Query 011530
Match_columns 483
No_of_seqs 347 out of 2489
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 02:23:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011530.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011530hhsearch_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 1.6E-53 3.4E-58 427.4 29.0 261 108-429 11-287 (289)
2 PRK11180 rluD 23S rRNA pseudou 100.0 9.1E-50 2E-54 407.7 29.3 258 109-428 17-300 (325)
3 PRK11025 23S rRNA pseudouridyl 100.0 1.2E-49 2.7E-54 405.4 28.8 258 109-428 19-301 (317)
4 TIGR00005 rluA_subfam pseudour 100.0 5.4E-49 1.2E-53 397.6 30.0 262 109-430 5-288 (299)
5 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 1E-45 2.2E-50 364.0 24.6 224 171-428 5-243 (246)
6 cd02557 PseudoU_synth_ScRIB2 P 100.0 3.8E-43 8.3E-48 338.7 21.2 196 217-474 15-212 (213)
7 TIGR01621 RluA-like pseudourid 100.0 1.2E-42 2.6E-47 336.1 21.2 196 218-475 2-201 (217)
8 KOG1919 RNA pseudouridylate sy 100.0 4E-42 8.7E-47 351.8 23.7 305 109-475 43-370 (371)
9 cd02563 PseudoU_synth_TruC tRN 100.0 2.2E-42 4.7E-47 335.7 20.4 196 218-428 1-221 (223)
10 PRK11112 tRNA pseudouridine sy 100.0 9.4E-42 2E-46 337.9 23.3 196 218-428 2-222 (257)
11 PRK10158 23S rRNA/tRNA pseudou 100.0 6.2E-42 1.3E-46 331.6 20.6 193 217-429 13-217 (219)
12 PRK10839 16S rRNA pseudouridyl 100.0 4.1E-37 9E-42 300.3 14.7 202 111-402 2-203 (232)
13 cd02869 PseudoU_synth_RluCD_li 100.0 8E-36 1.7E-40 279.7 17.0 161 227-405 1-166 (185)
14 PRK10700 23S rRNA pseudouridyl 100.0 2.7E-32 5.8E-37 274.2 19.7 207 110-401 3-212 (289)
15 PRK10475 23S rRNA pseudouridin 100.0 4.3E-32 9.3E-37 272.3 17.9 201 108-401 5-205 (290)
16 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 8.6E-32 1.9E-36 246.9 15.3 147 227-398 1-148 (154)
17 COG1187 RsuA 16S rRNA uridine- 100.0 3.4E-30 7.3E-35 251.3 17.5 208 110-402 3-213 (248)
18 cd02556 PseudoU_synth_RluB Pse 100.0 4.8E-30 1E-34 238.6 13.1 144 227-401 2-145 (167)
19 cd02870 PseudoU_synth_RsuA_lik 100.0 1.4E-30 2.9E-35 237.0 8.8 140 227-398 1-140 (146)
20 cd02553 PseudoU_synth_RsuA Pse 100.0 3.2E-30 6.8E-35 239.8 11.3 143 227-403 2-144 (167)
21 PF00849 PseudoU_synth_2: RNA 100.0 3.4E-29 7.4E-34 230.6 14.0 153 226-391 1-164 (164)
22 cd02566 PseudoU_synth_RluE Pse 100.0 2.2E-28 4.8E-33 227.7 11.9 156 227-402 1-158 (168)
23 PRK11394 23S rRNA pseudouridin 99.9 8E-27 1.7E-31 224.4 11.8 161 226-405 40-200 (217)
24 cd02555 PSSA_1 PSSA_1: Pseudou 99.9 1.3E-26 2.8E-31 217.4 12.5 142 226-403 5-154 (177)
25 TIGR00093 pseudouridine syntha 99.9 5.2E-25 1.1E-29 196.1 8.5 109 266-403 1-109 (128)
26 cd02554 PseudoU_synth_RluF Pse 99.9 1.2E-23 2.6E-28 194.8 11.9 138 227-402 2-139 (164)
27 cd02868 PseudoU_synth_hTruB2_l 99.1 1.4E-10 3.1E-15 112.7 7.7 75 227-307 2-76 (226)
28 cd00165 S4 S4/Hsp/ tRNA synthe 98.7 6.3E-08 1.4E-12 74.9 8.1 68 111-231 2-70 (70)
29 TIGR02988 YaaA_near_RecF S4 do 98.2 2.7E-06 5.8E-11 65.5 6.1 51 108-202 7-59 (59)
30 PF01479 S4: S4 domain; Inter 98.2 3.9E-06 8.5E-11 61.6 6.1 46 111-199 2-48 (48)
31 cd02572 PseudoU_synth_hDyskeri 97.6 0.00024 5.2E-09 67.2 8.1 70 225-307 2-71 (182)
32 smart00363 S4 S4 RNA-binding d 97.3 0.00075 1.6E-08 50.1 6.7 50 111-203 2-52 (60)
33 PRK00989 truB tRNA pseudouridi 97.3 0.0008 1.7E-08 65.7 7.4 70 226-307 10-79 (230)
34 PLN00051 RNA-binding S4 domain 97.2 0.00054 1.2E-08 68.6 6.1 53 109-204 191-243 (267)
35 TIGR00431 TruB tRNA pseudourid 97.2 0.0013 2.9E-08 63.4 7.9 69 226-307 3-71 (209)
36 cd00506 PseudoU_synth_TruB_lik 97.2 0.0013 2.7E-08 63.7 7.8 68 227-307 2-69 (210)
37 PRK04099 truB tRNA pseudouridi 97.2 0.0013 2.9E-08 65.8 8.0 70 225-307 2-71 (273)
38 COG1188 Ribosome-associated he 97.1 0.00091 2E-08 56.7 5.3 53 110-206 9-62 (100)
39 PRK00020 truB tRNA pseudouridi 97.1 0.0019 4.1E-08 63.6 8.1 70 225-307 10-79 (244)
40 TIGR03069 PS_II_S4 photosystem 97.0 0.00093 2E-08 66.6 5.8 54 108-204 182-235 (257)
41 PRK02484 truB tRNA pseudouridi 97.0 0.0024 5.1E-08 64.8 8.1 70 225-307 3-72 (294)
42 cd01291 PseudoU_synth PseudoU_ 97.0 0.0035 7.6E-08 51.8 7.7 28 261-307 24-51 (87)
43 PRK14124 tRNA pseudouridine sy 97.0 0.0029 6.2E-08 64.5 8.4 70 225-307 3-72 (308)
44 PRK14123 tRNA pseudouridine sy 97.0 0.0026 5.6E-08 64.8 8.1 70 225-307 3-72 (305)
45 PRK02193 truB tRNA pseudouridi 96.9 0.0025 5.5E-08 64.0 7.7 68 227-307 2-69 (279)
46 PRK03287 truB tRNA pseudouridi 96.9 0.0028 6E-08 64.3 7.9 71 224-307 8-78 (298)
47 PRK14846 truB tRNA pseudouridi 96.9 0.0032 6.9E-08 64.6 8.3 70 225-307 3-72 (345)
48 PRK00130 truB tRNA pseudouridi 96.9 0.0033 7.2E-08 63.6 8.2 70 225-307 2-71 (290)
49 PRK02755 truB tRNA pseudouridi 96.9 0.003 6.6E-08 64.0 7.8 69 225-307 3-71 (295)
50 TIGR01017 rpsD_bact ribosomal 96.8 0.0023 5E-08 61.5 6.4 52 110-204 90-142 (200)
51 PRK05389 truB tRNA pseudouridi 96.8 0.0037 8E-08 63.7 8.0 70 225-307 13-82 (305)
52 COG2302 Uncharacterized conser 96.8 0.0017 3.8E-08 63.5 5.2 54 109-205 180-233 (257)
53 cd02573 PseudoU_synth_EcTruB P 96.8 0.004 8.6E-08 62.7 7.9 68 227-307 2-69 (277)
54 PRK01528 truB tRNA pseudouridi 96.8 0.0044 9.5E-08 62.8 8.2 70 225-307 3-72 (292)
55 PRK04270 H/ACA RNA-protein com 96.8 0.0038 8.3E-08 63.6 7.7 71 224-307 21-91 (300)
56 PRK01550 truB tRNA pseudouridi 96.8 0.0048 1E-07 62.9 8.2 70 225-307 2-71 (304)
57 PRK01851 truB tRNA pseudouridi 96.7 0.0052 1.1E-07 62.5 8.2 70 225-307 16-85 (303)
58 PRK05033 truB tRNA pseudouridi 96.7 0.0054 1.2E-07 62.6 8.2 70 225-307 10-79 (312)
59 CHL00113 rps4 ribosomal protei 96.7 0.0031 6.8E-08 60.5 6.1 53 110-205 89-142 (201)
60 PRK14122 tRNA pseudouridine sy 96.5 0.0079 1.7E-07 61.4 7.8 68 227-307 3-70 (312)
61 TIGR00478 tly hemolysin TlyA f 96.4 0.0052 1.1E-07 60.2 5.6 49 111-202 1-50 (228)
62 PRK04642 truB tRNA pseudouridi 96.4 0.011 2.3E-07 60.1 7.9 70 225-307 10-79 (300)
63 TIGR00425 CBF5 rRNA pseudourid 96.4 0.0088 1.9E-07 61.5 7.3 70 225-307 34-103 (322)
64 PRK05327 rpsD 30S ribosomal pr 96.3 0.0079 1.7E-07 57.9 6.1 51 110-203 93-144 (203)
65 PRK10348 ribosome-associated h 96.2 0.014 3E-07 52.4 6.4 52 110-205 9-61 (133)
66 COG0130 TruB Pseudouridine syn 95.9 0.021 4.6E-07 57.3 7.4 69 226-307 16-84 (271)
67 COG0522 RpsD Ribosomal protein 95.9 0.014 3.1E-07 56.2 5.8 53 110-205 94-147 (205)
68 cd02867 PseudoU_synth_TruB_4 P 95.9 0.025 5.3E-07 57.8 7.7 69 227-307 2-98 (312)
69 COG1189 Predicted rRNA methyla 94.4 0.1 2.2E-06 51.3 6.4 51 110-203 3-54 (245)
70 PRK11507 ribosome-associated p 93.2 0.26 5.7E-06 39.3 5.8 50 110-202 12-62 (70)
71 PRK04051 rps4p 30S ribosomal p 91.9 0.35 7.5E-06 45.6 5.8 50 110-202 103-153 (177)
72 PRK04313 30S ribosomal protein 89.2 2.2 4.7E-05 42.1 8.8 71 109-232 37-109 (237)
73 COG2501 S4-like RNA binding pr 88.2 1.8 3.8E-05 34.9 6.2 55 105-202 7-62 (73)
74 PLN00189 40S ribosomal protein 87.5 0.52 1.1E-05 45.0 3.2 51 112-205 111-162 (194)
75 PF13275 S4_2: S4 domain; PDB: 86.9 0.16 3.4E-06 40.0 -0.5 52 108-202 6-58 (65)
76 PTZ00223 40S ribosomal protein 86.1 4.1 8.8E-05 41.0 8.7 71 109-232 38-110 (273)
77 PLN00036 40S ribosomal protein 86.0 4.3 9.4E-05 40.5 8.9 71 109-232 41-113 (261)
78 TIGR01018 rpsD_arch ribosomal 85.6 1.5 3.2E-05 40.8 5.1 49 110-201 104-153 (162)
79 PTZ00118 40S ribosomal protein 84.9 5.1 0.00011 40.1 8.8 70 109-231 41-112 (262)
80 PRK01777 hypothetical protein; 82.1 1.8 3.9E-05 36.7 3.8 58 102-204 19-76 (95)
81 KOG2559 Predicted pseudouridin 81.5 1 2.3E-05 44.2 2.4 22 262-283 90-111 (318)
82 PTZ00155 40S ribosomal protein 80.8 1.8 4E-05 40.9 3.8 51 110-203 107-158 (181)
83 PF06353 DUF1062: Protein of u 77.7 2.3 5.1E-05 38.7 3.3 29 110-138 103-131 (142)
84 PF01509 TruB_N: TruB family p 71.9 3.7 7.9E-05 37.7 3.1 42 262-307 8-49 (149)
85 PF14451 Ub-Mut7C: Mut7-C ubiq 70.9 7.6 0.00016 31.9 4.4 24 171-204 53-76 (81)
86 PRK05912 tyrosyl-tRNA syntheta 67.3 18 0.00039 38.6 7.5 29 109-137 342-371 (408)
87 COG4332 Uncharacterized protei 63.5 6.7 0.00015 36.9 3.0 28 110-137 139-166 (203)
88 PRK13354 tyrosyl-tRNA syntheta 60.2 12 0.00027 39.9 4.7 29 109-137 342-371 (410)
89 COG1471 RPS4A Ribosomal protei 56.9 22 0.00049 34.8 5.4 66 114-232 45-112 (241)
90 PF04225 OapA: Opacity-associa 46.5 28 0.00061 28.7 3.8 31 103-134 4-34 (85)
91 PRK08364 sulfur carrier protei 45.9 37 0.0008 26.7 4.3 22 171-202 43-64 (70)
92 cd00754 MoaD Ubiquitin domain 41.4 76 0.0016 24.9 5.5 22 171-202 53-74 (80)
93 PF02824 TGS: TGS domain; Int 40.3 32 0.00069 26.2 3.0 22 171-202 38-59 (60)
94 PRK05659 sulfur carrier protei 40.2 31 0.00068 26.4 3.0 26 171-202 35-60 (66)
95 cd00565 ThiS ThiaminS ubiquiti 34.2 81 0.0018 24.2 4.5 26 171-202 34-59 (65)
96 PLN02799 Molybdopterin synthas 30.6 1.9E+02 0.004 23.1 6.2 22 171-202 55-76 (82)
97 PF02597 ThiS: ThiS family; I 28.6 1.1E+02 0.0023 23.8 4.4 25 171-202 47-71 (77)
98 TIGR01764 excise DNA binding d 27.0 54 0.0012 22.7 2.2 22 115-136 6-27 (49)
99 cd01666 TGS_DRG_C TGS_DRG_C: 26.7 1.8E+02 0.0038 23.5 5.3 22 171-202 53-74 (75)
100 PRK06437 hypothetical protein; 26.3 66 0.0014 25.1 2.7 22 171-202 40-61 (67)
101 cd02563 PseudoU_synth_TruC tRN 25.9 53 0.0011 31.8 2.6 24 448-471 196-223 (223)
102 TIGR00005 rluA_subfam pseudour 23.6 36 0.00078 34.3 1.0 28 448-475 261-292 (299)
103 PF08068 DKCLD: DKCLD (NUC011) 23.5 36 0.00079 26.3 0.7 18 222-239 39-56 (59)
104 PRK11180 rluD 23S rRNA pseudou 22.5 32 0.0007 35.3 0.4 28 448-475 275-306 (325)
105 PF13021 DUF3885: Domain of un 22.5 1.1E+02 0.0024 21.5 3.0 24 272-295 5-28 (38)
106 cd04762 HTH_MerR-trunc Helix-T 21.6 80 0.0017 21.6 2.2 22 115-136 5-26 (49)
107 PRK07440 hypothetical protein; 21.4 94 0.002 24.5 2.7 26 171-202 39-64 (70)
108 PRK11130 moaD molybdopterin sy 21.1 2.1E+02 0.0046 22.9 4.9 23 171-203 54-76 (81)
109 PRK07696 sulfur carrier protei 20.2 1E+02 0.0022 24.0 2.7 26 171-202 36-61 (67)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-53 Score=427.39 Aligned_cols=261 Identities=24% Similarity=0.299 Sum_probs=209.9
Q ss_pred CCCcHHHHHHhccC-CCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccc
Q 011530 108 EGGPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRI 186 (483)
Q Consensus 108 ~~~rl~~~Ls~~l~-~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~ 186 (483)
++.||++||++ +. +||+++.++|++|+| .|||++++
T Consensus 11 ~g~rld~~L~~-l~~~sr~~~~~~i~~g~v----------------------------------~vNg~~v~-------- 47 (289)
T COG0564 11 AGQRLDKFLAK-LLPISRSRIQKLIRKGRV----------------------------------RVNGKKVK-------- 47 (289)
T ss_pred cCCCHHHHHHH-ccCcCHHHHHHHHHCCCE----------------------------------EECCEEcc--------
Confidence 34577799999 54 999999999999999 68999885
Q ss_pred cCCCceecCCCEEEEecCCCCC-CcccCCCCCceEEeecCeEEEEeCCCCCccCCCCCCccchHHHHHHHhccC-CCCCc
Q 011530 187 THVDQIVEAGTYLRVHVHPKRF-PRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL-TTPLR 264 (483)
Q Consensus 187 ~~~~~~v~~GD~I~v~~~~~~~-p~~~~~~~~~~IlyED~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~-~~~l~ 264 (483)
++++|..||+|.+....... ....+.+.++.|||||++++|||||+||+|||+..+...++...+....+. ...++
T Consensus 48 --~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~ 125 (289)
T COG0564 48 --PSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDGVERPG 125 (289)
T ss_pred --CCeeeCCCCEEEEecccccccccccccCCCccEEEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhccccCCcee
Confidence 78999999999999876443 222233445889999999999999999999999888888888877655432 34678
Q ss_pred cccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEEeccCC--ccceeecccccccCCccccCCeeeeeEEEee
Q 011530 265 TTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP--VGIMTHYMRPINIAPRLVSEGWYLCQLEVME 342 (483)
Q Consensus 265 ~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~G~~~--~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~ 342 (483)
+||||||+||||||||||..+++.|+++|+++.+.|+|+|+|.|.++ .|.|+.++....... ..+.+..
T Consensus 126 ~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~---------~~~~v~~ 196 (289)
T COG0564 126 IVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNR---------KKMAVVK 196 (289)
T ss_pred eeccCCCCCceEEEEECCHHHHHHHHHHHhcCcCcEEEEEEEECcccCCCCEEeeeeecCCcCC---------ceEEEec
Confidence 99999999999999999999999999999999999999999999886 478887654322111 1122222
Q ss_pred cccCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCCCChh---h---hhhc-----C
Q 011530 343 CKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPA---A---IAQL-----S 411 (483)
Q Consensus 343 ~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~YG~~---~---~~~~-----~ 411 (483)
.. . .+.+.|.|++++.. ....++++|+|+||||||||+||++|||||+||++||+. . ..++ .
T Consensus 197 ~~---~-gk~A~T~~~~l~~~---~~~~tlv~~~~~TGRTHQIRVHl~~lghPI~GD~~Yg~~~~~~~~~~~r~~LHA~~ 269 (289)
T COG0564 197 EG---S-GKPAITHYEVLERF---GDNYTLVELKPETGRTHQIRVHLAHLGHPIVGDPLYGGKDKSAGAGLKRQALHAYK 269 (289)
T ss_pred cC---C-CCceEEEEEehhcc---CCceEEEEEEeCCCCHhHHHHHHHHCCCCeeCCcccCCchhhcccCcchhhhhhce
Confidence 11 1 34567999999852 222689999999999999999999999999999999974 1 2233 3
Q ss_pred CCCCCCCCCceeeEecCh
Q 011530 412 SPGLNPFGKCQKEYASDD 429 (483)
Q Consensus 412 l~f~hP~t~~~~~f~~~~ 429 (483)
+.|.||.+++.+.|++|.
T Consensus 270 l~f~hp~t~~~~~~~a~~ 287 (289)
T COG0564 270 LSFTHPLTGEELEFEAPL 287 (289)
T ss_pred eEccCCCCCCEEEEecCC
Confidence 789999999999999863
No 2
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=9.1e-50 Score=407.73 Aligned_cols=258 Identities=17% Similarity=0.223 Sum_probs=201.9
Q ss_pred CCcHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeecccccccc
Q 011530 109 GGPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRIT 187 (483)
Q Consensus 109 ~~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~ 187 (483)
+.||++||++.+ .+||+.++++|+.|.| .|||+.+.
T Consensus 17 g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V----------------------------------~VNg~~v~--------- 53 (325)
T PRK11180 17 GQRLDQALAELFPDYSRSRIKEWILDQRV----------------------------------LVNGKVIN--------- 53 (325)
T ss_pred CccHHHHHHhhccccCHHHHHHHHHCCCE----------------------------------EECCEEcc---------
Confidence 467779999997 5899999999999999 58999875
Q ss_pred CCCceecCCCEEEEecCCCCCCcccCCCCCceEEeecCeEEEEeCCCCCccCCCCCCccchHHHHHHHhcc---CCCCCc
Q 011530 188 HVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALG---LTTPLR 264 (483)
Q Consensus 188 ~~~~~v~~GD~I~v~~~~~~~p~~~~~~~~~~IlyED~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~---~~~~l~ 264 (483)
++++.|..||.|.+.............+.++.|||||++|+|||||+||+||++..+...++.+.+...+. ....++
T Consensus 54 ~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~iiyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~ 133 (325)
T PRK11180 54 KPKEKVLGGEQVAIDAEIEEEARFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAG 133 (325)
T ss_pred CCCcCcCCCCEEEEeeccccccCCCCCCCCCcEEEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHhhhccCCcccc
Confidence 47889999999999865432211112234679999999999999999999999877666777776654432 123467
Q ss_pred cccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEEeccCC-ccceeecccccccCCccccCCeeeeeEEEeec
Q 011530 265 TTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP-VGIMTHYMRPINIAPRLVSEGWYLCQLEVMEC 343 (483)
Q Consensus 265 ~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~G~~~-~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~ 343 (483)
+|||||++||||||||||.+++..|+++|+++.++|+|+|+|.|.++ +|.++.++....... ..+.+
T Consensus 134 ~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~Y~A~v~G~~~~~~~i~~~l~~~~~~~---------~~~~~--- 201 (325)
T PRK11180 134 IVHRLDKDTTGLMVVAKTVPAQTRLVEALQKREITREYEAVAIGHMTAGGTVDEPISRHPTKR---------THMAV--- 201 (325)
T ss_pred eeccCCCCCceeEEEECCHHHHHHHHHHHHhCCcceEEEEEEecCCCCCCEEECceecCCCcC---------cEEEe---
Confidence 89999999999999999999999999999999999999999999886 667776553211100 00111
Q ss_pred ccCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCCCChhh----------------h
Q 011530 344 KKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAA----------------I 407 (483)
Q Consensus 344 ~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~YG~~~----------------~ 407 (483)
.+.+ +.+.|.|+++.. ....++++|+|+||||||||+||+++||||+||.+||+.. .
T Consensus 202 --~~~g-k~a~T~~~~l~~----~~~~slv~~~~~TGRtHQIRvhla~lG~PI~GD~~Yg~~~~~~~~~~~~~~~~~~~~ 274 (325)
T PRK11180 202 --HPMG-KPAVTHYRIMEH----FRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPPKGASEEFISTLRKF 274 (325)
T ss_pred --CCCC-cEEeEEEEEeEE----cCCeEEEEEEeCCCCHHHHHHHHHhCCCCEeCccccCCCcccccccchhhhhhcccc
Confidence 0112 345789999874 3457899999999999999999999999999999999642 1
Q ss_pred hh-----cCCCCCCCCCCceeeEecC
Q 011530 408 AQ-----LSSPGLNPFGKCQKEYASD 428 (483)
Q Consensus 408 ~~-----~~l~f~hP~t~~~~~f~~~ 428 (483)
.+ ..+.|.||++++.+.|++|
T Consensus 275 ~r~~Lha~~l~f~hP~~~~~~~~~a~ 300 (325)
T PRK11180 275 DRQALHATMLRLYHPITGIEMEWHAP 300 (325)
T ss_pred chhhhhcceeEeeCCCCCCeEEEECC
Confidence 12 2378999999999999976
No 3
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=1.2e-49 Score=405.37 Aligned_cols=258 Identities=21% Similarity=0.253 Sum_probs=197.1
Q ss_pred CCcHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeecccccccc
Q 011530 109 GGPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRIT 187 (483)
Q Consensus 109 ~~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~ 187 (483)
+.||++||++.+ .+||+.++++|+.|.| .|||+.++
T Consensus 19 g~RLd~~L~~~~~~~sr~~i~~li~~G~V----------------------------------~VNg~~v~--------- 55 (317)
T PRK11025 19 GQRIDNFLRTQLKGVPKSMIYRILRKGEV----------------------------------RVNKKRIK--------- 55 (317)
T ss_pred CchHHHHHHHhcccCCHHHHHHHHHcCCE----------------------------------EECCEEcC---------
Confidence 468889999887 5899999999999999 58998764
Q ss_pred CCCceecCCCEEEEecCCCCC----Cccc----CCCCCceEEeecCeEEEEeCCCCCccCCCCCCccchHHHHHHHhccC
Q 011530 188 HVDQIVEAGTYLRVHVHPKRF----PRCY----DIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL 259 (483)
Q Consensus 188 ~~~~~v~~GD~I~v~~~~~~~----p~~~----~~~~~~~IlyED~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~ 259 (483)
+++.|+.||.|.+....... |... .....+.|||||++|+|||||+|++||++.... .++.+.+......
T Consensus 56 -~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~-~~~~~~~~~~~~~ 133 (317)
T PRK11025 56 -PEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKVAALADVILYEDDHILVLNKPSGTAVHGGSGLS-FGVIEGLRALRPE 133 (317)
T ss_pred -cccccCCCCEEEeCCCCccccccccccccccccccCcCCEEEECCCEEEEECCCCCcCcCCCCCC-ccHHHHHHHhccC
Confidence 78999999999986422111 1100 012457899999999999999999999876543 3444444433222
Q ss_pred CCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEEeccCC--ccceeecccccccCCccccCCeeeee
Q 011530 260 TTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP--VGIMTHYMRPINIAPRLVSEGWYLCQ 337 (483)
Q Consensus 260 ~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~G~~~--~g~I~~~l~~~~~~~~~v~~g~~~~~ 337 (483)
...+++|||||++||||||||||+++++.|+++|+++.++|+|+|+|.|.++ .|.++.++....... +...
T Consensus 134 ~~~~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~v~K~Y~a~v~G~~~~~~~~i~~~i~~~~~~~-----~~~~-- 206 (317)
T PRK11025 134 ARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKVVQAPLLKNILQS-----GERI-- 206 (317)
T ss_pred CCcCceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCCccEEEEEEEeCcccCCCceEecccccCcccC-----CceE--
Confidence 2346789999999999999999999999999999999999999999999875 577887654321111 1000
Q ss_pred EEEeecccCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCCCChhhh---------h
Q 011530 338 LEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAI---------A 408 (483)
Q Consensus 338 ~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~YG~~~~---------~ 408 (483)
+.+ ...+ +.+.|+|++++. ....++++|+|+||||||||+||+++||||+||.+||.... .
T Consensus 207 ~~~-----~~~g-k~a~T~~~~l~~----~~~~sLv~~~~~TGRtHQIRvhla~lG~PIlGD~~Yg~~~~~~~~~~~~~~ 276 (317)
T PRK11025 207 VRV-----SQEG-KPSETRFKVEER----YAFATLVRASPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTGTGLN 276 (317)
T ss_pred Eec-----CCCC-ccceEEEEEeEE----cCCcEEEEEEeCCCCHHHHHHHHHHCCCCEECCcccCCcccchhhhccCCc
Confidence 001 0122 345799999974 34579999999999999999999999999999999996421 2
Q ss_pred hc-----CCCCCCCCCCceeeEecC
Q 011530 409 QL-----SSPGLNPFGKCQKEYASD 428 (483)
Q Consensus 409 ~~-----~l~f~hP~t~~~~~f~~~ 428 (483)
++ .+.|.||++++.+.|++|
T Consensus 277 r~~LHa~~l~f~~P~~~~~~~~~ap 301 (317)
T PRK11025 277 RLFLHAAALKFTHPGTGEVMRIEAP 301 (317)
T ss_pred chhhhcCcceeeCCCCCCeEEEEcC
Confidence 22 378999999999999987
No 4
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=100.00 E-value=5.4e-49 Score=397.56 Aligned_cols=262 Identities=21% Similarity=0.257 Sum_probs=204.4
Q ss_pred CCcHHHHHHhccC-CCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeecccccccc
Q 011530 109 GGPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRIT 187 (483)
Q Consensus 109 ~~rl~~~Ls~~l~-~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~ 187 (483)
+.||++||++.+. +||+.++++|+.|.| .|||+.+.
T Consensus 5 g~rLd~~L~~~~~~~Sr~~~~kli~~G~V----------------------------------~VNg~~~~--------- 41 (299)
T TIGR00005 5 GQRLDDFLASLLPDLSRSRIQKLIENGQV----------------------------------KVNGKVTA--------- 41 (299)
T ss_pred chhHHHHHHHhcccCCHHHHHHHHHCCcE----------------------------------EECCEecc---------
Confidence 4577799999996 999999999999999 58996543
Q ss_pred CCCceecCCCEEEEecCCCCCCcccCCCCCceEEeecCeEEEEeCCCCCccCCCCCCccchHHHHHHHhccC---CCCCc
Q 011530 188 HVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGL---TTPLR 264 (483)
Q Consensus 188 ~~~~~v~~GD~I~v~~~~~~~p~~~~~~~~~~IlyED~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~---~~~l~ 264 (483)
++++.|+.||.|.+.......+.....+..+.|+|||++|+|||||+|++||+.+.....++.+++...+.. ...++
T Consensus 42 ~~~~~v~~gd~I~i~~~~~~~~~~~~~~~~~~i~~ed~~~lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~ 121 (299)
T TIGR00005 42 NPKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDEDIIVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVG 121 (299)
T ss_pred CcccCCCCCCEEEEecCCcccccCCccCCCccEEEeCCCEEEEECCCCCeEeCCCCCCcccHHHHHHHhcccccCCCcCc
Confidence 488999999999997654222221222335789999999999999999999998877777888887665431 13578
Q ss_pred cccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEEeccCC--ccceeecccccccCCccccCCeeeeeEEEee
Q 011530 265 TTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP--VGIMTHYMRPINIAPRLVSEGWYLCQLEVME 342 (483)
Q Consensus 265 ~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~G~~~--~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~ 342 (483)
+|||||++||||||||||+++++.|+++|+++.++|+|+|+|.|.++ .|.|+.++....... +. +.+..
T Consensus 122 ~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~g~~~~~~~~i~~~l~~~~~~~-----~~----~~~~~ 192 (299)
T TIGR00005 122 IVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYVALVHGQFDSGGGTVDAPLGRVPNNR-----GL----MAVHP 192 (299)
T ss_pred eECCCCCCCceEEEEEcCHHHHHHHHHHHHhCCcceEEEEEEeccccCCCCEEeCceecCCCCC-----ce----EEEec
Confidence 99999999999999999999999999999999999999999999886 566776553321111 10 01110
Q ss_pred cccCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCCCChhhh-----------hhcC
Q 011530 343 CKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAI-----------AQLS 411 (483)
Q Consensus 343 ~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~YG~~~~-----------~~~~ 411 (483)
.. ..+.+.|.|+++.. ....++++|+|+|||+||||+||+++||||+||.+||+... .++.
T Consensus 193 ---~~-~~k~a~t~~~~l~~----~~~~slv~~~l~tGR~HQIR~hla~lG~pI~gD~~Yg~~~~~~~~~~~~~~~~r~~ 264 (299)
T TIGR00005 193 ---SS-EGKPAVTHFRVLER----FGNASLVECELETGRTHQIRVHLQYLGHPLAGDPLYGNKPVPGNNLNGLLNFDRQA 264 (299)
T ss_pred ---CC-CCCeeeEEEEEeEE----cCCeEEEEEEeCCCChHHHHHHHHHCCCcEeCccccCCccccccccccccCCcchh
Confidence 01 12345688998864 34578999999999999999999999999999999997432 2332
Q ss_pred -----CCCCCCCCCceeeEecChh
Q 011530 412 -----SPGLNPFGKCQKEYASDDD 430 (483)
Q Consensus 412 -----l~f~hP~t~~~~~f~~~~~ 430 (483)
+.|.||++++.+.|++|..
T Consensus 265 Lha~~l~f~~p~~~~~~~~~a~~p 288 (299)
T TIGR00005 265 LHAYELGFIHPATGEILEFEAPLP 288 (299)
T ss_pred hccCeeeccCCCCCCEEEEEcCCh
Confidence 7899999999999998743
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=1e-45 Score=364.01 Aligned_cols=224 Identities=20% Similarity=0.236 Sum_probs=173.0
Q ss_pred eeCCEEEeeccccccccCCCceecCCCEEEEecCCCCCCcccCCCCCceEEeecCeEEEEeCCCCCccCCCCCCccchHH
Q 011530 171 SIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCA 250 (483)
Q Consensus 171 ~vnGk~v~~~q~~~r~~~~~~~v~~GD~I~v~~~~~~~p~~~~~~~~~~IlyED~~liVvNKPaGl~v~~~~~~~~~tl~ 250 (483)
..||+.++ ++++|+.||.|.+.....+.+ ..+.++.|||||++|+|||||+|++||+.+....+++.
T Consensus 5 ~~ng~~~~----------~~~~l~~gd~i~~~~~~~~~~---~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~ 71 (246)
T cd02558 5 DADGEPLD----------PDSPYRPGTFVWYYRELPDEP---PIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLL 71 (246)
T ss_pred CCCCcCCC----------CCceecCCCEEEEeCCCCCCC---CCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHH
Confidence 46888764 789999999999975432211 22346899999999999999999999999887778888
Q ss_pred HHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEEeccCC--cc-ceeecccccccCCc
Q 011530 251 TFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLP--VG-IMTHYMRPINIAPR 327 (483)
Q Consensus 251 ~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~G~~~--~g-~I~~~l~~~~~~~~ 327 (483)
..+....+. ..+++|||||++||||||||||+++++.|+.+|++++++|+|+|+|.|.++ .+ .++..+. ....
T Consensus 72 ~~l~~~~~~-~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~YlA~v~G~~~~~~~~~~~~~i~---~~~~ 147 (246)
T cd02558 72 VRLRRQTGN-PDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYEAVAPYVPALTFPLTVRSRIV---KGRG 147 (246)
T ss_pred HHHHHHhCC-CcccccccCCCCceeEEEEEcCHHHHHHHHHHHHcCCccEEEEEEEecCCCCCCCcceecccc---ccCC
Confidence 777655443 357899999999999999999999999999999999999999999999875 22 2332221 1110
Q ss_pred cccCCeeeeeEEEeecccCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCCCChhh-
Q 011530 328 LVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAA- 406 (483)
Q Consensus 328 ~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~YG~~~- 406 (483)
. ....+. .+.+.+.|.|++++. ....++++|+|+||||||||+||+++||||+||.+||...
T Consensus 148 ~-------~~~~~~------~~~~~a~T~~~~l~~----~~~~slv~~~l~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~ 210 (246)
T cd02558 148 F-------FQAREV------EGEPNAETRIELLAR----RGGWGLYRLSPHTGKTHQLRVHMAALGVPILNDPFYPVLLD 210 (246)
T ss_pred c-------ceeecc------CCCCCceEEEEEEEe----cCCeEEEEEEeCCCCHHHHHHHHHHCCCcccCCccCCCCCc
Confidence 0 001111 123345789999874 3467899999999999999999999999999999999621
Q ss_pred -----h-h-----hcCCCCCCCCCCceeeEecC
Q 011530 407 -----I-A-----QLSSPGLNPFGKCQKEYASD 428 (483)
Q Consensus 407 -----~-~-----~~~l~f~hP~t~~~~~f~~~ 428 (483)
. . ...+.|.||++++.+.|++|
T Consensus 211 ~~~~~~~~~~~Lha~~l~f~hP~t~~~~~~~~~ 243 (246)
T cd02558 211 KDPDDFSRPLQLLAKELEFTDPLTGRPRRFESG 243 (246)
T ss_pred ccccccccCchhhhcccCccCCCCCCEEEEecC
Confidence 1 1 22378999999999999976
No 6
>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=3.8e-43 Score=338.72 Aligned_cols=196 Identities=27% Similarity=0.376 Sum_probs=157.2
Q ss_pred CceEEeecCeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcC
Q 011530 217 NSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREK 296 (483)
Q Consensus 217 ~~~IlyED~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~ 296 (483)
.++|||||++|+|+|||+|++|++.+.....++.+.+....+. ..+++|||||++||||||||||++++++|+++|+++
T Consensus 15 ~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~~-~~~~~vhRLD~~TSGllllak~~~~~~~l~~~f~~~ 93 (213)
T cd02557 15 PIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGL-TELRPCHRLDRLTSGLLLFAKTSQTASRLQQQIRSR 93 (213)
T ss_pred CCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcCC-CCccCccCCCCCCceEEEEECCHHHHHHHHHHHHcC
Confidence 6789999999999999999999988766677888888765543 357899999999999999999999999999999999
Q ss_pred CcceEEEEEEeccCC--ccceeecccccccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecCCCCCCCeeEEE
Q 011530 297 KVKKLYLALTTAPLP--VGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECK 374 (483)
Q Consensus 297 ~v~K~YlAlV~G~~~--~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~ 374 (483)
+++|+|+|+|.|.++ .+.++.++....... +.. .. . ....+.+.|.|+++... .....++++
T Consensus 94 ~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~-----~~~------~~--~-~~~~~~a~t~~~~~~~~--~~~~~slv~ 157 (213)
T cd02557 94 EVKKEYLARVKGEFPDGEVVVDQPIGLVSPKG-----GLR------ND--V-DEKGKDARTIFKRLSYN--GDLNTSVVL 157 (213)
T ss_pred CccEEEEEEEeCcCCCCCeEEecceeccCcCC-----cee------ec--c-CCCCceeeEEEEEEEEc--CCCCeEEEE
Confidence 999999999999886 566776553322111 100 00 0 11223446789888752 123678999
Q ss_pred EEEcCCcchHHHHHHHHcCCCeeecCCCChhhhhhcCCCCCCCCCCceeeEecChhhHHHHHHHHHhcCCCCCcceeEEE
Q 011530 375 IKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAIAQLSSPGLNPFGKCQKEYASDDDKEMAVIEWISQHGMEPSVAIGLQA 454 (483)
Q Consensus 375 l~l~TGRtHQIRvHla~lG~PIvGD~~YG~~~~~~~~l~f~hP~t~~~~~f~~~~~~~~~~~~~l~~h~~e~~~~I~LhA 454 (483)
|+|.|||+||||+||+++||||+||.+||. ..++|||
T Consensus 158 v~~~TGR~HQIR~hla~lG~PIlGD~~Yg~-------------------------------------------~~l~Lha 194 (213)
T cd02557 158 CKPITGRTHQIRVHLQYLGHPIVNDPIYNN-------------------------------------------LGIYLHA 194 (213)
T ss_pred EEeCCCCHHHHHHHHHHCCCCCcCccccCC-------------------------------------------cChhhhh
Confidence 999999999999999999999999999992 1478999
Q ss_pred EEeeecCcceEEEeCCCccc
Q 011530 455 CHISWDDGECCYEARSPWWR 474 (483)
Q Consensus 455 ~~~~~~g~~~~f~a~~P~W~ 474 (483)
++++|. ...|++++|.|.
T Consensus 195 ~~l~f~--~~~~~~~~p~~~ 212 (213)
T cd02557 195 LRYEGP--DWSYETELPDWA 212 (213)
T ss_pred ccCcCc--cEEEEeCCCccc
Confidence 999887 678999999885
No 7
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621. This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.
Probab=100.00 E-value=1.2e-42 Score=336.08 Aligned_cols=196 Identities=21% Similarity=0.292 Sum_probs=150.9
Q ss_pred ceEEeecCeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCC
Q 011530 218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKK 297 (483)
Q Consensus 218 ~~IlyED~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~ 297 (483)
++|||||++|+|||||+||+||+... ..++...+....+ ...+++|||||++||||||||||+++++.|+++|+++.
T Consensus 2 ~~ilyed~~~lvvnKP~Gl~v~~~~~--~~~l~~~l~~~~~-~~~~~~VhRLDr~TSGlll~Ak~~~~~~~L~~~~~~~~ 78 (217)
T TIGR01621 2 FEILFTHPDFLLINKHPGISVHKDDG--ETGLLQEVATQLG-VGQVWLVHRLDKMTSGILLLALNAESASELSQGFAKRK 78 (217)
T ss_pred ceEEEeCCCEEEEECCCCCeECCCCC--cChHHHHHHHhcC-CCCccEecCCCCCCceEEEEEcCHHHHHHHHHHHhcCC
Confidence 47999999999999999999998754 2455555544433 23578999999999999999999999999999999999
Q ss_pred cceEEEEEEeccCC--ccceeecccccccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecCCCCCCCeeEEEE
Q 011530 298 VKKLYLALTTAPLP--VGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKI 375 (483)
Q Consensus 298 v~K~YlAlV~G~~~--~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l 375 (483)
++|+|+|+|.|.++ +|.|+.++..... +. ..+.. . ..+.+.|.|+++.. ....++++|
T Consensus 79 v~K~YlAlV~g~~~~~~~~i~~~~~~~~~-------~~----~~~~~----~-~~k~a~t~~~~~~~----~~~~slv~~ 138 (217)
T TIGR01621 79 IEKTYLALSSKKPKKKQGLICGDMEKSRR-------GS----WKLVN----S-QENPAITRFFSASA----ATGLRLFIL 138 (217)
T ss_pred ccEEEEEEEeccccCCCCEEeCCcccCCC-------CC----EEEeC----C-CCCceeEEEEEEEE----cCCeEEEEE
Confidence 99999999999875 5777765532211 11 11111 1 12334688988864 346789999
Q ss_pred EEcCCcchHHHHHHHHcCCCeeecCCCChhhhhhcCCCCCCCCCCceeeEecChhhHHHHHHHHHhcCCCCCcceeEEEE
Q 011530 376 KLLTGRTHQVRAQLAACGAPIVGDSMYMPAAIAQLSSPGLNPFGKCQKEYASDDDKEMAVIEWISQHGMEPSVAIGLQAC 455 (483)
Q Consensus 376 ~l~TGRtHQIRvHla~lG~PIvGD~~YG~~~~~~~~l~f~hP~t~~~~~f~~~~~~~~~~~~~l~~h~~e~~~~I~LhA~ 455 (483)
+|.||||||||+||+++||||+||.+||... ....++|||+
T Consensus 139 ~~~TGR~HQIRvhla~lG~PIlGD~~Yg~~~---------------------------------------~~~~~~Lha~ 179 (217)
T TIGR01621 139 KPHTGKTHQLRVAMKSLGSPILGDPLYGTTD---------------------------------------ESDRGYLHAF 179 (217)
T ss_pred EeCCCCHHHHHHHHHHCCCceeCCcccCCCC---------------------------------------CccCceeeee
Confidence 9999999999999999999999999999421 0125789999
Q ss_pred Eeeec--CcceEEEeCCCcccc
Q 011530 456 HISWD--DGECCYEARSPWWRC 475 (483)
Q Consensus 456 ~~~~~--g~~~~f~a~~P~W~~ 475 (483)
++.|. |+...|++++|++.+
T Consensus 180 ~l~f~~~~~~~~~~~~~~~~~~ 201 (217)
T TIGR01621 180 ALRFDYQNEVIQWLCDPRQFQK 201 (217)
T ss_pred EeEEEECCeEEEEEECcHHHHH
Confidence 99884 566678888665543
No 8
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=100.00 E-value=4e-42 Score=351.78 Aligned_cols=305 Identities=27% Similarity=0.352 Sum_probs=220.4
Q ss_pred CCcHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeecccccccc
Q 011530 109 GGPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRIT 187 (483)
Q Consensus 109 ~~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~ 187 (483)
+..+.++++.++ ..++.+.+..|+.|.| .+||+.+.
T Consensus 43 ~k~~~~~~~~ef~~~~~~~~~~~i~~g~v----------------------------------~~n~~~~~--------- 79 (371)
T KOG1919|consen 43 GKKLVDVFVSEFRLRERAYYESAIKLGRV----------------------------------TVNGEQVR--------- 79 (371)
T ss_pred ccchHHHHHHHHhcCchHhhhhhhhcCce----------------------------------EECcEeee---------
Confidence 456678888887 5888999999999999 58999876
Q ss_pred CCCceecCCCEEEEecCCCCCCcccCCCCCceEEeecCeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCcccc
Q 011530 188 HVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTH 267 (483)
Q Consensus 188 ~~~~~v~~GD~I~v~~~~~~~p~~~~~~~~~~IlyED~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VH 267 (483)
.++.++.||.|...++.++.+... +.+.|+|||++|+|||||+|++||+++....+++..++..... ...+++||
T Consensus 80 -v~~i~k~~d~l~~~vhrh~p~~~~---~~~~Iv~ed~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~~~-~~~~~~~h 154 (371)
T KOG1919|consen 80 -VSLIVKNGDVLCHTVHRHEPPVAY---LPIRIVFEDKDYVVVNKPHGIPVHPTGRYRENTITKILAALHK-VEGLRPCH 154 (371)
T ss_pred -eEEEeccCCEEEEeeccCCCCccc---cccceEEecCCEEEEeCCCCCceeccCccccccchHHHHHhcc-cccccccc
Confidence 678999999999999888766433 4789999999999999999999999888888888777655422 24578999
Q ss_pred CCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEE-EEEEeccCC-ccceeecccccccCCccccCCeeeeeEEEeeccc
Q 011530 268 QIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLY-LALTTAPLP-VGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKK 345 (483)
Q Consensus 268 RLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~Y-lAlV~G~~~-~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~ 345 (483)
|||+.|||||+|||+++++..++++|+++++.|.| +|-|.|.+| .|.+.... +.....+ ..++.++...+.++
T Consensus 155 RLDr~tSGllvlAkt~~~~~~~~~~~r~~~~~k~Y~v~~v~g~fp~~~~~~i~~-~~~~~~~--~~~~~l~~~~~~~~-- 229 (371)
T KOG1919|consen 155 RLDRLTSGLLVLAKTKEAADKFHEVLRKRTVKKEYVVARVEGPFPVVGEVEIKE-PIGEEER--PLRMGLNAVGVRDE-- 229 (371)
T ss_pred ccCccccceEEEEechhHhHHHHHHHhcccceeEEEEEEEeccCCCCceEEeCC-Ccccccc--ccceEeeecccccc--
Confidence 99999999999999999999999999999999999 799999998 66665321 1111110 01222222222221
Q ss_pred CCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCCCChhhhhhcCCCCCCCCCCce-ee
Q 011530 346 VPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAIAQLSSPGLNPFGKCQ-KE 424 (483)
Q Consensus 346 ~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~YG~~~~~~~~l~f~hP~t~~~-~~ 424 (483)
...+.+.|.|+++.. .+..++|+|.|+||||||||+||+++|+||+||.+||+...... +++.......+ ..
T Consensus 230 --~~~k~a~T~~~~~~~----~~~ss~V~~~PlTGRtHQIRvHlq~lG~PI~gD~~Y~~~~~~~~-~P~~g~~~~~~~~~ 302 (371)
T KOG1919|consen 230 --VAAKDAKTLFKVLSY----DGGSSLVECRPLTGRTHQIRVHLQYLGHPIAGDPKYGNHIVWAG-LPFTGREGTAKKKS 302 (371)
T ss_pred --cccccceeEEEEccc----CCceEEEEeeccCCcHHHHHHHHHHhCCCcCCCccccccccccc-CCCCCCCCCccccC
Confidence 123556789999874 47789999999999999999999999999999999976332110 11111110000 00
Q ss_pred EecCh----------------hhHHHHHHHHHhcCCC---CCcceeEEEEEeeecCcceEEEeCCCcccc
Q 011530 425 YASDD----------------DKEMAVIEWISQHGME---PSVAIGLQACHISWDDGECCYEARSPWWRC 475 (483)
Q Consensus 425 f~~~~----------------~~~~~~~~~l~~h~~e---~~~~I~LhA~~~~~~g~~~~f~a~~P~W~~ 475 (483)
++.+. .......+-++..|.. ....+||||++|++. +|.|+++.|.|+.
T Consensus 303 ~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~~~~~Dl~~~lha~~y~~~--~~~~~~~~~~w~~ 370 (371)
T KOG1919|consen 303 LEEEIQRLIDVHLLENWLGFHPRTGPLIEELCQECKVPIDNDLELFLHALKYEMK--GWEYKTELPKWAL 370 (371)
T ss_pred ccccccccchhhccccccccccccccchhhhhhhCCCCCCchHhHhhhhcccccC--CccccCCcchhhc
Confidence 00000 0000112233334443 466799999999555 6889999999985
No 9
>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=2.2e-42 Score=335.66 Aligned_cols=196 Identities=20% Similarity=0.182 Sum_probs=147.4
Q ss_pred ceEEeecCeEEEEeCCCCCccCCCCCCccc--hHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhc
Q 011530 218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEE--SCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIRE 295 (483)
Q Consensus 218 ~~IlyED~~liVvNKPaGl~v~~~~~~~~~--tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~ 295 (483)
++|||||++|+|||||+|++||+....... .+...+...++ ..+++|||||++||||||||||+++++.|+++|++
T Consensus 1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~ 78 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLG--QHVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTE 78 (223)
T ss_pred CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHcC--CCcccccCCCCCCeEEEEEEECHHHHHHHHHHHhc
Confidence 369999999999999999999987643222 23333433332 45789999999999999999999999999999999
Q ss_pred CCcceEEEEEEeccCC-ccceeecccccccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecCC-------CCC
Q 011530 296 KKVKKLYLALTTAPLP-VGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGW-------PSR 367 (483)
Q Consensus 296 ~~v~K~YlAlV~G~~~-~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~-------~~~ 367 (483)
+.++|+|+|+|.|.++ +|.++.++........ . ..+. . ....+.+.|.|+++.... ...
T Consensus 79 ~~v~K~Y~alv~G~~~~~~~i~~~l~~~~~~~~-----~----~~~~-~---~~~~~~a~t~~~~l~~~~~~~~~~~~~~ 145 (223)
T cd02563 79 HRVHKTYLAVVRGYVPESGTIDYPLSEELDKLA-----D----KFAS-D---DKAPQAATTHYRLLAVEELPVVVGKYPT 145 (223)
T ss_pred CceeEEEEEEEECccCCCCeEEEeeeeCCCccc-----e----EEee-c---CCCCceeEEEEEEeeecccccccccCCC
Confidence 9999999999999875 6777765532211100 0 0010 0 112234578898886320 112
Q ss_pred CCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCCCChhhh----------hhc-----CCCCCCCCCCceeeEecC
Q 011530 368 DYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAI----------AQL-----SSPGLNPFGKCQKEYASD 428 (483)
Q Consensus 368 ~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~YG~~~~----------~~~-----~l~f~hP~t~~~~~f~~~ 428 (483)
...++++|+|+||||||||+||+++||||+||.+||+... .++ .+.|.||++++.+.|++|
T Consensus 146 ~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~rl~Lha~~L~F~hP~t~~~~~~~a~ 221 (223)
T cd02563 146 SRYSLVELTPHTGRKHQLRRHLAHIRHPIIGDTTHGDGRHNRFFREHFGCHRLLLAATRLEFTHPVTGERLLIEAP 221 (223)
T ss_pred CCeEEEEEEeCCCCHHHHHHHHHHcCCCeeCCcccCCcccChhHHhhcCCccceeecCeeEeeCCCCCCeEEEEcc
Confidence 3579999999999999999999999999999999996431 223 278999999999999986
No 10
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=100.00 E-value=9.4e-42 Score=337.87 Aligned_cols=196 Identities=18% Similarity=0.199 Sum_probs=146.5
Q ss_pred ceEEeecCeEEEEeCCCCCccCCCCCCccch--HHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhc
Q 011530 218 SRIIAVTESHVVLDKPAGTSVGGTTDNIEES--CATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIRE 295 (483)
Q Consensus 218 ~~IlyED~~liVvNKPaGl~v~~~~~~~~~t--l~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~ 295 (483)
++|||||++|||||||+||+||+.......+ +...+....+ ..+++|||||++||||||||||+++++.|+++|++
T Consensus 2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~ 79 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQIG--QHVFTAHRLDRPTSGVLLMALSSEVARLLAQQFEQ 79 (257)
T ss_pred CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHhC--CCceeeccCCCCCeeEEEEECCHHHHHHHHHHHHh
Confidence 4799999999999999999999875333332 3334433332 35789999999999999999999999999999999
Q ss_pred CCcceEEEEEEeccCC-ccceeecccccccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecCC-------CCC
Q 011530 296 KKVKKLYLALTTAPLP-VGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGW-------PSR 367 (483)
Q Consensus 296 ~~v~K~YlAlV~G~~~-~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~-------~~~ 367 (483)
+.|+|+|+|+|.|.++ +|.++.++...... ...+ +. . .....+.+.|.|+++.... ...
T Consensus 80 ~~v~K~Y~Alv~G~~~~~~~i~~~l~~~~~~---~~~~-------~~--~-~~~~~k~a~T~~~~l~~~~~~~~~~~~~~ 146 (257)
T PRK11112 80 HQIQKTYHAIVRGWLMEEAVLDYPLKEELDK---IADK-------FA--R-EDKAPQPAVTHYRGLATVEMPVATGRYPT 146 (257)
T ss_pred CCcceEEEEEEEeEeCCCCeEeeeeeecccc---ccee-------ec--c-cCCCCeEeEEEEEEEEEecccccccccCC
Confidence 9999999999999875 67777655321100 0000 00 0 0112234568888876320 012
Q ss_pred CCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCCCChhhh----------hhc-----CCCCCCCCCCceeeEecC
Q 011530 368 DYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAI----------AQL-----SSPGLNPFGKCQKEYASD 428 (483)
Q Consensus 368 ~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~YG~~~~----------~~~-----~l~f~hP~t~~~~~f~~~ 428 (483)
...++++|+|.||||||||+||+++||||+||.+||.... .++ .+.|.||++++.+.|++|
T Consensus 147 ~~~slv~i~~~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~rl~LHA~~L~F~hP~t~e~~~~~a~ 222 (257)
T PRK11112 147 TRYSLVELEPKTGRKHQLRRHMAHLRHPIIGDTKHGDLRQNRSLAEHFGCSRLMLHASELSLTHPFTGEPLTITAG 222 (257)
T ss_pred CCeEEEEEEcCCCChHHHHHHHHHcCCCEeCCcccCCcccchhhhhccCCcchhHhhCccCccCCCCCCEEEEEcC
Confidence 4579999999999999999999999999999999996321 122 378999999999999976
No 11
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=100.00 E-value=6.2e-42 Score=331.63 Aligned_cols=193 Identities=22% Similarity=0.260 Sum_probs=150.0
Q ss_pred CceEEeecCeEEEEeCCCCCccCCCCC-CccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhc
Q 011530 217 NSRIIAVTESHVVLDKPAGTSVGGTTD-NIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIRE 295 (483)
Q Consensus 217 ~~~IlyED~~liVvNKPaGl~v~~~~~-~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~ 295 (483)
.+.|||||++|+|||||+|++|++... ....++.+.+...+ ..+++|||||++||||||||||.++++.|+++|++
T Consensus 13 ~~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~---~~~~~vhRLDr~TSGlll~Akt~~~~~~l~~~f~~ 89 (219)
T PRK10158 13 WLVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY---PQAESVHRLDMATSGVIVVALTKAAERELKRQFRE 89 (219)
T ss_pred CCCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC---CCCCEECCCCCCCceEEEEECCHHHHHHHHHHHHh
Confidence 368999999999999999999998753 33456666665433 24789999999999999999999999999999999
Q ss_pred CCcceEEEEEEeccCC--ccceeecccccccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecCCCCCCCeeEE
Q 011530 296 KKVKKLYLALTTAPLP--VGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYEC 373 (483)
Q Consensus 296 ~~v~K~YlAlV~G~~~--~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv 373 (483)
++++|+|+|+|.|.++ .+.++.++........ ...+. ...+ +.+.|.|++++.. ....+++
T Consensus 90 ~~v~K~Yla~v~G~~~~~~~~i~~~i~~~~~~~~---------~~~~~----~~~g-k~a~t~~~~l~~~---~~~~sll 152 (219)
T PRK10158 90 REPKKQYVARVWGHPSPAEGLVDLPLICDWPNRP---------KQKVC----YETG-KPAQTEYEVVEYA---ADNTARV 152 (219)
T ss_pred CCccEEEEEEEecccCCCCcEEecceecCCCCCc---------eEEec----CCCC-ceeeEEEEEEEEc---CCCCEEE
Confidence 9999999999999885 5777765532211100 01111 0112 3456899998752 2334799
Q ss_pred EEEEcCCcchHHHHHHHHcCCCeeecCCCChhhh----hhc-----CCCCCCCCCCceeeEecCh
Q 011530 374 KIKLLTGRTHQVRAQLAACGAPIVGDSMYMPAAI----AQL-----SSPGLNPFGKCQKEYASDD 429 (483)
Q Consensus 374 ~l~l~TGRtHQIRvHla~lG~PIvGD~~YG~~~~----~~~-----~l~f~hP~t~~~~~f~~~~ 429 (483)
+|+|+||||||||+||+++||||+||.+||+... .++ .+.|.||++++.+.|.+|.
T Consensus 153 ~~~~~TGRtHQIR~hla~lG~PIvGD~~Yg~~~~~~~~~r~~Lha~~l~f~~P~~~~~~~~~a~~ 217 (219)
T PRK10158 153 VLKPITGRSHQLRVHMLALGHPILGDRFYASPEARAMAPRLLLHAEMLTITHPAYGNSMTFKAPA 217 (219)
T ss_pred EEEeCCCCHHHHHHHHHHCCCcEECCcccCCccccccccchhhhhCccCccCCCCCCeEEEEeCC
Confidence 9999999999999999999999999999996432 233 3799999999999999874
No 12
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=100.00 E-value=4.1e-37 Score=300.32 Aligned_cols=202 Identities=14% Similarity=0.219 Sum_probs=151.8
Q ss_pred cHHHHHHhccCCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccCCC
Q 011530 111 PVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVD 190 (483)
Q Consensus 111 rl~~~Ls~~l~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~~~ 190 (483)
||++||++.+.+||+.++++|+.|.| .|||+.++ +++
T Consensus 2 rld~~L~~~~~~Sr~~~~~li~~g~V----------------------------------~VNg~~~~---------~~~ 38 (232)
T PRK10839 2 RLDKFISQQLGVSRAIAGRELRANRV----------------------------------TVDGEIVK---------NGA 38 (232)
T ss_pred cHHHHHHHcCCCCHHHHHHHHHcCeE----------------------------------EECCEEec---------cCC
Confidence 67799999989999999999999999 58999875 478
Q ss_pred ceecCCCEEEEecCCCCCCcccCCCCCceEEeecCeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCC
Q 011530 191 QIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQID 270 (483)
Q Consensus 191 ~~v~~GD~I~v~~~~~~~p~~~~~~~~~~IlyED~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLD 270 (483)
++|+.||.|.+...+.. ..++++++|+|||+||+||++... ..++.+++... ....+++|||||
T Consensus 39 ~~l~~gd~I~l~~~~~~-------------~~~~~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~~--~~~~~~~v~RLD 102 (232)
T PRK10839 39 FKLLPEHDVAYDGNPLA-------------QQHGPRYFMLNKPQGYVCSTDDPD-HPTVLYFLDEP--VAYKLHAAGRLD 102 (232)
T ss_pred cCcCCCCEEEECCEEcc-------------cCCCCEEEEEECCCCeEecccCCC-CCeEEEecccc--cccCceecCCCC
Confidence 89999999988642110 113568999999999999987543 34554443321 122467999999
Q ss_pred CCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEEeccCCccceeecccccccCCccccCCeeeeeEEEeecccCCCCC
Q 011530 271 NCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPD 350 (483)
Q Consensus 271 r~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~G~~~~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~ 350 (483)
++||||||||||++++..|.. +++.++|+|+|.+.+++....+........ . .+
T Consensus 103 ~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~i~~~i~~~~~~~~~~~~~-----------------~------~g- 156 (232)
T PRK10839 103 IDTTGLVLMTDDGQWSHRITS--PRHHCEKTYLVTLESPVADDTAEQFAKGVQ-----------------L------HN- 156 (232)
T ss_pred CCceeEEEEecCHHHHHHHhC--CCCCCCeEEEEEECCCCCHHHHHHHHCCeE-----------------E------CC-
Confidence 999999999999999999975 788999999999998875332221100000 0 01
Q ss_pred CccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCCC
Q 011530 351 ATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMY 402 (483)
Q Consensus 351 ~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~Y 402 (483)
+.+.|.|.+++.. + .++++|+|+||||||||+||+++||||+|=...
T Consensus 157 ~~a~t~~~~~~~~---~--~sll~~~l~tGRtHQIR~h~~~~G~pi~gl~R~ 203 (232)
T PRK10839 157 EKDLTKPAVLEVI---T--PTQVRLTISEGRYHQVKRMFAAVGNHVVELHRE 203 (232)
T ss_pred CcccccccEEEEe---c--CCEEEEEEEcCcCHHHHHHHHHcCCeEeeEEEE
Confidence 1234677777642 1 279999999999999999999999999997643
No 13
>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=100.00 E-value=8e-36 Score=279.72 Aligned_cols=161 Identities=27% Similarity=0.370 Sum_probs=122.5
Q ss_pred EEEEeCCCCCccCCCCCCccchHHHHHH---HhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEE
Q 011530 227 HVVLDKPAGTSVGGTTDNIEESCATFAS---RALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYL 303 (483)
Q Consensus 227 liVvNKPaGl~v~~~~~~~~~tl~~~l~---~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~Yl 303 (483)
|+|+|||+|++|++.......++..++. ........+++|||||++||||||||+|+++++.|.++|+++.+.|+|+
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~tsGlll~ak~~~~~~~l~~~~~~~~~~K~Y~ 80 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYL 80 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhcCCCCcCceecccCCCCceEEEEEcCHHHHHHHHHHHhcCceeEEEE
Confidence 5899999999999988776777776542 1112335688999999999999999999999999999999999999999
Q ss_pred EEEeccCC--ccceeecccccccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCc
Q 011530 304 ALTTAPLP--VGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGR 381 (483)
Q Consensus 304 AlV~G~~~--~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGR 381 (483)
|+|.|.++ .+.++.++........ . .... ..+.+.+.|.|+++.. ....++++|+|.|||
T Consensus 81 a~v~g~~~~~~~~~~~~~~~~~~~~~--------~-~~~~-----~~~~~~~~t~~~~l~~----~~~~s~~~~~l~tGR 142 (185)
T cd02869 81 ALVDGKPPEDEGTIDAPLGRKKRKKR--------A-RVVV-----SEDGKPAITHYKVLER----FGNVTLVELQLETGR 142 (185)
T ss_pred EEEeCCCCCCccEEecccccCCccCc--------e-EEEE-----CCCCeEEEEEEEEEEE----cCCcEEEEEEeCcCC
Confidence 99999886 3444443322100000 0 0000 0122345678988864 346789999999999
Q ss_pred chHHHHHHHHcCCCeeecCCCChh
Q 011530 382 THQVRAQLAACGAPIVGDSMYMPA 405 (483)
Q Consensus 382 tHQIRvHla~lG~PIvGD~~YG~~ 405 (483)
+||||+||+++||||+||.+||..
T Consensus 143 ~HQIR~hl~~~G~pIvGD~~Yg~~ 166 (185)
T cd02869 143 THQIRVHLASIGHPIVGDPKYGGK 166 (185)
T ss_pred ccHHHHHHHHCCCCEeCccccCCc
Confidence 999999999999999999999953
No 14
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=100.00 E-value=2.7e-32 Score=274.24 Aligned_cols=207 Identities=15% Similarity=0.150 Sum_probs=150.5
Q ss_pred CcHHHHHHhccCCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccCC
Q 011530 110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (483)
Q Consensus 110 ~rl~~~Ls~~l~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~~ 189 (483)
.||++||++.+.+||++++++|+.|+| +|||++++ +
T Consensus 3 ~RL~k~La~~g~~SRr~a~~lI~~G~V----------------------------------~VNG~~~~----------~ 38 (289)
T PRK10700 3 EKLQKVLARAGHGSRREIESIIEAGRV----------------------------------SVDGKIAT----------L 38 (289)
T ss_pred hhHHHHHHHCCCCCHHHHHHHHHcCCE----------------------------------EECCEecc----------C
Confidence 467799999877999999999999999 58998763 7
Q ss_pred CceecCCC--EEEEecCCCCCCcccCCCCCceEEe-ecCeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccc
Q 011530 190 DQIVEAGT--YLRVHVHPKRFPRCYDIDWNSRIIA-VTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTT 266 (483)
Q Consensus 190 ~~~v~~GD--~I~v~~~~~~~p~~~~~~~~~~Ily-ED~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~V 266 (483)
++.|..+| .|.++...... ...+ ||++|+++|||+|++|++.+.....++.+++.... ...+++|
T Consensus 39 g~~V~~~~~d~I~v~g~~~~~----------~~~~~e~~~ylvlnKP~G~~~s~~d~~~~~tv~d~l~~~~--~~~~~~V 106 (289)
T PRK10700 39 GDRVEVTPGLKIRIDGHLISV----------KESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLR--GARWIAV 106 (289)
T ss_pred CCEeCCCCCeEEEECCEEeec----------ccccccCCeEEEEECCCCCEeecCCCCCCccHHHHhhhhc--CCceeEc
Confidence 78888774 45554211100 0111 56789999999999999887666678888876421 2357899
Q ss_pred cCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEEeccCCccceeecccccccCCccccCCeeeeeEEEeecccC
Q 011530 267 HQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKV 346 (483)
Q Consensus 267 HRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~G~~~~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~ 346 (483)
||||++||||||||+|+++++.|.+ +++.++|+|+|+|.|.+++..++....++.. ++.
T Consensus 107 gRLD~dTsGLLLlTndg~~~~~L~~--p~~~i~K~Y~v~V~G~~~~~~l~~l~~Gv~l------~~~------------- 165 (289)
T PRK10700 107 GRLDVNTCGLLLFTTDGELANRLMH--PSREVEREYAVRVFGQVDDAKLRQLSRGVQL------EDG------------- 165 (289)
T ss_pred cCCCCCCceEEEEEcCHHHHHHHhC--ccCCCCeEEEEEEccCCCHHHHHHHHcCCEe------CCc-------------
Confidence 9999999999999999999999966 8889999999999998875544421111110 000
Q ss_pred CCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCC
Q 011530 347 PWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSM 401 (483)
Q Consensus 347 ~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~ 401 (483)
. +.+..+... ......++++|+|.|||+||||+||+++|+||+.=..
T Consensus 166 ----~---~~~~~v~~~-~~~~~~s~l~v~L~EGk~hQIRrm~~~lG~~V~~L~R 212 (289)
T PRK10700 166 ----P---AAFKTIKFS-GGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIR 212 (289)
T ss_pred ----e---eeeEEEEec-cCCCCceEEEEEEeCCccHHHHHHHHHcCCEEeEEEE
Confidence 0 111111110 0112346899999999999999999999999987543
No 15
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=100.00 E-value=4.3e-32 Score=272.33 Aligned_cols=201 Identities=17% Similarity=0.198 Sum_probs=152.5
Q ss_pred CCCcHHHHHHhccCCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeecccccccc
Q 011530 108 EGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRIT 187 (483)
Q Consensus 108 ~~~rl~~~Ls~~l~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~ 187 (483)
++.||++||++.+.+||++++++|+.|.| .|||+++.
T Consensus 5 ~~~RL~k~La~~g~~SRr~a~~lI~~G~V----------------------------------~VNGk~v~--------- 41 (290)
T PRK10475 5 SSTRLNKYISESGICSRREADRYIEQGNV----------------------------------FINGKRAT--------- 41 (290)
T ss_pred hHHHHHHHHHhCCCCCHHHHHHHHHCCcE----------------------------------EECCEEcc---------
Confidence 44578899999888999999999999999 58998764
Q ss_pred CCCceecCCCEEEEecCCCCCCcccCCCCCceEEeecCeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCcccc
Q 011530 188 HVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTH 267 (483)
Q Consensus 188 ~~~~~v~~GD~I~v~~~~~~~p~~~~~~~~~~IlyED~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VH 267 (483)
+++.|.+||.|.|+....+. ..+||++|||+|||+|++|++.+. ...++.+++... ..+++||
T Consensus 42 -~~~~V~~gD~V~v~g~~i~~-----------~~~ed~~~lvlnKP~G~~~~~~~~-~~~tv~~~l~~~----~~l~~Vg 104 (290)
T PRK10475 42 -IGDQVKAGDVVKVNGQLIEP-----------REAEDLVLIALNKPVGIVSTTEDG-ERDNIVDFVNHS----KRVFPIG 104 (290)
T ss_pred -CCCCcCCCCEEEECCEEccc-----------cccCCCeEEEEECCCCCCcCCCCC-CCCcHHHHhhcc----ccccccc
Confidence 78899999999987421100 013788999999999999997655 457787777532 3578999
Q ss_pred CCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEEeccCCccceeecccccccCCccccCCeeeeeEEEeecccCC
Q 011530 268 QIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVP 347 (483)
Q Consensus 268 RLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~G~~~~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~ 347 (483)
|||++||||||||+|+++++.|.+ +.+.++|+|+|+|.|++.+..++....++... +.. +
T Consensus 105 RLDrdTsGLLLlT~dg~~~~~L~~--p~~~i~K~Y~v~V~g~~~~~~l~~l~~Gv~l~------~~~-~----------- 164 (290)
T PRK10475 105 RLDKDSQGLIFLTNHGDLVNKILR--AGNDHEKEYLVTVDKPITDEFIRGMGAGVPIL------GTV-T----------- 164 (290)
T ss_pred cCCCCCcceEEEecCHHHHHHhhC--cCCCCCeEEEEEECCCCCHHHHHHHhCCcEEC------CEE-e-----------
Confidence 999999999999999999999966 66789999999999999876665433222110 100 0
Q ss_pred CCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCC
Q 011530 348 WPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSM 401 (483)
Q Consensus 348 ~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~ 401 (483)
.. .....+ ..++++|.|.+||+||||+||+++|++|+-=..
T Consensus 165 --~~---~~v~~~--------~~~~~~i~l~eGk~rqIRrm~~~~G~~V~~L~R 205 (290)
T PRK10475 165 --KK---CKVKKE--------APFVFRITLVQGLNRQIRRMCEHFGYEVTKLER 205 (290)
T ss_pred --cc---eEEEec--------CCcEEEEEEECCcCHHHHHHHHHcCCEEeEEEE
Confidence 00 011111 124689999999999999999999999986443
No 16
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=99.98 E-value=8.6e-32 Score=246.87 Aligned_cols=147 Identities=21% Similarity=0.281 Sum_probs=111.2
Q ss_pred EEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEE
Q 011530 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (483)
Q Consensus 227 liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV 306 (483)
|+|+|||+|++||+++.....++...+.... ...+++|||||++||||||||+|+++++.|+++ +++++|+|+|+|
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~~--~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~v~K~Y~a~v 76 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLH--GPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEP--RREIEKEYLVTV 76 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhhccc--CCceeEeccCCCCCeeEEEEEcCHHHHHHHhhh--hccCcEEEEEEE
Confidence 5899999999999988766677776654332 245789999999999999999999999999997 788999999999
Q ss_pred eccCC-ccceeecccccccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHH
Q 011530 307 TAPLP-VGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQV 385 (483)
Q Consensus 307 ~G~~~-~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQI 385 (483)
.|.++ ++.+..++.. ..+. .+ +.. . +.+.+.|.|+++.. ....++++|+|.|||+|||
T Consensus 77 ~g~~~~~~~~~~~~~~---~~~~--~~-------~~~----~-~~~~~~t~~~~l~~----~~~~sll~~~l~tGR~HQI 135 (154)
T cd02550 77 RGELDEEGIEDLATVR---RGRL--SG-------LVD----E-GVPLAVTKVRVIGE----HGGTGRLRLTLKTGRTHQI 135 (154)
T ss_pred EeecCcchheeccccc---cCcc--ee-------EEc----C-CCcccceEEEEEEe----cCCcEEEEEEEcCCCcHHH
Confidence 99886 3433322211 0000 00 000 1 12334678998863 3456899999999999999
Q ss_pred HHHHHHcCCCeee
Q 011530 386 RAQLAACGAPIVG 398 (483)
Q Consensus 386 RvHla~lG~PIvG 398 (483)
|+||+++||||+.
T Consensus 136 R~hla~~G~pI~~ 148 (154)
T cd02550 136 RRHCAAVGFPVLR 148 (154)
T ss_pred HHHHHHcCCcEEe
Confidence 9999999999974
No 17
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=3.4e-30 Score=251.29 Aligned_cols=208 Identities=19% Similarity=0.198 Sum_probs=158.2
Q ss_pred CcHHHHHHhccCCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccCC
Q 011530 110 GPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (483)
Q Consensus 110 ~rl~~~Ls~~l~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~~ 189 (483)
.||++||++.+.+||++|+++|.+|+| +|||++++ ++
T Consensus 3 ~RL~K~La~~G~~SRr~ae~lI~~G~V----------------------------------~VnG~v~~---------~~ 39 (248)
T COG1187 3 MRLNKFLAEAGVGSRREAEKLIEEGRV----------------------------------TVNGKVAT---------LG 39 (248)
T ss_pred cchHHHHHHcCCCCHHHHHHHHHcCCE----------------------------------EECCEEec---------cC
Confidence 466799999999999999999999999 69999988 46
Q ss_pred CceecCC-CEEEEecCCCCCCcccCCCCCceEEe-ecCeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCcccc
Q 011530 190 DQIVEAG-TYLRVHVHPKRFPRCYDIDWNSRIIA-VTESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTH 267 (483)
Q Consensus 190 ~~~v~~G-D~I~v~~~~~~~p~~~~~~~~~~Ily-ED~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VH 267 (483)
...+.++ |.|.+.. ..+.+ +...|+++|||.|++|+..++....|+.+++.........+++|+
T Consensus 40 ~~~v~~~~~~i~v~g--------------~~~~~~~~~~y~llnKP~G~v~s~~D~~gr~tv~D~lp~~~~~~~~~~pvG 105 (248)
T COG1187 40 GVVVDPDDDVVEVDG--------------KRIELKEERVYLLLNKPRGYVSSTEDDEGRPTVFDLLPERLPRKKRLFPVG 105 (248)
T ss_pred CeEeCCCCcEEEECC--------------EEeeccccceEEEEECCCCeEecccCCCCCceeeeecccccccccceeecc
Confidence 6778877 4666653 22333 334499999999999998877788899888874322334589999
Q ss_pred CCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEEeccCCccceeecccccccCCccccCCeeeeeEEEeecccCC
Q 011530 268 QIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVP 347 (483)
Q Consensus 268 RLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~G~~~~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~ 347 (483)
|||+||+|||||++|++++++|.+ +..+++|+|+|.|.|.+.+..++....++..... .
T Consensus 106 RLD~dTeGLLLLTnDG~la~rL~~--P~~~~~K~Y~v~v~g~~~~~~l~~l~~Gv~l~d~-----~-------------- 164 (248)
T COG1187 106 RLDKDTEGLLLLTNDGELAHRLMH--PSSEVEKEYLVRVEGPVTEEDLEKLRKGVTLDDG-----E-------------- 164 (248)
T ss_pred ccCCCCeeEEEEeCCHHHHHHhcC--CCCCCCEEEEEEEecCCCHHHHHHHhCCcEecCc-----c--------------
Confidence 999999999999999999999955 9999999999999998876666543333222110 0
Q ss_pred CCCCcccee-EEeeecCCCCCCCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCCC
Q 011530 348 WPDATVGKA-YSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMY 402 (483)
Q Consensus 348 ~~~~~~~t~-~~vl~~~~~~~~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~Y 402 (483)
.. ... ..+... .....+++++.|.+||+||||+||+++|+|++.=..+
T Consensus 165 --~~--~~~~~~l~~~---~~~~~s~~~itl~EGrnrQVRRm~~a~G~~V~~L~R~ 213 (248)
T COG1187 165 --TK--PAKPASLEKE---PGKNNSWLRITLTEGRNRQVRRMFEAVGLEVLRLKRI 213 (248)
T ss_pred --cc--cceeEEEEec---CCCCceEEEEEEeCCcCHHHHHHHHHcCCEEeEEEEE
Confidence 00 011 111110 1115779999999999999999999999999876544
No 18
>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=99.97 E-value=4.8e-30 Score=238.60 Aligned_cols=144 Identities=14% Similarity=0.133 Sum_probs=109.5
Q ss_pred EEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEE
Q 011530 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (483)
Q Consensus 227 liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV 306 (483)
++|+|||+|++|++.+.....++.+++.... ...+++|||||++||||||||+|+++++.|.. +++.++|+|+|+|
T Consensus 2 ~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~--~~~~~~V~RLD~~TsGLll~ak~~~~~~~L~~--~~~~i~K~Y~a~V 77 (167)
T cd02556 2 VLIYHKPEGLICTRKDPKGRPTVFDLLPKLG--IPRWISVGRLDLNTEGLLLFTNDGELANRLMH--PSNEIEREYAVRV 77 (167)
T ss_pred EEEEECCCCcEECccCCCCCccHHHhhhhhc--cCceEEcCcCCCCCeeEEEEECCHHHHHHHhC--CcCCCCeEEEEEE
Confidence 7899999999999876555677877765431 23577999999999999999999999999965 8899999999999
Q ss_pred eccCCccceeecccccccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHH
Q 011530 307 TAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVR 386 (483)
Q Consensus 307 ~G~~~~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIR 386 (483)
.|.++...++.. .. |. . . .. .+.+.+.|+++.. ....++++|+|+|||+||||
T Consensus 78 ~g~~~~~~~~~~----~~-------gv-----~-~-----~~-~~~~~~~~~~~~~----~~~~sll~v~l~tGR~HQIR 130 (167)
T cd02556 78 FGQVTDEQLKSL----KK-------GV-----E-L-----ED-GFAGFKSIQLEGG----EGKNSWYRVTLREGRNREVR 130 (167)
T ss_pred CccCCHHHHHHH----Hc-------CC-----E-E-----CC-CcCcceEEEEEec----CCCcEEEEEEEEeCCCHHHH
Confidence 998864433211 00 10 0 0 01 1233468887753 23458999999999999999
Q ss_pred HHHHHcCCCeeecCC
Q 011530 387 AQLAACGAPIVGDSM 401 (483)
Q Consensus 387 vHla~lG~PIvGD~~ 401 (483)
+||+++||||+-=..
T Consensus 131 ~~~a~~G~pV~~L~R 145 (167)
T cd02556 131 RLWEAFGLQVSRLIR 145 (167)
T ss_pred HHHHHcCCeEeEEEE
Confidence 999999999986443
No 19
>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=99.96 E-value=1.4e-30 Score=236.96 Aligned_cols=140 Identities=19% Similarity=0.219 Sum_probs=106.2
Q ss_pred EEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEE
Q 011530 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (483)
Q Consensus 227 liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV 306 (483)
|+|+|||+|++|++.+.....++.+.+.. ....+++|||||++||||||||+|+++++.|.. +++.++|+|+|+|
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~---~~~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~v 75 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKD---VGERLFPVGRLDYDTEGLLLLTNDGELANRLTH--PRYGVEKTYLVKV 75 (146)
T ss_pred CEEEECCCCcEecccCCCCCCEEeeeccc---cCCCEEECCCCCCCCeeEEEEeCCHHHHHHhhC--ccCCCCeEEEEEE
Confidence 58999999999998776555566554432 224578999999999999999999999999976 6788999999999
Q ss_pred eccCCccceeecccccccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHH
Q 011530 307 TAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVR 386 (483)
Q Consensus 307 ~G~~~~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIR 386 (483)
.|.++...+..+. +|. ..+ +.+.+.|.|++++. ....++++|+|+|||+||||
T Consensus 76 ~g~~~~~~~~~~~-----------~~~------~~~------~~~~~~t~~~~l~~----~~~~sll~~~l~tGR~HQIR 128 (146)
T cd02870 76 RGVPSEEELRRLR-----------AGV------ELD------DGKTAPAKVKVLSR----DPKNTLLEVTLHEGRNRQVR 128 (146)
T ss_pred CCCCCHHHHHHHH-----------CCe------EeC------CceEcceEEEEecc----CCCCcEEEEEEEeCCcHHHH
Confidence 9988644332111 010 000 11234578888763 23468999999999999999
Q ss_pred HHHHHcCCCeee
Q 011530 387 AQLAACGAPIVG 398 (483)
Q Consensus 387 vHla~lG~PIvG 398 (483)
+||+++||||+.
T Consensus 129 ~hla~~G~pI~~ 140 (146)
T cd02870 129 RMFEAVGHPVLR 140 (146)
T ss_pred HHHHHcCCcCCe
Confidence 999999999974
No 20
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.
Probab=99.96 E-value=3.2e-30 Score=239.84 Aligned_cols=143 Identities=19% Similarity=0.259 Sum_probs=107.2
Q ss_pred EEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEE
Q 011530 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (483)
Q Consensus 227 liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV 306 (483)
|+|+|||+||+|++.. ....++.+++...+. ...+++|||||++||||||||||.++++.|.. +++.++|+|+|+|
T Consensus 2 ~ivvnKP~G~~~~~~~-~~~~tl~~~l~~~~~-~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~V 77 (167)
T cd02553 2 YLMLNKPAGVVCATKD-PHHPTVIDLLPEPDR-RRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTS--PKKHVPKTYEVTL 77 (167)
T ss_pred EEEEECCCCCEeCCCC-CCCCcHHHHhhhhcc-cCCeEEcccCCCCCEEEEEEEeCHHHHHHhhC--CcCCCceEEEEEE
Confidence 7999999999999554 446778887766543 23578999999999999999999999988866 6788999999999
Q ss_pred eccCCccceeecccccccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHH
Q 011530 307 TAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVR 386 (483)
Q Consensus 307 ~G~~~~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIR 386 (483)
.|.++...+..+..... ..++ .....+.+++++ .++++|+|.|||+||||
T Consensus 78 ~G~~~~~~~~~~~~~~~-----~~~~-----------------~~~~~~~~~~~~--------~sll~v~l~tGR~HQIR 127 (167)
T cd02553 78 AGPLTEDDIEAFAEGVL-----LHDG-----------------YPTKPAKLEILS--------PTTVRLTITEGKYHQVK 127 (167)
T ss_pred ccCCCHHHHHHHHCCeE-----EcCC-----------------CEeeeeEEEEeC--------CcEEEEEEEeCCCHHHH
Confidence 99886444332111100 0001 011123455542 17899999999999999
Q ss_pred HHHHHcCCCeeecCCCC
Q 011530 387 AQLAACGAPIVGDSMYM 403 (483)
Q Consensus 387 vHla~lG~PIvGD~~YG 403 (483)
+||+++||||++|..++
T Consensus 128 ~hla~lG~pI~~~~R~~ 144 (167)
T cd02553 128 RMFAAVGNKVVALHRIR 144 (167)
T ss_pred HHHHHcCCeEEEEEEEE
Confidence 99999999999997775
No 21
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family. This Prosite family is a subset of the Pfam family.; InterPro: IPR006145 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit). RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [, ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site. RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: RluB modifies uracil-2605. RluC modifies uracil-955, U-2504, and U-2580. RluD modifies uracil-1911, U-1915, and U-1917. RluE modifies uracil-3457. RluF modifies uracil-2604, and to a lesser extent U-2605. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [, ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 2GML_A 3DH3_B 1VIO_A 2I82_B 1XPI_B 1V9K_B 1PRZ_A 1V9F_A 2IST_A 1QYU_A ....
Probab=99.96 E-value=3.4e-29 Score=230.55 Aligned_cols=153 Identities=24% Similarity=0.317 Sum_probs=103.6
Q ss_pred eEEEEeCCCCCccCCCCCCccchH---HHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEE
Q 011530 226 SHVVLDKPAGTSVGGTTDNIEESC---ATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLY 302 (483)
Q Consensus 226 ~liVvNKPaGl~v~~~~~~~~~tl---~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~Y 302 (483)
||||||||+||+|++.+......+ .............+++|||||++||||||||+|+++++.|+++|+++.++|+|
T Consensus 1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~TsGlll~a~~~~~~~~l~~~f~~~~~~K~Y 80 (164)
T PF00849_consen 1 NLIVVNKPAGVPVHPSDGNESKSVKELPALSLKRGDDPPELYPVHRLDRDTSGLLLFAKDKEAAAKLSKQFPKRKVEKTY 80 (164)
T ss_dssp SEEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHHHCTTSGGGEESS---TT-EEEEEEESSHHHHHHHHHHHHTTCSEEEE
T ss_pred CEEEEECCCCCeEecCCCCCcccccchhhhhhhhccCCCceEECCCCCccccCCeeccCCcccccccccccccCCCcEEE
Confidence 589999999999999884322222 22222222444678999999999999999999999999999999999999999
Q ss_pred EEEEec-cCC-ccceeeccccc-ccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecC-----CCCCCCeeEEE
Q 011530 303 LALTTA-PLP-VGIMTHYMRPI-NIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCG-----WPSRDYAYECK 374 (483)
Q Consensus 303 lAlV~G-~~~-~g~I~~~l~~~-~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~-----~~~~~~~slv~ 374 (483)
+|+|.| +.+ .|.++.++... ....... ... .......+.|.|+++... .......++++
T Consensus 81 ~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~-----~~~~~~~~~t~~~~l~~~~~~~~~~~~~~~s~v~ 147 (164)
T PF00849_consen 81 LALVEGGPVEEEGKINSPLGKDVGKNKSSN--------KDP-----PGRDGKPAITRYRVLRSGSRTPSKDENAGCSLVE 147 (164)
T ss_dssp EEEECSSSSTTCEEEESHEEE-EECSSCTC--------CEE-----ETTTSBTSEEEEEEEEEETT---EECCSSEEEEE
T ss_pred EEeEcccccccceeeeccccccccccccce--------eee-----ecccccccceeeeeeccccccccccccCCCEEEE
Confidence 999994 443 67777665431 1110000 000 111233446788888753 11346789999
Q ss_pred EEEcCCcchHHHHHHHH
Q 011530 375 IKLLTGRTHQVRAQLAA 391 (483)
Q Consensus 375 l~l~TGRtHQIRvHla~ 391 (483)
|+|.|||+||||+|||+
T Consensus 148 ~~l~tGr~HQIR~hla~ 164 (164)
T PF00849_consen 148 CELITGRTHQIRVHLAH 164 (164)
T ss_dssp EEESS-STTHHHHHHHH
T ss_pred EEECcCCCHHHHHHhcC
Confidence 99999999999999996
No 22
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.
Probab=99.95 E-value=2.2e-28 Score=227.65 Aligned_cols=156 Identities=14% Similarity=0.138 Sum_probs=106.1
Q ss_pred EEEEeCCCCCccCCCCC-CccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEE
Q 011530 227 HVVLDKPAGTSVGGTTD-NIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLAL 305 (483)
Q Consensus 227 liVvNKPaGl~v~~~~~-~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAl 305 (483)
|+|+|||+|++|++.+. ....++.+++.. ..+++|||||++||||||||+|+++++.|.+ +++.++|+|+|+
T Consensus 1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l~~-----~~~~~v~RLD~~TsGlll~a~d~~~~~~l~~--~~~~v~K~Y~a~ 73 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYIDD-----PGVYAAGRLDRDSEGLLLLTDDGRLQHRITD--PSFKHPKTYYVQ 73 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCccHHHHcCc-----CCeEEccCCCCCCeEEEEEEeCHHHHHHHHC--CCCCCCEEEEEE
Confidence 58999999999998765 445677666531 3578999999999999999999999988877 456799999999
Q ss_pred EeccCCccceeecccccccCCccccCCe-eeeeEEEeecccCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchH
Q 011530 306 TTAPLPVGIMTHYMRPINIAPRLVSEGW-YLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQ 384 (483)
Q Consensus 306 V~G~~~~g~I~~~l~~~~~~~~~v~~g~-~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQ 384 (483)
|.|.++...+.....+.... ++. ..+.+...+ . .....+.|.++... .....++++|+|.|||+||
T Consensus 74 v~g~~~~~~~~~l~~g~~~~-----~~~~~~~~v~~~~-----~-~~~~~~~~~~~~~~--~~~~~sll~v~l~tGR~HQ 140 (168)
T cd02566 74 VEGVPTEDALEQLRNGVELG-----DGLTLPAKVEKVD-----E-PPWLWEREPPIRFR--KNIPTSWIEITICEGKNRQ 140 (168)
T ss_pred ECCcCCHHHHHHHhCCcEEC-----CeEecceEEEEec-----c-cccccccccccccc--cCCCccEEEEEEecCccHH
Confidence 99988643332111111100 000 111111111 0 11223444444421 1234579999999999999
Q ss_pred HHHHHHHcCCCeeecCCC
Q 011530 385 VRAQLAACGAPIVGDSMY 402 (483)
Q Consensus 385 IRvHla~lG~PIvGD~~Y 402 (483)
||+||+++||||+.....
T Consensus 141 IR~~la~lG~pV~~L~R~ 158 (168)
T cd02566 141 VRRMTAAVGFPTLRLIRV 158 (168)
T ss_pred HHHHHHHcCCeEeEEEEE
Confidence 999999999999987654
No 23
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.94 E-value=8e-27 Score=224.41 Aligned_cols=161 Identities=16% Similarity=0.150 Sum_probs=110.0
Q ss_pred eEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEE
Q 011530 226 SHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLAL 305 (483)
Q Consensus 226 ~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAl 305 (483)
.|+++|||+|++|+..+.....++.+++. ...+++|||||++||||||||+|+++++.|.+ +++.+.|+|+|+
T Consensus 40 ~ylllnKP~G~l~~~~d~~~~~tl~d~l~-----~~~~~~vgRLD~~TsGllLlt~d~~~~~~L~~--~~~~i~K~Y~~~ 112 (217)
T PRK11394 40 RVILFNKPYDVLPQFTDEAGRKTLKEFIP-----VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQ--PGKRTGKIYYVQ 112 (217)
T ss_pred EEEEEECCCCCEEeeCCccCCcchHHhcc-----cCCeEEecCCCCCCeeEEEEECCHHHHHHHhC--cccCCCEEEEEE
Confidence 48999999999999766655677777764 13578999999999999999999999999988 478899999999
Q ss_pred EeccCCccceeecccccccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHH
Q 011530 306 TTAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQV 385 (483)
Q Consensus 306 V~G~~~~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQI 385 (483)
|.|.++...++....++...... ...+..+++....... ..+..+... .....++++|.|.|||+|||
T Consensus 113 v~g~~~~~~l~~l~~Gv~i~~~~----~~p~~~~~i~~~~~~~------~~~~~~~~~--~~~~~s~l~I~L~eGR~hQI 180 (217)
T PRK11394 113 VEGIPTQDALEALRNGVTLNDGP----TLPAGAELVDEPAWLW------PRNPPIRER--KSIPTSWLKITLYEGRNRQV 180 (217)
T ss_pred ECCCCCHHHHHHHhCCeEECCcc----ccccEEEEeccccccc------ccccccccc--cCCCceEEEEEEeCCCCHHH
Confidence 99988654443211111110000 0011111211000000 001111100 12246789999999999999
Q ss_pred HHHHHHcCCCeeecCCCChh
Q 011530 386 RAQLAACGAPIVGDSMYMPA 405 (483)
Q Consensus 386 RvHla~lG~PIvGD~~YG~~ 405 (483)
|+||+++||||+||.+|+-.
T Consensus 181 Rrm~a~lG~pVl~L~Ry~iG 200 (217)
T PRK11394 181 RRMTAHVGFPTLRLIRYAMG 200 (217)
T ss_pred HHHHHHcCCeEeeeEEEEEC
Confidence 99999999999999999743
No 24
>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=99.94 E-value=1.3e-26 Score=217.38 Aligned_cols=142 Identities=14% Similarity=0.149 Sum_probs=100.8
Q ss_pred eEEEEeCCCCCccCCCCC--------CccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCC
Q 011530 226 SHVVLDKPAGTSVGGTTD--------NIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKK 297 (483)
Q Consensus 226 ~liVvNKPaGl~v~~~~~--------~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~ 297 (483)
.|+++|||+|++|+..+. ....+..+++...+ ..+++|||||++||||||||+|+++++.|++ +.+.
T Consensus 5 ~y~llnKP~G~l~s~~d~~~~~g~~~~~~~~~~~~l~~~~---~~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~--~~~~ 79 (177)
T cd02555 5 VTLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGHF---ARLAPIGPLDKDASGLLVFSQDGRVLRKLIG--DASR 79 (177)
T ss_pred EEEEEECCCceEecCCCcccccccccccccchhhhhhhcC---CceeEecCCCCCCeeEEEEECCHHHHHHHhC--hhcC
Confidence 479999999999975541 12234444554332 3588999999999999999999999999988 4578
Q ss_pred cceEEEEEEeccCCccceeecccccccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecCCCCCCCeeEEEEEE
Q 011530 298 VKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKL 377 (483)
Q Consensus 298 v~K~YlAlV~G~~~~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l 377 (483)
++|+|+|+|.|.+++..+...-.++. .+|.. .+.+++.. ...+++++.|
T Consensus 80 i~K~Y~v~v~g~~~~~~l~~l~~g~~------~~~~~-------------------~~~~~~~~------~~~~~l~i~l 128 (177)
T cd02555 80 LEQEYLVEVRGELTAGGLERLNHGLT------YDGRE-------------------LPPAKVSW------QNEQRLRFAL 128 (177)
T ss_pred CCEEEEEEEcccCCHHHHHHHhcCcc------cCCee-------------------cceEEEEE------cCCCEEEEEE
Confidence 99999999999886433211001110 01110 01222211 1236899999
Q ss_pred cCCcchHHHHHHHHcCCCeeecCCCC
Q 011530 378 LTGRTHQVRAQLAACGAPIVGDSMYM 403 (483)
Q Consensus 378 ~TGRtHQIRvHla~lG~PIvGD~~YG 403 (483)
.|||+||||+||+++||||+|+....
T Consensus 129 ~tGr~hQIR~~~~~~G~pV~~L~R~~ 154 (177)
T cd02555 129 KEPQPGQIRRMCESVGLEVVALRRIR 154 (177)
T ss_pred ECCcChHHHHHHHHcCCeEEEEEEEE
Confidence 99999999999999999999998764
No 25
>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=99.91 E-value=5.2e-25 Score=196.11 Aligned_cols=109 Identities=21% Similarity=0.288 Sum_probs=83.7
Q ss_pred ccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEEeccCCccceeecccccccCCccccCCeeeeeEEEeeccc
Q 011530 266 THQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTTAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKK 345 (483)
Q Consensus 266 VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~G~~~~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~ 345 (483)
|||||++||||||||+|+++++.|.+ ++++++|+|+|+|.|.+++..++. + . .|.. ++
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~--~~~~i~K~Y~a~v~g~~~~~~~~~-~---~-------~g~~------~~--- 58 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTH--PGHHCEKTYLVTVEGPVTDEDLEA-L---R-------KGVQ------LE--- 58 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhC--CCCCCCeEEEEEECCCCCHHHHHH-H---h-------CCeE------EC---
Confidence 79999999999999999999999987 788999999999999886443331 1 0 0110 00
Q ss_pred CCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHHHHHHHcCCCeeecCCCC
Q 011530 346 VPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVRAQLAACGAPIVGDSMYM 403 (483)
Q Consensus 346 ~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIRvHla~lG~PIvGD~~YG 403 (483)
......+.|+++.. ....++++|.|.|||+||||+||+++||||+||..|.
T Consensus 59 ---~~~~~~~~~~~l~~----~~~~~~l~~~l~tGR~HQIR~~~~~lG~pI~g~~R~~ 109 (128)
T TIGR00093 59 ---DGPTKPAKLEVITE----PGFPTWLRITLSEGRNRQVRRMFAAVGFPVLRLHRVR 109 (128)
T ss_pred ---CcEEeeeEEEEEcc----CCCceEEEEEEeCCCCHHHHHHHHHcCCeEeEEEEEE
Confidence 01112346777653 2335799999999999999999999999999998875
No 26
>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=99.90 E-value=1.2e-23 Score=194.78 Aligned_cols=138 Identities=16% Similarity=0.187 Sum_probs=100.7
Q ss_pred EEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEE
Q 011530 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (483)
Q Consensus 227 liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV 306 (483)
|+++|||+|++|++.+. ...++.+++.. ...+++|||||++||||||||+|+++++.|+. +.+.+.|+|+|.|
T Consensus 2 y~~lnKP~G~l~s~~~~-~~~tv~~~l~~----~~~~~~vgRLD~~tsGlll~t~dg~~~~~L~~--p~~~~~K~Y~V~v 74 (164)
T cd02554 2 YIAYNKPVGIDCTLERA-DEDNIIDFVNP----PPRIFPIGRLDKDSEGLILLTNDGDLVNKILH--ADNNHEKEYLVTV 74 (164)
T ss_pred EEEEECCCCcEeecCCC-CCCcHHHHhcC----cCCEEEccCCCCCCeeEEEEEcCHHHHHHHhh--hhcCCCeEEEEEE
Confidence 78999999999998765 35788777653 24689999999999999999999999999965 6778999999999
Q ss_pred eccCCccceeecccccccCCccccCCeeeeeEEEeecccCCCCCCccceeEEeeecCCCCCCCeeEEEEEEcCCcchHHH
Q 011530 307 TAPLPVGIMTHYMRPINIAPRLVSEGWYLCQLEVMECKKVPWPDATVGKAYSIEDCGWPSRDYAYECKIKLLTGRTHQVR 386 (483)
Q Consensus 307 ~G~~~~g~I~~~l~~~~~~~~~v~~g~~~~~~~vl~~~~~~~~~~~~~t~~~vl~~~~~~~~~~slv~l~l~TGRtHQIR 386 (483)
.|++.+..+.....++.. ++. .+....+... .. +.++|.|.+||+||||
T Consensus 75 ~~~l~~~~l~~l~~G~~~------~~~--------------------~~~~~~v~~~---~~--~~l~i~l~eGr~~qIR 123 (164)
T cd02554 75 NKPITDEFIEGMSNGVVI------LGT--------------------VTKPCKVERL---AK--DKFRIVLTQGLNRQIR 123 (164)
T ss_pred CCCCCHHHHHHHhCCCEE------CCe--------------------EEcceEEEEC---CC--CEEEEEEECCcCHHHH
Confidence 998875443321111110 000 0111111110 11 2489999999999999
Q ss_pred HHHHHcCCCeeecCCC
Q 011530 387 AQLAACGAPIVGDSMY 402 (483)
Q Consensus 387 vHla~lG~PIvGD~~Y 402 (483)
+||+++|+||+-=..+
T Consensus 124 rm~~~~G~~V~~L~Ri 139 (164)
T cd02554 124 RMCEALGYRVTDLKRV 139 (164)
T ss_pred HHHHHcCCEEEEEEEE
Confidence 9999999999875544
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=99.11 E-value=1.4e-10 Score=112.69 Aligned_cols=75 Identities=13% Similarity=0.177 Sum_probs=57.6
Q ss_pred EEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEE
Q 011530 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (483)
Q Consensus 227 liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV 306 (483)
++|||||+||.++... +.+...+.+.++.....++|||||++|||||+||++..+ +|.++|.++.+.|+|+|..
T Consensus 2 ilvvnKP~Gi~s~~~~----~~~~~~l~~~~~~~k~~~~vhrLD~~aSGvl~~a~~~~t--kl~~~~~~~~~~K~Y~~~~ 75 (226)
T cd02868 2 LFAVYKPPGVHWKHVR----DTIESNLLKYFPEDKVLVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYSNHPTRVYTIRG 75 (226)
T ss_pred EEEEEcCCCCChhHHH----HHHHHHHHHHccccceeeEccccCCCCceEEEEEeChhH--hHHHHHHhcCCCeEEEEEE
Confidence 7999999999886532 333333333344333367889999999999999999987 6999999999999999665
Q ss_pred e
Q 011530 307 T 307 (483)
Q Consensus 307 ~ 307 (483)
.
T Consensus 76 ~ 76 (226)
T cd02868 76 L 76 (226)
T ss_pred E
Confidence 4
No 28
>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=98.71 E-value=6.3e-08 Score=74.87 Aligned_cols=68 Identities=19% Similarity=0.214 Sum_probs=57.0
Q ss_pred cHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccCC
Q 011530 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (483)
Q Consensus 111 rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~~ 189 (483)
+|++||.+.+ ..||+.++++|+.|.| .+||+.++ ++
T Consensus 2 rl~~~l~~~~~~~sr~~~~~~i~~g~V----------------------------------~vn~~~~~---------~~ 38 (70)
T cd00165 2 RLDKILARLGLAPSRSEARQLIKHGHV----------------------------------LVNGKVVT---------KP 38 (70)
T ss_pred cHHHHHHHhccccCHHHHHHHHHcCCE----------------------------------EECCEEcc---------CC
Confidence 6779999885 6899999999999999 58999875 48
Q ss_pred CceecCCCEEEEecCCCCCCcccCCCCCceEEeecCeEEEEe
Q 011530 190 DQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLD 231 (483)
Q Consensus 190 ~~~v~~GD~I~v~~~~~~~p~~~~~~~~~~IlyED~~liVvN 231 (483)
++.+..||.|.+...+ +...|+|||++++|+|
T Consensus 39 ~~~v~~~d~i~i~~~~----------~~~~i~~ed~~~lvv~ 70 (70)
T cd00165 39 SYKVKPGDVIEVDGKS----------IEEDIVYEDKKLLVVN 70 (70)
T ss_pred ccCcCCCCEEEEcCCC----------cccceeeccCCEEEeC
Confidence 8899999999887422 1238999999999997
No 29
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=98.23 E-value=2.7e-06 Score=65.48 Aligned_cols=51 Identities=8% Similarity=0.017 Sum_probs=44.7
Q ss_pred CCCcHHHHHHhccCC--CHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeecccccc
Q 011530 108 EGGPVLEYICRELNL--PPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFR 185 (483)
Q Consensus 108 ~~~rl~~~Ls~~l~~--Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r 185 (483)
++.||++||++. ++ ||+.++++|+.|.| .|||++++
T Consensus 7 ~~~rLd~~L~~~-~~~~SR~~~k~li~~G~V----------------------------------~VNg~~~~------- 44 (59)
T TIGR02988 7 EYITLGQLLKEL-GIIDSGGQAKWFLQENEV----------------------------------LVNGELEN------- 44 (59)
T ss_pred hHHHHHHHHHHc-CCccCHHHHHHHHHcCCE----------------------------------EECCEEcc-------
Confidence 347889999999 66 99999999999999 58999875
Q ss_pred ccCCCceecCCCEEEEe
Q 011530 186 ITHVDQIVEAGTYLRVH 202 (483)
Q Consensus 186 ~~~~~~~v~~GD~I~v~ 202 (483)
.++++|+.||.|.|+
T Consensus 45 --~~~~~l~~Gd~v~i~ 59 (59)
T TIGR02988 45 --RRGKKLYPGDVIEIP 59 (59)
T ss_pred --CCCCCCCCCCEEEeC
Confidence 489999999999863
No 30
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=98.20 E-value=3.9e-06 Score=61.60 Aligned_cols=46 Identities=24% Similarity=0.299 Sum_probs=41.1
Q ss_pred cHHHHHHhccC-CCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccCC
Q 011530 111 PVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (483)
Q Consensus 111 rl~~~Ls~~l~-~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~~ 189 (483)
||++||++.+. .||++++++|+.|.| +|||+.++ ++
T Consensus 2 RLd~~L~~~~~~~sr~~a~~~I~~g~V----------------------------------~VNg~~v~---------~~ 38 (48)
T PF01479_consen 2 RLDKFLSRLGLASSRSEARRLIKQGRV----------------------------------KVNGKVVK---------DP 38 (48)
T ss_dssp BHHHHHHHTTSSSSHHHHHHHHHTTTE----------------------------------EETTEEES---------ST
T ss_pred CHHHHHHHcCCcCCHHHHHHhcCCCEE----------------------------------EECCEEEc---------CC
Confidence 67899997775 579999999999999 68999987 69
Q ss_pred CceecCCCEE
Q 011530 190 DQIVEAGTYL 199 (483)
Q Consensus 190 ~~~v~~GD~I 199 (483)
++.|++||.|
T Consensus 39 ~~~v~~~d~I 48 (48)
T PF01479_consen 39 SYIVKPGDVI 48 (48)
T ss_dssp TSBESTTEEE
T ss_pred CCCCCCcCCC
Confidence 9999999986
No 31
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like. This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl r
Probab=97.58 E-value=0.00024 Score=67.19 Aligned_cols=70 Identities=21% Similarity=0.379 Sum_probs=53.8
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.||.++ .+...+++.++. .++.-.+-||...||||+++-+.. .++.+.+.+ -.|+|.|
T Consensus 2 ~g~l~i~Kp~g~tS~--------~~v~~~k~~~~~-kkvGH~GTLDp~A~GvLiv~~g~~--Tk~~~~~~~--~~K~Y~a 68 (182)
T cd02572 2 YGVINLDKPSGPSSH--------EVVAWIKRILGV-EKTGHSGTLDPKVTGCLPVCIDRA--TRLVKSQQE--AGKEYVC 68 (182)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhCC-CccCcCCCCCCcCeeEEEEEECHH--hhhhHHHhC--CCCEEEE
Confidence 368999999999987 344566666665 357779999999999999999873 455555555 4499999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 69 ~v~ 71 (182)
T cd02572 69 VMR 71 (182)
T ss_pred EEE
Confidence 886
No 32
>smart00363 S4 S4 RNA-binding domain.
Probab=97.34 E-value=0.00075 Score=50.12 Aligned_cols=50 Identities=24% Similarity=0.294 Sum_probs=43.2
Q ss_pred cHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccCC
Q 011530 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (483)
Q Consensus 111 rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~~ 189 (483)
+|+.||.+.+ ..|++.++++|..|.| .|||+.++ ++
T Consensus 2 rl~~~l~~~~~~~s~~~~~~~i~~g~i----------------------------------~vng~~~~---------~~ 38 (60)
T smart00363 2 RLDKFLARLGLAPSRSQARKLIEQGRV----------------------------------KVNGKKVT---------KP 38 (60)
T ss_pred cHHHHHHHcCcccCHHHHHHHHHcCCE----------------------------------EECCEEec---------CC
Confidence 5679998874 6899999999999999 58999875 48
Q ss_pred CceecCCCEEEEec
Q 011530 190 DQIVEAGTYLRVHV 203 (483)
Q Consensus 190 ~~~v~~GD~I~v~~ 203 (483)
++.+..||.|.+..
T Consensus 39 ~~~l~~gd~i~~~~ 52 (60)
T smart00363 39 SYIVKPGDVISVRG 52 (60)
T ss_pred CeEeCCCCEEEEcc
Confidence 89999999998875
No 33
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.25 E-value=0.0008 Score=65.68 Aligned_cols=70 Identities=17% Similarity=0.243 Sum_probs=54.4
Q ss_pred eEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEE
Q 011530 226 SHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLAL 305 (483)
Q Consensus 226 ~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAl 305 (483)
.+++||||.|+.+| .+...+++.++.. ++.-.|.||...||||+++-.. .+.+|.+.+.+ ..|+|+|.
T Consensus 10 G~l~i~KP~g~TS~--------dvv~~ikk~~~~k-KvGH~GTLDP~AtGvLiv~vG~-~aTkl~~~~~~--~~K~Y~~~ 77 (230)
T PRK00989 10 GILLVDKPQGRTSF--------SLIRSLTKLIGVK-KIGHAGTLDPFATGVMVMLIGR-KFTRLSDILLF--EDKEYAAV 77 (230)
T ss_pred EEEEEeCCCCCCHH--------HHHHHHHHHhCCC-cCCcCccCCCCCeeEEEEEECC-chhhhHHHhcC--CCcEEEEE
Confidence 68999999999987 3455566666653 5777999999999999999776 33455565544 77999999
Q ss_pred Ee
Q 011530 306 TT 307 (483)
Q Consensus 306 V~ 307 (483)
+.
T Consensus 78 ~~ 79 (230)
T PRK00989 78 AH 79 (230)
T ss_pred EE
Confidence 86
No 34
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=97.22 E-value=0.00054 Score=68.59 Aligned_cols=53 Identities=15% Similarity=0.165 Sum_probs=47.8
Q ss_pred CCcHHHHHHhccCCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccC
Q 011530 109 GGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (483)
Q Consensus 109 ~~rl~~~Ls~~l~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~ 188 (483)
..|||.+|+..+++||+.++++|+.|.| +|||+.+. +
T Consensus 191 s~RLD~vla~~~~~SRsk~~~lI~~g~V----------------------------------~vN~~~v~---------~ 227 (267)
T PLN00051 191 SLRLDALASAGFRMSRSKLVDLISSGDV----------------------------------RVNWREVT---------K 227 (267)
T ss_pred cccHHHHHHHHhccCHHHHHHHHHcCcE----------------------------------EECCEEcC---------C
Confidence 4577899999999999999999999999 68999886 6
Q ss_pred CCceecCCCEEEEecC
Q 011530 189 VDQIVEAGTYLRVHVH 204 (483)
Q Consensus 189 ~~~~v~~GD~I~v~~~ 204 (483)
+++.|+.||.|.|...
T Consensus 228 ~s~~v~~gD~isiRG~ 243 (267)
T PLN00051 228 NGTTLKTGDVVSVSGK 243 (267)
T ss_pred CCCCCCCCCEEEEeeC
Confidence 9999999999999853
No 35
>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=97.17 E-value=0.0013 Score=63.39 Aligned_cols=69 Identities=19% Similarity=0.235 Sum_probs=54.5
Q ss_pred eEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEE
Q 011530 226 SHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLAL 305 (483)
Q Consensus 226 ~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAl 305 (483)
.+++||||.||.++ .+...+++.++.. ++.-.+-||-..||||+++-+... +|...+. .-.|+|.|.
T Consensus 3 G~l~v~KP~g~tS~--------~vv~~vkk~~~~k-KvGH~GTLDP~AsGvLiv~vG~~T--kl~~~~~--~~~K~Y~~~ 69 (209)
T TIGR00431 3 GVLLLDKPQGMTSF--------DALAKVRRLLNVK-KVGHTGTLDPFATGVLPILVGKAT--KLSPYLT--DLDKEYRAE 69 (209)
T ss_pred eEEEEECCCCCCHH--------HHHHHHHHHhCCC-cCCCCCCCCCcCceEEEEEEChHh--hhhHHHc--CCCCeEEEE
Confidence 58999999999976 3455566666653 567789999999999999999854 5666664 478999999
Q ss_pred Ee
Q 011530 306 TT 307 (483)
Q Consensus 306 V~ 307 (483)
+.
T Consensus 70 ~~ 71 (209)
T TIGR00431 70 IR 71 (209)
T ss_pred EE
Confidence 86
No 36
>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=97.16 E-value=0.0013 Score=63.66 Aligned_cols=68 Identities=18% Similarity=0.239 Sum_probs=53.1
Q ss_pred EEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEE
Q 011530 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (483)
Q Consensus 227 liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV 306 (483)
+++||||.|+.++ .+...+++.++. .++.-.|-||...||||+++-+.. .++...|.+ ..|+|.|.+
T Consensus 2 il~i~KP~g~tS~--------~vv~~ik~~~~~-kKvGH~GTLDP~AsGvLiv~vG~a--Tkl~~~~~~--~~K~Y~~~~ 68 (210)
T cd00506 2 LFAVDKPQGPSSH--------DVVDTIRRIFLA-EKVGHGGTLDPFATGVLVVGIGKA--TKLLKHLLA--ATKDYTAIG 68 (210)
T ss_pred EEEEEcCCCCCHH--------HHHHHHHHHhCc-cccCCCCcCCCcCeeEEEEEECHH--HhhhHHHhc--CCceEEEEE
Confidence 7899999999987 344556666654 357779999999999999999874 455555555 789999998
Q ss_pred e
Q 011530 307 T 307 (483)
Q Consensus 307 ~ 307 (483)
.
T Consensus 69 ~ 69 (210)
T cd00506 69 R 69 (210)
T ss_pred E
Confidence 6
No 37
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=97.15 E-value=0.0013 Score=65.76 Aligned_cols=70 Identities=23% Similarity=0.287 Sum_probs=54.5
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.++++|||+||.+| .+...+++.++. .++.-.+-||...||||+++-... .+|.+.+.+ -.|+|.|
T Consensus 2 ngil~vdKP~g~tS~--------~vv~~ikk~~~~-kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~--~~K~Y~a 68 (273)
T PRK04099 2 NRLFVANKPAGMSSN--------AFLSRLKRKYGV-KKAGFSGTLDPFAKGVLIVAFGQY--TKLFRFLKK--TPKTYRA 68 (273)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCC-CccccCccCCCCCeeEEEEEEChH--hhhHHHhcc--CCceEEE
Confidence 368999999999987 345566666654 356779999999999999999875 346565554 4899999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 69 ~~~ 71 (273)
T PRK04099 69 TLW 71 (273)
T ss_pred EEE
Confidence 886
No 38
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=97.10 E-value=0.00091 Score=56.66 Aligned_cols=53 Identities=15% Similarity=0.254 Sum_probs=45.3
Q ss_pred CcHHHHHHhc-cCCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccC
Q 011530 110 GPVLEYICRE-LNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (483)
Q Consensus 110 ~rl~~~Ls~~-l~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~ 188 (483)
.|||+||-.. +-=+|+.|+++|+.|+| .+||+.++
T Consensus 9 mRLDKwL~~aR~~KrRslAk~~~~~GrV----------------------------------~vNG~~aK---------- 44 (100)
T COG1188 9 MRLDKWLWAARFIKRRSLAKEMIEGGRV----------------------------------KVNGQRAK---------- 44 (100)
T ss_pred eehHHHHHHHHHhhhHHHHHHHHHCCeE----------------------------------EECCEEcc----------
Confidence 3555999877 56789999999999999 58999874
Q ss_pred CCceecCCCEEEEecCCC
Q 011530 189 VDQIVEAGTYLRVHVHPK 206 (483)
Q Consensus 189 ~~~~v~~GD~I~v~~~~~ 206 (483)
|+..|+.||.|.|.+...
T Consensus 45 pS~~VK~GD~l~i~~~~~ 62 (100)
T COG1188 45 PSKEVKVGDILTIRFGNK 62 (100)
T ss_pred cccccCCCCEEEEEeCCc
Confidence 899999999999997654
No 39
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=97.08 E-value=0.0019 Score=63.62 Aligned_cols=70 Identities=23% Similarity=0.301 Sum_probs=54.0
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.|+.+| .+...+++.++.. ++.-.+-||...||||+++-... .+|...+.+ ..|+|.|
T Consensus 10 ~Gil~vdKP~G~TS~--------dvv~~vkr~~~~k-KvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~--~~K~Y~a 76 (244)
T PRK00020 10 DGVLLLDKPVGLSSN--------HALQRAKRTVDAA-KAGHTGTLDPFATGLLVCCMGRA--TKISGRMLE--ADKTYQA 76 (244)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhCCC-CCCcCCcCCCcCeeEEEEEECHH--hhhhHHhcc--CCcEEEE
Confidence 369999999999987 3455666666654 56778999999999999999873 455555544 4599999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 77 ~~~ 79 (244)
T PRK00020 77 TLQ 79 (244)
T ss_pred EEE
Confidence 986
No 40
>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=97.05 E-value=0.00093 Score=66.61 Aligned_cols=54 Identities=17% Similarity=0.177 Sum_probs=47.6
Q ss_pred CCCcHHHHHHhccCCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeecccccccc
Q 011530 108 EGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRIT 187 (483)
Q Consensus 108 ~~~rl~~~Ls~~l~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~ 187 (483)
.+.||+.+++..+++||+.++++|+.|.| +|||+.++
T Consensus 182 ~s~RLD~lls~~~~~SRs~a~~lI~~G~V----------------------------------~VNg~~v~--------- 218 (257)
T TIGR03069 182 ASLRIDAIASAGFGLSRSKIVDQIKAGRL----------------------------------RLNWKTVT--------- 218 (257)
T ss_pred ccccHHHHHHhhhhhhHHHHHHHHHCCeE----------------------------------EECCEEcC---------
Confidence 44577799999889999999999999999 68999886
Q ss_pred CCCceecCCCEEEEecC
Q 011530 188 HVDQIVEAGTYLRVHVH 204 (483)
Q Consensus 188 ~~~~~v~~GD~I~v~~~ 204 (483)
++++.|++||.|.+...
T Consensus 219 ~~s~~v~~gD~IsvrG~ 235 (257)
T TIGR03069 219 QPSRELKVGDRLQLRGK 235 (257)
T ss_pred CCCCcCCCCCEEEEcCC
Confidence 58999999999999853
No 41
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=96.98 E-value=0.0024 Score=64.78 Aligned_cols=70 Identities=17% Similarity=0.166 Sum_probs=54.3
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.||.+| .+...+++.++. +++.-.|-||...||||+++-... .++.+.+.+ -.|+|.|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~~-kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~~--~~K~Y~a 69 (294)
T PRK02484 3 NGIINLKKEAGMTSH--------DAVFKLRKILQT-KKIGHGGTLDPDVVGVLPIAVGKA--TRLIEYMTE--AGKVYEG 69 (294)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhCC-CccccCCCCCCCCeeEEEEEEChh--hhhhHHhcc--CCcEEEE
Confidence 368999999999987 345566676665 357779999999999999999874 345555554 4599999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 70 ~~~ 72 (294)
T PRK02484 70 EIT 72 (294)
T ss_pred EEE
Confidence 986
No 42
>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=96.97 E-value=0.0035 Score=51.80 Aligned_cols=28 Identities=4% Similarity=-0.008 Sum_probs=25.2
Q ss_pred CCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEEe
Q 011530 261 TPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTT 307 (483)
Q Consensus 261 ~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~ 307 (483)
..+..++++|+.++|+++++ ++|...+.
T Consensus 24 ~~i~~aG~kDk~a~t~q~v~-------------------n~f~i~~r 51 (87)
T cd01291 24 KRVGYAGRKDKRAVTTQLVS-------------------NRFTITLR 51 (87)
T ss_pred heEEECccCCCCeeEEEEEc-------------------ccEEEEEE
Confidence 45788999999999999999 88999887
No 43
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=96.95 E-value=0.0029 Score=64.52 Aligned_cols=70 Identities=14% Similarity=0.253 Sum_probs=54.6
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.|+.+| .+...+++.++.. ++.-.+-||...||||+++-+.. .+|.+.+.+ -.|+|.|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~~k-KvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~--~~K~Y~a 69 (308)
T PRK14124 3 HGFLVAYKPKGPTSH--------DVVDEVRKKLKTR-KVGHAGTLDPFATGVLIVGVNKA--TRLLEYLKN--EKKVYYV 69 (308)
T ss_pred ceEEEEECCCCCCHH--------HHHHHHHHHcCCC-ccCcCcCCCCCCcEEEEEEEChH--HhhhHHHhc--CCceEEE
Confidence 368999999999987 3455667766653 57778999999999999999875 345565655 3799999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 70 ~~~ 72 (308)
T PRK14124 70 KMR 72 (308)
T ss_pred EEE
Confidence 986
No 44
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=96.95 E-value=0.0026 Score=64.85 Aligned_cols=70 Identities=13% Similarity=0.102 Sum_probs=55.1
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.||.+| .+...+++.++. +++.-.+-||-..||||+++-...+ +|.+.+.+ ..|+|.|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~~-kKvGH~GTLDP~AtGvL~v~vG~aT--kl~~~l~~--~~K~Y~~ 69 (305)
T PRK14123 3 NGILPVYKERGLTSH--------DVVFKLRKILKT-KKIGHTGTLDPEVAGVLPVCIGNAT--RVSDYVMD--MGKAYEA 69 (305)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhCC-CccccCcCCCCcCeeEEEEEEChhh--hhHHHhcC--CCcEEEE
Confidence 368999999999987 345566666665 3577799999999999999998754 56665544 6799999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 70 ~~~ 72 (305)
T PRK14123 70 TVS 72 (305)
T ss_pred EEE
Confidence 986
No 45
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=96.93 E-value=0.0025 Score=64.04 Aligned_cols=68 Identities=18% Similarity=0.229 Sum_probs=52.9
Q ss_pred EEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEE
Q 011530 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (483)
Q Consensus 227 liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV 306 (483)
++++|||.||.+| .+...+++.++. +++.-.|-||-..||||+++-... .++.+.+. ...|+|.|.+
T Consensus 2 il~i~KP~G~tS~--------dvv~~vrr~~~~-kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~--~~~K~Y~a~~ 68 (279)
T PRK02193 2 IKLLYKPKGISSF--------KFIKNFAKTNNI-KKIGHTGTLDPLASGLLLVATDED--TKLIDYLD--QKDKTYIAKI 68 (279)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHcCC-CccccCccCCCcCeeEEEEEEChh--hhhhHHhc--cCCcEEEEEE
Confidence 6899999999987 244556666665 357779999999999999999874 44555553 3679999998
Q ss_pred e
Q 011530 307 T 307 (483)
Q Consensus 307 ~ 307 (483)
.
T Consensus 69 ~ 69 (279)
T PRK02193 69 K 69 (279)
T ss_pred E
Confidence 6
No 46
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=96.91 E-value=0.0028 Score=64.33 Aligned_cols=71 Identities=23% Similarity=0.313 Sum_probs=54.7
Q ss_pred cCeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEE
Q 011530 224 TESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYL 303 (483)
Q Consensus 224 D~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~Yl 303 (483)
-+.+++||||.||.+| .+...+++.++.. ++.-.+-||...||||+++-... .++.+.+.+ -.|+|.
T Consensus 8 ~~Gil~i~KP~G~TS~--------dvv~~vrr~~~~k-KvGH~GTLDP~AtGvL~i~vG~a--TKl~~~l~~--~~K~Y~ 74 (298)
T PRK03287 8 GSGLVVVDKPAGMTSH--------DVVARCRRLFGTR-KVGHAGTLDPMATGVLVLGVERA--TKLLGHLTL--TDKSYT 74 (298)
T ss_pred cCeEEEEeCCCCCCHH--------HHHHHHHHHhCCC-CCCcCccCCCcceeEEEEEeChh--hhhhHHHhc--CCcEEE
Confidence 3469999999999987 3455666666653 57778999999999999999863 445555554 479999
Q ss_pred EEEe
Q 011530 304 ALTT 307 (483)
Q Consensus 304 AlV~ 307 (483)
|.+.
T Consensus 75 a~~~ 78 (298)
T PRK03287 75 ATIR 78 (298)
T ss_pred EEEE
Confidence 9986
No 47
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=96.90 E-value=0.0032 Score=64.61 Aligned_cols=70 Identities=19% Similarity=0.277 Sum_probs=54.3
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.||.+| .+...+++.++. +++.-.|-||...||||+++-... .++...+.+ -.|+|.|
T Consensus 3 nGiL~idKP~G~TS~--------dvv~~vrk~l~~-kKVGH~GTLDP~AtGVL~i~vG~a--TKl~~~l~~--~~K~Y~a 69 (345)
T PRK14846 3 NYWLNIYKPRGISSA--------QLVSIVKKILGK-TKIGHAGTLDVEAEGILPFAVGEA--TKLIHLLID--ARKTYIF 69 (345)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCC-CcCCcCccCCCcCceEEEEEEChh--hhhhHHHhc--CCceEEE
Confidence 469999999999987 345566666655 457779999999999999998874 455555544 6799999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 70 ~~~ 72 (345)
T PRK14846 70 TVK 72 (345)
T ss_pred EEE
Confidence 986
No 48
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=96.88 E-value=0.0033 Score=63.63 Aligned_cols=70 Identities=16% Similarity=0.152 Sum_probs=54.8
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.|+.+| .+...+++.++.. ++.-.+-||-..||||+++-... .+|.+.+.+ -.|+|.|
T Consensus 2 ~Gil~i~KP~G~tS~--------dvv~~vrr~~~~k-KvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~--~~K~Y~a 68 (290)
T PRK00130 2 DGILNILKPPGMTSF--------DVVRKIRKIAKIK-KVGHTGTLDPLASGVLPVCLGKA--TKIVDYLME--GKKTYRA 68 (290)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCCC-ccCcCCCCCCCCeeEEEEEEChh--hhhHHHhcc--CCcEEEE
Confidence 368999999999987 3455666766653 57778999999999999999874 346666654 4799999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 69 ~~~ 71 (290)
T PRK00130 69 EIK 71 (290)
T ss_pred EEE
Confidence 986
No 49
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=96.88 E-value=0.003 Score=64.03 Aligned_cols=69 Identities=22% Similarity=0.274 Sum_probs=54.4
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.||.+| .+...+++.++.. ++.-.+-||...||||+++-...+ +|.+.+. . .|+|.|
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~~k-KvGH~GTLDP~AtGvL~i~vG~aT--kl~~~l~--~-~K~Y~a 68 (295)
T PRK02755 3 FGFLNLDKPAGLTSH--------DCVARLRRLLRLK-RVGHGGTLDPAATGVLPIALGKAT--RLLPYLP--G-EKTYRG 68 (295)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhCCC-ccccCCCCCCcCeeEEEEEEChhh--hhHHHhC--C-CcEEEE
Confidence 368999999999987 3455667776654 577789999999999999998754 4656664 3 699999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 69 ~~~ 71 (295)
T PRK02755 69 TIR 71 (295)
T ss_pred EEE
Confidence 986
No 50
>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=96.85 E-value=0.0023 Score=61.47 Aligned_cols=52 Identities=15% Similarity=0.209 Sum_probs=45.7
Q ss_pred CcHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccC
Q 011530 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (483)
Q Consensus 110 ~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~ 188 (483)
.||+.+|.+.+ ..||+.|+++|..|.| .|||+.++ .
T Consensus 90 ~RLD~~L~~~g~~~SR~~ArqlI~~G~V----------------------------------~VNgk~v~---------~ 126 (200)
T TIGR01017 90 SRLDNVVYRLGFAPTRFAARQLVSHGHI----------------------------------LVNGKKVD---------I 126 (200)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHCCCE----------------------------------EECCEEeC---------C
Confidence 58889998776 5799999999999999 68999987 5
Q ss_pred CCceecCCCEEEEecC
Q 011530 189 VDQIVEAGTYLRVHVH 204 (483)
Q Consensus 189 ~~~~v~~GD~I~v~~~ 204 (483)
+++.|++||.|.|...
T Consensus 127 ps~~V~~GD~I~V~~~ 142 (200)
T TIGR01017 127 PSYQVRPGDIISIKEK 142 (200)
T ss_pred CCCCCCCCCEEEEeeC
Confidence 8999999999998754
No 51
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=96.82 E-value=0.0037 Score=63.70 Aligned_cols=70 Identities=16% Similarity=0.184 Sum_probs=54.1
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.|+.+| .+...+++.++.. ++.-.+-||...||||+++-... .++.+.+.+ -.|+|.|
T Consensus 13 ~Gil~i~KP~G~TS~--------dvv~~vrk~~~~k-KvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~--~~K~Y~a 79 (305)
T PRK05389 13 SGWLILDKPAGMTST--------EAVSKVKWLFDAQ-KAGHAGTLDPLASGVLPIALGEA--TKTVPYVMD--GTKRYRF 79 (305)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhccc-ccCCcccCCCCCceEEEEEEChh--hhhhHHhcc--CCcEEEE
Confidence 469999999999987 3455566666553 46778999999999999999874 455555544 4799999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 80 ~~~ 82 (305)
T PRK05389 80 TVA 82 (305)
T ss_pred EEE
Confidence 986
No 52
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=96.80 E-value=0.0017 Score=63.48 Aligned_cols=54 Identities=19% Similarity=0.166 Sum_probs=49.2
Q ss_pred CCcHHHHHHhccCCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccC
Q 011530 109 GGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (483)
Q Consensus 109 ~~rl~~~Ls~~l~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~ 188 (483)
.-|||.++++.+++||..++++|+.|.| +||.+.++ +
T Consensus 180 SlRLD~vis~~~~~SR~~a~~lIe~g~V----------------------------------kVN~k~v~---------~ 216 (257)
T COG2302 180 SLRLDVVISEGFGLSRAKAQQLIEKGKV----------------------------------KVNWKVVD---------K 216 (257)
T ss_pred hhhHHHHHHHHHhhhHHHHHHHHHcCce----------------------------------EEeeEEec---------c
Confidence 4589999999999999999999999999 79999998 5
Q ss_pred CCceecCCCEEEEecCC
Q 011530 189 VDQIVEAGTYLRVHVHP 205 (483)
Q Consensus 189 ~~~~v~~GD~I~v~~~~ 205 (483)
+++.|+.||.|.+....
T Consensus 217 ~s~~v~~GDliSirG~G 233 (257)
T COG2302 217 ASYEVQEGDLISIRGFG 233 (257)
T ss_pred ccceeccCCEEEEeccc
Confidence 89999999999997543
No 53
>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=96.80 E-value=0.004 Score=62.73 Aligned_cols=68 Identities=24% Similarity=0.332 Sum_probs=53.7
Q ss_pred EEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEE
Q 011530 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (483)
Q Consensus 227 liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV 306 (483)
++++|||.||.+| .+...+++.++.. ++.-.+-||...||||+++-+.. .+|...+.+ ..|+|+|.+
T Consensus 2 il~i~KP~G~tS~--------~vv~~vr~~~~~k-KvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~--~~K~Y~~~~ 68 (277)
T cd02573 2 ILLLDKPAGLTSH--------DVVQKVRRLLGTK-KVGHTGTLDPLATGVLPIALGEA--TKLSQYLLD--ADKTYRATV 68 (277)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHhCcC-ccCCCCCCCCcCeEEEEEEEChH--HhhHHHhcC--CCcEEEEEE
Confidence 7899999999987 3455666666653 56778999999999999999875 346666655 689999998
Q ss_pred e
Q 011530 307 T 307 (483)
Q Consensus 307 ~ 307 (483)
.
T Consensus 69 ~ 69 (277)
T cd02573 69 R 69 (277)
T ss_pred E
Confidence 6
No 54
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=96.80 E-value=0.0044 Score=62.77 Aligned_cols=70 Identities=20% Similarity=0.287 Sum_probs=54.2
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.||.+| .+...+++.++. .++.-.+-||...||||+++-... .++.+.+.+ -.|+|.|
T Consensus 3 ~GiL~i~KP~G~TS~--------dvv~~vrk~~~~-kKvGH~GTLDP~AtGvL~v~vG~a--TKl~~~l~~--~~K~Y~~ 69 (292)
T PRK01528 3 NYWLNIYKPRGISSA--------KLVSIVKKILGK-VKIGHAGTLDVEAEGVLPLAVGEA--TKLVQLLID--AKKTYIF 69 (292)
T ss_pred CEEEEEeCCCCCCHH--------HHHHHHHHHcCC-CccCcCccCCCcCceEEEEEEChH--hhhhHHHhc--CCceEEE
Confidence 469999999999987 345566666664 357778999999999999998874 445555544 5699999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 70 ~~~ 72 (292)
T PRK01528 70 TVK 72 (292)
T ss_pred EEE
Confidence 886
No 55
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=96.78 E-value=0.0038 Score=63.65 Aligned_cols=71 Identities=21% Similarity=0.276 Sum_probs=54.4
Q ss_pred cCeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEE
Q 011530 224 TESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYL 303 (483)
Q Consensus 224 D~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~Yl 303 (483)
.+.++++|||.|+.+| .+...+++.++. .++.-.+-||...||||+++-+.. .+|.+.+.+ -.|+|.
T Consensus 21 ~~g~l~i~Kp~g~tS~--------~~v~~~r~~~~~-kkvGH~GTLDp~A~GvL~v~~g~a--tk~~~~~~~--~~K~Y~ 87 (300)
T PRK04270 21 KFGVVNLDKPPGPTSH--------EVAAWVRDILGV-EKAGHGGTLDPKVTGVLPVALGKA--TKVVQALLE--SGKEYV 87 (300)
T ss_pred CCCEEEEECCCCCCHH--------HHHHHHHHHhcc-ccccCCCCCCCcCeEEEEEEEChH--hhhhHHhcc--CCcEEE
Confidence 3469999999999987 245556666654 356778999999999999999874 456565554 459999
Q ss_pred EEEe
Q 011530 304 ALTT 307 (483)
Q Consensus 304 AlV~ 307 (483)
|.+.
T Consensus 88 ~~~~ 91 (300)
T PRK04270 88 CVMH 91 (300)
T ss_pred EEEE
Confidence 9886
No 56
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=96.75 E-value=0.0048 Score=62.89 Aligned_cols=70 Identities=17% Similarity=0.249 Sum_probs=54.5
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.||.+| .+...+++.++.. ++.-.+-||-..||||+++-... .+|.+.+.+ -.|+|.|
T Consensus 2 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~~k-KvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~~--~~K~Y~a 68 (304)
T PRK01550 2 NGVLLLHKPRGMTSH--------DCVFKLRKILRTK-KVGHTGTLDPEVSGVLPICVGRA--TKIAEYLTD--EGKTYEG 68 (304)
T ss_pred CeEEEEECCCCCCHH--------HHHHHHHHHcCCC-CcccCCCCCCcCeeEEEEEEChh--hhhhHHhcC--CCcEEEE
Confidence 368999999999987 3455667766653 56678999999999999999875 346566654 4799999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 69 ~~~ 71 (304)
T PRK01550 69 EVT 71 (304)
T ss_pred EEE
Confidence 986
No 57
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=96.74 E-value=0.0052 Score=62.50 Aligned_cols=70 Identities=24% Similarity=0.304 Sum_probs=54.4
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.||.+| .+...+++.++.. ++.-.+-||...||||+++-... .+|.+.+.+ -.|+|.|
T Consensus 16 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~~k-KvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~--~~K~Y~~ 82 (303)
T PRK01851 16 DGVLLLDKPLGLSSN--------DALQRAKRLLRAK-KAGHTGTLDPLATGLLPLCFGEA--TKFSQDLLD--ADKTYEA 82 (303)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCcc-cCCCCCCCCCCCceEEEEEECHH--HhhhHHhcc--cCeEEEE
Confidence 469999999999987 3455667766653 46668999999999999999875 346565655 4599999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 83 ~~~ 85 (303)
T PRK01851 83 TLR 85 (303)
T ss_pred EEE
Confidence 986
No 58
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=96.71 E-value=0.0054 Score=62.62 Aligned_cols=70 Identities=19% Similarity=0.255 Sum_probs=54.6
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.||.+| .+...+++.++. .++.-.+-||-..||||+++-...+ +|.+.+.+ -.|+|.|
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~~-kKvGH~GTLDP~AtGvL~v~vG~aT--kl~~~~~~--~~K~Y~a 76 (312)
T PRK05033 10 NGVLLLDKPQGMSSN--------DALQKVKRLFNA-NKAGHTGALDPLATGMLPICLGEAT--KFSQYLLD--SDKRYRV 76 (312)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhCC-CCCCCCCcCCCcCeeEEEEEECHHh--hhhHHhcC--CCcEEEE
Confidence 469999999999987 245566666654 3567789999999999999998753 46666654 4799999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 77 ~~~ 79 (312)
T PRK05033 77 TAR 79 (312)
T ss_pred EEE
Confidence 986
No 59
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=96.71 E-value=0.0031 Score=60.53 Aligned_cols=53 Identities=11% Similarity=0.070 Sum_probs=46.2
Q ss_pred CcHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccC
Q 011530 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (483)
Q Consensus 110 ~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~ 188 (483)
.|||++|.+.+ ..||+.|+++|..|.| .|||+.++ .
T Consensus 89 ~RLD~~L~r~g~~~SR~~ArqlI~~G~V----------------------------------~VNGk~v~---------~ 125 (201)
T CHL00113 89 MRLDNILFRLGMAPTIPAARQLVNHGHI----------------------------------LVNGRIVD---------I 125 (201)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHCCcE----------------------------------EECCEEec---------C
Confidence 47889999887 5799999999999999 68999987 5
Q ss_pred CCceecCCCEEEEecCC
Q 011530 189 VDQIVEAGTYLRVHVHP 205 (483)
Q Consensus 189 ~~~~v~~GD~I~v~~~~ 205 (483)
+++.|++||.|.|....
T Consensus 126 ps~~Vk~GD~I~V~~~~ 142 (201)
T CHL00113 126 PSYRCKPKDIITVKDKQ 142 (201)
T ss_pred ccccCCCCCEEEEcccc
Confidence 89999999999987543
No 60
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=96.50 E-value=0.0079 Score=61.40 Aligned_cols=68 Identities=26% Similarity=0.322 Sum_probs=53.3
Q ss_pred EEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEE
Q 011530 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALT 306 (483)
Q Consensus 227 liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV 306 (483)
+++||||.||.+| .+...+++.++.. ++.-.+-||-..||||+++-...+ +|.+.+. ...|+|.|.+
T Consensus 3 il~idKP~G~TS~--------dvv~~vrr~l~~k-KvGH~GTLDP~AtGvL~i~iG~aT--Kl~~~l~--~~~K~Y~a~~ 69 (312)
T PRK14122 3 VYAVDKPLGLTSH--------DVVNRARRALGTR-RVGHTGTLDPLATGVLVLCTDDST--KLVPFLS--AEDKEYLAWV 69 (312)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHhCCC-CCCCCCCCCCcCeeeEEEEEChhh--hhhHHhc--CCCceEEEEE
Confidence 7899999999987 3455667766653 566789999999999999998753 3666663 3679999998
Q ss_pred e
Q 011530 307 T 307 (483)
Q Consensus 307 ~ 307 (483)
.
T Consensus 70 ~ 70 (312)
T PRK14122 70 S 70 (312)
T ss_pred E
Confidence 5
No 61
>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=96.41 E-value=0.0052 Score=60.25 Aligned_cols=49 Identities=18% Similarity=0.120 Sum_probs=42.8
Q ss_pred cHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccCC
Q 011530 111 PVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHV 189 (483)
Q Consensus 111 rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~~ 189 (483)
||++||.+.+ ..||+.|+++|..|.| .|||++++ ++
T Consensus 1 RLD~~L~~~g~~~SR~~a~~lI~~G~V----------------------------------~Vng~~v~---------k~ 37 (228)
T TIGR00478 1 RLDILLVRRGLFESREKAKRLILKGFV----------------------------------LVNGKKVD---------KP 37 (228)
T ss_pred CHHHHHHHcCCccHHHHHHHHHHCCcE----------------------------------EECCEEeC---------CC
Confidence 5779999987 4689999999999999 58999886 58
Q ss_pred CceecCCCEEEEe
Q 011530 190 DQIVEAGTYLRVH 202 (483)
Q Consensus 190 ~~~v~~GD~I~v~ 202 (483)
++.|..||.|.+.
T Consensus 38 s~~V~~~d~I~v~ 50 (228)
T TIGR00478 38 SALVDFDAKIELL 50 (228)
T ss_pred CCCCCCCCEEecc
Confidence 8999999988776
No 62
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=96.38 E-value=0.011 Score=60.11 Aligned_cols=70 Identities=24% Similarity=0.220 Sum_probs=54.5
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.||.+| .+...+++.++.. ++.-.+=||-..||||+++-... .+|.+.+.+ -.|+|.|
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~~k-KvGH~GTLDP~AtGvL~v~~G~a--Tkl~~~l~~--~~K~Y~a 76 (300)
T PRK04642 10 DGILLLDKPAGLSSN--------NALQAARRLLRAE-KGGHTGSLDPLATGLLPLCFGEA--TKIAGLLLG--SAKAYDA 76 (300)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhCCC-cccCCCccCCcCeeeEEEEEChh--hhhhHHhcC--CCcEEEE
Confidence 469999999999987 3456667776653 46668999999999999998874 455555544 6799999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 77 ~~~ 79 (300)
T PRK04642 77 EIV 79 (300)
T ss_pred EEE
Confidence 985
No 63
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=96.38 E-value=0.0088 Score=61.54 Aligned_cols=70 Identities=21% Similarity=0.322 Sum_probs=54.3
Q ss_pred CeEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEE
Q 011530 225 ESHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLA 304 (483)
Q Consensus 225 ~~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlA 304 (483)
+.+++||||.||.+| .+...+++.++. .++.-.+=||-..+|||+++-... .+|.+.+.+ -.|+|.|
T Consensus 34 ~G~l~i~KP~g~tS~--------~~v~~vr~~~~~-kkvGH~GTLDP~A~GvL~v~~G~a--Tkl~~~~~~--~~K~Y~~ 100 (322)
T TIGR00425 34 YGVVNLDKPSGPSSH--------EVVAWVRRILNV-EKTGHGGTLDPKVTGVLPVCIERA--TRLVKSLQE--APKEYVC 100 (322)
T ss_pred CCEEEEeCCCCCCHH--------HHHHHHHHHhcc-cccCCCCCCCCCCceEEEEEEChH--hhccHHhcc--CCCEEEE
Confidence 469999999999987 345556666654 356678999999999999999874 455565544 6799999
Q ss_pred EEe
Q 011530 305 LTT 307 (483)
Q Consensus 305 lV~ 307 (483)
.+.
T Consensus 101 ~v~ 103 (322)
T TIGR00425 101 LMR 103 (322)
T ss_pred EEE
Confidence 886
No 64
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=96.30 E-value=0.0079 Score=57.92 Aligned_cols=51 Identities=18% Similarity=0.189 Sum_probs=44.7
Q ss_pred CcHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccC
Q 011530 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (483)
Q Consensus 110 ~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~ 188 (483)
.||+.+|.+.+ ..||+.|+++|..|.| .|||+.++ .
T Consensus 93 ~RLD~iL~~~g~~~SR~~arqlI~~G~V----------------------------------~VNgk~v~---------~ 129 (203)
T PRK05327 93 SRLDNVVYRLGFAPTRRQARQLVSHGHI----------------------------------LVNGKKVN---------I 129 (203)
T ss_pred HHHHHHHHHcCccCCHHHHHHHHHCCcE----------------------------------EECCEEEC---------C
Confidence 68889997765 6899999999999999 58999886 5
Q ss_pred CCceecCCCEEEEec
Q 011530 189 VDQIVEAGTYLRVHV 203 (483)
Q Consensus 189 ~~~~v~~GD~I~v~~ 203 (483)
+++.|++||.|.+..
T Consensus 130 ps~~v~~GD~I~v~~ 144 (203)
T PRK05327 130 PSYRVKPGDVIEVRE 144 (203)
T ss_pred CCcCCCCCCEEEECC
Confidence 899999999999874
No 65
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=96.15 E-value=0.014 Score=52.42 Aligned_cols=52 Identities=15% Similarity=0.176 Sum_probs=43.7
Q ss_pred CcHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccC
Q 011530 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (483)
Q Consensus 110 ~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~ 188 (483)
.|||+||-... --||+.|+++|..|.| .|||.++ +
T Consensus 9 ~RlDk~L~~~rl~ktRs~A~~lI~~G~V----------------------------------~vnG~~~----------K 44 (133)
T PRK10348 9 VRLDKWLWAARFYKTRALAREMIEGGKV----------------------------------HYNGQRS----------K 44 (133)
T ss_pred ccHHHHHHHcCccccHHHHHHHHHCCCE----------------------------------EECCEEC----------C
Confidence 36669998886 5799999999999999 5899874 4
Q ss_pred CCceecCCCEEEEecCC
Q 011530 189 VDQIVEAGTYLRVHVHP 205 (483)
Q Consensus 189 ~~~~v~~GD~I~v~~~~ 205 (483)
|+..|..||.|.|....
T Consensus 45 ps~~V~~gd~l~v~~~~ 61 (133)
T PRK10348 45 PSKIVELNATLTLRQGN 61 (133)
T ss_pred CCCccCCCCEEEEEECC
Confidence 99999999999997543
No 66
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=95.95 E-value=0.021 Score=57.28 Aligned_cols=69 Identities=20% Similarity=0.327 Sum_probs=53.1
Q ss_pred eEEEEeCCCCCccCCCCCCccchHHHHHHHhccCCCCCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEE
Q 011530 226 SHVVLDKPAGTSVGGTTDNIEESCATFASRALGLTTPLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLAL 305 (483)
Q Consensus 226 ~liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAl 305 (483)
.++++|||.|+.+| .+...+++.++.. +..-.+-||-..||+|+++-. ++ .+|.+.+.+ -.|+|.|.
T Consensus 16 Gil~ldKP~G~tS~--------~~v~~vkkil~~~-K~GH~GTLDP~atGvLpi~ig-~a-TKl~~~l~~--~~K~Y~a~ 82 (271)
T COG0130 16 GVINLDKPPGPTSH--------EVVAWVKRILGVE-KAGHGGTLDPLATGVLPICLG-EA-TKLVQYLLD--ADKEYVAT 82 (271)
T ss_pred ceEEeeCCCCCCHH--------HHHHHHHHHhCcc-ccccccccCCcccceEEEEec-hh-HhHHHHHhh--CCcEEEEE
Confidence 69999999999987 3556677777654 455689999999999999998 33 344444443 57999999
Q ss_pred Ee
Q 011530 306 TT 307 (483)
Q Consensus 306 V~ 307 (483)
+.
T Consensus 83 ~~ 84 (271)
T COG0130 83 VR 84 (271)
T ss_pred EE
Confidence 86
No 67
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=95.92 E-value=0.014 Score=56.15 Aligned_cols=53 Identities=17% Similarity=0.191 Sum_probs=46.0
Q ss_pred CcHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccC
Q 011530 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (483)
Q Consensus 110 ~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~ 188 (483)
.||+.++-+.+ .-|+.+|+++|.-|.| .|||++|+ .
T Consensus 94 rRLd~vVyR~GfA~T~~qARQlV~HGHI----------------------------------~VnGk~V~---------i 130 (205)
T COG0522 94 RRLDNVVYRLGFAKTRRQARQLVSHGHI----------------------------------LVNGKRVN---------I 130 (205)
T ss_pred HHHHHHHHHhcccccHHHHHHHhhcceE----------------------------------EECCEEec---------c
Confidence 47777777776 5899999999999999 69999998 5
Q ss_pred CCceecCCCEEEEecCC
Q 011530 189 VDQIVEAGTYLRVHVHP 205 (483)
Q Consensus 189 ~~~~v~~GD~I~v~~~~ 205 (483)
|++.|.+||++.|....
T Consensus 131 PSy~V~~gdei~V~~k~ 147 (205)
T COG0522 131 PSYLVSPGDEISVREKS 147 (205)
T ss_pred CcEEecCCCEEEeeecc
Confidence 99999999999998544
No 68
>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=95.90 E-value=0.025 Score=57.85 Aligned_cols=69 Identities=13% Similarity=0.122 Sum_probs=48.5
Q ss_pred EEEEeCCCCCccCCCCCCccchHHHHHHHhccC----------------------------CCCCccccCCCCCCceEEE
Q 011530 227 HVVLDKPAGTSVGGTTDNIEESCATFASRALGL----------------------------TTPLRTTHQIDNCTEGCVV 278 (483)
Q Consensus 227 liVvNKPaGl~v~~~~~~~~~tl~~~l~~~~~~----------------------------~~~l~~VHRLDr~TSGLLL 278 (483)
+++||||.||.++. +...+++.++. ..++.-.+-||-..||||+
T Consensus 2 il~i~KP~G~TS~~--------vv~~lk~~l~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~KiGH~GTLDPlAsGVLv 73 (312)
T cd02867 2 VFAINKPSGITSAQ--------VLNDLKPLFLNSALFKDKIQRAVAKRGKKARRRKGRKRSKLKIGHGGTLDPLATGVLV 73 (312)
T ss_pred eEEEeCCCCCCHHH--------HHHHHHHHhcccccccchhhhhhhhhhhhhhhhccccccccccccccccCCccceeEE
Confidence 78999999999863 23333333321 1356668899999999999
Q ss_pred EEcCHHHHHHHHHHhhcCCcceEEEEEEe
Q 011530 279 LARTQEYCSIFHRKIREKKVKKLYLALTT 307 (483)
Q Consensus 279 ~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~ 307 (483)
++-... .+.+ ..|.. ..|+|.|.+.
T Consensus 74 vgvG~a-TK~l-~~~l~--~~K~Y~~~~~ 98 (312)
T cd02867 74 VGVGAG-TKQL-QDYLS--CSKTYEATGL 98 (312)
T ss_pred EEECcH-HHHH-HHHhc--CCceEEEEEE
Confidence 998864 3344 33443 7899999886
No 69
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=94.35 E-value=0.1 Score=51.29 Aligned_cols=51 Identities=18% Similarity=0.135 Sum_probs=44.5
Q ss_pred CcHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccC
Q 011530 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (483)
Q Consensus 110 ~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~ 188 (483)
.||+.+|.+.+ .-||..|+++|..|.| .|||..++ +
T Consensus 3 ~RLD~~Lv~rgl~~sR~~A~~~I~~G~V----------------------------------~Vng~~v~---------K 39 (245)
T COG1189 3 MRLDALLVERGLFESREKAKELILAGNV----------------------------------LVNGEKVT---------K 39 (245)
T ss_pred chHHHHHHHccchhhHHHHHHHHHcCeE----------------------------------EECCEEec---------C
Confidence 57779999996 5899999999999999 58999887 6
Q ss_pred CCceecCCCEEEEec
Q 011530 189 VDQIVEAGTYLRVHV 203 (483)
Q Consensus 189 ~~~~v~~GD~I~v~~ 203 (483)
|++.|..++.|++..
T Consensus 40 P~~~V~~~~~i~v~~ 54 (245)
T COG1189 40 PSQLVDIDDEIEVKG 54 (245)
T ss_pred cceecCCCceEEEcc
Confidence 999999888888864
No 70
>PRK11507 ribosome-associated protein; Provisional
Probab=93.21 E-value=0.26 Score=39.29 Aligned_cols=50 Identities=14% Similarity=-0.001 Sum_probs=41.9
Q ss_pred CcHHHHHHhccC-CCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccC
Q 011530 110 GPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (483)
Q Consensus 110 ~rl~~~Ls~~l~-~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~ 188 (483)
-+|.+||....- -|=-+|+.+|.+|.| +|||++.++
T Consensus 12 I~L~QlLK~~~~v~SGG~AK~~I~eg~V----------------------------------~VNGeve~r--------- 48 (70)
T PRK11507 12 VELCDLLKLEGWSESGAQAKIAIAEGQV----------------------------------KVDGAVETR--------- 48 (70)
T ss_pred EEHHHHHhhhCcccChHHHHHHHHcCce----------------------------------EECCEEecc---------
Confidence 588899988774 566899999999999 689998764
Q ss_pred CCceecCCCEEEEe
Q 011530 189 VDQIVEAGTYLRVH 202 (483)
Q Consensus 189 ~~~~v~~GD~I~v~ 202 (483)
-..+|.+||.|.+.
T Consensus 49 RgkKl~~GD~V~~~ 62 (70)
T PRK11507 49 KRCKIVAGQTVSFA 62 (70)
T ss_pred cCCCCCCCCEEEEC
Confidence 45689999999986
No 71
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=91.91 E-value=0.35 Score=45.62 Aligned_cols=50 Identities=14% Similarity=0.199 Sum_probs=41.2
Q ss_pred CcHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccC
Q 011530 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (483)
Q Consensus 110 ~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~ 188 (483)
.||+.+|.+.+ .-|+..|+++|..|.| .|||++|+ +
T Consensus 103 rRLd~il~r~gla~S~~~Ar~lI~hGhV----------------------------------~V~g~~V~---------~ 139 (177)
T PRK04051 103 RRLQTIVYRKGLARTPKQARQFIVHGHI----------------------------------AVNGRRVT---------S 139 (177)
T ss_pred hHHHHHHHHccCcCCHHHHHHHHHcCCE----------------------------------EECCEEeC---------C
Confidence 47778888876 5799999999999999 68999987 6
Q ss_pred CCceecCCCEEEEe
Q 011530 189 VDQIVEAGTYLRVH 202 (483)
Q Consensus 189 ~~~~v~~GD~I~v~ 202 (483)
|++.|..++.-.|.
T Consensus 140 Ps~~V~~~~ed~I~ 153 (177)
T PRK04051 140 PSYLVSVEEEDLID 153 (177)
T ss_pred CCeECCCCCcceEE
Confidence 99999998543333
No 72
>PRK04313 30S ribosomal protein S4e; Validated
Probab=89.17 E-value=2.2 Score=42.08 Aligned_cols=71 Identities=15% Similarity=0.116 Sum_probs=53.3
Q ss_pred CCcHHHHHHhccC--CCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccc
Q 011530 109 GGPVLEYICRELN--LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRI 186 (483)
Q Consensus 109 ~~rl~~~Ls~~l~--~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~ 186 (483)
.-+|.-+|...|+ .+.++|++.|.+|.| .|||++.+
T Consensus 37 siPL~iiLRd~L~yA~t~rEak~Il~~~~V----------------------------------~VDGkvr~-------- 74 (237)
T PRK04313 37 SIPLLVVLRDVLGYADTAREAKKIINEGKV----------------------------------LVDGRVRK-------- 74 (237)
T ss_pred ccccHHHHHhHhhhhccHHHHHHHHhCCcE----------------------------------EECCEEEc--------
Confidence 3467788988885 799999999999999 68999987
Q ss_pred cCCCceecCCCEEEEecCCCCCCcccCCCCCceEEeecCeEEEEeC
Q 011530 187 THVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDK 232 (483)
Q Consensus 187 ~~~~~~v~~GD~I~v~~~~~~~p~~~~~~~~~~IlyED~~liVvNK 232 (483)
|..+.+---|+|.|.-.. ...+++|+....+++.+
T Consensus 75 -D~~~PvGlmDVIsI~~~~----------e~yRvl~d~kgr~~l~~ 109 (237)
T PRK04313 75 -DYKFPVGLMDVISIPETG----------EYYRVLPDEKGRLVLIP 109 (237)
T ss_pred -ccccCcCceeEEEEccCC----------CeEEEEECCCCcEEEEE
Confidence 567777666999986322 24567777766555543
No 73
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=88.24 E-value=1.8 Score=34.87 Aligned_cols=55 Identities=11% Similarity=0.035 Sum_probs=43.7
Q ss_pred ecCCCCcHHHHHHhccC-CCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeecccc
Q 011530 105 VVSEGGPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKT 183 (483)
Q Consensus 105 ~~~~~~rl~~~Ls~~l~-~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~ 183 (483)
...|--+|.+||....- -|=.+|+.+|.+|.| .|||++-++
T Consensus 7 i~~e~I~L~qlLK~~g~i~sGG~AK~~i~eg~V----------------------------------~vNGe~EtR---- 48 (73)
T COG2501 7 IKTEFITLGQLLKLAGLIESGGQAKAFIAEGEV----------------------------------KVNGEVETR---- 48 (73)
T ss_pred eccceEEHHHHHHHhCcccCcHHHHHHHHCCeE----------------------------------EECCeeeec----
Confidence 34455689999988774 466799999999999 589998763
Q ss_pred ccccCCCceecCCCEEEEe
Q 011530 184 FRITHVDQIVEAGTYLRVH 202 (483)
Q Consensus 184 ~r~~~~~~~v~~GD~I~v~ 202 (483)
-..+|..||.|.+.
T Consensus 49 -----RgkKlr~gd~V~i~ 62 (73)
T COG2501 49 -----RGKKLRDGDVVEIP 62 (73)
T ss_pred -----cCCEeecCCEEEEC
Confidence 45689999999886
No 74
>PLN00189 40S ribosomal protein S9; Provisional
Probab=87.45 E-value=0.52 Score=44.99 Aligned_cols=51 Identities=8% Similarity=0.025 Sum_probs=39.9
Q ss_pred HHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccCCC
Q 011530 112 VLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVD 190 (483)
Q Consensus 112 l~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~~~ 190 (483)
|+-++.+.+ .-|...|.++|..|.| .|||++|+ .|+
T Consensus 111 L~~vv~r~g~a~si~~ARqlI~hgHI----------------------------------~V~~~~V~---------~Ps 147 (194)
T PLN00189 111 LQTLVFKSGMAKSIHHARVLIRQRHI----------------------------------RVGKQIVN---------VPS 147 (194)
T ss_pred hceeeeecCCcCCHHHHHHheeCCCE----------------------------------eECCEEEe---------cCc
Confidence 333343433 3678899999999999 69999998 599
Q ss_pred ceecCCCEEEEecCC
Q 011530 191 QIVEAGTYLRVHVHP 205 (483)
Q Consensus 191 ~~v~~GD~I~v~~~~ 205 (483)
+.|..|+++.|.+..
T Consensus 148 ~~V~~~~e~~Itw~~ 162 (194)
T PLN00189 148 FMVRVDSQKHIDFSL 162 (194)
T ss_pred EEEecCCEEEEEEec
Confidence 999999998887643
No 75
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=86.89 E-value=0.16 Score=40.05 Aligned_cols=52 Identities=13% Similarity=0.061 Sum_probs=34.0
Q ss_pred CCCcHHHHHHhccC-CCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccc
Q 011530 108 EGGPVLEYICRELN-LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRI 186 (483)
Q Consensus 108 ~~~rl~~~Ls~~l~-~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~ 186 (483)
+.-+|.+||....- -|=.+|+.+|.+|.| +|||+..++
T Consensus 6 e~I~L~qlLK~~glv~sGGeAK~~I~~g~V----------------------------------~VNGe~e~r------- 44 (65)
T PF13275_consen 6 EYITLGQLLKLAGLVSSGGEAKALIQEGEV----------------------------------KVNGEVETR------- 44 (65)
T ss_dssp S---HHHHHHHHTS-SSSSTTSHHHHHHHH----------------------------------EETTB-----------
T ss_pred CcEEHHHHHhHcCCcccHHHHHHHHHcCce----------------------------------EECCEEccc-------
Confidence 34578899988764 455689999999999 689998773
Q ss_pred cCCCceecCCCEEEEe
Q 011530 187 THVDQIVEAGTYLRVH 202 (483)
Q Consensus 187 ~~~~~~v~~GD~I~v~ 202 (483)
...+|.+||.|.+.
T Consensus 45 --rg~Kl~~GD~V~~~ 58 (65)
T PF13275_consen 45 --RGKKLRPGDVVEID 58 (65)
T ss_dssp --SS----SSEEEEET
T ss_pred --cCCcCCCCCEEEEC
Confidence 56789999999984
No 76
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=86.06 E-value=4.1 Score=40.96 Aligned_cols=71 Identities=18% Similarity=0.112 Sum_probs=52.6
Q ss_pred CCcHHHHHHhccC--CCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccc
Q 011530 109 GGPVLEYICRELN--LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRI 186 (483)
Q Consensus 109 ~~rl~~~Ls~~l~--~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~ 186 (483)
.-+|.-+|...|+ .+.++|++.+.+|.| .|||++.+
T Consensus 38 siPL~iiLRd~LkyA~t~rEak~Il~~~~V----------------------------------~VDGkvr~-------- 75 (273)
T PTZ00223 38 CLPLLIIIRNRLKYALNAREAQMILRQGLV----------------------------------CVDGKPRK-------- 75 (273)
T ss_pred ccccHHHHHHHhhhhccHHHHHHHHhCCeE----------------------------------EECCEEEc--------
Confidence 3467788988885 788899999999999 69999987
Q ss_pred cCCCceecCCCEEEEecCCCCCCcccCCCCCceEEeecCeEEEEeC
Q 011530 187 THVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDK 232 (483)
Q Consensus 187 ~~~~~~v~~GD~I~v~~~~~~~p~~~~~~~~~~IlyED~~liVvNK 232 (483)
|..+.+---|+|.|.-.. ...+++|+....+++.+
T Consensus 76 -D~~~PvGlMDVIsI~kt~----------e~yRvl~D~kGrf~l~~ 110 (273)
T PTZ00223 76 -DGKYPAGFMDVVEIPKTG----------DRFRILYDVKGRFALVK 110 (273)
T ss_pred -cCCCCCceeEEEEEcCCC----------CeEEEEECCCCcEEEEE
Confidence 466676666999886322 24567777666555543
No 77
>PLN00036 40S ribosomal protein S4; Provisional
Probab=86.02 E-value=4.3 Score=40.54 Aligned_cols=71 Identities=17% Similarity=0.107 Sum_probs=52.8
Q ss_pred CCcHHHHHHhccC--CCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccc
Q 011530 109 GGPVLEYICRELN--LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRI 186 (483)
Q Consensus 109 ~~rl~~~Ls~~l~--~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~ 186 (483)
.-+|.-+|...|+ .+.++|++.+.+|.| .|||++.+
T Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~~~V----------------------------------~VDGkvr~-------- 78 (261)
T PLN00036 41 CLPLLLILRNRLKYALTYREVQAILMQRHV----------------------------------KVDGKVRT-------- 78 (261)
T ss_pred ccccHHHHHhHhhhhccHHHHHHHHhCCeE----------------------------------EECCEEec--------
Confidence 3467788998885 788899999999999 69999987
Q ss_pred cCCCceecCCCEEEEecCCCCCCcccCCCCCceEEeecCeEEEEeC
Q 011530 187 THVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDK 232 (483)
Q Consensus 187 ~~~~~~v~~GD~I~v~~~~~~~p~~~~~~~~~~IlyED~~liVvNK 232 (483)
|..+.+---|+|.+.-.. ...+++|+....+++.+
T Consensus 79 -D~~fPvG~mDVIsI~kt~----------e~yRvl~D~kGrf~l~~ 113 (261)
T PLN00036 79 -DKTYPAGFMDVISIPKTN----------ENFRLLYDTKGRFRLHR 113 (261)
T ss_pred -cCCCCCceeEEEEEcCCC----------CeEEEEECCCceEEEEE
Confidence 466666666999886322 24577777776665543
No 78
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=85.58 E-value=1.5 Score=40.84 Aligned_cols=49 Identities=14% Similarity=0.173 Sum_probs=38.6
Q ss_pred CcHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccC
Q 011530 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (483)
Q Consensus 110 ~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~ 188 (483)
.||+-++.+.+ .-|..+|.++|..|.| .|||++|+ .
T Consensus 104 RRL~~vv~r~g~a~s~~~ArqlI~hgHI----------------------------------~V~~~~V~---------~ 140 (162)
T TIGR01018 104 RRLQTQVFKKGLARTIHQARQLIVHGHI----------------------------------AVDGRRVT---------S 140 (162)
T ss_pred HhHhhHhhhccCcCCHHHHHHHhhCCCe----------------------------------eECCEEec---------c
Confidence 35556666654 4788999999999999 68999998 6
Q ss_pred CCceecCCCEEEE
Q 011530 189 VDQIVEAGTYLRV 201 (483)
Q Consensus 189 ~~~~v~~GD~I~v 201 (483)
|++.|..|++-.|
T Consensus 141 Ps~~V~~~~Ed~I 153 (162)
T TIGR01018 141 PSYIVRREEEKKI 153 (162)
T ss_pred CceEecCCCCCee
Confidence 9999999844333
No 79
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=84.91 E-value=5.1 Score=40.08 Aligned_cols=70 Identities=16% Similarity=0.046 Sum_probs=51.6
Q ss_pred CCcHHHHHHhccC--CCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccc
Q 011530 109 GGPVLEYICRELN--LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRI 186 (483)
Q Consensus 109 ~~rl~~~Ls~~l~--~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~ 186 (483)
.-+|.-+|...|+ .+.++|+..|.+|.| .|||++.+
T Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~~~V----------------------------------~VDGkvr~-------- 78 (262)
T PTZ00118 41 CLPLVILLRNRLKYALTYDEVKLIVIQKIV----------------------------------KVDGKVRT-------- 78 (262)
T ss_pred ccccHHHHHhhhhhhccHHHHHHHHHCCcE----------------------------------EECCEEEc--------
Confidence 3467788988885 788999999999999 69999987
Q ss_pred cCCCceecCCCEEEEecCCCCCCcccCCCCCceEEeecCeEEEEe
Q 011530 187 THVDQIVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLD 231 (483)
Q Consensus 187 ~~~~~~v~~GD~I~v~~~~~~~p~~~~~~~~~~IlyED~~liVvN 231 (483)
|..+.+---|+|.|.--. ...+++|+....+++.
T Consensus 79 -D~~fPvG~mDVIsI~kt~----------e~yRvl~D~kGr~~l~ 112 (262)
T PTZ00118 79 -DCTYPVGFMDVVSLTKTN----------EYFRLLYDTKGRFVPH 112 (262)
T ss_pred -cCCCCCceeEEEEEcCCC----------CeEEEEECCCccEEEE
Confidence 466677666999886322 1456777666655544
No 80
>PRK01777 hypothetical protein; Validated
Probab=82.14 E-value=1.8 Score=36.70 Aligned_cols=58 Identities=19% Similarity=0.230 Sum_probs=39.6
Q ss_pred eeeecCCCCcHHHHHHhccCCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeecc
Q 011530 102 EHLVVSEGGPVLEYICRELNLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQ 181 (483)
Q Consensus 102 ~~~~~~~~~rl~~~Ls~~l~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q 181 (483)
..+.+.++.++.+.|... ++...+-+--+..+.| -|||+.+.
T Consensus 19 ~~l~vp~GtTv~dal~~s-gi~~~~pei~~~~~~v----------------------------------gI~Gk~v~--- 60 (95)
T PRK01777 19 QRLTLQEGATVEEAIRAS-GLLELRTDIDLAKNKV----------------------------------GIYSRPAK--- 60 (95)
T ss_pred EEEEcCCCCcHHHHHHHc-CCCccCcccccccceE----------------------------------EEeCeECC---
Confidence 345578888888988765 4433311112234455 58999875
Q ss_pred ccccccCCCceecCCCEEEEecC
Q 011530 182 KTFRITHVDQIVEAGTYLRVHVH 204 (483)
Q Consensus 182 ~~~r~~~~~~~v~~GD~I~v~~~ 204 (483)
.++.|+.||+|+|+.+
T Consensus 61 -------~d~~L~dGDRVeIyrP 76 (95)
T PRK01777 61 -------LTDVLRDGDRVEIYRP 76 (95)
T ss_pred -------CCCcCCCCCEEEEecC
Confidence 8899999999999854
No 81
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=81.54 E-value=1 Score=44.18 Aligned_cols=22 Identities=14% Similarity=0.308 Sum_probs=19.4
Q ss_pred CCccccCCCCCCceEEEEEcCH
Q 011530 262 PLRTTHQIDNCTEGCVVLARTQ 283 (483)
Q Consensus 262 ~l~~VHRLDr~TSGLLL~Ak~~ 283 (483)
.+.++||||-.|||++||+-+.
T Consensus 90 ~V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559|consen 90 DVQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred ceeeEEeecccccceEEEecCc
Confidence 3678999999999999998764
No 82
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=80.83 E-value=1.8 Score=40.91 Aligned_cols=51 Identities=8% Similarity=-0.014 Sum_probs=40.1
Q ss_pred CcHHHHHHhcc-CCCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccC
Q 011530 110 GPVLEYICREL-NLPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITH 188 (483)
Q Consensus 110 ~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~ 188 (483)
.||+-++.+.+ .-+...|.++|..|.| .|||++|+ +
T Consensus 107 RRL~~iv~r~g~A~ti~~ARqlI~HGHI----------------------------------~V~~~~V~---------~ 143 (181)
T PTZ00155 107 RRLQTKVFKLGLAKSIHHARVLIRQRHI----------------------------------RVGKQIVD---------I 143 (181)
T ss_pred HhhhhHHHhccCcCCHHHhhhheeCCCE----------------------------------EECCEEec---------c
Confidence 35556666655 4688899999999999 69999998 6
Q ss_pred CCceecCCCEEEEec
Q 011530 189 VDQIVEAGTYLRVHV 203 (483)
Q Consensus 189 ~~~~v~~GD~I~v~~ 203 (483)
|++.|..|+.=.|.+
T Consensus 144 Ps~~V~~~~Ed~I~~ 158 (181)
T PTZ00155 144 PSFLVRVDSEKHIDF 158 (181)
T ss_pred CceEeccCccCceee
Confidence 999999997655544
No 83
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=77.75 E-value=2.3 Score=38.68 Aligned_cols=29 Identities=21% Similarity=0.196 Sum_probs=27.1
Q ss_pred CcHHHHHHhccCCCHHHHHHHHHcCCEEe
Q 011530 110 GPVLEYICRELNLPPLFVADLIHFGAVYY 138 (483)
Q Consensus 110 ~rl~~~Ls~~l~~Sr~~~~~lI~~G~V~~ 138 (483)
-||+.+|++.+++||++++++++.|.|..
T Consensus 103 ~Rld~lLa~~L~lSrs~l~~l~~~G~I~~ 131 (142)
T PF06353_consen 103 LRLDRLLARQLGLSRSRLKRLIEQGLIRS 131 (142)
T ss_pred ccHHHHHHHHhCcCHHHHHHHHHCCCEEe
Confidence 58889999999999999999999999963
No 84
>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=71.87 E-value=3.7 Score=37.66 Aligned_cols=42 Identities=14% Similarity=0.203 Sum_probs=31.0
Q ss_pred CCccccCCCCCCceEEEEEcCHHHHHHHHHHhhcCCcceEEEEEEe
Q 011530 262 PLRTTHQIDNCTEGCVVLARTQEYCSIFHRKIREKKVKKLYLALTT 307 (483)
Q Consensus 262 ~l~~VHRLDr~TSGLLL~Ak~~~aa~~L~~~f~~~~v~K~YlAlV~ 307 (483)
++.-.+.||...||||+++-+... +|.+.+.+ ..|+|.|.+.
T Consensus 8 KvGH~GTLDP~AsGvL~v~vg~~T--kl~~~l~~--~~K~Y~~~~~ 49 (149)
T PF01509_consen 8 KVGHGGTLDPFASGVLVVGVGKAT--KLLSYLQN--SDKEYVATIR 49 (149)
T ss_dssp SEEESS-SSTT-EEEEEEEEGGGG--GGHHHHTT--SEEEEEEEEE
T ss_pred eeccccccCCcceEEEEEEECCcc--hHHHHhhc--cCCEEEEEEE
Confidence 466689999999999999997743 45566654 5599999885
No 85
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=70.91 E-value=7.6 Score=31.89 Aligned_cols=24 Identities=21% Similarity=0.295 Sum_probs=20.8
Q ss_pred eeCCEEEeeccccccccCCCceecCCCEEEEecC
Q 011530 171 SIKGKTVREAQKTFRITHVDQIVEAGTYLRVHVH 204 (483)
Q Consensus 171 ~vnGk~v~~~q~~~r~~~~~~~v~~GD~I~v~~~ 204 (483)
.|||+.+. .++.++.||.|.|+..
T Consensus 53 ~vNG~~v~----------~~~~~~~Gd~v~V~P~ 76 (81)
T PF14451_consen 53 LVNGRPVD----------FDYRLKDGDRVAVYPV 76 (81)
T ss_pred EECCEECC----------CcccCCCCCEEEEEec
Confidence 68999874 8999999999999853
No 86
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=67.30 E-value=18 Score=38.65 Aligned_cols=29 Identities=21% Similarity=0.104 Sum_probs=24.5
Q ss_pred CCcHHHHHHhcc-CCCHHHHHHHHHcCCEE
Q 011530 109 GGPVLEYICREL-NLPPLFVADLIHFGAVY 137 (483)
Q Consensus 109 ~~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~ 137 (483)
+..+.++|.... .-|+++|+++|++|.|+
T Consensus 342 ~~~~~~~l~~~~~~~S~~earr~i~~g~v~ 371 (408)
T PRK05912 342 GIDLLALLVEAGLVPSKSEARRLIKQGGVK 371 (408)
T ss_pred CCcHHHHHHHhCCCCCHHHHHHHHHcCCEE
Confidence 457888888775 47999999999999994
No 87
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.51 E-value=6.7 Score=36.91 Aligned_cols=28 Identities=21% Similarity=0.201 Sum_probs=26.4
Q ss_pred CcHHHHHHhccCCCHHHHHHHHHcCCEE
Q 011530 110 GPVLEYICRELNLPPLFVADLIHFGAVY 137 (483)
Q Consensus 110 ~rl~~~Ls~~l~~Sr~~~~~lI~~G~V~ 137 (483)
-+|+.+|++++++||+..+++|+.|.+.
T Consensus 139 lrl~~Ll~seL~LSrS~lq~lie~g~Ir 166 (203)
T COG4332 139 LRLDRLLASELGLSRSELQRLIETGQIR 166 (203)
T ss_pred hHHHHHHHHHhCcCHHHHHHHHHcCcee
Confidence 4888999999999999999999999994
No 88
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=60.22 E-value=12 Score=39.93 Aligned_cols=29 Identities=14% Similarity=0.072 Sum_probs=24.3
Q ss_pred CCcHHHHHHhcc-CCCHHHHHHHHHcCCEE
Q 011530 109 GGPVLEYICREL-NLPPLFVADLIHFGAVY 137 (483)
Q Consensus 109 ~~rl~~~Ls~~l-~~Sr~~~~~lI~~G~V~ 137 (483)
+..|.++|.... .-|+++|+++|.+|.|+
T Consensus 342 ~~~~~~~l~~~~~~~S~~earrli~~ggv~ 371 (410)
T PRK13354 342 TKNLVDLLVDLGLEPSKREARRLIQNGAIK 371 (410)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHcCCEE
Confidence 456778888775 57999999999999994
No 89
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=56.94 E-value=22 Score=34.85 Aligned_cols=66 Identities=15% Similarity=0.114 Sum_probs=44.4
Q ss_pred HHHHhccC--CCHHHHHHHHHcCCEEecccCCCCCCCCCchhhhhccccCCccccccceeeCCEEEeeccccccccCCCc
Q 011530 114 EYICRELN--LPPLFVADLIHFGAVYYALVCPKPPLTATPEQMRVFKEVTDPSVLSKRSSIKGKTVREAQKTFRITHVDQ 191 (483)
Q Consensus 114 ~~Ls~~l~--~Sr~~~~~lI~~G~V~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~vnGk~v~~~q~~~r~~~~~~ 191 (483)
-+|...|. -.-++|++.|.+|.| .|||++.++ ..+
T Consensus 45 ~iiRd~LkyAd~~REa~~Ii~~g~v----------------------------------~VDG~vRkd---------~kf 81 (241)
T COG1471 45 VIIRDYLKYADNAREARKILSEGKV----------------------------------LVDGKVRKD---------YKF 81 (241)
T ss_pred eeehhHHHhccchHHHHHHHhcCcE----------------------------------EECCEEecc---------ccC
Confidence 44555443 455799999999999 689998763 444
Q ss_pred eecCCCEEEEecCCCCCCcccCCCCCceEEeecCeEEEEeC
Q 011530 192 IVEAGTYLRVHVHPKRFPRCYDIDWNSRIIAVTESHVVLDK 232 (483)
Q Consensus 192 ~v~~GD~I~v~~~~~~~p~~~~~~~~~~IlyED~~liVvNK 232 (483)
.|--=|+|.|.--. ...+|||+....+++.+
T Consensus 82 PVGlmDVisip~tg----------E~yRvl~d~~grl~l~~ 112 (241)
T COG1471 82 PVGLMDVISIPKTG----------EHYRVLPDEKGRLVLHP 112 (241)
T ss_pred CcceEEEEEECCCC----------ceEEEEecCCccEEEEe
Confidence 44333888886322 24578887777777654
No 90
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=46.55 E-value=28 Score=28.68 Aligned_cols=31 Identities=13% Similarity=0.151 Sum_probs=20.9
Q ss_pred eeecCCCCcHHHHHHhccCCCHHHHHHHHHcC
Q 011530 103 HLVVSEGGPVLEYICRELNLPPLFVADLIHFG 134 (483)
Q Consensus 103 ~~~~~~~~rl~~~Ls~~l~~Sr~~~~~lI~~G 134 (483)
+++|..|.+|..++.+. ++|-+.+.+++...
T Consensus 4 ~~~V~~GDtLs~iF~~~-gls~~dl~~v~~~~ 34 (85)
T PF04225_consen 4 EYTVKSGDTLSTIFRRA-GLSASDLYAVLEAD 34 (85)
T ss_dssp EEE--TT--HHHHHHHT-T--HHHHHHHHHHG
T ss_pred EEEECCCCcHHHHHHHc-CCCHHHHHHHHhcc
Confidence 46788999999988775 99999999998864
No 91
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=45.91 E-value=37 Score=26.69 Aligned_cols=22 Identities=32% Similarity=0.530 Sum_probs=18.9
Q ss_pred eeCCEEEeeccccccccCCCceecCCCEEEEe
Q 011530 171 SIKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (483)
Q Consensus 171 ~vnGk~v~~~q~~~r~~~~~~~v~~GD~I~v~ 202 (483)
.+||+.+. .++.|+.||.|.+.
T Consensus 43 ~vNg~iv~----------~~~~l~~gD~Veii 64 (70)
T PRK08364 43 KVNGKVAL----------EDDPVKDGDYVEVI 64 (70)
T ss_pred EECCEECC----------CCcCcCCCCEEEEE
Confidence 58999875 68899999999886
No 92
>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=41.44 E-value=76 Score=24.92 Aligned_cols=22 Identities=23% Similarity=0.480 Sum_probs=18.8
Q ss_pred eeCCEEEeeccccccccCCCceecCCCEEEEe
Q 011530 171 SIKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (483)
Q Consensus 171 ~vnGk~v~~~q~~~r~~~~~~~v~~GD~I~v~ 202 (483)
.+||+.+. .++.|+.||.|.+.
T Consensus 53 ~vNg~~v~----------~~~~l~~gD~v~i~ 74 (80)
T cd00754 53 AVNGEYVR----------LDTPLKDGDEVAII 74 (80)
T ss_pred EECCeEcC----------CCcccCCCCEEEEe
Confidence 58999875 67899999999986
No 93
>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=40.32 E-value=32 Score=26.24 Aligned_cols=22 Identities=23% Similarity=0.496 Sum_probs=18.2
Q ss_pred eeCCEEEeeccccccccCCCceecCCCEEEEe
Q 011530 171 SIKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (483)
Q Consensus 171 ~vnGk~v~~~q~~~r~~~~~~~v~~GD~I~v~ 202 (483)
.|||+.+. .++.|+.||.|++.
T Consensus 38 ~Vng~~vd----------l~~~L~~~d~v~ii 59 (60)
T PF02824_consen 38 KVNGQLVD----------LDHPLEDGDVVEII 59 (60)
T ss_dssp EETTEEEE----------TTSBB-SSEEEEEE
T ss_pred EEcCEECC----------CCCCcCCCCEEEEE
Confidence 69998875 89999999999874
No 94
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=40.20 E-value=31 Score=26.43 Aligned_cols=26 Identities=19% Similarity=0.447 Sum_probs=20.4
Q ss_pred eeCCEEEeeccccccccCCCceecCCCEEEEe
Q 011530 171 SIKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (483)
Q Consensus 171 ~vnGk~v~~~q~~~r~~~~~~~v~~GD~I~v~ 202 (483)
.+||+.+...+ -.++.|+.||+|++.
T Consensus 35 ~vNg~iv~r~~------~~~~~l~~gD~vei~ 60 (66)
T PRK05659 35 EVNGEIVPRSQ------HASTALREGDVVEIV 60 (66)
T ss_pred EECCeEeCHHH------cCcccCCCCCEEEEE
Confidence 58998886433 378899999999885
No 95
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=34.24 E-value=81 Score=24.16 Aligned_cols=26 Identities=12% Similarity=0.349 Sum_probs=19.1
Q ss_pred eeCCEEEeeccccccccCCCceecCCCEEEEe
Q 011530 171 SIKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (483)
Q Consensus 171 ~vnGk~v~~~q~~~r~~~~~~~v~~GD~I~v~ 202 (483)
.+||+.+...+ -.++.|+.||.|.+.
T Consensus 34 ~vNg~~v~~~~------~~~~~L~~gD~V~ii 59 (65)
T cd00565 34 ALNGEIVPRSE------WASTPLQDGDRIEIV 59 (65)
T ss_pred EECCEEcCHHH------cCceecCCCCEEEEE
Confidence 58999886322 133789999999886
No 96
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=30.61 E-value=1.9e+02 Score=23.08 Aligned_cols=22 Identities=9% Similarity=0.176 Sum_probs=18.4
Q ss_pred eeCCEEEeeccccccccCCCceecCCCEEEEe
Q 011530 171 SIKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (483)
Q Consensus 171 ~vnGk~v~~~q~~~r~~~~~~~v~~GD~I~v~ 202 (483)
.+||+.+. .++.|+.||.|.+.
T Consensus 55 avN~~~v~----------~~~~l~dgDeVai~ 76 (82)
T PLN02799 55 ALNEEYTT----------ESAALKDGDELAII 76 (82)
T ss_pred EECCEEcC----------CCcCcCCCCEEEEe
Confidence 58998764 67899999999986
No 97
>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=28.60 E-value=1.1e+02 Score=23.82 Aligned_cols=25 Identities=16% Similarity=0.399 Sum_probs=20.1
Q ss_pred eeCCEEEeeccccccccCCCceecCCCEEEEe
Q 011530 171 SIKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (483)
Q Consensus 171 ~vnGk~v~~~q~~~r~~~~~~~v~~GD~I~v~ 202 (483)
.|||+.++. + -.++.|+.||.|.+.
T Consensus 47 ~vN~~~v~~-~------~~~~~l~~gD~V~i~ 71 (77)
T PF02597_consen 47 AVNGEIVPD-D------GLDTPLKDGDEVAIL 71 (77)
T ss_dssp EETTEEEGG-G------TTTSBEETTEEEEEE
T ss_pred EECCEEcCC-c------cCCcCcCCCCEEEEE
Confidence 689999873 2 248899999999886
No 98
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=26.96 E-value=54 Score=22.71 Aligned_cols=22 Identities=27% Similarity=0.212 Sum_probs=19.7
Q ss_pred HHHhccCCCHHHHHHHHHcCCE
Q 011530 115 YICRELNLPPLFVADLIHFGAV 136 (483)
Q Consensus 115 ~Ls~~l~~Sr~~~~~lI~~G~V 136 (483)
=+++.+++|++.+.++++.|.+
T Consensus 6 e~a~~lgis~~ti~~~~~~g~i 27 (49)
T TIGR01764 6 EAAEYLGVSKDTVYRLIHEGEL 27 (49)
T ss_pred HHHHHHCCCHHHHHHHHHcCCC
Confidence 4567789999999999999988
No 99
>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=26.69 E-value=1.8e+02 Score=23.46 Aligned_cols=22 Identities=14% Similarity=0.282 Sum_probs=17.8
Q ss_pred eeCCEEEeeccccccccCCCceecCCCEEEEe
Q 011530 171 SIKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (483)
Q Consensus 171 ~vnGk~v~~~q~~~r~~~~~~~v~~GD~I~v~ 202 (483)
..+|+.|. .++.|+.||+|+|.
T Consensus 53 ~~~gq~Vg----------l~~~L~d~DvVeI~ 74 (75)
T cd01666 53 KHSPQRVG----------LDHVLEDEDVVQIV 74 (75)
T ss_pred cCCCeECC----------CCCEecCCCEEEEe
Confidence 35777764 89999999999985
No 100
>PRK06437 hypothetical protein; Provisional
Probab=26.35 E-value=66 Score=25.13 Aligned_cols=22 Identities=18% Similarity=0.194 Sum_probs=18.9
Q ss_pred eeCCEEEeeccccccccCCCceecCCCEEEEe
Q 011530 171 SIKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (483)
Q Consensus 171 ~vnGk~v~~~q~~~r~~~~~~~v~~GD~I~v~ 202 (483)
.+||+.+. .++.|+.||.|++.
T Consensus 40 ~vNg~iv~----------~~~~L~dgD~Veiv 61 (67)
T PRK06437 40 IVNGSPVL----------EDHNVKKEDDVLIL 61 (67)
T ss_pred EECCEECC----------CceEcCCCCEEEEE
Confidence 58999885 78899999999886
No 101
>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=25.87 E-value=53 Score=31.77 Aligned_cols=24 Identities=17% Similarity=0.099 Sum_probs=20.3
Q ss_pred cceeEEEEEeeec----CcceEEEeCCC
Q 011530 448 VAIGLQACHISWD----DGECCYEARSP 471 (483)
Q Consensus 448 ~~I~LhA~~~~~~----g~~~~f~a~~P 471 (483)
..++|||++++|. |+...|+|++|
T Consensus 196 ~rl~Lha~~L~F~hP~t~~~~~~~a~~~ 223 (223)
T cd02563 196 HRLLLAATRLEFTHPVTGERLLIEAPLD 223 (223)
T ss_pred ccceeecCeeEeeCCCCCCeEEEEccCC
Confidence 4699999999994 67888999876
No 102
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=23.62 E-value=36 Score=34.31 Aligned_cols=28 Identities=18% Similarity=0.031 Sum_probs=22.7
Q ss_pred cceeEEEEEeeec----CcceEEEeCCCcccc
Q 011530 448 VAIGLQACHISWD----DGECCYEARSPWWRC 475 (483)
Q Consensus 448 ~~I~LhA~~~~~~----g~~~~f~a~~P~W~~ 475 (483)
..++|||++++|. |+...|++++|++..
T Consensus 261 ~r~~Lha~~l~f~~p~~~~~~~~~a~~p~~~~ 292 (299)
T TIGR00005 261 DRQALHAYELGFIHPATGEILEFEAPLPADLV 292 (299)
T ss_pred cchhhccCeeeccCCCCCCEEEEEcCChHHHH
Confidence 4689999999994 566789999997644
No 103
>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=23.49 E-value=36 Score=26.28 Aligned_cols=18 Identities=28% Similarity=0.445 Sum_probs=12.5
Q ss_pred eecCeEEEEeCCCCCccC
Q 011530 222 AVTESHVVLDKPAGTSVG 239 (483)
Q Consensus 222 yED~~liVvNKPaGl~v~ 239 (483)
|-...+|.+|||+|-.+|
T Consensus 39 ~i~~GvinlDKP~gPtSH 56 (59)
T PF08068_consen 39 YIKYGVINLDKPSGPTSH 56 (59)
T ss_dssp HHHTEEEEEEE-SSS-HH
T ss_pred HHhCCcEEeeCCCCCCcc
Confidence 345679999999997765
No 104
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=22.53 E-value=32 Score=35.34 Aligned_cols=28 Identities=18% Similarity=-0.031 Sum_probs=22.8
Q ss_pred cceeEEEEEeeec----CcceEEEeCCCcccc
Q 011530 448 VAIGLQACHISWD----DGECCYEARSPWWRC 475 (483)
Q Consensus 448 ~~I~LhA~~~~~~----g~~~~f~a~~P~W~~ 475 (483)
..++|||++++|. |+...|++++|++..
T Consensus 275 ~r~~Lha~~l~f~hP~~~~~~~~~a~~p~~~~ 306 (325)
T PRK11180 275 DRQALHATMLRLYHPITGIEMEWHAPLPQDMV 306 (325)
T ss_pred chhhhhcceeEeeCCCCCCeEEEECCChHHHH
Confidence 3589999999993 566789999998754
No 105
>PF13021 DUF3885: Domain of unknown function (DUF3885)
Probab=22.49 E-value=1.1e+02 Score=21.47 Aligned_cols=24 Identities=25% Similarity=0.375 Sum_probs=20.7
Q ss_pred CCceEEEEEcCHHHHHHHHHHhhc
Q 011530 272 CTEGCVVLARTQEYCSIFHRKIRE 295 (483)
Q Consensus 272 ~TSGLLL~Ak~~~aa~~L~~~f~~ 295 (483)
+-.|+-|+|+|++..+.|-+.|.+
T Consensus 5 DDRGcdvia~~~~~i~~ly~~y~~ 28 (38)
T PF13021_consen 5 DDRGCDVIANNKERIRPLYEKYND 28 (38)
T ss_pred cCCCcEEeeCCHHHHHHHHHHHHH
Confidence 567999999999999999887754
No 106
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=21.61 E-value=80 Score=21.65 Aligned_cols=22 Identities=14% Similarity=0.191 Sum_probs=19.7
Q ss_pred HHHhccCCCHHHHHHHHHcCCE
Q 011530 115 YICRELNLPPLFVADLIHFGAV 136 (483)
Q Consensus 115 ~Ls~~l~~Sr~~~~~lI~~G~V 136 (483)
=+++.+++|++.+.++++.|.+
T Consensus 5 e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 5 EAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHCcCHHHHHHHHHcCCC
Confidence 3677789999999999999998
No 107
>PRK07440 hypothetical protein; Provisional
Probab=21.38 E-value=94 Score=24.53 Aligned_cols=26 Identities=15% Similarity=0.252 Sum_probs=20.6
Q ss_pred eeCCEEEeeccccccccCCCceecCCCEEEEe
Q 011530 171 SIKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (483)
Q Consensus 171 ~vnGk~v~~~q~~~r~~~~~~~v~~GD~I~v~ 202 (483)
.+||+.+...+ -.++.|+.||.|+|-
T Consensus 39 ~~N~~iv~r~~------w~~~~L~~gD~IEIv 64 (70)
T PRK07440 39 EYNGEILHRQF------WEQTQVQPGDRLEIV 64 (70)
T ss_pred EECCEEeCHHH------cCceecCCCCEEEEE
Confidence 58999987443 377889999999875
No 108
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=21.09 E-value=2.1e+02 Score=22.87 Aligned_cols=23 Identities=13% Similarity=0.206 Sum_probs=18.2
Q ss_pred eeCCEEEeeccccccccCCCceecCCCEEEEec
Q 011530 171 SIKGKTVREAQKTFRITHVDQIVEAGTYLRVHV 203 (483)
Q Consensus 171 ~vnGk~v~~~q~~~r~~~~~~~v~~GD~I~v~~ 203 (483)
.||+..+. .++.|+.||.|.+..
T Consensus 54 aVN~~~~~----------~~~~l~dgDeVai~P 76 (81)
T PRK11130 54 AVNQTLVS----------FDHPLTDGDEVAFFP 76 (81)
T ss_pred EECCEEcC----------CCCCCCCCCEEEEeC
Confidence 58887653 678999999999873
No 109
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=20.18 E-value=1e+02 Score=24.04 Aligned_cols=26 Identities=15% Similarity=0.256 Sum_probs=20.4
Q ss_pred eeCCEEEeeccccccccCCCceecCCCEEEEe
Q 011530 171 SIKGKTVREAQKTFRITHVDQIVEAGTYLRVH 202 (483)
Q Consensus 171 ~vnGk~v~~~q~~~r~~~~~~~v~~GD~I~v~ 202 (483)
.+||+.+...+ -.++.|+.||.|+|-
T Consensus 36 ~vN~~iv~r~~------w~~~~L~~gD~iEIv 61 (67)
T PRK07696 36 ERNKDILQKDD------HTDTSVFDGDQIEIV 61 (67)
T ss_pred EECCEEeCHHH------cCceecCCCCEEEEE
Confidence 58999997544 366889999999874
Done!