Query psy17313
Match_columns 197
No_of_seqs 160 out of 1080
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 18:48:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17313.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17313hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09601 GTP-binding protein Y 100.0 1.7E-66 3.6E-71 470.9 18.4 180 5-187 184-364 (364)
2 TIGR00092 GTP-binding protein 100.0 1.3E-65 2.9E-70 465.5 17.8 182 5-187 184-368 (368)
3 PTZ00258 GTP-binding protein; 100.0 1.8E-64 3.9E-69 461.1 17.8 184 5-189 205-390 (390)
4 COG0012 Predicted GTPase, prob 100.0 3.3E-58 7.2E-63 415.6 11.7 179 6-187 192-372 (372)
5 KOG1491|consensus 100.0 3.4E-57 7.4E-62 405.2 13.6 183 5-187 209-391 (391)
6 PF06071 YchF-GTPase_C: Protei 100.0 1.2E-49 2.6E-54 293.9 6.1 84 103-186 1-84 (84)
7 cd04867 TGS_YchF_C TGS_YchF_C: 100.0 6.4E-49 1.4E-53 289.0 7.6 83 103-185 1-83 (83)
8 PRK09602 translation-associate 100.0 1.1E-35 2.3E-40 272.1 12.8 155 5-185 202-394 (396)
9 cd04938 TGS_Obg-like TGS_Obg-l 99.9 7.5E-22 1.6E-26 143.5 6.4 65 103-185 1-76 (76)
10 cd01900 YchF YchF subfamily. 99.8 1.2E-19 2.6E-24 159.6 7.9 94 5-101 180-274 (274)
11 COG1163 DRG Predicted GTPase [ 99.7 1.4E-16 3.1E-21 143.2 9.3 124 18-185 237-364 (365)
12 cd01669 TGS_Ygr210_C TGS_Ygr21 99.6 7.6E-16 1.6E-20 112.1 4.6 53 115-184 23-75 (76)
13 cd01666 TGS_DRG_C TGS_DRG_C: 99.4 4.6E-13 1E-17 97.3 5.0 70 103-184 1-74 (75)
14 PF08438 MMR_HSR1_C: GTPase of 98.9 2.5E-09 5.4E-14 83.0 4.4 77 26-110 1-108 (109)
15 PF02824 TGS: TGS domain; Int 98.6 3.5E-08 7.6E-13 68.3 4.1 59 104-184 1-59 (60)
16 KOG1486|consensus 98.5 7.9E-07 1.7E-11 79.0 9.8 122 19-184 237-362 (364)
17 cd01899 Ygr210 Ygr210 subfamil 98.3 2.3E-06 5.1E-11 76.9 7.0 89 5-101 199-318 (318)
18 TIGR00691 spoT_relA (p)ppGpp s 98.1 8E-06 1.7E-10 80.2 7.9 66 102-189 360-425 (683)
19 KOG1487|consensus 98.1 2.7E-06 5.9E-11 75.8 3.4 122 19-184 230-356 (358)
20 PRK10872 relA (p)ppGpp synthet 97.9 3.3E-05 7.2E-10 76.6 7.3 66 102-189 404-469 (743)
21 PRK11092 bifunctional (p)ppGpp 97.3 0.00087 1.9E-08 66.4 8.0 66 102-189 386-451 (702)
22 COG0317 SpoT Guanosine polypho 97.1 0.0021 4.6E-08 63.6 8.8 68 102-191 387-454 (701)
23 cd01616 TGS The TGS domain, na 96.7 0.0031 6.7E-08 40.5 4.0 51 115-184 9-59 (60)
24 PRK12296 obgE GTPase CgtA; Rev 95.2 0.057 1.2E-06 51.8 6.9 48 17-69 281-328 (500)
25 cd01896 DRG The developmentall 95.1 0.061 1.3E-06 45.9 6.2 60 18-109 174-233 (233)
26 PRK12297 obgE GTPase CgtA; Rev 94.2 0.12 2.5E-06 48.6 6.2 40 18-65 272-311 (424)
27 KOG1489|consensus 92.8 0.063 1.4E-06 49.3 1.9 47 17-69 309-355 (366)
28 cd01668 TGS_RelA_SpoT TGS_RelA 91.3 0.53 1.1E-05 30.9 4.7 50 116-184 10-59 (60)
29 PF02421 FeoB_N: Ferrous iron 89.9 0.51 1.1E-05 38.6 4.3 42 19-65 104-145 (156)
30 PRK06437 hypothetical protein; 89.6 2.2 4.8E-05 29.8 6.9 66 103-189 1-66 (67)
31 cd04138 H_N_K_Ras_like H-Ras/N 89.5 2 4.4E-05 32.4 7.2 42 18-64 104-145 (162)
32 cd01897 NOG NOG1 is a nucleola 88.7 1.7 3.6E-05 33.5 6.3 41 19-65 112-152 (168)
33 cd04139 RalA_RalB RalA/RalB su 87.9 1.8 3.9E-05 32.8 6.0 42 19-64 104-145 (164)
34 cd01881 Obg_like The Obg-like 87.7 1.3 2.9E-05 34.1 5.2 42 18-65 118-161 (176)
35 PRK12298 obgE GTPase CgtA; Rev 87.3 1.4 2.9E-05 40.9 5.8 59 19-101 274-332 (390)
36 COG0536 Obg Predicted GTPase [ 86.8 1.4 3.1E-05 40.8 5.5 50 12-64 266-316 (369)
37 TIGR02729 Obg_CgtA Obg family 86.7 1.5 3.3E-05 39.6 5.7 42 18-65 271-313 (329)
38 cd04136 Rap_like Rap-like subf 86.4 3.5 7.7E-05 31.3 6.9 43 19-65 105-147 (163)
39 cd04148 RGK RGK subfamily. Th 86.4 2.9 6.3E-05 35.0 6.9 68 18-110 104-171 (221)
40 cd04171 SelB SelB subfamily. 85.8 2.1 4.5E-05 32.5 5.2 47 19-65 103-150 (164)
41 cd04176 Rap2 Rap2 subgroup. T 85.2 4.5 9.8E-05 31.0 7.0 43 19-65 105-147 (163)
42 cd01859 MJ1464 MJ1464. This f 85.0 3.7 8.1E-05 31.9 6.5 41 19-65 40-80 (156)
43 smart00173 RAS Ras subfamily o 84.9 4.3 9.3E-05 31.1 6.7 43 19-65 104-146 (164)
44 cd04175 Rap1 Rap1 subgroup. T 84.5 5.1 0.00011 30.8 7.0 43 19-65 105-147 (164)
45 PRK12299 obgE GTPase CgtA; Rev 84.5 2.2 4.8E-05 38.7 5.6 43 18-65 269-312 (335)
46 cd01869 Rab1_Ypt1 Rab1/Ypt1 su 84.3 3.5 7.6E-05 31.8 6.0 43 19-65 106-148 (166)
47 TIGR03598 GTPase_YsxC ribosome 84.2 1.2 2.7E-05 35.5 3.5 46 20-65 129-174 (179)
48 COG5257 GCD11 Translation init 84.2 1.1 2.4E-05 41.6 3.5 64 3-68 123-189 (415)
49 PRK15467 ethanolamine utilizat 83.7 3.8 8.2E-05 32.4 6.1 44 19-67 90-133 (158)
50 PF00009 GTP_EFTU: Elongation 83.5 3.9 8.5E-05 32.9 6.2 61 19-101 121-186 (188)
51 cd01898 Obg Obg subfamily. Th 83.3 3.6 7.7E-05 31.6 5.7 43 19-65 113-155 (170)
52 cd01863 Rab18 Rab18 subfamily. 83.3 6.7 0.00015 29.9 7.2 43 18-65 104-146 (161)
53 cd04127 Rab27A Rab27a subfamil 82.9 5.7 0.00012 31.0 6.8 42 20-65 120-161 (180)
54 cd04145 M_R_Ras_like M-Ras/R-R 82.7 4.5 9.8E-05 30.8 6.0 41 20-64 107-147 (164)
55 cd04119 RJL RJL (RabJ-Like) su 81.5 5.3 0.00011 30.3 6.0 43 19-65 109-151 (168)
56 cd01861 Rab6 Rab6 subfamily. 81.5 6.8 0.00015 29.7 6.6 41 20-64 105-145 (161)
57 cd00881 GTP_translation_factor 80.6 6 0.00013 30.6 6.1 14 19-32 113-126 (189)
58 cd01888 eIF2_gamma eIF2-gamma 80.4 4.5 9.7E-05 33.3 5.6 47 19-65 136-183 (203)
59 cd01868 Rab11_like Rab11-like. 80.1 6.5 0.00014 30.1 6.1 41 20-64 108-148 (165)
60 cd04107 Rab32_Rab38 Rab38/Rab3 79.5 10 0.00022 30.7 7.3 43 19-65 109-152 (201)
61 cd04144 Ras2 Ras2 subfamily. 79.4 5 0.00011 32.2 5.4 43 19-65 105-147 (190)
62 cd04152 Arl4_Arl7 Arl4/Arl7 su 78.7 10 0.00022 30.3 7.0 16 17-32 106-121 (183)
63 TIGR02528 EutP ethanolamine ut 78.3 2.3 5.1E-05 32.0 3.0 41 21-65 89-129 (142)
64 cd04122 Rab14 Rab14 subfamily. 77.5 8.5 0.00018 29.7 6.1 43 19-65 106-148 (166)
65 cd04124 RabL2 RabL2 subfamily. 76.6 8.2 0.00018 29.9 5.8 40 19-65 103-142 (161)
66 cd04143 Rhes_like Rhes_like su 76.6 9.1 0.0002 32.9 6.5 44 19-65 112-155 (247)
67 cd01879 FeoB Ferrous iron tran 76.4 6.8 0.00015 29.5 5.1 41 20-65 101-141 (158)
68 TIGR00436 era GTP-binding prot 75.8 6.6 0.00014 33.9 5.5 44 19-66 106-149 (270)
69 cd01867 Rab8_Rab10_Rab13_like 75.7 10 0.00023 29.3 6.2 43 19-65 107-149 (167)
70 cd04137 RheB Rheb (Ras Homolog 75.7 14 0.0003 28.8 6.9 43 18-64 104-146 (180)
71 COG1159 Era GTPase [General fu 75.2 10 0.00022 34.5 6.6 56 7-67 102-158 (298)
72 cd04123 Rab21 Rab21 subfamily. 74.9 12 0.00026 28.0 6.2 42 20-65 105-146 (162)
73 cd01865 Rab3 Rab3 subfamily. 74.3 12 0.00026 28.9 6.1 41 20-64 106-146 (165)
74 cd01857 HSR1_MMR1 HSR1/MMR1. 74.3 4.9 0.00011 31.0 3.9 42 19-66 41-82 (141)
75 smart00175 RAB Rab subfamily o 74.0 12 0.00026 28.3 6.0 42 19-64 104-145 (164)
76 cd01862 Rab7 Rab7 subfamily. 73.3 14 0.0003 28.3 6.2 44 19-65 108-151 (172)
77 COG1188 Ribosome-associated he 73.0 3.9 8.5E-05 31.5 3.0 29 159-187 29-61 (100)
78 KOG0466|consensus 72.9 3.4 7.3E-05 38.4 3.0 66 3-70 162-230 (466)
79 cd04141 Rit_Rin_Ric Rit/Rin/Ri 72.9 15 0.00034 29.0 6.6 43 19-65 106-148 (172)
80 PF09138 Urm1: Urm1 (Ubiquitin 72.8 2 4.2E-05 32.8 1.3 16 170-185 76-91 (96)
81 cd04116 Rab9 Rab9 subfamily. 72.4 15 0.00032 28.3 6.3 43 19-65 113-155 (170)
82 cd04140 ARHI_like ARHI subfami 72.3 13 0.00027 28.8 5.8 43 19-65 107-149 (165)
83 PRK15494 era GTPase Era; Provi 72.2 11 0.00025 33.9 6.3 43 20-67 160-202 (339)
84 KOG4146|consensus 72.0 2.3 4.9E-05 32.6 1.4 17 169-185 80-96 (101)
85 cd04106 Rab23_lke Rab23-like s 71.6 7.8 0.00017 29.5 4.4 42 19-64 105-146 (162)
86 PRK04213 GTP-binding protein; 71.5 16 0.00034 29.3 6.4 14 19-32 129-142 (201)
87 COG1160 Predicted GTPases [Gen 70.8 12 0.00027 35.7 6.3 50 6-64 99-148 (444)
88 cd01855 YqeH YqeH. YqeH is an 70.3 13 0.00029 29.9 5.7 47 18-67 59-111 (190)
89 cd04112 Rab26 Rab26 subfamily. 70.3 14 0.00031 29.5 6.0 43 19-65 105-147 (191)
90 cd04121 Rab40 Rab40 subfamily. 70.0 15 0.00033 30.1 6.1 42 20-65 110-151 (189)
91 cd01864 Rab19 Rab19 subfamily. 69.9 18 0.0004 27.7 6.3 42 20-64 108-149 (165)
92 PF01043 SecA_PP_bind: SecA pr 69.8 2.7 5.9E-05 32.6 1.5 82 94-184 11-92 (113)
93 cd04101 RabL4 RabL4 (Rab-like4 69.2 20 0.00042 27.3 6.3 41 20-64 107-147 (164)
94 PRK13796 GTPase YqeH; Provisio 69.1 56 0.0012 29.9 10.1 147 19-183 95-259 (365)
95 COG5131 URM1 Ubiquitin-like pr 68.8 2.9 6.3E-05 31.8 1.4 17 169-185 75-91 (96)
96 cd01866 Rab2 Rab2 subfamily. 68.4 19 0.00042 27.9 6.1 43 19-65 108-150 (168)
97 cd01860 Rab5_related Rab5-rela 68.3 21 0.00046 27.0 6.2 42 19-64 105-146 (163)
98 PLN03118 Rab family protein; P 67.6 26 0.00057 28.5 7.1 42 19-64 119-160 (211)
99 cd04177 RSR1 RSR1 subgroup. R 67.3 27 0.00058 27.0 6.7 44 19-65 105-148 (168)
100 cd01892 Miro2 Miro2 subfamily. 66.9 15 0.00032 28.9 5.3 50 12-65 100-150 (169)
101 cd04103 Centaurin_gamma Centau 66.6 14 0.00031 29.0 5.1 45 20-65 99-143 (158)
102 cd04118 Rab24 Rab24 subfamily. 66.0 23 0.00049 28.1 6.2 44 20-65 105-150 (193)
103 cd01889 SelB_euk SelB subfamil 66.0 7.1 0.00015 31.4 3.3 47 20-66 120-171 (192)
104 cd04115 Rab33B_Rab33A Rab33B/R 65.9 15 0.00032 28.6 5.0 44 18-65 107-150 (170)
105 cd04156 ARLTS1 ARLTS1 subfamil 65.8 6 0.00013 30.1 2.7 14 19-32 100-113 (160)
106 cd01883 EF1_alpha Eukaryotic e 65.7 11 0.00023 31.5 4.4 52 19-70 136-194 (219)
107 PLN03108 Rab family protein; P 65.6 15 0.00032 30.3 5.2 43 19-65 110-152 (210)
108 cd04161 Arl2l1_Arl13_like Arl2 65.4 6.9 0.00015 30.7 3.1 16 17-32 97-112 (167)
109 cd00877 Ran Ran (Ras-related n 64.8 12 0.00026 29.3 4.3 42 20-67 104-145 (166)
110 cd00876 Ras Ras family. The R 64.5 18 0.00039 27.0 5.1 43 19-65 103-145 (160)
111 PTZ00099 rab6; Provisional 64.5 30 0.00064 28.0 6.7 43 19-65 84-126 (176)
112 PRK01777 hypothetical protein; 64.1 25 0.00054 26.5 5.7 59 115-194 19-82 (95)
113 TIGR03596 GTPase_YlqF ribosome 63.8 17 0.00037 31.6 5.4 45 19-69 47-91 (276)
114 smart00174 RHO Rho (Ras homolo 63.5 23 0.0005 27.3 5.7 14 19-32 101-114 (174)
115 PRK00089 era GTPase Era; Revie 63.1 27 0.00059 30.1 6.6 45 20-67 113-157 (292)
116 smart00178 SAR Sar1p-like memb 62.7 33 0.00071 27.4 6.6 44 18-65 116-169 (184)
117 PRK04000 translation initiatio 62.7 18 0.00039 33.5 5.7 56 12-67 131-187 (411)
118 cd01856 YlqF YlqF. Proteins o 62.6 19 0.0004 28.7 5.1 45 17-67 43-87 (171)
119 PRK00454 engB GTP-binding prot 62.6 18 0.0004 28.5 5.1 43 20-64 135-177 (196)
120 cd04160 Arfrp1 Arfrp1 subfamil 62.2 20 0.00043 27.4 5.1 44 18-65 105-153 (167)
121 cd04109 Rab28 Rab28 subfamily. 62.0 26 0.00056 28.8 6.0 41 21-65 110-150 (215)
122 PLN03110 Rab GTPase; Provision 61.8 24 0.00053 29.2 5.9 42 20-65 117-158 (216)
123 cd00154 Rab Rab family. Rab G 61.3 17 0.00038 26.7 4.5 41 20-64 105-145 (159)
124 cd04147 Ras_dva Ras-dva subfam 61.3 36 0.00079 27.4 6.7 67 19-108 103-169 (198)
125 cd01878 HflX HflX subfamily. 61.1 22 0.00048 28.5 5.4 38 19-65 152-189 (204)
126 cd04142 RRP22 RRP22 subfamily. 60.9 14 0.00031 30.3 4.2 44 19-65 115-158 (198)
127 cd04117 Rab15 Rab15 subfamily. 60.9 32 0.0007 26.6 6.1 42 20-65 105-146 (161)
128 PRK09554 feoB ferrous iron tra 60.6 14 0.0003 37.5 4.8 45 20-69 112-156 (772)
129 cd04154 Arl2 Arl2 subfamily. 60.4 22 0.00047 27.8 5.1 44 18-65 113-159 (173)
130 PRK09563 rbgA GTPase YlqF; Rev 59.8 20 0.00044 31.4 5.2 122 19-151 50-206 (287)
131 TIGR03597 GTPase_YqeH ribosome 59.8 73 0.0016 29.0 9.0 107 19-135 89-218 (360)
132 cd04146 RERG_RasL11_like RERG/ 59.4 18 0.00038 27.8 4.4 43 19-65 105-147 (165)
133 cd04120 Rab12 Rab12 subfamily. 58.6 34 0.00074 28.4 6.2 44 19-65 104-147 (202)
134 PTZ00327 eukaryotic translatio 58.3 21 0.00046 34.0 5.4 53 15-67 166-219 (460)
135 cd04158 ARD1 ARD1 subfamily. 58.3 52 0.0011 25.6 6.9 43 19-65 99-145 (169)
136 cd01890 LepA LepA subfamily. 58.1 34 0.00074 26.4 5.8 14 19-32 118-131 (179)
137 KOG1145|consensus 58.1 26 0.00056 34.9 6.0 41 20-65 253-300 (683)
138 cd01858 NGP_1 NGP-1. Autoanti 58.0 20 0.00042 28.0 4.4 12 21-32 40-51 (157)
139 cd01891 TypA_BipA TypA (tyrosi 57.9 24 0.00053 28.3 5.1 52 20-72 117-173 (194)
140 cd04132 Rho4_like Rho4-like su 57.7 31 0.00068 27.1 5.6 46 19-66 104-152 (187)
141 cd04104 p47_IIGP_like p47 (47- 57.3 24 0.00052 28.8 5.0 58 7-65 95-166 (197)
142 cd01895 EngA2 EngA2 subfamily. 57.3 12 0.00025 28.2 3.0 47 19-67 112-161 (174)
143 TIGR00437 feoB ferrous iron tr 57.0 16 0.00035 35.7 4.5 46 19-69 98-143 (591)
144 cd01764 Urm1 Urm1-like ubuitin 56.2 7.1 0.00015 29.2 1.5 20 168-187 72-91 (94)
145 cd04108 Rab36_Rab34 Rab34/Rab3 56.1 39 0.00084 26.6 5.9 42 21-65 107-149 (170)
146 PF03658 Ub-RnfH: RnfH family 56.0 34 0.00075 25.4 5.1 16 169-184 56-71 (84)
147 PTZ00369 Ras-like protein; Pro 55.9 63 0.0014 25.7 7.2 45 19-67 109-153 (189)
148 cd04162 Arl9_Arfrp2_like Arl9/ 55.8 11 0.00024 29.5 2.7 43 19-67 98-146 (164)
149 TIGR03680 eif2g_arch translati 55.6 25 0.00055 32.4 5.4 56 11-66 125-181 (406)
150 cd00157 Rho Rho (Ras homology) 55.1 29 0.00064 26.4 4.9 45 19-64 103-156 (171)
151 cd04159 Arl10_like Arl10-like 54.3 28 0.00061 25.6 4.6 15 18-32 99-113 (159)
152 cd04153 Arl5_Arl8 Arl5/Arl8 su 54.2 15 0.00032 29.0 3.1 43 19-65 115-160 (174)
153 cd04111 Rab39 Rab39 subfamily. 54.2 63 0.0014 26.6 7.1 41 20-64 109-149 (211)
154 cd04151 Arl1 Arl1 subfamily. 53.4 15 0.00033 28.1 3.0 43 19-65 99-144 (158)
155 TIGR00073 hypB hydrogenase acc 53.2 15 0.00033 30.2 3.2 44 19-64 147-190 (207)
156 cd04163 Era Era subfamily. Er 53.2 14 0.0003 27.4 2.8 45 20-67 111-155 (168)
157 PF11372 DUF3173: Domain of un 52.8 3.5 7.5E-05 28.9 -0.6 31 145-178 3-34 (59)
158 TIGR00231 small_GTP small GTP- 52.5 41 0.00089 24.2 5.2 41 20-65 108-148 (161)
159 PF14478 DUF4430: Domain of un 52.0 8.1 0.00018 26.8 1.2 14 171-184 55-68 (68)
160 cd01667 TGS_ThrRS_N TGS _ThrRS 51.8 31 0.00067 21.5 3.9 49 117-184 11-59 (61)
161 cd01884 EF_Tu EF-Tu subfamily. 51.7 25 0.00055 29.0 4.3 49 21-69 118-171 (195)
162 PF00071 Ras: Ras family; Int 51.3 42 0.0009 25.4 5.2 40 21-64 105-144 (162)
163 cd04157 Arl6 Arl6 subfamily. 51.2 24 0.00052 26.6 3.8 14 19-32 103-116 (162)
164 cd00880 Era_like Era (E. coli 50.8 42 0.00091 24.2 5.0 16 17-32 101-116 (163)
165 cd00878 Arf_Arl Arf (ADP-ribos 50.4 45 0.00098 25.2 5.3 43 18-64 98-143 (158)
166 cd01849 YlqF_related_GTPase Yl 50.3 17 0.00037 28.3 2.9 48 19-72 28-76 (155)
167 KOG0394|consensus 49.8 23 0.00051 30.5 3.8 44 20-64 118-161 (210)
168 cd04166 CysN_ATPS CysN_ATPS su 49.8 28 0.00061 28.6 4.3 53 20-72 130-185 (208)
169 cd04125 RabA_like RabA-like su 49.6 61 0.0013 25.6 6.1 42 20-65 105-146 (188)
170 smart00177 ARF ARF-like small 49.6 24 0.00052 27.9 3.7 13 20-32 114-126 (175)
171 PF13984 MsyB: MsyB protein 49.5 3.9 8.5E-05 32.0 -0.8 11 171-181 36-46 (122)
172 PLN00223 ADP-ribosylation fact 49.3 54 0.0012 26.2 5.8 14 19-32 117-130 (181)
173 PRK11171 hypothetical protein; 48.8 18 0.00038 31.7 3.1 58 113-190 185-242 (266)
174 cd04113 Rab4 Rab4 subfamily. 48.3 34 0.00074 25.9 4.3 41 20-64 105-145 (161)
175 cd04114 Rab30 Rab30 subfamily. 47.7 56 0.0012 24.9 5.5 13 20-32 112-124 (169)
176 PF06858 NOG1: Nucleolar GTP-b 47.6 17 0.00036 25.4 2.1 25 7-31 33-58 (58)
177 cd04168 TetM_like Tet(M)-like 47.4 72 0.0016 27.2 6.6 29 20-49 116-144 (237)
178 cd00879 Sar1 Sar1 subfamily. 47.4 84 0.0018 24.6 6.6 28 19-50 119-146 (190)
179 cd04164 trmE TrmE (MnmE, ThdF, 47.1 70 0.0015 23.6 5.8 36 18-64 105-140 (157)
180 TIGR03594 GTPase_EngA ribosome 46.7 30 0.00064 31.5 4.3 50 19-71 282-334 (429)
181 cd01894 EngA1 EngA1 subfamily. 46.5 44 0.00096 24.7 4.6 13 20-32 105-117 (157)
182 COG0370 FeoB Fe2+ transport sy 46.2 32 0.00069 34.5 4.6 42 19-65 107-148 (653)
183 PRK00093 GTP-binding protein D 45.9 31 0.00067 31.5 4.3 53 19-72 283-335 (435)
184 PRK03003 GTP-binding protein D 45.7 57 0.0012 30.6 6.2 80 19-100 321-403 (472)
185 PRK00098 GTPase RsgA; Reviewed 45.5 9 0.0002 33.9 0.7 74 19-102 110-189 (298)
186 cd01876 YihA_EngB The YihA (En 45.2 29 0.00064 25.7 3.5 45 20-64 110-154 (170)
187 cd01875 RhoG RhoG subfamily. 44.9 70 0.0015 25.7 5.8 45 19-64 106-160 (191)
188 COG2262 HflX GTPases [General 43.9 51 0.0011 31.3 5.4 70 10-110 295-365 (411)
189 COG0024 Map Methionine aminope 43.8 18 0.00038 32.1 2.3 58 118-187 31-99 (255)
190 PTZ00133 ADP-ribosylation fact 43.7 43 0.00094 26.7 4.4 14 19-32 117-130 (182)
191 PF09269 DUF1967: Domain of un 43.6 19 0.00041 25.4 2.0 22 152-183 41-62 (69)
192 TIGR02988 YaaA_near_RecF S4 do 43.3 22 0.00048 23.7 2.2 24 160-183 30-58 (59)
193 PF02311 AraC_binding: AraC-li 43.3 14 0.0003 26.7 1.3 26 162-187 32-57 (136)
194 cd04128 Spg1 Spg1p. Spg1p (se 43.2 71 0.0015 25.6 5.6 42 22-65 106-150 (182)
195 COG1917 Uncharacterized conser 43.0 14 0.00031 28.2 1.4 29 162-190 73-101 (131)
196 PRK11467 secY/secA suppressor 42.8 5.5 0.00012 31.3 -0.9 11 171-181 38-48 (124)
197 cd04150 Arf1_5_like Arf1-Arf5- 41.7 69 0.0015 24.7 5.2 14 19-32 100-113 (159)
198 PRK13768 GTPase; Provisional 41.3 60 0.0013 27.9 5.2 14 19-32 161-174 (253)
199 PRK12289 GTPase RsgA; Reviewed 40.6 22 0.00049 32.6 2.5 81 19-105 119-200 (352)
200 TIGR03595 Obg_CgtA_exten Obg f 40.0 31 0.00067 24.3 2.6 22 152-183 41-62 (69)
201 cd04130 Wrch_1 Wrch-1 subfamil 39.8 49 0.0011 25.7 4.1 45 19-65 103-158 (173)
202 cd01887 IF2_eIF5B IF2/eIF5B (i 39.3 37 0.00081 25.7 3.3 14 19-32 101-114 (168)
203 cd01854 YjeQ_engC YjeQ/EngC. 38.8 17 0.00036 32.0 1.4 77 19-101 108-185 (287)
204 COG1977 MoaD Molybdopterin con 38.8 20 0.00044 26.0 1.6 18 167-184 61-78 (84)
205 PF00498 FHA: FHA domain; Int 38.8 22 0.00048 23.7 1.7 15 169-183 53-67 (68)
206 COG0012 Predicted GTPase, prob 38.6 14 0.0003 34.6 0.8 57 80-144 279-346 (372)
207 cd04110 Rab35 Rab35 subfamily. 38.6 59 0.0013 26.2 4.5 42 19-64 109-150 (199)
208 cd04134 Rho3 Rho3 subfamily. 38.4 79 0.0017 25.2 5.2 14 19-32 103-116 (189)
209 PF13128 DUF3954: Protein of u 38.1 26 0.00056 23.8 1.9 20 169-190 9-28 (50)
210 PF09547 Spore_IV_A: Stage IV 37.7 91 0.002 30.2 6.1 48 8-63 169-217 (492)
211 PRK11507 ribosome-associated p 37.5 25 0.00054 25.3 1.8 36 148-183 20-61 (70)
212 TIGR02836 spore_IV_A stage IV 37.3 1E+02 0.0022 30.0 6.3 49 7-63 168-217 (492)
213 KOG1490|consensus 37.1 37 0.0008 33.5 3.4 63 3-69 261-329 (620)
214 cd01871 Rac1_like Rac1-like su 37.1 1.1E+02 0.0025 24.0 5.9 45 19-64 104-158 (174)
215 cd01893 Miro1 Miro1 subfamily. 36.9 52 0.0011 25.4 3.8 13 20-32 103-115 (166)
216 COG2229 Predicted GTPase [Gene 36.8 78 0.0017 27.0 5.0 40 21-64 122-161 (187)
217 cd01886 EF-G Elongation factor 36.7 34 0.00075 29.9 3.0 44 19-64 115-158 (270)
218 TIGR03156 GTP_HflX GTP-binding 36.6 83 0.0018 28.6 5.6 44 11-65 293-336 (351)
219 TIGR00157 ribosome small subun 36.5 25 0.00054 30.2 2.0 45 19-69 66-111 (245)
220 cd00882 Ras_like_GTPase Ras-li 35.9 92 0.002 21.8 4.7 47 15-65 97-144 (157)
221 cd04126 Rab20 Rab20 subfamily. 35.8 1.1E+02 0.0024 25.8 5.8 14 19-32 99-112 (220)
222 PF07883 Cupin_2: Cupin domain 35.4 16 0.00034 24.2 0.5 25 164-188 30-54 (71)
223 cd04129 Rho2 Rho2 subfamily. 35.2 1E+02 0.0022 24.4 5.4 46 19-65 104-157 (187)
224 CHL00189 infB translation init 35.0 1.3E+02 0.0027 30.7 7.0 42 19-65 346-394 (742)
225 smart00176 RAN Ran (Ras-relate 34.9 1.1E+02 0.0023 25.3 5.6 40 19-64 98-137 (200)
226 cd04149 Arf6 Arf6 subfamily. 34.8 72 0.0016 25.0 4.3 42 20-65 110-154 (168)
227 PRK08364 sulfur carrier protei 34.3 1.6E+02 0.0034 20.4 6.1 59 109-188 10-68 (70)
228 cd01873 RhoBTB RhoBTB subfamil 34.0 68 0.0015 26.3 4.2 44 19-64 119-179 (195)
229 PLN03071 GTP-binding nuclear p 33.6 1.1E+02 0.0025 25.3 5.6 40 19-64 116-155 (219)
230 cd07357 HN_L-whirlin_R2_like S 33.4 56 0.0012 24.3 3.2 41 65-105 8-53 (81)
231 cd04165 GTPBP1_like GTPBP1-lik 32.1 92 0.002 26.3 4.8 14 19-32 137-150 (224)
232 PRK10512 selenocysteinyl-tRNA- 31.5 60 0.0013 32.0 4.0 47 21-67 105-152 (614)
233 TIGR01683 thiS thiamine biosyn 31.4 49 0.0011 22.4 2.5 57 116-189 7-63 (64)
234 PRK13956 dut deoxyuridine 5'-t 31.4 94 0.002 25.2 4.5 48 114-181 59-118 (147)
235 cd01870 RhoA_like RhoA-like su 31.1 81 0.0018 24.2 4.0 14 19-32 104-117 (175)
236 KOG0073|consensus 30.7 51 0.0011 28.0 2.9 45 18-64 115-161 (185)
237 PF01479 S4: S4 domain; Inter 30.4 35 0.00075 21.5 1.5 19 163-181 25-48 (48)
238 CHL00075 rpl21 ribosomal prote 30.4 36 0.00079 26.3 1.8 19 166-184 7-25 (108)
239 PRK05659 sulfur carrier protei 30.2 45 0.00097 22.5 2.1 57 116-189 9-65 (66)
240 TIGR03214 ura-cupin putative a 30.2 26 0.00057 30.6 1.2 28 162-189 209-236 (260)
241 PLN00043 elongation factor 1-a 30.2 70 0.0015 30.1 4.1 54 17-70 142-202 (447)
242 PRK09435 membrane ATPase/prote 30.0 81 0.0018 28.8 4.3 43 23-65 197-244 (332)
243 PRK09518 bifunctional cytidyla 30.0 1.4E+02 0.003 29.8 6.3 100 19-126 560-665 (712)
244 PRK09518 bifunctional cytidyla 29.6 1.4E+02 0.0029 29.9 6.1 15 18-32 381-395 (712)
245 TIGR00061 L21 ribosomal protei 29.5 38 0.00083 25.8 1.8 19 166-184 4-22 (101)
246 PRK09866 hypothetical protein; 29.5 98 0.0021 31.5 5.1 60 7-69 275-341 (741)
247 PRK05291 trmE tRNA modificatio 29.5 98 0.0021 29.1 4.9 36 18-65 319-354 (449)
248 PTZ00141 elongation factor 1- 29.4 68 0.0015 30.2 3.8 56 15-70 140-202 (446)
249 COG3837 Uncharacterized conser 28.8 31 0.00068 28.7 1.3 27 163-189 74-100 (161)
250 COG1160 Predicted GTPases [Gen 28.6 2.1E+02 0.0046 27.5 6.9 84 12-99 281-371 (444)
251 cd01092 APP-like Similar to Pr 28.5 27 0.00059 28.1 0.9 61 120-187 23-83 (208)
252 PF14451 Ub-Mut7C: Mut7-C ubiq 28.5 41 0.00089 24.6 1.8 46 116-184 26-74 (81)
253 PRK09570 rpoH DNA-directed RNA 28.4 28 0.0006 25.7 0.8 23 72-94 18-41 (79)
254 PF00025 Arf: ADP-ribosylation 28.4 78 0.0017 25.2 3.6 44 17-64 112-159 (175)
255 COG0182 Predicted translation 28.2 78 0.0017 29.4 3.9 39 88-130 169-207 (346)
256 TIGR03594 GTPase_EngA ribosome 28.0 1.2E+02 0.0026 27.5 5.2 41 19-67 106-146 (429)
257 TIGR00487 IF-2 translation ini 27.9 1.8E+02 0.004 28.5 6.6 41 20-65 187-234 (587)
258 cd01874 Cdc42 Cdc42 subfamily. 27.7 79 0.0017 25.0 3.5 14 19-32 104-117 (175)
259 TIGR00483 EF-1_alpha translati 27.4 78 0.0017 29.2 3.8 53 20-72 141-198 (426)
260 PRK10463 hydrogenase nickel in 27.2 70 0.0015 28.8 3.4 49 15-65 225-273 (290)
261 TIGR02219 phage_NlpC_fam putat 27.1 53 0.0011 25.6 2.3 15 174-188 76-90 (134)
262 PRK06488 sulfur carrier protei 27.0 59 0.0013 22.0 2.3 18 172-189 47-64 (65)
263 cd07347 harmonin_N_like N-term 27.0 93 0.002 22.8 3.4 31 72-102 16-49 (78)
264 PRK12288 GTPase RsgA; Reviewed 26.8 48 0.001 30.3 2.3 76 19-103 149-231 (347)
265 TIGR00101 ureG urease accessor 26.3 2E+02 0.0043 23.8 5.8 40 23-64 140-179 (199)
266 COG1920 Predicted nucleotidylt 26.3 1.3E+02 0.0029 26.0 4.7 48 58-110 4-54 (210)
267 cd01882 BMS1 Bms1. Bms1 is an 26.1 1.6E+02 0.0034 24.8 5.2 45 20-64 132-179 (225)
268 PF02563 Poly_export: Polysacc 26.1 46 0.001 23.7 1.7 19 169-187 7-25 (82)
269 PRK03003 GTP-binding protein D 25.9 1.5E+02 0.0032 27.9 5.4 15 18-32 144-158 (472)
270 PRK13290 ectC L-ectoine syntha 25.9 35 0.00076 26.7 1.1 56 114-190 37-94 (125)
271 TIGR00750 lao LAO/AO transport 25.7 1.5E+02 0.0032 26.1 5.1 26 5-32 159-184 (300)
272 cd04133 Rop_like Rop subfamily 25.7 1.1E+02 0.0024 24.6 4.0 44 19-64 104-156 (176)
273 COG0218 Predicted GTPase [Gene 25.5 1.9E+02 0.0042 24.8 5.5 49 15-63 130-179 (200)
274 PRK05124 cysN sulfate adenylyl 25.3 1.3E+02 0.0028 28.6 4.9 52 20-73 160-217 (474)
275 PRK09943 DNA-binding transcrip 25.0 47 0.001 26.9 1.7 27 165-191 140-166 (185)
276 PF13543 KSR1-SAM: SAM like do 24.3 1E+02 0.0022 24.7 3.4 32 69-100 96-128 (129)
277 PRK05306 infB translation init 24.2 1.6E+02 0.0035 30.1 5.7 45 20-65 389-436 (787)
278 PF06241 DUF1012: Protein of u 24.1 52 0.0011 28.3 1.8 51 126-188 100-151 (206)
279 TIGR01663 PNK-3'Pase polynucle 24.1 79 0.0017 30.8 3.3 45 133-186 57-101 (526)
280 cd04172 Rnd3_RhoE_Rho8 Rnd3/Rh 24.1 1.3E+02 0.0027 24.4 4.1 44 19-64 108-162 (182)
281 PF00829 Ribosomal_L21p: Ribos 23.8 50 0.0011 24.8 1.5 19 166-184 5-23 (96)
282 PRK05573 rplU 50S ribosomal pr 23.0 60 0.0013 24.8 1.8 19 166-184 5-23 (103)
283 PF06249 EutQ: Ethanolamine ut 22.6 55 0.0012 26.9 1.7 18 166-183 108-125 (152)
284 PF10416 IBD: Transcription-in 22.3 49 0.0011 25.8 1.3 20 103-122 107-126 (128)
285 cd00559 Cyanase_C Cyanase C-te 22.2 81 0.0018 22.8 2.2 17 128-144 22-38 (69)
286 TIGR00485 EF-Tu translation el 22.0 1.1E+02 0.0023 28.1 3.6 56 10-65 118-177 (394)
287 cd04131 Rnd Rnd subfamily. Th 21.9 1.5E+02 0.0032 23.7 4.1 44 19-64 104-158 (178)
288 COG0756 Dut dUTPase [Nucleotid 21.9 71 0.0015 26.2 2.2 45 116-181 69-113 (148)
289 PRK07696 sulfur carrier protei 21.7 89 0.0019 21.6 2.4 19 171-189 48-66 (67)
290 PF13275 S4_2: S4 domain; PDB: 21.6 25 0.00055 24.8 -0.4 35 149-183 17-57 (65)
291 cd04174 Rnd1_Rho6 Rnd1/Rho6 su 21.5 1.6E+02 0.0035 25.1 4.4 44 19-64 116-170 (232)
292 cd01850 CDC_Septin CDC/Septin. 21.5 1.3E+02 0.0029 26.2 4.0 53 6-62 131-183 (276)
293 COG0261 RplU Ribosomal protein 21.4 68 0.0015 24.9 1.8 19 166-184 5-23 (103)
294 PF08006 DUF1700: Protein of u 21.2 74 0.0016 25.8 2.2 18 65-82 10-27 (181)
295 PRK07440 hypothetical protein; 20.9 94 0.002 21.7 2.4 19 171-189 51-69 (70)
296 PLN00051 RNA-binding S4 domain 20.7 72 0.0016 28.3 2.1 23 162-184 214-241 (267)
297 TIGR01394 TypA_BipA GTP-bindin 20.7 1.9E+02 0.0042 28.4 5.3 48 19-67 115-167 (594)
298 PRK12317 elongation factor 1-a 20.4 1.4E+02 0.0031 27.4 4.1 53 20-72 139-196 (425)
299 cd04135 Tc10 TC10 subfamily. 20.4 2.6E+02 0.0055 21.3 5.0 15 18-32 102-116 (174)
300 cd00565 ThiS ThiaminS ubiquiti 20.4 97 0.0021 20.9 2.3 53 116-189 8-64 (65)
301 PRK10348 ribosome-associated h 20.3 1.2E+02 0.0026 24.4 3.1 27 161-187 31-61 (133)
302 PRK05433 GTP-binding protein L 20.2 2.1E+02 0.0045 28.2 5.4 43 20-65 126-168 (600)
303 PRK05863 sulfur carrier protei 20.0 73 0.0016 21.8 1.6 56 116-189 9-64 (65)
No 1
>PRK09601 GTP-binding protein YchF; Reviewed
Probab=100.00 E-value=1.7e-66 Score=470.87 Aligned_cols=180 Identities=44% Similarity=0.763 Sum_probs=172.4
Q ss_pred ChHHHHHhhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHh
Q psy17313 5 HHLRIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQ 84 (197)
Q Consensus 5 ~~~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~ 84 (197)
.++|.+.|++++|||+||||||+|++|.|+.. ++++++++++|+.++ +.++||+||++|.+|++|+++++++||+++
T Consensus 184 ~~~e~~~l~~~~llt~KP~i~v~N~~e~~~~~-~~~~~~~i~~~~~~~--~~~~i~~sa~~E~el~~l~~ee~~~fl~~~ 260 (364)
T PRK09601 184 TDEEEKLLKSLQLLTAKPVLYVANVDEDDLAD-GNPYVKKVREIAAKE--GAEVVVICAKIEAEIAELDDEEKAEFLEEL 260 (364)
T ss_pred CHHHHHHHHHhcccccCCeEEEEECCcccccc-ccHHHHHHHHHHHHc--CCeEEEEEHHHHHHHHcCCHHHHHHHHHHc
Confidence 35788999999999999999999999988753 688999999999876 678999999999999999999999999999
Q ss_pred C-CcchHHHHHHHHHhhcCCeEEeecCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHc
Q psy17313 85 K-ATSVLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAA 163 (197)
Q Consensus 85 g-~~sgl~~li~~~y~lL~LitffT~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~ 163 (197)
| .+||++++|+++|++||||+|||||++|||||||++|+|||||||+|||||+|||||||||+|+||+++||++.||++
T Consensus 261 g~~~s~~~~ii~~~~~~L~li~fftvg~~evrawti~~GstA~~aAg~IHsD~~kgFI~AeVi~~~d~~~~g~~~~ak~~ 340 (364)
T PRK09601 261 GLEESGLDRLIRAGYELLGLITYFTAGPKEVRAWTIKKGTTAPQAAGVIHTDFEKGFIRAEVISYDDLIEYGSEAGAKEA 340 (364)
T ss_pred CCcchhHHHHHHHHHHHhCCEEEecCCCCeEEEEEeCCCCchHHHhhcchhhHhhccEEEEEecHHHHHHcCCHHHHHHc
Confidence 9 889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccCCceeecCCCEEEEEEcc
Q psy17313 164 GKYRQQGRAYTVEDGDIIFFKFNA 187 (197)
Q Consensus 164 Gk~r~eGkdYivqDGDIi~f~fn~ 187 (197)
||+|++||||+|||||||+||||+
T Consensus 341 gk~rleGkdY~v~DGDIi~f~fn~ 364 (364)
T PRK09601 341 GKVRLEGKDYIVQDGDVMHFRFNV 364 (364)
T ss_pred cceeccCCceEecCCCEEEEEcCC
Confidence 999999999999999999999996
No 2
>TIGR00092 GTP-binding protein YchF. This predicted GTP-binding protein is found in a single copy in every complete bacterial genome, and is found in Eukaryotes. A more distantly related protein, separated from this model, is found in the archaea. It is known to bind GTP and double-stranded nucleic acid. It is suggested to belong to a nucleoprotein complex and act as a translation factor.
Probab=100.00 E-value=1.3e-65 Score=465.45 Aligned_cols=182 Identities=40% Similarity=0.667 Sum_probs=168.9
Q ss_pred ChHHHHHhhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCC-CCeEEEechhhchhhcCCCHHHHHHHHHH
Q psy17313 5 HHLRIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDP-GATIIPFSGVFEHQLVDMPDDERQRYLDE 83 (197)
Q Consensus 5 ~~~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~-~~~vv~~sa~~E~el~~l~~ee~~~fl~~ 83 (197)
.++|..++++|+|||.||++||+|++|+++..++|.+.+.++ |++++++ +..++++||++|.||.+|++||+++||++
T Consensus 184 ~~ee~~~~~~~~llt~Kp~~~v~N~~e~~~~~~n~~~~~~~~-~~~~~~~~~~~~~~~~a~~E~el~~l~~ee~~~fl~~ 262 (368)
T TIGR00092 184 SKEELILIKSLNLLTKKPIILIANVSEDYLRNLNNNYLLIVE-WIAAYSKGDPKVVFVCALEESELSELDDEERQEFLQK 262 (368)
T ss_pred CHHHHHHHHhCcchhhCCEEEEEECCHHHhhhcccHHHHHHH-HHhhcCcCCCeEEEeEHHHHHHHhcCCHHHHHHHHHH
Confidence 357889999999999999999999999887532255666665 9988643 56789999999999999999999999999
Q ss_pred hC-Ccc-hHHHHHHHHHhhcCCeEEeecCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHH
Q psy17313 84 QK-ATS-VLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACR 161 (197)
Q Consensus 84 ~g-~~s-gl~~li~~~y~lL~LitffT~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak 161 (197)
+| .+| |+++||+++|++|+|+||||+|++|+|||||++|+|||||||+|||||+||||||||++|+||+++||++.||
T Consensus 263 ~g~~~s~~~~~ii~~~y~lL~L~sFfT~g~~EvRaWti~~G~~Ap~AAG~IHsDfekgFIrAEV~~yddl~~~gs~~~~k 342 (368)
T TIGR00092 263 LGLTESAGLNIIIRARYKLLLLSFFFTGGKEEVRAWTRKGGWAAPQAAGIIHTDFETGFIAAEVISWDDFIYKKSSQGAK 342 (368)
T ss_pred cCCcccchHHHHHHHHHHHhCeeEEEcCCCceeEEeecCCCCchhHhcCCcccccccCceEEEEecHHHHHHcCCHHHHH
Confidence 99 888 9999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HcCcccccCCceeecCCCEEEEEEcc
Q psy17313 162 AAGKYRQQGRAYTVEDGDIIFFKFNA 187 (197)
Q Consensus 162 ~~Gk~r~eGkdYivqDGDIi~f~fn~ 187 (197)
++||+|++||||+|||||||+|||||
T Consensus 343 ~~Gk~r~eGK~YivqDGDIi~f~fnv 368 (368)
T TIGR00092 343 KGGLMRLEGKYYVVDDGDVLFFAFNV 368 (368)
T ss_pred hcCchhhcCCeEEeeCCeEEEEecCC
Confidence 99999999999999999999999996
No 3
>PTZ00258 GTP-binding protein; Provisional
Probab=100.00 E-value=1.8e-64 Score=461.15 Aligned_cols=184 Identities=63% Similarity=1.030 Sum_probs=173.7
Q ss_pred ChHHHHHhhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCC-CHHHHHHHHHH
Q psy17313 5 HHLRIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDM-PDDERQRYLDE 83 (197)
Q Consensus 5 ~~~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l-~~ee~~~fl~~ 83 (197)
.++|.++|++++|||+||+|||+|++|.|+...++++++++++++.+++ +.++||+||++|.+|++| +++++.+||++
T Consensus 205 ~~~e~~~l~~l~llt~KP~iyv~N~~E~D~~~~~~~~~~~l~~~~~~~~-~~~~v~~sa~~E~el~~l~~~~e~~~fl~~ 283 (390)
T PTZ00258 205 TDKEIEILNEYQLLTAKPMIYLVNMSEKDFIRQKNKWLAKIKEWVGEKG-GGPIIPYSAEFEEELAELGSEEERKEYLEE 283 (390)
T ss_pred CHHHHHHHHHhchhhcCCEEEEEECchhhhcccchHHHHHHHHHHHhcC-CCeEEEeeHHHHHHHHhcCCHHHHHHHHHH
Confidence 4578899999999999999999999988873236789999999997752 368999999999999999 99999999999
Q ss_pred hC-CcchHHHHHHHHHhhcCCeEEeecCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHH
Q psy17313 84 QK-ATSVLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRA 162 (197)
Q Consensus 84 ~g-~~sgl~~li~~~y~lL~LitffT~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~ 162 (197)
+| .+||++++|+++|++||||||||+||+|+|||||++|+||+||||+|||||+|||||||||+|+||+++||+++||+
T Consensus 284 ~g~~~~gl~~li~~~~~lL~li~ffT~g~~e~raw~i~~Gsta~~aAg~IHsD~~kgFi~Aev~~~~d~~~~g~~~~ak~ 363 (390)
T PTZ00258 284 YGIKQSMLDKIIKTGYKLLNLIHFFTAGPDEVRCWTIQKGTKAPQAAGVIHSDFEKGFICAEVMKYEDFLELGSEAAVKA 363 (390)
T ss_pred cCCCcccHHHHHHHHHHHhCCEEEEcCCCCceeEEEeCCCCcHHHHHhhhhhHHhhCcEEEEECcHHHHHHcCCHHHHHh
Confidence 99 89999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcccccCCceeecCCCEEEEEEccCC
Q psy17313 163 AGKYRQQGRAYTVEDGDIIFFKFNAGA 189 (197)
Q Consensus 163 ~Gk~r~eGkdYivqDGDIi~f~fn~~~ 189 (197)
+|++|++||||+|||||||+|||||+.
T Consensus 364 ~g~~r~eGkdYiv~DGDIi~f~fnv~~ 390 (390)
T PTZ00258 364 EGKYRQEGKDYVVQDGDIIFFKFNVSK 390 (390)
T ss_pred cCceeeeCCceEecCCCEEEEEecCCC
Confidence 999999999999999999999999974
No 4
>COG0012 Predicted GTPase, probable translation factor [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-58 Score=415.59 Aligned_cols=179 Identities=46% Similarity=0.762 Sum_probs=171.0
Q ss_pred hHHHHHhhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCH-HHHHHHHHHh
Q psy17313 6 HLRIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPD-DERQRYLDEQ 84 (197)
Q Consensus 6 ~~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~-ee~~~fl~~~ 84 (197)
++|..++++++|||+||||||||++|.++.+ .|+|++++++++..+ +.++||+||++|.+|++|++ +++.+|+..+
T Consensus 192 ~e~~~~l~~l~llt~KP~lyvaN~~e~~~~~-~n~~~~~i~~~~~~~--~~~vV~~sA~~E~eL~~l~~~~e~~~F~~~~ 268 (372)
T COG0012 192 EEDLEALASLNLLTAKPMLYVANVSEDDLAN-LNEYVKRLKELAAKE--NAEVVPVSAAIELELRELADAEEKGEFLIEL 268 (372)
T ss_pred HHHHHHHHHhhhhhcCCeEEEEECCcccccc-hhHHHHHHHHHhhhc--CCcEEEeeHHHHHHHHhCccccchhhHHHhc
Confidence 4777889999999999999999999999864 378899999999876 57899999999999999987 8888999999
Q ss_pred C-CcchHHHHHHHHHhhcCCeEEeecCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHc
Q psy17313 85 K-ATSVLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAA 163 (197)
Q Consensus 85 g-~~sgl~~li~~~y~lL~LitffT~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~ 163 (197)
| ..+||+++|+++|.+|||++|||+|++|+|||||++|+|||||||.|||||++|||+|+|++|+|++.+||++.||++
T Consensus 269 g~~~~~l~~~i~~~y~~lgl~~~ft~g~~evrawti~~g~kap~aaG~Ih~Dfe~~fi~aevi~~~d~i~~~~~~~Akea 348 (372)
T COG0012 269 GQKESGLNELIRAGYGLLGLQTYFTAGVKEVRAWTIKDGSKAPDAAGVIHPDFEKGFIRAEVISYADLIHYGGEAAAKEA 348 (372)
T ss_pred CcchhHHHHHHHHHhcccchhHHHhhcCCeEEEEEeccCCcccccCCccccchhhccccceEeeHHHHHhcCcHHHHHHh
Confidence 9 889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccCCceeecCCCEEEEEEcc
Q psy17313 164 GKYRQQGRAYTVEDGDIIFFKFNA 187 (197)
Q Consensus 164 Gk~r~eGkdYivqDGDIi~f~fn~ 187 (197)
|++|++||||+||||||||||||+
T Consensus 349 g~~r~~GkdY~vqdGDVi~Fk~~~ 372 (372)
T COG0012 349 GKRRLEGKDYIVQDGDVIHFKFNV 372 (372)
T ss_pred cceeeccccceecCCCEEEEEecC
Confidence 999999999999999999999996
No 5
>KOG1491|consensus
Probab=100.00 E-value=3.4e-57 Score=405.18 Aligned_cols=183 Identities=63% Similarity=1.006 Sum_probs=178.1
Q ss_pred ChHHHHHhhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHh
Q psy17313 5 HHLRIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQ 84 (197)
Q Consensus 5 ~~~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~ 84 (197)
.++|+++|++++|||+||+||++|++|.|+.+.+|+++.++++|..++++++.+||+|+.+|.+|..|.+||+.++++++
T Consensus 209 ~d~eieiln~~~lLt~kP~Vyl~N~se~dy~r~knk~l~~i~~w~~~~~~g~~~i~fs~~~e~ql~~~~~EE~~~~~~~~ 288 (391)
T KOG1491|consen 209 NDEEIEILNKLFLLTAKPTVYLLNLSEHDYARKKNKKLPKIKEWVDEVSPGDVVIVFSAAFESQLFELYEEEAVKELEDL 288 (391)
T ss_pred CHHHHHHHHHhhhhhcCceEEEEecCcchhhhHHHHHHhhhhhhhhccCCCCeEEEehHHHHHHhhccCHHHHHHHHHhc
Confidence 36899999999999999999999999999988889999999999999999999999999999999999999999999999
Q ss_pred CCcchHHHHHHHHHhhcCCeEEeecCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcC
Q psy17313 85 KATSVLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAG 164 (197)
Q Consensus 85 g~~sgl~~li~~~y~lL~LitffT~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~G 164 (197)
+..|+|+++|.++|..|+|++|||+|++|||+|||++|++||||||+|||||++|||.|||+.|+||+.+||+.++|.+|
T Consensus 289 ~~~s~L~~iI~~~~~~L~li~fFt~G~~eV~~WtIr~gt~ap~aagvihsdf~k~Fi~aev~~f~D~~~~k~e~a~k~~G 368 (391)
T KOG1491|consen 289 GDSSALPKIIKTGYSALNLIVFFTCGEDEVRAWTIRKGTKAPQAAGVIHSDFEKGFIMAEVMKFEDFKEYKSESACKAAG 368 (391)
T ss_pred ccccchhHHHHHHHHhhCceEEEeeCCchheeeehhhccccccccceeeehhhhhccccceeeeehHHHhcCHHHHHHhc
Confidence 96699999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCceeecCCCEEEEEEcc
Q psy17313 165 KYRQQGRAYTVEDGDIIFFKFNA 187 (197)
Q Consensus 165 k~r~eGkdYivqDGDIi~f~fn~ 187 (197)
|.|++||+|+|+||||++||||.
T Consensus 369 k~~~~Gk~yiVedGDIi~FK~~~ 391 (391)
T KOG1491|consen 369 KYRQVGKEYIVEDGDIIFFKFNP 391 (391)
T ss_pred chhhcCceeeecCCCEEEEeecC
Confidence 99999999999999999999984
No 6
>PF06071 YchF-GTPase_C: Protein of unknown function (DUF933); InterPro: IPR013029 This domain is found at the C terminus of family of conserved hypothetical proteins found in both prokaryotes and eukaryotes. While the function of these proteins is not known, the crystal structure of P44681 from SWISSPROT from Haemophilus influenzae has been determined []. This protein consists of three domains: an N-terminal domain which has a mononucleotide binding fold typical for the P-loop NTPases, a central domain which forms an alpha-helical coiled coil, and this C-terminal domain which is composed of a six-stranded half-barrel curved around an alpha helix. The central domain and this domain are topologically similar to RNA-binding proteins, while the N-terminal region contains the features typical of GTP-dependent molecular switches. The purified protein was capable of binding both double-stranded nucleic acid and GTP. It was suggested, therefore, that this protein might be part of a nucleoprotein complex and could function as a GTP-dependent translation factor.; PDB: 1NI3_A 1JAL_A 2DWQ_B 2DBY_A 2OHF_A.
Probab=100.00 E-value=1.2e-49 Score=293.89 Aligned_cols=84 Identities=68% Similarity=1.097 Sum_probs=76.6
Q ss_pred CeEEeecCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEE
Q psy17313 103 LQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIF 182 (197)
Q Consensus 103 LitffT~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~ 182 (197)
|+||||+||+|+|||||++|+|||||||+|||||+||||+||||+|+||+++||++.+|++||+|++||||+|||||||+
T Consensus 1 L~tffT~G~~EvRaWti~~G~~Ap~aAG~IHsDfekgFI~Aevi~~~d~~~~~s~~~~k~~Gk~r~eGK~YivqDGDIi~ 80 (84)
T PF06071_consen 1 LITFFTAGPKEVRAWTIRKGTTAPQAAGVIHSDFEKGFIRAEVISYDDFVEYGSEAAAKEAGKLRLEGKDYIVQDGDIIH 80 (84)
T ss_dssp EEEEEEESSSEEEEEEEETT-BHHHHHHCC-THHHHHEEEEEEEEHHHHHHHTSHHHHHHTT-SEEEETT-B--TTEEEE
T ss_pred CceEEccCCCeEEEEEccCCCCHHHhHhHHHHHHHhhceEEEEEcHHHHHHcCCHHHHHHcCCccccCCceeEeCCCEEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEc
Q psy17313 183 FKFN 186 (197)
Q Consensus 183 f~fn 186 (197)
||||
T Consensus 81 f~fN 84 (84)
T PF06071_consen 81 FRFN 84 (84)
T ss_dssp EEE-
T ss_pred EEcC
Confidence 9998
No 7
>cd04867 TGS_YchF_C TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the family contain a C-terminal TGS domain. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=100.00 E-value=6.4e-49 Score=288.96 Aligned_cols=83 Identities=75% Similarity=1.193 Sum_probs=82.3
Q ss_pred CeEEeecCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEE
Q psy17313 103 LQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIF 182 (197)
Q Consensus 103 LitffT~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~ 182 (197)
|+||||+||+|+|||||++|+|||||||+|||||+|||||||||+|+||+++||+++||++||+|++||||+|||||||+
T Consensus 1 L~tffT~G~~EvRAWti~~g~tAp~AAG~IHsDfekgFIrAeVi~~~d~i~~g~~~~ak~~Gkir~eGK~Yiv~DGDi~~ 80 (83)
T cd04867 1 LISFFTAGPDEVRAWTIRKGTKAPQAAGVIHTDFEKGFIRAEVMKYEDLVELGSEAAAKEAGKYRQEGKDYVVQDGDIIF 80 (83)
T ss_pred CccEECCCCCeEEEEEccCCCChHHhcCCcccccccCcEEEEEEcHHHHHHcCCHHHHHHcChhhhhCCceEeeCCeEEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEE
Q psy17313 183 FKF 185 (197)
Q Consensus 183 f~f 185 (197)
|||
T Consensus 81 f~f 83 (83)
T cd04867 81 FKF 83 (83)
T ss_pred EEC
Confidence 997
No 8
>PRK09602 translation-associated GTPase; Reviewed
Probab=100.00 E-value=1.1e-35 Score=272.12 Aligned_cols=155 Identities=21% Similarity=0.281 Sum_probs=130.2
Q ss_pred ChHHHHHhhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcC-------------
Q psy17313 5 HHLRIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVD------------- 71 (197)
Q Consensus 5 ~~~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~------------- 71 (197)
.++|...|++++|+|.||+|||+|++|... .++++.++.++ . ...+||+||..|..+.+
T Consensus 202 ~~~~~~~I~~~~l~t~KPvI~VlNK~D~~~---~~~~l~~i~~~---~--~~~vvpISA~~e~~l~~~l~~~i~~~lp~~ 273 (396)
T PRK09602 202 TDEDLLELARELRKISKPMVIAANKADLPP---AEENIERLKEE---K--YYIVVPTSAEAELALRRAAKAGLIDYIPGD 273 (396)
T ss_pred CHHHHHHHHHhhhhcCCCEEEEEEchhccc---chHHHHHHHhc---C--CCcEEEEcchhhhhHHHHHHHhHHhhCCCC
Confidence 357788899999999999999999987431 24456666665 1 45799999999998765
Q ss_pred --------CCHHHH------HHHHHHhCCcchHHHHH-HHHHhhcCCeEEeecCC----------CceeeeEecCCCChh
Q psy17313 72 --------MPDDER------QRYLDEQKATSVLDKII-TQGYKSLQLQYFFTAGQ----------DEVKAWTIQKGTKAP 126 (197)
Q Consensus 72 --------l~~ee~------~~fl~~~g~~sgl~~li-~~~y~lL~LitffT~g~----------~EvRAWti~~GstA~ 126 (197)
++++++ .+||..+|. ||++++| +++|++||||+|||+++ +++|||++++|+||+
T Consensus 274 p~~~~~d~ltd~~~r~~E~IRk~l~~~g~-~~~~~~i~~~~~~~L~li~~yt~~~~~~~~~~~g~~~~~~~~l~~g~t~~ 352 (396)
T PRK09602 274 SDFEILGELSEKQKKALEYIREVLKKYGG-TGVQEAINTAVFDLLDMIVVYPVEDENKLTDKKGNVLPDAFLLPKGSTAR 352 (396)
T ss_pred CccCccccCCHHHHHHHHHHHHHHHHhCC-chHHHHHHHHHHHHhCCEEEEecCcccccccccCcccceeEEECCCCCHH
Confidence 565542 378999984 8999999 99999999999999986 677799999999999
Q ss_pred hhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEEE
Q psy17313 127 QAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKF 185 (197)
Q Consensus 127 ~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~f 185 (197)
|+||+|||||++|||||+. +| +.|++|+||+|+|||||+|.-
T Consensus 353 d~A~~IH~d~~~~fi~A~~--------------~~---~~~~~g~~~~l~dgDiv~i~~ 394 (396)
T PRK09602 353 DLAYKIHTDIGEGFLYAID--------------AR---TKRRIGEDYELKDGDVIKIVS 394 (396)
T ss_pred HHHHHHHHHHHhhceehhc--------------cc---CCcccCCCcEecCCCEEEEEe
Confidence 9999999999999999992 44 357899999999999999974
No 9
>cd04938 TGS_Obg-like TGS_Obg-like: The C-terminal TGS domain of Obg-like GTPases such as those present in DRG (developmentally regulated GTP-binding protein), and GTP-binding proteins Ygr210 and YchF. The TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=99.85 E-value=7.5e-22 Score=143.50 Aligned_cols=65 Identities=32% Similarity=0.418 Sum_probs=58.8
Q ss_pred CeEEeec-----------CCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCC
Q psy17313 103 LQYFFTA-----------GQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGR 171 (197)
Q Consensus 103 LitffT~-----------g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGk 171 (197)
|+.+||+ |+++.+||++++|+||+|+|+.|||||+++|++|+||+ .|++|+
T Consensus 1 li~VYpv~~~~~~~~~~~g~d~~~~~~l~~g~tv~d~a~~IH~d~~~~F~~A~v~~------------------~~~vg~ 62 (76)
T cd04938 1 LIPVYPVKNIHTFTNGSGGNVFRDCVLVKKGTTVGDVARKIHGDLEKGFIEAVGGR------------------RRLEGK 62 (76)
T ss_pred CEEEEEcCCCccccCcCCCCccceeEEEcCCCCHHHHHHHHhHHHHhccEEEEEcc------------------CEEECC
Confidence 5677774 46789999999999999999999999999999999987 367999
Q ss_pred ceeecCCCEEEEEE
Q psy17313 172 AYTVEDGDIIFFKF 185 (197)
Q Consensus 172 dYivqDGDIi~f~f 185 (197)
||+|+|||||+|++
T Consensus 63 d~~l~d~DVv~i~~ 76 (76)
T cd04938 63 DVILGKNDILKFKT 76 (76)
T ss_pred CEEecCCCEEEEEC
Confidence 99999999999975
No 10
>cd01900 YchF YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated with the ribosome. Several members of the family, including YchF, possess the TGS domain related to the RNA-binding proteins. Experimental data and genomic analysis suggest that YchF may be part of a nucleoprotein complex and may function as a GTP-dependent translational factor.
Probab=99.79 E-value=1.2e-19 Score=159.57 Aligned_cols=94 Identities=36% Similarity=0.575 Sum_probs=84.5
Q ss_pred ChHHHHHhhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHh
Q psy17313 5 HHLRIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQ 84 (197)
Q Consensus 5 ~~~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~ 84 (197)
.++|.+.|++++|||+||||||+|++|.|+.+ .+++..++..++.+. +.++||+||++|.+|++|+++|+++||+++
T Consensus 180 ~~~e~~~l~~~~llt~KP~i~v~N~~e~d~~~-~~~~~~~~~~~~~~~--~~~~i~~sa~~E~eL~~l~~ee~~~fl~~~ 256 (274)
T cd01900 180 TEEEIEILNSLQLLTAKPVLYVANVSEDDLAN-GNNKVLKVREIAAKE--GAEVIPISAKIEAELAELDEEEAAEFLEEL 256 (274)
T ss_pred CHHHHHHHHHHhHhhcCCceeecccCHHHhcc-ccHHHHHHHHHHhcC--CCeEEEeeHHHHHHHHcCCHHHHHHHHHHc
Confidence 35788999999999999999999999988753 466777888887664 678999999999999999999999999999
Q ss_pred C-CcchHHHHHHHHHhhc
Q psy17313 85 K-ATSVLDKIITQGYKSL 101 (197)
Q Consensus 85 g-~~sgl~~li~~~y~lL 101 (197)
| .+||++++|+++|++|
T Consensus 257 gi~es~l~riI~~~y~~L 274 (274)
T cd01900 257 GLEESGLDRLIRAGYELL 274 (274)
T ss_pred CCccccHHHHHHHHHhhC
Confidence 9 8999999999999987
No 11
>COG1163 DRG Predicted GTPase [General function prediction only]
Probab=99.68 E-value=1.4e-16 Score=143.24 Aligned_cols=124 Identities=21% Similarity=0.270 Sum_probs=101.4
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHhCCcchHHHHHHHH
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQKATSVLDKIITQG 97 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~g~~sgl~~li~~~ 97 (197)
...||.|||+|+.+.. +.+.+..+.+.. .++|+||+- +-+++.|.+.+
T Consensus 237 rvY~p~l~v~NKiD~~----~~e~~~~l~~~~-------~~v~isa~~---------------------~~nld~L~e~i 284 (365)
T COG1163 237 RVYKPALYVVNKIDLP----GLEELERLARKP-------NSVPISAKK---------------------GINLDELKERI 284 (365)
T ss_pred ceeeeeEEEEeccccc----CHHHHHHHHhcc-------ceEEEeccc---------------------CCCHHHHHHHH
Confidence 5689999999996532 233444444322 478999763 23688999999
Q ss_pred HhhcCCeEEeecCCCce----eeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCce
Q psy17313 98 YKSLQLQYFFTAGQDEV----KAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAY 173 (197)
Q Consensus 98 y~lL~LitffT~g~~Ev----RAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdY 173 (197)
|+.|||+.+||..|.+. .+-.+|+|+|+-|+|.+||+||.+.|-+|.||.-+ +|..| +++|.||
T Consensus 285 ~~~L~liRVYtK~~g~~pd~~~PlIlr~GsTV~Dvc~~IH~~l~~~FryA~VWGkS----------vk~~~--QrVG~dH 352 (365)
T COG1163 285 WDVLGLIRVYTKPPGEEPDFDEPLILRRGSTVGDVCRKIHRDLVENFRYARVWGKS----------VKHPG--QRVGLDH 352 (365)
T ss_pred HHhhCeEEEEecCCCCCCCCCCCeEEeCCCcHHHHHHHHHHHHHHhcceEEEeccC----------CCCCc--cccCcCc
Confidence 99999999999887554 48899999999999999999999999999999853 78888 5599999
Q ss_pred eecCCCEEEEEE
Q psy17313 174 TVEDGDIIFFKF 185 (197)
Q Consensus 174 ivqDGDIi~f~f 185 (197)
++.|+||+.|..
T Consensus 353 vLeD~DIV~I~~ 364 (365)
T COG1163 353 VLEDEDIVEIHA 364 (365)
T ss_pred CccCCCeEEEee
Confidence 999999999863
No 12
>cd01669 TGS_Ygr210_C TGS_Ygr210_C: The C-terminal TGS domain of Ygr210 GTP-binding protein which is a member of Obg-like family of GTPases, and present in archaea. Several Obg-like 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. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=99.60 E-value=7.6e-16 Score=112.07 Aligned_cols=53 Identities=36% Similarity=0.565 Sum_probs=47.2
Q ss_pred eeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEE
Q psy17313 115 KAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFK 184 (197)
Q Consensus 115 RAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~ 184 (197)
.+|++++|+||+|+|+.|||||.++|++|.+ +| .| +++|++|+|+|||||+|.
T Consensus 23 d~~~l~~GaTv~D~A~~IHtdi~~~f~~Ai~--------------~k-~~--~~vg~~~~L~dgDvV~Ii 75 (76)
T cd01669 23 DAFLLPKGSTARDLAYAIHTDIGDGFLHAID--------------AR-TG--RRVGEDYELKHRDVIKIV 75 (76)
T ss_pred ceEEECCCCCHHHHHHHHHHHHHhcceeeEE--------------ee-CC--EEeCCCcEecCCCEEEEe
Confidence 4999999999999999999999999999964 23 24 679999999999999984
No 13
>cd01666 TGS_DRG_C TGS_DRG_C: DRG (developmentally regulated GTP-binding protein) represents a family of GTP-binding proteins that includes two members, DRG1 and DRG2. DRG1 and DRG2 have a C-terminal TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) with a predominantly beta-sheet structure. The function of TGS is unknown but its presence in two types of regulatory proteins (the DRG GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=99.39 E-value=4.6e-13 Score=97.29 Aligned_cols=70 Identities=20% Similarity=0.289 Sum_probs=60.6
Q ss_pred CeEEeecCCC----ceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCC
Q psy17313 103 LQYFFTAGQD----EVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDG 178 (197)
Q Consensus 103 LitffT~g~~----EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDG 178 (197)
|+.+||..+. -.++..+++|+|+.|+|..||+|+.+.|.+|.||.=+ ++-.| ++.|.||+++||
T Consensus 1 lirvytk~~g~~~d~~~~liL~~GaTV~D~a~~iH~di~~~f~~A~v~g~s----------~~~~g--q~Vgl~~~L~d~ 68 (75)
T cd01666 1 LIRVYTKPKGQEPDFDEPVILRRGSTVEDVCNKIHKDLVKQFKYALVWGSS----------VKHSP--QRVGLDHVLEDE 68 (75)
T ss_pred CEEEEeCCCCCCCCCCCCEEECCCCCHHHHHHHHHHHHHHhCCeeEEeccC----------CcCCC--eECCCCCEecCC
Confidence 6889998764 4679999999999999999999999999999999622 55555 569999999999
Q ss_pred CEEEEE
Q psy17313 179 DIIFFK 184 (197)
Q Consensus 179 DIi~f~ 184 (197)
|||.|.
T Consensus 69 DvVeI~ 74 (75)
T cd01666 69 DVVQIV 74 (75)
T ss_pred CEEEEe
Confidence 999984
No 14
>PF08438 MMR_HSR1_C: GTPase of unknown function C-terminal; InterPro: IPR013646 This domain is found at the C terminus of IPR002917 from INTERPRO in archaeal and eukaryotic GTP-binding proteins. ; PDB: 1WXQ_A.
Probab=98.86 E-value=2.5e-09 Score=82.97 Aligned_cols=77 Identities=16% Similarity=0.262 Sum_probs=50.7
Q ss_pred EEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcC-----------------------CCHHHHH----
Q psy17313 26 LVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVD-----------------------MPDDERQ---- 78 (197)
Q Consensus 26 v~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~-----------------------l~~ee~~---- 78 (197)
++|+.|.+- +.+++++|++.. ++..+||+||..|..|+. |+++|++
T Consensus 1 AaNK~D~~~---a~~ni~kl~~~~----~~~~vVp~SA~aEl~Lr~a~k~g~I~Y~pGd~~F~i~~~~~l~~~q~~~Le~ 73 (109)
T PF08438_consen 1 AANKADLPA---ADENIEKLKEKY----PDEPVVPTSAAAELALRKAAKAGLIDYIPGDSDFEITDDDKLSDKQKKALEK 73 (109)
T ss_dssp EEE-GGG-S----HHHHHHHHHHH----TT-EEEEE-HHHHHHHHS-SSS----S----------------------TTH
T ss_pred CCccccccc---cHhHHHHHHHhC----CCCceeeccHHHHHHHHHHHHCCCEEeCCCCCceEeecccccCHHHHHHHHH
Confidence 689976532 467888888633 256899999999999872 5555543
Q ss_pred --H-HHHHhCCcchHHHHH-HHHHhhcCCeEEeecC
Q psy17313 79 --R-YLDEQKATSVLDKII-TQGYKSLQLQYFFTAG 110 (197)
Q Consensus 79 --~-fl~~~g~~sgl~~li-~~~y~lL~LitffT~g 110 (197)
+ ||..+| .||++++| +++|++|++|.+||+.
T Consensus 74 I~~~vl~~~g-~TGVq~aln~AVf~ll~~i~VyPVe 108 (109)
T PF08438_consen 74 IRDNVLERYG-STGVQEALNRAVFDLLGMIVVYPVE 108 (109)
T ss_dssp HHHHHTSSSS-S-SHHHHHHHHHHTTS-EEEEEEES
T ss_pred HHHHHHHhcC-CchHHHHHHHHHHHhcCCeeEeccC
Confidence 3 677777 89999999 6888999999999975
No 15
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=98.64 E-value=3.5e-08 Score=68.33 Aligned_cols=59 Identities=20% Similarity=0.291 Sum_probs=49.0
Q ss_pred eEEeecCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEE
Q psy17313 104 QYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFF 183 (197)
Q Consensus 104 itffT~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f 183 (197)
|..|| .....+. +++|+|+.|+|..||+++.+.|+.|.|.+ ++.+.+|+++|||+|.|
T Consensus 1 I~v~l-pdG~~~~--~~~g~T~~d~A~~I~~~l~~~~~~A~Vng-------------------~~vdl~~~L~~~d~v~i 58 (60)
T PF02824_consen 1 IRVYL-PDGSIKE--LPEGSTVLDVAYSIHSSLAKRAVAAKVNG-------------------QLVDLDHPLEDGDVVEI 58 (60)
T ss_dssp EEEEE-TTSCEEE--EETTBBHHHHHHHHSHHHHHCEEEEEETT-------------------EEEETTSBB-SSEEEEE
T ss_pred CEEEC-CCCCeee--CCCCCCHHHHHHHHCHHHHhheeEEEEcC-------------------EECCCCCCcCCCCEEEE
Confidence 45667 3355555 99999999999999999999999999764 55899999999999998
Q ss_pred E
Q psy17313 184 K 184 (197)
Q Consensus 184 ~ 184 (197)
.
T Consensus 59 i 59 (60)
T PF02824_consen 59 I 59 (60)
T ss_dssp E
T ss_pred E
Confidence 4
No 16
>KOG1486|consensus
Probab=98.50 E-value=7.9e-07 Score=79.02 Aligned_cols=122 Identities=19% Similarity=0.298 Sum_probs=92.3
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHhCCcchHHHHHHHHH
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQKATSVLDKIITQGY 98 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~g~~sgl~~li~~~y 98 (197)
..-|.+||-|+-+. -.++++...+.. |+..|| |... .-+|++++..+.
T Consensus 237 ~Y~~ClYvYnKID~-------vs~eevdrlAr~--PnsvVi--SC~m---------------------~lnld~lle~iW 284 (364)
T KOG1486|consen 237 VYIKCLYVYNKIDQ-------VSIEEVDRLARQ--PNSVVI--SCNM---------------------KLNLDRLLERIW 284 (364)
T ss_pred eEEEEEEEeeccce-------ecHHHHHHHhcC--CCcEEE--Eecc---------------------ccCHHHHHHHHH
Confidence 45689999998542 134455555543 355343 4321 225889999999
Q ss_pred hhcCCeEEeecCCCc----eeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCcee
Q psy17313 99 KSLQLQYFFTAGQDE----VKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYT 174 (197)
Q Consensus 99 ~lL~LitffT~g~~E----vRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYi 174 (197)
+.|+|..+||..+.. ..+..+|+|+|..+++..||.||..-|-+|-||.-. +|.. =++.|-.+.
T Consensus 285 e~l~L~rvYtKk~g~~Pdfdd~~vlr~g~tve~~C~~iHr~l~~qfkyAlVWGtS----------akhs--PQrvgl~h~ 352 (364)
T KOG1486|consen 285 EELNLVRVYTKKKGQRPDFDDPLVLRKGSTVEDVCHRIHRTLAAQFKYALVWGTS----------AKHS--PQRVGLGHT 352 (364)
T ss_pred HHhceEEEEecCCCCCCCCCCceEEeCCCcHHHHHHHHHHHHHHhhceeeEeccc----------cccC--cceeccccc
Confidence 999999999977433 349999999999999999999999999999999843 4442 245899999
Q ss_pred ecCCCEEEEE
Q psy17313 175 VEDGDIIFFK 184 (197)
Q Consensus 175 vqDGDIi~f~ 184 (197)
+.|-|||.+-
T Consensus 353 ~~dEdvvqi~ 362 (364)
T KOG1486|consen 353 LEDEDVVQIV 362 (364)
T ss_pred cccccceeee
Confidence 9999999763
No 17
>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=98.25 E-value=2.3e-06 Score=76.89 Aligned_cols=89 Identities=13% Similarity=0.180 Sum_probs=59.0
Q ss_pred ChHHHHHhhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCC-----------
Q psy17313 5 HHLRIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMP----------- 73 (197)
Q Consensus 5 ~~~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~----------- 73 (197)
.+.|...+.+++++|.||+|||+|+.|. .. .+++.+.+.. .. +...+||+||..|..+.+|.
T Consensus 199 ~~~~~~~~~~~~llt~KPvI~VlNK~Dl--~~-~~~~~~~l~~---~~-~~~~iI~iSA~~e~~L~~L~~~~i~~~lPe~ 271 (318)
T cd01899 199 TDEDLLRLARALRKRSKPMVIAANKADI--PD-AENNISKLRL---KY-PDEIVVPTSAEAELALRRAAKQGLIKYDPGD 271 (318)
T ss_pred CHHHHHHHHHHHHhcCCcEEEEEEHHHc--cC-hHHHHHHHHh---hC-CCCeEEEEeCcccccHHHHHHhhHHHhCCCC
Confidence 3567788999999999999999999863 22 3444443432 22 24679999999987776432
Q ss_pred ------------HHHHH-------HHHHHhCCcchHHHHH-HHHHhhc
Q psy17313 74 ------------DDERQ-------RYLDEQKATSVLDKII-TQGYKSL 101 (197)
Q Consensus 74 ------------~ee~~-------~fl~~~g~~sgl~~li-~~~y~lL 101 (197)
+++++ ++|..+| .||++.+| +++|++|
T Consensus 272 ~~f~~~~~~~~~~~~~~~l~~i~d~~~~~~~-~tgv~~~~~~a~~~~~ 318 (318)
T cd01899 272 SDFEITDELGLSEKQKEALESIRDEVLDRFG-STGVQEALNAAVFDLL 318 (318)
T ss_pred CCceecccCCCCHHHHHHHHHHHHHHHHhcC-CchHHHHHHHHHHhcC
Confidence 22221 3566666 67888888 4666543
No 18
>TIGR00691 spoT_relA (p)ppGpp synthetase, RelA/SpoT family. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species.
Probab=98.11 E-value=8e-06 Score=80.25 Aligned_cols=66 Identities=20% Similarity=0.211 Sum_probs=57.0
Q ss_pred CCeEEeecCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEE
Q psy17313 102 QLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDII 181 (197)
Q Consensus 102 ~LitffT~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi 181 (197)
.-+.+|| ..-+...+|+|+|+.|.|..||||+...++.|.|-+ +..+.||.+++||+|
T Consensus 360 ~~i~vfT---PkG~~~~lp~gst~~DfAy~ih~~~g~~~~~a~vng-------------------~~v~l~~~l~~gd~v 417 (683)
T TIGR00691 360 EEIYVFT---PKGDVVELPSGSTPVDFAYAVHTDVGNKCTGAKVNG-------------------KIVPLDKELENGDVV 417 (683)
T ss_pred CceEEEC---CCCeEEEcCCCCCHHHHHHHHhHHhHhceeEEEECC-------------------EECCCCccCCCCCEE
Confidence 7778888 345688999999999999999999999999998543 458899999999999
Q ss_pred EEEEccCC
Q psy17313 182 FFKFNAGA 189 (197)
Q Consensus 182 ~f~fn~~~ 189 (197)
.|..+-..
T Consensus 418 ei~t~~~~ 425 (683)
T TIGR00691 418 EIITGKNS 425 (683)
T ss_pred EEEeCCCC
Confidence 99987655
No 19
>KOG1487|consensus
Probab=98.06 E-value=2.7e-06 Score=75.83 Aligned_cols=122 Identities=16% Similarity=0.221 Sum_probs=88.1
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHhCCcchHHHHHHHHH
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQKATSVLDKIITQGY 98 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~g~~sgl~~li~~~y 98 (197)
..-|.+|+.|+-+.= +++++. +... ....+|+||..+- .+++++..+.
T Consensus 230 ~yVp~iyvLNkIdsI-------SiEELd-ii~~---iphavpISA~~~w---------------------n~d~lL~~mw 277 (358)
T KOG1487|consen 230 IYVPCIYVLNKIDSI-------SIEELD-IIYT---IPHAVPISAHTGW---------------------NFDKLLEKMW 277 (358)
T ss_pred eeeeeeeeeccccee-------eeeccc-eeee---ccceeeccccccc---------------------chHHHHHHHh
Confidence 457999999986531 122221 1111 2346899976422 4778888899
Q ss_pred hhcCCeEEeecCCCceee----eEe-cCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCce
Q psy17313 99 KSLQLQYFFTAGQDEVKA----WTI-QKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAY 173 (197)
Q Consensus 99 ~lL~LitffT~g~~EvRA----Wti-~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdY 173 (197)
+-|+|...||......-- =.+ ..-+|+.|.+..||+++.+-|-+|-||.-. +|.++ +++|+++
T Consensus 278 eyL~LvriYtkPKgq~PDy~~pVvLs~~~~sv~dfc~~ih~~~~~~fk~alvwg~s----------~kh~p--q~vg~~h 345 (358)
T KOG1487|consen 278 EYLKLVRIYTKPKGQPPDYTSPVVLSSERRSVEDFCNKIHKSILKQFKYALVWGSS----------VKHNP--QRVGKEH 345 (358)
T ss_pred hcchheEEecCCCCCCCCCCCCceecCCcccHHHHHHHHHHHHHHhhhhheEeccc----------cCcCh--hhcchhh
Confidence 999999999976444332 222 344889999999999999999999999854 66655 5699999
Q ss_pred eecCCCEEEEE
Q psy17313 174 TVEDGDIIFFK 184 (197)
Q Consensus 174 ivqDGDIi~f~ 184 (197)
++.|-|||.|.
T Consensus 346 ~l~dedvv~iv 356 (358)
T KOG1487|consen 346 VLEDEDVVQIV 356 (358)
T ss_pred eeccchhhhhc
Confidence 99999999763
No 20
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=97.87 E-value=3.3e-05 Score=76.62 Aligned_cols=66 Identities=24% Similarity=0.293 Sum_probs=55.8
Q ss_pred CCeEEeecCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEE
Q psy17313 102 QLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDII 181 (197)
Q Consensus 102 ~LitffT~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi 181 (197)
+-+.+||-. . +...+|+|+|+.|.|..||||+...++.|.| .| +..+.+|.+++||+|
T Consensus 404 d~V~VfTPk-G--~~~~Lp~gaT~lDfAy~iHt~iG~~~~gAkv-----------------ng--~~v~l~~~L~~GD~V 461 (743)
T PRK10872 404 DRVYVFTPK-G--DVVDLPAGSTPLDFAYHIHSDVGHRCIGAKI-----------------GG--RIVPFTYQLQMGDQI 461 (743)
T ss_pred CeEEEECCC-C--CeEEcCCCCcHHHHHHHHhHHHHhhceEEEE-----------------CC--EECCCCcCCCCCCEE
Confidence 668888832 2 3889999999999999999999999999873 24 457899999999999
Q ss_pred EEEEccCC
Q psy17313 182 FFKFNAGA 189 (197)
Q Consensus 182 ~f~fn~~~ 189 (197)
.|..+...
T Consensus 462 eIits~~~ 469 (743)
T PRK10872 462 EIITQKQP 469 (743)
T ss_pred EEEeCCCC
Confidence 99987654
No 21
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=97.27 E-value=0.00087 Score=66.37 Aligned_cols=66 Identities=20% Similarity=0.228 Sum_probs=53.9
Q ss_pred CCeEEeecCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEE
Q psy17313 102 QLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDII 181 (197)
Q Consensus 102 ~LitffT~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi 181 (197)
+-+-+||-. . .--.+|+|+|+.|.|..||||+..--+-|.|= | +...-+|.+++||+|
T Consensus 386 d~v~VfTP~-G--~v~~LP~GaT~lDFAY~iHt~iG~~c~gAkVN-----------------g--~~vpL~~~L~~Gd~V 443 (702)
T PRK11092 386 DEIYVFTPE-G--RIVELPAGATPVDFAYAVHTDIGHACVGARVD-----------------R--QPYPLSQPLTSGQTV 443 (702)
T ss_pred ceEEEECCC-C--CEEeCCCCCchhhhhHhhCchhhceeEEEEEC-----------------C--EECCCCccCCCCCEE
Confidence 567788842 3 45679999999999999999999888887743 4 447899999999999
Q ss_pred EEEEccCC
Q psy17313 182 FFKFNAGA 189 (197)
Q Consensus 182 ~f~fn~~~ 189 (197)
.|..+...
T Consensus 444 eIiT~~~~ 451 (702)
T PRK11092 444 EIITAPGA 451 (702)
T ss_pred EEEeCCCC
Confidence 99987654
No 22
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=97.12 E-value=0.0021 Score=63.58 Aligned_cols=68 Identities=28% Similarity=0.311 Sum_probs=55.1
Q ss_pred CCeEEeecCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEE
Q psy17313 102 QLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDII 181 (197)
Q Consensus 102 ~LitffT~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi 181 (197)
+-+.+|| |+- +--.+|+|+|+.|.|+.||||+...-+-|.| .| |+..-+|.++.||+|
T Consensus 387 d~VyvfT--PkG-~vi~LP~GatplDFAY~vHt~iG~~c~gAkV-----------------nG--~ivpl~~~Lk~Gd~V 444 (701)
T COG0317 387 DRVYVFT--PKG-KVIDLPKGATPLDFAYAVHTDIGHRCIGAKV-----------------NG--RIVPLTTKLQTGDQV 444 (701)
T ss_pred ceEEEEC--CCC-CEEeCCCCCcchhhhhhhhchhcceeeEEEE-----------------CC--EEeccceecCCCCEE
Confidence 4456666 332 7788999999999999999999998888773 35 568899999999999
Q ss_pred EEEEccCCCC
Q psy17313 182 FFKFNAGAGL 191 (197)
Q Consensus 182 ~f~fn~~~~~ 191 (197)
.|..+-....
T Consensus 445 EIit~k~~~P 454 (701)
T COG0317 445 EIITSKHAGP 454 (701)
T ss_pred EEEeCCCCCC
Confidence 9998876433
No 23
>cd01616 TGS The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=96.65 E-value=0.0031 Score=40.54 Aligned_cols=51 Identities=39% Similarity=0.481 Sum_probs=43.5
Q ss_pred eeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEE
Q psy17313 115 KAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFK 184 (197)
Q Consensus 115 RAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~ 184 (197)
+.|.++.|+|..+++..+|.++.+.++.|.|-+ +..+.++.+++||.|.|.
T Consensus 9 ~~~~~~~g~t~~~~~~~~~~~~~~~~~~~~vn~-------------------~~~~l~~~l~~~~~i~~i 59 (60)
T cd01616 9 SAVELPKGATAMDFALKIHTDLGKGFIGALVNG-------------------QLVDLSYTLQDGDTVSIV 59 (60)
T ss_pred CEEEcCCCCCHHHHHHHHHHHHHhheEEEEECC-------------------EECCCCcCcCCCCEEEEe
Confidence 678899999999999999999999998887432 346789999999998875
No 24
>PRK12296 obgE GTPase CgtA; Reviewed
Probab=95.16 E-value=0.057 Score=51.79 Aligned_cols=48 Identities=13% Similarity=0.156 Sum_probs=30.4
Q ss_pred ccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhh
Q psy17313 17 LLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQL 69 (197)
Q Consensus 17 lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el 69 (197)
-|..||+|+|+|+.|.. . .....+.+++...+. +.+++++||.-..-|
T Consensus 281 ~l~~kP~IVVlNKiDL~--d-a~el~e~l~~~l~~~--g~~Vf~ISA~tgeGL 328 (500)
T PRK12296 281 DLAERPRLVVLNKIDVP--D-ARELAEFVRPELEAR--GWPVFEVSAASREGL 328 (500)
T ss_pred hhcCCCEEEEEECccch--h-hHHHHHHHHHHHHHc--CCeEEEEECCCCCCH
Confidence 35679999999997642 1 223334444444443 568999998754433
No 25
>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=95.07 E-value=0.061 Score=45.90 Aligned_cols=60 Identities=13% Similarity=0.088 Sum_probs=43.1
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHhCCcchHHHHHHHH
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQKATSVLDKIITQG 97 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~g~~sgl~~li~~~ 97 (197)
...+|+++|+|+.|.. . .+.+..++.. ..++++||+- +.|++++...+
T Consensus 174 ~~y~p~iiV~NK~Dl~--~-----~~~~~~~~~~----~~~~~~SA~~---------------------g~gi~~l~~~i 221 (233)
T cd01896 174 RVYIPCLYVYNKIDLI--S-----IEELDLLARQ----PNSVVISAEK---------------------GLNLDELKERI 221 (233)
T ss_pred ceEeeEEEEEECccCC--C-----HHHHHHHhcC----CCEEEEcCCC---------------------CCCHHHHHHHH
Confidence 4668999999997642 1 1233344432 2478888762 45799999999
Q ss_pred HhhcCCeEEeec
Q psy17313 98 YKSLQLQYFFTA 109 (197)
Q Consensus 98 y~lL~LitffT~ 109 (197)
++.|+||.+||.
T Consensus 222 ~~~L~~irvy~k 233 (233)
T cd01896 222 WDKLGLIRVYTK 233 (233)
T ss_pred HHHhCcEEEecC
Confidence 999999999993
No 26
>PRK12297 obgE GTPase CgtA; Reviewed
Probab=94.18 E-value=0.12 Score=48.62 Aligned_cols=40 Identities=25% Similarity=0.324 Sum_probs=24.7
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
|..||+|+|+|+.|. .. ....++++.+ .. +.+++++||.-
T Consensus 272 L~~kP~IVV~NK~DL--~~-~~e~l~~l~~---~l--~~~i~~iSA~t 311 (424)
T PRK12297 272 LLERPQIVVANKMDL--PE-AEENLEEFKE---KL--GPKVFPISALT 311 (424)
T ss_pred ccCCcEEEEEeCCCC--cC-CHHHHHHHHH---Hh--CCcEEEEeCCC
Confidence 467999999999874 21 2223333333 22 24689999864
No 27
>KOG1489|consensus
Probab=92.78 E-value=0.063 Score=49.31 Aligned_cols=47 Identities=13% Similarity=0.191 Sum_probs=32.7
Q ss_pred ccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhh
Q psy17313 17 LLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQL 69 (197)
Q Consensus 17 lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el 69 (197)
-|+.||.++|||+.|... ..+.+++.+.+.++ +..|+|+||+.+..+
T Consensus 309 ~L~~rp~liVaNKiD~~e--ae~~~l~~L~~~lq----~~~V~pvsA~~~egl 355 (366)
T KOG1489|consen 309 GLADRPALIVANKIDLPE--AEKNLLSSLAKRLQ----NPHVVPVSAKSGEGL 355 (366)
T ss_pred hhccCceEEEEeccCchh--HHHHHHHHHHHHcC----CCcEEEeeeccccch
Confidence 578999999999976532 12334577776663 235999999976533
No 28
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown.
Probab=91.35 E-value=0.53 Score=30.88 Aligned_cols=50 Identities=24% Similarity=0.285 Sum_probs=39.5
Q ss_pred eeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEE
Q psy17313 116 AWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFK 184 (197)
Q Consensus 116 AWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~ 184 (197)
.-+++.|+|+.+++..++..+.+.++.+.+- | +....++.+++||.|.+.
T Consensus 10 ~~~~~~~~t~~~~~~~~~~~~~~~~va~~vn-----------------g--~~vdl~~~l~~~~~ve~v 59 (60)
T cd01668 10 IIELPAGATVLDFAYAIHTEIGNRCVGAKVN-----------------G--KLVPLSTVLKDGDIVEII 59 (60)
T ss_pred EEEcCCCCCHHHHHHHHChHhhhheEEEEEC-----------------C--EECCCCCCCCCCCEEEEE
Confidence 4568999999999999999888888876632 3 335688999999987763
No 29
>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=89.91 E-value=0.51 Score=38.55 Aligned_cols=42 Identities=19% Similarity=0.153 Sum_probs=27.2
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..+|+|+|+|+.|.--..+-.-..+++.++. +.||||+||.-
T Consensus 104 ~g~P~vvvlN~~D~a~~~g~~id~~~Ls~~L-----g~pvi~~sa~~ 145 (156)
T PF02421_consen 104 LGIPVVVVLNKMDEAERKGIEIDAEKLSERL-----GVPVIPVSART 145 (156)
T ss_dssp TTSSEEEEEETHHHHHHTTEEE-HHHHHHHH-----TS-EEEEBTTT
T ss_pred cCCCEEEEEeCHHHHHHcCCEECHHHHHHHh-----CCCEEEEEeCC
Confidence 4699999999976422111122456666665 68999999874
No 30
>PRK06437 hypothetical protein; Provisional
Probab=89.58 E-value=2.2 Score=29.85 Aligned_cols=66 Identities=9% Similarity=0.030 Sum_probs=47.4
Q ss_pred CeEEeecCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEE
Q psy17313 103 LQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIF 182 (197)
Q Consensus 103 LitffT~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~ 182 (197)
+++|+|+...+.+...++.|+|+.|+.....=+. +++ |.++. |.+ .-.++.++|||-|.
T Consensus 1 ~~~~~~v~g~~~~~~~i~~~~tv~dLL~~Lgi~~-~~v--aV~vN----------------g~i--v~~~~~L~dgD~Ve 59 (67)
T PRK06437 1 MIAMIRVKGHINKTIEIDHELTVNDIIKDLGLDE-EEY--VVIVN----------------GSP--VLEDHNVKKEDDVL 59 (67)
T ss_pred CcceEEecCCcceEEEcCCCCcHHHHHHHcCCCC-ccE--EEEEC----------------CEE--CCCceEcCCCCEEE
Confidence 5788888867777888899999999998875442 333 33343 222 33899999999999
Q ss_pred EEEccCC
Q psy17313 183 FKFNAGA 189 (197)
Q Consensus 183 f~fn~~~ 189 (197)
|.--++.
T Consensus 60 iv~~V~G 66 (67)
T PRK06437 60 ILEVFSG 66 (67)
T ss_pred EEecccC
Confidence 8766553
No 31
>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=89.51 E-value=2 Score=32.37 Aligned_cols=42 Identities=10% Similarity=-0.021 Sum_probs=27.0
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
...+|+++|+|+.|..- .......+.++.+.. +.+++++||+
T Consensus 104 ~~~~piivv~nK~Dl~~---~~~~~~~~~~~~~~~--~~~~~~~Sa~ 145 (162)
T cd04138 104 SDDVPMVLVGNKCDLAA---RTVSSRQGQDLAKSY--GIPYIETSAK 145 (162)
T ss_pred CCCCCEEEEEECccccc---ceecHHHHHHHHHHh--CCeEEEecCC
Confidence 35689999999976421 122344555665544 4678899975
No 32
>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=88.66 E-value=1.7 Score=33.54 Aligned_cols=41 Identities=20% Similarity=0.138 Sum_probs=24.2
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..+|+++|+|+.|..- ...+...+++.... +.+++++||+-
T Consensus 112 ~~~pvilv~NK~Dl~~----~~~~~~~~~~~~~~--~~~~~~~Sa~~ 152 (168)
T cd01897 112 KNKPVIVVLNKIDLLT----FEDLSEIEEEEELE--GEEVLKISTLT 152 (168)
T ss_pred CcCCeEEEEEccccCc----hhhHHHHHHhhhhc--cCceEEEEecc
Confidence 4689999999976421 11222234444332 46788889863
No 33
>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=87.90 E-value=1.8 Score=32.82 Aligned_cols=42 Identities=10% Similarity=0.001 Sum_probs=25.9
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
..+|+++|+|+.|..- ..+......+.+.+.. +.+++++||.
T Consensus 104 ~~~piiiv~NK~D~~~--~~~~~~~~~~~~~~~~--~~~~~~~Sa~ 145 (164)
T cd04139 104 DNVPLLLVGNKCDLED--KRQVSSEEAANLARQW--GVPYVETSAK 145 (164)
T ss_pred CCCCEEEEEEcccccc--ccccCHHHHHHHHHHh--CCeEEEeeCC
Confidence 4689999999976421 1122334444555544 4678888875
No 34
>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=87.71 E-value=1.3 Score=34.08 Aligned_cols=42 Identities=33% Similarity=0.392 Sum_probs=24.2
Q ss_pred cccCceEEEEeCCCccccccccccHHHH--HHHHhhcCCCCeEEEechhh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKI--KEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l--~~~~~~~~~~~~vv~~sa~~ 65 (197)
+..+|+++|+|+.|..- ....... ....... +.+++++||.-
T Consensus 118 ~~~~p~ivv~NK~Dl~~----~~~~~~~~~~~~~~~~--~~~~~~~Sa~~ 161 (176)
T cd01881 118 LTAKPVIYVLNKIDLDD----AEELEEELVRELALEE--GAEVVPISAKT 161 (176)
T ss_pred HhhCCeEEEEEchhcCc----hhHHHHHHHHHHhcCC--CCCEEEEehhh
Confidence 35799999999976432 1111221 1222222 45689999864
No 35
>PRK12298 obgE GTPase CgtA; Reviewed
Probab=87.26 E-value=1.4 Score=40.93 Aligned_cols=59 Identities=10% Similarity=-0.002 Sum_probs=35.5
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHhCCcchHHHHHHHHH
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQKATSVLDKIITQGY 98 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~g~~sgl~~li~~~y 98 (197)
..||+|+|+|+.|. .. .....+.++++.+......+++++||.- ..|++.++..+.
T Consensus 274 ~~kP~IlVlNKiDl--~~-~~el~~~l~~l~~~~~~~~~Vi~ISA~t---------------------g~GIdeLl~~I~ 329 (390)
T PRK12298 274 AEKPRWLVFNKIDL--LD-EEEAEERAKAIVEALGWEGPVYLISAAS---------------------GLGVKELCWDLM 329 (390)
T ss_pred cCCCEEEEEeCCcc--CC-hHHHHHHHHHHHHHhCCCCCEEEEECCC---------------------CcCHHHHHHHHH
Confidence 56999999999764 21 1222334444444322123689999864 336777777666
Q ss_pred hhc
Q psy17313 99 KSL 101 (197)
Q Consensus 99 ~lL 101 (197)
+.|
T Consensus 330 ~~L 332 (390)
T PRK12298 330 TFI 332 (390)
T ss_pred HHh
Confidence 655
No 36
>COG0536 Obg Predicted GTPase [General function prediction only]
Probab=86.75 E-value=1.4 Score=40.80 Aligned_cols=50 Identities=18% Similarity=0.132 Sum_probs=30.6
Q ss_pred hhcc-cccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 12 LNKL-NLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 12 i~~~-~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
|+.| .-|..||+++|+|+.|... ..+.++.+++...+...-....++||.
T Consensus 266 L~~Y~~~L~~K~~ivv~NKiD~~~---~~e~~~~~~~~l~~~~~~~~~~~ISa~ 316 (369)
T COG0536 266 LEKYSPKLAEKPRIVVLNKIDLPL---DEEELEELKKALAEALGWEVFYLISAL 316 (369)
T ss_pred HHHhhHHhccCceEEEEeccCCCc---CHHHHHHHHHHHHHhcCCCcceeeehh
Confidence 4556 5788999999999987433 345666666655543211112227764
No 37
>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=86.74 E-value=1.5 Score=39.58 Aligned_cols=42 Identities=21% Similarity=0.245 Sum_probs=25.7
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHH-HHhhcCCCCeEEEechhh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKE-WVDANDPGATIIPFSGVF 65 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~-~~~~~~~~~~vv~~sa~~ 65 (197)
+..||+|+|+|+.|..- ....+++.+ +.++. +.+++++||..
T Consensus 271 l~~kp~IIV~NK~DL~~----~~~~~~~~~~l~~~~--~~~vi~iSAkt 313 (329)
T TIGR02729 271 LAEKPRIVVLNKIDLLD----EEELAELLKELKKAL--GKPVFPISALT 313 (329)
T ss_pred hccCCEEEEEeCccCCC----hHHHHHHHHHHHHHc--CCcEEEEEccC
Confidence 45799999999976421 122333333 33333 45789999863
No 38
>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=86.40 E-value=3.5 Score=31.33 Aligned_cols=43 Identities=7% Similarity=-0.062 Sum_probs=25.5
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..+|+++|+|+.|.. ....-..+....+.+.. +.+++++||+-
T Consensus 105 ~~~piilv~nK~Dl~--~~~~~~~~~~~~~~~~~--~~~~~~~Sa~~ 147 (163)
T cd04136 105 ENVPMVLVGNKCDLE--DERVVSREEGQALARQW--GCPFYETSAKS 147 (163)
T ss_pred CCCCEEEEEECcccc--ccceecHHHHHHHHHHc--CCeEEEecCCC
Confidence 468999999997632 11111223344455544 46788999863
No 39
>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=86.37 E-value=2.9 Score=34.98 Aligned_cols=68 Identities=12% Similarity=0.076 Sum_probs=41.1
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHhCCcchHHHHHHHH
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQKATSVLDKIITQG 97 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~g~~sgl~~li~~~ 97 (197)
...+|+|+|+|+.|.. ....-..+..++++... +.+++++||.. +.|++.++..+
T Consensus 104 ~~~~piilV~NK~Dl~--~~~~v~~~~~~~~a~~~--~~~~~e~SA~~---------------------~~gv~~l~~~l 158 (221)
T cd04148 104 LEDRPIILVGNKSDLA--RSREVSVQEGRACAVVF--DCKFIETSAGL---------------------QHNVDELLEGI 158 (221)
T ss_pred CCCCCEEEEEEChhcc--ccceecHHHHHHHHHHc--CCeEEEecCCC---------------------CCCHHHHHHHH
Confidence 3468999999987632 11111233344555544 46788888763 34677777777
Q ss_pred HhhcCCeEEeecC
Q psy17313 98 YKSLQLQYFFTAG 110 (197)
Q Consensus 98 y~lL~LitffT~g 110 (197)
.+.+.+..-++..
T Consensus 159 ~~~~~~~~~~~~~ 171 (221)
T cd04148 159 VRQIRLRRDSKEK 171 (221)
T ss_pred HHHHHhhhccccc
Confidence 7777666666533
No 40
>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=85.75 E-value=2.1 Score=32.50 Aligned_cols=47 Identities=17% Similarity=0.075 Sum_probs=26.1
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcC-CCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAND-PGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~-~~~~vv~~sa~~ 65 (197)
..+|+++++|+.|..-........+++.++..... .+.+++++||.-
T Consensus 103 ~~~~~ilv~NK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~ 150 (164)
T cd04171 103 GIKRGLVVLTKADLVDEDWLELVEEEIRELLAGTFLADAPIFPVSAVT 150 (164)
T ss_pred CCCcEEEEEECccccCHHHHHHHHHHHHHHHHhcCcCCCcEEEEeCCC
Confidence 34699999999764210000122345555554310 146799999864
No 41
>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=85.22 E-value=4.5 Score=30.97 Aligned_cols=43 Identities=9% Similarity=-0.030 Sum_probs=25.2
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..+|+++|+|+.|..-. ..-.......++... +.+++++||.-
T Consensus 105 ~~~piviv~nK~Dl~~~--~~~~~~~~~~~~~~~--~~~~~~~Sa~~ 147 (163)
T cd04176 105 EKVPIILVGNKVDLESE--REVSSAEGRALAEEW--GCPFMETSAKS 147 (163)
T ss_pred CCCCEEEEEECccchhc--CccCHHHHHHHHHHh--CCEEEEecCCC
Confidence 56899999999764211 111122334444433 46788999863
No 42
>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=85.02 E-value=3.7 Score=31.91 Aligned_cols=41 Identities=17% Similarity=0.202 Sum_probs=24.0
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..||+++|+|+.|. .. .........+.... +.+++++||.-
T Consensus 40 ~~~p~iiv~NK~Dl--~~--~~~~~~~~~~~~~~--~~~~~~iSa~~ 80 (156)
T cd01859 40 LGKKLLIVLNKADL--VP--KEVLEKWKSIKESE--GIPVVYVSAKE 80 (156)
T ss_pred CCCcEEEEEEhHHh--CC--HHHHHHHHHHHHhC--CCcEEEEEccc
Confidence 46999999999763 21 11122222232222 46789999864
No 43
>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=84.95 E-value=4.3 Score=31.05 Aligned_cols=43 Identities=12% Similarity=-0.050 Sum_probs=26.8
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..+|+++|+|+.|..-. .....+.+..+++.. +.+++++||+-
T Consensus 104 ~~~pii~v~nK~Dl~~~--~~~~~~~~~~~~~~~--~~~~~~~Sa~~ 146 (164)
T smart00173 104 DDVPIVLVGNKCDLESE--RVVSTEEGKELARQW--GCPFLETSAKE 146 (164)
T ss_pred CCCCEEEEEECcccccc--ceEcHHHHHHHHHHc--CCEEEEeecCC
Confidence 36899999999764211 111233445555554 57889999864
No 44
>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=84.54 E-value=5.1 Score=30.79 Aligned_cols=43 Identities=9% Similarity=-0.041 Sum_probs=25.9
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+++|+|+.|..- ..........++++.. +.+++++||+-
T Consensus 105 ~~~piilv~nK~Dl~~--~~~~~~~~~~~~~~~~--~~~~~~~Sa~~ 147 (164)
T cd04175 105 EDVPMILVGNKCDLED--ERVVGKEQGQNLARQW--GCAFLETSAKA 147 (164)
T ss_pred CCCCEEEEEECCcchh--ccEEcHHHHHHHHHHh--CCEEEEeeCCC
Confidence 4579999999976421 1111223344555544 46789999863
No 45
>PRK12299 obgE GTPase CgtA; Reviewed
Probab=84.49 E-value=2.2 Score=38.72 Aligned_cols=43 Identities=19% Similarity=0.127 Sum_probs=25.9
Q ss_pred cccCceEEEEeCCCccccccccccH-HHHHHHHhhcCCCCeEEEechhh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWL-PKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~-~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
|..||+|+|+|+.|.. . ..... ..++.+.... +.+++++||.-
T Consensus 269 L~~kp~IIV~NKiDL~--~-~~~~~~~~~~~~~~~~--~~~i~~iSAkt 312 (335)
T PRK12299 269 LADKPRILVLNKIDLL--D-EEEEREKRAALELAAL--GGPVFLISAVT 312 (335)
T ss_pred cccCCeEEEEECcccC--C-chhHHHHHHHHHHHhc--CCCEEEEEcCC
Confidence 4579999999998642 1 11112 2233444333 46789999864
No 46
>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=84.28 E-value=3.5 Score=31.78 Aligned_cols=43 Identities=14% Similarity=0.086 Sum_probs=28.0
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+++|+|+.|..- ...-..+..+.++... +.+++++||.-
T Consensus 106 ~~~~~iiv~nK~Dl~~--~~~~~~~~~~~~~~~~--~~~~~~~Sa~~ 148 (166)
T cd01869 106 ENVNKLLVGNKCDLTD--KRVVDYSEAQEFADEL--GIPFLETSAKN 148 (166)
T ss_pred CCCcEEEEEEChhccc--ccCCCHHHHHHHHHHc--CCeEEEEECCC
Confidence 3579999999976421 1122345566666655 57899999864
No 47
>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=84.21 E-value=1.2 Score=35.47 Aligned_cols=46 Identities=20% Similarity=0.174 Sum_probs=26.6
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
.+|+++++|+.|..-........+++++++.....+..++++||.-
T Consensus 129 ~~pviiv~nK~D~~~~~~~~~~~~~i~~~l~~~~~~~~v~~~Sa~~ 174 (179)
T TIGR03598 129 GIPVLIVLTKADKLKKSELNKQLKKIKKALKKDADDPSVQLFSSLK 174 (179)
T ss_pred CCCEEEEEECcccCCHHHHHHHHHHHHHHHhhccCCCceEEEECCC
Confidence 5788888998754211101224556666665542234688888763
No 48
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=84.16 E-value=1.1 Score=41.64 Aligned_cols=64 Identities=27% Similarity=0.367 Sum_probs=46.4
Q ss_pred cCChHHHHHhhcccccccCceEEEEeCCCccccc--cccccHHHHHHHHhhcC-CCCeEEEechhhchh
Q psy17313 3 CEHHLRIEHLNKLNLLTAKTQIYLVNLSAKDYIK--KKNKWLPKIKEWVDAND-PGATIIPFSGVFEHQ 68 (197)
Q Consensus 3 ~~~~~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~--~~~~~~~~l~~~~~~~~-~~~~vv~~sa~~E~e 68 (197)
|-.|.-.+.|--+..+-.|-+|+|-|+-| +.+ .+.++.++|+++++..- +++|+||+||+...-
T Consensus 123 cPQPQT~EHl~AleIigik~iiIvQNKID--lV~~E~AlE~y~qIk~FvkGt~Ae~aPIIPiSA~~~~N 189 (415)
T COG5257 123 CPQPQTREHLMALEIIGIKNIIIVQNKID--LVSRERALENYEQIKEFVKGTVAENAPIIPISAQHKAN 189 (415)
T ss_pred CCCCchHHHHHHHhhhccceEEEEecccc--eecHHHHHHHHHHHHHHhcccccCCCceeeehhhhccC
Confidence 55666666677777888999999999964 332 24568888888886421 378999999986553
No 49
>PRK15467 ethanolamine utilization protein EutP; Provisional
Probab=83.71 E-value=3.8 Score=32.43 Aligned_cols=44 Identities=9% Similarity=0.050 Sum_probs=29.7
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhch
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEH 67 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~ 67 (197)
..+|+++++|+.|. . +...+.+.+++.+.+...+++++||.-..
T Consensus 90 ~~~~ii~v~nK~Dl--~---~~~~~~~~~~~~~~~~~~p~~~~Sa~~g~ 133 (158)
T PRK15467 90 VSKRQIAVISKTDM--P---DADVAATRKLLLETGFEEPIFELNSHDPQ 133 (158)
T ss_pred CCCCeEEEEEcccc--C---cccHHHHHHHHHHcCCCCCEEEEECCCcc
Confidence 46899999999763 2 22345667777665322489999987544
No 50
>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=83.48 E-value=3.9 Score=32.94 Aligned_cols=61 Identities=15% Similarity=0.131 Sum_probs=34.9
Q ss_pred ccCceEEEEeCCCccccccccccHHHHH-HHHhhcCC----CCeEEEechhhchhhcCCCHHHHHHHHHHhCCcchHHHH
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIK-EWVDANDP----GATIIPFSGVFEHQLVDMPDDERQRYLDEQKATSVLDKI 93 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~-~~~~~~~~----~~~vv~~sa~~E~el~~l~~ee~~~fl~~~g~~sgl~~l 93 (197)
...|+|+++|+.|.-..+ -.+..+++. .+.+.... ..+++|+||.- +.|++.|
T Consensus 121 ~~~p~ivvlNK~D~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~vi~~Sa~~---------------------g~gi~~L 178 (188)
T PF00009_consen 121 LGIPIIVVLNKMDLIEKE-LEEIIEEIKEKLLKEYGENGEEIVPVIPISALT---------------------GDGIDEL 178 (188)
T ss_dssp TT-SEEEEEETCTSSHHH-HHHHHHHHHHHHHHHTTSTTTSTEEEEEEBTTT---------------------TBTHHHH
T ss_pred cccceEEeeeeccchhhh-HHHHHHHHHHHhccccccCccccceEEEEecCC---------------------CCCHHHH
Confidence 458899999998754211 122334444 33333211 25899999863 4467777
Q ss_pred HHHHHhhc
Q psy17313 94 ITQGYKSL 101 (197)
Q Consensus 94 i~~~y~lL 101 (197)
+.++.+.|
T Consensus 179 l~~l~~~~ 186 (188)
T PF00009_consen 179 LEALVELL 186 (188)
T ss_dssp HHHHHHHS
T ss_pred HHHHHHhC
Confidence 77766654
No 51
>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=83.33 E-value=3.6 Score=31.63 Aligned_cols=43 Identities=19% Similarity=0.237 Sum_probs=25.1
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..+|+++|+|+.|.. . .....+.+..+..+.. +.+++++||+-
T Consensus 113 ~~~p~ivv~NK~Dl~--~-~~~~~~~~~~~~~~~~-~~~~~~~Sa~~ 155 (170)
T cd01898 113 LEKPRIVVLNKIDLL--D-EEELFELLKELLKELW-GKPVFPISALT 155 (170)
T ss_pred cccccEEEEEchhcC--C-chhhHHHHHHHHhhCC-CCCEEEEecCC
Confidence 469999999997642 1 1222233444444321 35688899763
No 52
>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=83.27 E-value=6.7 Score=29.86 Aligned_cols=43 Identities=9% Similarity=-0.021 Sum_probs=27.8
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
....|+++|+|+.|... .....+...+++... +.+++++||+-
T Consensus 104 ~~~~~~~iv~nK~D~~~---~~~~~~~~~~~~~~~--~~~~~~~Sa~~ 146 (161)
T cd01863 104 NNDIVKMLVGNKIDKEN---REVTREEGLKFARKH--NMLFIETSAKT 146 (161)
T ss_pred CCCCcEEEEEECCcccc---cccCHHHHHHHHHHc--CCEEEEEecCC
Confidence 35688999999976431 122344555666654 57788999763
No 53
>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=82.89 E-value=5.7 Score=31.01 Aligned_cols=42 Identities=12% Similarity=0.024 Sum_probs=26.5
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
.-|+++|+|+.|..- ......+.+.+++++. +.+++++||+-
T Consensus 120 ~~piiiv~nK~Dl~~--~~~v~~~~~~~~~~~~--~~~~~e~Sak~ 161 (180)
T cd04127 120 NPDIVLCGNKADLED--QRQVSEEQAKALADKY--GIPYFETSAAT 161 (180)
T ss_pred CCcEEEEEeCccchh--cCccCHHHHHHHHHHc--CCeEEEEeCCC
Confidence 458999999976421 1122334566777665 56788888764
No 54
>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=82.70 E-value=4.5 Score=30.75 Aligned_cols=41 Identities=12% Similarity=-0.048 Sum_probs=25.7
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
..|+++++|+.|..- ...-..+...++++.. +.+++++||.
T Consensus 107 ~~piiiv~NK~Dl~~--~~~~~~~~~~~~~~~~--~~~~~~~Sa~ 147 (164)
T cd04145 107 EFPMILVGNKADLEH--QRKVSREEGQELARKL--KIPYIETSAK 147 (164)
T ss_pred CCCEEEEeeCccccc--cceecHHHHHHHHHHc--CCcEEEeeCC
Confidence 569999999976421 1111334455666554 4678888975
No 55
>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=81.49 E-value=5.3 Score=30.26 Aligned_cols=43 Identities=9% Similarity=0.037 Sum_probs=24.3
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+++|+|+.|..- ......+..+.++.+. +.+++.+||+-
T Consensus 109 ~~~piilv~nK~Dl~~--~~~~~~~~~~~~~~~~--~~~~~~~Sa~~ 151 (168)
T cd04119 109 ENIVVVVCANKIDLTK--HRAVSEDEGRLWAESK--GFKYFETSACT 151 (168)
T ss_pred CCceEEEEEEchhccc--ccccCHHHHHHHHHHc--CCeEEEEECCC
Confidence 3478888888876421 0122334445566554 45677778653
No 56
>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=81.47 E-value=6.8 Score=29.73 Aligned_cols=41 Identities=12% Similarity=-0.018 Sum_probs=22.9
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
..|+++++|+.|.. .......+......+.. +.+++++||.
T Consensus 105 ~~~iilv~nK~D~~--~~~~~~~~~~~~~~~~~--~~~~~~~Sa~ 145 (161)
T cd01861 105 DVIIVLVGNKTDLS--DKRQVSTEEGEKKAKEL--NAMFIETSAK 145 (161)
T ss_pred CCEEEEEEEChhcc--ccCccCHHHHHHHHHHh--CCEEEEEeCC
Confidence 37888888876542 11222334444444443 4667777765
No 57
>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=80.57 E-value=6 Score=30.65 Aligned_cols=14 Identities=14% Similarity=0.064 Sum_probs=11.9
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
..+|+++++|+.|.
T Consensus 113 ~~~~i~iv~nK~D~ 126 (189)
T cd00881 113 GGLPIIVAINKIDR 126 (189)
T ss_pred CCCCeEEEEECCCC
Confidence 47999999999764
No 58
>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=80.39 E-value=4.5 Score=33.26 Aligned_cols=47 Identities=23% Similarity=0.181 Sum_probs=26.7
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcC-CCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAND-PGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~-~~~~vv~~sa~~ 65 (197)
-.+|+|+|+|+.|..-.......++.+++++.... .+.+++++||.-
T Consensus 136 ~~~~iiivvNK~Dl~~~~~~~~~~~~i~~~~~~~~~~~~~i~~vSA~~ 183 (203)
T cd01888 136 GLKHIIIVQNKIDLVKEEQALENYEQIKKFVKGTIAENAPIIPISAQL 183 (203)
T ss_pred CCCcEEEEEEchhccCHHHHHHHHHHHHHHHhccccCCCcEEEEeCCC
Confidence 34689999999764210001123455555554321 145799999864
No 59
>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=80.12 E-value=6.5 Score=30.14 Aligned_cols=41 Identities=17% Similarity=0.121 Sum_probs=24.2
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
..|+++|+|+.|..- ......+.+..++... +.+++++||.
T Consensus 108 ~~pi~vv~nK~Dl~~--~~~~~~~~~~~~~~~~--~~~~~~~Sa~ 148 (165)
T cd01868 108 NIVIMLVGNKSDLRH--LRAVPTEEAKAFAEKN--GLSFIETSAL 148 (165)
T ss_pred CCeEEEEEECccccc--cccCCHHHHHHHHHHc--CCEEEEEECC
Confidence 478888888876421 1122344555555543 4667888875
No 60
>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=79.46 E-value=10 Score=30.72 Aligned_cols=43 Identities=14% Similarity=0.051 Sum_probs=29.7
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCC-CeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPG-ATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~-~~vv~~sa~~ 65 (197)
...|+|+|+|+.|..- ......+++.++++.+ + ..++++||+-
T Consensus 109 ~~~piilv~NK~Dl~~--~~~~~~~~~~~~~~~~--~~~~~~e~Sak~ 152 (201)
T cd04107 109 EPIPCLLLANKCDLKK--RLAKDGEQMDQFCKEN--GFIGWFETSAKE 152 (201)
T ss_pred CCCcEEEEEECCCccc--ccccCHHHHHHHHHHc--CCceEEEEeCCC
Confidence 5679999999987421 1223456777888765 4 5788999874
No 61
>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=79.36 E-value=5 Score=32.21 Aligned_cols=43 Identities=14% Similarity=0.037 Sum_probs=26.1
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+|+|+|+.|... ...-......+++... +.+++++||+-
T Consensus 105 ~~~piilvgNK~Dl~~--~~~v~~~~~~~~~~~~--~~~~~e~SAk~ 147 (190)
T cd04144 105 ADVPIMIVGNKCDKVY--EREVSTEEGAALARRL--GCEFIEASAKT 147 (190)
T ss_pred CCCCEEEEEEChhccc--cCccCHHHHHHHHHHh--CCEEEEecCCC
Confidence 4579999999976421 1111223344555554 46789999874
No 62
>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=78.71 E-value=10 Score=30.35 Aligned_cols=16 Identities=13% Similarity=-0.062 Sum_probs=12.7
Q ss_pred ccccCceEEEEeCCCc
Q psy17313 17 LLTAKTQIYLVNLSAK 32 (197)
Q Consensus 17 lLT~KP~iyv~Nv~e~ 32 (197)
....+|+++|+|+.|.
T Consensus 106 ~~~~~p~iiv~NK~D~ 121 (183)
T cd04152 106 ENQGVPVLVLANKQDL 121 (183)
T ss_pred hcCCCcEEEEEECcCc
Confidence 3356999999999864
No 63
>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=78.29 E-value=2.3 Score=31.99 Aligned_cols=41 Identities=22% Similarity=0.181 Sum_probs=26.9
Q ss_pred CceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 21 KTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 21 KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
+|+++|+|+.|.. . .....+.+++++++.+ ..+++++||+-
T Consensus 89 ~p~ilv~NK~Dl~--~-~~~~~~~~~~~~~~~~-~~~~~~~Sa~~ 129 (142)
T TIGR02528 89 KPVIGLVTKIDLA--E-ADVDIERAKELLETAG-AEPIFEISSVD 129 (142)
T ss_pred CCeEEEEEeeccC--C-cccCHHHHHHHHHHcC-CCcEEEEecCC
Confidence 6999999997642 1 1234556667776552 23688999864
No 64
>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=77.50 E-value=8.5 Score=29.74 Aligned_cols=43 Identities=14% Similarity=0.180 Sum_probs=27.5
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+++|+|+.|..- ......+..++++++. +.+++.+||+-
T Consensus 106 ~~~~iiiv~nK~Dl~~--~~~~~~~~~~~~~~~~--~~~~~e~Sa~~ 148 (166)
T cd04122 106 PNTVIFLIGNKADLEA--QRDVTYEEAKQFADEN--GLLFLECSAKT 148 (166)
T ss_pred CCCeEEEEEECccccc--ccCcCHHHHHHHHHHc--CCEEEEEECCC
Confidence 3468999999976421 1122345666777665 57888889863
No 65
>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=76.60 E-value=8.2 Score=29.89 Aligned_cols=40 Identities=13% Similarity=-0.012 Sum_probs=25.0
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..+|+++|+|+.|.+- ....+..++++.. +.+++++||+-
T Consensus 103 ~~~p~ivv~nK~Dl~~-----~~~~~~~~~~~~~--~~~~~~~Sa~~ 142 (161)
T cd04124 103 PEIPCIVVANKIDLDP-----SVTQKKFNFAEKH--NLPLYYVSAAD 142 (161)
T ss_pred CCCcEEEEEECccCch-----hHHHHHHHHHHHc--CCeEEEEeCCC
Confidence 3689999999976421 1123334455444 46788899863
No 66
>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=76.58 E-value=9.1 Score=32.92 Aligned_cols=44 Identities=9% Similarity=0.134 Sum_probs=28.1
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..+|+|+|+|+.|.... .....+++.+++.... +..++++||+-
T Consensus 112 ~~~piIivgNK~Dl~~~--~~v~~~ei~~~~~~~~-~~~~~evSAkt 155 (247)
T cd04143 112 VKIPMVICGNKADRDFP--REVQRDEVEQLVGGDE-NCAYFEVSAKK 155 (247)
T ss_pred CCCcEEEEEECccchhc--cccCHHHHHHHHHhcC-CCEEEEEeCCC
Confidence 46899999999875321 1224456666664321 45689999863
No 67
>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=76.40 E-value=6.8 Score=29.48 Aligned_cols=41 Identities=12% Similarity=0.162 Sum_probs=24.5
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
.+|+++|+|+.|.. + ..........+.... +.+++++||.-
T Consensus 101 ~~~~iiv~NK~Dl~--~-~~~~~~~~~~~~~~~--~~~~~~iSa~~ 141 (158)
T cd01879 101 GLPVVVALNMIDEA--E-KRGIKIDLDKLSELL--GVPVVPTSARK 141 (158)
T ss_pred CCCEEEEEehhhhc--c-cccchhhHHHHHHhh--CCCeEEEEccC
Confidence 59999999997642 1 111122233444333 46789999864
No 68
>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=75.83 E-value=6.6 Score=33.85 Aligned_cols=44 Identities=23% Similarity=0.276 Sum_probs=26.1
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhc
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFE 66 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E 66 (197)
..+|+++|+|+.|.. . .....+.+..+....+ ..+++|+||.--
T Consensus 106 ~~~p~ilV~NK~Dl~--~-~~~~~~~~~~~~~~~~-~~~v~~iSA~~g 149 (270)
T TIGR00436 106 LKRPVVLTRNKLDNK--F-KDKLLPLIDKYAILED-FKDIVPISALTG 149 (270)
T ss_pred cCCCEEEEEECeeCC--C-HHHHHHHHHHHHhhcC-CCceEEEecCCC
Confidence 358999999997642 1 1223334444443331 237899999743
No 69
>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=75.73 E-value=10 Score=29.34 Aligned_cols=43 Identities=12% Similarity=0.024 Sum_probs=27.9
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+++|+|+.|..- ......+...+++... +.+++++||+-
T Consensus 107 ~~~p~iiv~nK~Dl~~--~~~~~~~~~~~~~~~~--~~~~~~~Sa~~ 149 (167)
T cd01867 107 EDVERMLVGNKCDMEE--KRVVSKEEGEALADEY--GIKFLETSAKA 149 (167)
T ss_pred CCCcEEEEEECccccc--ccCCCHHHHHHHHHHc--CCEEEEEeCCC
Confidence 4579999999976421 1122445566666655 46789999864
No 70
>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=75.65 E-value=14 Score=28.84 Aligned_cols=43 Identities=16% Similarity=0.046 Sum_probs=25.7
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
.+.+|+|+|+|+.|.... .......+..+..+. +.+++++||.
T Consensus 104 ~~~~p~ilv~NK~Dl~~~--~~~~~~~~~~~~~~~--~~~~~~~Sa~ 146 (180)
T cd04137 104 KESVPIVLVGNKSDLHTQ--RQVSTEEGKELAESW--GAAFLESSAR 146 (180)
T ss_pred CCCCCEEEEEEchhhhhc--CccCHHHHHHHHHHc--CCeEEEEeCC
Confidence 356899999999875321 111222344444443 4678899975
No 71
>COG1159 Era GTPase [General function prediction only]
Probab=75.22 E-value=10 Score=34.46 Aligned_cols=56 Identities=27% Similarity=0.180 Sum_probs=34.8
Q ss_pred HHHHHhhcccccccCceEEEEeCCCcccccccccc-HHHHHHHHhhcCCCCeEEEechhhch
Q psy17313 7 LRIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKW-LPKIKEWVDANDPGATIIPFSGVFEH 67 (197)
Q Consensus 7 ~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~-~~~l~~~~~~~~~~~~vv~~sa~~E~ 67 (197)
.+..+++.+.- +..|+|.+.|+-|.- .++. +..+.++.....+-..++|+||.--.
T Consensus 102 ~d~~il~~lk~-~~~pvil~iNKID~~----~~~~~l~~~~~~~~~~~~f~~ivpiSA~~g~ 158 (298)
T COG1159 102 GDEFILEQLKK-TKTPVILVVNKIDKV----KPKTVLLKLIAFLKKLLPFKEIVPISALKGD 158 (298)
T ss_pred cHHHHHHHHhh-cCCCeEEEEEccccC----CcHHHHHHHHHHHHhhCCcceEEEeeccccC
Confidence 44555665554 557999999997632 2333 34555555444345679999987543
No 72
>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=74.86 E-value=12 Score=28.04 Aligned_cols=42 Identities=12% Similarity=0.014 Sum_probs=24.5
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
.+|+++|+|+.|..-. ..-..+.+.++.... +.+++++|+.-
T Consensus 105 ~~piiiv~nK~D~~~~--~~~~~~~~~~~~~~~--~~~~~~~s~~~ 146 (162)
T cd04123 105 NISLVIVGNKIDLERQ--RVVSKSEAEEYAKSV--GAKHFETSAKT 146 (162)
T ss_pred CCeEEEEEECcccccc--cCCCHHHHHHHHHHc--CCEEEEEeCCC
Confidence 5789999998764311 111234455555544 46678888653
No 73
>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=74.29 E-value=12 Score=28.94 Aligned_cols=41 Identities=12% Similarity=-0.010 Sum_probs=22.8
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
..|+++|+|+.|..-. .....+...++++.. +.+++++||+
T Consensus 106 ~~piivv~nK~Dl~~~--~~~~~~~~~~~~~~~--~~~~~~~Sa~ 146 (165)
T cd01865 106 NAQVILVGNKCDMEDE--RVVSSERGRQLADQL--GFEFFEASAK 146 (165)
T ss_pred CCCEEEEEECcccCcc--cccCHHHHHHHHHHc--CCEEEEEECC
Confidence 5688888888654211 111234444455443 4567788875
No 74
>cd01857 HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows 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 sequence NKXD) are relocated to the N terminus.
Probab=74.27 E-value=4.9 Score=31.00 Aligned_cols=42 Identities=21% Similarity=0.314 Sum_probs=26.5
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhc
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFE 66 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E 66 (197)
..||.++|+|+.|- . ....+....++.++. +.+++++||.-.
T Consensus 41 ~~k~~iivlNK~DL--~--~~~~~~~~~~~~~~~--~~~ii~iSa~~~ 82 (141)
T cd01857 41 PRKKNILLLNKADL--L--TEEQRKAWAEYFKKE--GIVVVFFSALKE 82 (141)
T ss_pred CCCcEEEEEechhc--C--CHHHHHHHHHHHHhc--CCeEEEEEecCC
Confidence 36999999999763 2 122233444445443 467899998643
No 75
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=73.98 E-value=12 Score=28.30 Aligned_cols=42 Identities=10% Similarity=0.114 Sum_probs=25.6
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
...|+++++|+.|.. .......+.++++.... +.+++++||.
T Consensus 104 ~~~pivvv~nK~D~~--~~~~~~~~~~~~~~~~~--~~~~~e~Sa~ 145 (164)
T smart00175 104 PNVVIMLVGNKSDLE--DQRQVSREEAEAFAEEH--GLPFFETSAK 145 (164)
T ss_pred CCCeEEEEEEchhcc--cccCCCHHHHHHHHHHc--CCeEEEEeCC
Confidence 468999999986532 11112344555666554 5678888875
No 76
>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=73.26 E-value=14 Score=28.26 Aligned_cols=44 Identities=14% Similarity=0.067 Sum_probs=27.8
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..+|+++|+|+.|.... .....+.++.+.+..+ ..+++++||.-
T Consensus 108 ~~~p~ilv~nK~Dl~~~--~~~~~~~~~~~~~~~~-~~~~~~~Sa~~ 151 (172)
T cd01862 108 ENFPFVVLGNKIDLEEK--RQVSTKKAQQWCQSNG-NIPYFETSAKE 151 (172)
T ss_pred CCceEEEEEECcccccc--cccCHHHHHHHHHHcC-CceEEEEECCC
Confidence 36899999999764211 1224556666665542 25788888753
No 77
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=73.00 E-value=3.9 Score=31.46 Aligned_cols=29 Identities=24% Similarity=0.464 Sum_probs=23.8
Q ss_pred HHHHcCcccccC----CceeecCCCEEEEEEcc
Q psy17313 159 ACRAAGKYRQQG----RAYTVEDGDIIFFKFNA 187 (197)
Q Consensus 159 ~ak~~Gk~r~eG----kdYivqDGDIi~f~fn~ 187 (197)
++-+.|++++.| -.+.|+.||+|.|+|+.
T Consensus 29 ~~~~~GrV~vNG~~aKpS~~VK~GD~l~i~~~~ 61 (100)
T COG1188 29 EMIEGGRVKVNGQRAKPSKEVKVGDILTIRFGN 61 (100)
T ss_pred HHHHCCeEEECCEEcccccccCCCCEEEEEeCC
Confidence 355678898888 46889999999999974
No 78
>KOG0466|consensus
Probab=72.89 E-value=3.4 Score=38.43 Aligned_cols=66 Identities=26% Similarity=0.405 Sum_probs=42.3
Q ss_pred cCChHHHHHhhcccccccCceEEEEeCCCccccc--cccccHHHHHHHHhhc-CCCCeEEEechhhchhhc
Q psy17313 3 CEHHLRIEHLNKLNLLTAKTQIYLVNLSAKDYIK--KKNKWLPKIKEWVDAN-DPGATIIPFSGVFEHQLV 70 (197)
Q Consensus 3 ~~~~~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~--~~~~~~~~l~~~~~~~-~~~~~vv~~sa~~E~el~ 70 (197)
|..|.--+.|-.......|-+|++-|+-| +.. .+.+..+.+.++++.. .+++|+||+||++-..+.
T Consensus 162 CPQPQTsEHLaaveiM~LkhiiilQNKiD--li~e~~A~eq~e~I~kFi~~t~ae~aPiiPisAQlkyNId 230 (466)
T KOG0466|consen 162 CPQPQTSEHLAAVEIMKLKHIIILQNKID--LIKESQALEQHEQIQKFIQGTVAEGAPIIPISAQLKYNID 230 (466)
T ss_pred CCCCchhhHHHHHHHhhhceEEEEechhh--hhhHHHHHHHHHHHHHHHhccccCCCceeeehhhhccChH
Confidence 44443333344444566799999999854 332 1345667777777542 247899999999876553
No 79
>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=72.86 E-value=15 Score=28.98 Aligned_cols=43 Identities=5% Similarity=-0.055 Sum_probs=25.8
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+|+|+|+.|..-. ..-..+...+++++. +.+++.+||.-
T Consensus 106 ~~~piilvgNK~Dl~~~--~~v~~~~~~~~a~~~--~~~~~e~Sa~~ 148 (172)
T cd04141 106 EDIPLVLVGNKVDLESQ--RQVTTEEGRNLAREF--NCPFFETSAAL 148 (172)
T ss_pred CCCCEEEEEEChhhhhc--CccCHHHHHHHHHHh--CCEEEEEecCC
Confidence 45799999999764211 111223445566554 56788888874
No 80
>PF09138 Urm1: Urm1 (Ubiquitin related modifier); InterPro: IPR015221 Ubiquitin related modifier 1 (Urm1) is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like urmylation pathway []. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily []. ; GO: 0034227 tRNA thio-modification, 0005737 cytoplasm; PDB: 2AX5_A 2QJL_A 2PKO_A 1WGK_A 1XO3_A 2K9X_A.
Probab=72.80 E-value=2 Score=32.79 Aligned_cols=16 Identities=38% Similarity=0.567 Sum_probs=11.9
Q ss_pred CCceeecCCCEEEEEE
Q psy17313 170 GRAYTVEDGDIIFFKF 185 (197)
Q Consensus 170 GkdYivqDGDIi~f~f 185 (197)
+.+|+++|||.|.|--
T Consensus 76 ~~~y~l~~~D~I~FiS 91 (96)
T PF09138_consen 76 EEDYVLKDGDNITFIS 91 (96)
T ss_dssp CCCSB--TTEEEEEEE
T ss_pred CcceEcCCCCEEEEEc
Confidence 4699999999999964
No 81
>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=72.43 E-value=15 Score=28.31 Aligned_cols=43 Identities=12% Similarity=0.057 Sum_probs=27.3
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+++|+|+.|.. . .....+.+++++++.+ ..+++++||+-
T Consensus 113 ~~~piilv~nK~Dl~--~-~~~~~~~~~~~~~~~~-~~~~~e~Sa~~ 155 (170)
T cd04116 113 ESFPFVVLGNKNDIP--E-RQVSTEEAQAWCRENG-DYPYFETSAKD 155 (170)
T ss_pred CCCcEEEEEECcccc--c-cccCHHHHHHHHHHCC-CCeEEEEECCC
Confidence 346999999997642 1 2224556777776652 24678888763
No 82
>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=72.33 E-value=13 Score=28.81 Aligned_cols=43 Identities=7% Similarity=-0.080 Sum_probs=25.5
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+++|+|+.|..- ...-..+....++... +.+++++||+-
T Consensus 107 ~~~piilv~nK~Dl~~--~~~v~~~~~~~~~~~~--~~~~~e~SA~~ 149 (165)
T cd04140 107 EKIPIMLVGNKCDESH--KREVSSNEGAACATEW--NCAFMETSAKT 149 (165)
T ss_pred CCCCEEEEEECccccc--cCeecHHHHHHHHHHh--CCcEEEeecCC
Confidence 4579999999976421 0111223334455444 46788899864
No 83
>PRK15494 era GTPase Era; Provisional
Probab=72.23 E-value=11 Score=33.91 Aligned_cols=43 Identities=26% Similarity=0.444 Sum_probs=28.1
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhch
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEH 67 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~ 67 (197)
.+|.|+|+|+.|. . ++.+..+.+++.+..+...++|+||.-..
T Consensus 160 ~~p~IlViNKiDl--~---~~~~~~~~~~l~~~~~~~~i~~iSAktg~ 202 (339)
T PRK15494 160 NIVPIFLLNKIDI--E---SKYLNDIKAFLTENHPDSLLFPISALSGK 202 (339)
T ss_pred CCCEEEEEEhhcC--c---cccHHHHHHHHHhcCCCcEEEEEeccCcc
Confidence 4688999999764 2 22355666666554333579999996433
No 84
>KOG4146|consensus
Probab=72.02 E-value=2.3 Score=32.59 Aligned_cols=17 Identities=41% Similarity=0.667 Sum_probs=14.5
Q ss_pred cCCceeecCCCEEEEEE
Q psy17313 169 QGRAYTVEDGDIIFFKF 185 (197)
Q Consensus 169 eGkdYivqDGDIi~f~f 185 (197)
+-+||++||||.|-|.-
T Consensus 80 ekedy~ledgD~ivfiS 96 (101)
T KOG4146|consen 80 EKEDYPLEDGDHIVFIS 96 (101)
T ss_pred cccccCcccCCEEEEEE
Confidence 55899999999998864
No 85
>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=71.62 E-value=7.8 Score=29.46 Aligned_cols=42 Identities=2% Similarity=-0.236 Sum_probs=24.4
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
...|+++|+|+.|..- ...-..++..++++.. +.+++++||+
T Consensus 105 ~~~p~iiv~nK~Dl~~--~~~v~~~~~~~~~~~~--~~~~~~~Sa~ 146 (162)
T cd04106 105 GDIPMVLVQTKIDLLD--QAVITNEEAEALAKRL--QLPLFRTSVK 146 (162)
T ss_pred CCCCEEEEEEChhccc--ccCCCHHHHHHHHHHc--CCeEEEEECC
Confidence 3678888888865321 1111234455555554 4677888875
No 86
>PRK04213 GTP-binding protein; Provisional
Probab=71.55 E-value=16 Score=29.29 Aligned_cols=14 Identities=29% Similarity=0.128 Sum_probs=11.7
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
..+|+++|+|+.|.
T Consensus 129 ~~~p~iiv~NK~Dl 142 (201)
T PRK04213 129 LGIPPIVAVNKMDK 142 (201)
T ss_pred cCCCeEEEEECccc
Confidence 36899999999764
No 87
>COG1160 Predicted GTPases [General function prediction only]
Probab=70.77 E-value=12 Score=35.66 Aligned_cols=50 Identities=18% Similarity=-0.009 Sum_probs=27.5
Q ss_pred hHHHHHhhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 6 HLRIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 6 ~~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
+++..+.+-| +-..||+|.|+|+.|..- .-....++..- + -..++|+||.
T Consensus 99 ~~D~~ia~~L-r~~~kpviLvvNK~D~~~------~e~~~~efysl-G-~g~~~~ISA~ 148 (444)
T COG1160 99 PADEEIAKIL-RRSKKPVILVVNKIDNLK------AEELAYEFYSL-G-FGEPVPISAE 148 (444)
T ss_pred HHHHHHHHHH-HhcCCCEEEEEEcccCch------hhhhHHHHHhc-C-CCCceEeehh
Confidence 3444444433 355699999999987531 11223333321 1 1357899974
No 88
>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=70.35 E-value=13 Score=29.87 Aligned_cols=47 Identities=21% Similarity=0.189 Sum_probs=26.2
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHH-----hhcC-CCCeEEEechhhch
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWV-----DAND-PGATIIPFSGVFEH 67 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~-----~~~~-~~~~vv~~sa~~E~ 67 (197)
...+|+++|+|+.|. .. .......+..|. +... +...++++||.-..
T Consensus 59 ~~~~~~ilV~NK~Dl--~~-~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vSA~~~~ 111 (190)
T cd01855 59 GGNNPVILVGNKIDL--LP-KDKNLVRIKNWLRAKAAAGLGLKPKDVILISAKKGW 111 (190)
T ss_pred cCCCcEEEEEEchhc--CC-CCCCHHHHHHHHHHHHHhhcCCCcccEEEEECCCCC
Confidence 356999999999764 21 122233344443 2211 01258999987543
No 89
>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=70.32 E-value=14 Score=29.54 Aligned_cols=43 Identities=9% Similarity=-0.081 Sum_probs=25.7
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+++|+|+.|..-. .....+..+.+.... +.+++++||.-
T Consensus 105 ~~~piiiv~NK~Dl~~~--~~~~~~~~~~l~~~~--~~~~~e~Sa~~ 147 (191)
T cd04112 105 EDVVIMLLGNKADMSGE--RVVKREDGERLAKEY--GVPFMETSAKT 147 (191)
T ss_pred CCCcEEEEEEcccchhc--cccCHHHHHHHHHHc--CCeEEEEeCCC
Confidence 35799999999764211 111223445555544 46788888764
No 90
>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=69.98 E-value=15 Score=30.12 Aligned_cols=42 Identities=14% Similarity=0.180 Sum_probs=24.3
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
.-|+|+|+|+.|-... ..-..+.+++|++++ +.+++.+||+-
T Consensus 110 ~~piilVGNK~DL~~~--~~v~~~~~~~~a~~~--~~~~~e~SAk~ 151 (189)
T cd04121 110 GVPKILVGNRLHLAFK--RQVATEQAQAYAERN--GMTFFEVSPLC 151 (189)
T ss_pred CCCEEEEEECccchhc--cCCCHHHHHHHHHHc--CCEEEEecCCC
Confidence 4577888887653211 112344566676655 45677777663
No 91
>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=69.91 E-value=18 Score=27.72 Aligned_cols=42 Identities=7% Similarity=0.046 Sum_probs=24.6
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
..|+++|+|+.|..- ......+...++++..+ -..++++||+
T Consensus 108 ~~p~ivv~nK~Dl~~--~~~~~~~~~~~~~~~~~-~~~~~e~Sa~ 149 (165)
T cd01864 108 NVVLLLIGNKCDLEE--QREVLFEEACTLAEKNG-MLAVLETSAK 149 (165)
T ss_pred CCcEEEEEECccccc--ccccCHHHHHHHHHHcC-CcEEEEEECC
Confidence 468999999876421 12223445556655442 2357888875
No 92
>PF01043 SecA_PP_bind: SecA preprotein cross-linking domain; InterPro: IPR011130 The SecA ATPase is involved in the insertion and retraction of preproteins through the plasma membrane. This domain has been found to cross-link to preproteins, thought to indicate a role in preprotein binding. The pre-protein cross-linking domain is comprised of two sub domains that are inserted within the ATPase domain [].; GO: 0017038 protein import, 0016020 membrane; PDB: 3DIN_B 3JUX_A 3IQY_A 2IBM_A 3DL8_A 3JV2_B 3IQM_A 1TF2_A 1TF5_A 1M74_A ....
Probab=69.77 E-value=2.7 Score=32.64 Aligned_cols=82 Identities=16% Similarity=0.205 Sum_probs=47.3
Q ss_pred HHHHHhhcCCeEEeecCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCce
Q psy17313 94 ITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAY 173 (197)
Q Consensus 94 i~~~y~lL~LitffT~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdY 173 (197)
....-..|.--..|++.++.-..|+...|..-.+-.-.+..++-.. +.. ++..+ =.++.|.. .+-..++||
T Consensus 11 a~~~~~~L~~~~dy~vde~~~~v~LT~~G~~~~e~~~~~~~~l~~~----~~~---~~~~~-i~~AL~A~-~l~~rd~dY 81 (113)
T PF01043_consen 11 ADKFAKQLKEDEDYEVDEKQRTVELTEKGIEKAEKLLGISDNLYDE----ENS---ELYHH-INQALKAH-HLFKRDVDY 81 (113)
T ss_dssp HHHHHHHSHTTTSECECTSTTEEEESHHHHHHHHHHHTSSSSTTST----TCH---HHHHH-HHHHHHHH-HCSTTTTSE
T ss_pred HHHHHHhCCCCCCEEEeCCCCeeeEhHHHHHHHHHHhhhccccccc----ccH---HHHHH-HHHHHHHH-HHHhCCcce
Confidence 3334444555557999988889999999976665444443222211 100 11111 01223332 244589999
Q ss_pred eecCCCEEEEE
Q psy17313 174 TVEDGDIIFFK 184 (197)
Q Consensus 174 ivqDGDIi~f~ 184 (197)
+|+||.|+-+-
T Consensus 82 iV~dg~V~IVD 92 (113)
T PF01043_consen 82 IVRDGEVVIVD 92 (113)
T ss_dssp EEETTEEEEBC
T ss_pred EEEcCEEEEEE
Confidence 99999998764
No 93
>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=69.22 E-value=20 Score=27.32 Aligned_cols=41 Identities=12% Similarity=0.024 Sum_probs=22.2
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
..|+++|+|+.|..- ..+......+.+.... +.+++++||.
T Consensus 107 ~~p~ilv~nK~Dl~~--~~~~~~~~~~~~~~~~--~~~~~~~Sa~ 147 (164)
T cd04101 107 HMPGVLVGNKMDLAD--KAEVTDAQAQAFAQAN--QLKFFKTSAL 147 (164)
T ss_pred CCCEEEEEECccccc--ccCCCHHHHHHHHHHc--CCeEEEEeCC
Confidence 478999999876421 1111122233444333 4567888875
No 94
>PRK13796 GTPase YqeH; Provisional
Probab=69.12 E-value=56 Score=29.86 Aligned_cols=147 Identities=14% Similarity=0.178 Sum_probs=75.4
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHH----hhcCC-CCeEEEechhhchhhcCCCHHHHHHHHH-----HhC-Cc
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWV----DANDP-GATIIPFSGVFEHQLVDMPDDERQRYLD-----EQK-AT 87 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~----~~~~~-~~~vv~~sa~~E~el~~l~~ee~~~fl~-----~~g-~~ 87 (197)
..+|+++|+|+.|- .. .....+++++|. ++.+- ...++++||+--.-+.+|-. .-.++++ -.| .+
T Consensus 95 ~~kpviLViNK~DL--l~-~~~~~~~i~~~l~~~~k~~g~~~~~v~~vSAk~g~gI~eL~~-~I~~~~~~~~v~vvG~~N 170 (365)
T PRK13796 95 GNNPVLLVGNKADL--LP-KSVKKNKVKNWLRQEAKELGLRPVDVVLISAQKGHGIDELLE-AIEKYREGRDVYVVGVTN 170 (365)
T ss_pred CCCCEEEEEEchhh--CC-CccCHHHHHHHHHHHHHhcCCCcCcEEEEECCCCCCHHHHHH-HHHHhcCCCeEEEEcCCC
Confidence 47899999999764 21 122334455443 33210 11578899875433322210 0011111 124 55
Q ss_pred chHHHHHHHHHhhc----CCeEEeecCCCceee--e-EecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHH
Q psy17313 88 SVLDKIITQGYKSL----QLQYFFTAGQDEVKA--W-TIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAAC 160 (197)
Q Consensus 88 sgl~~li~~~y~lL----~LitffT~g~~EvRA--W-ti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~a 160 (197)
.|-..||.+..... ..++.= ..|.-++. | .+..|....|..|.++.+= -+..+.-+|+..+
T Consensus 171 vGKSTLiN~L~~~~~~~~~~~~~s-~~pGTT~~~~~~~l~~~~~l~DTPGi~~~~~-----~~~~l~~~~l~~~------ 238 (365)
T PRK13796 171 VGKSTLINRIIKEITGEKDVITTS-RFPGTTLDKIEIPLDDGSFLYDTPGIIHRHQ-----MAHYLSAKDLKII------ 238 (365)
T ss_pred CcHHHHHHHHHhhccCccceEEec-CCCCccceeEEEEcCCCcEEEECCCccccch-----hhhcCCHHHHhhc------
Confidence 66666776665432 222211 12344442 2 2467788889999886531 1233333454333
Q ss_pred HHcCcccccCCceeecCCCEEEE
Q psy17313 161 RAAGKYRQQGRAYTVEDGDIIFF 183 (197)
Q Consensus 161 k~~Gk~r~eGkdYivqDGDIi~f 183 (197)
... -++..+.|.++.|..++|
T Consensus 239 -~p~-k~i~p~~~~l~~gq~l~~ 259 (365)
T PRK13796 239 -SPK-KEIKPKTYQLNEEQTLFL 259 (365)
T ss_pred -CCC-cccCceEEEECCCCEEEE
Confidence 111 134578999999988875
No 95
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=68.82 E-value=2.9 Score=31.76 Aligned_cols=17 Identities=47% Similarity=0.782 Sum_probs=14.0
Q ss_pred cCCceeecCCCEEEEEE
Q psy17313 169 QGRAYTVEDGDIIFFKF 185 (197)
Q Consensus 169 eGkdYivqDGDIi~f~f 185 (197)
+-++|.++|||+|.|.-
T Consensus 75 eke~y~ledgDiIvfis 91 (96)
T COG5131 75 EKERYPLEDGDIIVFIS 91 (96)
T ss_pred hcccccCCCCCEEEEEe
Confidence 44689999999998853
No 96
>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=68.41 E-value=19 Score=27.93 Aligned_cols=43 Identities=9% Similarity=0.088 Sum_probs=26.2
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+++|+|+.|..- ...-..+..+.++... +.+++++||.-
T Consensus 108 ~~~pvivv~nK~Dl~~--~~~~~~~~~~~~~~~~--~~~~~e~Sa~~ 150 (168)
T cd01866 108 SNMTIMLIGNKCDLES--RREVSYEEGEAFAKEH--GLIFMETSAKT 150 (168)
T ss_pred CCCcEEEEEECccccc--ccCCCHHHHHHHHHHc--CCEEEEEeCCC
Confidence 4678999999865421 1122344555566554 56788888753
No 97
>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=68.30 E-value=21 Score=27.05 Aligned_cols=42 Identities=17% Similarity=0.133 Sum_probs=26.9
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
...|+++++|+.|..- ......+.+..++... +.+++++||.
T Consensus 105 ~~~~iivv~nK~D~~~--~~~~~~~~~~~~~~~~--~~~~~~~Sa~ 146 (163)
T cd01860 105 PNIIIALVGNKADLES--KRQVSTEEAQEYADEN--GLLFFETSAK 146 (163)
T ss_pred CCCeEEEEEECccccc--cCcCCHHHHHHHHHHc--CCEEEEEECC
Confidence 5678999999976421 1222444555666655 4678899976
No 98
>PLN03118 Rab family protein; Provisional
Probab=67.58 E-value=26 Score=28.54 Aligned_cols=42 Identities=7% Similarity=0.030 Sum_probs=24.7
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
...|+++|+|+.|.... .....+....++.++ +.+++++||+
T Consensus 119 ~~~~~ilv~NK~Dl~~~--~~i~~~~~~~~~~~~--~~~~~e~SAk 160 (211)
T PLN03118 119 QDCVKMLVGNKVDRESE--RDVSREEGMALAKEH--GCLFLECSAK 160 (211)
T ss_pred CCCCEEEEEECcccccc--CccCHHHHHHHHHHc--CCEEEEEeCC
Confidence 44689999999764211 111233444555544 5678888875
No 99
>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=67.25 E-value=27 Score=27.03 Aligned_cols=44 Identities=5% Similarity=-0.142 Sum_probs=24.1
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+|+++|+.|..- ...-..+....+....+ ..+++++||.-
T Consensus 105 ~~~piiiv~nK~D~~~--~~~~~~~~~~~~~~~~~-~~~~~~~SA~~ 148 (168)
T cd04177 105 DNVPMVLVGNKADLED--DRQVSREDGVSLSQQWG-NVPFYETSARK 148 (168)
T ss_pred CCCCEEEEEEChhccc--cCccCHHHHHHHHHHcC-CceEEEeeCCC
Confidence 4689999999875421 11112233334444431 25688888764
No 100
>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=66.89 E-value=15 Score=28.92 Aligned_cols=50 Identities=14% Similarity=0.252 Sum_probs=25.8
Q ss_pred hhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCC-eEEEechhh
Q psy17313 12 LNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGA-TIIPFSGVF 65 (197)
Q Consensus 12 i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~-~vv~~sa~~ 65 (197)
++.+......|+++|+|+.|.. ...........++.+.. +. .++++||.-
T Consensus 100 ~~~~~~~~~~p~iiv~NK~Dl~--~~~~~~~~~~~~~~~~~--~~~~~~~~Sa~~ 150 (169)
T cd01892 100 YKKYFMLGEIPCLFVAAKADLD--EQQQRYEVQPDEFCRKL--GLPPPLHFSSKL 150 (169)
T ss_pred HHHhccCCCCeEEEEEEccccc--ccccccccCHHHHHHHc--CCCCCEEEEecc
Confidence 3333223468999999997642 11111112234444443 22 357888764
No 101
>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=66.62 E-value=14 Score=28.96 Aligned_cols=45 Identities=4% Similarity=-0.070 Sum_probs=20.2
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
.-|+++|+|+++..-.....--.+..++++++.. +..++.+||+-
T Consensus 99 ~~piilvgnK~Dl~~~~~~~v~~~~~~~~~~~~~-~~~~~e~SAk~ 143 (158)
T cd04103 99 EIPLILVGTQDAISESNPRVIDDARARQLCADMK-RCSYYETCATY 143 (158)
T ss_pred CCCEEEEeeHHHhhhcCCcccCHHHHHHHHHHhC-CCcEEEEecCC
Confidence 3477888887442110000111122334444321 34667777653
No 102
>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=65.99 E-value=23 Score=28.12 Aligned_cols=44 Identities=9% Similarity=-0.080 Sum_probs=25.5
Q ss_pred cCceEEEEeCCCcccccc--ccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKK--KNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~--~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..|+++|+|+.|..-... .......+.+++... +.+++++||+-
T Consensus 105 ~~piilv~nK~Dl~~~~~~~~~v~~~~~~~~~~~~--~~~~~~~Sa~~ 150 (193)
T cd04118 105 HCKIYLCGTKSDLIEQDRSLRQVDFHDVQDFADEI--KAQHFETSSKT 150 (193)
T ss_pred CCCEEEEEEcccccccccccCccCHHHHHHHHHHc--CCeEEEEeCCC
Confidence 579999999976421000 011223455665544 46788888764
No 103
>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=65.97 E-value=7.1 Score=31.40 Aligned_cols=47 Identities=19% Similarity=0.157 Sum_probs=25.3
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhh-----cCCCCeEEEechhhc
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDA-----NDPGATIIPFSGVFE 66 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~-----~~~~~~vv~~sa~~E 66 (197)
.+|+++++|+.|..-.......++.+++.... ...+.+++++||.-.
T Consensus 120 ~~~~iiv~NK~Dl~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~vi~iSa~~g 171 (192)
T cd01889 120 CKKLIVVLNKIDLIPEEERERKIEKMKKKLQKTLEKTRFKNSPIIPVSAKPG 171 (192)
T ss_pred CCCEEEEEECcccCCHHHHHHHHHHHHHHHHHHHHhcCcCCCCEEEEeccCC
Confidence 67999999997642110011223344332211 112567999998643
No 104
>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=65.90 E-value=15 Score=28.62 Aligned_cols=44 Identities=11% Similarity=-0.047 Sum_probs=24.0
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
....|+++|+|+.|..-. ..-......++++.. +.+++.+||+-
T Consensus 107 ~~~~p~iiv~nK~Dl~~~--~~~~~~~~~~~~~~~--~~~~~e~Sa~~ 150 (170)
T cd04115 107 PNEVPRILVGNKCDLREQ--IQVPTDLAQRFADAH--SMPLFETSAKD 150 (170)
T ss_pred CCCCCEEEEEECccchhh--cCCCHHHHHHHHHHc--CCcEEEEeccC
Confidence 356788888888663211 111223334444443 45677778764
No 105
>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=65.78 E-value=6 Score=30.10 Aligned_cols=14 Identities=14% Similarity=0.102 Sum_probs=11.9
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
...|+++|+|+.|.
T Consensus 100 ~~~piilv~nK~Dl 113 (160)
T cd04156 100 KGVPVVLLANKQDL 113 (160)
T ss_pred cCCCEEEEEECccc
Confidence 57899999999875
No 106
>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=65.73 E-value=11 Score=31.45 Aligned_cols=52 Identities=17% Similarity=0.238 Sum_probs=29.1
Q ss_pred ccCceEEEEeCCCccccccc----cccHHHHHHHHhhcC---CCCeEEEechhhchhhc
Q psy17313 19 TAKTQIYLVNLSAKDYIKKK----NKWLPKIKEWVDAND---PGATIIPFSGVFEHQLV 70 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~----~~~~~~l~~~~~~~~---~~~~vv~~sa~~E~el~ 70 (197)
-.+|+|+++|+.|..-.... ....+.+++..+... .+.+++|+||.-..-|.
T Consensus 136 ~~~~iiivvNK~Dl~~~~~~~~~~~~i~~~l~~~l~~~~~~~~~~~ii~iSA~tg~gi~ 194 (219)
T cd01883 136 GVKQLIVAVNKMDDVTVNWSEERYDEIKKELSPFLKKVGYNPKDVPFIPISGLTGDNLI 194 (219)
T ss_pred CCCeEEEEEEccccccccccHHHHHHHHHHHHHHHHHcCCCcCCceEEEeecCcCCCCC
Confidence 34899999999875310001 122334433343321 13679999997666554
No 107
>PLN03108 Rab family protein; Provisional
Probab=65.58 E-value=15 Score=30.29 Aligned_cols=43 Identities=9% Similarity=0.070 Sum_probs=25.9
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+|+|+|+.|.. ....-..+...++++++ +.+++.+||+-
T Consensus 110 ~~~piiiv~nK~Dl~--~~~~~~~~~~~~~~~~~--~~~~~e~Sa~~ 152 (210)
T PLN03108 110 ANMTIMLIGNKCDLA--HRRAVSTEEGEQFAKEH--GLIFMEASAKT 152 (210)
T ss_pred CCCcEEEEEECccCc--cccCCCHHHHHHHHHHc--CCEEEEEeCCC
Confidence 457888999986532 11112344555666555 56788888753
No 108
>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=65.40 E-value=6.9 Score=30.73 Aligned_cols=16 Identities=25% Similarity=0.285 Sum_probs=12.9
Q ss_pred ccccCceEEEEeCCCc
Q psy17313 17 LLTAKTQIYLVNLSAK 32 (197)
Q Consensus 17 lLT~KP~iyv~Nv~e~ 32 (197)
-+..+|+++|+|+.|.
T Consensus 97 ~~~~~piliv~NK~Dl 112 (167)
T cd04161 97 RVSGKPILVLANKQDK 112 (167)
T ss_pred cccCCcEEEEEeCCCC
Confidence 3457899999999874
No 109
>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=64.76 E-value=12 Score=29.31 Aligned_cols=42 Identities=10% Similarity=-0.115 Sum_probs=25.3
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhch
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEH 67 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~ 67 (197)
..|+++|+|+.|..- .....+..++.+.+ +.+++++||+-..
T Consensus 104 ~~piiiv~nK~Dl~~----~~~~~~~~~~~~~~--~~~~~e~Sa~~~~ 145 (166)
T cd00877 104 NIPIVLCGNKVDIKD----RKVKAKQITFHRKK--NLQYYEISAKSNY 145 (166)
T ss_pred CCcEEEEEEchhccc----ccCCHHHHHHHHHc--CCEEEEEeCCCCC
Confidence 699999999976431 11112233444443 4678899987533
No 110
>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=64.53 E-value=18 Score=27.00 Aligned_cols=43 Identities=12% Similarity=-0.049 Sum_probs=26.8
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..+|+++++|+.|..-. .....+.+..+.... +.+++++|+.-
T Consensus 103 ~~~p~ivv~nK~D~~~~--~~~~~~~~~~~~~~~--~~~~~~~S~~~ 145 (160)
T cd00876 103 EDIPIVLVGNKCDLENE--RQVSKEEGKALAKEW--GCPFIETSAKD 145 (160)
T ss_pred CCCcEEEEEECCccccc--ceecHHHHHHHHHHc--CCcEEEeccCC
Confidence 47899999999775321 122344555555554 35788888763
No 111
>PTZ00099 rab6; Provisional
Probab=64.53 E-value=30 Score=27.96 Aligned_cols=43 Identities=5% Similarity=-0.150 Sum_probs=23.1
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+++|+|+.|..-. ..-..+....++... +..++++||+-
T Consensus 84 ~~~piilVgNK~DL~~~--~~v~~~e~~~~~~~~--~~~~~e~SAk~ 126 (176)
T PTZ00099 84 KDVIIALVGNKTDLGDL--RKVTYEEGMQKAQEY--NTMFHETSAKA 126 (176)
T ss_pred CCCeEEEEEECcccccc--cCCCHHHHHHHHHHc--CCEEEEEECCC
Confidence 34677888888653111 111233344555444 45677788763
No 112
>PRK01777 hypothetical protein; Validated
Probab=64.08 E-value=25 Score=26.49 Aligned_cols=59 Identities=19% Similarity=0.119 Sum_probs=34.2
Q ss_pred eeeEecCCCChhhhhhhhccccccCee-----EEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEEEccCC
Q psy17313 115 KAWTIQKGTKAPQAAGRIHTDFEKGFI-----MAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFNAGA 189 (197)
Q Consensus 115 RAWti~~GstA~~aAg~IHsDfekgFI-----~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~fn~~~ 189 (197)
..-.++.|+|+.||.... .+..-|- .+.|.= -| +...-|++++|||-|.|- -|=
T Consensus 19 ~~l~vp~GtTv~dal~~s--gi~~~~pei~~~~~~vgI---------------~G--k~v~~d~~L~dGDRVeIy--rPL 77 (95)
T PRK01777 19 QRLTLQEGATVEEAIRAS--GLLELRTDIDLAKNKVGI---------------YS--RPAKLTDVLRDGDRVEIY--RPL 77 (95)
T ss_pred EEEEcCCCCcHHHHHHHc--CCCccCcccccccceEEE---------------eC--eECCCCCcCCCCCEEEEe--cCC
Confidence 345579999999998765 2222221 011111 13 234679999999999874 233
Q ss_pred CCCCC
Q psy17313 190 GLNPK 194 (197)
Q Consensus 190 ~~~~~ 194 (197)
..+||
T Consensus 78 ~~DPk 82 (95)
T PRK01777 78 LADPK 82 (95)
T ss_pred CCCHH
Confidence 44444
No 113
>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=63.82 E-value=17 Score=31.64 Aligned_cols=45 Identities=7% Similarity=0.121 Sum_probs=25.8
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQL 69 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el 69 (197)
..||+|+|.|+.|- .. ....+...++.++. +.+++++||.-...+
T Consensus 47 ~~kp~IiVlNK~DL--~~--~~~~~~~~~~~~~~--~~~vi~iSa~~~~gi 91 (276)
T TIGR03596 47 GNKPRLIVLNKADL--AD--PAVTKQWLKYFEEK--GIKALAINAKKGKGV 91 (276)
T ss_pred CCCCEEEEEEcccc--CC--HHHHHHHHHHHHHc--CCeEEEEECCCcccH
Confidence 47999999999763 21 11122222223222 457899998765433
No 114
>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=63.51 E-value=23 Score=27.28 Aligned_cols=14 Identities=7% Similarity=-0.128 Sum_probs=12.0
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
..+|+++|+|+.|.
T Consensus 101 ~~~piilv~nK~Dl 114 (174)
T smart00174 101 PNTPIILVGTKLDL 114 (174)
T ss_pred CCCCEEEEecChhh
Confidence 47999999999764
No 115
>PRK00089 era GTPase Era; Reviewed
Probab=63.13 E-value=27 Score=30.09 Aligned_cols=45 Identities=24% Similarity=0.271 Sum_probs=26.3
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhch
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEH 67 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~ 67 (197)
.+|+++|+|+.|.. .......+.+..+.+.. +..+++++||.-..
T Consensus 113 ~~pvilVlNKiDl~--~~~~~l~~~~~~l~~~~-~~~~i~~iSA~~~~ 157 (292)
T PRK00089 113 KTPVILVLNKIDLV--KDKEELLPLLEELSELM-DFAEIVPISALKGD 157 (292)
T ss_pred CCCEEEEEECCcCC--CCHHHHHHHHHHHHhhC-CCCeEEEecCCCCC
Confidence 58999999997642 11122233344444332 24679999987543
No 116
>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=62.71 E-value=33 Score=27.40 Aligned_cols=44 Identities=14% Similarity=0.022 Sum_probs=24.9
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHHhhcC----------CCCeEEEechhh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAND----------PGATIIPFSGVF 65 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~----------~~~~vv~~sa~~ 65 (197)
+..+|+++|+|+.|... ....+++++.+.-.. ....++++||..
T Consensus 116 ~~~~piliv~NK~Dl~~----~~~~~~i~~~l~l~~~~~~~~~~~~~~~~i~~~Sa~~ 169 (184)
T smart00178 116 LATVPFLILGNKIDAPY----AASEDELRYALGLTNTTGSKGKVGVRPLEVFMCSVVR 169 (184)
T ss_pred hcCCCEEEEEeCccccC----CCCHHHHHHHcCCCcccccccccCCceeEEEEeeccc
Confidence 35689999999977421 123445554442110 123478888764
No 117
>PRK04000 translation initiation factor IF-2 subunit gamma; Validated
Probab=62.66 E-value=18 Score=33.52 Aligned_cols=56 Identities=23% Similarity=0.277 Sum_probs=30.8
Q ss_pred hhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhc-CCCCeEEEechhhch
Q psy17313 12 LNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAN-DPGATIIPFSGVFEH 67 (197)
Q Consensus 12 i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~-~~~~~vv~~sa~~E~ 67 (197)
+..+..+-.+|+++|+|+.|..-........++++++++.. ..+.+++++||.-..
T Consensus 131 l~~l~~~~i~~iiVVlNK~Dl~~~~~~~~~~~~i~~~l~~~~~~~~~ii~vSA~~g~ 187 (411)
T PRK04000 131 LMALDIIGIKNIVIVQNKIDLVSKERALENYEQIKEFVKGTVAENAPIIPVSALHKV 187 (411)
T ss_pred HHHHHHcCCCcEEEEEEeeccccchhHHHHHHHHHHHhccccCCCCeEEEEECCCCc
Confidence 33333445578999999976421000011234555655432 114679999987543
No 118
>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=62.62 E-value=19 Score=28.68 Aligned_cols=45 Identities=16% Similarity=0.217 Sum_probs=25.4
Q ss_pred ccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhch
Q psy17313 17 LLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEH 67 (197)
Q Consensus 17 lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~ 67 (197)
.+..||.++|+|+.|. .. ........++.... +..++++||.-..
T Consensus 43 ~~~~k~~ilVlNK~Dl--~~--~~~~~~~~~~~~~~--~~~vi~iSa~~~~ 87 (171)
T cd01856 43 ILGNKPRIIVLNKADL--AD--PKKTKKWLKYFESK--GEKVLFVNAKSGK 87 (171)
T ss_pred HhcCCCEEEEEehhhc--CC--hHHHHHHHHHHHhc--CCeEEEEECCCcc
Confidence 3456999999999763 21 11122222333222 3568899986543
No 119
>PRK00454 engB GTP-binding protein YsxC; Reviewed
Probab=62.60 E-value=18 Score=28.49 Aligned_cols=43 Identities=16% Similarity=0.213 Sum_probs=20.4
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
.+|+++++|+.|..-........+.+..+.... +.+++|+||.
T Consensus 135 ~~~~iiv~nK~Dl~~~~~~~~~~~~i~~~l~~~--~~~~~~~Sa~ 177 (196)
T PRK00454 135 GIPVLIVLTKADKLKKGERKKQLKKVRKALKFG--DDEVILFSSL 177 (196)
T ss_pred CCcEEEEEECcccCCHHHHHHHHHHHHHHHHhc--CCceEEEEcC
Confidence 467778888765311000111223344444332 2456777764
No 120
>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=62.15 E-value=20 Score=27.35 Aligned_cols=44 Identities=18% Similarity=0.170 Sum_probs=25.3
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHHhhc-----CCCCeEEEechhh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAN-----DPGATIIPFSGVF 65 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~-----~~~~~vv~~sa~~ 65 (197)
....|+++++|+.|..- ......+.++.+.. ..+.+++++||+-
T Consensus 105 ~~~~p~ilv~NK~D~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~ 153 (167)
T cd04160 105 LEGVPLLILANKQDLPD----ALSVEEIKEVFQDKAEEIGRRDCLVLPVSALE 153 (167)
T ss_pred hcCCCEEEEEEcccccc----CCCHHHHHHHhccccccccCCceEEEEeeCCC
Confidence 35689999999986421 12233444443321 0134788889763
No 121
>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=62.00 E-value=26 Score=28.81 Aligned_cols=41 Identities=15% Similarity=0.065 Sum_probs=24.3
Q ss_pred CceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 21 KTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 21 KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
.|+++|+|+.|.. .......++.++++..+ +.+++.+||+-
T Consensus 110 ~piilVgNK~DL~--~~~~v~~~~~~~~~~~~--~~~~~~iSAkt 150 (215)
T cd04109 110 PLVVLVGNKTDLE--HNRTVKDDKHARFAQAN--GMESCLVSAKT 150 (215)
T ss_pred ceEEEEEECcccc--cccccCHHHHHHHHHHc--CCEEEEEECCC
Confidence 3688899997642 11122334555666555 46678888764
No 122
>PLN03110 Rab GTPase; Provisional
Probab=61.83 E-value=24 Score=29.16 Aligned_cols=42 Identities=10% Similarity=0.014 Sum_probs=23.7
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..|+++|+|+.|..-. .....+..+.++..+ +.+++.+||.-
T Consensus 117 ~~piiiv~nK~Dl~~~--~~~~~~~~~~l~~~~--~~~~~e~SA~~ 158 (216)
T PLN03110 117 NIVIMMAGNKSDLNHL--RSVAEEDGQALAEKE--GLSFLETSALE 158 (216)
T ss_pred CCeEEEEEEChhcccc--cCCCHHHHHHHHHHc--CCEEEEEeCCC
Confidence 4688888888653211 111223444555444 56788888753
No 123
>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=61.32 E-value=17 Score=26.65 Aligned_cols=41 Identities=12% Similarity=0.054 Sum_probs=25.3
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
.+|+++++|+.|..-. .....+.++++..+. +.+++.+||.
T Consensus 105 ~~p~ivv~nK~D~~~~--~~~~~~~~~~~~~~~--~~~~~~~sa~ 145 (159)
T cd00154 105 NIPIILVGNKIDLEDQ--RQVSTEEAQQFAKEN--GLLFFETSAK 145 (159)
T ss_pred CCcEEEEEEccccccc--ccccHHHHHHHHHHc--CCeEEEEecC
Confidence 4788888888765211 122345566666554 4678888865
No 124
>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=61.26 E-value=36 Score=27.41 Aligned_cols=67 Identities=7% Similarity=-0.039 Sum_probs=35.4
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHhCCcchHHHHHHHHH
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQKATSVLDKIITQGY 98 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~g~~sgl~~li~~~y 98 (197)
..+|+++|+|+.|..-. ......+...+..... .+.+++.+||+- +.|+..+.+.+.
T Consensus 103 ~~~piilv~NK~Dl~~~-~~~v~~~~~~~~~~~~-~~~~~~~~Sa~~---------------------g~gv~~l~~~l~ 159 (198)
T cd04147 103 KFVPIVVVGNKADSLEE-ERQVPAKDALSTVELD-WNCGFVETSAKD---------------------NENVLEVFKELL 159 (198)
T ss_pred CCCcEEEEEEccccccc-cccccHHHHHHHHHhh-cCCcEEEecCCC---------------------CCCHHHHHHHHH
Confidence 46899999999764210 0000111222222111 134677788753 457777777777
Q ss_pred hhcCCeEEee
Q psy17313 99 KSLQLQYFFT 108 (197)
Q Consensus 99 ~lL~LitffT 108 (197)
+.+..-.-+|
T Consensus 160 ~~~~~~~~~~ 169 (198)
T cd04147 160 RQANLPYNLS 169 (198)
T ss_pred HHhhcccccc
Confidence 7666544444
No 125
>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=61.06 E-value=22 Score=28.55 Aligned_cols=38 Identities=16% Similarity=0.041 Sum_probs=21.9
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..+|+++|+|+.|..- ..... .+.... +.+++++||.-
T Consensus 152 ~~~~viiV~NK~Dl~~----~~~~~---~~~~~~--~~~~~~~Sa~~ 189 (204)
T cd01878 152 EDIPMILVLNKIDLLD----DEELE---ERLEAG--RPDAVFISAKT 189 (204)
T ss_pred CCCCEEEEEEccccCC----hHHHH---HHhhcC--CCceEEEEcCC
Confidence 3589999999976421 11111 222222 45688899763
No 126
>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=60.93 E-value=14 Score=30.33 Aligned_cols=44 Identities=7% Similarity=-0.066 Sum_probs=25.5
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+++|+|+.|..-. .....+.++.++.+.. +.+++++||+-
T Consensus 115 ~~~piiivgNK~Dl~~~--~~~~~~~~~~~~~~~~-~~~~~e~Sak~ 158 (198)
T cd04142 115 KEPPIVVVGNKRDQQRH--RFAPRHVLSVLVRKSW-KCGYLECSAKY 158 (198)
T ss_pred CCCCEEEEEECcccccc--ccccHHHHHHHHHHhc-CCcEEEecCCC
Confidence 44799999999765321 1112233445544321 46788999874
No 127
>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=60.92 E-value=32 Score=26.57 Aligned_cols=42 Identities=10% Similarity=0.025 Sum_probs=22.4
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..|+++|+|+.|..-. ..-..+....+++.. +.+++++||+-
T Consensus 105 ~~~iilvgnK~Dl~~~--~~v~~~~~~~~~~~~--~~~~~e~Sa~~ 146 (161)
T cd04117 105 GVQKILIGNKADEEQK--RQVGDEQGNKLAKEY--GMDFFETSACT 146 (161)
T ss_pred CCeEEEEEECcccccc--cCCCHHHHHHHHHHc--CCEEEEEeCCC
Confidence 4688888888653211 111223344444443 45677778763
No 128
>PRK09554 feoB ferrous iron transport protein B; Reviewed
Probab=60.61 E-value=14 Score=37.49 Aligned_cols=45 Identities=13% Similarity=0.096 Sum_probs=27.9
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQL 69 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el 69 (197)
.+|+++++|+.|..-. ......++++.+.. +.+++|+||.-..-+
T Consensus 112 giPvIvVlNK~Dl~~~---~~i~id~~~L~~~L--G~pVvpiSA~~g~GI 156 (772)
T PRK09554 112 GIPCIVALNMLDIAEK---QNIRIDIDALSARL--GCPVIPLVSTRGRGI 156 (772)
T ss_pred CCCEEEEEEchhhhhc---cCcHHHHHHHHHHh--CCCEEEEEeecCCCH
Confidence 5899999999875321 11222334444433 678999998765433
No 129
>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=60.41 E-value=22 Score=27.76 Aligned_cols=44 Identities=23% Similarity=0.129 Sum_probs=26.9
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHHhh---cCCCCeEEEechhh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDA---NDPGATIIPFSGVF 65 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~---~~~~~~vv~~sa~~ 65 (197)
+..+|+++|+|+.|..- ....+.+.++... +..+.+++++||+-
T Consensus 113 ~~~~p~iiv~nK~Dl~~----~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~ 159 (173)
T cd04154 113 LAGATLLILANKQDLPG----ALSEEEIREALELDKISSHHWRIQPCSAVT 159 (173)
T ss_pred hcCCCEEEEEECccccc----CCCHHHHHHHhCccccCCCceEEEeccCCC
Confidence 46789999999976421 1133455555422 11245789999864
No 130
>PRK09563 rbgA GTPase YlqF; Reviewed
Probab=59.80 E-value=20 Score=31.39 Aligned_cols=122 Identities=15% Similarity=0.184 Sum_probs=61.9
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHH----------------
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLD---------------- 82 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~---------------- 82 (197)
..||+++|.|+.|. .. ....+...++.++. +.+++++||.-...+.+|-.. -.+++.
T Consensus 50 ~~kp~iiVlNK~DL--~~--~~~~~~~~~~~~~~--~~~vi~vSa~~~~gi~~L~~~-l~~~l~~~~~~~~~~~~~~~~~ 122 (287)
T PRK09563 50 GNKPRLLILNKSDL--AD--PEVTKKWIEYFEEQ--GIKALAINAKKGQGVKKILKA-AKKLLKEKNERRKAKGMRPRAI 122 (287)
T ss_pred CCCCEEEEEEchhc--CC--HHHHHHHHHHHHHc--CCeEEEEECCCcccHHHHHHH-HHHHHHHHHhhhhhcccCcCce
Confidence 47999999999763 21 11122222323332 457899998765433332110 000000
Q ss_pred ---HhC-CcchHHHHHHHHHhhcCCeEEeecC--CCceeeeEe---cCCCChhhhhhhhcccccc----------CeeEE
Q psy17313 83 ---EQK-ATSVLDKIITQGYKSLQLQYFFTAG--QDEVKAWTI---QKGTKAPQAAGRIHTDFEK----------GFIMA 143 (197)
Q Consensus 83 ---~~g-~~sgl~~li~~~y~lL~LitffT~g--~~EvRAWti---~~GstA~~aAg~IHsDfek----------gFI~A 143 (197)
-.| .+.|-..+|.+.... ...+++ |.-+|.|.. ..+....|..|.++..+.. |-|+.
T Consensus 123 ~~~~~G~pnvGKSsliN~l~~~----~~~~~~~~~g~T~~~~~~~~~~~~~l~DtPGi~~~~~~~~~~~~~l~~~~~i~~ 198 (287)
T PRK09563 123 RAMIIGIPNVGKSTLINRLAGK----KIAKTGNRPGVTKAQQWIKLGKGLELLDTPGILWPKLEDQEVGLKLALTGAIKD 198 (287)
T ss_pred EEEEECCCCCCHHHHHHHHhcC----CccccCCCCCeEEEEEEEEeCCcEEEEECCCcCCCCCCcHHHHHHHHHhCCcch
Confidence 124 456666777665543 122222 233443322 2345577888888776554 55666
Q ss_pred EEecchhh
Q psy17313 144 EVMHFDDF 151 (197)
Q Consensus 144 eVi~~~D~ 151 (197)
+++..+++
T Consensus 199 ~~~~~~~~ 206 (287)
T PRK09563 199 EALDLEEV 206 (287)
T ss_pred hhcChHHH
Confidence 66655443
No 131
>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=59.76 E-value=73 Score=29.00 Aligned_cols=107 Identities=17% Similarity=0.176 Sum_probs=56.5
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHH----HhhcCCCC---eEEEechhhchhhcCCCHHHHHHHHHH--------
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEW----VDANDPGA---TIIPFSGVFEHQLVDMPDDERQRYLDE-------- 83 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~----~~~~~~~~---~vv~~sa~~E~el~~l~~ee~~~fl~~-------- 83 (197)
..+|+++|+|+.|- .. .....+++.+| +++. +. .++++||.--.-+.+| .+.+..
T Consensus 89 ~~~piilV~NK~DL--l~-k~~~~~~~~~~l~~~~k~~--g~~~~~i~~vSAk~g~gv~eL-----~~~l~~~~~~~~v~ 158 (360)
T TIGR03597 89 GGNPVLLVGNKIDL--LP-KSVNLSKIKEWMKKRAKEL--GLKPVDIILVSAKKGNGIDEL-----LDKIKKARNKKDVY 158 (360)
T ss_pred CCCCEEEEEEchhh--CC-CCCCHHHHHHHHHHHHHHc--CCCcCcEEEecCCCCCCHHHH-----HHHHHHHhCCCeEE
Confidence 47999999999763 21 12223444444 4433 32 4788998754433322 222322
Q ss_pred -hC-CcchHHHHHHHHHhhcCCe-EEeecC--CCceeee---EecCCCChhhhhhhhccc
Q psy17313 84 -QK-ATSVLDKIITQGYKSLQLQ-YFFTAG--QDEVKAW---TIQKGTKAPQAAGRIHTD 135 (197)
Q Consensus 84 -~g-~~sgl~~li~~~y~lL~Li-tffT~g--~~EvRAW---ti~~GstA~~aAg~IHsD 135 (197)
.| .+.|-..||.+....-+.. ...|++ |.-++.+ .+..+....|..|.++++
T Consensus 159 ~vG~~nvGKStliN~l~~~~~~~~~~~~~s~~pgtT~~~~~~~~~~~~~l~DtPG~~~~~ 218 (360)
T TIGR03597 159 VVGVTNVGKSSLINKLLKQNNGDKDVITTSPFPGTTLDLIEIPLDDGHSLYDTPGIINSH 218 (360)
T ss_pred EECCCCCCHHHHHHHHHhhccCCcceeeecCCCCeEeeEEEEEeCCCCEEEECCCCCChh
Confidence 14 5667777777766643321 112333 2333322 233566677888877663
No 132
>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=59.41 E-value=18 Score=27.82 Aligned_cols=43 Identities=9% Similarity=-0.055 Sum_probs=25.5
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+++|+|+.|.. ....-..+...++++.. +.+++++||+-
T Consensus 105 ~~~piilv~nK~Dl~--~~~~v~~~~~~~~~~~~--~~~~~e~Sa~~ 147 (165)
T cd04146 105 REIPVILVGNKADLL--HYRQVSTEEGEKLASEL--GCLFFEVSAAE 147 (165)
T ss_pred CCCCEEEEEECCchH--HhCccCHHHHHHHHHHc--CCEEEEeCCCC
Confidence 368999999987632 11111223445555554 46788888753
No 133
>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=58.57 E-value=34 Score=28.38 Aligned_cols=44 Identities=7% Similarity=-0.053 Sum_probs=25.2
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+|+|+|+.|..- ...-......+++++.. +..++.+||+-
T Consensus 104 ~~~piilVgNK~DL~~--~~~v~~~~~~~~a~~~~-~~~~~etSAkt 147 (202)
T cd04120 104 EDAELLLVGNKLDCET--DREISRQQGEKFAQQIT-GMRFCEASAKD 147 (202)
T ss_pred CCCcEEEEEECccccc--ccccCHHHHHHHHHhcC-CCEEEEecCCC
Confidence 4578999999876321 11112334455665431 45678888764
No 134
>PTZ00327 eukaryotic translation initiation factor 2 gamma subunit; Provisional
Probab=58.31 E-value=21 Score=33.96 Aligned_cols=53 Identities=21% Similarity=0.256 Sum_probs=30.2
Q ss_pred ccccccCceEEEEeCCCccccccccccHHHHHHHHhhc-CCCCeEEEechhhch
Q psy17313 15 LNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAN-DPGATIIPFSGVFEH 67 (197)
Q Consensus 15 ~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~-~~~~~vv~~sa~~E~ 67 (197)
+.++-.+|+|+|.|+.|..-.....+..++++++.... ..+.++||+||.-..
T Consensus 166 ~~~lgi~~iIVvlNKiDlv~~~~~~~~~~ei~~~l~~~~~~~~~iipVSA~~G~ 219 (460)
T PTZ00327 166 VEIMKLKHIIILQNKIDLVKEAQAQDQYEEIRNFVKGTIADNAPIIPISAQLKY 219 (460)
T ss_pred HHHcCCCcEEEEEecccccCHHHHHHHHHHHHHHHHhhccCCCeEEEeeCCCCC
Confidence 34555689999999976321000122344555544321 125789999987543
No 135
>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=58.26 E-value=52 Score=25.60 Aligned_cols=43 Identities=7% Similarity=-0.072 Sum_probs=23.2
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcC---C-CCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAND---P-GATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~---~-~~~vv~~sa~~ 65 (197)
..+|+++|+|+.|..- ....+.+++++...+ . ...++++||+-
T Consensus 99 ~~~piilv~NK~Dl~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~ 145 (169)
T cd04158 99 RDALLLIFANKQDVAG----ALSVEEMTELLSLHKLCCGRSWYIQGCDARS 145 (169)
T ss_pred CCCCEEEEEeCcCccc----CCCHHHHHHHhCCccccCCCcEEEEeCcCCC
Confidence 3479999999976421 112344555443211 0 12466778764
No 136
>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=58.12 E-value=34 Score=26.43 Aligned_cols=14 Identities=14% Similarity=-0.012 Sum_probs=11.5
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
..+|+++|+|+.|.
T Consensus 118 ~~~~iiiv~NK~Dl 131 (179)
T cd01890 118 NNLEIIPVINKIDL 131 (179)
T ss_pred cCCCEEEEEECCCC
Confidence 35799999999874
No 137
>KOG1145|consensus
Probab=58.09 E-value=26 Score=34.91 Aligned_cols=41 Identities=20% Similarity=0.186 Sum_probs=27.0
Q ss_pred cCceEEEEeCCCccccccccccHHHHHH-------HHhhcCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKE-------WVDANDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~-------~~~~~~~~~~vv~~sa~~ 65 (197)
.-|+|+++|+.|.+ +...+++.. .++..+.+.++||+||.-
T Consensus 253 ~VpiVvAinKiDkp-----~a~pekv~~eL~~~gi~~E~~GGdVQvipiSAl~ 300 (683)
T KOG1145|consen 253 NVPIVVAINKIDKP-----GANPEKVKRELLSQGIVVEDLGGDVQVIPISALT 300 (683)
T ss_pred CCCEEEEEeccCCC-----CCCHHHHHHHHHHcCccHHHcCCceeEEEeeccc
Confidence 37999999998754 333444442 223344457899999864
No 138
>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=57.98 E-value=20 Score=28.01 Aligned_cols=12 Identities=25% Similarity=0.373 Sum_probs=10.6
Q ss_pred CceEEEEeCCCc
Q psy17313 21 KTQIYLVNLSAK 32 (197)
Q Consensus 21 KP~iyv~Nv~e~ 32 (197)
+|+|+|+|+.|-
T Consensus 40 ~p~ilVlNKiDl 51 (157)
T cd01858 40 KHLIFVLNKCDL 51 (157)
T ss_pred CCEEEEEEchhc
Confidence 899999999764
No 139
>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=57.94 E-value=24 Score=28.29 Aligned_cols=52 Identities=6% Similarity=0.008 Sum_probs=29.6
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhc-----CCCCeEEEechhhchhhcCC
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAN-----DPGATIIPFSGVFEHQLVDM 72 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~-----~~~~~vv~~sa~~E~el~~l 72 (197)
.+|+++|+|+.|..-.. ....++++.++.... ..+.+++++||+-..-+.++
T Consensus 117 ~~p~iiv~NK~Dl~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iv~~Sa~~g~~~~~~ 173 (194)
T cd01891 117 GLKPIVVINKIDRPDAR-PEEVVDEVFDLFIELGATEEQLDFPVLYASAKNGWASLNL 173 (194)
T ss_pred CCCEEEEEECCCCCCCC-HHHHHHHHHHHHHHhCCccccCccCEEEeehhcccccccc
Confidence 57999999998752111 112244455544211 01467899998865545444
No 140
>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=57.66 E-value=31 Score=27.06 Aligned_cols=46 Identities=9% Similarity=-0.054 Sum_probs=26.5
Q ss_pred ccCceEEEEeCCCcccccccc--ccHHHHHHHHhhcCCCC-eEEEechhhc
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKN--KWLPKIKEWVDANDPGA-TIIPFSGVFE 66 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~--~~~~~l~~~~~~~~~~~-~vv~~sa~~E 66 (197)
...|+|+|+|+.|..-..... -.....++++... +. +++.+||+-.
T Consensus 104 ~~~piilv~nK~Dl~~~~~~~~~v~~~~~~~~~~~~--~~~~~~e~Sa~~~ 152 (187)
T cd04132 104 PGTPIMLVGLKTDLRKDKNLDRKVTPAQAESVAKKQ--GAFAYLECSAKTM 152 (187)
T ss_pred CCCCEEEEEeChhhhhCccccCCcCHHHHHHHHHHc--CCcEEEEccCCCC
Confidence 457999999997642110000 1234555666655 34 7888887643
No 141
>cd04104 p47_IIGP_like p47 (47-kDa) family. The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens. p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type II interferon (IFN-gamma). ITGP is critical for resistance to Toxoplasma gondii infection and in involved in inhibition of Coxsackievirus-B3-induced apoptosis. TGTP was shown to limit vesicular stomatitis virus (VSV) infection of fibroblasts in vitro. IRG-47 is involved in resistance to T. gondii infection. LRG-47 has been implicated in resistance to T. gondii, Listeria monocytogenes, Leishmania, and mycobacterial infections. IIGP1 has been shown to localize to the ER and to the Golgi membranes in IFN-induced cells and inflamed tissues. In macrophages, IIGP1 interacts with hook3, a microtubule binding protei
Probab=57.33 E-value=24 Score=28.76 Aligned_cols=58 Identities=9% Similarity=0.111 Sum_probs=32.5
Q ss_pred HHHHHhhcccccccCceEEEEeCCCcccccc---------ccccHHHHHHHHhh----cC-CCCeEEEechhh
Q psy17313 7 LRIEHLNKLNLLTAKTQIYLVNLSAKDYIKK---------KNKWLPKIKEWVDA----ND-PGATIIPFSGVF 65 (197)
Q Consensus 7 ~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~~---------~~~~~~~l~~~~~~----~~-~~~~vv~~sa~~ 65 (197)
.|..+++.+.- ..+|+++|.|+.|....+. .+..++.+++.+.+ .+ +..+|.++|+..
T Consensus 95 ~d~~~~~~l~~-~~~~~ilV~nK~D~~~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~~~~~~~p~v~~vS~~~ 166 (197)
T cd04104 95 NDVKLAKAIQC-MGKKFYFVRTKVDRDLSNEQRSKPRSFNREQVLQEIRDNCLENLQEAGVSEPPVFLVSNFD 166 (197)
T ss_pred HHHHHHHHHHH-hCCCEEEEEecccchhhhhhccccccccHHHHHHHHHHHHHHHHHHcCCCCCCEEEEeCCC
Confidence 34444443322 2589999999988643211 12456666654432 21 123688899864
No 142
>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=57.31 E-value=12 Score=28.24 Aligned_cols=47 Identities=19% Similarity=0.123 Sum_probs=26.0
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcC---CCCeEEEechhhch
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAND---PGATIIPFSGVFEH 67 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~---~~~~vv~~sa~~E~ 67 (197)
..+|+++++|+.|.. ...+...+.+.+.+.+.- +..+++++||.-+.
T Consensus 112 ~~~~~iiv~nK~Dl~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~~~~ 161 (174)
T cd01895 112 EGKALVIVVNKWDLV--EKDSKTMKEFKKEIRRKLPFLDYAPIVFISALTGQ 161 (174)
T ss_pred cCCCEEEEEeccccC--CccHHHHHHHHHHHHhhcccccCCceEEEeccCCC
Confidence 458999999997532 111123333333333211 13578999987543
No 143
>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=56.96 E-value=16 Score=35.70 Aligned_cols=46 Identities=13% Similarity=0.089 Sum_probs=27.5
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQL 69 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el 69 (197)
..+|+++|+|+.|..-. .......+++.+.. +.+++++||.-..-+
T Consensus 98 ~~~PiIIVlNK~Dl~~~---~~i~~d~~~L~~~l--g~pvv~tSA~tg~Gi 143 (591)
T TIGR00437 98 LGIPMILALNLVDEAEK---KGIRIDEEKLEERL--GVPVVPTSATEGRGI 143 (591)
T ss_pred cCCCEEEEEehhHHHHh---CCChhhHHHHHHHc--CCCEEEEECCCCCCH
Confidence 35899999999764211 11112233444443 578999998754433
No 144
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=56.23 E-value=7.1 Score=29.15 Aligned_cols=20 Identities=30% Similarity=0.463 Sum_probs=16.3
Q ss_pred ccCCceeecCCCEEEEEEcc
Q psy17313 168 QQGRAYTVEDGDIIFFKFNA 187 (197)
Q Consensus 168 ~eGkdYivqDGDIi~f~fn~ 187 (197)
..|.+|.|+|||.|.|---+
T Consensus 72 l~g~~t~L~dgD~v~i~P~v 91 (94)
T cd01764 72 LGEEDYILEDGDHVVFISTL 91 (94)
T ss_pred cCCcccCCCCcCEEEEECCC
Confidence 35899999999999986543
No 145
>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=56.09 E-value=39 Score=26.61 Aligned_cols=42 Identities=5% Similarity=-0.163 Sum_probs=21.3
Q ss_pred CceEEEEeCCCccccccccc-cHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 21 KTQIYLVNLSAKDYIKKKNK-WLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 21 KP~iyv~Nv~e~d~~~~~~~-~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
.|+++|+|+.|..-.. ... ..+....++.+. +.+++.+||+-
T Consensus 107 ~~iilVgnK~Dl~~~~-~~~~~~~~~~~~~~~~--~~~~~e~Sa~~ 149 (170)
T cd04108 107 VLLFLVGTKKDLSSPA-QYALMEQDAIKLAAEM--QAEYWSVSALS 149 (170)
T ss_pred CeEEEEEEChhcCccc-cccccHHHHHHHHHHc--CCeEEEEECCC
Confidence 4578888887632110 001 122334555444 45677777753
No 146
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=55.99 E-value=34 Score=25.40 Aligned_cols=16 Identities=19% Similarity=0.146 Sum_probs=8.7
Q ss_pred cCCceeecCCCEEEEE
Q psy17313 169 QGRAYTVEDGDIIFFK 184 (197)
Q Consensus 169 eGkdYivqDGDIi~f~ 184 (197)
..-|++++|||-|+|-
T Consensus 56 ~~~d~~L~~GDRVEIY 71 (84)
T PF03658_consen 56 VKLDTVLRDGDRVEIY 71 (84)
T ss_dssp --TT-B--TT-EEEEE
T ss_pred cCCCCcCCCCCEEEEe
Confidence 4589999999999874
No 147
>PTZ00369 Ras-like protein; Provisional
Probab=55.95 E-value=63 Score=25.72 Aligned_cols=45 Identities=13% Similarity=0.030 Sum_probs=25.4
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhch
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEH 67 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~ 67 (197)
...|+++|+|+.|.. ....-......++.+.. +.+++.+||+-..
T Consensus 109 ~~~piiiv~nK~Dl~--~~~~i~~~~~~~~~~~~--~~~~~e~Sak~~~ 153 (189)
T PTZ00369 109 DRVPMILVGNKCDLD--SERQVSTGEGQELAKSF--GIPFLETSAKQRV 153 (189)
T ss_pred CCCCEEEEEECcccc--cccccCHHHHHHHHHHh--CCEEEEeeCCCCC
Confidence 356999999987632 10011222344555444 4678888986533
No 148
>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=55.78 E-value=11 Score=29.51 Aligned_cols=43 Identities=7% Similarity=-0.100 Sum_probs=27.2
Q ss_pred ccCceEEEEeCCCccccccccccHHH------HHHHHhhcCCCCeEEEechhhch
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPK------IKEWVDANDPGATIIPFSGVFEH 67 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~------l~~~~~~~~~~~~vv~~sa~~E~ 67 (197)
..+|+++|+|+.|..- ...... +..+++++ +..++++||.-|.
T Consensus 98 ~~~piilv~NK~Dl~~----~~~~~~i~~~~~~~~~~~~~--~~~~~~~Sa~~~~ 146 (164)
T cd04162 98 PDLPLVVLANKQDLPA----ARSVQEIHKELELEPIARGR--RWILQGTSLDDDG 146 (164)
T ss_pred CCCcEEEEEeCcCCcC----CCCHHHHHHHhCChhhcCCC--ceEEEEeeecCCC
Confidence 6799999999987421 112222 23444433 5678888998776
No 149
>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=55.64 E-value=25 Score=32.38 Aligned_cols=56 Identities=27% Similarity=0.316 Sum_probs=30.9
Q ss_pred HhhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhc-CCCCeEEEechhhc
Q psy17313 11 HLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAN-DPGATIIPFSGVFE 66 (197)
Q Consensus 11 ~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~-~~~~~vv~~sa~~E 66 (197)
.+..+.++-.+|+++++|+.|..-.......+++++++.... ..+.+++|+||.-.
T Consensus 125 ~l~~l~~~gi~~iIVvvNK~Dl~~~~~~~~~~~~i~~~l~~~~~~~~~ii~vSA~~g 181 (406)
T TIGR03680 125 HLMALEIIGIKNIVIVQNKIDLVSKEKALENYEEIKEFVKGTVAENAPIIPVSALHN 181 (406)
T ss_pred HHHHHHHcCCCeEEEEEEccccCCHHHHHHHHHHHHhhhhhcccCCCeEEEEECCCC
Confidence 344444555689999999976421000011234555555432 11467999998753
No 150
>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=55.08 E-value=29 Score=26.38 Aligned_cols=45 Identities=4% Similarity=-0.169 Sum_probs=24.9
Q ss_pred ccCceEEEEeCCCcccccccc---------ccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKN---------KWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~---------~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
..+|+++|+|+.|..-..... -..+...++....+ ..+++.+||+
T Consensus 103 ~~~p~ivv~nK~Dl~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~-~~~~~~~Sa~ 156 (171)
T cd00157 103 PNVPIILVGTKIDLRDDENTLKKLEKGKEPITPEEGEKLAKEIG-AIGYMECSAL 156 (171)
T ss_pred CCCCEEEEEccHHhhhchhhhhhcccCCCccCHHHHHHHHHHhC-CeEEEEeecC
Confidence 369999999997642211000 01233445555442 2378888875
No 151
>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=54.35 E-value=28 Score=25.60 Aligned_cols=15 Identities=20% Similarity=0.078 Sum_probs=12.2
Q ss_pred cccCceEEEEeCCCc
Q psy17313 18 LTAKTQIYLVNLSAK 32 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~ 32 (197)
+..+|+++|+|+.|.
T Consensus 99 ~~~~p~iiv~nK~D~ 113 (159)
T cd04159 99 LEGIPLLVLGNKNDL 113 (159)
T ss_pred hcCCCEEEEEeCccc
Confidence 357899999999764
No 152
>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=54.22 E-value=15 Score=28.99 Aligned_cols=43 Identities=14% Similarity=-0.020 Sum_probs=23.4
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhh---cCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDA---NDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~---~~~~~~vv~~sa~~ 65 (197)
..+|+++++|+.|..- ....+++.+.... .+.+.+++++||.-
T Consensus 115 ~~~p~viv~NK~Dl~~----~~~~~~i~~~l~~~~~~~~~~~~~~~SA~~ 160 (174)
T cd04153 115 RKAVLLVLANKQDLKG----AMTPAEISESLGLTSIRDHTWHIQGCCALT 160 (174)
T ss_pred cCCCEEEEEECCCCCC----CCCHHHHHHHhCcccccCCceEEEecccCC
Confidence 4589999999987421 1112333322210 11134688888764
No 153
>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=54.17 E-value=63 Score=26.61 Aligned_cols=41 Identities=10% Similarity=0.003 Sum_probs=21.5
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
..|+++|+|+.|..- ......+....+++.. +.+++.+||+
T Consensus 109 ~~~iilvgNK~Dl~~--~~~v~~~~~~~~~~~~--~~~~~e~Sak 149 (211)
T cd04111 109 RPVFILVGHKCDLES--QRQVTREEAEKLAKDL--GMKYIETSAR 149 (211)
T ss_pred CCeEEEEEEcccccc--ccccCHHHHHHHHHHh--CCEEEEEeCC
Confidence 345677788765321 1112233445555544 4567777765
No 154
>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=53.38 E-value=15 Score=28.07 Aligned_cols=43 Identities=14% Similarity=0.032 Sum_probs=23.7
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhh---cCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDA---NDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~---~~~~~~vv~~sa~~ 65 (197)
..+|+++|+|+.|.. + .+ ...++.+.... ...+.+++++||.-
T Consensus 99 ~~~piiiv~nK~Dl~--~-~~-~~~~i~~~~~~~~~~~~~~~~~~~Sa~~ 144 (158)
T cd04151 99 KGAVLLVFANKQDMP--G-AL-SEAEISEKLGLSELKDRTWSIFKTSAIK 144 (158)
T ss_pred cCCcEEEEEeCCCCC--C-CC-CHHHHHHHhCccccCCCcEEEEEeeccC
Confidence 568999999997642 1 11 22334322211 11134689999853
No 155
>TIGR00073 hypB hydrogenase accessory protein HypB. HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.
Probab=53.22 E-value=15 Score=30.24 Aligned_cols=44 Identities=18% Similarity=0.114 Sum_probs=27.7
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
-.+|.++++|+.|. .+.......++.+.+.+..+..+++++||.
T Consensus 147 ~~~a~iiv~NK~Dl--~~~~~~~~~~~~~~l~~~~~~~~i~~~Sa~ 190 (207)
T TIGR00073 147 FKEADLIVINKADL--AEAVGFDVEKMKADAKKINPEAEIILMSLK 190 (207)
T ss_pred HhhCCEEEEEHHHc--cccchhhHHHHHHHHHHhCCCCCEEEEECC
Confidence 46899999999764 211122344555555444345789999986
No 156
>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=53.22 E-value=14 Score=27.38 Aligned_cols=45 Identities=20% Similarity=0.121 Sum_probs=24.2
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhch
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEH 67 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~ 67 (197)
..|.++|+|+.|... ....+..+........+..+++++|+.-..
T Consensus 111 ~~~~iiv~nK~Dl~~---~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~ 155 (168)
T cd04163 111 KTPVILVLNKIDLVK---DKEDLLPLLEKLKELGPFAEIFPISALKGE 155 (168)
T ss_pred CCCEEEEEEchhccc---cHHHHHHHHHHHHhccCCCceEEEEeccCC
Confidence 379999999976421 112223333333332223568888876443
No 157
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=52.78 E-value=3.5 Score=28.86 Aligned_cols=31 Identities=32% Similarity=0.446 Sum_probs=24.1
Q ss_pred EecchhhhhcC-CHHHHHHcCcccccCCceeecCC
Q psy17313 145 VMHFDDFKEHG-SEAACRAAGKYRQQGRAYTVEDG 178 (197)
Q Consensus 145 Vi~~~D~~~~g-~~~~ak~~Gk~r~eGkdYivqDG 178 (197)
.++++||+++| +...|+. +-++.|.+.|+.|
T Consensus 3 tv~k~dLi~lGf~~~tA~~---IIrqAK~~lV~~G 34 (59)
T PF11372_consen 3 TVTKKDLIELGFSESTARD---IIRQAKALLVQKG 34 (59)
T ss_pred ccCHHHHHHcCCCHHHHHH---HHHHHHHHHHHcC
Confidence 57899999998 6777775 4447888888876
No 158
>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=52.45 E-value=41 Score=24.24 Aligned_cols=41 Identities=20% Similarity=0.112 Sum_probs=24.4
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..|+++++|+.|... ....+.........+ ..+++++||.-
T Consensus 108 ~~p~ivv~nK~D~~~----~~~~~~~~~~~~~~~-~~~~~~~sa~~ 148 (161)
T TIGR00231 108 NVPIILVGNKIDLRD----AKLKTHVAFLFAKLN-GEPIIPLSAET 148 (161)
T ss_pred CCcEEEEEEcccCCc----chhhHHHHHHHhhcc-CCceEEeecCC
Confidence 789999999976421 112333433333322 45689999764
No 159
>PF14478 DUF4430: Domain of unknown function (DUF4430); PDB: 3U7Z_B 2BB5_A.
Probab=52.05 E-value=8.1 Score=26.76 Aligned_cols=14 Identities=36% Similarity=0.672 Sum_probs=9.1
Q ss_pred CceeecCCCEEEEE
Q psy17313 171 RAYTVEDGDIIFFK 184 (197)
Q Consensus 171 kdYivqDGDIi~f~ 184 (197)
.+|.|+|||.|.|+
T Consensus 55 ~~~~l~~GD~i~~~ 68 (68)
T PF14478_consen 55 GSYKLKDGDKITWY 68 (68)
T ss_dssp CC-B--TTEEEEE-
T ss_pred ceeEeCCCCEEEeC
Confidence 68999999999985
No 160
>cd01667 TGS_ThrRS_N TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and SpoT proteins where it occurs. The TGS domain is thought to interact with the tRNA acceptor arm along with an adjacent N-terminal domain. The specific function of TGS is not well understood.
Probab=51.80 E-value=31 Score=21.49 Aligned_cols=49 Identities=20% Similarity=0.175 Sum_probs=35.8
Q ss_pred eEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEE
Q psy17313 117 WTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFK 184 (197)
Q Consensus 117 Wti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~ 184 (197)
..++.|+|..++|..++.+..+.++.|.|= |++ ..-++.+.+|+.|.|.
T Consensus 11 ~~~~~~~t~~~~~~~~~~~~~~~~v~~~vn-----------------g~~--~dL~~~l~~~~~ie~i 59 (61)
T cd01667 11 KEFPKGTTPLDIAKSISPGLAKKAVAAKVN-----------------GEL--VDLSRPLEEDCELEII 59 (61)
T ss_pred EEeCCCCCHHHHHHHHHHHHHhheEEEEEC-----------------CEE--ecCCcCcCCCCEEEEE
Confidence 347789999999999999888888777632 333 3467778777766654
No 161
>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=51.67 E-value=25 Score=29.04 Aligned_cols=49 Identities=8% Similarity=-0.044 Sum_probs=27.1
Q ss_pred Cc-eEEEEeCCCccccccccc-cHHHHHHHHhhcC---CCCeEEEechhhchhh
Q psy17313 21 KT-QIYLVNLSAKDYIKKKNK-WLPKIKEWVDAND---PGATIIPFSGVFEHQL 69 (197)
Q Consensus 21 KP-~iyv~Nv~e~d~~~~~~~-~~~~l~~~~~~~~---~~~~vv~~sa~~E~el 69 (197)
+| +|+++|+.|.-......+ ..+++++.+...+ .+.++||+||.-....
T Consensus 118 ~~~iIvviNK~D~~~~~~~~~~~~~~i~~~l~~~g~~~~~v~iipiSa~~g~n~ 171 (195)
T cd01884 118 VPYIVVFLNKADMVDDEELLELVEMEVRELLSKYGFDGDNTPIVRGSALKALEG 171 (195)
T ss_pred CCcEEEEEeCCCCCCcHHHHHHHHHHHHHHHHHhcccccCCeEEEeeCccccCC
Confidence 56 778899976421000011 2234555554321 2478999999875543
No 162
>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=51.33 E-value=42 Score=25.41 Aligned_cols=40 Identities=15% Similarity=0.071 Sum_probs=18.8
Q ss_pred CceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 21 KTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 21 KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
.|+++++|+.|..-. ..-..+..+++++++ +.+++.+||+
T Consensus 105 ~~iivvg~K~D~~~~--~~v~~~~~~~~~~~~--~~~~~e~Sa~ 144 (162)
T PF00071_consen 105 IPIIVVGNKSDLSDE--REVSVEEAQEFAKEL--GVPYFEVSAK 144 (162)
T ss_dssp SEEEEEEETTTGGGG--SSSCHHHHHHHHHHT--TSEEEEEBTT
T ss_pred ccceeeecccccccc--ccchhhHHHHHHHHh--CCEEEEEECC
Confidence 466666666543210 111233445555554 3555555654
No 163
>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=51.15 E-value=24 Score=26.60 Aligned_cols=14 Identities=7% Similarity=0.088 Sum_probs=11.7
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
..+|+++|+|+.|.
T Consensus 103 ~~~p~iiv~NK~Dl 116 (162)
T cd04157 103 RRVPILFFANKMDL 116 (162)
T ss_pred CCCCEEEEEeCccc
Confidence 36899999999764
No 164
>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=50.85 E-value=42 Score=24.17 Aligned_cols=16 Identities=13% Similarity=0.023 Sum_probs=12.4
Q ss_pred ccccCceEEEEeCCCc
Q psy17313 17 LLTAKTQIYLVNLSAK 32 (197)
Q Consensus 17 lLT~KP~iyv~Nv~e~ 32 (197)
....+|+++|+|+.|.
T Consensus 101 ~~~~~~~ivv~nK~D~ 116 (163)
T cd00880 101 RERGKPVLLVLNKIDL 116 (163)
T ss_pred HhcCCeEEEEEEcccc
Confidence 3467999999999764
No 165
>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=50.44 E-value=45 Score=25.17 Aligned_cols=43 Identities=16% Similarity=0.078 Sum_probs=25.6
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHHhhc---CCCCeEEEechh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAN---DPGATIIPFSGV 64 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~---~~~~~vv~~sa~ 64 (197)
++..|+++++|+.|..- ....+++.+..... ....+++++||+
T Consensus 98 ~~~~piiiv~nK~D~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~Sa~ 143 (158)
T cd00878 98 LKGVPLLIFANKQDLPG----ALSVSELIEKLGLEKILGRRWHIQPCSAV 143 (158)
T ss_pred cCCCcEEEEeeccCCcc----ccCHHHHHHhhChhhccCCcEEEEEeeCC
Confidence 56899999999986432 12334454443221 113468888876
No 166
>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=50.26 E-value=17 Score=28.33 Aligned_cols=48 Identities=13% Similarity=0.084 Sum_probs=27.1
Q ss_pred ccCceEEEEeCCCccccccccccHHH-HHHHHhhcCCCCeEEEechhhchhhcCC
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPK-IKEWVDANDPGATIIPFSGVFEHQLVDM 72 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~-l~~~~~~~~~~~~vv~~sa~~E~el~~l 72 (197)
..||+|+|+|+.|. .. ...+.. +..+.... +..++++||.-..-+.+|
T Consensus 28 ~~~p~IiVlNK~Dl--~~--~~~~~~~~~~~~~~~--~~~ii~vSa~~~~gi~~L 76 (155)
T cd01849 28 KGKKLILVLNKADL--VP--KEVLRKWLAYLRHSY--PTIPFKISATNGQGIEKK 76 (155)
T ss_pred CCCCEEEEEechhc--CC--HHHHHHHHHHHHhhC--CceEEEEeccCCcChhhH
Confidence 46999999999764 21 111211 11221121 456899999876555444
No 167
>KOG0394|consensus
Probab=49.82 E-value=23 Score=30.51 Aligned_cols=44 Identities=16% Similarity=0.071 Sum_probs=31.2
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
.=|.|++.|+.+.+-......-.++.+.|++.++ +.|..-.||+
T Consensus 118 ~FPFVilGNKiD~~~~~~r~VS~~~Aq~WC~s~g-nipyfEtSAK 161 (210)
T KOG0394|consen 118 TFPFVILGNKIDVDGGKSRQVSEKKAQTWCKSKG-NIPYFETSAK 161 (210)
T ss_pred cccEEEEcccccCCCCccceeeHHHHHHHHHhcC-CceeEEeccc
Confidence 3489999999765431101235567889998875 7888889987
No 168
>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=49.79 E-value=28 Score=28.60 Aligned_cols=53 Identities=13% Similarity=0.085 Sum_probs=28.5
Q ss_pred cCceEEEEeCCCcccccc--ccccHHHHHHHHhhcC-CCCeEEEechhhchhhcCC
Q psy17313 20 AKTQIYLVNLSAKDYIKK--KNKWLPKIKEWVDAND-PGATIIPFSGVFEHQLVDM 72 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~--~~~~~~~l~~~~~~~~-~~~~vv~~sa~~E~el~~l 72 (197)
.+|+|+|+|+.|..-... -+....+++++....+ +..+++++||.-..-+.+.
T Consensus 130 ~~~iIvviNK~D~~~~~~~~~~~i~~~~~~~~~~~~~~~~~ii~iSA~~g~ni~~~ 185 (208)
T cd04166 130 IRHVVVAVNKMDLVDYSEEVFEEIVADYLAFAAKLGIEDITFIPISALDGDNVVSR 185 (208)
T ss_pred CCcEEEEEEchhcccCCHHHHHHHHHHHHHHHHHcCCCCceEEEEeCCCCCCCccC
Confidence 356788999976421000 0112334444444432 1246899999866555443
No 169
>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=49.64 E-value=61 Score=25.60 Aligned_cols=42 Identities=14% Similarity=-0.024 Sum_probs=23.8
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..|+|+++|+.|..- ...-.....+.++... +.+++.+||+-
T Consensus 105 ~~~~ivv~nK~Dl~~--~~~v~~~~~~~~~~~~--~~~~~evSa~~ 146 (188)
T cd04125 105 NVIKVIVANKSDLVN--NKVVDSNIAKSFCDSL--NIPFFETSAKQ 146 (188)
T ss_pred CCeEEEEEECCCCcc--cccCCHHHHHHHHHHc--CCeEEEEeCCC
Confidence 478899999876321 1111223334555444 45788888763
No 170
>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=49.56 E-value=24 Score=27.88 Aligned_cols=13 Identities=8% Similarity=0.020 Sum_probs=10.3
Q ss_pred cCceEEEEeCCCc
Q psy17313 20 AKTQIYLVNLSAK 32 (197)
Q Consensus 20 ~KP~iyv~Nv~e~ 32 (197)
..|+++|+|+.|.
T Consensus 114 ~~piilv~NK~Dl 126 (175)
T smart00177 114 DAVILVFANKQDL 126 (175)
T ss_pred CCcEEEEEeCcCc
Confidence 4799999999763
No 171
>PF13984 MsyB: MsyB protein
Probab=49.55 E-value=3.9 Score=32.04 Aligned_cols=11 Identities=45% Similarity=1.051 Sum_probs=9.6
Q ss_pred CceeecCCCEE
Q psy17313 171 RAYTVEDGDII 181 (197)
Q Consensus 171 kdYivqDGDIi 181 (197)
..|+||||||+
T Consensus 36 QKYvmqDGdim 46 (122)
T PF13984_consen 36 QKYVMQDGDIM 46 (122)
T ss_pred HHHhhhccchH
Confidence 56999999996
No 172
>PLN00223 ADP-ribosylation factor; Provisional
Probab=49.29 E-value=54 Score=26.20 Aligned_cols=14 Identities=7% Similarity=0.022 Sum_probs=10.5
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
...|+++|+|+.|.
T Consensus 117 ~~~piilv~NK~Dl 130 (181)
T PLN00223 117 RDAVLLVFANKQDL 130 (181)
T ss_pred CCCCEEEEEECCCC
Confidence 35788888888763
No 173
>PRK11171 hypothetical protein; Provisional
Probab=48.82 E-value=18 Score=31.72 Aligned_cols=58 Identities=22% Similarity=0.324 Sum_probs=39.4
Q ss_pred ceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEEEccCCC
Q psy17313 113 EVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFNAGAG 190 (197)
Q Consensus 113 EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~fn~~~~ 190 (197)
+.+-|+++.|+..+-.. -|..-+--|| .+-.|.++..|+.|.|+.||.|.|.-+++-.
T Consensus 185 ~~~~~~l~PG~~~~~~~--~~~~ee~i~V------------------l~G~~~~~~~~~~~~l~~GD~i~~~~~~~h~ 242 (266)
T PRK11171 185 HVNIVTFEPGASIPFVE--THVMEHGLYV------------------LEGKGVYRLNNDWVEVEAGDFIWMRAYCPQA 242 (266)
T ss_pred EEEEEEECCCCEEccCc--CCCceEEEEE------------------EeCEEEEEECCEEEEeCCCCEEEECCCCCEE
Confidence 55678899998766543 1333322222 1244678889999999999999998776643
No 174
>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=48.31 E-value=34 Score=25.95 Aligned_cols=41 Identities=15% Similarity=0.129 Sum_probs=21.0
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
..|+++++|+.|..- ......+.+..++.+. +.+++.+||.
T Consensus 105 ~~~iivv~nK~D~~~--~~~~~~~~~~~~~~~~--~~~~~~~Sa~ 145 (161)
T cd04113 105 NIVVILVGNKSDLAD--QREVTFLEASRFAQEN--GLLFLETSAL 145 (161)
T ss_pred CCeEEEEEEchhcch--hccCCHHHHHHHHHHc--CCEEEEEECC
Confidence 457777777754311 1122334444555444 3566666754
No 175
>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=47.74 E-value=56 Score=24.86 Aligned_cols=13 Identities=15% Similarity=-0.066 Sum_probs=9.1
Q ss_pred cCceEEEEeCCCc
Q psy17313 20 AKTQIYLVNLSAK 32 (197)
Q Consensus 20 ~KP~iyv~Nv~e~ 32 (197)
..|+++|+|+.|.
T Consensus 112 ~~~~i~v~NK~D~ 124 (169)
T cd04114 112 KVITILVGNKIDL 124 (169)
T ss_pred CCeEEEEEECccc
Confidence 4677888887653
No 176
>PF06858 NOG1: Nucleolar GTP-binding protein 1 (NOG1); InterPro: IPR010674 This domain represents a conserved region of approximately 60 residues in length within nucleolar GTP-binding protein 1 (NOG1). The NOG1 family includes eukaryotic, bacterial and archaeal proteins. In Saccharomyces cerevisiae, the NOG1 gene has been shown to be essential for cell viability, suggesting that NOG1 may play an important role in nucleolar functions. In particular, NOG1 is believed to be functionally linked to ribosome biogenesis, which occurs in the nucleolus. In eukaryotes, NOG1 mutants were found to disrupt the biogenesis of the 60S ribosomal subunit []. The DRG and OBG proteins as well as the prokaryotic NOG-like proteins are homologous throughout their length to the amino half of eukaryotic NOG1, which contains the GTP binding motifs (IPR006073 from INTERPRO); the N-terminal GTP-binding motif is required for function.; GO: 0005525 GTP binding; PDB: 2E87_A.
Probab=47.61 E-value=17 Score=25.38 Aligned_cols=25 Identities=16% Similarity=0.283 Sum_probs=12.8
Q ss_pred HHHHHhhccc-ccccCceEEEEeCCC
Q psy17313 7 LRIEHLNKLN-LLTAKTQIYLVNLSA 31 (197)
Q Consensus 7 ~E~~~i~~~~-lLT~KP~iyv~Nv~e 31 (197)
++..+.++.. +...||++.|+|+.|
T Consensus 33 ~Q~~L~~~ik~~F~~~P~i~V~nK~D 58 (58)
T PF06858_consen 33 EQLSLFKEIKPLFPNKPVIVVLNKID 58 (58)
T ss_dssp HHHHHHHHHHHHTTTS-EEEEE--TT
T ss_pred HHHHHHHHHHHHcCCCCEEEEEeccC
Confidence 3344444443 335789999988854
No 177
>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=47.40 E-value=72 Score=27.17 Aligned_cols=29 Identities=24% Similarity=0.158 Sum_probs=17.7
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHH
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWV 49 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~ 49 (197)
.+|+++++|+.|..-.+ ....++.+++..
T Consensus 116 ~~P~iivvNK~D~~~a~-~~~~~~~i~~~~ 144 (237)
T cd04168 116 NIPTIIFVNKIDRAGAD-LEKVYQEIKEKL 144 (237)
T ss_pred CCCEEEEEECccccCCC-HHHHHHHHHHHH
Confidence 58999999998753211 123455555544
No 178
>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=47.37 E-value=84 Score=24.65 Aligned_cols=28 Identities=7% Similarity=-0.084 Sum_probs=17.0
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVD 50 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~ 50 (197)
..+|+++++|+.|.. . ....++++++..
T Consensus 119 ~~~pvivv~NK~Dl~--~--~~~~~~~~~~~~ 146 (190)
T cd00879 119 ANVPFLILGNKIDLP--G--AVSEEELRQALG 146 (190)
T ss_pred cCCCEEEEEeCCCCC--C--CcCHHHHHHHhC
Confidence 458999999997642 1 113355655553
No 179
>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=47.11 E-value=70 Score=23.58 Aligned_cols=36 Identities=22% Similarity=0.115 Sum_probs=21.7
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
...+|+++|+|+.|..- .... .... .+.+++++||.
T Consensus 105 ~~~~~vi~v~nK~D~~~---~~~~------~~~~--~~~~~~~~Sa~ 140 (157)
T cd04164 105 PADKPIIVVLNKSDLLP---DSEL------LSLL--AGKPIIAISAK 140 (157)
T ss_pred hcCCCEEEEEEchhcCC---cccc------cccc--CCCceEEEECC
Confidence 56799999999976421 1111 1111 14678999975
No 180
>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=46.66 E-value=30 Score=31.49 Aligned_cols=50 Identities=18% Similarity=0.053 Sum_probs=28.0
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhc---CCCCeEEEechhhchhhcC
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAN---DPGATIIPFSGVFEHQLVD 71 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~---~~~~~vv~~sa~~E~el~~ 71 (197)
..+|+|+|+|+.|.. . .....+.+.+..... -+..+++++||.--.-+.+
T Consensus 282 ~~~~iiiv~NK~Dl~--~-~~~~~~~~~~~~~~~~~~~~~~~vi~~SA~~g~~v~~ 334 (429)
T TIGR03594 282 AGKALVIVVNKWDLV--K-DEKTREEFKKELRRKLPFLDFAPIVFISALTGQGVDK 334 (429)
T ss_pred cCCcEEEEEECcccC--C-CHHHHHHHHHHHHHhcccCCCCceEEEeCCCCCCHHH
Confidence 469999999997642 1 112223333222211 0146899999976554443
No 181
>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=46.53 E-value=44 Score=24.74 Aligned_cols=13 Identities=31% Similarity=0.304 Sum_probs=10.8
Q ss_pred cCceEEEEeCCCc
Q psy17313 20 AKTQIYLVNLSAK 32 (197)
Q Consensus 20 ~KP~iyv~Nv~e~ 32 (197)
.+|+++|+|+.|.
T Consensus 105 ~~piiiv~nK~D~ 117 (157)
T cd01894 105 KKPVILVVNKVDN 117 (157)
T ss_pred CCCEEEEEECccc
Confidence 4899999999764
No 182
>COG0370 FeoB Fe2+ transport system protein B [Inorganic ion transport and metabolism]
Probab=46.21 E-value=32 Score=34.51 Aligned_cols=42 Identities=12% Similarity=0.146 Sum_probs=27.4
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
.-+||+.+.|+.|..-..+-.-..+++.+.. |.||||+||.-
T Consensus 107 ~g~p~ilaLNm~D~A~~~Gi~ID~~~L~~~L-----GvPVv~tvA~~ 148 (653)
T COG0370 107 LGIPMILALNMIDEAKKRGIRIDIEKLSKLL-----GVPVVPTVAKR 148 (653)
T ss_pred cCCCeEEEeccHhhHHhcCCcccHHHHHHHh-----CCCEEEEEeec
Confidence 3589999999865432111122556666655 78999999874
No 183
>PRK00093 GTP-binding protein Der; Reviewed
Probab=45.94 E-value=31 Score=31.54 Aligned_cols=53 Identities=11% Similarity=0.066 Sum_probs=28.6
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCC
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDM 72 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l 72 (197)
..+|+|+|+|+.|..-........+.+....... +..+++++||.-..-+.+|
T Consensus 283 ~~~~~ivv~NK~Dl~~~~~~~~~~~~~~~~l~~~-~~~~i~~~SA~~~~gv~~l 335 (435)
T PRK00093 283 AGRALVIVVNKWDLVDEKTMEEFKKELRRRLPFL-DYAPIVFISALTGQGVDKL 335 (435)
T ss_pred cCCcEEEEEECccCCCHHHHHHHHHHHHHhcccc-cCCCEEEEeCCCCCCHHHH
Confidence 4599999999976421000011222232222111 2468999999766555444
No 184
>PRK03003 GTP-binding protein Der; Reviewed
Probab=45.71 E-value=57 Score=30.63 Aligned_cols=80 Identities=10% Similarity=0.010 Sum_probs=40.0
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHhC---CcchHHHHHH
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQK---ATSVLDKIIT 95 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~g---~~sgl~~li~ 95 (197)
..+|+|+|+|+.|..-........+.+.+..... ...+++++||+-..-+.+|-. .-...++.+. .-+-|++++.
T Consensus 321 ~~~piIiV~NK~Dl~~~~~~~~~~~~i~~~l~~~-~~~~~~~~SAk~g~gv~~lf~-~i~~~~~~~~~~i~t~~ln~~~~ 398 (472)
T PRK03003 321 AGRALVLAFNKWDLVDEDRRYYLEREIDRELAQV-PWAPRVNISAKTGRAVDKLVP-ALETALESWDTRIPTGRLNAWLG 398 (472)
T ss_pred cCCCEEEEEECcccCChhHHHHHHHHHHHhcccC-CCCCEEEEECCCCCCHHHHHH-HHHHHHHHhcccCCHHHHHHHHH
Confidence 5699999999976421000011122333222221 136789999986654544321 1112233333 2355777776
Q ss_pred HHHhh
Q psy17313 96 QGYKS 100 (197)
Q Consensus 96 ~~y~l 100 (197)
.+...
T Consensus 399 ~~~~~ 403 (472)
T PRK03003 399 ELVAA 403 (472)
T ss_pred HHHHc
Confidence 55543
No 185
>PRK00098 GTPase RsgA; Reviewed
Probab=45.55 E-value=9 Score=33.87 Aligned_cols=74 Identities=11% Similarity=0.055 Sum_probs=39.1
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHH-----HhC-CcchHHH
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLD-----EQK-ATSVLDK 92 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~-----~~g-~~sgl~~ 92 (197)
..+|.++|+|+.|. .. .........++..+. +.+++++||.-..-+.+| .+++. -.| .+.|-..
T Consensus 110 ~~ip~iIVlNK~DL--~~-~~~~~~~~~~~~~~~--g~~v~~vSA~~g~gi~~L-----~~~l~gk~~~~~G~sgvGKSt 179 (298)
T PRK00098 110 NGIKPIIVLNKIDL--LD-DLEEARELLALYRAI--GYDVLELSAKEGEGLDEL-----KPLLAGKVTVLAGQSGVGKST 179 (298)
T ss_pred CCCCEEEEEEhHHc--CC-CHHHHHHHHHHHHHC--CCeEEEEeCCCCccHHHH-----HhhccCceEEEECCCCCCHHH
Confidence 35899999999764 21 112223333444333 578999998754333222 11121 124 4556666
Q ss_pred HHHHHHhhcC
Q psy17313 93 IITQGYKSLQ 102 (197)
Q Consensus 93 li~~~y~lL~ 102 (197)
||++....+.
T Consensus 180 lin~l~~~~~ 189 (298)
T PRK00098 180 LLNALAPDLE 189 (298)
T ss_pred HHHHHhCCcC
Confidence 7766654443
No 186
>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=45.22 E-value=29 Score=25.72 Aligned_cols=45 Identities=20% Similarity=0.138 Sum_probs=21.6
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
..|+++|+|+.|.--..........+..+++......+++++||.
T Consensus 110 ~~~vi~v~nK~D~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Sa~ 154 (170)
T cd01876 110 GIPFLVVLTKADKLKKSELAKALKEIKKELKLFEIDPPIILFSSL 154 (170)
T ss_pred CCCEEEEEEchhcCChHHHHHHHHHHHHHHHhccCCCceEEEecC
Confidence 368888888865411110111223333333211123567788864
No 187
>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=44.86 E-value=70 Score=25.68 Aligned_cols=45 Identities=2% Similarity=-0.159 Sum_probs=24.5
Q ss_pred ccCceEEEEeCCCcccccc----------ccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIKK----------KNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~----------~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
..-|+++|+|+.|-.-... ..-..++.++++++.+ ..+++.+||+
T Consensus 106 ~~~piilvgNK~DL~~~~~~~~~~~~~~~~~v~~~~~~~~a~~~~-~~~~~e~SAk 160 (191)
T cd01875 106 PNVPILLVGTKKDLRNDADTLKKLKEQGQAPITPQQGGALAKQIH-AVKYLECSAL 160 (191)
T ss_pred CCCCEEEEEeChhhhcChhhHHHHhhccCCCCCHHHHHHHHHHcC-CcEEEEeCCC
Confidence 5689999999976421100 0011233445665541 1367788875
No 188
>COG2262 HflX GTPases [General function prediction only]
Probab=43.89 E-value=51 Score=31.27 Aligned_cols=70 Identities=16% Similarity=0.133 Sum_probs=40.8
Q ss_pred HHhhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHhCCcch
Q psy17313 10 EHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQKATSV 89 (197)
Q Consensus 10 ~~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~g~~sg 89 (197)
.+|..+.... +|+|+|.|+.|. .. ....+..+.. ..| ..|++||.- +.|
T Consensus 295 ~vL~el~~~~-~p~i~v~NKiD~--~~-~~~~~~~~~~----~~~--~~v~iSA~~---------------------~~g 343 (411)
T COG2262 295 DVLAEIGADE-IPIILVLNKIDL--LE-DEEILAELER----GSP--NPVFISAKT---------------------GEG 343 (411)
T ss_pred HHHHHcCCCC-CCEEEEEecccc--cC-chhhhhhhhh----cCC--CeEEEEecc---------------------CcC
Confidence 3455555444 999999999652 11 1111222222 211 478999863 347
Q ss_pred HHHHHHHHHhhcC-CeEEeecC
Q psy17313 90 LDKIITQGYKSLQ-LQYFFTAG 110 (197)
Q Consensus 90 l~~li~~~y~lL~-LitffT~g 110 (197)
++.|.+.+.+.|. ....+|..
T Consensus 344 l~~L~~~i~~~l~~~~~~~~l~ 365 (411)
T COG2262 344 LDLLRERIIELLSGLRTEVTLE 365 (411)
T ss_pred HHHHHHHHHHHhhhcccceEEE
Confidence 7777777777776 55555543
No 189
>COG0024 Map Methionine aminopeptidase [Translation, ribosomal structure and biogenesis]
Probab=43.77 E-value=18 Score=32.08 Aligned_cols=58 Identities=19% Similarity=0.362 Sum_probs=36.7
Q ss_pred EecCCCChhhhhhhhccccc-----------cCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEEEc
Q psy17313 118 TIQKGTKAPQAAGRIHTDFE-----------KGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFN 186 (197)
Q Consensus 118 ti~~GstA~~aAg~IHsDfe-----------kgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~fn 186 (197)
.++.|.|..+.+..+|.=+. +||=.+--+|-++-+-. | +- +.+++++|||||.+-+.
T Consensus 31 ~v~pGvtt~Eld~~~~~~i~~~ga~pa~~gy~g~~~~~ciSvNe~v~H---------g-iP--~d~~vlk~GDiv~IDvg 98 (255)
T COG0024 31 LVKPGVTTLELDEIAEEFIREKGAYPAFLGYKGFPFPTCISVNEVVAH---------G-IP--GDKKVLKEGDIVKIDVG 98 (255)
T ss_pred HcCCCCCHHHHHHHHHHHHHHcCceehhccCcCCCcceEeehhheeee---------c-CC--CCCcccCCCCEEEEEEE
Confidence 34588899888887765443 44444444444443222 2 22 17899999999998765
Q ss_pred c
Q psy17313 187 A 187 (197)
Q Consensus 187 ~ 187 (197)
+
T Consensus 99 ~ 99 (255)
T COG0024 99 A 99 (255)
T ss_pred E
Confidence 3
No 190
>PTZ00133 ADP-ribosylation factor; Provisional
Probab=43.65 E-value=43 Score=26.75 Aligned_cols=14 Identities=7% Similarity=0.022 Sum_probs=10.9
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
..+|+|+|+|+.|.
T Consensus 117 ~~~piilv~NK~Dl 130 (182)
T PTZ00133 117 RDAVLLVFANKQDL 130 (182)
T ss_pred cCCCEEEEEeCCCC
Confidence 45789999998764
No 191
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=43.56 E-value=19 Score=25.40 Aligned_cols=22 Identities=41% Similarity=0.632 Sum_probs=12.4
Q ss_pred hhcCCHHHHHHcCcccccCCceeecCCCEEEE
Q psy17313 152 KEHGSEAACRAAGKYRQQGRAYTVEDGDIIFF 183 (197)
Q Consensus 152 ~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f 183 (197)
..+|=+++.+++| ++|||+|.|
T Consensus 41 ~~~Gv~~~L~~~G----------~~~GD~V~I 62 (69)
T PF09269_consen 41 KKMGVEKALRKAG----------AKEGDTVRI 62 (69)
T ss_dssp HHTTHHHHHHTTT------------TT-EEEE
T ss_pred HHCCHHHHHHHcC----------CCCCCEEEE
Confidence 3445566666666 778998876
No 192
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=43.35 E-value=22 Score=23.72 Aligned_cols=24 Identities=17% Similarity=0.192 Sum_probs=18.0
Q ss_pred HHHcCcccccCC-----ceeecCCCEEEE
Q psy17313 160 CRAAGKYRQQGR-----AYTVEDGDIIFF 183 (197)
Q Consensus 160 ak~~Gk~r~eGk-----dYivqDGDIi~f 183 (197)
.-..|.+.+.|+ .|.|+.||+|.|
T Consensus 30 li~~G~V~VNg~~~~~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 30 FLQENEVLVNGELENRRGKKLYPGDVIEI 58 (59)
T ss_pred HHHcCCEEECCEEccCCCCCCCCCCEEEe
Confidence 335577777663 889999999875
No 193
>PF02311 AraC_binding: AraC-like ligand binding domain; InterPro: IPR003313 This entry defines the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The crystal structure of the arabinose-binding and dimerization domain of the Escherichia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1XJA_B 2ARA_A 2AAC_B 2ARC_A.
Probab=43.31 E-value=14 Score=26.75 Aligned_cols=26 Identities=19% Similarity=0.501 Sum_probs=18.1
Q ss_pred HcCcccccCCceeecCCCEEEEEEcc
Q psy17313 162 AAGKYRQQGRAYTVEDGDIIFFKFNA 187 (197)
Q Consensus 162 ~~Gk~r~eGkdYivqDGDIi~f~fn~ 187 (197)
-.|.+...|+.|.++.||++.|.-+.
T Consensus 32 G~~~~~~~~~~~~l~~g~~~li~p~~ 57 (136)
T PF02311_consen 32 GEGTLHIDGQEYPLKPGDLFLIPPGQ 57 (136)
T ss_dssp E-EEEEETTEEEEE-TT-EEEE-TTS
T ss_pred CEEEEEECCEEEEEECCEEEEecCCc
Confidence 45678899999999999999875443
No 194
>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=43.23 E-value=71 Score=25.59 Aligned_cols=42 Identities=12% Similarity=0.021 Sum_probs=23.0
Q ss_pred ceEEEEeCCCcc--cccc-ccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 22 TQIYLVNLSAKD--YIKK-KNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 22 P~iyv~Nv~e~d--~~~~-~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
+.++|+|+.|.. .... .....+...++++.. +.+++++||+-
T Consensus 106 ~pilVgnK~Dl~~~~~~~~~~~~~~~~~~~a~~~--~~~~~e~SAk~ 150 (182)
T cd04128 106 IPILVGTKYDLFADLPPEEQEEITKQARKYAKAM--KAPLIFCSTSH 150 (182)
T ss_pred CEEEEEEchhccccccchhhhhhHHHHHHHHHHc--CCEEEEEeCCC
Confidence 336789997631 0000 111234455666655 46788889863
No 195
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=43.04 E-value=14 Score=28.15 Aligned_cols=29 Identities=21% Similarity=0.390 Sum_probs=24.2
Q ss_pred HcCcccccCCceeecCCCEEEEEEccCCC
Q psy17313 162 AAGKYRQQGRAYTVEDGDIIFFKFNAGAG 190 (197)
Q Consensus 162 ~~Gk~r~eGkdYivqDGDIi~f~fn~~~~ 190 (197)
-+|++.++|..++++.||+|.+-.|+.=.
T Consensus 73 G~~~~~~~g~~~~l~~Gd~i~ip~g~~H~ 101 (131)
T COG1917 73 GEGTVQLEGEKKELKAGDVIIIPPGVVHG 101 (131)
T ss_pred cEEEEEecCCceEecCCCEEEECCCCeee
Confidence 45678889999999999999998876543
No 196
>PRK11467 secY/secA suppressor protein; Provisional
Probab=42.79 E-value=5.5 Score=31.27 Aligned_cols=11 Identities=45% Similarity=1.057 Sum_probs=9.5
Q ss_pred CceeecCCCEE
Q psy17313 171 RAYTVEDGDII 181 (197)
Q Consensus 171 kdYivqDGDIi 181 (197)
..|+||||||+
T Consensus 38 QKYvmqDGDim 48 (124)
T PRK11467 38 QKYVLQDGDIM 48 (124)
T ss_pred HHHHhhccchH
Confidence 56999999986
No 197
>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=41.65 E-value=69 Score=24.74 Aligned_cols=14 Identities=7% Similarity=0.022 Sum_probs=11.5
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
..+|+++++|+.|.
T Consensus 100 ~~~piilv~NK~Dl 113 (159)
T cd04150 100 RDAVLLVFANKQDL 113 (159)
T ss_pred cCCCEEEEEECCCC
Confidence 45899999999764
No 198
>PRK13768 GTPase; Provisional
Probab=41.34 E-value=60 Score=27.93 Aligned_cols=14 Identities=21% Similarity=0.116 Sum_probs=12.0
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
..+|+++|+|+.|.
T Consensus 161 ~~~~~i~v~nK~D~ 174 (253)
T PRK13768 161 LGLPQIPVLNKADL 174 (253)
T ss_pred cCCCEEEEEEhHhh
Confidence 57999999999764
No 199
>PRK12289 GTPase RsgA; Reviewed
Probab=40.62 E-value=22 Score=32.56 Aligned_cols=81 Identities=10% Similarity=0.009 Sum_probs=40.4
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHhC-CcchHHHHHHHH
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQK-ATSVLDKIITQG 97 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~g-~~sgl~~li~~~ 97 (197)
+.+|+|+|+|+.|- .. ....+...++.... +.+++++||.-..-+.+|-+.-.....--.| .+.|-..||++.
T Consensus 119 ~~ip~ILVlNK~DL--v~--~~~~~~~~~~~~~~--g~~v~~iSA~tg~GI~eL~~~L~~ki~v~iG~SgVGKSSLIN~L 192 (352)
T PRK12289 119 TGLEIVLCLNKADL--VS--PTEQQQWQDRLQQW--GYQPLFISVETGIGLEALLEQLRNKITVVAGPSGVGKSSLINRL 192 (352)
T ss_pred CCCCEEEEEEchhc--CC--hHHHHHHHHHHHhc--CCeEEEEEcCCCCCHHHHhhhhccceEEEEeCCCCCHHHHHHHH
Confidence 57999999999763 21 11122222222233 6789999987654443321100000001124 344555567666
Q ss_pred HhhcCCeE
Q psy17313 98 YKSLQLQY 105 (197)
Q Consensus 98 y~lL~Lit 105 (197)
...+.+.+
T Consensus 193 ~~~~~~~t 200 (352)
T PRK12289 193 IPDVELRV 200 (352)
T ss_pred cCcccccc
Confidence 65555443
No 200
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=40.02 E-value=31 Score=24.33 Aligned_cols=22 Identities=45% Similarity=0.655 Sum_probs=15.4
Q ss_pred hhcCCHHHHHHcCcccccCCceeecCCCEEEE
Q psy17313 152 KEHGSEAACRAAGKYRQQGRAYTVEDGDIIFF 183 (197)
Q Consensus 152 ~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f 183 (197)
...|=+++.+++| +++||.|.|
T Consensus 41 ~~~Gv~~~L~~~G----------~~~GD~V~I 62 (69)
T TIGR03595 41 KKLGVEDALRKAG----------AKDGDTVRI 62 (69)
T ss_pred HHCCHHHHHHHcC----------CCCCCEEEE
Confidence 3345566777777 678998876
No 201
>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=39.79 E-value=49 Score=25.74 Aligned_cols=45 Identities=13% Similarity=0.022 Sum_probs=25.8
Q ss_pred ccCceEEEEeCCCcccccc--------cc-c-cHHHHHHHHhhcCCCC-eEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKK--------KN-K-WLPKIKEWVDANDPGA-TIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~--------~~-~-~~~~l~~~~~~~~~~~-~vv~~sa~~ 65 (197)
...|+++|+|+.|..-..+ .. + -.++...++++. +. +++++||+-
T Consensus 103 ~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~a~~~--~~~~~~e~Sa~~ 158 (173)
T cd04130 103 PKAPIILVGTQADLRTDVNVLIQLARYGEKPVSQSRAKALAEKI--GACEYIECSALT 158 (173)
T ss_pred CCCCEEEEeeChhhccChhHHHHHhhcCCCCcCHHHHHHHHHHh--CCCeEEEEeCCC
Confidence 4689999999976321000 00 0 223455666554 33 788888763
No 202
>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=39.34 E-value=37 Score=25.70 Aligned_cols=14 Identities=21% Similarity=0.060 Sum_probs=11.5
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
..+|+++|+|+.|.
T Consensus 101 ~~~p~ivv~NK~Dl 114 (168)
T cd01887 101 ANVPFIVALNKIDK 114 (168)
T ss_pred cCCCEEEEEEceec
Confidence 45899999999763
No 203
>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=38.85 E-value=17 Score=32.00 Aligned_cols=77 Identities=8% Similarity=-0.053 Sum_probs=37.6
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHhC-CcchHHHHHHHH
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQK-ATSVLDKIITQG 97 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~g-~~sgl~~li~~~ 97 (197)
..+|.++|+|+.|- .. .........+.... +.+++++||.-..-+.+|...=+....--+| .+.|-..+|+..
T Consensus 108 ~~ip~iIVlNK~DL--~~--~~~~~~~~~~~~~~--g~~v~~vSA~~g~gi~~L~~~L~~k~~~~~G~sg~GKSTlin~l 181 (287)
T cd01854 108 AGIEPVIVLTKADL--LD--DEEEELELVEALAL--GYPVLAVSAKTGEGLDELREYLKGKTSVLVGQSGVGKSTLINAL 181 (287)
T ss_pred cCCCEEEEEEHHHC--CC--hHHHHHHHHHHHhC--CCeEEEEECCCCccHHHHHhhhccceEEEECCCCCCHHHHHHHH
Confidence 46899999999763 21 11111112222222 6789999987654333221100001111224 455666666655
Q ss_pred Hhhc
Q psy17313 98 YKSL 101 (197)
Q Consensus 98 y~lL 101 (197)
...+
T Consensus 182 ~~~~ 185 (287)
T cd01854 182 LPDL 185 (287)
T ss_pred hchh
Confidence 5443
No 204
>COG1977 MoaD Molybdopterin converting factor, small subunit [Coenzyme metabolism]
Probab=38.83 E-value=20 Score=25.97 Aligned_cols=18 Identities=28% Similarity=0.313 Sum_probs=15.6
Q ss_pred cccCCceeecCCCEEEEE
Q psy17313 167 RQQGRAYTVEDGDIIFFK 184 (197)
Q Consensus 167 r~eGkdYivqDGDIi~f~ 184 (197)
...|.|+.++|||.|-|-
T Consensus 61 ~~~~~~t~L~dGDeVa~~ 78 (84)
T COG1977 61 FLVGLDTPLKDGDEVAFF 78 (84)
T ss_pred eeccccccCCCCCEEEEe
Confidence 457899999999999875
No 205
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=38.76 E-value=22 Score=23.69 Aligned_cols=15 Identities=47% Similarity=0.820 Sum_probs=11.9
Q ss_pred cCCceeecCCCEEEE
Q psy17313 169 QGRAYTVEDGDIIFF 183 (197)
Q Consensus 169 eGkdYivqDGDIi~f 183 (197)
.+..|.+++||+|.|
T Consensus 53 ~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 53 PGEPVPLKDGDIIRF 67 (68)
T ss_dssp STSEEEE-TTEEEEE
T ss_pred CCCEEECCCCCEEEc
Confidence 357899999999986
No 206
>COG0012 Predicted GTPase, probable translation factor [Translation, ribosomal structure and biogenesis]
Probab=38.60 E-value=14 Score=34.59 Aligned_cols=57 Identities=21% Similarity=0.012 Sum_probs=47.5
Q ss_pred HHHHhCCcchHHHHHHHHHhhcCCeEEeecCCCceee-----------eEecCCCChhhhhhhhccccccCeeEEE
Q psy17313 80 YLDEQKATSVLDKIITQGYKSLQLQYFFTAGQDEVKA-----------WTIQKGTKAPQAAGRIHTDFEKGFIMAE 144 (197)
Q Consensus 80 fl~~~g~~sgl~~li~~~y~lL~LitffT~g~~EvRA-----------Wti~~GstA~~aAg~IHsDfekgFI~Ae 144 (197)
++..|+ ..||+..++++- +++..||+. ++.+| -....|+++.+.+..||++ ||++|.
T Consensus 279 i~~~y~-~lgl~~~ft~g~---~evrawti~-~g~kap~aaG~Ih~Dfe~~fi~aevi~~~d~i~~~---~~~~Ak 346 (372)
T COG0012 279 IRAGYG-LLGLQTYFTAGV---KEVRAWTIK-DGSKAPDAAGVIHPDFEKGFIRAEVISYADLIHYG---GEAAAK 346 (372)
T ss_pred HHHHhc-ccchhHHHhhcC---CeEEEEEec-cCCcccccCCccccchhhccccceEeeHHHHHhcC---cHHHHH
Confidence 777787 789999998777 899999987 66653 3567889999999999999 888876
No 207
>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=38.59 E-value=59 Score=26.23 Aligned_cols=42 Identities=10% Similarity=0.077 Sum_probs=23.0
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
...|+++|+|+.|.. .......+...+++... +.+++++||.
T Consensus 109 ~~~piivVgNK~Dl~--~~~~~~~~~~~~~~~~~--~~~~~e~Sa~ 150 (199)
T cd04110 109 DDVCKVLVGNKNDDP--ERKVVETEDAYKFAGQM--GISLFETSAK 150 (199)
T ss_pred CCCCEEEEEECcccc--cccccCHHHHHHHHHHc--CCEEEEEECC
Confidence 346888888886532 11111234444555444 4567777865
No 208
>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=38.41 E-value=79 Score=25.22 Aligned_cols=14 Identities=0% Similarity=-0.116 Sum_probs=11.5
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
...|+++|+|+.|.
T Consensus 103 ~~~piilvgNK~Dl 116 (189)
T cd04134 103 PGVKLVLVALKCDL 116 (189)
T ss_pred CCCCEEEEEEChhh
Confidence 46799999999764
No 209
>PF13128 DUF3954: Protein of unknown function (DUF3954)
Probab=38.06 E-value=26 Score=23.78 Aligned_cols=20 Identities=25% Similarity=0.611 Sum_probs=14.7
Q ss_pred cCCceeecCCCEEEEEEccCCC
Q psy17313 169 QGRAYTVEDGDIIFFKFNAGAG 190 (197)
Q Consensus 169 eGkdYivqDGDIi~f~fn~~~~ 190 (197)
+-.=|+|+||+|-.| +.|++
T Consensus 9 ~ngiYiV~~G~v~~i--~pP~s 28 (50)
T PF13128_consen 9 ENGIYIVKDGEVTFI--EPPES 28 (50)
T ss_pred CCeEEEEECCeEEEc--CCCCC
Confidence 345699999999877 55553
No 210
>PF09547 Spore_IV_A: Stage IV sporulation protein A (spore_IV_A); InterPro: IPR014201 This entry is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=37.67 E-value=91 Score=30.24 Aligned_cols=48 Identities=15% Similarity=0.277 Sum_probs=27.5
Q ss_pred HHHHhhcccccccCceEEEEeCCCccccccccccHHHHHH-HHhhcCCCCeEEEech
Q psy17313 8 RIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKE-WVDANDPGATIIPFSG 63 (197)
Q Consensus 8 E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~-~~~~~~~~~~vv~~sa 63 (197)
|.+.++.|.=+ .||.|++.|-.. ++ .+-..+|.+ .-+++ +.+|+|++.
T Consensus 169 EervI~ELk~i-gKPFvillNs~~-P~----s~et~~L~~eL~ekY--~vpVlpvnc 217 (492)
T PF09547_consen 169 EERVIEELKEI-GKPFVILLNSTK-PY----SEETQELAEELEEKY--DVPVLPVNC 217 (492)
T ss_pred HHHHHHHHHHh-CCCEEEEEeCCC-CC----CHHHHHHHHHHHHHh--CCcEEEeeh
Confidence 33444444322 399999999753 22 223344443 33445 688999983
No 211
>PRK11507 ribosome-associated protein; Provisional
Probab=37.47 E-value=25 Score=25.35 Aligned_cols=36 Identities=22% Similarity=0.522 Sum_probs=22.0
Q ss_pred chhhhhcCCHHH-HHHcCcccccC-----CceeecCCCEEEE
Q psy17313 148 FDDFKEHGSEAA-CRAAGKYRQQG-----RAYTVEDGDIIFF 183 (197)
Q Consensus 148 ~~D~~~~g~~~~-ak~~Gk~r~eG-----kdYivqDGDIi~f 183 (197)
|.+++.-|++++ .=..|.+++.| |.-.+.+||+|.|
T Consensus 20 ~~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~V~~ 61 (70)
T PRK11507 20 LEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSF 61 (70)
T ss_pred hhCcccChHHHHHHHHcCceEECCEEecccCCCCCCCCEEEE
Confidence 445555555543 22346666665 4556889999987
No 212
>TIGR02836 spore_IV_A stage IV sporulation protein A. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis.
Probab=37.29 E-value=1e+02 Score=29.96 Aligned_cols=49 Identities=14% Similarity=0.194 Sum_probs=27.1
Q ss_pred HHHHHhhcccccccCceEEEEeCCCccccccccccHHHHH-HHHhhcCCCCeEEEech
Q psy17313 7 LRIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIK-EWVDANDPGATIIPFSG 63 (197)
Q Consensus 7 ~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~-~~~~~~~~~~~vv~~sa 63 (197)
.|.+.++.|.= ..||.|+|.|..+- +. .+ ...+. ++-+++ +.+++++|.
T Consensus 168 aEe~~i~eLk~-~~kPfiivlN~~dp-~~---~e-t~~l~~~l~eky--~vpvl~v~c 217 (492)
T TIGR02836 168 AEERVIEELKE-LNKPFIILLNSTHP-YH---PE-TEALRQELEEKY--DVPVLAMDV 217 (492)
T ss_pred HHHHHHHHHHh-cCCCEEEEEECcCC-CC---ch-hHHHHHHHHHHh--CCceEEEEH
Confidence 45555554432 34999999999752 11 11 22222 332334 567888873
No 213
>KOG1490|consensus
Probab=37.14 E-value=37 Score=33.50 Aligned_cols=63 Identities=16% Similarity=0.278 Sum_probs=34.4
Q ss_pred cCCh--HHHHHhhcc-cccccCceEEEEeCCCcccccc---ccccHHHHHHHHhhcCCCCeEEEechhhchhh
Q psy17313 3 CEHH--LRIEHLNKL-NLLTAKTQIYLVNLSAKDYIKK---KNKWLPKIKEWVDANDPGATIIPFSGVFEHQL 69 (197)
Q Consensus 3 ~~~~--~E~~~i~~~-~lLT~KP~iyv~Nv~e~d~~~~---~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el 69 (197)
|-+. ++.++.++. .|...||+|+|+|+.|. ... ..+.-+-+....+.- +.+|+-.|..-|.-.
T Consensus 261 CGySva~QvkLfhsIKpLFaNK~~IlvlNK~D~--m~~edL~~~~~~ll~~~~~~~--~v~v~~tS~~~eegV 329 (620)
T KOG1490|consen 261 CGYSVAAQVKLYHSIKPLFANKVTILVLNKIDA--MRPEDLDQKNQELLQTIIDDG--NVKVVQTSCVQEEGV 329 (620)
T ss_pred hCCCHHHHHHHHHHhHHHhcCCceEEEeecccc--cCccccCHHHHHHHHHHHhcc--CceEEEecccchhce
Confidence 4444 445555554 46799999999999753 211 122222222322221 467777776554433
No 214
>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=37.10 E-value=1.1e+02 Score=24.05 Aligned_cols=45 Identities=9% Similarity=-0.069 Sum_probs=24.2
Q ss_pred ccCceEEEEeCCCccccccc----------cccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKK----------NKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~----------~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
...|+++|+|+.|..-.... .-..++..+++++.+ ..+++.+||+
T Consensus 104 ~~~piilvgnK~Dl~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~-~~~~~e~Sa~ 158 (174)
T cd01871 104 PNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIG-AVKYLECSAL 158 (174)
T ss_pred CCCCEEEEeeChhhccChhhHHHHhhccCCCCCHHHHHHHHHHcC-CcEEEEeccc
Confidence 35799999999764210000 011233445565542 2367778875
No 215
>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=36.89 E-value=52 Score=25.38 Aligned_cols=13 Identities=23% Similarity=0.005 Sum_probs=11.1
Q ss_pred cCceEEEEeCCCc
Q psy17313 20 AKTQIYLVNLSAK 32 (197)
Q Consensus 20 ~KP~iyv~Nv~e~ 32 (197)
..|+++|+|+.|.
T Consensus 103 ~~pviiv~nK~Dl 115 (166)
T cd01893 103 KVPIILVGNKSDL 115 (166)
T ss_pred CCCEEEEEEchhc
Confidence 6899999999764
No 216
>COG2229 Predicted GTPase [General function prediction only]
Probab=36.83 E-value=78 Score=26.97 Aligned_cols=40 Identities=13% Similarity=-0.021 Sum_probs=25.7
Q ss_pred CceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 21 KTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 21 KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
-|++++||+.|..- -.-.++++++.+....+.++|+.+|.
T Consensus 122 ip~vVa~NK~DL~~----a~ppe~i~e~l~~~~~~~~vi~~~a~ 161 (187)
T COG2229 122 IPVVVAINKQDLFD----ALPPEKIREALKLELLSVPVIEIDAT 161 (187)
T ss_pred CCEEEEeeccccCC----CCCHHHHHHHHHhccCCCceeeeecc
Confidence 69999999976421 22345677666543124678888875
No 217
>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=36.75 E-value=34 Score=29.87 Aligned_cols=44 Identities=18% Similarity=0.130 Sum_probs=26.4
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
..+|+|+++|+.|..-.+ ....++.+++...... -..++|+|+.
T Consensus 115 ~~~p~ivviNK~D~~~a~-~~~~~~~l~~~l~~~~-~~~~~Pisa~ 158 (270)
T cd01886 115 YNVPRIAFVNKMDRTGAD-FFRVVEQIREKLGANP-VPLQLPIGEE 158 (270)
T ss_pred cCCCEEEEEECCCCCCCC-HHHHHHHHHHHhCCCc-eEEEeccccC
Confidence 358999999998743111 1234666766654331 2346788875
No 218
>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=36.62 E-value=83 Score=28.64 Aligned_cols=44 Identities=14% Similarity=0.041 Sum_probs=24.3
Q ss_pred HhhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 11 HLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 11 ~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
+++.+. ...+|+++|+|+.|.. . .. .+.... .. ..+++++||+-
T Consensus 293 ~L~~l~-~~~~piIlV~NK~Dl~--~--~~---~v~~~~-~~--~~~~i~iSAkt 336 (351)
T TIGR03156 293 VLEELG-AEDIPQLLVYNKIDLL--D--EP---RIERLE-EG--YPEAVFVSAKT 336 (351)
T ss_pred HHHHhc-cCCCCEEEEEEeecCC--C--hH---hHHHHH-hC--CCCEEEEEccC
Confidence 444443 2468999999997642 1 11 222221 11 23578999864
No 219
>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=36.48 E-value=25 Score=30.22 Aligned_cols=45 Identities=11% Similarity=0.093 Sum_probs=26.1
Q ss_pred ccCceEEEEeCCCccccccccccH-HHHHHHHhhcCCCCeEEEechhhchhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWL-PKIKEWVDANDPGATIIPFSGVFEHQL 69 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~-~~l~~~~~~~~~~~~vv~~sa~~E~el 69 (197)
...|+++|+|+.|- .. ..... +.++.+. +. +.+++.+||+-..-+
T Consensus 66 ~~i~~vIV~NK~DL--~~-~~~~~~~~~~~~~-~~--g~~v~~~SAktg~gi 111 (245)
T TIGR00157 66 QNIEPIIVLNKIDL--LD-DEDMEKEQLDIYR-NI--GYQVLMTSSKNQDGL 111 (245)
T ss_pred CCCCEEEEEECccc--CC-CHHHHHHHHHHHH-HC--CCeEEEEecCCchhH
Confidence 45899999999764 21 11111 2233332 33 678999998754433
No 220
>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=35.89 E-value=92 Score=21.84 Aligned_cols=47 Identities=9% Similarity=-0.169 Sum_probs=26.1
Q ss_pred ccccccCceEEEEeCCCccccccccccHHH-HHHHHhhcCCCCeEEEechhh
Q psy17313 15 LNLLTAKTQIYLVNLSAKDYIKKKNKWLPK-IKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 15 ~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~-l~~~~~~~~~~~~vv~~sa~~ 65 (197)
......+|+++++|+.|..-. ....... ........ +.+++++|+.-
T Consensus 97 ~~~~~~~~~ivv~nk~D~~~~--~~~~~~~~~~~~~~~~--~~~~~~~s~~~ 144 (157)
T cd00882 97 NKEGENIPIILVGNKIDLPEE--RVVSEEELAEQLAKEL--GVPYFETSAKT 144 (157)
T ss_pred hhccCCCcEEEEEeccccccc--cchHHHHHHHHHHhhc--CCcEEEEecCC
Confidence 456678999999999764321 1111111 12222222 56788899763
No 221
>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=35.82 E-value=1.1e+02 Score=25.83 Aligned_cols=14 Identities=7% Similarity=-0.313 Sum_probs=11.1
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
...|+|+|+|+.|.
T Consensus 99 ~~~piIlVgNK~DL 112 (220)
T cd04126 99 EDCLFAVVGNKLDL 112 (220)
T ss_pred CCCcEEEEEECccc
Confidence 34799999999763
No 222
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=35.36 E-value=16 Score=24.20 Aligned_cols=25 Identities=20% Similarity=0.381 Sum_probs=20.6
Q ss_pred CcccccCCceeecCCCEEEEEEccC
Q psy17313 164 GKYRQQGRAYTVEDGDIIFFKFNAG 188 (197)
Q Consensus 164 Gk~r~eGkdYivqDGDIi~f~fn~~ 188 (197)
+.+...|..|.++.||.+.+.-+++
T Consensus 30 ~~~~~~~~~~~l~~Gd~~~i~~~~~ 54 (71)
T PF07883_consen 30 GTLTVDGERVELKPGDAIYIPPGVP 54 (71)
T ss_dssp EEEEETTEEEEEETTEEEEEETTSE
T ss_pred EEEEEccEEeEccCCEEEEECCCCe
Confidence 4567788999999999999977654
No 223
>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=35.21 E-value=1e+02 Score=24.41 Aligned_cols=46 Identities=7% Similarity=-0.117 Sum_probs=24.5
Q ss_pred ccCceEEEEeCCCccccccc------cc--cHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKK------NK--WLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~------~~--~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...|+++|+|+.|..-.... .. ..++...++++.+ -.+++.+||+-
T Consensus 104 ~~~piilvgnK~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~e~Sa~~ 157 (187)
T cd04129 104 PNVPVILVGLKKDLRQDAVAKEEYRTQRFVPIQQGKRVAKEIG-AKKYMECSALT 157 (187)
T ss_pred CCCCEEEEeeChhhhhCcccccccccCCcCCHHHHHHHHHHhC-CcEEEEccCCC
Confidence 35899999999764110000 11 1234445555441 13678888763
No 224
>CHL00189 infB translation initiation factor 2; Provisional
Probab=35.03 E-value=1.3e+02 Score=30.73 Aligned_cols=42 Identities=19% Similarity=0.136 Sum_probs=23.7
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHh-------hcCCCCeEEEechhh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVD-------ANDPGATIIPFSGVF 65 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~-------~~~~~~~vv~~sa~~ 65 (197)
...|+|+++|+.|..- ...+++.+.+. ..+...+++++||.-
T Consensus 346 ~~iPiIVViNKiDl~~-----~~~e~v~~eL~~~~ll~e~~g~~vpvv~VSAkt 394 (742)
T CHL00189 346 ANVPIIVAINKIDKAN-----ANTERIKQQLAKYNLIPEKWGGDTPMIPISASQ 394 (742)
T ss_pred cCceEEEEEECCCccc-----cCHHHHHHHHHHhccchHhhCCCceEEEEECCC
Confidence 3479999999976421 12233332221 111125789999864
No 225
>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=34.90 E-value=1.1e+02 Score=25.34 Aligned_cols=40 Identities=5% Similarity=-0.117 Sum_probs=21.8
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
..-|+|+|+|+.|... .....+. ..++... +..++.+||+
T Consensus 98 ~~~piilvgNK~Dl~~---~~v~~~~-~~~~~~~--~~~~~e~SAk 137 (200)
T smart00176 98 ENIPIVLCGNKVDVKD---RKVKAKS-ITFHRKK--NLQYYDISAK 137 (200)
T ss_pred CCCCEEEEEECccccc---ccCCHHH-HHHHHHc--CCEEEEEeCC
Confidence 3568888888876321 1111122 2444443 4677888876
No 226
>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=34.81 E-value=72 Score=25.00 Aligned_cols=42 Identities=12% Similarity=-0.014 Sum_probs=23.5
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhh---cCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDA---NDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~---~~~~~~vv~~sa~~ 65 (197)
.+|+++|+|+.|..- ....++++++.+. ......++++||+-
T Consensus 110 ~~piilv~NK~Dl~~----~~~~~~i~~~~~~~~~~~~~~~~~~~SAk~ 154 (168)
T cd04149 110 DALLLVFANKQDLPD----AMKPHEIQEKLGLTRIRDRNWYVQPSCATS 154 (168)
T ss_pred CCcEEEEEECcCCcc----CCCHHHHHHHcCCCccCCCcEEEEEeeCCC
Confidence 479999999976321 1123455554421 11123577888864
No 227
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=34.31 E-value=1.6e+02 Score=20.37 Aligned_cols=59 Identities=19% Similarity=0.190 Sum_probs=36.6
Q ss_pred cCCCceeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEEEccC
Q psy17313 109 AGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFNAG 188 (197)
Q Consensus 109 ~g~~EvRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~fn~~ 188 (197)
.|....+.+.++.|+|+.+..... ++..-.+ |..+. | +..-.++.++|||.|.|---++
T Consensus 10 ng~~~~~~~~~~~~~tv~~ll~~l--~~~~~~v-~v~vN----------------g--~iv~~~~~l~~gD~Veii~~V~ 68 (70)
T PRK08364 10 IGRGIEKEIEWRKGMKVADILRAV--GFNTESA-IAKVN----------------G--KVALEDDPVKDGDYVEVIPVVS 68 (70)
T ss_pred eccccceEEEcCCCCcHHHHHHHc--CCCCccE-EEEEC----------------C--EECCCCcCcCCCCEEEEEcccc
Confidence 344445677889999999888766 3332222 22111 2 2234799999999988765444
No 228
>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=33.96 E-value=68 Score=26.28 Aligned_cols=44 Identities=11% Similarity=-0.130 Sum_probs=26.3
Q ss_pred ccCceEEEEeCCCccccc-----------------cccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIK-----------------KKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~-----------------~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
...|+|+|+|+.|..-.. ...-..+..++++++. +.+++-+||+
T Consensus 119 ~~~piilvgNK~DL~~~~~~~~~~~~~~~~~~~~~~~~V~~~e~~~~a~~~--~~~~~E~SAk 179 (195)
T cd01873 119 PRVPVILVGCKLDLRYADLDEVNRARRPLARPIKNADILPPETGRAVAKEL--GIPYYETSVV 179 (195)
T ss_pred CCCCEEEEEEchhccccccchhhhcccccccccccCCccCHHHHHHHHHHh--CCEEEEcCCC
Confidence 457999999997632100 0011234556677665 5677777875
No 229
>PLN03071 GTP-binding nuclear protein Ran; Provisional
Probab=33.65 E-value=1.1e+02 Score=25.28 Aligned_cols=40 Identities=5% Similarity=-0.031 Sum_probs=21.1
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
...|+++|+|+.|.. . .....+.+ .+..++ +.+++.+||+
T Consensus 116 ~~~piilvgNK~Dl~--~-~~v~~~~~-~~~~~~--~~~~~e~SAk 155 (219)
T PLN03071 116 ENIPIVLCGNKVDVK--N-RQVKAKQV-TFHRKK--NLQYYEISAK 155 (219)
T ss_pred CCCcEEEEEEchhhh--h-ccCCHHHH-HHHHhc--CCEEEEcCCC
Confidence 457888888886532 1 11111223 444433 4567777776
No 230
>cd07357 HN_L-whirlin_R2_like Second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains. This subgroup contains the second of two harmonin_N_like domains found in the long isoform of whirlin, and related domains. Whirlin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds various components of the Usher protein network of the inner ear and the retina: erythrocyte protein p55, usherin, VlGR1, and myosin XVa. The long isoform of whirlin contains two harmonin_N_like domains, and three PDZ protein-binding domains, PDZ1-3. The short whirlin isoform, derived from an alternative start ATG, lacks the first harmonin_N_like domain but has in common with the long isoform, this second harmonin_N_like domain (designated repeat 2, included in this subgroup) and PDZ3. This second harmonin_N_like domain is a putative protein-binding module based on its sequence similarity to the harmonin N-domain.
Probab=33.44 E-value=56 Score=24.29 Aligned_cols=41 Identities=24% Similarity=0.370 Sum_probs=29.5
Q ss_pred hchhhc-CCCHHHHH---HHHHHhC-CcchHHHHHHHHHhhcCCeE
Q psy17313 65 FEHQLV-DMPDDERQ---RYLDEQK-ATSVLDKIITQGYKSLQLQY 105 (197)
Q Consensus 65 ~E~el~-~l~~ee~~---~fl~~~g-~~sgl~~li~~~y~lL~Lit 105 (197)
+|..-. -|+++|++ .|+++|. ..-+++.++.+.+++|+=-.
T Consensus 8 ~ee~Ar~lL~e~E~~tm~yyl~eY~~~~~tVealV~aL~elLnt~~ 53 (81)
T cd07357 8 VEEQARHLLSENERATLSYYLDEYRSGHISVDALVMALFELLNTHE 53 (81)
T ss_pred HHHHHHHHcCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhccHH
Confidence 444333 35887876 3788887 45689999999999998443
No 231
>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=32.11 E-value=92 Score=26.32 Aligned_cols=14 Identities=7% Similarity=-0.135 Sum_probs=11.4
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
..+|+++|+|+.|.
T Consensus 137 ~~ip~ivvvNK~D~ 150 (224)
T cd04165 137 LNIPVFVVVTKIDL 150 (224)
T ss_pred cCCCEEEEEECccc
Confidence 34899999999874
No 232
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=31.54 E-value=60 Score=32.00 Aligned_cols=47 Identities=4% Similarity=-0.070 Sum_probs=25.6
Q ss_pred CceEEEEeCCCccccccccccHHHHHHHHhhcC-CCCeEEEechhhch
Q psy17313 21 KTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAND-PGATIIPFSGVFEH 67 (197)
Q Consensus 21 KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~-~~~~vv~~sa~~E~ 67 (197)
+++++|+|+.|..-...-....+.+++++...+ .+.+++|+||.--.
T Consensus 105 ~~iIVVlNKiDlv~~~~~~~v~~ei~~~l~~~~~~~~~ii~VSA~tG~ 152 (614)
T PRK10512 105 PMLTVALTKADRVDEARIAEVRRQVKAVLREYGFAEAKLFVTAATEGR 152 (614)
T ss_pred CeEEEEEECCccCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEeCCCCC
Confidence 346799999864210001123345555554321 13679999987543
No 233
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=31.43 E-value=49 Score=22.39 Aligned_cols=57 Identities=16% Similarity=0.165 Sum_probs=33.0
Q ss_pred eeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEEEccCC
Q psy17313 116 AWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFNAGA 189 (197)
Q Consensus 116 AWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~fn~~~ 189 (197)
.+.++.|+|..++-....-+. +++.-| +. . +- + -|....++.++|||.|.|---++.
T Consensus 7 ~~~~~~~~tv~~ll~~l~~~~-~~v~v~--vN--~------~i-v-----~~~~~~~~~L~~gD~veii~~V~G 63 (64)
T TIGR01683 7 PVEVEDGLTLAALLESLGLDP-RRVAVA--VN--G------EI-V-----PRSEWDDTILKEGDRIEIVTFVGG 63 (64)
T ss_pred EEEcCCCCcHHHHHHHcCCCC-CeEEEE--EC--C------EE-c-----CHHHcCceecCCCCEEEEEEeccC
Confidence 456678888888877664332 333211 11 1 00 0 022356789999999998766554
No 234
>PRK13956 dut deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional
Probab=31.43 E-value=94 Score=25.17 Aligned_cols=48 Identities=19% Similarity=0.379 Sum_probs=33.6
Q ss_pred eeeeEecCCCChhh-------hhhhhccccc-----cCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEE
Q psy17313 114 VKAWTIQKGTKAPQ-------AAGRIHTDFE-----KGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDII 181 (197)
Q Consensus 114 vRAWti~~GstA~~-------aAg~IHsDfe-----kgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi 181 (197)
.-+|..++.+.|.. .+|+|++|+. +|=|.+.+++.. .+++.++.||-|
T Consensus 59 ~~~~I~~RSsla~k~Gl~l~n~~GvIDsdYrGe~~~~G~i~v~l~N~~--------------------~~~~~I~~GdRI 118 (147)
T PRK13956 59 EVLYLYDRSSNPRKKGLVLINSVGVIDGDYYGNPANEGHIFAQMKNIT--------------------DQEVVLEVGERI 118 (147)
T ss_pred eEEEEecCchhhhhCCEEEcCcCCeEcCCCCCCCCCCcEEEEEEEeCC--------------------CCCEEECCCCEE
Confidence 34677777766644 5999999996 566888877632 257778888743
No 235
>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=31.06 E-value=81 Score=24.18 Aligned_cols=14 Identities=14% Similarity=-0.040 Sum_probs=11.8
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
..+|+++|+|+.|.
T Consensus 104 ~~~piilv~nK~Dl 117 (175)
T cd01870 104 PNVPIILVGNKKDL 117 (175)
T ss_pred CCCCEEEEeeChhc
Confidence 47899999999763
No 236
>KOG0073|consensus
Probab=30.74 E-value=51 Score=27.98 Aligned_cols=45 Identities=13% Similarity=0.074 Sum_probs=25.5
Q ss_pred cccCceEEEEeCCCccccccccc--cHHHHHHHHhhcCCCCeEEEechh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNK--WLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~--~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
|--+|++++||+.+..-.-..+. ..-.+.++++.+ .-+++.+||-
T Consensus 115 laG~~~Lvlank~dl~~~l~~~~i~~~~~L~~l~ks~--~~~l~~cs~~ 161 (185)
T KOG0073|consen 115 LAGAPLLVLANKQDLPGALSLEEISKALDLEELAKSH--HWRLVKCSAV 161 (185)
T ss_pred hcCCceEEEEecCcCccccCHHHHHHhhCHHHhcccc--CceEEEEecc
Confidence 44489999999987641111222 222344555443 4667777764
No 237
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=30.44 E-value=35 Score=21.48 Aligned_cols=19 Identities=37% Similarity=0.810 Sum_probs=14.9
Q ss_pred cCcccccC-----CceeecCCCEE
Q psy17313 163 AGKYRQQG-----RAYTVEDGDII 181 (197)
Q Consensus 163 ~Gk~r~eG-----kdYivqDGDIi 181 (197)
+|.+++.| .+|.|+.||+|
T Consensus 25 ~g~V~VNg~~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 25 QGRVKVNGKVVKDPSYIVKPGDVI 48 (48)
T ss_dssp TTTEEETTEEESSTTSBESTTEEE
T ss_pred CCEEEECCEEEcCCCCCCCCcCCC
Confidence 47777766 67889999986
No 238
>CHL00075 rpl21 ribosomal protein L21
Probab=30.36 E-value=36 Score=26.34 Aligned_cols=19 Identities=21% Similarity=0.253 Sum_probs=16.3
Q ss_pred ccccCCceeecCCCEEEEE
Q psy17313 166 YRQQGRAYTVEDGDIIFFK 184 (197)
Q Consensus 166 ~r~eGkdYivqDGDIi~f~ 184 (197)
++.-||.|.|+.||++.+-
T Consensus 7 i~~gGkQykV~~Gd~i~ve 25 (108)
T CHL00075 7 IEAGGKQLWVEPGRFYDIN 25 (108)
T ss_pred EEECCEEEEEeCCCEEEEE
Confidence 4667999999999999874
No 239
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=30.21 E-value=45 Score=22.47 Aligned_cols=57 Identities=14% Similarity=0.254 Sum_probs=35.7
Q ss_pred eeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEEEccCC
Q psy17313 116 AWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFNAGA 189 (197)
Q Consensus 116 AWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~fn~~~ 189 (197)
...++.|+|..++... .++....+..+ +.- .+ +. |..-.++.++|||.|.|-.-++.
T Consensus 9 ~~~~~~~~tl~~lL~~--l~~~~~~vav~-vNg-~i--------v~-----r~~~~~~~l~~gD~vei~~~vgG 65 (66)
T PRK05659 9 PRELPDGESVAALLAR--EGLAGRRVAVE-VNG-EI--------VP-----RSQHASTALREGDVVEIVHALGG 65 (66)
T ss_pred EEEcCCCCCHHHHHHh--cCCCCCeEEEE-ECC-eE--------eC-----HHHcCcccCCCCCEEEEEEEecC
Confidence 5678899998888764 34555555443 220 00 00 12337889999999998766654
No 240
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=30.20 E-value=26 Score=30.57 Aligned_cols=28 Identities=25% Similarity=0.345 Sum_probs=24.1
Q ss_pred HcCcccccCCceeecCCCEEEEEEccCC
Q psy17313 162 AAGKYRQQGRAYTVEDGDIIFFKFNAGA 189 (197)
Q Consensus 162 ~~Gk~r~eGkdYivqDGDIi~f~fn~~~ 189 (197)
-+|.++..|+.|.|+-||+|++.-+++-
T Consensus 209 G~G~~~~~g~~~~V~~GD~i~i~~~~~h 236 (260)
T TIGR03214 209 GKGVYNLDNNWVPVEAGDYIWMGAYCPQ 236 (260)
T ss_pred ceEEEEECCEEEEecCCCEEEECCCCCE
Confidence 4678899999999999999999877653
No 241
>PLN00043 elongation factor 1-alpha; Provisional
Probab=30.19 E-value=70 Score=30.14 Aligned_cols=54 Identities=17% Similarity=0.279 Sum_probs=31.5
Q ss_pred ccccCceEEEEeCCCcc---cccc-ccccHHHHHHHHhhcC---CCCeEEEechhhchhhc
Q psy17313 17 LLTAKTQIYLVNLSAKD---YIKK-KNKWLPKIKEWVDAND---PGATIIPFSGVFEHQLV 70 (197)
Q Consensus 17 lLT~KP~iyv~Nv~e~d---~~~~-~~~~~~~l~~~~~~~~---~~~~vv~~sa~~E~el~ 70 (197)
.+-.+|+|+++|+.|.. +... -++..++++.++++.+ .+.++||+||.-..-+.
T Consensus 142 ~~gi~~iIV~vNKmD~~~~~~~~~~~~~i~~ei~~~l~~~g~~~~~~~~ipiSa~~G~ni~ 202 (447)
T PLN00043 142 TLGVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVGYNPDKIPFVPISGFEGDNMI 202 (447)
T ss_pred HcCCCcEEEEEEcccCCchhhhHHHHHHHHHHHHHHHHHcCCCcccceEEEEecccccccc
Confidence 34456788899998742 1100 1223566777776542 13679999986544443
No 242
>PRK09435 membrane ATPase/protein kinase; Provisional
Probab=29.99 E-value=81 Score=28.79 Aligned_cols=43 Identities=7% Similarity=0.043 Sum_probs=23.7
Q ss_pred eEEEEeCCCccccccccccHHHHHHHHhhcC-----CCCeEEEechhh
Q psy17313 23 QIYLVNLSAKDYIKKKNKWLPKIKEWVDAND-----PGATIIPFSGVF 65 (197)
Q Consensus 23 ~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~-----~~~~vv~~sa~~ 65 (197)
-|+|+|+.|..-....+.....+++...... ...+|+++||.-
T Consensus 197 DIiVVNKaDl~~~~~a~~~~~el~~~L~l~~~~~~~w~~pVi~vSA~~ 244 (332)
T PRK09435 197 DLIVINKADGDNKTAARRAAAEYRSALRLLRPKDPGWQPPVLTCSALE 244 (332)
T ss_pred heEEeehhcccchhHHHHHHHHHHHHHhcccccccCCCCCEEEEECCC
Confidence 3899999874321112334455555443211 125799999854
No 243
>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed
Probab=29.98 E-value=1.4e+02 Score=29.80 Aligned_cols=100 Identities=9% Similarity=0.071 Sum_probs=48.6
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhh---cCCCCeEEEechhhchhhcCCCHHHHHHHHHHhC---CcchHHH
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDA---NDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQK---ATSVLDK 92 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~---~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~g---~~sgl~~ 92 (197)
..+|+|+|+|+.|. .. ....+.+++.... .-+..+++++||.-..-+.+|-+. -.+.+..+. ..+-|++
T Consensus 560 ~~~piIiV~NK~DL--~~--~~~~~~~~~~~~~~l~~~~~~~ii~iSAktg~gv~~L~~~-i~~~~~~~~~~i~T~~Ln~ 634 (712)
T PRK09518 560 AGRALVLVFNKWDL--MD--EFRRQRLERLWKTEFDRVTWARRVNLSAKTGWHTNRLAPA-MQEALESWDQRIPTGKLNA 634 (712)
T ss_pred cCCCEEEEEEchhc--CC--hhHHHHHHHHHHHhccCCCCCCEEEEECCCCCCHHHHHHH-HHHHHHHhcccCChHHHHH
Confidence 46999999999753 21 1112223322211 112457899999766555444221 112223332 1345788
Q ss_pred HHHHHHhhcCCeEEeecCCCceeeeEecCCCChh
Q psy17313 93 IITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAP 126 (197)
Q Consensus 93 li~~~y~lL~LitffT~g~~EvRAWti~~GstA~ 126 (197)
.++..-..-- ..+ .+....|...+.++++.|
T Consensus 635 ~l~~~~~~~~-~p~--~~g~~~ki~y~~q~~~~P 665 (712)
T PRK09518 635 FLGKIQAEHP-HPL--RGGKQPRILFATQASTRP 665 (712)
T ss_pred HHHHHHhhCC-CCc--cCCeeeeEEEEECCCCCC
Confidence 8765543211 110 123555666665555544
No 244
>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed
Probab=29.64 E-value=1.4e+02 Score=29.87 Aligned_cols=15 Identities=20% Similarity=0.138 Sum_probs=12.7
Q ss_pred cccCceEEEEeCCCc
Q psy17313 18 LTAKTQIYLVNLSAK 32 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~ 32 (197)
...+|+|+|+|+.|.
T Consensus 381 ~~~~pvIlV~NK~D~ 395 (712)
T PRK09518 381 RAGKPVVLAVNKIDD 395 (712)
T ss_pred hcCCCEEEEEECccc
Confidence 367999999999874
No 245
>TIGR00061 L21 ribosomal protein L21. Eubacterial and chloroplast.
Probab=29.53 E-value=38 Score=25.85 Aligned_cols=19 Identities=26% Similarity=0.564 Sum_probs=16.0
Q ss_pred ccccCCceeecCCCEEEEE
Q psy17313 166 YRQQGRAYTVEDGDIIFFK 184 (197)
Q Consensus 166 ~r~eGkdYivqDGDIi~f~ 184 (197)
+..-||.|.|+.||++.+.
T Consensus 4 i~~gGkQykV~~Gd~i~Ve 22 (101)
T TIGR00061 4 VEIGGKQYKVEEGQTVRIE 22 (101)
T ss_pred EEECCEEEEEeCCCEEEEc
Confidence 4567999999999999873
No 246
>PRK09866 hypothetical protein; Provisional
Probab=29.53 E-value=98 Score=31.53 Aligned_cols=60 Identities=12% Similarity=0.058 Sum_probs=31.4
Q ss_pred HHHHHhhccccccc--CceEEEEeCCCccccccccccHHHHHHHHh----h-cCCCCeEEEechhhchhh
Q psy17313 7 LRIEHLNKLNLLTA--KTQIYLVNLSAKDYIKKKNKWLPKIKEWVD----A-NDPGATIIPFSGVFEHQL 69 (197)
Q Consensus 7 ~E~~~i~~~~lLT~--KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~----~-~~~~~~vv~~sa~~E~el 69 (197)
.+..+++.+.- +. +|+++|+|+.|. .+......+.+.+++. + ..+...|+|+||.-..-+
T Consensus 275 ~DeeIlk~Lkk-~~K~~PVILVVNKIDl--~dreeddkE~Lle~V~~~L~q~~i~f~eIfPVSAlkG~ni 341 (741)
T PRK09866 275 SDEEVREAILA-VGQSVPLYVLVNKFDQ--QDRNSDDADQVRALISGTLMKGCITPQQIFPVSSMWGYLA 341 (741)
T ss_pred hHHHHHHHHHh-cCCCCCEEEEEEcccC--CCcccchHHHHHHHHHHHHHhcCCCCceEEEEeCCCCCCH
Confidence 44455554432 23 399999999774 1101112334444332 1 112346999998765433
No 247
>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed
Probab=29.53 E-value=98 Score=29.10 Aligned_cols=36 Identities=25% Similarity=0.255 Sum_probs=21.9
Q ss_pred cccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 18 LTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
...+|+++|+|+.|.. . ..... ... +.+++++||+-
T Consensus 319 ~~~~piiiV~NK~DL~--~--~~~~~------~~~--~~~~i~iSAkt 354 (449)
T PRK05291 319 LKDKPVIVVLNKADLT--G--EIDLE------EEN--GKPVIRISAKT 354 (449)
T ss_pred cCCCCcEEEEEhhhcc--c--cchhh------hcc--CCceEEEEeeC
Confidence 4678999999997642 1 11111 111 35688999864
No 248
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=29.39 E-value=68 Score=30.21 Aligned_cols=56 Identities=14% Similarity=0.206 Sum_probs=30.6
Q ss_pred ccccccCceEEEEeCCCccccccc----cccHHHHHHHHhhcC---CCCeEEEechhhchhhc
Q psy17313 15 LNLLTAKTQIYLVNLSAKDYIKKK----NKWLPKIKEWVDAND---PGATIIPFSGVFEHQLV 70 (197)
Q Consensus 15 ~~lLT~KP~iyv~Nv~e~d~~~~~----~~~~~~l~~~~~~~~---~~~~vv~~sa~~E~el~ 70 (197)
...+--+++|+++|+.|....+-. ....+++++.....+ .+.++||+||.-..-+.
T Consensus 140 ~~~~gi~~iiv~vNKmD~~~~~~~~~~~~~i~~~i~~~l~~~g~~~~~~~~ipiSa~~g~ni~ 202 (446)
T PTZ00141 140 AFTLGVKQMIVCINKMDDKTVNYSQERYDEIKKEVSAYLKKVGYNPEKVPFIPISGWQGDNMI 202 (446)
T ss_pred HHHcCCCeEEEEEEccccccchhhHHHHHHHHHHHHHHHHhcCCCcccceEEEeecccCCCcc
Confidence 334444567899999874221001 223445555444321 14789999987655443
No 249
>COG3837 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=28.80 E-value=31 Score=28.70 Aligned_cols=27 Identities=26% Similarity=0.414 Sum_probs=22.8
Q ss_pred cCcccccCCceeecCCCEEEEEEccCC
Q psy17313 163 AGKYRQQGRAYTVEDGDIIFFKFNAGA 189 (197)
Q Consensus 163 ~Gk~r~eGkdYivqDGDIi~f~fn~~~ 189 (197)
.|-++..|..|+|+.||++-|..+++.
T Consensus 74 E~~l~~d~~e~~lrpGD~~gFpAG~~~ 100 (161)
T COG3837 74 EGTLREDGGETRLRPGDSAGFPAGVGN 100 (161)
T ss_pred ceEEEECCeeEEecCCceeeccCCCcc
Confidence 356788999999999999999888643
No 250
>COG1160 Predicted GTPases [General function prediction only]
Probab=28.57 E-value=2.1e+02 Score=27.50 Aligned_cols=84 Identities=13% Similarity=0.148 Sum_probs=48.8
Q ss_pred hhcccccccCceEEEEeCCCccccccccc----cHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHHhC--
Q psy17313 12 LNKLNLLTAKTQIYLVNLSAKDYIKKKNK----WLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDEQK-- 85 (197)
Q Consensus 12 i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~----~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~~g-- 85 (197)
|-++-.-..||+++|+|+-|. ....+. +.++++....-- ..++++.+||.--.-+..|-+ .-.+..+.++
T Consensus 281 ia~~i~~~g~~~vIvvNKWDl--~~~~~~~~~~~k~~i~~~l~~l-~~a~i~~iSA~~~~~i~~l~~-~i~~~~~~~~~r 356 (444)
T COG1160 281 IAGLIEEAGRGIVIVVNKWDL--VEEDEATMEEFKKKLRRKLPFL-DFAPIVFISALTGQGLDKLFE-AIKEIYECATRR 356 (444)
T ss_pred HHHHHHHcCCCeEEEEEcccc--CCchhhHHHHHHHHHHHHhccc-cCCeEEEEEecCCCChHHHHH-HHHHHHHHhccc
Confidence 445666678999999999652 211112 333333322211 257899999988777666532 2222334444
Q ss_pred -CcchHHHHHHHHHh
Q psy17313 86 -ATSVLDKIITQGYK 99 (197)
Q Consensus 86 -~~sgl~~li~~~y~ 99 (197)
..+-|+++++.+..
T Consensus 357 i~Ts~LN~~l~~a~~ 371 (444)
T COG1160 357 ISTSLLNRVLEDAVA 371 (444)
T ss_pred cCHHHHHHHHHHHHH
Confidence 34678888865544
No 251
>cd01092 APP-like Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline.
Probab=28.52 E-value=27 Score=28.07 Aligned_cols=61 Identities=23% Similarity=0.311 Sum_probs=35.0
Q ss_pred cCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEEEcc
Q psy17313 120 QKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFNA 187 (197)
Q Consensus 120 ~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~fn~ 187 (197)
+.|.|-.|.+..++.-+.+. -++-+.|.-++..|.... ..+....+-++++||+|.|-+.+
T Consensus 23 ~~G~te~ei~~~~~~~~~~~--g~~~~~~~~~v~~g~~~~-----~~h~~~~~~~l~~gd~v~id~g~ 83 (208)
T cd01092 23 KPGMTEREVAAELEYFMRKL--GAEGPSFDTIVASGPNSA-----LPHGVPSDRKIEEGDLVLIDFGA 83 (208)
T ss_pred cCCCCHHHHHHHHHHHHHHc--CCCCCCCCcEEEECcccc-----ccCCCCCCcCcCCCCEEEEEeee
Confidence 66778888888876654421 111123334444443211 22334456779999999998754
No 252
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=28.50 E-value=41 Score=24.57 Aligned_cols=46 Identities=22% Similarity=0.337 Sum_probs=33.2
Q ss_pred eeEecCCCChhh---hhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEE
Q psy17313 116 AWTIQKGTKAPQ---AAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFK 184 (197)
Q Consensus 116 AWti~~GstA~~---aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~ 184 (197)
++.+..++|+.+ +-|+=|++..-=++. | +..+-+|+++|||.|.+.
T Consensus 26 ~~~~~~~~tvkd~IEsLGVP~tEV~~i~vN---------------------G--~~v~~~~~~~~Gd~v~V~ 74 (81)
T PF14451_consen 26 THPFDGGATVKDVIESLGVPHTEVGLILVN---------------------G--RPVDFDYRLKDGDRVAVY 74 (81)
T ss_pred EEecCCCCcHHHHHHHcCCChHHeEEEEEC---------------------C--EECCCcccCCCCCEEEEE
Confidence 567788888764 568889987543322 3 346789999999998763
No 253
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=28.43 E-value=28 Score=25.67 Aligned_cols=23 Identities=26% Similarity=0.406 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHHhC-CcchHHHHH
Q psy17313 72 MPDDERQRYLDEQK-ATSVLDKII 94 (197)
Q Consensus 72 l~~ee~~~fl~~~g-~~sgl~~li 94 (197)
|++||++++|+.|+ ..+-|+++.
T Consensus 18 Ls~eE~~~lL~~y~i~~~qLP~I~ 41 (79)
T PRK09570 18 LSEEEAKKLLKEYGIKPEQLPKIK 41 (79)
T ss_pred CCHHHHHHHHHHcCCCHHHCCcee
Confidence 68999999999999 777787776
No 254
>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=28.43 E-value=78 Score=25.20 Aligned_cols=44 Identities=16% Similarity=0.039 Sum_probs=24.3
Q ss_pred ccccCceEEEEeCCCccccccccccHHHHHHHHhh--c--CCCCeEEEechh
Q psy17313 17 LLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDA--N--DPGATIIPFSGV 64 (197)
Q Consensus 17 lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~--~--~~~~~vv~~sa~ 64 (197)
-+..+|+++++|+.|..-. -....+.+...- . .-...++++||.
T Consensus 112 ~~~~~piLIl~NK~D~~~~----~~~~~i~~~l~l~~l~~~~~~~v~~~sa~ 159 (175)
T PF00025_consen 112 ELKDIPILILANKQDLPDA----MSEEEIKEYLGLEKLKNKRPWSVFSCSAK 159 (175)
T ss_dssp GGTTSEEEEEEESTTSTTS----STHHHHHHHTTGGGTTSSSCEEEEEEBTT
T ss_pred hcccceEEEEeccccccCc----chhhHHHhhhhhhhcccCCceEEEeeecc
Confidence 3467999999999764321 122334432211 0 113567778875
No 255
>COG0182 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]
Probab=28.23 E-value=78 Score=29.37 Aligned_cols=39 Identities=15% Similarity=0.122 Sum_probs=28.0
Q ss_pred chHHHHHHHHHhhcCCeEEeecCCCceeeeEecCCCChhhhhh
Q psy17313 88 SVLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAPQAAG 130 (197)
Q Consensus 88 sgl~~li~~~y~lL~LitffT~g~~EvRAWti~~GstA~~aAg 130 (197)
|+| -+||.+...=..+.+|. +|+|+|.=-.--||.++..
T Consensus 169 TAl-gviR~a~~~gk~i~v~a---~ETRP~lQGARLTawEL~~ 207 (346)
T COG0182 169 TAL-GVIRSAHEEGKDIRVFA---DETRPYLQGARLTAWELVQ 207 (346)
T ss_pred chH-HHHHHHHHCCCeeEEEe---CCCccccccceeeHHHHhh
Confidence 344 45666666667888887 8999998666678887753
No 256
>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=27.96 E-value=1.2e+02 Score=27.50 Aligned_cols=41 Identities=17% Similarity=0.133 Sum_probs=23.3
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhhch
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEH 67 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~E~ 67 (197)
..||+++|+|+.|..- ...... ++. +.+ -.+++++||.-..
T Consensus 106 ~~~piilVvNK~D~~~---~~~~~~---~~~-~lg-~~~~~~vSa~~g~ 146 (429)
T TIGR03594 106 SGKPVILVANKIDGKK---EDAVAA---EFY-SLG-FGEPIPISAEHGR 146 (429)
T ss_pred hCCCEEEEEECccCCc---ccccHH---HHH-hcC-CCCeEEEeCCcCC
Confidence 4699999999987421 111111 221 121 1268899987443
No 257
>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=27.85 E-value=1.8e+02 Score=28.53 Aligned_cols=41 Identities=15% Similarity=0.093 Sum_probs=23.3
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhh-------cCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDA-------NDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~-------~~~~~~vv~~sa~~ 65 (197)
..|+++++|+.|..- ...+++...+.+ .+...+++|+||.-
T Consensus 187 ~vPiIVviNKiDl~~-----~~~e~v~~~L~~~g~~~~~~~~~~~~v~iSAkt 234 (587)
T TIGR00487 187 NVPIIVAINKIDKPE-----ANPDRVKQELSEYGLVPEDWGGDTIFVPVSALT 234 (587)
T ss_pred CCCEEEEEECccccc-----CCHHHHHHHHHHhhhhHHhcCCCceEEEEECCC
Confidence 479999999987421 112233333222 11124689999864
No 258
>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=27.73 E-value=79 Score=24.98 Aligned_cols=14 Identities=0% Similarity=-0.156 Sum_probs=11.4
Q ss_pred ccCceEEEEeCCCc
Q psy17313 19 TAKTQIYLVNLSAK 32 (197)
Q Consensus 19 T~KP~iyv~Nv~e~ 32 (197)
...|+|+|+|+.|.
T Consensus 104 ~~~piilvgnK~Dl 117 (175)
T cd01874 104 PKTPFLLVGTQIDL 117 (175)
T ss_pred CCCCEEEEEECHhh
Confidence 45799999999763
No 259
>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=27.40 E-value=78 Score=29.19 Aligned_cols=53 Identities=11% Similarity=0.119 Sum_probs=30.9
Q ss_pred cCceEEEEeCCCcc-cccc-ccccHHHHHHHHhhcC---CCCeEEEechhhchhhcCC
Q psy17313 20 AKTQIYLVNLSAKD-YIKK-KNKWLPKIKEWVDAND---PGATIIPFSGVFEHQLVDM 72 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d-~~~~-~~~~~~~l~~~~~~~~---~~~~vv~~sa~~E~el~~l 72 (197)
.+|+|+++|+.|.. .... -....++++++++..+ ...+++|+||.-..-+.++
T Consensus 141 ~~~iIVviNK~Dl~~~~~~~~~~~~~ei~~~~~~~g~~~~~~~~i~iSA~~g~ni~~~ 198 (426)
T TIGR00483 141 INQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNPDTVPFIPISAWNGDNVIKK 198 (426)
T ss_pred CCeEEEEEEChhccCccHHHHHHHHHHHHHHHHHcCCCcccceEEEeecccccccccc
Confidence 46899999997641 1000 0112345556665432 1357999999877656543
No 260
>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional
Probab=27.19 E-value=70 Score=28.81 Aligned_cols=49 Identities=18% Similarity=0.092 Sum_probs=31.1
Q ss_pred ccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 15 LNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 15 ~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
|...-..+-++|+|+.|. .......++.+.+.+++.+|..+++++||.-
T Consensus 225 yp~~f~~ADIVVLNKiDL--l~~~~~dle~~~~~lr~lnp~a~I~~vSA~t 273 (290)
T PRK10463 225 YPHMFAAASLMLLNKVDL--LPYLNFDVEKCIACAREVNPEIEIILISATS 273 (290)
T ss_pred ccchhhcCcEEEEEhHHc--CcccHHHHHHHHHHHHhhCCCCcEEEEECCC
Confidence 434446788999999763 2101224555665565555678999999864
No 261
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=27.12 E-value=53 Score=25.63 Aligned_cols=15 Identities=27% Similarity=0.877 Sum_probs=12.1
Q ss_pred eecCCCEEEEEEccC
Q psy17313 174 TVEDGDIIFFKFNAG 188 (197)
Q Consensus 174 ivqDGDIi~f~fn~~ 188 (197)
.+|.||+|+|+++.+
T Consensus 76 ~~qpGDlvff~~~~~ 90 (134)
T TIGR02219 76 AAQPGDVLVFRWRPG 90 (134)
T ss_pred cCCCCCEEEEeeCCC
Confidence 479999999997543
No 262
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=26.98 E-value=59 Score=21.99 Aligned_cols=18 Identities=17% Similarity=0.239 Sum_probs=14.8
Q ss_pred ceeecCCCEEEEEEccCC
Q psy17313 172 AYTVEDGDIIFFKFNAGA 189 (197)
Q Consensus 172 dYivqDGDIi~f~fn~~~ 189 (197)
++.++|||.|.|---|+.
T Consensus 47 ~~~L~dgD~Ieiv~~V~G 64 (65)
T PRK06488 47 QFVLHEGDRIEILSPMQG 64 (65)
T ss_pred ccccCCCCEEEEEEeccC
Confidence 889999999998766554
No 263
>cd07347 harmonin_N_like N-terminal protein-binding module of harmonin and similar domains. This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain is found in either one or two copies. Harmonin contains a single copy, which is found at its N-terminus and binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network. Whirlin contains two copies of the harmonin_N_like domain; the first of these has been assayed for interaction with the cytoplasmic domain of cadherin 23 and no interaction could be detected.
Probab=26.95 E-value=93 Score=22.77 Aligned_cols=31 Identities=23% Similarity=0.429 Sum_probs=23.8
Q ss_pred CCHHHHHHH---HHHhCCcchHHHHHHHHHhhcC
Q psy17313 72 MPDDERQRY---LDEQKATSVLDKIITQGYKSLQ 102 (197)
Q Consensus 72 l~~ee~~~f---l~~~g~~sgl~~li~~~y~lL~ 102 (197)
|++.||..+ |++|..+.+++.++.+.+.+|+
T Consensus 16 L~~~Er~~~~~~L~~Y~~~~~Vd~LV~~L~~vLd 49 (78)
T cd07347 16 LTDAEREQVTRALERYHQERNVDDLVRDLYLVLD 49 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcC
Confidence 478888754 6666644589999999998886
No 264
>PRK12288 GTPase RsgA; Reviewed
Probab=26.78 E-value=48 Score=30.32 Aligned_cols=76 Identities=8% Similarity=0.067 Sum_probs=38.2
Q ss_pred ccCceEEEEeCCCccccccc-cccHHHHHHHHhhcCCCCeEEEechhhchhhcCCCHHHHHHHHHH-----hC-CcchHH
Q psy17313 19 TAKTQIYLVNLSAKDYIKKK-NKWLPKIKEWVDANDPGATIIPFSGVFEHQLVDMPDDERQRYLDE-----QK-ATSVLD 91 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~-~~~~~~l~~~~~~~~~~~~vv~~sa~~E~el~~l~~ee~~~fl~~-----~g-~~sgl~ 91 (197)
..+|.++|+|+.|- .... ...+.+..+..... +.+++++||.-..-+.+| .+++.. .| .+.|-.
T Consensus 149 ~~i~~VIVlNK~DL--~~~~~~~~~~~~~~~y~~~--g~~v~~vSA~tg~GideL-----~~~L~~ki~~~vG~sgVGKS 219 (347)
T PRK12288 149 LGIEPLIVLNKIDL--LDDEGRAFVNEQLDIYRNI--GYRVLMVSSHTGEGLEEL-----EAALTGRISIFVGQSGVGKS 219 (347)
T ss_pred cCCCEEEEEECccC--CCcHHHHHHHHHHHHHHhC--CCeEEEEeCCCCcCHHHH-----HHHHhhCCEEEECCCCCCHH
Confidence 34799999999764 2101 01222222222232 578999998754333222 122221 24 445555
Q ss_pred HHHHHHHhhcCC
Q psy17313 92 KIITQGYKSLQL 103 (197)
Q Consensus 92 ~li~~~y~lL~L 103 (197)
.||++...-..+
T Consensus 220 TLiN~Ll~~~~~ 231 (347)
T PRK12288 220 SLINALLPEAEI 231 (347)
T ss_pred HHHHHhccccce
Confidence 577665544444
No 265
>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=26.34 E-value=2e+02 Score=23.81 Aligned_cols=40 Identities=8% Similarity=-0.119 Sum_probs=24.4
Q ss_pred eEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechh
Q psy17313 23 QIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGV 64 (197)
Q Consensus 23 ~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~ 64 (197)
-+++.|+.|.. +.....++.+.++++..+++.+++.+||+
T Consensus 140 d~~~~~k~d~~--~~~~~~~~~~~~~~~~~~~~~~i~~~Sa~ 179 (199)
T TIGR00101 140 DLLVINKIDLA--PMVGADLGVMERDAKKMRGEKPFIFTNLK 179 (199)
T ss_pred cEEEEEhhhcc--ccccccHHHHHHHHHHhCCCCCEEEEECC
Confidence 47788886532 11123455666666654457788888875
No 266
>COG1920 Predicted nucleotidyltransferase, CobY/MobA/RfbA family [General function prediction only]
Probab=26.33 E-value=1.3e+02 Score=26.03 Aligned_cols=48 Identities=19% Similarity=0.194 Sum_probs=36.0
Q ss_pred EEEec--hhhchhhcC-CCHHHHHHHHHHhCCcchHHHHHHHHHhhcCCeEEeecC
Q psy17313 58 IIPFS--GVFEHQLVD-MPDDERQRYLDEQKATSVLDKIITQGYKSLQLQYFFTAG 110 (197)
Q Consensus 58 vv~~s--a~~E~el~~-l~~ee~~~fl~~~g~~sgl~~li~~~y~lL~LitffT~g 110 (197)
+||++ +..-..|+. |++|||++|...+ |..+|.+.-..++=|++-|..
T Consensus 4 iIPvk~~~~aKTRLs~~lS~eeRe~~~laM-----L~dvi~Al~~~~~~i~Vvtpd 54 (210)
T COG1920 4 IIPVKRLADAKTRLSPVLSAEERENFALAM-----LVDVLGALAGVLGEITVVTPD 54 (210)
T ss_pred EEeccccCcchhccccccCHHHHHHHHHHH-----HHHHHHHhhhhcCCceEEcCC
Confidence 67777 444455665 5899999997764 778888888878888888853
No 267
>cd01882 BMS1 Bms1. Bms1 is an essential, evolutionarily conserved, nucleolar protein. Its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. Bms1, the putative endonuclease Rc11, and the essential U3 small nucleolar RNA form a stable subcomplex that is believed to control an early step in the formation of the 40S subumit. The C-terminal domain of Bms1 contains a GTPase-activating protein (GAP) that functions intramolecularly. It is believed that Rc11 activates Bms1 by acting as a guanine-nucleotide exchange factor (GEF) to promote GDP/GTP exchange, and that activated (GTP-bound) Bms1 delivers Rc11 to the preribosomes.
Probab=26.14 E-value=1.6e+02 Score=24.76 Aligned_cols=45 Identities=16% Similarity=0.111 Sum_probs=23.7
Q ss_pred cCceE-EEEeCCCcccccc-ccccHHHHHH-HHhhcCCCCeEEEechh
Q psy17313 20 AKTQI-YLVNLSAKDYIKK-KNKWLPKIKE-WVDANDPGATIIPFSGV 64 (197)
Q Consensus 20 ~KP~i-yv~Nv~e~d~~~~-~~~~~~~l~~-~~~~~~~~~~vv~~sa~ 64 (197)
.+|.+ .|+|+.|.--... -.+..+.+++ +..+..++.+++++||.
T Consensus 132 g~p~vi~VvnK~D~~~~~~~~~~~~~~l~~~~~~~~~~~~ki~~iSa~ 179 (225)
T cd01882 132 GFPRVMGVLTHLDLFKKNKTLRKTKKRLKHRFWTEVYQGAKLFYLSGI 179 (225)
T ss_pred CCCeEEEEEeccccCCcHHHHHHHHHHHHHHHHHhhCCCCcEEEEeec
Confidence 36754 5999976310000 1123344444 22233346789999986
No 268
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=26.10 E-value=46 Score=23.66 Aligned_cols=19 Identities=16% Similarity=0.314 Sum_probs=9.3
Q ss_pred cCCceeecCCCEEEEEEcc
Q psy17313 169 QGRAYTVEDGDIIFFKFNA 187 (197)
Q Consensus 169 eGkdYivqDGDIi~f~fn~ 187 (197)
...+|.+..||++.|.+-.
T Consensus 7 ~~~~y~l~pGD~l~i~v~~ 25 (82)
T PF02563_consen 7 APPEYRLGPGDVLRISVFG 25 (82)
T ss_dssp HT------TT-EEEEEETT
T ss_pred CCCCCEECCCCEEEEEEec
Confidence 3579999999999998754
No 269
>PRK03003 GTP-binding protein Der; Reviewed
Probab=25.92 E-value=1.5e+02 Score=27.93 Aligned_cols=15 Identities=20% Similarity=0.122 Sum_probs=12.5
Q ss_pred cccCceEEEEeCCCc
Q psy17313 18 LTAKTQIYLVNLSAK 32 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~ 32 (197)
...+|+|+|+|+.|.
T Consensus 144 ~~~~piilV~NK~Dl 158 (472)
T PRK03003 144 RSGKPVILAANKVDD 158 (472)
T ss_pred HcCCCEEEEEECccC
Confidence 356999999999874
No 270
>PRK13290 ectC L-ectoine synthase; Reviewed
Probab=25.91 E-value=35 Score=26.68 Aligned_cols=56 Identities=14% Similarity=0.178 Sum_probs=35.4
Q ss_pred eeeeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCccc-cc-CCceeecCCCEEEEEEccCCC
Q psy17313 114 VKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYR-QQ-GRAYTVEDGDIIFFKFNAGAG 190 (197)
Q Consensus 114 vRAWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r-~e-GkdYivqDGDIi~f~fn~~~~ 190 (197)
++-++++.|++.+. ..|..-+ |++.- +-.|.+. .. |+.|.++.||.++|.-+.+=+
T Consensus 37 ~~~~~l~pG~~~~~---h~h~~~E--~~yVL----------------~G~~~~~~i~~g~~~~L~aGD~i~~~~~~~H~ 94 (125)
T PRK13290 37 FHETTIYAGTETHL---HYKNHLE--AVYCI----------------EGEGEVEDLATGEVHPIRPGTMYALDKHDRHY 94 (125)
T ss_pred EEEEEECCCCcccc---eeCCCEE--EEEEE----------------eCEEEEEEcCCCEEEEeCCCeEEEECCCCcEE
Confidence 35578888876654 2232122 44322 2234455 53 999999999999998887633
No 271
>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=25.75 E-value=1.5e+02 Score=26.14 Aligned_cols=26 Identities=19% Similarity=0.282 Sum_probs=17.0
Q ss_pred ChHHHHHhhcccccccCceEEEEeCCCc
Q psy17313 5 HHLRIEHLNKLNLLTAKTQIYLVNLSAK 32 (197)
Q Consensus 5 ~~~E~~~i~~~~lLT~KP~iyv~Nv~e~ 32 (197)
..+|...++. . +..+|.++|+|+.|.
T Consensus 159 ~~~el~~~~~-~-l~~~~~ivv~NK~Dl 184 (300)
T TIGR00750 159 TGDDLQGIKA-G-LMEIADIYVVNKADG 184 (300)
T ss_pred ccHHHHHHHH-H-HhhhccEEEEEcccc
Confidence 3355544442 2 357999999999864
No 272
>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=25.67 E-value=1.1e+02 Score=24.58 Aligned_cols=44 Identities=14% Similarity=-0.063 Sum_probs=25.6
Q ss_pred ccCceEEEEeCCCcccccc--------ccccHHHHHHHHhhcCCCC-eEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYIKK--------KNKWLPKIKEWVDANDPGA-TIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~--------~~~~~~~l~~~~~~~~~~~-~vv~~sa~ 64 (197)
..-|+++|+|+.|-.-... ..-..++.++++.+. +. .++.+||+
T Consensus 104 ~~~piilvgnK~Dl~~~~~~~~~~~~~~~v~~~~~~~~a~~~--~~~~~~E~SAk 156 (176)
T cd04133 104 PNVPIVLVGTKLDLRDDKQYLADHPGASPITTAQGEELRKQI--GAAAYIECSSK 156 (176)
T ss_pred CCCCEEEEEeChhhccChhhhhhccCCCCCCHHHHHHHHHHc--CCCEEEECCCC
Confidence 3569999999976411000 001344556677665 44 57788876
No 273
>COG0218 Predicted GTPase [General function prediction only]
Probab=25.45 E-value=1.9e+02 Score=24.81 Aligned_cols=49 Identities=22% Similarity=0.236 Sum_probs=26.8
Q ss_pred ccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCe-EEEech
Q psy17313 15 LNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGAT-IIPFSG 63 (197)
Q Consensus 15 ~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~-vv~~sa 63 (197)
+..-+..|+++|+|+.|.=-.+..++.+..+++.+....+..+ ++.+|+
T Consensus 130 ~l~~~~i~~~vv~tK~DKi~~~~~~k~l~~v~~~l~~~~~~~~~~~~~ss 179 (200)
T COG0218 130 FLLELGIPVIVVLTKADKLKKSERNKQLNKVAEELKKPPPDDQWVVLFSS 179 (200)
T ss_pred HHHHcCCCeEEEEEccccCChhHHHHHHHHHHHHhcCCCCccceEEEEec
Confidence 4445678999999998741111123455666654433322222 666663
No 274
>PRK05124 cysN sulfate adenylyltransferase subunit 1; Provisional
Probab=25.32 E-value=1.3e+02 Score=28.59 Aligned_cols=52 Identities=12% Similarity=0.122 Sum_probs=29.9
Q ss_pred cCceEEEEeCCCccccccccccHH----HHHHHHhhc--CCCCeEEEechhhchhhcCCC
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLP----KIKEWVDAN--DPGATIIPFSGVFEHQLVDMP 73 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~----~l~~~~~~~--~~~~~vv~~sa~~E~el~~l~ 73 (197)
.+|+|+++|+.|.. +.....++ ++..+.+.. .+..++||+||.-..-+..++
T Consensus 160 ~~~iIvvvNKiD~~--~~~~~~~~~i~~~l~~~~~~~~~~~~~~iipvSA~~g~ni~~~~ 217 (474)
T PRK05124 160 IKHLVVAVNKMDLV--DYSEEVFERIREDYLTFAEQLPGNLDIRFVPLSALEGDNVVSQS 217 (474)
T ss_pred CCceEEEEEeeccc--cchhHHHHHHHHHHHHHHHhcCCCCCceEEEEEeecCCCccccc
Confidence 47899999997642 11112223 333333321 124689999998776665543
No 275
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=25.00 E-value=47 Score=26.94 Aligned_cols=27 Identities=11% Similarity=0.171 Sum_probs=22.5
Q ss_pred cccccCCceeecCCCEEEEEEccCCCC
Q psy17313 165 KYRQQGRAYTVEDGDIIFFKFNAGAGL 191 (197)
Q Consensus 165 k~r~eGkdYivqDGDIi~f~fn~~~~~ 191 (197)
.+.+.|+.|.++.||.+.|.-+++-..
T Consensus 140 ~~~~~~~~~~l~~Gd~~~~~~~~~H~~ 166 (185)
T PRK09943 140 VLTINGQDYHLVAGQSYAINTGIPHSF 166 (185)
T ss_pred EEEECCEEEEecCCCEEEEcCCCCeee
Confidence 367789999999999999988877543
No 276
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=24.32 E-value=1e+02 Score=24.73 Aligned_cols=32 Identities=16% Similarity=0.195 Sum_probs=25.4
Q ss_pred hcCCCHHHHHHHHHHhC-CcchHHHHHHHHHhh
Q psy17313 69 LVDMPDDERQRYLDEQK-ATSVLDKIITQGYKS 100 (197)
Q Consensus 69 l~~l~~ee~~~fl~~~g-~~sgl~~li~~~y~l 100 (197)
|.+|+++|-++.|..+| .+-...+++++.+.+
T Consensus 96 Llemsd~el~~~l~~~g~~~EE~rRL~~Al~~L 128 (129)
T PF13543_consen 96 LLEMSDEELKEILNRCGAREEECRRLCRALSNL 128 (129)
T ss_pred HHhCCHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence 34678999899999999 666788898887653
No 277
>PRK05306 infB translation initiation factor IF-2; Validated
Probab=24.22 E-value=1.6e+02 Score=30.12 Aligned_cols=45 Identities=13% Similarity=0.083 Sum_probs=23.6
Q ss_pred cCceEEEEeCCCccccccccccHHHHHH---HHhhcCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKE---WVDANDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~---~~~~~~~~~~vv~~sa~~ 65 (197)
..|+|+++|+.|..-.+ .......+.+ +.+..+...+++++||.-
T Consensus 389 ~vPiIVviNKiDl~~a~-~e~V~~eL~~~~~~~e~~g~~vp~vpvSAkt 436 (787)
T PRK05306 389 GVPIIVAINKIDKPGAN-PDRVKQELSEYGLVPEEWGGDTIFVPVSAKT 436 (787)
T ss_pred CCcEEEEEECccccccC-HHHHHHHHHHhcccHHHhCCCceEEEEeCCC
Confidence 47999999998753110 0111222221 112222236799999864
No 278
>PF06241 DUF1012: Protein of unknown function (DUF1012); InterPro: IPR010420 This entry represents the CASTOR/POLLUX/SYM8 family of ion channels, which are found in plants. They have been implicated in modulating the nuclear membrane envelope potential [].
Probab=24.11 E-value=52 Score=28.26 Aligned_cols=51 Identities=24% Similarity=0.314 Sum_probs=41.0
Q ss_pred hhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccC-CceeecCCCEEEEEEccC
Q psy17313 126 PQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQG-RAYTVEDGDIIFFKFNAG 188 (197)
Q Consensus 126 ~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eG-kdYivqDGDIi~f~fn~~ 188 (197)
|+++|.=-.|..++|=-|.|++ ++..||+-..- -||+++.||-+.|..-+.
T Consensus 100 P~L~Gm~y~dvr~~Fpdav~CG------------v~r~GkI~fhP~Dd~vL~e~DklLvIa~~~ 151 (206)
T PF06241_consen 100 PQLDGMKYRDVRRSFPDAVVCG------------VKRDGKIVFHPDDDYVLREGDKLLVIAPVN 151 (206)
T ss_pred cccCCcCHHHHHhcCCcceeee------------eeeCCeeEECCCCCceeecCCEEEEEeecC
Confidence 7888888889999999999987 34568777655 579999999988876553
No 279
>TIGR01663 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase. Note that the EC number for the kinase function is: 2.7.1.78
Probab=24.10 E-value=79 Score=30.77 Aligned_cols=45 Identities=18% Similarity=0.316 Sum_probs=35.7
Q ss_pred ccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEEEc
Q psy17313 133 HTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFN 186 (197)
Q Consensus 133 HsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~fn 186 (197)
--|..+||+...+++-+. +.-.|++-.-|..|.+++||++++..+
T Consensus 57 ~a~~~~~~v~~k~lg~np---------~~~~~~~~~~~~~~~l~~g~~l~~v~~ 101 (526)
T TIGR01663 57 QADLEKATVALKQLGVNP---------CGTGGLELKPGGEGELGHGDLLEIVNG 101 (526)
T ss_pred eecccCceEEEEEccCCC---------cccCceEecCCCeeeecCCCEEEEecc
Confidence 368899999998877665 555677777889999999999987543
No 280
>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=24.06 E-value=1.3e+02 Score=24.36 Aligned_cols=44 Identities=14% Similarity=0.003 Sum_probs=26.0
Q ss_pred ccCceEEEEeCCCcccc----------ccccccHHHHHHHHhhcCCCC-eEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYI----------KKKNKWLPKIKEWVDANDPGA-TIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~----------~~~~~~~~~l~~~~~~~~~~~-~vv~~sa~ 64 (197)
...|+++|+|+.|..-. +...-..++.++++++. +. +++-+||+
T Consensus 108 ~~~piilVgNK~DL~~~~~~~~~~~~~~~~~v~~~~~~~~a~~~--~~~~~~E~SAk 162 (182)
T cd04172 108 PNTKMLLVGCKSDLRTDLTTLVELSNHRQTPVSYDQGANMAKQI--GAATYIECSAL 162 (182)
T ss_pred CCCCEEEEeEChhhhcChhhHHHHHhcCCCCCCHHHHHHHHHHc--CCCEEEECCcC
Confidence 35799999999763210 00011234566777665 43 67777875
No 281
>PF00829 Ribosomal_L21p: Ribosomal prokaryotic L21 protein; InterPro: IPR001787 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 L21 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L21 is known to bind to the 23S rRNA in the presence of L20. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Bacterial L21. Marchantia polymorpha chloroplast L21. Cyanelle L21. Plant chloroplast L21 (nuclear-encoded). Bacterial L21 is a protein of about 100 amino-acid residues, the mature form of the spinach chloroplast L21 has 200 residues.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XG0_V 2X9S_V 2XG2_V 3UZ1_2 2Y19_V 2WDL_V 3V23_V 2WRO_V 2WRL_V 2Y11_V ....
Probab=23.78 E-value=50 Score=24.81 Aligned_cols=19 Identities=37% Similarity=0.679 Sum_probs=16.2
Q ss_pred ccccCCceeecCCCEEEEE
Q psy17313 166 YRQQGRAYTVEDGDIIFFK 184 (197)
Q Consensus 166 ~r~eGkdYivqDGDIi~f~ 184 (197)
++..||.|.|+.||++.+-
T Consensus 5 i~~ggkQykV~~gd~i~v~ 23 (96)
T PF00829_consen 5 IEIGGKQYKVEEGDVIDVE 23 (96)
T ss_dssp EESSSEEEEESSSEEEEEE
T ss_pred EEECCEEEEEeCCCEEEEC
Confidence 4567999999999999875
No 282
>PRK05573 rplU 50S ribosomal protein L21; Validated
Probab=23.03 E-value=60 Score=24.79 Aligned_cols=19 Identities=37% Similarity=0.774 Sum_probs=16.1
Q ss_pred ccccCCceeecCCCEEEEE
Q psy17313 166 YRQQGRAYTVEDGDIIFFK 184 (197)
Q Consensus 166 ~r~eGkdYivqDGDIi~f~ 184 (197)
++.-|+.|.|+.||++.+.
T Consensus 5 i~~gGkQykV~~Gd~i~v~ 23 (103)
T PRK05573 5 IKTGGKQYKVEEGDVIKVE 23 (103)
T ss_pred EEECCEEEEEeCCCEEEEc
Confidence 4567999999999999875
No 283
>PF06249 EutQ: Ethanolamine utilisation protein EutQ; InterPro: IPR010424 The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear [].; PDB: 2PYT_B 3LWC_A.
Probab=22.62 E-value=55 Score=26.86 Aligned_cols=18 Identities=33% Similarity=0.652 Sum_probs=14.8
Q ss_pred ccccCCceeecCCCEEEE
Q psy17313 166 YRQQGRAYTVEDGDIIFF 183 (197)
Q Consensus 166 ~r~eGkdYivqDGDIi~f 183 (197)
++..|+-|.-+.||||+|
T Consensus 108 i~~~G~~~~A~~GDvi~i 125 (152)
T PF06249_consen 108 ISIDGQTVTAKPGDVIFI 125 (152)
T ss_dssp EEETTEEEEEETT-EEEE
T ss_pred EEECCEEEEEcCCcEEEE
Confidence 456799999999999987
No 284
>PF10416 IBD: Transcription-initiator DNA-binding domain IBD; InterPro: IPR018845 In Trichomonas vaginalis, thought to be the earliest extant eukaryote, the sole initiator element for control of the start of transcription is Inr, and this is recognised by the initiator binding protein IBP39. IBP39 contains an N-terminal Inr binding domain (IBD, represented by this entry) connected via a flexible, proteolytically sensitive, linker (residues 127-145) to a C-terminal domain. The IBD structure reveals a winged-helix-wing conformation with each element binding to DNA, the central helix-turn-helix contributing the majority of the specificity-determining contacts with the Inr core motif TCAPy(T/A). The binding of IBP39 to the Inr directly recruits RNA polymerase II and in this way initiates transcription []. ; PDB: 1PP8_O 1PP7_U.
Probab=22.29 E-value=49 Score=25.84 Aligned_cols=20 Identities=20% Similarity=0.635 Sum_probs=13.5
Q ss_pred CeEEeecCCCceeeeEecCC
Q psy17313 103 LQYFFTAGQDEVKAWTIQKG 122 (197)
Q Consensus 103 LitffT~g~~EvRAWti~~G 122 (197)
.+-|+-..+.|.|.||+|.-
T Consensus 107 ~~p~l~~n~~e~rqWtvR~~ 126 (128)
T PF10416_consen 107 FIPFLKGNPSELRQWTVRRK 126 (128)
T ss_dssp ---ECSEECTTBEEEEBTTE
T ss_pred HHHHhccCccccccceEecc
Confidence 33455566789999999864
No 285
>cd00559 Cyanase_C Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the toxicity of environmental cyanate and to use cyanate as a source of nitrogen for growth. This enzyme is a homodecamer, formed by five dimers. Each monomer is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain.
Probab=22.22 E-value=81 Score=22.76 Aligned_cols=17 Identities=29% Similarity=0.436 Sum_probs=15.0
Q ss_pred hhhhhccccccCeeEEE
Q psy17313 128 AAGRIHTDFEKGFIMAE 144 (197)
Q Consensus 128 aAg~IHsDfekgFI~Ae 144 (197)
.-..||..|.+|-+.|.
T Consensus 22 ~K~li~E~FGDGIMSAI 38 (69)
T cd00559 22 LKALIHEKFGDGIMSAI 38 (69)
T ss_pred HHHHHHHHcCCceeeeE
Confidence 34579999999999999
No 286
>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=22.02 E-value=1.1e+02 Score=28.07 Aligned_cols=56 Identities=14% Similarity=0.048 Sum_probs=27.8
Q ss_pred HHhhcccccccCceEEEEeCCCcccccc-ccccHHHHHHHHhhcC---CCCeEEEechhh
Q psy17313 10 EHLNKLNLLTAKTQIYLVNLSAKDYIKK-KNKWLPKIKEWVDAND---PGATIIPFSGVF 65 (197)
Q Consensus 10 ~~i~~~~lLT~KP~iyv~Nv~e~d~~~~-~~~~~~~l~~~~~~~~---~~~~vv~~sa~~ 65 (197)
+.+.-+..+..+++|+++|+.|.--... .+...++++++++..+ .+.+++++||.-
T Consensus 118 e~l~~~~~~gi~~iIvvvNK~Dl~~~~~~~~~~~~~i~~~l~~~~~~~~~~~ii~vSa~~ 177 (394)
T TIGR00485 118 EHILLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSEYDFPGDDTPIIRGSALK 177 (394)
T ss_pred HHHHHHHHcCCCEEEEEEEecccCCHHHHHHHHHHHHHHHHHhcCCCccCccEEECcccc
Confidence 3344333333344557899976310000 0111235666665542 126899999864
No 287
>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=21.89 E-value=1.5e+02 Score=23.66 Aligned_cols=44 Identities=7% Similarity=-0.067 Sum_probs=24.8
Q ss_pred ccCceEEEEeCCCcccc--------cccc--ccHHHHHHHHhhcCCCC-eEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYI--------KKKN--KWLPKIKEWVDANDPGA-TIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~--------~~~~--~~~~~l~~~~~~~~~~~-~vv~~sa~ 64 (197)
..-|+++|+|+.|-.-. .... -..++.++++++. +. +++-+||+
T Consensus 104 ~~~~iilVgnK~DL~~~~~~~~~~~~~~~~~v~~~e~~~~a~~~--~~~~~~E~SA~ 158 (178)
T cd04131 104 PNTKVLLVGCKTDLRTDLSTLMELSHQRQAPVSYEQGCAIAKQL--GAEIYLECSAF 158 (178)
T ss_pred CCCCEEEEEEChhhhcChhHHHHHHhcCCCCCCHHHHHHHHHHh--CCCEEEECccC
Confidence 35799999999763210 0000 1233455677665 43 56777765
No 288
>COG0756 Dut dUTPase [Nucleotide transport and metabolism]
Probab=21.87 E-value=71 Score=26.24 Aligned_cols=45 Identities=24% Similarity=0.561 Sum_probs=33.8
Q ss_pred eeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEE
Q psy17313 116 AWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDII 181 (197)
Q Consensus 116 AWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi 181 (197)
..-.+.|-+.....|.|+||- +|=|+.-+|++.| .++.++.||-|
T Consensus 69 gla~k~Gi~~~Ns~G~IDsDY-rGei~V~l~N~~~--------------------~~f~ie~GdRI 113 (148)
T COG0756 69 GLALKHGITLGNSPGTIDSDY-RGEIKVLLINLGD--------------------EDFVIEKGDRI 113 (148)
T ss_pred cCceeceEEEecCCceECCCC-CceEEEEEEeCCC--------------------CCEEecCCCEE
Confidence 344566777788899999996 5678888777654 67888888854
No 289
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=21.67 E-value=89 Score=21.58 Aligned_cols=19 Identities=32% Similarity=0.247 Sum_probs=15.1
Q ss_pred CceeecCCCEEEEEEccCC
Q psy17313 171 RAYTVEDGDIIFFKFNAGA 189 (197)
Q Consensus 171 kdYivqDGDIi~f~fn~~~ 189 (197)
.++.++|||.|.|.--++.
T Consensus 48 ~~~~L~~gD~iEIv~~VgG 66 (67)
T PRK07696 48 TDTSVFDGDQIEIVTFVGG 66 (67)
T ss_pred CceecCCCCEEEEEEEecC
Confidence 4588999999998776654
No 290
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=21.61 E-value=25 Score=24.83 Aligned_cols=35 Identities=23% Similarity=0.412 Sum_probs=16.9
Q ss_pred hhhhhcCCHHH-HHHcCcccccC-----CceeecCCCEEEE
Q psy17313 149 DDFKEHGSEAA-CRAAGKYRQQG-----RAYTVEDGDIIFF 183 (197)
Q Consensus 149 ~D~~~~g~~~~-ak~~Gk~r~eG-----kdYivqDGDIi~f 183 (197)
.++++-|++++ .=..|.+++.| |.-.+.+||+|.|
T Consensus 17 ~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~ 57 (65)
T PF13275_consen 17 AGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEI 57 (65)
T ss_dssp HTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEE
T ss_pred cCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEE
Confidence 34444555443 22334455555 5566999999987
No 291
>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=21.49 E-value=1.6e+02 Score=25.13 Aligned_cols=44 Identities=7% Similarity=-0.078 Sum_probs=26.6
Q ss_pred ccCceEEEEeCCCcccc--------c--cccccHHHHHHHHhhcCCCC-eEEEechh
Q psy17313 19 TAKTQIYLVNLSAKDYI--------K--KKNKWLPKIKEWVDANDPGA-TIIPFSGV 64 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~--------~--~~~~~~~~l~~~~~~~~~~~-~vv~~sa~ 64 (197)
...|+|+|+|+.|..-. . ...-..++.++++++. +. .++.+||+
T Consensus 116 ~~~piilVgNK~DL~~~~~~~~~l~~~~~~~Vs~~e~~~~a~~~--~~~~~~EtSAk 170 (232)
T cd04174 116 PSTRILLIGCKTDLRTDLSTLMELSNQKQAPISYEQGCALAKQL--GAEVYLECSAF 170 (232)
T ss_pred CCCCEEEEEECcccccccchhhhhccccCCcCCHHHHHHHHHHc--CCCEEEEccCC
Confidence 35799999999874210 0 0011344566788776 45 47777876
No 292
>cd01850 CDC_Septin CDC/Septin. Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities.
Probab=21.46 E-value=1.3e+02 Score=26.22 Aligned_cols=53 Identities=17% Similarity=0.238 Sum_probs=31.5
Q ss_pred hHHHHHhhcccccccCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEec
Q psy17313 6 HLRIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFS 62 (197)
Q Consensus 6 ~~E~~~i~~~~lLT~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~s 62 (197)
+.+.++++.+. ...|+|.|+|+.|.--........+.+.+.+..+ +.++.++.
T Consensus 131 ~~D~~~lk~l~--~~v~vi~VinK~D~l~~~e~~~~k~~i~~~l~~~--~i~~~~~~ 183 (276)
T cd01850 131 PLDIEFMKRLS--KRVNIIPVIAKADTLTPEELKEFKQRIMEDIEEH--NIKIYKFP 183 (276)
T ss_pred HHHHHHHHHHh--ccCCEEEEEECCCcCCHHHHHHHHHHHHHHHHHc--CCceECCC
Confidence 45677777765 3689999999976411000123445566667666 55666554
No 293
>COG0261 RplU Ribosomal protein L21 [Translation, ribosomal structure and biogenesis]
Probab=21.38 E-value=68 Score=24.87 Aligned_cols=19 Identities=37% Similarity=0.774 Sum_probs=15.6
Q ss_pred ccccCCceeecCCCEEEEE
Q psy17313 166 YRQQGRAYTVEDGDIIFFK 184 (197)
Q Consensus 166 ~r~eGkdYivqDGDIi~f~ 184 (197)
+..-||.|.|..||+|.+.
T Consensus 5 i~tGGKQykV~~G~~i~vE 23 (103)
T COG0261 5 IKTGGKQYKVEEGDVIKVE 23 (103)
T ss_pred EEECCEEEEEecCCEEEEE
Confidence 3457999999999998764
No 294
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=21.16 E-value=74 Score=25.82 Aligned_cols=18 Identities=33% Similarity=0.732 Sum_probs=8.3
Q ss_pred hchhhcCCCHHHHHHHHH
Q psy17313 65 FEHQLVDMPDDERQRYLD 82 (197)
Q Consensus 65 ~E~el~~l~~ee~~~fl~ 82 (197)
+|..|..|+++|+++.++
T Consensus 10 L~~~L~~lp~~e~~e~l~ 27 (181)
T PF08006_consen 10 LEKYLKKLPEEEREEILE 27 (181)
T ss_pred HHHHHHcCCHHHHHHHHH
Confidence 333444455555554333
No 295
>PRK07440 hypothetical protein; Provisional
Probab=20.93 E-value=94 Score=21.74 Aligned_cols=19 Identities=21% Similarity=0.212 Sum_probs=15.5
Q ss_pred CceeecCCCEEEEEEccCC
Q psy17313 171 RAYTVEDGDIIFFKFNAGA 189 (197)
Q Consensus 171 kdYivqDGDIi~f~fn~~~ 189 (197)
.++.++|||.|.+..-++.
T Consensus 51 ~~~~L~~gD~IEIv~~v~G 69 (70)
T PRK07440 51 EQTQVQPGDRLEIVTIVGG 69 (70)
T ss_pred CceecCCCCEEEEEEEecC
Confidence 7788999999998766654
No 296
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=20.71 E-value=72 Score=28.31 Aligned_cols=23 Identities=22% Similarity=0.398 Sum_probs=19.4
Q ss_pred HcCcccccC-----CceeecCCCEEEEE
Q psy17313 162 AAGKYRQQG-----RAYTVEDGDIIFFK 184 (197)
Q Consensus 162 ~~Gk~r~eG-----kdYivqDGDIi~f~ 184 (197)
++|++++.| .+|.|+.||+|.+|
T Consensus 214 ~~g~V~vN~~~v~~~s~~v~~gD~isiR 241 (267)
T PLN00051 214 SSGDVRVNWREVTKNGTTLKTGDVVSVS 241 (267)
T ss_pred HcCcEEECCEEcCCCCCCCCCCCEEEEe
Confidence 468888776 46999999999998
No 297
>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=20.68 E-value=1.9e+02 Score=28.41 Aligned_cols=48 Identities=10% Similarity=0.057 Sum_probs=26.7
Q ss_pred ccCceEEEEeCCCccccccccccHHHHHHHHhhcC-----CCCeEEEechhhch
Q psy17313 19 TAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAND-----PGATIIPFSGVFEH 67 (197)
Q Consensus 19 T~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~-----~~~~vv~~sa~~E~ 67 (197)
...|.|+++|+.|..-.+ ....++++.++....+ -..+++++||.-..
T Consensus 115 ~~ip~IVviNKiD~~~a~-~~~v~~ei~~l~~~~g~~~e~l~~pvl~~SA~~g~ 167 (594)
T TIGR01394 115 LGLKPIVVINKIDRPSAR-PDEVVDEVFDLFAELGADDEQLDFPIVYASGRAGW 167 (594)
T ss_pred CCCCEEEEEECCCCCCcC-HHHHHHHHHHHHHhhccccccccCcEEechhhcCc
Confidence 346899999998752111 1123445554442110 13578999987543
No 298
>PRK12317 elongation factor 1-alpha; Reviewed
Probab=20.42 E-value=1.4e+02 Score=27.43 Aligned_cols=53 Identities=13% Similarity=0.121 Sum_probs=29.9
Q ss_pred cCceEEEEeCCCccccccc--cccHHHHHHHHhhcC---CCCeEEEechhhchhhcCC
Q psy17313 20 AKTQIYLVNLSAKDYIKKK--NKWLPKIKEWVDAND---PGATIIPFSGVFEHQLVDM 72 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~--~~~~~~l~~~~~~~~---~~~~vv~~sa~~E~el~~l 72 (197)
.+|+++++|+.|..-.... +...++++++++..+ ...+++|+||.-..-+.++
T Consensus 139 ~~~iivviNK~Dl~~~~~~~~~~~~~~i~~~l~~~g~~~~~~~ii~iSA~~g~gi~~~ 196 (425)
T PRK12317 139 INQLIVAINKMDAVNYDEKRYEEVKEEVSKLLKMVGYKPDDIPFIPVSAFEGDNVVKK 196 (425)
T ss_pred CCeEEEEEEccccccccHHHHHHHHHHHHHHHHhhCCCcCcceEEEeecccCCCcccc
Confidence 3679999999764210000 112345555554332 1257999999876656554
No 299
>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=20.40 E-value=2.6e+02 Score=21.30 Aligned_cols=15 Identities=0% Similarity=-0.190 Sum_probs=12.4
Q ss_pred cccCceEEEEeCCCc
Q psy17313 18 LTAKTQIYLVNLSAK 32 (197)
Q Consensus 18 LT~KP~iyv~Nv~e~ 32 (197)
...+|+++|+|+.|.
T Consensus 102 ~~~~piivv~nK~Dl 116 (174)
T cd04135 102 APNVPYLLVGTQIDL 116 (174)
T ss_pred CCCCCEEEEeEchhh
Confidence 467999999999763
No 300
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=20.39 E-value=97 Score=20.89 Aligned_cols=53 Identities=15% Similarity=0.260 Sum_probs=32.2
Q ss_pred eeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCc----eeecCCCEEEEEEccCC
Q psy17313 116 AWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRA----YTVEDGDIIFFKFNAGA 189 (197)
Q Consensus 116 AWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkd----YivqDGDIi~f~fn~~~ 189 (197)
.+.++.++|..++-...- +....+. ..+. | +...++ +.++|||.|.|.--++.
T Consensus 8 ~~~~~~~~tv~~ll~~l~--~~~~~i~-V~vN----------------g--~~v~~~~~~~~~L~~gD~V~ii~~v~G 64 (65)
T cd00565 8 PREVEEGATLAELLEELG--LDPRGVA-VALN----------------G--EIVPRSEWASTPLQDGDRIEIVTAVGG 64 (65)
T ss_pred EEEcCCCCCHHHHHHHcC--CCCCcEE-EEEC----------------C--EEcCHHHcCceecCCCCEEEEEEeccC
Confidence 456677888887776652 3333332 2121 2 223444 99999999998765553
No 301
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=20.31 E-value=1.2e+02 Score=24.38 Aligned_cols=27 Identities=19% Similarity=0.226 Sum_probs=20.0
Q ss_pred HHcCcccccCC----ceeecCCCEEEEEEcc
Q psy17313 161 RAAGKYRQQGR----AYTVEDGDIIFFKFNA 187 (197)
Q Consensus 161 k~~Gk~r~eGk----dYivqDGDIi~f~fn~ 187 (197)
=.+|++++.|. -..|.+||+|.|+++.
T Consensus 31 I~~G~V~vnG~~~Kps~~V~~gd~l~v~~~~ 61 (133)
T PRK10348 31 IEGGKVHYNGQRSKPSKIVELNATLTLRQGN 61 (133)
T ss_pred HHCCCEEECCEECCCCCccCCCCEEEEEECC
Confidence 34577777764 4678899999998863
No 302
>PRK05433 GTP-binding protein LepA; Provisional
Probab=20.23 E-value=2.1e+02 Score=28.17 Aligned_cols=43 Identities=9% Similarity=0.034 Sum_probs=22.6
Q ss_pred cCceEEEEeCCCccccccccccHHHHHHHHhhcCCCCeEEEechhh
Q psy17313 20 AKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVF 65 (197)
Q Consensus 20 ~KP~iyv~Nv~e~d~~~~~~~~~~~l~~~~~~~~~~~~vv~~sa~~ 65 (197)
..|+|+|+|+.|..-.+ .....+.+.+...-. ...++++||.-
T Consensus 126 ~lpiIvViNKiDl~~a~-~~~v~~ei~~~lg~~--~~~vi~iSAkt 168 (600)
T PRK05433 126 DLEIIPVLNKIDLPAAD-PERVKQEIEDVIGID--ASDAVLVSAKT 168 (600)
T ss_pred CCCEEEEEECCCCCccc-HHHHHHHHHHHhCCC--cceEEEEecCC
Confidence 57999999998742110 011123333332111 13488999864
No 303
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=20.03 E-value=73 Score=21.75 Aligned_cols=56 Identities=13% Similarity=0.089 Sum_probs=32.5
Q ss_pred eeEecCCCChhhhhhhhccccccCeeEEEEecchhhhhcCCHHHHHHcCcccccCCceeecCCCEEEEEEccCC
Q psy17313 116 AWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFNAGA 189 (197)
Q Consensus 116 AWti~~GstA~~aAg~IHsDfekgFI~AeVi~~~D~~~~g~~~~ak~~Gk~r~eGkdYivqDGDIi~f~fn~~~ 189 (197)
...++.++|..++--.. ++....+..++-. ++ +++...+..++|||.|.|-.-|+.
T Consensus 9 ~~~~~~~~tl~~ll~~l--~~~~~~vav~~N~--~i--------------v~r~~~~~~L~~gD~ieIv~~VgG 64 (65)
T PRK05863 9 QVEVDEQTTVAALLDSL--GFPEKGIAVAVDW--SV--------------LPRSDWATKLRDGARLEVVTAVQG 64 (65)
T ss_pred EEEcCCCCcHHHHHHHc--CCCCCcEEEEECC--cC--------------cChhHhhhhcCCCCEEEEEeeccC
Confidence 44556788888777665 3444444444321 11 122223334999999998776654
Done!