Query 037167
Match_columns 353
No_of_seqs 322 out of 1856
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 09:21:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037167.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037167hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0564 RluA Pseudouridylate s 100.0 1E-64 2.2E-69 471.8 29.2 272 1-324 13-289 (289)
2 PRK11025 23S rRNA pseudouridyl 100.0 3.2E-62 7E-67 463.5 31.3 285 1-335 20-315 (317)
3 PRK11180 rluD 23S rRNA pseudou 100.0 1.7E-61 3.7E-66 460.3 32.7 295 1-336 18-315 (325)
4 TIGR00005 rluA_subfam pseudour 100.0 3.2E-61 7E-66 454.4 32.5 288 1-333 6-298 (299)
5 cd02558 PSRA_1 PSRA_1: Pseudou 100.0 1.9E-55 4.1E-60 402.8 25.2 242 28-323 3-245 (246)
6 PRK11112 tRNA pseudouridine sy 100.0 1.7E-53 3.7E-58 392.3 23.8 228 65-339 2-240 (257)
7 cd02563 PseudoU_synth_TruC tRN 100.0 1.2E-51 2.6E-56 373.0 24.1 212 65-323 1-223 (223)
8 PRK10158 23S rRNA/tRNA pseudou 100.0 1.4E-51 3.1E-56 371.1 22.6 204 65-323 14-218 (219)
9 TIGR01621 RluA-like pseudourid 100.0 5.3E-51 1.2E-55 366.7 24.9 203 65-331 2-204 (217)
10 cd02557 PseudoU_synth_ScRIB2 P 100.0 1.9E-50 4.1E-55 362.5 22.3 204 57-326 7-212 (213)
11 KOG1919 RNA pseudouridylate sy 100.0 1E-42 2.3E-47 329.7 26.0 296 2-335 45-354 (371)
12 cd02869 PseudoU_synth_RluCD_li 100.0 6E-41 1.3E-45 294.6 19.8 166 74-264 1-166 (185)
13 PRK10839 16S rRNA pseudouridyl 100.0 1.8E-41 3.8E-46 308.6 14.1 204 1-262 1-204 (232)
14 PRK10700 23S rRNA pseudouridyl 100.0 1.1E-36 2.4E-41 284.1 17.1 207 1-260 3-212 (289)
15 PRK10475 23S rRNA pseudouridin 100.0 9.5E-36 2.1E-40 277.0 15.6 198 1-259 7-204 (290)
16 cd02550 PseudoU_synth_Rsu_Rlu_ 100.0 2.6E-35 5.7E-40 251.5 15.3 147 74-256 1-147 (154)
17 COG1187 RsuA 16S rRNA uridine- 100.0 7.9E-35 1.7E-39 262.3 14.8 209 1-261 3-213 (248)
18 PF00849 PseudoU_synth_2: RNA 100.0 5.3E-33 1.2E-37 239.5 16.7 157 73-250 1-164 (164)
19 cd02556 PseudoU_synth_RluB Pse 100.0 8.2E-34 1.8E-38 245.3 11.1 145 74-261 2-146 (167)
20 cd02870 PseudoU_synth_RsuA_lik 100.0 4.8E-34 1E-38 241.6 6.6 140 74-257 1-140 (146)
21 cd02553 PseudoU_synth_RsuA Pse 100.0 5.7E-33 1.2E-37 239.9 9.5 144 74-264 2-146 (167)
22 cd02566 PseudoU_synth_RluE Pse 100.0 5.5E-31 1.2E-35 227.8 9.7 156 74-262 1-159 (168)
23 PRK11394 23S rRNA pseudouridin 100.0 4.5E-30 9.8E-35 228.4 10.2 148 73-264 40-200 (217)
24 cd02555 PSSA_1 PSSA_1: Pseudou 100.0 8.4E-30 1.8E-34 221.5 8.1 142 73-263 5-155 (177)
25 TIGR00093 pseudouridine syntha 99.9 1.1E-27 2.4E-32 198.0 7.3 111 121-264 1-111 (128)
26 cd02554 PseudoU_synth_RluF Pse 99.9 3E-26 6.6E-31 196.3 9.0 138 74-261 2-139 (164)
27 cd00165 S4 S4/Hsp/ tRNA synthe 99.2 1.6E-10 3.5E-15 83.8 8.6 70 1-78 1-70 (70)
28 cd02868 PseudoU_synth_hTruB2_l 99.1 2E-10 4.2E-15 103.3 7.3 75 73-177 1-75 (226)
29 PF01479 S4: S4 domain; Inter 98.9 4.9E-09 1.1E-13 71.1 5.9 48 1-49 1-48 (48)
30 TIGR02988 YaaA_near_RecF S4 do 98.6 1.5E-07 3.2E-12 66.7 6.2 50 1-51 9-58 (59)
31 smart00363 S4 S4 RNA-binding d 98.1 8.5E-06 1.8E-10 56.7 6.7 52 1-53 1-52 (60)
32 cd02572 PseudoU_synth_hDyskeri 98.0 3.1E-05 6.8E-10 67.6 8.0 70 72-178 2-71 (182)
33 TIGR01017 rpsD_bact ribosomal 97.9 2.6E-05 5.6E-10 69.2 6.9 54 1-55 90-143 (200)
34 COG1188 Ribosome-associated he 97.9 2.1E-05 4.6E-10 60.8 5.4 50 1-53 9-59 (100)
35 CHL00113 rps4 ribosomal protei 97.9 2.9E-05 6.2E-10 68.7 6.0 53 1-54 89-141 (201)
36 PLN00051 RNA-binding S4 domain 97.8 6.1E-05 1.3E-09 69.6 6.9 52 1-54 192-243 (267)
37 PRK00989 truB tRNA pseudouridi 97.8 8.4E-05 1.8E-09 66.8 7.4 70 73-178 10-79 (230)
38 TIGR03069 PS_II_S4 photosystem 97.7 5.9E-05 1.3E-09 69.6 6.0 52 1-54 184-235 (257)
39 cd00506 PseudoU_synth_TruB_lik 97.7 0.00014 3.1E-09 64.8 8.0 69 73-178 1-69 (210)
40 PRK04099 truB tRNA pseudouridi 97.7 0.00013 2.9E-09 67.2 8.0 70 72-178 2-71 (273)
41 TIGR00431 TruB tRNA pseudourid 97.7 0.00017 3.8E-09 64.1 8.0 69 73-178 3-71 (209)
42 PRK00020 truB tRNA pseudouridi 97.6 0.00021 4.5E-09 64.8 8.1 70 72-178 10-79 (244)
43 PRK10348 ribosome-associated h 97.6 0.00016 3.5E-09 59.4 6.6 50 1-52 9-58 (133)
44 PRK05327 rpsD 30S ribosomal pr 97.6 0.00012 2.6E-09 65.1 6.0 52 1-53 93-144 (203)
45 TIGR00478 tly hemolysin TlyA f 97.6 0.00013 2.9E-09 66.0 6.0 51 2-53 1-51 (228)
46 PRK02484 truB tRNA pseudouridi 97.5 0.00033 7.1E-09 65.6 8.0 70 72-178 3-72 (294)
47 PRK14123 tRNA pseudouridine sy 97.5 0.00034 7.3E-09 65.9 8.0 70 72-178 3-72 (305)
48 PRK02193 truB tRNA pseudouridi 97.5 0.00031 6.8E-09 65.2 7.7 68 74-178 2-69 (279)
49 PRK03287 truB tRNA pseudouridi 97.5 0.00033 7.1E-09 65.6 7.8 71 71-178 8-78 (298)
50 PRK00130 truB tRNA pseudouridi 97.5 0.00039 8.4E-09 65.0 8.2 70 72-178 2-71 (290)
51 cd02573 PseudoU_synth_EcTruB P 97.5 0.00044 9.4E-09 64.3 8.2 69 73-178 1-69 (277)
52 PRK05389 truB tRNA pseudouridi 97.5 0.00041 9E-09 65.2 8.1 70 72-178 13-82 (305)
53 PRK14846 truB tRNA pseudouridi 97.5 0.00044 9.6E-09 65.4 8.2 70 72-178 3-72 (345)
54 PRK14124 tRNA pseudouridine sy 97.5 0.00048 1E-08 64.8 8.2 70 72-178 3-72 (308)
55 PRK02755 truB tRNA pseudouridi 97.5 0.00046 1E-08 64.6 8.0 69 72-178 3-71 (295)
56 PRK04270 H/ACA RNA-protein com 97.4 0.00044 9.6E-09 65.2 7.9 71 71-178 21-91 (300)
57 PRK05033 truB tRNA pseudouridi 97.4 0.00053 1.1E-08 64.6 8.2 70 72-178 10-79 (312)
58 COG0522 RpsD Ribosomal protein 97.4 0.00029 6.3E-09 62.4 6.1 42 14-55 106-147 (205)
59 PRK01851 truB tRNA pseudouridi 97.4 0.0006 1.3E-08 64.0 8.5 70 72-178 16-85 (303)
60 PRK01550 truB tRNA pseudouridi 97.4 0.00057 1.2E-08 64.3 8.0 70 72-178 2-71 (304)
61 PRK01528 truB tRNA pseudouridi 97.4 0.0006 1.3E-08 63.7 8.0 70 72-178 3-72 (292)
62 COG2302 Uncharacterized conser 97.4 0.0003 6.4E-09 63.3 5.3 52 1-54 181-232 (257)
63 PRK14122 tRNA pseudouridine sy 97.3 0.001 2.2E-08 62.7 7.9 68 74-178 3-70 (312)
64 PRK11507 ribosome-associated p 97.2 0.00099 2.1E-08 48.3 5.8 51 2-53 13-63 (70)
65 TIGR00425 CBF5 rRNA pseudourid 97.2 0.00097 2.1E-08 63.4 7.5 70 72-178 34-103 (322)
66 COG1189 Predicted rRNA methyla 97.2 0.00066 1.4E-08 61.0 5.7 51 1-52 3-53 (245)
67 PRK04642 truB tRNA pseudouridi 97.2 0.0013 2.8E-08 61.7 7.8 70 72-178 10-79 (300)
68 COG0130 TruB Pseudouridine syn 97.1 0.0023 4.9E-08 59.2 8.0 69 73-178 16-84 (271)
69 cd01291 PseudoU_synth PseudoU_ 97.0 0.0046 9.9E-08 47.2 8.0 20 116-135 24-43 (87)
70 cd02867 PseudoU_synth_TruB_4 P 96.7 0.0062 1.3E-07 57.4 8.0 78 73-178 1-98 (312)
71 PRK04051 rps4p 30S ribosomal p 96.6 0.0056 1.2E-07 53.0 6.4 50 2-52 104-155 (177)
72 COG2501 S4-like RNA binding pr 96.5 0.009 2E-07 43.6 5.8 51 2-53 13-63 (73)
73 PF13275 S4_2: S4 domain; PDB: 96.4 0.00073 1.6E-08 48.5 -0.2 50 2-52 9-58 (65)
74 PRK04313 30S ribosomal protein 96.0 0.021 4.5E-07 51.6 6.9 72 1-79 38-109 (237)
75 PLN00036 40S ribosomal protein 95.7 0.032 7E-07 51.0 7.0 72 1-79 42-113 (261)
76 PLN00189 40S ribosomal protein 95.7 0.025 5.4E-07 49.5 5.7 38 15-52 122-159 (194)
77 PTZ00223 40S ribosomal protein 95.6 0.036 7.8E-07 51.0 6.8 72 1-79 39-110 (273)
78 TIGR01018 rpsD_arch ribosomal 95.6 0.028 6.1E-07 47.9 5.7 38 15-52 117-156 (162)
79 PTZ00118 40S ribosomal protein 95.5 0.04 8.7E-07 50.4 6.8 70 2-78 43-112 (262)
80 PTZ00155 40S ribosomal protein 94.5 0.04 8.6E-07 47.9 3.7 38 14-51 119-158 (181)
81 COG1471 RPS4A Ribosomal protei 93.6 0.1 2.2E-06 46.7 4.4 66 7-79 47-112 (241)
82 PRK13354 tyrosyl-tRNA syntheta 90.8 0.38 8.1E-06 47.6 5.1 46 2-48 344-389 (410)
83 PRK05912 tyrosyl-tRNA syntheta 89.0 1 2.2E-05 44.5 6.5 43 2-45 344-386 (408)
84 PF14451 Ub-Mut7C: Mut7-C ubiq 88.8 0.51 1.1E-05 35.5 3.2 26 27-53 50-75 (81)
85 PRK01777 hypothetical protein; 86.4 0.92 2E-05 35.2 3.5 30 25-55 48-77 (95)
86 KOG2559 Predicted pseudouridin 86.3 0.75 1.6E-05 41.5 3.4 22 117-138 90-111 (318)
87 PF01509 TruB_N: TruB family p 84.2 1.2 2.5E-05 37.6 3.5 43 116-178 7-49 (149)
88 COG4332 Uncharacterized protei 73.7 4.2 9.2E-05 35.0 3.6 51 1-53 139-189 (203)
89 cd00754 MoaD Ubiquitin domain 69.2 10 0.00023 27.6 4.6 25 27-52 50-74 (80)
90 COG0162 TyrS Tyrosyl-tRNA synt 68.9 6.3 0.00014 38.8 4.1 40 3-43 338-377 (401)
91 PRK11130 moaD molybdopterin sy 68.7 15 0.00033 27.2 5.4 43 3-52 31-75 (81)
92 PRK06437 hypothetical protein; 64.9 11 0.00024 27.0 3.8 24 28-52 38-61 (67)
93 PRK08364 sulfur carrier protei 59.0 13 0.00029 26.8 3.4 25 27-52 40-64 (70)
94 cd00565 ThiS ThiaminS ubiquiti 58.3 11 0.00023 26.7 2.7 24 28-52 32-59 (65)
95 PLN02799 Molybdopterin synthas 58.0 33 0.00071 25.3 5.5 24 28-52 53-76 (82)
96 TIGR01682 moaD molybdopterin c 57.5 23 0.0005 26.0 4.5 24 28-52 51-74 (80)
97 KOG2529 Pseudouridine synthase 56.9 15 0.00032 35.8 4.2 75 71-182 67-141 (395)
98 COG2104 ThiS Sulfur transfer p 53.4 16 0.00035 26.4 2.9 25 28-52 35-62 (68)
99 PF02824 TGS: TGS domain; Int 50.8 15 0.00031 25.7 2.3 23 28-51 36-58 (60)
100 KOG3301 Ribosomal protein S4 [ 50.7 16 0.00034 31.0 2.9 31 15-45 110-140 (183)
101 TIGR01687 moaD_arch MoaD famil 49.8 38 0.00083 25.3 4.8 24 28-52 57-82 (88)
102 PRK06488 sulfur carrier protei 49.3 24 0.00052 24.9 3.3 24 29-52 33-59 (65)
103 TIGR01683 thiS thiamine biosyn 48.8 25 0.00055 24.7 3.4 25 28-52 31-58 (64)
104 PF02597 ThiS: ThiS family; I 48.6 21 0.00045 25.7 3.0 26 27-52 44-71 (77)
105 PRK06944 sulfur carrier protei 47.5 28 0.0006 24.4 3.4 25 28-52 32-59 (65)
106 COG4043 Preprotein translocase 45.9 24 0.00052 27.5 3.0 36 17-52 8-43 (111)
107 PRK05659 sulfur carrier protei 45.1 28 0.00061 24.4 3.2 25 28-52 33-60 (66)
108 PF08068 DKCLD: DKCLD (NUC011) 43.3 12 0.00025 26.2 0.9 16 71-86 41-56 (59)
109 PRK07440 hypothetical protein; 41.6 36 0.00078 24.6 3.3 25 28-52 37-64 (70)
110 KOG4655 U3 small nucleolar rib 36.6 29 0.00064 29.5 2.4 35 16-50 121-157 (181)
111 PRK08053 sulfur carrier protei 35.6 51 0.0011 23.3 3.3 25 28-52 33-60 (66)
112 PF00498 FHA: FHA domain; Int 35.0 38 0.00082 23.6 2.5 26 26-51 41-67 (68)
113 cd01764 Urm1 Urm1-like ubuitin 33.8 48 0.001 25.5 3.0 48 3-52 34-88 (94)
114 PRK07696 sulfur carrier protei 31.7 51 0.0011 23.5 2.7 25 28-52 34-61 (67)
115 KOG2623 Tyrosyl-tRNA synthetas 29.9 80 0.0017 31.0 4.4 37 3-40 401-437 (467)
116 cd01666 TGS_DRG_C TGS_DRG_C: 29.6 52 0.0011 24.2 2.5 22 30-52 53-74 (75)
117 PF03658 Ub-RnfH: RnfH family 28.9 28 0.0006 26.3 1.0 30 25-55 45-74 (84)
118 KOG4837 Uncharacterized conser 27.5 96 0.0021 27.6 4.1 37 15-51 152-188 (248)
119 cd06919 Asp_decarbox Aspartate 26.8 49 0.0011 26.4 2.0 43 26-72 65-109 (111)
120 PRK06083 sulfur carrier protei 25.8 78 0.0017 23.8 2.9 25 28-52 51-78 (84)
121 cd01668 TGS_RelA_SpoT TGS_RelA 25.5 1E+02 0.0022 20.6 3.4 23 28-51 36-58 (60)
122 PF13021 DUF3885: Domain of un 23.8 1E+02 0.0022 19.6 2.7 24 127-150 5-28 (38)
123 cd01616 TGS The TGS domain, na 21.6 1.3E+02 0.0029 19.4 3.3 22 29-51 37-58 (60)
124 TIGR00223 panD L-aspartate-alp 21.2 67 0.0015 26.2 1.8 44 26-73 66-111 (126)
125 PRK05449 aspartate alpha-decar 20.7 71 0.0015 26.0 1.9 43 26-72 66-110 (126)
No 1
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1e-64 Score=471.80 Aligned_cols=272 Identities=38% Similarity=0.580 Sum_probs=227.4
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCC--CC--CCCCccEEEECCcEEE
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKE--PD--VPYLLEVLYEDDDLIA 76 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~--~~--~~~~~~Ilyed~~~iv 76 (353)
+||..||.+ +.. .||+.+.++|++|.|+|||+++. ++++|..||+|.+....... .. .+.+++|||||++++|
T Consensus 13 ~rld~~L~~-l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED~~llV 89 (289)
T COG0564 13 QRLDKFLAK-LLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDEDLLV 89 (289)
T ss_pred CCHHHHHHH-ccC-cCHHHHHHHHHCCCEEECCEEcc-CCeeeCCCCEEEEecccccccccccccCCCccEEEecCCEEE
Confidence 478888888 665 79999999999999999999997 99999999999885432111 11 1234789999999999
Q ss_pred EECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccccccc
Q 037167 77 LNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVID 156 (353)
Q Consensus 77 vnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~~~~ 156 (353)
||||+||+|||++.+...|+++++..+.... ..++++||||||+||||||+|||..++..|+++|++
T Consensus 90 vnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~-------~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~------ 156 (289)
T COG0564 90 VNKPAGLVVHPGGGHHEGTLVNALLRHCQDG-------VERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQ------ 156 (289)
T ss_pred EECCCCCcCcCCCCCccHhHHHHHHHhcccc-------CCceeeeccCCCCCceEEEEECCHHHHHHHHHHHhc------
Confidence 9999999999998888899999887664322 257899999999999999999999999999999987
Q ss_pred cchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCC-CCcceeEEEEEEEeCCCCeEEEEEE
Q 037167 157 ADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPS-GKPALSKVDVLERDVQRNCTLVQVE 235 (353)
Q Consensus 157 ~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~-gk~a~t~~~vl~~~~~~~~sll~~~ 235 (353)
+.+.|+|+|+|.|.++++++.|+.|+++..... ....+.... |++|.|.|+++++... ..||++|+
T Consensus 157 ----------r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~--~~~~v~~~~~gk~A~T~~~~l~~~~~-~~tlv~~~ 223 (289)
T COG0564 157 ----------RKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNR--KKMAVVKEGSGKPAITHYEVLERFGD-NYTLVELK 223 (289)
T ss_pred ----------CcCcEEEEEEEECcccCCCCEEeeeeecCCcCC--ceEEEeccCCCCceEEEEEehhccCC-ceEEEEEE
Confidence 589999999999999988899999999875433 223333333 8999999999998742 26999999
Q ss_pred eCCCchhHHHHHHHHcCCCeeCCcCCCCCCCCCCCCccccccccccCCCCCCCCCCCCccccccccceeeeeecCCCCCE
Q 037167 236 IQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEV 315 (353)
Q Consensus 236 l~TGR~HQIR~hla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~l~LHa~~l~f~hp~~~~~ 315 (353)
|.||||||||+||+++||||+||.+||.... ....+. .|++|||++|.|.||.+++.
T Consensus 224 ~~TGRTHQIRVHl~~lghPI~GD~~Yg~~~~-------------~~~~~~----------~r~~LHA~~l~f~hp~t~~~ 280 (289)
T COG0564 224 PETGRTHQIRVHLAHLGHPIVGDPLYGGKDK-------------SAGAGL----------KRQALHAYKLSFTHPLTGEE 280 (289)
T ss_pred eCCCCHhHHHHHHHHCCCCeeCCcccCCchh-------------hcccCc----------chhhhhhceeEccCCCCCCE
Confidence 9999999999999999999999999996310 000011 24899999999999999999
Q ss_pred EEEEeCCch
Q 037167 316 IKITAPLPS 324 (353)
Q Consensus 316 ~~~~aplP~ 324 (353)
+.|++|+|.
T Consensus 281 ~~~~a~~p~ 289 (289)
T COG0564 281 LEFEAPLPE 289 (289)
T ss_pred EEEecCCCC
Confidence 999999984
No 2
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=100.00 E-value=3.2e-62 Score=463.50 Aligned_cols=285 Identities=30% Similarity=0.414 Sum_probs=227.3
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCC----CC-------CCCCccEEE
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKE----PD-------VPYLLEVLY 69 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~----~~-------~~~~~~Ily 69 (353)
+||.+||...+.. .||+.++++|++|.|+|||+++ ++++.|+.||.|.+......+ |. ....++|+|
T Consensus 20 ~RLd~~L~~~~~~-~sr~~i~~li~~G~V~VNg~~v-~~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~~~~~Ily 97 (317)
T PRK11025 20 QRIDNFLRTQLKG-VPKSMIYRILRKGEVRVNKKRI-KPEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKVAALADVILY 97 (317)
T ss_pred chHHHHHHHhccc-CCHHHHHHHHHcCCEEECCEEc-CcccccCCCCEEEeCCCCccccccccccccccccccCcCCEEE
Confidence 5888999988865 6999999999999999999998 589999999999885322111 11 113568999
Q ss_pred ECCcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhh
Q 037167 70 EDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFA 149 (353)
Q Consensus 70 ed~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~ 149 (353)
||++++|||||+|++|||+... ..++.+.+...... ...+++|||||++||||||||||+.+++.|+++|+
T Consensus 98 ed~~~lvvnKP~gl~~~~~~~~-~~~~~~~~~~~~~~--------~~~~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~ 168 (317)
T PRK11025 98 EDDHILVLNKPSGTAVHGGSGL-SFGVIEGLRALRPE--------ARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLR 168 (317)
T ss_pred ECCCEEEEECCCCCcCcCCCCC-CccHHHHHHHhccC--------CCcCceeCCCCCCCceEEEEEcCHHHHHHHHHHHH
Confidence 9999999999999999998654 34555655432110 13467899999999999999999999999999998
Q ss_pred ccccccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEeCCCCe
Q 037167 150 DKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNC 229 (353)
Q Consensus 150 ~g~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~~~~~~ 229 (353)
+ +.|+|+|+|+|.|.+..+.+.++.|+.+...... .......++|++|.|+|++++.. .++
T Consensus 169 ~----------------~~v~K~Y~a~v~G~~~~~~~~i~~~i~~~~~~~~-~~~~~~~~~gk~a~T~~~~l~~~--~~~ 229 (317)
T PRK11025 169 E----------------KGMQKDYLALVRGQWQSHVKVVQAPLLKNILQSG-ERIVRVSQEGKPSETRFKVEERY--AFA 229 (317)
T ss_pred h----------------CCccEEEEEEEeCcccCCCceEecccccCcccCC-ceEEecCCCCccceEEEEEeEEc--CCc
Confidence 6 5899999999999998778899999986532211 12222346799999999999876 478
Q ss_pred EEEEEEeCCCchhHHHHHHHHcCCCeeCCcCCCCCCCCCCCCccccccccccCCCCCCCCCCCCccccccccceeeeeec
Q 037167 230 TLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSH 309 (353)
Q Consensus 230 sll~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~l~LHa~~l~f~h 309 (353)
|||+|+|.||||||||+|||++||||+||.+||...... .+. ..+.. +++|||++|+|.|
T Consensus 230 sLv~~~~~TGRtHQIRvhla~lG~PIlGD~~Yg~~~~~~---------~~~-~~~~~----------r~~LHa~~l~f~~ 289 (317)
T PRK11025 230 TLVRASPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQ---------QLT-GTGLN----------RLFLHAAALKFTH 289 (317)
T ss_pred EEEEEEeCCCCHHHHHHHHHHCCCCEECCcccCCcccch---------hhh-ccCCc----------chhhhcCcceeeC
Confidence 999999999999999999999999999999998531100 000 00111 4899999999999
Q ss_pred CCCCCEEEEEeCCchhHHHHHHhccc
Q 037167 310 PTTNEVIKITAPLPSVLKTREEGREV 335 (353)
Q Consensus 310 p~~~~~~~~~aplP~~f~~~~~~l~~ 335 (353)
|.+|+.+.|+||+|++|..+++.|..
T Consensus 290 P~~~~~~~~~aplP~~~~~~l~~l~~ 315 (317)
T PRK11025 290 PGTGEVMRIEAPLDEQLKRCLQKLRN 315 (317)
T ss_pred CCCCCeEEEEcCCCHHHHHHHHHHhh
Confidence 99999999999999999999876643
No 3
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=100.00 E-value=1.7e-61 Score=460.26 Aligned_cols=295 Identities=28% Similarity=0.406 Sum_probs=234.2
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCCC---CCCCCccEEEECCcEEEE
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEP---DVPYLLEVLYEDDDLIAL 77 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~~---~~~~~~~Ilyed~~~ivv 77 (353)
+||.++|.+.+.. +||+.++++|++|+|+|||+++..+++.|..||.|.+...+..+. ..+.+++|||||++++||
T Consensus 18 ~RLd~~L~~~~~~-~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~iiyed~~~lvv 96 (325)
T PRK11180 18 QRLDQALAELFPD-YSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQDIPLDIVYEDDDILVI 96 (325)
T ss_pred ccHHHHHHhhccc-cCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEeeccccccCCCCCCCCCcEEEECCCEEEE
Confidence 5889999998875 699999999999999999999877899999999999865332211 123457899999999999
Q ss_pred ECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcccccccc
Q 037167 78 NKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDA 157 (353)
Q Consensus 78 nKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~~~~~ 157 (353)
|||+|++|||++.....|+.+.+......... ..++.+|||||++||||||||||.+++..|+++|++
T Consensus 97 nKP~gl~~~~~~~~~~~tl~~~l~~~~~~~~~-----~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~------- 164 (325)
T PRK11180 97 NKPRDLVVHPGAGNPDGTVLNALLHYYPPIAD-----VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQK------- 164 (325)
T ss_pred ECCCCCeEeCCCCCCCCcHHHHHHHHhhhccC-----CcccceeccCCCCCceeEEEECCHHHHHHHHHHHHh-------
Confidence 99999999998776667888888765432111 245789999999999999999999999999999986
Q ss_pred chhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEeCCCCeEEEEEEeC
Q 037167 158 DSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQ 237 (353)
Q Consensus 158 ~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~~~~~~sll~~~l~ 237 (353)
+.|.|+|+|+|.|.++. ++.++.|+.+.... .......+.|++|.|.|+++... .+.|+++|+|.
T Consensus 165 ---------~~v~K~Y~A~v~G~~~~-~~~i~~~l~~~~~~---~~~~~~~~~gk~a~T~~~~l~~~--~~~slv~~~~~ 229 (325)
T PRK11180 165 ---------REITREYEAVAIGHMTA-GGTVDEPISRHPTK---RTHMAVHPMGKPAVTHYRIMEHF--RVHTRLRLRLE 229 (325)
T ss_pred ---------CCcceEEEEEEecCCCC-CCEEECceecCCCc---CcEEEeCCCCcEEeEEEEEeEEc--CCeEEEEEEeC
Confidence 58999999999999864 57889998764211 11222346789999999999876 47899999999
Q ss_pred CCchhHHHHHHHHcCCCeeCCcCCCCCCCCCCCCccccccccccCCCCCCCCCCCCccccccccceeeeeecCCCCCEEE
Q 037167 238 SGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEVIK 317 (353)
Q Consensus 238 TGR~HQIR~hla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~l~LHa~~l~f~hp~~~~~~~ 317 (353)
||||||||+|||++||||+||.+||...... . ...........++ .+++|||++|+|.||.+|+.+.
T Consensus 230 TGRtHQIRvhla~lG~PI~GD~~Yg~~~~~~--~-~~~~~~~~~~~~~----------~r~~Lha~~l~f~hP~~~~~~~ 296 (325)
T PRK11180 230 TGRTHQIRVHMAHITHPLVGDQVYGGRPRPP--K-GASEEFISTLRKF----------DRQALHATMLRLYHPITGIEME 296 (325)
T ss_pred CCCHHHHHHHHHhCCCCEeCccccCCCcccc--c-ccchhhhhhcccc----------chhhhhcceeEeeCCCCCCeEE
Confidence 9999999999999999999999998532110 0 0000000000011 2489999999999999999999
Q ss_pred EEeCCchhHHHHHHhcccc
Q 037167 318 ITAPLPSVLKTREEGREVD 336 (353)
Q Consensus 318 ~~aplP~~f~~~~~~l~~~ 336 (353)
|+||+|++|..+++.|+.+
T Consensus 297 ~~a~~p~~~~~~~~~l~~~ 315 (325)
T PRK11180 297 WHAPLPQDMVELIEALRAD 315 (325)
T ss_pred EECCChHHHHHHHHHhhhh
Confidence 9999999999999877543
No 4
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=100.00 E-value=3.2e-61 Score=454.39 Aligned_cols=288 Identities=38% Similarity=0.553 Sum_probs=231.7
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCCC---CCCCCccEEEECCcEEEE
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEP---DVPYLLEVLYEDDDLIAL 77 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~~---~~~~~~~Ilyed~~~ivv 77 (353)
+||.+||...+.. +||+.++++|++|.|+|||+++.++++.|+.||.|.+......++ .....++|+|||++|+||
T Consensus 6 ~rLd~~L~~~~~~-~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~I~i~~~~~~~~~~~~~~~~~~i~~ed~~~lvv 84 (299)
T TIGR00005 6 QRLDDFLASLLPD-LSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDEDIIVI 84 (299)
T ss_pred hhHHHHHHHhccc-CCHHHHHHHHHCCcEEECCEeccCcccCCCCCCEEEEecCCcccccCCccCCCccEEEeCCCEEEE
Confidence 5899999998864 799999999999999999976667899999999999854322211 122357899999999999
Q ss_pred ECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcccccccc
Q 037167 78 NKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDA 157 (353)
Q Consensus 78 nKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~~~~~ 157 (353)
|||+|++||+++.....|+.+.+..++.... ....+++|||||++||||||||+|+++++.|+++|.+
T Consensus 85 nKP~g~~~~~~~~~~~~tl~~~l~~~~~~~~-----~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~------- 152 (299)
T TIGR00005 85 NKPSGLVVHPGGGNPFGTVLNALLAHCPPIA-----GVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKN------- 152 (299)
T ss_pred ECCCCCeEeCCCCCCcccHHHHHHHhccccc-----CCCcCceECCCCCCCceEEEEEcCHHHHHHHHHHHHh-------
Confidence 9999999999887767889988875543111 1246889999999999999999999999999999976
Q ss_pred chhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEee--CCCCCcceeEEEEEEEeCCCCeEEEEEE
Q 037167 158 DSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVA--SPSGKPALSKVDVLERDVQRNCTLVQVE 235 (353)
Q Consensus 158 ~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~--~~~gk~a~t~~~vl~~~~~~~~sll~~~ 235 (353)
+.|.|+|+|+|.|.++.+.+.++.|+.+.... .+.... ..+|++|.|.|+++... .++|+++|+
T Consensus 153 ---------~~v~K~Y~a~v~g~~~~~~~~i~~~l~~~~~~---~~~~~~~~~~~~k~a~t~~~~l~~~--~~~slv~~~ 218 (299)
T TIGR00005 153 ---------RTVTKEYVALVHGQFDSGGGTVDAPLGRVPNN---RGLMAVHPSSEGKPAVTHFRVLERF--GNASLVECE 218 (299)
T ss_pred ---------CCcceEEEEEEeccccCCCCEEeCceecCCCC---CceEEEecCCCCCeeeEEEEEeEEc--CCeEEEEEE
Confidence 58999999999999988888999999764321 122222 23589999999999875 468999999
Q ss_pred eCCCchhHHHHHHHHcCCCeeCCcCCCCCCCCCCCCccccccccccCCCCCCCCCCCCccccccccceeeeeecCCCCCE
Q 037167 236 IQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEV 315 (353)
Q Consensus 236 l~TGR~HQIR~hla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~l~LHa~~l~f~hp~~~~~ 315 (353)
|.|||+||||+||+++||||+||.+||...... . . .... ++..+++|||++|+|.||.+++.
T Consensus 219 l~tGR~HQIR~hla~lG~pI~gD~~Yg~~~~~~--~-~-----~~~~----------~~~~r~~Lha~~l~f~~p~~~~~ 280 (299)
T TIGR00005 219 LETGRTHQIRVHLQYLGHPLAGDPLYGNKPVPG--N-N-----LNGL----------LNFDRQALHAYELGFIHPATGEI 280 (299)
T ss_pred eCCCChHHHHHHHHHCCCcEeCccccCCccccc--c-c-----cccc----------cCCcchhhccCeeeccCCCCCCE
Confidence 999999999999999999999999999532100 0 0 0000 01124899999999999999999
Q ss_pred EEEEeCCchhHHHHHHhc
Q 037167 316 IKITAPLPSVLKTREEGR 333 (353)
Q Consensus 316 ~~~~aplP~~f~~~~~~l 333 (353)
+.|+||+|++|..+++.+
T Consensus 281 ~~~~a~~p~~~~~~~~~~ 298 (299)
T TIGR00005 281 LEFEAPLPADLVLLLEAL 298 (299)
T ss_pred EEEEcCChHHHHHHHHhh
Confidence 999999999999988754
No 5
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.
Probab=100.00 E-value=1.9e-55 Score=402.83 Aligned_cols=242 Identities=26% Similarity=0.398 Sum_probs=191.8
Q ss_pred CEEECCEEccCCCceecCCCEEEEeeCCCCCCCCCCCccEEEECCcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhc
Q 037167 28 QITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQ 107 (353)
Q Consensus 28 ~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~~~~~~~~~Ilyed~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~ 107 (353)
.|..||+++ +++++++.||.|.+......++..+..++|||||++++|||||+|++|||++.+...|+++.+.....
T Consensus 3 ~~~~ng~~~-~~~~~l~~gd~i~~~~~~~~~~~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~~-- 79 (246)
T cd02558 3 VVDADGEPL-DPDSPYRPGTFVWYYRELPDEPPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTG-- 79 (246)
T ss_pred eECCCCcCC-CCCceecCCCEEEEeCCCCCCCCCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHhC--
Confidence 456899998 58999999999988643333444455689999999999999999999999887777888887764332
Q ss_pred CCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccccccccchhhhhhccceEEEEEEEEEeeeeCCCce-
Q 037167 108 SSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKV- 186 (353)
Q Consensus 108 ~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~- 186 (353)
...+++|||||++||||||||||+++++.++.+|++ +.++|+|+|+|.|.++.+..
T Consensus 80 -------~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~----------------~~v~K~YlA~v~G~~~~~~~~ 136 (246)
T cd02558 80 -------NPDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFAR----------------REVSKTYEAVAPYVPALTFPL 136 (246)
T ss_pred -------CCcccccccCCCCceeEEEEEcCHHHHHHHHHHHHc----------------CCccEEEEEEEecCCCCCCCc
Confidence 135789999999999999999999999999999976 58999999999998864333
Q ss_pred EEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEeCCCCeEEEEEEeCCCchhHHHHHHHHcCCCeeCCcCCCCCCC
Q 037167 187 IIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQ 266 (353)
Q Consensus 187 ~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~~~~~~sll~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg~~~~ 266 (353)
.++.++.+... .... ....+++.|.|+|++++.. .++|+++|+|.|||+||||+||+++||||+||.+||....
T Consensus 137 ~~~~~i~~~~~--~~~~--~~~~~~~~a~T~~~~l~~~--~~~slv~~~l~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~ 210 (246)
T cd02558 137 TVRSRIVKGRG--FFQA--REVEGEPNAETRIELLARR--GGWGLYRLSPHTGKTHQLRVHMAALGVPILNDPFYPVLLD 210 (246)
T ss_pred ceeccccccCC--ccee--eccCCCCCceEEEEEEEec--CCeEEEEEEeCCCCHHHHHHHHHHCCCcccCCccCCCCCc
Confidence 45656654321 1111 1224557899999999875 3789999999999999999999999999999999985311
Q ss_pred CCCCCccccccccccCCCCCCCCCCCCccccccccceeeeeecCCCCCEEEEEeCCc
Q 037167 267 PKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEVIKITAPLP 323 (353)
Q Consensus 267 ~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~l~LHa~~l~f~hp~~~~~~~~~aplP 323 (353)
... ..+.+ +++|||++|+|.||.|++.+.|+||+|
T Consensus 211 ~~~-------------~~~~~---------~~~Lha~~l~f~hP~t~~~~~~~~~~~ 245 (246)
T cd02558 211 KDP-------------DDFSR---------PLQLLAKELEFTDPLTGRPRRFESGRS 245 (246)
T ss_pred ccc-------------ccccc---------CchhhhcccCccCCCCCCEEEEecCCC
Confidence 000 00111 379999999999999999999999987
No 6
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=100.00 E-value=1.7e-53 Score=392.27 Aligned_cols=228 Identities=31% Similarity=0.422 Sum_probs=177.4
Q ss_pred ccEEEECCcEEEEECCCCCccccCCCCCcch--HHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHH
Q 037167 65 LEVLYEDDDLIALNKPSGLQVLPGGLFQQRT--VLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKT 142 (353)
Q Consensus 65 ~~Ilyed~~~ivvnKP~G~~~~~~~~~~~~t--l~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~ 142 (353)
++|||||++|||||||+|++||++......+ +...+.... ...+++|||||++||||||||||+++++
T Consensus 2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~----------~~~~~~VHRLDr~TSGlll~Ak~~~~~~ 71 (257)
T PRK11112 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQI----------GQHVFTAHRLDRPTSGVLLMALSSEVAR 71 (257)
T ss_pred CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHh----------CCCceeeccCCCCCeeEEEEECCHHHHH
Confidence 5699999999999999999999875333332 333333221 1357799999999999999999999999
Q ss_pred HHHHHhhccccccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEE
Q 037167 143 CIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLE 222 (353)
Q Consensus 143 ~L~~~f~~g~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~ 222 (353)
.|+++|++ +.|.|+|+|+|.|.++. ++.++.|+...... ..........++++|.|.|++++
T Consensus 72 ~L~~~f~~----------------~~v~K~Y~Alv~G~~~~-~~~i~~~l~~~~~~-~~~~~~~~~~~~k~a~T~~~~l~ 133 (257)
T PRK11112 72 LLAQQFEQ----------------HQIQKTYHAIVRGWLME-EAVLDYPLKEELDK-IADKFAREDKAPQPAVTHYRGLA 133 (257)
T ss_pred HHHHHHHh----------------CCcceEEEEEEEeEeCC-CCeEeeeeeecccc-cceeecccCCCCeEeEEEEEEEE
Confidence 99999987 58999999999999864 56788888764211 11112222346899999999997
Q ss_pred EeC---------CCCeEEEEEEeCCCchhHHHHHHHHcCCCeeCCcCCCCCCCCCCCCccccccccccCCCCCCCCCCCC
Q 037167 223 RDV---------QRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVP 293 (353)
Q Consensus 223 ~~~---------~~~~sll~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~ 293 (353)
... ..+.||++|+|.||||||||+||+++||||+||.+||...... .+....+.
T Consensus 134 ~~~~~~~~~~~~~~~~slv~i~~~TGRtHQIRvhla~lG~PIvGD~~Yg~~~~~~---------~~~~~~~~-------- 196 (257)
T PRK11112 134 TVEMPVATGRYPTTRYSLVELEPKTGRKHQLRRHMAHLRHPIIGDTKHGDLRQNR---------SLAEHFGC-------- 196 (257)
T ss_pred EecccccccccCCCCeEEEEEEcCCCChHHHHHHHHHcCCCEeCCcccCCcccch---------hhhhccCC--------
Confidence 641 2357999999999999999999999999999999998531110 00000011
Q ss_pred ccccccccceeeeeecCCCCCEEEEEeCCchhHHHHHHhccccccc
Q 037167 294 GDCGYYLHAYQLFLSHPTTNEVIKITAPLPSVLKTREEGREVDKSV 339 (353)
Q Consensus 294 ~~~~l~LHa~~l~f~hp~~~~~~~~~aplP~~f~~~~~~l~~~~~~ 339 (353)
.+++|||++|+|.||.+++.+.|+||+|++|+.+++.++++.-+
T Consensus 197 --~rl~LHA~~L~F~hP~t~e~~~~~a~~p~~~~~~~~~~~~~~~~ 240 (257)
T PRK11112 197 --SRLMLHASELSLTHPFTGEPLTITAGLDETWQQLLSQFGWRGLL 240 (257)
T ss_pred --cchhHhhCccCccCCCCCCEEEEEcCCCHHHHHHHHHcCCCCCC
Confidence 24899999999999999999999999999999999999887544
No 7
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.
Probab=100.00 E-value=1.2e-51 Score=373.01 Aligned_cols=212 Identities=33% Similarity=0.483 Sum_probs=163.3
Q ss_pred ccEEEECCcEEEEECCCCCccccCCCCCcc--hHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHH
Q 037167 65 LEVLYEDDDLIALNKPSGLQVLPGGLFQQR--TVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKT 142 (353)
Q Consensus 65 ~~Ilyed~~~ivvnKP~G~~~~~~~~~~~~--tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~ 142 (353)
++|||||++++|||||+|++||+++..... +++..+.... ...+++|||||++||||||||+|+++++
T Consensus 1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~----------~~~~~~vhRLD~~TSGlll~Ak~~~~~~ 70 (223)
T cd02563 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQL----------GQHVYPVHRLDRPTSGVLLFALSSEVAR 70 (223)
T ss_pred CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHc----------CCCcccccCCCCCCeEEEEEEECHHHHH
Confidence 369999999999999999999987543222 2333332221 1357899999999999999999999999
Q ss_pred HHHHHhhccccccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEE
Q 037167 143 CIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLE 222 (353)
Q Consensus 143 ~L~~~f~~g~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~ 222 (353)
.|+++|++ +.|+|+|+|+|.|.+++ ++.++.|+.+..... ..........++.|.|.|+++.
T Consensus 71 ~l~~~f~~----------------~~v~K~Y~alv~G~~~~-~~~i~~~l~~~~~~~-~~~~~~~~~~~~~a~t~~~~l~ 132 (223)
T cd02563 71 KLGEQFTE----------------HRVHKTYLAVVRGYVPE-SGTIDYPLSEELDKL-ADKFASDDKAPQAATTHYRLLA 132 (223)
T ss_pred HHHHHHhc----------------CceeEEEEEEEECccCC-CCeEEEeeeeCCCcc-ceEEeecCCCCceeEEEEEEee
Confidence 99999987 58999999999999875 678888887643211 1111122346789999999997
Q ss_pred EeC---------CCCeEEEEEEeCCCchhHHHHHHHHcCCCeeCCcCCCCCCCCCCCCccccccccccCCCCCCCCCCCC
Q 037167 223 RDV---------QRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVP 293 (353)
Q Consensus 223 ~~~---------~~~~sll~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~ 293 (353)
... ..++||++|+|.||||||||+||+++||||+||.+||....... +.+..+.
T Consensus 133 ~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~---------~~~~~~~-------- 195 (223)
T cd02563 133 VEELPVVVGKYPTSRYSLVELTPHTGRKHQLRRHLAHIRHPIIGDTTHGDGRHNRF---------FREHFGC-------- 195 (223)
T ss_pred ecccccccccCCCCCeEEEEEEeCCCCHHHHHHHHHHcCCCeeCCcccCCcccChh---------HHhhcCC--------
Confidence 531 23589999999999999999999999999999999995321100 0111011
Q ss_pred ccccccccceeeeeecCCCCCEEEEEeCCc
Q 037167 294 GDCGYYLHAYQLFLSHPTTNEVIKITAPLP 323 (353)
Q Consensus 294 ~~~~l~LHa~~l~f~hp~~~~~~~~~aplP 323 (353)
.+++|||++|+|+||.||+.+.|+||+|
T Consensus 196 --~rl~Lha~~L~F~hP~t~~~~~~~a~~~ 223 (223)
T cd02563 196 --HRLLLAATRLEFTHPVTGERLLIEAPLD 223 (223)
T ss_pred --ccceeecCeeEeeCCCCCCeEEEEccCC
Confidence 2489999999999999999999999987
No 8
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=100.00 E-value=1.4e-51 Score=371.10 Aligned_cols=204 Identities=32% Similarity=0.487 Sum_probs=167.9
Q ss_pred ccEEEECCcEEEEECCCCCccccCCC-CCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHH
Q 037167 65 LEVLYEDDDLIALNKPSGLQVLPGGL-FQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTC 143 (353)
Q Consensus 65 ~~Ilyed~~~ivvnKP~G~~~~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~ 143 (353)
++|||||++|+|||||+|++||++.. ....++.+.+...+ ..+++|||||++||||||||+|.++++.
T Consensus 14 ~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~-----------~~~~~vhRLDr~TSGlll~Akt~~~~~~ 82 (219)
T PRK10158 14 LVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY-----------PQAESVHRLDMATSGVIVVALTKAAERE 82 (219)
T ss_pred CCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC-----------CCCCEECCCCCCCceEEEEECCHHHHHH
Confidence 67999999999999999999998753 33457777665332 2477999999999999999999999999
Q ss_pred HHHHhhccccccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEE
Q 037167 144 IAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLER 223 (353)
Q Consensus 144 L~~~f~~g~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~ 223 (353)
|+++|++ ++|.|+|+|+|.|.++.+.+.++.|+........ ...+..++|+.|.|.|++++.
T Consensus 83 l~~~f~~----------------~~v~K~Yla~v~G~~~~~~~~i~~~i~~~~~~~~--~~~~~~~~gk~a~t~~~~l~~ 144 (219)
T PRK10158 83 LKRQFRE----------------REPKKQYVARVWGHPSPAEGLVDLPLICDWPNRP--KQKVCYETGKPAQTEYEVVEY 144 (219)
T ss_pred HHHHHHh----------------CCccEEEEEEEecccCCCCcEEecceecCCCCCc--eEEecCCCCceeeEEEEEEEE
Confidence 9999986 5899999999999998888899999876432211 122233578999999999987
Q ss_pred eCCCCeEEEEEEeCCCchhHHHHHHHHcCCCeeCCcCCCCCCCCCCCCccccccccccCCCCCCCCCCCCccccccccce
Q 037167 224 DVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAY 303 (353)
Q Consensus 224 ~~~~~~sll~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~l~LHa~ 303 (353)
.. ...++++|+|+|||+||||+||+++||||+||.+||..... .... +++|||+
T Consensus 145 ~~-~~~sll~~~~~TGRtHQIR~hla~lG~PIvGD~~Yg~~~~~---------------~~~~----------r~~Lha~ 198 (219)
T PRK10158 145 AA-DNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEAR---------------AMAP----------RLLLHAE 198 (219)
T ss_pred cC-CCCEEEEEEeCCCCHHHHHHHHHHCCCcEECCcccCCcccc---------------cccc----------chhhhhC
Confidence 64 23589999999999999999999999999999999952110 0011 4899999
Q ss_pred eeeeecCCCCCEEEEEeCCc
Q 037167 304 QLFLSHPTTNEVIKITAPLP 323 (353)
Q Consensus 304 ~l~f~hp~~~~~~~~~aplP 323 (353)
+|.|.||.+++.+.|.||.|
T Consensus 199 ~l~f~~P~~~~~~~~~a~~~ 218 (219)
T PRK10158 199 MLTITHPAYGNSMTFKAPAD 218 (219)
T ss_pred ccCccCCCCCCeEEEEeCCC
Confidence 99999999999999999976
No 9
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621. This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.
Probab=100.00 E-value=5.3e-51 Score=366.69 Aligned_cols=203 Identities=28% Similarity=0.419 Sum_probs=166.8
Q ss_pred ccEEEECCcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHH
Q 037167 65 LEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCI 144 (353)
Q Consensus 65 ~~Ilyed~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L 144 (353)
++|||||++|+|||||+|++||+++. ..++.+.+..... ...+++|||||++||||||||+|+++++.|
T Consensus 2 ~~ilyed~~~lvvnKP~Gl~v~~~~~--~~~l~~~l~~~~~---------~~~~~~VhRLDr~TSGlll~Ak~~~~~~~L 70 (217)
T TIGR01621 2 FEILFTHPDFLLINKHPGISVHKDDG--ETGLLQEVATQLG---------VGQVWLVHRLDKMTSGILLLALNAESASEL 70 (217)
T ss_pred ceEEEeCCCEEEEECCCCCeECCCCC--cChHHHHHHHhcC---------CCCccEecCCCCCCceEEEEEcCHHHHHHH
Confidence 56999999999999999999998754 3456655543211 245889999999999999999999999999
Q ss_pred HHHhhccccccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEe
Q 037167 145 AGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERD 224 (353)
Q Consensus 145 ~~~f~~g~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~ 224 (353)
+++|++ +.|+|+|+|+|.|.++.+++.++.++.... .....+....+++|.|+|+++...
T Consensus 71 ~~~~~~----------------~~v~K~YlAlV~g~~~~~~~~i~~~~~~~~----~~~~~~~~~~~k~a~t~~~~~~~~ 130 (217)
T TIGR01621 71 SQGFAK----------------RKIEKTYLALSSKKPKKKQGLICGDMEKSR----RGSWKLVNSQENPAITRFFSASAA 130 (217)
T ss_pred HHHHhc----------------CCccEEEEEEEeccccCCCCEEeCCcccCC----CCCEEEeCCCCCceeEEEEEEEEc
Confidence 999987 589999999999999888888988886532 112223345789999999999876
Q ss_pred CCCCeEEEEEEeCCCchhHHHHHHHHcCCCeeCCcCCCCCCCCCCCCccccccccccCCCCCCCCCCCCcccccccccee
Q 037167 225 VQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQ 304 (353)
Q Consensus 225 ~~~~~sll~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~l~LHa~~ 304 (353)
.+.++++|+|.|||+||||+||+++||||+||.+||... . .. +++|||++
T Consensus 131 --~~~slv~~~~~TGR~HQIRvhla~lG~PIlGD~~Yg~~~--~----------------~~----------~~~Lha~~ 180 (217)
T TIGR01621 131 --TGLRLFILKPHTGKTHQLRVAMKSLGSPILGDPLYGTTD--E----------------SD----------RGYLHAFA 180 (217)
T ss_pred --CCeEEEEEEeCCCCHHHHHHHHHHCCCceeCCcccCCCC--C----------------cc----------CceeeeeE
Confidence 368999999999999999999999999999999999521 0 01 38999999
Q ss_pred eeeecCCCCCEEEEEeCCchhHHHHHH
Q 037167 305 LFLSHPTTNEVIKITAPLPSVLKTREE 331 (353)
Q Consensus 305 l~f~hp~~~~~~~~~aplP~~f~~~~~ 331 (353)
|.|+| +|+.+.|+|| |++|..++.
T Consensus 181 l~f~~--~~~~~~~~~~-~~~~~~~~~ 204 (217)
T TIGR01621 181 LRFDY--QNEVIQWLCD-PRQFQKWHE 204 (217)
T ss_pred eEEEE--CCeEEEEEEC-cHHHHHHHH
Confidence 99998 4899999999 777755543
No 10
>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=1.9e-50 Score=362.45 Aligned_cols=204 Identities=36% Similarity=0.541 Sum_probs=172.0
Q ss_pred CCCCCC-CCccEEEECCcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEE
Q 037167 57 KEPDVP-YLLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCA 135 (353)
Q Consensus 57 ~~~~~~-~~~~Ilyed~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~a 135 (353)
+||+++ ..++|||||++++|+|||+|++|++++.....++.+.|..... ...+++|||||++||||||||
T Consensus 7 ~~~~~~~~~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~---------~~~~~~vhRLD~~TSGlllla 77 (213)
T cd02557 7 HEPPVTNDPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYG---------LTELRPCHRLDRLTSGLLLFA 77 (213)
T ss_pred cCCCCCCCCCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcC---------CCCccCccCCCCCCceEEEEE
Confidence 455544 4688999999999999999999999877667788888875432 135789999999999999999
Q ss_pred eChHHHHHHHHHhhccccccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccce-EeeCCCCCcc
Q 037167 136 KTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGL-YVASPSGKPA 214 (353)
Q Consensus 136 k~~~~~~~L~~~f~~g~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~-~~~~~~gk~a 214 (353)
||+++++.|+++|++ +.++|+|+|+|.|.++.+.+.++.|+.+... ..++ ......+++|
T Consensus 78 k~~~~~~~l~~~f~~----------------~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~---~~~~~~~~~~~~~~a 138 (213)
T cd02557 78 KTSQTASRLQQQIRS----------------REVKKEYLARVKGEFPDGEVVVDQPIGLVSP---KGGLRNDVDEKGKDA 138 (213)
T ss_pred CCHHHHHHHHHHHHc----------------CCccEEEEEEEeCcCCCCCeEEecceeccCc---CCceeeccCCCCcee
Confidence 999999999999986 5899999999999998888999999876432 2222 1224568899
Q ss_pred eeEEEEEEEeCCCCeEEEEEEeCCCchhHHHHHHHHcCCCeeCCcCCCCCCCCCCCCccccccccccCCCCCCCCCCCCc
Q 037167 215 LSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPG 294 (353)
Q Consensus 215 ~t~~~vl~~~~~~~~sll~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~ 294 (353)
.|.|+++......+.++++|+|.|||+||||+||+++||||+||.+||..
T Consensus 139 ~t~~~~~~~~~~~~~slv~v~~~TGR~HQIR~hla~lG~PIlGD~~Yg~~------------------------------ 188 (213)
T cd02557 139 RTIFKRLSYNGDLNTSVVLCKPITGRTHQIRVHLQYLGHPIVNDPIYNNL------------------------------ 188 (213)
T ss_pred eEEEEEEEEcCCCCeEEEEEEeCCCCHHHHHHHHHHCCCCCcCccccCCc------------------------------
Confidence 99999998764347899999999999999999999999999999999840
Q ss_pred cccccccceeeeeecCCCCCEEEEEeCCchhH
Q 037167 295 DCGYYLHAYQLFLSHPTTNEVIKITAPLPSVL 326 (353)
Q Consensus 295 ~~~l~LHa~~l~f~hp~~~~~~~~~aplP~~f 326 (353)
+++|||++|.|+ .+.|++|+|.+|
T Consensus 189 --~l~Lha~~l~f~------~~~~~~~~p~~~ 212 (213)
T cd02557 189 --GIYLHALRYEGP------DWSYETELPDWA 212 (213)
T ss_pred --ChhhhhccCcCc------cEEEEeCCCccc
Confidence 389999999996 799999999886
No 11
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=100.00 E-value=1e-42 Score=329.70 Aligned_cols=296 Identities=29% Similarity=0.394 Sum_probs=218.3
Q ss_pred cHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCCCCC-CCCccEEEECCcEEEEECC
Q 037167 2 TLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDV-PYLLEVLYEDDDLIALNKP 80 (353)
Q Consensus 2 ~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~~~~-~~~~~Ilyed~~~ivvnKP 80 (353)
.++++++++|.. .++...+..|+.|.|++||+.+. .++.++.+|.+... ....+|.. ..++.|+|||++|+|||||
T Consensus 45 ~~~~~~~~ef~~-~~~~~~~~~i~~g~v~~n~~~~~-v~~i~k~~d~l~~~-vhrh~p~~~~~~~~Iv~ed~~~vVvnKP 121 (371)
T KOG1919|consen 45 KLVDVFVSEFRL-RERAYYESAIKLGRVTVNGEQVR-VSLIVKNGDVLCHT-VHRHEPPVAYLPIRIVFEDKDYVVVNKP 121 (371)
T ss_pred chHHHHHHHHhc-CchHhhhhhhhcCceEECcEeee-eEEEeccCCEEEEe-eccCCCCccccccceEEecCCEEEEeCC
Confidence 468999999986 47777889999999999999995 89999999999763 33344443 3578999999999999999
Q ss_pred CCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccccccccchh
Q 037167 81 SGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADST 160 (353)
Q Consensus 81 ~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~~~~~~~~ 160 (353)
+|++|||++.+..+++...+..... ...+.+|||||+.|||||+||++++++..+.++|++
T Consensus 122 ~gipVhp~g~~~~n~i~~~l~~~~~---------~~~~~~~hRLDr~tSGllvlAkt~~~~~~~~~~~r~---------- 182 (371)
T KOG1919|consen 122 HGIPVHPTGRYRENTITKILAALHK---------VEGLRPCHRLDRLTSGLLVLAKTKEAADKFHEVLRK---------- 182 (371)
T ss_pred CCCceeccCccccccchHHHHHhcc---------ccccccccccCccccceEEEEechhHhHHHHHHHhc----------
Confidence 9999999999988988887765421 255789999999999999999999999999999986
Q ss_pred hhhhccceEEEEE-EEEEeeeeC-CCceEEecceeeecCCCcccceEeeCC----CCCcceeEEEEEEEeCCCCeEEEEE
Q 037167 161 VMELSQRKITKIY-RALVHGIVD-EDKVIIKQPIGIVRYPGVAKGLYVASP----SGKPALSKVDVLERDVQRNCTLVQV 234 (353)
Q Consensus 161 ~~~~~~~~v~K~Y-~alv~G~~~-~~~~~i~~~i~~~~~~~~~~~~~~~~~----~gk~a~t~~~vl~~~~~~~~sll~~ 234 (353)
+.+.|.| .|-|.|.++ .....+..|++....+ .+..+.-... .++.|.|.|+++.++ ...++|+|
T Consensus 183 ------~~~~k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~~-~~~~l~~~~~~~~~~~k~a~T~~~~~~~~--~~ss~V~~ 253 (371)
T KOG1919|consen 183 ------RTVKKEYVVARVEGPFPVVGEVEIKEPIGEEERP-LRMGLNAVGVRDEVAAKDAKTLFKVLSYD--GGSSLVEC 253 (371)
T ss_pred ------ccceeEEEEEEEeccCCCCceEEeCCCccccccc-cceEeeecccccccccccceeEEEEcccC--CceEEEEe
Confidence 5899999 799999988 5667777777664320 1112222222 379999999999987 58899999
Q ss_pred EeCCCchhHHHHHHHHcCCCeeCCcCCCCCCCCCCCCcc--ccccccccCCCCCCCCCCCCccccccccceeeeeecCCC
Q 037167 235 EIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSE--FADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTT 312 (353)
Q Consensus 235 ~l~TGR~HQIR~hla~lG~PIvGD~~Yg~~~~~~~~~~~--~~~~~~~~~~~~~r~~~~~~~~~~l~LHa~~l~f~hp~~ 312 (353)
.|+||||||||+||+++|+||+||.+|+........+.. ...... .... .........++++-... .||.+
T Consensus 254 ~PlTGRtHQIRvHlq~lG~PI~gD~~Y~~~~~~~~~P~~g~~~~~~~---~~~e---~~~~~~~~~~~~~~~~~-~~~~~ 326 (371)
T KOG1919|consen 254 RPLTGRTHQIRVHLQYLGHPIAGDPKYGNHIVWAGLPFTGREGTAKK---KSLE---EEIQRLIDVHLLENWLG-FHPRT 326 (371)
T ss_pred eccCCcHHHHHHHHHHhCCCcCCCcccccccccccCCCCCCCCCccc---cCcc---ccccccchhhccccccc-ccccc
Confidence 999999999999999999999999999753211100000 000000 0000 00011112344444333 67777
Q ss_pred C---CEEEEEeCCc--hhHHHHHHhccc
Q 037167 313 N---EVIKITAPLP--SVLKTREEGREV 335 (353)
Q Consensus 313 ~---~~~~~~aplP--~~f~~~~~~l~~ 335 (353)
+ +.+...++.| .|+..++..+.-
T Consensus 327 ~~~~~~~~~~C~~~~~~Dl~~~lha~~y 354 (371)
T KOG1919|consen 327 GPLIEELCQECKVPIDNDLELFLHALKY 354 (371)
T ss_pred ccchhhhhhhCCCCCCchHhHhhhhccc
Confidence 7 5677777777 777777776643
No 12
>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=6e-41 Score=294.55 Aligned_cols=166 Identities=42% Similarity=0.626 Sum_probs=134.0
Q ss_pred EEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcccc
Q 037167 74 LIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTS 153 (353)
Q Consensus 74 ~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~ 153 (353)
++|+|||+|++|++.......++.+.+........ ....+.+|||||++||||||||+|+++++.|+.+|++
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~v~RLD~~tsGlll~ak~~~~~~~l~~~~~~--- 72 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLG-----EEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKE--- 72 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhcC-----CCCcCceecccCCCCceEEEEEcCHHHHHHHHHHHhc---
Confidence 58999999999999887767777776522111111 1256889999999999999999999999999999976
Q ss_pred ccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEeCCCCeEEEE
Q 037167 154 VIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQ 233 (353)
Q Consensus 154 ~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~~~~~~sll~ 233 (353)
+.+.|+|+|+|.|.++.+.+.++.|+..... ..........+++.+.|+|+++... .++|+++
T Consensus 73 -------------~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~t~~~~l~~~--~~~s~~~ 135 (185)
T cd02869 73 -------------RKVKKTYLALVDGKPPEDEGTIDAPLGRKKR--KKRARVVVSEDGKPAITHYKVLERF--GNVTLVE 135 (185)
T ss_pred -------------CceeEEEEEEEeCCCCCCccEEecccccCCc--cCceEEEECCCCeEEEEEEEEEEEc--CCcEEEE
Confidence 5899999999999998888888777754311 1111222346788999999999865 3789999
Q ss_pred EEeCCCchhHHHHHHHHcCCCeeCCcCCCCC
Q 037167 234 VEIQSGRPHQIRIHLAFLGHPLLGDPLYVAG 264 (353)
Q Consensus 234 ~~l~TGR~HQIR~hla~lG~PIvGD~~Yg~~ 264 (353)
|+|.|||+||||+||+++|+||+||.+||..
T Consensus 136 ~~l~tGR~HQIR~hl~~~G~pIvGD~~Yg~~ 166 (185)
T cd02869 136 LQLETGRTHQIRVHLASIGHPIVGDPKYGGK 166 (185)
T ss_pred EEeCcCCccHHHHHHHHCCCCEeCccccCCc
Confidence 9999999999999999999999999999953
No 13
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=100.00 E-value=1.8e-41 Score=308.57 Aligned_cols=204 Identities=24% Similarity=0.255 Sum_probs=157.9
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCCCCCCCCccEEEECCcEEEEECC
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALNKP 80 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~~~~~~~~~Ilyed~~~ivvnKP 80 (353)
|||.+||++.+. +||+.++++|++|.|+|||+++.+++++|+.||.|.+...+.. + .++++++|+|||
T Consensus 1 ~rld~~L~~~~~--~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~I~l~~~~~~-~---------~~~~~~lvvnKP 68 (232)
T PRK10839 1 MRLDKFISQQLG--VSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDGNPLA-Q---------QHGPRYFMLNKP 68 (232)
T ss_pred CcHHHHHHHcCC--CCHHHHHHHHHcCeEEECCEEeccCCcCcCCCCEEEECCEEcc-c---------CCCCEEEEEECC
Confidence 688889988773 6999999999999999999998668999999999987532111 1 134689999999
Q ss_pred CCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccccccccchh
Q 037167 81 SGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADST 160 (353)
Q Consensus 81 ~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~~~~~~~~ 160 (353)
+||+||++... ..|+.+.+.... ...+.+|||||++||||||||||+++++.|..
T Consensus 69 ~G~~~~~~~~~-~~tl~~~l~~~~----------~~~~~~v~RLD~~TSGlll~ak~~~~~~~l~~-------------- 123 (232)
T PRK10839 69 QGYVCSTDDPD-HPTVLYFLDEPV----------AYKLHAAGRLDIDTTGLVLMTDDGQWSHRITS-------------- 123 (232)
T ss_pred CCeEecccCCC-CCeEEEeccccc----------ccCceecCCCCCCceeEEEEecCHHHHHHHhC--------------
Confidence 99999987543 356554432110 13577999999999999999999999888873
Q ss_pred hhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEeCCCCeEEEEEEeCCCc
Q 037167 161 VMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGR 240 (353)
Q Consensus 161 ~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~~~~~~sll~~~l~TGR 240 (353)
+.+.++|+|+|.+.+.+..+.. .....++. .+|+.|.|+|.+++... .++++|+|.|||
T Consensus 124 ----~~~~i~K~Y~a~i~~~i~~~~~-----------~~~~~~~~---~~g~~a~t~~~~~~~~~---~sll~~~l~tGR 182 (232)
T PRK10839 124 ----PRHHCEKTYLVTLESPVADDTA-----------EQFAKGVQ---LHNEKDLTKPAVLEVIT---PTQVRLTISEGR 182 (232)
T ss_pred ----CCCCCCeEEEEEECCCCCHHHH-----------HHHHCCeE---ECCCcccccccEEEEec---CCEEEEEEEcCc
Confidence 2368999999988777653211 01122222 25788999999998763 389999999999
Q ss_pred hhHHHHHHHHcCCCeeCCcCCC
Q 037167 241 PHQIRIHLAFLGHPLLGDPLYV 262 (353)
Q Consensus 241 ~HQIR~hla~lG~PIvGD~~Yg 262 (353)
|||||+||+++||||+|=....
T Consensus 183 tHQIR~h~~~~G~pi~gl~R~~ 204 (232)
T PRK10839 183 YHQVKRMFAAVGNHVVELHRER 204 (232)
T ss_pred CHHHHHHHHHcCCeEeeEEEEE
Confidence 9999999999999999976653
No 14
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=100.00 E-value=1.1e-36 Score=284.13 Aligned_cols=207 Identities=17% Similarity=0.189 Sum_probs=153.8
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCC--CEEEEeeCCCCCCCCCCCccEEEECCcEEEEE
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAG--SELVYHRLPWKEPDVPYLLEVLYEDDDLIALN 78 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~g--d~i~~~~~~~~~~~~~~~~~Ilyed~~~ivvn 78 (353)
|||.+||++. +. |||++++++|++|+|+|||+++ ++++.|.++ |.|.++......+ .+ .-||+.|+++|
T Consensus 3 ~RL~k~La~~-g~-~SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g~~~~~~-~~-----~~e~~~ylvln 73 (289)
T PRK10700 3 EKLQKVLARA-GH-GSRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRIDGHLISVK-ES-----AEQICRVLAYY 73 (289)
T ss_pred hhHHHHHHHC-CC-CCHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEECCEEeecc-cc-----cccCCeEEEEE
Confidence 5888888864 43 8999999999999999999988 689999877 5576653221111 00 01556899999
Q ss_pred CCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccccccccc
Q 037167 79 KPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDAD 158 (353)
Q Consensus 79 KP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~~~~~~ 158 (353)
||+|++|++.+.....|+++.+.... ..++++|||||++||||||||+|+++++.|..
T Consensus 74 KP~G~~~s~~d~~~~~tv~d~l~~~~----------~~~~~~VgRLD~dTsGLLLlTndg~~~~~L~~------------ 131 (289)
T PRK10700 74 KPEGELCTRNDPEGRPTVFDRLPKLR----------GARWIAVGRLDVNTCGLLLFTTDGELANRLMH------------ 131 (289)
T ss_pred CCCCCEeecCCCCCCccHHHHhhhhc----------CCceeEccCCCCCCceEEEEEcCHHHHHHHhC------------
Confidence 99999999887666689998886421 13578999999999999999999999999973
Q ss_pred hhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEeC-CCCeEEEEEEeC
Q 037167 159 STVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDV-QRNCTLVQVEIQ 237 (353)
Q Consensus 159 ~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~~-~~~~sll~~~l~ 237 (353)
+.+.|.|+|+|+|.|.++++... . +..++.+ .++. +.+..+.... ....++++|+|.
T Consensus 132 ------p~~~i~K~Y~v~V~G~~~~~~l~--~---------l~~Gv~l--~~~~---~~~~~v~~~~~~~~~s~l~v~L~ 189 (289)
T PRK10700 132 ------PSREVEREYAVRVFGQVDDAKLR--Q---------LSRGVQL--EDGP---AAFKTIKFSGGEGINQWYNVTLT 189 (289)
T ss_pred ------ccCCCCeEEEEEEccCCCHHHHH--H---------HHcCCEe--CCce---eeeEEEEeccCCCCceEEEEEEe
Confidence 55789999999999998654321 0 2334444 2232 2233332221 123478999999
Q ss_pred CCchhHHHHHHHHcCCCeeCCcC
Q 037167 238 SGRPHQIRIHLAFLGHPLLGDPL 260 (353)
Q Consensus 238 TGR~HQIR~hla~lG~PIvGD~~ 260 (353)
|||+||||.||+++|+||+.=..
T Consensus 190 EGk~hQIRrm~~~lG~~V~~L~R 212 (289)
T PRK10700 190 EGRNREVRRLWEAVGVQVSRLIR 212 (289)
T ss_pred CCccHHHHHHHHHcCCEEeEEEE
Confidence 99999999999999999976443
No 15
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=100.00 E-value=9.5e-36 Score=277.05 Aligned_cols=198 Identities=18% Similarity=0.197 Sum_probs=150.7
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCCCCCCCCccEEEECCcEEEEECC
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALNKP 80 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~~~~~~~~~Ilyed~~~ivvnKP 80 (353)
|||.+||+.. .. |||++++++|++|+|+|||+++ .+++.|.+||.|.++..... + ..+||++|||+|||
T Consensus 7 ~RL~k~La~~-g~-~SRr~a~~lI~~G~V~VNGk~v-~~~~~V~~gD~V~v~g~~i~-~-------~~~ed~~~lvlnKP 75 (290)
T PRK10475 7 TRLNKYISES-GI-CSRREADRYIEQGNVFINGKRA-TIGDQVKAGDVVKVNGQLIE-P-------REAEDLVLIALNKP 75 (290)
T ss_pred HHHHHHHHhC-CC-CCHHHHHHHHHCCcEEECCEEc-cCCCCcCCCCEEEECCEEcc-c-------cccCCCeEEEEECC
Confidence 5788888765 33 7999999999999999999998 58999999999988643211 1 11478899999999
Q ss_pred CCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccccccccchh
Q 037167 81 SGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADST 160 (353)
Q Consensus 81 ~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~~~~~~~~ 160 (353)
+|++||+.+.. ..|+++.+... .++++|||||++||||||||+|+++++.|..
T Consensus 76 ~G~~~~~~~~~-~~tv~~~l~~~------------~~l~~VgRLDrdTsGLLLlT~dg~~~~~L~~-------------- 128 (290)
T PRK10475 76 VGIVSTTEDGE-RDNIVDFVNHS------------KRVFPIGRLDKDSQGLIFLTNHGDLVNKILR-------------- 128 (290)
T ss_pred CCCCcCCCCCC-CCcHHHHhhcc------------ccccccccCCCCCcceEEEecCHHHHHHhhC--------------
Confidence 99999977654 57888877531 3578999999999999999999999998864
Q ss_pred hhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEeCCCCeEEEEEEeCCCc
Q 037167 161 VMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGR 240 (353)
Q Consensus 161 ~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~~~~~~sll~~~l~TGR 240 (353)
+.+.++|+|+|+|.|.+.++... .+..++.+. ++......++.+ +.++++|++.+||
T Consensus 129 ----p~~~i~K~Y~v~V~g~~~~~~l~-----------~l~~Gv~l~--~~~~~~~~v~~~------~~~~~~i~l~eGk 185 (290)
T PRK10475 129 ----AGNDHEKEYLVTVDKPITDEFIR-----------GMGAGVPIL--GTVTKKCKVKKE------APFVFRITLVQGL 185 (290)
T ss_pred ----cCCCCCeEEEEEECCCCCHHHHH-----------HHhCCcEEC--CEEecceEEEec------CCcEEEEEEECCc
Confidence 34679999999999998654321 123444442 121111122211 2357999999999
Q ss_pred hhHHHHHHHHcCCCeeCCc
Q 037167 241 PHQIRIHLAFLGHPLLGDP 259 (353)
Q Consensus 241 ~HQIR~hla~lG~PIvGD~ 259 (353)
+||||.||+++|++|+-=.
T Consensus 186 ~rqIRrm~~~~G~~V~~L~ 204 (290)
T PRK10475 186 NRQIRRMCEHFGYEVTKLE 204 (290)
T ss_pred CHHHHHHHHHcCCEEeEEE
Confidence 9999999999999997543
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=100.00 E-value=2.6e-35 Score=251.55 Aligned_cols=147 Identities=30% Similarity=0.392 Sum_probs=117.8
Q ss_pred EEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcccc
Q 037167 74 LIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTS 153 (353)
Q Consensus 74 ~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~ 153 (353)
|+|+|||+|++||+++.....++.+.+.... ..++++|||||++||||||||+|+++++.|+++ +
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~~----------~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~--- 65 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLH----------GPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEP--R--- 65 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhhccc----------CCceeEeccCCCCCeeEEEEEcCHHHHHHHhhh--h---
Confidence 5899999999999987766678777654221 246889999999999999999999999999987 2
Q ss_pred ccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEeCCCCeEEEE
Q 037167 154 VIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQ 233 (353)
Q Consensus 154 ~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~~~~~~sll~ 233 (353)
+.++|+|+|+|.|.++++ ..+..++... ....+ +..++++.+.|+|+++... .+.++++
T Consensus 66 -------------~~v~K~Y~a~v~g~~~~~-~~~~~~~~~~---~~~~~--~~~~~~~~~~t~~~~l~~~--~~~sll~ 124 (154)
T cd02550 66 -------------REIEKEYLVTVRGELDEE-GIEDLATVRR---GRLSG--LVDEGVPLAVTKVRVIGEH--GGTGRLR 124 (154)
T ss_pred -------------ccCcEEEEEEEEeecCcc-hheecccccc---Cccee--EEcCCCcccceEEEEEEec--CCcEEEE
Confidence 589999999999998754 4455555431 11111 2345688899999999754 3679999
Q ss_pred EEeCCCchhHHHHHHHHcCCCee
Q 037167 234 VEIQSGRPHQIRIHLAFLGHPLL 256 (353)
Q Consensus 234 ~~l~TGR~HQIR~hla~lG~PIv 256 (353)
|+|.|||+||||+||+++||||.
T Consensus 125 ~~l~tGR~HQIR~hla~~G~pI~ 147 (154)
T cd02550 125 LTLKTGRTHQIRRHCAAVGFPVL 147 (154)
T ss_pred EEEcCCCcHHHHHHHHHcCCcEE
Confidence 99999999999999999999997
No 17
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.9e-35 Score=262.30 Aligned_cols=209 Identities=22% Similarity=0.304 Sum_probs=161.1
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCC-CEEEEeeCCCCCCCCCCCccEEE-ECCcEEEEE
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAG-SELVYHRLPWKEPDVPYLLEVLY-EDDDLIALN 78 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~g-d~i~~~~~~~~~~~~~~~~~Ily-ed~~~ivvn 78 (353)
|||.+||+.... |||++++++|++|+|+|||++++++...+.++ |.|.+++.. +.+ +...|+++|
T Consensus 3 ~RL~K~La~~G~--~SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~-----------~~~~~~~~y~lln 69 (248)
T COG1187 3 MRLNKFLAEAGV--GSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKR-----------IELKEERVYLLLN 69 (248)
T ss_pred cchHHHHHHcCC--CCHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCEE-----------eeccccceEEEEE
Confidence 577777777644 79999999999999999999999999999988 567776543 333 233499999
Q ss_pred CCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccccccccc
Q 037167 79 KPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDAD 158 (353)
Q Consensus 79 KP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~~~~~~ 158 (353)
||.|++|+..+.....|+.+.++.... ...++++|+|||+|||||||+|+|++.+++|.
T Consensus 70 KP~G~v~s~~D~~gr~tv~D~lp~~~~--------~~~~~~pvGRLD~dTeGLLLLTnDG~la~rL~------------- 128 (248)
T COG1187 70 KPRGYVSSTEDDEGRPTVFDLLPERLP--------RKKRLFPVGRLDKDTEGLLLLTNDGELAHRLM------------- 128 (248)
T ss_pred CCCCeEecccCCCCCceeeeecccccc--------cccceeeccccCCCCeeEEEEeCCHHHHHHhc-------------
Confidence 999999998766678899988863211 02568999999999999999999999999887
Q ss_pred hhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEeCCCCeEEEEEEeCC
Q 037167 159 STVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQS 238 (353)
Q Consensus 159 ~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~~~~~~sll~~~l~T 238 (353)
+|+++++|+|+|.|.|.++++... .++.|+.+. +|....+....+......+.|+++++|.+
T Consensus 129 -----~P~~~~~K~Y~v~v~g~~~~~~l~-----------~l~~Gv~l~--d~~~~~~~~~~l~~~~~~~~s~~~itl~E 190 (248)
T COG1187 129 -----HPSSEVEKEYLVRVEGPVTEEDLE-----------KLRKGVTLD--DGETKPAKPASLEKEPGKNNSWLRITLTE 190 (248)
T ss_pred -----CCCCCCCEEEEEEEecCCCHHHHH-----------HHhCCcEec--CcccccceeEEEEecCCCCceEEEEEEeC
Confidence 688999999999999988654322 144555553 33333334233333221257899999999
Q ss_pred CchhHHHHHHHHcCCCeeCCcCC
Q 037167 239 GRPHQIRIHLAFLGHPLLGDPLY 261 (353)
Q Consensus 239 GR~HQIR~hla~lG~PIvGD~~Y 261 (353)
||+||||.||+++|+|++.=..+
T Consensus 191 GrnrQVRRm~~a~G~~V~~L~R~ 213 (248)
T COG1187 191 GRNRQVRRMFEAVGLEVLRLKRI 213 (248)
T ss_pred CcCHHHHHHHHHcCCEEeEEEEE
Confidence 99999999999999999865554
No 18
>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=100.00 E-value=5.3e-33 Score=239.45 Aligned_cols=157 Identities=36% Similarity=0.521 Sum_probs=116.5
Q ss_pred cEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccc
Q 037167 73 DLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKT 152 (353)
Q Consensus 73 ~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~ 152 (353)
+|||||||+||+|++.+................... ....+++|||||++||||||||+|+++++.|+++|.+
T Consensus 1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~v~RLD~~TsGlll~a~~~~~~~~l~~~f~~-- 73 (164)
T PF00849_consen 1 NLIVVNKPAGVPVHPSDGNESKSVKELPALSLKRGD-----DPPELYPVHRLDRDTSGLLLFAKDKEAAAKLSKQFPK-- 73 (164)
T ss_dssp SEEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHHHCT-----TSGGGEESS---TT-EEEEEEESSHHHHHHHHHHHHT--
T ss_pred CEEEEECCCCCeEecCCCCCcccccchhhhhhhhcc-----CCCceEECCCCCccccCCeeccCCccccccccccccc--
Confidence 589999999999999874333333333322222111 1367899999999999999999999999999999976
Q ss_pred cccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEe-------C
Q 037167 153 SVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERD-------V 225 (353)
Q Consensus 153 ~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~-------~ 225 (353)
+.++|+|+|+|.|.+.++.+.++.++.................+++.+.|.|+++... .
T Consensus 74 --------------~~~~K~Y~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~l~~~~~~~~~~~ 139 (164)
T PF00849_consen 74 --------------RKVEKTYLALVEGGPVEEEGKINSPLGKDVGKNKSSNKDPPGRDGKPAITRYRVLRSGSRTPSKDE 139 (164)
T ss_dssp --------------TCSEEEEEEEECSSSSTTCEEEESHEEE-EECSSCTCCEEETTTSBTSEEEEEEEEEETT---EEC
T ss_pred --------------CCCcEEEEEeEcccccccceeeeccccccccccccceeeeecccccccceeeeeeccccccccccc
Confidence 5899999999997777788999999887221112222333456789999999999987 4
Q ss_pred CCCeEEEEEEeCCCchhHHHHHHHH
Q 037167 226 QRNCTLVQVEIQSGRPHQIRIHLAF 250 (353)
Q Consensus 226 ~~~~sll~~~l~TGR~HQIR~hla~ 250 (353)
...+++++|+|.|||+||||+|||+
T Consensus 140 ~~~~s~v~~~l~tGr~HQIR~hla~ 164 (164)
T PF00849_consen 140 NAGCSLVECELITGRTHQIRVHLAH 164 (164)
T ss_dssp CSSEEEEEEEESS-STTHHHHHHHH
T ss_pred cCCCEEEEEEECcCCCHHHHHHhcC
Confidence 5689999999999999999999986
No 19
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.
Probab=100.00 E-value=8.2e-34 Score=245.27 Aligned_cols=145 Identities=19% Similarity=0.267 Sum_probs=115.7
Q ss_pred EEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcccc
Q 037167 74 LIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTS 153 (353)
Q Consensus 74 ~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~ 153 (353)
++|+|||+|++||+.+.....|+.+.+.... ..++++|||||++||||||||+|+++++.|+.
T Consensus 2 ~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~----------~~~~~~V~RLD~~TsGLll~ak~~~~~~~L~~------- 64 (167)
T cd02556 2 VLIYHKPEGLICTRKDPKGRPTVFDLLPKLG----------IPRWISVGRLDLNTEGLLLFTNDGELANRLMH------- 64 (167)
T ss_pred EEEEECCCCcEECccCCCCCccHHHhhhhhc----------cCceEEcCcCCCCCeeEEEEECCHHHHHHHhC-------
Confidence 7899999999999876655678888876431 14578999999999999999999999999973
Q ss_pred ccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEeCCCCeEEEE
Q 037167 154 VIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQ 233 (353)
Q Consensus 154 ~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~~~~~~sll~ 233 (353)
+++.++|+|+|+|.|.++++.. . . ...++.. .+|+.+.|+|+++... .+.++++
T Consensus 65 -----------~~~~i~K~Y~a~V~g~~~~~~~--~----~-----~~~gv~~--~~~~~~~~~~~~~~~~--~~~sll~ 118 (167)
T cd02556 65 -----------PSNEIEREYAVRVFGQVTDEQL--K----S-----LKKGVEL--EDGFAGFKSIQLEGGE--GKNSWYR 118 (167)
T ss_pred -----------CcCCCCeEEEEEECccCCHHHH--H----H-----HHcCCEE--CCCcCcceEEEEEecC--CCcEEEE
Confidence 3468999999999999875541 1 0 1223322 4578888999998654 3569999
Q ss_pred EEeCCCchhHHHHHHHHcCCCeeCCcCC
Q 037167 234 VEIQSGRPHQIRIHLAFLGHPLLGDPLY 261 (353)
Q Consensus 234 ~~l~TGR~HQIR~hla~lG~PIvGD~~Y 261 (353)
|+|.|||+||||+||+++||||+-=...
T Consensus 119 v~l~tGR~HQIR~~~a~~G~pV~~L~R~ 146 (167)
T cd02556 119 VTLREGRNREVRRLWEAFGLQVSRLIRI 146 (167)
T ss_pred EEEEeCCCHHHHHHHHHcCCeEeEEEEE
Confidence 9999999999999999999999865444
No 20
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.
Probab=100.00 E-value=4.8e-34 Score=241.59 Aligned_cols=140 Identities=31% Similarity=0.446 Sum_probs=111.0
Q ss_pred EEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcccc
Q 037167 74 LIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTS 153 (353)
Q Consensus 74 ~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~ 153 (353)
|+|+|||+|++|++.+.....++.+.+... ..++.+|||||++||||||||+|+++++.|..
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~~-----------~~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~------- 62 (146)
T cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDV-----------GERLFPVGRLDYDTEGLLLLTNDGELANRLTH------- 62 (146)
T ss_pred CEEEECCCCcEecccCCCCCCEEeeecccc-----------CCCEEECCCCCCCCeeEEEEeCCHHHHHHhhC-------
Confidence 689999999999988766566776554321 24688999999999999999999999998874
Q ss_pred ccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEeCCCCeEEEE
Q 037167 154 VIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQ 233 (353)
Q Consensus 154 ~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~~~~~~sll~ 233 (353)
+.+.++|+|+|+|.|.++++.+. . ...++.. .+++.+.|.|++++.. .+.++++
T Consensus 63 -----------~~~~i~K~Y~a~v~g~~~~~~~~--~---------~~~~~~~--~~~~~~~t~~~~l~~~--~~~sll~ 116 (146)
T cd02870 63 -----------PRYGVEKTYLVKVRGVPSEEELR--R---------LRAGVEL--DDGKTAPAKVKVLSRD--PKNTLLE 116 (146)
T ss_pred -----------ccCCCCeEEEEEECCCCCHHHHH--H---------HHCCeEe--CCceEcceEEEEeccC--CCCcEEE
Confidence 22579999999999998654321 0 1122222 4578899999999765 3579999
Q ss_pred EEeCCCchhHHHHHHHHcCCCeeC
Q 037167 234 VEIQSGRPHQIRIHLAFLGHPLLG 257 (353)
Q Consensus 234 ~~l~TGR~HQIR~hla~lG~PIvG 257 (353)
|+|.|||+||||+||+++|+||+.
T Consensus 117 ~~l~tGR~HQIR~hla~~G~pI~~ 140 (146)
T cd02870 117 VTLHEGRNRQVRRMFEAVGHPVLR 140 (146)
T ss_pred EEEEeCCcHHHHHHHHHcCCcCCe
Confidence 999999999999999999999973
No 21
>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=99.98 E-value=5.7e-33 Score=239.93 Aligned_cols=144 Identities=24% Similarity=0.403 Sum_probs=108.8
Q ss_pred EEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcccc
Q 037167 74 LIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTS 153 (353)
Q Consensus 74 ~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~ 153 (353)
|+|+|||+|++||+++. ...++.+.+..... ..++++|||||++||||||||+|.++++.+..
T Consensus 2 ~ivvnKP~G~~~~~~~~-~~~tl~~~l~~~~~---------~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~------- 64 (167)
T cd02553 2 YLMLNKPAGVVCATKDP-HHPTVIDLLPEPDR---------RRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTS------- 64 (167)
T ss_pred EEEEECCCCCEeCCCCC-CCCcHHHHhhhhcc---------cCCeEEcccCCCCCEEEEEEEeCHHHHHHhhC-------
Confidence 79999999999996544 46888887765431 24678999999999999999999998887763
Q ss_pred ccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCC-CcceeEEEEEEEeCCCCeEEE
Q 037167 154 VIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSG-KPALSKVDVLERDVQRNCTLV 232 (353)
Q Consensus 154 ~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~g-k~a~t~~~vl~~~~~~~~sll 232 (353)
+.+.++|+|+|+|.|.++++... . ...++.. .++ +...+.+++++ .+++
T Consensus 65 -----------~~~~i~K~Y~a~V~G~~~~~~~~--~---------~~~~~~~--~~~~~~~~~~~~~~~------~sll 114 (167)
T cd02553 65 -----------PKKHVPKTYEVTLAGPLTEDDIE--A---------FAEGVLL--HDGYPTKPAKLEILS------PTTV 114 (167)
T ss_pred -----------CcCCCceEEEEEEccCCCHHHHH--H---------HHCCeEE--cCCCEeeeeEEEEeC------CcEE
Confidence 23689999999999998654321 1 1112221 223 22344555552 2899
Q ss_pred EEEeCCCchhHHHHHHHHcCCCeeCCcCCCCC
Q 037167 233 QVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAG 264 (353)
Q Consensus 233 ~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg~~ 264 (353)
+|+|.|||+||||+||+++||||++|..++-+
T Consensus 115 ~v~l~tGR~HQIR~hla~lG~pI~~~~R~~~g 146 (167)
T cd02553 115 RLTITEGKYHQVKRMFAAVGNKVVALHRIRIG 146 (167)
T ss_pred EEEEEeCCCHHHHHHHHHcCCeEEEEEEEEEC
Confidence 99999999999999999999999999888653
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=99.97 E-value=5.5e-31 Score=227.84 Aligned_cols=156 Identities=20% Similarity=0.220 Sum_probs=106.2
Q ss_pred EEEEECCCCCccccCCC-CCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccc
Q 037167 74 LIALNKPSGLQVLPGGL-FQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKT 152 (353)
Q Consensus 74 ~ivvnKP~G~~~~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~ 152 (353)
++|+|||+|++||+++. ....++.+.+. ..++++|||||++||||||||+|+++++.|..
T Consensus 1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l~-------------~~~~~~v~RLD~~TsGlll~a~d~~~~~~l~~------ 61 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYID-------------DPGVYAAGRLDRDSEGLLLLTDDGRLQHRITD------ 61 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCccHHHHcC-------------cCCeEEccCCCCCCeEEEEEEeCHHHHHHHHC------
Confidence 58999999999998765 44567776653 13567999999999999999999988777763
Q ss_pred cccccchhhhhhccceEEEEEEEEEeeeeCCCceE-EecceeeecCCCcccceEee-CCCCCcceeEEEEEEEeCCCCeE
Q 037167 153 SVIDADSTVMELSQRKITKIYRALVHGIVDEDKVI-IKQPIGIVRYPGVAKGLYVA-SPSGKPALSKVDVLERDVQRNCT 230 (353)
Q Consensus 153 ~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~-i~~~i~~~~~~~~~~~~~~~-~~~gk~a~t~~~vl~~~~~~~~s 230 (353)
+.+.++|+|+|+|.|.++++... +...+... +.......+. ...+....+.+.++......+.|
T Consensus 62 ------------~~~~v~K~Y~a~v~g~~~~~~~~~l~~g~~~~--~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~s 127 (168)
T cd02566 62 ------------PSFKHPKTYYVQVEGVPTEDALEQLRNGVELG--DGLTLPAKVEKVDEPPWLWEREPPIRFRKNIPTS 127 (168)
T ss_pred ------------CCCCCCEEEEEEECCcCCHHHHHHHhCCcEEC--CeEecceEEEEecccccccccccccccccCCCcc
Confidence 33569999999999998654311 01111100 0000011111 11122233444445433223568
Q ss_pred EEEEEeCCCchhHHHHHHHHcCCCeeCCcCCC
Q 037167 231 LVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYV 262 (353)
Q Consensus 231 ll~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg 262 (353)
+++|+|.|||+||||+||+++||||+......
T Consensus 128 ll~v~l~tGR~HQIR~~la~lG~pV~~L~R~~ 159 (168)
T cd02566 128 WIEITICEGKNRQVRRMTAAVGFPTLRLIRVS 159 (168)
T ss_pred EEEEEEecCccHHHHHHHHHcCCeEeEEEEEE
Confidence 99999999999999999999999999887664
No 23
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=99.96 E-value=4.5e-30 Score=228.40 Aligned_cols=148 Identities=20% Similarity=0.299 Sum_probs=109.7
Q ss_pred cEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccc
Q 037167 73 DLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKT 152 (353)
Q Consensus 73 ~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~ 152 (353)
.|+++|||+|++|+..+.....++.+.+. ..++++|||||++||||||||+|+++++.|...
T Consensus 40 ~ylllnKP~G~l~~~~d~~~~~tl~d~l~-------------~~~~~~vgRLD~~TsGllLlt~d~~~~~~L~~~----- 101 (217)
T PRK11394 40 RVILFNKPYDVLPQFTDEAGRKTLKEFIP-------------VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQP----- 101 (217)
T ss_pred EEEEEECCCCCEEeeCCccCCcchHHhcc-------------cCCeEEecCCCCCCeeEEEEECCHHHHHHHhCc-----
Confidence 59999999999999766555678877763 135789999999999999999999999999853
Q ss_pred cccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEE---------
Q 037167 153 SVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLER--------- 223 (353)
Q Consensus 153 ~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~--------- 223 (353)
.+.+.|+|+|+|.|.+.++.+.. ...++.+. ++......++.+..
T Consensus 102 -------------~~~i~K~Y~~~v~g~~~~~~l~~-----------l~~Gv~i~--~~~~~p~~~~~i~~~~~~~~~~~ 155 (217)
T PRK11394 102 -------------GKRTGKIYYVQVEGIPTQDALEA-----------LRNGVTLN--DGPTLPAGAELVDEPAWLWPRNP 155 (217)
T ss_pred -------------ccCCCEEEEEEECCCCCHHHHHH-----------HhCCeEEC--CccccccEEEEeccccccccccc
Confidence 36899999999999986554321 12222221 11111112222211
Q ss_pred ----eCCCCeEEEEEEeCCCchhHHHHHHHHcCCCeeCCcCCCCC
Q 037167 224 ----DVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAG 264 (353)
Q Consensus 224 ----~~~~~~sll~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg~~ 264 (353)
....+.++++++|.|||+||||+||+++|+||+||.+|+-+
T Consensus 156 ~~~~~~~~~~s~l~I~L~eGR~hQIRrm~a~lG~pVl~L~Ry~iG 200 (217)
T PRK11394 156 PIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMG 200 (217)
T ss_pred ccccccCCCceEEEEEEeCCCCHHHHHHHHHcCCeEeeeEEEEEC
Confidence 11124689999999999999999999999999999999754
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=99.96 E-value=8.4e-30 Score=221.55 Aligned_cols=142 Identities=18% Similarity=0.228 Sum_probs=101.6
Q ss_pred cEEEEECCCCCccccCCC--------CCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHH
Q 037167 73 DLIALNKPSGLQVLPGGL--------FQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCI 144 (353)
Q Consensus 73 ~~ivvnKP~G~~~~~~~~--------~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L 144 (353)
.|+++|||+|++|+..+. ....++.+.+...+ .++++|||||++||||||||+|+++++.|
T Consensus 5 ~y~llnKP~G~l~s~~d~~~~~g~~~~~~~~~~~~l~~~~-----------~~l~~VgRLD~dTsGLLl~t~d~~~~~~L 73 (177)
T cd02555 5 VTLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGHF-----------ARLAPIGPLDKDASGLLVFSQDGRVLRKL 73 (177)
T ss_pred EEEEEECCCceEecCCCcccccccccccccchhhhhhhcC-----------CceeEecCCCCCCeeEEEEECCHHHHHHH
Confidence 579999999999975541 11233333433211 35789999999999999999999999999
Q ss_pred HHHhhccccccccchhhhhhccceEEEEEEEEEeeeeCCCceE-EecceeeecCCCcccceEeeCCCCCcceeEEEEEEE
Q 037167 145 AGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVI-IKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLER 223 (353)
Q Consensus 145 ~~~f~~g~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~-i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~ 223 (353)
+..+ +.|+|+|+|+|.|.++++... ++ .++.. +++. .+.+++..
T Consensus 74 ~~~~------------------~~i~K~Y~v~v~g~~~~~~l~~l~------------~g~~~---~~~~-~~~~~~~~- 118 (177)
T cd02555 74 IGDA------------------SRLEQEYLVEVRGELTAGGLERLN------------HGLTY---DGRE-LPPAKVSW- 118 (177)
T ss_pred hChh------------------cCCCEEEEEEEcccCCHHHHHHHh------------cCccc---CCee-cceEEEEE-
Confidence 8642 579999999999998754211 11 11111 1221 12222211
Q ss_pred eCCCCeEEEEEEeCCCchhHHHHHHHHcCCCeeCCcCCCC
Q 037167 224 DVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVA 263 (353)
Q Consensus 224 ~~~~~~sll~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg~ 263 (353)
.+.++++++|.|||+||||+||+++||||+|+....-
T Consensus 119 ---~~~~~l~i~l~tGr~hQIR~~~~~~G~pV~~L~R~~i 155 (177)
T cd02555 119 ---QNEQRLRFALKEPQPGQIRRMCESVGLEVVALRRIRI 155 (177)
T ss_pred ---cCCCEEEEEEECCcChHHHHHHHHcCCeEEEEEEEEE
Confidence 1357999999999999999999999999999998853
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=99.94 E-value=1.1e-27 Score=197.96 Aligned_cols=111 Identities=23% Similarity=0.367 Sum_probs=89.1
Q ss_pred cccCCCCCceEEEEEeChHHHHHHHHHhhccccccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCc
Q 037167 121 VHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGV 200 (353)
Q Consensus 121 vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~ 200 (353)
|||||++||||||||+|+++++.|.. +++.|.|+|+|+|.|.++++.. + + .
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~------------------~~~~i~K~Y~a~v~g~~~~~~~--~-~--------~ 51 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTH------------------PGHHCEKTYLVTVEGPVTDEDL--E-A--------L 51 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhC------------------CCCCCCeEEEEEECCCCCHHHH--H-H--------H
Confidence 79999999999999999999999874 3468999999999999865431 1 1 1
Q ss_pred ccceEeeCCCCCcceeEEEEEEEeCCCCeEEEEEEeCCCchhHHHHHHHHcCCCeeCCcCCCCC
Q 037167 201 AKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAG 264 (353)
Q Consensus 201 ~~~~~~~~~~gk~a~t~~~vl~~~~~~~~sll~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg~~ 264 (353)
..++.. .+++.+.+.++++... .+.++++|+|.|||+||||+||+++||||+||..|.-+
T Consensus 52 ~~g~~~--~~~~~~~~~~~~l~~~--~~~~~l~~~l~tGR~HQIR~~~~~lG~pI~g~~R~~~g 111 (128)
T TIGR00093 52 RKGVQL--EDGPTKPAKLEVITEP--GFPTWLRITLSEGRNRQVRRMFAAVGFPVLRLHRVRIG 111 (128)
T ss_pred hCCeEE--CCcEEeeeEEEEEccC--CCceEEEEEEeCCCCHHHHHHHHHcCCeEeEEEEEEEC
Confidence 122222 3456677888888654 34689999999999999999999999999999998643
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=99.93 E-value=3e-26 Score=196.31 Aligned_cols=138 Identities=19% Similarity=0.238 Sum_probs=103.0
Q ss_pred EEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcccc
Q 037167 74 LIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTS 153 (353)
Q Consensus 74 ~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~ 153 (353)
|+++|||+|++|++++.. ..++.+.+.. ..++++|||||++||||||||+|+++++.|+..
T Consensus 2 y~~lnKP~G~l~s~~~~~-~~tv~~~l~~------------~~~~~~vgRLD~~tsGlll~t~dg~~~~~L~~p------ 62 (164)
T cd02554 2 YIAYNKPVGIDCTLERAD-EDNIIDFVNP------------PPRIFPIGRLDKDSEGLILLTNDGDLVNKILHA------ 62 (164)
T ss_pred EEEEECCCCcEeecCCCC-CCcHHHHhcC------------cCCEEEccCCCCCCeeEEEEEcCHHHHHHHhhh------
Confidence 799999999999987653 5788877642 146899999999999999999999999999743
Q ss_pred ccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEeCCCCeEEEE
Q 037167 154 VIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQ 233 (353)
Q Consensus 154 ~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~~~~~~sll~ 233 (353)
.+.+.|+|+|.|.|.+.++... .+..++.. .++ .|....++... + +.++
T Consensus 63 ------------~~~~~K~Y~V~v~~~l~~~~l~-----------~l~~G~~~--~~~---~~~~~~v~~~~--~-~~l~ 111 (164)
T cd02554 63 ------------DNNHEKEYLVTVNKPITDEFIE-----------GMSNGVVI--LGT---VTKPCKVERLA--K-DKFR 111 (164)
T ss_pred ------------hcCCCeEEEEEECCCCCHHHHH-----------HHhCCCEE--CCe---EEcceEEEECC--C-CEEE
Confidence 3578999999999988754221 12233333 122 23333333321 2 3499
Q ss_pred EEeCCCchhHHHHHHHHcCCCeeCCcCC
Q 037167 234 VEIQSGRPHQIRIHLAFLGHPLLGDPLY 261 (353)
Q Consensus 234 ~~l~TGR~HQIR~hla~lG~PIvGD~~Y 261 (353)
|.+.+||+||||+||+++|+||+-=..+
T Consensus 112 i~l~eGr~~qIRrm~~~~G~~V~~L~Ri 139 (164)
T cd02554 112 IVLTQGLNRQIRRMCEALGYRVTDLKRV 139 (164)
T ss_pred EEEECCcCHHHHHHHHHcCCEEEEEEEE
Confidence 9999999999999999999999875554
No 27
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=99.17 E-value=1.6e-10 Score=83.82 Aligned_cols=70 Identities=21% Similarity=0.340 Sum_probs=59.3
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCCCCCCCCccEEEECCcEEEEE
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALN 78 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~~~~~~~~~Ilyed~~~ivvn 78 (353)
|||.++|.+.+.. +||+.+.++|++|.|+|||+.++.+++.+.+||.|.+...+ + ...|+|||++++|+|
T Consensus 1 ~rl~~~l~~~~~~-~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~~~~---~----~~~i~~ed~~~lvv~ 70 (70)
T cd00165 1 MRLDKILARLGLA-PSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKS---I----EEDIVYEDKKLLVVN 70 (70)
T ss_pred CcHHHHHHHhccc-cCHHHHHHHHHcCCEEECCEEccCCccCcCCCCEEEEcCCC---c----ccceeeccCCEEEeC
Confidence 6889999887554 69999999999999999999997799999999999875322 1 127999999999987
No 28
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=99.09 E-value=2e-10 Score=103.32 Aligned_cols=75 Identities=23% Similarity=0.221 Sum_probs=52.8
Q ss_pred cEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccc
Q 037167 73 DLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKT 152 (353)
Q Consensus 73 ~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~ 152 (353)
.++|||||+|+.++.. .+.+...+...+.. .....+|||||++|||||+||+++.+ ++.++|.+
T Consensus 1 GilvvnKP~Gi~s~~~----~~~~~~~l~~~~~~--------~k~~~~vhrLD~~aSGvl~~a~~~~t--kl~~~~~~-- 64 (226)
T cd02868 1 GLFAVYKPPGVHWKHV----RDTIESNLLKYFPE--------DKVLVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYS-- 64 (226)
T ss_pred CEEEEEcCCCCChhHH----HHHHHHHHHHHccc--------cceeeEccccCCCCceEEEEEeChhH--hHHHHHHh--
Confidence 3799999999988643 13333333222211 11255789999999999999999976 58888875
Q ss_pred cccccchhhhhhccceEEEEEEEEE
Q 037167 153 SVIDADSTVMELSQRKITKIYRALV 177 (353)
Q Consensus 153 ~~~~~~~~~~~~~~~~v~K~Y~alv 177 (353)
+.+.|+|+|..
T Consensus 65 --------------~~~~K~Y~~~~ 75 (226)
T cd02868 65 --------------NHPTRVYTIRG 75 (226)
T ss_pred --------------cCCCeEEEEEE
Confidence 46899999543
No 29
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=98.88 E-value=4.9e-09 Score=71.12 Aligned_cols=48 Identities=27% Similarity=0.459 Sum_probs=43.6
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEE
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSEL 49 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i 49 (353)
|||..||.+.... .||++++++|++|.|+|||++++++++.|++||+|
T Consensus 1 ~RLd~~L~~~~~~-~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 1 MRLDKFLSRLGLA-SSRSEARRLIKQGRVKVNGKVVKDPSYIVKPGDVI 48 (48)
T ss_dssp EBHHHHHHHTTSS-SSHHHHHHHHHTTTEEETTEEESSTTSBESTTEEE
T ss_pred CCHHHHHHHcCCc-CCHHHHHHhcCCCEEEECCEEEcCCCCCCCCcCCC
Confidence 6899999866654 58999999999999999999999999999999986
No 30
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=98.58 E-value=1.5e-07 Score=66.75 Aligned_cols=50 Identities=16% Similarity=0.084 Sum_probs=43.4
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEE
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVY 51 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~ 51 (353)
+||..||... ....||+.++++|+.|.|+|||++++.++++|.+||.|.+
T Consensus 9 ~rLd~~L~~~-~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 9 ITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEI 58 (59)
T ss_pred HHHHHHHHHc-CCccCHHHHHHHHHcCCEEECCEEccCCCCCCCCCCEEEe
Confidence 3788888888 3223999999999999999999999889999999999976
No 31
>smart00363 S4 S4 RNA-binding domain.
Probab=98.15 E-value=8.5e-06 Score=56.72 Aligned_cols=52 Identities=19% Similarity=0.303 Sum_probs=44.2
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEee
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHR 53 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~ 53 (353)
|+|..+|...+.. .|++.+.++|..|.|+|||+++++++..+..||.|.+..
T Consensus 1 ~rl~~~l~~~~~~-~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 1 RRLDKFLARLGLA-PSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred CcHHHHHHHcCcc-cCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 5777788766443 699999999999999999999977999999999998753
No 32
>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=97.96 E-value=3.1e-05 Score=67.58 Aligned_cols=70 Identities=19% Similarity=0.191 Sum_probs=52.9
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+++||||.|+.+| .+++.+++.+. ..+.+-.+-||...||||+++-+. +.++.+.|.+
T Consensus 2 ~g~l~i~Kp~g~tS~--------~~v~~~k~~~~---------~kkvGH~GTLDp~A~GvLiv~~g~--~Tk~~~~~~~- 61 (182)
T cd02572 2 YGVINLDKPSGPSSH--------EVVAWIKRILG---------VEKTGHSGTLDPKVTGCLPVCIDR--ATRLVKSQQE- 61 (182)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhC---------CCccCcCCCCCCcCeeEEEEEECH--HhhhhHHHhC-
Confidence 369999999999776 34566665443 246788999999999999999987 3455555543
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
-.|+|.|.+.
T Consensus 62 -----------------~~K~Y~a~v~ 71 (182)
T cd02572 62 -----------------AGKEYVCVMR 71 (182)
T ss_pred -----------------CCCEEEEEEE
Confidence 3599999875
No 33
>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=97.92 E-value=2.6e-05 Score=69.23 Aligned_cols=54 Identities=17% Similarity=0.138 Sum_probs=46.5
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCC
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLP 55 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~ 55 (353)
|||..+|.+.... .||+.+.++|+.|.|+|||++++.+++.|++||.|.+.+..
T Consensus 90 ~RLD~~L~~~g~~-~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~GD~I~V~~~~ 143 (200)
T TIGR01017 90 SRLDNVVYRLGFA-PTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKS 143 (200)
T ss_pred HHHHHHHHHcCCC-CCHHHHHHHHHCCCEEECCEEeCCCCCCCCCCCEEEEeeCc
Confidence 5777787666543 58999999999999999999999999999999999987654
No 34
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=97.91 E-value=2.1e-05 Score=60.77 Aligned_cols=50 Identities=16% Similarity=0.198 Sum_probs=43.6
Q ss_pred CcHHHHHHhh-cCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEee
Q 037167 1 LTLIEFYSTK-HKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHR 53 (353)
Q Consensus 1 ~~l~~~l~~~-~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~ 53 (353)
|||++||-.- |. -+|+-+++++..|+|.|||.++ +|+..|+.||+|.+..
T Consensus 9 mRLDKwL~~aR~~--KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~ 59 (100)
T COG1188 9 MRLDKWLWAARFI--KRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTIRF 59 (100)
T ss_pred eehHHHHHHHHHh--hhHHHHHHHHHCCeEEECCEEc-ccccccCCCCEEEEEe
Confidence 6889998665 44 3899999999999999999998 6999999999998853
No 35
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=97.86 E-value=2.9e-05 Score=68.72 Aligned_cols=53 Identities=17% Similarity=0.209 Sum_probs=46.1
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeC
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRL 54 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~ 54 (353)
|||..+|.+.... .||+.+.++|+.|.|+|||++++.+++.|++||.|.+...
T Consensus 89 ~RLD~~L~r~g~~-~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~~~ 141 (201)
T CHL00113 89 MRLDNILFRLGMA-PTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDK 141 (201)
T ss_pred HHHHHHHHHcCCC-CCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEccc
Confidence 4788888776654 5899999999999999999999999999999999988643
No 36
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=97.76 E-value=6.1e-05 Score=69.62 Aligned_cols=52 Identities=19% Similarity=0.216 Sum_probs=47.1
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeC
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRL 54 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~ 54 (353)
+||..+++..+. .||+.+.++|++|.|+|||+.+.++++.|++||.|.+.+.
T Consensus 192 ~RLD~vla~~~~--~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiRG~ 243 (267)
T PLN00051 192 LRLDALASAGFR--MSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVSGK 243 (267)
T ss_pred ccHHHHHHHHhc--cCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEeeC
Confidence 588898888884 7999999999999999999999899999999999988643
No 37
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=97.76 E-value=8.4e-05 Score=66.81 Aligned_cols=70 Identities=16% Similarity=0.222 Sum_probs=53.5
Q ss_pred cEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccc
Q 037167 73 DLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKT 152 (353)
Q Consensus 73 ~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~ 152 (353)
.+++||||.|+.+| .+++.+++.+. ..+.+-.|.||...||||+++-.. ++.+|.+.+.
T Consensus 10 G~l~i~KP~g~TS~--------dvv~~ikk~~~---------~kKvGH~GTLDP~AtGvLiv~vG~-~aTkl~~~~~--- 68 (230)
T PRK00989 10 GILLVDKPQGRTSF--------SLIRSLTKLIG---------VKKIGHAGTLDPFATGVMVMLIGR-KFTRLSDILL--- 68 (230)
T ss_pred EEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCcCCcCccCCCCCeeEEEEEECC-chhhhHHHhc---
Confidence 79999999999776 35566665543 256888999999999999999876 3345665553
Q ss_pred cccccchhhhhhccceEEEEEEEEEe
Q 037167 153 SVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 153 ~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
...|+|.|.+.
T Consensus 69 ---------------~~~K~Y~~~~~ 79 (230)
T PRK00989 69 ---------------FEDKEYAAVAH 79 (230)
T ss_pred ---------------CCCcEEEEEEE
Confidence 35799999875
No 38
>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=97.72 E-value=5.9e-05 Score=69.56 Aligned_cols=52 Identities=17% Similarity=0.252 Sum_probs=45.2
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeC
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRL 54 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~ 54 (353)
|||..+++..+. .||+.+.++|++|+|+|||+.++++++.|++||.|.+.+.
T Consensus 184 ~RLD~lls~~~~--~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~IsvrG~ 235 (257)
T TIGR03069 184 LRIDAIASAGFG--LSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRGK 235 (257)
T ss_pred ccHHHHHHhhhh--hhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEcCC
Confidence 578876666663 6999999999999999999999889999999999998643
No 39
>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=97.70 E-value=0.00014 Score=64.80 Aligned_cols=69 Identities=23% Similarity=0.214 Sum_probs=52.4
Q ss_pred cEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccc
Q 037167 73 DLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKT 152 (353)
Q Consensus 73 ~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~ 152 (353)
.+++||||.|+.+| .+++.+++.+. ..+.+-.+.||...||||+++-+.. .++...|.
T Consensus 1 Gil~i~KP~g~tS~--------~vv~~ik~~~~---------~kKvGH~GTLDP~AsGvLiv~vG~a--Tkl~~~~~--- 58 (210)
T cd00506 1 GLFAVDKPQGPSSH--------DVVDTIRRIFL---------AEKVGHGGTLDPFATGVLVVGIGKA--TKLLKHLL--- 58 (210)
T ss_pred CEEEEEcCCCCCHH--------HHHHHHHHHhC---------ccccCCCCcCCCcCeeEEEEEECHH--HhhhHHHh---
Confidence 37999999999776 35666665543 2467889999999999999999873 44555553
Q ss_pred cccccchhhhhhccceEEEEEEEEEe
Q 037167 153 SVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 153 ~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
...|+|.|.+.
T Consensus 59 ---------------~~~K~Y~~~~~ 69 (210)
T cd00506 59 ---------------AATKDYTAIGR 69 (210)
T ss_pred ---------------cCCceEEEEEE
Confidence 46799999775
No 40
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=97.70 E-value=0.00013 Score=67.25 Aligned_cols=70 Identities=24% Similarity=0.339 Sum_probs=54.0
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.++++|||+|+.+| .+++.+++.+. ..+.+..+-||...||||+++-... .+|.+.+.
T Consensus 2 ngil~vdKP~g~tS~--------~vv~~ikk~~~---------~kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~-- 60 (273)
T PRK04099 2 NRLFVANKPAGMSSN--------AFLSRLKRKYG---------VKKAGFSGTLDPFAKGVLIVAFGQY--TKLFRFLK-- 60 (273)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccccCccCCCCCeeEEEEEEChH--hhhHHHhc--
Confidence 369999999999776 35666665553 2567889999999999999999874 44666654
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
.-.|+|.|.+.
T Consensus 61 ----------------~~~K~Y~a~~~ 71 (273)
T PRK04099 61 ----------------KTPKTYRATLW 71 (273)
T ss_pred ----------------cCCceEEEEEE
Confidence 34799999875
No 41
>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=97.67 E-value=0.00017 Score=64.07 Aligned_cols=69 Identities=20% Similarity=0.326 Sum_probs=53.7
Q ss_pred cEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccc
Q 037167 73 DLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKT 152 (353)
Q Consensus 73 ~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~ 152 (353)
.+++||||.|+.+| .+++.+++.+. ..+.+-.+.||...||||+++-+..+ +|...+.
T Consensus 3 G~l~v~KP~g~tS~--------~vv~~vkk~~~---------~kKvGH~GTLDP~AsGvLiv~vG~~T--kl~~~~~--- 60 (209)
T TIGR00431 3 GVLLLDKPQGMTSF--------DALAKVRRLLN---------VKKVGHTGTLDPFATGVLPILVGKAT--KLSPYLT--- 60 (209)
T ss_pred eEEEEECCCCCCHH--------HHHHHHHHHhC---------CCcCCCCCCCCCcCceEEEEEEChHh--hhhHHHc---
Confidence 69999999999765 35666766554 25678899999999999999998743 5666664
Q ss_pred cccccchhhhhhccceEEEEEEEEEe
Q 037167 153 SVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 153 ~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
.-.|+|.|.+.
T Consensus 61 ---------------~~~K~Y~~~~~ 71 (209)
T TIGR00431 61 ---------------DLDKEYRAEIR 71 (209)
T ss_pred ---------------CCCCeEEEEEE
Confidence 45799999775
No 42
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=97.64 E-value=0.00021 Score=64.83 Aligned_cols=70 Identities=26% Similarity=0.420 Sum_probs=53.2
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+++||||.|+.+| .+++.+++.+. ..+.+-.+-||...||||+++-.. +.+|...|.
T Consensus 10 ~Gil~vdKP~G~TS~--------dvv~~vkr~~~---------~kKvGH~GTLDP~AtGvLiv~iG~--aTKl~~~l~-- 68 (244)
T PRK00020 10 DGVLLLDKPVGLSSN--------HALQRAKRTVD---------AAKAGHTGTLDPFATGLLVCCMGR--ATKISGRML-- 68 (244)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhC---------CCCCCcCCcCCCcCeeEEEEEECH--HhhhhHHhc--
Confidence 379999999999776 35666665443 256788999999999999999987 345555554
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
...|+|.|.+.
T Consensus 69 ----------------~~~K~Y~a~~~ 79 (244)
T PRK00020 69 ----------------EADKTYQATLQ 79 (244)
T ss_pred ----------------cCCcEEEEEEE
Confidence 34599999874
No 43
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=97.62 E-value=0.00016 Score=59.41 Aligned_cols=50 Identities=14% Similarity=0.197 Sum_probs=44.4
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEe
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYH 52 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~ 52 (353)
|||..||...-.. -||+.+.++|..|.|+|||.+ .+|+..|+.||.|.+.
T Consensus 9 ~RlDk~L~~~rl~-ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~ 58 (133)
T PRK10348 9 VRLDKWLWAARFY-KTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLR 58 (133)
T ss_pred ccHHHHHHHcCcc-ccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEE
Confidence 5788888887665 599999999999999999999 5899999999999874
No 44
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=97.60 E-value=0.00012 Score=65.10 Aligned_cols=52 Identities=19% Similarity=0.176 Sum_probs=43.9
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEee
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHR 53 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~ 53 (353)
+||+.+|.+.... .||+.+.++|..|.|+|||++++.+++.|++||.|.+..
T Consensus 93 ~RLD~iL~~~g~~-~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~GD~I~v~~ 144 (203)
T PRK05327 93 SRLDNVVYRLGFA-PTRRQARQLVSHGHILVNGKKVNIPSYRVKPGDVIEVRE 144 (203)
T ss_pred HHHHHHHHHcCcc-CCHHHHHHHHHCCcEEECCEEECCCCcCCCCCCEEEECC
Confidence 4676777665433 589999999999999999999988999999999998753
No 45
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=97.57 E-value=0.00013 Score=65.98 Aligned_cols=51 Identities=14% Similarity=0.187 Sum_probs=44.5
Q ss_pred cHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEee
Q 037167 2 TLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHR 53 (353)
Q Consensus 2 ~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~ 53 (353)
||..+|.++... .||+.++++|++|+|+|||++++++++.|..+|.|.+..
T Consensus 1 RLD~~L~~~g~~-~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~d~I~v~~ 51 (228)
T TIGR00478 1 RLDILLVRRGLF-ESREKAKRLILKGFVLVNGKKVDKPSALVDFDAKIELLQ 51 (228)
T ss_pred CHHHHHHHcCCc-cHHHHHHHHHHCCcEEECCEEeCCCCCCCCCCCEEeccC
Confidence 577788887654 589999999999999999999999999999999988753
No 46
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=97.52 E-value=0.00033 Score=65.61 Aligned_cols=70 Identities=20% Similarity=0.257 Sum_probs=53.2
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+++||||+|+.+| .+++.++..+. ..+.+-.+.||...||||+++-... .++.+.+.+
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~~- 62 (294)
T PRK02484 3 NGIINLKKEAGMTSH--------DAVFKLRKILQ---------TKKIGHGGTLDPDVVGVLPIAVGKA--TRLIEYMTE- 62 (294)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccccCCCCCCCCeeEEEEEEChh--hhhhHHhcc-
Confidence 369999999999876 35566665443 2568889999999999999999873 446665543
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
-.|+|.|.+.
T Consensus 63 -----------------~~K~Y~a~~~ 72 (294)
T PRK02484 63 -----------------AGKVYEGEIT 72 (294)
T ss_pred -----------------CCcEEEEEEE
Confidence 3599999875
No 47
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=97.52 E-value=0.00034 Score=65.86 Aligned_cols=70 Identities=19% Similarity=0.250 Sum_probs=53.6
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+++||||.|+.+| .+++.+++.+. ..+.+-.+.||...||||+++-.+.+ ++.+.+.
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~v~vG~aT--kl~~~l~-- 61 (305)
T PRK14123 3 NGILPVYKERGLTSH--------DVVFKLRKILK---------TKKIGHTGTLDPEVAGVLPVCIGNAT--RVSDYVM-- 61 (305)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccccCcCCCCcCeeEEEEEEChhh--hhHHHhc--
Confidence 369999999999776 35666665543 25688899999999999999998743 4665553
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
...|+|.|.+.
T Consensus 62 ----------------~~~K~Y~~~~~ 72 (305)
T PRK14123 62 ----------------DMGKAYEATVS 72 (305)
T ss_pred ----------------CCCcEEEEEEE
Confidence 35799999874
No 48
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=97.51 E-value=0.00031 Score=65.15 Aligned_cols=68 Identities=22% Similarity=0.293 Sum_probs=51.8
Q ss_pred EEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcccc
Q 037167 74 LIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTS 153 (353)
Q Consensus 74 ~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~ 153 (353)
++++|||.|+.+| .+++.+++.+. ..+.+-.+.||...||||+++-... .++.+.+.
T Consensus 2 il~i~KP~G~tS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~---- 58 (279)
T PRK02193 2 IKLLYKPKGISSF--------KFIKNFAKTNN---------IKKIGHTGTLDPLASGLLLVATDED--TKLIDYLD---- 58 (279)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHcC---------CCccccCccCCCcCeeEEEEEEChh--hhhhHHhc----
Confidence 7899999999876 34556665443 2567889999999999999999873 44555553
Q ss_pred ccccchhhhhhccceEEEEEEEEEe
Q 037167 154 VIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 154 ~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
...|+|.|.+.
T Consensus 59 --------------~~~K~Y~a~~~ 69 (279)
T PRK02193 59 --------------QKDKTYIAKIK 69 (279)
T ss_pred --------------cCCcEEEEEEE
Confidence 45799999874
No 49
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=97.51 E-value=0.00033 Score=65.61 Aligned_cols=71 Identities=18% Similarity=0.286 Sum_probs=53.9
Q ss_pred CCcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhc
Q 037167 71 DDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFAD 150 (353)
Q Consensus 71 d~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~ 150 (353)
-+.+++||||.|+.+| .+++.+++.+. ..+.+-.+-||...||||+++-.. +.++.+.+.
T Consensus 8 ~~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~i~vG~--aTKl~~~l~- 67 (298)
T PRK03287 8 GSGLVVVDKPAGMTSH--------DVVARCRRLFG---------TRKVGHAGTLDPMATGVLVLGVER--ATKLLGHLT- 67 (298)
T ss_pred cCeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCCCCcCccCCCcceeEEEEEeCh--hhhhhHHHh-
Confidence 3479999999999776 35666665554 256788999999999999999986 345555554
Q ss_pred cccccccchhhhhhccceEEEEEEEEEe
Q 037167 151 KTSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 151 g~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
.-.|+|.|.+.
T Consensus 68 -----------------~~~K~Y~a~~~ 78 (298)
T PRK03287 68 -----------------LTDKSYTATIR 78 (298)
T ss_pred -----------------cCCcEEEEEEE
Confidence 34799999774
No 50
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=97.50 E-value=0.00039 Score=65.02 Aligned_cols=70 Identities=26% Similarity=0.351 Sum_probs=53.8
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+++||||.|+.+| .+++.+++.+. ..+.+-.+-||...||||+++-... .++.+.+.+
T Consensus 2 ~Gil~i~KP~G~tS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~- 61 (290)
T PRK00130 2 DGILNILKPPGMTSF--------DVVRKIRKIAK---------IKKVGHTGTLDPLASGVLPVCLGKA--TKIVDYLME- 61 (290)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccCcCCCCCCCCeeEEEEEEChh--hhhHHHhcc-
Confidence 379999999999776 35666665543 2467889999999999999999873 456666643
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
-.|+|.|.+.
T Consensus 62 -----------------~~K~Y~a~~~ 71 (290)
T PRK00130 62 -----------------GKKTYRAEIK 71 (290)
T ss_pred -----------------CCcEEEEEEE
Confidence 4799999875
No 51
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Probab=97.48 E-value=0.00044 Score=64.32 Aligned_cols=69 Identities=25% Similarity=0.346 Sum_probs=53.0
Q ss_pred cEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccc
Q 037167 73 DLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKT 152 (353)
Q Consensus 73 ~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~ 152 (353)
.++++|||.|+.+| .+++.+++.+. ..+.+-.+-||...||||+++-+.. .+|...+.
T Consensus 1 Gil~i~KP~G~tS~--------~vv~~vr~~~~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~--- 58 (277)
T cd02573 1 GILLLDKPAGLTSH--------DVVQKVRRLLG---------TKKVGHTGTLDPLATGVLPIALGEA--TKLSQYLL--- 58 (277)
T ss_pred CEEEEECCCCCCHH--------HHHHHHHHHhC---------cCccCCCCCCCCcCeEEEEEEEChH--HhhHHHhc---
Confidence 37999999999776 35666665543 2467889999999999999999874 44666664
Q ss_pred cccccchhhhhhccceEEEEEEEEEe
Q 037167 153 SVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 153 ~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
.-.|+|.|.+.
T Consensus 59 ---------------~~~K~Y~~~~~ 69 (277)
T cd02573 59 ---------------DADKTYRATVR 69 (277)
T ss_pred ---------------CCCcEEEEEEE
Confidence 35799999875
No 52
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=97.48 E-value=0.00041 Score=65.20 Aligned_cols=70 Identities=26% Similarity=0.334 Sum_probs=53.6
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+++||||.|+.+| .+++.+++.+. ..+.+-.+-||...||||+++-.. +.++...+.
T Consensus 13 ~Gil~i~KP~G~TS~--------dvv~~vrk~~~---------~kKvGH~GTLDP~AtGvL~v~vG~--aTkl~~~l~-- 71 (305)
T PRK05389 13 SGWLILDKPAGMTST--------EAVSKVKWLFD---------AQKAGHAGTLDPLASGVLPIALGE--ATKTVPYVM-- 71 (305)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhc---------ccccCCcccCCCCCceEEEEEECh--hhhhhHHhc--
Confidence 379999999999876 35666665544 246788999999999999999987 345565554
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
.-.|+|.|.+.
T Consensus 72 ----------------~~~K~Y~a~~~ 82 (305)
T PRK05389 72 ----------------DGTKRYRFTVA 82 (305)
T ss_pred ----------------cCCcEEEEEEE
Confidence 34799999874
No 53
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=97.47 E-value=0.00044 Score=65.35 Aligned_cols=70 Identities=17% Similarity=0.172 Sum_probs=53.3
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+++||||.|+.+| .+++.++..+. ..+++-.|.||...||||+++-... .++...+.
T Consensus 3 nGiL~idKP~G~TS~--------dvv~~vrk~l~---------~kKVGH~GTLDP~AtGVL~i~vG~a--TKl~~~l~-- 61 (345)
T PRK14846 3 NYWLNIYKPRGISSA--------QLVSIVKKILG---------KTKIGHAGTLDVEAEGILPFAVGEA--TKLIHLLI-- 61 (345)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCcCCcCccCCCcCceEEEEEEChh--hhhhHHHh--
Confidence 479999999999776 35666665443 2568889999999999999999873 45555554
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
.-.|+|.|.+.
T Consensus 62 ----------------~~~K~Y~a~~~ 72 (345)
T PRK14846 62 ----------------DARKTYIFTVK 72 (345)
T ss_pred ----------------cCCceEEEEEE
Confidence 34689999774
No 54
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=97.45 E-value=0.00048 Score=64.82 Aligned_cols=70 Identities=17% Similarity=0.284 Sum_probs=53.4
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+++||||+|+.+| .+++.+++.+. ..+.+-.+-||...||||+++-+.. .++.+.+.+
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~- 62 (308)
T PRK14124 3 HGFLVAYKPKGPTSH--------DVVDEVRKKLK---------TRKVGHAGTLDPFATGVLIVGVNKA--TRLLEYLKN- 62 (308)
T ss_pred ceEEEEECCCCCCHH--------HHHHHHHHHcC---------CCccCcCcCCCCCCcEEEEEEEChH--HhhhHHHhc-
Confidence 369999999999876 35566665543 2467889999999999999999874 446666543
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
-.|+|.|.+.
T Consensus 63 -----------------~~K~Y~a~~~ 72 (308)
T PRK14124 63 -----------------EKKVYYVKMR 72 (308)
T ss_pred -----------------CCceEEEEEE
Confidence 3799999874
No 55
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=97.45 E-value=0.00046 Score=64.58 Aligned_cols=69 Identities=22% Similarity=0.292 Sum_probs=52.8
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+++||||.|+.+| .+++.++..+. ..+.+-.+-||...||+|+++-.+.+ +|.+.+.
T Consensus 3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~i~vG~aT--kl~~~l~-- 61 (295)
T PRK02755 3 FGFLNLDKPAGLTSH--------DCVARLRRLLR---------LKRVGHGGTLDPAATGVLPIALGKAT--RLLPYLP-- 61 (295)
T ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccccCCCCCCcCeeEEEEEEChhh--hhHHHhC--
Confidence 379999999999776 35666665443 25678899999999999999998743 5665552
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
. .|+|.|.+.
T Consensus 62 ----------------~-~K~Y~a~~~ 71 (295)
T PRK02755 62 ----------------G-EKTYRGTIR 71 (295)
T ss_pred ----------------C-CcEEEEEEE
Confidence 3 699999874
No 56
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=97.44 E-value=0.00044 Score=65.24 Aligned_cols=71 Identities=20% Similarity=0.181 Sum_probs=53.9
Q ss_pred CCcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhc
Q 037167 71 DDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFAD 150 (353)
Q Consensus 71 d~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~ 150 (353)
.+.++++|||.|+.+| .+++.+++.+. ..+.+-.+-||...||+|+++-+.. .++.+.+.+
T Consensus 21 ~~g~l~i~Kp~g~tS~--------~~v~~~r~~~~---------~kkvGH~GTLDp~A~GvL~v~~g~a--tk~~~~~~~ 81 (300)
T PRK04270 21 KFGVVNLDKPPGPTSH--------EVAAWVRDILG---------VEKAGHGGTLDPKVTGVLPVALGKA--TKVVQALLE 81 (300)
T ss_pred CCCEEEEECCCCCCHH--------HHHHHHHHHhc---------cccccCCCCCCCcCeEEEEEEEChH--hhhhHHhcc
Confidence 3589999999999776 35666665443 2467889999999999999999873 456666643
Q ss_pred cccccccchhhhhhccceEEEEEEEEEe
Q 037167 151 KTSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 151 g~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
-.|+|.|.+.
T Consensus 82 ------------------~~K~Y~~~~~ 91 (300)
T PRK04270 82 ------------------SGKEYVCVMH 91 (300)
T ss_pred ------------------CCcEEEEEEE
Confidence 4599998764
No 57
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=97.44 E-value=0.00053 Score=64.60 Aligned_cols=70 Identities=20% Similarity=0.285 Sum_probs=53.9
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+++||||.|+.+| .+++.+++.+. ..+.+-.+-||...||||+++-.+. .+|.+.+.
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~~~-- 68 (312)
T PRK05033 10 NGVLLLDKPQGMSSN--------DALQKVKRLFN---------ANKAGHTGALDPLATGMLPICLGEA--TKFSQYLL-- 68 (312)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCCCCCCCcCCCcCeeEEEEEECHH--hhhhHHhc--
Confidence 479999999999876 35666665543 2567889999999999999999874 34666654
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
.-.|+|.|.+.
T Consensus 69 ----------------~~~K~Y~a~~~ 79 (312)
T PRK05033 69 ----------------DSDKRYRVTAR 79 (312)
T ss_pred ----------------CCCcEEEEEEE
Confidence 34799999875
No 58
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=97.43 E-value=0.00029 Score=62.43 Aligned_cols=42 Identities=26% Similarity=0.404 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCC
Q 037167 14 SAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLP 55 (353)
Q Consensus 14 ~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~ 55 (353)
..|+.++.++|..|.|.|||++|+.|++.|.+||++.+....
T Consensus 106 A~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~ 147 (205)
T COG0522 106 AKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKS 147 (205)
T ss_pred cccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEeeecc
Confidence 369999999999999999999999999999999999886443
No 59
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=97.43 E-value=0.0006 Score=63.95 Aligned_cols=70 Identities=23% Similarity=0.251 Sum_probs=53.8
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+++||||.|+.+| .+++.+++.+. ..+.+-.+-||...||||+++-... .+|.+.+.+
T Consensus 16 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~- 75 (303)
T PRK01851 16 DGVLLLDKPLGLSSN--------DALQRAKRLLR---------AKKAGHTGTLDPLATGLLPLCFGEA--TKFSQDLLD- 75 (303)
T ss_pred CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------cccCCCCCCCCCCCceEEEEEECHH--HhhhHHhcc-
Confidence 479999999999876 35666666554 2467889999999999999999874 446666643
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
-.|+|.|.+.
T Consensus 76 -----------------~~K~Y~~~~~ 85 (303)
T PRK01851 76 -----------------ADKTYEATLR 85 (303)
T ss_pred -----------------cCeEEEEEEE
Confidence 4599999874
No 60
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=97.40 E-value=0.00057 Score=64.31 Aligned_cols=70 Identities=24% Similarity=0.298 Sum_probs=53.3
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+++||||.|+.+| .+++.+++.+. ..+.+-.+-||...||||+++-... .+|.+.+.+
T Consensus 2 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~~- 61 (304)
T PRK01550 2 NGVLLLHKPRGMTSH--------DCVFKLRKILR---------TKKVGHTGTLDPEVSGVLPICVGRA--TKIAEYLTD- 61 (304)
T ss_pred CeEEEEECCCCCCHH--------HHHHHHHHHcC---------CCCcccCCCCCCcCeeEEEEEEChh--hhhhHHhcC-
Confidence 369999999999876 35566665443 2567889999999999999999874 446666643
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
-.|+|.|.+.
T Consensus 62 -----------------~~K~Y~a~~~ 71 (304)
T PRK01550 62 -----------------EGKTYEGEVT 71 (304)
T ss_pred -----------------CCcEEEEEEE
Confidence 4799999875
No 61
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=97.39 E-value=0.0006 Score=63.71 Aligned_cols=70 Identities=16% Similarity=0.160 Sum_probs=52.9
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+|+||||.|+.+| .+++.++..+. ..+.+-.+-||...||+|+++-... .++.+.+.
T Consensus 3 ~GiL~i~KP~G~TS~--------dvv~~vrk~~~---------~kKvGH~GTLDP~AtGvL~v~vG~a--TKl~~~l~-- 61 (292)
T PRK01528 3 NYWLNIYKPRGISSA--------KLVSIVKKILG---------KVKIGHAGTLDVEAEGVLPLAVGEA--TKLVQLLI-- 61 (292)
T ss_pred CEEEEEeCCCCCCHH--------HHHHHHHHHcC---------CCccCcCccCCCcCceEEEEEEChH--hhhhHHHh--
Confidence 479999999999776 35566665443 2467889999999999999999873 45555554
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
.-.|+|.|.+.
T Consensus 62 ----------------~~~K~Y~~~~~ 72 (292)
T PRK01528 62 ----------------DAKKTYIFTVK 72 (292)
T ss_pred ----------------cCCceEEEEEE
Confidence 34689999774
No 62
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=97.36 E-value=0.0003 Score=63.27 Aligned_cols=52 Identities=19% Similarity=0.199 Sum_probs=45.9
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeC
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRL 54 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~ 54 (353)
|||....++-+. .||+.+.++|.+|.|+||.+.+.++++.|..||.|.+.+.
T Consensus 181 lRLD~vis~~~~--~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG~ 232 (257)
T COG2302 181 LRLDVVISEGFG--LSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRGF 232 (257)
T ss_pred hhHHHHHHHHHh--hhHHHHHHHHHcCceEEeeEEeccccceeccCCEEEEecc
Confidence 567777777776 5999999999999999999999999999999999998654
No 63
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=97.26 E-value=0.001 Score=62.70 Aligned_cols=68 Identities=22% Similarity=0.276 Sum_probs=52.3
Q ss_pred EEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcccc
Q 037167 74 LIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTS 153 (353)
Q Consensus 74 ~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~ 153 (353)
+++||||.|+.+| .+++.+++.+. ..+.+-.+-||...||||+++-... .+|.+.+.
T Consensus 3 il~idKP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~i~iG~a--TKl~~~l~---- 59 (312)
T PRK14122 3 VYAVDKPLGLTSH--------DVVNRARRALG---------TRRVGHTGTLDPLATGVLVLCTDDS--TKLVPFLS---- 59 (312)
T ss_pred EEEEECCCCCCHH--------HHHHHHHHHhC---------CCCCCCCCCCCCcCeeeEEEEEChh--hhhhHHhc----
Confidence 8999999999776 35666665443 2567889999999999999999874 34666653
Q ss_pred ccccchhhhhhccceEEEEEEEEEe
Q 037167 154 VIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 154 ~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
...|+|.|.+.
T Consensus 60 --------------~~~K~Y~a~~~ 70 (312)
T PRK14122 60 --------------AEDKEYLAWVS 70 (312)
T ss_pred --------------CCCceEEEEEE
Confidence 45799999874
No 64
>PRK11507 ribosome-associated protein; Provisional
Probab=97.22 E-value=0.00099 Score=48.34 Aligned_cols=51 Identities=20% Similarity=0.228 Sum_probs=40.5
Q ss_pred cHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEee
Q 037167 2 TLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHR 53 (353)
Q Consensus 2 ~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~ 53 (353)
+|..||-..-.. .|=.+++.+|.+|.|+|||++.+.-+.++.+||.|++.+
T Consensus 13 ~L~QlLK~~~~v-~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~V~~~g 63 (70)
T PRK11507 13 ELCDLLKLEGWS-ESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAG 63 (70)
T ss_pred EHHHHHhhhCcc-cChHHHHHHHHcCceEECCEEecccCCCCCCCCEEEECC
Confidence 445555444332 466789999999999999999999999999999998854
No 65
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=97.22 E-value=0.00097 Score=63.43 Aligned_cols=70 Identities=19% Similarity=0.220 Sum_probs=53.8
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+|+||||.|+.+| .+++.++..+. ..+.+-.+-||...||||+++-.+. .+|.+.+.
T Consensus 34 ~G~l~i~KP~g~tS~--------~~v~~vr~~~~---------~kkvGH~GTLDP~A~GvL~v~~G~a--Tkl~~~~~-- 92 (322)
T TIGR00425 34 YGVVNLDKPSGPSSH--------EVVAWVRRILN---------VEKTGHGGTLDPKVTGVLPVCIERA--TRLVKSLQ-- 92 (322)
T ss_pred CCEEEEeCCCCCCHH--------HHHHHHHHHhc---------ccccCCCCCCCCCCceEEEEEEChH--hhccHHhc--
Confidence 479999999999876 35666665543 2467889999999999999999873 45666654
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
.-.|+|.|.+.
T Consensus 93 ----------------~~~K~Y~~~v~ 103 (322)
T TIGR00425 93 ----------------EAPKEYVCLMR 103 (322)
T ss_pred ----------------cCCCEEEEEEE
Confidence 35799998774
No 66
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=97.20 E-value=0.00066 Score=61.03 Aligned_cols=51 Identities=16% Similarity=0.227 Sum_probs=46.7
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEe
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYH 52 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~ 52 (353)
|||..+|.++..- .||+.++.+|.+|.|+|||.++++|++.|..++.|.+.
T Consensus 3 ~RLD~~Lv~rgl~-~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~ 53 (245)
T COG1189 3 MRLDALLVERGLF-ESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVK 53 (245)
T ss_pred chHHHHHHHccch-hhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEc
Confidence 7899999999654 59999999999999999999999999999999999875
No 67
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=97.19 E-value=0.0013 Score=61.66 Aligned_cols=70 Identities=26% Similarity=0.279 Sum_probs=53.7
Q ss_pred CcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcc
Q 037167 72 DDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADK 151 (353)
Q Consensus 72 ~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g 151 (353)
+.+++||||.|+.+| .+++.+++.+. ..+.+-.+-||...||||+++-... .+|.+.+.
T Consensus 10 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~v~~G~a--Tkl~~~l~-- 68 (300)
T PRK04642 10 DGILLLDKPAGLSSN--------NALQAARRLLR---------AEKGGHTGSLDPLATGLLPLCFGEA--TKIAGLLL-- 68 (300)
T ss_pred CeEEEEecCCCCCHH--------HHHHHHHHHhC---------CCcccCCCccCCcCeeeEEEEEChh--hhhhHHhc--
Confidence 479999999999876 35666665544 2467889999999999999999863 45666654
Q ss_pred ccccccchhhhhhccceEEEEEEEEEe
Q 037167 152 TSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 152 ~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
.-.|+|.|.+.
T Consensus 69 ----------------~~~K~Y~a~~~ 79 (300)
T PRK04642 69 ----------------GSAKAYDAEIV 79 (300)
T ss_pred ----------------CCCcEEEEEEE
Confidence 34799999873
No 68
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=97.05 E-value=0.0023 Score=59.22 Aligned_cols=69 Identities=23% Similarity=0.226 Sum_probs=52.9
Q ss_pred cEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccc
Q 037167 73 DLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKT 152 (353)
Q Consensus 73 ~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~ 152 (353)
.++++|||.|+.+| .++..+++.+. ..+.+-.+-||...||+|.++-. ++ .+|...+.
T Consensus 16 Gil~ldKP~G~tS~--------~~v~~vkkil~---------~~K~GH~GTLDP~atGvLpi~ig-~a-TKl~~~l~--- 73 (271)
T COG0130 16 GVINLDKPPGPTSH--------EVVAWVKRILG---------VEKAGHGGTLDPLATGVLPICLG-EA-TKLVQYLL--- 73 (271)
T ss_pred ceEEeeCCCCCCHH--------HHHHHHHHHhC---------ccccccccccCCcccceEEEEec-hh-HhHHHHHh---
Confidence 79999999999776 35566666554 35678899999999999999998 33 44555543
Q ss_pred cccccchhhhhhccceEEEEEEEEEe
Q 037167 153 SVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 153 ~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
.-.|+|.|.+.
T Consensus 74 ---------------~~~K~Y~a~~~ 84 (271)
T COG0130 74 ---------------DADKEYVATVR 84 (271)
T ss_pred ---------------hCCcEEEEEEE
Confidence 34699999885
No 69
>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=96.99 E-value=0.0046 Score=47.16 Aligned_cols=20 Identities=10% Similarity=-0.047 Sum_probs=18.4
Q ss_pred CCCcccccCCCCCceEEEEE
Q 037167 116 SHPVPVHRLGRGTSGILLCA 135 (353)
Q Consensus 116 ~~~~~vhRLD~~TSGlll~a 135 (353)
.+++.++++|+.++|+++++
T Consensus 24 ~~i~~aG~kDk~a~t~q~v~ 43 (87)
T cd01291 24 KRVGYAGRKDKRAVTTQLVS 43 (87)
T ss_pred heEEECccCCCCeeEEEEEc
Confidence 56789999999999999998
No 70
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=96.72 E-value=0.0062 Score=57.42 Aligned_cols=78 Identities=21% Similarity=0.185 Sum_probs=50.6
Q ss_pred cEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcC--------------------CCccCCCCCCcccccCCCCCceEE
Q 037167 73 DLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQS--------------------SSLSSQASHPVPVHRLGRGTSGIL 132 (353)
Q Consensus 73 ~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~--------------------~~~~~~~~~~~~vhRLD~~TSGll 132 (353)
.+++||||.|+.+| .+++.+++.+.... ........+.+-.+-||-..||||
T Consensus 1 Gil~i~KP~G~TS~--------~vv~~lk~~l~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~KiGH~GTLDPlAsGVL 72 (312)
T cd02867 1 GVFAINKPSGITSA--------QVLNDLKPLFLNSALFKDKIQRAVAKRGKKARRRKGRKRSKLKIGHGGTLDPLATGVL 72 (312)
T ss_pred CeEEEeCCCCCCHH--------HHHHHHHHHhcccccccchhhhhhhhhhhhhhhhccccccccccccccccCCccceeE
Confidence 37999999999776 34555554433100 000001246788999999999999
Q ss_pred EEEeChHHHHHHHHHhhccccccccchhhhhhccceEEEEEEEEEe
Q 037167 133 LCAKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 133 l~ak~~~~~~~L~~~f~~g~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
+++-... .+.++ .|. ...|+|.|...
T Consensus 73 vvgvG~a-TK~l~-~~l------------------~~~K~Y~~~~~ 98 (312)
T cd02867 73 VVGVGAG-TKQLQ-DYL------------------SCSKTYEATGL 98 (312)
T ss_pred EEEECcH-HHHHH-HHh------------------cCCceEEEEEE
Confidence 9999863 33343 332 35799999764
No 71
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=96.60 E-value=0.0056 Score=52.97 Aligned_cols=50 Identities=26% Similarity=0.287 Sum_probs=39.8
Q ss_pred cHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCC--CEEEEe
Q 037167 2 TLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAG--SELVYH 52 (353)
Q Consensus 2 ~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~g--d~i~~~ 52 (353)
||.-.|.+.... .|+.++.++|..|.|+|||++|++|++.|..+ |.|.+.
T Consensus 104 RLd~il~r~gla-~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~ 155 (177)
T PRK04051 104 RLQTIVYRKGLA-RTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYY 155 (177)
T ss_pred HHHHHHHHccCc-CCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEe
Confidence 344444444443 59999999999999999999999999999988 567654
No 72
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=96.48 E-value=0.009 Score=43.63 Aligned_cols=51 Identities=18% Similarity=0.096 Sum_probs=40.6
Q ss_pred cHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEee
Q 037167 2 TLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHR 53 (353)
Q Consensus 2 ~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~ 53 (353)
+|-++|--.-.. -|=.+++.+|..|.|+|||++-+.-+.+|..||.|.+..
T Consensus 13 ~L~qlLK~~g~i-~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~ 63 (73)
T COG2501 13 TLGQLLKLAGLI-ESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPG 63 (73)
T ss_pred EHHHHHHHhCcc-cCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECC
Confidence 455555554433 355788999999999999999998999999999998753
No 73
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=96.40 E-value=0.00073 Score=48.48 Aligned_cols=50 Identities=20% Similarity=0.157 Sum_probs=30.5
Q ss_pred cHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEe
Q 037167 2 TLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYH 52 (353)
Q Consensus 2 ~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~ 52 (353)
+|..+|-..-.. .|=.+++.+|.+|.|+|||++.+..+.++.+||.|.+.
T Consensus 9 ~L~qlLK~~glv-~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~~ 58 (65)
T PF13275_consen 9 TLGQLLKLAGLV-SSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEID 58 (65)
T ss_dssp -HHHHHHHHTS--SSSSTTSHHHHHHHHEETTB----SS----SSEEEEET
T ss_pred EHHHHHhHcCCc-ccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEEC
Confidence 455555544332 24457788899999999999999999999999999874
No 74
>PRK04313 30S ribosomal protein S4e; Validated
Probab=96.01 E-value=0.021 Score=51.61 Aligned_cols=72 Identities=17% Similarity=0.170 Sum_probs=55.2
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCCCCCCCCccEEEECCcEEEEEC
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALNK 79 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~~~~~~~~~Ilyed~~~ivvnK 79 (353)
+.|+=+|...+....+.+++.+.|.+|.|+|||++.++..+.+---|+|++... ...++|+|.....+++.+
T Consensus 38 iPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~~~-------~e~yRvl~d~kgr~~l~~ 109 (237)
T PRK04313 38 IPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIPET-------GEYYRVLPDEKGRLVLIP 109 (237)
T ss_pred cccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEccC-------CCeEEEEECCCCcEEEEE
Confidence 356667888888777899999999999999999999888777766699987422 234667777776666553
No 75
>PLN00036 40S ribosomal protein S4; Provisional
Probab=95.74 E-value=0.032 Score=51.03 Aligned_cols=72 Identities=15% Similarity=0.208 Sum_probs=55.4
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCCCCCCCCccEEEECCcEEEEEC
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALNK 79 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~~~~~~~~~Ilyed~~~ivvnK 79 (353)
+.|.=+|...+.+..+.+++.+.+.+|.|+|||++.++..+.+---|+|++... ...++|+|.....+++.+
T Consensus 42 lPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt-------~e~yRvl~D~kGrf~l~~ 113 (261)
T PLN00036 42 LPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPKT-------NENFRLLYDTKGRFRLHR 113 (261)
T ss_pred cccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcCC-------CCeEEEEECCCceEEEEE
Confidence 356677888888767889999999999999999999887777766699987422 234678887777666654
No 76
>PLN00189 40S ribosomal protein S9; Provisional
Probab=95.66 E-value=0.025 Score=49.52 Aligned_cols=38 Identities=18% Similarity=0.246 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEe
Q 037167 15 APLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYH 52 (353)
Q Consensus 15 ~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~ 52 (353)
.|..++.++|..|.|.|||++|+.|++.|..|+++.+.
T Consensus 122 ~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~It 159 (194)
T PLN00189 122 KSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHID 159 (194)
T ss_pred CCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEE
Confidence 48899999999999999999999999999999887654
No 77
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=95.61 E-value=0.036 Score=50.99 Aligned_cols=72 Identities=18% Similarity=0.176 Sum_probs=55.1
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCCCCCCCCccEEEECCcEEEEEC
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALNK 79 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~~~~~~~~~Ilyed~~~ivvnK 79 (353)
+.|.=+|...+.+..+.+++.+.+.+|.|+|||++.++..+.+---|+|++... ...++|+|.....+++.+
T Consensus 39 iPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~kt-------~e~yRvl~D~kGrf~l~~ 110 (273)
T PTZ00223 39 LPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPKT-------GDRFRILYDVKGRFALVK 110 (273)
T ss_pred cccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcCC-------CCeEEEEECCCCcEEEEE
Confidence 356667888888767889999999999999999999887777766699987422 234667777777666653
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=95.59 E-value=0.028 Score=47.91 Aligned_cols=38 Identities=29% Similarity=0.462 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHcCCEEECCEEccCCCceecCC--CEEEEe
Q 037167 15 APLQGWLQRIQNGQITVDGRVVNDPNIILSAG--SELVYH 52 (353)
Q Consensus 15 ~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~g--d~i~~~ 52 (353)
.|..++.++|..|.|+|||++|+.|++.|..+ |.|.+.
T Consensus 117 ~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~ 156 (162)
T TIGR01018 117 RTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFA 156 (162)
T ss_pred CCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeee
Confidence 58999999999999999999999999999988 666553
No 79
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=95.52 E-value=0.04 Score=50.42 Aligned_cols=70 Identities=13% Similarity=0.151 Sum_probs=53.7
Q ss_pred cHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCCCCCCCCccEEEECCcEEEEE
Q 037167 2 TLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALN 78 (353)
Q Consensus 2 ~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~~~~~~~~~Ilyed~~~ivvn 78 (353)
.|.=+|...+.+..+.+++.+.+.+|.|+|||++.++..+.+---|+|++... ...++++|.....+++.
T Consensus 43 PL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt-------~e~yRvl~D~kGr~~l~ 112 (262)
T PTZ00118 43 PLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTKT-------NEYFRLLYDTKGRFVPH 112 (262)
T ss_pred ccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEcCC-------CCeEEEEECCCccEEEE
Confidence 46667888888767889999999999999999999887777766699987422 23466777766666555
No 80
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=94.54 E-value=0.04 Score=47.88 Aligned_cols=38 Identities=16% Similarity=0.308 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHcCCEEECCEEccCCCceecCCC--EEEE
Q 037167 14 SAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGS--ELVY 51 (353)
Q Consensus 14 ~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd--~i~~ 51 (353)
..|..++.++|..|.|.|||++|+.|++.|..++ .|.+
T Consensus 119 A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I~~ 158 (181)
T PTZ00155 119 AKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHIDF 158 (181)
T ss_pred cCCHHHhhhheeCCCEEECCEEeccCceEeccCccCceee
Confidence 3588999999999999999999999999999884 4544
No 81
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=93.61 E-value=0.1 Score=46.67 Aligned_cols=66 Identities=15% Similarity=0.166 Sum_probs=46.2
Q ss_pred HHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCCCCCCCCccEEEECCcEEEEEC
Q 037167 7 YSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALNK 79 (353)
Q Consensus 7 l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~~~~~~~~~Ilyed~~~ivvnK 79 (353)
+..-+.+.-.-+++++.|.+|.|+|||++.++..+.|--=|+|++.. .....+|+|.....+++.+
T Consensus 47 iRd~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~-------tgE~yRvl~d~~grl~l~~ 112 (241)
T COG1471 47 IRDYLKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPK-------TGEHYRVLPDEKGRLVLHP 112 (241)
T ss_pred ehhHHHhccchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECC-------CCceEEEEecCCccEEEEe
Confidence 33334333345799999999999999999876555554449998742 2234678888888888765
No 82
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=90.81 E-value=0.38 Score=47.56 Aligned_cols=46 Identities=22% Similarity=0.336 Sum_probs=37.5
Q ss_pred cHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCE
Q 037167 2 TLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSE 48 (353)
Q Consensus 2 ~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~ 48 (353)
+|.+.|.+.-. ..|+++++++|.+|.|+|||++++++++.+.+++.
T Consensus 344 ~~~~~l~~~~~-~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~~ 389 (410)
T PRK13354 344 NLVDLLVDLGL-EPSKREARRLIQNGAIKINGEKVTDVDAIINPEDA 389 (410)
T ss_pred CHHHHHHHhCC-CCCHHHHHHHHHcCCEEECCEEccCcccccChhhh
Confidence 57777775443 36999999999999999999999888888776663
No 83
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=89.04 E-value=1 Score=44.51 Aligned_cols=43 Identities=21% Similarity=0.324 Sum_probs=34.8
Q ss_pred cHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecC
Q 037167 2 TLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSA 45 (353)
Q Consensus 2 ~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~ 45 (353)
++++.|.+.- ...|+++++++|++|.|+|||++|++.+..+..
T Consensus 344 ~~~~~l~~~~-~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~ 386 (408)
T PRK05912 344 DLLALLVEAG-LVPSKSEARRLIKQGGVKINGEKVSDENYVLTA 386 (408)
T ss_pred cHHHHHHHhC-CCCCHHHHHHHHHcCCEEECCEEecCccccccc
Confidence 5777776543 336999999999999999999999877776665
No 84
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=88.77 E-value=0.51 Score=35.51 Aligned_cols=26 Identities=35% Similarity=0.452 Sum_probs=23.8
Q ss_pred CCEEECCEEccCCCceecCCCEEEEee
Q 037167 27 GQITVDGRVVNDPNIILSAGSELVYHR 53 (353)
Q Consensus 27 G~V~vNg~~v~~~~~~v~~gd~i~~~~ 53 (353)
|.|.|||+.+ ..++.++.||.|.++.
T Consensus 50 ~~i~vNG~~v-~~~~~~~~Gd~v~V~P 75 (81)
T PF14451_consen 50 GLILVNGRPV-DFDYRLKDGDRVAVYP 75 (81)
T ss_pred EEEEECCEEC-CCcccCCCCCEEEEEe
Confidence 8999999998 6999999999999864
No 85
>PRK01777 hypothetical protein; Validated
Probab=86.37 E-value=0.92 Score=35.21 Aligned_cols=30 Identities=13% Similarity=0.161 Sum_probs=25.4
Q ss_pred HcCCEEECCEEccCCCceecCCCEEEEeeCC
Q 037167 25 QNGQITVDGRVVNDPNIILSAGSELVYHRLP 55 (353)
Q Consensus 25 ~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~ 55 (353)
..+.|-|||+.+ ..++.|+.||+|++++.-
T Consensus 48 ~~~~vgI~Gk~v-~~d~~L~dGDRVeIyrPL 77 (95)
T PRK01777 48 AKNKVGIYSRPA-KLTDVLRDGDRVEIYRPL 77 (95)
T ss_pred ccceEEEeCeEC-CCCCcCCCCCEEEEecCC
Confidence 457899999999 589999999999997543
No 86
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=86.35 E-value=0.75 Score=41.51 Aligned_cols=22 Identities=36% Similarity=0.354 Sum_probs=19.1
Q ss_pred CCcccccCCCCCceEEEEEeCh
Q 037167 117 HPVPVHRLGRGTSGILLCAKTK 138 (353)
Q Consensus 117 ~~~~vhRLD~~TSGlll~ak~~ 138 (353)
....+||||-.|||+++|.-+.
T Consensus 90 ~V~v~h~l~~~~sgvl~~gVgh 111 (318)
T KOG2559|consen 90 DVQVVHVLPLATSGVLLFGVGH 111 (318)
T ss_pred ceeeEEeecccccceEEEecCc
Confidence 4578999999999999998764
No 87
>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=84.18 E-value=1.2 Score=37.65 Aligned_cols=43 Identities=23% Similarity=0.222 Sum_probs=31.1
Q ss_pred CCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccccccccchhhhhhccceEEEEEEEEEe
Q 037167 116 SHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVH 178 (353)
Q Consensus 116 ~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~~~~~~~~~~~~~~~~v~K~Y~alv~ 178 (353)
.+.+-.+.||...||||+++-+.. .+|.+.+.+ ..|+|.|...
T Consensus 7 ~KvGH~GTLDP~AsGvL~v~vg~~--Tkl~~~l~~------------------~~K~Y~~~~~ 49 (149)
T PF01509_consen 7 KKVGHGGTLDPFASGVLVVGVGKA--TKLLSYLQN------------------SDKEYVATIR 49 (149)
T ss_dssp SSEEESS-SSTT-EEEEEEEEGGG--GGGHHHHTT------------------SEEEEEEEEE
T ss_pred ceeccccccCCcceEEEEEEECCc--chHHHHhhc------------------cCCEEEEEEE
Confidence 467789999999999999999773 346666643 4599998763
No 88
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.69 E-value=4.2 Score=35.03 Aligned_cols=51 Identities=20% Similarity=0.126 Sum_probs=39.8
Q ss_pred CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEee
Q 037167 1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHR 53 (353)
Q Consensus 1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~ 53 (353)
++|...|.++++ .||+.++++|..|.|..+-.........++.|-.|.++-
T Consensus 139 lrl~~Ll~seL~--LSrS~lq~lie~g~Irgdtd~~~l~rkrlr~~~~i~Id~ 189 (203)
T COG4332 139 LRLDRLLASELG--LSRSELQRLIETGQIRGDTDKMLLLRKRLRAGYDIQIDV 189 (203)
T ss_pred hHHHHHHHHHhC--cCHHHHHHHHHcCceeecchHHHHhhhhhhcCcEEEEEc
Confidence 367888889987 599999999999999998775444455677787776653
No 89
>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=69.17 E-value=10 Score=27.61 Aligned_cols=25 Identities=28% Similarity=0.377 Sum_probs=21.7
Q ss_pred CCEEECCEEccCCCceecCCCEEEEe
Q 037167 27 GQITVDGRVVNDPNIILSAGSELVYH 52 (353)
Q Consensus 27 G~V~vNg~~v~~~~~~v~~gd~i~~~ 52 (353)
-.|.|||+.+. .++.|+.||+|.+.
T Consensus 50 ~~v~vNg~~v~-~~~~l~~gD~v~i~ 74 (80)
T cd00754 50 VRIAVNGEYVR-LDTPLKDGDEVAII 74 (80)
T ss_pred EEEEECCeEcC-CCcccCCCCEEEEe
Confidence 36899999996 78999999999874
No 90
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=68.89 E-value=6.3 Score=38.79 Aligned_cols=40 Identities=23% Similarity=0.364 Sum_probs=32.5
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCcee
Q 037167 3 LIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIIL 43 (353)
Q Consensus 3 l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v 43 (353)
+++.|...... .||+++++.|..|.|++||+++.+.+..+
T Consensus 338 ~~~~lv~~~L~-psr~earr~i~~g~v~in~~~v~d~~~~~ 377 (401)
T COG0162 338 LVDLLVDAGLA-PSRSEARRLIQQGGVKINGEKVEDENYVL 377 (401)
T ss_pred HHHHHHHhCCc-ccHHHHHhhcccCCEEECCEeccccccch
Confidence 56666666554 59999999999999999999998776554
No 91
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=68.73 E-value=15 Score=27.20 Aligned_cols=43 Identities=21% Similarity=0.433 Sum_probs=28.4
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHcC--CEEECCEEccCCCceecCCCEEEEe
Q 037167 3 LIEFYSTKHKNSAPLQGWLQRIQNG--QITVDGRVVNDPNIILSAGSELVYH 52 (353)
Q Consensus 3 l~~~l~~~~~~~~sr~~~~~~I~~G--~V~vNg~~v~~~~~~v~~gd~i~~~ 52 (353)
|++.|.++++. |......| .+.||+.-+ ..++.|+.||+|.+.
T Consensus 31 l~~~L~~~~~~------~~~~~~~~~~~~aVN~~~~-~~~~~l~dgDeVai~ 75 (81)
T PRK11130 31 LRQHLAQKGDR------WALALEDGKLLAAVNQTLV-SFDHPLTDGDEVAFF 75 (81)
T ss_pred HHHHHHHhCcc------HHhhhcCCCEEEEECCEEc-CCCCCCCCCCEEEEe
Confidence 45555555532 22223345 378899887 478999999999875
No 92
>PRK06437 hypothetical protein; Provisional
Probab=64.93 E-value=11 Score=27.04 Aligned_cols=24 Identities=13% Similarity=0.185 Sum_probs=20.6
Q ss_pred CEEECCEEccCCCceecCCCEEEEe
Q 037167 28 QITVDGRVVNDPNIILSAGSELVYH 52 (353)
Q Consensus 28 ~V~vNg~~v~~~~~~v~~gd~i~~~ 52 (353)
.|.+||+.+. .++.|+.||.|.+.
T Consensus 38 aV~vNg~iv~-~~~~L~dgD~Veiv 61 (67)
T PRK06437 38 VVIVNGSPVL-EDHNVKKEDDVLIL 61 (67)
T ss_pred EEEECCEECC-CceEcCCCCEEEEE
Confidence 4568999995 89999999999875
No 93
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=59.00 E-value=13 Score=26.77 Aligned_cols=25 Identities=16% Similarity=0.151 Sum_probs=21.3
Q ss_pred CCEEECCEEccCCCceecCCCEEEEe
Q 037167 27 GQITVDGRVVNDPNIILSAGSELVYH 52 (353)
Q Consensus 27 G~V~vNg~~v~~~~~~v~~gd~i~~~ 52 (353)
-.|.+||+.+. .++.++.||.|.+.
T Consensus 40 v~v~vNg~iv~-~~~~l~~gD~Veii 64 (70)
T PRK08364 40 AIAKVNGKVAL-EDDPVKDGDYVEVI 64 (70)
T ss_pred EEEEECCEECC-CCcCcCCCCEEEEE
Confidence 46788999995 79999999999874
No 94
>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=58.34 E-value=11 Score=26.69 Aligned_cols=24 Identities=17% Similarity=0.369 Sum_probs=19.5
Q ss_pred CEEECCEEccCCC----ceecCCCEEEEe
Q 037167 28 QITVDGRVVNDPN----IILSAGSELVYH 52 (353)
Q Consensus 28 ~V~vNg~~v~~~~----~~v~~gd~i~~~ 52 (353)
.|.+||+.+. .+ +.|+.||.|.+.
T Consensus 32 ~V~vNg~~v~-~~~~~~~~L~~gD~V~ii 59 (65)
T cd00565 32 AVALNGEIVP-RSEWASTPLQDGDRIEIV 59 (65)
T ss_pred EEEECCEEcC-HHHcCceecCCCCEEEEE
Confidence 4678999985 45 889999999874
No 95
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=57.99 E-value=33 Score=25.31 Aligned_cols=24 Identities=17% Similarity=0.264 Sum_probs=20.8
Q ss_pred CEEECCEEccCCCceecCCCEEEEe
Q 037167 28 QITVDGRVVNDPNIILSAGSELVYH 52 (353)
Q Consensus 28 ~V~vNg~~v~~~~~~v~~gd~i~~~ 52 (353)
.|.|||+.+ ..++.|+.||.|.+.
T Consensus 53 ~vavN~~~v-~~~~~l~dgDeVai~ 76 (82)
T PLN02799 53 VLALNEEYT-TESAALKDGDELAII 76 (82)
T ss_pred EEEECCEEc-CCCcCcCCCCEEEEe
Confidence 488999998 588999999999874
No 96
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=57.49 E-value=23 Score=26.04 Aligned_cols=24 Identities=21% Similarity=0.481 Sum_probs=20.9
Q ss_pred CEEECCEEccCCCceecCCCEEEEe
Q 037167 28 QITVDGRVVNDPNIILSAGSELVYH 52 (353)
Q Consensus 28 ~V~vNg~~v~~~~~~v~~gd~i~~~ 52 (353)
.|.|||+.+. .+..|+.||.|.+.
T Consensus 51 ~v~vn~~~v~-~~~~l~dgDevai~ 74 (80)
T TIGR01682 51 MVAVNEEYVT-DDALLNEGDEVAFI 74 (80)
T ss_pred EEEECCEEcC-CCcCcCCCCEEEEe
Confidence 5889999985 68999999999875
No 97
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=56.92 E-value=15 Score=35.83 Aligned_cols=75 Identities=13% Similarity=0.187 Sum_probs=48.1
Q ss_pred CCcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhc
Q 037167 71 DDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFAD 150 (353)
Q Consensus 71 d~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~ 150 (353)
-..+++++||++ |.. ..+++.+...+. ....+-.+-||-+.||+++...+........ +
T Consensus 67 ~sgv~~i~kpa~----pss----~e~~swvk~iL~---------~ek~Gh~gTlDP~vtg~l~v~~~~~tr~~~s-~--- 125 (395)
T KOG2529|consen 67 RSGVINIDKPAN----PSS----HEVVSWVKNILR---------VEKTGHSGTLDPEVTGCLIVCIDRATRLLKS-Q--- 125 (395)
T ss_pred hcCceeccCCCC----Cch----HHHHHHHHHHhh---------HHHhCCCCCCCccccceEEEEeecccccccc-h---
Confidence 346899999993 221 223333333222 1345678899999999999998865433222 2
Q ss_pred cccccccchhhhhhccceEEEEEEEEEeeeeC
Q 037167 151 KTSVIDADSTVMELSQRKITKIYRALVHGIVD 182 (353)
Q Consensus 151 g~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~ 182 (353)
....|+|.+++....+
T Consensus 126 ----------------~s~gk~yvg~~~lt~~ 141 (395)
T KOG2529|consen 126 ----------------QSAGKEYVGIGKLTPE 141 (395)
T ss_pred ----------------hccCcEEEEEEecCcc
Confidence 2567999888877654
No 98
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=53.39 E-value=16 Score=26.41 Aligned_cols=25 Identities=24% Similarity=0.490 Sum_probs=20.4
Q ss_pred CEEECCEEccC---CCceecCCCEEEEe
Q 037167 28 QITVDGRVVND---PNIILSAGSELVYH 52 (353)
Q Consensus 28 ~V~vNg~~v~~---~~~~v~~gd~i~~~ 52 (353)
.|.+||..+.+ .++.++.||+|++-
T Consensus 35 av~vNg~iVpr~~~~~~~l~~gD~ievv 62 (68)
T COG2104 35 AVAVNGEIVPRSQWADTILKEGDRIEVV 62 (68)
T ss_pred EEEECCEEccchhhhhccccCCCEEEEE
Confidence 46789999954 68899999999874
No 99
>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=50.76 E-value=15 Score=25.71 Aligned_cols=23 Identities=26% Similarity=0.380 Sum_probs=19.2
Q ss_pred CEEECCEEccCCCceecCCCEEEE
Q 037167 28 QITVDGRVVNDPNIILSAGSELVY 51 (353)
Q Consensus 28 ~V~vNg~~v~~~~~~v~~gd~i~~ 51 (353)
..+|||+.+ +.++.|+.||.|++
T Consensus 36 ~A~Vng~~v-dl~~~L~~~d~v~i 58 (60)
T PF02824_consen 36 AAKVNGQLV-DLDHPLEDGDVVEI 58 (60)
T ss_dssp EEEETTEEE-ETTSBB-SSEEEEE
T ss_pred EEEEcCEEC-CCCCCcCCCCEEEE
Confidence 567999998 68999999999976
No 100
>KOG3301 consensus Ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=50.74 E-value=16 Score=31.03 Aligned_cols=31 Identities=19% Similarity=0.282 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHcCCEEECCEEccCCCceecC
Q 037167 15 APLQGWLQRIQNGQITVDGRVVNDPNIILSA 45 (353)
Q Consensus 15 ~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~ 45 (353)
.|...+..+|..+.|.|+++.|.-|+++|+.
T Consensus 110 kSIhhARvLi~~rhI~V~~qiV~IPsf~vrl 140 (183)
T KOG3301|consen 110 KSIHHARVLIRQRHIRVGKQIVNIPSFMVRL 140 (183)
T ss_pred hhhHHHHHHhcCccEEecCeEeeccceeEee
Confidence 4777888999999999999999999999884
No 101
>TIGR01687 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.
Probab=49.83 E-value=38 Score=25.26 Aligned_cols=24 Identities=29% Similarity=0.372 Sum_probs=19.2
Q ss_pred CEEECCEEccCCCc--eecCCCEEEEe
Q 037167 28 QITVDGRVVNDPNI--ILSAGSELVYH 52 (353)
Q Consensus 28 ~V~vNg~~v~~~~~--~v~~gd~i~~~ 52 (353)
.|.|||+.+. .+. .|+.||+|.+.
T Consensus 57 ~v~vN~~~v~-~~~~~~l~dgdev~i~ 82 (88)
T TIGR01687 57 IILVNGRNVD-WGLGTELKDGDVVAIF 82 (88)
T ss_pred EEEECCEecC-ccCCCCCCCCCEEEEe
Confidence 4789999985 444 89999999874
No 102
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=49.29 E-value=24 Score=24.87 Aligned_cols=24 Identities=21% Similarity=0.476 Sum_probs=19.9
Q ss_pred EEECCEEccC---CCceecCCCEEEEe
Q 037167 29 ITVDGRVVND---PNIILSAGSELVYH 52 (353)
Q Consensus 29 V~vNg~~v~~---~~~~v~~gd~i~~~ 52 (353)
|-+|++.+.+ .++.|+.||+|.+.
T Consensus 33 vavN~~iv~~~~~~~~~L~dgD~Ieiv 59 (65)
T PRK06488 33 TAVNGELVHKEARAQFVLHEGDRIEIL 59 (65)
T ss_pred EEECCEEcCHHHcCccccCCCCEEEEE
Confidence 7889999853 37889999999875
No 103
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=48.84 E-value=25 Score=24.69 Aligned_cols=25 Identities=24% Similarity=0.482 Sum_probs=19.6
Q ss_pred CEEECCEEccC---CCceecCCCEEEEe
Q 037167 28 QITVDGRVVND---PNIILSAGSELVYH 52 (353)
Q Consensus 28 ~V~vNg~~v~~---~~~~v~~gd~i~~~ 52 (353)
.|.+||+.+.. .++.|+.||.|.+.
T Consensus 31 ~v~vN~~iv~~~~~~~~~L~~gD~veii 58 (64)
T TIGR01683 31 AVAVNGEIVPRSEWDDTILKEGDRIEIV 58 (64)
T ss_pred EEEECCEEcCHHHcCceecCCCCEEEEE
Confidence 57789999852 34689999999874
No 104
>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=48.59 E-value=21 Score=25.71 Aligned_cols=26 Identities=27% Similarity=0.432 Sum_probs=21.4
Q ss_pred CCEEECCEEccC--CCceecCCCEEEEe
Q 037167 27 GQITVDGRVVND--PNIILSAGSELVYH 52 (353)
Q Consensus 27 G~V~vNg~~v~~--~~~~v~~gd~i~~~ 52 (353)
=.|.|||+.+.. .++.|+.||.|.+.
T Consensus 44 ~~v~vN~~~v~~~~~~~~l~~gD~V~i~ 71 (77)
T PF02597_consen 44 VAVAVNGEIVPDDGLDTPLKDGDEVAIL 71 (77)
T ss_dssp EEEEETTEEEGGGTTTSBEETTEEEEEE
T ss_pred EEEEECCEEcCCccCCcCcCCCCEEEEE
Confidence 468899999963 38999999999875
No 105
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=47.53 E-value=28 Score=24.38 Aligned_cols=25 Identities=28% Similarity=0.388 Sum_probs=19.9
Q ss_pred CEEECCEEccCC---CceecCCCEEEEe
Q 037167 28 QITVDGRVVNDP---NIILSAGSELVYH 52 (353)
Q Consensus 28 ~V~vNg~~v~~~---~~~v~~gd~i~~~ 52 (353)
.|.+||..+... ++.|+.||+|.+.
T Consensus 32 ~v~vN~~~v~~~~~~~~~L~~gD~vei~ 59 (65)
T PRK06944 32 AVAVNGDFVARTQHAARALAAGDRLDLV 59 (65)
T ss_pred EEEECCEEcCchhcccccCCCCCEEEEE
Confidence 578899998533 6789999999875
No 106
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.91 E-value=24 Score=27.51 Aligned_cols=36 Identities=14% Similarity=0.439 Sum_probs=28.3
Q ss_pred HHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEe
Q 037167 17 LQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYH 52 (353)
Q Consensus 17 r~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~ 52 (353)
+.+...+|++|+=+|.+......-..+++||.|.++
T Consensus 8 ~eeylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~ 43 (111)
T COG4043 8 REEYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFN 43 (111)
T ss_pred HHHHHHHHHcccceEEEEecCHhhcCCCCCCEEEEc
Confidence 567788999999999887764344568999998775
No 107
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=45.10 E-value=28 Score=24.45 Aligned_cols=25 Identities=20% Similarity=0.357 Sum_probs=19.5
Q ss_pred CEEECCEEccC---CCceecCCCEEEEe
Q 037167 28 QITVDGRVVND---PNIILSAGSELVYH 52 (353)
Q Consensus 28 ~V~vNg~~v~~---~~~~v~~gd~i~~~ 52 (353)
.|.+||+.+.+ .++.|+.||+|++.
T Consensus 33 av~vNg~iv~r~~~~~~~l~~gD~vei~ 60 (66)
T PRK05659 33 AVEVNGEIVPRSQHASTALREGDVVEIV 60 (66)
T ss_pred EEEECCeEeCHHHcCcccCCCCCEEEEE
Confidence 46789987742 57889999999874
No 108
>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=43.28 E-value=12 Score=26.24 Aligned_cols=16 Identities=38% Similarity=0.499 Sum_probs=11.7
Q ss_pred CCcEEEEECCCCCccc
Q 037167 71 DDDLIALNKPSGLQVL 86 (353)
Q Consensus 71 d~~~ivvnKP~G~~~~ 86 (353)
...+|.+|||+|-.+|
T Consensus 41 ~~GvinlDKP~gPtSH 56 (59)
T PF08068_consen 41 KYGVINLDKPSGPTSH 56 (59)
T ss_dssp HTEEEEEEE-SSS-HH
T ss_pred hCCcEEeeCCCCCCcc
Confidence 3579999999998776
No 109
>PRK07440 hypothetical protein; Provisional
Probab=41.59 E-value=36 Score=24.57 Aligned_cols=25 Identities=12% Similarity=0.316 Sum_probs=19.4
Q ss_pred CEEECCEEccC---CCceecCCCEEEEe
Q 037167 28 QITVDGRVVND---PNIILSAGSELVYH 52 (353)
Q Consensus 28 ~V~vNg~~v~~---~~~~v~~gd~i~~~ 52 (353)
.|-+||+.+.. +++.|+.||.|++-
T Consensus 37 av~~N~~iv~r~~w~~~~L~~gD~IEIv 64 (70)
T PRK07440 37 AVEYNGEILHRQFWEQTQVQPGDRLEIV 64 (70)
T ss_pred EEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 46789999842 56789999999764
No 110
>KOG4655 consensus U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification]
Probab=36.58 E-value=29 Score=29.54 Aligned_cols=35 Identities=17% Similarity=0.428 Sum_probs=29.4
Q ss_pred CHHHHHHHHHcCCEEECCEEccCCCceecCC--CEEE
Q 037167 16 PLQGWLQRIQNGQITVDGRVVNDPNIILSAG--SELV 50 (353)
Q Consensus 16 sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~g--d~i~ 50 (353)
+-+++-++|++|.|+|..++|++|.+.|... |.|+
T Consensus 121 ~~k~A~~~vEqGHVRvGp~~vtDPa~lvtr~mEDfvt 157 (181)
T KOG4655|consen 121 SVKEAVRFVEQGHVRVGPKVVTDPAFLVTRSMEDFVT 157 (181)
T ss_pred hHHHHHHHHHcCceeeCCeeccCchHHhhhhhhhhhh
Confidence 5678889999999999999999999988754 5553
No 111
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=35.61 E-value=51 Score=23.28 Aligned_cols=25 Identities=8% Similarity=0.425 Sum_probs=19.0
Q ss_pred CEEECCEEccC---CCceecCCCEEEEe
Q 037167 28 QITVDGRVVND---PNIILSAGSELVYH 52 (353)
Q Consensus 28 ~V~vNg~~v~~---~~~~v~~gd~i~~~ 52 (353)
.|-+|++.+.+ ..+.|+.||.|.+-
T Consensus 33 aVavN~~iv~r~~w~~~~L~~gD~Ieii 60 (66)
T PRK08053 33 ALAINQQIIPREQWAQHIVQDGDQILLF 60 (66)
T ss_pred EEEECCEEeChHHcCccccCCCCEEEEE
Confidence 45789999852 35679999999874
No 112
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=35.04 E-value=38 Score=23.64 Aligned_cols=26 Identities=15% Similarity=0.303 Sum_probs=17.8
Q ss_pred cCCEEECCEEccC-CCceecCCCEEEE
Q 037167 26 NGQITVDGRVVND-PNIILSAGSELVY 51 (353)
Q Consensus 26 ~G~V~vNg~~v~~-~~~~v~~gd~i~~ 51 (353)
...++|||+++.. ..+.|..||+|.+
T Consensus 41 ~ngt~vng~~l~~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 41 TNGTFVNGQRLGPGEPVPLKDGDIIRF 67 (68)
T ss_dssp SS-EEETTEEESSTSEEEE-TTEEEEE
T ss_pred CCcEEECCEEcCCCCEEECCCCCEEEc
Confidence 4567899999853 2577889998865
No 113
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=33.75 E-value=48 Score=25.49 Aligned_cols=48 Identities=13% Similarity=0.342 Sum_probs=30.0
Q ss_pred HHHHHHhhcCCCCCHHHHH---HHHHcC-CEEECCEEcc---CCCceecCCCEEEEe
Q 037167 3 LIEFYSTKHKNSAPLQGWL---QRIQNG-QITVDGRVVN---DPNIILSAGSELVYH 52 (353)
Q Consensus 3 l~~~l~~~~~~~~sr~~~~---~~I~~G-~V~vNg~~v~---~~~~~v~~gd~i~~~ 52 (353)
|+++|.+++.. .|..+. .-++.| .|.|||..+. ..++.|+.||.|.+.
T Consensus 34 ll~~L~~~~~~--~~~~lf~~~g~lr~~i~VlvN~~di~~l~g~~t~L~dgD~v~i~ 88 (94)
T cd01764 34 LLDYVASNLLE--ERPDLFIEGGSVRPGIIVLINDTDWELLGEEDYILEDGDHVVFI 88 (94)
T ss_pred HHHHHHHhCch--hhhhhEecCCcccCCEEEEECCccccccCCcccCCCCcCEEEEE
Confidence 56677776642 232221 012222 6789999874 357899999999875
No 114
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=31.65 E-value=51 Score=23.49 Aligned_cols=25 Identities=4% Similarity=0.151 Sum_probs=19.0
Q ss_pred CEEECCEEccCC---CceecCCCEEEEe
Q 037167 28 QITVDGRVVNDP---NIILSAGSELVYH 52 (353)
Q Consensus 28 ~V~vNg~~v~~~---~~~v~~gd~i~~~ 52 (353)
.|-+||+.+.+. .+.|+.||.|++-
T Consensus 34 av~vN~~iv~r~~w~~~~L~~gD~iEIv 61 (67)
T PRK07696 34 VVERNKDILQKDDHTDTSVFDGDQIEIV 61 (67)
T ss_pred EEEECCEEeCHHHcCceecCCCCEEEEE
Confidence 367899998532 3789999999764
No 115
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=29.91 E-value=80 Score=30.99 Aligned_cols=37 Identities=14% Similarity=0.253 Sum_probs=27.0
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCC
Q 037167 3 LIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPN 40 (353)
Q Consensus 3 l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~ 40 (353)
+++.+.+.-.. .|++++.++|.+|.|.+|++++.+++
T Consensus 401 ~~~l~~ka~~~-~s~~~a~r~i~qG~vslnh~~v~~es 437 (467)
T KOG2623|consen 401 ILDLLRKASRF-PSGKEARRMIQQGGVSLNHEKVRDES 437 (467)
T ss_pred HHHHHHHhhcC-CCcHHHHHHHHccceeecCccccCch
Confidence 44555444332 36779999999999999999997633
No 116
>cd01666 TGS_DRG_C TGS_DRG_C: DRG (developmentally regulated GTP-binding protein) represents a family of GTP-binding proteins that includes two members, DRG1 and DRG2. DRG1 and DRG2 have a C-terminal TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) with a predominantly beta-sheet structure. The function of TGS is unknown but its presence in two types of regulatory proteins (the DRG GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=29.64 E-value=52 Score=24.20 Aligned_cols=22 Identities=9% Similarity=0.004 Sum_probs=18.7
Q ss_pred EECCEEccCCCceecCCCEEEEe
Q 037167 30 TVDGRVVNDPNIILSAGSELVYH 52 (353)
Q Consensus 30 ~vNg~~v~~~~~~v~~gd~i~~~ 52 (353)
.++|++| ..++.|+.||+|++.
T Consensus 53 ~~~gq~V-gl~~~L~d~DvVeI~ 74 (75)
T cd01666 53 KHSPQRV-GLDHVLEDEDVVQIV 74 (75)
T ss_pred cCCCeEC-CCCCEecCCCEEEEe
Confidence 3699998 589999999999874
No 117
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=28.93 E-value=28 Score=26.33 Aligned_cols=30 Identities=17% Similarity=0.340 Sum_probs=17.3
Q ss_pred HcCCEEECCEEccCCCceecCCCEEEEeeCC
Q 037167 25 QNGQITVDGRVVNDPNIILSAGSELVYHRLP 55 (353)
Q Consensus 25 ~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~ 55 (353)
....|=|=|+.+ ..++.|+.||+|++++.-
T Consensus 45 ~~~~vGIfGk~~-~~d~~L~~GDRVEIYRPL 74 (84)
T PF03658_consen 45 EKNKVGIFGKLV-KLDTVLRDGDRVEIYRPL 74 (84)
T ss_dssp TTSEEEEEE-S---TT-B--TT-EEEEE-S-
T ss_pred ccceeeeeeeEc-CCCCcCCCCCEEEEeccC
Confidence 456777889988 489999999999997643
No 118
>KOG4837 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.52 E-value=96 Score=27.57 Aligned_cols=37 Identities=3% Similarity=-0.054 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEE
Q 037167 15 APLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVY 51 (353)
Q Consensus 15 ~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~ 51 (353)
..|+.++-+.-++.+++|+....+.+..++.||.+-+
T Consensus 152 v~rnKVel~fye~e~R~N~~Kl~kkS~~i~vgds~d~ 188 (248)
T KOG4837|consen 152 VTRNKVELLFYEYEPRTNSFKLVKKSLRIDVGDSADF 188 (248)
T ss_pred cccchhhHhhhhcccccCcccccccceeeecccccce
Confidence 6788999999999999999998888999999998754
No 119
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=26.79 E-value=49 Score=26.35 Aligned_cols=43 Identities=14% Similarity=0.218 Sum_probs=26.0
Q ss_pred cCCEEECCEEccCCCceecCCCEEEEeeCCCCCC--CCCCCccEEEECC
Q 037167 26 NGQITVDGRVVNDPNIILSAGSELVYHRLPWKEP--DVPYLLEVLYEDD 72 (353)
Q Consensus 26 ~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~~--~~~~~~~Ilyed~ 72 (353)
+|.|.+||--. ..+++||.|.+-....-++ ......+|+|-|+
T Consensus 65 Sg~I~lNGAAA----r~~~~GD~vII~sy~~~~~~e~~~~~P~vv~vd~ 109 (111)
T cd06919 65 SGVICLNGAAA----RLGQPGDRVIIMAYALMDEEEAEGHKPKVVLVDE 109 (111)
T ss_pred CCEEEeCCHHH----hcCCCCCEEEEEECccCCHHHHhcCCCEEEEeCC
Confidence 47888888654 3678999998754332211 2233455776664
No 120
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=25.75 E-value=78 Score=23.83 Aligned_cols=25 Identities=20% Similarity=0.430 Sum_probs=18.4
Q ss_pred CEEECCEEccC---CCceecCCCEEEEe
Q 037167 28 QITVDGRVVND---PNIILSAGSELVYH 52 (353)
Q Consensus 28 ~V~vNg~~v~~---~~~~v~~gd~i~~~ 52 (353)
.|-+||..+.. .++.|+.||.|++.
T Consensus 51 AVevNg~iVpr~~w~~t~L~egD~IEIv 78 (84)
T PRK06083 51 VFAINNQVVPRSEWQSTVLSSGDAISLF 78 (84)
T ss_pred EEEECCEEeCHHHcCcccCCCCCEEEEE
Confidence 45789998853 35678899998764
No 121
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown.
Probab=25.47 E-value=1e+02 Score=20.56 Aligned_cols=23 Identities=22% Similarity=0.381 Sum_probs=18.4
Q ss_pred CEEECCEEccCCCceecCCCEEEE
Q 037167 28 QITVDGRVVNDPNIILSAGSELVY 51 (353)
Q Consensus 28 ~V~vNg~~v~~~~~~v~~gd~i~~ 51 (353)
.+.+||+.+ +.++.+..||.|.+
T Consensus 36 a~~vng~~v-dl~~~l~~~~~ve~ 58 (60)
T cd01668 36 GAKVNGKLV-PLSTVLKDGDIVEI 58 (60)
T ss_pred EEEECCEEC-CCCCCCCCCCEEEE
Confidence 356899987 57888999998865
No 122
>PF13021 DUF3885: Domain of unknown function (DUF3885)
Probab=23.82 E-value=1e+02 Score=19.56 Aligned_cols=24 Identities=17% Similarity=0.105 Sum_probs=20.5
Q ss_pred CCceEEEEEeChHHHHHHHHHhhc
Q 037167 127 GTSGILLCAKTKLAKTCIAGYFAD 150 (353)
Q Consensus 127 ~TSGlll~ak~~~~~~~L~~~f~~ 150 (353)
|-.|+-|+|++++..+.|-..|.+
T Consensus 5 DDRGcdvia~~~~~i~~ly~~y~~ 28 (38)
T PF13021_consen 5 DDRGCDVIANNKERIRPLYEKYND 28 (38)
T ss_pred cCCCcEEeeCCHHHHHHHHHHHHH
Confidence 557999999999999998887753
No 123
>cd01616 TGS The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=21.62 E-value=1.3e+02 Score=19.35 Aligned_cols=22 Identities=27% Similarity=0.452 Sum_probs=17.6
Q ss_pred EEECCEEccCCCceecCCCEEEE
Q 037167 29 ITVDGRVVNDPNIILSAGSELVY 51 (353)
Q Consensus 29 V~vNg~~v~~~~~~v~~gd~i~~ 51 (353)
+.+||+.+ +.++.+..||.|.+
T Consensus 37 ~~vn~~~~-~l~~~l~~~~~i~~ 58 (60)
T cd01616 37 ALVNGQLV-DLSYTLQDGDTVSI 58 (60)
T ss_pred EEECCEEC-CCCcCcCCCCEEEE
Confidence 46899987 57888999998765
No 124
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=21.18 E-value=67 Score=26.16 Aligned_cols=44 Identities=18% Similarity=0.173 Sum_probs=25.9
Q ss_pred cCCEEECCEEccCCCceecCCCEEEEeeCCCC-C-CCCCCCccEEEECCc
Q 037167 26 NGQITVDGRVVNDPNIILSAGSELVYHRLPWK-E-PDVPYLLEVLYEDDD 73 (353)
Q Consensus 26 ~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~-~-~~~~~~~~Ilyed~~ 73 (353)
+|.|-+||--. ..+++||.|.+-....- + ....+...|+|-|++
T Consensus 66 Sg~I~lNGAAA----rl~~~GD~VII~sy~~~~~~e~~~~~P~vv~vd~~ 111 (126)
T TIGR00223 66 SRIICVNGAAA----RCVSVGDIVIIASYVTMPDEEARTHRPNVAYFEGD 111 (126)
T ss_pred CCEEEeCCHHH----hcCCCCCEEEEEECCcCCHHHHhcCCCEEEEECCC
Confidence 46788888654 36789999987543322 1 112234457766643
No 125
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=20.72 E-value=71 Score=26.05 Aligned_cols=43 Identities=16% Similarity=0.289 Sum_probs=25.1
Q ss_pred cCCEEECCEEccCCCceecCCCEEEEeeCCCC-CC-CCCCCccEEEECC
Q 037167 26 NGQITVDGRVVNDPNIILSAGSELVYHRLPWK-EP-DVPYLLEVLYEDD 72 (353)
Q Consensus 26 ~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~-~~-~~~~~~~Ilyed~ 72 (353)
+|.|-+||--. ..+++||.|.+-....- +. ...+...|+|-|+
T Consensus 66 Sg~I~lNGAAA----r~~~~GD~vII~ay~~~~~~e~~~~~P~vv~vd~ 110 (126)
T PRK05449 66 SGVICLNGAAA----RLVQVGDLVIIAAYAQMDEEEAKTHKPKVVFVDE 110 (126)
T ss_pred CCEEEeCCHHH----hcCCCCCEEEEEECccCCHHHHhcCCCEEEEECC
Confidence 46788888654 36789999987533222 11 1223445666654
Done!