Query psy7060
Match_columns 160
No_of_seqs 117 out of 303
Neff 2.9
Searched_HMMs 46136
Date Fri Aug 16 17:06:34 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7060.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7060hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1486|consensus 100.0 5.7E-52 1.2E-56 360.5 12.6 124 1-160 146-269 (364)
2 COG1163 DRG Predicted GTPase [ 100.0 4.9E-41 1.1E-45 295.4 13.6 124 1-160 147-270 (365)
3 KOG1487|consensus 100.0 2.1E-37 4.6E-42 269.8 6.4 120 1-160 143-262 (358)
4 cd01896 DRG The developmentall 100.0 5.6E-35 1.2E-39 235.0 14.6 124 1-160 84-207 (233)
5 cd01899 Ygr210 Ygr210 subfamil 98.9 1.5E-10 3.2E-15 99.3 -0.5 118 7-160 127-249 (318)
6 PRK09602 translation-associate 98.7 5.4E-09 1.2E-13 92.1 2.0 116 7-160 130-251 (396)
7 KOG1486|consensus 94.9 0.0069 1.5E-07 54.4 -0.1 19 54-72 199-217 (364)
8 COG2262 HflX GTPases [General 94.6 0.033 7.1E-07 51.2 3.3 31 130-160 305-337 (411)
9 TIGR03156 GTP_HflX GTP-binding 90.9 0.38 8.3E-06 42.0 4.6 81 78-160 239-333 (351)
10 cd01858 NGP_1 NGP-1. Autoanti 90.2 0.35 7.5E-06 36.1 3.3 19 130-148 40-58 (157)
11 cd01857 HSR1_MMR1 HSR1/MMR1. 90.2 0.4 8.7E-06 35.4 3.5 32 118-149 31-62 (141)
12 cd04178 Nucleostemin_like Nucl 89.5 0.43 9.4E-06 37.6 3.4 21 130-150 31-51 (172)
13 COG1160 Predicted GTPases [Gen 88.7 1 2.3E-05 41.9 5.8 48 111-160 94-146 (444)
14 smart00174 RHO Rho (Ras homolo 88.3 1.7 3.8E-05 31.6 5.7 21 123-143 96-116 (174)
15 TIGR02528 EutP ethanolamine ut 87.0 1.7 3.7E-05 30.8 4.9 21 131-151 90-114 (142)
16 cd01849 YlqF_related_GTPase Yl 86.6 0.62 1.3E-05 34.8 2.6 19 130-148 30-48 (155)
17 cd01881 Obg_like The Obg-like 86.2 0.77 1.7E-05 33.1 2.8 22 128-149 119-140 (176)
18 cd01878 HflX HflX subfamily. 86.0 2 4.3E-05 32.8 5.2 19 130-148 154-172 (204)
19 PTZ00258 GTP-binding protein; 85.4 2.3 4.9E-05 38.6 6.0 53 91-150 186-245 (390)
20 cd01868 Rab11_like Rab11-like. 83.1 2 4.2E-05 31.1 3.8 23 130-152 109-136 (165)
21 cd01863 Rab18 Rab18 subfamily. 83.0 11 0.00024 27.0 7.6 28 127-154 104-135 (161)
22 cd01856 YlqF YlqF. Proteins o 83.0 1.2 2.7E-05 33.8 2.8 18 130-147 47-64 (171)
23 cd04164 trmE TrmE (MnmE, ThdF, 83.0 0.69 1.5E-05 32.4 1.3 20 128-147 106-125 (157)
24 cd01896 DRG The developmentall 82.6 1.4 3E-05 35.9 3.1 34 56-100 139-172 (233)
25 cd04141 Rit_Rin_Ric Rit/Rin/Ri 82.0 1.4 3E-05 33.3 2.8 26 128-153 106-136 (172)
26 cd01894 EngA1 EngA1 subfamily. 82.0 1.8 4E-05 30.3 3.2 18 130-147 106-123 (157)
27 cd04107 Rab32_Rab38 Rab38/Rab3 81.8 10 0.00022 29.2 7.5 28 128-155 109-141 (201)
28 cd04157 Arl6 Arl6 subfamily. 81.2 8.7 0.00019 27.3 6.5 15 129-143 104-118 (162)
29 cd04171 SelB SelB subfamily. 80.8 16 0.00035 25.8 7.7 15 130-144 105-119 (164)
30 cd01862 Rab7 Rab7 subfamily. 80.7 1.9 4.2E-05 31.0 3.0 26 129-154 109-139 (172)
31 smart00173 RAS Ras subfamily o 80.7 8.7 0.00019 27.6 6.4 25 129-153 105-134 (164)
32 cd01864 Rab19 Rab19 subfamily. 80.3 14 0.00031 26.8 7.5 26 128-153 107-137 (165)
33 cd04163 Era Era subfamily. Er 80.0 3.9 8.4E-05 28.4 4.2 19 130-148 112-131 (168)
34 PRK10463 hydrogenase nickel in 79.5 2 4.4E-05 37.6 3.3 67 76-143 156-244 (290)
35 cd04112 Rab26 Rab26 subfamily. 79.5 14 0.0003 28.2 7.5 26 128-153 105-135 (191)
36 PF00009 GTP_EFTU: Elongation 79.5 11 0.00023 28.8 6.9 51 90-142 80-135 (188)
37 cd04139 RalA_RalB RalA/RalB su 79.3 2 4.4E-05 30.4 2.7 14 130-143 106-119 (164)
38 cd01893 Miro1 Miro1 subfamily. 78.8 11 0.00023 27.7 6.5 46 98-144 65-118 (166)
39 cd01892 Miro2 Miro2 subfamily. 78.8 6.5 0.00014 29.5 5.4 15 129-143 108-122 (169)
40 cd01861 Rab6 Rab6 subfamily. 78.6 4 8.7E-05 29.2 4.1 26 129-154 105-135 (161)
41 cd01859 MJ1464 MJ1464. This f 78.4 1.7 3.7E-05 32.0 2.2 20 130-149 42-61 (156)
42 cd04127 Rab27A Rab27a subfamil 78.3 17 0.00037 26.7 7.4 24 130-153 121-149 (180)
43 cd01898 Obg Obg subfamily. Th 77.9 2.3 4.9E-05 30.7 2.6 19 128-146 113-131 (170)
44 cd04151 Arl1 Arl1 subfamily. 77.6 3.5 7.6E-05 29.9 3.6 15 129-143 100-114 (158)
45 COG1163 DRG Predicted GTPase [ 77.4 8.1 0.00018 35.6 6.6 23 56-78 202-224 (365)
46 cd00879 Sar1 Sar1 subfamily. 77.1 25 0.00054 26.2 8.2 25 129-153 120-147 (190)
47 PRK00089 era GTPase Era; Revie 76.9 10 0.00022 31.1 6.5 18 130-147 114-132 (292)
48 cd01866 Rab2 Rab2 subfamily. 76.6 4 8.7E-05 30.1 3.7 25 128-152 108-137 (168)
49 cd04106 Rab23_lke Rab23-like s 76.6 3.3 7.1E-05 29.7 3.1 24 129-152 106-134 (162)
50 PRK12289 GTPase RsgA; Reviewed 76.5 3.4 7.4E-05 36.6 3.8 20 130-149 121-140 (352)
51 cd01888 eIF2_gamma eIF2-gamma 76.4 15 0.00032 28.7 7.1 56 90-146 93-154 (203)
52 cd01867 Rab8_Rab10_Rab13_like 76.3 3 6.4E-05 30.6 2.9 25 128-152 107-136 (167)
53 cd04116 Rab9 Rab9 subfamily. 76.1 3.4 7.4E-05 30.1 3.2 27 128-154 113-143 (170)
54 cd04175 Rap1 Rap1 subgroup. T 76.0 2.5 5.5E-05 30.6 2.5 23 130-152 107-134 (164)
55 cd00881 GTP_translation_factor 76.0 2 4.3E-05 31.2 1.9 16 130-145 115-130 (189)
56 cd00880 Era_like Era (E. coli 75.8 2.8 6E-05 28.4 2.5 23 127-149 102-124 (163)
57 TIGR00231 small_GTP small GTP- 75.8 4.2 9E-05 27.5 3.4 15 129-143 108-122 (161)
58 cd01876 YihA_EngB The YihA (En 75.5 4.7 0.0001 28.1 3.6 27 119-147 102-128 (170)
59 PRK04213 GTP-binding protein; 75.4 2.7 5.9E-05 31.9 2.6 16 129-144 130-145 (201)
60 cd04110 Rab35 Rab35 subfamily. 75.3 4.6 0.0001 31.2 3.9 30 123-152 104-138 (199)
61 TIGR00436 era GTP-binding prot 75.3 3.6 7.8E-05 33.8 3.5 17 130-146 108-124 (270)
62 cd04160 Arfrp1 Arfrp1 subfamil 75.1 12 0.00025 27.0 5.7 17 128-144 106-122 (167)
63 cd04155 Arl3 Arl3 subfamily. 74.9 14 0.0003 26.9 6.1 17 128-144 114-130 (173)
64 cd04158 ARD1 ARD1 subfamily. 74.8 21 0.00046 26.4 7.2 24 130-153 101-127 (169)
65 cd04136 Rap_like Rap-like subf 74.6 3.5 7.6E-05 29.4 2.9 23 130-152 107-134 (163)
66 cd04101 RabL4 RabL4 (Rab-like4 74.5 2.1 4.6E-05 30.8 1.7 17 128-144 106-122 (164)
67 cd04146 RERG_RasL11_like RERG/ 74.3 4 8.6E-05 29.7 3.1 23 129-151 106-133 (165)
68 PLN00223 ADP-ribosylation fact 73.8 15 0.00032 28.2 6.3 26 129-154 118-146 (181)
69 TIGR02729 Obg_CgtA Obg family 73.7 3 6.6E-05 36.2 2.8 21 130-150 274-294 (329)
70 cd04144 Ras2 Ras2 subfamily. 73.7 5.5 0.00012 30.3 3.9 22 130-151 107-133 (190)
71 cd04138 H_N_K_Ras_like H-Ras/N 73.6 4.2 9.2E-05 28.6 3.0 24 128-151 105-132 (162)
72 TIGR03597 GTPase_YqeH ribosome 73.2 4.6 0.0001 35.3 3.8 51 89-143 48-104 (360)
73 cd04130 Wrch_1 Wrch-1 subfamil 72.8 5.2 0.00011 29.6 3.5 24 120-143 95-118 (173)
74 cd01897 NOG NOG1 is a nucleola 72.2 3.3 7.1E-05 29.9 2.3 19 130-148 114-132 (168)
75 cd04125 RabA_like RabA-like su 72.1 6.9 0.00015 29.5 4.1 24 129-152 105-133 (188)
76 cd04132 Rho4_like Rho4-like su 71.7 5.9 0.00013 29.5 3.6 25 129-153 105-138 (187)
77 PRK12288 GTPase RsgA; Reviewed 71.7 5.4 0.00012 35.2 3.9 16 130-145 151-166 (347)
78 cd01890 LepA LepA subfamily. 71.3 5.9 0.00013 29.0 3.5 14 130-143 120-133 (179)
79 TIGR03596 GTPase_YlqF ribosome 71.2 3.8 8.2E-05 34.1 2.7 20 130-149 49-68 (276)
80 cd01889 SelB_euk SelB subfamil 71.2 21 0.00046 27.2 6.6 17 129-145 120-136 (192)
81 cd04172 Rnd3_RhoE_Rho8 Rnd3/Rh 71.0 5.3 0.00011 31.1 3.3 14 128-141 108-121 (182)
82 cd04114 Rab30 Rab30 subfamily. 70.9 3.1 6.8E-05 30.1 1.9 14 130-143 113-126 (169)
83 cd04165 GTPBP1_like GTPBP1-lik 70.4 6.3 0.00014 32.2 3.8 56 91-148 95-157 (224)
84 cd04174 Rnd1_Rho6 Rnd1/Rho6 su 70.4 24 0.00052 29.2 7.2 20 123-142 111-130 (232)
85 cd01869 Rab1_Ypt1 Rab1/Ypt1 su 70.4 16 0.00035 26.4 5.6 25 129-153 107-136 (166)
86 cd01895 EngA2 EngA2 subfamily. 70.4 4.2 9.2E-05 28.7 2.4 15 130-144 114-128 (174)
87 cd04122 Rab14 Rab14 subfamily. 70.3 39 0.00085 24.6 8.0 25 129-153 107-136 (166)
88 cd04159 Arl10_like Arl10-like 70.3 3.2 6.9E-05 28.7 1.8 17 129-145 101-117 (159)
89 cd04124 RabL2 RabL2 subfamily. 70.1 3.9 8.5E-05 30.0 2.3 23 120-142 95-117 (161)
90 cd01855 YqeH YqeH. YqeH is an 69.9 6.7 0.00015 30.0 3.6 52 92-144 22-76 (190)
91 cd04137 RheB Rheb (Ras Homolog 69.9 4.9 0.00011 29.7 2.8 25 128-152 105-134 (180)
92 cd04167 Snu114p Snu114p subfam 69.5 14 0.0003 29.0 5.4 13 130-142 124-136 (213)
93 smart00178 SAR Sar1p-like memb 69.0 47 0.001 25.3 8.1 25 129-153 118-145 (184)
94 TIGR00157 ribosome small subun 68.9 6.2 0.00013 32.6 3.5 18 129-146 67-84 (245)
95 cd04115 Rab33B_Rab33A Rab33B/R 68.8 8.9 0.00019 28.3 4.0 27 128-154 108-139 (170)
96 cd04131 Rnd Rnd subfamily. Th 68.6 6.4 0.00014 30.3 3.3 13 129-141 105-117 (178)
97 TIGR00412 redox_disulf_2 small 68.6 6.7 0.00015 26.6 3.1 49 81-135 7-55 (76)
98 PRK00454 engB GTP-binding prot 68.5 5.6 0.00012 29.7 2.9 22 127-148 133-154 (196)
99 cd04154 Arl2 Arl2 subfamily. 68.1 6 0.00013 29.3 2.9 23 129-151 115-140 (173)
100 cd01860 Rab5_related Rab5-rela 68.0 9.4 0.0002 27.3 3.9 25 128-152 105-134 (163)
101 cd04161 Arl2l1_Arl13_like Arl2 67.9 25 0.00055 26.1 6.3 16 128-143 99-114 (167)
102 cd04152 Arl4_Arl7 Arl4/Arl7 su 67.4 44 0.00095 25.3 7.6 24 128-151 108-134 (183)
103 cd03418 GRX_GRXb_1_3_like Glut 67.4 13 0.00029 24.0 4.2 62 82-151 8-72 (75)
104 PRK12299 obgE GTPase CgtA; Rev 67.3 12 0.00027 32.6 5.2 17 130-146 272-288 (335)
105 cd04145 M_R_Ras_like M-Ras/R-R 66.9 2.7 5.9E-05 30.0 0.9 23 129-151 107-134 (164)
106 COG1084 Predicted GTPase [Gene 66.9 44 0.00094 30.7 8.6 67 84-151 228-302 (346)
107 TIGR03598 GTPase_YsxC ribosome 66.8 6 0.00013 29.8 2.8 17 129-145 129-145 (179)
108 cd04104 p47_IIGP_like p47 (47- 66.7 12 0.00025 29.2 4.4 48 94-143 69-121 (197)
109 cd00878 Arf_Arl Arf (ADP-ribos 66.6 6.4 0.00014 28.2 2.8 26 128-153 99-127 (158)
110 smart00053 DYNc Dynamin, GTPas 66.2 15 0.00033 31.0 5.3 54 91-144 148-207 (240)
111 cd04109 Rab28 Rab28 subfamily. 66.1 10 0.00023 29.6 4.1 25 129-153 109-138 (215)
112 cd04140 ARHI_like ARHI subfami 66.1 7.1 0.00015 28.6 3.0 15 129-143 108-122 (165)
113 TIGR00750 lao LAO/AO transport 65.9 5.6 0.00012 33.6 2.7 30 116-146 160-189 (300)
114 PRK11058 GTPase HflX; Provisio 65.9 24 0.00053 31.9 6.9 15 129-143 309-323 (426)
115 TIGR02194 GlrX_NrdH Glutaredox 65.8 17 0.00038 23.9 4.6 63 81-150 6-71 (72)
116 cd04134 Rho3 Rho3 subfamily. 65.5 10 0.00022 29.0 3.8 24 121-144 96-119 (189)
117 cd01850 CDC_Septin CDC/Septin. 65.1 14 0.00031 31.1 5.0 28 120-150 137-164 (276)
118 PRK09563 rbgA GTPase YlqF; Rev 64.9 25 0.00055 29.5 6.4 27 118-148 44-70 (287)
119 cd04142 RRP22 RRP22 subfamily. 64.8 9.5 0.00021 30.0 3.7 53 100-152 77-144 (198)
120 cd01865 Rab3 Rab3 subfamily. 64.7 52 0.0011 24.0 7.4 23 129-151 106-133 (165)
121 cd00882 Ras_like_GTPase Ras-li 64.5 8 0.00017 25.5 2.7 23 124-146 97-119 (157)
122 PLN03108 Rab family protein; P 64.4 58 0.0013 25.5 8.0 26 128-153 110-140 (210)
123 cd01871 Rac1_like Rac1-like su 64.3 11 0.00023 28.6 3.8 14 129-142 105-118 (174)
124 cd00154 Rab Rab family. Rab G 64.1 7.6 0.00016 26.7 2.7 24 130-153 106-134 (159)
125 cd01879 FeoB Ferrous iron tran 63.8 3.4 7.4E-05 29.2 0.9 15 130-144 102-116 (158)
126 PRK12298 obgE GTPase CgtA; Rev 63.7 7.5 0.00016 34.7 3.2 18 130-147 276-293 (390)
127 cd04119 RJL RJL (RabJ-Like) su 63.6 7.1 0.00015 27.7 2.5 23 130-152 111-138 (168)
128 smart00175 RAB Rab subfamily o 63.6 8.6 0.00019 27.3 2.9 24 129-152 105-133 (164)
129 cd01854 YjeQ_engC YjeQ/EngC. 63.5 7.6 0.00016 32.8 3.0 16 130-145 110-125 (287)
130 cd04162 Arl9_Arfrp2_like Arl9/ 63.3 7.7 0.00017 28.9 2.8 16 128-143 98-113 (164)
131 PRK00093 GTP-binding protein D 63.3 6.7 0.00015 34.0 2.8 19 129-147 284-302 (435)
132 PRK13796 GTPase YqeH; Provisio 63.3 20 0.00044 31.4 5.8 52 89-143 54-110 (365)
133 TIGR03594 GTPase_EngA ribosome 62.7 7 0.00015 33.7 2.8 16 130-145 284-300 (429)
134 PTZ00133 ADP-ribosylation fact 62.6 36 0.00077 26.0 6.4 14 129-142 118-131 (182)
135 PRK10597 DNA damage-inducible 62.5 22 0.00049 26.2 5.0 50 9-64 16-69 (81)
136 cd04149 Arf6 Arf6 subfamily. 62.3 55 0.0012 24.5 7.3 22 129-150 110-134 (168)
137 cd01875 RhoG RhoG subfamily. 62.0 14 0.00031 28.3 4.1 14 129-142 107-120 (191)
138 cd00157 Rho Rho (Ras homology) 61.9 5.5 0.00012 28.6 1.7 22 123-144 98-119 (171)
139 cd04148 RGK RGK subfamily. Th 61.9 4.4 9.6E-05 32.3 1.3 16 128-143 105-120 (221)
140 KOG4252|consensus 61.7 5.3 0.00012 34.7 1.8 94 60-155 35-155 (246)
141 cd04153 Arl5_Arl8 Arl5/Arl8 su 61.5 5.9 0.00013 29.6 1.9 14 129-142 116-129 (174)
142 cd04156 ARLTS1 ARLTS1 subfamil 61.5 56 0.0012 23.3 7.8 22 129-150 101-125 (160)
143 PLN03118 Rab family protein; P 60.9 69 0.0015 24.8 7.8 25 128-152 119-148 (211)
144 cd00876 Ras Ras family. The R 60.5 15 0.00033 25.7 3.8 25 128-152 103-132 (160)
145 cd04121 Rab40 Rab40 subfamily. 60.4 13 0.00028 29.3 3.7 26 128-153 109-139 (189)
146 PF13192 Thioredoxin_3: Thiore 60.3 18 0.00039 24.4 3.9 51 80-136 6-56 (76)
147 PRK12297 obgE GTPase CgtA; Rev 60.1 12 0.00027 34.1 4.0 23 129-151 274-297 (424)
148 PF06207 DUF1002: Protein of u 60.0 23 0.00051 30.1 5.4 53 30-116 53-106 (225)
149 COG2229 Predicted GTPase [Gene 59.9 24 0.00052 29.8 5.4 51 103-155 92-150 (187)
150 cd04120 Rab12 Rab12 subfamily. 59.3 13 0.00028 29.7 3.5 25 128-152 104-133 (202)
151 PRK05291 trmE tRNA modificatio 59.3 5.8 0.00013 35.7 1.7 18 130-147 322-339 (449)
152 PRK15494 era GTPase Era; Provi 59.1 35 0.00076 29.5 6.4 14 130-143 161-174 (339)
153 cd01887 IF2_eIF5B IF2/eIF5B (i 59.1 5.8 0.00013 28.4 1.4 14 130-143 103-116 (168)
154 cd04135 Tc10 TC10 subfamily. 58.9 15 0.00032 26.7 3.6 16 127-142 102-117 (174)
155 cd01886 EF-G Elongation factor 58.8 8.4 0.00018 32.4 2.5 49 93-143 77-130 (270)
156 PRK00098 GTPase RsgA; Reviewed 58.5 12 0.00025 31.8 3.3 14 129-142 111-124 (298)
157 PRK13675 GTP cyclohydrolase; P 57.7 14 0.0003 32.7 3.8 26 101-126 191-224 (308)
158 cd04143 Rhes_like Rhes_like su 57.4 42 0.00091 27.7 6.4 25 128-152 112-141 (247)
159 TIGR02200 GlrX_actino Glutared 57.3 24 0.00052 22.4 4.0 53 81-137 7-59 (77)
160 COG3052 CitD Citrate lyase, ga 57.2 14 0.0003 28.6 3.2 61 29-121 16-76 (98)
161 smart00177 ARF ARF-like small 56.6 73 0.0016 23.9 7.1 21 130-150 115-138 (175)
162 cd04113 Rab4 Rab4 subfamily. 56.6 12 0.00025 27.0 2.6 22 130-151 106-132 (161)
163 PF06857 ACP: Malonate decarbo 56.2 33 0.00072 25.3 5.0 30 90-119 44-73 (87)
164 KOG1752|consensus 56.2 24 0.00052 26.6 4.3 64 82-150 22-87 (104)
165 cd04133 Rop_like Rop subfamily 56.1 10 0.00023 29.4 2.5 25 130-154 106-145 (176)
166 cd04168 TetM_like Tet(M)-like 55.9 13 0.00029 30.4 3.2 24 118-143 107-130 (237)
167 cd01883 EF1_alpha Eukaryotic e 55.5 11 0.00024 29.9 2.6 13 130-142 138-150 (219)
168 PRK13768 GTPase; Provisional 55.3 7.8 0.00017 32.1 1.7 23 128-150 161-183 (253)
169 cd04123 Rab21 Rab21 subfamily. 55.0 14 0.0003 26.0 2.7 23 130-152 106-133 (162)
170 cd01873 RhoBTB RhoBTB subfamil 54.9 17 0.00036 28.7 3.5 14 129-142 120-133 (195)
171 cd04150 Arf1_5_like Arf1-Arf5- 54.6 57 0.0012 24.0 6.1 13 130-142 102-114 (159)
172 PLN03110 Rab GTPase; Provision 54.5 47 0.001 26.2 6.0 24 130-153 118-146 (216)
173 cd04129 Rho2 Rho2 subfamily. 54.3 19 0.00041 27.3 3.6 14 129-142 105-118 (187)
174 TIGR02183 GRXA Glutaredoxin, G 53.6 45 0.00099 23.0 5.2 68 82-154 8-81 (86)
175 PF01189 Nol1_Nop2_Fmu: NOL1/N 53.6 7.6 0.00016 33.0 1.5 45 9-65 193-238 (283)
176 PRK01889 GTPase RsgA; Reviewed 53.6 20 0.00043 31.4 4.1 26 117-144 132-157 (356)
177 PF08477 Miro: Miro-like prote 52.8 13 0.00027 25.6 2.2 13 128-140 107-119 (119)
178 KOG1489|consensus 52.3 13 0.00029 34.2 2.9 36 125-160 308-348 (366)
179 cd01885 EF2 EF2 (for archaea a 51.7 14 0.00031 30.3 2.7 13 130-142 126-138 (222)
180 PRK12296 obgE GTPase CgtA; Rev 51.2 12 0.00025 35.2 2.4 19 128-146 283-301 (500)
181 TIGR00483 EF-1_alpha translati 51.1 64 0.0014 28.5 6.8 14 130-143 142-155 (426)
182 TIGR02189 GlrX-like_plant Glut 51.0 47 0.001 23.9 5.0 64 82-150 16-81 (99)
183 cd04108 Rab36_Rab34 Rab34/Rab3 50.5 63 0.0014 24.2 5.9 14 130-143 107-120 (170)
184 PRK09518 bifunctional cytidyla 50.3 20 0.00044 34.2 3.8 18 129-146 561-578 (712)
185 cd04105 SR_beta Signal recogni 50.3 44 0.00095 26.4 5.2 15 129-143 109-123 (203)
186 PRK00093 GTP-binding protein D 50.2 18 0.00039 31.4 3.3 40 119-160 101-143 (435)
187 cd01884 EF_Tu EF-Tu subfamily. 50.0 15 0.00032 29.3 2.5 52 91-144 76-133 (195)
188 COG0536 Obg Predicted GTPase [ 49.9 15 0.00032 34.0 2.8 21 130-150 276-297 (369)
189 cd04117 Rab15 Rab15 subfamily. 49.6 19 0.00041 26.5 2.9 24 129-152 105-133 (161)
190 cd04176 Rap2 Rap2 subgroup. T 49.5 10 0.00022 27.3 1.4 14 129-142 106-119 (163)
191 PRK03003 GTP-binding protein D 49.2 15 0.00031 33.1 2.6 16 129-144 322-337 (472)
192 PF00025 Arf: ADP-ribosylation 49.0 27 0.00059 26.6 3.8 33 118-150 103-139 (175)
193 TIGR01393 lepA GTP-binding pro 48.7 72 0.0016 30.2 7.2 14 130-143 123-136 (595)
194 TIGR02181 GRX_bact Glutaredoxi 48.4 44 0.00095 22.0 4.3 64 81-151 6-70 (79)
195 cd01615 CIDE_N CIDE_N domain, 47.8 16 0.00034 26.9 2.1 59 64-129 4-67 (78)
196 PTZ00327 eukaryotic translatio 47.8 17 0.00036 33.5 2.8 56 91-147 128-189 (460)
197 cd04166 CysN_ATPS CysN_ATPS su 47.7 20 0.00044 28.1 2.9 13 131-143 132-144 (208)
198 cd04126 Rab20 Rab20 subfamily. 47.2 32 0.00068 28.1 4.1 15 129-143 100-114 (220)
199 TIGR00475 selB selenocysteine- 46.6 71 0.0015 30.1 6.7 18 130-147 103-121 (581)
200 cd02966 TlpA_like_family TlpA- 46.6 61 0.0013 20.9 4.6 43 90-138 64-106 (116)
201 cd01874 Cdc42 Cdc42 subfamily. 46.4 21 0.00046 27.0 2.8 15 129-143 105-119 (175)
202 cd04147 Ras_dva Ras-dva subfam 46.3 13 0.00029 28.5 1.6 15 129-143 104-118 (198)
203 PF06858 NOG1: Nucleolar GTP-b 46.2 12 0.00026 26.2 1.3 12 129-140 47-58 (58)
204 cd01891 TypA_BipA TypA (tyrosi 46.0 13 0.00029 28.3 1.6 14 129-142 117-130 (194)
205 TIGR03680 eif2g_arch translati 45.2 89 0.0019 27.7 6.8 55 91-146 91-151 (406)
206 COG0523 Putative GTPases (G3E 45.1 19 0.00041 31.8 2.6 18 133-150 149-166 (323)
207 cd04177 RSR1 RSR1 subgroup. R 44.9 26 0.00057 25.6 3.0 14 129-142 106-119 (168)
208 PRK03003 GTP-binding protein D 44.4 23 0.00049 31.9 3.0 24 118-143 137-160 (472)
209 PF02421 FeoB_N: Ferrous iron 43.8 31 0.00067 27.4 3.4 52 90-142 66-118 (156)
210 PTZ00369 Ras-like protein; Pro 43.5 24 0.00052 26.8 2.7 14 129-142 110-123 (189)
211 cd04173 Rnd2_Rho7 Rnd2/Rho7 su 43.2 1.4E+02 0.0029 24.5 7.2 14 129-142 105-118 (222)
212 PF05193 Peptidase_M16_C: Pept 43.1 61 0.0013 22.8 4.5 37 89-125 2-39 (184)
213 CHL00071 tufA elongation facto 43.0 23 0.00049 31.4 2.8 54 91-146 86-145 (409)
214 PRK12739 elongation factor G; 42.9 22 0.00047 33.8 2.8 25 118-144 116-140 (691)
215 TIGR00485 EF-Tu translation el 42.8 34 0.00074 30.0 3.8 19 127-145 125-144 (394)
216 TIGR00073 hypB hydrogenase acc 42.6 19 0.00042 28.3 2.1 14 130-143 149-162 (207)
217 PRK13674 putative GTP cyclohyd 42.5 21 0.00047 31.0 2.5 42 77-126 147-196 (271)
218 cd01870 RhoA_like RhoA-like su 42.4 26 0.00056 25.5 2.6 15 129-143 105-119 (175)
219 PHA01631 hypothetical protein 42.3 22 0.00048 29.9 2.5 49 91-139 57-107 (176)
220 cd00877 Ran Ran (Ras-related n 42.2 22 0.00047 26.4 2.2 14 129-142 104-117 (166)
221 PRK09866 hypothetical protein; 42.2 39 0.00085 33.8 4.5 13 131-143 291-303 (741)
222 cd04118 Rab24 Rab24 subfamily. 41.5 29 0.00063 26.0 2.8 14 130-143 106-119 (193)
223 PLN03126 Elongation factor Tu; 41.3 23 0.00051 32.6 2.7 54 91-146 155-214 (478)
224 cd06535 CIDE_N_CAD CIDE_N doma 40.9 23 0.0005 26.1 2.1 57 65-129 5-66 (77)
225 PF14297 DUF4373: Domain of un 40.5 23 0.0005 24.9 2.0 20 88-107 57-76 (87)
226 COG0012 Predicted GTPase, prob 40.4 22 0.00047 32.7 2.3 47 114-160 190-245 (372)
227 PRK09518 bifunctional cytidyla 39.5 1.1E+02 0.0024 29.3 6.9 52 91-144 342-398 (712)
228 cd04111 Rab39 Rab39 subfamily. 39.0 31 0.00067 27.2 2.7 24 130-153 110-138 (211)
229 KOG2484|consensus 38.8 35 0.00077 32.2 3.5 58 90-150 129-198 (435)
230 PF00071 Ras: Ras family; Int 38.6 44 0.00096 23.9 3.3 53 101-153 69-133 (162)
231 cd02997 PDI_a_PDIR PDIa family 38.6 43 0.00092 22.3 3.0 59 81-139 26-85 (104)
232 COG1161 Predicted GTPases [Gen 38.4 23 0.0005 30.7 2.1 55 91-149 21-81 (322)
233 TIGR00294 conserved hypothetic 38.4 33 0.00072 29.8 3.1 26 101-126 189-222 (308)
234 PRK12736 elongation factor Tu; 38.4 1E+02 0.0022 27.1 6.1 53 91-145 86-144 (394)
235 cd02995 PDI_a_PDI_a'_C PDIa fa 38.4 62 0.0013 21.5 3.8 59 80-140 26-84 (104)
236 smart00266 CAD Domains present 38.4 26 0.00057 25.5 2.1 58 65-129 3-65 (74)
237 TIGR01608 citD citrate lyase a 38.3 61 0.0013 24.7 4.1 30 91-120 46-75 (92)
238 PRK13580 serine hydroxymethylt 38.1 44 0.00096 31.5 4.0 37 12-48 384-421 (493)
239 COG0486 ThdF Predicted GTPase 37.9 32 0.0007 32.5 3.1 48 103-150 294-345 (454)
240 cd04103 Centaurin_gamma Centau 37.7 23 0.00049 26.6 1.7 23 130-152 100-129 (158)
241 PRK15467 ethanolamine utilizat 37.6 45 0.00098 25.1 3.3 15 129-143 91-105 (158)
242 PF03029 ATP_bind_1: Conserved 37.5 20 0.00043 29.8 1.5 18 126-143 153-170 (238)
243 PRK15367 type III secretion sy 37.3 3.5E+02 0.0076 25.3 10.6 120 10-151 140-274 (395)
244 TIGR02475 CobW cobalamin biosy 37.3 30 0.00065 30.3 2.6 19 132-150 176-194 (341)
245 PRK10076 pyruvate formate lyas 37.3 37 0.00081 28.0 3.1 100 38-152 38-152 (213)
246 KOG1487|consensus 37.3 21 0.00045 32.8 1.7 71 56-126 194-279 (358)
247 PTZ00099 rab6; Provisional 36.7 72 0.0016 24.7 4.4 23 129-151 85-112 (176)
248 KOG0395|consensus 36.7 33 0.00072 27.7 2.6 23 129-151 108-135 (196)
249 PLN03127 Elongation factor Tu; 36.6 51 0.0011 30.1 4.0 26 118-145 167-193 (447)
250 PRK05433 GTP-binding protein L 36.5 69 0.0015 30.4 5.0 14 130-143 127-140 (600)
251 smart00176 RAN Ran (Ras-relate 36.2 1.2E+02 0.0026 24.2 5.7 15 128-142 98-112 (200)
252 TIGR01295 PedC_BrcD bacterioci 35.9 1.8E+02 0.0039 21.6 6.6 72 80-151 31-120 (122)
253 TIGR00550 nadA quinolinate syn 35.5 61 0.0013 28.6 4.3 52 61-117 63-118 (310)
254 cd05025 S-100A1 S-100A1: S-100 35.4 42 0.0009 23.3 2.7 31 89-124 49-79 (92)
255 TIGR03594 GTPase_EngA ribosome 34.9 22 0.00047 30.7 1.4 24 119-144 99-122 (429)
256 KOG2485|consensus 34.8 88 0.0019 28.7 5.2 55 91-148 34-92 (335)
257 COG2151 PaaD Predicted metal-s 34.8 42 0.00091 25.9 2.8 39 81-119 59-100 (111)
258 PLN03071 GTP-binding nuclear p 34.7 28 0.00061 27.7 1.9 15 128-142 116-130 (219)
259 TIGR00450 mnmE_trmE_thdF tRNA 34.5 30 0.00066 31.4 2.3 16 129-144 310-325 (442)
260 PF10662 PduV-EutP: Ethanolami 33.6 35 0.00076 27.1 2.3 44 107-150 66-111 (143)
261 TIGR00484 EF-G translation elo 33.3 43 0.00093 31.8 3.1 24 118-143 118-141 (689)
262 PRK10512 selenocysteinyl-tRNA- 33.2 1.5E+02 0.0032 28.4 6.7 54 91-146 62-121 (614)
263 PF12307 DUF3631: Protein of u 33.0 65 0.0014 26.9 3.8 36 89-124 143-182 (184)
264 cd04169 RF3 RF3 subfamily. Pe 32.7 35 0.00075 28.7 2.2 14 130-143 124-137 (267)
265 cd02973 TRX_GRX_like Thioredox 32.6 46 0.001 21.1 2.3 53 81-138 8-61 (67)
266 PLN00043 elongation factor 1-a 32.5 48 0.001 30.1 3.2 52 90-142 95-158 (447)
267 cd02976 NrdH NrdH-redoxin (Nrd 32.4 72 0.0016 19.5 3.2 51 81-137 7-58 (73)
268 cd04170 EF-G_bact Elongation f 32.3 30 0.00065 28.2 1.7 25 118-144 107-131 (268)
269 PF07927 YcfA: YcfA-like prote 32.2 1.3E+02 0.0029 18.9 5.4 51 13-63 3-54 (56)
270 PRK12735 elongation factor Tu; 32.1 39 0.00084 29.8 2.5 25 118-144 118-143 (396)
271 PRK04000 translation initiatio 32.1 35 0.00075 30.4 2.2 16 131-146 141-156 (411)
272 cd06538 CIDE_N_FSP27 CIDE_N do 32.0 34 0.00074 25.3 1.8 58 65-129 5-66 (79)
273 COG5324 Uncharacterized conser 32.0 34 0.00073 33.9 2.2 74 58-133 502-576 (758)
274 PTZ00062 glutaredoxin; Provisi 31.7 1.1E+02 0.0024 25.4 5.0 66 80-151 124-189 (204)
275 PF06183 DinI: DinI-like famil 31.0 80 0.0017 22.1 3.5 49 10-64 5-55 (65)
276 PLN00023 GTP-binding protein; 30.9 53 0.0012 29.7 3.2 15 129-143 151-165 (334)
277 PRK11933 yebU rRNA (cytosine-C 30.0 29 0.00063 32.2 1.4 32 71-102 230-262 (470)
278 COG1100 GTPase SAR1 and relate 29.9 95 0.0021 23.6 4.0 55 90-144 63-126 (219)
279 cd03029 GRX_hybridPRX5 Glutare 29.9 1.5E+02 0.0032 19.2 4.5 52 81-138 8-59 (72)
280 PRK11200 grxA glutaredoxin 1; 29.7 62 0.0013 21.9 2.7 65 82-151 9-79 (85)
281 PF13590 DUF4136: Domain of un 29.7 77 0.0017 23.0 3.4 25 11-35 41-65 (151)
282 PF00462 Glutaredoxin: Glutare 29.6 1.1E+02 0.0023 19.3 3.7 49 82-136 7-56 (60)
283 TIGR00446 nop2p NOL1/NOP2/sun 29.2 33 0.00071 28.5 1.5 32 72-103 188-220 (264)
284 PRK10824 glutaredoxin-4; Provi 29.1 1.4E+02 0.0031 22.7 4.9 50 82-138 28-79 (115)
285 PRK09435 membrane ATPase/prote 29.0 37 0.0008 30.1 1.9 31 114-145 180-210 (332)
286 cd04128 Spg1 Spg1p. Spg1p (se 28.7 78 0.0017 24.3 3.4 12 130-142 106-117 (182)
287 PF02492 cobW: CobW/HypB/UreG, 28.5 25 0.00054 27.2 0.7 19 132-150 144-163 (178)
288 cd01853 Toc34_like Toc34-like 28.5 1.1E+02 0.0023 25.7 4.4 23 123-145 143-165 (249)
289 KOG1490|consensus 28.5 24 0.00052 34.5 0.7 62 84-148 228-300 (620)
290 PRK00007 elongation factor G; 28.2 58 0.0013 31.1 3.1 24 118-143 118-141 (693)
291 PF04320 DUF469: Protein with 28.2 1.8E+02 0.0039 22.3 5.2 38 113-150 33-78 (101)
292 COG5309 Exo-beta-1,3-glucanase 28.1 35 0.00075 30.9 1.5 53 75-127 98-162 (305)
293 PF05511 ATP-synt_F6: Mitochon 28.1 36 0.00078 26.2 1.4 48 59-106 39-86 (99)
294 cd04102 RabL3 RabL3 (Rab-like3 27.9 36 0.00078 27.4 1.5 15 130-144 130-144 (202)
295 KOG1122|consensus 27.8 68 0.0015 30.6 3.4 45 10-65 345-390 (460)
296 CHL00053 rps7 ribosomal protei 27.8 2.1E+02 0.0045 22.7 5.8 93 12-130 60-152 (155)
297 COG0144 Sun tRNA and rRNA cyto 27.8 1.1E+02 0.0024 27.0 4.6 40 10-65 267-307 (355)
298 PRK05124 cysN sulfate adenylyl 27.5 49 0.0011 30.2 2.5 14 130-143 161-174 (474)
299 COG0218 Predicted GTPase [Gene 27.5 50 0.0011 28.0 2.3 53 93-147 92-153 (200)
300 cd03028 GRX_PICOT_like Glutare 27.4 1.4E+02 0.003 20.7 4.2 63 83-151 22-84 (90)
301 KOG1532|consensus 27.4 47 0.001 30.7 2.3 18 129-146 181-198 (366)
302 PF08765 Mor: Mor transcriptio 26.8 28 0.00061 25.6 0.6 41 91-131 11-52 (108)
303 cd03027 GRX_DEP Glutaredoxin ( 26.4 1.7E+02 0.0037 19.0 4.3 62 82-150 9-71 (73)
304 COG3797 Uncharacterized protei 26.0 77 0.0017 26.8 3.1 88 58-151 24-120 (178)
305 COG2239 MgtE Mg/Co/Ni transpor 26.0 81 0.0018 29.4 3.6 40 86-125 210-254 (451)
306 PRK09554 feoB ferrous iron tra 25.9 1.1E+02 0.0024 30.1 4.7 14 129-142 112-125 (772)
307 TIGR00101 ureG urease accessor 25.8 68 0.0015 25.7 2.7 12 132-143 140-151 (199)
308 COG0780 Enzyme related to GTP 25.6 39 0.00084 27.4 1.3 42 80-124 49-107 (149)
309 TIGR02190 GlrX-dom Glutaredoxi 25.5 1.8E+02 0.004 19.4 4.5 50 82-137 16-65 (79)
310 PF00578 AhpC-TSA: AhpC/TSA fa 25.5 59 0.0013 22.4 2.0 42 83-124 37-78 (124)
311 PRK00049 elongation factor Tu; 25.4 63 0.0014 28.5 2.7 25 118-144 118-143 (396)
312 COG1281 Disulfide bond chapero 25.3 1.3E+02 0.0028 26.8 4.6 35 90-124 211-248 (286)
313 PF06784 UPF0240: Uncharacteri 25.0 77 0.0017 26.0 2.9 20 89-108 148-167 (179)
314 PRK14862 rimO ribosomal protei 25.0 88 0.0019 28.2 3.5 69 42-112 10-81 (440)
315 PF01189 Nol1_Nop2_Fmu: NOL1/N 24.8 26 0.00056 29.8 0.2 29 74-102 210-239 (283)
316 PF00571 CBS: CBS domain CBS d 24.6 1.5E+02 0.0033 17.8 3.6 34 90-123 17-55 (57)
317 PRK13808 adenylate kinase; Pro 24.5 1.5E+02 0.0033 26.6 4.9 24 1-24 82-106 (333)
318 PRK13253 citrate lyase subunit 24.0 2.3E+02 0.005 21.2 5.1 29 91-119 46-74 (92)
319 KOG2198|consensus 23.9 55 0.0012 30.3 2.1 31 71-101 284-315 (375)
320 cd00304 RT_like RT_like: Rever 23.8 1.2E+02 0.0025 20.3 3.2 24 10-33 62-85 (98)
321 PF00919 UPF0004: Uncharacteri 23.8 1.3E+02 0.0028 22.1 3.6 66 47-112 8-76 (98)
322 TIGR00550 nadA quinolinate syn 23.8 1.1E+02 0.0025 26.9 3.9 35 81-117 172-207 (310)
323 PF10678 DUF2492: Protein of u 23.6 2E+02 0.0043 21.2 4.5 39 91-132 23-65 (78)
324 TIGR01394 TypA_BipA GTP-bindin 23.6 51 0.0011 31.3 1.9 14 130-143 117-130 (594)
325 cd01882 BMS1 Bms1. Bms1 is an 23.5 1.1E+02 0.0025 24.6 3.6 24 118-143 123-147 (225)
326 PHA02992 hypothetical protein; 23.4 1.8E+02 0.0038 29.4 5.5 63 54-128 153-215 (728)
327 PF10281 Ish1: Putative stress 23.2 1.1E+02 0.0024 18.7 2.8 34 89-126 4-37 (38)
328 smart00115 CASc Caspase, inter 23.1 1.2E+02 0.0026 25.0 3.7 33 89-124 30-62 (241)
329 PRK13505 formate--tetrahydrofo 22.8 67 0.0015 31.1 2.5 35 114-150 359-393 (557)
330 PLN00116 translation elongatio 22.6 67 0.0015 31.6 2.5 49 92-142 110-163 (843)
331 PRK05506 bifunctional sulfate 22.5 69 0.0015 30.0 2.5 14 130-143 158-171 (632)
332 cd06536 CIDE_N_ICAD CIDE_N dom 22.4 79 0.0017 23.4 2.3 58 65-129 5-69 (80)
333 PF02017 CIDE-N: CIDE-N domain 22.2 26 0.00057 25.6 -0.3 58 65-129 5-67 (78)
334 PF13529 Peptidase_C39_2: Pept 22.0 2.6E+02 0.0057 19.1 4.8 44 88-137 64-107 (144)
335 cd03063 TRX_Fd_FDH_beta TRX-li 21.9 2.3E+02 0.005 20.9 4.7 61 9-103 18-79 (92)
336 TIGR00487 IF-2 translation ini 21.6 83 0.0018 29.9 2.8 21 128-148 186-208 (587)
337 TIGR00411 redox_disulf_1 small 21.6 1.6E+02 0.0035 18.8 3.4 53 80-138 7-61 (82)
338 PF13419 HAD_2: Haloacid dehal 21.4 3E+02 0.0064 19.2 5.4 67 54-125 103-169 (176)
339 cd02947 TRX_family TRX family; 21.4 2.1E+02 0.0046 17.6 4.2 54 81-139 19-73 (93)
340 TIGR00503 prfC peptide chain r 20.9 56 0.0012 30.5 1.5 23 118-142 123-145 (527)
341 COG1159 Era GTPase [General fu 20.9 6.3E+02 0.014 22.8 10.5 106 7-146 15-131 (298)
342 COG1258 Predicted pseudouridyl 20.7 1.2E+02 0.0025 28.6 3.5 41 85-125 262-305 (398)
343 PF11263 Attachment_P66: Borre 20.6 88 0.0019 27.4 2.5 48 66-113 71-122 (233)
344 COG0050 TufB GTPases - transla 20.4 77 0.0017 29.6 2.3 80 67-149 50-148 (394)
345 cd02961 PDI_a_family Protein D 20.4 2.4E+02 0.0052 17.8 4.2 58 80-139 23-81 (101)
346 COG4009 Uncharacterized protei 20.3 66 0.0014 24.5 1.5 19 11-29 62-80 (88)
347 COG1162 Predicted GTPases [Gen 20.2 76 0.0017 28.4 2.1 37 112-148 92-129 (301)
348 PRK00741 prfC peptide chain re 20.1 64 0.0014 30.1 1.7 15 129-143 131-145 (526)
349 cd01659 TRX_superfamily Thiore 20.0 1.7E+02 0.0036 15.8 4.6 56 81-138 6-62 (69)
No 1
>KOG1486|consensus
Probab=100.00 E-value=5.7e-52 Score=360.49 Aligned_cols=124 Identities=73% Similarity=1.165 Sum_probs=118.0
Q ss_pred CCCCCCchHHHHHHHHHHHhcCceeccCCCCeEEEEecCcceEEecccCCchhhHHHHHHHHHHhhhhhhHHhhhcCccc
Q psy7060 1 MLDATKQDVQRGLLEKELESVGIRLNKKKPNIYFKQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEQKKAGGIAF 80 (160)
Q Consensus 1 vLDa~k~~~q~~~le~ELe~~GIrLnkk~p~I~ikkk~~GGI~i~~t~~lt~~~~~~v~~~l~~yki~n~~~~~~~~~~~ 80 (160)
||||+|.+.||.+||+|||++||||||+||||+|++|+.|||.|+.|||+
T Consensus 146 vLDatk~e~qr~~le~ELe~vGiRLNk~~Pniy~k~kk~gGi~f~~T~~l------------------------------ 195 (364)
T KOG1486|consen 146 VLDATKSEDQREILEKELEAVGIRLNKRKPNIYFKKKKTGGISFNTTVPL------------------------------ 195 (364)
T ss_pred EecCCcchhHHHHHHHHHHHhceeccCCCCCeEEEeeccCCeEEeeeecc------------------------------
Confidence 79999999999999999999999999999999999998888877665555
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEEecCCCCCHHHHHHHhcCCCceeeC
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYNKIDQISIEEVDRIARQPNSVVVR 160 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~NKiD~is~eevd~i~~~p~~v~is 160 (160)
|++||++++.||||||||||+|+||||||.|||||+|.|||+|+||+|||||||++|+||+||+||+||||+||
T Consensus 196 ------T~~~ek~i~~ILheykI~Naevl~ReD~t~DdfIDvi~gnr~Y~~ClYvYnKID~vs~eevdrlAr~PnsvViS 269 (364)
T KOG1486|consen 196 ------THCDEKLIYTILHEYKIHNAEVLFREDCTVDDFIDVIEGNRVYIKCLYVYNKIDQVSIEEVDRLARQPNSVVIS 269 (364)
T ss_pred ------ccccHHHHHHHHHHHeeccceEEEecCCChHHHHHHHhccceEEEEEEEeeccceecHHHHHHHhcCCCcEEEE
Confidence 55999999999999999999999999999999999999999999999999999999999999999999999997
No 2
>COG1163 DRG Predicted GTPase [General function prediction only]
Probab=100.00 E-value=4.9e-41 Score=295.45 Aligned_cols=124 Identities=50% Similarity=0.849 Sum_probs=120.2
Q ss_pred CCCCCCchHHHHHHHHHHHhcCceeccCCCCeEEEEecCcceEEecccCCchhhHHHHHHHHHHhhhhhhHHhhhcCccc
Q psy7060 1 MLDATKQDVQRGLLEKELESVGIRLNKKKPNIYFKQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEQKKAGGIAF 80 (160)
Q Consensus 1 vLDa~k~~~q~~~le~ELe~~GIrLnkk~p~I~ikkk~~GGI~i~~t~~lt~~~~~~v~~~l~~yki~n~~~~~~~~~~~ 80 (160)
|||++++..|++.|++|||++|||||+.||+|+|++++.|||++++++++++
T Consensus 147 Vld~~~~~~~~~~i~~ELe~~GIrlnk~~p~V~I~kk~~gGI~i~~t~~l~~---------------------------- 198 (365)
T COG1163 147 VLDVFEDPHHRDIIERELEDVGIRLNKRPPDVTIKKKESGGIRINGTGPLTH---------------------------- 198 (365)
T ss_pred EEecCCChhHHHHHHHHHHhcCeEecCCCCceEEEEeccCCEEEeccccccc----------------------------
Confidence 5899999878999999999999999999999999999999999998888776
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEEecCCCCCHHHHHHHhcCCCceeeC
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYNKIDQISIEEVDRIARQPNSVVVR 160 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~NKiD~is~eevd~i~~~p~~v~is 160 (160)
+|+++|++||+|||||||+|+||||||+|||||++++||+|+|||||+||+|+++.|+++.+++.|++++||
T Consensus 199 --------~d~~~ir~iL~Ey~I~nA~V~Ir~dvTlDd~id~l~~nrvY~p~l~v~NKiD~~~~e~~~~l~~~~~~v~is 270 (365)
T COG1163 199 --------LDEDTVRAILREYRIHNADVLIREDVTLDDLIDALEGNRVYKPALYVVNKIDLPGLEELERLARKPNSVPIS 270 (365)
T ss_pred --------CCHHHHHHHHHHhCcccceEEEecCCcHHHHHHHHhhcceeeeeEEEEecccccCHHHHHHHHhccceEEEe
Confidence 999999999999999999999999999999999999999999999999999999999999999999999997
No 3
>KOG1487|consensus
Probab=100.00 E-value=2.1e-37 Score=269.79 Aligned_cols=120 Identities=48% Similarity=0.783 Sum_probs=117.1
Q ss_pred CCCCCCchHHHHHHHHHHHhcCceeccCCCCeEEEEecCcceEEecccCCchhhHHHHHHHHHHhhhhhhHHhhhcCccc
Q psy7060 1 MLDATKQDVQRGLLEKELESVGIRLNKKKPNIYFKQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEQKKAGGIAF 80 (160)
Q Consensus 1 vLDa~k~~~q~~~le~ELe~~GIrLnkk~p~I~ikkk~~GGI~i~~t~~lt~~~~~~v~~~l~~yki~n~~~~~~~~~~~ 80 (160)
|||+.|+..|+.++|+|||.+||||||+||||.+++|+.|||++++ ++
T Consensus 143 vld~~kp~~hk~~ie~eleg~girlnk~pp~i~~kkKdkgGInlt~----~~---------------------------- 190 (358)
T KOG1487|consen 143 VLDVLKPLSHKKIIEKELEGFGIRLNKQPPNIGTKKKDKGGINLTG----TH---------------------------- 190 (358)
T ss_pred EeeccCcccHHHHHHHhhhcceeeccCCCCCccccccccCceeeec----ch----------------------------
Confidence 6899999999999999999999999999999999999999999988 55
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEEecCCCCCHHHHHHHhcCCCceeeC
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYNKIDQISIEEVDRIARQPNSVVVR 160 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~NKiD~is~eevd~i~~~p~~v~is 160 (160)
++-++++++|.|||+|||++.+|.|+|+|||||++++||+|+||||++||||++|+||+|-+.+.||+|+||
T Consensus 191 --------LdlD~~rsil~eyR~hsAdi~Lr~DaT~DdLIdvVegnr~yVp~iyvLNkIdsISiEELdii~~iphavpIS 262 (358)
T KOG1487|consen 191 --------LDLDLQRSILSEYRIHSADIALRFDATADDLIDVVEGNRIYVPCIYVLNKIDSISIEELDIIYTIPHAVPIS 262 (358)
T ss_pred --------hhHHHHHHHHHHhhhcchheeeecCcchhhhhhhhccCceeeeeeeeecccceeeeeccceeeeccceeecc
Confidence 889999999999999999999999999999999999999999999999999999999999999999999997
No 4
>cd01896 DRG The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding.
Probab=100.00 E-value=5.6e-35 Score=234.98 Aligned_cols=124 Identities=64% Similarity=1.003 Sum_probs=118.6
Q ss_pred CCCCCCchHHHHHHHHHHHhcCceeccCCCCeEEEEecCcceEEecccCCchhhHHHHHHHHHHhhhhhhHHhhhcCccc
Q psy7060 1 MLDATKQDVQRGLLEKELESVGIRLNKKKPNIYFKQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEQKKAGGIAF 80 (160)
Q Consensus 1 vLDa~k~~~q~~~le~ELe~~GIrLnkk~p~I~ikkk~~GGI~i~~t~~lt~~~~~~v~~~l~~yki~n~~~~~~~~~~~ 80 (160)
|+|++.+..|+..++++|+++||++|+++|.|.|+++..|||+|++++++++
T Consensus 84 V~D~t~~~~~~~~~~~~l~~~gi~l~~~~~~v~~~~~~~ggi~~~~~~~~~~---------------------------- 135 (233)
T cd01896 84 VLDATKPEGHREILERELEGVGIRLNKRPPNITIKKKKKGGINITSTVPLTK---------------------------- 135 (233)
T ss_pred EecCCcchhHHHHHHHHHHHcCceecCCCCeEEEEEEecCCEEEeccCCCCC----------------------------
Confidence 5788888779999999999999999999999999999999999999888877
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEEecCCCCCHHHHHHHhcCCCceeeC
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYNKIDQISIEEVDRIARQPNSVVVR 160 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~NKiD~is~eevd~i~~~p~~v~is 160 (160)
+|+++|++||+|||||||+|.++|++|+|||||+|+|||+|+||++|+||+|+.+.++++.+++.|+.+++|
T Consensus 136 --------~~~~~v~~~l~~~~i~~~~v~~~~~~~~~~~~~~~~~~~~y~p~iiV~NK~Dl~~~~~~~~~~~~~~~~~~S 207 (233)
T cd01896 136 --------LDEKTIKAILREYKIHNADVLIREDITVDDLIDVIEGNRVYIPCLYVYNKIDLISIEELDLLARQPNSVVIS 207 (233)
T ss_pred --------CCHHHHHHHHHHhCeeeEEEEEccCCCHHHHHHHHhCCceEeeEEEEEECccCCCHHHHHHHhcCCCEEEEc
Confidence 999999999999999999999999999999999999999999999999999999999999999999888876
No 5
>cd01899 Ygr210 Ygr210 subfamily. Ygr210 is a member of Obg-like family and present in archaea and fungi. They are characterized by a distinct glycine-rich motif immediately following the Walker B motif. The Ygr210 and YyaF/YchF subfamilies appear to form one major branch of the Obg-like family. Among eukaryotes, the Ygr210 subfamily is represented only in fungi. These fungal proteins form a tight cluster with their archaeal orthologs, which suggests the possibility of horizontal transfer from archaea to fungi.
Probab=98.92 E-value=1.5e-10 Score=99.35 Aligned_cols=118 Identities=19% Similarity=0.050 Sum_probs=85.0
Q ss_pred chHHHHHHHHHHHhc-CceeccCCCCeEEEEecCcceEEecccCCchhhHHHHHHHHHHhhhhhhHHhhhcCccccccCC
Q psy7060 7 QDVQRGLLEKELESV-GIRLNKKKPNIYFKQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEQKKAGGIAFNSTCP 85 (160)
Q Consensus 7 ~~~q~~~le~ELe~~-GIrLnkk~p~I~ikkk~~GGI~i~~t~~lt~~~~~~v~~~l~~yki~n~~~~~~~~~~~~~~~~ 85 (160)
+..|...++.||+.. ...++++.+.+. ++..+||..++.+.... ..
T Consensus 127 p~~d~~~i~~El~~~d~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~--------------------------------~~ 173 (318)
T cd01899 127 PLEDIEFLENEIDMWIYGILEKNWEKIV-RKADAEKTDIVEALSEQ--------------------------------LS 173 (318)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhcCCccHHHHHHHH--------------------------------Hh
Confidence 355889999999986 777788877777 44455555544322110 01
Q ss_pred CcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEEecCCCCCHHHHHH-H-hc--CCCceeeC
Q psy7060 86 LTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYNKIDQISIEEVDR-I-AR--QPNSVVVR 160 (160)
Q Consensus 86 ~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~NKiD~is~eevd~-i-~~--~p~~v~is 160 (160)
+-+++++.|+.+| ++++++|.+.++++.++++|.+++.. .++|+|||+||+|+.+.++... + .. .+..+++|
T Consensus 174 ~~~~~~~~v~~~L-~~~~~~~~~~~~~~~~~~~~~~~~ll--t~KPvI~VlNK~Dl~~~~~~~~~l~~~~~~~~iI~iS 249 (318)
T cd01899 174 GFGVNEKDVIEAL-EELELPEDLSKWTDEDLLRLARALRK--RSKPMVIAANKADIPDAENNISKLRLKYPDEIVVPTS 249 (318)
T ss_pred hccccHHHHHHHH-HhCCCCCcccCCCHHHHHHHHHHHHh--cCCcEEEEEEHHHccChHHHHHHHHhhCCCCeEEEEe
Confidence 1248899999999 55999999999999999999999985 4589999999999876655332 2 22 33456665
No 6
>PRK09602 translation-associated GTPase; Reviewed
Probab=98.70 E-value=5.4e-09 Score=92.14 Aligned_cols=116 Identities=22% Similarity=0.236 Sum_probs=78.6
Q ss_pred chHHHHHHHHHHHhc--CceeccCCCCeEEEEecCcceEEecccCCchhhHHHHHHHHHHhhhhhhHHhhhcCccccccC
Q psy7060 7 QDVQRGLLEKELESV--GIRLNKKKPNIYFKQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEQKKAGGIAFNSTC 84 (160)
Q Consensus 7 ~~~q~~~le~ELe~~--GIrLnkk~p~I~ikkk~~GGI~i~~t~~lt~~~~~~v~~~l~~yki~n~~~~~~~~~~~~~~~ 84 (160)
+..|...++.||+.. ++ ++|+.+.+ .++.++|+..+.. .++..|.-
T Consensus 130 p~~d~~~i~~EL~~~d~~~-~~k~~~~~-~~~~~~~~~~~~~----------~~~~~l~~-------------------- 177 (396)
T PRK09602 130 PVEDIKFLEEELDMWIYGI-LEKNWEKF-SRKAQAEKFDIEE----------ALAEQLSG-------------------- 177 (396)
T ss_pred HHHHHHHHHHHHHHHhHHH-HHHHHHHH-HHHHhcCCcchHH----------HHHHHHhh--------------------
Confidence 356899999999985 88 77777777 4444455522111 11111111
Q ss_pred CCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcce-eceEEEEecCCCCC-HHHHHHHhcC--CCceeeC
Q psy7060 85 PLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVY-LPCIYAYNKIDQIS-IEEVDRIARQ--PNSVVVR 160 (160)
Q Consensus 85 ~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY-~P~iyv~NKiD~is-~eevd~i~~~--p~~v~is 160 (160)
-+++++.|+.+|++|++. |.+... +.+|+.++...++.+ +|+|||+||+|..+ .+.++.+.++ +..++||
T Consensus 178 --~~~~e~~v~~~L~~~g~~-~~~~~~---~~~~~~~I~~~~l~t~KPvI~VlNK~D~~~~~~~l~~i~~~~~~~vvpIS 251 (396)
T PRK09602 178 --LGINEEHVKEALRELGLP-EDPSKW---TDEDLLELARELRKISKPMVIAANKADLPPAEENIERLKEEKYYIVVPTS 251 (396)
T ss_pred --hccCHHHHHHHHHHcCCc-CcccCC---CHHHHHHHHHhhhhcCCCEEEEEEchhcccchHHHHHHHhcCCCcEEEEc
Confidence 137899999999999998 665554 457777777777665 99999999999874 4446666555 4567776
No 7
>KOG1486|consensus
Probab=94.92 E-value=0.0069 Score=54.40 Aligned_cols=19 Identities=68% Similarity=0.945 Sum_probs=17.5
Q ss_pred hHHHHHHHHHHhhhhhhHH
Q psy7060 54 NEKLVQLILHEYKIFNAEQ 72 (160)
Q Consensus 54 ~~~~v~~~l~~yki~n~~~ 72 (160)
|+++++.|||+||||||+-
T Consensus 199 ~ek~i~~ILheykI~Naev 217 (364)
T KOG1486|consen 199 DEKLIYTILHEYKIHNAEV 217 (364)
T ss_pred cHHHHHHHHHHHeeccceE
Confidence 5899999999999999984
No 8
>COG2262 HflX GTPases [General function prediction only]
Probab=94.55 E-value=0.033 Score=51.24 Aligned_cols=31 Identities=39% Similarity=0.651 Sum_probs=24.2
Q ss_pred eceEEEEecCCCCCHHH-HHHHhcC-CCceeeC
Q psy7060 130 LPCIYAYNKIDQISIEE-VDRIARQ-PNSVVVR 160 (160)
Q Consensus 130 ~P~iyv~NKiD~is~ee-vd~i~~~-p~~v~is 160 (160)
+|.|+|+||||+++.++ +..+.+. |+.|+||
T Consensus 305 ~p~i~v~NKiD~~~~~~~~~~~~~~~~~~v~iS 337 (411)
T COG2262 305 IPIILVLNKIDLLEDEEILAELERGSPNPVFIS 337 (411)
T ss_pred CCEEEEEecccccCchhhhhhhhhcCCCeEEEE
Confidence 89999999999997765 5555444 5678887
No 9
>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=90.88 E-value=0.38 Score=42.03 Aligned_cols=81 Identities=22% Similarity=0.447 Sum_probs=43.0
Q ss_pred ccccccCCC-cccCHHH---HHHHHHHcCccceEEEee-cCCC----hhHH---HHHHhcCcc-eeceEEEEecCCCCCH
Q psy7060 78 IAFNSTCPL-TQVNEKL---VQLILHEYKIFNAEVLFR-EDCN----ADEL---IDVINANRV-YLPCIYAYNKIDQISI 144 (160)
Q Consensus 78 ~~~~~~~~~-~~~~e~~---V~~IL~EYkI~NA~V~ir-ed~t----~Ddl---iDvi~~nrv-Y~P~iyv~NKiD~is~ 144 (160)
+.|--|+-+ ..++.+. .+..+.+ +.+|++.+- =|++ .+++ .+.+..-.. =+|+|+|+||+|+.+.
T Consensus 239 i~l~DT~G~~~~l~~~lie~f~~tle~--~~~ADlil~VvD~s~~~~~~~~~~~~~~L~~l~~~~~piIlV~NK~Dl~~~ 316 (351)
T TIGR03156 239 VLLTDTVGFIRDLPHELVAAFRATLEE--VREADLLLHVVDASDPDREEQIEAVEKVLEELGAEDIPQLLVYNKIDLLDE 316 (351)
T ss_pred EEEEecCcccccCCHHHHHHHHHHHHH--HHhCCEEEEEEECCCCchHHHHHHHHHHHHHhccCCCCEEEEEEeecCCCh
Confidence 344556555 3334444 4444554 456655432 2332 2222 233332111 2699999999999877
Q ss_pred HHHHHHhc-CCCceeeC
Q psy7060 145 EEVDRIAR-QPNSVVVR 160 (160)
Q Consensus 145 eevd~i~~-~p~~v~is 160 (160)
+++..+.. .|..+++|
T Consensus 317 ~~v~~~~~~~~~~i~iS 333 (351)
T TIGR03156 317 PRIERLEEGYPEAVFVS 333 (351)
T ss_pred HhHHHHHhCCCCEEEEE
Confidence 77665532 24566665
No 10
>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=90.23 E-value=0.35 Score=36.11 Aligned_cols=19 Identities=21% Similarity=0.176 Sum_probs=16.2
Q ss_pred eceEEEEecCCCCCHHHHH
Q psy7060 130 LPCIYAYNKIDQISIEEVD 148 (160)
Q Consensus 130 ~P~iyv~NKiD~is~eevd 148 (160)
+|.|.|+||+|+.+.+++.
T Consensus 40 ~p~ilVlNKiDl~~~~~~~ 58 (157)
T cd01858 40 KHLIFVLNKCDLVPTWVTA 58 (157)
T ss_pred CCEEEEEEchhcCCHHHHH
Confidence 7999999999999876554
No 11
>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=90.15 E-value=0.4 Score=35.38 Aligned_cols=32 Identities=19% Similarity=0.135 Sum_probs=21.6
Q ss_pred HHHHHHhcCcceeceEEEEecCCCCCHHHHHH
Q psy7060 118 ELIDVINANRVYLPCIYAYNKIDQISIEEVDR 149 (160)
Q Consensus 118 dliDvi~~nrvY~P~iyv~NKiD~is~eevd~ 149 (160)
++...+.....-+|+|+|+||+|+.+.+++..
T Consensus 31 ~l~~~l~~~~~~k~~iivlNK~DL~~~~~~~~ 62 (141)
T cd01857 31 DLERYVKEVDPRKKNILLLNKADLLTEEQRKA 62 (141)
T ss_pred HHHHHHHhccCCCcEEEEEechhcCCHHHHHH
Confidence 44454443223479999999999987766544
No 12
>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=89.46 E-value=0.43 Score=37.57 Aligned_cols=21 Identities=29% Similarity=0.414 Sum_probs=17.6
Q ss_pred eceEEEEecCCCCCHHHHHHH
Q psy7060 130 LPCIYAYNKIDQISIEEVDRI 150 (160)
Q Consensus 130 ~P~iyv~NKiD~is~eevd~i 150 (160)
.|+|+|+||+|+.+.+++...
T Consensus 31 kp~IlVlNK~DL~~~~~l~~~ 51 (172)
T cd04178 31 KKLVLVLNKIDLVPKENVEKW 51 (172)
T ss_pred CCEEEEEehhhcCCHHHHHHH
Confidence 699999999999987766543
No 13
>COG1160 Predicted GTPases [General function prediction only]
Probab=88.68 E-value=1 Score=41.93 Aligned_cols=48 Identities=25% Similarity=0.389 Sum_probs=29.1
Q ss_pred ecCCChhH--HHHHHhcCcceeceEEEEecCCCCCHHHHHH-HhcC--CCceeeC
Q psy7060 111 REDCNADE--LIDVINANRVYLPCIYAYNKIDQISIEEVDR-IARQ--PNSVVVR 160 (160)
Q Consensus 111 red~t~Dd--liDvi~~nrvY~P~iyv~NKiD~is~eevd~-i~~~--p~~v~is 160 (160)
++-+|.+| +.+.+. +.-+|+|.|+||+|-...|+... ..++ ...++||
T Consensus 94 ~~Git~~D~~ia~~Lr--~~~kpviLvvNK~D~~~~e~~~~efyslG~g~~~~IS 146 (444)
T COG1160 94 REGITPADEEIAKILR--RSKKPVILVVNKIDNLKAEELAYEFYSLGFGEPVPIS 146 (444)
T ss_pred CCCCCHHHHHHHHHHH--hcCCCEEEEEEcccCchhhhhHHHHHhcCCCCceEee
Confidence 55556544 334443 44489999999999885554332 3443 3556665
No 14
>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=88.29 E-value=1.7 Score=31.64 Aligned_cols=21 Identities=19% Similarity=0.118 Sum_probs=15.6
Q ss_pred HhcCcceeceEEEEecCCCCC
Q psy7060 123 INANRVYLPCIYAYNKIDQIS 143 (160)
Q Consensus 123 i~~nrvY~P~iyv~NKiD~is 143 (160)
+....--+|+|+|.||+|+.+
T Consensus 96 i~~~~~~~piilv~nK~Dl~~ 116 (174)
T smart00174 96 VKHFCPNTPIILVGTKLDLRE 116 (174)
T ss_pred HHhhCCCCCEEEEecChhhhh
Confidence 433344689999999999853
No 15
>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=86.98 E-value=1.7 Score=30.83 Aligned_cols=21 Identities=33% Similarity=0.415 Sum_probs=15.4
Q ss_pred ceEEEEecCCCCC----HHHHHHHh
Q psy7060 131 PCIYAYNKIDQIS----IEEVDRIA 151 (160)
Q Consensus 131 P~iyv~NKiD~is----~eevd~i~ 151 (160)
|+|+|.||+|+.. .+++.+++
T Consensus 90 p~ilv~NK~Dl~~~~~~~~~~~~~~ 114 (142)
T TIGR02528 90 PVIGLVTKIDLAEADVDIERAKELL 114 (142)
T ss_pred CeEEEEEeeccCCcccCHHHHHHHH
Confidence 9999999999864 24445544
No 16
>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=86.62 E-value=0.62 Score=34.79 Aligned_cols=19 Identities=26% Similarity=0.244 Sum_probs=16.3
Q ss_pred eceEEEEecCCCCCHHHHH
Q psy7060 130 LPCIYAYNKIDQISIEEVD 148 (160)
Q Consensus 130 ~P~iyv~NKiD~is~eevd 148 (160)
+|.|+|+||+|+.+.+++.
T Consensus 30 ~p~IiVlNK~Dl~~~~~~~ 48 (155)
T cd01849 30 KKLILVLNKADLVPKEVLR 48 (155)
T ss_pred CCEEEEEechhcCCHHHHH
Confidence 6999999999998876554
No 17
>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=86.17 E-value=0.77 Score=33.11 Aligned_cols=22 Identities=41% Similarity=0.566 Sum_probs=17.9
Q ss_pred ceeceEEEEecCCCCCHHHHHH
Q psy7060 128 VYLPCIYAYNKIDQISIEEVDR 149 (160)
Q Consensus 128 vY~P~iyv~NKiD~is~eevd~ 149 (160)
..+|.++|.||+|+.+.+++..
T Consensus 119 ~~~p~ivv~NK~Dl~~~~~~~~ 140 (176)
T cd01881 119 TAKPVIYVLNKIDLDDAEELEE 140 (176)
T ss_pred hhCCeEEEEEchhcCchhHHHH
Confidence 4789999999999987655544
No 18
>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=86.05 E-value=2 Score=32.79 Aligned_cols=19 Identities=42% Similarity=0.683 Sum_probs=15.9
Q ss_pred eceEEEEecCCCCCHHHHH
Q psy7060 130 LPCIYAYNKIDQISIEEVD 148 (160)
Q Consensus 130 ~P~iyv~NKiD~is~eevd 148 (160)
+|+++|.||+|+...++..
T Consensus 154 ~~viiV~NK~Dl~~~~~~~ 172 (204)
T cd01878 154 IPMILVLNKIDLLDDEELE 172 (204)
T ss_pred CCEEEEEEccccCChHHHH
Confidence 6999999999998765544
No 19
>PTZ00258 GTP-binding protein; Provisional
Probab=85.41 E-value=2.3 Score=38.56 Aligned_cols=53 Identities=26% Similarity=0.104 Sum_probs=35.9
Q ss_pred HHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcC---cceeceEEEEecC--CC--CCHHHHHHH
Q psy7060 91 EKLVQLILHEYKIFNAEVLFREDCNADELIDVINAN---RVYLPCIYAYNKI--DQ--ISIEEVDRI 150 (160)
Q Consensus 91 e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~n---rvY~P~iyv~NKi--D~--is~eevd~i 150 (160)
.+.|+..|.+++..++ .+.+.+| ..+..+ ..++|.|||.||. |+ .+.+.++.+
T Consensus 186 l~~v~~~L~~~~~~~~-----~~~~~~e--~~~l~~l~llt~KP~iyv~N~~E~D~~~~~~~~~~~l 245 (390)
T PTZ00258 186 LKKVLEWLEEGKPVRD-----GDWTDKE--IEILNEYQLLTAKPMIYLVNMSEKDFIRQKNKWLAKI 245 (390)
T ss_pred HHHHHHHHHcCCcccc-----CCCCHHH--HHHHHHhchhhcCCEEEEEECchhhhcccchHHHHHH
Confidence 3678999999888765 2445554 333333 6799999999999 86 244444444
No 20
>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=83.15 E-value=2 Score=31.11 Aligned_cols=23 Identities=26% Similarity=0.213 Sum_probs=17.6
Q ss_pred eceEEEEecCCCCC-----HHHHHHHhc
Q psy7060 130 LPCIYAYNKIDQIS-----IEEVDRIAR 152 (160)
Q Consensus 130 ~P~iyv~NKiD~is-----~eevd~i~~ 152 (160)
+|+++|.||+|+.. .++...+++
T Consensus 109 ~pi~vv~nK~Dl~~~~~~~~~~~~~~~~ 136 (165)
T cd01868 109 IVIMLVGNKSDLRHLRAVPTEEAKAFAE 136 (165)
T ss_pred CeEEEEEECccccccccCCHHHHHHHHH
Confidence 79999999999863 356666655
No 21
>cd01863 Rab18 Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of mos
Probab=83.04 E-value=11 Score=27.00 Aligned_cols=28 Identities=29% Similarity=0.202 Sum_probs=20.9
Q ss_pred cceeceEEEEecCCCC----CHHHHHHHhcCC
Q psy7060 127 RVYLPCIYAYNKIDQI----SIEEVDRIARQP 154 (160)
Q Consensus 127 rvY~P~iyv~NKiD~i----s~eevd~i~~~p 154 (160)
....|.++|.||+|+. +.++..++++..
T Consensus 104 ~~~~~~~iv~nK~D~~~~~~~~~~~~~~~~~~ 135 (161)
T cd01863 104 NNDIVKMLVGNKIDKENREVTREEGLKFARKH 135 (161)
T ss_pred CCCCcEEEEEECCcccccccCHHHHHHHHHHc
Confidence 4568999999999997 556776665543
No 22
>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=83.02 E-value=1.2 Score=33.80 Aligned_cols=18 Identities=28% Similarity=0.289 Sum_probs=15.1
Q ss_pred eceEEEEecCCCCCHHHH
Q psy7060 130 LPCIYAYNKIDQISIEEV 147 (160)
Q Consensus 130 ~P~iyv~NKiD~is~eev 147 (160)
.|.|+|+||+|+.+.+++
T Consensus 47 k~~ilVlNK~Dl~~~~~~ 64 (171)
T cd01856 47 KPRIIVLNKADLADPKKT 64 (171)
T ss_pred CCEEEEEehhhcCChHHH
Confidence 599999999999866554
No 23
>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=82.98 E-value=0.69 Score=32.37 Aligned_cols=20 Identities=30% Similarity=0.302 Sum_probs=16.2
Q ss_pred ceeceEEEEecCCCCCHHHH
Q psy7060 128 VYLPCIYAYNKIDQISIEEV 147 (160)
Q Consensus 128 vY~P~iyv~NKiD~is~eev 147 (160)
.-.|.+++.||+|+.+.++.
T Consensus 106 ~~~~vi~v~nK~D~~~~~~~ 125 (157)
T cd04164 106 ADKPIIVVLNKSDLLPDSEL 125 (157)
T ss_pred cCCCEEEEEEchhcCCcccc
Confidence 34799999999999876554
No 24
>cd01896 DRG The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding.
Probab=82.63 E-value=1.4 Score=35.92 Aligned_cols=34 Identities=26% Similarity=0.334 Sum_probs=25.7
Q ss_pred HHHHHHHHHhhhhhhHHhhhcCccccccCCCcccCHHHHHHHHHH
Q psy7060 56 KLVQLILHEYKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHE 100 (160)
Q Consensus 56 ~~v~~~l~~yki~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL~E 100 (160)
++|+.+|++|+||||+=+-.|. ++.+++...+..
T Consensus 139 ~~v~~~l~~~~i~~~~v~~~~~-----------~~~~~~~~~~~~ 172 (233)
T cd01896 139 KTIKAILREYKIHNADVLIRED-----------ITVDDLIDVIEG 172 (233)
T ss_pred HHHHHHHHHhCeeeEEEEEccC-----------CCHHHHHHHHhC
Confidence 6899999999999998876666 445555555543
No 25
>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=82.01 E-value=1.4 Score=33.27 Aligned_cols=26 Identities=31% Similarity=0.390 Sum_probs=19.3
Q ss_pred ceeceEEEEecCCCC-----CHHHHHHHhcC
Q psy7060 128 VYLPCIYAYNKIDQI-----SIEEVDRIARQ 153 (160)
Q Consensus 128 vY~P~iyv~NKiD~i-----s~eevd~i~~~ 153 (160)
.-+|+++|.||+|+. +.++...+++.
T Consensus 106 ~~~piilvgNK~Dl~~~~~v~~~~~~~~a~~ 136 (172)
T cd04141 106 EDIPLVLVGNKVDLESQRQVTTEEGRNLARE 136 (172)
T ss_pred CCCCEEEEEEChhhhhcCccCHHHHHHHHHH
Confidence 458999999999974 45666666543
No 26
>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=81.98 E-value=1.8 Score=30.33 Aligned_cols=18 Identities=39% Similarity=0.553 Sum_probs=15.3
Q ss_pred eceEEEEecCCCCCHHHH
Q psy7060 130 LPCIYAYNKIDQISIEEV 147 (160)
Q Consensus 130 ~P~iyv~NKiD~is~eev 147 (160)
.|+++|.||+|+...++.
T Consensus 106 ~piiiv~nK~D~~~~~~~ 123 (157)
T cd01894 106 KPVILVVNKVDNIKEEDE 123 (157)
T ss_pred CCEEEEEECcccCChHHH
Confidence 799999999999876554
No 27
>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=81.80 E-value=10 Score=29.16 Aligned_cols=28 Identities=25% Similarity=0.450 Sum_probs=21.9
Q ss_pred ceeceEEEEecCCCC-----CHHHHHHHhcCCC
Q psy7060 128 VYLPCIYAYNKIDQI-----SIEEVDRIARQPN 155 (160)
Q Consensus 128 vY~P~iyv~NKiD~i-----s~eevd~i~~~p~ 155 (160)
..+|.|+|.||+|+. +.+++..+++..+
T Consensus 109 ~~~piilv~NK~Dl~~~~~~~~~~~~~~~~~~~ 141 (201)
T cd04107 109 EPIPCLLLANKCDLKKRLAKDGEQMDQFCKENG 141 (201)
T ss_pred CCCcEEEEEECCCcccccccCHHHHHHHHHHcC
Confidence 467999999999985 6678888766543
No 28
>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=81.19 E-value=8.7 Score=27.34 Aligned_cols=15 Identities=27% Similarity=0.454 Sum_probs=13.3
Q ss_pred eeceEEEEecCCCCC
Q psy7060 129 YLPCIYAYNKIDQIS 143 (160)
Q Consensus 129 Y~P~iyv~NKiD~is 143 (160)
-+|+++|.||+|+.+
T Consensus 104 ~~p~iiv~NK~Dl~~ 118 (162)
T cd04157 104 RVPILFFANKMDLPD 118 (162)
T ss_pred CCCEEEEEeCccccC
Confidence 489999999999874
No 29
>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=80.76 E-value=16 Score=25.82 Aligned_cols=15 Identities=13% Similarity=0.085 Sum_probs=13.0
Q ss_pred eceEEEEecCCCCCH
Q psy7060 130 LPCIYAYNKIDQISI 144 (160)
Q Consensus 130 ~P~iyv~NKiD~is~ 144 (160)
.|.|++.||+|+.+.
T Consensus 105 ~~~ilv~NK~Dl~~~ 119 (164)
T cd04171 105 KRGLVVLTKADLVDE 119 (164)
T ss_pred CcEEEEEECccccCH
Confidence 399999999999864
No 30
>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=80.69 E-value=1.9 Score=31.04 Aligned_cols=26 Identities=23% Similarity=0.279 Sum_probs=20.0
Q ss_pred eeceEEEEecCCCC-----CHHHHHHHhcCC
Q psy7060 129 YLPCIYAYNKIDQI-----SIEEVDRIARQP 154 (160)
Q Consensus 129 Y~P~iyv~NKiD~i-----s~eevd~i~~~p 154 (160)
-+|.++|.||+|+. +.++++++.+..
T Consensus 109 ~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~~~ 139 (172)
T cd01862 109 NFPFVVLGNKIDLEEKRQVSTKKAQQWCQSN 139 (172)
T ss_pred CceEEEEEECcccccccccCHHHHHHHHHHc
Confidence 57999999999997 457777665443
No 31
>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=80.67 E-value=8.7 Score=27.58 Aligned_cols=25 Identities=40% Similarity=0.401 Sum_probs=18.1
Q ss_pred eeceEEEEecCCCCC-----HHHHHHHhcC
Q psy7060 129 YLPCIYAYNKIDQIS-----IEEVDRIARQ 153 (160)
Q Consensus 129 Y~P~iyv~NKiD~is-----~eevd~i~~~ 153 (160)
..|.++|.||+|+.. .++...+++.
T Consensus 105 ~~pii~v~nK~Dl~~~~~~~~~~~~~~~~~ 134 (164)
T smart00173 105 DVPIVLVGNKCDLESERVVSTEEGKELARQ 134 (164)
T ss_pred CCCEEEEEECccccccceEcHHHHHHHHHH
Confidence 579999999999853 3555555543
No 32
>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=80.26 E-value=14 Score=26.81 Aligned_cols=26 Identities=23% Similarity=0.164 Sum_probs=18.8
Q ss_pred ceeceEEEEecCCCCC-----HHHHHHHhcC
Q psy7060 128 VYLPCIYAYNKIDQIS-----IEEVDRIARQ 153 (160)
Q Consensus 128 vY~P~iyv~NKiD~is-----~eevd~i~~~ 153 (160)
.-+|.|+|.||+|+.. .++...+++.
T Consensus 107 ~~~p~ivv~nK~Dl~~~~~~~~~~~~~~~~~ 137 (165)
T cd01864 107 SNVVLLLIGNKCDLEEQREVLFEEACTLAEK 137 (165)
T ss_pred CCCcEEEEEECcccccccccCHHHHHHHHHH
Confidence 4579999999999863 3555566554
No 33
>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=79.99 E-value=3.9 Score=28.36 Aligned_cols=19 Identities=37% Similarity=0.529 Sum_probs=14.7
Q ss_pred eceEEEEecCCCC-CHHHHH
Q psy7060 130 LPCIYAYNKIDQI-SIEEVD 148 (160)
Q Consensus 130 ~P~iyv~NKiD~i-s~eevd 148 (160)
.|.++++||+|+. +.+++.
T Consensus 112 ~~~iiv~nK~Dl~~~~~~~~ 131 (168)
T cd04163 112 TPVILVLNKIDLVKDKEDLL 131 (168)
T ss_pred CCEEEEEEchhccccHHHHH
Confidence 5999999999998 444443
No 34
>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional
Probab=79.53 E-value=2 Score=37.57 Aligned_cols=67 Identities=16% Similarity=0.274 Sum_probs=49.5
Q ss_pred cCccccccCCCcccCHHHHHHHHHHcCccceEEEeecCCCh--h-------H-----HHHHHhcCc---ce-----eceE
Q psy7060 76 GGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNA--D-------E-----LIDVINANR---VY-----LPCI 133 (160)
Q Consensus 76 ~~~~~~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~--D-------d-----liDvi~~nr---vY-----~P~i 133 (160)
-++.+|+.| .-+++..++...|.++.-...+++|-|.+.. . + ++++.+|.. .| .+.+
T Consensus 156 pvvqi~tG~-~Chl~a~mv~~Al~~L~~~~~d~liIEnvGnLvcPa~fdlge~~~v~vlsV~eg~dkplKyp~~f~~ADI 234 (290)
T PRK10463 156 PAIQVNTGK-GCHLDAQMIADAAPRLPLDDNGILFIENVGNLVCPASFDLGEKHKVAVLSVTEGEDKPLKYPHMFAAASL 234 (290)
T ss_pred cEEEecCCC-CCcCcHHHHHHHHHHHhhcCCcEEEEECCCCccCCCccchhhceeEEEEECccccccchhccchhhcCcE
Confidence 466677765 4578888999999999888888888887541 2 2 455666632 44 7789
Q ss_pred EEEecCCCCC
Q psy7060 134 YAYNKIDQIS 143 (160)
Q Consensus 134 yv~NKiD~is 143 (160)
+++||+|+.+
T Consensus 235 VVLNKiDLl~ 244 (290)
T PRK10463 235 MLLNKVDLLP 244 (290)
T ss_pred EEEEhHHcCc
Confidence 9999999986
No 35
>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=79.51 E-value=14 Score=28.15 Aligned_cols=26 Identities=23% Similarity=0.224 Sum_probs=19.6
Q ss_pred ceeceEEEEecCCCC-----CHHHHHHHhcC
Q psy7060 128 VYLPCIYAYNKIDQI-----SIEEVDRIARQ 153 (160)
Q Consensus 128 vY~P~iyv~NKiD~i-----s~eevd~i~~~ 153 (160)
.-+|.++|.||+|+. +.++...+++.
T Consensus 105 ~~~piiiv~NK~Dl~~~~~~~~~~~~~l~~~ 135 (191)
T cd04112 105 EDVVIMLLGNKADMSGERVVKREDGERLAKE 135 (191)
T ss_pred CCCcEEEEEEcccchhccccCHHHHHHHHHH
Confidence 367999999999985 44667777543
No 36
>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=79.49 E-value=11 Score=28.85 Aligned_cols=51 Identities=18% Similarity=0.401 Sum_probs=32.4
Q ss_pred CHHHHHHHHHHcCccceEEEeec---CCChh--HHHHHHhcCcceeceEEEEecCCCC
Q psy7060 90 NEKLVQLILHEYKIFNAEVLFRE---DCNAD--ELIDVINANRVYLPCIYAYNKIDQI 142 (160)
Q Consensus 90 ~e~~V~~IL~EYkI~NA~V~ire---d~t~D--dliDvi~~nrvY~P~iyv~NKiD~i 142 (160)
..+.++....--+.-++-+++-. ..+.. +.+..+ ...=+|.|+|+||+|+.
T Consensus 80 ~~~f~~~~~~~~~~~D~ailvVda~~g~~~~~~~~l~~~--~~~~~p~ivvlNK~D~~ 135 (188)
T PF00009_consen 80 HEDFIKEMIRGLRQADIAILVVDANDGIQPQTEEHLKIL--RELGIPIIVVLNKMDLI 135 (188)
T ss_dssp SHHHHHHHHHHHTTSSEEEEEEETTTBSTHHHHHHHHHH--HHTT-SEEEEEETCTSS
T ss_pred ccceeecccceecccccceeeeecccccccccccccccc--cccccceEEeeeeccch
Confidence 46777888877777776555543 23322 233333 44446899999999998
No 37
>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=79.30 E-value=2 Score=30.43 Aligned_cols=14 Identities=29% Similarity=0.325 Sum_probs=12.9
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
+|.++|+||+|+..
T Consensus 106 ~piiiv~NK~D~~~ 119 (164)
T cd04139 106 VPLLLVGNKCDLED 119 (164)
T ss_pred CCEEEEEEcccccc
Confidence 89999999999975
No 38
>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=78.83 E-value=11 Score=27.74 Aligned_cols=46 Identities=22% Similarity=0.185 Sum_probs=26.6
Q ss_pred HHHcCccceEEEeecCCC----hhHH----HHHHhcCcceeceEEEEecCCCCCH
Q psy7060 98 LHEYKIFNAEVLFREDCN----ADEL----IDVINANRVYLPCIYAYNKIDQISI 144 (160)
Q Consensus 98 L~EYkI~NA~V~ired~t----~Ddl----iDvi~~nrvY~P~iyv~NKiD~is~ 144 (160)
...|+--++-+++- |++ .+++ ++.+...+--+|.++|.||+|+.+.
T Consensus 65 ~~~~~~ad~~ilv~-d~~~~~s~~~~~~~~~~~i~~~~~~~pviiv~nK~Dl~~~ 118 (166)
T cd01893 65 AAEIRKANVICLVY-SVDRPSTLERIRTKWLPLIRRLGVKVPIILVGNKSDLRDG 118 (166)
T ss_pred hhhcccCCEEEEEE-ECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEchhcccc
Confidence 34455555555554 333 3332 2334333335799999999999753
No 39
>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=78.79 E-value=6.5 Score=29.47 Aligned_cols=15 Identities=27% Similarity=0.592 Sum_probs=12.9
Q ss_pred eeceEEEEecCCCCC
Q psy7060 129 YLPCIYAYNKIDQIS 143 (160)
Q Consensus 129 Y~P~iyv~NKiD~is 143 (160)
=+|+++|.||+|+..
T Consensus 108 ~~p~iiv~NK~Dl~~ 122 (169)
T cd01892 108 EIPCLFVAAKADLDE 122 (169)
T ss_pred CCeEEEEEEcccccc
Confidence 379999999999863
No 40
>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=78.56 E-value=4 Score=29.15 Aligned_cols=26 Identities=27% Similarity=0.201 Sum_probs=19.7
Q ss_pred eeceEEEEecCCCC-----CHHHHHHHhcCC
Q psy7060 129 YLPCIYAYNKIDQI-----SIEEVDRIARQP 154 (160)
Q Consensus 129 Y~P~iyv~NKiD~i-----s~eevd~i~~~p 154 (160)
..|.++|.||+|+. +.++...+++..
T Consensus 105 ~~~iilv~nK~D~~~~~~~~~~~~~~~~~~~ 135 (161)
T cd01861 105 DVIIVLVGNKTDLSDKRQVSTEEGEKKAKEL 135 (161)
T ss_pred CCEEEEEEEChhccccCccCHHHHHHHHHHh
Confidence 68999999999993 556677765443
No 41
>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=78.42 E-value=1.7 Score=32.04 Aligned_cols=20 Identities=20% Similarity=0.295 Sum_probs=15.8
Q ss_pred eceEEEEecCCCCCHHHHHH
Q psy7060 130 LPCIYAYNKIDQISIEEVDR 149 (160)
Q Consensus 130 ~P~iyv~NKiD~is~eevd~ 149 (160)
+|.|+|+||+|+.+.++...
T Consensus 42 ~p~iiv~NK~Dl~~~~~~~~ 61 (156)
T cd01859 42 KKLLIVLNKADLVPKEVLEK 61 (156)
T ss_pred CcEEEEEEhHHhCCHHHHHH
Confidence 69999999999986654443
No 42
>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=78.25 E-value=17 Score=26.66 Aligned_cols=24 Identities=25% Similarity=0.187 Sum_probs=17.9
Q ss_pred eceEEEEecCCCC-----CHHHHHHHhcC
Q psy7060 130 LPCIYAYNKIDQI-----SIEEVDRIARQ 153 (160)
Q Consensus 130 ~P~iyv~NKiD~i-----s~eevd~i~~~ 153 (160)
.|.++|.||+|+. +.++...+++.
T Consensus 121 ~piiiv~nK~Dl~~~~~v~~~~~~~~~~~ 149 (180)
T cd04127 121 PDIVLCGNKADLEDQRQVSEEQAKALADK 149 (180)
T ss_pred CcEEEEEeCccchhcCccCHHHHHHHHHH
Confidence 5899999999985 44666666543
No 43
>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=77.89 E-value=2.3 Score=30.71 Aligned_cols=19 Identities=42% Similarity=0.480 Sum_probs=15.4
Q ss_pred ceeceEEEEecCCCCCHHH
Q psy7060 128 VYLPCIYAYNKIDQISIEE 146 (160)
Q Consensus 128 vY~P~iyv~NKiD~is~ee 146 (160)
...|.++|.||+|+.+.++
T Consensus 113 ~~~p~ivv~NK~Dl~~~~~ 131 (170)
T cd01898 113 LEKPRIVVLNKIDLLDEEE 131 (170)
T ss_pred cccccEEEEEchhcCCchh
Confidence 4689999999999976544
No 44
>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=77.59 E-value=3.5 Score=29.89 Aligned_cols=15 Identities=20% Similarity=-0.102 Sum_probs=13.0
Q ss_pred eeceEEEEecCCCCC
Q psy7060 129 YLPCIYAYNKIDQIS 143 (160)
Q Consensus 129 Y~P~iyv~NKiD~is 143 (160)
-+|++++.||+|+..
T Consensus 100 ~~piiiv~nK~Dl~~ 114 (158)
T cd04151 100 GAVLLVFANKQDMPG 114 (158)
T ss_pred CCcEEEEEeCCCCCC
Confidence 379999999999863
No 45
>COG1163 DRG Predicted GTPase [General function prediction only]
Probab=77.41 E-value=8.1 Score=35.58 Aligned_cols=23 Identities=35% Similarity=0.501 Sum_probs=19.6
Q ss_pred HHHHHHHHHhhhhhhHHhhhcCc
Q psy7060 56 KLVQLILHEYKIFNAEQKKAGGI 78 (160)
Q Consensus 56 ~~v~~~l~~yki~n~~~~~~~~~ 78 (160)
++|+.+|.+|+||||+-.-.|-+
T Consensus 202 ~~ir~iL~Ey~I~nA~V~Ir~dv 224 (365)
T COG1163 202 DTVRAILREYRIHNADVLIREDV 224 (365)
T ss_pred HHHHHHHHHhCcccceEEEecCC
Confidence 47999999999999997777653
No 46
>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=77.12 E-value=25 Score=26.19 Aligned_cols=25 Identities=32% Similarity=0.278 Sum_probs=19.4
Q ss_pred eeceEEEEecCCCC---CHHHHHHHhcC
Q psy7060 129 YLPCIYAYNKIDQI---SIEEVDRIARQ 153 (160)
Q Consensus 129 Y~P~iyv~NKiD~i---s~eevd~i~~~ 153 (160)
-.|.+++.||.|+. +.+++....+.
T Consensus 120 ~~pvivv~NK~Dl~~~~~~~~~~~~~~~ 147 (190)
T cd00879 120 NVPFLILGNKIDLPGAVSEEELRQALGL 147 (190)
T ss_pred CCCEEEEEeCCCCCCCcCHHHHHHHhCc
Confidence 48999999999986 66777666543
No 47
>PRK00089 era GTPase Era; Reviewed
Probab=76.89 E-value=10 Score=31.06 Aligned_cols=18 Identities=44% Similarity=0.648 Sum_probs=14.6
Q ss_pred eceEEEEecCCCC-CHHHH
Q psy7060 130 LPCIYAYNKIDQI-SIEEV 147 (160)
Q Consensus 130 ~P~iyv~NKiD~i-s~eev 147 (160)
.|+++|+||+|+. +.+++
T Consensus 114 ~pvilVlNKiDl~~~~~~l 132 (292)
T PRK00089 114 TPVILVLNKIDLVKDKEEL 132 (292)
T ss_pred CCEEEEEECCcCCCCHHHH
Confidence 6999999999998 54433
No 48
>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=76.64 E-value=4 Score=30.08 Aligned_cols=25 Identities=28% Similarity=0.228 Sum_probs=19.0
Q ss_pred ceeceEEEEecCCCC-----CHHHHHHHhc
Q psy7060 128 VYLPCIYAYNKIDQI-----SIEEVDRIAR 152 (160)
Q Consensus 128 vY~P~iyv~NKiD~i-----s~eevd~i~~ 152 (160)
-.+|.++|.||+|+. +.++.+.+++
T Consensus 108 ~~~pvivv~nK~Dl~~~~~~~~~~~~~~~~ 137 (168)
T cd01866 108 SNMTIMLIGNKCDLESRREVSYEEGEAFAK 137 (168)
T ss_pred CCCcEEEEEECcccccccCCCHHHHHHHHH
Confidence 468999999999986 4466666644
No 49
>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=76.59 E-value=3.3 Score=29.65 Aligned_cols=24 Identities=29% Similarity=0.512 Sum_probs=17.8
Q ss_pred eeceEEEEecCCCCC-----HHHHHHHhc
Q psy7060 129 YLPCIYAYNKIDQIS-----IEEVDRIAR 152 (160)
Q Consensus 129 Y~P~iyv~NKiD~is-----~eevd~i~~ 152 (160)
-+|.++|.||+|+.+ .++...+++
T Consensus 106 ~~p~iiv~nK~Dl~~~~~v~~~~~~~~~~ 134 (162)
T cd04106 106 DIPMVLVQTKIDLLDQAVITNEEAEALAK 134 (162)
T ss_pred CCCEEEEEEChhcccccCCCHHHHHHHHH
Confidence 479999999999864 455555654
No 50
>PRK12289 GTPase RsgA; Reviewed
Probab=76.48 E-value=3.4 Score=36.61 Aligned_cols=20 Identities=30% Similarity=0.375 Sum_probs=16.6
Q ss_pred eceEEEEecCCCCCHHHHHH
Q psy7060 130 LPCIYAYNKIDQISIEEVDR 149 (160)
Q Consensus 130 ~P~iyv~NKiD~is~eevd~ 149 (160)
+|.++|+||+|+++.++...
T Consensus 121 ip~ILVlNK~DLv~~~~~~~ 140 (352)
T PRK12289 121 LEIVLCLNKADLVSPTEQQQ 140 (352)
T ss_pred CCEEEEEEchhcCChHHHHH
Confidence 79999999999998765443
No 51
>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=76.45 E-value=15 Score=28.74 Aligned_cols=56 Identities=20% Similarity=0.267 Sum_probs=30.5
Q ss_pred CHHHHHHHHHHcCccce-EEEeecC---C--ChhHHHHHHhcCcceeceEEEEecCCCCCHHH
Q psy7060 90 NEKLVQLILHEYKIFNA-EVLFRED---C--NADELIDVINANRVYLPCIYAYNKIDQISIEE 146 (160)
Q Consensus 90 ~e~~V~~IL~EYkI~NA-~V~ired---~--t~DdliDvi~~nrvY~P~iyv~NKiD~is~ee 146 (160)
.++.+...+....--.+ -+.+... . ...+.+..+..... .|.|+|+||+|+.+.++
T Consensus 93 ~~~~~~~~~~~~~~~D~~llVvd~~~~~~~~~t~~~l~~~~~~~~-~~iiivvNK~Dl~~~~~ 154 (203)
T cd01888 93 HEILMATMLSGAAVMDGALLLIAANEPCPQPQTSEHLAALEIMGL-KHIIIVQNKIDLVKEEQ 154 (203)
T ss_pred hHHHHHHHHHhhhcCCEEEEEEECCCCCCCcchHHHHHHHHHcCC-CcEEEEEEchhccCHHH
Confidence 46667776666643333 3333322 1 12344444432222 47899999999987543
No 52
>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=76.30 E-value=3 Score=30.63 Aligned_cols=25 Identities=28% Similarity=0.147 Sum_probs=18.0
Q ss_pred ceeceEEEEecCCCC-----CHHHHHHHhc
Q psy7060 128 VYLPCIYAYNKIDQI-----SIEEVDRIAR 152 (160)
Q Consensus 128 vY~P~iyv~NKiD~i-----s~eevd~i~~ 152 (160)
...|+++|.||+|+. +.++...+++
T Consensus 107 ~~~p~iiv~nK~Dl~~~~~~~~~~~~~~~~ 136 (167)
T cd01867 107 EDVERMLVGNKCDMEEKRVVSKEEGEALAD 136 (167)
T ss_pred CCCcEEEEEECcccccccCCCHHHHHHHHH
Confidence 357999999999986 3355555543
No 53
>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=76.11 E-value=3.4 Score=30.11 Aligned_cols=27 Identities=30% Similarity=0.244 Sum_probs=20.4
Q ss_pred ceeceEEEEecCCCC----CHHHHHHHhcCC
Q psy7060 128 VYLPCIYAYNKIDQI----SIEEVDRIARQP 154 (160)
Q Consensus 128 vY~P~iyv~NKiD~i----s~eevd~i~~~p 154 (160)
.-+|.++|.||+|+. +.+++.++++..
T Consensus 113 ~~~piilv~nK~Dl~~~~~~~~~~~~~~~~~ 143 (170)
T cd04116 113 ESFPFVVLGNKNDIPERQVSTEEAQAWCREN 143 (170)
T ss_pred CCCcEEEEEECccccccccCHHHHHHHHHHC
Confidence 357999999999984 457777776543
No 54
>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=76.02 E-value=2.5 Score=30.61 Aligned_cols=23 Identities=35% Similarity=0.382 Sum_probs=17.2
Q ss_pred eceEEEEecCCCC-----CHHHHHHHhc
Q psy7060 130 LPCIYAYNKIDQI-----SIEEVDRIAR 152 (160)
Q Consensus 130 ~P~iyv~NKiD~i-----s~eevd~i~~ 152 (160)
+|.|+|.||+|+. +.++.+.+++
T Consensus 107 ~piilv~nK~Dl~~~~~~~~~~~~~~~~ 134 (164)
T cd04175 107 VPMILVGNKCDLEDERVVGKEQGQNLAR 134 (164)
T ss_pred CCEEEEEECCcchhccEEcHHHHHHHHH
Confidence 6999999999985 3455556654
No 55
>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=75.97 E-value=2 Score=31.25 Aligned_cols=16 Identities=56% Similarity=0.764 Sum_probs=14.0
Q ss_pred eceEEEEecCCCCCHH
Q psy7060 130 LPCIYAYNKIDQISIE 145 (160)
Q Consensus 130 ~P~iyv~NKiD~is~e 145 (160)
+|.++++||+|+...+
T Consensus 115 ~~i~iv~nK~D~~~~~ 130 (189)
T cd00881 115 LPIIVAINKIDRVGEE 130 (189)
T ss_pred CCeEEEEECCCCcchh
Confidence 7999999999998743
No 56
>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=75.81 E-value=2.8 Score=28.37 Aligned_cols=23 Identities=30% Similarity=0.375 Sum_probs=17.8
Q ss_pred cceeceEEEEecCCCCCHHHHHH
Q psy7060 127 RVYLPCIYAYNKIDQISIEEVDR 149 (160)
Q Consensus 127 rvY~P~iyv~NKiD~is~eevd~ 149 (160)
..-+|.++|.||+|+.+.++...
T Consensus 102 ~~~~~~ivv~nK~D~~~~~~~~~ 124 (163)
T cd00880 102 ERGKPVLLVLNKIDLLPEEEEEE 124 (163)
T ss_pred hcCCeEEEEEEccccCChhhHHH
Confidence 44579999999999997655543
No 57
>TIGR00231 small_GTP small GTP-binding protein domain. This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model.
Probab=75.81 E-value=4.2 Score=27.54 Aligned_cols=15 Identities=40% Similarity=0.428 Sum_probs=13.5
Q ss_pred eeceEEEEecCCCCC
Q psy7060 129 YLPCIYAYNKIDQIS 143 (160)
Q Consensus 129 Y~P~iyv~NKiD~is 143 (160)
-.|.+++.||+|+.+
T Consensus 108 ~~p~ivv~nK~D~~~ 122 (161)
T TIGR00231 108 NVPIILVGNKIDLRD 122 (161)
T ss_pred CCcEEEEEEcccCCc
Confidence 569999999999986
No 58
>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=75.45 E-value=4.7 Score=28.12 Aligned_cols=27 Identities=19% Similarity=0.425 Sum_probs=19.4
Q ss_pred HHHHHhcCcceeceEEEEecCCCCCHHHH
Q psy7060 119 LIDVINANRVYLPCIYAYNKIDQISIEEV 147 (160)
Q Consensus 119 liDvi~~nrvY~P~iyv~NKiD~is~eev 147 (160)
++..+...+ .|.+.+.||+|+.+.++.
T Consensus 102 ~~~~l~~~~--~~vi~v~nK~D~~~~~~~ 128 (170)
T cd01876 102 MLDWLEELG--IPFLVVLTKADKLKKSEL 128 (170)
T ss_pred HHHHHHHcC--CCEEEEEEchhcCChHHH
Confidence 455555443 699999999999876544
No 59
>PRK04213 GTP-binding protein; Provisional
Probab=75.43 E-value=2.7 Score=31.89 Aligned_cols=16 Identities=44% Similarity=0.511 Sum_probs=13.6
Q ss_pred eeceEEEEecCCCCCH
Q psy7060 129 YLPCIYAYNKIDQISI 144 (160)
Q Consensus 129 Y~P~iyv~NKiD~is~ 144 (160)
=+|.++|.||+|+...
T Consensus 130 ~~p~iiv~NK~Dl~~~ 145 (201)
T PRK04213 130 GIPPIVAVNKMDKIKN 145 (201)
T ss_pred CCCeEEEEECccccCc
Confidence 3799999999999753
No 60
>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=75.31 E-value=4.6 Score=31.16 Aligned_cols=30 Identities=23% Similarity=0.127 Sum_probs=20.7
Q ss_pred HhcCcceeceEEEEecCCCC-----CHHHHHHHhc
Q psy7060 123 INANRVYLPCIYAYNKIDQI-----SIEEVDRIAR 152 (160)
Q Consensus 123 i~~nrvY~P~iyv~NKiD~i-----s~eevd~i~~ 152 (160)
+..+.-..|.++|.||+|+. +.++..++++
T Consensus 104 i~~~~~~~piivVgNK~Dl~~~~~~~~~~~~~~~~ 138 (199)
T cd04110 104 IEQNCDDVCKVLVGNKNDDPERKVVETEDAYKFAG 138 (199)
T ss_pred HHHhCCCCCEEEEEECcccccccccCHHHHHHHHH
Confidence 33444568999999999985 3455665654
No 61
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=75.27 E-value=3.6 Score=33.79 Aligned_cols=17 Identities=24% Similarity=0.382 Sum_probs=14.4
Q ss_pred eceEEEEecCCCCCHHH
Q psy7060 130 LPCIYAYNKIDQISIEE 146 (160)
Q Consensus 130 ~P~iyv~NKiD~is~ee 146 (160)
.|+++|.||+|+...++
T Consensus 108 ~p~ilV~NK~Dl~~~~~ 124 (270)
T TIGR00436 108 RPVVLTRNKLDNKFKDK 124 (270)
T ss_pred CCEEEEEECeeCCCHHH
Confidence 69999999999986544
No 62
>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=75.07 E-value=12 Score=27.00 Aligned_cols=17 Identities=24% Similarity=0.120 Sum_probs=14.1
Q ss_pred ceeceEEEEecCCCCCH
Q psy7060 128 VYLPCIYAYNKIDQISI 144 (160)
Q Consensus 128 vY~P~iyv~NKiD~is~ 144 (160)
..+|++++.||+|+...
T Consensus 106 ~~~p~ilv~NK~D~~~~ 122 (167)
T cd04160 106 EGVPLLILANKQDLPDA 122 (167)
T ss_pred cCCCEEEEEEccccccC
Confidence 35899999999998643
No 63
>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=74.94 E-value=14 Score=26.88 Aligned_cols=17 Identities=24% Similarity=0.214 Sum_probs=14.3
Q ss_pred ceeceEEEEecCCCCCH
Q psy7060 128 VYLPCIYAYNKIDQISI 144 (160)
Q Consensus 128 vY~P~iyv~NKiD~is~ 144 (160)
..+|.+++.||+|+...
T Consensus 114 ~~~p~ivv~nK~D~~~~ 130 (173)
T cd04155 114 AGVPVLVFANKQDLATA 130 (173)
T ss_pred cCCCEEEEEECCCCccC
Confidence 35899999999999764
No 64
>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=74.76 E-value=21 Score=26.44 Aligned_cols=24 Identities=25% Similarity=0.202 Sum_probs=18.6
Q ss_pred eceEEEEecCCCC---CHHHHHHHhcC
Q psy7060 130 LPCIYAYNKIDQI---SIEEVDRIARQ 153 (160)
Q Consensus 130 ~P~iyv~NKiD~i---s~eevd~i~~~ 153 (160)
.|.++|.||.|+. +.+++..+++.
T Consensus 101 ~piilv~NK~Dl~~~~~~~~~~~~~~~ 127 (169)
T cd04158 101 ALLLIFANKQDVAGALSVEEMTELLSL 127 (169)
T ss_pred CCEEEEEeCcCcccCCCHHHHHHHhCC
Confidence 6999999999985 55777666543
No 65
>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=74.62 E-value=3.5 Score=29.40 Aligned_cols=23 Identities=35% Similarity=0.381 Sum_probs=16.5
Q ss_pred eceEEEEecCCCCC-----HHHHHHHhc
Q psy7060 130 LPCIYAYNKIDQIS-----IEEVDRIAR 152 (160)
Q Consensus 130 ~P~iyv~NKiD~is-----~eevd~i~~ 152 (160)
+|.|+|.||+|+.. .++...+++
T Consensus 107 ~piilv~nK~Dl~~~~~~~~~~~~~~~~ 134 (163)
T cd04136 107 VPMVLVGNKCDLEDERVVSREEGQALAR 134 (163)
T ss_pred CCEEEEEECccccccceecHHHHHHHHH
Confidence 69999999999853 344455543
No 66
>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=74.49 E-value=2.1 Score=30.81 Aligned_cols=17 Identities=24% Similarity=0.274 Sum_probs=14.1
Q ss_pred ceeceEEEEecCCCCCH
Q psy7060 128 VYLPCIYAYNKIDQISI 144 (160)
Q Consensus 128 vY~P~iyv~NKiD~is~ 144 (160)
...|.++|.||+|+.+.
T Consensus 106 ~~~p~ilv~nK~Dl~~~ 122 (164)
T cd04101 106 KHMPGVLVGNKMDLADK 122 (164)
T ss_pred CCCCEEEEEECcccccc
Confidence 45899999999998643
No 67
>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=74.30 E-value=4 Score=29.70 Aligned_cols=23 Identities=39% Similarity=0.523 Sum_probs=17.2
Q ss_pred eeceEEEEecCCCC-----CHHHHHHHh
Q psy7060 129 YLPCIYAYNKIDQI-----SIEEVDRIA 151 (160)
Q Consensus 129 Y~P~iyv~NKiD~i-----s~eevd~i~ 151 (160)
-+|+|+|.||+|+. +.++..+++
T Consensus 106 ~~piilv~nK~Dl~~~~~v~~~~~~~~~ 133 (165)
T cd04146 106 EIPVILVGNKADLLHYRQVSTEEGEKLA 133 (165)
T ss_pred CCCEEEEEECCchHHhCccCHHHHHHHH
Confidence 58999999999985 345555554
No 68
>PLN00223 ADP-ribosylation factor; Provisional
Probab=73.77 E-value=15 Score=28.18 Aligned_cols=26 Identities=15% Similarity=-0.061 Sum_probs=17.9
Q ss_pred eeceEEEEecCCCCC---HHHHHHHhcCC
Q psy7060 129 YLPCIYAYNKIDQIS---IEEVDRIARQP 154 (160)
Q Consensus 129 Y~P~iyv~NKiD~is---~eevd~i~~~p 154 (160)
-+|.+++.||+|+.. .+++.+....+
T Consensus 118 ~~piilv~NK~Dl~~~~~~~~~~~~l~l~ 146 (181)
T PLN00223 118 DAVLLVFANKQDLPNAMNAAEITDKLGLH 146 (181)
T ss_pred CCCEEEEEECCCCCCCCCHHHHHHHhCcc
Confidence 479999999999864 35555444433
No 69
>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=73.74 E-value=3 Score=36.18 Aligned_cols=21 Identities=38% Similarity=0.523 Sum_probs=16.5
Q ss_pred eceEEEEecCCCCCHHHHHHH
Q psy7060 130 LPCIYAYNKIDQISIEEVDRI 150 (160)
Q Consensus 130 ~P~iyv~NKiD~is~eevd~i 150 (160)
+|+|+|.||+|+.+.++++.+
T Consensus 274 kp~IIV~NK~DL~~~~~~~~~ 294 (329)
T TIGR02729 274 KPRIVVLNKIDLLDEEELAEL 294 (329)
T ss_pred CCEEEEEeCccCCChHHHHHH
Confidence 799999999999876554433
No 70
>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=73.70 E-value=5.5 Score=30.30 Aligned_cols=22 Identities=36% Similarity=0.474 Sum_probs=15.9
Q ss_pred eceEEEEecCCCC-----CHHHHHHHh
Q psy7060 130 LPCIYAYNKIDQI-----SIEEVDRIA 151 (160)
Q Consensus 130 ~P~iyv~NKiD~i-----s~eevd~i~ 151 (160)
.|.|+|.||+|+. +.++...++
T Consensus 107 ~piilvgNK~Dl~~~~~v~~~~~~~~~ 133 (190)
T cd04144 107 VPIMIVGNKCDKVYEREVSTEEGAALA 133 (190)
T ss_pred CCEEEEEEChhccccCccCHHHHHHHH
Confidence 6999999999984 444444444
No 71
>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=73.58 E-value=4.2 Score=28.64 Aligned_cols=24 Identities=21% Similarity=0.198 Sum_probs=17.3
Q ss_pred ceeceEEEEecCCCCC----HHHHHHHh
Q psy7060 128 VYLPCIYAYNKIDQIS----IEEVDRIA 151 (160)
Q Consensus 128 vY~P~iyv~NKiD~is----~eevd~i~ 151 (160)
--+|+++|.||+|+.+ .++..+++
T Consensus 105 ~~~piivv~nK~Dl~~~~~~~~~~~~~~ 132 (162)
T cd04138 105 DDVPMVLVGNKCDLAARTVSSRQGQDLA 132 (162)
T ss_pred CCCCEEEEEECcccccceecHHHHHHHH
Confidence 3579999999999864 34555553
No 72
>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=73.22 E-value=4.6 Score=35.27 Aligned_cols=51 Identities=24% Similarity=0.230 Sum_probs=34.2
Q ss_pred cCHHHHHHHHHHcCccceEEEeecCCC------hhHHHHHHhcCcceeceEEEEecCCCCC
Q psy7060 89 VNEKLVQLILHEYKIFNAEVLFREDCN------ADELIDVINANRVYLPCIYAYNKIDQIS 143 (160)
Q Consensus 89 ~~e~~V~~IL~EYkI~NA~V~ired~t------~DdliDvi~~nrvY~P~iyv~NKiD~is 143 (160)
++.+..+.++++|.-..+.|++-=|++ ..++.+.+. -.|.++|.||+|+.+
T Consensus 48 ~~~e~f~~~l~~~~~~~~~Il~VvD~~d~~~s~~~~l~~~~~----~~piilV~NK~DLl~ 104 (360)
T TIGR03597 48 LNDDDFLNLLNSLGDSNALIVYVVDIFDFEGSLIPELKRFVG----GNPVLLVGNKIDLLP 104 (360)
T ss_pred CCHHHHHHHHhhcccCCcEEEEEEECcCCCCCccHHHHHHhC----CCCEEEEEEchhhCC
Confidence 667889999999966655555444442 223444432 259999999999974
No 73
>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=72.84 E-value=5.2 Score=29.59 Aligned_cols=24 Identities=21% Similarity=0.164 Sum_probs=16.2
Q ss_pred HHHHhcCcceeceEEEEecCCCCC
Q psy7060 120 IDVINANRVYLPCIYAYNKIDQIS 143 (160)
Q Consensus 120 iDvi~~nrvY~P~iyv~NKiD~is 143 (160)
++.+.....-.|+++|.||+|+.+
T Consensus 95 ~~~~~~~~~~~piilv~nK~Dl~~ 118 (173)
T cd04130 95 IPEIRKHNPKAPIILVGTQADLRT 118 (173)
T ss_pred HHHHHhhCCCCCEEEEeeChhhcc
Confidence 334433223479999999999863
No 74
>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=72.23 E-value=3.3 Score=29.92 Aligned_cols=19 Identities=37% Similarity=0.641 Sum_probs=15.7
Q ss_pred eceEEEEecCCCCCHHHHH
Q psy7060 130 LPCIYAYNKIDQISIEEVD 148 (160)
Q Consensus 130 ~P~iyv~NKiD~is~eevd 148 (160)
+|.|+|.||+|+.+.+++.
T Consensus 114 ~pvilv~NK~Dl~~~~~~~ 132 (168)
T cd01897 114 KPVIVVLNKIDLLTFEDLS 132 (168)
T ss_pred CCeEEEEEccccCchhhHH
Confidence 6999999999998665544
No 75
>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=72.13 E-value=6.9 Score=29.46 Aligned_cols=24 Identities=13% Similarity=0.075 Sum_probs=17.3
Q ss_pred eeceEEEEecCCCC-----CHHHHHHHhc
Q psy7060 129 YLPCIYAYNKIDQI-----SIEEVDRIAR 152 (160)
Q Consensus 129 Y~P~iyv~NKiD~i-----s~eevd~i~~ 152 (160)
..|++++.||+|+. +.++...+++
T Consensus 105 ~~~~ivv~nK~Dl~~~~~v~~~~~~~~~~ 133 (188)
T cd04125 105 NVIKVIVANKSDLVNNKVVDSNIAKSFCD 133 (188)
T ss_pred CCeEEEEEECCCCcccccCCHHHHHHHHH
Confidence 47999999999987 3345555543
No 76
>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=71.73 E-value=5.9 Score=29.48 Aligned_cols=25 Identities=16% Similarity=0.157 Sum_probs=18.1
Q ss_pred eeceEEEEecCCCCC---------HHHHHHHhcC
Q psy7060 129 YLPCIYAYNKIDQIS---------IEEVDRIARQ 153 (160)
Q Consensus 129 Y~P~iyv~NKiD~is---------~eevd~i~~~ 153 (160)
-+|.|+|.||.|+.. .++...+++.
T Consensus 105 ~~piilv~nK~Dl~~~~~~~~~v~~~~~~~~~~~ 138 (187)
T cd04132 105 GTPIMLVGLKTDLRKDKNLDRKVTPAQAESVAKK 138 (187)
T ss_pred CCCEEEEEeChhhhhCccccCCcCHHHHHHHHHH
Confidence 479999999999864 4555555443
No 77
>PRK12288 GTPase RsgA; Reviewed
Probab=71.67 E-value=5.4 Score=35.19 Aligned_cols=16 Identities=31% Similarity=0.389 Sum_probs=14.2
Q ss_pred eceEEEEecCCCCCHH
Q psy7060 130 LPCIYAYNKIDQISIE 145 (160)
Q Consensus 130 ~P~iyv~NKiD~is~e 145 (160)
+|+++|+||+|+.+.+
T Consensus 151 i~~VIVlNK~DL~~~~ 166 (347)
T PRK12288 151 IEPLIVLNKIDLLDDE 166 (347)
T ss_pred CCEEEEEECccCCCcH
Confidence 7999999999998754
No 78
>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=71.31 E-value=5.9 Score=28.98 Aligned_cols=14 Identities=50% Similarity=0.392 Sum_probs=12.2
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
+|.+.|.||+|+..
T Consensus 120 ~~iiiv~NK~Dl~~ 133 (179)
T cd01890 120 LEIIPVINKIDLPS 133 (179)
T ss_pred CCEEEEEECCCCCc
Confidence 58999999999864
No 79
>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=71.21 E-value=3.8 Score=34.12 Aligned_cols=20 Identities=20% Similarity=0.202 Sum_probs=15.8
Q ss_pred eceEEEEecCCCCCHHHHHH
Q psy7060 130 LPCIYAYNKIDQISIEEVDR 149 (160)
Q Consensus 130 ~P~iyv~NKiD~is~eevd~ 149 (160)
.|.|+|+||+|+.+.++...
T Consensus 49 kp~IiVlNK~DL~~~~~~~~ 68 (276)
T TIGR03596 49 KPRLIVLNKADLADPAVTKQ 68 (276)
T ss_pred CCEEEEEEccccCCHHHHHH
Confidence 59999999999986654443
No 80
>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=71.16 E-value=21 Score=27.17 Aligned_cols=17 Identities=41% Similarity=0.348 Sum_probs=14.1
Q ss_pred eeceEEEEecCCCCCHH
Q psy7060 129 YLPCIYAYNKIDQISIE 145 (160)
Q Consensus 129 Y~P~iyv~NKiD~is~e 145 (160)
-+|.+++.||+|+.+.+
T Consensus 120 ~~~~iiv~NK~Dl~~~~ 136 (192)
T cd01889 120 CKKLIVVLNKIDLIPEE 136 (192)
T ss_pred CCCEEEEEECcccCCHH
Confidence 46999999999998543
No 81
>cd04172 Rnd3_RhoE_Rho8 Rnd3/RhoE/Rho8 subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7. Rnd3/RhoE is known to bind the serine-threonine kinase ROCK I. Unphosphorylated Rnd3/RhoE associates primarily with membranes, but ROCK I-phosphorylated Rnd3/RhoE localizes in the cytosol. Phosphorylation of Rnd3/RhoE correlates with its activity in disrupting RhoA-induced stress fibers and inhibiting Ras-induced fibroblast transformation. In cells that lack stress fibers, such as macrophages and monocytes, Rnd3/RhoE induces a redistribution of actin, causing morphological changes in the cell. In addition, Rnd3/RhoE has been shown to inhibit cell cycle progression in G1 phase at a point upstream of the pRb family pocket protein checkpoint. Rnd3/RhoE has also been shown to inhibit Ras- and Raf-induced fibroblast transformation. In mammary epithelial tumor cells, Rnd3/RhoE regulates the assembly of the apical junction complex and tight
Probab=70.99 E-value=5.3 Score=31.09 Aligned_cols=14 Identities=14% Similarity=-0.102 Sum_probs=12.2
Q ss_pred ceeceEEEEecCCC
Q psy7060 128 VYLPCIYAYNKIDQ 141 (160)
Q Consensus 128 vY~P~iyv~NKiD~ 141 (160)
--.|.|+|.||+|+
T Consensus 108 ~~~piilVgNK~DL 121 (182)
T cd04172 108 PNTKMLLVGCKSDL 121 (182)
T ss_pred CCCCEEEEeEChhh
Confidence 35799999999997
No 82
>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=70.93 E-value=3.1 Score=30.06 Aligned_cols=14 Identities=36% Similarity=0.294 Sum_probs=12.6
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
+|++++.||+|+.+
T Consensus 113 ~~~i~v~NK~D~~~ 126 (169)
T cd04114 113 VITILVGNKIDLAE 126 (169)
T ss_pred CeEEEEEECccccc
Confidence 79999999999863
No 83
>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=70.45 E-value=6.3 Score=32.15 Aligned_cols=56 Identities=16% Similarity=0.141 Sum_probs=31.6
Q ss_pred HHHHHHHHHHc---CccceEEEeecC--CChh--HHHHHHhcCcceeceEEEEecCCCCCHHHHH
Q psy7060 91 EKLVQLILHEY---KIFNAEVLFRED--CNAD--ELIDVINANRVYLPCIYAYNKIDQISIEEVD 148 (160)
Q Consensus 91 e~~V~~IL~EY---kI~NA~V~ired--~t~D--dliDvi~~nrvY~P~iyv~NKiD~is~eevd 148 (160)
++..+..++.. ...=|-+.+..+ .+-. +++..+.... +|.++|+||+|+.+.++++
T Consensus 95 ~~~~~~~~~~~~~~~~D~~llVvda~~g~~~~d~~~l~~l~~~~--ip~ivvvNK~D~~~~~~~~ 157 (224)
T cd04165 95 ERYLKTTLFGLTGYAPDYAMLVVAANAGIIGMTKEHLGLALALN--IPVFVVVTKIDLAPANILQ 157 (224)
T ss_pred HHHHHHHHHhhcccCCCEEEEEEECCCCCcHHHHHHHHHHHHcC--CCEEEEEECccccCHHHHH
Confidence 44444444433 333444555432 3332 3455555444 6999999999998765544
No 84
>cd04174 Rnd1_Rho6 Rnd1/Rho6 subfamily. Rnd1/Rho6 is a member of the novel Rho subfamily Rnd, together with Rnd2/Rho7 and Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not hydrolyze it to GDP, indicating that it is constitutively active. In rat, Rnd1/Rho6 is highly expressed in the cerebral cortex and hippocampus during synapse formation, and plays a role in spine formation. Rnd1/Rho6 is also expressed in the liver and in endothelial cells, and is upregulated in uterine myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8, Rnd1/Rho6 is believed to function as an antagonist to RhoA. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=70.40 E-value=24 Score=29.20 Aligned_cols=20 Identities=15% Similarity=-0.157 Sum_probs=14.4
Q ss_pred HhcCcceeceEEEEecCCCC
Q psy7060 123 INANRVYLPCIYAYNKIDQI 142 (160)
Q Consensus 123 i~~nrvY~P~iyv~NKiD~i 142 (160)
+....--.|.|+|.||+|+.
T Consensus 111 i~~~~~~~piilVgNK~DL~ 130 (232)
T cd04174 111 IMDYCPSTRILLIGCKTDLR 130 (232)
T ss_pred HHHhCCCCCEEEEEECcccc
Confidence 44333357999999999973
No 85
>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=70.39 E-value=16 Score=26.43 Aligned_cols=25 Identities=20% Similarity=0.186 Sum_probs=18.0
Q ss_pred eeceEEEEecCCCCC-----HHHHHHHhcC
Q psy7060 129 YLPCIYAYNKIDQIS-----IEEVDRIARQ 153 (160)
Q Consensus 129 Y~P~iyv~NKiD~is-----~eevd~i~~~ 153 (160)
-+|.++|.||+|+.. .++...+++.
T Consensus 107 ~~~~iiv~nK~Dl~~~~~~~~~~~~~~~~~ 136 (166)
T cd01869 107 NVNKLLVGNKCDLTDKRVVDYSEAQEFADE 136 (166)
T ss_pred CCcEEEEEEChhcccccCCCHHHHHHHHHH
Confidence 369999999999853 3556666543
No 86
>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=70.36 E-value=4.2 Score=28.67 Aligned_cols=15 Identities=20% Similarity=0.171 Sum_probs=13.4
Q ss_pred eceEEEEecCCCCCH
Q psy7060 130 LPCIYAYNKIDQISI 144 (160)
Q Consensus 130 ~P~iyv~NKiD~is~ 144 (160)
.|.++++||+|+.+.
T Consensus 114 ~~~iiv~nK~Dl~~~ 128 (174)
T cd01895 114 KALVIVVNKWDLVEK 128 (174)
T ss_pred CCEEEEEeccccCCc
Confidence 699999999999865
No 87
>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=70.27 E-value=39 Score=24.58 Aligned_cols=25 Identities=24% Similarity=0.163 Sum_probs=18.9
Q ss_pred eeceEEEEecCCCC-----CHHHHHHHhcC
Q psy7060 129 YLPCIYAYNKIDQI-----SIEEVDRIARQ 153 (160)
Q Consensus 129 Y~P~iyv~NKiD~i-----s~eevd~i~~~ 153 (160)
-.|+++|.||+|+. +.++...+++.
T Consensus 107 ~~~iiiv~nK~Dl~~~~~~~~~~~~~~~~~ 136 (166)
T cd04122 107 NTVIFLIGNKADLEAQRDVTYEEAKQFADE 136 (166)
T ss_pred CCeEEEEEECcccccccCcCHHHHHHHHHH
Confidence 47999999999985 44666766654
No 88
>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=70.27 E-value=3.2 Score=28.73 Aligned_cols=17 Identities=24% Similarity=0.059 Sum_probs=14.0
Q ss_pred eeceEEEEecCCCCCHH
Q psy7060 129 YLPCIYAYNKIDQISIE 145 (160)
Q Consensus 129 Y~P~iyv~NKiD~is~e 145 (160)
-+|.++|.||+|+.+.+
T Consensus 101 ~~p~iiv~nK~D~~~~~ 117 (159)
T cd04159 101 GIPLLVLGNKNDLPGAL 117 (159)
T ss_pred CCCEEEEEeCccccCCc
Confidence 46999999999987543
No 89
>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=70.13 E-value=3.9 Score=30.02 Aligned_cols=23 Identities=35% Similarity=0.508 Sum_probs=15.8
Q ss_pred HHHHhcCcceeceEEEEecCCCC
Q psy7060 120 IDVINANRVYLPCIYAYNKIDQI 142 (160)
Q Consensus 120 iDvi~~nrvY~P~iyv~NKiD~i 142 (160)
++.+....--+|.|+|.||+|+.
T Consensus 95 ~~~i~~~~~~~p~ivv~nK~Dl~ 117 (161)
T cd04124 95 YEELREYRPEIPCIVVANKIDLD 117 (161)
T ss_pred HHHHHHhCCCCcEEEEEECccCc
Confidence 33443332347999999999985
No 90
>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=69.90 E-value=6.7 Score=30.02 Aligned_cols=52 Identities=21% Similarity=0.142 Sum_probs=28.7
Q ss_pred HHHHHHHHHcCccceE-EEeecCCCh--hHHHHHHhcCcceeceEEEEecCCCCCH
Q psy7060 92 KLVQLILHEYKIFNAE-VLFREDCNA--DELIDVINANRVYLPCIYAYNKIDQISI 144 (160)
Q Consensus 92 ~~V~~IL~EYkI~NA~-V~ired~t~--DdliDvi~~nrvY~P~iyv~NKiD~is~ 144 (160)
..++..+.+| +.+|+ |++-=|++- .+..+.+.....=+|.++|+||+|+.+.
T Consensus 22 ~~~~~~l~~~-~~~ad~il~VvD~~~~~~~~~~~l~~~~~~~~~ilV~NK~Dl~~~ 76 (190)
T cd01855 22 DFILNLLSSI-SPKKALVVHVVDIFDFPGSLIPRLRLFGGNNPVILVGNKIDLLPK 76 (190)
T ss_pred HHHHHHHHhc-ccCCcEEEEEEECccCCCccchhHHHhcCCCcEEEEEEchhcCCC
Confidence 3378888888 55553 333333331 0111222111223699999999999753
No 91
>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=69.86 E-value=4.9 Score=29.65 Aligned_cols=25 Identities=28% Similarity=0.283 Sum_probs=17.8
Q ss_pred ceeceEEEEecCCCCC-----HHHHHHHhc
Q psy7060 128 VYLPCIYAYNKIDQIS-----IEEVDRIAR 152 (160)
Q Consensus 128 vY~P~iyv~NKiD~is-----~eevd~i~~ 152 (160)
..+|.|+|.||+|+.. .++...+++
T Consensus 105 ~~~p~ilv~NK~Dl~~~~~~~~~~~~~~~~ 134 (180)
T cd04137 105 ESVPIVLVGNKSDLHTQRQVSTEEGKELAE 134 (180)
T ss_pred CCCCEEEEEEchhhhhcCccCHHHHHHHHH
Confidence 4579999999999863 344555544
No 92
>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=69.48 E-value=14 Score=28.95 Aligned_cols=13 Identities=46% Similarity=0.846 Sum_probs=12.1
Q ss_pred eceEEEEecCCCC
Q psy7060 130 LPCIYAYNKIDQI 142 (160)
Q Consensus 130 ~P~iyv~NKiD~i 142 (160)
+|.+.|.||+|..
T Consensus 124 ~p~iiviNK~D~~ 136 (213)
T cd04167 124 LPIVLVINKIDRL 136 (213)
T ss_pred CCEEEEEECcccC
Confidence 7999999999986
No 93
>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=68.99 E-value=47 Score=25.27 Aligned_cols=25 Identities=28% Similarity=0.234 Sum_probs=19.0
Q ss_pred eeceEEEEecCCCC---CHHHHHHHhcC
Q psy7060 129 YLPCIYAYNKIDQI---SIEEVDRIARQ 153 (160)
Q Consensus 129 Y~P~iyv~NKiD~i---s~eevd~i~~~ 153 (160)
-.|.+++.||+|+. +.+++.....+
T Consensus 118 ~~piliv~NK~Dl~~~~~~~~i~~~l~l 145 (184)
T smart00178 118 TVPFLILGNKIDAPYAASEDELRYALGL 145 (184)
T ss_pred CCCEEEEEeCccccCCCCHHHHHHHcCC
Confidence 47999999999985 66777655433
No 94
>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=68.94 E-value=6.2 Score=32.60 Aligned_cols=18 Identities=33% Similarity=0.392 Sum_probs=14.4
Q ss_pred eeceEEEEecCCCCCHHH
Q psy7060 129 YLPCIYAYNKIDQISIEE 146 (160)
Q Consensus 129 Y~P~iyv~NKiD~is~ee 146 (160)
=+|.++|.||+|+.+..+
T Consensus 67 ~i~~vIV~NK~DL~~~~~ 84 (245)
T TIGR00157 67 NIEPIIVLNKIDLLDDED 84 (245)
T ss_pred CCCEEEEEECcccCCCHH
Confidence 379999999999975433
No 95
>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=68.76 E-value=8.9 Score=28.28 Aligned_cols=27 Identities=26% Similarity=0.202 Sum_probs=19.4
Q ss_pred ceeceEEEEecCCCC-----CHHHHHHHhcCC
Q psy7060 128 VYLPCIYAYNKIDQI-----SIEEVDRIARQP 154 (160)
Q Consensus 128 vY~P~iyv~NKiD~i-----s~eevd~i~~~p 154 (160)
..+|+++|.||+|+. +.++.+++++..
T Consensus 108 ~~~p~iiv~nK~Dl~~~~~~~~~~~~~~~~~~ 139 (170)
T cd04115 108 NEVPRILVGNKCDLREQIQVPTDLAQRFADAH 139 (170)
T ss_pred CCCCEEEEEECccchhhcCCCHHHHHHHHHHc
Confidence 468999999999974 445566665443
No 96
>cd04131 Rnd Rnd subfamily. The Rnd subfamily contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These novel Rho family proteins have substantial structural differences compared to other Rho members, including N- and C-terminal extensions relative to other Rhos. Rnd3/RhoE is farnesylated at the C-terminal prenylation site, unlike most other Rho proteins that are geranylgeranylated. In addition, Rnd members are unable to hydrolyze GTP and are resistant to GAP activity. They are believed to exist only in the GTP-bound conformation, and are antagonists of RhoA activity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=68.63 E-value=6.4 Score=30.27 Aligned_cols=13 Identities=15% Similarity=-0.010 Sum_probs=11.7
Q ss_pred eeceEEEEecCCC
Q psy7060 129 YLPCIYAYNKIDQ 141 (160)
Q Consensus 129 Y~P~iyv~NKiD~ 141 (160)
-.|.|+|.||.|+
T Consensus 105 ~~~iilVgnK~DL 117 (178)
T cd04131 105 NTKVLLVGCKTDL 117 (178)
T ss_pred CCCEEEEEEChhh
Confidence 4799999999997
No 97
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=68.62 E-value=6.7 Score=26.62 Aligned_cols=49 Identities=24% Similarity=0.272 Sum_probs=35.3
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEE
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYA 135 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv 135 (160)
.+.||.-+.-...++.++.||++. +++.--+ +.|+ +..-+-..+|++++
T Consensus 7 a~~C~~C~~~~~~~~~~~~e~~~~-~~~~~v~--~~~~---a~~~~v~~vPti~i 55 (76)
T TIGR00412 7 GTGCANCQMTEKNVKKAVEELGID-AEFEKVT--DMNE---ILEAGVTATPGVAV 55 (76)
T ss_pred CCCCcCHHHHHHHHHHHHHHcCCC-eEEEEeC--CHHH---HHHcCCCcCCEEEE
Confidence 478999999999999999999854 3331111 2443 55568888999998
No 98
>PRK00454 engB GTP-binding protein YsxC; Reviewed
Probab=68.48 E-value=5.6 Score=29.65 Aligned_cols=22 Identities=18% Similarity=0.291 Sum_probs=17.4
Q ss_pred cceeceEEEEecCCCCCHHHHH
Q psy7060 127 RVYLPCIYAYNKIDQISIEEVD 148 (160)
Q Consensus 127 rvY~P~iyv~NKiD~is~eevd 148 (160)
...+|++++.||+|+.+.++..
T Consensus 133 ~~~~~~iiv~nK~Dl~~~~~~~ 154 (196)
T PRK00454 133 EYGIPVLIVLTKADKLKKGERK 154 (196)
T ss_pred HcCCcEEEEEECcccCCHHHHH
Confidence 3468999999999999865544
No 99
>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=68.08 E-value=6 Score=29.28 Aligned_cols=23 Identities=26% Similarity=0.083 Sum_probs=17.1
Q ss_pred eeceEEEEecCCCC---CHHHHHHHh
Q psy7060 129 YLPCIYAYNKIDQI---SIEEVDRIA 151 (160)
Q Consensus 129 Y~P~iyv~NKiD~i---s~eevd~i~ 151 (160)
=.|.++|.||+|+. +.+++....
T Consensus 115 ~~p~iiv~nK~Dl~~~~~~~~~~~~~ 140 (173)
T cd04154 115 GATLLILANKQDLPGALSEEEIREAL 140 (173)
T ss_pred CCCEEEEEECcccccCCCHHHHHHHh
Confidence 47999999999986 345655554
No 100
>cd01860 Rab5_related Rab5-related subfamily. This subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence mo
Probab=68.00 E-value=9.4 Score=27.30 Aligned_cols=25 Identities=28% Similarity=0.128 Sum_probs=18.2
Q ss_pred ceeceEEEEecCCCC-----CHHHHHHHhc
Q psy7060 128 VYLPCIYAYNKIDQI-----SIEEVDRIAR 152 (160)
Q Consensus 128 vY~P~iyv~NKiD~i-----s~eevd~i~~ 152 (160)
.-.|.+++.||+|+. +.+++.++++
T Consensus 105 ~~~~iivv~nK~D~~~~~~~~~~~~~~~~~ 134 (163)
T cd01860 105 PNIIIALVGNKADLESKRQVSTEEAQEYAD 134 (163)
T ss_pred CCCeEEEEEECccccccCcCCHHHHHHHHH
Confidence 447899999999987 3456666543
No 101
>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=67.86 E-value=25 Score=26.12 Aligned_cols=16 Identities=25% Similarity=0.164 Sum_probs=13.5
Q ss_pred ceeceEEEEecCCCCC
Q psy7060 128 VYLPCIYAYNKIDQIS 143 (160)
Q Consensus 128 vY~P~iyv~NKiD~is 143 (160)
...|.++|.||+|+..
T Consensus 99 ~~~piliv~NK~Dl~~ 114 (167)
T cd04161 99 SGKPILVLANKQDKKN 114 (167)
T ss_pred cCCcEEEEEeCCCCcC
Confidence 3579999999999863
No 102
>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=67.43 E-value=44 Score=25.30 Aligned_cols=24 Identities=29% Similarity=0.380 Sum_probs=17.8
Q ss_pred ceeceEEEEecCCCC---CHHHHHHHh
Q psy7060 128 VYLPCIYAYNKIDQI---SIEEVDRIA 151 (160)
Q Consensus 128 vY~P~iyv~NKiD~i---s~eevd~i~ 151 (160)
.-+|+++|.||+|+. +.++++.+.
T Consensus 108 ~~~p~iiv~NK~D~~~~~~~~~~~~~~ 134 (183)
T cd04152 108 QGVPVLVLANKQDLPNALSVSEVEKLL 134 (183)
T ss_pred CCCcEEEEEECcCccccCCHHHHHHHh
Confidence 357999999999986 345566554
No 103
>cd03418 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known i
Probab=67.35 E-value=13 Score=23.96 Aligned_cols=62 Identities=15% Similarity=0.221 Sum_probs=39.5
Q ss_pred ccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHH---hcCcceeceEEEEecCCCCCHHHHHHHh
Q psy7060 82 STCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVI---NANRVYLPCIYAYNKIDQISIEEVDRIA 151 (160)
Q Consensus 82 ~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi---~~nrvY~P~iyv~NKiD~is~eevd~i~ 151 (160)
+.||.- ..++.+|++++|.-.++-+..+ .+..+.+ .+.+...|+|++=.+. .-+-+++.++.
T Consensus 8 ~~Cp~C----~~ak~~L~~~~i~~~~i~i~~~---~~~~~~~~~~~~~~~~vP~v~i~g~~-igg~~~~~~~~ 72 (75)
T cd03418 8 PNCPYC----VRAKALLDKKGVDYEEIDVDGD---PALREEMINRSGGRRTVPQIFIGDVH-IGGCDDLYALE 72 (75)
T ss_pred CCChHH----HHHHHHHHHCCCcEEEEECCCC---HHHHHHHHHHhCCCCccCEEEECCEE-EeChHHHHHHH
Confidence 556653 4689999999998888877765 3333333 3445588999865542 22456665554
No 104
>PRK12299 obgE GTPase CgtA; Reviewed
Probab=67.29 E-value=12 Score=32.64 Aligned_cols=17 Identities=47% Similarity=0.575 Sum_probs=14.2
Q ss_pred eceEEEEecCCCCCHHH
Q psy7060 130 LPCIYAYNKIDQISIEE 146 (160)
Q Consensus 130 ~P~iyv~NKiD~is~ee 146 (160)
+|+|+|.||+|+.+.++
T Consensus 272 kp~IIV~NKiDL~~~~~ 288 (335)
T PRK12299 272 KPRILVLNKIDLLDEEE 288 (335)
T ss_pred CCeEEEEECcccCCchh
Confidence 69999999999985543
No 105
>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=66.93 E-value=2.7 Score=30.01 Aligned_cols=23 Identities=35% Similarity=0.299 Sum_probs=16.5
Q ss_pred eeceEEEEecCCCCC-----HHHHHHHh
Q psy7060 129 YLPCIYAYNKIDQIS-----IEEVDRIA 151 (160)
Q Consensus 129 Y~P~iyv~NKiD~is-----~eevd~i~ 151 (160)
=+|+++|.||+|+.. .++...++
T Consensus 107 ~~piiiv~NK~Dl~~~~~~~~~~~~~~~ 134 (164)
T cd04145 107 EFPMILVGNKADLEHQRKVSREEGQELA 134 (164)
T ss_pred CCCEEEEeeCccccccceecHHHHHHHH
Confidence 369999999999863 34554444
No 106
>COG1084 Predicted GTPase [General function prediction only]
Probab=66.91 E-value=44 Score=30.73 Aligned_cols=67 Identities=25% Similarity=0.262 Sum_probs=50.0
Q ss_pred CCCcccCHHHHHHHHHHcCccceEEEeec---C--CChhHHHH---HHhcCcceeceEEEEecCCCCCHHHHHHHh
Q psy7060 84 CPLTQVNEKLVQLILHEYKIFNAEVLFRE---D--CNADELID---VINANRVYLPCIYAYNKIDQISIEEVDRIA 151 (160)
Q Consensus 84 ~~~~~~~e~~V~~IL~EYkI~NA~V~ire---d--~t~DdliD---vi~~nrvY~P~iyv~NKiD~is~eevd~i~ 151 (160)
-|+...|+=+-|+|+.=--+-++.+.|-. . .++++=+. -|.++-. .|.+.|+||+|....|+++++.
T Consensus 228 RPl~ErN~IE~qAi~AL~hl~~~IlF~~D~Se~cgy~lE~Q~~L~~eIk~~f~-~p~v~V~nK~D~~~~e~~~~~~ 302 (346)
T COG1084 228 RPLEERNEIERQAILALRHLAGVILFLFDPSETCGYSLEEQISLLEEIKELFK-APIVVVINKIDIADEEKLEEIE 302 (346)
T ss_pred CChHHhcHHHHHHHHHHHHhcCeEEEEEcCccccCCCHHHHHHHHHHHHHhcC-CCeEEEEecccccchhHHHHHH
Confidence 48888999999999987777777776643 2 34555444 4444444 7999999999999898888874
No 107
>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=66.78 E-value=6 Score=29.82 Aligned_cols=17 Identities=18% Similarity=0.368 Sum_probs=14.3
Q ss_pred eeceEEEEecCCCCCHH
Q psy7060 129 YLPCIYAYNKIDQISIE 145 (160)
Q Consensus 129 Y~P~iyv~NKiD~is~e 145 (160)
-+|.+++.||+|+.+.+
T Consensus 129 ~~pviiv~nK~D~~~~~ 145 (179)
T TIGR03598 129 GIPVLIVLTKADKLKKS 145 (179)
T ss_pred CCCEEEEEECcccCCHH
Confidence 36999999999998653
No 108
>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=66.69 E-value=12 Score=29.23 Aligned_cols=48 Identities=15% Similarity=0.144 Sum_probs=29.4
Q ss_pred HHHHHHHcCccceEEEee---cCCChhH--HHHHHhcCcceeceEEEEecCCCCC
Q psy7060 94 VQLILHEYKIFNAEVLFR---EDCNADE--LIDVINANRVYLPCIYAYNKIDQIS 143 (160)
Q Consensus 94 V~~IL~EYkI~NA~V~ir---ed~t~Dd--liDvi~~nrvY~P~iyv~NKiD~is 143 (160)
.+..+++.++..+++.+- ++.+..| ++..+... -.|+++|.||+|+..
T Consensus 69 ~~~~l~~~~~~~~d~~l~v~~~~~~~~d~~~~~~l~~~--~~~~ilV~nK~D~~~ 121 (197)
T cd04104 69 PDDYLEEMKFSEYDFFIIISSTRFSSNDVKLAKAIQCM--GKKFYFVRTKVDRDL 121 (197)
T ss_pred HHHHHHHhCccCcCEEEEEeCCCCCHHHHHHHHHHHHh--CCCEEEEEecccchh
Confidence 345566666666555443 3334333 44555443 369999999999974
No 109
>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=66.60 E-value=6.4 Score=28.23 Aligned_cols=26 Identities=19% Similarity=0.069 Sum_probs=18.7
Q ss_pred ceeceEEEEecCCCCC---HHHHHHHhcC
Q psy7060 128 VYLPCIYAYNKIDQIS---IEEVDRIARQ 153 (160)
Q Consensus 128 vY~P~iyv~NKiD~is---~eevd~i~~~ 153 (160)
--.|+++|.||+|+.. .+++....+.
T Consensus 99 ~~~piiiv~nK~D~~~~~~~~~~~~~~~~ 127 (158)
T cd00878 99 KGVPLLIFANKQDLPGALSVSELIEKLGL 127 (158)
T ss_pred CCCcEEEEeeccCCccccCHHHHHHhhCh
Confidence 3579999999999985 3455555443
No 110
>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=66.20 E-value=15 Score=30.98 Aligned_cols=54 Identities=11% Similarity=0.127 Sum_probs=31.7
Q ss_pred HHHHHHHHHHcC-----ccceEEEeecCCChhHHHHHHh-cCcceeceEEEEecCCCCCH
Q psy7060 91 EKLVQLILHEYK-----IFNAEVLFREDCNADELIDVIN-ANRVYLPCIYAYNKIDQISI 144 (160)
Q Consensus 91 e~~V~~IL~EYk-----I~NA~V~ired~t~DdliDvi~-~nrvY~P~iyv~NKiD~is~ 144 (160)
.+.|+....+|= |.=+.|--+.|.+..|..+... -.+...|+|.|+||+|..+.
T Consensus 148 ~~~i~~lv~~yi~~~~~IIL~Vvda~~d~~~~d~l~ia~~ld~~~~rti~ViTK~D~~~~ 207 (240)
T smart00053 148 EEQIKDMIKQFISKEECLILAVTPANVDLANSDALKLAKEVDPQGERTIGVITKLDLMDE 207 (240)
T ss_pred HHHHHHHHHHHHhCccCeEEEEEECCCCCCchhHHHHHHHHHHcCCcEEEEEECCCCCCc
Confidence 356777777772 2223333344544444333332 24566899999999999854
No 111
>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=66.13 E-value=10 Score=29.64 Aligned_cols=25 Identities=20% Similarity=0.092 Sum_probs=17.5
Q ss_pred eeceEEEEecCCCCC-----HHHHHHHhcC
Q psy7060 129 YLPCIYAYNKIDQIS-----IEEVDRIARQ 153 (160)
Q Consensus 129 Y~P~iyv~NKiD~is-----~eevd~i~~~ 153 (160)
-.|.++|.||+|+.. .++...+++.
T Consensus 109 ~~piilVgNK~DL~~~~~v~~~~~~~~~~~ 138 (215)
T cd04109 109 QPLVVLVGNKTDLEHNRTVKDDKHARFAQA 138 (215)
T ss_pred CceEEEEEECcccccccccCHHHHHHHHHH
Confidence 457899999999863 3556666543
No 112
>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=66.06 E-value=7.1 Score=28.56 Aligned_cols=15 Identities=27% Similarity=0.359 Sum_probs=13.0
Q ss_pred eeceEEEEecCCCCC
Q psy7060 129 YLPCIYAYNKIDQIS 143 (160)
Q Consensus 129 Y~P~iyv~NKiD~is 143 (160)
=+|+++|.||+|+..
T Consensus 108 ~~piilv~nK~Dl~~ 122 (165)
T cd04140 108 KIPIMLVGNKCDESH 122 (165)
T ss_pred CCCEEEEEECccccc
Confidence 369999999999864
No 113
>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=65.91 E-value=5.6 Score=33.60 Aligned_cols=30 Identities=23% Similarity=0.294 Sum_probs=20.7
Q ss_pred hhHHHHHHhcCcceeceEEEEecCCCCCHHH
Q psy7060 116 ADELIDVINANRVYLPCIYAYNKIDQISIEE 146 (160)
Q Consensus 116 ~DdliDvi~~nrvY~P~iyv~NKiD~is~ee 146 (160)
-||+.....+ -.=+|.++|+||+|+...++
T Consensus 160 ~~el~~~~~~-l~~~~~ivv~NK~Dl~~~~~ 189 (300)
T TIGR00750 160 GDDLQGIKAG-LMEIADIYVVNKADGEGATN 189 (300)
T ss_pred cHHHHHHHHH-HhhhccEEEEEcccccchhH
Confidence 4666554432 34578999999999986653
No 114
>PRK11058 GTPase HflX; Provisional
Probab=65.90 E-value=24 Score=31.91 Aligned_cols=15 Identities=33% Similarity=0.620 Sum_probs=13.2
Q ss_pred eeceEEEEecCCCCC
Q psy7060 129 YLPCIYAYNKIDQIS 143 (160)
Q Consensus 129 Y~P~iyv~NKiD~is 143 (160)
-+|.|+|+||+|+.+
T Consensus 309 ~~pvIiV~NKiDL~~ 323 (426)
T PRK11058 309 EIPTLLVMNKIDMLD 323 (426)
T ss_pred CCCEEEEEEcccCCC
Confidence 379999999999975
No 115
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase.
Probab=65.79 E-value=17 Score=23.93 Aligned_cols=63 Identities=17% Similarity=0.176 Sum_probs=39.8
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeecCCC-hhHHHHHHhcCcceeceEEEEec--CCCCCHHHHHHH
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCN-ADELIDVINANRVYLPCIYAYNK--IDQISIEEVDRI 150 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t-~DdliDvi~~nrvY~P~iyv~NK--iD~is~eevd~i 150 (160)
.++||. =..+++.|.+.+|.--++-+.++-. .+++.. ..+..+|++++-.+ +---+.++++.+
T Consensus 6 ~~~Cp~----C~~ak~~L~~~~i~~~~~di~~~~~~~~~~~~---~g~~~vP~v~~~g~~~~~G~~~~~~~~~ 71 (72)
T TIGR02194 6 KNNCVQ----CKMTKKALEEHGIAFEEINIDEQPEAIDYVKA---QGFRQVPVIVADGDLSWSGFRPDKLKAL 71 (72)
T ss_pred CCCCHH----HHHHHHHHHHCCCceEEEECCCCHHHHHHHHH---cCCcccCEEEECCCcEEeccCHHHHHhc
Confidence 356764 3568899999999888888876642 333332 24568999977554 222255666554
No 116
>cd04134 Rho3 Rho3 subfamily. Rho3 is a member of the Rho family found only in fungi. Rho3 is believed to regulate cell polarity by interacting with the diaphanous/formin family protein For3 to control both the actin cytoskeleton and microtubules. Rho3 is also believed to have a direct role in exocytosis that is independent of its role in regulating actin polarity. The function in exocytosis may be two-pronged: first, in the transport of post-Golgi vesicles from the mother cell to the bud, mediated by myosin (Myo2); second, in the docking and fusion of vesicles to the plasma membrane, mediated by an exocyst (Exo70) protein. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.
Probab=65.53 E-value=10 Score=28.95 Aligned_cols=24 Identities=13% Similarity=-0.058 Sum_probs=17.1
Q ss_pred HHHhcCcceeceEEEEecCCCCCH
Q psy7060 121 DVINANRVYLPCIYAYNKIDQISI 144 (160)
Q Consensus 121 Dvi~~nrvY~P~iyv~NKiD~is~ 144 (160)
+.+.....-.|.++|.||+|+...
T Consensus 96 ~~i~~~~~~~piilvgNK~Dl~~~ 119 (189)
T cd04134 96 GEIREHCPGVKLVLVALKCDLREA 119 (189)
T ss_pred HHHHHhCCCCCEEEEEEChhhccC
Confidence 344443346899999999998643
No 117
>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=65.13 E-value=14 Score=31.07 Aligned_cols=28 Identities=18% Similarity=0.264 Sum_probs=20.8
Q ss_pred HHHHhcCcceeceEEEEecCCCCCHHHHHHH
Q psy7060 120 IDVINANRVYLPCIYAYNKIDQISIEEVDRI 150 (160)
Q Consensus 120 iDvi~~nrvY~P~iyv~NKiD~is~eevd~i 150 (160)
+..+.+ .+|.|.|.||+|+.+.+|+..+
T Consensus 137 lk~l~~---~v~vi~VinK~D~l~~~e~~~~ 164 (276)
T cd01850 137 MKRLSK---RVNIIPVIAKADTLTPEELKEF 164 (276)
T ss_pred HHHHhc---cCCEEEEEECCCcCCHHHHHHH
Confidence 444443 5899999999999987766543
No 118
>PRK09563 rbgA GTPase YlqF; Reviewed
Probab=64.89 E-value=25 Score=29.48 Aligned_cols=27 Identities=26% Similarity=0.270 Sum_probs=18.9
Q ss_pred HHHHHHhcCcceeceEEEEecCCCCCHHHHH
Q psy7060 118 ELIDVINANRVYLPCIYAYNKIDQISIEEVD 148 (160)
Q Consensus 118 dliDvi~~nrvY~P~iyv~NKiD~is~eevd 148 (160)
++.+.+. + +|.|+|+||+|+.+.+...
T Consensus 44 ~l~~~~~-~---kp~iiVlNK~DL~~~~~~~ 70 (287)
T PRK09563 44 MIDKIIG-N---KPRLLILNKSDLADPEVTK 70 (287)
T ss_pred hHHHHhC-C---CCEEEEEEchhcCCHHHHH
Confidence 3455443 3 5999999999998765443
No 119
>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=64.83 E-value=9.5 Score=29.98 Aligned_cols=53 Identities=23% Similarity=0.219 Sum_probs=29.5
Q ss_pred HcCccceEEEeecCCChhHH------HHHHhcCc----ceeceEEEEecCCCC-----CHHHHHHHhc
Q psy7060 100 EYKIFNAEVLFREDCNADEL------IDVINANR----VYLPCIYAYNKIDQI-----SIEEVDRIAR 152 (160)
Q Consensus 100 EYkI~NA~V~ired~t~Ddl------iDvi~~nr----vY~P~iyv~NKiD~i-----s~eevd~i~~ 152 (160)
.|+--+|-+++..-.+.+.+ ++-+...+ .=+|+++|.||+|+. +.++...+++
T Consensus 77 ~~~~ad~iilv~D~~~~~S~~~~~~~~~~i~~~~~~~~~~~piiivgNK~Dl~~~~~~~~~~~~~~~~ 144 (198)
T cd04142 77 GLRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQQRHRFAPRHVLSVLVR 144 (198)
T ss_pred hhccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcccCCCCCCEEEEEECccccccccccHHHHHHHHH
Confidence 34545555555544344333 33343332 237999999999994 3345555543
No 120
>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=64.71 E-value=52 Score=23.97 Aligned_cols=23 Identities=26% Similarity=0.147 Sum_probs=16.8
Q ss_pred eeceEEEEecCCCCC-----HHHHHHHh
Q psy7060 129 YLPCIYAYNKIDQIS-----IEEVDRIA 151 (160)
Q Consensus 129 Y~P~iyv~NKiD~is-----~eevd~i~ 151 (160)
..|.++|.||+|+.. .++...++
T Consensus 106 ~~piivv~nK~Dl~~~~~~~~~~~~~~~ 133 (165)
T cd01865 106 NAQVILVGNKCDMEDERVVSSERGRQLA 133 (165)
T ss_pred CCCEEEEEECcccCcccccCHHHHHHHH
Confidence 579999999999863 35555553
No 121
>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=64.47 E-value=8 Score=25.46 Aligned_cols=23 Identities=30% Similarity=0.247 Sum_probs=17.9
Q ss_pred hcCcceeceEEEEecCCCCCHHH
Q psy7060 124 NANRVYLPCIYAYNKIDQISIEE 146 (160)
Q Consensus 124 ~~nrvY~P~iyv~NKiD~is~ee 146 (160)
.....-.|++++.||+|....++
T Consensus 97 ~~~~~~~~~ivv~nk~D~~~~~~ 119 (157)
T cd00882 97 NKEGENIPIILVGNKIDLPEERV 119 (157)
T ss_pred hhccCCCcEEEEEeccccccccc
Confidence 34556689999999999986544
No 122
>PLN03108 Rab family protein; Provisional
Probab=64.40 E-value=58 Score=25.51 Aligned_cols=26 Identities=27% Similarity=0.308 Sum_probs=20.0
Q ss_pred ceeceEEEEecCCCC-----CHHHHHHHhcC
Q psy7060 128 VYLPCIYAYNKIDQI-----SIEEVDRIARQ 153 (160)
Q Consensus 128 vY~P~iyv~NKiD~i-----s~eevd~i~~~ 153 (160)
..+|++.+.||+|+. +.++.+++++.
T Consensus 110 ~~~piiiv~nK~Dl~~~~~~~~~~~~~~~~~ 140 (210)
T PLN03108 110 ANMTIMLIGNKCDLAHRRAVSTEEGEQFAKE 140 (210)
T ss_pred CCCcEEEEEECccCccccCCCHHHHHHHHHH
Confidence 368999999999985 45677777653
No 123
>cd01871 Rac1_like Rac1-like subfamily. The Rac1-like subfamily consists of Rac1, Rac2, and Rac3 proteins, plus the splice variant Rac1b that contains a 19-residue insertion near switch II relative to Rac1. While Rac1 is ubiquitously expressed, Rac2 and Rac3 are largely restricted to hematopoietic and neural tissues respectively. Rac1 stimulates the formation of actin lamellipodia and membrane ruffles. It also plays a role in cell-matrix adhesion and cell anoikis. In intestinal epithelial cells, Rac1 is an important regulator of migration and mediates apoptosis. Rac1 is also essential for RhoA-regulated actin stress fiber and focal adhesion complex formation. In leukocytes, Rac1 and Rac2 have distinct roles in regulating cell morphology, migration, and invasion, but are not essential for macrophage migration or chemotaxis. Rac3 has biochemical properties that are closely related to Rac1, such as effector interaction, nucleotide binding, and hydrolysis; Rac2 has a slower nucleoti
Probab=64.32 E-value=11 Score=28.57 Aligned_cols=14 Identities=29% Similarity=0.266 Sum_probs=12.6
Q ss_pred eeceEEEEecCCCC
Q psy7060 129 YLPCIYAYNKIDQI 142 (160)
Q Consensus 129 Y~P~iyv~NKiD~i 142 (160)
..|.|+|.||+|+.
T Consensus 105 ~~piilvgnK~Dl~ 118 (174)
T cd01871 105 NTPIILVGTKLDLR 118 (174)
T ss_pred CCCEEEEeeChhhc
Confidence 58999999999984
No 124
>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=64.08 E-value=7.6 Score=26.74 Aligned_cols=24 Identities=42% Similarity=0.555 Sum_probs=18.4
Q ss_pred eceEEEEecCCCC-----CHHHHHHHhcC
Q psy7060 130 LPCIYAYNKIDQI-----SIEEVDRIARQ 153 (160)
Q Consensus 130 ~P~iyv~NKiD~i-----s~eevd~i~~~ 153 (160)
+|.+++.||+|+. +.+++..+++.
T Consensus 106 ~p~ivv~nK~D~~~~~~~~~~~~~~~~~~ 134 (159)
T cd00154 106 IPIILVGNKIDLEDQRQVSTEEAQQFAKE 134 (159)
T ss_pred CcEEEEEEcccccccccccHHHHHHHHHH
Confidence 6999999999995 44677666543
No 125
>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=63.81 E-value=3.4 Score=29.21 Aligned_cols=15 Identities=40% Similarity=0.580 Sum_probs=13.2
Q ss_pred eceEEEEecCCCCCH
Q psy7060 130 LPCIYAYNKIDQISI 144 (160)
Q Consensus 130 ~P~iyv~NKiD~is~ 144 (160)
+|.+++.||+|+...
T Consensus 102 ~~~iiv~NK~Dl~~~ 116 (158)
T cd01879 102 LPVVVALNMIDEAEK 116 (158)
T ss_pred CCEEEEEehhhhccc
Confidence 699999999999754
No 126
>PRK12298 obgE GTPase CgtA; Reviewed
Probab=63.68 E-value=7.5 Score=34.74 Aligned_cols=18 Identities=39% Similarity=0.532 Sum_probs=15.2
Q ss_pred eceEEEEecCCCCCHHHH
Q psy7060 130 LPCIYAYNKIDQISIEEV 147 (160)
Q Consensus 130 ~P~iyv~NKiD~is~eev 147 (160)
.|.|+|+||+|+.+.+++
T Consensus 276 kP~IlVlNKiDl~~~~el 293 (390)
T PRK12298 276 KPRWLVFNKIDLLDEEEA 293 (390)
T ss_pred CCEEEEEeCCccCChHHH
Confidence 699999999999876544
No 127
>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=63.64 E-value=7.1 Score=27.67 Aligned_cols=23 Identities=30% Similarity=0.231 Sum_probs=17.4
Q ss_pred eceEEEEecCCCC-----CHHHHHHHhc
Q psy7060 130 LPCIYAYNKIDQI-----SIEEVDRIAR 152 (160)
Q Consensus 130 ~P~iyv~NKiD~i-----s~eevd~i~~ 152 (160)
.|.++|.||+|+. +.++...+++
T Consensus 111 ~piilv~nK~Dl~~~~~~~~~~~~~~~~ 138 (168)
T cd04119 111 IVVVVCANKIDLTKHRAVSEDEGRLWAE 138 (168)
T ss_pred ceEEEEEEchhcccccccCHHHHHHHHH
Confidence 7999999999986 4566555543
No 128
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=63.64 E-value=8.6 Score=27.33 Aligned_cols=24 Identities=25% Similarity=0.183 Sum_probs=17.5
Q ss_pred eeceEEEEecCCCCC-----HHHHHHHhc
Q psy7060 129 YLPCIYAYNKIDQIS-----IEEVDRIAR 152 (160)
Q Consensus 129 Y~P~iyv~NKiD~is-----~eevd~i~~ 152 (160)
-+|++++.||+|+.. .+++..+++
T Consensus 105 ~~pivvv~nK~D~~~~~~~~~~~~~~~~~ 133 (164)
T smart00175 105 NVVIMLVGNKSDLEDQRQVSREEAEAFAE 133 (164)
T ss_pred CCeEEEEEEchhcccccCCCHHHHHHHHH
Confidence 479999999999874 245555543
No 129
>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=63.45 E-value=7.6 Score=32.75 Aligned_cols=16 Identities=19% Similarity=0.227 Sum_probs=13.9
Q ss_pred eceEEEEecCCCCCHH
Q psy7060 130 LPCIYAYNKIDQISIE 145 (160)
Q Consensus 130 ~P~iyv~NKiD~is~e 145 (160)
+|.+.|+||+|+.+..
T Consensus 110 ip~iIVlNK~DL~~~~ 125 (287)
T cd01854 110 IEPVIVLTKADLLDDE 125 (287)
T ss_pred CCEEEEEEHHHCCChH
Confidence 7999999999998653
No 130
>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=63.32 E-value=7.7 Score=28.91 Aligned_cols=16 Identities=31% Similarity=0.227 Sum_probs=13.5
Q ss_pred ceeceEEEEecCCCCC
Q psy7060 128 VYLPCIYAYNKIDQIS 143 (160)
Q Consensus 128 vY~P~iyv~NKiD~is 143 (160)
--+|.++|.||+|+..
T Consensus 98 ~~~piilv~NK~Dl~~ 113 (164)
T cd04162 98 PDLPLVVLANKQDLPA 113 (164)
T ss_pred CCCcEEEEEeCcCCcC
Confidence 3479999999999864
No 131
>PRK00093 GTP-binding protein Der; Reviewed
Probab=63.31 E-value=6.7 Score=34.02 Aligned_cols=19 Identities=16% Similarity=0.106 Sum_probs=15.4
Q ss_pred eeceEEEEecCCCCCHHHH
Q psy7060 129 YLPCIYAYNKIDQISIEEV 147 (160)
Q Consensus 129 Y~P~iyv~NKiD~is~eev 147 (160)
-.|+++|+||+|+.+.++.
T Consensus 284 ~~~~ivv~NK~Dl~~~~~~ 302 (435)
T PRK00093 284 GRALVIVVNKWDLVDEKTM 302 (435)
T ss_pred CCcEEEEEECccCCCHHHH
Confidence 4799999999999865443
No 132
>PRK13796 GTPase YqeH; Provisional
Probab=63.27 E-value=20 Score=31.44 Aligned_cols=52 Identities=17% Similarity=0.061 Sum_probs=33.3
Q ss_pred cCHHHHHHHHHHcCccceEEEeecCC-----ChhHHHHHHhcCcceeceEEEEecCCCCC
Q psy7060 89 VNEKLVQLILHEYKIFNAEVLFREDC-----NADELIDVINANRVYLPCIYAYNKIDQIS 143 (160)
Q Consensus 89 ~~e~~V~~IL~EYkI~NA~V~ired~-----t~DdliDvi~~nrvY~P~iyv~NKiD~is 143 (160)
++.++.+.+|++-+=.+|.|..-=|+ +....+.-+.++ .|.++|+||+|+.+
T Consensus 54 ~~~~~~~~~l~~i~~~~~lIv~VVD~~D~~~s~~~~L~~~~~~---kpviLViNK~DLl~ 110 (365)
T PRK13796 54 LTDDDFLKLLNGIGDSDALVVNVVDIFDFNGSWIPGLHRFVGN---NPVLLVGNKADLLP 110 (365)
T ss_pred CCHHHHHHHHHhhcccCcEEEEEEECccCCCchhHHHHHHhCC---CCEEEEEEchhhCC
Confidence 67778889999988666554443333 222222222233 48999999999974
No 133
>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=62.71 E-value=7 Score=33.66 Aligned_cols=16 Identities=19% Similarity=0.179 Sum_probs=13.8
Q ss_pred eceEEEEecCCCC-CHH
Q psy7060 130 LPCIYAYNKIDQI-SIE 145 (160)
Q Consensus 130 ~P~iyv~NKiD~i-s~e 145 (160)
+|+|+|.||+|+. +.+
T Consensus 284 ~~iiiv~NK~Dl~~~~~ 300 (429)
T TIGR03594 284 KALVIVVNKWDLVKDEK 300 (429)
T ss_pred CcEEEEEECcccCCCHH
Confidence 6999999999998 443
No 134
>PTZ00133 ADP-ribosylation factor; Provisional
Probab=62.63 E-value=36 Score=26.01 Aligned_cols=14 Identities=21% Similarity=-0.104 Sum_probs=12.6
Q ss_pred eeceEEEEecCCCC
Q psy7060 129 YLPCIYAYNKIDQI 142 (160)
Q Consensus 129 Y~P~iyv~NKiD~i 142 (160)
..|+|+|.||.|+.
T Consensus 118 ~~piilv~NK~Dl~ 131 (182)
T PTZ00133 118 DAVLLVFANKQDLP 131 (182)
T ss_pred CCCEEEEEeCCCCC
Confidence 47999999999986
No 135
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=62.52 E-value=22 Score=26.18 Aligned_cols=50 Identities=18% Similarity=0.226 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHhcCceeccCCCC----eEEEEecCcceEEecccCCchhhHHHHHHHHHH
Q psy7060 9 VQRGLLEKELESVGIRLNKKKPN----IYFKQKKAGGIAFNSTCPLTQVNEKLVQLILHE 64 (160)
Q Consensus 9 ~q~~~le~ELe~~GIrLnkk~p~----I~ikkk~~GGI~i~~t~~lt~~~~~~v~~~l~~ 64 (160)
.-...|+.||+. ||.+..|+ |.+++..+-|+++.+..+- |-+.+..+|.+
T Consensus 16 ga~~AL~~EL~k---Rl~~~fPd~~~~v~Vr~~s~n~lsv~g~~k~---dK~~i~eiLqE 69 (81)
T PRK10597 16 GAIDALAGELSR---RIQYAFPDNEGHVSVRYAAANNLSVIGATKE---DKDRISEILQE 69 (81)
T ss_pred hHHHHHHHHHHH---HHHhhCCCCCccEEEeecCCCceEecCCCcc---hHHHHHHHHHH
Confidence 456788888886 78888887 6777777789999776443 34555555554
No 136
>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=62.30 E-value=55 Score=24.48 Aligned_cols=22 Identities=18% Similarity=-0.016 Sum_probs=17.2
Q ss_pred eeceEEEEecCCCC---CHHHHHHH
Q psy7060 129 YLPCIYAYNKIDQI---SIEEVDRI 150 (160)
Q Consensus 129 Y~P~iyv~NKiD~i---s~eevd~i 150 (160)
-.|.++|.||+|+. +.+++...
T Consensus 110 ~~piilv~NK~Dl~~~~~~~~i~~~ 134 (168)
T cd04149 110 DALLLVFANKQDLPDAMKPHEIQEK 134 (168)
T ss_pred CCcEEEEEECcCCccCCCHHHHHHH
Confidence 37999999999986 45666664
No 137
>cd01875 RhoG RhoG subfamily. RhoG is a GTPase with high sequence similarity to members of the Rac subfamily, including the regions involved in effector recognition and binding. However, RhoG does not bind to known Rac1 and Cdc42 effectors, including proteins containing a Cdc42/Rac interacting binding (CRIB) motif. Instead, RhoG interacts directly with Elmo, an upstream regulator of Rac1, in a GTP-dependent manner and forms a ternary complex with Dock180 to induce activation of Rac1. The RhoG-Elmo-Dock180 pathway is required for activation of Rac1 and cell spreading mediated by integrin, as well as for neurite outgrowth induced by nerve growth factor. Thus RhoG activates Rac1 through Elmo and Dock180 to control cell morphology. RhoG has also been shown to play a role in caveolar trafficking and has a novel role in signaling the neutrophil respiratory burst stimulated by G protein-coupled receptor (GPCR) agonists. Most Rho proteins contain a lipid modification site at the C-termin
Probab=61.95 E-value=14 Score=28.31 Aligned_cols=14 Identities=21% Similarity=0.195 Sum_probs=12.5
Q ss_pred eeceEEEEecCCCC
Q psy7060 129 YLPCIYAYNKIDQI 142 (160)
Q Consensus 129 Y~P~iyv~NKiD~i 142 (160)
-+|.++|.||.|+.
T Consensus 107 ~~piilvgNK~DL~ 120 (191)
T cd01875 107 NVPILLVGTKKDLR 120 (191)
T ss_pred CCCEEEEEeChhhh
Confidence 47999999999985
No 138
>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=61.91 E-value=5.5 Score=28.64 Aligned_cols=22 Identities=27% Similarity=0.157 Sum_probs=16.2
Q ss_pred HhcCcceeceEEEEecCCCCCH
Q psy7060 123 INANRVYLPCIYAYNKIDQISI 144 (160)
Q Consensus 123 i~~nrvY~P~iyv~NKiD~is~ 144 (160)
+......+|.++|.||+|+...
T Consensus 98 ~~~~~~~~p~ivv~nK~Dl~~~ 119 (171)
T cd00157 98 IRHYCPNVPIILVGTKIDLRDD 119 (171)
T ss_pred HHhhCCCCCEEEEEccHHhhhc
Confidence 3333346999999999998744
No 139
>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=61.90 E-value=4.4 Score=32.31 Aligned_cols=16 Identities=31% Similarity=0.148 Sum_probs=13.8
Q ss_pred ceeceEEEEecCCCCC
Q psy7060 128 VYLPCIYAYNKIDQIS 143 (160)
Q Consensus 128 vY~P~iyv~NKiD~is 143 (160)
..+|.|+|.||+|+..
T Consensus 105 ~~~piilV~NK~Dl~~ 120 (221)
T cd04148 105 EDRPIILVGNKSDLAR 120 (221)
T ss_pred CCCCEEEEEEChhccc
Confidence 4689999999999853
No 140
>KOG4252|consensus
Probab=61.67 E-value=5.3 Score=34.73 Aligned_cols=94 Identities=23% Similarity=0.334 Sum_probs=54.5
Q ss_pred HHHHHhh--hhhhHHhhhcCccccccCCCcccCHHHHHHHH-------------H-HcCccceEEEeecCCChhHHH---
Q psy7060 60 LILHEYK--IFNAEQKKAGGIAFNSTCPLTQVNEKLVQLIL-------------H-EYKIFNAEVLFREDCNADELI--- 120 (160)
Q Consensus 60 ~~l~~yk--i~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL-------------~-EYkI~NA~V~ired~t~Ddli--- 120 (160)
+.+..|- ||--+-|+.=|..|- .---+++.++|+..| + -|+=--|-|++-.--+...|.
T Consensus 35 smiqryCkgifTkdykktIgvdfl--erqi~v~~Edvr~mlWdtagqeEfDaItkAyyrgaqa~vLVFSTTDr~SFea~~ 112 (246)
T KOG4252|consen 35 SMIQRYCKGIFTKDYKKTIGVDFL--ERQIKVLIEDVRSMLWDTAGQEEFDAITKAYYRGAQASVLVFSTTDRYSFEATL 112 (246)
T ss_pred HHHHHHhccccccccccccchhhh--hHHHHhhHHHHHHHHHHhccchhHHHHHHHHhccccceEEEEecccHHHHHHHH
Confidence 4455554 666666666665542 122234555555544 2 245556677765433333332
Q ss_pred ---HHHhcCcceeceEEEEecCCCC-----CHHHHHHHhcCCC
Q psy7060 121 ---DVINANRVYLPCIYAYNKIDQI-----SIEEVDRIARQPN 155 (160)
Q Consensus 121 ---Dvi~~nrvY~P~iyv~NKiD~i-----s~eevd~i~~~p~ 155 (160)
.-+....--+|.++|-||||++ +.+|++.+|+.-|
T Consensus 113 ~w~~kv~~e~~~IPtV~vqNKIDlveds~~~~~evE~lak~l~ 155 (246)
T KOG4252|consen 113 EWYNKVQKETERIPTVFVQNKIDLVEDSQMDKGEVEGLAKKLH 155 (246)
T ss_pred HHHHHHHHHhccCCeEEeeccchhhHhhhcchHHHHHHHHHhh
Confidence 2233444568999999999988 4488888876543
No 141
>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=61.47 E-value=5.9 Score=29.63 Aligned_cols=14 Identities=21% Similarity=-0.050 Sum_probs=12.6
Q ss_pred eeceEEEEecCCCC
Q psy7060 129 YLPCIYAYNKIDQI 142 (160)
Q Consensus 129 Y~P~iyv~NKiD~i 142 (160)
-+|++++.||+|+.
T Consensus 116 ~~p~viv~NK~Dl~ 129 (174)
T cd04153 116 KAVLLVLANKQDLK 129 (174)
T ss_pred CCCEEEEEECCCCC
Confidence 37999999999986
No 142
>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=61.46 E-value=56 Score=23.26 Aligned_cols=22 Identities=32% Similarity=0.365 Sum_probs=16.3
Q ss_pred eeceEEEEecCCCC---CHHHHHHH
Q psy7060 129 YLPCIYAYNKIDQI---SIEEVDRI 150 (160)
Q Consensus 129 Y~P~iyv~NKiD~i---s~eevd~i 150 (160)
-.|+++|.||+|+. +.+++...
T Consensus 101 ~~piilv~nK~Dl~~~~~~~~i~~~ 125 (160)
T cd04156 101 GVPVVLLANKQDLPGALTAEEITRR 125 (160)
T ss_pred CCCEEEEEECcccccCcCHHHHHHH
Confidence 47999999999985 34555433
No 143
>PLN03118 Rab family protein; Provisional
Probab=60.92 E-value=69 Score=24.80 Aligned_cols=25 Identities=28% Similarity=0.133 Sum_probs=17.3
Q ss_pred ceeceEEEEecCCCCC-----HHHHHHHhc
Q psy7060 128 VYLPCIYAYNKIDQIS-----IEEVDRIAR 152 (160)
Q Consensus 128 vY~P~iyv~NKiD~is-----~eevd~i~~ 152 (160)
.-.|.++|.||+|+.. .++...+++
T Consensus 119 ~~~~~ilv~NK~Dl~~~~~i~~~~~~~~~~ 148 (211)
T PLN03118 119 QDCVKMLVGNKVDRESERDVSREEGMALAK 148 (211)
T ss_pred CCCCEEEEEECccccccCccCHHHHHHHHH
Confidence 3468999999999863 355555544
No 144
>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=60.53 E-value=15 Score=25.70 Aligned_cols=25 Identities=28% Similarity=0.276 Sum_probs=18.7
Q ss_pred ceeceEEEEecCCCCC-----HHHHHHHhc
Q psy7060 128 VYLPCIYAYNKIDQIS-----IEEVDRIAR 152 (160)
Q Consensus 128 vY~P~iyv~NKiD~is-----~eevd~i~~ 152 (160)
...|++++.||+|+.. .+++.++++
T Consensus 103 ~~~p~ivv~nK~D~~~~~~~~~~~~~~~~~ 132 (160)
T cd00876 103 EDIPIVLVGNKCDLENERQVSKEEGKALAK 132 (160)
T ss_pred CCCcEEEEEECCcccccceecHHHHHHHHH
Confidence 5789999999999874 355555543
No 145
>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=60.38 E-value=13 Score=29.28 Aligned_cols=26 Identities=19% Similarity=0.233 Sum_probs=20.5
Q ss_pred ceeceEEEEecCCCC-----CHHHHHHHhcC
Q psy7060 128 VYLPCIYAYNKIDQI-----SIEEVDRIARQ 153 (160)
Q Consensus 128 vY~P~iyv~NKiD~i-----s~eevd~i~~~ 153 (160)
--.|.|+|.||+|+. +.++...+++.
T Consensus 109 ~~~piilVGNK~DL~~~~~v~~~~~~~~a~~ 139 (189)
T cd04121 109 PGVPKILVGNRLHLAFKRQVATEQAQAYAER 139 (189)
T ss_pred CCCCEEEEEECccchhccCCCHHHHHHHHHH
Confidence 357999999999974 56788877654
No 146
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=60.32 E-value=18 Score=24.42 Aligned_cols=51 Identities=14% Similarity=0.348 Sum_probs=35.5
Q ss_pred ccccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEE
Q psy7060 80 FNSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAY 136 (160)
Q Consensus 80 ~~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~ 136 (160)
|.++||--....+.++.++.+++ .++++. + ..++-+.-.-+-...|++++=
T Consensus 6 ~~~~C~~C~~~~~~~~~~~~~~~-i~~ei~--~---~~~~~~~~~ygv~~vPalvIn 56 (76)
T PF13192_consen 6 FSPGCPYCPELVQLLKEAAEELG-IEVEII--D---IEDFEEIEKYGVMSVPALVIN 56 (76)
T ss_dssp ECSSCTTHHHHHHHHHHHHHHTT-EEEEEE--E---TTTHHHHHHTT-SSSSEEEET
T ss_pred eCCCCCCcHHHHHHHHHHHHhcC-CeEEEE--E---ccCHHHHHHcCCCCCCEEEEC
Confidence 56778887788889999999998 555443 2 255555544567788999663
No 147
>PRK12297 obgE GTPase CgtA; Reviewed
Probab=60.12 E-value=12 Score=34.05 Aligned_cols=23 Identities=26% Similarity=0.299 Sum_probs=16.4
Q ss_pred eeceEEEEecCCCCCH-HHHHHHh
Q psy7060 129 YLPCIYAYNKIDQISI-EEVDRIA 151 (160)
Q Consensus 129 Y~P~iyv~NKiD~is~-eevd~i~ 151 (160)
-+|+|+|.||+|+... +.++.+.
T Consensus 274 ~kP~IVV~NK~DL~~~~e~l~~l~ 297 (424)
T PRK12297 274 ERPQIVVANKMDLPEAEENLEEFK 297 (424)
T ss_pred CCcEEEEEeCCCCcCCHHHHHHHH
Confidence 4799999999998533 4445553
No 148
>PF06207 DUF1002: Protein of unknown function (DUF1002); InterPro: IPR009343 This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.
Probab=60.02 E-value=23 Score=30.11 Aligned_cols=53 Identities=19% Similarity=0.287 Sum_probs=42.0
Q ss_pred CCeEEEEecCc-ceEEecccCCchhhHHHHHHHHHHhhhhhhHHhhhcCccccccCCCcccCHHHHHHHHHHcCccceEE
Q psy7060 30 PNIYFKQKKAG-GIAFNSTCPLTQVNEKLVQLILHEYKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEV 108 (160)
Q Consensus 30 p~I~ikkk~~G-GI~i~~t~~lt~~~~~~v~~~l~~yki~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL~EYkI~NA~V 108 (160)
..++|++.+.| ||++....|- + +|.+++++.+.-|--=||-||+|
T Consensus 53 SSa~V~~~~~g~Gi~V~i~tp~-N---------------------------------It~VT~~mY~NAl~TAGv~da~I 98 (225)
T PF06207_consen 53 SSAYVTPTDKGSGIKVEIVTPN-N---------------------------------ITWVTEEMYANALITAGVTDADI 98 (225)
T ss_pred EEEEEEECCCCCCeEEEEeccC-c---------------------------------ceeecHHHHHHHHHHcCCCcceE
Confidence 34789999999 9999872222 1 45599999999999999999999
Q ss_pred EeecCCCh
Q psy7060 109 LFREDCNA 116 (160)
Q Consensus 109 ~ired~t~ 116 (160)
.+.....+
T Consensus 99 ~Vasp~~V 106 (225)
T PF06207_consen 99 YVASPFPV 106 (225)
T ss_pred EEeccccC
Confidence 99876554
No 149
>COG2229 Predicted GTPase [General function prediction only]
Probab=59.91 E-value=24 Score=29.79 Aligned_cols=51 Identities=25% Similarity=0.332 Sum_probs=33.7
Q ss_pred ccceEEEeecCCChh----HHHHHHhc-CcceeceEEEEecCCCC---CHHHHHHHhcCCC
Q psy7060 103 IFNAEVLFREDCNAD----ELIDVINA-NRVYLPCIYAYNKIDQI---SIEEVDRIARQPN 155 (160)
Q Consensus 103 I~NA~V~ired~t~D----dliDvi~~-nrvY~P~iyv~NKiD~i---s~eevd~i~~~p~ 155 (160)
-.-|.|++..-.+.+ ++++.+.. |+ +|-+++.||-|+. ++|.+..+...++
T Consensus 92 a~gaivlVDss~~~~~~a~~ii~f~~~~~~--ip~vVa~NK~DL~~a~ppe~i~e~l~~~~ 150 (187)
T COG2229 92 AVGAIVLVDSSRPITFHAEEIIDFLTSRNP--IPVVVAINKQDLFDALPPEKIREALKLEL 150 (187)
T ss_pred cceEEEEEecCCCcchHHHHHHHHHhhccC--CCEEEEeeccccCCCCCHHHHHHHHHhcc
Confidence 334566665544433 45555543 22 9999999999998 5588877766663
No 150
>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=59.33 E-value=13 Score=29.73 Aligned_cols=25 Identities=20% Similarity=0.143 Sum_probs=17.9
Q ss_pred ceeceEEEEecCCCC-----CHHHHHHHhc
Q psy7060 128 VYLPCIYAYNKIDQI-----SIEEVDRIAR 152 (160)
Q Consensus 128 vY~P~iyv~NKiD~i-----s~eevd~i~~ 152 (160)
.-+|.|+|.||+|+. +.++...+++
T Consensus 104 ~~~piilVgNK~DL~~~~~v~~~~~~~~a~ 133 (202)
T cd04120 104 EDAELLLVGNKLDCETDREISRQQGEKFAQ 133 (202)
T ss_pred CCCcEEEEEECcccccccccCHHHHHHHHH
Confidence 357999999999984 3455555553
No 151
>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed
Probab=59.28 E-value=5.8 Score=35.75 Aligned_cols=18 Identities=28% Similarity=0.311 Sum_probs=14.7
Q ss_pred eceEEEEecCCCCCHHHH
Q psy7060 130 LPCIYAYNKIDQISIEEV 147 (160)
Q Consensus 130 ~P~iyv~NKiD~is~eev 147 (160)
.|.++|+||+|+.+....
T Consensus 322 ~piiiV~NK~DL~~~~~~ 339 (449)
T PRK05291 322 KPVIVVLNKADLTGEIDL 339 (449)
T ss_pred CCcEEEEEhhhccccchh
Confidence 699999999999865443
No 152
>PRK15494 era GTPase Era; Provisional
Probab=59.11 E-value=35 Score=29.54 Aligned_cols=14 Identities=43% Similarity=0.456 Sum_probs=12.1
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
.|.|+|.||+|+.+
T Consensus 161 ~p~IlViNKiDl~~ 174 (339)
T PRK15494 161 IVPIFLLNKIDIES 174 (339)
T ss_pred CCEEEEEEhhcCcc
Confidence 58899999999874
No 153
>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=59.06 E-value=5.8 Score=28.43 Aligned_cols=14 Identities=50% Similarity=0.700 Sum_probs=12.6
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
+|.++|+||+|+.+
T Consensus 103 ~p~ivv~NK~Dl~~ 116 (168)
T cd01887 103 VPFIVALNKIDKPN 116 (168)
T ss_pred CCEEEEEEceeccc
Confidence 69999999999874
No 154
>cd04135 Tc10 TC10 subfamily. TC10 is a Rho family protein that has been shown to induce microspike formation and neurite outgrowth in vitro. Its expression changes dramatically after peripheral nerve injury, suggesting an important role in promoting axonal outgrowth and regeneration. TC10 regulates translocation of insulin-stimulated GLUT4 in adipocytes and has also been shown to bind directly to Golgi COPI coat proteins. GTP-bound TC10 in vitro can bind numerous potential effectors. Depending on its subcellular localization and distinct functional domains, TC10 can differentially regulate two types of filamentous actin in adipocytes. TC10 mRNAs are highly expressed in three types of mouse muscle tissues: leg skeletal muscle, cardiac muscle, and uterus; they were also present in brain, with higher levels in adults than in newborns. TC10 has also been shown to play a role in regulating the expression of cystic fibrosis transmembrane conductance regulator (CFTR) through interacti
Probab=58.93 E-value=15 Score=26.73 Aligned_cols=16 Identities=19% Similarity=0.225 Sum_probs=13.2
Q ss_pred cceeceEEEEecCCCC
Q psy7060 127 RVYLPCIYAYNKIDQI 142 (160)
Q Consensus 127 rvY~P~iyv~NKiD~i 142 (160)
.--+|++++.||+|+.
T Consensus 102 ~~~~piivv~nK~Dl~ 117 (174)
T cd04135 102 APNVPYLLVGTQIDLR 117 (174)
T ss_pred CCCCCEEEEeEchhhh
Confidence 3457999999999975
No 155
>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=58.83 E-value=8.4 Score=32.43 Aligned_cols=49 Identities=12% Similarity=0.230 Sum_probs=26.6
Q ss_pred HHHHHHHHcCccceEEEeecC---CC--hhHHHHHHhcCcceeceEEEEecCCCCC
Q psy7060 93 LVQLILHEYKIFNAEVLFRED---CN--ADELIDVINANRVYLPCIYAYNKIDQIS 143 (160)
Q Consensus 93 ~V~~IL~EYkI~NA~V~ired---~t--~DdliDvi~~nrvY~P~iyv~NKiD~is 143 (160)
......+.++.-.+-+++-.- +. ...++..+.... +|.|+++||+|+..
T Consensus 77 f~~~~~~~l~~aD~ailVVDa~~g~~~~t~~~~~~~~~~~--~p~ivviNK~D~~~ 130 (270)
T cd01886 77 FTIEVERSLRVLDGAVAVFDAVAGVEPQTETVWRQADRYN--VPRIAFVNKMDRTG 130 (270)
T ss_pred HHHHHHHHHHHcCEEEEEEECCCCCCHHHHHHHHHHHHcC--CCEEEEEECCCCCC
Confidence 344444445444444444221 11 124455444333 69999999999974
No 156
>PRK00098 GTPase RsgA; Reviewed
Probab=58.45 E-value=12 Score=31.81 Aligned_cols=14 Identities=36% Similarity=0.368 Sum_probs=12.6
Q ss_pred eeceEEEEecCCCC
Q psy7060 129 YLPCIYAYNKIDQI 142 (160)
Q Consensus 129 Y~P~iyv~NKiD~i 142 (160)
=+|.++|+||+|+.
T Consensus 111 ~ip~iIVlNK~DL~ 124 (298)
T PRK00098 111 GIKPIIVLNKIDLL 124 (298)
T ss_pred CCCEEEEEEhHHcC
Confidence 37999999999997
No 157
>PRK13675 GTP cyclohydrolase; Provisional
Probab=57.71 E-value=14 Score=32.69 Aligned_cols=26 Identities=19% Similarity=0.437 Sum_probs=19.3
Q ss_pred cCccc----eEEEe--ec--CCChhHHHHHHhcC
Q psy7060 101 YKIFN----AEVLF--RE--DCNADELIDVINAN 126 (160)
Q Consensus 101 YkI~N----A~V~i--re--d~t~DdliDvi~~n 126 (160)
|+-|| |.|.+ +. ++.++|||+.++.+
T Consensus 191 ~~~HnQRs~~~l~v~~~~~~~i~iedLI~~~E~~ 224 (308)
T PRK13675 191 MATHNQRGRGTLTIEVPGDEDVSLEDIIDIIESS 224 (308)
T ss_pred CCCccCceEEEEEEEeCCCCccCHHHHHHHHHHh
Confidence 56677 55666 44 58999999999875
No 158
>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=57.40 E-value=42 Score=27.69 Aligned_cols=25 Identities=28% Similarity=0.426 Sum_probs=19.0
Q ss_pred ceeceEEEEecCCCC-----CHHHHHHHhc
Q psy7060 128 VYLPCIYAYNKIDQI-----SIEEVDRIAR 152 (160)
Q Consensus 128 vY~P~iyv~NKiD~i-----s~eevd~i~~ 152 (160)
.-+|.|+|.||+|+. +.+++..++.
T Consensus 112 ~~~piIivgNK~Dl~~~~~v~~~ei~~~~~ 141 (247)
T cd04143 112 VKIPMVICGNKADRDFPREVQRDEVEQLVG 141 (247)
T ss_pred CCCcEEEEEECccchhccccCHHHHHHHHH
Confidence 458999999999985 4466666644
No 159
>TIGR02200 GlrX_actino Glutaredoxin-like protein. This family of glutaredoxin-like proteins is limited to the Actinobacteria and contains the conserved CxxC motif.
Probab=57.31 E-value=24 Score=22.43 Aligned_cols=53 Identities=15% Similarity=0.145 Sum_probs=34.1
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEEe
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYN 137 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~N 137 (160)
.+.||... .++..|++.++..-.+-+.++-...+....++.+...+|+++.-+
T Consensus 7 ~~~C~~C~----~~~~~L~~~~~~~~~idi~~~~~~~~~~~~~~~~~~~vP~i~~~~ 59 (77)
T TIGR02200 7 TTWCGYCA----QLMRTLDKLGAAYEWVDIEEDEGAADRVVSVNNGNMTVPTVKFAD 59 (77)
T ss_pred CCCChhHH----HHHHHHHHcCCceEEEeCcCCHhHHHHHHHHhCCCceeCEEEECC
Confidence 45676543 367788888876666666655444455555555678999986444
No 160
>COG3052 CitD Citrate lyase, gamma subunit [Energy production and conversion]
Probab=57.17 E-value=14 Score=28.56 Aligned_cols=61 Identities=15% Similarity=0.158 Sum_probs=42.2
Q ss_pred CCCeEEEEecCcceEEecccCCchhhHHHHHHHHHHhhhhhhHHhhhcCccccccCCCcccCHHHHHHHHHHcCccceEE
Q psy7060 29 KPNIYFKQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEV 108 (160)
Q Consensus 29 ~p~I~ikkk~~GGI~i~~t~~lt~~~~~~v~~~l~~yki~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL~EYkI~NA~V 108 (160)
--.|+|.+...|||.+.-.....+ .| |= -=+.+|...|.+|++.||.|
T Consensus 16 DvmIri~P~~~~gI~i~i~SsV~k-------QF---------------G~----------~I~~tV~~~La~l~V~~A~V 63 (98)
T COG3052 16 DVMIRIAPLDTQGIDLQINSSVEK-------QF---------------GD----------AIRQTVLEVLARLGVRGAQV 63 (98)
T ss_pred ceEEEEccCCCCCeEEEeehHHHH-------HH---------------HH----------HHHHHHHHHHHHhCcccceE
Confidence 346888899999998865332221 11 10 22778999999999999999
Q ss_pred EeecCCChhHHHH
Q psy7060 109 LFREDCNADELID 121 (160)
Q Consensus 109 ~ired~t~DdliD 121 (160)
.+...=-+|=++.
T Consensus 64 ~v~DKGALdcvl~ 76 (98)
T COG3052 64 NVDDKGALDCILR 76 (98)
T ss_pred EEeccchHHHHHH
Confidence 9987665655443
No 161
>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=56.62 E-value=73 Score=23.91 Aligned_cols=21 Identities=19% Similarity=0.050 Sum_probs=15.7
Q ss_pred eceEEEEecCCCC---CHHHHHHH
Q psy7060 130 LPCIYAYNKIDQI---SIEEVDRI 150 (160)
Q Consensus 130 ~P~iyv~NKiD~i---s~eevd~i 150 (160)
+|.++|.||.|+. +.+++...
T Consensus 115 ~piilv~NK~Dl~~~~~~~~i~~~ 138 (175)
T smart00177 115 AVILVFANKQDLPDAMKAAEITEK 138 (175)
T ss_pred CcEEEEEeCcCcccCCCHHHHHHH
Confidence 7999999999986 33555443
No 162
>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=56.56 E-value=12 Score=26.97 Aligned_cols=22 Identities=32% Similarity=0.299 Sum_probs=16.2
Q ss_pred eceEEEEecCCCCC-----HHHHHHHh
Q psy7060 130 LPCIYAYNKIDQIS-----IEEVDRIA 151 (160)
Q Consensus 130 ~P~iyv~NKiD~is-----~eevd~i~ 151 (160)
+|.++|.||+|+.+ .+++..++
T Consensus 106 ~~iivv~nK~D~~~~~~~~~~~~~~~~ 132 (161)
T cd04113 106 IVVILVGNKSDLADQREVTFLEASRFA 132 (161)
T ss_pred CeEEEEEEchhcchhccCCHHHHHHHH
Confidence 69999999999863 34555554
No 163
>PF06857 ACP: Malonate decarboxylase delta subunit (MdcD); InterPro: IPR023439 This family consists of the acyl carrier protein found in malonate decarboxylase and citrate lyase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis.
Probab=56.22 E-value=33 Score=25.33 Aligned_cols=30 Identities=20% Similarity=0.203 Sum_probs=24.0
Q ss_pred CHHHHHHHHHHcCccceEEEeecCCChhHH
Q psy7060 90 NEKLVQLILHEYKIFNAEVLFREDCNADEL 119 (160)
Q Consensus 90 ~e~~V~~IL~EYkI~NA~V~ired~t~Ddl 119 (160)
=++.|...|.+|++-||.|.+..-=-+|=.
T Consensus 44 i~~vi~~~l~~~~i~~~~v~i~D~GAld~v 73 (87)
T PF06857_consen 44 IRAVIRETLEELGIEDAKVEINDKGALDCV 73 (87)
T ss_pred HHHHHHHHHHhcCCCceEEEEEeCCCCHHH
Confidence 367899999999999999999875444433
No 164
>KOG1752|consensus
Probab=56.17 E-value=24 Score=26.62 Aligned_cols=64 Identities=16% Similarity=0.284 Sum_probs=48.1
Q ss_pred ccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHh--cCcceeceEEEEecCCCCCHHHHHHH
Q psy7060 82 STCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVIN--ANRVYLPCIYAYNKIDQISIEEVDRI 150 (160)
Q Consensus 82 ~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~--~nrvY~P~iyv~NKiD~is~eevd~i 150 (160)
|.||.-+. ++.+|+++++.=+.|.+.++-.-.|+.+++. .-+.=.|.+++-.|-= =+.+++.++
T Consensus 22 s~C~~c~~----~k~ll~~~~v~~~vvELD~~~~g~eiq~~l~~~tg~~tvP~vFI~Gk~i-GG~~dl~~l 87 (104)
T KOG1752|consen 22 SSCPYCHR----AKELLSDLGVNPKVVELDEDEDGSEIQKALKKLTGQRTVPNVFIGGKFI-GGASDLMAL 87 (104)
T ss_pred CcCchHHH----HHHHHHhCCCCCEEEEccCCCCcHHHHHHHHHhcCCCCCCEEEECCEEE-cCHHHHHHH
Confidence 67887664 8999999999999999999988889999988 3444679998866641 134444444
No 165
>cd04133 Rop_like Rop subfamily. The Rop (Rho-related protein from plants) subfamily plays a role in diverse cellular processes, including cytoskeletal organization, pollen and vegetative cell growth, hormone responses, stress responses, and pathogen resistance. Rops are able to regulate several downstream pathways to amplify a specific signal by acting as master switches early in the signaling cascade. They transmit a variety of extracellular and intracellular signals. Rops are involved in establishing cell polarity in root-hair development, root-hair elongation, pollen-tube growth, cell-shape formation, responses to hormones such as abscisic acid (ABA) and auxin, responses to abiotic stresses such as oxygen deprivation, and disease resistance and disease susceptibility. An individual Rop can have a unique function or an overlapping function shared with other Rop proteins; in addition, a given Rop-regulated function can be controlled by one or multiple Rop proteins. For example,
Probab=56.15 E-value=10 Score=29.37 Aligned_cols=25 Identities=20% Similarity=0.381 Sum_probs=19.5
Q ss_pred eceEEEEecCCC---------------CCHHHHHHHhcCC
Q psy7060 130 LPCIYAYNKIDQ---------------ISIEEVDRIARQP 154 (160)
Q Consensus 130 ~P~iyv~NKiD~---------------is~eevd~i~~~p 154 (160)
.|.|+|.||.|+ ++.++...+++..
T Consensus 106 ~piilvgnK~Dl~~~~~~~~~~~~~~~v~~~~~~~~a~~~ 145 (176)
T cd04133 106 VPIVLVGTKLDLRDDKQYLADHPGASPITTAQGEELRKQI 145 (176)
T ss_pred CCEEEEEeChhhccChhhhhhccCCCCCCHHHHHHHHHHc
Confidence 799999999998 4566777776543
No 166
>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=55.86 E-value=13 Score=30.42 Aligned_cols=24 Identities=29% Similarity=0.427 Sum_probs=17.2
Q ss_pred HHHHHHhcCcceeceEEEEecCCCCC
Q psy7060 118 ELIDVINANRVYLPCIYAYNKIDQIS 143 (160)
Q Consensus 118 dliDvi~~nrvY~P~iyv~NKiD~is 143 (160)
.+++.+.. .=+|.++++||+|+..
T Consensus 107 ~~~~~~~~--~~~P~iivvNK~D~~~ 130 (237)
T cd04168 107 ILWRLLRK--LNIPTIIFVNKIDRAG 130 (237)
T ss_pred HHHHHHHH--cCCCEEEEEECccccC
Confidence 45555543 2369999999999874
No 167
>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=55.47 E-value=11 Score=29.90 Aligned_cols=13 Identities=38% Similarity=0.478 Sum_probs=11.7
Q ss_pred eceEEEEecCCCC
Q psy7060 130 LPCIYAYNKIDQI 142 (160)
Q Consensus 130 ~P~iyv~NKiD~i 142 (160)
.|.|+|+||+|+.
T Consensus 138 ~~iiivvNK~Dl~ 150 (219)
T cd01883 138 KQLIVAVNKMDDV 150 (219)
T ss_pred CeEEEEEEccccc
Confidence 5788899999998
No 168
>PRK13768 GTPase; Provisional
Probab=55.26 E-value=7.8 Score=32.10 Aligned_cols=23 Identities=48% Similarity=0.580 Sum_probs=18.5
Q ss_pred ceeceEEEEecCCCCCHHHHHHH
Q psy7060 128 VYLPCIYAYNKIDQISIEEVDRI 150 (160)
Q Consensus 128 vY~P~iyv~NKiD~is~eevd~i 150 (160)
.-+|.|.|+||+|..+.++.+.+
T Consensus 161 ~~~~~i~v~nK~D~~~~~~~~~~ 183 (253)
T PRK13768 161 LGLPQIPVLNKADLLSEEELERI 183 (253)
T ss_pred cCCCEEEEEEhHhhcCchhHHHH
Confidence 45799999999999987665544
No 169
>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=54.97 E-value=14 Score=26.03 Aligned_cols=23 Identities=26% Similarity=0.301 Sum_probs=16.6
Q ss_pred eceEEEEecCCCCC-----HHHHHHHhc
Q psy7060 130 LPCIYAYNKIDQIS-----IEEVDRIAR 152 (160)
Q Consensus 130 ~P~iyv~NKiD~is-----~eevd~i~~ 152 (160)
+|.++|.||+|+.. .++++.+++
T Consensus 106 ~piiiv~nK~D~~~~~~~~~~~~~~~~~ 133 (162)
T cd04123 106 ISLVIVGNKIDLERQRVVSKSEAEEYAK 133 (162)
T ss_pred CeEEEEEECcccccccCCCHHHHHHHHH
Confidence 69999999999873 345555543
No 170
>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=54.86 E-value=17 Score=28.70 Aligned_cols=14 Identities=29% Similarity=0.301 Sum_probs=12.3
Q ss_pred eeceEEEEecCCCC
Q psy7060 129 YLPCIYAYNKIDQI 142 (160)
Q Consensus 129 Y~P~iyv~NKiD~i 142 (160)
-.|.|+|.||+|+.
T Consensus 120 ~~piilvgNK~DL~ 133 (195)
T cd01873 120 RVPVILVGCKLDLR 133 (195)
T ss_pred CCCEEEEEEchhcc
Confidence 57999999999974
No 171
>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=54.58 E-value=57 Score=24.03 Aligned_cols=13 Identities=23% Similarity=-0.041 Sum_probs=12.0
Q ss_pred eceEEEEecCCCC
Q psy7060 130 LPCIYAYNKIDQI 142 (160)
Q Consensus 130 ~P~iyv~NKiD~i 142 (160)
.|.+++.||+|+.
T Consensus 102 ~piilv~NK~Dl~ 114 (159)
T cd04150 102 AVLLVFANKQDLP 114 (159)
T ss_pred CCEEEEEECCCCC
Confidence 6999999999986
No 172
>PLN03110 Rab GTPase; Provisional
Probab=54.53 E-value=47 Score=26.21 Aligned_cols=24 Identities=25% Similarity=0.209 Sum_probs=17.7
Q ss_pred eceEEEEecCCCC-----CHHHHHHHhcC
Q psy7060 130 LPCIYAYNKIDQI-----SIEEVDRIARQ 153 (160)
Q Consensus 130 ~P~iyv~NKiD~i-----s~eevd~i~~~ 153 (160)
+|.++|.||+|+. +.++...++..
T Consensus 118 ~piiiv~nK~Dl~~~~~~~~~~~~~l~~~ 146 (216)
T PLN03110 118 IVIMMAGNKSDLNHLRSVAEEDGQALAEK 146 (216)
T ss_pred CeEEEEEEChhcccccCCCHHHHHHHHHH
Confidence 6999999999984 34566666543
No 173
>cd04129 Rho2 Rho2 subfamily. Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction. Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall. Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for proper intracellular localization via membrane attachment. As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors).
Probab=54.35 E-value=19 Score=27.30 Aligned_cols=14 Identities=29% Similarity=0.166 Sum_probs=12.5
Q ss_pred eeceEEEEecCCCC
Q psy7060 129 YLPCIYAYNKIDQI 142 (160)
Q Consensus 129 Y~P~iyv~NKiD~i 142 (160)
..|.|+|.||+|+.
T Consensus 105 ~~piilvgnK~Dl~ 118 (187)
T cd04129 105 NVPVILVGLKKDLR 118 (187)
T ss_pred CCCEEEEeeChhhh
Confidence 48999999999984
No 174
>TIGR02183 GRXA Glutaredoxin, GrxA family. This model includes the E. coli glyutaredoxin GrxA which appears to have primary responsibility for the reduction of ribonucleotide reductase.
Probab=53.65 E-value=45 Score=23.02 Aligned_cols=68 Identities=12% Similarity=0.222 Sum_probs=38.3
Q ss_pred ccCCCcccCHHHHHHHHHHcCccceEEE-----eecCC-ChhHHHHHHhcCcceeceEEEEecCCCCCHHHHHHHhcCC
Q psy7060 82 STCPLTQVNEKLVQLILHEYKIFNAEVL-----FREDC-NADELIDVINANRVYLPCIYAYNKIDQISIEEVDRIARQP 154 (160)
Q Consensus 82 ~~~~~~~~~e~~V~~IL~EYkI~NA~V~-----ired~-t~DdliDvi~~nrvY~P~iyv~NKiD~is~eevd~i~~~p 154 (160)
++||.- ..+++.|.+.++-+..+. +.++- ...++.+.....+..+|.|++=.+. .-.-+++..+.+..
T Consensus 8 ~~Cp~C----~~ak~~L~~~~~~~~~i~~~~idi~~~~~~~~~l~~~~g~~~~tVP~ifi~g~~-igG~~dl~~~~~~~ 81 (86)
T TIGR02183 8 PGCPYC----VRAKQLAEKLAIERADFEFRYIDIHAEGISKADLEKTVGKPVETVPQIFVDEKH-VGGCTDFEQLVKEN 81 (86)
T ss_pred CCCccH----HHHHHHHHHhCcccCCCcEEEEECCCCHHHHHHHHHHhCCCCCCcCeEEECCEE-ecCHHHHHHHHHhc
Confidence 567764 457788888765443332 33222 2334555443234689999875544 33667777665543
No 175
>PF01189 Nol1_Nop2_Fmu: NOL1/NOP2/sun family; InterPro: IPR001678 This domain is found in archaeal, bacterial and eukaryotic proteins. In the archaea and bacteria, they are annotated as putative nucleolar protein, Sun (Fmu) family protein or tRNA/rRNA cytosine-C5-methylase. The majority have the S-adenosyl methionine (SAM) binding domain and are related to Escherichia coli Fmu (Sun) protein (16S rRNA m5C 967 methyltransferase) whose structure has been determined []. In the eukaryota, the majority are annotated as being 'hypothetical protein', nucleolar protein or the Nop2/Sun (Fmu) family. Unlike their bacterial homologues, few of the eukaryotic members in this family have a the SAM binding signature. Despite this, Saccharomyces cerevisiae (Baker's yeast) Nop2p is a probable RNA m5C methyltransferase []. It is essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis []; localized to the nucleolus and is essential for viability []. Reduced Nop2p expression limits yeast growth and decreases levels of mature 60S ribosomal subunits while altering rRNA processing []. There is substantial identity between Nop2p and Homo sapiens (Human) p120 (NOL1), which is also called the proliferation-associated nucleolar antigen [, ].; PDB: 3M4X_A 2FRX_B 2YXL_A 1IXK_A 1SQG_A 1SQF_A 3M6U_B 3M6V_B 3M6W_A 3M6X_A ....
Probab=53.64 E-value=7.6 Score=32.98 Aligned_cols=45 Identities=33% Similarity=0.520 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhcCceeccCCCCeEEEEecCcceEEecccCCc-hhhHHHHHHHHHHh
Q psy7060 9 VQRGLLEKELESVGIRLNKKKPNIYFKQKKAGGIAFNSTCPLT-QVNEKLVQLILHEY 65 (160)
Q Consensus 9 ~q~~~le~ELe~~GIrLnkk~p~I~ikkk~~GGI~i~~t~~lt-~~~~~~v~~~l~~y 65 (160)
.|+.+|+.-++-+|+- .+.||.-+-+||.+. .-||+.|+.||.++
T Consensus 193 ~Q~~iL~~a~~~~~~~------------~k~gG~lvYsTCS~~~eENE~vV~~fl~~~ 238 (283)
T PF01189_consen 193 LQREILDNAAKLLNID------------FKPGGRLVYSTCSLSPEENEEVVEKFLKRH 238 (283)
T ss_dssp HHHHHHHHHHHCEHHH------------BEEEEEEEEEESHHHGGGTHHHHHHHHHHS
T ss_pred HHHHHHHHHHHhhccc------------ccCCCeEEEEeccHHHHHHHHHHHHHHHhC
Confidence 4777777777776665 456788888888765 23455555555544
No 176
>PRK01889 GTPase RsgA; Reviewed
Probab=53.63 E-value=20 Score=31.44 Aligned_cols=26 Identities=8% Similarity=0.027 Sum_probs=17.2
Q ss_pred hHHHHHHhcCcceeceEEEEecCCCCCH
Q psy7060 117 DELIDVINANRVYLPCIYAYNKIDQISI 144 (160)
Q Consensus 117 DdliDvi~~nrvY~P~iyv~NKiD~is~ 144 (160)
|.+.-.+.... +|.++|+||+|+.+.
T Consensus 132 dr~L~~a~~~~--i~piIVLNK~DL~~~ 157 (356)
T PRK01889 132 ERYLALAWESG--AEPVIVLTKADLCED 157 (356)
T ss_pred HHHHHHHHHcC--CCEEEEEEChhcCCC
Confidence 34444444444 377999999999864
No 177
>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=52.80 E-value=13 Score=25.56 Aligned_cols=13 Identities=38% Similarity=0.417 Sum_probs=10.5
Q ss_pred ceeceEEEEecCC
Q psy7060 128 VYLPCIYAYNKID 140 (160)
Q Consensus 128 vY~P~iyv~NKiD 140 (160)
..+|+|+|.||.|
T Consensus 107 ~~~piilv~nK~D 119 (119)
T PF08477_consen 107 KNIPIILVGNKSD 119 (119)
T ss_dssp SCSEEEEEEE-TC
T ss_pred CCCCEEEEEeccC
Confidence 3499999999998
No 178
>KOG1489|consensus
Probab=52.30 E-value=13 Score=34.24 Aligned_cols=36 Identities=28% Similarity=0.358 Sum_probs=21.9
Q ss_pred cCcceeceEEEEecCCCCCHH-H-HHHHh---cCCCceeeC
Q psy7060 125 ANRVYLPCIYAYNKIDQISIE-E-VDRIA---RQPNSVVVR 160 (160)
Q Consensus 125 ~nrvY~P~iyv~NKiD~is~e-e-vd~i~---~~p~~v~is 160 (160)
.+-.=.|.++|.||||+...| + +..++ ..|+-+++|
T Consensus 308 k~L~~rp~liVaNKiD~~eae~~~l~~L~~~lq~~~V~pvs 348 (366)
T KOG1489|consen 308 KGLADRPALIVANKIDLPEAEKNLLSSLAKRLQNPHVVPVS 348 (366)
T ss_pred hhhccCceEEEEeccCchhHHHHHHHHHHHHcCCCcEEEee
Confidence 344557999999999985322 2 14442 234456665
No 179
>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=51.71 E-value=14 Score=30.34 Aligned_cols=13 Identities=31% Similarity=0.529 Sum_probs=11.9
Q ss_pred eceEEEEecCCCC
Q psy7060 130 LPCIYAYNKIDQI 142 (160)
Q Consensus 130 ~P~iyv~NKiD~i 142 (160)
+|.|+|+||+|+.
T Consensus 126 ~p~ilviNKiD~~ 138 (222)
T cd01885 126 VKPVLVINKIDRL 138 (222)
T ss_pred CCEEEEEECCCcc
Confidence 6999999999975
No 180
>PRK12296 obgE GTPase CgtA; Reviewed
Probab=51.21 E-value=12 Score=35.21 Aligned_cols=19 Identities=32% Similarity=0.312 Sum_probs=15.4
Q ss_pred ceeceEEEEecCCCCCHHH
Q psy7060 128 VYLPCIYAYNKIDQISIEE 146 (160)
Q Consensus 128 vY~P~iyv~NKiD~is~ee 146 (160)
..+|+|+|.||+|+...++
T Consensus 283 ~~kP~IVVlNKiDL~da~e 301 (500)
T PRK12296 283 AERPRLVVLNKIDVPDARE 301 (500)
T ss_pred cCCCEEEEEECccchhhHH
Confidence 4579999999999976543
No 181
>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=51.06 E-value=64 Score=28.48 Aligned_cols=14 Identities=36% Similarity=0.437 Sum_probs=11.8
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
.|.|+|+||+|+.+
T Consensus 142 ~~iIVviNK~Dl~~ 155 (426)
T TIGR00483 142 NQLIVAINKMDSVN 155 (426)
T ss_pred CeEEEEEEChhccC
Confidence 37888999999973
No 182
>TIGR02189 GlrX-like_plant Glutaredoxin-like family. This family of glutaredoxin-like proteins is aparrently limited to plants. Multiple isoforms are found in A. thaliana and O.sativa.
Probab=50.99 E-value=47 Score=23.91 Aligned_cols=64 Identities=14% Similarity=0.251 Sum_probs=44.1
Q ss_pred ccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhc--CcceeceEEEEecCCCCCHHHHHHH
Q psy7060 82 STCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINA--NRVYLPCIYAYNKIDQISIEEVDRI 150 (160)
Q Consensus 82 ~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~--nrvY~P~iyv~NKiD~is~eevd~i 150 (160)
++||.-. .++++|.+++|.-.++-+.++-...++.+.+.. ++.=+|.|++=.+. .-.-+++..+
T Consensus 16 ~~Cp~C~----~ak~~L~~~~i~~~~vdid~~~~~~~~~~~l~~~tg~~tvP~Vfi~g~~-iGG~ddl~~l 81 (99)
T TIGR02189 16 SSCCMCH----VVKRLLLTLGVNPAVHEIDKEPAGKDIENALSRLGCSPAVPAVFVGGKL-VGGLENVMAL 81 (99)
T ss_pred CCCHHHH----HHHHHHHHcCCCCEEEEcCCCccHHHHHHHHHHhcCCCCcCeEEECCEE-EcCHHHHHHH
Confidence 5677643 688899999998888888888777888777762 45566999765432 1133444444
No 183
>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=50.54 E-value=63 Score=24.24 Aligned_cols=14 Identities=21% Similarity=0.007 Sum_probs=11.8
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
.|.|+|.||+|+.+
T Consensus 107 ~~iilVgnK~Dl~~ 120 (170)
T cd04108 107 VLLFLVGTKKDLSS 120 (170)
T ss_pred CeEEEEEEChhcCc
Confidence 46899999999864
No 184
>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed
Probab=50.27 E-value=20 Score=34.15 Aligned_cols=18 Identities=17% Similarity=0.113 Sum_probs=15.0
Q ss_pred eeceEEEEecCCCCCHHH
Q psy7060 129 YLPCIYAYNKIDQISIEE 146 (160)
Q Consensus 129 Y~P~iyv~NKiD~is~ee 146 (160)
-+|+|+|+||+|+.+.+.
T Consensus 561 ~~piIiV~NK~DL~~~~~ 578 (712)
T PRK09518 561 GRALVLVFNKWDLMDEFR 578 (712)
T ss_pred CCCEEEEEEchhcCChhH
Confidence 479999999999987543
No 185
>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=50.26 E-value=44 Score=26.35 Aligned_cols=15 Identities=33% Similarity=0.512 Sum_probs=13.3
Q ss_pred eeceEEEEecCCCCC
Q psy7060 129 YLPCIYAYNKIDQIS 143 (160)
Q Consensus 129 Y~P~iyv~NKiD~is 143 (160)
-+|.++|.||.|+..
T Consensus 109 ~~pvliv~NK~Dl~~ 123 (203)
T cd04105 109 KIPVLIACNKQDLFT 123 (203)
T ss_pred CCCEEEEecchhhcc
Confidence 589999999999874
No 186
>PRK00093 GTP-binding protein Der; Reviewed
Probab=50.20 E-value=18 Score=31.38 Aligned_cols=40 Identities=13% Similarity=0.189 Sum_probs=23.1
Q ss_pred HHHHHhcCcceeceEEEEecCCCCCH-HHHHHHhcC--CCceeeC
Q psy7060 119 LIDVINANRVYLPCIYAYNKIDQISI-EEVDRIARQ--PNSVVVR 160 (160)
Q Consensus 119 liDvi~~nrvY~P~iyv~NKiD~is~-eevd~i~~~--p~~v~is 160 (160)
+.+.+... =+|.|+|.||+|..+. ++.....++ ++.+++|
T Consensus 101 ~~~~l~~~--~~piilv~NK~D~~~~~~~~~~~~~lg~~~~~~iS 143 (435)
T PRK00093 101 IAKILRKS--NKPVILVVNKVDGPDEEADAYEFYSLGLGEPYPIS 143 (435)
T ss_pred HHHHHHHc--CCcEEEEEECccCccchhhHHHHHhcCCCCCEEEE
Confidence 44444432 4799999999997652 333333333 2445554
No 187
>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=50.03 E-value=15 Score=29.30 Aligned_cols=52 Identities=10% Similarity=0.127 Sum_probs=27.2
Q ss_pred HHHHHHHHHHcCccce-EEEeecC--CChh--HHHHHHhcCcceece-EEEEecCCCCCH
Q psy7060 91 EKLVQLILHEYKIFNA-EVLFRED--CNAD--ELIDVINANRVYLPC-IYAYNKIDQISI 144 (160)
Q Consensus 91 e~~V~~IL~EYkI~NA-~V~ired--~t~D--dliDvi~~nrvY~P~-iyv~NKiD~is~ 144 (160)
.+.+....+....-.+ -+.+... .+.. +++..+.... +|+ |+++||+|+.+.
T Consensus 76 ~~~~~~~~~~~~~~D~~ilVvda~~g~~~~~~~~~~~~~~~~--~~~iIvviNK~D~~~~ 133 (195)
T cd01884 76 ADYIKNMITGAAQMDGAILVVSATDGPMPQTREHLLLARQVG--VPYIVVFLNKADMVDD 133 (195)
T ss_pred HHHHHHHHHHhhhCCEEEEEEECCCCCcHHHHHHHHHHHHcC--CCcEEEEEeCCCCCCc
Confidence 3455556555544443 3333322 2222 3444444333 585 588999999753
No 188
>COG0536 Obg Predicted GTPase [General function prediction only]
Probab=49.90 E-value=15 Score=33.96 Aligned_cols=21 Identities=38% Similarity=0.485 Sum_probs=17.1
Q ss_pred eceEEEEecCCCC-CHHHHHHH
Q psy7060 130 LPCIYAYNKIDQI-SIEEVDRI 150 (160)
Q Consensus 130 ~P~iyv~NKiD~i-s~eevd~i 150 (160)
+|.|+|.||+|+. +.|+++.+
T Consensus 276 K~~ivv~NKiD~~~~~e~~~~~ 297 (369)
T COG0536 276 KPRIVVLNKIDLPLDEEELEEL 297 (369)
T ss_pred CceEEEEeccCCCcCHHHHHHH
Confidence 6899999999955 77777665
No 189
>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=49.60 E-value=19 Score=26.48 Aligned_cols=24 Identities=25% Similarity=0.214 Sum_probs=17.6
Q ss_pred eeceEEEEecCCCC-----CHHHHHHHhc
Q psy7060 129 YLPCIYAYNKIDQI-----SIEEVDRIAR 152 (160)
Q Consensus 129 Y~P~iyv~NKiD~i-----s~eevd~i~~ 152 (160)
-+|++++.||.|+. +.++...+++
T Consensus 105 ~~~iilvgnK~Dl~~~~~v~~~~~~~~~~ 133 (161)
T cd04117 105 GVQKILIGNKADEEQKRQVGDEQGNKLAK 133 (161)
T ss_pred CCeEEEEEECcccccccCCCHHHHHHHHH
Confidence 47999999999985 3455555554
No 190
>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=49.55 E-value=10 Score=27.31 Aligned_cols=14 Identities=36% Similarity=0.401 Sum_probs=12.4
Q ss_pred eeceEEEEecCCCC
Q psy7060 129 YLPCIYAYNKIDQI 142 (160)
Q Consensus 129 Y~P~iyv~NKiD~i 142 (160)
=+|+++|.||+|+.
T Consensus 106 ~~piviv~nK~Dl~ 119 (163)
T cd04176 106 KVPIILVGNKVDLE 119 (163)
T ss_pred CCCEEEEEECccch
Confidence 37999999999985
No 191
>PRK03003 GTP-binding protein Der; Reviewed
Probab=49.25 E-value=15 Score=33.11 Aligned_cols=16 Identities=25% Similarity=0.260 Sum_probs=13.8
Q ss_pred eeceEEEEecCCCCCH
Q psy7060 129 YLPCIYAYNKIDQISI 144 (160)
Q Consensus 129 Y~P~iyv~NKiD~is~ 144 (160)
-+|+|+|.||+|+.+.
T Consensus 322 ~~piIiV~NK~Dl~~~ 337 (472)
T PRK03003 322 GRALVLAFNKWDLVDE 337 (472)
T ss_pred CCCEEEEEECcccCCh
Confidence 4699999999999853
No 192
>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=49.04 E-value=27 Score=26.63 Aligned_cols=33 Identities=30% Similarity=0.328 Sum_probs=21.6
Q ss_pred HHHHHHhcC-cceeceEEEEecCCCC---CHHHHHHH
Q psy7060 118 ELIDVINAN-RVYLPCIYAYNKIDQI---SIEEVDRI 150 (160)
Q Consensus 118 dliDvi~~n-rvY~P~iyv~NKiD~i---s~eevd~i 150 (160)
+|-+.++.. -.-+|.+++.||.|+. +.+++...
T Consensus 103 ~L~~ll~~~~~~~~piLIl~NK~D~~~~~~~~~i~~~ 139 (175)
T PF00025_consen 103 ELKELLNDPELKDIPILILANKQDLPDAMSEEEIKEY 139 (175)
T ss_dssp HHHHHHTSGGGTTSEEEEEEESTTSTTSSTHHHHHHH
T ss_pred chhhhcchhhcccceEEEEeccccccCcchhhHHHhh
Confidence 344444432 2358999999999986 45666654
No 193
>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=48.68 E-value=72 Score=30.21 Aligned_cols=14 Identities=50% Similarity=0.392 Sum_probs=12.4
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
+|.|.|+||+|+.+
T Consensus 123 ipiIiViNKiDl~~ 136 (595)
T TIGR01393 123 LEIIPVINKIDLPS 136 (595)
T ss_pred CCEEEEEECcCCCc
Confidence 69999999999863
No 194
>TIGR02181 GRX_bact Glutaredoxin, GrxC family. This family of glutaredoxins includes the E. coli protein GrxC (Grx3) which appears to have a secondary role in reducing ribonucleotide reductase (in the absence of GrxA) possibly indicating a role in the reduction of other protein disulfides.
Probab=48.43 E-value=44 Score=22.00 Aligned_cols=64 Identities=16% Similarity=0.215 Sum_probs=40.9
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeecCC-ChhHHHHHHhcCcceeceEEEEecCCCCCHHHHHHHh
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDC-NADELIDVINANRVYLPCIYAYNKIDQISIEEVDRIA 151 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~-t~DdliDvi~~nrvY~P~iyv~NKiD~is~eevd~i~ 151 (160)
.++||. =..++.+|+++++.-..+-+..+- ..+++.+. . ++...|.|++=.+. ..+-+++..+.
T Consensus 6 ~~~Cp~----C~~a~~~L~~~~i~~~~~di~~~~~~~~~~~~~-~-g~~~vP~i~i~g~~-igg~~~~~~~~ 70 (79)
T TIGR02181 6 KPYCPY----CTRAKALLSSKGVTFTEIRVDGDPALRDEMMQR-S-GRRTVPQIFIGDVH-VGGCDDLYALD 70 (79)
T ss_pred cCCChh----HHHHHHHHHHcCCCcEEEEecCCHHHHHHHHHH-h-CCCCcCEEEECCEE-EcChHHHHHHH
Confidence 355664 356899999999988888776653 23444432 3 37788999775543 22556665553
No 195
>cd01615 CIDE_N CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein.
Probab=47.81 E-value=16 Score=26.88 Aligned_cols=59 Identities=20% Similarity=0.421 Sum_probs=45.5
Q ss_pred HhhhhhhHHhhhcCccccccCCCcccCHHHHHHHHHHcCc--cceEEEeecC---CChhHHHHHHhcCcce
Q psy7060 64 EYKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKI--FNAEVLFRED---CNADELIDVINANRVY 129 (160)
Q Consensus 64 ~yki~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL~EYkI--~NA~V~ired---~t~DdliDvi~~nrvY 129 (160)
-|||.|.+....=||+-+|- +++......-+.+ ....+.+.+| +.-+|.-..+..|-++
T Consensus 4 p~kV~~~~r~~k~GV~A~sL-------~eL~~K~~~~l~l~~~~~~lvL~eDGTeVddEeYF~tLp~nT~l 67 (78)
T cd01615 4 PFKVCDSDRSRKKGVAASSL-------EELLSKACEKLKLPSAPVTLVLEEDGTEVDDEEYFQTLPDNTVL 67 (78)
T ss_pred CEEEecCCCCeeEEEEcCCH-------HHHHHHHHHHcCCCCCCeEEEEeCCCcEEccHHHHhcCCCCcEE
Confidence 37888999888889998874 7788899999999 4556677777 4457777777777655
No 196
>PTZ00327 eukaryotic translation initiation factor 2 gamma subunit; Provisional
Probab=47.77 E-value=17 Score=33.54 Aligned_cols=56 Identities=18% Similarity=0.270 Sum_probs=30.1
Q ss_pred HHHHHHHHHHcCccc-eEEEeecCC---C--hhHHHHHHhcCcceeceEEEEecCCCCCHHHH
Q psy7060 91 EKLVQLILHEYKIFN-AEVLFREDC---N--ADELIDVINANRVYLPCIYAYNKIDQISIEEV 147 (160)
Q Consensus 91 e~~V~~IL~EYkI~N-A~V~ired~---t--~DdliDvi~~nrvY~P~iyv~NKiD~is~eev 147 (160)
++.++..+..-..-. |-+.+..+- . ..+-+..+..-.+ .|.|+|+||+|+.+.+++
T Consensus 128 ~~fi~~m~~g~~~~D~alLVVda~~g~~~~qT~ehl~i~~~lgi-~~iIVvlNKiDlv~~~~~ 189 (460)
T PTZ00327 128 DILMATMLNGAAVMDAALLLIAANESCPQPQTSEHLAAVEIMKL-KHIIILQNKIDLVKEAQA 189 (460)
T ss_pred HHHHHHHHHHHhhCCEEEEEEECCCCccchhhHHHHHHHHHcCC-CcEEEEEecccccCHHHH
Confidence 566677666554333 444444331 1 1233333332222 367899999999875543
No 197
>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=47.71 E-value=20 Score=28.09 Aligned_cols=13 Identities=31% Similarity=0.473 Sum_probs=10.2
Q ss_pred ceEEEEecCCCCC
Q psy7060 131 PCIYAYNKIDQIS 143 (160)
Q Consensus 131 P~iyv~NKiD~is 143 (160)
|.|+|+||+|+..
T Consensus 132 ~iIvviNK~D~~~ 144 (208)
T cd04166 132 HVVVAVNKMDLVD 144 (208)
T ss_pred cEEEEEEchhccc
Confidence 3566899999974
No 198
>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=47.25 E-value=32 Score=28.08 Aligned_cols=15 Identities=20% Similarity=-0.013 Sum_probs=12.9
Q ss_pred eeceEEEEecCCCCC
Q psy7060 129 YLPCIYAYNKIDQIS 143 (160)
Q Consensus 129 Y~P~iyv~NKiD~is 143 (160)
-+|.|+|.||+|+..
T Consensus 100 ~~piIlVgNK~DL~~ 114 (220)
T cd04126 100 DCLFAVVGNKLDLTE 114 (220)
T ss_pred CCcEEEEEECccccc
Confidence 479999999999864
No 199
>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=46.61 E-value=71 Score=30.07 Aligned_cols=18 Identities=33% Similarity=0.610 Sum_probs=14.8
Q ss_pred ec-eEEEEecCCCCCHHHH
Q psy7060 130 LP-CIYAYNKIDQISIEEV 147 (160)
Q Consensus 130 ~P-~iyv~NKiD~is~eev 147 (160)
+| .|+|+||+|+.+.+.+
T Consensus 103 i~~iIVVlNK~Dlv~~~~~ 121 (581)
T TIGR00475 103 IPHTIVVITKADRVNEEEI 121 (581)
T ss_pred CCeEEEEEECCCCCCHHHH
Confidence 57 9999999999876543
No 200
>cd02966 TlpA_like_family TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases.
Probab=46.57 E-value=61 Score=20.90 Aligned_cols=43 Identities=23% Similarity=0.400 Sum_probs=19.8
Q ss_pred CHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEEec
Q psy7060 90 NEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYNK 138 (160)
Q Consensus 90 ~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~NK 138 (160)
+.+.++..+.+++ .+-.+....+ .++.+....+ ..|+++++++
T Consensus 64 ~~~~~~~~~~~~~-~~~~~~~~~~---~~~~~~~~~~--~~P~~~l~d~ 106 (116)
T cd02966 64 DPAAVKAFLKKYG-ITFPVLLDPD---GELAKAYGVR--GLPTTFLIDR 106 (116)
T ss_pred CHHHHHHHHHHcC-CCcceEEcCc---chHHHhcCcC--ccceEEEECC
Confidence 4556666666665 2333332221 2223322222 5577777654
No 201
>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=46.38 E-value=21 Score=26.99 Aligned_cols=15 Identities=20% Similarity=0.213 Sum_probs=12.9
Q ss_pred eeceEEEEecCCCCC
Q psy7060 129 YLPCIYAYNKIDQIS 143 (160)
Q Consensus 129 Y~P~iyv~NKiD~is 143 (160)
-.|.|+|.||+|+.+
T Consensus 105 ~~piilvgnK~Dl~~ 119 (175)
T cd01874 105 KTPFLLVGTQIDLRD 119 (175)
T ss_pred CCCEEEEEECHhhhh
Confidence 479999999999854
No 202
>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=46.26 E-value=13 Score=28.51 Aligned_cols=15 Identities=27% Similarity=0.569 Sum_probs=13.5
Q ss_pred eeceEEEEecCCCCC
Q psy7060 129 YLPCIYAYNKIDQIS 143 (160)
Q Consensus 129 Y~P~iyv~NKiD~is 143 (160)
.+|+|+|.||+|+..
T Consensus 104 ~~piilv~NK~Dl~~ 118 (198)
T cd04147 104 FVPIVVVGNKADSLE 118 (198)
T ss_pred CCcEEEEEEcccccc
Confidence 589999999999875
No 203
>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=46.21 E-value=12 Score=26.18 Aligned_cols=12 Identities=50% Similarity=0.634 Sum_probs=7.8
Q ss_pred eeceEEEEecCC
Q psy7060 129 YLPCIYAYNKID 140 (160)
Q Consensus 129 Y~P~iyv~NKiD 140 (160)
=.|-+.|+||+|
T Consensus 47 ~~P~i~V~nK~D 58 (58)
T PF06858_consen 47 NKPVIVVLNKID 58 (58)
T ss_dssp TS-EEEEE--TT
T ss_pred CCCEEEEEeccC
Confidence 469999999998
No 204
>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=46.01 E-value=13 Score=28.29 Aligned_cols=14 Identities=43% Similarity=0.316 Sum_probs=12.5
Q ss_pred eeceEEEEecCCCC
Q psy7060 129 YLPCIYAYNKIDQI 142 (160)
Q Consensus 129 Y~P~iyv~NKiD~i 142 (160)
-+|.++|.||+|+.
T Consensus 117 ~~p~iiv~NK~Dl~ 130 (194)
T cd01891 117 GLKPIVVINKIDRP 130 (194)
T ss_pred CCCEEEEEECCCCC
Confidence 46999999999986
No 205
>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=45.22 E-value=89 Score=27.65 Aligned_cols=55 Identities=20% Similarity=0.347 Sum_probs=28.8
Q ss_pred HHHHHHHHHHcCccce-EEEeecC--C---ChhHHHHHHhcCcceeceEEEEecCCCCCHHH
Q psy7060 91 EKLVQLILHEYKIFNA-EVLFRED--C---NADELIDVINANRVYLPCIYAYNKIDQISIEE 146 (160)
Q Consensus 91 e~~V~~IL~EYkI~NA-~V~ired--~---t~DdliDvi~~nrvY~P~iyv~NKiD~is~ee 146 (160)
++.++..+.....-.+ -+.+..+ + ...+.+..+....+ .|.++|+||+|+.+.++
T Consensus 91 ~~f~~~~~~g~~~aD~aIlVVDa~~g~~~~qt~e~l~~l~~~gi-~~iIVvvNK~Dl~~~~~ 151 (406)
T TIGR03680 91 ETLMATMLSGAALMDGALLVIAANEPCPQPQTKEHLMALEIIGI-KNIVIVQNKIDLVSKEK 151 (406)
T ss_pred HHHHHHHHHHHHHCCEEEEEEECCCCccccchHHHHHHHHHcCC-CeEEEEEEccccCCHHH
Confidence 5666666666543333 3333332 1 11222333322222 46899999999987543
No 206
>COG0523 Putative GTPases (G3E family) [General function prediction only]
Probab=45.12 E-value=19 Score=31.78 Aligned_cols=18 Identities=28% Similarity=0.532 Sum_probs=14.7
Q ss_pred EEEEecCCCCCHHHHHHH
Q psy7060 133 IYAYNKIDQISIEEVDRI 150 (160)
Q Consensus 133 iyv~NKiD~is~eevd~i 150 (160)
++++||+|+++.++++.+
T Consensus 149 ~ivlNK~Dlv~~~~l~~l 166 (323)
T COG0523 149 VIVLNKTDLVDAEELEAL 166 (323)
T ss_pred EEEEecccCCCHHHHHHH
Confidence 578999999998876554
No 207
>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=44.94 E-value=26 Score=25.64 Aligned_cols=14 Identities=29% Similarity=0.309 Sum_probs=12.3
Q ss_pred eeceEEEEecCCCC
Q psy7060 129 YLPCIYAYNKIDQI 142 (160)
Q Consensus 129 Y~P~iyv~NKiD~i 142 (160)
-+|.+++.||+|+.
T Consensus 106 ~~piiiv~nK~D~~ 119 (168)
T cd04177 106 NVPMVLVGNKADLE 119 (168)
T ss_pred CCCEEEEEEChhcc
Confidence 47999999999985
No 208
>PRK03003 GTP-binding protein Der; Reviewed
Probab=44.37 E-value=23 Score=31.90 Aligned_cols=24 Identities=29% Similarity=0.336 Sum_probs=16.9
Q ss_pred HHHHHHhcCcceeceEEEEecCCCCC
Q psy7060 118 ELIDVINANRVYLPCIYAYNKIDQIS 143 (160)
Q Consensus 118 dliDvi~~nrvY~P~iyv~NKiD~is 143 (160)
++.+.+.. .=+|+|+|.||+|+..
T Consensus 137 ~i~~~l~~--~~~piilV~NK~Dl~~ 160 (472)
T PRK03003 137 AVARVLRR--SGKPVILAANKVDDER 160 (472)
T ss_pred HHHHHHHH--cCCCEEEEEECccCCc
Confidence 34555542 3379999999999864
No 209
>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=43.78 E-value=31 Score=27.42 Aligned_cols=52 Identities=17% Similarity=0.167 Sum_probs=29.0
Q ss_pred CHHHHHHHHHHcCccceEEEeecCCChhHHHHHH-hcCcceeceEEEEecCCCC
Q psy7060 90 NEKLVQLILHEYKIFNAEVLFREDCNADELIDVI-NANRVYLPCIYAYNKIDQI 142 (160)
Q Consensus 90 ~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi-~~nrvY~P~iyv~NKiD~i 142 (160)
+|+..+..|.+-+..=..+.+.. -++++=.... .---.-+|.++|+||+|..
T Consensus 66 ee~v~~~~l~~~~~D~ii~VvDa-~~l~r~l~l~~ql~e~g~P~vvvlN~~D~a 118 (156)
T PF02421_consen 66 EERVARDYLLSEKPDLIIVVVDA-TNLERNLYLTLQLLELGIPVVVVLNKMDEA 118 (156)
T ss_dssp HHHHHHHHHHHTSSSEEEEEEEG-GGHHHHHHHHHHHHHTTSSEEEEEETHHHH
T ss_pred HHHHHHHHHhhcCCCEEEEECCC-CCHHHHHHHHHHHHHcCCCEEEEEeCHHHH
Confidence 45666777776664434444433 3333222211 1112338999999999976
No 210
>PTZ00369 Ras-like protein; Provisional
Probab=43.54 E-value=24 Score=26.82 Aligned_cols=14 Identities=36% Similarity=0.287 Sum_probs=12.2
Q ss_pred eeceEEEEecCCCC
Q psy7060 129 YLPCIYAYNKIDQI 142 (160)
Q Consensus 129 Y~P~iyv~NKiD~i 142 (160)
-+|.++|.||+|+.
T Consensus 110 ~~piiiv~nK~Dl~ 123 (189)
T PTZ00369 110 RVPMILVGNKCDLD 123 (189)
T ss_pred CCCEEEEEECcccc
Confidence 46999999999984
No 211
>cd04173 Rnd2_Rho7 Rnd2/Rho7 subfamily. Rnd2/Rho7 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed in radially migrating cells in the brain while they are within the subventricular zone of the hippocampus and cerebral cortex. These migrating cells typically develop into pyramidal neurons. Cells that exogenously expressed Rnd2/Rho7 failed to migrate to upper layers of the brain, suggesting that Rnd2/Rho7 plays a role in the radial migration and morphological changes of developing pyramidal neurons, and that Rnd2/Rho7 degradation is necessary for proper cellular migration. The Rnd2/Rho7 GEF Rapostlin is found primarily in the brain and together with Rnd2/Rho7 induces dendrite branching. Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA antagonists, Rnd2/Rho7 binds the GEF Pragmin and significantly stimulates RhoA activity and Rho-A mediated cell contraction. Rnd2/Rho7 is also found to be expressed in sperma
Probab=43.21 E-value=1.4e+02 Score=24.50 Aligned_cols=14 Identities=14% Similarity=0.038 Sum_probs=12.4
Q ss_pred eeceEEEEecCCCC
Q psy7060 129 YLPCIYAYNKIDQI 142 (160)
Q Consensus 129 Y~P~iyv~NKiD~i 142 (160)
-.|.|+|.||+|+.
T Consensus 105 ~~piiLVgnK~DL~ 118 (222)
T cd04173 105 NAKVVLVGCKLDMR 118 (222)
T ss_pred CCCEEEEEECcccc
Confidence 47999999999984
No 212
>PF05193 Peptidase_M16_C: Peptidase M16 inactive domain; InterPro: IPR007863 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. These metallopeptidases belong to MEROPS peptidase family M16 (clan ME). They include proteins, which are classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. The peptidases in this group of sequences include: Insulinase, insulin-degrading enzyme (3.4.24.56 from EC) Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64 from EC) Pitrlysin, Protease III precursor (3.4.24.55 from EC) Nardilysin, (3.4.24.61 from EC) Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2 from EC) Coenzyme PQQ synthesis protein F (3.4.99 from EC) These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The mitochondrial processing peptidase consists of two structurally related domains. One is the active peptidase whereas the other, the C-terminal region, is inactive. The two domains hold the substrate like a clamp [].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 1BE3_B 1PP9_B 2A06_B 1SQB_B 1SQP_B 1L0N_B 1SQX_B 1NU1_B 1L0L_B 2FYU_B ....
Probab=43.05 E-value=61 Score=22.78 Aligned_cols=37 Identities=19% Similarity=0.320 Sum_probs=29.7
Q ss_pred cCHHHHHHHHHH-cCccceEEEeecCCChhHHHHHHhc
Q psy7060 89 VNEKLVQLILHE-YKIFNAEVLFREDCNADELIDVINA 125 (160)
Q Consensus 89 ~~e~~V~~IL~E-YkI~NA~V~ired~t~DdliDvi~~ 125 (160)
+|.+++++..++ |.=.|+.+.+-||++.|++...+..
T Consensus 2 it~e~l~~f~~~~y~p~n~~l~i~Gd~~~~~~~~~i~~ 39 (184)
T PF05193_consen 2 ITLEDLRAFYKKFYRPSNMTLVIVGDIDPDELEKLIEK 39 (184)
T ss_dssp --HHHHHHHHHHHSSGGGEEEEEEESSGHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcCccceEEEEEcCccHHHHHHHHHh
Confidence 567788888775 4778999999999999999988763
No 213
>CHL00071 tufA elongation factor Tu
Probab=42.97 E-value=23 Score=31.36 Aligned_cols=54 Identities=20% Similarity=0.228 Sum_probs=28.6
Q ss_pred HHHHHHHHHHcCccceE-EEeecC--CChh--HHHHHHhcCcceec-eEEEEecCCCCCHHH
Q psy7060 91 EKLVQLILHEYKIFNAE-VLFRED--CNAD--ELIDVINANRVYLP-CIYAYNKIDQISIEE 146 (160)
Q Consensus 91 e~~V~~IL~EYkI~NA~-V~ired--~t~D--dliDvi~~nrvY~P-~iyv~NKiD~is~ee 146 (160)
.+.++...+....-.+- +.+..+ ..-. +++..+. ..-+| .|+|+||+|+.+.++
T Consensus 86 ~~~~~~~~~~~~~~D~~ilVvda~~g~~~qt~~~~~~~~--~~g~~~iIvvvNK~D~~~~~~ 145 (409)
T CHL00071 86 ADYVKNMITGAAQMDGAILVVSAADGPMPQTKEHILLAK--QVGVPNIVVFLNKEDQVDDEE 145 (409)
T ss_pred HHHHHHHHHHHHhCCEEEEEEECCCCCcHHHHHHHHHHH--HcCCCEEEEEEEccCCCCHHH
Confidence 35566666555444433 333222 2222 3344433 23358 568999999997543
No 214
>PRK12739 elongation factor G; Reviewed
Probab=42.95 E-value=22 Score=33.80 Aligned_cols=25 Identities=24% Similarity=0.268 Sum_probs=17.4
Q ss_pred HHHHHHhcCcceeceEEEEecCCCCCH
Q psy7060 118 ELIDVINANRVYLPCIYAYNKIDQISI 144 (160)
Q Consensus 118 dliDvi~~nrvY~P~iyv~NKiD~is~ 144 (160)
+++..+.. .-+|+|+++||+|+...
T Consensus 116 ~i~~~~~~--~~~p~iv~iNK~D~~~~ 140 (691)
T PRK12739 116 TVWRQADK--YGVPRIVFVNKMDRIGA 140 (691)
T ss_pred HHHHHHHH--cCCCEEEEEECCCCCCC
Confidence 44444433 33799999999999853
No 215
>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=42.80 E-value=34 Score=29.97 Aligned_cols=19 Identities=37% Similarity=0.412 Sum_probs=14.3
Q ss_pred cceeceE-EEEecCCCCCHH
Q psy7060 127 RVYLPCI-YAYNKIDQISIE 145 (160)
Q Consensus 127 rvY~P~i-yv~NKiD~is~e 145 (160)
...+|.+ +|+||+|+.+.+
T Consensus 125 ~~gi~~iIvvvNK~Dl~~~~ 144 (394)
T TIGR00485 125 QVGVPYIVVFLNKCDMVDDE 144 (394)
T ss_pred HcCCCEEEEEEEecccCCHH
Confidence 3357887 589999998654
No 216
>TIGR00073 hypB hydrogenase accessory protein HypB. HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.
Probab=42.56 E-value=19 Score=28.27 Aligned_cols=14 Identities=21% Similarity=0.109 Sum_probs=12.3
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
.|.++++||+|+.+
T Consensus 149 ~a~iiv~NK~Dl~~ 162 (207)
T TIGR00073 149 EADLIVINKADLAE 162 (207)
T ss_pred hCCEEEEEHHHccc
Confidence 47899999999985
No 217
>PRK13674 putative GTP cyclohydrolase; Provisional
Probab=42.47 E-value=21 Score=31.03 Aligned_cols=42 Identities=26% Similarity=0.446 Sum_probs=29.9
Q ss_pred CccccccCCCcccCHHHHHHHHHHcCccc----eEE--EeecC--CChhHHHHHHhcC
Q psy7060 77 GIAFNSTCPLTQVNEKLVQLILHEYKIFN----AEV--LFRED--CNADELIDVINAN 126 (160)
Q Consensus 77 ~~~~~~~~~~~~~~e~~V~~IL~EYkI~N----A~V--~ired--~t~DdliDvi~~n 126 (160)
.+...||||- -+-|.+|+-|| |.+ .++++ +.++||||.++.+
T Consensus 147 ~V~~~T~CPC--------S~~is~~~~HnQRs~~~i~v~~~~~~~i~iedLI~~~E~~ 196 (271)
T PRK13674 147 EVPVSSLCPC--------SKAISRYTAHSQRSVATVKVRLAADAQLWIEDLIDLAEAA 196 (271)
T ss_pred EEEEEECCcC--------hHhHccCCCccccEEEEEEEEeCCCCcCCHHHHHHHHHHh
Confidence 4556899994 34445689997 444 44556 7799999999865
No 218
>cd01870 RhoA_like RhoA-like subfamily. The RhoA subfamily consists of RhoA, RhoB, and RhoC. RhoA promotes the formation of stress fibers and focal adhesions, regulating cell shape, attachment, and motility. RhoA can bind to multiple effector proteins, thereby triggering different downstream responses. In many cell types, RhoA mediates local assembly of the contractile ring, which is necessary for cytokinesis. RhoA is vital for muscle contraction; in vascular smooth muscle cells, RhoA plays a key role in cell contraction, differentiation, migration, and proliferation. RhoA activities appear to be elaborately regulated in a time- and space-dependent manner to control cytoskeletal changes. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. RhoA and RhoC are observed only in geranyl
Probab=42.37 E-value=26 Score=25.50 Aligned_cols=15 Identities=33% Similarity=0.301 Sum_probs=12.9
Q ss_pred eeceEEEEecCCCCC
Q psy7060 129 YLPCIYAYNKIDQIS 143 (160)
Q Consensus 129 Y~P~iyv~NKiD~is 143 (160)
-+|.++|.||+|+..
T Consensus 105 ~~piilv~nK~Dl~~ 119 (175)
T cd01870 105 NVPIILVGNKKDLRN 119 (175)
T ss_pred CCCEEEEeeChhccc
Confidence 369999999999864
No 219
>PHA01631 hypothetical protein
Probab=42.30 E-value=22 Score=29.94 Aligned_cols=49 Identities=22% Similarity=0.424 Sum_probs=35.8
Q ss_pred HHHHHHHHHHcCccceEE--EeecCCChhHHHHHHhcCcceeceEEEEecC
Q psy7060 91 EKLVQLILHEYKIFNAEV--LFREDCNADELIDVINANRVYLPCIYAYNKI 139 (160)
Q Consensus 91 e~~V~~IL~EYkI~NA~V--~ired~t~DdliDvi~~nrvY~P~iyv~NKi 139 (160)
.+++..||++|.=-|-++ .+..|+.+-.+-..+.+.++|-|||.|++|-
T Consensus 57 Ak~Ll~Iln~~s~i~DDi~~iIDSDV~ipn~~~~~~~~~v~t~CiPA~~kp 107 (176)
T PHA01631 57 AKQLLTIVNFAKNIEDDIIAIIDSDLIIPNLREIIPNERVFTPCYWLYYDW 107 (176)
T ss_pred HHHHHHHHHhhccCCccEEEEeccceEecCccccccCCCccceeeeeeecC
Confidence 356778888887777777 5677776665543344459999999999985
No 220
>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=42.19 E-value=22 Score=26.45 Aligned_cols=14 Identities=29% Similarity=0.437 Sum_probs=12.8
Q ss_pred eeceEEEEecCCCC
Q psy7060 129 YLPCIYAYNKIDQI 142 (160)
Q Consensus 129 Y~P~iyv~NKiD~i 142 (160)
=+|+++|.||+|+.
T Consensus 104 ~~piiiv~nK~Dl~ 117 (166)
T cd00877 104 NIPIVLCGNKVDIK 117 (166)
T ss_pred CCcEEEEEEchhcc
Confidence 58999999999986
No 221
>PRK09866 hypothetical protein; Provisional
Probab=42.15 E-value=39 Score=33.84 Aligned_cols=13 Identities=38% Similarity=0.411 Sum_probs=12.2
Q ss_pred ceEEEEecCCCCC
Q psy7060 131 PCIYAYNKIDQIS 143 (160)
Q Consensus 131 P~iyv~NKiD~is 143 (160)
|.++|+||+|+.+
T Consensus 291 PVILVVNKIDl~d 303 (741)
T PRK09866 291 PLYVLVNKFDQQD 303 (741)
T ss_pred CEEEEEEcccCCC
Confidence 9999999999986
No 222
>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=41.45 E-value=29 Score=25.99 Aligned_cols=14 Identities=21% Similarity=0.045 Sum_probs=12.4
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
.|.++|.||+|+..
T Consensus 106 ~piilv~nK~Dl~~ 119 (193)
T cd04118 106 CKIYLCGTKSDLIE 119 (193)
T ss_pred CCEEEEEEcccccc
Confidence 69999999999863
No 223
>PLN03126 Elongation factor Tu; Provisional
Probab=41.34 E-value=23 Score=32.62 Aligned_cols=54 Identities=22% Similarity=0.224 Sum_probs=29.5
Q ss_pred HHHHHHHHHHcCccc-eEEEeec--CCCh--hHHHHHHhcCcceec-eEEEEecCCCCCHHH
Q psy7060 91 EKLVQLILHEYKIFN-AEVLFRE--DCNA--DELIDVINANRVYLP-CIYAYNKIDQISIEE 146 (160)
Q Consensus 91 e~~V~~IL~EYkI~N-A~V~ire--d~t~--DdliDvi~~nrvY~P-~iyv~NKiD~is~ee 146 (160)
++.++..+.....-. |-+.+.. .... .+.+..+. ..=+| .|+++||+|+.+.++
T Consensus 155 ~~f~~~~~~g~~~aD~ailVVda~~G~~~qt~e~~~~~~--~~gi~~iIvvvNK~Dl~~~~~ 214 (478)
T PLN03126 155 ADYVKNMITGAAQMDGAILVVSGADGPMPQTKEHILLAK--QVGVPNMVVFLNKQDQVDDEE 214 (478)
T ss_pred HHHHHHHHHHHhhCCEEEEEEECCCCCcHHHHHHHHHHH--HcCCCeEEEEEecccccCHHH
Confidence 556666665554333 4444432 2222 23444433 33358 678999999997543
No 224
>cd06535 CIDE_N_CAD CIDE_N domain of CAD nuclease. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of CAD/DFF40 and ICAD/DFF45 during apoptosis. In normal cells, DFF exists in the nucleus as a heterodimer composed of CAD/DFF40 as a latent nuclease and its chaperone and inhibitor subunit ICAD/DFF45. Apoptotic activation of caspase-3 results in the cleavage of DFF45/ICAD and the release of active DFF40/CAD nuclease.
Probab=40.86 E-value=23 Score=26.09 Aligned_cols=57 Identities=16% Similarity=0.174 Sum_probs=43.0
Q ss_pred hhhhhhHHhhhcCccccccCCCcccCHHHHHHHHHHcCccc--eEEEeecC---CChhHHHHHHhcCcce
Q psy7060 65 YKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFN--AEVLFRED---CNADELIDVINANRVY 129 (160)
Q Consensus 65 yki~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL~EYkI~N--A~V~ired---~t~DdliDvi~~nrvY 129 (160)
|||.|.+....=||+-+|- +++......-+.+.. ..+...|| +| ||+-..+..|-++
T Consensus 5 ~kV~~~~rs~k~GV~A~sL-------~eL~~K~~~~l~l~~~~~~l~L~eDGTeVt-EeyF~tLp~nT~l 66 (77)
T cd06535 5 VKIRSLNSAQKYGVAAKNL-------KELLRKGCRLLQLPCAGSRLCLYEDGTEVT-EEYFPTLPDNTEL 66 (77)
T ss_pred eEEecCCCCeeEeEEcCCH-------HHHHHHHHHHhCCCCCCcEEEEecCCcEeh-HHHHhcCCCCcEE
Confidence 6777777777778887764 778888888999984 46777887 54 7777777777665
No 225
>PF14297 DUF4373: Domain of unknown function (DUF4373)
Probab=40.48 E-value=23 Score=24.92 Aligned_cols=20 Identities=40% Similarity=0.725 Sum_probs=17.7
Q ss_pred ccCHHHHHHHHHHcCccceE
Q psy7060 88 QVNEKLVQLILHEYKIFNAE 107 (160)
Q Consensus 88 ~~~e~~V~~IL~EYkI~NA~ 107 (160)
+++++.|++|+.+|+.|+.+
T Consensus 57 ~~~~~~v~~II~~~~LF~~~ 76 (87)
T PF14297_consen 57 GVSEEYVEEIINEYGLFDIE 76 (87)
T ss_pred CcCHHHHHHHHHHhCCcccC
Confidence 48899999999999999954
No 226
>COG0012 Predicted GTPase, probable translation factor [Translation, ribosomal structure and biogenesis]
Probab=40.43 E-value=22 Score=32.74 Aligned_cols=47 Identities=19% Similarity=0.212 Sum_probs=28.2
Q ss_pred CChhHHHHHHhcC-cceeceEEEEecCCCCCHH---HHHHHhcC-C----CceeeC
Q psy7060 114 CNADELIDVINAN-RVYLPCIYAYNKIDQISIE---EVDRIARQ-P----NSVVVR 160 (160)
Q Consensus 114 ~t~DdliDvi~~n-rvY~P~iyv~NKiD~is~e---evd~i~~~-p----~~v~is 160 (160)
.+-+|+.-.-.-+ ..-+|.|||.||.|....+ .++++... + ..|++|
T Consensus 190 ~~~e~~~~l~~l~llt~KP~lyvaN~~e~~~~~~n~~~~~i~~~~~~~~~~vV~~s 245 (372)
T COG0012 190 WSEEDLEALASLNLLTAKPMLYVANVSEDDLANLNEYVKRLKELAAKENAEVVPVS 245 (372)
T ss_pred CCHHHHHHHHHhhhhhcCCeEEEEECCcccccchhHHHHHHHHHhhhcCCcEEEee
Confidence 4445444333334 3457999999999988633 36666333 2 256665
No 227
>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed
Probab=39.53 E-value=1.1e+02 Score=29.29 Aligned_cols=52 Identities=17% Similarity=0.256 Sum_probs=30.4
Q ss_pred HHHHHHHHHHcCccceEEEeecC---CC-hh-HHHHHHhcCcceeceEEEEecCCCCCH
Q psy7060 91 EKLVQLILHEYKIFNAEVLFRED---CN-AD-ELIDVINANRVYLPCIYAYNKIDQISI 144 (160)
Q Consensus 91 e~~V~~IL~EYkI~NA~V~ired---~t-~D-dliDvi~~nrvY~P~iyv~NKiD~is~ 144 (160)
.........-|.--++-+.+-.- .+ .| ++++.+.. .-+|+|+|.||+|+...
T Consensus 342 ~~~~~~~~~~~~~aD~iL~VvDa~~~~~~~d~~i~~~Lr~--~~~pvIlV~NK~D~~~~ 398 (712)
T PRK09518 342 SAIASQAQIAVSLADAVVFVVDGQVGLTSTDERIVRMLRR--AGKPVVLAVNKIDDQAS 398 (712)
T ss_pred HHHHHHHHHHHHhCCEEEEEEECCCCCCHHHHHHHHHHHh--cCCCEEEEEECcccccc
Confidence 33444555555555555555331 22 23 35566643 34799999999998753
No 228
>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=39.05 E-value=31 Score=27.23 Aligned_cols=24 Identities=29% Similarity=0.282 Sum_probs=17.4
Q ss_pred eceEEEEecCCCCC-----HHHHHHHhcC
Q psy7060 130 LPCIYAYNKIDQIS-----IEEVDRIARQ 153 (160)
Q Consensus 130 ~P~iyv~NKiD~is-----~eevd~i~~~ 153 (160)
.|.++|.||+|+.. .++.+.+++.
T Consensus 110 ~~iilvgNK~Dl~~~~~v~~~~~~~~~~~ 138 (211)
T cd04111 110 PVFILVGHKCDLESQRQVTREEAEKLAKD 138 (211)
T ss_pred CeEEEEEEccccccccccCHHHHHHHHHH
Confidence 57889999999863 4666666543
No 229
>KOG2484|consensus
Probab=38.83 E-value=35 Score=32.21 Aligned_cols=58 Identities=22% Similarity=0.339 Sum_probs=42.6
Q ss_pred CHHHHHHHHHHcC--ccceEEEee-----c--CCChhHHHHHHh---cCcceeceEEEEecCCCCCHHHHHHH
Q psy7060 90 NEKLVQLILHEYK--IFNAEVLFR-----E--DCNADELIDVIN---ANRVYLPCIYAYNKIDQISIEEVDRI 150 (160)
Q Consensus 90 ~e~~V~~IL~EYk--I~NA~V~ir-----e--d~t~DdliDvi~---~nrvY~P~iyv~NKiD~is~eevd~i 150 (160)
+++..++...|++ |-.++|.+. . -+.--+.++++. || +.-|.|+||+|+++.|-++.-
T Consensus 129 ~~~s~kaY~ke~rkvve~sDVVleVlDARDPlgtR~~~vE~~V~~~~gn---KkLILVLNK~DLVPrEv~e~W 198 (435)
T KOG2484|consen 129 NEESKKAYDKEFRKVVEASDVVLEVLDARDPLGTRCPEVEEAVLQAHGN---KKLILVLNKIDLVPREVVEKW 198 (435)
T ss_pred chhhHHHHHHHHHHHHhhhheEEEeeeccCCCCCCChhHHHHHHhccCC---ceEEEEeehhccCCHHHHHHH
Confidence 4566777777775 677888774 1 245567777775 77 456899999999999888754
No 230
>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=38.62 E-value=44 Score=23.86 Aligned_cols=53 Identities=23% Similarity=0.328 Sum_probs=31.4
Q ss_pred cCccceEEEeecCC------ChhHHHHHHhcCcc-eeceEEEEecCCCCC-----HHHHHHHhcC
Q psy7060 101 YKIFNAEVLFREDC------NADELIDVINANRV-YLPCIYAYNKIDQIS-----IEEVDRIARQ 153 (160)
Q Consensus 101 YkI~NA~V~ired~------t~DdliDvi~~nrv-Y~P~iyv~NKiD~is-----~eevd~i~~~ 153 (160)
|+=.+|-+.+-.-. ++..+...+...+- -.|.+++.||.|+.. .++..++++.
T Consensus 69 ~~~~~~~ii~fd~~~~~S~~~~~~~~~~i~~~~~~~~~iivvg~K~D~~~~~~v~~~~~~~~~~~ 133 (162)
T PF00071_consen 69 YRNSDAIIIVFDVTDEESFENLKKWLEEIQKYKPEDIPIIVVGNKSDLSDEREVSVEEAQEFAKE 133 (162)
T ss_dssp HTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGGSSSCHHHHHHHHHH
T ss_pred ccccccccccccccccccccccccccccccccccccccceeeeccccccccccchhhHHHHHHHH
Confidence 44455555554221 23344455554454 479999999999763 4667777554
No 231
>cd02997 PDI_a_PDIR PDIa family, PDIR subfamily; composed of proteins similar to human PDIR (for Protein Disulfide Isomerase Related). PDIR is composed of three redox active TRX (a) domains and an N-terminal redox inactive TRX-like (b) domain. Similar to PDI, it is involved in oxidative protein folding in the endoplasmic reticulum (ER) through its isomerase and chaperone activities. These activities are lower compared to PDI, probably due to PDIR acting only on a subset of proteins. PDIR is preferentially expressed in cells actively secreting proteins and its expression is induced by stress. Similar to PDI, the isomerase and chaperone activities of PDIR are independent; CXXC mutants lacking isomerase activity retain chaperone activity.
Probab=38.59 E-value=43 Score=22.34 Aligned_cols=59 Identities=17% Similarity=0.085 Sum_probs=31.4
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhc-CcceeceEEEEecC
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINA-NRVYLPCIYAYNKI 139 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~-nrvY~P~iyv~NKi 139 (160)
.+.||.-..-...++.+..+|+-...-+...=||+.++--+.... +....|+++++++-
T Consensus 26 a~wC~~C~~~~~~~~~~~~~~~~~~~~~~~~id~~~~~~~~~~~~~~i~~~Pt~~~~~~g 85 (104)
T cd02997 26 APWCGHCKKMKPEFTKAATELKEDGKGVLAAVDCTKPEHDALKEEYNVKGFPTFKYFENG 85 (104)
T ss_pred CCCCHHHHHhCHHHHHHHHHHhhCCceEEEEEECCCCccHHHHHhCCCccccEEEEEeCC
Confidence 455776555555566666666532222222335554322233332 33477999999854
No 232
>COG1161 Predicted GTPases [General function prediction only]
Probab=38.42 E-value=23 Score=30.70 Aligned_cols=55 Identities=20% Similarity=0.130 Sum_probs=32.9
Q ss_pred HHHHHHHHHHcCccceEEEe----ecC-CC-hhHHHHHHhcCcceeceEEEEecCCCCCHHHHHH
Q psy7060 91 EKLVQLILHEYKIFNAEVLF----RED-CN-ADELIDVINANRVYLPCIYAYNKIDQISIEEVDR 149 (160)
Q Consensus 91 e~~V~~IL~EYkI~NA~V~i----red-~t-~DdliDvi~~nrvY~P~iyv~NKiD~is~eevd~ 149 (160)
-+.....++++-.+...|.- |.. -| -.++.+.+.++. .|+|+||+|+.+.+....
T Consensus 21 ~~k~~~~~~~~~~~~d~vvevvDar~P~~s~~~~l~~~v~~k~----~i~vlNK~DL~~~~~~~~ 81 (322)
T COG1161 21 MKKAKRQLKEVLKSVDVVVEVVDARDPLGTRNPELERIVKEKP----KLLVLNKADLAPKEVTKK 81 (322)
T ss_pred hHHHHHHHHHhcccCCEEEEEEeccccccccCccHHHHHccCC----cEEEEehhhcCCHHHHHH
Confidence 34466677777666554432 322 22 344555555543 399999999998755443
No 233
>TIGR00294 conserved hypothetical protein TIGR00294.
Probab=38.41 E-value=33 Score=29.75 Aligned_cols=26 Identities=15% Similarity=0.330 Sum_probs=19.3
Q ss_pred cCccc----eEEEe----ecCCChhHHHHHHhcC
Q psy7060 101 YKIFN----AEVLF----REDCNADELIDVINAN 126 (160)
Q Consensus 101 YkI~N----A~V~i----red~t~DdliDvi~~n 126 (160)
|+-|| |.+.+ +.++.++||||.++.+
T Consensus 189 ~~aHnQRs~~~i~v~~~~~~~~~~edli~~~E~~ 222 (308)
T TIGR00294 189 FATHNQRGRGRIFTEVPSLPSIVIADLIDIAESS 222 (308)
T ss_pred CcCccCCcEEEEEEEeCCCCccCHHHHHHHHHHh
Confidence 67787 55555 4468999999999864
No 234
>PRK12736 elongation factor Tu; Reviewed
Probab=38.40 E-value=1e+02 Score=27.13 Aligned_cols=53 Identities=17% Similarity=0.187 Sum_probs=27.5
Q ss_pred HHHHHHHHHHcCccceEEEe-ecC--CCh--hHHHHHHhcCcceece-EEEEecCCCCCHH
Q psy7060 91 EKLVQLILHEYKIFNAEVLF-RED--CNA--DELIDVINANRVYLPC-IYAYNKIDQISIE 145 (160)
Q Consensus 91 e~~V~~IL~EYkI~NA~V~i-red--~t~--DdliDvi~~nrvY~P~-iyv~NKiD~is~e 145 (160)
++.+...++....-.+-+++ ..+ ... .+.+..+... -+|. |+|+||+|+.+.+
T Consensus 86 ~~f~~~~~~~~~~~d~~llVvd~~~g~~~~t~~~~~~~~~~--g~~~~IvviNK~D~~~~~ 144 (394)
T PRK12736 86 ADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLARQV--GVPYLVVFLNKVDLVDDE 144 (394)
T ss_pred HHHHHHHHHHHhhCCEEEEEEECCCCCchhHHHHHHHHHHc--CCCEEEEEEEecCCcchH
Confidence 45556665554433333333 221 122 2444444333 3685 6889999998543
No 235
>cd02995 PDI_a_PDI_a'_C PDIa family, C-terminal TRX domain (a') subfamily; composed of the C-terminal redox active a' domains of PDI, ERp72, ERp57 (or ERp60) and EFP1. PDI, ERp72 and ERp57 are endoplasmic reticulum (ER)-resident eukaryotic proteins involved in oxidative protein folding. They are oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. PDI and ERp57 have the abb'a' domain structure (where a and a' are redox active TRX domains while b and b' are redox inactive TRX-like domains). PDI also contains an acidic region (c domain) after the a' domain that is absent in ERp57. ERp72 has an additional a domain at the N-terminus (a"abb'a' domain structure). ERp57 interacts with the lectin chaperones, calnexin and calreticu
Probab=38.38 E-value=62 Score=21.46 Aligned_cols=59 Identities=14% Similarity=0.145 Sum_probs=36.9
Q ss_pred ccccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEEecCC
Q psy7060 80 FNSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYNKID 140 (160)
Q Consensus 80 ~~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~NKiD 140 (160)
+.+.|+.-+.=...++.+..+|+=..--...+=||+..++..... -...|+++++.+-.
T Consensus 26 ~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~id~~~~~~~~~~~--~~~~Pt~~~~~~~~ 84 (104)
T cd02995 26 YAPWCGHCKALAPIYEELAEKLKGDDNVVIAKMDATANDVPSEFV--VDGFPTILFFPAGD 84 (104)
T ss_pred ECCCCHHHHHHhhHHHHHHHHhcCCCCEEEEEEeCcchhhhhhcc--CCCCCEEEEEcCCC
Confidence 467788777666777777777754322333345666666544332 25679999997543
No 236
>smart00266 CAD Domains present in proteins implicated in post-mortem DNA fragmentation.
Probab=38.37 E-value=26 Score=25.54 Aligned_cols=58 Identities=17% Similarity=0.347 Sum_probs=44.4
Q ss_pred hhhhhhHHhhhcCccccccCCCcccCHHHHHHHHHHcCcc--ceEEEeecC---CChhHHHHHHhcCcce
Q psy7060 65 YKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIF--NAEVLFRED---CNADELIDVINANRVY 129 (160)
Q Consensus 65 yki~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL~EYkI~--NA~V~ired---~t~DdliDvi~~nrvY 129 (160)
|||.|.+....=||+-+|- +++......-+.+. ...+.+.+| +.-+|.-..+..|-++
T Consensus 3 ~kV~~~~r~~k~GV~A~sL-------~eL~~K~~~~l~l~~~~~~l~L~eDGT~VddEeyF~tLp~nt~l 65 (74)
T smart00266 3 FKVRDHDRNVRKGVAASSL-------EELLSKVCDKLALPDSPVTLVLEEDGTIVDDEEYFQTLPDNTEL 65 (74)
T ss_pred EEEecCCCCeeEEEEcCCH-------HHHHHHHHHHhCCCCCCcEEEEecCCcEEccHHHHhcCCCCcEE
Confidence 6788888888888888774 77888899999998 577777888 4456677777677654
No 237
>TIGR01608 citD citrate lyase acyl carrier protein. This is a model of the acyl carrier protein (aka gamma subunit) of the holoenzyme citrate lyase (EC 4.1.3.6) composed of alpha (EC 2.8.3.10), beta (EC 4.1.3.34), and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The acyl carrier protein covalently binds the coenzyme of citrate lyase. The seed contains an experimentally characterized member from Leuconostoc mesenteroides. The model covers a wide range of Gram positive bacteria. For Gram negative bacteria, it appears that only gamma proteobacteria hit this model. The model is quite robust with queries scoring either quite well or quite poorly against the model. There are currently no hits in-between the noise cutoff and trusted cutoff.
Probab=38.31 E-value=61 Score=24.67 Aligned_cols=30 Identities=23% Similarity=0.138 Sum_probs=24.2
Q ss_pred HHHHHHHHHHcCccceEEEeecCCChhHHH
Q psy7060 91 EKLVQLILHEYKIFNAEVLFREDCNADELI 120 (160)
Q Consensus 91 e~~V~~IL~EYkI~NA~V~ired~t~Ddli 120 (160)
.+.|...|.++++.||.|.+...=-+|=.|
T Consensus 46 r~~v~etL~~lgV~~~~v~v~DkGALDc~I 75 (92)
T TIGR01608 46 ESTVKETLKLLGVENAVVKVVDKGALNCVI 75 (92)
T ss_pred HHHHHHHHHHcCCceEEEEEEeCChHHHHH
Confidence 578999999999999999998755555444
No 238
>PRK13580 serine hydroxymethyltransferase; Provisional
Probab=38.11 E-value=44 Score=31.51 Aligned_cols=37 Identities=22% Similarity=0.194 Sum_probs=25.6
Q ss_pred HHHHHHHHhcCceeccC-CCCeEEEEecCcceEEeccc
Q psy7060 12 GLLEKELESVGIRLNKK-KPNIYFKQKKAGGIAFNSTC 48 (160)
Q Consensus 12 ~~le~ELe~~GIrLnkk-~p~I~ikkk~~GGI~i~~t~ 48 (160)
..+++.|++.||.+|+- +|.+--..-...||||..+.
T Consensus 384 ~~a~~~L~e~GI~vn~i~~Ptvp~g~~~~srLRIg~~A 421 (493)
T PRK13580 384 RQAESALLDAGIVTNRNSIPSDPNGAWYTSGIRLGTPA 421 (493)
T ss_pred HHHHHHHHHCCeEEccccCCCCCCCCCCCceEEeccch
Confidence 46888999999999974 45543222236789997654
No 239
>COG0486 ThdF Predicted GTPase [General function prediction only]
Probab=37.86 E-value=32 Score=32.46 Aligned_cols=48 Identities=25% Similarity=0.196 Sum_probs=28.5
Q ss_pred ccceEEE-eecCCCh--hHHHHHHhc-CcceeceEEEEecCCCCCHHHHHHH
Q psy7060 103 IFNAEVL-FREDCNA--DELIDVINA-NRVYLPCIYAYNKIDQISIEEVDRI 150 (160)
Q Consensus 103 I~NA~V~-ired~t~--DdliDvi~~-nrvY~P~iyv~NKiD~is~eevd~i 150 (160)
+-.|+.. +--|.+- ++--..+.. .+.=+|++.|+||+|+.+..+...+
T Consensus 294 i~~ADlvL~v~D~~~~~~~~d~~~~~~~~~~~~~i~v~NK~DL~~~~~~~~~ 345 (454)
T COG0486 294 IEEADLVLFVLDASQPLDKEDLALIELLPKKKPIIVVLNKADLVSKIELESE 345 (454)
T ss_pred HHhCCEEEEEEeCCCCCchhhHHHHHhcccCCCEEEEEechhcccccccchh
Confidence 4556543 3344443 222222333 5555789999999999987665544
No 240
>cd04103 Centaurin_gamma Centaurin gamma. The centaurins (alpha, beta, gamma, and delta) are large, multi-domain proteins that all contain an ArfGAP domain and ankyrin repeats, and in some cases, numerous additional domains. Centaurin gamma contains an additional GTPase domain near its N-terminus. The specific function of this GTPase domain has not been well characterized, but centaurin gamma 2 (CENTG2) may play a role in the development of autism. Centaurin gamma 1 is also called PIKE (phosphatidyl inositol (PI) 3-kinase enhancer) and centaurin gamma 2 is also known as AGAP (ArfGAP protein with a GTPase-like domain, ankyrin repeats and a Pleckstrin homology domain) or GGAP. Three isoforms of PIKE have been identified. PIKE-S (short) and PIKE-L (long) are brain-specific isoforms, with PIKE-S restricted to the nucleus and PIKE-L found in multiple cellular compartments. A third isoform, PIKE-A was identified in human glioblastoma brain cancers and has been found in various tissues.
Probab=37.66 E-value=23 Score=26.57 Aligned_cols=23 Identities=9% Similarity=0.065 Sum_probs=16.9
Q ss_pred eceEEEEecCCCC-------CHHHHHHHhc
Q psy7060 130 LPCIYAYNKIDQI-------SIEEVDRIAR 152 (160)
Q Consensus 130 ~P~iyv~NKiD~i-------s~eevd~i~~ 152 (160)
+|.++|.||.|+. +.++.+.+++
T Consensus 100 ~piilvgnK~Dl~~~~~~~v~~~~~~~~~~ 129 (158)
T cd04103 100 IPLILVGTQDAISESNPRVIDDARARQLCA 129 (158)
T ss_pred CCEEEEeeHHHhhhcCCcccCHHHHHHHHH
Confidence 7999999999973 3455566664
No 241
>PRK15467 ethanolamine utilization protein EutP; Provisional
Probab=37.63 E-value=45 Score=25.09 Aligned_cols=15 Identities=20% Similarity=-0.020 Sum_probs=12.7
Q ss_pred eeceEEEEecCCCCC
Q psy7060 129 YLPCIYAYNKIDQIS 143 (160)
Q Consensus 129 Y~P~iyv~NKiD~is 143 (160)
-.|.+.+.||+|+..
T Consensus 91 ~~~ii~v~nK~Dl~~ 105 (158)
T PRK15467 91 SKRQIAVISKTDMPD 105 (158)
T ss_pred CCCeEEEEEccccCc
Confidence 468999999999864
No 242
>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity.; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.
Probab=37.55 E-value=20 Score=29.78 Aligned_cols=18 Identities=39% Similarity=0.540 Sum_probs=13.4
Q ss_pred CcceeceEEEEecCCCCC
Q psy7060 126 NRVYLPCIYAYNKIDQIS 143 (160)
Q Consensus 126 nrvY~P~iyv~NKiD~is 143 (160)
-|.-+|.|.|+||+|+++
T Consensus 153 ~~~~lP~vnvlsK~Dl~~ 170 (238)
T PF03029_consen 153 LRLELPHVNVLSKIDLLS 170 (238)
T ss_dssp HHHTSEEEEEE--GGGS-
T ss_pred hhCCCCEEEeeeccCccc
Confidence 367899999999999998
No 243
>PRK15367 type III secretion system protein SsaD; Provisional
Probab=37.33 E-value=3.5e+02 Score=25.31 Aligned_cols=120 Identities=16% Similarity=0.156 Sum_probs=75.5
Q ss_pred HHHHHHHHHHhcCceeccCCCCeEEEEecCcceEEecccCCchhhHHHHHHHHHHhhhhhhHHhhhcCccccccCCCccc
Q psy7060 10 QRGLLEKELESVGIRLNKKKPNIYFKQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEQKKAGGIAFNSTCPLTQV 89 (160)
Q Consensus 10 q~~~le~ELe~~GIrLnkk~p~I~ikkk~~GGI~i~~t~~lt~~~~~~v~~~l~~yki~n~~~~~~~~~~~~~~~~~~~~ 89 (160)
.+..+.+.|..-|. ..|...-...|.+.+.+-|..+. .-..+|.+|. +-||.|-.-.- .
T Consensus 140 ~~~~l~~~L~~p~l------~~V~~~W~~dg~l~LsGyC~~s~-~~~~Lq~~L~-----------~~gi~yr~~lv---c 198 (395)
T PRK15367 140 LPLRVKFLLDKSNI------HYVRAQWKEDGSLQLSGYCSSSE-QMQKVRATLE-----------SWGVMYRDGVI---C 198 (395)
T ss_pred hHHHHHHHhhcccc------cceEEEECCCCcEEEEEEECChH-HHHHHHHHHH-----------hcCceeeecce---e
Confidence 45566666655543 56888888889999999998764 2333444443 44666633221 1
Q ss_pred CHH---HHHHHHHHcCccceEEE--------eecCCChh----HHHHHHhcCcceeceEEEEecCCCCCHHHHHHHh
Q psy7060 90 NEK---LVQLILHEYKIFNAEVL--------FREDCNAD----ELIDVINANRVYLPCIYAYNKIDQISIEEVDRIA 151 (160)
Q Consensus 90 ~e~---~V~~IL~EYkI~NA~V~--------ired~t~D----dliDvi~~nrvY~P~iyv~NKiD~is~eevd~i~ 151 (160)
++. .|+.||+.|+.++++|. |.++++.+ .+...+ .+--=+--.-+.|.++.-...-++++.
T Consensus 199 ~D~L~~~V~~IL~~~GY~~i~V~~~~pG~v~I~G~Iq~~~~w~~V~~lL-~~vpGL~gW~v~n~~~g~~~~li~~L~ 274 (395)
T PRK15367 199 DDLLIREVQDVLIKMGYPHAEVSSEGPGSVLIHDDIQMDQQWRKVQPLL-ADIPGLLHWQISHSHQSQGDDIISAII 274 (395)
T ss_pred HHHHHHHHHHHHHHcCcCceEEecCCCCeEEEEeeecCCcchHHHHHHH-HhCcCcceEEEEeccchhHHHHHHHHH
Confidence 233 57889999999999887 66666644 444444 333334445677777766666666653
No 244
>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=37.29 E-value=30 Score=30.31 Aligned_cols=19 Identities=21% Similarity=0.317 Sum_probs=16.3
Q ss_pred eEEEEecCCCCCHHHHHHH
Q psy7060 132 CIYAYNKIDQISIEEVDRI 150 (160)
Q Consensus 132 ~iyv~NKiD~is~eevd~i 150 (160)
-++++||+|+.+.++++++
T Consensus 176 D~IvlnK~Dl~~~~~l~~~ 194 (341)
T TIGR02475 176 DLVILNKADLLDAAGLARV 194 (341)
T ss_pred CEEEEeccccCCHHHHHHH
Confidence 4689999999999888766
No 245
>PRK10076 pyruvate formate lyase II activase; Provisional
Probab=37.26 E-value=37 Score=27.97 Aligned_cols=100 Identities=12% Similarity=0.108 Sum_probs=50.7
Q ss_pred cCcceEEecccCCchhhHHHHHHHHHHhhhhhhHHhhhcCccccccCCCccc--CHHHHHHHHHHcCccceEEEeec---
Q psy7060 38 KAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEQKKAGGIAFNSTCPLTQV--NEKLVQLILHEYKIFNAEVLFRE--- 112 (160)
Q Consensus 38 ~~GGI~i~~t~~lt~~~~~~v~~~l~~yki~n~~~~~~~~~~~~~~~~~~~~--~e~~V~~IL~EYkI~NA~V~ire--- 112 (160)
..|||.|++.-|+.+ .+.+..++..-| +. || .||--|.. +.+.++.++.--..++.++.--.
T Consensus 38 sggGVt~SGGEPllq--~~fl~~l~~~~k-------~~-gi---~~~leTnG~~~~~~~~~l~~~~D~~l~DiK~~d~~~ 104 (213)
T PRK10076 38 SGGGVTLSGGEVLMQ--AEFATRFLQRLR-------LW-GV---SCAIETAGDAPASKLLPLAKLCDEVLFDLKIMDATQ 104 (213)
T ss_pred CCCEEEEeCchHHcC--HHHHHHHHHHHH-------Hc-CC---CEEEECCCCCCHHHHHHHHHhcCEEEEeeccCCHHH
Confidence 568888888888876 444444444332 22 33 33333332 56667777765556666665421
Q ss_pred -----CCChhHHHHHH---h-cCcceeceEEEEecC-CCCCHHHHHHHhc
Q psy7060 113 -----DCNADELIDVI---N-ANRVYLPCIYAYNKI-DQISIEEVDRIAR 152 (160)
Q Consensus 113 -----d~t~DdliDvi---~-~nrvY~P~iyv~NKi-D~is~eevd~i~~ 152 (160)
-++.+.+.+-+ . .+.-+.-.+.++-.. | +.|+++++++
T Consensus 105 ~~~~tG~~~~~il~nl~~l~~~g~~v~iR~~vIPg~nd--~~e~i~~ia~ 152 (213)
T PRK10076 105 ARDVVKMNLPRVLENLRLLVSEGVNVIPRLPLIPGFTL--SRENMQQALD 152 (213)
T ss_pred HHHHHCCCHHHHHHHHHHHHhCCCcEEEEEEEECCCCC--CHHHHHHHHH
Confidence 13344444433 2 222233334444443 4 5677766653
No 246
>KOG1487|consensus
Probab=37.25 E-value=21 Score=32.75 Aligned_cols=71 Identities=21% Similarity=0.226 Sum_probs=45.2
Q ss_pred HHHHHHHHHhhhhhhHHhhh---------cCcccc-----ccCCCcccCHHHHHHHHHHcCccceEEEeec-CCChhHHH
Q psy7060 56 KLVQLILHEYKIFNAEQKKA---------GGIAFN-----STCPLTQVNEKLVQLILHEYKIFNAEVLFRE-DCNADELI 120 (160)
Q Consensus 56 ~~v~~~l~~yki~n~~~~~~---------~~~~~~-----~~~~~~~~~e~~V~~IL~EYkI~NA~V~ire-d~t~Ddli 120 (160)
.+++++|.+|++|||+..-+ |-+.+| +..-|.+++.=.+..+==+|+|-||.-.--+ +-|.|++.
T Consensus 194 D~~rsil~eyR~hsAdi~Lr~DaT~DdLIdvVegnr~yVp~iyvLNkIdsISiEELdii~~iphavpISA~~~wn~d~lL 273 (358)
T KOG1487|consen 194 DLQRSILSEYRIHSADIALRFDATADDLIDVVEGNRIYVPCIYVLNKIDSISIEELDIIYTIPHAVPISAHTGWNFDKLL 273 (358)
T ss_pred HHHHHHHHHhhhcchheeeecCcchhhhhhhhccCceeeeeeeeecccceeeeeccceeeeccceeecccccccchHHHH
Confidence 37899999999999997543 335555 2223444443333333346888887543333 57889998
Q ss_pred HHHhcC
Q psy7060 121 DVINAN 126 (160)
Q Consensus 121 Dvi~~n 126 (160)
+.+-+.
T Consensus 274 ~~mwey 279 (358)
T KOG1487|consen 274 EKMWEY 279 (358)
T ss_pred HHHhhc
Confidence 888664
No 247
>PTZ00099 rab6; Provisional
Probab=36.75 E-value=72 Score=24.71 Aligned_cols=23 Identities=26% Similarity=-0.010 Sum_probs=16.4
Q ss_pred eeceEEEEecCCCC-----CHHHHHHHh
Q psy7060 129 YLPCIYAYNKIDQI-----SIEEVDRIA 151 (160)
Q Consensus 129 Y~P~iyv~NKiD~i-----s~eevd~i~ 151 (160)
=.|.|+|.||+|+. +.++...++
T Consensus 85 ~~piilVgNK~DL~~~~~v~~~e~~~~~ 112 (176)
T PTZ00099 85 DVIIALVGNKTDLGDLRKVTYEEGMQKA 112 (176)
T ss_pred CCeEEEEEECcccccccCCCHHHHHHHH
Confidence 36889999999985 445555544
No 248
>KOG0395|consensus
Probab=36.69 E-value=33 Score=27.67 Aligned_cols=23 Identities=35% Similarity=0.263 Sum_probs=17.5
Q ss_pred eeceEEEEecCCCCC-----HHHHHHHh
Q psy7060 129 YLPCIYAYNKIDQIS-----IEEVDRIA 151 (160)
Q Consensus 129 Y~P~iyv~NKiD~is-----~eevd~i~ 151 (160)
.+|.+.|-||+|+.. .||-..+|
T Consensus 108 ~~PivlVGNK~Dl~~~R~V~~eeg~~la 135 (196)
T KOG0395|consen 108 DVPIILVGNKCDLERERQVSEEEGKALA 135 (196)
T ss_pred CCCEEEEEEcccchhccccCHHHHHHHH
Confidence 389999999999974 46655554
No 249
>PLN03127 Elongation factor Tu; Provisional
Probab=36.57 E-value=51 Score=30.05 Aligned_cols=26 Identities=31% Similarity=0.383 Sum_probs=16.9
Q ss_pred HHHHHHhcCcceece-EEEEecCCCCCHH
Q psy7060 118 ELIDVINANRVYLPC-IYAYNKIDQISIE 145 (160)
Q Consensus 118 dliDvi~~nrvY~P~-iyv~NKiD~is~e 145 (160)
+.+..+. ..-+|. |+|+||+|+.+.+
T Consensus 167 e~l~~~~--~~gip~iIvviNKiDlv~~~ 193 (447)
T PLN03127 167 EHILLAR--QVGVPSLVVFLNKVDVVDDE 193 (447)
T ss_pred HHHHHHH--HcCCCeEEEEEEeeccCCHH
Confidence 3444443 334695 6889999998643
No 250
>PRK05433 GTP-binding protein LepA; Provisional
Probab=36.47 E-value=69 Score=30.37 Aligned_cols=14 Identities=43% Similarity=0.382 Sum_probs=12.4
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
+|.|.|+||+|+..
T Consensus 127 lpiIvViNKiDl~~ 140 (600)
T PRK05433 127 LEIIPVLNKIDLPA 140 (600)
T ss_pred CCEEEEEECCCCCc
Confidence 69999999999863
No 251
>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=36.21 E-value=1.2e+02 Score=24.17 Aligned_cols=15 Identities=27% Similarity=0.375 Sum_probs=12.8
Q ss_pred ceeceEEEEecCCCC
Q psy7060 128 VYLPCIYAYNKIDQI 142 (160)
Q Consensus 128 vY~P~iyv~NKiD~i 142 (160)
--+|.|+|.||+|+.
T Consensus 98 ~~~piilvgNK~Dl~ 112 (200)
T smart00176 98 ENIPIVLCGNKVDVK 112 (200)
T ss_pred CCCCEEEEEECcccc
Confidence 357999999999974
No 252
>TIGR01295 PedC_BrcD bacteriocin transport accessory protein, putative. This model describes a small family of proteins believed to aid in the export of various class II bacteriocins, which are ribosomally-synthesized, non-lantibiotic bacterial peptide antibiotics. Members of this family are found in operons for pediocin PA-1 from Pediococcus acidilactici and brochocin-C from Brochothrix campestris.
Probab=35.95 E-value=1.8e+02 Score=21.55 Aligned_cols=72 Identities=13% Similarity=0.099 Sum_probs=43.6
Q ss_pred ccccCCCcccCHHHHHHHHHHcCccceEEEeecC-----CChhHHHHHHh-----cCcceeceEEEEecC--------CC
Q psy7060 80 FNSTCPLTQVNEKLVQLILHEYKIFNAEVLFRED-----CNADELIDVIN-----ANRVYLPCIYAYNKI--------DQ 141 (160)
Q Consensus 80 ~~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired-----~t~DdliDvi~-----~nrvY~P~iyv~NKi--------D~ 141 (160)
..++||--+.=...++.+..+.+..=.-|-+.++ .+-+++.+... .+-.++|+++++++= +.
T Consensus 31 ~~~~Cp~C~~~~P~l~~~~~~~~~~~y~vdvd~~~~~~~~~~~~~~~~~~~~~i~~~i~~~PT~v~~k~Gk~v~~~~G~~ 110 (122)
T TIGR01295 31 GRKTCPYCRKFSGTLSGVVAQTKAPIYYIDSENNGSFEMSSLNDLTAFRSRFGIPTSFMGTPTFVHITDGKQVSVRCGSS 110 (122)
T ss_pred ECCCChhHHHHhHHHHHHHHhcCCcEEEEECCCccCcCcccHHHHHHHHHHcCCcccCCCCCEEEEEeCCeEEEEEeCCC
Confidence 4688999888777888888885532122222211 11223333332 345679999999884 35
Q ss_pred CCHHHHHHHh
Q psy7060 142 ISIEEVDRIA 151 (160)
Q Consensus 142 is~eevd~i~ 151 (160)
.+.+++..+.
T Consensus 111 ~~~~~l~~~~ 120 (122)
T TIGR01295 111 TTAQELQDIA 120 (122)
T ss_pred CCHHHHHHHh
Confidence 5677777663
No 253
>TIGR00550 nadA quinolinate synthetase complex, A subunit. This protein, termed NadA, plays a role in the synthesis of pyridine, a precursor to NAD. The quinolinate synthetase complex consists of A protein (this protein) and B protein. B protein converts L-aspartate to iminoaspartate, an unstable reaction product which in the absence of A protein is spontaneously hydrolyzed to form oxaloacetate. The A protein, NadA, converts iminoaspartate to quinolate.
Probab=35.47 E-value=61 Score=28.59 Aligned_cols=52 Identities=17% Similarity=0.274 Sum_probs=37.0
Q ss_pred HHHHh-hhhhhHHhhhcCcc--ccccCCCccc-CHHHHHHHHHHcCccceEEEeecCCChh
Q psy7060 61 ILHEY-KIFNAEQKKAGGIA--FNSTCPLTQV-NEKLVQLILHEYKIFNAEVLFREDCNAD 117 (160)
Q Consensus 61 ~l~~y-ki~n~~~~~~~~~~--~~~~~~~~~~-~e~~V~~IL~EYkI~NA~V~ired~t~D 117 (160)
||++| ||.|-+++. +. .++.||+-+. +.+.++.+-++| -||.|+..-+++.+
T Consensus 63 fMae~a~~l~p~k~v---ilp~~~a~C~~a~~~~~~~i~~lk~~~--Pda~vvah~n~~ae 118 (310)
T TIGR00550 63 FMGETAKILNPEKTV---LMPDLGAGCSMADMCPPEEFKKLKERH--PDAFVVTYVNTTAE 118 (310)
T ss_pred hHHHHHHHhCCCCEE---EccCCCCCCccccccCHHHHHHHHHHC--CCCEEEEECCCCHH
Confidence 66666 344666432 33 5889999765 889999988888 57888777777765
No 254
>cd05025 S-100A1 S-100A1: S-100A1 domain found in proteins similar to S100A1. S100A1 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. As is the case with many other members of S100 protein family, S100A1 is implicated in intracellular and extracellular regulatory activities, including interaction with myosin-associated twitchin kinase, actin-capping protein CapZ, sinapsin I, and tubulin. Structural data suggests that S100A1 proteins exist within cells as antiparallel homodimers, while heterodimers with S100A4 and S100B also has been reported. Upon binding calcium S100A1 changes conformation to expose a hydrophobic cleft which is the interaction site of S100A1 with its more that 20 known target proteins.
Probab=35.43 E-value=42 Score=23.29 Aligned_cols=31 Identities=13% Similarity=0.227 Sum_probs=19.8
Q ss_pred cCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHh
Q psy7060 89 VNEKLVQLILHEYKIFNAEVLFREDCNADELIDVIN 124 (160)
Q Consensus 89 ~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~ 124 (160)
.+++.++.+++++...+ .+.++.++++..+.
T Consensus 49 ~s~~~v~~i~~~~D~d~-----~G~I~f~eF~~l~~ 79 (92)
T cd05025 49 KDADAVDKIMKELDENG-----DGEVDFQEFVVLVA 79 (92)
T ss_pred CCHHHHHHHHHHHCCCC-----CCcCcHHHHHHHHH
Confidence 36677777777765533 34577777776654
No 255
>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=34.85 E-value=22 Score=30.70 Aligned_cols=24 Identities=25% Similarity=0.236 Sum_probs=17.1
Q ss_pred HHHHHhcCcceeceEEEEecCCCCCH
Q psy7060 119 LIDVINANRVYLPCIYAYNKIDQISI 144 (160)
Q Consensus 119 liDvi~~nrvY~P~iyv~NKiD~is~ 144 (160)
+...+... =+|.++|+||+|+.+.
T Consensus 99 i~~~l~~~--~~piilVvNK~D~~~~ 122 (429)
T TIGR03594 99 IAKWLRKS--GKPVILVANKIDGKKE 122 (429)
T ss_pred HHHHHHHh--CCCEEEEEECccCCcc
Confidence 44555432 3699999999998764
No 256
>KOG2485|consensus
Probab=34.82 E-value=88 Score=28.71 Aligned_cols=55 Identities=20% Similarity=0.259 Sum_probs=38.4
Q ss_pred HHHHHHHHHHcCccceEEEeecC----CChhHHHHHHhcCcceeceEEEEecCCCCCHHHHH
Q psy7060 91 EKLVQLILHEYKIFNAEVLFRED----CNADELIDVINANRVYLPCIYAYNKIDQISIEEVD 148 (160)
Q Consensus 91 e~~V~~IL~EYkI~NA~V~ired----~t~DdliDvi~~nrvY~P~iyv~NKiD~is~eevd 148 (160)
.+.+++|=+.-+..++.|-+|.- -+..++.+-... =.|-|+||||.|+.+.-+..
T Consensus 34 akalr~i~~~l~~~D~iiEvrDaRiPLssrn~~~~~~~~---~k~riiVlNK~DLad~~~~k 92 (335)
T KOG2485|consen 34 AKALRAIQNRLPLVDCIIEVRDARIPLSSRNELFQDFLP---PKPRIIVLNKMDLADPKEQK 92 (335)
T ss_pred HHHHHHHHhhcccccEEEEeeccccCCccccHHHHHhcC---CCceEEEEecccccCchhhh
Confidence 45677887888889999999873 223333333333 57999999999999854433
No 257
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=34.79 E-value=42 Score=25.87 Aligned_cols=39 Identities=26% Similarity=0.410 Sum_probs=31.4
Q ss_pred cccCCCcccCHHHHHHHHHHcC-ccceEEEeecC--CChhHH
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYK-IFNAEVLFRED--CNADEL 119 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYk-I~NA~V~ired--~t~Ddl 119 (160)
++.||++.+=...|++.|.+.. +.+++|.+.-+ -|.|.+
T Consensus 59 ~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l~~~p~Wt~~~m 100 (111)
T COG2151 59 SPGCPLAEVIADQVEAALEEIPGVEDVEVELTLSPPWTPDRM 100 (111)
T ss_pred CCCCCccHHHHHHHHHHHHhcCCcceEEEEEEEcCCCchhhc
Confidence 3789999999999999999997 88888877655 444443
No 258
>PLN03071 GTP-binding nuclear protein Ran; Provisional
Probab=34.73 E-value=28 Score=27.68 Aligned_cols=15 Identities=27% Similarity=0.375 Sum_probs=13.0
Q ss_pred ceeceEEEEecCCCC
Q psy7060 128 VYLPCIYAYNKIDQI 142 (160)
Q Consensus 128 vY~P~iyv~NKiD~i 142 (160)
-.+|.++|.||+|+.
T Consensus 116 ~~~piilvgNK~Dl~ 130 (219)
T PLN03071 116 ENIPIVLCGNKVDVK 130 (219)
T ss_pred CCCcEEEEEEchhhh
Confidence 358999999999985
No 259
>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=34.52 E-value=30 Score=31.40 Aligned_cols=16 Identities=38% Similarity=0.295 Sum_probs=13.2
Q ss_pred eeceEEEEecCCCCCH
Q psy7060 129 YLPCIYAYNKIDQISI 144 (160)
Q Consensus 129 Y~P~iyv~NKiD~is~ 144 (160)
-.|.|+|.||+|+...
T Consensus 310 ~~piIlV~NK~Dl~~~ 325 (442)
T TIGR00450 310 KKPFILVLNKIDLKIN 325 (442)
T ss_pred CCCEEEEEECccCCCc
Confidence 3699999999998643
No 260
>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=33.56 E-value=35 Score=27.14 Aligned_cols=44 Identities=23% Similarity=0.197 Sum_probs=25.5
Q ss_pred EEEeecCCChhH-HHHHHhcCcceeceEEEEecCCCC-CHHHHHHH
Q psy7060 107 EVLFREDCNADE-LIDVINANRVYLPCIYAYNKIDQI-SIEEVDRI 150 (160)
Q Consensus 107 ~V~ired~t~Dd-liDvi~~nrvY~P~iyv~NKiD~i-s~eevd~i 150 (160)
.|.+--|+|-.. +.--=+++-.=.|+|=|++|+|+. +.+.+++.
T Consensus 66 ~V~ll~dat~~~~~~pP~fa~~f~~pvIGVITK~Dl~~~~~~i~~a 111 (143)
T PF10662_consen 66 VVLLLQDATEPRSVFPPGFASMFNKPVIGVITKIDLPSDDANIERA 111 (143)
T ss_pred EEEEEecCCCCCccCCchhhcccCCCEEEEEECccCccchhhHHHH
Confidence 344445555432 222222222336999999999999 66666654
No 261
>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=33.30 E-value=43 Score=31.81 Aligned_cols=24 Identities=29% Similarity=0.322 Sum_probs=16.9
Q ss_pred HHHHHHhcCcceeceEEEEecCCCCC
Q psy7060 118 ELIDVINANRVYLPCIYAYNKIDQIS 143 (160)
Q Consensus 118 dliDvi~~nrvY~P~iyv~NKiD~is 143 (160)
+++..+. +.-+|+|+++||+|+..
T Consensus 118 ~~~~~~~--~~~~p~ivviNK~D~~~ 141 (689)
T TIGR00484 118 TVWRQAN--RYEVPRIAFVNKMDKTG 141 (689)
T ss_pred HHHHHHH--HcCCCEEEEEECCCCCC
Confidence 3444433 33479999999999984
No 262
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=33.21 E-value=1.5e+02 Score=28.37 Aligned_cols=54 Identities=20% Similarity=0.239 Sum_probs=29.2
Q ss_pred HHHHHHHHHHcCccceEEEee-cC--CChh--HHHHHHhcCcceec-eEEEEecCCCCCHHH
Q psy7060 91 EKLVQLILHEYKIFNAEVLFR-ED--CNAD--ELIDVINANRVYLP-CIYAYNKIDQISIEE 146 (160)
Q Consensus 91 e~~V~~IL~EYkI~NA~V~ir-ed--~t~D--dliDvi~~nrvY~P-~iyv~NKiD~is~ee 146 (160)
++.++..+..+.--.+.+++- -+ +..+ +.++.+.... +| .|+|+||+|+.+.+.
T Consensus 62 e~fi~~m~~g~~~~D~~lLVVda~eg~~~qT~ehl~il~~lg--i~~iIVVlNKiDlv~~~~ 121 (614)
T PRK10512 62 EKFLSNMLAGVGGIDHALLVVACDDGVMAQTREHLAILQLTG--NPMLTVALTKADRVDEAR 121 (614)
T ss_pred HHHHHHHHHHhhcCCEEEEEEECCCCCcHHHHHHHHHHHHcC--CCeEEEEEECCccCCHHH
Confidence 666777776654444333332 11 1122 3344443222 46 479999999987543
No 263
>PF12307 DUF3631: Protein of unknown function (DUF3631); InterPro: IPR022081 This domain is found in uncharacterised proteins and in tripartite motif containing (TRIM) protein 41. This protein functions as an E3 ligase that catalyzes the ubiquitin-mediated degradation of protein kinase C [].
Probab=32.97 E-value=65 Score=26.87 Aligned_cols=36 Identities=17% Similarity=0.348 Sum_probs=29.5
Q ss_pred cCHHHHHHHHHHcCccceEEEeecC----CChhHHHHHHh
Q psy7060 89 VNEKLVQLILHEYKIFNAEVLFRED----CNADELIDVIN 124 (160)
Q Consensus 89 ~~e~~V~~IL~EYkI~NA~V~ired----~t~DdliDvi~ 124 (160)
+|...+...|++|+|....|.|-+. .+.++|.|+..
T Consensus 143 Lt~r~La~~L~~ygI~s~~ir~~~~~~KGY~r~~f~DAw~ 182 (184)
T PF12307_consen 143 LTPRQLAKLLKEYGIRSKNIRFGGSQAKGYRREDFADAWA 182 (184)
T ss_pred CCHHHHHHHHHHCCCCCCceeeCCCCCCceeHHHHHHHHH
Confidence 5688899999999999999998443 46788888764
No 264
>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=32.65 E-value=35 Score=28.66 Aligned_cols=14 Identities=36% Similarity=0.527 Sum_probs=12.5
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
+|.++++||+|+..
T Consensus 124 ~P~iivvNK~D~~~ 137 (267)
T cd04169 124 IPIITFINKLDREG 137 (267)
T ss_pred CCEEEEEECCccCC
Confidence 69999999999864
No 265
>cd02973 TRX_GRX_like Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacteri
Probab=32.63 E-value=46 Score=21.05 Aligned_cols=53 Identities=19% Similarity=0.244 Sum_probs=26.6
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhc-CcceeceEEEEec
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINA-NRVYLPCIYAYNK 138 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~-nrvY~P~iyv~NK 138 (160)
.++||.-+.-...++.+-.++ ..+.+.. +++|+.-+.... +...+|++++-+|
T Consensus 8 ~~~C~~C~~~~~~l~~l~~~~----~~i~~~~-id~~~~~~l~~~~~i~~vPti~i~~~ 61 (67)
T cd02973 8 SPTCPYCPDAVQAANRIAALN----PNISAEM-IDAAEFPDLADEYGVMSVPAIVINGK 61 (67)
T ss_pred CCCCCCcHHHHHHHHHHHHhC----CceEEEE-EEcccCHhHHHHcCCcccCEEEECCE
Confidence 467887755555555444333 2233322 233333333332 4456899987554
No 266
>PLN00043 elongation factor 1-alpha; Provisional
Probab=32.49 E-value=48 Score=30.14 Aligned_cols=52 Identities=13% Similarity=0.156 Sum_probs=29.0
Q ss_pred CHHHHHHHHHHcCccceEEEeecCCCh----------hHHHHHHh-cCcceece-EEEEecCCCC
Q psy7060 90 NEKLVQLILHEYKIFNAEVLFREDCNA----------DELIDVIN-ANRVYLPC-IYAYNKIDQI 142 (160)
Q Consensus 90 ~e~~V~~IL~EYkI~NA~V~ired~t~----------DdliDvi~-~nrvY~P~-iyv~NKiD~i 142 (160)
-++-++.....+..-++-+++-. ++- .+....+. .+..=+|. |+++||+|+.
T Consensus 95 h~df~~~~~~g~~~aD~aIlVVd-a~~G~~e~g~~~~~qT~eh~~~~~~~gi~~iIV~vNKmD~~ 158 (447)
T PLN00043 95 HRDFIKNMITGTSQADCAVLIID-STTGGFEAGISKDGQTREHALLAFTLGVKQMICCCNKMDAT 158 (447)
T ss_pred HHHHHHHHHhhhhhccEEEEEEE-cccCceecccCCCchHHHHHHHHHHcCCCcEEEEEEcccCC
Confidence 46677777776665554444422 221 23333322 33444665 7789999986
No 267
>cd02976 NrdH NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase activity that is dependent on TRX reductase, not glutathione (GSH). It is part of the NrdHIEF operon, where NrdEF codes for class Ib ribonucleotide reductase (RNR-Ib), an efficient enzyme at low oxygen levels. Under these conditions when GSH is mostly conjugated to spermidine, NrdH can still function and act as a hydrogen donor for RNR-Ib. It has been suggested that the NrdHEF system may be the oldest RNR reducing system, capable of functioning in a microaerophilic environment, where GSH was not yet available. NrdH from Corynebacterium ammoniagenes can form domain-swapped dimers, although it is unknown if this happens in vivo. Domain-swapped dimerization, which results in the blocking of the TRX reductase binding site, cou
Probab=32.39 E-value=72 Score=19.52 Aligned_cols=51 Identities=25% Similarity=0.309 Sum_probs=29.9
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeecCCC-hhHHHHHHhcCcceeceEEEEe
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCN-ADELIDVINANRVYLPCIYAYN 137 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t-~DdliDvi~~nrvY~P~iyv~N 137 (160)
.++||-.. .++.+|.+.++.-..+.+..+-. .+++. .+++ ..-+|+|+.-+
T Consensus 7 ~~~c~~c~----~~~~~l~~~~i~~~~~~i~~~~~~~~~~~-~~~~-~~~vP~i~~~~ 58 (73)
T cd02976 7 KPDCPYCK----ATKRFLDERGIPFEEVDVDEDPEALEELK-KLNG-YRSVPVVVIGD 58 (73)
T ss_pred CCCChhHH----HHHHHHHHCCCCeEEEeCCCCHHHHHHHH-HHcC-CcccCEEEECC
Confidence 34566543 47888999887666666654322 22222 2333 45679998755
No 268
>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=32.27 E-value=30 Score=28.25 Aligned_cols=25 Identities=24% Similarity=0.359 Sum_probs=17.2
Q ss_pred HHHHHHhcCcceeceEEEEecCCCCCH
Q psy7060 118 ELIDVINANRVYLPCIYAYNKIDQISI 144 (160)
Q Consensus 118 dliDvi~~nrvY~P~iyv~NKiD~is~ 144 (160)
.+.+.+...+ +|.++++||+|....
T Consensus 107 ~~~~~~~~~~--~p~iivvNK~D~~~~ 131 (268)
T cd04170 107 KLWEFADEAG--IPRIIFINKMDRERA 131 (268)
T ss_pred HHHHHHHHcC--CCEEEEEECCccCCC
Confidence 3444444333 699999999998853
No 269
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=32.15 E-value=1.3e+02 Score=18.91 Aligned_cols=51 Identities=22% Similarity=0.185 Sum_probs=26.1
Q ss_pred HHHHHHHhcCceeccCCCCeEEEEecCcce-EEecccCCchhhHHHHHHHHH
Q psy7060 13 LLEKELESVGIRLNKKKPNIYFKQKKAGGI-AFNSTCPLTQVNEKLVQLILH 63 (160)
Q Consensus 13 ~le~ELe~~GIrLnkk~p~I~ikkk~~GGI-~i~~t~~lt~~~~~~v~~~l~ 63 (160)
-+.+.|+..|..+.+.+++=.+-....++. .+...-+-.++..-+|+.||.
T Consensus 3 el~k~L~~~G~~~~r~~GSH~~~~~~~~~~~~~vp~h~~~ei~~~~~k~ilk 54 (56)
T PF07927_consen 3 ELIKLLEKAGFEEVRQKGSHHIFRHPGGRKIVTVPPHPGKEIKPGTVKQILK 54 (56)
T ss_dssp HHHHHHHHTT-EEEEEETTEEEEE-TTS-E-EEEE-SSS-S--HHHHHHHHH
T ss_pred HHHHHHHHCCCEEecCCCCEEEEEeCCCCcceEeCCCCccccCHHHHHHHHH
Confidence 477889999999887666655555555553 222211222344555555553
No 270
>PRK12735 elongation factor Tu; Reviewed
Probab=32.11 E-value=39 Score=29.79 Aligned_cols=25 Identities=28% Similarity=0.248 Sum_probs=16.2
Q ss_pred HHHHHHhcCcceeceE-EEEecCCCCCH
Q psy7060 118 ELIDVINANRVYLPCI-YAYNKIDQISI 144 (160)
Q Consensus 118 dliDvi~~nrvY~P~i-yv~NKiD~is~ 144 (160)
+.+..+.... +|.| +|+||+|+.+.
T Consensus 118 e~l~~~~~~g--i~~iivvvNK~Dl~~~ 143 (396)
T PRK12735 118 EHILLARQVG--VPYIVVFLNKCDMVDD 143 (396)
T ss_pred HHHHHHHHcC--CCeEEEEEEecCCcch
Confidence 3444444333 6877 47999999854
No 271
>PRK04000 translation initiation factor IF-2 subunit gamma; Validated
Probab=32.08 E-value=35 Score=30.45 Aligned_cols=16 Identities=38% Similarity=0.420 Sum_probs=13.0
Q ss_pred ceEEEEecCCCCCHHH
Q psy7060 131 PCIYAYNKIDQISIEE 146 (160)
Q Consensus 131 P~iyv~NKiD~is~ee 146 (160)
|.++|+||+|+.+.++
T Consensus 141 ~iiVVlNK~Dl~~~~~ 156 (411)
T PRK04000 141 NIVIVQNKIDLVSKER 156 (411)
T ss_pred cEEEEEEeeccccchh
Confidence 6899999999987543
No 272
>cd06538 CIDE_N_FSP27 CIDE_N domain of FSP27 proteins. The CIDE-N (cell death-inducing DFF45-like effector, N-terminal) domain is found in the FSP27/CIDE-C protein, which has been identified as a n adipocyte lipid droplet protein that negatively regulates lipolysis and promotes triglyceride accumulation. The CIDE protein family includes 3 members: CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence similarity with DFF40 and DFF45, CIDE proteins were initially characterized as mitochondrial activators of apoptosis. The CIDE-N domain of FSP27 is sufficient to increase apoptosis in vitro when overexpressed.
Probab=31.99 E-value=34 Score=25.26 Aligned_cols=58 Identities=22% Similarity=0.450 Sum_probs=43.3
Q ss_pred hhhhhhHHhhhcCccccccCCCcccCHHHHHHHHHHcCccc-eEEEeecC---CChhHHHHHHhcCcce
Q psy7060 65 YKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFN-AEVLFRED---CNADELIDVINANRVY 129 (160)
Q Consensus 65 yki~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL~EYkI~N-A~V~ired---~t~DdliDvi~~nrvY 129 (160)
|||.|.+....=||+-+|- +++..+...-+.+.. ..+...|| +.-+|.-..+..|-++
T Consensus 5 ~kV~~~~rs~k~GV~A~sL-------~eL~~K~~~~l~l~~~~~lvL~eDGT~Vd~EeyF~tLp~nt~l 66 (79)
T cd06538 5 FRVSNADRSLRKGIMADSL-------EDLLNKVLDALLLDCISSLVLDEDGTGVDTEEFFQALADNTVF 66 (79)
T ss_pred EEEecCCCceeEeEEcCCH-------HHHHHHHHHHcCCCCccEEEEecCCcEEccHHHHhhCCCCcEE
Confidence 7888888888888888774 778888888899943 23666777 4457777777777665
No 273
>COG5324 Uncharacterized conserved protein [Function unknown]
Probab=31.98 E-value=34 Score=33.85 Aligned_cols=74 Identities=22% Similarity=0.262 Sum_probs=53.6
Q ss_pred HHHHHHHhhhhhhHHhhhcCccc-cccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceE
Q psy7060 58 VQLILHEYKIFNAEQKKAGGIAF-NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCI 133 (160)
Q Consensus 58 v~~~l~~yki~n~~~~~~~~~~~-~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~i 133 (160)
..-|+..||-|||+.|.-.-.-- ----|+ ..+.+-.++|+++++ .|--.++-+|.+-||..-+++-.--|.|+.
T Consensus 502 mn~f~k~ykp~~~~~~~d~~~d~~ield~~-~~sl~nar~i~n~~~-k~~p~lip~~p~ddd~~~a~~~a~ey~pt~ 576 (758)
T COG5324 502 MNTFYKQYKPFDAGNKHDANYDDIIELDPL-IGSLENARRIVNYFK-KNIPELIPNDPSDDDYAAALNYAVEYVPTY 576 (758)
T ss_pred HHHHHHhcCCCCCCCCccccccceeecccc-cchhhhHHHHHHHHH-hhCccccCCCCCchHHHHHHhhhhhcCchh
Confidence 34588999999998875432211 011121 234567899999886 466778999999999999999988999974
No 274
>PTZ00062 glutaredoxin; Provisional
Probab=31.74 E-value=1.1e+02 Score=25.39 Aligned_cols=66 Identities=14% Similarity=0.136 Sum_probs=41.7
Q ss_pred ccccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEEecCCCCCHHHHHHHh
Q psy7060 80 FNSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYNKIDQISIEEVDRIA 151 (160)
Q Consensus 80 ~~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~NKiD~is~eevd~i~ 151 (160)
-.++||.. ..++.+|++++|.=.++-+.+|-.+.+-.....|-+. .|.||+=.+. .-..+++.++.
T Consensus 124 ~~p~C~~C----~~~k~~L~~~~i~y~~~DI~~d~~~~~~l~~~sg~~T-vPqVfI~G~~-IGG~d~l~~l~ 189 (204)
T PTZ00062 124 TFPFCRFS----NAVVNMLNSSGVKYETYNIFEDPDLREELKVYSNWPT-YPQLYVNGEL-IGGHDIIKELY 189 (204)
T ss_pred CCCCChhH----HHHHHHHHHcCCCEEEEEcCCCHHHHHHHHHHhCCCC-CCeEEECCEE-EcChHHHHHHH
Confidence 33467764 3588999999998777777766444444444555555 4999976553 12445555553
No 275
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=31.05 E-value=80 Score=22.06 Aligned_cols=49 Identities=22% Similarity=0.354 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhcCceeccCCCCeEEEEecC--cceEEecccCCchhhHHHHHHHHHH
Q psy7060 10 QRGLLEKELESVGIRLNKKKPNIYFKQKKA--GGIAFNSTCPLTQVNEKLVQLILHE 64 (160)
Q Consensus 10 q~~~le~ELe~~GIrLnkk~p~I~ikkk~~--GGI~i~~t~~lt~~~~~~v~~~l~~ 64 (160)
-+..|+.||. =||.+..|+..++-+.+ -|+++.++..- +-+.+..+|.+
T Consensus 5 a~~AL~~EL~---kRl~~~yPd~~v~Vr~~s~~~l~v~g~~~~---~k~~i~~iLqe 55 (65)
T PF06183_consen 5 ALEALESELT---KRLHRQYPDAEVRVRPGSANGLSVSGGKKD---DKERIEEILQE 55 (65)
T ss_dssp HHHHHHHHHH---HHHHHH-SS-EEEEEEESS-EEEEES--HH---HHHHHHHHHHH
T ss_pred HHHHHHHHHH---HHHHHHCCCceEeeeecccCccccCCcCch---HHHHHHHHHHH
Confidence 3678888888 47888888766655555 47777764321 23445555443
No 276
>PLN00023 GTP-binding protein; Provisional
Probab=30.85 E-value=53 Score=29.66 Aligned_cols=15 Identities=33% Similarity=0.279 Sum_probs=13.0
Q ss_pred eeceEEEEecCCCCC
Q psy7060 129 YLPCIYAYNKIDQIS 143 (160)
Q Consensus 129 Y~P~iyv~NKiD~is 143 (160)
-+|+++|.||+|+..
T Consensus 151 ~ipIILVGNK~DL~~ 165 (334)
T PLN00023 151 PVPYIVIGNKADIAP 165 (334)
T ss_pred CCcEEEEEECccccc
Confidence 479999999999854
No 277
>PRK11933 yebU rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
Probab=29.95 E-value=29 Score=32.18 Aligned_cols=32 Identities=28% Similarity=0.469 Sum_probs=26.9
Q ss_pred HHhhhcCccccccCCCccc-CHHHHHHHHHHcC
Q psy7060 71 EQKKAGGIAFNSTCPLTQV-NEKLVQLILHEYK 102 (160)
Q Consensus 71 ~~~~~~~~~~~~~~~~~~~-~e~~V~~IL~EYk 102 (160)
.-=+.||+.+=|||-++.- ||+.|..+|++|.
T Consensus 230 ~~LkpGG~LVYSTCT~~~eENE~vV~~~L~~~~ 262 (470)
T PRK11933 230 HALKPGGTLVYSTCTLNREENQAVCLWLKETYP 262 (470)
T ss_pred HHcCCCcEEEEECCCCCHHHHHHHHHHHHHHCC
Confidence 3446899999999998876 8889999999874
No 278
>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]
Probab=29.94 E-value=95 Score=23.56 Aligned_cols=55 Identities=22% Similarity=0.199 Sum_probs=34.4
Q ss_pred CHHHHHHHHHHcCccceEEEeecCCCh----hHHHH----HHhcCc-ceeceEEEEecCCCCCH
Q psy7060 90 NEKLVQLILHEYKIFNAEVLFREDCNA----DELID----VINANR-VYLPCIYAYNKIDQISI 144 (160)
Q Consensus 90 ~e~~V~~IL~EYkI~NA~V~ired~t~----DdliD----vi~~nr-vY~P~iyv~NKiD~is~ 144 (160)
+.+..+.+...|-..-.-+++--|.+. ++++. .+.... -..|.+.+.||+|+.+.
T Consensus 63 gq~~~~~~~~~y~~~~~~~l~~~d~~~~~~~~~~~~~~~~~l~~~~~~~~~iilv~nK~Dl~~~ 126 (219)
T COG1100 63 GQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFDE 126 (219)
T ss_pred CHHHHHHHHHHHhcCCCEEEEEEecccchhhhHHHHHHHHHHHHhCCCCceEEEEecccccccc
Confidence 678888899888444433333334433 33333 333333 36799999999999855
No 279
>cd03029 GRX_hybridPRX5 Glutaredoxin (GRX) family, PRX5 hybrid subfamily; composed of hybrid proteins containing peroxiredoxin (PRX) and GRX domains, which is found in some pathogenic bacteria and cyanobacteria. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins. PRX-GRX hybrid proteins from Haemophilus influenza and Neisseria meningitis exhibit GSH-dependent peroxidase activity. The flow of reducing equivalents in the catalytic cycle of the hybrid protein goes from NADPH - GSH reductase - GSH - GRX domain of hybrid - PRX domain of hybrid - peroxide substrate.
Probab=29.91 E-value=1.5e+02 Score=19.21 Aligned_cols=52 Identities=17% Similarity=0.341 Sum_probs=32.2
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEEec
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYNK 138 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~NK 138 (160)
-++||.- ..++++|+++++.=-++-+.++-..+++. .+ ..+..+|.|++=.+
T Consensus 8 ~~~Cp~C----~~ak~~L~~~~i~~~~~~v~~~~~~~~~~-~~-~g~~~vP~ifi~g~ 59 (72)
T cd03029 8 KPGCPFC----ARAKAALQENGISYEEIPLGKDITGRSLR-AV-TGAMTVPQVFIDGE 59 (72)
T ss_pred CCCCHHH----HHHHHHHHHcCCCcEEEECCCChhHHHHH-HH-hCCCCcCeEEECCE
Confidence 3567653 35789999998887666665544333222 11 35678899975444
No 280
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=29.72 E-value=62 Score=21.89 Aligned_cols=65 Identities=11% Similarity=0.108 Sum_probs=34.0
Q ss_pred ccCCCcccCHHHHHHHHHH-----cCccceEEEeecCC-ChhHHHHHHhcCcceeceEEEEecCCCCCHHHHHHHh
Q psy7060 82 STCPLTQVNEKLVQLILHE-----YKIFNAEVLFREDC-NADELIDVINANRVYLPCIYAYNKIDQISIEEVDRIA 151 (160)
Q Consensus 82 ~~~~~~~~~e~~V~~IL~E-----YkI~NA~V~ired~-t~DdliDvi~~nrvY~P~iyv~NKiD~is~eevd~i~ 151 (160)
++||.-. .+++.|.+ -++.=..+-+.++- +.+++..........+|.|++=.+. .-.-+++..+.
T Consensus 9 ~~C~~C~----~a~~~L~~l~~~~~~i~~~~idi~~~~~~~~el~~~~~~~~~~vP~ifi~g~~-igg~~~~~~~~ 79 (85)
T PRK11200 9 PGCPYCV----RAKELAEKLSEERDDFDYRYVDIHAEGISKADLEKTVGKPVETVPQIFVDQKH-IGGCTDFEAYV 79 (85)
T ss_pred CCChhHH----HHHHHHHhhcccccCCcEEEEECCCChHHHHHHHHHHCCCCCcCCEEEECCEE-EcCHHHHHHHH
Confidence 4677654 45555555 35555556565543 2445544332223578999864433 22445555543
No 281
>PF13590 DUF4136: Domain of unknown function (DUF4136)
Probab=29.69 E-value=77 Score=23.05 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=21.8
Q ss_pred HHHHHHHHHhcCceeccCCCCeEEE
Q psy7060 11 RGLLEKELESVGIRLNKKKPNIYFK 35 (160)
Q Consensus 11 ~~~le~ELe~~GIrLnkk~p~I~ik 35 (160)
+..++++|++.|.+.....|++.|.
T Consensus 41 ~~~v~~~L~~~G~~~~~~~aDl~V~ 65 (151)
T PF13590_consen 41 QDAVEQELAAKGYRRVPENADLLVS 65 (151)
T ss_pred HHHHHHHHHHCCCeecccCCCEEEE
Confidence 4688999999999999889998874
No 282
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=29.63 E-value=1.1e+02 Score=19.25 Aligned_cols=49 Identities=27% Similarity=0.318 Sum_probs=31.8
Q ss_pred ccCCCcccCHHHHHHHHHHcCccceEEEeecCC-ChhHHHHHHhcCcceeceEEEE
Q psy7060 82 STCPLTQVNEKLVQLILHEYKIFNAEVLFREDC-NADELIDVINANRVYLPCIYAY 136 (160)
Q Consensus 82 ~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~-t~DdliDvi~~nrvY~P~iyv~ 136 (160)
.+||-. ..++++|+++++.=.++-+..+- ..++|.+.. ...-.|+|++=
T Consensus 7 ~~C~~C----~~~~~~L~~~~i~y~~~dv~~~~~~~~~l~~~~--g~~~~P~v~i~ 56 (60)
T PF00462_consen 7 PGCPYC----KKAKEFLDEKGIPYEEVDVDEDEEAREELKELS--GVRTVPQVFID 56 (60)
T ss_dssp TTSHHH----HHHHHHHHHTTBEEEEEEGGGSHHHHHHHHHHH--SSSSSSEEEET
T ss_pred CCCcCH----HHHHHHHHHcCCeeeEcccccchhHHHHHHHHc--CCCccCEEEEC
Confidence 456533 45889999999887777777763 333333333 55566999873
No 283
>TIGR00446 nop2p NOL1/NOP2/sun family putative RNA methylase.
Probab=29.20 E-value=33 Score=28.47 Aligned_cols=32 Identities=34% Similarity=0.508 Sum_probs=27.1
Q ss_pred HhhhcCccccccCCCccc-CHHHHHHHHHHcCc
Q psy7060 72 QKKAGGIAFNSTCPLTQV-NEKLVQLILHEYKI 103 (160)
Q Consensus 72 ~~~~~~~~~~~~~~~~~~-~e~~V~~IL~EYkI 103 (160)
--+.||..+=|||.++.- ||+.|+.+|++|.=
T Consensus 188 ~lkpgG~lvYstcs~~~~Ene~vv~~~l~~~~~ 220 (264)
T TIGR00446 188 ALKPGGVLVYSTCSLEPEENEAVVDYLLEKRPD 220 (264)
T ss_pred hcCCCCEEEEEeCCCChHHHHHHHHHHHHhCCC
Confidence 346799999999999886 68899999998753
No 284
>PRK10824 glutaredoxin-4; Provisional
Probab=29.07 E-value=1.4e+02 Score=22.71 Aligned_cols=50 Identities=14% Similarity=0.139 Sum_probs=34.2
Q ss_pred ccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHh--cCcceeceEEEEec
Q psy7060 82 STCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVIN--ANRVYLPCIYAYNK 138 (160)
Q Consensus 82 ~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~--~nrvY~P~iyv~NK 138 (160)
++||.. ..++++|.++++.-..+-+.+| .++.+.+. .++--+|.|++=.|
T Consensus 28 p~Cpyc----~~ak~lL~~~~i~~~~idi~~d---~~~~~~l~~~sg~~TVPQIFI~G~ 79 (115)
T PRK10824 28 PSCGFS----AQAVQALSACGERFAYVDILQN---PDIRAELPKYANWPTFPQLWVDGE 79 (115)
T ss_pred CCCchH----HHHHHHHHHcCCCceEEEecCC---HHHHHHHHHHhCCCCCCeEEECCE
Confidence 468874 4688999999988877766655 24444443 25566799998554
No 285
>PRK09435 membrane ATPase/protein kinase; Provisional
Probab=29.02 E-value=37 Score=30.11 Aligned_cols=31 Identities=23% Similarity=0.158 Sum_probs=19.5
Q ss_pred CChhHHHHHHhcCcceeceEEEEecCCCCCHH
Q psy7060 114 CNADELIDVINANRVYLPCIYAYNKIDQISIE 145 (160)
Q Consensus 114 ~t~DdliDvi~~nrvY~P~iyv~NKiD~is~e 145 (160)
.+-|++.....+. .=+..|+|+||+|+.+.+
T Consensus 180 ~~gd~iq~~k~gi-~E~aDIiVVNKaDl~~~~ 210 (332)
T PRK09435 180 GAGDELQGIKKGI-MELADLIVINKADGDNKT 210 (332)
T ss_pred CchHHHHHHHhhh-hhhhheEEeehhcccchh
Confidence 5556665544322 223459999999998643
No 286
>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=28.69 E-value=78 Score=24.30 Aligned_cols=12 Identities=33% Similarity=0.490 Sum_probs=10.0
Q ss_pred eceEEEEecCCCC
Q psy7060 130 LPCIYAYNKIDQI 142 (160)
Q Consensus 130 ~P~iyv~NKiD~i 142 (160)
.| |.|.||+|+.
T Consensus 106 ~p-ilVgnK~Dl~ 117 (182)
T cd04128 106 IP-ILVGTKYDLF 117 (182)
T ss_pred CE-EEEEEchhcc
Confidence 56 7889999985
No 287
>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=28.50 E-value=25 Score=27.16 Aligned_cols=19 Identities=37% Similarity=0.593 Sum_probs=12.9
Q ss_pred eEEEEecCCCCCHHH-HHHH
Q psy7060 132 CIYAYNKIDQISIEE-VDRI 150 (160)
Q Consensus 132 ~iyv~NKiD~is~ee-vd~i 150 (160)
-++++||+|+++.++ ++++
T Consensus 144 DvIvlnK~D~~~~~~~i~~~ 163 (178)
T PF02492_consen 144 DVIVLNKIDLVSDEQKIERV 163 (178)
T ss_dssp SEEEEE-GGGHHHH--HHHH
T ss_pred CEEEEeccccCChhhHHHHH
Confidence 368999999998873 3554
No 288
>cd01853 Toc34_like Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts). This family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90. The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five copies of Toc34. Toc64 and Toc12 are associated with the translocon, but do not appear to be part of the core complex. The Toc translocon initiates the import of nuclear-encoded preproteins from the cytosol into the organelle. Toc34 and Toc159 are both GTPases, while Toc75 is a beta-barrel integral membrane protein. Toc159 is equally distributed between a soluble cytoplasmic form and a membrane-inserted form, suggesting that assembly of the Toc complex is dynamic. Toc34 and Toc75 act sequentially to mediate docking and insertion of Toc159 resulting in assembly of the functional translocon.
Probab=28.49 E-value=1.1e+02 Score=25.74 Aligned_cols=23 Identities=4% Similarity=0.017 Sum_probs=19.5
Q ss_pred HhcCcceeceEEEEecCCCCCHH
Q psy7060 123 INANRVYLPCIYAYNKIDQISIE 145 (160)
Q Consensus 123 i~~nrvY~P~iyv~NKiD~is~e 145 (160)
.+|..+|.++|+|.+|+|...++
T Consensus 143 ~fG~~i~~~~ivV~T~~d~~~p~ 165 (249)
T cd01853 143 SFGPSIWRNAIVVLTHAASSPPD 165 (249)
T ss_pred HhChhhHhCEEEEEeCCccCCCC
Confidence 36789999999999999998554
No 289
>KOG1490|consensus
Probab=28.48 E-value=24 Score=34.53 Aligned_cols=62 Identities=29% Similarity=0.338 Sum_probs=37.8
Q ss_pred CCCcccCHHHHHHHHHHcCccceEEEee---cCC--ChhHH------HHHHhcCcceeceEEEEecCCCCCHHHHH
Q psy7060 84 CPLTQVNEKLVQLILHEYKIFNAEVLFR---EDC--NADEL------IDVINANRVYLPCIYAYNKIDQISIEEVD 148 (160)
Q Consensus 84 ~~~~~~~e~~V~~IL~EYkI~NA~V~ir---ed~--t~Ddl------iDvi~~nrvY~P~iyv~NKiD~is~eevd 148 (160)
-|+.+.|.-+.+.|-.=--+..|..+|- |.| |+.+= |.-+++|+ |.|.|+||+|...+|.++
T Consensus 228 ~plEdrN~IEmqsITALAHLraaVLYfmDLSe~CGySva~QvkLfhsIKpLFaNK---~~IlvlNK~D~m~~edL~ 300 (620)
T KOG1490|consen 228 RPEEDRNIIEMQIITALAHLRSAVLYFMDLSEMCGYSVAAQVKLYHSIKPLFANK---VTILVLNKIDAMRPEDLD 300 (620)
T ss_pred cchhhhhHHHHHHHHHHHHhhhhheeeeechhhhCCCHHHHHHHHHHhHHHhcCC---ceEEEeecccccCccccC
Confidence 4666666656666544444556666553 233 33332 44566775 789999999999765543
No 290
>PRK00007 elongation factor G; Reviewed
Probab=28.25 E-value=58 Score=31.07 Aligned_cols=24 Identities=21% Similarity=0.238 Sum_probs=17.1
Q ss_pred HHHHHHhcCcceeceEEEEecCCCCC
Q psy7060 118 ELIDVINANRVYLPCIYAYNKIDQIS 143 (160)
Q Consensus 118 dliDvi~~nrvY~P~iyv~NKiD~is 143 (160)
.+++.+.. .-+|+|+++||+|...
T Consensus 118 ~~~~~~~~--~~~p~iv~vNK~D~~~ 141 (693)
T PRK00007 118 TVWRQADK--YKVPRIAFVNKMDRTG 141 (693)
T ss_pred HHHHHHHH--cCCCEEEEEECCCCCC
Confidence 34444443 3379999999999984
No 291
>PF04320 DUF469: Protein with unknown function (DUF469); InterPro: IPR007416 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.
Probab=28.16 E-value=1.8e+02 Score=22.33 Aligned_cols=38 Identities=21% Similarity=0.315 Sum_probs=28.5
Q ss_pred CCChhHHHHHHhcCccee--------ceEEEEecCCCCCHHHHHHH
Q psy7060 113 DCNADELIDVINANRVYL--------PCIYAYNKIDQISIEEVDRI 150 (160)
Q Consensus 113 d~t~DdliDvi~~nrvY~--------P~iyv~NKiD~is~eevd~i 150 (160)
|..+|++||+|++|-... -.+++..|+...+.|.-..+
T Consensus 33 D~~~D~fId~Ie~~gL~~~Ggg~~~~eG~vc~~~~gs~tee~R~~v 78 (101)
T PF04320_consen 33 DAFVDAFIDVIEPNGLAFGGGGYEQWEGFVCLQRYGSCTEEDRAAV 78 (101)
T ss_pred HHHHHHHHHHHHhCCCEEecCCccCEeEEEEeccCCCCCHHHHHHH
Confidence 456799999999887653 36777778888887766554
No 292
>COG5309 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]
Probab=28.11 E-value=35 Score=30.94 Aligned_cols=53 Identities=32% Similarity=0.337 Sum_probs=35.1
Q ss_pred hcCccccccCCCcccCHHHHH-HHHHHcCccce-----------EEEeecCCChhHHHHHHhcCc
Q psy7060 75 AGGIAFNSTCPLTQVNEKLVQ-LILHEYKIFNA-----------EVLFREDCNADELIDVINANR 127 (160)
Q Consensus 75 ~~~~~~~~~~~~~~~~e~~V~-~IL~EYkI~NA-----------~V~ired~t~DdliDvi~~nr 127 (160)
+-|+.++--.=+|.=-.+.+. .||..|.++|. |++.|.+||+++|++-|..=|
T Consensus 98 ~~g~kv~lGiw~tdd~~~~~~~til~ay~~~~~~d~v~~v~VGnEal~r~~~tasql~~~I~~vr 162 (305)
T COG5309 98 ASGFKVFLGIWPTDDIHDAVEKTILSAYLPYNGWDDVTTVTVGNEALNRNDLTASQLIEYIDDVR 162 (305)
T ss_pred hcCceEEEEEeeccchhhhHHHHHHHHHhccCCCCceEEEEechhhhhcCCCCHHHHHHHHHHHH
Confidence 344444433333322233333 89999998885 567899999999999887544
No 293
>PF05511 ATP-synt_F6: Mitochondrial ATP synthase coupling factor 6; InterPro: IPR008387 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit F6 (or coupling factor 6) found in the F0 complex of F-ATPases in mitochondria. The F6 subunit is part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D []. There is no homologue of subunit F6 in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o); PDB: 2WSS_V 2CLY_C 1VZS_A.
Probab=28.06 E-value=36 Score=26.16 Aligned_cols=48 Identities=15% Similarity=0.238 Sum_probs=32.8
Q ss_pred HHHHHHhhhhhhHHhhhcCccccccCCCcccCHHHHHHHHHHcCccce
Q psy7060 59 QLILHEYKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNA 106 (160)
Q Consensus 59 ~~~l~~yki~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL~EYkI~NA 106 (160)
|+||.|-+=++-.+|.+||=-..++--...-=++++.++-+.|+.-++
T Consensus 39 klFldKIREY~~Ksks~gGklVD~~Pe~~kel~eel~kL~r~YG~g~~ 86 (99)
T PF05511_consen 39 KLFLDKIREYNQKSKSSGGKLVDAGPEYEKELNEELEKLARQYGGGSG 86 (99)
T ss_dssp HHHHHHHHHHHHHHTTTSS-STT--THHHHHHHHHHHHHHHHHHSS--
T ss_pred HHHHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHHHHHhCCccc
Confidence 799999999999999999966666544444334566677777876654
No 294
>cd04102 RabL3 RabL3 (Rab-like3) subfamily. RabL3s 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, RabL3 lacks a prenylation site at the C-terminus. The specific function of RabL3 remains unknown.
Probab=27.92 E-value=36 Score=27.38 Aligned_cols=15 Identities=33% Similarity=0.476 Sum_probs=13.1
Q ss_pred eceEEEEecCCCCCH
Q psy7060 130 LPCIYAYNKIDQISI 144 (160)
Q Consensus 130 ~P~iyv~NKiD~is~ 144 (160)
+|.|+|-||.|+...
T Consensus 130 ~PiilVGnK~Dl~~~ 144 (202)
T cd04102 130 IPLLVIGTKLDQIPE 144 (202)
T ss_pred ceEEEEEECccchhh
Confidence 699999999998653
No 295
>KOG1122|consensus
Probab=27.83 E-value=68 Score=30.60 Aligned_cols=45 Identities=36% Similarity=0.512 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhcCceeccCCCCeEEEEecCcceEEecccCCc-hhhHHHHHHHHHHh
Q psy7060 10 QRGLLEKELESVGIRLNKKKPNIYFKQKKAGGIAFNSTCPLT-QVNEKLVQLILHEY 65 (160)
Q Consensus 10 q~~~le~ELe~~GIrLnkk~p~I~ikkk~~GGI~i~~t~~lt-~~~~~~v~~~l~~y 65 (160)
.+.-|.++|-..+|-+-+. |||-+-|||..+ .-||..|.-+|.||
T Consensus 345 ~~~~LQr~LllsAi~lv~~-----------GGvLVYSTCSI~~~ENE~vV~yaL~K~ 390 (460)
T KOG1122|consen 345 RYAHLQRELLLSAIDLVKA-----------GGVLVYSTCSITVEENEAVVDYALKKR 390 (460)
T ss_pred HhHHHHHHHHHHHHhhccC-----------CcEEEEEeeecchhhhHHHHHHHHHhC
Confidence 4556777777777777654 999999999876 44788888888887
No 296
>CHL00053 rps7 ribosomal protein S7
Probab=27.79 E-value=2.1e+02 Score=22.72 Aligned_cols=93 Identities=18% Similarity=0.290 Sum_probs=59.1
Q ss_pred HHHHHHHHhcCceeccCCCCeEEEEecCcceEEecccCCchhhHHHHHHHHHHhhhhhhHHhhhcCccccccCCCcccCH
Q psy7060 12 GLLEKELESVGIRLNKKKPNIYFKQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEQKKAGGIAFNSTCPLTQVNE 91 (160)
Q Consensus 12 ~~le~ELe~~GIrLnkk~p~I~ikkk~~GGI~i~~t~~lt~~~~~~v~~~l~~yki~n~~~~~~~~~~~~~~~~~~~~~e 91 (160)
.+|.+.++++ .|.+.++....||....-..++.. --+.+|+=.-|-.+-.+++| - .+.+
T Consensus 60 ~vl~~Ai~N~-------~P~~evk~~r~gG~~~qvPv~v~~----~rr~~lAirWil~~ar~r~~-~---------~~~~ 118 (155)
T CHL00053 60 SVLRQAIRNV-------TPDVEVKARRVGGSTYQVPIEIGS----TRGKALAIRWLLKASRKRSG-R---------NMAF 118 (155)
T ss_pred HHHHHHHHhC-------CCcEEEEEEeeCCEEEEEeeEcCH----HHHHHHHHHHHHHHHHhcCC-C---------CHHH
Confidence 4556666554 588999999999998766666642 35566666665555444432 1 2457
Q ss_pred HHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCccee
Q psy7060 92 KLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYL 130 (160)
Q Consensus 92 ~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~ 130 (160)
.+..+|+.-|+-....+.-+ ||+...-..||.|.
T Consensus 119 ~La~Eii~A~~~~g~aikkK-----~e~hk~A~aNRa~~ 152 (155)
T CHL00053 119 KLSSELVDAAKGSGNAIRKK-----EETHRMAEANRAFA 152 (155)
T ss_pred HHHHHHHHHHhCCCchhhhH-----HHHHHHHHHhHhHh
Confidence 78878887776655433333 56666667777663
No 297
>COG0144 Sun tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]
Probab=27.78 E-value=1.1e+02 Score=26.97 Aligned_cols=40 Identities=38% Similarity=0.609 Sum_probs=0.0
Q ss_pred HHHHHHHHHHhcCceeccCCCCeEEEEecCcceEEecccCCc-hhhHHHHHHHHHHh
Q psy7060 10 QRGLLEKELESVGIRLNKKKPNIYFKQKKAGGIAFNSTCPLT-QVNEKLVQLILHEY 65 (160)
Q Consensus 10 q~~~le~ELe~~GIrLnkk~p~I~ikkk~~GGI~i~~t~~lt-~~~~~~v~~~l~~y 65 (160)
|+.+|...+.-+ +.||.=+-|||.++ .-||+.|+.||.++
T Consensus 267 Q~~iL~~a~~~l----------------k~GG~LVYSTCS~~~eENE~vV~~~L~~~ 307 (355)
T COG0144 267 QKEILAAALKLL----------------KPGGVLVYSTCSLTPEENEEVVERFLERH 307 (355)
T ss_pred HHHHHHHHHHhc----------------CCCCEEEEEccCCchhcCHHHHHHHHHhC
No 298
>PRK05124 cysN sulfate adenylyltransferase subunit 1; Provisional
Probab=27.54 E-value=49 Score=30.23 Aligned_cols=14 Identities=29% Similarity=0.354 Sum_probs=11.9
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
.|.|+|+||+|+.+
T Consensus 161 ~~iIvvvNKiD~~~ 174 (474)
T PRK05124 161 KHLVVAVNKMDLVD 174 (474)
T ss_pred CceEEEEEeecccc
Confidence 37889999999983
No 299
>COG0218 Predicted GTPase [General function prediction only]
Probab=27.48 E-value=50 Score=27.97 Aligned_cols=53 Identities=19% Similarity=0.296 Sum_probs=31.2
Q ss_pred HHHHHHHHc-----CccceEEEeecC--CChh--HHHHHHhcCcceeceEEEEecCCCCCHHHH
Q psy7060 93 LVQLILHEY-----KIFNAEVLFRED--CNAD--ELIDVINANRVYLPCIYAYNKIDQISIEEV 147 (160)
Q Consensus 93 ~V~~IL~EY-----kI~NA~V~ired--~t~D--dliDvi~~nrvY~P~iyv~NKiD~is~eev 147 (160)
.++..+.+| .|-=+.+++... .+.+ ++++.+ ...=+|.++|.||+|-++..+.
T Consensus 92 ~w~~~i~~YL~~R~~L~~vvlliD~r~~~~~~D~em~~~l--~~~~i~~~vv~tK~DKi~~~~~ 153 (200)
T COG0218 92 KWKKLIEEYLEKRANLKGVVLLIDARHPPKDLDREMIEFL--LELGIPVIVVLTKADKLKKSER 153 (200)
T ss_pred HHHHHHHHHHhhchhheEEEEEEECCCCCcHHHHHHHHHH--HHcCCCeEEEEEccccCChhHH
Confidence 344444444 333344555443 3332 344444 3445699999999999987665
No 300
>cd03028 GRX_PICOT_like Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain followed by one to three GRX-like domains. It is interesting to note that PICOT from plants contain three repeats of the GRX-like domain, metazoan proteins (except for insect) have two repeats, while fungal sequences contain only one copy of the domain. PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli. Both GRX and TRX domains of PICOT are required for its activity. Characterized non-PICOT members of this family include CXIP1, a CAX-interacting protein
Probab=27.40 E-value=1.4e+02 Score=20.73 Aligned_cols=63 Identities=14% Similarity=0.187 Sum_probs=39.7
Q ss_pred cCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEEecCCCCCHHHHHHHh
Q psy7060 83 TCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYNKIDQISIEEVDRIA 151 (160)
Q Consensus 83 ~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~NKiD~is~eevd~i~ 151 (160)
.||.. ..++++|.+.++.=.++-+.+|-.+.+-...+.|.+. .|.|++=.+. .-+-+++..+.
T Consensus 22 ~Cp~C----~~ak~~L~~~~i~y~~idv~~~~~~~~~l~~~~g~~t-vP~vfi~g~~-iGG~~~l~~l~ 84 (90)
T cd03028 22 RCGFS----RKVVQILNQLGVDFGTFDILEDEEVRQGLKEYSNWPT-FPQLYVNGEL-VGGCDIVKEMH 84 (90)
T ss_pred CCcHH----HHHHHHHHHcCCCeEEEEcCCCHHHHHHHHHHhCCCC-CCEEEECCEE-EeCHHHHHHHH
Confidence 56653 4688999999988777777776433333344455544 6999774432 22556665553
No 301
>KOG1532|consensus
Probab=27.39 E-value=47 Score=30.66 Aligned_cols=18 Identities=39% Similarity=0.427 Sum_probs=14.9
Q ss_pred eeceEEEEecCCCCCHHH
Q psy7060 129 YLPCIYAYNKIDQISIEE 146 (160)
Q Consensus 129 Y~P~iyv~NKiD~is~ee 146 (160)
=+|.|+|+||.|..+.+-
T Consensus 181 klp~ivvfNK~Dv~d~~f 198 (366)
T KOG1532|consen 181 KLPFIVVFNKTDVSDSEF 198 (366)
T ss_pred cCCeEEEEecccccccHH
Confidence 369999999999986643
No 302
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=26.83 E-value=28 Score=25.58 Aligned_cols=41 Identities=15% Similarity=0.169 Sum_probs=22.0
Q ss_pred HHHHHHHHHHcC-ccceEEEeecCCChhHHHHHHhcCcceec
Q psy7060 91 EKLVQLILHEYK-IFNAEVLFREDCNADELIDVINANRVYLP 131 (160)
Q Consensus 91 e~~V~~IL~EYk-I~NA~V~ired~t~DdliDvi~~nrvY~P 131 (160)
.+.+...|.+++ ++-...-.-+.-.++.|.....|..+|+|
T Consensus 11 ~~~i~~~l~~~g~i~~~~a~~ig~~~~~~L~~~~gG~~iyiP 52 (108)
T PF08765_consen 11 ADVIAAELERLGEIDAELAEIIGEEVALKLCRYFGGQQIYIP 52 (108)
T ss_dssp HHHHHHHHHHTS-S-----TTSHHHHHHHHHHHH-SS-----
T ss_pred HHHHHHHHHHcCCcchhHHHHHHHHHHHHHHHHHCCEeEEee
Confidence 456788888888 77433333344567888889999999999
No 303
>cd03027 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions. GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions.
Probab=26.45 E-value=1.7e+02 Score=19.02 Aligned_cols=62 Identities=15% Similarity=0.185 Sum_probs=39.1
Q ss_pred ccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEEecCCCC-CHHHHHHH
Q psy7060 82 STCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYNKIDQI-SIEEVDRI 150 (160)
Q Consensus 82 ~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~NKiD~i-s~eevd~i 150 (160)
+.||. =+.++.+|.+.+|.-..+-+.++-...+-+-.+.+. ...|.+++=++ .+ +.+|+.+|
T Consensus 9 ~~C~~----C~ka~~~L~~~gi~~~~~di~~~~~~~~el~~~~g~-~~vP~v~i~~~--~iGg~~~~~~~ 71 (73)
T cd03027 9 LGCED----CTAVRLFLREKGLPYVEINIDIFPERKAELEERTGS-SVVPQIFFNEK--LVGGLTDLKSL 71 (73)
T ss_pred CCChh----HHHHHHHHHHCCCceEEEECCCCHHHHHHHHHHhCC-CCcCEEEECCE--EEeCHHHHHhh
Confidence 45654 456899999999988888777765433333344454 45699977554 23 44555443
No 304
>COG3797 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.03 E-value=77 Score=26.76 Aligned_cols=88 Identities=19% Similarity=0.362 Sum_probs=62.2
Q ss_pred HHHHHHHhhhhhhHHh-hhcCccccccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCc--------c
Q psy7060 58 VQLILHEYKIFNAEQK-KAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANR--------V 128 (160)
Q Consensus 58 v~~~l~~yki~n~~~~-~~~~~~~~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nr--------v 128 (160)
++.+|.+--.-|...- .+|-+.|-|+|..+++.+++=..+...|+.| .++++| +++|+...+.+|- -
T Consensus 24 Lka~~~dlGf~~v~T~iaSGNlvf~s~~~~~el~~klE~afe~~fg~~-~dilVr---s~~~~~~i~a~nPf~~~~~~~~ 99 (178)
T COG3797 24 LKAALTDLGFANVRTYIASGNLVFESEAGAAELEAKLEAAFEKRFGRH-VDILVR---SAEDWETIAAANPFPEEAAGEP 99 (178)
T ss_pred HHHHHHHcCcchhhHhhhcCCEEEEcCCChHHHHHHHHHHHHHHcCCC-ccEEEe---eHHHHHHHHhcCCCchhhccCc
Confidence 3444444444444433 3688999999999999999888888889865 677776 5788888887773 3
Q ss_pred eeceEEEEecCCCCCHHHHHHHh
Q psy7060 129 YLPCIYAYNKIDQISIEEVDRIA 151 (160)
Q Consensus 129 Y~P~iyv~NKiD~is~eevd~i~ 151 (160)
+--|+-+|+.- ++.|++..++
T Consensus 100 ~~~~v~f~~ep--~dvd~v~~l~ 120 (178)
T COG3797 100 ARVCVRFYREP--LDVDEVEALA 120 (178)
T ss_pred ceEEEEEEcCC--CcHHHHHHHH
Confidence 55567777764 4567777773
No 305
>COG2239 MgtE Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]
Probab=25.99 E-value=81 Score=29.44 Aligned_cols=40 Identities=23% Similarity=0.422 Sum_probs=34.5
Q ss_pred CcccCHHHHHHHHHHcCccceEEEeec-----CCChhHHHHHHhc
Q psy7060 86 LTQVNEKLVQLILHEYKIFNAEVLFRE-----DCNADELIDVINA 125 (160)
Q Consensus 86 ~~~~~e~~V~~IL~EYkI~NA~V~ire-----d~t~DdliDvi~~ 125 (160)
.++.|.+++.++.+.|.+-.+-|.=.+ -+|.||++|+|..
T Consensus 210 ~~~~dqeevA~~~~~ydl~a~PVVd~~~~LiG~itiDDiidvi~e 254 (451)
T COG2239 210 LADDDQEEVARLFEKYDLLAVPVVDEDNRLIGIITIDDIIDVIEE 254 (451)
T ss_pred cccCCHHHHHHHHHHhCCeecceECCCCceeeeeeHHHHHHHHHH
Confidence 456889999999999999998886555 7999999999975
No 306
>PRK09554 feoB ferrous iron transport protein B; Reviewed
Probab=25.92 E-value=1.1e+02 Score=30.12 Aligned_cols=14 Identities=43% Similarity=0.724 Sum_probs=12.7
Q ss_pred eeceEEEEecCCCC
Q psy7060 129 YLPCIYAYNKIDQI 142 (160)
Q Consensus 129 Y~P~iyv~NKiD~i 142 (160)
-+|++.|+||+|..
T Consensus 112 giPvIvVlNK~Dl~ 125 (772)
T PRK09554 112 GIPCIVALNMLDIA 125 (772)
T ss_pred CCCEEEEEEchhhh
Confidence 48999999999986
No 307
>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=25.83 E-value=68 Score=25.69 Aligned_cols=12 Identities=33% Similarity=0.354 Sum_probs=10.2
Q ss_pred eEEEEecCCCCC
Q psy7060 132 CIYAYNKIDQIS 143 (160)
Q Consensus 132 ~iyv~NKiD~is 143 (160)
-++++||+|+.+
T Consensus 140 d~~~~~k~d~~~ 151 (199)
T TIGR00101 140 DLLVINKIDLAP 151 (199)
T ss_pred cEEEEEhhhccc
Confidence 389999999975
No 308
>COG0780 Enzyme related to GTP cyclohydrolase I [General function prediction only]
Probab=25.57 E-value=39 Score=27.39 Aligned_cols=42 Identities=31% Similarity=0.605 Sum_probs=32.5
Q ss_pred ccccCCCcc-----------------cCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHh
Q psy7060 80 FNSTCPLTQ-----------------VNEKLVQLILHEYKIFNAEVLFREDCNADELIDVIN 124 (160)
Q Consensus 80 ~~~~~~~~~-----------------~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~ 124 (160)
|-|-||.|+ +..|-.++.|..|+=||. |.|+|+-.=+.|.+.
T Consensus 49 f~S~CpiTgqPD~~ti~I~Y~p~~~~ve~ksLk~yl~SFR~h~~---fHE~c~~~I~~dl~~ 107 (149)
T COG0780 49 FKSLCPITGQPDFATIYIEYIPDKACVESKSLKLYLFSFRNHGI---FHEQCANRIFNDLKA 107 (149)
T ss_pred ceecCCCcCCCCeEEEEEEEcCchhhhhhHHHHHHHHHHhccch---HHHHHHHHHHHHHHH
Confidence 567777775 677889999999999998 899998654444443
No 309
>TIGR02190 GlrX-dom Glutaredoxin-family domain. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain.
Probab=25.51 E-value=1.8e+02 Score=19.44 Aligned_cols=50 Identities=16% Similarity=0.269 Sum_probs=34.2
Q ss_pred ccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEEe
Q psy7060 82 STCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYN 137 (160)
Q Consensus 82 ~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~N 137 (160)
+.||.- ..+++.|.+++|.--++-+.++-...++.. +.|. .=+|.|++=.
T Consensus 16 ~~Cp~C----~~ak~~L~~~gi~y~~idi~~~~~~~~~~~-~~g~-~~vP~i~i~g 65 (79)
T TIGR02190 16 PGCPFC----AKAKATLKEKGYDFEEIPLGNDARGRSLRA-VTGA-TTVPQVFIGG 65 (79)
T ss_pred CCCHhH----HHHHHHHHHcCCCcEEEECCCChHHHHHHH-HHCC-CCcCeEEECC
Confidence 456543 468899999999988888877766555443 3443 4479997633
No 310
>PF00578 AhpC-TSA: AhpC/TSA family; InterPro: IPR000866 Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels which mediate signal transduction in mammalian cells. Prxs can be regulated by changes to phosphorylation, redox and possibly oligomerisation states. Prxs are divided into three classes: typical 2-Cys Prxs; atypical 2-Cys Prxs; and 1-Cys Prxs. All Prxs share the same basic catalytic mechanism, in which an active-site cysteine (the peroxidatic cysteine) is oxidised to a sulphenic acid by the peroxide substrate. The recycling of the sulphenic acid back to a thiol is what distinguishes the three enzyme classes. Using crystal structures, a detailed catalytic cycle has been derived for typical 2-Cys Prxs, including a model for the redox-regulated oligomeric state proposed to control enzyme activity []. Alkyl hydroperoxide reductase (AhpC) is responsible for directly reducing organic hyperoxides in its reduced dithiol form. Thiol specific antioxidant (TSA) is a physiologically important antioxidant which constitutes an enzymatic defence against sulphur-containing radicals. This family contains AhpC and TSA, as well as related proteins.; GO: 0016209 antioxidant activity, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1QMV_A 1PRX_B 3HJP_C 3HA9_A 2V41_G 2V32_C 2V2G_C 3LWA_A 3IA1_B 1ZYE_G ....
Probab=25.46 E-value=59 Score=22.37 Aligned_cols=42 Identities=17% Similarity=0.278 Sum_probs=22.6
Q ss_pred cCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHh
Q psy7060 83 TCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVIN 124 (160)
Q Consensus 83 ~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~ 124 (160)
.||........++....+|+-.|+.+..=..-+.+++...+.
T Consensus 37 ~c~~c~~~l~~l~~~~~~~~~~~~~vi~is~d~~~~~~~~~~ 78 (124)
T PF00578_consen 37 WCPFCQAELPELNELYKKYKDKGVQVIGISTDDPEEIKQFLE 78 (124)
T ss_dssp TSHHHHHHHHHHHHHHHHHHTTTEEEEEEESSSHHHHHHHHH
T ss_pred CccccccchhHHHHHhhhhccceEEeeecccccccchhhhhh
Confidence 366665555556666666665555554444444444444444
No 311
>PRK00049 elongation factor Tu; Reviewed
Probab=25.42 E-value=63 Score=28.54 Aligned_cols=25 Identities=28% Similarity=0.208 Sum_probs=16.3
Q ss_pred HHHHHHhcCcceeceE-EEEecCCCCCH
Q psy7060 118 ELIDVINANRVYLPCI-YAYNKIDQISI 144 (160)
Q Consensus 118 dliDvi~~nrvY~P~i-yv~NKiD~is~ 144 (160)
+++..+... -+|.+ +++||+|+.+.
T Consensus 118 ~~~~~~~~~--g~p~iiVvvNK~D~~~~ 143 (396)
T PRK00049 118 EHILLARQV--GVPYIVVFLNKCDMVDD 143 (396)
T ss_pred HHHHHHHHc--CCCEEEEEEeecCCcch
Confidence 344444432 36987 58999999854
No 312
>COG1281 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]
Probab=25.28 E-value=1.3e+02 Score=26.84 Aligned_cols=35 Identities=23% Similarity=0.491 Sum_probs=28.6
Q ss_pred CHHHHHHHHHH--cCccc-eEEEeecCCChhHHHHHHh
Q psy7060 90 NEKLVQLILHE--YKIFN-AEVLFREDCNADELIDVIN 124 (160)
Q Consensus 90 ~e~~V~~IL~E--YkI~N-A~V~ired~t~DdliDvi~ 124 (160)
.|+...+++|| ++++- ..|.|+.+|+-+.+.++|.
T Consensus 211 ~e~ll~rL~~e~~v~ile~~~v~f~C~CSrEr~~~aL~ 248 (286)
T COG1281 211 AEELLYRLFHEEGVQLLEPQPVEFRCSCSRERVAAALL 248 (286)
T ss_pred HHHHHHHHhccccccccCCccceEEcCCCHHHHHHHHH
Confidence 36678889986 57765 7799999999999988875
No 313
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=25.00 E-value=77 Score=26.01 Aligned_cols=20 Identities=35% Similarity=0.544 Sum_probs=17.6
Q ss_pred cCHHHHHHHHHHcCccceEE
Q psy7060 89 VNEKLVQLILHEYKIFNAEV 108 (160)
Q Consensus 89 ~~e~~V~~IL~EYkI~NA~V 108 (160)
+++++|+.||+-|+-|+..+
T Consensus 148 L~~~dv~~iL~yF~~F~v~i 167 (179)
T PF06784_consen 148 LDEKDVKNILKYFKPFEVKI 167 (179)
T ss_pred CCHHHHHHHHHhcCCceeeC
Confidence 89999999999999997644
No 314
>PRK14862 rimO ribosomal protein S12 methylthiotransferase; Provisional
Probab=24.99 E-value=88 Score=28.18 Aligned_cols=69 Identities=23% Similarity=0.274 Sum_probs=41.8
Q ss_pred eEEec-ccCCchhhHHHHHHHHHH--hhhhhhHHhhhcCccccccCCCcccCHHHHHHHHHHcCccceEEEeec
Q psy7060 42 IAFNS-TCPLTQVNEKLVQLILHE--YKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEVLFRE 112 (160)
Q Consensus 42 I~i~~-t~~lt~~~~~~v~~~l~~--yki~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ire 112 (160)
+.|.+ .|+.-..|.+.+...|.+ |.+-+.. ..|.=+.+| ||-.++-.++.+...+++++=.+..|.+-|
T Consensus 10 ~~i~t~GC~~N~~dse~~~~~l~~~G~~~~~~~-~~aD~ivin-TC~v~~~a~~k~~~~i~~~~~~~~~ivv~G 81 (440)
T PRK14862 10 IGFVSLGCPKALVDSERILTQLRAEGYEISPSY-DGADLVIVN-TCGFIDSAVQESLEAIGEALAENGKVIVTG 81 (440)
T ss_pred EEEEEcCCCCcHHHHHHHHHHHHHCcCEECCCc-ccCCEEEEe-cccccchHHHHHHHHHHHHHhcCCCEEEEC
Confidence 34433 778777888888888865 5555432 256667777 888888776655554444432233344433
No 315
>PF01189 Nol1_Nop2_Fmu: NOL1/NOP2/sun family; InterPro: IPR001678 This domain is found in archaeal, bacterial and eukaryotic proteins. In the archaea and bacteria, they are annotated as putative nucleolar protein, Sun (Fmu) family protein or tRNA/rRNA cytosine-C5-methylase. The majority have the S-adenosyl methionine (SAM) binding domain and are related to Escherichia coli Fmu (Sun) protein (16S rRNA m5C 967 methyltransferase) whose structure has been determined []. In the eukaryota, the majority are annotated as being 'hypothetical protein', nucleolar protein or the Nop2/Sun (Fmu) family. Unlike their bacterial homologues, few of the eukaryotic members in this family have a the SAM binding signature. Despite this, Saccharomyces cerevisiae (Baker's yeast) Nop2p is a probable RNA m5C methyltransferase []. It is essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis []; localized to the nucleolus and is essential for viability []. Reduced Nop2p expression limits yeast growth and decreases levels of mature 60S ribosomal subunits while altering rRNA processing []. There is substantial identity between Nop2p and Homo sapiens (Human) p120 (NOL1), which is also called the proliferation-associated nucleolar antigen [, ].; PDB: 3M4X_A 2FRX_B 2YXL_A 1IXK_A 1SQG_A 1SQF_A 3M6U_B 3M6V_B 3M6W_A 3M6X_A ....
Probab=24.78 E-value=26 Score=29.78 Aligned_cols=29 Identities=38% Similarity=0.557 Sum_probs=26.2
Q ss_pred hhcCccccccCCCccc-CHHHHHHHHHHcC
Q psy7060 74 KAGGIAFNSTCPLTQV-NEKLVQLILHEYK 102 (160)
Q Consensus 74 ~~~~~~~~~~~~~~~~-~e~~V~~IL~EYk 102 (160)
+.||..+=|||.+..- +|+.|+..|+++.
T Consensus 210 k~gG~lvYsTCS~~~eENE~vV~~fl~~~~ 239 (283)
T PF01189_consen 210 KPGGRLVYSTCSLSPEENEEVVEKFLKRHP 239 (283)
T ss_dssp EEEEEEEEEESHHHGGGTHHHHHHHHHHST
T ss_pred cCCCeEEEEeccHHHHHHHHHHHHHHHhCC
Confidence 7899999999999876 8999999999874
No 316
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=24.57 E-value=1.5e+02 Score=17.84 Aligned_cols=34 Identities=12% Similarity=0.113 Sum_probs=15.8
Q ss_pred CHHHHHHHHHHcCccceEEE-----eecCCChhHHHHHH
Q psy7060 90 NEKLVQLILHEYKIFNAEVL-----FREDCNADELIDVI 123 (160)
Q Consensus 90 ~e~~V~~IL~EYkI~NA~V~-----ired~t~DdliDvi 123 (160)
+-..+...+.++++..+-|. +.|-+|..||+.++
T Consensus 17 ~l~~~~~~~~~~~~~~~~V~d~~~~~~G~is~~dl~~~l 55 (57)
T PF00571_consen 17 SLEEALEIMRKNGISRLPVVDEDGKLVGIISRSDLLKAL 55 (57)
T ss_dssp BHHHHHHHHHHHTSSEEEEESTTSBEEEEEEHHHHHHHH
T ss_pred cHHHHHHHHHHcCCcEEEEEecCCEEEEEEEHHHHHhhh
Confidence 34445555555555444443 33334444444443
No 317
>PRK13808 adenylate kinase; Provisional
Probab=24.50 E-value=1.5e+02 Score=26.57 Aligned_cols=24 Identities=21% Similarity=0.249 Sum_probs=14.8
Q ss_pred CCCCCCc-hHHHHHHHHHHHhcCce
Q psy7060 1 MLDATKQ-DVQRGLLEKELESVGIR 24 (160)
Q Consensus 1 vLDa~k~-~~q~~~le~ELe~~GIr 24 (160)
|||.+-. ..|...|+..|...|+.
T Consensus 82 ILDGFPRt~~QA~~L~~ll~~~gi~ 106 (333)
T PRK13808 82 ILDGFPRTVPQAEALDALLKDKQLK 106 (333)
T ss_pred EEeCCCCCHHHHHHHHHHHHhcCCC
Confidence 3566544 45777777777666643
No 318
>PRK13253 citrate lyase subunit gamma; Provisional
Probab=23.98 E-value=2.3e+02 Score=21.22 Aligned_cols=29 Identities=17% Similarity=0.170 Sum_probs=23.1
Q ss_pred HHHHHHHHHHcCccceEEEeecCCChhHH
Q psy7060 91 EKLVQLILHEYKIFNAEVLFREDCNADEL 119 (160)
Q Consensus 91 e~~V~~IL~EYkI~NA~V~ired~t~Ddl 119 (160)
++.+...|.+|++.||.|.+..-=-+|-.
T Consensus 46 ~~vv~~~l~~~~v~~~~i~i~D~GAld~v 74 (92)
T PRK13253 46 RAVILETLAKLGVENAQVKVDDKGALDCV 74 (92)
T ss_pred HHHHHHHHHhcCCCceEEEEEcCCCCHHH
Confidence 67889999999999999999875444433
No 319
>KOG2198|consensus
Probab=23.94 E-value=55 Score=30.33 Aligned_cols=31 Identities=39% Similarity=0.527 Sum_probs=26.4
Q ss_pred HHhhhcCccccccCCCccc-CHHHHHHHHHHc
Q psy7060 71 EQKKAGGIAFNSTCPLTQV-NEKLVQLILHEY 101 (160)
Q Consensus 71 ~~~~~~~~~~~~~~~~~~~-~e~~V~~IL~EY 101 (160)
+.-+-||..+-|||-|..+ ||..|+.+|++-
T Consensus 284 ~lLk~GG~lVYSTCSLnpieNEaVV~~~L~~~ 315 (375)
T KOG2198|consen 284 RLLKVGGRLVYSTCSLNPIENEAVVQEALQKV 315 (375)
T ss_pred HHhcCCCEEEEeccCCCchhhHHHHHHHHHHh
Confidence 4457899999999999998 788899999763
No 320
>cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=23.84 E-value=1.2e+02 Score=20.33 Aligned_cols=24 Identities=25% Similarity=0.422 Sum_probs=20.0
Q ss_pred HHHHHHHHHHhcCceeccCCCCeE
Q psy7060 10 QRGLLEKELESVGIRLNKKKPNIY 33 (160)
Q Consensus 10 q~~~le~ELe~~GIrLnkk~p~I~ 33 (160)
-...+...|+..|+++|..|..+.
T Consensus 62 ~~~~l~~~l~~~gl~ln~~Kt~~~ 85 (98)
T cd00304 62 KKRELEEFLARLGLNLSDEKTQFT 85 (98)
T ss_pred HHHHHHHHHHHcCcEEChheeEEe
Confidence 456788999999999999997663
No 321
>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=23.78 E-value=1.3e+02 Score=22.07 Aligned_cols=66 Identities=14% Similarity=0.266 Sum_probs=37.7
Q ss_pred ccCCchhhHHHHHHHHHHhhhhhhHHhhhcCccccccCCCcccCHHHHHHHHHHcCccc---eEEEeec
Q psy7060 47 TCPLTQVNEKLVQLILHEYKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFN---AEVLFRE 112 (160)
Q Consensus 47 t~~lt~~~~~~v~~~l~~yki~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL~EYkI~N---A~V~ire 112 (160)
.|+.-..|.+.+.+.|...-.--.+.....-+.+=-||-.++-.++.+...+++++=.+ +.|.+-|
T Consensus 8 GC~~N~~Dse~i~~~l~~~G~~~~~~~e~AD~iiiNTC~V~~~Ae~k~~~~i~~l~~~~~~~~~ivv~G 76 (98)
T PF00919_consen 8 GCQMNQYDSERIASILQAAGYEIVDDPEEADVIIINTCTVRESAEQKSRNRIRKLKKLKKPGAKIVVTG 76 (98)
T ss_pred CCcccHHHHHHHHHHHHhcCCeeecccccCCEEEEEcCCCCcHHHHHHHHHHHHHHHhcCCCCEEEEEe
Confidence 56666667777777777633222333233344455567777766666666666655444 5555554
No 322
>TIGR00550 nadA quinolinate synthetase complex, A subunit. This protein, termed NadA, plays a role in the synthesis of pyridine, a precursor to NAD. The quinolinate synthetase complex consists of A protein (this protein) and B protein. B protein converts L-aspartate to iminoaspartate, an unstable reaction product which in the absence of A protein is spontaneously hydrolyzed to form oxaloacetate. The A protein, NadA, converts iminoaspartate to quinolate.
Probab=23.77 E-value=1.1e+02 Score=26.93 Aligned_cols=35 Identities=17% Similarity=0.523 Sum_probs=31.3
Q ss_pred cccCCCcc-cCHHHHHHHHHHcCccceEEEeecCCChh
Q psy7060 81 NSTCPLTQ-VNEKLVQLILHEYKIFNAEVLFREDCNAD 117 (160)
Q Consensus 81 ~~~~~~~~-~~e~~V~~IL~EYkI~NA~V~ired~t~D 117 (160)
++.||.-+ .+.+.|...+++| -+|.|.+.++|+.+
T Consensus 172 ~g~C~vh~~~t~e~v~~~~~~~--p~a~VvvhpEc~~e 207 (310)
T TIGR00550 172 QGHCSVHEKFTTEDLERLKEKY--PDAEILVHPECEPE 207 (310)
T ss_pred CCCCcChhhCCHHHHHHHHHHC--CCCeEEECCCCCHH
Confidence 79999977 6999999999999 57999999999865
No 323
>PF10678 DUF2492: Protein of unknown function (DUF2492); InterPro: IPR019620 This entry describes a family of small cytosolic proteins, about 80 amino acids in length, in which the eight invariant residues include three His residues and two Cys residues. Two pairs of these invariant residues occur in motifs HxH (where x is A or G) and CxH, both of which suggest metal-binding activity. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulphatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulphur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulphatase/maturase systems.
Probab=23.64 E-value=2e+02 Score=21.22 Aligned_cols=39 Identities=28% Similarity=0.568 Sum_probs=31.0
Q ss_pred HHHHHHHHHHcCccceEEEee----cCCChhHHHHHHhcCcceece
Q psy7060 91 EKLVQLILHEYKIFNAEVLFR----EDCNADELIDVINANRVYLPC 132 (160)
Q Consensus 91 e~~V~~IL~EYkI~NA~V~ir----ed~t~DdliDvi~~nrvY~P~ 132 (160)
+++++.|-..||- ++.|. ++.|+|+|++.+...-.++|.
T Consensus 23 ~~L~~ai~~~FG~---~arFhTCSae~m~a~eLv~FL~~rgKfi~~ 65 (78)
T PF10678_consen 23 EELKAAIIEKFGE---DARFHTCSAEGMTADELVDFLEERGKFIPS 65 (78)
T ss_pred HHHHHHHHHHhCC---CceEEecCCCCCCHHHHHHHHHHcCCEeec
Confidence 6788888888874 44443 689999999999998888874
No 324
>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=23.57 E-value=51 Score=31.30 Aligned_cols=14 Identities=50% Similarity=0.463 Sum_probs=12.4
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
+|.|+|+||+|+..
T Consensus 117 ip~IVviNKiD~~~ 130 (594)
T TIGR01394 117 LKPIVVINKIDRPS 130 (594)
T ss_pred CCEEEEEECCCCCC
Confidence 69999999999863
No 325
>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=23.52 E-value=1.1e+02 Score=24.60 Aligned_cols=24 Identities=13% Similarity=0.501 Sum_probs=15.6
Q ss_pred HHHHHHhcCcceeceEE-EEecCCCCC
Q psy7060 118 ELIDVINANRVYLPCIY-AYNKIDQIS 143 (160)
Q Consensus 118 dliDvi~~nrvY~P~iy-v~NKiD~is 143 (160)
++...+.... +|+++ |+||+|++.
T Consensus 123 ~i~~~l~~~g--~p~vi~VvnK~D~~~ 147 (225)
T cd01882 123 EFLNILQVHG--FPRVMGVLTHLDLFK 147 (225)
T ss_pred HHHHHHHHcC--CCeEEEEEeccccCC
Confidence 4455554332 58655 999999973
No 326
>PHA02992 hypothetical protein; Provisional
Probab=23.40 E-value=1.8e+02 Score=29.41 Aligned_cols=63 Identities=8% Similarity=0.273 Sum_probs=51.0
Q ss_pred hHHHHHHHHHHhhhhhhHHhhhcCccccccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcc
Q psy7060 54 NEKLVQLILHEYKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRV 128 (160)
Q Consensus 54 ~~~~v~~~l~~yki~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrv 128 (160)
|+.+.+-|.+.|+++++=-+..- .+-+-.+..|..|||-=+.--+.+.++.|+.+|++...|.
T Consensus 153 d~~~E~i~~~d~~m~~~lY~hQ~------------~s~~FL~~Mlyk~GI~P~N~Gi~~~~s~~~iieiL~~~~~ 215 (728)
T PHA02992 153 ESLTEKIFIQDYSMYDPLYEHQS------------FTSDFLTDMLYKYGIVPNNDGILDEISIELIIEILQSIKR 215 (728)
T ss_pred HHHHHHHHHhchhhhhHhhhcCc------------CCHHHHHHHHHHcCCCCCCccccccCCHHHHHHHHHhcCC
Confidence 34556778888888887544321 6788999999999999999999999999999999987654
No 327
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=23.22 E-value=1.1e+02 Score=18.66 Aligned_cols=34 Identities=18% Similarity=0.132 Sum_probs=24.8
Q ss_pred cCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcC
Q psy7060 89 VNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINAN 126 (160)
Q Consensus 89 ~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~n 126 (160)
-+++..+.-|.+|+|.-..-. .|-|+|++.+..|
T Consensus 4 Ws~~~L~~wL~~~gi~~~~~~----~~rd~Ll~~~k~~ 37 (38)
T PF10281_consen 4 WSDSDLKSWLKSHGIPVPKSA----KTRDELLKLAKKN 37 (38)
T ss_pred CCHHHHHHHHHHcCCCCCCCC----CCHHHHHHHHHHh
Confidence 467889999999988643222 4889998877654
No 328
>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
Probab=23.11 E-value=1.2e+02 Score=25.03 Aligned_cols=33 Identities=15% Similarity=0.364 Sum_probs=26.8
Q ss_pred cCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHh
Q psy7060 89 VNEKLVQLILHEYKIFNAEVLFREDCNADELIDVIN 124 (160)
Q Consensus 89 ~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~ 124 (160)
.|.+.+..+|++.+. +|.+..|+|.+|+.+++.
T Consensus 30 ~D~~~l~~~f~~lgF---~V~~~~dlt~~em~~~l~ 62 (241)
T smart00115 30 VDAENLTELFQSLGY---EVHVKNNLTAEEMLEELK 62 (241)
T ss_pred HHHHHHHHHHHHCCC---EEEEecCCCHHHHHHHHH
Confidence 466677777777665 999999999999999884
No 329
>PRK13505 formate--tetrahydrofolate ligase; Provisional
Probab=22.81 E-value=67 Score=31.14 Aligned_cols=35 Identities=23% Similarity=0.312 Sum_probs=27.0
Q ss_pred CChhHHHHHHhcCcceeceEEEEecCCCCCHHHHHHH
Q psy7060 114 CNADELIDVINANRVYLPCIYAYNKIDQISIEEVDRI 150 (160)
Q Consensus 114 ~t~DdliDvi~~nrvY~P~iyv~NKiD~is~eevd~i 150 (160)
.++...++.+. +.=+|+++++||-|.-+.+|++.+
T Consensus 359 ~NL~RHIenvr--~FGvPvVVAINKFd~DTe~Ei~~I 393 (557)
T PRK13505 359 ANLERHIENIR--KFGVPVVVAINKFVTDTDAEIAAL 393 (557)
T ss_pred HHHHHHHHHHH--HcCCCEEEEEeCCCCCCHHHHHHH
Confidence 45666666665 355799999999999888787766
No 330
>PLN00116 translation elongation factor EF-2 subunit; Provisional
Probab=22.63 E-value=67 Score=31.59 Aligned_cols=49 Identities=14% Similarity=0.173 Sum_probs=28.8
Q ss_pred HHHHHHHHHcCcc-ceEEEeecC--CC--hhHHHHHHhcCcceeceEEEEecCCCC
Q psy7060 92 KLVQLILHEYKIF-NAEVLFRED--CN--ADELIDVINANRVYLPCIYAYNKIDQI 142 (160)
Q Consensus 92 ~~V~~IL~EYkI~-NA~V~ired--~t--~DdliDvi~~nrvY~P~iyv~NKiD~i 142 (160)
+-+......-+.- .|.+.+... +. ...++..+...+ +|+|+++||+|..
T Consensus 110 dF~~e~~~al~~~D~ailVvda~~Gv~~~t~~~~~~~~~~~--~p~i~~iNK~D~~ 163 (843)
T PLN00116 110 DFSSEVTAALRITDGALVVVDCIEGVCVQTETVLRQALGER--IRPVLTVNKMDRC 163 (843)
T ss_pred HHHHHHHHHHhhcCEEEEEEECCCCCcccHHHHHHHHHHCC--CCEEEEEECCccc
Confidence 3445555544444 455555532 22 234555554444 5999999999998
No 331
>PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
Probab=22.48 E-value=69 Score=30.05 Aligned_cols=14 Identities=29% Similarity=0.413 Sum_probs=11.8
Q ss_pred eceEEEEecCCCCC
Q psy7060 130 LPCIYAYNKIDQIS 143 (160)
Q Consensus 130 ~P~iyv~NKiD~is 143 (160)
.|.|+|+||+|+.+
T Consensus 158 ~~iivvvNK~D~~~ 171 (632)
T PRK05506 158 RHVVLAVNKMDLVD 171 (632)
T ss_pred CeEEEEEEeccccc
Confidence 46788999999984
No 332
>cd06536 CIDE_N_ICAD CIDE_N domain of ICAD. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD (DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40 and ICAD/DFF45 during apoptosis. In normal cells, DFF exists in the nucleus as a heterodimer composed of CAD/DFF40 as a latent nuclease and its chaperone and inhibitor subunit ICAD/DFF45. Apoptotic activation of caspase-3 results in the cleavage of DFF45/ICAD and release of active DFF40/CAD nuclease.
Probab=22.41 E-value=79 Score=23.39 Aligned_cols=58 Identities=17% Similarity=0.245 Sum_probs=44.1
Q ss_pred hhhhhhHHhhhcCccccccCCCcccCHHHHHHHHHHcCcc--c--eEEEeecC---CChhHHHHHHhcCcce
Q psy7060 65 YKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIF--N--AEVLFRED---CNADELIDVINANRVY 129 (160)
Q Consensus 65 yki~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL~EYkI~--N--A~V~ired---~t~DdliDvi~~nrvY 129 (160)
|||.|.+....=||+-+|- +++......-+.+. + ..+.+.|| +.-+|.-..+..|-++
T Consensus 5 fkV~~~~r~~k~GV~A~sL-------~eL~~K~~~~l~l~~~~~~~~lvL~eDGT~VddEeyF~tLp~nT~l 69 (80)
T cd06536 5 CVVCNVSRQKQHGVAASSL-------EELRIKACESLGFDSSSAPITLVLAEDGTIVEDEDYFLCLPPNTKF 69 (80)
T ss_pred eEEecCCCCeeEeEEcCCH-------HHHHHHHHHHhCCCCCCCceEEEEecCCcEEccHHHHhhCCCCcEE
Confidence 6777888888888888774 77888889999997 3 67778888 4456777777777655
No 333
>PF02017 CIDE-N: CIDE-N domain; InterPro: IPR003508 This domain consists of caspase-activated (CAD) nucleases, which induce DNA fragmentation and chromatin condensation during apoptosis, and the cell death activator proteins CIDE-A and CIDE-B, which are inhibitors of CAD nuclease. The two proteins interact through the region defined by the method signatures.; GO: 0006915 apoptosis, 0005622 intracellular; PDB: 1IBX_A 2EEL_A 1F2R_I 1C9F_A 1D4B_A.
Probab=22.17 E-value=26 Score=25.61 Aligned_cols=58 Identities=21% Similarity=0.362 Sum_probs=41.9
Q ss_pred hhhhhhHHhhhcCccccccCCCcccCHHHHHHHHHHcCcc--ceEEEeecCCC---hhHHHHHHhcCcce
Q psy7060 65 YKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIF--NAEVLFREDCN---ADELIDVINANRVY 129 (160)
Q Consensus 65 yki~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL~EYkI~--NA~V~ired~t---~DdliDvi~~nrvY 129 (160)
|||.|.+....=||+-.|- +++..+...-+.+. .+.+.+.||=| -||+-..+..|-+.
T Consensus 5 ~kv~~~~r~~k~Gv~A~sL-------~eL~~K~~~~l~~~~~~~~lvL~eDGT~VddEeyF~tLp~nT~l 67 (78)
T PF02017_consen 5 FKVRNHDRSVKKGVAASSL-------EELLEKACDKLQLPEEPVRLVLEEDGTEVDDEEYFQTLPDNTVL 67 (78)
T ss_dssp EEEEETTSSCEEEEEESSH-------HHHHHHHHHHHT-SSSTCEEEETTTTCBESSCHHHCCSSSSEEE
T ss_pred EEEecCCCCceEeEEcCCH-------HHHHHHHHHHhCCCCcCcEEEEeCCCcEEccHHHHhhCCCCCEE
Confidence 6777777777778877653 78888999999998 67778888844 45666666666554
No 334
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=22.04 E-value=2.6e+02 Score=19.10 Aligned_cols=44 Identities=23% Similarity=0.309 Sum_probs=28.8
Q ss_pred ccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhcCcceeceEEEEe
Q psy7060 88 QVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINANRVYLPCIYAYN 137 (160)
Q Consensus 88 ~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~N 137 (160)
.+....+...++.|+. ........+.+++.+.|..++ |.|+-++
T Consensus 64 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~~i~~~i~~G~---Pvi~~~~ 107 (144)
T PF13529_consen 64 GTSPDDLARYLEKYGY---KATDTSDASFDDIKQEIDAGR---PVIVSVN 107 (144)
T ss_dssp ---HHHHHHHHHHH-T---TEEE-TTS-HHHHHHHHHTT-----EEEEEE
T ss_pred ccccHHHHHHHHHcCc---ceeeccCCcHHHHHHHHHCCC---cEEEEEE
Confidence 4678889999999999 333456788999999999876 6666664
No 335
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=21.87 E-value=2.3e+02 Score=20.92 Aligned_cols=61 Identities=20% Similarity=0.236 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHhcCceeccCCCCeEEEEecCcceEEecccCCchhhHHHHHHHHHHhhhhhhHHhhhcC-ccccccCCCc
Q psy7060 9 VQRGLLEKELESVGIRLNKKKPNIYFKQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEQKKAGG-IAFNSTCPLT 87 (160)
Q Consensus 9 ~q~~~le~ELe~~GIrLnkk~p~I~ikkk~~GGI~i~~t~~lt~~~~~~v~~~l~~yki~n~~~~~~~~-~~~~~~~~~~ 87 (160)
.=++.|++|+++.|+ +|.+++..--|+ -...|+..+ . ..+| + -..
T Consensus 18 ~V~~al~~ei~~~gl-------~v~v~~tGC~G~--C~~ePlV~V--------------~-----~p~g~v------~Y~ 63 (92)
T cd03063 18 EVAEAIEAEAAARGL-------AATIVRNGSRGM--YWLEPLVEV--------------E-----TPGGRV------AYG 63 (92)
T ss_pred HHHHHHHHHHHHcCC-------eEEEEEecCcee--cCCCCEEEE--------------E-----eCCCcE------EEE
Confidence 357899999999998 355544433344 445566541 0 0112 2 234
Q ss_pred ccCHHHHHHHHHHcCc
Q psy7060 88 QVNEKLVQLILHEYKI 103 (160)
Q Consensus 88 ~~~e~~V~~IL~EYkI 103 (160)
+++.+++.+|+.++-.
T Consensus 64 ~V~~edv~~Iv~~~~~ 79 (92)
T cd03063 64 PVTPADVASLLDAGAL 79 (92)
T ss_pred eCCHHHHHHHHHHHhh
Confidence 5788888888877644
No 336
>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=21.63 E-value=83 Score=29.92 Aligned_cols=21 Identities=38% Similarity=0.501 Sum_probs=15.5
Q ss_pred ceeceEEEEecCCCC--CHHHHH
Q psy7060 128 VYLPCIYAYNKIDQI--SIEEVD 148 (160)
Q Consensus 128 vY~P~iyv~NKiD~i--s~eevd 148 (160)
.-+|.|+|+||+|+. +.+++.
T Consensus 186 ~~vPiIVviNKiDl~~~~~e~v~ 208 (587)
T TIGR00487 186 ANVPIIVAINKIDKPEANPDRVK 208 (587)
T ss_pred cCCCEEEEEECcccccCCHHHHH
Confidence 347999999999986 344443
No 337
>TIGR00411 redox_disulf_1 small redox-active disulfide protein 1. This protein is homologous to a family of proteins that includes thioredoxins, glutaredoxins, protein-disulfide isomerases, and others, some of which have several such domains. The sequence of this protein at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although its overall sequence seems closer to thioredoxins. It is suggested to be a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.
Probab=21.56 E-value=1.6e+02 Score=18.81 Aligned_cols=53 Identities=17% Similarity=0.159 Sum_probs=31.6
Q ss_pred ccccCCCcccCHHHHHHHHHHcCc--cceEEEeecCCChhHHHHHHhcCcceeceEEEEec
Q psy7060 80 FNSTCPLTQVNEKLVQLILHEYKI--FNAEVLFREDCNADELIDVINANRVYLPCIYAYNK 138 (160)
Q Consensus 80 ~~~~~~~~~~~e~~V~~IL~EYkI--~NA~V~ired~t~DdliDvi~~nrvY~P~iyv~NK 138 (160)
..+.||.-+.-...+.++..+|+. .-..|-+.+ -.++... ....-+|++++ |.
T Consensus 7 ~~~~C~~C~~~~~~l~~l~~~~~~~~~~~~vd~~~---~~~~~~~--~~v~~vPt~~~-~g 61 (82)
T TIGR00411 7 TSPTCPYCPAAKRVVEEVAKEMGDAVEVEYINVME---NPQKAME--YGIMAVPAIVI-NG 61 (82)
T ss_pred ECCCCcchHHHHHHHHHHHHHhcCceEEEEEeCcc---CHHHHHH--cCCccCCEEEE-CC
Confidence 357899888888899999999973 222222221 1122222 23445799987 54
No 338
>PF13419 HAD_2: Haloacid dehalogenase-like hydrolase; PDB: 2FI1_A 2I6X_A 3SD7_A 4F71_A 4DFD_B 4F72_B 4DCC_A 3DDH_A 3KZX_A 2B0C_A ....
Probab=21.39 E-value=3e+02 Score=19.25 Aligned_cols=67 Identities=13% Similarity=0.128 Sum_probs=48.5
Q ss_pred hHHHHHHHHHHhhhhhhHHhhhcCccccccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHHHHhc
Q psy7060 54 NEKLVQLILHEYKIFNAEQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELIDVINA 125 (160)
Q Consensus 54 ~~~~v~~~l~~yki~n~~~~~~~~~~~~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliDvi~~ 125 (160)
+.+.+...|..+.+. .-...+...+.++...-+.+..+.+++++++.-.++++-+|-- .|+.-+...
T Consensus 103 ~~~~~~~~l~~~~~~----~~f~~i~~~~~~~~~Kp~~~~~~~~~~~~~~~p~~~~~vgD~~-~d~~~A~~~ 169 (176)
T PF13419_consen 103 SRERIERVLERLGLD----DYFDEIISSDDVGSRKPDPDAYRRALEKLGIPPEEILFVGDSP-SDVEAAKEA 169 (176)
T ss_dssp EHHHHHHHHHHTTHG----GGCSEEEEGGGSSSSTTSHHHHHHHHHHHTSSGGGEEEEESSH-HHHHHHHHT
T ss_pred Ccccccccccccccc----cccccccccchhhhhhhHHHHHHHHHHHcCCCcceEEEEeCCH-HHHHHHHHc
Confidence 456677777777665 2233555566667677789999999999999989999988755 666655543
No 339
>cd02947 TRX_family TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox state of target proteins via the reversible oxidation of an active site dithiol, present in a CXXC motif, partially exposed at the protein's surface. TRX reduces protein disulfide bonds, resulting in a disulfide bond at its active site. Oxidized TRX is converted to the active form by TRX reductase, using reducing equivalents derived from either NADPH or ferredoxins. By altering their redox state, TRX regulates the functions of at least 30 target proteins, some of which are enzymes and transcription factors. It also plays an important role in the defense against oxidative stress by directly reducing hydrogen peroxide and certain radicals, and by serving as a reductant for peroxiredoxins. At least two major types of functio
Probab=21.36 E-value=2.1e+02 Score=17.56 Aligned_cols=54 Identities=13% Similarity=0.213 Sum_probs=30.4
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeecCCCh-hHHHHHHhcCcceeceEEEEecC
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNA-DELIDVINANRVYLPCIYAYNKI 139 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~-DdliDvi~~nrvY~P~iyv~NKi 139 (160)
++.||.-+.-.+.++.+.+++ .....+.-|++- .++..... -...|+++++++-
T Consensus 19 ~~~C~~C~~~~~~~~~~~~~~---~~~~~~~i~~~~~~~~~~~~~--v~~~P~~~~~~~g 73 (93)
T cd02947 19 APWCGPCKAIAPVLEELAEEY---PKVKFVKVDVDENPELAEEYG--VRSIPTFLFFKNG 73 (93)
T ss_pred CCCChhHHHhhHHHHHHHHHC---CCceEEEEECCCChhHHHhcC--cccccEEEEEECC
Confidence 455777777777777777772 222222333442 33444332 3356999998764
No 340
>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=20.90 E-value=56 Score=30.52 Aligned_cols=23 Identities=26% Similarity=0.382 Sum_probs=16.2
Q ss_pred HHHHHHhcCcceeceEEEEecCCCC
Q psy7060 118 ELIDVINANRVYLPCIYAYNKIDQI 142 (160)
Q Consensus 118 dliDvi~~nrvY~P~iyv~NKiD~i 142 (160)
.++....... +|.|+++||+|+.
T Consensus 123 ~l~~~~~~~~--~PiivviNKiD~~ 145 (527)
T TIGR00503 123 KLMEVTRLRD--TPIFTFMNKLDRD 145 (527)
T ss_pred HHHHHHHhcC--CCEEEEEECcccc
Confidence 4444443322 6999999999996
No 341
>COG1159 Era GTPase [General function prediction only]
Probab=20.88 E-value=6.3e+02 Score=22.83 Aligned_cols=106 Identities=20% Similarity=0.262 Sum_probs=63.8
Q ss_pred chHHHHHHHHHHHhcCceeccCCCCeE------EEEecCcceEEecccCCchhhHHHHHHHHHHhhhhhhHHhhhcCccc
Q psy7060 7 QDVQRGLLEKELESVGIRLNKKKPNIY------FKQKKAGGIAFNSTCPLTQVNEKLVQLILHEYKIFNAEQKKAGGIAF 80 (160)
Q Consensus 7 ~~~q~~~le~ELe~~GIrLnkk~p~I~------ikkk~~GGI~i~~t~~lt~~~~~~v~~~l~~yki~n~~~~~~~~~~~ 80 (160)
+.+-+..|.+.|-..-|.+-.++|+-+ |.-.+..-|-|.-|+-+.
T Consensus 15 PNvGKSTLlN~l~G~KisIvS~k~QTTR~~I~GI~t~~~~QiIfvDTPGih----------------------------- 65 (298)
T COG1159 15 PNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNAQIIFVDTPGIH----------------------------- 65 (298)
T ss_pred CCCcHHHHHHHHhcCceEeecCCcchhhhheeEEEEcCCceEEEEeCCCCC-----------------------------
Confidence 334567788888888888888888743 111122234444443332
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeec-C--CCh-hHH-HHHHhcCcceeceEEEEecCCCCCHHH
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFRE-D--CNA-DEL-IDVINANRVYLPCIYAYNKIDQISIEE 146 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ire-d--~t~-Ddl-iDvi~~nrvY~P~iyv~NKiD~is~ee 146 (160)
-|-+.+++-+++.+-..++--.+.+.+-+ + .+. |++ ++-+.. .-.|-|.++||||+++.+.
T Consensus 66 ---~pk~~l~~~m~~~a~~sl~dvDlilfvvd~~~~~~~~d~~il~~lk~--~~~pvil~iNKID~~~~~~ 131 (298)
T COG1159 66 ---KPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLKK--TKTPVILVVNKIDKVKPKT 131 (298)
T ss_pred ---CcchHHHHHHHHHHHHHhccCcEEEEEEeccccCCccHHHHHHHHhh--cCCCeEEEEEccccCCcHH
Confidence 14444778888888888877666555432 2 222 222 222222 4569999999999997766
No 342
>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=20.70 E-value=1.2e+02 Score=28.58 Aligned_cols=41 Identities=22% Similarity=0.279 Sum_probs=34.9
Q ss_pred CCcccCHHHHHHHH---HHcCccceEEEeecCCChhHHHHHHhc
Q psy7060 85 PLTQVNEKLVQLIL---HEYKIFNAEVLFREDCNADELIDVINA 125 (160)
Q Consensus 85 ~~~~~~e~~V~~IL---~EYkI~NA~V~ired~t~DdliDvi~~ 125 (160)
+|.-++-+.++.|. +..|+|-|-|.++++++.+++.+++..
T Consensus 262 ~l~f~~~e~v~~ik~~~~~rK~YrAlV~~~~~v~~e~l~~~~~~ 305 (398)
T COG1258 262 DLEFVGREEVEEIKETERHRKVYRALVYSDRPVSDEKLEEVLGS 305 (398)
T ss_pred EEEecCHHHHHHHHhccccceeEEEEEEECCCcCHHHHHHHHhh
Confidence 56667888888888 578999999999999999999887754
No 343
>PF11263 Attachment_P66: Borrelia burgdorferi attachment protein P66 ; InterPro: IPR020967 Borrelia burgdorferi, the agent of Lyme disease, expresses several adhesion molecules that are probably required for initial establishment of infection in mammalian hosts, and for colonization of various tissues within the host. P66 is an outer membrane protein in B. burgdorferi, the agent of Lyme disease. P66 has a role in the attachment of Borrelia burgdorferi to human cell-surface receptors. Specifically p66 has been identified as a ligand for beta3-chain integrins as mutants in p66 show dramatically reduced attachment to the integrin alpha-v beta-3 [].
Probab=20.56 E-value=88 Score=27.36 Aligned_cols=48 Identities=33% Similarity=0.550 Sum_probs=34.6
Q ss_pred hhhhhHHhhhc---CccccccCCCcccCHHHHHHHHH-HcCccceEEEeecC
Q psy7060 66 KIFNAEQKKAG---GIAFNSTCPLTQVNEKLVQLILH-EYKIFNAEVLFRED 113 (160)
Q Consensus 66 ki~n~~~~~~~---~~~~~~~~~~~~~~e~~V~~IL~-EYkI~NA~V~ired 113 (160)
+||-+..||+| ||+..-..--..-+.++++.|-. .|+-.|||+.-.||
T Consensus 71 rifg~qdkksgig~GI~YGqnLY~~tssn~~iq~Ia~ksFqtlNaEiStYED 122 (233)
T PF11263_consen 71 RIFGEQDKKSGIGLGISYGQNLYKPTSSNKLIQKIAAKSFQTLNAEISTYED 122 (233)
T ss_pred hhhcccccccceeEeeecccccccCcchhHHHHHHHHHHHhhhceeeeeecc
Confidence 68888888887 44443222222456788999865 89999999988876
No 344
>COG0050 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]
Probab=20.44 E-value=77 Score=29.56 Aligned_cols=80 Identities=28% Similarity=0.359 Sum_probs=50.8
Q ss_pred hhhhHHhhhcCcccccc---------------CCCcccCHHHHHHHHHH-cCccceEEEeec-C-CChhHHHHHHhcCcc
Q psy7060 67 IFNAEQKKAGGIAFNST---------------CPLTQVNEKLVQLILHE-YKIFNAEVLFRE-D-CNADELIDVINANRV 128 (160)
Q Consensus 67 i~n~~~~~~~~~~~~~~---------------~~~~~~~e~~V~~IL~E-YkI~NA~V~ire-d-~t~DdliDvi~~nrv 128 (160)
|-||-..|+-||++|.. || .-.+-|+..+.. ....-|-..+.- | .--.--.-++-+..+
T Consensus 50 id~aPeEk~rGITIntahveyet~~rhyahVDcP---GHaDYvKNMItgAaqmDgAILVVsA~dGpmPqTrEHiLlarqv 126 (394)
T COG0050 50 IDNAPEEKARGITINTAHVEYETANRHYAHVDCP---GHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLARQV 126 (394)
T ss_pred hccCchHhhcCceeccceeEEecCCceEEeccCC---ChHHHHHHHhhhHHhcCccEEEEEcCCCCCCcchhhhhhhhhc
Confidence 77788899999999974 55 346778877653 344445444432 1 112223445666777
Q ss_pred eeceEE-EEecCCCCCHHHHHH
Q psy7060 129 YLPCIY-AYNKIDQISIEEVDR 149 (160)
Q Consensus 129 Y~P~iy-v~NKiD~is~eevd~ 149 (160)
=.|.|+ .+||+|+.+.+|+-.
T Consensus 127 Gvp~ivvflnK~Dmvdd~elle 148 (394)
T COG0050 127 GVPYIVVFLNKVDMVDDEELLE 148 (394)
T ss_pred CCcEEEEEEecccccCcHHHHH
Confidence 777665 579999998655433
No 345
>cd02961 PDI_a_family Protein Disulfide Isomerase (PDIa) family, redox active TRX domains; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI and PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5, PDIR, ERp46 and the transmembrane PDIs. PDI, ERp57, ERp72, P5, PDIR and ERp46 are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins usually contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and may also contain one or more redox inactive TRX-like (b) domains. Only one a domain is required for the oxidase function but multiple copies
Probab=20.37 E-value=2.4e+02 Score=17.83 Aligned_cols=58 Identities=17% Similarity=0.175 Sum_probs=33.4
Q ss_pred ccccCCCcccCHHHHHHHHHHcCccceEEEeecCCCh-hHHHHHHhcCcceeceEEEEecC
Q psy7060 80 FNSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNA-DELIDVINANRVYLPCIYAYNKI 139 (160)
Q Consensus 80 ~~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~-DdliDvi~~nrvY~P~iyv~NKi 139 (160)
+++.||.-+.-......+.+.++-.+.-..++-|+.- .++.+-. +-...|+++++.+-
T Consensus 23 ~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~--~i~~~Pt~~~~~~~ 81 (101)
T cd02961 23 YAPWCGHCKALAPEYEKLAKELKGDGKVVVAKVDCTANNDLCSEY--GVRGYPTIKLFPNG 81 (101)
T ss_pred ECCCCHHHHhhhHHHHHHHHHhccCCceEEEEeeccchHHHHHhC--CCCCCCEEEEEcCC
Confidence 3556887777677777887777411222223333432 3444433 33567999999765
No 346
>COG4009 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.27 E-value=66 Score=24.49 Aligned_cols=19 Identities=32% Similarity=0.602 Sum_probs=16.1
Q ss_pred HHHHHHHHHhcCceeccCC
Q psy7060 11 RGLLEKELESVGIRLNKKK 29 (160)
Q Consensus 11 ~~~le~ELe~~GIrLnkk~ 29 (160)
-+-+++|||++|.++|...
T Consensus 62 ~eev~~ele~mga~in~ds 80 (88)
T COG4009 62 EEEVERELEDMGAEINRDS 80 (88)
T ss_pred HHHHHHHHHHhCchhcccH
Confidence 4678999999999999753
No 347
>COG1162 Predicted GTPases [General function prediction only]
Probab=20.16 E-value=76 Score=28.37 Aligned_cols=37 Identities=27% Similarity=0.221 Sum_probs=22.1
Q ss_pred cCCChhHHHHHHh-cCcceeceEEEEecCCCCCHHHHH
Q psy7060 112 EDCNADELIDVIN-ANRVYLPCIYAYNKIDQISIEEVD 148 (160)
Q Consensus 112 ed~t~DdliDvi~-~nrvY~P~iyv~NKiD~is~eevd 148 (160)
.+.+...|-..+- ..--=+.-++++||+|+.+.|+..
T Consensus 92 P~~~~~~ldR~Lv~ae~~gi~pvIvlnK~DL~~~~~~~ 129 (301)
T COG1162 92 PDFNTNLLDRYLVLAEAGGIEPVIVLNKIDLLDDEEAA 129 (301)
T ss_pred CCCCHHHHHHHHHHHHHcCCcEEEEEEccccCcchHHH
Confidence 3455444443332 233334567779999999876665
No 348
>PRK00741 prfC peptide chain release factor 3; Provisional
Probab=20.09 E-value=64 Score=30.14 Aligned_cols=15 Identities=27% Similarity=0.248 Sum_probs=13.2
Q ss_pred eeceEEEEecCCCCC
Q psy7060 129 YLPCIYAYNKIDQIS 143 (160)
Q Consensus 129 Y~P~iyv~NKiD~is 143 (160)
=+|.|+++||+|...
T Consensus 131 ~iPiiv~iNK~D~~~ 145 (526)
T PRK00741 131 DTPIFTFINKLDRDG 145 (526)
T ss_pred CCCEEEEEECCcccc
Confidence 479999999999874
No 349
>cd01659 TRX_superfamily Thioredoxin (TRX) superfamily; a large, diverse group of proteins containing a TRX-fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include TRX, protein disulfide isomerase (PDI), tlpA-like, glutaredoxin, NrdH redoxin, and the bacterial Dsb (DsbA, DsbC, DsbG, DsbE, DsbDgamma) protein families. Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins and glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others.
Probab=20.05 E-value=1.7e+02 Score=15.82 Aligned_cols=56 Identities=9% Similarity=0.059 Sum_probs=29.1
Q ss_pred cccCCCcccCHHHHHHHHHHcCccceEEEeecCCChhHHHH-HHhcCcceeceEEEEec
Q psy7060 81 NSTCPLTQVNEKLVQLILHEYKIFNAEVLFREDCNADELID-VINANRVYLPCIYAYNK 138 (160)
Q Consensus 81 ~~~~~~~~~~e~~V~~IL~EYkI~NA~V~ired~t~DdliD-vi~~nrvY~P~iyv~NK 138 (160)
.+.||.-+.-...+.++ ++.-.+..+....--...+..+ ....+..+.|.+++++.
T Consensus 6 ~~~c~~c~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~ 62 (69)
T cd01659 6 APWCPFCQALRPVLAEL--ALLNKGVKFEAVDVDEDPALEKELKRYGVGGVPTLVVFGP 62 (69)
T ss_pred CCCChhHHhhhhHHHHH--HhhCCCcEEEEEEcCCChHHhhHHHhCCCccccEEEEEeC
Confidence 45666665555555555 3333344443333222222222 23456778899988874
Done!