Query 027979
Match_columns 216
No_of_seqs 198 out of 1486
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 04:25:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027979.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027979hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0523 Putative GTPases (G3E 100.0 4.6E-48 9.9E-53 334.2 18.6 203 1-215 33-246 (323)
2 KOG2743 Cobalamin synthesis pr 100.0 1.4E-46 3.1E-51 314.2 12.8 203 7-215 109-311 (391)
3 PRK11537 putative GTP-binding 100.0 7.2E-44 1.6E-48 308.7 18.7 198 1-215 36-245 (318)
4 TIGR02475 CobW cobalamin biosy 100.0 5.5E-43 1.2E-47 305.9 17.6 208 1-216 36-274 (341)
5 PF02492 cobW: CobW/HypB/UreG, 100.0 2.1E-32 4.4E-37 219.2 4.6 135 2-149 34-178 (178)
6 cd03112 CobW_like The function 99.9 1.9E-27 4.1E-32 187.1 10.1 111 5-121 40-158 (158)
7 TIGR00101 ureG urease accessor 99.7 9.2E-17 2E-21 130.9 9.8 127 13-161 57-188 (199)
8 PRK10463 hydrogenase nickel in 99.6 7E-15 1.5E-19 125.4 8.9 124 13-161 156-281 (290)
9 TIGR00073 hypB hydrogenase acc 99.5 3.9E-14 8.5E-19 115.8 10.1 114 13-151 74-188 (207)
10 COG0378 HypB Ni2+-binding GTPa 98.9 3.1E-09 6.8E-14 85.3 6.7 115 14-152 67-183 (202)
11 PRK09435 membrane ATPase/prote 98.3 3.8E-06 8.2E-11 73.5 10.3 125 15-162 121-253 (332)
12 COG2403 Predicted GTPase [Gene 98.3 1.9E-06 4.1E-11 75.4 6.4 94 28-150 212-305 (449)
13 cd04163 Era Era subfamily. Er 97.5 0.00022 4.9E-09 54.2 6.2 98 43-151 50-150 (168)
14 PF03308 ArgK: ArgK protein; 97.1 0.001 2.3E-08 56.1 5.7 93 36-152 115-212 (266)
15 COG1703 ArgK Putative periplas 97.0 0.0038 8.3E-08 53.7 8.2 78 41-141 141-218 (323)
16 TIGR00750 lao LAO/AO transport 96.9 0.017 3.6E-07 49.9 11.5 69 36-125 120-188 (300)
17 PRK00089 era GTPase Era; Revie 96.8 0.0044 9.6E-08 53.0 7.3 98 43-151 52-152 (292)
18 cd00881 GTP_translation_factor 96.6 0.0075 1.6E-07 47.2 6.6 85 43-140 61-145 (189)
19 cd03114 ArgK-like The function 96.5 0.028 6E-07 43.5 9.0 65 34-120 83-148 (148)
20 PRK13768 GTPase; Provisional 96.0 0.018 3.8E-07 48.6 5.9 78 41-126 94-179 (253)
21 cd01895 EngA2 EngA2 subfamily. 95.8 0.03 6.6E-07 42.7 6.3 98 43-150 49-155 (174)
22 PRK15494 era GTPase Era; Provi 95.7 0.032 6.8E-07 49.1 6.5 104 45-161 101-208 (339)
23 COG1159 Era GTPase [General fu 95.6 0.049 1.1E-06 46.8 7.3 99 43-152 53-154 (298)
24 cd04167 Snu114p Snu114p subfam 95.4 0.011 2.5E-07 48.1 2.6 94 44-150 71-167 (213)
25 cd00880 Era_like Era (E. coli 95.3 0.049 1.1E-06 40.4 5.6 99 43-151 44-145 (163)
26 TIGR00436 era GTP-binding prot 95.1 0.09 2E-06 44.5 7.2 104 44-161 48-156 (270)
27 cd03115 SRP The signal recogni 94.9 0.2 4.4E-06 39.2 8.4 75 41-125 80-155 (173)
28 TIGR03598 GTPase_YsxC ribosome 94.7 0.093 2E-06 41.3 6.0 97 45-151 65-171 (179)
29 PRK00093 GTP-binding protein D 93.9 0.13 2.8E-06 46.5 5.9 107 44-162 221-337 (435)
30 cd01878 HflX HflX subfamily. 93.8 0.18 3.9E-06 40.4 6.0 76 44-125 89-169 (204)
31 cd01858 NGP_1 NGP-1. Autoanti 93.6 0.19 4.1E-06 38.7 5.6 57 75-143 8-69 (157)
32 TIGR03594 GTPase_EngA ribosome 93.5 0.16 3.4E-06 45.7 5.6 107 45-162 221-337 (429)
33 COG0218 Predicted GTPase [Gene 93.4 0.13 2.9E-06 41.8 4.6 76 46-126 72-152 (200)
34 COG2262 HflX GTPases [General 93.2 0.32 6.9E-06 43.7 6.9 104 44-161 240-348 (411)
35 COG1160 Predicted GTPases [Gen 93.2 0.12 2.6E-06 46.9 4.3 120 24-151 207-332 (444)
36 cd01889 SelB_euk SelB subfamil 93.0 0.45 9.7E-06 37.8 7.1 95 43-151 67-167 (192)
37 PRK14974 cell division protein 93.0 1.1 2.4E-05 39.5 10.0 95 42-154 221-316 (336)
38 cd01884 EF_Tu EF-Tu subfamily. 92.6 0.66 1.4E-05 37.4 7.6 92 44-151 65-164 (195)
39 PF02421 FeoB_N: Ferrous iron 92.6 0.14 3E-06 40.1 3.4 91 44-151 47-142 (156)
40 cd01882 BMS1 Bms1. Bms1 is an 92.5 0.82 1.8E-05 37.7 8.2 93 45-159 84-188 (225)
41 PRK12298 obgE GTPase CgtA; Rev 92.2 0.45 9.7E-06 42.8 6.6 69 46-125 209-291 (390)
42 cd01898 Obg Obg subfamily. Th 92.1 0.75 1.6E-05 35.1 7.1 70 45-125 49-130 (170)
43 cd01894 EngA1 EngA1 subfamily. 92.0 0.7 1.5E-05 34.5 6.7 73 44-125 45-121 (157)
44 cd01857 HSR1_MMR1 HSR1/MMR1. 91.6 0.38 8.2E-06 36.4 4.8 61 75-149 11-76 (141)
45 TIGR03156 GTP_HflX GTP-binding 91.4 0.44 9.5E-06 42.2 5.6 73 44-124 237-316 (351)
46 TIGR00231 small_GTP small GTP- 91.4 1.4 3.1E-05 32.3 7.7 93 44-150 50-144 (161)
47 cd01887 IF2_eIF5B IF2/eIF5B (i 91.2 0.79 1.7E-05 34.9 6.4 69 43-124 49-117 (168)
48 cd04178 Nucleostemin_like Nucl 91.2 0.27 5.9E-06 39.0 3.7 55 77-143 1-60 (172)
49 cd01876 YihA_EngB The YihA (En 91.0 0.83 1.8E-05 34.3 6.2 97 45-150 46-151 (170)
50 cd04160 Arfrp1 Arfrp1 subfamil 90.8 2.1 4.6E-05 32.5 8.4 82 44-140 50-134 (167)
51 TIGR00959 ffh signal recogniti 90.7 3 6.6E-05 38.0 10.4 95 41-153 180-275 (428)
52 PRK01889 GTPase RsgA; Reviewed 90.5 0.54 1.2E-05 41.7 5.4 66 74-151 111-178 (356)
53 PTZ00327 eukaryotic translatio 90.4 0.85 1.8E-05 41.9 6.6 93 45-151 118-214 (460)
54 cd01854 YjeQ_engC YjeQ/EngC. 90.3 0.55 1.2E-05 40.3 5.1 95 18-124 16-124 (287)
55 PRK10867 signal recognition pa 90.1 3.7 8.1E-05 37.5 10.5 74 41-124 181-255 (433)
56 TIGR02729 Obg_CgtA Obg family 89.8 1.1 2.4E-05 39.3 6.6 91 45-151 206-310 (329)
57 PRK12296 obgE GTPase CgtA; Rev 89.7 0.96 2.1E-05 42.0 6.4 43 45-88 207-249 (500)
58 TIGR02528 EutP ethanolamine ut 89.4 1.4 3E-05 32.7 6.2 64 75-150 62-125 (142)
59 PRK09866 hypothetical protein; 89.3 2.3 5.1E-05 40.8 8.7 105 43-162 229-346 (741)
60 TIGR00064 ftsY signal recognit 89.3 5.9 0.00013 33.8 10.6 100 42-160 153-259 (272)
61 cd04145 M_R_Ras_like M-Ras/R-R 89.2 5.3 0.00012 30.0 9.5 88 45-151 51-145 (164)
62 cd04101 RabL4 RabL4 (Rab-like4 89.1 3.9 8.6E-05 30.9 8.7 67 44-125 52-123 (164)
63 cd01860 Rab5_related Rab5-rela 88.9 6.1 0.00013 29.7 9.6 65 76-151 74-144 (163)
64 cd03110 Fer4_NifH_child This p 88.9 5.5 0.00012 31.0 9.5 91 28-141 74-170 (179)
65 cd04105 SR_beta Signal recogni 88.8 2.4 5.1E-05 34.3 7.5 74 44-125 48-125 (203)
66 cd01864 Rab19 Rab19 subfamily. 88.8 5.9 0.00013 30.1 9.5 88 45-150 53-146 (165)
67 PRK12299 obgE GTPase CgtA; Rev 88.7 1.3 2.8E-05 39.0 6.3 69 45-125 207-287 (335)
68 cd01891 TypA_BipA TypA (tyrosi 88.5 2.6 5.6E-05 33.4 7.5 65 44-124 65-132 (194)
69 PF09439 SRPRB: Signal recogni 88.5 1.3 2.8E-05 35.5 5.7 70 44-125 49-128 (181)
70 cd01888 eIF2_gamma eIF2-gamma 88.3 1.7 3.6E-05 35.0 6.3 65 44-125 83-153 (203)
71 KOG0090 Signal recognition par 88.2 0.89 1.9E-05 37.6 4.5 53 68-126 101-162 (238)
72 cd00154 Rab Rab family. Rab G 87.9 7.1 0.00015 28.7 9.3 89 44-151 49-143 (159)
73 cd01881 Obg_like The Obg-like 87.7 1.9 4.1E-05 32.9 6.1 79 44-125 44-136 (176)
74 cd04164 trmE TrmE (MnmE, ThdF, 87.4 0.53 1.2E-05 35.2 2.7 74 44-125 49-123 (157)
75 cd01849 YlqF_related_GTPase Yl 87.4 1.2 2.5E-05 34.3 4.6 40 77-124 1-44 (155)
76 PRK10416 signal recognition pa 87.2 6.8 0.00015 34.2 9.8 97 41-154 194-296 (318)
77 cd04153 Arl5_Arl8 Arl5/Arl8 su 86.8 5.8 0.00013 30.7 8.5 66 44-123 59-130 (174)
78 cd01866 Rab2 Rab2 subfamily. 86.7 10 0.00022 29.0 9.8 66 75-151 76-147 (168)
79 TIGR01007 eps_fam capsular exo 86.7 3.5 7.6E-05 33.0 7.3 64 42-122 126-193 (204)
80 PRK09554 feoB ferrous iron tra 86.7 1.1 2.3E-05 44.0 4.9 72 44-125 50-128 (772)
81 cd04154 Arl2 Arl2 subfamily. 86.7 5.5 0.00012 30.7 8.2 88 45-150 59-155 (173)
82 cd04110 Rab35 Rab35 subfamily. 86.7 11 0.00023 30.0 10.1 98 46-162 57-160 (199)
83 cd01869 Rab1_Ypt1 Rab1/Ypt1 su 86.7 8.5 0.00019 29.2 9.2 96 47-161 54-156 (166)
84 cd04151 Arl1 Arl1 subfamily. 86.2 7.7 0.00017 29.3 8.7 71 43-124 42-115 (158)
85 cd04139 RalA_RalB RalA/RalB su 86.2 10 0.00022 28.4 9.3 99 44-161 48-154 (164)
86 cd04165 GTPBP1_like GTPBP1-lik 86.1 1.1 2.5E-05 36.9 4.2 72 43-125 83-154 (224)
87 PF00009 GTP_EFTU: Elongation 86.0 1.9 4E-05 34.2 5.3 64 44-123 70-136 (188)
88 PRK15467 ethanolamine utilizat 86.0 1.7 3.6E-05 33.6 4.9 74 75-161 64-139 (158)
89 cd04136 Rap_like Rap-like subf 85.5 11 0.00023 28.3 9.2 86 47-151 52-144 (163)
90 cd04114 Rab30 Rab30 subfamily. 85.4 12 0.00027 28.2 9.6 75 76-161 80-161 (169)
91 smart00173 RAS Ras subfamily o 85.4 12 0.00025 28.2 9.4 98 45-161 49-154 (164)
92 KOG0780 Signal recognition par 85.3 2.2 4.9E-05 38.4 5.8 74 41-124 181-255 (483)
93 PRK10512 selenocysteinyl-tRNA- 85.3 1.5 3.2E-05 41.9 5.0 72 74-151 73-147 (614)
94 COG3276 SelB Selenocysteine-sp 85.0 1.8 3.9E-05 39.3 5.1 92 45-152 51-144 (447)
95 cd01886 EF-G Elongation factor 85.0 2.7 5.8E-05 35.8 6.0 69 43-124 63-131 (270)
96 PRK12297 obgE GTPase CgtA; Rev 84.7 2.9 6.2E-05 38.1 6.4 68 45-123 207-288 (424)
97 cd01879 FeoB Ferrous iron tran 84.6 5.5 0.00012 29.7 7.2 66 44-125 43-117 (158)
98 cd01867 Rab8_Rab10_Rab13_like 84.4 15 0.00032 28.0 9.7 87 46-151 54-146 (167)
99 PTZ00099 rab6; Provisional 84.4 10 0.00022 29.8 8.8 101 43-162 28-135 (176)
100 cd04109 Rab28 Rab28 subfamily. 84.1 15 0.00032 29.6 9.9 98 45-161 51-158 (215)
101 cd00882 Ras_like_GTPase Ras-li 84.1 4.9 0.00011 28.8 6.5 98 43-152 44-142 (157)
102 cd04142 RRP22 RRP22 subfamily. 83.7 10 0.00022 30.4 8.7 78 75-162 80-167 (198)
103 PRK00771 signal recognition pa 83.7 3.8 8.2E-05 37.5 6.7 86 29-124 161-247 (437)
104 cd04166 CysN_ATPS CysN_ATPS su 83.5 3.2 6.8E-05 33.5 5.7 68 44-124 77-145 (208)
105 TIGR01425 SRP54_euk signal rec 83.4 4.6 0.0001 36.8 7.1 80 33-124 174-254 (429)
106 PRK11058 GTPase HflX; Provisio 83.3 2.8 6.2E-05 38.1 5.8 72 45-124 246-324 (426)
107 cd04137 RheB Rheb (Ras Homolog 82.9 12 0.00026 28.8 8.7 93 44-151 49-144 (180)
108 smart00178 SAR Sar1p-like memb 82.9 6.8 0.00015 30.7 7.3 80 44-138 61-143 (184)
109 cd00876 Ras Ras family. The R 82.9 17 0.00036 26.9 9.3 87 45-150 48-141 (160)
110 cd01861 Rab6 Rab6 subfamily. 82.5 13 0.00028 27.8 8.5 87 46-151 51-143 (161)
111 cd04158 ARD1 ARD1 subfamily. 82.4 6.9 0.00015 30.1 7.0 81 43-138 42-125 (169)
112 cd00878 Arf_Arl Arf (ADP-ribos 82.3 13 0.00027 27.9 8.4 82 44-140 43-127 (158)
113 cd01856 YlqF YlqF. Proteins o 82.3 2.2 4.7E-05 33.3 4.1 42 75-124 19-61 (171)
114 PRK00049 elongation factor Tu; 82.1 6.2 0.00013 35.4 7.5 92 44-151 75-174 (396)
115 COG1161 Predicted GTPases [Gen 81.8 2.1 4.5E-05 37.4 4.2 64 74-149 33-97 (322)
116 PRK12736 elongation factor Tu; 81.7 4.9 0.00011 36.0 6.7 92 44-151 75-174 (394)
117 cd01890 LepA LepA subfamily. 81.6 19 0.00042 27.5 9.4 66 43-124 66-134 (179)
118 cd04171 SelB SelB subfamily. 81.4 4.2 9.1E-05 30.5 5.4 93 45-151 52-147 (164)
119 cd01883 EF1_alpha Eukaryotic e 81.4 2.9 6.2E-05 34.1 4.7 37 43-87 76-112 (219)
120 PRK00454 engB GTP-binding prot 81.3 5.4 0.00012 31.2 6.2 76 44-125 70-151 (196)
121 PRK04000 translation initiatio 81.2 3.5 7.6E-05 37.2 5.6 94 44-151 85-182 (411)
122 KOG2484 GTPase [General functi 80.9 2.8 6.1E-05 37.7 4.7 64 77-152 148-216 (435)
123 PF00025 Arf: ADP-ribosylation 80.9 5.6 0.00012 31.1 6.1 54 75-138 81-140 (175)
124 cd04161 Arl2l1_Arl13_like Arl2 80.6 9.2 0.0002 29.4 7.2 67 43-124 42-115 (167)
125 TIGR00475 selB selenocysteine- 80.5 3.3 7.2E-05 39.2 5.4 93 45-151 51-147 (581)
126 cd04175 Rap1 Rap1 subgroup. T 80.3 20 0.00044 27.0 9.0 86 47-151 52-144 (164)
127 cd01855 YqeH YqeH. YqeH is an 80.1 4.7 0.0001 31.8 5.5 43 75-125 34-77 (190)
128 cd04122 Rab14 Rab14 subfamily. 79.9 24 0.00052 26.7 9.4 66 75-151 74-145 (166)
129 PTZ00369 Ras-like protein; Pro 79.8 25 0.00054 27.5 9.6 95 48-161 57-159 (189)
130 cd04149 Arf6 Arf6 subfamily. 79.7 14 0.00029 28.5 7.9 37 44-88 53-89 (168)
131 cd04143 Rhes_like Rhes_like su 79.7 27 0.00058 29.2 10.1 47 113-162 117-164 (247)
132 PRK12289 GTPase RsgA; Reviewed 79.7 5.6 0.00012 35.3 6.2 78 74-163 88-169 (352)
133 cd04119 RJL RJL (RabJ-Like) su 79.6 23 0.0005 26.4 9.3 98 45-161 50-159 (168)
134 PRK06731 flhF flagellar biosyn 79.5 26 0.00057 29.8 10.1 115 28-161 140-255 (270)
135 cd04123 Rab21 Rab21 subfamily. 79.4 23 0.00049 26.2 9.2 90 45-150 50-142 (162)
136 PRK05124 cysN sulfate adenylyl 79.4 8.7 0.00019 35.4 7.6 94 43-151 106-206 (474)
137 cd01885 EF2 EF2 (for archaea a 79.3 5.8 0.00013 32.7 5.9 83 43-144 72-163 (222)
138 cd04106 Rab23_lke Rab23-like s 79.1 20 0.00044 26.8 8.6 99 44-161 51-155 (162)
139 cd01863 Rab18 Rab18 subfamily. 79.1 24 0.00052 26.3 9.9 87 45-151 50-143 (161)
140 cd04144 Ras2 Ras2 subfamily. 78.7 23 0.00049 27.8 9.0 97 46-161 49-155 (190)
141 COG0370 FeoB Fe2+ transport sy 78.7 3.1 6.8E-05 39.7 4.5 88 45-150 51-144 (653)
142 PLN03127 Elongation factor Tu; 78.7 4.2 9.2E-05 37.2 5.3 65 45-125 125-193 (447)
143 PRK04213 GTP-binding protein; 78.7 10 0.00022 29.9 7.0 79 45-124 53-145 (201)
144 cd04170 EF-G_bact Elongation f 78.4 5.1 0.00011 33.7 5.4 77 43-141 63-143 (268)
145 cd01892 Miro2 Miro2 subfamily. 78.2 9.8 0.00021 29.3 6.7 43 75-124 77-123 (169)
146 cd04113 Rab4 Rab4 subfamily. 78.0 22 0.00047 26.6 8.5 66 75-151 72-143 (161)
147 smart00175 RAB Rab subfamily o 77.5 27 0.00058 26.0 9.0 66 76-152 73-144 (164)
148 cd04127 Rab27A Rab27a subfamil 77.3 22 0.00048 27.2 8.5 65 76-151 87-158 (180)
149 cd04138 H_N_K_Ras_like H-Ras/N 77.2 27 0.00058 25.8 9.5 94 48-161 53-154 (162)
150 TIGR03596 GTPase_YlqF ribosome 77.1 5.1 0.00011 34.0 5.1 60 55-124 3-63 (276)
151 PRK12735 elongation factor Tu; 76.7 8.9 0.00019 34.4 6.7 91 44-151 75-174 (396)
152 cd04115 Rab33B_Rab33A Rab33B/R 76.6 21 0.00045 27.3 8.1 44 75-125 75-125 (170)
153 cd04168 TetM_like Tet(M)-like 76.3 13 0.00027 30.9 7.1 66 43-124 63-131 (237)
154 cd01859 MJ1464 MJ1464. This f 76.2 4.4 9.6E-05 30.8 4.1 41 76-124 13-56 (156)
155 cd04150 Arf1_5_like Arf1-Arf5- 76.2 30 0.00064 26.2 8.8 37 44-88 44-80 (159)
156 PRK11889 flhF flagellar biosyn 76.1 39 0.00084 30.9 10.4 115 28-161 306-421 (436)
157 PF00919 UPF0004: Uncharacteri 76.0 2.3 5E-05 30.5 2.3 64 80-150 11-75 (98)
158 CHL00071 tufA elongation facto 75.5 6.2 0.00013 35.5 5.4 91 44-150 75-173 (409)
159 cd04108 Rab36_Rab34 Rab34/Rab3 75.5 21 0.00046 27.5 7.9 43 75-124 72-121 (170)
160 cd04141 Rit_Rin_Ric Rit/Rin/Ri 75.4 26 0.00056 27.0 8.4 100 46-161 52-156 (172)
161 COG3640 CooC CO dehydrogenase 75.1 12 0.00026 31.5 6.5 90 14-122 107-198 (255)
162 TIGR00157 ribosome small subun 75.0 8.8 0.00019 32.1 5.9 77 75-162 36-116 (245)
163 PTZ00141 elongation factor 1- 74.2 16 0.00035 33.4 7.8 96 43-151 84-194 (446)
164 PLN03118 Rab family protein; P 74.1 43 0.00093 26.7 10.3 99 45-162 63-170 (211)
165 PRK10218 GTP-binding protein; 73.8 10 0.00022 36.2 6.6 84 43-140 67-150 (607)
166 PRK00098 GTPase RsgA; Reviewed 73.8 7.4 0.00016 33.5 5.3 78 74-162 79-160 (298)
167 TIGR00485 EF-Tu translation el 73.7 6.1 0.00013 35.4 4.9 90 45-151 76-174 (394)
168 TIGR03680 eif2g_arch translati 73.6 6.1 0.00013 35.6 4.9 94 44-151 80-177 (406)
169 TIGR00176 mobB molybdopterin-g 73.5 3.1 6.7E-05 32.3 2.6 50 13-63 58-108 (155)
170 cd04130 Wrch_1 Wrch-1 subfamil 73.4 36 0.00077 26.0 8.7 65 46-124 50-119 (173)
171 cd04146 RERG_RasL11_like RERG/ 73.3 19 0.00041 27.2 7.0 86 46-151 49-144 (165)
172 KOG1424 Predicted GTP-binding 72.7 6.1 0.00013 36.7 4.6 58 76-142 175-234 (562)
173 cd04104 p47_IIGP_like p47 (47- 72.5 16 0.00035 29.0 6.7 71 44-124 52-122 (197)
174 cd01852 AIG1 AIG1 (avrRpt2-ind 72.2 13 0.00028 29.5 6.0 72 44-125 49-132 (196)
175 COG5257 GCD11 Translation init 72.2 2.6 5.7E-05 37.1 2.0 56 106-161 136-194 (415)
176 PLN03126 Elongation factor Tu; 71.8 7.1 0.00015 36.1 4.9 68 75-150 167-242 (478)
177 cd04157 Arl6 Arl6 subfamily. 71.5 27 0.00059 25.9 7.5 69 45-124 46-119 (162)
178 TIGR03594 GTPase_EngA ribosome 71.4 13 0.00029 33.3 6.5 72 45-125 48-123 (429)
179 cd04156 ARLTS1 ARLTS1 subfamil 71.3 27 0.00058 26.0 7.4 70 44-124 44-116 (160)
180 PRK09563 rbgA GTPase YlqF; Rev 71.3 5.1 0.00011 34.2 3.7 60 55-124 6-66 (287)
181 cd04121 Rab40 Rab40 subfamily. 71.3 48 0.001 26.3 9.1 96 47-161 58-159 (189)
182 PF14972 Mito_morph_reg: Mitoc 71.3 4.7 0.0001 31.6 3.1 29 27-57 17-45 (165)
183 TIGR00437 feoB ferrous iron tr 71.1 13 0.00027 35.4 6.5 69 45-125 42-115 (591)
184 cd04111 Rab39 Rab39 subfamily. 71.0 53 0.0011 26.4 9.8 75 76-161 76-158 (211)
185 cd04148 RGK RGK subfamily. Th 70.6 25 0.00053 28.6 7.5 98 44-161 50-155 (221)
186 cd01868 Rab11_like Rab11-like. 70.4 43 0.00093 25.1 9.3 98 45-161 53-157 (165)
187 PRK03003 GTP-binding protein D 69.9 15 0.00034 33.6 6.7 47 113-163 326-376 (472)
188 cd04112 Rab26 Rab26 subfamily. 69.8 39 0.00085 26.4 8.3 75 76-161 74-155 (191)
189 TIGR02034 CysN sulfate adenyly 69.6 8.5 0.00018 34.6 4.9 68 44-124 80-148 (406)
190 cd04107 Rab32_Rab38 Rab38/Rab3 69.6 53 0.0012 25.9 10.8 102 46-161 52-160 (201)
191 PLN03108 Rab family protein; P 69.0 57 0.0012 26.1 9.3 75 76-161 79-160 (210)
192 cd04176 Rap2 Rap2 subgroup. T 68.9 46 0.001 24.9 8.9 62 48-124 53-121 (163)
193 cd01862 Rab7 Rab7 subfamily. 68.9 47 0.001 24.9 9.0 70 76-151 73-148 (172)
194 KOG0461 Selenocysteine-specifi 68.8 17 0.00036 32.6 6.2 95 43-151 69-170 (522)
195 cd04152 Arl4_Arl7 Arl4/Arl7 su 68.8 53 0.0011 25.5 9.0 37 45-89 53-89 (183)
196 TIGR00483 EF-1_alpha translati 68.5 8.6 0.00019 34.7 4.7 99 43-151 84-188 (426)
197 cd00877 Ran Ran (Ras-related n 68.4 45 0.00098 25.4 8.2 65 45-124 50-119 (166)
198 PF01656 CbiA: CobQ/CobB/MinD/ 68.2 53 0.0012 25.3 9.1 74 31-124 84-163 (195)
199 cd04124 RabL2 RabL2 subfamily. 68.0 49 0.0011 24.9 8.7 64 45-123 50-118 (161)
200 cd00879 Sar1 Sar1 subfamily. 67.6 30 0.00065 26.8 7.2 54 76-139 87-146 (190)
201 cd01865 Rab3 Rab3 subfamily. 67.5 51 0.0011 24.8 9.6 88 45-151 51-144 (165)
202 PTZ00416 elongation factor 2; 67.4 4.8 0.0001 39.9 3.0 63 44-122 92-157 (836)
203 PF04670 Gtr1_RagA: Gtr1/RagA 67.1 13 0.00027 31.1 5.0 47 75-127 76-129 (232)
204 cd04162 Arl9_Arfrp2_like Arl9/ 67.0 48 0.0011 25.2 8.1 66 44-124 44-114 (164)
205 cd01897 NOG NOG1 is a nucleola 67.0 32 0.00068 25.9 7.1 43 77-125 81-129 (168)
206 COG0050 TufB GTPases - transla 66.9 3.8 8.3E-05 35.7 1.9 35 103-140 121-156 (394)
207 PRK00093 GTP-binding protein D 66.8 22 0.00048 31.9 7.0 74 44-123 49-123 (435)
208 PRK09518 bifunctional cytidyla 66.7 12 0.00026 36.3 5.5 50 110-163 562-615 (712)
209 PTZ00133 ADP-ribosylation fact 66.6 41 0.00088 26.3 7.7 38 44-89 61-98 (182)
210 PRK12740 elongation factor G; 66.5 15 0.00033 35.2 6.2 77 43-140 59-138 (668)
211 TIGR00484 EF-G translation elo 66.3 18 0.00039 35.0 6.6 70 43-125 74-143 (689)
212 PRK05291 trmE tRNA modificatio 66.0 5.9 0.00013 36.2 3.1 73 45-125 264-337 (449)
213 PRK05703 flhF flagellar biosyn 65.8 51 0.0011 30.0 9.1 111 28-161 288-401 (424)
214 cd04169 RF3 RF3 subfamily. Pe 65.8 20 0.00044 30.3 6.2 66 43-125 70-139 (267)
215 KOG0462 Elongation factor-type 65.6 21 0.00046 33.7 6.5 77 75-161 148-227 (650)
216 PRK13796 GTPase YqeH; Provisio 64.9 20 0.00044 31.8 6.2 41 77-125 71-112 (365)
217 smart00177 ARF ARF-like small 64.8 45 0.00098 25.7 7.7 37 44-88 57-93 (175)
218 PRK00007 elongation factor G; 64.7 11 0.00024 36.4 4.9 70 43-125 74-143 (693)
219 PRK12726 flagellar biosynthesi 64.1 36 0.00078 30.8 7.6 116 25-161 268-386 (407)
220 cd00157 Rho Rho (Ras homology) 64.1 59 0.0013 24.3 8.2 67 45-125 49-120 (171)
221 PF08885 GSCFA: GSCFA family; 63.7 14 0.0003 31.3 4.7 50 103-152 94-175 (251)
222 COG1160 Predicted GTPases [Gen 62.6 22 0.00048 32.5 6.0 76 43-124 50-127 (444)
223 cd04128 Spg1 Spg1p. Spg1p (se 62.5 49 0.0011 25.9 7.5 41 76-123 73-118 (182)
224 PRK14723 flhF flagellar biosyn 62.4 1.1E+02 0.0025 30.1 11.2 103 28-154 252-360 (767)
225 COG0541 Ffh Signal recognition 62.3 32 0.0007 31.5 6.9 73 42-124 181-254 (451)
226 TIGR03597 GTPase_YqeH ribosome 62.1 12 0.00025 33.3 4.1 41 77-125 65-106 (360)
227 PRK12727 flagellar biosynthesi 61.9 1E+02 0.0022 29.2 10.3 101 42-161 427-528 (559)
228 TIGR00503 prfC peptide chain r 61.8 26 0.00057 32.8 6.6 65 43-124 79-147 (527)
229 PLN00116 translation elongatio 61.2 10 0.00022 37.6 4.0 60 75-142 121-186 (843)
230 KOG1954 Endocytosis/signaling 60.6 10 0.00023 34.1 3.5 44 75-125 181-227 (532)
231 PF00448 SRP54: SRP54-type pro 59.2 92 0.002 25.0 10.9 95 41-153 81-176 (196)
232 PLN00043 elongation factor 1-a 58.9 15 0.00033 33.6 4.5 14 74-87 107-120 (447)
233 cd01893 Miro1 Miro1 subfamily. 58.3 78 0.0017 23.9 9.2 68 44-125 47-119 (166)
234 PRK03003 GTP-binding protein D 58.2 30 0.00065 31.7 6.3 70 46-124 88-161 (472)
235 PRK12739 elongation factor G; 57.5 18 0.00039 35.0 4.9 69 44-125 73-141 (691)
236 cd04155 Arl3 Arl3 subfamily. 57.1 26 0.00057 26.5 5.0 14 112-125 118-131 (173)
237 PRK14722 flhF flagellar biosyn 56.8 1.4E+02 0.003 26.8 10.1 111 28-159 204-323 (374)
238 PRK10076 pyruvate formate lyas 56.6 30 0.00065 28.4 5.4 46 16-63 36-86 (213)
239 smart00174 RHO Rho (Ras homolo 56.5 84 0.0018 23.7 8.5 67 44-124 46-117 (174)
240 cd04177 RSR1 RSR1 subgroup. R 56.0 86 0.0019 23.6 9.4 92 45-151 50-145 (168)
241 cd04125 RabA_like RabA-like su 55.8 94 0.002 24.0 9.4 97 46-161 51-154 (188)
242 TIGR01969 minD_arch cell divis 54.7 77 0.0017 25.7 7.7 37 42-88 107-143 (251)
243 cd04116 Rab9 Rab9 subfamily. 54.3 91 0.002 23.4 7.9 35 113-151 118-152 (170)
244 PRK12288 GTPase RsgA; Reviewed 53.8 22 0.00047 31.5 4.4 13 113-125 154-166 (347)
245 PRK05433 GTP-binding protein L 53.7 86 0.0019 29.9 8.7 65 44-124 74-141 (600)
246 PRK09518 bifunctional cytidyla 53.0 34 0.00074 33.2 6.0 71 45-124 324-398 (712)
247 cd04159 Arl10_like Arl10-like 52.9 86 0.0019 22.7 9.3 65 46-125 46-117 (159)
248 smart00053 DYNc Dynamin, GTPas 52.3 53 0.0011 27.5 6.3 73 44-125 125-208 (240)
249 KOG0460 Mitochondrial translat 52.0 19 0.00042 32.1 3.7 34 104-140 164-198 (449)
250 COG2229 Predicted GTPase [Gene 51.8 64 0.0014 26.0 6.3 63 76-150 92-158 (187)
251 KOG0781 Signal recognition par 51.5 39 0.00085 31.5 5.7 99 41-153 464-567 (587)
252 KOG1532 GTPase XAB1, interacts 51.3 1.1E+02 0.0023 26.8 7.9 99 15-125 83-197 (366)
253 PRK05506 bifunctional sulfate 50.8 22 0.00047 34.0 4.2 68 44-124 104-172 (632)
254 COG0552 FtsY Signal recognitio 50.6 64 0.0014 28.6 6.7 79 32-121 212-296 (340)
255 TIGR01394 TypA_BipA GTP-bindin 50.1 38 0.00083 32.2 5.7 64 44-124 64-131 (594)
256 CHL00189 infB translation init 50.0 68 0.0015 31.5 7.4 98 44-162 295-403 (742)
257 PF06858 NOG1: Nucleolar GTP-b 49.5 34 0.00073 22.2 3.6 11 77-87 15-25 (58)
258 TIGR00450 mnmE_trmE_thdF tRNA 49.3 32 0.00069 31.5 4.9 70 46-124 253-325 (442)
259 TIGR00487 IF-2 translation ini 49.2 1.3E+02 0.0028 28.7 9.0 75 45-140 136-213 (587)
260 COG4917 EutP Ethanolamine util 49.0 32 0.00069 26.3 4.0 34 113-151 94-127 (148)
261 PF02606 LpxK: Tetraacyldisacc 48.7 27 0.00059 30.6 4.2 42 80-124 149-192 (326)
262 KOG0458 Elongation factor 1 al 48.6 20 0.00044 33.8 3.5 103 74-178 277-383 (603)
263 KOG0070 GTP-binding ADP-ribosy 48.2 54 0.0012 26.3 5.4 55 75-139 84-144 (181)
264 cd04118 Rab24 Rab24 subfamily. 48.0 1.3E+02 0.0028 23.3 9.3 43 75-124 73-120 (193)
265 PRK13351 elongation factor G; 47.8 53 0.0011 31.7 6.4 66 44-125 73-141 (687)
266 PRK12723 flagellar biosynthesi 47.7 2E+02 0.0043 25.9 9.6 108 28-160 243-355 (388)
267 KOG1489 Predicted GTP-binding 47.6 67 0.0014 28.4 6.3 48 75-124 274-327 (366)
268 PLN00223 ADP-ribosylation fact 46.2 1.3E+02 0.0028 23.4 7.4 54 76-139 85-144 (181)
269 TIGR03029 EpsG chain length de 45.8 1.1E+02 0.0023 25.6 7.3 12 43-54 212-223 (274)
270 cd04117 Rab15 Rab15 subfamily. 45.5 1.3E+02 0.0028 22.6 9.3 66 75-151 72-143 (161)
271 COG1084 Predicted GTPase [Gene 45.3 51 0.0011 29.1 5.3 86 45-140 216-307 (346)
272 COG0486 ThdF Predicted GTPase 45.2 23 0.00051 32.5 3.3 73 44-125 265-340 (454)
273 cd04120 Rab12 Rab12 subfamily. 44.9 1.6E+02 0.0035 23.5 10.1 77 75-161 72-155 (202)
274 PRK12317 elongation factor 1-a 43.7 33 0.00071 30.9 4.1 37 43-87 83-119 (425)
275 COG1162 Predicted GTPases [Gen 43.7 83 0.0018 27.4 6.3 74 45-126 49-127 (301)
276 PF10662 PduV-EutP: Ethanolami 43.0 42 0.0009 25.9 3.9 66 72-150 60-126 (143)
277 COG2895 CysN GTPases - Sulfate 42.7 33 0.00072 30.7 3.7 83 43-141 85-169 (431)
278 TIGR00334 5S_RNA_mat_M5 ribonu 42.0 71 0.0015 25.5 5.2 104 44-166 21-130 (174)
279 cd04140 ARHI_like ARHI subfami 42.0 1.5E+02 0.0032 22.2 8.7 67 46-124 51-123 (165)
280 KOG0466 Translation initiation 40.3 20 0.00043 31.5 2.0 42 111-152 180-223 (466)
281 KOG0073 GTP-binding ADP-ribosy 40.3 57 0.0012 26.0 4.3 47 75-124 83-132 (185)
282 PRK00741 prfC peptide chain re 40.1 79 0.0017 29.7 6.1 65 44-125 79-147 (526)
283 COG1515 Nfi Deoxyinosine 3'end 39.7 29 0.00063 28.6 2.7 20 41-60 93-112 (212)
284 KOG0077 Vesicle coat complex C 39.5 81 0.0018 25.3 5.1 60 73-139 85-147 (193)
285 PF08438 MMR_HSR1_C: GTPase of 38.5 35 0.00076 25.0 2.8 31 115-152 1-31 (109)
286 KOG1490 GTP-binding protein CR 38.5 52 0.0011 30.9 4.4 39 112-151 284-322 (620)
287 PF12503 CMV_1a_C: Cucumber mo 38.5 24 0.00051 24.5 1.7 26 3-28 53-79 (85)
288 cd04132 Rho4_like Rho4-like su 38.4 1.8E+02 0.0039 22.2 8.7 43 76-124 73-120 (187)
289 COG1419 FlhF Flagellar GTP-bin 38.3 3.1E+02 0.0068 25.0 9.5 110 28-162 270-383 (407)
290 PRK05306 infB translation init 38.1 1.4E+02 0.003 29.7 7.5 63 45-124 338-404 (787)
291 PRK14331 (dimethylallyl)adenos 37.6 37 0.00081 30.8 3.5 49 108-161 35-90 (437)
292 cd01874 Cdc42 Cdc42 subfamily. 37.3 1.9E+02 0.0041 22.2 8.6 67 44-124 49-120 (175)
293 COG0621 MiaB 2-methylthioadeni 37.2 35 0.00076 31.3 3.2 65 80-150 14-78 (437)
294 TIGR01393 lepA GTP-binding pro 36.8 1.7E+02 0.0037 27.9 7.8 66 44-124 70-137 (595)
295 CHL00175 minD septum-site dete 36.4 2.5E+02 0.0054 23.4 8.2 37 43-89 126-162 (281)
296 PLN03110 Rab GTPase; Provision 36.3 2.2E+02 0.0049 22.7 9.0 76 76-162 85-167 (216)
297 cd00550 ArsA_ATPase Oxyanion-t 36.3 2.5E+02 0.0054 23.3 11.0 81 34-124 116-204 (254)
298 cd04147 Ras_dva Ras-dva subfam 34.4 2.2E+02 0.0049 22.2 9.5 69 45-124 48-119 (198)
299 TIGR01005 eps_transp_fam exopo 34.2 1.5E+02 0.0033 28.9 7.2 14 42-55 654-667 (754)
300 COG0536 Obg Predicted GTPase [ 33.7 60 0.0013 28.9 3.9 32 110-144 276-307 (369)
301 TIGR03018 pepcterm_TyrKin exop 33.5 2.4E+02 0.0052 22.4 7.3 10 80-89 151-160 (207)
302 PRK14329 (dimethylallyl)adenos 32.3 51 0.0011 30.3 3.4 74 80-163 35-115 (467)
303 COG4026 Uncharacterized protei 32.1 2E+02 0.0043 24.1 6.4 85 46-153 10-97 (290)
304 PRK11519 tyrosine kinase; Prov 32.1 1.8E+02 0.0038 28.4 7.3 14 42-55 634-647 (719)
305 PRK14464 ribosomal RNA large s 31.9 57 0.0012 28.9 3.5 37 19-58 108-154 (344)
306 cd01850 CDC_Septin CDC/Septin. 31.4 33 0.00072 29.1 2.0 67 74-150 113-182 (276)
307 KOG2485 Conserved ATP/GTP bind 31.4 45 0.00097 29.3 2.7 85 44-143 15-103 (335)
308 PRK14337 (dimethylallyl)adenos 31.1 52 0.0011 30.0 3.3 64 80-150 15-80 (446)
309 PRK07560 elongation factor EF- 30.5 1.2E+02 0.0026 29.6 5.9 63 44-123 87-153 (731)
310 TIGR01968 minD_bact septum sit 30.2 2.9E+02 0.0064 22.3 8.5 46 30-88 101-146 (261)
311 PF08123 DOT1: Histone methyla 30.2 74 0.0016 25.9 3.7 39 108-151 120-158 (205)
312 COG5258 GTPBP1 GTPase [General 30.2 52 0.0011 30.0 3.0 37 107-143 253-289 (527)
313 TIGR00313 cobQ cobyric acid sy 29.7 3.2E+02 0.007 25.2 8.3 13 42-54 121-133 (475)
314 KOG0072 GTP-binding ADP-ribosy 29.1 1.6E+02 0.0034 23.2 5.1 48 75-124 85-134 (182)
315 PF00071 Ras: Ras family; Int 29.1 2.3E+02 0.0051 20.8 9.0 90 44-152 48-143 (162)
316 KOG2423 Nucleolar GTPase [Gene 28.9 57 0.0012 29.8 3.0 45 113-161 248-295 (572)
317 PF11823 DUF3343: Protein of u 28.7 82 0.0018 20.8 3.2 35 5-39 25-60 (73)
318 KOG0071 GTP-binding ADP-ribosy 28.5 1.8E+02 0.0038 22.8 5.2 53 77-139 86-144 (180)
319 cd04126 Rab20 Rab20 subfamily. 28.4 3.3E+02 0.007 22.2 9.9 65 44-123 44-114 (220)
320 PF08477 Miro: Miro-like prote 28.3 1.3E+02 0.0028 21.0 4.4 10 108-117 71-80 (119)
321 KOG0094 GTPase Rab6/YPT6/Ryh1, 27.9 90 0.002 25.7 3.7 44 115-162 134-178 (221)
322 PRK03659 glutathione-regulated 27.9 3.9E+02 0.0084 25.4 8.7 113 16-163 398-510 (601)
323 PRK01077 cobyrinic acid a,c-di 27.8 3.4E+02 0.0075 24.7 8.1 45 42-87 80-125 (451)
324 TIGR00347 bioD dethiobiotin sy 27.8 67 0.0014 24.5 3.0 23 29-54 88-110 (166)
325 cd01899 Ygr210 Ygr210 subfamil 27.3 75 0.0016 27.7 3.5 42 113-161 218-260 (318)
326 PRK14340 (dimethylallyl)adenos 26.9 61 0.0013 29.6 3.0 77 80-162 18-97 (445)
327 cd02035 ArsA ArsA ATPase funct 26.4 3.4E+02 0.0074 21.8 8.9 67 43-123 113-184 (217)
328 PLN03071 GTP-binding nuclear p 26.3 2E+02 0.0043 23.2 5.7 65 45-124 63-132 (219)
329 smart00176 RAN Ran (Ras-relate 26.3 2.2E+02 0.0048 22.7 5.9 65 44-123 44-113 (200)
330 PF01926 MMR_HSR1: 50S ribosom 26.0 2E+02 0.0043 20.1 5.1 12 46-57 49-60 (116)
331 PRK14333 (dimethylallyl)adenos 26.0 66 0.0014 29.3 3.1 76 80-161 18-96 (448)
332 cd01169 HMPP_kinase 4-amino-5- 26.0 93 0.002 25.2 3.7 84 28-120 54-138 (242)
333 PRK12724 flagellar biosynthesi 25.6 5.3E+02 0.011 23.7 10.0 102 42-161 298-403 (432)
334 PRK00090 bioD dithiobiotin syn 25.4 72 0.0016 25.6 2.9 16 42-57 102-118 (222)
335 PRK14336 (dimethylallyl)adenos 25.1 74 0.0016 28.8 3.2 72 80-161 13-91 (418)
336 COG1217 TypA Predicted membran 25.1 1.1E+02 0.0025 28.5 4.3 83 44-142 68-152 (603)
337 PRK09841 cryptic autophosphory 25.0 2.9E+02 0.0063 27.0 7.4 13 43-55 640-652 (726)
338 PF01884 PcrB: PcrB family; I 24.8 3.7E+02 0.0079 22.4 7.0 26 33-58 143-169 (230)
339 TIGR01574 miaB-methiolase tRNA 24.8 80 0.0017 28.7 3.3 77 80-161 11-90 (438)
340 PRK10669 putative cation:proto 24.7 5.3E+02 0.011 24.1 8.9 102 16-152 415-516 (558)
341 KOG0076 GTP-binding ADP-ribosy 24.5 1.1E+02 0.0024 24.7 3.6 58 75-139 92-152 (197)
342 COG2213 MtlA Phosphotransferas 24.4 2E+02 0.0044 26.2 5.6 80 74-167 376-460 (472)
343 COG1533 SplB DNA repair photol 24.1 95 0.0021 26.9 3.5 45 17-62 39-99 (297)
344 PF01106 NifU: NifU-like domai 24.1 78 0.0017 20.9 2.4 27 14-40 30-57 (68)
345 PRK14327 (dimethylallyl)adenos 23.9 92 0.002 29.1 3.6 60 80-149 78-143 (509)
346 PRK14339 (dimethylallyl)adenos 23.8 89 0.0019 28.3 3.4 38 108-150 25-66 (420)
347 PRK14338 (dimethylallyl)adenos 23.8 99 0.0021 28.3 3.8 78 77-160 29-109 (459)
348 PF00056 Ldh_1_N: lactate/mala 23.7 2E+02 0.0044 21.6 4.9 46 106-151 65-118 (141)
349 TIGR00490 aEF-2 translation el 23.5 1.9E+02 0.004 28.3 5.7 65 43-124 85-153 (720)
350 PRK14328 (dimethylallyl)adenos 23.4 88 0.0019 28.4 3.3 64 80-149 13-78 (439)
351 PRK05692 hydroxymethylglutaryl 22.4 1.9E+02 0.004 24.8 5.0 23 42-64 167-190 (287)
352 PRK14325 (dimethylallyl)adenos 22.2 89 0.0019 28.4 3.1 77 80-162 15-94 (444)
353 PF04723 GRDA: Glycine reducta 22.1 1.5E+02 0.0033 22.8 3.8 36 13-49 32-71 (150)
354 TIGR02355 moeB molybdopterin s 22.1 1E+02 0.0022 25.7 3.2 81 44-157 25-105 (240)
355 TIGR00682 lpxK tetraacyldisacc 21.7 61 0.0013 28.2 1.9 39 80-121 142-182 (311)
356 KOG2749 mRNA cleavage and poly 21.4 1.4E+02 0.0031 26.9 4.0 78 43-139 211-288 (415)
357 PRK03094 hypothetical protein; 21.3 78 0.0017 21.9 1.9 48 13-64 23-75 (80)
358 PRK11617 endonuclease V; Provi 21.3 82 0.0018 26.2 2.4 20 41-60 95-114 (224)
359 PRK14326 (dimethylallyl)adenos 21.1 1.1E+02 0.0024 28.4 3.6 77 80-162 25-104 (502)
360 TIGR03453 partition_RepA plasm 20.9 4.6E+02 0.0099 23.2 7.4 37 42-88 233-269 (387)
361 cd01873 RhoBTB RhoBTB subfamil 20.8 4.3E+02 0.0092 20.8 7.7 11 113-123 124-134 (195)
362 PRK14845 translation initiatio 20.6 2.2E+02 0.0049 29.2 5.7 64 44-123 526-592 (1049)
363 TIGR03602 streptolysinS bacter 20.4 80 0.0017 19.7 1.6 13 13-25 18-30 (56)
364 cd06559 Endonuclease_V Endonuc 20.2 93 0.002 25.5 2.5 19 42-60 92-110 (208)
No 1
>COG0523 Putative GTPases (G3E family) [General function prediction only]
Probab=100.00 E-value=4.6e-48 Score=334.19 Aligned_cols=203 Identities=38% Similarity=0.624 Sum_probs=172.6
Q ss_pred Cccc----CCCc-eee----eeeeecCCCcEEeecchhHHHHHHHHHHhcCCCCEEEEecCCCCCcHHHHHHhhcCcccc
Q 027979 1 MINE----GEGG-ALV----EEWVELANGCICCTVKHSLVQALEQLVQRKERLDHILLETTGLANPAPLASVLWLDDQLE 71 (216)
Q Consensus 1 ~~ne----g~dg-~~~----~~v~eL~~GCiCCsl~~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~ 71 (216)
+||| |||| .++ ++++||+|||||||+|+|+++++.+|.+++.+||||+|||||+|+|.|++++++.++.+.
T Consensus 33 IVNEfGEvgID~~~~l~~~~e~~~El~nGCICCT~r~dl~~~~~~L~~~~~~~D~ivIEtTGlA~P~pv~~t~~~~~~l~ 112 (323)
T COG0523 33 IVNEFGEVGIDGGALLSDTGEEVVELTNGCICCTVRDDLLPALERLLRRRDRPDRLVIETTGLADPAPVIQTFLTDPELA 112 (323)
T ss_pred EEecCccccccCCCccccCCccEEEeCCceEEEeccchhHHHHHHHHhccCCCCEEEEeCCCCCCCHHHHHHhccccccc
Confidence 4899 8994 666 479999999999999999999999998856779999999999999999999998778899
Q ss_pred cceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 72 SAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 72 ~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
+.++++++||||||.+|...+... ..++.+||++||+|+|||+|+++++ .++++++.++++||.|+|+.++
T Consensus 113 ~~~~ld~vvtvVDa~~~~~~~~~~-----~~~~~~Qia~AD~ivlNK~Dlv~~~----~l~~l~~~l~~lnp~A~i~~~~ 183 (323)
T COG0523 113 DGVRLDGVVTVVDAAHFLEGLDAI-----AELAEDQLAFADVIVLNKTDLVDAE----ELEALEARLRKLNPRARIIETS 183 (323)
T ss_pred cceeeceEEEEEeHHHhhhhHHHH-----HHHHHHHHHhCcEEEEecccCCCHH----HHHHHHHHHHHhCCCCeEEEcc
Confidence 999999999999999999887531 3467899999999999999999986 4799999999999999999999
Q ss_pred cCCCChhhhhccCCCCccchhhhhhhhhhhcc--CCCCCCCCCCEEEEEEEcCCCCCHHHHHHhHc
Q 027979 152 RCQVDLSEVLNCRAYDATHVTRLEGLLEEHQY--KSSQNLHDNNVRTLSICEPLAVNLDKVILQIA 215 (216)
Q Consensus 152 ~~~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~h~~~v~t~~~~~~~p~~~~~~~~~l~ 215 (216)
++.+++..+++...|+..+. ..+...+.. ++.|++|+++++|+++..++|+||++|..||.
T Consensus 184 ~~~~~~~~ll~~~~~~~~~~---~~~~~~~~~~~~h~h~~~~~~i~s~~~~~~~p~~~~~l~~~l~ 246 (323)
T COG0523 184 YGDVDLAELLDEGLFDLDRD---VGRTSPLFSDHQHDHEHDEGGISSFSVRADRPFDPERLEAFLD 246 (323)
T ss_pred ccCCCHHHhhcccccccccc---ccccCccccccCCCchhcccCceEEEEecCCCCCHHHHHHHHH
Confidence 99999999999999986551 111111111 12233333479999999999999999999985
No 2
>KOG2743 consensus Cobalamin synthesis protein [Coenzyme transport and metabolism]
Probab=100.00 E-value=1.4e-46 Score=314.16 Aligned_cols=203 Identities=47% Similarity=0.717 Sum_probs=179.3
Q ss_pred CceeeeeeeecCCCcEEeecchhHHHHHHHHHHhcCCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEccc
Q 027979 7 GGALVEEWVELANGCICCTVKHSLVQALEQLVQRKERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAK 86 (216)
Q Consensus 7 dg~~~~~v~eL~~GCiCCsl~~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~ 86 (216)
.|.+.++.++|+|||+|||++++++.+|.+|.+++++||+|+|||||+|+|+|++++||.+..+...++||+|||||||.
T Consensus 109 gg~lyEewv~L~NGClCCtVk~~gvraie~lvqkkGkfD~IllETTGlAnPaPia~~Fw~dd~l~sdVkLDGIVTvvD~K 188 (391)
T KOG2743|consen 109 GGELYEEWVELRNGCLCCTVKDNGVRAIENLVQKKGKFDHILLETTGLANPAPIASMFWLDDELGSDVKLDGIVTVVDAK 188 (391)
T ss_pred cchHHHHHHHhcCCeEEEEecchHHHHHHHHHhcCCCcceEEEeccCCCCcHHHHHHHhhhhhhcCceeeeeEEEEEehh
Confidence 34455688999999999999999999999999989999999999999999999999999999999999999999999999
Q ss_pred chHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeecCCCChhhhhccCCC
Q 027979 87 NLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQVDLSEVLNCRAY 166 (216)
Q Consensus 87 ~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~~~l~~~~~~ 166 (216)
+.+..++.....+..+|+..||++||.|++||+|+++++ ++.+++++|+.+|.-|+++.|.||++|+..+++.++|
T Consensus 189 ~~~~~Lde~k~~g~i~EA~~QiA~AD~II~NKtDli~~e----~~~~l~q~I~~INslA~m~~Tky~~vdlsnvLdi~ay 264 (391)
T KOG2743|consen 189 HILKHLDEEKPDGLINEATRQIALADRIIMNKTDLVSEE----EVKKLRQRIRSINSLAQMIETKYSRVDLSNVLDIHAF 264 (391)
T ss_pred hHHhhhcccCcccchHHHHHHHhhhheeeeccccccCHH----HHHHHHHHHHHhhhHHHhhhhhhccccHHHhcccccc
Confidence 999999887666667899999999999999999999986 6899999999999999999999999999999999999
Q ss_pred CccchhhhhhhhhhhccCCCCCCCCCCEEEEEEEcCCCCCHHHHHHhHc
Q 027979 167 DATHVTRLEGLLEEHQYKSSQNLHDNNVRTLSICEPLAVNLDKVILQIA 215 (216)
Q Consensus 167 ~~~~~~~~~~~~~~~~~~~~~~~h~~~v~t~~~~~~~p~~~~~~~~~l~ 215 (216)
+......+ .|.. .++.+..+||+.+|.|+.|..+.-++.+.|..||+
T Consensus 265 ds~ss~nl-~~k~-~~~~~~~~h~d~~i~ti~~~~~~~~~~E~~n~wl~ 311 (391)
T KOG2743|consen 265 DSESSINL-DKKL-QHSGGTQIHLDQSIGTITFEVPGLAKEEHLNMWLQ 311 (391)
T ss_pred cccccchh-hhhh-ccCCCCCcccCCCcceEEEEeCCccCHHHHHHHHH
Confidence 97633222 2221 12222334567899999999999999999999986
No 3
>PRK11537 putative GTP-binding protein YjiA; Provisional
Probab=100.00 E-value=7.2e-44 Score=308.68 Aligned_cols=198 Identities=25% Similarity=0.416 Sum_probs=166.0
Q ss_pred Cccc----CCCceee----eeeeecCCCcEEeecchhHHHHHHHHHHh----cCCCCEEEEecCCCCCcHHHHHHhhcCc
Q 027979 1 MINE----GEGGALV----EEWVELANGCICCTVKHSLVQALEQLVQR----KERLDHILLETTGLANPAPLASVLWLDD 68 (216)
Q Consensus 1 ~~ne----g~dg~~~----~~v~eL~~GCiCCsl~~dl~~~L~~l~~~----~~~~d~IiIE~sG~a~P~~i~~~l~~~~ 68 (216)
++|| |+|+.++ .++++|+|||+||+++++|..+|.+++.+ ..+||+|||||||+|+|.+|+++|+.++
T Consensus 36 i~NEfG~v~iD~~ll~~~~~~v~eL~~GCiCCs~~~~l~~~l~~l~~~~~~~~~~~d~IvIEttG~a~p~~i~~~~~~~~ 115 (318)
T PRK11537 36 IENEFGEVSVDDQLIGDRATQIKTLTNGCICCSRSNELEDALLDLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHE 115 (318)
T ss_pred cccCcCCccccHHHHhCcCceEEEECCCEEEEccCchHHHHHHHHHHHHhccCCCCCEEEEECCCccCHHHHHHHHhcCh
Confidence 4788 6777766 36899999999999999999999999853 1369999999999999999999987778
Q ss_pred ccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEE
Q 027979 69 QLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVI 148 (216)
Q Consensus 69 ~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv 148 (216)
.+.+.++++++||||||.++..++++ ++++.+||++||+|||||+|++++ .+++++.|+.+||.|+|+
T Consensus 116 ~l~~~~~l~~vvtvvDa~~~~~~~~~------~~~~~~Qi~~AD~IvlnK~Dl~~~------~~~~~~~l~~lnp~a~i~ 183 (318)
T PRK11537 116 VLCQRYLLDGVIALVDAVHADEQMNQ------FTIAQSQVGYADRILLTKTDVAGE------AEKLRERLARINARAPVY 183 (318)
T ss_pred hhcccEEeccEEEEEEhhhhhhhccc------cHHHHHHHHhCCEEEEeccccCCH------HHHHHHHHHHhCCCCEEE
Confidence 89999999999999999999988754 456789999999999999999985 378999999999999999
Q ss_pred EeecCCCChhhhhccCCCCccchhhhhhhhhhhccCCCCCCCCCCEEEEEEEcCCCCCHHHHHHhHc
Q 027979 149 RSVRCQVDLSEVLNCRAYDATHVTRLEGLLEEHQYKSSQNLHDNNVRTLSICEPLAVNLDKVILQIA 215 (216)
Q Consensus 149 ~~~~~~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~v~t~~~~~~~p~~~~~~~~~l~ 215 (216)
.+.+|++++..+++...|+........ .....++++|+++|+|++|+.++|||+++|..||+
T Consensus 184 ~~~~~~v~~~~l~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~i~s~~~~~~~p~~~~~l~~~L~ 245 (318)
T PRK11537 184 TVVHGDIDLSLLFNTNGFMLEENVVST-----KPRFHFIADKQNDISSIVVELDYPVDISEVSRVME 245 (318)
T ss_pred EeccCCCCHHHHhCCCCcCcccccccc-----CcccccCCcccCceEEEEEEcCCCCCHHHHHHHHH
Confidence 999999999999998777643211000 00011122455789999999999999999999985
No 4
>TIGR02475 CobW cobalamin biosynthesis protein CobW. A broader CobW family is delineated by two PFAM models which identify the N- and C-terminal domains (pfam02492 and pfam07683).
Probab=100.00 E-value=5.5e-43 Score=305.88 Aligned_cols=208 Identities=27% Similarity=0.434 Sum_probs=163.6
Q ss_pred Cccc----CCCceeee----------eeeecCCCcEEeecchhHHHHHHHHHHhcCCCCEEEEecCCCCCcHHHHHHhhc
Q 027979 1 MINE----GEGGALVE----------EWVELANGCICCTVKHSLVQALEQLVQRKERLDHILLETTGLANPAPLASVLWL 66 (216)
Q Consensus 1 ~~ne----g~dg~~~~----------~v~eL~~GCiCCsl~~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~~ 66 (216)
++|| |+|+.++. +++||+||||||++++||..+|.+|+.++.+||+|||||||+|+|.+|+++|+
T Consensus 36 i~Ne~G~~~ID~~ll~~~~~~~~~~~~v~el~nGCiCCs~~~dl~~~l~~l~~~~~~~d~IvIEtsG~a~P~~i~~~~~- 114 (341)
T TIGR02475 36 IVNEFGDLGIDGEILKACGIEGCSEENIVELANGCICCTVADDFIPTMTKLLARRQRPDHILIETSGLALPKPLVQAFQ- 114 (341)
T ss_pred EECCCccccchHHHHhccccccCCcceEEEeCCCCccccCcHHHHHHHHHHHhccCCCCEEEEeCCCCCCHHHHHHHhc-
Confidence 4688 67777662 58999999999999999999999998656789999999999999999999984
Q ss_pred CcccccceeeccEEEEEcccchHHHHhh--------c-------ccCCCh-hHHHHHHhhccEEEEccCCCCCCCCccch
Q 027979 67 DDQLESAVRLDSIITVVDAKNLLFQIDK--------Y-------RHLSSY-PEAIHQIAFADVVILNKVDLVSPERSGDS 130 (216)
Q Consensus 67 ~~~l~~~~~l~~vI~vVDa~~~~~~l~~--------~-------~~~~~~-~~~~~QI~~AD~IvlnK~D~v~~~~~~~~ 130 (216)
.+.+...+++++|||||||.++..+... . ...+.+ ..+.+||++||+|||||+|+++++ +
T Consensus 115 ~~~l~~~~~l~~vvtvVDa~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Qi~~AD~IvlnK~Dl~~~~----~ 190 (341)
T TIGR02475 115 WPEIRSRVTVDGVVTVVDGPAVAAGRFAADPDALDAQRAADDNLDHETPLEELFEDQLACADLVILNKADLLDAA----G 190 (341)
T ss_pred CccccceEEeeeEEEEEECchhhhhccccchhhhhhhccccccccccchHHHHHHHHHHhCCEEEEeccccCCHH----H
Confidence 5788899999999999999988643210 0 000111 245799999999999999999975 5
Q ss_pred HHHHHHHHHhhCCC-CEEEEeecCCCChhhhhccCCCCccchhhhhhhhhhhccCCCCCCCCCCEEEEEEEcCCCCCHHH
Q 027979 131 LDELEKEIHEINSL-AHVIRSVRCQVDLSEVLNCRAYDATHVTRLEGLLEEHQYKSSQNLHDNNVRTLSICEPLAVNLDK 209 (216)
Q Consensus 131 l~~i~~~l~~lNP~-A~iv~~~~~~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~v~t~~~~~~~p~~~~~ 209 (216)
++++++.|+++||. |+|+++.+|++++..+++...++.........+. ....++++|+++|+|++++.++|+|+++
T Consensus 191 l~~~~~~l~~~~~~~a~i~~~~~~~v~~~~ll~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~i~s~~~~~~~p~~~~~ 267 (341)
T TIGR02475 191 LARVRAEIAAELPRAVKIVEASHGEVDARVLLGLGAAAEDDLDNRPSHH---DFEGGEEHDHDEFDSVVVDLGEVADPAA 267 (341)
T ss_pred HHHHHHHHHHhCCCCCEEEEcccCCCCHHHHhCCCCcChhhhhcCcccc---cccCCCCCCCCCEEEEEEEcCCCCCHHH
Confidence 79999999998885 6999999999999999998655432211111111 1011123345789999999999999999
Q ss_pred HHHhHcC
Q 027979 210 VILQIAS 216 (216)
Q Consensus 210 ~~~~l~~ 216 (216)
|..||++
T Consensus 268 ~~~~L~~ 274 (341)
T TIGR02475 268 LRQRLER 274 (341)
T ss_pred HHHHHHh
Confidence 9999964
No 5
>PF02492 cobW: CobW/HypB/UreG, nucleotide-binding domain; InterPro: IPR003495 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents CobW-like proteins, including P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [], and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site [].; PDB: 2WSM_B 1NIJ_A 2HF9_A 2HF8_B.
Probab=99.97 E-value=2.1e-32 Score=219.19 Aligned_cols=135 Identities=47% Similarity=0.739 Sum_probs=107.6
Q ss_pred ccc----CCCceeee----eeeecCCCcEEeecchhHHHHHHHHHHhcC--CCCEEEEecCCCCCcHHHHHHhhcCcccc
Q 027979 2 INE----GEGGALVE----EWVELANGCICCTVKHSLVQALEQLVQRKE--RLDHILLETTGLANPAPLASVLWLDDQLE 71 (216)
Q Consensus 2 ~ne----g~dg~~~~----~v~eL~~GCiCCsl~~dl~~~L~~l~~~~~--~~d~IiIE~sG~a~P~~i~~~l~~~~~l~ 71 (216)
+|| ++|+.++. .+++|+|||+||+++++|..+|.++.. .+ +||+||||+||+++|.++ .+ .++.+.
T Consensus 34 ~ne~g~~~iD~~~l~~~~~~v~~l~~gcicc~~~~~~~~~l~~l~~-~~~~~~d~IiIE~sG~a~p~~l--~~-~~~~~~ 109 (178)
T PF02492_consen 34 VNEFGEVNIDAELLQEDGVPVVELNNGCICCTLRDDLVEALRRLLR-EYEERPDRIIIETSGLADPAPL--IL-QDPPLK 109 (178)
T ss_dssp ECSTTSTHHHHHHHHTTT-EEEEECTTTESS-TTS-HHHHHHHHCC-CCHGC-SEEEEEEECSSGGGGH--HH-HSHHHH
T ss_pred EccccccccchhhhcccceEEEEecCCCcccccHHHHHHHHHHHHH-hcCCCcCEEEECCccccccchh--hh-cccccc
Confidence 677 45566553 589999999999999999999999976 55 899999999999999999 33 377888
Q ss_pred cceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEE
Q 027979 72 SAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIR 149 (216)
Q Consensus 72 ~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~ 149 (216)
..++++++|+||||.+|...... .+.+.+||++||+|+|||+|++++++ .++++++.+|++||+|+|+.
T Consensus 110 ~~~~~~~iI~vVDa~~~~~~~~~------~~~~~~Qi~~ADvIvlnK~D~~~~~~---~i~~~~~~ir~lnp~a~Iv~ 178 (178)
T PF02492_consen 110 EDFRLDSIITVVDATNFDELENI------PELLREQIAFADVIVLNKIDLVSDEQ---KIERVREMIRELNPKAPIVQ 178 (178)
T ss_dssp HHESESEEEEEEEGTTHGGHTTH------CHHHHHHHCT-SEEEEE-GGGHHHH-----HHHHHHHHHHH-TTSEEE-
T ss_pred ccccccceeEEeccccccccccc------hhhhhhcchhcCEEEEeccccCChhh---HHHHHHHHHHHHCCCCEEeC
Confidence 99999999999999999433221 34568999999999999999999862 36999999999999999973
No 6
>cd03112 CobW_like The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K.
Probab=99.95 E-value=1.9e-27 Score=187.05 Aligned_cols=111 Identities=49% Similarity=0.804 Sum_probs=96.3
Q ss_pred CCCceee----eeeeecCCCcEEeecchhHHHHHHHHHH----hcCCCCEEEEecCCCCCcHHHHHHhhcCcccccceee
Q 027979 5 GEGGALV----EEWVELANGCICCTVKHSLVQALEQLVQ----RKERLDHILLETTGLANPAPLASVLWLDDQLESAVRL 76 (216)
Q Consensus 5 g~dg~~~----~~v~eL~~GCiCCsl~~dl~~~L~~l~~----~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l 76 (216)
++|+..+ ..+++|+|||+||+++++|..+|.++++ +..+||+|+|||||+++|.++++.++.++.+...+++
T Consensus 40 ~~d~~~~~~~~~~v~~l~~GCiCC~~~~~l~~~l~~l~~~~~~~~~~~d~I~IEt~G~~~p~~~~~~~~~~~~~~~~~~~ 119 (158)
T cd03112 40 GIDNQLVVDTDEEIIEMNNGCICCTVRGDLIRALLDLLERLDAGKIAFDRIVIETTGLADPGPVAQTFFMDEELAERYLL 119 (158)
T ss_pred chhHHHHhCCCceEEEeCCCEeEeeCchhHHHHHHHHHHHHHhccCCCCEEEEECCCcCCHHHHHHHHhhchhhhcceee
Confidence 3555544 3689999999999999999999965543 3568999999999999999999987667788899999
Q ss_pred ccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCC
Q 027979 77 DSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDL 121 (216)
Q Consensus 77 ~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~ 121 (216)
++++++||+.+|..++++ .+.+.+||++||+||+||+|+
T Consensus 120 d~vv~vvDa~~~~~~~~~------~~~~~~Qi~~ad~ivlnk~dl 158 (158)
T cd03112 120 DGVITLVDAKHANQHLDQ------QTEAQSQIAFADRILLNKTDL 158 (158)
T ss_pred ccEEEEEEhhHhHHHhhc------cHHHHHHHHHCCEEEEecccC
Confidence 999999999999998865 356789999999999999996
No 7
>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=99.69 E-value=9.2e-17 Score=130.87 Aligned_cols=127 Identities=19% Similarity=0.283 Sum_probs=91.9
Q ss_pred eeeec-CCCcEEeecchhHH---HHHHHHHHhcCCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccch
Q 027979 13 EWVEL-ANGCICCTVKHSLV---QALEQLVQRKERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNL 88 (216)
Q Consensus 13 ~v~eL-~~GCiCCsl~~dl~---~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~ 88 (216)
.++.+ .|||.||+.+.++. .+|.++..+..++|+|+||++|.. +...+ ++.+ .+.+|+|+|+.++
T Consensus 57 ~~~~~~~~g~~~~~~~~~~~~~~~~L~~l~~~~~~~D~iiIEt~G~~----l~~~~--~~~l-----~~~~i~vvD~~~~ 125 (199)
T TIGR00101 57 RILGVETGGCPHTAIREDASMNLEAVAEMEARFPPLEMVFIESGGDN----LSATF--SPEL-----ADLTIFVIDVAAG 125 (199)
T ss_pred ceehhhcCCCccceeccCHHHHHHHHHHHHhcCCCCCEEEEECCCCC----ccccc--chhh-----hCcEEEEEEcchh
Confidence 34444 89999999999994 566776544457999999999962 33333 2323 3668999999988
Q ss_pred HHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 89 LFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 89 ~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
..... ....|+.+||++++||+|+.+... ..++.+++.++.+||.++++.++. ....++.++
T Consensus 126 ~~~~~---------~~~~qi~~ad~~~~~k~d~~~~~~--~~~~~~~~~~~~~~~~~~i~~~Sa~~g~gi~el~ 188 (199)
T TIGR00101 126 DKIPR---------KGGPGITRSDLLVINKIDLAPMVG--ADLGVMERDAKKMRGEKPFIFTNLKTKEGLDTVI 188 (199)
T ss_pred hhhhh---------hhHhHhhhccEEEEEhhhcccccc--ccHHHHHHHHHHhCCCCCEEEEECCCCCCHHHHH
Confidence 76432 123799999999999999986311 247889999999999999997653 233344443
No 8
>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional
Probab=99.58 E-value=7e-15 Score=125.40 Aligned_cols=124 Identities=21% Similarity=0.259 Sum_probs=91.1
Q ss_pred eeeecCCCcEEeecchhHHHHHHHHHHhcCCCCEEEEecCCC-CCcHHHHHHhhcCcccccceeeccEEEEEcccchHHH
Q 027979 13 EWVELANGCICCTVKHSLVQALEQLVQRKERLDHILLETTGL-ANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQ 91 (216)
Q Consensus 13 ~v~eL~~GCiCCsl~~dl~~~L~~l~~~~~~~d~IiIE~sG~-a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~ 91 (216)
.++++++||+||..+.++..+|..|.. .+.|++|||++|. +.|..+ .+...++ |+|++...+.+.
T Consensus 156 pvvqi~tG~~Chl~a~mv~~Al~~L~~--~~~d~liIEnvGnLvcPa~f--------dlge~~~----v~vlsV~eg~dk 221 (290)
T PRK10463 156 PAIQVNTGKGCHLDAQMIADAAPRLPL--DDNGILFIENVGNLVCPASF--------DLGEKHK----VAVLSVTEGEDK 221 (290)
T ss_pred cEEEecCCCCCcCcHHHHHHHHHHHhh--cCCcEEEEECCCCccCCCcc--------chhhcee----EEEEECcccccc
Confidence 689999999999999999999999853 4689999999996 678732 2334444 356666555332
Q ss_pred HhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 92 IDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 92 l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
..+ ++ .|++.||+|||||+|+++... ..++++.+.++++||.++|+..+. ....++.|+
T Consensus 222 plK------yp---~~f~~ADIVVLNKiDLl~~~~--~dle~~~~~lr~lnp~a~I~~vSA~tGeGld~L~ 281 (290)
T PRK10463 222 PLK------YP---HMFAAASLMLLNKVDLLPYLN--FDVEKCIACAREVNPEIEIILISATSGEGMDQWL 281 (290)
T ss_pred chh------cc---chhhcCcEEEEEhHHcCcccH--HHHHHHHHHHHhhCCCCcEEEEECCCCCCHHHHH
Confidence 111 33 789999999999999987421 257889999999999999997443 334444444
No 9
>TIGR00073 hypB hydrogenase accessory protein HypB. HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.
Probab=99.54 E-value=3.9e-14 Score=115.83 Aligned_cols=114 Identities=23% Similarity=0.333 Sum_probs=81.9
Q ss_pred eeeecCCCcEEeecchhHHHHHHHHHHhcCCCCEEEEecCC-CCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHH
Q 027979 13 EWVELANGCICCTVKHSLVQALEQLVQRKERLDHILLETTG-LANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQ 91 (216)
Q Consensus 13 ~v~eL~~GCiCCsl~~dl~~~L~~l~~~~~~~d~IiIE~sG-~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~ 91 (216)
+++++++||+||....++..+|.++.. .++|+||||||| +..|... .+...++ ++|+|+......
T Consensus 74 ~~~~l~~gcic~~~~~~~~~~l~~~~~--~~~d~IiIEt~G~l~~~~~~--------~~~~~~~----i~Vvd~~~~d~~ 139 (207)
T TIGR00073 74 PAIQINTGKECHLDAHMVAHALEDLPL--DDIDLLFIENVGNLVCPADF--------DLGEHMR----VVLLSVTEGDDK 139 (207)
T ss_pred cEEEEcCCCcccCChHHHHHHHHHhcc--CCCCEEEEecCCCcCCCccc--------ccccCeE----EEEEecCcccch
Confidence 689999999999877777777776643 368999999999 5544311 1223333 478888765433
Q ss_pred HhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 92 IDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 92 l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
+.. ...++..+++|++||+|+++... ....++.+.++++||.++++.++
T Consensus 140 ~~~---------~~~~~~~a~iiv~NK~Dl~~~~~--~~~~~~~~~l~~~~~~~~i~~~S 188 (207)
T TIGR00073 140 PLK---------YPGMFKEADLIVINKADLAEAVG--FDVEKMKADAKKINPEAEIILMS 188 (207)
T ss_pred hhh---------hHhHHhhCCEEEEEHHHccccch--hhHHHHHHHHHHhCCCCCEEEEE
Confidence 222 12578899999999999986431 13577888899999999998754
No 10
>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]
Probab=98.91 E-value=3.1e-09 Score=85.29 Aligned_cols=115 Identities=27% Similarity=0.375 Sum_probs=81.7
Q ss_pred eeecCCCcEEeecchhHH-HHHHHHHHhcCCCCEEEEecCC-CCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHH
Q 027979 14 WVELANGCICCTVKHSLV-QALEQLVQRKERLDHILLETTG-LANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQ 91 (216)
Q Consensus 14 v~eL~~GCiCCsl~~dl~-~~L~~l~~~~~~~d~IiIE~sG-~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~ 91 (216)
++....|=.| .+...|. .++.+|..+....|.+|||.-| ++-|. +|.+.+.++ |+|+|.....+.
T Consensus 67 i~~v~TG~~C-H~da~m~~~ai~~l~~~~~~~Dll~iEs~GNL~~~~--------sp~L~d~~~----v~VidvteGe~~ 133 (202)
T COG0378 67 IIGVETGKGC-HLDASMNLEAIEELVLDFPDLDLLFIESVGNLVCPF--------SPDLGDHLR----VVVIDVTEGEDI 133 (202)
T ss_pred eEEeccCCcc-CCcHHHHHHHHHHHhhcCCcCCEEEEecCcceeccc--------CcchhhceE----EEEEECCCCCCC
Confidence 3444444333 4665555 6688887643347999999999 66552 566666555 899999876643
Q ss_pred HhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec
Q 027979 92 IDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR 152 (216)
Q Consensus 92 l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~ 152 (216)
-.+ .+|. |-.||++||||+|+++.-+ ..++.+.+..+++||.++|+.++-
T Consensus 134 P~K-----~gP~----i~~aDllVInK~DLa~~v~--~dlevm~~da~~~np~~~ii~~n~ 183 (202)
T COG0378 134 PRK-----GGPG----IFKADLLVINKTDLAPYVG--ADLEVMARDAKEVNPEAPIIFTNL 183 (202)
T ss_pred ccc-----CCCc----eeEeeEEEEehHHhHHHhC--ccHHHHHHHHHHhCCCCCEEEEeC
Confidence 322 1333 3349999999999998764 478999999999999999998653
No 11
>PRK09435 membrane ATPase/protein kinase; Provisional
Probab=98.35 E-value=3.8e-06 Score=73.53 Aligned_cols=125 Identities=14% Similarity=0.116 Sum_probs=71.5
Q ss_pred eecCCCcEEeecch--hHHHHHHHHHHhcCCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHH
Q 027979 15 VELANGCICCTVKH--SLVQALEQLVQRKERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQI 92 (216)
Q Consensus 15 ~eL~~GCiCCsl~~--dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l 92 (216)
+...+| ||.+.+ +.+....+++. ...+|+|||||.|+......+.. .-|-++.|+++....+.
T Consensus 121 ~r~~~~--~~~l~~~a~~~~~~~~~~~-~~g~d~viieT~Gv~qs~~~i~~-----------~aD~vlvv~~p~~gd~i- 185 (332)
T PRK09435 121 IRPSPS--SGTLGGVARKTRETMLLCE-AAGYDVILVETVGVGQSETAVAG-----------MVDFFLLLQLPGAGDEL- 185 (332)
T ss_pred EEecCC--cccccchHHHHHHHHHHHh-ccCCCEEEEECCCCccchhHHHH-----------hCCEEEEEecCCchHHH-
Confidence 333444 888874 45544444444 46799999999999955433211 13345666664433322
Q ss_pred hhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCC-----CEEEEeec-CCCChhhhhc
Q 027979 93 DKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSL-----AHVIRSVR-CQVDLSEVLN 162 (216)
Q Consensus 93 ~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~-----A~iv~~~~-~~v~~~~l~~ 162 (216)
.. .-..+++.||++|+||+|+.+.........++++.++-.+|. .+|+.++- ..-..+.+++
T Consensus 186 q~--------~k~gi~E~aDIiVVNKaDl~~~~~a~~~~~el~~~L~l~~~~~~~w~~pVi~vSA~~g~GIdeL~~ 253 (332)
T PRK09435 186 QG--------IKKGIMELADLIVINKADGDNKTAARRAAAEYRSALRLLRPKDPGWQPPVLTCSALEGEGIDEIWQ 253 (332)
T ss_pred HH--------HHhhhhhhhheEEeehhcccchhHHHHHHHHHHHHHhcccccccCCCCCEEEEECCCCCCHHHHHH
Confidence 11 112589999999999999987542112345556666555543 45664332 2334445443
No 12
>COG2403 Predicted GTPase [General function prediction only]
Probab=98.26 E-value=1.9e-06 Score=75.36 Aligned_cols=94 Identities=31% Similarity=0.336 Sum_probs=73.4
Q ss_pred hhHHHHHHHHHHhcCCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHH
Q 027979 28 HSLVQALEQLVQRKERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQ 107 (216)
Q Consensus 28 ~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~Q 107 (216)
.|+..-|++-.. --|.|+.|-+|-+-| .|+-+..|+||||.+-...+.++. .+ -.
T Consensus 212 vdy~~vlke~~~---~aD~IlwdGgnndfP---------------fvkpd~~Ivvvda~rpg~ei~~~p-----Ge--~~ 266 (449)
T COG2403 212 VDYGTVLKEGEK---EADFILWDGGNNDFP---------------FVKPDLHIVVVDALRPGEEIGSFP-----GE--LR 266 (449)
T ss_pred eeHHHHHHHHhh---hccEEEEeCCCCCCC---------------cccCCeeEEEecCCCCchhhccCC-----Cc--ee
Confidence 456666666432 239999999999755 255667899999998766665532 12 35
Q ss_pred HhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 108 IAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 108 I~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
|+.||+||+||+|.+..+ ..+++++.++++||+|.|+.+
T Consensus 267 irlAD~VIItkveea~~~----kvrkI~~~I~~iNP~A~Vi~~ 305 (449)
T COG2403 267 IRLADLVIITKVEEAMAE----KVRKIVRNIEEINPKAEVILA 305 (449)
T ss_pred eeeccEEEEecccccchH----HHHHHHHHHHhhCCCcEEEec
Confidence 899999999999998875 579999999999999999987
No 13
>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=97.55 E-value=0.00022 Score=54.23 Aligned_cols=98 Identities=19% Similarity=0.277 Sum_probs=61.7
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEccC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNKV 119 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK~ 119 (216)
+.+++++++.|..++................-..+.++.|+|+.....+. .....+++. ...++++||+
T Consensus 50 ~~~~~liDtpG~~~~~~~~~~~~~~~~~~~~~~~d~i~~v~d~~~~~~~~--------~~~~~~~~~~~~~~~iiv~nK~ 121 (168)
T cd04163 50 DAQIIFVDTPGIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASEPIGEG--------DEFILELLKKSKTPVILVLNKI 121 (168)
T ss_pred CeEEEEEECCCCCcchHHHHHHHHHHHHHHHHhCCEEEEEEECCCccCch--------HHHHHHHHHHhCCCEEEEEEch
Confidence 46789999999998876543211111122345567899999998762211 112233343 5788999999
Q ss_pred CCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 120 DLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
|+.... ..+.+..+.++..+|..+++.++
T Consensus 122 Dl~~~~---~~~~~~~~~~~~~~~~~~~~~~s 150 (168)
T cd04163 122 DLVKDK---EDLLPLLEKLKELGPFAEIFPIS 150 (168)
T ss_pred hccccH---HHHHHHHHHHHhccCCCceEEEE
Confidence 998433 24567777777777766776543
No 14
>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.
Probab=97.11 E-value=0.001 Score=56.07 Aligned_cols=93 Identities=18% Similarity=0.306 Sum_probs=48.9
Q ss_pred HHHHhcCCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEE
Q 027979 36 QLVQRKERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVI 115 (216)
Q Consensus 36 ~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~Iv 115 (216)
.+++ ...||+|||||.|++.-.--+..+ .|.++.|+=+..- +.+... =..=++.||++|
T Consensus 115 ~ll~-aaG~D~IiiETVGvGQsE~~I~~~-----------aD~~v~v~~Pg~G-D~iQ~~--------KaGimEiaDi~v 173 (266)
T PF03308_consen 115 RLLD-AAGFDVIIIETVGVGQSEVDIADM-----------ADTVVLVLVPGLG-DEIQAI--------KAGIMEIADIFV 173 (266)
T ss_dssp HHHH-HTT-SEEEEEEESSSTHHHHHHTT-----------SSEEEEEEESSTC-CCCCTB---------TTHHHH-SEEE
T ss_pred HHHH-HcCCCEEEEeCCCCCccHHHHHHh-----------cCeEEEEecCCCc-cHHHHH--------hhhhhhhccEEE
Confidence 3444 467999999999999554222111 2334555444322 222111 013578899999
Q ss_pred EccCCCCCCCCccchHHHHHHHHHhhCC-----CCEEEEeec
Q 027979 116 LNKVDLVSPERSGDSLDELEKEIHEINS-----LAHVIRSVR 152 (216)
Q Consensus 116 lnK~D~v~~~~~~~~l~~i~~~l~~lNP-----~A~iv~~~~ 152 (216)
+||.|+...+ ....+++..+.-..+ .-+|+.++.
T Consensus 174 VNKaD~~gA~---~~~~~l~~~l~l~~~~~~~W~ppV~~tsA 212 (266)
T PF03308_consen 174 VNKADRPGAD---RTVRDLRSMLHLLREREDGWRPPVLKTSA 212 (266)
T ss_dssp EE--SHHHHH---HHHHHHHHHHHHCSTSCTSB--EEEEEBT
T ss_pred EeCCChHHHH---HHHHHHHHHHhhccccccCCCCCEEEEEe
Confidence 9999975543 245666666654443 246776543
No 15
>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]
Probab=97.00 E-value=0.0038 Score=53.67 Aligned_cols=78 Identities=19% Similarity=0.270 Sum_probs=46.1
Q ss_pred cCCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCC
Q 027979 41 KERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVD 120 (216)
Q Consensus 41 ~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D 120 (216)
...||.|||||+|++.-.--+..+ .|.++.|.=+. +-+.+.. .=..-++.||++++||.|
T Consensus 141 AaG~DvIIVETVGvGQsev~I~~~-----------aDt~~~v~~pg-~GD~~Q~--------iK~GimEiaDi~vINKaD 200 (323)
T COG1703 141 AAGYDVIIVETVGVGQSEVDIANM-----------ADTFLVVMIPG-AGDDLQG--------IKAGIMEIADIIVINKAD 200 (323)
T ss_pred hcCCCEEEEEecCCCcchhHHhhh-----------cceEEEEecCC-CCcHHHH--------HHhhhhhhhheeeEeccC
Confidence 457999999999999765332221 12233333332 2222211 112568999999999999
Q ss_pred CCCCCCccchHHHHHHHHHhh
Q 027979 121 LVSPERSGDSLDELEKEIHEI 141 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~l 141 (216)
+-+.+ .....++..++.+
T Consensus 201 ~~~A~---~a~r~l~~al~~~ 218 (323)
T COG1703 201 RKGAE---KAARELRSALDLL 218 (323)
T ss_pred hhhHH---HHHHHHHHHHHhh
Confidence 75543 2445555555544
No 16
>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=96.89 E-value=0.017 Score=49.90 Aligned_cols=69 Identities=19% Similarity=0.234 Sum_probs=40.8
Q ss_pred HHHHhcCCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEE
Q 027979 36 QLVQRKERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVI 115 (216)
Q Consensus 36 ~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~Iv 115 (216)
.++. ...+|+|||||.|++.+.- ..+. ..+.++.+.++... +.+.. + .......+++|+
T Consensus 120 ~~l~-~~g~D~viidT~G~~~~e~--~i~~---------~aD~i~vv~~~~~~-~el~~------~--~~~l~~~~~ivv 178 (300)
T TIGR00750 120 LLLD-AAGYDVIIVETVGVGQSEV--DIAN---------MADTFVVVTIPGTG-DDLQG------I--KAGLMEIADIYV 178 (300)
T ss_pred HHHH-hCCCCEEEEeCCCCchhhh--HHHH---------hhceEEEEecCCcc-HHHHH------H--HHHHhhhccEEE
Confidence 3344 4689999999999985541 1110 12344444444322 22222 1 113467889999
Q ss_pred EccCCCCCCC
Q 027979 116 LNKVDLVSPE 125 (216)
Q Consensus 116 lnK~D~v~~~ 125 (216)
+||+|+.+..
T Consensus 179 ~NK~Dl~~~~ 188 (300)
T TIGR00750 179 VNKADGEGAT 188 (300)
T ss_pred EEcccccchh
Confidence 9999998753
No 17
>PRK00089 era GTPase Era; Reviewed
Probab=96.81 E-value=0.0044 Score=52.97 Aligned_cols=98 Identities=21% Similarity=0.281 Sum_probs=59.5
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEccC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNKV 119 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK~ 119 (216)
....+++.|.|+.+|................-..+.++.|+|+....... ...+.+++. .-.++|+||+
T Consensus 52 ~~qi~~iDTPG~~~~~~~l~~~~~~~~~~~~~~~D~il~vvd~~~~~~~~--------~~~i~~~l~~~~~pvilVlNKi 123 (292)
T PRK00089 52 DAQIIFVDTPGIHKPKRALNRAMNKAAWSSLKDVDLVLFVVDADEKIGPG--------DEFILEKLKKVKTPVILVLNKI 123 (292)
T ss_pred CceEEEEECCCCCCchhHHHHHHHHHHHHHHhcCCEEEEEEeCCCCCChh--------HHHHHHHHhhcCCCEEEEEECC
Confidence 36789999999998864433211111112334678899999998721110 122334443 3578999999
Q ss_pred CCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 120 DLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
|+.... ..+....+.++...+..+++.++
T Consensus 124 Dl~~~~---~~l~~~~~~l~~~~~~~~i~~iS 152 (292)
T PRK00089 124 DLVKDK---EELLPLLEELSELMDFAEIVPIS 152 (292)
T ss_pred cCCCCH---HHHHHHHHHHHhhCCCCeEEEec
Confidence 998432 13455556666666777787644
No 18
>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=96.58 E-value=0.0075 Score=47.16 Aligned_cols=85 Identities=19% Similarity=0.124 Sum_probs=47.7
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLV 122 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v 122 (216)
+.+.++++++|..+........ .-..+.++.|+|+.......... .-....+....-++++||+|+.
T Consensus 61 ~~~~~liDtpG~~~~~~~~~~~--------~~~~d~~i~v~d~~~~~~~~~~~-----~~~~~~~~~~~i~iv~nK~D~~ 127 (189)
T cd00881 61 DRRVNFIDTPGHEDFSSEVIRG--------LSVSDGAILVVDANEGVQPQTRE-----HLRIAREGGLPIIVAINKIDRV 127 (189)
T ss_pred CEEEEEEeCCCcHHHHHHHHHH--------HHhcCEEEEEEECCCCCcHHHHH-----HHHHHHHCCCCeEEEEECCCCc
Confidence 3578999999987654433221 12577899999997543211100 0011223345569999999998
Q ss_pred CCCCccchHHHHHHHHHh
Q 027979 123 SPERSGDSLDELEKEIHE 140 (216)
Q Consensus 123 ~~~~~~~~l~~i~~~l~~ 140 (216)
++++.....+.+++.++.
T Consensus 128 ~~~~~~~~~~~~~~~~~~ 145 (189)
T cd00881 128 GEEDLEEVLREIKELLGL 145 (189)
T ss_pred chhcHHHHHHHHHHHHcc
Confidence 754311123344444443
No 19
>cd03114 ArgK-like The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.
Probab=96.47 E-value=0.028 Score=43.49 Aligned_cols=65 Identities=20% Similarity=0.292 Sum_probs=39.9
Q ss_pred HHHHHHhcCCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHH-HHHHhhcc
Q 027979 34 LEQLVQRKERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEA-IHQIAFAD 112 (216)
Q Consensus 34 L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~-~~QI~~AD 112 (216)
+.++++ ..++|+|||+|.|+. +..+ ..+. .-+.+|.|+.+.-...| +.. ..-.+.||
T Consensus 83 ~~~~~~-~~~~D~iiIDtaG~~-~~~~-~~~~---------~Ad~~ivv~tpe~~D~y----------~~~k~~~~~~~~ 140 (148)
T cd03114 83 VIRVLD-AAGFDVIIVETVGVG-QSEV-DIAS---------MADTTVVVMAPGAGDDI----------QAIKAGIMEIAD 140 (148)
T ss_pred HHHHHH-hcCCCEEEEECCccC-hhhh-hHHH---------hCCEEEEEECCCchhHH----------HHhhhhHhhhcC
Confidence 334444 357999999999986 3222 2221 11235777777633222 221 25678999
Q ss_pred EEEEccCC
Q 027979 113 VVILNKVD 120 (216)
Q Consensus 113 ~IvlnK~D 120 (216)
++++||+|
T Consensus 141 ~~~~~k~~ 148 (148)
T cd03114 141 IVVVNKAD 148 (148)
T ss_pred EEEEeCCC
Confidence 99999997
No 20
>PRK13768 GTPase; Provisional
Probab=95.95 E-value=0.018 Score=48.61 Aligned_cols=78 Identities=21% Similarity=0.246 Sum_probs=44.9
Q ss_pred cCCCCEEEEecCCCCCcHHHH---HHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHH-----HHHhhcc
Q 027979 41 KERLDHILLETTGLANPAPLA---SVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAI-----HQIAFAD 112 (216)
Q Consensus 41 ~~~~d~IiIE~sG~a~P~~i~---~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~-----~QI~~AD 112 (216)
+.+.|+|+|.+.|..+|.... ..+. ..+.... -+.++.|+|+.......+-. ..... .+...-=
T Consensus 94 ~~~~~~~~~d~~g~~~~~~~~~~~~~~~--~~l~~~~-~~~ii~liD~~~~~~~~d~~-----~~~~l~~~~~~~~~~~~ 165 (253)
T PRK13768 94 SLDADYVLVDTPGQMELFAFRESGRKLV--ERLSGSS-KSVVVFLIDAVLAKTPSDFV-----SLLLLALSVQLRLGLPQ 165 (253)
T ss_pred hcCCCEEEEeCCcHHHHHhhhHHHHHHH--HHHHhcC-CeEEEEEechHHhCCHHHHH-----HHHHHHHHHHHHcCCCE
Confidence 345799999999998876431 1111 0111111 56789999997643221110 00001 1334455
Q ss_pred EEEEccCCCCCCCC
Q 027979 113 VVILNKVDLVSPER 126 (216)
Q Consensus 113 ~IvlnK~D~v~~~~ 126 (216)
++++||+|+++..+
T Consensus 166 i~v~nK~D~~~~~~ 179 (253)
T PRK13768 166 IPVLNKADLLSEEE 179 (253)
T ss_pred EEEEEhHhhcCchh
Confidence 88899999998753
No 21
>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=95.81 E-value=0.03 Score=42.73 Aligned_cols=98 Identities=23% Similarity=0.297 Sum_probs=54.0
Q ss_pred CCCEEEEecCCCCCcHHHHHHh---hcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH---hhccEEEE
Q 027979 43 RLDHILLETTGLANPAPLASVL---WLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---AFADVVIL 116 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l---~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~~AD~Ivl 116 (216)
..++.+|.+.|..++...-..+ .....+...-..+.++.|+|+.+...... ..+..++ ...-++++
T Consensus 49 ~~~~~iiDtpG~~~~~~~~~~~e~~~~~~~~~~~~~~d~vi~v~d~~~~~~~~~--------~~~~~~~~~~~~~~iiv~ 120 (174)
T cd01895 49 GKKYTLIDTAGIRRKGKVEEGIEKYSVLRTLKAIERADVVLLVIDATEGITEQD--------LRIAGLILEEGKALVIVV 120 (174)
T ss_pred CeeEEEEECCCCccccchhccHHHHHHHHHHHHHhhcCeEEEEEeCCCCcchhH--------HHHHHHHHhcCCCEEEEE
Confidence 3568899999998764321111 00001111235678999999976533211 1122222 34558889
Q ss_pred ccCCCCCCCCccchHHHHHHHHHhhCC---CCEEEEe
Q 027979 117 NKVDLVSPERSGDSLDELEKEIHEINS---LAHVIRS 150 (216)
Q Consensus 117 nK~D~v~~~~~~~~l~~i~~~l~~lNP---~A~iv~~ 150 (216)
||+|+.+... ...+++.+.+++..+ ..+++.+
T Consensus 121 nK~Dl~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~ 155 (174)
T cd01895 121 NKWDLVEKDS--KTMKEFKKEIRRKLPFLDYAPIVFI 155 (174)
T ss_pred eccccCCccH--HHHHHHHHHHHhhcccccCCceEEE
Confidence 9999987631 135566666665544 3455543
No 22
>PRK15494 era GTPase Era; Provisional
Probab=95.67 E-value=0.032 Score=49.11 Aligned_cols=104 Identities=16% Similarity=0.252 Sum_probs=58.4
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHH---HHhhccEEEEccCCC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIH---QIAFADVVILNKVDL 121 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~---QI~~AD~IvlnK~D~ 121 (216)
..+++.|.|..++..-+............-..+.++.|+|+..-..... ..+.+ +....-++++||+|+
T Consensus 101 qi~~~DTpG~~~~~~~l~~~~~r~~~~~l~~aDvil~VvD~~~s~~~~~--------~~il~~l~~~~~p~IlViNKiDl 172 (339)
T PRK15494 101 QVILYDTPGIFEPKGSLEKAMVRCAWSSLHSADLVLLIIDSLKSFDDIT--------HNILDKLRSLNIVPIFLLNKIDI 172 (339)
T ss_pred EEEEEECCCcCCCcccHHHHHHHHHHHHhhhCCEEEEEEECCCCCCHHH--------HHHHHHHHhcCCCEEEEEEhhcC
Confidence 4578899999766322211000111111235678899999875322111 11222 233456789999999
Q ss_pred CCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 122 VSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 122 v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
.+. .+..+.+.++..++...+++++- ..-..+.++
T Consensus 173 ~~~-----~~~~~~~~l~~~~~~~~i~~iSAktg~gv~eL~ 208 (339)
T PRK15494 173 ESK-----YLNDIKAFLTENHPDSLLFPISALSGKNIDGLL 208 (339)
T ss_pred ccc-----cHHHHHHHHHhcCCCcEEEEEeccCccCHHHHH
Confidence 753 25677777877788788876543 123444444
No 23
>COG1159 Era GTPase [General function prediction only]
Probab=95.65 E-value=0.049 Score=46.79 Aligned_cols=99 Identities=19% Similarity=0.213 Sum_probs=71.2
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh---ccEEEEccC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF---ADVVILNKV 119 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~---AD~IvlnK~ 119 (216)
+...|+|-|.|+-.|..-+.-+.........=.+|-++.|||+..-.... -....+|+.. =.++++||+
T Consensus 53 ~~QiIfvDTPGih~pk~~l~~~m~~~a~~sl~dvDlilfvvd~~~~~~~~--------d~~il~~lk~~~~pvil~iNKI 124 (298)
T COG1159 53 NAQIIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADEGWGPG--------DEFILEQLKKTKTPVILVVNKI 124 (298)
T ss_pred CceEEEEeCCCCCCcchHHHHHHHHHHHHHhccCcEEEEEEeccccCCcc--------HHHHHHHHhhcCCCeEEEEEcc
Confidence 56789999999999976665443333334455688899999998622111 1224577766 478899999
Q ss_pred CCCCCCCccchHHHHHHHHHhhCCCCEEEEeec
Q 027979 120 DLVSPERSGDSLDELEKEIHEINSLAHVIRSVR 152 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~ 152 (216)
|.+..+. .+..+.+.++..-|...+++.+.
T Consensus 125 D~~~~~~---~l~~~~~~~~~~~~f~~ivpiSA 154 (298)
T COG1159 125 DKVKPKT---VLLKLIAFLKKLLPFKEIVPISA 154 (298)
T ss_pred ccCCcHH---HHHHHHHHHHhhCCcceEEEeec
Confidence 9999863 25788888999999999987554
No 24
>cd04167 Snu114p Snu114p subfamily. Snu114p is one of several proteins that make up the U5 small nuclear ribonucleoprotein (snRNP) particle. U5 is a component of the spliceosome, which catalyzes the splicing of pre-mRNA to remove introns. Snu114p is homologous to EF-2, but typically contains an additional N-terminal domain not found in Ef-2. This protein is part of the GTP translation factor family and the Ras superfamily, characterized by five G-box motifs.
Probab=95.41 E-value=0.011 Score=48.09 Aligned_cols=94 Identities=18% Similarity=0.170 Sum_probs=56.9
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVS 123 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~ 123 (216)
....++-|.|..+-..... ......+.+|.|+|+.......... .... ..+-....++++||+|++.
T Consensus 71 ~~i~iiDtpG~~~f~~~~~--------~~~~~aD~~llVvD~~~~~~~~~~~----~~~~-~~~~~~p~iiviNK~D~~~ 137 (213)
T cd04167 71 YLFNIIDTPGHVNFMDEVA--------AALRLSDGVVLVVDVVEGVTSNTER----LIRH-AILEGLPIVLVINKIDRLI 137 (213)
T ss_pred EEEEEEECCCCcchHHHHH--------HHHHhCCEEEEEEECCCCCCHHHHH----HHHH-HHHcCCCEEEEEECcccCc
Confidence 4567889999865432221 1224567899999997654221110 0011 1122367899999999873
Q ss_pred CCC---ccchHHHHHHHHHhhCCCCEEEEe
Q 027979 124 PER---SGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 124 ~~~---~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
.+. ..+..+++.+.++++||.+..+..
T Consensus 138 ~~~~l~~~~~~~~l~~~i~~~n~~~~~~~~ 167 (213)
T cd04167 138 LELKLPPNDAYFKLRHIIDEVNNIIASFST 167 (213)
T ss_pred ccccCCHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 210 012468889999999999877653
No 25
>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=95.26 E-value=0.049 Score=40.40 Aligned_cols=99 Identities=23% Similarity=0.168 Sum_probs=57.7
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLV 122 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v 122 (216)
..+.+++.+.|..++........ .......-..+.++.++|+.......... .-....+....-++++||+|++
T Consensus 44 ~~~~~~~Dt~g~~~~~~~~~~~~-~~~~~~~~~~d~il~v~~~~~~~~~~~~~-----~~~~~~~~~~~~ivv~nK~D~~ 117 (163)
T cd00880 44 LGPVVLIDTPGIDEAGGLGRERE-ELARRVLERADLILFVVDADLRADEEEEK-----LLELLRERGKPVLLVLNKIDLL 117 (163)
T ss_pred CCcEEEEECCCCCccccchhhHH-HHHHHHHHhCCEEEEEEeCCCCCCHHHHH-----HHHHHHhcCCeEEEEEEccccC
Confidence 46889999999987754332100 00001112456789999999765443220 0111234556679999999998
Q ss_pred CCCCccchHHHH---HHHHHhhCCCCEEEEee
Q 027979 123 SPERSGDSLDEL---EKEIHEINSLAHVIRSV 151 (216)
Q Consensus 123 ~~~~~~~~l~~i---~~~l~~lNP~A~iv~~~ 151 (216)
.+.. .... ........+.++++..+
T Consensus 118 ~~~~----~~~~~~~~~~~~~~~~~~~~~~~s 145 (163)
T cd00880 118 PEEE----EEELLELRLLILLLLLGLPVIAVS 145 (163)
T ss_pred Chhh----HHHHHHHHHhhcccccCCceEEEe
Confidence 8653 2332 23445566777777543
No 26
>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=95.07 E-value=0.09 Score=44.52 Aligned_cols=104 Identities=15% Similarity=0.139 Sum_probs=55.0
Q ss_pred CCEEEEecCCCCCcHH-HHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc---EEEEccC
Q 027979 44 LDHILLETTGLANPAP-LASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD---VVILNKV 119 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~-i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD---~IvlnK~ 119 (216)
...+++-|.|+.++.. +.+.+. .......-..+.++.|+|+....... ..+..++...+ ++|+||+
T Consensus 48 ~qii~vDTPG~~~~~~~l~~~~~-~~~~~~l~~aDvvl~VvD~~~~~~~~---------~~i~~~l~~~~~p~ilV~NK~ 117 (270)
T TIGR00436 48 SQIIFIDTPGFHEKKHSLNRLMM-KEARSAIGGVDLILFVVDSDQWNGDG---------EFVLTKLQNLKRPVVLTRNKL 117 (270)
T ss_pred cEEEEEECcCCCCCcchHHHHHH-HHHHHHHhhCCEEEEEEECCCCCchH---------HHHHHHHHhcCCCEEEEEECe
Confidence 3468999999987632 211110 00011123567799999998643211 12345555444 7889999
Q ss_pred CCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 120 DLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
|+++.+ .+......+....+..++++++- .....+.++
T Consensus 118 Dl~~~~----~~~~~~~~~~~~~~~~~v~~iSA~~g~gi~~L~ 156 (270)
T TIGR00436 118 DNKFKD----KLLPLIDKYAILEDFKDIVPISALTGDNTSFLA 156 (270)
T ss_pred eCCCHH----HHHHHHHHHHhhcCCCceEEEecCCCCCHHHHH
Confidence 998643 22223333334444446665433 223444443
No 27
>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.
Probab=94.93 E-value=0.2 Score=39.16 Aligned_cols=75 Identities=23% Similarity=0.271 Sum_probs=47.5
Q ss_pred cCCCCEEEEecCCCCC-cHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccC
Q 027979 41 KERLDHILLETTGLAN-PAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKV 119 (216)
Q Consensus 41 ~~~~d~IiIE~sG~a~-P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~ 119 (216)
...+|+|||.+.|... ..+.+..+. .+......+.++.|+|+..-.+.+.. ...+.++.. .+.+|+||.
T Consensus 80 ~~~~d~viiDt~g~~~~~~~~l~~l~---~l~~~~~~~~~~lVv~~~~~~~~~~~------~~~~~~~~~-~~~viltk~ 149 (173)
T cd03115 80 EENFDVVIVDTAGRLQIDENLMEELK---KIKRVVKPDEVLLVVDAMTGQDAVNQ------AKAFNEALG-ITGVILTKL 149 (173)
T ss_pred hCCCCEEEEECcccchhhHHHHHHHH---HHHhhcCCCeEEEEEECCCChHHHHH------HHHHHhhCC-CCEEEEECC
Confidence 3578999999999862 223333331 12233457889999999755443321 222334444 689999999
Q ss_pred CCCCCC
Q 027979 120 DLVSPE 125 (216)
Q Consensus 120 D~v~~~ 125 (216)
|.....
T Consensus 150 D~~~~~ 155 (173)
T cd03115 150 DGDARG 155 (173)
T ss_pred cCCCCc
Confidence 987754
No 28
>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=94.72 E-value=0.093 Score=41.30 Aligned_cols=97 Identities=15% Similarity=0.254 Sum_probs=50.9
Q ss_pred CEEEEecCCCCCcH-------HHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh---ccEE
Q 027979 45 DHILLETTGLANPA-------PLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF---ADVV 114 (216)
Q Consensus 45 d~IiIE~sG~a~P~-------~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~---AD~I 114 (216)
...++-+.|..... .....+ ...+...-..+.++.|+|+.+-...... .+...+.. -=++
T Consensus 65 ~~~liDtpG~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~~ii~vvd~~~~~~~~~~--------~~~~~~~~~~~pvii 134 (179)
T TIGR03598 65 GFRLVDLPGYGYAKVSKEEKEKWQKLI--EEYLEKRENLKGVVLLMDIRHPLKELDL--------EMLEWLRERGIPVLI 134 (179)
T ss_pred cEEEEeCCCCccccCChhHHHHHHHHH--HHHHHhChhhcEEEEEecCCCCCCHHHH--------HHHHHHHHcCCCEEE
Confidence 56889999976531 111111 1112222345789999999762211111 11222322 2368
Q ss_pred EEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 115 ILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 115 vlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
++||+|+.++++....++++++.++...+..+++.++
T Consensus 135 v~nK~D~~~~~~~~~~~~~i~~~l~~~~~~~~v~~~S 171 (179)
T TIGR03598 135 VLTKADKLKKSELNKQLKKIKKALKKDADDPSVQLFS 171 (179)
T ss_pred EEECcccCCHHHHHHHHHHHHHHHhhccCCCceEEEE
Confidence 8899999875422123455666666554445666543
No 29
>PRK00093 GTP-binding protein Der; Reviewed
Probab=93.93 E-value=0.13 Score=46.45 Aligned_cols=107 Identities=21% Similarity=0.277 Sum_probs=59.4
Q ss_pred CCEEEEecCCCCCcHHHHHHh---hcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH---hhccEEEEc
Q 027979 44 LDHILLETTGLANPAPLASVL---WLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---AFADVVILN 117 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l---~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~~AD~Ivln 117 (216)
.++.++.|.|+..+..+-+.+ .....+...-..+.+|.|+|+..-....+ ..+..++ ...-+|++|
T Consensus 221 ~~~~lvDT~G~~~~~~~~~~~e~~~~~~~~~~~~~ad~~ilViD~~~~~~~~~--------~~i~~~~~~~~~~~ivv~N 292 (435)
T PRK00093 221 QKYTLIDTAGIRRKGKVTEGVEKYSVIRTLKAIERADVVLLVIDATEGITEQD--------LRIAGLALEAGRALVIVVN 292 (435)
T ss_pred eeEEEEECCCCCCCcchhhHHHHHHHHHHHHHHHHCCEEEEEEeCCCCCCHHH--------HHHHHHHHHcCCcEEEEEE
Confidence 467899999987765543211 00001111224578899999985422111 1122333 356789999
Q ss_pred cCCCCCCCCccchHHHHHHHHHhhC---CCCEEEEeec-CCCChhhhhc
Q 027979 118 KVDLVSPERSGDSLDELEKEIHEIN---SLAHVIRSVR-CQVDLSEVLN 162 (216)
Q Consensus 118 K~D~v~~~~~~~~l~~i~~~l~~lN---P~A~iv~~~~-~~v~~~~l~~ 162 (216)
|+|+.+.+ ..+++.+.++... +.++++.++- ....+..+++
T Consensus 293 K~Dl~~~~----~~~~~~~~~~~~l~~~~~~~i~~~SA~~~~gv~~l~~ 337 (435)
T PRK00093 293 KWDLVDEK----TMEEFKKELRRRLPFLDYAPIVFISALTGQGVDKLLE 337 (435)
T ss_pred CccCCCHH----HHHHHHHHHHHhcccccCCCEEEEeCCCCCCHHHHHH
Confidence 99998643 3455665555433 3567775433 2345555554
No 30
>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=93.83 E-value=0.18 Score=40.37 Aligned_cols=76 Identities=25% Similarity=0.463 Sum_probs=44.6
Q ss_pred CCEEEEecCCCCC--cHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc---EEEEcc
Q 027979 44 LDHILLETTGLAN--PAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD---VVILNK 118 (216)
Q Consensus 44 ~d~IiIE~sG~a~--P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD---~IvlnK 118 (216)
..+.+++++|..+ +..+.+.+. . .+......+.++.|+|+......... .....+.+++...+ +||+||
T Consensus 89 ~~~~i~Dt~G~~~~~~~~~~~~~~-~-~~~~~~~~d~ii~v~D~~~~~~~~~~----~~~~~~l~~~~~~~~~viiV~NK 162 (204)
T cd01878 89 REVLLTDTVGFIRDLPHQLVEAFR-S-TLEEVAEADLLLHVVDASDPDYEEQI----ETVEKVLKELGAEDIPMILVLNK 162 (204)
T ss_pred ceEEEeCCCccccCCCHHHHHHHH-H-HHHHHhcCCeEEEEEECCCCChhhHH----HHHHHHHHHcCcCCCCEEEEEEc
Confidence 3678899999853 333333221 1 12223467889999999754322110 00123446666566 899999
Q ss_pred CCCCCCC
Q 027979 119 VDLVSPE 125 (216)
Q Consensus 119 ~D~v~~~ 125 (216)
+|+.+..
T Consensus 163 ~Dl~~~~ 169 (204)
T cd01878 163 IDLLDDE 169 (204)
T ss_pred cccCChH
Confidence 9997753
No 31
>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=93.59 E-value=0.19 Score=38.75 Aligned_cols=57 Identities=21% Similarity=0.180 Sum_probs=32.7
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc-----cEEEEccCCCCCCCCccchHHHHHHHHHhhCC
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA-----DVVILNKVDLVSPERSGDSLDELEKEIHEINS 143 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A-----D~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP 143 (216)
..|-++.|+|+....... ...+.+.+... =++|+||+|+++++ .+....+.+++..+
T Consensus 8 ~aD~il~VvD~~~p~~~~--------~~~i~~~l~~~~~~~p~ilVlNKiDl~~~~----~~~~~~~~~~~~~~ 69 (157)
T cd01858 8 SSDVVIQVLDARDPMGTR--------CKHVEEYLKKEKPHKHLIFVLNKCDLVPTW----VTARWVKILSKEYP 69 (157)
T ss_pred hCCEEEEEEECCCCcccc--------CHHHHHHHHhccCCCCEEEEEEchhcCCHH----HHHHHHHHHhcCCc
Confidence 346789999998643211 12233444432 28899999998753 23444444544443
No 32
>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=93.45 E-value=0.16 Score=45.72 Aligned_cols=107 Identities=22% Similarity=0.300 Sum_probs=58.3
Q ss_pred CEEEEecCCCCCcHHHHHH---hhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH---hhccEEEEcc
Q 027979 45 DHILLETTGLANPAPLASV---LWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---AFADVVILNK 118 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~---l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~~AD~IvlnK 118 (216)
.+.++.|.|+.....+.+. +.....+...-..+.+|.|+|+..-....+. .+..++ ...-+|++||
T Consensus 221 ~~~liDT~G~~~~~~~~~~~e~~~~~~~~~~~~~ad~~ilV~D~~~~~~~~~~--------~~~~~~~~~~~~iiiv~NK 292 (429)
T TIGR03594 221 KYLLIDTAGIRRKGKVTEGVEKYSVLRTLKAIERADVVLLVLDATEGITEQDL--------RIAGLILEAGKALVIVVNK 292 (429)
T ss_pred EEEEEECCCccccccchhhHHHHHHHHHHHHHHhCCEEEEEEECCCCccHHHH--------HHHHHHHHcCCcEEEEEEC
Confidence 5788999998765443211 1000011122345778999999854322111 122222 3567899999
Q ss_pred CCCCCCCCccchHHHHHHHHHhhCC---CCEEEEeec-CCCChhhhhc
Q 027979 119 VDLVSPERSGDSLDELEKEIHEINS---LAHVIRSVR-CQVDLSEVLN 162 (216)
Q Consensus 119 ~D~v~~~~~~~~l~~i~~~l~~lNP---~A~iv~~~~-~~v~~~~l~~ 162 (216)
+|+++.. ...+++++.++...+ .++++.++- ..-.+..++.
T Consensus 293 ~Dl~~~~---~~~~~~~~~~~~~~~~~~~~~vi~~SA~~g~~v~~l~~ 337 (429)
T TIGR03594 293 WDLVKDE---KTREEFKKELRRKLPFLDFAPIVFISALTGQGVDKLLD 337 (429)
T ss_pred cccCCCH---HHHHHHHHHHHHhcccCCCCceEEEeCCCCCCHHHHHH
Confidence 9998322 245666666665543 467775443 2334555543
No 33
>COG0218 Predicted GTPase [General function prediction only]
Probab=93.44 E-value=0.13 Score=41.76 Aligned_cols=76 Identities=17% Similarity=0.315 Sum_probs=52.9
Q ss_pred EEEEecCCCCCcH---HHHHHh--hcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCC
Q 027979 46 HILLETTGLANPA---PLASVL--WLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVD 120 (216)
Q Consensus 46 ~IiIE~sG~a~P~---~i~~~l--~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D 120 (216)
..+|--.|-+--. .+.+.. .....+..+-.|..+|.++|+.+.....+.. +=++..+....=+|++||+|
T Consensus 72 ~~lVDlPGYGyAkv~k~~~e~w~~~i~~YL~~R~~L~~vvlliD~r~~~~~~D~e-----m~~~l~~~~i~~~vv~tK~D 146 (200)
T COG0218 72 LRLVDLPGYGYAKVPKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPPKDLDRE-----MIEFLLELGIPVIVVLTKAD 146 (200)
T ss_pred EEEEeCCCcccccCCHHHHHHHHHHHHHHHhhchhheEEEEEEECCCCCcHHHHH-----HHHHHHHcCCCeEEEEEccc
Confidence 5677777765432 222210 0234677778899999999999998776542 33456788888899999999
Q ss_pred CCCCCC
Q 027979 121 LVSPER 126 (216)
Q Consensus 121 ~v~~~~ 126 (216)
.++..+
T Consensus 147 Ki~~~~ 152 (200)
T COG0218 147 KLKKSE 152 (200)
T ss_pred cCChhH
Confidence 999754
No 34
>COG2262 HflX GTPases [General function prediction only]
Probab=93.22 E-value=0.32 Score=43.66 Aligned_cols=104 Identities=24% Similarity=0.387 Sum_probs=65.3
Q ss_pred CCEEEEecCCCCC--cHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc---EEEEcc
Q 027979 44 LDHILLETTGLAN--PAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD---VVILNK 118 (216)
Q Consensus 44 ~d~IiIE~sG~a~--P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD---~IvlnK 118 (216)
...++-.|.|.-. |-.++++|. ..|.+-..-|-++.|||++.-. ..... ........+|...+ ++++||
T Consensus 240 ~~vlLtDTVGFI~~LP~~LV~AFk--sTLEE~~~aDlllhVVDaSdp~-~~~~~---~~v~~vL~el~~~~~p~i~v~NK 313 (411)
T COG2262 240 RKVLLTDTVGFIRDLPHPLVEAFK--STLEEVKEADLLLHVVDASDPE-ILEKL---EAVEDVLAEIGADEIPIILVLNK 313 (411)
T ss_pred ceEEEecCccCcccCChHHHHHHH--HHHHHhhcCCEEEEEeecCChh-HHHHH---HHHHHHHHHcCCCCCCEEEEEec
Confidence 3477778888754 778888874 3567778889999999999752 22111 01233457776666 788999
Q ss_pred CCCCCCCCccchHHHHHHHHHhhCCCCEEEEeecCCCChhhhh
Q 027979 119 VDLVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQVDLSEVL 161 (216)
Q Consensus 119 ~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~~~l~ 161 (216)
+|+++++ . ....+....| .+|+-+......++.|.
T Consensus 314 iD~~~~~------~-~~~~~~~~~~-~~v~iSA~~~~gl~~L~ 348 (411)
T COG2262 314 IDLLEDE------E-ILAELERGSP-NPVFISAKTGEGLDLLR 348 (411)
T ss_pred ccccCch------h-hhhhhhhcCC-CeEEEEeccCcCHHHHH
Confidence 9998864 1 3344444446 44544444445554444
No 35
>COG1160 Predicted GTPases [General function prediction only]
Probab=93.21 E-value=0.12 Score=46.90 Aligned_cols=120 Identities=17% Similarity=0.292 Sum_probs=70.9
Q ss_pred eecchhHHHHHHHHHHhcCCCCEEEEecCCCCCcHHHHHHhh---cCcccccceeeccEEEEEcccchHHHHhhcccCCC
Q 027979 24 CTVKHSLVQALEQLVQRKERLDHILLETTGLANPAPLASVLW---LDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSS 100 (216)
Q Consensus 24 Csl~~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~---~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~ 100 (216)
+.+.+.-.+++....+ ...=.+.+|.|.|+---..+.+.+. ....++.--+.+-++.|+||..-...-+..
T Consensus 207 ~~~aGTTRD~I~~~~e-~~~~~~~liDTAGiRrk~ki~e~~E~~Sv~rt~~aI~~a~vvllviDa~~~~~~qD~~----- 280 (444)
T COG1160 207 SDIAGTTRDSIDIEFE-RDGRKYVLIDTAGIRRKGKITESVEKYSVARTLKAIERADVVLLVIDATEGISEQDLR----- 280 (444)
T ss_pred cCCCCccccceeeeEE-ECCeEEEEEECCCCCcccccccceEEEeehhhHhHHhhcCEEEEEEECCCCchHHHHH-----
Confidence 3333333344433333 2234679999999987776665321 011123334456678999998743322210
Q ss_pred hhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCC---CCEEEEee
Q 027979 101 YPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINS---LAHVIRSV 151 (216)
Q Consensus 101 ~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP---~A~iv~~~ 151 (216)
..-+..--.-|.+|++||+|+++.++ ..++++++.++..-| .|+++..+
T Consensus 281 ia~~i~~~g~~~vIvvNKWDl~~~~~--~~~~~~k~~i~~~l~~l~~a~i~~iS 332 (444)
T COG1160 281 IAGLIEEAGRGIVIVVNKWDLVEEDE--ATMEEFKKKLRRKLPFLDFAPIVFIS 332 (444)
T ss_pred HHHHHHHcCCCeEEEEEccccCCchh--hHHHHHHHHHHHHhccccCCeEEEEE
Confidence 12234555678999999999998632 256777777777655 46776543
No 36
>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=93.03 E-value=0.45 Score=37.80 Aligned_cols=95 Identities=23% Similarity=0.333 Sum_probs=48.7
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc-EEEEccCCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD-VVILNKVDL 121 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD-~IvlnK~D~ 121 (216)
...+.++-+.|.. .+..... ...-..+.++.|+|+.......... . ....+..... ++++||+|+
T Consensus 67 ~~~~~i~DtpG~~---~~~~~~~-----~~~~~~d~vi~VvD~~~~~~~~~~~-----~-~~~~~~~~~~~iiv~NK~Dl 132 (192)
T cd01889 67 NLQITLVDCPGHA---SLIRTII-----GGAQIIDLMLLVVDATKGIQTQTAE-----C-LVIGEILCKKLIVVLNKIDL 132 (192)
T ss_pred CceEEEEECCCcH---HHHHHHH-----HHHhhCCEEEEEEECCCCccHHHHH-----H-HHHHHHcCCCEEEEEECccc
Confidence 4677889999973 2333221 1222467899999998632111000 0 0112222233 588899999
Q ss_pred CCCCCccchHHHHHHHHHhh-----CCCCEEEEee
Q 027979 122 VSPERSGDSLDELEKEIHEI-----NSLAHVIRSV 151 (216)
Q Consensus 122 v~~~~~~~~l~~i~~~l~~l-----NP~A~iv~~~ 151 (216)
++.+......+++++.++.. +...++++++
T Consensus 133 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~vi~iS 167 (192)
T cd01889 133 IPEEERERKIEKMKKKLQKTLEKTRFKNSPIIPVS 167 (192)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhcCcCCCCEEEEe
Confidence 86532111234444444332 3456666543
No 37
>PRK14974 cell division protein FtsY; Provisional
Probab=92.99 E-value=1.1 Score=39.45 Aligned_cols=95 Identities=22% Similarity=0.138 Sum_probs=56.3
Q ss_pred CCCCEEEEecCCCCC-cHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCC
Q 027979 42 ERLDHILLETTGLAN-PAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVD 120 (216)
Q Consensus 42 ~~~d~IiIE~sG~a~-P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D 120 (216)
.+.|+|||.|.|... +..+++.|. .+......+.++.|+||..-.+.+.. ...+.+....|-+|+||.|
T Consensus 221 ~~~DvVLIDTaGr~~~~~~lm~eL~---~i~~~~~pd~~iLVl~a~~g~d~~~~-------a~~f~~~~~~~giIlTKlD 290 (336)
T PRK14974 221 RGIDVVLIDTAGRMHTDANLMDELK---KIVRVTKPDLVIFVGDALAGNDAVEQ-------AREFNEAVGIDGVILTKVD 290 (336)
T ss_pred CCCCEEEEECCCccCCcHHHHHHHH---HHHHhhCCceEEEeeccccchhHHHH-------HHHHHhcCCCCEEEEeeec
Confidence 468999999999985 455555442 12233445678899999764432211 1112333457999999999
Q ss_pred CCCCCCccchHHHHHHHHHhhCCCCEEEEeecCC
Q 027979 121 LVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQ 154 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~ 154 (216)
....-. .+....... +.+|.....|+
T Consensus 291 ~~~~~G------~~ls~~~~~--~~Pi~~i~~Gq 316 (336)
T PRK14974 291 ADAKGG------AALSIAYVI--GKPILFLGVGQ 316 (336)
T ss_pred CCCCcc------HHHHHHHHH--CcCEEEEeCCC
Confidence 865432 222333222 56776655553
No 38
>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=92.64 E-value=0.66 Score=37.45 Aligned_cols=92 Identities=21% Similarity=0.232 Sum_probs=48.9
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc----EEEEccC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD----VVILNKV 119 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD----~IvlnK~ 119 (216)
..+.+|-|.|..+ +.... ....-..+.++.|||+..-...- ..+...++.... ++++||+
T Consensus 65 ~~i~~iDtPG~~~---~~~~~-----~~~~~~~D~~ilVvda~~g~~~~--------~~~~~~~~~~~~~~~iIvviNK~ 128 (195)
T cd01884 65 RHYAHVDCPGHAD---YIKNM-----ITGAAQMDGAILVVSATDGPMPQ--------TREHLLLARQVGVPYIVVFLNKA 128 (195)
T ss_pred eEEEEEECcCHHH---HHHHH-----HHHhhhCCEEEEEEECCCCCcHH--------HHHHHHHHHHcCCCcEEEEEeCC
Confidence 4578999999742 32221 12334678899999997532111 112233444332 3678999
Q ss_pred CCCCCCCccc-hHHHHHHHHHhh--CC-CCEEEEee
Q 027979 120 DLVSPERSGD-SLDELEKEIHEI--NS-LAHVIRSV 151 (216)
Q Consensus 120 D~v~~~~~~~-~l~~i~~~l~~l--NP-~A~iv~~~ 151 (216)
|+++.++.-. ..+++++.++.+ || .+++++.+
T Consensus 129 D~~~~~~~~~~~~~~i~~~l~~~g~~~~~v~iipiS 164 (195)
T cd01884 129 DMVDDEELLELVEMEVRELLSKYGFDGDNTPIVRGS 164 (195)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHhcccccCCeEEEee
Confidence 9985432100 112344555543 33 36777643
No 39
>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=92.61 E-value=0.14 Score=40.15 Aligned_cols=91 Identities=25% Similarity=0.225 Sum_probs=51.2
Q ss_pred CCEEEEecCCCCCcHHHH--HHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEcc
Q 027979 44 LDHILLETTGLANPAPLA--SVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNK 118 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~--~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK 118 (216)
-.+.+|=+.|+-.+.+.. +.+..+..+ .-..|.+|.|+||.++.+.+. +..|+. .==++++||
T Consensus 47 ~~~~lvDlPG~ysl~~~s~ee~v~~~~l~--~~~~D~ii~VvDa~~l~r~l~----------l~~ql~e~g~P~vvvlN~ 114 (156)
T PF02421_consen 47 QQVELVDLPGIYSLSSKSEEERVARDYLL--SEKPDLIIVVVDATNLERNLY----------LTLQLLELGIPVVVVLNK 114 (156)
T ss_dssp EEEEEEE----SSSSSSSHHHHHHHHHHH--HTSSSEEEEEEEGGGHHHHHH----------HHHHHHHTTSSEEEEEET
T ss_pred ceEEEEECCCcccCCCCCcHHHHHHHHHh--hcCCCEEEEECCCCCHHHHHH----------HHHHHHHcCCCEEEEEeC
Confidence 467888999976654332 222111111 225788999999999876542 234443 445799999
Q ss_pred CCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 119 VDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 119 ~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
+|.+.........+.+.+.+ +++++.++
T Consensus 115 ~D~a~~~g~~id~~~Ls~~L-----g~pvi~~s 142 (156)
T PF02421_consen 115 MDEAERKGIEIDAEKLSERL-----GVPVIPVS 142 (156)
T ss_dssp HHHHHHTTEEE-HHHHHHHH-----TS-EEEEB
T ss_pred HHHHHHcCCEECHHHHHHHh-----CCCEEEEE
Confidence 99988765323345555554 46777654
No 40
>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=92.54 E-value=0.82 Score=37.66 Aligned_cols=93 Identities=16% Similarity=0.216 Sum_probs=50.7
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH---hhccEE-EEccCC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---AFADVV-ILNKVD 120 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~~AD~I-vlnK~D 120 (216)
.+.+++|.|-. ..+++.. -..+.++.|+|+........ ..+...+ ...-+| ++||+|
T Consensus 84 ~i~~vDtPg~~--~~~l~~a---------k~aDvVllviDa~~~~~~~~--------~~i~~~l~~~g~p~vi~VvnK~D 144 (225)
T cd01882 84 RLTFIECPNDI--NAMIDIA---------KVADLVLLLIDASFGFEMET--------FEFLNILQVHGFPRVMGVLTHLD 144 (225)
T ss_pred eEEEEeCCchH--HHHHHHH---------HhcCEEEEEEecCcCCCHHH--------HHHHHHHHHcCCCeEEEEEeccc
Confidence 44677887632 3333322 23567899999974321110 1122222 233456 999999
Q ss_pred CCCCCCccchHHHHHHHHH-----hhCCCCEEEEee---cCCCChhh
Q 027979 121 LVSPERSGDSLDELEKEIH-----EINSLAHVIRSV---RCQVDLSE 159 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~-----~lNP~A~iv~~~---~~~v~~~~ 159 (216)
++++.+ .++++.+.|+ ++-|.++|+..+ .++++..+
T Consensus 145 ~~~~~~---~~~~~~~~l~~~~~~~~~~~~ki~~iSa~~~~~~~~~e 188 (225)
T cd01882 145 LFKKNK---TLRKTKKRLKHRFWTEVYQGAKLFYLSGIVHGRYPKTE 188 (225)
T ss_pred cCCcHH---HHHHHHHHHHHHHHHhhCCCCcEEEEeeccCCCCCHHH
Confidence 986432 2344444443 366889998866 44444433
No 41
>PRK12298 obgE GTPase CgtA; Reviewed
Probab=92.19 E-value=0.45 Score=42.77 Aligned_cols=69 Identities=19% Similarity=0.320 Sum_probs=40.2
Q ss_pred EEEEecCCCCCcHH----HHHHhhcCcccccceeeccEEEEEcccchH--HHHhhcccCCChhHHHHHHh--------hc
Q 027979 46 HILLETTGLANPAP----LASVLWLDDQLESAVRLDSIITVVDAKNLL--FQIDKYRHLSSYPEAIHQIA--------FA 111 (216)
Q Consensus 46 ~IiIE~sG~a~P~~----i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~--~~l~~~~~~~~~~~~~~QI~--------~A 111 (216)
.+++-+.|+-.+.. +-..+ ++..-+.+.++.|+|+..+. +.+.. +..+.+++. ..
T Consensus 209 i~~vDtPGi~~~a~~~~~Lg~~~-----l~~i~radvlL~VVD~s~~~~~d~~e~------~~~l~~eL~~~~~~L~~kP 277 (390)
T PRK12298 209 FVVADIPGLIEGASEGAGLGIRF-----LKHLERCRVLLHLIDIAPIDGSDPVEN------ARIIINELEKYSPKLAEKP 277 (390)
T ss_pred EEEEeCCCccccccchhhHHHHH-----HHHHHhCCEEEEEeccCcccccChHHH------HHHHHHHHHhhhhhhcCCC
Confidence 78899999976642 22211 12233567889999987431 11111 122333333 34
Q ss_pred cEEEEccCCCCCCC
Q 027979 112 DVVILNKVDLVSPE 125 (216)
Q Consensus 112 D~IvlnK~D~v~~~ 125 (216)
-+||+||+|+.+..
T Consensus 278 ~IlVlNKiDl~~~~ 291 (390)
T PRK12298 278 RWLVFNKIDLLDEE 291 (390)
T ss_pred EEEEEeCCccCChH
Confidence 59999999997653
No 42
>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=92.11 E-value=0.75 Score=35.14 Aligned_cols=70 Identities=21% Similarity=0.343 Sum_probs=37.9
Q ss_pred CEEEEecCCCCCcH----HHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH--------hhcc
Q 027979 45 DHILLETTGLANPA----PLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI--------AFAD 112 (216)
Q Consensus 45 d~IiIE~sG~a~P~----~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI--------~~AD 112 (216)
.+.++.|.|..+-. .+...++ ...-..+.++.|+|+....+.+.. +..+.+++ ...=
T Consensus 49 ~~~l~DtpG~~~~~~~~~~~~~~~~-----~~~~~~d~vi~v~D~~~~~~~~~~------~~~~~~~l~~~~~~~~~~p~ 117 (170)
T cd01898 49 SFVVADIPGLIEGASEGKGLGHRFL-----RHIERTRLLLHVIDLSGDDDPVED------YKTIRNELELYNPELLEKPR 117 (170)
T ss_pred eEEEEecCcccCcccccCCchHHHH-----HHHHhCCEEEEEEecCCCCCHHHH------HHHHHHHHHHhCcccccccc
Confidence 66788999974221 1222111 111236789999999864111111 11222222 2234
Q ss_pred EEEEccCCCCCCC
Q 027979 113 VVILNKVDLVSPE 125 (216)
Q Consensus 113 ~IvlnK~D~v~~~ 125 (216)
++|+||+|+.+..
T Consensus 118 ivv~NK~Dl~~~~ 130 (170)
T cd01898 118 IVVLNKIDLLDEE 130 (170)
T ss_pred EEEEEchhcCCch
Confidence 8999999998764
No 43
>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=91.96 E-value=0.7 Score=34.54 Aligned_cols=73 Identities=23% Similarity=0.325 Sum_probs=40.5
Q ss_pred CCEEEEecCCCCCcHH-HHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEccC
Q 027979 44 LDHILLETTGLANPAP-LASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNKV 119 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~-i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK~ 119 (216)
....++.|.|..+-.. +...+. +......-..+.++.|+|+........ ..+.+++. .-=++++||+
T Consensus 45 ~~~~i~DtpG~~~~~~~~~~~~~-~~~~~~~~~~d~ii~v~d~~~~~~~~~--------~~~~~~~~~~~~piiiv~nK~ 115 (157)
T cd01894 45 REFILIDTGGIEPDDEGISKEIR-EQAELAIEEADVILFVVDGREGLTPAD--------EEIAKYLRKSKKPVILVVNKV 115 (157)
T ss_pred eEEEEEECCCCCCchhHHHHHHH-HHHHHHHHhCCEEEEEEeccccCCccH--------HHHHHHHHhcCCCEEEEEECc
Confidence 5678999999987544 111111 001112234678999999975321111 11223332 2337888999
Q ss_pred CCCCCC
Q 027979 120 DLVSPE 125 (216)
Q Consensus 120 D~v~~~ 125 (216)
|+.+..
T Consensus 116 D~~~~~ 121 (157)
T cd01894 116 DNIKEE 121 (157)
T ss_pred ccCChH
Confidence 998753
No 44
>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=91.59 E-value=0.38 Score=36.43 Aligned_cols=61 Identities=25% Similarity=0.370 Sum_probs=33.7
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHh-----hccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEE
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA-----FADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIR 149 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~-----~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~ 149 (216)
..|.++.|+|+........ ..+.+.+. .-=++++||+|+++++ ...++.+.++... .+++.
T Consensus 11 ~aD~vl~ViD~~~p~~~~~--------~~l~~~l~~~~~~k~~iivlNK~DL~~~~----~~~~~~~~~~~~~--~~ii~ 76 (141)
T cd01857 11 RSDIVVQIVDARNPLLFRP--------PDLERYVKEVDPRKKNILLLNKADLLTEE----QRKAWAEYFKKEG--IVVVF 76 (141)
T ss_pred hCCEEEEEEEccCCcccCC--------HHHHHHHHhccCCCcEEEEEechhcCCHH----HHHHHHHHHHhcC--CeEEE
Confidence 3457899999975432111 12223332 2246778999998653 3445555555544 34544
No 45
>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=91.43 E-value=0.44 Score=42.17 Aligned_cols=73 Identities=26% Similarity=0.436 Sum_probs=45.4
Q ss_pred CCEEEEecCCC-CC-cHHHHHHhhcCcccccceeeccEEEEEcccchHH--HHhhcccCCChhHHHHHHhhcc---EEEE
Q 027979 44 LDHILLETTGL-AN-PAPLASVLWLDDQLESAVRLDSIITVVDAKNLLF--QIDKYRHLSSYPEAIHQIAFAD---VVIL 116 (216)
Q Consensus 44 ~d~IiIE~sG~-a~-P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~--~l~~~~~~~~~~~~~~QI~~AD---~Ivl 116 (216)
...+++.|.|. .+ |..+++.+. ..+...-..+.++.|+|++.... ++.. ......++...+ ++|+
T Consensus 237 ~~i~l~DT~G~~~~l~~~lie~f~--~tle~~~~ADlil~VvD~s~~~~~~~~~~------~~~~L~~l~~~~~piIlV~ 308 (351)
T TIGR03156 237 GEVLLTDTVGFIRDLPHELVAAFR--ATLEEVREADLLLHVVDASDPDREEQIEA------VEKVLEELGAEDIPQLLVY 308 (351)
T ss_pred ceEEEEecCcccccCCHHHHHHHH--HHHHHHHhCCEEEEEEECCCCchHHHHHH------HHHHHHHhccCCCCEEEEE
Confidence 46788999998 33 777766542 12223345678999999986432 1111 112345555444 8899
Q ss_pred ccCCCCCC
Q 027979 117 NKVDLVSP 124 (216)
Q Consensus 117 nK~D~v~~ 124 (216)
||+|+.+.
T Consensus 309 NK~Dl~~~ 316 (351)
T TIGR03156 309 NKIDLLDE 316 (351)
T ss_pred EeecCCCh
Confidence 99999764
No 46
>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=91.39 E-value=1.4 Score=32.30 Aligned_cols=93 Identities=20% Similarity=0.262 Sum_probs=46.1
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH--hhccEEEEccCCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI--AFADVVILNKVDL 121 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI--~~AD~IvlnK~D~ 121 (216)
+...++++.|..+-.++..... .....-.+..+.++.|+|+........ ..+..+. ...-++++||+|+
T Consensus 50 ~~~~~~D~~G~~~~~~~~~~~~-~~~~~~i~~~d~~~~v~~~~~~~~~~~--------~~~~~~~~~~~p~ivv~nK~D~ 120 (161)
T TIGR00231 50 YKFNLLDTAGQEDYRAIRRLYY-RAVESSLRVFDIVILVLDVEEILEKQT--------KEIIHHAESNVPIILVGNKIDL 120 (161)
T ss_pred EEEEEEECCCcccchHHHHHHH-hhhhEEEEEEEEeeeehhhhhHhHHHH--------HHHHHhcccCCcEEEEEEcccC
Confidence 4567789999665554443322 111112233444444455544432111 1111111 3456899999999
Q ss_pred CCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 122 VSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 122 v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
.... ...+..+.+..++.. +++++
T Consensus 121 ~~~~----~~~~~~~~~~~~~~~-~~~~~ 144 (161)
T TIGR00231 121 RDAK----LKTHVAFLFAKLNGE-PIIPL 144 (161)
T ss_pred Ccch----hhHHHHHHHhhccCC-ceEEe
Confidence 8753 235555555555443 35443
No 47
>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=91.25 E-value=0.79 Score=34.86 Aligned_cols=69 Identities=19% Similarity=0.127 Sum_probs=39.3
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLV 122 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v 122 (216)
+.+..++.|.|......+.... .-..+.++.|+|+......-.. ... ....+...--+|++||+|+.
T Consensus 49 ~~~~~iiDtpG~~~~~~~~~~~--------~~~~d~il~v~d~~~~~~~~~~----~~~-~~~~~~~~p~ivv~NK~Dl~ 115 (168)
T cd01887 49 IPGITFIDTPGHEAFTNMRARG--------ASLTDIAILVVAADDGVMPQTI----EAI-KLAKAANVPFIVALNKIDKP 115 (168)
T ss_pred cceEEEEeCCCcHHHHHHHHHH--------HhhcCEEEEEEECCCCccHHHH----HHH-HHHHHcCCCEEEEEEceecc
Confidence 4678999999985433332211 1245678999999763211000 001 11233344458999999997
Q ss_pred CC
Q 027979 123 SP 124 (216)
Q Consensus 123 ~~ 124 (216)
+.
T Consensus 116 ~~ 117 (168)
T cd01887 116 NA 117 (168)
T ss_pred cc
Confidence 54
No 48
>cd04178 Nucleostemin_like Nucleostemin-like. Nucleostemin (NS) is a nucleolar protein that functions as a regulator of cell growth and proliferation in stem cells and in several types of cancer cells, but is not expressed in the differentiated cells of most mammalian adult tissues. NS shuttles between the nucleolus and nucleoplasm bidirectionally at a rate that is fast and independent of cell type. Lowering GTP levels decreases the nucleolar retention of NS, and expression of NS is abruptly down-regulated during differentiation prior to terminal cell division. Found only in eukaryotes, NS consists of an N-terminal basic domain, a coiled-coil domain, a GTP-binding domain, an intermediate domain, and a C-terminal acidic domain. Experimental evidence indicates that NS uses its GTP-binding property as a molecular switch to control the transition between the nucleolus and nucleoplasm, and this process involves interaction between the basic, GTP-binding, and intermediate domains of the
Probab=91.21 E-value=0.27 Score=38.96 Aligned_cols=55 Identities=31% Similarity=0.344 Sum_probs=32.6
Q ss_pred ccEEEEEcccchHHHHhhcccCCChhHHHHH--Hhh---ccEEEEccCCCCCCCCccchHHHHHHHHHhhCC
Q 027979 77 DSIITVVDAKNLLFQIDKYRHLSSYPEAIHQ--IAF---ADVVILNKVDLVSPERSGDSLDELEKEIHEINS 143 (216)
Q Consensus 77 ~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~Q--I~~---AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP 143 (216)
|-|+.|+||....... .+.+.+. +.. --++|+||+|+++++ .+..+.+.+++..+
T Consensus 1 DvVl~VvDar~p~~~~--------~~~i~~~~~l~~~~kp~IlVlNK~DL~~~~----~l~~~~~~~~~~~~ 60 (172)
T cd04178 1 DVILEVLDARDPLGCR--------CPQVEEAVLQAGGNKKLVLVLNKIDLVPKE----NVEKWLKYLRREFP 60 (172)
T ss_pred CEEEEEEECCCCCCCC--------CHHHHHHHHhccCCCCEEEEEehhhcCCHH----HHHHHHHHHHhhCC
Confidence 4578999997643211 1233333 222 238899999998864 34555555555544
No 49
>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=90.97 E-value=0.83 Score=34.31 Aligned_cols=97 Identities=20% Similarity=0.254 Sum_probs=46.4
Q ss_pred CEEEEecCCCCCc------HHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc---cEEE
Q 027979 45 DHILLETTGLANP------APLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA---DVVI 115 (216)
Q Consensus 45 d~IiIE~sG~a~P------~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A---D~Iv 115 (216)
...++.+.|++.. ..-...+. ...+...=.++.++.++|......... ..+...+... -+++
T Consensus 46 ~~~~~D~~g~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~v~d~~~~~~~~~--------~~~~~~l~~~~~~vi~v 116 (170)
T cd01876 46 KFRLVDLPGYGYAKVSKEVKEKWGKLI-EEYLENRENLKGVVLLIDSRHGPTEID--------LEMLDWLEELGIPFLVV 116 (170)
T ss_pred eEEEecCCCccccccCHHHHHHHHHHH-HHHHHhChhhhEEEEEEEcCcCCCHhH--------HHHHHHHHHcCCCEEEE
Confidence 5667888998763 11111111 111122224566788988875421111 1122333333 4789
Q ss_pred EccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 116 LNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 116 lnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
+||+|+.+.++.......+...++...+..+++.+
T Consensus 117 ~nK~D~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 151 (170)
T cd01876 117 LTKADKLKKSELAKALKEIKKELKLFEIDPPIILF 151 (170)
T ss_pred EEchhcCChHHHHHHHHHHHHHHHhccCCCceEEE
Confidence 99999987643211112223333323455566543
No 50
>cd04160 Arfrp1 Arfrp1 subfamily. Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development.
Probab=90.76 E-value=2.1 Score=32.53 Aligned_cols=82 Identities=16% Similarity=0.243 Sum_probs=42.6
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH---hhccEEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---AFADVVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~~AD~IvlnK~D 120 (216)
....++.+.|...-..+..... -..+.+|.|+|+..... +.... ..+..+.++. ..-=++++||+|
T Consensus 50 ~~~~l~Dt~G~~~~~~~~~~~~--------~~~~~~v~vvd~~~~~~-~~~~~--~~~~~~~~~~~~~~~p~ilv~NK~D 118 (167)
T cd04160 50 ARLKFWDLGGQESLRSLWDKYY--------AECHAIIYVIDSTDRER-FEESK--SALEKVLRNEALEGVPLLILANKQD 118 (167)
T ss_pred EEEEEEECCCChhhHHHHHHHh--------CCCCEEEEEEECchHHH-HHHHH--HHHHHHHhChhhcCCCEEEEEEccc
Confidence 5567888888754333333221 13457899999976532 11100 0011111111 123378889999
Q ss_pred CCCCCCccchHHHHHHHHHh
Q 027979 121 LVSPERSGDSLDELEKEIHE 140 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~ 140 (216)
+.+.. ..+++.+.++.
T Consensus 119 ~~~~~----~~~~~~~~~~~ 134 (167)
T cd04160 119 LPDAL----SVEEIKEVFQD 134 (167)
T ss_pred cccCC----CHHHHHHHhcc
Confidence 86653 23555555544
No 51
>TIGR00959 ffh signal recognition particle protein. This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.
Probab=90.65 E-value=3 Score=37.97 Aligned_cols=95 Identities=16% Similarity=0.092 Sum_probs=54.1
Q ss_pred cCCCCEEEEecCCCCCc-HHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccC
Q 027979 41 KERLDHILLETTGLANP-APLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKV 119 (216)
Q Consensus 41 ~~~~d~IiIE~sG~a~P-~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~ 119 (216)
...+|+|||.|.|...- ..+++.+. .+...+..+.++.|+|+....+.... ...+.+++. -+-||+||.
T Consensus 180 ~~~~DvVIIDTaGr~~~d~~l~~eL~---~i~~~~~p~e~lLVvda~tgq~~~~~------a~~f~~~v~-i~giIlTKl 249 (428)
T TIGR00959 180 ENGFDVVIVDTAGRLQIDEELMEELA---AIKEILNPDEILLVVDAMTGQDAVNT------AKTFNERLG-LTGVVLTKL 249 (428)
T ss_pred hcCCCEEEEeCCCccccCHHHHHHHH---HHHHhhCCceEEEEEeccchHHHHHH------HHHHHhhCC-CCEEEEeCc
Confidence 35689999999997532 33444331 23345567789999999865433321 111223343 468889999
Q ss_pred CCCCCCCccchHHHHHHHHHhhCCCCEEEEeecC
Q 027979 120 DLVSPERSGDSLDELEKEIHEINSLAHVIRSVRC 153 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~ 153 (216)
|...... . +.......+ .||.....|
T Consensus 250 D~~~~~G---~---~lsi~~~~~--~PI~fi~~G 275 (428)
T TIGR00959 250 DGDARGG---A---ALSVRSVTG--KPIKFIGVG 275 (428)
T ss_pred cCccccc---H---HHHHHHHHC--cCEEEEeCC
Confidence 9644321 2 333333333 566554444
No 52
>PRK01889 GTPase RsgA; Reviewed
Probab=90.54 E-value=0.54 Score=41.65 Aligned_cols=66 Identities=18% Similarity=0.322 Sum_probs=37.5
Q ss_pred eeeccEEEEEcccc-hHH-HHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 74 VRLDSIITVVDAKN-LLF-QIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 74 ~~l~~vI~vVDa~~-~~~-~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
-.+|.++.|+++.. |.. .++. +=.+......--+|||||+|++++. +...+.++.++++.+|+.++
T Consensus 111 ANvD~vliV~s~~p~~~~~~ldr------~L~~a~~~~i~piIVLNK~DL~~~~------~~~~~~~~~~~~g~~Vi~vS 178 (356)
T PRK01889 111 ANVDTVFIVCSLNHDFNLRRIER------YLALAWESGAEPVIVLTKADLCEDA------EEKIAEVEALAPGVPVLAVS 178 (356)
T ss_pred EeCCEEEEEEecCCCCChhHHHH------HHHHHHHcCCCEEEEEEChhcCCCH------HHHHHHHHHhCCCCcEEEEE
Confidence 46777888888852 211 1111 1011222223348999999998752 33445566667888888644
No 53
>PTZ00327 eukaryotic translation initiation factor 2 gamma subunit; Provisional
Probab=90.36 E-value=0.85 Score=41.92 Aligned_cols=93 Identities=17% Similarity=0.278 Sum_probs=49.8
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccch--HHHHhhcccCCChhHHHHHHhhcc-EEEEccCCC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNL--LFQIDKYRHLSSYPEAIHQIAFAD-VVILNKVDL 121 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~--~~~l~~~~~~~~~~~~~~QI~~AD-~IvlnK~D~ 121 (216)
.+.+|-+.|-. .++..+. ...-..|.++.||||... ..+... +-.+.+.+...- +|++||+|+
T Consensus 118 ~i~~IDtPGH~---~fi~~m~-----~g~~~~D~alLVVda~~g~~~~qT~e------hl~i~~~lgi~~iIVvlNKiDl 183 (460)
T PTZ00327 118 HVSFVDCPGHD---ILMATML-----NGAAVMDAALLLIAANESCPQPQTSE------HLAAVEIMKLKHIIILQNKIDL 183 (460)
T ss_pred eEeeeeCCCHH---HHHHHHH-----HHHhhCCEEEEEEECCCCccchhhHH------HHHHHHHcCCCcEEEEEecccc
Confidence 46789999942 3443322 233456889999999852 222111 111223344444 569999999
Q ss_pred CCCCCccchHHHHHHHHHhh-CCCCEEEEee
Q 027979 122 VSPERSGDSLDELEKEIHEI-NSLAHVIRSV 151 (216)
Q Consensus 122 v~~~~~~~~l~~i~~~l~~l-NP~A~iv~~~ 151 (216)
++.+......+++++.++.. ...+++++.+
T Consensus 184 v~~~~~~~~~~ei~~~l~~~~~~~~~iipVS 214 (460)
T PTZ00327 184 VKEAQAQDQYEEIRNFVKGTIADNAPIIPIS 214 (460)
T ss_pred cCHHHHHHHHHHHHHHHHhhccCCCeEEEee
Confidence 87542111233344433332 2456777654
No 54
>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=90.31 E-value=0.55 Score=40.29 Aligned_cols=95 Identities=20% Similarity=0.245 Sum_probs=49.1
Q ss_pred CCCcEEeecchhHHHHHHHHHHhcCCCCEEEEecCCCCCcHHHH-HHhhcCccc-c-c--------ceeeccEEEEEccc
Q 027979 18 ANGCICCTVKHSLVQALEQLVQRKERLDHILLETTGLANPAPLA-SVLWLDDQL-E-S--------AVRLDSIITVVDAK 86 (216)
Q Consensus 18 ~~GCiCCsl~~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~-~~l~~~~~l-~-~--------~~~l~~vI~vVDa~ 86 (216)
.+|=+-|.+++.|... ... ----|+|.+|..+- + ..++ +.+-....| + . .-.+|.++.|+|+.
T Consensus 16 ~~~~~~~~~~g~~~~~-~~~---~~vGD~V~~~~~~~-~-~~~i~~i~~R~~~l~R~~~~~~~~~i~anvD~vllV~d~~ 89 (287)
T cd01854 16 EGGELRCRARGKLRKK-GIK---PVVGDWVEVEPDDD-G-EGVIVRVLPRKNLLSRPAAGGREQVIAANVDQLVIVVSLN 89 (287)
T ss_pred CCeEEEEEeccccccC-CCC---ccCCCEEEEEecCC-C-cEEEEEEECCCceEEccCCCCcceeEEEeCCEEEEEEEcC
Confidence 4677888888866421 000 01239999987541 1 1122 111111111 1 1 34577789999986
Q ss_pred chHHHHhhcccCCChhHHHHHHhhcc---EEEEccCCCCCC
Q 027979 87 NLLFQIDKYRHLSSYPEAIHQIAFAD---VVILNKVDLVSP 124 (216)
Q Consensus 87 ~~~~~l~~~~~~~~~~~~~~QI~~AD---~IvlnK~D~v~~ 124 (216)
........ .......+..++ +||+||+|+.++
T Consensus 90 ~p~~s~~~------ldr~L~~~~~~~ip~iIVlNK~DL~~~ 124 (287)
T cd01854 90 EPFFNPRL------LDRYLVAAEAAGIEPVIVLTKADLLDD 124 (287)
T ss_pred CCCCCHHH------HHHHHHHHHHcCCCEEEEEEHHHCCCh
Confidence 43200000 112233444455 889999999875
No 55
>PRK10867 signal recognition particle protein; Provisional
Probab=90.12 E-value=3.7 Score=37.47 Aligned_cols=74 Identities=24% Similarity=0.225 Sum_probs=44.3
Q ss_pred cCCCCEEEEecCCCCC-cHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccC
Q 027979 41 KERLDHILLETTGLAN-PAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKV 119 (216)
Q Consensus 41 ~~~~d~IiIE~sG~a~-P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~ 119 (216)
...+|+|||.|.|... ...+++.+. .+...+..+.++.|+|+..-.+.... ...+.+.+ .-+-+|+||.
T Consensus 181 ~~~~DvVIIDTaGrl~~d~~lm~eL~---~i~~~v~p~evllVlda~~gq~av~~------a~~F~~~~-~i~giIlTKl 250 (433)
T PRK10867 181 ENGYDVVIVDTAGRLHIDEELMDELK---AIKAAVNPDEILLVVDAMTGQDAVNT------AKAFNEAL-GLTGVILTKL 250 (433)
T ss_pred hcCCCEEEEeCCCCcccCHHHHHHHH---HHHHhhCCCeEEEEEecccHHHHHHH------HHHHHhhC-CCCEEEEeCc
Confidence 4579999999999653 234444332 23344566778999999765433221 11111222 2467999999
Q ss_pred CCCCC
Q 027979 120 DLVSP 124 (216)
Q Consensus 120 D~v~~ 124 (216)
|-...
T Consensus 251 D~~~r 255 (433)
T PRK10867 251 DGDAR 255 (433)
T ss_pred cCccc
Confidence 96443
No 56
>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=89.76 E-value=1.1 Score=39.28 Aligned_cols=91 Identities=25% Similarity=0.363 Sum_probs=46.3
Q ss_pred CEEEEecCCCCCcH----HHHHHhhcCcccccceeeccEEEEEcccchH--HHHhhcccCCChhHHHHHHh--------h
Q 027979 45 DHILLETTGLANPA----PLASVLWLDDQLESAVRLDSIITVVDAKNLL--FQIDKYRHLSSYPEAIHQIA--------F 110 (216)
Q Consensus 45 d~IiIE~sG~a~P~----~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~--~~l~~~~~~~~~~~~~~QI~--------~ 110 (216)
.+.|+-+.|+-+.. .+-..+ ++..-+.+.++.|+|+.... +.+.. +..+.+++. .
T Consensus 206 ~~~i~D~PGli~~a~~~~gLg~~f-----lrhierad~ll~VvD~s~~~~~~~~e~------l~~l~~EL~~~~~~l~~k 274 (329)
T TIGR02729 206 SFVIADIPGLIEGASEGAGLGHRF-----LKHIERTRVLLHLIDISPLDGRDPIED------YEIIRNELKKYSPELAEK 274 (329)
T ss_pred EEEEEeCCCcccCCcccccHHHHH-----HHHHHhhCEEEEEEcCccccccCHHHH------HHHHHHHHHHhhhhhccC
Confidence 46777888874322 122221 12223466789999998541 11111 122223332 2
Q ss_pred ccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 111 ADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 111 AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
.-+||+||+|+.++. ..+++.+.+.+... .+++.++
T Consensus 275 p~IIV~NK~DL~~~~----~~~~~~~~l~~~~~-~~vi~iS 310 (329)
T TIGR02729 275 PRIVVLNKIDLLDEE----ELAELLKELKKALG-KPVFPIS 310 (329)
T ss_pred CEEEEEeCccCCChH----HHHHHHHHHHHHcC-CcEEEEE
Confidence 348899999997753 23444444443222 3455443
No 57
>PRK12296 obgE GTPase CgtA; Reviewed
Probab=89.73 E-value=0.96 Score=41.98 Aligned_cols=43 Identities=26% Similarity=0.236 Sum_probs=23.4
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccch
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNL 88 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~ 88 (216)
.+.|+-+.|+-+...--.-+. ...++..-+.+.+|.|||+..+
T Consensus 207 ~f~laDtPGliegas~g~gLg-~~fLrhieradvLv~VVD~s~~ 249 (500)
T PRK12296 207 RFTVADVPGLIPGASEGKGLG-LDFLRHIERCAVLVHVVDCATL 249 (500)
T ss_pred EEEEEECCCCccccchhhHHH-HHHHHHHHhcCEEEEEECCccc
Confidence 467888889854332211110 0112222345778999999754
No 58
>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=89.42 E-value=1.4 Score=32.72 Aligned_cols=64 Identities=13% Similarity=0.175 Sum_probs=36.5
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
..+.+|.|+|+.+...... ..+...+...-++++||+|+.+... ..+++.+..+..+. .+++++
T Consensus 62 ~ad~vilv~d~~~~~s~~~--------~~~~~~~~~p~ilv~NK~Dl~~~~~---~~~~~~~~~~~~~~-~~~~~~ 125 (142)
T TIGR02528 62 DADVIALVQSATDPESRFP--------PGFASIFVKPVIGLVTKIDLAEADV---DIERAKELLETAGA-EPIFEI 125 (142)
T ss_pred cCCEEEEEecCCCCCcCCC--------hhHHHhccCCeEEEEEeeccCCccc---CHHHHHHHHHHcCC-CcEEEE
Confidence 5677899999976553321 1122233345677899999975332 24555555555432 345543
No 59
>PRK09866 hypothetical protein; Provisional
Probab=89.33 E-value=2.3 Score=40.78 Aligned_cols=105 Identities=21% Similarity=0.205 Sum_probs=59.2
Q ss_pred CCCEEEEecCCCCCcH-H-HHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc-----cEEE
Q 027979 43 RLDHILLETTGLANPA-P-LASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA-----DVVI 115 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~-~-i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A-----D~Iv 115 (216)
....|+|=|.|+-.|. . +-+.+. . . --..|-|+.|||+......-+ ..+.+++... =++|
T Consensus 229 ~~QIIFVDTPGIhk~~~~~L~k~M~-e-q---L~eADvVLFVVDat~~~s~~D--------eeIlk~Lkk~~K~~PVILV 295 (741)
T PRK09866 229 PGQLTLLDTPGPNEAGQPHLQKMLN-Q-Q---LARASAVLAVLDYTQLKSISD--------EEVREAILAVGQSVPLYVL 295 (741)
T ss_pred cCCEEEEECCCCCCccchHHHHHHH-H-H---HhhCCEEEEEEeCCCCCChhH--------HHHHHHHHhcCCCCCEEEE
Confidence 4678999999998763 2 222221 1 1 234578999999986432211 1234445443 3568
Q ss_pred EccCCCCCCCCccchHHHHHHHHHhh-----CCCCEEEEeec-CCCChhhhhc
Q 027979 116 LNKVDLVSPERSGDSLDELEKEIHEI-----NSLAHVIRSVR-CQVDLSEVLN 162 (216)
Q Consensus 116 lnK~D~v~~~~~~~~l~~i~~~l~~l-----NP~A~iv~~~~-~~v~~~~l~~ 162 (216)
+||+|+.+... ...+.+.+.++.. .+.+.|++.+- -....+.+++
T Consensus 296 VNKIDl~dree--ddkE~Lle~V~~~L~q~~i~f~eIfPVSAlkG~nid~LLd 346 (741)
T PRK09866 296 VNKFDQQDRNS--DDADQVRALISGTLMKGCITPQQIFPVSSMWGYLANRARH 346 (741)
T ss_pred EEcccCCCccc--chHHHHHHHHHHHHHhcCCCCceEEEEeCCCCCCHHHHHH
Confidence 89999976432 1245566655432 35677876443 2344445543
No 60
>TIGR00064 ftsY signal recognition particle-docking protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.
Probab=89.32 E-value=5.9 Score=33.75 Aligned_cols=100 Identities=15% Similarity=0.169 Sum_probs=56.4
Q ss_pred CCCCEEEEecCCCCCcH-HHHHHhhcCcccccce------eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEE
Q 027979 42 ERLDHILLETTGLANPA-PLASVLWLDDQLESAV------RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVV 114 (216)
Q Consensus 42 ~~~d~IiIE~sG~a~P~-~i~~~l~~~~~l~~~~------~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~I 114 (216)
.++|+|||.|.|..... .+++-|. .+.... ..+.++.|+|+..-.+.+.. . ..+.+....+-+
T Consensus 153 ~~~D~ViIDT~G~~~~d~~~~~el~---~~~~~~~~~~~~~~~~~~LVl~a~~~~~~~~~------~-~~f~~~~~~~g~ 222 (272)
T TIGR00064 153 RNIDVVLIDTAGRLQNKVNLMDELK---KIKRVIKKVDKDAPDEVLLVLDATTGQNALEQ------A-KVFNEAVGLTGI 222 (272)
T ss_pred CCCCEEEEeCCCCCcchHHHHHHHH---HHHHHHhcccCCCCceEEEEEECCCCHHHHHH------H-HHHHhhCCCCEE
Confidence 46999999999987432 2222111 011112 26678999999865443322 1 112233356899
Q ss_pred EEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeecCCCChhhh
Q 027979 115 ILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQVDLSEV 160 (216)
Q Consensus 115 vlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~~~l 160 (216)
|+||.|....-. .+.+..... +.+|.....|+= +++|
T Consensus 223 IlTKlDe~~~~G------~~l~~~~~~--~~Pi~~~~~Gq~-~~dl 259 (272)
T TIGR00064 223 ILTKLDGTAKGG------IILSIAYEL--KLPIKFIGVGEK-IDDL 259 (272)
T ss_pred EEEccCCCCCcc------HHHHHHHHH--CcCEEEEeCCCC-hHhC
Confidence 999999866542 233333333 367777666654 3444
No 61
>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=89.24 E-value=5.3 Score=30.04 Aligned_cols=88 Identities=15% Similarity=0.110 Sum_probs=47.8
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh----c---cEEEEc
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF----A---DVVILN 117 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~----A---D~Ivln 117 (216)
..-++.++|.-+...+.+.... ..+.++.|+|+..... +.. ...+..++.. . =+|++|
T Consensus 51 ~~~i~Dt~G~~~~~~~~~~~~~--------~~~~~ilv~d~~~~~s-~~~------~~~~~~~~~~~~~~~~~piiiv~N 115 (164)
T cd04145 51 ILDILDTAGQEEFSAMREQYMR--------TGEGFLLVFSVTDRGS-FEE------VDKFHTQILRVKDRDEFPMILVGN 115 (164)
T ss_pred EEEEEECCCCcchhHHHHHHHh--------hCCEEEEEEECCCHHH-HHH------HHHHHHHHHHHhCCCCCCEEEEee
Confidence 3456889998766665544321 2467899999987442 221 1122222221 1 167889
Q ss_pred cCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 118 KVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 118 K~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
|+|+.+.... ..++..+..+..+ .++++++
T Consensus 116 K~Dl~~~~~~--~~~~~~~~~~~~~--~~~~~~S 145 (164)
T cd04145 116 KADLEHQRKV--SREEGQELARKLK--IPYIETS 145 (164)
T ss_pred Ccccccccee--cHHHHHHHHHHcC--CcEEEee
Confidence 9999764321 2344555555432 4566544
No 62
>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=89.12 E-value=3.9 Score=30.88 Aligned_cols=67 Identities=18% Similarity=0.293 Sum_probs=38.5
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh-----ccEEEEcc
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF-----ADVVILNK 118 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~-----AD~IvlnK 118 (216)
....+..++|.-....+.+... -..+.++.|+|..+.... .. ...+..++.. -=++|.||
T Consensus 52 ~~l~i~Dt~G~~~~~~~~~~~~--------~~~d~ii~v~d~~~~~s~-~~------~~~~~~~~~~~~~~~p~ilv~nK 116 (164)
T cd04101 52 VELFIFDSAGQELYSDMVSNYW--------ESPSVFILVYDVSNKASF-EN------CSRWVNKVRTASKHMPGVLVGNK 116 (164)
T ss_pred EEEEEEECCCHHHHHHHHHHHh--------CCCCEEEEEEECcCHHHH-HH------HHHHHHHHHHhCCCCCEEEEEEC
Confidence 4556777777644333333221 135778999999865432 11 2223344433 23778899
Q ss_pred CCCCCCC
Q 027979 119 VDLVSPE 125 (216)
Q Consensus 119 ~D~v~~~ 125 (216)
+|+.+..
T Consensus 117 ~Dl~~~~ 123 (164)
T cd04101 117 MDLADKA 123 (164)
T ss_pred ccccccc
Confidence 9997654
No 63
>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=88.91 E-value=6.1 Score=29.73 Aligned_cols=65 Identities=18% Similarity=0.097 Sum_probs=37.2
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc------EEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEE
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD------VVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIR 149 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD------~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~ 149 (216)
.+.+|.|+|+.+-...- . ......++.... +|+.||+|+.+... ...+.+.+..+..+ .++++
T Consensus 74 ~~~~i~v~d~~~~~s~~-~------~~~~~~~~~~~~~~~~~iivv~nK~D~~~~~~--~~~~~~~~~~~~~~--~~~~~ 142 (163)
T cd01860 74 AAAAIVVYDITSEESFE-K------AKSWVKELQRNASPNIIIALVGNKADLESKRQ--VSTEEAQEYADENG--LLFFE 142 (163)
T ss_pred CCEEEEEEECcCHHHHH-H------HHHHHHHHHHhCCCCCeEEEEEECccccccCc--CCHHHHHHHHHHcC--CEEEE
Confidence 57889999998654321 1 122333343332 66779999875322 13455666666655 56665
Q ss_pred ee
Q 027979 150 SV 151 (216)
Q Consensus 150 ~~ 151 (216)
++
T Consensus 143 ~S 144 (163)
T cd01860 143 TS 144 (163)
T ss_pred EE
Confidence 44
No 64
>cd03110 Fer4_NifH_child This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.
Probab=88.88 E-value=5.5 Score=31.04 Aligned_cols=91 Identities=18% Similarity=0.193 Sum_probs=49.9
Q ss_pred hhHHHHHHHHHH---hcCCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHH
Q 027979 28 HSLVQALEQLVQ---RKERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEA 104 (216)
Q Consensus 28 ~dl~~~L~~l~~---~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~ 104 (216)
+.+...+.+.+. ...++|+|||-+.|...+. ....+. .-+.++.++.+...... . ...+
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~d~viiDtpp~~~~~-~~~~l~---------~aD~vliv~~~~~~~~~--~------~~~~ 135 (179)
T cd03110 74 GKLVTEVRKHAKEIAKAEGAELIIIDGPPGIGCP-VIASLT---------GADAALLVTEPTPSGLH--D------LERA 135 (179)
T ss_pred HHHHHHHHHHHHHhhhhcCCCEEEEECcCCCcHH-HHHHHH---------cCCEEEEEecCCcccHH--H------HHHH
Confidence 444445544331 1357999999999665542 233321 23567888888754211 1 1122
Q ss_pred HHHHhhc---cEEEEccCCCCCCCCccchHHHHHHHHHhh
Q 027979 105 IHQIAFA---DVVILNKVDLVSPERSGDSLDELEKEIHEI 141 (216)
Q Consensus 105 ~~QI~~A---D~IvlnK~D~v~~~~~~~~l~~i~~~l~~l 141 (216)
.++++.. =.+|+||.|.-.. ..+++++.+++.
T Consensus 136 ~~~l~~~~~~~~vV~N~~~~~~~-----~~~~~~~~~~~~ 170 (179)
T cd03110 136 VELVRHFGIPVGVVINKYDLNDE-----IAEEIEDYCEEE 170 (179)
T ss_pred HHHHHHcCCCEEEEEeCCCCCcc-----hHHHHHHHHHHc
Confidence 2233222 2689999987543 235566666654
No 65
>cd04105 SR_beta Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this typ
Probab=88.79 E-value=2.4 Score=34.26 Aligned_cols=74 Identities=16% Similarity=0.157 Sum_probs=38.8
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHH-HHH--hhcc-EEEEccC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAI-HQI--AFAD-VVILNKV 119 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~-~QI--~~AD-~IvlnK~ 119 (216)
..+.|+.+.|-......... .+... ++++|.|+|+......+..... ..+..+. .|. .... +|+.||+
T Consensus 48 ~~~~l~D~pG~~~~~~~~~~-----~~~~~--~~~vV~VvD~~~~~~~~~~~~~-~l~~il~~~~~~~~~~pvliv~NK~ 119 (203)
T cd04105 48 KKFRLVDVPGHPKLRDKLLE-----TLKNS--AKGIVFVVDSATFQKNLKDVAE-FLYDILTDLEKVKNKIPVLIACNKQ 119 (203)
T ss_pred ceEEEEECCCCHHHHHHHHH-----HHhcc--CCEEEEEEECccchhHHHHHHH-HHHHHHHHHhhccCCCCEEEEecch
Confidence 45678888887543322211 12222 6899999999987433322100 0001111 122 1333 5667999
Q ss_pred CCCCCC
Q 027979 120 DLVSPE 125 (216)
Q Consensus 120 D~v~~~ 125 (216)
|+.++.
T Consensus 120 Dl~~a~ 125 (203)
T cd04105 120 DLFTAK 125 (203)
T ss_pred hhcccC
Confidence 997754
No 66
>cd01864 Rab19 Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet chracterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=88.77 E-value=5.9 Score=30.06 Aligned_cols=88 Identities=15% Similarity=0.146 Sum_probs=44.8
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh---cc---EEEEcc
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF---AD---VVILNK 118 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~---AD---~IvlnK 118 (216)
...++++.|...-..+.+.+ + -..+.++.|+|+.+.... .. ......++.. .+ ++|.||
T Consensus 53 ~l~i~D~~G~~~~~~~~~~~-----~---~~~d~~llv~d~~~~~s~-~~------~~~~~~~i~~~~~~~~p~ivv~nK 117 (165)
T cd01864 53 KLQIWDTAGQERFRTITQSY-----Y---RSANGAIIAYDITRRSSF-ES------VPHWIEEVEKYGASNVVLLLIGNK 117 (165)
T ss_pred EEEEEECCChHHHHHHHHHH-----h---ccCCEEEEEEECcCHHHH-Hh------HHHHHHHHHHhCCCCCcEEEEEEC
Confidence 45677888853222222211 1 125788999999875432 11 1223333332 22 578899
Q ss_pred CCCCCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 119 VDLVSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 119 ~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
+|+....+. ..+...+..+..+. ..++++
T Consensus 118 ~Dl~~~~~~--~~~~~~~~~~~~~~-~~~~e~ 146 (165)
T cd01864 118 CDLEEQREV--LFEEACTLAEKNGM-LAVLET 146 (165)
T ss_pred ccccccccc--CHHHHHHHHHHcCC-cEEEEE
Confidence 999765421 23444444444332 344443
No 67
>PRK12299 obgE GTPase CgtA; Reviewed
Probab=88.67 E-value=1.3 Score=38.98 Aligned_cols=69 Identities=20% Similarity=0.405 Sum_probs=37.5
Q ss_pred CEEEEecCCCCCcHH----HHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH--------hhcc
Q 027979 45 DHILLETTGLANPAP----LASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI--------AFAD 112 (216)
Q Consensus 45 d~IiIE~sG~a~P~~----i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI--------~~AD 112 (216)
.++++.+.|+-+... +-..++ +..-+-+.+|.|+|+.... .+.. +..+...+ ...-
T Consensus 207 ~~~i~D~PGli~ga~~~~gLg~~fl-----rhie~a~vlI~ViD~s~~~-s~e~------~~~~~~EL~~~~~~L~~kp~ 274 (335)
T PRK12299 207 SFVIADIPGLIEGASEGAGLGHRFL-----KHIERTRLLLHLVDIEAVD-PVED------YKTIRNELEKYSPELADKPR 274 (335)
T ss_pred EEEEEeCCCccCCCCccccHHHHHH-----HHhhhcCEEEEEEcCCCCC-CHHH------HHHHHHHHHHhhhhcccCCe
Confidence 467888888854321 222211 1112356789999998542 1111 11122222 2345
Q ss_pred EEEEccCCCCCCC
Q 027979 113 VVILNKVDLVSPE 125 (216)
Q Consensus 113 ~IvlnK~D~v~~~ 125 (216)
+||+||+|+.+..
T Consensus 275 IIV~NKiDL~~~~ 287 (335)
T PRK12299 275 ILVLNKIDLLDEE 287 (335)
T ss_pred EEEEECcccCCch
Confidence 8899999997654
No 68
>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=88.51 E-value=2.6 Score=33.39 Aligned_cols=65 Identities=17% Similarity=0.241 Sum_probs=37.5
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHH---HHhhccEEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIH---QIAFADVVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~---QI~~AD~IvlnK~D 120 (216)
....++.|.|..+=........ -..+.++.|+|+..-.... ...... +...--+|++||+|
T Consensus 65 ~~~~l~DtpG~~~~~~~~~~~~--------~~~d~~ilV~d~~~~~~~~--------~~~~~~~~~~~~~p~iiv~NK~D 128 (194)
T cd01891 65 TKINIVDTPGHADFGGEVERVL--------SMVDGVLLLVDASEGPMPQ--------TRFVLKKALELGLKPIVVINKID 128 (194)
T ss_pred EEEEEEECCCcHHHHHHHHHHH--------HhcCEEEEEEECCCCccHH--------HHHHHHHHHHcCCCEEEEEECCC
Confidence 4557899999865333333221 2457889999997521000 011112 22334589999999
Q ss_pred CCCC
Q 027979 121 LVSP 124 (216)
Q Consensus 121 ~v~~ 124 (216)
+.+.
T Consensus 129 l~~~ 132 (194)
T cd01891 129 RPDA 132 (194)
T ss_pred CCCC
Confidence 9754
No 69
>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.
Probab=88.50 E-value=1.3 Score=35.54 Aligned_cols=70 Identities=20% Similarity=0.179 Sum_probs=36.0
Q ss_pred CCEEEEecCCCCCcHH-HHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHH----HHHh----hcc-E
Q 027979 44 LDHILLETTGLANPAP-LASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAI----HQIA----FAD-V 113 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~-i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~----~QI~----~AD-~ 113 (216)
..+-+|-..|=.-... +.+.+. ..-...+||+|||+..+...+.. .++.. .+.. .-+ +
T Consensus 49 ~~~~lvD~PGH~rlr~~~~~~~~------~~~~~k~IIfvvDSs~~~~~~~~------~Ae~Ly~iL~~~~~~~~~~piL 116 (181)
T PF09439_consen 49 KKLRLVDIPGHPRLRSKLLDELK------YLSNAKGIIFVVDSSTDQKELRD------VAEYLYDILSDTEVQKNKPPIL 116 (181)
T ss_dssp TCECEEEETT-HCCCHHHHHHHH------HHGGEEEEEEEEETTTHHHHHHH------HHHHHHHHHHHHHCCTT--EEE
T ss_pred CEEEEEECCCcHHHHHHHHHhhh------chhhCCEEEEEEeCccchhhHHH------HHHHHHHHHHhhhhccCCCCEE
Confidence 3556777777644322 222210 12237799999999988766544 22221 1111 122 4
Q ss_pred EEEccCCCCCCC
Q 027979 114 VILNKVDLVSPE 125 (216)
Q Consensus 114 IvlnK~D~v~~~ 125 (216)
|+.||.|+.++.
T Consensus 117 IacNK~Dl~~A~ 128 (181)
T PF09439_consen 117 IACNKQDLFTAK 128 (181)
T ss_dssp EEEE-TTSTT--
T ss_pred EEEeCccccccC
Confidence 667999998754
No 70
>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=88.35 E-value=1.7 Score=35.03 Aligned_cols=65 Identities=22% Similarity=0.349 Sum_probs=36.6
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccch--HHHHhhcccCCChhHHHHHH---hhcc-EEEEc
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNL--LFQIDKYRHLSSYPEAIHQI---AFAD-VVILN 117 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~--~~~l~~~~~~~~~~~~~~QI---~~AD-~Ivln 117 (216)
....+|-+.|-. .+.... +...-.++.++.|+|+... ..+. . +....+ ...- +|++|
T Consensus 83 ~~i~~iDtPG~~---~~~~~~-----~~~~~~~D~~llVvd~~~~~~~~~t--------~-~~l~~~~~~~~~~iiivvN 145 (203)
T cd01888 83 RHVSFVDCPGHE---ILMATM-----LSGAAVMDGALLLIAANEPCPQPQT--------S-EHLAALEIMGLKHIIIVQN 145 (203)
T ss_pred cEEEEEECCChH---HHHHHH-----HHhhhcCCEEEEEEECCCCCCCcch--------H-HHHHHHHHcCCCcEEEEEE
Confidence 346889999952 233322 2233457889999999852 1110 1 111222 2222 45999
Q ss_pred cCCCCCCC
Q 027979 118 KVDLVSPE 125 (216)
Q Consensus 118 K~D~v~~~ 125 (216)
|+|+.+++
T Consensus 146 K~Dl~~~~ 153 (203)
T cd01888 146 KIDLVKEE 153 (203)
T ss_pred chhccCHH
Confidence 99998753
No 71
>KOG0090 consensus Signal recognition particle receptor, beta subunit (small G protein superfamily) [Intracellular trafficking, secretion, and vesicular transport]
Probab=88.23 E-value=0.89 Score=37.56 Aligned_cols=53 Identities=21% Similarity=0.304 Sum_probs=36.7
Q ss_pred cccccceeeccEEEEEcccchHHHHhhcccCCChhHHH-HHHhhc-------c-EEEEccCCCCCCCC
Q 027979 68 DQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAI-HQIAFA-------D-VVILNKVDLVSPER 126 (216)
Q Consensus 68 ~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~-~QI~~A-------D-~IvlnK~D~v~~~~ 126 (216)
+.+..+++..++|.|||+..|...... .+|+. +=+..+ + +|.-||.|+..+..
T Consensus 101 e~~~~~~~akaiVFVVDSa~f~k~vrd------vaefLydil~~~~~~~~~~~vLIaCNKqDl~tAkt 162 (238)
T KOG0090|consen 101 EYLKHNYSAKAIVFVVDSATFLKNVRD------VAEFLYDILLDSRVKKNKPPVLIACNKQDLFTAKT 162 (238)
T ss_pred HHccccccceeEEEEEeccccchhhHH------HHHHHHHHHHhhccccCCCCEEEEecchhhhhcCc
Confidence 345666889999999999999877654 44543 333334 2 45569999988653
No 72
>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=87.91 E-value=7.1 Score=28.68 Aligned_cols=89 Identities=15% Similarity=0.164 Sum_probs=45.6
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh------ccEEEEc
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF------ADVVILN 117 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~------AD~Ivln 117 (216)
.+..++.+.|......+...+. + ..+.+|.|+|+..... +.. ...+..++.. -=+|++|
T Consensus 49 ~~~~l~D~~g~~~~~~~~~~~~-----~---~~d~ii~v~d~~~~~~-~~~------~~~~~~~~~~~~~~~~p~ivv~n 113 (159)
T cd00154 49 VKLQIWDTAGQERFRSITPSYY-----R---GAHGAILVYDITNRES-FEN------LDKWLKELKEYAPENIPIILVGN 113 (159)
T ss_pred EEEEEEecCChHHHHHHHHHHh-----c---CCCEEEEEEECCCHHH-HHH------HHHHHHHHHHhCCCCCcEEEEEE
Confidence 3445667777643333333221 1 2678999999987432 211 1112222222 2267789
Q ss_pred cCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 118 KVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 118 K~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
|+|+.++.+ ...+.+++..+. ...+++.++
T Consensus 114 K~D~~~~~~--~~~~~~~~~~~~--~~~~~~~~s 143 (159)
T cd00154 114 KIDLEDQRQ--VSTEEAQQFAKE--NGLLFFETS 143 (159)
T ss_pred ccccccccc--ccHHHHHHHHHH--cCCeEEEEe
Confidence 999973332 134555555544 245666544
No 73
>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=87.72 E-value=1.9 Score=32.95 Aligned_cols=79 Identities=27% Similarity=0.228 Sum_probs=38.5
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchH-----HHHhhcccCCChhHHHHH---------Hh
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLL-----FQIDKYRHLSSYPEAIHQ---------IA 109 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~-----~~l~~~~~~~~~~~~~~Q---------I~ 109 (216)
....++.+.|..+-..-.+.+. ...+...-..+.++.|+|+.... ........ ...++... ..
T Consensus 44 ~~~~i~DtpG~~~~~~~~~~~~-~~~~~~~~~~d~ii~v~d~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~ 120 (176)
T cd01881 44 ARIQVADIPGLIEGASEGRGLG-NQFLAHIRRADAILHVVDASEDDDIGGVDPLEDYEI--LNAELKLYDLETILGLLTA 120 (176)
T ss_pred CeEEEEeccccchhhhcCCCcc-HHHHHHHhccCEEEEEEeccCCccccccCHHHHHHH--HHHHHHHhhhhhHHHHHhh
Confidence 4568888888742111101010 00011122367889999998652 11111000 00111111 24
Q ss_pred hccEEEEccCCCCCCC
Q 027979 110 FADVVILNKVDLVSPE 125 (216)
Q Consensus 110 ~AD~IvlnK~D~v~~~ 125 (216)
..-++++||+|+.+..
T Consensus 121 ~p~ivv~NK~Dl~~~~ 136 (176)
T cd01881 121 KPVIYVLNKIDLDDAE 136 (176)
T ss_pred CCeEEEEEchhcCchh
Confidence 5668899999998764
No 74
>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=87.44 E-value=0.53 Score=35.15 Aligned_cols=74 Identities=23% Similarity=0.290 Sum_probs=41.7
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHH-HHhhccEEEEccCCCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIH-QIAFADVVILNKVDLV 122 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~-QI~~AD~IvlnK~D~v 122 (216)
....++.+.|..+...-.+...........-..+.++.|+|+.+...... . .... +-...-++++||+|+.
T Consensus 49 ~~~~i~DtpG~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~d~~~~~~~~~-------~-~~~~~~~~~~vi~v~nK~D~~ 120 (157)
T cd04164 49 IPVRLIDTAGIRETEDEIEKIGIERAREAIEEADLVLFVIDASRGLDEED-------L-EILELPADKPIIVVLNKSDLL 120 (157)
T ss_pred EEEEEEECCCcCCCcchHHHHHHHHHHHHHhhCCEEEEEEECCCCCCHHH-------H-HHHHhhcCCCEEEEEEchhcC
Confidence 46688999998765332211000001112236678899999986332211 1 1222 2345568899999998
Q ss_pred CCC
Q 027979 123 SPE 125 (216)
Q Consensus 123 ~~~ 125 (216)
+..
T Consensus 121 ~~~ 123 (157)
T cd04164 121 PDS 123 (157)
T ss_pred Ccc
Confidence 764
No 75
>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=87.37 E-value=1.2 Score=34.26 Aligned_cols=40 Identities=35% Similarity=0.412 Sum_probs=22.7
Q ss_pred ccEEEEEcccchHHHHhhcccCCChhHHH-HHHhhc---cEEEEccCCCCCC
Q 027979 77 DSIITVVDAKNLLFQIDKYRHLSSYPEAI-HQIAFA---DVVILNKVDLVSP 124 (216)
Q Consensus 77 ~~vI~vVDa~~~~~~l~~~~~~~~~~~~~-~QI~~A---D~IvlnK~D~v~~ 124 (216)
|-++.|+|+....... ...+. ..+... =++|+||+|++++
T Consensus 1 Dvvl~VvD~~~p~~~~--------~~~i~~~~~~~~~~p~IiVlNK~Dl~~~ 44 (155)
T cd01849 1 DVILEVLDARDPLGTR--------SPDIERVLIKEKGKKLILVLNKADLVPK 44 (155)
T ss_pred CEEEEEEeccCCcccc--------CHHHHHHHHhcCCCCEEEEEechhcCCH
Confidence 3478999997543221 11111 122222 4788899999875
No 76
>PRK10416 signal recognition particle-docking protein FtsY; Provisional
Probab=87.20 E-value=6.8 Score=34.22 Aligned_cols=97 Identities=15% Similarity=0.104 Sum_probs=54.8
Q ss_pred cCCCCEEEEecCCCCCcH-HHHHHhhc-----CcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEE
Q 027979 41 KERLDHILLETTGLANPA-PLASVLWL-----DDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVV 114 (216)
Q Consensus 41 ~~~~d~IiIE~sG~a~P~-~i~~~l~~-----~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~I 114 (216)
..++|+|||.|.|..... .+++-|.. +.. -....+.++.|+||..-...+.. . ....+....+-+
T Consensus 194 ~~~~D~ViIDTaGr~~~~~~l~~eL~~~~~v~~~~--~~~~p~~~~LVl~a~~g~~~~~~------a-~~f~~~~~~~gi 264 (318)
T PRK10416 194 ARGIDVLIIDTAGRLHNKTNLMEELKKIKRVIKKA--DPDAPHEVLLVLDATTGQNALSQ------A-KAFHEAVGLTGI 264 (318)
T ss_pred hCCCCEEEEeCCCCCcCCHHHHHHHHHHHHHHhhh--cCCCCceEEEEEECCCChHHHHH------H-HHHHhhCCCCEE
Confidence 357999999999996432 22221110 000 01234568999999965543321 0 111223346789
Q ss_pred EEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeecCC
Q 027979 115 ILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQ 154 (216)
Q Consensus 115 vlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~ 154 (216)
|+||.|..... -.+.+.+... +.||.....|+
T Consensus 265 IlTKlD~t~~~------G~~l~~~~~~--~~Pi~~v~~Gq 296 (318)
T PRK10416 265 ILTKLDGTAKG------GVVFAIADEL--GIPIKFIGVGE 296 (318)
T ss_pred EEECCCCCCCc------cHHHHHHHHH--CCCEEEEeCCC
Confidence 99999965443 2344444444 56787777775
No 77
>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=86.81 E-value=5.8 Score=30.69 Aligned_cols=66 Identities=18% Similarity=0.194 Sum_probs=35.2
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc---c---EEEEc
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA---D---VVILN 117 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A---D---~Ivln 117 (216)
..+.++.+.|...-...... .+ -..+.+|.|+|+......... ..++.+.+... + +|++|
T Consensus 59 ~~~~l~D~~G~~~~~~~~~~-----~~---~~~d~vi~V~D~s~~~~~~~~------~~~l~~~~~~~~~~~~p~viv~N 124 (174)
T cd04153 59 IRFLMWDIGGQESLRSSWNT-----YY---TNTDAVILVIDSTDRERLPLT------KEELYKMLAHEDLRKAVLLVLAN 124 (174)
T ss_pred eEEEEEECCCCHHHHHHHHH-----Hh---hcCCEEEEEEECCCHHHHHHH------HHHHHHHHhchhhcCCCEEEEEE
Confidence 35677788886422122111 11 245788999999865322111 11122222222 2 78889
Q ss_pred cCCCCC
Q 027979 118 KVDLVS 123 (216)
Q Consensus 118 K~D~v~ 123 (216)
|+|+..
T Consensus 125 K~Dl~~ 130 (174)
T cd04153 125 KQDLKG 130 (174)
T ss_pred CCCCCC
Confidence 999865
No 78
>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=86.69 E-value=10 Score=28.96 Aligned_cols=66 Identities=18% Similarity=0.046 Sum_probs=36.5
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh-----c-cEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEE
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF-----A-DVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVI 148 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~-----A-D~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv 148 (216)
..+.++.|+|+.+-... .. ...+..++.. . =+|+.||+|+.+.... ..++.+...+.. ++.++
T Consensus 76 ~~d~il~v~d~~~~~s~-~~------~~~~~~~~~~~~~~~~pvivv~nK~Dl~~~~~~--~~~~~~~~~~~~--~~~~~ 144 (168)
T cd01866 76 GAAGALLVYDITRRETF-NH------LTSWLEDARQHSNSNMTIMLIGNKCDLESRREV--SYEEGEAFAKEH--GLIFM 144 (168)
T ss_pred cCCEEEEEEECCCHHHH-HH------HHHHHHHHHHhCCCCCcEEEEEECcccccccCC--CHHHHHHHHHHc--CCEEE
Confidence 35679999998853322 11 2233344432 2 2677799999754321 334555555543 45666
Q ss_pred Eee
Q 027979 149 RSV 151 (216)
Q Consensus 149 ~~~ 151 (216)
+++
T Consensus 145 e~S 147 (168)
T cd01866 145 ETS 147 (168)
T ss_pred EEe
Confidence 544
No 79
>TIGR01007 eps_fam capsular exopolysaccharide family. This model describes the capsular exopolysaccharide proteins in bacteria. The exopolysaccharide gene cluster consists of several genes which encode a number of proteins which regulate the exoploysaccharide biosynthesis(EPS). Atleast 13 genes espA to espM in streptococcus species seem to direct the EPS proteins and all of which share high homology. Functional roles were characterized by gene disruption experiments which resulted in exopolysaccharide-deficient phenotypes.
Probab=86.69 E-value=3.5 Score=33.01 Aligned_cols=64 Identities=25% Similarity=0.311 Sum_probs=37.2
Q ss_pred CCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc----EEEEc
Q 027979 42 ERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD----VVILN 117 (216)
Q Consensus 42 ~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD----~Ivln 117 (216)
.++|+|||.++.+...... ..+. . ..+.+|.|+++......- .....++++.++ -+|+|
T Consensus 126 ~~yD~ViiD~pp~~~~~~~-~~~~------~--~~D~vilV~~~~~~~~~~--------~~~~~~~l~~~~~~~~gvVlN 188 (204)
T TIGR01007 126 KYFDYIIIDTPPIGTVTDA-AIIA------R--ACDASILVTDAGEIKKRD--------VQKAKEQLEQTGSNFLGVVLN 188 (204)
T ss_pred hcCCEEEEeCCCccccchH-HHHH------H--hCCeEEEEEECCCCCHHH--------HHHHHHHHHhCCCCEEEEEEe
Confidence 4689999999875432111 1111 1 246789999987543211 223456666553 37889
Q ss_pred cCCCC
Q 027979 118 KVDLV 122 (216)
Q Consensus 118 K~D~v 122 (216)
|.+.-
T Consensus 189 ~~~~~ 193 (204)
T TIGR01007 189 KVDIS 193 (204)
T ss_pred Ccccc
Confidence 98754
No 80
>PRK09554 feoB ferrous iron transport protein B; Reviewed
Probab=86.68 E-value=1.1 Score=43.95 Aligned_cols=72 Identities=26% Similarity=0.312 Sum_probs=41.3
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccc----eeeccEEEEEcccchHHHHhhcccCCChhHHHHHH---hhccEEEE
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESA----VRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---AFADVVIL 116 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~----~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~~AD~Ivl 116 (216)
.+..++-+.|..+-.........++..... -..|.+|.|+|+.++...+. +..|+ ..-=++++
T Consensus 50 ~~i~lvDtPG~ysl~~~~~~~s~~E~i~~~~l~~~~aD~vI~VvDat~ler~l~----------l~~ql~e~giPvIvVl 119 (772)
T PRK09554 50 HQVTLVDLPGTYSLTTISSQTSLDEQIACHYILSGDADLLINVVDASNLERNLY----------LTLQLLELGIPCIVAL 119 (772)
T ss_pred eEEEEEECCCccccccccccccHHHHHHHHHHhccCCCEEEEEecCCcchhhHH----------HHHHHHHcCCCEEEEE
Confidence 456788889986543211100001111111 15688999999998765331 22333 34458999
Q ss_pred ccCCCCCCC
Q 027979 117 NKVDLVSPE 125 (216)
Q Consensus 117 nK~D~v~~~ 125 (216)
||+|+.+..
T Consensus 120 NK~Dl~~~~ 128 (772)
T PRK09554 120 NMLDIAEKQ 128 (772)
T ss_pred Echhhhhcc
Confidence 999997654
No 81
>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=86.68 E-value=5.5 Score=30.66 Aligned_cols=88 Identities=19% Similarity=0.126 Sum_probs=43.1
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh-----hc-cEEEEcc
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA-----FA-DVVILNK 118 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~-----~A-D~IvlnK 118 (216)
...++.+.|......+.... + -..+.+|.|+|+..-...... ...+...+. .. =+|++||
T Consensus 59 ~l~l~D~~G~~~~~~~~~~~-----~---~~~d~~i~v~d~~~~~s~~~~------~~~~~~~~~~~~~~~~p~iiv~nK 124 (173)
T cd04154 59 KLNIWDVGGQKTLRPYWRNY-----F---ESTDALIWVVDSSDRLRLDDC------KRELKELLQEERLAGATLLILANK 124 (173)
T ss_pred EEEEEECCCCHHHHHHHHHH-----h---CCCCEEEEEEECCCHHHHHHH------HHHHHHHHhChhhcCCCEEEEEEC
Confidence 34667888864322222211 1 135678999999875321110 011111111 12 2677799
Q ss_pred CCCCCCCCccchHHHHHHHHHhh---CCCCEEEEe
Q 027979 119 VDLVSPERSGDSLDELEKEIHEI---NSLAHVIRS 150 (216)
Q Consensus 119 ~D~v~~~~~~~~l~~i~~~l~~l---NP~A~iv~~ 150 (216)
+|+.... ..+++.+.++.. ....+++++
T Consensus 125 ~Dl~~~~----~~~~~~~~~~~~~~~~~~~~~~~~ 155 (173)
T cd04154 125 QDLPGAL----SEEEIREALELDKISSHHWRIQPC 155 (173)
T ss_pred cccccCC----CHHHHHHHhCccccCCCceEEEec
Confidence 9997643 235555554332 234456554
No 82
>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=86.68 E-value=11 Score=30.02 Aligned_cols=98 Identities=15% Similarity=0.169 Sum_probs=50.9
Q ss_pred EEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh-----ccEEEEccCC
Q 027979 46 HILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF-----ADVVILNKVD 120 (216)
Q Consensus 46 ~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~-----AD~IvlnK~D 120 (216)
..|++++|-.....+..... . ..+++|.|+|+.+... +.. ......++.. .=+||.||+|
T Consensus 57 l~l~D~~G~~~~~~~~~~~~-----~---~a~~iilv~D~~~~~s-~~~------~~~~~~~i~~~~~~~piivVgNK~D 121 (199)
T cd04110 57 LQIWDTAGQERFRTITSTYY-----R---GTHGVIVVYDVTNGES-FVN------VKRWLQEIEQNCDDVCKVLVGNKND 121 (199)
T ss_pred EEEEeCCCchhHHHHHHHHh-----C---CCcEEEEEEECCCHHH-HHH------HHHHHHHHHHhCCCCCEEEEEECcc
Confidence 44667777544333333221 1 1356899999976542 111 1222333322 2277889999
Q ss_pred CCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhhc
Q 027979 121 LVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVLN 162 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~~ 162 (216)
+.+.... ..+...+..+..+ .++++++- .......++.
T Consensus 122 l~~~~~~--~~~~~~~~~~~~~--~~~~e~Sa~~~~gi~~lf~ 160 (199)
T cd04110 122 DPERKVV--ETEDAYKFAGQMG--ISLFETSAKENINVEEMFN 160 (199)
T ss_pred ccccccc--CHHHHHHHHHHcC--CEEEEEECCCCcCHHHHHH
Confidence 9764321 2344455555544 66776543 2345555553
No 83
>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=86.67 E-value=8.5 Score=29.15 Aligned_cols=96 Identities=15% Similarity=0.193 Sum_probs=48.2
Q ss_pred EEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh------hccEEEEccCC
Q 027979 47 ILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA------FADVVILNKVD 120 (216)
Q Consensus 47 IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~------~AD~IvlnK~D 120 (216)
-+++++|.-....+..... -..+.+|.|+|+.+.... .. ...+...+. .--+++.||+|
T Consensus 54 ~i~D~~G~~~~~~~~~~~~--------~~~~~ii~v~d~~~~~s~-~~------l~~~~~~~~~~~~~~~~~iiv~nK~D 118 (166)
T cd01869 54 QIWDTAGQERFRTITSSYY--------RGAHGIIIVYDVTDQESF-NN------VKQWLQEIDRYASENVNKLLVGNKCD 118 (166)
T ss_pred EEEECCCcHhHHHHHHHHh--------CcCCEEEEEEECcCHHHH-Hh------HHHHHHHHHHhCCCCCcEEEEEEChh
Confidence 4557777543333332221 135788999999875422 11 122222222 12377889999
Q ss_pred CCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 121 LVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
+...... ..++..+..+.. ++++++++- ...+...++
T Consensus 119 l~~~~~~--~~~~~~~~~~~~--~~~~~~~Sa~~~~~v~~~~ 156 (166)
T cd01869 119 LTDKRVV--DYSEAQEFADEL--GIPFLETSAKNATNVEQAF 156 (166)
T ss_pred cccccCC--CHHHHHHHHHHc--CCeEEEEECCCCcCHHHHH
Confidence 8765432 234444444433 456776543 223444443
No 84
>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=86.23 E-value=7.7 Score=29.25 Aligned_cols=71 Identities=18% Similarity=0.160 Sum_probs=37.1
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEccC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNKV 119 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK~ 119 (216)
+....++.+.|...-..+..... -..+.+|.|+|+.......... .......++.. .-=+|++||+
T Consensus 42 ~~~~~i~Dt~G~~~~~~~~~~~~--------~~~~~ii~v~d~~~~~~~~~~~---~~~~~~~~~~~~~~~piiiv~nK~ 110 (158)
T cd04151 42 NLKFQVWDLGGQTSIRPYWRCYY--------SNTDAIIYVVDSTDRDRLGTAK---EELHAMLEEEELKGAVLLVFANKQ 110 (158)
T ss_pred CEEEEEEECCCCHHHHHHHHHHh--------cCCCEEEEEEECCCHHHHHHHH---HHHHHHHhchhhcCCcEEEEEeCC
Confidence 34567889999864433333221 1366789999998653211000 00111111111 1226778999
Q ss_pred CCCCC
Q 027979 120 DLVSP 124 (216)
Q Consensus 120 D~v~~ 124 (216)
|+.+.
T Consensus 111 Dl~~~ 115 (158)
T cd04151 111 DMPGA 115 (158)
T ss_pred CCCCC
Confidence 99754
No 85
>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=86.17 E-value=10 Score=28.36 Aligned_cols=99 Identities=14% Similarity=0.167 Sum_probs=50.2
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH-------hhccEEEE
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI-------AFADVVIL 116 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI-------~~AD~Ivl 116 (216)
..+.++.+.|......+..... . ..+.++.++|...-.. +.+ ......++ ..-=+|++
T Consensus 48 ~~~~i~D~~g~~~~~~~~~~~~-----~---~~~~~i~v~d~~~~~s-~~~------~~~~~~~~~~~~~~~~~piiiv~ 112 (164)
T cd04139 48 VQLNILDTAGQEDYAAIRDNYH-----R---SGEGFLLVFSITDMES-FTA------TAEFREQILRVKDDDNVPLLLVG 112 (164)
T ss_pred EEEEEEECCChhhhhHHHHHHh-----h---cCCEEEEEEECCCHHH-HHH------HHHHHHHHHHhcCCCCCCEEEEE
Confidence 3467788888766555544332 1 2256788888764321 111 11111111 22337899
Q ss_pred ccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 117 NKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 117 nK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
||+|+.+... .......+..+.++ .++++++. -...+++++
T Consensus 113 NK~D~~~~~~--~~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~ 154 (164)
T cd04139 113 NKCDLEDKRQ--VSSEEAANLARQWG--VPYVETSAKTRQNVEKAF 154 (164)
T ss_pred Eccccccccc--cCHHHHHHHHHHhC--CeEEEeeCCCCCCHHHHH
Confidence 9999977321 12344445544443 56665442 233444444
No 86
>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=86.11 E-value=1.1 Score=36.88 Aligned_cols=72 Identities=15% Similarity=0.151 Sum_probs=36.3
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLV 122 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v 122 (216)
...+.+|-+.|..+ ....... .+.. ...+.++.|||+..-....... +-.+..+....=+|++||+|++
T Consensus 83 ~~~i~liDtpG~~~---~~~~~~~--~~~~-~~~D~~llVvda~~g~~~~d~~-----~l~~l~~~~ip~ivvvNK~D~~ 151 (224)
T cd04165 83 SKLVTFIDLAGHER---YLKTTLF--GLTG-YAPDYAMLVVAANAGIIGMTKE-----HLGLALALNIPVFVVVTKIDLA 151 (224)
T ss_pred CcEEEEEECCCcHH---HHHHHHH--hhcc-cCCCEEEEEEECCCCCcHHHHH-----HHHHHHHcCCCEEEEEECcccc
Confidence 34567788888642 2221110 1111 2456788999987533211110 0011122222238999999998
Q ss_pred CCC
Q 027979 123 SPE 125 (216)
Q Consensus 123 ~~~ 125 (216)
+++
T Consensus 152 ~~~ 154 (224)
T cd04165 152 PAN 154 (224)
T ss_pred CHH
Confidence 764
No 87
>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=85.98 E-value=1.9 Score=34.15 Aligned_cols=64 Identities=25% Similarity=0.349 Sum_probs=36.0
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK~D 120 (216)
....+|-+.|-.+= +.++. ...-..|.+|.|||+....... ..+...++. .-=+|++||+|
T Consensus 70 ~~i~~iDtPG~~~f--~~~~~------~~~~~~D~ailvVda~~g~~~~--------~~~~l~~~~~~~~p~ivvlNK~D 133 (188)
T PF00009_consen 70 RKITLIDTPGHEDF--IKEMI------RGLRQADIAILVVDANDGIQPQ--------TEEHLKILRELGIPIIVVLNKMD 133 (188)
T ss_dssp EEEEEEEESSSHHH--HHHHH------HHHTTSSEEEEEEETTTBSTHH--------HHHHHHHHHHTT-SEEEEEETCT
T ss_pred cceeecccccccce--eeccc------ceecccccceeeeecccccccc--------cccccccccccccceEEeeeecc
Confidence 45677888886431 11221 1123457789999997543211 112223333 33588999999
Q ss_pred CCC
Q 027979 121 LVS 123 (216)
Q Consensus 121 ~v~ 123 (216)
+..
T Consensus 134 ~~~ 136 (188)
T PF00009_consen 134 LIE 136 (188)
T ss_dssp SSH
T ss_pred chh
Confidence 984
No 88
>PRK15467 ethanolamine utilization protein EutP; Provisional
Probab=85.95 E-value=1.7 Score=33.58 Aligned_cols=74 Identities=11% Similarity=0.173 Sum_probs=43.5
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHH-HHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIH-QIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR- 152 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~-QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~- 152 (216)
..+.++.|+|+......+. ..+.+ .....-++++||+|+.+.. .+.+.+.++++....+++.++-
T Consensus 64 ~ad~il~v~d~~~~~s~~~--------~~~~~~~~~~~ii~v~nK~Dl~~~~-----~~~~~~~~~~~~~~~p~~~~Sa~ 130 (158)
T PRK15467 64 DVDMLIYVHGANDPESRLP--------AGLLDIGVSKRQIAVISKTDMPDAD-----VAATRKLLLETGFEEPIFELNSH 130 (158)
T ss_pred cCCEEEEEEeCCCcccccC--------HHHHhccCCCCeEEEEEccccCccc-----HHHHHHHHHHcCCCCCEEEEECC
Confidence 5688999999986542211 01111 0112347899999986542 4667777777766567775433
Q ss_pred CCCChhhhh
Q 027979 153 CQVDLSEVL 161 (216)
Q Consensus 153 ~~v~~~~l~ 161 (216)
..-..+.++
T Consensus 131 ~g~gi~~l~ 139 (158)
T PRK15467 131 DPQSVQQLV 139 (158)
T ss_pred CccCHHHHH
Confidence 233454554
No 89
>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=85.49 E-value=11 Score=28.32 Aligned_cols=86 Identities=15% Similarity=0.115 Sum_probs=43.4
Q ss_pred EEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hc-c---EEEEccC
Q 027979 47 ILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FA-D---VVILNKV 119 (216)
Q Consensus 47 IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~A-D---~IvlnK~ 119 (216)
-|..++|.-....+..... -.-+.++.|+|...-... .. ...+..++. .. + +|+.||+
T Consensus 52 ~i~Dt~G~~~~~~~~~~~~--------~~~~~~ilv~d~~~~~s~-~~------~~~~~~~i~~~~~~~~~piilv~nK~ 116 (163)
T cd04136 52 EILDTAGTEQFTAMRDLYI--------KNGQGFVLVYSITSQSSF-ND------LQDLREQILRVKDTENVPMVLVGNKC 116 (163)
T ss_pred EEEECCCccccchHHHHHh--------hcCCEEEEEEECCCHHHH-HH------HHHHHHHHHHhcCCCCCCEEEEEECc
Confidence 4578888765554443322 124567888887654321 11 112223332 11 1 5688999
Q ss_pred CCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 120 DLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
|+.+.... ..+...+..+..+ .++++++
T Consensus 117 Dl~~~~~~--~~~~~~~~~~~~~--~~~~~~S 144 (163)
T cd04136 117 DLEDERVV--SREEGQALARQWG--CPFYETS 144 (163)
T ss_pred ccccccee--cHHHHHHHHHHcC--CeEEEec
Confidence 99764321 2233333334443 6676654
No 90
>cd04114 Rab30 Rab30 subfamily. Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=85.42 E-value=12 Score=28.24 Aligned_cols=75 Identities=15% Similarity=0.189 Sum_probs=38.8
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHHHHH---hhcc---EEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEE
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---AFAD---VVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIR 149 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~~AD---~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~ 149 (216)
.+.++.|+|+..-... .. .+....++ ...+ +++.||+|+.+..+. ...+.+.+...++ .++++
T Consensus 80 ~d~~i~v~d~~~~~s~-~~------~~~~~~~l~~~~~~~~~~i~v~NK~D~~~~~~i---~~~~~~~~~~~~~-~~~~~ 148 (169)
T cd04114 80 ANALILTYDITCEESF-RC------LPEWLREIEQYANNKVITILVGNKIDLAERREV---SQQRAEEFSDAQD-MYYLE 148 (169)
T ss_pred CCEEEEEEECcCHHHH-HH------HHHHHHHHHHhCCCCCeEEEEEECccccccccc---CHHHHHHHHHHcC-CeEEE
Confidence 4568999998754321 11 22233333 2223 788899999765432 2334445555554 55554
Q ss_pred eec-CCCChhhhh
Q 027979 150 SVR-CQVDLSEVL 161 (216)
Q Consensus 150 ~~~-~~v~~~~l~ 161 (216)
++- .+.+...++
T Consensus 149 ~Sa~~~~gv~~l~ 161 (169)
T cd04114 149 TSAKESDNVEKLF 161 (169)
T ss_pred eeCCCCCCHHHHH
Confidence 332 233444444
No 91
>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=85.35 E-value=12 Score=28.22 Aligned_cols=98 Identities=17% Similarity=0.150 Sum_probs=51.0
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH----hhcc---EEEEc
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI----AFAD---VVILN 117 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI----~~AD---~Ivln 117 (216)
..-++.++|......+..... -..++++.|+|+..-.. +.+ ......++ ...+ +++.|
T Consensus 49 ~l~i~Dt~g~~~~~~~~~~~~--------~~~~~~i~v~d~~~~~s-~~~------~~~~~~~i~~~~~~~~~pii~v~n 113 (164)
T smart00173 49 LLDILDTAGQEEFSAMRDQYM--------RTGEGFLLVYSITDRQS-FEE------IKKFREQILRVKDRDDVPIVLVGN 113 (164)
T ss_pred EEEEEECCCcccchHHHHHHH--------hhCCEEEEEEECCCHHH-HHH------HHHHHHHHHHhcCCCCCCEEEEEE
Confidence 345688999877666554432 12467899999876432 111 11111122 1112 56889
Q ss_pred cCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 118 KVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 118 K~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
|+|+.+... ...+...+..+..+ +++++++- ...+.+.++
T Consensus 114 K~Dl~~~~~--~~~~~~~~~~~~~~--~~~~~~Sa~~~~~i~~l~ 154 (164)
T smart00173 114 KCDLESERV--VSTEEGKELARQWG--CPFLETSAKERVNVDEAF 154 (164)
T ss_pred Cccccccce--EcHHHHHHHHHHcC--CEEEEeecCCCCCHHHHH
Confidence 999976432 12344444555444 56665442 233444444
No 92
>KOG0780 consensus Signal recognition particle, subunit Srp54 [Intracellular trafficking, secretion, and vesicular transport]
Probab=85.31 E-value=2.2 Score=38.36 Aligned_cols=74 Identities=28% Similarity=0.299 Sum_probs=49.7
Q ss_pred cCCCCEEEEecCCCCCcH-HHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccC
Q 027979 41 KERLDHILLETTGLANPA-PLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKV 119 (216)
Q Consensus 41 ~~~~d~IiIE~sG~a~P~-~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~ 119 (216)
+.++|.||+-|||=-.-. .+.+-+. .....+..+.||.|+||...+.... ...++.|-..---|||+|.
T Consensus 181 ke~fdvIIvDTSGRh~qe~sLfeEM~---~v~~ai~Pd~vi~VmDasiGQaae~-------Qa~aFk~~vdvg~vIlTKl 250 (483)
T KOG0780|consen 181 KENFDVIIVDTSGRHKQEASLFEEMK---QVSKAIKPDEIIFVMDASIGQAAEA-------QARAFKETVDVGAVILTKL 250 (483)
T ss_pred hcCCcEEEEeCCCchhhhHHHHHHHH---HHHhhcCCCeEEEEEeccccHhHHH-------HHHHHHHhhccceEEEEec
Confidence 458999999999975432 2332221 2456788999999999987764432 1234556566667899999
Q ss_pred CCCCC
Q 027979 120 DLVSP 124 (216)
Q Consensus 120 D~v~~ 124 (216)
|--..
T Consensus 251 DGhak 255 (483)
T KOG0780|consen 251 DGHAK 255 (483)
T ss_pred ccCCC
Confidence 96443
No 93
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=85.27 E-value=1.5 Score=41.88 Aligned_cols=72 Identities=17% Similarity=0.179 Sum_probs=36.1
Q ss_pred eeeccEEEEEcccchHH-HHhhcccCCChhHHHHHHhhcc-EEEEccCCCCCCCCccchHHHHHHHHHhhC-CCCEEEEe
Q 027979 74 VRLDSIITVVDAKNLLF-QIDKYRHLSSYPEAIHQIAFAD-VVILNKVDLVSPERSGDSLDELEKEIHEIN-SLAHVIRS 150 (216)
Q Consensus 74 ~~l~~vI~vVDa~~~~~-~l~~~~~~~~~~~~~~QI~~AD-~IvlnK~D~v~~~~~~~~l~~i~~~l~~lN-P~A~iv~~ 150 (216)
-..|.++.|||+..... +... +-.+...+...- +|++||+|+++++......+++++.++..+ ..++++++
T Consensus 73 ~~~D~~lLVVda~eg~~~qT~e------hl~il~~lgi~~iIVVlNKiDlv~~~~~~~v~~ei~~~l~~~~~~~~~ii~V 146 (614)
T PRK10512 73 GGIDHALLVVACDDGVMAQTRE------HLAILQLTGNPMLTVALTKADRVDEARIAEVRRQVKAVLREYGFAEAKLFVT 146 (614)
T ss_pred hcCCEEEEEEECCCCCcHHHHH------HHHHHHHcCCCeEEEEEECCccCCHHHHHHHHHHHHHHHHhcCCCCCcEEEE
Confidence 45678899999875321 1111 101122333333 589999999875421111233444444332 23667754
Q ss_pred e
Q 027979 151 V 151 (216)
Q Consensus 151 ~ 151 (216)
+
T Consensus 147 S 147 (614)
T PRK10512 147 A 147 (614)
T ss_pred e
Confidence 4
No 94
>COG3276 SelB Selenocysteine-specific translation elongation factor [Translation, ribosomal structure and biogenesis]
Probab=85.02 E-value=1.8 Score=39.31 Aligned_cols=92 Identities=16% Similarity=0.281 Sum_probs=52.9
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEccc-chHHHHhhcccCCChhHHHHHHhhcc-EEEEccCCCC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAK-NLLFQIDKYRHLSSYPEAIHQIAFAD-VVILNKVDLV 122 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~-~~~~~l~~~~~~~~~~~~~~QI~~AD-~IvlnK~D~v 122 (216)
-.-+|+++|= |.-|...+ ....-++..+.|||+. .+..+... +=.+.+.+..-. +|++||+|++
T Consensus 51 ~~~fIDvpgh--~~~i~~mi------ag~~~~d~alLvV~~deGl~~qtgE------hL~iLdllgi~~giivltk~D~~ 116 (447)
T COG3276 51 VMGFIDVPGH--PDFISNLL------AGLGGIDYALLVVAADEGLMAQTGE------HLLILDLLGIKNGIIVLTKADRV 116 (447)
T ss_pred ceEEeeCCCc--HHHHHHHH------hhhcCCceEEEEEeCccCcchhhHH------HHHHHHhcCCCceEEEEeccccc
Confidence 4457888886 55444433 2334566678999993 44433322 223457777777 8999999999
Q ss_pred CCCCccchHHHHHHHHHhhCCCCEEEEeec
Q 027979 123 SPERSGDSLDELEKEIHEINSLAHVIRSVR 152 (216)
Q Consensus 123 ~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~ 152 (216)
++++....++++.+.+. -+.++++.++.
T Consensus 117 d~~r~e~~i~~Il~~l~--l~~~~i~~~s~ 144 (447)
T COG3276 117 DEARIEQKIKQILADLS--LANAKIFKTSA 144 (447)
T ss_pred cHHHHHHHHHHHHhhcc--ccccccccccc
Confidence 87532112222222222 35566665443
No 95
>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=84.99 E-value=2.7 Score=35.77 Aligned_cols=69 Identities=16% Similarity=0.101 Sum_probs=38.9
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLV 122 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v 122 (216)
+..+.+|-|.|..+...-... ..-..+.+|.|||+......-... .-....+...-=++++||+|+.
T Consensus 63 ~~~i~liDTPG~~df~~~~~~--------~l~~aD~ailVVDa~~g~~~~t~~-----~~~~~~~~~~p~ivviNK~D~~ 129 (270)
T cd01886 63 DHRINIIDTPGHVDFTIEVER--------SLRVLDGAVAVFDAVAGVEPQTET-----VWRQADRYNVPRIAFVNKMDRT 129 (270)
T ss_pred CEEEEEEECCCcHHHHHHHHH--------HHHHcCEEEEEEECCCCCCHHHHH-----HHHHHHHcCCCEEEEEECCCCC
Confidence 356788999998654322211 122356889999997643211100 0011223333458999999997
Q ss_pred CC
Q 027979 123 SP 124 (216)
Q Consensus 123 ~~ 124 (216)
+.
T Consensus 130 ~a 131 (270)
T cd01886 130 GA 131 (270)
T ss_pred CC
Confidence 64
No 96
>PRK12297 obgE GTPase CgtA; Reviewed
Probab=84.71 E-value=2.9 Score=38.09 Aligned_cols=68 Identities=24% Similarity=0.369 Sum_probs=35.9
Q ss_pred CEEEEecCCCCCcHH----HHHHhhcCcccccceeeccEEEEEcccchH--HHHhhcccCCChhHHHHHH--------hh
Q 027979 45 DHILLETTGLANPAP----LASVLWLDDQLESAVRLDSIITVVDAKNLL--FQIDKYRHLSSYPEAIHQI--------AF 110 (216)
Q Consensus 45 d~IiIE~sG~a~P~~----i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~--~~l~~~~~~~~~~~~~~QI--------~~ 110 (216)
..+++-+.|+.+-.. +...+ ++..-+.+.+|.|+|+.... +.+.. +..+..++ ..
T Consensus 207 ~~~laD~PGliega~~~~gLg~~f-----Lrhier~~llI~VID~s~~~~~dp~e~------~~~i~~EL~~y~~~L~~k 275 (424)
T PRK12297 207 SFVMADIPGLIEGASEGVGLGHQF-----LRHIERTRVIVHVIDMSGSEGRDPIED------YEKINKELKLYNPRLLER 275 (424)
T ss_pred eEEEEECCCCcccccccchHHHHH-----HHHHhhCCEEEEEEeCCccccCChHHH------HHHHHHHHhhhchhccCC
Confidence 467788888753211 22211 22233467899999996431 11111 11122222 23
Q ss_pred ccEEEEccCCCCC
Q 027979 111 ADVVILNKVDLVS 123 (216)
Q Consensus 111 AD~IvlnK~D~v~ 123 (216)
--+||+||+|+..
T Consensus 276 P~IVV~NK~DL~~ 288 (424)
T PRK12297 276 PQIVVANKMDLPE 288 (424)
T ss_pred cEEEEEeCCCCcC
Confidence 4588999999843
No 97
>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=84.63 E-value=5.5 Score=29.68 Aligned_cols=66 Identities=26% Similarity=0.279 Sum_probs=39.5
Q ss_pred CCEEEEecCCCCCcHH------HHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEE
Q 027979 44 LDHILLETTGLANPAP------LASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVV 114 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~------i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~I 114 (216)
.++.++.|.|..+-.. +...+. .. -..+.+|.|+|+....... ....|+. ..=++
T Consensus 43 ~~~~liDtpG~~~~~~~~~~~~~~~~~~-----~~-~~~d~vi~v~d~~~~~~~~----------~~~~~~~~~~~~~ii 106 (158)
T cd01879 43 KEIEIVDLPGTYSLSPYSEDEKVARDFL-----LG-EKPDLIVNVVDATNLERNL----------YLTLQLLELGLPVVV 106 (158)
T ss_pred eEEEEEECCCccccCCCChhHHHHHHHh-----cC-CCCcEEEEEeeCCcchhHH----------HHHHHHHHcCCCEEE
Confidence 4678999999865332 122111 10 2567899999998753221 1222332 33478
Q ss_pred EEccCCCCCCC
Q 027979 115 ILNKVDLVSPE 125 (216)
Q Consensus 115 vlnK~D~v~~~ 125 (216)
++||+|+.+..
T Consensus 107 v~NK~Dl~~~~ 117 (158)
T cd01879 107 ALNMIDEAEKR 117 (158)
T ss_pred EEehhhhcccc
Confidence 88999998764
No 98
>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=84.40 E-value=15 Score=27.95 Aligned_cols=87 Identities=16% Similarity=0.174 Sum_probs=44.9
Q ss_pred EEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh-----cc-EEEEccC
Q 027979 46 HILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF-----AD-VVILNKV 119 (216)
Q Consensus 46 ~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~-----AD-~IvlnK~ 119 (216)
..+.+++|.-....+..... . ..+.+|.|.|+..-.. +.. ......++.. .- +|+.||+
T Consensus 54 l~l~D~~g~~~~~~~~~~~~-----~---~ad~~i~v~d~~~~~s-~~~------~~~~~~~i~~~~~~~~p~iiv~nK~ 118 (167)
T cd01867 54 LQIWDTAGQERFRTITTAYY-----R---GAMGIILVYDITDEKS-FEN------IRNWMRNIEEHASEDVERMLVGNKC 118 (167)
T ss_pred EEEEeCCchHHHHHHHHHHh-----C---CCCEEEEEEECcCHHH-HHh------HHHHHHHHHHhCCCCCcEEEEEECc
Confidence 34567777543333332221 1 3477899999876432 222 2222333322 22 7788999
Q ss_pred CCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 120 DLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
|+.+..+. ..++..+..+..+ .++++++
T Consensus 119 Dl~~~~~~--~~~~~~~~~~~~~--~~~~~~S 146 (167)
T cd01867 119 DMEEKRVV--SKEEGEALADEYG--IKFLETS 146 (167)
T ss_pred ccccccCC--CHHHHHHHHHHcC--CEEEEEe
Confidence 99864321 3345555555433 4556543
No 99
>PTZ00099 rab6; Provisional
Probab=84.37 E-value=10 Score=29.79 Aligned_cols=101 Identities=18% Similarity=0.169 Sum_probs=54.0
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH---hhcc---EEEE
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---AFAD---VVIL 116 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~~AD---~Ivl 116 (216)
.....|..|+|......+..... -.-+.+|.|+|...-.. +.. ......++ ...+ ++|.
T Consensus 28 ~v~l~iwDt~G~e~~~~~~~~~~--------~~ad~~ilv~D~t~~~s-f~~------~~~w~~~i~~~~~~~~piilVg 92 (176)
T PTZ00099 28 PVRLQLWDTAGQERFRSLIPSYI--------RDSAAAIVVYDITNRQS-FEN------TTKWIQDILNERGKDVIIALVG 92 (176)
T ss_pred EEEEEEEECCChHHhhhccHHHh--------CCCcEEEEEEECCCHHH-HHH------HHHHHHHHHHhcCCCCeEEEEE
Confidence 45778889999876655544322 13467899999887332 111 11222222 1223 5788
Q ss_pred ccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee-cCCCChhhhhc
Q 027979 117 NKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV-RCQVDLSEVLN 162 (216)
Q Consensus 117 nK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~-~~~v~~~~l~~ 162 (216)
||+|+.+.... ..++.....+..+ ..+++++ ........++.
T Consensus 93 NK~DL~~~~~v--~~~e~~~~~~~~~--~~~~e~SAk~g~nV~~lf~ 135 (176)
T PTZ00099 93 NKTDLGDLRKV--TYEEGMQKAQEYN--TMFHETSAKAGHNIKVLFK 135 (176)
T ss_pred ECcccccccCC--CHHHHHHHHHHcC--CEEEEEECCCCCCHHHHHH
Confidence 99999753221 2344444444443 3555443 22345555553
No 100
>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=84.10 E-value=15 Score=29.64 Aligned_cols=98 Identities=10% Similarity=0.008 Sum_probs=50.4
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh--------cc-EEE
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF--------AD-VVI 115 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~--------AD-~Iv 115 (216)
...|..+.|--.+..+...+. -.-+.+|.|+|..+.... .+ ...+..++.. .- ++|
T Consensus 51 ~~~i~Dt~G~~~~~~l~~~~~--------~~ad~iilV~D~t~~~s~-~~------~~~w~~~l~~~~~~~~~~~piilV 115 (215)
T cd04109 51 TLQVWDIGGQSIGGKMLDKYI--------YGAHAVFLVYDVTNSQSF-EN------LEDWYSMVRKVLKSSETQPLVVLV 115 (215)
T ss_pred EEEEEECCCcHHHHHHHHHHh--------hcCCEEEEEEECCCHHHH-HH------HHHHHHHHHHhccccCCCceEEEE
Confidence 445678888655555544432 245788999999875432 11 1222233321 11 457
Q ss_pred EccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 116 LNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 116 lnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
.||+|+.+.... ..++..+..+..+ ++.+.++. ..-....++
T Consensus 116 gNK~DL~~~~~v--~~~~~~~~~~~~~--~~~~~iSAktg~gv~~lf 158 (215)
T cd04109 116 GNKTDLEHNRTV--KDDKHARFAQANG--MESCLVSAKTGDRVNLLF 158 (215)
T ss_pred EECccccccccc--CHHHHHHHHHHcC--CEEEEEECCCCCCHHHHH
Confidence 799999754321 2234444444332 45554332 234455554
No 101
>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=84.10 E-value=4.9 Score=28.81 Aligned_cols=98 Identities=16% Similarity=0.051 Sum_probs=50.8
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLV 122 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v 122 (216)
..+..++++.|..+-....... .-..+.++.|+|+......................-...-++++||+|+.
T Consensus 44 ~~~~~l~D~~g~~~~~~~~~~~--------~~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivv~nk~D~~ 115 (157)
T cd00882 44 KVKLQIWDTAGQERFRSLRRLY--------YRGADGIILVYDVTDRESFENVKEWLLLILINKEGENIPIILVGNKIDLP 115 (157)
T ss_pred EEEEEEEecCChHHHHhHHHHH--------hcCCCEEEEEEECcCHHHHHHHHHHHHHHHHhhccCCCcEEEEEeccccc
Confidence 4567888999976554433221 12456789999999755322110000000000122234458888999998
Q ss_pred CCCCccchHHHHH-HHHHhhCCCCEEEEeec
Q 027979 123 SPERSGDSLDELE-KEIHEINSLAHVIRSVR 152 (216)
Q Consensus 123 ~~~~~~~~l~~i~-~~l~~lNP~A~iv~~~~ 152 (216)
..... .... .......+..+++.++.
T Consensus 116 ~~~~~----~~~~~~~~~~~~~~~~~~~~s~ 142 (157)
T cd00882 116 EERVV----SEEELAEQLAKELGVPYFETSA 142 (157)
T ss_pred cccch----HHHHHHHHHHhhcCCcEEEEec
Confidence 76532 2211 22333455677776543
No 102
>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=83.67 E-value=10 Score=30.38 Aligned_cols=78 Identities=14% Similarity=-0.049 Sum_probs=41.1
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh---------ccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCC
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF---------ADVVILNKVDLVSPERSGDSLDELEKEIHEINSLA 145 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~---------AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A 145 (216)
..+.+|.|+|+.+-... .. ...+.+++.. .=+|+.||+|+...... ..+.+.+..++.+ ++
T Consensus 80 ~ad~iilv~D~~~~~S~-~~------~~~~~~~i~~~~~~~~~~~piiivgNK~Dl~~~~~~--~~~~~~~~~~~~~-~~ 149 (198)
T cd04142 80 NSRAFILVYDICSPDSF-HY------VKLLRQQILETRPAGNKEPPIVVVGNKRDQQRHRFA--PRHVLSVLVRKSW-KC 149 (198)
T ss_pred cCCEEEEEEECCCHHHH-HH------HHHHHHHHHHhcccCCCCCCEEEEEECccccccccc--cHHHHHHHHHHhc-CC
Confidence 46788999999865322 11 1223333322 12788899999654321 1222333222222 46
Q ss_pred EEEEeec-CCCChhhhhc
Q 027979 146 HVIRSVR-CQVDLSEVLN 162 (216)
Q Consensus 146 ~iv~~~~-~~v~~~~l~~ 162 (216)
++++++- ...+...++.
T Consensus 150 ~~~e~Sak~g~~v~~lf~ 167 (198)
T cd04142 150 GYLECSAKYNWHILLLFK 167 (198)
T ss_pred cEEEecCCCCCCHHHHHH
Confidence 6776543 3456666663
No 103
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=83.66 E-value=3.8 Score=37.46 Aligned_cols=86 Identities=20% Similarity=0.259 Sum_probs=47.0
Q ss_pred hHHHHHHHHHHhcCCCCEEEEecCCCCCc-HHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHH
Q 027979 29 SLVQALEQLVQRKERLDHILLETTGLANP-APLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQ 107 (216)
Q Consensus 29 dl~~~L~~l~~~~~~~d~IiIE~sG~a~P-~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~Q 107 (216)
+....+.+.+++....|+|||-|.|.... ..+++-+. .+...+.-+.++.|+||..-.+.+.. . ..+.+
T Consensus 161 d~~~i~~~al~~~~~~DvVIIDTAGr~~~d~~lm~El~---~l~~~~~pdevlLVvda~~gq~av~~------a-~~F~~ 230 (437)
T PRK00771 161 DAVEIAKEGLEKFKKADVIIVDTAGRHALEEDLIEEMK---EIKEAVKPDEVLLVIDATIGQQAKNQ------A-KAFHE 230 (437)
T ss_pred CHHHHHHHHHHHhhcCCEEEEECCCcccchHHHHHHHH---HHHHHhcccceeEEEeccccHHHHHH------H-HHHHh
Confidence 33333444333223359999999997643 33333221 12234456678999999775433211 1 11111
Q ss_pred HhhccEEEEccCCCCCC
Q 027979 108 IAFADVVILNKVDLVSP 124 (216)
Q Consensus 108 I~~AD~IvlnK~D~v~~ 124 (216)
--.-+-||+||.|....
T Consensus 231 ~l~i~gvIlTKlD~~a~ 247 (437)
T PRK00771 231 AVGIGGIIITKLDGTAK 247 (437)
T ss_pred cCCCCEEEEecccCCCc
Confidence 12247899999997544
No 104
>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=83.50 E-value=3.2 Score=33.54 Aligned_cols=68 Identities=24% Similarity=0.300 Sum_probs=35.3
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEE-EEccCCCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVV-ILNKVDLV 122 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~I-vlnK~D~v 122 (216)
..+.++-|.|..+ +..... ...-..+.+|.|+|+..-...-.. ....+..+...--+| ++||+|+.
T Consensus 77 ~~~~liDTpG~~~---~~~~~~-----~~~~~ad~~llVvD~~~~~~~~~~-----~~~~~~~~~~~~~iIvviNK~D~~ 143 (208)
T cd04166 77 RKFIIADTPGHEQ---YTRNMV-----TGASTADLAILLVDARKGVLEQTR-----RHSYILSLLGIRHVVVAVNKMDLV 143 (208)
T ss_pred ceEEEEECCcHHH---HHHHHH-----HhhhhCCEEEEEEECCCCccHhHH-----HHHHHHHHcCCCcEEEEEEchhcc
Confidence 4678899999642 211110 112356788999999753211100 011112222222345 68999997
Q ss_pred CC
Q 027979 123 SP 124 (216)
Q Consensus 123 ~~ 124 (216)
+.
T Consensus 144 ~~ 145 (208)
T cd04166 144 DY 145 (208)
T ss_pred cC
Confidence 64
No 105
>TIGR01425 SRP54_euk signal recognition particle protein SRP54. This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.
Probab=83.39 E-value=4.6 Score=36.81 Aligned_cols=80 Identities=25% Similarity=0.308 Sum_probs=49.6
Q ss_pred HHHHHHHhcCCCCEEEEecCCCCCcH-HHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc
Q 027979 33 ALEQLVQRKERLDHILLETTGLANPA-PLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA 111 (216)
Q Consensus 33 ~L~~l~~~~~~~d~IiIE~sG~a~P~-~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A 111 (216)
++.++. ...+|+|||-|.|--... .+.+.+. .+......+.++.|+||..-...... ...+.+...-
T Consensus 174 ~l~~~~--~~~~DvViIDTaGr~~~d~~lm~El~---~i~~~~~p~e~lLVlda~~Gq~a~~~-------a~~F~~~~~~ 241 (429)
T TIGR01425 174 GVEKFK--KENFDIIIVDTSGRHKQEDSLFEEML---QVAEAIQPDNIIFVMDGSIGQAAEAQ-------AKAFKDSVDV 241 (429)
T ss_pred HHHHHH--hCCCCEEEEECCCCCcchHHHHHHHH---HHhhhcCCcEEEEEeccccChhHHHH-------HHHHHhccCC
Confidence 444442 246899999999987663 3443332 12334556778999999765433211 1223444456
Q ss_pred cEEEEccCCCCCC
Q 027979 112 DVVILNKVDLVSP 124 (216)
Q Consensus 112 D~IvlnK~D~v~~ 124 (216)
+-+|+||.|....
T Consensus 242 ~g~IlTKlD~~ar 254 (429)
T TIGR01425 242 GSVIITKLDGHAK 254 (429)
T ss_pred cEEEEECccCCCC
Confidence 8899999998554
No 106
>PRK11058 GTPase HflX; Provisional
Probab=83.29 E-value=2.8 Score=38.09 Aligned_cols=72 Identities=21% Similarity=0.441 Sum_probs=43.4
Q ss_pred CEEEEecCCC-CC-cHHHHHHhhcCcccccceeeccEEEEEcccchHH--HHhhcccCCChhHHHHHHhh---ccEEEEc
Q 027979 45 DHILLETTGL-AN-PAPLASVLWLDDQLESAVRLDSIITVVDAKNLLF--QIDKYRHLSSYPEAIHQIAF---ADVVILN 117 (216)
Q Consensus 45 d~IiIE~sG~-a~-P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~--~l~~~~~~~~~~~~~~QI~~---AD~Ivln 117 (216)
..+++-|.|. .+ |..+.+.+.. .+...-.-+.++.|+|+++-.. .+.. ......++.. --++|+|
T Consensus 246 ~~~l~DTaG~~r~lp~~lve~f~~--tl~~~~~ADlIL~VvDaS~~~~~e~l~~------v~~iL~el~~~~~pvIiV~N 317 (426)
T PRK11058 246 ETVLADTVGFIRHLPHDLVAAFKA--TLQETRQATLLLHVVDAADVRVQENIEA------VNTVLEEIDAHEIPTLLVMN 317 (426)
T ss_pred eEEEEecCcccccCCHHHHHHHHH--HHHHhhcCCEEEEEEeCCCccHHHHHHH------HHHHHHHhccCCCCEEEEEE
Confidence 5588999998 33 7777665431 2333445677999999986431 1110 1122344432 2378899
Q ss_pred cCCCCCC
Q 027979 118 KVDLVSP 124 (216)
Q Consensus 118 K~D~v~~ 124 (216)
|+|+.+.
T Consensus 318 KiDL~~~ 324 (426)
T PRK11058 318 KIDMLDD 324 (426)
T ss_pred cccCCCc
Confidence 9999754
No 107
>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=82.92 E-value=12 Score=28.77 Aligned_cols=93 Identities=16% Similarity=0.174 Sum_probs=45.2
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK~D 120 (216)
+...++.++|..+-..+.... .-..+.+|.++|....... .... ..+..+.++.. ..-+++.||+|
T Consensus 49 ~~~~l~D~~g~~~~~~~~~~~--------~~~~~~~i~v~d~~~~~~~-~~~~--~~~~~~~~~~~~~~~p~ilv~NK~D 117 (180)
T cd04137 49 YHLEIVDTAGQDEYSILPQKY--------SIGIHGYILVYSVTSRKSF-EVVK--VIYDKILDMLGKESVPIVLVGNKSD 117 (180)
T ss_pred EEEEEEECCChHhhHHHHHHH--------HhhCCEEEEEEECCCHHHH-HHHH--HHHHHHHHhcCCCCCCEEEEEEchh
Confidence 345678888875433222221 1235567888888865422 1100 00111222222 24589999999
Q ss_pred CCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 121 LVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
+...... ..+......+..+ .++++++
T Consensus 118 l~~~~~~--~~~~~~~~~~~~~--~~~~~~S 144 (180)
T cd04137 118 LHTQRQV--STEEGKELAESWG--AAFLESS 144 (180)
T ss_pred hhhcCcc--CHHHHHHHHHHcC--CeEEEEe
Confidence 8754321 2233333334333 5666543
No 108
>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=82.90 E-value=6.8 Score=30.73 Aligned_cols=80 Identities=18% Similarity=0.194 Sum_probs=41.6
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHH--Hh-hccEEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQ--IA-FADVVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~Q--I~-~AD~IvlnK~D 120 (216)
....++.++|......+.... + -..+.+|.|+|+.......... .....+.+. +. ..=+|++||+|
T Consensus 61 ~~~~~~D~~G~~~~~~~~~~~-----~---~~ad~ii~vvD~~~~~~~~~~~---~~l~~l~~~~~~~~~piliv~NK~D 129 (184)
T smart00178 61 IKFTTFDLGGHQQARRLWKDY-----F---PEVNGIVYLVDAYDKERFAESK---RELDALLSDEELATVPFLILGNKID 129 (184)
T ss_pred EEEEEEECCCCHHHHHHHHHH-----h---CCCCEEEEEEECCcHHHHHHHH---HHHHHHHcChhhcCCCEEEEEeCcc
Confidence 345678888875444443322 1 2467899999998753221110 001111111 11 22357889999
Q ss_pred CCCCCCccchHHHHHHHH
Q 027979 121 LVSPERSGDSLDELEKEI 138 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l 138 (216)
+...- ..+++++.+
T Consensus 130 l~~~~----~~~~i~~~l 143 (184)
T smart00178 130 APYAA----SEDELRYAL 143 (184)
T ss_pred ccCCC----CHHHHHHHc
Confidence 85432 245666655
No 109
>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=82.89 E-value=17 Score=26.92 Aligned_cols=87 Identities=21% Similarity=0.163 Sum_probs=47.1
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh-cc------EEEEc
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF-AD------VVILN 117 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~-AD------~Ivln 117 (216)
...++++.|......+..... . ..+.+|.|+|..+.... .. ...+..++.. .. ++++|
T Consensus 48 ~~~l~D~~g~~~~~~~~~~~~-----~---~~~~~i~v~d~~~~~s~-~~------~~~~~~~~~~~~~~~~~p~ivv~n 112 (160)
T cd00876 48 TLDILDTAGQEEFSAMRDLYI-----R---QGDGFILVYSITDRESF-EE------IKGYREQILRVKDDEDIPIVLVGN 112 (160)
T ss_pred EEEEEECCChHHHHHHHHHHH-----h---cCCEEEEEEECCCHHHH-HH------HHHHHHHHHHhcCCCCCcEEEEEE
Confidence 455788888765444433322 1 24678999998764421 11 1122222222 12 68889
Q ss_pred cCCCCCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 118 KVDLVSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 118 K~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
|+|+..... ...+.+.+..+..+ ++++.+
T Consensus 113 K~D~~~~~~--~~~~~~~~~~~~~~--~~~~~~ 141 (160)
T cd00876 113 KCDLENERQ--VSKEEGKALAKEWG--CPFIET 141 (160)
T ss_pred CCcccccce--ecHHHHHHHHHHcC--CcEEEe
Confidence 999987432 13455556666555 455543
No 110
>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=82.45 E-value=13 Score=27.82 Aligned_cols=87 Identities=25% Similarity=0.225 Sum_probs=45.2
Q ss_pred EEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh------hccEEEEccC
Q 027979 46 HILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA------FADVVILNKV 119 (216)
Q Consensus 46 ~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~------~AD~IvlnK~ 119 (216)
..+++++|-.....+...+. . ..+.+|.|+|....... .. ......++. ..=++++||+
T Consensus 51 l~~~D~~G~~~~~~~~~~~~-----~---~~~~ii~v~d~~~~~s~-~~------~~~~~~~~~~~~~~~~~iilv~nK~ 115 (161)
T cd01861 51 LQLWDTAGQERFRSLIPSYI-----R---DSSVAVVVYDITNRQSF-DN------TDKWIDDVRDERGNDVIIVLVGNKT 115 (161)
T ss_pred EEEEECCCcHHHHHHHHHHh-----c---cCCEEEEEEECcCHHHH-HH------HHHHHHHHHHhCCCCCEEEEEEECh
Confidence 45778888654444433322 1 23568999999764321 11 111222322 2345677999
Q ss_pred CCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 120 DLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
|+....+. ..++.....+..+ +++++++
T Consensus 116 D~~~~~~~--~~~~~~~~~~~~~--~~~~~~S 143 (161)
T cd01861 116 DLSDKRQV--STEEGEKKAKELN--AMFIETS 143 (161)
T ss_pred hccccCcc--CHHHHHHHHHHhC--CEEEEEe
Confidence 99654321 2344444444433 6666543
No 111
>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=82.41 E-value=6.9 Score=30.07 Aligned_cols=81 Identities=17% Similarity=0.287 Sum_probs=41.9
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc---EEEEccC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD---VVILNKV 119 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD---~IvlnK~ 119 (216)
+....++++.|.....++..... -.-+.+|.|+|+...... .+.. ..+..+.++-...+ +|+.||+
T Consensus 42 ~~~i~l~Dt~G~~~~~~~~~~~~--------~~ad~ii~V~D~s~~~s~-~~~~--~~~~~~~~~~~~~~~piilv~NK~ 110 (169)
T cd04158 42 NLKFTIWDVGGKHKLRPLWKHYY--------LNTQAVVFVVDSSHRDRV-SEAH--SELAKLLTEKELRDALLLIFANKQ 110 (169)
T ss_pred CEEEEEEECCCChhcchHHHHHh--------ccCCEEEEEEeCCcHHHH-HHHH--HHHHHHhcChhhCCCCEEEEEeCc
Confidence 34567889998765444433221 234788999999874322 1100 00111222222222 4667999
Q ss_pred CCCCCCCccchHHHHHHHH
Q 027979 120 DLVSPERSGDSLDELEKEI 138 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l 138 (216)
|+...- ..+++++.+
T Consensus 111 Dl~~~~----~~~~~~~~~ 125 (169)
T cd04158 111 DVAGAL----SVEEMTELL 125 (169)
T ss_pred CcccCC----CHHHHHHHh
Confidence 996532 235555554
No 112
>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=82.32 E-value=13 Score=27.87 Aligned_cols=82 Identities=20% Similarity=0.244 Sum_probs=42.4
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc---EEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD---VVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD---~IvlnK~D 120 (216)
....+++++|--.-..+...+. . ..+.++.|+|+..-...-.-. ..+..+..+....+ +++.||+|
T Consensus 43 ~~~~i~D~~G~~~~~~~~~~~~-----~---~~~~~i~v~D~~~~~~~~~~~---~~~~~~~~~~~~~~~piiiv~nK~D 111 (158)
T cd00878 43 VSFTVWDVGGQDKIRPLWKHYY-----E---NTNGIIFVVDSSDRERIEEAK---EELHKLLNEEELKGVPLLIFANKQD 111 (158)
T ss_pred EEEEEEECCCChhhHHHHHHHh-----c---cCCEEEEEEECCCHHHHHHHH---HHHHHHHhCcccCCCcEEEEeeccC
Confidence 4667888888643222322221 1 237889999998643111000 00111112222233 56679999
Q ss_pred CCCCCCccchHHHHHHHHHh
Q 027979 121 LVSPERSGDSLDELEKEIHE 140 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~ 140 (216)
+.... ..+++.+.++.
T Consensus 112 ~~~~~----~~~~~~~~~~~ 127 (158)
T cd00878 112 LPGAL----SVSELIEKLGL 127 (158)
T ss_pred Ccccc----CHHHHHHhhCh
Confidence 98754 24566666554
No 113
>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=82.32 E-value=2.2 Score=33.34 Aligned_cols=42 Identities=31% Similarity=0.392 Sum_probs=24.7
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc-cEEEEccCCCCCC
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA-DVVILNKVDLVSP 124 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A-D~IvlnK~D~v~~ 124 (216)
..|-++.|+|+....... ..++...+... -++|+||+|+.++
T Consensus 19 ~aD~il~v~D~~~~~~~~--------~~~i~~~~~~k~~ilVlNK~Dl~~~ 61 (171)
T cd01856 19 LVDLVIEVRDARIPLSSR--------NPLLEKILGNKPRIIVLNKADLADP 61 (171)
T ss_pred hCCEEEEEeeccCccCcC--------ChhhHhHhcCCCEEEEEehhhcCCh
Confidence 456679999996433211 11122333233 4888899999754
No 114
>PRK00049 elongation factor Tu; Reviewed
Probab=82.05 E-value=6.2 Score=35.41 Aligned_cols=92 Identities=22% Similarity=0.209 Sum_probs=47.8
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc---E-EEEccC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD---V-VILNKV 119 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD---~-IvlnK~ 119 (216)
..+++|-|.|.. .+..... ...-..|.++.|||+..-...- -.+...++.... + |++||+
T Consensus 75 ~~i~~iDtPG~~---~f~~~~~-----~~~~~aD~~llVVDa~~g~~~q--------t~~~~~~~~~~g~p~iiVvvNK~ 138 (396)
T PRK00049 75 RHYAHVDCPGHA---DYVKNMI-----TGAAQMDGAILVVSAADGPMPQ--------TREHILLARQVGVPYIVVFLNKC 138 (396)
T ss_pred eEEEEEECCCHH---HHHHHHH-----hhhccCCEEEEEEECCCCCchH--------HHHHHHHHHHcCCCEEEEEEeec
Confidence 457899999973 3333322 2234578899999997532110 112233333322 4 368999
Q ss_pred CCCCCCCccc-hHHHHHHHHHhhC---CCCEEEEee
Q 027979 120 DLVSPERSGD-SLDELEKEIHEIN---SLAHVIRSV 151 (216)
Q Consensus 120 D~v~~~~~~~-~l~~i~~~l~~lN---P~A~iv~~~ 151 (216)
|+++.++.-. ...++++.++.+. ..++++..+
T Consensus 139 D~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~iv~iS 174 (396)
T PRK00049 139 DMVDDEELLELVEMEVRELLSKYDFPGDDTPIIRGS 174 (396)
T ss_pred CCcchHHHHHHHHHHHHHHHHhcCCCccCCcEEEee
Confidence 9986432100 1124444554432 246676533
No 115
>COG1161 Predicted GTPases [General function prediction only]
Probab=81.82 E-value=2.1 Score=37.45 Aligned_cols=64 Identities=22% Similarity=0.304 Sum_probs=39.5
Q ss_pred eeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh-hccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEE
Q 027979 74 VRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA-FADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIR 149 (216)
Q Consensus 74 ~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~-~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~ 149 (216)
-..+.|+-|+||..+...... .+.+.+. ...++|+||+|+++.. .+++..+....-++...+..
T Consensus 33 ~~~d~vvevvDar~P~~s~~~--------~l~~~v~~k~~i~vlNK~DL~~~~----~~~~W~~~~~~~~~~~~~~v 97 (322)
T COG1161 33 KSVDVVVEVVDARDPLGTRNP--------ELERIVKEKPKLLVLNKADLAPKE----VTKKWKKYFKKEEGIKPIFV 97 (322)
T ss_pred ccCCEEEEEEeccccccccCc--------cHHHHHccCCcEEEEehhhcCCHH----HHHHHHHHHHhcCCCccEEE
Confidence 456788999999877643321 2222222 2227889999999975 35666666666554444443
No 116
>PRK12736 elongation factor Tu; Reviewed
Probab=81.74 E-value=4.9 Score=36.04 Aligned_cols=92 Identities=27% Similarity=0.221 Sum_probs=47.4
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh---cc-EEEEccC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF---AD-VVILNKV 119 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~---AD-~IvlnK~ 119 (216)
..+.+|-|.|-. ..+... +...-..+.++.|||+..-.... -.+...++.. .- +|++||+
T Consensus 75 ~~i~~iDtPGh~---~f~~~~-----~~~~~~~d~~llVvd~~~g~~~~--------t~~~~~~~~~~g~~~~IvviNK~ 138 (394)
T PRK12736 75 RHYAHVDCPGHA---DYVKNM-----ITGAAQMDGAILVVAATDGPMPQ--------TREHILLARQVGVPYLVVFLNKV 138 (394)
T ss_pred cEEEEEECCCHH---HHHHHH-----HHHHhhCCEEEEEEECCCCCchh--------HHHHHHHHHHcCCCEEEEEEEec
Confidence 456888999843 222221 12223567889999997532110 0122233332 33 3679999
Q ss_pred CCCCCCCccch-HHHHHHHHHhhCC---CCEEEEee
Q 027979 120 DLVSPERSGDS-LDELEKEIHEINS---LAHVIRSV 151 (216)
Q Consensus 120 D~v~~~~~~~~-l~~i~~~l~~lNP---~A~iv~~~ 151 (216)
|+++.++.-+. .+++++.++.++- .++++..+
T Consensus 139 D~~~~~~~~~~i~~~i~~~l~~~~~~~~~~~ii~vS 174 (394)
T PRK12736 139 DLVDDEELLELVEMEVRELLSEYDFPGDDIPVIRGS 174 (394)
T ss_pred CCcchHHHHHHHHHHHHHHHHHhCCCcCCccEEEee
Confidence 99864321011 1245555555542 36777644
No 117
>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=81.57 E-value=19 Score=27.47 Aligned_cols=66 Identities=18% Similarity=0.124 Sum_probs=38.4
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEccC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNKV 119 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK~ 119 (216)
+....++-|.|..+...+..... -..+.+|.|+|+..-.... . ...+ .++. .-=++++||+
T Consensus 66 ~~~~~l~Dt~G~~~~~~~~~~~~--------~~ad~~i~v~D~~~~~~~~-~------~~~~-~~~~~~~~~iiiv~NK~ 129 (179)
T cd01890 66 EYLLNLIDTPGHVDFSYEVSRSL--------AACEGALLLVDATQGVEAQ-T------LANF-YLALENNLEIIPVINKI 129 (179)
T ss_pred cEEEEEEECCCChhhHHHHHHHH--------HhcCeEEEEEECCCCccHh-h------HHHH-HHHHHcCCCEEEEEECC
Confidence 34566899999977655544322 2357789999997532110 0 1111 1111 2247889999
Q ss_pred CCCCC
Q 027979 120 DLVSP 124 (216)
Q Consensus 120 D~v~~ 124 (216)
|+.+.
T Consensus 130 Dl~~~ 134 (179)
T cd01890 130 DLPSA 134 (179)
T ss_pred CCCcC
Confidence 98653
No 118
>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=81.38 E-value=4.2 Score=30.51 Aligned_cols=93 Identities=18% Similarity=0.211 Sum_probs=43.2
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccch-HHHHhhcccCCChhHHHHHHhh-ccEEEEccCCCC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNL-LFQIDKYRHLSSYPEAIHQIAF-ADVVILNKVDLV 122 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~-~~~l~~~~~~~~~~~~~~QI~~-AD~IvlnK~D~v 122 (216)
...++-|.|.-. ..... ....-..+.++.|+|+..- ..+.... . ...++... -=++++||+|+.
T Consensus 52 ~~~~~DtpG~~~---~~~~~-----~~~~~~ad~ii~V~d~~~~~~~~~~~~-----~-~~~~~~~~~~~ilv~NK~Dl~ 117 (164)
T cd04171 52 RLGFIDVPGHEK---FIKNM-----LAGAGGIDLVLLVVAADEGIMPQTREH-----L-EILELLGIKRGLVVLTKADLV 117 (164)
T ss_pred EEEEEECCChHH---HHHHH-----HhhhhcCCEEEEEEECCCCccHhHHHH-----H-HHHHHhCCCcEEEEEECcccc
Confidence 456677777632 21111 1122356789999999751 1111000 1 11222322 225888999997
Q ss_pred CCCCccchHHHHHHHHHhhC-CCCEEEEee
Q 027979 123 SPERSGDSLDELEKEIHEIN-SLAHVIRSV 151 (216)
Q Consensus 123 ~~~~~~~~l~~i~~~l~~lN-P~A~iv~~~ 151 (216)
+........+++.+.++... ...++++++
T Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~S 147 (164)
T cd04171 118 DEDWLELVEEEIRELLAGTFLADAPIFPVS 147 (164)
T ss_pred CHHHHHHHHHHHHHHHHhcCcCCCcEEEEe
Confidence 64210011234444444321 234566543
No 119
>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=81.37 E-value=2.9 Score=34.12 Aligned_cols=37 Identities=22% Similarity=0.435 Sum_probs=22.8
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccc
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKN 87 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~ 87 (216)
.+.+.+|.+.|..+ ..... +...-..+.+|.|||+..
T Consensus 76 ~~~i~liDtpG~~~---~~~~~-----~~~~~~~d~~i~VvDa~~ 112 (219)
T cd01883 76 KYRFTILDAPGHRD---FVPNM-----ITGASQADVAVLVVDARK 112 (219)
T ss_pred CeEEEEEECCChHH---HHHHH-----HHHhhhCCEEEEEEECCC
Confidence 45678899999632 11111 112234678899999986
No 120
>PRK00454 engB GTP-binding protein YsxC; Reviewed
Probab=81.30 E-value=5.4 Score=31.21 Aligned_cols=76 Identities=16% Similarity=0.252 Sum_probs=35.5
Q ss_pred CCEEEEecCCCCCc---HHHH---HHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEc
Q 027979 44 LDHILLETTGLANP---APLA---SVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILN 117 (216)
Q Consensus 44 ~d~IiIE~sG~a~P---~~i~---~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~Ivln 117 (216)
....|+-+.|.... .... ..+. ...+...-.++.++.|+|+..-....... ..........--++++|
T Consensus 70 ~~l~l~DtpG~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~v~d~~~~~~~~~~~-----i~~~l~~~~~~~iiv~n 143 (196)
T PRK00454 70 DKLRLVDLPGYGYAKVSKEEKEKWQKLI-EEYLRTRENLKGVVLLIDSRHPLKELDLQ-----MIEWLKEYGIPVLIVLT 143 (196)
T ss_pred CeEEEeCCCCCCCcCCCchHHHHHHHHH-HHHHHhCccceEEEEEEecCCCCCHHHHH-----HHHHHHHcCCcEEEEEE
Confidence 35677899996432 1111 1111 11222222445677888876422111100 11111221112368899
Q ss_pred cCCCCCCC
Q 027979 118 KVDLVSPE 125 (216)
Q Consensus 118 K~D~v~~~ 125 (216)
|+|+.+..
T Consensus 144 K~Dl~~~~ 151 (196)
T PRK00454 144 KADKLKKG 151 (196)
T ss_pred CcccCCHH
Confidence 99998754
No 121
>PRK04000 translation initiation factor IF-2 subunit gamma; Validated
Probab=81.16 E-value=3.5 Score=37.22 Aligned_cols=94 Identities=23% Similarity=0.327 Sum_probs=46.7
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchH--HHHhhcccCCChhHHHHHHhhcc-EEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLL--FQIDKYRHLSSYPEAIHQIAFAD-VVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~--~~l~~~~~~~~~~~~~~QI~~AD-~IvlnK~D 120 (216)
....++-|.|-. .+.... +...-..+.++.|+|+.... .+.... . .......... +|++||+|
T Consensus 85 ~~i~liDtPG~~---~f~~~~-----~~~~~~~D~~llVVDa~~~~~~~~t~~~-----l-~~l~~~~i~~iiVVlNK~D 150 (411)
T PRK04000 85 RRVSFVDAPGHE---TLMATM-----LSGAALMDGAILVIAANEPCPQPQTKEH-----L-MALDIIGIKNIVIVQNKID 150 (411)
T ss_pred cEEEEEECCCHH---HHHHHH-----HHHHhhCCEEEEEEECCCCCCChhHHHH-----H-HHHHHcCCCcEEEEEEeec
Confidence 356788999852 232221 22334567899999998531 111110 1 1112222223 66689999
Q ss_pred CCCCCCccchHHHHHHHHHhh-CCCCEEEEee
Q 027979 121 LVSPERSGDSLDELEKEIHEI-NSLAHVIRSV 151 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~l-NP~A~iv~~~ 151 (216)
++++++.....+++++.++.. ....++++++
T Consensus 151 l~~~~~~~~~~~~i~~~l~~~~~~~~~ii~vS 182 (411)
T PRK04000 151 LVSKERALENYEQIKEFVKGTVAENAPIIPVS 182 (411)
T ss_pred cccchhHHHHHHHHHHHhccccCCCCeEEEEE
Confidence 987542101123344444332 2346676544
No 122
>KOG2484 consensus GTPase [General function prediction only]
Probab=80.92 E-value=2.8 Score=37.71 Aligned_cols=64 Identities=25% Similarity=0.347 Sum_probs=44.6
Q ss_pred ccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc-----EEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 77 DSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD-----VVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 77 ~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD-----~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
|-|+-|+||.--+... .+++.+|+..|. ++||||+|+++.+ .+++....++.--|.+.....+
T Consensus 148 DVVleVlDARDPlgtR--------~~~vE~~V~~~~gnKkLILVLNK~DLVPrE----v~e~Wl~YLr~~~ptv~fkast 215 (435)
T KOG2484|consen 148 DVVLEVLDARDPLGTR--------CPEVEEAVLQAHGNKKLILVLNKIDLVPRE----VVEKWLVYLRREGPTVAFKAST 215 (435)
T ss_pred heEEEeeeccCCCCCC--------ChhHHHHHHhccCCceEEEEeehhccCCHH----HHHHHHHHHHhhCCcceeeccc
Confidence 4468899997443211 244556774332 5788999999985 6788999999999987765443
Q ss_pred c
Q 027979 152 R 152 (216)
Q Consensus 152 ~ 152 (216)
.
T Consensus 216 ~ 216 (435)
T KOG2484|consen 216 Q 216 (435)
T ss_pred c
Confidence 3
No 123
>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=80.91 E-value=5.6 Score=31.11 Aligned_cols=54 Identities=24% Similarity=0.274 Sum_probs=29.5
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHH-----HHhhcc-EEEEccCCCCCCCCccchHHHHHHHH
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIH-----QIAFAD-VVILNKVDLVSPERSGDSLDELEKEI 138 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~-----QI~~AD-~IvlnK~D~v~~~~~~~~l~~i~~~l 138 (216)
..+++|.|||+..... +... ..++.+ ++...- +|++||.|+.+.. ..+++...+
T Consensus 81 ~~~~iIfVvDssd~~~-l~e~-----~~~L~~ll~~~~~~~~piLIl~NK~D~~~~~----~~~~i~~~l 140 (175)
T PF00025_consen 81 NADGIIFVVDSSDPER-LQEA-----KEELKELLNDPELKDIPILILANKQDLPDAM----SEEEIKEYL 140 (175)
T ss_dssp TESEEEEEEETTGGGG-HHHH-----HHHHHHHHTSGGGTTSEEEEEEESTTSTTSS----THHHHHHHT
T ss_pred ccceeEEEEeccccee-eccc-----ccchhhhcchhhcccceEEEEeccccccCcc----hhhHHHhhh
Confidence 4688999999986532 1110 111222 222233 4556999987654 245666554
No 124
>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=80.61 E-value=9.2 Score=29.39 Aligned_cols=67 Identities=16% Similarity=0.191 Sum_probs=36.8
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH-hh------ccEEE
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI-AF------ADVVI 115 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI-~~------AD~Iv 115 (216)
+....++++.|.....++.... + -.-+.+|.|+|+..... +.. ......++ .. -=+|+
T Consensus 42 ~~~~~i~D~~G~~~~~~~~~~~-----~---~~a~~ii~V~D~s~~~s-~~~------~~~~l~~l~~~~~~~~~piliv 106 (167)
T cd04161 42 KYEVCIFDLGGGANFRGIWVNY-----Y---AEAHGLVFVVDSSDDDR-VQE------VKEILRELLQHPRVSGKPILVL 106 (167)
T ss_pred CEEEEEEECCCcHHHHHHHHHH-----H---cCCCEEEEEEECCchhH-HHH------HHHHHHHHHcCccccCCcEEEE
Confidence 3456788999975444333221 1 23467899999987542 111 11112222 11 12678
Q ss_pred EccCCCCCC
Q 027979 116 LNKVDLVSP 124 (216)
Q Consensus 116 lnK~D~v~~ 124 (216)
+||+|+.+.
T Consensus 107 ~NK~Dl~~~ 115 (167)
T cd04161 107 ANKQDKKNA 115 (167)
T ss_pred EeCCCCcCC
Confidence 899998664
No 125
>TIGR00475 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.
Probab=80.49 E-value=3.3 Score=39.18 Aligned_cols=93 Identities=15% Similarity=0.200 Sum_probs=46.8
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchH-HHHhhcccCCChhHHHHHHhhc-cEEEEccCCCC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLL-FQIDKYRHLSSYPEAIHQIAFA-DVVILNKVDLV 122 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~-~~l~~~~~~~~~~~~~~QI~~A-D~IvlnK~D~v 122 (216)
...+|.+.|-. ...... +...-..+.++.|||+..-. .+... +-........- =+|++||+|++
T Consensus 51 ~v~~iDtPGhe---~f~~~~-----~~g~~~aD~aILVVDa~~G~~~qT~e------hl~il~~lgi~~iIVVlNK~Dlv 116 (581)
T TIGR00475 51 RLGFIDVPGHE---KFISNA-----IAGGGGIDAALLVVDADEGVMTQTGE------HLAVLDLLGIPHTIVVITKADRV 116 (581)
T ss_pred EEEEEECCCHH---HHHHHH-----HhhhccCCEEEEEEECCCCCcHHHHH------HHHHHHHcCCCeEEEEEECCCCC
Confidence 34567777742 222221 12334578899999998621 11111 10112233333 37888999998
Q ss_pred CCCCccchHHHHHHHHHhh--CCCCEEEEee
Q 027979 123 SPERSGDSLDELEKEIHEI--NSLAHVIRSV 151 (216)
Q Consensus 123 ~~~~~~~~l~~i~~~l~~l--NP~A~iv~~~ 151 (216)
+++......+++++.++.. .+.+++++++
T Consensus 117 ~~~~~~~~~~ei~~~l~~~~~~~~~~ii~vS 147 (581)
T TIGR00475 117 NEEEIKRTEMFMKQILNSYIFLKNAKIFKTS 147 (581)
T ss_pred CHHHHHHHHHHHHHHHHHhCCCCCCcEEEEe
Confidence 7642100122344444433 2357787654
No 126
>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=80.35 E-value=20 Score=26.95 Aligned_cols=86 Identities=13% Similarity=0.136 Sum_probs=42.8
Q ss_pred EEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh----hcc---EEEEccC
Q 027979 47 ILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA----FAD---VVILNKV 119 (216)
Q Consensus 47 IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~----~AD---~IvlnK~ 119 (216)
-+..++|.-....+..... -..+++|.|+|....... .. ......++. ..+ +|+.||+
T Consensus 52 ~i~Dt~G~~~~~~~~~~~~--------~~~d~~ilv~d~~~~~s~-~~------~~~~~~~i~~~~~~~~~piilv~nK~ 116 (164)
T cd04175 52 EILDTAGTEQFTAMRDLYM--------KNGQGFVLVYSITAQSTF-ND------LQDLREQILRVKDTEDVPMILVGNKC 116 (164)
T ss_pred EEEECCCcccchhHHHHHH--------hhCCEEEEEEECCCHHHH-HH------HHHHHHHHHHhcCCCCCCEEEEEECC
Confidence 4677888765555544332 123567888887654321 11 111122221 111 6788999
Q ss_pred CCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 120 DLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
|+.+.... ......+..+..+ .++++++
T Consensus 117 Dl~~~~~~--~~~~~~~~~~~~~--~~~~~~S 144 (164)
T cd04175 117 DLEDERVV--GKEQGQNLARQWG--CAFLETS 144 (164)
T ss_pred cchhccEE--cHHHHHHHHHHhC--CEEEEee
Confidence 99764321 2233333334443 5666544
No 127
>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=80.10 E-value=4.7 Score=31.85 Aligned_cols=43 Identities=19% Similarity=0.190 Sum_probs=25.7
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh-ccEEEEccCCCCCCC
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF-ADVVILNKVDLVSPE 125 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~-AD~IvlnK~D~v~~~ 125 (216)
+.+.++.|+|+......+. ..+..+... -=++|+||+|+.+.+
T Consensus 34 ~ad~il~VvD~~~~~~~~~--------~~l~~~~~~~~~ilV~NK~Dl~~~~ 77 (190)
T cd01855 34 KKALVVHVVDIFDFPGSLI--------PRLRLFGGNNPVILVGNKIDLLPKD 77 (190)
T ss_pred CCcEEEEEEECccCCCccc--------hhHHHhcCCCcEEEEEEchhcCCCC
Confidence 3567899999986542221 122222222 236889999998654
No 128
>cd04122 Rab14 Rab14 subfamily. Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles. Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments. Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation. In addition, Rab14 is believed to play a role in the regulation of phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GT
Probab=79.86 E-value=24 Score=26.71 Aligned_cols=66 Identities=14% Similarity=0.053 Sum_probs=35.8
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh---c---cEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEE
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF---A---DVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVI 148 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~---A---D~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv 148 (216)
..+++|.|+|..+-.. +.. ...+...+.. . =+||.||+|+.+..+. ..++..+..+.. +.+++
T Consensus 74 ~~~~~ilv~d~~~~~s-~~~------~~~~~~~~~~~~~~~~~iiiv~nK~Dl~~~~~~--~~~~~~~~~~~~--~~~~~ 142 (166)
T cd04122 74 GAAGALMVYDITRRST-YNH------LSSWLTDARNLTNPNTVIFLIGNKADLEAQRDV--TYEEAKQFADEN--GLLFL 142 (166)
T ss_pred CCCEEEEEEECCCHHH-HHH------HHHHHHHHHHhCCCCCeEEEEEECcccccccCc--CHHHHHHHHHHc--CCEEE
Confidence 3578999999986432 111 1222333322 1 2677899999765431 234555554443 35666
Q ss_pred Eee
Q 027979 149 RSV 151 (216)
Q Consensus 149 ~~~ 151 (216)
+++
T Consensus 143 e~S 145 (166)
T cd04122 143 ECS 145 (166)
T ss_pred EEE
Confidence 544
No 129
>PTZ00369 Ras-like protein; Provisional
Probab=79.81 E-value=25 Score=27.53 Aligned_cols=95 Identities=16% Similarity=0.189 Sum_probs=49.6
Q ss_pred EEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh----hcc---EEEEccCC
Q 027979 48 LLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA----FAD---VVILNKVD 120 (216)
Q Consensus 48 iIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~----~AD---~IvlnK~D 120 (216)
+..++|..+...+..... . ..+++|.|+|...-.. +.+ ...+..++. ..+ +|+.||+|
T Consensus 57 i~Dt~G~~~~~~l~~~~~-----~---~~d~iilv~D~s~~~s-~~~------~~~~~~~i~~~~~~~~~piiiv~nK~D 121 (189)
T PTZ00369 57 ILDTAGQEEYSAMRDQYM-----R---TGQGFLCVYSITSRSS-FEE------IASFREQILRVKDKDRVPMILVGNKCD 121 (189)
T ss_pred EEeCCCCccchhhHHHHh-----h---cCCEEEEEEECCCHHH-HHH------HHHHHHHHHHhcCCCCCCEEEEEECcc
Confidence 678899877766654332 1 3567899999876542 111 112222221 112 56889999
Q ss_pred CCCCCCccchHHHHHHHHHhhCCCCEEEEee-cCCCChhhhh
Q 027979 121 LVSPERSGDSLDELEKEIHEINSLAHVIRSV-RCQVDLSEVL 161 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~-~~~v~~~~l~ 161 (216)
+.+.... ...+..+..+..+ .++++++ .....+..++
T Consensus 122 l~~~~~i--~~~~~~~~~~~~~--~~~~e~Sak~~~gi~~~~ 159 (189)
T PTZ00369 122 LDSERQV--STGEGQELAKSFG--IPFLETSAKQRVNVDEAF 159 (189)
T ss_pred ccccccc--CHHHHHHHHHHhC--CEEEEeeCCCCCCHHHHH
Confidence 8654221 1233334444443 4666543 2334555554
No 130
>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=79.71 E-value=14 Score=28.53 Aligned_cols=37 Identities=19% Similarity=0.273 Sum_probs=23.1
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccch
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNL 88 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~ 88 (216)
....+.+++|......+..... -.-+.+|.|+|+..-
T Consensus 53 ~~~~l~Dt~G~~~~~~~~~~~~--------~~a~~ii~v~D~t~~ 89 (168)
T cd04149 53 VKFNVWDVGGQDKIRPLWRHYY--------TGTQGLIFVVDSADR 89 (168)
T ss_pred EEEEEEECCCCHHHHHHHHHHh--------ccCCEEEEEEeCCch
Confidence 4456778888754444332221 135678999999874
No 131
>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=79.70 E-value=27 Score=29.16 Aligned_cols=47 Identities=21% Similarity=0.174 Sum_probs=26.8
Q ss_pred EEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhhc
Q 027979 113 VVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVLN 162 (216)
Q Consensus 113 ~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~~ 162 (216)
+|+.||+|+....+ ...+++.+.+...+ ...+++++- ...+.+.++.
T Consensus 117 IivgNK~Dl~~~~~--v~~~ei~~~~~~~~-~~~~~evSAktg~gI~elf~ 164 (247)
T cd04143 117 VICGNKADRDFPRE--VQRDEVEQLVGGDE-NCAYFEVSAKKNSNLDEMFR 164 (247)
T ss_pred EEEEECccchhccc--cCHHHHHHHHHhcC-CCEEEEEeCCCCCCHHHHHH
Confidence 78889999975322 13456666655433 456665442 2345555553
No 132
>PRK12289 GTPase RsgA; Reviewed
Probab=79.69 E-value=5.6 Score=35.28 Aligned_cols=78 Identities=18% Similarity=0.221 Sum_probs=38.5
Q ss_pred eeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 74 VRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 74 ~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
-.+|.++.|+|+......... ...+...+. .-=+||+||+|+++++ ..+.+.+.++..+ .+++.+
T Consensus 88 aNvD~vLlV~d~~~p~~~~~~------LdR~L~~a~~~~ip~ILVlNK~DLv~~~----~~~~~~~~~~~~g--~~v~~i 155 (352)
T PRK12289 88 ANADQILLVFALAEPPLDPWQ------LSRFLVKAESTGLEIVLCLNKADLVSPT----EQQQWQDRLQQWG--YQPLFI 155 (352)
T ss_pred hcCCEEEEEEECCCCCCCHHH------HHHHHHHHHHCCCCEEEEEEchhcCChH----HHHHHHHHHHhcC--CeEEEE
Confidence 457788999998632100000 111111221 1226888999998753 2344445554433 345543
Q ss_pred e-cCCCChhhhhcc
Q 027979 151 V-RCQVDLSEVLNC 163 (216)
Q Consensus 151 ~-~~~v~~~~l~~~ 163 (216)
+ .....++.|+..
T Consensus 156 SA~tg~GI~eL~~~ 169 (352)
T PRK12289 156 SVETGIGLEALLEQ 169 (352)
T ss_pred EcCCCCCHHHHhhh
Confidence 2 223445555543
No 133
>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=79.58 E-value=23 Score=26.38 Aligned_cols=98 Identities=13% Similarity=0.107 Sum_probs=48.5
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh-hc----------cE
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA-FA----------DV 113 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~-~A----------D~ 113 (216)
..-++.++|.-....+..... -.-+.+|.|+|+.+-... .. ......++. .. =+
T Consensus 50 ~l~i~Dt~G~~~~~~~~~~~~--------~~~d~~ilv~D~~~~~s~-~~------~~~~~~~~~~~~~~~~~~~~~pii 114 (168)
T cd04119 50 RVNFFDLSGHPEYLEVRNEFY--------KDTQGVLLVYDVTDRQSF-EA------LDSWLKEMKQEGGPHGNMENIVVV 114 (168)
T ss_pred EEEEEECCccHHHHHHHHHHh--------ccCCEEEEEEECCCHHHH-Hh------HHHHHHHHHHhccccccCCCceEE
Confidence 345678888754443333221 124678999999864321 11 111222221 11 27
Q ss_pred EEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 114 VILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 114 IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
+|.||+|+.++.. ...++.++..+..+ .++++++. .+.....++
T Consensus 115 lv~nK~Dl~~~~~--~~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~ 159 (168)
T cd04119 115 VCANKIDLTKHRA--VSEDEGRLWAESKG--FKYFETSACTGEGVNEMF 159 (168)
T ss_pred EEEEchhcccccc--cCHHHHHHHHHHcC--CeEEEEECCCCCCHHHHH
Confidence 7789999974322 12344445555443 56665543 233444443
No 134
>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=79.47 E-value=26 Score=29.84 Aligned_cols=115 Identities=17% Similarity=0.141 Sum_probs=65.5
Q ss_pred hhHHHHHHHHHHhcCCCCEEEEecCCCCCc-HHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHH
Q 027979 28 HSLVQALEQLVQRKERLDHILLETTGLANP-APLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIH 106 (216)
Q Consensus 28 ~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P-~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~ 106 (216)
.++..+|..+.. ..++|+|||-|.|-..- .+.++.+. .+......+.++.|+||..-...+... -..+.
T Consensus 140 ~~l~~~l~~l~~-~~~~D~ViIDt~Gr~~~~~~~l~el~---~~~~~~~~~~~~LVl~a~~~~~d~~~~------~~~f~ 209 (270)
T PRK06731 140 AAMTRALTYFKE-EARVDYILIDTAGKNYRASETVEEMI---ETMGQVEPDYICLTLSASMKSKDMIEI------ITNFK 209 (270)
T ss_pred HHHHHHHHHHHh-cCCCCEEEEECCCCCcCCHHHHHHHH---HHHhhhCCCeEEEEEcCccCHHHHHHH------HHHhC
Confidence 456666766643 34799999999999732 23333221 111233444578899997544333221 01112
Q ss_pred HHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeecCCCChhhhh
Q 027979 107 QIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQVDLSEVL 161 (216)
Q Consensus 107 QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~~~l~ 161 (216)
. ..-|-+|++|.|-...- -.+.+..... +.+|.....|+-=++++.
T Consensus 210 ~-~~~~~~I~TKlDet~~~------G~~l~~~~~~--~~Pi~~it~Gq~vp~di~ 255 (270)
T PRK06731 210 D-IHIDGIVFTKFDETASS------GELLKIPAVS--SAPIVLMTDGQDVKKNIH 255 (270)
T ss_pred C-CCCCEEEEEeecCCCCc------cHHHHHHHHH--CcCEEEEeCCCCCCcchh
Confidence 2 45689999999987653 2333333332 567777777754444443
No 135
>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=79.45 E-value=23 Score=26.23 Aligned_cols=90 Identities=21% Similarity=0.266 Sum_probs=45.2
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEccCCC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNKVDL 121 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK~D~ 121 (216)
...+++++|-..+..+..... -..+.++.|+|...-... .... .+-+...+.. ..=++++||+|+
T Consensus 50 ~~~~~D~~g~~~~~~~~~~~~--------~~~~~~i~v~d~~~~~s~-~~~~---~~~~~i~~~~~~~~piiiv~nK~D~ 117 (162)
T cd04123 50 DLAIWDTAGQERYHALGPIYY--------RDADGAILVYDITDADSF-QKVK---KWIKELKQMRGNNISLVIVGNKIDL 117 (162)
T ss_pred EEEEEECCchHHHHHhhHHHh--------ccCCEEEEEEECCCHHHH-HHHH---HHHHHHHHhCCCCCeEEEEEECccc
Confidence 356678888544443333221 135788999998764421 1100 0001112222 345677899999
Q ss_pred CCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 122 VSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 122 v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
....+. ..+.+.+..+..+ .+++++
T Consensus 118 ~~~~~~--~~~~~~~~~~~~~--~~~~~~ 142 (162)
T cd04123 118 ERQRVV--SKSEAEEYAKSVG--AKHFET 142 (162)
T ss_pred ccccCC--CHHHHHHHHHHcC--CEEEEE
Confidence 754321 2345555555443 445543
No 136
>PRK05124 cysN sulfate adenylyltransferase subunit 1; Provisional
Probab=79.35 E-value=8.7 Score=35.43 Aligned_cols=94 Identities=17% Similarity=0.239 Sum_probs=49.1
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc-EEEEccCCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD-VVILNKVDL 121 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD-~IvlnK~D~ 121 (216)
+..+++|-|.|-. .+..... ...-..|.++.|||+......... ..-.+...+..-- +|++||+|+
T Consensus 106 ~~~i~~iDTPGh~---~f~~~~~-----~~l~~aD~allVVDa~~G~~~qt~-----~~~~l~~~lg~~~iIvvvNKiD~ 172 (474)
T PRK05124 106 KRKFIIADTPGHE---QYTRNMA-----TGASTCDLAILLIDARKGVLDQTR-----RHSFIATLLGIKHLVVAVNKMDL 172 (474)
T ss_pred CcEEEEEECCCcH---HHHHHHH-----HHHhhCCEEEEEEECCCCccccch-----HHHHHHHHhCCCceEEEEEeecc
Confidence 3467899999942 3332221 122456788999999753211000 0111222222223 569999999
Q ss_pred CCCCCccchHHHHHHHHHh----h--CCCCEEEEee
Q 027979 122 VSPERSGDSLDELEKEIHE----I--NSLAHVIRSV 151 (216)
Q Consensus 122 v~~~~~~~~l~~i~~~l~~----l--NP~A~iv~~~ 151 (216)
++..+ ..++++++.++. + .+.+++++.+
T Consensus 173 ~~~~~--~~~~~i~~~l~~~~~~~~~~~~~~iipvS 206 (474)
T PRK05124 173 VDYSE--EVFERIREDYLTFAEQLPGNLDIRFVPLS 206 (474)
T ss_pred ccchh--HHHHHHHHHHHHHHHhcCCCCCceEEEEE
Confidence 85432 134455554433 2 3467777644
No 137
>cd01885 EF2 EF2 (for archaea and eukarya). Translocation requires hydrolysis of a molecule of GTP and is mediated by EF-G in bacteria and by eEF2 in eukaryotes. The eukaryotic elongation factor eEF2 is a GTPase involved in the translocation of the peptidyl-tRNA from the A site to the P site on the ribosome. The 95-kDa protein is highly conserved, with 60% amino acid sequence identity between the human and yeast proteins. Two major mechanisms are known to regulate protein elongation and both involve eEF2. First, eEF2 can be modulated by reversible phosphorylation. Increased levels of phosphorylated eEF2 reduce elongation rates presumably because phosphorylated eEF2 fails to bind the ribosomes. Treatment of mammalian cells with agents that raise the cytoplasmic Ca2+ and cAMP levels reduce elongation rates by activating the kinase responsible for phosphorylating eEF2. In contrast, treatment of cells with insulin increases elongation rates by promoting eEF2 dephosphorylation. Seco
Probab=79.28 E-value=5.8 Score=32.72 Aligned_cols=83 Identities=22% Similarity=0.320 Sum_probs=48.2
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEccC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNKV 119 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK~ 119 (216)
+....+|-|.|..+-...... ..-..++++.|||+..-...- -.+..+|.. .-=++++||+
T Consensus 72 ~~~i~iiDTPG~~~f~~~~~~--------~l~~aD~~ilVvD~~~g~~~~--------t~~~l~~~~~~~~p~ilviNKi 135 (222)
T cd01885 72 EYLINLIDSPGHVDFSSEVTA--------ALRLCDGALVVVDAVEGVCVQ--------TETVLRQALKERVKPVLVINKI 135 (222)
T ss_pred ceEEEEECCCCccccHHHHHH--------HHHhcCeeEEEEECCCCCCHH--------HHHHHHHHHHcCCCEEEEEECC
Confidence 345677999998765443322 113456789999997542111 011223322 2347888999
Q ss_pred CCC------CCCCccchHHHHHHHHHhhCCC
Q 027979 120 DLV------SPERSGDSLDELEKEIHEINSL 144 (216)
Q Consensus 120 D~v------~~~~~~~~l~~i~~~l~~lNP~ 144 (216)
|+. +++ +...++.+.+.++|..
T Consensus 136 D~~~~e~~~~~~---~~~~~~~~ii~~~n~~ 163 (222)
T cd01885 136 DRLILELKLSPE---EAYQRLARIIEQVNAI 163 (222)
T ss_pred CcchhhhcCCHH---HHHHHHHHHHHHHhHH
Confidence 986 332 2456677777777763
No 138
>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=79.14 E-value=20 Score=26.76 Aligned_cols=99 Identities=13% Similarity=0.188 Sum_probs=49.3
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh-c----cEEEEcc
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF-A----DVVILNK 118 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~-A----D~IvlnK 118 (216)
.+..|..+.|...-..+..... -.-+.++.|.|+..-... .. ...+..++.. + =+|+.||
T Consensus 51 ~~~~i~D~~G~~~~~~~~~~~~--------~~~~~~v~v~d~~~~~s~-~~------l~~~~~~~~~~~~~~p~iiv~nK 115 (162)
T cd04106 51 VRLMLWDTAGQEEFDAITKAYY--------RGAQACILVFSTTDRESF-EA------IESWKEKVEAECGDIPMVLVQTK 115 (162)
T ss_pred EEEEEeeCCchHHHHHhHHHHh--------cCCCEEEEEEECCCHHHH-HH------HHHHHHHHHHhCCCCCEEEEEEC
Confidence 4566778888543333333221 134567888887654321 11 1222333321 1 1788899
Q ss_pred CCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 119 VDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 119 ~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
+|+.+.... ..++..+..+.++ .++++++. .+.+.+.++
T Consensus 116 ~Dl~~~~~v--~~~~~~~~~~~~~--~~~~~~Sa~~~~~v~~l~ 155 (162)
T cd04106 116 IDLLDQAVI--TNEEAEALAKRLQ--LPLFRTSVKDDFNVTELF 155 (162)
T ss_pred hhcccccCC--CHHHHHHHHHHcC--CeEEEEECCCCCCHHHHH
Confidence 999775432 2344444555443 46665442 223444443
No 139
>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=79.13 E-value=24 Score=26.33 Aligned_cols=87 Identities=16% Similarity=0.140 Sum_probs=45.9
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH-h------hccEEEEc
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI-A------FADVVILN 117 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI-~------~AD~Ivln 117 (216)
...+++++|...-..+...+. + ..+.++.|+|+...... .. ...+...+ . ..-+|+.|
T Consensus 50 ~~~l~D~~g~~~~~~~~~~~~-----~---~~d~~i~v~d~~~~~s~-~~------~~~~~~~i~~~~~~~~~~~~iv~n 114 (161)
T cd01863 50 KLAIWDTAGQERFRTLTSSYY-----R---GAQGVILVYDVTRRDTF-TN------LETWLNELETYSTNNDIVKMLVGN 114 (161)
T ss_pred EEEEEECCCchhhhhhhHHHh-----C---CCCEEEEEEECCCHHHH-Hh------HHHHHHHHHHhCCCCCCcEEEEEE
Confidence 456668888543322222211 1 35789999998865432 11 11122222 1 22488899
Q ss_pred cCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 118 KVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 118 K~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
|+|+..... ..+...+..+.. .+++++++
T Consensus 115 K~D~~~~~~---~~~~~~~~~~~~--~~~~~~~S 143 (161)
T cd01863 115 KIDKENREV---TREEGLKFARKH--NMLFIETS 143 (161)
T ss_pred CCccccccc---CHHHHHHHHHHc--CCEEEEEe
Confidence 999974432 235555555543 46676543
No 140
>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=78.73 E-value=23 Score=27.80 Aligned_cols=97 Identities=16% Similarity=0.139 Sum_probs=47.2
Q ss_pred EEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc--------c-EEEE
Q 027979 46 HILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA--------D-VVIL 116 (216)
Q Consensus 46 ~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A--------D-~Ivl 116 (216)
.-|+.+.|...-..+..... -.-+.+|.|+|..+.... .. ...+..++... - +||.
T Consensus 49 l~i~Dt~G~~~~~~~~~~~~--------~~ad~~ilv~d~~~~~s~-~~------~~~~~~~i~~~~~~~~~~~piilvg 113 (190)
T cd04144 49 LEVLDTAGQEEYTALRDQWI--------REGEGFILVYSITSRSTF-ER------VERFREQIQRVKDESAADVPIMIVG 113 (190)
T ss_pred EEEEECCCchhhHHHHHHHH--------HhCCEEEEEEECCCHHHH-HH------HHHHHHHHHHHhcccCCCCCEEEEE
Confidence 44577788654443332211 124677888898765321 11 12222333221 1 5677
Q ss_pred ccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 117 NKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 117 nK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
||+|+.+..+. ......+..+.++ ++.++++- -......++
T Consensus 114 NK~Dl~~~~~v--~~~~~~~~~~~~~--~~~~e~SAk~~~~v~~l~ 155 (190)
T cd04144 114 NKCDKVYEREV--STEEGAALARRLG--CEFIEASAKTNVNVERAF 155 (190)
T ss_pred EChhccccCcc--CHHHHHHHHHHhC--CEEEEecCCCCCCHHHHH
Confidence 99999754321 2233334444443 46665432 234454554
No 141
>COG0370 FeoB Fe2+ transport system protein B [Inorganic ion transport and metabolism]
Probab=78.72 E-value=3.1 Score=39.72 Aligned_cols=88 Identities=19% Similarity=0.223 Sum_probs=52.4
Q ss_pred CEEEEecCCCCCcHHH------HHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEcc
Q 027979 45 DHILLETTGLANPAPL------ASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNK 118 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i------~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK 118 (216)
++-+|-..|+-...+. .+-+.. .=..|-+|.||||+|++..+.= ..-...+..==++.+|+
T Consensus 51 ~i~ivDLPG~YSL~~~S~DE~Var~~ll------~~~~D~ivnVvDAtnLeRnLyl-------tlQLlE~g~p~ilaLNm 117 (653)
T COG0370 51 EIEIVDLPGTYSLTAYSEDEKVARDFLL------EGKPDLIVNVVDATNLERNLYL-------TLQLLELGIPMILALNM 117 (653)
T ss_pred eEEEEeCCCcCCCCCCCchHHHHHHHHh------cCCCCEEEEEcccchHHHHHHH-------HHHHHHcCCCeEEEecc
Confidence 4567788887655433 222211 1245789999999999876521 10012333345788999
Q ss_pred CCCCCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 119 VDLVSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 119 ~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
+|.+......-..+++.+.+ +++++++
T Consensus 118 ~D~A~~~Gi~ID~~~L~~~L-----GvPVv~t 144 (653)
T COG0370 118 IDEAKKRGIRIDIEKLSKLL-----GVPVVPT 144 (653)
T ss_pred HhhHHhcCCcccHHHHHHHh-----CCCEEEE
Confidence 99887655433456666665 4666653
No 142
>PLN03127 Elongation factor Tu; Provisional
Probab=78.68 E-value=4.2 Score=37.21 Aligned_cols=65 Identities=29% Similarity=0.286 Sum_probs=37.2
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh---cc-EEEEccCC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF---AD-VVILNKVD 120 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~---AD-~IvlnK~D 120 (216)
.+++|-|.|..+ .+.... ......|.++.|||+......- -.+...++.. -- ++++||+|
T Consensus 125 ~i~~iDtPGh~~---f~~~~~-----~g~~~aD~allVVda~~g~~~q--------t~e~l~~~~~~gip~iIvviNKiD 188 (447)
T PLN03127 125 HYAHVDCPGHAD---YVKNMI-----TGAAQMDGGILVVSAPDGPMPQ--------TKEHILLARQVGVPSLVVFLNKVD 188 (447)
T ss_pred EEEEEECCCccc---hHHHHH-----HHHhhCCEEEEEEECCCCCchh--------HHHHHHHHHHcCCCeEEEEEEeec
Confidence 568999999853 332221 1223478899999997432110 1122333333 33 35799999
Q ss_pred CCCCC
Q 027979 121 LVSPE 125 (216)
Q Consensus 121 ~v~~~ 125 (216)
+++.+
T Consensus 189 lv~~~ 193 (447)
T PLN03127 189 VVDDE 193 (447)
T ss_pred cCCHH
Confidence 98643
No 143
>PRK04213 GTP-binding protein; Provisional
Probab=78.65 E-value=10 Score=29.90 Aligned_cols=79 Identities=22% Similarity=0.248 Sum_probs=37.9
Q ss_pred CEEEEecCCCCCcH-------HHHHHhhcCcccc-cceeeccEEEEEcccchHHHHhhcccCCCh---hHHHHHHhh---
Q 027979 45 DHILLETTGLANPA-------PLASVLWLDDQLE-SAVRLDSIITVVDAKNLLFQIDKYRHLSSY---PEAIHQIAF--- 110 (216)
Q Consensus 45 d~IiIE~sG~a~P~-------~i~~~l~~~~~l~-~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~---~~~~~QI~~--- 110 (216)
++.++.+.|.+.-. .-.+.++ ...+. ..-.++.++.|+|+..+......+...... .++...+..
T Consensus 53 ~~~l~Dt~G~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~vi~v~d~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 131 (201)
T PRK04213 53 DFILTDLPGFGFMSGVPKEVQEKIKDEI-VRYIEDNADRILAAVLVVDGKSFIEIIERWEGRGEIPIDVEMFDFLRELGI 131 (201)
T ss_pred ceEEEeCCccccccccCHHHHHHHHHHH-HHHHHhhhhhheEEEEEEeCccccccccccccCCCcHHHHHHHHHHHHcCC
Confidence 57889999964311 1222221 11111 122456789999997654221111000000 112223322
Q ss_pred ccEEEEccCCCCCC
Q 027979 111 ADVVILNKVDLVSP 124 (216)
Q Consensus 111 AD~IvlnK~D~v~~ 124 (216)
-=+||+||+|+.+.
T Consensus 132 p~iiv~NK~Dl~~~ 145 (201)
T PRK04213 132 PPIVAVNKMDKIKN 145 (201)
T ss_pred CeEEEEECccccCc
Confidence 22889999999764
No 144
>cd04170 EF-G_bact Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group
Probab=78.36 E-value=5.1 Score=33.65 Aligned_cols=77 Identities=18% Similarity=0.201 Sum_probs=43.8
Q ss_pred CCCEEEEecCCCCCcHH-HHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH---hhccEEEEcc
Q 027979 43 RLDHILLETTGLANPAP-LASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---AFADVVILNK 118 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~-i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~~AD~IvlnK 118 (216)
..+..+|-|.|..+-.. +...+ -..+.++.|+|+........ ..+.+++ ..--++++||
T Consensus 63 ~~~i~liDtPG~~~f~~~~~~~l---------~~aD~~i~Vvd~~~g~~~~~--------~~~~~~~~~~~~p~iivvNK 125 (268)
T cd04170 63 GHKINLIDTPGYADFVGETRAAL---------RAADAALVVVSAQSGVEVGT--------EKLWEFADEAGIPRIIFINK 125 (268)
T ss_pred CEEEEEEECcCHHHHHHHHHHHH---------HHCCEEEEEEeCCCCCCHHH--------HHHHHHHHHcCCCEEEEEEC
Confidence 34667888888754222 22222 24577899999986432110 1122233 3345789999
Q ss_pred CCCCCCCCccchHHHHHHHHHhh
Q 027979 119 VDLVSPERSGDSLDELEKEIHEI 141 (216)
Q Consensus 119 ~D~v~~~~~~~~l~~i~~~l~~l 141 (216)
+|+.... .++..+.+++.
T Consensus 126 ~D~~~~~-----~~~~~~~l~~~ 143 (268)
T cd04170 126 MDRERAD-----FDKTLAALQEA 143 (268)
T ss_pred CccCCCC-----HHHHHHHHHHH
Confidence 9998653 34455555543
No 145
>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=78.25 E-value=9.8 Score=29.33 Aligned_cols=43 Identities=16% Similarity=0.108 Sum_probs=26.0
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHh----hccEEEEccCCCCCC
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA----FADVVILNKVDLVSP 124 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~----~AD~IvlnK~D~v~~ 124 (216)
..+.++.|+|+..... +.. ..++.+++. .-=++|+||+|+.+.
T Consensus 77 ~~d~~llv~d~~~~~s-~~~------~~~~~~~~~~~~~~p~iiv~NK~Dl~~~ 123 (169)
T cd01892 77 ACDVACLVYDSSDPKS-FSY------CAEVYKKYFMLGEIPCLFVAAKADLDEQ 123 (169)
T ss_pred cCCEEEEEEeCCCHHH-HHH------HHHHHHHhccCCCCeEEEEEEccccccc
Confidence 5677899999976532 211 123334442 223688899999654
No 146
>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=77.97 E-value=22 Score=26.62 Aligned_cols=66 Identities=17% Similarity=0.126 Sum_probs=37.1
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHH---HHhhc---cEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEE
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIH---QIAFA---DVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVI 148 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~---QI~~A---D~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv 148 (216)
..+.+|.|+|+.+....- + ...+.. +.... =+|+.||+|+....+. ..+.+....+..+ .+++
T Consensus 72 ~~~~~i~v~d~~~~~s~~-~------~~~~~~~~~~~~~~~~~iivv~nK~D~~~~~~~--~~~~~~~~~~~~~--~~~~ 140 (161)
T cd04113 72 GAAGALLVYDITNRTSFE-A------LPTWLSDARALASPNIVVILVGNKSDLADQREV--TFLEASRFAQENG--LLFL 140 (161)
T ss_pred CCCEEEEEEECCCHHHHH-H------HHHHHHHHHHhCCCCCeEEEEEEchhcchhccC--CHHHHHHHHHHcC--CEEE
Confidence 356899999998754321 1 122222 22222 3567799999764321 3455556666554 5666
Q ss_pred Eee
Q 027979 149 RSV 151 (216)
Q Consensus 149 ~~~ 151 (216)
+++
T Consensus 141 ~~S 143 (161)
T cd04113 141 ETS 143 (161)
T ss_pred EEE
Confidence 543
No 147
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=77.54 E-value=27 Score=26.00 Aligned_cols=66 Identities=17% Similarity=0.111 Sum_probs=36.4
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHHHHHh------hccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEE
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA------FADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIR 149 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~------~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~ 149 (216)
.+.+|.|+|+.+.... .. ...+..++. .-=+++.||+|+....+. ..+.+.+..+..+ .++++
T Consensus 73 ~d~~ilv~d~~~~~s~-~~------~~~~l~~~~~~~~~~~pivvv~nK~D~~~~~~~--~~~~~~~~~~~~~--~~~~e 141 (164)
T smart00175 73 AVGALLVYDITNRESF-EN------LKNWLKELREYADPNVVIMLVGNKSDLEDQRQV--SREEAEAFAEEHG--LPFFE 141 (164)
T ss_pred CCEEEEEEECCCHHHH-HH------HHHHHHHHHHhCCCCCeEEEEEEchhcccccCC--CHHHHHHHHHHcC--CeEEE
Confidence 5789999999875432 11 111222221 235677799998764321 2355555555443 56665
Q ss_pred eec
Q 027979 150 SVR 152 (216)
Q Consensus 150 ~~~ 152 (216)
++.
T Consensus 142 ~Sa 144 (164)
T smart00175 142 TSA 144 (164)
T ss_pred EeC
Confidence 443
No 148
>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=77.30 E-value=22 Score=27.18 Aligned_cols=65 Identities=14% Similarity=0.080 Sum_probs=34.7
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHHHHHhh------c-cEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEE
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF------A-DVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVI 148 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~------A-D~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv 148 (216)
.+.+|.|+|+.+-.... + ...+..++.. . =+||.||+|+.+.... ..++..+..++.+ .+++
T Consensus 87 ~~~~i~v~d~~~~~s~~-~------~~~~~~~i~~~~~~~~~piiiv~nK~Dl~~~~~v--~~~~~~~~~~~~~--~~~~ 155 (180)
T cd04127 87 AMGFLLIFDLTNEQSFL-N------VRNWMSQLQTHAYCENPDIVLCGNKADLEDQRQV--SEEQAKALADKYG--IPYF 155 (180)
T ss_pred CCEEEEEEECCCHHHHH-H------HHHHHHHHHHhcCCCCCcEEEEEeCccchhcCcc--CHHHHHHHHHHcC--CeEE
Confidence 56789999987644321 1 1222233321 2 2566799999764321 2344555555443 4566
Q ss_pred Eee
Q 027979 149 RSV 151 (216)
Q Consensus 149 ~~~ 151 (216)
+++
T Consensus 156 e~S 158 (180)
T cd04127 156 ETS 158 (180)
T ss_pred EEe
Confidence 544
No 149
>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=77.16 E-value=27 Score=25.82 Aligned_cols=94 Identities=16% Similarity=0.161 Sum_probs=46.4
Q ss_pred EEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh----hcc---EEEEccCC
Q 027979 48 LLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA----FAD---VVILNKVD 120 (216)
Q Consensus 48 iIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~----~AD---~IvlnK~D 120 (216)
++.++|......+..... . .-+.++.|+|...-.. +.+ ......++. ..+ +|+.||+|
T Consensus 53 i~Dt~G~~~~~~l~~~~~-----~---~~~~~i~v~~~~~~~s-~~~------~~~~~~~i~~~~~~~~~piivv~nK~D 117 (162)
T cd04138 53 ILDTAGQEEYSAMRDQYM-----R---TGEGFLCVFAINSRKS-FED------IHTYREQIKRVKDSDDVPMVLVGNKCD 117 (162)
T ss_pred EEECCCCcchHHHHHHHH-----h---cCCEEEEEEECCCHHH-HHH------HHHHHHHHHHhcCCCCCCEEEEEECcc
Confidence 578888766555544322 1 2456778878765331 111 111222222 122 67889999
Q ss_pred CCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 121 LVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
+.+... ...++.+..+..+ .++++++. ...+.++++
T Consensus 118 l~~~~~---~~~~~~~~~~~~~--~~~~~~Sa~~~~gi~~l~ 154 (162)
T cd04138 118 LAARTV---SSRQGQDLAKSYG--IPYIETSAKTRQGVEEAF 154 (162)
T ss_pred ccccee---cHHHHHHHHHHhC--CeEEEecCCCCCCHHHHH
Confidence 976431 2344444444433 45665432 233444443
No 150
>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=77.07 E-value=5.1 Score=34.00 Aligned_cols=60 Identities=27% Similarity=0.243 Sum_probs=31.0
Q ss_pred CCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc-cEEEEccCCCCCC
Q 027979 55 ANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA-DVVILNKVDLVSP 124 (216)
Q Consensus 55 a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A-D~IvlnK~D~v~~ 124 (216)
|-|..+..++.. .....=..|-++.|+||....... .+.+.+.+..- =++|+||+|++++
T Consensus 3 WfpgHm~k~~~~--~~~~l~~aDvVl~V~Dar~p~~~~--------~~~i~~~l~~kp~IiVlNK~DL~~~ 63 (276)
T TIGR03596 3 WFPGHMAKARRE--IKEKLKLVDVVIEVLDARIPLSSR--------NPMIDEIRGNKPRLIVLNKADLADP 63 (276)
T ss_pred cChHHHHHHHHH--HHHHHhhCCEEEEEEeCCCCCCCC--------ChhHHHHHCCCCEEEEEEccccCCH
Confidence 346656554321 111122456679999996432110 11223333222 3688899999765
No 151
>PRK12735 elongation factor Tu; Reviewed
Probab=76.68 E-value=8.9 Score=34.40 Aligned_cols=91 Identities=23% Similarity=0.245 Sum_probs=47.8
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccch-HHHHhhcccCCChhHHHHHHhhcc---EE-EEcc
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNL-LFQIDKYRHLSSYPEAIHQIAFAD---VV-ILNK 118 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~-~~~l~~~~~~~~~~~~~~QI~~AD---~I-vlnK 118 (216)
..+.+|-|.|.. .++.... ...-..+.++.|||+..- ..+. .+...++.... +| ++||
T Consensus 75 ~~i~~iDtPGh~---~f~~~~~-----~~~~~aD~~llVvda~~g~~~qt---------~e~l~~~~~~gi~~iivvvNK 137 (396)
T PRK12735 75 RHYAHVDCPGHA---DYVKNMI-----TGAAQMDGAILVVSAADGPMPQT---------REHILLARQVGVPYIVVFLNK 137 (396)
T ss_pred cEEEEEECCCHH---HHHHHHH-----hhhccCCEEEEEEECCCCCchhH---------HHHHHHHHHcCCCeEEEEEEe
Confidence 356899999973 3333221 233467888999999752 2111 12233444333 43 5899
Q ss_pred CCCCCCCCccchH-HHHHHHHHhhC-C--CCEEEEee
Q 027979 119 VDLVSPERSGDSL-DELEKEIHEIN-S--LAHVIRSV 151 (216)
Q Consensus 119 ~D~v~~~~~~~~l-~~i~~~l~~lN-P--~A~iv~~~ 151 (216)
+|+++.++....+ +++++.++.+. + .++++..+
T Consensus 138 ~Dl~~~~~~~~~~~~ei~~~l~~~~~~~~~~~ii~~S 174 (396)
T PRK12735 138 CDMVDDEELLELVEMEVRELLSKYDFPGDDTPIIRGS 174 (396)
T ss_pred cCCcchHHHHHHHHHHHHHHHHHcCCCcCceeEEecc
Confidence 9998643210011 24444555442 2 35666543
No 152
>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=76.59 E-value=21 Score=27.27 Aligned_cols=44 Identities=20% Similarity=0.270 Sum_probs=25.8
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc-------cEEEEccCCCCCCC
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA-------DVVILNKVDLVSPE 125 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A-------D~IvlnK~D~v~~~ 125 (216)
..+.+|.|+|+.+-... .. ...+..++... =+|+.||+|+....
T Consensus 75 ~~d~~i~v~d~~~~~s~-~~------~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~~ 125 (170)
T cd04115 75 NVHAVVFVYDVTNMASF-HS------LPSWIEECEQHSLPNEVPRILVGNKCDLREQI 125 (170)
T ss_pred CCCEEEEEEECCCHHHH-Hh------HHHHHHHHHHhcCCCCCCEEEEEECccchhhc
Confidence 35778999999864422 11 22233333322 26788999986543
No 153
>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=76.27 E-value=13 Score=30.93 Aligned_cols=66 Identities=18% Similarity=0.155 Sum_probs=38.2
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEccC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNKV 119 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK~ 119 (216)
+....++.|.|..+-...... ..-..+.+|.|+|+..-.... ...+.+++. .-=+|++||+
T Consensus 63 ~~~i~liDTPG~~~f~~~~~~--------~l~~aD~~IlVvd~~~g~~~~--------~~~~~~~~~~~~~P~iivvNK~ 126 (237)
T cd04168 63 DTKVNLIDTPGHMDFIAEVER--------SLSVLDGAILVISAVEGVQAQ--------TRILWRLLRKLNIPTIIFVNKI 126 (237)
T ss_pred CEEEEEEeCCCccchHHHHHH--------HHHHhCeEEEEEeCCCCCCHH--------HHHHHHHHHHcCCCEEEEEECc
Confidence 456788899998754332221 112357889999998642211 111222232 2237899999
Q ss_pred CCCCC
Q 027979 120 DLVSP 124 (216)
Q Consensus 120 D~v~~ 124 (216)
|+...
T Consensus 127 D~~~a 131 (237)
T cd04168 127 DRAGA 131 (237)
T ss_pred cccCC
Confidence 99764
No 154
>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=76.25 E-value=4.4 Score=30.82 Aligned_cols=41 Identities=24% Similarity=0.308 Sum_probs=23.9
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEccCCCCCC
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNKVDLVSP 124 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK~D~v~~ 124 (216)
.+.++.|+|+....... ..++...+. .-=++++||+|+.+.
T Consensus 13 aD~vl~V~D~~~~~~~~--------~~~l~~~~~~~~~p~iiv~NK~Dl~~~ 56 (156)
T cd01859 13 SDVVLEVLDARDPELTR--------SRKLERYVLELGKKLLIVLNKADLVPK 56 (156)
T ss_pred CCEEEEEeeCCCCcccC--------CHHHHHHHHhCCCcEEEEEEhHHhCCH
Confidence 56789999996532111 112222232 223788899999764
No 155
>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=76.21 E-value=30 Score=26.24 Aligned_cols=37 Identities=19% Similarity=0.306 Sum_probs=21.6
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccch
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNL 88 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~ 88 (216)
....+..+.|......+..... -.-+.+|.|+|+...
T Consensus 44 ~~~~l~D~~G~~~~~~~~~~~~--------~~ad~~i~v~D~~~~ 80 (159)
T cd04150 44 ISFTVWDVGGQDKIRPLWRHYF--------QNTQGLIFVVDSNDR 80 (159)
T ss_pred EEEEEEECCCCHhHHHHHHHHh--------cCCCEEEEEEeCCCH
Confidence 3456677777643333322211 234788999999864
No 156
>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=76.13 E-value=39 Score=30.88 Aligned_cols=115 Identities=17% Similarity=0.141 Sum_probs=64.9
Q ss_pred hhHHHHHHHHHHhcCCCCEEEEecCCCCCc-HHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHH
Q 027979 28 HSLVQALEQLVQRKERLDHILLETTGLANP-APLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIH 106 (216)
Q Consensus 28 ~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P-~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~ 106 (216)
.++..+|..+.. ..++|+|||-|.|-..- ...++.+. .+......+.++.|+||..-...+.. .-..+.
T Consensus 306 ~~L~~aL~~lk~-~~~~DvVLIDTaGRs~kd~~lm~EL~---~~lk~~~PdevlLVLsATtk~~d~~~------i~~~F~ 375 (436)
T PRK11889 306 AAMTRALTYFKE-EARVDYILIDTAGKNYRASETVEEMI---ETMGQVEPDYICLTLSASMKSKDMIE------IITNFK 375 (436)
T ss_pred HHHHHHHHHHHh-ccCCCEEEEeCccccCcCHHHHHHHH---HHHhhcCCCeEEEEECCccChHHHHH------HHHHhc
Confidence 566677766643 23689999999999653 22232221 11122334567888998654433322 111112
Q ss_pred HHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeecCCCChhhhh
Q 027979 107 QIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQVDLSEVL 161 (216)
Q Consensus 107 QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~~~l~ 161 (216)
. ..-|-+|++|.|-...- -.+.+.+... +.+|.....|+-=+++|.
T Consensus 376 ~-~~idglI~TKLDET~k~------G~iLni~~~~--~lPIsyit~GQ~VPeDI~ 421 (436)
T PRK11889 376 D-IHIDGIVFTKFDETASS------GELLKIPAVS--SAPIVLMTDGQDVKKNIH 421 (436)
T ss_pred C-CCCCEEEEEcccCCCCc------cHHHHHHHHH--CcCEEEEeCCCCCCcchh
Confidence 2 34589999999987653 2333444333 467777677754444544
No 157
>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PDOC50926 from PROSITEDOC). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [, , ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [, ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PDOC00155 from PROSITEDOC) []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit []. ; GO: 0003824 catalytic activity, 0051539 4 iron, 4 sulfur cluster binding, 0009451 RNA modification
Probab=76.04 E-value=2.3 Score=30.51 Aligned_cols=64 Identities=16% Similarity=0.328 Sum_probs=37.5
Q ss_pred EEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhC-CCCEEEEe
Q 027979 80 ITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEIN-SLAHVIRS 150 (216)
Q Consensus 80 I~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lN-P~A~iv~~ 150 (216)
.-.+|+..+...+... .+ +.....+.||+||+|=+--...++. ..+..+ ..+++.+ |+++|+.+
T Consensus 11 ~N~~Dse~i~~~l~~~----G~-~~~~~~e~AD~iiiNTC~V~~~Ae~-k~~~~i-~~l~~~~~~~~~ivv~ 75 (98)
T PF00919_consen 11 MNQYDSERIASILQAA----GY-EIVDDPEEADVIIINTCTVRESAEQ-KSRNRI-RKLKKLKKPGAKIVVT 75 (98)
T ss_pred ccHHHHHHHHHHHHhc----CC-eeecccccCCEEEEEcCCCCcHHHH-HHHHHH-HHHHHhcCCCCEEEEE
Confidence 4455666666666442 11 2235568999999999877665431 222333 3334455 88888754
No 158
>CHL00071 tufA elongation factor Tu
Probab=75.46 E-value=6.2 Score=35.54 Aligned_cols=91 Identities=20% Similarity=0.185 Sum_probs=48.0
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccE-EEEccC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADV-VILNKV 119 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~-IvlnK~ 119 (216)
..+++|-|.|.. ..+.... ...-..|.++.|||+..-..... .+...++. .--+ +++||+
T Consensus 75 ~~~~~iDtPGh~---~~~~~~~-----~~~~~~D~~ilVvda~~g~~~qt--------~~~~~~~~~~g~~~iIvvvNK~ 138 (409)
T CHL00071 75 RHYAHVDCPGHA---DYVKNMI-----TGAAQMDGAILVVSAADGPMPQT--------KEHILLAKQVGVPNIVVFLNKE 138 (409)
T ss_pred eEEEEEECCChH---HHHHHHH-----HHHHhCCEEEEEEECCCCCcHHH--------HHHHHHHHHcCCCEEEEEEEcc
Confidence 356889999953 3333221 22335688999999975321110 11223333 3324 579999
Q ss_pred CCCCCCCccch-HHHHHHHHHhhC--C-CCEEEEe
Q 027979 120 DLVSPERSGDS-LDELEKEIHEIN--S-LAHVIRS 150 (216)
Q Consensus 120 D~v~~~~~~~~-l~~i~~~l~~lN--P-~A~iv~~ 150 (216)
|+++.++..+. .+++.+.++.++ + .++++..
T Consensus 139 D~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~ii~~ 173 (409)
T CHL00071 139 DQVDDEELLELVELEVRELLSKYDFPGDDIPIVSG 173 (409)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHhCCCCCcceEEEc
Confidence 99875421011 135555665543 2 2566653
No 159
>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=75.46 E-value=21 Score=27.45 Aligned_cols=43 Identities=21% Similarity=0.230 Sum_probs=24.2
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHh--hcc-----EEEEccCCCCCC
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA--FAD-----VVILNKVDLVSP 124 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~--~AD-----~IvlnK~D~v~~ 124 (216)
..+.++.|.|+..-... .. ...+..++. ... ++|.||+|+.+.
T Consensus 72 ~ad~~ilv~d~~~~~s~-~~------~~~~~~~~~~~~~~~~~~iilVgnK~Dl~~~ 121 (170)
T cd04108 72 GAQAIIIVFDLTDVASL-EH------TRQWLEDALKENDPSSVLLFLVGTKKDLSSP 121 (170)
T ss_pred CCCEEEEEEECcCHHHH-HH------HHHHHHHHHHhcCCCCCeEEEEEEChhcCcc
Confidence 45678999999763221 11 122233321 122 578899998764
No 160
>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=75.38 E-value=26 Score=27.03 Aligned_cols=100 Identities=15% Similarity=0.168 Sum_probs=48.2
Q ss_pred EEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc----EEEEccCCC
Q 027979 46 HILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD----VVILNKVDL 121 (216)
Q Consensus 46 ~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD----~IvlnK~D~ 121 (216)
.-|+.++|......+..... -.-+++|.|+|..+-...-.-. ..-....+..... ++|.||+|+
T Consensus 52 l~i~Dt~G~~~~~~l~~~~~--------~~~d~~ilv~d~~~~~Sf~~~~----~~~~~i~~~~~~~~~piilvgNK~Dl 119 (172)
T cd04141 52 LDILDTAGQAEFTAMRDQYM--------RCGEGFIICYSVTDRHSFQEAS----EFKKLITRVRLTEDIPLVLVGNKVDL 119 (172)
T ss_pred EEEEeCCCchhhHHHhHHHh--------hcCCEEEEEEECCchhHHHHHH----HHHHHHHHhcCCCCCCEEEEEEChhh
Confidence 44567777655444433221 1346778888886543221100 0111123332211 678899998
Q ss_pred CCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 122 VSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 122 v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
.+..+. ..++..+..+.. ++++++++- ...+.++++
T Consensus 120 ~~~~~v--~~~~~~~~a~~~--~~~~~e~Sa~~~~~v~~~f 156 (172)
T cd04141 120 ESQRQV--TTEEGRNLAREF--NCPFFETSAALRHYIDDAF 156 (172)
T ss_pred hhcCcc--CHHHHHHHHHHh--CCEEEEEecCCCCCHHHHH
Confidence 654321 223344444433 467776543 234454544
No 161
>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]
Probab=75.13 E-value=12 Score=31.52 Aligned_cols=90 Identities=24% Similarity=0.370 Sum_probs=49.3
Q ss_pred eeecCCCcEEeecchhHHHHHHHHHHhcCCCCEEEEecC-CCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHH
Q 027979 14 WVELANGCICCTVKHSLVQALEQLVQRKERLDHILLETT-GLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQI 92 (216)
Q Consensus 14 v~eL~~GCiCCsl~~dl~~~L~~l~~~~~~~d~IiIE~s-G~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l 92 (216)
+-+-..||.| .+..=+..-|++|. ..+.|+|||-|= |+ +-|- .... =.+|-+|.|+|++.=.-.+
T Consensus 107 ie~~GeGC~C-p~~allR~~l~~l~--~~~~e~VivDtEAGi-------EHfg--Rg~~--~~vD~vivVvDpS~~sl~t 172 (255)
T COG3640 107 IEEGGEGCAC-PMNALLRRLLRHLI--LNRYEVVIVDTEAGI-------EHFG--RGTI--EGVDLVIVVVDPSYKSLRT 172 (255)
T ss_pred ccCCCCcccc-hHHHHHHHHHHHHh--cccCcEEEEecccch-------hhhc--cccc--cCCCEEEEEeCCcHHHHHH
Confidence 4456789998 44443333444553 345899999663 44 2221 1111 2467799999997321111
Q ss_pred hhcccCCChhHHHHHHhhc-cEEEEccCCCC
Q 027979 93 DKYRHLSSYPEAIHQIAFA-DVVILNKVDLV 122 (216)
Q Consensus 93 ~~~~~~~~~~~~~~QI~~A-D~IvlnK~D~v 122 (216)
.. ...++.+++..= =.+|+||.|-.
T Consensus 173 ae-----ri~~L~~elg~k~i~~V~NKv~e~ 198 (255)
T COG3640 173 AE-----RIKELAEELGIKRIFVVLNKVDEE 198 (255)
T ss_pred HH-----HHHHHHHHhCCceEEEEEeeccch
Confidence 11 133445555522 25788999864
No 162
>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=74.97 E-value=8.8 Score=32.06 Aligned_cols=77 Identities=21% Similarity=0.262 Sum_probs=36.8
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc---EEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD---VVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD---~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
.++.++.|.|+..-...+.. ...+...+...+ +||+||+|+.+..+ ...+..+..++. +.+++.++
T Consensus 36 n~D~viiV~d~~~p~~s~~~------l~r~l~~~~~~~i~~vIV~NK~DL~~~~~---~~~~~~~~~~~~--g~~v~~~S 104 (245)
T TIGR00157 36 NIDQIVIVSSAVLPELSLNQ------LDRFLVVAEAQNIEPIIVLNKIDLLDDED---MEKEQLDIYRNI--GYQVLMTS 104 (245)
T ss_pred cCCEEEEEEECCCCCCCHHH------HHHHHHHHHHCCCCEEEEEECcccCCCHH---HHHHHHHHHHHC--CCeEEEEe
Confidence 45678888887632211100 111122222222 58889999976532 112233344433 35666544
Q ss_pred c-CCCChhhhhc
Q 027979 152 R-CQVDLSEVLN 162 (216)
Q Consensus 152 ~-~~v~~~~l~~ 162 (216)
. ..-.++.++.
T Consensus 105 Aktg~gi~eLf~ 116 (245)
T TIGR00157 105 SKNQDGLKELIE 116 (245)
T ss_pred cCCchhHHHHHh
Confidence 2 2334555554
No 163
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=74.17 E-value=16 Score=33.37 Aligned_cols=96 Identities=20% Similarity=0.261 Sum_probs=47.5
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchH--HHHhhcccCCChhHHH---HHHhhccE-EEE
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLL--FQIDKYRHLSSYPEAI---HQIAFADV-VIL 116 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~--~~l~~~~~~~~~~~~~---~QI~~AD~-Ivl 116 (216)
...+.||-+.|-.+ .+..+ ....-..|.+|.||||..-. ..+... ..-.+.. ..+..-.+ |++
T Consensus 84 ~~~i~lIDtPGh~~---f~~~~-----~~g~~~aD~ailVVda~~G~~e~~~~~~---~qT~eh~~~~~~~gi~~iiv~v 152 (446)
T PTZ00141 84 KYYFTIIDAPGHRD---FIKNM-----ITGTSQADVAILVVASTAGEFEAGISKD---GQTREHALLAFTLGVKQMIVCI 152 (446)
T ss_pred CeEEEEEECCChHH---HHHHH-----HHhhhhcCEEEEEEEcCCCceecccCCC---ccHHHHHHHHHHcCCCeEEEEE
Confidence 34667899999532 22221 12234667889999997532 111000 0011222 22333344 799
Q ss_pred ccCCC--CCCCCccchHHHHHHHHHh------hCC-CCEEEEee
Q 027979 117 NKVDL--VSPERSGDSLDELEKEIHE------INS-LAHVIRSV 151 (216)
Q Consensus 117 nK~D~--v~~~~~~~~l~~i~~~l~~------lNP-~A~iv~~~ 151 (216)
||+|. ++..+ ..++++.+.++. +++ ..++++.+
T Consensus 153 NKmD~~~~~~~~--~~~~~i~~~i~~~l~~~g~~~~~~~~ipiS 194 (446)
T PTZ00141 153 NKMDDKTVNYSQ--ERYDEIKKEVSAYLKKVGYNPEKVPFIPIS 194 (446)
T ss_pred EccccccchhhH--HHHHHHHHHHHHHHHhcCCCcccceEEEee
Confidence 99994 33211 134444444443 233 46777654
No 164
>PLN03118 Rab family protein; Provisional
Probab=74.08 E-value=43 Score=26.69 Aligned_cols=99 Identities=16% Similarity=0.140 Sum_probs=50.3
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhH-HHHHHhh-------ccEEEE
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPE-AIHQIAF-------ADVVIL 116 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~-~~~QI~~-------AD~Ivl 116 (216)
...|+.+.|......+..... . ..+.+|.|+|..+..... + ... +..++.. --+||.
T Consensus 63 ~l~l~Dt~G~~~~~~~~~~~~-----~---~~d~~vlv~D~~~~~sf~-~------~~~~~~~~~~~~~~~~~~~~ilv~ 127 (211)
T PLN03118 63 KLTIWDTAGQERFRTLTSSYY-----R---NAQGIILVYDVTRRETFT-N------LSDVWGKEVELYSTNQDCVKMLVG 127 (211)
T ss_pred EEEEEECCCchhhHHHHHHHH-----h---cCCEEEEEEECCCHHHHH-H------HHHHHHHHHHHhcCCCCCCEEEEE
Confidence 346778888755444433321 1 346789999998754321 1 111 1122221 135788
Q ss_pred ccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhhc
Q 027979 117 NKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVLN 162 (216)
Q Consensus 117 nK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~~ 162 (216)
||+|+...... ..+......+.. .+.+++++. .....+.++.
T Consensus 128 NK~Dl~~~~~i--~~~~~~~~~~~~--~~~~~e~SAk~~~~v~~l~~ 170 (211)
T PLN03118 128 NKVDRESERDV--SREEGMALAKEH--GCLFLECSAKTRENVEQCFE 170 (211)
T ss_pred ECccccccCcc--CHHHHHHHHHHc--CCEEEEEeCCCCCCHHHHHH
Confidence 99999765321 223333444433 356665432 2345555553
No 165
>PRK10218 GTP-binding protein; Provisional
Probab=73.80 E-value=10 Score=36.17 Aligned_cols=84 Identities=18% Similarity=0.199 Sum_probs=46.6
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLV 122 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v 122 (216)
+....++-|.|.++-........ -..+++|.|||+..-...-... .-....+....-+|++||+|+.
T Consensus 67 ~~~inliDTPG~~df~~~v~~~l--------~~aDg~ILVVDa~~G~~~qt~~-----~l~~a~~~gip~IVviNKiD~~ 133 (607)
T PRK10218 67 DYRINIVDTPGHADFGGEVERVM--------SMVDSVLLVVDAFDGPMPQTRF-----VTKKAFAYGLKPIVVINKVDRP 133 (607)
T ss_pred CEEEEEEECCCcchhHHHHHHHH--------HhCCEEEEEEecccCccHHHHH-----HHHHHHHcCCCEEEEEECcCCC
Confidence 34567889999987765544322 2467889999997532110000 0001122333458999999986
Q ss_pred CCCCccchHHHHHHHHHh
Q 027979 123 SPERSGDSLDELEKEIHE 140 (216)
Q Consensus 123 ~~~~~~~~l~~i~~~l~~ 140 (216)
+..- ...++++.+.+..
T Consensus 134 ~a~~-~~vl~ei~~l~~~ 150 (607)
T PRK10218 134 GARP-DWVVDQVFDLFVN 150 (607)
T ss_pred CCch-hHHHHHHHHHHhc
Confidence 5421 1234555555433
No 166
>PRK00098 GTPase RsgA; Reviewed
Probab=73.79 E-value=7.4 Score=33.49 Aligned_cols=78 Identities=22% Similarity=0.231 Sum_probs=37.7
Q ss_pred eeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc---cEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 74 VRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA---DVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 74 ~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A---D~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
-.+|.++.|+|+........- ...+...+..+ =+||+||+|+.+.. .......+..+.++ .+++.+
T Consensus 79 aniD~vllV~d~~~p~~~~~~------idr~L~~~~~~~ip~iIVlNK~DL~~~~---~~~~~~~~~~~~~g--~~v~~v 147 (298)
T PRK00098 79 ANVDQAVLVFAAKEPDFSTDL------LDRFLVLAEANGIKPIIVLNKIDLLDDL---EEARELLALYRAIG--YDVLEL 147 (298)
T ss_pred ecCCEEEEEEECCCCCCCHHH------HHHHHHHHHHCCCCEEEEEEhHHcCCCH---HHHHHHHHHHHHCC--CeEEEE
Confidence 467778999999642110000 11122223333 35889999997432 12233344444433 456543
Q ss_pred ec-CCCChhhhhc
Q 027979 151 VR-CQVDLSEVLN 162 (216)
Q Consensus 151 ~~-~~v~~~~l~~ 162 (216)
+. ..-.++.|+.
T Consensus 148 SA~~g~gi~~L~~ 160 (298)
T PRK00098 148 SAKEGEGLDELKP 160 (298)
T ss_pred eCCCCccHHHHHh
Confidence 32 2334555543
No 167
>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=73.67 E-value=6.1 Score=35.35 Aligned_cols=90 Identities=24% Similarity=0.252 Sum_probs=45.8
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchH-HHHhhcccCCChhHHHHHHhh---ccE-EEEccC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLL-FQIDKYRHLSSYPEAIHQIAF---ADV-VILNKV 119 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~-~~l~~~~~~~~~~~~~~QI~~---AD~-IvlnK~ 119 (216)
.+.+|-|.|-.+ ..... +...-..+.++.|||+..-. .+. .+....+.. --+ |++||+
T Consensus 76 ~~~liDtpGh~~---f~~~~-----~~~~~~~D~~ilVvda~~g~~~qt---------~e~l~~~~~~gi~~iIvvvNK~ 138 (394)
T TIGR00485 76 HYAHVDCPGHAD---YVKNM-----ITGAAQMDGAILVVSATDGPMPQT---------REHILLARQVGVPYIVVFLNKC 138 (394)
T ss_pred EEEEEECCchHH---HHHHH-----HHHHhhCCEEEEEEECCCCCcHHH---------HHHHHHHHHcCCCEEEEEEEec
Confidence 467888888632 22221 12233567889999997521 111 112222222 234 368999
Q ss_pred CCCCCCCccc-hHHHHHHHHHhhC-C--CCEEEEee
Q 027979 120 DLVSPERSGD-SLDELEKEIHEIN-S--LAHVIRSV 151 (216)
Q Consensus 120 D~v~~~~~~~-~l~~i~~~l~~lN-P--~A~iv~~~ 151 (216)
|+++.++..+ ..+++++.++.+. + .++++.++
T Consensus 139 Dl~~~~~~~~~~~~~i~~~l~~~~~~~~~~~ii~vS 174 (394)
T TIGR00485 139 DMVDDEELLELVEMEVRELLSEYDFPGDDTPIIRGS 174 (394)
T ss_pred ccCCHHHHHHHHHHHHHHHHHhcCCCccCccEEECc
Confidence 9987532100 0124555666543 1 26777644
No 168
>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=73.57 E-value=6.1 Score=35.55 Aligned_cols=94 Identities=21% Similarity=0.299 Sum_probs=45.7
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchH--HHHhhcccCCChhHHHHHHhhcc-EEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLL--FQIDKYRHLSSYPEAIHQIAFAD-VVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~--~~l~~~~~~~~~~~~~~QI~~AD-~IvlnK~D 120 (216)
....+|-+.|-. .....+. ...-..+.++.|||+..-. .+...+ . .......... +|++||+|
T Consensus 80 ~~i~liDtPGh~---~f~~~~~-----~g~~~aD~aIlVVDa~~g~~~~qt~e~-----l-~~l~~~gi~~iIVvvNK~D 145 (406)
T TIGR03680 80 RRVSFVDAPGHE---TLMATML-----SGAALMDGALLVIAANEPCPQPQTKEH-----L-MALEIIGIKNIVIVQNKID 145 (406)
T ss_pred cEEEEEECCCHH---HHHHHHH-----HHHHHCCEEEEEEECCCCccccchHHH-----H-HHHHHcCCCeEEEEEEccc
Confidence 346788888853 2222211 1223457889999998532 111000 0 0112222223 57799999
Q ss_pred CCCCCCccchHHHHHHHHHhhC-CCCEEEEee
Q 027979 121 LVSPERSGDSLDELEKEIHEIN-SLAHVIRSV 151 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~lN-P~A~iv~~~ 151 (216)
+++.+......+++.+.++... ...++++++
T Consensus 146 l~~~~~~~~~~~~i~~~l~~~~~~~~~ii~vS 177 (406)
T TIGR03680 146 LVSKEKALENYEEIKEFVKGTVAENAPIIPVS 177 (406)
T ss_pred cCCHHHHHHHHHHHHhhhhhcccCCCeEEEEE
Confidence 9875421011234444444321 245676543
No 169
>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB. This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.
Probab=73.51 E-value=3.1 Score=32.27 Aligned_cols=50 Identities=28% Similarity=0.282 Sum_probs=31.4
Q ss_pred eeeecCCCcEEeecchh-HHHHHHHHHHhcCCCCEEEEecCCCCCcHHHHHH
Q 027979 13 EWVELANGCICCTVKHS-LVQALEQLVQRKERLDHILLETTGLANPAPLASV 63 (216)
Q Consensus 13 ~v~eL~~GCiCCsl~~d-l~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~ 63 (216)
..+.+.+||.||..... ....|.+++.+...+|+||||.-+-. |.+-+..
T Consensus 58 ~~v~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~D~vlVEG~k~~-~~pki~v 108 (155)
T TIGR00176 58 DQVIVASSRRYAFMHETQEERDLEALLDRLPDLDIILVEGFKDS-PLPKIVV 108 (155)
T ss_pred CEEEEecCCeEEEEEecCCCcCHHHHHhhCCCCCEEEECCCCCC-CCCEEEE
Confidence 46778899999975531 12344454443334899999998864 4444433
No 170
>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=73.38 E-value=36 Score=26.01 Aligned_cols=65 Identities=15% Similarity=0.065 Sum_probs=32.4
Q ss_pred EEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh--c---cEEEEccCC
Q 027979 46 HILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF--A---DVVILNKVD 120 (216)
Q Consensus 46 ~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~--A---D~IvlnK~D 120 (216)
..+++++|.-....+... .+ -..+.+|.|.|..+-...- .. ...+..++.. . =+++.||+|
T Consensus 50 ~~i~Dt~G~~~~~~~~~~-----~~---~~a~~~i~v~d~~~~~sf~-~~-----~~~~~~~~~~~~~~~piilv~nK~D 115 (173)
T cd04130 50 LQLCDTAGQDEFDKLRPL-----CY---PDTDVFLLCFSVVNPSSFQ-NI-----SEKWIPEIRKHNPKAPIILVGTQAD 115 (173)
T ss_pred EEEEECCCChhhcccccc-----cc---CCCcEEEEEEECCCHHHHH-HH-----HHHHHHHHHhhCCCCCEEEEeeChh
Confidence 456777877433222111 11 1346788888877643211 10 0112233321 1 278889999
Q ss_pred CCCC
Q 027979 121 LVSP 124 (216)
Q Consensus 121 ~v~~ 124 (216)
+.+.
T Consensus 116 l~~~ 119 (173)
T cd04130 116 LRTD 119 (173)
T ss_pred hccC
Confidence 9753
No 171
>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=73.29 E-value=19 Score=27.23 Aligned_cols=86 Identities=20% Similarity=0.183 Sum_probs=43.3
Q ss_pred EEEEecCCCCC--cHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh--------ccEEE
Q 027979 46 HILLETTGLAN--PAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF--------ADVVI 115 (216)
Q Consensus 46 ~IiIE~sG~a~--P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~--------AD~Iv 115 (216)
.-++.++|... .......+ -..+.+|.++|+.+.... .. ...+..++.. -=++|
T Consensus 49 ~~i~D~~g~~~~~~~~~~~~~---------~~~d~~i~v~d~~~~~s~-~~------~~~~~~~~~~~~~~~~~~piilv 112 (165)
T cd04146 49 LEILDTAGQQQADTEQLERSI---------RWADGFVLVYSITDRSSF-DE------ISQLKQLIREIKKRDREIPVILV 112 (165)
T ss_pred EEEEECCCCcccccchHHHHH---------HhCCEEEEEEECCCHHHH-HH------HHHHHHHHHHHhcCCCCCCEEEE
Confidence 34778888763 22111111 124678999999876432 11 1112222221 12577
Q ss_pred EccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 116 LNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 116 lnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
.||+|+...... ..+...+..+..+ ++.++++
T Consensus 113 ~nK~Dl~~~~~v--~~~~~~~~~~~~~--~~~~e~S 144 (165)
T cd04146 113 GNKADLLHYRQV--STEEGEKLASELG--CLFFEVS 144 (165)
T ss_pred EECCchHHhCcc--CHHHHHHHHHHcC--CEEEEeC
Confidence 899998654321 2233444444444 5666654
No 172
>KOG1424 consensus Predicted GTP-binding protein MMR1 [General function prediction only]
Probab=72.66 E-value=6.1 Score=36.75 Aligned_cols=58 Identities=26% Similarity=0.411 Sum_probs=34.9
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHHHHH--hhccEEEEccCCCCCCCCccchHHHHHHHHHhhC
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI--AFADVVILNKVDLVSPERSGDSLDELEKEIHEIN 142 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI--~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lN 142 (216)
=|-||-||||.+-+-+.... ....+.-+ .-+.++++||+|++++++ .....+.-+.-|
T Consensus 175 SDivvqIVDARnPllfr~~d-----Le~Yvke~d~~K~~~LLvNKaDLl~~~q----r~aWa~YF~~~n 234 (562)
T KOG1424|consen 175 SDIVVQIVDARNPLLFRSPD-----LEDYVKEVDPSKANVLLVNKADLLPPEQ----RVAWAEYFRQNN 234 (562)
T ss_pred cceEEEEeecCCccccCChh-----HHHHHhccccccceEEEEehhhcCCHHH----HHHHHHHHHhcC
Confidence 35679999999865332210 11112111 256799999999999863 355555555545
No 173
>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=72.47 E-value=16 Score=29.05 Aligned_cols=71 Identities=15% Similarity=0.057 Sum_probs=34.2
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVS 123 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~ 123 (216)
++..++.+.|+.+.....+..... ......+.++.+.| ..+...-.. .-....+...--++|+||+|+..
T Consensus 52 ~~l~l~DtpG~~~~~~~~~~~l~~---~~~~~~d~~l~v~~-~~~~~~d~~------~~~~l~~~~~~~ilV~nK~D~~~ 121 (197)
T cd04104 52 PNVTLWDLPGIGSTAFPPDDYLEE---MKFSEYDFFIIISS-TRFSSNDVK------LAKAIQCMGKKFYFVRTKVDRDL 121 (197)
T ss_pred CCceEEeCCCCCcccCCHHHHHHH---hCccCcCEEEEEeC-CCCCHHHHH------HHHHHHHhCCCEEEEEecccchh
Confidence 577899999998753322221100 01123444555544 334321111 11112222223379999999965
Q ss_pred C
Q 027979 124 P 124 (216)
Q Consensus 124 ~ 124 (216)
+
T Consensus 122 ~ 122 (197)
T cd04104 122 S 122 (197)
T ss_pred h
Confidence 3
No 174
>cd01852 AIG1 AIG1 (avrRpt2-induced gene 1). This represents Arabidoposis protein AIG1 that appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 exhibits RPS2- and avrRpt1-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2. This subfamily also includes IAN-4 protein, which has GTP-binding activity and shares sequence homology with a novel family of putative GTP-binding proteins: the immuno-associated nucleotide (IAN) family. The evolutionary conservation of the IAN family provides a unique example of a plant pathogen response gene conserved in animals. The IAN/IMAP subfamily has been proposed to regulate apoptosis in vertebrates and angiosperm plants, particularly in relation to cancer, diabetes, and infections. The human IAN genes were renamed GIMAP (GTPase of the immunity associated proteins).
Probab=72.25 E-value=13 Score=29.49 Aligned_cols=72 Identities=15% Similarity=0.129 Sum_probs=40.7
Q ss_pred CCEEEEecCCCCCcH----HHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh--------c
Q 027979 44 LDHILLETTGLANPA----PLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF--------A 111 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~----~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~--------A 111 (216)
....+|.|.|+.++. .+...+. .......-.++.++.|+|+.++...- ..+.+++.. -
T Consensus 49 ~~i~viDTPG~~d~~~~~~~~~~~i~-~~~~~~~~g~~~illVi~~~~~t~~d---------~~~l~~l~~~fg~~~~~~ 118 (196)
T cd01852 49 RRVNVIDTPGLFDTSVSPEQLSKEIV-RCLSLSAPGPHAFLLVVPLGRFTEEE---------EQAVETLQELFGEKVLDH 118 (196)
T ss_pred eEEEEEECcCCCCccCChHHHHHHHH-HHHHhcCCCCEEEEEEEECCCcCHHH---------HHHHHHHHHHhChHhHhc
Confidence 467899999999874 2222211 00011112456799999998743221 122333322 2
Q ss_pred cEEEEccCCCCCCC
Q 027979 112 DVVILNKVDLVSPE 125 (216)
Q Consensus 112 D~IvlnK~D~v~~~ 125 (216)
=+|++||.|.....
T Consensus 119 ~ivv~T~~d~l~~~ 132 (196)
T cd01852 119 TIVLFTRGDDLEGG 132 (196)
T ss_pred EEEEEECccccCCC
Confidence 26888999987653
No 175
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=72.21 E-value=2.6 Score=37.08 Aligned_cols=56 Identities=21% Similarity=0.436 Sum_probs=34.6
Q ss_pred HHHhhccEEEE-ccCCCCCCCCccchHHHHHHHHHh-hCCCCEEEEeec-CCCChhhhh
Q 027979 106 HQIAFADVVIL-NKVDLVSPERSGDSLDELEKEIHE-INSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 106 ~QI~~AD~Ivl-nK~D~v~~~~~~~~l~~i~~~l~~-lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
+=|..=++||+ ||+|+++.++.-+.-++++++++. ..-+|+|++.+- -+++.+.++
T Consensus 136 eIigik~iiIvQNKIDlV~~E~AlE~y~qIk~FvkGt~Ae~aPIIPiSA~~~~NIDal~ 194 (415)
T COG5257 136 EIIGIKNIIIVQNKIDLVSRERALENYEQIKEFVKGTVAENAPIIPISAQHKANIDALI 194 (415)
T ss_pred hhhccceEEEEecccceecHHHHHHHHHHHHHHhcccccCCCceeeehhhhccCHHHHH
Confidence 33344444444 999999987543455677777775 345789986443 245555554
No 176
>PLN03126 Elongation factor Tu; Provisional
Probab=71.84 E-value=7.1 Score=36.10 Aligned_cols=68 Identities=22% Similarity=0.189 Sum_probs=33.6
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh---ccE-EEEccCCCCCCCCccchH-HHHHHHHHhh--CC-CCE
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF---ADV-VILNKVDLVSPERSGDSL-DELEKEIHEI--NS-LAH 146 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~---AD~-IvlnK~D~v~~~~~~~~l-~~i~~~l~~l--NP-~A~ 146 (216)
..|.++.||||......- -.+...++.. .-+ |++||+|+++.++..+.+ +++++.++.+ ++ .++
T Consensus 167 ~aD~ailVVda~~G~~~q--------t~e~~~~~~~~gi~~iIvvvNK~Dl~~~~~~~~~i~~~i~~~l~~~g~~~~~~~ 238 (478)
T PLN03126 167 QMDGAILVVSGADGPMPQ--------TKEHILLAKQVGVPNMVVFLNKQDQVDDEELLELVELEVRELLSSYEFPGDDIP 238 (478)
T ss_pred hCCEEEEEEECCCCCcHH--------HHHHHHHHHHcCCCeEEEEEecccccCHHHHHHHHHHHHHHHHHhcCCCcCcce
Confidence 456677888876432110 0122222322 223 579999998753210111 2455555554 22 566
Q ss_pred EEEe
Q 027979 147 VIRS 150 (216)
Q Consensus 147 iv~~ 150 (216)
++..
T Consensus 239 ~vp~ 242 (478)
T PLN03126 239 IISG 242 (478)
T ss_pred EEEE
Confidence 7654
No 177
>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=71.53 E-value=27 Score=25.94 Aligned_cols=69 Identities=17% Similarity=0.214 Sum_probs=36.0
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHH--Hh---hccEEEEccC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQ--IA---FADVVILNKV 119 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~Q--I~---~AD~IvlnK~ 119 (216)
..-++.+.|...-..+..... -..+.+|.|+|+......-... .....+... +. .-=+|++||+
T Consensus 46 ~~~l~Dt~G~~~~~~~~~~~~--------~~~d~ii~v~D~~~~~~~~~~~---~~~~~~~~~~~~~~~~~p~iiv~NK~ 114 (162)
T cd04157 46 SFTAFDMSGQGKYRGLWEHYY--------KNIQGIIFVIDSSDRLRLVVVK---DELELLLNHPDIKHRRVPILFFANKM 114 (162)
T ss_pred EEEEEECCCCHhhHHHHHHHH--------ccCCEEEEEEeCCcHHHHHHHH---HHHHHHHcCcccccCCCCEEEEEeCc
Confidence 346788888754444333221 2467899999998654221000 001111111 11 1227788999
Q ss_pred CCCCC
Q 027979 120 DLVSP 124 (216)
Q Consensus 120 D~v~~ 124 (216)
|+.+.
T Consensus 115 Dl~~~ 119 (162)
T cd04157 115 DLPDA 119 (162)
T ss_pred cccCC
Confidence 99764
No 178
>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=71.38 E-value=13 Score=33.27 Aligned_cols=72 Identities=22% Similarity=0.301 Sum_probs=37.7
Q ss_pred CEEEEecCCCCCc-HHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc---EEEEccCC
Q 027979 45 DHILLETTGLANP-APLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD---VVILNKVD 120 (216)
Q Consensus 45 d~IiIE~sG~a~P-~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD---~IvlnK~D 120 (216)
...++.|.|+... ..+.+.+. .......-..+.++.|+|+..-....+ .++.+.++..+ ++++||+|
T Consensus 48 ~~~liDTpG~~~~~~~~~~~~~-~~~~~~~~~ad~vl~vvD~~~~~~~~d--------~~i~~~l~~~~~piilVvNK~D 118 (429)
T TIGR03594 48 EFILIDTGGIEEDDDGLDKQIR-EQAEIAIEEADVILFVVDGREGLTPED--------EEIAKWLRKSGKPVILVANKID 118 (429)
T ss_pred EEEEEECCCCCCcchhHHHHHH-HHHHHHHhhCCEEEEEEeCCCCCCHHH--------HHHHHHHHHhCCCEEEEEECcc
Confidence 4678999997433 11111111 000111123567899999975322211 12233343333 77889999
Q ss_pred CCCCC
Q 027979 121 LVSPE 125 (216)
Q Consensus 121 ~v~~~ 125 (216)
+.+.+
T Consensus 119 ~~~~~ 123 (429)
T TIGR03594 119 GKKED 123 (429)
T ss_pred CCccc
Confidence 97654
No 179
>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=71.32 E-value=27 Score=26.03 Aligned_cols=70 Identities=20% Similarity=0.256 Sum_probs=34.4
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHH--HH-hhccEEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIH--QI-AFADVVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~--QI-~~AD~IvlnK~D 120 (216)
....+.+++|...-..+.... + -..+.+|.|+|+.+.... .... ..+.++.+ .+ ..-=+|++||+|
T Consensus 44 ~~l~i~D~~G~~~~~~~~~~~-----~---~~~~~iv~v~D~~~~~~~-~~~~--~~~~~~~~~~~~~~~piilv~nK~D 112 (160)
T cd04156 44 LSLTVWDVGGQEKMRTVWKCY-----L---ENTDGLVYVVDSSDEARL-DESQ--KELKHILKNEHIKGVPVVLLANKQD 112 (160)
T ss_pred eEEEEEECCCCHhHHHHHHHH-----h---ccCCEEEEEEECCcHHHH-HHHH--HHHHHHHhchhhcCCCEEEEEECcc
Confidence 345667777764322222211 1 124678999999875421 1100 00111111 11 122377889999
Q ss_pred CCCC
Q 027979 121 LVSP 124 (216)
Q Consensus 121 ~v~~ 124 (216)
+.+.
T Consensus 113 l~~~ 116 (160)
T cd04156 113 LPGA 116 (160)
T ss_pred cccC
Confidence 8653
No 180
>PRK09563 rbgA GTPase YlqF; Reviewed
Probab=71.27 E-value=5.1 Score=34.23 Aligned_cols=60 Identities=30% Similarity=0.303 Sum_probs=33.0
Q ss_pred CCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH-hhccEEEEccCCCCCC
Q 027979 55 ANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI-AFADVVILNKVDLVSP 124 (216)
Q Consensus 55 a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI-~~AD~IvlnK~D~v~~ 124 (216)
|-|..+..++. ......-..|-++.|+|+....... .+.+.+.+ ..--++|+||+|+++.
T Consensus 6 wfpgHm~k~~~--~l~~~l~~aDvIL~VvDar~p~~~~--------~~~l~~~~~~kp~iiVlNK~DL~~~ 66 (287)
T PRK09563 6 WFPGHMAKARR--EIKENLKLVDVVIEVLDARIPLSSE--------NPMIDKIIGNKPRLLILNKSDLADP 66 (287)
T ss_pred CcHHHHHHHHH--HHHHHhhhCCEEEEEEECCCCCCCC--------ChhHHHHhCCCCEEEEEEchhcCCH
Confidence 55666665532 1112223457789999996443211 11222222 2334899999999764
No 181
>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=71.27 E-value=48 Score=26.31 Aligned_cols=96 Identities=16% Similarity=0.174 Sum_probs=49.9
Q ss_pred EEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh----hcc-EEEEccCCC
Q 027979 47 ILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA----FAD-VVILNKVDL 121 (216)
Q Consensus 47 IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~----~AD-~IvlnK~D~ 121 (216)
-+..++|.-....+..... -..+++|.|.|..+-... .+ ...+.+||. .+= +||-||.|+
T Consensus 58 ~iwDt~G~~~~~~l~~~~~--------~~ad~illVfD~t~~~Sf-~~------~~~w~~~i~~~~~~~piilVGNK~DL 122 (189)
T cd04121 58 QLWDTSGQGRFCTIFRSYS--------RGAQGIILVYDITNRWSF-DG------IDRWIKEIDEHAPGVPKILVGNRLHL 122 (189)
T ss_pred EEEeCCCcHHHHHHHHHHh--------cCCCEEEEEEECcCHHHH-HH------HHHHHHHHHHhCCCCCEEEEEECccc
Confidence 3456777654444433221 245788999998764422 11 122333342 222 455699999
Q ss_pred CCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 122 VSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 122 v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
...... ..++.++..+..+ .++++++- ...+.+.+|
T Consensus 123 ~~~~~v--~~~~~~~~a~~~~--~~~~e~SAk~g~~V~~~F 159 (189)
T cd04121 123 AFKRQV--ATEQAQAYAERNG--MTFFEVSPLCNFNITESF 159 (189)
T ss_pred hhccCC--CHHHHHHHHHHcC--CEEEEecCCCCCCHHHHH
Confidence 653221 2455556655543 56776542 234455554
No 182
>PF14972 Mito_morph_reg: Mitochondrial morphogenesis regulator
Probab=71.25 E-value=4.7 Score=31.63 Aligned_cols=29 Identities=21% Similarity=0.407 Sum_probs=24.0
Q ss_pred chhHHHHHHHHHHhcCCCCEEEEecCCCCCc
Q 027979 27 KHSLVQALEQLVQRKERLDHILLETTGLANP 57 (216)
Q Consensus 27 ~~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P 57 (216)
.+.|...|++-++ .++++|+||++.++|-
T Consensus 17 ~e~FE~eLe~ALe--~~~~~IVIEP~~LGde 45 (165)
T PF14972_consen 17 HEQFEAELERALE--AKVSYIVIEPTRLGDE 45 (165)
T ss_pred HHHHHHHHHHHHH--hCCCEEEECCccccHH
Confidence 4678888998876 3689999999999864
No 183
>TIGR00437 feoB ferrous iron transporter FeoB. FeoB (773 amino acids in E. coli), a cytoplasmic membrane protein required for iron(II) update, is encoded in an operon with FeoA (75 amino acids), which is also required, and is regulated by Fur. There appear to be two copies in Archaeoglobus fulgidus and Clostridium acetobutylicum.
Probab=71.06 E-value=13 Score=35.43 Aligned_cols=69 Identities=23% Similarity=0.234 Sum_probs=38.7
Q ss_pred CEEEEecCCCCCcHHHH--HHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh---ccEEEEccC
Q 027979 45 DHILLETTGLANPAPLA--SVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF---ADVVILNKV 119 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~--~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~---AD~IvlnK~ 119 (216)
...++.+.|..+-.+.. +.+..+ .+. .-..+.++.|+|+.++.+.+. ...|+.. -=++++||+
T Consensus 42 ~i~lvDtPG~~~~~~~s~~e~v~~~-~l~-~~~aDvvI~VvDat~ler~l~----------l~~ql~~~~~PiIIVlNK~ 109 (591)
T TIGR00437 42 DIEIVDLPGIYSLTTFSLEEEVARD-YLL-NEKPDLVVNVVDASNLERNLY----------LTLQLLELGIPMILALNLV 109 (591)
T ss_pred EEEEEECCCccccCccchHHHHHHH-HHh-hcCCCEEEEEecCCcchhhHH----------HHHHHHhcCCCEEEEEehh
Confidence 45788899876543221 111100 001 114578999999998654331 2234432 336888999
Q ss_pred CCCCCC
Q 027979 120 DLVSPE 125 (216)
Q Consensus 120 D~v~~~ 125 (216)
|+.+..
T Consensus 110 Dl~~~~ 115 (591)
T TIGR00437 110 DEAEKK 115 (591)
T ss_pred HHHHhC
Confidence 997654
No 184
>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=71.03 E-value=53 Score=26.39 Aligned_cols=75 Identities=16% Similarity=0.201 Sum_probs=38.2
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHHHHHhh----cc---EEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEE
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF----AD---VVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVI 148 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~----AD---~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv 148 (216)
.+.+|.|+|..+... +.+ ......++.. .. +||.||+|+.+.... ..++..+..+..+ ..++
T Consensus 76 ~d~iilv~D~~~~~S-f~~------l~~~~~~i~~~~~~~~~~iilvgNK~Dl~~~~~v--~~~~~~~~~~~~~--~~~~ 144 (211)
T cd04111 76 SVGVLLVFDITNRES-FEH------VHDWLEEARSHIQPHRPVFILVGHKCDLESQRQV--TREEAEKLAKDLG--MKYI 144 (211)
T ss_pred CcEEEEEEECCCHHH-HHH------HHHHHHHHHHhcCCCCCeEEEEEEcccccccccc--CHHHHHHHHHHhC--CEEE
Confidence 467889999887532 111 1222333321 12 456799999764321 2334444444433 6677
Q ss_pred Eeec-CCCChhhhh
Q 027979 149 RSVR-CQVDLSEVL 161 (216)
Q Consensus 149 ~~~~-~~v~~~~l~ 161 (216)
+++- ..-+..+++
T Consensus 145 e~Sak~g~~v~e~f 158 (211)
T cd04111 145 ETSARTGDNVEEAF 158 (211)
T ss_pred EEeCCCCCCHHHHH
Confidence 6543 233444544
No 185
>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=70.56 E-value=25 Score=28.62 Aligned_cols=98 Identities=14% Similarity=0.082 Sum_probs=47.9
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh-------ccEEEE
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF-------ADVVIL 116 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~-------AD~Ivl 116 (216)
....++.++|.. . .....+ ..+..+.++.|+|+.+-... .. ...+..++.. -=+||.
T Consensus 50 ~~l~i~Dt~G~~--~-~~~~~~------~~~~ad~iilV~d~td~~S~-~~------~~~~~~~l~~~~~~~~~piilV~ 113 (221)
T cd04148 50 STLVVIDHWEQE--M-WTEDSC------MQYQGDAFVVVYSVTDRSSF-ER------ASELRIQLRRNRQLEDRPIILVG 113 (221)
T ss_pred EEEEEEeCCCcc--h-HHHhHH------hhcCCCEEEEEEECCCHHHH-HH------HHHHHHHHHHhcCCCCCCEEEEE
Confidence 345577888875 1 111111 01156788999999875432 11 1222233322 126777
Q ss_pred ccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 117 NKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 117 nK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
||+|+....+. ..++..+..... .+++++++- -+.+.+.++
T Consensus 114 NK~Dl~~~~~v--~~~~~~~~a~~~--~~~~~e~SA~~~~gv~~l~ 155 (221)
T cd04148 114 NKSDLARSREV--SVQEGRACAVVF--DCKFIETSAGLQHNVDELL 155 (221)
T ss_pred EChhcccccee--cHHHHHHHHHHc--CCeEEEecCCCCCCHHHHH
Confidence 99999765431 223233332222 356666442 233444444
No 186
>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=70.36 E-value=43 Score=25.08 Aligned_cols=98 Identities=13% Similarity=0.109 Sum_probs=47.7
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh-----cc-EEEEcc
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF-----AD-VVILNK 118 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~-----AD-~IvlnK 118 (216)
..-++.++|......+..... . ..+.+|.|+|+...... .+ ...+..++.. .- +|+.||
T Consensus 53 ~~~l~D~~g~~~~~~~~~~~~-----~---~~~~~i~v~d~~~~~s~-~~------~~~~~~~~~~~~~~~~pi~vv~nK 117 (165)
T cd01868 53 KAQIWDTAGQERYRAITSAYY-----R---GAVGALLVYDITKKQTF-EN------VERWLKELRDHADSNIVIMLVGNK 117 (165)
T ss_pred EEEEEeCCChHHHHHHHHHHH-----C---CCCEEEEEEECcCHHHH-HH------HHHHHHHHHHhCCCCCeEEEEEEC
Confidence 345667777643333332211 1 23568999999754432 11 1222333321 11 467899
Q ss_pred CCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 119 VDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 119 ~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
+|+.+..+. ..++..+..+. + +.++++++. .....+.++
T Consensus 118 ~Dl~~~~~~--~~~~~~~~~~~-~-~~~~~~~Sa~~~~~v~~l~ 157 (165)
T cd01868 118 SDLRHLRAV--PTEEAKAFAEK-N-GLSFIETSALDGTNVEEAF 157 (165)
T ss_pred ccccccccC--CHHHHHHHHHH-c-CCEEEEEECCCCCCHHHHH
Confidence 999764321 23444444443 2 456666443 233444443
No 187
>PRK03003 GTP-binding protein Der; Reviewed
Probab=69.95 E-value=15 Score=33.64 Aligned_cols=47 Identities=26% Similarity=0.312 Sum_probs=25.4
Q ss_pred EEEEccCCCCCCCCccchHHHHHHHHHh-h--CCCCEEEEeec-CCCChhhhhcc
Q 027979 113 VVILNKVDLVSPERSGDSLDELEKEIHE-I--NSLAHVIRSVR-CQVDLSEVLNC 163 (216)
Q Consensus 113 ~IvlnK~D~v~~~~~~~~l~~i~~~l~~-l--NP~A~iv~~~~-~~v~~~~l~~~ 163 (216)
+|++||+|+.+++. ...+...++. + .+.++++.++- ..-..+.++..
T Consensus 326 IiV~NK~Dl~~~~~----~~~~~~~i~~~l~~~~~~~~~~~SAk~g~gv~~lf~~ 376 (472)
T PRK03003 326 VLAFNKWDLVDEDR----RYYLEREIDRELAQVPWAPRVNISAKTGRAVDKLVPA 376 (472)
T ss_pred EEEEECcccCChhH----HHHHHHHHHHhcccCCCCCEEEEECCCCCCHHHHHHH
Confidence 78889999986431 2333333332 1 24567765432 34456666543
No 188
>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=69.80 E-value=39 Score=26.42 Aligned_cols=75 Identities=12% Similarity=0.146 Sum_probs=36.8
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHHHHHhh------ccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEE
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF------ADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIR 149 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~------AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~ 149 (216)
.+.+|.|+|+.+... +.+ ......++.. -=+|+.||+|+..+... ..++..+..+..+ .++++
T Consensus 74 ad~~i~v~D~~~~~s-~~~------~~~~~~~i~~~~~~~~piiiv~NK~Dl~~~~~~--~~~~~~~l~~~~~--~~~~e 142 (191)
T cd04112 74 AHALLLLYDITNKAS-FDN------IRAWLTEIKEYAQEDVVIMLLGNKADMSGERVV--KREDGERLAKEYG--VPFME 142 (191)
T ss_pred CCEEEEEEECCCHHH-HHH------HHHHHHHHHHhCCCCCcEEEEEEcccchhcccc--CHHHHHHHHHHcC--CeEEE
Confidence 467899999987532 111 1112222221 12477799999754321 2234444444333 45665
Q ss_pred eec-CCCChhhhh
Q 027979 150 SVR-CQVDLSEVL 161 (216)
Q Consensus 150 ~~~-~~v~~~~l~ 161 (216)
++- .....+.++
T Consensus 143 ~Sa~~~~~v~~l~ 155 (191)
T cd04112 143 TSAKTGLNVELAF 155 (191)
T ss_pred EeCCCCCCHHHHH
Confidence 432 123444444
No 189
>TIGR02034 CysN sulfate adenylyltransferase, large subunit. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules. With members of the Rhizobiaceae family, nodQ often appears as a fusion of cysN (large subunit of ATP sulfurase) and cysC (APS kinase).
Probab=69.65 E-value=8.5 Score=34.65 Aligned_cols=68 Identities=21% Similarity=0.260 Sum_probs=36.4
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc-EEEEccCCCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD-VVILNKVDLV 122 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD-~IvlnK~D~v 122 (216)
..+.+|-|.|..+ +...+. ...-..|.++.|||+..-...-.. .+-.+...+..-. +|++||+|++
T Consensus 80 ~~~~liDtPGh~~---f~~~~~-----~~~~~aD~allVVda~~G~~~qt~-----~~~~~~~~~~~~~iivviNK~D~~ 146 (406)
T TIGR02034 80 RKFIVADTPGHEQ---YTRNMA-----TGASTADLAVLLVDARKGVLEQTR-----RHSYIASLLGIRHVVLAVNKMDLV 146 (406)
T ss_pred eEEEEEeCCCHHH---HHHHHH-----HHHhhCCEEEEEEECCCCCccccH-----HHHHHHHHcCCCcEEEEEEecccc
Confidence 3568889999532 222211 122356778999999743211000 0111223333334 4589999998
Q ss_pred CC
Q 027979 123 SP 124 (216)
Q Consensus 123 ~~ 124 (216)
+.
T Consensus 147 ~~ 148 (406)
T TIGR02034 147 DY 148 (406)
T ss_pred cc
Confidence 64
No 190
>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=69.61 E-value=53 Score=25.88 Aligned_cols=102 Identities=12% Similarity=0.113 Sum_probs=48.6
Q ss_pred EEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh---c---cEEEEccC
Q 027979 46 HILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF---A---DVVILNKV 119 (216)
Q Consensus 46 ~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~---A---D~IvlnK~ 119 (216)
..+.+++|...-..+..... -..+++|.|+|...-... ..... -..++...+.. . =+||.||+
T Consensus 52 l~l~Dt~G~~~~~~~~~~~~--------~~a~~~ilv~D~t~~~s~-~~~~~--~~~~i~~~~~~~~~~~~piilv~NK~ 120 (201)
T cd04107 52 LQLWDIAGQERFGGMTRVYY--------RGAVGAIIVFDVTRPSTF-EAVLK--WKADLDSKVTLPNGEPIPCLLLANKC 120 (201)
T ss_pred EEEEECCCchhhhhhHHHHh--------CCCCEEEEEEECCCHHHH-HHHHH--HHHHHHHhhcccCCCCCcEEEEEECC
Confidence 44556777643333322221 134678999998764321 11000 01111122211 1 17788999
Q ss_pred CCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 120 DLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
|+.+... ...+++.+..+..+ ..++++++- ...+...++
T Consensus 121 Dl~~~~~--~~~~~~~~~~~~~~-~~~~~e~Sak~~~~v~e~f 160 (201)
T cd04107 121 DLKKRLA--KDGEQMDQFCKENG-FIGWFETSAKEGINIEEAM 160 (201)
T ss_pred Ccccccc--cCHHHHHHHHHHcC-CceEEEEeCCCCCCHHHHH
Confidence 9974221 13456666666544 345665443 234555554
No 191
>PLN03108 Rab family protein; Provisional
Probab=69.05 E-value=57 Score=26.08 Aligned_cols=75 Identities=17% Similarity=0.115 Sum_probs=39.0
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHHHHHh-h--cc---EEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEE
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA-F--AD---VVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIR 149 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~-~--AD---~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~ 149 (216)
.+.+|.|+|+.+....- . .......+. . .+ +++.||+|+.+... ...+...+..+..+ .++++
T Consensus 79 ad~~vlv~D~~~~~s~~-~------l~~~~~~~~~~~~~~~piiiv~nK~Dl~~~~~--~~~~~~~~~~~~~~--~~~~e 147 (210)
T PLN03108 79 AAGALLVYDITRRETFN-H------LASWLEDARQHANANMTIMLIGNKCDLAHRRA--VSTEEGEQFAKEHG--LIFME 147 (210)
T ss_pred CCEEEEEEECCcHHHHH-H------HHHHHHHHHHhcCCCCcEEEEEECccCccccC--CCHHHHHHHHHHcC--CEEEE
Confidence 56789999998754221 1 111122121 1 12 68889999976432 13455555555543 56665
Q ss_pred eec-CCCChhhhh
Q 027979 150 SVR-CQVDLSEVL 161 (216)
Q Consensus 150 ~~~-~~v~~~~l~ 161 (216)
++- ......++|
T Consensus 148 ~Sa~~~~~v~e~f 160 (210)
T PLN03108 148 ASAKTAQNVEEAF 160 (210)
T ss_pred EeCCCCCCHHHHH
Confidence 442 233444444
No 192
>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=68.92 E-value=46 Score=24.86 Aligned_cols=62 Identities=24% Similarity=0.215 Sum_probs=32.6
Q ss_pred EEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh-------ccEEEEccCC
Q 027979 48 LLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF-------ADVVILNKVD 120 (216)
Q Consensus 48 iIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~-------AD~IvlnK~D 120 (216)
|..++|.-.-..+..... -.-+.+|.|.|...-.. +.+ ..++..++.. -=+|+.||+|
T Consensus 53 i~Dt~G~~~~~~~~~~~~--------~~ad~~i~v~d~~~~~s-~~~------~~~~~~~~~~~~~~~~~piviv~nK~D 117 (163)
T cd04176 53 ILDTAGTEQFASMRDLYI--------KNGQGFIVVYSLVNQQT-FQD------IKPMRDQIVRVKGYEKVPIILVGNKVD 117 (163)
T ss_pred EEECCCcccccchHHHHH--------hhCCEEEEEEECCCHHH-HHH------HHHHHHHHHHhcCCCCCCEEEEEECcc
Confidence 567888644333333221 13466788888876432 111 1222223321 2367889999
Q ss_pred CCCC
Q 027979 121 LVSP 124 (216)
Q Consensus 121 ~v~~ 124 (216)
+.+.
T Consensus 118 l~~~ 121 (163)
T cd04176 118 LESE 121 (163)
T ss_pred chhc
Confidence 8654
No 193
>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=68.87 E-value=47 Score=24.92 Aligned_cols=70 Identities=19% Similarity=0.094 Sum_probs=34.1
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHHHHHh-----hcc-EEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEE
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA-----FAD-VVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIR 149 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~-----~AD-~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~ 149 (216)
.+.+|.++|+..-.. +.+... -..++..+.. ... ++++||+|+..+.. ...+.+++..+..+ ..++++
T Consensus 73 ~d~~i~v~d~~~~~~-~~~~~~--~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~--~~~~~~~~~~~~~~-~~~~~~ 146 (172)
T cd01862 73 ADCCVLVYDVTNPKS-FESLDS--WRDEFLIQASPSDPENFPFVVLGNKIDLEEKRQ--VSTKKAQQWCQSNG-NIPYFE 146 (172)
T ss_pred CCEEEEEEECCCHHH-HHHHHH--HHHHHHHhcCccCCCCceEEEEEECcccccccc--cCHHHHHHHHHHcC-CceEEE
Confidence 577899999875432 111000 0111222221 122 56779999984322 12355555555433 356665
Q ss_pred ee
Q 027979 150 SV 151 (216)
Q Consensus 150 ~~ 151 (216)
++
T Consensus 147 ~S 148 (172)
T cd01862 147 TS 148 (172)
T ss_pred EE
Confidence 43
No 194
>KOG0461 consensus Selenocysteine-specific elongation factor [Translation, ribosomal structure and biogenesis]
Probab=68.85 E-value=17 Score=32.59 Aligned_cols=95 Identities=17% Similarity=0.301 Sum_probs=59.3
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccE-EEEccCCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADV-VILNKVDL 121 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~-IvlnK~D~ 121 (216)
+...-+|.+.|=| .+++++. ...--+|-++.|||+......- . ..-.+..|+.+-.+ ||+||+|.
T Consensus 69 ~lq~tlvDCPGHa---sLIRtii-----ggaqiiDlm~lviDv~kG~QtQ-t-----AEcLiig~~~c~klvvvinkid~ 134 (522)
T KOG0461|consen 69 QLQFTLVDCPGHA---SLIRTII-----GGAQIIDLMILVIDVQKGKQTQ-T-----AECLIIGELLCKKLVVVINKIDV 134 (522)
T ss_pred cceeEEEeCCCcH---HHHHHHH-----hhhheeeeeeEEEehhcccccc-c-----chhhhhhhhhccceEEEEecccc
Confidence 4566788999876 6777653 2334567789999997543210 0 01124567766665 56799999
Q ss_pred CCCCCccchHHHHHHHHHh------hCCCCEEEEee
Q 027979 122 VSPERSGDSLDELEKEIHE------INSLAHVIRSV 151 (216)
Q Consensus 122 v~~~~~~~~l~~i~~~l~~------lNP~A~iv~~~ 151 (216)
..+.++...+++...++++ ...+++|++.+
T Consensus 135 lpE~qr~ski~k~~kk~~KtLe~t~f~g~~PI~~vs 170 (522)
T KOG0461|consen 135 LPENQRASKIEKSAKKVRKTLESTGFDGNSPIVEVS 170 (522)
T ss_pred ccchhhhhHHHHHHHHHHHHHHhcCcCCCCceeEEe
Confidence 9886554455666555553 34457777644
No 195
>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=68.83 E-value=53 Score=25.51 Aligned_cols=37 Identities=22% Similarity=0.215 Sum_probs=21.1
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchH
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLL 89 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~ 89 (216)
...+.+++|...-.++...+. -..+.+|.|+|+....
T Consensus 53 ~l~l~Dt~G~~~~~~~~~~~~--------~~~d~ii~v~D~~~~~ 89 (183)
T cd04152 53 TFHFWDVGGQEKLRPLWKSYT--------RCTDGIVFVVDSVDVE 89 (183)
T ss_pred EEEEEECCCcHhHHHHHHHHh--------ccCCEEEEEEECCCHH
Confidence 455667777643222222211 1356789999998754
No 196
>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=68.47 E-value=8.6 Score=34.74 Aligned_cols=99 Identities=14% Similarity=0.220 Sum_probs=46.7
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccE-EEEccCCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADV-VILNKVDL 121 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~-IvlnK~D~ 121 (216)
+....|+-+.|-. .+.... +...-..+.+|.|+|+..-....... . ...-.+.+++...-+ |++||+|+
T Consensus 84 ~~~i~iiDtpGh~---~f~~~~-----~~~~~~aD~~ilVvDa~~~~~~~~~~-t-~~~~~~~~~~~~~~iIVviNK~Dl 153 (426)
T TIGR00483 84 KYEVTIVDCPGHR---DFIKNM-----ITGASQADAAVLVVAVGDGEFEVQPQ-T-REHAFLARTLGINQLIVAINKMDS 153 (426)
T ss_pred CeEEEEEECCCHH---HHHHHH-----HhhhhhCCEEEEEEECCCCCcccCCc-h-HHHHHHHHHcCCCeEEEEEEChhc
Confidence 3566788888842 222221 11223467889999998642111000 0 000011222332234 47899999
Q ss_pred CCCCCc--cchHHHHHHHHHhhC---CCCEEEEee
Q 027979 122 VSPERS--GDSLDELEKEIHEIN---SLAHVIRSV 151 (216)
Q Consensus 122 v~~~~~--~~~l~~i~~~l~~lN---P~A~iv~~~ 151 (216)
++..+. ....+++++.++..+ ...++++++
T Consensus 154 ~~~~~~~~~~~~~ei~~~~~~~g~~~~~~~~i~iS 188 (426)
T TIGR00483 154 VNYDEEEFEAIKKEVSNLIKKVGYNPDTVPFIPIS 188 (426)
T ss_pred cCccHHHHHHHHHHHHHHHHHcCCCcccceEEEee
Confidence 853210 011234444555443 135666543
No 197
>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=68.37 E-value=45 Score=25.38 Aligned_cols=65 Identities=17% Similarity=0.133 Sum_probs=35.8
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh----cc-EEEEccC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF----AD-VVILNKV 119 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~----AD-~IvlnK~ 119 (216)
...+..++|.-+...+.+.. ....+.+|.|+|...-... .+ .+.+..++.. .- +||.||+
T Consensus 50 ~l~i~Dt~G~~~~~~~~~~~--------~~~~d~~i~v~d~~~~~s~-~~------~~~~~~~i~~~~~~~piiiv~nK~ 114 (166)
T cd00877 50 RFNVWDTAGQEKFGGLRDGY--------YIGGQCAIIMFDVTSRVTY-KN------VPNWHRDLVRVCGNIPIVLCGNKV 114 (166)
T ss_pred EEEEEECCCChhhccccHHH--------hcCCCEEEEEEECCCHHHH-HH------HHHHHHHHHHhCCCCcEEEEEEch
Confidence 34566777775443332221 1246788999999865432 11 2223344432 22 4668999
Q ss_pred CCCCC
Q 027979 120 DLVSP 124 (216)
Q Consensus 120 D~v~~ 124 (216)
|+...
T Consensus 115 Dl~~~ 119 (166)
T cd00877 115 DIKDR 119 (166)
T ss_pred hcccc
Confidence 99743
No 198
>PF01656 CbiA: CobQ/CobB/MinD/ParA nucleotide binding domain; InterPro: IPR002586 This entry consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from Salmonella typhimurium []., and CobQ from Rhodobacter capsulatus []. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [].; PDB: 3K9G_A 3K9H_B 3EZ9_B 3EZF_A 3EZ2_B 3EZ6_A 3EZ7_A 1G3Q_A 1G3R_A 1DTS_A ....
Probab=68.21 E-value=53 Score=25.33 Aligned_cols=74 Identities=20% Similarity=0.248 Sum_probs=43.0
Q ss_pred HHHHHHHHHhcCCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh
Q 027979 31 VQALEQLVQRKERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF 110 (216)
Q Consensus 31 ~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~ 110 (216)
...+..+.. ..+|+|||.+.+.-... +...+. .-+.+|.++++.... +.+ ...+.+.++.
T Consensus 84 ~~~l~~l~~--~~yD~iiiD~~~~~~~~-~~~~l~---------~ad~viv~~~~~~~~--i~~------~~~~~~~l~~ 143 (195)
T PF01656_consen 84 REILESLIK--SDYDYIIIDTPPGLSDP-VRNALA---------AADYVIVPIEPDPSS--IEG------AERLIELLKR 143 (195)
T ss_dssp HHHHHHHHH--TTSSEEEEEECSSSSHH-HHHHHH---------TSSEEEEEEESSHHH--HHH------HHHHHHHHHH
T ss_pred HHHHHHhhh--ccccceeecccccccHH-HHHHHH---------hCceeeeecCCcHHH--HHH------HHHHHHHHHH
Confidence 334444432 34999999998765443 333332 234578899987654 222 2223444444
Q ss_pred cc------EEEEccCCCCCC
Q 027979 111 AD------VVILNKVDLVSP 124 (216)
Q Consensus 111 AD------~IvlnK~D~v~~ 124 (216)
.. .+|+||.+.-..
T Consensus 144 ~~~~~~~~~vv~N~v~~~~~ 163 (195)
T PF01656_consen 144 LGKKLKIIGVVINRVDPGNE 163 (195)
T ss_dssp HTHTEEEEEEEEEEETSCCH
T ss_pred hccccceEEEEEeeeCCCcc
Confidence 33 789999987643
No 199
>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=68.04 E-value=49 Score=24.89 Aligned_cols=64 Identities=16% Similarity=0.178 Sum_probs=34.6
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh-----ccEEEEccC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF-----ADVVILNKV 119 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~-----AD~IvlnK~ 119 (216)
..-+..++|-.....+..... -.-+.+|.|+|+..-... .+ ...+..++.. -=++++||+
T Consensus 50 ~~~i~Dt~G~~~~~~~~~~~~--------~~~d~~i~v~d~~~~~s~-~~------~~~~~~~i~~~~~~~p~ivv~nK~ 114 (161)
T cd04124 50 LVDFWDTAGQERFQTMHASYY--------HKAHACILVFDVTRKITY-KN------LSKWYEELREYRPEIPCIVVANKI 114 (161)
T ss_pred EEEEEeCCCchhhhhhhHHHh--------CCCCEEEEEEECCCHHHH-HH------HHHHHHHHHHhCCCCcEEEEEECc
Confidence 344667888654444433221 134678999998754322 11 1222333321 227888999
Q ss_pred CCCC
Q 027979 120 DLVS 123 (216)
Q Consensus 120 D~v~ 123 (216)
|+..
T Consensus 115 Dl~~ 118 (161)
T cd04124 115 DLDP 118 (161)
T ss_pred cCch
Confidence 9853
No 200
>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=67.59 E-value=30 Score=26.80 Aligned_cols=54 Identities=24% Similarity=0.228 Sum_probs=28.2
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHHHHHhh------ccEEEEccCCCCCCCCccchHHHHHHHHH
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF------ADVVILNKVDLVSPERSGDSLDELEKEIH 139 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~------AD~IvlnK~D~v~~~~~~~~l~~i~~~l~ 139 (216)
.+.+|.|+|+...... ... ...+...+.. .=+|+.||+|+.... ..+++++.++
T Consensus 87 ad~iilV~D~~~~~s~-~~~-----~~~~~~i~~~~~~~~~pvivv~NK~Dl~~~~----~~~~~~~~~~ 146 (190)
T cd00879 87 VDGIVFLVDAADPERF-QES-----KEELDSLLSDEELANVPFLILGNKIDLPGAV----SEEELRQALG 146 (190)
T ss_pred CCEEEEEEECCcHHHH-HHH-----HHHHHHHHcCccccCCCEEEEEeCCCCCCCc----CHHHHHHHhC
Confidence 3678999999864321 110 1111111221 126677999986532 2456665554
No 201
>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=67.46 E-value=51 Score=24.84 Aligned_cols=88 Identities=14% Similarity=0.118 Sum_probs=41.9
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH---h--hc-cEEEEcc
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---A--FA-DVVILNK 118 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~--~A-D~IvlnK 118 (216)
...+..++|......+..... -..+.++.|+|...... +.. ...+...+ . .. =+|+.||
T Consensus 51 ~~~l~Dt~g~~~~~~~~~~~~--------~~~~~~l~v~d~~~~~s-~~~------~~~~~~~i~~~~~~~~piivv~nK 115 (165)
T cd01865 51 KLQIWDTAGQERYRTITTAYY--------RGAMGFILMYDITNEES-FNA------VQDWSTQIKTYSWDNAQVILVGNK 115 (165)
T ss_pred EEEEEECCChHHHHHHHHHHc--------cCCcEEEEEEECCCHHH-HHH------HHHHHHHHHHhCCCCCCEEEEEEC
Confidence 345567777543333322211 23566788899875432 211 12222222 1 11 2677799
Q ss_pred CCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 119 VDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 119 ~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
+|+.+.... ..++..+..+.++ .++++++
T Consensus 116 ~Dl~~~~~~--~~~~~~~~~~~~~--~~~~~~S 144 (165)
T cd01865 116 CDMEDERVV--SSERGRQLADQLG--FEFFEAS 144 (165)
T ss_pred cccCccccc--CHHHHHHHHHHcC--CEEEEEE
Confidence 999765321 1233333333332 3566543
No 202
>PTZ00416 elongation factor 2; Provisional
Probab=67.41 E-value=4.8 Score=39.86 Aligned_cols=63 Identities=21% Similarity=0.188 Sum_probs=38.0
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh---ccEEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF---ADVVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~---AD~IvlnK~D 120 (216)
.-+.+|-|.|..+= .... ....-..|++|.|||+..-...- -..+.+|+.. .=++++||+|
T Consensus 92 ~~i~liDtPG~~~f---~~~~-----~~al~~~D~ailVvda~~g~~~~--------t~~~~~~~~~~~~p~iv~iNK~D 155 (836)
T PTZ00416 92 FLINLIDSPGHVDF---SSEV-----TAALRVTDGALVVVDCVEGVCVQ--------TETVLRQALQERIRPVLFINKVD 155 (836)
T ss_pred eEEEEEcCCCHHhH---HHHH-----HHHHhcCCeEEEEEECCCCcCcc--------HHHHHHHHHHcCCCEEEEEEChh
Confidence 34678999998652 1111 11223477899999997632111 1223455554 3489999999
Q ss_pred CC
Q 027979 121 LV 122 (216)
Q Consensus 121 ~v 122 (216)
+.
T Consensus 156 ~~ 157 (836)
T PTZ00416 156 RA 157 (836)
T ss_pred hh
Confidence 97
No 203
>PF04670 Gtr1_RagA: Gtr1/RagA G protein conserved region; InterPro: IPR006762 GTR1 was first identified in Saccharomyces cerevisiae (Baker's yeast) as a suppressor of a mutation in RCC1. RCC1 catalyzes guanine nucleotide exchange on Ran, a well characterised nuclear Ras-like small G protein that plays an essential role in the import and export of proteins and RNAs across the nuclear membrane through the nuclear pore complex. RCC1 is located inside the nucleus, bound to chromatin. The concentration of GTP within the cell is ~30 times higher than the concentration of GDP, thus resulting in the preferential production of the GTP form of Ran by RCC1 within the nucleus. Gtr1p is located within both the cytoplasm and the nucleus and has been reported to play a role in cell growth. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1 and Rag A and Gtr1p belong to the sixth subfamily of the Ras-like small GTPase superfamily []. ; GO: 0005525 GTP binding, 0005634 nucleus, 0005737 cytoplasm; PDB: 3R7W_B 2Q3F_B 3LLU_A.
Probab=67.10 E-value=13 Score=31.06 Aligned_cols=47 Identities=23% Similarity=0.355 Sum_probs=25.8
Q ss_pred eeccEEEEEccc--chHHHHhhcccCCChhHHHH---HHh-hcc-EEEEccCCCCCCCCc
Q 027979 75 RLDSIITVVDAK--NLLFQIDKYRHLSSYPEAIH---QIA-FAD-VVILNKVDLVSPERS 127 (216)
Q Consensus 75 ~l~~vI~vVDa~--~~~~~l~~~~~~~~~~~~~~---QI~-~AD-~IvlnK~D~v~~~~~ 127 (216)
.+..+|.|+|+. .+...+.. +...+. |.. .|- -|++.|+|++.++.+
T Consensus 76 ~v~~LIyV~D~qs~~~~~~l~~------~~~~i~~l~~~sp~~~v~vfiHK~D~l~~~~r 129 (232)
T PF04670_consen 76 NVGVLIYVFDAQSDDYDEDLAY------LSDCIEALRQYSPNIKVFVFIHKMDLLSEDER 129 (232)
T ss_dssp TESEEEEEEETT-STCHHHHHH------HHHHHHHHHHHSTT-EEEEEEE-CCCS-HHHH
T ss_pred ccCEEEEEEEcccccHHHHHHH------HHHHHHHHHHhCCCCeEEEEEeecccCCHHHH
Confidence 467899999998 44444433 222221 211 111 477899999987653
No 204
>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=67.03 E-value=48 Score=25.20 Aligned_cols=66 Identities=27% Similarity=0.191 Sum_probs=35.9
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh--cc---EEEEcc
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF--AD---VVILNK 118 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~--AD---~IvlnK 118 (216)
....+.++.|...-..+..... -..+.+|.|+|+....... . ......++.. .+ +++.||
T Consensus 44 ~~l~i~Dt~G~~~~~~~~~~~~--------~~ad~ii~V~D~t~~~s~~-~------~~~~l~~~~~~~~~~piilv~NK 108 (164)
T cd04162 44 AIMELLEIGGSQNLRKYWKRYL--------SGSQGLIFVVDSADSERLP-L------ARQELHQLLQHPPDLPLVVLANK 108 (164)
T ss_pred eEEEEEECCCCcchhHHHHHHH--------hhCCEEEEEEECCCHHHHH-H------HHHHHHHHHhCCCCCcEEEEEeC
Confidence 4556678888765444433211 1346789999998754221 1 1111222321 12 477899
Q ss_pred CCCCCC
Q 027979 119 VDLVSP 124 (216)
Q Consensus 119 ~D~v~~ 124 (216)
+|+.++
T Consensus 109 ~Dl~~~ 114 (164)
T cd04162 109 QDLPAA 114 (164)
T ss_pred cCCcCC
Confidence 998654
No 205
>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=67.02 E-value=32 Score=25.88 Aligned_cols=43 Identities=21% Similarity=0.317 Sum_probs=23.7
Q ss_pred ccEEEEEcccchHHH-HhhcccCCChhHHHHHHh-----hccEEEEccCCCCCCC
Q 027979 77 DSIITVVDAKNLLFQ-IDKYRHLSSYPEAIHQIA-----FADVVILNKVDLVSPE 125 (216)
Q Consensus 77 ~~vI~vVDa~~~~~~-l~~~~~~~~~~~~~~QI~-----~AD~IvlnK~D~v~~~ 125 (216)
+.++.|+|+...... +.. ...+..++. .-=++++||+|+.+..
T Consensus 81 d~~l~v~d~~~~~~~~~~~------~~~~~~~l~~~~~~~pvilv~NK~Dl~~~~ 129 (168)
T cd01897 81 AAVLFLFDPSETCGYSLEE------QLSLFEEIKPLFKNKPVIVVLNKIDLLTFE 129 (168)
T ss_pred CcEEEEEeCCcccccchHH------HHHHHHHHHhhcCcCCeEEEEEccccCchh
Confidence 678999999753211 000 011222332 2236777999998754
No 206
>COG0050 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]
Probab=66.91 E-value=3.8 Score=35.70 Aligned_cols=35 Identities=40% Similarity=0.475 Sum_probs=23.1
Q ss_pred HHHHHHhh-ccEEEEccCCCCCCCCccchHHHHHHHHHh
Q 027979 103 EAIHQIAF-ADVVILNKVDLVSPERSGDSLDELEKEIHE 140 (216)
Q Consensus 103 ~~~~QI~~-AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~ 140 (216)
.+.+|+.. .=++++||+|+++.++ -++.+.-.+|.
T Consensus 121 LlarqvGvp~ivvflnK~Dmvdd~e---llelVemEvre 156 (394)
T COG0050 121 LLARQVGVPYIVVFLNKVDMVDDEE---LLELVEMEVRE 156 (394)
T ss_pred hhhhhcCCcEEEEEEecccccCcHH---HHHHHHHHHHH
Confidence 35689888 5567789999999653 24444444444
No 207
>PRK00093 GTP-binding protein Der; Reviewed
Probab=66.76 E-value=22 Score=31.93 Aligned_cols=74 Identities=20% Similarity=0.262 Sum_probs=38.2
Q ss_pred CCEEEEecCCCCCcHH-HHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCC
Q 027979 44 LDHILLETTGLANPAP-LASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLV 122 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~-i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v 122 (216)
....++.|.|..+... +.+.+. .......-..+.++.|+|+..-....+.. .....++...-=++++||+|+.
T Consensus 49 ~~~~liDT~G~~~~~~~~~~~~~-~~~~~~~~~ad~il~vvd~~~~~~~~~~~-----~~~~l~~~~~piilv~NK~D~~ 122 (435)
T PRK00093 49 REFILIDTGGIEPDDDGFEKQIR-EQAELAIEEADVILFVVDGRAGLTPADEE-----IAKILRKSNKPVILVVNKVDGP 122 (435)
T ss_pred cEEEEEECCCCCCcchhHHHHHH-HHHHHHHHhCCEEEEEEECCCCCCHHHHH-----HHHHHHHcCCcEEEEEECccCc
Confidence 5678999999976222 211111 00011123467799999997632221110 1111222233347888999976
Q ss_pred C
Q 027979 123 S 123 (216)
Q Consensus 123 ~ 123 (216)
+
T Consensus 123 ~ 123 (435)
T PRK00093 123 D 123 (435)
T ss_pred c
Confidence 5
No 208
>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed
Probab=66.73 E-value=12 Score=36.32 Aligned_cols=50 Identities=18% Similarity=0.121 Sum_probs=28.9
Q ss_pred hccEEEEccCCCCCCCCccchHHHHHHHHHhh---CCCCEEEEee-cCCCChhhhhcc
Q 027979 110 FADVVILNKVDLVSPERSGDSLDELEKEIHEI---NSLAHVIRSV-RCQVDLSEVLNC 163 (216)
Q Consensus 110 ~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~l---NP~A~iv~~~-~~~v~~~~l~~~ 163 (216)
..=+||+||+|+++.+ ..+.+++.++.. .+.++++.++ .....+..++..
T Consensus 562 ~piIiV~NK~DL~~~~----~~~~~~~~~~~~l~~~~~~~ii~iSAktg~gv~~L~~~ 615 (712)
T PRK09518 562 RALVLVFNKWDLMDEF----RRQRLERLWKTEFDRVTWARRVNLSAKTGWHTNRLAPA 615 (712)
T ss_pred CCEEEEEEchhcCChh----HHHHHHHHHHHhccCCCCCCEEEEECCCCCCHHHHHHH
Confidence 4568889999998753 234455545432 3456766433 233456666643
No 209
>PTZ00133 ADP-ribosylation factor; Provisional
Probab=66.57 E-value=41 Score=26.26 Aligned_cols=38 Identities=21% Similarity=0.311 Sum_probs=22.3
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchH
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLL 89 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~ 89 (216)
....++.++|.....++..... -.-+.+|.|+|+....
T Consensus 61 ~~~~l~D~~G~~~~~~~~~~~~--------~~ad~iI~v~D~t~~~ 98 (182)
T PTZ00133 61 LKFTMWDVGGQDKLRPLWRHYY--------QNTNGLIFVVDSNDRE 98 (182)
T ss_pred EEEEEEECCCCHhHHHHHHHHh--------cCCCEEEEEEeCCCHH
Confidence 3456677788744333322221 2356789999997643
No 210
>PRK12740 elongation factor G; Reviewed
Probab=66.54 E-value=15 Score=35.18 Aligned_cols=77 Identities=17% Similarity=0.158 Sum_probs=45.3
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH---hhccEEEEccC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---AFADVVILNKV 119 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~~AD~IvlnK~ 119 (216)
+.++.+|-|.|..+-...... ..-..|.++.|+|+........ .....++ ...-+|++||+
T Consensus 59 ~~~i~liDtPG~~~~~~~~~~--------~l~~aD~vllvvd~~~~~~~~~--------~~~~~~~~~~~~p~iiv~NK~ 122 (668)
T PRK12740 59 GHKINLIDTPGHVDFTGEVER--------ALRVLDGAVVVVCAVGGVEPQT--------ETVWRQAEKYGVPRIIFVNKM 122 (668)
T ss_pred CEEEEEEECCCcHHHHHHHHH--------HHHHhCeEEEEEeCCCCcCHHH--------HHHHHHHHHcCCCEEEEEECC
Confidence 467889999998653222211 1124678999999986432111 1122233 33458999999
Q ss_pred CCCCCCCccchHHHHHHHHHh
Q 027979 120 DLVSPERSGDSLDELEKEIHE 140 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l~~ 140 (216)
|+.... ..++.+.++.
T Consensus 123 D~~~~~-----~~~~~~~l~~ 138 (668)
T PRK12740 123 DRAGAD-----FFRVLAQLQE 138 (668)
T ss_pred CCCCCC-----HHHHHHHHHH
Confidence 998643 3455555554
No 211
>TIGR00484 EF-G translation elongation factor EF-G. After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G.
Probab=66.30 E-value=18 Score=35.00 Aligned_cols=70 Identities=16% Similarity=0.130 Sum_probs=39.4
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLV 122 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v 122 (216)
+....+|-|.|..+-...... ..-..+.+|.|||+..-...-... .-....+...-=+|++||+|+.
T Consensus 74 ~~~i~liDTPG~~~~~~~~~~--------~l~~~D~~ilVvda~~g~~~~~~~-----~~~~~~~~~~p~ivviNK~D~~ 140 (689)
T TIGR00484 74 GHRINIIDTPGHVDFTVEVER--------SLRVLDGAVAVLDAVGGVQPQSET-----VWRQANRYEVPRIAFVNKMDKT 140 (689)
T ss_pred CeEEEEEECCCCcchhHHHHH--------HHHHhCEEEEEEeCCCCCChhHHH-----HHHHHHHcCCCEEEEEECCCCC
Confidence 345788899999765432221 112347899999997532111000 0001122233457899999998
Q ss_pred CCC
Q 027979 123 SPE 125 (216)
Q Consensus 123 ~~~ 125 (216)
+..
T Consensus 141 ~~~ 143 (689)
T TIGR00484 141 GAN 143 (689)
T ss_pred CCC
Confidence 753
No 212
>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed
Probab=66.01 E-value=5.9 Score=36.23 Aligned_cols=73 Identities=22% Similarity=0.289 Sum_probs=40.9
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh-hccEEEEccCCCCC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA-FADVVILNKVDLVS 123 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~-~AD~IvlnK~D~v~ 123 (216)
...++-|.|.-++...++.+.....+...-..+.++.|+|+......- . . ....+.. .-=++|+||+|+.+
T Consensus 264 ~i~l~DT~G~~~~~~~ie~~gi~~~~~~~~~aD~il~VvD~s~~~s~~-~------~-~~l~~~~~~piiiV~NK~DL~~ 335 (449)
T PRK05291 264 PLRLIDTAGIRETDDEVEKIGIERSREAIEEADLVLLVLDASEPLTEE-D------D-EILEELKDKPVIVVLNKADLTG 335 (449)
T ss_pred EEEEEeCCCCCCCccHHHHHHHHHHHHHHHhCCEEEEEecCCCCCChh-H------H-HHHHhcCCCCcEEEEEhhhccc
Confidence 457789999987766554321111112234467789999997543111 0 1 1122211 12378889999976
Q ss_pred CC
Q 027979 124 PE 125 (216)
Q Consensus 124 ~~ 125 (216)
..
T Consensus 336 ~~ 337 (449)
T PRK05291 336 EI 337 (449)
T ss_pred cc
Confidence 53
No 213
>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=65.85 E-value=51 Score=30.01 Aligned_cols=111 Identities=22% Similarity=0.188 Sum_probs=58.4
Q ss_pred hhHHHHHHHHHHhcCCCCEEEEecCCCCCcH-HHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHH
Q 027979 28 HSLVQALEQLVQRKERLDHILLETTGLANPA-PLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIH 106 (216)
Q Consensus 28 ~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~-~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~ 106 (216)
.++...|.++ .++|+|||-|.|...-. ..++.+. ..+.....-..++.|+++..=...+. .+.+
T Consensus 288 ~~l~~~l~~~----~~~DlVlIDt~G~~~~d~~~~~~L~--~ll~~~~~~~~~~LVl~a~~~~~~l~---------~~~~ 352 (424)
T PRK05703 288 KELAKALEQL----RDCDVILIDTAGRSQRDKRLIEELK--ALIEFSGEPIDVYLVLSATTKYEDLK---------DIYK 352 (424)
T ss_pred HhHHHHHHHh----CCCCEEEEeCCCCCCCCHHHHHHHH--HHHhccCCCCeEEEEEECCCCHHHHH---------HHHH
Confidence 4555555543 35899999999995321 1111110 01110111135677888865443332 2223
Q ss_pred HHhh--ccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeecCCCChhhhh
Q 027979 107 QIAF--ADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQVDLSEVL 161 (216)
Q Consensus 107 QI~~--AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~~~l~ 161 (216)
+.+. .+-+|+||.|-... ...+.+.+... +.++.....|+-=+++|.
T Consensus 353 ~f~~~~~~~vI~TKlDet~~------~G~i~~~~~~~--~lPv~yit~Gq~VpdDl~ 401 (424)
T PRK05703 353 HFSRLPLDGLIFTKLDETSS------LGSILSLLIES--GLPISYLTNGQRVPDDIK 401 (424)
T ss_pred HhCCCCCCEEEEeccccccc------ccHHHHHHHHH--CCCEEEEeCCCCChhhhh
Confidence 3332 35699999998554 24455555443 457776677753334443
No 214
>cd04169 RF3 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and activate the release of the nascent polypeptide. The class II release factor RF3 then initiates the release of the class I RF from the ribosome. RF3 binds to the RF/ribosome complex in the inactive (GDP-bound) state. GDP/GTP exchange occurs, followed by the release of the class I RF. Subsequent hydrolysis of GTP to GDP triggers the release of RF3 from the ribosome. RF3 also enhances the efficiency of class I RFs at less preferred stop codons and at stop codons in weak contexts.
Probab=65.75 E-value=20 Score=30.27 Aligned_cols=66 Identities=20% Similarity=0.184 Sum_probs=37.7
Q ss_pred CCCEEEEecCCCCCcHH-HHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEcc
Q 027979 43 RLDHILLETTGLANPAP-LASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNK 118 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~-i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK 118 (216)
+..+.++-|.|..+-.. ....+ -..+.+|.|+|+..-..... ..+.++.. .-=+|++||
T Consensus 70 ~~~i~liDTPG~~df~~~~~~~l---------~~aD~~IlVvda~~g~~~~~--------~~i~~~~~~~~~P~iivvNK 132 (267)
T cd04169 70 DCVINLLDTPGHEDFSEDTYRTL---------TAVDSAVMVIDAAKGVEPQT--------RKLFEVCRLRGIPIITFINK 132 (267)
T ss_pred CEEEEEEECCCchHHHHHHHHHH---------HHCCEEEEEEECCCCccHHH--------HHHHHHHHhcCCCEEEEEEC
Confidence 46778899999864332 11221 23578899999976321110 11222221 223788899
Q ss_pred CCCCCCC
Q 027979 119 VDLVSPE 125 (216)
Q Consensus 119 ~D~v~~~ 125 (216)
+|+....
T Consensus 133 ~D~~~a~ 139 (267)
T cd04169 133 LDREGRD 139 (267)
T ss_pred CccCCCC
Confidence 9986653
No 215
>KOG0462 consensus Elongation factor-type GTP-binding protein [Translation, ribosomal structure and biogenesis]
Probab=65.65 E-value=21 Score=33.67 Aligned_cols=77 Identities=26% Similarity=0.374 Sum_probs=44.0
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhh--CCCCEEEE-ee
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEI--NSLAHVIR-SV 151 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~l--NP~A~iv~-~~ 151 (216)
..++++.||||...... ... .++-. .-+-..+=+.||||+|+-+++ .+++...+..+ +|.++++. +.
T Consensus 148 ac~G~lLvVDA~qGvqA-QT~---anf~l-Afe~~L~iIpVlNKIDlp~ad-----pe~V~~q~~~lF~~~~~~~i~vSA 217 (650)
T KOG0462|consen 148 ACDGALLVVDASQGVQA-QTV---ANFYL-AFEAGLAIIPVLNKIDLPSAD-----PERVENQLFELFDIPPAEVIYVSA 217 (650)
T ss_pred hcCceEEEEEcCcCchH-HHH---HHHHH-HHHcCCeEEEeeeccCCCCCC-----HHHHHHHHHHHhcCCccceEEEEe
Confidence 46789999999864421 000 00111 234455668899999997764 46666666653 45556654 33
Q ss_pred cCCCChhhhh
Q 027979 152 RCQVDLSEVL 161 (216)
Q Consensus 152 ~~~v~~~~l~ 161 (216)
......+.++
T Consensus 218 K~G~~v~~lL 227 (650)
T KOG0462|consen 218 KTGLNVEELL 227 (650)
T ss_pred ccCccHHHHH
Confidence 3334554444
No 216
>PRK13796 GTPase YqeH; Provisional
Probab=64.90 E-value=20 Score=31.82 Aligned_cols=41 Identities=20% Similarity=0.215 Sum_probs=23.6
Q ss_pred ccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc-EEEEccCCCCCCC
Q 027979 77 DSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD-VVILNKVDLVSPE 125 (216)
Q Consensus 77 ~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD-~IvlnK~D~v~~~ 125 (216)
.-|+.|||+..+...+ .+++.+-+..-. ++|+||+|+.+.+
T Consensus 71 ~lIv~VVD~~D~~~s~--------~~~L~~~~~~kpviLViNK~DLl~~~ 112 (365)
T PRK13796 71 ALVVNVVDIFDFNGSW--------IPGLHRFVGNNPVLLVGNKADLLPKS 112 (365)
T ss_pred cEEEEEEECccCCCch--------hHHHHHHhCCCCEEEEEEchhhCCCc
Confidence 3689999987654322 122222122222 6688999998643
No 217
>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=64.81 E-value=45 Score=25.68 Aligned_cols=37 Identities=19% Similarity=0.324 Sum_probs=22.7
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccch
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNL 88 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~ 88 (216)
....+..++|......+...+. -.-+.+|.|+|++.-
T Consensus 57 ~~l~l~D~~G~~~~~~~~~~~~--------~~ad~ii~v~D~t~~ 93 (175)
T smart00177 57 ISFTVWDVGGQDKIRPLWRHYY--------TNTQGLIFVVDSNDR 93 (175)
T ss_pred EEEEEEECCCChhhHHHHHHHh--------CCCCEEEEEEECCCH
Confidence 4556778888754444433321 124578999998764
No 218
>PRK00007 elongation factor G; Reviewed
Probab=64.73 E-value=11 Score=36.40 Aligned_cols=70 Identities=17% Similarity=0.144 Sum_probs=38.8
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLV 122 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v 122 (216)
+..+.+|-|.|..+- +.++. ...-..+.+|.||||......-... .-....+....-++++||+|+.
T Consensus 74 ~~~~~liDTPG~~~f--~~ev~------~al~~~D~~vlVvda~~g~~~qt~~-----~~~~~~~~~~p~iv~vNK~D~~ 140 (693)
T PRK00007 74 DHRINIIDTPGHVDF--TIEVE------RSLRVLDGAVAVFDAVGGVEPQSET-----VWRQADKYKVPRIAFVNKMDRT 140 (693)
T ss_pred CeEEEEEeCCCcHHH--HHHHH------HHHHHcCEEEEEEECCCCcchhhHH-----HHHHHHHcCCCEEEEEECCCCC
Confidence 346688888886532 11211 1122447899999987543211100 1011233334568999999998
Q ss_pred CCC
Q 027979 123 SPE 125 (216)
Q Consensus 123 ~~~ 125 (216)
+++
T Consensus 141 ~~~ 143 (693)
T PRK00007 141 GAD 143 (693)
T ss_pred CCC
Confidence 754
No 219
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=64.13 E-value=36 Score=30.83 Aligned_cols=116 Identities=17% Similarity=0.117 Sum_probs=61.2
Q ss_pred ecchhHHHHHHHHHHhcCCCCEEEEecCCCCCc-HHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhH
Q 027979 25 TVKHSLVQALEQLVQRKERLDHILLETTGLANP-APLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPE 103 (216)
Q Consensus 25 sl~~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P-~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~ 103 (216)
.-..++..+|..+.. ....|+|||-|.|...- ...++.+. .+...+..+-++.|+++..-...+. .
T Consensus 268 ~dp~dL~~al~~l~~-~~~~D~VLIDTAGr~~~d~~~l~EL~---~l~~~~~p~~~~LVLsag~~~~d~~---------~ 334 (407)
T PRK12726 268 TSPAELEEAVQYMTY-VNCVDHILIDTVGRNYLAEESVSEIS---AYTDVVHPDLTCFTFSSGMKSADVM---------T 334 (407)
T ss_pred CCHHHHHHHHHHHHh-cCCCCEEEEECCCCCccCHHHHHHHH---HHhhccCCceEEEECCCcccHHHHH---------H
Confidence 344677777777642 24689999999999642 22222221 1122233344566777643222211 1
Q ss_pred HHHH--HhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeecCCCChhhhh
Q 027979 104 AIHQ--IAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQVDLSEVL 161 (216)
Q Consensus 104 ~~~Q--I~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~~~l~ 161 (216)
+.++ .-.-|-+|+||.|-...- -.+.+..... +.+|.....|+-=+++++
T Consensus 335 i~~~f~~l~i~glI~TKLDET~~~------G~~Lsv~~~t--glPIsylt~GQ~VpdDi~ 386 (407)
T PRK12726 335 ILPKLAEIPIDGFIITKMDETTRI------GDLYTVMQET--NLPVLYMTDGQNITENIF 386 (407)
T ss_pred HHHhcCcCCCCEEEEEcccCCCCc------cHHHHHHHHH--CCCEEEEecCCCCCcccC
Confidence 1121 233578999999986543 2333333332 456776666643333443
No 220
>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=64.08 E-value=59 Score=24.33 Aligned_cols=67 Identities=16% Similarity=0.115 Sum_probs=35.7
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh-----hccEEEEccC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA-----FADVVILNKV 119 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~-----~AD~IvlnK~ 119 (216)
...++.++|.-+...+.... .-..+.++.|+|+.+....... ...+...+. ..=++|.||+
T Consensus 49 ~l~~~D~~g~~~~~~~~~~~--------~~~~~~~i~v~d~~~~~s~~~~------~~~~~~~~~~~~~~~p~ivv~nK~ 114 (171)
T cd00157 49 NLGLWDTAGQEEYDRLRPLS--------YPNTDVFLICFSVDSPSSFENV------KTKWIPEIRHYCPNVPIILVGTKI 114 (171)
T ss_pred EEEEEeCCCcccccccchhh--------cCCCCEEEEEEECCCHHHHHHH------HHHHHHHHHhhCCCCCEEEEEccH
Confidence 35677788865432221111 1235788999999874332111 111222222 1237778999
Q ss_pred CCCCCC
Q 027979 120 DLVSPE 125 (216)
Q Consensus 120 D~v~~~ 125 (216)
|+....
T Consensus 115 Dl~~~~ 120 (171)
T cd00157 115 DLRDDE 120 (171)
T ss_pred Hhhhch
Confidence 998764
No 221
>PF08885 GSCFA: GSCFA family; InterPro: IPR014982 This group of proteins are functionally uncharacterised. They have been named GSCFA after a highly conserved N-terminal motif in the alignment, they are functionally uncharacterised.
Probab=63.69 E-value=14 Score=31.25 Aligned_cols=50 Identities=24% Similarity=0.257 Sum_probs=34.6
Q ss_pred HHHHHHhhccEEEEccC---------------------------CC-----CCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 103 EAIHQIAFADVVILNKV---------------------------DL-----VSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 103 ~~~~QI~~AD~IvlnK~---------------------------D~-----v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
...+++..||++|++=- ++ .+.++.-..++++.+.|+++||.++|+-|
T Consensus 94 ~~~~~l~~ad~~iiTLGtaevw~~~~~g~vv~nc~k~p~~~F~~~~~~f~~ls~~ei~~~l~~~~~~l~~~nP~~kiilT 173 (251)
T PF08885_consen 94 EVREALEEADVFIITLGTAEVWRDRETGRVVANCHKVPAGQFDPERYEFRNLSVEEILEDLEAIIDLLRSINPDIKIILT 173 (251)
T ss_pred HHHHHHHhCCEEEEeCCcHHHheeCCCCEEEecCCCccccccchhhhhhccCCHHHHHHHHHHHHHHHHhhCCCceEEEE
Confidence 45689999999998731 11 11111124567778889999999999987
Q ss_pred ec
Q 027979 151 VR 152 (216)
Q Consensus 151 ~~ 152 (216)
..
T Consensus 174 VS 175 (251)
T PF08885_consen 174 VS 175 (251)
T ss_pred ec
Confidence 53
No 222
>COG1160 Predicted GTPases [General function prediction only]
Probab=62.59 E-value=22 Score=32.54 Aligned_cols=76 Identities=21% Similarity=0.337 Sum_probs=44.6
Q ss_pred CCCEEEEecCCCCCc--HHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCC
Q 027979 43 RLDHILLETTGLANP--APLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVD 120 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P--~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D 120 (216)
...+.+|-|-|+.+- .++.+.+. ...+...-.-|-++.|||+.......+.. .....+.-.--=++++||+|
T Consensus 50 ~~~f~lIDTgGl~~~~~~~l~~~i~-~Qa~~Ai~eADvilfvVD~~~Git~~D~~-----ia~~Lr~~~kpviLvvNK~D 123 (444)
T COG1160 50 GREFILIDTGGLDDGDEDELQELIR-EQALIAIEEADVILFVVDGREGITPADEE-----IAKILRRSKKPVILVVNKID 123 (444)
T ss_pred CceEEEEECCCCCcCCchHHHHHHH-HHHHHHHHhCCEEEEEEeCCCCCCHHHHH-----HHHHHHhcCCCEEEEEEccc
Confidence 456899999999742 35554433 22233444567789999998755433321 22222222223467889999
Q ss_pred CCCC
Q 027979 121 LVSP 124 (216)
Q Consensus 121 ~v~~ 124 (216)
....
T Consensus 124 ~~~~ 127 (444)
T COG1160 124 NLKA 127 (444)
T ss_pred Cchh
Confidence 8744
No 223
>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=62.49 E-value=49 Score=25.88 Aligned_cols=41 Identities=17% Similarity=0.090 Sum_probs=23.5
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHHHHHhh-----ccEEEEccCCCCC
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF-----ADVVILNKVDLVS 123 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~-----AD~IvlnK~D~v~ 123 (216)
-+.++.|+|..+-... .+ ...+..++.. .=++|.||+|+..
T Consensus 73 a~~iilv~D~t~~~s~-~~------i~~~~~~~~~~~~~~~pilVgnK~Dl~~ 118 (182)
T cd04128 73 AVAILFMFDLTRKSTL-NS------IKEWYRQARGFNKTAIPILVGTKYDLFA 118 (182)
T ss_pred CCEEEEEEECcCHHHH-HH------HHHHHHHHHHhCCCCCEEEEEEchhccc
Confidence 4568899998765432 11 1223333321 1257889999963
No 224
>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=62.43 E-value=1.1e+02 Score=30.11 Aligned_cols=103 Identities=17% Similarity=0.120 Sum_probs=57.9
Q ss_pred hhHHHHHHHHHHhcCCCCEEEEecCCCCCc-HHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHH
Q 027979 28 HSLVQALEQLVQRKERLDHILLETTGLANP-APLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIH 106 (216)
Q Consensus 28 ~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P-~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~ 106 (216)
.++..+|.++ .+.|+|||-|.|...- ..+.+.+. .+........++.|+|+..=.+.+. ++.+
T Consensus 252 ~~l~~al~~~----~~~D~VLIDTAGRs~~d~~l~eel~---~l~~~~~p~e~~LVLsAt~~~~~l~---------~i~~ 315 (767)
T PRK14723 252 ADLRFALAAL----GDKHLVLIDTVGMSQRDRNVSEQIA---MLCGVGRPVRRLLLLNAASHGDTLN---------EVVH 315 (767)
T ss_pred HHHHHHHHHh----cCCCEEEEeCCCCCccCHHHHHHHH---HHhccCCCCeEEEEECCCCcHHHHH---------HHHH
Confidence 4555566554 3569999999997642 23333322 1112233445789999985433332 2222
Q ss_pred HHh-----hccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeecCC
Q 027979 107 QIA-----FADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQ 154 (216)
Q Consensus 107 QI~-----~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~ 154 (216)
... .-+-+|++|.|-...- -.+...+... +.+|.....|+
T Consensus 316 ~f~~~~~~~i~glIlTKLDEt~~~------G~iL~i~~~~--~lPI~yit~GQ 360 (767)
T PRK14723 316 AYRHGAGEDVDGCIITKLDEATHL------GPALDTVIRH--RLPVHYVSTGQ 360 (767)
T ss_pred HHhhcccCCCCEEEEeccCCCCCc------cHHHHHHHHH--CCCeEEEecCC
Confidence 222 3578999999987643 3344444333 45666655653
No 225
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=62.34 E-value=32 Score=31.49 Aligned_cols=73 Identities=22% Similarity=0.219 Sum_probs=47.4
Q ss_pred CCCCEEEEecCCCCCc-HHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCC
Q 027979 42 ERLDHILLETTGLANP-APLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVD 120 (216)
Q Consensus 42 ~~~d~IiIE~sG~a~P-~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D 120 (216)
..+|+|||-|.|=-.- .++++-+. .+...+..+.++.||||...++..+. ...+-+++.. .=|||+|.|
T Consensus 181 ~~~DvvIvDTAGRl~ide~Lm~El~---~Ik~~~~P~E~llVvDam~GQdA~~~------A~aF~e~l~i-tGvIlTKlD 250 (451)
T COG0541 181 EGYDVVIVDTAGRLHIDEELMDELK---EIKEVINPDETLLVVDAMIGQDAVNT------AKAFNEALGI-TGVILTKLD 250 (451)
T ss_pred cCCCEEEEeCCCcccccHHHHHHHH---HHHhhcCCCeEEEEEecccchHHHHH------HHHHhhhcCC-ceEEEEccc
Confidence 4579999999996543 23333322 34567888899999999988765533 1122345544 457899999
Q ss_pred CCCC
Q 027979 121 LVSP 124 (216)
Q Consensus 121 ~v~~ 124 (216)
--..
T Consensus 251 GdaR 254 (451)
T COG0541 251 GDAR 254 (451)
T ss_pred CCCc
Confidence 6443
No 226
>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=62.06 E-value=12 Score=33.26 Aligned_cols=41 Identities=24% Similarity=0.285 Sum_probs=24.6
Q ss_pred ccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc-EEEEccCCCCCCC
Q 027979 77 DSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD-VVILNKVDLVSPE 125 (216)
Q Consensus 77 ~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD-~IvlnK~D~v~~~ 125 (216)
+.++.|+|+..+...+ .+++.+-+..-. ++|+||+|+.+..
T Consensus 65 ~~Il~VvD~~d~~~s~--------~~~l~~~~~~~piilV~NK~DLl~k~ 106 (360)
T TIGR03597 65 ALIVYVVDIFDFEGSL--------IPELKRFVGGNPVLLVGNKIDLLPKS 106 (360)
T ss_pred cEEEEEEECcCCCCCc--------cHHHHHHhCCCCEEEEEEchhhCCCC
Confidence 5789999986554322 122333332333 5677999998754
No 227
>PRK12727 flagellar biosynthesis regulator FlhF; Provisional
Probab=61.89 E-value=1e+02 Score=29.23 Aligned_cols=101 Identities=16% Similarity=0.154 Sum_probs=54.1
Q ss_pred CCCCEEEEecCCCCCcHHH-HHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCC
Q 027979 42 ERLDHILLETTGLANPAPL-ASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVD 120 (216)
Q Consensus 42 ~~~d~IiIE~sG~a~P~~i-~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D 120 (216)
.++|+|||-|.|+..-... ++.+. .+... .-...+.|+++..-...+... . ..+.++ .-+-+|+||.|
T Consensus 427 ~~~DLVLIDTaG~s~~D~~l~eeL~---~L~aa-~~~a~lLVLpAtss~~Dl~ei-----i-~~f~~~-~~~gvILTKlD 495 (559)
T PRK12727 427 RDYKLVLIDTAGMGQRDRALAAQLN---WLRAA-RQVTSLLVLPANAHFSDLDEV-----V-RRFAHA-KPQGVVLTKLD 495 (559)
T ss_pred ccCCEEEecCCCcchhhHHHHHHHH---HHHHh-hcCCcEEEEECCCChhHHHHH-----H-HHHHhh-CCeEEEEecCc
Confidence 3589999999999743222 22111 11111 123568888887543333221 1 111222 34779999999
Q ss_pred CCCCCCccchHHHHHHHHHhhCCCCEEEEeecCCCChhhhh
Q 027979 121 LVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQVDLSEVL 161 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~~~l~ 161 (216)
.... +-.+...+... +.+|.....|+-=+++|.
T Consensus 496 Et~~------lG~aLsv~~~~--~LPI~yvt~GQ~VPeDL~ 528 (559)
T PRK12727 496 ETGR------FGSALSVVVDH--QMPITWVTDGQRVPDDLH 528 (559)
T ss_pred Cccc------hhHHHHHHHHh--CCCEEEEeCCCCchhhhh
Confidence 8553 34455555443 357777667643334443
No 228
>TIGR00503 prfC peptide chain release factor 3. This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. More recently, RF-3 was shown to be active primarily at UGA stop codons in E. coli. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis PCC6803, and in Staphylococcus aureus.
Probab=61.80 E-value=26 Score=32.82 Aligned_cols=65 Identities=17% Similarity=0.083 Sum_probs=36.9
Q ss_pred CCCEEEEecCCCCCcHH-HHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEcc
Q 027979 43 RLDHILLETTGLANPAP-LASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNK 118 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~-i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK 118 (216)
+..+.++-|.|..+-.. .... .-..+.+|.|||+....... ...+.++.. .-=++++||
T Consensus 79 ~~~inliDTPG~~df~~~~~~~---------l~~aD~aIlVvDa~~gv~~~--------t~~l~~~~~~~~~PiivviNK 141 (527)
T TIGR00503 79 DCLVNLLDTPGHEDFSEDTYRT---------LTAVDNCLMVIDAAKGVETR--------TRKLMEVTRLRDTPIFTFMNK 141 (527)
T ss_pred CeEEEEEECCChhhHHHHHHHH---------HHhCCEEEEEEECCCCCCHH--------HHHHHHHHHhcCCCEEEEEEC
Confidence 45667888999853322 1122 13467899999998632111 011222222 234678899
Q ss_pred CCCCCC
Q 027979 119 VDLVSP 124 (216)
Q Consensus 119 ~D~v~~ 124 (216)
+|+...
T Consensus 142 iD~~~~ 147 (527)
T TIGR00503 142 LDRDIR 147 (527)
T ss_pred ccccCC
Confidence 999653
No 229
>PLN00116 translation elongation factor EF-2 subunit; Provisional
Probab=61.18 E-value=10 Score=37.59 Aligned_cols=60 Identities=20% Similarity=0.184 Sum_probs=32.7
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc---EEEEccCCCCCCCCc---cchHHHHHHHHHhhC
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD---VVILNKVDLVSPERS---GDSLDELEKEIHEIN 142 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD---~IvlnK~D~v~~~~~---~~~l~~i~~~l~~lN 142 (216)
..|+.|.||||......- -..+.+|+.... ++++||+|+..-+-. .+..+.+.+.|.++|
T Consensus 121 ~~D~ailVvda~~Gv~~~--------t~~~~~~~~~~~~p~i~~iNK~D~~~~~~~~~~~~~~~~~~~vi~~in 186 (843)
T PLN00116 121 ITDGALVVVDCIEGVCVQ--------TETVLRQALGERIRPVLTVNKMDRCFLELQVDGEEAYQTFSRVIENAN 186 (843)
T ss_pred hcCEEEEEEECCCCCccc--------HHHHHHHHHHCCCCEEEEEECCcccchhhcCCHHHHHHHHHHHHHHHH
Confidence 356677777776432110 112345555443 899999999831100 013456666666666
No 230
>KOG1954 consensus Endocytosis/signaling protein EHD1 [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=60.59 E-value=10 Score=34.11 Aligned_cols=44 Identities=34% Similarity=0.501 Sum_probs=31.0
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc---EEEEccCCCCCCC
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD---VVILNKVDLVSPE 125 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD---~IvlnK~D~v~~~ 125 (216)
+.|.||.+.||..+. +.. .+.+++.|++.-+ .|||||+|.++.+
T Consensus 181 R~D~IiLlfD~hKLD--Isd-----Ef~~vi~aLkG~EdkiRVVLNKADqVdtq 227 (532)
T KOG1954|consen 181 RVDRIILLFDAHKLD--ISD-----EFKRVIDALKGHEDKIRVVLNKADQVDTQ 227 (532)
T ss_pred hccEEEEEechhhcc--ccH-----HHHHHHHHhhCCcceeEEEeccccccCHH
Confidence 567889999997653 111 1455667776544 6999999999975
No 231
>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....
Probab=59.21 E-value=92 Score=24.99 Aligned_cols=95 Identities=21% Similarity=0.111 Sum_probs=54.8
Q ss_pred cCCCCEEEEecCCCCCcH-HHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccC
Q 027979 41 KERLDHILLETTGLANPA-PLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKV 119 (216)
Q Consensus 41 ~~~~d~IiIE~sG~a~P~-~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~ 119 (216)
..+.|+|+|=|.|...-. ..++-+. .+.....-..++.|++|..-...+.. . ....+.-.-+-+|++|.
T Consensus 81 ~~~~D~vlIDT~Gr~~~d~~~~~el~---~~~~~~~~~~~~LVlsa~~~~~~~~~------~-~~~~~~~~~~~lIlTKl 150 (196)
T PF00448_consen 81 KKGYDLVLIDTAGRSPRDEELLEELK---KLLEALNPDEVHLVLSATMGQEDLEQ------A-LAFYEAFGIDGLILTKL 150 (196)
T ss_dssp HTTSSEEEEEE-SSSSTHHHHHHHHH---HHHHHHSSSEEEEEEEGGGGGHHHHH------H-HHHHHHSSTCEEEEEST
T ss_pred hcCCCEEEEecCCcchhhHHHHHHHH---HHhhhcCCccceEEEecccChHHHHH------H-HHHhhcccCceEEEEee
Confidence 346899999999998533 2222221 12233456678999999877655432 1 11122223478999999
Q ss_pred CCCCCCCccchHHHHHHHHHhhCCCCEEEEeecC
Q 027979 120 DLVSPERSGDSLDELEKEIHEINSLAHVIRSVRC 153 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~ 153 (216)
|....- -.+-..+.+. +.+|-....|
T Consensus 151 Det~~~------G~~l~~~~~~--~~Pi~~it~G 176 (196)
T PF00448_consen 151 DETARL------GALLSLAYES--GLPISYITTG 176 (196)
T ss_dssp TSSSTT------HHHHHHHHHH--TSEEEEEESS
T ss_pred cCCCCc------ccceeHHHHh--CCCeEEEECC
Confidence 986643 4444554443 3466655555
No 232
>PLN00043 elongation factor 1-alpha; Provisional
Probab=58.91 E-value=15 Score=33.55 Aligned_cols=14 Identities=14% Similarity=0.423 Sum_probs=10.1
Q ss_pred eeeccEEEEEcccc
Q 027979 74 VRLDSIITVVDAKN 87 (216)
Q Consensus 74 ~~l~~vI~vVDa~~ 87 (216)
-..+..|.|||+..
T Consensus 107 ~~aD~aIlVVda~~ 120 (447)
T PLN00043 107 SQADCAVLIIDSTT 120 (447)
T ss_pred hhccEEEEEEEccc
Confidence 35567788888875
No 233
>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=58.29 E-value=78 Score=23.86 Aligned_cols=68 Identities=12% Similarity=0.101 Sum_probs=33.4
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh----cc-EEEEcc
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF----AD-VVILNK 118 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~----AD-~IvlnK 118 (216)
.+..++-++|........... + -.-+.++.|+|+.+-... ... ...+...++. .- +|+.||
T Consensus 47 ~~~~i~Dt~G~~~~~~~~~~~-----~---~~ad~~ilv~d~~~~~s~-~~~-----~~~~~~~i~~~~~~~pviiv~nK 112 (166)
T cd01893 47 VPTTIVDTSSRPQDRANLAAE-----I---RKANVICLVYSVDRPSTL-ERI-----RTKWLPLIRRLGVKVPIILVGNK 112 (166)
T ss_pred EEEEEEeCCCchhhhHHHhhh-----c---ccCCEEEEEEECCCHHHH-HHH-----HHHHHHHHHHhCCCCCEEEEEEc
Confidence 455677888875433222211 1 234557888887763321 110 0011122221 11 566799
Q ss_pred CCCCCCC
Q 027979 119 VDLVSPE 125 (216)
Q Consensus 119 ~D~v~~~ 125 (216)
+|+.+..
T Consensus 113 ~Dl~~~~ 119 (166)
T cd01893 113 SDLRDGS 119 (166)
T ss_pred hhccccc
Confidence 9997654
No 234
>PRK03003 GTP-binding protein Der; Reviewed
Probab=58.25 E-value=30 Score=31.75 Aligned_cols=70 Identities=19% Similarity=0.145 Sum_probs=36.4
Q ss_pred EEEEecCCCCC-cHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh---ccEEEEccCCC
Q 027979 46 HILLETTGLAN-PAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF---ADVVILNKVDL 121 (216)
Q Consensus 46 ~IiIE~sG~a~-P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~---AD~IvlnK~D~ 121 (216)
..++.|.|.-. +..+.+.+. .......-..+.++.|+|+..-..... ..+..++.. -=++|+||+|+
T Consensus 88 ~~l~DT~G~~~~~~~~~~~~~-~~~~~~~~~aD~il~VvD~~~~~s~~~--------~~i~~~l~~~~~piilV~NK~Dl 158 (472)
T PRK03003 88 FTVVDTGGWEPDAKGLQASVA-EQAEVAMRTADAVLFVVDATVGATATD--------EAVARVLRRSGKPVILAANKVDD 158 (472)
T ss_pred EEEEeCCCcCCcchhHHHHHH-HHHHHHHHhCCEEEEEEECCCCCCHHH--------HHHHHHHHHcCCCEEEEEECccC
Confidence 56788889753 222221111 000011124578999999986432211 122333333 34677899998
Q ss_pred CCC
Q 027979 122 VSP 124 (216)
Q Consensus 122 v~~ 124 (216)
...
T Consensus 159 ~~~ 161 (472)
T PRK03003 159 ERG 161 (472)
T ss_pred Ccc
Confidence 653
No 235
>PRK12739 elongation factor G; Reviewed
Probab=57.50 E-value=18 Score=34.99 Aligned_cols=69 Identities=19% Similarity=0.186 Sum_probs=36.9
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVS 123 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~ 123 (216)
..+.+|-|.|..+= +.++. ...-..|.+|.|||+......-... .-....+....=++++||+|+.+
T Consensus 73 ~~i~liDTPG~~~f--~~e~~------~al~~~D~~ilVvDa~~g~~~qt~~-----i~~~~~~~~~p~iv~iNK~D~~~ 139 (691)
T PRK12739 73 HRINIIDTPGHVDF--TIEVE------RSLRVLDGAVAVFDAVSGVEPQSET-----VWRQADKYGVPRIVFVNKMDRIG 139 (691)
T ss_pred EEEEEEcCCCHHHH--HHHHH------HHHHHhCeEEEEEeCCCCCCHHHHH-----HHHHHHHcCCCEEEEEECCCCCC
Confidence 45677888887431 11111 1223457899999997542111000 00011222234589999999987
Q ss_pred CC
Q 027979 124 PE 125 (216)
Q Consensus 124 ~~ 125 (216)
.+
T Consensus 140 ~~ 141 (691)
T PRK12739 140 AD 141 (691)
T ss_pred CC
Confidence 53
No 236
>cd04155 Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.
Probab=57.14 E-value=26 Score=26.51 Aligned_cols=14 Identities=36% Similarity=0.434 Sum_probs=10.2
Q ss_pred cEEEEccCCCCCCC
Q 027979 112 DVVILNKVDLVSPE 125 (216)
Q Consensus 112 D~IvlnK~D~v~~~ 125 (216)
-++++||+|+.+..
T Consensus 118 ~ivv~nK~D~~~~~ 131 (173)
T cd04155 118 VLVFANKQDLATAA 131 (173)
T ss_pred EEEEEECCCCccCC
Confidence 35677999987653
No 237
>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=56.82 E-value=1.4e+02 Score=26.79 Aligned_cols=111 Identities=17% Similarity=0.097 Sum_probs=59.0
Q ss_pred hhHHHHHHHHHHhcCCCCEEEEecCCCCCcHH-HHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHH
Q 027979 28 HSLVQALEQLVQRKERLDHILLETTGLANPAP-LASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIH 106 (216)
Q Consensus 28 ~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~~-i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~ 106 (216)
.++...+.++ .+.|.|+|-|.|...-.. +.+.+. .+........++.|++|.+-.+.+... . ..+.
T Consensus 204 ~~l~~~l~~l----~~~DlVLIDTaG~~~~d~~l~e~La---~L~~~~~~~~~lLVLsAts~~~~l~ev-----i-~~f~ 270 (374)
T PRK14722 204 GDLQLALAEL----RNKHMVLIDTIGMSQRDRTVSDQIA---MLHGADTPVQRLLLLNATSHGDTLNEV-----V-QAYR 270 (374)
T ss_pred ccHHHHHHHh----cCCCEEEEcCCCCCcccHHHHHHHH---HHhccCCCCeEEEEecCccChHHHHHH-----H-HHHH
Confidence 3454445443 357999999999984322 333221 111112223468899998755544321 0 0112
Q ss_pred HHh--------hccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeecCCCChhh
Q 027979 107 QIA--------FADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQVDLSE 159 (216)
Q Consensus 107 QI~--------~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~~~ 159 (216)
... .-+-+|++|.|-...- -.+.+.+... +.+|.....|+-=+++
T Consensus 271 ~~~~~p~~~~~~~~~~I~TKlDEt~~~------G~~l~~~~~~--~lPi~yvt~Gq~VPed 323 (374)
T PRK14722 271 SAAGQPKAALPDLAGCILTKLDEASNL------GGVLDTVIRY--KLPVHYVSTGQKVPEN 323 (374)
T ss_pred HhhcccccccCCCCEEEEeccccCCCc------cHHHHHHHHH--CcCeEEEecCCCCCcc
Confidence 221 2478999999986643 3344444332 4667766666443333
No 238
>PRK10076 pyruvate formate lyase II activase; Provisional
Probab=56.61 E-value=30 Score=28.36 Aligned_cols=46 Identities=15% Similarity=0.112 Sum_probs=30.0
Q ss_pred ecCCCcEEeecch-----hHHHHHHHHHHhcCCCCEEEEecCCCCCcHHHHHH
Q 027979 16 ELANGCICCTVKH-----SLVQALEQLVQRKERLDHILLETTGLANPAPLASV 63 (216)
Q Consensus 16 eL~~GCiCCsl~~-----dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~ 63 (216)
.-++|+||-|..+ +|+..+.+.+. +.. =++.|||||...+..+.+.
T Consensus 36 ~~sggGVt~SGGEPllq~~fl~~l~~~~k-~~g-i~~~leTnG~~~~~~~~~l 86 (213)
T PRK10076 36 RTSGGGVTLSGGEVLMQAEFATRFLQRLR-LWG-VSCAIETAGDAPASKLLPL 86 (213)
T ss_pred cCCCCEEEEeCchHHcCHHHHHHHHHHHH-HcC-CCEEEECCCCCCHHHHHHH
Confidence 3478999998665 44444444443 233 3689999999977655443
No 239
>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=56.49 E-value=84 Score=23.67 Aligned_cols=67 Identities=12% Similarity=0.114 Sum_probs=35.3
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh----hcc-EEEEcc
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA----FAD-VVILNK 118 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~----~AD-~IvlnK 118 (216)
+...+..++|......+.... + -..+.+|.|+|..+.... .+. ...+..++. ..- +|+.||
T Consensus 46 ~~~~i~Dt~G~~~~~~~~~~~-----~---~~~d~~ilv~d~~~~~s~-~~~-----~~~~~~~i~~~~~~~piilv~nK 111 (174)
T smart00174 46 VELGLWDTAGQEDYDRLRPLS-----Y---PDTDVFLICFSVDSPASF-ENV-----KEKWYPEVKHFCPNTPIILVGTK 111 (174)
T ss_pred EEEEEEECCCCcccchhchhh-----c---CCCCEEEEEEECCCHHHH-HHH-----HHHHHHHHHhhCCCCCEEEEecC
Confidence 456778888875443332221 1 134778888998765322 110 011223332 222 566699
Q ss_pred CCCCCC
Q 027979 119 VDLVSP 124 (216)
Q Consensus 119 ~D~v~~ 124 (216)
+|+.+.
T Consensus 112 ~Dl~~~ 117 (174)
T smart00174 112 LDLRED 117 (174)
T ss_pred hhhhhC
Confidence 999763
No 240
>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=55.96 E-value=86 Score=23.63 Aligned_cols=92 Identities=14% Similarity=0.130 Sum_probs=43.6
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc-c---EEEEccCC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA-D---VVILNKVD 120 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A-D---~IvlnK~D 120 (216)
..-++.++|...-..+.+... . ..+++|.|+|..+.... .+.. .......++... + +++.||.|
T Consensus 50 ~~~i~Dt~G~~~~~~~~~~~~-----~---~~~~~vlv~~~~~~~s~-~~~~---~~~~~i~~~~~~~~~piiiv~nK~D 117 (168)
T cd04177 50 DLEILDTAGTEQFTAMRELYI-----K---SGQGFLLVYSVTSEASL-NELG---ELREQVLRIKDSDNVPMVLVGNKAD 117 (168)
T ss_pred EEEEEeCCCcccchhhhHHHH-----h---hCCEEEEEEECCCHHHH-HHHH---HHHHHHHHhhCCCCCCEEEEEEChh
Confidence 345678888765444443322 1 23566778887754322 1100 011112222211 2 67889999
Q ss_pred CCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 121 LVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
+.+.... ..+...+..+..+ ..++++++
T Consensus 118 ~~~~~~~--~~~~~~~~~~~~~-~~~~~~~S 145 (168)
T cd04177 118 LEDDRQV--SREDGVSLSQQWG-NVPFYETS 145 (168)
T ss_pred ccccCcc--CHHHHHHHHHHcC-CceEEEee
Confidence 9764321 2233334434333 35566543
No 241
>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=55.82 E-value=94 Score=24.02 Aligned_cols=97 Identities=14% Similarity=0.143 Sum_probs=46.5
Q ss_pred EEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---h--cc-EEEEccC
Q 027979 46 HILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---F--AD-VVILNKV 119 (216)
Q Consensus 46 ~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~--AD-~IvlnK~ 119 (216)
.-+.++.|......+...+. -..+.+|.|+|..+-.. +.+ ...+..++. . .- +++.||+
T Consensus 51 ~~i~Dt~g~~~~~~~~~~~~--------~~~d~iilv~d~~~~~s-~~~------i~~~~~~i~~~~~~~~~~ivv~nK~ 115 (188)
T cd04125 51 LQIWDTNGQERFRSLNNSYY--------RGAHGYLLVYDVTDQES-FEN------LKFWINEINRYARENVIKVIVANKS 115 (188)
T ss_pred EEEEECCCcHHHHhhHHHHc--------cCCCEEEEEEECcCHHH-HHH------HHHHHHHHHHhCCCCCeEEEEEECC
Confidence 34567777543333322221 13578899999976442 221 122222222 1 22 6677999
Q ss_pred CCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 120 DLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
|+.+.... ..+..+...+.. +.++++++- ...+...++
T Consensus 116 Dl~~~~~v--~~~~~~~~~~~~--~~~~~evSa~~~~~i~~~f 154 (188)
T cd04125 116 DLVNNKVV--DSNIAKSFCDSL--NIPFFETSAKQSINVEEAF 154 (188)
T ss_pred CCcccccC--CHHHHHHHHHHc--CCeEEEEeCCCCCCHHHHH
Confidence 98754321 122333333332 345665442 234454444
No 242
>TIGR01969 minD_arch cell division ATPase MinD, archaeal. This model represents the archaeal branch of the MinD family. MinD, a weak ATPase, works in bacteria with MinC as a generalized cell division inhibitor and, through interaction with MinE, prevents septum placement inappropriate sites. Often several members of this family are found in archaeal genomes, and the function is uncharacterized. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. The exact roles of the various archaeal MinD homologs are unknown.
Probab=54.65 E-value=77 Score=25.69 Aligned_cols=37 Identities=16% Similarity=0.276 Sum_probs=24.8
Q ss_pred CCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccch
Q 027979 42 ERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNL 88 (216)
Q Consensus 42 ~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~ 88 (216)
.++|+|||.+.+..++..... +. .-+.+|.++++...
T Consensus 107 ~~yD~VIiD~p~~~~~~~~~~-l~---------~ad~vliv~~~~~~ 143 (251)
T TIGR01969 107 DDTDFLLIDAPAGLERDAVTA-LA---------AADELLLVVNPEIS 143 (251)
T ss_pred hhCCEEEEeCCCccCHHHHHH-HH---------hCCeEEEEECCCCc
Confidence 369999999998877654332 21 12457888888744
No 243
>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=54.27 E-value=91 Score=23.41 Aligned_cols=35 Identities=23% Similarity=0.150 Sum_probs=21.2
Q ss_pred EEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 113 VVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 113 ~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
+|+.||+|+.... ...+++.+..+..+. .++++++
T Consensus 118 ilv~nK~Dl~~~~---~~~~~~~~~~~~~~~-~~~~e~S 152 (170)
T cd04116 118 VVLGNKNDIPERQ---VSTEEAQAWCRENGD-YPYFETS 152 (170)
T ss_pred EEEEECccccccc---cCHHHHHHHHHHCCC-CeEEEEE
Confidence 6888999986432 134566666666542 3555543
No 244
>PRK12288 GTPase RsgA; Reviewed
Probab=53.76 E-value=22 Score=31.47 Aligned_cols=13 Identities=46% Similarity=0.922 Sum_probs=11.1
Q ss_pred EEEEccCCCCCCC
Q 027979 113 VVILNKVDLVSPE 125 (216)
Q Consensus 113 ~IvlnK~D~v~~~ 125 (216)
+||+||+|+++..
T Consensus 154 VIVlNK~DL~~~~ 166 (347)
T PRK12288 154 LIVLNKIDLLDDE 166 (347)
T ss_pred EEEEECccCCCcH
Confidence 7899999998753
No 245
>PRK05433 GTP-binding protein LepA; Provisional
Probab=53.74 E-value=86 Score=29.93 Aligned_cols=65 Identities=22% Similarity=0.190 Sum_probs=37.0
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH---hhccEEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---AFADVVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~~AD~IvlnK~D 120 (216)
+...++-|.|..+-......- + -..+++|.|||+..-...- . ... ..+. ..-=++++||+|
T Consensus 74 ~~lnLiDTPGh~dF~~~v~~s-----l---~~aD~aILVVDas~gv~~q-t------~~~-~~~~~~~~lpiIvViNKiD 137 (600)
T PRK05433 74 YILNLIDTPGHVDFSYEVSRS-----L---AACEGALLVVDASQGVEAQ-T------LAN-VYLALENDLEIIPVLNKID 137 (600)
T ss_pred EEEEEEECCCcHHHHHHHHHH-----H---HHCCEEEEEEECCCCCCHH-H------HHH-HHHHHHCCCCEEEEEECCC
Confidence 445788999998765443321 1 1356789999997632110 0 101 1111 112378999999
Q ss_pred CCCC
Q 027979 121 LVSP 124 (216)
Q Consensus 121 ~v~~ 124 (216)
+.+.
T Consensus 138 l~~a 141 (600)
T PRK05433 138 LPAA 141 (600)
T ss_pred CCcc
Confidence 8654
No 246
>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed
Probab=52.99 E-value=34 Score=33.22 Aligned_cols=71 Identities=21% Similarity=0.243 Sum_probs=36.7
Q ss_pred CEEEEecCCCCCcH-HHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEccCC
Q 027979 45 DHILLETTGLANPA-PLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNKVD 120 (216)
Q Consensus 45 d~IiIE~sG~a~P~-~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK~D 120 (216)
...++-|.|..... .+-..+. .......-..+.++.|+|+..-....+ .++.+.+. .-=++|+||+|
T Consensus 324 ~~~liDT~G~~~~~~~~~~~~~-~~~~~~~~~aD~iL~VvDa~~~~~~~d--------~~i~~~Lr~~~~pvIlV~NK~D 394 (712)
T PRK09518 324 DFKLVDTGGWEADVEGIDSAIA-SQAQIAVSLADAVVFVVDGQVGLTSTD--------ERIVRMLRRAGKPVVLAVNKID 394 (712)
T ss_pred EEEEEeCCCcCCCCccHHHHHH-HHHHHHHHhCCEEEEEEECCCCCCHHH--------HHHHHHHHhcCCCEEEEEECcc
Confidence 56788999976421 1111110 000111234678999999975322211 11223333 23368889999
Q ss_pred CCCC
Q 027979 121 LVSP 124 (216)
Q Consensus 121 ~v~~ 124 (216)
+...
T Consensus 395 ~~~~ 398 (712)
T PRK09518 395 DQAS 398 (712)
T ss_pred cccc
Confidence 8654
No 247
>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=52.87 E-value=86 Score=22.69 Aligned_cols=65 Identities=18% Similarity=0.140 Sum_probs=33.9
Q ss_pred EEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH------hhcc-EEEEcc
Q 027979 46 HILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI------AFAD-VVILNK 118 (216)
Q Consensus 46 ~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI------~~AD-~IvlnK 118 (216)
..++.+.|...-..+..... -..+.++.|+|+......... .....++ ...- +|++||
T Consensus 46 ~~~~D~~g~~~~~~~~~~~~--------~~~d~ii~v~d~~~~~~~~~~-------~~~~~~~~~~~~~~~~p~iiv~nK 110 (159)
T cd04159 46 LKVWDLGGQPRFRSMWERYC--------RGVNAIVYVVDAADRTALEAA-------KNELHDLLEKPSLEGIPLLVLGNK 110 (159)
T ss_pred EEEEECCCCHhHHHHHHHHH--------hcCCEEEEEEECCCHHHHHHH-------HHHHHHHHcChhhcCCCEEEEEeC
Confidence 45667777643333332221 234678999999875432211 0111111 1112 567899
Q ss_pred CCCCCCC
Q 027979 119 VDLVSPE 125 (216)
Q Consensus 119 ~D~v~~~ 125 (216)
.|+.+..
T Consensus 111 ~D~~~~~ 117 (159)
T cd04159 111 NDLPGAL 117 (159)
T ss_pred ccccCCc
Confidence 9987653
No 248
>smart00053 DYNc Dynamin, GTPase. Large GTPases that mediate vesicle trafficking. Dynamin participates in the endocytic uptake of receptors, associated ligands, and plasma membrane following an exocytic event.
Probab=52.32 E-value=53 Score=27.49 Aligned_cols=73 Identities=18% Similarity=0.274 Sum_probs=38.6
Q ss_pred CCEEEEecCCCCC------cHHHHHHhhcCccccccee-e-ccEEEEEcccchHHHHhhcccCCChhHHHHHHhh---cc
Q 027979 44 LDHILLETTGLAN------PAPLASVLWLDDQLESAVR-L-DSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF---AD 112 (216)
Q Consensus 44 ~d~IiIE~sG~a~------P~~i~~~l~~~~~l~~~~~-l-~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~---AD 112 (216)
|+..+|=+.|+.. +..+...+. ......++ - +-+++|+||..-....+ .-++.+++.- =-
T Consensus 125 ~~ltLIDlPGl~~~~~~~~~~~~~~~i~--~lv~~yi~~~~~IIL~Vvda~~d~~~~d-------~l~ia~~ld~~~~rt 195 (240)
T smart00053 125 LNLTLIDLPGITKVAVGDQPPDIEEQIK--DMIKQFISKEECLILAVTPANVDLANSD-------ALKLAKEVDPQGERT 195 (240)
T ss_pred CceEEEeCCCccccccCCccHHHHHHHH--HHHHHHHhCccCeEEEEEECCCCCCchh-------HHHHHHHHHHcCCcE
Confidence 8999999999974 233322111 11112222 1 14689999864221100 0123344433 23
Q ss_pred EEEEccCCCCCCC
Q 027979 113 VVILNKVDLVSPE 125 (216)
Q Consensus 113 ~IvlnK~D~v~~~ 125 (216)
++|+||+|..++.
T Consensus 196 i~ViTK~D~~~~~ 208 (240)
T smart00053 196 IGVITKLDLMDEG 208 (240)
T ss_pred EEEEECCCCCCcc
Confidence 5689999998764
No 249
>KOG0460 consensus Mitochondrial translation elongation factor Tu [Translation, ribosomal structure and biogenesis]
Probab=52.00 E-value=19 Score=32.08 Aligned_cols=34 Identities=38% Similarity=0.568 Sum_probs=22.8
Q ss_pred HHHHHhhccEEE-EccCCCCCCCCccchHHHHHHHHHh
Q 027979 104 AIHQIAFADVVI-LNKVDLVSPERSGDSLDELEKEIHE 140 (216)
Q Consensus 104 ~~~QI~~AD~Iv-lnK~D~v~~~~~~~~l~~i~~~l~~ 140 (216)
+.+|+..-++|| +||.|++++++ -++-++-.+|+
T Consensus 164 LArQVGV~~ivvfiNKvD~V~d~e---~leLVEmE~RE 198 (449)
T KOG0460|consen 164 LARQVGVKHIVVFINKVDLVDDPE---MLELVEMEIRE 198 (449)
T ss_pred HHHHcCCceEEEEEecccccCCHH---HHHHHHHHHHH
Confidence 568999988765 59999996543 34444444444
No 250
>COG2229 Predicted GTPase [General function prediction only]
Probab=51.80 E-value=64 Score=26.03 Aligned_cols=63 Identities=21% Similarity=0.138 Sum_probs=39.7
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHH--HHHhh-ccE-EEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAI--HQIAF-ADV-VILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~--~QI~~-AD~-IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
..+.|.+||++.-... . ..++. -++.+ ..+ |..||.|+-+.. -.+++++.+..-|-..+++..
T Consensus 92 a~gaivlVDss~~~~~--~------a~~ii~f~~~~~~ip~vVa~NK~DL~~a~----ppe~i~e~l~~~~~~~~vi~~ 158 (187)
T COG2229 92 AVGAIVLVDSSRPITF--H------AEEIIDFLTSRNPIPVVVAINKQDLFDAL----PPEKIREALKLELLSVPVIEI 158 (187)
T ss_pred cceEEEEEecCCCcch--H------HHHHHHHHhhccCCCEEEEeeccccCCCC----CHHHHHHHHHhccCCCceeee
Confidence 4567888998876543 0 11222 34444 454 556999998864 358888888876645566643
No 251
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=51.48 E-value=39 Score=31.49 Aligned_cols=99 Identities=21% Similarity=0.232 Sum_probs=57.5
Q ss_pred cCCCCEEEEecCCCC-CcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHH---HHHhhccEEEE
Q 027979 41 KERLDHILLETTGLA-NPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAI---HQIAFADVVIL 116 (216)
Q Consensus 41 ~~~~d~IiIE~sG~a-~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~---~QI~~AD~Ivl 116 (216)
...+|.|+|-|.|=- +-.+++..|. .+...-+.|.|+.|-.|--..+.++.. ..|..+. .|=+.-|-|+|
T Consensus 464 ~~gfDVvLiDTAGR~~~~~~lm~~l~---k~~~~~~pd~i~~vgealvg~dsv~q~---~~fn~al~~~~~~r~id~~~l 537 (587)
T KOG0781|consen 464 NQGFDVVLIDTAGRMHNNAPLMTSLA---KLIKVNKPDLILFVGEALVGNDSVDQL---KKFNRALADHSTPRLIDGILL 537 (587)
T ss_pred hcCCCEEEEeccccccCChhHHHHHH---HHHhcCCCceEEEehhhhhCcHHHHHH---HHHHHHHhcCCCccccceEEE
Confidence 458999999999954 4456666653 344455677788876654322222110 0022221 34456789999
Q ss_pred ccCCCCCCCCccchHHHHHHHHHh-hCCCCEEEEeecC
Q 027979 117 NKVDLVSPERSGDSLDELEKEIHE-INSLAHVIRSVRC 153 (216)
Q Consensus 117 nK~D~v~~~~~~~~l~~i~~~l~~-lNP~A~iv~~~~~ 153 (216)
+|.|.+++ .+-..+.- ...++||+...-|
T Consensus 538 tk~dtv~d--------~vg~~~~m~y~~~~pi~fvg~g 567 (587)
T KOG0781|consen 538 TKFDTVDD--------KVGAAVSMVYITGKPILFVGVG 567 (587)
T ss_pred Eeccchhh--------HHHHHhhheeecCCceEEEecC
Confidence 99999984 33333332 3456677654433
No 252
>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]
Probab=51.26 E-value=1.1e+02 Score=26.81 Aligned_cols=99 Identities=21% Similarity=0.377 Sum_probs=49.7
Q ss_pred eec-CCCcEEeecchhHH---HHHHHHHHh-cCCCCEEEEecCCCCC------cHHH-HHHhhcCcccccceeeccEEEE
Q 027979 15 VEL-ANGCICCTVKHSLV---QALEQLVQR-KERLDHILLETTGLAN------PAPL-ASVLWLDDQLESAVRLDSIITV 82 (216)
Q Consensus 15 ~eL-~~GCiCCsl~~dl~---~~L~~l~~~-~~~~d~IiIE~sG~a~------P~~i-~~~l~~~~~l~~~~~l~~vI~v 82 (216)
++| .||-|--+++- |. ++..+++++ ...+++++|-|.|=-+ +..| .++|. ..+ ..-|+.|
T Consensus 83 Y~LGPNGgI~TsLNL-F~tk~dqv~~~iek~~~~~~~~liDTPGQIE~FtWSAsGsIIte~la------ss~-ptvv~Yv 154 (366)
T KOG1532|consen 83 YQLGPNGGIVTSLNL-FATKFDQVIELIEKRAEEFDYVLIDTPGQIEAFTWSASGSIITETLA------SSF-PTVVVYV 154 (366)
T ss_pred hCCCCCcchhhhHHH-HHHHHHHHHHHHHHhhcccCEEEEcCCCceEEEEecCCccchHhhHh------hcC-CeEEEEE
Confidence 344 46666555542 22 222233332 3468999999988532 2333 24443 222 2236889
Q ss_pred EcccchHH---HHhhcccCCChh-HHHHHHhhccEEEEccCCCCCCC
Q 027979 83 VDAKNLLF---QIDKYRHLSSYP-EAIHQIAFADVVILNKVDLVSPE 125 (216)
Q Consensus 83 VDa~~~~~---~l~~~~~~~~~~-~~~~QI~~AD~IvlnK~D~v~~~ 125 (216)
||..+-.. .+.++- ++ -+.---+.-=+|++||+|+.+.+
T Consensus 155 vDt~rs~~p~tFMSNMl----YAcSilyktklp~ivvfNK~Dv~d~~ 197 (366)
T KOG1532|consen 155 VDTPRSTSPTTFMSNML----YACSILYKTKLPFIVVFNKTDVSDSE 197 (366)
T ss_pred ecCCcCCCchhHHHHHH----HHHHHHHhccCCeEEEEecccccccH
Confidence 99865321 111110 00 01111223347899999998864
No 253
>PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
Probab=50.76 E-value=22 Score=34.01 Aligned_cols=68 Identities=22% Similarity=0.259 Sum_probs=35.4
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc-EEEEccCCCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD-VVILNKVDLV 122 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD-~IvlnK~D~v 122 (216)
..++||-|.|..+ +...+. ...-..|.++.|||+......-.. .+-.+..++..-- +|++||+|++
T Consensus 104 ~~~~liDtPG~~~---f~~~~~-----~~~~~aD~~llVvda~~g~~~~t~-----e~~~~~~~~~~~~iivvvNK~D~~ 170 (632)
T PRK05506 104 RKFIVADTPGHEQ---YTRNMV-----TGASTADLAIILVDARKGVLTQTR-----RHSFIASLLGIRHVVLAVNKMDLV 170 (632)
T ss_pred ceEEEEECCChHH---HHHHHH-----HHHHhCCEEEEEEECCCCccccCH-----HHHHHHHHhCCCeEEEEEEecccc
Confidence 3568889999642 222111 122355678999999643211000 0111223333333 4579999998
Q ss_pred CC
Q 027979 123 SP 124 (216)
Q Consensus 123 ~~ 124 (216)
+.
T Consensus 171 ~~ 172 (632)
T PRK05506 171 DY 172 (632)
T ss_pred cc
Confidence 63
No 254
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=50.65 E-value=64 Score=28.55 Aligned_cols=79 Identities=20% Similarity=0.230 Sum_probs=46.0
Q ss_pred HHHHHHHHhcCCCCEEEEecCCCCCc-HHHHHHhh-----cCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHH
Q 027979 32 QALEQLVQRKERLDHILLETTGLANP-APLASVLW-----LDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAI 105 (216)
Q Consensus 32 ~~L~~l~~~~~~~d~IiIE~sG~a~P-~~i~~~l~-----~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~ 105 (216)
++++.-. ..++|++||-|.|=-+- ..+++-|. ..+... -....++.++||....+-+.. ...+
T Consensus 212 DAi~~Ak--ar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~--~ap~e~llvlDAttGqnal~Q-------Ak~F 280 (340)
T COG0552 212 DAIQAAK--ARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDP--DAPHEILLVLDATTGQNALSQ-------AKIF 280 (340)
T ss_pred HHHHHHH--HcCCCEEEEeCcccccCchhHHHHHHHHHHHhccccC--CCCceEEEEEEcccChhHHHH-------HHHH
Confidence 4555543 34789999999995433 23333221 011111 012236777799988766543 2334
Q ss_pred HHHhhccEEEEccCCC
Q 027979 106 HQIAFADVVILNKVDL 121 (216)
Q Consensus 106 ~QI~~AD~IvlnK~D~ 121 (216)
...-.=|=||++|.|-
T Consensus 281 ~eav~l~GiIlTKlDg 296 (340)
T COG0552 281 NEAVGLDGIILTKLDG 296 (340)
T ss_pred HHhcCCceEEEEeccc
Confidence 5555679999999994
No 255
>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=50.06 E-value=38 Score=32.24 Aligned_cols=64 Identities=20% Similarity=0.223 Sum_probs=36.2
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchH-HHHhhcccCCChhHHHHHH---hhccEEEEccC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLL-FQIDKYRHLSSYPEAIHQI---AFADVVILNKV 119 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~-~~l~~~~~~~~~~~~~~QI---~~AD~IvlnK~ 119 (216)
..+-||-|.|-++-....... .-..+.++.|||+..-. .+. .....++ ..-=+|++||+
T Consensus 64 ~kinlIDTPGh~DF~~ev~~~--------l~~aD~alLVVDa~~G~~~qT---------~~~l~~a~~~~ip~IVviNKi 126 (594)
T TIGR01394 64 TKINIVDTPGHADFGGEVERV--------LGMVDGVLLLVDASEGPMPQT---------RFVLKKALELGLKPIVVINKI 126 (594)
T ss_pred EEEEEEECCCHHHHHHHHHHH--------HHhCCEEEEEEeCCCCCcHHH---------HHHHHHHHHCCCCEEEEEECC
Confidence 345678888887644333221 12457899999997521 111 1112222 22238999999
Q ss_pred CCCCC
Q 027979 120 DLVSP 124 (216)
Q Consensus 120 D~v~~ 124 (216)
|+.+.
T Consensus 127 D~~~a 131 (594)
T TIGR01394 127 DRPSA 131 (594)
T ss_pred CCCCc
Confidence 99654
No 256
>CHL00189 infB translation initiation factor 2; Provisional
Probab=49.97 E-value=68 Score=31.50 Aligned_cols=98 Identities=19% Similarity=0.280 Sum_probs=48.3
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc---EEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD---VVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD---~IvlnK~D 120 (216)
....++-|.|-..=..+... ..-..+.+|.|||+...... ... +...++..++ +|++||+|
T Consensus 295 ~kItfiDTPGhe~F~~mr~r--------g~~~aDiaILVVDA~dGv~~-------QT~-E~I~~~k~~~iPiIVViNKiD 358 (742)
T CHL00189 295 QKIVFLDTPGHEAFSSMRSR--------GANVTDIAILIIAADDGVKP-------QTI-EAINYIQAANVPIIVAINKID 358 (742)
T ss_pred eEEEEEECCcHHHHHHHHHH--------HHHHCCEEEEEEECcCCCCh-------hhH-HHHHHHHhcCceEEEEEECCC
Confidence 34566777776422222111 11245678889988643210 001 2233333333 68899999
Q ss_pred CCCCCCccchHHHHHHHHHhh-------CCCCEEEEeec-CCCChhhhhc
Q 027979 121 LVSPERSGDSLDELEKEIHEI-------NSLAHVIRSVR-CQVDLSEVLN 162 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~l-------NP~A~iv~~~~-~~v~~~~l~~ 162 (216)
+.+.. ..++.+.++.. ....++++++- ....+..++.
T Consensus 359 l~~~~-----~e~v~~eL~~~~ll~e~~g~~vpvv~VSAktG~GIdeLle 403 (742)
T CHL00189 359 KANAN-----TERIKQQLAKYNLIPEKWGGDTPMIPISASQGTNIDKLLE 403 (742)
T ss_pred ccccC-----HHHHHHHHHHhccchHhhCCCceEEEEECCCCCCHHHHHH
Confidence 97642 34555555432 22356665432 2234445443
No 257
>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=49.51 E-value=34 Score=22.18 Aligned_cols=11 Identities=27% Similarity=0.685 Sum_probs=6.9
Q ss_pred ccEEEEEcccc
Q 027979 77 DSIITVVDAKN 87 (216)
Q Consensus 77 ~~vI~vVDa~~ 87 (216)
+.|+.++|++.
T Consensus 15 ~~ilfi~D~Se 25 (58)
T PF06858_consen 15 DAILFIIDPSE 25 (58)
T ss_dssp SEEEEEE-TT-
T ss_pred ceEEEEEcCCC
Confidence 35789999874
No 258
>TIGR00450 mnmE_trmE_thdF tRNA modification GTPase TrmE. TrmE, also called MnmE and previously designated ThdF (thiophene and furan oxidation protein), is a GTPase involved in tRNA modification to create 5-methylaminomethyl-2-thiouridine in the wobble position of some tRNAs. This protein and GidA form an alpha2/beta2 heterotetramer.
Probab=49.34 E-value=32 Score=31.49 Aligned_cols=70 Identities=26% Similarity=0.307 Sum_probs=35.9
Q ss_pred EEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh--c-cEEEEccCCCC
Q 027979 46 HILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF--A-DVVILNKVDLV 122 (216)
Q Consensus 46 ~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~--A-D~IvlnK~D~v 122 (216)
..++-|.|..+....++...........-..+.++.|+|+.+-...- ..+..++.. . =++|+||+|+.
T Consensus 253 v~l~DTaG~~~~~~~ie~~gi~~~~~~~~~aD~il~V~D~s~~~s~~---------~~~l~~~~~~~~piIlV~NK~Dl~ 323 (442)
T TIGR00450 253 IKLLDTAGIREHADFVERLGIEKSFKAIKQADLVIYVLDASQPLTKD---------DFLIIDLNKSKKPFILVLNKIDLK 323 (442)
T ss_pred EEEeeCCCcccchhHHHHHHHHHHHHHHhhCCEEEEEEECCCCCChh---------HHHHHHHhhCCCCEEEEEECccCC
Confidence 35677788765544433211000011122467889999997532110 012233321 1 26888999996
Q ss_pred CC
Q 027979 123 SP 124 (216)
Q Consensus 123 ~~ 124 (216)
..
T Consensus 324 ~~ 325 (442)
T TIGR00450 324 IN 325 (442)
T ss_pred Cc
Confidence 54
No 259
>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=49.15 E-value=1.3e+02 Score=28.70 Aligned_cols=75 Identities=24% Similarity=0.279 Sum_probs=37.9
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh---ccEEEEccCCC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF---ADVVILNKVDL 121 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~---AD~IvlnK~D~ 121 (216)
...|+-|.|-.+-..+.. ...-..|.+|.|+|+......- .-+...+... -=+|++||+|+
T Consensus 136 ~i~~iDTPGhe~F~~~r~--------rga~~aDiaILVVda~dgv~~q--------T~e~i~~~~~~~vPiIVviNKiDl 199 (587)
T TIGR00487 136 MITFLDTPGHEAFTSMRA--------RGAKVTDIVVLVVAADDGVMPQ--------TIEAISHAKAANVPIIVAINKIDK 199 (587)
T ss_pred EEEEEECCCCcchhhHHH--------hhhccCCEEEEEEECCCCCCHh--------HHHHHHHHHHcCCCEEEEEECccc
Confidence 345667777543322221 1123456788899886421100 0112233332 24788899999
Q ss_pred CCCCCccchHHHHHHHHHh
Q 027979 122 VSPERSGDSLDELEKEIHE 140 (216)
Q Consensus 122 v~~~~~~~~l~~i~~~l~~ 140 (216)
.+.. .+++.+.++.
T Consensus 200 ~~~~-----~e~v~~~L~~ 213 (587)
T TIGR00487 200 PEAN-----PDRVKQELSE 213 (587)
T ss_pred ccCC-----HHHHHHHHHH
Confidence 6532 3455555544
No 260
>COG4917 EutP Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=48.99 E-value=32 Score=26.28 Aligned_cols=34 Identities=12% Similarity=0.281 Sum_probs=25.4
Q ss_pred EEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 113 VVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 113 ~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
+=|++|+|+++.+ .++..+++|++.. .-+|+.++
T Consensus 94 IgvVTK~DLaed~----dI~~~~~~L~eaG-a~~IF~~s 127 (148)
T COG4917 94 IGVVTKADLAEDA----DISLVKRWLREAG-AEPIFETS 127 (148)
T ss_pred EEEEecccccchH----hHHHHHHHHHHcC-CcceEEEe
Confidence 4578999999654 4799999999876 44666543
No 261
>PF02606 LpxK: Tetraacyldisaccharide-1-P 4'-kinase; InterPro: IPR003758 Tetraacyldisaccharide 4'-kinase phosphorylates the 4'-position of a tetraacyldisaccharide 1-phosphate precursor (DS-1-P) of lipid A, but the enzyme has not yet been purified because of instability []. This enzyme is involved in the synthesis of lipid A portion of the bacterial lipopolysaccharide layer (LPS).; GO: 0005524 ATP binding, 0009029 tetraacyldisaccharide 4'-kinase activity, 0009245 lipid A biosynthetic process
Probab=48.73 E-value=27 Score=30.58 Aligned_cols=42 Identities=26% Similarity=0.327 Sum_probs=25.9
Q ss_pred EEEEcccchHHHHhhc--ccCCChhHHHHHHhhccEEEEccCCCCCC
Q 027979 80 ITVVDAKNLLFQIDKY--RHLSSYPEAIHQIAFADVVILNKVDLVSP 124 (216)
Q Consensus 80 I~vVDa~~~~~~l~~~--~~~~~~~~~~~QI~~AD~IvlnK~D~v~~ 124 (216)
|.++|+.+.. .+. -..+...|-..++..||+||+||.+....
T Consensus 149 Ivl~D~~~~~---gng~lLPaG~LREp~~~l~rAD~vi~~~~~~~~~ 192 (326)
T PF02606_consen 149 IVLVDADRPF---GNGFLLPAGPLREPLSALKRADAVIVTGCDASDP 192 (326)
T ss_pred EEEEeCCCCC---cCCccCCCCcccCChhHhCcccEEEEcCCCcchh
Confidence 7777775432 111 01122334457999999999999887543
No 262
>KOG0458 consensus Elongation factor 1 alpha [Translation, ribosomal structure and biogenesis]
Probab=48.56 E-value=20 Score=33.83 Aligned_cols=103 Identities=17% Similarity=0.174 Sum_probs=49.7
Q ss_pred eeeccEEEEEcccch--HHHHhhcccCCChhHHHHHHhhcc-EEEEccCCCCCCCCccchHHHHHHHHHhhC-CCCEEEE
Q 027979 74 VRLDSIITVVDAKNL--LFQIDKYRHLSSYPEAIHQIAFAD-VVILNKVDLVSPERSGDSLDELEKEIHEIN-SLAHVIR 149 (216)
Q Consensus 74 ~~l~~vI~vVDa~~~--~~~l~~~~~~~~~~~~~~QI~~AD-~IvlnK~D~v~~~~~~~~l~~i~~~l~~lN-P~A~iv~ 149 (216)
-..|.-|.|||+.+- +.-++.....+.+..+.+-+.-.. +|.+||.|+++=.+ ..++.|+..|...- -.|.+..
T Consensus 277 sqaD~avLvvd~s~~~FE~gfd~~gQtrEha~llr~Lgi~qlivaiNKmD~V~Wsq--~RF~eIk~~l~~fL~~~~gf~e 354 (603)
T KOG0458|consen 277 SQADVAVLVVDASTGEFESGFDPGGQTREHALLLRSLGISQLIVAINKMDLVSWSQ--DRFEEIKNKLSSFLKESCGFKE 354 (603)
T ss_pred cccceEEEEEECCcchhhhccCCCCchHHHHHHHHHcCcceEEEEeecccccCccH--HHHHHHHHHHHHHHHHhcCccc
Confidence 344556888888753 222221000011122334444444 45679999998654 24555555544433 3445554
Q ss_pred eecCCCChhhhhccCCCCccchhhhhhhh
Q 027979 150 SVRCQVDLSEVLNCRAYDATHVTRLEGLL 178 (216)
Q Consensus 150 ~~~~~v~~~~l~~~~~~~~~~~~~~~~~~ 178 (216)
.+..=||..-+.+...........+..|.
T Consensus 355 s~v~FIPiSGl~GeNL~k~~~~~~l~~WY 383 (603)
T KOG0458|consen 355 SSVKFIPISGLSGENLIKIEQENELSQWY 383 (603)
T ss_pred CCcceEecccccCCcccccccchhhhhhh
Confidence 44333555556555444332222344554
No 263
>KOG0070 consensus GTP-binding ADP-ribosylation factor Arf1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=48.19 E-value=54 Score=26.32 Aligned_cols=55 Identities=24% Similarity=0.223 Sum_probs=30.6
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc-----E-EEEccCCCCCCCCccchHHHHHHHHH
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD-----V-VILNKVDLVSPERSGDSLDELEKEIH 139 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD-----~-IvlnK~D~v~~~~~~~~l~~i~~~l~ 139 (216)
.-+++|.|||+..-...-.. -.++.+++..-+ + |.-||-|+-++- ...++.+.+.
T Consensus 84 ~t~~lIfVvDS~Dr~Ri~ea------k~eL~~~l~~~~l~~~~llv~aNKqD~~~al----s~~ei~~~L~ 144 (181)
T KOG0070|consen 84 NTQGLIFVVDSSDRERIEEA------KEELHRMLAEPELRNAPLLVFANKQDLPGAL----SAAEITNKLG 144 (181)
T ss_pred CCcEEEEEEeCCcHHHHHHH------HHHHHHHHcCcccCCceEEEEechhhccccC----CHHHHHhHhh
Confidence 34678999999855432111 233444444443 3 444899986653 2455555543
No 264
>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=47.96 E-value=1.3e+02 Score=23.26 Aligned_cols=43 Identities=12% Similarity=0.021 Sum_probs=24.4
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc-----cEEEEccCCCCCC
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA-----DVVILNKVDLVSP 124 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A-----D~IvlnK~D~v~~ 124 (216)
..+.++.|+|....... .+ ...+.+.+... =+||.||+|+.+.
T Consensus 73 ~~d~iilv~d~~~~~s~-~~------~~~~~~~i~~~~~~~piilv~nK~Dl~~~ 120 (193)
T cd04118 73 GAKAAIVCYDLTDSSSF-ER------AKFWVKELQNLEEHCKIYLCGTKSDLIEQ 120 (193)
T ss_pred CCCEEEEEEECCCHHHH-HH------HHHHHHHHHhcCCCCCEEEEEEccccccc
Confidence 35778999998765322 11 11122333221 2588899998754
No 265
>PRK13351 elongation factor G; Reviewed
Probab=47.81 E-value=53 Score=31.70 Aligned_cols=66 Identities=20% Similarity=0.185 Sum_probs=37.3
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH---hhccEEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---AFADVVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~~AD~IvlnK~D 120 (216)
....++-|.|..+-....... .-..+.+|.|+|+..-...-. .....++ ..-=++++||+|
T Consensus 73 ~~i~liDtPG~~df~~~~~~~--------l~~aD~~ilVvd~~~~~~~~~--------~~~~~~~~~~~~p~iiviNK~D 136 (687)
T PRK13351 73 HRINLIDTPGHIDFTGEVERS--------LRVLDGAVVVFDAVTGVQPQT--------ETVWRQADRYGIPRLIFINKMD 136 (687)
T ss_pred EEEEEEECCCcHHHHHHHHHH--------HHhCCEEEEEEeCCCCCCHHH--------HHHHHHHHhcCCCEEEEEECCC
Confidence 456778888886543332221 123477899999975322110 0111222 223478899999
Q ss_pred CCCCC
Q 027979 121 LVSPE 125 (216)
Q Consensus 121 ~v~~~ 125 (216)
+...+
T Consensus 137 ~~~~~ 141 (687)
T PRK13351 137 RVGAD 141 (687)
T ss_pred CCCCC
Confidence 98753
No 266
>PRK12723 flagellar biosynthesis regulator FlhF; Provisional
Probab=47.72 E-value=2e+02 Score=25.92 Aligned_cols=108 Identities=22% Similarity=0.248 Sum_probs=59.8
Q ss_pred hhHHHHHHHHHHhcCCCCEEEEecCCCCCcH--HHHHHhhcCcccccceeec-cEEEEEcccchHHHHhhcccCCChhHH
Q 027979 28 HSLVQALEQLVQRKERLDHILLETTGLANPA--PLASVLWLDDQLESAVRLD-SIITVVDAKNLLFQIDKYRHLSSYPEA 104 (216)
Q Consensus 28 ~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~--~i~~~l~~~~~l~~~~~l~-~vI~vVDa~~~~~~l~~~~~~~~~~~~ 104 (216)
.++..+|.++ .+.|+|||=|.|...-. .+.+. ...+ ..+..+ .++.|+||..-...+. +.
T Consensus 243 ~~l~~~L~~~----~~~DlVLIDTaGr~~~~~~~l~el---~~~l-~~~~~~~e~~LVlsat~~~~~~~---------~~ 305 (388)
T PRK12723 243 KDLKEEITQS----KDFDLVLVDTIGKSPKDFMKLAEM---KELL-NACGRDAEFHLAVSSTTKTSDVK---------EI 305 (388)
T ss_pred HHHHHHHHHh----CCCCEEEEcCCCCCccCHHHHHHH---HHHH-HhcCCCCeEEEEEcCCCCHHHHH---------HH
Confidence 4444444433 46899999999997422 21121 0111 111112 5789999987654432 34
Q ss_pred HHHHhh--ccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeecCCCChhhh
Q 027979 105 IHQIAF--ADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQVDLSEV 160 (216)
Q Consensus 105 ~~QI~~--AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~~~l 160 (216)
+.+... -+-+|++|.|-...- -.+...+... +.++.....|+-=+++|
T Consensus 306 ~~~~~~~~~~~~I~TKlDet~~~------G~~l~~~~~~--~~Pi~yit~Gq~vPeDl 355 (388)
T PRK12723 306 FHQFSPFSYKTVIFTKLDETTCV------GNLISLIYEM--RKEVSYVTDGQIVPHNI 355 (388)
T ss_pred HHHhcCCCCCEEEEEeccCCCcc------hHHHHHHHHH--CCCEEEEeCCCCChhhh
Confidence 455543 689999999986643 3344444333 35666666664333344
No 267
>KOG1489 consensus Predicted GTP-binding protein (ODN superfamily) [General function prediction only]
Probab=47.61 E-value=67 Score=28.42 Aligned_cols=48 Identities=21% Similarity=0.266 Sum_probs=25.4
Q ss_pred eeccEEEEEcccchHH--HHhhcccCCChhHH--H--HHHhhccEEEEccCCCCCC
Q 027979 75 RLDSIITVVDAKNLLF--QIDKYRHLSSYPEA--I--HQIAFADVVILNKVDLVSP 124 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~--~l~~~~~~~~~~~~--~--~QI~~AD~IvlnK~D~v~~ 124 (216)
+-+..+.|||.+.+.. -+.....+ ..|+ . .-....-+||.||+|+-+.
T Consensus 274 R~~~l~fVvD~s~~~~~~p~~~~~lL--~~ELe~yek~L~~rp~liVaNKiD~~ea 327 (366)
T KOG1489|consen 274 RCKGLLFVVDLSGKQLRNPWQQLQLL--IEELELYEKGLADRPALIVANKIDLPEA 327 (366)
T ss_pred hhceEEEEEECCCcccCCHHHHHHHH--HHHHHHHhhhhccCceEEEEeccCchhH
Confidence 4456799999998721 00000000 0111 1 1223457899999999644
No 268
>PLN00223 ADP-ribosylation factor; Provisional
Probab=46.18 E-value=1.3e+02 Score=23.38 Aligned_cols=54 Identities=22% Similarity=0.231 Sum_probs=28.4
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHH-----HHHhhcc-EEEEccCCCCCCCCccchHHHHHHHHH
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAI-----HQIAFAD-VVILNKVDLVSPERSGDSLDELEKEIH 139 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~-----~QI~~AD-~IvlnK~D~v~~~~~~~~l~~i~~~l~ 139 (216)
.+.+|.|+|+......-.- ..++. .++...- +|+.||.|+.+.. ..+++.+.+.
T Consensus 85 a~~iI~V~D~s~~~s~~~~------~~~l~~~l~~~~~~~~piilv~NK~Dl~~~~----~~~~~~~~l~ 144 (181)
T PLN00223 85 TQGLIFVVDSNDRDRVVEA------RDELHRMLNEDELRDAVLLVFANKQDLPNAM----NAAEITDKLG 144 (181)
T ss_pred CCEEEEEEeCCcHHHHHHH------HHHHHHHhcCHhhCCCCEEEEEECCCCCCCC----CHHHHHHHhC
Confidence 4779999999865422110 01111 1222233 4555999986643 2455555543
No 269
>TIGR03029 EpsG chain length determinant protein tyrosine kinase EpsG. The proteins in this family are homologs of the EpsG protein found in Methylobacillus strain 12S and are generally found in operons with other Eps homologs. The protein is believed to function as the protein tyrosine kinase component of the chain length regulator (along with the transmembrane component EpsF).
Probab=45.84 E-value=1.1e+02 Score=25.57 Aligned_cols=12 Identities=17% Similarity=0.407 Sum_probs=8.3
Q ss_pred CCCEEEEecCCC
Q 027979 43 RLDHILLETTGL 54 (216)
Q Consensus 43 ~~d~IiIE~sG~ 54 (216)
.+|+|||-+..+
T Consensus 212 ~yD~ViiD~pp~ 223 (274)
T TIGR03029 212 DYDVVIVDTPSA 223 (274)
T ss_pred cCCEEEEeCCCc
Confidence 577777777654
No 270
>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=45.52 E-value=1.3e+02 Score=22.58 Aligned_cols=66 Identities=17% Similarity=0.160 Sum_probs=33.0
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHHHHHh-hcc-----EEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEE
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA-FAD-----VVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVI 148 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~-~AD-----~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv 148 (216)
..+.++.|+|..+-.. +.. ...+..++. .+. ++|-||.|+....+. ..++.....+..+ ++++
T Consensus 72 ~~~~~i~v~d~~~~~s-f~~------~~~~~~~~~~~~~~~~~iilvgnK~Dl~~~~~v--~~~~~~~~~~~~~--~~~~ 140 (161)
T cd04117 72 RAQGIFLVYDISSERS-YQH------IMKWVSDVDEYAPEGVQKILIGNKADEEQKRQV--GDEQGNKLAKEYG--MDFF 140 (161)
T ss_pred CCcEEEEEEECCCHHH-HHH------HHHHHHHHHHhCCCCCeEEEEEECcccccccCC--CHHHHHHHHHHcC--CEEE
Confidence 3567888988775432 111 112222221 122 677799999765421 1233333334343 5666
Q ss_pred Eee
Q 027979 149 RSV 151 (216)
Q Consensus 149 ~~~ 151 (216)
+++
T Consensus 141 e~S 143 (161)
T cd04117 141 ETS 143 (161)
T ss_pred EEe
Confidence 554
No 271
>COG1084 Predicted GTPase [General function prediction only]
Probab=45.35 E-value=51 Score=29.11 Aligned_cols=86 Identities=22% Similarity=0.235 Sum_probs=41.8
Q ss_pred CEEEEecCCCCCc-HHHHHHhhcCcccccceeeccEEEEEcccchH-----HHHhhcccCCChhHHHHHHhhccEEEEcc
Q 027979 45 DHILLETTGLANP-APLASVLWLDDQLESAVRLDSIITVVDAKNLL-----FQIDKYRHLSSYPEAIHQIAFADVVILNK 118 (216)
Q Consensus 45 d~IiIE~sG~a~P-~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~-----~~l~~~~~~~~~~~~~~QI~~AD~IvlnK 118 (216)
.+=+|-|.|+-|= ..=.+.+.....++=+.-=+.|+.++|++-.- .+..= +.++..-+..-=++|+||
T Consensus 216 R~QvIDTPGlLDRPl~ErN~IE~qAi~AL~hl~~~IlF~~D~Se~cgy~lE~Q~~L------~~eIk~~f~~p~v~V~nK 289 (346)
T COG1084 216 RIQVIDTPGLLDRPLEERNEIERQAILALRHLAGVILFLFDPSETCGYSLEEQISL------LEEIKELFKAPIVVVINK 289 (346)
T ss_pred eEEEecCCcccCCChHHhcHHHHHHHHHHHHhcCeEEEEEcCccccCCCHHHHHHH------HHHHHHhcCCCeEEEEec
Confidence 3456788888652 21111111111111122224468899987432 11110 222233333235678899
Q ss_pred CCCCCCCCccchHHHHHHHHHh
Q 027979 119 VDLVSPERSGDSLDELEKEIHE 140 (216)
Q Consensus 119 ~D~v~~~~~~~~l~~i~~~l~~ 140 (216)
+|.++.+ .++++...+..
T Consensus 290 ~D~~~~e----~~~~~~~~~~~ 307 (346)
T COG1084 290 IDIADEE----KLEEIEASVLE 307 (346)
T ss_pred ccccchh----HHHHHHHHHHh
Confidence 9999875 35666655443
No 272
>COG0486 ThdF Predicted GTPase [General function prediction only]
Probab=45.20 E-value=23 Score=32.49 Aligned_cols=73 Identities=25% Similarity=0.318 Sum_probs=43.6
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc---EEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD---VVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD---~IvlnK~D 120 (216)
.-..++-|.|+=+-..+++.+-.....+.-=.-|-|+.|+|+.......+ ..+.. ....+ ++|+||+|
T Consensus 265 ~pv~l~DTAGiRet~d~VE~iGIeRs~~~i~~ADlvL~v~D~~~~~~~~d--------~~~~~-~~~~~~~~i~v~NK~D 335 (454)
T COG0486 265 IPVRLVDTAGIRETDDVVERIGIERAKKAIEEADLVLFVLDASQPLDKED--------LALIE-LLPKKKPIIVVLNKAD 335 (454)
T ss_pred EEEEEEecCCcccCccHHHHHHHHHHHHHHHhCCEEEEEEeCCCCCchhh--------HHHHH-hcccCCCEEEEEechh
Confidence 44567788888887777765433222333344567899999986421111 11223 22232 78889999
Q ss_pred CCCCC
Q 027979 121 LVSPE 125 (216)
Q Consensus 121 ~v~~~ 125 (216)
+.++.
T Consensus 336 L~~~~ 340 (454)
T COG0486 336 LVSKI 340 (454)
T ss_pred ccccc
Confidence 99874
No 273
>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=44.86 E-value=1.6e+02 Score=23.55 Aligned_cols=77 Identities=22% Similarity=0.189 Sum_probs=37.5
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHH---HHHHhh--c-cEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEE
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEA---IHQIAF--A-DVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVI 148 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~---~~QI~~--A-D~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv 148 (216)
.-+++|.|+|..+-... .+ ...+ .++... . =+||.||+|+.+..+. ..+...+..+++ .+..++
T Consensus 72 ~ad~iIlVfDvtd~~Sf-~~------l~~w~~~i~~~~~~~~piilVgNK~DL~~~~~v--~~~~~~~~a~~~-~~~~~~ 141 (202)
T cd04120 72 SAKGIILVYDITKKETF-DD------LPKWMKMIDKYASEDAELLLVGNKLDCETDREI--SRQQGEKFAQQI-TGMRFC 141 (202)
T ss_pred CCCEEEEEEECcCHHHH-HH------HHHHHHHHHHhCCCCCcEEEEEECccccccccc--CHHHHHHHHHhc-CCCEEE
Confidence 35678999998765422 11 1112 222211 1 1567799999754322 223333333333 235666
Q ss_pred Eeec-CCCChhhhh
Q 027979 149 RSVR-CQVDLSEVL 161 (216)
Q Consensus 149 ~~~~-~~v~~~~l~ 161 (216)
+++- ......++|
T Consensus 142 etSAktg~gV~e~F 155 (202)
T cd04120 142 EASAKDNFNVDEIF 155 (202)
T ss_pred EecCCCCCCHHHHH
Confidence 6543 233455554
No 274
>PRK12317 elongation factor 1-alpha; Reviewed
Probab=43.72 E-value=33 Score=30.92 Aligned_cols=37 Identities=16% Similarity=0.347 Sum_probs=22.3
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccc
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKN 87 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~ 87 (216)
+....++-|.|.-+ ....+ ....-..+.++.|||+..
T Consensus 83 ~~~i~liDtpG~~~---~~~~~-----~~~~~~aD~~ilVvDa~~ 119 (425)
T PRK12317 83 KYYFTIVDCPGHRD---FVKNM-----ITGASQADAAVLVVAADD 119 (425)
T ss_pred CeEEEEEECCCccc---chhhH-----hhchhcCCEEEEEEEccc
Confidence 34667888898632 11111 112235778899999974
No 275
>COG1162 Predicted GTPases [General function prediction only]
Probab=43.67 E-value=83 Score=27.37 Aligned_cols=74 Identities=19% Similarity=0.313 Sum_probs=36.4
Q ss_pred CEEEEecCCCCCcHHHHHHh-----hcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccC
Q 027979 45 DHILLETTGLANPAPLASVL-----WLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKV 119 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l-----~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~ 119 (216)
|++++|..-.. .-|...+ ...|........--|++.+++.-=...++.+ =.+..--.-.=+|+|||+
T Consensus 49 D~V~~~~~~~~--g~I~~i~~Rkn~L~Rp~v~n~d~~iiIvs~~~P~~~~~~ldR~------Lv~ae~~gi~pvIvlnK~ 120 (301)
T COG1162 49 DRVVFEDENNN--GVIEKILPRKNVLIRPPVANNDQAIIVVSLVDPDFNTNLLDRY------LVLAEAGGIEPVIVLNKI 120 (301)
T ss_pred CeEEEecCCCc--ceEEEEecccCceeCCcccccceEEEEEeccCCCCCHHHHHHH------HHHHHHcCCcEEEEEEcc
Confidence 89999988543 1111111 1123333333333345555554222222221 011222334458999999
Q ss_pred CCCCCCC
Q 027979 120 DLVSPER 126 (216)
Q Consensus 120 D~v~~~~ 126 (216)
|++++++
T Consensus 121 DL~~~~~ 127 (301)
T COG1162 121 DLLDDEE 127 (301)
T ss_pred ccCcchH
Confidence 9999864
No 276
>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways. Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process
Probab=42.96 E-value=42 Score=25.86 Aligned_cols=66 Identities=17% Similarity=0.296 Sum_probs=40.4
Q ss_pred cceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEE-EEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 72 SAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVV-ILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 72 ~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~I-vlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
.....+.|+.|.||..-... +|.-+.+.-..-+| |+||+|+.+.+ ..+++.++.|+...-. +|+..
T Consensus 60 ta~dad~V~ll~dat~~~~~---------~pP~fa~~f~~pvIGVITK~Dl~~~~---~~i~~a~~~L~~aG~~-~if~v 126 (143)
T PF10662_consen 60 TAQDADVVLLLQDATEPRSV---------FPPGFASMFNKPVIGVITKIDLPSDD---ANIERAKKWLKNAGVK-EIFEV 126 (143)
T ss_pred HHhhCCEEEEEecCCCCCcc---------CCchhhcccCCCEEEEEECccCccch---hhHHHHHHHHHHcCCC-CeEEE
Confidence 34677889999999864422 22222222233444 78999998332 2578888888876554 45543
No 277
>COG2895 CysN GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]
Probab=42.67 E-value=33 Score=30.75 Aligned_cols=83 Identities=20% Similarity=0.244 Sum_probs=43.9
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchH-HHHhhcccCCChhHHHHHHhhccE-EEEccCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLL-FQIDKYRHLSSYPEAIHQIAFADV-VILNKVD 120 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~-~~l~~~~~~~~~~~~~~QI~~AD~-IvlnK~D 120 (216)
+-++||.-|.|=. +-.+.+.+. .=+-+..|.+|||..-. .+-.. ++-+...+..=-+ +.+||+|
T Consensus 85 KRkFIiADTPGHe---QYTRNMaTG-----ASTadlAIlLVDAR~Gvl~QTrR------Hs~I~sLLGIrhvvvAVNKmD 150 (431)
T COG2895 85 KRKFIIADTPGHE---QYTRNMATG-----ASTADLAILLVDARKGVLEQTRR------HSFIASLLGIRHVVVAVNKMD 150 (431)
T ss_pred cceEEEecCCcHH---HHhhhhhcc-----cccccEEEEEEecchhhHHHhHH------HHHHHHHhCCcEEEEEEeeec
Confidence 3467888877753 222222221 12334468888887543 22211 3333444444444 4469999
Q ss_pred CCCCCCccchHHHHHHHHHhh
Q 027979 121 LVSPERSGDSLDELEKEIHEI 141 (216)
Q Consensus 121 ~v~~~~~~~~l~~i~~~l~~l 141 (216)
+++-.+ +..+++++.-..+
T Consensus 151 Lvdy~e--~~F~~I~~dy~~f 169 (431)
T COG2895 151 LVDYSE--EVFEAIVADYLAF 169 (431)
T ss_pred ccccCH--HHHHHHHHHHHHH
Confidence 999765 3555555544433
No 278
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=42.01 E-value=71 Score=25.48 Aligned_cols=104 Identities=13% Similarity=0.150 Sum_probs=62.7
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCC-
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLV- 122 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v- 122 (216)
+|.-+|||+|.+=+...++.+. ....-.+||...|+..--..+.. .+.+.+-.|-...+.|.+..
T Consensus 21 ~d~~~I~T~Gs~i~~~~i~~i~------~~~~~rgVIIfTDpD~~GekIRk--------~i~~~vp~~khafi~~~~a~~ 86 (174)
T TIGR00334 21 FDVDVIETNGSALKDETINLIK------KAQKKQGVIILTDPDFPGEKIRK--------KIEQHLPGYENCFIPKHLAKP 86 (174)
T ss_pred cCceEEEECCCccCHHHHHHHH------HHhhcCCEEEEeCCCCchHHHHH--------HHHHHCCCCeEEeeeHHhcCc
Confidence 5778899999997777776542 33456789999999754333322 12344555777777765543
Q ss_pred -----CCCCccchHHHHHHHHHhhCCCCEEEEeecCCCChhhhhccCCC
Q 027979 123 -----SPERSGDSLDELEKEIHEINSLAHVIRSVRCQVDLSEVLNCRAY 166 (216)
Q Consensus 123 -----~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~~~l~~~~~~ 166 (216)
.-+. ...+.+++.|...... .......+..++++..+..
T Consensus 87 ~~~~iGVE~--As~e~I~~AL~~~~~~---~~~~~~~it~~dl~~~gL~ 130 (174)
T TIGR00334 87 NKKKIGVEE--ASVEAIIAALENVHEE---TKAQQSDISWEDLLELGLI 130 (174)
T ss_pred CCCCcccCC--CCHHHHHHHHHHhccc---ccCcccccCHHHHHHCCCC
Confidence 2222 2356777777654421 1122334778888876654
No 279
>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=41.98 E-value=1.5e+02 Score=22.23 Aligned_cols=67 Identities=16% Similarity=0.098 Sum_probs=32.8
Q ss_pred EEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh------ccEEEEccC
Q 027979 46 HILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF------ADVVILNKV 119 (216)
Q Consensus 46 ~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~------AD~IvlnK~ 119 (216)
.-++.++|.-.-..+..... -..+.+|.|.|..+-... .+.. ..-+...++.. .=+||.||+
T Consensus 51 l~i~Dt~G~~~~~~~~~~~~--------~~~~~~ilv~d~~~~~s~-~~~~---~~~~~i~~~~~~~~~~~piilv~nK~ 118 (165)
T cd04140 51 LQITDTTGSHQFPAMQRLSI--------SKGHAFILVYSVTSKQSL-EELK---PIYELICEIKGNNIEKIPIMLVGNKC 118 (165)
T ss_pred EEEEECCCCCcchHHHHHHh--------hcCCEEEEEEECCCHHHH-HHHH---HHHHHHHHHhcCCCCCCCEEEEEECc
Confidence 34667777654333322211 134567888888764421 1100 00011233321 126888999
Q ss_pred CCCCC
Q 027979 120 DLVSP 124 (216)
Q Consensus 120 D~v~~ 124 (216)
|+...
T Consensus 119 Dl~~~ 123 (165)
T cd04140 119 DESHK 123 (165)
T ss_pred ccccc
Confidence 99663
No 280
>KOG0466 consensus Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=40.32 E-value=20 Score=31.54 Aligned_cols=42 Identities=24% Similarity=0.357 Sum_probs=26.9
Q ss_pred ccEEEE-ccCCCCCCCCccchHHHHHHHHHhhC-CCCEEEEeec
Q 027979 111 ADVVIL-NKVDLVSPERSGDSLDELEKEIHEIN-SLAHVIRSVR 152 (216)
Q Consensus 111 AD~Ivl-nK~D~v~~~~~~~~l~~i~~~l~~lN-P~A~iv~~~~ 152 (216)
-.+++| ||+|++.+++.-+.-+++.++++.-| .+|+|++.+.
T Consensus 180 khiiilQNKiDli~e~~A~eq~e~I~kFi~~t~ae~aPiiPisA 223 (466)
T KOG0466|consen 180 KHIIILQNKIDLIKESQALEQHEQIQKFIQGTVAEGAPIIPISA 223 (466)
T ss_pred ceEEEEechhhhhhHHHHHHHHHHHHHHHhccccCCCceeeehh
Confidence 344444 99999998754344556666776544 4678887543
No 281
>KOG0073 consensus GTP-binding ADP-ribosylation factor-like protein ARL2 [Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=40.29 E-value=57 Score=26.04 Aligned_cols=47 Identities=28% Similarity=0.381 Sum_probs=26.8
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHH--HHHHhhccEEEE-ccCCCCCC
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEA--IHQIAFADVVIL-NKVDLVSP 124 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~--~~QI~~AD~Ivl-nK~D~v~~ 124 (216)
.-+++|.|||.+--.. +.... ....++ -+|++.+-++|+ ||.|+.++
T Consensus 83 stdglIwvvDssD~~r-~~e~~--~~L~~lL~eerlaG~~~Lvlank~dl~~~ 132 (185)
T KOG0073|consen 83 STDGLIWVVDSSDRMR-MQECK--QELTELLVEERLAGAPLLVLANKQDLPGA 132 (185)
T ss_pred ccCeEEEEEECchHHH-HHHHH--HHHHHHHhhhhhcCCceEEEEecCcCccc
Confidence 4678899998854322 22110 001111 378888666555 89998754
No 282
>PRK00741 prfC peptide chain release factor 3; Provisional
Probab=40.12 E-value=79 Score=29.66 Aligned_cols=65 Identities=22% Similarity=0.149 Sum_probs=37.2
Q ss_pred CCEEEEecCCCCCcHH-HHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH---hhccEEEEccC
Q 027979 44 LDHILLETTGLANPAP-LASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---AFADVVILNKV 119 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~-i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~~AD~IvlnK~ 119 (216)
....+|-|.|..+-.. ....+ -..+++|.|+|+..-.... ...+.++. ..-=++++||+
T Consensus 79 ~~inliDTPG~~df~~~~~~~l---------~~aD~aIlVvDa~~gv~~~--------t~~l~~~~~~~~iPiiv~iNK~ 141 (526)
T PRK00741 79 CLINLLDTPGHEDFSEDTYRTL---------TAVDSALMVIDAAKGVEPQ--------TRKLMEVCRLRDTPIFTFINKL 141 (526)
T ss_pred EEEEEEECCCchhhHHHHHHHH---------HHCCEEEEEEecCCCCCHH--------HHHHHHHHHhcCCCEEEEEECC
Confidence 4567888888765433 22222 2468899999997532111 01122222 22346888999
Q ss_pred CCCCCC
Q 027979 120 DLVSPE 125 (216)
Q Consensus 120 D~v~~~ 125 (216)
|+....
T Consensus 142 D~~~a~ 147 (526)
T PRK00741 142 DRDGRE 147 (526)
T ss_pred cccccC
Confidence 987653
No 283
>COG1515 Nfi Deoxyinosine 3'endonuclease (endonuclease V) [DNA replication, recombination, and repair]
Probab=39.66 E-value=29 Score=28.57 Aligned_cols=20 Identities=30% Similarity=0.574 Sum_probs=17.0
Q ss_pred cCCCCEEEEecCCCCCcHHH
Q 027979 41 KERLDHILLETTGLANPAPL 60 (216)
Q Consensus 41 ~~~~d~IiIE~sG~a~P~~i 60 (216)
..+||.|+|.-+|+++|..+
T Consensus 93 ~~~~d~ilVDG~GiaHPR~~ 112 (212)
T COG1515 93 SVKPDLLLVDGHGIAHPRRL 112 (212)
T ss_pred CCCCCEEEEcCcceecCccc
Confidence 45799999999999999643
No 284
>KOG0077 consensus Vesicle coat complex COPII, GTPase subunit SAR1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=39.52 E-value=81 Score=25.28 Aligned_cols=60 Identities=23% Similarity=0.264 Sum_probs=35.7
Q ss_pred ceeeccEEEEEcccchHHHHhhcccCCChhH--HHHHHhhccEEEE-ccCCCCCCCCccchHHHHHHHHH
Q 027979 73 AVRLDSIITVVDAKNLLFQIDKYRHLSSYPE--AIHQIAFADVVIL-NKVDLVSPERSGDSLDELEKEIH 139 (216)
Q Consensus 73 ~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~--~~~QI~~AD~Ivl-nK~D~v~~~~~~~~l~~i~~~l~ 139 (216)
...++++|.+||+.-.......... ... ..++++.+..+|+ ||+|.-.+.. -++++..+-
T Consensus 85 f~~v~~iv~lvda~d~er~~es~~e---ld~ll~~e~la~vp~lilgnKId~p~a~s----e~~l~~~l~ 147 (193)
T KOG0077|consen 85 FPQVDAIVYLVDAYDQERFAESKKE---LDALLSDESLATVPFLILGNKIDIPYAAS----EDELRFHLG 147 (193)
T ss_pred HhhhceeEeeeehhhHHHhHHHHHH---HHHHHhHHHHhcCcceeecccccCCCccc----HHHHHHHHH
Confidence 4567889999999765543222100 111 1367888887766 9999876642 355554443
No 285
>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=38.48 E-value=35 Score=25.04 Aligned_cols=31 Identities=26% Similarity=0.246 Sum_probs=16.1
Q ss_pred EEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec
Q 027979 115 ILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR 152 (216)
Q Consensus 115 vlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~ 152 (216)
++||+|+-.+ ++-.++|++-.|.-+++.++-
T Consensus 1 AaNK~D~~~a-------~~ni~kl~~~~~~~~vVp~SA 31 (109)
T PF08438_consen 1 AANKADLPAA-------DENIEKLKEKYPDEPVVPTSA 31 (109)
T ss_dssp EEE-GGG-S--------HHHHHHHHHHHTT-EEEEE-H
T ss_pred CCcccccccc-------HhHHHHHHHhCCCCceeeccH
Confidence 4799997443 233344444458888887654
No 286
>KOG1490 consensus GTP-binding protein CRFG/NOG1 (ODN superfamily) [General function prediction only]
Probab=38.47 E-value=52 Score=30.93 Aligned_cols=39 Identities=26% Similarity=0.414 Sum_probs=25.1
Q ss_pred cEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 112 DVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 112 D~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
=++++||+|...++...++-+++...+... +.++|+.++
T Consensus 284 ~IlvlNK~D~m~~edL~~~~~~ll~~~~~~-~~v~v~~tS 322 (620)
T KOG1490|consen 284 TILVLNKIDAMRPEDLDQKNQELLQTIIDD-GNVKVVQTS 322 (620)
T ss_pred eEEEeecccccCccccCHHHHHHHHHHHhc-cCceEEEec
Confidence 468899999998876544444555555442 236777644
No 287
>PF12503 CMV_1a_C: Cucumber mosaic virus 1a protein C terminal ; InterPro: IPR022184 This domain family is found in viruses, and is approximately 90 amino acids in length. The family is found in association with PF01443 from PFAM, PF01660 from PFAM. There is a conserved GLG sequence motif. 1a protein is the major virulence factor of the (Cucumber mosaic virus. The Ns strain of CMV causes necrotic lesions to Nicotiana spp. while other strains cause systemic mosaic. The determinant of the pathogenesis of these different strains is the specific amino acid residue at the 461 residue of the 1a protein. ; GO: 0008168 methyltransferase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=38.46 E-value=24 Score=24.49 Aligned_cols=26 Identities=23% Similarity=0.382 Sum_probs=19.0
Q ss_pred cc-CCCceeeeeeeecCCCcEEeecch
Q 027979 3 NE-GEGGALVEEWVELANGCICCTVKH 28 (216)
Q Consensus 3 ne-g~dg~~~~~v~eL~~GCiCCsl~~ 28 (216)
|| |..--+-.+.+-.+.-|+||....
T Consensus 53 Ne~GLGpK~~~ElyiVnk~Cvi~N~~~ 79 (85)
T PF12503_consen 53 NESGLGPKFDGELYIVNKDCVISNSES 79 (85)
T ss_pred cCCCCCcCcCCeEEEEcCcEEEechHH
Confidence 56 555555567788999999998653
No 288
>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=38.40 E-value=1.8e+02 Score=22.22 Aligned_cols=43 Identities=14% Similarity=0.108 Sum_probs=22.8
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHHHHHhh----c-cEEEEccCCCCCC
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF----A-DVVILNKVDLVSP 124 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~----A-D~IvlnK~D~v~~ 124 (216)
-+.+|.|+|..+-... .+. ...+...+.. . =+|+.||+|+...
T Consensus 73 ad~ii~v~d~~~~~s~-~~~-----~~~~~~~~~~~~~~~piilv~nK~Dl~~~ 120 (187)
T cd04132 73 VDVLLICYAVDNPTSL-DNV-----EDKWFPEVNHFCPGTPIMLVGLKTDLRKD 120 (187)
T ss_pred CCEEEEEEECCCHHHH-HHH-----HHHHHHHHHHhCCCCCEEEEEeChhhhhC
Confidence 5778999999764321 110 0011222221 1 1667799998663
No 289
>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]
Probab=38.25 E-value=3.1e+02 Score=24.96 Aligned_cols=110 Identities=21% Similarity=0.253 Sum_probs=64.8
Q ss_pred hhHHHHHHHHHHhcCCCCEEEEecCCCCCc--HHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHH
Q 027979 28 HSLVQALEQLVQRKERLDHILLETTGLANP--APLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAI 105 (216)
Q Consensus 28 ~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P--~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~ 105 (216)
.||..++..+- ..|.|+|-|.|...- ..+.+. ...+.....+ .+..|++|..=... ..+++
T Consensus 270 ~el~~ai~~l~----~~d~ILVDTaGrs~~D~~~i~el---~~~~~~~~~i-~~~Lvlsat~K~~d---------lkei~ 332 (407)
T COG1419 270 KELAEAIEALR----DCDVILVDTAGRSQYDKEKIEEL---KELIDVSHSI-EVYLVLSATTKYED---------LKEII 332 (407)
T ss_pred HHHHHHHHHhh----cCCEEEEeCCCCCccCHHHHHHH---HHHHhccccc-eEEEEEecCcchHH---------HHHHH
Confidence 57888888874 359999999999743 333221 1111222222 24555666533323 33456
Q ss_pred HHHhhc--cEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeecCCCChhhhhc
Q 027979 106 HQIAFA--DVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQVDLSEVLN 162 (216)
Q Consensus 106 ~QI~~A--D~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~~~l~~ 162 (216)
+|.+.. +-+|++|.|-.+. +-.+...+.+- +-+|.....|+-=|++|.-
T Consensus 333 ~~f~~~~i~~~I~TKlDET~s------~G~~~s~~~e~--~~PV~YvT~GQ~VPeDI~v 383 (407)
T COG1419 333 KQFSLFPIDGLIFTKLDETTS------LGNLFSLMYET--RLPVSYVTNGQRVPEDIVV 383 (407)
T ss_pred HHhccCCcceeEEEcccccCc------hhHHHHHHHHh--CCCeEEEeCCCCCCchhhh
Confidence 666665 4689999997664 44555555443 3466666777665666653
No 290
>PRK05306 infB translation initiation factor IF-2; Validated
Probab=38.05 E-value=1.4e+02 Score=29.68 Aligned_cols=63 Identities=27% Similarity=0.288 Sum_probs=33.4
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchH-HHHhhcccCCChhHHHHHHhhc---cEEEEccCC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLL-FQIDKYRHLSSYPEAIHQIAFA---DVVILNKVD 120 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~-~~l~~~~~~~~~~~~~~QI~~A---D~IvlnK~D 120 (216)
...|+-|.|-.+=..+.. ...-..|.+|.|||+..-. .+. . +...++..+ =+|++||+|
T Consensus 338 ~ItfiDTPGhe~F~~m~~--------rga~~aDiaILVVdAddGv~~qT--------~-e~i~~a~~~~vPiIVviNKiD 400 (787)
T PRK05306 338 KITFLDTPGHEAFTAMRA--------RGAQVTDIVVLVVAADDGVMPQT--------I-EAINHAKAAGVPIIVAINKID 400 (787)
T ss_pred EEEEEECCCCccchhHHH--------hhhhhCCEEEEEEECCCCCCHhH--------H-HHHHHHHhcCCcEEEEEECcc
Confidence 345677777654332221 1122356788899886421 110 1 122333322 378889999
Q ss_pred CCCC
Q 027979 121 LVSP 124 (216)
Q Consensus 121 ~v~~ 124 (216)
+.+.
T Consensus 401 l~~a 404 (787)
T PRK05306 401 KPGA 404 (787)
T ss_pred cccc
Confidence 9654
No 291
>PRK14331 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=37.59 E-value=37 Score=30.82 Aligned_cols=49 Identities=20% Similarity=0.152 Sum_probs=31.6
Q ss_pred HhhccEEEEccCCCCCCCCccchHHHHH------HHHHhhCCCCEEEEee-cCCCChhhhh
Q 027979 108 IAFADVVILNKVDLVSPERSGDSLDELE------KEIHEINSLAHVIRSV-RCQVDLSEVL 161 (216)
Q Consensus 108 I~~AD~IvlnK~D~v~~~~~~~~l~~i~------~~l~~lNP~A~iv~~~-~~~v~~~~l~ 161 (216)
...||+||+|=|--...++ ++.+ +.+++.||+++|+.+. +.+..++.++
T Consensus 35 ~~~aDviiiNTC~v~~~a~-----~k~~~~i~~~~~~k~~~p~~~ivv~Gc~a~~~~e~~~ 90 (437)
T PRK14331 35 WEEADLILVNTCTIREKPD-----QKVLSHLGEYKKIKEKNPNALIGVCGCLAQRAGYEIV 90 (437)
T ss_pred cccCCEEEEeCcceecHHH-----HHHHHHHHHHHHHHHhCCCCEEEEEcchhcCChHHHH
Confidence 4569999999887655542 3333 4457889999888643 3344444443
No 292
>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=37.30 E-value=1.9e+02 Score=22.17 Aligned_cols=67 Identities=12% Similarity=0.166 Sum_probs=33.9
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc--c---EEEEcc
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA--D---VVILNK 118 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A--D---~IvlnK 118 (216)
....|..++|-..-..+... .+ -.-+.+|.|.|..+-.. +.+. ...+..++... + +||.||
T Consensus 49 ~~l~i~Dt~G~~~~~~~~~~-----~~---~~a~~~ilv~d~~~~~s-~~~~-----~~~w~~~i~~~~~~~piilvgnK 114 (175)
T cd01874 49 YTLGLFDTAGQEDYDRLRPL-----SY---PQTDVFLVCFSVVSPSS-FENV-----KEKWVPEITHHCPKTPFLLVGTQ 114 (175)
T ss_pred EEEEEEECCCccchhhhhhh-----hc---ccCCEEEEEEECCCHHH-HHHH-----HHHHHHHHHHhCCCCCEEEEEEC
Confidence 34456677777543322211 11 13467888999876432 1110 01122333221 2 678899
Q ss_pred CCCCCC
Q 027979 119 VDLVSP 124 (216)
Q Consensus 119 ~D~v~~ 124 (216)
+|+.+.
T Consensus 115 ~Dl~~~ 120 (175)
T cd01874 115 IDLRDD 120 (175)
T ss_pred HhhhhC
Confidence 998654
No 293
>COG0621 MiaB 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]
Probab=37.19 E-value=35 Score=31.27 Aligned_cols=65 Identities=18% Similarity=0.287 Sum_probs=38.0
Q ss_pred EEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 80 ITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 80 I~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
.-.+|+......+... .+.+..+-...||+||+|-|--.+.++. ..-.....+++.||.+.|+.+
T Consensus 14 ~N~~DSe~m~~~L~~~----G~~~~~~~~~eADvviiNTC~V~~~a~~--k~~~~i~~~~~~~p~~~iiVt 78 (437)
T COG0621 14 MNLYDSERMAGLLEAA----GYEELVEDPEEADVVIINTCAVREKAEQ--KVRSAIGELKKLKPDAKIIVT 78 (437)
T ss_pred ccHHHHHHHHHHHHHc----CCccccCCcccCCEEEEecCeeeehHHH--HHHHHHHHHHHhCCCCEEEEe
Confidence 4456666666655431 0112233445699999999877665431 222233445567899999753
No 294
>TIGR01393 lepA GTP-binding protein LepA. LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function is unknown.
Probab=36.81 E-value=1.7e+02 Score=27.89 Aligned_cols=66 Identities=18% Similarity=0.148 Sum_probs=36.8
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHH--HHHhhccEEEEccCCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAI--HQIAFADVVILNKVDL 121 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~--~QI~~AD~IvlnK~D~ 121 (216)
+...|+-|.|..+-....... .-..+.+|.|+|+..-...- . ...+. .+-..-=++++||+|+
T Consensus 70 ~~l~liDTPG~~dF~~~v~~~--------l~~aD~aILVvDat~g~~~q-t------~~~~~~~~~~~ipiIiViNKiDl 134 (595)
T TIGR01393 70 YVLNLIDTPGHVDFSYEVSRS--------LAACEGALLLVDAAQGIEAQ-T------LANVYLALENDLEIIPVINKIDL 134 (595)
T ss_pred EEEEEEECCCcHHHHHHHHHH--------HHhCCEEEEEecCCCCCCHh-H------HHHHHHHHHcCCCEEEEEECcCC
Confidence 345788999998755443321 12346789999997632110 0 11111 1111223788999998
Q ss_pred CCC
Q 027979 122 VSP 124 (216)
Q Consensus 122 v~~ 124 (216)
.+.
T Consensus 135 ~~~ 137 (595)
T TIGR01393 135 PSA 137 (595)
T ss_pred Ccc
Confidence 654
No 295
>CHL00175 minD septum-site determining protein; Validated
Probab=36.35 E-value=2.5e+02 Score=23.41 Aligned_cols=37 Identities=14% Similarity=0.128 Sum_probs=24.3
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchH
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLL 89 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~ 89 (216)
.+|+|||.+.+..++. ....+. .-+.+|.|+++....
T Consensus 126 ~yD~VIiDtpp~~~~~-~~~~l~---------~aD~viiV~~p~~~s 162 (281)
T CHL00175 126 GYDYILIDCPAGIDVG-FINAIA---------PAQEAIVVTTPEITA 162 (281)
T ss_pred CCCEEEEeCCCCCCHH-HHHHHH---------hcCeeEEEcCCChHH
Confidence 6999999999876442 223331 235678888887543
No 296
>PLN03110 Rab GTPase; Provisional
Probab=36.28 E-value=2.2e+02 Score=22.72 Aligned_cols=76 Identities=12% Similarity=0.080 Sum_probs=37.0
Q ss_pred eccEEEEEcccchHHHHhhcccCCChhHHH---HHHhhcc---EEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEE
Q 027979 76 LDSIITVVDAKNLLFQIDKYRHLSSYPEAI---HQIAFAD---VVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIR 149 (216)
Q Consensus 76 l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~---~QI~~AD---~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~ 149 (216)
.+++|.|+|...-.. +.+ ...+. .+....+ +++.||+|+....+. ..+..+ .+... ...++++
T Consensus 85 ~~~~ilv~d~~~~~s-~~~------~~~~~~~~~~~~~~~~piiiv~nK~Dl~~~~~~--~~~~~~-~l~~~-~~~~~~e 153 (216)
T PLN03110 85 AVGALLVYDITKRQT-FDN------VQRWLRELRDHADSNIVIMMAGNKSDLNHLRSV--AEEDGQ-ALAEK-EGLSFLE 153 (216)
T ss_pred CCEEEEEEECCChHH-HHH------HHHHHHHHHHhCCCCCeEEEEEEChhcccccCC--CHHHHH-HHHHH-cCCEEEE
Confidence 456899999865332 111 11122 2222122 677799998654321 112222 33222 3567776
Q ss_pred eec-CCCChhhhhc
Q 027979 150 SVR-CQVDLSEVLN 162 (216)
Q Consensus 150 ~~~-~~v~~~~l~~ 162 (216)
++- ...+.+.++.
T Consensus 154 ~SA~~g~~v~~lf~ 167 (216)
T PLN03110 154 TSALEATNVEKAFQ 167 (216)
T ss_pred EeCCCCCCHHHHHH
Confidence 543 3445555553
No 297
>cd00550 ArsA_ATPase Oxyanion-translocating ATPase (ArsA). This ATPase is involved in transport of arsenite, antimonite or other oxyanions across biological membranes in all three kingdoms of life. ArsA contains a highly conserved AAA motif present in the AAA+ ATPase superfamily associated with a variety of cellular activities. To form a functional ATP-driven pump, ArsA interacts with the permease ArsB, which is a channel-forming integral membrane protein. One of the most interesting features of ArsA is the allosteric activation by its transport substrates. A divalent cation, typically Mg2+, is required for its enzymatic activity.
Probab=36.26 E-value=2.5e+02 Score=23.29 Aligned_cols=81 Identities=17% Similarity=0.176 Sum_probs=42.8
Q ss_pred HHHHHHhcCCCCEEEEecCCCCCcHHHHHH---hh-cCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh
Q 027979 34 LEQLVQRKERLDHILLETTGLANPAPLASV---LW-LDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA 109 (216)
Q Consensus 34 L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~---l~-~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~ 109 (216)
+.++++ ..++|+|||=|...++...++.. +. ....+. .-..++++.|+.+......- ...+.+++.
T Consensus 116 ~~~~l~-~~~yD~VVvDtpPtg~tlrlL~lp~~l~~~~~~l~-d~~~~~~vlV~~p~~~~~~e--------~~r~~~~L~ 185 (254)
T cd00550 116 FSRYID-EAEYDVVVFDTAPTGHTLRLLSLPTVLSWAREILS-DPERTSFRLVCIPEKMSLYE--------TERAIQELA 185 (254)
T ss_pred HHHHHh-cCCCCEEEECCCCcHHHHHHHHhHHHHHHHHHHhc-CCcceEEEEEeCCChhHHHH--------HHHHHHHHH
Confidence 445554 45899999999887654433321 00 000111 11234578888877543221 112334444
Q ss_pred hcc----EEEEccCCCCCC
Q 027979 110 FAD----VVILNKVDLVSP 124 (216)
Q Consensus 110 ~AD----~IvlnK~D~v~~ 124 (216)
..+ -+|+||...-..
T Consensus 186 ~~g~~v~gvV~N~v~~~~~ 204 (254)
T cd00550 186 KYGIDVDAVIVNQLLPEDV 204 (254)
T ss_pred HCCCCCCEEEEecCccccc
Confidence 443 599999876443
No 298
>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=34.36 E-value=2.2e+02 Score=22.17 Aligned_cols=69 Identities=16% Similarity=0.061 Sum_probs=33.4
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHH---hhccEEEEccCCC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQI---AFADVVILNKVDL 121 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI---~~AD~IvlnK~D~ 121 (216)
...++.+.|...-..+.... .-..+.+|.|+|+..-...- .... -...+.+.. ...=+|++||+|+
T Consensus 48 ~l~i~D~~G~~~~~~~~~~~--------~~~ad~vilv~d~~~~~s~~-~~~~--~~~~i~~~~~~~~~piilv~NK~Dl 116 (198)
T cd04147 48 TLDILDTSGSYSFPAMRKLS--------IQNSDAFALVYAVDDPESFE-EVER--LREEILEVKEDKFVPIVVVGNKADS 116 (198)
T ss_pred EEEEEECCCchhhhHHHHHH--------hhcCCEEEEEEECCCHHHHH-HHHH--HHHHHHHhcCCCCCcEEEEEEcccc
Confidence 34467777764333322211 12356789999987643221 1000 001111111 1223788899999
Q ss_pred CCC
Q 027979 122 VSP 124 (216)
Q Consensus 122 v~~ 124 (216)
...
T Consensus 117 ~~~ 119 (198)
T cd04147 117 LEE 119 (198)
T ss_pred ccc
Confidence 763
No 299
>TIGR01005 eps_transp_fam exopolysaccharide transport protein family. The model describes the exopolysaccharide transport protein family in bacteria. The transport protein is part of a large genetic locus which is associated with exopolysaccharide (EPS) biosynthesis. Detailed molecular characterization and gene fusion analysis revealed atleast seven gene products are involved in the overall regulation, which among other things, include exopolysaccharide biosynthesis, property of conferring virulence and exopolysaccharide export.
Probab=34.15 E-value=1.5e+02 Score=28.88 Aligned_cols=14 Identities=7% Similarity=0.060 Sum_probs=10.1
Q ss_pred CCCCEEEEecCCCC
Q 027979 42 ERLDHILLETTGLA 55 (216)
Q Consensus 42 ~~~d~IiIE~sG~a 55 (216)
..+|+|||-+.++.
T Consensus 654 ~~yD~IiID~pp~~ 667 (754)
T TIGR01005 654 LYSDCVVVDVGTAD 667 (754)
T ss_pred hhCCEEEEcCCCcc
Confidence 35788888877765
No 300
>COG0536 Obg Predicted GTPase [General function prediction only]
Probab=33.69 E-value=60 Score=28.93 Aligned_cols=32 Identities=38% Similarity=0.534 Sum_probs=21.1
Q ss_pred hccEEEEccCCCCCCCCccchHHHHHHHHHhhCCC
Q 027979 110 FADVVILNKVDLVSPERSGDSLDELEKEIHEINSL 144 (216)
Q Consensus 110 ~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~ 144 (216)
-.-+|++||+|+..++ +.++++.+.+.+....
T Consensus 276 K~~ivv~NKiD~~~~~---e~~~~~~~~l~~~~~~ 307 (369)
T COG0536 276 KPRIVVLNKIDLPLDE---EELEELKKALAEALGW 307 (369)
T ss_pred CceEEEEeccCCCcCH---HHHHHHHHHHHHhcCC
Confidence 3456999999965554 2567777777654443
No 301
>TIGR03018 pepcterm_TyrKin exopolysaccharide/PEPCTERM locus tyrosine autokinase. Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine residues are likely to be autophosphorylation sites. Some members of this family are fusion proteins.
Probab=33.50 E-value=2.4e+02 Score=22.41 Aligned_cols=10 Identities=40% Similarity=0.713 Sum_probs=5.6
Q ss_pred EEEEcccchH
Q 027979 80 ITVVDAKNLL 89 (216)
Q Consensus 80 I~vVDa~~~~ 89 (216)
++++|+....
T Consensus 151 ~IiiD~pp~~ 160 (207)
T TIGR03018 151 IIIIDTPPLL 160 (207)
T ss_pred EEEEECCCCc
Confidence 5666665443
No 302
>PRK14329 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=32.30 E-value=51 Score=30.33 Aligned_cols=74 Identities=14% Similarity=0.167 Sum_probs=42.6
Q ss_pred EEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHH------HHHhhCCCCEEEE-eec
Q 027979 80 ITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEK------EIHEINSLAHVIR-SVR 152 (216)
Q Consensus 80 I~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~------~l~~lNP~A~iv~-~~~ 152 (216)
+-.+|+..+...+... .+. .......||+|++|=|--..+++ +++.+ .+++.||.++|+. --+
T Consensus 35 ~N~~dse~~~~~l~~~----G~~-~~~~~~~ADiviiNTC~v~~~a~-----~k~~~~i~~~~~~k~~~p~~~ivvgGc~ 104 (467)
T PRK14329 35 MNFADSEIVASILQMA----GYN-TTENLEEADLVLVNTCSIRDNAE-----QKVRKRLEKFNALKKKNPKLIVGVLGCM 104 (467)
T ss_pred CcHHHHHHHHHHHHHC----cCE-ECCCcccCCEEEEeCcceechHH-----HHHHHHHHHHHHHHhhCCCcEEEEECCh
Confidence 4455666665555331 011 12345679999999887665542 33333 3467899998875 333
Q ss_pred CCCChhhhhcc
Q 027979 153 CQVDLSEVLNC 163 (216)
Q Consensus 153 ~~v~~~~l~~~ 163 (216)
.+..++.++..
T Consensus 105 a~~~~~~~l~~ 115 (467)
T PRK14329 105 AERLKDKLLEE 115 (467)
T ss_pred hcCcHHHHHhc
Confidence 44555555543
No 303
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=32.11 E-value=2e+02 Score=24.09 Aligned_cols=85 Identities=21% Similarity=0.246 Sum_probs=49.3
Q ss_pred EEEEecCCCCCcHHHHHHhhcCccccc--ceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEE-ccCCCC
Q 027979 46 HILLETTGLANPAPLASVLWLDDQLES--AVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVIL-NKVDLV 122 (216)
Q Consensus 46 ~IiIE~sG~a~P~~i~~~l~~~~~l~~--~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~Ivl-nK~D~v 122 (216)
+||+| |.+|...|..++. .-.|.. .+++.++| -.++ ...+.+-.+.||++++ +..|.+
T Consensus 10 RIiVE--GAsDvE~iSkalQ-r~aLG~eYnITisSIi---PTT~-------------~eIA~raaeGADlvlIATDaD~~ 70 (290)
T COG4026 10 RIIVE--GASDVEVISKALQ-RLALGSEYNITISSII---PTTN-------------VEIAKRAAEGADLVLIATDADRV 70 (290)
T ss_pred EEEee--ccchHHHHHHHHH-HhhhcccceeEEEeec---cCch-------------HHHHHHhhccCCEEEEeecCcch
Confidence 57777 6777766666552 222333 34444443 2221 2234577899999998 567776
Q ss_pred CCCCccchHHHHHHHHHhhCCCCEEEEeecC
Q 027979 123 SPERSGDSLDELEKEIHEINSLAHVIRSVRC 153 (216)
Q Consensus 123 ~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~ 153 (216)
.-+ -.+++.+.++..-.+..-+...+|
T Consensus 71 GRe----LA~kf~eeLrg~VGhiERmK~PiG 97 (290)
T COG4026 71 GRE----LAEKFFEELRGMVGHIERMKIPIG 97 (290)
T ss_pred hHH----HHHHHHHHHHHhhhhhheeccCCC
Confidence 642 346777778877666555544443
No 304
>PRK11519 tyrosine kinase; Provisional
Probab=32.07 E-value=1.8e+02 Score=28.41 Aligned_cols=14 Identities=21% Similarity=0.465 Sum_probs=9.9
Q ss_pred CCCCEEEEecCCCC
Q 027979 42 ERLDHILLETTGLA 55 (216)
Q Consensus 42 ~~~d~IiIE~sG~a 55 (216)
.++|+|||-+..+.
T Consensus 634 ~~yD~ViiDtpP~~ 647 (719)
T PRK11519 634 KNYDLVLIDTPPIL 647 (719)
T ss_pred hcCCEEEEeCCCcc
Confidence 35788888777654
No 305
>PRK14464 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=31.91 E-value=57 Score=28.92 Aligned_cols=37 Identities=19% Similarity=0.562 Sum_probs=24.1
Q ss_pred CCcEEeecc----------hhHHHHHHHHHHhcCCCCEEEEecCCCCCcH
Q 027979 19 NGCICCTVK----------HSLVQALEQLVQRKERLDHILLETTGLANPA 58 (216)
Q Consensus 19 ~GCiCCsl~----------~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~ 58 (216)
-||..|... ++.+.++..+.. ..+++.|++ +|+++|.
T Consensus 108 ~~C~FC~tg~~g~~RnLs~~EI~~Qv~~~~~-~~~i~nIVf--mGmGEPl 154 (344)
T PRK14464 108 VGCVFCMTGRSGLLRQLGSAEIVAQVVLARR-RRAVKKVVF--MGMGEPA 154 (344)
T ss_pred CCCCcCcCCCCCCCCCCCHHHHHHHHHHHHh-cCCCCEEEE--eccCccc
Confidence 467778422 566666666544 345788875 7888885
No 306
>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=31.39 E-value=33 Score=29.14 Aligned_cols=67 Identities=16% Similarity=0.306 Sum_probs=35.1
Q ss_pred eeeccEEEEEcccch-HHHHhhcccCCChhHHHHHHhh--ccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEe
Q 027979 74 VRLDSIITVVDAKNL-LFQIDKYRHLSSYPEAIHQIAF--ADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRS 150 (216)
Q Consensus 74 ~~l~~vI~vVDa~~~-~~~l~~~~~~~~~~~~~~QI~~--AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~ 150 (216)
-+++.++.++++..- ...++ -++.+++.. -=++|+||+|+++.++.....+.+.+.++..+ .+++..
T Consensus 113 ~rvh~~ly~i~~~~~~l~~~D--------~~~lk~l~~~v~vi~VinK~D~l~~~e~~~~k~~i~~~l~~~~--i~~~~~ 182 (276)
T cd01850 113 TRVHACLYFIEPTGHGLKPLD--------IEFMKRLSKRVNIIPVIAKADTLTPEELKEFKQRIMEDIEEHN--IKIYKF 182 (276)
T ss_pred CceEEEEEEEeCCCCCCCHHH--------HHHHHHHhccCCEEEEEECCCcCCHHHHHHHHHHHHHHHHHcC--CceECC
Confidence 357778899988641 11110 012344432 23678899999886432122334444555443 556543
No 307
>KOG2485 consensus Conserved ATP/GTP binding protein [General function prediction only]
Probab=31.35 E-value=45 Score=29.29 Aligned_cols=85 Identities=21% Similarity=0.203 Sum_probs=45.7
Q ss_pred CCEEEEecCCC--CCcHHHHHHhhcCccccccee-eccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc-cEEEEccC
Q 027979 44 LDHILLETTGL--ANPAPLASVLWLDDQLESAVR-LDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA-DVVILNKV 119 (216)
Q Consensus 44 ~d~IiIE~sG~--a~P~~i~~~l~~~~~l~~~~~-l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A-D~IvlnK~ 119 (216)
+.++..+.++- |-|..++.++. .++..+. +|-||=|=||.--+... .+.+.+++.-. -+||+||+
T Consensus 15 ~~~~~~~~~~~~~wfpgHmakalr---~i~~~l~~~D~iiEvrDaRiPLssr--------n~~~~~~~~~k~riiVlNK~ 83 (335)
T KOG2485|consen 15 DAVIFAKYNMPRRWFPGHMAKALR---AIQNRLPLVDCIIEVRDARIPLSSR--------NELFQDFLPPKPRIIVLNKM 83 (335)
T ss_pred hcccccccCCccccCchHHHHHHH---HHHhhcccccEEEEeeccccCCccc--------cHHHHHhcCCCceEEEEecc
Confidence 34455555543 56777776653 2233333 34567777776443211 12234555532 47888999
Q ss_pred CCCCCCCccchHHHHHHHHHhhCC
Q 027979 120 DLVSPERSGDSLDELEKEIHEINS 143 (216)
Q Consensus 120 D~v~~~~~~~~l~~i~~~l~~lNP 143 (216)
|++++.+ ...+.+.++.-|-
T Consensus 84 DLad~~~----~k~~iq~~~~~~~ 103 (335)
T KOG2485|consen 84 DLADPKE----QKKIIQYLEWQNL 103 (335)
T ss_pred cccCchh----hhHHHHHHHhhcc
Confidence 9999532 3444444444333
No 308
>PRK14337 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=31.11 E-value=52 Score=30.02 Aligned_cols=64 Identities=17% Similarity=0.145 Sum_probs=36.2
Q ss_pred EEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHH--HHHHhhCCCCEEEEe
Q 027979 80 ITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELE--KEIHEINSLAHVIRS 150 (216)
Q Consensus 80 I~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~--~~l~~lNP~A~iv~~ 150 (216)
+-.+|+..+...+... .+.. ... +.||+||||=|--...++. ...+.+. +.+++.||.++|+.+
T Consensus 15 ~N~~dse~~~~~l~~~----G~~~-~~~-~~ADiiiiNTC~v~~~A~~-~~~~~i~~~~~~k~~~p~~~ivv~ 80 (446)
T PRK14337 15 MNVNDSDWLARALVAR----GFTE-APE-EEARVFIVNTCSVRDKPEQ-KVYSLLGRIRHATKKNPDVFVAVG 80 (446)
T ss_pred CcHHHHHHHHHHHHHC----CCEE-CCc-CCCCEEEEeccCeecHHHH-HHHHHHHHHHHHHHhCCCCEEEEE
Confidence 4556777666666431 1211 122 5699999998876655431 1122222 224667899988753
No 309
>PRK07560 elongation factor EF-2; Reviewed
Probab=30.51 E-value=1.2e+02 Score=29.62 Aligned_cols=63 Identities=24% Similarity=0.228 Sum_probs=36.2
Q ss_pred CCEEEEecCCCCCcHHHH-HHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHH---HhhccEEEEccC
Q 027979 44 LDHILLETTGLANPAPLA-SVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQ---IAFADVVILNKV 119 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~-~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~Q---I~~AD~IvlnK~ 119 (216)
.-..+|-|.|..+-..-+ ..+ -..|.+|.|||+......- -....+| ...-=++++||+
T Consensus 87 ~~i~liDtPG~~df~~~~~~~l---------~~~D~avlVvda~~g~~~~--------t~~~~~~~~~~~~~~iv~iNK~ 149 (731)
T PRK07560 87 YLINLIDTPGHVDFGGDVTRAM---------RAVDGAIVVVDAVEGVMPQ--------TETVLRQALRERVKPVLFINKV 149 (731)
T ss_pred EEEEEEcCCCccChHHHHHHHH---------HhcCEEEEEEECCCCCCcc--------HHHHHHHHHHcCCCeEEEEECc
Confidence 345689999987743222 222 2357889999987542110 0112222 122348999999
Q ss_pred CCCC
Q 027979 120 DLVS 123 (216)
Q Consensus 120 D~v~ 123 (216)
|+..
T Consensus 150 D~~~ 153 (731)
T PRK07560 150 DRLI 153 (731)
T ss_pred hhhc
Confidence 9874
No 310
>TIGR01968 minD_bact septum site-determining protein MinD. This model describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model.
Probab=30.25 E-value=2.9e+02 Score=22.27 Aligned_cols=46 Identities=13% Similarity=0.233 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhcCCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccch
Q 027979 30 LVQALEQLVQRKERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNL 88 (216)
Q Consensus 30 l~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~ 88 (216)
+...|..+. ..+|+|||.+.|..... ....+. .-+.+|.++.+...
T Consensus 101 l~~~l~~l~---~~~D~viiD~p~~~~~~-~~~~l~---------~aD~viiv~~~~~~ 146 (261)
T TIGR01968 101 MKKLVNELK---EEFDYVIIDCPAGIESG-FRNAVA---------PADEAIVVTTPEVS 146 (261)
T ss_pred HHHHHHHHH---HhCCEEEEeCCCCcCHH-HHHHHH---------hCCeEEEEcCCCcH
Confidence 444555553 25899999998765442 222221 23457888888744
No 311
>PF08123 DOT1: Histone methylation protein DOT1 ; InterPro: IPR013110 The DOT1 domain regulates gene expression by methylating histone H3 []. H3 methylation by DOT1 has been shown to be required for the DNA damage checkpoint in yeast [].; GO: 0018024 histone-lysine N-methyltransferase activity; PDB: 4ER3_A 4ER6_A 4EQZ_A 1NW3_A 3UWP_A 4ER5_A 3QOX_A 3SX0_A 4ER7_A 3SR4_A ....
Probab=30.24 E-value=74 Score=25.90 Aligned_cols=39 Identities=26% Similarity=0.282 Sum_probs=25.6
Q ss_pred HhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee
Q 027979 108 IAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 108 I~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
++.||+|++|..-- +++ ...++.+.+..+.|+++|+.+.
T Consensus 120 ~s~AdvVf~Nn~~F-~~~----l~~~L~~~~~~lk~G~~IIs~~ 158 (205)
T PF08123_consen 120 WSDADVVFVNNTCF-DPD----LNLALAELLLELKPGARIISTK 158 (205)
T ss_dssp GHC-SEEEE--TTT--HH----HHHHHHHHHTTS-TT-EEEESS
T ss_pred hcCCCEEEEecccc-CHH----HHHHHHHHHhcCCCCCEEEECC
Confidence 48999999998733 322 4678889999999999998754
No 312
>COG5258 GTPBP1 GTPase [General function prediction only]
Probab=30.20 E-value=52 Score=30.00 Aligned_cols=37 Identities=16% Similarity=0.435 Sum_probs=25.3
Q ss_pred HHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCC
Q 027979 107 QIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINS 143 (216)
Q Consensus 107 QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP 143 (216)
-++.-=+|+++|+|+++++......+++.+.|+..+.
T Consensus 253 a~~lPviVvvTK~D~~~ddr~~~v~~ei~~~Lk~v~R 289 (527)
T COG5258 253 AMELPVIVVVTKIDMVPDDRFQGVVEEISALLKRVGR 289 (527)
T ss_pred hhcCCEEEEEEecccCcHHHHHHHHHHHHHHHHHhcc
Confidence 4555668999999999986544445566666665554
No 313
>TIGR00313 cobQ cobyric acid synthase CobQ.
Probab=29.65 E-value=3.2e+02 Score=25.19 Aligned_cols=13 Identities=23% Similarity=0.478 Sum_probs=10.9
Q ss_pred CCCCEEEEecCCC
Q 027979 42 ERLDHILLETTGL 54 (216)
Q Consensus 42 ~~~d~IiIE~sG~ 54 (216)
.++|+||||..|-
T Consensus 121 ~~~D~vIIEGaGG 133 (475)
T TIGR00313 121 REYDYVVIEGAGS 133 (475)
T ss_pred hcCCEEEEECCCC
Confidence 3689999999973
No 314
>KOG0072 consensus GTP-binding ADP-ribosylation factor-like protein ARL1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.11 E-value=1.6e+02 Score=23.15 Aligned_cols=48 Identities=21% Similarity=0.172 Sum_probs=26.2
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHH-HHHHhhccEEE-EccCCCCCC
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEA-IHQIAFADVVI-LNKVDLVSP 124 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~-~~QI~~AD~Iv-lnK~D~v~~ 124 (216)
..+.+|.|||+.+....--.... -+..+ .+.+..|-++| .||.|....
T Consensus 85 dt~avIyVVDssd~dris~a~~e--l~~mL~E~eLq~a~llv~anKqD~~~~ 134 (182)
T KOG0072|consen 85 DTDAVIYVVDSSDRDRISIAGVE--LYSMLQEEELQHAKLLVFANKQDYSGA 134 (182)
T ss_pred ccceEEEEEeccchhhhhhhHHH--HHHHhccHhhcCceEEEEeccccchhh
Confidence 46889999999876432111000 00111 14556666554 599997543
No 315
>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=29.09 E-value=2.3e+02 Score=20.76 Aligned_cols=90 Identities=18% Similarity=0.265 Sum_probs=49.7
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh-----hccEEEE-c
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA-----FADVVIL-N 117 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~-----~AD~Ivl-n 117 (216)
...-+.+++|...-..+...+. -..+.+|.+.|..+-... .. ...+..++. ..-++|+ |
T Consensus 48 ~~l~i~D~~g~~~~~~~~~~~~--------~~~~~~ii~fd~~~~~S~-~~------~~~~~~~i~~~~~~~~~iivvg~ 112 (162)
T PF00071_consen 48 VNLEIWDTSGQERFDSLRDIFY--------RNSDAIIIVFDVTDEESF-EN------LKKWLEEIQKYKPEDIPIIVVGN 112 (162)
T ss_dssp EEEEEEEETTSGGGHHHHHHHH--------TTESEEEEEEETTBHHHH-HT------HHHHHHHHHHHSTTTSEEEEEEE
T ss_pred cccccccccccccccccccccc--------cccccccccccccccccc-cc------cccccccccccccccccceeeec
Confidence 3456677888654444433322 235677888888764432 11 222222222 2344444 9
Q ss_pred cCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec
Q 027979 118 KVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR 152 (216)
Q Consensus 118 K~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~ 152 (216)
|.|+.+..+. ..++.++..++.+ .+.++++.
T Consensus 113 K~D~~~~~~v--~~~~~~~~~~~~~--~~~~e~Sa 143 (162)
T PF00071_consen 113 KSDLSDEREV--SVEEAQEFAKELG--VPYFEVSA 143 (162)
T ss_dssp TTTGGGGSSS--CHHHHHHHHHHTT--SEEEEEBT
T ss_pred cccccccccc--hhhHHHHHHHHhC--CEEEEEEC
Confidence 9998764332 4566777777766 77777553
No 316
>KOG2423 consensus Nucleolar GTPase [General function prediction only]
Probab=28.92 E-value=57 Score=29.85 Aligned_cols=45 Identities=20% Similarity=0.178 Sum_probs=30.0
Q ss_pred EEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEE---EeecCCCChhhhh
Q 027979 113 VVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVI---RSVRCQVDLSEVL 161 (216)
Q Consensus 113 ~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv---~~~~~~v~~~~l~ 161 (216)
+.||||+||+.. +..++..+.+.+..|..... ..++|.-.+-.||
T Consensus 248 i~vLNKvDLVPt----wvt~~Wv~~lSkeyPTiAfHAsi~nsfGKgalI~ll 295 (572)
T KOG2423|consen 248 IYVLNKVDLVPT----WVTAKWVRHLSKEYPTIAFHASINNSFGKGALIQLL 295 (572)
T ss_pred EEEeeccccccH----HHHHHHHHHHhhhCcceeeehhhcCccchhHHHHHH
Confidence 568899999986 46677778888888865554 3344544444444
No 317
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=28.75 E-value=82 Score=20.82 Aligned_cols=35 Identities=14% Similarity=0.278 Sum_probs=24.5
Q ss_pred CCCceeeeeeeecCCCcEEe-ecchhHHHHHHHHHH
Q 027979 5 GEGGALVEEWVELANGCICC-TVKHSLVQALEQLVQ 39 (216)
Q Consensus 5 g~dg~~~~~v~eL~~GCiCC-sl~~dl~~~L~~l~~ 39 (216)
|+.+.++.--.+++.||-=| -...+-.+.+.++++
T Consensus 25 gi~~~liP~P~~i~~~CG~al~~~~~d~~~i~~~l~ 60 (73)
T PF11823_consen 25 GIPVRLIPTPREISAGCGLALRFEPEDLEKIKEILE 60 (73)
T ss_pred CCcEEEeCCChhccCCCCEEEEEChhhHHHHHHHHH
Confidence 77788777777889998544 455555666777765
No 318
>KOG0071 consensus GTP-binding ADP-ribosylation factor Arf6 (dArf3) [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.50 E-value=1.8e+02 Score=22.80 Aligned_cols=53 Identities=26% Similarity=0.321 Sum_probs=31.2
Q ss_pred ccEEEEEcccchHHHHhhcccCCChhHH-----HHHHhhccEEEE-ccCCCCCCCCccchHHHHHHHHH
Q 027979 77 DSIITVVDAKNLLFQIDKYRHLSSYPEA-----IHQIAFADVVIL-NKVDLVSPERSGDSLDELEKEIH 139 (216)
Q Consensus 77 ~~vI~vVDa~~~~~~l~~~~~~~~~~~~-----~~QI~~AD~Ivl-nK~D~v~~~~~~~~l~~i~~~l~ 139 (216)
.++|.|+|+..- +.+... -.|+ -+|.+.+=++|+ ||-|+.++- ..+++...+.
T Consensus 86 qglIFV~Dsa~~-dr~eeA-----r~ELh~ii~~~em~~~~~LvlANkQDlp~A~----~pqei~d~le 144 (180)
T KOG0071|consen 86 QGLIFVVDSADR-DRIEEA-----RNELHRIINDREMRDAIILILANKQDLPDAM----KPQEIQDKLE 144 (180)
T ss_pred ceEEEEEeccch-hhHHHH-----HHHHHHHhCCHhhhcceEEEEecCccccccc----CHHHHHHHhc
Confidence 467999998754 222211 1122 167776666555 899987764 3466666553
No 319
>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=28.38 E-value=3.3e+02 Score=22.17 Aligned_cols=65 Identities=22% Similarity=0.250 Sum_probs=34.4
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHH---HHHhhcc---EEEEc
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAI---HQIAFAD---VVILN 117 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~---~QI~~AD---~Ivln 117 (216)
+...|..+.|--....+..... -..+.+|.|+|...-... .+ ..... .+....+ +||.|
T Consensus 44 ~~l~iwDt~G~e~~~~l~~~~~--------~~ad~~IlV~Dvt~~~Sf-~~------l~~~~~~l~~~~~~~~piIlVgN 108 (220)
T cd04126 44 YNISIWDTAGREQFHGLGSMYC--------RGAAAVILTYDVSNVQSL-EE------LEDRFLGLTDTANEDCLFAVVGN 108 (220)
T ss_pred EEEEEEeCCCcccchhhHHHHh--------ccCCEEEEEEECCCHHHH-HH------HHHHHHHHHHhcCCCCcEEEEEE
Confidence 3455677777654444433221 245778999998864321 11 11111 1222222 57779
Q ss_pred cCCCCC
Q 027979 118 KVDLVS 123 (216)
Q Consensus 118 K~D~v~ 123 (216)
|+|+.+
T Consensus 109 K~DL~~ 114 (220)
T cd04126 109 KLDLTE 114 (220)
T ss_pred Cccccc
Confidence 999976
No 320
>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.
Probab=28.34 E-value=1.3e+02 Score=21.04 Aligned_cols=10 Identities=50% Similarity=0.517 Sum_probs=6.4
Q ss_pred HhhccEEEEc
Q 027979 108 IAFADVVILN 117 (216)
Q Consensus 108 I~~AD~Ivln 117 (216)
+..+|.+++-
T Consensus 71 ~~~~d~~ilv 80 (119)
T PF08477_consen 71 LKKADAVILV 80 (119)
T ss_dssp HHHSCEEEEE
T ss_pred hhcCcEEEEE
Confidence 6667766663
No 321
>KOG0094 consensus GTPase Rab6/YPT6/Ryh1, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.95 E-value=90 Score=25.66 Aligned_cols=44 Identities=23% Similarity=0.420 Sum_probs=27.1
Q ss_pred EEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEee-cCCCChhhhhc
Q 027979 115 ILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSV-RCQVDLSEVLN 162 (216)
Q Consensus 115 vlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~-~~~v~~~~l~~ 162 (216)
|-||+||+++.+. ..++-...-+++|- ..++++ ....+.+.+++
T Consensus 134 VGnKtDL~dkrqv--s~eEg~~kAkel~a--~f~etsak~g~NVk~lFr 178 (221)
T KOG0094|consen 134 VGNKTDLSDKRQV--SIEEGERKAKELNA--EFIETSAKAGENVKQLFR 178 (221)
T ss_pred Ecccccccchhhh--hHHHHHHHHHHhCc--EEEEecccCCCCHHHHHH
Confidence 3399999998753 55555566667764 555433 33455666653
No 322
>PRK03659 glutathione-regulated potassium-efflux system protein KefB; Provisional
Probab=27.85 E-value=3.9e+02 Score=25.42 Aligned_cols=113 Identities=12% Similarity=0.137 Sum_probs=68.6
Q ss_pred ecCCCcEEeecchhHHHHHHHHHHhcCCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhc
Q 027979 16 ELANGCICCTVKHSLVQALEQLVQRKERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKY 95 (216)
Q Consensus 16 eL~~GCiCCsl~~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~ 95 (216)
+..+.-|=|+.. .+-..+.+.+. +.+.++++||. ||..+-. +. + .+.-+..=|+.+.... .
T Consensus 398 ~~~~~vII~G~G-r~G~~va~~L~-~~g~~vvvID~----d~~~v~~-~~-~--------~g~~v~~GDat~~~~L-~-- 458 (601)
T PRK03659 398 DDKPQVIIVGFG-RFGQVIGRLLM-ANKMRITVLER----DISAVNL-MR-K--------YGYKVYYGDATQLELL-R-- 458 (601)
T ss_pred cccCCEEEecCc-hHHHHHHHHHH-hCCCCEEEEEC----CHHHHHH-HH-h--------CCCeEEEeeCCCHHHH-H--
Confidence 345666667654 35666666555 45678999995 4654433 21 1 1223556677654321 1
Q ss_pred ccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeecCCCChhhhhcc
Q 027979 96 RHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQVDLSEVLNC 163 (216)
Q Consensus 96 ~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~~~l~~~ 163 (216)
...+..||.+|+.--|.. .-..+...+|+.||+.+|+...+.+-..+.+...
T Consensus 459 ---------~agi~~A~~vv~~~~d~~-------~n~~i~~~~r~~~p~~~IiaRa~~~~~~~~L~~~ 510 (601)
T PRK03659 459 ---------AAGAEKAEAIVITCNEPE-------DTMKIVELCQQHFPHLHILARARGRVEAHELLQA 510 (601)
T ss_pred ---------hcCCccCCEEEEEeCCHH-------HHHHHHHHHHHHCCCCeEEEEeCCHHHHHHHHhC
Confidence 135778999999855531 2246667889999999999766655555555443
No 323
>PRK01077 cobyrinic acid a,c-diamide synthase; Validated
Probab=27.84 E-value=3.4e+02 Score=24.71 Aligned_cols=45 Identities=20% Similarity=0.193 Sum_probs=22.4
Q ss_pred CCCCEEEEecC-CCCCcHHHHHHhhcCcccccceeeccEEEEEcccc
Q 027979 42 ERLDHILLETT-GLANPAPLASVLWLDDQLESAVRLDSIITVVDAKN 87 (216)
Q Consensus 42 ~~~d~IiIE~s-G~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~ 87 (216)
.+.|++|||-+ |+.++.+....-.....+...+.+ .+|.|+|+..
T Consensus 80 ~~~D~vlVEGagGl~~g~~~~~~~~s~adiA~~l~~-pviLV~~~~~ 125 (451)
T PRK01077 80 QGADIAVIEGVMGLFDGAGSDPDEGSTADIAKLLGA-PVVLVVDASG 125 (451)
T ss_pred ccCCEEEEECCCccccCCccCCCCCCHHHHHHHhCC-CEEEEECCch
Confidence 35899999998 454431100000000111222222 4888999875
No 324
>TIGR00347 bioD dethiobiotin synthase. Dethiobiotin synthase is involved in biotin biosynthesis and catalyses the reaction (CO2 + 7,8-diaminononanoate + ATP = dethiobiotin + phosphate + ADP). The enzyme binds ATP (see motif in first 12 residues of the SEED alignment) and requires magnesium as a co-factor.
Probab=27.75 E-value=67 Score=24.47 Aligned_cols=23 Identities=30% Similarity=0.533 Sum_probs=15.2
Q ss_pred hHHHHHHHHHHhcCCCCEEEEecCCC
Q 027979 29 SLVQALEQLVQRKERLDHILLETTGL 54 (216)
Q Consensus 29 dl~~~L~~l~~~~~~~d~IiIE~sG~ 54 (216)
++.+.+.++ ...+|+||||+.|-
T Consensus 88 ~i~~~~~~l---~~~~D~viid~~g~ 110 (166)
T TIGR00347 88 ELSKHLRTL---EQKYDFVLVEGAGG 110 (166)
T ss_pred HHHHHHHHH---HhcCCEEEEEcCCc
Confidence 344445443 24689999999974
No 325
>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=27.33 E-value=75 Score=27.71 Aligned_cols=42 Identities=17% Similarity=0.175 Sum_probs=22.7
Q ss_pred EEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec-CCCChhhhh
Q 027979 113 VVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR-CQVDLSEVL 161 (216)
Q Consensus 113 ~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~-~~v~~~~l~ 161 (216)
++++||+|+.+.+ +..+.++...+...++..+- ...++..+.
T Consensus 218 I~VlNK~Dl~~~~-------~~~~~l~~~~~~~~iI~iSA~~e~~L~~L~ 260 (318)
T cd01899 218 VIAANKADIPDAE-------NNISKLRLKYPDEIVVPTSAEAELALRRAA 260 (318)
T ss_pred EEEEEHHHccChH-------HHHHHHHhhCCCCeEEEEeCcccccHHHHH
Confidence 4888999986543 22334444445566665332 234454444
No 326
>PRK14340 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=26.90 E-value=61 Score=29.63 Aligned_cols=77 Identities=16% Similarity=0.064 Sum_probs=41.3
Q ss_pred EEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHH--HHHHhhCCCCEEEEe-ecCCCC
Q 027979 80 ITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELE--KEIHEINSLAHVIRS-VRCQVD 156 (216)
Q Consensus 80 I~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~--~~l~~lNP~A~iv~~-~~~~v~ 156 (216)
.-.+|+..+...+... .+ +...-.+.||+||+|=|--...++. .....++ +.+++.||.++|+.+ =+.+..
T Consensus 18 ~N~~dse~~~~~l~~~----G~-~~~~~~~~ADviiiNTC~v~~~A~~-k~~~~i~~~~~~k~~~~~~~ivv~GC~a~~~ 91 (445)
T PRK14340 18 MNQADSEIITALLQDE----GY-VPAASEEDADIVLLNTCAVRENAVE-RIGHYLQHLKGAKRRRKGLLVGVLGCVPQYE 91 (445)
T ss_pred CcHHHHHHHHHHHHHC----cC-EECCCcccCCEEEEEeeeeeccHHH-HHHHHHHHHHHHhhcCCCCEEEEeCcccccc
Confidence 4556666666665431 01 1123345699999999877665431 1122222 134567999887752 223344
Q ss_pred hhhhhc
Q 027979 157 LSEVLN 162 (216)
Q Consensus 157 ~~~l~~ 162 (216)
.+.+..
T Consensus 92 ~~e~~~ 97 (445)
T PRK14340 92 REEMFS 97 (445)
T ss_pred hHHHHh
Confidence 445443
No 327
>cd02035 ArsA ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two subunits, the catalytic ArsA subunit and the membrane subunit ArsB, which are encoded by arsA and arsB genes respectively. Arsenic efflux in bacteria is catalyzed by either ArsB alone or by ArsAB complex. The ATP-coupled pump, however, is more efficient. ArsA is composed of two homologous halves, A1 and A2, connected by a short linker sequence.
Probab=26.42 E-value=3.4e+02 Score=21.75 Aligned_cols=67 Identities=24% Similarity=0.216 Sum_probs=35.3
Q ss_pred CCCEEEEecCCCCCcHHHH-HHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc----cEEEEc
Q 027979 43 RLDHILLETTGLANPAPLA-SVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA----DVVILN 117 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~-~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A----D~Ivln 117 (216)
++|+|||=+.........+ .....+ -..+.++.|+.+......- ...+.+.++.. .-+|+|
T Consensus 113 ~yD~IIiD~pp~~~~~~~l~~~~l~~------~~~~~vllV~~p~~~s~~~--------~~~~l~~l~~~~~~~~glVlN 178 (217)
T cd02035 113 LYDVIVFDTAPTGHTLRLLVRELLTD------PERTSFRLVTLPEKLPLYE--------TERAITELALYGIPVDAVVVN 178 (217)
T ss_pred CCCEEEECCCCchHHHHHHHHHHccC------CCceEEEEEeCCCccHHHH--------HHHHHHHHHHCCCCCCEEEEe
Confidence 4999999988654332221 111111 1235678888887543211 11223344333 358999
Q ss_pred cCCCCC
Q 027979 118 KVDLVS 123 (216)
Q Consensus 118 K~D~v~ 123 (216)
|.....
T Consensus 179 ~~~~~~ 184 (217)
T cd02035 179 RVLPAE 184 (217)
T ss_pred CCcCcc
Confidence 987543
No 328
>PLN03071 GTP-binding nuclear protein Ran; Provisional
Probab=26.29 E-value=2e+02 Score=23.19 Aligned_cols=65 Identities=18% Similarity=0.165 Sum_probs=34.4
Q ss_pred CEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh-----hccEEEEccC
Q 027979 45 DHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA-----FADVVILNKV 119 (216)
Q Consensus 45 d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~-----~AD~IvlnK~ 119 (216)
..-+..++|......+..... -.-+.+|.|+|..+-...- + ...+..+|. ..=+||.||+
T Consensus 63 ~l~i~Dt~G~~~~~~~~~~~~--------~~~~~~ilvfD~~~~~s~~-~------i~~w~~~i~~~~~~~piilvgNK~ 127 (219)
T PLN03071 63 RFYCWDTAGQEKFGGLRDGYY--------IHGQCAIIMFDVTARLTYK-N------VPTWHRDLCRVCENIPIVLCGNKV 127 (219)
T ss_pred EEEEEECCCchhhhhhhHHHc--------ccccEEEEEEeCCCHHHHH-H------HHHHHHHHHHhCCCCcEEEEEEch
Confidence 445567777655544433221 1335678899988754321 1 122223332 1224677999
Q ss_pred CCCCC
Q 027979 120 DLVSP 124 (216)
Q Consensus 120 D~v~~ 124 (216)
|+.+.
T Consensus 128 Dl~~~ 132 (219)
T PLN03071 128 DVKNR 132 (219)
T ss_pred hhhhc
Confidence 98643
No 329
>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=26.28 E-value=2.2e+02 Score=22.68 Aligned_cols=65 Identities=17% Similarity=0.173 Sum_probs=33.6
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhh----cc-EEEEcc
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAF----AD-VVILNK 118 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~----AD-~IvlnK 118 (216)
...-|..++|--.-..+..... -..+.+|.|+|...-...- + ...+..+|.. .- ++|.||
T Consensus 44 ~~l~iwDt~G~e~~~~l~~~~~--------~~ad~~ilV~D~t~~~S~~-~------i~~w~~~i~~~~~~~piilvgNK 108 (200)
T smart00176 44 IRFNVWDTAGQEKFGGLRDGYY--------IQGQCAIIMFDVTARVTYK-N------VPNWHRDLVRVCENIPIVLCGNK 108 (200)
T ss_pred EEEEEEECCCchhhhhhhHHHh--------cCCCEEEEEEECCChHHHH-H------HHHHHHHHHHhCCCCCEEEEEEC
Confidence 3444667777643222222211 1235678889998754321 1 1223333332 22 467799
Q ss_pred CCCCC
Q 027979 119 VDLVS 123 (216)
Q Consensus 119 ~D~v~ 123 (216)
+|+..
T Consensus 109 ~Dl~~ 113 (200)
T smart00176 109 VDVKD 113 (200)
T ss_pred ccccc
Confidence 99854
No 330
>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been 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 both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....
Probab=26.05 E-value=2e+02 Score=20.14 Aligned_cols=12 Identities=33% Similarity=0.686 Sum_probs=7.1
Q ss_pred EEEEecCCCCCc
Q 027979 46 HILLETTGLANP 57 (216)
Q Consensus 46 ~IiIE~sG~a~P 57 (216)
++++-+.|+.++
T Consensus 49 ~~~vDtpG~~~~ 60 (116)
T PF01926_consen 49 FILVDTPGINDG 60 (116)
T ss_dssp EEEEESSSCSSS
T ss_pred EEEEeCCCCccc
Confidence 456666666554
No 331
>PRK14333 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=26.01 E-value=66 Score=29.34 Aligned_cols=76 Identities=13% Similarity=0.152 Sum_probs=42.7
Q ss_pred EEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHH--HHhhCCCCEEEEee-cCCCC
Q 027979 80 ITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKE--IHEINSLAHVIRSV-RCQVD 156 (216)
Q Consensus 80 I~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~--l~~lNP~A~iv~~~-~~~v~ 156 (216)
+-.+|+..+...+... .+ +..+..+.||+||+|=|--...++. ..+..+.+. .++.||.++|+.+. +.+..
T Consensus 18 ~N~~ds~~~~~~l~~~----G~-~~~~~~~~ADiiiiNTC~v~~~a~~-~~~~~i~~~~~~k~~~p~~~vvv~Gc~a~~~ 91 (448)
T PRK14333 18 MNKADSERMAGILEDM----GY-QWAEDELQADLVLYNTCTIRDNAEQ-KVYSYLGRQAKRKHKNPDLTLVVAGCVAQQE 91 (448)
T ss_pred CcHHHHHHHHHHHHHC----cC-EECCCcccCCEEEEEeeeeeehHHH-HHHHHHHHHHHHHhcCCCCEEEEECccCccC
Confidence 4556666666655431 01 1223445799999999876665431 122222222 26678999887533 44555
Q ss_pred hhhhh
Q 027979 157 LSEVL 161 (216)
Q Consensus 157 ~~~l~ 161 (216)
++.++
T Consensus 92 ~~~~~ 96 (448)
T PRK14333 92 GESLL 96 (448)
T ss_pred HHHHH
Confidence 66555
No 332
>cd01169 HMPP_kinase 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of the hydroxyl group of HMP to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate (HMP-P) and then the phophorylation of HMP-P to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine pyrophosphate (HMP-PP), which is the substrate for the thiamine synthase coupling reaction.
Probab=25.99 E-value=93 Score=25.21 Aligned_cols=84 Identities=14% Similarity=0.176 Sum_probs=43.0
Q ss_pred hhHHHHHHHHHHhcCCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHH
Q 027979 28 HSLVQALEQLVQRKERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQ 107 (216)
Q Consensus 28 ~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~Q 107 (216)
+.+.++++.+++ ..+++.|.+ |+---.+.++.+. ..++. + .++..++|+......-...........+.++
T Consensus 54 ~~~~~~l~~~~~-~~~~~~i~~---G~l~~~~~~~~i~--~~~~~-~--~~~~vv~Dpv~~~~~~~~~~~~~~~~~~~~~ 124 (242)
T cd01169 54 EFVAAQLDAVLE-DIPVDAIKI---GMLGSAEIIEAVA--EALKD-Y--PDIPVVLDPVMVAKSGDSLLDDDAIEALREL 124 (242)
T ss_pred HHHHHHHHHHHh-CCCCCEEEE---CCCCCHHHHHHHH--HHHHh-C--CCCcEEECCceeCCCCCcccCHHHHHHHHHH
Confidence 445677888775 468999999 6654333444332 11111 1 2456778875321100000000001122334
Q ss_pred H-hhccEEEEccCC
Q 027979 108 I-AFADVVILNKVD 120 (216)
Q Consensus 108 I-~~AD~IvlnK~D 120 (216)
+ ..+|+|..|..+
T Consensus 125 ll~~~dvitpN~~E 138 (242)
T cd01169 125 LLPLATLITPNLPE 138 (242)
T ss_pred hhccCeEEeCCHHH
Confidence 3 889999999876
No 333
>PRK12724 flagellar biosynthesis regulator FlhF; Provisional
Probab=25.64 E-value=5.3e+02 Score=23.71 Aligned_cols=102 Identities=12% Similarity=0.023 Sum_probs=56.5
Q ss_pred CCCCEEEEecCCCCCc-HHHHHHhhcCcccccce---eeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEc
Q 027979 42 ERLDHILLETTGLANP-APLASVLWLDDQLESAV---RLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILN 117 (216)
Q Consensus 42 ~~~d~IiIE~sG~a~P-~~i~~~l~~~~~l~~~~---~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~Ivln 117 (216)
..+|+|||-|.|.... ...++.|. . +...+ .-..++.|+||..-...+... .... +--..+-+|++
T Consensus 298 ~~~D~VLIDTaGr~~rd~~~l~eL~--~-~~~~~~~~~~~e~~LVLsAt~~~~~~~~~------~~~f-~~~~~~glIlT 367 (432)
T PRK12724 298 DGSELILIDTAGYSHRNLEQLERMQ--S-FYSCFGEKDSVENLLVLSSTSSYHHTLTV------LKAY-ESLNYRRILLT 367 (432)
T ss_pred CCCCEEEEeCCCCCccCHHHHHHHH--H-HHHhhcCCCCCeEEEEEeCCCCHHHHHHH------HHHh-cCCCCCEEEEE
Confidence 5789999999998632 23333221 0 01111 122468899998665444321 1111 23346899999
Q ss_pred cCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeecCCCChhhhh
Q 027979 118 KVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVRCQVDLSEVL 161 (216)
Q Consensus 118 K~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~~~l~ 161 (216)
|.|-...- -.+...+... +.+|.....|+--+++|.
T Consensus 368 KLDEt~~~------G~il~i~~~~--~lPI~ylt~GQ~VPeDi~ 403 (432)
T PRK12724 368 KLDEADFL------GSFLELADTY--SKSFTYLSVGQEVPFDIL 403 (432)
T ss_pred cccCCCCc------cHHHHHHHHH--CCCEEEEecCCCCCCCHH
Confidence 99986543 3344444333 467776667654444443
No 334
>PRK00090 bioD dithiobiotin synthetase; Reviewed
Probab=25.39 E-value=72 Score=25.64 Aligned_cols=16 Identities=31% Similarity=0.509 Sum_probs=12.0
Q ss_pred CCCCEEEEecCCC-CCc
Q 027979 42 ERLDHILLETTGL-ANP 57 (216)
Q Consensus 42 ~~~d~IiIE~sG~-a~P 57 (216)
.++|+||||+.|- ..|
T Consensus 102 ~~~D~viIEg~gg~~~~ 118 (222)
T PRK00090 102 QQYDLVLVEGAGGLLVP 118 (222)
T ss_pred hhCCEEEEECCCceecc
Confidence 4699999998864 345
No 335
>PRK14336 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=25.14 E-value=74 Score=28.77 Aligned_cols=72 Identities=11% Similarity=0.190 Sum_probs=38.8
Q ss_pred EEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHH------HHHHhhCCCCEEEEe-ec
Q 027979 80 ITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELE------KEIHEINSLAHVIRS-VR 152 (216)
Q Consensus 80 I~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~------~~l~~lNP~A~iv~~-~~ 152 (216)
.-.+|+..+...+... .+. .....+.||+||+|=|--...++ ++.. +.+++.||.++|+.+ =.
T Consensus 13 ~N~~dse~~~~~l~~~----G~~-~~~~~~~AD~viiNTC~v~~~a~-----~~~~~~i~~~~~~~~~~~~~~ivv~GC~ 82 (418)
T PRK14336 13 MNQAESERLGRLFELW----GYS-LADKAEDAELVLVNSCVVREHAE-----NKVINRLHLLRKLKNKNPKLKIALTGCL 82 (418)
T ss_pred CcHHHHHHHHHHHHHC----cCE-ECCCcccCCEEEEecccEecHHH-----HHHHHHHHHHHHHHhhCCCCEEEEECCh
Confidence 4455666666555431 011 11223569999999887665542 2332 334667898877652 12
Q ss_pred CCCChhhhh
Q 027979 153 CQVDLSEVL 161 (216)
Q Consensus 153 ~~v~~~~l~ 161 (216)
.+...+.+.
T Consensus 83 ~~~~~~~l~ 91 (418)
T PRK14336 83 VGQDISLIR 91 (418)
T ss_pred hcCCHHHHH
Confidence 233444444
No 336
>COG1217 TypA Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]
Probab=25.10 E-value=1.1e+02 Score=28.54 Aligned_cols=83 Identities=17% Similarity=0.264 Sum_probs=45.3
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHH--HHhhccEEEEccCCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIH--QIAFADVVILNKVDL 121 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~--QI~~AD~IvlnK~D~ 121 (216)
...=||-|.|=||=..=++-+. =-+|+++.+|||.....- . ..| .+.+ -...-=+||+||+|.
T Consensus 68 ~~INIvDTPGHADFGGEVERvl--------~MVDgvlLlVDA~EGpMP--Q----TrF-VlkKAl~~gL~PIVVvNKiDr 132 (603)
T COG1217 68 TRINIVDTPGHADFGGEVERVL--------SMVDGVLLLVDASEGPMP--Q----TRF-VLKKALALGLKPIVVINKIDR 132 (603)
T ss_pred eEEEEecCCCcCCccchhhhhh--------hhcceEEEEEEcccCCCC--c----hhh-hHHHHHHcCCCcEEEEeCCCC
Confidence 3444688889888754443221 137899999999743210 0 001 0111 123446899999999
Q ss_pred CCCCCccchHHHHHHHHHhhC
Q 027979 122 VSPERSGDSLDELEKEIHEIN 142 (216)
Q Consensus 122 v~~~~~~~~l~~i~~~l~~lN 142 (216)
-++.- ++...++-...-++.
T Consensus 133 p~Arp-~~Vvd~vfDLf~~L~ 152 (603)
T COG1217 133 PDARP-DEVVDEVFDLFVELG 152 (603)
T ss_pred CCCCH-HHHHHHHHHHHHHhC
Confidence 66532 234444444444443
No 337
>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional
Probab=24.95 E-value=2.9e+02 Score=26.96 Aligned_cols=13 Identities=15% Similarity=0.422 Sum_probs=8.2
Q ss_pred CCCEEEEecCCCC
Q 027979 43 RLDHILLETTGLA 55 (216)
Q Consensus 43 ~~d~IiIE~sG~a 55 (216)
++|+|||-+..+.
T Consensus 640 ~yD~IIIDtPP~~ 652 (726)
T PRK09841 640 HYDLVIVDTPPML 652 (726)
T ss_pred cCCEEEEeCCCcc
Confidence 5677777766443
No 338
>PF01884 PcrB: PcrB family; InterPro: IPR008205 This entry represents geranylgeranylglyceryl phosphate (GGGP) synthase, which is a prenyltransferase that catalyses the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). This reaction is the first ether-bond-formation step in the biosynthesis of archaeal membrane lipids. This entry also matches putative glycerol-1-phosphate prenyltransferases that may catalyse the transfer of a prenyl moiety to sn-glycerol-1-phosphate (G1P) []. Some of the prokaryotic proteins in this family are related to pcrB. The Staphylococcus aureus chromosomal gene pcrA encodes a protein with significant similarity (40% identity) to two Escherichia coli helicases: the helicase II encoded by the uvrD gene and the Rep helicase. PcrB gene seems to belong to an operon containing at least one other gene, pcrBA, downstream from pcrB []. The PcrB proteins often contain an FMN binding site although the function of these proteins is still unknown.; GO: 0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups; PDB: 1VIZ_A 2F6X_B 2F6U_B 3VKD_A 3VKA_A 3VK5_B 3VKC_B 3VKB_B.
Probab=24.85 E-value=3.7e+02 Score=22.43 Aligned_cols=26 Identities=27% Similarity=0.313 Sum_probs=16.9
Q ss_pred HHHHHHHhcCCCCEEEEec-CCCCCcH
Q 027979 33 ALEQLVQRKERLDHILLET-TGLANPA 58 (216)
Q Consensus 33 ~L~~l~~~~~~~d~IiIE~-sG~a~P~ 58 (216)
+-..+..+...+..|-+|+ ||.-.|.
T Consensus 143 a~~alA~~~~g~~~iYLEaGSGa~~~v 169 (230)
T PF01884_consen 143 AAAALAAEYLGMPIIYLEAGSGAYGPV 169 (230)
T ss_dssp HHHHHHHHHTT-SEEEEE--TTSSS-H
T ss_pred HHHHHHHHHhCCCEEEEEeCCCCCCCc
Confidence 3444555566899999999 9997665
No 339
>TIGR01574 miaB-methiolase tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB. Hits to this model span all major groups of bacteria and eukaryotes, but not archaea, which are known to lack this particular tRNA modification. The enzyme from Thermotoga maritima has been cloned, expressed, spectroscopically characterized and shown to complement the E. coli MiaB enzyme.
Probab=24.83 E-value=80 Score=28.69 Aligned_cols=77 Identities=16% Similarity=0.188 Sum_probs=39.1
Q ss_pred EEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHH--HHHHhhCCCCEEEE-eecCCCC
Q 027979 80 ITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELE--KEIHEINSLAHVIR-SVRCQVD 156 (216)
Q Consensus 80 I~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~--~~l~~lNP~A~iv~-~~~~~v~ 156 (216)
+-.+|+..+...+.... .+. .....+.||+||+|=|--...++. ...+.+. +.+++.||.++|+. .-+.+..
T Consensus 11 ~N~~dse~~~~~l~~~~---G~~-~~~~~~~aDv~iiNTC~v~~~a~~-k~~~~i~~~~~~k~~~~~~~ivv~GC~a~~~ 85 (438)
T TIGR01574 11 MNVRDSEHMAALLTAKE---GYA-LTEDAKEADVLLINTCSVREKAEH-KVFGELGGFKKLKKKNPDLIIGVCGCMASHL 85 (438)
T ss_pred CcHHHHHHHHHHHHhcC---CcE-ECCCcccCCEEEEeccCeechHHH-HHHHHHHHHHHHHhhCCCcEEEEeCcccccc
Confidence 44456665555553210 011 112345699999998876555421 1112221 23456789998854 2333444
Q ss_pred hhhhh
Q 027979 157 LSEVL 161 (216)
Q Consensus 157 ~~~l~ 161 (216)
++.+.
T Consensus 86 ~~~~~ 90 (438)
T TIGR01574 86 GNEIF 90 (438)
T ss_pred HHHHH
Confidence 45544
No 340
>PRK10669 putative cation:proton antiport protein; Provisional
Probab=24.72 E-value=5.3e+02 Score=24.10 Aligned_cols=102 Identities=12% Similarity=0.127 Sum_probs=59.6
Q ss_pred ecCCCcEEeecchhHHHHHHHHHHhcCCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhc
Q 027979 16 ELANGCICCTVKHSLVQALEQLVQRKERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKY 95 (216)
Q Consensus 16 eL~~GCiCCsl~~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~ 95 (216)
++.|.-+=|+... +-..+.+.+. +.+.++++||. ||..+ +.+. + .+.-+..-|+.+-.. +.
T Consensus 415 ~~~~hiiI~G~G~-~G~~la~~L~-~~g~~vvvId~----d~~~~-~~~~-~--------~g~~~i~GD~~~~~~-L~-- 475 (558)
T PRK10669 415 DICNHALLVGYGR-VGSLLGEKLL-AAGIPLVVIET----SRTRV-DELR-E--------RGIRAVLGNAANEEI-MQ-- 475 (558)
T ss_pred ccCCCEEEECCCh-HHHHHHHHHH-HCCCCEEEEEC----CHHHH-HHHH-H--------CCCeEEEcCCCCHHH-HH--
Confidence 4456667777654 5555555444 34578999995 45443 3221 1 122355557764321 11
Q ss_pred ccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHHHHhhCCCCEEEEeec
Q 027979 96 RHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKEIHEINSLAHVIRSVR 152 (216)
Q Consensus 96 ~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~lNP~A~iv~~~~ 152 (216)
...++.||.+++.-.|-.+ -..+...+++.||.++++...+
T Consensus 476 ---------~a~i~~a~~viv~~~~~~~-------~~~iv~~~~~~~~~~~iiar~~ 516 (558)
T PRK10669 476 ---------LAHLDCARWLLLTIPNGYE-------AGEIVASAREKRPDIEIIARAH 516 (558)
T ss_pred ---------hcCccccCEEEEEcCChHH-------HHHHHHHHHHHCCCCeEEEEEC
Confidence 1467899988887554211 2346667888999999986544
No 341
>KOG0076 consensus GTP-binding ADP-ribosylation factor-like protein yARL3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.51 E-value=1.1e+02 Score=24.72 Aligned_cols=58 Identities=22% Similarity=0.255 Sum_probs=31.9
Q ss_pred eeccEEEEEcccchHHHHhhcccCCChhHHH--HHHhhccEEE-EccCCCCCCCCccchHHHHHHHHH
Q 027979 75 RLDSIITVVDAKNLLFQIDKYRHLSSYPEAI--HQIAFADVVI-LNKVDLVSPERSGDSLDELEKEIH 139 (216)
Q Consensus 75 ~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~--~QI~~AD~Iv-lnK~D~v~~~~~~~~l~~i~~~l~ 139 (216)
...++|.+|||.+-...-... ..+..+. +-++.|-+++ +||-|+-+.. +.++++....
T Consensus 92 ~~H~ii~viDa~~~eR~~~~~---t~~~~v~~~E~leg~p~L~lankqd~q~~~----~~~El~~~~~ 152 (197)
T KOG0076|consen 92 LAHGIIYVIDATDRERFEESK---TAFEKVVENEKLEGAPVLVLANKQDLQNAM----EAAELDGVFG 152 (197)
T ss_pred HhceeEEeecCCCHHHHHHHH---HHHHHHHHHHHhcCCchhhhcchhhhhhhh----hHHHHHHHhh
Confidence 456789999998733211110 0122222 4455666554 5999987764 3455555544
No 342
>COG2213 MtlA Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]
Probab=24.44 E-value=2e+02 Score=26.19 Aligned_cols=80 Identities=15% Similarity=0.113 Sum_probs=50.9
Q ss_pred eeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhcc---EEEEccC-CCCC-CCCccchHHHHHHHHHhhCCCCEEE
Q 027979 74 VRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFAD---VVILNKV-DLVS-PERSGDSLDELEKEIHEINSLAHVI 148 (216)
Q Consensus 74 ~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD---~IvlnK~-D~v~-~~~~~~~l~~i~~~l~~lNP~A~iv 148 (216)
-.+..++.+.||..-...+.. ..++++++.|. +=|.|+. +..+ +++.--..+.+.++.++-+|.|..+
T Consensus 376 ~~v~~iifaCDAGMGSSAMGA-------silrkk~k~agl~~I~V~n~AIn~Lp~d~d~VITh~~LtdRak~k~p~A~hi 448 (472)
T COG2213 376 SNVKKIIFACDAGMGSSAMGA-------SILRKKLKNAGLNDISVTNYAINNLPADADLVITHKDLTDRAKRKVPDAQHI 448 (472)
T ss_pred cceeEEEEEEcCCCChhhhhH-------HHHHHHHHhCCCCceeEeehhhhcCCccccEEEEhHHhhHHHHhcCCCCeEE
Confidence 457789999999877655532 34566777664 4466653 2222 2211134578889999999999986
Q ss_pred EeecCCCChhhhhccCCCC
Q 027979 149 RSVRCQVDLSEVLNCRAYD 167 (216)
Q Consensus 149 ~~~~~~v~~~~l~~~~~~~ 167 (216)
. ++.+++...|+
T Consensus 449 s-------i~nFL~s~~Y~ 460 (472)
T COG2213 449 S-------INNFLDSPKYD 460 (472)
T ss_pred e-------HHhhcccHhHH
Confidence 5 44566665554
No 343
>COG1533 SplB DNA repair photolyase [DNA replication, recombination, and repair]
Probab=24.14 E-value=95 Score=26.88 Aligned_cols=45 Identities=20% Similarity=0.480 Sum_probs=29.8
Q ss_pred cCCCcEEeecc----------------hhHHHHHHHHHHhcCCCCEEEEecCCCCCcHHHHH
Q 027979 17 LANGCICCTVK----------------HSLVQALEQLVQRKERLDHILLETTGLANPAPLAS 62 (216)
Q Consensus 17 L~~GCiCCsl~----------------~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~ 62 (216)
=.+||+.|-++ .++.+.|.+-+. +..+....|..+.+.||-+-.+
T Consensus 39 C~h~C~YCYa~~~~~~~~~~~~~v~vk~n~~e~l~~el~-~~~~k~~~i~is~~TDpyqp~E 99 (297)
T COG1533 39 CSHGCIYCYARPMHGYLPKSPTKVNVKENLLELLERELR-KPGPKRTVIAISSVTDPYQPIE 99 (297)
T ss_pred CCCCCceeecccccccccCCCceeeechhHHHHHHHHHh-hccCCceEEEEecCCCCCCcch
Confidence 36899999654 234444555443 2357888888888888876544
No 344
>PF01106 NifU: NifU-like domain; InterPro: IPR001075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal (IPR002871 from INTERPRO) and a C-terminal domain []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 2JNV_A 2Z51_A 1TH5_A 1VEH_A 1XHJ_A.
Probab=24.05 E-value=78 Score=20.88 Aligned_cols=27 Identities=30% Similarity=0.592 Sum_probs=19.6
Q ss_pred eeecCCCcEEeecchh-HHHHHHHHHHh
Q 027979 14 WVELANGCICCTVKHS-LVQALEQLVQR 40 (216)
Q Consensus 14 v~eL~~GCiCCsl~~d-l~~~L~~l~~~ 40 (216)
.+.|.|+|--|..... +...+++.+..
T Consensus 30 ~V~l~GaC~gC~~s~~Tl~~~Ie~~L~~ 57 (68)
T PF01106_consen 30 YVRLTGACSGCPSSDMTLKQGIEQALRE 57 (68)
T ss_dssp EEEEESSCCSSCCHHHHHHHHHHHHHHH
T ss_pred EEEEEeCCCCCCCHHHHHHHHHHHHHHH
Confidence 5789999999987754 44667776653
No 345
>PRK14327 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=23.94 E-value=92 Score=29.14 Aligned_cols=60 Identities=17% Similarity=0.180 Sum_probs=35.8
Q ss_pred EEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHHHH------HHhhCCCCEEEE
Q 027979 80 ITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELEKE------IHEINSLAHVIR 149 (216)
Q Consensus 80 I~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~~~------l~~lNP~A~iv~ 149 (216)
.-.+|+..+...|... .+ +.....+.||+||+|=|--...++ +++... +++-||.+.|+.
T Consensus 78 ~N~~Dse~~~~~L~~~----Gy-~~~~~~~~ADviiiNTC~V~~~Ae-----~k~~~~i~~l~~~k~~~p~~~i~v 143 (509)
T PRK14327 78 MNEHDTEVMAGIFEAL----GY-EPTDDTEDADVILLNTCAIRENAE-----NKVFGEIGHLKHLKRENPDLLIGV 143 (509)
T ss_pred ccHHHHHHHHHHHHHC----cC-EECCCcCCCCEEEEECCCCccHHH-----HHHHHHHHHHHHHHhhCCCCEEEE
Confidence 5556666666555431 01 112334569999999987766543 333333 467789987764
No 346
>PRK14339 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=23.85 E-value=89 Score=28.28 Aligned_cols=38 Identities=21% Similarity=0.199 Sum_probs=24.8
Q ss_pred HhhccEEEEccCCCCCCCCccchHHHHHHHHHh----hCCCCEEEEe
Q 027979 108 IAFADVVILNKVDLVSPERSGDSLDELEKEIHE----INSLAHVIRS 150 (216)
Q Consensus 108 I~~AD~IvlnK~D~v~~~~~~~~l~~i~~~l~~----lNP~A~iv~~ 150 (216)
.+.||+||+|=|--...++ ++.++.|++ -+|.+.|+.+
T Consensus 25 ~~~ADv~iiNTC~v~~~a~-----~k~~~~i~~~~~~~~~~~~ivv~ 66 (420)
T PRK14339 25 IKEADLILINTCSVREKPV-----HKLFSEIGQFNKIKKEGAKIGVC 66 (420)
T ss_pred cccCCEEEEeccCccchHH-----HHHHHHHHHHHHhhCCCCeEEEE
Confidence 4569999999887766543 344444433 5777777654
No 347
>PRK14338 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=23.83 E-value=99 Score=28.34 Aligned_cols=78 Identities=13% Similarity=0.185 Sum_probs=43.5
Q ss_pred ccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHH--HHHHHhhCCCCEEEEe-ecC
Q 027979 77 DSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDEL--EKEIHEINSLAHVIRS-VRC 153 (216)
Q Consensus 77 ~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i--~~~l~~lNP~A~iv~~-~~~ 153 (216)
.--.-.+|+..+...+... .+. .....+.||+||+|=|--...++. .....+ .+.+++.||.++|+.+ =+.
T Consensus 29 GC~~N~~dse~~~~~l~~~----G~~-~~~~~~~AD~~iiNTC~v~~~a~~-~~~~~i~~~~~~k~~~p~~~ivv~GC~a 102 (459)
T PRK14338 29 GCQMNVSDSERLEAALQGV----GYS-PAERPEDADFIVLNSCSVRASAEE-RILGKLGELQRLKRQRPDTRIVLWGCMV 102 (459)
T ss_pred CCCCCHHHHHHHHHHHHHC----cCE-ECCCcccCCEEEEeccceeeHHHH-HHHHHHHHHHHHHhhCCCCEEEEeCCcc
Confidence 3335667777777766442 011 123345799999999877665431 111111 2345678999988742 233
Q ss_pred CCChhhh
Q 027979 154 QVDLSEV 160 (216)
Q Consensus 154 ~v~~~~l 160 (216)
+...+.+
T Consensus 103 ~~~~~~~ 109 (459)
T PRK14338 103 GPNNQSI 109 (459)
T ss_pred ccChhHh
Confidence 4445554
No 348
>PF00056 Ldh_1_N: lactate/malate dehydrogenase, NAD binding domain Prosite entry for lactate dehydrogenase Prosite entry for malate dehydrogenase; InterPro: IPR001236 L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis []. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate []. The enzyme participates in the citric acid cycle. This entry represents the N-terminal, and is thought to be a Rossmann NAD-binding fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1IB6_B 3HHP_C 1IE3_A 2PWZ_A 1EMD_A 2CMD_A 1EZ4_D 9LDT_B 9LDB_B 2D4A_C ....
Probab=23.68 E-value=2e+02 Score=21.57 Aligned_cols=46 Identities=24% Similarity=0.218 Sum_probs=30.9
Q ss_pred HHHhhccEEEEccCCCCCCCCcc--------chHHHHHHHHHhhCCCCEEEEee
Q 027979 106 HQIAFADVVILNKVDLVSPERSG--------DSLDELEKEIHEINSLAHVIRSV 151 (216)
Q Consensus 106 ~QI~~AD~IvlnK~D~v~~~~~~--------~~l~~i~~~l~~lNP~A~iv~~~ 151 (216)
+.++.||+||++=.-...+.+.+ .-++++.+.+++.+|++.++..+
T Consensus 65 ~~~~~aDivvitag~~~~~g~sR~~ll~~N~~i~~~~~~~i~~~~p~~~vivvt 118 (141)
T PF00056_consen 65 EALKDADIVVITAGVPRKPGMSRLDLLEANAKIVKEIAKKIAKYAPDAIVIVVT 118 (141)
T ss_dssp GGGTTESEEEETTSTSSSTTSSHHHHHHHHHHHHHHHHHHHHHHSTTSEEEE-S
T ss_pred cccccccEEEEeccccccccccHHHHHHHhHhHHHHHHHHHHHhCCccEEEEeC
Confidence 67899999999854433332211 34556677888999999887654
No 349
>TIGR00490 aEF-2 translation elongation factor aEF-2. This model represents archaeal elongation factor 2, a protein more similar to eukaryotic EF-2 than to bacterial EF-G, both in sequence similarity and in sharing with eukaryotes the property of having a diphthamide (modified His) residue at a conserved position. The diphthamide can be ADP-ribosylated by diphtheria toxin in the presence of NAD.
Probab=23.46 E-value=1.9e+02 Score=28.30 Aligned_cols=65 Identities=22% Similarity=0.217 Sum_probs=37.7
Q ss_pred CCCEEEEecCCCCCcHH-HHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHh---hccEEEEcc
Q 027979 43 RLDHILLETTGLANPAP-LASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIA---FADVVILNK 118 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~-i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~---~AD~IvlnK 118 (216)
++...+|=|.|..+-.. +...+ -..|.+|.|+|+..-...- .....+++. .-=++++||
T Consensus 85 ~~~i~liDTPG~~~f~~~~~~al---------~~aD~~llVvda~~g~~~~--------t~~~~~~~~~~~~p~ivviNK 147 (720)
T TIGR00490 85 EYLINLIDTPGHVDFGGDVTRAM---------RAVDGAIVVVCAVEGVMPQ--------TETVLRQALKENVKPVLFINK 147 (720)
T ss_pred ceEEEEEeCCCccccHHHHHHHH---------HhcCEEEEEEecCCCCCcc--------HHHHHHHHHHcCCCEEEEEEC
Confidence 45678899999876432 22222 2457889999987532110 111222321 122789999
Q ss_pred CCCCCC
Q 027979 119 VDLVSP 124 (216)
Q Consensus 119 ~D~v~~ 124 (216)
+|+...
T Consensus 148 iD~~~~ 153 (720)
T TIGR00490 148 VDRLIN 153 (720)
T ss_pred hhcccc
Confidence 998753
No 350
>PRK14328 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=23.43 E-value=88 Score=28.43 Aligned_cols=64 Identities=19% Similarity=0.210 Sum_probs=35.0
Q ss_pred EEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHH--HHHHHhhCCCCEEEE
Q 027979 80 ITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDEL--EKEIHEINSLAHVIR 149 (216)
Q Consensus 80 I~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i--~~~l~~lNP~A~iv~ 149 (216)
+-.+|+..+...+... .+ +..+..+.||+||+|=|--..+++. ..+..+ .+.+++.||.++|+.
T Consensus 13 ~N~~ds~~~~~~l~~~----G~-~~~~~~~~ADv~iiNTC~v~~~a~~-k~~~~i~~~~~~~~~~~~~~vvv 78 (439)
T PRK14328 13 MNEEDSEKLAGMLKSM----GY-ERTENREEADIIIFNTCCVRENAEN-KVFGNLGELKKLKEKNPNLIIGV 78 (439)
T ss_pred CCHHHHHHHHHHHHHC----cC-EECCCcCcCCEEEEecccEechHHH-HHHHHHHHHHHHHhhCCCCEEEE
Confidence 3345565555555331 01 1224456799999998876655421 111111 233566789998875
No 351
>PRK05692 hydroxymethylglutaryl-CoA lyase; Provisional
Probab=22.39 E-value=1.9e+02 Score=24.80 Aligned_cols=23 Identities=30% Similarity=0.433 Sum_probs=15.9
Q ss_pred CCCCEEEE-ecCCCCCcHHHHHHh
Q 027979 42 ERLDHILL-ETTGLANPAPLASVL 64 (216)
Q Consensus 42 ~~~d~IiI-E~sG~a~P~~i~~~l 64 (216)
...|+|-| -|.|++.|..+.+.+
T Consensus 167 ~G~d~i~l~DT~G~~~P~~v~~lv 190 (287)
T PRK05692 167 LGCYEISLGDTIGVGTPGQVRAVL 190 (287)
T ss_pred cCCcEEEeccccCccCHHHHHHHH
Confidence 34666655 677888888777654
No 352
>PRK14325 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=22.20 E-value=89 Score=28.40 Aligned_cols=77 Identities=18% Similarity=0.218 Sum_probs=42.1
Q ss_pred EEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHHHHH--HHHHhhCCCCEEEEee-cCCCC
Q 027979 80 ITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLDELE--KEIHEINSLAHVIRSV-RCQVD 156 (216)
Q Consensus 80 I~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~~i~--~~l~~lNP~A~iv~~~-~~~v~ 156 (216)
+-.+|+..+...+... .+ +.......||+|++|=|--...++. .....++ +.+++.||+++|+.+. +....
T Consensus 15 ~N~~ds~~~~~~l~~~----g~-~~~~~~~~aDvviinTC~v~~~a~~-~~~~~i~~~~~~k~~~p~~~vvvgGc~as~~ 88 (444)
T PRK14325 15 MNEYDSSKMADLLGAE----GY-ELTDDPEEADLILLNTCSIREKAQE-KVFSELGRWRKLKEKNPDLIIGVGGCVAQQE 88 (444)
T ss_pred CcHHHHHHHHHHHHHC----cC-EECCCcCCCCEEEEEcceeeehHHH-HHHHHHHHHHHHHHhCCCCEEEEECchhccC
Confidence 4455666665555331 01 1224456799999998865554321 1112222 3357789999888633 34455
Q ss_pred hhhhhc
Q 027979 157 LSEVLN 162 (216)
Q Consensus 157 ~~~l~~ 162 (216)
++.++.
T Consensus 89 ~ee~~~ 94 (444)
T PRK14325 89 GEEILK 94 (444)
T ss_pred HHHHHh
Confidence 565553
No 353
>PF04723 GRDA: Glycine reductase complex selenoprotein A; InterPro: IPR006812 Found in clostridia, this protein contains one active site selenocysteine and catalyses the reductive deamination of glycine, which is coupled to the esterification of orthophosphate resulting in the formation of ATP []. A member of this family may also exist in Treponema denticola [].; GO: 0030699 glycine reductase activity, 0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor, 0055114 oxidation-reduction process, 0030700 glycine reductase complex
Probab=22.12 E-value=1.5e+02 Score=22.80 Aligned_cols=36 Identities=22% Similarity=0.418 Sum_probs=23.7
Q ss_pred eeeecCCCcEEeecch--hHHH--HHHHHHHhcCCCCEEEE
Q 027979 13 EWVELANGCICCTVKH--SLVQ--ALEQLVQRKERLDHILL 49 (216)
Q Consensus 13 ~v~eL~~GCiCCsl~~--dl~~--~L~~l~~~~~~~d~IiI 49 (216)
+++=-+.-|.-||..+ ||.. .++++.+ ++.++-+++
T Consensus 32 evvfs~TeCFVctaagaMDLEnQ~rvk~~aE-k~g~enlvV 71 (150)
T PF04723_consen 32 EVVFSSTECFVCTAAGAMDLENQQRVKDLAE-KYGAENLVV 71 (150)
T ss_pred eEEEEeeeEEEecccccccHHHHHHHHHHHH-hcCCccEEE
Confidence 4566678899999664 5554 4888887 455544443
No 354
>TIGR02355 moeB molybdopterin synthase sulfurylase MoeB. This model describes the molybdopterin biosynthesis protein MoeB in E. coli and related species. The enzyme covalently modifies the molybdopterin synthase MoaD by sulfurylation. This enzyme is closely related to ThiF, a thiamine biosynthesis enzyme that modifies ThiS by an analogous adenylation. Both MoeB and ThiF belong to the HesA/MoeB/ThiF family (pfam00899).
Probab=22.11 E-value=1e+02 Score=25.66 Aligned_cols=81 Identities=14% Similarity=0.220 Sum_probs=47.9
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVS 123 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~ 123 (216)
...+|+=.-|++- .++..|.. ..+ +-|+++|...+... -+-+|+- .+..|.-.
T Consensus 25 ~~VlvvG~GglGs--~va~~La~-----~Gv---g~i~lvD~D~ve~s-----------NL~RQ~l------~~~~diG~ 77 (240)
T TIGR02355 25 SRVLIVGLGGLGC--AASQYLAA-----AGV---GNLTLLDFDTVSLS-----------NLQRQVL------HSDANIGQ 77 (240)
T ss_pred CcEEEECcCHHHH--HHHHHHHH-----cCC---CEEEEEeCCccccc-----------Cccccee------eeHhhCCC
Confidence 5678887777863 34444431 111 35899999876521 1336652 33334322
Q ss_pred CCCccchHHHHHHHHHhhCCCCEEEEeecCCCCh
Q 027979 124 PERSGDSLDELEKEIHEINSLAHVIRSVRCQVDL 157 (216)
Q Consensus 124 ~~~~~~~l~~i~~~l~~lNP~A~iv~~~~~~v~~ 157 (216)
. ..+.+.+.++++||.++|... ...++.
T Consensus 78 ~-----Ka~~a~~~l~~inp~v~i~~~-~~~i~~ 105 (240)
T TIGR02355 78 P-----KVESAKDALTQINPHIAINPI-NAKLDD 105 (240)
T ss_pred c-----HHHHHHHHHHHHCCCcEEEEE-eccCCH
Confidence 2 357778999999999998643 334443
No 355
>TIGR00682 lpxK tetraacyldisaccharide 4'-kinase. Also called lipid-A 4'-kinase. This essential gene encodes an enzyme in the pathway of lipid A biosynthesis in Gram-negative organisms. A single copy of this protein is found in Gram-negative bacteria. PSI-BLAST converges on this set of apparent orthologs without identifying any other homologs.
Probab=21.74 E-value=61 Score=28.24 Aligned_cols=39 Identities=26% Similarity=0.213 Sum_probs=23.5
Q ss_pred EEEEcccchHHHHhhcc--cCCChhHHHHHHhhccEEEEccCCC
Q 027979 80 ITVVDAKNLLFQIDKYR--HLSSYPEAIHQIAFADVVILNKVDL 121 (216)
Q Consensus 80 I~vVDa~~~~~~l~~~~--~~~~~~~~~~QI~~AD~IvlnK~D~ 121 (216)
|.++|+.+.. .+.. ..+...|-..+++.||.||+||...
T Consensus 142 IvlvD~~~~f---gng~lLPaGpLREp~~~l~raD~vvv~~~~~ 182 (311)
T TIGR00682 142 IVVVDGQRPF---GNGFLLPAGPLREFPKRLKSADAVIVNGGEN 182 (311)
T ss_pred EEEECCCCCC---CCCcccCCcCCCCChhhhhhCCEEEEeCCcc
Confidence 6777775531 1110 1112234468999999999999753
No 356
>KOG2749 consensus mRNA cleavage and polyadenylation factor IA/II complex, subunit CLP1 [RNA processing and modification]
Probab=21.43 E-value=1.4e+02 Score=26.86 Aligned_cols=78 Identities=22% Similarity=0.293 Sum_probs=51.5
Q ss_pred CCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCC
Q 027979 43 RLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLV 122 (216)
Q Consensus 43 ~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v 122 (216)
+..-+||+|.|..++..-...+. ....|.++ +|.|+|..++-..++.. ++ . =.+-+++.|.|.+.+
T Consensus 211 r~sG~iInT~g~i~~egy~~llh----ai~~f~v~-vviVLg~ErLy~~lkk~-----~~---~-~~~v~vv~lpKsgGv 276 (415)
T KOG2749|consen 211 RVSGCIINTCGWIEGEGYAALLH----AIKAFEVD-VVIVLGQERLYSSLKKD-----LP---P-KKNVRVVKLPKSGGV 276 (415)
T ss_pred cccceEEeccceeccccHHHHHH----HHHHcCcc-EEEEeccHHHHHHHHhh-----cc---c-cccceEEEecCCCCe
Confidence 45668999999998766555432 34667776 56678887776665442 11 1 167789999999987
Q ss_pred CCCCccchHHHHHHHHH
Q 027979 123 SPERSGDSLDELEKEIH 139 (216)
Q Consensus 123 ~~~~~~~~l~~i~~~l~ 139 (216)
-+- -.++++..|
T Consensus 277 ~~R-----s~~~r~~~r 288 (415)
T KOG2749|consen 277 VAR-----SKEVRRKLR 288 (415)
T ss_pred Eee-----hHHHHHHHh
Confidence 653 245555544
No 357
>PRK03094 hypothetical protein; Provisional
Probab=21.28 E-value=78 Score=21.90 Aligned_cols=48 Identities=21% Similarity=0.468 Sum_probs=30.3
Q ss_pred eeeecC-----CCcEEeecchhHHHHHHHHHHhcCCCCEEEEecCCCCCcHHHHHHh
Q 027979 13 EWVELA-----NGCICCTVKHSLVQALEQLVQRKERLDHILLETTGLANPAPLASVL 64 (216)
Q Consensus 13 ~v~eL~-----~GCiCCsl~~dl~~~L~~l~~~~~~~d~IiIE~sG~a~P~~i~~~l 64 (216)
+|+.|. .||-||-..+.=..-+ .+ + .......+|+++|+. |.+|.+.+
T Consensus 23 eVv~l~~~~~~~~~Da~VitG~d~n~m-gi-~-d~~t~~pVI~A~G~T-aeEI~~~v 75 (80)
T PRK03094 23 EVVQLRSEQDAQGCDCCVVTGQDSNVM-GI-A-DTSTKGSVITASGLT-ADEICQQV 75 (80)
T ss_pred EEEecCcccccCCcCEEEEeCCCccee-cc-c-ccccCCcEEEcCCCC-HHHHHHHH
Confidence 466664 5799997664111111 11 1 234677899999996 88888765
No 358
>PRK11617 endonuclease V; Provisional
Probab=21.25 E-value=82 Score=26.17 Aligned_cols=20 Identities=25% Similarity=0.605 Sum_probs=16.9
Q ss_pred cCCCCEEEEecCCCCCcHHH
Q 027979 41 KERLDHILLETTGLANPAPL 60 (216)
Q Consensus 41 ~~~~d~IiIE~sG~a~P~~i 60 (216)
+..||.|+|--.|+++|..+
T Consensus 95 ~~~PdlllvDG~G~~HPR~~ 114 (224)
T PRK11617 95 SQKPDLVFVDGHGIAHPRRL 114 (224)
T ss_pred CcCCCEEEEcCceeECCCCc
Confidence 35799999999999999643
No 359
>PRK14326 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=21.09 E-value=1.1e+02 Score=28.42 Aligned_cols=77 Identities=17% Similarity=0.140 Sum_probs=42.9
Q ss_pred EEEEcccchHHHHhhcccCCChhHHHHHHhhccEEEEccCCCCCCCCccchHH--HHHHHHHhhCCCCEEEEee-cCCCC
Q 027979 80 ITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFADVVILNKVDLVSPERSGDSLD--ELEKEIHEINSLAHVIRSV-RCQVD 156 (216)
Q Consensus 80 I~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~AD~IvlnK~D~v~~~~~~~~l~--~i~~~l~~lNP~A~iv~~~-~~~v~ 156 (216)
.-.+|+..+...+... .+ +.....+.||+||+|=|--...++. +... ...+.+++.||+++|+.+. +....
T Consensus 25 ~N~~dse~~~~~L~~~----G~-~~~~~~e~ADvvviNTCtv~~~A~~-k~~~~i~~~~~~k~~~p~~~VvvgGc~a~~~ 98 (502)
T PRK14326 25 MNVHDSERLAGLLEAA----GY-VRAAEGQDADVVVFNTCAVRENADN-RLYGNLGHLAPVKRANPGMQIAVGGCLAQKD 98 (502)
T ss_pred CcHHHHHHHHHHHHHC----CC-EECCCcCCCCEEEEECCCeeehHHH-HHHHHHHHHHHHHHhCCCCEEEEECcccccC
Confidence 4556666666665431 01 1112335699999998876555421 1111 1123457789999888643 44555
Q ss_pred hhhhhc
Q 027979 157 LSEVLN 162 (216)
Q Consensus 157 ~~~l~~ 162 (216)
++.++.
T Consensus 99 ~ee~~~ 104 (502)
T PRK14326 99 RDTILK 104 (502)
T ss_pred HHHHHh
Confidence 666653
No 360
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=20.92 E-value=4.6e+02 Score=23.21 Aligned_cols=37 Identities=11% Similarity=0.218 Sum_probs=23.6
Q ss_pred CCCCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccch
Q 027979 42 ERLDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNL 88 (216)
Q Consensus 42 ~~~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~ 88 (216)
..+|+|||=+.+......+.... .-+.+|..+.+..+
T Consensus 233 ~~yD~IiiD~pp~~~~~~~~al~----------aad~viipv~p~~~ 269 (387)
T TIGR03453 233 DDYDVVVIDCPPQLGFLTLSALC----------AATGVLITVHPQML 269 (387)
T ss_pred hcCCEEEEeCCccHhHHHHHHHH----------HcCeeEEcCCCchh
Confidence 46999999999887554333222 22456777777554
No 361
>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=20.77 E-value=4.3e+02 Score=20.83 Aligned_cols=11 Identities=27% Similarity=0.353 Sum_probs=8.6
Q ss_pred EEEEccCCCCC
Q 027979 113 VVILNKVDLVS 123 (216)
Q Consensus 113 ~IvlnK~D~v~ 123 (216)
++|.||+|+.+
T Consensus 124 ilvgNK~DL~~ 134 (195)
T cd01873 124 ILVGCKLDLRY 134 (195)
T ss_pred EEEEEchhccc
Confidence 66779999864
No 362
>PRK14845 translation initiation factor IF-2; Provisional
Probab=20.59 E-value=2.2e+02 Score=29.24 Aligned_cols=64 Identities=25% Similarity=0.250 Sum_probs=34.7
Q ss_pred CCEEEEecCCCCCcHHHHHHhhcCcccccceeeccEEEEEcccchHHHHhhcccCCChhHHHHHHhhc---cEEEEccCC
Q 027979 44 LDHILLETTGLANPAPLASVLWLDDQLESAVRLDSIITVVDAKNLLFQIDKYRHLSSYPEAIHQIAFA---DVVILNKVD 120 (216)
Q Consensus 44 ~d~IiIE~sG~a~P~~i~~~l~~~~~l~~~~~l~~vI~vVDa~~~~~~l~~~~~~~~~~~~~~QI~~A---D~IvlnK~D 120 (216)
|...|+-|.|-..-..+.. ...-..+.++.|+|+......-. . +....+... =++++||+|
T Consensus 526 p~i~fiDTPGhe~F~~lr~--------~g~~~aDivlLVVDa~~Gi~~qT-------~-e~I~~lk~~~iPiIVViNKiD 589 (1049)
T PRK14845 526 PGLLFIDTPGHEAFTSLRK--------RGGSLADLAVLVVDINEGFKPQT-------I-EAINILRQYKTPFVVAANKID 589 (1049)
T ss_pred CcEEEEECCCcHHHHHHHH--------hhcccCCEEEEEEECcccCCHhH-------H-HHHHHHHHcCCCEEEEEECCC
Confidence 3478889999532221111 11123567899999975311100 1 122333333 368899999
Q ss_pred CCC
Q 027979 121 LVS 123 (216)
Q Consensus 121 ~v~ 123 (216)
+.+
T Consensus 590 L~~ 592 (1049)
T PRK14845 590 LIP 592 (1049)
T ss_pred Ccc
Confidence 975
No 363
>TIGR03602 streptolysinS bacteriocin protoxin, streptolysin S family. Members of this family are bacteriocin precursors. These small, ribosomally produced polypeptide precursors are extensively processed post-translationally. This family belongs to a class of heterocycle-containing bacteriocins, including streptolysin S from Streptococcus pyogenes, and related bacteriocins from Streptococcus iniae and Clostridium botulinum. Streptolysin S is hemolytic. Bacteriocin genes in general are small and highly diverse, with odd sequence composition, and are easily missed by many gene-finding programs.
Probab=20.38 E-value=80 Score=19.68 Aligned_cols=13 Identities=31% Similarity=0.915 Sum_probs=9.2
Q ss_pred eeeecCCCcEEee
Q 027979 13 EWVELANGCICCT 25 (216)
Q Consensus 13 ~v~eL~~GCiCCs 25 (216)
++..-.+||-||.
T Consensus 18 qvtvapggccccc 30 (56)
T TIGR03602 18 KVTVAPGGCCCCC 30 (56)
T ss_pred eeEecCCCeEEEe
Confidence 3456688998885
No 364
>cd06559 Endonuclease_V Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases. Endonuclease_V (EndoV) is an enzyme that can initiate repair of all possible deaminated DNA bases. EndoV cleaves the DNA strand containing lesions at the second phosphodiester bond 3' to the lesion using Mg2+ as a cofactor. EndoV homologs are conserved throughout all domains of life from bacteria to humans. EndoV is encoded by the nfi gene and nfi null mutant mice have a phenotype prone to cancer. The ability of endonuclease V to recognize mismatches and abnormal replicative DNA structures suggests that the enzyme plays an important role in DNA metabolism. The details of downstream processing for the EndoV pathway remain unknown.
Probab=20.15 E-value=93 Score=25.45 Aligned_cols=19 Identities=26% Similarity=0.599 Sum_probs=16.4
Q ss_pred CCCCEEEEecCCCCCcHHH
Q 027979 42 ERLDHILLETTGLANPAPL 60 (216)
Q Consensus 42 ~~~d~IiIE~sG~a~P~~i 60 (216)
..||.|+|--.|+++|..+
T Consensus 92 ~~PDlilVDG~G~~HpR~~ 110 (208)
T cd06559 92 TKPDLLLVDGHGIAHPRRF 110 (208)
T ss_pred CCCCEEEEeCCccccCCCc
Confidence 3699999999999999644
Done!