Query psy5542
Match_columns 86
No_of_seqs 119 out of 1026
Neff 7.0
Searched_HMMs 46136
Date Fri Aug 16 20:13:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5542.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5542hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0442 ProS Prolyl-tRNA synth 100.0 2E-29 4.4E-34 192.2 5.5 86 1-86 117-202 (500)
2 KOG2324|consensus 99.9 6E-29 1.3E-33 183.3 4.0 82 5-86 127-208 (457)
3 cd00772 ProRS_core Prolyl-tRNA 99.9 2.9E-27 6.3E-32 168.2 7.6 86 1-86 107-193 (264)
4 PRK12325 prolyl-tRNA synthetas 99.9 5.7E-27 1.2E-31 176.3 7.4 86 1-86 117-202 (439)
5 cd00779 ProRS_core_prok Prolyl 99.9 8.1E-27 1.8E-31 164.9 6.6 86 1-86 101-186 (255)
6 cd00778 ProRS_core_arch_euk Pr 99.9 8.7E-27 1.9E-31 165.2 6.7 86 1-86 107-193 (261)
7 TIGR00409 proS_fam_II prolyl-t 99.9 2.6E-26 5.7E-31 177.4 7.0 86 1-86 117-202 (568)
8 PRK09194 prolyl-tRNA synthetas 99.9 2.9E-26 6.3E-31 176.6 7.1 86 1-86 117-202 (565)
9 PF00587 tRNA-synt_2b: tRNA sy 99.9 8.6E-26 1.9E-30 150.8 6.9 84 2-86 71-156 (173)
10 cd00770 SerRS_core Seryl-tRNA 99.9 8.5E-26 1.8E-30 162.8 7.2 85 1-86 119-207 (297)
11 PRK05431 seryl-tRNA synthetase 99.9 1.4E-25 3E-30 168.5 7.3 85 1-86 238-326 (425)
12 TIGR00414 serS seryl-tRNA synt 99.9 6E-25 1.3E-29 164.8 7.0 85 1-86 240-328 (418)
13 PRK03991 threonyl-tRNA synthet 99.9 1.1E-24 2.5E-29 169.5 7.1 84 1-84 296-381 (613)
14 PRK08661 prolyl-tRNA synthetas 99.9 8.7E-24 1.9E-28 160.5 6.8 82 1-83 119-201 (477)
15 TIGR00408 proS_fam_I prolyl-tR 99.9 5.8E-24 1.3E-28 161.4 5.4 83 1-83 113-196 (472)
16 PLN02837 threonine-tRNA ligase 99.9 1.4E-23 3E-28 163.3 7.5 84 1-85 317-401 (614)
17 PLN02678 seryl-tRNA synthetase 99.9 1.5E-22 3.1E-27 153.2 7.6 86 1-86 243-333 (448)
18 PLN02320 seryl-tRNA synthetase 99.9 4.4E-22 9.6E-27 152.1 8.0 85 1-86 301-389 (502)
19 cd00771 ThrRS_core Threonyl-tR 99.8 3E-21 6.6E-26 139.1 6.1 84 1-85 99-183 (298)
20 PRK14799 thrS threonyl-tRNA sy 99.8 1.2E-20 2.6E-25 145.6 7.5 79 1-80 237-319 (545)
21 PLN02908 threonyl-tRNA synthet 99.8 1.3E-20 2.8E-25 148.2 7.7 81 1-82 390-471 (686)
22 TIGR00418 thrS threonyl-tRNA s 99.8 1.3E-20 2.8E-25 144.6 7.3 84 1-85 270-354 (563)
23 PRK12444 threonyl-tRNA synthet 99.8 1.3E-20 2.8E-25 146.9 7.0 78 1-79 343-421 (639)
24 cd00670 Gly_His_Pro_Ser_Thr_tR 99.8 3.7E-20 8.1E-25 127.4 6.4 84 1-85 76-159 (235)
25 PRK04173 glycyl-tRNA synthetas 99.8 1.3E-20 2.8E-25 142.8 4.4 73 2-75 174-247 (456)
26 PRK00960 seryl-tRNA synthetase 99.8 9.2E-20 2E-24 139.9 7.7 79 1-80 323-403 (517)
27 COG0172 SerS Seryl-tRNA synthe 99.8 5E-19 1.1E-23 133.2 7.3 85 1-86 241-329 (429)
28 cd00774 GlyRS-like_core Glycyl 99.8 2.2E-19 4.7E-24 127.0 3.2 71 4-75 97-168 (254)
29 TIGR00415 serS_MJ seryl-tRNA s 99.8 1.6E-18 3.4E-23 132.7 7.9 81 1-82 323-404 (520)
30 PRK12305 thrS threonyl-tRNA sy 99.8 1.1E-18 2.4E-23 134.4 6.8 84 1-85 276-360 (575)
31 COG0441 ThrS Threonyl-tRNA syn 99.8 1.5E-18 3.3E-23 134.7 6.5 82 1-83 289-371 (589)
32 KOG4163|consensus 99.7 2E-18 4.3E-23 130.0 2.1 79 1-79 173-252 (551)
33 PRK00413 thrS threonyl-tRNA sy 99.7 8.3E-17 1.8E-21 125.1 7.5 82 1-83 340-422 (638)
34 KOG2509|consensus 99.7 1.1E-16 2.3E-21 120.3 5.5 84 2-86 255-342 (455)
35 KOG1637|consensus 99.6 1.5E-15 3.2E-20 115.3 6.2 80 1-81 261-341 (560)
36 PRK14894 glycyl-tRNA synthetas 99.3 2E-12 4.4E-17 99.4 5.5 67 8-75 160-226 (539)
37 TIGR00389 glyS_dimeric glycyl- 99.3 8.2E-13 1.8E-17 102.4 3.1 45 8-52 178-222 (551)
38 PLN02734 glycyl-tRNA synthetas 99.3 1.9E-12 4.2E-17 102.2 3.7 66 10-75 272-378 (684)
39 CHL00201 syh histidine-tRNA sy 99.2 1.6E-11 3.5E-16 92.5 6.2 72 6-83 95-167 (430)
40 COG0423 GRS1 Glycyl-tRNA synth 99.2 9.5E-12 2.1E-16 95.8 4.3 44 9-52 183-226 (558)
41 COG0124 HisS Histidyl-tRNA syn 99.2 4.5E-11 9.7E-16 90.6 5.5 68 11-84 99-167 (429)
42 TIGR00442 hisS histidyl-tRNA s 99.0 1.1E-09 2.3E-14 81.2 7.0 70 8-83 92-162 (397)
43 cd00773 HisRS-like_core Class 99.0 2.1E-09 4.5E-14 75.9 6.3 62 10-77 79-140 (261)
44 KOG2298|consensus 98.9 2.9E-10 6.3E-15 87.1 0.6 55 9-63 205-259 (599)
45 PRK00037 hisS histidyl-tRNA sy 98.9 3.5E-09 7.6E-14 78.7 5.3 61 12-78 97-157 (412)
46 PLN02530 histidine-tRNA ligase 98.9 3.5E-09 7.7E-14 81.0 5.3 59 11-75 162-220 (487)
47 cd00768 class_II_aaRS-like_cor 98.8 1.5E-08 3.2E-13 67.8 6.9 68 10-79 72-141 (211)
48 PRK12420 histidyl-tRNA synthet 98.7 1.4E-08 3E-13 76.2 5.2 67 10-82 96-162 (423)
49 TIGR00443 hisZ_biosyn_reg ATP 98.7 3.5E-08 7.6E-13 71.5 6.1 65 9-79 83-148 (314)
50 PRK12292 hisZ ATP phosphoribos 98.6 9.2E-08 2E-12 71.3 6.0 64 10-79 95-159 (391)
51 PRK12421 ATP phosphoribosyltra 98.4 5.2E-07 1.1E-11 67.6 6.3 64 11-80 99-163 (392)
52 PRK09537 pylS pyrolysyl-tRNA s 98.4 7.4E-07 1.6E-11 67.6 6.6 64 8-79 277-340 (417)
53 PLN02972 Histidyl-tRNA synthet 98.4 4.3E-07 9.3E-12 73.0 5.5 64 11-80 415-480 (763)
54 TIGR02367 PylS pyrrolysyl-tRNA 98.2 4.1E-06 8.9E-11 64.1 6.1 62 10-79 315-376 (453)
55 PF13393 tRNA-synt_His: Histid 98.1 1.7E-05 3.7E-10 56.9 7.0 65 10-80 85-151 (311)
56 PRK12295 hisZ ATP phosphoribos 98.1 1.1E-05 2.3E-10 60.3 5.9 61 10-79 79-141 (373)
57 PRK12293 hisZ ATP phosphoribos 97.9 2.3E-05 4.9E-10 56.6 4.9 53 10-77 92-144 (281)
58 PRK07080 hypothetical protein; 97.8 6.3E-05 1.4E-09 55.4 6.5 62 18-82 157-218 (317)
59 cd00669 Asp_Lys_Asn_RS_core As 97.7 0.00012 2.6E-09 52.5 5.6 40 15-57 71-110 (269)
60 PTZ00326 phenylalanyl-tRNA syn 97.6 9.9E-05 2.1E-09 57.2 4.9 56 12-75 356-411 (494)
61 PRK04172 pheS phenylalanyl-tRN 97.4 0.00031 6.6E-09 54.1 4.8 59 9-75 346-404 (489)
62 PRK09350 poxB regulator PoxA; 97.4 0.00012 2.6E-09 53.3 2.4 44 15-61 80-123 (306)
63 TIGR00462 genX lysyl-tRNA synt 97.3 0.00021 4.6E-09 52.0 3.0 57 15-77 75-131 (304)
64 TIGR00459 aspS_bact aspartyl-t 97.3 0.00055 1.2E-08 54.1 5.3 45 15-62 208-252 (583)
65 cd00777 AspRS_core Asp tRNA sy 97.3 0.00059 1.3E-08 49.3 4.9 45 15-62 71-115 (280)
66 PLN02903 aminoacyl-tRNA ligase 97.2 0.00066 1.4E-08 54.3 5.3 50 15-70 274-323 (652)
67 KOG1936|consensus 97.2 0.00021 4.5E-09 54.9 2.2 60 11-76 148-210 (518)
68 PF00152 tRNA-synt_2: tRNA syn 97.2 0.0016 3.4E-08 47.6 6.5 44 15-61 95-139 (335)
69 cd00775 LysRS_core Lys_tRNA sy 97.2 0.0011 2.4E-08 48.8 5.5 45 15-62 78-122 (329)
70 COG0173 AspS Aspartyl-tRNA syn 97.1 0.0012 2.6E-08 52.0 5.3 50 15-71 211-261 (585)
71 PRK00484 lysS lysyl-tRNA synth 97.0 0.0017 3.6E-08 50.3 5.8 44 15-61 242-285 (491)
72 PRK12820 bifunctional aspartyl 97.0 0.00094 2E-08 53.8 4.5 45 15-62 226-270 (706)
73 PRK00476 aspS aspartyl-tRNA sy 97.0 0.0012 2.6E-08 52.1 4.8 45 15-62 211-255 (588)
74 PRK06462 asparagine synthetase 97.0 0.0013 2.8E-08 48.6 4.6 46 15-60 104-149 (335)
75 PRK12445 lysyl-tRNA synthetase 96.8 0.0021 4.5E-08 50.0 4.8 45 15-62 254-298 (505)
76 cd00776 AsxRS_core Asx tRNA sy 96.8 0.003 6.5E-08 46.3 5.4 46 15-62 91-137 (322)
77 KOG2411|consensus 96.8 0.0014 3.1E-08 51.3 3.4 46 15-63 249-294 (628)
78 PTZ00385 lysyl-tRNA synthetase 96.8 0.0025 5.5E-08 51.1 4.9 44 15-61 303-346 (659)
79 PF01409 tRNA-synt_2d: tRNA sy 96.8 0.0084 1.8E-07 42.7 7.0 61 7-75 96-157 (247)
80 PLN02502 lysyl-tRNA synthetase 96.7 0.0019 4.2E-08 50.8 4.0 44 15-61 299-342 (553)
81 PRK05159 aspC aspartyl-tRNA sy 96.6 0.0043 9.4E-08 47.2 5.1 43 15-59 204-247 (437)
82 PTZ00417 lysine-tRNA ligase; P 96.6 0.0034 7.5E-08 49.7 4.6 44 15-61 323-366 (585)
83 TIGR00499 lysS_bact lysyl-tRNA 96.6 0.0027 5.9E-08 49.2 4.0 45 15-62 242-286 (496)
84 TIGR00458 aspS_arch aspartyl-t 96.4 0.0078 1.7E-07 45.8 5.5 45 15-61 201-245 (428)
85 PRK03932 asnC asparaginyl-tRNA 96.4 0.008 1.7E-07 46.0 5.2 44 15-61 209-253 (450)
86 COG2269 Truncated, possibly in 96.2 0.0055 1.2E-07 45.1 3.3 46 15-63 91-136 (322)
87 PRK02983 lysS lysyl-tRNA synth 96.2 0.0055 1.2E-07 51.5 3.6 45 15-62 840-884 (1094)
88 PLN02850 aspartate-tRNA ligase 96.0 0.0081 1.8E-07 47.0 3.6 42 15-59 293-336 (530)
89 TIGR00457 asnS asparaginyl-tRN 95.9 0.017 3.7E-07 44.4 5.1 43 15-59 212-254 (453)
90 PTZ00401 aspartyl-tRNA synthet 95.7 0.014 2.9E-07 46.1 3.7 45 15-61 281-326 (550)
91 PLN02532 asparagine-tRNA synth 95.6 0.024 5.2E-07 45.4 5.0 54 15-70 391-445 (633)
92 TIGR00470 sepS O-phosphoseryl- 95.6 0.03 6.5E-07 43.9 5.3 59 9-75 203-262 (533)
93 PTZ00425 asparagine-tRNA ligas 95.3 0.048 1.1E-06 43.4 5.6 43 15-59 345-387 (586)
94 PLN02221 asparaginyl-tRNA synt 95.3 0.044 9.5E-07 43.5 5.3 38 15-55 328-366 (572)
95 COG3705 HisZ ATP phosphoribosy 95.1 0.013 2.7E-07 44.5 1.9 68 8-81 90-158 (390)
96 cd00496 PheRS_alpha_core Pheny 95.0 0.077 1.7E-06 36.7 5.4 55 11-73 78-132 (218)
97 PLN02603 asparaginyl-tRNA synt 94.8 0.081 1.8E-06 41.9 5.6 39 15-55 323-361 (565)
98 PLN02853 Probable phenylalanyl 94.7 0.064 1.4E-06 41.9 4.7 55 12-74 341-395 (492)
99 COG0017 AsnS Aspartyl/asparagi 94.6 0.065 1.4E-06 41.3 4.4 53 15-70 201-255 (435)
100 TIGR00468 pheS phenylalanyl-tR 94.4 0.067 1.5E-06 38.8 4.0 56 12-75 149-204 (294)
101 PRK00488 pheS phenylalanyl-tRN 94.0 0.13 2.9E-06 38.4 5.0 55 10-72 182-236 (339)
102 COG0016 PheS Phenylalanyl-tRNA 91.4 0.4 8.8E-06 35.8 4.5 53 13-73 192-244 (335)
103 KOG2784|consensus 90.2 0.18 3.9E-06 38.6 1.7 56 12-75 332-387 (483)
104 COG2024 Phenylalanyl-tRNA synt 87.1 0.11 2.4E-06 40.0 -1.2 63 6-75 200-262 (536)
105 PRK12294 hisZ ATP phosphoribos 86.2 1.6 3.5E-05 31.5 4.4 51 11-75 82-132 (272)
106 COG1190 LysU Lysyl-tRNA synthe 85.6 0.7 1.5E-05 36.3 2.4 37 15-54 250-286 (502)
107 PRK09616 pheT phenylalanyl-tRN 80.9 5.9 0.00013 31.2 5.9 61 9-77 434-494 (552)
108 TIGR02049 gshA_ferroox glutama 73.4 8.9 0.00019 29.5 4.8 48 38-85 216-268 (403)
109 PF15518 L_protein_N: L protei 72.9 13 0.00028 25.6 5.1 37 45-81 93-129 (183)
110 PRK06253 O-phosphoseryl-tRNA s 71.7 7.8 0.00017 30.8 4.3 62 7-75 202-263 (529)
111 PF08886 GshA: Glutamate-cyste 70.3 12 0.00026 28.8 4.9 49 37-85 218-271 (404)
112 PLN02788 phenylalanine-tRNA sy 66.1 12 0.00026 28.7 4.2 57 15-74 149-213 (402)
113 KOG0556|consensus 65.0 5.3 0.00011 31.3 2.1 35 9-45 285-324 (533)
114 KOG0554|consensus 61.6 4.7 0.0001 31.2 1.3 34 15-50 207-240 (446)
115 PF14552 Tautomerase_2: Tautom 60.7 20 0.00044 21.3 3.8 42 31-75 21-63 (82)
116 KOG0081|consensus 56.2 21 0.00045 24.8 3.6 20 66-85 148-167 (219)
117 PF02042 RWP-RK: RWP-RK domain 54.9 13 0.00029 20.5 2.1 33 47-79 14-49 (52)
118 cd00769 PheRS_beta_core Phenyl 52.9 22 0.00049 23.8 3.4 61 7-75 72-140 (198)
119 KOG1885|consensus 52.6 4.4 9.5E-05 32.1 -0.1 38 15-55 295-332 (560)
120 KOG0555|consensus 51.5 13 0.00027 29.2 2.2 55 15-71 310-365 (545)
121 PF14791 DNA_pol_B_thumb: DNA 48.8 11 0.00025 21.4 1.2 13 66-78 46-58 (64)
122 PF14719 PID_2: Phosphotyrosin 48.2 88 0.0019 21.5 5.7 44 20-70 81-124 (182)
123 TIGR00471 pheT_arch phenylalan 47.6 92 0.002 24.6 6.5 61 9-77 436-496 (551)
124 COG0408 HemF Coproporphyrinoge 46.6 21 0.00045 26.3 2.6 52 21-76 177-229 (303)
125 PF00462 Glutaredoxin: Glutare 44.9 32 0.0007 18.2 2.7 22 62-83 12-33 (60)
126 PF12683 DUF3798: Protein of u 43.5 56 0.0012 24.0 4.4 37 45-83 137-173 (275)
127 cd01646 RT_Bac_retron_I RT_Bac 43.3 60 0.0013 20.8 4.2 34 40-77 88-121 (158)
128 PF04175 DUF406: Protein of un 42.6 80 0.0017 19.4 4.8 44 41-84 28-71 (94)
129 PLN02265 probable phenylalanyl 40.6 60 0.0013 26.0 4.5 58 10-75 474-531 (597)
130 PF00078 RVT_1: Reverse transc 33.6 93 0.002 20.0 4.0 34 39-76 160-193 (214)
131 PF03462 PCRF: PCRF domain; I 33.6 1.2E+02 0.0026 18.8 4.6 43 42-85 50-92 (115)
132 cd03487 RT_Bac_retron_II RT_Ba 33.4 95 0.0021 20.9 4.1 35 40-76 140-174 (214)
133 COG3691 Uncharacterized protei 32.3 1.3E+02 0.0028 18.8 4.6 43 42-84 32-75 (98)
134 PF07870 DUF1657: Protein of u 32.1 42 0.00091 18.1 1.8 29 44-72 18-46 (50)
135 PF09830 ATP_transf: ATP adeny 32.0 73 0.0016 17.8 2.8 29 44-75 34-62 (62)
136 cd03029 GRX_hybridPRX5 Glutare 29.9 94 0.002 16.9 3.1 20 64-83 16-35 (72)
137 cd01651 RT_G2_intron RT_G2_int 29.4 1.3E+02 0.0027 19.8 4.2 33 41-77 173-205 (226)
138 PRK10329 glutaredoxin-like pro 28.8 1.1E+02 0.0024 17.6 3.4 21 63-83 15-35 (81)
139 smart00460 TGc Transglutaminas 28.7 1E+02 0.0022 16.4 3.6 21 61-81 12-32 (68)
140 COG3195 Uncharacterized protei 28.5 1.2E+02 0.0027 20.8 3.9 20 58-80 109-128 (176)
141 cd03418 GRX_GRXb_1_3_like Glut 27.9 1.1E+02 0.0024 16.5 3.2 21 63-83 14-34 (75)
142 TIGR02190 GlrX-dom Glutaredoxi 27.6 1E+02 0.0022 17.3 3.0 21 63-83 22-42 (79)
143 PRK08179 prfH peptide chain re 27.5 2.1E+02 0.0046 19.9 5.1 34 52-85 13-46 (200)
144 PF00586 AIRS: AIR synthase re 26.7 1.1E+02 0.0023 17.9 3.1 23 55-77 70-92 (96)
145 TIGR03191 benz_CoA_bzdO benzoy 26.3 1.2E+02 0.0026 23.3 4.0 48 35-85 355-403 (430)
146 cd03027 GRX_DEP Glutaredoxin ( 26.0 1.2E+02 0.0025 16.6 3.0 21 63-83 15-35 (73)
147 PTZ00217 flap endonuclease-1; 25.8 1.4E+02 0.003 22.8 4.2 22 59-80 137-158 (393)
148 PRK05330 coproporphyrinogen II 25.8 74 0.0016 23.7 2.7 50 21-76 174-226 (300)
149 COG1435 Tdk Thymidine kinase [ 25.6 2.4E+02 0.0053 19.8 5.9 61 22-83 37-120 (201)
150 TIGR02194 GlrX_NrdH Glutaredox 25.3 1.3E+02 0.0028 16.5 3.2 20 64-83 14-33 (72)
151 COG0695 GrxC Glutaredoxin and 25.2 1.4E+02 0.0031 17.1 3.4 22 63-84 15-36 (80)
152 PF03445 DUF294: Putative nucl 25.0 1.9E+02 0.0041 18.4 4.5 56 13-76 49-105 (138)
153 TIGR03072 release_prfH putativ 24.7 2.4E+02 0.0053 19.6 5.0 34 52-85 12-45 (200)
154 TIGR03279 cyano_FeS_chp putati 24.7 1.6E+02 0.0035 23.0 4.4 44 32-78 223-266 (433)
155 PRK03980 flap endonuclease-1; 24.6 1.5E+02 0.0032 21.6 4.1 20 61-80 84-103 (292)
156 PF09182 PuR_N: Bacterial puri 24.5 99 0.0021 18.1 2.5 33 52-84 31-64 (70)
157 PRK10638 glutaredoxin 3; Provi 24.0 1.4E+02 0.0029 16.9 3.2 22 63-84 16-37 (83)
158 PLN02873 coproporphyrinogen-II 24.0 81 0.0018 23.2 2.5 49 22-76 148-199 (274)
159 PF13521 AAA_28: AAA domain; P 23.3 1.3E+02 0.0028 19.0 3.3 23 58-80 134-156 (163)
160 PF04908 SH3BGR: SH3-binding, 23.2 1.9E+02 0.0041 17.7 4.2 38 45-83 4-41 (99)
161 TIGR02189 GlrX-like_plant Glut 23.1 1.5E+02 0.0032 17.7 3.3 22 62-83 21-42 (99)
162 TIGR00365 monothiol glutaredox 23.0 1.6E+02 0.0036 17.4 3.5 21 62-82 30-50 (97)
163 KOG2520|consensus 22.8 79 0.0017 26.7 2.5 22 59-80 465-486 (815)
164 PF09967 DUF2201: VWA-like dom 22.3 2.1E+02 0.0046 17.9 4.8 30 54-83 12-41 (126)
165 cd08025 RNR_PFL_like_DUF711 Un 22.0 3.4E+02 0.0073 21.1 5.6 52 33-84 14-75 (400)
166 COG0072 PheT Phenylalanyl-tRNA 21.9 92 0.002 25.3 2.7 67 9-82 424-497 (650)
167 TIGR02200 GlrX_actino Glutared 21.7 1.5E+02 0.0032 15.8 3.1 18 66-83 17-34 (77)
168 PF02120 Flg_hook: Flagellar h 21.6 1.7E+02 0.0036 16.5 4.1 34 51-84 46-79 (85)
169 COG4071 Uncharacterized protei 21.6 1.3E+02 0.0029 21.7 3.2 35 47-84 135-169 (278)
170 TIGR02260 benz_CoA_red_B benzo 21.6 1.4E+02 0.0031 22.8 3.6 43 41-85 350-393 (413)
171 PF09003 Phage_integ_N: Bacter 21.4 1.9E+02 0.0041 17.1 3.5 41 10-55 10-50 (75)
172 COG0562 Glf UDP-galactopyranos 21.3 1.4E+02 0.003 23.0 3.3 38 21-63 39-76 (374)
173 COG1791 Uncharacterized conser 21.2 72 0.0016 22.0 1.7 30 32-61 58-87 (181)
174 COG4921 Uncharacterized protei 20.4 2.2E+02 0.0047 18.5 3.7 43 41-86 39-81 (131)
175 PF10454 DUF2458: Protein of u 20.1 2.2E+02 0.0047 18.8 3.8 23 59-81 104-126 (150)
176 TIGR00743 conserved hypothetic 20.1 2.3E+02 0.005 17.5 5.1 43 42-84 29-72 (95)
No 1
>COG0442 ProS Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=2e-29 Score=192.16 Aligned_cols=86 Identities=47% Similarity=0.739 Sum_probs=83.6
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI 80 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~ 80 (86)
|+++||.||||||+++|||+++||+|.||++||+|.|||+|+|+|+||.+.++|+++|.++.++|.+||.++|+.+..+.
T Consensus 117 ~~~~~i~SYkdLPl~lYQi~~kfRdE~rpr~gllR~REF~mkdaySfh~~~e~a~~~y~~~~~~Y~~if~~i~l~~~~~~ 196 (500)
T COG0442 117 MFRKWIRSYKDLPLKLYQIQSKFRDEKRPRFGLLRGREFLMKDAYSFHADEEDAEETYEKMLDAYSRIFLRLPLIFGPVP 196 (500)
T ss_pred HHHHHhhhhhhCCcceeeeeeEEeccccCCCCccchheeeecccccccCCHHHHHHHHHHHHHHHHHHHHhCCceEEeec
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCC
Q psy5542 81 VRHGAV 86 (86)
Q Consensus 81 ~~~g~~ 86 (86)
+++|.+
T Consensus 197 ad~g~~ 202 (500)
T COG0442 197 ADEGFI 202 (500)
T ss_pred ccCCCC
Confidence 999864
No 2
>KOG2324|consensus
Probab=99.95 E-value=6e-29 Score=183.30 Aligned_cols=82 Identities=50% Similarity=0.931 Sum_probs=79.6
Q ss_pred ccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEecCC
Q psy5542 5 MKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHG 84 (86)
Q Consensus 5 ~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~~g 84 (86)
..+||+|||+++||++++||||.+|++||+|.|||.|+|+|+|+.+++.|.++|+.+.++|.++|+.||+||+.|.|++|
T Consensus 127 ~~lsykqlPi~vYQigrKfRDElrpRfGLlRgREFlMKDmYsFd~~~etA~qTy~~v~~aY~~iFkqL~~pfVkv~AdsG 206 (457)
T KOG2324|consen 127 IPLSYKQLPIRVYQIGRKFRDELRPRFGLLRGREFLMKDMYSFDSDEETAQQTYQLVDQAYDRIFKQLGLPFVKVWADSG 206 (457)
T ss_pred CccccccCcEEeeeechhhhhccCccccchhhHHHHHhhhhcccCCHHHHHHHHHHHHHHHHHHHHHcCCCeEEEeeccc
Confidence 34699999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CC
Q psy5542 85 AV 86 (86)
Q Consensus 85 ~~ 86 (86)
+|
T Consensus 207 ~i 208 (457)
T KOG2324|consen 207 DI 208 (457)
T ss_pred cc
Confidence 86
No 3
>cd00772 ProRS_core Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.
Probab=99.94 E-value=2.9e-27 Score=168.21 Aligned_cols=86 Identities=35% Similarity=0.545 Sum_probs=82.0
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcC-CcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLG-IKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lg-i~~~~~ 79 (86)
|+++++.||++||+++||+++|||+|++|+.||+|+|||+|+|+|+||.+.+++++++..++++|.+++++|| +||+++
T Consensus 107 ~~~~~i~s~~~LPlrl~~~~~~fR~E~r~~~Gl~R~reF~~~e~~~~~~~~e~a~~e~~~~~~~~~~i~~~l~~lp~~~~ 186 (264)
T cd00772 107 IAAKFIKSWKDLPQHLNQIGNKFRDEIRPRFGFLRAREFIMKDGHSAHADAEEADEEFLNMLSAYAEIARDLAAIDFIEG 186 (264)
T ss_pred HHHhhhhhhhccCeeEEEEeCeEeCcCCCCCCcceeeEEEEeeeEEecCCHHHHHHHHHHHHHHHHHHHHhcCCccEEEE
Confidence 4688999999999999999999999999989999999999999999988888999999999999999999999 999999
Q ss_pred EecCCCC
Q psy5542 80 IVRHGAV 86 (86)
Q Consensus 80 ~~~~g~~ 86 (86)
.+++|++
T Consensus 187 ~~~~~d~ 193 (264)
T cd00772 187 EADEGAK 193 (264)
T ss_pred EcCCCcc
Confidence 9999983
No 4
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=99.94 E-value=5.7e-27 Score=176.27 Aligned_cols=86 Identities=43% Similarity=0.677 Sum_probs=81.7
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI 80 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~ 80 (86)
|+++++.|||+||+++||++++||+|.+|+.||+|+|||+|+|+|+||.+.+++.+++.+++++|.++|+.||++++.+.
T Consensus 117 ~~~~~~~syrdLPlrl~q~~~~fR~E~~~~~GL~R~reF~~~D~h~f~~~~~~a~~~~~~~~~~~~~i~~~lgl~~~~v~ 196 (439)
T PRK12325 117 IFRSYVKSYKDLPLNLYHIQWKFRDEIRPRFGVMRGREFLMKDAYSFDLDEEGARHSYNRMFVAYLRTFARLGLKAIPMR 196 (439)
T ss_pred HHHHHhhhchhhchHheEecCEecCCCCCCCCccccceEeEeccEEEeCCHHHHHHHHHHHHHHHHHHHHHcCCceEEEE
Confidence 47889999999999999999999999999889999999999999999999999999999999999999999999999999
Q ss_pred ecCCCC
Q psy5542 81 VRHGAV 86 (86)
Q Consensus 81 ~~~g~~ 86 (86)
+++|.|
T Consensus 197 ~~~~~~ 202 (439)
T PRK12325 197 ADTGPI 202 (439)
T ss_pred EccCCC
Confidence 988863
No 5
>cd00779 ProRS_core_prok Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from prokaryotes and from the mitochondria of eukaryotes.
Probab=99.94 E-value=8.1e-27 Score=164.94 Aligned_cols=86 Identities=48% Similarity=0.822 Sum_probs=81.9
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI 80 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~ 80 (86)
++++++.||++||+++||+++|||+|++|+.||+|+|||+|.|+|+||.++++++++++++++++.++|++|||||+++.
T Consensus 101 ~~~~~i~s~~~LPlr~~~~~~~FR~E~~~~~Gl~R~reF~q~e~~~~~~~~~~a~~~~~~i~~~~~~il~~Lgl~~~~~~ 180 (255)
T cd00779 101 LVANEIKSYKQLPLNLYQIQTKFRDEIRPRFGLMRGREFLMKDAYSFDIDEESLEETYEKMYQAYSRIFKRLGLPFVKVE 180 (255)
T ss_pred HHHhccccHhhCCHHHHhCcceecCCCCCCCceeeeeeEeHhhheeccCCHHHHHHHHHHHHHHHHHHHHHcCCcEEEEE
Confidence 46789999999999999999999999999999999999999999999999888999999999999999999999999999
Q ss_pred ecCCCC
Q psy5542 81 VRHGAV 86 (86)
Q Consensus 81 ~~~g~~ 86 (86)
+++|+|
T Consensus 181 ~~~~~~ 186 (255)
T cd00779 181 ADSGAI 186 (255)
T ss_pred ecCCCC
Confidence 999876
No 6
>cd00778 ProRS_core_arch_euk Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from archaea, the cytoplasm of eukaryotes and some bacteria.
Probab=99.93 E-value=8.7e-27 Score=165.24 Aligned_cols=86 Identities=24% Similarity=0.280 Sum_probs=80.3
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHc-CCcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTL-GIKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~l-gi~~~~~ 79 (86)
++++++.|||+||+++||+++|||+|.+++.||+|+|||+|+|+|+++.+++++.+++++++++|++||++| ||||+.+
T Consensus 107 ~~~~~i~s~r~LPlr~~~~~~~fR~E~~~~~Gl~R~reF~~~d~h~~~~~~e~~~~~~~~~~~~~~~i~~~llgl~~~~~ 186 (261)
T cd00778 107 MFSKWIRSYRDLPLKINQWVNVFRWETKTTRPFLRTREFLWQEGHTAHATEEEAEEEVLQILDLYKEFYEDLLAIPVVKG 186 (261)
T ss_pred HHHhhccchhhcCHHHHhhhhhccCCCCCCCceeEeeeeeeeceeeccCCHHHHHHHHHHHHHHHHHHHHHhCCCeEEEe
Confidence 468899999999999999999999999999999999999999999877778899999999999999999998 9999999
Q ss_pred EecCCCC
Q psy5542 80 IVRHGAV 86 (86)
Q Consensus 80 ~~~~g~~ 86 (86)
..+++++
T Consensus 187 ~~~~~d~ 193 (261)
T cd00778 187 RKTEWEK 193 (261)
T ss_pred cCCcccc
Confidence 9887663
No 7
>TIGR00409 proS_fam_II prolyl-tRNA synthetase, family II. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent groups. This group includes enzymes from Escherichia coli, Bacillus subtilis, Aquifex aeolicus, the spirochete Treponema pallidum, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. The other group includes the Pro-specific domain of a human multifunctional tRNA ligase and the prolyl-tRNA synthetases from the Archaea, the Mycoplasmas, and the spirochete Borrelia burgdorferi.
Probab=99.93 E-value=2.6e-26 Score=177.41 Aligned_cols=86 Identities=44% Similarity=0.820 Sum_probs=82.5
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI 80 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~ 80 (86)
++++++.|||+||+++||+++|||+|.+|+.||+|+|||+|.|+|+||.+++++++++..+.++|.++|++|||||+++.
T Consensus 117 ~~~~~i~syr~LPlrlyqi~~~fR~E~rpr~Gl~R~REF~~~d~~~f~~~~~~a~~e~~~~~~~y~~if~~LgL~~~~v~ 196 (568)
T TIGR00409 117 LARNEIKSYKQLPLNLYQIQTKFRDEIRPRFGLMRGREFIMKDAYSFHSDEESLDATYQKMYQAYSNIFSRLGLDFRPVQ 196 (568)
T ss_pred HHHHHHhhccccCeEEEEeeCEeeCCCCCCCCccccccEEEEEEEEEeCChHHHHHHHHHHHHHHHHHHHHhCCcceEEE
Confidence 35788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCC
Q psy5542 81 VRHGAV 86 (86)
Q Consensus 81 ~~~g~~ 86 (86)
+++|+|
T Consensus 197 ~~~g~~ 202 (568)
T TIGR00409 197 ADSGAI 202 (568)
T ss_pred eccccC
Confidence 999986
No 8
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=99.93 E-value=2.9e-26 Score=176.64 Aligned_cols=86 Identities=47% Similarity=0.852 Sum_probs=82.7
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI 80 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~ 80 (86)
|+++++.||++||+++||++++||+|++|+.||+|+|||+|.|+|+||.+++++++++.+++++|.++|++|||||+++.
T Consensus 117 ~~~~~~~s~~~LP~r~yqi~~~fR~E~rp~~Gl~R~reF~q~d~~~f~~~~~~a~~~~~~~~~~~~~i~~~lgl~~~~~~ 196 (565)
T PRK09194 117 LVRNEIKSYKQLPLNLYQIQTKFRDEIRPRFGLMRGREFIMKDAYSFHADEESLDETYDAMYQAYSRIFDRLGLDFRAVE 196 (565)
T ss_pred HHHhhhhhcccCCeEEEEeeCCccCCCCCCCcccccccEEEeeEEEEcCChHHHHHHHHHHHHHHHHHHHHhCCccEEEE
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCC
Q psy5542 81 VRHGAV 86 (86)
Q Consensus 81 ~~~g~~ 86 (86)
+++|+|
T Consensus 197 ~~~g~~ 202 (565)
T PRK09194 197 ADSGAI 202 (565)
T ss_pred cccccC
Confidence 999986
No 9
>PF00587 tRNA-synt_2b: tRNA synthetase class II core domain (G, H, P, S and T) This Prosite entry contains all class II enzymes. seryl tRNA synthetase structure; InterPro: IPR002314 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 includes the glycine, histidine, proline, threonine and serine tRNA synthetases.; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 3UH0_A 3UGT_C 3UGQ_A 1B76_B 1GGM_B 1ATI_A 1ADY_C 1ADJ_C 2I4O_A 2I4M_B ....
Probab=99.93 E-value=8.6e-26 Score=150.84 Aligned_cols=84 Identities=32% Similarity=0.593 Sum_probs=78.3
Q ss_pred cccccCC-cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCC-cEEEE
Q psy5542 2 VADMKLS-HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGI-KYRKV 79 (86)
Q Consensus 2 ~~~~i~S-yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi-~~~~~ 79 (86)
+++.+.| |++||++++|+|+|||+|+++..|+.|+|||+|.|+|+||++ +++.++++++++.+.++++.||| +|+++
T Consensus 71 ~~~~~~~~~~~LP~~~~~~g~~fR~E~~~~~gl~R~reF~~~e~~~f~~~-~~~~~~~~~~~~~~~~i~~~lgl~~~~~~ 149 (173)
T PF00587_consen 71 FKNEIRSSYRDLPLKLYQIGTCFRNEARPTRGLFRLREFTMDEMHIFCTP-EQSEEEFEELLELYKEILEKLGLEPYRIV 149 (173)
T ss_dssp HHHHEEBHGGGSSEEEEEEEEEEBSSSSSBSTTTS-SEEEEEEEEEEESS-HHHHHHHHHHHHHHHHHHHHTTSGCEEEE
T ss_pred ecceeeeccccCCeEEeecccccccccccccccceeeEeeeeceEEEeCC-cccHHHHHHHHHHHHHHHHHcCCceEEEE
Confidence 5677888 999999999999999999988889999999999999999998 77888999999999999999999 99999
Q ss_pred EecCCCC
Q psy5542 80 IVRHGAV 86 (86)
Q Consensus 80 ~~~~g~~ 86 (86)
.+++|++
T Consensus 150 ~~~~~~~ 156 (173)
T PF00587_consen 150 LSSSGEL 156 (173)
T ss_dssp EEETCTS
T ss_pred EcCCCcc
Confidence 9999875
No 10
>cd00770 SerRS_core Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. SerRS synthetase is a homodimer.
Probab=99.92 E-value=8.5e-26 Score=162.85 Aligned_cols=85 Identities=24% Similarity=0.398 Sum_probs=79.8
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCC----CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPK----FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKY 76 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~----~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~ 76 (86)
|+++++.||++||++++|+++|||+|++|+ .||+|+|||+|+|+|+||++ +++++++.++++.+.+++++||||+
T Consensus 119 l~~~~~~s~~~LPlr~~~~~~~fR~E~~~~g~~~~GL~R~reF~~~e~~~f~~~-e~~~~~~~~~l~~~~~i~~~lgl~~ 197 (297)
T cd00770 119 LHRDEILEEEELPLKYAGYSPCFRKEAGSAGRDTRGLFRVHQFEKVEQFVFTKP-EESWEELEELISNAEEILQELGLPY 197 (297)
T ss_pred HHhcccCCHhhCCchheecChhHhCccccCCCCCCCceEEEeeeeeeEEEEECc-hHHHHHHHHHHHHHHHHHHHcCCcE
Confidence 478899999999999999999999999975 59999999999999999998 6778899999999999999999999
Q ss_pred EEEEecCCCC
Q psy5542 77 RKVIVRHGAV 86 (86)
Q Consensus 77 ~~~~~~~g~~ 86 (86)
+.+.+++|+|
T Consensus 198 ~~~~~~~~dl 207 (297)
T cd00770 198 RVVNICTGDL 207 (297)
T ss_pred EEEEccCccc
Confidence 9999999975
No 11
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=99.92 E-value=1.4e-25 Score=168.53 Aligned_cols=85 Identities=25% Similarity=0.405 Sum_probs=79.8
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCC----CCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRP----KFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKY 76 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~----~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~ 76 (86)
|++++++||++||++++|+++|||+|+++ +.||+|+|||+|+|+|+||++ +++.+++++++++++++|+.|||||
T Consensus 238 l~~~~~~s~~dLPlr~~~~s~~fR~Eag~~g~~~~GL~Rv~qF~k~E~~~f~~~-e~s~~~~~~~l~~~~~i~~~Lglpy 316 (425)
T PRK05431 238 LHRDEILDEEELPLKYTAYSPCFRSEAGSAGRDTRGLIRVHQFDKVELVKFTKP-EDSYAELEELTANAEEILQKLELPY 316 (425)
T ss_pred HHhcccCCHHhCCeeEEEEcCEecCCCCcCCCCCCceeeeeeeeeeeEEEEECH-HHHHHHHHHHHHHHHHHHHHcCCcE
Confidence 57899999999999999999999999976 359999999999999999997 6778899999999999999999999
Q ss_pred EEEEecCCCC
Q psy5542 77 RKVIVRHGAV 86 (86)
Q Consensus 77 ~~~~~~~g~~ 86 (86)
+++.+++|+|
T Consensus 317 r~v~~~s~dl 326 (425)
T PRK05431 317 RVVLLCTGDL 326 (425)
T ss_pred EEEEcCCccc
Confidence 9999999986
No 12
>TIGR00414 serS seryl-tRNA synthetase. This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.
Probab=99.91 E-value=6e-25 Score=164.82 Aligned_cols=85 Identities=20% Similarity=0.327 Sum_probs=78.8
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCC----CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPK----FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKY 76 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~----~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~ 76 (86)
|++++++||++||++++|+++|||+|++|. .||+|+|||+|+|+|+||++ +++.++++++++.+.++|+.|||||
T Consensus 240 ~~~~~i~s~~~LPlr~~~~s~~FR~E~g~~G~~t~GL~Rv~qF~k~E~~~f~~~-e~s~~~~~~~~~~~~~i~~~Lglp~ 318 (418)
T TIGR00414 240 LHRNEILEEEELPIKYTAHSPCFRSEAGSYGKDTKGLIRVHQFNKVELVKFCKP-EESAEELEEMTSDAEQILQELELPY 318 (418)
T ss_pred HHhCcCCChHhCCeeEEEEcccccCCCCccCCCCCccccccceeeeeEEEEcCH-HHHHHHHHHHHHHHHHHHHHcCCce
Confidence 578999999999999999999999999764 39999999999999999997 4566799999999999999999999
Q ss_pred EEEEecCCCC
Q psy5542 77 RKVIVRHGAV 86 (86)
Q Consensus 77 ~~~~~~~g~~ 86 (86)
+++.+++|+|
T Consensus 319 r~v~~~t~dl 328 (418)
T TIGR00414 319 RVVNLCSGDL 328 (418)
T ss_pred EEEecCcccc
Confidence 9999999986
No 13
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=99.91 E-value=1.1e-24 Score=169.54 Aligned_cols=84 Identities=30% Similarity=0.415 Sum_probs=79.1
Q ss_pred CcccccCCcCCcchhhheeec-eeecCCCCCC-CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTS-KFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRK 78 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~-~fR~E~~~~~-Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~ 78 (86)
||+++++|||+||++++|+++ |||+|++|+. ||+|+|||+|+|+|+||++.+++.+++..+++++.++++.||++|++
T Consensus 296 ~~~~~~~SyrdLPlr~~e~~~~~fR~E~~g~l~GL~RvReF~~~D~h~f~~~~eqa~~e~~~~l~~~~~i~~~lGl~~~~ 375 (613)
T PRK03991 296 MLKDMTISYKNLPLKMYELSTYSFRLEQRGELVGLKRLRAFTMPDMHTLCKDMEQAMEEFEKQYEMILETGEDLGRDYEV 375 (613)
T ss_pred HHhCCcCchhhCChhhheecchheeCCCCCCCcCcccccceEeeeEEEEECCHHHHHHHHHHHHHHHHHHHHHcCCCeEE
Confidence 578999999999999999999 9999999975 99999999999999999987888999999999999999999999999
Q ss_pred EEecCC
Q psy5542 79 VIVRHG 84 (86)
Q Consensus 79 ~~~~~g 84 (86)
+..+++
T Consensus 376 ~~~~t~ 381 (613)
T PRK03991 376 AIRFTE 381 (613)
T ss_pred EecCHH
Confidence 887664
No 14
>PRK08661 prolyl-tRNA synthetase; Provisional
Probab=99.89 E-value=8.7e-24 Score=160.54 Aligned_cols=82 Identities=26% Similarity=0.267 Sum_probs=76.3
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHH-HHcCCcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVF-NTLGIKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~-~~lgi~~~~~ 79 (86)
++++++.|||+||+++||+++|||+|.+ ..||+|+|||+|+|+|+||.+++++.+++.+++++|.+++ +.||||++.+
T Consensus 119 ~~~~~i~SyrdLPlrl~q~~~vfR~E~~-~rgl~R~rEF~~~E~h~~~~~~eea~~e~~~~l~~y~~i~~~~Lglp~~~~ 197 (477)
T PRK08661 119 MYKKWIQSYRDLPLLYNQWVNVVRWETK-TRPFLRTREFLWQEGHTAHATEEEAEEETLEMLEIYKEFFEDYLAIPVIIG 197 (477)
T ss_pred HHHhhhcchhhcCHHHhcccceeeCCCC-CCCcceeeeEEEcceeeeeCCHHHHHHHHHHHHHHHHHHHHHhcCCeEEEE
Confidence 4789999999999999999999999998 4599999999999999998889999999999999999999 8899999988
Q ss_pred EecC
Q psy5542 80 IVRH 83 (86)
Q Consensus 80 ~~~~ 83 (86)
..+.
T Consensus 198 ~~~~ 201 (477)
T PRK08661 198 KKTE 201 (477)
T ss_pred ecCh
Confidence 7664
No 15
>TIGR00408 proS_fam_I prolyl-tRNA synthetase, family I. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi. The other family includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae.
Probab=99.89 E-value=5.8e-24 Score=161.37 Aligned_cols=83 Identities=23% Similarity=0.267 Sum_probs=77.6
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHH-HcCCcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFN-TLGIKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~-~lgi~~~~~ 79 (86)
||++++.|||+||+++||+++|||+|.+++.||+|+|||+|+|+|+++.+.+++.+++..++++|.++|+ .||||++.+
T Consensus 113 ~~~~~i~S~rdLPlr~~q~~~vfR~E~~~~~gl~R~rEF~~~e~h~~~~~~e~a~~e~~~~l~~y~~i~~~~lglp~~~~ 192 (472)
T TIGR00408 113 MFKKWVKSYTDLPLKINQWVNVFRYETKHTRPFLRTREFTWQEAHTAHATAEEAEEQVLRALDIYKEFIENSLAIPYFVG 192 (472)
T ss_pred HHhccccChhhcCHHHhheeeeecCCCCCCCCcceeeeeehhhhhhhhCCHHHHHHHHHHHHHHHHHHHHhccCCeEEEE
Confidence 5789999999999999999999999999888999999999999998777789999999999999999998 899999988
Q ss_pred EecC
Q psy5542 80 IVRH 83 (86)
Q Consensus 80 ~~~~ 83 (86)
..+.
T Consensus 193 ~~~~ 196 (472)
T TIGR00408 193 RKPE 196 (472)
T ss_pred ecCc
Confidence 7654
No 16
>PLN02837 threonine-tRNA ligase
Probab=99.89 E-value=1.4e-23 Score=163.29 Aligned_cols=84 Identities=19% Similarity=0.272 Sum_probs=77.5
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCC-CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~-Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~ 79 (86)
||+++++|||+||++++|+++|||+|++|.. ||+|+|||+|+|+|+||++ +++++++..+++.+.++++.||+|++.+
T Consensus 317 ~~~~~~~SyrdLPlr~~~~~~~~R~E~~g~~~GL~RvreF~~~e~h~f~~~-~q~~~e~~~~l~~~~~~~~~lg~~~~~~ 395 (614)
T PLN02837 317 VYKRKLHSYRDLPIRVAELGTVYRYELSGSLHGLFRVRGFTQDDAHIFCLE-DQIKDEIRGVLDLTEEILKQFGFSKYEI 395 (614)
T ss_pred HHhCccCChhHCCHhhEeecccccCCCCCCCcCcccccceEECeEEEEeCH-HHHHHHHHHHHHHHHHHHHHcCCCeEEE
Confidence 5789999999999999999999999998754 9999999999999999997 4578899999999999999999999998
Q ss_pred EecCCC
Q psy5542 80 IVRHGA 85 (86)
Q Consensus 80 ~~~~g~ 85 (86)
.++++.
T Consensus 396 ~~~t~~ 401 (614)
T PLN02837 396 NLSTRP 401 (614)
T ss_pred EecCCc
Confidence 888763
No 17
>PLN02678 seryl-tRNA synthetase
Probab=99.87 E-value=1.5e-22 Score=153.23 Aligned_cols=86 Identities=22% Similarity=0.392 Sum_probs=78.9
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCC----CCCceeeceeeeeeeeEEcCChH-hHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRP----KFGLMRSREFLMKDLYAFTASEV-DANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~----~~Gl~R~reF~~~d~~~f~~~~~-~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
+++++++||++||++++++++|||.|+++ ..||+|+|||+|+|++.||.+++ ++.++++++++.++.||+.||||
T Consensus 243 ~h~~~~~s~~eLPlr~~~~s~cfR~Eags~G~~~~GL~RvhqF~KvE~f~~~~pe~~~s~~~~e~~l~~~~~i~~~L~lp 322 (448)
T PLN02678 243 YHRGDWIDPKELPIRYAGYSTCFRKEAGSHGRDTLGIFRVHQFEKVEQFCITSPNGNESWEMHEEMLKNSEDFYQSLGIP 322 (448)
T ss_pred HHhcccCCHHhCCceeEEeccccccccccCCCcCCcceEEEEEEEEEEEEEECCCchhHHHHHHHHHHHHHHHHHHcCCC
Confidence 46789999999999999999999999973 34999999999999999999864 36779999999999999999999
Q ss_pred EEEEEecCCCC
Q psy5542 76 YRKVIVRHGAV 86 (86)
Q Consensus 76 ~~~~~~~~g~~ 86 (86)
|+++.+|+|||
T Consensus 323 yrvv~~~sgdl 333 (448)
T PLN02678 323 YQVVSIVSGAL 333 (448)
T ss_pred eEEEeeccccc
Confidence 99999999997
No 18
>PLN02320 seryl-tRNA synthetase
Probab=99.87 E-value=4.4e-22 Score=152.09 Aligned_cols=85 Identities=21% Similarity=0.377 Sum_probs=78.2
Q ss_pred CcccccCCcCCcchhhheeeceeecCCC--CC--CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELR--PK--FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKY 76 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~--~~--~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~ 76 (86)
++.++++||++||++++.+++|||.|++ |+ .||+|+|||+++|+|+||.+ ++++++++++++..+++|+.|||||
T Consensus 301 ~~~~~ils~~dLPlRy~~~s~cFR~EAgs~G~d~rGL~RvhQF~KvE~~if~~p-eqs~~e~e~ll~~~e~i~~~LgLpy 379 (502)
T PLN02320 301 IHMDSILLESALPLKYVAFSHCFRTEAGAAGAATRGLYRVHQFSKVEMFVICRP-EESESFHEELIQIEEDLFTSLGLHF 379 (502)
T ss_pred cccccccCHhhCCceeEEeccccccccccCCCcCCCceeeeeeecccEEEEECH-HHHHHHHHHHHHHHHHHHHHcCCCe
Confidence 3568899999999999999999999998 42 39999999999999999997 5567799999999999999999999
Q ss_pred EEEEecCCCC
Q psy5542 77 RKVIVRHGAV 86 (86)
Q Consensus 77 ~~~~~~~g~~ 86 (86)
+++..++|||
T Consensus 380 rvv~l~tgDL 389 (502)
T PLN02320 380 KTLDMATADL 389 (502)
T ss_pred EEEEecCCcc
Confidence 9999999997
No 19
>cd00771 ThrRS_core Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.
Probab=99.84 E-value=3e-21 Score=139.08 Aligned_cols=84 Identities=24% Similarity=0.265 Sum_probs=75.1
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCC-CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPK-FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~-~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~ 79 (86)
++++++.||++||+|++++++|||+|+++. .||+|+|||+|.|+|+||++ +++++++.++++++.++++.||++...+
T Consensus 99 ~~~~~~~s~~~LPlr~~~~g~vfR~E~~~~~~Gl~R~reF~q~e~~i~~~~-e~~~~e~~e~l~~~~~~l~~lgl~~~~i 177 (298)
T cd00771 99 IFKSKPRSYRDLPLRLAEFGTVHRYEQSGALHGLTRVRGFTQDDAHIFCTP-DQIKEEIKGVLDLIKEVYSDFGFFDYKV 177 (298)
T ss_pred HHHhhccchhhCCeEEEEecCcccCCCCCCCCCccccccEEECCEEEEeCC-cchHHHHHHHHHHHHHHHHHcCCCcEEE
Confidence 467889999999999999999999998874 59999999999999999997 5667788999999999999999998888
Q ss_pred EecCCC
Q psy5542 80 IVRHGA 85 (86)
Q Consensus 80 ~~~~g~ 85 (86)
..++++
T Consensus 178 ~l~~~~ 183 (298)
T cd00771 178 ELSTRP 183 (298)
T ss_pred EEEcCh
Confidence 777653
No 20
>PRK14799 thrS threonyl-tRNA synthetase; Provisional
Probab=99.83 E-value=1.2e-20 Score=145.59 Aligned_cols=79 Identities=19% Similarity=0.325 Sum_probs=70.6
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCC-CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc---E
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK---Y 76 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~-Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~---~ 76 (86)
||+++++|||+||++++|+++|||+|.+++. ||+|+|||+|+|+|+||++ +++.+++.++++++.++|+.||++ +
T Consensus 237 ~~~~~~~SyrdLPlR~~e~g~vfR~E~sg~l~GL~RvReF~Q~DaHif~~~-~q~~~E~~~~l~~i~~vy~~fG~~~~~~ 315 (545)
T PRK14799 237 IYKSKPRTYRDLPIRFSEFGHVYRWEKKGELYGLLRVRGFVQDDGHIFLRE-DQLREEIKMLISKTVEVWHKFGFKDDDI 315 (545)
T ss_pred HHhccccChhhCCHhhEEecceecCCCCCCccccccceeEEEcccEEEeCH-HHHHHHHHHHHHHHHHHHHHhCCCcccE
Confidence 5789999999999999999999999999876 9999999999999999996 566567889999999999999996 5
Q ss_pred EEEE
Q psy5542 77 RKVI 80 (86)
Q Consensus 77 ~~~~ 80 (86)
....
T Consensus 316 ~i~l 319 (545)
T PRK14799 316 KPYL 319 (545)
T ss_pred EEEE
Confidence 5443
No 21
>PLN02908 threonyl-tRNA synthetase
Probab=99.83 E-value=1.3e-20 Score=148.19 Aligned_cols=81 Identities=30% Similarity=0.370 Sum_probs=73.6
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCC-CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~-Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~ 79 (86)
||++++.|||+||++++++++|||+|.+|.. ||+|+|||+|+|+|+||++ +++.+++.++++.+.++|+.||++|+..
T Consensus 390 ~~~~~~~s~r~LPlr~~~~g~~fR~E~~~~l~Gl~RvReF~q~d~~if~~~-~q~~~e~~~~l~~~~~v~~~lG~~~~~~ 468 (686)
T PLN02908 390 MFAHRVRSYRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCRE-DQIKDEVKGVLDFLDYVYEVFGFTYELK 468 (686)
T ss_pred HHhccccChhhCCHhHEEeeccccCCCCcCCcCccccccEEEeeEEEEcCH-HHHHHHHHHHHHHHHHHHHHCCCcEEEE
Confidence 5788999999999999999999999999865 9999999999999999996 5667788999999999999999998876
Q ss_pred Eec
Q psy5542 80 IVR 82 (86)
Q Consensus 80 ~~~ 82 (86)
..+
T Consensus 469 ls~ 471 (686)
T PLN02908 469 LST 471 (686)
T ss_pred EeC
Confidence 544
No 22
>TIGR00418 thrS threonyl-tRNA synthetase. This model represents the threonyl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. Note that B. subtilis has closely related isozymes thrS and thrZ. The N-terminal regions are quite dissimilar between archaeal and eubacterial forms, while some eukaryotic forms are missing sequence there altogether..
Probab=99.83 E-value=1.3e-20 Score=144.62 Aligned_cols=84 Identities=21% Similarity=0.305 Sum_probs=77.1
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCC-CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPK-FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~-~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~ 79 (86)
+|+++++||++||+++|+++++||+|++|+ .||+|+|||+|.|+|+||. .+++++++.++++++.++++.||+++..+
T Consensus 270 ~~~~~~~s~~~lP~rl~~~g~~fR~E~~g~~~Gl~R~reF~q~~~~~~~~-~~~~~~e~~~~i~~~~~~~~~lgl~~~~~ 348 (563)
T TIGR00418 270 IFKSSLRSYRDLPLRIAELGYSHRYEQSGELHGLMRVRGFTQDDAHIFCT-EDQIKEEFKNQFRLIQKVYSDFGFSFDKY 348 (563)
T ss_pred HHhCcCCChHHCCceeeEeccccCCCCCcCCcCcccccceEEeeeEEEcC-HHHHHHHHHHHHHHHHHHHHHcCCCeEEE
Confidence 367889999999999999999999999985 5999999999999999999 67888899999999999999999998888
Q ss_pred EecCCC
Q psy5542 80 IVRHGA 85 (86)
Q Consensus 80 ~~~~g~ 85 (86)
.+++|+
T Consensus 349 ~l~~~~ 354 (563)
T TIGR00418 349 ELSTRD 354 (563)
T ss_pred EEeCCC
Confidence 888764
No 23
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=99.82 E-value=1.3e-20 Score=146.88 Aligned_cols=78 Identities=27% Similarity=0.404 Sum_probs=70.9
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCC-CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPK-FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~-~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~ 79 (86)
+|++++.||++||+++||+++|||+|.+|. .||+|+|||+|+|+|+||+++ ++++++..+++++.++|+.||++|+..
T Consensus 343 ~~~~~~~sy~~LP~r~~~~g~~fR~E~~~~~~Gl~R~reF~q~d~~~f~~~~-~~~~e~~~~~~~~~~i~~~lgl~~~~~ 421 (639)
T PRK12444 343 MFKNKLHSYRELPIRMCEFGQVHRHEFSGALNGLLRVRTFCQDDAHLFVTPD-QIEDEIKSVMAQIDYVYKTFGFEYEVE 421 (639)
T ss_pred HHhCcccChhhCCceeEEeccccCCCCCcCCcCcceeeeeEEccEEEECCHH-HHHHHHHHHHHHHHHHHHHcCCcEEEE
Confidence 468899999999999999999999998874 599999999999999999964 578889999999999999999998753
No 24
>cd00670 Gly_His_Pro_Ser_Thr_tRS_core Gly_His_Pro_Ser_Thr_tRNA synthetase class II core domain. This domain is the core catalytic domain of tRNA synthetases of the subgroup containing glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. These enzymes belong to class II aminoacyl-tRNA synthetases (aaRS) based upon their structure and the presence of three characteristic sequence motifs in the core domain. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ and the accessory subunit of mitochondrial polymerase gamma (Pol gamma b) . Most class II tRNA synthetases are dimers, with this subgroup consisting of mostly homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.
Probab=99.81 E-value=3.7e-20 Score=127.42 Aligned_cols=84 Identities=30% Similarity=0.367 Sum_probs=75.8
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVI 80 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~ 80 (86)
++++++.||++||++++|+++|||+|.++..|+.|+|||+|.|+|+||.++ ++.+...++++.+.++++.||+++.++.
T Consensus 76 ~~~~~~~~~~~lP~r~~~~g~~fR~E~~~~~gl~R~reF~q~e~~~~~~~~-~~~~~~~e~~~~~~~~l~~lgl~~~i~~ 154 (235)
T cd00670 76 IFSGEILSYRALPLRLDQIGPCFRHEPSGRRGLMRVREFRQVEYVVFGEPE-EAEEERREWLELAEEIARELGLPVRVVV 154 (235)
T ss_pred HHhccCccchhcCeeeeeecccccCCCCCCCCChhheeeeeceEEEEcCHH-HHHHHHHHHHHHHHHHHHHcCCcEEEEE
Confidence 357788999999999999999999999888789999999999999999975 5566789999999999999999999988
Q ss_pred ecCCC
Q psy5542 81 VRHGA 85 (86)
Q Consensus 81 ~~~g~ 85 (86)
++.++
T Consensus 155 ~~~~~ 159 (235)
T cd00670 155 ADDPF 159 (235)
T ss_pred ccChh
Confidence 87764
No 25
>PRK04173 glycyl-tRNA synthetase; Provisional
Probab=99.81 E-value=1.3e-20 Score=142.79 Aligned_cols=73 Identities=23% Similarity=0.350 Sum_probs=68.1
Q ss_pred cccccCCcC-CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 2 VADMKLSHK-ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 2 ~~~~i~Syr-~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
|++++.||| +||++++|+++|||+|.+|..||+|+|||+|+|+|+||++ +++.+++..+++.+..++..||++
T Consensus 174 f~~~~~syr~dLPlr~aq~g~~~RnE~s~~~gL~RvReF~q~e~hiF~~p-eq~~~e~~~~l~~~~~~l~~lG~~ 247 (456)
T PRK04173 174 FKNVLRTARKKLPFGIAQIGKSFRNEITPRNFIFRTREFEQMELEFFVKP-GTDNEWFAYWIELRKNWLLDLGID 247 (456)
T ss_pred HHHHHHhccccCCeeeeEEchhHhCccCCCCCceeeceeeeeEEEEEECc-ChHHHHHHHHHHHHHHHHHHcCCC
Confidence 678889999 9999999999999999999779999999999999999997 456778899999999999999997
No 26
>PRK00960 seryl-tRNA synthetase; Provisional
Probab=99.80 E-value=9.2e-20 Score=139.88 Aligned_cols=79 Identities=16% Similarity=0.213 Sum_probs=70.5
Q ss_pred CcccccCCcCCcchhhhe-eeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEE
Q psy5542 1 MVADMKLSHKALPLLLYQ-FTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRK 78 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q-~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~ 78 (86)
||+++++||++||+++++ .++|||+|.++..||+|+|||+|.|+|.||++ +++.+++.++++....+++.|||| ++.
T Consensus 323 ~~~~~ils~rdLPLrl~e~sG~cFR~EsGs~~GL~RV~eF~kvE~h~f~tp-Eqs~ee~e~ll~~~e~i~~~LgLp~~r~ 401 (517)
T PRK00960 323 FFQGETVDVDELPIKFFDRSGWTYRWEGGGAHGLERVNEFHRIEIVWLGTP-EQVEEIRDELLKYAHILAEKLDLEYWRE 401 (517)
T ss_pred HHhCCcCChhhCCHHHhhccCCceeCCCCCCCCCcccceeEEEEEEEEeCH-HHHHHHHHHHHHHHHHHHHHcCCCceEE
Confidence 478899999999999999 55999999666669999999999999999996 566778899999999999999999 776
Q ss_pred EE
Q psy5542 79 VI 80 (86)
Q Consensus 79 ~~ 80 (86)
+.
T Consensus 402 v~ 403 (517)
T PRK00960 402 VG 403 (517)
T ss_pred ec
Confidence 66
No 27
>COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=99.78 E-value=5e-19 Score=133.24 Aligned_cols=85 Identities=24% Similarity=0.353 Sum_probs=79.3
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCC----CCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRP----KFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKY 76 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~----~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~ 76 (86)
|++++|++-.+||++++.+++|||.|+++ +.||+|+|||.+.|+..||.++++ .++++++....+++++.|+|||
T Consensus 241 l~~~Eil~~~~LP~k~~~~S~cFR~EAGs~GrdtrGliRvHQF~KVE~v~~~~Pe~S-~~~~E~m~~~ae~il~~LeLPy 319 (429)
T COG0172 241 LHRDEILDEEDLPIKYTAYSPCFRSEAGSAGKDTRGLIRVHQFDKVELVVITKPEES-EEELEEMLGNAEEVLQELELPY 319 (429)
T ss_pred hhcccccccccCCeeeEEEChhhhcccccccccccceeeeeeeeeEEEEEEeCcchh-HHHHHHHHHHHHHHHHHhCCCc
Confidence 57899999999999999999999999988 559999999999999999998666 4578999999999999999999
Q ss_pred EEEEecCCCC
Q psy5542 77 RKVIVRHGAV 86 (86)
Q Consensus 77 ~~~~~~~g~~ 86 (86)
+++..|||||
T Consensus 320 Rvv~lctGDl 329 (429)
T COG0172 320 RVVNLCTGDL 329 (429)
T ss_pred eEeeeccCCc
Confidence 9999999997
No 28
>cd00774 GlyRS-like_core Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP binding and hydrolysis. This alignment contains only sequences from the GlyRS form which homodimerizes. The heterotetramer glyQ is in a different family of class II aaRS. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the N-terminus of the accessory subunit of mitochondrial polymerase gamma (Pol gamma b). Pol gamma b stimulates processive DNA synthesis and is functional as a homodimer, which can associate with the catalytic subunit Pol gamma alpha to form a heterotrimer. Despite significant both structural and sequence similarity with Gly
Probab=99.76 E-value=2.2e-19 Score=127.01 Aligned_cols=71 Identities=21% Similarity=0.359 Sum_probs=63.6
Q ss_pred cccCCc-CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 4 DMKLSH-KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 4 ~~i~Sy-r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
+...|+ ++||++++|+++|||+|.+|+.||+|+|||+|.|+|+||+++ ++.+++..+.+.+.++++++|++
T Consensus 97 ~~~~~~~~~lP~~~~qig~~fR~E~~~~~gl~R~ReF~q~d~~~f~~~~-~~~e~~~~v~~~~~~~l~~~G~~ 168 (254)
T cd00774 97 NLLEFNRRKLPFGVAQIGKSFRNEISPRNGLFRVREFTQAEIEFFVDPE-KSHPWFDYWADQRLKWLPKFAQS 168 (254)
T ss_pred HHHHHhCCCCCchhhhhchhhccccCcccceeeeccchhhheeeeECCC-CchHHHHHHHHHHHHHHHHcCCC
Confidence 334455 599999999999999999999999999999999999999865 66779999999999999999974
No 29
>TIGR00415 serS_MJ seryl-tRNA synthetase, Methanococcus jannaschii family. The seryl-tRNA synthetases from a few of the Archaea, represented by this model, are very different from the set of mutually more closely related seryl-tRNA synthetases from Eubacteria, Eukaryotes, and other Archaea. Although distantly homologous, the present set differs enough not to be recognized by the pfam model tRNA-synt_2b that recognizes the remainder of seryl-tRNA synthetases among oither class II amino-acyl tRNA synthetases.
Probab=99.76 E-value=1.6e-18 Score=132.71 Aligned_cols=81 Identities=14% Similarity=0.200 Sum_probs=73.9
Q ss_pred CcccccCCcCCcchhhheee-ceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFT-SKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~-~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~ 79 (86)
|++++++|+++||++++|++ +|||+|.++..||+|++||.|.|+|.++++ +++.+..+++++.+..+++.|||||+++
T Consensus 323 ~~a~~Ils~~dLPlk~~~~s~~CFR~EaGstrGL~RvhEF~kvE~v~~~tp-Eea~e~~e~mle~~~~~l~~L~Lpyrv~ 401 (520)
T TIGR00415 323 FFEGEVIDAEDKPIKFFDRSGWTYRWEAGGAKGLDRVHEFLRVECVWIAEP-EETEEIRDKTLELAEDAADELDLEWWTE 401 (520)
T ss_pred HHhccccChhhCCeeEEEEecCeEeCCCCCCCCCceeeEEEEEEEEEEeCH-HHHHHHHHHHHHHHHHHHHHcCCCeEEe
Confidence 57899999999999999955 799999988899999999999999998775 5667788999999999999999999999
Q ss_pred Eec
Q psy5542 80 IVR 82 (86)
Q Consensus 80 ~~~ 82 (86)
.|+
T Consensus 402 ~ad 404 (520)
T TIGR00415 402 VGD 404 (520)
T ss_pred ecC
Confidence 766
No 30
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=99.76 E-value=1.1e-18 Score=134.39 Aligned_cols=84 Identities=23% Similarity=0.253 Sum_probs=72.8
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCC-CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPK-FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~-~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~ 79 (86)
+++++..||++||++++++++|||+|.++. .|+.|+|||+|.|+|+||.++ ++.+++.++++++.++++.||++...+
T Consensus 276 ~~~~~~~s~~~lP~r~~~~g~~fR~E~~~~~~Gl~R~reF~q~~~~if~~~~-~~~~e~~e~i~l~~~~~~~lgl~~~~i 354 (575)
T PRK12305 276 IYKSRLRSYRDLPLRLAEFGTVYRYEKSGVLHGLTRVRGFTQDDAHIFCTPD-QIEDEILKVLDFVLELLKDFGFKDYYL 354 (575)
T ss_pred HHhcccCChhhCCHhhEEecccccCCCCCCCcCcccccCeEEcceEEEeCHH-HHHHHHHHHHHHHHHHHHHcCCCeEEE
Confidence 367788899999999999999999998754 599999999999999999854 445577999999999999999997667
Q ss_pred EecCCC
Q psy5542 80 IVRHGA 85 (86)
Q Consensus 80 ~~~~g~ 85 (86)
..++++
T Consensus 355 ~l~~r~ 360 (575)
T PRK12305 355 ELSTRE 360 (575)
T ss_pred EEeCCC
Confidence 777764
No 31
>COG0441 ThrS Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=99.75 E-value=1.5e-18 Score=134.74 Aligned_cols=82 Identities=24% Similarity=0.314 Sum_probs=73.4
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCC-CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~-Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~ 79 (86)
||++..+|||+||+++++.+.|||+|++|.. ||.|+|.|+|+|+|+||+ .+++.+++..+++....+++.+|++...+
T Consensus 289 ifk~~~~SYR~LP~r~~E~g~v~R~E~SGal~GL~RvR~ftqdDaHifc~-~dQi~~E~~~~~~~i~~v~~~fg~~~y~~ 367 (589)
T COG0441 289 IFKSGLRSYRELPLRLAEFGYVYRYEKSGALHGLMRVRGFTQDDAHIFCT-PDQIKDEFKGILELILEVYKDFGFTDYEV 367 (589)
T ss_pred HHhcCCcceeccchhhhhcceeecccCcchhhccccccceeecccceecc-HHHHHHHHHHHHHHHHHHHHhcCCceEEE
Confidence 4788999999999999999999999999998 999999999999999999 67777788999999999999999984444
Q ss_pred EecC
Q psy5542 80 IVRH 83 (86)
Q Consensus 80 ~~~~ 83 (86)
..++
T Consensus 368 ~ls~ 371 (589)
T COG0441 368 KLST 371 (589)
T ss_pred EEec
Confidence 4443
No 32
>KOG4163|consensus
Probab=99.71 E-value=2e-18 Score=130.01 Aligned_cols=79 Identities=28% Similarity=0.318 Sum_probs=73.8
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHH-cCCcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNT-LGIKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~-lgi~~~~~ 79 (86)
+|+.||+||||||++|+||+++-|.|-+....++|.|||+|+|+|+-+.+.++|+++..+++++|..++.. |.+|++.-
T Consensus 173 ~yakWi~ShRDLPlkLNQW~nVvRWEfk~p~PFlRtrEFLWQEGHTAfat~~eA~eEvlqiLdlYa~vy~ellAiPVvkG 252 (551)
T KOG4163|consen 173 YYAKWIQSHRDLPLKLNQWCNVVRWEFKHPQPFLRTREFLWQEGHTAFATPEEAEEEVLQILDLYARVYEELLAIPVVKG 252 (551)
T ss_pred HHHHHHHhhccCchhhhhhhhheeeeccCCCcchhhhHHHHhcCcchhCCHhHHHHHHHHHHHHHHHHHHhhhccccccC
Confidence 47899999999999999999999999997778999999999999999999999999999999999999997 78898753
No 33
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=99.68 E-value=8.3e-17 Score=125.09 Aligned_cols=82 Identities=27% Similarity=0.300 Sum_probs=68.9
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCC-CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPK-FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~-~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~ 79 (86)
+++++..||++||+|+|++++|||+|.++. .||.|+|||+|.|+|+||.+++ +.+++.++++++.++|+.||++-..+
T Consensus 340 ~~~~~~~s~~~lP~r~~~~g~~fR~E~~~~~~Gl~R~reF~q~~~~~~g~~~~-~~~e~~eii~l~~~~~~~lg~~~~~i 418 (638)
T PRK00413 340 IYKQGLRSYRDLPLRLAEFGTVHRYEPSGALHGLMRVRGFTQDDAHIFCTPEQ-IEEEVKKVIDLILDVYKDFGFEDYEV 418 (638)
T ss_pred HHhCcCCChhhCCceeeeccCeecCCCCCCCcCcceeeeeEEeeEEEEcCHHH-HHHHHHHHHHHHHHHHHHcCCceEEE
Confidence 356788999999999999999999997765 4999999999999999998644 44466999999999999999964444
Q ss_pred EecC
Q psy5542 80 IVRH 83 (86)
Q Consensus 80 ~~~~ 83 (86)
..++
T Consensus 419 ~l~~ 422 (638)
T PRK00413 419 KLST 422 (638)
T ss_pred EEec
Confidence 4444
No 34
>KOG2509|consensus
Probab=99.66 E-value=1.1e-16 Score=120.28 Aligned_cols=84 Identities=21% Similarity=0.342 Sum_probs=76.2
Q ss_pred cccccCCcCCcchhhheeeceeecCCCCCC----CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEE
Q psy5542 2 VADMKLSHKALPLLLYQFTSKFRDELRPKF----GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYR 77 (86)
Q Consensus 2 ~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~----Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~ 77 (86)
++++...-.+||+++..+++|||.|.++.+ ||+|+|||++.|+...|.++++. +.+++|++.-+++|+.|||||+
T Consensus 255 ~~~e~~~~~~lPiK~vg~S~CfR~EaGs~G~d~~GlyRVHqF~KVE~Fvit~Pe~S~-~~~eEmi~~~eef~qsLgip~r 333 (455)
T KOG2509|consen 255 HRDEWLEEDQLPIKYVGVSRCFRAEAGSHGKDTKGLYRVHQFEKVEQFVITGPEDSW-EMLEEMINNQEEFYQSLGLPYR 333 (455)
T ss_pred hcccccccccCceeeeehhHHHHHHhhhcccccccceeeeeeeeeEEEEecCcchhH-HHHHHHHHHHHHHHHHhCCcee
Confidence 567778889999999999999999985543 99999999999999999998764 4889999999999999999999
Q ss_pred EEEecCCCC
Q psy5542 78 KVIVRHGAV 86 (86)
Q Consensus 78 ~~~~~~g~~ 86 (86)
++...+|++
T Consensus 334 vl~m~S~eL 342 (455)
T KOG2509|consen 334 VLNMPSGEL 342 (455)
T ss_pred EecCCchhh
Confidence 999999875
No 35
>KOG1637|consensus
Probab=99.60 E-value=1.5e-15 Score=115.34 Aligned_cols=80 Identities=24% Similarity=0.337 Sum_probs=72.2
Q ss_pred CcccccCCcCCcchhhheeeceeecCCCCCC-CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542 1 MVADMKLSHKALPLLLYQFTSKFRDELRPKF-GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV 79 (86)
Q Consensus 1 ~~~~~i~Syr~LP~~l~q~~~~fR~E~~~~~-Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~ 79 (86)
||+...+|||+||+++..++.++|||.+|.+ ||.|+|.|.|+|+|+||++ ++..+++.-.++.++.+|.-+|..+...
T Consensus 261 mf~~r~rS~reLPlR~aDFg~LHRnE~SGaLsGLTRvRrFqQDDaHIFCt~-~Qi~~Eik~~l~fl~~vY~~fgf~f~l~ 339 (560)
T KOG1637|consen 261 MFAHRDRSYRELPLRFADFGVLHRNEASGALSGLTRVRRFQQDDAHIFCTP-DQVKEEIKGCLDFLDYVYGVFGFTFKLN 339 (560)
T ss_pred ccccCCccHhhCCccccCcceeeeccccccccccceeeeecccCceEEecC-ccHHHHHHHHHHHHHHHHHhccccceeE
Confidence 6889999999999999999999999999998 9999999999999999997 5667788999999999999888777654
Q ss_pred Ee
Q psy5542 80 IV 81 (86)
Q Consensus 80 ~~ 81 (86)
..
T Consensus 340 lS 341 (560)
T KOG1637|consen 340 LS 341 (560)
T ss_pred ec
Confidence 43
No 36
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=99.32 E-value=2e-12 Score=99.42 Aligned_cols=67 Identities=24% Similarity=0.318 Sum_probs=60.8
Q ss_pred CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
+-+.||+.++|+|.+||||.+|+.||+|+|||+|.|+-.|+.+.+ +.+++...++.....+.++||+
T Consensus 160 ~~~klPFgiaQIGk~FRNEIsPr~~l~R~REF~q~EiE~Fv~P~~-~~~~~~y~~~~~~~fl~~iGi~ 226 (539)
T PRK14894 160 SARKLPFGIAQVGKAFRNEINPRNFLFRVREFEQMEIEYFVMPGT-DEEWHQRWLEARLAWWEQIGIP 226 (539)
T ss_pred cCCCCCeeEEeeeccccCccCCCCceeecccchhheEEEEeCCCc-hHHHHHHHHHHHHHHHHHhCCC
Confidence 446999999999999999999999999999999999999999854 4668888888888999999996
No 37
>TIGR00389 glyS_dimeric glycyl-tRNA synthetase, dimeric type. This model describes a glycyl-tRNA synthetase distinct from the two alpha and two beta chains of the tetrameric E. coli glycyl-tRNA synthetase. This enzyme is a homodimeric class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes His, Ser, Pro, and this set of glycyl-tRNA synthetases.
Probab=99.32 E-value=8.2e-13 Score=102.41 Aligned_cols=45 Identities=31% Similarity=0.500 Sum_probs=42.0
Q ss_pred CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChH
Q psy5542 8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEV 52 (86)
Q Consensus 8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~ 52 (86)
+-..||+.++|||.+||||.+|+.||+|+|||+|.|+..||.+++
T Consensus 178 ~~~klPfgiaQiGk~fRNEIsPr~~l~R~REF~q~EiE~F~~p~~ 222 (551)
T TIGR00389 178 FRRKLPFGVAQIGKSFRNEISPRNGLFRVREFEQAEIEFFVHPLD 222 (551)
T ss_pred cCCCCCeeehhhhHhhhcccCcccceEEeehhhhchhheecCccc
Confidence 345999999999999999999999999999999999999999853
No 38
>PLN02734 glycyl-tRNA synthetase
Probab=99.29 E-value=1.9e-12 Score=102.19 Aligned_cols=66 Identities=29% Similarity=0.453 Sum_probs=56.7
Q ss_pred CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHh------------------------------------
Q psy5542 10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVD------------------------------------ 53 (86)
Q Consensus 10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~------------------------------------ 53 (86)
..||+..+|||..||||.+|+.||+|+|||+|.|+-.|+.+++.
T Consensus 272 ~klPF~~AQIGk~FRNEIsPR~gl~R~REF~qaEiE~Fv~P~~k~h~~f~~v~~~~l~l~~~~~q~~~~~~~~~t~~eAv 351 (684)
T PLN02734 272 GKLPFAAAQIGQAFRNEISPRQGLLRVREFTLAEIEHFVDPEDKSHPKFSEVADLEFLLFPREEQLGGQKAKPMRLGEAV 351 (684)
T ss_pred CCCCeeeeeccHhhhcccCcccceeeechhhhhhhheecCcccccccchhhhhhhhhhcccHhhhhccCCcccccHHHHH
Confidence 48999999999999999999999999999999999999998632
Q ss_pred -----HHHHHHHHHHHHHHHHHHcCCc
Q psy5542 54 -----ANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 54 -----~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
+++++...+.-....+.++||+
T Consensus 352 ~~gii~ne~l~Y~~~r~~~fl~~iGi~ 378 (684)
T PLN02734 352 SKGIVNNETLGYFIGRTYLFLTKLGID 378 (684)
T ss_pred HcCccchHHHHHHHHHHHHHHHHcCCC
Confidence 1346677777777778888885
No 39
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=99.24 E-value=1.6e-11 Score=92.46 Aligned_cols=72 Identities=25% Similarity=0.245 Sum_probs=61.1
Q ss_pred cCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEEecC
Q psy5542 6 KLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVIVRH 83 (86)
Q Consensus 6 i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~~~~ 83 (86)
..|++++|+|+|++++|||+| +|..| |.|||+|.+++.|+.+...++ .+++.+..++++.||++ +.....+.
T Consensus 95 ~~~~~~~p~R~~y~g~vfR~e-~~q~G--R~Ref~Q~g~EiiG~~~~~aD---~Evi~l~~~~l~~lGl~~~~i~l~~~ 167 (430)
T CHL00201 95 KMDYHSNLQRLWYSGPMFRYE-RPQSG--RQRQFHQLGIEFIGSIDARAD---TEVIHLAMQIFNELQVKNLILDINSI 167 (430)
T ss_pred cccccCCCeEEEEEcceecCC-CCcCC--ccceeEEeceEEECCCChhhH---HHHHHHHHHHHHHcCCCceEEEECCC
Confidence 346788999999999999999 55567 999999999999999888887 77899999999999996 55544443
No 40
>COG0423 GRS1 Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=99.22 E-value=9.5e-12 Score=95.78 Aligned_cols=44 Identities=34% Similarity=0.604 Sum_probs=42.0
Q ss_pred cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChH
Q psy5542 9 HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEV 52 (86)
Q Consensus 9 yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~ 52 (86)
-+.||+.++|||..||||.+|+.||+|+|||+|.|+-.|+.+++
T Consensus 183 r~klPFgiaQIGKsfRNEISPr~gl~R~REF~QaEiE~Fv~P~~ 226 (558)
T COG0423 183 RNKLPFGIAQIGKSFRNEISPRNGLFRTREFEQAEIEFFVDPEE 226 (558)
T ss_pred ccCCCeEEEeechhhccccCcccceeehhhhhhhheeeEECCCc
Confidence 45899999999999999999999999999999999999999877
No 41
>COG0124 HisS Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=99.17 E-value=4.5e-11 Score=90.57 Aligned_cols=68 Identities=32% Similarity=0.460 Sum_probs=60.2
Q ss_pred CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEEecCC
Q psy5542 11 ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVIVRHG 84 (86)
Q Consensus 11 ~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~~~~g 84 (86)
.+|+|+|.++++||+| +|+.| |.|||.|.++.+|..+...++ .+++.+..+++++|||. |....-+.|
T Consensus 99 ~~p~k~yy~g~vfRyE-rPQ~G--R~RqF~Q~g~E~iG~~~~~~D---AEvi~l~~~~l~~lGi~~~~l~iN~~g 167 (429)
T COG0124 99 PKPLKLYYFGPVFRYE-RPQKG--RYRQFYQFGVEVIGSDSPDAD---AEVIALAVEILEALGIGGFTLEINSRG 167 (429)
T ss_pred cCCeeEEEecceecCC-CCCCC--CceeeEEcCeEEeCCCCcccC---HHHHHHHHHHHHHcCCCcEEEEEcCcc
Confidence 3899999999999999 88889 999999999999999888888 77999999999999997 655555444
No 42
>TIGR00442 hisS histidyl-tRNA synthetase. This model finds a histidyl-tRNA synthetase in every completed genome. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and actually serve as regulatory subunits for an enzyme of histidine biosynthesis. They were excluded from the seed alignment and score much lower than do single copy histidyl-tRNA synthetases of other genomes not included in the seed alignment. These putative second copies of HisS score below the trusted cutoff. The regulatory protein kinase GCN2 of Saccharomyces cerevisiae (YDR283c), and related proteins from other species designated eIF-2 alpha kinase, have a domain closely related to histidyl-tRNA synthetase that may serve to detect and respond to uncharged tRNA(his), an indicator of amino acid starvation; these regulatory proteins are not orthologous and so score below the noise cutoff.
Probab=99.01 E-value=1.1e-09 Score=81.17 Aligned_cols=70 Identities=23% Similarity=0.243 Sum_probs=57.6
Q ss_pred CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEEecC
Q psy5542 8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVIVRH 83 (86)
Q Consensus 8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~~~~ 83 (86)
+++++|+|+|++++|||+|.. ..| |.|||+|.++++|+.+...++ .+++.++.++++.||++ +.....+.
T Consensus 92 ~~~~~p~r~~y~g~vfR~e~~-~~g--r~ref~Q~g~eiig~~~~~~d---~E~i~l~~e~l~~lg~~~~~i~i~~~ 162 (397)
T TIGR00442 92 LLLPKPFKLYYIGPMFRYERP-QKG--RYRQFHQFGVEVIGSDSPLAD---AEIIALAAEILKELGIKDFTLEINSL 162 (397)
T ss_pred cccCCCeEEEEEcCeecCCCC-CCC--cccceEEcCeeeeCCCCHHHH---HHHHHHHHHHHHHcCCCceEEEecCc
Confidence 357899999999999999954 345 999999999999999866665 57899999999999997 55554443
No 43
>cd00773 HisRS-like_core Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ. HisZ along with HisG catalyze the first reaction in histidine biosynthesis. HisZ is found only in a subset of bacteria and differs from HisRS in lacking a C-terminal anti-codon binding domain.
Probab=98.95 E-value=2.1e-09 Score=75.91 Aligned_cols=62 Identities=29% Similarity=0.302 Sum_probs=53.7
Q ss_pred CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEE
Q psy5542 10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYR 77 (86)
Q Consensus 10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~ 77 (86)
+++|+|+|++++|||+|.++ .| |.|||+|.+++.|+.+...++ .+++.+..++++.||++-.
T Consensus 79 ~~~p~k~~y~g~vfR~e~~~-~g--~~re~~Q~g~Eiig~~~~~~d---aE~i~l~~~~l~~lg~~~~ 140 (261)
T cd00773 79 LPLPLKLYYIGPVFRYERPQ-KG--RYREFYQVGVEIIGSDSPLAD---AEVIALAVEILEALGLKDF 140 (261)
T ss_pred CCCCeEEEEEcCEEecCCCC-CC--CccceEEeceeeeCCCChHHH---HHHHHHHHHHHHHcCCCce
Confidence 57999999999999999655 44 999999999999999766665 7799999999999998633
No 44
>KOG2298|consensus
Probab=98.90 E-value=2.9e-10 Score=87.10 Aligned_cols=55 Identities=31% Similarity=0.578 Sum_probs=46.8
Q ss_pred cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHH
Q psy5542 9 HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGK 63 (86)
Q Consensus 9 yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~ 63 (86)
-+.||+.-+|||..||||.+|+.||+|+|||+|.|+++|+.+......-|..+.+
T Consensus 205 ~~KlPFA~AqiG~~fRNEISpRsGLlRvrEF~maEIEHFvdP~~K~h~kF~~V~~ 259 (599)
T KOG2298|consen 205 QGKLPFASAQIGKSFRNEISPRSGLLRVREFTMAEIEHFVDPLLKSHPKFSLVAA 259 (599)
T ss_pred CCCCcchHHHhchHhhhccCcccCceeEEEeehHHhhccCCCCCCCChhhhhhhh
Confidence 4689999999999999999999999999999999999999987654444444443
No 45
>PRK00037 hisS histidyl-tRNA synthetase; Reviewed
Probab=98.87 E-value=3.5e-09 Score=78.68 Aligned_cols=61 Identities=28% Similarity=0.303 Sum_probs=52.4
Q ss_pred cchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEE
Q psy5542 12 LPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRK 78 (86)
Q Consensus 12 LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~ 78 (86)
+|+|+|+++++||+|.. ..| |.|||+|.++++|+.+...++ .+++.++.++++.||++...
T Consensus 97 ~p~r~~~~g~vfR~e~~-~~g--r~ref~Q~g~ei~g~~~~~~d---~E~i~~~~~~l~~lg~~~~~ 157 (412)
T PRK00037 97 QPFKLYYIGPMFRYERP-QKG--RYRQFHQFGVEVIGSDSPLAD---AEVIALAADILKALGLKGLK 157 (412)
T ss_pred CCeEEEEEcCccccCCC-CCC--cccceEEcCeeeeCCCCcchh---HHHHHHHHHHHHHcCCCcee
Confidence 99999999999999954 445 999999999999999866666 55888999999999997443
No 46
>PLN02530 histidine-tRNA ligase
Probab=98.86 E-value=3.5e-09 Score=80.99 Aligned_cols=59 Identities=25% Similarity=0.344 Sum_probs=53.1
Q ss_pred CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 11 ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 11 ~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
.+|+|+|++++|||+| ++..| |.|||+|.++..|+.+...++ .+++.+..++++.||++
T Consensus 162 ~~P~r~~y~g~vfR~e-~~q~g--r~REf~Q~giEiiG~~~~~aD---aEvi~l~~~~l~~lgl~ 220 (487)
T PLN02530 162 SLPLKWFAIGQCWRYE-RMTRG--RRREHYQWNMDIIGVPGVEAE---AELLAAIVTFFKRVGIT 220 (487)
T ss_pred CCCeEEEEEcCEEcCc-CCCCC--CccceEEcCeeEeCCCCcchh---HHHHHHHHHHHHHcCCC
Confidence 6899999999999999 56677 999999999999999877677 67889999999999995
No 47
>cd00768 class_II_aaRS-like_core Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial ATP phosphoribosyltransferase regulatory subunit HisZ.
Probab=98.83 E-value=1.5e-08 Score=67.76 Aligned_cols=68 Identities=28% Similarity=0.367 Sum_probs=55.8
Q ss_pred CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCC--cEEEE
Q psy5542 10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGI--KYRKV 79 (86)
Q Consensus 10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi--~~~~~ 79 (86)
+++|+++|++++|||+|..+ .++.|++||.|.+++.++.+.+++ ..+..+...+..+++.+|+ ++..+
T Consensus 72 ~~~~~~lfeig~vfr~e~~~-~~~~~~~ef~~l~~~~~g~~~~~~-~~~~~~~~~~~~~l~~lg~~~~~~~~ 141 (211)
T cd00768 72 RKLPLRLAEIGPAFRNEGGR-RGLRRVREFTQLEGEVFGEDGEEA-SEFEELIELTEELLRALGIKLDIVFV 141 (211)
T ss_pred ccCCEEEEEEcceeecCCCc-cccccceeEEEcCEEEEcCCchhH-HHHHHHHHHHHHHHHHcCCCcceEEE
Confidence 68999999999999999754 335689999999999999865433 3578899999999999997 45544
No 48
>PRK12420 histidyl-tRNA synthetase; Provisional
Probab=98.75 E-value=1.4e-08 Score=76.21 Aligned_cols=67 Identities=25% Similarity=0.274 Sum_probs=56.9
Q ss_pred CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEec
Q psy5542 10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVR 82 (86)
Q Consensus 10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~ 82 (86)
..+|+|+|++++|||+|. +..| |.|||+|.++..|..+...++ .+++.+..++++.||+++.....+
T Consensus 96 ~~~p~r~~y~g~vfR~~~-~~~g--r~rE~~Q~g~EiiG~~~~~ad---aEvi~la~~~l~~lg~~~~i~l~~ 162 (423)
T PRK12420 96 IRLPFKRYEIGKVFRDGP-IKQG--RFREFIQCDVDIVGVESVMAE---AELMSMAFELFRRLNLEVTIQYNN 162 (423)
T ss_pred CCCCeeEEEEcceECCCC-CCCC--ccceeEECCeeeECCCCCccc---HHHHHHHHHHHHHCCCCEEEEEcC
Confidence 467999999999999994 4456 999999999999998777777 779999999999999987655444
No 49
>TIGR00443 hisZ_biosyn_reg ATP phosphoribosyltransferase, regulatory subunit. Apparant second copies of histidyl-tRNA synthetase, found in Bacillus subtilis, Synechocystis sp., Aquifex aeolicus, and others, are in fact a regulatory subunit of ATP phosphoribosyltransferase, and usually encoded by a gene adjacent to that encoding the catalytic subunit.
Probab=98.71 E-value=3.5e-08 Score=71.55 Aligned_cols=65 Identities=28% Similarity=0.336 Sum_probs=55.1
Q ss_pred cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEE
Q psy5542 9 HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKV 79 (86)
Q Consensus 9 yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~ 79 (86)
+.++|+|++.+++|||+|..+ .| |.|||+|.+++.|..+...++ .+++.+..++++.||++ +...
T Consensus 83 ~~~~p~r~~y~g~VfR~~~~~-~g--r~re~~Q~g~Eiig~~~~~ad---aEvi~l~~~~l~~lg~~~~~i~ 148 (314)
T TIGR00443 83 DRPLPLRLCYAGNVFRTNESG-AG--RSREFTQAGVELIGAGGPAAD---AEVIALLIEALKALGLKDFKIE 148 (314)
T ss_pred cCCCCeEEEEeceEeecCCCc-CC--CcccccccceEEeCCCCchhH---HHHHHHHHHHHHHcCCCCeEEE
Confidence 457899999999999999643 45 999999999999998766666 68999999999999995 4443
No 50
>PRK12292 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=98.61 E-value=9.2e-08 Score=71.32 Aligned_cols=64 Identities=25% Similarity=0.340 Sum_probs=55.2
Q ss_pred CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEE
Q psy5542 10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKV 79 (86)
Q Consensus 10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~ 79 (86)
...|+|+|.+++|||+| ++..| |.|||+|.++.+|..+...++ .+++.+..++++.||++ +...
T Consensus 95 ~~~p~r~~y~g~vfR~~-~~~~g--r~ref~Q~g~EiiG~~~~~aD---aEvi~l~~~~l~~lgl~~~~i~ 159 (391)
T PRK12292 95 RPGPLRLCYAGNVFRAQ-ERGLG--RSREFLQSGVELIGDAGLEAD---AEVILLLLEALKALGLPNFTLD 159 (391)
T ss_pred CCCCeEEEeeceeeecC-CCcCC--CccchhccceEEeCCCCchHH---HHHHHHHHHHHHHcCCCCeEEE
Confidence 46899999999999999 56667 999999999999998777777 68999999999999996 4443
No 51
>PRK12421 ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=98.45 E-value=5.2e-07 Score=67.55 Aligned_cols=64 Identities=11% Similarity=-0.024 Sum_probs=54.7
Q ss_pred CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEE
Q psy5542 11 ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVI 80 (86)
Q Consensus 11 ~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~ 80 (86)
..|+|+|.+++|||.+. +..| |.|||+|.++-.+..+...++ .+++.+..++++.||++ +....
T Consensus 99 ~~p~R~~Y~g~VfR~~~-~~~g--r~rEf~Q~GvEiiG~~~~~aD---aEvi~l~~e~l~~lgi~~~~l~i 163 (392)
T PRK12421 99 EGVARLCYAGSVLHTLP-QGLF--GSRTPLQLGAELYGHAGIEAD---LEIIRLMLGLLRNAGVPALHLDL 163 (392)
T ss_pred CCceEEEEeeeEEEcCC-CcCC--CcCccceeceEEeCCCCchhH---HHHHHHHHHHHHHcCCCCeEEEe
Confidence 67999999999999884 5556 999999999999998877777 77999999999999996 44433
No 52
>PRK09537 pylS pyrolysyl-tRNA synthetase; Reviewed
Probab=98.42 E-value=7.4e-07 Score=67.63 Aligned_cols=64 Identities=20% Similarity=0.324 Sum_probs=52.4
Q ss_pred CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542 8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV 79 (86)
Q Consensus 8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~ 79 (86)
++.++|++++++++|||+|..+.. +++||+|.++..+..+ ..+..+..+.+.+++.|||+|...
T Consensus 277 k~~~~P~RIFEIG~VFR~E~~g~~---hlrEf~Ql~~~iiGs~-----~~f~dL~~lleeLL~~LGI~f~i~ 340 (417)
T PRK09537 277 RILPDPIKIFEIGPCYRKESDGKE---HLEEFTMVNFCQMGSG-----CTRENLENIIDDFLKHLGIDYEII 340 (417)
T ss_pred hcccCCeeEEEEeceEecCCCCCC---CcceEEEEEEEEeCCc-----hHHHHHHHHHHHHHHHCCCCcEEe
Confidence 457889999999999999964433 8999999999988543 234668899999999999998766
No 53
>PLN02972 Histidyl-tRNA synthetase
Probab=98.42 E-value=4.3e-07 Score=73.04 Aligned_cols=64 Identities=22% Similarity=0.340 Sum_probs=52.5
Q ss_pred CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCC-hHhHHHHHHHHHHHHHHHHHHcCCc-EEEEE
Q psy5542 11 ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTAS-EVDANDVYNLVGKCYDDVFNTLGIK-YRKVI 80 (86)
Q Consensus 11 ~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~-~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~ 80 (86)
..|+|+|+++++||+| +|..| |.|||+|.++.++... ...++ .+++.+..++++.||++ +.+..
T Consensus 415 ~~p~KrYyiG~VFR~e-~pqkG--R~REF~Q~G~EIIG~~~~~~aD---AEVI~La~E~L~~LGi~df~I~I 480 (763)
T PLN02972 415 ITSFKRYQIAKVYRRD-NPSKG--RYREFYQCDFDIAGVYEPMGPD---FEIIKVLTELLDELDIGTYEVKL 480 (763)
T ss_pred CCcceEEEeccEEecC-CCCCC--CCccceEEeEEEEcCCCcchhh---HHHHHHHHHHHHhCCCCceEEEe
Confidence 4599999999999999 46778 9999999999999873 33356 67999999999999995 44433
No 54
>TIGR02367 PylS pyrrolysyl-tRNA synthetase. PylS is the archaeal enzyme responsible for charging the pyrrolysine tRNA, PylT, by ligating a free molecule of pyrrolysine. Pyrrolysine is encoded at an in-frame UAG (amber) at least in several corrinoid-dependent methyltransferases of the archaeal genera Methanosarcina and Methanococcoides, such as trimethylamine methyltransferase.
Probab=98.19 E-value=4.1e-06 Score=64.07 Aligned_cols=62 Identities=16% Similarity=0.265 Sum_probs=49.5
Q ss_pred CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEE
Q psy5542 10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKV 79 (86)
Q Consensus 10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~ 79 (86)
..+|+++|+++.|||+|.. ..| |+|||+|.++.+++.+..- .++......+++.||++|...
T Consensus 315 l~~PqKIFEIGkVFR~E~~-~~t--hlREF~QL~~eIaG~~atf-----aDlealL~e~Lr~LGIdfeit 376 (453)
T TIGR02367 315 LPDPIKIFEIGPCYRKESD-GKE--HLEEFTMLNFCQMGSGCTR-----ENLEAIIKDFLDHLEIDFEIV 376 (453)
T ss_pred ccCCeeEEEEcCeEecCCC-CCC--CcCeEEEEEEEEECCCCCH-----HHHHHHHHHHHHHCCCceEEe
Confidence 3689999999999999954 445 8999999999999775332 345568888999999987664
No 55
>PF13393 tRNA-synt_His: Histidyl-tRNA synthetase; PDB: 3HRI_E 3HRK_A 3LC0_A 1Z7N_A 1Z7M_D 3NET_A 1H4V_B 3OD1_A 4E51_B 3RAC_A ....
Probab=98.07 E-value=1.7e-05 Score=56.88 Aligned_cols=65 Identities=29% Similarity=0.417 Sum_probs=54.2
Q ss_pred CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHH-HcCCc-EEEEE
Q psy5542 10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFN-TLGIK-YRKVI 80 (86)
Q Consensus 10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~-~lgi~-~~~~~ 80 (86)
...|.|+|.++++||++. +..| |.|||.|.++.++..+...++ .+++.+..++++ .||+. +....
T Consensus 85 ~~~~~r~~y~g~vfR~~~-~~~g--~~re~~Q~g~Eiig~~~~~~d---aEvi~l~~e~l~~~l~~~~~~i~i 151 (311)
T PF13393_consen 85 LPRPKRYYYIGPVFRYER-PGKG--RPREFYQCGFEIIGSSSLEAD---AEVIKLADEILDRELGLENFTIRI 151 (311)
T ss_dssp SSSSEEEEEEEEEEEEET-TTTT--BESEEEEEEEEEESSSSHHHH---HHHHHHHHHHHHHHHTTTSEEEEE
T ss_pred cCCCceEEEEcceeeccc-cCCC--CCceeEEEEEEEECCCCHHHH---HHHHHHHHHHHHhhcCCCCcEEEE
Confidence 678999999999999994 4355 999999999999998866666 779999999997 89994 44443
No 56
>PRK12295 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=98.06 E-value=1.1e-05 Score=60.34 Aligned_cols=61 Identities=21% Similarity=0.243 Sum_probs=50.2
Q ss_pred CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCCh-HhHHHHHHHHHHHHHHHHHHcCCc-EEEE
Q psy5542 10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASE-VDANDVYNLVGKCYDDVFNTLGIK-YRKV 79 (86)
Q Consensus 10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~-~~~~~~~~~~~~~~~~i~~~lgi~-~~~~ 79 (86)
...|+|+|.++++||+| + | |.|||+|.++..|..+. ..++ .+++.+..++++.||++ +...
T Consensus 79 ~~~p~R~~Y~g~VfR~~-~---g--r~rEf~Q~GvEiiG~~~~~~aD---aEvi~l~~~~L~~lgl~~~~i~ 141 (373)
T PRK12295 79 GGEPARYAYLGEVFRQR-R---D--RASEFLQAGIESFGRADPAAAD---AEVLALALEALAALGPGDLEVR 141 (373)
T ss_pred CCCCeEEEEEccEEECC-C---C--CCCcceEeeEEeeCCCCCccch---HHHHHHHHHHHHHcCCCceEEE
Confidence 46799999999999999 3 4 89999999999998633 4556 67999999999999985 4443
No 57
>PRK12293 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=97.89 E-value=2.3e-05 Score=56.57 Aligned_cols=53 Identities=9% Similarity=0.078 Sum_probs=45.9
Q ss_pred CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEE
Q psy5542 10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYR 77 (86)
Q Consensus 10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~ 77 (86)
..+|+|+|.++++||+|. |||+|.++-.+..+.. .+++.+..+++++||+++.
T Consensus 92 ~~~p~r~~Y~g~vfR~~~---------rEf~Q~GvEliG~~~~------~Evi~la~~~l~~lgl~~~ 144 (281)
T PRK12293 92 STEHKKWFYIQPVFRYPS---------NEIYQIGAELIGEEDL------SEILNIAAEIFEELELEPI 144 (281)
T ss_pred CCCceeEEEeccEEecCC---------CcccccCeEeeCCCCH------HHHHHHHHHHHHHcCCCCE
Confidence 368999999999999983 8999999999988643 3688999999999999865
No 58
>PRK07080 hypothetical protein; Validated
Probab=97.84 E-value=6.3e-05 Score=55.45 Aligned_cols=62 Identities=13% Similarity=0.077 Sum_probs=51.2
Q ss_pred eeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEec
Q psy5542 18 QFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVR 82 (86)
Q Consensus 18 q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~ 82 (86)
-.+.|||+|. ..++-|+.+|.|-|..-+.++ +++.+.-+..++....+.+.|||++.+..|+
T Consensus 157 v~g~CFR~E~--s~dl~Rl~~F~mrE~V~iGt~-e~v~~~r~~w~e~~~~l~~~LgL~~~ve~An 218 (317)
T PRK07080 157 VASYCFRHEP--SLDPARMQLFRMREYVRIGTP-EQIVAFRQSWIERGTAMADALGLPVEIDLAN 218 (317)
T ss_pred eeeeeeccCC--CCCcHHHhheeeeEEEEecCH-HHHHHHHHHHHHHHHHHHHHhCCceeEeecC
Confidence 3467999996 368999999999999888875 5666666788888888899999999988776
No 59
>cd00669 Asp_Lys_Asn_RS_core Asp_Lys_Asn_tRNA synthetase class II core domain. This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.
Probab=97.66 E-value=0.00012 Score=52.55 Aligned_cols=40 Identities=25% Similarity=0.339 Sum_probs=30.9
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDV 57 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~ 57 (86)
++|++++|||+| ..+.+ +++||+|.|++.-..+-+++.+.
T Consensus 71 ~vf~i~~~fR~e-~~~~~--hl~EF~~le~e~~~~~~~dvm~~ 110 (269)
T cd00669 71 RVFEINRNFRNE-DLRAR--HQPEFTMMDLEMAFADYEDVIEL 110 (269)
T ss_pred cEEEEecceeCC-CCCCC--cccceeEEEEEEecCCHHHHHHH
Confidence 889999999999 55555 99999999999554455554433
No 60
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=97.62 E-value=9.9e-05 Score=57.24 Aligned_cols=56 Identities=16% Similarity=0.223 Sum_probs=46.5
Q ss_pred cchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 12 LPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 12 LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
-|++++.++.|||+|. ...+ +++||+|.|+.++..+. .+..++.+...+|+++|+.
T Consensus 356 ~P~k~fsigrVfR~d~-~Dat--H~~eFhQ~Eg~vi~~~~-----s~~~L~~~l~~f~~~lG~~ 411 (494)
T PTZ00326 356 KPKKYFSIDRVFRNET-LDAT--HLAEFHQVEGFVIDRNL-----TLGDLIGTIREFFRRIGIT 411 (494)
T ss_pred CCceEEecCCEecCCC-CCCC--cCceeEEEEEEEEeCCC-----CHHHHHHHHHHHHHhcCCC
Confidence 3999999999999995 4444 99999999999997754 2356888888999999873
No 61
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=97.38 E-value=0.00031 Score=54.12 Aligned_cols=59 Identities=12% Similarity=0.179 Sum_probs=48.0
Q ss_pred cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 9 HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 9 yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
....|+++|++++|||+|.. ..+ |++||.|.++.....+. .+..+..+...++..||++
T Consensus 346 ~~~~p~rlFeiGrVFR~e~~-d~~--~l~Ef~ql~~~i~G~~~-----~f~elkg~l~~ll~~lGi~ 404 (489)
T PRK04172 346 RPEPPQKYFSIGRVFRPDTI-DAT--HLPEFYQLEGIVMGEDV-----SFRDLLGILKEFYKRLGFE 404 (489)
T ss_pred cCCCCeEEEEecceEcCCCC-Ccc--cCCchheEEEEEEeCCC-----CHHHHHHHHHHHHHHhCCc
Confidence 55789999999999999953 333 56899999999998642 2467888999999999994
No 62
>PRK09350 poxB regulator PoxA; Provisional
Probab=97.37 E-value=0.00012 Score=53.32 Aligned_cols=44 Identities=18% Similarity=0.170 Sum_probs=33.3
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV 61 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~ 61 (86)
++|++++|||+|.++ .+ ++.||+|.|++....+-++..+..+.+
T Consensus 80 rvf~i~~~FR~e~~~-~~--H~~EFt~lE~y~~~~d~~dlm~~~E~l 123 (306)
T PRK09350 80 PIFQICKSFRNEEAG-RY--HNPEFTMLEWYRPHYDMYRLMNEVDDL 123 (306)
T ss_pred ceEEecceeecCCCC-CC--CCcHHHhhhhhhhCCCHHHHHHHHHHH
Confidence 899999999999774 34 899999999997766655544333333
No 63
>TIGR00462 genX lysyl-tRNA synthetase-like protein GenX. Many Gram-negative bacteria have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS. The protein is termed GenX after its designation in E. coli. Interestingly, genX often is located near a homolog of lysine-2,3-aminomutase. Its function is unknown.
Probab=97.29 E-value=0.00021 Score=52.03 Aligned_cols=57 Identities=18% Similarity=0.205 Sum_probs=37.8
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEE
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYR 77 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~ 77 (86)
++|+++++||+|.++.. -+-||+|.|++....+-++.. ..+-+++..+++.+..|+.
T Consensus 75 rVfeigp~FRaE~~~~r---Hl~EFtmLE~e~~~~d~~d~m---~~~e~li~~i~~~~~~~~~ 131 (304)
T TIGR00462 75 PIFQICKVFRNGERGRR---HNPEFTMLEWYRPGFDYHDLM---DEVEALLQELLGDPFAPWE 131 (304)
T ss_pred CEEEEcCceeCCCCCCC---cccHHHhHHHHHHcCCHHHHH---HHHHHHHHHHHHhcCCCcE
Confidence 67999999999987544 688999999996655544444 3333344444544434443
No 64
>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.
Probab=97.27 E-value=0.00055 Score=54.08 Aligned_cols=45 Identities=24% Similarity=0.213 Sum_probs=33.6
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG 62 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~ 62 (86)
++||+++|||+|...+. |--||+|.|++.-..+.++..+..+.++
T Consensus 208 rvfqI~~~FR~E~~~t~---r~pEFT~le~E~af~d~~dvm~~~E~li 252 (583)
T TIGR00459 208 RYYQIARCFRDEDLRAD---RQPEFTQIDMEMSFMTQEDVMELIEKLV 252 (583)
T ss_pred cEEEEcceeeCCCCCCC---CCcccCcceeeecCCCHHHHHHHHHHHH
Confidence 68999999999976655 8899999999965556555554444433
No 65
>cd00777 AspRS_core Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. AspRS in this family differ from those found in the AsxRS family by a GAD insert in the core domain.
Probab=97.26 E-value=0.00059 Score=49.25 Aligned_cols=45 Identities=22% Similarity=0.177 Sum_probs=33.4
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG 62 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~ 62 (86)
++|+++++||+|...+ | |..||+|.|++.-..+-++..+..+.++
T Consensus 71 ~v~~i~~~fR~e~~~~-~--r~~Ef~~~e~e~~~~~~~dlm~~~e~li 115 (280)
T cd00777 71 RYFQIARCFRDEDLRA-D--RQPEFTQIDIEMSFVDQEDIMSLIEGLL 115 (280)
T ss_pred cEEEeccceeCCCCCC-C--ccceeEEeEeeeccCCHHHHHHHHHHHH
Confidence 6799999999997554 4 8889999999977666555544444433
No 66
>PLN02903 aminoacyl-tRNA ligase
Probab=97.23 E-value=0.00066 Score=54.28 Aligned_cols=50 Identities=26% Similarity=0.216 Sum_probs=35.6
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFN 70 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~ 70 (86)
++||+++|||+|...+. |--||+|.|++.-..+.++..+..+.+ +..+++
T Consensus 274 RvFqIa~~FR~E~~~t~---RhpEFTqLE~E~sf~d~~dvm~~~E~l---i~~v~~ 323 (652)
T PLN02903 274 RYYQIARCFRDEDLRAD---RQPEFTQLDMELAFTPLEDMLKLNEDL---IRQVFK 323 (652)
T ss_pred cEEEEehhhccCCCCCC---cccceeeeeeeecCCCHHHHHHHHHHH---HHHHHH
Confidence 58999999999976655 889999999996555555554343433 344444
No 67
>KOG1936|consensus
Probab=97.20 E-value=0.00021 Score=54.91 Aligned_cols=60 Identities=22% Similarity=0.268 Sum_probs=47.0
Q ss_pred CcchhhheeeceeecCCCC--CCCceeeceeeeeeeeEEcCChH-hHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542 11 ALPLLLYQFTSKFRDELRP--KFGLMRSREFLMKDLYAFTASEV-DANDVYNLVGKCYDDVFNTLGIKY 76 (86)
Q Consensus 11 ~LP~~l~q~~~~fR~E~~~--~~Gl~R~reF~~~d~~~f~~~~~-~~~~~~~~~~~~~~~i~~~lgi~~ 76 (86)
---++.|+|+.+||.+. | +.| |.|||.|.|..+...-++ -++ .+++.+..+++..|||.-
T Consensus 148 i~sikRy~iAkVyRRd~-P~mtrG--R~REFYQcDFDIAG~~d~M~pd---aE~lkiv~e~L~~l~Igd 210 (518)
T KOG1936|consen 148 ITSIKRYHIAKVYRRDQ-PAMTRG--RYREFYQCDFDIAGQFDPMIPD---AECLKIVVEILSRLGIGD 210 (518)
T ss_pred cccceeeeEEEEEeccC-chhhch--hhhhhhccCccccccCCCCCch---HHHHHHHHHHHhhcCccc
Confidence 33467899999999994 5 458 999999999999875322 234 568888999999999953
No 68
>PF00152 tRNA-synt_2: tRNA synthetases class II (D, K and N) ; InterPro: IPR004364 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 includes the asparagine, aspartic acid and lysine tRNA synthetases.; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 1N9W_B 1BBU_A 1BBW_A 4EX5_B 3E9I_A 3E9H_C 3A74_C 1NNH_A 3M4P_C 3M4Q_B ....
Probab=97.18 E-value=0.0016 Score=47.60 Aligned_cols=44 Identities=20% Similarity=0.195 Sum_probs=31.7
Q ss_pred hhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYNLV 61 (86)
Q Consensus 15 ~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~ 61 (86)
++||+++|||+|.+ +.. =+-||+|.|++.-..+.+.+.+..+.+
T Consensus 95 ~vf~i~~~FR~E~~~~~r---Hl~EFtmLE~e~a~~~~~~lm~~~e~l 139 (335)
T PF00152_consen 95 RVFEIGPCFRNEESRTRR---HLPEFTMLEWEMAFADYDDLMDLIEEL 139 (335)
T ss_dssp EEEEEEEEE-BSSSCBTT---BSSEEEEEEEEEETSSHHHHHHHHHHH
T ss_pred hhhheecceeccCccccc---chhhhhhhhhccccCcHHHhHHHHHHH
Confidence 58999999999977 444 467999999999777665554343433
No 69
>cd00775 LysRS_core Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three characteristic sequence motifs in the core domain. It is found in eukaryotes as well as some prokaryotes and archaea. However, LysRS belongs to class I aaRS's in some prokaryotes and archaea. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.
Probab=97.15 E-value=0.0011 Score=48.76 Aligned_cols=45 Identities=24% Similarity=0.251 Sum_probs=32.9
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG 62 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~ 62 (86)
++||++++||+|..++. .+-||+|.|++.-..+-++..+..+.++
T Consensus 78 ~vf~i~~~FR~E~~~~r---Hl~EFt~le~e~~~~~~~~~m~~~e~li 122 (329)
T cd00775 78 RVYEIGRNFRNEGIDLT---HNPEFTMIEFYEAYADYNDMMDLTEDLF 122 (329)
T ss_pred cEEEEeccccCCCCCCC---CCCceEEEEEeeecCCHHHHHHHHHHHH
Confidence 68999999999987654 7889999999865555455443434333
No 70
>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=97.09 E-value=0.0012 Score=52.00 Aligned_cols=50 Identities=34% Similarity=0.426 Sum_probs=34.6
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeee-EEcCChHhHHHHHHHHHHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLY-AFTASEVDANDVYNLVGKCYDDVFNT 71 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~-~f~~~~~~~~~~~~~~~~~~~~i~~~ 71 (86)
|+|||.+|||+|- .+.- |.-||+|.|+- ||+. +++..+..+ +++.++|+.
T Consensus 211 RYyQIarCFRDED-lRaD--RQPEFTQiD~EmSF~~-~edv~~~~E---~l~~~vf~~ 261 (585)
T COG0173 211 RYYQIARCFRDED-LRAD--RQPEFTQIDLEMSFVD-EEDVMELIE---KLLRYVFKE 261 (585)
T ss_pred ceeeeeeeecccc-cccc--cCCcceeEeEEeecCC-HHHHHHHHH---HHHHHHHHH
Confidence 7899999999995 3333 88999999996 5655 555554444 444555553
No 71
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=97.04 E-value=0.0017 Score=50.30 Aligned_cols=44 Identities=25% Similarity=0.312 Sum_probs=32.8
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV 61 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~ 61 (86)
++||++++||+|...+. ++-||+|.|++.-..+-++..+..+.+
T Consensus 242 rVfei~~~FR~E~~~~r---H~pEFt~lE~e~a~~d~~d~m~~~E~l 285 (491)
T PRK00484 242 RVYEIGRNFRNEGIDTR---HNPEFTMLEFYQAYADYNDMMDLTEEL 285 (491)
T ss_pred cEEEEecceecCCCCCC---cCCceEEEEEEEecCCHHHHHHHHHHH
Confidence 68999999999987654 889999999985555555554343433
No 72
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=97.04 E-value=0.00094 Score=53.83 Aligned_cols=45 Identities=24% Similarity=0.168 Sum_probs=33.3
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG 62 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~ 62 (86)
++||+++|||+|...+. |--||+|.|++.-..+.++..+..+.++
T Consensus 226 rvfqI~~~FR~E~~~t~---r~pEFT~LE~E~af~d~~dvm~l~E~li 270 (706)
T PRK12820 226 RYFQLARCFRDEDLRPN---RQPEFTQLDIEASFIDEEFIFELIEELT 270 (706)
T ss_pred cEEEEechhcCCCCCCC---cCccccccceeeccCCHHHHHHHHHHHH
Confidence 67999999999977655 7899999999954455555554444443
No 73
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=97.00 E-value=0.0012 Score=52.14 Aligned_cols=45 Identities=24% Similarity=0.174 Sum_probs=32.0
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG 62 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~ 62 (86)
++||+++|||+|..-+. |--||+|.|++.-..+.++..+..+.++
T Consensus 211 rvfqi~~~FR~E~~~~~---r~~EFt~le~e~af~~~~dvm~~~E~li 255 (588)
T PRK00476 211 RYYQIARCFRDEDLRAD---RQPEFTQIDIEMSFVTQEDVMALMEGLI 255 (588)
T ss_pred ceEEEeceeecCCCCCC---cCcccccceeeecCCCHHHHHHHHHHHH
Confidence 68999999999974333 6669999999965556555554444433
No 74
>PRK06462 asparagine synthetase A; Reviewed
Probab=96.99 E-value=0.0013 Score=48.58 Aligned_cols=46 Identities=20% Similarity=0.067 Sum_probs=32.5
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNL 60 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~ 60 (86)
++||++++||+|...+.+=--+-||+|.|++....+-++..+..+.
T Consensus 104 rVfeI~p~FR~E~~~~~~~rHl~EFtmlE~e~~~~d~~dlm~~~e~ 149 (335)
T PRK06462 104 KIFYLSPNFRLEPVDKDTGRHLYEFTQLDIEIEGADLDEVMDLIED 149 (335)
T ss_pred cEEEEeccccCCCCCCCCCCCCCchheeeehhhcCCHHHHHHHHHH
Confidence 6799999999998766112268899999999655555554433333
No 75
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=96.84 E-value=0.0021 Score=50.02 Aligned_cols=45 Identities=22% Similarity=0.253 Sum_probs=34.0
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG 62 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~ 62 (86)
++|+++++||+|..+.. .+-||+|.|++.-..+-++..+..+.++
T Consensus 254 rVfeIg~~FRnE~~~~r---H~pEFTmlE~y~a~~d~~d~m~l~E~li 298 (505)
T PRK12445 254 RVFEINRNFRNEGISVR---HNPEFTMMELYMAYADYHDLIELTESLF 298 (505)
T ss_pred cEEEEehhccCCCCCCC---cCcccceeeeeeecCCHHHHHHHHHHHH
Confidence 57999999999976544 7899999999987666666554444443
No 76
>cd00776 AsxRS_core Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as a subgroup of AspRS. AsnRS and AspRS are homodimers, which attach either asparagine or aspartate to the 3'OH group of ribose of the appropriate tRNA. While archaea lack asnRS, they possess a non-discriminating aspRS, which can mischarge Asp-tRNA with Asn. Subsequently, a tRNA-dependent aspartate amidotransferase converts the bound aspartate to asparagine. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.
Probab=96.83 E-value=0.003 Score=46.34 Aligned_cols=46 Identities=17% Similarity=0.113 Sum_probs=32.0
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcC-ChHhHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTA-SEVDANDVYNLVG 62 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~-~~~~~~~~~~~~~ 62 (86)
++|+++++||+|.+-+. --+.||+|.|++.... +-++..+..+.++
T Consensus 91 ~vf~i~~~FR~E~~~~~--rHl~EFtmlE~e~~~~~~~~dlm~~~e~ll 137 (322)
T cd00776 91 RVYEIGPVFRAEKSNTR--RHLSEFWMLEAEMAFIEDYNEVMDLIEELI 137 (322)
T ss_pred hhEEeccccccCCCCcC--CCcceeeccceeeeccCCHHHHHHHHHHHH
Confidence 68999999999963321 2578999999996655 5555544434333
No 77
>KOG2411|consensus
Probab=96.77 E-value=0.0014 Score=51.27 Aligned_cols=46 Identities=24% Similarity=0.234 Sum_probs=33.6
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGK 63 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~ 63 (86)
++||++.|||+|. .+.- |--||+|.|+..-..+.+...+.++.++.
T Consensus 249 rYyQiARCfRDEd-lR~D--RQPEFTQvD~EMsF~~~~dim~liEdll~ 294 (628)
T KOG2411|consen 249 RYYQIARCFRDED-LRAD--RQPEFTQVDMEMSFTDQEDIMKLIEDLLR 294 (628)
T ss_pred hHHhHHhhhcccc-cCcc--cCCcceeeeeEEeccCHHHHHHHHHHHHH
Confidence 6899999999994 3334 89999999998666666665544444433
No 78
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=96.77 E-value=0.0025 Score=51.08 Aligned_cols=44 Identities=20% Similarity=0.254 Sum_probs=33.9
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV 61 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~ 61 (86)
++||++++||+|...+. .+-||+|.|++....+-++..+..+++
T Consensus 303 rVyeIg~~FRnE~~~~r---H~pEFTmlE~y~a~~d~~d~m~l~E~l 346 (659)
T PTZ00385 303 RIYEIGKVFRNEDADRS---HNPEFTSCEFYAAYHTYEDLMPMTEDI 346 (659)
T ss_pred CEEEEeceecCCCCCCC---ccccccceeeeeecCCHHHHHHHHHHH
Confidence 68999999999987654 889999999997766655555443443
No 79
>PF01409 tRNA-synt_2d: tRNA synthetases class II core domain (F); InterPro: IPR002319 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. Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases [].; GO: 0000049 tRNA binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0043039 tRNA aminoacylation, 0005737 cytoplasm; PDB: 3TUP_A 3HFV_A 3CMQ_A 3TEG_A 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B ....
Probab=96.75 E-value=0.0084 Score=42.70 Aligned_cols=61 Identities=13% Similarity=0.275 Sum_probs=48.6
Q ss_pred CCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHc-CCc
Q psy5542 7 LSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTL-GIK 75 (86)
Q Consensus 7 ~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~l-gi~ 75 (86)
.+.+..|++++++|.|||+|.-... .+.+|.|.|+-....+- .+..+...++.+++.| |..
T Consensus 96 ~~~~~~p~kif~iG~VyR~D~~D~t---h~~~f~Qleg~~~~~~~-----~f~~Lk~~l~~l~~~lfG~~ 157 (247)
T PF01409_consen 96 NKHRPPPIKIFEIGKVYRRDEIDAT---HLPEFHQLEGLVVDKNV-----TFEDLKGTLEELLKELFGID 157 (247)
T ss_dssp TTTSHSSEEEEEEEEEESSSCSBSS---BESEEEEEEEEEEETTE------HHHHHHHHHHHHHHHHTTT
T ss_pred HHhcCCCeEEEecCceEecCCcccc---cCccceeEeeEEEeccc-----chhHHHHHHHHHHHHHhhcc
Confidence 3567889999999999999986655 67899999998876531 3466888888888887 886
No 80
>PLN02502 lysyl-tRNA synthetase
Probab=96.75 E-value=0.0019 Score=50.77 Aligned_cols=44 Identities=20% Similarity=0.278 Sum_probs=32.7
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV 61 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~ 61 (86)
++|+++++||+|...+ -.+-||+|.|++.-..+-++..+..+.+
T Consensus 299 rVfeIg~~FRnE~~~~---rH~pEFtmlE~y~a~~d~~dlm~~~E~l 342 (553)
T PLN02502 299 RVYEIGRQFRNEGIST---RHNPEFTTCEFYQAYADYNDMMELTEEM 342 (553)
T ss_pred CEEEEcCeeeCCCCCC---ccccceeehhhhhhcCCHHHHHHHHHHH
Confidence 5799999999997765 4889999999985555555554444433
No 81
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=96.62 E-value=0.0043 Score=47.24 Aligned_cols=43 Identities=16% Similarity=0.150 Sum_probs=29.6
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCC-hHhHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTAS-EVDANDVYN 59 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~-~~~~~~~~~ 59 (86)
++||++++||+|...+. -=+-||+|.|++.-..+ -++..+..+
T Consensus 204 rVf~i~~~FR~E~~~t~--rHl~EFt~lE~e~a~~~~~~~lm~~~e 247 (437)
T PRK05159 204 RVFEIGPVFRAEEHNTS--RHLNEYTSIDVEMGFIDDHEDVMDLLE 247 (437)
T ss_pred cEEEEeceeeCCCCCCc--ccchhhheeeeeeeecccHHHHHHHHH
Confidence 67999999999976542 02579999999954444 444443333
No 82
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=96.62 E-value=0.0034 Score=49.69 Aligned_cols=44 Identities=20% Similarity=0.139 Sum_probs=33.0
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV 61 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~ 61 (86)
++|+++++||+|...+. ..-||+|.|+|.-..+-++..+..+.+
T Consensus 323 rVfeIgp~FRnE~~~~r---HnpEFTmlE~y~ay~dy~dlM~l~E~L 366 (585)
T PTZ00417 323 KVYEIGKVFRNEGIDNT---HNPEFTSCEFYWAYADFYDLIKWSEDF 366 (585)
T ss_pred CEEEEcccccCCCCCCC---ccceeeeeeeeeecCCHHHHHHHHHHH
Confidence 67999999999986654 778999999996666655554343433
No 83
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=96.61 E-value=0.0027 Score=49.23 Aligned_cols=45 Identities=24% Similarity=0.275 Sum_probs=33.2
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG 62 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~ 62 (86)
++|+++++||+|...+. .+-||+|.|+|.-..+-++..+..+.++
T Consensus 242 rVfeIg~~FRnE~~~~r---H~pEFTmlE~y~a~~d~~dlm~~~E~li 286 (496)
T TIGR00499 242 KVYEIGRNFRNEGVDTT---HNPEFTMIEFYQAYADYEDLMDLTENLF 286 (496)
T ss_pred ceEEEecceecCCCCCc---ccchhheeehhhhcCCHHHHHHHHHHHH
Confidence 57999999999987654 7889999999965556555544444433
No 84
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=96.44 E-value=0.0078 Score=45.81 Aligned_cols=45 Identities=18% Similarity=0.162 Sum_probs=31.8
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV 61 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~ 61 (86)
++||++++||+|...+. --+-||+|.|++.-..+.++..+..+++
T Consensus 201 rVf~i~~~FR~E~~~t~--rHl~EFt~lE~e~a~~~~~dlm~~~e~l 245 (428)
T TIGR00458 201 RVYEIGPIFRAEEHNTH--RHLNEATSIDIEMAFEDHHDVMDILEEL 245 (428)
T ss_pred cEEEEecccccCCCCCc--cchheeeEeeeeeccCCHHHHHHHHHHH
Confidence 68999999999976542 1356999999996655655554444433
No 85
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=96.36 E-value=0.008 Score=46.04 Aligned_cols=44 Identities=25% Similarity=0.246 Sum_probs=30.3
Q ss_pred hhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYNLV 61 (86)
Q Consensus 15 ~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~ 61 (86)
++||+++|||+|.. +.. =+-||+|.|++.-..+-++.....+.+
T Consensus 209 rVf~i~~~FR~E~~~t~r---Hl~EFt~lE~e~~~~~~~~~m~~~e~l 253 (450)
T PRK03932 209 KVYTFGPTFRAENSNTRR---HLAEFWMIEPEMAFADLEDNMDLAEEM 253 (450)
T ss_pred CeEEeeeccccCCCCCcc---ccccccccceEEeccCHHHHHHHHHHH
Confidence 57999999999965 222 356999999996555555544343433
No 86
>COG2269 Truncated, possibly inactive, lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=96.19 E-value=0.0055 Score=45.10 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=35.2
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGK 63 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~ 63 (86)
.+||++.||||+-.|+. ---||+|.|.|..+-+-....++...+++
T Consensus 91 ~ifql~kvfRN~E~G~~---H~PEFTMLEWYrv~~d~~~lm~e~~~Ll~ 136 (322)
T COG2269 91 PIFQLGKVFRNEEMGRL---HNPEFTMLEWYRVGCDYYRLMNEVDDLLQ 136 (322)
T ss_pred cchhhhHHHhccccccc---CCCceeEeeeeccCCcHHHHHHHHHHHHH
Confidence 47999999999987755 45699999999999887665544444444
No 87
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=96.16 E-value=0.0055 Score=51.55 Aligned_cols=45 Identities=18% Similarity=0.217 Sum_probs=34.6
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVG 62 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~ 62 (86)
++||++++||+|...+. ..-||+|.|+|.-..+-++..+..++++
T Consensus 840 rVFEIg~~FRnE~~~~r---HnpEFTmLE~y~a~~dy~d~m~l~E~li 884 (1094)
T PRK02983 840 RVFELGRNFRNEGVDAT---HNPEFTLLEAYQAHADYDTMRDLTRELI 884 (1094)
T ss_pred ceEEEcceecCCCCCCC---ccccccchhhhhhcCCHHHHHHHHHHHH
Confidence 67999999999987654 7889999999987776666554444443
No 88
>PLN02850 aspartate-tRNA ligase
Probab=95.99 E-value=0.0081 Score=47.04 Aligned_cols=42 Identities=21% Similarity=0.204 Sum_probs=29.7
Q ss_pred hhheeeceeecCCC-CCCCceeeceeeeeeee-EEcCChHhHHHHHH
Q psy5542 15 LLYQFTSKFRDELR-PKFGLMRSREFLMKDLY-AFTASEVDANDVYN 59 (86)
Q Consensus 15 ~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~-~f~~~~~~~~~~~~ 59 (86)
++|+++++||+|.+ +.. =+-||+|.|++ .|..+-++..+..+
T Consensus 293 rVfeIgp~FRaE~s~t~R---Hl~EFt~Le~Em~~~~~y~evm~~~E 336 (530)
T PLN02850 293 RVFEIGPVFRAEDSFTHR---HLCEFTGLDLEMEIKEHYSEVLDVVD 336 (530)
T ss_pred ceEEEecccccCCCCCCc---cchhhccchhhhhhhcCHHHHHHHHH
Confidence 68999999999974 322 35799999999 77655444433333
No 89
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=95.93 E-value=0.017 Score=44.36 Aligned_cols=43 Identities=23% Similarity=0.191 Sum_probs=29.4
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYN 59 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~ 59 (86)
++||++++||+|...+. -=+-||+|.|++.-..+.+++.+..+
T Consensus 212 rVf~i~~~FR~E~~~t~--rHl~EFt~le~e~~~~~~~dvm~~~E 254 (453)
T TIGR00457 212 KVYTFGPTFRAEKSNTS--RHLSEFWMIEPEMAFANLNDLLQLAE 254 (453)
T ss_pred CceEeeeccccCCCCCC--cCcchhccceeeeecCCHHHHHHHHH
Confidence 57999999999976532 12469999999955445555443333
No 90
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=95.67 E-value=0.014 Score=46.05 Aligned_cols=45 Identities=16% Similarity=0.203 Sum_probs=31.1
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeee-eEEcCChHhHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDL-YAFTASEVDANDVYNLV 61 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~-~~f~~~~~~~~~~~~~~ 61 (86)
++||++++||+|.+.+. --+-||+|.|+ +.|..+-++..+..+.+
T Consensus 281 rVfeI~p~FRaE~s~T~--RHl~EFt~Le~E~~~~~~y~evm~~~e~l 326 (550)
T PTZ00401 281 RVFEVGPVFRSENSNTH--RHLTEFVGLDVEMRINEHYYEVLDLAESL 326 (550)
T ss_pred CEEEEeCeEeCCCCCCC--CCccchhhhhhhhHhcCCHHHHHHHHHHH
Confidence 57999999999976532 12569999999 57766544444343433
No 91
>PLN02532 asparagine-tRNA synthetase
Probab=95.63 E-value=0.024 Score=45.42 Aligned_cols=54 Identities=17% Similarity=0.092 Sum_probs=34.8
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHH-HHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLV-GKCYDDVFN 70 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~-~~~~~~i~~ 70 (86)
++|+++++||+|.+-+. --+-||+|.|++.--.+-+++.+..+.+ ..++..+++
T Consensus 391 rVYeIgP~FRAE~s~T~--RHL~EFtmlE~Emaf~d~~dvM~l~E~lI~~v~k~v~~ 445 (633)
T PLN02532 391 NVYTFGPRFRADRIDSA--RHLAEMWMVEVEMAFSELEDAMNCAEDYFKFLCKWVLE 445 (633)
T ss_pred ceEEEccceecCCCCCC--cccccccceeeeehhcCHHHHHHHHHHHHHHHHHHHHh
Confidence 57999999999977533 0378999999995444555544343433 333444443
No 92
>TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains. Recently, it was shown to act in a proposed pathway of tRNA(Cys) indirect aminoacylation, resulting in Cys biosynthesis from O-phosphoserine, in certain archaea. It charges tRNA(Cys) with O-phosphoserine. The pscS gene product converts the phosphoserine to Cys.
Probab=95.62 E-value=0.03 Score=43.85 Aligned_cols=59 Identities=15% Similarity=0.231 Sum_probs=46.6
Q ss_pred cCCcchhhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 9 HKALPLLLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 9 yr~LP~~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
...+|++++.++.|||+|.. ... ++++|.|.++-..+.+- ++..+......+++.||..
T Consensus 203 ~~~~PiRIFsIGRVfRrD~~~DaT---Hl~eFhQlEGLVVdedV-----Sf~DLKgvLe~LLr~LG~~ 262 (533)
T TIGR00470 203 KRKLPLKLFSIDRCFRREQREDRS---HLMTYHSASCVVVDEEV-----SVDDGKAVAEGLLAQFGFT 262 (533)
T ss_pred cCCCCeEEEeeeeEEecCCCCCCc---cCceeeeEEEEEECCCC-----CHHHHHHHHHHHHHHhCCc
Confidence 56799999999999999963 323 68999999999986642 3466777888888888864
No 93
>PTZ00425 asparagine-tRNA ligase; Provisional
Probab=95.30 E-value=0.048 Score=43.37 Aligned_cols=43 Identities=23% Similarity=0.196 Sum_probs=29.2
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYN 59 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~ 59 (86)
++|+++++||+|.+-+. --+-||+|.|++.-..+.++..+..+
T Consensus 345 rVf~i~p~FRaE~s~t~--RHL~EFt~lE~E~af~d~~d~m~~~E 387 (586)
T PTZ00425 345 DVYTFGPTFRAENSHTS--RHLAEFWMIEPEIAFADLYDNMELAE 387 (586)
T ss_pred CEEEEeceEeCCCCCCC--CCCcccceEEEEEecCCHHHHHHHHH
Confidence 67999999999975322 13469999999955445454443333
No 94
>PLN02221 asparaginyl-tRNA synthetase
Probab=95.28 E-value=0.044 Score=43.47 Aligned_cols=38 Identities=26% Similarity=0.229 Sum_probs=28.2
Q ss_pred hhheeeceeecCCC-CCCCceeeceeeeeeeeEEcCChHhHH
Q psy5542 15 LLYQFTSKFRDELR-PKFGLMRSREFLMKDLYAFTASEVDAN 55 (86)
Q Consensus 15 ~l~q~~~~fR~E~~-~~~Gl~R~reF~~~d~~~f~~~~~~~~ 55 (86)
+.|+++++||+|.+ ... =+-||+|.|++.-..+-++..
T Consensus 328 rVfeIgP~FRAE~s~T~R---HL~EFtmlE~Emaf~d~~dvm 366 (572)
T PLN02221 328 SVYTFGPTFRAENSHTSR---HLAEFWMVEPEIAFADLEDDM 366 (572)
T ss_pred CeEEEccceecCCCCCCc---ccccccceeeeeecCCHHHHH
Confidence 68999999999986 333 478999999994434444443
No 95
>COG3705 HisZ ATP phosphoribosyltransferase involved in histidine biosynthesis [Amino acid transport and metabolism]
Probab=95.14 E-value=0.013 Score=44.55 Aligned_cols=68 Identities=21% Similarity=0.214 Sum_probs=55.3
Q ss_pred CcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc-EEEEEe
Q psy5542 8 SHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK-YRKVIV 81 (86)
Q Consensus 8 Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~~ 81 (86)
+-...|.|++..+++||.. ++..| |..||+|.-+-.+..+...|+ .+++......++.+|++ +.....
T Consensus 90 ~~~~~P~Rl~Y~G~Vfr~~-~~~~g--~~~Ef~QaGiEllG~~~~~AD---aEvi~la~~~L~~~gl~~~~l~LG 158 (390)
T COG3705 90 LLAGTPLRLSYAGKVFRAR-EGRHG--RRAEFLQAGIELLGDDSAAAD---AEVIALALAALKALGLADLKLELG 158 (390)
T ss_pred hcCCCCceeeecchhhhcc-hhccC--cccchhhhhhHHhCCCcchhh---HHHHHHHHHHHHHcCCcCeEEEec
Confidence 4445899999999999999 77778 888999998888888767777 67888888899999985 444433
No 96
>cd00496 PheRS_alpha_core Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer.
Probab=95.02 E-value=0.077 Score=36.70 Aligned_cols=55 Identities=9% Similarity=0.129 Sum_probs=41.7
Q ss_pred CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcC
Q psy5542 11 ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLG 73 (86)
Q Consensus 11 ~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lg 73 (86)
..|++++++|++||.+..+.. ++.||.+..+.....+ . .+..+..+.+.+++.+|
T Consensus 78 ~~~~~lFEiG~Vf~~~~~~~~---~~~E~~~l~~~~~g~~---~--df~dlkg~ve~ll~~l~ 132 (218)
T cd00496 78 KPPIRIFSIGRVYRNDEIDAT---HLPEFHQIEGLVVDKG---L--TFADLKGTLEEFAKELF 132 (218)
T ss_pred CCCeeEEEEcCeEECCCCCCC---cCCccEEEEEEEECCC---C--CHHHHHHHHHHHHHHhc
Confidence 679999999999998743222 2459999998887642 1 25778888888888888
No 97
>PLN02603 asparaginyl-tRNA synthetase
Probab=94.81 E-value=0.081 Score=41.93 Aligned_cols=39 Identities=26% Similarity=0.178 Sum_probs=27.9
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDAN 55 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~ 55 (86)
++|+++++||+|.+-+. --+-||+|.|++.-..+-++..
T Consensus 323 rVy~igp~FRaE~s~T~--RHL~EF~mlE~E~af~dl~d~m 361 (565)
T PLN02603 323 DVYTFGPTFRAENSNTS--RHLAEFWMIEPELAFADLNDDM 361 (565)
T ss_pred ceEEEecceeCCCCCCc--cccccceeeeeeeecCCHHHHH
Confidence 47999999999976432 0357999999996444544443
No 98
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=94.68 E-value=0.064 Score=41.91 Aligned_cols=55 Identities=18% Similarity=0.239 Sum_probs=43.2
Q ss_pred cchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCC
Q psy5542 12 LPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGI 74 (86)
Q Consensus 12 LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi 74 (86)
-|++++.++.|||+|.--.. -+.+|+|.|+.+...+- ++..+......+++++|+
T Consensus 341 ~p~k~fsigrVfR~d~iDat---H~~eFhQ~EG~vvd~~~-----t~~~L~g~l~~f~~~lg~ 395 (492)
T PLN02853 341 KPKRYFSIDRVFRNEAVDRT---HLAEFHQVEGLVCDRGL-----TLGDLIGVLEDFFSRLGM 395 (492)
T ss_pred CCcEEEeccceecCCCCCcc---cCccceeEEEEEEeCCC-----CHHHHHHHHHHHHHHcCC
Confidence 69999999999999974433 57899999999996532 235577778888888876
No 99
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=94.57 E-value=0.065 Score=41.29 Aligned_cols=53 Identities=23% Similarity=0.231 Sum_probs=36.8
Q ss_pred hhheeeceeecCCCCCCCcee-eceeeeeeeeEEcCChHhHHHHHHH-HHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMR-SREFLMKDLYAFTASEVDANDVYNL-VGKCYDDVFN 70 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R-~reF~~~d~~~f~~~~~~~~~~~~~-~~~~~~~i~~ 70 (86)
+.|.+++.||.|.+-+. | +-||+|.|+-.-..+.++..+..+. +.-+++++++
T Consensus 201 rVf~igP~FRAE~s~T~---RHL~EF~~ld~Emaf~~~~d~m~l~E~~i~~i~~~v~e 255 (435)
T COG0017 201 RVFTIGPTFRAEKSNTR---RHLSEFWMLDPEMAFADLNDVMDLAEELIKYLFKKVLE 255 (435)
T ss_pred ceEEecCceecCCCCCc---chhhhHheecceeccCcHHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999988766 5 8899999998777665554434333 2333444443
No 100
>TIGR00468 pheS phenylalanyl-tRNA synthetase, alpha subunit. Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This model describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this model. An interesting feature of the alignment of all sequences captured by this model is a deep split between non-spirochete bacterial examples and all other examples; supporting this split is a relative deletion of about 50 residues in the former set between two motifs well conserved throughout the alignment.
Probab=94.37 E-value=0.067 Score=38.85 Aligned_cols=56 Identities=9% Similarity=0.152 Sum_probs=41.5
Q ss_pred cchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 12 LPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 12 LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
.|++++++|.|||++..... ++.||.+.++-.... .. .+..+....+.+++.+|++
T Consensus 149 ~pirlFEiGrVfr~d~~d~~---~~pef~ql~gl~~~~---~~--~f~dLKg~le~ll~~l~~~ 204 (294)
T TIGR00468 149 PPIRIFSPGRVFRNDTVDAT---HLPEFHQVEGLVIDK---NV--SFTNLKGFLEEFLKKMFGE 204 (294)
T ss_pred CCceEEEecceEEcCCCCCc---cCChhhEEEEEEECC---CC--CHHHHHHHHHHHHHHhCCC
Confidence 89999999999999853322 245899888885542 11 2577888888888988885
No 101
>PRK00488 pheS phenylalanyl-tRNA synthetase subunit alpha; Validated
Probab=94.03 E-value=0.13 Score=38.40 Aligned_cols=55 Identities=9% Similarity=0.132 Sum_probs=41.3
Q ss_pred CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHc
Q psy5542 10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTL 72 (86)
Q Consensus 10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~l 72 (86)
+..|+++..+|.|||++.-... ++.+|+|.|+-..+.+- .+..+......+++.+
T Consensus 182 ~~~Pirif~~G~VyR~D~~Dat---H~~~FhQleglvvd~~v-----tf~dLK~~L~~fl~~~ 236 (339)
T PRK00488 182 QKPPIRIIAPGRVYRNDSDDAT---HSPMFHQVEGLVVDKNI-----SFADLKGTLEDFLKAF 236 (339)
T ss_pred cCCCeEEEEeeeEEEcCCCCcc---cCcceeeEEEEEEeCCC-----CHHHHHHHHHHHHHHH
Confidence 6789999999999999964433 68899999999997642 2355556666666654
No 102
>COG0016 PheS Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]
Probab=91.42 E-value=0.4 Score=35.85 Aligned_cols=53 Identities=9% Similarity=0.136 Sum_probs=40.4
Q ss_pred chhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcC
Q psy5542 13 PLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLG 73 (86)
Q Consensus 13 P~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lg 73 (86)
|+++..++.|||+|.--.. -+.+|.|.|+-+...+-. +..+.-.++.++++++
T Consensus 192 P~k~~~~grvyR~D~~DaT---Hs~~FhQiEGlvvd~~~s-----~~~Lkg~L~~f~~~~f 244 (335)
T COG0016 192 PIKIFSPGRVYRNDTVDAT---HSPEFHQIEGLVVDKNIS-----FADLKGTLEEFAKKFF 244 (335)
T ss_pred CceEecccceecCCCCCcc---cchheeeeEEEEEeCCcc-----HHHHHHHHHHHHHHhc
Confidence 9999999999999965544 678999999988866422 3556666677777654
No 103
>KOG2784|consensus
Probab=90.17 E-value=0.18 Score=38.62 Aligned_cols=56 Identities=16% Similarity=0.130 Sum_probs=44.3
Q ss_pred cchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 12 LPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 12 LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
-|.+++.|..+||||.--+. -+-||.|.|+.+....- +.-.++.....++.++|+.
T Consensus 332 ~p~K~FSIDrVFRNEtvDaT---HLAEFHQVEGviad~gl-----tLgdLig~l~~ff~~lg~t 387 (483)
T KOG2784|consen 332 KPAKYFSIDRVFRNETVDAT---HLAEFHQVEGVIADKGL-----TLGDLIGILMEFFTKLGAT 387 (483)
T ss_pred CcccccchhhhhhccccchH---HHHHHhhhceeeecCCC-----cHHHHHHHHHHHHhccCCc
Confidence 38899999999999975544 57799999999987643 2345778888888888874
No 104
>COG2024 Phenylalanyl-tRNA synthetase alpha subunit (archaeal type) [Translation, ribosomal structure and biogenesis]
Probab=87.07 E-value=0.11 Score=39.96 Aligned_cols=63 Identities=16% Similarity=0.231 Sum_probs=36.7
Q ss_pred cCCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 6 KLSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 6 i~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
|+..+++|++++.|..|||.|++--.. ++-.+...-+.+...+ -..+ .=..+.+.+++.+|+.
T Consensus 200 i~~r~~~PlklFSIDRCFRREQ~ED~s--hLmtYhSASCVvvde~-vtvD----~GKaVAEglL~qfGFe 262 (536)
T COG2024 200 ILKREDPPLKLFSIDRCFRREQREDAS--HLMTYHSASCVVVDED-VTVD----DGKAVAEGLLRQFGFE 262 (536)
T ss_pred HHhccCCCceeeehhHHhhhhhhcchh--hhhhhccceEEEEcCc-cccc----ccHHHHHHHHHHhCcc
Confidence 455679999999999999999876432 3333333444444221 1111 1123345566777763
No 105
>PRK12294 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=86.20 E-value=1.6 Score=31.53 Aligned_cols=51 Identities=6% Similarity=-0.081 Sum_probs=35.9
Q ss_pred CcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 11 ALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 11 ~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
.-|.|++.++++||++. +|+|..+-.+..+ .+++ .+++.+..+.++.+|.+
T Consensus 82 ~~~~Rl~Y~g~VfR~~~----------~~~Q~GvEliG~~-~~a~---~e~l~la~~~l~~~g~~ 132 (272)
T PRK12294 82 TAATKVAYAGLIIRNNE----------AAVQVGIENYAPS-LANV---QQSFKLFIQFIQQQLRD 132 (272)
T ss_pred CCCceEEEeccEeccCC----------CcceeceEEECCC-chhH---HHHHHHHHHHHHHhCCC
Confidence 45779999999999983 3789988888743 2333 44556666777777543
No 106
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=85.59 E-value=0.7 Score=36.31 Aligned_cols=37 Identities=24% Similarity=0.333 Sum_probs=27.9
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDA 54 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~ 54 (86)
++|+++..||||--... -.-||+|.|.|-.-++-+..
T Consensus 250 rVfEIgr~FRNEGid~t---HNPEFTmlE~Y~AYaDy~D~ 286 (502)
T COG1190 250 RVFEIGRNFRNEGIDTT---HNPEFTMLEFYQAYADYEDL 286 (502)
T ss_pred hheeeccccccCCCccc---cCcchhhHHHHHHHhHHHHH
Confidence 78999999999954433 45699999999766654443
No 107
>PRK09616 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=80.92 E-value=5.9 Score=31.20 Aligned_cols=61 Identities=13% Similarity=0.219 Sum_probs=41.5
Q ss_pred cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEE
Q psy5542 9 HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYR 77 (86)
Q Consensus 9 yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~ 77 (86)
.+..|++++++|.+|+.+..+.. -.+|+.+..+-.... .. .|..+..+.+.++..+|+++.
T Consensus 434 ~~~~~~~lFEiG~Vf~~~~~~~~---~~~e~~~l~~~~~g~---~~--df~dlKg~ve~ll~~lgi~~~ 494 (552)
T PRK09616 434 HREYPQKIFEIGDVVLIDESTET---GTRTERKLAAAIAHS---EA--SFTEIKSVVQALLRELGIEYE 494 (552)
T ss_pred CCCCCeeEEEeeEEEecCCcccc---CcchhhEEEEEEECC---CC--CHHHHHHHHHHHHHHcCCeEE
Confidence 45789999999999987642211 124666666554443 22 267788888999999998643
No 108
>TIGR02049 gshA_ferroox glutamate--cysteine ligase, T. ferrooxidans family. This family consists of a rare family of glutamate--cysteine ligases, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria. It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase.
Probab=73.44 E-value=8.9 Score=29.46 Aligned_cols=48 Identities=21% Similarity=0.160 Sum_probs=35.7
Q ss_pred eeeeeeeeEEcCC--hHhHHHHHHHHHHHHHHHHHHcCC---cEEEEEecCCC
Q psy5542 38 EFLMKDLYAFTAS--EVDANDVYNLVGKCYDDVFNTLGI---KYRKVIVRHGA 85 (86)
Q Consensus 38 eF~~~d~~~f~~~--~~~~~~~~~~~~~~~~~i~~~lgi---~~~~~~~~~g~ 85 (86)
-|..++..-|+.. .++..+..+.+++.+.+=|+.-|| ||++|+||.|.
T Consensus 216 ~f~~c~~vdF~~~~G~e~lA~~Vd~~L~kir~KY~eYgI~e~PfViVKADaGT 268 (403)
T TIGR02049 216 YFEKCDGIDFDDREGEDALATAVDQVLSKTQKKYEEYGIHTQPYVIVKADAGT 268 (403)
T ss_pred hhhccCCcCCCccccHHHHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEcCCCC
Confidence 4666777777764 344455567778888888889998 79999999984
No 109
>PF15518 L_protein_N: L protein N-terminus; PDB: 2XI5_D 2XI7_D.
Probab=72.93 E-value=13 Score=25.62 Aligned_cols=37 Identities=27% Similarity=0.594 Sum_probs=27.7
Q ss_pred eEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEe
Q psy5542 45 YAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIV 81 (86)
Q Consensus 45 ~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~ 81 (86)
|-+.-+.++.+.++++--+.+..++..+||++.+|..
T Consensus 93 yKVSV~~eSs~iT~eKY~~~~~~i~~~lgi~~EivII 129 (183)
T PF15518_consen 93 YKVSVDNESSEITYEKYNEIFGDIFSQLGIDYEIVII 129 (183)
T ss_dssp EEE-SSSHHHHHHHHHHHHHHHHHHHHHT--EEEEEE
T ss_pred EEEeccCcccHHHHHHHHHHHHHHHhhcCCCeEEEEE
Confidence 4444566788889999999999999999999877643
No 110
>PRK06253 O-phosphoseryl-tRNA synthetase; Reviewed
Probab=71.69 E-value=7.8 Score=30.85 Aligned_cols=62 Identities=19% Similarity=0.306 Sum_probs=37.3
Q ss_pred CCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 7 LSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 7 ~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
++.+..|++++++++|||.+..... .++..+..-... .. .+.+ .|..+..+.+.+++.||++
T Consensus 202 l~Rg~~piRLFEIGRVFr~d~~eE~--t~La~llsGs~W--~~-~e~v--DFfDlKGiLE~LL~~LGI~ 263 (529)
T PRK06253 202 LEKRPLPIKLFSIDRCFRREQREDA--SRLMTYHSASCV--IA-DEDV--TVDDGKAVAEGLLSQFGFT 263 (529)
T ss_pred HhCCCCCEEEEEEeeEEecCCccch--hheeEEEEcccc--cc-CCCC--CHHHHHHHHHHHHHHcCCC
Confidence 4467899999999999988632110 022222222111 11 1222 2677888888999999986
No 111
>PF08886 GshA: Glutamate-cysteine ligase; InterPro: IPR011718 This entry represents a rare family of glutamate--cysteine ligases, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria []. It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase.; PDB: 3K1T_A.
Probab=70.26 E-value=12 Score=28.79 Aligned_cols=49 Identities=14% Similarity=0.071 Sum_probs=29.2
Q ss_pred ceeeeeeeeEEcCC--hHhHHHHHHHHHHHHHHHHHHcCC---cEEEEEecCCC
Q psy5542 37 REFLMKDLYAFTAS--EVDANDVYNLVGKCYDDVFNTLGI---KYRKVIVRHGA 85 (86)
Q Consensus 37 reF~~~d~~~f~~~--~~~~~~~~~~~~~~~~~i~~~lgi---~~~~~~~~~g~ 85 (86)
-.|.+.+..-|... .+++.+....++.-+.+=|+..|| ||+.|+||.|.
T Consensus 218 p~f~~c~~vdF~~~~G~~~La~~Vd~lL~kir~KY~eygI~e~PfV~VKAD~GT 271 (404)
T PF08886_consen 218 PYFEQCGGVDFQEREGEECLASAVDQLLAKIRKKYKEYGIKEKPFVFVKADAGT 271 (404)
T ss_dssp --EEEEE---TTSSTTHHHHHHHHHHHHHHHHHHHHHHT--S---EEEEEE-GG
T ss_pred cchhccCCccCCccccHHHHHHHHHHHHHHHHHHHHHcCCCCCceEEEEcCCCC
Confidence 34677777777764 244444556777777777889998 79999999884
No 112
>PLN02788 phenylalanine-tRNA synthetase
Probab=66.07 E-value=12 Score=28.74 Aligned_cols=57 Identities=11% Similarity=0.008 Sum_probs=38.8
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChH-------hHHHHHHHHHHHHHHHHHHc-CC
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEV-------DANDVYNLVGKCYDDVFNTL-GI 74 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~-------~~~~~~~~~~~~~~~i~~~l-gi 74 (86)
++.-.|.|||+|.--+. -+.+|.|.|+......++ ..+-.+..+....+.+++.+ |+
T Consensus 149 ~~~~~g~VyRrD~iD~t---H~p~FhQ~EG~~v~~~~~~~~~~~~~~~~~~~dLKg~Le~l~~~lfg~ 213 (402)
T PLN02788 149 HFLVTGDVYRRDSIDAT---HYPVFHQMEGVRVFSPEEWEASGLDGTDLAAEDLKKTLEGLARHLFGD 213 (402)
T ss_pred cEEEEeeEeecCCCCcc---cCccceeEEEEEEecccccccccccccccCHHHHHHHHHHHHHHhcCC
Confidence 88899999999964433 467899999988864321 11112456667777777776 76
No 113
>KOG0556|consensus
Probab=65.01 E-value=5.3 Score=31.26 Aligned_cols=35 Identities=26% Similarity=0.329 Sum_probs=24.1
Q ss_pred cCCcch-----hhheeeceeecCCCCCCCceeeceeeeeeee
Q psy5542 9 HKALPL-----LLYQFTSKFRDELRPKFGLMRSREFLMKDLY 45 (86)
Q Consensus 9 yr~LP~-----~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~ 45 (86)
|+|+-+ +.|+||++||.|-+.+.- -+-||+=.|+.
T Consensus 285 yKQMaI~gdf~rVyeIGpVfRAEdSnthR--hltEFvGLD~E 324 (533)
T KOG0556|consen 285 YKQMAICGDFERVYEIGPVFRAEDSNTHR--HLTEFVGLDLE 324 (533)
T ss_pred HHHHHHhcchhheeeecceeeccccchhh--hhHHhhCcchh
Confidence 555544 689999999999877652 34567655553
No 114
>KOG0554|consensus
Probab=61.56 E-value=4.7 Score=31.19 Aligned_cols=34 Identities=26% Similarity=0.261 Sum_probs=24.7
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCC
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTAS 50 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~ 50 (86)
+.|-+++.||.|.+-..- -+-||+|.|+-.-..+
T Consensus 207 rvyTfgP~FRAEnS~tsR--HLAEFwMlEaE~AF~~ 240 (446)
T KOG0554|consen 207 RVYTFGPTFRAENSHTSR--HLAEFWMLEAELAFAE 240 (446)
T ss_pred ceEeeccceecccCCchh--HHhhhhhhhhHHHHHH
Confidence 467889999999765431 3568999999765554
No 115
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=60.74 E-value=20 Score=21.27 Aligned_cols=42 Identities=21% Similarity=0.428 Sum_probs=21.5
Q ss_pred CCceeeceeeeeeeeEE-cCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 31 FGLMRSREFLMKDLYAF-TASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 31 ~Gl~R~reF~~~d~~~f-~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
+|.-|...|+..++..+ .++.++-.+.|+.+.+ ++-+++||+
T Consensus 21 lg~~Rs~~~v~I~It~~~gRs~e~K~~ly~~l~~---~L~~~~gi~ 63 (82)
T PF14552_consen 21 LGIDRSDDFVIIQITSGAGRSTEQKKALYRALAE---RLAEKLGIR 63 (82)
T ss_dssp S--TS-TT-EEEEEEECS---HHHHHHHHHHHHH---HHHHHH---
T ss_pred CCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHH---HHHHHcCCC
Confidence 46779999999999999 6666665544444443 333678884
No 116
>KOG0081|consensus
Probab=56.19 E-value=21 Score=24.78 Aligned_cols=20 Identities=15% Similarity=0.315 Sum_probs=16.4
Q ss_pred HHHHHHcCCcEEEEEecCCC
Q psy5542 66 DDVFNTLGIKYRKVIVRHGA 85 (86)
Q Consensus 66 ~~i~~~lgi~~~~~~~~~g~ 85 (86)
..+-++.||||....|++|.
T Consensus 148 ~~La~kyglPYfETSA~tg~ 167 (219)
T KOG0081|consen 148 AALADKYGLPYFETSACTGT 167 (219)
T ss_pred HHHHHHhCCCeeeeccccCc
Confidence 34556899999999999984
No 117
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=54.86 E-value=13 Score=20.47 Aligned_cols=33 Identities=24% Similarity=0.319 Sum_probs=24.4
Q ss_pred EcCChHhHHHHHHHHHHHHHHHHHHcCC---cEEEE
Q psy5542 47 FTASEVDANDVYNLVGKCYDDVFNTLGI---KYRKV 79 (86)
Q Consensus 47 f~~~~~~~~~~~~~~~~~~~~i~~~lgi---~~~~~ 79 (86)
||.+.++|...+.--....+++++++|| ||+.+
T Consensus 14 fhlp~~eAA~~Lgv~~T~LKr~CR~~GI~RWP~Rkl 49 (52)
T PF02042_consen 14 FHLPIKEAAKELGVSVTTLKRRCRRLGIPRWPYRKL 49 (52)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHcCCCCCCchhh
Confidence 6677777766666667888999999998 46543
No 118
>cd00769 PheRS_beta_core Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer. While the alpha chain contains a catalytic core domain, the beta chain has a non-catalytic core domain.
Probab=52.86 E-value=22 Score=23.83 Aligned_cols=61 Identities=16% Similarity=0.120 Sum_probs=35.1
Q ss_pred CCcCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcC--------ChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 7 LSHKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTA--------SEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 7 ~Syr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~--------~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
.+.+..|++++++|.+|..+.. . .+|....=+-.... ....+ .+..+..+.+.++..+|++
T Consensus 72 ~~~~~~~~~lFEiG~vf~~~~~--~----~~e~~~l~~~~~g~~~~~~w~~~~~~~--~f~~~Kg~ve~ll~~l~~~ 140 (198)
T cd00769 72 LNRKNKPLRLFEIGRVFLKDED--G----PEEEEHLAALLSGNREPESWQGKGRPV--DFYDAKGILEALLRALGII 140 (198)
T ss_pred hcCCCCCEeEEEeEeEEecCCC--C----CcchheEEEEEECCCccccccCCCCcc--CHhhHHHHHHHHHHHcCCe
Confidence 3456689999999999965421 0 01222111111111 11112 3677888889999999963
No 119
>KOG1885|consensus
Probab=52.61 E-value=4.4 Score=32.07 Aligned_cols=38 Identities=26% Similarity=0.329 Sum_probs=27.7
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDAN 55 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~ 55 (86)
|.|+||..||||--. +.-.-||+..|.|---++-++..
T Consensus 295 rVYEIGr~FRNEGID---lTHNPEFTTcEfY~AYady~dlm 332 (560)
T KOG1885|consen 295 RVYEIGRQFRNEGID---LTHNPEFTTCEFYMAYADYEDLM 332 (560)
T ss_pred HHHHHHHHhhhcCcc---cccCCCcchHHHHHHHhhHHHHH
Confidence 689999999999433 44567999998886655544443
No 120
>KOG0555|consensus
Probab=51.51 E-value=13 Score=29.21 Aligned_cols=55 Identities=16% Similarity=0.108 Sum_probs=38.8
Q ss_pred hhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHH-HHHHHHHHHHHHH
Q psy5542 15 LLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVY-NLVGKCYDDVFNT 71 (86)
Q Consensus 15 ~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~-~~~~~~~~~i~~~ 71 (86)
..|-|++.||.|++-++- -+-|++..|+.--..+-++..+.+ +-+++...++++.
T Consensus 310 dvy~I~~SyRAEkSrTRR--HLsEytHVEaE~afltfd~ll~~iE~lvc~~vdr~l~d 365 (545)
T KOG0555|consen 310 DVYCIQQSYRAEKSRTRR--HLSEYTHVEAECAFLTFDDLLDRIEALVCDSVDRLLED 365 (545)
T ss_pred ceeEecHhhhhhhhhhhh--hhhhheeeeeecccccHHHHHHHHHHHHHHHHHHHHhC
Confidence 378899999999865442 366899998876655556654444 3577777777775
No 121
>PF14791 DNA_pol_B_thumb: DNA polymerase beta thumb ; PDB: 1HUZ_A 3K75_D 1HUO_A 2BPC_A 1RPL_A 1NOM_A 1ZQX_A 1ZQU_A 1ZQZ_A 1ZQV_A ....
Probab=48.83 E-value=11 Score=21.37 Aligned_cols=13 Identities=38% Similarity=0.971 Sum_probs=7.5
Q ss_pred HHHHHHcCCcEEE
Q psy5542 66 DDVFNTLGIKYRK 78 (86)
Q Consensus 66 ~~i~~~lgi~~~~ 78 (86)
++||+.||+||+.
T Consensus 46 ~dif~~Lgl~yip 58 (64)
T PF14791_consen 46 EDIFDALGLPYIP 58 (64)
T ss_dssp HHHHHHTTS----
T ss_pred HHHHHHcCCCCCC
Confidence 4688999999874
No 122
>PF14719 PID_2: Phosphotyrosine interaction domain (PTB/PID)
Probab=48.16 E-value=88 Score=21.49 Aligned_cols=44 Identities=14% Similarity=0.174 Sum_probs=23.7
Q ss_pred eceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHH
Q psy5542 20 TSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFN 70 (86)
Q Consensus 20 ~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~ 70 (86)
+-+||.|.+.....+|.|.| +|..++.|.+.-..+.+.+...|+
T Consensus 81 awIyrhe~~~~~~~L~CHAv-------lC~k~~~Akama~~L~~af~~Af~ 124 (182)
T PF14719_consen 81 AWIYRHEGKKLKVELRCHAV-------LCSKEEKAKAMARALYQAFRSAFQ 124 (182)
T ss_pred EEEEEcccCCCcccEEEEEE-------EECCHHHHHHHHHHHHHHHHHHHH
Confidence 34678875433344455444 255556666554455555555544
No 123
>TIGR00471 pheT_arch phenylalanyl-tRNA synthetase, beta subunit. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from eukaryotic cytosol, the Archaea, and spirochetes.
Probab=47.60 E-value=92 Score=24.63 Aligned_cols=61 Identities=21% Similarity=0.314 Sum_probs=36.7
Q ss_pred cCCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEE
Q psy5542 9 HKALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYR 77 (86)
Q Consensus 9 yr~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~ 77 (86)
.+..|++++++|.+|....... .+.+++...-+-... . .+ .|..+....+.++..||+++.
T Consensus 436 ~~~~~~~lFEiG~Vf~~~~~~~---~~e~~~~~l~~~~~g-~--~~--df~d~Kg~ve~ll~~l~i~~~ 496 (551)
T TIGR00471 436 HHELPQKIFEIGDVVVKDDKSE---TRSRVVTKLAVGITH-S--EA--NFNEIKSIVAALARELGIEYE 496 (551)
T ss_pred cCCCCeeEEEEEEEEEcCCccc---cccceeeEEEEEEEC-C--CC--CHHHHHHHHHHHHHHcCCceE
Confidence 5688999999999995432111 122323322222221 1 22 267788888999999998643
No 124
>COG0408 HemF Coproporphyrinogen III oxidase [Coenzyme metabolism]
Probab=46.61 E-value=21 Score=26.34 Aligned_cols=52 Identities=19% Similarity=0.132 Sum_probs=29.0
Q ss_pred ceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHH-cCCcE
Q psy5542 21 SKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNT-LGIKY 76 (86)
Q Consensus 21 ~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~-lgi~~ 76 (86)
-++|+|.||-+||+ |...+--.|..+-.=....-..++.+|-.|.++ .+.++
T Consensus 177 LkHR~E~RGiGGiF----fD~l~~~~~~~~Faf~qdvG~afl~aY~pIV~~r~~~~~ 229 (303)
T COG0408 177 LKHRNEPRGIGGIF----FDDLNEPDFERDFAFTQDVGKAFLPAYLPIVERRKNMPW 229 (303)
T ss_pred ecccCCCCCcceee----cccccCCCHHHHHHHHHHHHHHHhhhhHHHHHHhcCCCC
Confidence 47899999998976 322222112111111233445667777777774 66665
No 125
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=44.93 E-value=32 Score=18.20 Aligned_cols=22 Identities=27% Similarity=0.365 Sum_probs=17.4
Q ss_pred HHHHHHHHHHcCCcEEEEEecC
Q psy5542 62 GKCYDDVFNTLGIKYRKVIVRH 83 (86)
Q Consensus 62 ~~~~~~i~~~lgi~~~~~~~~~ 83 (86)
+...+++++..|++|..+..+.
T Consensus 12 C~~~~~~L~~~~i~y~~~dv~~ 33 (60)
T PF00462_consen 12 CKKAKEFLDEKGIPYEEVDVDE 33 (60)
T ss_dssp HHHHHHHHHHTTBEEEEEEGGG
T ss_pred HHHHHHHHHHcCCeeeEccccc
Confidence 4566778899999999887764
No 126
>PF12683 DUF3798: Protein of unknown function (DUF3798); InterPro: IPR024258 This entry represents functionally uncharacterised proteins that are found in bacteria. They are typically between 247 and 417 amino acids in length. Most of the proteins in this entry have an N-terminal lipoprotein attachment site. These proteins have distant similarity to periplasmic ligand binding families suggesting that this family has a similar role.; PDB: 3QI7_A.
Probab=43.51 E-value=56 Score=24.02 Aligned_cols=37 Identities=19% Similarity=0.346 Sum_probs=24.9
Q ss_pred eEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEecC
Q psy5542 45 YAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRH 83 (86)
Q Consensus 45 ~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~~ 83 (86)
++|-+ .-+.+....-++..++.+++||++|+.+.+..
T Consensus 137 ~sfpr--hms~~~l~~Rr~~M~~~C~~lGi~fv~~taPD 173 (275)
T PF12683_consen 137 YSFPR--HMSYELLARRRDIMEEACKDLGIKFVEVTAPD 173 (275)
T ss_dssp EEETT--GGGSHHHHHHHHHHHHHHHHCT--EEEEEE--
T ss_pred Eechh--hcchHHHHHHHHHHHHHHHHcCCeEEEEeCCC
Confidence 34644 34455667888889999999999999988753
No 127
>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=43.27 E-value=60 Score=20.82 Aligned_cols=34 Identities=18% Similarity=0.341 Sum_probs=25.2
Q ss_pred eeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEE
Q psy5542 40 LMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYR 77 (86)
Q Consensus 40 ~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~ 77 (86)
.++|+..++.+.+.+ .++.+.+.+.++.+|+...
T Consensus 88 Y~DD~~i~~~~~~~~----~~~~~~i~~~l~~~gL~ln 121 (158)
T cd01646 88 YVDDIRIFADSKEEA----EEILEELKEFLAELGLSLN 121 (158)
T ss_pred ecCcEEEEcCCHHHH----HHHHHHHHHHHHHCCCEEC
Confidence 489999999875544 5677778888888887643
No 128
>PF04175 DUF406: Protein of unknown function (DUF406) ; InterPro: IPR005272 These small proteins are approximately 100 amino acids in length and appear to be found only in gamma proteobacteria. The function of this protein family is unknown. ; PDB: 2JZ5_A 2KHD_A 2K3I_A.
Probab=42.63 E-value=80 Score=19.42 Aligned_cols=44 Identities=18% Similarity=0.154 Sum_probs=32.8
Q ss_pred eeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEecCC
Q psy5542 41 MKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHG 84 (86)
Q Consensus 41 ~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~~g 84 (86)
..+...+..++++|+..+..+.+..+.+++..+|.+.......|
T Consensus 28 ~~~~~~~~~~~~~Ae~~l~~l~~kAk~v~ep~~I~~~i~~~e~g 71 (94)
T PF04175_consen 28 VAEVSIVFASEAEAEAALAKLTEKAKQVEEPCNIESEITPVEDG 71 (94)
T ss_dssp EEEEEEEESSHHHHHHHHHHHHHHHHHHST-TTEEEEEEE-TT-
T ss_pred EEEEEEEeCCHHHHHHHHHHHHHHHHhhcccceeeEEEEEcCCc
Confidence 34566677778889999999999999988668888887766655
No 129
>PLN02265 probable phenylalanyl-tRNA synthetase beta chain
Probab=40.60 E-value=60 Score=26.02 Aligned_cols=58 Identities=14% Similarity=0.265 Sum_probs=33.9
Q ss_pred CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
+.+|++++++|.+|-.+.....| .+|-...= -.++.. .+ .|..+..+.+.++..||++
T Consensus 474 ~~~p~klFEiG~V~~~~~~~~~~---~~e~~~la-~~~~g~--~~--~f~~ikg~le~ll~~l~i~ 531 (597)
T PLN02265 474 APKPIKLFEVSDVVLLDESKDVG---ARNSRRLA-ALYCGT--TS--GFEVIHGLVDRIMEVLGIP 531 (597)
T ss_pred CCCCeeEEEeEeEEecCCcccCC---cchhhEEE-EEEECC--CC--CHhhHHHHHHHHHHHcCCc
Confidence 45699999999999443211111 12332221 222221 12 2677888889999999984
No 130
>PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons. The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) (2.7.7.49 from EC). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Retroviral reverse transcriptase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [].; GO: 0003723 RNA binding, 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 3RWE_C 3DU6_B 3DU5_A 3KYL_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B ....
Probab=33.63 E-value=93 Score=20.01 Aligned_cols=34 Identities=15% Similarity=0.214 Sum_probs=23.9
Q ss_pred eeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542 39 FLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKY 76 (86)
Q Consensus 39 F~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~ 76 (86)
..++|+..++.+.+.+ ..+++.+...++++|+..
T Consensus 160 rY~DD~~i~~~~~~~~----~~~~~~i~~~~~~~gl~l 193 (214)
T PF00078_consen 160 RYADDILIISKSKEEL----QKILEKISQWLEELGLKL 193 (214)
T ss_dssp EETTEEEEEESSHHHH----HHHHHHHHHHHHHTTSBC
T ss_pred EeccccEEEECCHHHH----HHHHHHHHHHHHHCCCEE
Confidence 4589999999985554 456666666777777653
No 131
>PF03462 PCRF: PCRF domain; InterPro: IPR005139 This domain is found in peptide chain release factors. Peptide chain release factors are important for protein synthesis since they direct the termination of translation in response to the peptide chain termination codons UAG and UAA. These are structurally distinct but both contain the PCRF domain [].; GO: 0016149 translation release factor activity, codon specific, 0006415 translational termination, 0005737 cytoplasm; PDB: 3D5A_X 3D5C_X 3MR8_V 3MS0_V 3F1G_X 3F1E_X 1ZBT_A 2IHR_1 2X9R_Y 2X9T_Y ....
Probab=33.58 E-value=1.2e+02 Score=18.82 Aligned_cols=43 Identities=14% Similarity=0.021 Sum_probs=29.5
Q ss_pred eeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEecCCC
Q psy5542 42 KDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHGA 85 (86)
Q Consensus 42 ~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~~g~ 85 (86)
.+++.=.-. .+|.-+...+..+|.+..++-|.++.++....|+
T Consensus 50 leI~aG~GG-~EA~lfa~~L~~MY~~~a~~~gw~~~~l~~~~~~ 92 (115)
T PF03462_consen 50 LEIRAGAGG-DEACLFAEELFRMYQRYAERRGWKVEVLDYSPGE 92 (115)
T ss_dssp EEEEE-SST-HHHHHHHHHHHHHHHHHHHHTT-EEEEEEEEE-S
T ss_pred EEEecCCCc-hHHHHHHHHHHHHHHHHHHHcCCEEEEEecCCCC
Confidence 344444343 4455577899999999999999999888877654
No 132
>cd03487 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=33.37 E-value=95 Score=20.92 Aligned_cols=35 Identities=9% Similarity=0.175 Sum_probs=24.8
Q ss_pred eeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542 40 LMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKY 76 (86)
Q Consensus 40 ~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~ 76 (86)
..+|+..++.+... +...++.+.+.+.++..|+..
T Consensus 140 YaDD~~i~~~~~~~--~~~~~~~~~i~~~l~~~gL~l 174 (214)
T cd03487 140 YADDITFSSNKKLK--EALDKLLEIIRSILSEEGFKI 174 (214)
T ss_pred EeccEEEEccccch--hHHHHHHHHHHHHHHHCCcee
Confidence 47999999887653 234667777777788777654
No 133
>COG3691 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.27 E-value=1.3e+02 Score=18.75 Aligned_cols=43 Identities=19% Similarity=0.226 Sum_probs=33.4
Q ss_pred eeeeEEcCChHhHHHHHHHHHHHHHHHHHH-cCCcEEEEEecCC
Q psy5542 42 KDLYAFTASEVDANDVYNLVGKCYDDVFNT-LGIKYRKVIVRHG 84 (86)
Q Consensus 42 ~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~-lgi~~~~~~~~~g 84 (86)
.+.+-|-++..+|++....+.+..+.+... +.|.+.+.....|
T Consensus 32 ~~~s~~~as~a~ae~~La~lt~kAr~veSepc~I~~ei~~vedg 75 (98)
T COG3691 32 AEYSRFFATRAEAEEALAALTEKARAVESEPCEIEYEITDVEDG 75 (98)
T ss_pred EEEEEEecCHHHHHHHHHHHHHHHHhhccCcceeeeeeEeccCc
Confidence 455667777889998888888888888775 7888887766655
No 134
>PF07870 DUF1657: Protein of unknown function (DUF1657); InterPro: IPR012452 This domain appears to be restricted to the Bacillales.
Probab=32.14 E-value=42 Score=18.09 Aligned_cols=29 Identities=14% Similarity=0.456 Sum_probs=22.1
Q ss_pred eeEEcCChHhHHHHHHHHHHHHHHHHHHc
Q psy5542 44 LYAFTASEVDANDVYNLVGKCYDDVFNTL 72 (86)
Q Consensus 44 ~~~f~~~~~~~~~~~~~~~~~~~~i~~~l 72 (86)
.++..+.+++|.+.|.+..+..+.|...|
T Consensus 18 ~fal~T~d~~AK~~y~~~a~~l~~ii~~L 46 (50)
T PF07870_consen 18 TFALQTQDQEAKQMYEQAAQQLEEIIQDL 46 (50)
T ss_pred HHHhhcCCHHHHHHHHHHHHHHHHHHHHh
Confidence 34455667788889998888888888775
No 135
>PF09830 ATP_transf: ATP adenylyltransferase; InterPro: IPR019200 Diadenosine 5',5'''-P-1,P-4-tetraphosphate (Ap4A) and related diadenosine oligoposphates such as Ap3A are important intracellular and extracellular signalling molecules in prokaryotes and eukaryotes []. They are implicated in the regulation of many vital celluar functions including stress response, cell division and apoptosis. Synthesis primarily occurs via aminoacyl-tRNA synthetases adding the AMP moiety of an aminoacyl-AMP to an acceptor nucleotide, and is an inevitable byproduct of protein synthesis. The concentration of these compounds must thus be controlled both to ensure the proper regulation of various celluar processes, but also to prevent their buildup to potentially toxic levels. This domain is found in a group of ATP adenylyltransferases found in bacteria and lower eukaryotes which catalyse the interconversion of Ap4A to ATP and ADP [, , ]. While these enzymes are thought to act primarily to break down Ap4A, there is evidence to suggest that in some circumstances they may also act in a biosynthetic role. Some variability in substrate range is apparent eg the cyanobacterial enzyme can also utilise Ap3A as a substrate, while the Saccharomyces enzymes apparently cannot.; GO: 0003877 ATP adenylyltransferase activity
Probab=31.99 E-value=73 Score=17.82 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=17.9
Q ss_pred eeEEcCChHhHHHHHHHHHHHHHHHHHHcCCc
Q psy5542 44 LYAFTASEVDANDVYNLVGKCYDDVFNTLGIK 75 (86)
Q Consensus 44 ~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~ 75 (86)
+..+++++++.+ ...+.--. ++++++|+|
T Consensus 34 G~llvk~~~~~~-~~~~~gp~--~iL~~vg~P 62 (62)
T PF09830_consen 34 GMLLVKSEEELD-WLKEDGPM--KILREVGFP 62 (62)
T ss_pred eeeeeCCHHHHH-HHHHcCHH--HHHHHhcCC
Confidence 456677766655 33443332 788888886
No 136
>cd03029 GRX_hybridPRX5 Glutaredoxin (GRX) family, PRX5 hybrid subfamily; composed of hybrid proteins containing peroxiredoxin (PRX) and GRX domains, which is found in some pathogenic bacteria and cyanobacteria. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins. PRX-GRX hybrid proteins from Haemophilus influenza and Neisseria meningitis exhibit GSH-dependent peroxidase activity. The flow of reducing equivalents in the catalytic cycle of the hybrid protein goes from NADPH - GSH reductase - GSH - GRX domain of hybrid - PRX domain of hybrid - peroxide substrate.
Probab=29.93 E-value=94 Score=16.92 Aligned_cols=20 Identities=15% Similarity=0.293 Sum_probs=14.2
Q ss_pred HHHHHHHHcCCcEEEEEecC
Q psy5542 64 CYDDVFNTLGIKYRKVIVRH 83 (86)
Q Consensus 64 ~~~~i~~~lgi~~~~~~~~~ 83 (86)
..++++++.|++|..+..+.
T Consensus 16 ~ak~~L~~~~i~~~~~~v~~ 35 (72)
T cd03029 16 RAKAALQENGISYEEIPLGK 35 (72)
T ss_pred HHHHHHHHcCCCcEEEECCC
Confidence 33566677899988877654
No 137
>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).
Probab=29.42 E-value=1.3e+02 Score=19.79 Aligned_cols=33 Identities=12% Similarity=0.218 Sum_probs=24.1
Q ss_pred eeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEE
Q psy5542 41 MKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYR 77 (86)
Q Consensus 41 ~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~ 77 (86)
.+|+..++.+++.+ .++.+.+...++..|+...
T Consensus 173 ~DD~~i~~~~~~~~----~~~~~~i~~~~~~~gl~ln 205 (226)
T cd01651 173 ADDFVIGVRGPKEA----EEIKELIREFLEELGLELN 205 (226)
T ss_pred cCceEEecCCHHHH----HHHHHHHHHHHHHcCCeec
Confidence 69999999876664 4566667777778887554
No 138
>PRK10329 glutaredoxin-like protein; Provisional
Probab=28.82 E-value=1.1e+02 Score=17.62 Aligned_cols=21 Identities=10% Similarity=0.279 Sum_probs=15.3
Q ss_pred HHHHHHHHHcCCcEEEEEecC
Q psy5542 63 KCYDDVFNTLGIKYRKVIVRH 83 (86)
Q Consensus 63 ~~~~~i~~~lgi~~~~~~~~~ 83 (86)
...+..+++.||+|..+..+.
T Consensus 15 ~~ak~~L~~~gI~~~~idi~~ 35 (81)
T PRK10329 15 HATKRAMESRGFDFEMINVDR 35 (81)
T ss_pred HHHHHHHHHCCCceEEEECCC
Confidence 345566688899998887764
No 139
>smart00460 TGc Transglutaminase/protease-like homologues. Transglutaminases are enzymes that establish covalent links between proteins. A subset of transglutaminase homologues appear to catalyse the reverse reaction, the hydrolysis of peptide bonds. Proteins with this domain are both extracellular and intracellular, and it is likely that the eukaryotic intracellular proteins are involved in signalling events.
Probab=28.74 E-value=1e+02 Score=16.36 Aligned_cols=21 Identities=24% Similarity=0.308 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHcCCcEEEEEe
Q psy5542 61 VGKCYDDVFNTLGIKYRKVIV 81 (86)
Q Consensus 61 ~~~~~~~i~~~lgi~~~~~~~ 81 (86)
...++..+++.+|||.+.+..
T Consensus 12 ~a~l~~~llr~~GIpar~v~g 32 (68)
T smart00460 12 FAALFVALLRSLGIPARVVSG 32 (68)
T ss_pred HHHHHHHHHHHCCCCeEEEee
Confidence 345566788999999988765
No 140
>COG3195 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.54 E-value=1.2e+02 Score=20.81 Aligned_cols=20 Identities=10% Similarity=0.393 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHcCCcEEEEE
Q psy5542 58 YNLVGKCYDDVFNTLGIKYRKVI 80 (86)
Q Consensus 58 ~~~~~~~~~~i~~~lgi~~~~~~ 80 (86)
|..+-+.|. +++|+||+...
T Consensus 109 f~~LN~aY~---~rFgfPfI~aV 128 (176)
T COG3195 109 FTELNAAYV---ERFGFPFIIAV 128 (176)
T ss_pred HHHHHHHHH---HhcCCceEEee
Confidence 344444454 89999988654
No 141
>cd03418 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known i
Probab=27.86 E-value=1.1e+02 Score=16.52 Aligned_cols=21 Identities=14% Similarity=0.298 Sum_probs=14.8
Q ss_pred HHHHHHHHHcCCcEEEEEecC
Q psy5542 63 KCYDDVFNTLGIKYRKVIVRH 83 (86)
Q Consensus 63 ~~~~~i~~~lgi~~~~~~~~~ 83 (86)
....+++++.|++|..+..+.
T Consensus 14 ~~ak~~L~~~~i~~~~i~i~~ 34 (75)
T cd03418 14 VRAKALLDKKGVDYEEIDVDG 34 (75)
T ss_pred HHHHHHHHHCCCcEEEEECCC
Confidence 344566777899998887654
No 142
>TIGR02190 GlrX-dom Glutaredoxin-family domain. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain.
Probab=27.59 E-value=1e+02 Score=17.35 Aligned_cols=21 Identities=5% Similarity=0.177 Sum_probs=15.0
Q ss_pred HHHHHHHHHcCCcEEEEEecC
Q psy5542 63 KCYDDVFNTLGIKYRKVIVRH 83 (86)
Q Consensus 63 ~~~~~i~~~lgi~~~~~~~~~ 83 (86)
...+++++..|++|..+..+.
T Consensus 22 ~~ak~~L~~~gi~y~~idi~~ 42 (79)
T TIGR02190 22 AKAKATLKEKGYDFEEIPLGN 42 (79)
T ss_pred HHHHHHHHHcCCCcEEEECCC
Confidence 444566678899998887654
No 143
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=27.52 E-value=2.1e+02 Score=19.87 Aligned_cols=34 Identities=6% Similarity=-0.060 Sum_probs=28.2
Q ss_pred HhHHHHHHHHHHHHHHHHHHcCCcEEEEEecCCC
Q psy5542 52 VDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHGA 85 (86)
Q Consensus 52 ~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~~g~ 85 (86)
+++.-+...++.+|.+..+..|+.+.++....|+
T Consensus 13 ~Ea~~fa~~L~~my~~~a~~~g~~~~ii~~~~~~ 46 (200)
T PRK08179 13 AECCLAVAKALERLLKEAARQGVRVTVLETETGR 46 (200)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCeEEEEeCCCCC
Confidence 4445477899999999999999999999887765
No 144
>PF00586 AIRS: AIR synthase related protein, N-terminal domain; InterPro: IPR000728 This family includes Hydrogen expression/formation protein, HypE, which may be involved in the maturation of NifE hydrogenase; AIR synthase and FGAM synthase, which are involved in de novo purine biosynthesis; and selenide, water dikinase, an enzyme which synthesizes selenophosphate from selenide and ATP.; GO: 0003824 catalytic activity; PDB: 3VIU_A 2Z1T_A 2Z1U_A 3C9U_B 3C9S_A 3C9R_A 1VQV_A 3C9T_B 3M84_A 3QTY_A ....
Probab=26.72 E-value=1.1e+02 Score=17.86 Aligned_cols=23 Identities=13% Similarity=0.138 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHcCCcEE
Q psy5542 55 NDVYNLVGKCYDDVFNTLGIKYR 77 (86)
Q Consensus 55 ~~~~~~~~~~~~~i~~~lgi~~~ 77 (86)
.+.+.++++-+.+..+.+|++++
T Consensus 70 ~~~l~~~~~Gi~~~~~~~g~~iv 92 (96)
T PF00586_consen 70 PEELKEIVKGIAEACREFGIPIV 92 (96)
T ss_dssp HHHHHHHHHHHHHHHHHHT-EEE
T ss_pred HHHHHHHHHHHHHHHHHhCCcEe
Confidence 44678888889999999999875
No 145
>TIGR03191 benz_CoA_bzdO benzoyl-CoA reductase, bzd-type, O subunit. Members of this family are the O subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=26.31 E-value=1.2e+02 Score=23.30 Aligned_cols=48 Identities=8% Similarity=-0.174 Sum_probs=31.3
Q ss_pred eeceeeeeeeeEEcCChHhHHHHHH-HHHHHHHHHHHHcCCcEEEEEecCCC
Q psy5542 35 RSREFLMKDLYAFTASEVDANDVYN-LVGKCYDDVFNTLGIKYRKVIVRHGA 85 (86)
Q Consensus 35 R~reF~~~d~~~f~~~~~~~~~~~~-~~~~~~~~i~~~lgi~~~~~~~~~g~ 85 (86)
++-+=.+.|+.+++...-+- .+. ... .+++.++++|||+..++.|..+
T Consensus 355 ~li~e~~vDGVI~~~~~~C~--~~s~e~~-~ik~~l~~~GIP~L~ietD~~d 403 (430)
T TIGR03191 355 NIARDWNVDGCMLHLNRGCE--GLSIGIM-ENRLAIAKAGIPIMTFEGNMGD 403 (430)
T ss_pred HHHHHHCCCEEEEcCCCCCc--cchHhHH-HHHHHHHHcCCCEEEEECCCCC
Confidence 33333479999998864442 222 222 3556667899999999988765
No 146
>cd03027 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions. GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions.
Probab=25.98 E-value=1.2e+02 Score=16.62 Aligned_cols=21 Identities=10% Similarity=0.194 Sum_probs=14.9
Q ss_pred HHHHHHHHHcCCcEEEEEecC
Q psy5542 63 KCYDDVFNTLGIKYRKVIVRH 83 (86)
Q Consensus 63 ~~~~~i~~~lgi~~~~~~~~~ 83 (86)
.....+++..||+|..+....
T Consensus 15 ~ka~~~L~~~gi~~~~~di~~ 35 (73)
T cd03027 15 TAVRLFLREKGLPYVEINIDI 35 (73)
T ss_pred HHHHHHHHHCCCceEEEECCC
Confidence 444566778899998877654
No 147
>PTZ00217 flap endonuclease-1; Provisional
Probab=25.82 E-value=1.4e+02 Score=22.78 Aligned_cols=22 Identities=9% Similarity=0.070 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHcCCcEEEEE
Q psy5542 59 NLVGKCYDDVFNTLGIKYRKVI 80 (86)
Q Consensus 59 ~~~~~~~~~i~~~lgi~~~~~~ 80 (86)
..+...+.++++.+||||+.+.
T Consensus 137 ~~~~~~~~~lL~~~Gip~i~AP 158 (393)
T PTZ00217 137 KEQNEDAKKLLRLMGIPVIEAP 158 (393)
T ss_pred HHHHHHHHHHHHHcCCceEECC
Confidence 3466778889999999998653
No 148
>PRK05330 coproporphyrinogen III oxidase; Provisional
Probab=25.79 E-value=74 Score=23.66 Aligned_cols=50 Identities=22% Similarity=0.236 Sum_probs=28.2
Q ss_pred ceeecCCCCCCCceeeceeeeeeeeE--EcCChHhHHHHHHHHHHHHHHHHHH-cCCcE
Q psy5542 21 SKFRDELRPKFGLMRSREFLMKDLYA--FTASEVDANDVYNLVGKCYDDVFNT-LGIKY 76 (86)
Q Consensus 21 ~~fR~E~~~~~Gl~R~reF~~~d~~~--f~~~~~~~~~~~~~~~~~~~~i~~~-lgi~~ 76 (86)
-.+|+|.||-+|++ .+|+.. |-.+-.=+.+.-..++++|..|+++ ...||
T Consensus 174 i~HR~E~RGvGGiF------fD~l~~~~~e~~f~F~~~vg~~fl~aY~pIv~rr~~~~~ 226 (300)
T PRK05330 174 LKHRNEPRGVGGIF------FDDLNSPGFERDFAFTQAVGDAFLDAYLPIVERRKDTPY 226 (300)
T ss_pred hhhcCCCCCCCeee------cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC
Confidence 36899999988865 233322 2111111233445677888888774 55554
No 149
>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]
Probab=25.60 E-value=2.4e+02 Score=19.77 Aligned_cols=61 Identities=13% Similarity=0.129 Sum_probs=41.4
Q ss_pred eeecCCCCCC--CceeeceeeeeeeeEEcCChHhHHHHH---------------------HHHHHHHHHHHHHcCCcEEE
Q psy5542 22 KFRDELRPKF--GLMRSREFLMKDLYAFTASEVDANDVY---------------------NLVGKCYDDVFNTLGIKYRK 78 (86)
Q Consensus 22 ~fR~E~~~~~--Gl~R~reF~~~d~~~f~~~~~~~~~~~---------------------~~~~~~~~~i~~~lgi~~~~ 78 (86)
+|..+.-.+. |.+.+|-....+++.+..+.+-.+ .+ .++.....++-+.||+|+..
T Consensus 37 vfkp~iD~R~~~~~V~Sr~G~~~~A~~i~~~~~i~~-~i~~~~~~~~~~~v~IDEaQF~~~~~v~~l~~lad~lgi~Vi~ 115 (201)
T COG1435 37 VFKPAIDTRYGVGKVSSRIGLSSEAVVIPSDTDIFD-EIAALHEKPPVDCVLIDEAQFFDEELVYVLNELADRLGIPVIC 115 (201)
T ss_pred EEecccccccccceeeeccCCcccceecCChHHHHH-HHHhcccCCCcCEEEEehhHhCCHHHHHHHHHHHhhcCCEEEE
Confidence 5555554443 888889898889888876543222 11 24667788888899999987
Q ss_pred EEecC
Q psy5542 79 VIVRH 83 (86)
Q Consensus 79 ~~~~~ 83 (86)
.-.++
T Consensus 116 ~GL~~ 120 (201)
T COG1435 116 YGLDT 120 (201)
T ss_pred ecccc
Confidence 65543
No 150
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase.
Probab=25.33 E-value=1.3e+02 Score=16.48 Aligned_cols=20 Identities=10% Similarity=0.328 Sum_probs=12.9
Q ss_pred HHHHHHHHcCCcEEEEEecC
Q psy5542 64 CYDDVFNTLGIKYRKVIVRH 83 (86)
Q Consensus 64 ~~~~i~~~lgi~~~~~~~~~ 83 (86)
..++.+++.|++|..+..+.
T Consensus 14 ~ak~~L~~~~i~~~~~di~~ 33 (72)
T TIGR02194 14 MTKKALEEHGIAFEEINIDE 33 (72)
T ss_pred HHHHHHHHCCCceEEEECCC
Confidence 34455667788887776654
No 151
>COG0695 GrxC Glutaredoxin and related proteins [Posttranslational modification, protein turnover, chaperones]
Probab=25.24 E-value=1.4e+02 Score=17.10 Aligned_cols=22 Identities=18% Similarity=0.383 Sum_probs=16.6
Q ss_pred HHHHHHHHHcCCcEEEEEecCC
Q psy5542 63 KCYDDVFNTLGIKYRKVIVRHG 84 (86)
Q Consensus 63 ~~~~~i~~~lgi~~~~~~~~~g 84 (86)
...++++++.|++|..+..+.+
T Consensus 15 ~~ak~~L~~~g~~~~~i~~~~~ 36 (80)
T COG0695 15 KRAKRLLDRKGVDYEEIDVDDD 36 (80)
T ss_pred HHHHHHHHHcCCCcEEEEecCC
Confidence 4456777899999998777654
No 152
>PF03445 DUF294: Putative nucleotidyltransferase DUF294; InterPro: IPR005105 This domain is found associated with an N-terminal cyclic nucleotide-binding domain (IPR000595 from INTERPRO) and two CBS domains (IPR000644 from INTERPRO). This domain, normally represents the C-terminal region, is uncharacterised; however, it seems to be similar to the nucleotidyltransferase domain (IPR002934 from INTERPRO), conserving the DXD motif, which strongly suggests that proteins containing this domain are also nucleotidyltransferases.; GO: 0008773 [protein-PII] uridylyltransferase activity
Probab=25.00 E-value=1.9e+02 Score=18.38 Aligned_cols=56 Identities=13% Similarity=0.134 Sum_probs=36.0
Q ss_pred chhhheeeceeecCCCCCCCceeeceeeeeeeeEEcC-ChHhHHHHHHHHHHHHHHHHHHcCCcE
Q psy5542 13 PLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTA-SEVDANDVYNLVGKCYDDVFNTLGIKY 76 (86)
Q Consensus 13 P~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~-~~~~~~~~~~~~~~~~~~i~~~lgi~~ 76 (86)
|+-+...|+.=|.|+-+..- ++-+-+|.. ..+...+.+..+.+.+...+..+|+|.
T Consensus 49 ~~a~lalGS~GR~E~~~~sD--------qD~alv~~d~~~~~~~~~f~~~a~~~~~~L~~~G~~~ 105 (138)
T PF03445_consen 49 PFAWLALGSYGRREQTLYSD--------QDNALVFEDEESEEDRAYFEAFAERLVDALDECGFPP 105 (138)
T ss_pred CEEEEEECcccccCCCcCcc--------ccceeeecCccchhHHHHHHHHHHHHHHHHHHcCCCC
Confidence 45566677777788765321 222233322 124456678899999999999999985
No 153
>TIGR03072 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.
Probab=24.70 E-value=2.4e+02 Score=19.59 Aligned_cols=34 Identities=6% Similarity=-0.037 Sum_probs=27.7
Q ss_pred HhHHHHHHHHHHHHHHHHHHcCCcEEEEEecCCC
Q psy5542 52 VDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHGA 85 (86)
Q Consensus 52 ~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~~g~ 85 (86)
+++.-+...++.+|.+..+..|..+.++....|+
T Consensus 12 ~Ea~lfa~~L~~my~~~a~~~g~~~eii~~~~~~ 45 (200)
T TIGR03072 12 AECCLAVAKALERLTREAAARGVRVEVLEQEPGE 45 (200)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCeEEEEeCCCCC
Confidence 3445477899999999999999999998887654
No 154
>TIGR03279 cyano_FeS_chp putative FeS-containing Cyanobacterial-specific oxidoreductase. Members of this protein family are predicted FeS-containing oxidoreductases of unknown function, apparently restricted to and universal across the Cyanobacteria. The high trusted cutoff score for this model, 700 bits, excludes homologs from other lineages. This exclusion seems justified because a significant number of sequence positions are simultaneously unique to and invariant across the Cyanobacteria, suggesting a specialized, conserved function, perhaps related to photosynthesis. A distantly related protein family, TIGR03278, in universal in and restricted to archaeal methanogens, and may be linked to methanogenesis.
Probab=24.70 E-value=1.6e+02 Score=23.02 Aligned_cols=44 Identities=23% Similarity=0.187 Sum_probs=31.8
Q ss_pred CceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEE
Q psy5542 32 GLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRK 78 (86)
Q Consensus 32 Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~ 78 (86)
||.|.|+-. ..+..| +.++|.+.+..+...-++..+++|-+++.
T Consensus 223 GlTk~R~~l-~~l~~~--~~e~A~~vi~~ie~~q~~~~~~~g~~fv~ 266 (433)
T TIGR03279 223 GLTRFRPEE-DELTPV--TPECARRVIAQVEALQTQFQRQLGSRFAW 266 (433)
T ss_pred ccccCCCCC-CCCccC--CHHHHHHHHHHHHHHHHHHHHHcCCceEE
Confidence 677777642 455666 45778878788877778888899988764
No 155
>PRK03980 flap endonuclease-1; Provisional
Probab=24.57 E-value=1.5e+02 Score=21.61 Aligned_cols=20 Identities=15% Similarity=0.321 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHcCCcEEEEE
Q psy5542 61 VGKCYDDVFNTLGIKYRKVI 80 (86)
Q Consensus 61 ~~~~~~~i~~~lgi~~~~~~ 80 (86)
+.+...++++.+||||+.+.
T Consensus 84 ~~~~~k~lL~~~GIp~i~AP 103 (292)
T PRK03980 84 IVEDSKKLLDLMGIPYVQAP 103 (292)
T ss_pred HHHHHHHHHHHCCCCEEecC
Confidence 77788899999999998764
No 156
>PF09182 PuR_N: Bacterial purine repressor, N-terminal; InterPro: IPR015265 The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1O57_B 1P4A_D.
Probab=24.48 E-value=99 Score=18.11 Aligned_cols=33 Identities=15% Similarity=0.070 Sum_probs=21.9
Q ss_pred HhHHHHHHHHHHHHHHHHHHcCCc-EEEEEecCC
Q psy5542 52 VDANDVYNLVGKCYDDVFNTLGIK-YRKVIVRHG 84 (86)
Q Consensus 52 ~~~~~~~~~~~~~~~~i~~~lgi~-~~~~~~~~g 84 (86)
+.|..++.+-+.++++.|+..|+- ...+...+|
T Consensus 31 ~~AKSsISEDl~iik~~~~~~g~G~ieT~~GaaG 64 (70)
T PF09182_consen 31 GAAKSSISEDLSIIKETFEKEGLGRIETVPGAAG 64 (70)
T ss_dssp T--HHHHHHHHHHHHHHHHHTTSEEEEEE-STT-
T ss_pred cccccchHHHHHHHHHHHHHcCCceEEEecCCCC
Confidence 456667788999999999999985 444444333
No 157
>PRK10638 glutaredoxin 3; Provisional
Probab=24.05 E-value=1.4e+02 Score=16.88 Aligned_cols=22 Identities=9% Similarity=0.350 Sum_probs=15.7
Q ss_pred HHHHHHHHHcCCcEEEEEecCC
Q psy5542 63 KCYDDVFNTLGIKYRKVIVRHG 84 (86)
Q Consensus 63 ~~~~~i~~~lgi~~~~~~~~~g 84 (86)
.....+++..|++|..+..+..
T Consensus 16 ~~a~~~L~~~gi~y~~~dv~~~ 37 (83)
T PRK10638 16 HRAKALLNSKGVSFQEIPIDGD 37 (83)
T ss_pred HHHHHHHHHcCCCcEEEECCCC
Confidence 4445667788999988877643
No 158
>PLN02873 coproporphyrinogen-III oxidase
Probab=24.00 E-value=81 Score=23.17 Aligned_cols=49 Identities=27% Similarity=0.202 Sum_probs=27.4
Q ss_pred eeecCCCCCCCceeeceeeeeeeeE--EcCChHhHHHHHHHHHHHHHHHHHH-cCCcE
Q psy5542 22 KFRDELRPKFGLMRSREFLMKDLYA--FTASEVDANDVYNLVGKCYDDVFNT-LGIKY 76 (86)
Q Consensus 22 ~fR~E~~~~~Gl~R~reF~~~d~~~--f~~~~~~~~~~~~~~~~~~~~i~~~-lgi~~ 76 (86)
.+|+|.||-+|++ .+|+-. |.....=+.+.-..++.+|..|+++ .+.+|
T Consensus 148 ~HR~E~RGvGGiF------fDdln~~~~e~~f~f~~~vg~afl~aY~pIv~rr~~~~~ 199 (274)
T PLN02873 148 KHRGERRGLGGIF------FDDLNDRDQEDLLAFATDVANSVVPAYLPIVEKRKDDPF 199 (274)
T ss_pred hhcCCCCCCceee------cCCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhCCCCC
Confidence 6899999988865 233221 1111111233445677778887774 44444
No 159
>PF13521 AAA_28: AAA domain; PDB: 1LW7_A.
Probab=23.33 E-value=1.3e+02 Score=19.05 Aligned_cols=23 Identities=17% Similarity=0.287 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHcCCcEEEEE
Q psy5542 58 YNLVGKCYDDVFNTLGIKYRKVI 80 (86)
Q Consensus 58 ~~~~~~~~~~i~~~lgi~~~~~~ 80 (86)
-..+-+.+..+++++|++|..+.
T Consensus 134 r~~~~~~~~~~l~~~~~~~~~v~ 156 (163)
T PF13521_consen 134 RERIDELLKELLERHGIPYIIVP 156 (163)
T ss_dssp HHHHHHHHHHHHHGGG---EEEE
T ss_pred HHHHHHHHHHHHHHCCCeEEEeC
Confidence 35778888889999999999885
No 160
>PF04908 SH3BGR: SH3-binding, glutamic acid-rich protein; InterPro: IPR006993 This family of proteins, which contains SH3BGRL3, is functionally uncharacterised. SH3BGRL3 is a highly conserved small protein, which is widely expressed and shows a significant similarity to glutaredoxin 1 (GRX1) of Escherichia coli which is predicted to belong to the thioredoxin superfamily. However, SH3BGRL3 lacks both conserved cysteine residues, which characterise the enzymatic active site of GRX. This structural feature raises the possibility that SH3BGRL3 and its homologues could function as endogenous modulators of GRX activity []. ; PDB: 1SJ6_A 1U6T_A 1WRY_A 1T1V_B 1J0F_A 2CT6_A.
Probab=23.23 E-value=1.9e+02 Score=17.74 Aligned_cols=38 Identities=8% Similarity=0.015 Sum_probs=23.6
Q ss_pred eEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEecC
Q psy5542 45 YAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRH 83 (86)
Q Consensus 45 ~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~~ 83 (86)
++|.++-.. ...+.+-.+-+..|++..+|+|..+..++
T Consensus 4 ~vy~ss~sg-~~~ikk~q~~v~~iL~a~kI~fe~vDIa~ 41 (99)
T PF04908_consen 4 KVYISSISG-SREIKKRQQRVLMILEAKKIPFEEVDIAM 41 (99)
T ss_dssp EEEE-SS-S-SHHHHHHHHHHHHHHHHTT--EEEEETTT
T ss_pred EEEEecccC-CHHHHHHHHHHHHHHHHcCCCcEEEeCcC
Confidence 455554333 33456667778888999999999887765
No 161
>TIGR02189 GlrX-like_plant Glutaredoxin-like family. This family of glutaredoxin-like proteins is aparrently limited to plants. Multiple isoforms are found in A. thaliana and O.sativa.
Probab=23.09 E-value=1.5e+02 Score=17.70 Aligned_cols=22 Identities=14% Similarity=0.135 Sum_probs=16.4
Q ss_pred HHHHHHHHHHcCCcEEEEEecC
Q psy5542 62 GKCYDDVFNTLGIKYRKVIVRH 83 (86)
Q Consensus 62 ~~~~~~i~~~lgi~~~~~~~~~ 83 (86)
+...+++++++|++|..+..+.
T Consensus 21 C~~ak~~L~~~~i~~~~vdid~ 42 (99)
T TIGR02189 21 CHVVKRLLLTLGVNPAVHEIDK 42 (99)
T ss_pred HHHHHHHHHHcCCCCEEEEcCC
Confidence 3445668888999998887764
No 162
>TIGR00365 monothiol glutaredoxin, Grx4 family. The gene for the member of this glutaredoxin family in E. coli, originally designated ydhD, is now designated grxD. Its protein, Grx4, is a monothiol glutaredoxin similar to Grx5 of yeast, which is involved in iron-sulfur cluster formation.
Probab=22.95 E-value=1.6e+02 Score=17.45 Aligned_cols=21 Identities=14% Similarity=0.191 Sum_probs=15.8
Q ss_pred HHHHHHHHHHcCCcEEEEEec
Q psy5542 62 GKCYDDVFNTLGIKYRKVIVR 82 (86)
Q Consensus 62 ~~~~~~i~~~lgi~~~~~~~~ 82 (86)
+...+++|+.+|++|..+...
T Consensus 30 C~~ak~lL~~~~i~~~~~di~ 50 (97)
T TIGR00365 30 SARAVQILKACGVPFAYVNVL 50 (97)
T ss_pred HHHHHHHHHHcCCCEEEEECC
Confidence 445567788899999887764
No 163
>KOG2520|consensus
Probab=22.79 E-value=79 Score=26.71 Aligned_cols=22 Identities=18% Similarity=0.194 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHcCCcEEEEE
Q psy5542 59 NLVGKCYDDVFNTLGIKYRKVI 80 (86)
Q Consensus 59 ~~~~~~~~~i~~~lgi~~~~~~ 80 (86)
..|..-...+++.|||||+.+-
T Consensus 465 ~~m~~e~QElL~~fGIPyI~AP 486 (815)
T KOG2520|consen 465 SDMFKELQELLRLFGIPYIIAP 486 (815)
T ss_pred HHHHHHHHHHHHHcCCceeccc
Confidence 4566677888999999999873
No 164
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=22.25 E-value=2.1e+02 Score=17.90 Aligned_cols=30 Identities=0% Similarity=-0.023 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHHHHcCCcEEEEEecC
Q psy5542 54 ANDVYNLVGKCYDDVFNTLGIKYRKVIVRH 83 (86)
Q Consensus 54 ~~~~~~~~~~~~~~i~~~lgi~~~~~~~~~ 83 (86)
.++.+.+++.-+..+++.++..+.++.+|+
T Consensus 12 s~~~l~~fl~ev~~i~~~~~~~v~vi~~D~ 41 (126)
T PF09967_consen 12 SDEELRRFLSEVAGILRRFPAEVHVIQFDA 41 (126)
T ss_pred CHHHHHHHHHHHHHHHHhCCCCEEEEEECC
Confidence 355677788888888888877777777765
No 165
>cd08025 RNR_PFL_like_DUF711 Uncharacterized proteins with similarity to Ribonucleotide reductase and Pyruvate formate lyase. This subfamily contains Streptococcus pneumoniae Sp0239 and similar uncharacterized proteins. Sp0239 is structurally similar to ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL), which are believed to have diverged from a common ancestor. RNR and PFL possess a ten-stranded alpha-beta barrel domain that hosts the active site, and are radical enzymes. RNRs are found in all organisms and provide the only mechanism by which nucleotides are converted to deoxynucleotides. PFL is an essential enzyme in anaerobic bacteria that catalyzes the conversion of pyruvate and CoA to acteylCoA and formate.
Probab=22.02 E-value=3.4e+02 Score=21.11 Aligned_cols=52 Identities=8% Similarity=-0.035 Sum_probs=32.2
Q ss_pred ceeeceeeeeeeeEEcCCh---HhHH-------HHHHHHHHHHHHHHHHcCCcEEEEEecCC
Q psy5542 33 LMRSREFLMKDLYAFTASE---VDAN-------DVYNLVGKCYDDVFNTLGIKYRKVIVRHG 84 (86)
Q Consensus 33 l~R~reF~~~d~~~f~~~~---~~~~-------~~~~~~~~~~~~i~~~lgi~~~~~~~~~g 84 (86)
.+++|.-||-=--.-|.+. ...+ .....+.+..+.++++.|+|++..+.+..
T Consensus 14 ~ldiRTiT~gisL~~c~~~d~~~~~~~i~~ki~~~a~~lv~~~~~i~~e~GipI~nkRIsvt 75 (400)
T cd08025 14 NLDIRTVTLGISLLDCIDPDIDELCENIYEKITSAAKRLVETVEEVSSELGVPIVNKRISVT 75 (400)
T ss_pred CCCeEEEeeeecccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCeEEEEEEeeC
Confidence 5677777764333333332 1112 23345678888899999999988877654
No 166
>COG0072 PheT Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis]
Probab=21.92 E-value=92 Score=25.30 Aligned_cols=67 Identities=10% Similarity=0.179 Sum_probs=39.6
Q ss_pred cCCcc-hhhheeeceeecCCCCC------CCceeeceeeeeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEe
Q psy5542 9 HKALP-LLLYQFTSKFRDELRPK------FGLMRSREFLMKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIV 81 (86)
Q Consensus 9 yr~LP-~~l~q~~~~fR~E~~~~------~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~ 81 (86)
.++.| ++++++|.+|-.+.... .|+.-.... .-.+-.. ... .|..+....+.+++.||+++.....
T Consensus 424 ~r~~~~~~iFEiG~v~~~~~~~~~~~~~~~~l~~g~~~----~~~w~~~-~~v--~f~d~Kg~ve~ll~~lg~~~~~~~~ 496 (650)
T COG0072 424 NRKNPDVRIFEIGDVFVKDEEAERETRHLAGLAAGLAG----EESWQGK-RPV--DFYDAKGDLEALLEALGVEYEFEPA 496 (650)
T ss_pred ccCCCCeeEEEeeeeEecCCcccchhHHHHHHhhcccc----ccccccC-CCc--CHHHHHHHHHHHHHHhCCceEEEEc
Confidence 57889 99999999998752211 022222111 1111111 122 3577888889999999977666554
Q ss_pred c
Q psy5542 82 R 82 (86)
Q Consensus 82 ~ 82 (86)
.
T Consensus 497 ~ 497 (650)
T COG0072 497 E 497 (650)
T ss_pred c
Confidence 4
No 167
>TIGR02200 GlrX_actino Glutaredoxin-like protein. This family of glutaredoxin-like proteins is limited to the Actinobacteria and contains the conserved CxxC motif.
Probab=21.67 E-value=1.5e+02 Score=15.83 Aligned_cols=18 Identities=22% Similarity=0.346 Sum_probs=11.0
Q ss_pred HHHHHHcCCcEEEEEecC
Q psy5542 66 DDVFNTLGIKYRKVIVRH 83 (86)
Q Consensus 66 ~~i~~~lgi~~~~~~~~~ 83 (86)
..+++++|++|..+..+.
T Consensus 17 ~~~L~~~~~~~~~idi~~ 34 (77)
T TIGR02200 17 MRTLDKLGAAYEWVDIEE 34 (77)
T ss_pred HHHHHHcCCceEEEeCcC
Confidence 345566777777665543
No 168
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=21.59 E-value=1.7e+02 Score=16.48 Aligned_cols=34 Identities=9% Similarity=0.182 Sum_probs=24.1
Q ss_pred hHhHHHHHHHHHHHHHHHHHHcCCcEEEEEecCC
Q psy5542 51 EVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHG 84 (86)
Q Consensus 51 ~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~~g 84 (86)
.+++.+.+..-.......+...|+....+....|
T Consensus 46 ~~~~~~~L~~~~~~L~~~L~~~G~~~~~~~v~~~ 79 (85)
T PF02120_consen 46 NPETKELLRQNLPELKERLQAQGLEVVNLSVSQG 79 (85)
T ss_dssp SSHHHHHHHHTHHHHHHHHHTTT-EEEEEEEESS
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCeEEEEEEEC
Confidence 4455657788888888888999998776665544
No 169
>COG4071 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.56 E-value=1.3e+02 Score=21.70 Aligned_cols=35 Identities=11% Similarity=0.228 Sum_probs=24.9
Q ss_pred EcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEecCC
Q psy5542 47 FTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHG 84 (86)
Q Consensus 47 f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~~g 84 (86)
.|.-.++...+ ..+.+++|.+++|.++.++.+||.
T Consensus 135 a~plPenp~~v---A~el~~Ei~rr~GvDV~v~v~DTD 169 (278)
T COG4071 135 ACPLPENPKKV---AEELYKEIKRRLGVDVVVMVADTD 169 (278)
T ss_pred eccCCCChHHH---HHHHHHHHHHHhCCceEEEEecCc
Confidence 34434555544 345677888999999999999875
No 170
>TIGR02260 benz_CoA_red_B benzoyl-CoA reductase, bcr type, subunit B. This model describes B, or beta, subunit of the bcr type of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA.
Probab=21.56 E-value=1.4e+02 Score=22.76 Aligned_cols=43 Identities=5% Similarity=-0.160 Sum_probs=27.7
Q ss_pred eeeeeEEcCChHhHHHHHH-HHHHHHHHHHHHcCCcEEEEEecCCC
Q psy5542 41 MKDLYAFTASEVDANDVYN-LVGKCYDDVFNTLGIKYRKVIVRHGA 85 (86)
Q Consensus 41 ~~d~~~f~~~~~~~~~~~~-~~~~~~~~i~~~lgi~~~~~~~~~g~ 85 (86)
..|+.+++...-+- .+. ....+-+.+.+++|||+..++.|.++
T Consensus 350 ~aDGVI~~~~~~C~--~~~~e~~~~~~~l~e~~GIP~L~iE~D~~d 393 (413)
T TIGR02260 350 EADGLLINSIKSCN--SFSAGQLLMMREIEKRTGKPAAFIETDLVD 393 (413)
T ss_pred CCCEEEEeccCCCC--cchhhhHHHHHHHHHHcCCCEEEEEcCCCC
Confidence 68888888754331 222 23344445556799999999888654
No 171
>PF09003 Phage_integ_N: Bacteriophage lambda integrase, N-terminal domain ; InterPro: IPR015094 The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage []. ; GO: 0003677 DNA binding, 0008907 integrase activity, 0015074 DNA integration; PDB: 1Z1G_B 1Z1B_A 2WCC_3 1KJK_A.
Probab=21.37 E-value=1.9e+02 Score=17.05 Aligned_cols=41 Identities=22% Similarity=0.270 Sum_probs=22.9
Q ss_pred CCcchhhheeeceeecCCCCCCCceeeceeeeeeeeEEcCChHhHH
Q psy5542 10 KALPLLLYQFTSKFRDELRPKFGLMRSREFLMKDLYAFTASEVDAN 55 (86)
Q Consensus 10 r~LP~~l~q~~~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~ 55 (86)
++||--||. |..++...|.++.|.-.--..|++.++..+|.
T Consensus 10 ~~lP~NLy~-----~~dkr~~k~Yy~Yr~P~tGk~~~LG~d~~~Ai 50 (75)
T PF09003_consen 10 RDLPPNLYC-----RKDKRNGKGYYQYRNPITGKEHGLGTDRAEAI 50 (75)
T ss_dssp GGS-TTEEE-----ETT-----SEEEEE-TTTS-EEEEES-HHHHH
T ss_pred CCCCCCccc-----cCCcCcceeEEEEecCCCCceeeCCCCHHHHH
Confidence 788877764 34444445677777766777899999776665
No 172
>COG0562 Glf UDP-galactopyranose mutase [Cell envelope biogenesis, outer membrane]
Probab=21.34 E-value=1.4e+02 Score=22.95 Aligned_cols=38 Identities=16% Similarity=0.184 Sum_probs=24.9
Q ss_pred ceeecCCCCCCCceeeceeeeeeeeEEcCChHhHHHHHHHHHH
Q psy5542 21 SKFRDELRPKFGLMRSREFLMKDLYAFTASEVDANDVYNLVGK 63 (86)
Q Consensus 21 ~~fR~E~~~~~Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~~~ 63 (86)
+|| +|.-++.|++ +.+=-.|+||++.+..-+....+.+
T Consensus 39 NaY-de~d~~tGIl----vHkYGpHIFHT~~~~Vwdyv~~F~e 76 (374)
T COG0562 39 NAY-DEADDQTGIL----VHKYGPHIFHTDNKRVWDYVNQFTE 76 (374)
T ss_pred ccc-cccCCCCCeE----EeeccCceeecCchHHHHHHhhhhh
Confidence 566 6655556654 7778899999987665444444433
No 173
>COG1791 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=21.20 E-value=72 Score=22.03 Aligned_cols=30 Identities=17% Similarity=0.328 Sum_probs=23.8
Q ss_pred CceeeceeeeeeeeEEcCChHhHHHHHHHH
Q psy5542 32 GLMRSREFLMKDLYAFTASEVDANDVYNLV 61 (86)
Q Consensus 32 Gl~R~reF~~~d~~~f~~~~~~~~~~~~~~ 61 (86)
+|.|-|.|.+.|..+.+.+....++..+++
T Consensus 58 ~l~~e~Gyk~~Dvvsv~~~~pk~del~akF 87 (181)
T COG1791 58 RLIRERGYKNRDVVSVSPSNPKLDELRAKF 87 (181)
T ss_pred HHHHhhCCceeeEEEeCCCCccHHHHHHHH
Confidence 588999999999999999877766444443
No 174
>COG4921 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.35 E-value=2.2e+02 Score=18.51 Aligned_cols=43 Identities=9% Similarity=0.110 Sum_probs=29.4
Q ss_pred eeeeeEEcCChHhHHHHHHHHHHHHHHHHHHcCCcEEEEEecCCCC
Q psy5542 41 MKDLYAFTASEVDANDVYNLVGKCYDDVFNTLGIKYRKVIVRHGAV 86 (86)
Q Consensus 41 ~~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~lgi~~~~~~~~~g~~ 86 (86)
+.+...||..+..- ...+.+-.++.+..|+-....+.|-.|++
T Consensus 39 ~v~v~v~~~~~~p~---Lrd~v~ev~~~~n~l~~e~~~IvaE~Gef 81 (131)
T COG4921 39 DVNVFVVCTREPPN---LRDLVEEVSRALNGLDKEDEMIVAEPGEF 81 (131)
T ss_pred eeeEEEEEecCCCc---HHHHHHHHHHHHhccCccCcEEEEcChhh
Confidence 56777788753332 25577777888888888776777777764
No 175
>PF10454 DUF2458: Protein of unknown function (DUF2458); InterPro: IPR018858 This entry represents a family of uncharacterised proteins.
Probab=20.11 E-value=2.2e+02 Score=18.85 Aligned_cols=23 Identities=13% Similarity=0.192 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHcCCcEEEEEe
Q psy5542 59 NLVGKCYDDVFNTLGIKYRKVIV 81 (86)
Q Consensus 59 ~~~~~~~~~i~~~lgi~~~~~~~ 81 (86)
..+.......+++|||||....-
T Consensus 104 ~~m~~~~~~~L~~LgVPfF~~~~ 126 (150)
T PF10454_consen 104 KQMSKEQQAELKELGVPFFYIKE 126 (150)
T ss_pred HHHHHHHHHHHHhcCCCeeeCCC
Confidence 45555666678899999876543
No 176
>TIGR00743 conserved hypothetical protein. These small proteins are approximately 100 amino acids in length and appear to be found only in gamma proteobacteria. The function of this protein family is unknown.
Probab=20.11 E-value=2.3e+02 Score=17.49 Aligned_cols=43 Identities=16% Similarity=0.117 Sum_probs=31.7
Q ss_pred eeeeEEcCChHhHHHHHHHHHHHHHHHHHH-cCCcEEEEEecCC
Q psy5542 42 KDLYAFTASEVDANDVYNLVGKCYDDVFNT-LGIKYRKVIVRHG 84 (86)
Q Consensus 42 ~d~~~f~~~~~~~~~~~~~~~~~~~~i~~~-lgi~~~~~~~~~g 84 (86)
.+.-.+..+.++|+...+.+.+..+.+... +.|.+.+.....|
T Consensus 29 a~~~~~~~~~~~Ae~~l~~l~ekAk~vesepc~I~~~i~~~e~g 72 (95)
T TIGR00743 29 SKFSRFFATRAEAESFLAKLTEKARAVESEPCEIASEITDVEDG 72 (95)
T ss_pred EEEEEEeCCHHHHHHHHHHHHHHHHHhhcCCceeEEEEEEcCCc
Confidence 344455567888999999999999988875 6777776665544
Done!