTQ--PGKRTGKIYYVQVEGIPTQDA 121 (217)
T ss_pred eEEEEECCHHHHHHHhC--cccCCCEEEEEEECCCCCHHH
Confidence 99999999999999999 577899999999999986544
No 24
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=1.2e-20 Score=160.98 Aligned_cols=164 Identities=20% Similarity=0.223 Sum_probs=114.4
Q ss_pred eEEecCeecC-CCceecCCC-EEEEEecCCCCccCCCCCCCccEEE-ecCcEEEEECCCCceeecCCCCCCCCHHHHHHH
Q 026204 15 ALFLSMDKLS-VSHNVKGGD-MVNCTISELQPLRAEAEDIPLDIVY-EDDNVLVVNKPAHMVVHPAPGNATGTLVNGILH 91 (241)
Q Consensus 15 ~v~vng~~~~-~~~~l~~GD-~i~~~~~~~~~~~~~~~~~~~~Ily-ed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~ 91 (241)
.|.|||++++ .+..+.+++ .|.+.... +.+ +...|+++|||.|+.|+......+.|+.+.+..
T Consensus 28 ~V~VnG~v~~~~~~~v~~~~~~i~v~g~~--------------~~~~~~~~y~llnKP~G~v~s~~D~~gr~tv~D~lp~ 93 (248)
T COG1187 28 RVTVNGKVATLGGVVVDPDDDVVEVDGKR--------------IELKEERVYLLLNKPRGYVSSTEDDEGRPTVFDLLPE 93 (248)
T ss_pred CEEECCEEeccCCeEeCCCCcEEEECCEE--------------eeccccceEEEEECCCCeEecccCCCCCceeeeeccc
Confidence 4899999876 677888774 66663311 222 233399999999999998766667788777654
Q ss_pred hcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEE
Q 026204 92 HCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISL 171 (241)
Q Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~Al 171 (241)
.. +...++++|+|||++||||||++.|.+++++|.+ ++..++|+|+|.
T Consensus 94 ~~------------------------------~~~~~~~pvGRLD~dTeGLLLLTnDG~la~rL~~--P~~~~~K~Y~v~ 141 (248)
T COG1187 94 RL------------------------------PRKKRLFPVGRLDKDTEGLLLLTNDGELAHRLMH--PSSEVEKEYLVR 141 (248)
T ss_pred cc------------------------------ccccceeeccccCCCCeeEEEEeCCHHHHHHhcC--CCCCCCEEEEEE
Confidence 31 1135688999999999999999999999999988 999999999999
Q ss_pred EecccCCCcc-EEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204 172 TSGVPSQSSG-RIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 172 V~G~~~~~~~-~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ 241 (241)
|.|.++++.. .+...+. .. ++....+....+......+.|++++.|..||+||
T Consensus 142 v~g~~~~~~l~~l~~Gv~----------l~-------d~~~~~~~~~~l~~~~~~~~s~~~itl~EGrnrQ 195 (248)
T COG1187 142 VEGPVTEEDLEKLRKGVT----------LD-------DGETKPAKPASLEKEPGKNNSWLRITLTEGRNRQ 195 (248)
T ss_pred EecCCCHHHHHHHhCCcE----------ec-------CcccccceeEEEEecCCCCceEEEEEEeCCcCHH
Confidence 9998754321 0111111 11 2222233322232221226799999999999998
No 25
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.
Probab=99.81 E-value=4.3e-20 Score=149.34 Aligned_cols=120 Identities=17% Similarity=0.155 Sum_probs=84.9
Q ss_pred EEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceE
Q 026204 63 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 142 (241)
Q Consensus 63 llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGl 142 (241)
|+++|||+|++|++... ...++.+++.. ..++++|||||++||||
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 68999999999998754 34677766532 13578899999999999
Q ss_pred EEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEe
Q 026204 143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL 222 (241)
Q Consensus 143 ll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~ 222 (241)
||||+|.+++++|+. +...+.|+|+|.|.|.+..... ..-..+ +.. . + +.|....++..
T Consensus 47 ll~t~dg~~~~~L~~--p~~~~~K~Y~V~v~~~l~~~~l------~~l~~G---~~~-~------~---~~~~~~~v~~~ 105 (164)
T cd02554 47 ILLTNDGDLVNKILH--ADNNHEKEYLVTVNKPITDEFI------EGMSNG---VVI-L------G---TVTKPCKVERL 105 (164)
T ss_pred EEEEcCHHHHHHHhh--hhcCCCeEEEEEECCCCCHHHH------HHHhCC---CEE-C------C---eEEcceEEEEC
Confidence 999999999999976 6677999999999998764321 000000 000 1 1 23333334432
Q ss_pred cCCCEEEEEEEcCCCCCCC
Q 026204 223 AGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 223 ~~~~~slv~~~l~TGR~HQ 241 (241)
. . +.++|.|.+||+||
T Consensus 106 ~--~-~~l~i~l~eGr~~q 121 (164)
T cd02554 106 A--K-DKFRIVLTQGLNRQ 121 (164)
T ss_pred C--C-CEEEEEEECCcCHH
Confidence 1 2 35999999999998
No 26
>TIGR00093 pseudouridine synthase. This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc.
Probab=99.79 E-value=1.2e-19 Score=141.17 Aligned_cols=90 Identities=22% Similarity=0.396 Sum_probs=70.9
Q ss_pred cccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcc
Q 026204 132 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH 211 (241)
Q Consensus 132 vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~ 211 (241)
|||||++||||||||+|+++++.|.. +.+.+.|+|+|+|.|.++.+. ++ ++.. ... .. +++.
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~--~~~~i~K~Y~a~v~g~~~~~~--~~-~~~~------g~~-~~------~~~~ 62 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTH--PGHHCEKTYLVTVEGPVTDED--LE-ALRK------GVQ-LE------DGPT 62 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhC--CCCCCCeEEEEEECCCCCHHH--HH-HHhC------CeE-EC------CcEE
Confidence 79999999999999999999999988 788899999999999886543 11 1210 011 11 4556
Q ss_pred eEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204 212 AASRYKVIEILAGGGSALVEWRLETGRTHQ 241 (241)
Q Consensus 212 a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ 241 (241)
+.+.|+++.. ..+.++++|+|.|||+||
T Consensus 63 ~~~~~~~l~~--~~~~~~l~~~l~tGR~HQ 90 (128)
T TIGR00093 63 KPAKLEVITE--PGFPTWLRITLSEGRNRQ 90 (128)
T ss_pred eeeEEEEEcc--CCCceEEEEEEeCCCCHH
Confidence 7888998875 245789999999999999
No 27
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=99.27 E-value=7e-12 Score=106.18 Aligned_cols=76 Identities=24% Similarity=0.243 Sum_probs=56.6
Q ss_pred cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204 62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 141 (241)
Q Consensus 62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 141 (241)
.++|||||+||.++... +.+...+...+. .....+.|||||.+|||
T Consensus 1 GilvvnKP~Gi~s~~~~----~~~~~~l~~~~~------------------------------~~k~~~~vhrLD~~aSG 46 (226)
T cd02868 1 GLFAVYKPPGVHWKHVR----DTIESNLLKYFP------------------------------EDKVLVGVHRLDAFSSG 46 (226)
T ss_pred CEEEEEcCCCCChhHHH----HHHHHHHHHHcc------------------------------ccceeeEccccCCCCce
Confidence 37999999999876431 333333333322 11235678999999999
Q ss_pred EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
+|+||+++.+ +|...|..+.+.|+|+|...
T Consensus 47 vl~~a~~~~t--kl~~~~~~~~~~K~Y~~~~~ 76 (226)
T cd02868 47 VLVLGVNHGN--KLLSHLYSNHPTRVYTIRGL 76 (226)
T ss_pred EEEEEeChhH--hHHHHHHhcCCCeEEEEEEE
Confidence 9999999986 69999999999999997644
No 28
>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=98.02 E-value=1.7e-05 Score=65.33 Aligned_cols=70 Identities=21% Similarity=0.256 Sum_probs=54.8
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.++++|||.|+-+| .++..+...+. ..+++..+-||-..|
T Consensus 2 ~g~l~i~Kp~g~tS~--------~~v~~~k~~~~-------------------------------~kkvGH~GTLDp~A~ 42 (182)
T cd02572 2 YGVINLDKPSGPSSH--------EVVAWIKRILG-------------------------------VEKTGHSGTLDPKVT 42 (182)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhC-------------------------------CCccCcCCCCCCcCe
Confidence 469999999999775 46777776654 246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-+. +.++...+.. ..|+|.|.+.
T Consensus 43 GvLiv~~g~--~Tk~~~~~~~--~~K~Y~a~v~ 71 (182)
T cd02572 43 GCLPVCIDR--ATRLVKSQQE--AGKEYVCVMR 71 (182)
T ss_pred eEEEEEECH--HhhhhHHHhC--CCCEEEEEEE
Confidence 999999997 3555555554 4599999876
No 29
>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=97.79 E-value=3.8e-05 Score=51.68 Aligned_cols=43 Identities=35% Similarity=0.505 Sum_probs=35.2
Q ss_pred eEEecCeec-CCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEE
Q 026204 15 ALFLSMDKL-SVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVN 67 (241)
Q Consensus 15 ~v~vng~~~-~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVin 67 (241)
+|.+||+++ +++..+.+||.|.+..... +..|+|||++++|+|
T Consensus 27 ~V~vn~~~~~~~~~~v~~~d~i~i~~~~~----------~~~i~~ed~~~lvv~ 70 (70)
T cd00165 27 HVLVNGKVVTKPSYKVKPGDVIEVDGKSI----------EEDIVYEDKKLLVVN 70 (70)
T ss_pred CEEECCEEccCCccCcCCCCEEEEcCCCc----------ccceeeccCCEEEeC
Confidence 488999998 7999999999998864211 127999999999986
No 30
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.77 E-value=5.8e-05 Score=64.08 Aligned_cols=71 Identities=18% Similarity=0.341 Sum_probs=56.4
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.+++||||.|+-+| .++..+...+. ..+++..+.||-..|
T Consensus 9 ~G~l~i~KP~g~TS~--------dvv~~ikk~~~-------------------------------~kKvGH~GTLDP~At 49 (230)
T PRK00989 9 EGILLVDKPQGRTSF--------SLIRSLTKLIG-------------------------------VKKIGHAGTLDPFAT 49 (230)
T ss_pred CEEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCcCCcCccCCCCCe
Confidence 479999999999775 46777777654 256788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-.+ .+.+|.+.+.. ..|+|+|.+.
T Consensus 50 GvLiv~vG~-~aTkl~~~~~~--~~K~Y~~~~~ 79 (230)
T PRK00989 50 GVMVMLIGR-KFTRLSDILLF--EDKEYAAVAH 79 (230)
T ss_pred eEEEEEECC-chhhhHHHhcC--CCcEEEEEEE
Confidence 999999876 34556666655 7899999876
No 31
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker
Probab=97.76 E-value=7.9e-05 Score=62.62 Aligned_cols=69 Identities=22% Similarity=0.287 Sum_probs=55.1
Q ss_pred cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204 62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 141 (241)
Q Consensus 62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 141 (241)
.++.||||.|+-+| .+++.++..+. ..+++..+.||-..||
T Consensus 1 Gil~i~KP~g~tS~--------~vv~~ik~~~~-------------------------------~kKvGH~GTLDP~AsG 41 (210)
T cd00506 1 GLFAVDKPQGPSSH--------DVVDTIRRIFL-------------------------------AEKVGHGGTLDPFATG 41 (210)
T ss_pred CEEEEEcCCCCCHH--------HHHHHHHHHhC-------------------------------ccccCCCCcCCCcCee
Confidence 37899999999775 46777776653 2467889999999999
Q ss_pred EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
+|+++-+.. .++...|.. ..|+|.|.+.
T Consensus 42 vLiv~vG~a--Tkl~~~~~~--~~K~Y~~~~~ 69 (210)
T cd00506 42 VLVVGIGKA--TKLLKHLLA--ATKDYTAIGR 69 (210)
T ss_pred EEEEEECHH--HhhhHHHhc--CCceEEEEEE
Confidence 999999973 556666655 8999999876
No 32
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=97.74 E-value=8.7e-05 Score=64.60 Aligned_cols=70 Identities=23% Similarity=0.319 Sum_probs=56.1
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.++++|||+|+-+| .++.+++..+. ..+.+..+-||-..|
T Consensus 2 ngil~vdKP~g~tS~--------~vv~~ikk~~~-------------------------------~kKvGH~GTLDP~At 42 (273)
T PRK04099 2 NRLFVANKPAGMSSN--------AFLSRLKRKYG-------------------------------VKKAGFSGTLDPFAK 42 (273)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccccCccCCCCCe
Confidence 368999999999875 47788887654 256788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-.+. .+|...+.. ..|+|.|.+.
T Consensus 43 GvLiv~iG~a--TKl~~~l~~--~~K~Y~a~~~ 71 (273)
T PRK04099 43 GVLIVAFGQY--TKLFRFLKK--TPKTYRATLW 71 (273)
T ss_pred eEEEEEEChH--hhhHHHhcc--CCceEEEEEE
Confidence 9999999975 446666655 4899999866
No 33
>TIGR00431 TruB tRNA pseudouridine 55 synthase. TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific
Probab=97.73 E-value=9.2e-05 Score=62.11 Aligned_cols=70 Identities=19% Similarity=0.291 Sum_probs=56.1
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.+++||||.|+-+| .+++.+...+. ..+++..+.||-..|
T Consensus 2 ~G~l~v~KP~g~tS~--------~vv~~vkk~~~-------------------------------~kKvGH~GTLDP~As 42 (209)
T TIGR00431 2 NGVLLLDKPQGMTSF--------DALAKVRRLLN-------------------------------VKKVGHTGTLDPFAT 42 (209)
T ss_pred CeEEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------CCcCCCCCCCCCcCc
Confidence 368999999999764 46777777654 246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-+..+ +|...+. ...|+|.|.+.
T Consensus 43 GvLiv~vG~~T--kl~~~~~--~~~K~Y~~~~~ 71 (209)
T TIGR00431 43 GVLPILVGKAT--KLSPYLT--DLDKEYRAEIR 71 (209)
T ss_pred eEEEEEEChHh--hhhHHHc--CCCCeEEEEEE
Confidence 99999999853 6666665 48999999865
No 34
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=97.68 E-value=0.00013 Score=62.50 Aligned_cols=70 Identities=20% Similarity=0.327 Sum_probs=55.1
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.++++|||.|+-+| .++..++..+. ..+++..+-||-..|
T Consensus 10 ~Gil~vdKP~G~TS~--------dvv~~vkr~~~-------------------------------~kKvGH~GTLDP~At 50 (244)
T PRK00020 10 DGVLLLDKPVGLSSN--------HALQRAKRTVD-------------------------------AAKAGHTGTLDPFAT 50 (244)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhC-------------------------------CCCCCcCCcCCCcCe
Confidence 479999999999775 46777777654 256788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-.. +.+|...+.. ..|+|+|.+.
T Consensus 51 GvLiv~iG~--aTKl~~~l~~--~~K~Y~a~~~ 79 (244)
T PRK00020 51 GLLVCCMGR--ATKISGRMLE--ADKTYQATLQ 79 (244)
T ss_pred eEEEEEECH--HhhhhHHhcc--CCcEEEEEEE
Confidence 999999997 3555555544 5599999865
No 35
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=97.60 E-value=0.00018 Score=63.39 Aligned_cols=70 Identities=21% Similarity=0.245 Sum_probs=55.4
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.++++|||+|+-+| .++..++..+. ..+++..+.||-..|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~At 43 (294)
T PRK02484 3 NGIINLKKEAGMTSH--------DAVFKLRKILQ-------------------------------TKKIGHGGTLDPDVV 43 (294)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccccCCCCCCCCe
Confidence 368999999999875 46777777654 256788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-... .++.+.+.. ..|+|.|.+.
T Consensus 44 GvL~i~vG~a--Tkl~~~l~~--~~K~Y~a~~~ 72 (294)
T PRK02484 44 GVLPIAVGKA--TRLIEYMTE--AGKVYEGEIT 72 (294)
T ss_pred eEEEEEEChh--hhhhHHhcc--CCcEEEEEEE
Confidence 9999999974 446665654 4599999876
No 36
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=97.57 E-value=0.00025 Score=62.85 Aligned_cols=70 Identities=24% Similarity=0.330 Sum_probs=55.7
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.++++|||.|+-+| .++..++..+. ..+++..+-||-..|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~At 43 (308)
T PRK14124 3 HGFLVAYKPKGPTSH--------DVVDEVRKKLK-------------------------------TRKVGHAGTLDPFAT 43 (308)
T ss_pred ceEEEEECCCCCCHH--------HHHHHHHHHcC-------------------------------CCccCcCcCCCCCCc
Confidence 368999999999875 46777777654 256788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-+.. .+|.+.+.. -.|+|+|.+.
T Consensus 44 GvL~v~vG~a--Tkl~~~l~~--~~K~Y~a~~~ 72 (308)
T PRK14124 44 GVLIVGVNKA--TRLLEYLKN--EKKVYYVKMR 72 (308)
T ss_pred EEEEEEEChH--HhhhHHHhc--CCceEEEEEE
Confidence 9999999974 446666655 3899999876
No 37
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=97.55 E-value=0.00023 Score=63.06 Aligned_cols=70 Identities=20% Similarity=0.253 Sum_probs=56.2
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.+++||||.|+-+| .++..++..+. ..+++..+.||-..|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At 43 (305)
T PRK14123 3 NGILPVYKERGLTSH--------DVVFKLRKILK-------------------------------TKKIGHTGTLDPEVA 43 (305)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccccCcCCCCcCe
Confidence 369999999999875 46777777654 256788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-.+. .+|.+.+.. ..|+|.|.+.
T Consensus 44 GvL~v~vG~a--Tkl~~~l~~--~~K~Y~~~~~ 72 (305)
T PRK14123 44 GVLPVCIGNA--TRVSDYVMD--MGKAYEATVS 72 (305)
T ss_pred eEEEEEEChh--hhhHHHhcC--CCcEEEEEEE
Confidence 9999999985 356666655 7899999875
No 38
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=97.53 E-value=0.00023 Score=62.81 Aligned_cols=71 Identities=24% Similarity=0.384 Sum_probs=56.0
Q ss_pred cCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCC
Q 026204 60 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 139 (241)
Q Consensus 60 d~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T 139 (241)
-+.+++||||.|+-+| .++..++..+. ..+++..+-||-..
T Consensus 8 ~~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~A 48 (298)
T PRK03287 8 GSGLVVVDKPAGMTSH--------DVVARCRRLFG-------------------------------TRKVGHAGTLDPMA 48 (298)
T ss_pred cCeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCCCCcCccCCCcc
Confidence 3579999999999775 46777777654 24678899999999
Q ss_pred ceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 140 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 140 SGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
||+|+++-.. +.++...+.+ ..|+|.|.+.
T Consensus 49 tGvL~i~vG~--aTKl~~~l~~--~~K~Y~a~~~ 78 (298)
T PRK03287 49 TGVLVLGVER--ATKLLGHLTL--TDKSYTATIR 78 (298)
T ss_pred eeEEEEEeCh--hhhhhHHHhc--CCcEEEEEEE
Confidence 9999999996 3555555655 4899999865
No 39
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=97.53 E-value=0.00024 Score=62.10 Aligned_cols=68 Identities=24% Similarity=0.362 Sum_probs=53.7
Q ss_pred EEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceE
Q 026204 63 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 142 (241)
Q Consensus 63 llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGl 142 (241)
++++|||.|+-+| .++..+...+. ..+++..+.||-..||+
T Consensus 2 il~i~KP~G~tS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~AtGv 42 (279)
T PRK02193 2 IKLLYKPKGISSF--------KFIKNFAKTNN-------------------------------IKKIGHTGTLDPLASGL 42 (279)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHcC-------------------------------CCccccCccCCCcCeeE
Confidence 6899999999875 36677776653 25678899999999999
Q ss_pred EEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 143 ll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+++-.+. .++...+.+ ..|+|.|.+.
T Consensus 43 L~v~vG~a--Tkl~~~l~~--~~K~Y~a~~~ 69 (279)
T PRK02193 43 LLVATDED--TKLIDYLDQ--KDKTYIAKIK 69 (279)
T ss_pred EEEEEChh--hhhhHHhcc--CCcEEEEEEE
Confidence 99999973 556666633 7899999866
No 40
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=97.53 E-value=0.00027 Score=62.22 Aligned_cols=70 Identities=21% Similarity=0.248 Sum_probs=55.8
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.++++|||.|+-+| .++..++..+. ..+++..+-||-..|
T Consensus 2 ~Gil~i~KP~G~tS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At 42 (290)
T PRK00130 2 DGILNILKPPGMTSF--------DVVRKIRKIAK-------------------------------IKKVGHTGTLDPLAS 42 (290)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccCcCCCCCCCCe
Confidence 368999999999775 46777777654 246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-... .+|.+.+.. ..|+|.|.+.
T Consensus 43 GvL~v~vG~a--Tkl~~~l~~--~~K~Y~a~~~ 71 (290)
T PRK00130 43 GVLPVCLGKA--TKIVDYLME--GKKTYRAEIK 71 (290)
T ss_pred eEEEEEEChh--hhhHHHhcc--CCcEEEEEEE
Confidence 9999999973 456666655 4899999876
No 41
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=97.50 E-value=0.00031 Score=62.73 Aligned_cols=70 Identities=21% Similarity=0.218 Sum_probs=55.3
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.+++||||.|+-+| .+++.++..+. ..+++..+.||-..|
T Consensus 3 nGiL~idKP~G~TS~--------dvv~~vrk~l~-------------------------------~kKVGH~GTLDP~At 43 (345)
T PRK14846 3 NYWLNIYKPRGISSA--------QLVSIVKKILG-------------------------------KTKIGHAGTLDVEAE 43 (345)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCcCCcCccCCCcCc
Confidence 479999999999875 46777777654 256788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-... .++...+.. ..|+|+|.+.
T Consensus 44 GVL~i~vG~a--TKl~~~l~~--~~K~Y~a~~~ 72 (345)
T PRK14846 44 GILPFAVGEA--TKLIHLLID--ARKTYIFTVK 72 (345)
T ss_pred eEEEEEEChh--hhhhHHHhc--CCceEEEEEE
Confidence 9999999873 555555544 6789999865
No 42
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Probab=97.50 E-value=0.0003 Score=61.55 Aligned_cols=69 Identities=23% Similarity=0.363 Sum_probs=55.2
Q ss_pred cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204 62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 141 (241)
Q Consensus 62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 141 (241)
.++.+|||.|+-+| .++..++..+. ..+++..+-||-..||
T Consensus 1 Gil~i~KP~G~tS~--------~vv~~vr~~~~-------------------------------~kKvGH~GTLDP~AtG 41 (277)
T cd02573 1 GILLLDKPAGLTSH--------DVVQKVRRLLG-------------------------------TKKVGHTGTLDPLATG 41 (277)
T ss_pred CEEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------cCccCCCCCCCCcCeE
Confidence 37899999999875 46777777654 2467889999999999
Q ss_pred EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
+|+++-+.. .+|...+.. ..|+|+|.+.
T Consensus 42 vL~v~vG~a--Tkl~~~l~~--~~K~Y~~~~~ 69 (277)
T cd02573 42 VLPIALGEA--TKLSQYLLD--ADKTYRATVR 69 (277)
T ss_pred EEEEEEChH--HhhHHHhcC--CCcEEEEEEE
Confidence 999999974 456666655 6999999876
No 43
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=97.50 E-value=0.00029 Score=62.41 Aligned_cols=70 Identities=21% Similarity=0.204 Sum_probs=55.6
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.+++||||.|+-+| .++..++..+. ..+++..+-||-..|
T Consensus 13 ~Gil~i~KP~G~TS~--------dvv~~vrk~~~-------------------------------~kKvGH~GTLDP~At 53 (305)
T PRK05389 13 SGWLILDKPAGMTST--------EAVSKVKWLFD-------------------------------AQKAGHAGTLDPLAS 53 (305)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhc-------------------------------ccccCCcccCCCCCc
Confidence 579999999999875 46777777654 246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-.. +.+|...+.. ..|+|+|.+.
T Consensus 54 GvL~v~vG~--aTkl~~~l~~--~~K~Y~a~~~ 82 (305)
T PRK05389 54 GVLPIALGE--ATKTVPYVMD--GTKRYRFTVA 82 (305)
T ss_pred eEEEEEECh--hhhhhHHhcc--CCcEEEEEEE
Confidence 999999987 3555565644 4899999865
No 44
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=97.49 E-value=0.00031 Score=61.95 Aligned_cols=69 Identities=23% Similarity=0.252 Sum_probs=55.1
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.++++|||.|+-+| .++..++..+. ..+++..+-||-..|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At 43 (295)
T PRK02755 3 FGFLNLDKPAGLTSH--------DCVARLRRLLR-------------------------------LKRVGHGGTLDPAAT 43 (295)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccccCCCCCCcCe
Confidence 369999999999875 46777777654 246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-.+.+ +|.+.+.. .|+|.|.+.
T Consensus 44 GvL~i~vG~aT--kl~~~l~~---~K~Y~a~~~ 71 (295)
T PRK02755 44 GVLPIALGKAT--RLLPYLPG---EKTYRGTIR 71 (295)
T ss_pred eEEEEEEChhh--hhHHHhCC---CcEEEEEEE
Confidence 99999999854 56666642 699999865
No 45
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=97.47 E-value=0.00033 Score=62.12 Aligned_cols=71 Identities=17% Similarity=0.209 Sum_probs=55.7
Q ss_pred cCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCC
Q 026204 60 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 139 (241)
Q Consensus 60 d~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T 139 (241)
-+.++++|||.|+-+| .+++.++..+. ..+++..+-||-..
T Consensus 21 ~~g~l~i~Kp~g~tS~--------~~v~~~r~~~~-------------------------------~kkvGH~GTLDp~A 61 (300)
T PRK04270 21 KFGVVNLDKPPGPTSH--------EVAAWVRDILG-------------------------------VEKAGHGGTLDPKV 61 (300)
T ss_pred CCCEEEEECCCCCCHH--------HHHHHHHHHhc-------------------------------cccccCCCCCCCcC
Confidence 4579999999999775 46777777653 24678899999999
Q ss_pred ceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 140 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 140 SGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
||+|+++-+.. .+|.+.+.. ..|+|.|.+.
T Consensus 62 ~GvL~v~~g~a--tk~~~~~~~--~~K~Y~~~~~ 91 (300)
T PRK04270 62 TGVLPVALGKA--TKVVQALLE--SGKEYVCVMH 91 (300)
T ss_pred eEEEEEEEChH--hhhhHHhcc--CCcEEEEEEE
Confidence 99999999873 566666654 4599999865
No 46
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=97.46 E-value=0.00038 Score=61.24 Aligned_cols=70 Identities=21% Similarity=0.253 Sum_probs=54.8
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.+++||||.|+-+| .++..++..+. ..+++..+-||-..|
T Consensus 3 ~GiL~i~KP~G~TS~--------dvv~~vrk~~~-------------------------------~kKvGH~GTLDP~At 43 (292)
T PRK01528 3 NYWLNIYKPRGISSA--------KLVSIVKKILG-------------------------------KVKIGHAGTLDVEAE 43 (292)
T ss_pred CEEEEEeCCCCCCHH--------HHHHHHHHHcC-------------------------------CCccCcCccCCCcCc
Confidence 479999999999775 46777777653 256788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-... .++...+.. ..|+|.|.+.
T Consensus 44 GvL~v~vG~a--TKl~~~l~~--~~K~Y~~~~~ 72 (292)
T PRK01528 44 GVLPLAVGEA--TKLVQLLID--AKKTYIFTVK 72 (292)
T ss_pred eEEEEEEChH--hhhhHHHhc--CCceEEEEEE
Confidence 9999999873 455555544 5699999865
No 47
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=97.45 E-value=0.00039 Score=61.69 Aligned_cols=70 Identities=19% Similarity=0.289 Sum_probs=56.0
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.+++||||.|+-+| .++..++..+. ..+++..+-||-..|
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~At 50 (312)
T PRK05033 10 NGVLLLDKPQGMSSN--------DALQKVKRLFN-------------------------------ANKAGHTGALDPLAT 50 (312)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCCCCCCCcCCCcCe
Confidence 579999999999875 36777777653 256788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-.+. .+|.+.+.. ..|+|.|.+.
T Consensus 51 GvL~v~vG~a--Tkl~~~~~~--~~K~Y~a~~~ 79 (312)
T PRK05033 51 GMLPICLGEA--TKFSQYLLD--SDKRYRVTAR 79 (312)
T ss_pred eEEEEEECHH--hhhhHHhcC--CCcEEEEEEE
Confidence 9999999974 446666655 5899999876
No 48
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=97.44 E-value=0.00043 Score=61.19 Aligned_cols=70 Identities=20% Similarity=0.288 Sum_probs=55.6
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.+++||||.|+-+| .++..++..+. ..+++..+-||-..|
T Consensus 16 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~At 56 (303)
T PRK01851 16 DGVLLLDKPLGLSSN--------DALQRAKRLLR-------------------------------AKKAGHTGTLDPLAT 56 (303)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------cccCCCCCCCCCCCc
Confidence 589999999999875 46777777654 246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-... .+|.+.+.. ..|+|.|.+.
T Consensus 57 GvL~v~vG~a--Tkl~~~l~~--~~K~Y~~~~~ 85 (303)
T PRK01851 57 GLLPLCFGEA--TKFSQDLLD--ADKTYEATLR 85 (303)
T ss_pred eEEEEEECHH--HhhhHHhcc--cCeEEEEEEE
Confidence 9999999974 446666655 4599999865
No 49
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=97.43 E-value=0.00041 Score=61.43 Aligned_cols=70 Identities=21% Similarity=0.293 Sum_probs=55.6
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.+++||||.||-+| .++..++..+. ..+++..+-||-..|
T Consensus 2 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At 42 (304)
T PRK01550 2 NGVLLLHKPRGMTSH--------DCVFKLRKILR-------------------------------TKKVGHTGTLDPEVS 42 (304)
T ss_pred CeEEEEECCCCCCHH--------HHHHHHHHHcC-------------------------------CCCcccCCCCCCcCe
Confidence 368999999999875 46777777654 246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-... .+|.+.+.. ..|+|.|.+.
T Consensus 43 GvL~i~vG~a--Tkl~~~l~~--~~K~Y~a~~~ 71 (304)
T PRK01550 43 GVLPICVGRA--TKIAEYLTD--EGKTYEGEVT 71 (304)
T ss_pred eEEEEEEChh--hhhhHHhcC--CCcEEEEEEE
Confidence 9999999974 446666655 4899999876
No 50
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=97.28 E-value=0.00074 Score=59.93 Aligned_cols=69 Identities=26% Similarity=0.396 Sum_probs=54.6
Q ss_pred cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204 62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 141 (241)
Q Consensus 62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 141 (241)
.+++||||.|+-+| .++..++..+. ..+++..+-||-..||
T Consensus 2 ~il~idKP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~AtG 42 (312)
T PRK14122 2 PVYAVDKPLGLTSH--------DVVNRARRALG-------------------------------TRRVGHTGTLDPLATG 42 (312)
T ss_pred cEEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------CCCCCCCCCCCCcCee
Confidence 37899999999775 46777777654 2567889999999999
Q ss_pred EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
+|+++-... .+|...+. ...|+|.|.+.
T Consensus 43 vL~i~iG~a--TKl~~~l~--~~~K~Y~a~~~ 70 (312)
T PRK14122 43 VLVLCTDDS--TKLVPFLS--AEDKEYLAWVS 70 (312)
T ss_pred eEEEEEChh--hhhhHHhc--CCCceEEEEEE
Confidence 999999974 34766663 37899999875
No 51
>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=97.24 E-value=0.00073 Score=60.46 Aligned_cols=71 Identities=20% Similarity=0.276 Sum_probs=56.2
Q ss_pred cCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCC
Q 026204 60 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT 139 (241)
Q Consensus 60 d~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T 139 (241)
.+.++++|||.|+-+| .++..++..+. ..+++..+-||-..
T Consensus 33 ~~G~l~i~KP~g~tS~--------~~v~~vr~~~~-------------------------------~kkvGH~GTLDP~A 73 (322)
T TIGR00425 33 SYGVVNLDKPSGPSSH--------EVVAWVRRILN-------------------------------VEKTGHGGTLDPKV 73 (322)
T ss_pred CCCEEEEeCCCCCCHH--------HHHHHHHHHhc-------------------------------ccccCCCCCCCCCC
Confidence 3579999999999875 46777777654 24678899999999
Q ss_pred ceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 140 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 140 SGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
||+|+++-.. +.+|.+.+.. ..|+|+|.+.
T Consensus 74 ~GvL~v~~G~--aTkl~~~~~~--~~K~Y~~~v~ 103 (322)
T TIGR00425 74 TGVLPVCIER--ATRLVKSLQE--APKEYVCLMR 103 (322)
T ss_pred ceEEEEEECh--HhhccHHhcc--CCCEEEEEEE
Confidence 9999999987 3566666654 7899998875
No 52
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=97.21 E-value=0.00096 Score=58.91 Aligned_cols=70 Identities=19% Similarity=0.244 Sum_probs=56.0
Q ss_pred CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204 61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS 140 (241)
Q Consensus 61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS 140 (241)
+.+++||||.|+-+| .+++.++..+. ..+++..+-||-..|
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At 50 (300)
T PRK04642 10 DGILLLDKPAGLSSN--------NALQAARRLLR-------------------------------AEKGGHTGSLDPLAT 50 (300)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhC-------------------------------CCcccCCCccCCcCe
Confidence 579999999999875 47788877764 246788999999999
Q ss_pred eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
|+|+++-.. +.+|.+.+.. ..|+|+|.+.
T Consensus 51 GvL~v~~G~--aTkl~~~l~~--~~K~Y~a~~~ 79 (300)
T PRK04642 51 GLLPLCFGE--ATKIAGLLLG--SAKAYDAEIV 79 (300)
T ss_pred eeEEEEECh--hhhhhHHhcC--CCcEEEEEEE
Confidence 999999987 3566666654 6899999874
No 53
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=96.97 E-value=0.002 Score=56.11 Aligned_cols=69 Identities=17% Similarity=0.241 Sum_probs=55.0
Q ss_pred cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204 62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG 141 (241)
Q Consensus 62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG 141 (241)
.++++|||.|+-+| .++.++...++ ..+.+..+-||-..||
T Consensus 16 Gil~ldKP~G~tS~--------~~v~~vkkil~-------------------------------~~K~GH~GTLDP~atG 56 (271)
T COG0130 16 GVINLDKPPGPTSH--------EVVAWVKRILG-------------------------------VEKAGHGGTLDPLATG 56 (271)
T ss_pred ceEEeeCCCCCCHH--------HHHHHHHHHhC-------------------------------ccccccccccCCcccc
Confidence 89999999999775 46777777764 2566789999999999
Q ss_pred EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
+|.+|-. + +.+|.+.+.. ..|+|.|.+.
T Consensus 57 vLpi~ig-~-aTKl~~~l~~--~~K~Y~a~~~ 84 (271)
T COG0130 57 VLPICLG-E-ATKLVQYLLD--ADKEYVATVR 84 (271)
T ss_pred eEEEEec-h-hHhHHHHHhh--CCcEEEEEEE
Confidence 9999998 3 4555555544 7899999976
No 54
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=96.82 E-value=0.0035 Score=55.72 Aligned_cols=93 Identities=17% Similarity=0.207 Sum_probs=55.3
Q ss_pred cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCcccccccccccccccccccccccc-----ccCCCCCCccccccCC
Q 026204 62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSS-----SISGASIRPGIVHRLD 136 (241)
Q Consensus 62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~vhRLD 136 (241)
.+++||||.|+-++ .+++.++..+.....-.. .+..+ .... |+. .......+++..+-||
T Consensus 1 Gil~i~KP~G~TS~--------~vv~~lk~~l~~s~~~~~---~~~~~---~~~~-~~~~~~~~~~~~~~~KiGH~GTLD 65 (312)
T cd02867 1 GVFAINKPSGITSA--------QVLNDLKPLFLNSALFKD---KIQRA---VAKR-GKKARRRKGRKRSKLKIGHGGTLD 65 (312)
T ss_pred CeEEEeCCCCCCHH--------HHHHHHHHHhcccccccc---hhhhh---hhhh-hhhhhhhccccccccccccccccC
Confidence 37899999999775 467777776642100000 00000 0000 000 0011125788899999
Q ss_pred CCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 137 KGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 137 ~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
-..||+|+++-... .+.++ .|.. ..|+|.|.+.
T Consensus 66 PlAsGVLvvgvG~a-TK~l~-~~l~--~~K~Y~~~~~ 98 (312)
T cd02867 66 PLATGVLVVGVGAG-TKQLQ-DYLS--CSKTYEATGL 98 (312)
T ss_pred CccceeEEEEECcH-HHHHH-HHhc--CCceEEEEEE
Confidence 99999999999874 34444 4444 8999999865
No 55
>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=94.17 E-value=0.19 Score=35.82 Aligned_cols=29 Identities=21% Similarity=0.179 Sum_probs=25.8
Q ss_pred CCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 126 SIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 126 ~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
..+++.++++|+.++|+++++ ++|...+.
T Consensus 23 ~~~i~~aG~kDk~a~t~q~v~-------------------n~f~i~~r 51 (87)
T cd01291 23 PKRVGYAGRKDKRAVTTQLVS-------------------NRFTITLR 51 (87)
T ss_pred hheEEECccCCCCeeEEEEEc-------------------ccEEEEEE
Confidence 356789999999999999999 88888887
No 56
>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=93.87 E-value=0.056 Score=35.82 Aligned_cols=23 Identities=9% Similarity=0.209 Sum_probs=20.9
Q ss_pred eEEecCeec-CCCceecCCCEEEE
Q 026204 15 ALFLSMDKL-SVSHNVKGGDMVNC 37 (241)
Q Consensus 15 ~v~vng~~~-~~~~~l~~GD~i~~ 37 (241)
.|+|||+++ +++++|++||.|.+
T Consensus 35 ~V~VNg~~~~~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 35 EVLVNGELENRRGKKLYPGDVIEI 58 (59)
T ss_pred CEEECCEEccCCCCCCCCCCEEEe
Confidence 489999998 68999999999986
No 57
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=93.47 E-value=0.13 Score=36.63 Aligned_cols=28 Identities=18% Similarity=0.171 Sum_probs=24.9
Q ss_pred eeeEEecCeecCCCceecCCCEEEEEec
Q 026204 13 VLALFLSMDKLSVSHNVKGGDMVNCTIS 40 (241)
Q Consensus 13 ~~~v~vng~~~~~~~~l~~GD~i~~~~~ 40 (241)
|..|.|||+.+..++++++||+|.++..
T Consensus 49 V~~i~vNG~~v~~~~~~~~Gd~v~V~P~ 76 (81)
T PF14451_consen 49 VGLILVNGRPVDFDYRLKDGDRVAVYPV 76 (81)
T ss_pred eEEEEECCEECCCcccCCCCCEEEEEec
Confidence 4568999999999999999999999754
No 58
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=93.34 E-value=0.1 Score=38.46 Aligned_cols=27 Identities=19% Similarity=0.272 Sum_probs=24.6
Q ss_pred eEEecCeecCCCceecCCCEEEEEecC
Q 026204 15 ALFLSMDKLSVSHNVKGGDMVNCTISE 41 (241)
Q Consensus 15 ~v~vng~~~~~~~~l~~GD~i~~~~~~ 41 (241)
.|.+||.+++++..|+.||+|.+.+..
T Consensus 35 rV~vNG~~aKpS~~VK~GD~l~i~~~~ 61 (100)
T COG1188 35 RVKVNGQRAKPSKEVKVGDILTIRFGN 61 (100)
T ss_pred eEEECCEEcccccccCCCCEEEEEeCC
Confidence 499999999999999999999998754
No 59
>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=92.59 E-value=0.1 Score=32.82 Aligned_cols=21 Identities=24% Similarity=0.227 Sum_probs=19.2
Q ss_pred eEEecCeecC-CCceecCCCEE
Q 026204 15 ALFLSMDKLS-VSHNVKGGDMV 35 (241)
Q Consensus 15 ~v~vng~~~~-~~~~l~~GD~i 35 (241)
.|+|||++++ +++.|.+||+|
T Consensus 27 ~V~VNg~~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 27 RVKVNGKVVKDPSYIVKPGDVI 48 (48)
T ss_dssp TEEETTEEESSTTSBESTTEEE
T ss_pred EEEECCEEEcCCCCCCCCcCCC
Confidence 4899999988 99999999986
No 60
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=92.03 E-value=0.11 Score=44.30 Aligned_cols=22 Identities=32% Similarity=0.416 Sum_probs=19.3
Q ss_pred CccccccCCCCCceEEEeecCH
Q 026204 128 RPGIVHRLDKGTSGLLVVAKDE 149 (241)
Q Consensus 128 ~~~~vhRLD~~TSGlll~Ak~~ 149 (241)
.+.++||||-.|||+++|.-+-
T Consensus 90 ~V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559|consen 90 DVQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred ceeeEEeecccccceEEEecCc
Confidence 4688999999999999998764
No 61
>PRK01777 hypothetical protein; Validated
Probab=91.28 E-value=0.25 Score=36.28 Aligned_cols=28 Identities=11% Similarity=0.037 Sum_probs=24.9
Q ss_pred eeEEecCeecCCCceecCCCEEEEEecC
Q 026204 14 LALFLSMDKLSVSHNVKGGDMVNCTISE 41 (241)
Q Consensus 14 ~~v~vng~~~~~~~~l~~GD~i~~~~~~ 41 (241)
..+-|||+.++.++.|+.||+|+++.+.
T Consensus 50 ~~vgI~Gk~v~~d~~L~dGDRVeIyrPL 77 (95)
T PRK01777 50 NKVGIYSRPAKLTDVLRDGDRVEIYRPL 77 (95)
T ss_pred ceEEEeCeECCCCCcCCCCCEEEEecCC
Confidence 4578999999999999999999998654
No 62
>smart00363 S4 S4 RNA-binding domain.
Probab=91.06 E-value=0.25 Score=31.38 Aligned_cols=26 Identities=23% Similarity=0.142 Sum_probs=22.9
Q ss_pred eeEEecCeec-CCCceecCCCEEEEEe
Q 026204 14 LALFLSMDKL-SVSHNVKGGDMVNCTI 39 (241)
Q Consensus 14 ~~v~vng~~~-~~~~~l~~GD~i~~~~ 39 (241)
.+|+|||+++ .++..+..||.|.+..
T Consensus 26 g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 26 GRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred CCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 3589999998 7999999999998865
No 63
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. This entry represents pseudouridine synthase TruB, as well as Cbf5p that modifies rRNA [].; GO: 0006396 RNA processing; PDB: 1SGV_B 2AUS_C 3UAI_A 3U28_A 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=89.31 E-value=0.46 Score=37.80 Aligned_cols=43 Identities=23% Similarity=0.282 Sum_probs=32.7
Q ss_pred CCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204 127 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173 (241)
Q Consensus 127 ~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~ 173 (241)
.+++..+.||-..||||+++-+.. .+|...+.. ..|+|.|.+.
T Consensus 7 ~KvGH~GTLDP~AsGvL~v~vg~~--Tkl~~~l~~--~~K~Y~~~~~ 49 (149)
T PF01509_consen 7 KKVGHGGTLDPFASGVLVVGVGKA--TKLLSYLQN--SDKEYVATIR 49 (149)
T ss_dssp SSEEESS-SSTT-EEEEEEEEGGG--GGGHHHHTT--SEEEEEEEEE
T ss_pred ceeccccccCCcceEEEEEEECCc--chHHHHhhc--cCCEEEEEEE
Confidence 577889999999999999999873 446666655 5599999865
No 64
>PRK06437 hypothetical protein; Provisional
Probab=86.95 E-value=0.92 Score=30.91 Aligned_cols=25 Identities=24% Similarity=0.159 Sum_probs=22.6
Q ss_pred eEEecCeecCCCceecCCCEEEEEe
Q 026204 15 ALFLSMDKLSVSHNVKGGDMVNCTI 39 (241)
Q Consensus 15 ~v~vng~~~~~~~~l~~GD~i~~~~ 39 (241)
++-+||+.+..++.|+.||+|.+..
T Consensus 38 aV~vNg~iv~~~~~L~dgD~Veiv~ 62 (67)
T PRK06437 38 VVIVNGSPVLEDHNVKKEDDVLILE 62 (67)
T ss_pred EEEECCEECCCceEcCCCCEEEEEe
Confidence 7789999999999999999999853
No 65
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=86.22 E-value=0.82 Score=38.35 Aligned_cols=27 Identities=15% Similarity=0.210 Sum_probs=24.1
Q ss_pred eEEecCeecC-CCceecCCCEEEEEecC
Q 026204 15 ALFLSMDKLS-VSHNVKGGDMVNCTISE 41 (241)
Q Consensus 15 ~v~vng~~~~-~~~~l~~GD~i~~~~~~ 41 (241)
.|.|||+++. |++.|.+||.+.|....
T Consensus 120 HI~VnGk~V~iPSy~V~~gdei~V~~k~ 147 (205)
T COG0522 120 HILVNGKRVNIPSYLVSPGDEISVREKS 147 (205)
T ss_pred eEEECCEEeccCcEEecCCCEEEeeecc
Confidence 4899999988 99999999999997654
No 66
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=82.80 E-value=1.6 Score=30.18 Aligned_cols=28 Identities=14% Similarity=0.250 Sum_probs=25.1
Q ss_pred eeeeeEEecCeecCCCceecCCCEEEEE
Q 026204 11 VSVLALFLSMDKLSVSHNVKGGDMVNCT 38 (241)
Q Consensus 11 ~~~~~v~vng~~~~~~~~l~~GD~i~~~ 38 (241)
.+...+.|||+.++.++.|+.||+|.+.
T Consensus 47 ~~~~~v~vNg~~v~~~~~l~~gD~v~i~ 74 (80)
T cd00754 47 LARVRIAVNGEYVRLDTPLKDGDEVAII 74 (80)
T ss_pred hhcEEEEECCeEcCCCcccCCCCEEEEe
Confidence 4667899999999999999999999985
No 67
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=82.36 E-value=1.5 Score=34.17 Aligned_cols=25 Identities=8% Similarity=-0.039 Sum_probs=22.9
Q ss_pred eEEecCeecCCCceecCCCEEEEEe
Q 026204 15 ALFLSMDKLSVSHNVKGGDMVNCTI 39 (241)
Q Consensus 15 ~v~vng~~~~~~~~l~~GD~i~~~~ 39 (241)
.|.|||+++|++..|..||.|.|..
T Consensus 35 ~V~vnG~~~Kps~~V~~gd~l~v~~ 59 (133)
T PRK10348 35 KVHYNGQRSKPSKIVELNATLTLRQ 59 (133)
T ss_pred CEEECCEECCCCCccCCCCEEEEEE
Confidence 4899999999999999999999965
No 68
>PRK11507 ribosome-associated protein; Provisional
Probab=81.63 E-value=1.6 Score=30.18 Aligned_cols=24 Identities=8% Similarity=0.062 Sum_probs=21.1
Q ss_pred eEEecCeecC-CCceecCCCEEEEE
Q 026204 15 ALFLSMDKLS-VSHNVKGGDMVNCT 38 (241)
Q Consensus 15 ~v~vng~~~~-~~~~l~~GD~i~~~ 38 (241)
.|.|||+... .+.+|.+||.|.+.
T Consensus 38 ~V~VNGeve~rRgkKl~~GD~V~~~ 62 (70)
T PRK11507 38 QVKVDGAVETRKRCKIVAGQTVSFA 62 (70)
T ss_pred ceEECCEEecccCCCCCCCCEEEEC
Confidence 4899999865 79999999999994
No 69
>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=81.11 E-value=1.6 Score=29.26 Aligned_cols=26 Identities=19% Similarity=0.286 Sum_probs=22.3
Q ss_pred eeEEecCeecCCC----ceecCCCEEEEEe
Q 026204 14 LALFLSMDKLSVS----HNVKGGDMVNCTI 39 (241)
Q Consensus 14 ~~v~vng~~~~~~----~~l~~GD~i~~~~ 39 (241)
.+|-+||+.+..+ +.|+.||+|.+..
T Consensus 31 i~V~vNg~~v~~~~~~~~~L~~gD~V~ii~ 60 (65)
T cd00565 31 VAVALNGEIVPRSEWASTPLQDGDRIEIVT 60 (65)
T ss_pred EEEEECCEEcCHHHcCceecCCCCEEEEEE
Confidence 3788999999877 8999999999853
No 70
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=81.02 E-value=2 Score=29.43 Aligned_cols=25 Identities=20% Similarity=0.106 Sum_probs=22.4
Q ss_pred eeEEecCeecCCCceecCCCEEEEE
Q 026204 14 LALFLSMDKLSVSHNVKGGDMVNCT 38 (241)
Q Consensus 14 ~~v~vng~~~~~~~~l~~GD~i~~~ 38 (241)
-++-+||+.+..++.|+.||+|.+.
T Consensus 40 v~v~vNg~iv~~~~~l~~gD~Veii 64 (70)
T PRK08364 40 AIAKVNGKVALEDDPVKDGDYVEVI 64 (70)
T ss_pred EEEEECCEECCCCcCcCCCCEEEEE
Confidence 5678999999999999999999985
No 71
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=80.33 E-value=2.2 Score=29.75 Aligned_cols=29 Identities=10% Similarity=0.105 Sum_probs=24.9
Q ss_pred ceeeeeEEecCeecCCCceecCCCEEEEE
Q 026204 10 QVSVLALFLSMDKLSVSHNVKGGDMVNCT 38 (241)
Q Consensus 10 ~~~~~~v~vng~~~~~~~~l~~GD~i~~~ 38 (241)
..+...|.+|++.+..+..|+.||+|.+.
T Consensus 46 ~~~~~~v~vn~~~v~~~~~l~dgDevai~ 74 (80)
T TIGR01682 46 SRGQVMVAVNEEYVTDDALLNEGDEVAFI 74 (80)
T ss_pred hccceEEEECCEEcCCCcCcCCCCEEEEe
Confidence 34556799999999999999999999985
No 72
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=77.95 E-value=2.1 Score=30.69 Aligned_cols=30 Identities=10% Similarity=-0.009 Sum_probs=17.2
Q ss_pred eeeeEEecCeecCCCceecCCCEEEEEecC
Q 026204 12 SVLALFLSMDKLSVSHNVKGGDMVNCTISE 41 (241)
Q Consensus 12 ~~~~v~vng~~~~~~~~l~~GD~i~~~~~~ 41 (241)
+-..+=|-|+.++.++.|+.||+|+|+.+.
T Consensus 45 ~~~~vGIfGk~~~~d~~L~~GDRVEIYRPL 74 (84)
T PF03658_consen 45 EKNKVGIFGKLVKLDTVLRDGDRVEIYRPL 74 (84)
T ss_dssp TTSEEEEEE-S--TT-B--TT-EEEEE-S-
T ss_pred ccceeeeeeeEcCCCCcCCCCCEEEEeccC
Confidence 345567889999999999999999999754
No 73
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=75.78 E-value=3.8 Score=27.37 Aligned_cols=26 Identities=19% Similarity=0.304 Sum_probs=21.0
Q ss_pred eeeEEecCeecC----CCceecCCCEEEEE
Q 026204 13 VLALFLSMDKLS----VSHNVKGGDMVNCT 38 (241)
Q Consensus 13 ~~~v~vng~~~~----~~~~l~~GD~i~~~ 38 (241)
..++-+||+.+. .++.|+.||+|.+.
T Consensus 31 ~vav~vNg~iv~r~~~~~~~l~~gD~vei~ 60 (66)
T PRK05659 31 RVAVEVNGEIVPRSQHASTALREGDVVEIV 60 (66)
T ss_pred eEEEEECCeEeCHHHcCcccCCCCCEEEEE
Confidence 346779997765 78899999999985
No 74
>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=75.70 E-value=3.2 Score=27.47 Aligned_cols=26 Identities=19% Similarity=0.341 Sum_probs=21.9
Q ss_pred eeeeEEecCeecCCCceecCCCEEEE
Q 026204 12 SVLALFLSMDKLSVSHNVKGGDMVNC 37 (241)
Q Consensus 12 ~~~~v~vng~~~~~~~~l~~GD~i~~ 37 (241)
.+.+..|||+.+..++.|..||.|++
T Consensus 33 ~~~~A~Vng~~vdl~~~L~~~d~v~i 58 (60)
T PF02824_consen 33 RAVAAKVNGQLVDLDHPLEDGDVVEI 58 (60)
T ss_dssp CEEEEEETTEEEETTSBB-SSEEEEE
T ss_pred heeEEEEcCEECCCCCCcCCCCEEEE
Confidence 34567799999999999999999987
No 75
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=75.35 E-value=3.3 Score=28.39 Aligned_cols=30 Identities=17% Similarity=0.280 Sum_probs=23.7
Q ss_pred ccceeeeeEEecCeecC----CCceecCCCEEEEE
Q 026204 8 FNQVSVLALFLSMDKLS----VSHNVKGGDMVNCT 38 (241)
Q Consensus 8 ~~~~~~~~v~vng~~~~----~~~~l~~GD~i~~~ 38 (241)
|+... -++-+||..+. .++.++.||+|.+-
T Consensus 29 ~~~~~-vav~vNg~iVpr~~~~~~~l~~gD~ievv 62 (68)
T COG2104 29 LNPEG-VAVAVNGEIVPRSQWADTILKEGDRIEVV 62 (68)
T ss_pred CCCce-EEEEECCEEccchhhhhccccCCCEEEEE
Confidence 44433 36889999988 89999999999984
No 76
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=75.34 E-value=1.5 Score=29.85 Aligned_cols=23 Identities=13% Similarity=0.237 Sum_probs=14.4
Q ss_pred eEEecCeecC-CCceecCCCEEEE
Q 026204 15 ALFLSMDKLS-VSHNVKGGDMVNC 37 (241)
Q Consensus 15 ~v~vng~~~~-~~~~l~~GD~i~~ 37 (241)
.|.|||+... .+.+|.+||.|.+
T Consensus 34 ~V~VNGe~e~rrg~Kl~~GD~V~~ 57 (65)
T PF13275_consen 34 EVKVNGEVETRRGKKLRPGDVVEI 57 (65)
T ss_dssp HHEETTB----SS----SSEEEEE
T ss_pred ceEECCEEccccCCcCCCCCEEEE
Confidence 3789999865 8999999999998
No 77
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=75.25 E-value=3.2 Score=27.74 Aligned_cols=27 Identities=15% Similarity=0.144 Sum_probs=22.5
Q ss_pred eeeeEEecCeecCC----CceecCCCEEEEE
Q 026204 12 SVLALFLSMDKLSV----SHNVKGGDMVNCT 38 (241)
Q Consensus 12 ~~~~v~vng~~~~~----~~~l~~GD~i~~~ 38 (241)
...+|-+|++.+.. ++.|+.||+|.+.
T Consensus 29 ~~vavavN~~iv~~~~~~~~~L~dgD~Ieiv 59 (65)
T PRK06488 29 NWLATAVNGELVHKEARAQFVLHEGDRIEIL 59 (65)
T ss_pred CeEEEEECCEEcCHHHcCccccCCCCEEEEE
Confidence 34578999999875 7899999999985
No 78
>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=74.69 E-value=3.8 Score=27.93 Aligned_cols=28 Identities=18% Similarity=0.158 Sum_probs=24.5
Q ss_pred eeeeEEecCeecCC---CceecCCCEEEEEe
Q 026204 12 SVLALFLSMDKLSV---SHNVKGGDMVNCTI 39 (241)
Q Consensus 12 ~~~~v~vng~~~~~---~~~l~~GD~i~~~~ 39 (241)
....+.|||+.+.. ++.|+.||+|.+..
T Consensus 42 ~~~~v~vN~~~v~~~~~~~~l~~gD~V~i~p 72 (77)
T PF02597_consen 42 DRVAVAVNGEIVPDDGLDTPLKDGDEVAILP 72 (77)
T ss_dssp TTEEEEETTEEEGGGTTTSBEETTEEEEEEE
T ss_pred ccEEEEECCEEcCCccCCcCcCCCCEEEEEC
Confidence 55678999999998 99999999999853
No 79
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=72.09 E-value=4.9 Score=27.95 Aligned_cols=24 Identities=13% Similarity=0.252 Sum_probs=21.0
Q ss_pred eEEecCeecC-CCceecCCCEEEEE
Q 026204 15 ALFLSMDKLS-VSHNVKGGDMVNCT 38 (241)
Q Consensus 15 ~v~vng~~~~-~~~~l~~GD~i~~~ 38 (241)
.|.|||+.-. .+.+|..||.|.+.
T Consensus 38 ~V~vNGe~EtRRgkKlr~gd~V~i~ 62 (73)
T COG2501 38 EVKVNGEVETRRGKKLRDGDVVEIP 62 (73)
T ss_pred eEEECCeeeeccCCEeecCCEEEEC
Confidence 5899999854 79999999999994
No 80
>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=72.07 E-value=3.9 Score=34.09 Aligned_cols=26 Identities=19% Similarity=0.316 Sum_probs=22.6
Q ss_pred eEEecCeec-CCCceecCCCEEEEEec
Q 026204 15 ALFLSMDKL-SVSHNVKGGDMVNCTIS 40 (241)
Q Consensus 15 ~v~vng~~~-~~~~~l~~GD~i~~~~~ 40 (241)
.|.|||+++ ++++.|++||.|.+...
T Consensus 116 ~V~VNgk~v~~ps~~V~~GD~I~V~~~ 142 (200)
T TIGR01017 116 HILVNGKKVDIPSYQVRPGDIISIKEK 142 (200)
T ss_pred CEEECCEEeCCCCCCCCCCCEEEEeeC
Confidence 489999997 58999999999999754
No 81
>PRK07440 hypothetical protein; Provisional
Probab=71.88 E-value=5.2 Score=27.40 Aligned_cols=26 Identities=19% Similarity=0.244 Sum_probs=20.5
Q ss_pred eeeEEecCeecC----CCceecCCCEEEEE
Q 026204 13 VLALFLSMDKLS----VSHNVKGGDMVNCT 38 (241)
Q Consensus 13 ~~~v~vng~~~~----~~~~l~~GD~i~~~ 38 (241)
-.+|-+||+.+. .++.|++||+|++.
T Consensus 35 ~vav~~N~~iv~r~~w~~~~L~~gD~IEIv 64 (70)
T PRK07440 35 LVAVEYNGEILHRQFWEQTQVQPGDRLEIV 64 (70)
T ss_pred eEEEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 346778998877 78888999998874
No 82
>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=70.41 E-value=6.1 Score=27.93 Aligned_cols=26 Identities=15% Similarity=0.261 Sum_probs=21.8
Q ss_pred eeeEEecCeecCCCc--eecCCCEEEEE
Q 026204 13 VLALFLSMDKLSVSH--NVKGGDMVNCT 38 (241)
Q Consensus 13 ~~~v~vng~~~~~~~--~l~~GD~i~~~ 38 (241)
-..|.|||+.+..+. .|+.||+|.+.
T Consensus 55 ~~~v~vN~~~v~~~~~~~l~dgdev~i~ 82 (88)
T TIGR01687 55 NVIILVNGRNVDWGLGTELKDGDVVAIF 82 (88)
T ss_pred cEEEEECCEecCccCCCCCCCCCEEEEe
Confidence 357899999987665 99999999985
No 83
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=70.11 E-value=4.1 Score=34.08 Aligned_cols=25 Identities=12% Similarity=0.094 Sum_probs=22.1
Q ss_pred eEEecCeec-CCCceecCCCEEEEEe
Q 026204 15 ALFLSMDKL-SVSHNVKGGDMVNCTI 39 (241)
Q Consensus 15 ~v~vng~~~-~~~~~l~~GD~i~~~~ 39 (241)
.|.|||+++ .+++.|++||.|.+..
T Consensus 115 ~V~VNGk~v~~ps~~Vk~GD~I~V~~ 140 (201)
T CHL00113 115 HILVNGRIVDIPSYRCKPKDIITVKD 140 (201)
T ss_pred cEEECCEEecCccccCCCCCEEEEcc
Confidence 489999998 4899999999999965
No 84
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=69.70 E-value=6.2 Score=27.54 Aligned_cols=24 Identities=25% Similarity=0.264 Sum_probs=22.0
Q ss_pred eEEecCeecCCCceecCCCEEEEE
Q 026204 15 ALFLSMDKLSVSHNVKGGDMVNCT 38 (241)
Q Consensus 15 ~v~vng~~~~~~~~l~~GD~i~~~ 38 (241)
.+.+||+.+..++.|+.||+|.+.
T Consensus 53 ~vavN~~~v~~~~~l~dgDeVai~ 76 (82)
T PLN02799 53 VLALNEEYTTESAALKDGDELAII 76 (82)
T ss_pred EEEECCEEcCCCcCcCCCCEEEEe
Confidence 588999999999999999999985
No 85
>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=68.64 E-value=4.4 Score=26.91 Aligned_cols=26 Identities=23% Similarity=0.383 Sum_probs=20.1
Q ss_pred eeeeEEecCeecCC--CceecCCCEEEE
Q 026204 12 SVLALFLSMDKLSV--SHNVKGGDMVNC 37 (241)
Q Consensus 12 ~~~~v~vng~~~~~--~~~l~~GD~i~~ 37 (241)
|-..++|||+++.+ .+.|..||.|.+
T Consensus 40 s~ngt~vng~~l~~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 40 STNGTFVNGQRLGPGEPVPLKDGDIIRF 67 (68)
T ss_dssp SSS-EEETTEEESSTSEEEE-TTEEEEE
T ss_pred CCCcEEECCEEcCCCCEEECCCCCEEEc
Confidence 56678999999887 778899999976
No 86
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=68.53 E-value=4.6 Score=33.76 Aligned_cols=25 Identities=24% Similarity=0.363 Sum_probs=22.2
Q ss_pred eEEecCeecC-CCceecCCCEEEEEe
Q 026204 15 ALFLSMDKLS-VSHNVKGGDMVNCTI 39 (241)
Q Consensus 15 ~v~vng~~~~-~~~~l~~GD~i~~~~ 39 (241)
.|.|||+++. +++.|.+||.|.+..
T Consensus 119 ~V~VNgk~v~~ps~~v~~GD~I~v~~ 144 (203)
T PRK05327 119 HILVNGKKVNIPSYRVKPGDVIEVRE 144 (203)
T ss_pred cEEECCEEECCCCcCCCCCCEEEECC
Confidence 4899999987 899999999999864
No 87
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=67.98 E-value=5.7 Score=26.93 Aligned_cols=26 Identities=19% Similarity=0.255 Sum_probs=20.7
Q ss_pred eeeEEecCeecCCC----ceecCCCEEEEE
Q 026204 13 VLALFLSMDKLSVS----HNVKGGDMVNCT 38 (241)
Q Consensus 13 ~~~v~vng~~~~~~----~~l~~GD~i~~~ 38 (241)
--+|-+||+.+..+ +.|+.||+|++-
T Consensus 32 ~vav~vN~~iv~r~~w~~~~L~~gD~iEIv 61 (67)
T PRK07696 32 IVVVERNKDILQKDDHTDTSVFDGDQIEIV 61 (67)
T ss_pred eEEEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 44688899987754 889999999884
No 88
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=65.87 E-value=7.4 Score=25.78 Aligned_cols=27 Identities=15% Similarity=0.213 Sum_probs=21.5
Q ss_pred eeeEEecCeecCC----CceecCCCEEEEEe
Q 026204 13 VLALFLSMDKLSV----SHNVKGGDMVNCTI 39 (241)
Q Consensus 13 ~~~v~vng~~~~~----~~~l~~GD~i~~~~ 39 (241)
-.++.+||+.+.. +..|+.||+|.+..
T Consensus 30 ~~~v~vN~~~v~~~~~~~~~L~~gD~vei~~ 60 (65)
T PRK06944 30 PFAVAVNGDFVARTQHAARALAAGDRLDLVQ 60 (65)
T ss_pred CeEEEECCEEcCchhcccccCCCCCEEEEEe
Confidence 3578999998753 67899999999853
No 89
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=62.11 E-value=8.9 Score=35.22 Aligned_cols=47 Identities=21% Similarity=0.352 Sum_probs=35.9
Q ss_pred CccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCC
Q 026204 128 RPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQ 178 (241)
Q Consensus 128 ~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~ 178 (241)
..+-..-||=+.||+++..-+.......+. ....|+|.+++.+.++-
T Consensus 96 k~Gh~gTlDP~vtg~l~v~~~~~tr~~~s~----~s~gk~yvg~~~lt~~v 142 (395)
T KOG2529|consen 96 KTGHSGTLDPEVTGCLIVCIDRATRLLKSQ----QSAGKEYVGIGKLTPEV 142 (395)
T ss_pred HhCCCCCCCccccceEEEEeecccccccch----hccCcEEEEEEecCcch
Confidence 345678899999999999998765544433 55899999998887643
No 90
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=62.05 E-value=10 Score=25.43 Aligned_cols=27 Identities=22% Similarity=0.247 Sum_probs=20.9
Q ss_pred eeeeEEecCeecC----CCceecCCCEEEEE
Q 026204 12 SVLALFLSMDKLS----VSHNVKGGDMVNCT 38 (241)
Q Consensus 12 ~~~~v~vng~~~~----~~~~l~~GD~i~~~ 38 (241)
+--+|-+|++.+. ..+.|++||.|.+.
T Consensus 30 ~~vaVavN~~iv~r~~w~~~~L~~gD~Ieii 60 (66)
T PRK08053 30 PGAALAINQQIIPREQWAQHIVQDGDQILLF 60 (66)
T ss_pred CcEEEEECCEEeChHHcCccccCCCCEEEEE
Confidence 3467889999876 45688999999884
No 91
>COG2914 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.81 E-value=9.2 Score=27.99 Aligned_cols=34 Identities=12% Similarity=0.189 Sum_probs=26.7
Q ss_pred ccceee--eeEEecCeecCCCceecCCCEEEEEecC
Q 026204 8 FNQVSV--LALFLSMDKLSVSHNVKGGDMVNCTISE 41 (241)
Q Consensus 8 ~~~~~~--~~v~vng~~~~~~~~l~~GD~i~~~~~~ 41 (241)
|.+.++ ..+=|-|++++.+..|+.||+|+++.+.
T Consensus 42 ~~~idl~~n~~GI~~k~~kl~~~l~dgDRVEIyRPL 77 (99)
T COG2914 42 FPDIDLHENKVGIYSKPVKLDDELHDGDRVEIYRPL 77 (99)
T ss_pred cccCCccccceeEEccccCccccccCCCEEEEeccc
Confidence 555555 4456778899999999999999998754
No 92
>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=61.46 E-value=8.6 Score=26.82 Aligned_cols=21 Identities=19% Similarity=0.341 Sum_probs=19.3
Q ss_pred ecCeecCCCceecCCCEEEEE
Q 026204 18 LSMDKLSVSHNVKGGDMVNCT 38 (241)
Q Consensus 18 vng~~~~~~~~l~~GD~i~~~ 38 (241)
.+|+++..++.|+.||+|++.
T Consensus 54 ~~gq~Vgl~~~L~d~DvVeI~ 74 (75)
T cd01666 54 HSPQRVGLDHVLEDEDVVQIV 74 (75)
T ss_pred CCCeECCCCCEecCCCEEEEe
Confidence 499999999999999999984
No 93
>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=60.92 E-value=8.2 Score=33.47 Aligned_cols=25 Identities=24% Similarity=0.218 Sum_probs=22.2
Q ss_pred eEEecCeec-CCCceecCCCEEEEEe
Q 026204 15 ALFLSMDKL-SVSHNVKGGDMVNCTI 39 (241)
Q Consensus 15 ~v~vng~~~-~~~~~l~~GD~i~~~~ 39 (241)
.|.|||+.+ ++++.|++||.|.+..
T Consensus 209 ~V~VNg~~v~~~s~~v~~gD~IsvrG 234 (257)
T TIGR03069 209 RLRLNWKTVTQPSRELKVGDRLQLRG 234 (257)
T ss_pred eEEECCEEcCCCCCcCCCCCEEEEcC
Confidence 489999988 6999999999999964
No 94
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=60.45 E-value=11 Score=26.36 Aligned_cols=24 Identities=21% Similarity=0.224 Sum_probs=21.5
Q ss_pred eEEecCeecCCCceecCCCEEEEE
Q 026204 15 ALFLSMDKLSVSHNVKGGDMVNCT 38 (241)
Q Consensus 15 ~v~vng~~~~~~~~l~~GD~i~~~ 38 (241)
.+.||++-+..++.|+.||+|.+.
T Consensus 52 ~~aVN~~~~~~~~~l~dgDeVai~ 75 (81)
T PRK11130 52 LAAVNQTLVSFDHPLTDGDEVAFF 75 (81)
T ss_pred EEEECCEEcCCCCCCCCCCEEEEe
Confidence 488999988899999999999985
No 95
>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=58.79 E-value=13 Score=24.61 Aligned_cols=27 Identities=15% Similarity=0.183 Sum_probs=21.4
Q ss_pred eeeeEEecCeecC----CCceecCCCEEEEE
Q 026204 12 SVLALFLSMDKLS----VSHNVKGGDMVNCT 38 (241)
Q Consensus 12 ~~~~v~vng~~~~----~~~~l~~GD~i~~~ 38 (241)
..-+|-+||+.+. ..+.|+.||+|.+.
T Consensus 28 ~~v~v~vN~~iv~~~~~~~~~L~~gD~veii 58 (64)
T TIGR01683 28 RRVAVAVNGEIVPRSEWDDTILKEGDRIEIV 58 (64)
T ss_pred CeEEEEECCEEcCHHHcCceecCCCCEEEEE
Confidence 4457889999875 34689999999985
No 96
>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=58.20 E-value=12 Score=27.13 Aligned_cols=29 Identities=10% Similarity=0.075 Sum_probs=23.5
Q ss_pred eeeeeEEecCeecC----CCceecCCCEEEEEe
Q 026204 11 VSVLALFLSMDKLS----VSHNVKGGDMVNCTI 39 (241)
Q Consensus 11 ~~~~~v~vng~~~~----~~~~l~~GD~i~~~~ 39 (241)
+|-.-|+|||+.+. .++.|+.||.|.+..
T Consensus 57 r~~i~VlvN~~di~~l~g~~t~L~dgD~v~i~P 89 (94)
T cd01764 57 RPGIIVLINDTDWELLGEEDYILEDGDHVVFIS 89 (94)
T ss_pred cCCEEEEECCccccccCCcccCCCCcCEEEEEC
Confidence 45667999998753 579999999999953
No 97
>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=58.00 E-value=15 Score=23.33 Aligned_cols=26 Identities=19% Similarity=0.271 Sum_probs=22.3
Q ss_pred eeeeEEecCeecCCCceecCCCEEEE
Q 026204 12 SVLALFLSMDKLSVSHNVKGGDMVNC 37 (241)
Q Consensus 12 ~~~~v~vng~~~~~~~~l~~GD~i~~ 37 (241)
.+.++.+||+.+..++.+..||+|.+
T Consensus 33 ~~va~~vng~~vdl~~~l~~~~~ve~ 58 (60)
T cd01668 33 RCVGAKVNGKLVPLSTVLKDGDIVEI 58 (60)
T ss_pred heEEEEECCEECCCCCCCCCCCEEEE
Confidence 45677899999999999999999876
No 98
>PF14478 DUF4430: Domain of unknown function (DUF4430); PDB: 3U7Z_B 2BB5_A.
Probab=54.94 E-value=12 Score=25.18 Aligned_cols=23 Identities=17% Similarity=0.309 Sum_probs=15.2
Q ss_pred eEEecCeecC---CCceecCCCEEEE
Q 026204 15 ALFLSMDKLS---VSHNVKGGDMVNC 37 (241)
Q Consensus 15 ~v~vng~~~~---~~~~l~~GD~i~~ 37 (241)
.++|||+.+. ..+.|++||.|.+
T Consensus 42 ~~~vNG~~~~~ga~~~~l~~GD~i~~ 67 (68)
T PF14478_consen 42 MYYVNGESANVGAGSYKLKDGDKITW 67 (68)
T ss_dssp EEEETTEE-SS-CCC-B--TTEEEEE
T ss_pred EEEECCEEhhcCcceeEeCCCCEEEe
Confidence 3678998765 4679999999986
No 99
>PLN00189 40S ribosomal protein S9; Provisional
Probab=54.93 E-value=16 Score=30.30 Aligned_cols=27 Identities=11% Similarity=0.001 Sum_probs=23.6
Q ss_pred EEecCeecC-CCceecCCCEEEEEecCC
Q 026204 16 LFLSMDKLS-VSHNVKGGDMVNCTISEL 42 (241)
Q Consensus 16 v~vng~~~~-~~~~l~~GD~i~~~~~~~ 42 (241)
|.|||+++. |++.|..|+.+.|.+.+.
T Consensus 136 I~V~~~~V~~Ps~~V~~~~e~~Itw~~~ 163 (194)
T PLN00189 136 IRVGKQIVNVPSFMVRVDSQKHIDFSLT 163 (194)
T ss_pred EeECCEEEecCcEEEecCCEEEEEEecC
Confidence 889999877 999999999999987653
No 100
>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=52.41 E-value=21 Score=22.02 Aligned_cols=26 Identities=15% Similarity=0.316 Sum_probs=21.9
Q ss_pred eeeeEEecCeecCCCceecCCCEEEE
Q 026204 12 SVLALFLSMDKLSVSHNVKGGDMVNC 37 (241)
Q Consensus 12 ~~~~v~vng~~~~~~~~l~~GD~i~~ 37 (241)
.+.+..+||+.+..++.|..||.|.+
T Consensus 33 ~~~~~~vn~~~~~l~~~l~~~~~i~~ 58 (60)
T cd01616 33 GFIGALVNGQLVDLSYTLQDGDTVSI 58 (60)
T ss_pred heEEEEECCEECCCCcCcCCCCEEEE
Confidence 55667799999999999999998876
No 101
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=51.84 E-value=15 Score=32.13 Aligned_cols=26 Identities=15% Similarity=0.250 Sum_probs=22.6
Q ss_pred eEEecCeec-CCCceecCCCEEEEEec
Q 026204 15 ALFLSMDKL-SVSHNVKGGDMVNCTIS 40 (241)
Q Consensus 15 ~v~vng~~~-~~~~~l~~GD~i~~~~~ 40 (241)
.|.||++.+ ++++.|++||.|.+...
T Consensus 217 ~V~vN~~~v~~~s~~v~~gD~isiRG~ 243 (267)
T PLN00051 217 DVRVNWREVTKNGTTLKTGDVVSVSGK 243 (267)
T ss_pred cEEECCEEcCCCCCCCCCCCEEEEeeC
Confidence 389999987 69999999999999754
No 102
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=48.29 E-value=22 Score=25.31 Aligned_cols=23 Identities=13% Similarity=0.238 Sum_probs=12.9
Q ss_pred eEEecCeecC----CCceecCCCEEEE
Q 026204 15 ALFLSMDKLS----VSHNVKGGDMVNC 37 (241)
Q Consensus 15 ~v~vng~~~~----~~~~l~~GD~i~~ 37 (241)
+|-+||+.+. ..+.|+.||+|.+
T Consensus 51 AVevNg~iVpr~~w~~t~L~egD~IEI 77 (84)
T PRK06083 51 VFAINNQVVPRSEWQSTVLSSGDAISL 77 (84)
T ss_pred EEEECCEEeCHHHcCcccCCCCCEEEE
Confidence 4556665543 2445666666665
No 103
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=47.96 E-value=21 Score=23.62 Aligned_cols=19 Identities=21% Similarity=0.015 Sum_probs=9.2
Q ss_pred cCeecCCCceecCCCEEEE
Q 026204 19 SMDKLSVSHNVKGGDMVNC 37 (241)
Q Consensus 19 ng~~~~~~~~l~~GD~i~~ 37 (241)
||=+++.+..|++||.|.+
T Consensus 35 NGF~~~~d~~L~e~D~v~~ 53 (57)
T PF14453_consen 35 NGFPTKEDIELKEGDEVFL 53 (57)
T ss_pred cCcccCCccccCCCCEEEE
Confidence 4444444445555554443
No 104
>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=44.98 E-value=9.2 Score=25.43 Aligned_cols=16 Identities=25% Similarity=0.401 Sum_probs=11.5
Q ss_pred cCcEEEEECCCCceee
Q 026204 60 DDNVLVVNKPAHMVVH 75 (241)
Q Consensus 60 d~~llVinKPaGl~~~ 75 (241)
...+|.+|||+|-.+|
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 4679999999997665
No 105
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=44.68 E-value=21 Score=23.86 Aligned_cols=27 Identities=11% Similarity=0.212 Sum_probs=19.3
Q ss_pred eeeeEEecCeec---CCCceecCCCEEEEE
Q 026204 12 SVLALFLSMDKL---SVSHNVKGGDMVNCT 38 (241)
Q Consensus 12 ~~~~v~vng~~~---~~~~~l~~GD~i~~~ 38 (241)
.-.+|-+|+..+ ..+..|+.||+|.+.
T Consensus 30 ~~vav~~N~~iv~r~~~~~~L~~gD~ieIv 59 (65)
T PRK05863 30 KGIAVAVDWSVLPRSDWATKLRDGARLEVV 59 (65)
T ss_pred CcEEEEECCcCcChhHhhhhcCCCCEEEEE
Confidence 345778888843 345568999999884
No 106
>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=44.37 E-value=23 Score=24.71 Aligned_cols=20 Identities=10% Similarity=0.195 Sum_probs=18.4
Q ss_pred cCeecCCCceecCCCEEEEE
Q 026204 19 SMDKLSVSHNVKGGDMVNCT 38 (241)
Q Consensus 19 ng~~~~~~~~l~~GD~i~~~ 38 (241)
||+.+..++.|+.||.|++.
T Consensus 56 ~~~~vg~~~~L~dgDvV~Ii 75 (76)
T cd01669 56 TGRRVGEDYELKHRDVIKIV 75 (76)
T ss_pred CCEEeCCCcEecCCCEEEEe
Confidence 89999999999999999873
No 107
>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=41.63 E-value=22 Score=30.29 Aligned_cols=25 Identities=12% Similarity=-0.007 Sum_probs=22.0
Q ss_pred eEEecCeec-CCCceecCCCEEEEEe
Q 026204 15 ALFLSMDKL-SVSHNVKGGDMVNCTI 39 (241)
Q Consensus 15 ~v~vng~~~-~~~~~l~~GD~i~~~~ 39 (241)
.|+|||+++ ++++.|..||.|.+..
T Consensus 26 ~V~Vng~~v~k~s~~V~~~d~I~v~~ 51 (228)
T TIGR00478 26 FVLVNGKKVDKPSALVDFDAKIELLQ 51 (228)
T ss_pred cEEECCEEeCCCCCCCCCCCEEeccC
Confidence 488999987 6999999999999864
No 108
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=35.79 E-value=78 Score=21.66 Aligned_cols=25 Identities=20% Similarity=0.113 Sum_probs=17.8
Q ss_pred EecCeecCCCceecCCCEEEEEecC
Q 026204 17 FLSMDKLSVSHNVKGGDMVNCTISE 41 (241)
Q Consensus 17 ~vng~~~~~~~~l~~GD~i~~~~~~ 41 (241)
++.|+--+...++.+||+|.+...+
T Consensus 33 ~i~GKmr~~rI~I~~GD~V~Ve~sp 57 (68)
T TIGR00008 33 HISGKIRMHYIRILPGDKVKVELSP 57 (68)
T ss_pred EecCcchhccEEECCCCEEEEEECc
Confidence 4555555566778899999997644
No 109
>cd00060 FHA Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
Probab=33.62 E-value=44 Score=23.33 Aligned_cols=29 Identities=17% Similarity=0.259 Sum_probs=22.2
Q ss_pred ceeeeeEEecCeecC--CCceecCCCEEEEE
Q 026204 10 QVSVLALFLSMDKLS--VSHNVKGGDMVNCT 38 (241)
Q Consensus 10 ~~~~~~v~vng~~~~--~~~~l~~GD~i~~~ 38 (241)
..|-..++|||+++. ....|..||.|.+-
T Consensus 62 ~~s~~g~~vn~~~~~~~~~~~l~~gd~i~ig 92 (102)
T cd00060 62 LGSTNGTFVNGQRVSPGEPVRLRDGDVIRLG 92 (102)
T ss_pred CCCCCCeEECCEECCCCCcEECCCCCEEEEC
Confidence 345556889999887 56778899999883
No 110
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=33.04 E-value=41 Score=33.55 Aligned_cols=30 Identities=10% Similarity=0.184 Sum_probs=25.6
Q ss_pred eeeeEEecCeecCCCceecCCCEEEEEecC
Q 026204 12 SVLALFLSMDKLSVSHNVKGGDMVNCTISE 41 (241)
Q Consensus 12 ~~~~v~vng~~~~~~~~l~~GD~i~~~~~~ 41 (241)
...+..|||+.+..++.|+.||.|+|--..
T Consensus 420 ~c~gAkVNg~~vpL~~~L~~Gd~VeIiT~~ 449 (702)
T PRK11092 420 ACVGARVDRQPYPLSQPLTSGQTVEIITAP 449 (702)
T ss_pred eeEEEEECCEECCCCccCCCCCEEEEEeCC
Confidence 445678999999999999999999997544
No 111
>PF13021 DUF3885: Domain of unknown function (DUF3885)
Probab=30.65 E-value=75 Score=19.13 Aligned_cols=24 Identities=21% Similarity=0.272 Sum_probs=20.4
Q ss_pred CCceEEEeecCHHHHHHHHHHhhc
Q 026204 138 GTSGLLVVAKDEHSHAHLSEQFKL 161 (241)
Q Consensus 138 ~TSGlll~Ak~~~~~~~L~~~f~~ 161 (241)
+-.|+-|+|.|++..+.|-+.|.+
T Consensus 5 DDRGcdvia~~~~~i~~ly~~y~~ 28 (38)
T PF13021_consen 5 DDRGCDVIANNKERIRPLYEKYND 28 (38)
T ss_pred cCCCcEEeeCCHHHHHHHHHHHHH
Confidence 457999999999999998887754
No 112
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=30.62 E-value=49 Score=28.64 Aligned_cols=27 Identities=15% Similarity=0.183 Sum_probs=23.2
Q ss_pred eEEecCeecC-CCceecCCCEEEEEecC
Q 026204 15 ALFLSMDKLS-VSHNVKGGDMVNCTISE 41 (241)
Q Consensus 15 ~v~vng~~~~-~~~~l~~GD~i~~~~~~ 41 (241)
.|.||.+.+. +++.|+.||.|.+....
T Consensus 206 ~VkVN~k~v~~~s~~v~~GDliSirG~G 233 (257)
T COG2302 206 KVKVNWKVVDKASYEVQEGDLISIRGFG 233 (257)
T ss_pred ceEEeeEEeccccceeccCCEEEEeccc
Confidence 3789999876 89999999999997643
No 113
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=30.25 E-value=68 Score=31.98 Aligned_cols=29 Identities=14% Similarity=0.226 Sum_probs=25.2
Q ss_pred eeeEEecCeecCCCceecCCCEEEEEecC
Q 026204 13 VLALFLSMDKLSVSHNVKGGDMVNCTISE 41 (241)
Q Consensus 13 ~~~v~vng~~~~~~~~l~~GD~i~~~~~~ 41 (241)
..+..|||+.+..++.|+.||.|+|-...
T Consensus 422 c~gAkVnG~ivpl~~~Lk~Gd~VEIit~k 450 (701)
T COG0317 422 CIGAKVNGRIVPLTTKLQTGDQVEIITSK 450 (701)
T ss_pred eeEEEECCEEeccceecCCCCEEEEEeCC
Confidence 45678999999999999999999997654
No 114
>TIGR00691 spoT_relA (p)ppGpp synthetase, RelA/SpoT family. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species.
Probab=29.60 E-value=72 Score=31.73 Aligned_cols=30 Identities=10% Similarity=0.171 Sum_probs=25.3
Q ss_pred eeeEEecCeecCCCceecCCCEEEEEecCC
Q 026204 13 VLALFLSMDKLSVSHNVKGGDMVNCTISEL 42 (241)
Q Consensus 13 ~~~v~vng~~~~~~~~l~~GD~i~~~~~~~ 42 (241)
.....|||+.+..++.|+.||.|+|-....
T Consensus 395 ~~~a~vng~~v~l~~~l~~gd~vei~t~~~ 424 (683)
T TIGR00691 395 CTGAKVNGKIVPLDKELENGDVVEIITGKN 424 (683)
T ss_pred eeEEEECCEECCCCccCCCCCEEEEEeCCC
Confidence 345679999999999999999999976543
No 115
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=29.15 E-value=1.2e+02 Score=21.87 Aligned_cols=38 Identities=16% Similarity=0.106 Sum_probs=25.4
Q ss_pred EecCeecCCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecC
Q 026204 17 FLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDD 61 (241)
Q Consensus 17 ~vng~~~~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~ 61 (241)
++.|+--+...++.+||+|.+..++-. ...-+|+|.-.
T Consensus 35 ~isGKmR~~rIrIl~GD~V~VE~spYD-------ltkGRIiyR~~ 72 (87)
T PRK12442 35 YASGRMRKHRIRILAGDRVTLELSPYD-------LTKGRINFRHK 72 (87)
T ss_pred EeccceeeeeEEecCCCEEEEEECccc-------CCceeEEEEec
Confidence 456665566778889999999665421 12456888863
No 116
>PRK04313 30S ribosomal protein S4e; Validated
Probab=28.90 E-value=84 Score=26.99 Aligned_cols=44 Identities=9% Similarity=0.030 Sum_probs=31.4
Q ss_pred eEEecCeecC-CCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEEC
Q 026204 15 ALFLSMDKLS-VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNK 68 (241)
Q Consensus 15 ~v~vng~~~~-~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinK 68 (241)
.|.|||++.+ ..+.+---|+|++.... ...+++|.....+++.+
T Consensus 65 ~V~VDGkvr~D~~~PvGlmDVIsI~~~~----------e~yRvl~d~kgr~~l~~ 109 (237)
T PRK04313 65 KVLVDGRVRKDYKFPVGLMDVISIPETG----------EYYRVLPDEKGRLVLIP 109 (237)
T ss_pred cEEECCEEEcccccCcCceeEEEEccCC----------CeEEEEECCCCcEEEEE
Confidence 4899999865 88999889999994322 24667777666555544
No 117
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=28.83 E-value=1.1e+02 Score=21.38 Aligned_cols=34 Identities=24% Similarity=0.150 Sum_probs=20.9
Q ss_pred cCeecCCCceecCCCEEEEEecCCCCccCCCCCCCccEEEe
Q 026204 19 SMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYE 59 (241)
Q Consensus 19 ng~~~~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilye 59 (241)
.|+--+..-.+.+||.|.+...+.. ....+|+|.
T Consensus 37 ~GKmr~~~i~I~~GD~V~Ve~~~~d-------~~kg~I~~R 70 (75)
T COG0361 37 SGKMRKNRIRILPGDVVLVELSPYD-------LTKGRIVYR 70 (75)
T ss_pred cCcchheeEEeCCCCEEEEEecccc-------cccccEEEE
Confidence 3333344667889999999654421 224567775
No 118
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=27.74 E-value=57 Score=26.82 Aligned_cols=27 Identities=7% Similarity=0.028 Sum_probs=22.1
Q ss_pred EEecCeecC-CCceecCCCEEEEEecCC
Q 026204 16 LFLSMDKLS-VSHNVKGGDMVNCTISEL 42 (241)
Q Consensus 16 v~vng~~~~-~~~~l~~GD~i~~~~~~~ 42 (241)
|.|||+++. |++.|..|+.=.|.+.+.
T Consensus 134 I~V~~~~V~~Ps~~V~~~~Ed~I~~~~~ 161 (181)
T PTZ00155 134 IRVGKQIVDIPSFLVRVDSEKHIDFADT 161 (181)
T ss_pred EEECCEEeccCceEeccCccCceeeecC
Confidence 889999887 999999998777766543
No 119
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=25.65 E-value=95 Score=27.23 Aligned_cols=44 Identities=11% Similarity=0.024 Sum_probs=31.4
Q ss_pred eEEecCeecC-CCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEEC
Q 026204 15 ALFLSMDKLS-VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNK 68 (241)
Q Consensus 15 ~v~vng~~~~-~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinK 68 (241)
.|.|||++.+ ..+.+---|+|++.... ...+++|.....+++.+
T Consensus 66 ~V~VDGkvr~D~~~PvGlMDVIsI~kt~----------e~yRvl~D~kGrf~l~~ 110 (273)
T PTZ00223 66 LVCVDGKPRKDGKYPAGFMDVVEIPKTG----------DRFRILYDVKGRFALVK 110 (273)
T ss_pred eEEECCEEEccCCCCCceeEEEEEcCCC----------CeEEEEECCCCcEEEEE
Confidence 4899999865 78888888999994322 24667777766655554
No 120
>PLN00036 40S ribosomal protein S4; Provisional
Probab=25.42 E-value=1e+02 Score=26.93 Aligned_cols=44 Identities=5% Similarity=0.070 Sum_probs=31.7
Q ss_pred eEEecCeecC-CCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEEC
Q 026204 15 ALFLSMDKLS-VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNK 68 (241)
Q Consensus 15 ~v~vng~~~~-~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinK 68 (241)
.|.|||++.+ ..+.+---|+|++.... ...+++|.....+++++
T Consensus 69 ~V~VDGkvr~D~~fPvG~mDVIsI~kt~----------e~yRvl~D~kGrf~l~~ 113 (261)
T PLN00036 69 HVKVDGKVRTDKTYPAGFMDVISIPKTN----------ENFRLLYDTKGRFRLHR 113 (261)
T ss_pred eEEECCEEeccCCCCCceeEEEEEcCCC----------CeEEEEECCCceEEEEE
Confidence 4899999865 78888888999994322 24667777776666554
No 121
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=24.62 E-value=93 Score=31.33 Aligned_cols=29 Identities=7% Similarity=0.135 Sum_probs=24.7
Q ss_pred eeeEEecCeecCCCceecCCCEEEEEecC
Q 026204 13 VLALFLSMDKLSVSHNVKGGDMVNCTISE 41 (241)
Q Consensus 13 ~~~v~vng~~~~~~~~l~~GD~i~~~~~~ 41 (241)
.....|||+.+..++.|+.||.|+|-...
T Consensus 439 ~~gAkvng~~v~l~~~L~~GD~VeIits~ 467 (743)
T PRK10872 439 CIGAKIGGRIVPFTYQLQMGDQIEIITQK 467 (743)
T ss_pred ceEEEECCEECCCCcCCCCCCEEEEEeCC
Confidence 34457999999999999999999997654
No 122
>PRK11840 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional
Probab=23.65 E-value=80 Score=28.44 Aligned_cols=27 Identities=11% Similarity=0.128 Sum_probs=22.3
Q ss_pred eeeEEecCeecC----CCceecCCCEEEEEe
Q 026204 13 VLALFLSMDKLS----VSHNVKGGDMVNCTI 39 (241)
Q Consensus 13 ~~~v~vng~~~~----~~~~l~~GD~i~~~~ 39 (241)
-.+|-+||+.+. .++.|+.||+|++..
T Consensus 31 ~VAVeVNgeIVpr~~w~~t~LkeGD~IEII~ 61 (326)
T PRK11840 31 KVAVERNLEIVPRSEYGQVALEEGDELEIVH 61 (326)
T ss_pred eEEEEECCEECCHHHcCccccCCCCEEEEEE
Confidence 346779999987 577999999999964
No 123
>PF07732 Cu-oxidase_3: Multicopper oxidase; InterPro: IPR011707 Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment. Multicopper oxidases oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water []. There are three spectroscopically different copper centres found in multicopper oxidases: type 1 (or blue), type 2 (or normal) and type 3 (or coupled binuclear) [, ]. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology to the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel []. Multicopper oxidases include: Ceruloplasmin (1.16.3.1 from EC) (ferroxidase), a 6-domain enzyme found in the serum of mammals and birds that oxidizes different inorganic and organic substances; exhibits internal sequence homology that appears to have evolved from the triplication of a Cu-binding domain similar to that of laccase and ascorbate oxidase. Laccase (1.10.3.2 from EC) (urishiol oxidase), a 3-domain enzyme found in fungi and plants, which oxidizes different phenols and diamines. CueO is a laccase found in Escherichia coli that is involved in copper-resistance []. Ascorbate oxidase (1.10.3.3 from EC), a 3-domain enzyme found in higher plants. Nitrite reductase (1.7.2.1 from EC), a 2-domain enzyme containing type-1 and type-2 copper centres [, ]. In addition to the above enzymes there are a number of other proteins that are similar to the multi-copper oxidases in terms of structure and sequence, some of which have lost the ability to bind copper. These include: copper resistance protein A (copA) from a plasmid in Pseudomonas syringae; domain A of (non-copper binding) blood coagulation factors V (Fa V) and VIII (Fa VIII) []; yeast FET3 required for ferrous iron uptake []; yeast hypothetical protein YFL041w; and the fission yeast homologue SpAC1F7.08. This entry represents multicopper oxidase type 3 (or coupled binuclear) domains. ; GO: 0005507 copper ion binding; PDB: 2QT6_B 3KW7_B 2R7E_A 3CDZ_A 1SDD_A 3G5W_D 3UAC_A 2YXV_A 3OD3_A 3NSY_A ....
Probab=23.40 E-value=75 Score=23.82 Aligned_cols=33 Identities=15% Similarity=0.056 Sum_probs=26.5
Q ss_pred ccceeeeeEEecCeecCCCceecCCCEEEEEec
Q 026204 8 FNQVSVLALFLSMDKLSVSHNVKGGDMVNCTIS 40 (241)
Q Consensus 8 ~~~~~~~~v~vng~~~~~~~~l~~GD~i~~~~~ 40 (241)
+.+.....+.+||...-+--+++.||.|.+.+.
T Consensus 9 ~~~~~~~~~~~ng~~pGPtI~v~~Gd~v~i~~~ 41 (117)
T PF07732_consen 9 PDGGTRKVWTYNGQFPGPTIRVREGDTVRITVT 41 (117)
T ss_dssp TTSTEEEEEEETTBSSEEEEEEETTEEEEEEEE
T ss_pred eCCcEEEEEEECCCCCCCEEEEEcCCeeEEEEE
Confidence 444456678899998888899999999999764
No 124
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=22.68 E-value=91 Score=25.52 Aligned_cols=27 Identities=7% Similarity=-0.123 Sum_probs=20.2
Q ss_pred eEEecCeecC-CCceecCCCEEEEEecC
Q 026204 15 ALFLSMDKLS-VSHNVKGGDMVNCTISE 41 (241)
Q Consensus 15 ~v~vng~~~~-~~~~l~~GD~i~~~~~~ 41 (241)
.|.|||+++. |++.|..++.-.|.+.+
T Consensus 129 hV~V~g~~V~~Ps~~V~~~~ed~I~~~~ 156 (177)
T PRK04051 129 HIAVNGRRVTSPSYLVSVEEEDLIDYYP 156 (177)
T ss_pred CEEECCEEeCCCCeECCCCCcceEEEeC
Confidence 4899999865 99999999655554444
No 125
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=22.40 E-value=1.2e+02 Score=26.54 Aligned_cols=44 Identities=16% Similarity=0.126 Sum_probs=30.9
Q ss_pred eEEecCeecC-CCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEEC
Q 026204 15 ALFLSMDKLS-VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNK 68 (241)
Q Consensus 15 ~v~vng~~~~-~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinK 68 (241)
.|.|||++.+ ..+.+---|+|++.... ...+++|.....+++.+
T Consensus 69 ~V~VDGkvr~D~~fPvG~mDVIsI~kt~----------e~yRvl~D~kGr~~l~~ 113 (262)
T PTZ00118 69 IVKVDGKVRTDCTYPVGFMDVVSLTKTN----------EYFRLLYDTKGRFVPHK 113 (262)
T ss_pred cEEECCEEEccCCCCCceeEEEEEcCCC----------CeEEEEECCCccEEEEE
Confidence 4899999865 78899888999994322 24667777666555543
No 126
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=21.64 E-value=1.4e+02 Score=21.59 Aligned_cols=10 Identities=40% Similarity=0.497 Sum_probs=7.1
Q ss_pred eecCCCEEEE
Q 026204 28 NVKGGDMVNC 37 (241)
Q Consensus 28 ~l~~GD~i~~ 37 (241)
.|+.||.|.+
T Consensus 53 ~Vk~GD~Vl~ 62 (91)
T PRK14533 53 DIKVGDKVIF 62 (91)
T ss_pred cccCCCEEEE
Confidence 4677887776
No 127
>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=21.03 E-value=70 Score=23.90 Aligned_cols=15 Identities=40% Similarity=0.857 Sum_probs=12.8
Q ss_pred CccEEEecCcEEEEE
Q 026204 53 PLDIVYEDDNVLVVN 67 (241)
Q Consensus 53 ~~~Ilyed~~llVin 67 (241)
+-+|+|+|+++++++
T Consensus 13 ~~~vly~d~~~v~~~ 27 (116)
T PF11969_consen 13 PERVLYEDDDFVVFK 27 (116)
T ss_dssp GGGESEEETSEEEEE
T ss_pred CCcEEEEeCCEEEee
Confidence 457999999999986
No 128
>PRK03427 cell division protein ZipA; Provisional
Probab=20.94 E-value=1.3e+02 Score=27.24 Aligned_cols=17 Identities=29% Similarity=0.462 Sum_probs=12.2
Q ss_pred cccccC-CCCCceEEEee
Q 026204 130 GIVHRL-DKGTSGLLVVA 146 (241)
Q Consensus 130 ~~vhRL-D~~TSGlll~A 146 (241)
.+-||. |.+.+|-+||+
T Consensus 231 ~IFHRh~~~~g~G~vLFS 248 (333)
T PRK03427 231 NIFHRHLSPDGSGPVLFS 248 (333)
T ss_pred cceeecccCCCCCceEEE
Confidence 446774 77778888887
No 129
>COG1977 MoaD Molybdopterin converting factor, small subunit [Coenzyme metabolism]
Probab=20.12 E-value=1.3e+02 Score=21.02 Aligned_cols=21 Identities=19% Similarity=0.115 Sum_probs=16.8
Q ss_pred ecCeecCCCceecCCCEEEEE
Q 026204 18 LSMDKLSVSHNVKGGDMVNCT 38 (241)
Q Consensus 18 vng~~~~~~~~l~~GD~i~~~ 38 (241)
+|......++.|+.||+|.+.
T Consensus 58 ~~~~~~~~~t~L~dGDeVa~~ 78 (84)
T COG1977 58 NNEFLVGLDTPLKDGDEVAFF 78 (84)
T ss_pred eceeeccccccCCCCCEEEEe
Confidence 344556789999999999985
No 130
>cd01667 TGS_ThrRS_N TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and SpoT proteins where it occurs. The TGS domain is thought to interact with the tRNA acceptor arm along with an adjacent N-terminal domain. The specific function of TGS is not well understood.
Probab=20.02 E-value=1.5e+02 Score=17.99 Aligned_cols=26 Identities=8% Similarity=0.059 Sum_probs=20.0
Q ss_pred eeeeEEecCeecCCCceecCCCEEEE
Q 026204 12 SVLALFLSMDKLSVSHNVKGGDMVNC 37 (241)
Q Consensus 12 ~~~~v~vng~~~~~~~~l~~GD~i~~ 37 (241)
.+.+..+||+.....+.+..++.|.+
T Consensus 33 ~~v~~~vng~~~dL~~~l~~~~~ie~ 58 (61)
T cd01667 33 KAVAAKVNGELVDLSRPLEEDCELEI 58 (61)
T ss_pred heEEEEECCEEecCCcCcCCCCEEEE
Confidence 44566689988888888888887765
Done!