Query psy938
Match_columns 241
No_of_seqs 169 out of 1271
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 17:37:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy938.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/938hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2623|consensus 100.0 8E-54 1.7E-58 392.6 19.8 212 3-215 255-467 (467)
2 PRK13354 tyrosyl-tRNA syntheta 100.0 4.8E-50 1E-54 377.9 23.7 200 2-215 211-410 (410)
3 PRK05912 tyrosyl-tRNA syntheta 100.0 1.4E-48 3.1E-53 367.8 22.9 195 3-214 214-408 (408)
4 COG0162 TyrS Tyrosyl-tRNA synt 100.0 3.3E-44 7.1E-49 335.9 19.1 198 1-215 204-401 (401)
5 TIGR00234 tyrS tyrosyl-tRNA sy 100.0 9.8E-34 2.1E-38 264.8 17.4 169 3-189 203-372 (377)
6 cd00395 Tyr_Trp_RS_core cataly 99.9 1.1E-21 2.3E-26 176.6 10.2 93 4-96 181-273 (273)
7 cd00805 TyrRS_core catalytic c 99.8 1.3E-19 2.8E-24 162.7 10.6 93 3-96 177-269 (269)
8 PF00579 tRNA-synt_1b: tRNA sy 99.5 9.2E-15 2E-19 132.1 5.7 111 4-115 180-292 (292)
9 PLN02486 aminoacyl-tRNA ligase 99.4 5.7E-13 1.2E-17 125.2 9.2 96 7-105 249-366 (383)
10 PTZ00126 tyrosyl-tRNA syntheta 99.4 4.5E-13 9.7E-18 126.0 7.9 94 5-101 239-360 (383)
11 cd00806 TrpRS_core catalytic c 99.4 1.6E-12 3.5E-17 117.5 10.2 81 11-95 179-279 (280)
12 PRK08560 tyrosyl-tRNA syntheta 99.4 2.2E-12 4.7E-17 119.1 9.4 93 4-99 195-315 (329)
13 PRK12284 tryptophanyl-tRNA syn 99.3 2E-12 4.3E-17 122.7 7.6 88 7-99 188-288 (431)
14 PRK12285 tryptophanyl-tRNA syn 99.3 3.3E-12 7.1E-17 119.6 8.4 92 5-99 235-346 (368)
15 PRK12556 tryptophanyl-tRNA syn 99.3 4.1E-12 8.9E-17 117.5 7.4 87 10-99 191-288 (332)
16 PRK00927 tryptophanyl-tRNA syn 99.3 7.3E-12 1.6E-16 115.8 8.6 84 11-100 181-288 (333)
17 PRK12282 tryptophanyl-tRNA syn 99.3 1.2E-11 2.5E-16 114.5 9.0 87 11-101 185-288 (333)
18 PRK12283 tryptophanyl-tRNA syn 99.3 6.1E-12 1.3E-16 118.4 6.9 84 11-99 254-353 (398)
19 TIGR00233 trpS tryptophanyl-tR 99.2 3.2E-11 6.9E-16 111.4 9.0 88 10-100 181-288 (328)
20 COG0180 TrpS Tryptophanyl-tRNA 99.1 1.4E-10 3E-15 106.3 8.2 83 12-99 188-289 (314)
21 PTZ00348 tyrosyl-tRNA syntheta 99.1 3.9E-10 8.4E-15 112.7 8.8 92 5-99 204-332 (682)
22 PF01479 S4: S4 domain; Inter 98.8 8.9E-09 1.9E-13 68.8 5.5 44 148-191 2-45 (48)
23 PLN02886 aminoacyl-tRNA ligase 98.8 9.5E-09 2.1E-13 96.9 6.3 85 11-99 239-341 (389)
24 KOG2144|consensus 98.2 5.4E-06 1.2E-10 75.2 7.6 93 5-100 205-327 (360)
25 PF13275 S4_2: S4 domain; PDB: 98.0 2.9E-06 6.3E-11 60.9 1.8 47 145-191 6-52 (65)
26 PRK11507 ribosome-associated p 97.9 6.5E-05 1.4E-09 54.6 7.6 47 145-191 10-56 (70)
27 KOG2713|consensus 97.9 1.7E-05 3.6E-10 72.0 5.3 80 18-101 207-303 (347)
28 cd00165 S4 S4/Hsp/ tRNA synthe 97.9 3E-05 6.4E-10 53.4 5.5 44 148-191 2-45 (70)
29 PRK04051 rps4p 30S ribosomal p 97.9 4.9E-05 1.1E-09 64.7 7.3 94 89-191 54-147 (177)
30 smart00363 S4 S4 RNA-binding d 97.8 6.9E-05 1.5E-09 50.0 5.5 44 148-191 2-45 (60)
31 TIGR02988 YaaA_near_RecF S4 do 97.8 5.5E-05 1.2E-09 52.7 4.9 46 146-191 8-53 (59)
32 PRK10348 ribosome-associated h 97.6 0.00037 8E-09 56.8 8.4 60 146-212 8-67 (133)
33 TIGR01018 rpsD_arch ribosomal 97.6 0.00019 4.2E-09 60.3 6.6 95 89-191 54-148 (162)
34 PTZ00348 tyrosyl-tRNA syntheta 97.3 0.00072 1.6E-08 68.3 8.2 83 8-99 549-655 (682)
35 COG1187 RsuA 16S rRNA uridine- 97.3 0.00056 1.2E-08 61.2 6.6 46 146-192 2-47 (248)
36 COG1189 Predicted rRNA methyla 97.3 0.00037 8E-09 61.9 4.8 45 147-191 3-47 (245)
37 COG2501 S4-like RNA binding pr 97.1 0.0018 3.9E-08 47.5 6.2 45 145-189 10-54 (73)
38 TIGR01017 rpsD_bact ribosomal 97.1 0.0011 2.4E-08 57.5 5.5 45 147-191 90-134 (200)
39 COG0522 RpsD Ribosomal protein 97.0 0.00079 1.7E-08 58.7 4.3 45 147-191 94-138 (205)
40 KOG2145|consensus 97.0 0.0024 5.1E-08 58.5 7.2 95 5-103 260-377 (397)
41 TIGR00478 tly hemolysin TlyA f 96.9 0.0014 3E-08 57.9 5.4 44 148-191 1-44 (228)
42 CHL00113 rps4 ribosomal protei 96.9 0.0015 3.2E-08 56.8 5.3 45 147-191 89-133 (201)
43 COG1188 Ribosome-associated he 96.9 0.0036 7.8E-08 48.6 6.5 60 146-212 8-67 (100)
44 PTZ00155 40S ribosomal protein 96.8 0.0012 2.5E-08 56.6 3.4 45 147-191 107-151 (181)
45 PRK05327 rpsD 30S ribosomal pr 96.7 0.0032 6.8E-08 54.7 5.4 45 147-191 93-137 (203)
46 PLN00189 40S ribosomal protein 96.4 0.0016 3.4E-08 56.3 1.5 44 148-191 110-153 (194)
47 TIGR03069 PS_II_S4 photosystem 96.2 0.012 2.6E-07 52.9 6.2 45 146-191 183-227 (257)
48 PRK10700 23S rRNA pseudouridyl 96.0 0.012 2.5E-07 53.8 5.2 42 147-190 3-44 (289)
49 cd00818 IleRS_core catalytic c 95.9 0.0026 5.7E-08 59.0 0.9 28 7-34 285-312 (338)
50 PRK10475 23S rRNA pseudouridin 95.9 0.012 2.7E-07 53.7 4.9 44 146-191 6-49 (290)
51 PRK00750 lysK lysyl-tRNA synth 95.3 0.012 2.5E-07 57.8 2.8 32 2-33 261-292 (510)
52 PLN00051 RNA-binding S4 domain 95.2 0.06 1.3E-06 48.7 6.9 45 146-191 191-235 (267)
53 cd00668 Ile_Leu_Val_MetRS_core 94.9 0.0096 2.1E-07 54.3 0.8 44 8-62 260-303 (312)
54 COG2302 Uncharacterized conser 94.8 0.067 1.4E-06 47.9 5.8 64 150-214 183-253 (257)
55 PRK12418 cysteinyl-tRNA synthe 94.7 0.012 2.5E-07 55.9 0.9 25 9-33 249-273 (384)
56 COG0060 IleS Isoleucyl-tRNA sy 94.7 0.016 3.5E-07 60.3 2.0 23 8-30 589-611 (933)
57 cd00812 LeuRS_core catalytic c 94.6 0.0089 1.9E-07 54.8 -0.1 19 16-34 270-288 (314)
58 cd00817 ValRS_core catalytic c 94.6 0.012 2.5E-07 55.5 0.5 42 8-60 330-371 (382)
59 PF00133 tRNA-synt_1: tRNA syn 94.5 0.022 4.7E-07 56.9 2.3 24 8-31 548-571 (601)
60 PRK11893 methionyl-tRNA synthe 94.4 0.017 3.8E-07 55.9 1.2 42 7-49 286-329 (511)
61 PTZ00427 isoleucine-tRNA ligas 94.2 0.031 6.7E-07 60.1 2.8 24 8-31 707-730 (1205)
62 PLN02381 valyl-tRNA synthetase 94.2 0.026 5.7E-07 60.0 2.3 23 8-30 642-664 (1066)
63 PLN02882 aminoacyl-tRNA ligase 94.1 0.034 7.5E-07 59.5 3.0 26 7-32 600-625 (1159)
64 PRK05743 ileS isoleucyl-tRNA s 94.1 0.033 7.2E-07 58.2 2.8 25 8-32 579-603 (912)
65 PRK05729 valS valyl-tRNA synth 94.1 0.02 4.4E-07 59.5 1.1 43 7-49 506-550 (874)
66 PRK14900 valS valyl-tRNA synth 94.0 0.021 4.5E-07 60.6 0.9 41 8-48 525-567 (1052)
67 PRK13208 valS valyl-tRNA synth 93.9 0.02 4.4E-07 58.9 0.7 41 8-48 520-562 (800)
68 TIGR03447 mycothiol_MshC cyste 93.9 0.018 3.9E-07 55.2 0.3 21 13-33 280-300 (411)
69 COG0525 ValS Valyl-tRNA synthe 93.8 0.037 8E-07 57.3 2.4 22 9-30 513-534 (877)
70 COG0215 CysS Cysteinyl-tRNA sy 93.8 0.025 5.5E-07 54.7 1.1 35 15-49 262-298 (464)
71 PRK06039 ileS isoleucyl-tRNA s 93.7 0.024 5.1E-07 59.7 0.9 42 8-49 579-622 (975)
72 PRK11180 rluD 23S rRNA pseudou 93.7 0.12 2.5E-06 47.7 5.3 45 146-190 17-61 (325)
73 PRK13804 ileS isoleucyl-tRNA s 93.7 0.045 9.8E-07 57.6 2.8 27 7-33 616-642 (961)
74 PTZ00419 valyl-tRNA synthetase 93.6 0.034 7.4E-07 58.7 1.8 23 8-30 572-594 (995)
75 PF01406 tRNA-synt_1e: tRNA sy 93.6 0.035 7.6E-07 51.0 1.7 19 16-34 247-265 (300)
76 PRK04313 30S ribosomal protein 93.5 0.25 5.4E-06 44.1 6.7 73 146-219 37-115 (237)
77 TIGR00422 valS valyl-tRNA synt 93.3 0.029 6.3E-07 58.2 0.7 43 7-49 511-555 (861)
78 TIGR00392 ileS isoleucyl-tRNA 93.3 0.03 6.5E-07 58.1 0.8 41 9-49 599-641 (861)
79 PLN02943 aminoacyl-tRNA ligase 93.3 0.031 6.7E-07 58.8 0.8 41 8-48 570-612 (958)
80 cd00672 CysRS_core catalytic c 93.2 0.023 5.1E-07 49.6 -0.2 25 10-34 163-187 (213)
81 PRK12300 leuS leucyl-tRNA synt 93.0 0.034 7.4E-07 58.1 0.6 40 9-49 566-607 (897)
82 PRK12268 methionyl-tRNA synthe 92.9 0.029 6.2E-07 55.2 -0.1 32 17-48 330-363 (556)
83 PRK00133 metG methionyl-tRNA s 92.8 0.039 8.5E-07 55.8 0.8 38 9-47 318-357 (673)
84 PLN02843 isoleucyl-tRNA synthe 92.8 0.053 1.2E-06 57.2 1.8 27 7-33 597-623 (974)
85 TIGR00005 rluA_subfam pseudour 92.8 0.19 4.2E-06 45.4 5.2 46 146-191 5-50 (299)
86 cd00814 MetRS_core catalytic c 92.8 0.03 6.4E-07 51.4 -0.1 35 16-61 275-309 (319)
87 PF09334 tRNA-synt_1g: tRNA sy 92.7 0.025 5.4E-07 53.7 -0.8 18 17-34 323-340 (391)
88 PRK10839 16S rRNA pseudouridyl 92.7 0.26 5.6E-06 43.1 5.6 43 148-191 2-44 (232)
89 KOG0432|consensus 92.5 0.05 1.1E-06 56.1 1.1 23 8-30 580-602 (995)
90 PTZ00223 40S ribosomal protein 92.3 0.46 1E-05 43.2 6.8 73 146-219 38-116 (273)
91 PLN02610 probable methionyl-tR 92.3 0.067 1.5E-06 55.3 1.6 34 16-49 343-379 (801)
92 TIGR00395 leuS_arch leucyl-tRN 92.3 0.049 1.1E-06 57.2 0.7 40 9-49 609-650 (938)
93 COG0143 MetG Methionyl-tRNA sy 92.3 0.08 1.7E-06 52.6 2.1 18 17-34 329-346 (558)
94 PRK00260 cysS cysteinyl-tRNA s 92.3 0.042 9.1E-07 53.2 0.1 37 12-48 257-295 (463)
95 PLN02224 methionine-tRNA ligas 92.1 0.042 9.2E-07 55.2 -0.0 33 16-48 361-395 (616)
96 PRK14535 cysS cysteinyl-tRNA s 92.1 0.19 4.1E-06 51.1 4.5 41 7-48 495-537 (699)
97 TIGR00435 cysS cysteinyl-tRNA 92.0 0.041 9E-07 53.4 -0.3 18 16-33 260-277 (465)
98 PLN02946 cysteine-tRNA ligase 91.7 0.062 1.3E-06 53.4 0.6 26 8-34 311-336 (557)
99 cd00418 GlxRS_core catalytic c 91.6 0.16 3.4E-06 45.1 3.0 46 4-49 136-183 (230)
100 PTZ00118 40S ribosomal protein 91.4 0.68 1.5E-05 41.9 6.8 73 146-219 41-119 (262)
101 TIGR00398 metG methionyl-tRNA 91.2 0.072 1.6E-06 52.1 0.5 38 10-48 317-356 (530)
102 PRK12267 methionyl-tRNA synthe 91.1 0.059 1.3E-06 54.2 -0.2 32 17-48 295-328 (648)
103 PLN00036 40S ribosomal protein 91.1 0.76 1.6E-05 41.5 6.9 73 146-219 41-119 (261)
104 KOG0437|consensus 91.0 0.41 8.8E-06 49.1 5.4 77 17-101 706-803 (1080)
105 cd00674 LysRS_core_class_I cat 90.9 0.1 2.2E-06 49.0 1.2 30 4-33 258-287 (353)
106 PLN02959 aminoacyl-tRNA ligase 90.6 0.085 1.8E-06 56.3 0.4 21 12-33 710-730 (1084)
107 PRK14536 cysS cysteinyl-tRNA s 90.5 0.074 1.6E-06 52.1 -0.2 19 16-34 274-292 (490)
108 KOG4655|consensus 90.4 0.13 2.8E-06 43.4 1.2 40 152-191 112-151 (181)
109 PRK11025 23S rRNA pseudouridyl 90.2 0.54 1.2E-05 43.2 5.2 46 145-191 18-63 (317)
110 KOG0436|consensus 90.0 0.15 3.3E-06 49.1 1.5 24 16-46 339-362 (578)
111 PTZ00399 cysteinyl-tRNA-synthe 90.0 0.083 1.8E-06 53.4 -0.3 35 15-49 309-345 (651)
112 PRK01611 argS arginyl-tRNA syn 90.0 0.16 3.4E-06 49.7 1.7 26 9-34 310-335 (507)
113 cd00808 GluRS_core catalytic c 89.9 0.29 6.2E-06 43.6 3.1 44 6-49 147-192 (239)
114 PRK14534 cysS cysteinyl-tRNA s 89.7 0.088 1.9E-06 51.5 -0.4 19 16-34 274-292 (481)
115 COG0564 RluA Pseudouridylate s 87.3 1.6 3.5E-05 39.8 6.3 45 145-191 11-55 (289)
116 KOG2007|consensus 85.8 1.4 2.9E-05 43.5 5.1 33 17-49 301-335 (586)
117 PF01921 tRNA-synt_1f: tRNA sy 85.7 1.8 3.8E-05 41.0 5.7 31 3-33 264-294 (360)
118 KOG3301|consensus 85.6 0.7 1.5E-05 39.0 2.6 44 147-190 97-140 (183)
119 COG0495 LeuS Leucyl-tRNA synth 85.0 0.53 1.2E-05 48.8 2.1 38 12-49 570-609 (814)
120 TIGR00467 lysS_arch lysyl-tRNA 84.8 0.38 8.2E-06 47.5 0.9 18 17-34 270-287 (515)
121 PLN02563 aminoacyl-tRNA ligase 84.4 0.86 1.9E-05 48.2 3.3 14 20-33 722-735 (963)
122 KOG0433|consensus 82.6 0.73 1.6E-05 47.2 1.8 22 9-30 601-622 (937)
123 TIGR00396 leuS_bact leucyl-tRN 80.1 0.5 1.1E-05 49.2 -0.3 28 21-48 604-633 (842)
124 COG0008 GlnS Glutamyl- and glu 76.5 5.5 0.00012 39.0 5.7 31 2-33 231-261 (472)
125 COG1471 RPS4A Ribosomal protei 73.6 6.9 0.00015 34.9 5.0 33 156-188 51-83 (241)
126 TIGR00464 gltX_bact glutamyl-t 71.6 24 0.00051 34.5 8.7 45 4-49 224-271 (470)
127 PRK14895 gltX glutamyl-tRNA sy 71.3 3.1 6.7E-05 41.1 2.6 46 4-49 223-270 (513)
128 PRK12558 glutamyl-tRNA synthet 66.7 4.1 8.9E-05 39.6 2.3 46 4-49 223-270 (445)
129 PRK05710 glutamyl-Q tRNA(Asp) 65.9 4.6 9.9E-05 37.2 2.4 26 3-28 218-243 (299)
130 COG1384 LysS Lysyl-tRNA synthe 64.8 2.9 6.2E-05 41.3 0.9 30 5-34 261-290 (521)
131 PRK12410 glutamylglutaminyl-tR 63.0 5.1 0.00011 38.8 2.2 44 6-49 220-265 (433)
132 PLN02627 glutamyl-tRNA synthet 62.9 5.7 0.00012 39.5 2.6 46 4-49 276-323 (535)
133 TIGR03838 queuosine_YadB gluta 60.8 5.5 0.00012 36.2 1.9 29 4-33 212-240 (272)
134 KOG0434|consensus 57.7 4.9 0.00011 41.3 1.1 30 9-45 589-618 (1070)
135 PRK00390 leuS leucyl-tRNA synt 57.3 5.7 0.00012 41.3 1.6 28 21-48 570-599 (805)
136 PF00749 tRNA-synt_1c: tRNA sy 50.8 11 0.00025 34.6 2.3 26 4-29 226-251 (314)
137 PRK01406 gltX glutamyl-tRNA sy 46.8 10 0.00022 37.1 1.4 43 5-48 235-280 (476)
138 PLN02286 arginine-tRNA ligase 35.9 22 0.00049 35.5 1.9 29 6-34 363-391 (576)
139 KOG2716|consensus 35.2 1.1E+02 0.0023 27.4 5.8 35 5-42 14-57 (230)
140 PF13877 RPAP3_C: Potential Mo 34.3 60 0.0013 24.0 3.6 36 37-74 5-41 (94)
141 TIGR00234 tyrS tyrosyl-tRNA sy 33.6 1.1E+02 0.0024 29.0 6.1 44 13-59 220-271 (377)
142 TIGR00456 argS arginyl-tRNA sy 31.1 23 0.00051 35.2 1.1 16 19-34 370-385 (566)
143 PF00750 tRNA-synt_1d: tRNA sy 29.9 16 0.00035 34.1 -0.2 27 8-34 274-301 (354)
144 PRK01151 rps17E 30S ribosomal 27.3 1.3E+02 0.0029 21.0 4.1 51 45-97 7-57 (58)
145 cd08818 CARD_MDA5_1 Caspase ac 23.5 1.9E+02 0.0042 21.9 4.6 38 57-95 24-61 (88)
146 PRK04156 gltX glutamyl-tRNA sy 22.4 55 0.0012 32.9 1.9 23 3-26 321-343 (567)
147 PRK12451 arginyl-tRNA syntheta 21.5 40 0.00086 33.6 0.7 24 10-34 361-384 (562)
No 1
>KOG2623|consensus
Probab=100.00 E-value=8e-54 Score=392.59 Aligned_cols=212 Identities=36% Similarity=0.570 Sum_probs=199.0
Q ss_pred CCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCCh
Q psy938 3 VTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEE 82 (241)
Q Consensus 3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~ 82 (241)
++.+||+|+||||+++|.|+|||+|||||||+++||||++||||.++||++|++||++|||+|.+||++++++|.+.|.+
T Consensus 255 ~~~vfGlT~PLlTsstG~KlGKSaGnAvWLdp~~tspy~lYQfF~~~pDd~v~k~LklfTfl~l~eI~~I~~~H~k~P~~ 334 (467)
T KOG2623|consen 255 QAFVFGLTFPLLTSSTGAKLGKSAGNAVWLDPSKTSPYHLYQFFASLPDDDVEKFLKLFTFLPLEEIKQILEEHRKEPSQ 334 (467)
T ss_pred ccceeeeeeeeEecCcchhhccCCCceEEecCccCCcHHHHHHHHhCchhHHHHHHHHHhcCCHHHHHHHHHHHhcChhh
Confidence 46799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCCCH
Q psy938 83 RRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRD 162 (241)
Q Consensus 83 ~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~Sk 162 (241)
|.+|+.||+|||.+|||+++++.|+++|++||++....+..++..++.++|+++|...+..++++++.+++++++.++|+
T Consensus 335 r~aQ~~LA~eVTr~VHG~egL~~A~r~T~al~g~~~~~~~~ls~~ei~~lfk~a~~~~l~~~~~~s~~~l~~ka~~~~s~ 414 (467)
T KOG2623|consen 335 RIAQKLLAAEVTRMVHGKEGLEVAERCTKALFGAKKAGLSGLSLSEILQLFKDATFIDLKDEPGVSILDLLRKASRFPSG 414 (467)
T ss_pred hhHHHHHHHHHHHHHcccchHHHHHHHHHHhhcccccccccCCHHHHHHHHhcCCceecccCCCCcHHHHHHHhhcCCCc
Confidence 99999999999999999999999999999999997777889999999999999999888766799999999999999999
Q ss_pred HHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCC-eEEEEeccccEEEEEEc
Q psy938 163 KEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNS-LTLLRVEVSANIIAKSA 215 (241)
Q Consensus 163 sEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~-~~llr~GKk~~~~i~~~ 215 (241)
+||||+|+|||||+|++++++++.. ..+.++++++ +.+||+|||+|++|+|.
T Consensus 415 ~~a~r~i~qG~vslnh~~v~~es~~-~~~~~i~~nr~L~lLr~GKrnf~ivr~~ 467 (467)
T KOG2623|consen 415 KEARRMIQQGGVSLNHEKVRDESVS-IAGPFILNNRGLSLLRAGKRNFVIVRWV 467 (467)
T ss_pred HHHHHHHHccceeecCccccCchhh-ccccceecCCCeEEEEecCcceEEEEeC
Confidence 9999999999999999999995543 3345888884 55999999999999984
No 2
>PRK13354 tyrosyl-tRNA synthetase; Provisional
Probab=100.00 E-value=4.8e-50 Score=377.90 Aligned_cols=200 Identities=32% Similarity=0.496 Sum_probs=181.8
Q ss_pred CCCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCC
Q psy938 2 EVTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPE 81 (241)
Q Consensus 2 ~~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~ 81 (241)
+...+|++|+|||+|+||.|||||.||+|||++++||||++||||++++|++|.+|+++||+++.++|+++++.|..+++
T Consensus 211 ~~~~~~~lt~PlL~g~dG~KMsKS~~naI~L~d~~tsp~~i~qki~~~~D~~v~~~l~~~t~l~~~ei~~l~~~~~~~~~ 290 (410)
T PRK13354 211 EGEEQFGLTMPLLEGADGTKMGKSAGGAIWLDPEKTSPYEFYQFWMNIDDRDVVKYLKLFTDLSPDEIDELEAQLETEPN 290 (410)
T ss_pred CCCCceEeccCCccCCCCCccCCCCCCceeccCCCCCHHHHHHHHHcCChHHHHHHHHHHhCCCHHHHHHHHHHHhcCCC
Confidence 34568999999999999999999999999999999999999999999999999999999999999999999999998888
Q ss_pred hHHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCCC
Q psy938 82 ERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPR 161 (241)
Q Consensus 82 ~~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~S 161 (241)
++++|+.||++|++++||.+++++|+++++++|+++... + . ++|.+++. ..+.++.++|+.+|+++|
T Consensus 291 ~~~~Kk~LA~~v~~~vhg~~~~~~a~~~~~~~f~~~~~~---~--~-------~~p~~~~~-~~~~~~~~~l~~~~~~~S 357 (410)
T PRK13354 291 PRDAKKVLAEEITKFVHGEEAAEEAEKIFKALFSGDVKP---L--K-------DIPTFEVS-AETKNLVDLLVDLGLEPS 357 (410)
T ss_pred hHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHhCCCCCC---c--C-------CCCeEEec-CCCCCHHHHHHHhCCCCC
Confidence 999999999999999999999999999999999865211 1 1 45665553 236789999999999999
Q ss_pred HHHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEEEEc
Q psy938 162 DKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSA 215 (241)
Q Consensus 162 ksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i~~~ 215 (241)
++||||+|+||||+|||++++|+++.+... +++++++++||+|||+|++|+|.
T Consensus 358 ~~earrli~~ggv~in~~~v~~~~~~~~~~-~~l~~~~~~lr~GKk~~~~i~~~ 410 (410)
T PRK13354 358 KREARRLIQNGAIKINGEKVTDVDAIINPE-DAFDGKFVILRRGKKKFFLVKLK 410 (410)
T ss_pred HHHHHHHHHcCCEEECCEEccCcccccChh-hhcCCCEEEEEeCCccEEEEEEC
Confidence 999999999999999999999999888765 68899999999999999999873
No 3
>PRK05912 tyrosyl-tRNA synthetase; Validated
Probab=100.00 E-value=1.4e-48 Score=367.81 Aligned_cols=195 Identities=34% Similarity=0.487 Sum_probs=177.9
Q ss_pred CCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCCh
Q psy938 3 VTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEE 82 (241)
Q Consensus 3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~ 82 (241)
..++|++|+|||||+||+|||||.||+|||+++||||+++||||+|++|++|++|+++||+++.++|++++++|..++++
T Consensus 214 ~~~~~~l~~plL~~~~G~KMsKS~~naI~L~d~~tsp~~i~qki~~~~D~~v~~~l~~~t~~~~~ei~~l~~~~~~g~~~ 293 (408)
T PRK05912 214 GKPQFGLTMPLLTGLDGKKMGKSEGNAVWLDEEKTSPYEMYQKWMNISDADVWRYLKLLTFLSLEEIEELEEELAEGPNP 293 (408)
T ss_pred CCCeEEEecCCcCCCCCCcccCCCCCceeCCCCCCCHHHHHHHHhcCChHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCh
Confidence 34789999999999999999999999999999999999999999999999999999999999999999999999888899
Q ss_pred HHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCCCH
Q psy938 83 RRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRD 162 (241)
Q Consensus 83 ~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~Sk 162 (241)
+++|+.||++|++++||++++++|+++++++|+++. ++ .++|.+++. .+.++.++|+.+|+++|+
T Consensus 294 ~~~Kk~LA~~v~~~lhg~~~~~~a~~~~~~~f~~~~-----~~--------~~~~~~~~~--~~~~~~~~l~~~~~~~S~ 358 (408)
T PRK05912 294 REAKKVLAEEITALVHGEEAAEAAEEAFEALFGSGE-----LP--------DDLPEVELE--LGIDLLALLVEAGLVPSK 358 (408)
T ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHhcCCC-----Cc--------cCCCeEEec--CCCcHHHHHHHhCCCCCH
Confidence 999999999999999999999999999999998641 11 135555552 267899999999999999
Q ss_pred HHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEEEE
Q psy938 163 KEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKS 214 (241)
Q Consensus 163 sEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i~~ 214 (241)
+||||+|+||||+|||++|+|++..+... ++ ++++++||+|||+|++|+|
T Consensus 359 ~earr~i~~g~v~in~~~v~~~~~~~~~~-~~-~~~~~~lr~GKk~~~~i~~ 408 (408)
T PRK05912 359 SEARRLIKQGGVKINGEKVSDENYVLTAD-DR-FGKYTVLQRGKKKFARVTL 408 (408)
T ss_pred HHHHHHHHcCCEEECCEEecCcccccccc-cc-CCCEEEEEeCCCceEEEeC
Confidence 99999999999999999999998888754 56 8889999999999999975
No 4
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-44 Score=335.90 Aligned_cols=198 Identities=33% Similarity=0.507 Sum_probs=181.7
Q ss_pred CCCCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCC
Q psy938 1 MEVTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKP 80 (241)
Q Consensus 1 ~~~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~ 80 (241)
+++.++||+|+|||+|+||.|||||+||++|+++++||||+|||||+|++|.++.+|+.+||+++.++|.++++.+..++
T Consensus 204 ~g~~~~~~lt~PLL~~ldG~KmgKs~~~a~~~~s~~~Sp~~~yq~~~~i~D~~~~~~~~~~t~l~~~eI~~i~~~~~~~~ 283 (401)
T COG0162 204 LGQKKVVGLTTPLLTGLDGKKMGKSEGGAVWLDSEKTSPYDFYQYWMNIEDADVKRFLKLLTFLSLEEIEEIEKYVLKGP 283 (401)
T ss_pred hCCCCeEEEEeccccCCCCCcccccCCCceEccCCCCCcHhhhhcHhcCcHHHHHHHHHHhCcCChHHHHHHHHHhhcCC
Confidence 35678999999999999999999999999999999999999999999999999999999999998899999999888888
Q ss_pred ChHHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCC
Q psy938 81 EERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFP 160 (241)
Q Consensus 81 ~~~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~ 160 (241)
+++.+|+.||.++|..+||++++.+|.+.++.+|.++ ..+++++.++.. .+ ..+++++|+.+|+++
T Consensus 284 ~~r~~k~~LA~e~~~~~hG~~~a~~a~~~~~~~F~~g--~~~~l~~~dlk~--------~~----~~~~~~~lv~~~L~p 349 (401)
T COG0162 284 EPREAKKLLAKEVTKLVHGEEAAEAAEEEFEKLFSEG--LPENLPPADLKQ--------KL----EDGLVDLLVDAGLAP 349 (401)
T ss_pred ChHHHHHHHHHHhhHhhcCHHHHHHHHHHHHHHHhcC--CcccCCHHHHhh--------hh----HHHHHHHHHHhCCcc
Confidence 9999999999999999999999999999999999986 345777777765 11 126899999999999
Q ss_pred CHHHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEEEEc
Q psy938 161 RDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSA 215 (241)
Q Consensus 161 SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i~~~ 215 (241)
|++||||+|++|||++||++++|++..+ .+++++++.+||+|||+|++|.+.
T Consensus 350 sr~earr~i~~g~v~in~~~v~d~~~~~---~~~~~~~~~~l~~GKkk~~~i~~~ 401 (401)
T COG0162 350 SRSEARRLIQQGGVKINGEKVEDENYVL---SDLLDNGLLVLRRGKKKFALIVLK 401 (401)
T ss_pred cHHHHHhhcccCCEEECCEeccccccch---hhccCCceEEEecccccEEEEeeC
Confidence 9999999999999999999999998777 367888999999999999999874
No 5
>TIGR00234 tyrS tyrosyl-tRNA synthetase. This tyrosyl-tRNA synthetase model starts picking up tryptophanyl-tRNA synthetases at scores of 0 and below. The proteins found by this model have a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples.
Probab=100.00 E-value=9.8e-34 Score=264.76 Aligned_cols=169 Identities=32% Similarity=0.496 Sum_probs=149.9
Q ss_pred CCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCCh
Q psy938 3 VTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEE 82 (241)
Q Consensus 3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~ 82 (241)
...+|++|+|||+++||.|||||.||+|||++ +||++||||++.+|..+.+|+++||+++.+||+++++ ..++++
T Consensus 203 ~~~~~~~t~pLl~~~dg~KmgKS~~~~i~l~~---~~~~~~i~~~d~~D~~~~Ki~k~~t~~~~~ei~~l~~--~~~~~~ 277 (377)
T TIGR00234 203 PSLGFGLTVPLLTPADGEKMGKSGGGAVSLDE---GKYDFYQFWINTPDEDVKKILKLFTFLGLEEIEALVE--LKGPSP 277 (377)
T ss_pred CCCceeeceeeecCCCCCCccCCCCCcccCCc---cHhhhhhhhcCCcHHHHHHHHHHcCCCcHHHHHHHHH--hcccCH
Confidence 35689999999999999999999999999999 8899999999999999999999999999999999976 466899
Q ss_pred HHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCC-CCcHHHHHHhcCCCCC
Q psy938 83 RRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEP-GMSMLELSLATKCFPR 161 (241)
Q Consensus 83 ~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~-~~~l~~lLv~~gl~~S 161 (241)
+.+|+.||.+||+++||++++++|+++++.+|+++. + ..++|...+.... +.++.++++.+|+++|
T Consensus 278 ~~~q~~la~ei~~~vhg~~~~~~a~~~~~~~f~~~~-----~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~S 344 (377)
T TIGR00234 278 REVKENLAKEITKYVHGEEAALAAEEISEAIFSGGL-----N--------PDELPIFRPEKFGGDITLADLLVLSGLFPS 344 (377)
T ss_pred HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhcCCC-----C--------ccCCCEEeecccCCCcCHHHHHHHcCCCcC
Confidence 999999999999999999999999999999998652 1 1234554443222 3789999999999999
Q ss_pred HHHHHHHHHhCCeEEccEEecCCCCccC
Q psy938 162 DKEANLTISEGGFYVNYKKVQNPQEVLS 189 (241)
Q Consensus 162 ksEARRlI~qGgV~VNg~~v~d~~~~l~ 189 (241)
+++|||+|++|||+||+.++++++.+..
T Consensus 345 ~~~arr~ik~g~v~vn~~~i~~~~~v~~ 372 (377)
T TIGR00234 345 KSEARRDIKQGGVYINGEKVTDLEPIRK 372 (377)
T ss_pred hHHHHHHHHhCCEEECCEeccCchhhhc
Confidence 9999999999999999999999877654
No 6
>cd00395 Tyr_Trp_RS_core catalytic core domain of tyrosinyl-tRNA and tryptophanyl-tRNA synthetase. Tyrosinyl-tRNA synthetase (TyrRS)/Tryptophanyl-tRNA synthetase (TrpRS) catalytic core domain. These enzymes attach Tyr or Trp, respectively, to the appropriate tRNA. These class I enzymes are homodimers, which aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding.
Probab=99.86 E-value=1.1e-21 Score=176.63 Aligned_cols=93 Identities=41% Similarity=0.647 Sum_probs=88.8
Q ss_pred CCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCChH
Q psy938 4 TGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEER 83 (241)
Q Consensus 4 ~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~~ 83 (241)
.++++++.|+|||++|.|||||.+|+|||++.++||+++||||+++.|++|.+|+++||+++.+||+++++++.++++++
T Consensus 181 ~~p~~l~~p~l~~l~G~KMSKS~~~~i~l~~~~dsp~~i~~ki~~a~d~~v~~~~~~~t~~~~~ei~~i~~~~~~~~~~~ 260 (273)
T cd00395 181 TIAEGLTIPLVTKLDGPKFGKSESGPKWLDTEKTSPYEFYQFWINAVDSDVINILKYFTFLSKEEIERLEQEQYEAPGYR 260 (273)
T ss_pred CCCeEEeeccccCCCCCcCCCCCCCCccccccCCCHHHHHHHHHcccHhHHHHHHHHHcCCCHHHHHHHHHHHhcCCCHH
Confidence 46899999999999999999999999999988889999999999999999999999999999999999999998888999
Q ss_pred HHHHHHHHHHHhh
Q psy938 84 RAQKKLAEDLTLL 96 (241)
Q Consensus 84 ~~Kk~LA~~i~~~ 96 (241)
++|+.||++|+++
T Consensus 261 ~~K~~La~~i~~~ 273 (273)
T cd00395 261 VAQKTLAEEVTKT 273 (273)
T ss_pred HHHHHHHHHHHhC
Confidence 9999999999863
No 7
>cd00805 TyrRS_core catalytic core domain of tyrosinyl-tRNA synthetase. Tyrosinyl-tRNA synthetase (TyrRS) catalytic core domain. TyrRS is a homodimer which attaches Tyr to the appropriate tRNA. TyrRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formationof the enzyme bound aminoacyl-adenylate. It contains the class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding.
Probab=99.81 E-value=1.3e-19 Score=162.70 Aligned_cols=93 Identities=40% Similarity=0.633 Sum_probs=87.0
Q ss_pred CCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCCh
Q psy938 3 VTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEE 82 (241)
Q Consensus 3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~ 82 (241)
..++++++.|+|++++|+|||||.+|++| +.-.+||+++||||+++.|++|.+|+++|++++.+++++++++|..++.+
T Consensus 177 ~~~~~~l~~~ll~~l~G~KMSKS~~~~~~-i~l~dsp~~i~~Ki~~a~~~~v~~~l~~~~~~~~~~~eel~~~~~~~~~~ 255 (269)
T cd00805 177 YKKVVGLTTPLLTGLDGGKMSKSEGNAIW-DPVLDSPYDVYQKIRNAFDPDVLEFLKLFTFLDYEEIEELEEEHAEGPLP 255 (269)
T ss_pred CCCcEEEeeccccCCCCCcccCCCCCccc-ccCCCCHHHHHHHHHcCCcHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCH
Confidence 35789999999999999999999999998 77777999999999999999999999999999999999999999888779
Q ss_pred HHHHHHHHHHHHhh
Q psy938 83 RRAQKKLAEDLTLL 96 (241)
Q Consensus 83 ~~~Kk~LA~~i~~~ 96 (241)
+++|+.||++|+++
T Consensus 256 ~~~K~~la~~i~~l 269 (269)
T cd00805 256 RDAKKALAEELTKL 269 (269)
T ss_pred HHHHHHHHHHHHhC
Confidence 99999999999864
No 8
>PF00579 tRNA-synt_1b: tRNA synthetases class I (W and Y); InterPro: IPR002305 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. The class Ia aminoacyl-tRNA synthetases consist of the isoleucyl, methionyl, valyl, leucyl, cysteinyl, and arginyl-tRNA synthetases; the class Ib include the glutamyl and glutaminyl-tRNA synthetases, and the class Ic are the tyrosyl and tryptophanyl-tRNA synthetases [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2JAN_A 3P0J_B 3P0I_B 3P0H_B 1YID_C 2A4M_C 1YIA_C 1YI8_C 2EL7_A 3PRH_A ....
Probab=99.52 E-value=9.2e-15 Score=132.08 Aligned_cols=111 Identities=25% Similarity=0.233 Sum_probs=92.9
Q ss_pred CCceeeecccccCCCCC-ccccCCCC-eEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCC
Q psy938 4 TGDGGLTTPIIESESGE-KFGKSARN-AIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPE 81 (241)
Q Consensus 4 ~~~~~lt~pLL~g~dG~-KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~ 81 (241)
..+++++.|+||++||. |||||.+| +|||+++.+++++.++++++.+|.++..++.+.++++.++++.++..+.+.+
T Consensus 180 ~~p~~l~~~~l~~l~G~~KMSKS~~ns~I~L~d~~~~i~~Ki~~a~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~- 258 (292)
T PF00579_consen 180 PKPAGLTSPLLPGLDGQKKMSKSDPNSAIFLDDSPEEIRKKIKKAFCDPDRENPRLLKGRPFISPFLIERLEAFHGNDD- 258 (292)
T ss_dssp SS-EEEEETCBBSTTSSSBTTTTTTGGS-BTTTTHHHHHHHHHHSHTSTTSHHHHHHHHHHTHHHHHHHHHHHHHHHHH-
T ss_pred cCchheeeccccccCCccccCccCCccEEEEeccchhHHHHHHHHhhCCCcccccccccCCCCCHHHHHHHHHhcCCcc-
Confidence 47899999999999997 99999999 9999995555555555556668889999999999998888888887665444
Q ss_pred hHHHHHHHHHHHHhhccCHHHHHHHHHHHHHhcc
Q psy938 82 ERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYS 115 (241)
Q Consensus 82 ~~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~ 115 (241)
++.+++.++++++..+|+.+..+++.++...+|+
T Consensus 259 ~~~~~~~~~~~~~g~l~~~~~K~~~~e~~~~~le 292 (292)
T PF00579_consen 259 YRSLEELLADYVSGELHPGDLKKALAEALNEFLE 292 (292)
T ss_dssp ESHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHccCCcChHHHHHHHHHHHHHhhC
Confidence 6789999999999999999999999998888773
No 9
>PLN02486 aminoacyl-tRNA ligase
Probab=99.42 E-value=5.7e-13 Score=125.20 Aligned_cols=96 Identities=21% Similarity=0.233 Sum_probs=78.6
Q ss_pred eeeecccccCCCC--CccccCCCC-eEeecCCCCCHHHHHHHhhc-C---------------CChhHHHHHHHhcCC--C
Q psy938 7 GGLTTPIIESESG--EKFGKSARN-AIWLDSKLSSSFELYQYLIR-T---------------KDSEVYDLLKLFSFD--S 65 (241)
Q Consensus 7 ~~lt~pLL~g~dG--~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~-~---------------~D~~v~~~l~~~t~l--~ 65 (241)
..+..+.||+++| .|||||.+| +|||++ +|+++++|+++ + .|++++..+.||+++ +
T Consensus 249 ~~~~~~~lp~L~g~~~KMSkS~~nsaI~L~D---~p~~i~~KI~k~A~t~~~~t~~~~~~~gg~p~v~~~~~~l~~f~~d 325 (383)
T PLN02486 249 ALIESRFFPALQGESGKMSASDPNSAIYVTD---TPKEIKNKINKYAFSGGQDTVEEHRELGANLEVDIPWKYLNFFLED 325 (383)
T ss_pred ceeccccccCCCCCCCcCcCcCCCCeeeccC---CHHHHHHHHhcCCCCCCCCcccccccCCCCCccchHHHHHHHHcCC
Confidence 3445678888887 699999987 799999 99999999999 3 256666666666666 3
Q ss_pred HHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHHHHH
Q psy938 66 LAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEGLKS 105 (241)
Q Consensus 66 ~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~a~~ 105 (241)
.++++++.+.+..| .++.++|+.||+.|++++++-.+..+
T Consensus 326 d~~~eei~~~y~~G~l~~ge~K~~lae~i~~~l~~~qerr~ 366 (383)
T PLN02486 326 DAELERIKKEYGSGRMLTGEVKKRLIEVLTEIVERHQRARA 366 (383)
T ss_pred chHHHHHHHHhccCCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999766 68999999999999999999766543
No 10
>PTZ00126 tyrosyl-tRNA synthetase; Provisional
Probab=99.41 E-value=4.5e-13 Score=125.98 Aligned_cols=94 Identities=18% Similarity=0.257 Sum_probs=80.0
Q ss_pred CceeeecccccCC-CC-CccccCCCC-eEeecCCCCCHHHHHHHhhc-------CCChhHHHHHHHhcC-----------
Q psy938 5 GDGGLTTPIIESE-SG-EKFGKSARN-AIWLDSKLSSSFELYQYLIR-------TKDSEVYDLLKLFSF----------- 63 (241)
Q Consensus 5 ~~~~lt~pLL~g~-dG-~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~-------~~D~~v~~~l~~~t~----------- 63 (241)
+++.++.|+|+|+ || +|||||.+| +|||++ +|+++++|+++ .+++.+..|+++++|
T Consensus 239 ~~~~~~~~~lpgL~dg~~KMSKS~~ns~I~L~D---spe~I~kKI~kA~t~p~~~~~npv~~~~~~~~~~~~~~~~I~r~ 315 (383)
T PTZ00126 239 KPIILSHHMLPGLLEGQEKMSKSDPNSAIFMED---SEEDVNRKIKKAYCPPGVIEGNPILAYFKSIVFPAFNSFTVLRK 315 (383)
T ss_pred CceeecccccccCCCCCCCCCcCCCCCeecCCC---CHHHHHHHHHhCcCCCCCCCCCcchhhhhhcccccccceeEecc
Confidence 5677789999999 67 799999977 799999 99999999999 466789999998775
Q ss_pred ------CCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHH
Q psy938 64 ------DSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEE 101 (241)
Q Consensus 64 ------l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~ 101 (241)
++.++++++++.+..+ .+|.++|+.||+.|++++..-.
T Consensus 316 ~k~gg~~~~~~~eel~~~y~~g~l~p~dlK~~lae~i~~~L~PIR 360 (383)
T PTZ00126 316 EKNGGDVTYTTYEELEKDYLSGALHPGDLKPALAKYLNLMLQPVR 360 (383)
T ss_pred ccccCccCcCCHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 1225789999998776 6999999999999999987543
No 11
>cd00806 TrpRS_core catalytic core domain of tryptophanyl-tRNA synthetase. Tryptophanyl-tRNA synthetase (TrpRS) catalytic core domain. TrpRS is a homodimer which attaches Tyr to the appropriate tRNA. TrpRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding
Probab=99.39 E-value=1.6e-12 Score=117.53 Aligned_cols=81 Identities=22% Similarity=0.288 Sum_probs=71.3
Q ss_pred cccccCCCC--CccccCCC-CeEeecCCCCCHHHHHHHhhcC-C---------------ChhHHHHHHHhcCCCHHHHHH
Q psy938 11 TPIIESESG--EKFGKSAR-NAIWLDSKLSSSFELYQYLIRT-K---------------DSEVYDLLKLFSFDSLAAIED 71 (241)
Q Consensus 11 ~pLL~g~dG--~KmsKS~g-n~I~L~~~~Tsp~~~yq~~~~~-~---------------D~~v~~~l~~~t~l~~eei~~ 71 (241)
+|+|+|++| +|||||.+ |+|||++ +|+++++|++++ + ++.+..|+++|++.+.+++++
T Consensus 179 ~~~i~~l~g~~~KMSKS~~~~~I~L~d---~~~~i~~KI~~a~td~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 255 (280)
T cd00806 179 GAFLPGLQGPSKKMSKSDPNNAIFLTD---SPKEIKKKIMKAATDGGRTEHRRDGGGPGVSNLVEIYSAFFNDDDEELEE 255 (280)
T ss_pred CCccccCCCCCCcccCCCCCCeEEeeC---CHHHHHHHHHhccCCCCCceecCCCCCCCcChHHHHHHHHhCCCHHHHHH
Confidence 599999998 49999998 9999999 999999999996 2 268899999999999999998
Q ss_pred HHHHhh-cCCChHHHHHHHHHHHHh
Q psy938 72 FKRQNE-HKPEERRAQKKLAEDLTL 95 (241)
Q Consensus 72 i~~~~~-~~~~~~~~Kk~LA~~i~~ 95 (241)
+ +++. .+.+++++|+.||+.|++
T Consensus 256 ~-~~~~~g~~~~~~~K~~lae~i~~ 279 (280)
T cd00806 256 I-DEYRSGGLGYGECKKLLAEAIQE 279 (280)
T ss_pred H-HHhhcCCCCHHHHHHHHHHHHHh
Confidence 8 5554 458999999999999986
No 12
>PRK08560 tyrosyl-tRNA synthetase; Validated
Probab=99.36 E-value=2.2e-12 Score=119.13 Aligned_cols=93 Identities=19% Similarity=0.288 Sum_probs=80.1
Q ss_pred CCceeeecccccCCCCC--ccccCC-CCeEeecCCCCCHHHHHHHhhcC-------CChhHHHHHHHhcCCC--------
Q psy938 4 TGDGGLTTPIIESESGE--KFGKSA-RNAIWLDSKLSSSFELYQYLIRT-------KDSEVYDLLKLFSFDS-------- 65 (241)
Q Consensus 4 ~~~~~lt~pLL~g~dG~--KmsKS~-gn~I~L~~~~Tsp~~~yq~~~~~-------~D~~v~~~l~~~t~l~-------- 65 (241)
..+++++.|+|||++|. |||||. +|+|||++ +|+++++|++++ .++.+..|+++|.+..
T Consensus 195 ~~p~~l~~~~l~~L~g~~~KMSKS~p~~~I~L~D---~~~~I~~KI~kA~t~~~~~~~n~v~~~~~~~~~~~~~~~~~~r 271 (329)
T PRK08560 195 KKPVCIHTPLLTGLDGGGIKMSKSKPGSAIFVHD---SPEEIRRKIKKAYCPPGEVEGNPVLEIAKYHIFPRYDPFVIER 271 (329)
T ss_pred CCceEEEcCccCCCCCCCCCCcCCCCCCeecccC---CHHHHHHHHHhccCCCCCcCCCcHHHHHHHHhhccccceEEec
Confidence 46789999999999996 999999 99999999 999999999995 4578999999987531
Q ss_pred ---------HHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccC
Q psy938 66 ---------LAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHG 99 (241)
Q Consensus 66 ---------~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG 99 (241)
.++++++++++..+ .++.++|+.||+.|++.+..
T Consensus 272 ~~~~g~~~~~~~~eel~~~y~~g~l~~~~lK~~la~~i~~~l~p 315 (329)
T PRK08560 272 PEKYGGDLEYESYEELERDYAEGKLHPMDLKNAVAEYLIEILEP 315 (329)
T ss_pred hhhcCCCCCcCCHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence 15688899998776 58999999999999888754
No 13
>PRK12284 tryptophanyl-tRNA synthetase; Reviewed
Probab=99.34 E-value=2e-12 Score=122.65 Aligned_cols=88 Identities=19% Similarity=0.180 Sum_probs=73.4
Q ss_pred eeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcC-CC------------hhHHHHHHHhcCCCHHHHHHHH
Q psy938 7 GGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRT-KD------------SEVYDLLKLFSFDSLAAIEDFK 73 (241)
Q Consensus 7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~-~D------------~~v~~~l~~~t~l~~eei~~i~ 73 (241)
+....|+|+|+||+|||||.+|+|+|.+ ||+++++|++++ +| +.+..|+++|+. .+++++++
T Consensus 188 i~~~~~~I~gLdg~KMSKS~~n~I~L~D---s~~~I~kKI~~A~TDs~~~~~~~~pe~snLl~i~~~~~~--~~~~eel~ 262 (431)
T PRK12284 188 IEESVATLPGLDGRKMSKSYDNTIPLFA---PREELKKAIFSIVTDSRAPGEPKDTEGSALFQLYQAFAT--PEETAAFR 262 (431)
T ss_pred cccccccccCCCCccccCCCCCEeeecC---CHHHHHHHHhcCCCCCCCCCCCCCCCcchHHHHHHHhCC--cchHHHHH
Confidence 3345789999999999999999999999 999999999997 22 356666666653 46788888
Q ss_pred HHhhcCCChHHHHHHHHHHHHhhccC
Q psy938 74 RQNEHKPEERRAQKKLAEDLTLLVHG 99 (241)
Q Consensus 74 ~~~~~~~~~~~~Kk~LA~~i~~~vhG 99 (241)
+++..+.++.++|+.||+.|++.+..
T Consensus 263 ~~~~~g~~~g~~K~~Lae~i~~~L~P 288 (431)
T PRK12284 263 QALADGIGWGDAKQRLFERIDRELAP 288 (431)
T ss_pred HHHhcCCChHHHHHHHHHHHHHHHHH
Confidence 88876689999999999999988763
No 14
>PRK12285 tryptophanyl-tRNA synthetase; Reviewed
Probab=99.33 E-value=3.3e-12 Score=119.63 Aligned_cols=92 Identities=14% Similarity=0.197 Sum_probs=77.9
Q ss_pred CceeeecccccCCCCCccccCC-CCeEeecCCCCCHHHHHHHhhcC-CC-----------------hhHHHHHHHhcCCC
Q psy938 5 GDGGLTTPIIESESGEKFGKSA-RNAIWLDSKLSSSFELYQYLIRT-KD-----------------SEVYDLLKLFSFDS 65 (241)
Q Consensus 5 ~~~~lt~pLL~g~dG~KmsKS~-gn~I~L~~~~Tsp~~~yq~~~~~-~D-----------------~~v~~~l~~~t~l~ 65 (241)
.+..+..|+|||++|+|||||. +|+|+|++ +|+++++|++++ +| +.+..|+++|...+
T Consensus 235 ~P~~l~~~~lpgL~G~KMSkS~~~s~I~L~D---~p~~I~kKI~kA~Td~~~t~~~~~~~~g~p~~~~v~~~l~~~~~~~ 311 (368)
T PRK12285 235 KPSSTYHKFMPGLTGGKMSSSKPESAIYLTD---DPETVKKKIMKALTGGRATLEEQRKLGGEPDECVVYELLLYHLEED 311 (368)
T ss_pred CchhHhhhcccCCCCCcCCCCCCCCeeeccC---CHHHHHHHHHhCcCCCCcccccccccCCCCCcchHHHHHHHHhcCC
Confidence 4455667899999999999998 67999999 999999999997 22 56777777776555
Q ss_pred HHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccC
Q psy938 66 LAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHG 99 (241)
Q Consensus 66 ~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG 99 (241)
.++++++.+.+..+ .++.++|+.||+.|++.+..
T Consensus 312 d~~~eei~~~y~~g~~~~g~~K~~lae~i~~~l~~ 346 (368)
T PRK12285 312 DKELKEIYEECRSGELLCGECKKEAAEKIAEFLKE 346 (368)
T ss_pred CccHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 67899999999776 69999999999999999854
No 15
>PRK12556 tryptophanyl-tRNA synthetase; Provisional
Probab=99.30 E-value=4.1e-12 Score=117.50 Aligned_cols=87 Identities=20% Similarity=0.215 Sum_probs=71.3
Q ss_pred ecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCC-C---------hhHHHHHHHhcCC-CHHHHHHHHHHhhc
Q psy938 10 TTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTK-D---------SEVYDLLKLFSFD-SLAAIEDFKRQNEH 78 (241)
Q Consensus 10 t~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~-D---------~~v~~~l~~~t~l-~~eei~~i~~~~~~ 78 (241)
+.|+|+|+||+|||||.+|+|+|.+ +|+++++|++++. | +++..++.++..+ +.++++++++++..
T Consensus 191 ~~~~l~gLdg~KMSKS~~n~I~L~D---~p~~I~kKI~ka~Td~~~~~~~~~p~~~~l~~i~~~~~~~~~~eei~~~y~~ 267 (332)
T PRK12556 191 EGAILPGLDGRKMSKSYGNVIPLFA---EQEKLRKLIFKIKTDSSLPNEPKDPETSALFTIYKEFATEEEVQSMREKYET 267 (332)
T ss_pred ccccccCCCCCCCCCCCCCcccccC---CHHHHHHHHHHhccCCCcccCCCCcchhHHHHHHHHHCCchhHHHHHHHHhc
Confidence 5899999999999999999999999 9999999999962 2 2344444444433 34678999998876
Q ss_pred CCChHHHHHHHHHHHHhhccC
Q psy938 79 KPEERRAQKKLAEDLTLLVHG 99 (241)
Q Consensus 79 ~~~~~~~Kk~LA~~i~~~vhG 99 (241)
+.++.++|+.||+.|++.+..
T Consensus 268 ~~~~~~~K~~lae~i~~~l~p 288 (332)
T PRK12556 268 GIGWGDVKKELFRVVDRELAG 288 (332)
T ss_pred CCChHHHHHHHHHHHHHHHHH
Confidence 778999999999999988764
No 16
>PRK00927 tryptophanyl-tRNA synthetase; Reviewed
Probab=99.29 E-value=7.3e-12 Score=115.82 Aligned_cols=84 Identities=20% Similarity=0.192 Sum_probs=70.3
Q ss_pred cccccCCCCC--ccccCCC---CeEeecCCCCCHHHHHHHhhcCC-Ch-----------------hHHHHHHHhcCCCHH
Q psy938 11 TPIIESESGE--KFGKSAR---NAIWLDSKLSSSFELYQYLIRTK-DS-----------------EVYDLLKLFSFDSLA 67 (241)
Q Consensus 11 ~pLL~g~dG~--KmsKS~g---n~I~L~~~~Tsp~~~yq~~~~~~-D~-----------------~v~~~l~~~t~l~~e 67 (241)
+|+|+|++|. |||||.+ |+|+|++ +|+++++|++++. |+ .+..|+++|+. +
T Consensus 181 ~~~l~gL~g~~~KMSKS~~~~~~~I~l~D---~~~~I~~KI~~a~td~~~~~~~~~~~~~~p~~~~l~~~~~~~~~---~ 254 (333)
T PRK00927 181 GARVMGLDGPTKKMSKSDPNDNNTINLLD---DPKTIAKKIKKAVTDSERLREIRYDLPNKPEVSNLLTIYSALSG---E 254 (333)
T ss_pred cccccCCCCCCCCCCCCCCCCCCeEEeeC---CHHHHHHHHHhCCCCCCcccccccCCCCCCccccHHHHHHHhCC---C
Confidence 4999999995 9999998 8999999 9999999999984 43 57778888875 4
Q ss_pred HHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCH
Q psy938 68 AIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGE 100 (241)
Q Consensus 68 ei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~ 100 (241)
+++++.+++..+ .+++++|+.||+.|++.+..-
T Consensus 255 ~~eel~~~~~~g~~~~~~lK~~la~~i~~~l~pi 288 (333)
T PRK00927 255 SIEELEAEYEAGGKGYGDFKKDLAEAVVEFLAPI 288 (333)
T ss_pred CHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHH
Confidence 566777777655 689999999999999987653
No 17
>PRK12282 tryptophanyl-tRNA synthetase II; Reviewed
Probab=99.28 E-value=1.2e-11 Score=114.54 Aligned_cols=87 Identities=21% Similarity=0.294 Sum_probs=73.9
Q ss_pred cccccCCCC-CccccCCCCeEeecCCCCCHHHHHHHhhcC-CC--------------hhHHHHHHHhcCCCHHHHHHHHH
Q psy938 11 TPIIESESG-EKFGKSARNAIWLDSKLSSSFELYQYLIRT-KD--------------SEVYDLLKLFSFDSLAAIEDFKR 74 (241)
Q Consensus 11 ~pLL~g~dG-~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~-~D--------------~~v~~~l~~~t~l~~eei~~i~~ 74 (241)
+|+|+|++| .|||||.+|+|||++ +|+++++|++++ +| +.+..|+++|. .+.++++++++
T Consensus 185 ~~~i~~L~g~~KMSKS~~~~I~L~D---~pe~I~kKI~~A~td~~~~~~~~~~~~~~~~l~~~~~~f~-~~~~~~e~l~~ 260 (333)
T PRK12282 185 AGRLPGLDGKAKMSKSLGNAIYLSD---DADTIKKKVMSMYTDPNHIRVEDPGKVEGNVVFTYLDAFD-PDKAEVAELKA 260 (333)
T ss_pred CCcccCCCCCCcCCCCCCCeeeeeC---CHHHHHHHHHhCcCCCCCccCCCCCCCCcChHHHHHHHhC-CCCchHHHHHH
Confidence 789999999 799999999999999 999999999997 33 56777888763 13578899999
Q ss_pred HhhcC-CChHHHHHHHHHHHHhhccCHH
Q psy938 75 QNEHK-PEERRAQKKLAEDLTLLVHGEE 101 (241)
Q Consensus 75 ~~~~~-~~~~~~Kk~LA~~i~~~vhG~~ 101 (241)
++..+ .++.++|+.||+.|++.+-.-.
T Consensus 261 ~y~~g~~~~~dlK~~lae~i~~~l~pir 288 (333)
T PRK12282 261 HYQRGGLGDVKCKRYLEEVLQELLAPIR 288 (333)
T ss_pred HHhcCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 98766 6999999999999999876543
No 18
>PRK12283 tryptophanyl-tRNA synthetase; Reviewed
Probab=99.27 E-value=6.1e-12 Score=118.41 Aligned_cols=84 Identities=14% Similarity=0.134 Sum_probs=68.8
Q ss_pred cccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcC-CC--------------hhHHHHHHHhcCCCHHHHHHHHHH
Q psy938 11 TPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRT-KD--------------SEVYDLLKLFSFDSLAAIEDFKRQ 75 (241)
Q Consensus 11 ~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~-~D--------------~~v~~~l~~~t~l~~eei~~i~~~ 75 (241)
.++|+|+||+|||||.+|+|+|.+ ||+++++|++++ +| +.+.+++.+|+ +.++++++.+.
T Consensus 254 ~~~I~gLdg~KMSKS~~n~I~L~D---s~~~I~kKI~~a~TDs~~~~~~~~g~Pe~~nl~~i~~~~~--~~~~~~~i~~~ 328 (398)
T PRK12283 254 ASKMPGLDGQKMSKSYGNTIGLRE---DPESVTKKIRTMPTDPARVRRTDPGDPEKCPVWQLHQVYS--DEETKEWVQKG 328 (398)
T ss_pred CCcccCCCCCcCCCCCCCeeeCcC---CHHHHHHHHHhCCCCCcccccCCCCCCCcCHHHHHHHHhC--CChHHHHHHHH
Confidence 579999999999999999999999 999999999996 33 34555555554 34468888888
Q ss_pred hhcC-CChHHHHHHHHHHHHhhccC
Q psy938 76 NEHK-PEERRAQKKLAEDLTLLVHG 99 (241)
Q Consensus 76 ~~~~-~~~~~~Kk~LA~~i~~~vhG 99 (241)
|+.+ .++.++|+.||+.|++.+..
T Consensus 329 ~~~g~~~~g~~K~~lae~v~e~L~~ 353 (398)
T PRK12283 329 CRSAGIGCLECKQPVIDAILREQQP 353 (398)
T ss_pred HhcCCCChHHHHHHHHHHHHHHHHH
Confidence 8765 68999999999999887653
No 19
>TIGR00233 trpS tryptophanyl-tRNA synthetase. This model represents tryptophanyl-tRNA synthetase. Some members of the family have a pfam00458 domain amino-terminal to the region described by this model.
Probab=99.23 E-value=3.2e-11 Score=111.41 Aligned_cols=88 Identities=19% Similarity=0.217 Sum_probs=74.8
Q ss_pred ecccccCCCCCccccCCCC-eEeecCCCCCHHHHHHHhhcC-CC---------------hhHHHHHHHhcCCC--HHHHH
Q psy938 10 TTPIIESESGEKFGKSARN-AIWLDSKLSSSFELYQYLIRT-KD---------------SEVYDLLKLFSFDS--LAAIE 70 (241)
Q Consensus 10 t~pLL~g~dG~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~~-~D---------------~~v~~~l~~~t~l~--~eei~ 70 (241)
.+|.|+|++|+|||||.+| +|+|++ +|+++++|++++ .| +++..++.+|++++ .++++
T Consensus 181 ~~~~l~gl~~~KMSKS~~~s~I~L~D---~~e~I~~KI~~a~td~~~~~~~~~~~~~g~~~l~~i~~~~~~~~~~~~~~~ 257 (328)
T TIGR00233 181 FFPRLMGLSGKKMSKSDPNSAIFLTD---TPKQIKKKIRKAATDGGRVTLFEHREKGGVPNLLVIYQYLSFFLIDDDKLK 257 (328)
T ss_pred ccCCCCCCCCCcCCCCCCCCeEeecC---CHHHHHHHHHhcCCCCCCCcccCcCCCCCCchHHHHHHHhhccCCCcchHH
Confidence 5789999999999999986 999999 999999999995 33 35778888888774 35788
Q ss_pred HHHHHhhcC-CChHHHHHHHHHHHHhhccCH
Q psy938 71 DFKRQNEHK-PEERRAQKKLAEDLTLLVHGE 100 (241)
Q Consensus 71 ~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~ 100 (241)
++.+.+..+ .++.++|+.||+.|.+.+..-
T Consensus 258 ~~~~~~~~g~~~~~~lK~~lae~i~~~l~pi 288 (328)
T TIGR00233 258 EIYEKYKSGKLLYGELKKALIEVLQEFLKEI 288 (328)
T ss_pred HHHHHHhcCCCChHHHHHHHHHHHHHHHHHH
Confidence 888888766 689999999999999988763
No 20
>COG0180 TrpS Tryptophanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=99.13 E-value=1.4e-10 Score=106.30 Aligned_cols=83 Identities=18% Similarity=0.242 Sum_probs=69.5
Q ss_pred ccccCCCC-CccccCCCC-eEeecCCCCCHHHHHHHhhcC-CC---------------hhHHHHHHHhcCCCHHHHHHHH
Q psy938 12 PIIESESG-EKFGKSARN-AIWLDSKLSSSFELYQYLIRT-KD---------------SEVYDLLKLFSFDSLAAIEDFK 73 (241)
Q Consensus 12 pLL~g~dG-~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~~-~D---------------~~v~~~l~~~t~l~~eei~~i~ 73 (241)
++++|++| .|||||.+| +|+|.+ +|.++.+|++++ +| +.+..|+.+|+. .+++.++.
T Consensus 188 ~~i~gL~g~~KMSkS~~ns~I~L~D---~~~~i~kKI~~~~td~~~~~~~~~~g~Pe~~~l~~~~~~~~~--~~~~~ei~ 262 (314)
T COG0180 188 ARLPGLDGPGKMSKSDPNSAIFLLD---DPKTIRKKIKKAATDGPTLIEYRKGGKPEVCNLFEIYSAFFE--DDSILEIE 262 (314)
T ss_pred CcccCCCCCCcccccCCCCeeeccC---CHHHHHHHHHHhccCCCCccccCCCCCCCcchHHHHHHHhcC--CCcHHHHH
Confidence 79999999 899999999 999999 999999999993 33 355556555553 55666999
Q ss_pred HHhhcC-CChHHHHHHHHHHHHhhccC
Q psy938 74 RQNEHK-PEERRAQKKLAEDLTLLVHG 99 (241)
Q Consensus 74 ~~~~~~-~~~~~~Kk~LA~~i~~~vhG 99 (241)
++|+.| .++.+||+.||+.|.+.+-.
T Consensus 263 ~~~~~G~~~~ge~K~~lae~i~~fL~~ 289 (314)
T COG0180 263 AEYRGGELGCGECKKELAEAIQEFLKP 289 (314)
T ss_pred HHHhccccchHHHHHHHHHHHHHHHHH
Confidence 999887 79999999999999888765
No 21
>PTZ00348 tyrosyl-tRNA synthetase; Provisional
Probab=99.06 E-value=3.9e-10 Score=112.65 Aligned_cols=92 Identities=15% Similarity=0.225 Sum_probs=77.1
Q ss_pred CceeeecccccCCCC--CccccCC-CCeEeecCCCCCHHHHHHHhhcC----------------------CChhHHHHHH
Q psy938 5 GDGGLTTPIIESESG--EKFGKSA-RNAIWLDSKLSSSFELYQYLIRT----------------------KDSEVYDLLK 59 (241)
Q Consensus 5 ~~~~lt~pLL~g~dG--~KmsKS~-gn~I~L~~~~Tsp~~~yq~~~~~----------------------~D~~v~~~l~ 59 (241)
+++.+..|+|+|++| .|||||. +|+|+|++ +|+++++|++++ +++.+..|++
T Consensus 204 kpvil~~~~LpGL~gg~~KMSKS~p~naI~L~D---spe~I~kKI~kA~td~~~~~~~~~~d~g~p~~~~e~npvl~i~~ 280 (682)
T PTZ00348 204 KPVILSHHMLAGLKQGQAKMSKSDPDSAIFMED---TEEDVARKIRQAYCPRVKQSASEITDDGAPVATDDRNPVLDYFQ 280 (682)
T ss_pred CceecccccCcCCCCCCCcCCCCCCCCeecccC---CHHHHHHHHHhCCCCCCcCcccccCCCCCccccCCCCcHHHHHH
Confidence 456667899999974 6999999 68999999 999999999998 2267888999
Q ss_pred HhcCCCH-----------HHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccC
Q psy938 60 LFSFDSL-----------AAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHG 99 (241)
Q Consensus 60 ~~t~l~~-----------eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG 99 (241)
++.|... ++++++++.+..+ .++.++|+.||+.|++.+..
T Consensus 281 ~~if~~~g~~~~i~~~~~~~~eele~~y~~g~l~~~dlK~~lae~l~~~L~P 332 (682)
T PTZ00348 281 CVVYARPGAVATIDGTTYATYEDLEQAFVSDEVSEEALKSCLIDEVNALLEP 332 (682)
T ss_pred HHhccccchhcccCCcccCcHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 8865322 5688999999765 69999999999999998865
No 22
>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=98.82 E-value=8.9e-09 Score=68.78 Aligned_cols=44 Identities=23% Similarity=0.251 Sum_probs=41.0
Q ss_pred cHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 148 SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 148 ~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
+|..+|..+|+++|+++|+++|.+|+|+|||+++++|++.+...
T Consensus 2 RLd~~L~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~ 45 (48)
T PF01479_consen 2 RLDKFLSRLGLASSRSEARRLIKQGRVKVNGKVVKDPSYIVKPG 45 (48)
T ss_dssp BHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEESSTTSBESTT
T ss_pred CHHHHHHHcCCcCCHHHHHHhcCCCEEEECCEEEcCCCCCCCCc
Confidence 57889999999999999999999999999999999999988765
No 23
>PLN02886 aminoacyl-tRNA ligase
Probab=98.78 E-value=9.5e-09 Score=96.87 Aligned_cols=85 Identities=19% Similarity=0.128 Sum_probs=65.4
Q ss_pred cccccCCCC--CccccCCC---CeEeecCCCCCHHHHHHHhhcCC-C------------hhHHHHHHHhcCCCHHHHHHH
Q psy938 11 TPIIESESG--EKFGKSAR---NAIWLDSKLSSSFELYQYLIRTK-D------------SEVYDLLKLFSFDSLAAIEDF 72 (241)
Q Consensus 11 ~pLL~g~dG--~KmsKS~g---n~I~L~~~~Tsp~~~yq~~~~~~-D------------~~v~~~l~~~t~l~~eei~~i 72 (241)
.++|++++| .|||||.. |+|+|.| +|+++++|++++. | +.+.+++.+|..++..+++++
T Consensus 239 ~~ri~~L~~g~~KMSKS~p~~~s~I~L~D---s~e~I~kKI~~a~TD~~~~i~~~~p~~p~v~nl~~i~~~~~~~~~eei 315 (389)
T PLN02886 239 GARVMSLTDGTSKMSKSAPSDQSRINLLD---PPDVIANKIKRCKTDSFPGLEFDNPERPECNNLLSIYQLVTGKTKEEV 315 (389)
T ss_pred cceeeeCCCCCCcCCCCCCCCCCeEEecC---CHHHHHHHHhcCCCCCCCCccCCCCCCcccccHHHHHHHccCCCHHHH
Confidence 347888854 69999984 6999999 9999999999972 2 344556666655545566777
Q ss_pred HHHhhcCCChHHHHHHHHHHHHhhccC
Q psy938 73 KRQNEHKPEERRAQKKLAEDLTLLVHG 99 (241)
Q Consensus 73 ~~~~~~~~~~~~~Kk~LA~~i~~~vhG 99 (241)
.+++. +.++.++|+.||+.|++.+..
T Consensus 316 ~~~~~-~~~~g~~K~~Lae~I~~~L~P 341 (389)
T PLN02886 316 LAECG-DMRWGDFKPLLTDALIEHLSP 341 (389)
T ss_pred HHHhc-CCCCchHHHHHHHHHHHHHHH
Confidence 77765 568889999999999888754
No 24
>KOG2144|consensus
Probab=98.18 E-value=5.4e-06 Score=75.21 Aligned_cols=93 Identities=18% Similarity=0.230 Sum_probs=76.5
Q ss_pred CceeeecccccCCC-CCccccCCCC-eEeecCCCCCHHHHHHHhhcC-------CChhHHHHHHHhcCCCHH--------
Q psy938 5 GDGGLTTPIIESES-GEKFGKSARN-AIWLDSKLSSSFELYQYLIRT-------KDSEVYDLLKLFSFDSLA-------- 67 (241)
Q Consensus 5 ~~~~lt~pLL~g~d-G~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~~-------~D~~v~~~l~~~t~l~~e-------- 67 (241)
....+..|.|||+. |+|||+|..+ .|.|-+ +|.+++.++.+. .++....|+++..|.-.+
T Consensus 205 KrihLmnpMvPGL~q~~KMSsSd~~SkIdllD---~~~~V~kKI~kAfCePg~ve~Ng~L~fvkyvvfP~~~e~~~~~i~ 281 (360)
T KOG2144|consen 205 KRIHLMNPMVPGLAQGEKMSSSDPLSKIDLLD---EPADVNKKIKKAFCEPGNVEGNGCLSFVKYVVFPIFEEFGVEVID 281 (360)
T ss_pred cceeecCCCCccccccCccccCCccccccccc---CHHHHHHHHHHhcCCCCCcCCCcHHHHHHHHHhhhHHhcCceeec
Confidence 45667889999998 7999999977 599999 999999999985 678888888876653222
Q ss_pred ------------HHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCH
Q psy938 68 ------------AIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGE 100 (241)
Q Consensus 68 ------------ei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~ 100 (241)
..+++++.+..+ .||.++|+-|+..|.+++.+-
T Consensus 282 r~ek~GG~~tf~syed~e~~y~~~~lhPgDLK~~l~~alN~lL~~i 327 (360)
T KOG2144|consen 282 RPEKFGGNKTFKSYEDIEKDYEEGELHPGDLKKGLEKALNELLQPI 327 (360)
T ss_pred chhhcCCcchhHHHHHHHHHHHhCCcChHHHHHHHHHHHHHHHHHH
Confidence 177888888766 799999999999999998753
No 25
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=97.99 E-value=2.9e-06 Score=60.91 Aligned_cols=47 Identities=21% Similarity=0.157 Sum_probs=32.6
Q ss_pred CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 145 PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 145 ~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
+.+.|.++|..+|+++|.+||+.+|++|.|+|||+..+.....+...
T Consensus 6 e~I~L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~G 52 (65)
T PF13275_consen 6 EYITLGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPG 52 (65)
T ss_dssp S---HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS----SS
T ss_pred CcEEHHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccCCcCCCC
Confidence 35789999999999999999999999999999999998877666544
No 26
>PRK11507 ribosome-associated protein; Provisional
Probab=97.91 E-value=6.5e-05 Score=54.64 Aligned_cols=47 Identities=15% Similarity=0.157 Sum_probs=40.8
Q ss_pred CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 145 PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 145 ~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
+-+.|.++|+.+|+++|.++|+-+|++|.|+|||+..+.-...+-..
T Consensus 10 e~I~L~QlLK~~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~G 56 (70)
T PRK11507 10 PHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAG 56 (70)
T ss_pred CeEEHHHHHhhhCcccChHHHHHHHHcCceEECCEEecccCCCCCCC
Confidence 34789999999999999999999999999999999887766555544
No 27
>KOG2713|consensus
Probab=97.90 E-value=1.7e-05 Score=71.96 Aligned_cols=80 Identities=19% Similarity=0.196 Sum_probs=62.6
Q ss_pred CC-CccccCCCC---eEeecCCCCCHHHHHHHhhcC-CC------------hhHHHHHHHhcCCCHHHHHHHHHHhhcCC
Q psy938 18 SG-EKFGKSARN---AIWLDSKLSSSFELYQYLIRT-KD------------SEVYDLLKLFSFDSLAAIEDFKRQNEHKP 80 (241)
Q Consensus 18 dG-~KmsKS~gn---~I~L~~~~Tsp~~~yq~~~~~-~D------------~~v~~~l~~~t~l~~eei~~i~~~~~~~~ 80 (241)
|+ +|||||.+| +|.|.| ||..+-+|+.+. +| +.|.+++.++..++-..++++++++ .+.
T Consensus 207 dpekKMSKSd~n~~s~I~l~D---S~~~I~~Ki~ka~TD~~~~vtYd~~~RpgvsNLlni~aaVt~~s~eeV~~~~-a~~ 282 (347)
T KOG2713|consen 207 DPEKKMSKSDPNPKSRINLTD---SPDLIVKKIKKAQTDNTSGVTYDPANRPGVSNLLNIYAAVTGKSIEEVVEES-ANM 282 (347)
T ss_pred ChhhhcccCCCCCcceEEecC---CHHHHHHHHHHHhcccccceeeCCccccchhHHHHHHHHHcCCCHHHHHHHh-ccC
Confidence 66 699999976 799999 999999999996 22 4677777777666555666666543 345
Q ss_pred ChHHHHHHHHHHHHhhccCHH
Q psy938 81 EERRAQKKLAEDLTLLVHGEE 101 (241)
Q Consensus 81 ~~~~~Kk~LA~~i~~~vhG~~ 101 (241)
..++.|-.+|+.|++.+.+-.
T Consensus 283 ~~~~fK~~vaeAvie~L~PIr 303 (347)
T KOG2713|consen 283 STADFKDNVAEAVIEHLAPIR 303 (347)
T ss_pred CHHHHHHHHHHHHHHHhccHH
Confidence 678999999999999888744
No 28
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=97.90 E-value=3e-05 Score=53.38 Aligned_cols=44 Identities=25% Similarity=0.268 Sum_probs=38.1
Q ss_pred cHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 148 SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 148 ~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
++.++|.+.+...|+++++++|++|+|+|||+++++++..+...
T Consensus 2 rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~ 45 (70)
T cd00165 2 RLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPG 45 (70)
T ss_pred cHHHHHHHhccccCHHHHHHHHHcCCEEECCEEccCCccCcCCC
Confidence 56788888877789999999999999999999998888766544
No 29
>PRK04051 rps4p 30S ribosomal protein S4P; Validated
Probab=97.86 E-value=4.9e-05 Score=64.72 Aligned_cols=94 Identities=16% Similarity=0.143 Sum_probs=60.7
Q ss_pred HHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCCCHHHHHHH
Q psy938 89 LAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLT 168 (241)
Q Consensus 89 LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~SksEARRl 168 (241)
+|..+.. ...+.........-+.||.-+.-+ . ...|..+. .+.+..+ -..+|..+|+..|++.|..+||++
T Consensus 54 ~Ar~Ll~-~~~~~r~~~~~~Ll~kL~~~Gil~--~--~~~L~~vl-~L~v~~~---lerRLd~il~r~gla~S~~~Ar~l 124 (177)
T PRK04051 54 QARSLLA-LPPEERAKEEEQLLGKLKRYGILK--E--NATLDDVL-SLTVEDI---LERRLQTIVYRKGLARTPKQARQF 124 (177)
T ss_pred HHHHHhc-CCchHHHHHHHHHHHHHHHcCCCC--C--CCCHHHHH-hccHHHH---HHhHHHHHHHHccCcCCHHHHHHH
Confidence 4444443 223444445556667777765311 1 11233222 1211111 124788899999999999999999
Q ss_pred HHhCCeEEccEEecCCCCccCCC
Q psy938 169 ISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 169 I~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
|.+|-|+|||++|++|.+.+..+
T Consensus 125 I~hGhV~V~g~~V~~Ps~~V~~~ 147 (177)
T PRK04051 125 IVHGHIAVNGRRVTSPSYLVSVE 147 (177)
T ss_pred HHcCCEEECCEEeCCCCeECCCC
Confidence 99999999999999999988754
No 30
>smart00363 S4 S4 RNA-binding domain.
Probab=97.77 E-value=6.9e-05 Score=50.03 Aligned_cols=44 Identities=25% Similarity=0.314 Sum_probs=37.4
Q ss_pred cHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 148 SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 148 ~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
++..+|...+...|+++++++|.+|+|+|||+++++++..+...
T Consensus 2 rl~~~l~~~~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~g 45 (60)
T smart00363 2 RLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPG 45 (60)
T ss_pred cHHHHHHHcCcccCHHHHHHHHHcCCEEECCEEecCCCeEeCCC
Confidence 45667888877789999999999999999999998888777654
No 31
>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=97.76 E-value=5.5e-05 Score=52.72 Aligned_cols=46 Identities=15% Similarity=0.096 Sum_probs=40.6
Q ss_pred CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
+.+|.++|...++..|++.++++|++|.|+|||.+++.|+..+...
T Consensus 8 ~~rLd~~L~~~~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~G 53 (59)
T TIGR02988 8 YITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPG 53 (59)
T ss_pred HHHHHHHHHHcCCccCHHHHHHHHHcCCEEECCEEccCCCCCCCCC
Confidence 5778889998888889999999999999999999998888777655
No 32
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=97.60 E-value=0.00037 Score=56.78 Aligned_cols=60 Identities=13% Similarity=0.165 Sum_probs=49.6
Q ss_pred CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEE
Q psy938 146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIA 212 (241)
Q Consensus 146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i 212 (241)
.++|..+|+.+++++|++.|.++|.+|.|.|||++ +.|...+..+ ..+.|+.|...+.+.
T Consensus 8 ~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~g------d~l~v~~~~~~~~v~ 67 (133)
T PRK10348 8 EVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELN------ATLTLRQGNDERTVI 67 (133)
T ss_pred cccHHHHHHHcCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCC------CEEEEEECCEEEEEE
Confidence 46899999999999999999999999999999999 7888766544 356788887665433
No 33
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=97.58 E-value=0.00019 Score=60.28 Aligned_cols=95 Identities=15% Similarity=0.163 Sum_probs=62.4
Q ss_pred HHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCCCHHHHHHH
Q psy938 89 LAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLT 168 (241)
Q Consensus 89 LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~SksEARRl 168 (241)
+|.++..+- ++.-.......-+.||.-+.- .+ +...+..+. .+.+..+. ..+|.-++...|+++|-.+||.+
T Consensus 54 ~Ar~L~~l~-d~~r~~~~~~LL~kL~~~Gll--~e-~~~~Ld~vl-~Ltv~~~l---eRRL~~vv~r~g~a~s~~~Arql 125 (162)
T TIGR01018 54 AARELLGLD-DEQRLFEGNQLLRRLVRLGIL--DE-ENAKLDDVL-GLTVEDFL---ERRLQTQVFKKGLARTIHQARQL 125 (162)
T ss_pred HHHHHHcCC-cHHHHHHHHHHHHHHHHcCCC--cc-ccCCHHHHH-hccHHHHH---HHhHhhHhhhccCcCCHHHHHHH
Confidence 566665555 555555556677778775531 10 011233222 11111110 23577778899999999999999
Q ss_pred HHhCCeEEccEEecCCCCccCCC
Q psy938 169 ISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 169 I~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
|.+|-|+|||++|++|.+.+..+
T Consensus 126 I~hgHI~V~~~~V~~Ps~~V~~~ 148 (162)
T TIGR01018 126 IVHGHIAVDGRRVTSPSYIVRRE 148 (162)
T ss_pred hhCCCeeECCEEeccCceEecCC
Confidence 99999999999999999888765
No 34
>PTZ00348 tyrosyl-tRNA synthetase; Provisional
Probab=97.33 E-value=0.00072 Score=68.27 Aligned_cols=83 Identities=10% Similarity=0.161 Sum_probs=64.7
Q ss_pred eeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcC------CChhHHHHHHHhcCCC----------------
Q psy938 8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRT------KDSEVYDLLKLFSFDS---------------- 65 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~------~D~~v~~~l~~~t~l~---------------- 65 (241)
|+..|++.++ +||| +++|++++ |+.++.+|++++ .++.|..|++|+ +..
T Consensus 549 ~l~~~~~~~~---~~s~--~s~i~~~D---~~~~i~~Ki~kA~Cpp~~~~Npvl~~~~y~-~~~~~~~~i~R~e~~Gg~~ 619 (682)
T PTZ00348 549 ALHRPGAAPA---VLGA--DDVLYLDD---NDMDIRRKIKKAYSAPNEEANPVISVAQHL-LAQQGALSIERGEANGGNV 619 (682)
T ss_pred cccccccccC---CCCC--CCeeeecC---CHHHHHHHHHhCCCCCCCCCCcHHHHHHHH-hcCCCeEEEecccccCCCe
Confidence 4444444333 4544 88999999 999999999997 568899999987 321
Q ss_pred -HHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccC
Q psy938 66 -LAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHG 99 (241)
Q Consensus 66 -~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG 99 (241)
-+.++++++.+.++ .||.++|..+|+.+.+++..
T Consensus 620 ~y~s~eeL~~dy~~g~lhP~DLK~av~~~l~~~l~p 655 (682)
T PTZ00348 620 AYNTPEALVADCGSGALHPADLKAAVSQLLLDRSAA 655 (682)
T ss_pred eeCCHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence 11389999999877 79999999999999998765
No 35
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=97.32 E-value=0.00056 Score=61.22 Aligned_cols=46 Identities=24% Similarity=0.195 Sum_probs=40.9
Q ss_pred CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCC
Q psy938 146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSA 192 (241)
Q Consensus 146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~ 192 (241)
.++|.++|..+|++ |++||.++|.+|.|+|||+.++++...+..+.
T Consensus 2 ~~RL~K~La~~G~~-SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~ 47 (248)
T COG1187 2 SMRLNKFLAEAGVG-SRREAEKLIEEGRVTVNGKVATLGGVVVDPDD 47 (248)
T ss_pred ccchHHHHHHcCCC-CHHHHHHHHHcCCEEECCEEeccCCeEeCCCC
Confidence 35788999999998 99999999999999999999999887777653
No 36
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=97.26 E-value=0.00037 Score=61.92 Aligned_cols=45 Identities=24% Similarity=0.324 Sum_probs=41.4
Q ss_pred CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
++|..+|++-|++.|++.|+++|..|-|+|||++++.|.+.+..+
T Consensus 3 ~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~ 47 (245)
T COG1189 3 MRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDID 47 (245)
T ss_pred chHHHHHHHccchhhHHHHHHHHHcCeEEECCEEecCcceecCCC
Confidence 578899999999999999999999999999999999999887643
No 37
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=97.10 E-value=0.0018 Score=47.48 Aligned_cols=45 Identities=18% Similarity=0.082 Sum_probs=39.0
Q ss_pred CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccC
Q psy938 145 PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLS 189 (241)
Q Consensus 145 ~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~ 189 (241)
+-+.|.++|..+|+++|.++|+-+|++|.|+|||+.-+.-...+-
T Consensus 10 e~I~L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr 54 (73)
T COG2501 10 EFITLGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLR 54 (73)
T ss_pred ceEEHHHHHHHhCcccCcHHHHHHHHCCeEEECCeeeeccCCEee
Confidence 357899999999999999999999999999999998776554443
No 38
>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=97.05 E-value=0.0011 Score=57.47 Aligned_cols=45 Identities=24% Similarity=0.243 Sum_probs=40.7
Q ss_pred CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
.+|..+|..+|++.|+++|+++|.+|.|.|||.+++.|.+.+..+
T Consensus 90 ~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~G 134 (200)
T TIGR01017 90 SRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPG 134 (200)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCC
Confidence 567788889999999999999999999999999999998877654
No 39
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=97.02 E-value=0.00079 Score=58.66 Aligned_cols=45 Identities=22% Similarity=0.274 Sum_probs=40.5
Q ss_pred CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
.+|..+....|+++|..+||.||..|-|.|||.+|+.|.+.+..+
T Consensus 94 rRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~g 138 (205)
T COG0522 94 RRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPG 138 (205)
T ss_pred HHHHHHHHHhcccccHHHHHHHhhcceEEECCEEeccCcEEecCC
Confidence 356667778999999999999999999999999999999988765
No 40
>KOG2145|consensus
Probab=96.99 E-value=0.0024 Score=58.46 Aligned_cols=95 Identities=16% Similarity=0.209 Sum_probs=68.8
Q ss_pred CceeeecccccCCCC--CccccCCCC-eEeecCCCCCHHHHHHHhhcC----------------CChhH---HHHHHHhc
Q psy938 5 GDGGLTTPIIESESG--EKFGKSARN-AIWLDSKLSSSFELYQYLIRT----------------KDSEV---YDLLKLFS 62 (241)
Q Consensus 5 ~~~~lt~pLL~g~dG--~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~~----------------~D~~v---~~~l~~~t 62 (241)
.+.-+..-.+|.+.| .|||-|..| +|+|++ +|.++..++.+- .+++| ..||++|-
T Consensus 260 Kpali~stffpaLqG~~~KMSASdpns~Ifltd---t~~qIk~KI~~~afSGGr~tiEeHRe~GGn~dVDV~~~YLsFFl 336 (397)
T KOG2145|consen 260 KPALIHSTFFPALQGAQTKMSASDPNSAIFLTD---TAKQIKNKINKYAFSGGRDTIEEHRELGGNPDVDVSFQYLSFFL 336 (397)
T ss_pred CcceeehhhchhhhCcccccccCCCCceEEecC---cHHHHHHHHHHhhccCCcchHHHHHHhCCCCcceehHHHHHHHh
Confidence 344566677888999 599999977 699999 999999999874 23344 44555443
Q ss_pred CCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHHH
Q psy938 63 FDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEGL 103 (241)
Q Consensus 63 ~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~a 103 (241)
. +.++.+++...+..| .--.+.|+.+-+.++..|.--.++
T Consensus 337 d-DD~kLeq~r~~Y~~G~mltgEmKk~~ievLq~~V~~hQa~ 377 (397)
T KOG2145|consen 337 D-DDDKLEQIRKDYTSGEMLTGEMKKLCIEVLQEFVSRHQAA 377 (397)
T ss_pred c-cHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHHHH
Confidence 1 566788888777666 455788999999888887644433
No 41
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=96.95 E-value=0.0014 Score=57.89 Aligned_cols=44 Identities=25% Similarity=0.246 Sum_probs=39.1
Q ss_pred cHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 148 SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 148 ~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
+|..+|+..|++.|+++|+++|.+|.|+|||+++++|...+..+
T Consensus 1 RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~ 44 (228)
T TIGR00478 1 RLDILLVRRGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFD 44 (228)
T ss_pred CHHHHHHHcCCccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCC
Confidence 36678899999999999999999999999999999998877644
No 42
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=96.94 E-value=0.0015 Score=56.81 Aligned_cols=45 Identities=20% Similarity=0.212 Sum_probs=40.8
Q ss_pred CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
.+|..+|...|+++|+++||++|.+|.|.|||.+++.|.+.+..+
T Consensus 89 ~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~G 133 (201)
T CHL00113 89 MRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPK 133 (201)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCC
Confidence 468889999999999999999999999999999999998877654
No 43
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=96.89 E-value=0.0036 Score=48.55 Aligned_cols=60 Identities=17% Similarity=0.189 Sum_probs=49.7
Q ss_pred CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEE
Q psy938 146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIA 212 (241)
Q Consensus 146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i 212 (241)
.++|...|..+.++++++-|+.+|.+|.|.|||.++ .|...+..+ ..+-|+.|.+.+-+-
T Consensus 8 ~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~G------D~l~i~~~~~~~~v~ 67 (100)
T COG1188 8 RMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVG------DILTIRFGNKEFTVK 67 (100)
T ss_pred ceehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEEc-ccccccCCC------CEEEEEeCCcEEEEE
Confidence 478999999999999999999999999999999988 566555544 467899998876443
No 44
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=96.78 E-value=0.0012 Score=56.55 Aligned_cols=45 Identities=11% Similarity=0.017 Sum_probs=40.8
Q ss_pred CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
.+|.-++...|+++|..+||.+|.+|-|.|||++|++|.+.+..+
T Consensus 107 RRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~ 151 (181)
T PTZ00155 107 RRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVD 151 (181)
T ss_pred HhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceEeccC
Confidence 356777889999999999999999999999999999999988765
No 45
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=96.68 E-value=0.0032 Score=54.72 Aligned_cols=45 Identities=24% Similarity=0.297 Sum_probs=39.9
Q ss_pred CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
.+|..+|...|++.|+++|+++|..|.|.|||.+++.|.+.+..+
T Consensus 93 ~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~G 137 (203)
T PRK05327 93 SRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPG 137 (203)
T ss_pred HHHHHHHHHcCccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCC
Confidence 457778888999999999999999999999999998898877655
No 46
>PLN00189 40S ribosomal protein S9; Provisional
Probab=96.37 E-value=0.0016 Score=56.28 Aligned_cols=44 Identities=14% Similarity=0.104 Sum_probs=39.2
Q ss_pred cHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 148 SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 148 ~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
+|.-++...|+++|..+||.+|.+|-|.|||++|++|.+.+..+
T Consensus 110 RL~~vv~r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~ 153 (194)
T PLN00189 110 RLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVD 153 (194)
T ss_pred hhceeeeecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecC
Confidence 45556678999999999999999999999999999999988755
No 47
>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=96.16 E-value=0.012 Score=52.87 Aligned_cols=45 Identities=16% Similarity=0.146 Sum_probs=37.4
Q ss_pred CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
+.+|. .+...++.-|++.|+++|++|.|.|||..+++|++.+...
T Consensus 183 s~RLD-~lls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~g 227 (257)
T TIGR03069 183 SLRID-AIASAGFGLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVG 227 (257)
T ss_pred cccHH-HHHHhhhhhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCC
Confidence 45666 5556677669999999999999999999999998877654
No 48
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=95.97 E-value=0.012 Score=53.77 Aligned_cols=42 Identities=12% Similarity=0.030 Sum_probs=35.9
Q ss_pred CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCC
Q psy938 147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSP 190 (241)
Q Consensus 147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~ 190 (241)
++|.++|..+|.+ |+++|+++|++|.|+|||..+ ++...+..
T Consensus 3 ~RL~k~La~~g~~-SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~ 44 (289)
T PRK10700 3 EKLQKVLARAGHG-SRREIESIIEAGRVSVDGKIA-TLGDRVEV 44 (289)
T ss_pred hhHHHHHHHCCCC-CHHHHHHHHHcCCEEECCEec-cCCCEeCC
Confidence 5688899999976 999999999999999999977 57766653
No 49
>cd00818 IleRS_core catalytic core domain of isoleucyl-tRNA synthetases. Isoleucine amino-acyl tRNA synthetases (IleRS) catalytic core domain . This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. IleRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=95.95 E-value=0.0026 Score=58.96 Aligned_cols=28 Identities=21% Similarity=0.212 Sum_probs=23.6
Q ss_pred eeeecccccCCCCCccccCCCCeEeecC
Q psy938 7 GGLTTPIIESESGEKFGKSARNAIWLDS 34 (241)
Q Consensus 7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~~ 34 (241)
-.++...+...+|+|||||.||+||+++
T Consensus 285 ~~~~hg~~~~~~g~KmSKS~gn~i~~~~ 312 (338)
T cd00818 285 NVIVHGFVLDEDGRKMSKSLGNYVDPQE 312 (338)
T ss_pred eEEEEeeEECCCCCCCCCCCCCcCCHHH
Confidence 4456678888899999999999998874
No 50
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=95.86 E-value=0.012 Score=53.67 Aligned_cols=44 Identities=14% Similarity=0.223 Sum_probs=37.0
Q ss_pred CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
+++|.++|..+|++ |+++|+++|.+|.|.|||+++ .++..+...
T Consensus 6 ~~RL~k~La~~g~~-SRr~a~~lI~~G~V~VNGk~v-~~~~~V~~g 49 (290)
T PRK10475 6 STRLNKYISESGIC-SRREADRYIEQGNVFINGKRA-TIGDQVKAG 49 (290)
T ss_pred HHHHHHHHHhCCCC-CHHHHHHHHHCCcEEECCEEc-cCCCCcCCC
Confidence 56789999999976 999999999999999999987 466666543
No 51
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=95.31 E-value=0.012 Score=57.83 Aligned_cols=32 Identities=22% Similarity=0.233 Sum_probs=27.0
Q ss_pred CCCCceeeecccccCCCCCccccCCCCeEeec
Q psy938 2 EVTGDGGLTTPIIESESGEKFGKSARNAIWLD 33 (241)
Q Consensus 2 ~~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~ 33 (241)
+..+++.+..+++...+|+|||||.||.|.++
T Consensus 261 g~~~P~~~~y~~v~~~~G~KMSKSkGN~i~~~ 292 (510)
T PRK00750 261 GGEPPEPFVYELFLDKKGEKISKSKGNVITIE 292 (510)
T ss_pred CCCCCeeeeeeeEEeCCCCcccccCCCccCHH
Confidence 34567788889999888999999999999765
No 52
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=95.21 E-value=0.06 Score=48.73 Aligned_cols=45 Identities=18% Similarity=0.175 Sum_probs=36.7
Q ss_pred CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
+.+|..++. +++--|++.|..+|++|.|+||+..+++|++.+..+
T Consensus 191 s~RLD~vla-~~~~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~g 235 (267)
T PLN00051 191 SLRLDALAS-AGFRMSRSKLVDLISSGDVRVNWREVTKNGTTLKTG 235 (267)
T ss_pred cccHHHHHH-HHhccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCC
Confidence 355666544 455679999999999999999999999999887765
No 53
>cd00668 Ile_Leu_Val_MetRS_core catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. Catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. These class I enzymes are all monomers. However, in some species, MetRS functions as a homodimer, as a result of an additional C-terminal domain. These enzymes aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. Enzymes in this subfamily share an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. MetRS has a significantly shorter insertion, which lacks the editing function.
Probab=94.87 E-value=0.0096 Score=54.28 Aligned_cols=44 Identities=18% Similarity=0.123 Sum_probs=29.4
Q ss_pred eeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhc
Q psy938 8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFS 62 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t 62 (241)
.++...+...+|+|||||.||+||+++ +-+. -++++.+|+-+.+
T Consensus 260 ~~~~g~~~~~~g~KmSKS~gn~v~~~d-------~~~~----~~~da~R~~l~~~ 303 (312)
T cd00668 260 LLVHGFVLDEGGQKMSKSKGNVIDPSD-------VVEK----YGADALRYYLTSL 303 (312)
T ss_pred eEECcEEEcCCCccccccCCCcCCHHH-------HHHH----cCcHHHHHHHHhc
Confidence 445566777777999999999998875 2222 2356666655443
No 54
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=94.80 E-value=0.067 Score=47.93 Aligned_cols=64 Identities=16% Similarity=0.207 Sum_probs=49.3
Q ss_pred HHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCccc----CCCeEEEEec---cccEEEEEE
Q psy938 150 LELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHIL----PNSLTLLRVE---VSANIIAKS 214 (241)
Q Consensus 150 ~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~----~~~~~llr~G---Kk~~~~i~~ 214 (241)
+|.+...++--|++.|..+|.+|-|+||.+.++++++.+..+ |++ .|+.-+++.+ ||.-++|++
T Consensus 183 LD~vis~~~~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~G-DliSirG~GR~~i~~i~g~TKKdK~ri~l 253 (257)
T COG2302 183 LDVVISEGFGLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEG-DLISIRGFGRLKILEINGVTKKDKFRITL 253 (257)
T ss_pred HHHHHHHHHhhhHHHHHHHHHcCceEEeeEEeccccceeccC-CEEEEeccccEEEEeecCccccccEEEEE
Confidence 456667777779999999999999999999999999988876 443 4666666666 555555554
No 55
>PRK12418 cysteinyl-tRNA synthetase; Provisional
Probab=94.71 E-value=0.012 Score=55.93 Aligned_cols=25 Identities=24% Similarity=0.324 Sum_probs=19.8
Q ss_pred eecccccCCCCCccccCCCCeEeec
Q psy938 9 LTTPIIESESGEKFGKSARNAIWLD 33 (241)
Q Consensus 9 lt~pLL~g~dG~KmsKS~gn~I~L~ 33 (241)
....-..+.+|+|||||.||.|++.
T Consensus 249 w~H~g~l~~~G~KMSKSlGN~i~~~ 273 (384)
T PRK12418 249 YVHAGMIGLDGEKMSKSRGNLVFVS 273 (384)
T ss_pred EEECCEECCCCCcccCcCCCcCCHH
Confidence 3444566789999999999998665
No 56
>COG0060 IleS Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=94.69 E-value=0.016 Score=60.35 Aligned_cols=23 Identities=35% Similarity=0.424 Sum_probs=20.5
Q ss_pred eeecccccCCCCCccccCCCCeE
Q psy938 8 GLTTPIIESESGEKFGKSARNAI 30 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I 30 (241)
++|.-.+.+.+|+|||||.||+|
T Consensus 589 vltHGfvlDe~GrKMSKSlGN~v 611 (933)
T COG0060 589 VLTHGFVLDEKGRKMSKSLGNVV 611 (933)
T ss_pred HhhcccEECCCCCCccccCCCcC
Confidence 56777888999999999999997
No 57
>cd00812 LeuRS_core catalytic core domain of leucyl-tRNA synthetases. Leucyl tRNA synthetase (LeuRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. In Aquifex aeolicus, the gene encoding LeuRS is split in two, just before the KMSKS motif. Consequently, LeuRS is a heterodimer, which likely superimposes with the LeuRS monomer found in most other organisms. LeuRS has an insertion in the core domain, which is subject to both deletions and rearrangements and thus differs between prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=94.63 E-value=0.0089 Score=54.82 Aligned_cols=19 Identities=37% Similarity=0.366 Sum_probs=17.0
Q ss_pred CCCCCccccCCCCeEeecC
Q psy938 16 SESGEKFGKSARNAIWLDS 34 (241)
Q Consensus 16 g~dG~KmsKS~gn~I~L~~ 34 (241)
..+|+|||||.||+||+++
T Consensus 270 ~~~g~KmSkS~Gn~v~~~d 288 (314)
T cd00812 270 LLEGEKMSKSKGNVVTPDE 288 (314)
T ss_pred ecCccccCCcCCCCCCHHH
Confidence 4689999999999999886
No 58
>cd00817 ValRS_core catalytic core domain of valyl-tRNA synthetases. Valine amino-acyl tRNA synthetase (ValRS) catalytic core domain. This enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=94.55 E-value=0.012 Score=55.54 Aligned_cols=42 Identities=17% Similarity=0.111 Sum_probs=29.6
Q ss_pred eeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHH
Q psy938 8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKL 60 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~ 60 (241)
.+....+.+.+|+|||||.||+|++++ +-+. -+.+..+|+-+
T Consensus 330 v~~hg~v~~~~g~KMSKS~Gn~v~~~d-------ll~~----~g~Da~R~~ll 371 (382)
T cd00817 330 VYLHGLVRDEDGRKMSKSLGNVIDPLD-------VIDG----YGADALRFTLA 371 (382)
T ss_pred eEeeeeEECCCCCCccccCCCCCCHHH-------HHHh----cCcHHHHHHHH
Confidence 455667888999999999999997664 3332 23566666544
No 59
>PF00133 tRNA-synt_1: tRNA synthetases class I (I, L, M and V); InterPro: IPR002300 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. The class Ia aminoacyl-tRNA synthetases consist of the isoleucyl, methionyl, valyl, leucyl, cysteinyl, and arginyl-tRNA synthetases; the class Ib include the glutamyl and glutaminyl-tRNA synthetases, and the class Ic are the tyrosyl and tryptophanyl-tRNA synthetases [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 1OBC_A 2AJH_B 4ARI_A 2AJG_B 4AQ7_D 2AJI_B 4ARC_A 4AS1_A 1QU3_A 1QU2_A ....
Probab=94.50 E-value=0.022 Score=56.87 Aligned_cols=24 Identities=33% Similarity=0.347 Sum_probs=16.7
Q ss_pred eeecccccCCCCCccccCCCCeEe
Q psy938 8 GLTTPIIESESGEKFGKSARNAIW 31 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I~ 31 (241)
.++...+.+.+|+|||||.||+|.
T Consensus 548 v~~hG~vld~~G~KMSKS~GNvi~ 571 (601)
T PF00133_consen 548 VITHGFVLDEDGRKMSKSKGNVID 571 (601)
T ss_dssp EEEE--EEETTSSB-BTTTTB--B
T ss_pred eeecccccccceeecccCCCcccC
Confidence 467788999999999999999983
No 60
>PRK11893 methionyl-tRNA synthetase; Reviewed
Probab=94.36 E-value=0.017 Score=55.85 Aligned_cols=42 Identities=21% Similarity=0.147 Sum_probs=27.1
Q ss_pred eeeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938 7 GGLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT 49 (241)
Q Consensus 7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~ 49 (241)
..++.-.+. .+|+|||||.||+||+.+ +.-+++.++=++++.
T Consensus 286 ~~~~~g~v~-~~G~KMSKS~GN~i~~~dll~~~g~DalR~~ll~~ 329 (511)
T PRK11893 286 RVFAHGFLT-LDGEKMSKSLGNVIDPFDLVDEYGVDAVRYFLLRE 329 (511)
T ss_pred EEEeeccEE-ECCeeecccCCcEEcHHHHHHHcCcHHHHHHHHhc
Confidence 344455555 489999999999999863 123455555445443
No 61
>PTZ00427 isoleucine-tRNA ligase, putative; Provisional
Probab=94.23 E-value=0.031 Score=60.08 Aligned_cols=24 Identities=17% Similarity=0.183 Sum_probs=21.1
Q ss_pred eeecccccCCCCCccccCCCCeEe
Q psy938 8 GLTTPIIESESGEKFGKSARNAIW 31 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I~ 31 (241)
.++..++.+.+|+|||||.||+|.
T Consensus 707 VlvHG~Vld~dG~KMSKSlGNvID 730 (1205)
T PTZ00427 707 LICNGLVLASDGKKMSKRLKNYPD 730 (1205)
T ss_pred eEEccEEEcCCCCCcccCCCCCCC
Confidence 567788999999999999999873
No 62
>PLN02381 valyl-tRNA synthetase
Probab=94.22 E-value=0.026 Score=59.97 Aligned_cols=23 Identities=35% Similarity=0.482 Sum_probs=21.1
Q ss_pred eeecccccCCCCCccccCCCCeE
Q psy938 8 GLTTPIIESESGEKFGKSARNAI 30 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I 30 (241)
.++.+++.+.+|+|||||.||.|
T Consensus 642 v~~hG~V~D~~G~KMSKS~GNvI 664 (1066)
T PLN02381 642 VYLHPMIRDAHGRKMSKSLGNVI 664 (1066)
T ss_pred heecceEECCCCCCCCCCCCCCC
Confidence 46788999999999999999998
No 63
>PLN02882 aminoacyl-tRNA ligase
Probab=94.14 E-value=0.034 Score=59.55 Aligned_cols=26 Identities=23% Similarity=0.219 Sum_probs=22.1
Q ss_pred eeeecccccCCCCCccccCCCCeEee
Q psy938 7 GGLTTPIIESESGEKFGKSARNAIWL 32 (241)
Q Consensus 7 ~~lt~pLL~g~dG~KmsKS~gn~I~L 32 (241)
-.++..++.+.+|+|||||.||+|+-
T Consensus 600 ~VivhG~vlde~G~KMSKSlGNvIdP 625 (1159)
T PLN02882 600 NLICNGLVLAEDGKKMSKSLKNYPDP 625 (1159)
T ss_pred eeEEccEEECCCCCCcccCCCCCCCH
Confidence 35677888999999999999999854
No 64
>PRK05743 ileS isoleucyl-tRNA synthetase; Reviewed
Probab=94.13 E-value=0.033 Score=58.25 Aligned_cols=25 Identities=32% Similarity=0.207 Sum_probs=21.1
Q ss_pred eeecccccCCCCCccccCCCCeEee
Q psy938 8 GLTTPIIESESGEKFGKSARNAIWL 32 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I~L 32 (241)
.++...+.+.+|+|||||.||.|..
T Consensus 579 vl~HG~vld~~G~KMSKSlGNvIdP 603 (912)
T PRK05743 579 VLTHGFTVDGKGRKMSKSLGNVIDP 603 (912)
T ss_pred eEEeeeEECCCCCCCCCCCCCcCCH
Confidence 4567788899999999999998843
No 65
>PRK05729 valS valyl-tRNA synthetase; Reviewed
Probab=94.07 E-value=0.02 Score=59.47 Aligned_cols=43 Identities=21% Similarity=0.084 Sum_probs=29.5
Q ss_pred eeeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938 7 GGLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT 49 (241)
Q Consensus 7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~ 49 (241)
-.+...++.+.+|+|||||.||.|+..+ ++-.++.++=++++.
T Consensus 506 ~v~~hG~v~d~~G~KMSKSlGNvIdP~dvi~~yGaDalR~~ll~~ 550 (874)
T PRK05729 506 DVYIHGLVRDEQGRKMSKSKGNVIDPLDLIDKYGADALRFTLAAL 550 (874)
T ss_pred heEEeeeEECCCCCCcccCCCCCCCHHHHHHHhChHHHHHHHHhC
Confidence 3556778899999999999999997652 112344455445543
No 66
>PRK14900 valS valyl-tRNA synthetase; Provisional
Probab=93.97 E-value=0.021 Score=60.64 Aligned_cols=41 Identities=22% Similarity=0.165 Sum_probs=29.4
Q ss_pred eeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938 8 GLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR 48 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~ 48 (241)
.++..++.+.+|+|||||.||.|+..+ ++-.++.++=+++.
T Consensus 525 V~~hG~v~d~~G~KMSKSkGNvIdP~dvIe~yGaDalR~~L~~ 567 (1052)
T PRK14900 525 VYLHPMVRDEKGQKMSKTKGNVIDPLVITEQYGADALRFTLAA 567 (1052)
T ss_pred eEecccEECCCCCCccCCCCCCCCHHHHHHHhCcHHHHHHHHh
Confidence 567788999999999999999998763 12234445444544
No 67
>PRK13208 valS valyl-tRNA synthetase; Reviewed
Probab=93.89 E-value=0.02 Score=58.86 Aligned_cols=41 Identities=12% Similarity=0.135 Sum_probs=28.2
Q ss_pred eeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938 8 GLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR 48 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~ 48 (241)
.++...+.+.+|+|||||.||+|+..+ +.-.++.++=+++.
T Consensus 520 v~~hg~v~~~~G~KMSKS~GN~i~p~~~i~~yg~D~lR~~l~~ 562 (800)
T PRK13208 520 IMISGMVLDPDGKKMSKSKGNVVTPEELLEKYGADAVRYWAAS 562 (800)
T ss_pred EEEeeEEECCCCCCCCCCCCCCCCHHHHHHHcCccHHHHHHhc
Confidence 356677888999999999999998652 11234455545553
No 68
>TIGR03447 mycothiol_MshC cysteine--1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase. Members of this protein family are MshC, l-cysteine:1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase, an enzyme that uses ATP to ligate a Cys residue to a mycothiol precursor molecule, in the second to last step in mycothiol biosynthesis. This enzyme shows considerable homology to Cys--tRNA ligases, and many instances are misannotated as such. Mycothiol is found in Mycobacterium tuberculosis, Corynebacterium glutamicum, Streptomyces coelicolor, and various other members of the Actinobacteria. Mycothiol is an analog to glutathione.
Probab=93.89 E-value=0.018 Score=55.16 Aligned_cols=21 Identities=29% Similarity=0.376 Sum_probs=17.4
Q ss_pred cccCCCCCccccCCCCeEeec
Q psy938 13 IIESESGEKFGKSARNAIWLD 33 (241)
Q Consensus 13 LL~g~dG~KmsKS~gn~I~L~ 33 (241)
=....+|+|||||.||.|.+.
T Consensus 280 g~l~~~G~KMSKSlGN~i~~~ 300 (411)
T TIGR03447 280 GMIGLDGEKMSKSLGNLVFVS 300 (411)
T ss_pred CEECcCCCCccCcCCCCCCHH
Confidence 355779999999999998665
No 69
>COG0525 ValS Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=93.83 E-value=0.037 Score=57.34 Aligned_cols=22 Identities=32% Similarity=0.489 Sum_probs=19.7
Q ss_pred eecccccCCCCCccccCCCCeE
Q psy938 9 LTTPIIESESGEKFGKSARNAI 30 (241)
Q Consensus 9 lt~pLL~g~dG~KmsKS~gn~I 30 (241)
+-..|+-+.+|+|||||.||.|
T Consensus 513 ~ihGLVrDe~G~KMSKS~GNvI 534 (877)
T COG0525 513 YIHGLVRDEQGRKMSKSKGNVI 534 (877)
T ss_pred EEeeeEEcCCCCCCcccCCCcC
Confidence 4568999999999999999987
No 70
>COG0215 CysS Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=93.79 E-value=0.025 Score=54.73 Aligned_cols=35 Identities=29% Similarity=0.255 Sum_probs=26.2
Q ss_pred cCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938 15 ESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT 49 (241)
Q Consensus 15 ~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~ 49 (241)
...+|+|||||.||.|-+-+ +.-+|..++=++++.
T Consensus 262 l~i~geKMSKSLGNfiti~d~l~~~~p~~lR~~lls~ 298 (464)
T COG0215 262 LNIDGEKMSKSLGNFITVRDLLKKYDPEVLRLFLLSS 298 (464)
T ss_pred eeecCcCcccccCCeeEHHHHHhhcCHHHHHHHHHHH
Confidence 45689999999999998764 224677777666664
No 71
>PRK06039 ileS isoleucyl-tRNA synthetase; Reviewed
Probab=93.74 E-value=0.024 Score=59.73 Aligned_cols=42 Identities=24% Similarity=0.161 Sum_probs=29.1
Q ss_pred eeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938 8 GLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT 49 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~ 49 (241)
.+...++.+.+|+|||||.||+|+..+ ++-.++.++=++++.
T Consensus 579 v~~hG~Vld~~G~KMSKSlGNvIdP~dli~~yGaDalR~~lls~ 622 (975)
T PRK06039 579 VLVHGHVLDEDGQKMSKSLGNYVDPFEVFDKYGADALRWYLLSS 622 (975)
T ss_pred EEEeeeEECCCCCCcCCCCCCcCCHHHHHHHhChHHHHHHHHhC
Confidence 455667788899999999999997652 122455555555554
No 72
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=93.73 E-value=0.12 Score=47.74 Aligned_cols=45 Identities=16% Similarity=0.009 Sum_probs=37.5
Q ss_pred CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCC
Q psy938 146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSP 190 (241)
Q Consensus 146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~ 190 (241)
+.+|.++|.......|++.++++|.+|.|+|||.++..++..+..
T Consensus 17 g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~ 61 (325)
T PRK11180 17 GQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLG 61 (325)
T ss_pred CccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCcCcCC
Confidence 678999998765456999999999999999999998777655543
No 73
>PRK13804 ileS isoleucyl-tRNA synthetase; Provisional
Probab=93.66 E-value=0.045 Score=57.59 Aligned_cols=27 Identities=33% Similarity=0.310 Sum_probs=22.3
Q ss_pred eeeecccccCCCCCccccCCCCeEeec
Q psy938 7 GGLTTPIIESESGEKFGKSARNAIWLD 33 (241)
Q Consensus 7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~ 33 (241)
-.++...+.+.+|+|||||.||.|...
T Consensus 616 ~V~~HG~vld~~G~KMSKSlGNvIdP~ 642 (961)
T PRK13804 616 AVLTHGFTLDEKGEKMSKSLGNTVSPQ 642 (961)
T ss_pred hEEEeccEECCCCCCccCCCCCcCCHH
Confidence 356778889999999999999998543
No 74
>PTZ00419 valyl-tRNA synthetase-like protein; Provisional
Probab=93.65 E-value=0.034 Score=58.65 Aligned_cols=23 Identities=30% Similarity=0.459 Sum_probs=20.9
Q ss_pred eeecccccCCCCCccccCCCCeE
Q psy938 8 GLTTPIIESESGEKFGKSARNAI 30 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I 30 (241)
.++.+++.+.+|+|||||.||.|
T Consensus 572 v~~HG~v~d~~G~KMSKSlGNvI 594 (995)
T PTZ00419 572 VFLHAMVRDSQGEKMSKSKGNVI 594 (995)
T ss_pred HhccceEECCCCCCcccCCCCcC
Confidence 56778899999999999999998
No 75
>PF01406 tRNA-synt_1e: tRNA synthetases class I (C) catalytic domain; InterPro: IPR015803 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Cysteinyl-tRNA synthetase (6.1.1.16 from EC) is an alpha monomer and belongs to class Ia.; GO: 0000166 nucleotide binding, 0004817 cysteine-tRNA ligase activity, 0005524 ATP binding, 0006423 cysteinyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3SP1_B 3TQO_A 3C8Z_B 1LI5_B 1LI7_B 1U0B_B.
Probab=93.62 E-value=0.035 Score=51.04 Aligned_cols=19 Identities=37% Similarity=0.407 Sum_probs=11.5
Q ss_pred CCCCCccccCCCCeEeecC
Q psy938 16 SESGEKFGKSARNAIWLDS 34 (241)
Q Consensus 16 g~dG~KmsKS~gn~I~L~~ 34 (241)
..+|+|||||.||.|.+.+
T Consensus 247 ~~~g~KMSKSlgN~~~i~d 265 (300)
T PF01406_consen 247 NVDGEKMSKSLGNFITIRD 265 (300)
T ss_dssp EETTCE--TTTT---BHHH
T ss_pred hhcCccccccCCCEEEHHH
Confidence 3489999999999998874
No 76
>PRK04313 30S ribosomal protein S4e; Validated
Probab=93.47 E-value=0.25 Score=44.06 Aligned_cols=73 Identities=14% Similarity=0.081 Sum_probs=51.5
Q ss_pred CCcHHHHHHh-cCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcc-----cCCCeEEEEeccccEEEEEEcccch
Q psy938 146 GMSMLELSLA-TKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHI-----LPNSLTLLRVEVSANIIAKSANIIA 219 (241)
Q Consensus 146 ~~~l~~lLv~-~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~-----~~~~~~llr~GKk~~~~i~~~~~~~ 219 (241)
.++|.=+|.. .|++.+.+||++.+.||-|.|||...+|+.+-+-.= |+ .+..|-+|-=-|.+|.+.+...+-|
T Consensus 37 siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlm-DVIsI~~~~e~yRvl~d~kgr~~l~~I~~eea 115 (237)
T PRK04313 37 SIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLM-DVISIPETGEYYRVLPDEKGRLVLIPISEEEA 115 (237)
T ss_pred ccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCce-eEEEEccCCCeEEEEECCCCcEEEEECChHHc
Confidence 5677777775 799999999999999999999999999988755322 11 1223445555556666666554444
No 77
>TIGR00422 valS valyl-tRNA synthetase. The valyl-tRNA synthetase (ValS) is a class I amino acyl-tRNA ligase and is particularly closely related to the isoleucyl tRNA synthetase.
Probab=93.35 E-value=0.029 Score=58.22 Aligned_cols=43 Identities=21% Similarity=0.079 Sum_probs=30.0
Q ss_pred eeeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938 7 GGLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT 49 (241)
Q Consensus 7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~ 49 (241)
-.+...++.+.+|+|||||.||+|+..+ +.-.++.++=++++.
T Consensus 511 ~v~~hG~v~d~~G~KMSKS~GN~i~p~~~i~~ygaDalR~~l~~~ 555 (861)
T TIGR00422 511 EVYIHGLVRDEQGRKMSKSLGNVIDPLDVIEKYGADALRFTLASL 555 (861)
T ss_pred eEEEeeEEECCCCCCCCcCCCCCCCHHHHHHHhChHHHHHHHHhC
Confidence 3456788899999999999999998653 112445555555544
No 78
>TIGR00392 ileS isoleucyl-tRNA synthetase. The isoleucyl tRNA synthetase (IleS) is a class I amino acyl-tRNA ligase and is particularly closely related to the valyl tRNA synthetase. This model may recognize IleS from every species, including eukaryotic cytosolic and mitochondrial forms.
Probab=93.32 E-value=0.03 Score=58.09 Aligned_cols=41 Identities=22% Similarity=0.148 Sum_probs=26.5
Q ss_pred eecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938 9 LTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT 49 (241)
Q Consensus 9 lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~ 49 (241)
++...+.+.+|+|||||.||+|+..+ ++-.++.++=++++.
T Consensus 599 ~~hG~vl~~~G~KMSKSkGNvI~p~d~i~~yGaDalR~~ll~~ 641 (861)
T TIGR00392 599 ITHGFTLDEKGRKMSKSLGNVVDPLKVINKYGADILRLYVASS 641 (861)
T ss_pred EecceEECCCCCCcCCCCCCCCCHHHHHHHcCHHHHHHHHHhC
Confidence 34556667899999999999997652 122344444444443
No 79
>PLN02943 aminoacyl-tRNA ligase
Probab=93.29 E-value=0.031 Score=58.81 Aligned_cols=41 Identities=22% Similarity=0.058 Sum_probs=29.2
Q ss_pred eeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938 8 GLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR 48 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~ 48 (241)
.+....+.+.+|+|||||.||.|+..+ ++-.|+.++=++..
T Consensus 570 v~~hg~v~~~~G~KMSKS~GN~i~p~~~i~~ygaDalR~~l~~ 612 (958)
T PLN02943 570 VYLHGLIRDSQGRKMSKTLGNVIDPLDTIKEFGTDALRFTLAL 612 (958)
T ss_pred EEEeccEECCCCCcccCcCCCCCCHHHHHHhcCChHHHHHHHh
Confidence 456788889999999999999998763 12245555544443
No 80
>cd00672 CysRS_core catalytic core domain of cysteinyl tRNA synthetase. Cysteinyl tRNA synthetase (CysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.
Probab=93.23 E-value=0.023 Score=49.56 Aligned_cols=25 Identities=28% Similarity=0.147 Sum_probs=19.9
Q ss_pred ecccccCCCCCccccCCCCeEeecC
Q psy938 10 TTPIIESESGEKFGKSARNAIWLDS 34 (241)
Q Consensus 10 t~pLL~g~dG~KmsKS~gn~I~L~~ 34 (241)
...-+.+.+|+|||||.||.|.+.+
T Consensus 163 ~h~~~v~~~g~KMSKs~Gn~v~~~d 187 (213)
T cd00672 163 LHTGHLTIDGEKMSKSLGNFITVRD 187 (213)
T ss_pred EEEEEEeccCcchhhcCCCccCHHH
Confidence 3444567899999999999997765
No 81
>PRK12300 leuS leucyl-tRNA synthetase; Reviewed
Probab=92.98 E-value=0.034 Score=58.06 Aligned_cols=40 Identities=23% Similarity=0.221 Sum_probs=27.6
Q ss_pred eecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938 9 LTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT 49 (241)
Q Consensus 9 lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~ 49 (241)
++...+.. +|+|||||.||+|+..+ ++-.++.++=++++.
T Consensus 566 ~~hG~vl~-~G~KMSKS~GNvVdp~eii~~yGaDalRl~L~~~ 607 (897)
T PRK12300 566 VVNGFVLL-EGKKMSKSKGNVIPLRKAIEEYGADVVRLYLTSS 607 (897)
T ss_pred EEcceEEE-CCccccCcCCCCCCHHHHHHHcChHHHHHHHHhC
Confidence 44555666 89999999999998762 223556666666654
No 82
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=92.85 E-value=0.029 Score=55.18 Aligned_cols=32 Identities=34% Similarity=0.431 Sum_probs=21.3
Q ss_pred CCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938 17 ESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR 48 (241)
Q Consensus 17 ~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~ 48 (241)
.+|+|||||.||+||..+ ++-.++.++=+++.
T Consensus 330 ~~G~KMSKS~GN~I~p~dli~~yGaDalR~~ll~ 363 (556)
T PRK12268 330 LEGGKFSKSRGWGIWVDDALERYPPDYLRYYLAA 363 (556)
T ss_pred ECCeeeccCCCcccCHHHHHHHcCcHHHHHHHHh
Confidence 489999999999998773 11234444444443
No 83
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=92.84 E-value=0.039 Score=55.78 Aligned_cols=38 Identities=24% Similarity=0.329 Sum_probs=25.3
Q ss_pred eecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhh
Q psy938 9 LTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLI 47 (241)
Q Consensus 9 lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~ 47 (241)
+....++. +|+|||||.||+||..+ ++-.++.++=+++
T Consensus 318 ~~hg~v~~-~G~KMSKS~GNvV~p~dlie~ygaDalR~~ll 357 (673)
T PRK00133 318 FAHGFLTV-EGAKMSKSRGTFIWARTYLDHLDPDYLRYYLA 357 (673)
T ss_pred eeeccEEe-cCCcccccCCcccCHHHHHHHcCchHHHHHHH
Confidence 34455555 99999999999999763 1234455555555
No 84
>PLN02843 isoleucyl-tRNA synthetase
Probab=92.84 E-value=0.053 Score=57.16 Aligned_cols=27 Identities=30% Similarity=0.218 Sum_probs=22.8
Q ss_pred eeeecccccCCCCCccccCCCCeEeec
Q psy938 7 GGLTTPIIESESGEKFGKSARNAIWLD 33 (241)
Q Consensus 7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~ 33 (241)
-.++.+.+.+.+|+|||||.||.|...
T Consensus 597 ~v~~HG~vld~~G~KMSKSlGNvI~p~ 623 (974)
T PLN02843 597 SVLTHGFVLDEKGFKMSKSLGNVVDPR 623 (974)
T ss_pred eEEEeccEECCCCCCcCCCCCCcCCHH
Confidence 356778899999999999999998654
No 85
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=92.81 E-value=0.19 Score=45.40 Aligned_cols=46 Identities=17% Similarity=0.097 Sum_probs=36.5
Q ss_pred CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
+.+|.++|......-|+++++++|.+|.|+|||.++.+++..+...
T Consensus 5 g~rLd~~L~~~~~~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~g 50 (299)
T TIGR00005 5 GQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDG 50 (299)
T ss_pred chhHHHHHHHhcccCCHHHHHHHHHCCcEEECCEeccCcccCCCCC
Confidence 5778899987654239999999999999999997666666666543
No 86
>cd00814 MetRS_core catalytic core domain of methioninyl-tRNA synthetases. Methionine tRNA synthetase (MetRS) catalytic core domain. This class I enzyme aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. MetRS, which consists of the core domain and an anti-codon binding domain, functions as a monomer. However, in some species the anti-codon binding domain is followed by an EMAP domain. In this case, MetRS functions as a homodimer. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. As a result of a deletion event, MetRS has a significantly shorter core domain insertion than IleRS, ValRS, and LeuR. Consequently, the MetRS insertion lacks the editing function.
Probab=92.79 E-value=0.03 Score=51.38 Aligned_cols=35 Identities=23% Similarity=0.247 Sum_probs=24.1
Q ss_pred CCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHh
Q psy938 16 SESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLF 61 (241)
Q Consensus 16 g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~ 61 (241)
..+|+|||||.||+||+.+ +- ..-.+++.+|+-+.
T Consensus 275 ~~~g~kmSkS~gn~i~~~~-------~l----~~~~~d~~R~~l~~ 309 (319)
T cd00814 275 TVEGKKMSKSRGNVVDPDD-------LL----ERYGADALRYYLLR 309 (319)
T ss_pred EECCeeecccCCcccCHHH-------HH----HHcCchHHHHHHHh
Confidence 4589999999999998874 21 22355666766543
No 87
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=92.67 E-value=0.025 Score=53.67 Aligned_cols=18 Identities=50% Similarity=0.776 Sum_probs=16.3
Q ss_pred CCCCccccCCCCeEeecC
Q psy938 17 ESGEKFGKSARNAIWLDS 34 (241)
Q Consensus 17 ~dG~KmsKS~gn~I~L~~ 34 (241)
.+|+|||||.||+||.++
T Consensus 323 ~~g~K~SkS~gn~i~~~~ 340 (391)
T PF09334_consen 323 LDGEKMSKSRGNVIWPDD 340 (391)
T ss_dssp ETTCCEETTTTESSBHHH
T ss_pred ECCeeccccCCcccCHHH
Confidence 589999999999999874
No 88
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=92.66 E-value=0.26 Score=43.10 Aligned_cols=43 Identities=14% Similarity=-0.018 Sum_probs=33.8
Q ss_pred cHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 148 SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 148 ~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
++.++|...+ .-|++.++++|++|.|+|||.++.+++..+...
T Consensus 2 rld~~L~~~~-~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~g 44 (232)
T PRK10839 2 RLDKFISQQL-GVSRAIAGRELRANRVTVDGEIVKNGAFKLLPE 44 (232)
T ss_pred cHHHHHHHcC-CCCHHHHHHHHHcCeEEECCEEeccCCcCcCCC
Confidence 4566777665 358999999999999999999887666666543
No 89
>KOG0432|consensus
Probab=92.52 E-value=0.05 Score=56.12 Aligned_cols=23 Identities=30% Similarity=0.398 Sum_probs=20.8
Q ss_pred eeecccccCCCCCccccCCCCeE
Q psy938 8 GLTTPIIESESGEKFGKSARNAI 30 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I 30 (241)
.+..|++-+..|+|||||.||.|
T Consensus 580 V~LH~mVRDa~GRKMSKSLGNVI 602 (995)
T KOG0432|consen 580 VLLHGLVRDAHGRKMSKSLGNVI 602 (995)
T ss_pred eeechhhccccccccchhhcccc
Confidence 45679999999999999999987
No 90
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=92.32 E-value=0.46 Score=43.17 Aligned_cols=73 Identities=14% Similarity=0.086 Sum_probs=52.6
Q ss_pred CCcHHHHHHh-cCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcc-----cCCCeEEEEeccccEEEEEEcccch
Q psy938 146 GMSMLELSLA-TKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHI-----LPNSLTLLRVEVSANIIAKSANIIA 219 (241)
Q Consensus 146 ~~~l~~lLv~-~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~-----~~~~~~llr~GKk~~~~i~~~~~~~ 219 (241)
.++|.=+|.. .+++.+.+||++.+.||-|.|||...+|+.+-+-.= |+ .+..|-+|-=-|.+|.+.++...-|
T Consensus 38 siPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlM-DVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA 116 (273)
T PTZ00223 38 CLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFM-DVVEIPKTGDRFRILYDVKGRFALVKVSEAEA 116 (273)
T ss_pred ccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCcee-EEEEEcCCCCeEEEEECCCCcEEEEEcChHHc
Confidence 5677777875 799999999999999999999999999988765322 11 1233555655566666666655544
No 91
>PLN02610 probable methionyl-tRNA synthetase
Probab=92.27 E-value=0.067 Score=55.31 Aligned_cols=34 Identities=21% Similarity=0.218 Sum_probs=25.1
Q ss_pred CCCCCccccCCCCeEeecCCC---CCHHHHHHHhhcC
Q psy938 16 SESGEKFGKSARNAIWLDSKL---SSSFELYQYLIRT 49 (241)
Q Consensus 16 g~dG~KmsKS~gn~I~L~~~~---Tsp~~~yq~~~~~ 49 (241)
..+|+|||||.||.||..+-. -+++.++=|+++.
T Consensus 343 ~~eG~KMSKS~GNvV~p~~~i~~~yg~D~lRyyLl~~ 379 (801)
T PLN02610 343 NYEGGKFSKSKGVGVFGNDAKDTNIPVEVWRYYLLTN 379 (801)
T ss_pred ecCCceecCcCCcccCHHHHHhccCCchHhHHHhhhc
Confidence 468999999999999988532 3566666666664
No 92
>TIGR00395 leuS_arch leucyl-tRNA synthetase, archaeal and cytosolic family. The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both archaeal and cytosolic eukaryotic leucyl-tRNA synthetases; the eubacterial and mitochondrial forms differ so substantially that some other tRNA ligases score higher by this model than does any eubacterial LeuS.
Probab=92.26 E-value=0.049 Score=57.16 Aligned_cols=40 Identities=18% Similarity=0.195 Sum_probs=27.7
Q ss_pred eecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938 9 LTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT 49 (241)
Q Consensus 9 lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~ 49 (241)
+....+.. +|+|||||.||.|++.+ ++-+++.++=++++.
T Consensus 609 ~~~G~vl~-~G~KMSKSlGNvI~p~d~i~~yGaDalRl~Ll~~ 650 (938)
T TIGR00395 609 VVNGYVML-EGKKMSKSKGNVLTLEQAVEKFGADVARLYIADA 650 (938)
T ss_pred EEeceEEe-CCccccCcCCCCCCHHHHHHHcChHHHHHHHHhc
Confidence 34445554 89999999999998763 223566666666665
No 93
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=92.26 E-value=0.08 Score=52.60 Aligned_cols=18 Identities=33% Similarity=0.355 Sum_probs=15.8
Q ss_pred CCCCccccCCCCeEeecC
Q psy938 17 ESGEKFGKSARNAIWLDS 34 (241)
Q Consensus 17 ~dG~KmsKS~gn~I~L~~ 34 (241)
.+|+|||||.||.||-++
T Consensus 329 ~~G~KmSKSrG~~V~~~~ 346 (558)
T COG0143 329 LEGQKMSKSRGNVVDPDE 346 (558)
T ss_pred ECCccccccCCcEEeHHH
Confidence 578999999999998773
No 94
>PRK00260 cysS cysteinyl-tRNA synthetase; Validated
Probab=92.26 E-value=0.042 Score=53.20 Aligned_cols=37 Identities=24% Similarity=0.186 Sum_probs=24.5
Q ss_pred ccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938 12 PIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR 48 (241)
Q Consensus 12 pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~ 48 (241)
.-+.+.+|+|||||.||.|.+.+ +.-+|..++=++++
T Consensus 257 ~g~v~~~G~KMSKS~GN~i~~~dll~~~~~d~lR~~ll~ 295 (463)
T PRK00260 257 NGFVTVNGEKMSKSLGNFFTIRDLLKKYDPEVLRFFLLS 295 (463)
T ss_pred ccEEccCCCcccCcCCCCCCHHHHHHHcCchHhHHHHHh
Confidence 34456899999999999997753 12345555544444
No 95
>PLN02224 methionine-tRNA ligase
Probab=92.10 E-value=0.042 Score=55.16 Aligned_cols=33 Identities=21% Similarity=0.249 Sum_probs=23.5
Q ss_pred CCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938 16 SESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR 48 (241)
Q Consensus 16 g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~ 48 (241)
..+|+|||||.||+||..+ +.-+|+.++=|+++
T Consensus 361 ~~eG~KMSKS~GN~i~p~e~l~~ygaD~~R~yLl~ 395 (616)
T PLN02224 361 TKDGMKMGKSLGNTLEPFELVQKFGPDAVRYFFLR 395 (616)
T ss_pred ecCCccccccCCccCCHHHHHHHcCcHHHHHHHHh
Confidence 5799999999999998873 22345555555554
No 96
>PRK14535 cysS cysteinyl-tRNA synthetase; Provisional
Probab=92.06 E-value=0.19 Score=51.05 Aligned_cols=41 Identities=24% Similarity=0.217 Sum_probs=26.6
Q ss_pred eeeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938 7 GGLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR 48 (241)
Q Consensus 7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~ 48 (241)
|=+..-.|. .+|+|||||.||.|.+.+ ++-+|..++=++++
T Consensus 495 yWmHnG~V~-vdGeKMSKSLGN~it~~dlLe~ygpdalRl~lLs 537 (699)
T PRK14535 495 YWLHNGFIR-VDGEKMSKSLGNFFTIREVLKQYDPEVVRFFILR 537 (699)
T ss_pred EEEECCeEe-eCCCccCCCCCCcCCHHHHHHhCCHHHHHHHHHc
Confidence 445555565 899999999999986542 12345555544444
No 97
>TIGR00435 cysS cysteinyl-tRNA synthetase. This model finds the cysteinyl-tRNA synthetase from most but not from all species. The enzyme from one archaeal species, Archaeoglobus fulgidus, is found but the equivalent enzymes from some other Archaea, including Methanococcus jannaschii, are not found, although biochemical evidence suggests that tRNA(Cys) in these species are charged directly with Cys rather than through a misacylation and correction pathway as for tRNA(Gln).
Probab=91.99 E-value=0.041 Score=53.35 Aligned_cols=18 Identities=28% Similarity=0.174 Sum_probs=16.0
Q ss_pred CCCCCccccCCCCeEeec
Q psy938 16 SESGEKFGKSARNAIWLD 33 (241)
Q Consensus 16 g~dG~KmsKS~gn~I~L~ 33 (241)
..+|+|||||.||.|.+.
T Consensus 260 ~~~g~KMSKS~GN~i~~~ 277 (465)
T TIGR00435 260 MIDNEKMSKSLGNFFTVR 277 (465)
T ss_pred EecCccccccCCCcCCHH
Confidence 479999999999999775
No 98
>PLN02946 cysteine-tRNA ligase
Probab=91.68 E-value=0.062 Score=53.39 Aligned_cols=26 Identities=19% Similarity=0.183 Sum_probs=19.8
Q ss_pred eeecccccCCCCCccccCCCCeEeecC
Q psy938 8 GLTTPIIESESGEKFGKSARNAIWLDS 34 (241)
Q Consensus 8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~ 34 (241)
-+..-.|. .+|+|||||.||.|.+.+
T Consensus 311 W~H~G~v~-~~G~KMSKSlGN~itl~d 336 (557)
T PLN02946 311 WIHNGFVT-VDSEKMSKSLGNFFTIRQ 336 (557)
T ss_pred eeEeeEEE-eCCCCcCCcCCCcCCHHH
Confidence 34444555 799999999999997763
No 99
>cd00418 GlxRS_core catalytic core domain of glutamyl-tRNA and glutaminyl-tRNA synthetase. Glutamyl-tRNA synthetase(GluRS)/Glutaminyl-tRNA synthetase (GlnRS) cataytic core domain. These enzymes attach Glu or Gln, respectively, to the appropriate tRNA. Like other class I tRNA synthetases, they aminoacylate the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. These enzymes function as monomers. Archaea, cellular organelles, and some bacteria lack GlnRS. In these cases, the "non-discriminating" form of GluRS aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu, which is converted to Gln when appropriate by a transamidation enzyme. The discriminating form of GluRS differs from GlnRS and the non-discriminating form of GluRS in their C-terminal anti-codon bind
Probab=91.57 E-value=0.16 Score=45.06 Aligned_cols=46 Identities=22% Similarity=0.130 Sum_probs=31.4
Q ss_pred CCceeeecccccCCCCCccccCCCCe-E-eecCCCCCHHHHHHHhhcC
Q psy938 4 TGDGGLTTPIIESESGEKFGKSARNA-I-WLDSKLSSSFELYQYLIRT 49 (241)
Q Consensus 4 ~~~~~lt~pLL~g~dG~KmsKS~gn~-I-~L~~~~Tsp~~~yq~~~~~ 49 (241)
..+....+|+|.+.+|+||||+.++. | ++-..--+|..+..++..+
T Consensus 136 ~~P~~~H~pll~~~~g~KLSKr~~~~~i~~~r~~G~~p~ai~~~l~~l 183 (230)
T cd00418 136 EPPRFYHFPRLLLEDGTKLSKRKLNTTLRALRRRGYLPEALRNYLALI 183 (230)
T ss_pred CCCeEEEeeeeeCCCCCCccCcCCCcCHHHHHHCCCcHHHHHHHHHHc
Confidence 45667899999999999999999872 2 2212223566666665544
No 100
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=91.37 E-value=0.68 Score=41.85 Aligned_cols=73 Identities=15% Similarity=-0.019 Sum_probs=51.0
Q ss_pred CCcHHHHHH-hcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcc-----cCCCeEEEEeccccEEEEEEcccch
Q psy938 146 GMSMLELSL-ATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHI-----LPNSLTLLRVEVSANIIAKSANIIA 219 (241)
Q Consensus 146 ~~~l~~lLv-~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~-----~~~~~~llr~GKk~~~~i~~~~~~~ 219 (241)
.++|.=+|. ..+++.+.+||++.+.||-|.|||...+|+.+-+-.= |+ .+..|-+|-=-|.+|.+.++...-|
T Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~m-DVIsI~kt~e~yRvl~D~kGr~~l~~I~~eeA 119 (262)
T PTZ00118 41 CLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFM-DVVSLTKTNEYFRLLYDTKGRFVPHKITNEEA 119 (262)
T ss_pred ccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCcee-EEEEEcCCCCeEEEEECCCccEEEEEcCHHHh
Confidence 467777776 4689999999999999999999999999987655321 11 1223445555556666666654444
No 101
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=91.21 E-value=0.072 Score=52.10 Aligned_cols=38 Identities=24% Similarity=0.226 Sum_probs=23.4
Q ss_pred ecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938 10 TTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR 48 (241)
Q Consensus 10 t~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~ 48 (241)
+.-.+..- |+|||||.||+||+++ +.-.++.++=++++
T Consensus 317 ~~g~v~~~-g~KmSKS~Gn~i~~~d~i~~~g~D~lR~~l~~ 356 (530)
T TIGR00398 317 SHGYLTVE-GGKMSKSLGNVVDPSDLLARFGADILRYYLLK 356 (530)
T ss_pred eeccEEEC-CceecccCCceecHHHHHHHcCchHHHHHHhh
Confidence 34444433 9999999999998773 11234444444444
No 102
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=91.15 E-value=0.059 Score=54.19 Aligned_cols=32 Identities=25% Similarity=0.200 Sum_probs=22.3
Q ss_pred CCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938 17 ESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR 48 (241)
Q Consensus 17 ~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~ 48 (241)
.+|+|||||.||+||..+ +.-+|+.++=|+++
T Consensus 295 ~eg~KMSKS~GN~i~p~d~l~~ygaD~lR~~L~~ 328 (648)
T PRK12267 295 MKDGKMSKSKGNVVDPEELVDRYGLDALRYYLLR 328 (648)
T ss_pred ECCceecccCCcccCHHHHHHHcCCcHHHHHHHh
Confidence 368999999999999763 12345555555654
No 103
>PLN00036 40S ribosomal protein S4; Provisional
Probab=91.13 E-value=0.76 Score=41.54 Aligned_cols=73 Identities=11% Similarity=-0.016 Sum_probs=51.5
Q ss_pred CCcHHHHHHh-cCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcc-----cCCCeEEEEeccccEEEEEEcccch
Q psy938 146 GMSMLELSLA-TKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHI-----LPNSLTLLRVEVSANIIAKSANIIA 219 (241)
Q Consensus 146 ~~~l~~lLv~-~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~-----~~~~~~llr~GKk~~~~i~~~~~~~ 219 (241)
.++|.=+|.. .+++.+.+||++.+.||-|.|||...+|+.+-+-.= |+ .+..|-+|-=-|.+|.+.++...-|
T Consensus 41 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~m-DVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA 119 (261)
T PLN00036 41 CLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFM-DVISIPKTNENFRLLYDTKGRFRLHRINDEEA 119 (261)
T ss_pred ccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCcee-EEEEEcCCCCeEEEEECCCceEEEEEcChHHc
Confidence 4677777764 699999999999999999999999999988765321 11 1223445555566666666654444
No 104
>KOG0437|consensus
Probab=90.96 E-value=0.41 Score=49.12 Aligned_cols=77 Identities=19% Similarity=0.294 Sum_probs=45.2
Q ss_pred CCCCccccCCCCeEeecCCCCCHHHHHHHhhcC------------------CChhHHHHHHHhcCCCHHHHHHHHHH---
Q psy938 17 ESGEKFGKSARNAIWLDSKLSSSFELYQYLIRT------------------KDSEVYDLLKLFSFDSLAAIEDFKRQ--- 75 (241)
Q Consensus 17 ~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~------------------~D~~v~~~l~~~t~l~~eei~~i~~~--- 75 (241)
++++|||||.||+.-|+. +-+.|=--=+++ .|.-| |++||. .+=++++++.
T Consensus 706 LNsEKMSKSTGNfmTL~q---aieKFgad~tRlalAdaGD~veDANF~ea~AnAaI---LRLyt~--~ew~eEm~~~~s~ 777 (1080)
T KOG0437|consen 706 LNSEKMSKSTGNFMTLEQ---AIEKFGADGTRLALADAGDGVEDANFVEANANAAI---LRLYTY--VEWIEEMCENRSS 777 (1080)
T ss_pred ecchhhccccCCeeeHHH---HHHHhCccceeeeeecccCCcccchhHHhcccHHH---HHHHHH--HHHHHHHHhhHHh
Confidence 356899999999988876 443332222222 22333 444442 2335555543
Q ss_pred hhcCCChHHHHHHHHHHHHhhccCHH
Q psy938 76 NEHKPEERRAQKKLAEDLTLLVHGEE 101 (241)
Q Consensus 76 ~~~~~~~~~~Kk~LA~~i~~~vhG~~ 101 (241)
.+.||...-+-+.++.++..++.-.+
T Consensus 778 LrtGp~~~FaDrvf~nemN~~i~~t~ 803 (1080)
T KOG0437|consen 778 LRTGPASTFADRVFENEMNALIAKTE 803 (1080)
T ss_pred hccCchhhHHHHHHHHHHHHHHHHHH
Confidence 34566555788889999887765433
No 105
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=90.90 E-value=0.1 Score=49.02 Aligned_cols=30 Identities=20% Similarity=0.110 Sum_probs=22.6
Q ss_pred CCceeeecccccCCCCCccccCCCCeEeec
Q psy938 4 TGDGGLTTPIIESESGEKFGKSARNAIWLD 33 (241)
Q Consensus 4 ~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~ 33 (241)
.+++.+...++....|.|||||.||.|.++
T Consensus 258 ~~P~~~~ye~V~l~gg~KMSKSkGnvI~~~ 287 (353)
T cd00674 258 EPPVPVMYEFIGLKGGGKMSSSKGNVITPS 287 (353)
T ss_pred CCCeEEEeeeEEeCCCCccCCCCCCcCCHH
Confidence 445667777776555679999999998665
No 106
>PLN02959 aminoacyl-tRNA ligase
Probab=90.63 E-value=0.085 Score=56.26 Aligned_cols=21 Identities=29% Similarity=0.221 Sum_probs=17.3
Q ss_pred ccccCCCCCccccCCCCeEeec
Q psy938 12 PIIESESGEKFGKSARNAIWLD 33 (241)
Q Consensus 12 pLL~g~dG~KmsKS~gn~I~L~ 33 (241)
.++. .+|+|||||.||.|++.
T Consensus 710 G~V~-~~G~KMSKSkGNvI~p~ 730 (1084)
T PLN02959 710 GHLM-LNSEKMSKSTGNFLTLR 730 (1084)
T ss_pred cEEe-cCCcCccccCCCcCCHH
Confidence 3444 79999999999999875
No 107
>PRK14536 cysS cysteinyl-tRNA synthetase; Provisional
Probab=90.48 E-value=0.074 Score=52.06 Aligned_cols=19 Identities=32% Similarity=0.200 Sum_probs=16.7
Q ss_pred CCCCCccccCCCCeEeecC
Q psy938 16 SESGEKFGKSARNAIWLDS 34 (241)
Q Consensus 16 g~dG~KmsKS~gn~I~L~~ 34 (241)
..+|+|||||.||.|+|.+
T Consensus 274 ~~~g~KMSKSlGN~itl~d 292 (490)
T PRK14536 274 LMNKGKMSKSAGQFLTLSS 292 (490)
T ss_pred eecCccccccCCCcccHHH
Confidence 4689999999999999863
No 108
>KOG4655|consensus
Probab=90.39 E-value=0.13 Score=43.39 Aligned_cols=40 Identities=23% Similarity=0.159 Sum_probs=35.8
Q ss_pred HHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 152 LSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 152 lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
++...+++.|-.+|-++|+||-|+|+-..|+||.+.++.+
T Consensus 112 Vm~~l~m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lvtr~ 151 (181)
T KOG4655|consen 112 VMGRLRMAESVKEAVRFVEQGHVRVGPKVVTDPAFLVTRS 151 (181)
T ss_pred eeeechhhhhHHHHHHHHHcCceeeCCeeccCchHHhhhh
Confidence 4556789999999999999999999999999999988744
No 109
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=90.16 E-value=0.54 Score=43.23 Aligned_cols=46 Identities=15% Similarity=0.124 Sum_probs=36.6
Q ss_pred CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 145 PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 145 ~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
.+.+|.++|.......|++.++++|++|.|+|||.++ .++..+...
T Consensus 18 ~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v-~~~~~v~~G 63 (317)
T PRK11025 18 AGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAG 63 (317)
T ss_pred CCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEc-CcccccCCC
Confidence 3688999998654445999999999999999999987 466655443
No 110
>KOG0436|consensus
Probab=90.04 E-value=0.15 Score=49.08 Aligned_cols=24 Identities=38% Similarity=0.537 Sum_probs=20.4
Q ss_pred CCCCCccccCCCCeEeecCCCCCHHHHHHHh
Q psy938 16 SESGEKFGKSARNAIWLDSKLSSSFELYQYL 46 (241)
Q Consensus 16 g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~ 46 (241)
+-+|.|||||.||.| +|+++-|+.
T Consensus 339 t~ngmKMsKSLGNvv-------dP~~l~~ky 362 (578)
T KOG0436|consen 339 TKNGMKMSKSLGNVV-------DPFELVQKY 362 (578)
T ss_pred eecceecchhhcccc-------CHHHHHHHh
Confidence 347999999999997 788888875
No 111
>PTZ00399 cysteinyl-tRNA-synthetase; Provisional
Probab=90.03 E-value=0.083 Score=53.43 Aligned_cols=35 Identities=17% Similarity=0.134 Sum_probs=24.8
Q ss_pred cCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938 15 ESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT 49 (241)
Q Consensus 15 ~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~ 49 (241)
...+|+|||||.||.|.+.+ ++-+|..++=++++.
T Consensus 309 L~i~G~KMSKSLGNfItp~dlLekygaDaLR~~lLs~ 345 (651)
T PTZ00399 309 LHIKGLKMSKSLKNFITIRQALSKYTARQIRLLFLLH 345 (651)
T ss_pred EEeccchhhhcCCCcccHHHHHHHcChHHHHHHHHhc
Confidence 35799999999999998873 123566666556543
No 112
>PRK01611 argS arginyl-tRNA synthetase; Reviewed
Probab=90.00 E-value=0.16 Score=49.71 Aligned_cols=26 Identities=23% Similarity=0.337 Sum_probs=22.5
Q ss_pred eecccccCCCCCccccCCCCeEeecC
Q psy938 9 LTTPIIESESGEKFGKSARNAIWLDS 34 (241)
Q Consensus 9 lt~pLL~g~dG~KmsKS~gn~I~L~~ 34 (241)
..+.++.+.+|+|||||.||+|++++
T Consensus 310 ~~~glv~~~~g~KMSkR~Gn~i~l~d 335 (507)
T PRK01611 310 QMVGLVRGGEGVKMSTRAGNVVTLDD 335 (507)
T ss_pred EEEEeeECCCCCcccCCCCceeEHHH
Confidence 34568889999999999999998885
No 113
>cd00808 GluRS_core catalytic core domain of discriminating glutamyl-tRNA synthetase. Discriminating Glutamyl-tRNA synthetase (GluRS) catalytic core domain . The discriminating form of GluRS is only found in bacteria and cellular organelles. GluRS is a monomer that attaches Glu to the appropriate tRNA. Like other class I tRNA synthetases, GluRS aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.
Probab=89.93 E-value=0.29 Score=43.64 Aligned_cols=44 Identities=20% Similarity=0.159 Sum_probs=31.7
Q ss_pred ceeeecccccCCCCCccccCCCCe-E-eecCCCCCHHHHHHHhhcC
Q psy938 6 DGGLTTPIIESESGEKFGKSARNA-I-WLDSKLSSSFELYQYLIRT 49 (241)
Q Consensus 6 ~~~lt~pLL~g~dG~KmsKS~gn~-I-~L~~~~Tsp~~~yq~~~~~ 49 (241)
+.-...|+|++.+|.||||+.|+. | ++-+.-.+|..+..|+..+
T Consensus 147 p~~~h~pll~~~~g~KLSKR~~~~~l~~lr~~G~~p~ai~~~l~~l 192 (239)
T cd00808 147 PKFAHLPLILNPDGKKLSKRKGDTSISDYREEGYLPEALLNYLALL 192 (239)
T ss_pred CceEeeccccCCCCCcccCCCCCccHHHHHHCCCCHHHHHHHHHHc
Confidence 444588999999999999999982 2 3323334677777777654
No 114
>PRK14534 cysS cysteinyl-tRNA synthetase; Provisional
Probab=89.68 E-value=0.088 Score=51.45 Aligned_cols=19 Identities=32% Similarity=0.220 Sum_probs=16.6
Q ss_pred CCCCCccccCCCCeEeecC
Q psy938 16 SESGEKFGKSARNAIWLDS 34 (241)
Q Consensus 16 g~dG~KmsKS~gn~I~L~~ 34 (241)
..+|+|||||.||.|+|.+
T Consensus 274 ~~~g~KMSKSlGN~i~l~d 292 (481)
T PRK14534 274 IMEYEKMSKSNNNFITIKD 292 (481)
T ss_pred EecCceecccCCCcccHHH
Confidence 3589999999999999974
No 115
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=87.29 E-value=1.6 Score=39.81 Aligned_cols=45 Identities=24% Similarity=0.226 Sum_probs=37.7
Q ss_pred CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938 145 PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS 191 (241)
Q Consensus 145 ~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~ 191 (241)
.+.++..+|.+... -|+++..++|.+|.|.|||+++. +++.+..+
T Consensus 11 ~g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~g 55 (289)
T COG0564 11 AGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPG 55 (289)
T ss_pred cCCCHHHHHHHccC-cCHHHHHHHHHCCCEEECCEEcc-CCeeeCCC
Confidence 36789999988433 59999999999999999999998 77777654
No 116
>KOG2007|consensus
Probab=85.76 E-value=1.4 Score=43.46 Aligned_cols=33 Identities=30% Similarity=0.274 Sum_probs=26.9
Q ss_pred CCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938 17 ESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT 49 (241)
Q Consensus 17 ~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~ 49 (241)
.+|+|||||.+|+|-+-+ ++-||.+++=+|+..
T Consensus 301 i~g~KMSKSLkNFiTIke~Lk~~sp~qLRl~fl~~ 335 (586)
T KOG2007|consen 301 INGEKMSKSLKNFITIKEALKKYSPRQLRLAFLLH 335 (586)
T ss_pred eccchhhhhhccceeHHHHHHhcCHHHHHHHHHHH
Confidence 478999999999988762 456899999888775
No 117
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=85.74 E-value=1.8 Score=40.98 Aligned_cols=31 Identities=16% Similarity=0.107 Sum_probs=7.4
Q ss_pred CCCceeeecccccCCCCCccccCCCCeEeec
Q psy938 3 VTGDGGLTTPIIESESGEKFGKSARNAIWLD 33 (241)
Q Consensus 3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~ 33 (241)
..+++++.--++..-.|+|||||.||.|-+.
T Consensus 264 ~~pP~~~~YE~~~~~g~~kmSsSkG~~~t~~ 294 (360)
T PF01921_consen 264 YEPPVPFPYEFFLDKGGGKMSSSKGNGITPE 294 (360)
T ss_dssp ----EEEEE--EEES--------------HH
T ss_pred CCCCCCCCeeEEEeCCCcccccCCCCccCHH
Confidence 4466677766777777789999999987554
No 118
>KOG3301|consensus
Probab=85.58 E-value=0.7 Score=38.99 Aligned_cols=44 Identities=11% Similarity=0.044 Sum_probs=38.1
Q ss_pred CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCC
Q psy938 147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSP 190 (241)
Q Consensus 147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~ 190 (241)
.+|...+.++|+++|-..||-+|.++.|.|+++.|.-|.+.+..
T Consensus 97 rRLqt~vFklGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrl 140 (183)
T KOG3301|consen 97 RRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRL 140 (183)
T ss_pred HHHHHHHHHHhhhhhhHHHHHHhcCccEEecCeEeeccceeEee
Confidence 34666778899999999999999999999999999888877653
No 119
>COG0495 LeuS Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=85.04 E-value=0.53 Score=48.80 Aligned_cols=38 Identities=21% Similarity=0.267 Sum_probs=24.1
Q ss_pred ccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938 12 PIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT 49 (241)
Q Consensus 12 pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~ 49 (241)
-.+.+.+|+|||||.||.|-+++ ++-.++..+=|+|.+
T Consensus 570 GmVl~~~g~KMSKSKgN~v~p~~~i~~yGADt~Rl~~m~~ 609 (814)
T COG0495 570 GMVLGEEGEKMSKSKGNVVDPEEAVEKYGADTVRLYIMFA 609 (814)
T ss_pred ceEEecCCCccccccCCCCCHHHHHHHhCchHHHHHHHhh
Confidence 34555589999999999996663 111233444455554
No 120
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=84.78 E-value=0.38 Score=47.46 Aligned_cols=18 Identities=22% Similarity=0.316 Sum_probs=14.8
Q ss_pred CCCCccccCCCCeEeecC
Q psy938 17 ESGEKFGKSARNAIWLDS 34 (241)
Q Consensus 17 ~dG~KmsKS~gn~I~L~~ 34 (241)
-+|+|||||.||.|.+++
T Consensus 270 ~~g~KMSKS~Gn~itl~d 287 (515)
T TIGR00467 270 GKGGKMSSSKGDVISVKD 287 (515)
T ss_pred CCCccccCCCCCCccHHH
Confidence 357899999999997763
No 121
>PLN02563 aminoacyl-tRNA ligase
Probab=84.40 E-value=0.86 Score=48.24 Aligned_cols=14 Identities=36% Similarity=0.363 Sum_probs=11.6
Q ss_pred CccccCCCCeEeec
Q psy938 20 EKFGKSARNAIWLD 33 (241)
Q Consensus 20 ~KmsKS~gn~I~L~ 33 (241)
+|||||.||.|+.+
T Consensus 722 eKMSKSKGNvVdP~ 735 (963)
T PLN02563 722 HKMSKSRGNVVNPD 735 (963)
T ss_pred cccccccCCcCCHH
Confidence 39999999998544
No 122
>KOG0433|consensus
Probab=82.56 E-value=0.73 Score=47.24 Aligned_cols=22 Identities=27% Similarity=0.401 Sum_probs=18.0
Q ss_pred eecccccCCCCCccccCCCCeE
Q psy938 9 LTTPIIESESGEKFGKSARNAI 30 (241)
Q Consensus 9 lt~pLL~g~dG~KmsKS~gn~I 30 (241)
+|.--..+..|.|||||.||.|
T Consensus 601 ivHGFtlDE~G~KMSKSlGNVi 622 (937)
T KOG0433|consen 601 IVHGFTLDENGNKMSKSLGNVV 622 (937)
T ss_pred eeeeeEecCCccchhhcccCcC
Confidence 4455567889999999999987
No 123
>TIGR00396 leuS_bact leucyl-tRNA synthetase, eubacterial and mitochondrial family. The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both eubacterial and mitochondrial leucyl-tRNA synthetases. It generates higher scores for some valyl-tRNA synthetases than for any archaeal or eukaryotic cytosolic leucyl-tRNA synthetase. Note that the enzyme from Aquifex aeolicus is split into alpha and beta chains; neither chain is long enough to score above the trusted cutoff, but the alpha chain scores well above the noise cutoff. The beta chain must be found by a model and search designed for partial length matches.
Probab=80.05 E-value=0.5 Score=49.23 Aligned_cols=28 Identities=29% Similarity=0.234 Sum_probs=17.9
Q ss_pred ccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938 21 KFGKSARNAIWLDS--KLSSSFELYQYLIR 48 (241)
Q Consensus 21 KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~ 48 (241)
|||||.||.|.+++ ++-.++.++=+++.
T Consensus 604 KMSKS~GN~v~p~~ii~~ygaDalRl~~l~ 633 (842)
T TIGR00396 604 KMSKSKGNGIDPQEIVKKHGADALRLYIMF 633 (842)
T ss_pred hhhhcCCCcCCHHHHHHHcCchHHHHHHHh
Confidence 99999999997652 11234455555553
No 124
>COG0008 GlnS Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=76.51 E-value=5.5 Score=39.02 Aligned_cols=31 Identities=19% Similarity=0.215 Sum_probs=24.5
Q ss_pred CCCCceeeecccccCCCCCccccCCCCeEeec
Q psy938 2 EVTGDGGLTTPIIESESGEKFGKSARNAIWLD 33 (241)
Q Consensus 2 ~~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~ 33 (241)
+-.++.-..+|||.+.+|+||||+.+ ++.+.
T Consensus 231 g~~~P~~~H~~li~~~~g~kLSKr~~-~~~~~ 261 (472)
T COG0008 231 GWPPPVYAHLPLLLNEDGKKLSKRKG-AVSIG 261 (472)
T ss_pred CCCCCcEEEeeeeecCCCCeecCccC-ccccc
Confidence 44567778999999999999999988 54444
No 125
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=73.63 E-value=6.9 Score=34.90 Aligned_cols=33 Identities=24% Similarity=0.186 Sum_probs=28.0
Q ss_pred cCCCCCHHHHHHHHHhCCeEEccEEecCCCCcc
Q psy938 156 TKCFPRDKEANLTISEGGFYVNYKKVQNPQEVL 188 (241)
Q Consensus 156 ~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l 188 (241)
.+++...+|||+.|.+|.|.|||...+|..+-+
T Consensus 51 LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPV 83 (241)
T COG1471 51 LKYADNAREARKILSEGKVLVDGKVRKDYKFPV 83 (241)
T ss_pred HHhccchHHHHHHHhcCcEEECCEEeccccCCc
Confidence 356678899999999999999999988876544
No 126
>TIGR00464 gltX_bact glutamyl-tRNA synthetase, bacterial family. The glutamyl-tRNA synthetases of the eukaryotic cytosol and of the Archaea are more similar to glutaminyl-tRNA synthetases than to bacterial glutamyl-tRNA synthetases. This alignment models just the bacterial and mitochondrial forms of the enzyme. In many species, the charging of tRNA(gln) proceeds first through misacylation with Glu and then transamidation. For this reason, glutamyl-tRNA synthetases may act on both tRNA(gln) and tRNA(glu). This model is highly specific. Proteins with positive scores below the trusted cutoff may be fragments rather than full-length sequences.
Probab=71.56 E-value=24 Score=34.51 Aligned_cols=45 Identities=22% Similarity=0.107 Sum_probs=32.2
Q ss_pred CCceeeecccccCCCCCccccCCCCeEeec---CCCCCHHHHHHHhhcC
Q psy938 4 TGDGGLTTPIIESESGEKFGKSARNAIWLD---SKLSSSFELYQYLIRT 49 (241)
Q Consensus 4 ~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~---~~~Tsp~~~yq~~~~~ 49 (241)
..+.-...|++.+.+|+||||-.| ++.|+ +.-..|..+..++.++
T Consensus 224 ~~p~~~H~p~l~~~~g~kLSKR~g-~~~l~~l~~~g~~p~a~~~~~~~l 271 (470)
T TIGR00464 224 KIPVFAHLPMILDEDGKKLSKRDG-ATSIMQFKEQGYLPEALINYLALL 271 (470)
T ss_pred CCCeEEEEeeeecCCCccccccCC-CccHHHHHHCCCCHHHHHHHHHHc
Confidence 345667889999999999999877 55554 2223577777777654
No 127
>PRK14895 gltX glutamyl-tRNA synthetase; Provisional
Probab=71.29 E-value=3.1 Score=41.12 Aligned_cols=46 Identities=20% Similarity=0.166 Sum_probs=33.5
Q ss_pred CCceeeecccccCCCCCccccCCCCe--EeecCCCCCHHHHHHHhhcC
Q psy938 4 TGDGGLTTPIIESESGEKFGKSARNA--IWLDSKLSSSFELYQYLIRT 49 (241)
Q Consensus 4 ~~~~~lt~pLL~g~dG~KmsKS~gn~--I~L~~~~Tsp~~~yq~~~~~ 49 (241)
..+.....|+|.+.+|.||||..|.. -.+-+.-..|..+..|+..+
T Consensus 223 ~~p~~~H~plv~~~~g~KLSKR~g~~~i~~~r~~G~~Peai~n~la~L 270 (513)
T PRK14895 223 AVPSMTHIPLIHGADGAKLSKRHGALGIEAYKDMGYLPESLCNYLLRL 270 (513)
T ss_pred CCCeEEEEEeEEcCCCCccccccCchhHHHHHHCCCCHHHHHHHHHHh
Confidence 45667789999999999999987753 22223445788888888743
No 128
>PRK12558 glutamyl-tRNA synthetase; Provisional
Probab=66.74 E-value=4.1 Score=39.58 Aligned_cols=46 Identities=13% Similarity=0.081 Sum_probs=34.2
Q ss_pred CCceeeecccccCCCCCccccCCCCe-E-eecCCCCCHHHHHHHhhcC
Q psy938 4 TGDGGLTTPIIESESGEKFGKSARNA-I-WLDSKLSSSFELYQYLIRT 49 (241)
Q Consensus 4 ~~~~~lt~pLL~g~dG~KmsKS~gn~-I-~L~~~~Tsp~~~yq~~~~~ 49 (241)
..+.-...|||.+.||+|+||..|.+ | ++-+.--.|..+..|+..+
T Consensus 223 ~~P~f~H~pli~~~~g~KLSKR~g~~sv~~~r~~G~~Peai~n~la~l 270 (445)
T PRK12558 223 KPPVFAHLSLLTGADGKGLSKRLGGLSIRSLREDGIEPMAIASLLARL 270 (445)
T ss_pred CCCeEEEcccccCCCcccccccCCCcCHHHHHHCCCCHHHHHHHHHHH
Confidence 34556789999999999999987652 2 3334455788888888775
No 129
>PRK05710 glutamyl-Q tRNA(Asp) synthetase; Reviewed
Probab=65.85 E-value=4.6 Score=37.23 Aligned_cols=26 Identities=19% Similarity=0.326 Sum_probs=21.3
Q ss_pred CCCceeeecccccCCCCCccccCCCC
Q psy938 3 VTGDGGLTTPIIESESGEKFGKSARN 28 (241)
Q Consensus 3 ~~~~~~lt~pLL~g~dG~KmsKS~gn 28 (241)
-..+.-...|||.+.+|+|+||+.+.
T Consensus 218 ~~~P~y~H~pll~~~~g~kLSKr~~~ 243 (299)
T PRK05710 218 LPTPRYLHLPLVLNADGQKLSKQNGA 243 (299)
T ss_pred CCCCeEEEeecccCCCCCcccccCCc
Confidence 34566778999999999999998654
No 130
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=64.82 E-value=2.9 Score=41.27 Aligned_cols=30 Identities=23% Similarity=0.144 Sum_probs=20.3
Q ss_pred CceeeecccccCCCCCccccCCCCeEeecC
Q psy938 5 GDGGLTTPIIESESGEKFGKSARNAIWLDS 34 (241)
Q Consensus 5 ~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~ 34 (241)
+++++.--+++--.|+|||||.||.|.+++
T Consensus 261 pP~~~~YE~i~lkg~~~mSsSkG~~i~~~d 290 (521)
T COG1384 261 PPVPFVYEWILLKGGGKMSSSKGNVISLSD 290 (521)
T ss_pred CCCCCceEEEEecCCcccccCCCcEEcHHH
Confidence 444444444444447999999999997773
No 131
>PRK12410 glutamylglutaminyl-tRNA synthetase; Provisional
Probab=63.05 E-value=5.1 Score=38.78 Aligned_cols=44 Identities=27% Similarity=0.292 Sum_probs=32.5
Q ss_pred ceeeecccccCCCCCccccCCCCe--EeecCCCCCHHHHHHHhhcC
Q psy938 6 DGGLTTPIIESESGEKFGKSARNA--IWLDSKLSSSFELYQYLIRT 49 (241)
Q Consensus 6 ~~~lt~pLL~g~dG~KmsKS~gn~--I~L~~~~Tsp~~~yq~~~~~ 49 (241)
+.-...||+.+.+|+|+||..|.. -++-+.--.|..+..|+..+
T Consensus 220 p~f~Hlpli~~~~g~KLSKR~~~~~v~~~r~~G~~PeAi~n~l~~l 265 (433)
T PRK12410 220 ITYAHLPIILNEEGKKMSKRDNASSVKWLLEQGFLPSAIANYLILL 265 (433)
T ss_pred CeEEEeeeeeCCCCCeeecccChhhHHHHHHCCCCHHHHHHHHHHh
Confidence 356788999999999999987742 22334445788888887766
No 132
>PLN02627 glutamyl-tRNA synthetase
Probab=62.86 E-value=5.7 Score=39.49 Aligned_cols=46 Identities=11% Similarity=-0.065 Sum_probs=34.0
Q ss_pred CCceeeecccccCCCCCccccCCCCe--EeecCCCCCHHHHHHHhhcC
Q psy938 4 TGDGGLTTPIIESESGEKFGKSARNA--IWLDSKLSSSFELYQYLIRT 49 (241)
Q Consensus 4 ~~~~~lt~pLL~g~dG~KmsKS~gn~--I~L~~~~Tsp~~~yq~~~~~ 49 (241)
..+.-...|||.+.||+|+||..|.. -++-+.--.|..+..|+..+
T Consensus 276 ~~P~f~Hlpli~~~~g~KLSKR~~~~~v~~~r~~G~~PeAi~nyla~L 323 (535)
T PLN02627 276 PMPRFAHVSLILAPDRSKLSKRHGATSVGQFREMGYLPDAMVNYLALL 323 (535)
T ss_pred CCCeEEEccceeCCCCCccccccCCccHHHHHHCCCCHHHHHHHHHHh
Confidence 44566789999999999999987542 12334455788888888765
No 133
>TIGR03838 queuosine_YadB glutamyl-queuosine tRNA(Asp) synthetase. This protein resembles a shortened glutamyl-tRNA ligase, but its purpose is to modify tRNA(Asp) at a queuosine position in the anticodon rather than to charge a tRNA with its cognate amino acid.
Probab=60.84 E-value=5.5 Score=36.16 Aligned_cols=29 Identities=28% Similarity=0.327 Sum_probs=22.3
Q ss_pred CCceeeecccccCCCCCccccCCCCeEeec
Q psy938 4 TGDGGLTTPIIESESGEKFGKSARNAIWLD 33 (241)
Q Consensus 4 ~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~ 33 (241)
..+.-...|||.+.+|+|+||+.+. ..|.
T Consensus 212 ~~P~y~H~pll~~~~g~kLSKR~~~-~~i~ 240 (272)
T TIGR03838 212 PPPRYLHLPLVVNADGEKLSKQNGA-PALD 240 (272)
T ss_pred CCCeEEechhhhCCCCCeeeccCCc-cchh
Confidence 3456678999999999999998654 3444
No 134
>KOG0434|consensus
Probab=57.67 E-value=4.9 Score=41.34 Aligned_cols=30 Identities=17% Similarity=0.285 Sum_probs=23.0
Q ss_pred eecccccCCCCCccccCCCCeEeecCCCCCHHHHHHH
Q psy938 9 LTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQY 45 (241)
Q Consensus 9 lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~ 45 (241)
+..-|+.-.||+||||+..|| + +|-.+.++
T Consensus 589 IvnGlVLAeDG~KMSKrlkNY----P---dP~~iink 618 (1070)
T KOG0434|consen 589 IVNGLVLAEDGKKMSKRLKNY----P---DPSLIINK 618 (1070)
T ss_pred eEeeeEEecccHHHhhhhhcC----C---CHHHHHHh
Confidence 455688889999999999998 4 56555554
No 135
>PRK00390 leuS leucyl-tRNA synthetase; Validated
Probab=57.31 E-value=5.7 Score=41.25 Aligned_cols=28 Identities=18% Similarity=0.062 Sum_probs=18.3
Q ss_pred ccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938 21 KFGKSARNAIWLDS--KLSSSFELYQYLIR 48 (241)
Q Consensus 21 KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~ 48 (241)
|||||.||.|...+ ++-.++.++=+++.
T Consensus 570 KMSKS~GN~i~p~~~i~~ygaD~lRl~l~~ 599 (805)
T PRK00390 570 KMSKSKGNVVDPDDIIEKYGADTARLFEMF 599 (805)
T ss_pred EeCCCCCCCCCHHHHHHHcChHHHHHHHHh
Confidence 99999999986652 12245555555555
No 136
>PF00749 tRNA-synt_1c: tRNA synthetases class I (E and Q), catalytic domain; InterPro: IPR020058 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Glutamyl-tRNA synthetase (6.1.1.17 from EC) is a class Ic synthetase and shows several similarities with glutaminyl-tRNA synthetase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamyl-tRNA synthetase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I synthetases and resembles the corresponding part of Escherichia coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure []. ; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0016876 ligase activity, forming aminoacyl-tRNA and related compounds, 0043039 tRNA aminoacylation, 0005737 cytoplasm; PDB: 2HZ7_A 2CFO_A 4A91_A 1NZJ_A 1N78_A 1G59_C 2CV2_A 2CV1_A 2CV0_B 1GLN_A ....
Probab=50.83 E-value=11 Score=34.62 Aligned_cols=26 Identities=23% Similarity=0.262 Sum_probs=20.3
Q ss_pred CCceeeecccccCCCCCccccCCCCe
Q psy938 4 TGDGGLTTPIIESESGEKFGKSARNA 29 (241)
Q Consensus 4 ~~~~~lt~pLL~g~dG~KmsKS~gn~ 29 (241)
..+.-...|++.+.+|+|+||+.+..
T Consensus 226 ~~P~~~H~pl~l~~~g~kLSKR~~~~ 251 (314)
T PF00749_consen 226 PPPPYAHLPLILNEDGKKLSKRKGAK 251 (314)
T ss_dssp SS-EEEEEEEEEETTSSBSSTTCSHH
T ss_pred CCcceEeeeeeecCCCcEechhhccc
Confidence 33444677999999999999988764
No 137
>PRK01406 gltX glutamyl-tRNA synthetase; Reviewed
Probab=46.77 E-value=10 Score=37.08 Aligned_cols=43 Identities=21% Similarity=0.118 Sum_probs=30.4
Q ss_pred CceeeecccccCCCCCccccCCCCeEeec---CCCCCHHHHHHHhhc
Q psy938 5 GDGGLTTPIIESESGEKFGKSARNAIWLD---SKLSSSFELYQYLIR 48 (241)
Q Consensus 5 ~~~~lt~pLL~g~dG~KmsKS~gn~I~L~---~~~Tsp~~~yq~~~~ 48 (241)
.+.-...|+|.+.+|+||||-.| ++.|+ +.--.|..+..|+..
T Consensus 235 ~p~~~H~pli~~~~g~klSKR~g-~~~l~~l~~~G~~p~Ai~n~l~~ 280 (476)
T PRK01406 235 VPVFAHLPLILGPDGKKLSKRHG-ATSVEQYRDMGYLPEALLNYLAL 280 (476)
T ss_pred CCeEEEeeeeeCCCCCcccCcCC-ccCHHHHHHCCCCHHHHHHHHHH
Confidence 44556789999999999999877 55554 222356666666654
No 138
>PLN02286 arginine-tRNA ligase
Probab=35.87 E-value=22 Score=35.52 Aligned_cols=29 Identities=14% Similarity=0.219 Sum_probs=24.1
Q ss_pred ceeeecccccCCCCCccccCCCCeEeecC
Q psy938 6 DGGLTTPIIESESGEKFGKSARNAIWLDS 34 (241)
Q Consensus 6 ~~~lt~pLL~g~dG~KmsKS~gn~I~L~~ 34 (241)
...+..-++.+.+|+||||=.||+|.|++
T Consensus 363 l~h~~~g~V~~~~g~kmStR~G~~v~L~d 391 (576)
T PLN02286 363 LEHVGFGLVLGEDGKRFRTRSGEVVRLVD 391 (576)
T ss_pred eEEEeeccEECCCCCcccCCCCCeeEHHH
Confidence 44566677778899999999999999985
No 139
>KOG2716|consensus
Probab=35.21 E-value=1.1e+02 Score=27.37 Aligned_cols=35 Identities=14% Similarity=0.173 Sum_probs=26.4
Q ss_pred CceeeecccccCCCC--Ccc-------ccCCCCeEeecCCCCCHHHH
Q psy938 5 GDGGLTTPIIESESG--EKF-------GKSARNAIWLDSKLSSSFEL 42 (241)
Q Consensus 5 ~~~~lt~pLL~g~dG--~Km-------sKS~gn~I~L~~~~Tsp~~~ 42 (241)
..|--+..-||..|| ++| .++..|.|++|. ||..|
T Consensus 14 ~~F~Tsk~TLtk~dg~fk~m~e~~i~~~~d~s~~IFIDR---SpKHF 57 (230)
T KOG2716|consen 14 TIFKTSKSTLTKFDGFFKTMLETDIPVEKDESGCIFIDR---SPKHF 57 (230)
T ss_pred eEEEeehhhhhhhhhHHHHHhhcCCccccCCcCcEEecC---ChhHH
Confidence 466667778888888 444 555678999999 99765
No 140
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=34.33 E-value=60 Score=24.01 Aligned_cols=36 Identities=17% Similarity=0.200 Sum_probs=26.4
Q ss_pred CCHHHHHHHhhcC-CChhHHHHHHHhcCCCHHHHHHHHH
Q psy938 37 SSSFELYQYLIRT-KDSEVYDLLKLFSFDSLAAIEDFKR 74 (241)
Q Consensus 37 Tsp~~~yq~~~~~-~D~~v~~~l~~~t~l~~eei~~i~~ 74 (241)
+++++|.+-|.++ .+++ ..++|+..++.+.+..+-.
T Consensus 5 ~~~~eF~~~w~~~~~~~~--~~~~yL~~i~p~~l~~if~ 41 (94)
T PF13877_consen 5 KNSYEFERDWRRLKKDPE--ERYEYLKSIPPDSLPKIFK 41 (94)
T ss_pred CCHHHHHHHHHHHcCCHH--HHHHHHHhCChHHHHHHHH
Confidence 6899999999998 3333 4456666677888877764
No 141
>TIGR00234 tyrS tyrosyl-tRNA synthetase. This tyrosyl-tRNA synthetase model starts picking up tryptophanyl-tRNA synthetases at scores of 0 and below. The proteins found by this model have a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples.
Probab=33.57 E-value=1.1e+02 Score=28.97 Aligned_cols=44 Identities=11% Similarity=0.012 Sum_probs=34.0
Q ss_pred cccCCC-CCccccCCC---CeEeecCCCCCHHHHHHHhhcC----CChhHHHHHH
Q psy938 13 IIESES-GEKFGKSAR---NAIWLDSKLSSSFELYQYLIRT----KDSEVYDLLK 59 (241)
Q Consensus 13 LL~g~d-G~KmsKS~g---n~I~L~~~~Tsp~~~yq~~~~~----~D~~v~~~l~ 59 (241)
..+|.+ |.|||.|.. .++++.+ +|+++.++++++ +.+.+..+..
T Consensus 220 ~KmgKS~~~~i~l~~~~~~~~i~~~d---~~D~~~~Ki~k~~t~~~~~ei~~l~~ 271 (377)
T TIGR00234 220 EKMGKSGGGAVSLDEGKYDFYQFWIN---TPDEDVKKILKLFTFLGLEEIEALVE 271 (377)
T ss_pred CCccCCCCCcccCCccHhhhhhhhcC---CcHHHHHHHHHHcCCCcHHHHHHHHH
Confidence 667776 589999998 7899999 999999999886 3345555543
No 142
>TIGR00456 argS arginyl-tRNA synthetase. This model recognizes arginyl-tRNA synthetase in every completed genome to date. An interesting feature of the alignment of all arginyl-tRNA synthetases is a fairly deep split between two families. One family includes archaeal, eukaryotic and organellar, spirochete, E. coli, and Synechocystis sp. The second, sharing a deletion of about 25 residues in the central region relative to the first, includes Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas and Mycobacteria, and the Gram-negative bacterium Helicobacter pylori.
Probab=31.15 E-value=23 Score=35.18 Aligned_cols=16 Identities=25% Similarity=0.167 Sum_probs=14.1
Q ss_pred CCccccCCCCeEeecC
Q psy938 19 GEKFGKSARNAIWLDS 34 (241)
Q Consensus 19 G~KmsKS~gn~I~L~~ 34 (241)
|.|||||.||+|.+++
T Consensus 370 ~~kmSkr~Gn~V~~~d 385 (566)
T TIGR00456 370 LGSMKTRRGNVISLDN 385 (566)
T ss_pred CCCCCccCCceeeHHH
Confidence 4699999999999885
No 143
>PF00750 tRNA-synt_1d: tRNA synthetases class I (R); InterPro: IPR015945 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the core region of arginyl-tRNA synthetase (6.1.1.19 from EC), which has been crystallized and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes is available []. ; GO: 0000166 nucleotide binding, 0004814 arginine-tRNA ligase activity, 0005524 ATP binding, 0006420 arginyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 2ZUE_A 2ZUF_A 3FNR_A 1IQ0_A 1F7V_A 1F7U_A 1BS2_A 3GDZ_B.
Probab=29.93 E-value=16 Score=34.11 Aligned_cols=27 Identities=22% Similarity=0.325 Sum_probs=20.1
Q ss_pred eeecccccCCCCC-ccccCCCCeEeecC
Q psy938 8 GLTTPIIESESGE-KFGKSARNAIWLDS 34 (241)
Q Consensus 8 ~lt~pLL~g~dG~-KmsKS~gn~I~L~~ 34 (241)
.+....+.+.||+ |||+-.||+|.|++
T Consensus 274 H~~~g~vl~~~gk~~mstR~G~~i~l~d 301 (354)
T PF00750_consen 274 HVSFGVVLLKDGKVKMSTRKGNVITLDD 301 (354)
T ss_dssp EEEE-EEEETTBEESS-TTTTSSTBHHH
T ss_pred EEEEEEEEcCCCCccccCCCCCceEHHH
Confidence 3555666677997 99999999998885
No 144
>PRK01151 rps17E 30S ribosomal protein S17e; Validated
Probab=27.33 E-value=1.3e+02 Score=21.02 Aligned_cols=51 Identities=16% Similarity=0.264 Sum_probs=36.5
Q ss_pred HhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhc
Q psy938 45 YLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEERRAQKKLAEDLTLLV 97 (241)
Q Consensus 45 ~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~~~~Kk~LA~~i~~~v 97 (241)
++.++....+++|...||. +-++-..+.++...-+. ...+-.+|..||.++
T Consensus 7 ~IKr~a~~lieky~~~ft~-DFe~NK~~v~e~a~i~S-K~lRNrIAGYiT~~~ 57 (58)
T PRK01151 7 YIKRTAEELLEKYPDLFTT-DFETNKKLVEELTNIES-KKVRNRIAGYITRKV 57 (58)
T ss_pred HHHHHHHHHHHHhHHHhcc-cHHHHHHHHHHHhcCcc-HhHHHHHhhhhhhcc
Confidence 4556778899999999984 66777777766554443 346778888888754
No 145
>cd08818 CARD_MDA5_1 Caspase activation and recruitment domain found in MDA5, first repeat. Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), first repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-
Probab=23.48 E-value=1.9e+02 Score=21.93 Aligned_cols=38 Identities=16% Similarity=0.189 Sum_probs=22.8
Q ss_pred HHHHhcCCCHHHHHHHHHHhhcCCChHHHHHHHHHHHHh
Q psy938 57 LLKLFSFDSLAAIEDFKRQNEHKPEERRAQKKLAEDLTL 95 (241)
Q Consensus 57 ~l~~~t~l~~eei~~i~~~~~~~~~~~~~Kk~LA~~i~~ 95 (241)
.+.++++++.|+.+.|.++.... |...|-..|-+.+.+
T Consensus 24 VL~~l~~L~~e~ke~I~a~~~~~-Gn~~AA~~LL~~l~~ 61 (88)
T cd08818 24 VLDYLTFLEAEVKERIRAAAATR-GNIAAAELLLSTLEK 61 (88)
T ss_pred HhhhcccCCHHHHHHHHHHHHcc-CcHHHHHHHHHHHHH
Confidence 44555788899988888765432 334444444444444
No 146
>PRK04156 gltX glutamyl-tRNA synthetase; Provisional
Probab=22.41 E-value=55 Score=32.93 Aligned_cols=23 Identities=9% Similarity=-0.083 Sum_probs=18.8
Q ss_pred CCCceeeecccccCCCCCccccCC
Q psy938 3 VTGDGGLTTPIIESESGEKFGKSA 26 (241)
Q Consensus 3 ~~~~~~lt~pLL~g~dG~KmsKS~ 26 (241)
-..++-..+|+|. .+|.|||||.
T Consensus 321 ~~~P~~~H~~~L~-~~g~kLSKR~ 343 (567)
T PRK04156 321 WEYPETIHYGRLK-IEGFVLSTSK 343 (567)
T ss_pred CCCceEEEcceec-CCCceeeccc
Confidence 3456778999997 6899999997
No 147
>PRK12451 arginyl-tRNA synthetase; Reviewed
Probab=21.52 E-value=40 Score=33.63 Aligned_cols=24 Identities=17% Similarity=0.324 Sum_probs=18.6
Q ss_pred ecccccCCCCCccccCCCCeEeecC
Q psy938 10 TTPIIESESGEKFGKSARNAIWLDS 34 (241)
Q Consensus 10 t~pLL~g~dG~KmsKS~gn~I~L~~ 34 (241)
.+-++. ++|+||||=.|++|.|++
T Consensus 361 ~~g~V~-~~g~kmStR~G~~v~l~d 384 (562)
T PRK12451 361 PFGLIL-KDGKKMSTRKGRVVLLEE 384 (562)
T ss_pred eeeeEe-cCCCCCcCCCCCeeEHHH
Confidence 333343 488899999999999996
Done!