Query psy5461
Match_columns 221
No_of_seqs 158 out of 1597
Neff 7.7
Searched_HMMs 46136
Date Fri Aug 16 18:10:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5461.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5461hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0465|consensus 100.0 6.3E-35 1.4E-39 265.5 11.4 193 22-218 249-473 (721)
2 PRK00007 elongation factor G; 100.0 4.2E-33 9.1E-38 266.5 18.0 177 42-218 239-445 (693)
3 TIGR00503 prfC peptide chain r 100.0 6.5E-33 1.4E-37 257.2 18.1 167 50-218 242-430 (527)
4 TIGR00484 EF-G translation elo 100.0 7.8E-33 1.7E-37 264.6 18.2 194 23-218 221-443 (689)
5 PRK00741 prfC peptide chain re 100.0 1.8E-32 3.8E-37 254.3 19.4 169 49-218 240-429 (526)
6 PRK12739 elongation factor G; 100.0 1.1E-32 2.5E-37 263.5 18.0 177 42-218 237-442 (691)
7 PRK13351 elongation factor G; 100.0 1.9E-32 4.1E-37 262.0 18.6 193 23-217 220-440 (687)
8 COG0480 FusA Translation elong 100.0 5.1E-32 1.1E-36 256.3 17.4 195 22-218 219-443 (697)
9 PRK12740 elongation factor G; 100.0 7.9E-31 1.7E-35 250.2 17.6 175 43-217 222-423 (668)
10 PRK10218 GTP-binding protein; 100.0 8.3E-27 1.8E-31 219.1 20.5 187 23-217 119-351 (607)
11 PRK07560 elongation factor EF- 99.9 3.5E-27 7.5E-32 227.0 17.6 159 59-217 198-426 (731)
12 TIGR01394 TypA_BipA GTP-bindin 99.9 3.8E-26 8.2E-31 214.6 20.6 188 23-218 115-348 (594)
13 TIGR01393 lepA GTP-binding pro 99.9 2.5E-25 5.4E-30 209.3 21.4 185 23-217 121-329 (595)
14 PRK05433 GTP-binding protein L 99.9 3.7E-25 8E-30 208.4 20.6 184 23-216 125-332 (600)
15 TIGR00490 aEF-2 translation el 99.9 2.7E-25 5.9E-30 213.5 17.0 148 71-218 243-427 (720)
16 COG4108 PrfC Peptide chain rel 99.9 2.2E-25 4.9E-30 197.4 11.2 166 51-216 244-430 (528)
17 PLN00116 translation elongatio 99.9 4.9E-25 1.1E-29 214.7 12.6 161 48-215 313-522 (843)
18 PTZ00416 elongation factor 2; 99.9 6.1E-24 1.3E-28 206.8 15.2 157 47-215 312-516 (836)
19 COG0481 LepA Membrane GTPase L 99.9 2E-23 4.3E-28 186.6 17.1 186 22-219 126-337 (603)
20 COG1217 TypA Predicted membran 99.9 3.8E-22 8.2E-27 178.0 16.9 185 23-215 119-349 (603)
21 KOG0464|consensus 99.9 2E-23 4.4E-28 184.2 5.8 174 45-219 280-495 (753)
22 cd03690 Tet_II Tet_II: This su 99.9 6.1E-22 1.3E-26 141.8 11.0 85 98-183 1-85 (85)
23 KOG0462|consensus 99.9 6.6E-22 1.4E-26 179.2 13.2 188 22-219 175-387 (650)
24 cd04092 mtEFG2_II_like mtEFG2_ 99.9 1.2E-21 2.5E-26 139.6 11.0 83 101-183 1-83 (83)
25 cd04088 EFG_mtEFG_II EFG_mtEFG 99.9 4.7E-21 1E-25 136.3 10.7 83 101-183 1-83 (83)
26 cd03689 RF3_II RF3_II: this su 99.8 9.1E-21 2E-25 135.7 10.8 81 103-183 1-84 (85)
27 cd04091 mtEFG1_II_like mtEFG1_ 99.8 1.3E-20 2.8E-25 133.7 10.8 81 101-183 1-81 (81)
28 cd03691 BipA_TypA_II BipA_TypA 99.8 9.4E-20 2E-24 130.5 11.2 83 101-183 1-86 (86)
29 cd03699 lepA_II lepA_II: This 99.8 2.4E-19 5.3E-24 128.5 10.5 82 101-183 1-86 (86)
30 KOG0469|consensus 99.8 9E-19 1.9E-23 157.7 7.8 146 72-218 332-525 (842)
31 cd03700 eEF2_snRNP_like_II EF2 99.8 5.9E-18 1.3E-22 123.0 10.1 82 101-182 1-92 (93)
32 cd04090 eEF2_II_snRNP Loc2 eEF 99.7 4.3E-17 9.2E-22 118.8 11.0 81 101-181 1-91 (94)
33 PRK05306 infB translation init 99.7 8.3E-16 1.8E-20 148.3 16.6 182 23-215 388-621 (787)
34 PRK12736 elongation factor Tu; 99.6 4E-14 8.6E-19 127.8 16.4 149 24-184 127-296 (394)
35 TIGR00487 IF-2 translation ini 99.6 5.3E-14 1.1E-18 132.5 17.6 176 23-215 186-419 (587)
36 CHL00189 infB translation init 99.6 3.1E-14 6.8E-19 136.4 14.1 147 23-184 346-501 (742)
37 CHL00071 tufA elongation facto 99.6 3.9E-14 8.5E-19 128.4 13.5 150 23-184 126-306 (409)
38 TIGR00485 EF-Tu translation el 99.6 9.4E-14 2E-18 125.4 14.6 117 56-184 166-296 (394)
39 KOG0460|consensus 99.5 7.3E-15 1.6E-19 127.4 6.8 148 25-184 171-340 (449)
40 PRK12735 elongation factor Tu; 99.5 4.3E-13 9.3E-18 121.2 15.1 117 56-184 166-298 (396)
41 PRK00049 elongation factor Tu; 99.5 1.3E-12 2.9E-17 118.0 15.1 150 23-184 126-298 (396)
42 PTZ00327 eukaryotic translatio 99.5 2E-12 4.3E-17 118.7 15.1 147 26-184 173-350 (460)
43 TIGR00483 EF-1_alpha translati 99.4 1.2E-12 2.6E-17 119.2 13.2 147 25-184 142-311 (426)
44 PRK12317 elongation factor 1-a 99.4 1.8E-12 3.9E-17 118.0 13.1 148 25-185 140-310 (425)
45 PRK04000 translation initiatio 99.4 6.3E-12 1.4E-16 114.1 16.1 149 25-185 140-318 (411)
46 PRK10512 selenocysteinyl-tRNA- 99.4 2.7E-12 5.8E-17 121.8 13.4 145 27-184 107-259 (614)
47 PLN00043 elongation factor 1-a 99.4 4.6E-12 1E-16 116.1 13.8 146 26-184 147-317 (447)
48 PLN03127 Elongation factor Tu; 99.4 7.8E-12 1.7E-16 114.6 14.6 150 23-184 175-349 (447)
49 PTZ00141 elongation factor 1- 99.4 6.1E-12 1.3E-16 115.3 13.5 146 26-184 147-317 (446)
50 PF03144 GTP_EFTU_D2: Elongati 99.4 6.1E-13 1.3E-17 92.2 5.0 68 115-182 1-74 (74)
51 TIGR03680 eif2g_arch translati 99.4 2.1E-11 4.5E-16 110.6 15.5 149 25-185 135-313 (406)
52 KOG0468|consensus 99.4 5.4E-12 1.2E-16 117.3 11.2 144 73-216 428-621 (971)
53 PLN03126 Elongation factor Tu; 99.3 3.3E-11 7.1E-16 111.3 14.5 149 24-184 196-375 (478)
54 COG0050 TufB GTPases - transla 99.3 4.5E-12 9.8E-17 108.4 7.9 148 25-184 129-296 (394)
55 COG5258 GTPBP1 GTPase [General 99.3 5.9E-11 1.3E-15 104.8 13.0 120 53-184 309-436 (527)
56 cd01342 Translation_Factor_II_ 99.2 1.6E-10 3.5E-15 79.6 9.7 78 101-182 1-82 (83)
57 TIGR00475 selB selenocysteine- 99.2 1.3E-10 2.8E-15 109.8 12.1 149 24-183 102-259 (581)
58 PRK05124 cysN sulfate adenylyl 99.1 9.5E-10 2.1E-14 101.6 14.6 146 25-184 161-327 (474)
59 COG5256 TEF1 Translation elong 99.1 1.8E-09 3.9E-14 96.3 15.3 145 25-184 146-315 (428)
60 COG3276 SelB Selenocysteine-sp 99.1 5.1E-10 1.1E-14 100.4 11.3 145 28-185 107-256 (447)
61 TIGR02034 CysN sulfate adenyly 99.1 1.6E-09 3.5E-14 98.3 14.7 148 25-186 134-301 (406)
62 KOG1145|consensus 99.1 8.4E-10 1.8E-14 101.2 10.4 148 22-184 251-407 (683)
63 PRK04004 translation initiatio 99.1 1.5E-09 3.2E-14 102.7 12.4 121 56-183 191-327 (586)
64 cd03698 eRF3_II_like eRF3_II_l 99.0 2.8E-09 6E-14 75.7 10.3 79 100-183 1-83 (83)
65 COG0532 InfB Translation initi 99.0 2.6E-09 5.7E-14 97.8 9.9 150 22-183 105-260 (509)
66 cd03693 EF1_alpha_II EF1_alpha 99.0 6.7E-09 1.5E-13 75.0 10.1 83 98-184 2-88 (91)
67 PRK05506 bifunctional sulfate 99.0 9.8E-09 2.1E-13 98.1 14.1 148 25-185 158-324 (632)
68 PRK14845 translation initiatio 99.0 6.5E-09 1.4E-13 103.2 12.4 127 55-184 645-783 (1049)
69 TIGR00491 aIF-2 translation in 98.9 2.8E-08 6.1E-13 94.0 14.1 125 55-182 188-324 (590)
70 cd04089 eRF3_II eRF3_II: domai 98.8 4.4E-08 9.6E-13 69.3 10.0 78 100-183 1-82 (82)
71 KOG0467|consensus 98.7 1.7E-08 3.7E-13 95.5 6.9 122 95-216 354-506 (887)
72 cd03695 CysN_NodQ_II CysN_NodQ 98.7 1.7E-07 3.8E-12 66.2 10.1 79 101-183 1-81 (81)
73 cd03696 selB_II selB_II: this 98.7 1.5E-07 3.2E-12 66.7 8.9 79 101-183 1-83 (83)
74 cd03694 GTPBP_II Domain II of 98.7 3.1E-07 6.7E-12 65.7 10.2 78 102-183 2-87 (87)
75 cd04168 TetM_like Tet(M)-like 98.6 1.4E-08 3.1E-13 85.8 2.4 62 22-85 176-237 (237)
76 cd03697 EFTU_II EFTU_II: Elong 98.6 3.1E-07 6.7E-12 65.7 8.6 78 102-183 2-85 (87)
77 cd01886 EF-G Elongation factor 98.5 3.8E-08 8.2E-13 84.8 2.4 62 22-85 209-270 (270)
78 cd04169 RF3 RF3 subfamily. Pe 98.5 4.1E-08 8.8E-13 84.4 2.3 62 22-85 206-267 (267)
79 cd03702 IF2_mtIF2_II This fami 98.5 1.4E-06 3.1E-11 63.4 9.3 78 102-184 2-80 (95)
80 cd03692 mtIF2_IVc mtIF2_IVc: t 98.4 3.9E-06 8.5E-11 59.6 10.4 74 104-181 4-82 (84)
81 COG5257 GCD11 Translation init 98.4 3.1E-06 6.6E-11 73.9 11.2 149 25-183 141-312 (415)
82 KOG0461|consensus 98.4 1.4E-06 3.1E-11 76.6 9.2 136 23-170 121-268 (522)
83 KOG0465|consensus 98.4 1.1E-07 2.5E-12 88.3 2.3 80 1-82 300-392 (721)
84 cd04170 EF-G_bact Elongation f 98.4 1.8E-07 3.8E-12 80.2 2.2 62 22-85 207-268 (268)
85 KOG0459|consensus 98.4 2E-06 4.4E-11 76.8 8.8 122 57-184 260-389 (501)
86 cd03701 IF2_IF5B_II IF2_IF5B_I 98.3 7.7E-06 1.7E-10 59.6 9.0 78 102-184 2-80 (95)
87 KOG0458|consensus 98.3 8.2E-06 1.8E-10 75.8 10.8 115 57-184 356-489 (603)
88 COG2895 CysN GTPases - Sulfate 98.0 6.5E-05 1.4E-09 66.4 10.1 144 25-185 140-306 (431)
89 KOG0464|consensus 97.9 1.4E-06 2.9E-11 78.3 -1.0 73 1-75 310-382 (753)
90 cd03703 aeIF5B_II aeIF5B_II: T 97.9 0.00021 4.5E-09 53.3 9.9 81 102-182 2-93 (110)
91 KOG0463|consensus 97.8 9.5E-05 2.1E-09 66.0 7.7 117 56-184 331-455 (641)
92 TIGR00503 prfC peptide chain r 97.8 1.2E-05 2.6E-10 75.4 2.2 75 1-76 267-345 (527)
93 cd03688 eIF2_gamma_II eIF2_gam 97.6 0.00064 1.4E-08 50.7 9.2 81 97-181 2-104 (113)
94 PRK00741 prfC peptide chain re 97.5 3.5E-05 7.6E-10 72.3 1.9 65 1-66 266-334 (526)
95 COG0480 FusA Translation elong 97.5 4.9E-05 1.1E-09 73.3 2.0 67 1-68 270-348 (697)
96 PRK00007 elongation factor G; 97.4 6.1E-05 1.3E-09 73.0 1.2 61 1-62 272-344 (693)
97 PRK12739 elongation factor G; 97.4 6.6E-05 1.4E-09 72.7 1.4 63 1-64 270-343 (691)
98 PF00009 GTP_EFTU: Elongation 97.3 0.00031 6.6E-09 56.8 4.0 62 23-84 121-188 (188)
99 TIGR00484 EF-G translation elo 97.2 0.00011 2.4E-09 71.1 1.3 61 1-62 271-342 (689)
100 KOG1143|consensus 97.2 0.0018 3.9E-08 58.0 8.6 129 53-188 358-494 (591)
101 PF14578 GTP_EFTU_D4: Elongati 97.1 0.0078 1.7E-07 42.4 9.4 72 103-182 7-80 (81)
102 PF14492 EFG_II: Elongation Fa 97.0 0.00058 1.3E-08 47.4 2.9 26 193-218 17-42 (75)
103 PRK13351 elongation factor G; 97.0 0.00025 5.4E-09 68.6 1.1 63 1-64 270-342 (687)
104 PRK07560 elongation factor EF- 97.0 0.00026 5.6E-09 69.0 1.1 63 1-64 248-327 (731)
105 PTZ00416 elongation factor 2; 96.9 0.00028 6.1E-09 69.7 0.6 58 1-58 329-404 (836)
106 TIGR00490 aEF-2 translation el 96.8 0.00031 6.6E-09 68.4 0.2 58 1-58 247-321 (720)
107 PLN00116 translation elongatio 96.7 0.00062 1.3E-08 67.4 1.5 58 1-58 333-408 (843)
108 PRK12740 elongation factor G; 96.6 0.00098 2.1E-08 64.3 1.6 64 1-65 254-326 (668)
109 cd03690 Tet_II Tet_II: This su 95.9 0.0027 5.9E-08 45.0 0.6 33 25-57 2-34 (85)
110 COG4108 PrfC Peptide chain rel 95.8 0.0044 9.6E-08 56.5 1.7 70 1-71 268-341 (528)
111 TIGR00487 IF-2 translation ini 95.5 0.061 1.3E-06 51.4 8.4 80 103-183 495-576 (587)
112 PF10662 PduV-EutP: Ethanolami 95.4 0.036 7.8E-07 43.3 5.3 57 21-79 86-142 (143)
113 KOG0466|consensus 95.3 0.038 8.2E-07 48.5 5.7 109 48-169 207-336 (466)
114 cd01889 SelB_euk SelB subfamil 95.3 0.015 3.3E-07 46.8 3.1 63 24-86 120-189 (192)
115 CHL00189 infB translation init 95.3 0.12 2.5E-06 50.7 9.5 77 105-183 654-732 (742)
116 PRK05306 infB translation init 95.2 0.12 2.5E-06 51.1 9.3 81 102-183 696-778 (787)
117 cd00881 GTP_translation_factor 95.1 0.045 9.8E-07 43.0 5.2 63 23-85 113-189 (189)
118 cd04091 mtEFG1_II_like mtEFG1_ 95.1 0.0053 1.1E-07 42.9 -0.2 35 27-63 1-35 (81)
119 cd01888 eIF2_gamma eIF2-gamma 95.1 0.028 6E-07 46.0 4.0 62 25-86 138-202 (203)
120 cd04092 mtEFG2_II_like mtEFG2_ 94.8 0.0069 1.5E-07 42.5 -0.2 32 27-58 1-32 (83)
121 cd01890 LepA LepA subfamily. 94.6 0.066 1.4E-06 42.0 4.9 61 24-85 119-179 (179)
122 COG0532 InfB Translation initi 94.4 0.32 7E-06 45.4 9.4 81 102-183 415-497 (509)
123 cd04088 EFG_mtEFG_II EFG_mtEFG 94.3 0.0089 1.9E-07 41.8 -0.6 35 27-62 1-35 (83)
124 cd03699 lepA_II lepA_II: This 93.9 0.027 5.9E-07 39.8 1.1 36 27-63 1-36 (86)
125 PRK10218 GTP-binding protein; 93.6 0.028 6.1E-07 53.8 1.0 50 1-58 187-236 (607)
126 cd04165 GTPBP1_like GTPBP1-lik 93.2 0.11 2.5E-06 43.3 3.9 29 56-85 196-224 (224)
127 cd01884 EF_Tu EF-Tu subfamily. 93.1 0.098 2.1E-06 42.8 3.4 62 24-85 117-195 (195)
128 cd01891 TypA_BipA TypA (tyrosi 93.0 0.16 3.4E-06 40.9 4.5 62 24-85 117-194 (194)
129 KOG1144|consensus 92.8 0.18 3.9E-06 49.0 5.1 79 56-139 660-738 (1064)
130 TIGR00436 era GTP-binding prot 92.8 0.19 4.1E-06 43.0 4.8 62 23-86 106-167 (270)
131 TIGR01393 lepA GTP-binding pro 92.6 0.067 1.4E-06 51.2 1.9 55 1-64 172-226 (595)
132 TIGR01394 TypA_BipA GTP-bindin 92.2 0.074 1.6E-06 50.9 1.8 54 1-63 183-236 (594)
133 PRK15467 ethanolamine utilizat 92.1 0.26 5.7E-06 38.5 4.5 58 24-85 91-149 (158)
134 cd01885 EF2 EF2 (for archaea a 91.9 0.19 4.1E-06 42.1 3.6 26 60-85 189-222 (222)
135 cd04139 RalA_RalB RalA/RalB su 91.9 0.22 4.7E-06 38.1 3.8 58 23-82 104-161 (164)
136 COG1160 Predicted GTPases [Gen 91.7 0.27 5.8E-06 45.2 4.7 58 23-87 111-168 (444)
137 PRK05433 GTP-binding protein L 91.7 0.09 1.9E-06 50.4 1.7 56 1-65 176-231 (600)
138 cd01897 NOG NOG1 is a nucleola 91.5 0.26 5.6E-06 38.1 3.8 55 24-82 113-167 (168)
139 cd04145 M_R_Ras_like M-Ras/R-R 91.2 0.33 7.1E-06 37.2 4.2 58 23-82 106-163 (164)
140 cd03689 RF3_II RF3_II: this su 91.2 0.056 1.2E-06 38.2 -0.2 30 29-58 1-33 (85)
141 cd04136 Rap_like Rap-like subf 91.1 0.49 1.1E-05 36.2 5.0 57 23-81 105-161 (163)
142 cd04147 Ras_dva Ras-dva subfam 90.9 0.43 9.3E-06 38.5 4.8 62 24-85 104-165 (198)
143 smart00173 RAS Ras subfamily o 90.9 0.34 7.3E-06 37.3 3.9 58 24-83 105-162 (164)
144 TIGR02528 EutP ethanolamine ut 90.8 0.42 9E-06 36.0 4.3 54 24-79 88-141 (142)
145 cd04157 Arl6 Arl6 subfamily. 90.7 0.54 1.2E-05 35.9 5.0 55 23-80 103-161 (162)
146 cd01860 Rab5_related Rab5-rela 90.7 0.5 1.1E-05 36.2 4.8 59 23-83 105-163 (163)
147 TIGR00491 aIF-2 translation in 90.6 1.6 3.4E-05 41.9 8.9 71 115-189 480-555 (590)
148 PF02421 FeoB_N: Ferrous iron 90.6 0.26 5.6E-06 39.1 3.0 53 22-78 103-156 (156)
149 cd04116 Rab9 Rab9 subfamily. 90.5 0.5 1.1E-05 36.7 4.6 56 24-81 114-169 (170)
150 cd04138 H_N_K_Ras_like H-Ras/N 90.5 0.55 1.2E-05 35.7 4.8 55 24-81 106-160 (162)
151 cd01865 Rab3 Rab3 subfamily. 90.4 0.36 7.7E-06 37.5 3.7 58 24-83 106-163 (165)
152 cd04160 Arfrp1 Arfrp1 subfamil 90.3 0.62 1.3E-05 35.9 5.0 54 24-80 107-166 (167)
153 cd03691 BipA_TypA_II BipA_TypA 90.0 0.091 2E-06 36.9 -0.0 35 27-62 1-35 (86)
154 cd01862 Rab7 Rab7 subfamily. 89.9 0.51 1.1E-05 36.4 4.2 58 24-82 109-166 (172)
155 cd04154 Arl2 Arl2 subfamily. 89.9 0.79 1.7E-05 35.9 5.3 55 23-80 114-172 (173)
156 cd04175 Rap1 Rap1 subgroup. T 89.5 0.52 1.1E-05 36.4 4.0 58 23-82 105-162 (164)
157 cd01863 Rab18 Rab18 subfamily. 89.5 0.79 1.7E-05 35.1 5.0 55 24-81 106-160 (161)
158 cd00880 Era_like Era (E. coli 89.4 0.77 1.7E-05 34.1 4.8 59 23-81 103-162 (163)
159 PRK04004 translation initiatio 89.3 2.4 5.3E-05 40.6 9.0 66 115-184 482-552 (586)
160 cd04151 Arl1 Arl1 subfamily. 89.2 0.68 1.5E-05 35.5 4.4 55 23-80 99-157 (158)
161 cd04106 Rab23_lke Rab23-like s 88.9 0.55 1.2E-05 35.9 3.7 56 24-81 106-161 (162)
162 cd04177 RSR1 RSR1 subgroup. R 88.8 0.86 1.9E-05 35.4 4.8 60 23-83 105-164 (168)
163 cd04158 ARD1 ARD1 subfamily. 88.7 0.99 2.1E-05 35.3 5.1 58 24-84 100-162 (169)
164 cd04156 ARLTS1 ARLTS1 subfamil 88.5 0.99 2.1E-05 34.5 5.0 55 23-80 100-159 (160)
165 cd01855 YqeH YqeH. YqeH is an 88.5 0.88 1.9E-05 36.5 4.8 62 23-84 60-126 (190)
166 cd04143 Rhes_like Rhes_like su 88.5 0.95 2.1E-05 38.3 5.2 63 24-87 113-175 (247)
167 cd04107 Rab32_Rab38 Rab38/Rab3 88.5 0.66 1.4E-05 37.5 4.1 61 24-85 110-170 (201)
168 cd04119 RJL RJL (RabJ-Like) su 88.3 0.84 1.8E-05 34.9 4.4 57 24-82 110-166 (168)
169 cd01864 Rab19 Rab19 subfamily. 88.3 1.1 2.3E-05 34.6 5.0 58 23-81 107-164 (165)
170 cd00876 Ras Ras family. The R 88.3 0.88 1.9E-05 34.4 4.4 57 24-82 104-160 (160)
171 cd04090 eEF2_II_snRNP Loc2 eEF 88.1 0.13 2.9E-06 36.9 -0.3 32 27-58 1-33 (94)
172 cd04150 Arf1_5_like Arf1-Arf5- 88.1 1.1 2.3E-05 34.8 4.9 57 24-80 101-158 (159)
173 cd01887 IF2_eIF5B IF2/eIF5B (i 88.0 1 2.2E-05 34.6 4.7 59 23-81 101-164 (168)
174 cd03700 eEF2_snRNP_like_II EF2 88.0 0.13 2.9E-06 36.8 -0.4 32 27-58 1-33 (93)
175 cd00879 Sar1 Sar1 subfamily. 87.9 1.1 2.3E-05 35.5 4.9 57 23-82 119-190 (190)
176 cd04153 Arl5_Arl8 Arl5/Arl8 su 87.8 1.3 2.8E-05 34.8 5.3 54 24-80 116-173 (174)
177 cd04113 Rab4 Rab4 subfamily. 87.8 1.1 2.3E-05 34.3 4.7 57 23-81 104-160 (161)
178 cd04155 Arl3 Arl3 subfamily. 87.7 0.86 1.9E-05 35.4 4.2 57 24-80 115-172 (173)
179 cd01859 MJ1464 MJ1464. This f 87.6 0.63 1.4E-05 36.0 3.3 58 23-84 40-97 (156)
180 TIGR02729 Obg_CgtA Obg family 87.5 0.82 1.8E-05 40.5 4.3 56 24-82 273-328 (329)
181 COG0481 LepA Membrane GTPase L 87.4 0.16 3.5E-06 47.1 -0.2 64 1-73 178-241 (603)
182 COG4917 EutP Ethanolamine util 87.2 1.7 3.8E-05 33.4 5.3 56 23-81 89-144 (148)
183 smart00175 RAB Rab subfamily o 87.2 0.7 1.5E-05 35.3 3.3 59 23-83 104-162 (164)
184 PRK00089 era GTPase Era; Revie 87.2 1.3 2.8E-05 38.1 5.3 59 24-84 113-172 (292)
185 cd01898 Obg Obg subfamily. Th 87.2 1.2 2.6E-05 34.3 4.6 55 24-81 114-169 (170)
186 TIGR03594 GTPase_EngA ribosome 87.0 0.71 1.5E-05 41.9 3.8 59 23-83 282-344 (429)
187 cd04152 Arl4_Arl7 Arl4/Arl7 su 87.0 1.2 2.6E-05 35.4 4.7 58 23-83 108-170 (183)
188 cd04149 Arf6 Arf6 subfamily. 87.0 1.1 2.3E-05 35.2 4.3 54 24-80 110-167 (168)
189 PRK00093 GTP-binding protein D 86.8 0.74 1.6E-05 42.0 3.8 60 23-82 283-343 (435)
190 PRK04213 GTP-binding protein; 86.8 1.2 2.6E-05 35.8 4.6 60 23-84 129-193 (201)
191 cd04159 Arl10_like Arl10-like 86.8 1.1 2.5E-05 33.5 4.3 56 24-80 101-158 (159)
192 cd01861 Rab6 Rab6 subfamily. 86.7 1.1 2.3E-05 34.2 4.2 56 24-81 105-160 (161)
193 cd00878 Arf_Arl Arf (ADP-ribos 86.6 1.5 3.3E-05 33.4 5.0 55 23-80 99-157 (158)
194 cd04142 RRP22 RRP22 subfamily. 86.6 1.3 2.8E-05 36.0 4.8 61 24-85 116-176 (198)
195 cd01868 Rab11_like Rab11-like. 86.3 1.1 2.3E-05 34.5 4.0 57 24-82 108-164 (165)
196 PRK12299 obgE GTPase CgtA; Rev 86.3 0.9 2E-05 40.4 3.9 59 24-84 271-329 (335)
197 cd04134 Rho3 Rho3 subfamily. 86.0 1.3 2.9E-05 35.3 4.5 64 24-87 104-178 (189)
198 COG1159 Era GTPase [General fu 86.0 1.4 3.1E-05 38.4 4.8 59 25-85 115-174 (298)
199 cd04135 Tc10 TC10 subfamily. 85.8 1.4 3E-05 34.2 4.5 59 23-81 103-172 (174)
200 cd01894 EngA1 EngA1 subfamily. 85.7 0.91 2E-05 34.2 3.3 54 23-82 104-157 (157)
201 cd04176 Rap2 Rap2 subgroup. T 85.7 1.3 2.9E-05 33.9 4.2 58 23-82 105-162 (163)
202 cd01869 Rab1_Ypt1 Rab1/Ypt1 su 85.7 1 2.2E-05 34.7 3.6 57 24-82 107-163 (166)
203 cd00154 Rab Rab family. Rab G 85.7 1.6 3.4E-05 32.6 4.6 55 23-79 104-158 (159)
204 cd04114 Rab30 Rab30 subfamily. 85.6 1.3 2.8E-05 34.2 4.1 56 24-81 112-167 (169)
205 PRK15494 era GTPase Era; Provi 85.5 1.7 3.7E-05 38.6 5.3 57 24-84 160-217 (339)
206 cd01870 RhoA_like RhoA-like su 85.5 1.8 4E-05 33.5 5.0 26 57-82 149-174 (175)
207 cd01878 HflX HflX subfamily. 85.4 1.3 2.9E-05 35.6 4.3 51 24-81 153-203 (204)
208 PRK03003 GTP-binding protein D 85.1 1 2.2E-05 41.8 3.8 62 23-84 321-383 (472)
209 PTZ00369 Ras-like protein; Pro 85.1 1.2 2.6E-05 35.6 3.8 59 24-84 110-168 (189)
210 TIGR00101 ureG urease accessor 84.9 1.4 3.1E-05 36.0 4.2 27 56-82 169-195 (199)
211 PRK14845 translation initiatio 84.8 6.4 0.00014 40.3 9.4 71 115-189 938-1013(1049)
212 cd04101 RabL4 RabL4 (Rab-like4 84.8 1.6 3.5E-05 33.4 4.3 56 24-81 107-162 (164)
213 cd04164 trmE TrmE (MnmE, ThdF, 84.8 1.6 3.4E-05 32.8 4.2 51 23-82 106-156 (157)
214 cd04124 RabL2 RabL2 subfamily. 84.6 1.3 2.8E-05 34.2 3.7 55 24-83 104-158 (161)
215 cd04127 Rab27A Rab27a subfamil 84.5 1.1 2.3E-05 35.1 3.2 57 24-82 120-176 (180)
216 PRK09435 membrane ATPase/prote 84.4 0.78 1.7E-05 40.8 2.6 27 58-84 235-261 (332)
217 COG1160 Predicted GTPases [Gen 84.3 1.1 2.4E-05 41.2 3.6 61 22-82 287-350 (444)
218 smart00177 ARF ARF-like small 84.1 1.9 4.1E-05 34.0 4.5 56 24-82 114-173 (175)
219 cd01881 Obg_like The Obg-like 84.1 1.5 3.3E-05 33.8 3.9 56 24-81 120-175 (176)
220 cd04110 Rab35 Rab35 subfamily. 84.1 1.3 2.7E-05 35.8 3.5 57 24-82 110-166 (199)
221 PTZ00133 ADP-ribosylation fact 84.0 1.7 3.7E-05 34.6 4.2 56 24-82 118-177 (182)
222 PLN00223 ADP-ribosylation fact 83.8 2 4.3E-05 34.3 4.5 56 24-82 118-177 (181)
223 smart00174 RHO Rho (Ras homolo 83.7 1.9 4.2E-05 33.4 4.4 60 23-82 101-171 (174)
224 cd04123 Rab21 Rab21 subfamily. 83.7 1.7 3.7E-05 32.9 4.0 56 24-81 105-160 (162)
225 cd04171 SelB SelB subfamily. 83.2 1.3 2.7E-05 33.8 3.1 55 26-80 106-163 (164)
226 PTZ00099 rab6; Provisional 83.0 1.4 3.1E-05 35.1 3.4 61 24-86 85-145 (176)
227 TIGR00073 hypB hydrogenase acc 82.9 1.7 3.6E-05 35.6 3.8 55 26-81 150-205 (207)
228 cd00157 Rho Rho (Ras homology) 82.9 2 4.3E-05 33.0 4.1 57 24-80 104-170 (171)
229 cd04112 Rab26 Rab26 subfamily. 82.8 1.4 2.9E-05 35.3 3.2 60 24-85 106-165 (191)
230 PRK12298 obgE GTPase CgtA; Rev 82.4 1.8 3.9E-05 39.3 4.2 59 24-84 275-334 (390)
231 TIGR03594 GTPase_EngA ribosome 82.3 4.3 9.2E-05 36.8 6.6 58 23-86 106-163 (429)
232 COG1703 ArgK Putative periplas 82.3 1.3 2.9E-05 38.8 3.1 53 29-83 194-254 (323)
233 cd04140 ARHI_like ARHI subfami 82.0 2.3 5E-05 32.8 4.2 57 23-81 107-163 (165)
234 PRK09518 bifunctional cytidyla 82.0 1.2 2.6E-05 43.5 3.1 62 23-84 560-622 (712)
235 cd04109 Rab28 Rab28 subfamily. 81.8 1.7 3.7E-05 35.6 3.5 57 25-83 110-166 (215)
236 PLN03110 Rab GTPase; Provision 81.6 1.9 4.1E-05 35.5 3.7 60 23-84 116-175 (216)
237 cd04132 Rho4_like Rho4-like su 81.6 2.7 5.8E-05 33.1 4.5 60 24-83 105-167 (187)
238 cd01895 EngA2 EngA2 subfamily. 81.6 2.5 5.4E-05 32.2 4.2 58 23-80 112-172 (174)
239 cd04167 Snu114p Snu114p subfam 81.3 0.89 1.9E-05 37.2 1.7 26 60-85 180-213 (213)
240 PRK13768 GTPase; Provisional 81.2 2.9 6.3E-05 35.5 4.8 29 57-85 221-249 (253)
241 cd04163 Era Era subfamily. Er 81.1 2.8 6.1E-05 31.4 4.3 57 24-82 111-168 (168)
242 cd04125 RabA_like RabA-like su 80.7 2 4.3E-05 34.1 3.5 59 24-84 105-163 (188)
243 cd04141 Rit_Rin_Ric Rit/Rin/Ri 80.5 2 4.4E-05 33.8 3.4 58 23-82 106-163 (172)
244 cd00882 Ras_like_GTPase Ras-li 80.5 3.5 7.6E-05 29.8 4.6 56 23-79 101-156 (157)
245 cd04137 RheB Rheb (Ras Homolog 80.4 2.2 4.7E-05 33.4 3.5 58 24-83 106-163 (180)
246 cd01849 YlqF_related_GTPase Yl 80.3 2.8 6E-05 32.4 4.1 59 22-83 27-85 (155)
247 cd04130 Wrch_1 Wrch-1 subfamil 80.2 2.9 6.3E-05 32.6 4.2 57 24-80 104-171 (173)
248 cd01879 FeoB Ferrous iron tran 79.7 2.3 5.1E-05 32.1 3.5 55 23-81 100-155 (158)
249 smart00178 SAR Sar1p-like memb 79.4 4.6 0.0001 32.1 5.2 55 24-81 118-183 (184)
250 PF00025 Arf: ADP-ribosylation 79.4 4.5 9.8E-05 32.0 5.1 55 24-81 115-174 (175)
251 cd04122 Rab14 Rab14 subfamily. 79.3 2.6 5.7E-05 32.5 3.7 57 23-81 106-162 (166)
252 PF03308 ArgK: ArgK protein; 79.1 1.9 4.1E-05 37.1 2.9 26 57-82 204-229 (266)
253 cd04148 RGK RGK subfamily. Th 78.8 2.7 5.9E-05 34.7 3.8 60 23-84 105-164 (221)
254 cd01875 RhoG RhoG subfamily. 78.4 4 8.6E-05 32.7 4.6 63 24-86 107-180 (191)
255 cd04144 Ras2 Ras2 subfamily. 78.0 3.3 7.1E-05 33.0 3.9 58 23-82 105-162 (190)
256 cd04120 Rab12 Rab12 subfamily. 77.9 4.3 9.3E-05 33.2 4.7 58 24-82 105-162 (202)
257 cd01871 Rac1_like Rac1-like su 77.9 4.5 9.7E-05 31.8 4.7 57 24-80 105-172 (174)
258 PRK12297 obgE GTPase CgtA; Rev 77.8 3.2 6.9E-05 38.2 4.2 55 24-84 274-328 (424)
259 PRK12296 obgE GTPase CgtA; Rev 77.5 2.8 6E-05 39.4 3.8 58 24-84 284-341 (500)
260 cd01876 YihA_EngB The YihA (En 77.3 3.4 7.4E-05 31.1 3.7 58 23-82 109-170 (170)
261 cd01867 Rab8_Rab10_Rab13_like 77.2 3.4 7.3E-05 32.0 3.7 57 24-82 108-164 (167)
262 PLN03118 Rab family protein; P 76.9 3.6 7.8E-05 33.4 4.0 58 25-84 121-178 (211)
263 KOG0072|consensus 76.8 3 6.5E-05 32.9 3.2 56 24-82 119-178 (182)
264 cd04103 Centaurin_gamma Centau 76.8 3.7 8.1E-05 31.8 3.9 58 24-81 99-157 (158)
265 cd01874 Cdc42 Cdc42 subfamily. 76.5 5.2 0.00011 31.5 4.7 25 57-81 149-173 (175)
266 PRK00454 engB GTP-binding prot 76.4 4.1 8.9E-05 32.2 4.1 59 23-82 134-193 (196)
267 TIGR00231 small_GTP small GTP- 75.7 5.5 0.00012 29.3 4.5 53 24-79 108-160 (161)
268 cd04117 Rab15 Rab15 subfamily. 75.1 4.8 0.0001 31.0 4.1 56 24-81 105-160 (161)
269 cd04118 Rab24 Rab24 subfamily. 75.1 5.3 0.00012 31.6 4.5 58 24-82 105-165 (193)
270 cd01883 EF1_alpha Eukaryotic e 74.4 2.4 5.1E-05 35.0 2.3 57 25-81 138-215 (219)
271 COG0370 FeoB Fe2+ transport sy 74.4 3.3 7.2E-05 40.0 3.4 61 22-86 106-167 (653)
272 cd04129 Rho2 Rho2 subfamily. 74.0 5.7 0.00012 31.5 4.4 61 24-84 105-174 (187)
273 PRK09518 bifunctional cytidyla 74.0 5 0.00011 39.3 4.7 56 23-84 382-437 (712)
274 PRK03003 GTP-binding protein D 73.6 5.3 0.00012 37.1 4.6 56 23-84 145-200 (472)
275 PF00071 Ras: Ras family; Int 73.5 5.2 0.00011 30.4 3.9 56 24-81 104-159 (162)
276 PLN03071 GTP-binding nuclear p 73.4 4.6 0.0001 33.3 3.8 56 24-83 117-172 (219)
277 COG2262 HflX GTPases [General 73.2 4.9 0.00011 36.6 4.1 55 23-84 303-357 (411)
278 cd01873 RhoBTB RhoBTB subfamil 72.3 9.2 0.0002 30.9 5.2 56 24-80 120-193 (195)
279 cd01866 Rab2 Rab2 subfamily. 71.9 5.7 0.00012 30.7 3.8 58 23-82 108-165 (168)
280 cd01893 Miro1 Miro1 subfamily. 71.2 6.8 0.00015 30.2 4.1 58 24-82 103-163 (166)
281 TIGR00437 feoB ferrous iron tr 71.1 4.8 0.0001 38.6 3.8 57 22-82 97-154 (591)
282 KOG1145|consensus 70.3 15 0.00032 35.1 6.6 105 71-183 558-666 (683)
283 TIGR00157 ribosome small subun 70.1 6.6 0.00014 33.1 4.1 54 23-79 66-119 (245)
284 PRK10463 hydrogenase nickel in 70.1 5.7 0.00012 34.7 3.7 54 26-80 232-286 (290)
285 cd01892 Miro2 Miro2 subfamily. 69.9 4.8 0.0001 31.4 3.0 56 24-82 108-165 (169)
286 cd00877 Ran Ran (Ras-related n 69.8 8.6 0.00019 29.8 4.4 55 24-82 104-158 (166)
287 cd04146 RERG_RasL11_like RERG/ 69.8 8.3 0.00018 29.5 4.3 57 24-82 106-163 (165)
288 cd04111 Rab39 Rab39 subfamily. 69.6 6.9 0.00015 32.0 4.0 57 25-83 110-166 (211)
289 cd04108 Rab36_Rab34 Rab34/Rab3 69.1 6.5 0.00014 30.7 3.6 57 25-82 107-164 (170)
290 cd04133 Rop_like Rop subfamily 69.1 10 0.00022 30.1 4.8 59 24-82 105-172 (176)
291 cd01858 NGP_1 NGP-1. Autoanti 68.5 9.8 0.00021 29.3 4.5 55 24-82 39-94 (157)
292 PLN03108 Rab family protein; P 67.6 7.6 0.00016 31.6 3.8 57 24-82 111-167 (210)
293 cd01856 YlqF YlqF. Proteins o 67.1 6.8 0.00015 30.8 3.4 57 24-84 46-102 (171)
294 COG2229 Predicted GTPase [Gene 66.9 11 0.00024 30.7 4.5 58 25-85 122-181 (187)
295 smart00176 RAN Ran (Ras-relate 66.0 8.2 0.00018 31.5 3.7 56 23-82 98-153 (200)
296 cd04128 Spg1 Spg1p. Spg1p (se 65.3 4.9 0.00011 32.0 2.2 26 58-83 141-166 (182)
297 COG0378 HypB Ni2+-binding GTPa 64.3 8.6 0.00019 31.7 3.4 26 56-81 174-199 (202)
298 cd04121 Rab40 Rab40 subfamily. 64.2 8.8 0.00019 30.9 3.5 59 24-84 110-168 (189)
299 PRK05291 trmE tRNA modificatio 63.8 6.3 0.00014 36.4 2.9 51 24-84 321-371 (449)
300 cd04162 Arl9_Arfrp2_like Arl9/ 62.2 16 0.00035 28.2 4.6 55 23-80 98-163 (164)
301 cd04126 Rab20 Rab20 subfamily. 61.8 6.3 0.00014 32.7 2.3 25 58-82 165-189 (220)
302 KOG1423|consensus 60.9 7.3 0.00016 34.6 2.6 25 60-84 248-272 (379)
303 PRK12288 GTPase RsgA; Reviewed 59.6 15 0.00033 32.8 4.5 57 23-80 149-205 (347)
304 cd04174 Rnd1_Rho6 Rnd1/Rho6 su 59.3 20 0.00043 30.1 4.9 59 24-82 117-187 (232)
305 PRK00098 GTPase RsgA; Reviewed 59.1 11 0.00025 32.6 3.6 53 23-78 110-162 (298)
306 cd01854 YjeQ_engC YjeQ/EngC. 58.2 13 0.00028 32.1 3.7 53 23-79 108-160 (287)
307 KOG0092|consensus 57.6 11 0.00025 30.9 3.0 45 42-87 127-171 (200)
308 TIGR03156 GTP_HflX GTP-binding 57.5 8 0.00017 34.6 2.3 50 24-81 301-350 (351)
309 TIGR03597 GTPase_YqeH ribosome 57.4 17 0.00038 32.5 4.5 58 24-81 90-151 (360)
310 cd01899 Ygr210 Ygr210 subfamil 57.1 15 0.00033 32.4 4.0 57 23-84 213-270 (318)
311 PRK09866 hypothetical protein; 56.7 18 0.00038 35.4 4.6 55 26-82 291-352 (741)
312 KOG1489|consensus 56.7 13 0.00028 33.1 3.4 54 23-81 311-365 (366)
313 COG3596 Predicted GTPase [Gene 56.0 10 0.00022 33.1 2.5 29 56-84 195-223 (296)
314 cd04172 Rnd3_RhoE_Rho8 Rnd3/Rh 55.7 27 0.00059 27.8 5.0 57 24-80 109-177 (182)
315 COG0536 Obg Predicted GTPase [ 54.6 14 0.0003 33.2 3.2 61 23-85 274-335 (369)
316 PRK09554 feoB ferrous iron tra 53.7 15 0.00032 36.6 3.6 58 22-83 110-168 (772)
317 PRK09602 translation-associate 53.2 21 0.00045 32.6 4.3 56 23-84 216-272 (396)
318 PRK00093 GTP-binding protein D 52.9 18 0.00039 32.9 3.9 56 23-84 108-163 (435)
319 PRK12289 GTPase RsgA; Reviewed 52.8 17 0.00037 32.6 3.7 53 24-80 120-172 (352)
320 PRK11058 GTPase HflX; Provisio 52.8 25 0.00055 32.3 4.9 55 23-84 308-363 (426)
321 TIGR03596 GTPase_YlqF ribosome 52.6 20 0.00044 30.6 4.0 57 24-85 48-105 (276)
322 TIGR00750 lao LAO/AO transport 52.5 11 0.00023 32.9 2.2 26 58-83 213-238 (300)
323 cd04131 Rnd Rnd subfamily. Th 51.6 35 0.00075 26.9 5.0 57 24-80 105-173 (178)
324 COG1217 TypA Predicted membran 50.5 20 0.00044 33.6 3.7 47 2-56 188-234 (603)
325 PRK13796 GTPase YqeH; Provisio 50.0 27 0.00059 31.3 4.5 24 59-82 135-158 (365)
326 cd04115 Rab33B_Rab33A Rab33B/R 49.0 22 0.00047 27.4 3.4 58 23-82 108-168 (170)
327 KOG0394|consensus 48.6 28 0.00061 28.6 3.9 60 24-83 118-178 (210)
328 cd01896 DRG The developmentall 45.8 18 0.00039 30.2 2.5 25 58-82 201-225 (233)
329 KOG0462|consensus 45.6 5 0.00011 38.1 -0.9 57 1-65 227-283 (650)
330 TIGR03598 GTPase_YsxC ribosome 41.2 14 0.00031 29.0 1.2 50 23-72 128-179 (179)
331 KOG0076|consensus 39.1 19 0.00042 29.3 1.6 62 24-85 126-189 (197)
332 cd04161 Arl2l1_Arl13_like Arl2 38.6 61 0.0013 24.9 4.5 56 24-79 100-165 (167)
333 PF08669 GCV_T_C: Glycine clea 38.4 1.4E+02 0.0029 20.8 5.9 43 98-140 43-86 (95)
334 PF00181 Ribosomal_L2: Ribosom 38.1 76 0.0016 21.7 4.3 28 99-126 31-59 (77)
335 PRK01889 GTPase RsgA; Reviewed 38.0 49 0.0011 29.6 4.2 53 23-79 141-193 (356)
336 cd04166 CysN_ATPS CysN_ATPS su 36.4 41 0.00089 27.2 3.2 16 57-72 168-183 (208)
337 PF03193 DUF258: Protein of un 36.0 32 0.00068 27.4 2.4 28 53-80 8-35 (161)
338 COG1326 Uncharacterized archae 30.7 85 0.0018 25.8 4.1 49 119-172 66-115 (201)
339 PRK09563 rbgA GTPase YlqF; Rev 30.5 30 0.00066 29.8 1.6 57 24-85 51-108 (287)
340 COG0486 ThdF Predicted GTPase 29.5 35 0.00076 31.7 1.9 28 58-85 351-378 (454)
341 COG0218 Predicted GTPase [Gene 28.7 44 0.00095 27.6 2.1 59 22-82 133-196 (200)
342 KOG0093|consensus 27.8 54 0.0012 26.1 2.4 58 23-82 125-182 (193)
343 PF09631 Sen15: Sen15 protein; 25.5 1.5E+02 0.0033 21.3 4.3 17 115-131 84-100 (101)
344 PRK11556 multidrug efflux syst 25.5 2.3E+02 0.0049 25.8 6.5 32 152-183 359-390 (415)
345 PTZ00180 60S ribosomal protein 24.1 3.9E+02 0.0084 23.0 7.1 36 101-136 41-77 (260)
346 COG1163 DRG Predicted GTPase [ 24.0 1.3E+02 0.0027 27.1 4.2 48 26-82 241-288 (365)
347 COG1162 Predicted GTPases [Gen 21.8 1.4E+02 0.003 26.3 4.0 53 25-80 111-164 (301)
348 PRK09578 periplasmic multidrug 21.4 2.4E+02 0.0051 25.2 5.7 32 151-182 341-372 (385)
349 PF03607 DCX: Doublecortin; I 21.0 79 0.0017 20.5 1.9 29 144-172 28-56 (60)
350 PRK15452 putative protease; Pr 21.0 5.2E+02 0.011 24.0 7.9 66 99-171 359-427 (443)
351 PTZ00132 GTP-binding nuclear p 21.0 1.5E+02 0.0033 23.7 4.1 26 57-82 142-167 (215)
352 PRK00556 minC septum formation 20.6 2.7E+02 0.0058 22.9 5.2 17 120-136 93-109 (194)
353 cd06462 Peptidase_S24_S26 The 20.4 1.6E+02 0.0034 19.4 3.4 13 124-136 11-23 (84)
354 PF13533 Biotin_lipoyl_2: Biot 20.2 2.2E+02 0.0049 17.4 4.4 27 112-138 8-35 (50)
No 1
>KOG0465|consensus
Probab=100.00 E-value=6.3e-35 Score=265.52 Aligned_cols=193 Identities=29% Similarity=0.460 Sum_probs=167.0
Q ss_pred CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCccccccc-------
Q psy5461 22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMF------- 94 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~------- 94 (221)
+.|+.++..+.. ......+-....||+.++++.++|||+|||++|.||++|||+|++|+|+|.+..++.+.
T Consensus 249 d~DE~l~e~fLe--e~~ps~~~l~~aIRr~Ti~r~fvPVl~GSAlKNkGVQPlLDAVvdYLPsP~Ev~n~a~~ke~~~~e 326 (721)
T KOG0465|consen 249 DVDETLAEMFLE--EEEPSAQQLKAAIRRATIKRSFVPVLCGSALKNKGVQPLLDAVVDYLPSPSEVENYALNKETNSKE 326 (721)
T ss_pred hhhHHHHHHHhc--cCCCCHHHHHHHHHHHHhhcceeeEEechhhcccCcchHHHHHHHhCCChhhhcccccccCCCCcc
Confidence 346666555544 11235667788999999999999999999999999999999999999999987765321
Q ss_pred -----CCCCC-CcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEE
Q psy5461 95 -----QHFGD-SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA 168 (221)
Q Consensus 95 -----~~~~~-~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~ 168 (221)
...++ ||+|.+||+..+++ |.++|+|||+|+|++||.+||.++++++|+.+|..|++...++++++.|||||+
T Consensus 327 kv~l~~~~d~~Pfv~LAFKle~g~f-GqLTyvRvYqG~L~kG~~iyN~rtgKKvrv~RL~rmHa~~medV~~v~AG~I~a 405 (721)
T KOG0465|consen 327 KVTLSPSRDKDPFVALAFKLEEGRF-GQLTYVRVYQGTLSKGDTIYNVRTGKKVRVGRLVRMHANDMEDVNEVLAGDICA 405 (721)
T ss_pred ceEeccCCCCCceeeeEEEeeecCc-cceEEEEEeeeeecCCcEEEecCCCceeEhHHHhHhcccccchhhhhhccceee
Confidence 22333 99999999999999 999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCCCCccCcEEecCC---------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461 169 VTGLKRERGKDKRTRVI---------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQ 218 (221)
Q Consensus 169 i~gl~~~~~Gdtl~~~~---------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~ 218 (221)
+.|+ ++.+||||++.. .-|.|++ |.+++++||.++.+|||++.+..|-.
T Consensus 406 lfGi-dcasGDTftd~~~~~~~m~si~vPePVis~aikP~~k~d~~~fskaL~rf~~EDPtFrv~~d~E 473 (721)
T KOG0465|consen 406 LFGI-DCASGDTFTDKQNLALSMESIHIPEPVISVAIKPVNKKDADNFSKALNRFTKEDPTFRVSLDPE 473 (721)
T ss_pred eecc-ccccCceeccCccccceeeeeecCCCeeEEEecccccccHHHHHHHHHhhcccCCceEEEeccc
Confidence 9999 899999998861 2355666 78899999999999999999988753
No 2
>PRK00007 elongation factor G; Reviewed
Probab=100.00 E-value=4.2e-33 Score=266.45 Aligned_cols=177 Identities=32% Similarity=0.493 Sum_probs=155.6
Q ss_pred cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc------------cccCCCCCCcEEEEEEEe
Q psy5461 42 AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL------------AMFQHFGDSLCARAFKVV 109 (221)
Q Consensus 42 ~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~------------~~~~~~~~~~~~~Vfk~~ 109 (221)
+.....+++++..+..+||++|||.++.||++|||+|++++|+|.+++.. .+.|++++|++|+|||+.
T Consensus 239 ~~l~~~l~~~~~~~~~~Pv~~gSa~~~~Gv~~LLd~I~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~l~a~VfK~~ 318 (693)
T PRK00007 239 EEIKAALRKATIANEIVPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPAIKGILPDGEEEEVERKASDDEPFSALAFKIM 318 (693)
T ss_pred HHHHHHHHHHHhcCcEEEEEecccccCcCHHHHHHHHHHHCCChhhcccccccCCCccccceeecCCCCCCeEEEEEEee
Confidence 44456667778888999999999999999999999999999999865421 234677899999999999
Q ss_pred ecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC----
Q psy5461 110 HDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI---- 185 (221)
Q Consensus 110 ~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~---- 185 (221)
+|++.|+++|+|||||+|++||+|++.++++++++++|+.+.|.+..+++++.|||||++.|++++++||||++..
T Consensus 319 ~d~~~G~ia~~RV~sGtl~~g~~v~~~~~~~~eki~~l~~~~g~~~~~v~~~~aGdI~~i~gl~~~~~GdtL~~~~~~~~ 398 (693)
T PRK00007 319 TDPFVGKLTFFRVYSGVLESGSYVLNSTKGKKERIGRILQMHANKREEIKEVRAGDIAAAVGLKDTTTGDTLCDEKNPII 398 (693)
T ss_pred ecCCCCcEEEEEEeeeEEcCCCEEEeCCCCceeEeceeEEeccCCcccccccCCCcEEEEeCCccCCcCCEeeCCCCccc
Confidence 9999999999999999999999999988888899999999999999999999999999999999999999997641
Q ss_pred ----CCCCCce----------ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461 186 ----PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQ 218 (221)
Q Consensus 186 ----~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~ 218 (221)
..|.|++ |.++|.+||++|+++||+|++.++..
T Consensus 399 l~~~~~~~Pv~~~aIep~~~~d~~kL~~aL~~L~~eDpsl~v~~~~e 445 (693)
T PRK00007 399 LESMEFPEPVISVAVEPKTKADQEKMGIALQKLAEEDPSFRVSTDEE 445 (693)
T ss_pred cCCCCCCCceEEEEEEECCcccHHHHHHHHHHHHHhCCeEEEEEcCC
Confidence 1233555 78999999999999999999988753
No 3
>TIGR00503 prfC peptide chain release factor 3. This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. More recently, RF-3 was shown to be active primarily at UGA stop codons in E. coli. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis PCC6803, and in Staphylococcus aureus.
Probab=100.00 E-value=6.5e-33 Score=257.20 Aligned_cols=167 Identities=21% Similarity=0.314 Sum_probs=146.0
Q ss_pred hccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCccccc--ccCCCCCCcEEEEEEEee--c-CCCceEEEEEEEc
Q psy5461 50 SGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALA--MFQHFGDSLCARAFKVVH--D-KHRGAVTFFRIYS 124 (221)
Q Consensus 50 ~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~--~~~~~~~~~~~~Vfk~~~--d-~~~G~i~~~RV~s 124 (221)
+++.++..+|||||||.+|.||++|||+|++++|+|.++.... +.+ .+++|+|+|||+.+ | +|+|+++|+||||
T Consensus 242 ~~~~~~~~~PV~~GSA~~n~Gv~~LLd~i~~~~PsP~~~~~~~~~~~~-~~~~~~~~VFK~~~~mdp~~~griaf~RV~s 320 (527)
T TIGR00503 242 AAFHGGEMTPVFFGTALGNFGVDHFLDGLLQWAPKPEARQSDTRTVEP-TEEKFSGFVFKIQANMDPKHRDRVAFMRVVS 320 (527)
T ss_pred HHHhcCCeeEEEEeecccCccHHHHHHHHHHHCCCCccccCCceecCC-CCCCeeEEEEEEEeccCcccCceEEEEEEee
Confidence 4567889999999999999999999999999999998654221 112 35789999999998 7 5999999999999
Q ss_pred eEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC-------CCCCCce-----
Q psy5461 125 GAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI-------PKPTSVV----- 192 (221)
Q Consensus 125 G~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~-------~~p~~~v----- 192 (221)
|++++|++|++.++++++++++++.++|.+++++++|.||||+++.|++++++||||+... +.|.|++
T Consensus 321 G~l~~g~~v~~~~~~k~~ri~~~~~~~g~~~~~v~~a~aGDI~~~~~~~~~~~GDtl~~~~~~~~~~i~~~~P~~~~~v~ 400 (527)
T TIGR00503 321 GKYEKGMKLKHVRTGKDVVISDALTFMAGDREHVEEAYAGDIIGLHNHGTIQIGDTFTQGEKIKFTGIPNFAPELFRRIR 400 (527)
T ss_pred eEEcCCCEEEecCCCCcEEecchhhhhcCCceEcceeCCCCEEEEECCCCcccCCEecCCCceeecCCCCCCcceEEEEE
Confidence 9999999999999999999999999999999999999999999999999999999998751 2233444
Q ss_pred -----ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461 193 -----QCSARWTLNLEVGASSPIISKSKRRQ 218 (221)
Q Consensus 193 -----~~~~l~~~L~~L~~~Dp~l~~~~~~~ 218 (221)
|.++|.+||++|++||| +++.++.+
T Consensus 401 ~~~~~d~~kl~~aL~~L~eED~-l~v~~~~~ 430 (527)
T TIGR00503 401 LKDPLKQKQLLKGLVQLSEEGA-VQVFRPLD 430 (527)
T ss_pred ECChhhHHHHHHHHHHHHhhCC-eEEEEcCC
Confidence 78999999999999999 88887754
No 4
>TIGR00484 EF-G translation elongation factor EF-G. After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G.
Probab=100.00 E-value=7.8e-33 Score=264.59 Aligned_cols=194 Identities=30% Similarity=0.457 Sum_probs=162.2
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc-----------
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL----------- 91 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~----------- 91 (221)
.|+++...++. .+....+.....+++++..+..+|||+|||++|.|+++|||+|++++|+|.+++..
T Consensus 221 ~dd~lle~yle--~~~~~~~~l~~~l~~~~~~~~~~PV~~gSa~~~~Gv~~LLd~I~~~lPsP~~~~~~~~~~~~~~~~~ 298 (689)
T TIGR00484 221 FDEELMEKYLE--GEELTIEEIKNAIRKGVLNCEFFPVLCGSAFKNKGVQLLLDAVVDYLPSPTDVPAIKGIDPDTEKEI 298 (689)
T ss_pred cCHHHHHHHhC--CCCCCHHHHHHHHHHHHhcCCEEEEEeccccCCccHHHHHHHHHHHCCCchhcccccccCCCCCcee
Confidence 45555545443 12222233455677788889999999999999999999999999999999865321
Q ss_pred cccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcC
Q psy5461 92 AMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTG 171 (221)
Q Consensus 92 ~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~g 171 (221)
.+.|++++||+|+|||+++|++.|+++|+|||||+|++||+|++.+.++++++++|+.+.|.+..+++++.|||||++.|
T Consensus 299 ~~~~~~~~~l~a~VfK~~~d~~~G~i~~~RV~sGtL~~g~~v~~~~~~~~~~i~~l~~~~g~~~~~v~~~~aGdI~~i~g 378 (689)
T TIGR00484 299 ERKASDDEPFSALAFKVATDPFVGQLTFVRVYSGVLKSGSYVKNSRKNKKERVGRLVKMHANNREEIKEVRAGDICAAIG 378 (689)
T ss_pred eecCCCCCceEEEEEEeeecCCCCeEEEEEEEEeEEcCCCEEEeCCCCceEEecceEEeecCCcccccccCCCCEEEEcC
Confidence 23466788999999999999999999999999999999999999888888999999999999999999999999999999
Q ss_pred CCCCccCcEEecCC--------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461 172 LKRERGKDKRTRVI--------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQ 218 (221)
Q Consensus 172 l~~~~~Gdtl~~~~--------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~ 218 (221)
++++++||||++.. ..|.|++ |.++|++||++|+++||+|++.++..
T Consensus 379 l~~~~~gdtl~~~~~~~~~~~~~~~~Pvl~~~i~p~~~~d~~kL~~aL~~L~~eDpsl~v~~~~e 443 (689)
T TIGR00484 379 LKDTTTGDTLCDPKIDVILERMEFPEPVISLAVEPKTKADQEKMGIALGKLAEEDPTFRTFTDPE 443 (689)
T ss_pred CCCCCCCCEEeCCCCccccCCCCCCCceEEEEEEECCcccHHHHHHHHHHHHHhCCEEEEEECCC
Confidence 99999999997641 1234555 88999999999999999999988653
No 5
>PRK00741 prfC peptide chain release factor 3; Provisional
Probab=100.00 E-value=1.8e-32 Score=254.28 Aligned_cols=169 Identities=22% Similarity=0.313 Sum_probs=146.5
Q ss_pred hhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCC-CCCCcEEEEEEEee---cCCCceEEEEEEEc
Q psy5461 49 YSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQH-FGDSLCARAFKVVH---DKHRGAVTFFRIYS 124 (221)
Q Consensus 49 ~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~-~~~~~~~~Vfk~~~---d~~~G~i~~~RV~s 124 (221)
++++.++..+|||||||++|+||++|||+|++++|+|.++.......+ ..++|+|+|||+.+ ++|+|+++|+||||
T Consensus 240 ~~~~~~~~~~PV~~GSA~~n~Gv~~LLd~i~~~~P~P~~~~~~~~~~~~~~~~~~~~VFK~~~~m~~~~~grlafvRV~s 319 (526)
T PRK00741 240 LEAFLAGELTPVFFGSALNNFGVQEFLDAFVEWAPAPQPRQTDEREVEPTEEKFSGFVFKIQANMDPKHRDRIAFVRVCS 319 (526)
T ss_pred HHHHhcCCeEEEEEeecccCcCHHHHHHHHHHHCCCCCcccccceeecCCCCceEEEEEEEEecCCCCcCceEEEEEEec
Confidence 667788999999999999999999999999999999986542211112 24579999999994 57999999999999
Q ss_pred eEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC-------CCCCCce-----
Q psy5461 125 GAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI-------PKPTSVV----- 192 (221)
Q Consensus 125 G~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~-------~~p~~~v----- 192 (221)
|++++|++|++.++++++++++++.++|.+++++++|.||||+++.|++++++||||+... +.|.|++
T Consensus 320 G~l~~g~~v~~~~~~k~~ri~~~~~~~g~~~~~v~~a~aGDIv~v~~l~~~~~GDTL~~~~~~~~~~i~~~~P~~~~~v~ 399 (526)
T PRK00741 320 GKFEKGMKVRHVRTGKDVRISNALTFMAQDREHVEEAYAGDIIGLHNHGTIQIGDTFTQGEKLKFTGIPNFAPELFRRVR 399 (526)
T ss_pred cEECCCCEEEeccCCceEEecceEEEecCCceECceeCCCCEEEEECCCCCccCCCccCCCccccCCCCCCCccEEEEEE
Confidence 9999999999999999999999999999999999999999999999999999999998652 2233444
Q ss_pred -----ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461 193 -----QCSARWTLNLEVGASSPIISKSKRRQ 218 (221)
Q Consensus 193 -----~~~~l~~~L~~L~~~Dp~l~~~~~~~ 218 (221)
|.++|.+||++|++||| +++.++..
T Consensus 400 p~~~~d~~kl~~aL~~L~eED~-l~~~~~~~ 429 (526)
T PRK00741 400 LKNPLKQKQLQKGLVQLSEEGA-VQVFRPLD 429 (526)
T ss_pred ECCchhHHHHHHHHHHHhhcCC-eEEEECCC
Confidence 78999999999999996 88887754
No 6
>PRK12739 elongation factor G; Reviewed
Probab=100.00 E-value=1.1e-32 Score=263.48 Aligned_cols=177 Identities=32% Similarity=0.487 Sum_probs=156.4
Q ss_pred cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc-----------cccCCCCCCcEEEEEEEee
Q psy5461 42 AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL-----------AMFQHFGDSLCARAFKVVH 110 (221)
Q Consensus 42 ~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~-----------~~~~~~~~~~~~~Vfk~~~ 110 (221)
+.....+++++.++..+||++|||.++.|+++|||+|++++|+|.+++.. .+.|++++||+|+|||+++
T Consensus 237 ~~l~~~l~~~~~~~~~~Pv~~gSa~~~~Gv~~LLd~I~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~pl~a~VfK~~~ 316 (691)
T PRK12739 237 EEIKAAIRKATINMEFFPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPAIKGINPDTEEEIERPASDDEPFAALAFKIMT 316 (691)
T ss_pred HHHHHHHHHHHHcCCEEEEEeccccCCccHHHHHHHHHHHCCChhhccccccccCCCCcceeeccCCCCCeEEEEEEeee
Confidence 34455677788888999999999999999999999999999999865432 1346778999999999999
Q ss_pred cCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC-----
Q psy5461 111 DKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI----- 185 (221)
Q Consensus 111 d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~----- 185 (221)
|+++|+++|+|||||+|++||.|++.++++++++.+|+.++|++..+++++.|||||+|.|++++++||||++..
T Consensus 317 d~~~G~i~~~RV~sGtL~~g~~v~~~~~~~~~~v~~l~~~~g~~~~~v~~~~aGdI~~i~gl~~~~~gdtl~~~~~~~~l 396 (691)
T PRK12739 317 DPFVGRLTFFRVYSGVLESGSYVLNTTKGKKERIGRLLQMHANKREEIKEVYAGDIAAAVGLKDTTTGDTLCDEKAPIIL 396 (691)
T ss_pred CCCCCeEEEEEEeeeEEcCCCEEEeCCCCceEEecceEEEecCCcccccccCCCCEEEEeCCCcccCCCEEeCCCCcccc
Confidence 999999999999999999999999998888899999999999999999999999999999999999999997642
Q ss_pred ---CCCCCce----------ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461 186 ---PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQ 218 (221)
Q Consensus 186 ---~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~ 218 (221)
..|.|++ |.++|++||++|+++||+|.+.+|..
T Consensus 397 ~~~~~~~Pv~~~aiep~~~~d~~kL~~aL~~L~~eDpsl~v~~~~e 442 (691)
T PRK12739 397 ESMEFPEPVISLAVEPKTKADQDKMGLALQKLAEEDPTFRVETDEE 442 (691)
T ss_pred CCCCCCCceEEEEEEECCcccHHHHHHHHHHHHHhCCeEEEEEcCC
Confidence 1234555 88999999999999999999998753
No 7
>PRK13351 elongation factor G; Reviewed
Probab=100.00 E-value=1.9e-32 Score=262.02 Aligned_cols=193 Identities=30% Similarity=0.411 Sum_probs=164.2
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc----------c
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL----------A 92 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~----------~ 92 (221)
.|+.+...+++ ..+...+.....+++++..+..+|||+|||++|.||++|||+|++++|+|.+++.. .
T Consensus 220 ~d~~lle~~l~--~~~l~~~~l~~~~~~~~~~~~~~PV~~gSA~~~~Gv~~LLd~I~~~lPsP~~~~~~~~~~~~~~~~~ 297 (687)
T PRK13351 220 FDDELLELYLE--GEELSAEQLRAPLREGTRSGHLVPVLFGSALKNIGIEPLLDAVVDYLPSPLEVPPPRGSKDNGKPVK 297 (687)
T ss_pred cCHHHHHHHhC--CCCCCHHHHHHHHHHHHHhCCEEEEEecccCcCccHHHHHHHHHHHCCChhhcccccccCCCCCcee
Confidence 45555555554 22233344567778888888999999999999999999999999999999765322 1
Q ss_pred ccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCC
Q psy5461 93 MFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGL 172 (221)
Q Consensus 93 ~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl 172 (221)
+.|++++|++|+|||++++++.|+++|+|||||+|++||+|++.++++.+++++|+.++|.+..+++++.||||+++.|+
T Consensus 298 ~~~~~~~pl~a~VfK~~~d~~~G~i~~~RV~sGtl~~g~~v~~~~~~~~~~i~~i~~~~g~~~~~v~~~~aGdI~~i~gl 377 (687)
T PRK13351 298 VDPDPEKPLLALVFKVQYDPYAGKLTYLRVYSGTLRAGSQLYNGTGGKREKVGRLFRLQGNKREEVDRAKAGDIVAVAGL 377 (687)
T ss_pred ecCCCCCCeEEEEEEeeecCCCceEEEEEEeEEEEcCCCEEEeCCCCCceEeeeEEEEccCCeeECCccCCCCEEEEECc
Confidence 34577889999999999999999999999999999999999999988889999999999999999999999999999999
Q ss_pred CCCccCcEEecCC--------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461 173 KRERGKDKRTRVI--------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRR 217 (221)
Q Consensus 173 ~~~~~Gdtl~~~~--------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~ 217 (221)
+++.+||||++.. ..|.|++ |.++|++||++|+++||++++.++.
T Consensus 378 ~~~~~gdtl~~~~~~~~~~~~~~~~pv~~~~Iep~~~~d~~kL~~aL~~L~~eDpsl~v~~~~ 440 (687)
T PRK13351 378 KELETGDTLHDSADPVLLELLTFPEPVVSLAVEPERRGDEQKLAEALEKLVWEDPSLRVEEDE 440 (687)
T ss_pred ccCccCCEEeCCCCccccCCCCCCCccEEEEEEECCcccHHHHHHHHHHHHHhCCeEEEEECC
Confidence 9999999998641 1244555 7899999999999999999999874
No 8
>COG0480 FusA Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.1e-32 Score=256.31 Aligned_cols=195 Identities=30% Similarity=0.476 Sum_probs=169.0
Q ss_pred CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCccccc---------
Q psy5461 22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALA--------- 92 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~--------- 92 (221)
++|+++...+.. ......+.....++++++++.++|++||||.+|.|++.|||++++++|+|.+.+.+.
T Consensus 219 e~de~l~e~yl~--g~e~~~~~i~~~i~~~~~~~~~~pvl~gsa~kn~gv~~lLdav~~~lPsP~e~~~~~g~~~~~~~~ 296 (697)
T COG0480 219 EFDEELMEKYLE--GEEPTEEEIKKALRKGTIAGKIVPVLCGSAFKNKGVQPLLDAVVDYLPSPLDVPPIKGDLDDEIEK 296 (697)
T ss_pred hcCHHHHHHHhc--CCCccHHHHHHHHHHhhhccceeeEEeeecccCCcHHHHHHHHHHHCCChhhcccccccCCccccc
Confidence 456666666666 222334566788888999999999999999999999999999999999998876431
Q ss_pred ---ccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE
Q psy5461 93 ---MFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV 169 (221)
Q Consensus 93 ---~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i 169 (221)
.+++.++||+|+|||+..|++.|+++|+|||||+|++|+.+++.+.+++++|.+|+.|+|.++++++++.||||+++
T Consensus 297 ~~~~~~~~e~p~~a~vfKi~~d~~~g~l~~~RvysGtl~~G~~v~n~~~~~~erv~~l~~~~~~~~~~v~~~~AG~I~a~ 376 (697)
T COG0480 297 AVLRKASDEGPLSALVFKIMTDPFVGKLTFVRVYSGTLKSGSEVLNSTKGKKERVGRLLLMHGNEREEVDEVPAGDIVAL 376 (697)
T ss_pred hhcccCCCCCceEEEEEEeEecCCCCeEEEEEEeccEEcCCCEEEeCCCCccEEEEEEEEccCCceeecccccCccEEEE
Confidence 12345789999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCccCcEEecCC--------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461 170 TGLKRERGKDKRTRVI--------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQ 218 (221)
Q Consensus 170 ~gl~~~~~Gdtl~~~~--------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~ 218 (221)
.|+++..+|||+|+.. .-|.|++ |+++|+.||.+|+++||++.+..|-.
T Consensus 377 ~Gl~~~~tGdTl~~~~~~v~~~~~~~pePVi~vavepk~~~d~~Kl~~aL~~l~~eDPt~~v~~d~E 443 (697)
T COG0480 377 VGLKDATTGDTLCDENKPVILESMEFPEPVISVAVEPKTKADQEKLSEALNKLAEEDPTFRVETDEE 443 (697)
T ss_pred EcccccccCCeeecCCCccccccccCCCceEEEEEeECChhhHHHHHHHHHHHHhhCCceEEEEcCC
Confidence 9999999999999654 1134666 88999999999999999999998753
No 9
>PRK12740 elongation factor G; Reviewed
Probab=99.97 E-value=7.9e-31 Score=250.18 Aligned_cols=175 Identities=30% Similarity=0.455 Sum_probs=152.9
Q ss_pred chHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc---------cccCCCCCCcEEEEEEEeecCC
Q psy5461 43 VTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL---------AMFQHFGDSLCARAFKVVHDKH 113 (221)
Q Consensus 43 l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~---------~~~~~~~~~~~~~Vfk~~~d~~ 113 (221)
.....+++.+..+..+|||+|||++|.|+++|||+|++++|+|.+++.. ...|++++|++|+|||+.++++
T Consensus 222 ~~~~~~~~~~~~~~~~Pv~~gSA~~~~Gv~~LLd~i~~~lPsp~~~~~~~~~~~~~~~~~~~~~~~~l~a~v~k~~~~~~ 301 (668)
T PRK12740 222 EIKAGLRKATLAGEIVPVFCGSALKNKGVQRLLDAVVDYLPSPLEVPPVDGEDGEEGAELAPDPDGPLVALVFKTMDDPF 301 (668)
T ss_pred HHHHHHHHHHHcCCEEEEEeccccCCccHHHHHHHHHHHCCChhhcccccCCCCccccccccCCCCCeEEEEEEeeecCC
Confidence 3345566777888999999999999999999999999999999764421 1245678899999999999999
Q ss_pred CceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC--------
Q psy5461 114 RGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI-------- 185 (221)
Q Consensus 114 ~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~-------- 185 (221)
.|+++++|||+|+|++||+|++.++++.+++.+|+.++|.+.++++++.||||+++.|++.+.+||||++..
T Consensus 302 ~G~i~~~RV~sG~L~~g~~v~~~~~~~~~~i~~l~~l~g~~~~~v~~~~aGdI~~i~gl~~~~~Gdtl~~~~~~~~~~~~ 381 (668)
T PRK12740 302 VGKLSLVRVYSGTLKKGDTLYNSGTGKKERVGRLYRMHGKQREEVDEAVAGDIVAVAKLKDAATGDTLCDKGDPILLEPM 381 (668)
T ss_pred CCcEEEEEEeeeEEcCCCEEEeCCCCCcEEecceeeecCCCccccCccCCCCEEEEeccCccCCCCEEeCCCCccccCCC
Confidence 999999999999999999999998887899999999999999999999999999999999999999997641
Q ss_pred CCCCCce----------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461 186 PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRR 217 (221)
Q Consensus 186 ~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~ 217 (221)
..|.|++ |.++|++||++|+++||+|++.++.
T Consensus 382 ~~~~P~~~~~i~p~~~~d~~~L~~aL~~l~~~Dpsl~v~~~~ 423 (668)
T PRK12740 382 EFPEPVISLAIEPKDKGDEEKLSEALGKLAEEDPTLRVERDE 423 (668)
T ss_pred CCCCcceEEEEEECCcchHHHHHHHHHHHHHhCCeEEEEECC
Confidence 1233555 7899999999999999999998863
No 10
>PRK10218 GTP-binding protein; Provisional
Probab=99.95 E-value=8.3e-27 Score=219.12 Aligned_cols=187 Identities=17% Similarity=0.177 Sum_probs=147.9
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhc------cccccCceeEecCCCccc----------cHHHHHHHHHhhCCCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG------AFKKNHVPVLCGSSYKNI----------GVQKLMDAIVDILPSPT 86 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~------~~~~~~~Pv~~gSa~~~~----------Gi~~LLd~I~~~~PsP~ 86 (221)
.+.|.+..+||++......+-....+... ......+||+++||++|+ |+.+|||+|++++|+|.
T Consensus 119 ~gip~IVviNKiD~~~a~~~~vl~ei~~l~~~l~~~~~~~~~PVi~~SA~~G~~~~~~~~~~~~i~~Lld~Ii~~iP~P~ 198 (607)
T PRK10218 119 YGLKPIVVINKVDRPGARPDWVVDQVFDLFVNLDATDEQLDFPIVYASALNGIAGLDHEDMAEDMTPLYQAIVDHVPAPD 198 (607)
T ss_pred cCCCEEEEEECcCCCCCchhHHHHHHHHHHhccCccccccCCCEEEeEhhcCcccCCccccccchHHHHHHHHHhCCCCC
Confidence 45678899999764432222222333322 123356999999999998 69999999999999996
Q ss_pred CcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccC-Cc--eeeeceeEeeecCCeeeeCcccc
Q psy5461 87 ERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHL-DQ--SEQITRLLLAEADDYKEVNEIQC 163 (221)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~-~~--~~~v~~i~~~~g~~~~~v~~a~a 163 (221)
. +.++||+++|||++++++.|+++++||++|+|++||.|++... ++ +++|++|+.+.|.++.++++|.|
T Consensus 199 ~--------~~~~Pl~~~V~k~~~d~~~G~i~~gRV~sG~lk~Gd~v~~~~~~~~~~~~rv~~l~~~~g~~~~~v~~a~A 270 (607)
T PRK10218 199 V--------DLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPNQQVTIIDSEGKTRNAKVGKVLGHLGLERIETDLAEA 270 (607)
T ss_pred C--------CCCCCeEEEEEeeEecCCCcEEEEEEEEeCcCcCCCEEEEecCCCcEeeEEEEEEEEEecCCceECCEEcC
Confidence 4 5678999999999999999999999999999999999999876 43 57899999999999999999999
Q ss_pred CCEEEEcCCCCCccCcEEecCC-CC-------CCCce-------------ehHHHHH---HHHHHhh---cCCceEEEcc
Q psy5461 164 GNIAAVTGLKRERGKDKRTRVI-PK-------PTSVV-------------QCSARWT---LNLEVGA---SSPIISKSKR 216 (221)
Q Consensus 164 GdIv~i~gl~~~~~Gdtl~~~~-~~-------p~~~v-------------~~~~l~~---~L~~L~~---~Dp~l~~~~~ 216 (221)
||||++.|++++.+|||||+.. +. |.|++ +.+++.+ ++++|.+ +||+|.+.++
T Consensus 271 GdIvai~gl~~~~~GdTl~~~~~~~~l~~~~~~~P~~~~~~~~~~sp~~g~e~k~~t~~~~~~rL~~~~~~D~sl~v~~~ 350 (607)
T PRK10218 271 GDIVAITGLGELNISDTVCDTQNVEALPALSVDEPTVSMFFCVNTSPFCGKEGKFVTSRQILDRLNKELVHNVALRVEET 350 (607)
T ss_pred CCEEEEECccccccCcEEecCCCcccCCCCCCCCCeEEEEEEeCCCccccchhhhhhHHHHHHHHHHhhCCCCeEEEEEc
Confidence 9999999999999999998651 11 12332 4466644 5555555 9999999887
Q ss_pred c
Q psy5461 217 R 217 (221)
Q Consensus 217 ~ 217 (221)
.
T Consensus 351 ~ 351 (607)
T PRK10218 351 E 351 (607)
T ss_pred C
Confidence 4
No 11
>PRK07560 elongation factor EF-2; Reviewed
Probab=99.95 E-value=3.5e-27 Score=226.95 Aligned_cols=159 Identities=26% Similarity=0.376 Sum_probs=140.4
Q ss_pred eeEecCCCccccHH----------------------------------HHHHHHHhhCCCCCCcccc-------------
Q psy5461 59 PVLCGSSYKNIGVQ----------------------------------KLMDAIVDILPSPTERPAL------------- 91 (221)
Q Consensus 59 Pv~~gSa~~~~Gi~----------------------------------~LLd~I~~~~PsP~~~~~~------------- 91 (221)
.|+++||+.++|+. .|||+|++++|+|.+++..
T Consensus 198 ~v~~~sa~~~~~~~~~~~~~~~~~~~~l~e~~~~~~~~~l~~~~Pv~~~Lld~I~~~lPsP~~~~~~~~~~~~~~~~~~~ 277 (731)
T PRK07560 198 TVAFGSALYNWAISVPMMQKTGIKFKDIIDYYEKGKQKELAEKAPLHEVVLDMVVKHLPNPIEAQKYRIPKIWKGDLNSE 277 (731)
T ss_pred cEeeeecccccceeHHHHHHhCCCHHHHHHHHhcCCHHHHHhhccchhHHHHHHHHhCCChhhhhhhcccccccCCCCcc
Confidence 47899999999886 8999999999999864421
Q ss_pred ----cccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEE
Q psy5461 92 ----AMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA 167 (221)
Q Consensus 92 ----~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv 167 (221)
...|++++|++|+|||+.+|+++|+++|+|||||+|++||+|++.+.++++++++|+.++|++..+++++.|||||
T Consensus 278 ~~~~~~~~d~~~p~~a~VfK~~~d~~~G~va~~RV~sGtL~~Gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~AGdIv 357 (731)
T PRK07560 278 VGKAMLNCDPNGPLVMMVTDIIVDPHAGEVATGRVFSGTLRKGQEVYLVGAKKKNRVQQVGIYMGPEREEVEEIPAGNIA 357 (731)
T ss_pred ccceeeccCCCCCEEEEEEeeEEcCCCCeEEEEEEEEeEEcCCCEEEEcCCCCceEeheehhhhcCCCceeeeECCCCEE
Confidence 1235677899999999999999999999999999999999999999888899999999999999999999999999
Q ss_pred EEcCCCCCccCcEEecCC---------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461 168 AVTGLKRERGKDKRTRVI---------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRR 217 (221)
Q Consensus 168 ~i~gl~~~~~Gdtl~~~~---------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~ 217 (221)
++.|++++.+||||+... ..|.|++ |.++|.+||++|+++||+|.+.++.
T Consensus 358 ~i~gl~~~~~GdtL~~~~~~~~~~~~~~~p~Pv~~~aI~p~~~~d~~kL~~aL~~L~~eDPsl~v~~~~ 426 (731)
T PRK07560 358 AVTGLKDARAGETVVSVEDMTPFESLKHISEPVVTVAIEAKNPKDLPKLIEVLRQLAKEDPTLVVKINE 426 (731)
T ss_pred EEEcccccccCCEEeCCCccccccccccCCCCeEEEEEEECCHHHHHHHHHHHHHHHhhCCcEEEEEcC
Confidence 999999999999998641 1234555 7899999999999999999998874
No 12
>TIGR01394 TypA_BipA GTP-binding protein TypA/BipA. This bacterial (and Arabidopsis) protein, termed TypA or BipA, a GTP-binding protein, is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown.
Probab=99.95 E-value=3.8e-26 Score=214.64 Aligned_cols=188 Identities=19% Similarity=0.205 Sum_probs=150.9
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhcc------ccccCceeEecCCCccc----------cHHHHHHHHHhhCCCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA------FKKNHVPVLCGSSYKNI----------GVQKLMDAIVDILPSPT 86 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~------~~~~~~Pv~~gSa~~~~----------Gi~~LLd~I~~~~PsP~ 86 (221)
.+-|++..+||++.......-....+.... .+...+|++++||++|+ |+.+||+.|++++|+|.
T Consensus 115 ~~ip~IVviNKiD~~~a~~~~v~~ei~~l~~~~g~~~e~l~~pvl~~SA~~g~~~~~~~~~~~gi~~Lld~Iv~~lP~P~ 194 (594)
T TIGR01394 115 LGLKPIVVINKIDRPSARPDEVVDEVFDLFAELGADDEQLDFPIVYASGRAGWASLDLDDPSDNMAPLFDAIVRHVPAPK 194 (594)
T ss_pred CCCCEEEEEECCCCCCcCHHHHHHHHHHHHHhhccccccccCcEEechhhcCcccccCcccccCHHHHHHHHHHhCCCCC
Confidence 456889999996643221111222222211 13346899999999997 89999999999999997
Q ss_pred CcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCc---eeeeceeEeeecCCeeeeCcccc
Q psy5461 87 ERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ---SEQITRLLLAEADDYKEVNEIQC 163 (221)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~---~~~v~~i~~~~g~~~~~v~~a~a 163 (221)
. +.++||+++||+++++++.|+++++||++|+|++||+|++.+.+. +++|++|+.+.|.++.++++|.|
T Consensus 195 ~--------~~~~pl~~~V~~i~~d~~~Grv~~gRV~sG~lk~G~~V~~~~~~~~~~~~kV~~i~~~~g~~~~~v~~a~a 266 (594)
T TIGR01394 195 G--------DLDEPLQMLVTNLDYDEYLGRIAIGRVHRGTVKKGQQVALMKRDGTIENGRISKLLGFEGLERVEIDEAGA 266 (594)
T ss_pred C--------CCCCCEEEEEEEEEeeCCCceEEEEEEEeCEEccCCEEEEecCCCceeEEEEEEEEEccCCCceECCEECC
Confidence 5 567999999999999999999999999999999999999987632 47999999999999999999999
Q ss_pred CCEEEEcCCCCCccCcEEecCC-CC-------CCCce-------------eh-H-----HHHHHHHHHhhcCCceEEEcc
Q psy5461 164 GNIAAVTGLKRERGKDKRTRVI-PK-------PTSVV-------------QC-S-----ARWTLNLEVGASSPIISKSKR 216 (221)
Q Consensus 164 GdIv~i~gl~~~~~Gdtl~~~~-~~-------p~~~v-------------~~-~-----~l~~~L~~L~~~Dp~l~~~~~ 216 (221)
||||++.|++++.+|||||+.. +. |.|++ +. . +|.++|.+++++||+|.+.++
T Consensus 267 GDiv~i~gl~~i~~Gdtl~~~~~~~~l~~~~~~~P~~~~~~~~~~~p~~~~e~k~~t~~~l~~~L~k~~~~d~sl~v~~~ 346 (594)
T TIGR01394 267 GDIVAVAGLEDINIGETIADPEVPEALPTITVDEPTLSMTFSVNDSPLAGKEGKKVTSRHIRDRLMRELETNVALRVEDT 346 (594)
T ss_pred CCEEEEeCCcccCCCCEEeCCCccccCCCCCCCCCeEEEEEEecCCCcccccchhhhHHHHHHHHHHhhccCCeEEEEEe
Confidence 9999999999999999998752 11 12333 11 2 399999999999999999887
Q ss_pred cc
Q psy5461 217 RQ 218 (221)
Q Consensus 217 ~~ 218 (221)
.+
T Consensus 347 ~~ 348 (594)
T TIGR01394 347 ES 348 (594)
T ss_pred cC
Confidence 54
No 13
>TIGR01393 lepA GTP-binding protein LepA. LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function is unknown.
Probab=99.94 E-value=2.5e-25 Score=209.35 Aligned_cols=185 Identities=17% Similarity=0.222 Sum_probs=146.3
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcE
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLC 102 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~ 102 (221)
.+.+++..+||++......+.....+.+. ......+++++||++|.||++|++.|.+.+|+|.. +.++||+
T Consensus 121 ~~ipiIiViNKiDl~~~~~~~~~~el~~~-lg~~~~~vi~vSAktG~GI~~Lle~I~~~lp~p~~--------~~~~pl~ 191 (595)
T TIGR01393 121 NDLEIIPVINKIDLPSADPERVKKEIEEV-IGLDASEAILASAKTGIGIEEILEAIVKRVPPPKG--------DPDAPLK 191 (595)
T ss_pred cCCCEEEEEECcCCCccCHHHHHHHHHHH-hCCCcceEEEeeccCCCCHHHHHHHHHHhCCCCCC--------CCCCCeE
Confidence 35688999999664321111112233221 11112258999999999999999999999999976 5678999
Q ss_pred EEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc-C---CCCCccC
Q psy5461 103 ARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT-G---LKRERGK 178 (221)
Q Consensus 103 ~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~-g---l~~~~~G 178 (221)
|+||++++|+++|+++++||++|+|++||+|++.++++.+++.+|+.+.+ +..+++++.||||+.+. | ++++++|
T Consensus 192 ~~V~~~~~d~~~G~v~~~rV~sG~lk~Gd~v~~~~~~~~~~v~~i~~~~~-~~~~v~~~~aGdIg~i~~~~~~~~~~~~G 270 (595)
T TIGR01393 192 ALIFDSHYDNYRGVVALVRVFEGTIKPGDKIRFMSTGKEYEVDEVGVFTP-KLTKTDELSAGEVGYIIAGIKDVSDVRVG 270 (595)
T ss_pred EEEEEEEEeCCCcEEEEEEEECCEEecCCEEEEecCCCeeEEeEEEEecC-CceECCEEcCCCEEEEeccccccCccCCC
Confidence 99999999999999999999999999999999999888899999996554 55899999999999664 4 4568999
Q ss_pred cEEecCC-C---------CCCCce----------ehHHHHHHHHHHhhcCCceEEEccc
Q psy5461 179 DKRTRVI-P---------KPTSVV----------QCSARWTLNLEVGASSPIISKSKRR 217 (221)
Q Consensus 179 dtl~~~~-~---------~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~ 217 (221)
||++... + .|.|++ |.++|.+||++|+++||+|++...-
T Consensus 271 dtl~~~~~~~~~~l~~~~~~~P~v~~~i~p~~~~d~~kL~~aL~kL~~eD~sl~~~~e~ 329 (595)
T TIGR01393 271 DTITHVKNPAKEPLPGFKEVKPMVFAGLYPIDTEDYEDLRDALEKLKLNDASLTYEPES 329 (595)
T ss_pred CEEECCCCccccCCCCCcCCCcEEEEEEEECCcccHHHHHHHHHHHhccCCeEEEEecC
Confidence 9998652 1 123666 7789999999999999999998643
No 14
>PRK05433 GTP-binding protein LepA; Provisional
Probab=99.94 E-value=3.7e-25 Score=208.39 Aligned_cols=184 Identities=17% Similarity=0.212 Sum_probs=145.9
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcE
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLC 102 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~ 102 (221)
.+.+++..+||++......+-....+.+. ......+++++||++|.||++|+++|.+.+|+|.. +.++||.
T Consensus 125 ~~lpiIvViNKiDl~~a~~~~v~~ei~~~-lg~~~~~vi~iSAktG~GI~~Ll~~I~~~lp~P~~--------~~~~pl~ 195 (600)
T PRK05433 125 NDLEIIPVLNKIDLPAADPERVKQEIEDV-IGIDASDAVLVSAKTGIGIEEVLEAIVERIPPPKG--------DPDAPLK 195 (600)
T ss_pred CCCCEEEEEECCCCCcccHHHHHHHHHHH-hCCCcceEEEEecCCCCCHHHHHHHHHHhCccccC--------CCCCCce
Confidence 35688999999654321111112222221 11111248899999999999999999999999975 5678999
Q ss_pred EEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc-C---CCCCccC
Q psy5461 103 ARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT-G---LKRERGK 178 (221)
Q Consensus 103 ~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~-g---l~~~~~G 178 (221)
|+|||+++|+++|+++++||++|+|++||+|++..+++.++|.+|+.+ +++..+++++.||||+.+. | ++++++|
T Consensus 196 ~~Vfd~~~d~~~G~v~~~rV~sG~Lk~Gd~i~~~~~~~~~~V~~i~~~-~~~~~~v~~~~aGdIg~i~~~ik~~~~~~~G 274 (600)
T PRK05433 196 ALIFDSWYDNYRGVVVLVRVVDGTLKKGDKIKMMSTGKEYEVDEVGVF-TPKMVPVDELSAGEVGYIIAGIKDVRDARVG 274 (600)
T ss_pred EEEEEEEecCCCceEEEEEEEcCEEecCCEEEEecCCceEEEEEeecc-CCCceECcEEcCCCEEEEecccccccccCCC
Confidence 999999999999999999999999999999999998888999999955 4588999999999999764 4 4578999
Q ss_pred cEEecCC-C---------CCCCce----------ehHHHHHHHHHHhhcCCceEEEcc
Q psy5461 179 DKRTRVI-P---------KPTSVV----------QCSARWTLNLEVGASSPIISKSKR 216 (221)
Q Consensus 179 dtl~~~~-~---------~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~ 216 (221)
|||+... + .|.|++ |.++|.+||++|+++||+|++...
T Consensus 275 dtl~~~~~~~~~~l~~~~~~~P~v~~~i~p~~~~d~~kL~~aL~kL~~eD~sl~~~~e 332 (600)
T PRK05433 275 DTITLAKNPAEEPLPGFKEVKPMVFAGLYPVDSDDYEDLRDALEKLQLNDASLTYEPE 332 (600)
T ss_pred CEEECCCCccccCCCCCCCCCcEEEEEEEECCccCHHHHHHHHHHHHHhCCeEEEEec
Confidence 9998652 1 233666 678999999999999999999744
No 15
>TIGR00490 aEF-2 translation elongation factor aEF-2. This model represents archaeal elongation factor 2, a protein more similar to eukaryotic EF-2 than to bacterial EF-G, both in sequence similarity and in sharing with eukaryotes the property of having a diphthamide (modified His) residue at a conserved position. The diphthamide can be ADP-ribosylated by diphtheria toxin in the presence of NAD.
Probab=99.93 E-value=2.7e-25 Score=213.48 Aligned_cols=148 Identities=26% Similarity=0.351 Sum_probs=129.9
Q ss_pred HHHHHHHHHhhCCCCCCccc-----------------ccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEE
Q psy5461 71 VQKLMDAIVDILPSPTERPA-----------------LAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKF 133 (221)
Q Consensus 71 i~~LLd~I~~~~PsP~~~~~-----------------~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v 133 (221)
++.|||+|++++|+|.+++. ..+.|++++|++++|||+.++++.|+++|+|||||+|++||+|
T Consensus 243 ~~~Lld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~pl~a~VfK~~~~~~~G~ia~~RV~sGtL~~G~~l 322 (720)
T TIGR00490 243 HQVVLDMVIRHLPSPIEAQKYRIPVIWKGDLNSEVGKAMLNCDPKGPLALMITKIVVDKHAGEVAVGRLYSGTIRPGMEV 322 (720)
T ss_pred HHHHHHHHHHhCCChhhhhhhcccccccCCCCccchhhcccCCCCCCeEEEEEEEEecCCCcEEEEEEEEeCEEcCCCEE
Confidence 57999999999999976421 0134667889999999999999999999999999999999999
Q ss_pred EeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC------C----CCCCce----------e
Q psy5461 134 YNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI------P----KPTSVV----------Q 193 (221)
Q Consensus 134 ~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~------~----~p~~~v----------~ 193 (221)
++.++++.++|++|+.++|++.++++++.|||||++.|++++.+||||++.. + .|.|++ |
T Consensus 323 ~~~~~~~~~kv~~l~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~GdtL~~~~~~~~~~~~~~~~~~Pv~~~~i~p~~~~d 402 (720)
T TIGR00490 323 YIVDRKAKARIQQVGVYMGPERVEVDEIPAGNIVAVIGLKDAVAGETICTTVENITPFESIKHISEPVVTVAIEAKNTKD 402 (720)
T ss_pred EEcCCCCeeEeeEEEEeccCCccCccEECCCCEEEEECccccccCceeecCCcccccCcccccCCCceEEEEEEECCHHH
Confidence 9999998899999999999999999999999999999999999999997541 1 134666 7
Q ss_pred hHHHHHHHHHHhhcCCceEEEcccc
Q psy5461 194 CSARWTLNLEVGASSPIISKSKRRQ 218 (221)
Q Consensus 194 ~~~l~~~L~~L~~~Dp~l~~~~~~~ 218 (221)
.++|.++|++|+++||+|++.++..
T Consensus 403 ~~kL~~aL~~L~~eDPsl~v~~d~e 427 (720)
T TIGR00490 403 LPKLIEVLRQVAKEDPTVHVEINEE 427 (720)
T ss_pred HHHHHHHHHHHHhhCCeEEEEECCC
Confidence 8999999999999999999988653
No 16
>COG4108 PrfC Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=2.2e-25 Score=197.37 Aligned_cols=166 Identities=24% Similarity=0.303 Sum_probs=141.5
Q ss_pred ccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCC-CCCcEEEEEEEeec---CCCceEEEEEEEceE
Q psy5461 51 GAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHF-GDSLCARAFKVVHD---KHRGAVTFFRIYSGA 126 (221)
Q Consensus 51 ~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~-~~~~~~~Vfk~~~d---~~~G~i~~~RV~sG~ 126 (221)
..+++..+|||||||++|.||+.|||++++|.|+|..+........+ +..|.+||||+... +|+.++||+||+||.
T Consensus 244 ~fl~G~~TPVFFGSAl~NFGV~~~L~~~~~~AP~P~~~~a~~~~v~p~e~kfsGFVFKIQANMDp~HRDRIAFmRv~SGk 323 (528)
T COG4108 244 AFLAGELTPVFFGSALGNFGVDHFLDALVDWAPSPRARQADTREVEPTEDKFSGFVFKIQANMDPKHRDRIAFMRVCSGK 323 (528)
T ss_pred HHhcCCccceEehhhhhccCHHHHHHHHHhhCCCCCcccCCcCcccCCCCccceEEEEEEcCCCcccccceeEEEecccc
Confidence 35778899999999999999999999999999999887554322233 34699999999873 689999999999999
Q ss_pred EcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecC---------CCCCC--Cce---
Q psy5461 127 FKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRV---------IPKPT--SVV--- 192 (221)
Q Consensus 127 L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~---------~~~p~--~~v--- 192 (221)
+.+|+++...++|+..++.+-..+++.+++.+++|.||||++|.+-..+++|||++.. .+.|. .+|
T Consensus 324 ferGMkv~h~rtGK~~~ls~~~~f~A~dRe~ve~A~aGDIIGl~nhG~~~IGDT~t~Ge~l~f~giP~FaPE~frrvr~k 403 (528)
T COG4108 324 FERGMKVTHVRTGKDVKLSDALTFMAQDRETVEEAYAGDIIGLHNHGTIQIGDTFTEGEKLKFTGIPNFAPELFRRVRLK 403 (528)
T ss_pred ccCCceeeeeecCCceEecchHhhhhhhhhhhhhccCCCeEeccCCCceeecceeecCceeeecCCCCCCHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999998899999999886 12232 333
Q ss_pred ---ehHHHHHHHHHHhhcCCceEEEcc
Q psy5461 193 ---QCSARWTLNLEVGASSPIISKSKR 216 (221)
Q Consensus 193 ---~~~~l~~~L~~L~~~Dp~l~~~~~ 216 (221)
...+|.+||++|++|....-|+..
T Consensus 404 d~~K~Kql~Kgl~QL~eEGavQ~f~p~ 430 (528)
T COG4108 404 DPLKQKQLKKGLEQLAEEGAVQVFKPL 430 (528)
T ss_pred ChHHHHHHHHHHHHHhhcCeeEEEecC
Confidence 668999999999999877555543
No 17
>PLN00116 translation elongation factor EF-2 subunit; Provisional
Probab=99.92 E-value=4.9e-25 Score=214.69 Aligned_cols=161 Identities=19% Similarity=0.239 Sum_probs=134.2
Q ss_pred HhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc-----------------cccCCCCCCcEEEEEEEee
Q psy5461 48 IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL-----------------AMFQHFGDSLCARAFKVVH 110 (221)
Q Consensus 48 l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~-----------------~~~~~~~~~~~~~Vfk~~~ 110 (221)
+++++.+...+|+|++| +.|||+|++++|+|.+++.. .+.|++++|++|+|||+.+
T Consensus 313 ~~~~l~~~~~~pv~~~s-------~~Lld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~pl~a~VfK~~~ 385 (843)
T PLN00116 313 MGKALMKRVMQTWLPAS-------DALLEMIIFHLPSPAKAQRYRVENLYEGPLDDKYATAIRNCDPNGPLMLYVSKMIP 385 (843)
T ss_pred hhHHHHHHHHHhhcCCh-------HHHHHHHHHhCCChHHhhhHHhhhccCCCCCccccchhhcCCCCCCeEEEEEeeee
Confidence 57778888899999987 69999999999999754311 1346778899999999999
Q ss_pred cCCCce-EEEEEEEceEEcCCCEEEe----ccCCce-----eeeceeEeeecCCeeeeCccccCCEEEEcCCCCC-ccCc
Q psy5461 111 DKHRGA-VTFFRIYSGAFKKGQKFYN----IHLDQS-----EQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE-RGKD 179 (221)
Q Consensus 111 d~~~G~-i~~~RV~sG~L~~gd~v~~----~~~~~~-----~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~-~~Gd 179 (221)
+++.|+ ++|+|||||+|++||+|++ .+.+++ +++.+|+.++|.+.++++++.|||||++.|+++. ..||
T Consensus 386 ~~~~g~~l~~~RVysGtL~~g~~v~v~~~n~~~~~~~~~~~~~v~~l~~~~g~~~~~v~~~~AGdI~ai~gl~~~~~~gd 465 (843)
T PLN00116 386 ASDKGRFFAFGRVFSGTVATGMKVRIMGPNYVPGEKKDLYVKSVQRTVIWMGKKQESVEDVPCGNTVAMVGLDQFITKNA 465 (843)
T ss_pred cCCCCeEEEEEEEEeeeecCCCEEEEeCCCCCCCCccccceeEhheEEEecCCCceECcEECCCCEEEEEeecccccCCc
Confidence 998888 9999999999999999984 333332 5889999999999999999999999999999876 4499
Q ss_pred EEecCC--C--------CC-CCce----------ehHHHHHHHHHHhhcCCceEEEc
Q psy5461 180 KRTRVI--P--------KP-TSVV----------QCSARWTLNLEVGASSPIISKSK 215 (221)
Q Consensus 180 tl~~~~--~--------~p-~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~ 215 (221)
||++.. . .| .|++ |.++|++||++|+++||++++..
T Consensus 466 TL~~~~~~~~~~l~~~~~~~~Pv~~~aIeP~~~~d~~kL~~aL~~L~~eDPsl~v~~ 522 (843)
T PLN00116 466 TLTNEKEVDAHPIKAMKFSVSPVVRVAVQCKNASDLPKLVEGLKRLAKSDPMVQCTI 522 (843)
T ss_pred eecCCcccCCccccccccCCCceEEEEEEECChhhHHHHHHHHHHHHHhCCCeEEEE
Confidence 997642 1 12 3555 88999999999999999999854
No 18
>PTZ00416 elongation factor 2; Provisional
Probab=99.91 E-value=6.1e-24 Score=206.78 Aligned_cols=157 Identities=22% Similarity=0.317 Sum_probs=129.5
Q ss_pred HHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccc-----------------cccCCCCCCcEEEEEEEe
Q psy5461 47 RIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL-----------------AMFQHFGDSLCARAFKVV 109 (221)
Q Consensus 47 ~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~-----------------~~~~~~~~~~~~~Vfk~~ 109 (221)
.+.+++. +..+|+ ++.|||+|++++|+|.+++.. .+.|++++|++|+|||+.
T Consensus 312 ~l~~~~~-~~~~Pv----------~~~Lld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~plva~VfK~~ 380 (836)
T PTZ00416 312 PLLKAVM-QKWLPA----------ADTLLEMIVDHLPSPKEAQKYRVENLYEGPMDDEAANAIRNCDPNGPLMMYISKMV 380 (836)
T ss_pred HHHHHHH-HHHhch----------HHHHHHHHHHhCCChhHhCchhhhccccCCCCccccceeeccCCCCCeEEEEEeee
Confidence 3455555 567776 789999999999999764321 134677889999999999
Q ss_pred ecCCCce-EEEEEEEceEEcCCCEEEecc----CCcee-----eeceeEeeecCCeeeeCccccCCEEEEcCCCC--Ccc
Q psy5461 110 HDKHRGA-VTFFRIYSGAFKKGQKFYNIH----LDQSE-----QITRLLLAEADDYKEVNEIQCGNIAAVTGLKR--ERG 177 (221)
Q Consensus 110 ~d~~~G~-i~~~RV~sG~L~~gd~v~~~~----~~~~~-----~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~--~~~ 177 (221)
++++.|+ ++|+|||||+|+.||+|++.+ .++++ ++++|+.++|++..+++++.|||||+|.|+++ .++
T Consensus 381 ~~~~~g~~~s~~RV~SGtL~~g~~v~v~~~~~~~~~~e~~~~~~i~~l~~~~g~~~~~v~~v~AGdI~~i~gl~~~~~~t 460 (836)
T PTZ00416 381 PTSDKGRFYAFGRVFSGTVATGQKVRIQGPNYVPGKKEDLFEKNIQRTVLMMGRYVEQIEDVPCGNTVGLVGVDQYLVKS 460 (836)
T ss_pred ecCCCCcEEEEEEEEeeeecCCCEEEEeCCCCCCCCcccchheecceeEEecCCCceECcEECCCCEEEEEecccceecc
Confidence 9999999 899999999999999999543 33334 59999999999999999999999999999988 799
Q ss_pred CcEEecCC---------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEc
Q psy5461 178 KDKRTRVI---------PKPTSVV----------QCSARWTLNLEVGASSPIISKSK 215 (221)
Q Consensus 178 Gdtl~~~~---------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~ 215 (221)
| ||++.. .+|.|++ |+++|++||++|+++||++.+..
T Consensus 461 g-TL~~~~~~~~l~~i~~~~~Pv~~vaIep~~~~d~~kL~~aL~~L~~eDPsl~~~~ 516 (836)
T PTZ00416 461 G-TITTSETAHNIRDMKYSVSPVVRVAVEPKNPKDLPKLVEGLKRLAKSDPLVVCTT 516 (836)
T ss_pred e-eecCCCCcccccccccCCCCeEEEEEEECCHHHHHHHHHHHHHHHhhCCceEEEE
Confidence 9 997542 1124555 88999999999999999998854
No 19
>COG0481 LepA Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]
Probab=99.91 E-value=2e-23 Score=186.59 Aligned_cols=186 Identities=18% Similarity=0.239 Sum_probs=150.2
Q ss_pred CCCCceeeeeeeecccccCCcchHHHHhh--ccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCC
Q psy5461 22 HFGDSLCARAFKVVHDKHRGAVTFFRIYS--GAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGD 99 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~--~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~ 99 (221)
+.+.+++--+||++-+.-..+-....+.. |.... -.+..||++|.||+++|++|++.+|+|.. +++.
T Consensus 126 e~~LeIiPViNKIDLP~Adpervk~eIe~~iGid~~---dav~~SAKtG~gI~~iLe~Iv~~iP~P~g--------~~~~ 194 (603)
T COG0481 126 ENNLEIIPVLNKIDLPAADPERVKQEIEDIIGIDAS---DAVLVSAKTGIGIEDVLEAIVEKIPPPKG--------DPDA 194 (603)
T ss_pred HcCcEEEEeeecccCCCCCHHHHHHHHHHHhCCCcc---hheeEecccCCCHHHHHHHHHhhCCCCCC--------CCCC
Confidence 46788999999986443222222222221 22222 24567999999999999999999999987 7899
Q ss_pred CcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEE-EEcCCC---CC
Q psy5461 100 SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA-AVTGLK---RE 175 (221)
Q Consensus 100 ~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv-~i~gl~---~~ 175 (221)
|+.|.+|+.|+|+++|.++++||+.|++++||++....+|++..|.++.++ .++..+.+++.||+++ .++|++ +.
T Consensus 195 pLkALifDS~yD~Y~GVv~~vRi~dG~ik~gdki~~m~tg~~y~V~evGvf-tP~~~~~~~L~aGeVG~~~a~iK~v~d~ 273 (603)
T COG0481 195 PLKALIFDSWYDNYLGVVVLVRIFDGTLKKGDKIRMMSTGKEYEVDEVGIF-TPKMVKVDELKAGEVGYIIAGIKDVRDA 273 (603)
T ss_pred cceEEEEeccccccceEEEEEEEeeceecCCCEEEEEecCCEEEEEEEeec-cCCccccccccCCceeEEEEeeeecccC
Confidence 999999999999999999999999999999999999999999999999966 4688999999999999 455655 67
Q ss_pred ccCcEEecCC-C---------CCCCce----------ehHHHHHHHHHHhhcCCceEEEccccc
Q psy5461 176 RGKDKRTRVI-P---------KPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQN 219 (221)
Q Consensus 176 ~~Gdtl~~~~-~---------~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~~ 219 (221)
++|||++... | ++.|+| |-+.|.+||++|.++|.+|+|...-+.
T Consensus 274 ~VGDTiT~~~~p~~e~LpGfk~~~P~Vf~GlyPid~~dye~LrdAleKL~LNDasl~~E~EtS~ 337 (603)
T COG0481 274 RVGDTITLASNPATEPLPGFKEVKPMVFAGLYPVDSDDYEDLRDALEKLQLNDASLTYEPETSQ 337 (603)
T ss_pred cccceEeccCCCccccCCCCCcCCceEEEeecccChhHHHHHHHHHHhcccccceeeeccccch
Confidence 9999998542 1 223777 568999999999999999999876553
No 20
>COG1217 TypA Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]
Probab=99.89 E-value=3.8e-22 Score=178.04 Aligned_cols=185 Identities=17% Similarity=0.216 Sum_probs=149.5
Q ss_pred CCCceeeeeeeecccccCCcchHHHHh------hccccccCceeEecCCCccc----------cHHHHHHHHHhhCCCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIY------SGAFKKNHVPVLCGSSYKNI----------GVQKLMDAIVDILPSPT 86 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~------~~~~~~~~~Pv~~gSa~~~~----------Gi~~LLd~I~~~~PsP~ 86 (221)
.+.+.+.-|||++-+..+..-....+. .+..++.+||++|+||+.|+ .+.+|+|+|.+++|+|.
T Consensus 119 ~gL~PIVVvNKiDrp~Arp~~Vvd~vfDLf~~L~A~deQLdFPivYAS~~~G~a~~~~~~~~~~m~pLfe~I~~hvp~P~ 198 (603)
T COG1217 119 LGLKPIVVINKIDRPDARPDEVVDEVFDLFVELGATDEQLDFPIVYASARNGTASLDPEDEADDMAPLFETILDHVPAPK 198 (603)
T ss_pred cCCCcEEEEeCCCCCCCCHHHHHHHHHHHHHHhCCChhhCCCcEEEeeccCceeccCccccccchhHHHHHHHHhCCCCC
Confidence 456777899998655333333333333 34567789999999999995 58999999999999998
Q ss_pred CcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC---ceeeeceeEeeecCCeeeeCcccc
Q psy5461 87 ERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD---QSEQITRLLLAEADDYKEVNEIQC 163 (221)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~---~~~~v~~i~~~~g~~~~~v~~a~a 163 (221)
. +.++||.++|+.+.++++.|++.++||++|++++|+++.....+ +..||++++-+.|-++.++++|.|
T Consensus 199 ~--------~~d~PlQ~qvt~Ldyn~y~GrIgigRi~~G~vk~~q~V~~i~~~g~~~~gri~kllgf~GL~R~ei~eA~A 270 (603)
T COG1217 199 G--------DLDEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPNQQVALIKSDGTTENGRITKLLGFLGLERIEIEEAEA 270 (603)
T ss_pred C--------CCCCCeEEEEEeeccccccceeEEEEEecCcccCCCeEEEEcCCCcEEeeEEEeeeeccceeeeecccccc
Confidence 6 78999999999999999999999999999999999999998765 357999999999999999999999
Q ss_pred CCEEEEcCCCCCccCcEEecCC-CCCC-------Cce-------------------ehHHHHHHHHHHhhcCCceEEEc
Q psy5461 164 GNIAAVTGLKRERGKDKRTRVI-PKPT-------SVV-------------------QCSARWTLNLEVGASSPIISKSK 215 (221)
Q Consensus 164 GdIv~i~gl~~~~~Gdtl~~~~-~~p~-------~~v-------------------~~~~l~~~L~~L~~~Dp~l~~~~ 215 (221)
|||++|+|++++.+|||+|+.. +.+. |.+ ---++.+.|.+=...+-+|.+..
T Consensus 271 GDIVaiaG~~~~~igdTi~d~~~~~aLp~l~iDePTlsMtf~vN~SPfAG~EGk~vTSR~i~dRL~~El~~NValrVe~ 349 (603)
T COG1217 271 GDIVAIAGLEDINIGDTICDPDNPEALPALSVDEPTLSMTFSVNDSPFAGKEGKFVTSRQIRDRLNKELETNVALRVEE 349 (603)
T ss_pred cCEEEEcCcccccccccccCCCCccCCCCcccCCCceEEEEEecCCCCCCcCCceeeHHHHHHHHHHHhhhceeEEEee
Confidence 9999999999999999999862 2111 111 11366777777777777776654
No 21
>KOG0464|consensus
Probab=99.88 E-value=2e-23 Score=184.18 Aligned_cols=174 Identities=34% Similarity=0.515 Sum_probs=147.8
Q ss_pred HHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEc
Q psy5461 45 FFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYS 124 (221)
Q Consensus 45 ~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~s 124 (221)
...+++.+..+...||+||||.++.||++|||++.-|+|+|.++. +++.---...++|..||+.+|+.+|.++|+|||+
T Consensus 280 ksai~~lt~aq~a~~i~cgsaiknkgiqplldavtmylpspeern-yeflqwykddlcalafkvlhdkqrg~l~fmriys 358 (753)
T KOG0464|consen 280 KSAIHELTCAQKAAPILCGSAIKNKGIQPLLDAVTMYLPSPEERN-YEFLQWYKDDLCALAFKVLHDKQRGPLSFMRIYS 358 (753)
T ss_pred HHHHHHHhhhhhhcceehhhhhcccCccchhhhhhhccCChhhcc-hHHHhhhhhhHHHHhhhhhcccccCceeEEEEec
Confidence 445566677788999999999999999999999999999998863 2110012356899999999999999999999999
Q ss_pred eEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcEEecCC-------------------
Q psy5461 125 GAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDKRTRVI------------------- 185 (221)
Q Consensus 125 G~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~~~------------------- 185 (221)
|+++..-.++|.+....+.+.+++...+++...++++.||+|....|++...+|||+....
T Consensus 359 gsi~~~~ai~nin~~~se~~~kl~~pfade~~~i~qlsagnialt~glk~tatgdtivaskasa~aa~qk~~~egekk~~ 438 (753)
T KOG0464|consen 359 GSIHNNLAIFNINGMCSEGILKLFLPFADEHREIEQLSAGNIALTAGLKHTATGDTIVASKASAEAAAQKAAGEGEKKHL 438 (753)
T ss_pred ccccCceeeeecccccccchHhhhccchhhhhhhhhcccccEEEEecceeeccCCeEEecchhHHHHHHHhhccchhhcc
Confidence 9999999999998777889999999999999999999999999999999999999996530
Q ss_pred -------------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEccccc
Q psy5461 186 -------------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQN 219 (221)
Q Consensus 186 -------------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~~ 219 (221)
..|.++. +++++..||+.|..+|||+.++.++.+
T Consensus 439 q~~daerll~agie~pd~vffc~iepps~~k~~d~ehale~lqredpslkir~d~ds 495 (753)
T KOG0464|consen 439 QNKDAERLLFAGIEIPDAVFFCCIEPPSLRKLNDFEHALECLQREDPSLKIRFDPDS 495 (753)
T ss_pred CCccccceeeecccCCCceEEEeccCcccccchhHHHHHHHHhccCCceeEEecCCC
Confidence 0132333 678999999999999999999988754
No 22
>cd03690 Tet_II Tet_II: This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.
Probab=99.88 E-value=6.1e-22 Score=141.82 Aligned_cols=85 Identities=24% Similarity=0.380 Sum_probs=80.2
Q ss_pred CCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCcc
Q psy5461 98 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERG 177 (221)
Q Consensus 98 ~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~ 177 (221)
++||+|+|||+.+|++.|+++|+|||||+|++||.+++.+ ++.+++.+|+.++|.+..+++++.||||+++.|++++.+
T Consensus 1 ~~p~~~~Vfkv~~d~~~G~la~~RV~sG~l~~g~~v~~~~-~~~~~v~~l~~~~g~~~~~v~~~~aGdI~ai~gl~~~~~ 79 (85)
T cd03690 1 ESELSGTVFKIERDDKGERLAYLRLYSGTLRLRDSVRVNR-EEKIKITELRVFNNGEVVTADTVTAGDIAILTGLKGLRV 79 (85)
T ss_pred CCCcEEEEEEeEECCCCCeEEEEEEccCEEcCCCEEEeCC-CcEEEeceeEEEeCCCeEECcEECCCCEEEEECCCCCcC
Confidence 3789999999999999999999999999999999999877 566899999999999999999999999999999999999
Q ss_pred CcEEec
Q psy5461 178 KDKRTR 183 (221)
Q Consensus 178 Gdtl~~ 183 (221)
||||++
T Consensus 80 Gdtl~~ 85 (85)
T cd03690 80 GDVLGD 85 (85)
T ss_pred ccccCC
Confidence 999863
No 23
>KOG0462|consensus
Probab=99.87 E-value=6.6e-22 Score=179.22 Aligned_cols=188 Identities=15% Similarity=0.171 Sum_probs=149.3
Q ss_pred CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCc
Q psy5461 22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSL 101 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~ 101 (221)
+....++--+||++-.....+-+...+.+..... --++++.||++|+|+.++|++|++.+|+|.. ..++||
T Consensus 175 e~~L~iIpVlNKIDlp~adpe~V~~q~~~lF~~~-~~~~i~vSAK~G~~v~~lL~AII~rVPpP~~--------~~d~pl 245 (650)
T KOG0462|consen 175 EAGLAIIPVLNKIDLPSADPERVENQLFELFDIP-PAEVIYVSAKTGLNVEELLEAIIRRVPPPKG--------IRDAPL 245 (650)
T ss_pred HcCCeEEEeeeccCCCCCCHHHHHHHHHHHhcCC-ccceEEEEeccCccHHHHHHHHHhhCCCCCC--------CCCcch
Confidence 4577888999998644333333344444433333 3379999999999999999999999999987 678999
Q ss_pred EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEE-EEcC---CCCCcc
Q psy5461 102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA-AVTG---LKRERG 177 (221)
Q Consensus 102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv-~i~g---l~~~~~ 177 (221)
.|.+|++++|+|+|.++++||..|.+++||+|....+++.+.+..+.+|. ++..++.++.||+++ .+++ +++.++
T Consensus 246 r~Lifds~yD~y~G~I~~vrv~~G~vrkGdkV~~~~t~~~yev~~vgvm~-p~~~~~~~l~agqvGyIi~~mr~~~ea~I 324 (650)
T KOG0462|consen 246 RMLIFDSEYDEYRGVIALVRVVDGVVRKGDKVQSAATGKSYEVKVVGVMR-PEMTPVVELDAGQVGYIICNMRNVKEAQI 324 (650)
T ss_pred HHHhhhhhhhhhcceEEEEEEeeeeeecCCEEEEeecCcceEeEEeEEec-cCceeeeeecccccceeEecccccccccc
Confidence 99999999999999999999999999999999999999888888888664 667777777776666 3344 557799
Q ss_pred CcEEecCC-----------CCCCCce----------ehHHHHHHHHHHhhcCCceEEEccccc
Q psy5461 178 KDKRTRVI-----------PKPTSVV----------QCSARWTLNLEVGASSPIISKSKRRQN 219 (221)
Q Consensus 178 Gdtl~~~~-----------~~p~~~v----------~~~~l~~~L~~L~~~Dp~l~~~~~~~~ 219 (221)
||||+... .++.|+| |-..|-+++++|+++|+++.+...-++
T Consensus 325 GdTi~~~~~~~~v~tl~~~~~~~pMvFvg~fP~dgsd~~~l~~a~erL~lnd~sv~v~~~~s~ 387 (650)
T KOG0462|consen 325 GDTIAHKSVTKAVETLPGFEPTKPMVFVGLFPLDGSDYETLRDAIERLVLNDESVTVIKESSG 387 (650)
T ss_pred cceeeecccCcccCcCCCCCCCcceEEeccccCccchhhhHHHHHHHHhcccccceeeecCCc
Confidence 99998752 1223666 557889999999999999998876654
No 24
>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n
Probab=99.87 E-value=1.2e-21 Score=139.61 Aligned_cols=83 Identities=48% Similarity=0.839 Sum_probs=79.4
Q ss_pred cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcE
Q psy5461 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDK 180 (221)
Q Consensus 101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdt 180 (221)
|+|+|||+++|++.|+++|+|||+|+|++||.+++.+.++++++.+|+.++|.+..+++++.||||+++.|++++++|||
T Consensus 1 ~~a~VfK~~~d~~~g~i~~~Ri~sGtl~~g~~v~~~~~~~~~~v~~l~~~~g~~~~~v~~~~aGdI~~i~gl~~~~~Gdt 80 (83)
T cd04092 1 LCALAFKVVHDPQRGPLTFVRVYSGTLKRGSALYNTNTGKKERISRLLQPFADQYQEIPSLSAGNIGVITGLKQTRTGDT 80 (83)
T ss_pred CEEEEEecccCCCCCeEEEEEEecCEECCCCEEEECCCCCEEEeeEEEEEECCCceECCeeCCCCEEEEECCCCcccCCE
Confidence 57999999999999999999999999999999999888878899999999999999999999999999999999999999
Q ss_pred Eec
Q psy5461 181 RTR 183 (221)
Q Consensus 181 l~~ 183 (221)
++.
T Consensus 81 l~~ 83 (83)
T cd04092 81 LVT 83 (83)
T ss_pred EeC
Confidence 974
No 25
>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl
Probab=99.86 E-value=4.7e-21 Score=136.30 Aligned_cols=83 Identities=36% Similarity=0.597 Sum_probs=79.4
Q ss_pred cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcE
Q psy5461 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDK 180 (221)
Q Consensus 101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdt 180 (221)
|+|+|||+++|++.|+++++|||+|+|++||++++.+.++.+++.+|+.++|.+..+++++.||||+++.|++++++|||
T Consensus 1 ~~a~Vfk~~~d~~~G~~~~~Rv~sG~l~~g~~v~~~~~~~~~~v~~l~~~~g~~~~~v~~~~aGdI~~i~g~~~~~~Gdt 80 (83)
T cd04088 1 FVALVFKTIHDPFVGKLSFVRVYSGTLKAGSTLYNSTKGKKERVGRLLRMHGKKQEEVEEAGAGDIGAVAGLKDTATGDT 80 (83)
T ss_pred CEEEEEEcccCCCCceEEEEEEecCEEcCCCEEEECCCCcEEEeeEEEEEcCCCceECCEeCCCCEEEEECCCCCccCCE
Confidence 57999999999999999999999999999999999988888899999999999999999999999999999999999999
Q ss_pred Eec
Q psy5461 181 RTR 183 (221)
Q Consensus 181 l~~ 183 (221)
+++
T Consensus 81 l~~ 83 (83)
T cd04088 81 LCD 83 (83)
T ss_pred eeC
Confidence 973
No 26
>cd03689 RF3_II RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of class II release factors with elongation factors shows that prokaryotic RF3 is more similar to EF-G whereas eukaryotic eRF3 is more similar to eEF1A, implying that their precise function may differ.
Probab=99.85 E-value=9.1e-21 Score=135.71 Aligned_cols=81 Identities=25% Similarity=0.351 Sum_probs=77.7
Q ss_pred EEEEEEee---cCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCc
Q psy5461 103 ARAFKVVH---DKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKD 179 (221)
Q Consensus 103 ~~Vfk~~~---d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gd 179 (221)
|+|||+.+ +++.|+++|+|||||+|++||.|++...++.+++++|+.++|.+..+++++.||||+++.|++++.+||
T Consensus 1 ~~vfKv~~~~~~~~~Gkla~~Rv~sG~l~~g~~v~~~~~~~~~kv~~l~~~~g~~~~~v~~a~aGdIv~v~gl~~~~~Gd 80 (85)
T cd03689 1 GFVFKIQANMDPAHRDRIAFVRVCSGKFERGMKVKHVRLGKEVRLSNPQQFFAQDRETVDEAYPGDIIGLVNPGNFQIGD 80 (85)
T ss_pred CEEEEEecccCCCCCcEEEEEEEECCEEcCCCEEEEcCCCCEEEeeEeEEEecCCeeEcCEECCCCEEEEECCCCccccC
Confidence 58999999 999999999999999999999999998777889999999999999999999999999999999999999
Q ss_pred EEec
Q psy5461 180 KRTR 183 (221)
Q Consensus 180 tl~~ 183 (221)
|||+
T Consensus 81 tl~~ 84 (85)
T cd03689 81 TLTE 84 (85)
T ss_pred EeeC
Confidence 9985
No 27
>cd04091 mtEFG1_II_like mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals
Probab=99.85 E-value=1.3e-20 Score=133.68 Aligned_cols=81 Identities=31% Similarity=0.589 Sum_probs=77.1
Q ss_pred cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCccCcE
Q psy5461 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERGKDK 180 (221)
Q Consensus 101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdt 180 (221)
|+|+|||+.+|++ |+++|+|||+|+|++||+|++.+.++++++.+|+.++|.+..+++++.||||+++.|++ +++|||
T Consensus 1 ~~a~vfK~~~~~~-G~i~~~Rv~sG~lk~gd~v~~~~~~~~~~v~~i~~~~g~~~~~~~~~~aGdI~~i~g~~-~~~Gdt 78 (81)
T cd04091 1 FVGLAFKLEEGRF-GQLTYMRIYQGKLKKGDTIYNVRTGKKVRVPRLVRMHSNEMEEVEEAGAGDICAIFGID-CASGDT 78 (81)
T ss_pred CeEEEEEeecCCC-CCEEEEEEecCEEcCCCEEEEcCCCCEEEEeEEEEEeCCCceEccEECCCCEEEEECCC-cccCCE
Confidence 5799999999988 99999999999999999999998888899999999999999999999999999999998 999999
Q ss_pred Eec
Q psy5461 181 RTR 183 (221)
Q Consensus 181 l~~ 183 (221)
|++
T Consensus 79 l~~ 81 (81)
T cd04091 79 FTD 81 (81)
T ss_pred ecC
Confidence 963
No 28
>cd03691 BipA_TypA_II BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion.
Probab=99.82 E-value=9.4e-20 Score=130.49 Aligned_cols=83 Identities=27% Similarity=0.320 Sum_probs=77.1
Q ss_pred cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC---ceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCCcc
Q psy5461 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD---QSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRERG 177 (221)
Q Consensus 101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~---~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~~~ 177 (221)
|.|+|||+++|++.|+++|+|||+|+|++||+|++...+ +++++++|+.++|++..+++++.||||+++.|++++.+
T Consensus 1 ~~~~vfk~~~d~~~g~i~~~Rv~sG~l~~g~~v~~~~~~~~~~~~~v~~l~~~~g~~~~~v~~~~aG~I~~i~gl~~~~~ 80 (86)
T cd03691 1 LQMLVTTLDYDDYVGRIAIGRIFRGTVKVGQQVAVVKRDGKIEKAKITKLFGFEGLKRVEVEEAEAGDIVAIAGIEDITI 80 (86)
T ss_pred CeEEEEEeEecCCCCeEEEEEEEeCEEcCCCEEEEEcCCCCEEEEEEeeEeeeeCCCeeECcEECCCCEEEEECCCCCcc
Confidence 579999999999999999999999999999999988763 25789999999999999999999999999999999999
Q ss_pred CcEEec
Q psy5461 178 KDKRTR 183 (221)
Q Consensus 178 Gdtl~~ 183 (221)
|||+++
T Consensus 81 Gdtl~~ 86 (86)
T cd03691 81 GDTICD 86 (86)
T ss_pred cceecC
Confidence 999963
No 29
>cd03699 lepA_II lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu and IF2 have all been demonstrated to interact at overlapping sites on the ribosome. Chemical protection studies demonstrate that they all include the universally conserved alpha-sarcin loop as part of their binding site. These data indicate that LepA may bind to this location on the ribosome as well. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage.
Probab=99.81 E-value=2.4e-19 Score=128.52 Aligned_cols=82 Identities=23% Similarity=0.372 Sum_probs=74.4
Q ss_pred cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc-C---CCCCc
Q psy5461 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT-G---LKRER 176 (221)
Q Consensus 101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~-g---l~~~~ 176 (221)
|+|+|||++++++.|+++|+|||+|+|++||.+++...++++++++|+ +.+.+..+++++.||||+++. | ++++.
T Consensus 1 ~~~~Vfk~~~d~~~G~i~~~Rv~sG~l~~~~~v~~~~~~~~~~i~~l~-~~~~~~~~~~~~~aGdI~~v~~g~~~l~~~~ 79 (86)
T cd03699 1 LRALIFDSWYDPYRGVIALVRVFDGTLKKGDKIRFMSTGKEYEVEEVG-IFRPEMTPTDELSAGQVGYIIAGIKTVKDAR 79 (86)
T ss_pred CEEEEEEeeccCCCCEEEEEEEEcCEEcCCCEEEEecCCCeEEEEEEE-EECCCccCCceECCCCEEEEEccccccCccc
Confidence 589999999999999999999999999999999998877788999999 558888999999999999885 4 66789
Q ss_pred cCcEEec
Q psy5461 177 GKDKRTR 183 (221)
Q Consensus 177 ~Gdtl~~ 183 (221)
+||||+.
T Consensus 80 ~Gdtl~~ 86 (86)
T cd03699 80 VGDTITL 86 (86)
T ss_pred cccEeeC
Confidence 9999974
No 30
>KOG0469|consensus
Probab=99.76 E-value=9e-19 Score=157.72 Aligned_cols=146 Identities=20% Similarity=0.203 Sum_probs=121.0
Q ss_pred HHHHHHHHhhCCCCCCccccc-----------------ccCCCCCCcEEEEEEEeecCCCce-EEEEEEEceEEcCCCEE
Q psy5461 72 QKLMDAIVDILPSPTERPALA-----------------MFQHFGDSLCARAFKVVHDKHRGA-VTFFRIYSGAFKKGQKF 133 (221)
Q Consensus 72 ~~LLd~I~~~~PsP~~~~~~~-----------------~~~~~~~~~~~~Vfk~~~d~~~G~-i~~~RV~sG~L~~gd~v 133 (221)
+.||++|..++|||..+++++ ..|++++|++++|.|.......|+ ++|+|||||++..|.++
T Consensus 332 dallemIalhLPSPvtaQkyR~e~LYEGP~DDe~a~aik~CD~~aplmmYvSKMvPtsDkgRFyAFGRVFsG~v~~G~Kv 411 (842)
T KOG0469|consen 332 DALLEMIALHLPSPVTAQKYRAEYLYEGPADDEAAVAIKNCDPKAPLMMYVSKMVPTSDKGRFYAFGRVFSGKVFTGLKV 411 (842)
T ss_pred HHHHHHHHhhCCCchHHHHHHHHHhhcCCCchHHhhHhhccCCCCCeEEeeeeccccCCCceEEEEeeeecceeccCcEE
Confidence 689999999999999988874 258999999999999998777776 99999999999999999
Q ss_pred EeccCC----cee-----eeceeEeeecCCeeeeCccccCCEEEEcCCCCC--ccCcEEecC-C--------CCCCCce-
Q psy5461 134 YNIHLD----QSE-----QITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE--RGKDKRTRV-I--------PKPTSVV- 192 (221)
Q Consensus 134 ~~~~~~----~~~-----~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~--~~Gdtl~~~-~--------~~p~~~v- 192 (221)
++.+.+ +++ .|.+...|+|+..++++..+||+|+.+.|+++. ++| ||+.. . +.-+|+|
T Consensus 412 RiqgPnY~PGkkedl~~K~iqRtvlMMGr~vepied~PaGNIiGlvGvDqfLvKtG-TiTt~e~AHNmrvMKFSVSPVV~ 490 (842)
T KOG0469|consen 412 RIQGPNYVPGKKEDLYIKAIQRTVLMMGRFVEPIEDCPAGNIIGLVGVDQFLVKTG-TITTSEAAHNMRVMKFSVSPVVR 490 (842)
T ss_pred EEeCCCCCCCcHHHHHHHHHHHHHHHhcccccccccCCCCcEEEEeehhHhhhccC-ceeehhhhccceEEEeeccceEE
Confidence 998764 322 455556699999999999999999999999974 676 66543 1 1223555
Q ss_pred ---------ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461 193 ---------QCSARWTLNLEVGASSPIISKSKRRQ 218 (221)
Q Consensus 193 ---------~~~~l~~~L~~L~~~Dp~l~~~~~~~ 218 (221)
|+++|.++|.+|+++||++..-.+.+
T Consensus 491 VAVe~Knp~DLpKLvEGLkrLakSDP~v~~~~~es 525 (842)
T KOG0469|consen 491 VAVEAKNPADLPKLVEGLKRLAKSDPMVQCIIEES 525 (842)
T ss_pred EEEecCChhhhHHHHHHHHHHhccCCeEEEEeccC
Confidence 88999999999999999988766543
No 31
>cd03700 eEF2_snRNP_like_II EF2_snRNP_like_II: this subfamily represents domain II of elongation factor (EF) EF-2 found eukaryotes and archaea and, the C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. This translocation step is catalyzed by EF-2_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p.
Probab=99.76 E-value=5.9e-18 Score=123.04 Aligned_cols=82 Identities=29% Similarity=0.412 Sum_probs=75.1
Q ss_pred cEEEEEEEeecC-CCceEEEEEEEceEEcCCCEEEecc---------CCceeeeceeEeeecCCeeeeCccccCCEEEEc
Q psy5461 101 LCARAFKVVHDK-HRGAVTFFRIYSGAFKKGQKFYNIH---------LDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT 170 (221)
Q Consensus 101 ~~~~Vfk~~~d~-~~G~i~~~RV~sG~L~~gd~v~~~~---------~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~ 170 (221)
++++|||+.+++ +.|+++|+|||||+|+.|+.+++.. ..+++++++|+.++|.+..+++++.|||||++.
T Consensus 1 ~v~~v~Ki~~~~~~~g~la~~RV~sGtl~~g~~v~~~~~~~~~~~~~~~~~~~v~~l~~~~g~~~~~v~~a~aGdIv~i~ 80 (93)
T cd03700 1 LVMYVTKMVPTPDKGGFIAFGRVFSGTIRKGQKVRVLGPNYSPEDEEDLSKKTIQRLYLMMGRYREPVDEVPAGNIVLIV 80 (93)
T ss_pred CeEEEEeCeECCCCCEEEEEEEEeeCeEeCCCEEEEECCCCCCCccCcEEEEEEeEEEEEcCCCEEEccccCCCCEEEEE
Confidence 478999999999 8999999999999999999999876 234578999999999999999999999999999
Q ss_pred CCCCCccCcEEe
Q psy5461 171 GLKRERGKDKRT 182 (221)
Q Consensus 171 gl~~~~~Gdtl~ 182 (221)
|++++++|||.+
T Consensus 81 g~~~~~~g~~~~ 92 (93)
T cd03700 81 GLDQLKSGTTAT 92 (93)
T ss_pred CCccCceEeEec
Confidence 999999999864
No 32
>cd04090 eEF2_II_snRNP Loc2 eEF2_C_snRNP, cd01514/C terminal domain:eEF2_C_snRNP: This family includes C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to domain II of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=99.73 E-value=4.3e-17 Score=118.77 Aligned_cols=81 Identities=30% Similarity=0.321 Sum_probs=71.3
Q ss_pred cEEEEEEEeecCCC-ceEEEEEEEceEEcCCCEEEeccCC---------ceeeeceeEeeecCCeeeeCccccCCEEEEc
Q psy5461 101 LCARAFKVVHDKHR-GAVTFFRIYSGAFKKGQKFYNIHLD---------QSEQITRLLLAEADDYKEVNEIQCGNIAAVT 170 (221)
Q Consensus 101 ~~~~Vfk~~~d~~~-G~i~~~RV~sG~L~~gd~v~~~~~~---------~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~ 170 (221)
++|+|||+.++++. |+++|+|||||+|++||.|++.+.+ ..+++.+|+.++|.+..+++++.||||+++.
T Consensus 1 ~~a~VfK~~~~~~~~~~la~~RV~sGtl~~g~~v~~~~~~~~~~~~~~~~~~~i~~l~~~~g~~~~~v~~a~aGdIv~v~ 80 (94)
T cd04090 1 LVVHVTKLYSTSDGGSFWAFGRIYSGTIKKGQKVKVLGENYSLDDEEDMTICTIGRLWILGGRYKIEVNEAPAGNWVLIK 80 (94)
T ss_pred CEEEEEeeeecCCCCEEEEEEEEeeCeEcCCCEEEEECCCCCCccCCcEEEEEEeEEEEecCCCEEEcceeCCCCEEEEE
Confidence 47899999999997 6799999999999999999885432 3579999999999999999999999999999
Q ss_pred CCCCCccCcEE
Q psy5461 171 GLKRERGKDKR 181 (221)
Q Consensus 171 gl~~~~~Gdtl 181 (221)
|+++...+.+.
T Consensus 81 gl~~~~~~~~t 91 (94)
T cd04090 81 GIDSSIVKTAT 91 (94)
T ss_pred CcchheeceEE
Confidence 99987655544
No 33
>PRK05306 infB translation initiation factor IF-2; Validated
Probab=99.69 E-value=8.3e-16 Score=148.25 Aligned_cols=182 Identities=14% Similarity=0.076 Sum_probs=135.2
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhh-ccc---cccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYS-GAF---KKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFG 98 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~-~~~---~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~ 98 (221)
.+-|++..++|++......+-....+.. +.. .+..+|++++||++|.||++|++.|....... .+.++++
T Consensus 388 ~~vPiIVviNKiDl~~a~~e~V~~eL~~~~~~~e~~g~~vp~vpvSAktG~GI~eLle~I~~~~e~~------~l~~~~~ 461 (787)
T PRK05306 388 AGVPIIVAINKIDKPGANPDRVKQELSEYGLVPEEWGGDTIFVPVSAKTGEGIDELLEAILLQAEVL------ELKANPD 461 (787)
T ss_pred cCCcEEEEEECccccccCHHHHHHHHHHhcccHHHhCCCceEEEEeCCCCCCchHHHHhhhhhhhhh------hcccCCC
Confidence 4678999999965422111111111111 111 13458999999999999999999998632110 1123567
Q ss_pred CCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCC-cc
Q psy5461 99 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE-RG 177 (221)
Q Consensus 99 ~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~-~~ 177 (221)
.++.++||++..++++|+++++||++|+|+.||.|++. .++++|+.+.+.+..++++|.|||+|.|.|++++ .+
T Consensus 462 ~~~~g~V~es~~dkg~G~v~~v~V~sGtLk~Gd~vv~g-----~~~gkVr~m~~~~~~~v~~A~pGd~V~I~gl~~~p~~ 536 (787)
T PRK05306 462 RPARGTVIEAKLDKGRGPVATVLVQNGTLKVGDIVVAG-----TTYGRVRAMVDDNGKRVKEAGPSTPVEILGLSGVPQA 536 (787)
T ss_pred CCcEEEEEEEEEcCCCeEEEEEEEecCeEecCCEEEEC-----CcEEEEEEEECCCCCCCCEEcCCCeEEEeCCCCCCCC
Confidence 89999999999999999999999999999999999985 2567777788878889999999999999999988 99
Q ss_pred CcEEecCCC---------------------------------C---C----CCce-------ehHHHHHHHHHHhhcCCc
Q psy5461 178 KDKRTRVIP---------------------------------K---P----TSVV-------QCSARWTLNLEVGASSPI 210 (221)
Q Consensus 178 Gdtl~~~~~---------------------------------~---p----~~~v-------~~~~l~~~L~~L~~~Dp~ 210 (221)
||+|+.... . + ..++ ..+.|..+|.+|..+|+.
T Consensus 537 Gd~l~~~~~e~~a~~~~~~r~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~iikad~~Gs~eai~~~l~~l~~~~v~ 616 (787)
T PRK05306 537 GDEFVVVEDEKKAREIAEYRQEKAREKKLARQQRVSLENLFEQMKEGEVKELNLIIKADVQGSVEALKDSLEKLSTDEVK 616 (787)
T ss_pred CCEEEEcCCHHHHHHHHHHHHHHHHHHHhhhccccCHHHhhhhhhcCCceEEEEEEEeCCcchHHHHHHHHHhhcccCCc
Confidence 999983200 0 0 0222 568999999999999998
Q ss_pred eEEEc
Q psy5461 211 ISKSK 215 (221)
Q Consensus 211 l~~~~ 215 (221)
+.+-+
T Consensus 617 ~~i~~ 621 (787)
T PRK05306 617 VNIIH 621 (787)
T ss_pred eEEEe
Confidence 88754
No 34
>PRK12736 elongation factor Tu; Reviewed
Probab=99.60 E-value=4e-14 Score=127.83 Aligned_cols=149 Identities=21% Similarity=0.274 Sum_probs=113.8
Q ss_pred CCc-eeeeeeeecc-cc-cCCcchHHHHhhcc----ccccCceeEecCCCccc--------cHHHHHHHHHhhCCCCCCc
Q psy5461 24 GDS-LCARAFKVVH-DK-HRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNI--------GVQKLMDAIVDILPSPTER 88 (221)
Q Consensus 24 ~~~-~~~~vfk~~~-d~-~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~--------Gi~~LLd~I~~~~PsP~~~ 88 (221)
+.+ ++..++|.+. +. ..-+.....+.+.. .+....|++++||++|. ++..|+++|.+++|.|..
T Consensus 127 g~~~~IvviNK~D~~~~~~~~~~i~~~i~~~l~~~~~~~~~~~ii~vSa~~g~~~~~~~~~~i~~Ll~~l~~~lp~~~~- 205 (394)
T PRK12736 127 GVPYLVVFLNKVDLVDDEELLELVEMEVRELLSEYDFPGDDIPVIRGSALKALEGDPKWEDAIMELMDAVDEYIPTPER- 205 (394)
T ss_pred CCCEEEEEEEecCCcchHHHHHHHHHHHHHHHHHhCCCcCCccEEEeeccccccCCCcchhhHHHHHHHHHHhCCCCCC-
Confidence 445 6788999652 11 11111122232221 22235799999999983 789999999999998754
Q ss_pred ccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccC--CceeeeceeEeeecCCeeeeCccccCCE
Q psy5461 89 PALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHL--DQSEQITRLLLAEADDYKEVNEIQCGNI 166 (221)
Q Consensus 89 ~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~--~~~~~v~~i~~~~g~~~~~v~~a~aGdI 166 (221)
+.++||.+.|++++.+++.|+++++||.+|+|+.||+|++.+. +...+|++|... ..+++++.|||+
T Consensus 206 -------~~~~p~r~~I~~~~~~~g~G~Vv~G~v~~G~l~~gd~v~i~p~~~~~~~~V~sI~~~----~~~~~~a~aGd~ 274 (394)
T PRK12736 206 -------DTDKPFLMPVEDVFTITGRGTVVTGRVERGTVKVGDEVEIVGIKETQKTVVTGVEMF----RKLLDEGQAGDN 274 (394)
T ss_pred -------CCCCCeEEEEEEEEecCCcEEEEEEEEeecEEecCCEEEEecCCCCeEEEEEEEEEC----CEEccEECCCCE
Confidence 4578999999999999999999999999999999999998765 456789998742 457899999999
Q ss_pred EE--EcCCC--CCccCcEEecC
Q psy5461 167 AA--VTGLK--RERGKDKRTRV 184 (221)
Q Consensus 167 v~--i~gl~--~~~~Gdtl~~~ 184 (221)
++ +.|++ +++.||+++..
T Consensus 275 v~l~l~~i~~~~i~~G~vl~~~ 296 (394)
T PRK12736 275 VGVLLRGVDRDEVERGQVLAKP 296 (394)
T ss_pred EEEEECCCcHHhCCcceEEecC
Confidence 95 47874 68999999875
No 35
>TIGR00487 IF-2 translation initiation factor IF-2. This model discriminates eubacterial (and mitochondrial) translation initiation factor 2 (IF-2), encoded by the infB gene in bacteria, from similar proteins in the Archaea and Eukaryotes. In the bacteria and in organelles, the initiator tRNA is charged with N-formyl-Met instead of Met. This translation factor acts in delivering the initator tRNA to the ribosome. It is one of a number of GTP-binding translation factors recognized by the pfam model GTP_EFTU.
Probab=99.59 E-value=5.3e-14 Score=132.55 Aligned_cols=176 Identities=13% Similarity=0.068 Sum_probs=129.1
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccc--------cccCceeEecCCCccccHHHHHHHHHhh--CCCCCCccccc
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAF--------KKNHVPVLCGSSYKNIGVQKLMDAIVDI--LPSPTERPALA 92 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~--------~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~--~PsP~~~~~~~ 92 (221)
.+-|++..++|++.... ...++.+... -+...|++.+||++|.||++|++.|... ++.+.
T Consensus 186 ~~vPiIVviNKiDl~~~----~~e~v~~~L~~~g~~~~~~~~~~~~v~iSAktGeGI~eLl~~I~~~~~~~~l~------ 255 (587)
T TIGR00487 186 ANVPIIVAINKIDKPEA----NPDRVKQELSEYGLVPEDWGGDTIFVPVSALTGDGIDELLDMILLQSEVEELK------ 255 (587)
T ss_pred cCCCEEEEEECcccccC----CHHHHHHHHHHhhhhHHhcCCCceEEEEECCCCCChHHHHHhhhhhhhhcccc------
Confidence 46789999999653221 1122222111 1224689999999999999999999753 12211
Q ss_pred ccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCC
Q psy5461 93 MFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGL 172 (221)
Q Consensus 93 ~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl 172 (221)
.+++.|+.+.|+++..++++|++++++|++|+|++||.+..... ..+|..|+ .....++++|.||+++.+.|+
T Consensus 256 --~~~~~~~~~~V~ev~~~~g~G~v~~~~V~~GtL~~Gd~iv~~~~--~~kVr~l~---~~~g~~v~~a~~g~~v~i~Gl 328 (587)
T TIGR00487 256 --ANPNGQASGVVIEAQLDKGRGPVATVLVQSGTLRVGDIVVVGAA--YGRVRAMI---DENGKSVKEAGPSKPVEILGL 328 (587)
T ss_pred --CCCCCCceeEEEEEEEeCCCcEEEEEEEEeCEEeCCCEEEECCC--ccEEEEEE---CCCCCCCCEECCCCEEEEeCC
Confidence 24678999999999999999999999999999999999988653 24555554 444567899999999999999
Q ss_pred CCC-ccCcEEecCC-----------------------CC----------------CC-Cce-------ehHHHHHHHHHH
Q psy5461 173 KRE-RGKDKRTRVI-----------------------PK----------------PT-SVV-------QCSARWTLNLEV 204 (221)
Q Consensus 173 ~~~-~~Gdtl~~~~-----------------------~~----------------p~-~~v-------~~~~l~~~L~~L 204 (221)
+++ .+||++.... .. |. .++ ..++|.++|++|
T Consensus 329 ~~~p~aGd~~~~~~~e~~a~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viikad~~Gs~eal~~~l~~~ 408 (587)
T TIGR00487 329 SDVPAAGDEFIVFKDEKDARLVAEKRAGKLRQKALSRSVKVTLDNLFEQIKEGELKELNIILKADVQGSLEAIKNSLEKL 408 (587)
T ss_pred CCCCCCCCEEEEcCCHHHHHHHHHHHHHHHHHHhhhhccccchhHhhhhhhccCCceEEEEEEeCCcchHHHHHHHHHhh
Confidence 886 9999997320 00 10 222 568999999999
Q ss_pred hhcCCceEEEc
Q psy5461 205 GASSPIISKSK 215 (221)
Q Consensus 205 ~~~Dp~l~~~~ 215 (221)
..+|+.+.+.+
T Consensus 409 ~~~~~~~~v~~ 419 (587)
T TIGR00487 409 NNEEVKVKVIH 419 (587)
T ss_pred cccCCeEEEEE
Confidence 99999887754
No 36
>CHL00189 infB translation initiation factor 2; Provisional
Probab=99.57 E-value=3.1e-14 Score=136.42 Aligned_cols=147 Identities=12% Similarity=0.056 Sum_probs=114.0
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhcc--------ccccCceeEecCCCccccHHHHHHHHHhhCCCCCCccccccc
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA--------FKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMF 94 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~--------~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~ 94 (221)
.+-|++..++|++.... .+.++.+.. ..+..+|++.+||++|.||++|++.|..+...+. +.
T Consensus 346 ~~iPiIVViNKiDl~~~----~~e~v~~eL~~~~ll~e~~g~~vpvv~VSAktG~GIdeLle~I~~l~e~~~------lk 415 (742)
T CHL00189 346 ANVPIIVAINKIDKANA----NTERIKQQLAKYNLIPEKWGGDTPMIPISASQGTNIDKLLETILLLAEIED------LK 415 (742)
T ss_pred cCceEEEEEECCCcccc----CHHHHHHHHHHhccchHhhCCCceEEEEECCCCCCHHHHHHhhhhhhhhhc------cc
Confidence 46789999999654321 122222211 1134689999999999999999999988753211 11
Q ss_pred CCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCC-
Q psy5461 95 QHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK- 173 (221)
Q Consensus 95 ~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~- 173 (221)
++++.|+.++||++..|+++|++++++|++|+|++||.|++.. +.++|+.+.+....++++|.|||+|.|.|++
T Consensus 416 ~~~~~~~~g~V~e~~iD~~~G~V~~~~V~sGtLr~GD~vv~g~-----~~gkVr~m~~~~~~~v~~a~pgdiV~I~gl~~ 490 (742)
T CHL00189 416 ADPTQLAQGIILEAHLDKTKGPVATILVQNGTLHIGDIIVIGT-----SYAKIRGMINSLGNKINLATPSSVVEIWGLSS 490 (742)
T ss_pred CCCCCCceEEEEEEEEcCCCceEEEEEEEcCEEecCCEEEECC-----cceEEEEEEcCCCcCccEEcCCCceEecCccc
Confidence 2456889999999999999999999999999999999998864 4567777778888899999999999999994
Q ss_pred CCccCcEEecC
Q psy5461 174 RERGKDKRTRV 184 (221)
Q Consensus 174 ~~~~Gdtl~~~ 184 (221)
...+||+|...
T Consensus 491 ~~~~Gd~l~v~ 501 (742)
T CHL00189 491 VPATGEHFQVF 501 (742)
T ss_pred CCCCCCEEEEe
Confidence 56899999643
No 37
>CHL00071 tufA elongation factor Tu
Probab=99.57 E-value=3.9e-14 Score=128.45 Aligned_cols=150 Identities=19% Similarity=0.245 Sum_probs=112.7
Q ss_pred CCCc-eeeeeeeecc-cc-cCCcchHHHHhhcc----ccccCceeEecCCCccc------------------cHHHHHHH
Q psy5461 23 FGDS-LCARAFKVVH-DK-HRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNI------------------GVQKLMDA 77 (221)
Q Consensus 23 ~~~~-~~~~vfk~~~-d~-~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~------------------Gi~~LLd~ 77 (221)
.+-| ++..++|.+. ++ ..-+.....+.... .+...+|++++||++|+ |+..||++
T Consensus 126 ~g~~~iIvvvNK~D~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~ii~~Sa~~g~n~~~~~~~~~~~~~~w~~~~~~ll~~ 205 (409)
T CHL00071 126 VGVPNIVVFLNKEDQVDDEELLELVELEVRELLSKYDFPGDDIPIVSGSALLALEALTENPKIKRGENKWVDKIYNLMDA 205 (409)
T ss_pred cCCCEEEEEEEccCCCCHHHHHHHHHHHHHHHHHHhCCCCCcceEEEcchhhcccccccCccccccCCchhhhHHHHHHH
Confidence 3456 7789999652 11 11111122333222 12335899999999986 47899999
Q ss_pred HHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccC--CceeeeceeEeeecCCe
Q psy5461 78 IVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHL--DQSEQITRLLLAEADDY 155 (221)
Q Consensus 78 I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~--~~~~~v~~i~~~~g~~~ 155 (221)
|.+++|+|.. +.++||++.|.+++.+++.|+++++||++|+++.||+|...+. +...+|++|... .
T Consensus 206 l~~~~~~p~~--------~~~~p~r~~I~~v~~~~g~G~Vv~G~V~sG~l~~Gd~v~i~p~~~~~~~~VksI~~~----~ 273 (409)
T CHL00071 206 VDSYIPTPER--------DTDKPFLMAIEDVFSITGRGTVATGRIERGTVKVGDTVEIVGLRETKTTTVTGLEMF----Q 273 (409)
T ss_pred HHhhCCCCCC--------CCCCCEEEEEEEEEEeCCCeEEEEEEEecCEEeeCCEEEEeeCCCCcEEEEEEEEEc----C
Confidence 9999988864 4578999999999999999999999999999999999987643 455789998743 2
Q ss_pred eeeCccccCCEEE--EcCCC--CCccCcEEecC
Q psy5461 156 KEVNEIQCGNIAA--VTGLK--RERGKDKRTRV 184 (221)
Q Consensus 156 ~~v~~a~aGdIv~--i~gl~--~~~~Gdtl~~~ 184 (221)
+++++|.|||+++ +.|++ +++.||+|++.
T Consensus 274 ~~v~~a~aGd~v~i~l~~i~~~~i~~G~vl~~~ 306 (409)
T CHL00071 274 KTLDEGLAGDNVGILLRGIQKEDIERGMVLAKP 306 (409)
T ss_pred cCCCEECCCceeEEEEcCCCHHHcCCeEEEecC
Confidence 4789999999995 55765 68999999876
No 38
>TIGR00485 EF-Tu translation elongation factor TU. This alignment models orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts, one of several GTP-binding translation factors found by the more general pfam model GTP_EFTU. The eukaryotic conterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this model. EF-Tu is one of the most abundant proteins in bacteria, as well as one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation.
Probab=99.55 E-value=9.4e-14 Score=125.40 Aligned_cols=117 Identities=22% Similarity=0.337 Sum_probs=99.3
Q ss_pred cCceeEecCCCccc--------cHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEE
Q psy5461 56 NHVPVLCGSSYKNI--------GVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAF 127 (221)
Q Consensus 56 ~~~Pv~~gSa~~~~--------Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L 127 (221)
..+|++++||++|. ++..||++|.+++|.|.. +.++||++.|++++.+++.|+++++||.+|++
T Consensus 166 ~~~~ii~vSa~~g~~g~~~~~~~~~~ll~~l~~~~~~~~~--------~~~~p~r~~V~~vf~~~g~G~Vv~G~v~~G~l 237 (394)
T TIGR00485 166 DDTPIIRGSALKALEGDAEWEAKILELMDAVDEYIPTPER--------ETDKPFLMPIEDVFSITGRGTVVTGRVERGIV 237 (394)
T ss_pred cCccEEECccccccccCCchhHhHHHHHHHHHhcCCCCCC--------CCCCCeEEEEEEEEeeCCceEEEEEEEEeeEE
Confidence 34899999999874 578999999999888764 45789999999999999999999999999999
Q ss_pred cCCCEEEeccC--CceeeeceeEeeecCCeeeeCccccCCEEEE--cCCC--CCccCcEEecC
Q psy5461 128 KKGQKFYNIHL--DQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLK--RERGKDKRTRV 184 (221)
Q Consensus 128 ~~gd~v~~~~~--~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~--~~~~Gdtl~~~ 184 (221)
++||+|+.... ++..+|++|... ..++++|.|||.+++ .|++ +++.||++++.
T Consensus 238 ~~gd~v~i~p~~~~~~~~VksI~~~----~~~~~~a~aGd~v~l~l~~i~~~~i~rG~vl~~~ 296 (394)
T TIGR00485 238 KVGEEVEIVGLKDTRKTTVTGVEMF----RKELDEGRAGDNVGLLLRGIKREEIERGMVLAKP 296 (394)
T ss_pred eCCCEEEEecCCCCcEEEEEEEEEC----CeEEEEECCCCEEEEEeCCccHHHCCccEEEecC
Confidence 99999998763 456789998743 357889999999954 7764 68999999885
No 39
>KOG0460|consensus
Probab=99.55 E-value=7.3e-15 Score=127.41 Aligned_cols=148 Identities=22% Similarity=0.290 Sum_probs=124.7
Q ss_pred Cceeeeeeeec-c-cccCCcchHHHHhhcc----ccccCceeEecCCCcc-------c---cHHHHHHHHHhhCCCCCCc
Q psy5461 25 DSLCARAFKVV-H-DKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKN-------I---GVQKLMDAIVDILPSPTER 88 (221)
Q Consensus 25 ~~~~~~vfk~~-~-d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~-------~---Gi~~LLd~I~~~~PsP~~~ 88 (221)
..++.|+||++ + |++.-++.+..+|+.. +++..+||++|||+-- + -|..|||++.+|+|.|..
T Consensus 171 ~~ivvfiNKvD~V~d~e~leLVEmE~RElLse~gf~Gd~~PvI~GSAL~ALeg~~peig~~aI~kLldavDsyip~P~R- 249 (449)
T KOG0460|consen 171 KHIVVFINKVDLVDDPEMLELVEMEIRELLSEFGFDGDNTPVIRGSALCALEGRQPEIGLEAIEKLLDAVDSYIPTPER- 249 (449)
T ss_pred ceEEEEEecccccCCHHHHHHHHHHHHHHHHHcCCCCCCCCeeecchhhhhcCCCccccHHHHHHHHHHHhccCCCccc-
Confidence 58999999985 4 6778888888888765 6788999999999754 2 389999999999999976
Q ss_pred ccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCc--eeeeceeEeeecCCeeeeCccccCCE
Q psy5461 89 PALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ--SEQITRLLLAEADDYKEVNEIQCGNI 166 (221)
Q Consensus 89 ~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~--~~~v~~i~~~~g~~~~~v~~a~aGdI 166 (221)
+.+.||++-|-.++.-+++|+++++|+.+|+|++||++...+.++ +..|+.|..++ ..++++.|||-
T Consensus 250 -------~~~~pFl~pie~vfsI~GRGTVvtGrlERG~lKkG~e~eivG~~~~lkttvtgiemF~----K~ld~a~AGDn 318 (449)
T KOG0460|consen 250 -------DLDKPFLLPIEDVFSIPGRGTVVTGRLERGVLKKGDEVEIVGHNKTLKTTVTGIEMFR----KSLDEAQAGDN 318 (449)
T ss_pred -------ccCCCceeehhheeeecCCceEEEEEEeecccccCCEEEEeccCcceeeEeehHHHHH----HHHHhcccccc
Confidence 678999999999999999999999999999999999999887654 46778776442 36899999999
Q ss_pred EE--EcCCC--CCccCcEEecC
Q psy5461 167 AA--VTGLK--RERGKDKRTRV 184 (221)
Q Consensus 167 v~--i~gl~--~~~~Gdtl~~~ 184 (221)
+. ++|++ +++.|..++..
T Consensus 319 ~G~LlRGik~~dvkRGmvl~~p 340 (449)
T KOG0460|consen 319 LGALLRGIKREDVKRGMVLAKP 340 (449)
T ss_pred eehhhhcCCHHHHhcccEEecC
Confidence 94 57775 78999998753
No 40
>PRK12735 elongation factor Tu; Reviewed
Probab=99.51 E-value=4.3e-13 Score=121.20 Aligned_cols=117 Identities=23% Similarity=0.320 Sum_probs=100.5
Q ss_pred cCceeEecCCCccc----------cHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEce
Q psy5461 56 NHVPVLCGSSYKNI----------GVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSG 125 (221)
Q Consensus 56 ~~~Pv~~gSa~~~~----------Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG 125 (221)
..+|++++||++|. |+..|+++|.+.+|.|.. +.++||.+.|..++..++.|.++++||.+|
T Consensus 166 ~~~~ii~~Sa~~g~n~~~~~~w~~~~~~Ll~~l~~~~~~p~~--------~~~~p~r~~I~~~f~v~g~Gtvv~G~v~~G 237 (396)
T PRK12735 166 DDTPIIRGSALKALEGDDDEEWEAKILELMDAVDSYIPEPER--------AIDKPFLMPIEDVFSISGRGTVVTGRVERG 237 (396)
T ss_pred CceeEEecchhccccCCCCCcccccHHHHHHHHHhcCCCCCc--------cCCCCeEEEEEEEEecCCceEEEEEEEEec
Confidence 35899999999983 789999999999998754 457899999999999999999999999999
Q ss_pred EEcCCCEEEeccC--CceeeeceeEeeecCCeeeeCccccCCEEEE--cCCC--CCccCcEEecC
Q psy5461 126 AFKKGQKFYNIHL--DQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLK--RERGKDKRTRV 184 (221)
Q Consensus 126 ~L~~gd~v~~~~~--~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~--~~~~Gdtl~~~ 184 (221)
++++||+|++... +++.+|++|... ..++++|.|||.+++ .|++ +++.|++++..
T Consensus 238 ~i~~gd~v~i~p~~~~~~~~VksI~~~----~~~v~~a~aGd~v~l~L~~i~~~~i~rG~vl~~~ 298 (396)
T PRK12735 238 IVKVGDEVEIVGIKETQKTTVTGVEMF----RKLLDEGQAGDNVGVLLRGTKREDVERGQVLAKP 298 (396)
T ss_pred EEeCCCEEEEecCCCCeEEEEEEEEEC----CeEeCEECCCCEEEEEeCCCcHHHCCcceEEEcC
Confidence 9999999998865 356788988742 468899999999965 6774 68999999986
No 41
>PRK00049 elongation factor Tu; Reviewed
Probab=99.47 E-value=1.3e-12 Score=118.00 Aligned_cols=150 Identities=19% Similarity=0.210 Sum_probs=112.8
Q ss_pred CCCcee-eeeeeeccc--ccCCcchHHHHhhccc----cccCceeEecCCCccc----------cHHHHHHHHHhhCCCC
Q psy5461 23 FGDSLC-ARAFKVVHD--KHRGAVTFFRIYSGAF----KKNHVPVLCGSSYKNI----------GVQKLMDAIVDILPSP 85 (221)
Q Consensus 23 ~~~~~~-~~vfk~~~d--~~~g~l~~~~l~~~~~----~~~~~Pv~~gSa~~~~----------Gi~~LLd~I~~~~PsP 85 (221)
.+.|.+ ..++|++.- +..-+.....+.+... .....|++++||++|. |+..||++|.+++|.|
T Consensus 126 ~g~p~iiVvvNK~D~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~iv~iSa~~g~~~~~~~~w~~~~~~ll~~l~~~~~~p 205 (396)
T PRK00049 126 VGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSKYDFPGDDTPIIRGSALKALEGDDDEEWEKKILELMDAVDSYIPTP 205 (396)
T ss_pred cCCCEEEEEEeecCCcchHHHHHHHHHHHHHHHHhcCCCccCCcEEEeecccccCCCCcccccccHHHHHHHHHhcCCCC
Confidence 345754 689996421 1111111222322221 2345899999999874 7899999999999987
Q ss_pred CCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccC--CceeeeceeEeeecCCeeeeCcccc
Q psy5461 86 TERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHL--DQSEQITRLLLAEADDYKEVNEIQC 163 (221)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~--~~~~~v~~i~~~~g~~~~~v~~a~a 163 (221)
.. ..++||.+.|..++..++.|.++.+||.+|++++||++.+... ++..+|++|... .++++++.|
T Consensus 206 ~~--------~~~~p~r~~I~~~f~v~g~G~Vv~G~v~~G~i~~gd~v~i~p~~~~~~~~VksI~~~----~~~~~~a~~ 273 (396)
T PRK00049 206 ER--------AIDKPFLMPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIRDTQKTTVTGVEMF----RKLLDEGQA 273 (396)
T ss_pred CC--------CCCCCeEEEEEEEEeeCCceEEEEEEEeeeEEecCCEEEEeecCCCceEEEEEEEEC----CcEeCEEcC
Confidence 54 4578999999999999999999999999999999999988764 456789998743 357899999
Q ss_pred CCEEEE--cCCC--CCccCcEEecC
Q psy5461 164 GNIAAV--TGLK--RERGKDKRTRV 184 (221)
Q Consensus 164 GdIv~i--~gl~--~~~~Gdtl~~~ 184 (221)
||.+++ .|++ +++.|+++++.
T Consensus 274 Gd~v~l~l~~i~~~~i~~G~vl~~~ 298 (396)
T PRK00049 274 GDNVGALLRGIKREDVERGQVLAKP 298 (396)
T ss_pred CCEEEEEeCCCCHHHCCcceEEecC
Confidence 999865 6764 68999999986
No 42
>PTZ00327 eukaryotic translation initiation factor 2 gamma subunit; Provisional
Probab=99.45 E-value=2e-12 Score=118.70 Aligned_cols=147 Identities=13% Similarity=0.102 Sum_probs=107.4
Q ss_pred ceeeeeeeecc-cccCCcchHHHHhhccc--cccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcE
Q psy5461 26 SLCARAFKVVH-DKHRGAVTFFRIYSGAF--KKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLC 102 (221)
Q Consensus 26 ~~~~~vfk~~~-d~~~g~l~~~~l~~~~~--~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~ 102 (221)
+++..++|++. ++...+-.+..+++... .....|++..||++|.|++.|+++|.+.+|.|.. +.+.||.
T Consensus 173 ~iIVvlNKiDlv~~~~~~~~~~ei~~~l~~~~~~~~~iipVSA~~G~nI~~Ll~~L~~~lp~~~r--------~~~~p~r 244 (460)
T PTZ00327 173 HIIILQNKIDLVKEAQAQDQYEEIRNFVKGTIADNAPIIPISAQLKYNIDVVLEYICTQIPIPKR--------DLTSPPR 244 (460)
T ss_pred cEEEEEecccccCHHHHHHHHHHHHHHHHhhccCCCeEEEeeCCCCCCHHHHHHHHHhhCCCCCC--------CCCCCcE
Confidence 57788999652 22211222333333111 1357899999999999999999999999998854 4568898
Q ss_pred EEEEEEee--------cCCCceEEEEEEEceEEcCCCEEEeccCC-------------ceeeeceeEeeecCCeeeeCcc
Q psy5461 103 ARAFKVVH--------DKHRGAVTFFRIYSGAFKKGQKFYNIHLD-------------QSEQITRLLLAEADDYKEVNEI 161 (221)
Q Consensus 103 ~~Vfk~~~--------d~~~G~i~~~RV~sG~L~~gd~v~~~~~~-------------~~~~v~~i~~~~g~~~~~v~~a 161 (221)
+.|..++. ++++|.++.++|.+|++++||+|.+...+ ...+|++|.. ...++++|
T Consensus 245 ~~Idr~F~V~~~g~~~~~~~GtVv~G~v~~G~l~~Gd~v~i~P~~~~~~~~g~~~~~~~~~~VksI~~----~~~~v~~a 320 (460)
T PTZ00327 245 MIVIRSFDVNKPGEDIENLKGGVAGGSILQGVLKVGDEIEIRPGIISKDSGGEFTCRPIRTRIVSLFA----ENNELQYA 320 (460)
T ss_pred EEEEEEEeecccCCcccCCceEEEEEEEeeceEecCCEEEEccCcccccccCccccccceEEEEEEEE----CCeECCEE
Confidence 88876543 34479999999999999999999998643 2357888863 34688999
Q ss_pred ccCCEEEEc-----CCC--CCccCcEEecC
Q psy5461 162 QCGNIAAVT-----GLK--RERGKDKRTRV 184 (221)
Q Consensus 162 ~aGdIv~i~-----gl~--~~~~Gdtl~~~ 184 (221)
.|||.+++. +++ ++..|+.++..
T Consensus 321 ~aG~~vai~l~ld~~v~~~dv~rG~Vl~~~ 350 (460)
T PTZ00327 321 VPGGLIGVGTTIDPTLTRADRLVGQVLGYP 350 (460)
T ss_pred cCCCEEEEEeccCCCcchhhcccccEEEcC
Confidence 999998774 332 56799999875
No 43
>TIGR00483 EF-1_alpha translation elongation factor EF-1 alpha. This model represents the counterpart of bacterial EF-Tu for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1 alpha). The trusted cutoff is set fairly high so that incomplete sequences will score between suggested and trusted cutoff levels.
Probab=99.44 E-value=1.2e-12 Score=119.24 Aligned_cols=147 Identities=17% Similarity=0.168 Sum_probs=110.7
Q ss_pred CceeeeeeeecccccCC---cchHHHHhhcc----ccccCceeEecCCCccccHHH------------HHHHHHhhCCCC
Q psy5461 25 DSLCARAFKVVHDKHRG---AVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQK------------LMDAIVDILPSP 85 (221)
Q Consensus 25 ~~~~~~vfk~~~d~~~g---~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~------------LLd~I~~~~PsP 85 (221)
.+++..++|.+.-.... +.....+.+-. ......|++..||++|.||.+ |+++|.+ +|+|
T Consensus 142 ~~iIVviNK~Dl~~~~~~~~~~~~~ei~~~~~~~g~~~~~~~~i~iSA~~g~ni~~~~~~~~w~~g~~l~~~l~~-~~~~ 220 (426)
T TIGR00483 142 NQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNPDTVPFIPISAWNGDNVIKKSENTPWYKGKTLLEALDA-LEPP 220 (426)
T ss_pred CeEEEEEEChhccCccHHHHHHHHHHHHHHHHHcCCCcccceEEEeeccccccccccccCCccccchHHHHHHhc-CCCC
Confidence 46888999965311111 11122222211 122347899999999999974 9999965 6666
Q ss_pred CCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCC
Q psy5461 86 TERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGN 165 (221)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGd 165 (221)
.. ..++||.+.|..++..++.|+++.+||.+|+++.||+|.+...+...+|++|... ..++++|.|||
T Consensus 221 ~~--------~~~~p~r~~i~~v~~~~g~G~vv~G~v~~G~i~~gd~v~i~P~~~~~~VksI~~~----~~~~~~a~aG~ 288 (426)
T TIGR00483 221 EK--------PTDKPLRIPIQDVYSITGVGTVPVGRVETGVLKPGDKVVFEPAGVSGEVKSIEMH----HEQIEQAEPGD 288 (426)
T ss_pred CC--------ccCCCcEEEEEEEEecCCCeEEEEEEEccceeecCCEEEECCCCcEEEEEEEEEC----CcccCEEcCCC
Confidence 43 4568999999999999999999999999999999999999988888899999743 34789999999
Q ss_pred EEEE--cCCC--CCccCcEEecC
Q psy5461 166 IAAV--TGLK--RERGKDKRTRV 184 (221)
Q Consensus 166 Iv~i--~gl~--~~~~Gdtl~~~ 184 (221)
.+++ .+++ +++.||++++.
T Consensus 289 ~v~i~l~~i~~~~i~rG~vl~~~ 311 (426)
T TIGR00483 289 NIGFNVRGVSKKDIRRGDVCGHP 311 (426)
T ss_pred EEEEEECCCChhhcccceEEecC
Confidence 9965 6653 68999999875
No 44
>PRK12317 elongation factor 1-alpha; Reviewed
Probab=99.43 E-value=1.8e-12 Score=118.05 Aligned_cols=148 Identities=16% Similarity=0.160 Sum_probs=111.2
Q ss_pred CceeeeeeeecccccCC---cchHHHHhhcc----ccccCceeEecCCCccccHHH------------HHHHHHhhCCCC
Q psy5461 25 DSLCARAFKVVHDKHRG---AVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQK------------LMDAIVDILPSP 85 (221)
Q Consensus 25 ~~~~~~vfk~~~d~~~g---~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~------------LLd~I~~~~PsP 85 (221)
.+++..++|++...... ......+.+-. ......|++..||++|.||.+ |+++|.. +|.|
T Consensus 140 ~~iivviNK~Dl~~~~~~~~~~~~~~i~~~l~~~g~~~~~~~ii~iSA~~g~gi~~~~~~~~wy~g~~L~~~l~~-~~~~ 218 (425)
T PRK12317 140 NQLIVAINKMDAVNYDEKRYEEVKEEVSKLLKMVGYKPDDIPFIPVSAFEGDNVVKKSENMPWYNGPTLLEALDN-LKPP 218 (425)
T ss_pred CeEEEEEEccccccccHHHHHHHHHHHHHHHHhhCCCcCcceEEEeecccCCCccccccCCCcccHHHHHHHHhc-CCCC
Confidence 36888999965322111 11122222211 122247899999999999975 8898765 6766
Q ss_pred CCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCC
Q psy5461 86 TERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGN 165 (221)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGd 165 (221)
.. ..++||.+.|..++..++.|+++.+||.+|++++||+|++...+...+|++|... ..++++|.|||
T Consensus 219 ~~--------~~~~p~r~~i~~~~~~~g~G~vv~G~v~~G~v~~Gd~v~i~P~~~~~~VksI~~~----~~~~~~a~aG~ 286 (425)
T PRK12317 219 EK--------PTDKPLRIPIQDVYSISGVGTVPVGRVETGVLKVGDKVVFMPAGVVGEVKSIEMH----HEELPQAEPGD 286 (425)
T ss_pred cc--------ccCCCcEEEEEEEEeeCCCeEEEEEEEeeccEecCCEEEECCCCCeEEEEEEEEC----CcccCEECCCC
Confidence 43 4578999999999999999999999999999999999999988888899998743 35789999999
Q ss_pred EEEE--cCCC--CCccCcEEecCC
Q psy5461 166 IAAV--TGLK--RERGKDKRTRVI 185 (221)
Q Consensus 166 Iv~i--~gl~--~~~~Gdtl~~~~ 185 (221)
.+++ .+++ +++.||+++...
T Consensus 287 ~v~i~l~~~~~~~i~rG~vl~~~~ 310 (425)
T PRK12317 287 NIGFNVRGVGKKDIKRGDVCGHPD 310 (425)
T ss_pred eEEEEECCCCHHHccCccEecCCC
Confidence 9854 5664 578999998763
No 45
>PRK04000 translation initiation factor IF-2 subunit gamma; Validated
Probab=99.42 E-value=6.3e-12 Score=114.14 Aligned_cols=149 Identities=15% Similarity=0.174 Sum_probs=108.4
Q ss_pred Cceeeeeeeecccc-cCCcchHHHHhhccc--cccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCc
Q psy5461 25 DSLCARAFKVVHDK-HRGAVTFFRIYSGAF--KKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSL 101 (221)
Q Consensus 25 ~~~~~~vfk~~~d~-~~g~l~~~~l~~~~~--~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~ 101 (221)
.+++..++|++... ......+..++.... .....|++..||++|.|+++|++.|...+|.|.. ..+.||
T Consensus 140 ~~iiVVlNK~Dl~~~~~~~~~~~~i~~~l~~~~~~~~~ii~vSA~~g~gI~~L~~~L~~~l~~~~~--------~~~~~~ 211 (411)
T PRK04000 140 KNIVIVQNKIDLVSKERALENYEQIKEFVKGTVAENAPIIPVSALHKVNIDALIEAIEEEIPTPER--------DLDKPP 211 (411)
T ss_pred CcEEEEEEeeccccchhHHHHHHHHHHHhccccCCCCeEEEEECCCCcCHHHHHHHHHHhCCCCCC--------CCCCCc
Confidence 35778889965322 111112333333221 1235789999999999999999999999988754 457899
Q ss_pred EEEEEEEee--------cCCCceEEEEEEEceEEcCCCEEEeccCCc------------eeeeceeEeeecCCeeeeCcc
Q psy5461 102 CARAFKVVH--------DKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ------------SEQITRLLLAEADDYKEVNEI 161 (221)
Q Consensus 102 ~~~Vfk~~~--------d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~------------~~~v~~i~~~~g~~~~~v~~a 161 (221)
.+.|..++. ++++|.++.+||.+|+|++||.|.+...++ ..+|++|... ..++++|
T Consensus 212 r~~I~~~f~v~~~g~~~~~~~G~Vv~G~v~~G~l~~gd~v~i~P~~~~~~~~~~~~~~~~~~VksI~~~----~~~~~~a 287 (411)
T PRK04000 212 RMYVARSFDVNKPGTPPEKLKGGVIGGSLIQGVLKVGDEIEIRPGIKVEEGGKTKWEPITTKIVSLRAG----GEKVEEA 287 (411)
T ss_pred eEEEEeeeeecCCCccccCCcceEEEEEEEeCEEecCCEEEEcCCcceecccccccccceEEEeEEEEC----CEECCEE
Confidence 999988763 345788999999999999999999987542 3578888632 3678999
Q ss_pred ccCCEEEEc-----CCC--CCccCcEEecCC
Q psy5461 162 QCGNIAAVT-----GLK--RERGKDKRTRVI 185 (221)
Q Consensus 162 ~aGdIv~i~-----gl~--~~~~Gdtl~~~~ 185 (221)
.|||.+++. +++ +++.|+.++...
T Consensus 288 ~~G~~v~i~l~~~~~i~~~~i~~G~vl~~~~ 318 (411)
T PRK04000 288 RPGGLVGVGTKLDPSLTKADALAGSVAGKPG 318 (411)
T ss_pred cCCCEEEEEeccCCCCCHHHccCccEEEcCC
Confidence 999998764 332 578999999763
No 46
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=99.41 E-value=2.7e-12 Score=121.76 Aligned_cols=145 Identities=14% Similarity=0.108 Sum_probs=109.9
Q ss_pred eeeeeeeecc-cccCCcchHHHHhhcccc--ccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEE
Q psy5461 27 LCARAFKVVH-DKHRGAVTFFRIYSGAFK--KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCA 103 (221)
Q Consensus 27 ~~~~vfk~~~-d~~~g~l~~~~l~~~~~~--~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~ 103 (221)
++..++|++. ++..-+.....+.+.... ....|++..||++|.|++.|++.|..+. .|.. ..++||.+
T Consensus 107 iIVVlNKiDlv~~~~~~~v~~ei~~~l~~~~~~~~~ii~VSA~tG~gI~~L~~~L~~~~-~~~~--------~~~~~~rl 177 (614)
T PRK10512 107 LTVALTKADRVDEARIAEVRRQVKAVLREYGFAEAKLFVTAATEGRGIDALREHLLQLP-EREH--------AAQHRFRL 177 (614)
T ss_pred EEEEEECCccCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEeCCCCCCCHHHHHHHHHhh-cccc--------CcCCCceE
Confidence 5688899653 221111222333332211 1247899999999999999999998764 4432 34689999
Q ss_pred EEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cC-CC--CCccC
Q psy5461 104 RAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TG-LK--RERGK 178 (221)
Q Consensus 104 ~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~g-l~--~~~~G 178 (221)
.|-.++..++.|++++++|.+|++++||++.+.+.+...+|++|.. + ..+++++.|||.+++ .| ++ +++.|
T Consensus 178 ~Id~vf~v~G~GtVvtGtv~sG~l~~Gd~v~i~p~~~~~~VrsIq~-~---~~~v~~a~aG~rval~l~g~~~~~~i~rG 253 (614)
T PRK10512 178 AIDRAFTVKGAGLVVTGTALSGEVKVGDTLWLTGVNKPMRVRGLHA-Q---NQPTEQAQAGQRIALNIAGDAEKEQINRG 253 (614)
T ss_pred EEEEEeccCCCeEEEEEEEecceEecCCEEEEcCCCCcEEEEEEec-C---CcCCCEEeCCCeEEEEecCCCChhhCCCc
Confidence 9999998999999999999999999999999988877789999873 2 357899999999965 55 53 68999
Q ss_pred cEEecC
Q psy5461 179 DKRTRV 184 (221)
Q Consensus 179 dtl~~~ 184 (221)
|+++..
T Consensus 254 dvl~~~ 259 (614)
T PRK10512 254 DWLLAD 259 (614)
T ss_pred CEEeCC
Confidence 999875
No 47
>PLN00043 elongation factor 1-alpha; Provisional
Probab=99.40 E-value=4.6e-12 Score=116.12 Aligned_cols=146 Identities=13% Similarity=0.137 Sum_probs=109.9
Q ss_pred ceeeeeeeecccc-cCCcchHHHHhhcc--------ccccCceeEecCCCccccHH------------HHHHHHHhhCCC
Q psy5461 26 SLCARAFKVVHDK-HRGAVTFFRIYSGA--------FKKNHVPVLCGSSYKNIGVQ------------KLMDAIVDILPS 84 (221)
Q Consensus 26 ~~~~~vfk~~~d~-~~g~l~~~~l~~~~--------~~~~~~Pv~~gSa~~~~Gi~------------~LLd~I~~~~Ps 84 (221)
+++..++|++... ..-+..+.++.+.. .+...+|++..||++|.||. .||++|.. ++.
T Consensus 147 ~iIV~vNKmD~~~~~~~~~~~~~i~~ei~~~l~~~g~~~~~~~~ipiSa~~G~ni~~~~~~~~Wy~g~tLl~~l~~-i~~ 225 (447)
T PLN00043 147 QMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVGYNPDKIPFVPISGFEGDNMIERSTNLDWYKGPTLLEALDQ-INE 225 (447)
T ss_pred cEEEEEEcccCCchhhhHHHHHHHHHHHHHHHHHcCCCcccceEEEEeccccccccccccCCcccchHHHHHHHhh-cCC
Confidence 5788999965321 10112222222211 11234789999999999974 48998875 565
Q ss_pred CCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccC
Q psy5461 85 PTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCG 164 (221)
Q Consensus 85 P~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aG 164 (221)
|.. ..+.||++.|..++..++.|+++.+||.+|++++||+|.....+...+|++|... ..++++|.||
T Consensus 226 p~~--------~~~~plr~~I~~v~~~~g~G~vv~G~V~~G~l~~Gd~v~~~P~~~~~~VksI~~~----~~~v~~a~aG 293 (447)
T PLN00043 226 PKR--------PSDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFGPTGLTTEVKSVEMH----HESLQEALPG 293 (447)
T ss_pred Ccc--------ccCCCcEEEEEEEEEeCCcEEEEEEEEECCEEeeCCEEEEcCCCCEEEEEEEEEC----CeEeCEecCC
Confidence 543 4578999999999999999999999999999999999999988888899998742 4688999999
Q ss_pred CEEE--EcCC--CCCccCcEEecC
Q psy5461 165 NIAA--VTGL--KRERGKDKRTRV 184 (221)
Q Consensus 165 dIv~--i~gl--~~~~~Gdtl~~~ 184 (221)
|.+. +.++ ++++.|+.++..
T Consensus 294 d~v~i~l~~~~~~~i~rG~vl~~~ 317 (447)
T PLN00043 294 DNVGFNVKNVAVKDLKRGYVASNS 317 (447)
T ss_pred CeEEEEECCCCHhhCCCccEEccC
Confidence 9995 5566 368999999875
No 48
>PLN03127 Elongation factor Tu; Provisional
Probab=99.39 E-value=7.8e-12 Score=114.59 Aligned_cols=150 Identities=21% Similarity=0.273 Sum_probs=110.6
Q ss_pred CCCc-eeeeeeeecc-c-ccCCcchHHHHhhcc----ccccCceeEecCCC---cccc-------HHHHHHHHHhhCCCC
Q psy5461 23 FGDS-LCARAFKVVH-D-KHRGAVTFFRIYSGA----FKKNHVPVLCGSSY---KNIG-------VQKLMDAIVDILPSP 85 (221)
Q Consensus 23 ~~~~-~~~~vfk~~~-d-~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~---~~~G-------i~~LLd~I~~~~PsP 85 (221)
.+-+ ++..++|++. + +..-+.....+.+.. .....+|++.+||. +|.| +..|+++|.+++|.|
T Consensus 175 ~gip~iIvviNKiDlv~~~~~~~~i~~~i~~~l~~~~~~~~~vpiip~Sa~sa~~g~n~~~~~~~i~~Ll~~l~~~lp~p 254 (447)
T PLN03127 175 VGVPSLVVFLNKVDVVDDEELLELVEMELRELLSFYKFPGDEIPIIRGSALSALQGTNDEIGKNAILKLMDAVDEYIPEP 254 (447)
T ss_pred cCCCeEEEEEEeeccCCHHHHHHHHHHHHHHHHHHhCCCCCcceEEEeccceeecCCCcccccchHHHHHHHHHHhCCCC
Confidence 3456 5788999752 1 111111111222211 22346899999886 3444 789999999999988
Q ss_pred CCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccC----CceeeeceeEeeecCCeeeeCcc
Q psy5461 86 TERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHL----DQSEQITRLLLAEADDYKEVNEI 161 (221)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~----~~~~~v~~i~~~~g~~~~~v~~a 161 (221)
.. ..++||.+.|..++..++.|.++.+||.+|++++||+|++.+. +...+|++|... ..+++++
T Consensus 255 ~r--------~~~~pfr~~I~~vf~v~g~GtVvtG~v~~G~i~~Gd~v~i~p~~~~g~~~~~VksI~~~----~~~v~~a 322 (447)
T PLN03127 255 VR--------VLDKPFLMPIEDVFSIQGRGTVATGRVEQGTIKVGEEVEIVGLRPGGPLKTTVTGVEMF----KKILDQG 322 (447)
T ss_pred Cc--------ccccceEeeEEEEEEcCCceEEEEEEEEccEEecCCEEEEcccCCCCcEEEEEEEEEEE----CcEeCEE
Confidence 54 4578999999999999999999999999999999999998854 246789998744 2468999
Q ss_pred ccCCEEE--EcCCC--CCccCcEEecC
Q psy5461 162 QCGNIAA--VTGLK--RERGKDKRTRV 184 (221)
Q Consensus 162 ~aGdIv~--i~gl~--~~~~Gdtl~~~ 184 (221)
.|||.++ +.|++ +++.||++++.
T Consensus 323 ~aGd~v~l~L~~i~~~~i~rG~Vl~~~ 349 (447)
T PLN03127 323 QAGDNVGLLLRGLKREDVQRGQVICKP 349 (447)
T ss_pred cCCCEEEEEeCCCCHHHCCCccEEecC
Confidence 9999996 46764 68999999985
No 49
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=99.38 E-value=6.1e-12 Score=115.30 Aligned_cols=146 Identities=12% Similarity=0.104 Sum_probs=110.0
Q ss_pred ceeeeeeeecccc-----cCCcchHHHHhhcc----ccccCceeEecCCCccccHH------------HHHHHHHhhCCC
Q psy5461 26 SLCARAFKVVHDK-----HRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQ------------KLMDAIVDILPS 84 (221)
Q Consensus 26 ~~~~~vfk~~~d~-----~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~------------~LLd~I~~~~Ps 84 (221)
.++..++|.+.+. ..-+-....+.... .+...+|++..||.+|.|+. .|+++|.+. +.
T Consensus 147 ~iiv~vNKmD~~~~~~~~~~~~~i~~~i~~~l~~~g~~~~~~~~ipiSa~~g~ni~~~~~~~~Wy~G~tL~~~l~~~-~~ 225 (446)
T PTZ00141 147 QMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVGYNPEKVPFIPISGWQGDNMIEKSDNMPWYKGPTLLEALDTL-EP 225 (446)
T ss_pred eEEEEEEccccccchhhHHHHHHHHHHHHHHHHhcCCCcccceEEEeecccCCCcccCCCCCcccchHHHHHHHhCC-CC
Confidence 4778999965222 11122222332221 12235899999999999986 499998664 44
Q ss_pred CCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccC
Q psy5461 85 PTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCG 164 (221)
Q Consensus 85 P~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aG 164 (221)
|.. ..++||.+.|..++..++.|+++.+||.+|+|+.||+|.+...+...+|++|... ..++++|.||
T Consensus 226 ~~~--------~~~~p~r~~I~~v~~v~g~Gtvv~G~V~~G~l~~Gd~v~i~P~~~~~~VksI~~~----~~~~~~a~aG 293 (446)
T PTZ00141 226 PKR--------PVDKPLRLPLQDVYKIGGIGTVPVGRVETGILKPGMVVTFAPSGVTTEVKSVEMH----HEQLAEAVPG 293 (446)
T ss_pred CCc--------CCCCCeEEEEEEEEecCCceEEEEEEEEcceEecCCEEEEccCCcEEEEEEEEec----CcccCEECCC
Confidence 543 3568999999999999999999999999999999999999988878899998743 3578999999
Q ss_pred CEEEE--cCCC--CCccCcEEecC
Q psy5461 165 NIAAV--TGLK--RERGKDKRTRV 184 (221)
Q Consensus 165 dIv~i--~gl~--~~~~Gdtl~~~ 184 (221)
|.+++ .+++ +++.||+|+..
T Consensus 294 ~~v~i~L~~i~~~~v~rG~vl~~~ 317 (446)
T PTZ00141 294 DNVGFNVKNVSVKDIKRGYVASDS 317 (446)
T ss_pred CEEEEEECCCCHHHcCCceEEecC
Confidence 99954 5654 58999999875
No 50
>PF03144 GTP_EFTU_D2: Elongation factor Tu domain 2; InterPro: IPR004161 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents domain 2 of EF2, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA []. This domain is structurally related to the C-terminal domain of EF2 (IPR004160 from INTERPRO), to which it displays weak sequence matches. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3MCA_A 3AGJ_E 1SKQ_B 1JNY_A 1S0U_A 1ZUN_B 3SFS_W 3UOQ_W 2H5E_B 2XEX_A ....
Probab=99.38 E-value=6.1e-13 Score=92.16 Aligned_cols=68 Identities=31% Similarity=0.428 Sum_probs=62.5
Q ss_pred ceEEEEEEEceEEcCCCEEEe--ccCCce---eeeceeEeeecCCeeeeCccccCCEEEEcCCCC-CccCcEEe
Q psy5461 115 GAVTFFRIYSGAFKKGQKFYN--IHLDQS---EQITRLLLAEADDYKEVNEIQCGNIAAVTGLKR-ERGKDKRT 182 (221)
Q Consensus 115 G~i~~~RV~sG~L~~gd~v~~--~~~~~~---~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~-~~~Gdtl~ 182 (221)
|+++++||+||+|++||++++ .+++++ .+|.+|+.+++...+.+..+.||+++.+.++++ +++|||||
T Consensus 1 G~v~~grV~sG~l~~gd~v~~~~~~~~~~~~~~~I~~i~~~~~~~~~~~~~~~~G~~~~~~~~~~~i~~Gdtl~ 74 (74)
T PF03144_consen 1 GRVATGRVYSGTLKKGDKVRVLPNGTGKKGQVVKIKSIFMFNGDVQEAVAGANAGDIVAIIGLNDAIRRGDTLT 74 (74)
T ss_dssp EEEEEEEEEESEEETTEEEEEESTTTTEECEEEEEEEEEETTEEESEEETTEEEEEEEESSSGCSCSSTTEEEE
T ss_pred CEEEEEEEEEeEEcCCCEEEECccCCcceeeeeecccccccccCccEeCCceeeEEEEEEcCCCCCcCcCCEEC
Confidence 789999999999999999999 545555 899999999999999999999999999999999 89999996
No 51
>TIGR03680 eif2g_arch translation initiation factor 2 subunit gamma. eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA.
Probab=99.36 E-value=2.1e-11 Score=110.59 Aligned_cols=149 Identities=16% Similarity=0.160 Sum_probs=108.1
Q ss_pred Cceeeeeeeecccc-cCCcchHHHHhhcccc--ccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCc
Q psy5461 25 DSLCARAFKVVHDK-HRGAVTFFRIYSGAFK--KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSL 101 (221)
Q Consensus 25 ~~~~~~vfk~~~d~-~~g~l~~~~l~~~~~~--~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~ 101 (221)
.+++..++|++... ......+..+.+.... ....|++..||++|.|+++|++.|...+|.|.. +.+.||
T Consensus 135 ~~iIVvvNK~Dl~~~~~~~~~~~~i~~~l~~~~~~~~~ii~vSA~~g~gi~~L~e~L~~~l~~~~~--------~~~~~~ 206 (406)
T TIGR03680 135 KNIVIVQNKIDLVSKEKALENYEEIKEFVKGTVAENAPIIPVSALHNANIDALLEAIEKFIPTPER--------DLDKPP 206 (406)
T ss_pred CeEEEEEEccccCCHHHHHHHHHHHHhhhhhcccCCCeEEEEECCCCCChHHHHHHHHHhCCCCCC--------CCCCCc
Confidence 35788899965321 1111223344332211 125789999999999999999999999987754 457899
Q ss_pred EEEEEEEee--------cCCCceEEEEEEEceEEcCCCEEEeccCCc------------eeeeceeEeeecCCeeeeCcc
Q psy5461 102 CARAFKVVH--------DKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ------------SEQITRLLLAEADDYKEVNEI 161 (221)
Q Consensus 102 ~~~Vfk~~~--------d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~------------~~~v~~i~~~~g~~~~~v~~a 161 (221)
.+.|..++. ++++|.++.+||.+|+|++||+|.+...+. ..+|++|... ..++++|
T Consensus 207 ~~~I~~~f~v~~~g~~~~~~~G~Vv~G~v~~G~i~~gd~v~i~P~~~~~~~g~~~~~~~~~~V~sI~~~----~~~~~~a 282 (406)
T TIGR03680 207 LMYVARSFDVNKPGTPPEKLKGGVIGGSLIQGKLKVGDEIEIRPGIKVEKGGKTKWEPIYTEITSLRAG----GYKVEEA 282 (406)
T ss_pred EEEEEEEEeecCCCccccCCceeEEEEEEEeCEEeCCCEEEEccCccccccccccccccceEEeEEEEC----CEECCEE
Confidence 999998774 344788999999999999999999986531 2478887632 4688999
Q ss_pred ccCCEEEEc-----CCC--CCccCcEEecCC
Q psy5461 162 QCGNIAAVT-----GLK--RERGKDKRTRVI 185 (221)
Q Consensus 162 ~aGdIv~i~-----gl~--~~~~Gdtl~~~~ 185 (221)
.|||.+++. +++ ++..||.++...
T Consensus 283 ~~G~~v~i~l~~~~~i~~~dv~~G~vl~~~~ 313 (406)
T TIGR03680 283 RPGGLVGVGTKLDPALTKADALAGQVVGKPG 313 (406)
T ss_pred cCCCEEEEeeccCCCCCHHHcccccEEEcCC
Confidence 999999863 332 567899998763
No 52
>KOG0468|consensus
Probab=99.35 E-value=5.4e-12 Score=117.29 Aligned_cols=144 Identities=19% Similarity=0.210 Sum_probs=117.5
Q ss_pred HHHHHHHhhCCCCCCccccc-----------------ccCCCCCCcEEEEEEEeecCC-CceEEEEEEEceEEcCCCEEE
Q psy5461 73 KLMDAIVDILPSPTERPALA-----------------MFQHFGDSLCARAFKVVHDKH-RGAVTFFRIYSGAFKKGQKFY 134 (221)
Q Consensus 73 ~LLd~I~~~~PsP~~~~~~~-----------------~~~~~~~~~~~~Vfk~~~d~~-~G~i~~~RV~sG~L~~gd~v~ 134 (221)
.+.|++++++|+|.+.+.+. ..|+..+|++.++.|.+.... .-..+|+||+||++++|+.|.
T Consensus 428 gfvd~~v~hi~sP~e~a~~K~~hsy~G~~~~~i~~~m~~c~~~~pLm~h~tklyp~dD~~~f~~f~rv~Sg~~~~~q~V~ 507 (971)
T KOG0468|consen 428 GFVDMPVEHIPSPRENAARKAEHSYTGTKDSLIYEGMVECNASGPLMVHVTKLYPRDDTVQFHVFGRVYSGQVVTGQDVR 507 (971)
T ss_pred hhhHhhHhhcCChhhhhccccceeecCCCcchHHHHHHhhCCCCceeEEeecceecCCceeeeeeeeeeecceeecceee
Confidence 58899999999998865441 358889999999999997443 456999999999999999999
Q ss_pred eccCC---------ceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCC-ccCcEEecC-------CCCC-----CCce
Q psy5461 135 NIHLD---------QSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE-RGKDKRTRV-------IPKP-----TSVV 192 (221)
Q Consensus 135 ~~~~~---------~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~-~~Gdtl~~~-------~~~p-----~~~v 192 (221)
+.+++ ....|+++++..+++..+++++.+|.++.|.|+++. -...|+++. .++| .++|
T Consensus 508 vlgeny~leDEeD~~~~~v~el~v~~arY~i~V~~~~~G~~VLI~Gidq~i~KtaTi~~~~~ked~yiFrpl~~~t~~Vv 587 (971)
T KOG0468|consen 508 VLGENYSLEDEEDMVICEVGELWVVRARYRIPVSRAPAGLWVLIEGVDQSIVKTATIKSLEYKEDVYIFRPLKFNTEPVV 587 (971)
T ss_pred EeeccccCCCcccceeeeeeeeeeeeeeEEEEecccCCCcEEEEeccchHHhhhhheeccccccceeeccchhcCCcceE
Confidence 98764 235788999999999999999999999999999863 444577653 2333 3555
Q ss_pred ----------ehHHHHHHHHHHhhcCCceEEEcc
Q psy5461 193 ----------QCSARWTLNLEVGASSPIISKSKR 216 (221)
Q Consensus 193 ----------~~~~l~~~L~~L~~~Dp~l~~~~~ 216 (221)
.+++|++||++.+|+.|++..+..
T Consensus 588 KiaveP~nPsELPKmldgLrKinKsYPl~~tkVE 621 (971)
T KOG0468|consen 588 KVAVEPLNPSELPKMLDGLRKINKSYPLVITKVE 621 (971)
T ss_pred EEEeccCChhhhhHHHHHHHhhcccCCcEEEehh
Confidence 779999999999999999876543
No 53
>PLN03126 Elongation factor Tu; Provisional
Probab=99.32 E-value=3.3e-11 Score=111.26 Aligned_cols=149 Identities=19% Similarity=0.237 Sum_probs=110.9
Q ss_pred CCc-eeeeeeeecc-cc-cCCcchHHHHhhcc----ccccCceeEecCCCccc------------------cHHHHHHHH
Q psy5461 24 GDS-LCARAFKVVH-DK-HRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNI------------------GVQKLMDAI 78 (221)
Q Consensus 24 ~~~-~~~~vfk~~~-d~-~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~------------------Gi~~LLd~I 78 (221)
+-+ ++..++|.+. ++ ..-+.....+.... +....+|++.+||.+|. ++..||++|
T Consensus 196 gi~~iIvvvNK~Dl~~~~~~~~~i~~~i~~~l~~~g~~~~~~~~vp~Sa~~g~n~~~~~~~~~~g~~~wy~~i~~Ll~~l 275 (478)
T PLN03126 196 GVPNMVVFLNKQDQVDDEELLELVELEVRELLSSYEFPGDDIPIISGSALLALEALMENPNIKRGDNKWVDKIYELMDAV 275 (478)
T ss_pred CCCeEEEEEecccccCHHHHHHHHHHHHHHHHHhcCCCcCcceEEEEEccccccccccccccccCCCchhhhHHHHHHHH
Confidence 445 7889999652 21 11111112222221 23347899999998873 367899999
Q ss_pred HhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC--ceeeeceeEeeecCCee
Q psy5461 79 VDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD--QSEQITRLLLAEADDYK 156 (221)
Q Consensus 79 ~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~--~~~~v~~i~~~~g~~~~ 156 (221)
.++.|.|.. ..++||.+.|..++..++.|.++.+||.+|++++||+|++...+ ...+|++|... ..
T Consensus 276 ~~~~~~p~r--------~~~~p~r~~I~~vf~v~g~GtVv~G~V~sG~i~~Gd~v~i~p~~~~~~~~VksI~~~----~~ 343 (478)
T PLN03126 276 DSYIPIPQR--------QTDLPFLLAVEDVFSITGRGTVATGRVERGTVKVGETVDIVGLRETRSTTVTGVEMF----QK 343 (478)
T ss_pred HHhCCCCCC--------ccccceeeEEEEEEEeCCceEEEEEEEEcCeEecCCEEEEecCCCceEEEEEEEEEC----Ce
Confidence 998877754 45689999999999999999999999999999999999998654 35688888743 36
Q ss_pred eeCccccCCEEEE--cCCC--CCccCcEEecC
Q psy5461 157 EVNEIQCGNIAAV--TGLK--RERGKDKRTRV 184 (221)
Q Consensus 157 ~v~~a~aGdIv~i--~gl~--~~~~Gdtl~~~ 184 (221)
++++|.|||.+++ .|++ +++.|++++..
T Consensus 344 ~v~~A~aG~~v~l~L~~i~~~di~rG~VL~~~ 375 (478)
T PLN03126 344 ILDEALAGDNVGLLLRGIQKADIQRGMVLAKP 375 (478)
T ss_pred ECCEEeCCceeeeeccCCcHHHcCCccEEecC
Confidence 7899999999865 6765 58999999876
No 54
>COG0050 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]
Probab=99.32 E-value=4.5e-12 Score=108.44 Aligned_cols=148 Identities=20% Similarity=0.264 Sum_probs=118.6
Q ss_pred Cceeeeeeeec-c-cccCCcchHHHHhhcc----ccccCceeEecCCCccc--------cHHHHHHHHHhhCCCCCCccc
Q psy5461 25 DSLCARAFKVV-H-DKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNI--------GVQKLMDAIVDILPSPTERPA 90 (221)
Q Consensus 25 ~~~~~~vfk~~-~-d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~--------Gi~~LLd~I~~~~PsP~~~~~ 90 (221)
..++.|++|++ + |++..++....++..+ ..+.+.||+.|||++-. -|.+|||++.+|+|.|..
T Consensus 129 p~ivvflnK~Dmvdd~ellelVemEvreLLs~y~f~gd~~Pii~gSal~ale~~~~~~~~i~eLm~avd~yip~Per--- 205 (394)
T COG0050 129 PYIVVFLNKVDMVDDEELLELVEMEVRELLSEYGFPGDDTPIIRGSALKALEGDAKWEAKIEELMDAVDSYIPTPER--- 205 (394)
T ss_pred cEEEEEEecccccCcHHHHHHHHHHHHHHHHHcCCCCCCcceeechhhhhhcCCcchHHHHHHHHHHHHhcCCCCCC---
Confidence 37889999994 4 5777888888887654 45678999999998763 389999999999999986
Q ss_pred ccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC--ceeeeceeEeeecCCeeeeCccccCCEE-
Q psy5461 91 LAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD--QSEQITRLLLAEADDYKEVNEIQCGNIA- 167 (221)
Q Consensus 91 ~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~--~~~~v~~i~~~~g~~~~~v~~a~aGdIv- 167 (221)
+.+.||++-|-++..-.++|+++++||-+|+|+.|+.+...+-. ++..++.+..+ ++..++..|||-+
T Consensus 206 -----~~dkPflmpvEdvfsIsgrgtvvtGrVeRG~lkvg~eveivG~~~~~kttvtgvemf----rk~ld~~~AGdnvg 276 (394)
T COG0050 206 -----DIDKPFLMPVEDVFSISGRGTVVTGRVERGILKVGEEVEIVGIKETQKTTVTGVEMF----RKLLDEGQAGDNVG 276 (394)
T ss_pred -----cccccccccceeeEEEcCceeEEEEEEeeeeeccCCEEEEecccccceeEEEhHHHH----HHHHhccccCCCcc
Confidence 67899999999999999999999999999999999999887644 34456655533 2346788999988
Q ss_pred -EEcCCC--CCccCcEEecC
Q psy5461 168 -AVTGLK--RERGKDKRTRV 184 (221)
Q Consensus 168 -~i~gl~--~~~~Gdtl~~~ 184 (221)
.++|.+ ++..|..|+..
T Consensus 277 ~llRg~~r~~veRGqvLakp 296 (394)
T COG0050 277 VLLRGVKREDVERGQVLAKP 296 (394)
T ss_pred eEEEeccccceecceEeecC
Confidence 356654 67888888754
No 55
>COG5258 GTPBP1 GTPase [General function prediction only]
Probab=99.28 E-value=5.9e-11 Score=104.80 Aligned_cols=120 Identities=17% Similarity=0.165 Sum_probs=98.4
Q ss_pred ccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCE
Q psy5461 53 FKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQK 132 (221)
Q Consensus 53 ~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~ 132 (221)
.++...|||..|+.+|.|++ ||+-+..++|.-.. .+..+||.+||-|++...+.|.++.+-|.+|.|+.||+
T Consensus 309 ~~~~vvPi~~tSsVTg~Gld-lL~e~f~~Lp~rr~-------~~d~g~flmYId~iYsVtGVGtVvsGsV~~G~l~~gd~ 380 (527)
T COG5258 309 AGRGVVPIFYTSSVTGEGLD-LLDEFFLLLPKRRR-------WDDEGPFLMYIDKIYSVTGVGTVVSGSVKSGILHVGDT 380 (527)
T ss_pred cCCceEEEEEEecccCccHH-HHHHHHHhCCcccc-------cCCCCCeEEEEEeeEEEeeeEEEEeeeEEeeeeccCCE
Confidence 34458999999999999987 56666677876421 15678999999999999999999999999999999999
Q ss_pred EEeccCC----ceeeeceeEeeecCCeeeeCccccCCEE--EEcCCC--CCccCcEEecC
Q psy5461 133 FYNIHLD----QSEQITRLLLAEADDYKEVNEIQCGNIA--AVTGLK--RERGKDKRTRV 184 (221)
Q Consensus 133 v~~~~~~----~~~~v~~i~~~~g~~~~~v~~a~aGdIv--~i~gl~--~~~~Gdtl~~~ 184 (221)
++..... ++.+|++|. | .+.++++|.||+|+ ++.|++ .+..|+.+...
T Consensus 381 vllGP~~~G~fr~v~vkSIe-m---h~~rvdsa~aG~iig~Al~gv~~e~lerGMVl~~~ 436 (527)
T COG5258 381 VLLGPFKDGKFREVVVKSIE-M---HHYRVDSAKAGSIIGIALKGVEKEELERGMVLSAG 436 (527)
T ss_pred EEEccCCCCcEEEEEEEEEE-E---eeEEeccccCCcEEEEEecccCHHHHhcceEecCC
Confidence 9997643 356888886 3 35689999999999 567876 48999999764
No 56
>cd01342 Translation_Factor_II_like Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=99.21 E-value=1.6e-10 Score=79.58 Aligned_cols=78 Identities=32% Similarity=0.321 Sum_probs=66.9
Q ss_pred cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEecc--CCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCC--Cc
Q psy5461 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIH--LDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKR--ER 176 (221)
Q Consensus 101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~--~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~--~~ 176 (221)
+.++|+++..+++.|+++++||++|+|++||.+++.. ...+.++.+|+... .+++++.|||++.+.+.+. ++
T Consensus 1 ~~~~v~~~~~~~~~g~v~~~rv~~G~l~~g~~v~~~~~~~~~~~~i~~i~~~~----~~~~~~~aG~~~~~~~~~~~~~~ 76 (83)
T cd01342 1 LRALVFKVFKDKGRGTVATGRVESGTLKKGDKVRVGPGGGGVKGKVKSLKRFK----GEVDEAVAGDIVGIVLKDKDDIK 76 (83)
T ss_pred CeeEEEEEEEeCCceEEEEEEEeeCEEecCCEEEEecCCceeEEEEeEeEecC----ceeceecCCCEEEEEEccccccC
Confidence 4678999999999999999999999999999999987 55567888887654 5678899999998877654 89
Q ss_pred cCcEEe
Q psy5461 177 GKDKRT 182 (221)
Q Consensus 177 ~Gdtl~ 182 (221)
+||+++
T Consensus 77 ~g~~l~ 82 (83)
T cd01342 77 IGDTLT 82 (83)
T ss_pred CCCEec
Confidence 999885
No 57
>TIGR00475 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.
Probab=99.21 E-value=1.3e-10 Score=109.84 Aligned_cols=149 Identities=13% Similarity=0.093 Sum_probs=109.7
Q ss_pred CCc-eeeeeeeecc-cccCCcchHHHHhhcccc---ccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCC
Q psy5461 24 GDS-LCARAFKVVH-DKHRGAVTFFRIYSGAFK---KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFG 98 (221)
Q Consensus 24 ~~~-~~~~vfk~~~-d~~~g~l~~~~l~~~~~~---~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~ 98 (221)
+-+ ++..++|++. |+..-+.....+.+-... ....|++..||++|.||++|.+.|..+++..... ..+
T Consensus 102 gi~~iIVVlNK~Dlv~~~~~~~~~~ei~~~l~~~~~~~~~~ii~vSA~tG~GI~eL~~~L~~l~~~~~~~-------~~~ 174 (581)
T TIGR00475 102 GIPHTIVVITKADRVNEEEIKRTEMFMKQILNSYIFLKNAKIFKTSAKTGQGIGELKKELKNLLESLDIK-------RIQ 174 (581)
T ss_pred CCCeEEEEEECCCCCCHHHHHHHHHHHHHHHHHhCCCCCCcEEEEeCCCCCCchhHHHHHHHHHHhCCCc-------CcC
Confidence 345 8899999653 222111122223221111 1147899999999999999999988776553221 236
Q ss_pred CCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCC--C
Q psy5461 99 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLK--R 174 (221)
Q Consensus 99 ~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~--~ 174 (221)
+||.+.|-.++..++.|+++.++|.+|+++.||++.+...+...+|++|.. + ..++++|.|||.+++ .|++ +
T Consensus 175 ~p~r~~Id~~f~v~G~GtVv~G~v~~G~i~~Gd~l~i~P~~~~~~Vr~iq~-~---~~~v~~a~aG~rval~L~~i~~~~ 250 (581)
T TIGR00475 175 KPLRMAIDRAFKVKGAGTVVTGTAFSGEVKVGDNLRLLPINHEVRVKAIQA-Q---NQDVEIAYAGQRIALNLMDVEPES 250 (581)
T ss_pred CCcEEEEEEEEecCCcEEEEEEEEecceEecCCEEEECCCCceEEEeEEEE-C---CccCCEEECCCEEEEEeCCCCHHH
Confidence 899999999998899999999999999999999999998888889999974 3 347899999999964 5664 5
Q ss_pred CccCcEEec
Q psy5461 175 ERGKDKRTR 183 (221)
Q Consensus 175 ~~~Gdtl~~ 183 (221)
++.|..++.
T Consensus 251 i~rG~~~~~ 259 (581)
T TIGR00475 251 LKRGLLILT 259 (581)
T ss_pred cCCceEEcC
Confidence 789966554
No 58
>PRK05124 cysN sulfate adenylyltransferase subunit 1; Provisional
Probab=99.15 E-value=9.5e-10 Score=101.63 Aligned_cols=146 Identities=12% Similarity=0.034 Sum_probs=100.9
Q ss_pred CceeeeeeeecccccCCcchHHHHhhcc---cc----ccCceeEecCCCccccHHH------------HHHHHHhhCCCC
Q psy5461 25 DSLCARAFKVVHDKHRGAVTFFRIYSGA---FK----KNHVPVLCGSSYKNIGVQK------------LMDAIVDILPSP 85 (221)
Q Consensus 25 ~~~~~~vfk~~~d~~~g~l~~~~l~~~~---~~----~~~~Pv~~gSa~~~~Gi~~------------LLd~I~~~~PsP 85 (221)
.+++..++|++..... +-.+..+.... .+ ....|++..||++|.|+.. |+++| +.+|.|
T Consensus 161 ~~iIvvvNKiD~~~~~-~~~~~~i~~~l~~~~~~~~~~~~~~iipvSA~~g~ni~~~~~~~~wy~G~tLl~~L-~~i~~~ 238 (474)
T PRK05124 161 KHLVVAVNKMDLVDYS-EEVFERIREDYLTFAEQLPGNLDIRFVPLSALEGDNVVSQSESMPWYSGPTLLEVL-ETVDIQ 238 (474)
T ss_pred CceEEEEEeeccccch-hHHHHHHHHHHHHHHHhcCCCCCceEEEEEeecCCCcccccccccccchhhHHHHH-hhcCCC
Confidence 4688899996532111 11122222211 11 2357899999999999864 67755 456665
Q ss_pred CCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCC
Q psy5461 86 TERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGN 165 (221)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGd 165 (221)
.. ..+.||.+.|..++...+..+-..+||.+|+|+.||+|++...++..+|++|.... .++++|.|||
T Consensus 239 ~~--------~~~~p~r~~I~~v~~~~~~~~g~~G~V~sG~l~~Gd~v~i~P~~~~~~VksI~~~~----~~v~~A~aG~ 306 (474)
T PRK05124 239 RV--------VDAQPFRFPVQYVNRPNLDFRGYAGTLASGVVKVGDRVKVLPSGKESNVARIVTFD----GDLEEAFAGE 306 (474)
T ss_pred CC--------CCCCCceeeEEEEEecCCcccceEEEEEeEEEecCCEEEEecCCceEEEEEEEEcC----ccccCcCCCC
Confidence 43 35689998887765432211224689999999999999999888888999998442 3688999999
Q ss_pred EEEEc--CCCCCccCcEEecC
Q psy5461 166 IAAVT--GLKRERGKDKRTRV 184 (221)
Q Consensus 166 Iv~i~--gl~~~~~Gdtl~~~ 184 (221)
.+++. +..+++.||+|+..
T Consensus 307 ~V~l~L~~~~~i~rG~VL~~~ 327 (474)
T PRK05124 307 AITLVLEDEIDISRGDLLVAA 327 (474)
T ss_pred EEEEEeCCccccCCccEEECC
Confidence 99764 34468999999976
No 59
>COG5256 TEF1 Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]
Probab=99.14 E-value=1.8e-09 Score=96.31 Aligned_cols=145 Identities=21% Similarity=0.245 Sum_probs=109.6
Q ss_pred CceeeeeeeecccccC-CcchHHHHhh-------cc-ccccCceeEecCCCccccHH------------HHHHHHHhhCC
Q psy5461 25 DSLCARAFKVVHDKHR-GAVTFFRIYS-------GA-FKKNHVPVLCGSSYKNIGVQ------------KLMDAIVDILP 83 (221)
Q Consensus 25 ~~~~~~vfk~~~d~~~-g~l~~~~l~~-------~~-~~~~~~Pv~~gSa~~~~Gi~------------~LLd~I~~~~P 83 (221)
..++..+||. |... -+--|+.+.+ .. ++...+|.+..||.+|.++. .||++|. .+.
T Consensus 146 ~~lIVavNKM--D~v~wde~rf~ei~~~v~~l~k~~G~~~~~v~FIPiSg~~G~Nl~~~s~~~pWY~GpTLleaLd-~~~ 222 (428)
T COG5256 146 KQLIVAVNKM--DLVSWDEERFEEIVSEVSKLLKMVGYNPKDVPFIPISGFKGDNLTKKSENMPWYKGPTLLEALD-QLE 222 (428)
T ss_pred ceEEEEEEcc--cccccCHHHHHHHHHHHHHHHHHcCCCccCCeEEecccccCCcccccCcCCcCccCChHHHHHh-ccC
Confidence 5889999994 3211 0111222221 11 23336789999999997654 6888887 555
Q ss_pred CCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCcccc
Q psy5461 84 SPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQC 163 (221)
Q Consensus 84 sP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~a 163 (221)
.|.. ..+.||++-|-+++.-...|++.++||.+|.|++||.|+....+....|+++.. + .++++.+.|
T Consensus 223 ~p~~--------~~d~Plr~pI~~v~~i~~~gtv~vGrVEsG~i~~g~~v~~~p~~~~~evksie~-~---~~~~~~a~~ 290 (428)
T COG5256 223 PPER--------PLDKPLRLPIQDVYSISGIGTVPVGRVESGVIKPGQKVTFMPAGVVGEVKSIEM-H---HEEISQAEP 290 (428)
T ss_pred CCCC--------CCCCCeEeEeeeEEEecCCceEEEEEEeeeeeccCCEEEEecCcceEEEeeeee-c---ccccccCCC
Confidence 5544 357999999999998788899999999999999999999998887788888873 2 678999999
Q ss_pred CCEEE--EcCCC--CCccCcEEecC
Q psy5461 164 GNIAA--VTGLK--RERGKDKRTRV 184 (221)
Q Consensus 164 GdIv~--i~gl~--~~~~Gdtl~~~ 184 (221)
||.+. ++|++ ++++||.+++.
T Consensus 291 GD~i~~~vrgv~~~dI~~Gdv~~~~ 315 (428)
T COG5256 291 GDNVGFNVRGVEKNDIRRGDVIGHS 315 (428)
T ss_pred CCeEEEEecCCchhccCCccEeccC
Confidence 99994 67765 69999999876
No 60
>COG3276 SelB Selenocysteine-specific translation elongation factor [Translation, ribosomal structure and biogenesis]
Probab=99.12 E-value=5.1e-10 Score=100.40 Aligned_cols=145 Identities=17% Similarity=0.186 Sum_probs=112.2
Q ss_pred eeeeeeec-ccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEE
Q psy5461 28 CARAFKVV-HDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAF 106 (221)
Q Consensus 28 ~~~vfk~~-~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vf 106 (221)
+..+.|.+ .|+..-+.....+...+. -...|+|..|+++|.||++|=+.|.+..- +.++ +.+.||..+|-
T Consensus 107 iivltk~D~~d~~r~e~~i~~Il~~l~-l~~~~i~~~s~~~g~GI~~Lk~~l~~L~~-~~e~-------d~~~~fri~ID 177 (447)
T COG3276 107 IIVLTKADRVDEARIEQKIKQILADLS-LANAKIFKTSAKTGRGIEELKNELIDLLE-EIER-------DEQKPFRIAID 177 (447)
T ss_pred EEEEeccccccHHHHHHHHHHHHhhcc-cccccccccccccCCCHHHHHHHHHHhhh-hhhh-------ccCCceEEEEe
Confidence 44455532 333333334455555554 45678899999999999999999998764 2222 56899999888
Q ss_pred EEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--CCccCcEEe
Q psy5461 107 KVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK--RERGKDKRT 182 (221)
Q Consensus 107 k~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~--~~~~Gdtl~ 182 (221)
.....++.|+++++.++||+++.||+++..+.+++.+|++|... -.++++|.||+.|+ +.|.+ ++..||.+.
T Consensus 178 raFtVKGvGTVVtGtv~sG~V~v~D~L~l~p~~k~v~VRsIq~~----d~d~~~a~AG~RVgLaL~~v~~eei~RG~~L~ 253 (447)
T COG3276 178 RAFTVKGVGTVVTGTVLSGEVKVGDKLYLSPINKEVRVRSIQAH----DVDVEEAKAGQRVGLALKGVEKEEIERGDWLL 253 (447)
T ss_pred eEEEeccccEEEEeEEeeeeEEECCEEEEecCCCeEEEEeeeec----CcchhhccccceeeeecCCCCHHHhhcccEec
Confidence 88888999999999999999999999999999999999998732 34689999999996 45653 689999988
Q ss_pred cCC
Q psy5461 183 RVI 185 (221)
Q Consensus 183 ~~~ 185 (221)
+..
T Consensus 254 ~~~ 256 (447)
T COG3276 254 KPE 256 (447)
T ss_pred cCC
Confidence 763
No 61
>TIGR02034 CysN sulfate adenylyltransferase, large subunit. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules. With members of the Rhizobiaceae family, nodQ often appears as a fusion of cysN (large subunit of ATP sulfurase) and cysC (APS kinase).
Probab=99.12 E-value=1.6e-09 Score=98.29 Aligned_cols=148 Identities=13% Similarity=0.029 Sum_probs=100.0
Q ss_pred CceeeeeeeecccccCCcchHHHHhhcc------ccccCceeEecCCCccccHHH------------HHHHHHhhCCCCC
Q psy5461 25 DSLCARAFKVVHDKHRGAVTFFRIYSGA------FKKNHVPVLCGSSYKNIGVQK------------LMDAIVDILPSPT 86 (221)
Q Consensus 25 ~~~~~~vfk~~~d~~~g~l~~~~l~~~~------~~~~~~Pv~~gSa~~~~Gi~~------------LLd~I~~~~PsP~ 86 (221)
.+++..++|++..... +-.+..+.... ..-...|++..||++|.|+.. |+++|.. +|.|.
T Consensus 134 ~~iivviNK~D~~~~~-~~~~~~i~~~~~~~~~~~~~~~~~iipiSA~~g~ni~~~~~~~~wy~g~tL~~~L~~-~~~~~ 211 (406)
T TIGR02034 134 RHVVLAVNKMDLVDYD-EEVFENIKKDYLAFAEQLGFRDVTFIPLSALKGDNVVSRSESMPWYSGPTLLEILET-VEVER 211 (406)
T ss_pred CcEEEEEEecccccch-HHHHHHHHHHHHHHHHHcCCCCccEEEeecccCCCCcccccCCCccchhHHHHHHHh-cCCCC
Confidence 3588899996532211 11112222111 111346899999999999874 7787765 45554
Q ss_pred CcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCE
Q psy5461 87 ERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNI 166 (221)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdI 166 (221)
. ..++||.+.|..++.....+.-..++|.+|+|++||+|++...+...+|++|... + .++++|.|||.
T Consensus 212 ~--------~~~~p~r~~i~~v~~~~~~~~g~~G~v~~G~l~~gd~v~i~P~~~~~~VksI~~~-~---~~~~~a~~G~~ 279 (406)
T TIGR02034 212 D--------AQDLPLRFPVQYVNRPNLDFRGYAGTIASGSVHVGDEVVVLPSGRSSRVARIVTF-D---GDLEQARAGQA 279 (406)
T ss_pred C--------cCCCCcccceEEEeecCCCcEEEEEEEecceeecCCEEEEeCCCcEEEEEEEEEC-C---cccCEeCCCCE
Confidence 3 3467888866655432222222569999999999999999888888899999743 2 36899999999
Q ss_pred EEEc--CCCCCccCcEEecCCC
Q psy5461 167 AAVT--GLKRERGKDKRTRVIP 186 (221)
Q Consensus 167 v~i~--gl~~~~~Gdtl~~~~~ 186 (221)
+++. +.++++.||+++....
T Consensus 280 v~l~l~~~~~i~rG~vl~~~~~ 301 (406)
T TIGR02034 280 VTLTLDDEIDISRGDLLAAADS 301 (406)
T ss_pred EEEEECCccccCCccEEEcCCC
Confidence 9764 3346899999998643
No 62
>KOG1145|consensus
Probab=99.07 E-value=8.4e-10 Score=101.18 Aligned_cols=148 Identities=16% Similarity=0.077 Sum_probs=116.2
Q ss_pred CCCCceeeeeeeecccccCCcchHHHHhhcc--------ccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccc
Q psy5461 22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGA--------FKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAM 93 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~--------~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~ 93 (221)
+.+.|++..++|++.+ ....+++++.. .-+++++++..||++|.|++.|.++|....--- .+
T Consensus 251 ~A~VpiVvAinKiDkp----~a~pekv~~eL~~~gi~~E~~GGdVQvipiSAl~g~nl~~L~eaill~Ae~m------dL 320 (683)
T KOG1145|consen 251 SANVPIVVAINKIDKP----GANPEKVKRELLSQGIVVEDLGGDVQVIPISALTGENLDLLEEAILLLAEVM------DL 320 (683)
T ss_pred hcCCCEEEEEeccCCC----CCCHHHHHHHHHHcCccHHHcCCceeEEEeecccCCChHHHHHHHHHHHHHh------hc
Confidence 4688999999997633 23333444332 335789999999999999999999998654221 23
Q ss_pred cCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCC
Q psy5461 94 FQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLK 173 (221)
Q Consensus 94 ~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~ 173 (221)
+.++.+|+.++|.....|+++|.++++-|-.|||++|+.+..... -.||+.++= ..-.++++|.||..+-|.|++
T Consensus 321 kA~p~g~~eg~VIES~vdkg~G~~aT~iVkrGTLkKG~vlV~G~~--w~KVr~l~D---~nGk~i~~A~Ps~pv~V~Gwk 395 (683)
T KOG1145|consen 321 KADPKGPAEGWVIESSVDKGRGPVATVIVKRGTLKKGSVLVAGKS--WCKVRALFD---HNGKPIDEATPSQPVEVLGWK 395 (683)
T ss_pred ccCCCCCceEEEEEeeecCCccceeEEEEeccccccccEEEEech--hhhhhhhhh---cCCCCccccCCCCceEeeccc
Confidence 447889999999999999999999999999999999999887522 246666553 444589999999999999999
Q ss_pred CC-ccCcEEecC
Q psy5461 174 RE-RGKDKRTRV 184 (221)
Q Consensus 174 ~~-~~Gdtl~~~ 184 (221)
++ ..||-+...
T Consensus 396 dlP~aGD~vleV 407 (683)
T KOG1145|consen 396 DLPIAGDEVLEV 407 (683)
T ss_pred CCCCCCceEEEE
Confidence 87 899988654
No 63
>PRK04004 translation initiation factor IF-2; Validated
Probab=99.07 E-value=1.5e-09 Score=102.71 Aligned_cols=121 Identities=16% Similarity=0.221 Sum_probs=94.5
Q ss_pred cCceeEecCCCccccHHHHHHHHHhh----CCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCC
Q psy5461 56 NHVPVLCGSSYKNIGVQKLMDAIVDI----LPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQ 131 (221)
Q Consensus 56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~----~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd 131 (221)
...|++..||++|.|+.+|++.+... ++.+.. .+.+.|+.+.|+++..+++.|++++++|++|+|++||
T Consensus 191 ~~v~ivpiSA~tGeGi~dLl~~i~~~~~~~l~~~l~-------~~~~~~~~~~V~ev~~~~g~G~v~~~~v~~GtL~~Gd 263 (586)
T PRK04004 191 KTVAIVPVSAKTGEGIPDLLMVLAGLAQRYLEERLK-------IDVEGPGKGTVLEVKEERGLGTTIDVILYDGTLRKGD 263 (586)
T ss_pred CCceEeeccCCCCCChHHHHHHHHHHHHHHHHHhhc-------cCCCCCeEEEEEEEEEeCCCceEEEEEEEcCEEECCC
Confidence 46889999999999999999988642 343332 2467899999999999999999999999999999999
Q ss_pred EEEeccCCc--eeeeceeEeee--------cCCeeeeCccccCCEEEE--cCCCCCccCcEEec
Q psy5461 132 KFYNIHLDQ--SEQITRLLLAE--------ADDYKEVNEIQCGNIAAV--TGLKRERGKDKRTR 183 (221)
Q Consensus 132 ~v~~~~~~~--~~~v~~i~~~~--------g~~~~~v~~a~aGdIv~i--~gl~~~~~Gdtl~~ 183 (221)
.|.....+. ..+|+.|.... +.....++++.|...+-+ .|++.+..||.+.-
T Consensus 264 ~vv~~~~~~~i~~kVr~l~~~~~~~e~~~~~~~~~~~~~~~~~~~v~i~~~gl~~~~~g~~~~v 327 (586)
T PRK04004 264 TIVVGGKDGPIVTKVRALLKPRPLDEMRDPEDKFKPVDEVVAAAGVKISAPDLEDALAGSPLRV 327 (586)
T ss_pred EEEECcCCCcceEEEEEEecCcchhhccccccccccccccCCCCceEEEeCCccccCCCCeEEE
Confidence 998877653 34788877542 124466777777776644 48888888988754
No 64
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=99.05 E-value=2.8e-09 Score=75.66 Aligned_cols=79 Identities=16% Similarity=0.216 Sum_probs=67.8
Q ss_pred CcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--CC
Q psy5461 100 SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK--RE 175 (221)
Q Consensus 100 ~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~--~~ 175 (221)
||.+.|..++..+ .|++..+||.+|++++||+++....+...+|++|... ..++++|.|||.+. +.+++ ++
T Consensus 1 p~r~~V~~v~~~~-~g~vv~G~v~~G~i~~Gd~v~i~P~~~~~~V~si~~~----~~~~~~a~aGd~v~~~l~~~~~~~v 75 (83)
T cd03698 1 PFRLPISDKYKDQ-GGTVVSGKVESGSIQKGDTLLVMPSKESVEVKSIYVD----DEEVDYAVAGENVRLKLKGIDEEDI 75 (83)
T ss_pred CeEEEEEeEEEcC-CCcEEEEEEeeeEEeCCCEEEEeCCCcEEEEEEEEEC----CeECCEECCCCEEEEEECCCCHHHC
Confidence 5788888888777 8999999999999999999999998888899998743 36789999999996 66765 68
Q ss_pred ccCcEEec
Q psy5461 176 RGKDKRTR 183 (221)
Q Consensus 176 ~~Gdtl~~ 183 (221)
+.||+|++
T Consensus 76 ~~G~vl~~ 83 (83)
T cd03698 76 SPGDVLCS 83 (83)
T ss_pred CCCCEEeC
Confidence 99999874
No 65
>COG0532 InfB Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=98.98 E-value=2.6e-09 Score=97.84 Aligned_cols=150 Identities=16% Similarity=0.129 Sum_probs=113.2
Q ss_pred CCCCceeeeeeeeccccc-----CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCC
Q psy5461 22 HFGDSLCARAFKVVHDKH-----RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQH 96 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~~-----~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~ 96 (221)
..+-|++..+||++-.+. ..++....+....+.+ ++.++.+||++|+||.+||++|....-- ++++..
T Consensus 105 ~a~vP~iVAiNKiDk~~~np~~v~~el~~~gl~~E~~gg-~v~~VpvSA~tg~Gi~eLL~~ill~aev------~elka~ 177 (509)
T COG0532 105 AAGVPIVVAINKIDKPEANPDKVKQELQEYGLVPEEWGG-DVIFVPVSAKTGEGIDELLELILLLAEV------LELKAN 177 (509)
T ss_pred HCCCCEEEEEecccCCCCCHHHHHHHHHHcCCCHhhcCC-ceEEEEeeccCCCCHHHHHHHHHHHHHH------HhhhcC
Confidence 367899999999753321 2233333333333444 5789999999999999999999865322 234456
Q ss_pred CCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCC-
Q psy5461 97 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE- 175 (221)
Q Consensus 97 ~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~- 175 (221)
++++..+.|..+..++++|.++..-++.|+|++||.+..... .+.+..+......++..+.++--+.+.|++++
T Consensus 178 ~~~~a~gtviE~~~dkG~G~vatviv~~GtL~~GD~iv~g~~-----~g~I~t~v~~~~~~i~~a~ps~~v~i~g~~evp 252 (509)
T COG0532 178 PEGPARGTVIEVKLDKGLGPVATVIVQDGTLKKGDIIVAGGE-----YGRVRTMVDDLGKPIKEAGPSKPVEILGLSEVP 252 (509)
T ss_pred CCCcceEEEEEEEeccCCCceEEEEEecCeEecCCEEEEccC-----CCceEEeehhcCCCccccCCCCCeEEecccccc
Confidence 789999999999999999999999999999999999999743 33444455566678888999988889998876
Q ss_pred ccCcEEec
Q psy5461 176 RGKDKRTR 183 (221)
Q Consensus 176 ~~Gdtl~~ 183 (221)
..||.+..
T Consensus 253 ~Ag~~~~v 260 (509)
T COG0532 253 AAGDVFIV 260 (509)
T ss_pred ccCceEEe
Confidence 67877754
No 66
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=98.98 E-value=6.7e-09 Score=75.01 Aligned_cols=83 Identities=14% Similarity=0.105 Sum_probs=70.9
Q ss_pred CCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--
Q psy5461 98 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK-- 173 (221)
Q Consensus 98 ~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~-- 173 (221)
++||++.|.+++..++.|+++.+||.+|+++.||++++...+...+|++|... ..++++|.|||.+. +.+++
T Consensus 2 ~~p~r~~V~~vf~~~g~g~vv~G~v~~G~i~~gd~v~i~P~~~~~~V~sI~~~----~~~~~~a~aG~~v~i~l~~i~~~ 77 (91)
T cd03693 2 DKPLRLPIQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPAGVTGEVKSVEMH----HEPLEEALPGDNVGFNVKNVSKK 77 (91)
T ss_pred CCCeEEEEEEEEEeCCceEEEEEEEecceeecCCEEEECCCCcEEEEEEEEEC----CcCcCEECCCCEEEEEECCCCHH
Confidence 46899999999988888999999999999999999999988888899999743 34688999999995 55654
Q ss_pred CCccCcEEecC
Q psy5461 174 RERGKDKRTRV 184 (221)
Q Consensus 174 ~~~~Gdtl~~~ 184 (221)
+++.||.|+..
T Consensus 78 ~v~~G~vl~~~ 88 (91)
T cd03693 78 DIKRGDVAGDS 88 (91)
T ss_pred HcCCcCEEccC
Confidence 57999999864
No 67
>PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
Probab=98.98 E-value=9.8e-09 Score=98.08 Aligned_cols=148 Identities=11% Similarity=0.027 Sum_probs=100.0
Q ss_pred CceeeeeeeecccccCCc-c--hHHHHhhcc--ccccCceeEecCCCccccHH------------HHHHHHHhhCCCCCC
Q psy5461 25 DSLCARAFKVVHDKHRGA-V--TFFRIYSGA--FKKNHVPVLCGSSYKNIGVQ------------KLMDAIVDILPSPTE 87 (221)
Q Consensus 25 ~~~~~~vfk~~~d~~~g~-l--~~~~l~~~~--~~~~~~Pv~~gSa~~~~Gi~------------~LLd~I~~~~PsP~~ 87 (221)
.+++..++|++.-....+ + ....+.+-. ..-...|+++.||++|.|+. .|+++|... |.|..
T Consensus 158 ~~iivvvNK~D~~~~~~~~~~~i~~~i~~~~~~~~~~~~~iipiSA~~g~ni~~~~~~~~wy~g~tL~~~l~~~-~~~~~ 236 (632)
T PRK05506 158 RHVVLAVNKMDLVDYDQEVFDEIVADYRAFAAKLGLHDVTFIPISALKGDNVVTRSARMPWYEGPSLLEHLETV-EIASD 236 (632)
T ss_pred CeEEEEEEecccccchhHHHHHHHHHHHHHHHHcCCCCccEEEEecccCCCccccccCCCcccHhHHHHHHhcC-CCCCC
Confidence 468889999753111111 1 111221111 11134679999999999987 588877654 44433
Q ss_pred cccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEE
Q psy5461 88 RPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA 167 (221)
Q Consensus 88 ~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv 167 (221)
..++||.+.|..++...+.++-..++|.+|+|++||+|.+...++..+|++|... ..+++++.|||.+
T Consensus 237 --------~~~~p~r~~i~~v~~~~~~~~g~~G~v~~G~l~~gd~v~i~P~~~~~~VksI~~~----~~~~~~a~aG~~v 304 (632)
T PRK05506 237 --------RNLKDFRFPVQYVNRPNLDFRGFAGTVASGVVRPGDEVVVLPSGKTSRVKRIVTP----DGDLDEAFAGQAV 304 (632)
T ss_pred --------cCCCCceeeEEEEEecCCCceEEEEEEecceeecCCEEEEcCCCceEEEEEEEEC----CceeCEEcCCCeE
Confidence 3468998877766543222222569999999999999999988888899999743 2358999999999
Q ss_pred EEc--CCCCCccCcEEecCC
Q psy5461 168 AVT--GLKRERGKDKRTRVI 185 (221)
Q Consensus 168 ~i~--gl~~~~~Gdtl~~~~ 185 (221)
++. +-.+++.|++|++..
T Consensus 305 ~i~l~~~~~i~rG~vL~~~~ 324 (632)
T PRK05506 305 TLTLADEIDISRGDMLARAD 324 (632)
T ss_pred EEEecCccccCCccEEecCC
Confidence 764 334688999999863
No 68
>PRK14845 translation initiation factor IF-2; Provisional
Probab=98.96 E-value=6.5e-09 Score=103.18 Aligned_cols=127 Identities=17% Similarity=0.214 Sum_probs=96.6
Q ss_pred ccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEE
Q psy5461 55 KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFY 134 (221)
Q Consensus 55 ~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~ 134 (221)
+..+|++..||++|.||+.|+++|....+.-.+. .+..+.++|+.+.|..+..+++.|.++.+.|++|+|++||.|.
T Consensus 645 ~~~v~iVpVSA~tGeGId~Ll~~l~~l~~~~l~~---~L~~~~~~~~~g~VlEv~~~kG~G~vvt~iv~~G~Lk~GD~iv 721 (1049)
T PRK14845 645 TRTVAIVPVSAKTGEGIPELLMMVAGLAQKYLEE---RLKLNVEGYAKGTILEVKEEKGLGTTIDAIIYDGTLRRGDTIV 721 (1049)
T ss_pred CCCceEEEEEcCCCCCHHHHHHHHHHhhHHhhhh---hhccCCCCceEEEEEEEEEecCceeEEEEEEEcCEEecCCEEE
Confidence 3578999999999999999999987654421110 0112456899999999999999999999999999999999999
Q ss_pred eccCCc--eeeeceeEee--------ecCCeeeeCccccCCEEEE--cCCCCCccCcEEecC
Q psy5461 135 NIHLDQ--SEQITRLLLA--------EADDYKEVNEIQCGNIAAV--TGLKRERGKDKRTRV 184 (221)
Q Consensus 135 ~~~~~~--~~~v~~i~~~--------~g~~~~~v~~a~aGdIv~i--~gl~~~~~Gdtl~~~ 184 (221)
....++ ..+|+.|... .+.+..+++++.|+.-+-| .|++.+..||.+...
T Consensus 722 ~g~~~~~i~~kVRaLl~p~pl~e~r~~~~~~~~~~~~~~a~~vki~a~gl~~~~aG~~~~v~ 783 (1049)
T PRK14845 722 VGGPDDVIVTKVRALLKPKPLDEIRDPRDKFDPVDEVTAAAGVKIAAPGLEEVLAGSPIRIV 783 (1049)
T ss_pred EccCCCcceEEEEEecCcccccccccccccccccccccCCCceEEecCCccccCCCCeEEEe
Confidence 987654 3566665421 1224567888888888866 488888999988543
No 69
>TIGR00491 aIF-2 translation initiation factor aIF-2/yIF-2. This model describes archaeal and eukaryotic orthologs of bacterial IF-2. Like IF-2, it helps convey the initiator tRNA to the ribosome, although the initiator is N-formyl-Met in bacteria and Met here. This protein is not closely related to the subunits of eIF-2 of eukaryotes, which is also involved in the initiation of translation. The aIF-2 of Methanococcus jannaschii contains a large intein interrupting a region of very strongly conserved sequence very near the amino end; this model does not correctly align the sequences from Methanococcus jannaschii and Pyrococcus horikoshii in this region.
Probab=98.90 E-value=2.8e-08 Score=93.97 Aligned_cols=125 Identities=17% Similarity=0.218 Sum_probs=90.8
Q ss_pred ccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEE
Q psy5461 55 KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFY 134 (221)
Q Consensus 55 ~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~ 134 (221)
+..+|++..||++|.|+++|++.|..+.-.-.. ..+..+.++|+.+.|..+..+++.|.++.++|++|+|++||.|.
T Consensus 188 ~~~v~iVpVSA~tGeGideLl~~l~~l~~~~l~---~~l~~~~~~~~~~~V~e~~~~~G~G~v~t~~v~~G~l~~GD~iv 264 (590)
T TIGR00491 188 TKTVAIIPISAITGEGIPELLTMLAGLAQQYLE---EQLKLEEEGPARGTILEVKEETGLGMTIDAVIYDGILRKGDTIA 264 (590)
T ss_pred CCCceEEEeecCCCCChhHHHHHHHHHHHHHhh---hhhccCCCCCeEEEEEEEEEcCCCceEEEEEEEcCEEeCCCEEE
Confidence 346899999999999999999998754211000 00112457899999999999999999999999999999999999
Q ss_pred eccCCc--eeeeceeEeeec--------CCeeeeCcccc--CCEEEEcCCCCCccCcEEe
Q psy5461 135 NIHLDQ--SEQITRLLLAEA--------DDYKEVNEIQC--GNIAAVTGLKRERGKDKRT 182 (221)
Q Consensus 135 ~~~~~~--~~~v~~i~~~~g--------~~~~~v~~a~a--GdIv~i~gl~~~~~Gdtl~ 182 (221)
....+. ..+|+.|.-..+ .+...+.++.| |--+.+.|++....|+.+.
T Consensus 265 ~~~~~~~i~~kVr~l~~~~~l~e~r~~~~~~~~~~~~~~~~~~~v~~~~l~~~~aG~~~~ 324 (590)
T TIGR00491 265 MAGSDDVIVTRVRALLKPRPLEEMRESRKKFQKVDEVVAAAGVKIAAPGLDDVMAGSPIR 324 (590)
T ss_pred EccCCCcccEEEEEecCCCccccccccccccCCcceecCCCceeEEecCCCCCCCCCEEE
Confidence 987653 346776654321 12345566444 4445667888888888874
No 70
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=98.84 E-value=4.4e-08 Score=69.31 Aligned_cols=78 Identities=18% Similarity=0.170 Sum_probs=63.3
Q ss_pred CcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCC--CC
Q psy5461 100 SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLK--RE 175 (221)
Q Consensus 100 ~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~--~~ 175 (221)
||.+.|..++... |++..+||.+|++++||+++....+...+|++|... ..++++|.|||.+++ .+++ ++
T Consensus 1 plr~~I~~v~~~~--g~vv~G~v~~G~i~~G~~v~i~P~~~~~~V~si~~~----~~~~~~a~aGd~v~l~l~~i~~~~v 74 (82)
T cd04089 1 PLRLPIIDKYKDM--GTVVLGKVESGTIKKGDKLLVMPNKTQVEVLSIYNE----DVEVRYARPGENVRLRLKGIEEEDI 74 (82)
T ss_pred CeEEEEEeEEEcC--CEEEEEEEeeeEEecCCEEEEeCCCcEEEEEEEEEC----CEECCEECCCCEEEEEecCCCHHHC
Confidence 5677777776543 899999999999999999999998888889998743 357899999999964 4554 57
Q ss_pred ccCcEEec
Q psy5461 176 RGKDKRTR 183 (221)
Q Consensus 176 ~~Gdtl~~ 183 (221)
+.||.+++
T Consensus 75 ~~G~vl~~ 82 (82)
T cd04089 75 SPGFVLCS 82 (82)
T ss_pred CCCCEEeC
Confidence 89998874
No 71
>KOG0467|consensus
Probab=98.75 E-value=1.7e-08 Score=95.51 Aligned_cols=122 Identities=17% Similarity=0.221 Sum_probs=96.3
Q ss_pred CCCCCCcEEEEEEEeec-----CCCceEEEEEEEceEEcCCCEEEeccCC-------ceeeeceeEeeecCCeeeeCccc
Q psy5461 95 QHFGDSLCARAFKVVHD-----KHRGAVTFFRIYSGAFKKGQKFYNIHLD-------QSEQITRLLLAEADDYKEVNEIQ 162 (221)
Q Consensus 95 ~~~~~~~~~~Vfk~~~d-----~~~G~i~~~RV~sG~L~~gd~v~~~~~~-------~~~~v~~i~~~~g~~~~~v~~a~ 162 (221)
|++.+|...+|.|.... +...-++++|||||+++.|+.+++.+.+ .+.+|.++|+++|.+..+.+++.
T Consensus 354 ~~~~~pviv~Vskm~~~~~k~lp~~~l~~~ari~sgTlr~g~~v~v~~pd~~~~e~i~~~~ie~lyl~mgqelv~~d~v~ 433 (887)
T KOG0467|consen 354 CSKESPVLVFVSKMLATPLKYLPQSRLLAFARIFSGTLRVGQVVYVLGPDPLSPEHITECTVESLYLFMGQELVPLDEVP 433 (887)
T ss_pred CCCCCcEEEEEEeeeccchhhCchhhheeeeeeccCceeeccEeeecCCCCCCcceeeeeeehhhHHhhcccceeeeccC
Confidence 56678999999998763 2323589999999999999999999863 24689999999999999999999
Q ss_pred cCCEEEEcCCCCCccCcEEecCCCC-----------CCCce--------ehHHHHHHHHHHhhcCCceEEEcc
Q psy5461 163 CGNIAAVTGLKRERGKDKRTRVIPK-----------PTSVV--------QCSARWTLNLEVGASSPIISKSKR 216 (221)
Q Consensus 163 aGdIv~i~gl~~~~~Gdtl~~~~~~-----------p~~~v--------~~~~l~~~L~~L~~~Dp~l~~~~~ 216 (221)
+|++++|.|-+......|+|+..+. |.-+| ++++|-++|+.|+.-||++++..+
T Consensus 434 ~gnv~~I~g~~~vlks~TL~s~~~~~p~~~~~f~~tp~vrvaiep~~p~em~~L~~glkll~~adp~v~i~v~ 506 (887)
T KOG0467|consen 434 SGNVVAIGGAGIVLKSATLCSKVPCGPNLVVNFQITPIVRVAIEPDDPDEMDKLVEGLKLLNQADPFVKIRVE 506 (887)
T ss_pred CCcEEEecccceEeccceecccCCCcceeeeeeeeeeEEEEEeecCChHHhHHHHHHHHhhcccchhhHHHHh
Confidence 9999999983334455588876221 22111 789999999999999999876543
No 72
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=98.73 E-value=1.7e-07 Score=66.19 Aligned_cols=79 Identities=11% Similarity=0.033 Sum_probs=62.7
Q ss_pred cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCccC
Q psy5461 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERGK 178 (221)
Q Consensus 101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~G 178 (221)
|++-|.+++.....|+.+.+||.+|++++||+++....+...+|.+|... ..+++.+.|||.+++ .+-+++++|
T Consensus 1 lr~~V~dv~k~~~~~~~v~Gkv~~G~v~~Gd~v~~~P~~~~~~V~si~~~----~~~~~~a~aGd~v~l~l~~~~~i~~G 76 (81)
T cd03695 1 FRFPVQYVIRPNADFRGYAGTIASGSIRVGDEVVVLPSGKTSRVKSIETF----DGELDEAGAGESVTLTLEDEIDVSRG 76 (81)
T ss_pred CEeeEEEEEeeCCCcEEEEEEEccceEECCCEEEEcCCCCeEEEEEEEEC----CcEeCEEcCCCEEEEEECCccccCCC
Confidence 34556666655556778999999999999999999998888899998743 357889999999954 455578999
Q ss_pred cEEec
Q psy5461 179 DKRTR 183 (221)
Q Consensus 179 dtl~~ 183 (221)
|.|+.
T Consensus 77 ~vl~~ 81 (81)
T cd03695 77 DVIVA 81 (81)
T ss_pred CEEeC
Confidence 99873
No 73
>cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
Probab=98.69 E-value=1.5e-07 Score=66.66 Aligned_cols=79 Identities=23% Similarity=0.280 Sum_probs=63.4
Q ss_pred cEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--CCc
Q psy5461 101 LCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK--RER 176 (221)
Q Consensus 101 ~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~--~~~ 176 (221)
|.+.|.+++..++.|.+..+||.+|++++|+++.+...+...+|++|... ..+++++.|||-+. +.+++ +++
T Consensus 1 lr~~i~~~~~~~~~g~vv~G~v~sG~i~~g~~v~~~p~~~~~~V~sI~~~----~~~~~~a~aGd~v~i~l~~~~~~~i~ 76 (83)
T cd03696 1 FRLPIDRVFTVKGQGTVVTGTVLSGSVKVGDKVEILPLGEETRVRSIQVH----GKDVEEAKAGDRVALNLTGVDAKDLE 76 (83)
T ss_pred CEEEEEEEEEcCCcEEEEEEEEeecEEeCCCEEEECCCCceEEEEEEEEC----CcCcCEEcCCCEEEEEEcCCCHHHcC
Confidence 35566677666788999999999999999999999988777888888632 35688999999995 45553 678
Q ss_pred cCcEEec
Q psy5461 177 GKDKRTR 183 (221)
Q Consensus 177 ~Gdtl~~ 183 (221)
.||.+++
T Consensus 77 ~G~vl~~ 83 (83)
T cd03696 77 RGDVLSS 83 (83)
T ss_pred CccEEcC
Confidence 9998864
No 74
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=98.68 E-value=3.1e-07 Score=65.75 Aligned_cols=78 Identities=10% Similarity=0.017 Sum_probs=61.0
Q ss_pred EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccC--C--ceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--
Q psy5461 102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHL--D--QSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK-- 173 (221)
Q Consensus 102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~--~--~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~-- 173 (221)
.+.|-.++..+..|++..+|+.+|++++||++++... + ...+|.+|... ..++++|.|||.+. +.+++
T Consensus 2 ~~~I~~vf~v~g~GtVv~G~v~~G~v~~g~~v~~~P~~~g~~~~~~V~sI~~~----~~~~~~a~aGd~v~l~l~~i~~~ 77 (87)
T cd03694 2 EFQIDEIYSVPGVGTVVGGTVSKGVIRLGDTLLLGPDQDGSFRPVTVKSIHRN----RSPVRVVRAGQSASLALKKIDRS 77 (87)
T ss_pred EEEEEeEEEcCCcceEEEEEEecCEEeCCCEEEECCCCCCCEeEEEEEEEEEC----CeECCEECCCCEEEEEEcCCCHH
Confidence 3455555556788999999999999999999999876 3 46788888632 45788999999995 45654
Q ss_pred CCccCcEEec
Q psy5461 174 RERGKDKRTR 183 (221)
Q Consensus 174 ~~~~Gdtl~~ 183 (221)
+++.|+.+++
T Consensus 78 ~i~~G~vl~~ 87 (87)
T cd03694 78 LLRKGMVLVS 87 (87)
T ss_pred HcCCccEEeC
Confidence 6788998874
No 75
>cd04168 TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria. Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site. This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative. Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G. EF-G and Tet(M) compete for binding on the ribosomes. Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind. Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity. These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB.
Probab=98.63 E-value=1.4e-08 Score=85.77 Aligned_cols=62 Identities=21% Similarity=0.333 Sum_probs=51.8
Q ss_pred CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
+.|+++...+|. .+....+-.+.++++++.++.++|||||||.++.|+++|||+|++++|+|
T Consensus 176 e~dd~l~e~yl~--~~~~~~~el~~~l~~~~~~~~~~Pv~~gsa~~~~Gv~~ll~~~~~~~p~~ 237 (237)
T cd04168 176 EGDDELLEKYLE--GGPIEELELDNELSARIAKRKVFPVYHGSALKGIGIEELLEGITKLFPTS 237 (237)
T ss_pred cCCHHHHHHHhC--CCCCCHHHHHHHHHHHHHhCCeEEEEEccccCCcCHHHHHHHHHHhcCCC
Confidence 467788888876 22333445578888889999999999999999999999999999999998
No 76
>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher
Probab=98.61 E-value=3.1e-07 Score=65.68 Aligned_cols=78 Identities=19% Similarity=0.201 Sum_probs=60.8
Q ss_pred EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccC--CceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--CC
Q psy5461 102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHL--DQSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK--RE 175 (221)
Q Consensus 102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~--~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~--~~ 175 (221)
++.|..++.-++.|++..+||.+|+++.||++.+... +.+.+|++|... ..++++|.|||.++ +.+++ ++
T Consensus 2 r~~V~~v~~~~g~G~vv~G~v~~G~v~~gd~v~~~p~~~~~~~~V~si~~~----~~~~~~a~~G~~v~l~l~~~~~~~v 77 (87)
T cd03697 2 LMPIEDVFSIPGRGTVVTGRIERGTIKVGDEVEIVGFGETLKTTVTGIEMF----RKTLDEAEAGDNVGVLLRGVKREDV 77 (87)
T ss_pred EeeEEEEEeCCCcEEEEEEEECCCCCccCCEEEEeCCCCCceEEEEEEEEC----CcCCCEECCCCEEEEEECCCCHHHc
Confidence 4556666666788999999999999999999998764 445688888633 34788999999995 45653 57
Q ss_pred ccCcEEec
Q psy5461 176 RGKDKRTR 183 (221)
Q Consensus 176 ~~Gdtl~~ 183 (221)
..|+.|++
T Consensus 78 ~rG~vl~~ 85 (87)
T cd03697 78 ERGMVLAK 85 (87)
T ss_pred CCccEEec
Confidence 89999875
No 77
>cd01886 EF-G Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group conta
Probab=98.53 E-value=3.8e-08 Score=84.77 Aligned_cols=62 Identities=42% Similarity=0.683 Sum_probs=51.0
Q ss_pred CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
+.|+.+...+|. .++...+.....+++++.++.++|||||||.++.||++|||+|+.++|+|
T Consensus 209 e~dd~L~e~yl~--~~~~~~~el~~~l~~~~~~~~~~PV~~gSa~~~~Gi~~lld~i~~~~p~p 270 (270)
T cd01886 209 EFDDELMEKYLE--GEEITEEEIKAAIRKGTIANKIVPVLCGSAFKNKGVQPLLDAVVDYLPSP 270 (270)
T ss_pred cCCHHHHHHHhC--CCCCCHHHHHHHHHHHHHcCcEEEEEeCcCCCCcCHHHHHHHHHHhcCCC
Confidence 467778777776 22333445567777888889999999999999999999999999999998
No 78
>cd04169 RF3 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and activate the release of the nascent polypeptide. The class II release factor RF3 then initiates the release of the class I RF from the ribosome. RF3 binds to the RF/ribosome complex in the inactive (GDP-bound) state. GDP/GTP exchange occurs, followed by the release of the class I RF. Subsequent hydrolysis of GTP to GDP triggers the release of RF3 from the ribosome. RF3 also enhances the efficiency of class I RFs at less preferred stop codons and at stop codons in weak contexts.
Probab=98.52 E-value=4.1e-08 Score=84.42 Aligned_cols=62 Identities=27% Similarity=0.367 Sum_probs=50.5
Q ss_pred CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
+.++.++..++.. |....+-....+++++.++.++|||||||.+|.||++|||+|++++|+|
T Consensus 206 e~~~~l~e~~~e~--~~~~~~~~~~~~~~~~~~~~~~Pv~~gsa~~~~Gv~~Lld~i~~~~P~p 267 (267)
T cd04169 206 ELGGDLAEQLREE--LELLEGAGPEFDQEAFLAGELTPVFFGSALNNFGVQELLDALVDLAPAP 267 (267)
T ss_pred hcCHHHHHHHhCC--CccchhhhHHHhHHHHHcCCEEEEEecccccCcCHHHHHHHHHHHCCCC
Confidence 4567777777773 3333333556778899999999999999999999999999999999998
No 79
>cd03702 IF2_mtIF2_II This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2.
Probab=98.49 E-value=1.4e-06 Score=63.38 Aligned_cols=78 Identities=22% Similarity=0.233 Sum_probs=64.5
Q ss_pred EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCC-ccCcE
Q psy5461 102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE-RGKDK 180 (221)
Q Consensus 102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~-~~Gdt 180 (221)
.+.|.....++..|.++.+-|.+|+|++||.+..... ..||+.|+ .....++++|.||+.+.|.|++++ ..||.
T Consensus 2 ~g~VlE~~~~~g~G~vatviV~~GtL~~Gd~iv~G~~--~gkVr~l~---d~~g~~v~~a~Ps~~V~I~G~~~~P~aGd~ 76 (95)
T cd03702 2 EGVVIESKLDKGRGPVATVLVQNGTLKVGDVLVAGTT--YGKVRAMF---DENGKRVKEAGPSTPVEILGLKGVPQAGDK 76 (95)
T ss_pred eEEEEEEEecCCCCccEEEEEEcCeEeCCCEEEEccc--ccEEEEEE---CCCCCCCCEECCCCcEEEcCCCCCCCCCCE
Confidence 5789999999999999999999999999999998632 23555554 455578999999999999999877 88988
Q ss_pred EecC
Q psy5461 181 RTRV 184 (221)
Q Consensus 181 l~~~ 184 (221)
+...
T Consensus 77 ~~~~ 80 (95)
T cd03702 77 FLVV 80 (95)
T ss_pred EEEe
Confidence 8643
No 80
>cd03692 mtIF2_IVc mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=98.44 E-value=3.9e-06 Score=59.64 Aligned_cols=74 Identities=15% Similarity=0.135 Sum_probs=58.1
Q ss_pred EEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCC---ceeeeceeEeeecCCeeeeCccccCCEEE--EcCCCCCccC
Q psy5461 104 RAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLD---QSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLKRERGK 178 (221)
Q Consensus 104 ~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~---~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~~~~~G 178 (221)
.|-+++.....|.++.+||-+|++++|+.+.+.+.+ .+.++.+|... ...++++.+|+-|. +.++++++.|
T Consensus 4 ~V~~vf~~~~~g~vag~kV~~G~l~~g~~v~vlr~~~~~~~g~i~sl~~~----~~~v~~a~~G~ecgi~l~~~~d~~~G 79 (84)
T cd03692 4 EVRAVFKISKVGNIAGCYVTDGKIKRNAKVRVLRNGEVIYEGKISSLKRF----KDDVKEVKKGYECGITLENFNDIKVG 79 (84)
T ss_pred EEEEEEECCCCcEEEEEEEEECEEeCCCEEEEEcCCCEEEEEEEEEEEEc----CcccCEECCCCEEEEEEeCcccCCCC
Confidence 344444334568999999999999999999999887 34577777643 45788999999995 4578899999
Q ss_pred cEE
Q psy5461 179 DKR 181 (221)
Q Consensus 179 dtl 181 (221)
|+|
T Consensus 80 dvi 82 (84)
T cd03692 80 DII 82 (84)
T ss_pred CEE
Confidence 987
No 81
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=98.42 E-value=3.1e-06 Score=73.85 Aligned_cols=149 Identities=16% Similarity=0.211 Sum_probs=103.8
Q ss_pred Cceeeeeeeec-ccccCCcchHHHHh---hccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCC
Q psy5461 25 DSLCARAFKVV-HDKHRGAVTFFRIY---SGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDS 100 (221)
Q Consensus 25 ~~~~~~vfk~~-~d~~~g~l~~~~l~---~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~ 100 (221)
+.++..=||++ ++++...-.|..+. +|+.. +..||+..||.++.+|+.|+++|.+++|.|.. +.+.|
T Consensus 141 k~iiIvQNKIDlV~~E~AlE~y~qIk~FvkGt~A-e~aPIIPiSA~~~~NIDal~e~i~~~IptP~r--------d~~~~ 211 (415)
T COG5257 141 KNIIIVQNKIDLVSRERALENYEQIKEFVKGTVA-ENAPIIPISAQHKANIDALIEAIEKYIPTPER--------DLDKP 211 (415)
T ss_pred ceEEEEecccceecHHHHHHHHHHHHHHhccccc-CCCceeeehhhhccCHHHHHHHHHHhCCCCcc--------CCCCC
Confidence 45566668874 55555555555554 34443 46799999999999999999999999999976 78889
Q ss_pred cEEEEEEEeec--------CCCceEEEEEEEceEEcCCCEEEeccC-----Cceee----eceeEeeecCCeeeeCcccc
Q psy5461 101 LCARAFKVVHD--------KHRGAVTFFRIYSGAFKKGQKFYNIHL-----DQSEQ----ITRLLLAEADDYKEVNEIQC 163 (221)
Q Consensus 101 ~~~~Vfk~~~d--------~~~G~i~~~RV~sG~L~~gd~v~~~~~-----~~~~~----v~~i~~~~g~~~~~v~~a~a 163 (221)
..++|...... +-.|=+.=+-+.+|.++.||++.+... +.+.. .++|..++. ....+++|.|
T Consensus 212 p~m~v~RSFDVNkPGt~~~~L~GGViGGsl~~G~l~vGDEIEIrPGi~v~k~~k~~~~pi~T~i~Sl~a-g~~~~~ea~P 290 (415)
T COG5257 212 PRMYVARSFDVNKPGTPPEELKGGVIGGSLVQGVLRVGDEIEIRPGIVVEKGGKTVWEPITTEIVSLQA-GGEDVEEARP 290 (415)
T ss_pred ceEEEEeecccCCCCCCHHHccCceecceeeeeeEecCCeEEecCCeEeecCCceEEEEeeEEEEEEEe-CCeeeeeccC
Confidence 99999887653 234556677889999999999988642 11111 223333333 3457899999
Q ss_pred CCEEEE-cCCC-CCccCcEEec
Q psy5461 164 GNIAAV-TGLK-RERGKDKRTR 183 (221)
Q Consensus 164 GdIv~i-~gl~-~~~~Gdtl~~ 183 (221)
|-.+++ ++++ .+..+|.+..
T Consensus 291 GGLvgvGT~lDP~ltKaD~L~G 312 (415)
T COG5257 291 GGLVGVGTKLDPTLTKADALVG 312 (415)
T ss_pred CceEEEecccCcchhhhhhhcc
Confidence 998876 4566 3466666543
No 82
>KOG0461|consensus
Probab=98.42 E-value=1.4e-06 Score=76.59 Aligned_cols=136 Identities=13% Similarity=0.109 Sum_probs=106.9
Q ss_pred CCCceeeeeeeecccccCC---cch--HHHHhhcccc---ccCceeEecCCCcc----ccHHHHHHHHHhhCCCCCCccc
Q psy5461 23 FGDSLCARAFKVVHDKHRG---AVT--FFRIYSGAFK---KNHVPVLCGSSYKN----IGVQKLMDAIVDILPSPTERPA 90 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g---~l~--~~~l~~~~~~---~~~~Pv~~gSa~~~----~Gi~~LLd~I~~~~PsP~~~~~ 90 (221)
+-..++.-++|++.=++.. .+. ..++++...+ ++..||+..||+.| .+|.+|.++|.+.+--|..
T Consensus 121 ~c~klvvvinkid~lpE~qr~ski~k~~kk~~KtLe~t~f~g~~PI~~vsa~~G~~~~~~i~eL~e~l~s~if~P~R--- 197 (522)
T KOG0461|consen 121 LCKKLVVVINKIDVLPENQRASKIEKSAKKVRKTLESTGFDGNSPIVEVSAADGYFKEEMIQELKEALESRIFEPKR--- 197 (522)
T ss_pred hccceEEEEeccccccchhhhhHHHHHHHHHHHHHHhcCcCCCCceeEEecCCCccchhHHHHHHHHHHHhhcCCCc---
Confidence 3468899999986544422 222 3334433222 34689999999999 8999999999999988876
Q ss_pred ccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc
Q psy5461 91 LAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT 170 (221)
Q Consensus 91 ~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~ 170 (221)
+..+||.+.|-.-..-++-|++.++.+.+|+++.|+.|....-+..-||+.+..++ .++.+|.+||..++.
T Consensus 198 -----d~~gpflm~vDHCF~IKGQGTV~TGTvl~G~~~ln~~iE~PAL~e~rkVKslqmf~----~~vtsa~~GdR~g~c 268 (522)
T KOG0461|consen 198 -----DEEGPFLMAVDHCFAIKGQGTVLTGTVLRGVLRLNTEIEFPALNEKRKVKSLQMFK----QRVTSAAAGDRAGFC 268 (522)
T ss_pred -----CCCCCeEEEeeeeEEeccCceEEeeeEEEeEEecCcEEeecccchhhhhhhHHHHh----hhhhhhhcccceeee
Confidence 78899999998888889999999999999999999999998777666788776443 468899999988653
No 83
>KOG0465|consensus
Probab=98.41 E-value=1.1e-07 Score=88.26 Aligned_cols=80 Identities=30% Similarity=0.501 Sum_probs=68.9
Q ss_pred ChhhhhcCCCCCCCCcccccc------------C-CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCc
Q psy5461 1 MDAIVDILPSPTERPALAMFQ------------H-FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYK 67 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~~~------------~-~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~ 67 (221)
||+|++|+|||+|..+++... . ++.||++..||+.++++ |+++|.|+|+|+++.+.+ ||+.-..+
T Consensus 300 LDAVvdYLPsP~Ev~n~a~~ke~~~~ekv~l~~~~d~~Pfv~LAFKle~g~f-GqLTyvRvYqG~L~kG~~-iyN~rtgK 377 (721)
T KOG0465|consen 300 LDAVVDYLPSPSEVENYALNKETNSKEKVTLSPSRDKDPFVALAFKLEEGRF-GQLTYVRVYQGTLSKGDT-IYNVRTGK 377 (721)
T ss_pred HHHHHHhCCChhhhcccccccCCCCccceEeccCCCCCceeeeEEEeeecCc-cceEEEEEeeeeecCCcE-EEecCCCc
Confidence 799999999999999987651 1 22399999999999999 999999999999999988 99998888
Q ss_pred cccHHHHHHHHHhhC
Q psy5461 68 NIGVQKLMDAIVDIL 82 (221)
Q Consensus 68 ~~Gi~~LLd~I~~~~ 82 (221)
..-+.+|+.+-.+..
T Consensus 378 Kvrv~RL~rmHa~~m 392 (721)
T KOG0465|consen 378 KVRVGRLVRMHANDM 392 (721)
T ss_pred eeEhHHHhHhccccc
Confidence 888889887755443
No 84
>cd04170 EF-G_bact Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group
Probab=98.36 E-value=1.8e-07 Score=80.20 Aligned_cols=62 Identities=34% Similarity=0.517 Sum_probs=51.6
Q ss_pred CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
+.|+.+...+|. ..+...+.....+++++.++..+|||+|||+++.|+++|||+|.+++|+|
T Consensus 207 ~~dd~l~e~yl~--~~~~~~~~l~~~l~~~~~~~~~~pv~~gSa~~~~G~~~ll~~~~~~~p~p 268 (268)
T cd04170 207 ETDDELMEKYLE--GGELTEEELHAGLRRALRAGLLVPVLCGSALTNIGVRELLDALVHLLPSP 268 (268)
T ss_pred hCCHHHHHHHhC--CCCCCHHHHHHHHHHHHHhCCEEEEEEeeCCCCcCHHHHHHHHHHhCCCC
Confidence 467788888876 22333455566788899999999999999999999999999999999998
No 85
>KOG0459|consensus
Probab=98.36 E-value=2e-06 Score=76.80 Aligned_cols=122 Identities=14% Similarity=0.117 Sum_probs=88.4
Q ss_pred CceeEecCCCccccHHHHHHHHHhhCCCCCCcccc----cccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCE
Q psy5461 57 HVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPAL----AMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQK 132 (221)
Q Consensus 57 ~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~----~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~ 132 (221)
+.-.+.+|+.+|.++.+..+.++-|---|.-...+ .++.+.++||++-|..=+. ..|++.++++-||++++|++
T Consensus 260 d~~f~p~sg~tG~~~k~~~~s~cpwy~gp~fl~~ld~l~~~~R~~~GP~~~pI~~Kyk--dmGTvv~GKvEsGsi~kg~~ 337 (501)
T KOG0459|consen 260 DKHFVPVSGLTGANVKDRTDSVCPWYKGPIFLEYLDELPHLERILNGPIRCPVANKYK--DMGTVVGGKVESGSIKKGQQ 337 (501)
T ss_pred CceeeecccccccchhhcccccCCcccCCccceehhccCcccccCCCCEEeehhhhcc--ccceEEEEEecccceecCCe
Confidence 33456799999999887776333222111110000 0123678999998886553 46899999999999999999
Q ss_pred EEeccCCceeeeceeEeeecCCeeeeCccccCCEE--EEcCCC--CCccCcEEecC
Q psy5461 133 FYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIA--AVTGLK--RERGKDKRTRV 184 (221)
Q Consensus 133 v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv--~i~gl~--~~~~Gdtl~~~ 184 (221)
+.+...+....|.+|+ .+-.+++++.|||.+ -+.|++ ++.+|-+||+.
T Consensus 338 lvvMPnk~~veV~~I~----~ddvE~~~~~pGenvk~rlkgieeedi~~GfiL~~~ 389 (501)
T KOG0459|consen 338 LVVMPNKTNVEVLGIY----SDDVETDRVAPGENVKLRLKGIEEEDISPGFILCSP 389 (501)
T ss_pred EEEccCCcceEEEEEe----cccceeeeccCCcceEEEecccchhhccCceEEecC
Confidence 9999887777888876 236789999999999 466875 68999888876
No 86
>cd03701 IF2_IF5B_II IF2_IF5B_II: This family represents the domain II of prokaryotic Initiation Factor 2 (IF2) and its archeal and eukaryotic homologue aeIF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma.
Probab=98.28 E-value=7.7e-06 Score=59.56 Aligned_cols=78 Identities=22% Similarity=0.196 Sum_probs=63.5
Q ss_pred EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCCCCC-ccCcE
Q psy5461 102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGLKRE-RGKDK 180 (221)
Q Consensus 102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl~~~-~~Gdt 180 (221)
.+.|.....++.+|.++.+-|.+|+|++||.+..... ..+|.. +.......+.++.||+.+.+.|+++. ..||.
T Consensus 2 ~g~ViE~~~~~g~G~vatviV~~GtL~~Gd~iv~G~~--~GkVr~---~~d~~g~~v~~a~Ps~~v~i~g~~~~p~aGd~ 76 (95)
T cd03701 2 EGTVIESKLDKGRGPVATVIVQNGTLKKGDVIVAGGT--YGKIRT---MVDENGKALLEAGPSTPVEILGLKDVPKAGDG 76 (95)
T ss_pred eEEEEEEEecCCCCeeEEEEEEcCeEecCCEEEECCc--cceEEE---EECCCCCCccccCCCCCEEEeeecCCccCCCE
Confidence 4789999999999999999999999999999998642 235554 44555668999999999999998764 88988
Q ss_pred EecC
Q psy5461 181 RTRV 184 (221)
Q Consensus 181 l~~~ 184 (221)
+...
T Consensus 77 ~~~~ 80 (95)
T cd03701 77 VLVV 80 (95)
T ss_pred EEEe
Confidence 7543
No 87
>KOG0458|consensus
Probab=98.26 E-value=8.2e-06 Score=75.78 Aligned_cols=115 Identities=16% Similarity=0.121 Sum_probs=92.1
Q ss_pred CceeEecCCCccccHH---------------HHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEE
Q psy5461 57 HVPVLCGSSYKNIGVQ---------------KLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFR 121 (221)
Q Consensus 57 ~~Pv~~gSa~~~~Gi~---------------~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~R 121 (221)
.+-.+..|+++|.++. .||+.|.. +-.|.. ..+.||++-|..++..+.-|..+++|
T Consensus 356 ~v~FIPiSGl~GeNL~k~~~~~~l~~WY~Gp~LL~~id~-~~~p~~--------~~~kPl~ltIsdi~~~~~~~~~i~gk 426 (603)
T KOG0458|consen 356 SVKFIPISGLSGENLIKIEQENELSQWYKGPTLLSQIDS-FKIPER--------PIDKPLRLTISDIYPLPSSGVSISGK 426 (603)
T ss_pred CcceEecccccCCcccccccchhhhhhhcCChHHHHHhh-ccCCCC--------cccCCeEEEhhheeecCCCeeEEEEE
Confidence 3346668999997643 67888887 555654 34679999999999999989999999
Q ss_pred EEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEE--EcCCC--CCccCcEEecC
Q psy5461 122 IYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAA--VTGLK--RERGKDKRTRV 184 (221)
Q Consensus 122 V~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~--i~gl~--~~~~Gdtl~~~ 184 (221)
|.+|.|.+||+|++........|.+|.. + ..+...+.|||-|. +.|++ .+..||+++..
T Consensus 427 iesG~iq~gqkl~i~~s~e~~~vk~l~~--~--~~~~~~a~AGD~Vsl~L~~i~~n~v~~g~i~~~~ 489 (603)
T KOG0458|consen 427 IESGYIQPGQKLYIMTSREDATVKGLTS--N--DEPKTWAVAGDNVSLKLPGILPNLVQVGDIADSG 489 (603)
T ss_pred EeccccccCCEEEEecCcceEEEEeeec--C--CCcceeEeeCCEEEEecCccChhhcccceeeecC
Confidence 9999999999999998877788888752 2 45677899999995 45654 67999999853
No 88
>COG2895 CysN GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]
Probab=97.97 E-value=6.5e-05 Score=66.42 Aligned_cols=144 Identities=13% Similarity=0.097 Sum_probs=92.5
Q ss_pred Cceeeeeeeec-ccccCCcchHHHHhhc------cccccCceeEecCCCccccHH------------HHHHHHHhhCCCC
Q psy5461 25 DSLCARAFKVV-HDKHRGAVTFFRIYSG------AFKKNHVPVLCGSSYKNIGVQ------------KLMDAIVDILPSP 85 (221)
Q Consensus 25 ~~~~~~vfk~~-~d~~~g~l~~~~l~~~------~~~~~~~Pv~~gSa~~~~Gi~------------~LLd~I~~~~PsP 85 (221)
.+++..|||.+ +|-. +-.|++|+.. .+.....-.+..||+.|.+|. .||+.+...-..
T Consensus 140 rhvvvAVNKmDLvdy~--e~~F~~I~~dy~~fa~~L~~~~~~~IPiSAl~GDNV~~~s~~mpWY~GptLLe~LE~v~i~- 216 (431)
T COG2895 140 RHVVVAVNKMDLVDYS--EEVFEAIVADYLAFAAQLGLKDVRFIPISALLGDNVVSKSENMPWYKGPTLLEILETVEIA- 216 (431)
T ss_pred cEEEEEEeeecccccC--HHHHHHHHHHHHHHHHHcCCCcceEEechhccCCcccccccCCCcccCccHHHHHhhcccc-
Confidence 58999999974 3321 3334444332 222233346779999996543 344444321111
Q ss_pred CCcccccccCCCCCCcEEEEEEEee--cCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCcccc
Q psy5461 86 TERPALAMFQHFGDSLCARAFKVVH--DKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQC 163 (221)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~Vfk~~~--d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~a 163 (221)
.. ...++|+.-|--+.. ..++|. -++|-||++++||+|.+..+|+..+|.+|..+.|. .++|.|
T Consensus 217 ~~--------~~~~~~RfPVQ~V~Rp~~dfRGy--aGtiasG~v~~Gd~vvvlPsG~~s~V~~Ivt~dg~----~~~A~a 282 (431)
T COG2895 217 DD--------RSAKAFRFPVQYVNRPNLDFRGY--AGTIASGSVKVGDEVVVLPSGKTSRVKRIVTFDGE----LAQASA 282 (431)
T ss_pred cc--------ccccceeeceEEecCCCCccccc--ceeeeccceecCCeEEEccCCCeeeEEEEeccCCc----hhhccC
Confidence 11 234556555544433 234443 35778999999999999999999999999988664 688999
Q ss_pred CCEEEEcCCC--CCccCcEEecCC
Q psy5461 164 GNIAAVTGLK--RERGKDKRTRVI 185 (221)
Q Consensus 164 GdIv~i~gl~--~~~~Gdtl~~~~ 185 (221)
|+-+.+.=-+ +++.||.|+...
T Consensus 283 G~aVtl~L~deidisRGd~i~~~~ 306 (431)
T COG2895 283 GEAVTLVLADEIDISRGDLIVAAD 306 (431)
T ss_pred CceEEEEEcceeecccCcEEEccC
Confidence 9999765323 569999998763
No 89
>KOG0464|consensus
Probab=97.93 E-value=1.4e-06 Score=78.31 Aligned_cols=73 Identities=44% Similarity=0.729 Sum_probs=64.4
Q ss_pred ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHH
Q psy5461 1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLM 75 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LL 75 (221)
||++.-|+|||.||+.... +=..+++++..||+.+|+.+|+++|.|+|+|.+++... ||+.+....+|+..|+
T Consensus 310 ldavtmylpspeernyefl-qwykddlcalafkvlhdkqrg~l~fmriysgsi~~~~a-i~nin~~~se~~~kl~ 382 (753)
T KOG0464|consen 310 LDAVTMYLPSPEERNYEFL-QWYKDDLCALAFKVLHDKQRGPLSFMRIYSGSIHNNLA-IFNINGMCSEGILKLF 382 (753)
T ss_pred hhhhhhccCChhhcchHHH-hhhhhhHHHHhhhhhcccccCceeEEEEecccccCcee-eeecccccccchHhhh
Confidence 6899999999999876443 45678999999999999999999999999999998665 9999999999988775
No 90
>cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma.
Probab=97.87 E-value=0.00021 Score=53.31 Aligned_cols=81 Identities=15% Similarity=0.250 Sum_probs=62.9
Q ss_pred EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCc--eeeeceeEeeecC-------CeeeeCccc--cCCEEEEc
Q psy5461 102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ--SEQITRLLLAEAD-------DYKEVNEIQ--CGNIAAVT 170 (221)
Q Consensus 102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~--~~~v~~i~~~~g~-------~~~~v~~a~--aGdIv~i~ 170 (221)
.+.|..+..++++|.++.+-+++|+|++||.|...+... ..||+.|....+. ++.+++++. +|--+...
T Consensus 2 ~gtVlEvk~~~G~G~t~dvIl~~GtL~~GD~Iv~g~~~Gpi~tkVRaLl~~~~~~E~r~~~~~~~vk~v~aa~gvkI~~~ 81 (110)
T cd03703 2 QGTVLEVKEEEGLGTTIDVILYDGTLREGDTIVVCGLNGPIVTKVRALLKPQPLKELRVKSRFIHVKEVKAAAGVKILAP 81 (110)
T ss_pred cEEEEEEEEcCCCceEEEEEEECCeEecCCEEEEccCCCCceEEEeEecCCCCchhhccccccceeeEEecCCCcEEEeC
Confidence 467888999999999999999999999999999976542 2367766655442 335777776 67777778
Q ss_pred CCCCCccCcEEe
Q psy5461 171 GLKRERGKDKRT 182 (221)
Q Consensus 171 gl~~~~~Gdtl~ 182 (221)
|++++..|+.|.
T Consensus 82 gL~~v~aG~~~~ 93 (110)
T cd03703 82 DLEKAIAGSPLL 93 (110)
T ss_pred CCccccCCCEEE
Confidence 899888898764
No 91
>KOG0463|consensus
Probab=97.77 E-value=9.5e-05 Score=65.98 Aligned_cols=117 Identities=15% Similarity=0.127 Sum_probs=92.9
Q ss_pred cCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEe
Q psy5461 56 NHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYN 135 (221)
Q Consensus 56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~ 135 (221)
...|||-.|..+|.++. ||.+..+.++.-..- ..+.|.--+|-+++..++.|+++-+..++|+++-+|.+..
T Consensus 331 r~CPIFQvSNVtG~NL~-LLkmFLNlls~R~~~-------~E~~PAeFQIDD~Y~VpGVGTvvSGT~L~GtIrLND~LlL 402 (641)
T KOG0463|consen 331 RVCPIFQVSNVTGTNLP-LLKMFLNLLSLRRQL-------NENDPAEFQIDDIYWVPGVGTVVSGTLLSGTIRLNDILLL 402 (641)
T ss_pred cccceEEeccccCCChH-HHHHHHhhcCccccc-------ccCCCcceeecceEecCCcceEeecceeeeeEEeccEEEe
Confidence 36799999999999975 889888888764331 3456777889999999999999999999999999999988
Q ss_pred ccCC--c--eeeeceeEeeecCCeeeeCccccCCEE--EEcCCC--CCccCcEEecC
Q psy5461 136 IHLD--Q--SEQITRLLLAEADDYKEVNEIQCGNIA--AVTGLK--RERGKDKRTRV 184 (221)
Q Consensus 136 ~~~~--~--~~~v~~i~~~~g~~~~~v~~a~aGdIv--~i~gl~--~~~~Gdtl~~~ 184 (221)
.... . ...|++|. +++.++..+.+|+-. ++.+++ .++.|.++.+.
T Consensus 403 GPd~~G~F~pI~iKSIH----RKRMpV~~VrcGQtASFALKKIkr~~vRKGMVmVsp 455 (641)
T KOG0463|consen 403 GPDSNGDFMPIPIKSIH----RKRMPVGIVRCGQTASFALKKIKRKDVRKGMVMVSP 455 (641)
T ss_pred cCCCCCCeeeeehhhhh----hccccceEEeccchhhhHhhhcchhhhhcceEEecC
Confidence 6542 1 34566654 577889999999987 455665 67899888765
No 92
>TIGR00503 prfC peptide chain release factor 3. This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. More recently, RF-3 was shown to be active primarily at UGA stop codons in E. coli. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis PCC6803, and in Staphylococcus aureus.
Probab=97.76 E-value=1.2e-05 Score=75.41 Aligned_cols=75 Identities=23% Similarity=0.414 Sum_probs=56.8
Q ss_pred ChhhhhcCCCCCCCCcccc-ccCCCCceeeeeeeecc--c-ccCCcchHHHHhhccccccCceeEecCCCccccHHHHHH
Q psy5461 1 MDAIVDILPSPTERPALAM-FQHFGDSLCARAFKVVH--D-KHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMD 76 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~-~~~~~~~~~~~vfk~~~--d-~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd 76 (221)
||++++|+|+|.++..... ....+++++++|||+.+ | +|.|++++.|+++|+++.+.. +++....+..-+..+..
T Consensus 267 Ld~i~~~~PsP~~~~~~~~~~~~~~~~~~~~VFK~~~~mdp~~~griaf~RV~sG~l~~g~~-v~~~~~~k~~ri~~~~~ 345 (527)
T TIGR00503 267 LDGLLQWAPKPEARQSDTRTVEPTEEKFSGFVFKIQANMDPKHRDRVAFMRVVSGKYEKGMK-LKHVRTGKDVVISDALT 345 (527)
T ss_pred HHHHHHHCCCCccccCCceecCCCCCCeeEEEEEEEeccCcccCceEEEEEEeeeEEcCCCE-EEecCCCCcEEecchhh
Confidence 6899999999988753211 12356789999999987 8 599999999999999998765 77766655554554443
No 93
>cd03688 eIF2_gamma_II eIF2_gamma_II: this subfamily represents the domain II of the gamma subunit of eukaryotic translation initiation factor 2 (eIF2-gamma) found in Eukaryota and Archaea. eIF2 is a G protein that delivers the methionyl initiator tRNA to the small ribosomal subunit and releases it upon GTP hydrolysis after the recognition of the initiation codon. eIF2 is composed three subunits, alpha, beta and gamma. Subunit gamma shows strongest conservation, and it confers both tRNA binding and GTP/GDP binding.
Probab=97.63 E-value=0.00064 Score=50.67 Aligned_cols=81 Identities=17% Similarity=0.156 Sum_probs=55.5
Q ss_pred CCCCcEEEEEEEeecC--------CCceEEEEEEEceEEcCCCEEEeccC------C------ceeeeceeEeeecCCee
Q psy5461 97 FGDSLCARAFKVVHDK--------HRGAVTFFRIYSGAFKKGQKFYNIHL------D------QSEQITRLLLAEADDYK 156 (221)
Q Consensus 97 ~~~~~~~~Vfk~~~d~--------~~G~i~~~RV~sG~L~~gd~v~~~~~------~------~~~~v~~i~~~~g~~~~ 156 (221)
.+.|+.|+|..+..-. .+|.++-+++.+|.|+.||+|.+..- + ...+|.+|+. ...
T Consensus 2 ~~~pp~M~V~RsFdinkPG~~~~~l~GgVigGsi~~G~lkvgdeIEIrpg~~~~~~~~~~~~pi~T~I~sl~~----~~~ 77 (113)
T cd03688 2 FTSPPRMIVIRSFDVNKPGTEVDDLKGGVAGGSLLQGVLKVGDEIEIRPGIVVKDEGKIKCRPIFTKIVSLKA----ENN 77 (113)
T ss_pred CCCCceEEEEEEEecCCCCCccccceeeEEEEEEEEEEEeCCCEEEEeeceeeecCCCeeEEEEEEEEEEEEe----cCc
Confidence 3567777777766543 77889999999999999999976521 1 1235556552 345
Q ss_pred eeCccccCCEEEE-cCCC-CCccCcEE
Q psy5461 157 EVNEIQCGNIAAV-TGLK-RERGKDKR 181 (221)
Q Consensus 157 ~v~~a~aGdIv~i-~gl~-~~~~Gdtl 181 (221)
.+++|.||+.+++ ++++ .+..+|.+
T Consensus 78 ~l~~a~pGgliGvgT~Ldpsltk~D~l 104 (113)
T cd03688 78 DLQEAVPGGLIGVGTKLDPTLTKADRL 104 (113)
T ss_pred cccEEeCCCeEEEccccCcccccccee
Confidence 7899999999987 3454 33444544
No 94
>PRK00741 prfC peptide chain release factor 3; Provisional
Probab=97.54 E-value=3.5e-05 Score=72.29 Aligned_cols=65 Identities=28% Similarity=0.428 Sum_probs=50.1
Q ss_pred ChhhhhcCCCCCCCCcccc-ccCCCCceeeeeeeec---ccccCCcchHHHHhhccccccCceeEecCCC
Q psy5461 1 MDAIVDILPSPTERPALAM-FQHFGDSLCARAFKVV---HDKHRGAVTFFRIYSGAFKKNHVPVLCGSSY 66 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~-~~~~~~~~~~~vfk~~---~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~ 66 (221)
||++++|+|+|.++..... ....+++++++|||+. .|+|.|++++.|+++|.++.+.. +++....
T Consensus 266 Ld~i~~~~P~P~~~~~~~~~~~~~~~~~~~~VFK~~~~m~~~~~grlafvRV~sG~l~~g~~-v~~~~~~ 334 (526)
T PRK00741 266 LDAFVEWAPAPQPRQTDEREVEPTEEKFSGFVFKIQANMDPKHRDRIAFVRVCSGKFEKGMK-VRHVRTG 334 (526)
T ss_pred HHHHHHHCCCCCcccccceeecCCCCceEEEEEEEEecCCCCcCceEEEEEEeccEECCCCE-EEeccCC
Confidence 6899999999988654211 1224567999999997 46799999999999999998665 6655443
No 95
>COG0480 FusA Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]
Probab=97.48 E-value=4.9e-05 Score=73.29 Aligned_cols=67 Identities=37% Similarity=0.563 Sum_probs=55.0
Q ss_pred ChhhhhcCCCCCCCCccccc------------cCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCcc
Q psy5461 1 MDAIVDILPSPTERPALAMF------------QHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKN 68 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~~------------~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~ 68 (221)
||++++|+|+|.|.+.+... .+.++|+++++||+..|++.|.+++.|+++|+++.+.. |+.+...+.
T Consensus 270 Ldav~~~lPsP~e~~~~~g~~~~~~~~~~~~~~~~e~p~~a~vfKi~~d~~~g~l~~~RvysGtl~~G~~-v~n~~~~~~ 348 (697)
T COG0480 270 LDAVVDYLPSPLDVPPIKGDLDDEIEKAVLRKASDEGPLSALVFKIMTDPFVGKLTFVRVYSGTLKSGSE-VLNSTKGKK 348 (697)
T ss_pred HHHHHHHCCChhhcccccccCCccccchhcccCCCCCceEEEEEEeEecCCCCeEEEEEEeccEEcCCCE-EEeCCCCcc
Confidence 68999999999998854332 13478999999999999999999999999999998774 666655533
No 96
>PRK00007 elongation factor G; Reviewed
Probab=97.37 E-value=6.1e-05 Score=72.95 Aligned_cols=61 Identities=41% Similarity=0.674 Sum_probs=49.8
Q ss_pred ChhhhhcCCCCCCCCcccc------------ccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEe
Q psy5461 1 MDAIVDILPSPTERPALAM------------FQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLC 62 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~------------~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~ 62 (221)
||+|++++|+|.+++.... .-+++.+++++|||+..|++.|.+++.|+++|+++.+.. ++.
T Consensus 272 Ld~I~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~l~a~VfK~~~d~~~G~ia~~RV~sGtl~~g~~-v~~ 344 (693)
T PRK00007 272 LDAVVDYLPSPLDVPAIKGILPDGEEEEVERKASDDEPFSALAFKIMTDPFVGKLTFFRVYSGVLESGSY-VLN 344 (693)
T ss_pred HHHHHHHCCChhhcccccccCCCccccceeecCCCCCCeEEEEEEeeecCCCCcEEEEEEeeeEEcCCCE-EEe
Confidence 6899999999988654311 124678999999999999999999999999999988664 543
No 97
>PRK12739 elongation factor G; Reviewed
Probab=97.37 E-value=6.6e-05 Score=72.68 Aligned_cols=63 Identities=40% Similarity=0.654 Sum_probs=50.7
Q ss_pred ChhhhhcCCCCCCCCcccc-----------ccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecC
Q psy5461 1 MDAIVDILPSPTERPALAM-----------FQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGS 64 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~-----------~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gS 64 (221)
||+|++++|+|.+++.... ..+++.+++++|||+..|++.|.+++.|+++|+++.+.. ++...
T Consensus 270 Ld~I~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~pl~a~VfK~~~d~~~G~i~~~RV~sGtL~~g~~-v~~~~ 343 (691)
T PRK12739 270 LDAVVDYLPSPLDVPAIKGINPDTEEEIERPASDDEPFAALAFKIMTDPFVGRLTFFRVYSGVLESGSY-VLNTT 343 (691)
T ss_pred HHHHHHHCCChhhccccccccCCCCcceeeccCCCCCeEEEEEEeeeCCCCCeEEEEEEeeeEEcCCCE-EEeCC
Confidence 6899999999988654321 124678999999999999999999999999999987663 54433
No 98
>PF00009 GTP_EFTU: Elongation factor Tu GTP binding domain; InterPro: IPR000795 Elongation factors belong to a family of proteins that promote the GTP-dependent binding of aminoacyl tRNA to the A site of ribosomes during protein biosynthesis, and catalyse the translocation of the synthesised protein chain from the A to the P site. The proteins are all relatively similar in the vicinity of their C-termini, and are also highly similar to a range of proteins that includes the nodulation Q protein from Rhizobium meliloti (Sinorhizobium meliloti), bacterial tetracycline resistance proteins [] and the omnipotent suppressor protein 2 from yeast. In both prokaryotes and eukaryotes, there are three distinct types of elongation factors, EF-1alpha (EF-Tu), which binds GTP and an aminoacyl-tRNAand delivers the latter to the A site of ribosomes; EF-1beta (EF-Ts), which interacts with EF-1a/EF-Tu to displace GDP and thus allows the regeneration of GTP-EF-1a; and EF-2 (EF-G), which binds GTP and peptidyl-tRNA and translocates the latter from the A site to the P site. In EF-1-alpha, a specific region has been shown [] to be involved in a conformational change mediated by the hydrolysis of GTP to GDP. This region is conserved in both EF-1alpha/EF-Tu as well as EF-2/EF-G and thus seems typical for GTP-dependent proteins which bind non-initiator tRNAs to the ribosome. The GTP-binding protein synthesis factor family also includes the eukaryotic peptide chain release factor GTP-binding subunits [] and prokaryotic peptide chain release factor 3 (RF-3) []; the prokaryotic GTP-binding protein lepA and its homologue in yeast (GUF1) and Caenorhabditis elegans (ZK1236.1); yeast HBS1 []; rat statin S1 []; and the prokaryotic selenocysteine-specific elongation factor selB [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 3IZW_C 1DG1_G 2BVN_B 3IZV_C 3MMP_C 1OB2_A 1EFU_A 3FIH_Z 3TR5_A 1TUI_C ....
Probab=97.27 E-value=0.00031 Score=56.78 Aligned_cols=62 Identities=23% Similarity=0.227 Sum_probs=40.2
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhc----c-ccc-cCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG----A-FKK-NHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~----~-~~~-~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
.+-|++..++|++.-...-+.....+++. . .++ ..+||+++||++|+|++.|+++|.+++|+
T Consensus 121 ~~~p~ivvlNK~D~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~vi~~Sa~~g~gi~~Ll~~l~~~~P~ 188 (188)
T PF00009_consen 121 LGIPIIVVLNKMDLIEKELEEIIEEIKEKLLKEYGENGEEIVPVIPISALTGDGIDELLEALVELLPS 188 (188)
T ss_dssp TT-SEEEEEETCTSSHHHHHHHHHHHHHHHHHHTTSTTTSTEEEEEEBTTTTBTHHHHHHHHHHHS--
T ss_pred cccceEEeeeeccchhhhHHHHHHHHHHHhccccccCccccceEEEEecCCCCCHHHHHHHHHHhCcC
Confidence 56789999999543211111222222211 1 222 37999999999999999999999999996
No 99
>TIGR00484 EF-G translation elongation factor EF-G. After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G.
Probab=97.23 E-value=0.00011 Score=71.07 Aligned_cols=61 Identities=43% Similarity=0.630 Sum_probs=49.6
Q ss_pred ChhhhhcCCCCCCCCcccc-----------ccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEe
Q psy5461 1 MDAIVDILPSPTERPALAM-----------FQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLC 62 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~-----------~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~ 62 (221)
||+|++++|+|.+++.... ..+++.+++++|||+..|++.|.+++.|+++|+++.+.. ++.
T Consensus 271 Ld~I~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~l~a~VfK~~~d~~~G~i~~~RV~sGtL~~g~~-v~~ 342 (689)
T TIGR00484 271 LDAVVDYLPSPTDVPAIKGIDPDTEKEIERKASDDEPFSALAFKVATDPFVGQLTFVRVYSGVLKSGSY-VKN 342 (689)
T ss_pred HHHHHHHCCCchhcccccccCCCCCceeeecCCCCCceEEEEEEeeecCCCCeEEEEEEEEeEEcCCCE-EEe
Confidence 6899999999987654221 124578999999999999999999999999999987665 543
No 100
>KOG1143|consensus
Probab=97.23 E-value=0.0018 Score=57.98 Aligned_cols=129 Identities=13% Similarity=0.127 Sum_probs=90.3
Q ss_pred ccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCE
Q psy5461 53 FKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQK 132 (221)
Q Consensus 53 ~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~ 132 (221)
..+.++|||+.|...|.|++ ||..+.+.+|+-..+..+.. -...|.--+|-.++..++.|.++=+-+-+|.++.|+.
T Consensus 358 ~s~nivPif~vSsVsGegl~-ll~~fLn~Lsp~~~~~e~~~--L~q~~~eFqvdEiy~Vp~VG~VVGG~Ls~G~l~Eg~~ 434 (591)
T KOG1143|consen 358 CSGNIVPIFAVSSVSGEGLR-LLRTFLNCLSPAGTAEERIQ--LVQLPAEFQVDEIYNVPHVGQVVGGMLSEGQLHEGAD 434 (591)
T ss_pred ccCCceeEEEEeecCccchh-HHHHHHhhcCCcCChHHHHH--HhcCcceeeHhHeecCCcccccccceeeeceeccCce
Confidence 44578999999999999987 55556555554332211100 0123455578888899999999999999999999999
Q ss_pred EEeccCC----ceeeeceeEeeecCCeeeeCccccCCEEEEcC--CC--CCccCcEEecCCCCC
Q psy5461 133 FYNIHLD----QSEQITRLLLAEADDYKEVNEIQCGNIAAVTG--LK--RERGKDKRTRVIPKP 188 (221)
Q Consensus 133 v~~~~~~----~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~g--l~--~~~~Gdtl~~~~~~p 188 (221)
+.+...+ .+.+|+.|. +.+..+.-+.||+-..++= .+ .++.|.++.+....|
T Consensus 435 ~~vGP~~DG~F~~itV~sI~----Rnr~acrvvraGqaAslsl~d~D~~~LR~GMVl~~~~~nP 494 (591)
T KOG1143|consen 435 VLVGPMKDGTFEKITVGSIR----RNRQACRVVRAGQAASLSLNDPDGVSLRRGMVLAEIDHNP 494 (591)
T ss_pred eEeecCCCCceeEEEeeeee----ccccceeeecCccceeeeccCCCccchhcceEEeecCCCC
Confidence 9997653 245777775 3445677789999886652 12 468999987653333
No 101
>PF14578 GTP_EFTU_D4: Elongation factor Tu domain 4; PDB: 1G7R_A 1G7S_A 1G7T_A 1XE1_A.
Probab=97.13 E-value=0.0078 Score=42.40 Aligned_cols=72 Identities=21% Similarity=0.235 Sum_probs=47.3
Q ss_pred EEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCccCcE
Q psy5461 103 ARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERGKDK 180 (221)
Q Consensus 103 ~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~Gdt 180 (221)
..|.....-..++ +..++|..|+|++|..+ .|. +++.+..++. +.+++++|.+||-|++ .|.-+++-||+
T Consensus 7 i~Ilp~~vFr~~~-~IvG~V~~G~ik~G~~l----~G~--~iG~I~sIe~-~~k~v~~A~~G~eVai~Ieg~~~i~eGDi 78 (81)
T PF14578_consen 7 IRILPVCVFRQSD-AIVGEVLEGIIKPGYPL----DGR--KIGRIKSIED-NGKNVDEAKKGDEVAISIEGPTQIKEGDI 78 (81)
T ss_dssp EEEEEEEEECTCC-EEEEEEEEEEEETT-EE----CSS--CEEEEEEEEE-TTEEESEEETT-EEEEEEET--TB-TT-E
T ss_pred EEECCcCEEecCC-eEEEEEeeeEEeCCCcc----CCE--EEEEEEEeEE-CCcCccccCCCCEEEEEEeCCccCCCCCE
Confidence 3344444445666 77889999999999999 332 3666666654 4579999999999965 46558889998
Q ss_pred Ee
Q psy5461 181 RT 182 (221)
Q Consensus 181 l~ 182 (221)
|.
T Consensus 79 Ly 80 (81)
T PF14578_consen 79 LY 80 (81)
T ss_dssp EE
T ss_pred Ee
Confidence 74
No 102
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=97.02 E-value=0.00058 Score=47.39 Aligned_cols=26 Identities=4% Similarity=0.028 Sum_probs=23.2
Q ss_pred ehHHHHHHHHHHhhcCCceEEEcccc
Q psy5461 193 QCSARWTLNLEVGASSPIISKSKRRQ 218 (221)
Q Consensus 193 ~~~~l~~~L~~L~~~Dp~l~~~~~~~ 218 (221)
|.++|++||++|+++||++++.+|.+
T Consensus 17 d~~kl~~aL~~l~~eDP~l~~~~d~e 42 (75)
T PF14492_consen 17 DEPKLSEALQKLSEEDPSLRVERDEE 42 (75)
T ss_dssp HHHHHHHHHHHHHHH-TTSEEEEETT
T ss_pred HHHHHHHHHHHHHhcCCeEEEEEcch
Confidence 78999999999999999999999864
No 103
>PRK13351 elongation factor G; Reviewed
Probab=96.99 E-value=0.00025 Score=68.63 Aligned_cols=63 Identities=37% Similarity=0.547 Sum_probs=50.4
Q ss_pred ChhhhhcCCCCCCCCcccc----------ccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecC
Q psy5461 1 MDAIVDILPSPTERPALAM----------FQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGS 64 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~----------~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gS 64 (221)
||++++++|+|.+++.... .-+++.+++++|||+..|++.|.+++.|+++|+++.+.. ++...
T Consensus 270 Ld~I~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~pl~a~VfK~~~d~~~G~i~~~RV~sGtl~~g~~-v~~~~ 342 (687)
T PRK13351 270 LDAVVDYLPSPLEVPPPRGSKDNGKPVKVDPDPEKPLLALVFKVQYDPYAGKLTYLRVYSGTLRAGSQ-LYNGT 342 (687)
T ss_pred HHHHHHHCCChhhcccccccCCCCCceeecCCCCCCeEEEEEEeeecCCCceEEEEEEeEEEEcCCCE-EEeCC
Confidence 6899999999987654321 114578999999999999999999999999999987665 54443
No 104
>PRK07560 elongation factor EF-2; Reviewed
Probab=96.97 E-value=0.00026 Score=69.05 Aligned_cols=63 Identities=25% Similarity=0.388 Sum_probs=49.6
Q ss_pred ChhhhhcCCCCCCCCcccc-----------------ccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEec
Q psy5461 1 MDAIVDILPSPTERPALAM-----------------FQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCG 63 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~-----------------~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~g 63 (221)
||+|++|+|||.+++.... ..+++.|++++|||+..|++.|.+++.|+++|+++.+.. ++..
T Consensus 248 ld~I~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~p~~a~VfK~~~d~~~G~va~~RV~sGtL~~Gd~-v~~~ 326 (731)
T PRK07560 248 LDMVVKHLPNPIEAQKYRIPKIWKGDLNSEVGKAMLNCDPNGPLVMMVTDIIVDPHAGEVATGRVFSGTLRKGQE-VYLV 326 (731)
T ss_pred HHHHHHhCCChhhhhhhcccccccCCCCccccceeeccCCCCCEEEEEEeeEEcCCCCeEEEEEEEEeEEcCCCE-EEEc
Confidence 6899999999987543110 014567999999999999999999999999999998765 5443
Q ss_pred C
Q psy5461 64 S 64 (221)
Q Consensus 64 S 64 (221)
.
T Consensus 327 ~ 327 (731)
T PRK07560 327 G 327 (731)
T ss_pred C
Confidence 3
No 105
>PTZ00416 elongation factor 2; Provisional
Probab=96.90 E-value=0.00028 Score=69.72 Aligned_cols=58 Identities=28% Similarity=0.393 Sum_probs=46.8
Q ss_pred ChhhhhcCCCCCCCCcccc-----------------ccCCCCceeeeeeeecccccCCc-chHHHHhhccccccCc
Q psy5461 1 MDAIVDILPSPTERPALAM-----------------FQHFGDSLCARAFKVVHDKHRGA-VTFFRIYSGAFKKNHV 58 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~-----------------~~~~~~~~~~~vfk~~~d~~~g~-l~~~~l~~~~~~~~~~ 58 (221)
||+|++|+|||.+++.... .-++++|++++|||+..|++.|+ +++.|+++|+++.+..
T Consensus 329 ld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~plva~VfK~~~~~~~g~~~s~~RV~SGtL~~g~~ 404 (836)
T PTZ00416 329 LEMIVDHLPSPKEAQKYRVENLYEGPMDDEAANAIRNCDPNGPLMMYISKMVPTSDKGRFYAFGRVFSGTVATGQK 404 (836)
T ss_pred HHHHHHhCCChhHhCchhhhccccCCCCccccceeeccCCCCCeEEEEEeeeecCCCCcEEEEEEEEeeeecCCCE
Confidence 6899999999987543210 01457799999999999999999 7999999999987654
No 106
>TIGR00490 aEF-2 translation elongation factor aEF-2. This model represents archaeal elongation factor 2, a protein more similar to eukaryotic EF-2 than to bacterial EF-G, both in sequence similarity and in sharing with eukaryotes the property of having a diphthamide (modified His) residue at a conserved position. The diphthamide can be ADP-ribosylated by diphtheria toxin in the presence of NAD.
Probab=96.83 E-value=0.00031 Score=68.42 Aligned_cols=58 Identities=31% Similarity=0.441 Sum_probs=47.0
Q ss_pred ChhhhhcCCCCCCCCccc-----------------cccCCCCceeeeeeeecccccCCcchHHHHhhccccccCc
Q psy5461 1 MDAIVDILPSPTERPALA-----------------MFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHV 58 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~-----------------~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~ 58 (221)
||+|++|+|||.+++... ...+++.+++++|||+..|++.|.+++.|+++|+++.+..
T Consensus 247 ld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~pl~a~VfK~~~~~~~G~ia~~RV~sGtL~~G~~ 321 (720)
T TIGR00490 247 LDMVIRHLPSPIEAQKYRIPVIWKGDLNSEVGKAMLNCDPKGPLALMITKIVVDKHAGEVAVGRLYSGTIRPGME 321 (720)
T ss_pred HHHHHHhCCChhhhhhhcccccccCCCCccchhhcccCCCCCCeEEEEEEEEecCCCcEEEEEEEEeCEEcCCCE
Confidence 689999999998753211 0124578999999999999999999999999999887654
No 107
>PLN00116 translation elongation factor EF-2 subunit; Provisional
Probab=96.73 E-value=0.00062 Score=67.43 Aligned_cols=58 Identities=21% Similarity=0.318 Sum_probs=46.6
Q ss_pred ChhhhhcCCCCCCCCcccc-----------------ccCCCCceeeeeeeecccccCCc-chHHHHhhccccccCc
Q psy5461 1 MDAIVDILPSPTERPALAM-----------------FQHFGDSLCARAFKVVHDKHRGA-VTFFRIYSGAFKKNHV 58 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~-----------------~~~~~~~~~~~vfk~~~d~~~g~-l~~~~l~~~~~~~~~~ 58 (221)
||++++|+|||.+++.... .-++++|++++|||+..+++.|+ +++.|+++|+++.+..
T Consensus 333 ld~i~~~lPsP~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~pl~a~VfK~~~~~~~g~~l~~~RVysGtL~~g~~ 408 (843)
T PLN00116 333 LEMIIFHLPSPAKAQRYRVENLYEGPLDDKYATAIRNCDPNGPLMLYVSKMIPASDKGRFFAFGRVFSGTVATGMK 408 (843)
T ss_pred HHHHHHhCCChHHhhhHHhhhccCCCCCccccchhhcCCCCCCeEEEEEeeeecCCCCeEEEEEEEEeeeecCCCE
Confidence 6899999999987543211 11457899999999988888888 8999999999988665
No 108
>PRK12740 elongation factor G; Reviewed
Probab=96.56 E-value=0.00098 Score=64.33 Aligned_cols=64 Identities=34% Similarity=0.603 Sum_probs=51.1
Q ss_pred ChhhhhcCCCCCCCCccc---------cccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCC
Q psy5461 1 MDAIVDILPSPTERPALA---------MFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSS 65 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~---------~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa 65 (221)
||++++++|+|.+++.+. ...+++++++++|||+.+|++.|.+++.|+++|+++.+.. ++....
T Consensus 254 Ld~i~~~lPsp~~~~~~~~~~~~~~~~~~~~~~~~l~a~v~k~~~~~~~G~i~~~RV~sG~L~~g~~-v~~~~~ 326 (668)
T PRK12740 254 LDAVVDYLPSPLEVPPVDGEDGEEGAELAPDPDGPLVALVFKTMDDPFVGKLSLVRVYSGTLKKGDT-LYNSGT 326 (668)
T ss_pred HHHHHHHCCChhhcccccCCCCccccccccCCCCCeEEEEEEeeecCCCCcEEEEEEeeeEEcCCCE-EEeCCC
Confidence 688999999998755321 1124578999999999999999999999999999998765 655543
No 109
>cd03690 Tet_II Tet_II: This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.
Probab=95.89 E-value=0.0027 Score=44.99 Aligned_cols=33 Identities=24% Similarity=0.587 Sum_probs=30.8
Q ss_pred CceeeeeeeecccccCCcchHHHHhhccccccC
Q psy5461 25 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNH 57 (221)
Q Consensus 25 ~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~ 57 (221)
+||+++|||+..|++.|++++.|+++|+++...
T Consensus 2 ~p~~~~Vfkv~~d~~~G~la~~RV~sG~l~~g~ 34 (85)
T cd03690 2 SELSGTVFKIERDDKGERLAYLRLYSGTLRLRD 34 (85)
T ss_pred CCcEEEEEEeEECCCCCeEEEEEEccCEEcCCC
Confidence 689999999999999999999999999998765
No 110
>COG4108 PrfC Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]
Probab=95.80 E-value=0.0044 Score=56.45 Aligned_cols=70 Identities=31% Similarity=0.489 Sum_probs=51.7
Q ss_pred ChhhhhcCCCCCCCCcc-ccccCCCCceeeeeeeec---ccccCCcchHHHHhhccccccCceeEecCCCccccH
Q psy5461 1 MDAIVDILPSPTERPAL-AMFQHFGDSLCARAFKVV---HDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGV 71 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~-~~~~~~~~~~~~~vfk~~---~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi 71 (221)
||.+++|.|+|..+..- ......+++|+++|||++ ..+|+-++++.|+++|.++++.. +-.....+...+
T Consensus 268 L~~~~~~AP~P~~~~a~~~~v~p~e~kfsGFVFKIQANMDp~HRDRIAFmRv~SGkferGMk-v~h~rtGK~~~l 341 (528)
T COG4108 268 LDALVDWAPSPRARQADTREVEPTEDKFSGFVFKIQANMDPKHRDRIAFMRVCSGKFERGMK-VTHVRTGKDVKL 341 (528)
T ss_pred HHHHHhhCCCCCcccCCcCcccCCCCccceEEEEEEcCCCcccccceeEEEeccccccCCce-eeeeecCCceEe
Confidence 57899999999887653 233445778999999995 33799999999999999988644 444444444443
No 111
>TIGR00487 IF-2 translation initiation factor IF-2. This model discriminates eubacterial (and mitochondrial) translation initiation factor 2 (IF-2), encoded by the infB gene in bacteria, from similar proteins in the Archaea and Eukaryotes. In the bacteria and in organelles, the initiator tRNA is charged with N-formyl-Met instead of Met. This translation factor acts in delivering the initator tRNA to the ribosome. It is one of a number of GTP-binding translation factors recognized by the pfam model GTP_EFTU.
Probab=95.55 E-value=0.061 Score=51.37 Aligned_cols=80 Identities=14% Similarity=0.084 Sum_probs=59.7
Q ss_pred EEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCccCcE
Q psy5461 103 ARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERGKDK 180 (221)
Q Consensus 103 ~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~Gdt 180 (221)
|.|-++......|.++=++|..|++++|..+++.+.++....+.|..++ +....++++..|+-|+| .+..+++.||.
T Consensus 495 a~v~~vf~~~~~~~iaG~~V~~G~i~~~~~~~v~r~~~~i~~g~i~sl~-~~k~~v~ev~~g~ecgi~~~~~~~~~~gD~ 573 (587)
T TIGR00487 495 AEVRQVFNVPKIGNIAGCYVTEGVIKRGNPLRVIRDGVVIFEGEIDSLK-RFKDDVKEVSNGYECGIGIKNYNDIKEGDI 573 (587)
T ss_pred EEEEEEEecCCCCEEEEEEEecCEEecCCeEEEEeCCEEEEeccchHhh-ccCccccEECCCCEEEEEEeccccCCCCCE
Confidence 4455555555668999999999999999999999877543334444333 34467999999999965 56778999999
Q ss_pred Eec
Q psy5461 181 RTR 183 (221)
Q Consensus 181 l~~ 183 (221)
|-.
T Consensus 574 i~~ 576 (587)
T TIGR00487 574 IEA 576 (587)
T ss_pred EEE
Confidence 854
No 112
>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways. Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process
Probab=95.40 E-value=0.036 Score=43.30 Aligned_cols=57 Identities=12% Similarity=0.060 Sum_probs=40.3
Q ss_pred cCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHH
Q psy5461 21 QHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIV 79 (221)
Q Consensus 21 ~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~ 79 (221)
+-|..|++.-|.|++.++... ..++.++.....+.-.+|..|+.+|.||++|.+.|.
T Consensus 86 ~~f~~pvIGVITK~Dl~~~~~--~i~~a~~~L~~aG~~~if~vS~~~~eGi~eL~~~L~ 142 (143)
T PF10662_consen 86 SMFNKPVIGVITKIDLPSDDA--NIERAKKWLKNAGVKEIFEVSAVTGEGIEELKDYLE 142 (143)
T ss_pred cccCCCEEEEEECccCccchh--hHHHHHHHHHHcCCCCeEEEECCCCcCHHHHHHHHh
Confidence 347889999999987663212 233333444444455679999999999999999885
No 113
>KOG0466|consensus
Probab=95.34 E-value=0.038 Score=48.50 Aligned_cols=109 Identities=19% Similarity=0.260 Sum_probs=78.4
Q ss_pred HhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEee--------cCCCceEEE
Q psy5461 48 IYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVH--------DKHRGAVTF 119 (221)
Q Consensus 48 l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~--------d~~~G~i~~ 119 (221)
+.+++.. +.-||+..||--+.+|+.+.++|+..+|-|.. +...|..+.|..... +.-.|-++=
T Consensus 207 Fi~~t~a-e~aPiiPisAQlkyNId~v~eyivkkIPvPvR--------df~s~prlIVIRSFDVNkPG~ev~~lkGgvag 277 (466)
T KOG0466|consen 207 FIQGTVA-EGAPIIPISAQLKYNIDVVCEYIVKKIPVPVR--------DFTSPPRLIVIRSFDVNKPGSEVDDLKGGVAG 277 (466)
T ss_pred HHhcccc-CCCceeeehhhhccChHHHHHHHHhcCCCCcc--------ccCCCCcEEEEEeeccCCCCchhhcccCcccc
Confidence 3344433 35699999999999999999999999999976 677777777776654 334567888
Q ss_pred EEEEceEEcCCCEEEeccC----C--cee-------eeceeEeeecCCeeeeCccccCCEEEE
Q psy5461 120 FRIYSGAFKKGQKFYNIHL----D--QSE-------QITRLLLAEADDYKEVNEIQCGNIAAV 169 (221)
Q Consensus 120 ~RV~sG~L~~gd~v~~~~~----~--~~~-------~v~~i~~~~g~~~~~v~~a~aGdIv~i 169 (221)
+-+..|.|+.||.+.+... + ... ++..+| .++.+...|.||-.+.+
T Consensus 278 gsil~Gvlkvg~~IEiRPGiv~kd~~g~~~C~Pi~SrI~sL~----AE~n~L~~AvPGGLIGV 336 (466)
T KOG0466|consen 278 GSILKGVLKVGQEIEIRPGIVTKDENGNIKCRPIFSRIVSLF----AEQNDLQFAVPGGLIGV 336 (466)
T ss_pred chhhhhhhhcCcEEEecCceeeecCCCcEEEeeHHHHHHHHH----hhhccceeecCCceeee
Confidence 8999999999999988532 1 011 333333 34556777888876655
No 114
>cd01889 SelB_euk SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and euk
Probab=95.32 E-value=0.015 Score=46.83 Aligned_cols=63 Identities=11% Similarity=0.073 Sum_probs=42.1
Q ss_pred CCceeeeeeeeccc-ccCCcchHHHHhhcc---c---cccCceeEecCCCccccHHHHHHHHHhhCCCCC
Q psy5461 24 GDSLCARAFKVVHD-KHRGAVTFFRIYSGA---F---KKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPT 86 (221)
Q Consensus 24 ~~~~~~~vfk~~~d-~~~g~l~~~~l~~~~---~---~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~ 86 (221)
..+++..++|++.- ...-+.....+.+.. . .....|++..||++|.|+++|++.|.+.+|.|.
T Consensus 120 ~~~~iiv~NK~Dl~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~vi~iSa~~g~gi~~L~~~l~~~~~~~~ 189 (192)
T cd01889 120 CKKLIVVLNKIDLIPEEERERKIEKMKKKLQKTLEKTRFKNSPIIPVSAKPGGGEAELGKDLNNLIVLPL 189 (192)
T ss_pred CCCEEEEEECcccCCHHHHHHHHHHHHHHHHHHHHhcCcCCCCEEEEeccCCCCHHHHHHHHHhcccccc
Confidence 45888999996532 111111222222211 1 123578999999999999999999999999985
No 115
>CHL00189 infB translation initiation factor 2; Provisional
Probab=95.30 E-value=0.12 Score=50.71 Aligned_cols=77 Identities=17% Similarity=0.079 Sum_probs=56.8
Q ss_pred EEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCccCcEEe
Q psy5461 105 AFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERGKDKRT 182 (221)
Q Consensus 105 Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~Gdtl~ 182 (221)
|-++..-.. |.+|=|+|.+|+++++..+++.+.++..--+.|..++ +....++++..|.-|+| .+..+++.||+|-
T Consensus 654 v~~vF~~~k-~~iaGc~V~~G~i~~~~~~rv~R~~~~i~~G~i~slk-~~k~~v~ev~~g~ecgi~i~~~~d~~~gD~ie 731 (742)
T CHL00189 654 VKTVFPLAK-RFVAGCRVTEGKITKNALIKVIRENKLIYEGKITSLK-RVKEDVEEAQEGNECGIFIEEFQLWQSGDKIH 731 (742)
T ss_pred eeEEEecCC-CEEEEEEEecCEEecCCeEEEEeCCeEEEEeEEhhHh-hcCccccEeCCCCEEEEEeeCCCCCCcCCEEE
Confidence 334433344 8999999999999999999999877543333443333 33467999999999965 4677899999984
Q ss_pred c
Q psy5461 183 R 183 (221)
Q Consensus 183 ~ 183 (221)
.
T Consensus 732 ~ 732 (742)
T CHL00189 732 A 732 (742)
T ss_pred E
Confidence 3
No 116
>PRK05306 infB translation initiation factor IF-2; Validated
Probab=95.19 E-value=0.12 Score=51.05 Aligned_cols=81 Identities=14% Similarity=0.077 Sum_probs=60.3
Q ss_pred EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCccCc
Q psy5461 102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERGKD 179 (221)
Q Consensus 102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~Gd 179 (221)
.|.|-++......|.++=|+|..|+++++..+++.+.++..--++|..++ +....+.++..|+-|+| .+..+++.||
T Consensus 696 ~a~v~~vF~~~k~~~iaGc~V~~G~i~~~~~~rv~R~~~~i~~g~i~slk-~~k~~v~ev~~g~ecgi~~~~~~d~~~gD 774 (787)
T PRK05306 696 QAEVREVFKVSKVGTIAGCMVTEGKIKRNAKVRVLRDGVVIYEGELESLK-RFKDDVKEVRAGYECGIGLENYNDIKEGD 774 (787)
T ss_pred eEEEEEEEecCCCCeEEEEEEeeCEEecCCeEEEEeCCEEEEEeEEehhc-ccCcCccEeCCCCEEEEEeeccccCCCCC
Confidence 34455555556679999999999999999999999877533333343333 34567999999999965 5777899999
Q ss_pred EEec
Q psy5461 180 KRTR 183 (221)
Q Consensus 180 tl~~ 183 (221)
+|-.
T Consensus 775 ~ie~ 778 (787)
T PRK05306 775 IIEA 778 (787)
T ss_pred EEEE
Confidence 9843
No 117
>cd00881 GTP_translation_factor GTP translation factor family. This family consists primarily of translation initiation, elongation, and release factors, which play specific roles in protein translation. In addition, the family includes Snu114p, a component of the U5 small nuclear riboprotein particle which is a component of the spliceosome and is involved in excision of introns, TetM, a tetracycline resistance gene that protects the ribosome from tetracycline binding, and the unusual subfamily CysN/ATPS, which has an unrelated function (ATP sulfurylase) acquired through lateral transfer of the EF1-alpha gene and development of a new function.
Probab=95.12 E-value=0.045 Score=43.05 Aligned_cols=63 Identities=27% Similarity=0.286 Sum_probs=42.4
Q ss_pred CCCceeeeeeeecccc-cCCcchHHHHhhccc-------------cccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 23 FGDSLCARAFKVVHDK-HRGAVTFFRIYSGAF-------------KKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~-~~g~l~~~~l~~~~~-------------~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
.+.+++..++|++.-. ..-+.....+.+... .....|++..||++|.|++++++.|..++|.|
T Consensus 113 ~~~~i~iv~nK~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~Sa~~g~gi~~l~~~l~~~l~~~ 189 (189)
T cd00881 113 GGLPIIVAINKIDRVGEEDLEEVLREIKELLGLIGFISTKEEGTRNGLLVPIVPGSALTGIGVEELLEAIVEHLPPP 189 (189)
T ss_pred CCCCeEEEEECCCCcchhcHHHHHHHHHHHHccccccchhhhhcccCCcceEEEEecccCcCHHHHHHHHHhhCCCC
Confidence 4678899999954221 111111222222221 23478999999999999999999999999865
No 118
>cd04091 mtEFG1_II_like mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals
Probab=95.10 E-value=0.0053 Score=42.94 Aligned_cols=35 Identities=31% Similarity=0.604 Sum_probs=30.1
Q ss_pred eeeeeeeecccccCCcchHHHHhhccccccCceeEec
Q psy5461 27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCG 63 (221)
Q Consensus 27 ~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~g 63 (221)
|+++|||+.+|++ |.+++.|+++|+++..+. +...
T Consensus 1 ~~a~vfK~~~~~~-G~i~~~Rv~sG~lk~gd~-v~~~ 35 (81)
T cd04091 1 FVGLAFKLEEGRF-GQLTYMRIYQGKLKKGDT-IYNV 35 (81)
T ss_pred CeEEEEEeecCCC-CCEEEEEEecCEEcCCCE-EEEc
Confidence 5799999999998 999999999999998664 5543
No 119
>cd01888 eIF2_gamma eIF2-gamma (gamma subunit of initiation factor 2). eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits. The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome. The gamma subunit has no intrinsic GTPase activity, but is stimulated by the GTPase activating protein (GAP) eIF5, and GDP/GTP exchange is stimulated by the guanine nucleotide exchange factor (GEF) eIF2B. eIF2B is a heteropentamer, and the epsilon chain binds eIF2. Both eIF5 and eIF2B-epsilon are known to bind strongly to eIF2-beta, but have also been shown to bind directly to eIF2-gamma. It is possible that eIF2-beta serves simply as a high-affinity docking site for eIF5 and eIF2B-epsilon, or that eIF2-beta serves a regulatory role. eIF2-gamma is found only in eukaryotes and archaea. It is closely related to SelB, the sel
Probab=95.08 E-value=0.028 Score=46.01 Aligned_cols=62 Identities=16% Similarity=0.192 Sum_probs=40.5
Q ss_pred Cceeeeeeeecccc-cCCcchHHHHhhcccc--ccCceeEecCCCccccHHHHHHHHHhhCCCCC
Q psy5461 25 DSLCARAFKVVHDK-HRGAVTFFRIYSGAFK--KNHVPVLCGSSYKNIGVQKLMDAIVDILPSPT 86 (221)
Q Consensus 25 ~~~~~~vfk~~~d~-~~g~l~~~~l~~~~~~--~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~ 86 (221)
.+++..++|++... ..-......+.+.... ....|++..||++|.||++|++.|.+.+|.|.
T Consensus 138 ~~iiivvNK~Dl~~~~~~~~~~~~i~~~~~~~~~~~~~i~~vSA~~g~gi~~L~~~l~~~l~~~~ 202 (203)
T cd01888 138 KHIIIVQNKIDLVKEEQALENYEQIKKFVKGTIAENAPIIPISAQLKYNIDVLLEYIVKKIPTPP 202 (203)
T ss_pred CcEEEEEEchhccCHHHHHHHHHHHHHHHhccccCCCcEEEEeCCCCCCHHHHHHHHHHhCCCCC
Confidence 36788999954321 1011112333322211 13568999999999999999999999999874
No 120
>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n
Probab=94.84 E-value=0.0069 Score=42.49 Aligned_cols=32 Identities=59% Similarity=1.068 Sum_probs=29.0
Q ss_pred eeeeeeeecccccCCcchHHHHhhccccccCc
Q psy5461 27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHV 58 (221)
Q Consensus 27 ~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~ 58 (221)
|+++|||+..|++.|.+++.|+++|+++....
T Consensus 1 ~~a~VfK~~~d~~~g~i~~~Ri~sGtl~~g~~ 32 (83)
T cd04092 1 LCALAFKVVHDPQRGPLTFVRVYSGTLKRGSA 32 (83)
T ss_pred CEEEEEecccCCCCCeEEEEEEecCEECCCCE
Confidence 57999999999999999999999999998654
No 121
>cd01890 LepA LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and eukaryota (e.g. yeast GUF1p), but is missing from archaea. This pattern of phyletic distribution suggests that LepA evolved through a duplication of the EF-G gene in bacteria, followed by early transfer into the eukaryotic lineage, most likely from the promitochondrial endosymbiont. Yeast GUF1p is not essential and mutant cells did not reveal any marked phenotype.
Probab=94.61 E-value=0.066 Score=42.04 Aligned_cols=61 Identities=18% Similarity=0.171 Sum_probs=39.2
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
+-+++..++|.+............+.+.. .....+++..||++|.||++|++.|...+|.|
T Consensus 119 ~~~iiiv~NK~Dl~~~~~~~~~~~~~~~~-~~~~~~~~~~Sa~~g~gi~~l~~~l~~~~~~~ 179 (179)
T cd01890 119 NLEIIPVINKIDLPSADPERVKQQIEDVL-GLDPSEAILVSAKTGLGVEDLLEAIVERIPPP 179 (179)
T ss_pred CCCEEEEEECCCCCcCCHHHHHHHHHHHh-CCCcccEEEeeccCCCCHHHHHHHHHhhCCCC
Confidence 45788888896542211111112222211 11123488999999999999999999999887
No 122
>COG0532 InfB Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=94.38 E-value=0.32 Score=45.40 Aligned_cols=81 Identities=14% Similarity=0.076 Sum_probs=62.2
Q ss_pred EEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCCCCCccCc
Q psy5461 102 CARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGLKRERGKD 179 (221)
Q Consensus 102 ~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl~~~~~Gd 179 (221)
.+.+-++...+..|.++=++|..|+++.|..++..+.+....-++|..++ +....++++.+|.-|+| .+-.+++.||
T Consensus 415 ~~~~r~v~~~~k~g~IaG~~V~~G~ikr~~~v~~~rd~~vi~~G~i~sLk-~~kddv~ev~~G~ecgI~i~~~~di~~gD 493 (509)
T COG0532 415 LAEVRAVFKLPKVGAIAGCMVTEGVIKRGAPVRVVRDGVVIYEGEVESLK-RFKDDVKEVRKGQECGIAIENYRDIKEGD 493 (509)
T ss_pred ceEEEEEEEcCCCCeEEEEEEecCEEecCCcEEEEeCCeEEEeeEEEeee-ccCccHhHhccCcEEEEEecCcccCCCCC
Confidence 45566666667789999999999999999999999765432225555554 45678999999999965 5667899999
Q ss_pred EEec
Q psy5461 180 KRTR 183 (221)
Q Consensus 180 tl~~ 183 (221)
+|..
T Consensus 494 ~le~ 497 (509)
T COG0532 494 ILEV 497 (509)
T ss_pred EEEE
Confidence 9854
No 123
>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl
Probab=94.34 E-value=0.0089 Score=41.77 Aligned_cols=35 Identities=34% Similarity=0.669 Sum_probs=30.2
Q ss_pred eeeeeeeecccccCCcchHHHHhhccccccCceeEe
Q psy5461 27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLC 62 (221)
Q Consensus 27 ~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~ 62 (221)
++++|||+..|++.|++++.|+++|+++.... +..
T Consensus 1 ~~a~Vfk~~~d~~~G~~~~~Rv~sG~l~~g~~-v~~ 35 (83)
T cd04088 1 FVALVFKTIHDPFVGKLSFVRVYSGTLKAGST-LYN 35 (83)
T ss_pred CEEEEEEcccCCCCceEEEEEEecCEEcCCCE-EEE
Confidence 57899999999999999999999999988654 443
No 124
>cd03699 lepA_II lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu and IF2 have all been demonstrated to interact at overlapping sites on the ribosome. Chemical protection studies demonstrate that they all include the universally conserved alpha-sarcin loop as part of their binding site. These data indicate that LepA may bind to this location on the ribosome as well. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage.
Probab=93.86 E-value=0.027 Score=39.77 Aligned_cols=36 Identities=28% Similarity=0.433 Sum_probs=30.7
Q ss_pred eeeeeeeecccccCCcchHHHHhhccccccCceeEec
Q psy5461 27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCG 63 (221)
Q Consensus 27 ~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~g 63 (221)
|.++|||++.|++.|++++.|+++|+++.... ++..
T Consensus 1 ~~~~Vfk~~~d~~~G~i~~~Rv~sG~l~~~~~-v~~~ 36 (86)
T cd03699 1 LRALIFDSWYDPYRGVIALVRVFDGTLKKGDK-IRFM 36 (86)
T ss_pred CEEEEEEeeccCCCCEEEEEEEEcCEEcCCCE-EEEe
Confidence 57899999999999999999999999987553 5443
No 125
>PRK10218 GTP-binding protein; Provisional
Probab=93.61 E-value=0.028 Score=53.84 Aligned_cols=50 Identities=24% Similarity=0.325 Sum_probs=43.5
Q ss_pred ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCc
Q psy5461 1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHV 58 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~ 58 (221)
||++.+++|+|.. +.+.||.++|||+..|++.|.+++.|+++|+++.+..
T Consensus 187 ld~Ii~~iP~P~~--------~~~~Pl~~~V~k~~~d~~~G~i~~gRV~sG~lk~Gd~ 236 (607)
T PRK10218 187 YQAIVDHVPAPDV--------DLDGPFQMQISQLDYNSYVGVIGIGRIKRGKVKPNQQ 236 (607)
T ss_pred HHHHHHhCCCCCC--------CCCCCeEEEEEeeEecCCCcEEEEEEEEeCcCcCCCE
Confidence 4788999999952 4578999999999999999999999999999887654
No 126
>cd04165 GTPBP1_like GTPBP1-like. Mammalian GTP binding protein 1 (GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1 are GTPases whose specific functions remain unknown. In mouse, GTPBP1 is expressed in macrophages, in smooth muscle cells of various tissues and in some neurons of the cerebral cortex; GTPBP2 tissue distribution appears to overlap that of GTPBP1. In human leukemia and macrophage cell lines, expression of both GTPBP1 and GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The chromosomal location of both genes has been identified in humans, with GTPBP1 located in chromosome 22q12-13.1 and GTPBP2 located in chromosome 6p21-12. Human glioblastoma multiforme (GBM), a highly-malignant astrocytic glioma and the most common cancer in the central nervous system, has been linked to chromosomal deletions and a translocation on chromosome 6. The GBM translocation results in a fusion of GTPBP2 and PTPRZ1, a protein involved in oligodendrocyte differentiation, recovery, and
Probab=93.16 E-value=0.11 Score=43.35 Aligned_cols=29 Identities=24% Similarity=0.319 Sum_probs=24.0
Q ss_pred cCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 56 NHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
...|+|..||.+|.|++.|+..|. .+|+|
T Consensus 196 ~~~pi~~vSavtg~Gi~~L~~~L~-~lp~~ 224 (224)
T cd04165 196 RIVPIFQVSNVTGEGLDLLHAFLN-LLPLR 224 (224)
T ss_pred ccCcEEEeeCCCccCHHHHHHHHH-hcCCC
Confidence 466999999999999999988774 56764
No 127
>cd01884 EF_Tu EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors. The eukaryotic counterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this family. EF-Tu is one of the most abundant proteins in bacteria, as well as, one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation.
Probab=93.11 E-value=0.098 Score=42.76 Aligned_cols=62 Identities=21% Similarity=0.350 Sum_probs=39.9
Q ss_pred CCc-eeeeeeeecc-c-ccCCcchHHHHhhcc----ccccCceeEecCCCcccc----------HHHHHHHHHhhCCCC
Q psy5461 24 GDS-LCARAFKVVH-D-KHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIG----------VQKLMDAIVDILPSP 85 (221)
Q Consensus 24 ~~~-~~~~vfk~~~-d-~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~G----------i~~LLd~I~~~~PsP 85 (221)
+.+ ++..++|++. + +..-+.....+++.. .+...+|++++||++|.+ +..|+++|.+..|+|
T Consensus 117 ~~~~iIvviNK~D~~~~~~~~~~~~~~i~~~l~~~g~~~~~v~iipiSa~~g~n~~~~~~w~~~~~~l~~~l~~~~~~~ 195 (195)
T cd01884 117 GVPYIVVFLNKADMVDDEELLELVEMEVRELLSKYGFDGDNTPIVRGSALKALEGDDPNKWVKKILELLDALDSYIPTP 195 (195)
T ss_pred CCCcEEEEEeCCCCCCcHHHHHHHHHHHHHHHHHhcccccCCeEEEeeCccccCCCCCCcchhcHhHHHHHHHhCCCCC
Confidence 444 7788999652 1 111122222343332 233468999999999875 679999999988876
No 128
>cd01891 TypA_BipA TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella typhimurium after exposure to bactericidal/permeability-inducing protein (a cationic antimicrobial protein produced by neutrophils), and has since been identified in E. coli as well. The properties thus far described for BipA are related to its role in the process of pathogenesis by enteropathogenic E. coli. It appears to be involved in the regulation of several processes important for infection, including rearrangements of the cytoskeleton of the host, bacterial resistance to host defense peptides, flagellum-mediated cell motility, and expression of K5 capsular genes. It has been proposed that BipA may utilize a novel mechanism to regulate the expression of target genes. In addition, BipA from enteropathogenic E. co
Probab=93.04 E-value=0.16 Score=40.92 Aligned_cols=62 Identities=19% Similarity=0.255 Sum_probs=39.9
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhcc------ccccCceeEecCCCccc----------cHHHHHHHHHhhCCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGA------FKKNHVPVLCGSSYKNI----------GVQKLMDAIVDILPSP 85 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~------~~~~~~Pv~~gSa~~~~----------Gi~~LLd~I~~~~PsP 85 (221)
+-|++..++|++............+.+.. .+...+|++++||++|. ++.+|++.|..++|.|
T Consensus 117 ~~p~iiv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iv~~Sa~~g~~~~~~~~~~~~~~~l~~~~~~~~~~~ 194 (194)
T cd01891 117 GLKPIVVINKIDRPDARPEEVVDEVFDLFIELGATEEQLDFPVLYASAKNGWASLNLEDPSEDLEPLFDTIIEHVPAP 194 (194)
T ss_pred CCCEEEEEECCCCCCCCHHHHHHHHHHHHHHhCCccccCccCEEEeehhccccccccccchhhHHHHHHHHHhcCCCC
Confidence 45788889996543221221222222211 12235689999999995 4679999999999987
No 129
>KOG1144|consensus
Probab=92.83 E-value=0.18 Score=49.01 Aligned_cols=79 Identities=14% Similarity=0.207 Sum_probs=61.9
Q ss_pred cCceeEecCCCccccHHHHHHHHHhhCCCCCCcccccccCCCCCCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEe
Q psy5461 56 NHVPVLCGSSYKNIGVQKLMDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYN 135 (221)
Q Consensus 56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~~~~~~~~~~~~~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~ 135 (221)
..+-++..||..|.||..||-.|+++.-.-... . ..--..+.+.|..+-.-++.|+..=+-+..|.|+.||+|.+
T Consensus 660 ~~vsiVPTSA~sGeGipdLl~llv~ltQk~m~~-k----l~y~~ev~cTVlEVKvieG~GtTIDViLvNG~L~eGD~Ivv 734 (1064)
T KOG1144|consen 660 ETVSIVPTSAISGEGIPDLLLLLVQLTQKTMVE-K----LAYVDEVQCTVLEVKVIEGHGTTIDVILVNGELHEGDQIVV 734 (1064)
T ss_pred ceEEeeecccccCCCcHHHHHHHHHHHHHHHHH-H----HhhhhheeeEEEEEEeecCCCceEEEEEEcceeccCCEEEE
Confidence 455678899999999999999999886442110 0 01235678889999888999987777788999999999999
Q ss_pred ccCC
Q psy5461 136 IHLD 139 (221)
Q Consensus 136 ~~~~ 139 (221)
++.+
T Consensus 735 cG~~ 738 (1064)
T KOG1144|consen 735 CGLQ 738 (1064)
T ss_pred cCCC
Confidence 8865
No 130
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=92.77 E-value=0.19 Score=42.97 Aligned_cols=62 Identities=13% Similarity=-0.041 Sum_probs=39.5
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPT 86 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~ 86 (221)
.+.|++..++|++.-. -+.....+..........+++..||++|.|+++|++.|.+++|...
T Consensus 106 ~~~p~ilV~NK~Dl~~--~~~~~~~~~~~~~~~~~~~v~~iSA~~g~gi~~L~~~l~~~l~~~~ 167 (270)
T TIGR00436 106 LKRPVVLTRNKLDNKF--KDKLLPLIDKYAILEDFKDIVPISALTGDNTSFLAAFIEVHLPEGP 167 (270)
T ss_pred cCCCEEEEEECeeCCC--HHHHHHHHHHHHhhcCCCceEEEecCCCCCHHHHHHHHHHhCCCCC
Confidence 4568888999965321 1111111111111112237999999999999999999999998643
No 131
>TIGR01393 lepA GTP-binding protein LepA. LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function is unknown.
Probab=92.56 E-value=0.067 Score=51.19 Aligned_cols=55 Identities=29% Similarity=0.440 Sum_probs=45.6
Q ss_pred ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecC
Q psy5461 1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGS 64 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gS 64 (221)
|+.+++++|+|.+ +.+.|+.++|||+..|++.|.+++.++++|+++.++. +++.+
T Consensus 172 le~I~~~lp~p~~--------~~~~pl~~~V~~~~~d~~~G~v~~~rV~sG~lk~Gd~-v~~~~ 226 (595)
T TIGR01393 172 LEAIVKRVPPPKG--------DPDAPLKALIFDSHYDNYRGVVALVRVFEGTIKPGDK-IRFMS 226 (595)
T ss_pred HHHHHHhCCCCCC--------CCCCCeEEEEEEEEEeCCCcEEEEEEEECCEEecCCE-EEEec
Confidence 4677888998854 4578999999999999999999999999999988765 54443
No 132
>TIGR01394 TypA_BipA GTP-binding protein TypA/BipA. This bacterial (and Arabidopsis) protein, termed TypA or BipA, a GTP-binding protein, is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown.
Probab=92.24 E-value=0.074 Score=50.88 Aligned_cols=54 Identities=26% Similarity=0.335 Sum_probs=45.1
Q ss_pred ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEec
Q psy5461 1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCG 63 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~g 63 (221)
|+.+++++|+|.. +.+.||.++||++..|++.|.+++.++++|+++.+.. |+..
T Consensus 183 ld~Iv~~lP~P~~--------~~~~pl~~~V~~i~~d~~~Grv~~gRV~sG~lk~G~~-V~~~ 236 (594)
T TIGR01394 183 FDAIVRHVPAPKG--------DLDEPLQMLVTNLDYDEYLGRIAIGRVHRGTVKKGQQ-VALM 236 (594)
T ss_pred HHHHHHhCCCCCC--------CCCCCEEEEEEEEEeeCCCceEEEEEEEeCEEccCCE-EEEe
Confidence 4678899999943 4578999999999999999999999999999987654 5443
No 133
>PRK15467 ethanolamine utilization protein EutP; Provisional
Probab=92.12 E-value=0.26 Score=38.55 Aligned_cols=58 Identities=14% Similarity=0.050 Sum_probs=39.4
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhcccccc-CceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKN-HVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~-~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
..|++..++|.+.... ....+.+...+.. ..|++..||++|.||++|++.|.+.++.-
T Consensus 91 ~~~ii~v~nK~Dl~~~----~~~~~~~~~~~~~~~~p~~~~Sa~~g~gi~~l~~~l~~~~~~~ 149 (158)
T PRK15467 91 SKRQIAVISKTDMPDA----DVAATRKLLLETGFEEPIFELNSHDPQSVQQLVDYLASLTKQE 149 (158)
T ss_pred CCCeEEEEEccccCcc----cHHHHHHHHHHcCCCCCEEEEECCCccCHHHHHHHHHHhchhh
Confidence 4578889999653221 2233333222222 25999999999999999999999887654
No 134
>cd01885 EF2 EF2 (for archaea and eukarya). Translocation requires hydrolysis of a molecule of GTP and is mediated by EF-G in bacteria and by eEF2 in eukaryotes. The eukaryotic elongation factor eEF2 is a GTPase involved in the translocation of the peptidyl-tRNA from the A site to the P site on the ribosome. The 95-kDa protein is highly conserved, with 60% amino acid sequence identity between the human and yeast proteins. Two major mechanisms are known to regulate protein elongation and both involve eEF2. First, eEF2 can be modulated by reversible phosphorylation. Increased levels of phosphorylated eEF2 reduce elongation rates presumably because phosphorylated eEF2 fails to bind the ribosomes. Treatment of mammalian cells with agents that raise the cytoplasmic Ca2+ and cAMP levels reduce elongation rates by activating the kinase responsible for phosphorylating eEF2. In contrast, treatment of cells with insulin increases elongation rates by promoting eEF2 dephosphorylation. Seco
Probab=91.90 E-value=0.19 Score=42.06 Aligned_cols=26 Identities=35% Similarity=0.653 Sum_probs=24.1
Q ss_pred eEecCCCcccc--------HHHHHHHHHhhCCCC
Q psy5461 60 VLCGSSYKNIG--------VQKLMDAIVDILPSP 85 (221)
Q Consensus 60 v~~gSa~~~~G--------i~~LLd~I~~~~PsP 85 (221)
|.|+||+.||+ +-.|+++|++++|+|
T Consensus 189 v~f~S~~~gw~f~~~~f~~~~~~~~~~~~~~~~p 222 (222)
T cd01885 189 VAFGSALHGWGFTIIKFARIYAVLEMVVKHLPSP 222 (222)
T ss_pred EEEEecccCEEeccccccchHHHHHHHHhhCCCC
Confidence 99999999985 779999999999998
No 135
>cd04139 RalA_RalB RalA/RalB subfamily. The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exo
Probab=91.88 E-value=0.22 Score=38.13 Aligned_cols=58 Identities=16% Similarity=0.017 Sum_probs=37.8
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+-|++..++|++.... .+........ ..+....|++..||++|.|+++|++.+.+.+
T Consensus 104 ~~~piiiv~NK~D~~~~-~~~~~~~~~~-~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~ 161 (164)
T cd04139 104 DNVPLLLVGNKCDLEDK-RQVSSEEAAN-LARQWGVPYVETSAKTRQNVEKAFYDLVREI 161 (164)
T ss_pred CCCCEEEEEEccccccc-cccCHHHHHH-HHHHhCCeEEEeeCCCCCCHHHHHHHHHHHH
Confidence 46788999999653221 1122222221 1222236899999999999999999988654
No 136
>COG1160 Predicted GTPases [General function prediction only]
Probab=91.75 E-value=0.27 Score=45.18 Aligned_cols=58 Identities=22% Similarity=0.271 Sum_probs=41.8
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTE 87 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~ 87 (221)
.+.|++.-+||++..+ .+......++. +.-..+..||.+|.|+..|+|.|.+.+| +.+
T Consensus 111 ~~kpviLvvNK~D~~~--~e~~~~efysl----G~g~~~~ISA~Hg~Gi~dLld~v~~~l~-~~e 168 (444)
T COG1160 111 SKKPVILVVNKIDNLK--AEELAYEFYSL----GFGEPVPISAEHGRGIGDLLDAVLELLP-PDE 168 (444)
T ss_pred cCCCEEEEEEcccCch--hhhhHHHHHhc----CCCCceEeehhhccCHHHHHHHHHhhcC-Ccc
Confidence 4589999999965542 23333333332 3334677999999999999999999998 544
No 137
>PRK05433 GTP-binding protein LepA; Provisional
Probab=91.69 E-value=0.09 Score=50.38 Aligned_cols=56 Identities=30% Similarity=0.446 Sum_probs=46.2
Q ss_pred ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCC
Q psy5461 1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSS 65 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa 65 (221)
|+.+++++|+|.+ +.+.|+.++|||+..|++.|.+++.++.+|.++.+.. +++.+.
T Consensus 176 l~~I~~~lp~P~~--------~~~~pl~~~Vfd~~~d~~~G~v~~~rV~sG~Lk~Gd~-i~~~~~ 231 (600)
T PRK05433 176 LEAIVERIPPPKG--------DPDAPLKALIFDSWYDNYRGVVVLVRVVDGTLKKGDK-IKMMST 231 (600)
T ss_pred HHHHHHhCccccC--------CCCCCceEEEEEEEecCCCceEEEEEEEcCEEecCCE-EEEecC
Confidence 4677888998853 4578999999999999999999999999999988765 555444
No 138
>cd01897 NOG NOG1 is a nucleolar GTP-binding protein present in eukaryotes ranging from trypanosomes to humans. NOG1 is functionally linked to ribosome biogenesis and found in association with the nuclear pore complexes and identified in many preribosomal complexes. Thus, defects in NOG1 can lead to defects in 60S biogenesis. The S. cerevisiae NOG1 gene is essential for cell viability, and mutations in the predicted G motifs abrogate function. It is a member of the ODN family of GTP-binding proteins that also includes the bacterial Obg and DRG proteins.
Probab=91.47 E-value=0.26 Score=38.12 Aligned_cols=55 Identities=15% Similarity=0.077 Sum_probs=36.5
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+.|++..++|.+.-.. .++.. . +...+....|++..||++|.|++++++.|.+.+
T Consensus 113 ~~pvilv~NK~Dl~~~-~~~~~--~-~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~~ 167 (168)
T cd01897 113 NKPVIVVLNKIDLLTF-EDLSE--I-EEEEELEGEEVLKISTLTEEGVDEVKNKACELL 167 (168)
T ss_pred cCCeEEEEEccccCch-hhHHH--H-HHhhhhccCceEEEEecccCCHHHHHHHHHHHh
Confidence 6788888999543211 12221 1 112233457899999999999999999988653
No 139
>cd04145 M_R_Ras_like M-Ras/R-Ras-like subfamily. This subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells. It interacts with some of the known Ras effectors, but appears to also have its own effectors. Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts. Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum. In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras. TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an ali
Probab=91.24 E-value=0.33 Score=37.25 Aligned_cols=58 Identities=16% Similarity=0.089 Sum_probs=39.3
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+-|++...+|.+.... ..+......+-. +...+|++..||++|.||+++++.|...+
T Consensus 106 ~~~piiiv~NK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~~i~~l~~~l~~~~ 163 (164)
T cd04145 106 DEFPMILVGNKADLEHQ-RKVSREEGQELA-RKLKIPYIETSAKDRLNVDKAFHDLVRVI 163 (164)
T ss_pred CCCCEEEEeeCcccccc-ceecHHHHHHHH-HHcCCcEEEeeCCCCCCHHHHHHHHHHhh
Confidence 35689999999654332 233333333322 22235899999999999999999998653
No 140
>cd03689 RF3_II RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of class II release factors with elongation factors shows that prokaryotic RF3 is more similar to EF-G whereas eukaryotic eRF3 is more similar to eEF1A, implying that their precise function may differ.
Probab=91.16 E-value=0.056 Score=38.24 Aligned_cols=30 Identities=30% Similarity=0.582 Sum_probs=26.9
Q ss_pred eeeeeecc---cccCCcchHHHHhhccccccCc
Q psy5461 29 ARAFKVVH---DKHRGAVTFFRIYSGAFKKNHV 58 (221)
Q Consensus 29 ~~vfk~~~---d~~~g~l~~~~l~~~~~~~~~~ 58 (221)
+++||+.+ |++.|++++.|+++|+++....
T Consensus 1 ~~vfKv~~~~~~~~~Gkla~~Rv~sG~l~~g~~ 33 (85)
T cd03689 1 GFVFKIQANMDPAHRDRIAFVRVCSGKFERGMK 33 (85)
T ss_pred CEEEEEecccCCCCCcEEEEEEEECCEEcCCCE
Confidence 57999999 9999999999999999997554
No 141
>cd04136 Rap_like Rap-like subfamily. The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres.
Probab=91.05 E-value=0.49 Score=36.21 Aligned_cols=57 Identities=14% Similarity=0.031 Sum_probs=37.0
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
.+-|++...+|.+.... .++.......-. +....|++..||++|.||.++++.|...
T Consensus 105 ~~~piilv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~~v~~l~~~l~~~ 161 (163)
T cd04136 105 ENVPMVLVGNKCDLEDE-RVVSREEGQALA-RQWGCPFYETSAKSKINVDEVFADLVRQ 161 (163)
T ss_pred CCCCEEEEEECcccccc-ceecHHHHHHHH-HHcCCeEEEecCCCCCCHHHHHHHHHHh
Confidence 35688888999653221 223332222211 1222789999999999999999999864
No 142
>cd04147 Ras_dva Ras-dva subfamily. Ras-dva (Ras - dorsal-ventral anterior localization) subfamily consists of a set of proteins characterized only in Xenopus leavis, to date. In Xenopus Ras-dva expression is activated by the transcription factor Otx2 and begins during gastrulation throughout the anterior ectoderm. Ras-dva expression is inhibited in the anterior neural plate by factor Xanf1. Downregulation of Ras-dva results in head development abnormalities through the inhibition of several regulators of the anterior neural plate and folds patterning, including Otx2, BF-1, Xag2, Pax6, Slug, and Sox9. Downregulation of Ras-dva also interferes with the FGF-8a signaling within the anterior ectoderm. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.
Probab=90.92 E-value=0.43 Score=38.53 Aligned_cols=62 Identities=11% Similarity=-0.052 Sum_probs=40.9
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
+-|++...+|.+..+....+......+........+++..||++|.||.++++.|.+.+..+
T Consensus 104 ~~piilv~NK~Dl~~~~~~v~~~~~~~~~~~~~~~~~~~~Sa~~g~gv~~l~~~l~~~~~~~ 165 (198)
T cd04147 104 FVPIVVVGNKADSLEEERQVPAKDALSTVELDWNCGFVETSAKDNENVLEVFKELLRQANLP 165 (198)
T ss_pred CCcEEEEEEccccccccccccHHHHHHHHHhhcCCcEEEecCCCCCCHHHHHHHHHHHhhcc
Confidence 56888999996532222333333333222212235789999999999999999999887643
No 143
>smart00173 RAS Ras subfamily of RAS small GTPases. Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades
Probab=90.87 E-value=0.34 Score=37.29 Aligned_cols=58 Identities=14% Similarity=0.043 Sum_probs=39.1
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
+.|++...+|.+.... ..+..+....-. +....|++..||++|.|++++++.|.+.+.
T Consensus 105 ~~pii~v~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~~i~~l~~~l~~~~~ 162 (164)
T smart00173 105 DVPIVLVGNKCDLESE-RVVSTEEGKELA-RQWGCPFLETSAKERVNVDEAFYDLVREIR 162 (164)
T ss_pred CCCEEEEEECcccccc-ceEcHHHHHHHH-HHcCCEEEEeecCCCCCHHHHHHHHHHHHh
Confidence 5688888999664332 223333322222 222378999999999999999999987654
No 144
>TIGR02528 EutP ethanolamine utilization protein, EutP. This protein is found within operons which code for polyhedral organelles containing the enzyme ethanolamine ammonia lyase. The function of this gene is unknown, although the presence of an N-terminal GxxGxGK motif implies a GTP-binding site.
Probab=90.76 E-value=0.42 Score=36.00 Aligned_cols=54 Identities=17% Similarity=0.080 Sum_probs=34.1
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHH
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIV 79 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~ 79 (221)
..|++..++|++..+. ....+.+.+........|++..||++|.|+++|++.|.
T Consensus 88 ~~p~ilv~NK~Dl~~~--~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~ 141 (142)
T TIGR02528 88 VKPVIGLVTKIDLAEA--DVDIERAKELLETAGAEPIFEISSVDEQGLEALVDYLN 141 (142)
T ss_pred cCCeEEEEEeeccCCc--ccCHHHHHHHHHHcCCCcEEEEecCCCCCHHHHHHHHh
Confidence 3488888899764321 12222222222222234789999999999999998874
No 145
>cd04157 Arl6 Arl6 subfamily. Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that A
Probab=90.71 E-value=0.54 Score=35.91 Aligned_cols=55 Identities=11% Similarity=-0.019 Sum_probs=35.3
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhcc--c--cccCceeEecCCCccccHHHHHHHHHh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA--F--KKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~--~--~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
.+-|++...+|.+.... .....+.... . ....++++..||++|.|++++++.|.+
T Consensus 103 ~~~p~iiv~NK~Dl~~~---~~~~~~~~~l~~~~~~~~~~~~~~~Sa~~g~gv~~~~~~l~~ 161 (162)
T cd04157 103 RRVPILFFANKMDLPDA---LTAVKITQLLGLENIKDKPWHIFASNALTGEGLDEGVQWLQA 161 (162)
T ss_pred CCCCEEEEEeCccccCC---CCHHHHHHHhCCccccCceEEEEEeeCCCCCchHHHHHHHhc
Confidence 35789999999653221 1122222211 1 223456899999999999999998864
No 146
>cd01860 Rab5_related Rab5-related subfamily. This subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence mo
Probab=90.70 E-value=0.5 Score=36.21 Aligned_cols=59 Identities=15% Similarity=0.017 Sum_probs=38.8
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
.+-+++...+|.+.... .......+.+-.... ..+++..||++|.|+.++++.|...+|
T Consensus 105 ~~~~iivv~nK~D~~~~-~~~~~~~~~~~~~~~-~~~~~~~Sa~~~~~v~~l~~~l~~~l~ 163 (163)
T cd01860 105 PNIIIALVGNKADLESK-RQVSTEEAQEYADEN-GLLFFETSAKTGENVNELFTEIAKKLP 163 (163)
T ss_pred CCCeEEEEEECcccccc-CcCCHHHHHHHHHHc-CCEEEEEECCCCCCHHHHHHHHHHHhC
Confidence 34578888899653221 222333333222222 367999999999999999999998775
No 147
>TIGR00491 aIF-2 translation initiation factor aIF-2/yIF-2. This model describes archaeal and eukaryotic orthologs of bacterial IF-2. Like IF-2, it helps convey the initiator tRNA to the ribosome, although the initiator is N-formyl-Met in bacteria and Met here. This protein is not closely related to the subunits of eIF-2 of eukaryotes, which is also involved in the initiation of translation. The aIF-2 of Methanococcus jannaschii contains a large intein interrupting a region of very strongly conserved sequence very near the amino end; this model does not correctly align the sequences from Methanococcus jannaschii and Pyrococcus horikoshii in this region.
Probab=90.63 E-value=1.6 Score=41.88 Aligned_cols=71 Identities=13% Similarity=0.203 Sum_probs=52.8
Q ss_pred ceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCC---CCCccCcEEecCCCCCC
Q psy5461 115 GAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGL---KRERGKDKRTRVIPKPT 189 (221)
Q Consensus 115 G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl---~~~~~Gdtl~~~~~~p~ 189 (221)
+.++=+||..|+|++|..|.. +.+ ..++.|..++. ...+++++.+|+-|+| .|. .+++.||+|.+..+.++
T Consensus 480 ~~i~G~~V~~G~i~~~~~v~r-~~~--~~iG~i~slk~-~k~~V~ev~~G~Ecgi~i~~~~~g~~~~~gD~l~~~i~~~~ 555 (590)
T TIGR00491 480 PAIVGVEVLTGVIRQGYPLMK-DDG--ETVGTVRSMQD-KGENVKSASAGQEVAIAIKDVVYGRTIHEGDTLYVDVPENH 555 (590)
T ss_pred CeEEEEEEecCEEecCCeEEe-cCC--EEEEEEchhcc-cCccccEECCCCEEEEEEeCccccCCCCCCCEEEEeCCHHH
Confidence 689999999999999998743 222 23455555543 4568999999999975 354 47899999998866554
No 148
>PF02421 FeoB_N: Ferrous iron transport protein B; InterPro: IPR011619 Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system and may play a role in the transport of ferrous iron. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent [].; GO: 0005525 GTP binding, 0015093 ferrous iron transmembrane transporter activity, 0015684 ferrous iron transport, 0016021 integral to membrane; PDB: 3TAH_B 3B1X_A 3SS8_A 3B1W_C 3B1V_A 3LX5_A 3B1Y_A 3LX8_A 3B1Z_A 3K53_B ....
Probab=90.59 E-value=0.26 Score=39.06 Aligned_cols=53 Identities=21% Similarity=0.225 Sum_probs=38.0
Q ss_pred CCCCceeeeeeeec-ccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHH
Q psy5461 22 HFGDSLCARAFKVV-HDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAI 78 (221)
Q Consensus 22 ~~~~~~~~~vfk~~-~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I 78 (221)
+.+.|++.-++|++ ..+....+...++.+.. .+||+..||.++.|+++|+++|
T Consensus 103 e~g~P~vvvlN~~D~a~~~g~~id~~~Ls~~L----g~pvi~~sa~~~~g~~~L~~~I 156 (156)
T PF02421_consen 103 ELGIPVVVVLNKMDEAERKGIEIDAEKLSERL----GVPVIPVSARTGEGIDELKDAI 156 (156)
T ss_dssp HTTSSEEEEEETHHHHHHTTEEE-HHHHHHHH----TS-EEEEBTTTTBTHHHHHHHH
T ss_pred HcCCCEEEEEeCHHHHHHcCCEECHHHHHHHh----CCCEEEEEeCCCcCHHHHHhhC
Confidence 46789999999964 22333355566665543 4799999999999999999986
No 149
>cd04116 Rab9 Rab9 subfamily. Rab9 is found in late endosomes, together with mannose 6-phosphate receptors (MPRs) and the tail-interacting protein of 47 kD (TIP47). Rab9 is a key mediator of vesicular transport from late endosomes to the trans-Golgi network (TGN) by redirecting the MPRs. Rab9 has been identified as a key component for the replication of several viruses, including HIV1, Ebola, Marburg, and measles, making it a potential target for inhibiting a variety of viruses. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CX
Probab=90.47 E-value=0.5 Score=36.67 Aligned_cols=56 Identities=11% Similarity=-0.044 Sum_probs=38.6
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+-|++...+|.+.. ..+++...+.+-..+....|++..||++|.|+.++++.+...
T Consensus 114 ~~piilv~nK~Dl~--~~~~~~~~~~~~~~~~~~~~~~e~Sa~~~~~v~~~~~~~~~~ 169 (170)
T cd04116 114 SFPFVVLGNKNDIP--ERQVSTEEAQAWCRENGDYPYFETSAKDATNVAAAFEEAVRR 169 (170)
T ss_pred CCcEEEEEECcccc--ccccCHHHHHHHHHHCCCCeEEEEECCCCCCHHHHHHHHHhh
Confidence 35788888995432 234444444443333344689999999999999999998754
No 150
>cd04138 H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1.
Probab=90.46 E-value=0.55 Score=35.66 Aligned_cols=55 Identities=15% Similarity=0.019 Sum_probs=36.3
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+.|++...+|.+... .......+.+- .+....|++..||++|.||+++++.+...
T Consensus 106 ~~piivv~nK~Dl~~--~~~~~~~~~~~-~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~ 160 (162)
T cd04138 106 DVPMVLVGNKCDLAA--RTVSSRQGQDL-AKSYGIPYIETSAKTRQGVEEAFYTLVRE 160 (162)
T ss_pred CCCEEEEEECccccc--ceecHHHHHHH-HHHhCCeEEEecCCCCCCHHHHHHHHHHH
Confidence 568888889954322 22333332221 12234589999999999999999998764
No 151
>cd01865 Rab3 Rab3 subfamily. The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D. All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression. Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules. Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promot
Probab=90.37 E-value=0.36 Score=37.51 Aligned_cols=58 Identities=17% Similarity=0.141 Sum_probs=38.4
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
+.|++...+|.+..+. ..+..+...+ ..+....|++..||++|.|+.+|++.+...++
T Consensus 106 ~~piivv~nK~Dl~~~-~~~~~~~~~~-~~~~~~~~~~~~Sa~~~~gv~~l~~~l~~~~~ 163 (165)
T cd01865 106 NAQVILVGNKCDMEDE-RVVSSERGRQ-LADQLGFEFFEASAKENINVKQVFERLVDIIC 163 (165)
T ss_pred CCCEEEEEECcccCcc-cccCHHHHHH-HHHHcCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence 4578899999664332 1222222222 22223458999999999999999999987654
No 152
>cd04160 Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.
Probab=90.34 E-value=0.62 Score=35.92 Aligned_cols=54 Identities=22% Similarity=0.147 Sum_probs=35.9
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhcc------ccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGA------FKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~------~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
+-|++..++|.+... ......+.... ......|++..||++|.|++++++.|.+
T Consensus 107 ~~p~ilv~NK~D~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gv~e~~~~l~~ 166 (167)
T cd04160 107 GVPLLILANKQDLPD---ALSVEEIKEVFQDKAEEIGRRDCLVLPVSALEGTGVREGIEWLVE 166 (167)
T ss_pred CCCEEEEEEcccccc---CCCHHHHHHHhccccccccCCceEEEEeeCCCCcCHHHHHHHHhc
Confidence 568999999965322 22222222211 1223568999999999999999998864
No 153
>cd03691 BipA_TypA_II BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion.
Probab=89.98 E-value=0.091 Score=36.87 Aligned_cols=35 Identities=23% Similarity=0.236 Sum_probs=29.9
Q ss_pred eeeeeeeecccccCCcchHHHHhhccccccCceeEe
Q psy5461 27 LCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLC 62 (221)
Q Consensus 27 ~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~ 62 (221)
|.++|||++.|++.|++++.|+++|+++.... +..
T Consensus 1 ~~~~vfk~~~d~~~g~i~~~Rv~sG~l~~g~~-v~~ 35 (86)
T cd03691 1 LQMLVTTLDYDDYVGRIAIGRIFRGTVKVGQQ-VAV 35 (86)
T ss_pred CeEEEEEeEecCCCCeEEEEEEEeCEEcCCCE-EEE
Confidence 45899999999999999999999999998654 443
No 154
>cd01862 Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-
Probab=89.89 E-value=0.51 Score=36.45 Aligned_cols=58 Identities=12% Similarity=0.114 Sum_probs=39.6
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+-|++...+|++.... ..+..+.+..........+++..||++|.|++++++.|.+.+
T Consensus 109 ~~p~ilv~nK~Dl~~~-~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~l~~~i~~~~ 166 (172)
T cd01862 109 NFPFVVLGNKIDLEEK-RQVSTKKAQQWCQSNGNIPYFETSAKEAINVEQAFETIARKA 166 (172)
T ss_pred CceEEEEEECcccccc-cccCHHHHHHHHHHcCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence 5688888899754321 223333333333333457899999999999999999998754
No 155
>cd04154 Arl2 Arl2 subfamily. Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis.
Probab=89.88 E-value=0.79 Score=35.87 Aligned_cols=55 Identities=20% Similarity=0.074 Sum_probs=36.9
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhcc----ccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
.+.|++...+|++..... ....+.... .+....|++..||++|.||+++++.+.+
T Consensus 114 ~~~p~iiv~nK~Dl~~~~---~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gi~~l~~~l~~ 172 (173)
T cd04154 114 AGATLLILANKQDLPGAL---SEEEIREALELDKISSHHWRIQPCSAVTGEGLLQGIDWLVD 172 (173)
T ss_pred cCCCEEEEEECcccccCC---CHHHHHHHhCccccCCCceEEEeccCCCCcCHHHHHHHHhc
Confidence 456888999996543221 222332221 1234678999999999999999998864
No 156
>cd04175 Rap1 Rap1 subgroup. The Rap1 subgroup is part of the Rap subfamily of the Ras family. It can be further divided into the Rap1a and Rap1b isoforms. In humans, Rap1a and Rap1b share 95% sequence homology, but are products of two different genes located on chromosomes 1 and 12, respectively. Rap1a is sometimes called smg p21 or Krev1 in the older literature. Rap1 proteins are believed to perform different cellular functions, depending on the isoform, its subcellular localization, and the effector proteins it binds. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and the microsomal membrane of pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. High expression of Rap1 has been observed in the n
Probab=89.52 E-value=0.52 Score=36.36 Aligned_cols=58 Identities=12% Similarity=-0.012 Sum_probs=38.0
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+-|++...+|.+.... ..+....... ..+....|++..||++|.|++++++.|.+.+
T Consensus 105 ~~~piilv~nK~Dl~~~-~~~~~~~~~~-~~~~~~~~~~~~Sa~~~~~v~~~~~~l~~~l 162 (164)
T cd04175 105 EDVPMILVGNKCDLEDE-RVVGKEQGQN-LARQWGCAFLETSAKAKINVNEIFYDLVRQI 162 (164)
T ss_pred CCCCEEEEEECCcchhc-cEEcHHHHHH-HHHHhCCEEEEeeCCCCCCHHHHHHHHHHHh
Confidence 45689999999654322 1233322221 2222336899999999999999999998643
No 157
>cd01863 Rab18 Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of mos
Probab=89.47 E-value=0.79 Score=35.07 Aligned_cols=55 Identities=18% Similarity=0.044 Sum_probs=36.2
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+.+++...+|.+.. ..........+-.. ...+|++..||++|.|++++++.+.+.
T Consensus 106 ~~~~~iv~nK~D~~--~~~~~~~~~~~~~~-~~~~~~~~~Sa~~~~gi~~~~~~~~~~ 160 (161)
T cd01863 106 DIVKMLVGNKIDKE--NREVTREEGLKFAR-KHNMLFIETSAKTRDGVQQAFEELVEK 160 (161)
T ss_pred CCcEEEEEECCccc--ccccCHHHHHHHHH-HcCCEEEEEecCCCCCHHHHHHHHHHh
Confidence 45677778885432 12223333333222 235789999999999999999998764
No 158
>cd00880 Era_like Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the se
Probab=89.41 E-value=0.77 Score=34.05 Aligned_cols=59 Identities=14% Similarity=0.103 Sum_probs=37.6
Q ss_pred CCCceeeeeeeecccccCCcchHH-HHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFF-RIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~-~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
...|++..++|.+.-......... ............|++..||+++.|+.++++.+.+.
T Consensus 103 ~~~~~ivv~nK~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sa~~~~~v~~l~~~l~~~ 162 (163)
T cd00880 103 RGKPVLLVLNKIDLLPEEEEEELLELRLLILLLLLGLPVIAVSALTGEGIDELREALIEA 162 (163)
T ss_pred cCCeEEEEEEccccCChhhHHHHHHHHHhhcccccCCceEEEeeeccCCHHHHHHHHHhh
Confidence 467888889995422211111111 01122334457789999999999999999999865
No 159
>PRK04004 translation initiation factor IF-2; Validated
Probab=89.32 E-value=2.4 Score=40.59 Aligned_cols=66 Identities=17% Similarity=0.195 Sum_probs=49.2
Q ss_pred ceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEE--cCC---CCCccCcEEecC
Q psy5461 115 GAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAV--TGL---KRERGKDKRTRV 184 (221)
Q Consensus 115 G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i--~gl---~~~~~Gdtl~~~ 184 (221)
+.++=+||..|+|++|..|.-. .+ ..++.|..++ ....+++++.+|+-|+| .+. .+++.||+|-..
T Consensus 482 ~~IaGc~V~~G~i~~~~~v~r~-~g--~~iG~i~Slk-~~k~~V~ev~~G~Ecgi~i~~~~~g~~~~~gD~i~~~ 552 (586)
T PRK04004 482 PAIVGVEVLGGTIKPGVPLIKE-DG--KRVGTIKQIQ-DQGENVKEAKAGMEVAISIDGPTVGRQIKEGDILYVD 552 (586)
T ss_pred CeEEEEEEEeCEEecCCEEEEE-CC--EEEEEEehhh-ccCCcccEeCCCCEEEEEEecccccCCCCCCCEEEEE
Confidence 6899999999999999986431 33 2345555554 34568999999999965 455 578999998765
No 160
>cd04151 Arl1 Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi complex, where it is believed to recruit effector proteins to the trans-Golgi network. Like most members of the Arf family, Arl1 is myristoylated at its N-terminal helix and mutation of the myristoylation site disrupts Golgi targeting. In humans, the Golgi-localized proteins golgin-97 and golgin-245 have been identified as Arl1 effectors. Golgins are large coiled-coil proteins found in the Golgi, and these golgins contain a C-terminal GRIP domain, which is the site of Arl1 binding. Additional Arl1 effectors include the GARP (Golgi-associated retrograde protein)/VFT (Vps53) vesicle-tethering complex and Arfaptin 2. Arl1 is not required for exocytosis, but appears necessary for trafficking from the endosomes to the Golgi. In Drosophila zygotes, mutation of Arl1 is lethal, and in the host-bloodstream form of Trypanosoma brucei, Arl1 is essential for viability.
Probab=89.17 E-value=0.68 Score=35.53 Aligned_cols=55 Identities=22% Similarity=0.114 Sum_probs=35.9
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhc----cccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG----AFKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~----~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
.+.|++...+|.+..... ...++.+. .......+++..||++|.||+++++.|.+
T Consensus 99 ~~~piiiv~nK~Dl~~~~---~~~~i~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~ 157 (158)
T cd04151 99 KGAVLLVFANKQDMPGAL---SEAEISEKLGLSELKDRTWSIFKTSAIKGEGLDEGMDWLVN 157 (158)
T ss_pred cCCcEEEEEeCCCCCCCC---CHHHHHHHhCccccCCCcEEEEEeeccCCCCHHHHHHHHhc
Confidence 357999999996432211 12222221 11223358999999999999999998864
No 161
>cd04106 Rab23_lke Rab23-like subfamily. Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signalling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. GTPase activating proteins (GAPs) interact with G
Probab=88.88 E-value=0.55 Score=35.94 Aligned_cols=56 Identities=13% Similarity=0.111 Sum_probs=36.8
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+-|++...+|.+.... .++..+.... ..+....|++..||++|.|++++++.|...
T Consensus 106 ~~p~iiv~nK~Dl~~~-~~v~~~~~~~-~~~~~~~~~~~~Sa~~~~~v~~l~~~l~~~ 161 (162)
T cd04106 106 DIPMVLVQTKIDLLDQ-AVITNEEAEA-LAKRLQLPLFRTSVKDDFNVTELFEYLAEK 161 (162)
T ss_pred CCCEEEEEEChhcccc-cCCCHHHHHH-HHHHcCCeEEEEECCCCCCHHHHHHHHHHh
Confidence 5688888999654332 2233333222 122234589999999999999999998753
No 162
>cd04177 RSR1 RSR1 subgroup. RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with RSR1 in vivo. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key featu
Probab=88.80 E-value=0.86 Score=35.42 Aligned_cols=60 Identities=15% Similarity=0.002 Sum_probs=39.1
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
.+-|++...+|.+.... -+++.+....-..+....|++..||++|.||.++++.|+..+.
T Consensus 105 ~~~piiiv~nK~D~~~~-~~~~~~~~~~~~~~~~~~~~~~~SA~~~~~i~~~f~~i~~~~~ 164 (168)
T cd04177 105 DNVPMVLVGNKADLEDD-RQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVRQII 164 (168)
T ss_pred CCCCEEEEEEChhcccc-CccCHHHHHHHHHHcCCceEEEeeCCCCCCHHHHHHHHHHHHh
Confidence 35688888899643222 1233333222222223478999999999999999999987654
No 163
>cd04158 ARD1 ARD1 subfamily. ARD1 (ADP-ribosylation factor domain protein 1) is an unusual member of the Arf family. In addition to the C-terminal Arf domain, ARD1 has an additional 46-kDa N-terminal domain that contains a RING finger domain, two predicted B-Boxes, and a coiled-coil protein interaction motif. This domain belongs to the TRIM (tripartite motif) or RBCC (RING, B-Box, coiled-coil) family. Like most Arfs, the ARD1 Arf domain lacks detectable GTPase activity. However, unlike most Arfs, the full-length ARD1 protein has significant GTPase activity due to the GAP (GTPase-activating protein) activity exhibited by the 46-kDa N-terminal domain. The GAP domain of ARD1 is specific for its own Arf domain and does not bind other Arfs. The rate of GDP dissociation from the ARD1 Arf domain is slowed by the adjacent 15 amino acids, which act as a GDI (GDP-dissociation inhibitor) domain. ARD1 is ubiquitously expressed in cells and localizes to the Golgi and to the lysosomal membra
Probab=88.71 E-value=0.99 Score=35.25 Aligned_cols=58 Identities=12% Similarity=-0.074 Sum_probs=37.8
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccc-----cccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAF-----KKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~-----~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
+.|++...+|.+... .+....+.+... .+...+++.+||++|.||+++++.|.+.++.
T Consensus 100 ~~piilv~NK~Dl~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~g~gv~~~f~~l~~~~~~ 162 (169)
T cd04158 100 DALLLIFANKQDVAG---ALSVEEMTELLSLHKLCCGRSWYIQGCDARSGMGLYEGLDWLSRQLVA 162 (169)
T ss_pred CCCEEEEEeCcCccc---CCCHHHHHHHhCCccccCCCcEEEEeCcCCCCCCHHHHHHHHHHHHhh
Confidence 358889999955322 233333332211 1123467889999999999999999877653
No 164
>cd04156 ARLTS1 ARLTS1 subfamily. ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in h
Probab=88.55 E-value=0.99 Score=34.46 Aligned_cols=55 Identities=15% Similarity=-0.034 Sum_probs=35.4
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhc-----cccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG-----AFKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~-----~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
.+.|++...+|.+.... .....+... .......+++..||++|.||+++++.|..
T Consensus 100 ~~~piilv~nK~Dl~~~---~~~~~i~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~~~~~i~~ 159 (160)
T cd04156 100 KGVPVVLLANKQDLPGA---LTAEEITRRFKLKKYCSDRDWYVQPCSAVTGEGLAEAFRKLAS 159 (160)
T ss_pred cCCCEEEEEECcccccC---cCHHHHHHHcCCcccCCCCcEEEEecccccCCChHHHHHHHhc
Confidence 35689999999654221 112222211 11113457899999999999999998864
No 165
>cd01855 YqeH YqeH. YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases.
Probab=88.54 E-value=0.88 Score=36.46 Aligned_cols=62 Identities=18% Similarity=0.128 Sum_probs=37.9
Q ss_pred CCCceeeeeeeeccc-ccCCcchHHHHh--h--ccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 23 FGDSLCARAFKVVHD-KHRGAVTFFRIY--S--GAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d-~~~g~l~~~~l~--~--~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
.+.+++..++|++.- +........... . ........+++..||++|.|+++|++.|.+++|.
T Consensus 60 ~~~~~ilV~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vSA~~~~gi~eL~~~l~~~l~~ 126 (190)
T cd01855 60 GNNPVILVGNKIDLLPKDKNLVRIKNWLRAKAAAGLGLKPKDVILISAKKGWGVEELINAIKKLAKK 126 (190)
T ss_pred CCCcEEEEEEchhcCCCCCCHHHHHHHHHHHHHhhcCCCcccEEEEECCCCCCHHHHHHHHHHHhhc
Confidence 356888999997532 211111111111 0 0111112368899999999999999999999874
No 166
>cd04143 Rhes_like Rhes_like subfamily. This subfamily includes Rhes (Ras homolog enriched in striatum) and Dexras1/AGS1 (activator of G-protein signaling 1). These proteins are homologous, but exhibit significant differences in tissue distribution and subcellular localization. Rhes is found primarily in the striatum of the brain, but is also expressed in other areas of the brain, such as the cerebral cortex, hippocampus, inferior colliculus, and cerebellum. Rhes expression is controlled by thyroid hormones. In rat PC12 cells, Rhes is farnesylated and localizes to the plasma membrane. Rhes binds and activates PI3K, and plays a role in coupling serpentine membrane receptors with heterotrimeric G-protein signaling. Rhes has recently been shown to be reduced under conditions of dopamine supersensitivity and may play a role in determining dopamine receptor sensitivity. Dexras1/AGS1 is a dexamethasone-induced Ras protein that is expressed primarily in the brain, with low expression l
Probab=88.47 E-value=0.95 Score=38.33 Aligned_cols=63 Identities=14% Similarity=0.044 Sum_probs=44.2
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTE 87 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~ 87 (221)
+-|++...+|.+.... -++....+.+........+++..||++|.||++|++.|....-.|.+
T Consensus 113 ~~piIivgNK~Dl~~~-~~v~~~ei~~~~~~~~~~~~~evSAktg~gI~elf~~L~~~~~~p~e 175 (247)
T cd04143 113 KIPMVICGNKADRDFP-REVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMFRALFSLAKLPNE 175 (247)
T ss_pred CCcEEEEEECccchhc-cccCHHHHHHHHHhcCCCEEEEEeCCCCCCHHHHHHHHHHHhccccc
Confidence 5688899999654332 23444555443322234678999999999999999999998766655
No 167
>cd04107 Rab32_Rab38 Rab38/Rab32 subfamily. Rab32 and Rab38 are members of the Rab family of small GTPases. Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
Probab=88.46 E-value=0.66 Score=37.46 Aligned_cols=61 Identities=15% Similarity=-0.037 Sum_probs=42.8
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
+-|++...+|.+... ...+..+.+.+........+++..||++|.||+++++.|.+.+...
T Consensus 110 ~~piilv~NK~Dl~~-~~~~~~~~~~~~~~~~~~~~~~e~Sak~~~~v~e~f~~l~~~l~~~ 170 (201)
T cd04107 110 PIPCLLLANKCDLKK-RLAKDGEQMDQFCKENGFIGWFETSAKEGINIEEAMRFLVKNILAN 170 (201)
T ss_pred CCcEEEEEECCCccc-ccccCHHHHHHHHHHcCCceEEEEeCCCCCCHHHHHHHHHHHHHHh
Confidence 458888899965432 1334455554444444446899999999999999999999877543
No 168
>cd04119 RJL RJL (RabJ-Like) subfamily. RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.
Probab=88.32 E-value=0.84 Score=34.86 Aligned_cols=57 Identities=19% Similarity=0.065 Sum_probs=37.9
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
..|++.-.+|.+..+. ..+..........+. ..|++..||++|.||+++++.|.+.+
T Consensus 110 ~~piilv~nK~Dl~~~-~~~~~~~~~~~~~~~-~~~~~~~Sa~~~~gi~~l~~~l~~~l 166 (168)
T cd04119 110 NIVVVVCANKIDLTKH-RAVSEDEGRLWAESK-GFKYFETSACTGEGVNEMFQTLFSSI 166 (168)
T ss_pred CceEEEEEEchhcccc-cccCHHHHHHHHHHc-CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence 4678888899654321 233333333322222 36899999999999999999988653
No 169
>cd01864 Rab19 Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet chracterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=88.28 E-value=1.1 Score=34.63 Aligned_cols=58 Identities=17% Similarity=0.026 Sum_probs=38.4
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
.+-|++...+|.+.... .+.......+........+++..||++|.|++++++.+...
T Consensus 107 ~~~p~ivv~nK~Dl~~~-~~~~~~~~~~~~~~~~~~~~~e~Sa~~~~~v~~~~~~l~~~ 164 (165)
T cd01864 107 SNVVLLLIGNKCDLEEQ-REVLFEEACTLAEKNGMLAVLETSAKESQNVEEAFLLMATE 164 (165)
T ss_pred CCCcEEEEEECcccccc-cccCHHHHHHHHHHcCCcEEEEEECCCCCCHHHHHHHHHHh
Confidence 35678888999653221 23333333333333344568899999999999999998764
No 170
>cd00876 Ras Ras family. The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of m
Probab=88.26 E-value=0.88 Score=34.45 Aligned_cols=57 Identities=14% Similarity=0.052 Sum_probs=39.5
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
..|++...+|.+..+. .++....+.+...+ ...|++..|++++.|++++++.|.+.+
T Consensus 104 ~~p~ivv~nK~D~~~~-~~~~~~~~~~~~~~-~~~~~~~~S~~~~~~i~~l~~~l~~~i 160 (160)
T cd00876 104 DIPIVLVGNKCDLENE-RQVSKEEGKALAKE-WGCPFIETSAKDNINIDEVFKLLVREI 160 (160)
T ss_pred CCcEEEEEECCccccc-ceecHHHHHHHHHH-cCCcEEEeccCCCCCHHHHHHHHHhhC
Confidence 5788899999654332 33444444333222 237899999999999999999998653
No 171
>cd04090 eEF2_II_snRNP Loc2 eEF2_C_snRNP, cd01514/C terminal domain:eEF2_C_snRNP: This family includes C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to domain II of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=88.09 E-value=0.13 Score=36.85 Aligned_cols=32 Identities=31% Similarity=0.386 Sum_probs=27.7
Q ss_pred eeeeeeeecccccC-CcchHHHHhhccccccCc
Q psy5461 27 LCARAFKVVHDKHR-GAVTFFRIYSGAFKKNHV 58 (221)
Q Consensus 27 ~~~~vfk~~~d~~~-g~l~~~~l~~~~~~~~~~ 58 (221)
++++|||+..|++. +.+++.|+++|+++....
T Consensus 1 ~~a~VfK~~~~~~~~~~la~~RV~sGtl~~g~~ 33 (94)
T cd04090 1 LVVHVTKLYSTSDGGSFWAFGRIYSGTIKKGQK 33 (94)
T ss_pred CEEEEEeeeecCCCCEEEEEEEEeeCeEcCCCE
Confidence 57899999999997 568999999999998654
No 172
>cd04150 Arf1_5_like Arf1-Arf5-like subfamily. This subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and related proteins. Arfs1-5 are soluble proteins that are crucial for assembling coat proteins during vesicle formation. Each contains an N-terminal myristoylated amphipathic helix that is folded into the protein in the GDP-bound state. GDP/GTP exchange exposes the helix, which anchors to the membrane. Following GTP hydrolysis, the helix dissociates from the membrane and folds back into the protein. A general feature of Arf1-5 signaling may be the cooperation of two Arfs at the same site. Arfs1-5 are generally considered to be interchangeable in function and location, but some specific functions have been assigned. Arf1 localizes to the early/cis-Golgi, where it is activated by GBF1 and recruits the coat protein COPI. It also localizes to the trans-Golgi network (TGN), where it is activated by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA proteins. Humans, but not rodents
Probab=88.05 E-value=1.1 Score=34.80 Aligned_cols=57 Identities=11% Similarity=-0.027 Sum_probs=34.3
Q ss_pred CCceeeeeeeecccccCCc-chHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 24 GDSLCARAFKVVHDKHRGA-VTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~-l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
+.|++...+|.+....... -....+..........+++..||++|.||+++++.|.+
T Consensus 101 ~~piilv~NK~Dl~~~~~~~~i~~~~~~~~~~~~~~~~~~~Sak~g~gv~~~~~~l~~ 158 (159)
T cd04150 101 DAVLLVFANKQDLPNAMSAAEVTDKLGLHSLRNRNWYIQATCATSGDGLYEGLDWLSN 158 (159)
T ss_pred CCCEEEEEECCCCCCCCCHHHHHHHhCccccCCCCEEEEEeeCCCCCCHHHHHHHHhc
Confidence 4688899999654322111 11111111111223456788999999999999998864
No 173
>cd01887 IF2_eIF5B IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases, IF2/IF5B undergoes conformational changes between its GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess three characteristic segments, including a divergent N-terminal region followed by conserved central and C-terminal segments. This core region is conserved among all known eukaryotic and archaeal IF2/eIF5Bs and eubacterial IF2s.
Probab=88.01 E-value=1 Score=34.60 Aligned_cols=59 Identities=12% Similarity=0.035 Sum_probs=37.1
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhcc-----ccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA-----FKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~-----~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
.+.|++..++|++......+-....+.... ..+...|++..||++|.|+.+|++.|.++
T Consensus 101 ~~~p~ivv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~ 164 (168)
T cd01887 101 ANVPFIVALNKIDKPNANPERVKNELSELGLQGEDEWGGDVQIVPTSAKTGEGIDDLLEAILLL 164 (168)
T ss_pred cCCCEEEEEEceecccccHHHHHHHHHHhhccccccccCcCcEEEeecccCCCHHHHHHHHHHh
Confidence 466888899996532211111112221111 11235789999999999999999999865
No 174
>cd03700 eEF2_snRNP_like_II EF2_snRNP_like_II: this subfamily represents domain II of elongation factor (EF) EF-2 found eukaryotes and archaea and, the C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. This translocation step is catalyzed by EF-2_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p.
Probab=87.95 E-value=0.13 Score=36.77 Aligned_cols=32 Identities=28% Similarity=0.463 Sum_probs=28.3
Q ss_pred eeeeeeeecccc-cCCcchHHHHhhccccccCc
Q psy5461 27 LCARAFKVVHDK-HRGAVTFFRIYSGAFKKNHV 58 (221)
Q Consensus 27 ~~~~vfk~~~d~-~~g~l~~~~l~~~~~~~~~~ 58 (221)
+++++||+..|+ +.+.+++.|+++|+++....
T Consensus 1 ~v~~v~Ki~~~~~~~g~la~~RV~sGtl~~g~~ 33 (93)
T cd03700 1 LVMYVTKMVPTPDKGGFIAFGRVFSGTIRKGQK 33 (93)
T ss_pred CeEEEEeCeECCCCCEEEEEEEEeeCeEeCCCE
Confidence 478999999999 88999999999999987643
No 175
>cd00879 Sar1 Sar1 subfamily. Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation.
Probab=87.94 E-value=1.1 Score=35.55 Aligned_cols=57 Identities=16% Similarity=0.026 Sum_probs=38.4
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccc---------------cccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAF---------------KKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~---------------~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+.|++...+|.+.. ..+....+..... .....+++..||++|.||+++++.|..++
T Consensus 119 ~~~pvivv~NK~Dl~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~e~~~~l~~~~ 190 (190)
T cd00879 119 ANVPFLILGNKIDLP---GAVSEEELRQALGLYGTTTGKGVSLKVSGIRPIEVFMCSVVKRQGYGEAFRWLSQYL 190 (190)
T ss_pred cCCCEEEEEeCCCCC---CCcCHHHHHHHhCcccccccccccccccCceeEEEEEeEecCCCChHHHHHHHHhhC
Confidence 357899999995432 1333444443321 11335789999999999999999987653
No 176
>cd04153 Arl5_Arl8 Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date.
Probab=87.81 E-value=1.3 Score=34.77 Aligned_cols=54 Identities=17% Similarity=0.048 Sum_probs=35.4
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhcc----ccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
+.|++..++|.+... ......+.+.. .+...+|++..||++|.||+++++.|..
T Consensus 116 ~~p~viv~NK~Dl~~---~~~~~~i~~~l~~~~~~~~~~~~~~~SA~~g~gi~e~~~~l~~ 173 (174)
T cd04153 116 KAVLLVLANKQDLKG---AMTPAEISESLGLTSIRDHTWHIQGCCALTGEGLPEGLDWIAS 173 (174)
T ss_pred CCCEEEEEECCCCCC---CCCHHHHHHHhCcccccCCceEEEecccCCCCCHHHHHHHHhc
Confidence 568899999965322 22222322221 1223468999999999999999998864
No 177
>cd04113 Rab4 Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to p
Probab=87.76 E-value=1.1 Score=34.34 Aligned_cols=57 Identities=14% Similarity=-0.041 Sum_probs=39.1
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
++-|++...+|.+... ..++....+..-..+. ..+++..||+++.|+.++++.++..
T Consensus 104 ~~~~iivv~nK~D~~~-~~~~~~~~~~~~~~~~-~~~~~~~Sa~~~~~i~~~~~~~~~~ 160 (161)
T cd04113 104 PNIVVILVGNKSDLAD-QREVTFLEASRFAQEN-GLLFLETSALTGENVEEAFLKCARS 160 (161)
T ss_pred CCCeEEEEEEchhcch-hccCCHHHHHHHHHHc-CCEEEEEECCCCCCHHHHHHHHHHh
Confidence 4668888889965332 2344444443333333 3789999999999999999998764
No 178
>cd04155 Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.
Probab=87.74 E-value=0.86 Score=35.36 Aligned_cols=57 Identities=12% Similarity=0.000 Sum_probs=33.6
Q ss_pred CCceeeeeeeecccccC-CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 24 GDSLCARAFKVVHDKHR-GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~-g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
+-|++..++|.+..... .+.....+.-........+++..||++|.|++++++.|++
T Consensus 115 ~~p~ivv~nK~D~~~~~~~~~i~~~l~~~~~~~~~~~~~~~Sa~~~~gi~~~~~~l~~ 172 (173)
T cd04155 115 GVPVLVFANKQDLATAAPAEEIAEALNLHDLRDRTWHIQACSAKTGEGLQEGMNWVCK 172 (173)
T ss_pred CCCEEEEEECCCCccCCCHHHHHHHcCCcccCCCeEEEEEeECCCCCCHHHHHHHHhc
Confidence 46788888896432211 1111111111111222456888999999999999998864
No 179
>cd01859 MJ1464 MJ1464. This family represents archaeal GTPase typified by the protein MJ1464 from Methanococcus jannaschii. The members of this family show a circular permutation of the GTPase signature motifs so that C-terminal strands 5, 6, and 7 (strands 6 contain the NKxD motif) are relocated to the N terminus.
Probab=87.62 E-value=0.63 Score=35.99 Aligned_cols=58 Identities=16% Similarity=0.138 Sum_probs=38.9
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
.+.|++..++|++.-+. ... .... ...+....|+++.||+++.|+++|++.|.+.+|.
T Consensus 40 ~~~p~iiv~NK~Dl~~~-~~~--~~~~-~~~~~~~~~~~~iSa~~~~gi~~L~~~l~~~~~~ 97 (156)
T cd01859 40 LGKKLLIVLNKADLVPK-EVL--EKWK-SIKESEGIPVVYVSAKERLGTKILRRTIKELAKI 97 (156)
T ss_pred CCCcEEEEEEhHHhCCH-HHH--HHHH-HHHHhCCCcEEEEEccccccHHHHHHHHHHHHhh
Confidence 46788999999653111 011 1111 1112234689999999999999999999999875
No 180
>TIGR02729 Obg_CgtA Obg family GTPase CgtA. This model describes a univeral, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. This GTPase, related to the nucleolar protein Obg, is designated CgtA in bacteria. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome structure. Recent work done in Vibrio cholerae shows an essential role in the stringent response, in which RelA-dependent ability to synthesize the alarmone ppGpp is required for deletion of this GTPase to be lethal.
Probab=87.48 E-value=0.82 Score=40.51 Aligned_cols=56 Identities=16% Similarity=0.105 Sum_probs=37.7
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
..|++..++|++.... .....+.+...+....+++..||+++.||++|++.|.+.+
T Consensus 273 ~kp~IIV~NK~DL~~~---~~~~~~~~~l~~~~~~~vi~iSAktg~GI~eL~~~I~~~l 328 (329)
T TIGR02729 273 EKPRIVVLNKIDLLDE---EELAELLKELKKALGKPVFPISALTGEGLDELLYALAELL 328 (329)
T ss_pred cCCEEEEEeCccCCCh---HHHHHHHHHHHHHcCCcEEEEEccCCcCHHHHHHHHHHHh
Confidence 5688888999653221 1123333333222235799999999999999999998765
No 181
>COG0481 LepA Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]
Probab=87.36 E-value=0.16 Score=47.08 Aligned_cols=64 Identities=30% Similarity=0.413 Sum_probs=53.6
Q ss_pred ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHH
Q psy5461 1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQK 73 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~ 73 (221)
|+.|++..|.|. ++.+.|+-+.+|+.+.|+..|-+.+.|+..|..+.++. |.+.|..+...|.+
T Consensus 178 Le~Iv~~iP~P~--------g~~~~pLkALifDS~yD~Y~GVv~~vRi~dG~ik~gdk-i~~m~tg~~y~V~e 241 (603)
T COG0481 178 LEAIVEKIPPPK--------GDPDAPLKALIFDSWYDNYLGVVVLVRIFDGTLKKGDK-IRMMSTGKEYEVDE 241 (603)
T ss_pred HHHHHhhCCCCC--------CCCCCcceEEEEeccccccceEEEEEEEeeceecCCCE-EEEEecCCEEEEEE
Confidence 467888899984 46789999999999999999999999999999998776 77777776665543
No 182
>COG4917 EutP Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=87.23 E-value=1.7 Score=33.42 Aligned_cols=56 Identities=14% Similarity=0.134 Sum_probs=39.2
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+..++++.|-|++.-+ ..+++ +.++-..+.+-.|||..|+..+.||++|+|.+...
T Consensus 89 ~~k~vIgvVTK~DLae-d~dI~--~~~~~L~eaGa~~IF~~s~~d~~gv~~l~~~L~~~ 144 (148)
T COG4917 89 GVKKVIGVVTKADLAE-DADIS--LVKRWLREAGAEPIFETSAVDNQGVEELVDYLASL 144 (148)
T ss_pred cccceEEEEecccccc-hHhHH--HHHHHHHHcCCcceEEEeccCcccHHHHHHHHHhh
Confidence 3456899999964322 22333 33344444457789999999999999999998754
No 183
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=87.22 E-value=0.7 Score=35.31 Aligned_cols=59 Identities=12% Similarity=0.040 Sum_probs=39.8
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
.+-|++..++|.+..+. -++..+...+-. +...++++..||.+|.|+.++++.|.+.++
T Consensus 104 ~~~pivvv~nK~D~~~~-~~~~~~~~~~~~-~~~~~~~~e~Sa~~~~~i~~l~~~i~~~~~ 162 (164)
T smart00175 104 PNVVIMLVGNKSDLEDQ-RQVSREEAEAFA-EEHGLPFFETSAKTNTNVEEAFEELAREIL 162 (164)
T ss_pred CCCeEEEEEEchhcccc-cCCCHHHHHHHH-HHcCCeEEEEeCCCCCCHHHHHHHHHHHHh
Confidence 45799999999654331 122222222222 233468999999999999999999988653
No 184
>PRK00089 era GTPase Era; Reviewed
Probab=87.16 E-value=1.3 Score=38.13 Aligned_cols=59 Identities=17% Similarity=0.164 Sum_probs=38.6
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhcc-ccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGA-FKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~-~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
+.|++..++|++.-....+ .....+.. ......+++..||+++.|+++|++.|..++|.
T Consensus 113 ~~pvilVlNKiDl~~~~~~--l~~~~~~l~~~~~~~~i~~iSA~~~~gv~~L~~~L~~~l~~ 172 (292)
T PRK00089 113 KTPVILVLNKIDLVKDKEE--LLPLLEELSELMDFAEIVPISALKGDNVDELLDVIAKYLPE 172 (292)
T ss_pred CCCEEEEEECCcCCCCHHH--HHHHHHHHHhhCCCCeEEEecCCCCCCHHHHHHHHHHhCCC
Confidence 4688888899643211111 11111211 11235678999999999999999999999975
No 185
>cd01898 Obg Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis. Members of the subfamily contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain.
Probab=87.15 E-value=1.2 Score=34.34 Aligned_cols=55 Identities=15% Similarity=0.134 Sum_probs=34.9
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccc-cCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKK-NHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~-~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
..|++...+|++..+. ... ...+.. .... ...|++..||+++.|++++++.|.+.
T Consensus 114 ~~p~ivv~NK~Dl~~~-~~~-~~~~~~-~~~~~~~~~~~~~Sa~~~~gi~~l~~~i~~~ 169 (170)
T cd01898 114 EKPRIVVLNKIDLLDE-EEL-FELLKE-LLKELWGKPVFPISALTGEGLDELLRKLAEL 169 (170)
T ss_pred ccccEEEEEchhcCCc-hhh-HHHHHH-HHhhCCCCCEEEEecCCCCCHHHHHHHHHhh
Confidence 4678888899653221 111 111111 1122 24678999999999999999998764
No 186
>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA. EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability.
Probab=87.05 E-value=0.71 Score=41.90 Aligned_cols=59 Identities=24% Similarity=0.158 Sum_probs=39.1
Q ss_pred CCCceeeeeeeecccccCCcchHHHH----hhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRI----YSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l----~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
.+.+++..+||.+... .+.....+ .+....-...|+++.||++|.|+.++++.+....-
T Consensus 282 ~~~~iiiv~NK~Dl~~--~~~~~~~~~~~~~~~~~~~~~~~vi~~SA~~g~~v~~l~~~i~~~~~ 344 (429)
T TIGR03594 282 AGKALVIVVNKWDLVK--DEKTREEFKKELRRKLPFLDFAPIVFISALTGQGVDKLLDAIDEVYE 344 (429)
T ss_pred cCCcEEEEEECcccCC--CHHHHHHHHHHHHHhcccCCCCceEEEeCCCCCCHHHHHHHHHHHHH
Confidence 4678999999965321 12222222 22222223579999999999999999999887653
No 187
>cd04152 Arl4_Arl7 Arl4/Arl7 subfamily. Arl4 (Arf-like 4) is highly expressed in testicular germ cells, and is found in the nucleus and nucleolus. In mice, Arl4 is developmentally expressed during embryogenesis, and a role in somite formation and central nervous system differentiation has been proposed. Arl7 has been identified as the only Arf/Arl protein to be induced by agonists of liver X-receptor and retinoid X-receptor and by cholesterol loading in human macrophages. Arl7 is proposed to play a role in transport between a perinuclear compartment and the plasma membrane, apparently linked to the ABCA1-mediated cholesterol secretion pathway. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.
Probab=87.05 E-value=1.2 Score=35.40 Aligned_cols=58 Identities=12% Similarity=0.017 Sum_probs=37.0
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhc-----cccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSG-----AFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~-----~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
.+.|++..++|.+... ......+... .......|++..||++|.|+++|++.|.+.+-
T Consensus 108 ~~~p~iiv~NK~D~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~SA~~~~gi~~l~~~l~~~l~ 170 (183)
T cd04152 108 QGVPVLVLANKQDLPN---ALSVSEVEKLLALHELSASTPWHVQPACAIIGEGLQEGLEKLYEMIL 170 (183)
T ss_pred CCCcEEEEEECcCccc---cCCHHHHHHHhCccccCCCCceEEEEeecccCCCHHHHHHHHHHHHH
Confidence 3568899999964322 1222222211 11112357889999999999999999887663
No 188
>cd04149 Arf6 Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins localize to the plasma membrane, where they perform a wide variety of functions. In its active, GTP-bound form, Arf6 is involved in cell spreading, Rac-induced formation of plasma membrane ruffles, cell migration, wound healing, and Fc-mediated phagocytosis. Arf6 appears to change the actin structure at the plasma membrane by activating Rac, a Rho family protein involved in membrane ruffling. Arf6 is required for and enhances Rac formation of ruffles. Arf6 can regulate dendritic branching in hippocampal neurons, and in yeast it localizes to the growing bud, where it plays a role in polarized growth and bud site selection. In leukocytes, Arf6 is required for chemokine-stimulated migration across endothelial cells. Arf6 also plays a role in down-regulation of beta2-adrenergic receptors and luteinizing hormone receptors by facilitating the release of sequestered arrestin to allow endocytosis. Arf6 is believed t
Probab=86.95 E-value=1.1 Score=35.24 Aligned_cols=54 Identities=13% Similarity=-0.034 Sum_probs=35.6
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhcc----ccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
+.|++...+|.+... ......+.+.. .++...+++..||++|.||+++++.|.+
T Consensus 110 ~~piilv~NK~Dl~~---~~~~~~i~~~~~~~~~~~~~~~~~~~SAk~g~gv~~~~~~l~~ 167 (168)
T cd04149 110 DALLLVFANKQDLPD---AMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLSS 167 (168)
T ss_pred CCcEEEEEECcCCcc---CCCHHHHHHHcCCCccCCCcEEEEEeeCCCCCChHHHHHHHhc
Confidence 568999999955322 22333333322 1223457888999999999999998864
No 189
>PRK00093 GTP-binding protein Der; Reviewed
Probab=86.84 E-value=0.74 Score=41.96 Aligned_cols=60 Identities=18% Similarity=0.067 Sum_probs=39.5
Q ss_pred CCCceeeeeeeeccc-ccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHD-KHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d-~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+.+++..++|.+.. +...+.....+..........|+++.||++|.||.+|++.+....
T Consensus 283 ~~~~~ivv~NK~Dl~~~~~~~~~~~~~~~~l~~~~~~~i~~~SA~~~~gv~~l~~~i~~~~ 343 (435)
T PRK00093 283 AGRALVIVVNKWDLVDEKTMEEFKKELRRRLPFLDYAPIVFISALTGQGVDKLLEAIDEAY 343 (435)
T ss_pred cCCcEEEEEECccCCCHHHHHHHHHHHHHhcccccCCCEEEEeCCCCCCHHHHHHHHHHHH
Confidence 467899999996532 211122223333333233457999999999999999999987643
No 190
>PRK04213 GTP-binding protein; Provisional
Probab=86.82 E-value=1.2 Score=35.76 Aligned_cols=60 Identities=20% Similarity=0.061 Sum_probs=38.6
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhcccc-----ccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFK-----KNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~-----~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
.+.|++..++|++..... +-....+.+...- .-..|++..||++| ||+++++.|.+.++.
T Consensus 129 ~~~p~iiv~NK~Dl~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~SA~~g-gi~~l~~~l~~~~~~ 193 (201)
T PRK04213 129 LGIPPIVAVNKMDKIKNR-DEVLDEIAERLGLYPPWRQWQDIIAPISAKKG-GIEELKEAIRKRLHE 193 (201)
T ss_pred cCCCeEEEEECccccCcH-HHHHHHHHHHhcCCccccccCCcEEEEecccC-CHHHHHHHHHHhhcC
Confidence 467899999996542211 1122333322110 11237899999999 999999999998754
No 191
>cd04159 Arl10_like Arl10-like subfamily. Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.
Probab=86.82 E-value=1.1 Score=33.47 Aligned_cols=56 Identities=13% Similarity=0.062 Sum_probs=34.2
Q ss_pred CCceeeeeeeecccccCCcch--HHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVT--FFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~--~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
+-|++...+|.+.... .... ...+..........+++..|+++|.|+.++++.|..
T Consensus 101 ~~p~iiv~nK~D~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~l~~ 158 (159)
T cd04159 101 GIPLLVLGNKNDLPGA-LSVDELIEQMNLKSITDREVSCYSISCKEKTNIDIVLDWLIK 158 (159)
T ss_pred CCCEEEEEeCccccCC-cCHHHHHHHhCcccccCCceEEEEEEeccCCChHHHHHHHhh
Confidence 4578888888542221 1111 111111112233468999999999999999998864
No 192
>cd01861 Rab6 Rab6 subfamily. Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate
Probab=86.69 E-value=1.1 Score=34.23 Aligned_cols=56 Identities=13% Similarity=-0.048 Sum_probs=38.0
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+.|++...+|++.... .+............ ...+++..||+++.|++++++.|.+.
T Consensus 105 ~~~iilv~nK~D~~~~-~~~~~~~~~~~~~~-~~~~~~~~Sa~~~~~v~~l~~~i~~~ 160 (161)
T cd01861 105 DVIIVLVGNKTDLSDK-RQVSTEEGEKKAKE-LNAMFIETSAKAGHNVKELFRKIASA 160 (161)
T ss_pred CCEEEEEEEChhcccc-CccCHHHHHHHHHH-hCCEEEEEeCCCCCCHHHHHHHHHHh
Confidence 4789999999665322 23333332222222 23778999999999999999999865
No 193
>cd00878 Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thu
Probab=86.63 E-value=1.5 Score=33.35 Aligned_cols=55 Identities=13% Similarity=-0.023 Sum_probs=37.3
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhcc----ccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGA----FKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~----~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
.+.|++...+|.+..... ..+.+.+.. ......|++..||++|.|++++++.|..
T Consensus 99 ~~~piiiv~nK~D~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~gv~~~~~~l~~ 157 (158)
T cd00878 99 KGVPLLIFANKQDLPGAL---SVSELIEKLGLEKILGRRWHIQPCSAVTGDGLDEGLDWLLQ 157 (158)
T ss_pred CCCcEEEEeeccCCcccc---CHHHHHHhhChhhccCCcEEEEEeeCCCCCCHHHHHHHHhh
Confidence 467888889996543321 222333322 1234678999999999999999998864
No 194
>cd04142 RRP22 RRP22 subfamily. RRP22 (Ras-related protein on chromosome 22) subfamily consists of proteins that inhibit cell growth and promote caspase-independent cell death. Unlike most Ras proteins, RRP22 is down-regulated in many human tumor cells due to promoter methylation. RRP22 localizes to the nucleolus in a GTP-dependent manner, suggesting a novel function in modulating transport of nucleolar components. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Like most Ras family proteins, RRP22 is farnesylated.
Probab=86.57 E-value=1.3 Score=35.98 Aligned_cols=61 Identities=11% Similarity=-0.049 Sum_probs=39.6
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
+-|++...+|.+.... .......+.....+....|++..||++|.||++|++.+...+-..
T Consensus 116 ~~piiivgNK~Dl~~~-~~~~~~~~~~~~~~~~~~~~~e~Sak~g~~v~~lf~~i~~~~~~~ 176 (198)
T cd04142 116 EPPIVVVGNKRDQQRH-RFAPRHVLSVLVRKSWKCGYLECSAKYNWHILLLFKELLISATTR 176 (198)
T ss_pred CCCEEEEEECcccccc-ccccHHHHHHHHHHhcCCcEEEecCCCCCCHHHHHHHHHHHhhcc
Confidence 4688899999765332 122222222211122346899999999999999999998766443
No 195
>cd01868 Rab11_like Rab11-like. Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP
Probab=86.33 E-value=1.1 Score=34.52 Aligned_cols=57 Identities=14% Similarity=0.005 Sum_probs=38.0
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+.|++...+|.+.... -++......+.... ...+++..||++|.|++++++.|.+.+
T Consensus 108 ~~pi~vv~nK~Dl~~~-~~~~~~~~~~~~~~-~~~~~~~~Sa~~~~~v~~l~~~l~~~i 164 (165)
T cd01868 108 NIVIMLVGNKSDLRHL-RAVPTEEAKAFAEK-NGLSFIETSALDGTNVEEAFKQLLTEI 164 (165)
T ss_pred CCeEEEEEECcccccc-ccCCHHHHHHHHHH-cCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence 4688888999654332 22333333332222 246799999999999999999998754
No 196
>PRK12299 obgE GTPase CgtA; Reviewed
Probab=86.31 E-value=0.9 Score=40.39 Aligned_cols=59 Identities=15% Similarity=0.044 Sum_probs=38.5
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
+.|++..++|++.... .+.....+.. ..+....|++..||+++.||++|++.|.+.++.
T Consensus 271 ~kp~IIV~NKiDL~~~-~~~~~~~~~~-~~~~~~~~i~~iSAktg~GI~eL~~~L~~~l~~ 329 (335)
T PRK12299 271 DKPRILVLNKIDLLDE-EEEREKRAAL-ELAALGGPVFLISAVTGEGLDELLRALWELLEE 329 (335)
T ss_pred cCCeEEEEECcccCCc-hhHHHHHHHH-HHHhcCCCEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence 5688999999754221 1122111111 112223679999999999999999999988754
No 197
>cd04134 Rho3 Rho3 subfamily. Rho3 is a member of the Rho family found only in fungi. Rho3 is believed to regulate cell polarity by interacting with the diaphanous/formin family protein For3 to control both the actin cytoskeleton and microtubules. Rho3 is also believed to have a direct role in exocytosis that is independent of its role in regulating actin polarity. The function in exocytosis may be two-pronged: first, in the transport of post-Golgi vesicles from the mother cell to the bud, mediated by myosin (Myo2); second, in the docking and fusion of vesicles to the plasma membrane, mediated by an exocyst (Exo70) protein. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.
Probab=85.97 E-value=1.3 Score=35.34 Aligned_cols=64 Identities=19% Similarity=0.127 Sum_probs=41.4
Q ss_pred CCceeeeeeeecccccCC-----------cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCC
Q psy5461 24 GDSLCARAFKVVHDKHRG-----------AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTE 87 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g-----------~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~ 87 (221)
+-|++...+|.+...... .+..+...+...+....+++..||++|.||+++++.|...+-.|..
T Consensus 104 ~~piilvgNK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~e~SAk~~~~v~e~f~~l~~~~~~~~~ 178 (189)
T cd04134 104 GVKLVLVALKCDLREARNERDDLQRYGKHTISYEEGLAVAKRINALRYLECSAKLNRGVNEAFTEAARVALNVRP 178 (189)
T ss_pred CCCEEEEEEChhhccChhhHHHHhhccCCCCCHHHHHHHHHHcCCCEEEEccCCcCCCHHHHHHHHHHHHhcccc
Confidence 567888888865332211 1222222222222234678999999999999999999988876653
No 198
>COG1159 Era GTPase [General function prediction only]
Probab=85.97 E-value=1.4 Score=38.42 Aligned_cols=59 Identities=15% Similarity=0.129 Sum_probs=39.2
Q ss_pred CceeeeeeeecccccCCc-chHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 25 DSLCARAFKVVHDKHRGA-VTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 25 ~~~~~~vfk~~~d~~~g~-l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
-|++..+||++.-...-. +.....+ ........++..||++|.|++.|++.+..++|.-
T Consensus 115 ~pvil~iNKID~~~~~~~l~~~~~~~--~~~~~f~~ivpiSA~~g~n~~~L~~~i~~~Lpeg 174 (298)
T COG1159 115 TPVILVVNKIDKVKPKTVLLKLIAFL--KKLLPFKEIVPISALKGDNVDTLLEIIKEYLPEG 174 (298)
T ss_pred CCeEEEEEccccCCcHHHHHHHHHHH--HhhCCcceEEEeeccccCCHHHHHHHHHHhCCCC
Confidence 488899999652211111 2222222 2223344688899999999999999999999863
No 199
>cd04135 Tc10 TC10 subfamily. TC10 is a Rho family protein that has been shown to induce microspike formation and neurite outgrowth in vitro. Its expression changes dramatically after peripheral nerve injury, suggesting an important role in promoting axonal outgrowth and regeneration. TC10 regulates translocation of insulin-stimulated GLUT4 in adipocytes and has also been shown to bind directly to Golgi COPI coat proteins. GTP-bound TC10 in vitro can bind numerous potential effectors. Depending on its subcellular localization and distinct functional domains, TC10 can differentially regulate two types of filamentous actin in adipocytes. TC10 mRNAs are highly expressed in three types of mouse muscle tissues: leg skeletal muscle, cardiac muscle, and uterus; they were also present in brain, with higher levels in adults than in newborns. TC10 has also been shown to play a role in regulating the expression of cystic fibrosis transmembrane conductance regulator (CFTR) through interacti
Probab=85.84 E-value=1.4 Score=34.17 Aligned_cols=59 Identities=10% Similarity=-0.079 Sum_probs=36.0
Q ss_pred CCCceeeeeeeecccccC-----------CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 23 FGDSLCARAFKVVHDKHR-----------GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~-----------g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
++.|++...+|.+..... -+++.+....-..+-...+++..||++|.||+++++.+...
T Consensus 103 ~~~piivv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~e~Sa~~~~gi~~~f~~~~~~ 172 (174)
T cd04135 103 PNVPYLLVGTQIDLRDDPKTLARLNDMKEKPVTVEQGQKLAKEIGAHCYVECSALTQKGLKTVFDEAILA 172 (174)
T ss_pred CCCCEEEEeEchhhhcChhhHHHHhhccCCCCCHHHHHHHHHHcCCCEEEEecCCcCCCHHHHHHHHHHH
Confidence 456788888886421110 12332222222222233478899999999999999998764
No 200
>cd01894 EngA1 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.
Probab=85.74 E-value=0.91 Score=34.22 Aligned_cols=54 Identities=20% Similarity=0.146 Sum_probs=35.3
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
...|++..++|++.... ......+. +....+++..|+++|.|++++++.|.+.+
T Consensus 104 ~~~piiiv~nK~D~~~~--~~~~~~~~----~~~~~~~~~~Sa~~~~gv~~l~~~l~~~~ 157 (157)
T cd01894 104 SKKPVILVVNKVDNIKE--EDEAAEFY----SLGFGEPIPISAEHGRGIGDLLDAILELL 157 (157)
T ss_pred cCCCEEEEEECcccCCh--HHHHHHHH----hcCCCCeEEEecccCCCHHHHHHHHHhhC
Confidence 35788888999643322 11111211 12233688999999999999999998653
No 201
>cd04176 Rap2 Rap2 subgroup. The Rap2 subgroup is part of the Rap subfamily of the Ras family. It consists of Rap2a, Rap2b, and Rap2c. Both isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK) are putative effectors of Rap2 in mediating the activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton. In human platelets, Rap2 was shown to interact with the cytoskeleton by binding the actin filaments. In embryonic Xenopus development, Rap2 is necessary for the Wnt/beta-catenin signaling pathway. The Rap2 interacting protein 9 (RPIP9) is highly expressed in human breast carcinomas and correlates with a poor prognosis, suggesting a role for Rap2 in breast cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a, or Rap1b, is expressed in human red blood cells, where it is believed to be involved in vesiculation. A number of additional effector proteins for Rap2 have been identified, incl
Probab=85.67 E-value=1.3 Score=33.88 Aligned_cols=58 Identities=16% Similarity=0.024 Sum_probs=36.4
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+.|++.-.+|.+.... ..+...... ...+....|++..||++|.|+.++++.+...+
T Consensus 105 ~~~piviv~nK~Dl~~~-~~~~~~~~~-~~~~~~~~~~~~~Sa~~~~~v~~l~~~l~~~l 162 (163)
T cd04176 105 EKVPIILVGNKVDLESE-REVSSAEGR-ALAEEWGCPFMETSAKSKTMVNELFAEIVRQM 162 (163)
T ss_pred CCCCEEEEEECccchhc-CccCHHHHH-HHHHHhCCEEEEecCCCCCCHHHHHHHHHHhc
Confidence 45688888899653222 122221111 11122235889999999999999999988653
No 202
>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily. Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to t
Probab=85.67 E-value=1 Score=34.70 Aligned_cols=57 Identities=12% Similarity=0.032 Sum_probs=37.7
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+.|++...+|.+.... -++.......-. +....|++..||++|.||.++++.|.+.+
T Consensus 107 ~~~~iiv~nK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~~v~~~~~~i~~~~ 163 (166)
T cd01869 107 NVNKLLVGNKCDLTDK-RVVDYSEAQEFA-DELGIPFLETSAKNATNVEQAFMTMAREI 163 (166)
T ss_pred CCcEEEEEEChhcccc-cCCCHHHHHHHH-HHcCCeEEEEECCCCcCHHHHHHHHHHHH
Confidence 4578888888553222 233333333322 22346899999999999999999988643
No 203
>cd00154 Rab Rab family. Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide di
Probab=85.65 E-value=1.6 Score=32.61 Aligned_cols=55 Identities=13% Similarity=0.015 Sum_probs=38.0
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHH
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIV 79 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~ 79 (221)
.+.|++..++|.+... ..+...+.+.+-.. ....|++..||+++.|+.++++.|.
T Consensus 104 ~~~p~ivv~nK~D~~~-~~~~~~~~~~~~~~-~~~~~~~~~sa~~~~~i~~~~~~i~ 158 (159)
T cd00154 104 ENIPIILVGNKIDLED-QRQVSTEEAQQFAK-ENGLLFFETSAKTGENVEELFQSLA 158 (159)
T ss_pred CCCcEEEEEEcccccc-cccccHHHHHHHHH-HcCCeEEEEecCCCCCHHHHHHHHh
Confidence 3578999999965421 12333444443222 2467899999999999999999875
No 204
>cd04114 Rab30 Rab30 subfamily. Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=85.57 E-value=1.3 Score=34.17 Aligned_cols=56 Identities=13% Similarity=-0.100 Sum_probs=36.0
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+.+.+...+|++.... -++... +.+...+....+++..||++|.|++++++.|...
T Consensus 112 ~~~~i~v~NK~D~~~~-~~i~~~-~~~~~~~~~~~~~~~~Sa~~~~gv~~l~~~i~~~ 167 (169)
T cd04114 112 KVITILVGNKIDLAER-REVSQQ-RAEEFSDAQDMYYLETSAKESDNVEKLFLDLACR 167 (169)
T ss_pred CCeEEEEEECcccccc-cccCHH-HHHHHHHHcCCeEEEeeCCCCCCHHHHHHHHHHH
Confidence 4567788888664322 122222 1122222233678999999999999999999864
No 205
>PRK15494 era GTPase Era; Provisional
Probab=85.49 E-value=1.7 Score=38.57 Aligned_cols=57 Identities=9% Similarity=-0.090 Sum_probs=38.2
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhcccc-ccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFK-KNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~-~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
+.+.+..++|++.... . ...+.+.... ....+++..||++|.|+++|++.|..++|.
T Consensus 160 ~~p~IlViNKiDl~~~--~--~~~~~~~l~~~~~~~~i~~iSAktg~gv~eL~~~L~~~l~~ 217 (339)
T PRK15494 160 NIVPIFLLNKIDIESK--Y--LNDIKAFLTENHPDSLLFPISALSGKNIDGLLEYITSKAKI 217 (339)
T ss_pred CCCEEEEEEhhcCccc--c--HHHHHHHHHhcCCCcEEEEEeccCccCHHHHHHHHHHhCCC
Confidence 4566778899653221 1 2222222222 223578999999999999999999999975
No 206
>cd01870 RhoA_like RhoA-like subfamily. The RhoA subfamily consists of RhoA, RhoB, and RhoC. RhoA promotes the formation of stress fibers and focal adhesions, regulating cell shape, attachment, and motility. RhoA can bind to multiple effector proteins, thereby triggering different downstream responses. In many cell types, RhoA mediates local assembly of the contractile ring, which is necessary for cytokinesis. RhoA is vital for muscle contraction; in vascular smooth muscle cells, RhoA plays a key role in cell contraction, differentiation, migration, and proliferation. RhoA activities appear to be elaborately regulated in a time- and space-dependent manner to control cytoskeletal changes. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. RhoA and RhoC are observed only in geranyl
Probab=85.45 E-value=1.8 Score=33.55 Aligned_cols=26 Identities=12% Similarity=0.115 Sum_probs=22.6
Q ss_pred CceeEecCCCccccHHHHHHHHHhhC
Q psy5461 57 HVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 57 ~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
..+++..||++|.||+++++.|...+
T Consensus 149 ~~~~~~~Sa~~~~~v~~lf~~l~~~~ 174 (175)
T cd01870 149 AFGYMECSAKTKEGVREVFEMATRAA 174 (175)
T ss_pred CcEEEEeccccCcCHHHHHHHHHHHh
Confidence 45789999999999999999998643
No 207
>cd01878 HflX HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.
Probab=85.44 E-value=1.3 Score=35.61 Aligned_cols=51 Identities=12% Similarity=0.053 Sum_probs=35.0
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+.+++..++|++..+. .... ........|++..||++|.|+.++++.|...
T Consensus 153 ~~~viiV~NK~Dl~~~--~~~~-----~~~~~~~~~~~~~Sa~~~~gi~~l~~~L~~~ 203 (204)
T cd01878 153 DIPMILVLNKIDLLDD--EELE-----ERLEAGRPDAVFISAKTGEGLDELLEAIEEL 203 (204)
T ss_pred CCCEEEEEEccccCCh--HHHH-----HHhhcCCCceEEEEcCCCCCHHHHHHHHHhh
Confidence 4578888888543221 1111 1223446689999999999999999998765
No 208
>PRK03003 GTP-binding protein Der; Reviewed
Probab=85.15 E-value=1 Score=41.83 Aligned_cols=62 Identities=21% Similarity=0.027 Sum_probs=41.2
Q ss_pred CCCceeeeeeeecccc-cCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 23 FGDSLCARAFKVVHDK-HRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~-~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
.+.+++..++|.+... .........+.+........|+++.||++|.||++|++.|...+..
T Consensus 321 ~~~piIiV~NK~Dl~~~~~~~~~~~~i~~~l~~~~~~~~~~~SAk~g~gv~~lf~~i~~~~~~ 383 (472)
T PRK03003 321 AGRALVLAFNKWDLVDEDRRYYLEREIDRELAQVPWAPRVNISAKTGRAVDKLVPALETALES 383 (472)
T ss_pred cCCCEEEEEECcccCChhHHHHHHHHHHHhcccCCCCCEEEEECCCCCCHHHHHHHHHHHHHH
Confidence 4678999999965322 1111122333333333345799999999999999999999886653
No 209
>PTZ00369 Ras-like protein; Provisional
Probab=85.13 E-value=1.2 Score=35.58 Aligned_cols=59 Identities=15% Similarity=0.045 Sum_probs=37.8
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
+-|++...+|.+.... -++....... ..+....|++..||++|.||.++++.|.+.+..
T Consensus 110 ~~piiiv~nK~Dl~~~-~~i~~~~~~~-~~~~~~~~~~e~Sak~~~gi~~~~~~l~~~l~~ 168 (189)
T PTZ00369 110 RVPMILVGNKCDLDSE-RQVSTGEGQE-LAKSFGIPFLETSAKQRVNVDEAFYELVREIRK 168 (189)
T ss_pred CCCEEEEEECcccccc-cccCHHHHHH-HHHHhCCEEEEeeCCCCCCHHHHHHHHHHHHHH
Confidence 5588888899654221 1222222111 112223689999999999999999999877643
No 210
>TIGR00101 ureG urease accessory protein UreG. This model represents UreG, a GTP hydrolase that acts in the assembly of the nickel metallocenter of urease. It is found only in urease-positive species, although some urease-positive species (e.g. Bacillus subtilis) lack this protein. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel.
Probab=84.92 E-value=1.4 Score=36.00 Aligned_cols=27 Identities=15% Similarity=0.224 Sum_probs=23.8
Q ss_pred cCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 56 NHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
...|++..||++|.|++++++.|.++.
T Consensus 169 ~~~~i~~~Sa~~g~gi~el~~~i~~~~ 195 (199)
T TIGR00101 169 GEKPFIFTNLKTKEGLDTVIDWIEHYA 195 (199)
T ss_pred CCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence 357899999999999999999998754
No 211
>PRK14845 translation initiation factor IF-2; Provisional
Probab=84.82 E-value=6.4 Score=40.35 Aligned_cols=71 Identities=14% Similarity=0.224 Sum_probs=51.5
Q ss_pred ceEEEEEEEceEEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEc--CC---CCCccCcEEecCCCCCC
Q psy5461 115 GAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVT--GL---KRERGKDKRTRVIPKPT 189 (221)
Q Consensus 115 G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~--gl---~~~~~Gdtl~~~~~~p~ 189 (221)
+.++=++|..|++++|..|.-. .+ ..++.|..++ .....++++.+|+-|+|. |. .++..||++....+...
T Consensus 938 ~~IaG~~V~~G~i~~~~~l~r~-~~--~~iG~i~Slk-~~k~~V~ev~~G~ecgI~i~~~~~gr~~~~gD~l~~~i~~~~ 1013 (1049)
T PRK14845 938 PAIVGVEVLEGTLRVGVTLIKE-DG--MKVGTVRSIK-DRGENVKEAKAGKAVAIAIEGAILGRHVDEGETLYVDVPESH 1013 (1049)
T ss_pred CeEEEEEEeeCEEecCcEEEec-CC--EEEEEEchHh-ccCccccEeCCCCEEEEEEecccccCCCCCCCEEEEecCHHH
Confidence 7899999999999999877531 22 3345555554 344689999999999763 43 27889999988755543
No 212
>cd04101 RabL4 RabL4 (Rab-like4) subfamily. RabL4s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL4 lacks a prenylation site at the C-terminus. The specific function of RabL4 remains unknown.
Probab=84.81 E-value=1.6 Score=33.43 Aligned_cols=56 Identities=11% Similarity=0.045 Sum_probs=36.0
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+.|++...+|.+..+. .++.......- ......|++..||++|.|++++++.+.+.
T Consensus 107 ~~p~ilv~nK~Dl~~~-~~~~~~~~~~~-~~~~~~~~~~~Sa~~~~gi~~l~~~l~~~ 162 (164)
T cd04101 107 HMPGVLVGNKMDLADK-AEVTDAQAQAF-AQANQLKFFKTSALRGVGYEEPFESLARA 162 (164)
T ss_pred CCCEEEEEECcccccc-cCCCHHHHHHH-HHHcCCeEEEEeCCCCCChHHHHHHHHHH
Confidence 4678888889654222 23333222111 12223678999999999999999998764
No 213
>cd04164 trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance.
Probab=84.76 E-value=1.6 Score=32.80 Aligned_cols=51 Identities=12% Similarity=0.063 Sum_probs=36.3
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+.+++..++|++.-..... .......|++..||+++.|+++|++.|..++
T Consensus 106 ~~~~vi~v~nK~D~~~~~~~---------~~~~~~~~~~~~Sa~~~~~v~~l~~~l~~~~ 156 (157)
T cd04164 106 ADKPIIVVLNKSDLLPDSEL---------LSLLAGKPIIAISAKTGEGLDELKEALLELA 156 (157)
T ss_pred cCCCEEEEEEchhcCCcccc---------ccccCCCceEEEECCCCCCHHHHHHHHHHhh
Confidence 46788888888642221111 2344467899999999999999999988653
No 214
>cd04124 RabL2 RabL2 subfamily. RabL2 (Rab-like2) subfamily. RabL2s are novel Rab proteins identified recently which display features that are distinct from other Rabs, and have been termed Rab-like. RabL2 contains RabL2a and RabL2b, two very similar Rab proteins that share 98% sequence identity in humans. RabL2b maps to the subtelomeric region of chromosome 22q13.3 and RabL2a maps to 2q13, a region that suggests it is also a subtelomeric gene. Both genes are believed to be expressed ubiquitously, suggesting that RabL2s are the first example of duplicated genes in human proximal subtelomeric regions that are both expressed actively. Like other Rab-like proteins, RabL2s lack a prenylation site at the C-terminus. The specific functions of RabL2a and RabL2b remain unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-b
Probab=84.56 E-value=1.3 Score=34.21 Aligned_cols=55 Identities=20% Similarity=0.155 Sum_probs=36.8
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
+.|++...+|.+.++. ...+ ... ..+....|++..||++|.|++++++.+...+.
T Consensus 104 ~~p~ivv~nK~Dl~~~---~~~~-~~~-~~~~~~~~~~~~Sa~~~~gv~~l~~~l~~~~~ 158 (161)
T cd04124 104 EIPCIVVANKIDLDPS---VTQK-KFN-FAEKHNLPLYYVSAADGTNVVKLFQDAIKLAV 158 (161)
T ss_pred CCcEEEEEECccCchh---HHHH-HHH-HHHHcCCeEEEEeCCCCCCHHHHHHHHHHHHH
Confidence 5688889999654321 1111 111 11222468999999999999999999987654
No 215
>cd04127 Rab27A Rab27a subfamily. The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated
Probab=84.48 E-value=1.1 Score=35.10 Aligned_cols=57 Identities=14% Similarity=0.157 Sum_probs=36.5
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+.|++.-.+|.+.... -++....... ..+...+|++..||++|.|++++++.|.+.+
T Consensus 120 ~~piiiv~nK~Dl~~~-~~v~~~~~~~-~~~~~~~~~~e~Sak~~~~v~~l~~~l~~~~ 176 (180)
T cd04127 120 NPDIVLCGNKADLEDQ-RQVSEEQAKA-LADKYGIPYFETSAATGTNVEKAVERLLDLV 176 (180)
T ss_pred CCcEEEEEeCccchhc-CccCHHHHHH-HHHHcCCeEEEEeCCCCCCHHHHHHHHHHHH
Confidence 4467777888553222 2333333322 2222246899999999999999999987643
No 216
>PRK09435 membrane ATPase/protein kinase; Provisional
Probab=84.37 E-value=0.78 Score=40.79 Aligned_cols=27 Identities=30% Similarity=0.416 Sum_probs=25.1
Q ss_pred ceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 58 VPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 58 ~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
.||+..||+++.||++|++.|.+++|.
T Consensus 235 ~pVi~vSA~~g~GIdeL~~~I~~~~~~ 261 (332)
T PRK09435 235 PPVLTCSALEGEGIDEIWQAIEDHRAA 261 (332)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHH
Confidence 689999999999999999999998764
No 217
>COG1160 Predicted GTPases [General function prediction only]
Probab=84.32 E-value=1.1 Score=41.19 Aligned_cols=61 Identities=16% Similarity=0.121 Sum_probs=43.2
Q ss_pred CCCCceeeeeeeec-ccc--cCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 22 HFGDSLCARAFKVV-HDK--HRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 22 ~~~~~~~~~vfk~~-~d~--~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+...+++..++|-+ .++ .........+++....-...|+++.||++|.|+..|++++..-.
T Consensus 287 ~~g~~~vIvvNKWDl~~~~~~~~~~~k~~i~~~l~~l~~a~i~~iSA~~~~~i~~l~~~i~~~~ 350 (444)
T COG1160 287 EAGRGIVIVVNKWDLVEEDEATMEEFKKKLRRKLPFLDFAPIVFISALTGQGLDKLFEAIKEIY 350 (444)
T ss_pred HcCCCeEEEEEccccCCchhhHHHHHHHHHHHHhccccCCeEEEEEecCCCChHHHHHHHHHHH
Confidence 35778999999965 333 22233344555544444677999999999999999999987644
No 218
>smart00177 ARF ARF-like small GTPases; ARF, ADP-ribosylation factor. Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).
Probab=84.09 E-value=1.9 Score=33.98 Aligned_cols=56 Identities=11% Similarity=-0.006 Sum_probs=34.6
Q ss_pred CCceeeeeeeecccccCCcchHHHHhh--cc--ccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYS--GA--FKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~--~~--~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+-|++...+|.+.... .....+.+ +. .....+.++..||++|.||.++++.|.+.+
T Consensus 114 ~~piilv~NK~Dl~~~---~~~~~i~~~~~~~~~~~~~~~~~~~Sa~~g~gv~e~~~~l~~~~ 173 (175)
T smart00177 114 DAVILVFANKQDLPDA---MKAAEITEKLGLHSIRDRNWYIQPTCATSGDGLYEGLTWLSNNL 173 (175)
T ss_pred CCcEEEEEeCcCcccC---CCHHHHHHHhCccccCCCcEEEEEeeCCCCCCHHHHHHHHHHHh
Confidence 4578888899653221 11222222 11 112234466799999999999999987653
No 219
>cd01881 Obg_like The Obg-like subfamily consists of five well-delimited, ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210, and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and Ygr210) are characterized by a distinct glycine-rich motif immediately following the Walker B motif (G3 box). Obg/CgtA is an essential gene that is involved in the initiation of sporulation and DNA replication in the bacteria Caulobacter and Bacillus, but its exact molecular role is unknown. Furthermore, several OBG family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. Nog1 is a nucleolar protein that might function in ribosome assembly. The DRG and Nog1 subfamilies are ubiquitous in archaea and eukaryotes, the Ygr210 subfamily is present in archaea and fungi, and the Obg and YyaF/YchF subfamilies are ubiquitous in bacteria and eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
Probab=84.08 E-value=1.5 Score=33.76 Aligned_cols=56 Identities=14% Similarity=0.076 Sum_probs=35.7
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
..|++..++|++..... ......... .......+++..||+++.|+++|++.+...
T Consensus 120 ~~p~ivv~NK~Dl~~~~-~~~~~~~~~-~~~~~~~~~~~~Sa~~~~gl~~l~~~l~~~ 175 (176)
T cd01881 120 AKPVIYVLNKIDLDDAE-ELEEELVRE-LALEEGAEVVPISAKTEEGLDELIRAIYEL 175 (176)
T ss_pred hCCeEEEEEchhcCchh-HHHHHHHHH-HhcCCCCCEEEEehhhhcCHHHHHHHHHhh
Confidence 56888888996543221 111111111 122234678999999999999999998764
No 220
>cd04110 Rab35 Rab35 subfamily. Rab35 is one of several Rab proteins to be found to participate in the regulation of osteoclast cells in rats. In addition, Rab35 has been identified as a protein that interacts with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in human cells. Overexpression of NPM-ALK is a key oncogenic event in some anaplastic large-cell lymphomas; since Rab35 interacts with N|PM-ALK, it may provide a target for cancer treatments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is
Probab=84.08 E-value=1.3 Score=35.83 Aligned_cols=57 Identities=16% Similarity=0.145 Sum_probs=37.3
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+-|++...+|.+..+. ..+......+-. +....+++..||++|.||.++++.|...+
T Consensus 110 ~~piivVgNK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~e~Sa~~~~gi~~lf~~l~~~~ 166 (199)
T cd04110 110 DVCKVLVGNKNDDPER-KVVETEDAYKFA-GQMGISLFETSAKENINVEEMFNCITELV 166 (199)
T ss_pred CCCEEEEEECcccccc-cccCHHHHHHHH-HHcCCEEEEEECCCCcCHHHHHHHHHHHH
Confidence 4577788888553322 223333322222 22337899999999999999999998876
No 221
>PTZ00133 ADP-ribosylation factor; Provisional
Probab=83.96 E-value=1.7 Score=34.63 Aligned_cols=56 Identities=11% Similarity=0.022 Sum_probs=35.1
Q ss_pred CCceeeeeeeecccccCCcchHHHHhh--cc--ccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYS--GA--FKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~--~~--~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+.|++...+|.+.... .....+.. +. .+...++++..||++|.||+++++.|.+.+
T Consensus 118 ~~piilv~NK~Dl~~~---~~~~~i~~~l~~~~~~~~~~~~~~~Sa~tg~gv~e~~~~l~~~i 177 (182)
T PTZ00133 118 DAVLLVFANKQDLPNA---MSTTEVTEKLGLHSVRQRNWYIQGCCATTAQGLYEGLDWLSANI 177 (182)
T ss_pred CCCEEEEEeCCCCCCC---CCHHHHHHHhCCCcccCCcEEEEeeeCCCCCCHHHHHHHHHHHH
Confidence 4688888899654221 11122211 11 222235677899999999999999998653
No 222
>PLN00223 ADP-ribosylation factor; Provisional
Probab=83.81 E-value=2 Score=34.25 Aligned_cols=56 Identities=13% Similarity=0.036 Sum_probs=35.8
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhc--cc--cccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSG--AF--KKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~--~~--~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+-|++...+|.+.... .....+.+. .. +.....++.+||++|.||.++++.|.+.+
T Consensus 118 ~~piilv~NK~Dl~~~---~~~~~~~~~l~l~~~~~~~~~~~~~Sa~~g~gv~e~~~~l~~~~ 177 (181)
T PLN00223 118 DAVLLVFANKQDLPNA---MNAAEITDKLGLHSLRQRHWYIQSTCATSGEGLYEGLDWLSNNI 177 (181)
T ss_pred CCCEEEEEECCCCCCC---CCHHHHHHHhCccccCCCceEEEeccCCCCCCHHHHHHHHHHHH
Confidence 4688899999654322 222333321 11 12234566799999999999999997654
No 223
>smart00174 RHO Rho (Ras homology) subfamily of Ras-like small GTPases. Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.
Probab=83.72 E-value=1.9 Score=33.37 Aligned_cols=60 Identities=15% Similarity=0.097 Sum_probs=38.2
Q ss_pred CCCceeeeeeeecccccCC-----------cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRG-----------AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g-----------~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+.|++...+|.+...... .++.....+...+....+.+..||++|.||+++++.+...+
T Consensus 101 ~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~e~Sa~~~~~v~~lf~~l~~~~ 171 (174)
T smart00174 101 PNTPIILVGTKLDLREDKSTLRELSKQKQEPVTYEQGEALAKRIGAVKYLECSALTQEGVREVFEEAIRAA 171 (174)
T ss_pred CCCCEEEEecChhhhhChhhhhhhhcccCCCccHHHHHHHHHHcCCcEEEEecCCCCCCHHHHHHHHHHHh
Confidence 3678888889965332111 13333322222233345788899999999999999988654
No 224
>cd04123 Rab21 Rab21 subfamily. The localization and function of Rab21 are not clearly defined, with conflicting data reported. Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker. More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site
Probab=83.69 E-value=1.7 Score=32.87 Aligned_cols=56 Identities=16% Similarity=0.061 Sum_probs=37.6
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+.|++...+|.+.... -++....+.+-. +....+++..|+++|.|++++++.+.+.
T Consensus 105 ~~piiiv~nK~D~~~~-~~~~~~~~~~~~-~~~~~~~~~~s~~~~~gi~~~~~~l~~~ 160 (162)
T cd04123 105 NISLVIVGNKIDLERQ-RVVSKSEAEEYA-KSVGAKHFETSAKTGKGIEELFLSLAKR 160 (162)
T ss_pred CCeEEEEEECcccccc-cCCCHHHHHHHH-HHcCCEEEEEeCCCCCCHHHHHHHHHHH
Confidence 5688888999654321 233333333322 2234678999999999999999998764
No 225
>cd04171 SelB SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryo
Probab=83.22 E-value=1.3 Score=33.77 Aligned_cols=55 Identities=11% Similarity=-0.039 Sum_probs=34.6
Q ss_pred ceeeeeeeecccccC-CcchHHHHhhccccc--cCceeEecCCCccccHHHHHHHHHh
Q psy5461 26 SLCARAFKVVHDKHR-GAVTFFRIYSGAFKK--NHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 26 ~~~~~vfk~~~d~~~-g~l~~~~l~~~~~~~--~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
+++..++|++..... -+.....+.+..... ...|++..||++|.|+++|++.+..
T Consensus 106 ~~ilv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~~v~~l~~~l~~ 163 (164)
T cd04171 106 RGLVVLTKADLVDEDWLELVEEEIRELLAGTFLADAPIFPVSAVTGEGIEELKEYLDE 163 (164)
T ss_pred cEEEEEECccccCHHHHHHHHHHHHHHHHhcCcCCCcEEEEeCCCCcCHHHHHHHHhh
Confidence 788999996432210 011222333322221 3478999999999999999998864
No 226
>PTZ00099 rab6; Provisional
Probab=82.99 E-value=1.4 Score=35.12 Aligned_cols=61 Identities=15% Similarity=0.018 Sum_probs=38.3
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPT 86 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~ 86 (221)
+-+++...+|++.... -++........... ...+++-.||++|.||.++++.|...+|...
T Consensus 85 ~~piilVgNK~DL~~~-~~v~~~e~~~~~~~-~~~~~~e~SAk~g~nV~~lf~~l~~~l~~~~ 145 (176)
T PTZ00099 85 DVIIALVGNKTDLGDL-RKVTYEEGMQKAQE-YNTMFHETSAKAGHNIKVLFKKIAAKLPNLD 145 (176)
T ss_pred CCeEEEEEECcccccc-cCCCHHHHHHHHHH-cCCEEEEEECCCCCCHHHHHHHHHHHHHhcc
Confidence 3466778888653221 12333222221111 2235778999999999999999999987643
No 227
>TIGR00073 hypB hydrogenase accessory protein HypB. HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.
Probab=82.88 E-value=1.7 Score=35.57 Aligned_cols=55 Identities=7% Similarity=-0.044 Sum_probs=34.0
Q ss_pred ceeeeeeeecccccCCcchHHHHhhccc-cccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 26 SLCARAFKVVHDKHRGAVTFFRIYSGAF-KKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 26 ~~~~~vfk~~~d~~~g~l~~~~l~~~~~-~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+.+..++|++..... ......+.+... .....|++..||++|.|++++++.+.++
T Consensus 150 a~iiv~NK~Dl~~~~-~~~~~~~~~~l~~~~~~~~i~~~Sa~~g~gv~~l~~~i~~~ 205 (207)
T TIGR00073 150 ADLIVINKADLAEAV-GFDVEKMKADAKKINPEAEIILMSLKTGEGLDEWLEFLEGQ 205 (207)
T ss_pred CCEEEEEHHHccccc-hhhHHHHHHHHHHhCCCCCEEEEECCCCCCHHHHHHHHHHh
Confidence 557888996532211 111112221111 1134789999999999999999999865
No 228
>cd00157 Rho Rho (Ras homology) family. Members of the Rho family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho protein
Probab=82.86 E-value=2 Score=33.04 Aligned_cols=57 Identities=11% Similarity=0.019 Sum_probs=36.9
Q ss_pred CCceeeeeeeecccccCC----------cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 24 GDSLCARAFKVVHDKHRG----------AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g----------~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
..|++...+|.+.-.... .+......+-.......+++..||++|.|+.++++.|..
T Consensus 104 ~~p~ivv~nK~Dl~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~Sa~~~~gi~~l~~~i~~ 170 (171)
T cd00157 104 NVPIILVGTKIDLRDDENTLKKLEKGKEPITPEEGEKLAKEIGAIGYMECSALTQEGVKEVFEEAIR 170 (171)
T ss_pred CCCEEEEEccHHhhhchhhhhhcccCCCccCHHHHHHHHHHhCCeEEEEeecCCCCCHHHHHHHHhh
Confidence 578888889965322211 222333333222333448999999999999999999875
No 229
>cd04112 Rab26 Rab26 subfamily. First identified in rat pancreatic acinar cells, Rab26 is believed to play a role in recruiting mature granules to the plasma membrane upon beta-adrenergic stimulation. Rab26 belongs to the Rab functional group III, which are considered key regulators of intracellular vesicle transport during exocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
Probab=82.75 E-value=1.4 Score=35.30 Aligned_cols=60 Identities=15% Similarity=-0.011 Sum_probs=39.8
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
+-|++...+|.+.... .++.......- .+....|++..||++|.|+++|++.|...++..
T Consensus 106 ~~piiiv~NK~Dl~~~-~~~~~~~~~~l-~~~~~~~~~e~Sa~~~~~v~~l~~~l~~~~~~~ 165 (191)
T cd04112 106 DVVIMLLGNKADMSGE-RVVKREDGERL-AKEYGVPFMETSAKTGLNVELAFTAVAKELKHR 165 (191)
T ss_pred CCcEEEEEEcccchhc-cccCHHHHHHH-HHHcCCeEEEEeCCCCCCHHHHHHHHHHHHHHh
Confidence 4588888899654322 12222222221 222346899999999999999999999887653
No 230
>PRK12298 obgE GTPase CgtA; Reviewed
Probab=82.39 E-value=1.8 Score=39.31 Aligned_cols=59 Identities=14% Similarity=-0.050 Sum_probs=37.8
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhcccc-ccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFK-KNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~-~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
+.|.+..++|++... .+.....+.+-... +...+++..||+++.||++|++.|.+++|.
T Consensus 275 ~kP~IlVlNKiDl~~--~~el~~~l~~l~~~~~~~~~Vi~ISA~tg~GIdeLl~~I~~~L~~ 334 (390)
T PRK12298 275 EKPRWLVFNKIDLLD--EEEAEERAKAIVEALGWEGPVYLISAASGLGVKELCWDLMTFIEE 334 (390)
T ss_pred CCCEEEEEeCCccCC--hHHHHHHHHHHHHHhCCCCCEEEEECCCCcCHHHHHHHHHHHhhh
Confidence 578888999965321 11111222111111 112368899999999999999999999875
No 231
>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA. EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability.
Probab=82.33 E-value=4.3 Score=36.82 Aligned_cols=58 Identities=24% Similarity=0.280 Sum_probs=40.6
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPT 86 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~ 86 (221)
.+.|++..++|++...... . ...++ +-+.-+++..||.+|.|+.+|++.+...+|...
T Consensus 106 ~~~piilVvNK~D~~~~~~-~-~~~~~----~lg~~~~~~vSa~~g~gv~~ll~~i~~~l~~~~ 163 (429)
T TIGR03594 106 SGKPVILVANKIDGKKEDA-V-AAEFY----SLGFGEPIPISAEHGRGIGDLLDAILELLPEEE 163 (429)
T ss_pred hCCCEEEEEECccCCcccc-c-HHHHH----hcCCCCeEEEeCCcCCChHHHHHHHHHhcCccc
Confidence 4678999999976433211 1 11222 223446889999999999999999999997743
No 232
>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]
Probab=82.31 E-value=1.3 Score=38.80 Aligned_cols=53 Identities=23% Similarity=0.176 Sum_probs=37.3
Q ss_pred eeeeeecccccCCcchHHHHhhcc--------ccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 29 ARAFKVVHDKHRGAVTFFRIYSGA--------FKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 29 ~~vfk~~~d~~~g~l~~~~l~~~~--------~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
-.||| .|..-.+.++..++.+. .++-..||+-.||.+|.||++|+++|.++.-
T Consensus 194 ~vINK--aD~~~A~~a~r~l~~al~~~~~~~~~~~W~ppv~~t~A~~g~Gi~~L~~ai~~h~~ 254 (323)
T COG1703 194 IVINK--ADRKGAEKAARELRSALDLLREVWRENGWRPPVVTTSALEGEGIDELWDAIEDHRK 254 (323)
T ss_pred eeEec--cChhhHHHHHHHHHHHHHhhcccccccCCCCceeEeeeccCCCHHHHHHHHHHHHH
Confidence 45777 56544455554444433 2234679999999999999999999998753
No 233
>cd04140 ARHI_like ARHI subfamily. ARHI (A Ras homolog member I) is a member of the Ras family with several unique structural and functional properties. ARHI is expressed in normal human ovarian and breast tissue, but its expression is decreased or eliminated in breast and ovarian cancer. ARHI contains an N-terminal extension of 34 residues (human) that is required to retain its tumor suppressive activity. Unlike most other Ras family members, ARHI is maintained in the constitutively active (GTP-bound) state in resting cells and has modest GTPase activity. ARHI inhibits STAT3 (signal transducers and activators of transcription 3), a latent transcription factor whose abnormal activation plays a critical role in oncogenesis. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to
Probab=81.98 E-value=2.3 Score=32.82 Aligned_cols=57 Identities=14% Similarity=0.036 Sum_probs=35.9
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
.+-|++...+|.+..+. -++.......-..+ ...+++..||++|.||+++++.|.++
T Consensus 107 ~~~piilv~nK~Dl~~~-~~v~~~~~~~~~~~-~~~~~~e~SA~~g~~v~~~f~~l~~~ 163 (165)
T cd04140 107 EKIPIMLVGNKCDESHK-REVSSNEGAACATE-WNCAFMETSAKTNHNVQELFQELLNL 163 (165)
T ss_pred CCCCEEEEEECcccccc-CeecHHHHHHHHHH-hCCcEEEeecCCCCCHHHHHHHHHhc
Confidence 34688888889654321 22333222211111 23578899999999999999998764
No 234
>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed
Probab=81.96 E-value=1.2 Score=43.54 Aligned_cols=62 Identities=16% Similarity=-0.040 Sum_probs=40.6
Q ss_pred CCCceeeeeeeecc-cccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 23 FGDSLCARAFKVVH-DKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~-d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
.+.|++..++|.+. ++...+.....+..........|+++.||++|.||.+|++.+.+..+.
T Consensus 560 ~~~piIiV~NK~DL~~~~~~~~~~~~~~~~l~~~~~~~ii~iSAktg~gv~~L~~~i~~~~~~ 622 (712)
T PRK09518 560 AGRALVLVFNKWDLMDEFRRQRLERLWKTEFDRVTWARRVNLSAKTGWHTNRLAPAMQEALES 622 (712)
T ss_pred cCCCEEEEEEchhcCChhHHHHHHHHHHHhccCCCCCCEEEEECCCCCCHHHHHHHHHHHHHH
Confidence 46789999999653 221111112222222222235688999999999999999999988775
No 235
>cd04109 Rab28 Rab28 subfamily. First identified in maize, Rab28 has been shown to be a late embryogenesis-abundant (Lea) protein that is regulated by the plant hormone abcisic acid (ABA). In Arabidopsis, Rab28 is expressed during embryo development and is generally restricted to provascular tissues in mature embryos. Unlike maize Rab28, it is not ABA-inducible. Characterization of the human Rab28 homolog revealed two isoforms, which differ by a 95-base pair insertion, producing an alternative sequence for the 30 amino acids at the C-terminus. The two human isoforms are presumbly the result of alternative splicing. Since they differ at the C-terminus but not in the GTP-binding region, they are predicted to be targeted to different cellular locations. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs
Probab=81.85 E-value=1.7 Score=35.58 Aligned_cols=57 Identities=14% Similarity=-0.063 Sum_probs=37.0
Q ss_pred CceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 25 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 25 ~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
.+++...+|.+... .-+++.+....-. +....|.+..||++|.||+++++.|...+-
T Consensus 110 ~piilVgNK~DL~~-~~~v~~~~~~~~~-~~~~~~~~~iSAktg~gv~~lf~~l~~~l~ 166 (215)
T cd04109 110 PLVVLVGNKTDLEH-NRTVKDDKHARFA-QANGMESCLVSAKTGDRVNLLFQQLAAELL 166 (215)
T ss_pred ceEEEEEECccccc-ccccCHHHHHHHH-HHcCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence 35777888965322 1233333333222 222357888999999999999999998764
No 236
>PLN03110 Rab GTPase; Provisional
Probab=81.61 E-value=1.9 Score=35.45 Aligned_cols=60 Identities=15% Similarity=0.005 Sum_probs=40.5
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
.+-|++...+|++..... ++..+... ........|++..||++|.||+++++.|.+.+..
T Consensus 116 ~~~piiiv~nK~Dl~~~~-~~~~~~~~-~l~~~~~~~~~e~SA~~g~~v~~lf~~l~~~i~~ 175 (216)
T PLN03110 116 SNIVIMMAGNKSDLNHLR-SVAEEDGQ-ALAEKEGLSFLETSALEATNVEKAFQTILLEIYH 175 (216)
T ss_pred CCCeEEEEEEChhccccc-CCCHHHHH-HHHHHcCCEEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence 356788888997643321 23322222 2223345789999999999999999999887754
No 237
>cd04132 Rho4_like Rho4-like subfamily. Rho4 is a GTPase that controls septum degradation by regulating secretion of Eng1 or Agn1 during cytokinesis. Rho4 also plays a role in cell morphogenesis. Rho4 regulates septation and cell morphology by controlling the actin cytoskeleton and cytoplasmic microtubules. The localization of Rho4 is modulated by Rdi1, which may function as a GDI, and by Rga9, which is believed to function as a GAP. In S. pombe, both Rho4 deletion and Rho4 overexpression result in a defective cell wall, suggesting a role for Rho4 in maintaining cell wall integrity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.
Probab=81.60 E-value=2.7 Score=33.13 Aligned_cols=60 Identities=20% Similarity=0.098 Sum_probs=39.3
Q ss_pred CCceeeeeeeeccccc---CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 24 GDSLCARAFKVVHDKH---RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~---~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
+.|++...+|.+..+. ...+......+-.......|++..||++|.||.++++.+...+.
T Consensus 105 ~~piilv~nK~Dl~~~~~~~~~v~~~~~~~~~~~~~~~~~~e~Sa~~~~~v~~~f~~l~~~~~ 167 (187)
T cd04132 105 GTPIMLVGLKTDLRKDKNLDRKVTPAQAESVAKKQGAFAYLECSAKTMENVEEVFDTAIEEAL 167 (187)
T ss_pred CCCEEEEEeChhhhhCccccCCcCHHHHHHHHHHcCCcEEEEccCCCCCCHHHHHHHHHHHHH
Confidence 5688888899653221 11233433333222333448899999999999999999887664
No 238
>cd01895 EngA2 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.
Probab=81.57 E-value=2.5 Score=32.15 Aligned_cols=58 Identities=22% Similarity=0.077 Sum_probs=36.1
Q ss_pred CCCceeeeeeeecccccC---CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 23 FGDSLCARAFKVVHDKHR---GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~---g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
.+.+++..++|.+..... .+.....+.+........|++..||+++.|+.++++.+..
T Consensus 112 ~~~~~iiv~nK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~~i~~~~~~l~~ 172 (174)
T cd01895 112 EGKALVIVVNKWDLVEKDSKTMKEFKKEIRRKLPFLDYAPIVFISALTGQGVDKLFDAIDE 172 (174)
T ss_pred cCCCEEEEEeccccCCccHHHHHHHHHHHHhhcccccCCceEEEeccCCCCHHHHHHHHHH
Confidence 357888888996422211 1111223322222223478999999999999999998865
No 239
>cd04167 Snu114p Snu114p subfamily. Snu114p is one of several proteins that make up the U5 small nuclear ribonucleoprotein (snRNP) particle. U5 is a component of the spliceosome, which catalyzes the splicing of pre-mRNA to remove introns. Snu114p is homologous to EF-2, but typically contains an additional N-terminal domain not found in Ef-2. This protein is part of the GTP translation factor family and the Ras superfamily, characterized by five G-box motifs.
Probab=81.32 E-value=0.89 Score=37.23 Aligned_cols=26 Identities=38% Similarity=0.459 Sum_probs=24.4
Q ss_pred eEecCCCccccHH--------HHHHHHHhhCCCC
Q psy5461 60 VLCGSSYKNIGVQ--------KLMDAIVDILPSP 85 (221)
Q Consensus 60 v~~gSa~~~~Gi~--------~LLd~I~~~~PsP 85 (221)
|+++||+.+|+.. +|||+|.+.+|+|
T Consensus 180 v~~~s~~~~w~~~~~~~~~~~~~~~~~~~~~~~~ 213 (213)
T cd04167 180 VCFASSKFGFCFTLESFAKKYGLVDSIVSNIPSP 213 (213)
T ss_pred EEEEecCCCeEEecHHHHhhhhHHHHHHhhCCCC
Confidence 8899999999887 9999999999997
No 240
>PRK13768 GTPase; Provisional
Probab=81.19 E-value=2.9 Score=35.49 Aligned_cols=29 Identities=24% Similarity=0.242 Sum_probs=26.4
Q ss_pred CceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 57 HVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 57 ~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
..+++..|++++.|+++|++.|.+++|+=
T Consensus 221 ~~~vi~iSa~~~~gl~~L~~~I~~~l~~~ 249 (253)
T PRK13768 221 PVRVIPVSAKTGEGFDELYAAIQEVFCGG 249 (253)
T ss_pred CCcEEEEECCCCcCHHHHHHHHHHHcCCC
Confidence 46899999999999999999999999874
No 241
>cd04163 Era Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.
Probab=81.13 E-value=2.8 Score=31.45 Aligned_cols=57 Identities=16% Similarity=0.140 Sum_probs=36.1
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhcccc-ccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFK-KNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~-~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
..+++..++|++......++ ......... ....|++..|++++.|+++|++.|.+++
T Consensus 111 ~~~~iiv~nK~Dl~~~~~~~--~~~~~~~~~~~~~~~~~~~s~~~~~~~~~l~~~l~~~~ 168 (168)
T cd04163 111 KTPVILVLNKIDLVKDKEDL--LPLLEKLKELGPFAEIFPISALKGENVDELLEEIVKYL 168 (168)
T ss_pred CCCEEEEEEchhccccHHHH--HHHHHHHHhccCCCceEEEEeccCCChHHHHHHHHhhC
Confidence 46788888886432111111 222222222 2256899999999999999999997653
No 242
>cd04125 RabA_like RabA-like subfamily. RabA was first identified in D. discoideum, where its expression levels were compared to other Rabs in growing and developing cells. The RabA mRNA levels were below the level of detection by Northern blot analysis, suggesting a very low level of expression. The function of RabA remains unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
Probab=80.71 E-value=2 Score=34.09 Aligned_cols=59 Identities=15% Similarity=0.008 Sum_probs=37.6
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
+.+++...+|.+..+. ..+.......- .+...+|++..||++|.||+++++.+.+.+..
T Consensus 105 ~~~~ivv~nK~Dl~~~-~~v~~~~~~~~-~~~~~~~~~evSa~~~~~i~~~f~~l~~~~~~ 163 (188)
T cd04125 105 NVIKVIVANKSDLVNN-KVVDSNIAKSF-CDSLNIPFFETSAKQSINVEEAFILLVKLIIK 163 (188)
T ss_pred CCeEEEEEECCCCccc-ccCCHHHHHHH-HHHcCCeEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence 4578888888653221 22222222221 12223489999999999999999998887754
No 243
>cd04141 Rit_Rin_Ric Rit/Rin/Ric subfamily. Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics. These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains. Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42. Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells. Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42. This ternary complex is proposed to have physiological function in processes such as tumorigenesis. Activated Ric is likely to sign
Probab=80.49 E-value=2 Score=33.76 Aligned_cols=58 Identities=16% Similarity=0.008 Sum_probs=39.4
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+-|++...+|.+.... .+++.+....-. +....|++..||++|.||+++++.+...+
T Consensus 106 ~~~piilvgNK~Dl~~~-~~v~~~~~~~~a-~~~~~~~~e~Sa~~~~~v~~~f~~l~~~~ 163 (172)
T cd04141 106 EDIPLVLVGNKVDLESQ-RQVTTEEGRNLA-REFNCPFFETSAALRHYIDDAFHGLVREI 163 (172)
T ss_pred CCCCEEEEEEChhhhhc-CccCHHHHHHHH-HHhCCEEEEEecCCCCCHHHHHHHHHHHH
Confidence 35688899999654322 234443333222 22346899999999999999999988654
No 244
>cd00882 Ras_like_GTPase Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulate initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Memb
Probab=80.48 E-value=3.5 Score=29.84 Aligned_cols=56 Identities=14% Similarity=0.035 Sum_probs=36.1
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHH
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIV 79 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~ 79 (221)
...+++..++|++........ ..............|++..|+.++.|+.++++.|.
T Consensus 101 ~~~~~ivv~nk~D~~~~~~~~-~~~~~~~~~~~~~~~~~~~s~~~~~~i~~~~~~l~ 156 (157)
T cd00882 101 ENIPIILVGNKIDLPEERVVS-EEELAEQLAKELGVPYFETSAKTGENVEELFEELA 156 (157)
T ss_pred CCCcEEEEEeccccccccchH-HHHHHHHHHhhcCCcEEEEecCCCCChHHHHHHHh
Confidence 467888889996533221111 11112222333467899999999999999999875
No 245
>cd04137 RheB Rheb (Ras Homolog Enriched in Brain) subfamily. Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that le
Probab=80.38 E-value=2.2 Score=33.41 Aligned_cols=58 Identities=12% Similarity=0.016 Sum_probs=37.6
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
+.|++..++|.+.... ..+....+.... +....|++..||++|.|+.++++.+.+.+.
T Consensus 106 ~~p~ilv~NK~Dl~~~-~~~~~~~~~~~~-~~~~~~~~~~Sa~~~~gv~~l~~~l~~~~~ 163 (180)
T cd04137 106 SVPIVLVGNKSDLHTQ-RQVSTEEGKELA-ESWGAAFLESSARENENVEEAFELLIEEIE 163 (180)
T ss_pred CCCEEEEEEchhhhhc-CccCHHHHHHHH-HHcCCeEEEEeCCCCCCHHHHHHHHHHHHH
Confidence 5688999999664321 222222222111 112257899999999999999999987653
No 246
>cd01849 YlqF_related_GTPase YlqF-related GTPases. These proteins are found in bacteria, eukaryotes, and archaea. They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases.
Probab=80.31 E-value=2.8 Score=32.42 Aligned_cols=59 Identities=12% Similarity=-0.072 Sum_probs=37.5
Q ss_pred CCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 22 HFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
....|++..++|++.-+. .++ ........+....++++.||+++.|+++|++.|.+..+
T Consensus 27 ~~~~p~IiVlNK~Dl~~~-~~~--~~~~~~~~~~~~~~ii~vSa~~~~gi~~L~~~i~~~~~ 85 (155)
T cd01849 27 EKGKKLILVLNKADLVPK-EVL--RKWLAYLRHSYPTIPFKISATNGQGIEKKESAFTKQTN 85 (155)
T ss_pred cCCCCEEEEEechhcCCH-HHH--HHHHHHHHhhCCceEEEEeccCCcChhhHHHHHHHHhH
Confidence 346799999999653111 111 11111111112467899999999999999999987643
No 247
>cd04130 Wrch_1 Wrch-1 subfamily. Wrch-1 (Wnt-1 responsive Cdc42 homolog) is a Rho family GTPase that shares significant sequence and functional similarity with Cdc42. Wrch-1 was first identified in mouse mammary epithelial cells, where its transcription is upregulated in Wnt-1 transformation. Wrch-1 contains N- and C-terminal extensions relative to cdc42, suggesting potential differences in cellular localization and function. The Wrch-1 N-terminal extension contains putative SH3 domain-binding motifs and has been shown to bind the SH3 domain-containing protein Grb2, which increases the level of active Wrch-1 in cells. Unlike Cdc42, which localizes to the cytosol and perinuclear membranes, Wrch-1 localizes extensively with the plasma membrane and endosomes. The membrane association, localization, and biological activity of Wrch-1 indicate an atypical model of regulation distinct from other Rho family GTPases. Most Rho proteins contain a lipid modification site at the C-terminus,
Probab=80.18 E-value=2.9 Score=32.60 Aligned_cols=57 Identities=11% Similarity=-0.013 Sum_probs=35.8
Q ss_pred CCceeeeeeeecccccC-----------CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 24 GDSLCARAFKVVHDKHR-----------GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~-----------g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
+-|++.-.+|.+..+.. -++..+....-..+....+++..||++|.||+++++.+..
T Consensus 104 ~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~a~~~~~~~~~e~Sa~~~~~v~~lf~~~~~ 171 (173)
T cd04130 104 KAPIILVGTQADLRTDVNVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSALTQKNLKEVFDTAIL 171 (173)
T ss_pred CCCEEEEeeChhhccChhHHHHHhhcCCCCcCHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHHHHHHh
Confidence 56788888886532211 1233333332222223447999999999999999998763
No 248
>cd01879 FeoB Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.
Probab=79.73 E-value=2.3 Score=32.08 Aligned_cols=55 Identities=22% Similarity=0.258 Sum_probs=36.3
Q ss_pred CCCceeeeeeeeccc-ccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 23 FGDSLCARAFKVVHD-KHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d-~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
.+.|++..++|++.. ...-......+ .+....|++..||.+|.|+.++++.+...
T Consensus 100 ~~~~~iiv~NK~Dl~~~~~~~~~~~~~----~~~~~~~~~~iSa~~~~~~~~l~~~l~~~ 155 (158)
T cd01879 100 LGLPVVVALNMIDEAEKRGIKIDLDKL----SELLGVPVVPTSARKGEGIDELKDAIAEL 155 (158)
T ss_pred cCCCEEEEEehhhhcccccchhhHHHH----HHhhCCCeEEEEccCCCCHHHHHHHHHHH
Confidence 467899999997532 21111112222 12223689999999999999999998865
No 249
>smart00178 SAR Sar1p-like members of the Ras-family of small GTPases. Yeast SAR1 is an essential gene required for transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus.
Probab=79.42 E-value=4.6 Score=32.05 Aligned_cols=55 Identities=9% Similarity=-0.082 Sum_probs=37.0
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccc-----------cccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAF-----------KKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~-----------~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+.|++...+|.+.. ..+..+.+++... .....-++..||++|.|++++++.|.+.
T Consensus 118 ~~piliv~NK~Dl~---~~~~~~~i~~~l~l~~~~~~~~~~~~~~~~i~~~Sa~~~~g~~~~~~wl~~~ 183 (184)
T smart00178 118 TVPFLILGNKIDAP---YAASEDELRYALGLTNTTGSKGKVGVRPLEVFMCSVVRRMGYGEGFKWLSQY 183 (184)
T ss_pred CCCEEEEEeCcccc---CCCCHHHHHHHcCCCcccccccccCCceeEEEEeecccCCChHHHHHHHHhh
Confidence 56889999995532 2344444443321 1123348999999999999999999764
No 250
>PF00025 Arf: ADP-ribosylation factor family The prints entry specific to Sar1 proteins The Prosite entry specific to Sar1 proteins; InterPro: IPR006689 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. This entry represents a branch of the small GTPase superfamily that includes the ADP ribosylation factor Arf, Arl (Arf-like), Arp (Arf-related proteins) and the remotely related Sar (Secretion-associated and Ras-related) proteins. Arf proteins are major regulators of vesicle biogenesis in intracellular traffic []. They cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. The classical structural GDP/GTP switch is characterised by conformational changes at the so-called switch 1 and switch 2 regions, which bind tightly to the gamma-phosphate of GTP but poorly or not at all to the GDP nucleotide. Structural studies of Arf1 and Arf6 have revealed that although these proteins feature the switch 1 and 2 conformational changes, they depart from other small GTP-binding proteins in that they use an additional, unique switch to propagate structural information from one side of the protein to the other. The GDP/GTP structural cycles of human Arf1 and Arf6 feature a unique conformational change that affects the beta2-beta3 strands connecting switch 1 and switch 2 (interswitch) and also the amphipathic helical N terminus. In GDP-bound Arf1 and Arf6, the interswitch is retracted and forms a pocket to which the N-terminal helix binds, the latter serving as a molecular hasp to maintain the inactive conformation. In the GTP-bound form of these proteins, the interswitch undergoes a two-residue register shift that pulls switch 1 and switch 2 up, restoring an active conformation that can bind GTP. In this conformation, the interswitch projects out of the protein and extrudes the N-terminal hasp by occluding its binding pocket.; GO: 0005525 GTP binding; PDB: 2H57_B 2W83_B 3N5C_B 2J5X_A 3LVR_E 2BAO_A 3LVQ_E 2A5F_A 3PCR_B 1E0S_A ....
Probab=79.38 E-value=4.5 Score=31.98 Aligned_cols=55 Identities=16% Similarity=0.018 Sum_probs=37.5
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhc-----cccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSG-----AFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~-----~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+-|+..+.+|.+... .+....+.+. ..+...+.++..||.+|.|+.+.++-|.+.
T Consensus 115 ~~piLIl~NK~D~~~---~~~~~~i~~~l~l~~l~~~~~~~v~~~sa~~g~Gv~e~l~WL~~~ 174 (175)
T PF00025_consen 115 DIPILILANKQDLPD---AMSEEEIKEYLGLEKLKNKRPWSVFSCSAKTGEGVDEGLEWLIEQ 174 (175)
T ss_dssp TSEEEEEEESTTSTT---SSTHHHHHHHTTGGGTTSSSCEEEEEEBTTTTBTHHHHHHHHHHH
T ss_pred cceEEEEeccccccC---cchhhHHHhhhhhhhcccCCceEEEeeeccCCcCHHHHHHHHHhc
Confidence 579999999954322 2233333321 122456779999999999999999988764
No 251
>cd04122 Rab14 Rab14 subfamily. Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles. Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments. Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation. In addition, Rab14 is believed to play a role in the regulation of phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GT
Probab=79.31 E-value=2.6 Score=32.47 Aligned_cols=57 Identities=14% Similarity=-0.049 Sum_probs=37.5
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
.+.+++...+|.+.... .+++.+...+... ....|++..||++|.||.++++.+...
T Consensus 106 ~~~~iiiv~nK~Dl~~~-~~~~~~~~~~~~~-~~~~~~~e~Sa~~~~~i~e~f~~l~~~ 162 (166)
T cd04122 106 PNTVIFLIGNKADLEAQ-RDVTYEEAKQFAD-ENGLLFLECSAKTGENVEDAFLETAKK 162 (166)
T ss_pred CCCeEEEEEECcccccc-cCcCHHHHHHHHH-HcCCEEEEEECCCCCCHHHHHHHHHHH
Confidence 34578888899654332 2344344333222 234689999999999999998887754
No 252
>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.
Probab=79.12 E-value=1.9 Score=37.11 Aligned_cols=26 Identities=31% Similarity=0.404 Sum_probs=22.4
Q ss_pred CceeEecCCCccccHHHHHHHHHhhC
Q psy5461 57 HVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 57 ~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
..||+-.||.++.||++|+++|.++-
T Consensus 204 ~ppV~~tsA~~~~Gi~eL~~~i~~~~ 229 (266)
T PF03308_consen 204 RPPVLKTSALEGEGIDELWEAIDEHR 229 (266)
T ss_dssp --EEEEEBTTTTBSHHHHHHHHHHHH
T ss_pred CCCEEEEEeCCCCCHHHHHHHHHHHH
Confidence 46999999999999999999998763
No 253
>cd04148 RGK RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Kir) subfamily of Ras GTPases are expressed in a tissue-specific manner and are dynamically regulated by transcriptional and posttranscriptional mechanisms in response to environmental cues. RGK proteins bind to the beta subunit of L-type calcium channels, causing functional down-regulation of these voltage-dependent calcium channels, and either termination of calcium-dependent secretion or modulation of electrical conduction and contractile function. Inhibition of L-type calcium channels by Rem2 may provide a mechanism for modulating calcium-triggered exocytosis in hormone-secreting cells, and has been proposed to influence the secretion of insulin in pancreatic beta cells. RGK proteins also interact with and inhibit the Rho/Rho kinase pathway to modulate remodeling of the cytoskeleton. Two characteristics of RGK proteins cited in the literature are N-terminal and C-terminal extensions beyond the GTPase domain typical of Ra
Probab=78.78 E-value=2.7 Score=34.71 Aligned_cols=60 Identities=12% Similarity=-0.023 Sum_probs=39.2
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
.+-|++...+|.+.... .+++.....+ .......+++..||++|.||+++++.|...+-.
T Consensus 105 ~~~piilV~NK~Dl~~~-~~v~~~~~~~-~a~~~~~~~~e~SA~~~~gv~~l~~~l~~~~~~ 164 (221)
T cd04148 105 EDRPIILVGNKSDLARS-REVSVQEGRA-CAVVFDCKFIETSAGLQHNVDELLEGIVRQIRL 164 (221)
T ss_pred CCCCEEEEEEChhcccc-ceecHHHHHH-HHHHcCCeEEEecCCCCCCHHHHHHHHHHHHHh
Confidence 35688888899653222 2333332221 122223578899999999999999999987744
No 254
>cd01875 RhoG RhoG subfamily. RhoG is a GTPase with high sequence similarity to members of the Rac subfamily, including the regions involved in effector recognition and binding. However, RhoG does not bind to known Rac1 and Cdc42 effectors, including proteins containing a Cdc42/Rac interacting binding (CRIB) motif. Instead, RhoG interacts directly with Elmo, an upstream regulator of Rac1, in a GTP-dependent manner and forms a ternary complex with Dock180 to induce activation of Rac1. The RhoG-Elmo-Dock180 pathway is required for activation of Rac1 and cell spreading mediated by integrin, as well as for neurite outgrowth induced by nerve growth factor. Thus RhoG activates Rac1 through Elmo and Dock180 to control cell morphology. RhoG has also been shown to play a role in caveolar trafficking and has a novel role in signaling the neutrophil respiratory burst stimulated by G protein-coupled receptor (GPCR) agonists. Most Rho proteins contain a lipid modification site at the C-termin
Probab=78.40 E-value=4 Score=32.69 Aligned_cols=63 Identities=17% Similarity=0.050 Sum_probs=39.6
Q ss_pred CCceeeeeeeecccccCC-----------cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCC
Q psy5461 24 GDSLCARAFKVVHDKHRG-----------AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPT 86 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g-----------~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~ 86 (221)
+-|++..-+|.+...... .++.+....-..+....+.+-.||++|.||+++++.+.+.+-.|.
T Consensus 107 ~~piilvgNK~DL~~~~~~~~~~~~~~~~~v~~~~~~~~a~~~~~~~~~e~SAk~g~~v~e~f~~l~~~~~~~~ 180 (191)
T cd01875 107 NVPILLVGTKKDLRNDADTLKKLKEQGQAPITPQQGGALAKQIHAVKYLECSALNQDGVKEVFAEAVRAVLNPT 180 (191)
T ss_pred CCCEEEEEeChhhhcChhhHHHHhhccCCCCCHHHHHHHHHHcCCcEEEEeCCCCCCCHHHHHHHHHHHHhccc
Confidence 568888888865432211 122222111111222357899999999999999999998776554
No 255
>cd04144 Ras2 Ras2 subfamily. The Ras2 subfamily, found exclusively in fungi, was first identified in Ustilago maydis. In U. maydis, Ras2 is regulated by Sql2, a protein that is homologous to GEFs (guanine nucleotide exchange factors) of the CDC25 family. Ras2 has been shown to induce filamentous growth, but the signaling cascade through which Ras2 and Sql2 regulate cell morphology is not known. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins.
Probab=77.99 E-value=3.3 Score=33.03 Aligned_cols=58 Identities=12% Similarity=0.013 Sum_probs=37.6
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+.|++...+|.+.... .++....... ..+....|.+..||++|.||+++++.+...+
T Consensus 105 ~~~piilvgNK~Dl~~~-~~v~~~~~~~-~~~~~~~~~~e~SAk~~~~v~~l~~~l~~~l 162 (190)
T cd04144 105 ADVPIMIVGNKCDKVYE-REVSTEEGAA-LARRLGCEFIEASAKTNVNVERAFYTLVRAL 162 (190)
T ss_pred CCCCEEEEEEChhcccc-CccCHHHHHH-HHHHhCCEEEEecCCCCCCHHHHHHHHHHHH
Confidence 35688888899653221 2333333222 1122235789999999999999999998754
No 256
>cd04120 Rab12 Rab12 subfamily. Rab12 was first identified in canine cells, where it was localized to the Golgi complex. The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported. More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic
Probab=77.88 E-value=4.3 Score=33.19 Aligned_cols=58 Identities=14% Similarity=0.032 Sum_probs=36.3
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+-+++...+|.+.... -+++.....+-..+....+++..||++|.||+++++.+...+
T Consensus 105 ~~piilVgNK~DL~~~-~~v~~~~~~~~a~~~~~~~~~etSAktg~gV~e~F~~l~~~~ 162 (202)
T cd04120 105 DAELLLVGNKLDCETD-REISRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDI 162 (202)
T ss_pred CCcEEEEEECcccccc-cccCHHHHHHHHHhcCCCEEEEecCCCCCCHHHHHHHHHHHH
Confidence 5678888899654322 233332222111111135788999999999999998887655
No 257
>cd01871 Rac1_like Rac1-like subfamily. The Rac1-like subfamily consists of Rac1, Rac2, and Rac3 proteins, plus the splice variant Rac1b that contains a 19-residue insertion near switch II relative to Rac1. While Rac1 is ubiquitously expressed, Rac2 and Rac3 are largely restricted to hematopoietic and neural tissues respectively. Rac1 stimulates the formation of actin lamellipodia and membrane ruffles. It also plays a role in cell-matrix adhesion and cell anoikis. In intestinal epithelial cells, Rac1 is an important regulator of migration and mediates apoptosis. Rac1 is also essential for RhoA-regulated actin stress fiber and focal adhesion complex formation. In leukocytes, Rac1 and Rac2 have distinct roles in regulating cell morphology, migration, and invasion, but are not essential for macrophage migration or chemotaxis. Rac3 has biochemical properties that are closely related to Rac1, such as effector interaction, nucleotide binding, and hydrolysis; Rac2 has a slower nucleoti
Probab=77.87 E-value=4.5 Score=31.84 Aligned_cols=57 Identities=14% Similarity=0.133 Sum_probs=35.1
Q ss_pred CCceeeeeeeecccccC-----------CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 24 GDSLCARAFKVVHDKHR-----------GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~-----------g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
+-|++...+|.+..... -+++.....+-..+-...+++-.||++|.||+++++.+..
T Consensus 105 ~~piilvgnK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~e~Sa~~~~~i~~~f~~l~~ 172 (174)
T cd01871 105 NTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQKGLKTVFDEAIR 172 (174)
T ss_pred CCCEEEEeeChhhccChhhHHHHhhccCCCCCHHHHHHHHHHcCCcEEEEecccccCCHHHHHHHHHH
Confidence 45788888886532210 1122222222222222357899999999999999998875
No 258
>PRK12297 obgE GTPase CgtA; Reviewed
Probab=77.84 E-value=3.2 Score=38.20 Aligned_cols=55 Identities=15% Similarity=0.090 Sum_probs=37.7
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
+.|.+..++|++... .+-....+++.. . .|++..||+++.|+++|++.|...++.
T Consensus 274 ~kP~IVV~NK~DL~~--~~e~l~~l~~~l-~---~~i~~iSA~tgeGI~eL~~~L~~~l~~ 328 (424)
T PRK12297 274 ERPQIVVANKMDLPE--AEENLEEFKEKL-G---PKVFPISALTGQGLDELLYAVAELLEE 328 (424)
T ss_pred CCcEEEEEeCCCCcC--CHHHHHHHHHHh-C---CcEEEEeCCCCCCHHHHHHHHHHHHHh
Confidence 578889999965421 111123333322 1 578999999999999999999887743
No 259
>PRK12296 obgE GTPase CgtA; Reviewed
Probab=77.50 E-value=2.8 Score=39.43 Aligned_cols=58 Identities=12% Similarity=0.005 Sum_probs=38.4
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
+.|.+..+||++.... .-..+.+.... .....||+..||+++.|+++|++.|.+.+..
T Consensus 284 ~kP~IVVlNKiDL~da--~el~e~l~~~l-~~~g~~Vf~ISA~tgeGLdEL~~~L~ell~~ 341 (500)
T PRK12296 284 ERPRLVVLNKIDVPDA--RELAEFVRPEL-EARGWPVFEVSAASREGLRELSFALAELVEE 341 (500)
T ss_pred CCCEEEEEECccchhh--HHHHHHHHHHH-HHcCCeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence 5688999999654221 11122222222 2224689999999999999999998887743
No 260
>cd01876 YihA_EngB The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target.
Probab=77.28 E-value=3.4 Score=31.12 Aligned_cols=58 Identities=21% Similarity=0.151 Sum_probs=36.4
Q ss_pred CCCceeeeeeeecccccCC-cc--hHHHHhhccc-cccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRG-AV--TFFRIYSGAF-KKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g-~l--~~~~l~~~~~-~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
...+++..++|++ ...+ +. ....+..... .....|++..||+++.|+.++++.|.+++
T Consensus 109 ~~~~vi~v~nK~D--~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Sa~~~~~~~~l~~~l~~~~ 170 (170)
T cd01876 109 LGIPFLVVLTKAD--KLKKSELAKALKEIKKELKLFEIDPPIILFSSLKGQGIDELRALIEKWL 170 (170)
T ss_pred cCCCEEEEEEchh--cCChHHHHHHHHHHHHHHHhccCCCceEEEecCCCCCHHHHHHHHHHhC
Confidence 3457777788853 3211 11 1222222221 23456899999999999999999998763
No 261
>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2. Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhi
Probab=77.17 E-value=3.4 Score=31.95 Aligned_cols=57 Identities=12% Similarity=-0.044 Sum_probs=36.8
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+-|++...+|.+.... -++..+....- .+....|++..||++|.||.++++.|...+
T Consensus 108 ~~p~iiv~nK~Dl~~~-~~~~~~~~~~~-~~~~~~~~~~~Sa~~~~~v~~~~~~i~~~~ 164 (167)
T cd01867 108 DVERMLVGNKCDMEEK-RVVSKEEGEAL-ADEYGIKFLETSAKANINVEEAFFTLAKDI 164 (167)
T ss_pred CCcEEEEEECcccccc-cCCCHHHHHHH-HHHcCCEEEEEeCCCCCCHHHHHHHHHHHH
Confidence 4577777888543321 23333333322 223346899999999999999999987643
No 262
>PLN03118 Rab family protein; Provisional
Probab=76.90 E-value=3.6 Score=33.42 Aligned_cols=58 Identities=14% Similarity=-0.038 Sum_probs=36.6
Q ss_pred CceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 25 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 25 ~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
.+++...+|.+.... .++......... .....+++..||++|.|++++++.|...+..
T Consensus 121 ~~~ilv~NK~Dl~~~-~~i~~~~~~~~~-~~~~~~~~e~SAk~~~~v~~l~~~l~~~~~~ 178 (211)
T PLN03118 121 CVKMLVGNKVDRESE-RDVSREEGMALA-KEHGCLFLECSAKTRENVEQCFEELALKIME 178 (211)
T ss_pred CCEEEEEECcccccc-CccCHHHHHHHH-HHcCCEEEEEeCCCCCCHHHHHHHHHHHHHh
Confidence 466677788543222 223322222211 1223578999999999999999999987754
No 263
>KOG0072|consensus
Probab=76.78 E-value=3 Score=32.92 Aligned_cols=56 Identities=25% Similarity=0.188 Sum_probs=38.4
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhc----cccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSG----AFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~----~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+..++.+.+| .|. .|.++...+... .++...+.|+-.||.+|.|+++.+|-+.+-+
T Consensus 119 ~a~llv~anK--qD~-~~~~t~~E~~~~L~l~~Lk~r~~~Iv~tSA~kg~Gld~~~DWL~~~l 178 (182)
T KOG0072|consen 119 HAKLLVFANK--QDY-SGALTRSEVLKMLGLQKLKDRIWQIVKTSAVKGEGLDPAMDWLQRPL 178 (182)
T ss_pred CceEEEEecc--ccc-hhhhhHHHHHHHhChHHHhhheeEEEeeccccccCCcHHHHHHHHHH
Confidence 4567777777 443 255554444332 2444568899999999999999999887644
No 264
>cd04103 Centaurin_gamma Centaurin gamma. The centaurins (alpha, beta, gamma, and delta) are large, multi-domain proteins that all contain an ArfGAP domain and ankyrin repeats, and in some cases, numerous additional domains. Centaurin gamma contains an additional GTPase domain near its N-terminus. The specific function of this GTPase domain has not been well characterized, but centaurin gamma 2 (CENTG2) may play a role in the development of autism. Centaurin gamma 1 is also called PIKE (phosphatidyl inositol (PI) 3-kinase enhancer) and centaurin gamma 2 is also known as AGAP (ArfGAP protein with a GTPase-like domain, ankyrin repeats and a Pleckstrin homology domain) or GGAP. Three isoforms of PIKE have been identified. PIKE-S (short) and PIKE-L (long) are brain-specific isoforms, with PIKE-S restricted to the nucleus and PIKE-L found in multiple cellular compartments. A third isoform, PIKE-A was identified in human glioblastoma brain cancers and has been found in various tissues.
Probab=76.76 E-value=3.7 Score=31.84 Aligned_cols=58 Identities=5% Similarity=-0.052 Sum_probs=35.6
Q ss_pred CCceeeeeeeecccc-cCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDK-HRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~-~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+-|++..-+|.+-+. ..-+++.+...+-..+....+++-.||++|.||+++++.+...
T Consensus 99 ~~piilvgnK~Dl~~~~~~~v~~~~~~~~~~~~~~~~~~e~SAk~~~~i~~~f~~~~~~ 157 (158)
T cd04103 99 EIPLILVGTQDAISESNPRVIDDARARQLCADMKRCSYYETCATYGLNVERVFQEAAQK 157 (158)
T ss_pred CCCEEEEeeHHHhhhcCCcccCHHHHHHHHHHhCCCcEEEEecCCCCCHHHHHHHHHhh
Confidence 347777788843221 1123443332222222234678899999999999999988754
No 265
>cd01874 Cdc42 Cdc42 subfamily. Cdc42 is an essential GTPase that belongs to the Rho family of Ras-like GTPases. These proteins act as molecular switches by responding to exogenous and/or endogenous signals and relaying those signals to activate downstream components of a biological pathway. Cdc42 transduces signals to the actin cytoskeleton to initiate and maintain polarized growth and to mitogen-activated protein morphogenesis. In the budding yeast Saccharomyces cerevisiae, Cdc42 plays an important role in multiple actin-dependent morphogenetic events such as bud emergence, mating-projection formation, and pseudohyphal growth. In mammalian cells, Cdc42 regulates a variety of actin-dependent events and induces the JNK/SAPK protein kinase cascade, which leads to the activation of transcription factors within the nucleus. Cdc42 mediates these processes through interactions with a myriad of downstream effectors, whose number and regulation we are just starting to understand. In addi
Probab=76.47 E-value=5.2 Score=31.52 Aligned_cols=25 Identities=16% Similarity=0.215 Sum_probs=21.9
Q ss_pred CceeEecCCCccccHHHHHHHHHhh
Q psy5461 57 HVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 57 ~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
..+++..||++|.||+++++.+...
T Consensus 149 ~~~~~e~SA~tg~~v~~~f~~~~~~ 173 (175)
T cd01874 149 AVKYVECSALTQKGLKNVFDEAILA 173 (175)
T ss_pred CcEEEEecCCCCCCHHHHHHHHHHH
Confidence 4678999999999999999988763
No 266
>PRK00454 engB GTP-binding protein YsxC; Reviewed
Probab=76.44 E-value=4.1 Score=32.20 Aligned_cols=59 Identities=20% Similarity=0.120 Sum_probs=36.3
Q ss_pred CCCceeeeeeeeccccc-CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKH-RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~-~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+.+++...+|++.... ..+.....+.+..... ..+++..||+++.|++++++.|..++
T Consensus 134 ~~~~~iiv~nK~Dl~~~~~~~~~~~~i~~~l~~~-~~~~~~~Sa~~~~gi~~l~~~i~~~~ 193 (196)
T PRK00454 134 YGIPVLIVLTKADKLKKGERKKQLKKVRKALKFG-DDEVILFSSLKKQGIDELRAAIAKWL 193 (196)
T ss_pred cCCcEEEEEECcccCCHHHHHHHHHHHHHHHHhc-CCceEEEEcCCCCCHHHHHHHHHHHh
Confidence 34566777778542211 0112222233333221 46788999999999999999998765
No 267
>TIGR00231 small_GTP small GTP-binding protein domain. This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model.
Probab=75.72 E-value=5.5 Score=29.27 Aligned_cols=53 Identities=9% Similarity=-0.063 Sum_probs=34.4
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHH
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIV 79 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~ 79 (221)
+.|++..++|.+.-.. . ......+........|++..||++|.|+.++++.|.
T Consensus 108 ~~p~ivv~nK~D~~~~--~-~~~~~~~~~~~~~~~~~~~~sa~~~~gv~~~~~~l~ 160 (161)
T TIGR00231 108 NVPIILVGNKIDLRDA--K-LKTHVAFLFAKLNGEPIIPLSAETGKNIDSAFKIVE 160 (161)
T ss_pred CCcEEEEEEcccCCcc--h-hhHHHHHHHhhccCCceEEeecCCCCCHHHHHHHhh
Confidence 5578888888543221 1 222333333333456799999999999999998864
No 268
>cd04117 Rab15 Rab15 subfamily. Rab15 colocalizes with the transferrin receptor in early endosome compartments, but not with late endosomal markers. It codistributes with Rab4 and Rab5 on early/sorting endosomes, and with Rab11 on pericentriolar recycling endosomes. It is believed to function as an inhibitory GTPase that regulates distinct steps in early endocytic trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to
Probab=75.13 E-value=4.8 Score=31.01 Aligned_cols=56 Identities=11% Similarity=0.032 Sum_probs=34.1
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+-+++..-+|.+.... .++..... ....+....|.+..||++|.||+++++.|...
T Consensus 105 ~~~iilvgnK~Dl~~~-~~v~~~~~-~~~~~~~~~~~~e~Sa~~~~~v~~~f~~l~~~ 160 (161)
T cd04117 105 GVQKILIGNKADEEQK-RQVGDEQG-NKLAKEYGMDFFETSACTNSNIKESFTRLTEL 160 (161)
T ss_pred CCeEEEEEECcccccc-cCCCHHHH-HHHHHHcCCEEEEEeCCCCCCHHHHHHHHHhh
Confidence 3467777777543222 22222221 11122223678999999999999999998754
No 269
>cd04118 Rab24 Rab24 subfamily. Rab24 is distinct from other Rabs in several ways. It exists primarily in the GTP-bound state, having a low intrinsic GTPase activity; it is not efficiently geranyl-geranylated at the C-terminus; it does not form a detectable complex with Rab GDP-dissociation inhibitors (GDIs); and it has recently been shown to undergo tyrosine phosphorylation when overexpressed in vitro. The specific function of Rab24 still remains unknown. It is found in a transport route between ER-cis-Golgi and late endocytic compartments. It is putatively involved in an autophagic pathway, possibly directing misfolded proteins in the ER to degradative pathways. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilita
Probab=75.10 E-value=5.3 Score=31.61 Aligned_cols=58 Identities=14% Similarity=0.033 Sum_probs=37.4
Q ss_pred CCceeeeeeeecccc---cCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDK---HRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~---~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+-|++...+|.+..+ ...++....+.+-. +....+++..||++|.||++|++.|.+.+
T Consensus 105 ~~piilv~nK~Dl~~~~~~~~~v~~~~~~~~~-~~~~~~~~~~Sa~~~~gv~~l~~~i~~~~ 165 (193)
T cd04118 105 HCKIYLCGTKSDLIEQDRSLRQVDFHDVQDFA-DEIKAQHFETSSKTGQNVDELFQKVAEDF 165 (193)
T ss_pred CCCEEEEEEcccccccccccCccCHHHHHHHH-HHcCCeEEEEeCCCCCCHHHHHHHHHHHH
Confidence 467888888865321 11233333332211 22236789999999999999999998766
No 270
>cd01883 EF1_alpha Eukaryotic elongation factor 1 (EF1) alpha subfamily. EF1 is responsible for the GTP-dependent binding of aminoacyl-tRNAs to the ribosomes. EF1 is composed of four subunits: the alpha chain which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This subfamily is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha interacts with the actin of the eukaryotic cytoskeleton and may thereby play a role in cellular transformation and apoptosis. EF-Tu can have no such role in bacteria. In humans, the isoform eEF1A2 is overexpressed in 2/3 of breast cancers and has been identified as a putative oncogene. This subfamily also includes Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation in
Probab=74.43 E-value=2.4 Score=34.97 Aligned_cols=57 Identities=14% Similarity=0.136 Sum_probs=32.8
Q ss_pred Cceeeeeeeeccccc-CCcchHHHHhhcc--------ccccCceeEecCCCccccHH------------HHHHHHHhh
Q psy5461 25 DSLCARAFKVVHDKH-RGAVTFFRIYSGA--------FKKNHVPVLCGSSYKNIGVQ------------KLMDAIVDI 81 (221)
Q Consensus 25 ~~~~~~vfk~~~d~~-~g~l~~~~l~~~~--------~~~~~~Pv~~gSa~~~~Gi~------------~LLd~I~~~ 81 (221)
.+++..++|++.... .-+-.+..+.+.. ......|++..||++|.||. .||++|...
T Consensus 138 ~~iiivvNK~Dl~~~~~~~~~~~~i~~~l~~~l~~~~~~~~~~~ii~iSA~tg~gi~~~~~~~~w~~g~~l~~~l~~~ 215 (219)
T cd01883 138 KQLIVAVNKMDDVTVNWSEERYDEIKKELSPFLKKVGYNPKDVPFIPISGLTGDNLIEKSENMPWYKGPTLLEALDSL 215 (219)
T ss_pred CeEEEEEEccccccccccHHHHHHHHHHHHHHHHHcCCCcCCceEEEeecCcCCCCCcCCCCCCCccCCcHHHHHhCC
Confidence 578889999654310 0111122222211 12235789999999999875 566666544
No 271
>COG0370 FeoB Fe2+ transport system protein B [Inorganic ion transport and metabolism]
Probab=74.36 E-value=3.3 Score=39.99 Aligned_cols=61 Identities=18% Similarity=0.199 Sum_probs=47.0
Q ss_pred CCCCceeeeeeeecccc-cCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCC
Q psy5461 22 HFGDSLCARAFKVVHDK-HRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPT 86 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~-~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~ 86 (221)
+.+-|.+...|.++.-+ .-.++..+++.+.. -+||+..||++|.|+++|++.+.+..++..
T Consensus 106 E~g~p~ilaLNm~D~A~~~Gi~ID~~~L~~~L----GvPVv~tvA~~g~G~~~l~~~i~~~~~~~~ 167 (653)
T COG0370 106 ELGIPMILALNMIDEAKKRGIRIDIEKLSKLL----GVPVVPTVAKRGEGLEELKRAIIELAESKT 167 (653)
T ss_pred HcCCCeEEEeccHhhHHhcCCcccHHHHHHHh----CCCEEEEEeecCCCHHHHHHHHHHhccccc
Confidence 56778888888865333 33377777775533 579999999999999999999998877654
No 272
>cd04129 Rho2 Rho2 subfamily. Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction. Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall. Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for proper intracellular localization via membrane attachment. As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors).
Probab=74.05 E-value=5.7 Score=31.49 Aligned_cols=61 Identities=11% Similarity=-0.045 Sum_probs=37.3
Q ss_pred CCceeeeeeeecccccC--------C-cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 24 GDSLCARAFKVVHDKHR--------G-AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~--------g-~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
+-|++...+|.+..... . .+.......-..+-...+.+..||++|.||+++++.+...+..
T Consensus 105 ~~piilvgnK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~Sa~~~~~v~~~f~~l~~~~~~ 174 (187)
T cd04129 105 NVPVILVGLKKDLRQDAVAKEEYRTQRFVPIQQGKRVAKEIGAKKYMECSALTGEGVDDVFEAATRAALL 174 (187)
T ss_pred CCCEEEEeeChhhhhCcccccccccCCcCCHHHHHHHHHHhCCcEEEEccCCCCCCHHHHHHHHHHHHhc
Confidence 56888888997532210 1 1112222111112223578999999999999999999866543
No 273
>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed
Probab=74.03 E-value=5 Score=39.30 Aligned_cols=56 Identities=16% Similarity=0.068 Sum_probs=37.3
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
.+.|++..+||++..... .. ....+.. + .-.+++.||++|.||.+|++.|.+.+|.
T Consensus 382 ~~~pvIlV~NK~D~~~~~-~~-~~~~~~l---g-~~~~~~iSA~~g~GI~eLl~~i~~~l~~ 437 (712)
T PRK09518 382 AGKPVVLAVNKIDDQASE-YD-AAEFWKL---G-LGEPYPISAMHGRGVGDLLDEALDSLKV 437 (712)
T ss_pred cCCCEEEEEECcccccch-hh-HHHHHHc---C-CCCeEEEECCCCCCchHHHHHHHHhccc
Confidence 567999999996543211 11 1222221 1 1124678999999999999999999876
No 274
>PRK03003 GTP-binding protein Der; Reviewed
Probab=73.57 E-value=5.3 Score=37.06 Aligned_cols=56 Identities=23% Similarity=0.209 Sum_probs=37.4
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
...|++..+||++...... .....+.. +... .+..||++|.||++|++.|.+.+|.
T Consensus 145 ~~~piilV~NK~Dl~~~~~--~~~~~~~~---g~~~-~~~iSA~~g~gi~eL~~~i~~~l~~ 200 (472)
T PRK03003 145 SGKPVILAANKVDDERGEA--DAAALWSL---GLGE-PHPVSALHGRGVGDLLDAVLAALPE 200 (472)
T ss_pred cCCCEEEEEECccCCccch--hhHHHHhc---CCCC-eEEEEcCCCCCcHHHHHHHHhhccc
Confidence 4579999999976433211 11222221 1112 3579999999999999999999876
No 275
>PF00071 Ras: Ras family; InterPro: IPR001806 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction; PDB: 1M7B_A 2V55_B 3EG5_C 3LAW_A 1YHN_A 1T91_B 1HE8_B 3SEA_B 3T5G_A 1XTS_A ....
Probab=73.52 E-value=5.2 Score=30.40 Aligned_cols=56 Identities=13% Similarity=0.032 Sum_probs=40.3
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+-|++...+|.+... .-++......+-..+.. .|.+-.||+++.||.+++..+++.
T Consensus 104 ~~~iivvg~K~D~~~-~~~v~~~~~~~~~~~~~-~~~~e~Sa~~~~~v~~~f~~~i~~ 159 (162)
T PF00071_consen 104 DIPIIVVGNKSDLSD-EREVSVEEAQEFAKELG-VPYFEVSAKNGENVKEIFQELIRK 159 (162)
T ss_dssp TSEEEEEEETTTGGG-GSSSCHHHHHHHHHHTT-SEEEEEBTTTTTTHHHHHHHHHHH
T ss_pred cccceeeeccccccc-cccchhhHHHHHHHHhC-CEEEEEECCCCCCHHHHHHHHHHH
Confidence 467777778865443 23566655555444444 889999999999999999988764
No 276
>PLN03071 GTP-binding nuclear protein Ran; Provisional
Probab=73.42 E-value=4.6 Score=33.25 Aligned_cols=56 Identities=14% Similarity=0.046 Sum_probs=36.5
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
+-|++...+|.+.... ......+ + ..+....+.+..||++|.||.++++.|...+.
T Consensus 117 ~~piilvgNK~Dl~~~--~v~~~~~-~-~~~~~~~~~~e~SAk~~~~i~~~f~~l~~~~~ 172 (219)
T PLN03071 117 NIPIVLCGNKVDVKNR--QVKAKQV-T-FHRKKNLQYYEISAKSNYNFEKPFLYLARKLA 172 (219)
T ss_pred CCcEEEEEEchhhhhc--cCCHHHH-H-HHHhcCCEEEEcCCCCCCCHHHHHHHHHHHHH
Confidence 4578888888653221 1222222 1 11223467899999999999999999887664
No 277
>COG2262 HflX GTPases [General function prediction only]
Probab=73.22 E-value=4.9 Score=36.65 Aligned_cols=55 Identities=13% Similarity=0.074 Sum_probs=37.3
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
.+.|.+.-+||++ ..........+..+. . +.++.||++|.|++.|.+.|.+.++.
T Consensus 303 ~~~p~i~v~NKiD--~~~~~~~~~~~~~~~--~---~~v~iSA~~~~gl~~L~~~i~~~l~~ 357 (411)
T COG2262 303 DEIPIILVLNKID--LLEDEEILAELERGS--P---NPVFISAKTGEGLDLLRERIIELLSG 357 (411)
T ss_pred CCCCEEEEEeccc--ccCchhhhhhhhhcC--C---CeEEEEeccCcCHHHHHHHHHHHhhh
Confidence 4579999999964 221111222222222 1 37778999999999999999998874
No 278
>cd01873 RhoBTB RhoBTB subfamily. Members of the RhoBTB subfamily of Rho GTPases are present in vertebrates, Drosophila, and Dictyostelium. RhoBTB proteins are characterized by a modular organization, consisting of a GTPase domain, a proline rich region, a tandem of two BTB (Broad-Complex, Tramtrack, and Bric a brac) domains, and a C-terminal region of unknown function. RhoBTB proteins may act as docking points for multiple components participating in signal transduction cascades. RhoBTB genes appeared upregulated in some cancer cell lines, suggesting a participation of RhoBTB proteins in the pathogenesis of particular tumors. Note that the Dictyostelium RacA GTPase domain is more closely related to Rac proteins than to RhoBTB proteins, where RacA actually belongs. Thus, the Dictyostelium RacA is not included here. Most Rho proteins contain a lipid modification site at the C-terminus; however, RhoBTB is one of few Rho subfamilies that lack this feature.
Probab=72.30 E-value=9.2 Score=30.93 Aligned_cols=56 Identities=13% Similarity=0.002 Sum_probs=36.6
Q ss_pred CCceeeeeeeeccccc------------------CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 24 GDSLCARAFKVVHDKH------------------RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~------------------~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
+-|++.-.+|.+-... .-.++.+...+-..+ ...|.+-.||++|.||+++++.+..
T Consensus 120 ~~piilvgNK~DL~~~~~~~~~~~~~~~~~~~~~~~~V~~~e~~~~a~~-~~~~~~E~SAkt~~~V~e~F~~~~~ 193 (195)
T cd01873 120 RVPVILVGCKLDLRYADLDEVNRARRPLARPIKNADILPPETGRAVAKE-LGIPYYETSVVTQFGVKDVFDNAIR 193 (195)
T ss_pred CCCEEEEEEchhccccccchhhhcccccccccccCCccCHHHHHHHHHH-hCCEEEEcCCCCCCCHHHHHHHHHH
Confidence 4577777888653210 124444444333333 3358999999999999999998875
No 279
>cd01866 Rab2 Rab2 subfamily. Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key featur
Probab=71.88 E-value=5.7 Score=30.71 Aligned_cols=58 Identities=9% Similarity=-0.065 Sum_probs=38.7
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+-|++...+|.+..+. ..++.+........ ...+++..||+++.||.++++.+.+.+
T Consensus 108 ~~~pvivv~nK~Dl~~~-~~~~~~~~~~~~~~-~~~~~~e~Sa~~~~~i~~~~~~~~~~~ 165 (168)
T cd01866 108 SNMTIMLIGNKCDLESR-REVSYEEGEAFAKE-HGLIFMETSAKTASNVEEAFINTAKEI 165 (168)
T ss_pred CCCcEEEEEECcccccc-cCCCHHHHHHHHHH-cCCEEEEEeCCCCCCHHHHHHHHHHHH
Confidence 35678888899653321 23444444332222 345789999999999999999888754
No 280
>cd01893 Miro1 Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
Probab=71.20 E-value=6.8 Score=30.22 Aligned_cols=58 Identities=9% Similarity=-0.093 Sum_probs=35.8
Q ss_pred CCceeeeeeeecccccCCc-chHHHHhhc--cccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGA-VTFFRIYSG--AFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~-l~~~~l~~~--~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+.|++...+|++..+.... .....+... ..+ ...+++..||++|.|++++++.+...+
T Consensus 103 ~~pviiv~nK~Dl~~~~~~~~~~~~~~~~~~~~~-~~~~~~e~Sa~~~~~v~~lf~~~~~~~ 163 (166)
T cd01893 103 KVPIILVGNKSDLRDGSSQAGLEEEMLPIMNEFR-EIETCVECSAKTLINVSEVFYYAQKAV 163 (166)
T ss_pred CCCEEEEEEchhcccccchhHHHHHHHHHHHHHh-cccEEEEeccccccCHHHHHHHHHHHh
Confidence 5688888999764332111 111222111 111 124789999999999999999987654
No 281
>TIGR00437 feoB ferrous iron transporter FeoB. FeoB (773 amino acids in E. coli), a cytoplasmic membrane protein required for iron(II) update, is encoded in an operon with FeoA (75 amino acids), which is also required, and is regulated by Fur. There appear to be two copies in Archaeoglobus fulgidus and Clostridium acetobutylicum.
Probab=71.13 E-value=4.8 Score=38.63 Aligned_cols=57 Identities=21% Similarity=0.281 Sum_probs=38.9
Q ss_pred CCCCceeeeeeeecccccCC-cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 22 HFGDSLCARAFKVVHDKHRG-AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~~~g-~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+.+.|++..+||.+..+..+ ......+.+ ....|++..||++|.|++++++.+.+..
T Consensus 97 ~~~~PiIIVlNK~Dl~~~~~i~~d~~~L~~----~lg~pvv~tSA~tg~Gi~eL~~~i~~~~ 154 (591)
T TIGR00437 97 ELGIPMILALNLVDEAEKKGIRIDEEKLEE----RLGVPVVPTSATEGRGIERLKDAIRKAI 154 (591)
T ss_pred hcCCCEEEEEehhHHHHhCCChhhHHHHHH----HcCCCEEEEECCCCCCHHHHHHHHHHHh
Confidence 35678999999965432212 222223322 2236899999999999999999998764
No 282
>KOG1145|consensus
Probab=70.30 E-value=15 Score=35.12 Aligned_cols=105 Identities=17% Similarity=0.178 Sum_probs=66.2
Q ss_pred HHHHHHHHHhhCCCCCCcccccccCCCCC-CcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCceeeeceeEe
Q psy5461 71 VQKLMDAIVDILPSPTERPALAMFQHFGD-SLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQSEQITRLLL 149 (221)
Q Consensus 71 i~~LLd~I~~~~PsP~~~~~~~~~~~~~~-~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~~~~v~~i~~ 149 (221)
|+.+-+.+...+|+-.+. ..-+ .-+...|++..-..+-.+|=|||-.|++++...+++.+.|+..--+.+-.
T Consensus 558 ieDv~~~ls~rlp~v~e~-------~vvGea~Vl~~F~i~~~rkr~~VAGC~V~~G~~~K~~~~rlvR~g~vV~~G~l~S 630 (683)
T KOG1145|consen 558 IEDVRELLSERLPPVEEQ-------EVVGEAEVLATFDIREKRKRVPVAGCRVNNGVIKKSCKIRLVRNGKVVFEGELDS 630 (683)
T ss_pred HHHHHHHHHhhCCCceEE-------eeccceeeeeeEeeccccccccccceEeecceEeecceEEEEeCCcEEEEechhH
Confidence 344445566667765442 1112 22334565543322224999999999999999999998776443344443
Q ss_pred eecCCeeeeCccccCCEEEEc--CCC-CCccCcEEec
Q psy5461 150 AEADDYKEVNEIQCGNIAAVT--GLK-RERGKDKRTR 183 (221)
Q Consensus 150 ~~g~~~~~v~~a~aGdIv~i~--gl~-~~~~Gdtl~~ 183 (221)
+. ...+.+.++..|.-|+|. ..+ +.+.||.|-.
T Consensus 631 lK-h~KedV~~vkkg~ECGl~~~d~~~~f~~GD~i~~ 666 (683)
T KOG1145|consen 631 LK-HLKEDVTEVKKGHECGLTFDDGNEDFKEGDKIQC 666 (683)
T ss_pred Hh-hhhhhhhhhcCCCeeeeEeccCCcCCCcCCEEEE
Confidence 33 234678899999999764 222 6789999843
No 283
>TIGR00157 ribosome small subunit-dependent GTPase A. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option).
Probab=70.11 E-value=6.6 Score=33.14 Aligned_cols=54 Identities=15% Similarity=0.075 Sum_probs=34.3
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHH
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIV 79 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~ 79 (221)
.+-+.+...+|.+-... .+...+.+ + .++...++++..||++|.||++|++.+.
T Consensus 66 ~~i~~vIV~NK~DL~~~-~~~~~~~~-~-~~~~~g~~v~~~SAktg~gi~eLf~~l~ 119 (245)
T TIGR00157 66 QNIEPIIVLNKIDLLDD-EDMEKEQL-D-IYRNIGYQVLMTSSKNQDGLKELIEALQ 119 (245)
T ss_pred CCCCEEEEEECcccCCC-HHHHHHHH-H-HHHHCCCeEEEEecCCchhHHHHHhhhc
Confidence 45678888999653221 12221111 1 1122346899999999999999998775
No 284
>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional
Probab=70.05 E-value=5.7 Score=34.67 Aligned_cols=54 Identities=9% Similarity=-0.036 Sum_probs=33.1
Q ss_pred ceeeeeeeecccccCCcchHHHHhhcccc-ccCceeEecCCCccccHHHHHHHHHh
Q psy5461 26 SLCARAFKVVHDKHRGAVTFFRIYSGAFK-KNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 26 ~~~~~vfk~~~d~~~g~l~~~~l~~~~~~-~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
.=+..++|++.-+.. ....+.+.+...+ ....||+..||++|.|+++|++.|..
T Consensus 232 ADIVVLNKiDLl~~~-~~dle~~~~~lr~lnp~a~I~~vSA~tGeGld~L~~~L~~ 286 (290)
T PRK10463 232 ASLMLLNKVDLLPYL-NFDVEKCIACAREVNPEIEIILISATSGEGMDQWLNWLET 286 (290)
T ss_pred CcEEEEEhHHcCccc-HHHHHHHHHHHHhhCCCCcEEEEECCCCCCHHHHHHHHHH
Confidence 336778886432211 1122222222211 23578999999999999999999875
No 285
>cd01892 Miro2 Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
Probab=69.90 E-value=4.8 Score=31.42 Aligned_cols=56 Identities=16% Similarity=-0.046 Sum_probs=34.5
Q ss_pred CCceeeeeeeecccccCCc--chHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGA--VTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~--l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+-|++...+|.+..+.... ....++.+.. ...+++..||++|.|++++++.|.+.+
T Consensus 108 ~~p~iiv~NK~Dl~~~~~~~~~~~~~~~~~~---~~~~~~~~Sa~~~~~v~~lf~~l~~~~ 165 (169)
T cd01892 108 EIPCLFVAAKADLDEQQQRYEVQPDEFCRKL---GLPPPLHFSSKLGDSSNELFTKLATAA 165 (169)
T ss_pred CCeEEEEEEcccccccccccccCHHHHHHHc---CCCCCEEEEeccCccHHHHHHHHHHHh
Confidence 5688888999754322111 1122332211 122357789999999999999998765
No 286
>cd00877 Ran Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases. Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily. Ran may therefore interact with a wide range of proteins in various intracellular locations. Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors. Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins. The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is
Probab=69.81 E-value=8.6 Score=29.81 Aligned_cols=55 Identities=16% Similarity=0.038 Sum_probs=36.8
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+-|++...+|.+-... +...... + ..+....+++..||++|.||+++++.|...+
T Consensus 104 ~~piiiv~nK~Dl~~~--~~~~~~~-~-~~~~~~~~~~e~Sa~~~~~v~~~f~~l~~~~ 158 (166)
T cd00877 104 NIPIVLCGNKVDIKDR--KVKAKQI-T-FHRKKNLQYYEISAKSNYNFEKPFLWLARKL 158 (166)
T ss_pred CCcEEEEEEchhcccc--cCCHHHH-H-HHHHcCCEEEEEeCCCCCChHHHHHHHHHHH
Confidence 5788888899653321 1212221 1 1223456789999999999999999998765
No 287
>cd04146 RERG_RasL11_like RERG/RasL11-like subfamily. RERG (Ras-related and Estrogen- Regulated Growth inhibitor) and Ras-like 11 are members of a novel subfamily of Ras that were identified based on their behavior in breast and prostate tumors, respectively. RERG expression was decreased or lost in a significant fraction of primary human breast tumors that lack estrogen receptor and are correlated with poor clinical prognosis. Elevated RERG expression correlated with favorable patient outcome in a breast tumor subtype that is positive for estrogen receptor expression. In contrast to most Ras proteins, RERG overexpression inhibited the growth of breast tumor cells in vitro and in vivo. RasL11 was found to be ubiquitously expressed in human tissue, but down-regulated in prostate tumors. Both RERG and RasL11 lack the C-terminal CaaX prenylation motif, where a = an aliphatic amino acid and X = any amino acid, and are localized primarily in the cytoplasm. Both are believed to have tu
Probab=69.77 E-value=8.3 Score=29.54 Aligned_cols=57 Identities=11% Similarity=-0.129 Sum_probs=35.9
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCcc-ccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKN-IGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~-~Gi~~LLd~I~~~~ 82 (221)
+-|++...+|.+.... ..+......+-... ...|++..||++| .||.++++.+...+
T Consensus 106 ~~piilv~nK~Dl~~~-~~v~~~~~~~~~~~-~~~~~~e~Sa~~~~~~v~~~f~~l~~~~ 163 (165)
T cd04146 106 EIPVILVGNKADLLHY-RQVSTEEGEKLASE-LGCLFFEVSAAEDYDGVHSVFHELCREV 163 (165)
T ss_pred CCCEEEEEECCchHHh-CccCHHHHHHHHHH-cCCEEEEeCCCCCchhHHHHHHHHHHHH
Confidence 5678888899653221 23333222221111 2268899999999 59999999988643
No 288
>cd04111 Rab39 Rab39 subfamily. Found in eukaryotes, Rab39 is mainly found in epithelial cell lines, but is distributed widely in various human tissues and cell lines. It is believed to be a novel Rab protein involved in regulating Golgi-associated vesicular transport during cellular endocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
Probab=69.59 E-value=6.9 Score=31.98 Aligned_cols=57 Identities=12% Similarity=-0.016 Sum_probs=36.0
Q ss_pred CceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 25 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 25 ~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
.+++...+|.+.... .++......+-. +....|++..||++|.||+++++.|...+.
T Consensus 110 ~~iilvgNK~Dl~~~-~~v~~~~~~~~~-~~~~~~~~e~Sak~g~~v~e~f~~l~~~~~ 166 (211)
T cd04111 110 PVFILVGHKCDLESQ-RQVTREEAEKLA-KDLGMKYIETSARTGDNVEEAFELLTQEIY 166 (211)
T ss_pred CeEEEEEEccccccc-cccCHHHHHHHH-HHhCCEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence 345666788543221 233333332222 222378999999999999999999987664
No 289
>cd04108 Rab36_Rab34 Rab34/Rab36 subfamily. Rab34, found primarily in the Golgi, interacts with its effector, Rab-interacting lysosomal protein (RILP). This enables its participation in microtubular dynenin-dynactin-mediated repositioning of lysosomes from the cell periphery to the Golgi. A Rab34 (Rah) isoform that lacks the consensus GTP-binding region has been identified in mice. This isoform is associated with membrane ruffles and promotes macropinosome formation. Rab36 has been mapped to human chromosome 22q11.2, a region that is homozygously deleted in malignant rhabdoid tumors (MRTs). However, experimental assessments do not implicate Rab36 as a tumor suppressor that would enable tumor formation through a loss-of-function mechanism. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further re
Probab=69.11 E-value=6.5 Score=30.73 Aligned_cols=57 Identities=9% Similarity=-0.111 Sum_probs=34.3
Q ss_pred Cceeeeeeeeccccc-CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 25 DSLCARAFKVVHDKH-RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 25 ~~~~~~vfk~~~d~~-~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.|++.-.+|.+..+. ..+......... .++...+++..||++|.||.++++.|...+
T Consensus 107 ~~iilVgnK~Dl~~~~~~~~~~~~~~~~-~~~~~~~~~e~Sa~~g~~v~~lf~~l~~~~ 164 (170)
T cd04108 107 VLLFLVGTKKDLSSPAQYALMEQDAIKL-AAEMQAEYWSVSALSGENVREFFFRVAALT 164 (170)
T ss_pred CeEEEEEEChhcCccccccccHHHHHHH-HHHcCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence 346777788653221 112222222221 122235788999999999999999988765
No 290
>cd04133 Rop_like Rop subfamily. The Rop (Rho-related protein from plants) subfamily plays a role in diverse cellular processes, including cytoskeletal organization, pollen and vegetative cell growth, hormone responses, stress responses, and pathogen resistance. Rops are able to regulate several downstream pathways to amplify a specific signal by acting as master switches early in the signaling cascade. They transmit a variety of extracellular and intracellular signals. Rops are involved in establishing cell polarity in root-hair development, root-hair elongation, pollen-tube growth, cell-shape formation, responses to hormones such as abscisic acid (ABA) and auxin, responses to abiotic stresses such as oxygen deprivation, and disease resistance and disease susceptibility. An individual Rop can have a unique function or an overlapping function shared with other Rop proteins; in addition, a given Rop-regulated function can be controlled by one or multiple Rop proteins. For example,
Probab=69.07 E-value=10 Score=30.12 Aligned_cols=59 Identities=12% Similarity=0.046 Sum_probs=38.0
Q ss_pred CCceeeeeeeecccccC---------CcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHR---------GAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~---------g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+-|++.--+|.+..+.. -.++.+...+-..+....+.+-.||++|.||+++++.+.+.+
T Consensus 105 ~~piilvgnK~Dl~~~~~~~~~~~~~~~v~~~~~~~~a~~~~~~~~~E~SAk~~~nV~~~F~~~~~~~ 172 (176)
T cd04133 105 NVPIVLVGTKLDLRDDKQYLADHPGASPITTAQGEELRKQIGAAAYIECSSKTQQNVKAVFDAAIKVV 172 (176)
T ss_pred CCCEEEEEeChhhccChhhhhhccCCCCCCHHHHHHHHHHcCCCEEEECCCCcccCHHHHHHHHHHHH
Confidence 45777777886532211 124444443333333333689999999999999999998754
No 291
>cd01858 NGP_1 NGP-1. Autoantigen NGP-1 (Nucleolar G-protein gene 1) has been shown to localize in the nucleolus and nucleolar organizers in all cell types analyzed, which is indicative of a function in ribosomal assembly. NGP-1 and its homologs show a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with NKXD motif) are relocated to the N terminus.
Probab=68.50 E-value=9.8 Score=29.32 Aligned_cols=55 Identities=13% Similarity=-0.041 Sum_probs=34.2
Q ss_pred CCceeeeeeeecc-cccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVH-DKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~-d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+.|.+..++|++- ++. ++ ....+...+...+-++..||+++.|+++|++.|.+++
T Consensus 39 ~~p~ilVlNKiDl~~~~--~~--~~~~~~~~~~~~~~~~~iSa~~~~~~~~L~~~l~~~~ 94 (157)
T cd01858 39 HKHLIFVLNKCDLVPTW--VT--ARWVKILSKEYPTIAFHASINNPFGKGSLIQLLRQFS 94 (157)
T ss_pred CCCEEEEEEchhcCCHH--HH--HHHHHHHhcCCcEEEEEeeccccccHHHHHHHHHHHH
Confidence 4788999999753 221 11 1112222221111157799999999999999998763
No 292
>PLN03108 Rab family protein; Provisional
Probab=67.60 E-value=7.6 Score=31.61 Aligned_cols=57 Identities=14% Similarity=-0.030 Sum_probs=36.1
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+-|++...+|.+... ...++.....+-. +...+|++..||+++.||+++++.++..+
T Consensus 111 ~~piiiv~nK~Dl~~-~~~~~~~~~~~~~-~~~~~~~~e~Sa~~~~~v~e~f~~l~~~~ 167 (210)
T PLN03108 111 NMTIMLIGNKCDLAH-RRAVSTEEGEQFA-KEHGLIFMEASAKTAQNVEEAFIKTAAKI 167 (210)
T ss_pred CCcEEEEEECccCcc-ccCCCHHHHHHHH-HHcCCEEEEEeCCCCCCHHHHHHHHHHHH
Confidence 567888888854322 1233333322222 22346899999999999999887776554
No 293
>cd01856 YlqF YlqF. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The YlqF subfamily is represented in a phylogenetically diverse array of bacteria (including gram-positive bacteria, proteobacteria, Synechocystis, Borrelia, and Thermotoga) and in all eukaryotes.
Probab=67.12 E-value=6.8 Score=30.77 Aligned_cols=57 Identities=18% Similarity=0.110 Sum_probs=37.0
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
+.+....++|++.-.. ..+ ....+ .++....+++..||+++.|+++|++.+...+|.
T Consensus 46 ~k~~ilVlNK~Dl~~~-~~~--~~~~~-~~~~~~~~vi~iSa~~~~gi~~L~~~l~~~l~~ 102 (171)
T cd01856 46 NKPRIIVLNKADLADP-KKT--KKWLK-YFESKGEKVLFVNAKSGKGVKKLLKAAKKLLKD 102 (171)
T ss_pred CCCEEEEEehhhcCCh-HHH--HHHHH-HHHhcCCeEEEEECCCcccHHHHHHHHHHHHHH
Confidence 4678899999653211 111 11111 111123568899999999999999999998864
No 294
>COG2229 Predicted GTPase [General function prediction only]
Probab=66.95 E-value=11 Score=30.66 Aligned_cols=58 Identities=17% Similarity=0.109 Sum_probs=43.7
Q ss_pred CceeeeeeeecccccCCcchHHHHhhccccc-cCceeEecCCCccccHHHHHHHHHhh-CCCC
Q psy5461 25 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKK-NHVPVLCGSSYKNIGVQKLMDAIVDI-LPSP 85 (221)
Q Consensus 25 ~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~-~~~Pv~~gSa~~~~Gi~~LLd~I~~~-~PsP 85 (221)
-|++.++|| .|-+ .....+.+++..... ...||+..+|.+++|..+.|+.+..+ .+.+
T Consensus 122 ip~vVa~NK--~DL~-~a~ppe~i~e~l~~~~~~~~vi~~~a~e~~~~~~~L~~ll~~~~~~~ 181 (187)
T COG2229 122 IPVVVAINK--QDLF-DALPPEKIREALKLELLSVPVIEIDATEGEGARDQLDVLLLKDLLGS 181 (187)
T ss_pred CCEEEEeec--cccC-CCCCHHHHHHHHHhccCCCceeeeecccchhHHHHHHHHHhhcccCc
Confidence 689999999 4433 344555666655444 47899999999999999999998877 5554
No 295
>smart00176 RAN Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases. Ran is involved in the active transport of proteins through nuclear pores.
Probab=66.04 E-value=8.2 Score=31.45 Aligned_cols=56 Identities=16% Similarity=-0.016 Sum_probs=37.3
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+-|++...+|.+.... .+....+. ..+....+.+..||++|.||.++++.|...+
T Consensus 98 ~~~piilvgNK~Dl~~~--~v~~~~~~--~~~~~~~~~~e~SAk~~~~v~~~F~~l~~~i 153 (200)
T smart00176 98 ENIPIVLCGNKVDVKDR--KVKAKSIT--FHRKKNLQYYDISAKSNYNFEKPFLWLARKL 153 (200)
T ss_pred CCCCEEEEEECcccccc--cCCHHHHH--HHHHcCCEEEEEeCCCCCCHHHHHHHHHHHH
Confidence 35688899999653221 22222221 1223346789999999999999999998765
No 296
>cd04128 Spg1 Spg1p. Spg1p (septum-promoting GTPase) was first identified in the fission yeast S. pombe, where it regulates septum formation in the septation initiation network (SIN) through the cdc7 protein kinase. Spg1p is an essential gene that localizes to the spindle pole bodies. When GTP-bound, it binds cdc7 and causes it to translocate to spindle poles. Sid4p (septation initiation defective) is required for localization of Spg1p to the spindle pole body, and the ability of Spg1p to promote septum formation from any point in the cell cycle depends on Sid4p. Spg1p is negatively regulated by Byr4 and cdc16, which form a two-component GTPase activating protein (GAP) for Spg1p. The existence of a SIN-related pathway in plants has been proposed. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are
Probab=65.32 E-value=4.9 Score=31.99 Aligned_cols=26 Identities=23% Similarity=0.362 Sum_probs=23.2
Q ss_pred ceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 58 VPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 58 ~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
.|++..||++|.||+++++.+...+.
T Consensus 141 ~~~~e~SAk~g~~v~~lf~~l~~~l~ 166 (182)
T cd04128 141 APLIFCSTSHSINVQKIFKIVLAKAF 166 (182)
T ss_pred CEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence 68899999999999999999987664
No 297
>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]
Probab=64.34 E-value=8.6 Score=31.73 Aligned_cols=26 Identities=12% Similarity=0.197 Sum_probs=23.0
Q ss_pred cCceeEecCCCccccHHHHHHHHHhh
Q psy5461 56 NHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
...|+++.|+++|.|++++++.+...
T Consensus 174 p~~~ii~~n~ktg~G~~~~~~~i~~~ 199 (202)
T COG0378 174 PEAPIIFTNLKTGEGLDEWLRFIEPQ 199 (202)
T ss_pred CCCCEEEEeCCCCcCHHHHHHHHHhh
Confidence 46799999999999999999988754
No 298
>cd04121 Rab40 Rab40 subfamily. This subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide d
Probab=64.16 E-value=8.8 Score=30.91 Aligned_cols=59 Identities=12% Similarity=0.032 Sum_probs=38.4
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
+-|++..-+|.+.+.. -+++.+....-. +....+.+..||++|.||+++++.|...+..
T Consensus 110 ~~piilVGNK~DL~~~-~~v~~~~~~~~a-~~~~~~~~e~SAk~g~~V~~~F~~l~~~i~~ 168 (189)
T cd04121 110 GVPKILVGNRLHLAFK-RQVATEQAQAYA-ERNGMTFFEVSPLCNFNITESFTELARIVLM 168 (189)
T ss_pred CCCEEEEEECccchhc-cCCCHHHHHHHH-HHcCCEEEEecCCCCCCHHHHHHHHHHHHHH
Confidence 4577777788554322 133443333322 2234689999999999999999998876543
No 299
>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed
Probab=63.84 E-value=6.3 Score=36.44 Aligned_cols=51 Identities=18% Similarity=0.158 Sum_probs=34.6
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
+.|++..++|++..... ... .....|++..||++|.|+++|++.|.+.++.
T Consensus 321 ~~piiiV~NK~DL~~~~-~~~---------~~~~~~~i~iSAktg~GI~~L~~~L~~~l~~ 371 (449)
T PRK05291 321 DKPVIVVLNKADLTGEI-DLE---------EENGKPVIRISAKTGEGIDELREAIKELAFG 371 (449)
T ss_pred CCCcEEEEEhhhccccc-hhh---------hccCCceEEEEeeCCCCHHHHHHHHHHHHhh
Confidence 45777777885432110 100 1223578899999999999999999988753
No 300
>cd04162 Arl9_Arfrp2_like Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first identified as part of the Human Cancer Genome Project. It maps to chromosome 4q12 and is sometimes referred to as Arfrp2 (Arf-related protein 2). This is a novel subfamily identified in human cancers that is uncharacterized to date.
Probab=62.16 E-value=16 Score=28.22 Aligned_cols=55 Identities=15% Similarity=-0.005 Sum_probs=34.4
Q ss_pred CCCceeeeeeeecccccCCcchHHHHh-----hccccccCceeEecCCCc------cccHHHHHHHHHh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIY-----SGAFKKNHVPVLCGSSYK------NIGVQKLMDAIVD 80 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~-----~~~~~~~~~Pv~~gSa~~------~~Gi~~LLd~I~~ 80 (221)
.+-|++...+|.+..... ....+. ....+....+++..||++ +.||.++++.+++
T Consensus 98 ~~~piilv~NK~Dl~~~~---~~~~i~~~~~~~~~~~~~~~~~~~~Sa~~~~s~~~~~~v~~~~~~~~~ 163 (164)
T cd04162 98 PDLPLVVLANKQDLPAAR---SVQEIHKELELEPIARGRRWILQGTSLDDDGSPSRMEAVKDLLSQLIN 163 (164)
T ss_pred CCCcEEEEEeCcCCcCCC---CHHHHHHHhCChhhcCCCceEEEEeeecCCCChhHHHHHHHHHHHHhc
Confidence 456888899996543322 221211 112233346677788888 9999999998875
No 301
>cd04126 Rab20 Rab20 subfamily. Rab20 is one of several Rab proteins that appear to be restricted in expression to the apical domain of murine polarized epithelial cells. It is expressed on the apical side of polarized kidney tubule and intestinal epithelial cells, and in non-polarized cells. It also localizes to vesico-tubular structures below the apical brush border of renal proximal tubule cells and in the apical region of duodenal epithelial cells. Rab20 has also been shown to colocalize with vacuolar H+-ATPases (V-ATPases) in mouse kidney cells, suggesting a role in the regulation of V-ATPase traffic in specific portions of the nephron. It was also shown to be one of several proteins whose expression is upregulated in human myelodysplastic syndrome (MDS) patients. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bo
Probab=61.85 E-value=6.3 Score=32.72 Aligned_cols=25 Identities=12% Similarity=0.222 Sum_probs=22.5
Q ss_pred ceeEecCCCccccHHHHHHHHHhhC
Q psy5461 58 VPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 58 ~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.|.+..||++|.||+++++.+...+
T Consensus 165 ~~~~E~SA~tg~~V~elf~~i~~~~ 189 (220)
T cd04126 165 KMCFETSAKTGYNVDELFEYLFNLV 189 (220)
T ss_pred ceEEEeeCCCCCCHHHHHHHHHHHH
Confidence 6889999999999999999988665
No 302
>KOG1423|consensus
Probab=60.93 E-value=7.3 Score=34.55 Aligned_cols=25 Identities=20% Similarity=0.307 Sum_probs=23.5
Q ss_pred eEecCCCccccHHHHHHHHHhhCCC
Q psy5461 60 VLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 60 v~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
||..||++|.||++|-++|...+|.
T Consensus 248 vF~vSaL~G~GikdlkqyLmsqa~~ 272 (379)
T KOG1423|consen 248 VFMVSALYGEGIKDLKQYLMSQAPP 272 (379)
T ss_pred EEEEecccccCHHHHHHHHHhcCCC
Confidence 8999999999999999999998865
No 303
>PRK12288 GTPase RsgA; Reviewed
Probab=59.63 E-value=15 Score=32.79 Aligned_cols=57 Identities=18% Similarity=0.095 Sum_probs=35.3
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
.+-+.+..++|++..+............ .++...+|++..||+++.|+++|++.|..
T Consensus 149 ~~i~~VIVlNK~DL~~~~~~~~~~~~~~-~y~~~g~~v~~vSA~tg~GideL~~~L~~ 205 (347)
T PRK12288 149 LGIEPLIVLNKIDLLDDEGRAFVNEQLD-IYRNIGYRVLMVSSHTGEGLEELEAALTG 205 (347)
T ss_pred cCCCEEEEEECccCCCcHHHHHHHHHHH-HHHhCCCeEEEEeCCCCcCHHHHHHHHhh
Confidence 3567888899965322111111111111 12223478999999999999999998864
No 304
>cd04174 Rnd1_Rho6 Rnd1/Rho6 subfamily. Rnd1/Rho6 is a member of the novel Rho subfamily Rnd, together with Rnd2/Rho7 and Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not hydrolyze it to GDP, indicating that it is constitutively active. In rat, Rnd1/Rho6 is highly expressed in the cerebral cortex and hippocampus during synapse formation, and plays a role in spine formation. Rnd1/Rho6 is also expressed in the liver and in endothelial cells, and is upregulated in uterine myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8, Rnd1/Rho6 is believed to function as an antagonist to RhoA. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=59.30 E-value=20 Score=30.06 Aligned_cols=59 Identities=7% Similarity=0.014 Sum_probs=36.6
Q ss_pred CCceeeeeeeeccccc-----------CCcchHHHHhhccccccCceeEecCCCccc-cHHHHHHHHHhhC
Q psy5461 24 GDSLCARAFKVVHDKH-----------RGAVTFFRIYSGAFKKNHVPVLCGSSYKNI-GVQKLMDAIVDIL 82 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~-----------~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~-Gi~~LLd~I~~~~ 82 (221)
+.|++.-.+|.+.... .-+++.+...+-..+.+..+.+..||++|. ||+++++.+...+
T Consensus 117 ~~piilVgNK~DL~~~~~~~~~l~~~~~~~Vs~~e~~~~a~~~~~~~~~EtSAktg~~~V~e~F~~~~~~~ 187 (232)
T cd04174 117 STRILLIGCKTDLRTDLSTLMELSNQKQAPISYEQGCALAKQLGAEVYLECSAFTSEKSIHSIFRSASLLC 187 (232)
T ss_pred CCCEEEEEECcccccccchhhhhccccCCcCCHHHHHHHHHHcCCCEEEEccCCcCCcCHHHHHHHHHHHH
Confidence 4577778888653221 123444444333333333367889999997 8999999886543
No 305
>PRK00098 GTPase RsgA; Reviewed
Probab=59.05 E-value=11 Score=32.65 Aligned_cols=53 Identities=13% Similarity=-0.021 Sum_probs=32.9
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHH
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAI 78 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I 78 (221)
.+.+++..++|++-... .+ ......+ ..+...+|++..||+++.|+++|++.+
T Consensus 110 ~~ip~iIVlNK~DL~~~-~~-~~~~~~~-~~~~~g~~v~~vSA~~g~gi~~L~~~l 162 (298)
T PRK00098 110 NGIKPIIVLNKIDLLDD-LE-EARELLA-LYRAIGYDVLELSAKEGEGLDELKPLL 162 (298)
T ss_pred CCCCEEEEEEhHHcCCC-HH-HHHHHHH-HHHHCCCeEEEEeCCCCccHHHHHhhc
Confidence 35678888999653211 11 1111111 122234689999999999999998876
No 306
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=58.22 E-value=13 Score=32.11 Aligned_cols=53 Identities=15% Similarity=-0.030 Sum_probs=32.8
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHH
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIV 79 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~ 79 (221)
.+-+.+..++|++-... .+.. ..........+|+++.||+++.|+++|.+.|.
T Consensus 108 ~~ip~iIVlNK~DL~~~-~~~~---~~~~~~~~~g~~v~~vSA~~g~gi~~L~~~L~ 160 (287)
T cd01854 108 AGIEPVIVLTKADLLDD-EEEE---LELVEALALGYPVLAVSAKTGEGLDELREYLK 160 (287)
T ss_pred cCCCEEEEEEHHHCCCh-HHHH---HHHHHHHhCCCeEEEEECCCCccHHHHHhhhc
Confidence 35677888999653221 1111 11111122347899999999999999887664
No 307
>KOG0092|consensus
Probab=57.60 E-value=11 Score=30.90 Aligned_cols=45 Identities=20% Similarity=0.228 Sum_probs=33.2
Q ss_pred cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCCCC
Q psy5461 42 AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSPTE 87 (221)
Q Consensus 42 ~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP~~ 87 (221)
++.++....-- +....+.+-+||++|.||++|+..|.+.+|....
T Consensus 127 ~V~~~ea~~yA-e~~gll~~ETSAKTg~Nv~~if~~Ia~~lp~~~~ 171 (200)
T KOG0092|consen 127 EVEFEEAQAYA-ESQGLLFFETSAKTGENVNEIFQAIAEKLPCSDP 171 (200)
T ss_pred cccHHHHHHHH-HhcCCEEEEEecccccCHHHHHHHHHHhccCccc
Confidence 44444443322 2345678999999999999999999999998644
No 308
>TIGR03156 GTP_HflX GTP-binding protein HflX. This protein family is one of a number of homologous small, well-conserved GTP-binding proteins with pleiotropic effects. Bacterial members are designated HflX, following the naming convention in Escherichia coli where HflX is encoded immediately downstream of the RNA chaperone Hfq, and immediately upstream of HflKC, a membrane-associated protease pair with an important housekeeping function. Over large numbers of other bacterial genomes, the pairing with hfq is more significant than with hflK and hlfC. The gene from Homo sapiens in this family has been named PGPL (pseudoautosomal GTP-binding protein-like).
Probab=57.49 E-value=8 Score=34.56 Aligned_cols=50 Identities=14% Similarity=0.046 Sum_probs=33.1
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+.|++..+||++.... .++. .+. . ...|++..||++|.|+++|++.|.+.
T Consensus 301 ~~piIlV~NK~Dl~~~-~~v~--~~~----~-~~~~~i~iSAktg~GI~eL~~~I~~~ 350 (351)
T TIGR03156 301 DIPQLLVYNKIDLLDE-PRIE--RLE----E-GYPEAVFVSAKTGEGLDLLLEAIAER 350 (351)
T ss_pred CCCEEEEEEeecCCCh-HhHH--HHH----h-CCCCEEEEEccCCCCHHHHHHHHHhh
Confidence 5678888888653211 1111 111 1 12468899999999999999999765
No 309
>TIGR03597 GTPase_YqeH ribosome biogenesis GTPase YqeH. This family describes YqeH, a member of a larger family of GTPases involved in ribosome biogenesis. Like YqlF, it shows a cyclical permutation relative to GTPases EngA (in which the GTPase domain is duplicated), Era, and others. Members of this protein family are found in a relatively small number of bacterial species, including Bacillus subtilis but not Escherichia coli.
Probab=57.45 E-value=17 Score=32.46 Aligned_cols=58 Identities=19% Similarity=0.133 Sum_probs=34.1
Q ss_pred CCceeeeeeeecc-cccCC-cchHHHHhhccccccC--ceeEecCCCccccHHHHHHHHHhh
Q psy5461 24 GDSLCARAFKVVH-DKHRG-AVTFFRIYSGAFKKNH--VPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 24 ~~~~~~~vfk~~~-d~~~g-~l~~~~l~~~~~~~~~--~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
+.+++..++|++. ++... +-....+++...+.+. ..++..||++|+|+++|++.|.++
T Consensus 90 ~~piilV~NK~DLl~k~~~~~~~~~~l~~~~k~~g~~~~~i~~vSAk~g~gv~eL~~~l~~~ 151 (360)
T TIGR03597 90 GNPVLLVGNKIDLLPKSVNLSKIKEWMKKRAKELGLKPVDIILVSAKKGNGIDELLDKIKKA 151 (360)
T ss_pred CCCEEEEEEchhhCCCCCCHHHHHHHHHHHHHHcCCCcCcEEEecCCCCCCHHHHHHHHHHH
Confidence 5688888899653 22111 1111111111111112 247889999999999999999876
No 310
>cd01899 Ygr210 Ygr210 subfamily. Ygr210 is a member of Obg-like family and present in archaea and fungi. They are characterized by a distinct glycine-rich motif immediately following the Walker B motif. The Ygr210 and YyaF/YchF subfamilies appear to form one major branch of the Obg-like family. Among eukaryotes, the Ygr210 subfamily is represented only in fungi. These fungal proteins form a tight cluster with their archaeal orthologs, which suggests the possibility of horizontal transfer from archaea to fungi.
Probab=57.09 E-value=15 Score=32.35 Aligned_cols=57 Identities=11% Similarity=0.066 Sum_probs=38.4
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHH-HHHhhCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMD-AIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd-~I~~~~Ps 84 (221)
...|++..+||.+.. ..+-....+.. .....+++..||+.+.|+.+|.+ .|.+++|.
T Consensus 213 t~KPvI~VlNK~Dl~--~~~~~~~~l~~---~~~~~~iI~iSA~~e~~L~~L~~~~i~~~lPe 270 (318)
T cd01899 213 RSKPMVIAANKADIP--DAENNISKLRL---KYPDEIVVPTSAEAELALRRAAKQGLIKYDPG 270 (318)
T ss_pred cCCcEEEEEEHHHcc--ChHHHHHHHHh---hCCCCeEEEEeCcccccHHHHHHhhHHHhCCC
Confidence 357999999996521 11111222221 11245789999999999999998 69999975
No 311
>PRK09866 hypothetical protein; Provisional
Probab=56.71 E-value=18 Score=35.43 Aligned_cols=55 Identities=11% Similarity=-0.031 Sum_probs=35.1
Q ss_pred ceeeeeeeecc-cccCCcchHHHHhhc---c-cc--ccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 26 SLCARAFKVVH-DKHRGAVTFFRIYSG---A-FK--KNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 26 ~~~~~vfk~~~-d~~~g~l~~~~l~~~---~-~~--~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
|+..-+||++. +.. +...+.+... . .+ .....||.+||++|.|++.|++.|..+-
T Consensus 291 PVILVVNKIDl~dre--eddkE~Lle~V~~~L~q~~i~f~eIfPVSAlkG~nid~LLdeI~~~~ 352 (741)
T PRK09866 291 PLYVLVNKFDQQDRN--SDDADQVRALISGTLMKGCITPQQIFPVSSMWGYLANRARHELANNG 352 (741)
T ss_pred CEEEEEEcccCCCcc--cchHHHHHHHHHHHHHhcCCCCceEEEEeCCCCCCHHHHHHHHHhCC
Confidence 89999999763 222 1112222221 1 11 1233588899999999999999998753
No 312
>KOG1489|consensus
Probab=56.69 E-value=13 Score=33.09 Aligned_cols=54 Identities=11% Similarity=0.085 Sum_probs=37.0
Q ss_pred CCCceeeeeeeecccccCCcchH-HHHhhccccccCceeEecCCCccccHHHHHHHHHhh
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTF-FRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDI 81 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~-~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~ 81 (221)
.+.|...-.||++.. .++-.+ ..+.+-+.+.. |+..||++++|+.+|++.+.+.
T Consensus 311 ~~rp~liVaNKiD~~--eae~~~l~~L~~~lq~~~---V~pvsA~~~egl~~ll~~lr~~ 365 (366)
T KOG1489|consen 311 ADRPALIVANKIDLP--EAEKNLLSSLAKRLQNPH---VVPVSAKSGEGLEELLNGLREL 365 (366)
T ss_pred ccCceEEEEeccCch--hHHHHHHHHHHHHcCCCc---EEEeeeccccchHHHHHHHhhc
Confidence 467777888996653 123332 45555444443 6669999999999999998764
No 313
>COG3596 Predicted GTPase [General function prediction only]
Probab=55.95 E-value=10 Score=33.08 Aligned_cols=29 Identities=28% Similarity=0.434 Sum_probs=27.1
Q ss_pred cCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 56 NHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 56 ~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
...||+++|+..++|+..|+.+++..+|.
T Consensus 195 ~V~pV~~~~~r~~wgl~~l~~ali~~lp~ 223 (296)
T COG3596 195 EVKPVVAVSGRLPWGLKELVRALITALPV 223 (296)
T ss_pred hcCCeEEeccccCccHHHHHHHHHHhCcc
Confidence 47899999999999999999999999985
No 314
>cd04172 Rnd3_RhoE_Rho8 Rnd3/RhoE/Rho8 subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7. Rnd3/RhoE is known to bind the serine-threonine kinase ROCK I. Unphosphorylated Rnd3/RhoE associates primarily with membranes, but ROCK I-phosphorylated Rnd3/RhoE localizes in the cytosol. Phosphorylation of Rnd3/RhoE correlates with its activity in disrupting RhoA-induced stress fibers and inhibiting Ras-induced fibroblast transformation. In cells that lack stress fibers, such as macrophages and monocytes, Rnd3/RhoE induces a redistribution of actin, causing morphological changes in the cell. In addition, Rnd3/RhoE has been shown to inhibit cell cycle progression in G1 phase at a point upstream of the pRb family pocket protein checkpoint. Rnd3/RhoE has also been shown to inhibit Ras- and Raf-induced fibroblast transformation. In mammary epithelial tumor cells, Rnd3/RhoE regulates the assembly of the apical junction complex and tight
Probab=55.66 E-value=27 Score=27.79 Aligned_cols=57 Identities=11% Similarity=0.011 Sum_probs=37.0
Q ss_pred CCceeeeeeeeccccc----------C-CcchHHHHhhccccccCceeEecCCCcccc-HHHHHHHHHh
Q psy5461 24 GDSLCARAFKVVHDKH----------R-GAVTFFRIYSGAFKKNHVPVLCGSSYKNIG-VQKLMDAIVD 80 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~----------~-g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~G-i~~LLd~I~~ 80 (221)
+-|++.--+|.+.... . -+++.+...+-..+....+.+-.||++|.| |+++++.+..
T Consensus 109 ~~piilVgNK~DL~~~~~~~~~~~~~~~~~v~~~~~~~~a~~~~~~~~~E~SAk~~~n~v~~~F~~~~~ 177 (182)
T cd04172 109 NTKMLLVGCKSDLRTDLTTLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSENSVRDIFHVATL 177 (182)
T ss_pred CCCEEEEeEChhhhcChhhHHHHHhcCCCCCCHHHHHHHHHHcCCCEEEECCcCCCCCCHHHHHHHHHH
Confidence 4577777788653221 1 135554444433333335899999999998 9999998876
No 315
>COG0536 Obg Predicted GTPase [General function prediction only]
Probab=54.57 E-value=14 Score=33.18 Aligned_cols=61 Identities=10% Similarity=0.029 Sum_probs=38.7
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccc-cCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKK-NHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~-~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
.+.+-....+|++... .+-..+.+.+...+. ...+.++.||.++.|+++|++.+.+++..-
T Consensus 274 ~~K~~ivv~NKiD~~~--~~e~~~~~~~~l~~~~~~~~~~~ISa~t~~g~~~L~~~~~~~l~~~ 335 (369)
T COG0536 274 AEKPRIVVLNKIDLPL--DEEELEELKKALAEALGWEVFYLISALTREGLDELLRALAELLEET 335 (369)
T ss_pred ccCceEEEEeccCCCc--CHHHHHHHHHHHHHhcCCCcceeeehhcccCHHHHHHHHHHHHHHh
Confidence 4678888899965222 222233334434332 233333399999999999999998887654
No 316
>PRK09554 feoB ferrous iron transport protein B; Reviewed
Probab=53.69 E-value=15 Score=36.59 Aligned_cols=58 Identities=14% Similarity=0.067 Sum_probs=41.0
Q ss_pred CCCCceeeeeeeecccccCC-cchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 22 HFGDSLCARAFKVVHDKHRG-AVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~~~g-~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
+.+.|++..+||.+..+..+ ....+++.+ ....|++..||.+|.|+++|.+.+.+..+
T Consensus 110 e~giPvIvVlNK~Dl~~~~~i~id~~~L~~----~LG~pVvpiSA~~g~GIdeL~~~I~~~~~ 168 (772)
T PRK09554 110 ELGIPCIVALNMLDIAEKQNIRIDIDALSA----RLGCPVIPLVSTRGRGIEALKLAIDRHQA 168 (772)
T ss_pred HcCCCEEEEEEchhhhhccCcHHHHHHHHH----HhCCCEEEEEeecCCCHHHHHHHHHHhhh
Confidence 35679999999976432222 233333332 23468999999999999999999988764
No 317
>PRK09602 translation-associated GTPase; Reviewed
Probab=53.23 E-value=21 Score=32.56 Aligned_cols=56 Identities=13% Similarity=0.156 Sum_probs=39.6
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHH-HHHHHHhhCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQK-LMDAIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~-LLd~I~~~~Ps 84 (221)
...|++..+||++... ..-....+.+. ...+++..||+.+.++.+ |++.+.+++|.
T Consensus 216 t~KPvI~VlNK~D~~~--~~~~l~~i~~~----~~~~vvpISA~~e~~l~~~l~~~i~~~lp~ 272 (396)
T PRK09602 216 ISKPMVIAANKADLPP--AEENIERLKEE----KYYIVVPTSAEAELALRRAAKAGLIDYIPG 272 (396)
T ss_pred cCCCEEEEEEchhccc--chHHHHHHHhc----CCCcEEEEcchhhhhHHHHHHHhHHhhCCC
Confidence 3579999999965321 11123344443 345688999999999999 89999999976
No 318
>PRK00093 GTP-binding protein Der; Reviewed
Probab=52.89 E-value=18 Score=32.90 Aligned_cols=56 Identities=20% Similarity=0.185 Sum_probs=36.1
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
.+.|++..++|++.... +......+ +.+...++..||++|.|+.+|++.|....+.
T Consensus 108 ~~~piilv~NK~D~~~~--~~~~~~~~----~lg~~~~~~iSa~~g~gv~~l~~~I~~~~~~ 163 (435)
T PRK00093 108 SNKPVILVVNKVDGPDE--EADAYEFY----SLGLGEPYPISAEHGRGIGDLLDAILEELPE 163 (435)
T ss_pred cCCcEEEEEECccCccc--hhhHHHHH----hcCCCCCEEEEeeCCCCHHHHHHHHHhhCCc
Confidence 35788999999653221 11112222 1122236778999999999999999986554
No 319
>PRK12289 GTPase RsgA; Reviewed
Probab=52.81 E-value=17 Score=32.57 Aligned_cols=53 Identities=13% Similarity=0.039 Sum_probs=33.7
Q ss_pred CCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
+-+++..++|++--.. .++ ..... .++...+++++.||+++.|+++|++.|..
T Consensus 120 ~ip~ILVlNK~DLv~~-~~~--~~~~~-~~~~~g~~v~~iSA~tg~GI~eL~~~L~~ 172 (352)
T PRK12289 120 GLEIVLCLNKADLVSP-TEQ--QQWQD-RLQQWGYQPLFISVETGIGLEALLEQLRN 172 (352)
T ss_pred CCCEEEEEEchhcCCh-HHH--HHHHH-HHHhcCCeEEEEEcCCCCCHHHHhhhhcc
Confidence 5688888999653111 111 11111 11223467999999999999999998864
No 320
>PRK11058 GTPase HflX; Provisional
Probab=52.76 E-value=25 Score=32.29 Aligned_cols=55 Identities=13% Similarity=0.017 Sum_probs=35.3
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCce-eEecCCCccccHHHHHHHHHhhCCC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVP-VLCGSSYKNIGVQKLMDAIVDILPS 84 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~P-v~~gSa~~~~Gi~~LLd~I~~~~Ps 84 (221)
.+.|++..+||++...... ...... . ...| ++..||++|.|+++|++.|.+.++.
T Consensus 308 ~~~pvIiV~NKiDL~~~~~--~~~~~~----~-~~~~~~v~ISAktG~GIdeL~e~I~~~l~~ 363 (426)
T PRK11058 308 HEIPTLLVMNKIDMLDDFE--PRIDRD----E-ENKPIRVWLSAQTGAGIPLLFQALTERLSG 363 (426)
T ss_pred CCCCEEEEEEcccCCCchh--HHHHHH----h-cCCCceEEEeCCCCCCHHHHHHHHHHHhhh
Confidence 3568888899965321111 111111 1 1223 4778999999999999999998854
No 321
>TIGR03596 GTPase_YlqF ribosome biogenesis GTP-binding protein YlqF. Members of this protein family are GTP-binding proteins involved in ribosome biogenesis, including the essential YlqF protein of Bacillus subtilis, which is an essential protein. They are related to Era, EngA, and other GTPases of ribosome biogenesis, but are circularly permuted. This family is not universal, and is not present in Escherichia coli, and so is not as well studied as some other GTPases. This model is built for bacterial members.
Probab=52.60 E-value=20 Score=30.63 Aligned_cols=57 Identities=16% Similarity=0.091 Sum_probs=37.8
Q ss_pred CCceeeeeeeecc-cccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 24 GDSLCARAFKVVH-DKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 24 ~~~~~~~vfk~~~-d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
+.+++.-++|++. ++. .. ....+.. +....++++.||+++.|+..|++.|.+.+|.-
T Consensus 48 ~kp~IiVlNK~DL~~~~--~~--~~~~~~~-~~~~~~vi~iSa~~~~gi~~L~~~i~~~~~~~ 105 (276)
T TIGR03596 48 NKPRLIVLNKADLADPA--VT--KQWLKYF-EEKGIKALAINAKKGKGVKKIIKAAKKLLKEK 105 (276)
T ss_pred CCCEEEEEEccccCCHH--HH--HHHHHHH-HHcCCeEEEEECCCcccHHHHHHHHHHHHHHh
Confidence 5688899999653 221 11 1111111 11235789999999999999999999988653
No 322
>TIGR00750 lao LAO/AO transport system ATPase. Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.
Probab=52.53 E-value=11 Score=32.86 Aligned_cols=26 Identities=35% Similarity=0.456 Sum_probs=23.2
Q ss_pred ceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 58 VPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 58 ~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
.|++..||+++.|+++|++.|.++..
T Consensus 213 ~~v~~iSA~~g~Gi~~L~~~i~~~~~ 238 (300)
T TIGR00750 213 PPVLTTSAVEGRGIDELWDAIEEHKT 238 (300)
T ss_pred CCEEEEEccCCCCHHHHHHHHHHHHH
Confidence 47999999999999999999988744
No 323
>cd04131 Rnd Rnd subfamily. The Rnd subfamily contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These novel Rho family proteins have substantial structural differences compared to other Rho members, including N- and C-terminal extensions relative to other Rhos. Rnd3/RhoE is farnesylated at the C-terminal prenylation site, unlike most other Rho proteins that are geranylgeranylated. In addition, Rnd members are unable to hydrolyze GTP and are resistant to GAP activity. They are believed to exist only in the GTP-bound conformation, and are antagonists of RhoA activity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=51.61 E-value=35 Score=26.94 Aligned_cols=57 Identities=11% Similarity=0.008 Sum_probs=36.0
Q ss_pred CCceeeeeeeeccccc-----------CCcchHHHHhhccccccCceeEecCCCcccc-HHHHHHHHHh
Q psy5461 24 GDSLCARAFKVVHDKH-----------RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIG-VQKLMDAIVD 80 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~-----------~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~G-i~~LLd~I~~ 80 (221)
+-+++.--+|.+.... .-+++.+...+-..+.+..+.+-.||++|.+ |+++++.++.
T Consensus 105 ~~~iilVgnK~DL~~~~~~~~~~~~~~~~~v~~~e~~~~a~~~~~~~~~E~SA~~~~~~v~~~F~~~~~ 173 (178)
T cd04131 105 NTKVLLVGCKTDLRTDLSTLMELSHQRQAPVSYEQGCAIAKQLGAEIYLECSAFTSEKSVRDIFHVATM 173 (178)
T ss_pred CCCEEEEEEChhhhcChhHHHHHHhcCCCCCCHHHHHHHHHHhCCCEEEECccCcCCcCHHHHHHHHHH
Confidence 4577777788653221 1124444433333333344789999999995 9999998876
No 324
>COG1217 TypA Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]
Probab=50.47 E-value=20 Score=33.64 Aligned_cols=47 Identities=23% Similarity=0.441 Sum_probs=39.8
Q ss_pred hhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhcccccc
Q psy5461 2 DAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKN 56 (221)
Q Consensus 2 ~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~ 56 (221)
+.|.+.+|+|. .+.++||-.++.-.+++++.|++..-|+++|+.+..
T Consensus 188 e~I~~hvp~P~--------~~~d~PlQ~qvt~Ldyn~y~GrIgigRi~~G~vk~~ 234 (603)
T COG1217 188 ETILDHVPAPK--------GDLDEPLQMQVTQLDYNSYVGRIGIGRIFRGTVKPN 234 (603)
T ss_pred HHHHHhCCCCC--------CCCCCCeEEEEEeeccccccceeEEEEEecCcccCC
Confidence 56778888884 267899999999999999999999999999987753
No 325
>PRK13796 GTPase YqeH; Provisional
Probab=50.04 E-value=27 Score=31.31 Aligned_cols=24 Identities=29% Similarity=0.347 Sum_probs=21.8
Q ss_pred eeEecCCCccccHHHHHHHHHhhC
Q psy5461 59 PVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 59 Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.++..||+++.|+++|++.|.++.
T Consensus 135 ~v~~vSAk~g~gI~eL~~~I~~~~ 158 (365)
T PRK13796 135 DVVLISAQKGHGIDELLEAIEKYR 158 (365)
T ss_pred cEEEEECCCCCCHHHHHHHHHHhc
Confidence 588999999999999999998764
No 326
>cd04115 Rab33B_Rab33A Rab33B/Rab33A subfamily. Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine
Probab=48.97 E-value=22 Score=27.41 Aligned_cols=58 Identities=12% Similarity=-0.060 Sum_probs=35.8
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCc---cccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYK---NIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~---~~Gi~~LLd~I~~~~ 82 (221)
.+-|++...+|.+.... -++...... ...+....|++-.||++ +.+|.+++..++..+
T Consensus 108 ~~~p~iiv~nK~Dl~~~-~~~~~~~~~-~~~~~~~~~~~e~Sa~~~~~~~~i~~~f~~l~~~~ 168 (170)
T cd04115 108 NEVPRILVGNKCDLREQ-IQVPTDLAQ-RFADAHSMPLFETSAKDPSENDHVEAIFMTLAHKL 168 (170)
T ss_pred CCCCEEEEEECccchhh-cCCCHHHHH-HHHHHcCCcEEEEeccCCcCCCCHHHHHHHHHHHh
Confidence 35688888899653322 122222111 11222347789999999 889999998887643
No 327
>KOG0394|consensus
Probab=48.58 E-value=28 Score=28.61 Aligned_cols=60 Identities=13% Similarity=0.040 Sum_probs=48.3
Q ss_pred CCceeeeeeeeccccc-CCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCC
Q psy5461 24 GDSLCARAFKVVHDKH-RGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILP 83 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~-~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~P 83 (221)
+=||+..=+|++.|.- .-+++..+...-...++.+|-|-.||+.+.+|..-.+.+....=
T Consensus 118 ~FPFVilGNKiD~~~~~~r~VS~~~Aq~WC~s~gnipyfEtSAK~~~NV~~AFe~ia~~aL 178 (210)
T KOG0394|consen 118 TFPFVILGNKIDVDGGKSRQVSEKKAQTWCKSKGNIPYFETSAKEATNVDEAFEEIARRAL 178 (210)
T ss_pred cccEEEEcccccCCCCccceeeHHHHHHHHHhcCCceeEEecccccccHHHHHHHHHHHHH
Confidence 4599999999887753 34677777777778888999999999999999988877766543
No 328
>cd01896 DRG The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding.
Probab=45.76 E-value=18 Score=30.19 Aligned_cols=25 Identities=24% Similarity=0.236 Sum_probs=21.5
Q ss_pred ceeEecCCCccccHHHHHHHHHhhC
Q psy5461 58 VPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 58 ~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+++..||++|.|+++|++.|.+.+
T Consensus 201 ~~~~~~SA~~g~gi~~l~~~i~~~L 225 (233)
T cd01896 201 PNSVVISAEKGLNLDELKERIWDKL 225 (233)
T ss_pred CCEEEEcCCCCCCHHHHHHHHHHHh
Confidence 3578889999999999999998754
No 329
>KOG0462|consensus
Probab=45.63 E-value=5 Score=38.10 Aligned_cols=57 Identities=21% Similarity=0.362 Sum_probs=45.7
Q ss_pred ChhhhhcCCCCCCCCccccccCCCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCC
Q psy5461 1 MDAIVDILPSPTERPALAMFQHFGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSS 65 (221)
Q Consensus 1 l~~~~~~~p~p~~~~~~~~~~~~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa 65 (221)
|++|.+..|.|.. ..|.||-..+|..+.|.+.|.+...++..|..+.++-=..+.|.
T Consensus 227 L~AII~rVPpP~~--------~~d~plr~Lifds~yD~y~G~I~~vrv~~G~vrkGdkV~~~~t~ 283 (650)
T KOG0462|consen 227 LEAIIRRVPPPKG--------IRDAPLRMLIFDSEYDEYRGVIALVRVVDGVVRKGDKVQSAATG 283 (650)
T ss_pred HHHHHhhCCCCCC--------CCCcchHHHhhhhhhhhhcceEEEEEEeeeeeecCCEEEEeecC
Confidence 5778888888843 46889999999999999999999999999998876653333333
No 330
>TIGR03598 GTPase_YsxC ribosome biogenesis GTP-binding protein YsxC/EngB. Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes.
Probab=41.18 E-value=14 Score=28.96 Aligned_cols=50 Identities=20% Similarity=0.042 Sum_probs=29.4
Q ss_pred CCCceeeeeeeeccc-ccCCcchHHHHhhccccc-cCceeEecCCCccccHH
Q psy5461 23 FGDSLCARAFKVVHD-KHRGAVTFFRIYSGAFKK-NHVPVLCGSSYKNIGVQ 72 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d-~~~g~l~~~~l~~~~~~~-~~~Pv~~gSa~~~~Gi~ 72 (221)
...|++..++|++.. ....+.....+++..... ...+++..||++|.||+
T Consensus 128 ~~~pviiv~nK~D~~~~~~~~~~~~~i~~~l~~~~~~~~v~~~Sa~~g~gi~ 179 (179)
T TIGR03598 128 RGIPVLIVLTKADKLKKSELNKQLKKIKKALKKDADDPSVQLFSSLKKTGID 179 (179)
T ss_pred cCCCEEEEEECcccCCHHHHHHHHHHHHHHHhhccCCCceEEEECCCCCCCC
Confidence 456888889996432 111122344444433222 23478999999999873
No 331
>KOG0076|consensus
Probab=39.12 E-value=19 Score=29.28 Aligned_cols=62 Identities=16% Similarity=0.134 Sum_probs=41.2
Q ss_pred CCceeeeeeeecccccCCcchHHHHhh--ccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIYS--GAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~~--~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
..|+...++|-......+......+.. ..+...+.|+...||.+|.||++=..-++..+|.-
T Consensus 126 g~p~L~lankqd~q~~~~~~El~~~~~~~e~~~~rd~~~~pvSal~gegv~egi~w~v~~~~kn 189 (197)
T KOG0076|consen 126 GAPVLVLANKQDLQNAMEAAELDGVFGLAELIPRRDNPFQPVSALTGEGVKEGIEWLVKKLEKN 189 (197)
T ss_pred CCchhhhcchhhhhhhhhHHHHHHHhhhhhhcCCccCccccchhhhcccHHHHHHHHHHHHhhc
Confidence 568888888843333323333333333 34455688999999999999998877777777654
No 332
>cd04161 Arl2l1_Arl13_like Arl2l1/Arl13 subfamily. Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene.
Probab=38.58 E-value=61 Score=24.93 Aligned_cols=56 Identities=9% Similarity=0.001 Sum_probs=33.0
Q ss_pred CCceeeeeeeecccccCCcchHHHHh--hccc--cccCceeEecCCCcc------ccHHHHHHHHH
Q psy5461 24 GDSLCARAFKVVHDKHRGAVTFFRIY--SGAF--KKNHVPVLCGSSYKN------IGVQKLMDAIV 79 (221)
Q Consensus 24 ~~~~~~~vfk~~~d~~~g~l~~~~l~--~~~~--~~~~~Pv~~gSa~~~------~Gi~~LLd~I~ 79 (221)
+.|++...+|.+.+............ .... .+...+++..||++| .|+.+-++-|.
T Consensus 100 ~~piliv~NK~Dl~~~~~~~~i~~~~~l~~~~~~~~~~~~~~~~Sa~~g~~~~~~~g~~~~~~wl~ 165 (167)
T cd04161 100 GKPILVLANKQDKKNALLGADVIEYLSLEKLVNENKSLCHIEPCSAIEGLGKKIDPSIVEGLRWLL 165 (167)
T ss_pred CCcEEEEEeCCCCcCCCCHHHHHHhcCcccccCCCCceEEEEEeEceeCCCCccccCHHHHHHHHh
Confidence 56899999996543322111111110 1111 123467888999998 78998888775
No 333
>PF08669 GCV_T_C: Glycine cleavage T-protein C-terminal barrel domain; InterPro: IPR013977 This entry shows glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. ; PDB: 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 3GIR_A 1WOO_A 1WOS_A 1WOR_A ....
Probab=38.36 E-value=1.4e+02 Score=20.80 Aligned_cols=43 Identities=7% Similarity=-0.030 Sum_probs=35.0
Q ss_pred CCCcEEEEEEEeecCCCce-EEEEEEEceEEcCCCEEEeccCCc
Q psy5461 98 GDSLCARAFKVVHDKHRGA-VTFFRIYSGAFKKGQKFYNIHLDQ 140 (221)
Q Consensus 98 ~~~~~~~Vfk~~~d~~~G~-i~~~RV~sG~L~~gd~v~~~~~~~ 140 (221)
++..+++|....+.+..|+ ++++.|-......|+++.+.-.++
T Consensus 43 ~g~~vG~vTS~~~sp~~~~~Iala~v~~~~~~~g~~l~v~~~g~ 86 (95)
T PF08669_consen 43 DGKPVGRVTSGAYSPTLGKNIALAYVDREYAEPGTELEVEIRGK 86 (95)
T ss_dssp TTEEEEEEEEEEEETTTTEEEEEEEEEGGGGSTTSEEEEEETTE
T ss_pred CCcEEeEEEEEeECCCCCceEEEEEECHHHcCCCCEEEEEECCE
Confidence 6778999999988887665 899999888889999988864443
No 334
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=38.15 E-value=76 Score=21.75 Aligned_cols=28 Identities=14% Similarity=0.296 Sum_probs=21.2
Q ss_pred CCcEEEEEEEeecCCCce-EEEEEEEceE
Q psy5461 99 DSLCARAFKVVHDKHRGA-VTFFRIYSGA 126 (221)
Q Consensus 99 ~~~~~~Vfk~~~d~~~G~-i~~~RV~sG~ 126 (221)
....+.|.++.+||.+.. +|.++...|.
T Consensus 31 ~~~~g~V~~i~~DP~Rsa~iAlV~~~~g~ 59 (77)
T PF00181_consen 31 GNIKGIVIDIEYDPNRSAPIALVKYEDGE 59 (77)
T ss_dssp TSEEEEEEEEEEETTTSSEEEEEEETTSE
T ss_pred CCCcEEEEEEEecCCcCccEEEEEecCCc
Confidence 346799999999998754 8887755543
No 335
>PRK01889 GTPase RsgA; Reviewed
Probab=38.03 E-value=49 Score=29.57 Aligned_cols=53 Identities=17% Similarity=0.066 Sum_probs=33.6
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHH
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIV 79 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~ 79 (221)
.+-+.+..++|++--+. .+-....+... ...+||+..|++++.|++.|.+.|.
T Consensus 141 ~~i~piIVLNK~DL~~~-~~~~~~~~~~~---~~g~~Vi~vSa~~g~gl~~L~~~L~ 193 (356)
T PRK01889 141 SGAEPVIVLTKADLCED-AEEKIAEVEAL---APGVPVLAVSALDGEGLDVLAAWLS 193 (356)
T ss_pred cCCCEEEEEEChhcCCC-HHHHHHHHHHh---CCCCcEEEEECCCCccHHHHHHHhh
Confidence 34566778999653221 11112223222 3457999999999999999988773
No 336
>cd04166 CysN_ATPS CysN_ATPS subfamily. CysN, together with protein CysD, form the ATP sulfurylase (ATPS) complex in some bacteria and lower eukaryotes. ATPS catalyzes the production of ATP sulfurylase (APS) and pyrophosphate (PPi) from ATP and sulfate. CysD, which catalyzes ATP hydrolysis, is a member of the ATP pyrophosphatase (ATP PPase) family. CysN hydrolysis of GTP is required for CysD hydrolysis of ATP; however, CysN hydrolysis of GTP is not dependent on CysD hydrolysis of ATP. CysN is an example of lateral gene transfer followed by acquisition of new function. In many organisms, an ATPS exists which is not GTP-dependent and shares no sequence or structural similarity to CysN.
Probab=36.36 E-value=41 Score=27.21 Aligned_cols=16 Identities=13% Similarity=0.036 Sum_probs=13.6
Q ss_pred CceeEecCCCccccHH
Q psy5461 57 HVPVLCGSSYKNIGVQ 72 (221)
Q Consensus 57 ~~Pv~~gSa~~~~Gi~ 72 (221)
..|++..||++|.|+.
T Consensus 168 ~~~ii~iSA~~g~ni~ 183 (208)
T cd04166 168 DITFIPISALDGDNVV 183 (208)
T ss_pred CceEEEEeCCCCCCCc
Confidence 3579999999999985
No 337
>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis. RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.
Probab=36.05 E-value=32 Score=27.36 Aligned_cols=28 Identities=21% Similarity=0.342 Sum_probs=21.7
Q ss_pred ccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 53 FKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 53 ~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
++...++|+..|++++.|+++|.+.+..
T Consensus 8 y~~~gy~v~~~S~~~~~g~~~l~~~l~~ 35 (161)
T PF03193_consen 8 YEKLGYPVFFISAKTGEGIEELKELLKG 35 (161)
T ss_dssp HHHTTSEEEE-BTTTTTTHHHHHHHHTT
T ss_pred HHHcCCcEEEEeCCCCcCHHHHHHHhcC
Confidence 3445788999999999999999887753
No 338
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=30.67 E-value=85 Score=25.81 Aligned_cols=49 Identities=22% Similarity=0.255 Sum_probs=36.5
Q ss_pred EEEEEce-EEcCCCEEEeccCCceeeeceeEeeecCCeeeeCccccCCEEEEcCC
Q psy5461 119 FFRIYSG-AFKKGQKFYNIHLDQSEQITRLLLAEADDYKEVNEIQCGNIAAVTGL 172 (221)
Q Consensus 119 ~~RV~sG-~L~~gd~v~~~~~~~~~~v~~i~~~~g~~~~~v~~a~aGdIv~i~gl 172 (221)
..+++.| +|++||.+.+-+ ....|++|..-.| ..+++|.+.||-.+.|-
T Consensus 66 ~vel~~gE~l~vGDei~vd~--e~veITSIE~~~g---kRV~~A~veeIeTVWgr 115 (201)
T COG1326 66 EVELDPGETLKVGDEIEVDG--EEVEITSIELGGG---KRVKSAKVEEIETVWGR 115 (201)
T ss_pred eEecCCCCeEecCCEEEEcC--CEEEEEEEeeCCC---ccccccccceeeeEeee
Confidence 4466777 689999998853 3478888874433 36888999999988874
No 339
>PRK09563 rbgA GTPase YlqF; Reviewed
Probab=30.46 E-value=30 Score=29.76 Aligned_cols=57 Identities=16% Similarity=0.092 Sum_probs=37.7
Q ss_pred CCceeeeeeeecc-cccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 24 GDSLCARAFKVVH-DKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 24 ~~~~~~~vfk~~~-d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
+.+++.-++|++. ++. +. ....+.. +....++++.||.++.|++.|++.|.+.+|..
T Consensus 51 ~kp~iiVlNK~DL~~~~--~~--~~~~~~~-~~~~~~vi~vSa~~~~gi~~L~~~l~~~l~~~ 108 (287)
T PRK09563 51 NKPRLLILNKSDLADPE--VT--KKWIEYF-EEQGIKALAINAKKGQGVKKILKAAKKLLKEK 108 (287)
T ss_pred CCCEEEEEEchhcCCHH--HH--HHHHHHH-HHcCCeEEEEECCCcccHHHHHHHHHHHHHHH
Confidence 5688899999653 221 11 1111111 11135789999999999999999999988764
No 340
>COG0486 ThdF Predicted GTPase [General function prediction only]
Probab=29.49 E-value=35 Score=31.72 Aligned_cols=28 Identities=18% Similarity=0.229 Sum_probs=25.1
Q ss_pred ceeEecCCCccccHHHHHHHHHhhCCCC
Q psy5461 58 VPVLCGSSYKNIGVQKLMDAIVDILPSP 85 (221)
Q Consensus 58 ~Pv~~gSa~~~~Gi~~LLd~I~~~~PsP 85 (221)
.|++..|+++|.|++.|.++|.+++..-
T Consensus 351 ~~~i~iSa~t~~Gl~~L~~~i~~~~~~~ 378 (454)
T COG0486 351 DAIISISAKTGEGLDALREAIKQLFGKG 378 (454)
T ss_pred CceEEEEecCccCHHHHHHHHHHHHhhc
Confidence 3789999999999999999999988764
No 341
>COG0218 Predicted GTPase [General function prediction only]
Probab=28.68 E-value=44 Score=27.61 Aligned_cols=59 Identities=20% Similarity=0.187 Sum_probs=37.5
Q ss_pred CCCCceeeeeeeecccccC-Ccch--HHHHhhcc-ccccCce-eEecCCCccccHHHHHHHHHhhC
Q psy5461 22 HFGDSLCARAFKVVHDKHR-GAVT--FFRIYSGA-FKKNHVP-VLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 22 ~~~~~~~~~vfk~~~d~~~-g~l~--~~~l~~~~-~~~~~~P-v~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
+.+-|+...+.| .|+.. ++.. ...+++.. ......+ ++..|+.++.|+++|.+.|.+++
T Consensus 133 ~~~i~~~vv~tK--~DKi~~~~~~k~l~~v~~~l~~~~~~~~~~~~~ss~~k~Gi~~l~~~i~~~~ 196 (200)
T COG0218 133 ELGIPVIVVLTK--ADKLKKSERNKQLNKVAEELKKPPPDDQWVVLFSSLKKKGIDELKAKILEWL 196 (200)
T ss_pred HcCCCeEEEEEc--cccCChhHHHHHHHHHHHHhcCCCCccceEEEEecccccCHHHHHHHHHHHh
Confidence 356788888888 66542 2221 23333222 1122222 78889999999999999998875
No 342
>KOG0093|consensus
Probab=27.82 E-value=54 Score=26.11 Aligned_cols=58 Identities=19% Similarity=0.126 Sum_probs=42.9
Q ss_pred CCCceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 23 FGDSLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 23 ~~~~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
.+.+++..-+|++.|.+ --++.++.+....+ .-+-.|-.||+.|.+|..+.+.++..+
T Consensus 125 ~naqvilvgnKCDmd~e-Rvis~e~g~~l~~~-LGfefFEtSaK~NinVk~~Fe~lv~~I 182 (193)
T KOG0093|consen 125 DNAQVILVGNKCDMDSE-RVISHERGRQLADQ-LGFEFFETSAKENINVKQVFERLVDII 182 (193)
T ss_pred cCceEEEEecccCCccc-eeeeHHHHHHHHHH-hChHHhhhcccccccHHHHHHHHHHHH
Confidence 57788888899888876 34566776654433 345688899999999998887776654
No 343
>PF09631 Sen15: Sen15 protein; InterPro: IPR018593 The Sen15 subunit of the tRNA intron-splicing endonuclease is one of the two structural subunits of this heterotetrameric enzyme. Residues 36-157 of this subunit possess a novel homodimeric fold. Each monomer consists of three alpha-helices and a mixed antiparallel/parallel beta-sheet. Two monomers of Sen15 fold with two monomers of Sen34, one of the two catalytic subunits, to form an alpha2-beta2 tetramer as part of the functional endonuclease assembly []. ; PDB: 2GW6_B.
Probab=25.53 E-value=1.5e+02 Score=21.28 Aligned_cols=17 Identities=24% Similarity=0.579 Sum_probs=7.7
Q ss_pred ceEEEEEEEceEEcCCC
Q psy5461 115 GAVTFFRIYSGAFKKGQ 131 (221)
Q Consensus 115 G~i~~~RV~sG~L~~gd 131 (221)
|+++|-++..|-+++.+
T Consensus 84 sTiVYY~i~~GivkP~~ 100 (101)
T PF09631_consen 84 STIVYYKIHDGIVKPRQ 100 (101)
T ss_dssp S-EEEEEEE--------
T ss_pred CCEEEEEEeCCccCCCC
Confidence 89999999999988764
No 344
>PRK11556 multidrug efflux system subunit MdtA; Provisional
Probab=25.53 E-value=2.3e+02 Score=25.80 Aligned_cols=32 Identities=13% Similarity=0.143 Sum_probs=24.2
Q ss_pred cCCeeeeCccccCCEEEEcCCCCCccCcEEec
Q psy5461 152 ADDYKEVNEIQCGNIAAVTGLKRERGKDKRTR 183 (221)
Q Consensus 152 g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~~ 183 (221)
+.+.+-.+.+.+||.+++.|...++-|+.+--
T Consensus 359 ~~~v~I~~GL~~Gd~VV~~g~~~L~~G~~V~v 390 (415)
T PRK11556 359 SQKVVISAGLSAGDRVVTDGIDRLTEGAKVEV 390 (415)
T ss_pred CCEEEEECCCCCCCEEEECCcccCCCcCEeee
Confidence 33344456799999999999888888988743
No 345
>PTZ00180 60S ribosomal protein L8; Provisional
Probab=24.10 E-value=3.9e+02 Score=23.05 Aligned_cols=36 Identities=19% Similarity=0.105 Sum_probs=22.7
Q ss_pred cEEEEEEEeecCCCce-EEEEEEEceEEcCCCEEEec
Q psy5461 101 LCARAFKVVHDKHRGA-VTFFRIYSGAFKKGQKFYNI 136 (221)
Q Consensus 101 ~~~~Vfk~~~d~~~G~-i~~~RV~sG~L~~gd~v~~~ 136 (221)
..+.|..+++||.+.- +|+++.-.|..-+|..-|++
T Consensus 41 ~~g~V~~IeyDPnRsA~IAlv~~~d~~~~~g~~~YIl 77 (260)
T PTZ00180 41 IRGVVKDIEHDPGRGAPLARVEFRDPYKYKRVKELMV 77 (260)
T ss_pred cCEEEEEEEECCCCCceEEEEEecCCccccCceEEEE
Confidence 3588999999998654 77776555543233333443
No 346
>COG1163 DRG Predicted GTPase [General function prediction only]
Probab=24.01 E-value=1.3e+02 Score=27.14 Aligned_cols=48 Identities=21% Similarity=0.144 Sum_probs=30.7
Q ss_pred ceeeeeeeecccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHhhC
Q psy5461 26 SLCARAFKVVHDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 26 ~~~~~vfk~~~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
|-..-++|++.- +.-....+.+.. ..+..||++++|+++|.+.|-..+
T Consensus 241 p~l~v~NKiD~~---~~e~~~~l~~~~------~~v~isa~~~~nld~L~e~i~~~L 288 (365)
T COG1163 241 PALYVVNKIDLP---GLEELERLARKP------NSVPISAKKGINLDELKERIWDVL 288 (365)
T ss_pred eeEEEEeccccc---CHHHHHHHHhcc------ceEEEecccCCCHHHHHHHHHHhh
Confidence 455667774322 222333443322 577799999999999999887654
No 347
>COG1162 Predicted GTPases [General function prediction only]
Probab=21.80 E-value=1.4e+02 Score=26.34 Aligned_cols=53 Identities=17% Similarity=0.149 Sum_probs=33.7
Q ss_pred Cceeeeeeeec-ccccCCcchHHHHhhccccccCceeEecCCCccccHHHHHHHHHh
Q psy5461 25 DSLCARAFKVV-HDKHRGAVTFFRIYSGAFKKNHVPVLCGSSYKNIGVQKLMDAIVD 80 (221)
Q Consensus 25 ~~~~~~vfk~~-~d~~~g~l~~~~l~~~~~~~~~~Pv~~gSa~~~~Gi~~LLd~I~~ 80 (221)
-.-+..++|++ .|.+ .. .. +-+...+...-+|++..|++++.|+.+|.+.+..
T Consensus 111 i~pvIvlnK~DL~~~~-~~-~~-~~~~~~y~~~gy~v~~~s~~~~~~~~~l~~~l~~ 164 (301)
T COG1162 111 IEPVIVLNKIDLLDDE-EA-AV-KELLREYEDIGYPVLFVSAKNGDGLEELAELLAG 164 (301)
T ss_pred CcEEEEEEccccCcch-HH-HH-HHHHHHHHhCCeeEEEecCcCcccHHHHHHHhcC
Confidence 34456689964 2222 11 11 2233344555789999999999999999887753
No 348
>PRK09578 periplasmic multidrug efflux lipoprotein precursor; Reviewed
Probab=21.35 E-value=2.4e+02 Score=25.20 Aligned_cols=32 Identities=9% Similarity=0.043 Sum_probs=23.8
Q ss_pred ecCCeeeeCccccCCEEEEcCCCCCccCcEEe
Q psy5461 151 EADDYKEVNEIQCGNIAAVTGLKRERGKDKRT 182 (221)
Q Consensus 151 ~g~~~~~v~~a~aGdIv~i~gl~~~~~Gdtl~ 182 (221)
.+...+-++.+.+||.+++.|...++-|+.+.
T Consensus 341 ~~~~~~V~~GL~~Gd~VV~~g~~~l~~G~~V~ 372 (385)
T PRK09578 341 SGRDWIVTRGLAGGERVIVDNAAQFAPGTAVK 372 (385)
T ss_pred cCCEEEEecCCCCCCEEEEcCHhhCCCcCEee
Confidence 34444445678999999999988888888874
No 349
>PF03607 DCX: Doublecortin; InterPro: IPR003533 X-linked lissencephaly is a severe brain malformation affecting males. Recently it has been demonstrated that the doublecortin gene is implicated in this disorder []. Doublecortin was found to bind to the microtubule cytoskeleton. In vivo and in vitro assays show that Doublecortin stabilises microtubules and causes bundling []. Doublecortin is a basic protein with an iso-electric point of 10, typical of microtubule-binding proteins. However, its sequence contains no known microtubule-binding domain(s). The detailed sequence analysis of Doublecortin and Doublecortin-like proteins allowed the identification of an evolutionarily conserved Doublecortin (DC) domain. This domain is found in the N terminus of proteins and consists of one or two tandemly repeated copies of an around 80 amino acids region. It has been suggested that the first DC domain of Doublecortin binds tubulin and enhances microtubule polymerisation []. Some proteins known to contain a DC domain are listed below: Doublecortin. It is required for neuronal migration []. A large number of point mutations in the human DCX gene leading to lissencephaly are located within the DC domains []. Human serine/threonine-protein kinase DCAMKL1. It is a probable kinase that may be involved in a calcium-signaling pathway controling neuronal migration in the developing brain []. Retinitis pigmentosa 1 protein. It could play a role in the differentiation of photoreceptor cells. Mutation in the human RP1 gene cause retinitis pigmentosa of type 1 []. ; GO: 0035556 intracellular signal transduction; PDB: 1UF0_A 1MG4_A 1MFW_A 2DNF_A 2XRP_I 2BQQ_A 1MJD_A.
Probab=21.00 E-value=79 Score=20.46 Aligned_cols=29 Identities=17% Similarity=0.355 Sum_probs=14.9
Q ss_pred eceeEeeecCCeeeeCccccCCEEEEcCC
Q psy5461 144 ITRLLLAEADDYKEVNEIQCGNIAAVTGL 172 (221)
Q Consensus 144 v~~i~~~~g~~~~~v~~a~aGdIv~i~gl 172 (221)
|.+||.+.|.....++++.-|+..+.+|-
T Consensus 28 Vr~lyt~~G~~V~~l~~l~dg~~yVa~g~ 56 (60)
T PF03607_consen 28 VRKLYTLDGKRVKSLDELEDGGSYVASGR 56 (60)
T ss_dssp -SEEEETTSSEESSGGGS-TTEEEEEESS
T ss_pred cceEECCCCCEeCCHHHHCCCCEEEEEcC
Confidence 55555565644445555666666554443
No 350
>PRK15452 putative protease; Provisional
Probab=20.98 E-value=5.2e+02 Score=23.95 Aligned_cols=66 Identities=6% Similarity=0.029 Sum_probs=40.4
Q ss_pred CCcEEEEEEEeecCCCceEEEEEEEceEEcCCCEEEeccCCc--eeeeceeEeeecCCeeeeCccc-cCCEEEEcC
Q psy5461 99 DSLCARAFKVVHDKHRGAVTFFRIYSGAFKKGQKFYNIHLDQ--SEQITRLLLAEADDYKEVNEIQ-CGNIAAVTG 171 (221)
Q Consensus 99 ~~~~~~Vfk~~~d~~~G~i~~~RV~sG~L~~gd~v~~~~~~~--~~~v~~i~~~~g~~~~~v~~a~-aGdIv~i~g 171 (221)
+.+++.|.+.. +. +..+.+++.. .++.||.|.+.+.+. ..++.+++ ..+..+++.+. +|+++.+.-
T Consensus 359 ~~~~g~v~~~~--~~-~~~~~v~~~~-~~~~gd~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~ 427 (443)
T PRK15452 359 QQFVGEFTGER--AG-TGLAEVEVKN-KFSVGDSLELMTPQGNINFTLERME---NRKGEAMEVAPGSGHTVWLPV 427 (443)
T ss_pred ceEEEEEEEEe--cC-CCEEEEEEeC-CCCCCCEEEEeecCCceEEEeehhc---cCCCCEeeeecCCCcEEEEeC
Confidence 45666666543 22 2345566554 699999999886542 34555543 33445677774 889887753
No 351
>PTZ00132 GTP-binding nuclear protein Ran; Provisional
Probab=20.96 E-value=1.5e+02 Score=23.71 Aligned_cols=26 Identities=15% Similarity=-0.001 Sum_probs=21.1
Q ss_pred CceeEecCCCccccHHHHHHHHHhhC
Q psy5461 57 HVPVLCGSSYKNIGVQKLMDAIVDIL 82 (221)
Q Consensus 57 ~~Pv~~gSa~~~~Gi~~LLd~I~~~~ 82 (221)
..+.+..||++|.|+++.+..|...+
T Consensus 142 ~~~~~e~Sa~~~~~v~~~f~~ia~~l 167 (215)
T PTZ00132 142 NLQYYDISAKSNYNFEKPFLWLARRL 167 (215)
T ss_pred CCEEEEEeCCCCCCHHHHHHHHHHHH
Confidence 35678899999999998887777655
No 352
>PRK00556 minC septum formation inhibitor; Reviewed
Probab=20.65 E-value=2.7e+02 Score=22.92 Aligned_cols=17 Identities=24% Similarity=0.612 Sum_probs=14.4
Q ss_pred EEEEceEEcCCCEEEec
Q psy5461 120 FRIYSGAFKKGQKFYNI 136 (221)
Q Consensus 120 ~RV~sG~L~~gd~v~~~ 136 (221)
.+++.|+++.|+.++.-
T Consensus 93 ~~i~~~~iRSGQ~I~~~ 109 (194)
T PRK00556 93 TTIYDRVIRSGEEIYSA 109 (194)
T ss_pred cEEEeCceeCCCEEEeC
Confidence 57789999999999884
No 353
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=20.38 E-value=1.6e+02 Score=19.36 Aligned_cols=13 Identities=8% Similarity=-0.008 Sum_probs=7.7
Q ss_pred ceEEcCCCEEEec
Q psy5461 124 SGAFKKGQKFYNI 136 (221)
Q Consensus 124 sG~L~~gd~v~~~ 136 (221)
..++..||.+.+-
T Consensus 11 ~P~i~~gd~v~i~ 23 (84)
T cd06462 11 EPTIPDGDLVLVD 23 (84)
T ss_pred cCcccCCCEEEEE
Confidence 3456667766664
No 354
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=20.25 E-value=2.2e+02 Score=17.42 Aligned_cols=27 Identities=22% Similarity=0.283 Sum_probs=17.5
Q ss_pred CCCceEEEEEEEce-EEcCCCEEEeccC
Q psy5461 112 KHRGAVTFFRIYSG-AFKKGQKFYNIHL 138 (221)
Q Consensus 112 ~~~G~i~~~RV~sG-~L~~gd~v~~~~~ 138 (221)
+..|++.-+.|-.| .+++||.|..+..
T Consensus 8 ~~~G~V~~v~V~~G~~VkkGd~L~~ld~ 35 (50)
T PF13533_consen 8 PVSGRVESVYVKEGQQVKKGDVLLVLDS 35 (50)
T ss_pred CCCEEEEEEEecCCCEEcCCCEEEEECc
Confidence 34466666666666 5678887777654
Done!