Query 038356
Match_columns 78
No_of_seqs 195 out of 1287
Neff 9.1
Searched_HMMs 46136
Date Fri Mar 29 10:09:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038356.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038356hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0084 GTPase Rab1/YPT1, smal 99.9 3.8E-24 8.2E-29 128.6 5.4 70 1-71 73-142 (205)
2 KOG0078 GTP-binding protein SE 99.9 6.2E-24 1.4E-28 128.6 4.4 76 1-77 76-151 (207)
3 KOG0087 GTPase Rab11/YPT3, sma 99.9 1.8E-23 3.9E-28 126.8 5.2 77 1-78 78-154 (222)
4 KOG0098 GTPase Rab2, small G p 99.9 1.2E-23 2.7E-28 125.8 4.4 77 1-78 70-146 (216)
5 KOG0092 GTPase Rab5/YPT51 and 99.9 1.1E-22 2.3E-27 121.9 5.7 67 1-68 69-135 (200)
6 KOG0094 GTPase Rab6/YPT6/Ryh1, 99.8 3.6E-21 7.8E-26 115.9 5.0 76 1-77 86-162 (221)
7 KOG0093 GTPase Rab3, small G p 99.8 5.7E-21 1.2E-25 111.2 5.6 64 2-66 86-149 (193)
8 KOG0088 GTPase Rab21, small G 99.8 6E-21 1.3E-25 112.4 4.6 66 1-67 77-142 (218)
9 KOG0080 GTPase Rab18, small G 99.8 2.4E-21 5.3E-26 114.1 2.9 77 1-78 75-152 (209)
10 KOG0086 GTPase Rab4, small G p 99.8 1.4E-20 3E-25 110.4 5.1 76 1-77 73-148 (214)
11 KOG0079 GTP-binding protein H- 99.8 8.7E-20 1.9E-24 106.4 4.3 66 2-69 73-138 (198)
12 KOG0083 GTPase Rab26/Rab37, sm 99.8 1.3E-20 2.8E-25 108.5 0.7 77 1-78 62-138 (192)
13 cd04120 Rab12 Rab12 subfamily. 99.8 4.7E-19 1E-23 107.9 6.1 64 2-66 65-128 (202)
14 cd04121 Rab40 Rab40 subfamily. 99.8 4.3E-19 9.4E-24 107.1 5.7 63 2-66 71-133 (189)
15 cd04133 Rop_like Rop subfamily 99.8 1.3E-18 2.8E-23 103.9 6.2 56 2-59 65-121 (176)
16 KOG0081 GTPase Rab27, small G 99.8 3.2E-19 7E-24 105.2 3.0 76 1-77 82-158 (219)
17 KOG0091 GTPase Rab39, small G 99.8 7.6E-19 1.6E-23 103.9 4.2 76 1-77 73-150 (213)
18 cd04172 Rnd3_RhoE_Rho8 Rnd3/Rh 99.7 2.7E-18 5.8E-23 103.0 5.7 54 2-57 69-123 (182)
19 cd04131 Rnd Rnd subfamily. Th 99.7 4.5E-18 9.7E-23 101.6 6.0 54 2-57 65-119 (178)
20 PTZ00099 rab6; Provisional 99.7 1E-17 2.2E-22 100.1 6.6 63 2-65 45-107 (176)
21 cd04102 RabL3 RabL3 (Rab-like3 99.7 9.4E-18 2E-22 102.3 6.6 61 2-63 70-149 (202)
22 KOG0395 Ras-related GTPase [Ge 99.7 7.4E-18 1.6E-22 102.4 5.7 75 2-77 67-142 (196)
23 cd01873 RhoBTB RhoBTB subfamil 99.7 1.8E-17 3.8E-22 100.4 6.4 54 2-57 80-134 (195)
24 KOG0095 GTPase Rab30, small G 99.7 6.7E-18 1.5E-22 98.8 4.2 67 1-68 71-137 (213)
25 cd04174 Rnd1_Rho6 Rnd1/Rho6 su 99.7 1.7E-17 3.6E-22 103.0 5.9 54 2-57 77-131 (232)
26 cd01875 RhoG RhoG subfamily. 99.7 2.9E-17 6.3E-22 98.8 6.0 56 2-59 67-123 (191)
27 cd04122 Rab14 Rab14 subfamily. 99.7 3.5E-17 7.6E-22 95.9 6.1 61 2-63 67-127 (166)
28 cd04117 Rab15 Rab15 subfamily. 99.7 4.1E-17 8.9E-22 95.5 6.4 64 2-66 65-128 (161)
29 cd04141 Rit_Rin_Ric Rit/Rin/Ri 99.7 4.1E-17 8.8E-22 96.7 5.3 64 2-66 66-130 (172)
30 PF00071 Ras: Ras family; Int 99.7 5.1E-17 1.1E-21 94.5 4.3 64 3-67 65-128 (162)
31 KOG0097 GTPase Rab14, small G 99.7 4.7E-17 1E-21 94.7 3.5 71 2-73 76-146 (215)
32 KOG0394 Ras-related GTPase [Ge 99.7 2.4E-16 5.1E-21 94.5 5.7 67 1-68 73-145 (210)
33 cd04127 Rab27A Rab27a subfamil 99.7 2.1E-16 4.6E-21 93.4 5.5 62 2-64 79-141 (180)
34 cd04126 Rab20 Rab20 subfamily. 99.7 3.2E-16 6.8E-21 96.6 6.0 55 2-57 60-114 (220)
35 cd01874 Cdc42 Cdc42 subfamily. 99.7 3.1E-16 6.8E-21 93.2 5.7 55 2-58 65-120 (175)
36 smart00176 RAN Ran (Ras-relate 99.6 7.5E-16 1.6E-20 93.7 7.0 58 2-62 60-117 (200)
37 PLN00023 GTP-binding protein; 99.6 6.5E-16 1.4E-20 99.7 6.5 56 2-58 99-166 (334)
38 cd04144 Ras2 Ras2 subfamily. 99.6 5E-16 1.1E-20 93.2 5.2 62 2-64 63-127 (190)
39 cd01865 Rab3 Rab3 subfamily. 99.6 8E-16 1.7E-20 90.1 6.0 60 2-62 66-125 (165)
40 cd01867 Rab8_Rab10_Rab13_like 99.6 8.3E-16 1.8E-20 90.2 6.0 59 3-62 69-127 (167)
41 cd04103 Centaurin_gamma Centau 99.6 6.2E-16 1.3E-20 90.7 5.3 61 4-65 60-123 (158)
42 cd04109 Rab28 Rab28 subfamily. 99.6 9E-16 2E-20 93.7 6.1 62 2-64 66-130 (215)
43 cd04136 Rap_like Rap-like subf 99.6 9E-16 2E-20 89.1 5.7 61 2-63 65-126 (163)
44 PLN03110 Rab GTPase; Provision 99.6 8.1E-16 1.8E-20 94.2 5.7 65 2-67 77-141 (216)
45 cd04115 Rab33B_Rab33A Rab33B/R 99.6 8.4E-16 1.8E-20 90.5 5.6 63 2-65 68-131 (170)
46 cd04176 Rap2 Rap2 subgroup. T 99.6 1E-15 2.2E-20 89.2 5.5 60 2-62 65-125 (163)
47 cd04175 Rap1 Rap1 subgroup. T 99.6 1E-15 2.2E-20 89.3 5.2 61 2-63 65-126 (164)
48 cd04107 Rab32_Rab38 Rab38/Rab3 99.6 1.5E-15 3.3E-20 91.7 6.2 60 2-62 66-129 (201)
49 cd01869 Rab1_Ypt1 Rab1/Ypt1 su 99.6 1.3E-15 2.9E-20 89.0 5.7 59 3-62 68-126 (166)
50 cd04125 RabA_like RabA-like su 99.6 1.9E-15 4.1E-20 90.3 6.3 62 2-64 65-126 (188)
51 cd04173 Rnd2_Rho7 Rnd2/Rho7 su 99.6 1.6E-15 3.4E-20 93.7 6.0 54 2-57 65-119 (222)
52 cd01871 Rac1_like Rac1-like su 99.6 1.8E-15 3.8E-20 89.9 5.8 55 2-58 65-120 (174)
53 cd04134 Rho3 Rho3 subfamily. 99.6 3.8E-15 8.3E-20 89.3 7.2 57 2-60 64-121 (189)
54 cd01868 Rab11_like Rab11-like. 99.6 2.2E-15 4.8E-20 87.9 6.0 60 2-62 68-127 (165)
55 cd04112 Rab26 Rab26 subfamily. 99.6 2.1E-15 4.6E-20 90.5 5.9 59 3-62 67-125 (191)
56 PLN03071 GTP-binding nuclear p 99.6 4E-15 8.6E-20 91.4 7.1 54 2-57 78-131 (219)
57 cd04140 ARHI_like ARHI subfami 99.6 2.2E-15 4.8E-20 88.2 5.5 61 3-64 66-129 (165)
58 cd04106 Rab23_lke Rab23-like s 99.6 2.7E-15 5.8E-20 87.1 5.5 60 2-63 67-126 (162)
59 cd04162 Arl9_Arfrp2_like Arl9/ 99.6 5.7E-15 1.2E-19 86.9 6.9 65 2-68 60-124 (164)
60 cd04111 Rab39 Rab39 subfamily. 99.6 3.6E-15 7.7E-20 91.1 6.1 63 2-65 68-131 (211)
61 PTZ00369 Ras-like protein; Pro 99.6 3.5E-15 7.5E-20 89.4 5.8 61 2-63 69-130 (189)
62 cd04146 RERG_RasL11_like RERG/ 99.6 2.6E-15 5.6E-20 87.8 5.0 59 4-63 66-126 (165)
63 cd04110 Rab35 Rab35 subfamily. 99.6 5.2E-15 1.1E-19 89.4 6.0 59 2-62 71-129 (199)
64 cd01864 Rab19 Rab19 subfamily. 99.6 6E-15 1.3E-19 86.2 6.0 59 3-62 69-127 (165)
65 cd01866 Rab2 Rab2 subfamily. 99.6 6.1E-15 1.3E-19 86.7 6.0 61 2-63 69-129 (168)
66 KOG4252 GTP-binding protein [S 99.6 1.7E-15 3.8E-20 90.9 3.3 59 2-62 85-143 (246)
67 PLN03108 Rab family protein; P 99.6 6.8E-15 1.5E-19 89.7 6.0 62 2-64 71-132 (210)
68 cd04119 RJL RJL (RabJ-Like) su 99.6 8.2E-15 1.8E-19 85.1 6.0 60 2-62 65-129 (168)
69 cd04128 Spg1 Spg1p. Spg1p (se 99.6 5.7E-15 1.2E-19 88.4 5.4 53 2-56 65-117 (182)
70 cd04108 Rab36_Rab34 Rab34/Rab3 99.6 1.9E-14 4.1E-19 85.1 7.4 58 2-60 65-123 (170)
71 smart00174 RHO Rho (Ras homolo 99.6 8E-15 1.7E-19 86.2 5.7 55 2-58 62-117 (174)
72 cd04142 RRP22 RRP22 subfamily. 99.6 1.4E-14 3.1E-19 87.8 6.3 59 5-64 76-137 (198)
73 cd04113 Rab4 Rab4 subfamily. 99.6 1.5E-14 3.2E-19 84.1 6.1 59 3-62 66-124 (161)
74 cd00877 Ran Ran (Ras-related n 99.5 3.6E-14 7.7E-19 83.6 7.3 54 2-57 65-118 (166)
75 cd04161 Arl2l1_Arl13_like Arl2 99.5 3.5E-14 7.5E-19 83.7 7.2 66 2-68 59-125 (167)
76 cd04148 RGK RGK subfamily. Th 99.5 1.7E-14 3.6E-19 88.7 5.8 60 4-64 66-127 (221)
77 cd04145 M_R_Ras_like M-Ras/R-R 99.5 1.6E-14 3.6E-19 83.8 5.4 61 2-63 66-127 (164)
78 cd04101 RabL4 RabL4 (Rab-like4 99.5 2.5E-14 5.5E-19 83.2 6.0 60 2-63 68-127 (164)
79 cd04132 Rho4_like Rho4-like su 99.5 2.6E-14 5.5E-19 85.1 5.5 55 2-58 65-120 (187)
80 smart00173 RAS Ras subfamily o 99.5 2.6E-14 5.7E-19 83.2 5.3 60 2-62 64-124 (164)
81 cd04130 Wrch_1 Wrch-1 subfamil 99.5 4.6E-14 1E-18 83.3 6.1 54 2-57 64-118 (173)
82 smart00177 ARF ARF-like small 99.5 6.9E-14 1.5E-18 83.0 6.9 66 2-68 73-139 (175)
83 cd04116 Rab9 Rab9 subfamily. 99.5 5.5E-14 1.2E-18 82.4 6.3 59 2-62 70-132 (170)
84 KOG0393 Ras-related small GTPa 99.5 4.2E-14 9.1E-19 85.9 5.9 55 2-58 69-124 (198)
85 PLN00223 ADP-ribosylation fact 99.5 7.9E-14 1.7E-18 83.4 6.8 67 2-69 77-144 (181)
86 cd04143 Rhes_like Rhes_like su 99.5 9E-14 1.9E-18 87.0 7.1 60 2-62 64-132 (247)
87 cd04123 Rab21 Rab21 subfamily. 99.5 8.6E-14 1.9E-18 80.4 6.4 60 2-62 65-124 (162)
88 smart00175 RAB Rab subfamily o 99.5 7.9E-14 1.7E-18 80.9 5.9 59 3-62 66-124 (164)
89 cd04150 Arf1_5_like Arf1-Arf5- 99.5 1.3E-13 2.9E-18 80.6 6.7 61 2-63 60-121 (159)
90 cd04138 H_N_K_Ras_like H-Ras/N 99.5 9.7E-14 2.1E-18 80.2 5.3 55 2-57 65-120 (162)
91 cd01892 Miro2 Miro2 subfamily. 99.5 1E-13 2.2E-18 81.9 5.5 56 2-60 70-125 (169)
92 cd04149 Arf6 Arf6 subfamily. 99.5 2.4E-13 5.3E-18 80.2 7.0 57 3-60 70-127 (168)
93 cd01861 Rab6 Rab6 subfamily. 99.5 2.1E-13 4.6E-18 79.1 6.2 59 3-62 66-124 (161)
94 cd04177 RSR1 RSR1 subgroup. R 99.5 1.9E-13 4.1E-18 80.2 5.9 60 2-62 65-125 (168)
95 cd04118 Rab24 Rab24 subfamily. 99.5 2.9E-13 6.3E-18 81.0 6.4 54 2-57 66-119 (193)
96 cd04114 Rab30 Rab30 subfamily. 99.4 2.9E-13 6.2E-18 79.1 6.1 61 3-64 73-133 (169)
97 cd04124 RabL2 RabL2 subfamily. 99.4 3.9E-13 8.4E-18 78.6 6.4 54 2-57 65-118 (161)
98 cd04158 ARD1 ARD1 subfamily. 99.4 5.3E-13 1.2E-17 78.6 6.9 59 3-62 60-119 (169)
99 PTZ00133 ADP-ribosylation fact 99.4 6.1E-13 1.3E-17 79.5 7.2 67 2-69 77-144 (182)
100 PLN03118 Rab family protein; P 99.4 3.1E-13 6.7E-18 82.3 5.9 60 2-62 78-139 (211)
101 cd01860 Rab5_related Rab5-rela 99.4 7.2E-13 1.6E-17 76.9 6.1 59 3-62 67-125 (163)
102 cd01863 Rab18 Rab18 subfamily. 99.4 2E-12 4.2E-17 75.1 6.7 54 2-56 65-119 (161)
103 cd04129 Rho2 Rho2 subfamily. 99.4 1.2E-12 2.6E-17 78.3 5.8 52 4-57 67-119 (187)
104 cd04135 Tc10 TC10 subfamily. 99.4 3.5E-12 7.5E-17 74.9 7.3 55 2-58 64-119 (174)
105 cd04157 Arl6 Arl6 subfamily. 99.4 2.9E-12 6.4E-17 74.2 6.7 58 2-60 61-121 (162)
106 cd01893 Miro1 Miro1 subfamily. 99.4 3.2E-12 6.9E-17 75.0 6.9 55 4-60 65-120 (166)
107 cd04154 Arl2 Arl2 subfamily. 99.3 4.2E-12 9.2E-17 74.9 6.5 60 3-63 75-135 (173)
108 KOG3883 Ras family small GTPas 99.3 4E-12 8.7E-17 74.8 6.1 66 2-68 77-143 (198)
109 TIGR00157 ribosome small subun 99.3 3.9E-12 8.5E-17 79.5 6.2 58 1-62 28-86 (245)
110 cd01870 RhoA_like RhoA-like su 99.3 1E-11 2.2E-16 73.0 7.3 53 3-57 66-119 (175)
111 cd04156 ARLTS1 ARLTS1 subfamil 99.3 9.7E-12 2.1E-16 72.1 7.2 62 3-65 61-123 (160)
112 cd04139 RalA_RalB RalA/RalB su 99.3 4.3E-12 9.3E-17 73.5 5.6 58 3-61 65-123 (164)
113 cd04147 Ras_dva Ras-dva subfam 99.3 1.3E-11 2.9E-16 74.4 7.3 60 2-62 63-124 (198)
114 smart00178 SAR Sar1p-like memb 99.3 9.5E-12 2.1E-16 74.4 6.5 67 2-69 77-144 (184)
115 cd04153 Arl5_Arl8 Arl5/Arl8 su 99.3 1.3E-11 2.8E-16 73.0 7.0 65 3-68 76-141 (174)
116 cd01862 Rab7 Rab7 subfamily. 99.3 1.6E-11 3.4E-16 71.7 7.2 58 2-60 65-126 (172)
117 PF08477 Miro: Miro-like prote 99.3 8.8E-12 1.9E-16 69.3 5.7 47 6-54 70-119 (119)
118 cd00876 Ras Ras family. The R 99.3 7.2E-12 1.6E-16 72.1 5.3 59 3-62 64-123 (160)
119 cd04152 Arl4_Arl7 Arl4/Arl7 su 99.3 2.1E-11 4.6E-16 72.7 7.0 60 2-62 68-128 (183)
120 cd00878 Arf_Arl Arf (ADP-ribos 99.3 3.1E-11 6.7E-16 69.9 6.9 64 3-67 60-124 (158)
121 PTZ00132 GTP-binding nuclear p 99.3 3.4E-11 7.4E-16 73.4 7.4 54 2-57 74-127 (215)
122 cd04151 Arl1 Arl1 subfamily. 99.3 4.7E-11 1E-15 69.3 7.4 63 3-66 60-123 (158)
123 cd04137 RheB Rheb (Ras Homolog 99.2 1.7E-11 3.7E-16 72.4 5.3 59 3-62 66-125 (180)
124 cd00154 Rab Rab family. Rab G 99.2 2.9E-11 6.2E-16 69.1 6.0 53 3-56 66-118 (159)
125 cd00157 Rho Rho (Ras homology) 99.2 3.4E-11 7.4E-16 70.2 5.8 55 3-59 65-120 (171)
126 cd00879 Sar1 Sar1 subfamily. 99.2 6.8E-11 1.5E-15 70.5 7.1 62 3-65 80-142 (190)
127 COG1100 GTPase SAR1 and relate 99.2 4.8E-11 1E-15 72.4 6.3 58 2-60 70-128 (219)
128 KOG0070 GTP-binding ADP-ribosy 99.2 1E-10 2.2E-15 70.1 7.0 67 2-69 77-144 (181)
129 cd04160 Arfrp1 Arfrp1 subfamil 99.2 9.4E-11 2E-15 68.3 6.4 57 3-60 67-124 (167)
130 PF00025 Arf: ADP-ribosylation 99.2 2.4E-10 5.2E-15 68.0 8.0 66 2-68 74-140 (175)
131 cd01898 Obg Obg subfamily. Th 99.1 1.4E-10 3E-15 67.7 5.3 55 9-63 77-134 (170)
132 KOG0096 GTPase Ran/TC4/GSP1 (n 99.1 5.8E-11 1.3E-15 71.8 3.7 54 2-57 75-128 (216)
133 cd04159 Arl10_like Arl10-like 99.1 4.5E-10 9.7E-15 64.2 6.9 61 3-64 61-122 (159)
134 KOG0071 GTP-binding ADP-ribosy 99.0 9.7E-10 2.1E-14 64.1 6.1 66 2-68 77-143 (180)
135 cd04155 Arl3 Arl3 subfamily. 99.0 3.9E-09 8.5E-14 61.8 7.1 65 4-69 76-141 (173)
136 PRK12299 obgE GTPase CgtA; Rev 99.0 1.1E-09 2.3E-14 71.4 5.1 54 9-62 235-290 (335)
137 cd01878 HflX HflX subfamily. 98.9 4.4E-09 9.6E-14 63.5 6.4 54 7-61 118-171 (204)
138 KOG0075 GTP-binding ADP-ribosy 98.9 2.5E-09 5.4E-14 62.8 4.8 68 1-69 80-148 (186)
139 smart00010 small_GTPase Small 98.9 7.2E-09 1.6E-13 57.5 6.4 57 3-62 40-96 (124)
140 KOG0073 GTP-binding ADP-ribosy 98.9 9.1E-09 2E-13 61.1 6.3 61 2-63 76-137 (185)
141 KOG4423 GTP-binding protein-li 98.9 1.7E-09 3.7E-14 65.6 2.7 55 2-57 91-149 (229)
142 cd01890 LepA LepA subfamily. 98.8 6.6E-09 1.4E-13 61.2 4.9 51 3-58 84-134 (179)
143 cd04105 SR_beta Signal recogni 98.8 1E-08 2.2E-13 62.4 5.6 57 4-61 66-127 (203)
144 KOG1707 Predicted Ras related/ 98.8 8.5E-09 1.8E-13 70.7 5.5 53 9-61 78-133 (625)
145 TIGR02528 EutP ethanolamine ut 98.8 4.8E-09 1E-13 59.8 3.4 44 6-57 59-102 (142)
146 cd01897 NOG NOG1 is a nucleola 98.8 1.4E-08 3.1E-13 59.1 5.5 52 10-62 79-132 (168)
147 cd01881 Obg_like The Obg-like 98.8 1.5E-08 3.3E-13 59.2 5.5 57 6-63 71-140 (176)
148 KOG1673 Ras GTPases [General f 98.8 1.5E-08 3.3E-13 60.1 4.9 50 4-55 87-136 (205)
149 TIGR03156 GTP_HflX GTP-binding 98.8 2.6E-08 5.7E-13 65.2 6.1 55 6-61 265-319 (351)
150 KOG0076 GTP-binding ADP-ribosy 98.7 6.3E-09 1.4E-13 62.4 1.8 65 1-66 84-149 (197)
151 TIGR02729 Obg_CgtA Obg family 98.7 2.9E-08 6.3E-13 64.6 4.7 53 10-62 235-292 (329)
152 cd00882 Ras_like_GTPase Ras-li 98.7 2.2E-07 4.7E-12 51.9 7.1 56 5-61 64-120 (157)
153 TIGR00450 mnmE_trmE_thdF tRNA 98.6 8.7E-08 1.9E-12 64.5 5.8 49 4-58 277-325 (442)
154 PRK11058 GTPase HflX; Provisio 98.6 1.1E-07 2.4E-12 63.7 6.3 51 6-57 273-323 (426)
155 KOG0074 GTP-binding ADP-ribosy 98.6 4.7E-08 1E-12 57.2 3.8 67 2-69 78-145 (185)
156 PRK12289 GTPase RsgA; Reviewed 98.6 1.1E-07 2.4E-12 62.4 5.4 54 2-59 82-136 (352)
157 cd01891 TypA_BipA TypA (tyrosi 98.5 2.5E-07 5.5E-12 55.6 5.2 52 3-59 82-133 (194)
158 cd01854 YjeQ_engC YjeQ/EngC. 98.5 3.1E-07 6.8E-12 58.7 4.6 49 6-58 75-124 (287)
159 TIGR00231 small_GTP small GTP- 98.4 6.4E-07 1.4E-11 50.6 5.1 55 4-59 68-124 (161)
160 KOG0072 GTP-binding ADP-ribosy 98.4 5.5E-07 1.2E-11 52.9 4.7 66 3-69 79-145 (182)
161 PRK05291 trmE tRNA modificatio 98.4 3.1E-07 6.8E-12 61.9 4.0 49 5-60 290-338 (449)
162 cd01879 FeoB Ferrous iron tran 98.4 9.6E-07 2.1E-11 50.7 5.3 52 4-62 67-120 (158)
163 PRK03003 GTP-binding protein D 98.4 1.1E-06 2.4E-11 59.4 6.0 47 6-57 290-336 (472)
164 cd04171 SelB SelB subfamily. 98.4 1.6E-06 3.4E-11 50.0 5.7 47 5-58 70-119 (164)
165 PRK12297 obgE GTPase CgtA; Rev 98.4 9.5E-07 2E-11 59.3 5.3 49 9-57 235-288 (424)
166 PRK03003 GTP-binding protein D 98.4 1.1E-06 2.5E-11 59.4 5.7 49 4-57 112-160 (472)
167 cd01855 YqeH YqeH. YqeH is an 98.3 8E-07 1.7E-11 53.3 3.5 49 3-58 28-76 (190)
168 COG2229 Predicted GTPase [Gene 98.3 3.1E-06 6.7E-11 51.1 5.8 63 2-68 84-146 (187)
169 cd01857 HSR1_MMR1 HSR1/MMR1. 98.3 1E-06 2.3E-11 50.7 3.7 50 9-62 10-61 (141)
170 PRK15467 ethanolamine utilizat 98.3 1.6E-06 3.5E-11 50.8 4.1 44 7-57 62-105 (158)
171 PRK00098 GTPase RsgA; Reviewed 98.2 1.5E-06 3.2E-11 55.9 3.8 46 9-57 79-125 (298)
172 PRK12288 GTPase RsgA; Reviewed 98.2 4.9E-06 1.1E-10 54.7 6.1 46 10-58 120-165 (347)
173 cd04164 trmE TrmE (MnmE, ThdF, 98.2 3.5E-06 7.6E-11 48.0 4.7 49 5-60 76-124 (157)
174 cd01887 IF2_eIF5B IF2/eIF5B (i 98.2 4.4E-06 9.6E-11 48.4 5.1 47 4-58 68-117 (168)
175 PRK12298 obgE GTPase CgtA; Rev 98.2 4.5E-06 9.7E-11 55.6 5.6 55 7-62 235-294 (390)
176 cd01885 EF2 EF2 (for archaea a 98.2 8.1E-06 1.8E-10 50.6 6.0 48 4-56 91-138 (222)
177 TIGR01393 lepA GTP-binding pro 98.1 5E-06 1.1E-10 57.9 5.1 50 4-58 88-137 (595)
178 TIGR00436 era GTP-binding prot 98.1 7.6E-06 1.6E-10 51.7 5.1 49 5-59 75-123 (270)
179 KOG0077 Vesicle coat complex C 98.1 6.2E-06 1.3E-10 49.4 4.2 60 3-63 81-141 (193)
180 TIGR03597 GTPase_YqeH ribosome 98.1 4.1E-06 8.8E-11 55.2 3.8 48 3-57 57-104 (360)
181 PRK04213 GTP-binding protein; 98.1 4.5E-07 9.8E-12 54.5 -0.7 18 42-59 129-146 (201)
182 cd01895 EngA2 EngA2 subfamily. 98.1 1.4E-05 3E-10 46.1 5.5 48 6-58 81-128 (174)
183 TIGR03594 GTPase_EngA ribosome 98.1 9.9E-06 2.2E-10 53.9 5.4 47 5-56 250-296 (429)
184 PRK12296 obgE GTPase CgtA; Rev 98.0 1E-05 2.3E-10 55.4 5.0 53 9-61 235-302 (500)
185 cd00881 GTP_translation_factor 98.0 2.2E-05 4.8E-10 46.1 5.9 50 4-58 80-129 (189)
186 TIGR00491 aIF-2 translation in 98.0 9.1E-06 2E-10 56.6 4.6 47 3-57 86-135 (590)
187 PRK09518 bifunctional cytidyla 98.0 1.8E-05 4E-10 56.1 5.8 48 6-58 529-576 (712)
188 cd01894 EngA1 EngA1 subfamily. 98.0 2.7E-05 5.9E-10 44.4 5.2 52 5-61 72-123 (157)
189 cd00066 G-alpha G protein alph 97.9 2E-05 4.3E-10 51.2 4.7 54 2-56 177-241 (317)
190 cd04169 RF3 RF3 subfamily. Pe 97.9 5.9E-05 1.3E-09 47.9 6.3 50 5-59 90-139 (267)
191 smart00275 G_alpha G protein a 97.9 3.1E-05 6.7E-10 50.8 5.0 54 2-56 200-264 (342)
192 PRK00093 GTP-binding protein D 97.9 7E-05 1.5E-09 50.1 6.7 46 5-57 76-123 (435)
193 PF09439 SRPRB: Signal recogni 97.9 4.4E-05 9.6E-10 46.2 5.2 56 6-62 72-131 (181)
194 cd04167 Snu114p Snu114p subfam 97.9 3.7E-05 8E-10 46.9 5.0 47 5-56 90-136 (213)
195 cd04168 TetM_like Tet(M)-like 97.9 3.6E-05 7.8E-10 48.1 4.9 49 4-57 82-130 (237)
196 cd00880 Era_like Era (E. coli 97.9 3.4E-05 7.3E-10 43.4 4.3 54 5-63 71-124 (163)
197 PRK15494 era GTPase Era; Provi 97.9 2.9E-05 6.3E-10 50.8 4.5 47 6-58 128-175 (339)
198 PRK05433 GTP-binding protein L 97.8 4.8E-05 1E-09 53.2 5.4 50 4-58 92-141 (600)
199 cd01859 MJ1464 MJ1464. This f 97.7 2.2E-05 4.7E-10 45.7 2.3 49 4-57 7-55 (156)
200 PRK00093 GTP-binding protein D 97.7 8.6E-05 1.9E-09 49.6 5.2 48 6-58 252-299 (435)
201 PF06858 NOG1: Nucleolar GTP-b 97.7 0.00036 7.8E-09 34.8 5.8 43 11-54 14-58 (58)
202 PRK04004 translation initiatio 97.7 9.2E-05 2E-09 51.7 5.0 45 4-56 89-136 (586)
203 TIGR00483 EF-1_alpha translati 97.7 6.1E-05 1.3E-09 50.5 3.9 50 6-57 105-155 (426)
204 CHL00189 infB translation init 97.6 7.5E-05 1.6E-09 53.4 4.2 47 3-57 312-361 (742)
205 PRK09518 bifunctional cytidyla 97.6 0.00013 2.8E-09 51.8 5.3 47 5-57 350-397 (712)
206 TIGR03594 GTPase_EngA ribosome 97.6 0.00027 5.9E-09 47.1 6.5 49 5-60 74-124 (429)
207 TIGR00437 feoB ferrous iron tr 97.6 7.3E-05 1.6E-09 52.2 3.8 47 10-62 72-118 (591)
208 cd01888 eIF2_gamma eIF2-gamma 97.6 0.0002 4.3E-09 43.5 5.1 44 9-58 105-152 (203)
209 TIGR01394 TypA_BipA GTP-bindin 97.6 0.0002 4.3E-09 50.1 5.4 50 5-59 83-132 (594)
210 cd04163 Era Era subfamily. Er 97.6 0.00016 3.4E-09 41.2 4.1 46 6-57 79-125 (168)
211 cd01858 NGP_1 NGP-1. Autoanti 97.5 0.00018 3.9E-09 41.9 4.2 48 9-60 7-56 (157)
212 TIGR00475 selB selenocysteine- 97.5 0.00029 6.3E-09 49.2 5.6 47 5-59 69-119 (581)
213 KOG1707 Predicted Ras related/ 97.5 0.00012 2.6E-09 51.0 3.6 49 10-60 495-543 (625)
214 PRK13351 elongation factor G; 97.5 0.00028 6E-09 49.9 5.4 50 4-58 91-140 (687)
215 cd01889 SelB_euk SelB subfamil 97.5 0.00047 1E-08 41.3 5.7 45 9-57 90-134 (192)
216 TIGR03598 GTPase_YsxC ribosome 97.5 0.00034 7.4E-09 41.5 4.9 49 5-58 93-144 (179)
217 PRK00089 era GTPase Era; Revie 97.5 0.00027 5.8E-09 45.0 4.6 46 6-57 81-127 (292)
218 cd01849 YlqF_related_GTPase Yl 97.5 0.00017 3.7E-09 42.0 3.4 45 12-59 1-45 (155)
219 TIGR00487 IF-2 translation ini 97.5 0.00022 4.7E-09 49.9 4.3 47 3-57 152-201 (587)
220 PRK05306 infB translation init 97.5 0.00016 3.6E-09 52.0 3.8 47 3-57 354-403 (787)
221 PRK14845 translation initiatio 97.4 0.00041 8.8E-09 51.3 5.1 46 4-57 544-592 (1049)
222 PRK12317 elongation factor 1-a 97.3 0.00048 1E-08 46.2 4.3 47 9-57 106-153 (425)
223 TIGR00503 prfC peptide chain r 97.3 0.00097 2.1E-08 46.2 5.8 48 5-57 99-146 (527)
224 PRK00741 prfC peptide chain re 97.3 0.0011 2.5E-08 45.8 5.9 50 5-59 98-147 (526)
225 PRK10218 GTP-binding protein; 97.2 0.0016 3.4E-08 45.9 6.0 51 4-59 86-136 (607)
226 KOG1489 Predicted GTP-binding 97.2 0.0015 3.3E-08 43.0 5.5 47 10-56 274-325 (366)
227 TIGR00484 EF-G translation elo 97.1 0.0017 3.6E-08 46.2 5.9 49 5-58 94-142 (689)
228 cd01856 YlqF YlqF. Proteins o 97.0 0.00051 1.1E-08 40.6 2.4 44 9-58 18-61 (171)
229 PRK09554 feoB ferrous iron tra 97.0 0.002 4.3E-08 46.5 5.6 47 10-62 85-131 (772)
230 COG2262 HflX GTPases [General 97.0 0.0034 7.4E-08 42.2 6.4 49 9-57 270-318 (411)
231 cd01896 DRG The developmentall 97.0 0.0024 5.2E-08 39.8 5.1 26 5-31 73-99 (233)
232 cd01883 EF1_alpha Eukaryotic e 97.0 0.002 4.3E-08 39.6 4.7 46 9-57 99-151 (219)
233 PRK04000 translation initiatio 96.9 0.0038 8.2E-08 42.0 6.0 43 10-58 108-154 (411)
234 cd04166 CysN_ATPS CysN_ATPS su 96.9 0.004 8.8E-08 37.9 5.5 48 6-57 97-144 (208)
235 cd04170 EF-G_bact Elongation f 96.9 0.0034 7.4E-08 39.6 5.3 49 5-58 83-131 (268)
236 cd01886 EF-G Elongation factor 96.9 0.0053 1.2E-07 39.1 6.2 49 5-58 83-131 (270)
237 PF00009 GTP_EFTU: Elongation 96.9 0.0069 1.5E-07 36.2 6.2 44 9-56 92-135 (188)
238 cd01876 YihA_EngB The YihA (En 96.8 0.0048 1E-07 35.1 5.2 41 11-57 82-124 (170)
239 cd04104 p47_IIGP_like p47 (47- 96.8 0.0017 3.6E-08 39.3 3.4 42 7-56 78-120 (197)
240 TIGR03596 GTPase_YlqF ribosome 96.8 0.0013 2.8E-08 41.9 2.7 44 9-58 20-63 (276)
241 TIGR03680 eif2g_arch translati 96.7 0.0039 8.5E-08 41.8 4.8 44 9-58 102-149 (406)
242 PRK13796 GTPase YqeH; Provisio 96.7 0.0041 9E-08 41.2 4.8 42 10-57 68-110 (365)
243 PRK12740 elongation factor G; 96.6 0.0054 1.2E-07 43.4 5.2 49 5-58 79-127 (668)
244 PRK00454 engB GTP-binding prot 96.6 0.0053 1.2E-07 36.4 4.6 47 5-58 99-150 (196)
245 cd04178 Nucleostemin_like Nucl 96.6 0.003 6.6E-08 37.7 3.2 53 12-66 1-53 (172)
246 PLN00043 elongation factor 1-a 96.4 0.0015 3.3E-08 44.4 1.4 49 6-56 105-158 (447)
247 PRK09563 rbgA GTPase YlqF; Rev 96.4 0.003 6.5E-08 40.5 2.7 44 9-58 23-66 (287)
248 cd04165 GTPBP1_like GTPBP1-lik 96.3 0.019 4E-07 35.7 5.7 45 10-58 109-153 (224)
249 PF04670 Gtr1_RagA: Gtr1/RagA 96.3 0.018 3.9E-07 36.2 5.5 52 4-57 71-125 (232)
250 COG1084 Predicted GTPase [Gene 96.3 0.015 3.3E-07 38.4 5.3 53 11-65 248-302 (346)
251 PRK01889 GTPase RsgA; Reviewed 96.3 0.018 3.9E-07 38.2 5.6 47 9-58 111-157 (356)
252 PRK10512 selenocysteinyl-tRNA- 96.2 0.019 4.1E-07 40.6 6.0 43 9-58 73-119 (614)
253 PRK13768 GTPase; Provisional 96.2 0.011 2.4E-07 37.3 4.2 50 11-61 129-180 (253)
254 TIGR00485 EF-Tu translation el 96.2 0.023 5E-07 37.9 5.8 43 9-58 97-143 (394)
255 COG1160 Predicted GTPases [Gen 95.9 0.042 9.2E-07 37.6 6.1 44 9-58 82-127 (444)
256 PRK12736 elongation factor Tu; 95.9 0.038 8.2E-07 37.0 5.8 45 9-57 97-142 (394)
257 KOG4273 Uncharacterized conser 95.8 0.007 1.5E-07 39.1 2.0 45 11-57 79-123 (418)
258 PRK09866 hypothetical protein; 95.7 0.037 8.1E-07 39.8 5.6 47 9-57 257-303 (741)
259 cd01884 EF_Tu EF-Tu subfamily. 95.7 0.066 1.4E-06 32.5 6.1 45 9-57 87-132 (195)
260 COG0486 ThdF Predicted GTPase 95.6 0.029 6.2E-07 38.5 4.5 46 9-60 295-341 (454)
261 cd01850 CDC_Septin CDC/Septin. 95.6 0.015 3.4E-07 37.1 3.1 16 42-57 142-157 (276)
262 TIGR00490 aEF-2 translation el 95.4 0.03 6.6E-07 40.2 4.3 48 5-57 105-152 (720)
263 KOG0090 Signal recognition par 95.3 0.11 2.4E-06 32.6 6.1 53 10-62 108-164 (238)
264 PF02421 FeoB_N: Ferrous iron 95.3 0.042 9.1E-07 32.6 4.1 57 9-71 77-137 (156)
265 COG0536 Obg Predicted GTPase [ 95.3 0.075 1.6E-06 35.4 5.5 49 10-58 237-290 (369)
266 PRK12739 elongation factor G; 95.3 0.07 1.5E-06 38.2 5.8 48 6-58 93-140 (691)
267 KOG3886 GTP-binding protein [S 94.9 0.18 4E-06 32.3 6.3 53 4-58 76-131 (295)
268 PF01926 MMR_HSR1: 50S ribosom 94.9 0.22 4.8E-06 27.2 6.0 37 9-52 78-116 (116)
269 PF00503 G-alpha: G-protein al 94.9 0.046 1E-06 36.4 3.7 52 3-55 253-315 (389)
270 KOG0082 G-protein alpha subuni 94.7 0.086 1.9E-06 35.2 4.6 54 3-57 212-276 (354)
271 PRK12735 elongation factor Tu; 94.7 0.18 3.9E-06 33.8 6.1 45 9-57 97-142 (396)
272 PRK00007 elongation factor G; 94.3 0.19 4.1E-06 36.1 5.9 46 9-58 97-142 (693)
273 PLN03126 Elongation factor Tu; 94.1 0.2 4.4E-06 34.6 5.6 45 9-57 166-211 (478)
274 CHL00071 tufA elongation facto 93.9 0.25 5.3E-06 33.3 5.6 45 9-57 97-142 (409)
275 COG1159 Era GTPase [General fu 93.9 0.3 6.5E-06 31.9 5.7 47 9-60 84-131 (298)
276 PTZ00416 elongation factor 2; 93.9 0.14 3.1E-06 37.5 4.7 44 9-56 114-157 (836)
277 PLN00116 translation elongatio 93.8 0.18 3.9E-06 37.0 5.0 44 9-56 120-163 (843)
278 PTZ00327 eukaryotic translatio 93.7 0.23 4.9E-06 34.2 5.2 47 9-57 139-185 (460)
279 cd03110 Fer4_NifH_child This p 93.7 0.51 1.1E-05 27.8 6.2 45 9-57 113-157 (179)
280 COG0532 InfB Translation initi 93.6 0.3 6.4E-06 34.1 5.6 41 10-57 78-121 (509)
281 PRK00049 elongation factor Tu; 93.5 0.34 7.4E-06 32.5 5.7 45 9-57 97-142 (396)
282 PF14331 ImcF-related_N: ImcF- 93.2 0.36 7.8E-06 30.8 5.3 49 9-57 24-83 (266)
283 KOG1424 Predicted GTP-binding 93.1 0.11 2.5E-06 36.3 3.0 57 10-68 174-230 (562)
284 TIGR03348 VI_IcmF type VI secr 93.0 0.24 5.2E-06 37.6 4.7 48 9-56 200-256 (1169)
285 PLN03127 Elongation factor Tu; 92.8 0.38 8.2E-06 33.0 5.1 45 9-57 146-191 (447)
286 KOG1490 GTP-binding protein CR 92.7 0.32 7E-06 34.3 4.7 51 13-64 250-302 (620)
287 TIGR02034 CysN sulfate adenyly 92.7 0.29 6.2E-06 33.0 4.4 46 9-57 102-147 (406)
288 KOG0468 U5 snRNP-specific prot 92.6 0.2 4.3E-06 36.5 3.7 43 9-55 219-261 (971)
289 PRK07560 elongation factor EF- 92.5 0.27 5.8E-06 35.6 4.3 44 9-56 109-152 (731)
290 COG1161 Predicted GTPases [Gen 92.2 0.096 2.1E-06 34.3 1.7 52 9-66 33-84 (322)
291 PF00350 Dynamin_N: Dynamin fa 92.2 0.55 1.2E-05 27.1 4.8 47 3-53 122-168 (168)
292 KOG0705 GTPase-activating prot 91.7 0.16 3.4E-06 36.2 2.3 51 5-56 91-142 (749)
293 PRK05124 cysN sulfate adenylyl 91.7 0.4 8.7E-06 33.0 4.3 46 9-57 129-174 (474)
294 PRK05506 bifunctional sulfate 91.4 0.46 1E-05 33.8 4.4 46 9-57 126-171 (632)
295 PF10662 PduV-EutP: Ethanolami 91.3 0.32 6.9E-06 28.5 3.0 48 10-64 63-111 (143)
296 KOG0462 Elongation factor-type 90.9 1.3 2.9E-05 31.6 6.1 47 9-59 147-193 (650)
297 COG4963 CpaE Flp pilus assembl 90.4 2.2 4.7E-05 28.8 6.6 63 5-69 235-297 (366)
298 TIGR00101 ureG urease accessor 90.3 0.29 6.2E-06 29.9 2.4 38 10-57 112-151 (199)
299 smart00053 DYNc Dynamin, GTPas 90.3 1.1 2.3E-05 28.4 4.9 49 4-57 156-206 (240)
300 cd01882 BMS1 Bms1. Bms1 is an 90.2 1.1 2.4E-05 27.7 5.0 45 9-57 102-147 (225)
301 COG1162 Predicted GTPases [Gen 89.7 2.1 4.6E-05 28.1 6.0 49 10-61 79-128 (301)
302 KOG2484 GTPase [General functi 89.4 0.6 1.3E-05 31.9 3.5 53 10-66 146-200 (435)
303 COG1149 MinD superfamily P-loo 89.3 3 6.4E-05 27.2 6.4 57 9-70 184-240 (284)
304 KOG1423 Ras-like GTPase ERA [C 88.9 0.36 7.9E-06 32.1 2.2 46 9-57 154-199 (379)
305 cd02067 B12-binding B12 bindin 88.5 1.8 3.9E-05 23.9 4.6 40 14-53 52-91 (119)
306 KOG1191 Mitochondrial GTPase [ 87.9 0.78 1.7E-05 32.1 3.3 50 9-58 347-404 (531)
307 KOG1145 Mitochondrial translat 87.4 2.2 4.8E-05 30.6 5.2 42 9-57 223-267 (683)
308 PF03709 OKR_DC_1_N: Orn/Lys/A 86.8 2.6 5.7E-05 23.4 4.6 40 10-53 38-77 (115)
309 KOG1954 Endocytosis/signaling 85.9 1 2.2E-05 31.0 2.9 53 9-64 180-232 (532)
310 COG3640 CooC CO dehydrogenase 85.7 5.3 0.00011 25.7 5.9 45 9-56 154-198 (255)
311 COG0218 Predicted GTPase [Gene 85.3 3.6 7.8E-05 25.5 4.9 44 11-58 107-150 (200)
312 COG1160 Predicted GTPases [Gen 85.2 7.2 0.00016 27.1 6.7 46 9-58 259-304 (444)
313 COG0480 FusA Translation elong 84.6 1.8 4E-05 31.5 3.9 45 9-57 98-142 (697)
314 PF14784 ECIST_Cterm: C-termin 83.7 3.4 7.3E-05 23.8 4.1 38 11-48 84-123 (126)
315 COG3523 IcmF Type VI protein s 83.4 2.9 6.3E-05 32.3 4.6 49 9-57 213-270 (1188)
316 PF08468 MTS_N: Methyltransfer 83.4 5.5 0.00012 23.6 5.0 51 10-66 69-119 (155)
317 cd02071 MM_CoA_mut_B12_BD meth 82.0 6.9 0.00015 21.8 5.0 42 10-53 50-91 (122)
318 COG0481 LepA Membrane GTPase L 79.3 10 0.00023 27.0 5.8 46 9-58 98-143 (603)
319 KOG2423 Nucleolar GTPase [Gene 79.2 4.9 0.00011 28.0 4.2 50 9-60 212-261 (572)
320 COG2813 RsmC 16S RNA G1207 met 79.2 8.1 0.00018 25.5 5.1 54 9-68 36-89 (300)
321 COG1010 CobJ Precorrin-3B meth 78.9 8.5 0.00018 24.7 4.9 44 10-53 154-197 (249)
322 KOG3929 Uncharacterized conser 78.5 6.4 0.00014 25.9 4.4 14 43-56 190-203 (363)
323 PRK09435 membrane ATPase/prote 78.2 7.8 0.00017 25.8 4.9 42 9-58 168-209 (332)
324 TIGR00073 hypB hydrogenase acc 78.0 3.2 6.9E-05 25.2 2.9 15 44-58 149-163 (207)
325 cd01852 AIG1 AIG1 (avrRpt2-ind 78.0 12 0.00026 22.3 6.4 47 9-57 82-130 (196)
326 PRK04017 hypothetical protein; 77.2 6.9 0.00015 22.7 3.9 32 23-55 3-34 (132)
327 PTZ00141 elongation factor 1- 77.2 10 0.00022 26.1 5.4 43 9-55 107-157 (446)
328 PF10551 MULE: MULE transposas 77.1 6.9 0.00015 20.3 3.8 39 12-51 25-63 (93)
329 TIGR00750 lao LAO/AO transport 77.0 5 0.00011 25.9 3.7 43 9-59 146-188 (300)
330 COG0050 TufB GTPases - transla 77.0 6.6 0.00014 26.3 4.2 45 10-61 98-146 (394)
331 cd03111 CpaE_like This protein 76.8 9.8 0.00021 20.6 5.2 43 9-52 63-106 (106)
332 PF10995 DUF2819: Protein of u 76.6 12 0.00026 24.9 5.3 48 9-56 102-149 (316)
333 TIGR02836 spore_IV_A stage IV 75.5 9.9 0.00021 26.7 4.9 43 10-55 144-192 (492)
334 COG1163 DRG Predicted GTPase [ 74.1 9.5 0.0002 25.8 4.4 28 9-36 139-167 (365)
335 PRK13505 formate--tetrahydrofo 74.1 7.4 0.00016 27.8 4.1 33 26-61 358-390 (557)
336 COG4502 5'(3')-deoxyribonucleo 70.5 14 0.00031 22.1 4.2 41 12-53 85-125 (180)
337 KOG1532 GTPase XAB1, interacts 70.2 6.9 0.00015 26.0 3.1 18 42-59 180-197 (366)
338 PRK14719 bifunctional RNAse/5- 69.8 9.5 0.0002 25.7 3.8 34 21-55 2-35 (360)
339 KOG0447 Dynamin-like GTP bindi 69.7 11 0.00024 27.6 4.1 68 2-73 441-511 (980)
340 COG0523 Putative GTPases (G3E 69.5 15 0.00033 24.3 4.6 48 10-62 116-164 (323)
341 cd03112 CobW_like The function 69.1 14 0.00031 21.5 4.1 40 10-55 118-158 (158)
342 KOG0099 G protein subunit Galp 68.6 8.8 0.00019 25.4 3.3 51 5-56 221-282 (379)
343 PRK09489 rsmC 16S ribosomal RN 68.6 22 0.00048 23.7 5.3 42 10-55 76-117 (342)
344 cd02038 FleN-like FleN is a me 67.7 20 0.00044 20.3 5.3 45 9-55 65-109 (139)
345 PF03029 ATP_bind_1: Conserved 67.6 5.7 0.00012 25.0 2.3 44 12-57 124-170 (238)
346 KOG1144 Translation initiation 67.5 8.3 0.00018 29.0 3.3 40 9-55 562-604 (1064)
347 TIGR03369 cellulose_bcsE cellu 67.5 24 0.00052 23.6 5.2 48 9-56 107-154 (322)
348 TIGR03677 rpl7ae 50S ribosomal 66.8 8.2 0.00018 21.7 2.6 40 11-56 43-82 (117)
349 KOG2485 Conserved ATP/GTP bind 66.6 15 0.00032 24.7 4.0 48 9-62 45-92 (335)
350 COG5256 TEF1 Translation elong 66.6 15 0.00032 25.5 4.1 49 9-59 107-161 (428)
351 PRK02261 methylaspartate mutas 66.3 22 0.00048 20.4 4.4 40 10-51 54-93 (137)
352 PF01656 CbiA: CobQ/CobB/MinD/ 64.3 16 0.00034 21.3 3.7 53 9-62 115-167 (195)
353 PF09827 CRISPR_Cas2: CRISPR a 64.3 11 0.00023 19.3 2.6 25 13-37 3-27 (78)
354 COG5257 GCD11 Translation init 62.3 12 0.00025 25.5 3.0 44 12-57 111-154 (415)
355 PRK06756 flavodoxin; Provision 60.7 29 0.00063 19.7 4.3 43 9-51 48-91 (148)
356 PF10087 DUF2325: Uncharacteri 60.0 25 0.00054 18.7 5.0 35 9-49 47-81 (97)
357 PRK15478 cbiH cobalt-precorrin 59.8 41 0.0009 21.2 5.5 45 9-53 150-194 (241)
358 cd02117 NifH_like This family 59.7 37 0.0008 20.5 6.0 44 10-56 141-188 (212)
359 cd07379 MPP_239FB Homo sapiens 58.6 28 0.00062 19.4 3.9 45 9-55 18-62 (135)
360 PF11111 CENP-M: Centromere pr 58.5 34 0.00075 20.9 4.4 28 10-37 64-91 (176)
361 PRK15045 cellulose biosynthesi 58.2 41 0.00089 24.0 5.2 48 9-56 255-302 (519)
362 COG1358 RPL8A Ribosomal protei 57.6 15 0.00033 20.8 2.6 42 10-57 43-84 (116)
363 TIGR02370 pyl_corrinoid methyl 57.5 38 0.00083 20.6 4.6 38 15-52 138-176 (197)
364 cd05295 MDH_like Malate dehydr 57.4 28 0.00061 24.3 4.3 48 7-55 197-255 (452)
365 PRK04175 rpl7ae 50S ribosomal 57.2 15 0.00033 20.8 2.6 40 11-56 47-86 (122)
366 cd01832 SGNH_hydrolase_like_1 57.2 36 0.00078 19.7 4.6 39 10-51 67-113 (185)
367 PF05783 DLIC: Dynein light in 57.1 24 0.00051 24.8 3.9 25 12-36 102-127 (472)
368 PF02492 cobW: CobW/HypB/UreG, 56.1 24 0.00052 20.8 3.5 44 10-59 113-157 (178)
369 cd05294 LDH-like_MDH_nadp A la 54.7 46 0.00099 21.7 4.8 47 7-55 70-126 (309)
370 PRK15029 arginine decarboxylas 53.3 37 0.0008 25.3 4.5 44 10-54 53-96 (755)
371 COG2895 CysN GTPases - Sulfate 52.6 72 0.0016 22.1 5.5 48 10-60 109-156 (431)
372 cd02070 corrinoid_protein_B12- 52.5 50 0.0011 20.0 4.5 38 15-52 136-174 (201)
373 PF13124 DUF3963: Protein of u 52.2 17 0.00037 16.3 1.8 15 23-37 10-24 (40)
374 cd01844 SGNH_hydrolase_like_6 51.9 46 0.001 19.3 5.6 43 10-53 57-103 (177)
375 TIGR01753 flav_short flavodoxi 51.4 41 0.00088 18.5 4.0 43 9-51 44-88 (140)
376 cd01339 LDH-like_MDH L-lactate 51.2 45 0.00098 21.5 4.4 46 9-55 65-120 (300)
377 TIGR01757 Malate-DH_plant mala 50.3 32 0.00069 23.5 3.7 47 9-55 119-175 (387)
378 KOG0458 Elongation factor 1 al 50.2 70 0.0015 23.3 5.3 47 10-59 278-331 (603)
379 PF00072 Response_reg: Respons 49.7 37 0.0008 17.6 3.8 39 11-54 44-82 (112)
380 cd01338 MDH_choloroplast_like 49.4 47 0.001 21.9 4.3 47 9-55 77-133 (322)
381 PRK13660 hypothetical protein; 49.2 55 0.0012 20.0 4.2 38 9-49 128-166 (182)
382 KOG3905 Dynein light intermedi 49.0 40 0.00086 23.2 3.9 26 13-38 130-156 (473)
383 COG0370 FeoB Fe2+ transport sy 48.8 55 0.0012 24.1 4.7 56 10-71 81-140 (653)
384 PRK13185 chlL protochlorophyll 48.7 66 0.0014 20.1 5.4 45 9-54 139-185 (270)
385 PRK05569 flavodoxin; Provision 48.5 48 0.001 18.5 3.9 44 9-52 47-92 (141)
386 COG4917 EutP Ethanolamine util 47.6 17 0.00038 21.3 1.8 19 44-62 91-109 (148)
387 cd01853 Toc34_like Toc34-like 47.6 71 0.0015 20.2 5.2 46 10-56 114-162 (249)
388 PRK15001 SAM-dependent 23S rib 47.4 89 0.0019 21.3 5.8 43 9-55 105-147 (378)
389 KOG1496 Malate dehydrogenase [ 47.1 42 0.00092 22.0 3.6 49 6-55 77-135 (332)
390 PF00701 DHDPS: Dihydrodipicol 46.6 65 0.0014 20.6 4.6 41 9-51 95-135 (289)
391 COG5258 GTPBP1 GTPase [General 46.5 17 0.00037 25.4 1.9 20 43-62 255-274 (527)
392 PHA02763 hypothetical protein; 46.4 24 0.00051 19.2 2.1 18 23-40 64-81 (102)
393 TIGR01756 LDH_protist lactate 46.3 27 0.0006 23.0 2.8 47 9-55 59-115 (313)
394 cd08166 MPP_Cdc1_like_1 unchar 45.7 21 0.00045 22.0 2.1 47 10-57 42-94 (195)
395 PF06490 FleQ: Flagellar regul 45.1 53 0.0011 18.0 4.6 25 30-55 57-81 (109)
396 cd01899 Ygr210 Ygr210 subfamil 43.9 17 0.00037 24.0 1.6 16 6-22 96-111 (318)
397 cd00300 LDH_like L-lactate deh 43.7 41 0.00088 21.8 3.3 46 9-55 65-120 (300)
398 cd00704 MDH Malate dehydrogena 43.4 64 0.0014 21.3 4.2 47 9-55 75-131 (323)
399 cd01611 GABARAP Ubiquitin doma 43.3 48 0.001 18.5 3.2 33 23-55 4-37 (112)
400 COG4108 PrfC Peptide chain rel 42.2 72 0.0016 22.7 4.4 43 10-57 104-147 (528)
401 cd07393 MPP_DR1119 Deinococcus 42.0 68 0.0015 19.8 4.0 40 10-51 41-80 (232)
402 PF00056 Ldh_1_N: lactate/mala 41.8 51 0.0011 18.8 3.3 46 9-55 68-123 (141)
403 cd02069 methionine_synthase_B1 41.4 86 0.0019 19.4 4.4 37 14-51 141-177 (213)
404 PF08438 MMR_HSR1_C: GTPase of 41.2 7.5 0.00016 21.8 -0.3 19 49-67 1-20 (109)
405 cd05292 LDH_2 A subgroup of L- 40.7 57 0.0012 21.2 3.7 46 9-55 66-121 (308)
406 PTZ00380 microtubule-associate 40.6 57 0.0012 18.7 3.2 27 23-49 7-33 (121)
407 TIGR01759 MalateDH-SF1 malate 40.4 83 0.0018 20.8 4.4 47 9-55 78-134 (323)
408 PF12327 FtsZ_C: FtsZ family, 40.4 61 0.0013 17.4 5.0 47 6-54 32-78 (95)
409 COG0420 SbcD DNA repair exonuc 40.3 69 0.0015 21.4 4.1 47 10-56 40-88 (390)
410 TIGR01771 L-LDH-NAD L-lactate 40.3 50 0.0011 21.5 3.3 46 9-55 63-118 (299)
411 PLN00135 malate dehydrogenase 40.1 91 0.002 20.6 4.5 47 9-55 57-113 (309)
412 PRK13602 putative ribosomal pr 39.9 35 0.00075 17.9 2.2 15 42-56 52-66 (82)
413 PF00319 SRF-TF: SRF-type tran 39.7 34 0.00073 16.4 1.9 14 9-22 31-44 (51)
414 COG1217 TypA Predicted membran 39.4 67 0.0015 23.1 3.9 48 9-60 90-137 (603)
415 KOG1143 Predicted translation 39.4 31 0.00066 24.2 2.3 21 42-62 302-322 (591)
416 KOG0460 Mitochondrial translat 39.3 97 0.0021 21.5 4.5 49 10-61 140-188 (449)
417 PLN00112 malate dehydrogenase 38.8 58 0.0013 22.7 3.6 47 9-55 175-231 (444)
418 TIGR00991 3a0901s02IAP34 GTP-b 38.8 1.2E+02 0.0026 20.3 5.3 46 10-56 118-166 (313)
419 cd05291 HicDH_like L-2-hydroxy 38.7 78 0.0017 20.5 4.0 46 9-55 67-122 (306)
420 PF02310 B12-binding: B12 bind 38.6 66 0.0014 17.3 5.0 35 16-51 55-89 (121)
421 cd00954 NAL N-Acetylneuraminic 38.2 86 0.0019 20.1 4.2 39 10-49 96-134 (288)
422 COG4328 Predicted nuclease (RN 37.8 57 0.0012 21.0 3.1 31 10-40 22-52 (266)
423 PRK11148 cyclic 3',5'-adenosin 37.6 66 0.0014 20.4 3.5 40 10-52 55-95 (275)
424 TIGR03566 FMN_reduc_MsuE FMN r 37.6 70 0.0015 18.8 3.5 40 9-51 67-109 (174)
425 cd00945 Aldolase_Class_I Class 37.0 69 0.0015 18.6 3.4 42 10-51 78-121 (201)
426 PRK06242 flavodoxin; Provision 36.9 80 0.0017 17.7 4.4 42 9-52 42-83 (150)
427 TIGR02313 HpaI-NOT-DapA 2,4-di 36.9 81 0.0017 20.4 3.9 46 10-56 95-144 (294)
428 PRK01018 50S ribosomal protein 36.7 52 0.0011 17.8 2.6 39 11-56 33-72 (99)
429 PF04684 BAF1_ABF1: BAF1 / ABF 36.4 19 0.00041 25.3 1.0 26 23-48 25-51 (496)
430 cd05293 LDH_1 A subgroup of L- 35.9 39 0.00083 22.2 2.3 46 9-55 70-125 (312)
431 TIGR00683 nanA N-acetylneurami 35.7 1E+02 0.0022 19.9 4.2 39 10-49 96-134 (290)
432 PRK07308 flavodoxin; Validated 35.2 88 0.0019 17.7 4.4 43 9-51 47-90 (146)
433 PF08309 LVIVD: LVIVD repeat; 34.8 30 0.00064 15.8 1.2 13 13-25 21-33 (42)
434 KOG0085 G protein subunit Galp 34.7 85 0.0019 20.6 3.6 18 42-59 265-282 (359)
435 cd00650 LDH_MDH_like NAD-depen 34.6 69 0.0015 20.2 3.3 46 9-55 69-124 (263)
436 PF00532 Peripla_BP_1: Peripla 34.5 1.1E+02 0.0025 19.3 4.3 38 9-56 55-92 (279)
437 COG0329 DapA Dihydrodipicolina 34.4 92 0.002 20.3 3.9 38 10-49 99-136 (299)
438 COG2179 Predicted hydrolase of 33.7 70 0.0015 19.6 3.0 29 22-53 44-72 (175)
439 KOG0448 Mitofusin 1 GTPase, in 33.5 1.6E+02 0.0036 22.1 5.2 45 9-57 231-275 (749)
440 TIGR00640 acid_CoA_mut_C methy 32.6 1E+02 0.0022 17.6 5.0 39 15-53 56-94 (132)
441 TIGR01758 MDH_euk_cyt malate d 32.4 1.2E+02 0.0025 20.1 4.1 47 9-55 74-130 (324)
442 PTZ00222 60S ribosomal protein 32.3 52 0.0011 21.4 2.4 41 10-56 148-188 (263)
443 PRK06223 malate dehydrogenase; 32.3 94 0.002 20.0 3.7 46 9-55 69-124 (307)
444 KOG2455 Delta-1-pyrroline-5-ca 31.5 66 0.0014 22.9 2.9 37 19-58 387-423 (561)
445 cd01840 SGNH_hydrolase_yrhL_li 31.5 1E+02 0.0022 17.4 4.9 39 10-52 50-88 (150)
446 PRK05442 malate dehydrogenase; 31.3 1.6E+02 0.0035 19.6 5.1 47 9-55 79-135 (326)
447 cd00952 CHBPH_aldolase Trans-o 31.2 1.1E+02 0.0024 19.9 3.9 39 10-49 103-141 (309)
448 PTZ00082 L-lactate dehydrogena 31.2 1E+02 0.0022 20.4 3.7 46 9-55 73-133 (321)
449 TIGR01573 cas2 CRISPR-associat 31.1 91 0.002 16.6 3.6 10 14-23 3-12 (95)
450 TIGR02475 CobW cobalamin biosy 31.0 30 0.00066 23.0 1.3 19 47-65 177-195 (341)
451 PF05193 Peptidase_M16_C: Pept 30.9 68 0.0015 17.9 2.6 27 25-53 3-29 (184)
452 TIGR01303 IMP_DH_rel_1 IMP deh 30.7 1.5E+02 0.0032 20.9 4.5 41 10-55 237-277 (475)
453 PF11176 DUF2962: Protein of u 30.6 47 0.001 19.7 1.9 18 15-32 121-138 (155)
454 KOG0467 Translation elongation 30.4 1.1E+02 0.0023 23.4 3.9 38 9-54 94-135 (887)
455 PRK00066 ldh L-lactate dehydro 30.3 64 0.0014 21.2 2.7 46 9-55 72-127 (315)
456 TIGR00381 cdhD CO dehydrogenas 30.2 84 0.0018 21.7 3.2 43 10-52 153-197 (389)
457 KOG1752 Glutaredoxin and relat 30.0 97 0.0021 17.1 3.0 35 17-53 43-77 (104)
458 PRK13601 putative L7Ae-like ri 30.0 75 0.0016 16.7 2.4 15 42-56 49-63 (82)
459 PHA02518 ParA-like protein; Pr 29.6 1.3E+02 0.0027 17.8 5.6 45 9-55 97-145 (211)
460 TIGR01763 MalateDH_bact malate 29.5 1.7E+02 0.0036 19.1 4.5 46 9-55 68-123 (305)
461 cd06299 PBP1_LacI_like_13 Liga 29.3 1.3E+02 0.0028 18.1 3.8 12 42-53 77-88 (265)
462 PRK12399 tagatose 1,6-diphosph 29.2 1.4E+02 0.0031 20.1 4.1 40 10-49 118-161 (324)
463 TIGR01007 eps_fam capsular exo 29.1 1.3E+02 0.0029 17.9 6.0 46 9-57 149-194 (204)
464 PHA03050 glutaredoxin; Provisi 29.1 89 0.0019 17.1 2.8 37 15-53 43-79 (108)
465 PF00462 Glutaredoxin: Glutare 28.9 73 0.0016 14.9 2.3 11 42-52 48-58 (60)
466 KOG2733 Uncharacterized membra 28.9 63 0.0014 22.4 2.4 18 12-29 63-80 (423)
467 COG1343 CRISPR-associated prot 28.5 1.1E+02 0.0023 16.6 3.5 11 14-24 3-13 (89)
468 TIGR03371 cellulose_yhjQ cellu 28.1 1.5E+02 0.0032 18.1 5.1 47 9-56 135-181 (246)
469 PRK04161 tagatose 1,6-diphosph 27.8 1.6E+02 0.0034 19.9 4.1 40 10-49 120-163 (329)
470 PF13788 DUF4180: Domain of un 27.7 99 0.0022 17.5 2.8 46 5-51 31-77 (113)
471 COG0012 Predicted GTPase, prob 27.2 66 0.0014 22.0 2.3 17 42-58 205-221 (372)
472 PF14606 Lipase_GDSL_3: GDSL-l 27.1 1.5E+02 0.0033 18.0 5.0 40 10-50 59-100 (178)
473 KOG1036 Mitotic spindle checkp 26.8 50 0.0011 22.1 1.7 24 9-32 250-273 (323)
474 PRK09602 translation-associate 26.8 95 0.0021 21.2 3.1 14 7-21 100-113 (396)
475 TIGR03567 FMN_reduc_SsuE FMN r 26.6 1.1E+02 0.0024 17.9 3.0 10 9-18 64-73 (171)
476 COG1660 Predicted P-loop-conta 26.6 2E+02 0.0043 19.1 5.1 29 12-40 52-80 (286)
477 TIGR01232 lacD tagatose 1,6-di 26.4 1.7E+02 0.0038 19.7 4.1 45 10-54 119-167 (325)
478 cd02037 MRP-like MRP (Multiple 26.3 1.4E+02 0.003 17.2 5.9 43 10-55 91-133 (169)
479 TIGR03249 KdgD 5-dehydro-4-deo 26.1 1.4E+02 0.0031 19.2 3.7 39 9-49 98-136 (296)
480 cd02036 MinD Bacterial cell di 25.9 1.4E+02 0.003 17.0 6.6 46 9-57 83-128 (179)
481 cd02032 Bchl_like This family 25.9 1.7E+02 0.0038 18.2 5.2 46 9-55 137-184 (267)
482 KOG0463 GTP-binding protein GP 25.8 40 0.00087 23.6 1.2 17 42-58 272-288 (641)
483 COG0252 AnsB L-asparaginase/ar 25.7 1.7E+02 0.0037 19.8 4.0 39 11-55 101-139 (351)
484 PF10923 DUF2791: P-loop Domai 25.6 1.9E+02 0.0042 20.1 4.3 46 10-55 237-293 (416)
485 TIGR01772 MDH_euk_gproteo mala 25.5 2.1E+02 0.0045 18.9 4.9 48 6-55 64-121 (312)
486 PRK11340 phosphodiesterase Yae 25.4 1.1E+02 0.0025 19.4 3.1 42 10-52 80-122 (271)
487 PF08630 Dfp1_Him1_M: Dfp1/Him 25.1 24 0.00052 20.3 0.0 25 5-32 74-98 (125)
488 smart00432 MADS MADS domain. 25.1 78 0.0017 15.6 1.9 15 9-23 38-52 (59)
489 PRK06843 inosine 5-monophospha 25.1 2.1E+02 0.0045 19.9 4.4 36 15-53 168-203 (404)
490 PLN00106 malate dehydrogenase 25.0 2.2E+02 0.0047 19.0 5.2 46 7-54 84-139 (323)
491 PRK10569 NAD(P)H-dependent FMN 24.9 1.3E+02 0.0028 18.2 3.2 41 9-52 65-108 (191)
492 PF00975 Thioesterase: Thioest 24.8 1.3E+02 0.0028 17.9 3.2 27 24-51 46-73 (229)
493 cd01833 XynB_like SGNH_hydrola 24.6 1.4E+02 0.003 16.7 5.4 40 10-50 40-86 (157)
494 KOG0466 Translation initiation 24.5 41 0.00089 22.9 1.0 19 44-62 180-198 (466)
495 PF00158 Sigma54_activat: Sigm 24.3 1.6E+02 0.0034 17.4 3.4 21 31-51 10-30 (168)
496 PF01653 DNA_ligase_aden: NAD- 24.2 69 0.0015 21.2 2.0 39 16-54 78-116 (315)
497 cd02042 ParA ParA and ParB of 24.0 1.2E+02 0.0026 15.7 5.1 25 9-34 60-84 (104)
498 PF09419 PGP_phosphatase: Mito 23.9 1.8E+02 0.0038 17.6 4.7 44 10-54 38-88 (168)
499 PF13692 Glyco_trans_1_4: Glyc 23.9 1.3E+02 0.0029 16.1 4.9 32 22-54 13-45 (135)
500 COG3967 DltE Short-chain dehyd 23.8 1E+02 0.0022 19.8 2.5 23 13-35 52-74 (245)
No 1
>KOG0084 consensus GTPase Rab1/YPT1, small G protein superfamily, and related GTP-binding proteins [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.90 E-value=3.8e-24 Score=128.56 Aligned_cols=70 Identities=36% Similarity=0.625 Sum_probs=63.6
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhccCc
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSLSGL 71 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~~~ 71 (78)
|++++|| |+|||+|+|||+|+++||+++..|+.++.++..+++|++|||||+|+.+.+.|+...++..+.
T Consensus 73 tit~syY-R~ahGii~vyDiT~~~SF~~v~~Wi~Ei~~~~~~~v~~lLVGNK~Dl~~~~~v~~~~a~~fa~ 142 (205)
T KOG0084|consen 73 TITSSYY-RGAHGIIFVYDITKQESFNNVKRWIQEIDRYASENVPKLLVGNKCDLTEKRVVSTEEAQEFAD 142 (205)
T ss_pred hhhHhhc-cCCCeEEEEEEcccHHHhhhHHHHHHHhhhhccCCCCeEEEeeccccHhheecCHHHHHHHHH
Confidence 4678999 999999999999999999999999999999998889999999999999999999776654443
No 2
>KOG0078 consensus GTP-binding protein SEC4, small G protein superfamily, and related Ras family GTP-binding proteins [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.89 E-value=6.2e-24 Score=128.59 Aligned_cols=76 Identities=37% Similarity=0.718 Sum_probs=68.4
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhccCccccccc
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSLSGLLFKLIF 77 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~~~~f~~~f 77 (78)
+++++|| |+|+++++|||+++..||+++..|++.++++.++++|++|||||+||.++|+|+.+.++..+..+.+.|
T Consensus 76 ti~~sYy-rgA~gi~LvyDitne~Sfeni~~W~~~I~e~a~~~v~~~LvGNK~D~~~~R~V~~e~ge~lA~e~G~~F 151 (207)
T KOG0078|consen 76 TITTAYY-RGAMGILLVYDITNEKSFENIRNWIKNIDEHASDDVVKILVGNKCDLEEKRQVSKERGEALAREYGIKF 151 (207)
T ss_pred HHHHHHH-hhcCeeEEEEEccchHHHHHHHHHHHHHHhhCCCCCcEEEeeccccccccccccHHHHHHHHHHhCCeE
Confidence 3678999 999999999999999999999999999999998899999999999999999999877777666665554
No 3
>KOG0087 consensus GTPase Rab11/YPT3, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.89 E-value=1.8e-23 Score=126.80 Aligned_cols=77 Identities=58% Similarity=0.886 Sum_probs=70.5
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhccCcccccccC
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSLSGLLFKLIFI 78 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~~~~f~~~f~ 78 (78)
++++.|| |+|.|+++|||+|++.||+++..|+.++++|.+++++++|||||+||.+.|.|+.+.++..+....+.|+
T Consensus 78 AitSaYY-rgAvGAllVYDITr~~Tfenv~rWL~ELRdhad~nivimLvGNK~DL~~lraV~te~~k~~Ae~~~l~f~ 154 (222)
T KOG0087|consen 78 AITSAYY-RGAVGALLVYDITRRQTFENVERWLKELRDHADSNIVIMLVGNKSDLNHLRAVPTEDGKAFAEKEGLFFL 154 (222)
T ss_pred cccchhh-cccceeEEEEechhHHHHHHHHHHHHHHHhcCCCCeEEEEeecchhhhhccccchhhhHhHHHhcCceEE
Confidence 4678999 9999999999999999999999999999999999999999999999999999998888887776666653
No 4
>KOG0098 consensus GTPase Rab2, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.89 E-value=1.2e-23 Score=125.82 Aligned_cols=77 Identities=40% Similarity=0.703 Sum_probs=72.5
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhccCcccccccC
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSLSGLLFKLIFI 78 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~~~~f~~~f~ 78 (78)
|++++|| |+|.|++||||+++++||+.+..|+.+++++..+++.++|+|||+||...|.|+++.++..+.+..++|+
T Consensus 70 sv~~syY-r~a~GalLVydit~r~sF~hL~~wL~D~rq~~~~NmvImLiGNKsDL~~rR~Vs~EEGeaFA~ehgLifm 146 (216)
T KOG0098|consen 70 SVTRSYY-RGAAGALLVYDITRRESFNHLTSWLEDARQHSNENMVIMLIGNKSDLEARREVSKEEGEAFAREHGLIFM 146 (216)
T ss_pred HHHHHHh-ccCcceEEEEEccchhhHHHHHHHHHHHHHhcCCCcEEEEEcchhhhhccccccHHHHHHHHHHcCceee
Confidence 4678999 9999999999999999999999999999999879999999999999999999999999999988888875
No 5
>KOG0092 consensus GTPase Rab5/YPT51 and related small G protein superfamily GTPases [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.88 E-value=1.1e-22 Score=121.94 Aligned_cols=67 Identities=37% Similarity=0.619 Sum_probs=61.5
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhc
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSL 68 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~ 68 (78)
||.|+|| |||+++|+|||+|+.+||..++.|+.++++..++++.+.|||||+||.+.|.|+...++.
T Consensus 69 slapMYy-RgA~AAivvYDit~~~SF~~aK~WvkeL~~~~~~~~vialvGNK~DL~~~R~V~~~ea~~ 135 (200)
T KOG0092|consen 69 SLAPMYY-RGANAAIVVYDITDEESFEKAKNWVKELQRQASPNIVIALVGNKADLLERREVEFEEAQA 135 (200)
T ss_pred cccccee-cCCcEEEEEEecccHHHHHHHHHHHHHHHhhCCCCeEEEEecchhhhhhcccccHHHHHH
Confidence 5789999 999999999999999999999999999999998999999999999999989888554443
No 6
>KOG0094 consensus GTPase Rab6/YPT6/Ryh1, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.84 E-value=3.6e-21 Score=115.94 Aligned_cols=76 Identities=29% Similarity=0.500 Sum_probs=67.4
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCC-CCeEEEEeeCCCCCCCCCchHHHHhccCccccccc
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADS-NIVIMMIGNKTDLKHLPTSMSIFQSLSGLLFKLIF 77 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~-~~~~~lvgnK~Dl~~~~~v~~~~~~~~~~~f~~~f 77 (78)
+|.|+|+ |+++++|+|||++++.||+++.+|++.++...++ ++.++|||||.||.++|+++.+.++..+.+++..|
T Consensus 86 slipsY~-Rds~vaviVyDit~~~Sfe~t~kWi~dv~~e~gs~~viI~LVGnKtDL~dkrqvs~eEg~~kAkel~a~f 162 (221)
T KOG0094|consen 86 SLIPSYI-RDSSVAVIVYDITDRNSFENTSKWIEDVRRERGSDDVIIFLVGNKTDLSDKRQVSIEEGERKAKELNAEF 162 (221)
T ss_pred hhhhhhc-cCCeEEEEEEeccccchHHHHHHHHHHHHhccCCCceEEEEEcccccccchhhhhHHHHHHHHHHhCcEE
Confidence 5789999 9999999999999999999999999999877754 58899999999999999999888877666666554
No 7
>KOG0093 consensus GTPase Rab3, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.84 E-value=5.7e-21 Score=111.22 Aligned_cols=64 Identities=31% Similarity=0.623 Sum_probs=58.9
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQ 66 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~ 66 (78)
++..|| |+|+|+|++||+++.+||++++.|..+++..+-.++|+++|||||||..+|.++.+..
T Consensus 86 iTTayy-RgamgfiLmyDitNeeSf~svqdw~tqIktysw~naqvilvgnKCDmd~eRvis~e~g 149 (193)
T KOG0093|consen 86 ITTAYY-RGAMGFILMYDITNEESFNSVQDWITQIKTYSWDNAQVILVGNKCDMDSERVISHERG 149 (193)
T ss_pred HHHHHh-hccceEEEEEecCCHHHHHHHHHHHHHheeeeccCceEEEEecccCCccceeeeHHHH
Confidence 578899 9999999999999999999999999999988778999999999999999999985443
No 8
>KOG0088 consensus GTPase Rab21, small G protein superfamily [General function prediction only]
Probab=99.83 E-value=6e-21 Score=112.40 Aligned_cols=66 Identities=33% Similarity=0.636 Sum_probs=60.7
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHh
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQS 67 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~ 67 (78)
+|.|.|| |+++|+++|||+||++||+.++.|..+++...+..+.+++||||+||+++|+|+...+.
T Consensus 77 ALGPIYY-RgSnGalLVyDITDrdSFqKVKnWV~Elr~mlGnei~l~IVGNKiDLEeeR~Vt~qeAe 142 (218)
T KOG0088|consen 77 ALGPIYY-RGSNGALLVYDITDRDSFQKVKNWVLELRTMLGNEIELLIVGNKIDLEEERQVTRQEAE 142 (218)
T ss_pred ccCceEE-eCCCceEEEEeccchHHHHHHHHHHHHHHHHhCCeeEEEEecCcccHHHhhhhhHHHHH
Confidence 4678999 99999999999999999999999999999998888999999999999999999855443
No 9
>KOG0080 consensus GTPase Rab18, small G protein superfamily [General function prediction only]
Probab=99.83 E-value=2.4e-21 Score=114.11 Aligned_cols=77 Identities=34% Similarity=0.535 Sum_probs=69.3
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHHHHhccCcccccccC
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSIFQSLSGLLFKLIFI 78 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~~~~f~~~f~ 78 (78)
+|+++|| |+|+|+|+|||+|+++||.++..|.+++...+ .+++..++||||+|-+.+|.|+++.+.-.+...+++|+
T Consensus 75 tLTpSyy-RgaqGiIlVYDVT~Rdtf~kLd~W~~Eld~Ystn~diikmlVgNKiDkes~R~V~reEG~kfAr~h~~LFi 152 (209)
T KOG0080|consen 75 TLTPSYY-RGAQGIILVYDVTSRDTFVKLDIWLKELDLYSTNPDIIKMLVGNKIDKESERVVDREEGLKFARKHRCLFI 152 (209)
T ss_pred ccCHhHh-ccCceeEEEEEccchhhHHhHHHHHHHHHhhcCCccHhHhhhcccccchhcccccHHHHHHHHHhhCcEEE
Confidence 5889999 99999999999999999999999999998877 47899999999999888899998888777777777664
No 10
>KOG0086 consensus GTPase Rab4, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.82 E-value=1.4e-20 Score=110.41 Aligned_cols=76 Identities=38% Similarity=0.617 Sum_probs=68.0
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhccCccccccc
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSLSGLLFKLIF 77 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~~~~f~~~f 77 (78)
|.+++|| |||.|.++|||+|+++||+.+..|+..++...++++.++++|||.||.++|+|+.+.+...+.+-++.|
T Consensus 73 SVtRsYY-RGAAGAlLVYD~TsrdsfnaLtnWL~DaR~lAs~nIvviL~GnKkDL~~~R~VtflEAs~FaqEnel~f 148 (214)
T KOG0086|consen 73 SVTRSYY-RGAAGALLVYDITSRDSFNALTNWLTDARTLASPNIVVILCGNKKDLDPEREVTFLEASRFAQENELMF 148 (214)
T ss_pred HHHHHHh-ccccceEEEEeccchhhHHHHHHHHHHHHhhCCCcEEEEEeCChhhcChhhhhhHHHHHhhhcccceee
Confidence 3568999 999999999999999999999999999999988999999999999999999999887777666555544
No 11
>KOG0079 consensus GTP-binding protein H-ray, small G protein superfamily [General function prediction only]
Probab=99.79 E-value=8.7e-20 Score=106.43 Aligned_cols=66 Identities=33% Similarity=0.616 Sum_probs=59.0
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhcc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSLS 69 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~ 69 (78)
++..|| |+.+++++|||+|+.+||.+++.|+++++.++ +++|.++||||.|+.+.|.|....+...
T Consensus 73 itstyy-rgthgv~vVYDVTn~ESF~Nv~rWLeei~~nc-dsv~~vLVGNK~d~~~RrvV~t~dAr~~ 138 (198)
T KOG0079|consen 73 ITSTYY-RGTHGVIVVYDVTNGESFNNVKRWLEEIRNNC-DSVPKVLVGNKNDDPERRVVDTEDARAF 138 (198)
T ss_pred HHHHHc-cCCceEEEEEECcchhhhHhHHHHHHHHHhcC-ccccceecccCCCCccceeeehHHHHHH
Confidence 567899 99999999999999999999999999999998 6899999999999998888875555443
No 12
>KOG0083 consensus GTPase Rab26/Rab37, small G protein superfamily [General function prediction only]
Probab=99.79 E-value=1.3e-20 Score=108.50 Aligned_cols=77 Identities=29% Similarity=0.543 Sum_probs=68.9
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhccCcccccccC
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSLSGLLFKLIFI 78 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~~~~f~~~f~ 78 (78)
|.+..|| |+||+.+++||++++.||++++.|+.++.+.....+.+.++|||+|+.++|.|++..++-.+..|.+.||
T Consensus 62 svt~ayy-rda~allllydiankasfdn~~~wlsei~ey~k~~v~l~llgnk~d~a~er~v~~ddg~kla~~y~ipfm 138 (192)
T KOG0083|consen 62 SVTHAYY-RDADALLLLYDIANKASFDNCQAWLSEIHEYAKEAVALMLLGNKCDLAHERAVKRDDGEKLAEAYGIPFM 138 (192)
T ss_pred hhhHhhh-cccceeeeeeecccchhHHHHHHHHHHHHHHHHhhHhHhhhccccccchhhccccchHHHHHHHHCCCce
Confidence 4678999 9999999999999999999999999999999877889999999999999999997777777666777664
No 13
>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=99.78 E-value=4.7e-19 Score=107.87 Aligned_cols=64 Identities=36% Similarity=0.634 Sum_probs=56.7
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQ 66 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~ 66 (78)
+++.|| ++|+++|+|||+++++||++++.|+..+++...+++|+++||||+||.+.++++...+
T Consensus 65 l~~~y~-~~ad~iIlVfDvtd~~Sf~~l~~w~~~i~~~~~~~~piilVgNK~DL~~~~~v~~~~~ 128 (202)
T cd04120 65 ITSAYY-RSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETDREISRQQG 128 (202)
T ss_pred HHHHHh-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCcEEEEEECcccccccccCHHHH
Confidence 567899 9999999999999999999999999998877667899999999999988788775444
No 14
>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=99.78 E-value=4.3e-19 Score=107.05 Aligned_cols=63 Identities=32% Similarity=0.652 Sum_probs=55.7
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQ 66 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~ 66 (78)
+++.|| ++||++++|||+++++||++++.|++++.++. +++|++|||||+||.+.+.++...+
T Consensus 71 l~~~~~-~~ad~illVfD~t~~~Sf~~~~~w~~~i~~~~-~~~piilVGNK~DL~~~~~v~~~~~ 133 (189)
T cd04121 71 IFRSYS-RGAQGIILVYDITNRWSFDGIDRWIKEIDEHA-PGVPKILVGNRLHLAFKRQVATEQA 133 (189)
T ss_pred HHHHHh-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCEEEEEECccchhccCCCHHHH
Confidence 456789 99999999999999999999999999998776 6899999999999988777764443
No 15
>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=99.76 E-value=1.3e-18 Score=103.93 Aligned_cols=56 Identities=30% Similarity=0.599 Sum_probs=50.4
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
+++.|| ++|+++|+|||+++++||+++ +.|+.++++.. +++|++|||||+||.+.+
T Consensus 65 ~~~~~~-~~a~~~ilvyd~~~~~Sf~~~~~~w~~~i~~~~-~~~piilvgnK~Dl~~~~ 121 (176)
T cd04133 65 LRPLSY-RGADVFVLAFSLISRASYENVLKKWVPELRHYA-PNVPIVLVGTKLDLRDDK 121 (176)
T ss_pred cchhhc-CCCcEEEEEEEcCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEeChhhccCh
Confidence 567899 999999999999999999999 78999998775 679999999999997653
No 16
>KOG0081 consensus GTPase Rab27, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.76 E-value=3.2e-19 Score=105.18 Aligned_cols=76 Identities=32% Similarity=0.520 Sum_probs=66.3
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHHHHhccCccccccc
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSIFQSLSGLLFKLIF 77 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~~~~f~~~f 77 (78)
|++..|| |+|.|++++||+|++.||-++++|+.+++-+. ..+..++++|||+||.+.|+|++..+...+..+.+.|
T Consensus 82 SLTTAFf-RDAMGFlLiFDlT~eqSFLnvrnWlSQL~~hAYcE~PDivlcGNK~DL~~~R~Vs~~qa~~La~kyglPY 158 (219)
T KOG0081|consen 82 SLTTAFF-RDAMGFLLIFDLTSEQSFLNVRNWLSQLQTHAYCENPDIVLCGNKADLEDQRVVSEDQAAALADKYGLPY 158 (219)
T ss_pred HHHHHHH-HhhccceEEEeccchHHHHHHHHHHHHHHHhhccCCCCEEEEcCccchhhhhhhhHHHHHHHHHHhCCCe
Confidence 5678899 99999999999999999999999999998876 4677899999999999999999777766666665554
No 17
>KOG0091 consensus GTPase Rab39, small G protein superfamily [General function prediction only]
Probab=99.76 E-value=7.6e-19 Score=103.87 Aligned_cols=76 Identities=29% Similarity=0.580 Sum_probs=64.7
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC-C-CCeEEEEeeCCCCCCCCCchHHHHhccCccccccc
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD-S-NIVIMMIGNKTDLKHLPTSMSIFQSLSGLLFKLIF 77 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~-~~~~~lvgnK~Dl~~~~~v~~~~~~~~~~~f~~~f 77 (78)
|++.+|| |++-|+++|||++|++||+.++.|..+...+.+ | .+...|||.|+||...|+|+.+.++..+..-++.|
T Consensus 73 sitksyy-rnsvgvllvyditnr~sfehv~~w~~ea~m~~q~P~k~VFlLVGhKsDL~SqRqVt~EEaEklAa~hgM~F 150 (213)
T KOG0091|consen 73 SITKSYY-RNSVGVLLVYDITNRESFEHVENWVKEAAMATQGPDKVVFLLVGHKSDLQSQRQVTAEEAEKLAASHGMAF 150 (213)
T ss_pred HHHHHHh-hcccceEEEEeccchhhHHHHHHHHHHHHHhcCCCCeeEEEEeccccchhhhccccHHHHHHHHHhcCceE
Confidence 5788999 999999999999999999999999999987774 4 45567999999999999999777776665555544
No 18
>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=99.75 E-value=2.7e-18 Score=103.00 Aligned_cols=54 Identities=20% Similarity=0.594 Sum_probs=49.5
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+++.|| ++||++++|||+++++||+++ ..|++++++.. ++.|++|||||+||.+
T Consensus 69 ~~~~~~-~~ad~~ilvyDit~~~Sf~~~~~~w~~~i~~~~-~~~piilVgNK~DL~~ 123 (182)
T cd04172 69 VRPLSY-PDSDAVLICFDISRPETLDSVLKKWKGEIQEFC-PNTKMLLVGCKSDLRT 123 (182)
T ss_pred hhhhhc-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHC-CCCCEEEEeEChhhhc
Confidence 567899 999999999999999999998 89999998876 6799999999999964
No 19
>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=99.74 E-value=4.5e-18 Score=101.59 Aligned_cols=54 Identities=22% Similarity=0.612 Sum_probs=49.3
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+++.|| ++|+++++|||+++++||+++ ..|+.++++.. +++|++|||||+||.+
T Consensus 65 ~~~~~~-~~a~~~ilvfdit~~~Sf~~~~~~w~~~i~~~~-~~~~iilVgnK~DL~~ 119 (178)
T cd04131 65 VRPLCY-PDSDAVLICFDISRPETLDSVLKKWRGEIQEFC-PNTKVLLVGCKTDLRT 119 (178)
T ss_pred cchhhc-CCCCEEEEEEECCChhhHHHHHHHHHHHHHHHC-CCCCEEEEEEChhhhc
Confidence 567899 999999999999999999996 89999998876 6899999999999964
No 20
>PTZ00099 rab6; Provisional
Probab=99.73 E-value=1e-17 Score=100.09 Aligned_cols=63 Identities=32% Similarity=0.644 Sum_probs=54.4
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIF 65 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~ 65 (78)
+++.|| ++||++|+|||+++++||+.+..|+..+.+..++++|++|||||+||.+.+.++...
T Consensus 45 ~~~~~~-~~ad~~ilv~D~t~~~sf~~~~~w~~~i~~~~~~~~piilVgNK~DL~~~~~v~~~e 107 (176)
T PTZ00099 45 LIPSYI-RDSAAAIVVYDITNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEE 107 (176)
T ss_pred ccHHHh-CCCcEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCeEEEEEECcccccccCCCHHH
Confidence 467789 999999999999999999999999999976655679999999999998766666433
No 21
>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=99.73 E-value=9.4e-18 Score=102.26 Aligned_cols=61 Identities=25% Similarity=0.416 Sum_probs=52.5
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-------------------CCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-------------------DSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-------------------~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+++.|| ++++++|+|||+++++||++++.|+.++.... ++++|++|||||+||.++|.++
T Consensus 70 l~~~~y-r~ad~iIlVyDvtn~~Sf~~l~~W~~ei~~~~~~~~~~~~~~~~~~~~~~~~~~~PiilVGnK~Dl~~~r~~~ 148 (202)
T cd04102 70 TRAVFY-NQVNGIILVHDLTNRKSSQNLQRWSLEALNKDTFPTGLLVTNGDYDSEQFGGNQIPLLVIGTKLDQIPEKESS 148 (202)
T ss_pred HHHHHh-CcCCEEEEEEECcChHHHHHHHHHHHHHHHhhccccccccccccccccccCCCCceEEEEEECccchhhcccc
Confidence 467899 99999999999999999999999999996531 2579999999999998777555
Q ss_pred H
Q 038356 63 S 63 (78)
Q Consensus 63 ~ 63 (78)
.
T Consensus 149 ~ 149 (202)
T cd04102 149 G 149 (202)
T ss_pred h
Confidence 3
No 22
>KOG0395 consensus Ras-related GTPase [General function prediction only]
Probab=99.73 E-value=7.4e-18 Score=102.38 Aligned_cols=75 Identities=23% Similarity=0.351 Sum_probs=62.4
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC-CCCeEEEEeeCCCCCCCCCchHHHHhccCccccccc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD-SNIVIMMIGNKTDLKHLPTSMSIFQSLSGLLFKLIF 77 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~lvgnK~Dl~~~~~v~~~~~~~~~~~f~~~f 77 (78)
+...|. +++||+++||+++++.||+.++.++..+.+... ..+|+++||||+||...|+|+...++..+..+++.|
T Consensus 67 ~~~~~~-~~~~gF~lVysitd~~SF~~~~~l~~~I~r~~~~~~~PivlVGNK~Dl~~~R~V~~eeg~~la~~~~~~f 142 (196)
T KOG0395|consen 67 MRDLYI-RNGDGFLLVYSITDRSSFEEAKQLREQILRVKGRDDVPIILVGNKCDLERERQVSEEEGKALARSWGCAF 142 (196)
T ss_pred HHHHhh-ccCcEEEEEEECCCHHHHHHHHHHHHHHHHhhCcCCCCEEEEEEcccchhccccCHHHHHHHHHhcCCcE
Confidence 456788 999999999999999999999999999966543 668999999999999999999877555555555444
No 23
>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=99.72 E-value=1.8e-17 Score=100.42 Aligned_cols=54 Identities=19% Similarity=0.418 Sum_probs=48.1
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHH-HHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVS-RWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+++.|| ++||++++|||+++++||++++ .|.+++++.. +++|+++||||+||.+
T Consensus 80 ~~~~~~-~~ad~iilv~d~t~~~Sf~~~~~~w~~~i~~~~-~~~piilvgNK~DL~~ 134 (195)
T cd01873 80 DRRFAY-GRSDVVLLCFSIASPNSLRNVKTMWYPEIRHFC-PRVPVILVGCKLDLRY 134 (195)
T ss_pred hhcccC-CCCCEEEEEEECCChhHHHHHHHHHHHHHHHhC-CCCCEEEEEEchhccc
Confidence 356789 9999999999999999999996 6999998765 6799999999999964
No 24
>KOG0095 consensus GTPase Rab30, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.72 E-value=6.7e-18 Score=98.85 Aligned_cols=67 Identities=27% Similarity=0.571 Sum_probs=61.4
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhc
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSL 68 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~ 68 (78)
|++++|| |.|+++|+|||++=++||+.+.+|+.++++..+..+..++||||.|+.+.|++++..++.
T Consensus 71 sitqsyy-rsahalilvydiscqpsfdclpewlreie~yan~kvlkilvgnk~d~~drrevp~qigee 137 (213)
T KOG0095|consen 71 SITQSYY-RSAHALILVYDISCQPSFDCLPEWLREIEQYANNKVLKILVGNKIDLADRREVPQQIGEE 137 (213)
T ss_pred HHHHHHh-hhcceEEEEEecccCcchhhhHHHHHHHHHHhhcceEEEeeccccchhhhhhhhHHHHHH
Confidence 5788999 999999999999999999999999999999988889999999999999999998665544
No 25
>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=99.71 E-value=1.7e-17 Score=103.02 Aligned_cols=54 Identities=26% Similarity=0.572 Sum_probs=48.8
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+++.|| ++|+++++|||+++++||+++ ..|+.++++.. ++.|++|||||+||.+
T Consensus 77 ~~~~~~-~~ad~vIlVyDit~~~Sf~~~~~~w~~~i~~~~-~~~piilVgNK~DL~~ 131 (232)
T cd04174 77 VRPLCY-SDSDAVLLCFDISRPETVDSALKKWKAEIMDYC-PSTRILLIGCKTDLRT 131 (232)
T ss_pred HHHHHc-CCCcEEEEEEECCChHHHHHHHHHHHHHHHHhC-CCCCEEEEEECccccc
Confidence 467899 999999999999999999985 89999998776 6789999999999964
No 26
>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=99.71 E-value=2.9e-17 Score=98.79 Aligned_cols=56 Identities=21% Similarity=0.565 Sum_probs=49.4
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHH-HHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVS-RWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
+++.|| ++||++|+|||+++++||+++. .|...+.... +++|++|||||+||.+.+
T Consensus 67 l~~~~~-~~a~~~ilvydit~~~Sf~~~~~~w~~~i~~~~-~~~piilvgNK~DL~~~~ 123 (191)
T cd01875 67 LRTLSY-PQTNVFIICFSIASPSSYENVRHKWHPEVCHHC-PNVPILLVGTKKDLRNDA 123 (191)
T ss_pred hhhhhc-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhC-CCCCEEEEEeChhhhcCh
Confidence 567899 9999999999999999999996 6998887665 679999999999997653
No 27
>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=99.70 E-value=3.5e-17 Score=95.90 Aligned_cols=61 Identities=43% Similarity=0.809 Sum_probs=53.6
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
+++.|| ++++++++|||+++++||+.+..|+..+.....++.|+++||||+|+.+.+.++.
T Consensus 67 ~~~~~~-~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~iiiv~nK~Dl~~~~~~~~ 127 (166)
T cd04122 67 VTRSYY-RGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADLEAQRDVTY 127 (166)
T ss_pred HHHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccccccCcCH
Confidence 346788 9999999999999999999999999998776667899999999999987776653
No 28
>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=99.70 E-value=4.1e-17 Score=95.53 Aligned_cols=64 Identities=28% Similarity=0.575 Sum_probs=55.2
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQ 66 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~ 66 (78)
+++.|+ +++|++++|||+++++||+.+..|++.+....+.++|+++||||.|+.+.+.+....+
T Consensus 65 ~~~~~~-~~~~~~i~v~d~~~~~sf~~~~~~~~~~~~~~~~~~~iilvgnK~Dl~~~~~v~~~~~ 128 (161)
T cd04117 65 ITKQYY-RRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIGNKADEEQKRQVGDEQG 128 (161)
T ss_pred hHHHHh-cCCcEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccccccCCCHHHH
Confidence 456788 9999999999999999999999999999877656799999999999988777654333
No 29
>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=99.69 E-value=4.1e-17 Score=96.71 Aligned_cols=64 Identities=23% Similarity=0.400 Sum_probs=54.7
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHHHH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSIFQ 66 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~~~ 66 (78)
+++.|| ++++++++|||+++++||+.+..|...+.+.. .+++|+++||||+|+.+.++++...+
T Consensus 66 l~~~~~-~~~d~~ilv~d~~~~~Sf~~~~~~~~~i~~~~~~~~~piilvgNK~Dl~~~~~v~~~~~ 130 (172)
T cd04141 66 MRDQYM-RCGEGFIICYSVTDRHSFQEASEFKKLITRVRLTEDIPLVLVGNKVDLESQRQVTTEEG 130 (172)
T ss_pred HhHHHh-hcCCEEEEEEECCchhHHHHHHHHHHHHHHhcCCCCCCEEEEEEChhhhhcCccCHHHH
Confidence 567889 99999999999999999999999988887654 36799999999999987777764433
No 30
>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=99.68 E-value=5.1e-17 Score=94.50 Aligned_cols=64 Identities=28% Similarity=0.563 Sum_probs=56.1
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHh
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQS 67 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~ 67 (78)
++.++ ++++++|+|||+++++||+++..|++.+....+.++|++|+|||.|+.+.+.++...++
T Consensus 65 ~~~~~-~~~~~~ii~fd~~~~~S~~~~~~~~~~i~~~~~~~~~iivvg~K~D~~~~~~v~~~~~~ 128 (162)
T PF00071_consen 65 RDIFY-RNSDAIIIVFDVTDEESFENLKKWLEEIQKYKPEDIPIIVVGNKSDLSDEREVSVEEAQ 128 (162)
T ss_dssp HHHHH-TTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGGSSSCHHHHH
T ss_pred ccccc-cccccccccccccccccccccccccccccccccccccceeeeccccccccccchhhHHH
Confidence 45678 99999999999999999999999999999888667999999999999887877754433
No 31
>KOG0097 consensus GTPase Rab14, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.67 E-value=4.7e-17 Score=94.74 Aligned_cols=71 Identities=37% Similarity=0.602 Sum_probs=62.4
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhccCccc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSLSGLLF 73 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~~~~f 73 (78)
++++|| |+|.+.++|||++++++++.+..|+...+....++..++++|||.||+..|.|+-+.++..+..-
T Consensus 76 vtrsyy-rgaagalmvyditrrstynhlsswl~dar~ltnpnt~i~lignkadle~qrdv~yeeak~faeen 146 (215)
T KOG0097|consen 76 VTRSYY-RGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADLESQRDVTYEEAKEFAEEN 146 (215)
T ss_pred HHHHHh-ccccceeEEEEehhhhhhhhHHHHHhhhhccCCCceEEEEecchhhhhhcccCcHHHHHHHHhhc
Confidence 467899 99999999999999999999999999998887899999999999999999999866555544433
No 32
>KOG0394 consensus Ras-related GTPase [General function prediction only]
Probab=99.66 E-value=2.4e-16 Score=94.53 Aligned_cols=67 Identities=30% Similarity=0.487 Sum_probs=56.8
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC----CCCeEEEEeeCCCCCCC--CCchHHHHhc
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD----SNIVIMMIGNKTDLKHL--PTSMSIFQSL 68 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~----~~~~~~lvgnK~Dl~~~--~~v~~~~~~~ 68 (78)
||...+| ||||++++|||+++++||+++..|.+++....+ ...|.||+|||+|+.+. |+|+...++.
T Consensus 73 sLg~aFY-RgaDcCvlvydv~~~~Sfe~L~~Wr~EFl~qa~~~~Pe~FPFVilGNKiD~~~~~~r~VS~~~Aq~ 145 (210)
T KOG0394|consen 73 SLGVAFY-RGADCCVLVYDVNNPKSFENLENWRKEFLIQASPQDPETFPFVILGNKIDVDGGKSRQVSEKKAQT 145 (210)
T ss_pred hccccee-cCCceEEEEeecCChhhhccHHHHHHHHHHhcCCCCCCcccEEEEcccccCCCCccceeeHHHHHH
Confidence 4667899 999999999999999999999999999976653 45899999999999763 8888655544
No 33
>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=99.66 E-value=2.1e-16 Score=93.42 Aligned_cols=62 Identities=35% Similarity=0.646 Sum_probs=53.2
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSI 64 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~ 64 (78)
+++.|+ +++|++++|||+++++||.+++.|+..+.... .++.|+++||||+|+.+.+.++..
T Consensus 79 ~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~piiiv~nK~Dl~~~~~v~~~ 141 (180)
T cd04127 79 LTTAFF-RDAMGFLLIFDLTNEQSFLNVRNWMSQLQTHAYCENPDIVLCGNKADLEDQRQVSEE 141 (180)
T ss_pred HHHHHh-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEeCccchhcCccCHH
Confidence 356788 99999999999999999999999999997764 367899999999999877666543
No 34
>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=99.65 E-value=3.2e-16 Score=96.63 Aligned_cols=55 Identities=33% Similarity=0.599 Sum_probs=48.7
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+++.|| ++++++|+|||+++++||+++..|+..+.+...+++|++|||||+||.+
T Consensus 60 l~~~~~-~~ad~~IlV~Dvt~~~Sf~~l~~~~~~l~~~~~~~~piIlVgNK~DL~~ 114 (220)
T cd04126 60 LGSMYC-RGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKLDLTE 114 (220)
T ss_pred hHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECccccc
Confidence 456789 9999999999999999999998888887766557799999999999975
No 35
>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=99.65 E-value=3.1e-16 Score=93.19 Aligned_cols=55 Identities=22% Similarity=0.529 Sum_probs=48.4
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHH-HHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVS-RWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
+++.|| ++++++|+|||+++++||+++. .|..+++... +++|+++||||+|+.+.
T Consensus 65 ~~~~~~-~~a~~~ilv~d~~~~~s~~~~~~~w~~~i~~~~-~~~piilvgnK~Dl~~~ 120 (175)
T cd01874 65 LRPLSY-PQTDVFLVCFSVVSPSSFENVKEKWVPEITHHC-PKTPFLLVGTQIDLRDD 120 (175)
T ss_pred hhhhhc-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEECHhhhhC
Confidence 456788 9999999999999999999996 6999887765 67999999999999654
No 36
>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=99.64 E-value=7.5e-16 Score=93.71 Aligned_cols=58 Identities=34% Similarity=0.617 Sum_probs=51.3
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+++.|| ++++++|+|||+++++||++++.|+.++++.. +++|++|||||+|+.. +.+.
T Consensus 60 l~~~~~-~~ad~~ilV~D~t~~~S~~~i~~w~~~i~~~~-~~~piilvgNK~Dl~~-~~v~ 117 (200)
T smart00176 60 LRDGYY-IQGQCAIIMFDVTARVTYKNVPNWHRDLVRVC-ENIPIVLCGNKVDVKD-RKVK 117 (200)
T ss_pred hhHHHh-cCCCEEEEEEECCChHHHHHHHHHHHHHHHhC-CCCCEEEEEECccccc-ccCC
Confidence 567899 99999999999999999999999999998876 6899999999999964 3443
No 37
>PLN00023 GTP-binding protein; Provisional
Probab=99.64 E-value=6.5e-16 Score=99.74 Aligned_cols=56 Identities=21% Similarity=0.456 Sum_probs=49.5
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC------------CCCeEEEEeeCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD------------SNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~------------~~~~~~lvgnK~Dl~~~ 58 (78)
+++.|| ++++++|+|||+++++||+++..|++++..... .++|++|||||+||.++
T Consensus 99 L~~~yy-r~AdgiILVyDITdr~SFenL~kWl~eI~~~~~~s~p~~s~~~~~~~ipIILVGNK~DL~~~ 166 (334)
T PLN00023 99 CRSLFY-SQINGVIFVHDLSQRRTKTSLQKWASEVAATGTFSAPLGSGGPGGLPVPYIVIGNKADIAPK 166 (334)
T ss_pred hhHHhc-cCCCEEEEEEeCCCHHHHHHHHHHHHHHHHhcccccccccccccCCCCcEEEEEECcccccc
Confidence 567899 999999999999999999999999999987631 25899999999999754
No 38
>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=99.63 E-value=5e-16 Score=93.16 Aligned_cols=62 Identities=27% Similarity=0.459 Sum_probs=52.6
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc---CCCCeEEEEeeCCCCCCCCCchHH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA---DSNIVIMMIGNKTDLKHLPTSMSI 64 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~---~~~~~~~lvgnK~Dl~~~~~v~~~ 64 (78)
+++.|| +++|++++|||+++++||+++..|+..+.+.. .++.|+++||||+|+.+.+.++..
T Consensus 63 ~~~~~~-~~ad~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilvgNK~Dl~~~~~v~~~ 127 (190)
T cd04144 63 LRDQWI-REGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKVYEREVSTE 127 (190)
T ss_pred HHHHHH-HhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcccCCCCCEEEEEEChhccccCccCHH
Confidence 456788 99999999999999999999999999886654 257899999999999776666543
No 39
>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=99.63 E-value=8e-16 Score=90.12 Aligned_cols=60 Identities=33% Similarity=0.682 Sum_probs=52.6
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
++..++ ++++++++|||+++++||+.+..|++.+.+...++.|+++||||+|+.+.+.+.
T Consensus 66 ~~~~~~-~~~~~~l~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piivv~nK~Dl~~~~~~~ 125 (165)
T cd01865 66 ITTAYY-RGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGNKCDMEDERVVS 125 (165)
T ss_pred HHHHHc-cCCcEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCCEEEEEECcccCcccccC
Confidence 356788 999999999999999999999999999987665689999999999997766554
No 40
>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=99.63 E-value=8.3e-16 Score=90.22 Aligned_cols=59 Identities=39% Similarity=0.871 Sum_probs=52.3
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+..++ +++|++++|||+++++||+.+..|+..+.+....+.|+++||||+|+.+.+.+.
T Consensus 69 ~~~~~-~~ad~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~p~iiv~nK~Dl~~~~~~~ 127 (167)
T cd01867 69 TTAYY-RGAMGIILVYDITDEKSFENIRNWMRNIEEHASEDVERMLVGNKCDMEEKRVVS 127 (167)
T ss_pred HHHHh-CCCCEEEEEEECcCHHHHHhHHHHHHHHHHhCCCCCcEEEEEECcccccccCCC
Confidence 45678 999999999999999999999999999988766789999999999998766554
No 41
>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=99.63 E-value=6.2e-16 Score=90.74 Aligned_cols=61 Identities=11% Similarity=0.266 Sum_probs=51.4
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC-CCCeEEEEeeCCCCC--CCCCchHHH
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD-SNIVIMMIGNKTDLK--HLPTSMSIF 65 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~lvgnK~Dl~--~~~~v~~~~ 65 (78)
..|+ +++|++++|||+++++||+++..|++++..... +++|+++||||.||. ..+.++...
T Consensus 60 ~~~~-~~~~~~ilv~d~~~~~sf~~~~~~~~~i~~~~~~~~~piilvgnK~Dl~~~~~~~v~~~~ 123 (158)
T cd04103 60 AQFA-SWVDAVIFVFSLENEASFQTVYNLYHQLSSYRNISEIPLILVGTQDAISESNPRVIDDAR 123 (158)
T ss_pred hhHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEeeHHHhhhcCCcccCHHH
Confidence 3578 999999999999999999999999999977653 679999999999985 346666443
No 42
>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=99.63 E-value=9e-16 Score=93.73 Aligned_cols=62 Identities=35% Similarity=0.580 Sum_probs=52.6
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC---CCCeEEEEeeCCCCCCCCCchHH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD---SNIVIMMIGNKTDLKHLPTSMSI 64 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~---~~~~~~lvgnK~Dl~~~~~v~~~ 64 (78)
+.+.|| +++|++|+|||+++++||+++..|...+.+... .++|+++||||+|+.+.+.++..
T Consensus 66 l~~~~~-~~ad~iilV~D~t~~~s~~~~~~w~~~l~~~~~~~~~~~piilVgNK~DL~~~~~v~~~ 130 (215)
T cd04109 66 MLDKYI-YGAHAVFLVYDVTNSQSFENLEDWYSMVRKVLKSSETQPLVVLVGNKTDLEHNRTVKDD 130 (215)
T ss_pred HHHHHh-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhccccCCCceEEEEEECcccccccccCHH
Confidence 356788 999999999999999999999999999987652 45789999999999877766643
No 43
>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=99.62 E-value=9e-16 Score=89.10 Aligned_cols=61 Identities=21% Similarity=0.444 Sum_probs=52.4
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
+++.|+ ++++++++|||+++++||+.+..|...+.+.. .++.|+++||||+|+.+.+.+..
T Consensus 65 ~~~~~~-~~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~ 126 (163)
T cd04136 65 MRDLYI-KNGQGFVLVYSITSQSSFNDLQDLREQILRVKDTENVPMVLVGNKCDLEDERVVSR 126 (163)
T ss_pred HHHHHh-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccceecH
Confidence 456788 99999999999999999999999999987654 36799999999999977666553
No 44
>PLN03110 Rab GTPase; Provisional
Probab=99.62 E-value=8.1e-16 Score=94.17 Aligned_cols=65 Identities=66% Similarity=1.031 Sum_probs=56.0
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHh
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQS 67 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~ 67 (78)
+++.|+ ++++++++|||+++++||+++..|+..+.+..+.++|+++||||+|+.+.+.+++....
T Consensus 77 ~~~~~~-~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~piiiv~nK~Dl~~~~~~~~~~~~ 141 (216)
T PLN03110 77 ITSAYY-RGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVIMMAGNKSDLNHLRSVAEEDGQ 141 (216)
T ss_pred HHHHHh-CCCCEEEEEEECCChHHHHHHHHHHHHHHHhCCCCCeEEEEEEChhcccccCCCHHHHH
Confidence 356788 99999999999999999999999999998876678999999999999877777654333
No 45
>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=99.62 E-value=8.4e-16 Score=90.50 Aligned_cols=63 Identities=25% Similarity=0.575 Sum_probs=54.2
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHHH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSIF 65 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~~ 65 (78)
+++.|+ +++|++++|||+++++||+.+..|..++.... ..++|+++||||+|+.+.++++...
T Consensus 68 ~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~~~~~~~~ 131 (170)
T cd04115 68 MVQHYY-RNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLREQIQVPTDL 131 (170)
T ss_pred hHHHhh-cCCCEEEEEEECCCHHHHHhHHHHHHHHHHhcCCCCCCEEEEEECccchhhcCCCHHH
Confidence 356788 99999999999999999999999999997765 3679999999999998877766433
No 46
>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=99.62 E-value=1e-15 Score=89.15 Aligned_cols=60 Identities=20% Similarity=0.414 Sum_probs=51.8
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+++.|+ +++|++++|||+++++||+++..|...+.+.. ..+.|+++||||+|+.+.+.+.
T Consensus 65 ~~~~~~-~~ad~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piviv~nK~Dl~~~~~~~ 125 (163)
T cd04176 65 MRDLYI-KNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLESEREVS 125 (163)
T ss_pred hHHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccchhcCccC
Confidence 467788 99999999999999999999999999987654 3679999999999997655554
No 47
>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=99.61 E-value=1e-15 Score=89.33 Aligned_cols=61 Identities=21% Similarity=0.435 Sum_probs=52.5
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
+++.|+ +++|++++|||+++++||+.+.+|...+.+.. .++.|+++||||+|+.+.+.++.
T Consensus 65 ~~~~~~-~~~d~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~nK~Dl~~~~~~~~ 126 (164)
T cd04175 65 MRDLYM-KNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGK 126 (164)
T ss_pred HHHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECCcchhccEEcH
Confidence 456788 99999999999999999999999999987654 36799999999999987666553
No 48
>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=99.61 E-value=1.5e-15 Score=91.71 Aligned_cols=60 Identities=40% Similarity=0.736 Sum_probs=50.9
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc----CCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA----DSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~----~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+++.|| ++++++|+|||+++++||+++..|+.++.... ..++|+++||||+|+.+.+.++
T Consensus 66 ~~~~~~-~~a~~~ilv~D~t~~~s~~~~~~~~~~i~~~~~~~~~~~~piilv~NK~Dl~~~~~~~ 129 (201)
T cd04107 66 MTRVYY-RGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPCLLLANKCDLKKRLAKD 129 (201)
T ss_pred hHHHHh-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhcccCCCCCcEEEEEECCCcccccccC
Confidence 467889 99999999999999999999999999886542 2678999999999997555544
No 49
>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=99.61 E-value=1.3e-15 Score=89.02 Aligned_cols=59 Identities=41% Similarity=0.767 Sum_probs=52.2
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+..|+ ++++++++|||+++++||+++..|+..+++...++.|+++||||+|+.+.+.+.
T Consensus 68 ~~~~~-~~~~~ii~v~d~~~~~s~~~l~~~~~~~~~~~~~~~~~iiv~nK~Dl~~~~~~~ 126 (166)
T cd01869 68 TSSYY-RGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTDKRVVD 126 (166)
T ss_pred HHHHh-CcCCEEEEEEECcCHHHHHhHHHHHHHHHHhCCCCCcEEEEEEChhcccccCCC
Confidence 45788 999999999999999999999999999987765679999999999997766655
No 50
>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=99.61 E-value=1.9e-15 Score=90.27 Aligned_cols=62 Identities=40% Similarity=0.715 Sum_probs=53.7
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSI 64 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~ 64 (78)
+++.++ +++|++++|||+++++||+++..|+.++......+.|++++|||+|+.+.+.++..
T Consensus 65 ~~~~~~-~~~d~iilv~d~~~~~s~~~i~~~~~~i~~~~~~~~~~ivv~nK~Dl~~~~~v~~~ 126 (188)
T cd04125 65 LNNSYY-RGAHGYLLVYDVTDQESFENLKFWINEINRYARENVIKVIVANKSDLVNNKVVDSN 126 (188)
T ss_pred hHHHHc-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECCCCcccccCCHH
Confidence 356788 99999999999999999999999999998776567999999999999877766543
No 51
>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=99.61 E-value=1.6e-15 Score=93.65 Aligned_cols=54 Identities=19% Similarity=0.541 Sum_probs=47.8
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+++.|| +++|++++|||+++++||+++ ..|..+++... +++|++|||||+||.+
T Consensus 65 l~~~~~-~~~d~illvfdis~~~Sf~~i~~~w~~~~~~~~-~~~piiLVgnK~DL~~ 119 (222)
T cd04173 65 VRPLAY-PDSDAVLICFDISRPETLDSVLKKWQGETQEFC-PNAKVVLVGCKLDMRT 119 (222)
T ss_pred HhHHhc-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhC-CCCCEEEEEECccccc
Confidence 467889 999999999999999999999 67888776655 7899999999999965
No 52
>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=99.61 E-value=1.8e-15 Score=89.88 Aligned_cols=55 Identities=25% Similarity=0.542 Sum_probs=48.1
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHH-HHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVS-RWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
+++.|+ +++|++|+|||+++++||+++. .|+..+.... +++|+++||||+||.+.
T Consensus 65 ~~~~~~-~~~d~~ilv~d~~~~~sf~~~~~~~~~~~~~~~-~~~piilvgnK~Dl~~~ 120 (174)
T cd01871 65 LRPLSY-PQTDVFLICFSLVSPASFENVRAKWYPEVRHHC-PNTPIILVGTKLDLRDD 120 (174)
T ss_pred hhhhhc-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEeeChhhccC
Confidence 457789 9999999999999999999994 7998887665 68999999999999643
No 53
>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=99.61 E-value=3.8e-15 Score=89.33 Aligned_cols=57 Identities=23% Similarity=0.522 Sum_probs=50.1
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHH-HHHHHHhhhcCCCCeEEEEeeCCCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVS-RWLKDLGDHADSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~ 60 (78)
+++.|| ++++++++|||+++++||+++. .|+..+.... ++.|+++||||+||.+.++
T Consensus 64 l~~~~~-~~a~~~ilv~dv~~~~sf~~~~~~~~~~i~~~~-~~~piilvgNK~Dl~~~~~ 121 (189)
T cd04134 64 LRSLSY-ADTDVIMLCFSVDSPDSLENVESKWLGEIREHC-PGVKLVLVALKCDLREARN 121 (189)
T ss_pred cccccc-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEEChhhccChh
Confidence 567889 9999999999999999999995 6999998765 6899999999999976553
No 54
>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=99.61 E-value=2.2e-15 Score=87.91 Aligned_cols=60 Identities=73% Similarity=1.179 Sum_probs=52.8
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+++.|+ ++++++++|||+++++||+++..|+..+.+....+.|+++||||+|+.+.+.+.
T Consensus 68 ~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~pi~vv~nK~Dl~~~~~~~ 127 (165)
T cd01868 68 ITSAYY-RGAVGALLVYDITKKQTFENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVP 127 (165)
T ss_pred HHHHHH-CCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECccccccccCC
Confidence 456788 999999999999999999999999999988775679999999999998766554
No 55
>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=99.60 E-value=2.1e-15 Score=90.50 Aligned_cols=59 Identities=37% Similarity=0.753 Sum_probs=52.2
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+..|+ +++|++++|||+++++||+++..|+..+.+....++|+++||||+|+...+.+.
T Consensus 67 ~~~~~-~~ad~~i~v~D~~~~~s~~~~~~~~~~i~~~~~~~~piiiv~NK~Dl~~~~~~~ 125 (191)
T cd04112 67 THAYY-RDAHALLLLYDITNKASFDNIRAWLTEIKEYAQEDVVIMLLGNKADMSGERVVK 125 (191)
T ss_pred hHHHc-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEEcccchhccccC
Confidence 45688 999999999999999999999999999988766689999999999997666554
No 56
>PLN03071 GTP-binding nuclear protein Ran; Provisional
Probab=99.60 E-value=4e-15 Score=91.37 Aligned_cols=54 Identities=37% Similarity=0.681 Sum_probs=49.3
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+++.|| ++++++|+|||+++++||+++..|++++.+.. +++|+++||||+|+.+
T Consensus 78 ~~~~~~-~~~~~~ilvfD~~~~~s~~~i~~w~~~i~~~~-~~~piilvgNK~Dl~~ 131 (219)
T PLN03071 78 LRDGYY-IHGQCAIIMFDVTARLTYKNVPTWHRDLCRVC-ENIPIVLCGNKVDVKN 131 (219)
T ss_pred hhHHHc-ccccEEEEEEeCCCHHHHHHHHHHHHHHHHhC-CCCcEEEEEEchhhhh
Confidence 457789 99999999999999999999999999998775 6799999999999964
No 57
>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=99.60 E-value=2.2e-15 Score=88.25 Aligned_cols=61 Identities=25% Similarity=0.279 Sum_probs=51.3
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc---CCCCeEEEEeeCCCCCCCCCchHH
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA---DSNIVIMMIGNKTDLKHLPTSMSI 64 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~---~~~~~~~lvgnK~Dl~~~~~v~~~ 64 (78)
+..++ ++++++++|||+++++||++++.|++.+++.. .+++|+++||||+|+.+.+.+...
T Consensus 66 ~~~~~-~~~~~~ilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~piilv~nK~Dl~~~~~v~~~ 129 (165)
T cd04140 66 QRLSI-SKGHAFILVYSVTSKQSLEELKPIYELICEIKGNNIEKIPIMLVGNKCDESHKREVSSN 129 (165)
T ss_pred HHHHh-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcCCCCCCCEEEEEECccccccCeecHH
Confidence 45678 99999999999999999999999988886643 267999999999999876666543
No 58
>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=99.59 E-value=2.7e-15 Score=87.14 Aligned_cols=60 Identities=28% Similarity=0.587 Sum_probs=52.3
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
++..|+ ++++++++|||+++++||+.+..|...+.... +++|+++||||.|+...+.++.
T Consensus 67 ~~~~~~-~~~~~~v~v~d~~~~~s~~~l~~~~~~~~~~~-~~~p~iiv~nK~Dl~~~~~v~~ 126 (162)
T cd04106 67 ITKAYY-RGAQACILVFSTTDRESFEAIESWKEKVEAEC-GDIPMVLVQTKIDLLDQAVITN 126 (162)
T ss_pred hHHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCEEEEEEChhcccccCCCH
Confidence 456788 99999999999999999999999999987665 6799999999999977666553
No 59
>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=99.59 E-value=5.7e-15 Score=86.88 Aligned_cols=65 Identities=23% Similarity=0.362 Sum_probs=55.0
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSL 68 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~ 68 (78)
+++.|| +++|++++|||.+++.+|+.++.|+.++.... +++|+++||||+|+.+.+.+++.....
T Consensus 60 ~~~~~~-~~ad~ii~V~D~t~~~s~~~~~~~l~~~~~~~-~~~piilv~NK~Dl~~~~~~~~i~~~~ 124 (164)
T cd04162 60 YWKRYL-SGSQGLIFVVDSADSERLPLARQELHQLLQHP-PDLPLVVLANKQDLPAARSVQEIHKEL 124 (164)
T ss_pred HHHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHhCC-CCCcEEEEEeCcCCcCCCCHHHHHHHh
Confidence 456789 99999999999999999999999998886554 689999999999998888776544443
No 60
>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=99.59 E-value=3.6e-15 Score=91.10 Aligned_cols=63 Identities=33% Similarity=0.663 Sum_probs=53.2
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC-CCCeEEEEeeCCCCCCCCCchHHH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD-SNIVIMMIGNKTDLKHLPTSMSIF 65 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~lvgnK~Dl~~~~~v~~~~ 65 (78)
+++.|| +++|++++|||+++++||+++..|+.++.+... ...|+++||||+|+.+.+.+....
T Consensus 68 ~~~~~~-~~~d~iilv~D~~~~~Sf~~l~~~~~~i~~~~~~~~~~iilvgNK~Dl~~~~~v~~~~ 131 (211)
T cd04111 68 ITRSYY-RNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCDLESQRQVTREE 131 (211)
T ss_pred HHHHHh-cCCcEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEccccccccccCHHH
Confidence 346788 999999999999999999999999999977653 468899999999998766665433
No 61
>PTZ00369 Ras-like protein; Provisional
Probab=99.59 E-value=3.5e-15 Score=89.44 Aligned_cols=61 Identities=23% Similarity=0.470 Sum_probs=52.5
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
+++.|+ ++++++++|||+++++||+.+..|...+.+.. .+++|+++||||+|+.+.+.++.
T Consensus 69 l~~~~~-~~~d~iilv~D~s~~~s~~~~~~~~~~i~~~~~~~~~piiiv~nK~Dl~~~~~i~~ 130 (189)
T PTZ00369 69 MRDQYM-RTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDSERQVST 130 (189)
T ss_pred hHHHHh-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECcccccccccCH
Confidence 456789 99999999999999999999999999987654 35899999999999977666553
No 62
>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=99.59 E-value=2.6e-15 Score=87.80 Aligned_cols=59 Identities=29% Similarity=0.481 Sum_probs=50.7
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc--CCCCeEEEEeeCCCCCCCCCchH
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA--DSNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~--~~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
..++ +++|++++|||+++++||+.++.|+..+.+.. ..+.|+++||||+|+.+.+.++.
T Consensus 66 ~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~v~~ 126 (165)
T cd04146 66 ERSI-RWADGFVLVYSITDRSSFDEISQLKQLIREIKKRDREIPVILVGNKADLLHYRQVST 126 (165)
T ss_pred HHHH-HhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECCchHHhCccCH
Confidence 4678 99999999999999999999999999887754 35799999999999976666653
No 63
>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=99.58 E-value=5.2e-15 Score=89.42 Aligned_cols=59 Identities=37% Similarity=0.750 Sum_probs=52.0
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
++..|+ ++++++++|||+++++||+.+..|+..+.... +..|+++||||+|+.+.+.+.
T Consensus 71 ~~~~~~-~~a~~iilv~D~~~~~s~~~~~~~~~~i~~~~-~~~piivVgNK~Dl~~~~~~~ 129 (199)
T cd04110 71 ITSTYY-RGTHGVIVVYDVTNGESFVNVKRWLQEIEQNC-DDVCKVLVGNKNDDPERKVVE 129 (199)
T ss_pred HHHHHh-CCCcEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCCEEEEEECcccccccccC
Confidence 456788 99999999999999999999999999987765 679999999999998766655
No 64
>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=99.58 E-value=6e-15 Score=86.23 Aligned_cols=59 Identities=37% Similarity=0.813 Sum_probs=52.1
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+..++ +++|++++|||+++++||+.++.|+..+......++|+++||||+|+.+.+.+.
T Consensus 69 ~~~~~-~~~d~~llv~d~~~~~s~~~~~~~~~~i~~~~~~~~p~ivv~nK~Dl~~~~~~~ 127 (165)
T cd01864 69 TQSYY-RSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIGNKCDLEEQREVL 127 (165)
T ss_pred HHHHh-ccCCEEEEEEECcCHHHHHhHHHHHHHHHHhCCCCCcEEEEEECcccccccccC
Confidence 46788 999999999999999999999999999987665789999999999997766554
No 65
>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=99.58 E-value=6.1e-15 Score=86.67 Aligned_cols=61 Identities=49% Similarity=0.874 Sum_probs=52.8
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
++..|+ +++|++++|||+++++||+.+..|+.++++...++.|+++||||.|+.+.+.++.
T Consensus 69 ~~~~~~-~~~d~il~v~d~~~~~s~~~~~~~~~~~~~~~~~~~pvivv~nK~Dl~~~~~~~~ 129 (168)
T cd01866 69 ITRSYY-RGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIGNKCDLESRREVSY 129 (168)
T ss_pred HHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEECcccccccCCCH
Confidence 345688 9999999999999999999999999999877657899999999999976555543
No 66
>KOG4252 consensus GTP-binding protein [Signal transduction mechanisms]
Probab=99.57 E-value=1.7e-15 Score=90.94 Aligned_cols=59 Identities=31% Similarity=0.527 Sum_probs=54.2
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
++..|| |||++.++||+.||+.||+.+..|++.++..+ .++|.++|-||+||-+..+++
T Consensus 85 ItkAyy-rgaqa~vLVFSTTDr~SFea~~~w~~kv~~e~-~~IPtV~vqNKIDlveds~~~ 143 (246)
T KOG4252|consen 85 ITKAYY-RGAQASVLVFSTTDRYSFEATLEWYNKVQKET-ERIPTVFVQNKIDLVEDSQMD 143 (246)
T ss_pred HHHHHh-ccccceEEEEecccHHHHHHHHHHHHHHHHHh-ccCCeEEeeccchhhHhhhcc
Confidence 567899 99999999999999999999999999998887 789999999999998776665
No 67
>PLN03108 Rab family protein; Provisional
Probab=99.57 E-value=6.8e-15 Score=89.70 Aligned_cols=62 Identities=50% Similarity=0.891 Sum_probs=53.7
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSI 64 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~ 64 (78)
+++.|+ +++|++++|||+++++||+.+..|+..+.....++.|+++||||+|+.+.+.++..
T Consensus 71 ~~~~~~-~~ad~~vlv~D~~~~~s~~~l~~~~~~~~~~~~~~~piiiv~nK~Dl~~~~~~~~~ 132 (210)
T PLN03108 71 ITRSYY-RGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKCDLAHRRAVSTE 132 (210)
T ss_pred HHHHHh-ccCCEEEEEEECCcHHHHHHHHHHHHHHHHhcCCCCcEEEEEECccCccccCCCHH
Confidence 356788 99999999999999999999999999887766678999999999999877666543
No 68
>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=99.57 E-value=8.2e-15 Score=85.11 Aligned_cols=60 Identities=35% Similarity=0.699 Sum_probs=51.2
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC-----CCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD-----SNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-----~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+++.++ ++++++|+|||+++++||+.+..|+.++.+... ...|+++||||+|+.+++.+.
T Consensus 65 ~~~~~~-~~~d~~ilv~D~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~ 129 (168)
T cd04119 65 VRNEFY-KDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKIDLTKHRAVS 129 (168)
T ss_pred HHHHHh-ccCCEEEEEEECCCHHHHHhHHHHHHHHHHhccccccCCCceEEEEEEchhcccccccC
Confidence 456788 999999999999999999999999999987653 469999999999997555444
No 69
>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=99.57 E-value=5.7e-15 Score=88.42 Aligned_cols=53 Identities=21% Similarity=0.496 Sum_probs=46.8
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
+++.|+ ++|+++++|||+++++||+++..|++++.+..+...| ++||||+||.
T Consensus 65 ~~~~~~-~~a~~iilv~D~t~~~s~~~i~~~~~~~~~~~~~~~p-ilVgnK~Dl~ 117 (182)
T cd04128 65 MLPLVC-NDAVAILFMFDLTRKSTLNSIKEWYRQARGFNKTAIP-ILVGTKYDLF 117 (182)
T ss_pred hhHHHC-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCE-EEEEEchhcc
Confidence 456788 9999999999999999999999999999877655677 6889999995
No 70
>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=99.56 E-value=1.9e-14 Score=85.12 Aligned_cols=58 Identities=33% Similarity=0.692 Sum_probs=49.5
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~ 60 (78)
+++.|| +++|++++|||+++++||+.+..|++++.+.. +.+.|+++||||.|+.+.+.
T Consensus 65 ~~~~~~-~~ad~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~iilVgnK~Dl~~~~~ 123 (170)
T cd04108 65 IASTYY-RGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDLSSPAQ 123 (170)
T ss_pred hHHHHh-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEChhcCcccc
Confidence 456788 99999999999999999999999999986543 45689999999999965543
No 71
>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=99.56 E-value=8e-15 Score=86.16 Aligned_cols=55 Identities=25% Similarity=0.523 Sum_probs=48.3
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHH-HHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVS-RWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
+++.++ +++|++++|||+++++||+++. .|+..+.... ++.|+++||||+|+.+.
T Consensus 62 ~~~~~~-~~~d~~ilv~d~~~~~s~~~~~~~~~~~i~~~~-~~~piilv~nK~Dl~~~ 117 (174)
T smart00174 62 LRPLSY-PDTDVFLICFSVDSPASFENVKEKWYPEVKHFC-PNTPIILVGTKLDLRED 117 (174)
T ss_pred hchhhc-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhC-CCCCEEEEecChhhhhC
Confidence 456788 9999999999999999999995 6999988765 68999999999999653
No 72
>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=99.55 E-value=1.4e-14 Score=87.83 Aligned_cols=59 Identities=20% Similarity=0.289 Sum_probs=50.5
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc---CCCCeEEEEeeCCCCCCCCCchHH
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA---DSNIVIMMIGNKTDLKHLPTSMSI 64 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~---~~~~~~~lvgnK~Dl~~~~~v~~~ 64 (78)
.++ +++|++++|||+++++||+.+..|++.+.+.. .+++|+++||||+|+.+.+.++..
T Consensus 76 ~~~-~~ad~iilv~D~~~~~S~~~~~~~~~~i~~~~~~~~~~~piiivgNK~Dl~~~~~~~~~ 137 (198)
T cd04142 76 RGL-RNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQQRHRFAPRH 137 (198)
T ss_pred hhh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcccCCCCCCEEEEEECccccccccccHH
Confidence 457 89999999999999999999999999887654 367999999999999776665543
No 73
>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=99.55 E-value=1.5e-14 Score=84.09 Aligned_cols=59 Identities=47% Similarity=0.842 Sum_probs=52.3
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
++.++ +++|++++|||++++++|+++..|+..++....+++|++++|||.|+.+.+.+.
T Consensus 66 ~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iivv~nK~D~~~~~~~~ 124 (161)
T cd04113 66 TRSYY-RGAAGALLVYDITNRTSFEALPTWLSDARALASPNIVVILVGNKSDLADQREVT 124 (161)
T ss_pred HHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEEchhcchhccCC
Confidence 46678 999999999999999999999999999877766889999999999997666554
No 74
>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=99.54 E-value=3.6e-14 Score=83.55 Aligned_cols=54 Identities=39% Similarity=0.739 Sum_probs=49.1
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+++.+| +++|++|+|||+++++||++++.|+.++.+.. +++|+++||||+|+.+
T Consensus 65 ~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~piiiv~nK~Dl~~ 118 (166)
T cd00877 65 LRDGYY-IGGQCAIIMFDVTSRVTYKNVPNWHRDLVRVC-GNIPIVLCGNKVDIKD 118 (166)
T ss_pred ccHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCcEEEEEEchhccc
Confidence 456788 99999999999999999999999999998876 4899999999999973
No 75
>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=99.54 E-value=3.5e-14 Score=83.67 Aligned_cols=66 Identities=27% Similarity=0.404 Sum_probs=55.1
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC-CCCeEEEEeeCCCCCCCCCchHHHHhc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD-SNIVIMMIGNKTDLKHLPTSMSIFQSL 68 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~lvgnK~Dl~~~~~v~~~~~~~ 68 (78)
+++.|| ++++++++|||.+++++|++++.|+..+.+... .+.|+++||||+|+.+.+...+....+
T Consensus 59 ~~~~~~-~~a~~ii~V~D~s~~~s~~~~~~~l~~l~~~~~~~~~piliv~NK~Dl~~~~~~~~i~~~~ 125 (167)
T cd04161 59 IWVNYY-AEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGADVIEYL 125 (167)
T ss_pred HHHHHH-cCCCEEEEEEECCchhHHHHHHHHHHHHHcCccccCCcEEEEEeCCCCcCCCCHHHHHHhc
Confidence 356789 999999999999999999999999998876532 579999999999998877665555543
No 76
>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=99.54 E-value=1.7e-14 Score=88.73 Aligned_cols=60 Identities=23% Similarity=0.310 Sum_probs=51.4
Q ss_pred ccchhc-CCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHH
Q 038356 4 SAYYNR-GALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSI 64 (78)
Q Consensus 4 ~~y~~~-~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~ 64 (78)
..++ + ++|++++|||+++++||+.+..|+..+.+.. ..+.|+++||||+|+.+.+.++..
T Consensus 66 ~~~~-~~~ad~iilV~d~td~~S~~~~~~~~~~l~~~~~~~~~piilV~NK~Dl~~~~~v~~~ 127 (221)
T cd04148 66 DSCM-QYQGDAFVVVYSVTDRSSFERASELRIQLRRNRQLEDRPIILVGNKSDLARSREVSVQ 127 (221)
T ss_pred hHHh-hcCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEChhccccceecHH
Confidence 4556 7 9999999999999999999999999987764 367999999999999877776644
No 77
>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=99.54 E-value=1.6e-14 Score=83.85 Aligned_cols=61 Identities=28% Similarity=0.506 Sum_probs=51.8
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
++..|+ +++|++++|||++++++|+.+..|...+.+.. ..+.|++++|||+|+.+.+.+..
T Consensus 66 ~~~~~~-~~~~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~piiiv~NK~Dl~~~~~~~~ 127 (164)
T cd04145 66 MREQYM-RTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEHQRKVSR 127 (164)
T ss_pred HHHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCCEEEEeeCccccccceecH
Confidence 356788 99999999999999999999999999887653 36799999999999977665553
No 78
>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=99.53 E-value=2.5e-14 Score=83.24 Aligned_cols=60 Identities=30% Similarity=0.565 Sum_probs=51.9
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
+.+.++ +++|++++|||+++++||+.+..|+..+.... ++.|+++||||+|+.+.+++..
T Consensus 68 ~~~~~~-~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~-~~~p~ilv~nK~Dl~~~~~~~~ 127 (164)
T cd04101 68 MVSNYW-ESPSVFILVYDVSNKASFENCSRWVNKVRTAS-KHMPGVLVGNKMDLADKAEVTD 127 (164)
T ss_pred HHHHHh-CCCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCEEEEEECcccccccCCCH
Confidence 345778 99999999999999999999999999987765 6799999999999977666554
No 79
>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=99.52 E-value=2.6e-14 Score=85.10 Aligned_cols=55 Identities=27% Similarity=0.533 Sum_probs=47.3
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHH-HHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVS-RWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
+++.|+ +++|++++|||+++++||+++. .|+..+.... ++.|+++||||+|+...
T Consensus 65 ~~~~~~-~~ad~ii~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~~ 120 (187)
T cd04132 65 LRPLSY-PDVDVLLICYAVDNPTSLDNVEDKWFPEVNHFC-PGTPIMLVGLKTDLRKD 120 (187)
T ss_pred HHHHhC-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEeChhhhhC
Confidence 345688 9999999999999999999995 6998887654 67999999999999654
No 80
>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=99.52 E-value=2.6e-14 Score=83.18 Aligned_cols=60 Identities=27% Similarity=0.511 Sum_probs=50.9
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+++.++ ++++++++|||+++++||+++..|...+.+.. ..+.|+++||||+|+.+.+.++
T Consensus 64 ~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~pii~v~nK~Dl~~~~~~~ 124 (164)
T smart00173 64 MRDQYM-RTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDLESERVVS 124 (164)
T ss_pred HHHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccceEc
Confidence 345678 99999999999999999999999998886654 3578999999999997766554
No 81
>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=99.51 E-value=4.6e-14 Score=83.27 Aligned_cols=54 Identities=22% Similarity=0.605 Sum_probs=47.2
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+++.|+ +++|++++|||+++++||+++ ..|+..++... ++.|++++|||+|+..
T Consensus 64 ~~~~~~-~~a~~~i~v~d~~~~~sf~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~ 118 (173)
T cd04130 64 LRPLCY-PDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHN-PKAPIILVGTQADLRT 118 (173)
T ss_pred cccccc-CCCcEEEEEEECCCHHHHHHHHHHHHHHHHhhC-CCCCEEEEeeChhhcc
Confidence 456788 999999999999999999999 57998887654 5799999999999964
No 82
>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=99.51 E-value=6.9e-14 Score=83.00 Aligned_cols=66 Identities=21% Similarity=0.335 Sum_probs=51.7
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHHHHhc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSIFQSL 68 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~~~~~ 68 (78)
+++.|| ++|+++|+|||++++++|+++..|+..+.... .+++|++|||||+||.+.....+.....
T Consensus 73 ~~~~~~-~~ad~ii~v~D~t~~~s~~~~~~~l~~~~~~~~~~~~piilv~NK~Dl~~~~~~~~i~~~~ 139 (175)
T smart00177 73 LWRHYY-TNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKL 139 (175)
T ss_pred HHHHHh-CCCCEEEEEEECCCHHHHHHHHHHHHHHhhCHhhcCCcEEEEEeCcCcccCCCHHHHHHHh
Confidence 356789 99999999999999999999988887775432 2579999999999997655444444433
No 83
>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=99.51 E-value=5.5e-14 Score=82.40 Aligned_cols=59 Identities=29% Similarity=0.545 Sum_probs=49.4
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc----CCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA----DSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~----~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+++.|+ ++++++++|||+++++||+.+..|..++.... ..++|+++||||+|+. .+.+.
T Consensus 70 ~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~-~~~~~ 132 (170)
T cd04116 70 LRTPFY-RGSDCCLLTFAVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVVLGNKNDIP-ERQVS 132 (170)
T ss_pred hHHHHh-cCCCEEEEEEECCCHHHHHhHHHHHHHHHHhcccccCCCCcEEEEEECcccc-ccccC
Confidence 456789 99999999999999999999999999886644 2568999999999996 34443
No 84
>KOG0393 consensus Ras-related small GTPase, Rho type [General function prediction only]
Probab=99.51 E-value=4.2e-14 Score=85.85 Aligned_cols=55 Identities=31% Similarity=0.626 Sum_probs=50.7
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
+++.-| .++|.++++|++.+++||+++ .+|+.+++.++ +++|++|||+|.||+++
T Consensus 69 lRplsY-~~tdvfl~cfsv~~p~S~~nv~~kW~pEi~~~c-p~vpiiLVGtk~DLr~d 124 (198)
T KOG0393|consen 69 LRPLSY-PQTDVFLLCFSVVSPESFENVKSKWIPEIKHHC-PNVPIILVGTKADLRDD 124 (198)
T ss_pred ccccCC-CCCCEEEEEEEcCChhhHHHHHhhhhHHHHhhC-CCCCEEEEeehHHhhhC
Confidence 456778 999999999999999999999 88999999998 89999999999999854
No 85
>PLN00223 ADP-ribosylation factor; Provisional
Probab=99.51 E-value=7.9e-14 Score=83.36 Aligned_cols=67 Identities=18% Similarity=0.294 Sum_probs=53.3
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhh-cCCCCeEEEEeeCCCCCCCCCchHHHHhcc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDH-ADSNIVIMMIGNKTDLKHLPTSMSIFQSLS 69 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~-~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~ 69 (78)
+++.|| +++|++|+|||++++++|+.+..|+..+... ..+++|++|+|||+|+.+.....+....++
T Consensus 77 ~~~~~~-~~a~~iI~V~D~s~~~s~~~~~~~l~~~l~~~~~~~~piilv~NK~Dl~~~~~~~~~~~~l~ 144 (181)
T PLN00223 77 LWRHYF-QNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLG 144 (181)
T ss_pred HHHHHh-ccCCEEEEEEeCCcHHHHHHHHHHHHHHhcCHhhCCCCEEEEEECCCCCCCCCHHHHHHHhC
Confidence 456789 9999999999999999999998777766432 226799999999999987666555555544
No 86
>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=99.50 E-value=9e-14 Score=86.96 Aligned_cols=60 Identities=18% Similarity=0.264 Sum_probs=50.3
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhh---------cCCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDH---------ADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~---------~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+++.|+ +++|++|+|||+++++||+++..|.+++.+. ...+.|+++||||+|+.+.+.+.
T Consensus 64 ~~~~~~-~~ad~iIlVfdv~~~~Sf~~i~~~~~~I~~~k~~~~~~~~~~~~~piIivgNK~Dl~~~~~v~ 132 (247)
T cd04143 64 MRRLSI-LTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICGNKADRDFPREVQ 132 (247)
T ss_pred HHHHHh-ccCCEEEEEEeCCCHHHHHHHHHHHHHHHHhhcccccccccCCCCcEEEEEECccchhccccC
Confidence 345678 9999999999999999999999999998653 22579999999999997655554
No 87
>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=99.50 E-value=8.6e-14 Score=80.38 Aligned_cols=60 Identities=38% Similarity=0.772 Sum_probs=52.5
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+++.++ +++|++++|||++++++++.+..|..++....+.+.|++++|||+|+.+.+.+.
T Consensus 65 ~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piiiv~nK~D~~~~~~~~ 124 (162)
T cd04123 65 LGPIYY-RDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKIDLERQRVVS 124 (162)
T ss_pred hhHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccccccCCC
Confidence 456788 999999999999999999999999999987765689999999999998666554
No 88
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=99.49 E-value=7.9e-14 Score=80.88 Aligned_cols=59 Identities=54% Similarity=0.972 Sum_probs=51.6
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
++.++ +++|++++|||+++++|++.+..|+..+.....+++|++++|||+|+...+.+.
T Consensus 66 ~~~~~-~~~d~~ilv~d~~~~~s~~~~~~~l~~~~~~~~~~~pivvv~nK~D~~~~~~~~ 124 (164)
T smart00175 66 TSSYY-RGAVGALLVYDITNRESFENLKNWLKELREYADPNVVIMLVGNKSDLEDQRQVS 124 (164)
T ss_pred HHHHh-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEEchhcccccCCC
Confidence 45678 999999999999999999999999999987766789999999999997655444
No 89
>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=99.49 E-value=1.3e-13 Score=80.60 Aligned_cols=61 Identities=16% Similarity=0.308 Sum_probs=48.3
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhh-cCCCCeEEEEeeCCCCCCCCCchH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDH-ADSNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~-~~~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
+++.|| +++|++++|||.++++||+++..|+..+... ...+.|++|+|||+|+.+.....+
T Consensus 60 ~~~~~~-~~ad~~i~v~D~~~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~~~~~~ 121 (159)
T cd04150 60 LWRHYF-QNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNAMSAAE 121 (159)
T ss_pred HHHHHh-cCCCEEEEEEeCCCHHHHHHHHHHHHHHHhcHHhcCCCEEEEEECCCCCCCCCHHH
Confidence 356789 9999999999999999999998877766432 225689999999999976443333
No 90
>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=99.47 E-value=9.7e-14 Score=80.16 Aligned_cols=55 Identities=22% Similarity=0.520 Sum_probs=48.6
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~ 57 (78)
+++.|+ ++++++++|||++++++|+++..|...+.+.. ..+.|+++||||+|+.+
T Consensus 65 l~~~~~-~~~~~~i~v~~~~~~~s~~~~~~~~~~i~~~~~~~~~piivv~nK~Dl~~ 120 (162)
T cd04138 65 MRDQYM-RTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLAA 120 (162)
T ss_pred HHHHHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccc
Confidence 456788 99999999999999999999999999987765 35799999999999965
No 91
>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=99.47 E-value=1e-13 Score=81.87 Aligned_cols=56 Identities=23% Similarity=0.262 Sum_probs=47.7
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~ 60 (78)
+++.|| +++|++++|||.++++||+.+..|+..+... .++|+++||||+|+.+.+.
T Consensus 70 ~~~~~~-~~~d~~llv~d~~~~~s~~~~~~~~~~~~~~--~~~p~iiv~NK~Dl~~~~~ 125 (169)
T cd01892 70 LNDAEL-AACDVACLVYDSSDPKSFSYCAEVYKKYFML--GEIPCLFVAAKADLDEQQQ 125 (169)
T ss_pred cchhhh-hcCCEEEEEEeCCCHHHHHHHHHHHHHhccC--CCCeEEEEEEccccccccc
Confidence 456788 9999999999999999999999999876432 4799999999999975553
No 92
>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=99.47 E-value=2.4e-13 Score=80.24 Aligned_cols=57 Identities=19% Similarity=0.354 Sum_probs=47.0
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~ 60 (78)
++.|| +++|++++|||.+++.+|+++..|+.++.... .+++|++|||||+|+.+...
T Consensus 70 ~~~~~-~~a~~ii~v~D~t~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~~~ 127 (168)
T cd04149 70 WRHYY-TGTQGLIFVVDSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAMK 127 (168)
T ss_pred HHHHh-ccCCEEEEEEeCCchhhHHHHHHHHHHHhcCHhhcCCcEEEEEECcCCccCCC
Confidence 46788 99999999999999999999988777665432 36789999999999975433
No 93
>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=99.46 E-value=2.1e-13 Score=79.06 Aligned_cols=59 Identities=32% Similarity=0.683 Sum_probs=50.4
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
.+.++ ++++++++|||+++++||+.+..|+..+....+.+.|++++|||+|+.+.+.+.
T Consensus 66 ~~~~~-~~~~~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilv~nK~D~~~~~~~~ 124 (161)
T cd01861 66 IPSYI-RDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLSDKRQVS 124 (161)
T ss_pred HHHHh-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCEEEEEEEChhccccCccC
Confidence 45678 999999999999999999999999999876654579999999999996555444
No 94
>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=99.46 E-value=1.9e-13 Score=80.24 Aligned_cols=60 Identities=23% Similarity=0.427 Sum_probs=52.0
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+++.++ ++++++++|||++++++|+.+..|...+.+.. ..+.|++++|||.|+.+.+.++
T Consensus 65 ~~~~~~-~~~~~~vlv~~~~~~~s~~~~~~~~~~i~~~~~~~~~piiiv~nK~D~~~~~~~~ 125 (168)
T cd04177 65 MRELYI-KSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLEDDRQVS 125 (168)
T ss_pred hhHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCCEEEEEEChhccccCccC
Confidence 467788 99999999999999999999999999987644 3679999999999997766554
No 95
>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=99.45 E-value=2.9e-13 Score=80.97 Aligned_cols=54 Identities=37% Similarity=0.714 Sum_probs=47.8
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
++..|| +++|++++|||+++++||+++..|++.++... ++.|+++||||+|+.+
T Consensus 66 ~~~~~~-~~~d~iilv~d~~~~~s~~~~~~~~~~i~~~~-~~~piilv~nK~Dl~~ 119 (193)
T cd04118 66 MSRIYY-RGAKAAIVCYDLTDSSSFERAKFWVKELQNLE-EHCKIYLCGTKSDLIE 119 (193)
T ss_pred hhHhhc-CCCCEEEEEEECCCHHHHHHHHHHHHHHHhcC-CCCCEEEEEEcccccc
Confidence 345678 99999999999999999999999999987764 5799999999999853
No 96
>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=99.45 E-value=2.9e-13 Score=79.11 Aligned_cols=61 Identities=28% Similarity=0.613 Sum_probs=52.3
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHH
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSI 64 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~ 64 (78)
+..|+ +++|++++|||+++++||+.+..|+.++......++|++++|||+|+.+.+++...
T Consensus 73 ~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~l~~~~~~~~~~i~v~NK~D~~~~~~i~~~ 133 (169)
T cd04114 73 TQSYY-RSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVGNKIDLAERREVSQQ 133 (169)
T ss_pred HHHHh-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccccccccCHH
Confidence 35678 99999999999999999999999999887766567999999999999876666543
No 97
>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=99.44 E-value=3.9e-13 Score=78.58 Aligned_cols=54 Identities=33% Similarity=0.713 Sum_probs=48.4
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+++.|+ +++|++++|||++++.+|+.+..|+..+++.. ++.|+++||||+|+.+
T Consensus 65 ~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~p~ivv~nK~Dl~~ 118 (161)
T cd04124 65 MHASYY-HKAHACILVFDVTRKITYKNLSKWYEELREYR-PEIPCIVVANKIDLDP 118 (161)
T ss_pred hhHHHh-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHhC-CCCcEEEEEECccCch
Confidence 456789 99999999999999999999999999997764 6799999999999853
No 98
>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=99.44 E-value=5.3e-13 Score=78.61 Aligned_cols=59 Identities=15% Similarity=0.206 Sum_probs=49.0
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCch
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+..|+ +++|++++|||.+++++|+++..|+..+.+.. ..+.|+++||||+|+.+.....
T Consensus 60 ~~~~~-~~ad~ii~V~D~s~~~s~~~~~~~~~~~~~~~~~~~~piilv~NK~Dl~~~~~~~ 119 (169)
T cd04158 60 WKHYY-LNTQAVVFVVDSSHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVE 119 (169)
T ss_pred HHHHh-ccCCEEEEEEeCCcHHHHHHHHHHHHHHhcChhhCCCCEEEEEeCcCcccCCCHH
Confidence 45788 99999999999999999999999998886543 2568999999999997543333
No 99
>PTZ00133 ADP-ribosylation factor; Provisional
Probab=99.44 E-value=6.1e-13 Score=79.52 Aligned_cols=67 Identities=18% Similarity=0.321 Sum_probs=50.8
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhh-cCCCCeEEEEeeCCCCCCCCCchHHHHhcc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDH-ADSNIVIMMIGNKTDLKHLPTSMSIFQSLS 69 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~-~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~ 69 (78)
+++.|| +++|++|+|||++++++|+.+..|+..+... ...+.|++|||||.|+.+.....+.....+
T Consensus 77 ~~~~~~-~~ad~iI~v~D~t~~~s~~~~~~~l~~~~~~~~~~~~piilv~NK~Dl~~~~~~~~i~~~l~ 144 (182)
T PTZ00133 77 LWRHYY-QNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKLG 144 (182)
T ss_pred HHHHHh-cCCCEEEEEEeCCCHHHHHHHHHHHHHHHhCHhhcCCCEEEEEeCCCCCCCCCHHHHHHHhC
Confidence 356789 9999999999999999999997777666332 225689999999999976544444444443
No 100
>PLN03118 Rab family protein; Provisional
Probab=99.44 E-value=3.1e-13 Score=82.25 Aligned_cols=60 Identities=40% Similarity=0.664 Sum_probs=49.2
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHH-HHHHHhhhc-CCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSR-WLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~-~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
++..|+ +++|++++|||+++++||+++.. |...+.... ..+.|+++||||+|+...+.++
T Consensus 78 ~~~~~~-~~~d~~vlv~D~~~~~sf~~~~~~~~~~~~~~~~~~~~~~ilv~NK~Dl~~~~~i~ 139 (211)
T PLN03118 78 LTSSYY-RNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGNKVDRESERDVS 139 (211)
T ss_pred HHHHHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEECccccccCccC
Confidence 356788 99999999999999999999965 777665543 2568999999999998766665
No 101
>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=99.41 E-value=7.2e-13 Score=76.94 Aligned_cols=59 Identities=41% Similarity=0.776 Sum_probs=51.2
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
++.++ +++|++++|||.+++++|+.+..|+..+.....+++|+++++||+|+.+.+.+.
T Consensus 67 ~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iivv~nK~D~~~~~~~~ 125 (163)
T cd01860 67 APMYY-RGAAAAIVVYDITSEESFEKAKSWVKELQRNASPNIIIALVGNKADLESKRQVS 125 (163)
T ss_pred HHHHh-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECccccccCcCC
Confidence 45678 999999999999999999999999999987766789999999999997555433
No 102
>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=99.38 E-value=2e-12 Score=75.06 Aligned_cols=54 Identities=48% Similarity=0.916 Sum_probs=48.2
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLK 56 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~ 56 (78)
+++.++ +++|++++|||.++++||+.+..|+..+.+.. ..+.|++++|||+|+.
T Consensus 65 ~~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~~~~~iv~nK~D~~ 119 (161)
T cd01863 65 LTSSYY-RGAQGVILVYDVTRRDTFTNLETWLNELETYSTNNDIVKMLVGNKIDKE 119 (161)
T ss_pred hhHHHh-CCCCEEEEEEECCCHHHHHhHHHHHHHHHHhCCCCCCcEEEEEECCccc
Confidence 345678 99999999999999999999999999998775 3679999999999997
No 103
>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=99.38 E-value=1.2e-12 Score=78.32 Aligned_cols=52 Identities=25% Similarity=0.548 Sum_probs=45.8
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHH-HHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVS-RWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~-~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+.++ +++++++++||+++++||+.+. .|...++... +++|+++||||+|+.+
T Consensus 67 ~~~~-~~a~~~llv~~i~~~~s~~~~~~~~~~~i~~~~-~~~piilvgnK~Dl~~ 119 (187)
T cd04129 67 PLSY-SKAHVILIGFAVDTPDSLENVRTKWIEEVRRYC-PNVPVILVGLKKDLRQ 119 (187)
T ss_pred hhhc-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEeeChhhhh
Confidence 4567 8999999999999999999995 6999998765 5799999999999954
No 104
>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=99.37 E-value=3.5e-12 Score=74.90 Aligned_cols=55 Identities=22% Similarity=0.491 Sum_probs=47.7
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
+++.++ ++++++++|||+++++||+.+ ..|...+... .++.|++++|||+|+.+.
T Consensus 64 ~~~~~~-~~~~~~ilv~~~~~~~s~~~~~~~~~~~l~~~-~~~~piivv~nK~Dl~~~ 119 (174)
T cd04135 64 LRPLSY-PMTDVFLICFSVVNPASFQNVKEEWVPELKEY-APNVPYLLVGTQIDLRDD 119 (174)
T ss_pred cccccC-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHhh-CCCCCEEEEeEchhhhcC
Confidence 456788 999999999999999999999 5798888766 478999999999998643
No 105
>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=99.37 E-value=2.9e-12 Score=74.21 Aligned_cols=58 Identities=26% Similarity=0.369 Sum_probs=48.6
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc---CCCCeEEEEeeCCCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA---DSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~---~~~~~~~lvgnK~Dl~~~~~ 60 (78)
++..|+ ++++++++|+|.+++.+|..+..|+..+.+.. ..+.|+++||||+|+.+...
T Consensus 61 ~~~~~~-~~~d~ii~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~iiv~NK~Dl~~~~~ 121 (162)
T cd04157 61 LWEHYY-KNIQGIIFVIDSSDRLRLVVVKDELELLLNHPDIKHRRVPILFFANKMDLPDALT 121 (162)
T ss_pred HHHHHH-ccCCEEEEEEeCCcHHHHHHHHHHHHHHHcCcccccCCCCEEEEEeCccccCCCC
Confidence 356788 99999999999999999999999988875532 25799999999999976543
No 106
>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=99.37 E-value=3.2e-12 Score=74.97 Aligned_cols=55 Identities=31% Similarity=0.537 Sum_probs=47.6
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~ 60 (78)
..++ +++|++++|||+++++||+.+ ..|.+.+++.. ++.|+++||||+|+.+.+.
T Consensus 65 ~~~~-~~ad~~ilv~d~~~~~s~~~~~~~~~~~i~~~~-~~~pviiv~nK~Dl~~~~~ 120 (166)
T cd01893 65 AAEI-RKANVICLVYSVDRPSTLERIRTKWLPLIRRLG-VKVPIILVGNKSDLRDGSS 120 (166)
T ss_pred hhhc-ccCCEEEEEEECCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEEEchhcccccc
Confidence 4567 899999999999999999998 57988887765 5899999999999977654
No 107
>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=99.34 E-value=4.2e-12 Score=74.86 Aligned_cols=60 Identities=18% Similarity=0.278 Sum_probs=49.0
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhh-cCCCCeEEEEeeCCCCCCCCCchH
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDH-ADSNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~-~~~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
+..|+ +++|++++|||.+++++|+++..|+..+... ...+.|+++||||+|+.+.....+
T Consensus 75 ~~~~~-~~~d~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~iiv~nK~Dl~~~~~~~~ 135 (173)
T cd04154 75 WRNYF-ESTDALIWVVDSSDRLRLDDCKRELKELLQEERLAGATLLILANKQDLPGALSEEE 135 (173)
T ss_pred HHHHh-CCCCEEEEEEECCCHHHHHHHHHHHHHHHhChhhcCCCEEEEEECcccccCCCHHH
Confidence 45688 9999999999999999999998888877543 236799999999999976554333
No 108
>KOG3883 consensus Ras family small GTPase [Signal transduction mechanisms]
Probab=99.34 E-value=4e-12 Score=74.85 Aligned_cols=66 Identities=21% Similarity=0.324 Sum_probs=53.8
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC-CCCeEEEEeeCCCCCCCCCchHHHHhc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD-SNIVIMMIGNKTDLKHLPTSMSIFQSL 68 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~lvgnK~Dl~~~~~v~~~~~~~ 68 (78)
|.+.|+ .-+||+++||+..|++||+.+.-..+++.++.. ..+||++.|||.|+.+.+++....++.
T Consensus 77 Lprhy~-q~aDafVLVYs~~d~eSf~rv~llKk~Idk~KdKKEvpiVVLaN~rdr~~p~~vd~d~A~~ 143 (198)
T KOG3883|consen 77 LPRHYF-QFADAFVLVYSPMDPESFQRVELLKKEIDKHKDKKEVPIVVLANKRDRAEPREVDMDVAQI 143 (198)
T ss_pred hhHhHh-ccCceEEEEecCCCHHHHHHHHHHHHHHhhccccccccEEEEechhhcccchhcCHHHHHH
Confidence 346788 999999999999999999998766666666553 679999999999998888877544443
No 109
>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=99.33 E-value=3.9e-12 Score=79.53 Aligned_cols=58 Identities=16% Similarity=0.136 Sum_probs=49.3
Q ss_pred CccccchhcCCcEEEEEEECCChh-hHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 1 VINSAYYNRGALGALLVYDVTKST-TFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+|.+.|+ +++|++++|||+++++ ||+.+..|+..+.. .++|+++|+||+||.+.+.+.
T Consensus 28 ~L~r~~~-~n~D~viiV~d~~~p~~s~~~l~r~l~~~~~---~~i~~vIV~NK~DL~~~~~~~ 86 (245)
T TIGR00157 28 ELTRPIV-ANIDQIVIVSSAVLPELSLNQLDRFLVVAEA---QNIEPIIVLNKIDLLDDEDME 86 (245)
T ss_pred eEECccc-ccCCEEEEEEECCCCCCCHHHHHHHHHHHHH---CCCCEEEEEECcccCCCHHHH
Confidence 3667899 9999999999999988 89999999987653 568999999999997655554
No 110
>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=99.33 E-value=1e-11 Score=72.98 Aligned_cols=53 Identities=23% Similarity=0.571 Sum_probs=46.1
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
++.++ +++|++++|||+++++||+++ ..|...++... ++.|+++||||+|+.+
T Consensus 66 ~~~~~-~~~d~~i~v~~~~~~~s~~~~~~~~~~~~~~~~-~~~piilv~nK~Dl~~ 119 (175)
T cd01870 66 RPLSY-PDTDVILMCFSIDSPDSLENIPEKWTPEVKHFC-PNVPIILVGNKKDLRN 119 (175)
T ss_pred ccccc-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhC-CCCCEEEEeeChhccc
Confidence 45678 999999999999999999999 56988887654 6799999999999864
No 111
>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=99.33 E-value=9.7e-12 Score=72.06 Aligned_cols=62 Identities=19% Similarity=0.279 Sum_probs=49.2
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHHH
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSIF 65 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~~ 65 (78)
+..|+ ++++++++|+|.+++.++..+..|+.++.+.. ..+.|+++|+||+|+.+.....+..
T Consensus 61 ~~~~~-~~~~~iv~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~~~~~~~~i~ 123 (160)
T cd04156 61 WKCYL-ENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGALTAEEIT 123 (160)
T ss_pred HHHHh-ccCCEEEEEEECCcHHHHHHHHHHHHHHHhchhhcCCCEEEEEECcccccCcCHHHHH
Confidence 45678 99999999999999999999988888875443 2579999999999997544333333
No 112
>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=99.32 E-value=4.3e-12 Score=73.45 Aligned_cols=58 Identities=26% Similarity=0.488 Sum_probs=49.4
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCc
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTS 61 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v 61 (78)
+..++ +++++++++||+++++||+++..|...+.+.. ..+.|+++|+||+|+.+.+..
T Consensus 65 ~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~piiiv~NK~D~~~~~~~ 123 (164)
T cd04139 65 RDNYH-RSGEGFLLVFSITDMESFTATAEFREQILRVKDDDNVPLLLVGNKCDLEDKRQV 123 (164)
T ss_pred HHHHh-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEcccccccccc
Confidence 45678 99999999999999999999999999887764 357999999999999764433
No 113
>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=99.31 E-value=1.3e-11 Score=74.42 Aligned_cols=60 Identities=22% Similarity=0.304 Sum_probs=50.6
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC-CCCeEEEEeeCCCCCC-CCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD-SNIVIMMIGNKTDLKH-LPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~lvgnK~Dl~~-~~~v~ 62 (78)
+++.|+ +++|++++|||++++++|+.+..|+..+.+... .+.|+++||||.|+.. .+.+.
T Consensus 63 ~~~~~~-~~ad~vilv~d~~~~~s~~~~~~~~~~i~~~~~~~~~piilv~NK~Dl~~~~~~v~ 124 (198)
T cd04147 63 MRKLSI-QNSDAFALVYAVDDPESFEEVERLREEILEVKEDKFVPIVVVGNKADSLEEERQVP 124 (198)
T ss_pred HHHHHh-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEEcccccccccccc
Confidence 345788 999999999999999999999999988877653 5799999999999965 35444
No 114
>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=99.31 E-value=9.5e-12 Score=74.38 Aligned_cols=67 Identities=18% Similarity=0.270 Sum_probs=53.2
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHHHHhcc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSIFQSLS 69 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~ 69 (78)
++..|| ++++++++|+|.+++++++....|+.++.+.. ..+.|+++|+||+|+.+.....+....++
T Consensus 77 ~~~~~~-~~ad~ii~vvD~~~~~~~~~~~~~l~~l~~~~~~~~~piliv~NK~Dl~~~~~~~~i~~~l~ 144 (184)
T smart00178 77 LWKDYF-PEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAASEDELRYALG 144 (184)
T ss_pred HHHHHh-CCCCEEEEEEECCcHHHHHHHHHHHHHHHcChhhcCCCEEEEEeCccccCCCCHHHHHHHcC
Confidence 346788 99999999999999999999988887775432 25789999999999976555555555554
No 115
>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=99.31 E-value=1.3e-11 Score=73.04 Aligned_cols=65 Identities=28% Similarity=0.324 Sum_probs=49.7
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHHHHhc
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSIFQSL 68 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~~~~~ 68 (78)
++.|| +++|++++|+|.+++++|..++.|+..+.+.. ..+.|+++++||+|+.+.....+....+
T Consensus 76 ~~~~~-~~~d~vi~V~D~s~~~~~~~~~~~l~~~~~~~~~~~~p~viv~NK~Dl~~~~~~~~i~~~l 141 (174)
T cd04153 76 WNTYY-TNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAMTPAEISESL 141 (174)
T ss_pred HHHHh-hcCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhcCCCEEEEEECCCCCCCCCHHHHHHHh
Confidence 45678 99999999999999999999987777765433 2579999999999997643333333333
No 116
>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=99.30 E-value=1.6e-11 Score=71.73 Aligned_cols=58 Identities=36% Similarity=0.651 Sum_probs=48.2
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC----CCCeEEEEeeCCCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD----SNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~----~~~~~~lvgnK~Dl~~~~~ 60 (78)
++..|+ +++++++++||++++++|+++..|...+..... .++|+++||||+|+...+.
T Consensus 65 ~~~~~~-~~~d~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~ 126 (172)
T cd01862 65 LGVAFY-RGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPSDPENFPFVVLGNKIDLEEKRQ 126 (172)
T ss_pred HHHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCccCCCCceEEEEEECcccccccc
Confidence 346788 999999999999999999999999888755442 3799999999999974433
No 117
>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=99.30 E-value=8.8e-12 Score=69.34 Aligned_cols=47 Identities=36% Similarity=0.767 Sum_probs=38.2
Q ss_pred chhcCCcEEEEEEECCChhhHHHHHH---HHHHHhhhcCCCCeEEEEeeCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVSR---WLKDLGDHADSNIVIMMIGNKTD 54 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~~---~~~~~~~~~~~~~~~~lvgnK~D 54 (78)
.+ .++|++++|||+++++||+.+.+ |+..+.... +++|+++||||.|
T Consensus 70 ~~-~~~d~~ilv~D~s~~~s~~~~~~~~~~l~~~~~~~-~~~piilv~nK~D 119 (119)
T PF08477_consen 70 FL-KKADAVILVYDLSDPESLEYLSQLLKWLKNIRKRD-KNIPIILVGNKSD 119 (119)
T ss_dssp HH-HHSCEEEEEEECCGHHHHHHHHHHHHHHHHHHHHS-SCSEEEEEEE-TC
T ss_pred hh-hcCcEEEEEEcCCChHHHHHHHHHHHHHHHHHccC-CCCCEEEEEeccC
Confidence 46 88999999999999999999844 566665544 6699999999998
No 118
>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=99.29 E-value=7.2e-12 Score=72.15 Aligned_cols=59 Identities=29% Similarity=0.505 Sum_probs=50.2
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC-CCCeEEEEeeCCCCCCCCCch
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD-SNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+..++ ++++++++|||++++++++++..|...+.+... ...|++++|||+|+.+.+.++
T Consensus 64 ~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~~~~~~~ 123 (160)
T cd00876 64 RDLYI-RQGDGFILVYSITDRESFEEIKGYREQILRVKDDEDIPIVLVGNKCDLENERQVS 123 (160)
T ss_pred HHHHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEECCcccccceec
Confidence 34567 899999999999999999999999988877654 589999999999998755544
No 119
>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=99.28 E-value=2.1e-11 Score=72.74 Aligned_cols=60 Identities=18% Similarity=0.315 Sum_probs=49.4
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCch
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+++.|+ ++++++++|+|.+++++++.+..|+.++.+.. ..+.|+++|+||+|+.+.....
T Consensus 68 ~~~~~~-~~~d~ii~v~D~~~~~~~~~~~~~~~~i~~~~~~~~~p~iiv~NK~D~~~~~~~~ 128 (183)
T cd04152 68 LWKSYT-RCTDGIVFVVDSVDVERMEEAKTELHKITRFSENQGVPVLVLANKQDLPNALSVS 128 (183)
T ss_pred HHHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHhhhhcCCCcEEEEEECcCccccCCHH
Confidence 346788 99999999999999999999999998886653 2578999999999997544333
No 120
>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=99.26 E-value=3.1e-11 Score=69.90 Aligned_cols=64 Identities=19% Similarity=0.311 Sum_probs=51.3
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHHHHh
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSIFQS 67 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~~~~ 67 (78)
++.++ +++|++++|||++++++|..+..|+..+.... ..+.|+++++||+|+.+.+...+....
T Consensus 60 ~~~~~-~~~~~~i~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~piiiv~nK~D~~~~~~~~~~~~~ 124 (158)
T cd00878 60 WKHYY-ENTNGIIFVVDSSDRERIEEAKEELHKLLNEEELKGVPLLIFANKQDLPGALSVSELIEK 124 (158)
T ss_pred HHHHh-ccCCEEEEEEECCCHHHHHHHHHHHHHHHhCcccCCCcEEEEeeccCCccccCHHHHHHh
Confidence 45678 99999999999999999999988888775543 367999999999999776544444333
No 121
>PTZ00132 GTP-binding nuclear protein Ran; Provisional
Probab=99.26 E-value=3.4e-11 Score=73.37 Aligned_cols=54 Identities=35% Similarity=0.699 Sum_probs=48.1
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
++..|+ ++++++++|||++++.||..+..|+..+.+.. +++|++++|||+|+.+
T Consensus 74 ~~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~-~~~~i~lv~nK~Dl~~ 127 (215)
T PTZ00132 74 LRDGYY-IKGQCAIIMFDVTSRITYKNVPNWHRDIVRVC-ENIPIVLVGNKVDVKD 127 (215)
T ss_pred hhHHHh-ccCCEEEEEEECcCHHHHHHHHHHHHHHHHhC-CCCCEEEEEECccCcc
Confidence 346688 99999999999999999999999999998765 6799999999999964
No 122
>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=99.25 E-value=4.7e-11 Score=69.34 Aligned_cols=63 Identities=17% Similarity=0.258 Sum_probs=47.3
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHH-hhhcCCCCeEEEEeeCCCCCCCCCchHHHH
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDL-GDHADSNIVIMMIGNKTDLKHLPTSMSIFQ 66 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~-~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~ 66 (78)
++.|+ ++++++++|+|.+++.++.....|+..+ ++....+.|+++++||+|+.+.....+...
T Consensus 60 ~~~~~-~~~~~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~piiiv~nK~Dl~~~~~~~~i~~ 123 (158)
T cd04151 60 WRCYY-SNTDAIIYVVDSTDRDRLGTAKEELHAMLEEEELKGAVLLVFANKQDMPGALSEAEISE 123 (158)
T ss_pred HHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhcCCcEEEEEeCCCCCCCCCHHHHHH
Confidence 46788 9999999999999999998886665544 332235799999999999975543344333
No 123
>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=99.25 E-value=1.7e-11 Score=72.43 Aligned_cols=59 Identities=31% Similarity=0.452 Sum_probs=49.0
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCch
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+..++ +++++++++||+++.++|+.+..|+..+.+.. ..+.|+++|+||+|+...+.+.
T Consensus 66 ~~~~~-~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~NK~Dl~~~~~~~ 125 (180)
T cd04137 66 PQKYS-IGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDLHTQRQVS 125 (180)
T ss_pred HHHHH-hhCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEchhhhhcCccC
Confidence 45677 89999999999999999999999888876644 3678999999999997655444
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=99.24 E-value=2.9e-11 Score=69.07 Aligned_cols=53 Identities=53% Similarity=0.998 Sum_probs=47.8
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
...++ +++|++++|+|.+++++++.+..|+..+.....++.|+++++||+|+.
T Consensus 66 ~~~~~-~~~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~ 118 (159)
T cd00154 66 TPSYY-RGAHGAILVYDITNRESFENLDKWLKELKEYAPENIPIILVGNKIDLE 118 (159)
T ss_pred HHHHh-cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEEccccc
Confidence 35677 999999999999999999999999999987765789999999999996
No 125
>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=99.22 E-value=3.4e-11 Score=70.24 Aligned_cols=55 Identities=25% Similarity=0.556 Sum_probs=47.2
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
++.++ +.+|++++|||+++++||... ..|...+.... ++.|+++||||+|+.+.+
T Consensus 65 ~~~~~-~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~-~~~p~ivv~nK~Dl~~~~ 120 (171)
T cd00157 65 RPLSY-PNTDVFLICFSVDSPSSFENVKTKWIPEIRHYC-PNVPIILVGTKIDLRDDE 120 (171)
T ss_pred chhhc-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhC-CCCCEEEEEccHHhhhch
Confidence 45677 899999999999999999988 67888887665 589999999999997654
No 126
>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=99.22 E-value=6.8e-11 Score=70.47 Aligned_cols=62 Identities=19% Similarity=0.311 Sum_probs=49.2
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHHH
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSIF 65 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~~ 65 (78)
+..|+ ++++++++|+|.+++++|+....|+..+.+.. ..+.|++++|||+|+.+.....+..
T Consensus 80 ~~~~~-~~ad~iilV~D~~~~~s~~~~~~~~~~i~~~~~~~~~pvivv~NK~Dl~~~~~~~~~~ 142 (190)
T cd00879 80 WKDYF-PEVDGIVFLVDAADPERFQESKEELDSLLSDEELANVPFLILGNKIDLPGAVSEEELR 142 (190)
T ss_pred HHHHh-ccCCEEEEEEECCcHHHHHHHHHHHHHHHcCccccCCCEEEEEeCCCCCCCcCHHHHH
Confidence 45688 99999999999999999999988888876543 2569999999999997543333333
No 127
>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]
Probab=99.21 E-value=4.8e-11 Score=72.42 Aligned_cols=58 Identities=38% Similarity=0.683 Sum_probs=49.5
Q ss_pred ccccchhcCCcEEEEEEECCCh-hhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKS-TTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~-~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~ 60 (78)
+++.|| +++++++++||.+++ .+++.+..|..++....+.+.|+++||||+||...+.
T Consensus 70 ~~~~y~-~~~~~~l~~~d~~~~~~~~~~~~~~~~~l~~~~~~~~~iilv~nK~Dl~~~~~ 128 (219)
T COG1100 70 LRPEYY-RGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFDEQS 128 (219)
T ss_pred HHHHHh-cCCCEEEEEEecccchhhhHHHHHHHHHHHHhCCCCceEEEEecccccccchh
Confidence 567899 999999999999995 4555569999999888766799999999999987653
No 128
>KOG0070 consensus GTP-binding ADP-ribosylation factor Arf1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.20 E-value=1e-10 Score=70.10 Aligned_cols=67 Identities=19% Similarity=0.333 Sum_probs=57.5
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC-CCCeEEEEeeCCCCCCCCCchHHHHhcc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD-SNIVIMMIGNKTDLKHLPTSMSIFQSLS 69 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~lvgnK~Dl~~~~~v~~~~~~~~ 69 (78)
+++.|| ++.+++|+|.|.+|++.+...+.-+..+..+.. .++|+++.+||.|+++...+.+..+.++
T Consensus 77 lW~~Y~-~~t~~lIfVvDS~Dr~Ri~eak~eL~~~l~~~~l~~~~llv~aNKqD~~~als~~ei~~~L~ 144 (181)
T KOG0070|consen 77 LWKHYF-QNTQGLIFVVDSSDRERIEEAKEELHRMLAEPELRNAPLLVFANKQDLPGALSAAEITNKLG 144 (181)
T ss_pred chhhhc-cCCcEEEEEEeCCcHHHHHHHHHHHHHHHcCcccCCceEEEEechhhccccCCHHHHHhHhh
Confidence 678999 999999999999999999999776666655543 6899999999999999988887777665
No 129
>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=99.19 E-value=9.4e-11 Score=68.32 Aligned_cols=57 Identities=21% Similarity=0.319 Sum_probs=47.6
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~ 60 (78)
+..++ ++++++++|+|.+++++++....|+..+.+.. ..+.|+++++||+|+.+...
T Consensus 67 ~~~~~-~~~~~~v~vvd~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~NK~D~~~~~~ 124 (167)
T cd04160 67 WDKYY-AECHAIIYVIDSTDRERFEESKSALEKVLRNEALEGVPLLILANKQDLPDALS 124 (167)
T ss_pred HHHHh-CCCCEEEEEEECchHHHHHHHHHHHHHHHhChhhcCCCEEEEEEccccccCCC
Confidence 45678 99999999999999999999988888876543 36799999999999976443
No 130
>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=99.18 E-value=2.4e-10 Score=68.03 Aligned_cols=66 Identities=24% Similarity=0.380 Sum_probs=53.6
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHHHHhc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSIFQSL 68 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~~~~~ 68 (78)
+++.|| ++++++|+|.|.++++.+...+..+.++.... -.++|+++++||+|+.+.....+....+
T Consensus 74 ~w~~y~-~~~~~iIfVvDssd~~~l~e~~~~L~~ll~~~~~~~~piLIl~NK~D~~~~~~~~~i~~~l 140 (175)
T PF00025_consen 74 LWKSYF-QNADGIIFVVDSSDPERLQEAKEELKELLNDPELKDIPILILANKQDLPDAMSEEEIKEYL 140 (175)
T ss_dssp GGGGGH-TTESEEEEEEETTGGGGHHHHHHHHHHHHTSGGGTTSEEEEEEESTTSTTSSTHHHHHHHT
T ss_pred cceeec-cccceeEEEEecccceeecccccchhhhcchhhcccceEEEEeccccccCcchhhHHHhhh
Confidence 578999 99999999999999999999987777775433 3679999999999998766655554444
No 131
>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=99.13 E-value=1.4e-10 Score=67.72 Aligned_cols=55 Identities=16% Similarity=0.061 Sum_probs=45.8
Q ss_pred cCCcEEEEEEECCCh-hhHHHHHHHHHHHhhhcC--CCCeEEEEeeCCCCCCCCCchH
Q 038356 9 RGALGALLVYDVTKS-TTFENVSRWLKDLGDHAD--SNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~-~s~~~~~~~~~~~~~~~~--~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
+.+|++++|+|.+++ ++++++..|.+++.+..+ .+.|+++|+||+|+.+...+.+
T Consensus 77 ~~~d~vi~v~D~~~~~~~~~~~~~~~~~l~~~~~~~~~~p~ivv~NK~Dl~~~~~~~~ 134 (170)
T cd01898 77 ERTRLLLHVIDLSGDDDPVEDYKTIRNELELYNPELLEKPRIVVLNKIDLLDEEELFE 134 (170)
T ss_pred HhCCEEEEEEecCCCCCHHHHHHHHHHHHHHhCccccccccEEEEEchhcCCchhhHH
Confidence 359999999999999 899999999998877642 4689999999999976555543
No 132
>KOG0096 consensus GTPase Ran/TC4/GSP1 (nuclear protein transport pathway), small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.13 E-value=5.8e-11 Score=71.82 Aligned_cols=54 Identities=39% Similarity=0.690 Sum_probs=49.4
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
++.-|| -+++|.|++||++++-++.++..|.+++.+.+ .++||+++|||.|.+.
T Consensus 75 lrdgyy-I~~qcAiimFdVtsr~t~~n~~rwhrd~~rv~-~NiPiv~cGNKvDi~~ 128 (216)
T KOG0096|consen 75 LRDGYY-IQGQCAIIMFDVTSRFTYKNVPRWHRDLVRVR-ENIPIVLCGNKVDIKA 128 (216)
T ss_pred cccccE-EecceeEEEeeeeehhhhhcchHHHHHHHHHh-cCCCeeeeccceeccc
Confidence 456788 89999999999999999999999999999988 6699999999999865
No 133
>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=99.12 E-value=4.5e-10 Score=64.20 Aligned_cols=61 Identities=26% Similarity=0.356 Sum_probs=48.5
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHH
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSI 64 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~ 64 (78)
+..|+ +++|++++|+|.++++++.....|+..+.... ..+.|+++|+||+|+.+.......
T Consensus 61 ~~~~~-~~~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~p~iiv~nK~D~~~~~~~~~~ 122 (159)
T cd04159 61 WERYC-RGVNAIVYVVDAADRTALEAAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDEL 122 (159)
T ss_pred HHHHH-hcCCEEEEEEECCCHHHHHHHHHHHHHHHcChhhcCCCEEEEEeCccccCCcCHHHH
Confidence 45678 99999999999999999999887777765432 367899999999999766554433
No 134
>KOG0071 consensus GTP-binding ADP-ribosylation factor Arf6 (dArf3) [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.04 E-value=9.7e-10 Score=64.07 Aligned_cols=66 Identities=23% Similarity=0.404 Sum_probs=54.4
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC-CCCeEEEEeeCCCCCCCCCchHHHHhc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD-SNIVIMMIGNKTDLKHLPTSMSIFQSL 68 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~lvgnK~Dl~~~~~v~~~~~~~ 68 (78)
+++.|| .++.|+|+|.|..+++..++.+.-+..+-.+.+ .++|+++.+||.|+++.+.+.+....+
T Consensus 77 lWrhYy-~gtqglIFV~Dsa~~dr~eeAr~ELh~ii~~~em~~~~~LvlANkQDlp~A~~pqei~d~l 143 (180)
T KOG0071|consen 77 LWRHYY-TGTQGLIFVVDSADRDRIEEARNELHRIINDREMRDAIILILANKQDLPDAMKPQEIQDKL 143 (180)
T ss_pred HHHhhc-cCCceEEEEEeccchhhHHHHHHHHHHHhCCHhhhcceEEEEecCcccccccCHHHHHHHh
Confidence 578999 999999999999999999999766555544433 679999999999999988887766544
No 135
>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=98.98 E-value=3.9e-09 Score=61.84 Aligned_cols=65 Identities=18% Similarity=0.296 Sum_probs=50.0
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchHHHHhcc
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMSIFQSLS 69 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~ 69 (78)
..++ ++++++++|+|.++..++.....|...+.+.. ..++|+++++||+|+.+.....+.....+
T Consensus 76 ~~~~-~~~~~ii~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~~~~~~~~i~~~l~ 141 (173)
T cd04155 76 RNYF-ENTDCLIYVIDSADKKRLEEAGAELVELLEEEKLAGVPVLVFANKQDLATAAPAEEIAEALN 141 (173)
T ss_pred HHHh-cCCCEEEEEEeCCCHHHHHHHHHHHHHHHhChhhcCCCEEEEEECCCCccCCCHHHHHHHcC
Confidence 4577 89999999999999999999877766664432 35799999999999976555555544443
No 136
>PRK12299 obgE GTPase CgtA; Reviewed
Probab=98.97 E-value=1.1e-09 Score=71.35 Aligned_cols=54 Identities=15% Similarity=0.107 Sum_probs=45.8
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC--CCCeEEEEeeCCCCCCCCCch
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHAD--SNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
..++++++|+|+++.++++.+..|.+++....+ .+.|+++|+||+|+.+...+.
T Consensus 235 e~a~vlI~ViD~s~~~s~e~~~~~~~EL~~~~~~L~~kp~IIV~NKiDL~~~~~~~ 290 (335)
T PRK12299 235 ERTRLLLHLVDIEAVDPVEDYKTIRNELEKYSPELADKPRILVLNKIDLLDEEEER 290 (335)
T ss_pred hhcCEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhcccCCeEEEEECcccCCchhHH
Confidence 578999999999998899999999999987653 468999999999997655443
No 137
>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=98.93 E-value=4.4e-09 Score=63.45 Aligned_cols=54 Identities=22% Similarity=0.126 Sum_probs=45.4
Q ss_pred hhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCc
Q 038356 7 YNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTS 61 (78)
Q Consensus 7 ~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v 61 (78)
+ +++|++++|+|.+++.++..+..|.+.+......+.|+++|+||+|+.+....
T Consensus 118 ~-~~~d~ii~v~D~~~~~~~~~~~~~~~~l~~~~~~~~~viiV~NK~Dl~~~~~~ 171 (204)
T cd01878 118 V-AEADLLLHVVDASDPDYEEQIETVEKVLKELGAEDIPMILVLNKIDLLDDEEL 171 (204)
T ss_pred H-hcCCeEEEEEECCCCChhhHHHHHHHHHHHcCcCCCCEEEEEEccccCChHHH
Confidence 5 78999999999999999998888888777655467899999999999765443
No 138
>KOG0075 consensus GTP-binding ADP-ribosylation factor-like protein [General function prediction only]
Probab=98.92 E-value=2.5e-09 Score=62.79 Aligned_cols=68 Identities=24% Similarity=0.408 Sum_probs=54.1
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcC-CCCeEEEEeeCCCCCCCCCchHHHHhcc
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHAD-SNIVIMMIGNKTDLKHLPTSMSIFQSLS 69 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~lvgnK~Dl~~~~~v~~~~~~~~ 69 (78)
+++..|+ |+.++++.|.|..+++.++..++-++.+....+ ..+|+++.|||.|+++.-.-.....+++
T Consensus 80 smWeryc-R~v~aivY~VDaad~~k~~~sr~EL~~LL~k~~l~gip~LVLGnK~d~~~AL~~~~li~rmg 148 (186)
T KOG0075|consen 80 SMWERYC-RGVSAIVYVVDAADPDKLEASRSELHDLLDKPSLTGIPLLVLGNKIDLPGALSKIALIERMG 148 (186)
T ss_pred HHHHHHh-hcCcEEEEEeecCCcccchhhHHHHHHHhcchhhcCCcEEEecccccCcccccHHHHHHHhC
Confidence 4677889 999999999999999999988776666654433 6899999999999988766555555544
No 139
>smart00010 small_GTPase Small GTPase of the Ras superfamily; ill-defined subfamily. SMART predicts Ras-like small GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies. Others that could not be classified in this way are predicted to be members of the small GTPase superfamily without predictions of the subfamily.
Probab=98.91 E-value=7.2e-09 Score=57.50 Aligned_cols=57 Identities=16% Similarity=0.163 Sum_probs=47.1
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
...++ ++++++++||+.++++|++.+ |...+......++|.+++|||.|+.+++.+.
T Consensus 40 ~~~~~-~s~~~~~~v~~~~~~~s~~~~--~~~~i~~~~k~dl~~~~~~nk~dl~~~~~~~ 96 (124)
T smart00010 40 DPTSY-ESFDVVLQCWRVDDRDSADNK--NVPEVLVGNKSDLPILVGGNRDVLEEERQVA 96 (124)
T ss_pred ccccc-CCCCEEEEEEEccCHHHHHHH--hHHHHHhcCCCCCcEEEEeechhhHhhCcCC
Confidence 46788 999999999999999999877 8877765555679999999999996555444
No 140
>KOG0073 consensus GTP-binding ADP-ribosylation factor-like protein ARL2 [Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=98.88 E-value=9.1e-09 Score=61.14 Aligned_cols=61 Identities=16% Similarity=0.248 Sum_probs=47.7
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHH-hhhcCCCCeEEEEeeCCCCCCCCCchH
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDL-GDHADSNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~-~~~~~~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
.|+.|| ..+||.|+|+|.+|+..|+....-+.++ .+..-...|+++++||.|+.+.-+..+
T Consensus 76 ~W~nYf-estdglIwvvDssD~~r~~e~~~~L~~lL~eerlaG~~~Lvlank~dl~~~l~~~~ 137 (185)
T KOG0073|consen 76 YWKNYF-ESTDGLIWVVDSSDRMRMQECKQELTELLVEERLAGAPLLVLANKQDLPGALSLEE 137 (185)
T ss_pred HHHHhh-hccCeEEEEEECchHHHHHHHHHHHHHHHhhhhhcCCceEEEEecCcCccccCHHH
Confidence 478999 9999999999999999999986655554 333225689999999999986544443
No 141
>KOG4423 consensus GTP-binding protein-like, RAS superfamily [Signal transduction mechanisms]
Probab=98.86 E-value=1.7e-09 Score=65.56 Aligned_cols=55 Identities=38% Similarity=0.729 Sum_probs=48.6
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc----CCCCeEEEEeeCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA----DSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~----~~~~~~~lvgnK~Dl~~ 57 (78)
|+.-|| +.|++..+|||+++.-+|+.+..|..++.... +..+|+++.+||||+..
T Consensus 91 mtrVyy-kea~~~~iVfdvt~s~tfe~~skwkqdldsk~qLpng~Pv~~vllankCd~e~ 149 (229)
T KOG4423|consen 91 MTRVYY-KEAHGAFIVFDVTRSLTFEPVSKWKQDLDSKLQLPNGTPVPCVLLANKCDQEK 149 (229)
T ss_pred eEEEEe-cCCcceEEEEEccccccccHHHHHHHhccCcccCCCCCcchheeccchhccCh
Confidence 678899 99999999999999999999999999986654 24688999999999864
No 142
>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=98.85 E-value=6.6e-09 Score=61.17 Aligned_cols=51 Identities=27% Similarity=0.333 Sum_probs=40.4
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
+..++ +++|++|+|+|.++..++.....|..... .++|+++|+||+|+.+.
T Consensus 84 ~~~~~-~~ad~~i~v~D~~~~~~~~~~~~~~~~~~----~~~~iiiv~NK~Dl~~~ 134 (179)
T cd01890 84 VSRSL-AACEGALLLVDATQGVEAQTLANFYLALE----NNLEIIPVINKIDLPSA 134 (179)
T ss_pred HHHHH-HhcCeEEEEEECCCCccHhhHHHHHHHHH----cCCCEEEEEECCCCCcC
Confidence 34678 99999999999999888777777754322 45789999999999653
No 143
>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=98.84 E-value=1e-08 Score=62.44 Aligned_cols=57 Identities=19% Similarity=0.304 Sum_probs=44.5
Q ss_pred ccchhcCC-cEEEEEEECCCh-hhHHHHHHHHHHHhhhc---CCCCeEEEEeeCCCCCCCCCc
Q 038356 4 SAYYNRGA-LGALLVYDVTKS-TTFENVSRWLKDLGDHA---DSNIVIMMIGNKTDLKHLPTS 61 (78)
Q Consensus 4 ~~y~~~~a-~~~ilv~d~~~~-~s~~~~~~~~~~~~~~~---~~~~~~~lvgnK~Dl~~~~~v 61 (78)
..|+ +++ +++|+|+|.++. +++..+..|+..+.... .+.+|+++++||+|+...+..
T Consensus 66 ~~~~-~~~~~~vV~VvD~~~~~~~~~~~~~~l~~il~~~~~~~~~~pvliv~NK~Dl~~a~~~ 127 (203)
T cd04105 66 LETL-KNSAKGIVFVVDSATFQKNLKDVAEFLYDILTDLEKVKNKIPVLIACNKQDLFTAKPA 127 (203)
T ss_pred HHHH-hccCCEEEEEEECccchhHHHHHHHHHHHHHHHHhhccCCCCEEEEecchhhcccCCH
Confidence 4577 898 999999999998 78888877766553321 367999999999999765544
No 144
>KOG1707 consensus Predicted Ras related/Rac-GTP binding protein [Defense mechanisms]
Probab=98.83 E-value=8.5e-09 Score=70.73 Aligned_cols=53 Identities=25% Similarity=0.415 Sum_probs=46.6
Q ss_pred cCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcC--CCCeEEEEeeCCCCCCCCCc
Q 038356 9 RGALGALLVYDVTKSTTFENV-SRWLKDLGDHAD--SNIVIMMIGNKTDLKHLPTS 61 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~--~~~~~~lvgnK~Dl~~~~~v 61 (78)
|.|+++.++|++++++|++.+ ..|+..+++..+ .++|++|||||+|+.....-
T Consensus 78 rkA~vi~lvyavd~~~T~D~ist~WLPlir~~~~~~~~~PVILvGNK~d~~~~~~~ 133 (625)
T KOG1707|consen 78 RKADVICLVYAVDDESTVDRISTKWLPLIRQLFGDYHETPVILVGNKSDNGDNENN 133 (625)
T ss_pred hhcCEEEEEEecCChHHhhhhhhhhhhhhhcccCCCccCCEEEEeeccCCcccccc
Confidence 789999999999999999999 789999987763 57999999999999765443
No 145
>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=98.81 E-value=4.8e-09 Score=59.84 Aligned_cols=44 Identities=16% Similarity=0.004 Sum_probs=34.8
Q ss_pred chhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
++ +++|++++|||++++.|+.. ..|.... . .|+++|+||+|+.+
T Consensus 59 ~~-~~ad~vilv~d~~~~~s~~~-~~~~~~~-----~-~p~ilv~NK~Dl~~ 102 (142)
T TIGR02528 59 TA-ADADVIALVQSATDPESRFP-PGFASIF-----V-KPVIGLVTKIDLAE 102 (142)
T ss_pred Hh-hcCCEEEEEecCCCCCcCCC-hhHHHhc-----c-CCeEEEEEeeccCC
Confidence 47 89999999999999999865 3454321 1 39999999999965
No 146
>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=98.81 E-value=1.4e-08 Score=59.09 Aligned_cols=52 Identities=15% Similarity=0.240 Sum_probs=41.4
Q ss_pred CCcEEEEEEECCChhhH--HHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 10 GALGALLVYDVTKSTTF--ENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~--~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
.+|++++|+|.+++.++ +....|+..+++.. ++.|+++|+||+|+.+.+.+.
T Consensus 79 ~~d~~l~v~d~~~~~~~~~~~~~~~~~~l~~~~-~~~pvilv~NK~Dl~~~~~~~ 132 (168)
T cd01897 79 LRAAVLFLFDPSETCGYSLEEQLSLFEEIKPLF-KNKPVIVVLNKIDLLTFEDLS 132 (168)
T ss_pred ccCcEEEEEeCCcccccchHHHHHHHHHHHhhc-CcCCeEEEEEccccCchhhHH
Confidence 36899999999998764 66677888887654 579999999999997665554
No 147
>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=98.81 E-value=1.5e-08 Score=59.18 Aligned_cols=57 Identities=19% Similarity=0.111 Sum_probs=46.2
Q ss_pred chhcCCcEEEEEEECCCh------hhHHHHHHHHHHHhhhcC-------CCCeEEEEeeCCCCCCCCCchH
Q 038356 6 YYNRGALGALLVYDVTKS------TTFENVSRWLKDLGDHAD-------SNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~------~s~~~~~~~~~~~~~~~~-------~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
++ ++++++++|+|.+++ ++++....|..++..... .+.|+++|+||+|+...+....
T Consensus 71 ~~-~~~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ivv~NK~Dl~~~~~~~~ 140 (176)
T cd01881 71 HI-RRADAILHVVDASEDDDIGGVDPLEDYEILNAELKLYDLETILGLLTAKPVIYVLNKIDLDDAEELEE 140 (176)
T ss_pred HH-hccCEEEEEEeccCCccccccCHHHHHHHHHHHHHHhhhhhHHHHHhhCCeEEEEEchhcCchhHHHH
Confidence 46 789999999999998 688888888888865532 3689999999999976555544
No 148
>KOG1673 consensus Ras GTPases [General function prediction only]
Probab=98.78 E-value=1.5e-08 Score=60.06 Aligned_cols=50 Identities=20% Similarity=0.539 Sum_probs=42.8
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
|.-. .++.+++++||++++++++++..|+.+.+.....-+| ++||+|.|+
T Consensus 87 Piac-~dsvaIlFmFDLt~r~TLnSi~~WY~QAr~~NktAiP-ilvGTKyD~ 136 (205)
T KOG1673|consen 87 PIAC-KDSVAILFMFDLTRRSTLNSIKEWYRQARGLNKTAIP-ILVGTKYDL 136 (205)
T ss_pred ceee-cCcEEEEEEEecCchHHHHHHHHHHHHHhccCCccce-EEeccchHh
Confidence 3345 7899999999999999999999999999877655566 689999996
No 149
>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=98.76 E-value=2.6e-08 Score=65.24 Aligned_cols=55 Identities=25% Similarity=0.184 Sum_probs=44.9
Q ss_pred chhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCc
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTS 61 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v 61 (78)
++ ++||++++|+|.+++.+++.+..|...+.+....+.|+++|+||+|+.+...+
T Consensus 265 ~~-~~ADlil~VvD~s~~~~~~~~~~~~~~L~~l~~~~~piIlV~NK~Dl~~~~~v 319 (351)
T TIGR03156 265 EV-READLLLHVVDASDPDREEQIEAVEKVLEELGAEDIPQLLVYNKIDLLDEPRI 319 (351)
T ss_pred HH-HhCCEEEEEEECCCCchHHHHHHHHHHHHHhccCCCCEEEEEEeecCCChHhH
Confidence 46 89999999999999999988887777666654457899999999999754443
No 150
>KOG0076 consensus GTP-binding ADP-ribosylation factor-like protein yARL3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.71 E-value=6.3e-09 Score=62.35 Aligned_cols=65 Identities=20% Similarity=0.287 Sum_probs=52.7
Q ss_pred CccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhh-hcCCCCeEEEEeeCCCCCCCCCchHHHH
Q 038356 1 VINSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGD-HADSNIVIMMIGNKTDLKHLPTSMSIFQ 66 (78)
Q Consensus 1 sl~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~-~~~~~~~~~lvgnK~Dl~~~~~v~~~~~ 66 (78)
||+..|| ..+|++|.++|.++++.|+....-++.+.. ....++|+++.+||.|+.+..++.+...
T Consensus 84 Slw~~yY-~~~H~ii~viDa~~~eR~~~~~t~~~~v~~~E~leg~p~L~lankqd~q~~~~~~El~~ 149 (197)
T KOG0076|consen 84 SLWKKYY-WLAHGIIYVIDATDRERFEESKTAFEKVVENEKLEGAPVLVLANKQDLQNAMEAAELDG 149 (197)
T ss_pred HHHHHHH-HHhceeEEeecCCCHHHHHHHHHHHHHHHHHHHhcCCchhhhcchhhhhhhhhHHHHHH
Confidence 5778899 999999999999999999998665555533 3347899999999999988766665443
No 151
>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=98.70 E-value=2.9e-08 Score=64.57 Aligned_cols=53 Identities=15% Similarity=0.085 Sum_probs=43.4
Q ss_pred CCcEEEEEEECCCh---hhHHHHHHHHHHHhhhcC--CCCeEEEEeeCCCCCCCCCch
Q 038356 10 GALGALLVYDVTKS---TTFENVSRWLKDLGDHAD--SNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 10 ~a~~~ilv~d~~~~---~s~~~~~~~~~~~~~~~~--~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
.++++++|+|+++. ++++++..|.+++..... .+.|+++|+||+|+.+.....
T Consensus 235 rad~ll~VvD~s~~~~~~~~e~l~~l~~EL~~~~~~l~~kp~IIV~NK~DL~~~~~~~ 292 (329)
T TIGR02729 235 RTRVLLHLIDISPLDGRDPIEDYEIIRNELKKYSPELAEKPRIVVLNKIDLLDEEELA 292 (329)
T ss_pred hhCEEEEEEcCccccccCHHHHHHHHHHHHHHhhhhhccCCEEEEEeCccCCChHHHH
Confidence 69999999999987 788888899888876542 468999999999997654433
No 152
>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=98.66 E-value=2.2e-07 Score=51.86 Aligned_cols=56 Identities=48% Similarity=0.765 Sum_probs=43.8
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHH-HHhhhcCCCCeEEEEeeCCCCCCCCCc
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLK-DLGDHADSNIVIMMIGNKTDLKHLPTS 61 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~-~~~~~~~~~~~~~lvgnK~Dl~~~~~v 61 (78)
.++ +.++++++|+|.++..+++....|.. ..........|+++++||+|+.+....
T Consensus 64 ~~~-~~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivv~nk~D~~~~~~~ 120 (157)
T cd00882 64 LYY-RGADGIILVYDVTDRESFENVKEWLLLILINKEGENIPIILVGNKIDLPEERVV 120 (157)
T ss_pred HHh-cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhhccCCCcEEEEEeccccccccch
Confidence 466 89999999999999999999988732 223333478999999999999765443
No 153
>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=98.64 E-value=8.7e-08 Score=64.48 Aligned_cols=49 Identities=24% Similarity=0.232 Sum_probs=40.1
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
..|+ +++|++++|+|.+++.+++.. |+..+.. .+.|+++|+||+|+.+.
T Consensus 277 ~~~~-~~aD~il~V~D~s~~~s~~~~--~l~~~~~---~~~piIlV~NK~Dl~~~ 325 (442)
T TIGR00450 277 FKAI-KQADLVIYVLDASQPLTKDDF--LIIDLNK---SKKPFILVLNKIDLKIN 325 (442)
T ss_pred HHHH-hhCCEEEEEEECCCCCChhHH--HHHHHhh---CCCCEEEEEECccCCCc
Confidence 3578 999999999999999988875 7666542 46799999999999643
No 154
>PRK11058 GTPase HflX; Provisional
Probab=98.64 E-value=1.1e-07 Score=63.71 Aligned_cols=51 Identities=24% Similarity=0.169 Sum_probs=41.7
Q ss_pred chhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
++ ++||++++|+|.+++.+++.+..|...+......+.|+++|+||+|+.+
T Consensus 273 ~~-~~ADlIL~VvDaS~~~~~e~l~~v~~iL~el~~~~~pvIiV~NKiDL~~ 323 (426)
T PRK11058 273 ET-RQATLLLHVVDAADVRVQENIEAVNTVLEEIDAHEIPTLLVMNKIDMLD 323 (426)
T ss_pred Hh-hcCCEEEEEEeCCCccHHHHHHHHHHHHHHhccCCCCEEEEEEcccCCC
Confidence 46 8999999999999999998886666555554445789999999999964
No 155
>KOG0074 consensus GTP-binding ADP-ribosylation factor-like protein ARL3 [General function prediction only]
Probab=98.63 E-value=4.7e-08 Score=57.20 Aligned_cols=67 Identities=27% Similarity=0.377 Sum_probs=52.6
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHH-hhhcCCCCeEEEEeeCCCCCCCCCchHHHHhcc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDL-GDHADSNIVIMMIGNKTDLKHLPTSMSIFQSLS 69 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~-~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~ 69 (78)
.|..|| .+.|++|+|.|.+|+..|+++..-+.++ .+..-..+|+.+.+||.|+-....+++.+.+++
T Consensus 78 yWsNYy-envd~lIyVIDS~D~krfeE~~~el~ELleeeKl~~vpvlIfankQdlltaa~~eeia~kln 145 (185)
T KOG0074|consen 78 YWSNYY-ENVDGLIYVIDSTDEKRFEEISEELVELLEEEKLAEVPVLIFANKQDLLTAAKVEEIALKLN 145 (185)
T ss_pred hhhhhh-hccceEEEEEeCCchHhHHHHHHHHHHHhhhhhhhccceeehhhhhHHHhhcchHHHHHhcc
Confidence 367899 9999999999999999999995544444 444446799999999999977666666665554
No 156
>PRK12289 GTPase RsgA; Reviewed
Probab=98.60 E-value=1.1e-07 Score=62.44 Aligned_cols=54 Identities=22% Similarity=0.259 Sum_probs=41.7
Q ss_pred ccccchhcCCcEEEEEEECCChh-hHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKST-TFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
|.+..+ +++|.+++|+|+++++ +...+..|+..+.. .++|+++|+||+||....
T Consensus 82 L~R~~~-aNvD~vLlV~d~~~p~~~~~~LdR~L~~a~~---~~ip~ILVlNK~DLv~~~ 136 (352)
T PRK12289 82 LDRPPV-ANADQILLVFALAEPPLDPWQLSRFLVKAES---TGLEIVLCLNKADLVSPT 136 (352)
T ss_pred eechhh-hcCCEEEEEEECCCCCCCHHHHHHHHHHHHH---CCCCEEEEEEchhcCChH
Confidence 345567 8999999999999876 55567778766532 568999999999996443
No 157
>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=98.53 E-value=2.5e-07 Score=55.55 Aligned_cols=52 Identities=17% Similarity=0.123 Sum_probs=37.3
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
...|+ +++|++++|+|.++. .+.....|+..+.. .++|+++|+||+|+.+.+
T Consensus 82 ~~~~~-~~~d~~ilV~d~~~~-~~~~~~~~~~~~~~---~~~p~iiv~NK~Dl~~~~ 133 (194)
T cd01891 82 VERVL-SMVDGVLLLVDASEG-PMPQTRFVLKKALE---LGLKPIVVINKIDRPDAR 133 (194)
T ss_pred HHHHH-HhcCEEEEEEECCCC-ccHHHHHHHHHHHH---cCCCEEEEEECCCCCCCC
Confidence 35678 999999999999874 23344444444432 468999999999996543
No 158
>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=98.46 E-value=3.1e-07 Score=58.70 Aligned_cols=49 Identities=14% Similarity=0.110 Sum_probs=41.6
Q ss_pred chhcCCcEEEEEEECCChh-hHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 6 YYNRGALGALLVYDVTKST-TFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
.+ .++|.+++|+|.+++. ++..+..|+..+.. .++|+++|.||+||.+.
T Consensus 75 i~-anvD~vllV~d~~~p~~s~~~ldr~L~~~~~---~~ip~iIVlNK~DL~~~ 124 (287)
T cd01854 75 IA-ANVDQLVIVVSLNEPFFNPRLLDRYLVAAEA---AGIEPVIVLTKADLLDD 124 (287)
T ss_pred EE-EeCCEEEEEEEcCCCCCCHHHHHHHHHHHHH---cCCCEEEEEEHHHCCCh
Confidence 36 7999999999999998 88988889887654 45899999999999654
No 159
>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=98.44 E-value=6.4e-07 Score=50.59 Aligned_cols=55 Identities=33% Similarity=0.567 Sum_probs=45.0
Q ss_pred ccchhcCCcEEEEEEECCCh-hhHHHHH-HHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKS-TTFENVS-RWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~-~s~~~~~-~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
+.++ +.+++++.++|+... .+++... .|...+.+....+.|+++++||.|+...+
T Consensus 68 ~~~~-~~~~~~i~~~d~~~~v~~~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~~~~ 124 (161)
T TIGR00231 68 RLYY-RAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESNVPIILVGNKIDLRDAK 124 (161)
T ss_pred HHHH-hhhhEEEEEEEEeeeehhhhhHhHHHHHHHHHhcccCCcEEEEEEcccCCcch
Confidence 4557 889999999999998 8888874 78887776664489999999999997644
No 160
>KOG0072 consensus GTP-binding ADP-ribosylation factor-like protein ARL1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.43 E-value=5.5e-07 Score=52.89 Aligned_cols=66 Identities=15% Similarity=0.209 Sum_probs=50.2
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhcc
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSLS 69 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~ 69 (78)
|+.|| .+.+++|.|.|.+|++..... ...+..+++..-.+..+++++||.|.......++....++
T Consensus 79 WRcYy-~dt~avIyVVDssd~dris~a~~el~~mL~E~eLq~a~llv~anKqD~~~~~t~~E~~~~L~ 145 (182)
T KOG0072|consen 79 WRCYY-ADTDAVIYVVDSSDRDRISIAGVELYSMLQEEELQHAKLLVFANKQDYSGALTRSEVLKMLG 145 (182)
T ss_pred HHHHh-cccceEEEEEeccchhhhhhhHHHHHHHhccHhhcCceEEEEeccccchhhhhHHHHHHHhC
Confidence 57899 999999999999999987776 4455555554436688999999999987666555544443
No 161
>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed
Probab=98.42 E-value=3.1e-07 Score=61.90 Aligned_cols=49 Identities=22% Similarity=0.109 Sum_probs=39.5
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~ 60 (78)
.++ +++|++++|+|.+++.+++....|.. ..+.|+++|+||+|+.+...
T Consensus 290 ~~~-~~aD~il~VvD~s~~~s~~~~~~l~~------~~~~piiiV~NK~DL~~~~~ 338 (449)
T PRK05291 290 EAI-EEADLVLLVLDASEPLTEEDDEILEE------LKDKPVIVVLNKADLTGEID 338 (449)
T ss_pred HHH-HhCCEEEEEecCCCCCChhHHHHHHh------cCCCCcEEEEEhhhccccch
Confidence 467 89999999999999988887655543 25689999999999965433
No 162
>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=98.40 E-value=9.6e-07 Score=50.68 Aligned_cols=52 Identities=12% Similarity=-0.078 Sum_probs=37.2
Q ss_pred ccchhc--CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 4 SAYYNR--GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 4 ~~y~~~--~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
..++ + ++|++++|+|.+++++.. .|...+.+ .+.|+++|+||+|+.+...+.
T Consensus 67 ~~~~-~~~~~d~vi~v~d~~~~~~~~---~~~~~~~~---~~~~~iiv~NK~Dl~~~~~~~ 120 (158)
T cd01879 67 RDFL-LGEKPDLIVNVVDATNLERNL---YLTLQLLE---LGLPVVVALNMIDEAEKRGIK 120 (158)
T ss_pred HHHh-cCCCCcEEEEEeeCCcchhHH---HHHHHHHH---cCCCEEEEEehhhhcccccch
Confidence 4455 5 999999999999876533 34444433 358999999999997654443
No 163
>PRK03003 GTP-binding protein Der; Reviewed
Probab=98.38 E-value=1.1e-06 Score=59.45 Aligned_cols=47 Identities=17% Similarity=0.132 Sum_probs=38.1
Q ss_pred chhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
++ ++||++++|+|.++..++..++ ++..+.+ .+.|+++|+||+||.+
T Consensus 290 ~i-~~ad~vilV~Da~~~~s~~~~~-~~~~~~~---~~~piIiV~NK~Dl~~ 336 (472)
T PRK03003 290 AI-EAAEVAVVLIDASEPISEQDQR-VLSMVIE---AGRALVLAFNKWDLVD 336 (472)
T ss_pred HH-hcCCEEEEEEeCCCCCCHHHHH-HHHHHHH---cCCCEEEEEECcccCC
Confidence 57 8999999999999998888764 4444432 5689999999999964
No 164
>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=98.37 E-value=1.6e-06 Score=49.99 Aligned_cols=47 Identities=23% Similarity=0.048 Sum_probs=33.0
Q ss_pred cchhcCCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTK---STTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
.++ +++|++++|+|.++ +++++.+.. ++.. ...|+++++||+|+.+.
T Consensus 70 ~~~-~~ad~ii~V~d~~~~~~~~~~~~~~~----~~~~--~~~~~ilv~NK~Dl~~~ 119 (164)
T cd04171 70 AGA-GGIDLVLLVVAADEGIMPQTREHLEI----LELL--GIKRGLVVLTKADLVDE 119 (164)
T ss_pred hhh-hcCCEEEEEEECCCCccHhHHHHHHH----HHHh--CCCcEEEEEECccccCH
Confidence 457 89999999999987 455554331 2211 22489999999999754
No 165
>PRK12297 obgE GTPase CgtA; Reviewed
Probab=98.37 E-value=9.5e-07 Score=59.34 Aligned_cols=49 Identities=20% Similarity=0.179 Sum_probs=40.4
Q ss_pred cCCcEEEEEEECCCh---hhHHHHHHHHHHHhhhcC--CCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKS---TTFENVSRWLKDLGDHAD--SNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~---~s~~~~~~~~~~~~~~~~--~~~~~~lvgnK~Dl~~ 57 (78)
..++++++|+|+++. +++++...|.+++....+ .+.|.++|+||+||.+
T Consensus 235 er~~llI~VID~s~~~~~dp~e~~~~i~~EL~~y~~~L~~kP~IVV~NK~DL~~ 288 (424)
T PRK12297 235 ERTRVIVHVIDMSGSEGRDPIEDYEKINKELKLYNPRLLERPQIVVANKMDLPE 288 (424)
T ss_pred hhCCEEEEEEeCCccccCChHHHHHHHHHHHhhhchhccCCcEEEEEeCCCCcC
Confidence 358999999999865 788888888888877643 4689999999999854
No 166
>PRK03003 GTP-binding protein Der; Reviewed
Probab=98.37 E-value=1.1e-06 Score=59.41 Aligned_cols=49 Identities=24% Similarity=0.222 Sum_probs=37.0
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
..++ ++||++++|+|.++..++.. ..|...++. .+.|+++|+||+|+..
T Consensus 112 ~~~~-~~aD~il~VvD~~~~~s~~~-~~i~~~l~~---~~~piilV~NK~Dl~~ 160 (472)
T PRK03003 112 EVAM-RTADAVLFVVDATVGATATD-EAVARVLRR---SGKPVILAANKVDDER 160 (472)
T ss_pred HHHH-HhCCEEEEEEECCCCCCHHH-HHHHHHHHH---cCCCEEEEEECccCCc
Confidence 3467 89999999999999866543 344444442 4689999999999864
No 167
>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=98.31 E-value=8e-07 Score=53.33 Aligned_cols=49 Identities=20% Similarity=0.153 Sum_probs=35.4
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
...|+ +++|++++|+|+++... .|...+.... .+.|+++|+||+|+.+.
T Consensus 28 l~~~~-~~ad~il~VvD~~~~~~-----~~~~~l~~~~-~~~~~ilV~NK~Dl~~~ 76 (190)
T cd01855 28 LSSIS-PKKALVVHVVDIFDFPG-----SLIPRLRLFG-GNNPVILVGNKIDLLPK 76 (190)
T ss_pred HHhcc-cCCcEEEEEEECccCCC-----ccchhHHHhc-CCCcEEEEEEchhcCCC
Confidence 45688 99999999999988642 2333332222 46799999999998643
No 168
>COG2229 Predicted GTPase [General function prediction only]
Probab=98.29 E-value=3.1e-06 Score=51.11 Aligned_cols=63 Identities=25% Similarity=0.345 Sum_probs=47.1
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSL 68 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~ 68 (78)
++..+. +|+.+.|++.|.++...+ .....++.+... ..+|+++..||.||.+.+..+...+-+
T Consensus 84 m~~~l~-~ga~gaivlVDss~~~~~-~a~~ii~f~~~~--~~ip~vVa~NK~DL~~a~ppe~i~e~l 146 (187)
T COG2229 84 MWEILS-RGAVGAIVLVDSSRPITF-HAEEIIDFLTSR--NPIPVVVAINKQDLFDALPPEKIREAL 146 (187)
T ss_pred HHHHHh-CCcceEEEEEecCCCcch-HHHHHHHHHhhc--cCCCEEEEeeccccCCCCCHHHHHHHH
Confidence 345677 999999999999999999 444444444433 229999999999999887776555444
No 169
>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=98.29 E-value=1e-06 Score=50.68 Aligned_cols=50 Identities=16% Similarity=0.228 Sum_probs=36.0
Q ss_pred cCCcEEEEEEECCChhhHH--HHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 9 RGALGALLVYDVTKSTTFE--NVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~--~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
..+|++++|+|..++.+.. .+..|+... . ++.|+++|.||+|+.++..+.
T Consensus 10 ~~aD~vl~ViD~~~p~~~~~~~l~~~l~~~---~-~~k~~iivlNK~DL~~~~~~~ 61 (141)
T cd01857 10 ERSDIVVQIVDARNPLLFRPPDLERYVKEV---D-PRKKNILLLNKADLLTEEQRK 61 (141)
T ss_pred hhCCEEEEEEEccCCcccCCHHHHHHHHhc---c-CCCcEEEEEechhcCCHHHHH
Confidence 6899999999998876644 445554432 2 467999999999996544433
No 170
>PRK15467 ethanolamine utilization protein EutP; Provisional
Probab=98.26 E-value=1.6e-06 Score=50.83 Aligned_cols=44 Identities=14% Similarity=0.094 Sum_probs=34.5
Q ss_pred hhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 7 YNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 7 ~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+ +++|++++|+|.++.+++ +..|...+ ..+.|+++++||+|+.+
T Consensus 62 ~-~~ad~il~v~d~~~~~s~--~~~~~~~~----~~~~~ii~v~nK~Dl~~ 105 (158)
T PRK15467 62 L-QDVDMLIYVHGANDPESR--LPAGLLDI----GVSKRQIAVISKTDMPD 105 (158)
T ss_pred H-hcCCEEEEEEeCCCcccc--cCHHHHhc----cCCCCeEEEEEccccCc
Confidence 6 799999999999998876 33455443 14578999999999965
No 171
>PRK00098 GTPase RsgA; Reviewed
Probab=98.23 E-value=1.5e-06 Score=55.85 Aligned_cols=46 Identities=22% Similarity=0.255 Sum_probs=37.8
Q ss_pred cCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
.++|.+++|+|+++++++... ..|+..+.. .++|+++|+||+||.+
T Consensus 79 aniD~vllV~d~~~p~~~~~~idr~L~~~~~---~~ip~iIVlNK~DL~~ 125 (298)
T PRK00098 79 ANVDQAVLVFAAKEPDFSTDLLDRFLVLAEA---NGIKPIIVLNKIDLLD 125 (298)
T ss_pred ecCCEEEEEEECCCCCCCHHHHHHHHHHHHH---CCCCEEEEEEhHHcCC
Confidence 789999999999998776654 778776653 4689999999999963
No 172
>PRK12288 GTPase RsgA; Reviewed
Probab=98.23 E-value=4.9e-06 Score=54.65 Aligned_cols=46 Identities=20% Similarity=0.182 Sum_probs=38.8
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
++|.+++|++++...++..+..|+..+.. .++|.++|.||+||.+.
T Consensus 120 NvD~vlIV~s~~p~~s~~~Ldr~L~~a~~---~~i~~VIVlNK~DL~~~ 165 (347)
T PRK12288 120 NIDQIVIVSAVLPELSLNIIDRYLVACET---LGIEPLIVLNKIDLLDD 165 (347)
T ss_pred EccEEEEEEeCCCCCCHHHHHHHHHHHHh---cCCCEEEEEECccCCCc
Confidence 38999999999988999999999875542 45889999999999653
No 173
>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=98.21 E-value=3.5e-06 Score=48.05 Aligned_cols=49 Identities=20% Similarity=0.133 Sum_probs=38.6
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~ 60 (78)
.++ +++|++++|+|.+++.+....+.|.. ..+.|+++|+||+|+.+...
T Consensus 76 ~~~-~~~~~~v~v~d~~~~~~~~~~~~~~~------~~~~~vi~v~nK~D~~~~~~ 124 (157)
T cd04164 76 EAI-EEADLVLFVIDASRGLDEEDLEILEL------PADKPIIVVLNKSDLLPDSE 124 (157)
T ss_pred HHH-hhCCEEEEEEECCCCCCHHHHHHHHh------hcCCCEEEEEEchhcCCccc
Confidence 356 78999999999999888877655433 25689999999999875443
No 174
>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=98.21 E-value=4.4e-06 Score=48.40 Aligned_cols=47 Identities=19% Similarity=0.099 Sum_probs=33.9
Q ss_pred ccchhcCCcEEEEEEECCCh---hhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKS---TTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~---~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
..++ +.+|++++|+|.++. ++++.+.. +.. .+.|+++|+||+|+.+.
T Consensus 68 ~~~~-~~~d~il~v~d~~~~~~~~~~~~~~~----~~~---~~~p~ivv~NK~Dl~~~ 117 (168)
T cd01887 68 ARGA-SLTDIAILVVAADDGVMPQTIEAIKL----AKA---ANVPFIVALNKIDKPNA 117 (168)
T ss_pred HHHH-hhcCEEEEEEECCCCccHHHHHHHHH----HHH---cCCCEEEEEEceecccc
Confidence 4567 899999999999984 44443322 222 45799999999999643
No 175
>PRK12298 obgE GTPase CgtA; Reviewed
Probab=98.20 E-value=4.5e-06 Score=55.59 Aligned_cols=55 Identities=18% Similarity=0.135 Sum_probs=43.6
Q ss_pred hhcCCcEEEEEEECC---ChhhHHHHHHHHHHHhhhcC--CCCeEEEEeeCCCCCCCCCch
Q 038356 7 YNRGALGALLVYDVT---KSTTFENVSRWLKDLGDHAD--SNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 7 ~~~~a~~~ilv~d~~---~~~s~~~~~~~~~~~~~~~~--~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+ ..++++++|+|++ +.+.++....|.+++..... .+.|+++|.||+|+.+...+.
T Consensus 235 i-~radvlL~VVD~s~~~~~d~~e~~~~l~~eL~~~~~~L~~kP~IlVlNKiDl~~~~el~ 294 (390)
T PRK12298 235 L-ERCRVLLHLIDIAPIDGSDPVENARIIINELEKYSPKLAEKPRWLVFNKIDLLDEEEAE 294 (390)
T ss_pred H-HhCCEEEEEeccCcccccChHHHHHHHHHHHHhhhhhhcCCCEEEEEeCCccCChHHHH
Confidence 5 7889999999998 56788888889888876542 368999999999997554443
No 176
>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=98.17 E-value=8.1e-06 Score=50.64 Aligned_cols=48 Identities=21% Similarity=0.165 Sum_probs=34.5
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
..++ +.+|++++|+|.++..+......|. ... ..++|+++++||+|+.
T Consensus 91 ~~~l-~~aD~~ilVvD~~~g~~~~t~~~l~-~~~---~~~~p~ilviNKiD~~ 138 (222)
T cd01885 91 TAAL-RLCDGALVVVDAVEGVCVQTETVLR-QAL---KERVKPVLVINKIDRL 138 (222)
T ss_pred HHHH-HhcCeeEEEEECCCCCCHHHHHHHH-HHH---HcCCCEEEEEECCCcc
Confidence 3567 8999999999999876554432222 222 2457999999999975
No 177
>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=98.14 E-value=5e-06 Score=57.93 Aligned_cols=50 Identities=24% Similarity=0.286 Sum_probs=39.6
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
..++ +++|++++|+|.++..+......|..... .++|+++|+||+|+.+.
T Consensus 88 ~~~l-~~aD~aILVvDat~g~~~qt~~~~~~~~~----~~ipiIiViNKiDl~~~ 137 (595)
T TIGR01393 88 SRSL-AACEGALLLVDAAQGIEAQTLANVYLALE----NDLEIIPVINKIDLPSA 137 (595)
T ss_pred HHHH-HhCCEEEEEecCCCCCCHhHHHHHHHHHH----cCCCEEEEEECcCCCcc
Confidence 4578 99999999999999777777766654432 45799999999999643
No 178
>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=98.11 E-value=7.6e-06 Score=51.74 Aligned_cols=49 Identities=20% Similarity=0.079 Sum_probs=37.0
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
.++ +++|++++|+|.++..+.+ ..+...++. .+.|+++|+||+|+.+..
T Consensus 75 ~~l-~~aDvvl~VvD~~~~~~~~--~~i~~~l~~---~~~p~ilV~NK~Dl~~~~ 123 (270)
T TIGR00436 75 SAI-GGVDLILFVVDSDQWNGDG--EFVLTKLQN---LKRPVVLTRNKLDNKFKD 123 (270)
T ss_pred HHH-hhCCEEEEEEECCCCCchH--HHHHHHHHh---cCCCEEEEEECeeCCCHH
Confidence 456 8999999999999987775 344444443 458999999999996433
No 179
>KOG0077 consensus Vesicle coat complex COPII, GTPase subunit SAR1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.10 E-value=6.2e-06 Score=49.43 Aligned_cols=60 Identities=15% Similarity=0.238 Sum_probs=47.3
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCCCCCchH
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
++.|| -.+++++..+|..+.+.|...+.-++.+.... -.++|+++.|||+|.+......+
T Consensus 81 wkdyf-~~v~~iv~lvda~d~er~~es~~eld~ll~~e~la~vp~lilgnKId~p~a~se~~ 141 (193)
T KOG0077|consen 81 WKDYF-PQVDAIVYLVDAYDQERFAESKKELDALLSDESLATVPFLILGNKIDIPYAASEDE 141 (193)
T ss_pred HHHHH-hhhceeEeeeehhhHHHhHHHHHHHHHHHhHHHHhcCcceeecccccCCCcccHHH
Confidence 46788 89999999999999999999876665553322 26899999999999987654443
No 180
>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=98.10 E-value=4.1e-06 Score=55.16 Aligned_cols=48 Identities=17% Similarity=0.205 Sum_probs=37.7
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
.+.|+ ++++++++|+|+.+.. ..|.+++.+.. .+.|+++|+||+||.+
T Consensus 57 l~~~~-~~~~~Il~VvD~~d~~-----~s~~~~l~~~~-~~~piilV~NK~DLl~ 104 (360)
T TIGR03597 57 LNSLG-DSNALIVYVVDIFDFE-----GSLIPELKRFV-GGNPVLLVGNKIDLLP 104 (360)
T ss_pred Hhhcc-cCCcEEEEEEECcCCC-----CCccHHHHHHh-CCCCEEEEEEchhhCC
Confidence 45678 8999999999997765 34666776665 4679999999999964
No 181
>PRK04213 GTP-binding protein; Provisional
Probab=98.09 E-value=4.5e-07 Score=54.50 Aligned_cols=18 Identities=22% Similarity=0.030 Sum_probs=15.0
Q ss_pred CCCeEEEEeeCCCCCCCC
Q 038356 42 SNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 42 ~~~~~~lvgnK~Dl~~~~ 59 (78)
.++|+++|+||+|+.+.+
T Consensus 129 ~~~p~iiv~NK~Dl~~~~ 146 (201)
T PRK04213 129 LGIPPIVAVNKMDKIKNR 146 (201)
T ss_pred cCCCeEEEEECccccCcH
Confidence 568999999999996544
No 182
>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=98.09 E-value=1.4e-05 Score=46.14 Aligned_cols=48 Identities=23% Similarity=0.154 Sum_probs=36.0
Q ss_pred chhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
++ +++|++++|+|.+++.+..... +...+.. .+.|+++++||+|+.+.
T Consensus 81 ~~-~~~d~vi~v~d~~~~~~~~~~~-~~~~~~~---~~~~~iiv~nK~Dl~~~ 128 (174)
T cd01895 81 AI-ERADVVLLVIDATEGITEQDLR-IAGLILE---EGKALVIVVNKWDLVEK 128 (174)
T ss_pred HH-hhcCeEEEEEeCCCCcchhHHH-HHHHHHh---cCCCEEEEEeccccCCc
Confidence 45 7999999999999988765542 3333332 35899999999999765
No 183
>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=98.08 E-value=9.9e-06 Score=53.89 Aligned_cols=47 Identities=23% Similarity=0.178 Sum_probs=36.1
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
.++ +.+|++++|+|.++..+....+ +...+.+ .+.|+++|+||+|+.
T Consensus 250 ~~~-~~ad~~ilV~D~~~~~~~~~~~-~~~~~~~---~~~~iiiv~NK~Dl~ 296 (429)
T TIGR03594 250 KAI-ERADVVLLVLDATEGITEQDLR-IAGLILE---AGKALVIVVNKWDLV 296 (429)
T ss_pred HHH-HhCCEEEEEEECCCCccHHHHH-HHHHHHH---cCCcEEEEEECcccC
Confidence 367 8999999999999887766643 3333332 458999999999996
No 184
>PRK12296 obgE GTPase CgtA; Reviewed
Probab=98.04 E-value=1e-05 Score=55.38 Aligned_cols=53 Identities=13% Similarity=0.119 Sum_probs=38.7
Q ss_pred cCCcEEEEEEECCC----hhhHHHHHHHHHHHhhhcC-----------CCCeEEEEeeCCCCCCCCCc
Q 038356 9 RGALGALLVYDVTK----STTFENVSRWLKDLGDHAD-----------SNIVIMMIGNKTDLKHLPTS 61 (78)
Q Consensus 9 ~~a~~~ilv~d~~~----~~s~~~~~~~~~~~~~~~~-----------~~~~~~lvgnK~Dl~~~~~v 61 (78)
..++++++|+|+++ ++.++.+..|..++..... .+.|+++|+||+|+.+.+..
T Consensus 235 eradvLv~VVD~s~~e~~rdp~~d~~~i~~EL~~y~~~l~~~~~~~~l~~kP~IVVlNKiDL~da~el 302 (500)
T PRK12296 235 ERCAVLVHVVDCATLEPGRDPLSDIDALEAELAAYAPALDGDLGLGDLAERPRLVVLNKIDVPDAREL 302 (500)
T ss_pred HhcCEEEEEECCcccccccCchhhHHHHHHHHHHhhhcccccchhhhhcCCCEEEEEECccchhhHHH
Confidence 67899999999986 3456666666666654431 36899999999999765443
No 185
>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=98.04 E-value=2.2e-05 Score=46.11 Aligned_cols=50 Identities=20% Similarity=0.142 Sum_probs=36.6
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
..++ +++|++++|+|.++..+... ..++..... .+.|+++++||+|+...
T Consensus 80 ~~~~-~~~d~~i~v~d~~~~~~~~~-~~~~~~~~~---~~~~i~iv~nK~D~~~~ 129 (189)
T cd00881 80 IRGL-SVSDGAILVVDANEGVQPQT-REHLRIARE---GGLPIIVAINKIDRVGE 129 (189)
T ss_pred HHHH-HhcCEEEEEEECCCCCcHHH-HHHHHHHHH---CCCCeEEEEECCCCcch
Confidence 4567 89999999999988665433 334444332 56899999999999753
No 186
>TIGR00491 aIF-2 translation initiation factor aIF-2/yIF-2. This model describes archaeal and eukaryotic orthologs of bacterial IF-2. Like IF-2, it helps convey the initiator tRNA to the ribosome, although the initiator is N-formyl-Met in bacteria and Met here. This protein is not closely related to the subunits of eIF-2 of eukaryotes, which is also involved in the initiation of translation. The aIF-2 of Methanococcus jannaschii contains a large intein interrupting a region of very strongly conserved sequence very near the amino end; this model does not correctly align the sequences from Methanococcus jannaschii and Pyrococcus horikoshii in this region.
Probab=98.03 E-value=9.1e-06 Score=56.63 Aligned_cols=47 Identities=19% Similarity=0.051 Sum_probs=36.6
Q ss_pred cccchhcCCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTK---STTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+..++ +.+|++++|+|.++ +.+++.+..+ +. .++|+++++||+|+.+
T Consensus 86 ~~~~~-~~aD~~IlVvD~~~g~~~qt~e~i~~l----~~---~~vpiIVv~NK~Dl~~ 135 (590)
T TIGR00491 86 RKRGG-ALADLAILIVDINEGFKPQTQEALNIL----RM---YKTPFVVAANKIDRIP 135 (590)
T ss_pred HHHHH-hhCCEEEEEEECCcCCCHhHHHHHHHH----HH---cCCCEEEEEECCCccc
Confidence 45678 99999999999997 6777766433 11 3589999999999963
No 187
>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed
Probab=98.01 E-value=1.8e-05 Score=56.05 Aligned_cols=48 Identities=17% Similarity=0.167 Sum_probs=37.8
Q ss_pred chhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
++ +.+|++++|+|.++..++..++-| ..+.+ .+.|+++|+||+|+.+.
T Consensus 529 ~i-~~advvilViDat~~~s~~~~~i~-~~~~~---~~~piIiV~NK~DL~~~ 576 (712)
T PRK09518 529 AI-ERSELALFLFDASQPISEQDLKVM-SMAVD---AGRALVLVFNKWDLMDE 576 (712)
T ss_pred Hh-hcCCEEEEEEECCCCCCHHHHHHH-HHHHH---cCCCEEEEEEchhcCCh
Confidence 46 899999999999999888876533 34432 45899999999999653
No 188
>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=97.97 E-value=2.7e-05 Score=44.39 Aligned_cols=52 Identities=21% Similarity=0.075 Sum_probs=35.7
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCc
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTS 61 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v 61 (78)
.++ +++|++++|+|.++..+.... .....+++ .+.|+++|+||+|+.+....
T Consensus 72 ~~~-~~~d~ii~v~d~~~~~~~~~~-~~~~~~~~---~~~piiiv~nK~D~~~~~~~ 123 (157)
T cd01894 72 LAI-EEADVILFVVDGREGLTPADE-EIAKYLRK---SKKPVILVVNKVDNIKEEDE 123 (157)
T ss_pred HHH-HhCCEEEEEEeccccCCccHH-HHHHHHHh---cCCCEEEEEECcccCChHHH
Confidence 356 899999999999876554432 12222222 34899999999999765443
No 189
>cd00066 G-alpha G protein alpha subunit. The alpha subunit of G proteins contains the guanine nucleotide binding site. The heterotrimeric GNP-binding proteins are signal transducers that communicate signals from many hormones, neurotransmitters, chemokines, and autocrine and paracrine factors. Extracellular signals are received by receptors, which activate the G proteins, which in turn route the signals to several distinct intracellular signaling pathways. The alpha subunit of G proteins is a weak GTPase. In the resting state, heterotrimeric G proteins are associated at the cytosolic face of the plasma membrane and the alpha subunit binds to GDP. Upon activation by a receptor GDP is replaced with GTP, and the G-alpha/GTP complex dissociates from the beta and gamma subunits. This results in activation of downstream signaling pathways, such as cAMP synthesis by adenylyl cyclase, which is terminated when GTP is hydrolized and the heterotrimers reconstitute.
Probab=97.94 E-value=2e-05 Score=51.15 Aligned_cols=54 Identities=13% Similarity=0.175 Sum_probs=40.5
Q ss_pred ccccchhcCCcEEEEEEECCCh----------hhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKS----------TTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLK 56 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~----------~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~ 56 (78)
.|..|| .+++++++|.|+++. ..+......++.+-.+. -.+.|++|++||.|+-
T Consensus 177 kW~~~f-~~v~~iifvv~lsd~d~~~~e~~~~nrl~esl~~f~~i~~~~~~~~~pill~~NK~D~f 241 (317)
T cd00066 177 KWIHCF-EDVTAIIFVVALSEYDQVLFEDESTNRMQESLNLFDSICNSRWFANTSIILFLNKKDLF 241 (317)
T ss_pred hHHHHh-CCCCEEEEEEEchhcccccccCCcchHHHHHHHHHHHHHhCccccCCCEEEEccChHHH
Confidence 356789 999999999999984 45666655555554332 2679999999999974
No 190
>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=97.90 E-value=5.9e-05 Score=47.91 Aligned_cols=50 Identities=18% Similarity=0.126 Sum_probs=34.5
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
.++ +.+|++++|+|.++.-. .....++..... .++|+++++||+|+.+..
T Consensus 90 ~~l-~~aD~~IlVvda~~g~~-~~~~~i~~~~~~---~~~P~iivvNK~D~~~a~ 139 (267)
T cd04169 90 RTL-TAVDSAVMVIDAAKGVE-PQTRKLFEVCRL---RGIPIITFINKLDREGRD 139 (267)
T ss_pred HHH-HHCCEEEEEEECCCCcc-HHHHHHHHHHHh---cCCCEEEEEECCccCCCC
Confidence 456 89999999999987532 222334443332 468999999999986543
No 191
>smart00275 G_alpha G protein alpha subunit. Subunit of G proteins that contains the guanine nucleotide binding site
Probab=97.89 E-value=3.1e-05 Score=50.78 Aligned_cols=54 Identities=11% Similarity=0.152 Sum_probs=40.8
Q ss_pred ccccchhcCCcEEEEEEECCCh----------hhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCC
Q 038356 2 INSAYYNRGALGALLVYDVTKS----------TTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLK 56 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~----------~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~ 56 (78)
.|..|| .+++++|+|.|+++. ..++.....++.+-.+. -.++|++|+.||.|+-
T Consensus 200 kW~~~f-~~v~~IiFvvdlSd~d~~~~Ed~~~nrl~esl~~f~~l~~~~~~~~~piil~~NK~D~~ 264 (342)
T smart00275 200 KWIHCF-DNVTAIIFCVALSEYDQVLEEDESTNRMQESLNLFESICNSRWFANTSIILFLNKIDLF 264 (342)
T ss_pred hHHHHh-CCCCEEEEEEECcccccchhccCcchHHHHHHHHHHHHHcCccccCCcEEEEEecHHhH
Confidence 456789 999999999999973 45666655555554332 2679999999999984
No 192
>PRK00093 GTP-binding protein Der; Reviewed
Probab=97.89 E-value=7e-05 Score=50.05 Aligned_cols=46 Identities=24% Similarity=0.200 Sum_probs=33.7
Q ss_pred cchhcCCcEEEEEEECCChhhHH--HHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFE--NVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~--~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
.++ +++|++++|+|.++..+.. .+..|+.. .+.|+++|+||+|+.+
T Consensus 76 ~~~-~~ad~il~vvd~~~~~~~~~~~~~~~l~~------~~~piilv~NK~D~~~ 123 (435)
T PRK00093 76 LAI-EEADVILFVVDGRAGLTPADEEIAKILRK------SNKPVILVVNKVDGPD 123 (435)
T ss_pred HHH-HhCCEEEEEEECCCCCCHHHHHHHHHHHH------cCCcEEEEEECccCcc
Confidence 457 8999999999998854432 33445432 2589999999999754
No 193
>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.
Probab=97.88 E-value=4.4e-05 Score=46.18 Aligned_cols=56 Identities=23% Similarity=0.361 Sum_probs=35.7
Q ss_pred chhcCCcEEEEEEECCC-hhhHHHHHHHHHHHhhhc---CCCCeEEEEeeCCCCCCCCCch
Q 038356 6 YYNRGALGALLVYDVTK-STTFENVSRWLKDLGDHA---DSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~-~~s~~~~~~~~~~~~~~~---~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
|. +++.|+|+|.|.+. +..+..+.+++-.+.... ...+|++|++||+|+...+...
T Consensus 72 ~~-~~~k~IIfvvDSs~~~~~~~~~Ae~Ly~iL~~~~~~~~~~piLIacNK~Dl~~A~~~~ 131 (181)
T PF09439_consen 72 YL-SNAKGIIFVVDSSTDQKELRDVAEYLYDILSDTEVQKNKPPILIACNKQDLFTAKPPK 131 (181)
T ss_dssp HH-GGEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHCCTT--EEEEEEE-TTSTT---HH
T ss_pred ch-hhCCEEEEEEeCccchhhHHHHHHHHHHHHHhhhhccCCCCEEEEEeCccccccCCHH
Confidence 45 78999999999874 556777755544443222 3679999999999997655433
No 194
>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=97.88 E-value=3.7e-05 Score=46.93 Aligned_cols=47 Identities=28% Similarity=0.278 Sum_probs=35.0
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
.++ +.+|++++|+|.++..++.. ..|+..... .+.|+++|+||+|+.
T Consensus 90 ~~~-~~aD~~llVvD~~~~~~~~~-~~~~~~~~~---~~~p~iiviNK~D~~ 136 (213)
T cd04167 90 AAL-RLSDGVVLVVDVVEGVTSNT-ERLIRHAIL---EGLPIVLVINKIDRL 136 (213)
T ss_pred HHH-HhCCEEEEEEECCCCCCHHH-HHHHHHHHH---cCCCEEEEEECcccC
Confidence 457 89999999999988776643 344444432 348999999999974
No 195
>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=97.87 E-value=3.6e-05 Score=48.07 Aligned_cols=49 Identities=20% Similarity=0.134 Sum_probs=36.7
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
..++ +.+|++++|+|.++.-+. ....|+..+++ .+.|+++++||+|+.+
T Consensus 82 ~~~l-~~aD~~IlVvd~~~g~~~-~~~~~~~~~~~---~~~P~iivvNK~D~~~ 130 (237)
T cd04168 82 ERSL-SVLDGAILVISAVEGVQA-QTRILWRLLRK---LNIPTIIFVNKIDRAG 130 (237)
T ss_pred HHHH-HHhCeEEEEEeCCCCCCH-HHHHHHHHHHH---cCCCEEEEEECccccC
Confidence 3567 899999999999886543 34455555544 3589999999999875
No 196
>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=97.86 E-value=3.4e-05 Score=43.42 Aligned_cols=54 Identities=20% Similarity=0.113 Sum_probs=40.7
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchH
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMS 63 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~ 63 (78)
.++ +.+|++++|+|.++..+..... |..... ..+.|+++|+||+|+........
T Consensus 71 ~~~-~~~d~il~v~~~~~~~~~~~~~-~~~~~~---~~~~~~ivv~nK~D~~~~~~~~~ 124 (163)
T cd00880 71 RVL-ERADLILFVVDADLRADEEEEK-LLELLR---ERGKPVLLVLNKIDLLPEEEEEE 124 (163)
T ss_pred HHH-HhCCEEEEEEeCCCCCCHHHHH-HHHHHH---hcCCeEEEEEEccccCChhhHHH
Confidence 367 8999999999999988877655 333332 25789999999999976555443
No 197
>PRK15494 era GTPase Era; Provisional
Probab=97.86 E-value=2.9e-05 Score=50.79 Aligned_cols=47 Identities=30% Similarity=0.388 Sum_probs=33.4
Q ss_pred chhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
++ ++||++++|+|.++ +|+.. ..|+..++.. +.|.++|+||+|+.+.
T Consensus 128 ~l-~~aDvil~VvD~~~--s~~~~~~~il~~l~~~---~~p~IlViNKiDl~~~ 175 (339)
T PRK15494 128 SL-HSADLVLLIIDSLK--SFDDITHNILDKLRSL---NIVPIFLLNKIDIESK 175 (339)
T ss_pred Hh-hhCCEEEEEEECCC--CCCHHHHHHHHHHHhc---CCCEEEEEEhhcCccc
Confidence 46 79999999998544 66666 4455555432 3566789999999653
No 198
>PRK05433 GTP-binding protein LepA; Provisional
Probab=97.83 E-value=4.8e-05 Score=53.19 Aligned_cols=50 Identities=26% Similarity=0.303 Sum_probs=37.6
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
..++ +.+|++++|+|.++.........|..... .++|+++|+||+|+.+.
T Consensus 92 ~~sl-~~aD~aILVVDas~gv~~qt~~~~~~~~~----~~lpiIvViNKiDl~~a 141 (600)
T PRK05433 92 SRSL-AACEGALLVVDASQGVEAQTLANVYLALE----NDLEIIPVLNKIDLPAA 141 (600)
T ss_pred HHHH-HHCCEEEEEEECCCCCCHHHHHHHHHHHH----CCCCEEEEEECCCCCcc
Confidence 4567 99999999999998765555555643321 46789999999999653
No 199
>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=97.75 E-value=2.2e-05 Score=45.66 Aligned_cols=49 Identities=14% Similarity=0.106 Sum_probs=32.8
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+.+. +++|.+++|+|.+++.+... ..+...+. ..+.|+++|.||+|+.+
T Consensus 7 ~~i~-~~aD~vl~V~D~~~~~~~~~-~~l~~~~~---~~~~p~iiv~NK~Dl~~ 55 (156)
T cd01859 7 RRII-KESDVVLEVLDARDPELTRS-RKLERYVL---ELGKKLLIVLNKADLVP 55 (156)
T ss_pred HHHH-hhCCEEEEEeeCCCCcccCC-HHHHHHHH---hCCCcEEEEEEhHHhCC
Confidence 4556 88999999999987643222 12222222 13579999999999854
No 200
>PRK00093 GTP-binding protein Der; Reviewed
Probab=97.72 E-value=8.6e-05 Score=49.62 Aligned_cols=48 Identities=23% Similarity=0.126 Sum_probs=35.9
Q ss_pred chhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
++ +.+|++++|+|.++..+....+ +...+.+ .+.|+++++||+|+.+.
T Consensus 252 ~~-~~ad~~ilViD~~~~~~~~~~~-i~~~~~~---~~~~~ivv~NK~Dl~~~ 299 (435)
T PRK00093 252 AI-ERADVVLLVIDATEGITEQDLR-IAGLALE---AGRALVIVVNKWDLVDE 299 (435)
T ss_pred HH-HHCCEEEEEEeCCCCCCHHHHH-HHHHHHH---cCCcEEEEEECccCCCH
Confidence 56 8999999999999887766543 3333332 35799999999999743
No 201
>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=97.68 E-value=0.00036 Score=34.84 Aligned_cols=43 Identities=21% Similarity=0.295 Sum_probs=27.5
Q ss_pred CcEEEEEEECCChhhH--HHHHHHHHHHhhhcCCCCeEEEEeeCCC
Q 038356 11 ALGALLVYDVTKSTTF--ENVSRWLKDLGDHADSNIVIMMIGNKTD 54 (78)
Q Consensus 11 a~~~ilv~d~~~~~s~--~~~~~~~~~~~~~~~~~~~~~lvgnK~D 54 (78)
++++++++|.+..-.+ +.=.+.+++++..- ++.|+++|.||+|
T Consensus 14 ~~~ilfi~D~Se~CGysie~Q~~L~~~ik~~F-~~~P~i~V~nK~D 58 (58)
T PF06858_consen 14 ADAILFIIDPSEQCGYSIEEQLSLFKEIKPLF-PNKPVIVVLNKID 58 (58)
T ss_dssp -SEEEEEE-TT-TTSS-HHHHHHHHHHHHHHT-TTS-EEEEE--TT
T ss_pred cceEEEEEcCCCCCCCCHHHHHHHHHHHHHHc-CCCCEEEEEeccC
Confidence 4678899999987644 43345667776665 6899999999998
No 202
>PRK04004 translation initiation factor IF-2; Validated
Probab=97.68 E-value=9.2e-05 Score=51.67 Aligned_cols=45 Identities=22% Similarity=0.128 Sum_probs=35.2
Q ss_pred ccchhcCCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTK---STTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
..++ +.+|++++|+|.++ +.+++.+..+ .. .++|+++++||+|+.
T Consensus 89 ~~~~-~~aD~~IlVvDa~~g~~~qt~e~i~~~----~~---~~vpiIvviNK~D~~ 136 (586)
T PRK04004 89 KRGG-ALADIAILVVDINEGFQPQTIEAINIL----KR---RKTPFVVAANKIDRI 136 (586)
T ss_pred HHhH-hhCCEEEEEEECCCCCCHhHHHHHHHH----HH---cCCCEEEEEECcCCc
Confidence 3456 78999999999998 7788776433 21 468999999999985
No 203
>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=97.68 E-value=6.1e-05 Score=50.46 Aligned_cols=50 Identities=18% Similarity=-0.059 Sum_probs=32.6
Q ss_pred chhcCCcEEEEEEECCChhhHHHHHH-HHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVSR-WLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~~-~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
++ +++|++++|+|.++.+++...+. +...+.+.. ...|+++++||+|+.+
T Consensus 105 ~~-~~aD~~ilVvDa~~~~~~~~~~t~~~~~~~~~~-~~~~iIVviNK~Dl~~ 155 (426)
T TIGR00483 105 GA-SQADAAVLVVAVGDGEFEVQPQTREHAFLARTL-GINQLIVAINKMDSVN 155 (426)
T ss_pred hh-hhCCEEEEEEECCCCCcccCCchHHHHHHHHHc-CCCeEEEEEEChhccC
Confidence 45 78999999999999865422211 111222222 3357999999999964
No 204
>CHL00189 infB translation initiation factor 2; Provisional
Probab=97.65 E-value=7.5e-05 Score=53.36 Aligned_cols=47 Identities=21% Similarity=0.189 Sum_probs=35.1
Q ss_pred cccchhcCCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTK---STTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+..++ +.+|++|+|+|.++ +.+++.+.. +. ..++|+++++||+|+.+
T Consensus 312 r~rg~-~~aDiaILVVDA~dGv~~QT~E~I~~----~k---~~~iPiIVViNKiDl~~ 361 (742)
T CHL00189 312 RSRGA-NVTDIAILIIAADDGVKPQTIEAINY----IQ---AANVPIIVAINKIDKAN 361 (742)
T ss_pred HHHHH-HHCCEEEEEEECcCCCChhhHHHHHH----HH---hcCceEEEEEECCCccc
Confidence 44677 89999999999887 455554432 22 24689999999999965
No 205
>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed
Probab=97.64 E-value=0.00013 Score=51.83 Aligned_cols=47 Identities=17% Similarity=0.111 Sum_probs=34.5
Q ss_pred cchhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
.++ +++|++++|+|.++. +... ..|...++. .+.|+++|+||+|+..
T Consensus 350 ~~~-~~aD~iL~VvDa~~~--~~~~d~~i~~~Lr~---~~~pvIlV~NK~D~~~ 397 (712)
T PRK09518 350 IAV-SLADAVVFVVDGQVG--LTSTDERIVRMLRR---AGKPVVLAVNKIDDQA 397 (712)
T ss_pred HHH-HhCCEEEEEEECCCC--CCHHHHHHHHHHHh---cCCCEEEEEECccccc
Confidence 467 899999999999763 2223 345555543 5689999999999864
No 206
>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=97.63 E-value=0.00027 Score=47.08 Aligned_cols=49 Identities=27% Similarity=0.324 Sum_probs=34.7
Q ss_pred cchhcCCcEEEEEEECCChhhHHH--HHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFEN--VSRWLKDLGDHADSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~--~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~ 60 (78)
.++ +++|++++|+|.++.-+... +..|+ ++ .+.|+++|+||+|+.+...
T Consensus 74 ~~~-~~ad~vl~vvD~~~~~~~~d~~i~~~l---~~---~~~piilVvNK~D~~~~~~ 124 (429)
T TIGR03594 74 IAI-EEADVILFVVDGREGLTPEDEEIAKWL---RK---SGKPVILVANKIDGKKEDA 124 (429)
T ss_pred HHH-hhCCEEEEEEeCCCCCCHHHHHHHHHH---HH---hCCCEEEEEECccCCcccc
Confidence 467 89999999999987544332 33343 32 3579999999999875443
No 207
>TIGR00437 feoB ferrous iron transporter FeoB. FeoB (773 amino acids in E. coli), a cytoplasmic membrane protein required for iron(II) update, is encoded in an operon with FeoA (75 amino acids), which is also required, and is regulated by Fur. There appear to be two copies in Archaeoglobus fulgidus and Clostridium acetobutylicum.
Probab=97.62 E-value=7.3e-05 Score=52.18 Aligned_cols=47 Identities=13% Similarity=-0.074 Sum_probs=32.7
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
++|+++.|+|.++.+. ...+..++. +.+.|+++|+||+|+.+.+.+.
T Consensus 72 ~aDvvI~VvDat~ler---~l~l~~ql~---~~~~PiIIVlNK~Dl~~~~~i~ 118 (591)
T TIGR00437 72 KPDLVVNVVDASNLER---NLYLTLQLL---ELGIPMILALNLVDEAEKKGIR 118 (591)
T ss_pred CCCEEEEEecCCcchh---hHHHHHHHH---hcCCCEEEEEehhHHHHhCCCh
Confidence 7899999999987432 223333333 2468999999999996555443
No 208
>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=97.61 E-value=0.0002 Score=43.52 Aligned_cols=44 Identities=25% Similarity=0.208 Sum_probs=30.1
Q ss_pred cCCcEEEEEEECCCh----hhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 9 RGALGALLVYDVTKS----TTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~----~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
+++|++++|+|.++. .+++.+..| ... ...|+++|+||+|+.+.
T Consensus 105 ~~~D~~llVvd~~~~~~~~~t~~~l~~~----~~~--~~~~iiivvNK~Dl~~~ 152 (203)
T cd01888 105 AVMDGALLLIAANEPCPQPQTSEHLAAL----EIM--GLKHIIIVQNKIDLVKE 152 (203)
T ss_pred hcCCEEEEEEECCCCCCCcchHHHHHHH----HHc--CCCcEEEEEEchhccCH
Confidence 567999999999873 445544433 111 22478999999999653
No 209
>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=97.58 E-value=0.0002 Score=50.14 Aligned_cols=50 Identities=18% Similarity=0.131 Sum_probs=37.7
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
.++ +.+|++++|+|.++. .....+.|+..+.. .++|.+++.||+|+.+.+
T Consensus 83 ~~l-~~aD~alLVVDa~~G-~~~qT~~~l~~a~~---~~ip~IVviNKiD~~~a~ 132 (594)
T TIGR01394 83 RVL-GMVDGVLLLVDASEG-PMPQTRFVLKKALE---LGLKPIVVINKIDRPSAR 132 (594)
T ss_pred HHH-HhCCEEEEEEeCCCC-CcHHHHHHHHHHHH---CCCCEEEEEECCCCCCcC
Confidence 467 899999999999763 34555667666654 357899999999996544
No 210
>cd04163 Era Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.
Probab=97.57 E-value=0.00016 Score=41.22 Aligned_cols=46 Identities=22% Similarity=0.192 Sum_probs=32.4
Q ss_pred chhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
++ +++|++++|+|.++.. ... ..+...+.. .+.|+++|+||+|+..
T Consensus 79 ~~-~~~d~i~~v~d~~~~~--~~~~~~~~~~~~~---~~~~~iiv~nK~Dl~~ 125 (168)
T cd04163 79 AL-KDVDLVLFVVDASEPI--GEGDEFILELLKK---SKTPVILVLNKIDLVK 125 (168)
T ss_pred HH-HhCCEEEEEEECCCcc--CchHHHHHHHHHH---hCCCEEEEEEchhccc
Confidence 46 8999999999999872 222 223333332 2579999999999973
No 211
>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=97.55 E-value=0.00018 Score=41.94 Aligned_cols=48 Identities=17% Similarity=0.180 Sum_probs=32.9
Q ss_pred cCCcEEEEEEECCChhh--HHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCC
Q 038356 9 RGALGALLVYDVTKSTT--FENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s--~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~ 60 (78)
.++|.+++|.|..++.+ -..+..+ +... ..+.|+++|.||+|+.+...
T Consensus 7 ~~aD~il~VvD~~~p~~~~~~~i~~~---l~~~-~~~~p~ilVlNKiDl~~~~~ 56 (157)
T cd01858 7 DSSDVVIQVLDARDPMGTRCKHVEEY---LKKE-KPHKHLIFVLNKCDLVPTWV 56 (157)
T ss_pred hhCCEEEEEEECCCCccccCHHHHHH---HHhc-cCCCCEEEEEEchhcCCHHH
Confidence 78999999999988632 2223333 2222 24589999999999965443
No 212
>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=97.52 E-value=0.00029 Score=49.17 Aligned_cols=47 Identities=28% Similarity=0.172 Sum_probs=34.2
Q ss_pred cchhcCCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCe-EEEEeeCCCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTK---STTFENVSRWLKDLGDHADSNIV-IMMIGNKTDLKHLP 59 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~-~~lvgnK~Dl~~~~ 59 (78)
.++ .++|++++|+|.++ +.+++.+. + +.. .++| +++|+||+|+.+..
T Consensus 69 ~g~-~~aD~aILVVDa~~G~~~qT~ehl~-i---l~~---lgi~~iIVVlNK~Dlv~~~ 119 (581)
T TIGR00475 69 AGG-GGIDAALLVVDADEGVMTQTGEHLA-V---LDL---LGIPHTIVVITKADRVNEE 119 (581)
T ss_pred hhh-ccCCEEEEEEECCCCCcHHHHHHHH-H---HHH---cCCCeEEEEEECCCCCCHH
Confidence 356 79999999999998 56666553 1 222 2466 99999999997644
No 213
>KOG1707 consensus Predicted Ras related/Rac-GTP binding protein [Defense mechanisms]
Probab=97.51 E-value=0.00012 Score=50.96 Aligned_cols=49 Identities=29% Similarity=0.411 Sum_probs=38.7
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~ 60 (78)
.+|.+.++||.+++.||+.+..-++..... ...|+++|+.|+||.+..+
T Consensus 495 ~cDv~~~~YDsS~p~sf~~~a~v~~~~~~~--~~~Pc~~va~K~dlDe~~Q 543 (625)
T KOG1707|consen 495 ACDVACLVYDSSNPRSFEYLAEVYNKYFDL--YKIPCLMVATKADLDEVPQ 543 (625)
T ss_pred eeeeEEEecccCCchHHHHHHHHHHHhhhc--cCCceEEEeeccccchhhh
Confidence 468899999999999999886654443322 6799999999999976553
No 214
>PRK13351 elongation factor G; Reviewed
Probab=97.51 E-value=0.00028 Score=49.94 Aligned_cols=50 Identities=20% Similarity=0.218 Sum_probs=38.5
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
..++ +.+|++++|+|.++..+......|. .+.. .++|+++++||+|+.+.
T Consensus 91 ~~~l-~~aD~~ilVvd~~~~~~~~~~~~~~-~~~~---~~~p~iiviNK~D~~~~ 140 (687)
T PRK13351 91 ERSL-RVLDGAVVVFDAVTGVQPQTETVWR-QADR---YGIPRLIFINKMDRVGA 140 (687)
T ss_pred HHHH-HhCCEEEEEEeCCCCCCHHHHHHHH-HHHh---cCCCEEEEEECCCCCCC
Confidence 4567 8999999999999887776655553 3332 35899999999998764
No 215
>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=97.50 E-value=0.00047 Score=41.25 Aligned_cols=45 Identities=24% Similarity=0.199 Sum_probs=30.0
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+.+|++++|+|.++..+......|. +... .+.|+++++||+|+..
T Consensus 90 ~~~d~vi~VvD~~~~~~~~~~~~~~--~~~~--~~~~~iiv~NK~Dl~~ 134 (192)
T cd01889 90 QIIDLMLLVVDATKGIQTQTAECLV--IGEI--LCKKLIVVLNKIDLIP 134 (192)
T ss_pred hhCCEEEEEEECCCCccHHHHHHHH--HHHH--cCCCEEEEEECcccCC
Confidence 3568999999998854443333332 1122 2469999999999864
No 216
>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=97.48 E-value=0.00034 Score=41.45 Aligned_cols=49 Identities=18% Similarity=0.276 Sum_probs=33.2
Q ss_pred cchhcC---CcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 5 AYYNRG---ALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 5 ~y~~~~---a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
.|+ +. ++++++|+|.+++-+..... +...+.. .+.|+++++||+|+.+.
T Consensus 93 ~~l-~~~~~~~~ii~vvd~~~~~~~~~~~-~~~~~~~---~~~pviiv~nK~D~~~~ 144 (179)
T TIGR03598 93 EYL-EKRENLKGVVLLMDIRHPLKELDLE-MLEWLRE---RGIPVLIVLTKADKLKK 144 (179)
T ss_pred HHH-HhChhhcEEEEEecCCCCCCHHHHH-HHHHHHH---cCCCEEEEEECcccCCH
Confidence 455 54 57999999998865555442 2233332 35899999999998643
No 217
>PRK00089 era GTPase Era; Reviewed
Probab=97.47 E-value=0.00027 Score=45.02 Aligned_cols=46 Identities=20% Similarity=0.257 Sum_probs=31.5
Q ss_pred chhcCCcEEEEEEECCChhhHHHHHHH-HHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVSRW-LKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~~~-~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
.+ .++|++++|+|.++. +.....+ .+.+. ..+.|+++|+||+|+..
T Consensus 81 ~~-~~~D~il~vvd~~~~--~~~~~~~i~~~l~---~~~~pvilVlNKiDl~~ 127 (292)
T PRK00089 81 SL-KDVDLVLFVVDADEK--IGPGDEFILEKLK---KVKTPVILVLNKIDLVK 127 (292)
T ss_pred HH-hcCCEEEEEEeCCCC--CChhHHHHHHHHh---hcCCCEEEEEECCcCCC
Confidence 45 789999999999882 2222222 22222 24689999999999973
No 218
>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=97.46 E-value=0.00017 Score=41.97 Aligned_cols=45 Identities=16% Similarity=0.028 Sum_probs=30.0
Q ss_pred cEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 12 LGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 12 ~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
|.+++|.|..++.+... .|+.. ......+.|+++|.||+|+.+..
T Consensus 1 Dvvl~VvD~~~p~~~~~--~~i~~-~~~~~~~~p~IiVlNK~Dl~~~~ 45 (155)
T cd01849 1 DVILEVLDARDPLGTRS--PDIER-VLIKEKGKKLILVLNKADLVPKE 45 (155)
T ss_pred CEEEEEEeccCCccccC--HHHHH-HHHhcCCCCEEEEEechhcCCHH
Confidence 57899999988765542 23331 11112568999999999996543
No 219
>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=97.46 E-value=0.00022 Score=49.91 Aligned_cols=47 Identities=21% Similarity=0.163 Sum_probs=33.7
Q ss_pred cccchhcCCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTK---STTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+..++ +.+|++++|+|.++ +.+.+.+. ... ..++|+++++||+|+.+
T Consensus 152 r~rga-~~aDiaILVVda~dgv~~qT~e~i~----~~~---~~~vPiIVviNKiDl~~ 201 (587)
T TIGR00487 152 RARGA-KVTDIVVLVVAADDGVMPQTIEAIS----HAK---AANVPIIVAINKIDKPE 201 (587)
T ss_pred HHhhh-ccCCEEEEEEECCCCCCHhHHHHHH----HHH---HcCCCEEEEEECccccc
Confidence 34567 89999999999886 44544332 111 24689999999999964
No 220
>PRK05306 infB translation initiation factor IF-2; Validated
Probab=97.46 E-value=0.00016 Score=51.98 Aligned_cols=47 Identities=17% Similarity=0.110 Sum_probs=33.9
Q ss_pred cccchhcCCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTK---STTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+..++ +.+|++|+|+|.++ +.+.+.+.. +. ..++|+++++||+|+.+
T Consensus 354 ~~rga-~~aDiaILVVdAddGv~~qT~e~i~~----a~---~~~vPiIVviNKiDl~~ 403 (787)
T PRK05306 354 RARGA-QVTDIVVLVVAADDGVMPQTIEAINH----AK---AAGVPIIVAINKIDKPG 403 (787)
T ss_pred HHhhh-hhCCEEEEEEECCCCCCHhHHHHHHH----HH---hcCCcEEEEEECccccc
Confidence 34566 78999999999987 455544321 11 25689999999999965
No 221
>PRK14845 translation initiation factor IF-2; Provisional
Probab=97.37 E-value=0.00041 Score=51.32 Aligned_cols=46 Identities=24% Similarity=0.156 Sum_probs=34.9
Q ss_pred ccchhcCCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTK---STTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
...+ +.+|++++|+|.++ +.+++.+..+ +. .++|+++++||+|+..
T Consensus 544 ~~g~-~~aDivlLVVDa~~Gi~~qT~e~I~~l----k~---~~iPiIVViNKiDL~~ 592 (1049)
T PRK14845 544 KRGG-SLADLAVLVVDINEGFKPQTIEAINIL----RQ---YKTPFVVAANKIDLIP 592 (1049)
T ss_pred Hhhc-ccCCEEEEEEECcccCCHhHHHHHHHH----HH---cCCCEEEEEECCCCcc
Confidence 3456 78999999999987 6777766432 22 3579999999999953
No 222
>PRK12317 elongation factor 1-alpha; Reviewed
Probab=97.28 E-value=0.00048 Score=46.18 Aligned_cols=47 Identities=15% Similarity=-0.012 Sum_probs=29.8
Q ss_pred cCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+++|++++|+|.+++.++... ..+...+.. . ...|+++++||+|+.+
T Consensus 106 ~~aD~~ilVvDa~~~~~~~~~~~~~~~~~~~-~-~~~~iivviNK~Dl~~ 153 (425)
T PRK12317 106 SQADAAVLVVAADDAGGVMPQTREHVFLART-L-GINQLIVAINKMDAVN 153 (425)
T ss_pred hcCCEEEEEEEcccCCCCCcchHHHHHHHHH-c-CCCeEEEEEEcccccc
Confidence 689999999999874222221 222222222 2 2347899999999964
No 223
>TIGR00503 prfC peptide chain release factor 3. This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. More recently, RF-3 was shown to be active primarily at UGA stop codons in E. coli. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis PCC6803, and in Staphylococcus aureus.
Probab=97.27 E-value=0.00097 Score=46.18 Aligned_cols=48 Identities=17% Similarity=0.105 Sum_probs=33.2
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
.++ +.+|++++|+|.++. --...+.+++..+. .++|+++++||+|+..
T Consensus 99 ~~l-~~aD~aIlVvDa~~g-v~~~t~~l~~~~~~---~~~PiivviNKiD~~~ 146 (527)
T TIGR00503 99 RTL-TAVDNCLMVIDAAKG-VETRTRKLMEVTRL---RDTPIFTFMNKLDRDI 146 (527)
T ss_pred HHH-HhCCEEEEEEECCCC-CCHHHHHHHHHHHh---cCCCEEEEEECccccC
Confidence 356 889999999998863 11223444443332 4689999999999864
No 224
>PRK00741 prfC peptide chain release factor 3; Provisional
Probab=97.25 E-value=0.0011 Score=45.84 Aligned_cols=50 Identities=18% Similarity=0.118 Sum_probs=34.7
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
.++ +.+|++++|+|.++.-. ...+.++..... .++|+++++||+|+....
T Consensus 98 ~~l-~~aD~aIlVvDa~~gv~-~~t~~l~~~~~~---~~iPiiv~iNK~D~~~a~ 147 (526)
T PRK00741 98 RTL-TAVDSALMVIDAAKGVE-PQTRKLMEVCRL---RDTPIFTFINKLDRDGRE 147 (526)
T ss_pred HHH-HHCCEEEEEEecCCCCC-HHHHHHHHHHHh---cCCCEEEEEECCcccccC
Confidence 457 89999999999987421 123344433332 468999999999986543
No 225
>PRK10218 GTP-binding protein; Provisional
Probab=97.17 E-value=0.0016 Score=45.90 Aligned_cols=51 Identities=16% Similarity=-0.022 Sum_probs=35.1
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
..++ +.+|++++|+|.++...- ..+.++..+.. .++|.+++.||+|+.+.+
T Consensus 86 ~~~l-~~aDg~ILVVDa~~G~~~-qt~~~l~~a~~---~gip~IVviNKiD~~~a~ 136 (607)
T PRK10218 86 ERVM-SMVDSVLLVVDAFDGPMP-QTRFVTKKAFA---YGLKPIVVINKVDRPGAR 136 (607)
T ss_pred HHHH-HhCCEEEEEEecccCccH-HHHHHHHHHHH---cCCCEEEEEECcCCCCCc
Confidence 4577 999999999999874322 23333333332 457889999999987543
No 226
>KOG1489 consensus Predicted GTP-binding protein (ODN superfamily) [General function prediction only]
Probab=97.17 E-value=0.0015 Score=42.95 Aligned_cols=47 Identities=19% Similarity=0.354 Sum_probs=38.2
Q ss_pred CCcEEEEEEECCCh---hhHHHHHHHHHHHhhhcC--CCCeEEEEeeCCCCC
Q 038356 10 GALGALLVYDVTKS---TTFENVSRWLKDLGDHAD--SNIVIMMIGNKTDLK 56 (78)
Q Consensus 10 ~a~~~ilv~d~~~~---~s~~~~~~~~~~~~~~~~--~~~~~~lvgnK~Dl~ 56 (78)
.+...++|.|++.. +-++.++....++..+.. .+-|.++|+||+|+.
T Consensus 274 R~~~l~fVvD~s~~~~~~p~~~~~lL~~ELe~yek~L~~rp~liVaNKiD~~ 325 (366)
T KOG1489|consen 274 RCKGLLFVVDLSGKQLRNPWQQLQLLIEELELYEKGLADRPALIVANKIDLP 325 (366)
T ss_pred hhceEEEEEECCCcccCCHHHHHHHHHHHHHHHhhhhccCceEEEEeccCch
Confidence 57889999999998 888888777777754432 678999999999995
No 227
>TIGR00484 EF-G translation elongation factor EF-G. After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G.
Probab=97.13 E-value=0.0017 Score=46.17 Aligned_cols=49 Identities=18% Similarity=0.191 Sum_probs=34.7
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
.++ +.+|++++|+|.++.........| ..++. .++|+++++||+|+.+.
T Consensus 94 ~~l-~~~D~~ilVvda~~g~~~~~~~~~-~~~~~---~~~p~ivviNK~D~~~~ 142 (689)
T TIGR00484 94 RSL-RVLDGAVAVLDAVGGVQPQSETVW-RQANR---YEVPRIAFVNKMDKTGA 142 (689)
T ss_pred HHH-HHhCEEEEEEeCCCCCChhHHHHH-HHHHH---cCCCEEEEEECCCCCCC
Confidence 456 899999999999875544433333 23332 35889999999999753
No 228
>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=97.05 E-value=0.00051 Score=40.63 Aligned_cols=44 Identities=20% Similarity=0.038 Sum_probs=29.6
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
.+||.+++|+|.+++.+-.. ..+... . .+.|.++|.||+|+.+.
T Consensus 18 ~~aD~il~v~D~~~~~~~~~-~~i~~~----~-~~k~~ilVlNK~Dl~~~ 61 (171)
T cd01856 18 KLVDLVIEVRDARIPLSSRN-PLLEKI----L-GNKPRIIVLNKADLADP 61 (171)
T ss_pred hhCCEEEEEeeccCccCcCC-hhhHhH----h-cCCCEEEEEehhhcCCh
Confidence 78999999999987643221 112111 1 34688999999999644
No 229
>PRK09554 feoB ferrous iron transport protein B; Reviewed
Probab=97.04 E-value=0.002 Score=46.52 Aligned_cols=47 Identities=15% Similarity=-0.038 Sum_probs=34.8
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
.+|+++.|.|.++.+. ...|..++.+ .+.|++++.||+|+.+.+.+.
T Consensus 85 ~aD~vI~VvDat~ler---~l~l~~ql~e---~giPvIvVlNK~Dl~~~~~i~ 131 (772)
T PRK09554 85 DADLLINVVDASNLER---NLYLTLQLLE---LGIPCIVALNMLDIAEKQNIR 131 (772)
T ss_pred CCCEEEEEecCCcchh---hHHHHHHHHH---cCCCEEEEEEchhhhhccCcH
Confidence 7899999999988654 2335555544 358999999999997655544
No 230
>COG2262 HflX GTPases [General function prediction only]
Probab=97.04 E-value=0.0034 Score=42.25 Aligned_cols=49 Identities=24% Similarity=0.245 Sum_probs=39.2
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
..||.++.|.|.+++...+.+..-.+-+.+..-.+.|+++|-||+|+-.
T Consensus 270 ~~aDlllhVVDaSdp~~~~~~~~v~~vL~el~~~~~p~i~v~NKiD~~~ 318 (411)
T COG2262 270 KEADLLLHVVDASDPEILEKLEAVEDVLAEIGADEIPIILVLNKIDLLE 318 (411)
T ss_pred hcCCEEEEEeecCChhHHHHHHHHHHHHHHcCCCCCCEEEEEecccccC
Confidence 4789999999999998777776665556555446699999999999653
No 231
>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=96.99 E-value=0.0024 Score=39.75 Aligned_cols=26 Identities=38% Similarity=0.270 Sum_probs=19.3
Q ss_pred cchhcCCcEEEEEEECCChh-hHHHHHH
Q 038356 5 AYYNRGALGALLVYDVTKST-TFENVSR 31 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~-s~~~~~~ 31 (78)
.++ +++|++++|+|.++++ ..+.+.+
T Consensus 73 ~~~-~~ad~il~V~D~t~~~~~~~~~~~ 99 (233)
T cd01896 73 AVA-RTADLILMVLDATKPEGHREILER 99 (233)
T ss_pred Hhh-ccCCEEEEEecCCcchhHHHHHHH
Confidence 367 9999999999998876 3443333
No 232
>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=96.99 E-value=0.002 Score=39.59 Aligned_cols=46 Identities=24% Similarity=0.100 Sum_probs=29.3
Q ss_pred cCCcEEEEEEECCChhh---H----HHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTT---F----ENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s---~----~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+.+|++++|.|.++... | ...+.|. ... .. ...|++++.||+|+..
T Consensus 99 ~~~d~~i~VvDa~~~~~~~~~~~~~~~~~~~~-~~~-~~-~~~~iiivvNK~Dl~~ 151 (219)
T cd01883 99 SQADVAVLVVDARKGEFEAGFEKGGQTREHAL-LAR-TL-GVKQLIVAVNKMDDVT 151 (219)
T ss_pred hhCCEEEEEEECCCCccccccccccchHHHHH-HHH-Hc-CCCeEEEEEEcccccc
Confidence 56999999999988421 1 1122232 222 21 3368999999999973
No 233
>PRK04000 translation initiation factor IF-2 subunit gamma; Validated
Probab=96.93 E-value=0.0038 Score=41.97 Aligned_cols=43 Identities=26% Similarity=0.181 Sum_probs=28.5
Q ss_pred CCcEEEEEEECCC----hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 10 GALGALLVYDVTK----STTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 10 ~a~~~ilv~d~~~----~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
++|++++|+|.++ ..+.+.+..+ ... ...|+++|+||+|+.+.
T Consensus 108 ~~D~~llVVDa~~~~~~~~t~~~l~~l----~~~--~i~~iiVVlNK~Dl~~~ 154 (411)
T PRK04000 108 LMDGAILVIAANEPCPQPQTKEHLMAL----DII--GIKNIVIVQNKIDLVSK 154 (411)
T ss_pred hCCEEEEEEECCCCCCChhHHHHHHHH----HHc--CCCcEEEEEEeeccccc
Confidence 3599999999995 4445444322 211 22368999999999653
No 234
>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=96.90 E-value=0.004 Score=37.91 Aligned_cols=48 Identities=25% Similarity=0.079 Sum_probs=29.5
Q ss_pred chhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
.+ +.+|++++|+|.++... .........+... ...++++|.||+|+.+
T Consensus 97 ~~-~~ad~~llVvD~~~~~~-~~~~~~~~~~~~~--~~~~iIvviNK~D~~~ 144 (208)
T cd04166 97 GA-STADLAILLVDARKGVL-EQTRRHSYILSLL--GIRHVVVAVNKMDLVD 144 (208)
T ss_pred hh-hhCCEEEEEEECCCCcc-HhHHHHHHHHHHc--CCCcEEEEEEchhccc
Confidence 45 78999999999987531 1122222222221 2245788999999864
No 235
>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=96.90 E-value=0.0034 Score=39.62 Aligned_cols=49 Identities=22% Similarity=0.222 Sum_probs=35.3
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
.++ +.+|++++|+|.++.........|. .+.. .+.|.+++.||+|+.+.
T Consensus 83 ~~l-~~aD~~i~Vvd~~~g~~~~~~~~~~-~~~~---~~~p~iivvNK~D~~~~ 131 (268)
T cd04170 83 AAL-RAADAALVVVSAQSGVEVGTEKLWE-FADE---AGIPRIIFINKMDRERA 131 (268)
T ss_pred HHH-HHCCEEEEEEeCCCCCCHHHHHHHH-HHHH---cCCCEEEEEECCccCCC
Confidence 456 8899999999999876554334442 2322 45899999999998754
No 236
>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=96.90 E-value=0.0053 Score=39.15 Aligned_cols=49 Identities=18% Similarity=0.131 Sum_probs=32.5
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
.++ +.+|++++|.|.++.-.= .....+..+.. .+.|++++.||+|+.+.
T Consensus 83 ~~l-~~aD~ailVVDa~~g~~~-~t~~~~~~~~~---~~~p~ivviNK~D~~~a 131 (270)
T cd01886 83 RSL-RVLDGAVAVFDAVAGVEP-QTETVWRQADR---YNVPRIAFVNKMDRTGA 131 (270)
T ss_pred HHH-HHcCEEEEEEECCCCCCH-HHHHHHHHHHH---cCCCEEEEEECCCCCCC
Confidence 456 899999999998764221 11223333332 45789999999998653
No 237
>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=96.86 E-value=0.0069 Score=36.17 Aligned_cols=44 Identities=34% Similarity=0.322 Sum_probs=29.7
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
+.+|++|+|.|..+.-.-.. ...+..+.. .++|+++|.||+|+.
T Consensus 92 ~~~D~ailvVda~~g~~~~~-~~~l~~~~~---~~~p~ivvlNK~D~~ 135 (188)
T PF00009_consen 92 RQADIAILVVDANDGIQPQT-EEHLKILRE---LGIPIIVVLNKMDLI 135 (188)
T ss_dssp TTSSEEEEEEETTTBSTHHH-HHHHHHHHH---TT-SEEEEEETCTSS
T ss_pred cccccceeeeeccccccccc-ccccccccc---cccceEEeeeeccch
Confidence 68999999999986533222 222233332 457899999999997
No 238
>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=96.84 E-value=0.0048 Score=35.13 Aligned_cols=41 Identities=20% Similarity=0.320 Sum_probs=27.8
Q ss_pred CcEEEEEEECCChh--hHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 11 ALGALLVYDVTKST--TFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 11 a~~~ilv~d~~~~~--s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
.+++++++|.++.. ....+..|+.. .+.|+++++||+|+..
T Consensus 82 ~~~~~~v~d~~~~~~~~~~~~~~~l~~------~~~~vi~v~nK~D~~~ 124 (170)
T cd01876 82 LKGVVLLIDSRHGPTEIDLEMLDWLEE------LGIPFLVVLTKADKLK 124 (170)
T ss_pred hhEEEEEEEcCcCCCHhHHHHHHHHHH------cCCCEEEEEEchhcCC
Confidence 46788899887663 22334455443 2478999999999853
No 239
>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=96.84 E-value=0.0017 Score=39.28 Aligned_cols=42 Identities=12% Similarity=0.111 Sum_probs=29.5
Q ss_pred hhcCCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 7 YNRGALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 7 ~~~~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
+ .++|.++++-+ ++|.+. ..|++.+++. +.|+++|+||+|+.
T Consensus 78 ~-~~~d~~l~v~~----~~~~~~d~~~~~~l~~~---~~~~ilV~nK~D~~ 120 (197)
T cd04104 78 F-SEYDFFIIISS----TRFSSNDVKLAKAIQCM---GKKFYFVRTKVDRD 120 (197)
T ss_pred c-cCcCEEEEEeC----CCCCHHHHHHHHHHHHh---CCCEEEEEecccch
Confidence 5 67888888732 345555 4566666654 46889999999983
No 240
>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=96.77 E-value=0.0013 Score=41.92 Aligned_cols=44 Identities=18% Similarity=0.160 Sum_probs=30.0
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
..||.+++|.|...+.+-++ .++.+.. .+.|+++|.||+|+.+.
T Consensus 20 ~~aDvVl~V~Dar~p~~~~~--~~i~~~l----~~kp~IiVlNK~DL~~~ 63 (276)
T TIGR03596 20 KLVDVVIEVLDARIPLSSRN--PMIDEIR----GNKPRLIVLNKADLADP 63 (276)
T ss_pred hhCCEEEEEEeCCCCCCCCC--hhHHHHH----CCCCEEEEEEccccCCH
Confidence 78999999999977644322 1111211 24689999999999643
No 241
>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=96.73 E-value=0.0039 Score=41.75 Aligned_cols=44 Identities=30% Similarity=0.212 Sum_probs=29.0
Q ss_pred cCCcEEEEEEECCCh----hhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 9 RGALGALLVYDVTKS----TTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~----~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
..+|++++|+|.++. .+.+.+. .+... ...|++++.||+|+.+.
T Consensus 102 ~~aD~aIlVVDa~~g~~~~qt~e~l~----~l~~~--gi~~iIVvvNK~Dl~~~ 149 (406)
T TIGR03680 102 ALMDGALLVIAANEPCPQPQTKEHLM----ALEII--GIKNIVIVQNKIDLVSK 149 (406)
T ss_pred HHCCEEEEEEECCCCccccchHHHHH----HHHHc--CCCeEEEEEEccccCCH
Confidence 467999999999853 3444332 22222 22468999999999753
No 242
>PRK13796 GTPase YqeH; Provisional
Probab=96.71 E-value=0.0041 Score=41.21 Aligned_cols=42 Identities=24% Similarity=0.381 Sum_probs=30.3
Q ss_pred CCc-EEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 10 GAL-GALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 10 ~a~-~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
.++ .+++|.|+.+.. ..|...+.+.. .+.|+++|+||+||.+
T Consensus 68 ~~~~lIv~VVD~~D~~-----~s~~~~L~~~~-~~kpviLViNK~DLl~ 110 (365)
T PRK13796 68 DSDALVVNVVDIFDFN-----GSWIPGLHRFV-GNNPVLLVGNKADLLP 110 (365)
T ss_pred ccCcEEEEEEECccCC-----CchhHHHHHHh-CCCCEEEEEEchhhCC
Confidence 445 677899987754 33666666554 3678999999999964
No 243
>PRK12740 elongation factor G; Reviewed
Probab=96.65 E-value=0.0054 Score=43.40 Aligned_cols=49 Identities=16% Similarity=0.123 Sum_probs=36.1
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
.++ +.+|++++|+|.++..+......|. .+.. .+.|++++.||+|+...
T Consensus 79 ~~l-~~aD~vllvvd~~~~~~~~~~~~~~-~~~~---~~~p~iiv~NK~D~~~~ 127 (668)
T PRK12740 79 RAL-RVLDGAVVVVCAVGGVEPQTETVWR-QAEK---YGVPRIIFVNKMDRAGA 127 (668)
T ss_pred HHH-HHhCeEEEEEeCCCCcCHHHHHHHH-HHHH---cCCCEEEEEECCCCCCC
Confidence 456 8999999999998876665544443 3332 45899999999998753
No 244
>PRK00454 engB GTP-binding protein YsxC; Reviewed
Probab=96.65 E-value=0.0053 Score=36.43 Aligned_cols=47 Identities=21% Similarity=0.371 Sum_probs=30.0
Q ss_pred cchhcCC---cEEEEEEECCChhhHHH--HHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 5 AYYNRGA---LGALLVYDVTKSTTFEN--VSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 5 ~y~~~~a---~~~ilv~d~~~~~s~~~--~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
.|+ +.+ +++++++|.+++.+... +..|+ .. .+.|+++++||+|+...
T Consensus 99 ~~~-~~~~~~~~~~~v~d~~~~~~~~~~~i~~~l---~~---~~~~~iiv~nK~Dl~~~ 150 (196)
T PRK00454 99 EYL-RTRENLKGVVLLIDSRHPLKELDLQMIEWL---KE---YGIPVLIVLTKADKLKK 150 (196)
T ss_pred HHH-HhCccceEEEEEEecCCCCCHHHHHHHHHH---HH---cCCcEEEEEECcccCCH
Confidence 455 554 57788888877654432 22232 21 45889999999998654
No 245
>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=96.59 E-value=0.003 Score=37.75 Aligned_cols=53 Identities=17% Similarity=0.073 Sum_probs=31.2
Q ss_pred cEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHH
Q 038356 12 LGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQ 66 (78)
Q Consensus 12 ~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~ 66 (78)
|++++|.|..++.+-.+ ..+.+.+. ....+.|+++|.||+||.+...+..+.+
T Consensus 1 DvVl~VvDar~p~~~~~-~~i~~~~~-l~~~~kp~IlVlNK~DL~~~~~l~~~~~ 53 (172)
T cd04178 1 DVILEVLDARDPLGCRC-PQVEEAVL-QAGGNKKLVLVLNKIDLVPKENVEKWLK 53 (172)
T ss_pred CEEEEEEECCCCCCCCC-HHHHHHHH-hccCCCCEEEEEehhhcCCHHHHHHHHH
Confidence 67899999877533211 12222221 1124579999999999965444443333
No 246
>PLN00043 elongation factor 1-alpha; Provisional
Probab=96.43 E-value=0.0015 Score=44.35 Aligned_cols=49 Identities=24% Similarity=0.145 Sum_probs=30.2
Q ss_pred chhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc----CCCC-eEEEEeeCCCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA----DSNI-VIMMIGNKTDLK 56 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~----~~~~-~~~lvgnK~Dl~ 56 (78)
.. +.+|++|+|+|.++ .+|+....|..+.+++. ..++ +++++.||+|+.
T Consensus 105 g~-~~aD~aIlVVda~~-G~~e~g~~~~~qT~eh~~~~~~~gi~~iIV~vNKmD~~ 158 (447)
T PLN00043 105 GT-SQADCAVLIIDSTT-GGFEAGISKDGQTREHALLAFTLGVKQMICCCNKMDAT 158 (447)
T ss_pred hh-hhccEEEEEEEccc-CceecccCCCchHHHHHHHHHHcCCCcEEEEEEcccCC
Confidence 45 79999999999986 44542211211111111 1345 578899999985
No 247
>PRK09563 rbgA GTPase YlqF; Reviewed
Probab=96.43 E-value=0.003 Score=40.48 Aligned_cols=44 Identities=23% Similarity=0.157 Sum_probs=30.4
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
..||.++.|.|...+.+.++ .++.+.. .+.|+++|.||+||.+.
T Consensus 23 ~~aDvIL~VvDar~p~~~~~--~~l~~~~----~~kp~iiVlNK~DL~~~ 66 (287)
T PRK09563 23 KLVDVVIEVLDARIPLSSEN--PMIDKII----GNKPRLLILNKSDLADP 66 (287)
T ss_pred hhCCEEEEEEECCCCCCCCC--hhHHHHh----CCCCEEEEEEchhcCCH
Confidence 68999999999877654332 1222222 25789999999999643
No 248
>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=96.33 E-value=0.019 Score=35.68 Aligned_cols=45 Identities=20% Similarity=0.093 Sum_probs=29.7
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
.+|++++|.|.....+ .....++..+.. .+.|+++|.||+|+.+.
T Consensus 109 ~~D~~llVvda~~g~~-~~d~~~l~~l~~---~~ip~ivvvNK~D~~~~ 153 (224)
T cd04165 109 APDYAMLVVAANAGII-GMTKEHLGLALA---LNIPVFVVVTKIDLAPA 153 (224)
T ss_pred CCCEEEEEEECCCCCc-HHHHHHHHHHHH---cCCCEEEEEECccccCH
Confidence 5789999999765432 222334444433 34789999999998544
No 249
>PF04670 Gtr1_RagA: Gtr1/RagA G protein conserved region; InterPro: IPR006762 GTR1 was first identified in Saccharomyces cerevisiae (Baker's yeast) as a suppressor of a mutation in RCC1. RCC1 catalyzes guanine nucleotide exchange on Ran, a well characterised nuclear Ras-like small G protein that plays an essential role in the import and export of proteins and RNAs across the nuclear membrane through the nuclear pore complex. RCC1 is located inside the nucleus, bound to chromatin. The concentration of GTP within the cell is ~30 times higher than the concentration of GDP, thus resulting in the preferential production of the GTP form of Ran by RCC1 within the nucleus. Gtr1p is located within both the cytoplasm and the nucleus and has been reported to play a role in cell growth. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1 and Rag A and Gtr1p belong to the sixth subfamily of the Ras-like small GTPase superfamily []. ; GO: 0005525 GTP binding, 0005634 nucleus, 0005737 cytoplasm; PDB: 3R7W_B 2Q3F_B 3LLU_A.
Probab=96.28 E-value=0.018 Score=36.19 Aligned_cols=52 Identities=17% Similarity=0.256 Sum_probs=35.3
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHH---HHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVS---RWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~---~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
...| +++.++|+|+|+.+.+-.+.+. ..+..+.+.. +++.+.+.-+|.|+-.
T Consensus 71 ~~if-~~v~~LIyV~D~qs~~~~~~l~~~~~~i~~l~~~s-p~~~v~vfiHK~D~l~ 125 (232)
T PF04670_consen 71 EEIF-SNVGVLIYVFDAQSDDYDEDLAYLSDCIEALRQYS-PNIKVFVFIHKMDLLS 125 (232)
T ss_dssp HHHH-CTESEEEEEEETT-STCHHHHHHHHHHHHHHHHHS-TT-EEEEEEE-CCCS-
T ss_pred HHHH-hccCEEEEEEEcccccHHHHHHHHHHHHHHHHHhC-CCCeEEEEEeecccCC
Confidence 3457 9999999999999665444444 3444445554 8999999999999853
No 250
>COG1084 Predicted GTPase [General function prediction only]
Probab=96.28 E-value=0.015 Score=38.35 Aligned_cols=53 Identities=19% Similarity=0.228 Sum_probs=38.3
Q ss_pred CcEEEEEEECCChh--hHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHH
Q 038356 11 ALGALLVYDVTKST--TFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIF 65 (78)
Q Consensus 11 a~~~ilv~d~~~~~--s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~ 65 (78)
++++++++|.+... |.+.=.+.+++++.... .|+++|.||.|+.+...+.+..
T Consensus 248 ~~~IlF~~D~Se~cgy~lE~Q~~L~~eIk~~f~--~p~v~V~nK~D~~~~e~~~~~~ 302 (346)
T COG1084 248 AGVILFLFDPSETCGYSLEEQISLLEEIKELFK--APIVVVINKIDIADEEKLEEIE 302 (346)
T ss_pred cCeEEEEEcCccccCCCHHHHHHHHHHHHHhcC--CCeEEEEecccccchhHHHHHH
Confidence 35678899988765 44554567778877653 8999999999998655555443
No 251
>PRK01889 GTPase RsgA; Reviewed
Probab=96.26 E-value=0.018 Score=38.15 Aligned_cols=47 Identities=15% Similarity=0.168 Sum_probs=33.7
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
.++|.+++|.+....-+...+..++..+.. .+++.++|.||+||.+.
T Consensus 111 ANvD~vliV~s~~p~~~~~~ldr~L~~a~~---~~i~piIVLNK~DL~~~ 157 (356)
T PRK01889 111 ANVDTVFIVCSLNHDFNLRRIERYLALAWE---SGAEPVIVLTKADLCED 157 (356)
T ss_pred EeCCEEEEEEecCCCCChhHHHHHHHHHHH---cCCCEEEEEEChhcCCC
Confidence 578999999999644444455666655543 34677889999999654
No 252
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=96.24 E-value=0.019 Score=40.62 Aligned_cols=43 Identities=23% Similarity=0.112 Sum_probs=29.5
Q ss_pred cCCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCe-EEEEeeCCCCCCC
Q 038356 9 RGALGALLVYDVTK---STTFENVSRWLKDLGDHADSNIV-IMMIGNKTDLKHL 58 (78)
Q Consensus 9 ~~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~-~~lvgnK~Dl~~~ 58 (78)
.++|++++|+|.++ +.+.+.+. .+.. .++| +++|.||+|+.++
T Consensus 73 ~~~D~~lLVVda~eg~~~qT~ehl~----il~~---lgi~~iIVVlNKiDlv~~ 119 (614)
T PRK10512 73 GGIDHALLVVACDDGVMAQTREHLA----ILQL---TGNPMLTVALTKADRVDE 119 (614)
T ss_pred hcCCEEEEEEECCCCCcHHHHHHHH----HHHH---cCCCeEEEEEECCccCCH
Confidence 68999999999887 45555442 2222 1244 5799999999653
No 253
>PRK13768 GTPase; Provisional
Probab=96.19 E-value=0.011 Score=37.32 Aligned_cols=50 Identities=14% Similarity=-0.018 Sum_probs=31.5
Q ss_pred CcEEEEEEECCChhhHHHH--HHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCc
Q 038356 11 ALGALLVYDVTKSTTFENV--SRWLKDLGDHADSNIVIMMIGNKTDLKHLPTS 61 (78)
Q Consensus 11 a~~~ilv~d~~~~~s~~~~--~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v 61 (78)
+++++++.|.+...+-... ..|....... ..+.|+++|.||+|+....+.
T Consensus 129 ~~~ii~liD~~~~~~~~d~~~~~~l~~~~~~-~~~~~~i~v~nK~D~~~~~~~ 180 (253)
T PRK13768 129 KSVVVFLIDAVLAKTPSDFVSLLLLALSVQL-RLGLPQIPVLNKADLLSEEEL 180 (253)
T ss_pred CeEEEEEechHHhCCHHHHHHHHHHHHHHHH-HcCCCEEEEEEhHhhcCchhH
Confidence 7899999999654433222 2333322222 246899999999998655443
No 254
>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=96.16 E-value=0.023 Score=37.94 Aligned_cols=43 Identities=23% Similarity=0.189 Sum_probs=27.1
Q ss_pred cCCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCeE-EEEeeCCCCCCC
Q 038356 9 RGALGALLVYDVTK---STTFENVSRWLKDLGDHADSNIVI-MMIGNKTDLKHL 58 (78)
Q Consensus 9 ~~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~-~lvgnK~Dl~~~ 58 (78)
.++|++++|+|.++ ..+.+.+ ..+.. .++|. +++.||+|+.+.
T Consensus 97 ~~~D~~ilVvda~~g~~~qt~e~l----~~~~~---~gi~~iIvvvNK~Dl~~~ 143 (394)
T TIGR00485 97 AQMDGAILVVSATDGPMPQTREHI----LLARQ---VGVPYIVVFLNKCDMVDD 143 (394)
T ss_pred hhCCEEEEEEECCCCCcHHHHHHH----HHHHH---cCCCEEEEEEEecccCCH
Confidence 35699999999987 3333222 22322 24554 578999998653
No 255
>COG1160 Predicted GTPases [General function prediction only]
Probab=95.90 E-value=0.042 Score=37.56 Aligned_cols=44 Identities=23% Similarity=0.225 Sum_probs=29.7
Q ss_pred cCCcEEEEEEECCCh-hhHH-HHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 9 RGALGALLVYDVTKS-TTFE-NVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~-~s~~-~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
..||++++|.|...- ...+ .+.+|+ + ..+.|+++|.||+|-...
T Consensus 82 ~eADvilfvVD~~~Git~~D~~ia~~L---r---~~~kpviLvvNK~D~~~~ 127 (444)
T COG1160 82 EEADVILFVVDGREGITPADEEIAKIL---R---RSKKPVILVVNKIDNLKA 127 (444)
T ss_pred HhCCEEEEEEeCCCCCCHHHHHHHHHH---H---hcCCCEEEEEEcccCchh
Confidence 689999999997652 2222 223333 2 256899999999997643
No 256
>PRK12736 elongation factor Tu; Reviewed
Probab=95.86 E-value=0.038 Score=36.98 Aligned_cols=45 Identities=20% Similarity=0.203 Sum_probs=27.8
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCe-EEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIV-IMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~~lvgnK~Dl~~ 57 (78)
+.+|++++|.|.++.-. ......+..+.. .++| ++++.||+|+.+
T Consensus 97 ~~~d~~llVvd~~~g~~-~~t~~~~~~~~~---~g~~~~IvviNK~D~~~ 142 (394)
T PRK12736 97 AQMDGAILVVAATDGPM-PQTREHILLARQ---VGVPYLVVFLNKVDLVD 142 (394)
T ss_pred hhCCEEEEEEECCCCCc-hhHHHHHHHHHH---cCCCEEEEEEEecCCcc
Confidence 46799999999876211 111222223332 2466 678999999864
No 257
>KOG4273 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.76 E-value=0.007 Score=39.06 Aligned_cols=45 Identities=20% Similarity=0.429 Sum_probs=33.9
Q ss_pred CcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 11 ALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 11 a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
..++++|||.+....+..++.|+....-+. --..+.+|||.|-..
T Consensus 79 l~a~vmvfdlse~s~l~alqdwl~htdins--fdillcignkvdrvp 123 (418)
T KOG4273|consen 79 LQAFVMVFDLSEKSGLDALQDWLPHTDINS--FDILLCIGNKVDRVP 123 (418)
T ss_pred eeeEEEEEeccchhhhHHHHhhcccccccc--chhheeccccccccc
Confidence 478999999999999999999986543321 123467899999643
No 258
>PRK09866 hypothetical protein; Provisional
Probab=95.75 E-value=0.037 Score=39.77 Aligned_cols=47 Identities=17% Similarity=0.178 Sum_probs=31.7
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+++|++++|.|.++.-+... ....+.+++. +...|+++|.||+|+.+
T Consensus 257 ~eADvVLFVVDat~~~s~~D-eeIlk~Lkk~-~K~~PVILVVNKIDl~d 303 (741)
T PRK09866 257 ARASAVLAVLDYTQLKSISD-EEVREAILAV-GQSVPLYVLVNKFDQQD 303 (741)
T ss_pred hhCCEEEEEEeCCCCCChhH-HHHHHHHHhc-CCCCCEEEEEEcccCCC
Confidence 78999999999987543332 1223333332 23469999999999854
No 259
>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=95.75 E-value=0.066 Score=32.53 Aligned_cols=45 Identities=22% Similarity=0.223 Sum_probs=28.4
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCe-EEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIV-IMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~~lvgnK~Dl~~ 57 (78)
+.+|++++|.|.+..-+ ......+..+.. .+.| ++++.||+|+..
T Consensus 87 ~~~D~~ilVvda~~g~~-~~~~~~~~~~~~---~~~~~iIvviNK~D~~~ 132 (195)
T cd01884 87 AQMDGAILVVSATDGPM-PQTREHLLLARQ---VGVPYIVVFLNKADMVD 132 (195)
T ss_pred hhCCEEEEEEECCCCCc-HHHHHHHHHHHH---cCCCcEEEEEeCCCCCC
Confidence 57999999999876321 112223333333 2355 778899999853
No 260
>COG0486 ThdF Predicted GTPase [General function prediction only]
Probab=95.60 E-value=0.029 Score=38.46 Aligned_cols=46 Identities=20% Similarity=0.061 Sum_probs=32.5
Q ss_pred cCCcEEEEEEECCCh-hhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCC
Q 038356 9 RGALGALLVYDVTKS-TTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~-~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~ 60 (78)
..||.+++|.|.+.+ +..+...-+ ..+++.|+++|.||.||..+..
T Consensus 295 ~~ADlvL~v~D~~~~~~~~d~~~~~------~~~~~~~~i~v~NK~DL~~~~~ 341 (454)
T COG0486 295 EEADLVLFVLDASQPLDKEDLALIE------LLPKKKPIIVVLNKADLVSKIE 341 (454)
T ss_pred HhCCEEEEEEeCCCCCchhhHHHHH------hcccCCCEEEEEechhcccccc
Confidence 689999999999985 222221111 2346789999999999976544
No 261
>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=95.60 E-value=0.015 Score=37.13 Aligned_cols=16 Identities=19% Similarity=0.179 Sum_probs=13.4
Q ss_pred CCCeEEEEeeCCCCCC
Q 038356 42 SNIVIMMIGNKTDLKH 57 (78)
Q Consensus 42 ~~~~~~lvgnK~Dl~~ 57 (78)
..+|+++|+||+|+-.
T Consensus 142 ~~v~vi~VinK~D~l~ 157 (276)
T cd01850 142 KRVNIIPVIAKADTLT 157 (276)
T ss_pred ccCCEEEEEECCCcCC
Confidence 3689999999999844
No 262
>TIGR00490 aEF-2 translation elongation factor aEF-2. This model represents archaeal elongation factor 2, a protein more similar to eukaryotic EF-2 than to bacterial EF-G, both in sequence similarity and in sharing with eukaryotes the property of having a diphthamide (modified His) residue at a conserved position. The diphthamide can be ADP-ribosylated by diphtheria toxin in the presence of NAD.
Probab=95.42 E-value=0.03 Score=40.20 Aligned_cols=48 Identities=17% Similarity=0.075 Sum_probs=30.6
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
..+ +.+|++++|+|..+--.-+....|.. .. ..+.|.+++.||+|...
T Consensus 105 ~al-~~aD~~llVvda~~g~~~~t~~~~~~-~~---~~~~p~ivviNKiD~~~ 152 (720)
T TIGR00490 105 RAM-RAVDGAIVVVCAVEGVMPQTETVLRQ-AL---KENVKPVLFINKVDRLI 152 (720)
T ss_pred HHH-HhcCEEEEEEecCCCCCccHHHHHHH-HH---HcCCCEEEEEEChhccc
Confidence 356 89999999999877322111122321 21 24467789999999853
No 263
>KOG0090 consensus Signal recognition particle receptor, beta subunit (small G protein superfamily) [Intracellular trafficking, secretion, and vesicular transport]
Probab=95.33 E-value=0.11 Score=32.63 Aligned_cols=53 Identities=23% Similarity=0.285 Sum_probs=34.6
Q ss_pred CCcEEEEEEECCC-hhhHHHHHHHHHHH-hhh--cCCCCeEEEEeeCCCCCCCCCch
Q 038356 10 GALGALLVYDVTK-STTFENVSRWLKDL-GDH--ADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 10 ~a~~~ilv~d~~~-~~s~~~~~~~~~~~-~~~--~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
.+-++++|.|..- ..-...+..++-.+ .+. +...+|++++.||.|+-..+..+
T Consensus 108 ~akaiVFVVDSa~f~k~vrdvaefLydil~~~~~~~~~~~vLIaCNKqDl~tAkt~~ 164 (238)
T KOG0090|consen 108 SAKAIVFVVDSATFLKNVRDVAEFLYDILLDSRVKKNKPPVLIACNKQDLFTAKTAE 164 (238)
T ss_pred cceeEEEEEeccccchhhHHHHHHHHHHHHhhccccCCCCEEEEecchhhhhcCcHH
Confidence 6788888887543 34455554444444 333 24679999999999997655433
No 264
>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=95.33 E-value=0.042 Score=32.56 Aligned_cols=57 Identities=16% Similarity=0.012 Sum_probs=36.9
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCc----hHHHHhccCc
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTS----MSIFQSLSGL 71 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v----~~~~~~~~~~ 71 (78)
...|+++.|.|.++.+.= .....++.+ -+.|++++.||+|....+.+ ....+.++.+
T Consensus 77 ~~~D~ii~VvDa~~l~r~---l~l~~ql~e---~g~P~vvvlN~~D~a~~~g~~id~~~Ls~~Lg~p 137 (156)
T PF02421_consen 77 EKPDLIIVVVDATNLERN---LYLTLQLLE---LGIPVVVVLNKMDEAERKGIEIDAEKLSERLGVP 137 (156)
T ss_dssp TSSSEEEEEEEGGGHHHH---HHHHHHHHH---TTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-
T ss_pred cCCCEEEEECCCCCHHHH---HHHHHHHHH---cCCCEEEEEeCHHHHHHcCCEECHHHHHHHhCCC
Confidence 578999999999875432 223334443 35899999999998654433 3445555443
No 265
>COG0536 Obg Predicted GTPase [General function prediction only]
Probab=95.31 E-value=0.075 Score=35.44 Aligned_cols=49 Identities=18% Similarity=0.114 Sum_probs=34.6
Q ss_pred CCcEEEEEEECCChhh---HHHHHHHHHHHhhhcC--CCCeEEEEeeCCCCCCC
Q 038356 10 GALGALLVYDVTKSTT---FENVSRWLKDLGDHAD--SNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s---~~~~~~~~~~~~~~~~--~~~~~~lvgnK~Dl~~~ 58 (78)
.+...+.|.|++..+- .+..+....++..+.+ .+.|.+||.||+|+...
T Consensus 237 Rt~vL~hviD~s~~~~~dp~~~~~~i~~EL~~Y~~~L~~K~~ivv~NKiD~~~~ 290 (369)
T COG0536 237 RTRVLLHVIDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKPRIVVLNKIDLPLD 290 (369)
T ss_pred hhheeEEEEecCcccCCCHHHHHHHHHHHHHHhhHHhccCceEEEEeccCCCcC
Confidence 4567888999987653 5555556666655542 56789999999996443
No 266
>PRK12739 elongation factor G; Reviewed
Probab=95.28 E-value=0.07 Score=38.19 Aligned_cols=48 Identities=17% Similarity=0.138 Sum_probs=31.9
Q ss_pred chhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
.+ +.+|++++|.|.++.-.-.. +..+..+.. .+.|.+++.||+|+.+.
T Consensus 93 al-~~~D~~ilVvDa~~g~~~qt-~~i~~~~~~---~~~p~iv~iNK~D~~~~ 140 (691)
T PRK12739 93 SL-RVLDGAVAVFDAVSGVEPQS-ETVWRQADK---YGVPRIVFVNKMDRIGA 140 (691)
T ss_pred HH-HHhCeEEEEEeCCCCCCHHH-HHHHHHHHH---cCCCEEEEEECCCCCCC
Confidence 45 78999999999876532221 222223332 45788999999999753
No 267
>KOG3886 consensus GTP-binding protein [Signal transduction mechanisms]
Probab=94.94 E-value=0.18 Score=32.27 Aligned_cols=53 Identities=19% Similarity=0.244 Sum_probs=39.4
Q ss_pred ccchhcCCcEEEEEEECCChhhHHHHHHHHH---HHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 4 SAYYNRGALGALLVYDVTKSTTFENVSRWLK---DLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 4 ~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~---~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
..-| ++.++.|.|||+.+++--..+..+.+ .+.++ +|...++..-.|.||...
T Consensus 76 d~iF-~nV~vli~vFDves~e~~~D~~~yqk~Le~ll~~-SP~AkiF~l~hKmDLv~~ 131 (295)
T KOG3886|consen 76 DNIF-RNVQVLIYVFDVESREMEKDFHYYQKCLEALLQN-SPEAKIFCLLHKMDLVQE 131 (295)
T ss_pred hhhh-eeheeeeeeeeccchhhhhhHHHHHHHHHHHHhc-CCcceEEEEEeechhccc
Confidence 3456 89999999999999875555544443 33444 488899999999999654
No 268
>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....
Probab=94.87 E-value=0.22 Score=27.20 Aligned_cols=37 Identities=22% Similarity=0.284 Sum_probs=26.0
Q ss_pred cCCcEEEEEEECCChh--hHHHHHHHHHHHhhhcCCCCeEEEEeeC
Q 038356 9 RGALGALLVYDVTKST--TFENVSRWLKDLGDHADSNIVIMMIGNK 52 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~--s~~~~~~~~~~~~~~~~~~~~~~lvgnK 52 (78)
+.+|++++|+|.+++. +..++ +++++ ...|+++|.||
T Consensus 78 ~~~d~ii~vv~~~~~~~~~~~~~---~~~l~----~~~~~i~v~NK 116 (116)
T PF01926_consen 78 SKSDLIIYVVDASNPITEDDKNI---LRELK----NKKPIILVLNK 116 (116)
T ss_dssp CTESEEEEEEETTSHSHHHHHHH---HHHHH----TTSEEEEEEES
T ss_pred HHCCEEEEEEECCCCCCHHHHHH---HHHHh----cCCCEEEEEcC
Confidence 6889999999987742 33333 33332 56899999998
No 269
>PF00503 G-alpha: G-protein alpha subunit; InterPro: IPR001019 Guanine nucleotide binding proteins (G proteins) are membrane-associated, heterotrimeric proteins composed of three subunits: alpha (IPR001019 from INTERPRO), beta (IPR001632 from INTERPRO) and gamma (IPR001770 from INTERPRO) []. G proteins and their receptors (GPCRs) form one of the most prevalent signalling systems in mammalian cells, regulating systems as diverse as sensory perception, cell growth and hormonal regulation []. At the cell surface, the binding of ligands such as hormones and neurotransmitters to a GPCR activates the receptor by causing a conformational change, which in turn activates the bound G protein on the intracellular-side of the membrane. The activated receptor promotes the exchange of bound GDP for GTP on the G protein alpha subunit. GTP binding changes the conformation of switch regions within the alpha subunit, which allows the bound trimeric G protein (inactive) to be released from the receptor, and to dissociate into active alpha subunit (GTP-bound) and beta/gamma dimer. The alpha subunit and the beta/gamma dimer go on to activate distinct downstream effectors, such as adenylyl cyclase, phosphodiesterases, phospholipase C, and ion channels. These effectors in turn regulate the intracellular concentrations of secondary messengers, such as cAMP, diacylglycerol, sodium or calcium cations, which ultimately lead to a physiological response, usually via the downstream regulation of gene transcription. The cycle is completed by the hydrolysis of alpha subunit-bound GTP to GDP, resulting in the re-association of the alpha and beta/gamma subunits and their binding to the receptor, which terminates the signal []. The length of the G protein signal is controlled by the duration of the GTP-bound alpha subunit, which can be regulated by RGS (regulator of G protein signalling) proteins (IPR000342 from INTERPRO) or by covalent modifications []. There are several isoforms of each subunit, many of which have splice variants, which together can make up hundreds of combinations of G proteins. The specific combination of subunits in heterotrimeric G proteins affects not only which receptor it can bind to, but also which downstream target is affected, providing the means to target specific physiological processes in response to specific external stimuli [, ]. G proteins carry lipid modifications on one or more of their subunits to target them to the plasma membrane and to contribute to protein interactions. This family consists of the G protein alpha subunit, which acts as a weak GTPase. G protein classes are defined based on the sequence and function of their alpha subunits, which in mammals fall into four main categories: G(S)alpha, G(Q)alpha, G(I)alpha and G(12)alpha; there are also fungal and plant classes of alpha subunits. The alpha subunit consists of two domains: a GTP-binding domain and a helical insertion domain (IPR011025 from INTERPRO). The GTP-binding domain is homologous to Ras-like small GTPases, and includes switch regions I and II, which change conformation during activation. The switch regions are loops of alpha-helices with conformations sensitive to guanine nucleotides. The helical insertion domain is inserted into the GTP-binding domain before switch region I and is unique to heterotrimeric G proteins. This helical insertion domain functions to sequester the guanine nucleotide at the interface with the GTP-binding domain and must be displaced to enable nucleotide dissociation.; GO: 0004871 signal transducer activity, 0019001 guanyl nucleotide binding, 0007186 G-protein coupled receptor protein signaling pathway; PDB: 3QI2_B 3QE0_A 2IK8_A 2OM2_A 2GTP_B 2XNS_B 3ONW_B 1KJY_A 2EBC_A 1Y3A_B ....
Probab=94.86 E-value=0.046 Score=36.41 Aligned_cols=52 Identities=13% Similarity=0.225 Sum_probs=35.2
Q ss_pred cccchhcCCcEEEEEEECCCh----------hhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTKS----------TTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDL 55 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~----------~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl 55 (78)
|-.+| .+++++|+|.++++- ..+......++.+-... -.+.|++|+-||.|+
T Consensus 253 W~~~F-~~v~~vif~vsls~ydq~~~ed~~~nrl~esl~lF~~i~~~~~~~~~~iil~lnK~D~ 315 (389)
T PF00503_consen 253 WIHCF-EDVTAVIFVVSLSEYDQTLYEDPNTNRLHESLNLFESICNNPWFKNTPIILFLNKIDL 315 (389)
T ss_dssp GGGGG-TTESEEEEEEEGGGGGSBESSSTTSBHHHHHHHHHHHHHTSGGGTTSEEEEEEE-HHH
T ss_pred HHHHh-ccccEEEEeecccchhhhhcccchHHHHHHHHHHHHHHHhCcccccCceEEeeecHHH
Confidence 45788 999999999997642 22444444444443322 267999999999997
No 270
>KOG0082 consensus G-protein alpha subunit (small G protein superfamily) [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=94.67 E-value=0.086 Score=35.16 Aligned_cols=54 Identities=11% Similarity=0.198 Sum_probs=36.9
Q ss_pred cccchhcCCcEEEEEEECCChh----------hHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCC
Q 038356 3 NSAYYNRGALGALLVYDVTKST----------TFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~----------s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~ 57 (78)
|.++| .+++++|+|.++++-+ .+....+.++.+-.+. =.+.+++|.-||.||-+
T Consensus 212 WihcF-e~v~aviF~vslSeYdq~l~ED~~~NRM~eS~~LF~sI~n~~~F~~tsiiLFLNK~DLFe 276 (354)
T KOG0082|consen 212 WIHCF-EDVTAVIFCVSLSEYDQVLEEDETTNRMHESLKLFESICNNKWFANTSIILFLNKKDLFE 276 (354)
T ss_pred HHHhh-cCCCEEEEEEehhhhhhhcccccchhHHHHHHHHHHHHhcCcccccCcEEEEeecHHHHH
Confidence 34678 9999999999988743 2222334444443332 25799999999999954
No 271
>PRK12735 elongation factor Tu; Reviewed
Probab=94.67 E-value=0.18 Score=33.83 Aligned_cols=45 Identities=16% Similarity=0.164 Sum_probs=27.8
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEE-EEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIM-MIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~-lvgnK~Dl~~ 57 (78)
.++|++++|+|.++... ......+..+.. .++|.+ ++.||+|+.+
T Consensus 97 ~~aD~~llVvda~~g~~-~qt~e~l~~~~~---~gi~~iivvvNK~Dl~~ 142 (396)
T PRK12735 97 AQMDGAILVVSAADGPM-PQTREHILLARQ---VGVPYIVVFLNKCDMVD 142 (396)
T ss_pred ccCCEEEEEEECCCCCc-hhHHHHHHHHHH---cCCCeEEEEEEecCCcc
Confidence 46799999999886321 122223333332 346754 6799999964
No 272
>PRK00007 elongation factor G; Reviewed
Probab=94.30 E-value=0.19 Score=36.07 Aligned_cols=46 Identities=20% Similarity=0.260 Sum_probs=30.1
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
+.+|++++|.|...--.-.....| ..+.+ .+.|.+++.||+|+.+.
T Consensus 97 ~~~D~~vlVvda~~g~~~qt~~~~-~~~~~---~~~p~iv~vNK~D~~~~ 142 (693)
T PRK00007 97 RVLDGAVAVFDAVGGVEPQSETVW-RQADK---YKVPRIAFVNKMDRTGA 142 (693)
T ss_pred HHcCEEEEEEECCCCcchhhHHHH-HHHHH---cCCCEEEEEECCCCCCC
Confidence 678999999997654322222223 23332 34788999999998753
No 273
>PLN03126 Elongation factor Tu; Provisional
Probab=94.14 E-value=0.2 Score=34.56 Aligned_cols=45 Identities=16% Similarity=0.128 Sum_probs=29.5
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCe-EEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIV-IMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~~lvgnK~Dl~~ 57 (78)
..+|++++|.|.++-.. ...+.++..+.. .++| ++++.||+|+.+
T Consensus 166 ~~aD~ailVVda~~G~~-~qt~e~~~~~~~---~gi~~iIvvvNK~Dl~~ 211 (478)
T PLN03126 166 AQMDGAILVVSGADGPM-PQTKEHILLAKQ---VGVPNMVVFLNKQDQVD 211 (478)
T ss_pred hhCCEEEEEEECCCCCc-HHHHHHHHHHHH---cCCCeEEEEEecccccC
Confidence 46799999999875422 222333334433 3466 778999999965
No 274
>CHL00071 tufA elongation factor Tu
Probab=93.91 E-value=0.25 Score=33.30 Aligned_cols=45 Identities=18% Similarity=0.164 Sum_probs=29.0
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCe-EEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIV-IMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~~lvgnK~Dl~~ 57 (78)
+.+|++++|.|.+..-. ......+..+.. .++| ++++.||+|+.+
T Consensus 97 ~~~D~~ilVvda~~g~~-~qt~~~~~~~~~---~g~~~iIvvvNK~D~~~ 142 (409)
T CHL00071 97 AQMDGAILVVSAADGPM-PQTKEHILLAKQ---VGVPNIVVFLNKEDQVD 142 (409)
T ss_pred HhCCEEEEEEECCCCCc-HHHHHHHHHHHH---cCCCEEEEEEEccCCCC
Confidence 57899999999875321 222233333332 3467 778999999965
No 275
>COG1159 Era GTPase [General function prediction only]
Probab=93.88 E-value=0.3 Score=31.92 Aligned_cols=47 Identities=19% Similarity=0.186 Sum_probs=31.5
Q ss_pred cCCcEEEEEEECCCh-hhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCC
Q 038356 9 RGALGALLVYDVTKS-TTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~-~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~ 60 (78)
.++|.+++|.|.+.. ...+. .-++.+++ .+.|++++.||+|......
T Consensus 84 ~dvDlilfvvd~~~~~~~~d~--~il~~lk~---~~~pvil~iNKID~~~~~~ 131 (298)
T COG1159 84 KDVDLILFVVDADEGWGPGDE--FILEQLKK---TKTPVILVVNKIDKVKPKT 131 (298)
T ss_pred ccCcEEEEEEeccccCCccHH--HHHHHHhh---cCCCeEEEEEccccCCcHH
Confidence 789999999998873 22222 12222332 4579999999999765544
No 276
>PTZ00416 elongation factor 2; Provisional
Probab=93.85 E-value=0.14 Score=37.52 Aligned_cols=44 Identities=23% Similarity=0.221 Sum_probs=29.7
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
+.+|++|+|.|.++--.-..-.-| ..+.. .+.|++++.||+|+.
T Consensus 114 ~~~D~ailVvda~~g~~~~t~~~~-~~~~~---~~~p~iv~iNK~D~~ 157 (836)
T PTZ00416 114 RVTDGALVVVDCVEGVCVQTETVL-RQALQ---ERIRPVLFINKVDRA 157 (836)
T ss_pred hcCCeEEEEEECCCCcCccHHHHH-HHHHH---cCCCEEEEEEChhhh
Confidence 789999999998764222211223 33332 357999999999986
No 277
>PLN00116 translation elongation factor EF-2 subunit; Provisional
Probab=93.78 E-value=0.18 Score=37.04 Aligned_cols=44 Identities=23% Similarity=0.139 Sum_probs=29.9
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
+.+|++|+|.|.+.--.-...+.|. .+. ..+.|++++.||+|..
T Consensus 120 ~~~D~ailVvda~~Gv~~~t~~~~~-~~~---~~~~p~i~~iNK~D~~ 163 (843)
T PLN00116 120 RITDGALVVVDCIEGVCVQTETVLR-QAL---GERIRPVLTVNKMDRC 163 (843)
T ss_pred hhcCEEEEEEECCCCCcccHHHHHH-HHH---HCCCCEEEEEECCccc
Confidence 6789999999987643222223332 222 2468999999999986
No 278
>PTZ00327 eukaryotic translation initiation factor 2 gamma subunit; Provisional
Probab=93.72 E-value=0.23 Score=34.24 Aligned_cols=47 Identities=23% Similarity=0.166 Sum_probs=27.9
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
..+|++++|.|.++...-...+..+..+... .-.++++|-||+|+.+
T Consensus 139 ~~~D~alLVVda~~g~~~~qT~ehl~i~~~l--gi~~iIVvlNKiDlv~ 185 (460)
T PTZ00327 139 AVMDAALLLIAANESCPQPQTSEHLAAVEIM--KLKHIIILQNKIDLVK 185 (460)
T ss_pred hhCCEEEEEEECCCCccchhhHHHHHHHHHc--CCCcEEEEEecccccC
Confidence 4689999999998631111111222222211 2246889999999965
No 279
>cd03110 Fer4_NifH_child This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.
Probab=93.69 E-value=0.51 Score=27.78 Aligned_cols=45 Identities=29% Similarity=0.347 Sum_probs=33.2
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
..+|.++++...+ ..+...+..+.+.+++. +.|+.+|.||.|...
T Consensus 113 ~~aD~vliv~~~~-~~~~~~~~~~~~~l~~~---~~~~~vV~N~~~~~~ 157 (179)
T cd03110 113 TGADAALLVTEPT-PSGLHDLERAVELVRHF---GIPVGVVINKYDLND 157 (179)
T ss_pred HcCCEEEEEecCC-cccHHHHHHHHHHHHHc---CCCEEEEEeCCCCCc
Confidence 6899999998766 44666777777666543 356789999999754
No 280
>COG0532 InfB Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=93.65 E-value=0.3 Score=34.14 Aligned_cols=41 Identities=22% Similarity=0.172 Sum_probs=30.7
Q ss_pred CCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 10 GALGALLVYDVTK---STTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 10 ~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
=+|.+|||.++++ +.+.+.+.+- + ..++|+++..||+|..+
T Consensus 78 vtDIaILVVa~dDGv~pQTiEAI~ha----k---~a~vP~iVAiNKiDk~~ 121 (509)
T COG0532 78 VTDIAILVVAADDGVMPQTIEAINHA----K---AAGVPIVVAINKIDKPE 121 (509)
T ss_pred cccEEEEEEEccCCcchhHHHHHHHH----H---HCCCCEEEEEecccCCC
Confidence 3588999999887 5666655332 1 25799999999999874
No 281
>PRK00049 elongation factor Tu; Reviewed
Probab=93.48 E-value=0.34 Score=32.53 Aligned_cols=45 Identities=16% Similarity=0.164 Sum_probs=29.0
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEE-EEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIM-MIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~-lvgnK~Dl~~ 57 (78)
..+|++++|.|.++.-. ...+..+..+.. .++|.+ ++.||+|+.+
T Consensus 97 ~~aD~~llVVDa~~g~~-~qt~~~~~~~~~---~g~p~iiVvvNK~D~~~ 142 (396)
T PRK00049 97 AQMDGAILVVSAADGPM-PQTREHILLARQ---VGVPYIVVFLNKCDMVD 142 (396)
T ss_pred ccCCEEEEEEECCCCCc-hHHHHHHHHHHH---cCCCEEEEEEeecCCcc
Confidence 68999999999876321 222333333433 346765 6899999864
No 282
>PF14331 ImcF-related_N: ImcF-related N-terminal domain
Probab=93.23 E-value=0.36 Score=30.80 Aligned_cols=49 Identities=18% Similarity=0.249 Sum_probs=33.5
Q ss_pred cCCcEEEEEEECCChh-------hHHH----HHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKST-------TFEN----VSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~-------s~~~----~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+..+|+|++.|+.+.- .+.. ++.-+.++.+..+-.+|+.++-||+|+-.
T Consensus 24 ~PlnGvil~vs~~~Ll~~~~~~r~l~~~a~~lR~rL~el~~~lg~~~PVYvv~Tk~D~l~ 83 (266)
T PF14331_consen 24 QPLNGVILTVSVDDLLNADEAERELEALARALRQRLEELQRTLGVRLPVYVVFTKCDLLP 83 (266)
T ss_pred CCCCEEEEEEEHHHHhcCChhhhHHHHHHHHHHHHHHHHHHHhCCCCCeEeeeECCCccc
Confidence 4569999999976421 1222 23445555555567899999999999853
No 283
>KOG1424 consensus Predicted GTP-binding protein MMR1 [General function prediction only]
Probab=93.09 E-value=0.11 Score=36.28 Aligned_cols=57 Identities=11% Similarity=0.071 Sum_probs=38.6
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhc
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSL 68 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~ 68 (78)
.+|.++.+.|.-++--|.. .+....+++.. ++...+|+-||+||....++..++.-.
T Consensus 174 rSDivvqIVDARnPllfr~-~dLe~Yvke~d-~~K~~~LLvNKaDLl~~~qr~aWa~YF 230 (562)
T KOG1424|consen 174 RSDIVVQIVDARNPLLFRS-PDLEDYVKEVD-PSKANVLLVNKADLLPPEQRVAWAEYF 230 (562)
T ss_pred hcceEEEEeecCCccccCC-hhHHHHHhccc-cccceEEEEehhhcCCHHHHHHHHHHH
Confidence 6899999999988866543 22333333332 456678999999998776666555444
No 284
>TIGR03348 VI_IcmF type VI secretion protein IcmF. Members of this protein family are IcmF homologs and tend to be associated with type VI secretion systems.
Probab=92.96 E-value=0.24 Score=37.63 Aligned_cols=48 Identities=15% Similarity=0.265 Sum_probs=37.0
Q ss_pred cCCcEEEEEEECCChhh---------HHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 9 RGALGALLVYDVTKSTT---------FENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s---------~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
+..+|+|++.|+.+.-+ -..++..+.++.+..+-.+|+.++-+|+|+-
T Consensus 200 ~plnGvil~vs~~~Ll~~~~~~~~~~a~~lR~rl~el~~~lg~~~PVYvv~Tk~Dll 256 (1169)
T TIGR03348 200 QPLNGVVVTVSLADLLTADPAERKAHARAIRQRLQELREQLGARFPVYLVLTKADLL 256 (1169)
T ss_pred CCCCeEEEEEEHHHHhCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCEEEEEecchhh
Confidence 46799999999776421 1345677777777777899999999999975
No 285
>PLN03127 Elongation factor Tu; Provisional
Probab=92.75 E-value=0.38 Score=32.98 Aligned_cols=45 Identities=13% Similarity=0.164 Sum_probs=27.8
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCe-EEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIV-IMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~~lvgnK~Dl~~ 57 (78)
..+|++++|.|.++... ...+..+..+.. .++| ++++.||+|+.+
T Consensus 146 ~~aD~allVVda~~g~~-~qt~e~l~~~~~---~gip~iIvviNKiDlv~ 191 (447)
T PLN03127 146 AQMDGGILVVSAPDGPM-PQTKEHILLARQ---VGVPSLVVFLNKVDVVD 191 (447)
T ss_pred hhCCEEEEEEECCCCCc-hhHHHHHHHHHH---cCCCeEEEEEEeeccCC
Confidence 46899999999865321 112222222332 3467 578899999964
No 286
>KOG1490 consensus GTP-binding protein CRFG/NOG1 (ODN superfamily) [General function prediction only]
Probab=92.73 E-value=0.32 Score=34.26 Aligned_cols=51 Identities=14% Similarity=0.129 Sum_probs=33.9
Q ss_pred EEEEEEECCChh--hHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHH
Q 038356 13 GALLVYDVTKST--TFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSI 64 (78)
Q Consensus 13 ~~ilv~d~~~~~--s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~ 64 (78)
+++++.|++..- |.+.=-+.++.++... .+-|+++|.||+|+.....+++.
T Consensus 250 aVLYfmDLSe~CGySva~QvkLfhsIKpLF-aNK~~IlvlNK~D~m~~edL~~~ 302 (620)
T KOG1490|consen 250 AVLYFMDLSEMCGYSVAAQVKLYHSIKPLF-ANKVTILVLNKIDAMRPEDLDQK 302 (620)
T ss_pred hheeeeechhhhCCCHHHHHHHHHHhHHHh-cCCceEEEeecccccCccccCHH
Confidence 567777888764 3333334555555444 67899999999999766555543
No 287
>TIGR02034 CysN sulfate adenylyltransferase, large subunit. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules. With members of the Rhizobiaceae family, nodQ often appears as a fusion of cysN (large subunit of ATP sulfurase) and cysC (APS kinase).
Probab=92.65 E-value=0.29 Score=33.00 Aligned_cols=46 Identities=20% Similarity=0.016 Sum_probs=27.3
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
..+|++++|.|.+..-.-...+.|. .+... ...+++++.||+|+.+
T Consensus 102 ~~aD~allVVda~~G~~~qt~~~~~-~~~~~--~~~~iivviNK~D~~~ 147 (406)
T TIGR02034 102 STADLAVLLVDARKGVLEQTRRHSY-IASLL--GIRHVVLAVNKMDLVD 147 (406)
T ss_pred hhCCEEEEEEECCCCCccccHHHHH-HHHHc--CCCcEEEEEEeccccc
Confidence 6889999999986532111111221 12221 2236889999999864
No 288
>KOG0468 consensus U5 snRNP-specific protein [Translation, ribosomal structure and biogenesis]
Probab=92.63 E-value=0.2 Score=36.48 Aligned_cols=43 Identities=28% Similarity=0.398 Sum_probs=30.4
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
+-+|++++|+|+..-=+++- ...++.. ...+.|+++|.||.|.
T Consensus 219 ~~sDgvVlvvDv~EGVmlnt-Er~ikha---iq~~~~i~vviNKiDR 261 (971)
T KOG0468|consen 219 RLSDGVVLVVDVAEGVMLNT-ERIIKHA---IQNRLPIVVVINKVDR 261 (971)
T ss_pred hhcceEEEEEEcccCceeeH-HHHHHHH---HhccCcEEEEEehhHH
Confidence 78999999999876555542 2222222 2367899999999995
No 289
>PRK07560 elongation factor EF-2; Reviewed
Probab=92.48 E-value=0.27 Score=35.55 Aligned_cols=44 Identities=18% Similarity=0.144 Sum_probs=28.3
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
+.+|++++|.|...--.-..-..|. .+.+ .+.|.+++.||+|+.
T Consensus 109 ~~~D~avlVvda~~g~~~~t~~~~~-~~~~---~~~~~iv~iNK~D~~ 152 (731)
T PRK07560 109 RAVDGAIVVVDAVEGVMPQTETVLR-QALR---ERVKPVLFINKVDRL 152 (731)
T ss_pred HhcCEEEEEEECCCCCCccHHHHHH-HHHH---cCCCeEEEEECchhh
Confidence 7899999999977643222223333 2222 235678999999975
No 290
>COG1161 Predicted GTPases [General function prediction only]
Probab=92.25 E-value=0.096 Score=34.31 Aligned_cols=52 Identities=15% Similarity=0.088 Sum_probs=34.6
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHH
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQ 66 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~ 66 (78)
...|.++-|.|.-++.+..+ ..+.+.. .+.|.++|.||+||.+......+..
T Consensus 33 ~~~d~vvevvDar~P~~s~~-----~~l~~~v-~~k~~i~vlNK~DL~~~~~~~~W~~ 84 (322)
T COG1161 33 KSVDVVVEVVDARDPLGTRN-----PELERIV-KEKPKLLVLNKADLAPKEVTKKWKK 84 (322)
T ss_pred ccCCEEEEEEeccccccccC-----ccHHHHH-ccCCcEEEEehhhcCCHHHHHHHHH
Confidence 57899999999999876543 2333333 3344499999999987554443333
No 291
>PF00350 Dynamin_N: Dynamin family; InterPro: IPR001401 Membrane transport between compartments in eukaryotic cells requires proteins that allow the budding and scission of nascent cargo vesicles from one compartment and their targeting and fusion with another. Dynamins are large GTPases that belong to a protein superfamily [] that, in eukaryotic cells, includes classical dynamins, dynamin-like proteins, OPA1, Mx proteins, mitofusins and guanylate-binding proteins/atlastins [, , , ], and are involved in the scission of a wide range of vesicles and organelles. They play a role in many processes including budding of transport vesicles, division of organelles, cytokinesis and pathogen resistance. The minimal distinguishing architectural features that are common to all dynamins and are distinct from other GTPases are the structure of the large GTPase domain (300 amino acids) and the presence of two additional domains; the middle domain and the GTPase effector domain (GED), which are involved in oligomerization and regulation of the GTPase activity. This entry represents the GTPase domain, containing the GTP-binding motifs that are needed for guanine-nucleotide binding and hydrolysis. The conservation of these motifs is absolute except for the the final motif in guanylate-binding proteins. The GTPase catalytic activity can be stimulated by oligomerisation of the protein, which is mediated by interactions between the GTPase domain, the middle domain and the GED.; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 1JWY_B 1JX2_B 3ZVR_A 2AKA_B 3L43_B 2X2F_D 2X2E_D 3SNH_A 3ZYS_D 3ZYC_D ....
Probab=92.21 E-value=0.55 Score=27.09 Aligned_cols=47 Identities=17% Similarity=0.140 Sum_probs=31.1
Q ss_pred cccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCC
Q 038356 3 NSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKT 53 (78)
Q Consensus 3 ~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~ 53 (78)
+..|. +.+|++++|.+.+..-+-.....|.+...... ...++|-||.
T Consensus 122 ~~~~~-~~~d~vi~V~~~~~~~~~~~~~~l~~~~~~~~---~~~i~V~nk~ 168 (168)
T PF00350_consen 122 TEEYL-PKADVVIFVVDANQDLTESDMEFLKQMLDPDK---SRTIFVLNKA 168 (168)
T ss_dssp HHHHH-STTEEEEEEEETTSTGGGHHHHHHHHHHTTTC---SSEEEEEE-G
T ss_pred HHHhh-ccCCEEEEEeccCcccchHHHHHHHHHhcCCC---CeEEEEEcCC
Confidence 45678 99999999999988655444455554444332 3377888874
No 292
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=91.74 E-value=0.16 Score=36.18 Aligned_cols=51 Identities=12% Similarity=0.363 Sum_probs=41.2
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLK 56 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~ 56 (78)
+|. ..+|++|+||.+.+..+|+.++.....+.... ...+|++++|++.-..
T Consensus 91 Qft-~wvdavIfvf~~~d~~s~q~v~~l~~~l~~~r~r~~i~l~lvgtqd~iS 142 (749)
T KOG0705|consen 91 QFC-QWVDAVVFVFSVEDEQSFQAVQALAHEMSSYRNISDLPLILVGTQDHIS 142 (749)
T ss_pred hhh-hhccceEEEEEeccccCHHHHHHHHhhcccccccccchHHhhcCcchhh
Confidence 455 78899999999999999999988877775443 3678999999976543
No 293
>PRK05124 cysN sulfate adenylyltransferase subunit 1; Provisional
Probab=91.67 E-value=0.4 Score=33.04 Aligned_cols=46 Identities=17% Similarity=0.002 Sum_probs=26.9
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+.+|++++|.|.+..-.=.....|. .+... ...|++++.||+|+.+
T Consensus 129 ~~aD~allVVDa~~G~~~qt~~~~~-l~~~l--g~~~iIvvvNKiD~~~ 174 (474)
T PRK05124 129 STCDLAILLIDARKGVLDQTRRHSF-IATLL--GIKHLVVAVNKMDLVD 174 (474)
T ss_pred hhCCEEEEEEECCCCccccchHHHH-HHHHh--CCCceEEEEEeecccc
Confidence 6889999999986531100011121 11111 1237889999999864
No 294
>PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
Probab=91.35 E-value=0.46 Score=33.76 Aligned_cols=46 Identities=20% Similarity=0.054 Sum_probs=27.8
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
..+|++++|.|.+.... ...+.....+... ...+++++.||+|+.+
T Consensus 126 ~~aD~~llVvda~~g~~-~~t~e~~~~~~~~--~~~~iivvvNK~D~~~ 171 (632)
T PRK05506 126 STADLAIILVDARKGVL-TQTRRHSFIASLL--GIRHVVLAVNKMDLVD 171 (632)
T ss_pred HhCCEEEEEEECCCCcc-ccCHHHHHHHHHh--CCCeEEEEEEeccccc
Confidence 67899999999865321 1111111122222 2357889999999864
No 295
>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=91.28 E-value=0.32 Score=28.52 Aligned_cols=48 Identities=19% Similarity=0.072 Sum_probs=31.4
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC-CCCCchHH
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK-HLPTSMSI 64 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~-~~~~v~~~ 64 (78)
+||.++++.|.+++.+.- -..+... =+.|++=|-||+|+. +..++...
T Consensus 63 dad~V~ll~dat~~~~~~-----pP~fa~~--f~~pvIGVITK~Dl~~~~~~i~~a 111 (143)
T PF10662_consen 63 DADVVLLLQDATEPRSVF-----PPGFASM--FNKPVIGVITKIDLPSDDANIERA 111 (143)
T ss_pred hCCEEEEEecCCCCCccC-----Cchhhcc--cCCCEEEEEECccCccchhhHHHH
Confidence 789999999999875421 0111111 146899999999998 44455543
No 296
>KOG0462 consensus Elongation factor-type GTP-binding protein [Translation, ribosomal structure and biogenesis]
Probab=90.85 E-value=1.3 Score=31.61 Aligned_cols=47 Identities=26% Similarity=0.385 Sum_probs=29.6
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
.-++|+++|.|.+.---=.-+..++..+ +.+..++.|-||+|++..+
T Consensus 147 aac~G~lLvVDA~qGvqAQT~anf~lAf----e~~L~iIpVlNKIDlp~ad 193 (650)
T KOG0462|consen 147 AACDGALLVVDASQGVQAQTVANFYLAF----EAGLAIIPVLNKIDLPSAD 193 (650)
T ss_pred hhcCceEEEEEcCcCchHHHHHHHHHHH----HcCCeEEEeeeccCCCCCC
Confidence 4579999999976532111122222222 2567889999999998653
No 297
>COG4963 CpaE Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]
Probab=90.39 E-value=2.2 Score=28.83 Aligned_cols=63 Identities=13% Similarity=0.196 Sum_probs=47.8
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhcc
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSLS 69 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~ 69 (78)
.+. .++|.+++|.+. +-.|+.+.++.++.+++..+++.+..++.||.+-....+.++..+.++
T Consensus 235 ~vL-~~Sd~iviv~e~-sl~slR~ak~lld~l~~~r~~~~~p~lv~n~~~~~~~~~~~dl~~~~~ 297 (366)
T COG4963 235 QVL-SGSDEIVIVAEP-SLASLRNAKELLDELKRLRPNDPKPILVLNRVGVPKRPEPSDLEEILG 297 (366)
T ss_pred HHH-hcCCeEEEEecc-cHHHHHHHHHHHHHHHHhCCCCCCceEEeeecCCCCCCCHHHHHHHhC
Confidence 455 799999999976 467888889999999888877888899999998754444344444443
No 298
>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=90.35 E-value=0.29 Score=29.88 Aligned_cols=38 Identities=24% Similarity=0.193 Sum_probs=25.2
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeE--EEEeeCCCCCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVI--MMIGNKTDLKH 57 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~--~lvgnK~Dl~~ 57 (78)
-++++|.|+|.++-++... .+. +.+.. +++.||+|+.+
T Consensus 112 l~~~~i~vvD~~~~~~~~~--~~~--------~qi~~ad~~~~~k~d~~~ 151 (199)
T TIGR00101 112 LADLTIFVIDVAAGDKIPR--KGG--------PGITRSDLLVINKIDLAP 151 (199)
T ss_pred hhCcEEEEEEcchhhhhhh--hhH--------hHhhhccEEEEEhhhccc
Confidence 3678999999987666321 111 22333 88999999974
No 299
>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=90.25 E-value=1.1 Score=28.40 Aligned_cols=49 Identities=10% Similarity=-0.010 Sum_probs=27.9
Q ss_pred ccchhcCC-cEEEEEEECCC-hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 4 SAYYNRGA-LGALLVYDVTK-STTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 4 ~~y~~~~a-~~~ilv~d~~~-~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
..|. ++. +.+++|.|.+. ....+ .... ++...+...|+++|.||.|..+
T Consensus 156 ~~yi-~~~~~IIL~Vvda~~d~~~~d-~l~i---a~~ld~~~~rti~ViTK~D~~~ 206 (240)
T smart00053 156 KQFI-SKEECLILAVTPANVDLANSD-ALKL---AKEVDPQGERTIGVITKLDLMD 206 (240)
T ss_pred HHHH-hCccCeEEEEEECCCCCCchh-HHHH---HHHHHHcCCcEEEEEECCCCCC
Confidence 4567 744 46677776543 22111 1122 2222235689999999999864
No 300
>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=90.25 E-value=1.1 Score=27.68 Aligned_cols=45 Identities=22% Similarity=0.146 Sum_probs=27.3
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCe-EEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIV-IMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~-~~lvgnK~Dl~~ 57 (78)
+.+|.++++.|.+....-.. ......+.. .+.| +++|.||.|+.+
T Consensus 102 k~aDvVllviDa~~~~~~~~-~~i~~~l~~---~g~p~vi~VvnK~D~~~ 147 (225)
T cd01882 102 KVADLVLLLIDASFGFEMET-FEFLNILQV---HGFPRVMGVLTHLDLFK 147 (225)
T ss_pred HhcCEEEEEEecCcCCCHHH-HHHHHHHHH---cCCCeEEEEEeccccCC
Confidence 57899999999875432211 222223322 2356 455999999853
No 301
>COG1162 Predicted GTPases [General function prediction only]
Probab=89.70 E-value=2.1 Score=28.14 Aligned_cols=49 Identities=18% Similarity=0.171 Sum_probs=32.1
Q ss_pred CCcEEEEEEECCChh-hHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCc
Q 038356 10 GALGALLVYDVTKST-TFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTS 61 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v 61 (78)
+.|-.+++++..+++ +...+..++-.+.. .++.-++|-||+||.+....
T Consensus 79 n~d~~iiIvs~~~P~~~~~~ldR~Lv~ae~---~gi~pvIvlnK~DL~~~~~~ 128 (301)
T COG1162 79 NNDQAIIVVSLVDPDFNTNLLDRYLVLAEA---GGIEPVIVLNKIDLLDDEEA 128 (301)
T ss_pred ccceEEEEEeccCCCCCHHHHHHHHHHHHH---cCCcEEEEEEccccCcchHH
Confidence 567777777877776 55555555544332 45666778999999765433
No 302
>KOG2484 consensus GTPase [General function prediction only]
Probab=89.42 E-value=0.6 Score=31.90 Aligned_cols=53 Identities=17% Similarity=0.079 Sum_probs=35.9
Q ss_pred CCcEEEEEEECCChhhHHH--HHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHH
Q 038356 10 GALGALLVYDVTKSTTFEN--VSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQ 66 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~--~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~ 66 (78)
.+|++|-|.|.-|+.+-.+ +..|.-. . +++-..|+|-||.||-....+..+..
T Consensus 146 ~sDVVleVlDARDPlgtR~~~vE~~V~~--~--~gnKkLILVLNK~DLVPrEv~e~Wl~ 200 (435)
T KOG2484|consen 146 ASDVVLEVLDARDPLGTRCPEVEEAVLQ--A--HGNKKLILVLNKIDLVPREVVEKWLV 200 (435)
T ss_pred hhheEEEeeeccCCCCCCChhHHHHHHh--c--cCCceEEEEeehhccCCHHHHHHHHH
Confidence 5799999999999876443 3444322 1 24477899999999976544444433
No 303
>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]
Probab=89.28 E-value=3 Score=27.23 Aligned_cols=57 Identities=19% Similarity=0.131 Sum_probs=39.2
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhccC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSLSG 70 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~~~ 70 (78)
.+||.+|+|-..| +.++..++.-++-++.. ++|..+|-||.++... .+.+...+.+.
T Consensus 184 ~~aD~ai~VTEPT-p~glhD~kr~~el~~~f---~ip~~iViNr~~~g~s-~ie~~~~e~gi 240 (284)
T COG1149 184 KGADLAILVTEPT-PFGLHDLKRALELVEHF---GIPTGIVINRYNLGDS-EIEEYCEEEGI 240 (284)
T ss_pred ccCCEEEEEecCC-ccchhHHHHHHHHHHHh---CCceEEEEecCCCCch-HHHHHHHHcCC
Confidence 6899999986554 45666666655555443 4899999999976554 56666555543
No 304
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=88.94 E-value=0.36 Score=32.10 Aligned_cols=46 Identities=26% Similarity=0.235 Sum_probs=31.0
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
..||++++++|.++....-+ ..-++.+... ..+|-++|-||.|...
T Consensus 154 q~AD~vvVv~Das~tr~~l~-p~vl~~l~~y--s~ips~lvmnkid~~k 199 (379)
T KOG1423|consen 154 QNADCVVVVVDASATRTPLH-PRVLHMLEEY--SKIPSILVMNKIDKLK 199 (379)
T ss_pred hhCCEEEEEEeccCCcCccC-hHHHHHHHHH--hcCCceeeccchhcch
Confidence 57999999999997443322 2223333333 4688899999999753
No 305
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=88.47 E-value=1.8 Score=23.86 Aligned_cols=40 Identities=10% Similarity=0.116 Sum_probs=29.2
Q ss_pred EEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCC
Q 038356 14 ALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKT 53 (78)
Q Consensus 14 ~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~ 53 (78)
-+++.+.++...+..+.++.+.+++..++++++++-|+=.
T Consensus 52 dvV~iS~~~~~~~~~~~~~i~~l~~~~~~~~~i~vGG~~~ 91 (119)
T cd02067 52 DAIGLSGLLTTHMTLMKEVIEELKEAGLDDIPVLVGGAIV 91 (119)
T ss_pred CEEEEeccccccHHHHHHHHHHHHHcCCCCCeEEEECCCC
Confidence 3556677778888999999999988753277777766543
No 306
>KOG1191 consensus Mitochondrial GTPase [Translation, ribosomal structure and biogenesis]
Probab=87.88 E-value=0.78 Score=32.14 Aligned_cols=50 Identities=26% Similarity=0.255 Sum_probs=32.8
Q ss_pred cCCcEEEEEEEC--CChhhHHHHHHHHHHHhhhc------CCCCeEEEEeeCCCCCCC
Q 038356 9 RGALGALLVYDV--TKSTTFENVSRWLKDLGDHA------DSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 9 ~~a~~~ilv~d~--~~~~s~~~~~~~~~~~~~~~------~~~~~~~lvgnK~Dl~~~ 58 (78)
+.||.+++|+|. ++.++-..+...+.....-. ...-|++++.||.|+...
T Consensus 347 ~~advi~~vvda~~~~t~sd~~i~~~l~~~~~g~~~~~~~~~~~~~i~~~nk~D~~s~ 404 (531)
T KOG1191|consen 347 ERADVILLVVDAEESDTESDLKIARILETEGVGLVVIVNKMEKQRIILVANKSDLVSK 404 (531)
T ss_pred hhcCEEEEEecccccccccchHHHHHHHHhccceEEEeccccccceEEEechhhccCc
Confidence 579999999998 55554444434443332221 134789999999999654
No 307
>KOG1145 consensus Mitochondrial translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=87.39 E-value=2.2 Score=30.63 Aligned_cols=42 Identities=21% Similarity=0.192 Sum_probs=30.4
Q ss_pred cCCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTK---STTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+.+|.+++|....| +.+.+.+++ -.+.++|+++.-||+|-++
T Consensus 223 ~vtDIvVLVVAadDGVmpQT~EaIkh-------Ak~A~VpiVvAinKiDkp~ 267 (683)
T KOG1145|consen 223 NVTDIVVLVVAADDGVMPQTLEAIKH-------AKSANVPIVVAINKIDKPG 267 (683)
T ss_pred ccccEEEEEEEccCCccHhHHHHHHH-------HHhcCCCEEEEEeccCCCC
Confidence 35688999997766 566665533 1236799999999999654
No 308
>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure. Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, P43099 from SWISSPROT) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 106 Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].; GO: 0016831 carboxy-lyase activity; PDB: 3Q16_C 3N75_A 1C4K_A 1ORD_A 2VYC_D.
Probab=86.79 E-value=2.6 Score=23.43 Aligned_cols=40 Identities=8% Similarity=0.293 Sum_probs=27.5
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKT 53 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~ 53 (78)
...|+++-|| .+..+.....++.++... .++|+++++++.
T Consensus 38 ~i~avvi~~d---~~~~~~~~~ll~~i~~~~-~~iPVFl~~~~~ 77 (115)
T PF03709_consen 38 DIAAVVISWD---GEEEDEAQELLDKIRERN-FGIPVFLLAERD 77 (115)
T ss_dssp TEEEEEEECH---HHHHHHHHHHHHHHHHHS-TT-EEEEEESCC
T ss_pred CeeEEEEEcc---cccchhHHHHHHHHHHhC-CCCCEEEEecCC
Confidence 4456666666 555556677777777665 889999999855
No 309
>KOG1954 consensus Endocytosis/signaling protein EHD1 [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=85.94 E-value=1 Score=30.96 Aligned_cols=53 Identities=19% Similarity=0.205 Sum_probs=33.3
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHH
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSI 64 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~ 64 (78)
..+|.+|++||....+--++.+.-+..++. ..-.+-+|-||.|.-+..+.-+.
T Consensus 180 eR~D~IiLlfD~hKLDIsdEf~~vi~aLkG---~EdkiRVVLNKADqVdtqqLmRV 232 (532)
T KOG1954|consen 180 ERVDRIILLFDAHKLDISDEFKRVIDALKG---HEDKIRVVLNKADQVDTQQLMRV 232 (532)
T ss_pred HhccEEEEEechhhccccHHHHHHHHHhhC---CcceeEEEeccccccCHHHHHHH
Confidence 578999999997665544444444444443 33445677899998665444433
No 310
>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]
Probab=85.69 E-value=5.3 Score=25.68 Aligned_cols=45 Identities=20% Similarity=0.242 Sum_probs=29.0
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
+++|.+|+|.|.+ .+|+...+... ++-+.. .=-++.+|.||.|-.
T Consensus 154 ~~vD~vivVvDpS-~~sl~taeri~-~L~~el-g~k~i~~V~NKv~e~ 198 (255)
T COG3640 154 EGVDLVIVVVDPS-YKSLRTAERIK-ELAEEL-GIKRIFVVLNKVDEE 198 (255)
T ss_pred cCCCEEEEEeCCc-HHHHHHHHHHH-HHHHHh-CCceEEEEEeeccch
Confidence 6889999999875 44554443332 222222 135789999999954
No 311
>COG0218 Predicted GTPase [General function prediction only]
Probab=85.26 E-value=3.6 Score=25.52 Aligned_cols=44 Identities=16% Similarity=0.166 Sum_probs=26.2
Q ss_pred CcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 11 ALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 11 a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
-.+++++.|....-.=.. ++.++-+.. .++|++++.||+|--..
T Consensus 107 L~~vvlliD~r~~~~~~D-~em~~~l~~---~~i~~~vv~tK~DKi~~ 150 (200)
T COG0218 107 LKGVVLLIDARHPPKDLD-REMIEFLLE---LGIPVIVVLTKADKLKK 150 (200)
T ss_pred heEEEEEEECCCCCcHHH-HHHHHHHHH---cCCCeEEEEEccccCCh
Confidence 456777777655433211 122222222 56999999999997543
No 312
>COG1160 Predicted GTPases [General function prediction only]
Probab=85.17 E-value=7.2 Score=27.11 Aligned_cols=46 Identities=26% Similarity=0.219 Sum_probs=31.3
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
..|+.+++|.|.+..-+-... .....+.+ ...++++|-||.|+-++
T Consensus 259 ~~a~vvllviDa~~~~~~qD~-~ia~~i~~---~g~~~vIvvNKWDl~~~ 304 (444)
T COG1160 259 ERADVVLLVIDATEGISEQDL-RIAGLIEE---AGRGIVIVVNKWDLVEE 304 (444)
T ss_pred hhcCEEEEEEECCCCchHHHH-HHHHHHHH---cCCCeEEEEEccccCCc
Confidence 578999999999886543322 12222222 45788999999998665
No 313
>COG0480 FusA Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]
Probab=84.59 E-value=1.8 Score=31.48 Aligned_cols=45 Identities=20% Similarity=0.235 Sum_probs=29.7
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
|-+|++++|+|...--.-..-.-|. ++. ..++|.+++-||+|...
T Consensus 98 rvlDgavvVvdaveGV~~QTEtv~r-qa~---~~~vp~i~fiNKmDR~~ 142 (697)
T COG0480 98 RVLDGAVVVVDAVEGVEPQTETVWR-QAD---KYGVPRILFVNKMDRLG 142 (697)
T ss_pred HhhcceEEEEECCCCeeecHHHHHH-HHh---hcCCCeEEEEECccccc
Confidence 6789999999976532222223343 222 25689999999999754
No 314
>PF14784 ECIST_Cterm: C-terminal domain of the ECSIT protein
Probab=83.71 E-value=3.4 Score=23.80 Aligned_cols=38 Identities=13% Similarity=0.406 Sum_probs=27.8
Q ss_pred CcEEEEEEECCChhhHHHHHHHHHHHhhhcC--CCCeEEE
Q 038356 11 ALGALLVYDVTKSTTFENVSRWLKDLGDHAD--SNIVIMM 48 (78)
Q Consensus 11 a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~--~~~~~~l 48 (78)
-||.|+..-++...+=..+..|+..+++..+ ..+|++.
T Consensus 84 ~dGti~Amc~tg~~~~~sL~~WI~~Lq~~NP~L~~ipV~F 123 (126)
T PF14784_consen 84 EDGTIFAMCMTGTSDKDSLLSWIRGLQETNPNLAQIPVLF 123 (126)
T ss_pred ccceEEEEEeccCCCHHHHHHHHHHHHhhCCchhcceEEE
Confidence 4677777777777777777889999988653 4677654
No 315
>COG3523 IcmF Type VI protein secretion system component VasK [Intracellular trafficking, secretion, and vesicular transport]
Probab=83.42 E-value=2.9 Score=32.30 Aligned_cols=49 Identities=20% Similarity=0.300 Sum_probs=35.3
Q ss_pred cCCcEEEEEEECCChhh---------HHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTT---------FENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s---------~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+..+|+|+..|+.+.-+ ...++.-+.++.+...-..|+.++.||.|+-.
T Consensus 213 ~piNGiiltlsv~~L~~~~~~~~~~~~~~LR~RL~El~~tL~~~~PVYl~lTk~Dll~ 270 (1188)
T COG3523 213 RPLNGIILTLSVSDLLTADPAEREALARTLRARLQELRETLHARLPVYLVLTKADLLP 270 (1188)
T ss_pred CCCceEEEEEEHHHHcCCCHHHHHHHHHHHHHHHHHHHHhhccCCceEEEEecccccc
Confidence 56789999998765211 22345556677666667899999999999853
No 316
>PF08468 MTS_N: Methyltransferase small domain N-terminal; InterPro: IPR013675 This domain is found to the N terminus of the methyltransferase small domain (IPR007848 from INTERPRO) in bacterial proteins []. ; GO: 0008990 rRNA (guanine-N2-)-methyltransferase activity, 0006364 rRNA processing; PDB: 2PJD_A.
Probab=83.38 E-value=5.5 Score=23.56 Aligned_cols=51 Identities=12% Similarity=0.157 Sum_probs=31.3
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHH
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQ 66 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~ 66 (78)
.+|.+|+-|.- +=+.+..++..+....+++.+++|||-|.. +-+++....+
T Consensus 69 ~~D~vvly~PK----aK~e~~~lL~~l~~~L~~g~~i~vVGEnk~--GIkSa~K~L~ 119 (155)
T PF08468_consen 69 DFDTVVLYWPK----AKAEAQYLLANLLSHLPPGTEIFVVGENKG--GIKSAEKQLA 119 (155)
T ss_dssp T-SEEEEE--S----SHHHHHHHHHHHHTTS-TT-EEEEEEEGGG--TGGGHHHHHT
T ss_pred CCCEEEEEccC----cHHHHHHHHHHHHHhCCCCCEEEEEecCcc--cHHHHHHHHH
Confidence 57888888844 334556677788887778999999998763 3344444433
No 317
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=82.00 E-value=6.9 Score=21.84 Aligned_cols=42 Identities=7% Similarity=-0.055 Sum_probs=29.0
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKT 53 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~ 53 (78)
+++.+. .+.++..+.+.++.+.+.+++...+++++++-|+..
T Consensus 50 ~~d~V~--iS~~~~~~~~~~~~~~~~L~~~~~~~i~i~~GG~~~ 91 (122)
T cd02071 50 DVDVIG--LSSLSGGHMTLFPEVIELLRELGAGDILVVGGGIIP 91 (122)
T ss_pred CCCEEE--EcccchhhHHHHHHHHHHHHhcCCCCCEEEEECCCC
Confidence 444444 455667788888999999988754567777776643
No 318
>COG0481 LepA Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]
Probab=79.26 E-value=10 Score=26.99 Aligned_cols=46 Identities=28% Similarity=0.369 Sum_probs=29.0
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
..+.|+++|.|.+.-=-=..+.+.+-.+ +.+..++-|-||+||+..
T Consensus 98 AACEGalLvVDAsQGveAQTlAN~YlAl----e~~LeIiPViNKIDLP~A 143 (603)
T COG0481 98 AACEGALLVVDASQGVEAQTLANVYLAL----ENNLEIIPVLNKIDLPAA 143 (603)
T ss_pred hhCCCcEEEEECccchHHHHHHHHHHHH----HcCcEEEEeeecccCCCC
Confidence 4678899999987532111222222222 356889999999999753
No 319
>KOG2423 consensus Nucleolar GTPase [General function prediction only]
Probab=79.19 E-value=4.9 Score=28.00 Aligned_cols=50 Identities=14% Similarity=0.033 Sum_probs=32.5
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~ 60 (78)
..+|.+|-|.|.-|+-.-. +.+.-+.+++.. +...++.|-||+||-....
T Consensus 212 DSSDVvvqVlDARDPmGTr-c~~ve~ylkke~-phKHli~vLNKvDLVPtwv 261 (572)
T KOG2423|consen 212 DSSDVVVQVLDARDPMGTR-CKHVEEYLKKEK-PHKHLIYVLNKVDLVPTWV 261 (572)
T ss_pred cccceeEEeeeccCCcccc-cHHHHHHHhhcC-CcceeEEEeeccccccHHH
Confidence 3678999999988874311 122222344444 6678899999999975433
No 320
>COG2813 RsmC 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]
Probab=79.19 E-value=8.1 Score=25.47 Aligned_cols=54 Identities=17% Similarity=0.174 Sum_probs=37.1
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCchHHHHhc
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSMSIFQSL 68 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~~~~~~~ 68 (78)
.++|++++-+.-+.. ..+.++.++....+++..++++|.|-|- -++..+..++.
T Consensus 36 ~~~d~~l~~~pK~~~----e~e~qLa~ll~~~~~g~~i~v~g~~~~g--~~s~~k~l~~~ 89 (300)
T COG2813 36 DDFDAVLLYWPKHKA----EAEFQLAQLLARLPPGGEIVVVGEKRDG--VRSAEKMLEKY 89 (300)
T ss_pred CCCCEEEEEccCchH----HHHHHHHHHHhhCCCCCeEEEEecccch--HHHHHHHHHHh
Confidence 467888888865544 4566777777777789999999999875 23444444433
No 321
>COG1010 CobJ Precorrin-3B methylase [Coenzyme metabolism]
Probab=78.91 E-value=8.5 Score=24.68 Aligned_cols=44 Identities=16% Similarity=0.190 Sum_probs=35.0
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKT 53 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~ 53 (78)
.+|-++..|..-++..=+++..-++-+.++.+++.|+.++-|=-
T Consensus 154 ~adfVi~~YNP~s~~R~~~~~~a~eil~~~r~~~tpVgivrnag 197 (249)
T COG1010 154 EADFVIALYNPISKRRPEQLGRAFEILREHRSPDTPVGIVRNAG 197 (249)
T ss_pred hCCEEEEEECCccccchHHHHHHHHHHHHhcCCCCcEEEEecCC
Confidence 67889999988887766666666777788888899999987755
No 322
>KOG3929 consensus Uncharacterized conserved protein [Function unknown]
Probab=78.53 E-value=6.4 Score=25.94 Aligned_cols=14 Identities=21% Similarity=0.541 Sum_probs=12.1
Q ss_pred CCeEEEEeeCCCCC
Q 038356 43 NIVIMMIGNKTDLK 56 (78)
Q Consensus 43 ~~~~~lvgnK~Dl~ 56 (78)
.+|+++||.|.|.-
T Consensus 190 P~PV~IVgsKYDvF 203 (363)
T KOG3929|consen 190 PVPVVIVGSKYDVF 203 (363)
T ss_pred CCceEEeccchhhh
Confidence 47999999999963
No 323
>PRK09435 membrane ATPase/protein kinase; Provisional
Probab=78.16 E-value=7.8 Score=25.77 Aligned_cols=42 Identities=14% Similarity=0.031 Sum_probs=24.0
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
.-||.++++.+....+....++ ..+.+. .-++|.||.|+.+.
T Consensus 168 ~~aD~vlvv~~p~~gd~iq~~k---~gi~E~-----aDIiVVNKaDl~~~ 209 (332)
T PRK09435 168 GMVDFFLLLQLPGAGDELQGIK---KGIMEL-----ADLIVINKADGDNK 209 (332)
T ss_pred HhCCEEEEEecCCchHHHHHHH---hhhhhh-----hheEEeehhcccch
Confidence 4578888886533333333322 222222 23799999998653
No 324
>TIGR00073 hypB hydrogenase accessory protein HypB. HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.
Probab=78.05 E-value=3.2 Score=25.20 Aligned_cols=15 Identities=27% Similarity=0.282 Sum_probs=12.3
Q ss_pred CeEEEEeeCCCCCCC
Q 038356 44 IVIMMIGNKTDLKHL 58 (78)
Q Consensus 44 ~~~~lvgnK~Dl~~~ 58 (78)
.|.+++.||.|+.+.
T Consensus 149 ~a~iiv~NK~Dl~~~ 163 (207)
T TIGR00073 149 EADLIVINKADLAEA 163 (207)
T ss_pred hCCEEEEEHHHcccc
Confidence 567999999999754
No 325
>cd01852 AIG1 AIG1 (avrRpt2-induced gene 1). This represents Arabidoposis protein AIG1 that appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 exhibits RPS2- and avrRpt1-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2. This subfamily also includes IAN-4 protein, which has GTP-binding activity and shares sequence homology with a novel family of putative GTP-binding proteins: the immuno-associated nucleotide (IAN) family. The evolutionary conservation of the IAN family provides a unique example of a plant pathogen response gene conserved in animals. The IAN/IMAP subfamily has been proposed to regulate apoptosis in vertebrates and angiosperm plants, particularly in relation to cancer, diabetes, and infections. The human IAN genes were renamed GIMAP (GTPase of the immunity associated proteins).
Probab=77.98 E-value=12 Score=22.29 Aligned_cols=47 Identities=17% Similarity=0.087 Sum_probs=26.9
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCC--CCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADS--NIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~--~~~~~lvgnK~Dl~~ 57 (78)
.++|++++|.+..+. +-+. ..-++.+++..++ -.+++++-|+.|--.
T Consensus 82 ~g~~~illVi~~~~~-t~~d-~~~l~~l~~~fg~~~~~~~ivv~T~~d~l~ 130 (196)
T cd01852 82 PGPHAFLLVVPLGRF-TEEE-EQAVETLQELFGEKVLDHTIVLFTRGDDLE 130 (196)
T ss_pred CCCEEEEEEEECCCc-CHHH-HHHHHHHHHHhChHhHhcEEEEEECccccC
Confidence 688999999998762 2111 2223333333222 136677788887543
No 326
>PRK04017 hypothetical protein; Provisional
Probab=77.23 E-value=6.9 Score=22.72 Aligned_cols=32 Identities=19% Similarity=0.465 Sum_probs=23.1
Q ss_pred hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 23 STTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 23 ~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
++.|+.+.+|++++++.+..+.+++|=| |.|.
T Consensus 3 ~~~~~~~~e~i~~L~e~s~~g~vIVVEG-k~D~ 34 (132)
T PRK04017 3 RENYERFEEIIEELKEFSEAGAPIIVEG-KRDV 34 (132)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCEEEEeC-ccHH
Confidence 4668899999999998875556655544 5553
No 327
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=77.17 E-value=10 Score=26.12 Aligned_cols=43 Identities=21% Similarity=0.040 Sum_probs=26.3
Q ss_pred cCCcEEEEEEECCChh---hH---HHH-HHHHHHHhhhcCCCCe-EEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKST---TF---ENV-SRWLKDLGDHADSNIV-IMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~---s~---~~~-~~~~~~~~~~~~~~~~-~~lvgnK~Dl 55 (78)
..+|++++|.|.+.-. .| ... ++|. .+.. -++| ++++-||+|.
T Consensus 107 ~~aD~ailVVda~~G~~e~~~~~~~qT~eh~~-~~~~---~gi~~iiv~vNKmD~ 157 (446)
T PTZ00141 107 SQADVAILVVASTAGEFEAGISKDGQTREHAL-LAFT---LGVKQMIVCINKMDD 157 (446)
T ss_pred hhcCEEEEEEEcCCCceecccCCCccHHHHHH-HHHH---cCCCeEEEEEEcccc
Confidence 5789999999987531 11 122 2232 2222 2455 6789999995
No 328
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=77.10 E-value=6.9 Score=20.32 Aligned_cols=39 Identities=15% Similarity=0.263 Sum_probs=28.9
Q ss_pred cEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEee
Q 038356 12 LGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGN 51 (78)
Q Consensus 12 ~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgn 51 (78)
.++++.|.+.+.++-+.....++.+++..+.. |.+++..
T Consensus 25 ~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~-p~~ii~D 63 (93)
T PF10551_consen 25 RGFPVAFALVSSESEESYEWFLEKLKEAMPQK-PKVIISD 63 (93)
T ss_pred CEEEEEEEEEcCCChhhhHHHHHHhhhccccC-ceeeecc
Confidence 66888898888888888887777777766445 7666543
No 329
>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=77.01 E-value=5 Score=25.92 Aligned_cols=43 Identities=19% Similarity=0.033 Sum_probs=24.3
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
..+|.++++-+ +++-+.+......+ .+.|.+++.||+|+.+..
T Consensus 146 ~~aD~i~vv~~---~~~~~el~~~~~~l-----~~~~~ivv~NK~Dl~~~~ 188 (300)
T TIGR00750 146 NMADTFVVVTI---PGTGDDLQGIKAGL-----MEIADIYVVNKADGEGAT 188 (300)
T ss_pred HhhceEEEEec---CCccHHHHHHHHHH-----hhhccEEEEEcccccchh
Confidence 34566666532 33334443333322 245679999999997543
No 330
>COG0050 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]
Probab=76.98 E-value=6.6 Score=26.35 Aligned_cols=45 Identities=24% Similarity=0.203 Sum_probs=27.7
Q ss_pred CCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCC-eEEEEeeCCCCCCCCCc
Q 038356 10 GALGALLVYDVTK---STTFENVSRWLKDLGDHADSNI-VIMMIGNKTDLKHLPTS 61 (78)
Q Consensus 10 ~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~-~~~lvgnK~Dl~~~~~v 61 (78)
+.|+.|||.+.++ +.+-+.+ -..+ .-.+ -++++-||+||-+.++.
T Consensus 98 qmDgAILVVsA~dGpmPqTrEHi----Llar---qvGvp~ivvflnK~Dmvdd~el 146 (394)
T COG0050 98 QMDGAILVVAATDGPMPQTREHI----LLAR---QVGVPYIVVFLNKVDMVDDEEL 146 (394)
T ss_pred hcCccEEEEEcCCCCCCcchhhh----hhhh---hcCCcEEEEEEecccccCcHHH
Confidence 4689999998877 3333322 0111 1335 46788999999875543
No 331
>cd03111 CpaE_like This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains 7 genes: pilA, cpaA, cpaB, cpaC, cpaD, cpaE and cpaF. These genes are clustered together on chromosome.
Probab=76.75 E-value=9.8 Score=20.58 Aligned_cols=43 Identities=23% Similarity=0.150 Sum_probs=29.3
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCC-CCeEEEEeeC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADS-NIVIMMIGNK 52 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~-~~~~~lvgnK 52 (78)
..+|.++++.+ .+..++..+..+.+.+++...+ ...+.+|.|+
T Consensus 63 ~~aD~vlvvv~-~~~~s~~~~~~~~~~l~~~~~~~~~~~~lVvNr 106 (106)
T cd03111 63 DQADRVFLVTQ-QDLPSIRNAKRLLELLRVLDYSLPAKIELVLNR 106 (106)
T ss_pred HHcCeEEEEec-CChHHHHHHHHHHHHHHHcCCCCcCceEEEecC
Confidence 67888888774 4567777777777777665433 4456677775
No 332
>PF10995 DUF2819: Protein of unknown function (DUF2819); InterPro: IPR017745 This protein, called BcsE (bacterial cellulose synthase E) or YhjS, is required for cellulose biosynthesis in Salmonella enteritidis. Its role is this process across multiple bacterial species is implied by the partial phylogenetic profiling algorithm []. The protein is encoded in the vicinity of other cellulose biosynthesis genes and has been [] suggested to act as a protease.
Probab=76.55 E-value=12 Score=24.91 Aligned_cols=48 Identities=19% Similarity=0.290 Sum_probs=40.8
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
.+|.+.-++|++++.+-.+.+-.....+++.+++...|+|--.+.-|+
T Consensus 102 ~~a~AATvifs~~~~~qi~~LA~~ih~LRr~~G~~LKIvVRE~~~~LR 149 (316)
T PF10995_consen 102 DTAQAATVIFSCTQNDQIEQLARQIHQLRRQRGSALKIVVREMGQCLR 149 (316)
T ss_pred cccceeEEEEEeCChHHHHHHHHHHHHHHHhcCccceEEEEecchhHH
Confidence 468899999999999999999999999999988888888876665553
No 333
>TIGR02836 spore_IV_A stage IV sporulation protein A. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis.
Probab=75.54 E-value=9.9 Score=26.68 Aligned_cols=43 Identities=19% Similarity=0.219 Sum_probs=30.4
Q ss_pred CCcEEEEEE-ECC----ChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 10 GALGALLVY-DVT----KSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 10 ~a~~~ilv~-d~~----~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
.++..++|. |-+ .++.+... ..|++++++ .+.|.+++-||.|-
T Consensus 144 hstIgivVtTDgsi~dI~Re~y~~aEe~~i~eLk~---~~kPfiivlN~~dp 192 (492)
T TIGR02836 144 HSTIGVVVTTDGTITDIPREDYVEAEERVIEELKE---LNKPFIILLNSTHP 192 (492)
T ss_pred cCcEEEEEEcCCCccccccccchHHHHHHHHHHHh---cCCCEEEEEECcCC
Confidence 677777776 442 23455555 678888775 45899999999993
No 334
>COG1163 DRG Predicted GTPase [General function prediction only]
Probab=74.07 E-value=9.5 Score=25.75 Aligned_cols=28 Identities=29% Similarity=0.321 Sum_probs=21.3
Q ss_pred cCCcEEEEEEECCChhh-HHHHHHHHHHH
Q 038356 9 RGALGALLVYDVTKSTT-FENVSRWLKDL 36 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s-~~~~~~~~~~~ 36 (78)
|+||.+++|.|+....+ .+.+..-++..
T Consensus 139 R~ADlIiiVld~~~~~~~~~~i~~ELe~~ 167 (365)
T COG1163 139 RNADLIIIVLDVFEDPHHRDIIERELEDV 167 (365)
T ss_pred ccCCEEEEEEecCCChhHHHHHHHHHHhc
Confidence 89999999999997776 66665554444
No 335
>PRK13505 formate--tetrahydrofolate ligase; Provisional
Probab=74.06 E-value=7.4 Score=27.81 Aligned_cols=33 Identities=15% Similarity=0.207 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCc
Q 038356 26 FENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTS 61 (78)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v 61 (78)
+.++..-++.++. =++|++++-||.|...+.++
T Consensus 358 l~NL~RHIenvr~---FGvPvVVAINKFd~DTe~Ei 390 (557)
T PRK13505 358 FANLERHIENIRK---FGVPVVVAINKFVTDTDAEI 390 (557)
T ss_pred HHHHHHHHHHHHH---cCCCEEEEEeCCCCCCHHHH
Confidence 3344344444433 35999999999998765443
No 336
>COG4502 5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism]
Probab=70.55 E-value=14 Score=22.05 Aligned_cols=41 Identities=22% Similarity=0.278 Sum_probs=28.9
Q ss_pred cEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCC
Q 038356 12 LGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKT 53 (78)
Q Consensus 12 ~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~ 53 (78)
+..|..-.+.-+.|++.--+|+.+.--.. +..-+++||||-
T Consensus 85 ~vYivtaamdhp~s~~dK~eWl~E~FPFi-~~qn~vfCgnKn 125 (180)
T COG4502 85 NVYIVTAAMDHPKSCEDKGEWLKEKFPFI-SYQNIVFCGNKN 125 (180)
T ss_pred eEEEEEeccCCchhHHHHHHHHHHHCCCC-ChhhEEEecCCC
Confidence 44555555667889998889987765443 445688999986
No 337
>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]
Probab=70.21 E-value=6.9 Score=26.01 Aligned_cols=18 Identities=22% Similarity=0.375 Sum_probs=15.5
Q ss_pred CCCeEEEEeeCCCCCCCC
Q 038356 42 SNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 42 ~~~~~~lvgnK~Dl~~~~ 59 (78)
...|.+++-||+|+.+..
T Consensus 180 tklp~ivvfNK~Dv~d~~ 197 (366)
T KOG1532|consen 180 TKLPFIVVFNKTDVSDSE 197 (366)
T ss_pred ccCCeEEEEecccccccH
Confidence 679999999999997653
No 338
>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
Probab=69.81 E-value=9.5 Score=25.68 Aligned_cols=34 Identities=26% Similarity=0.388 Sum_probs=24.9
Q ss_pred CChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 21 TKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 21 ~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
..++.++.+..|++++++....+.|+++=| |.|.
T Consensus 2 ~~~~~~~~~~~~~~~l~~~~~~~~~ilveg-~~d~ 35 (360)
T PRK14719 2 DKQESLEKLLLIIDDLKLLAEKGIPILVEG-PNDI 35 (360)
T ss_pred CHHHHHHHHHHHHHHHHHhhhCCCEEEEEc-chHH
Confidence 346679999999999998875567765544 5554
No 339
>KOG0447 consensus Dynamin-like GTP binding protein [General function prediction only]
Probab=69.71 E-value=11 Score=27.55 Aligned_cols=68 Identities=21% Similarity=0.225 Sum_probs=39.5
Q ss_pred ccccchhcCCcEEEEEEECCChhhHHHHHHHHHHHhh-hcCCCCeEEEEeeCCCCCCCC--CchHHHHhccCccc
Q 038356 2 INSAYYNRGALGALLVYDVTKSTTFENVSRWLKDLGD-HADSNIVIMMIGNKTDLKHLP--TSMSIFQSLSGLLF 73 (78)
Q Consensus 2 l~~~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~-~~~~~~~~~lvgnK~Dl~~~~--~v~~~~~~~~~~~f 73 (78)
|+..|. .+.+++|+|.-=.+-+ .=+.-...+-. ..+.+-..++|-+|.||.++. ..++...-+.+..|
T Consensus 441 msKayM-~NPNAIILCIQDGSVD---AERSnVTDLVsq~DP~GrRTIfVLTKVDlAEknlA~PdRI~kIleGKLF 511 (980)
T KOG0447|consen 441 ISKAYM-QNPNAIILCIQDGSVD---AERSIVTDLVSQMDPHGRRTIFVLTKVDLAEKNVASPSRIQQIIEGKLF 511 (980)
T ss_pred HHHHHh-cCCCeEEEEeccCCcc---hhhhhHHHHHHhcCCCCCeeEEEEeecchhhhccCCHHHHHHHHhcCcc
Confidence 456788 9999999987422222 11222222222 224557788999999997653 33344444444444
No 340
>COG0523 Putative GTPases (G3E family) [General function prediction only]
Probab=69.46 E-value=15 Score=24.35 Aligned_cols=48 Identities=19% Similarity=0.083 Sum_probs=27.2
Q ss_pred CCcEEEEEEECCChhhHHH-HHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 10 GALGALLVYDVTKSTTFEN-VSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~-~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
..|+++-|.|..+-..... +.....+.-.. .=+|+.||.||-+..++.
T Consensus 116 ~ld~vvtvVDa~~~~~~~~~~~~~~~~Qia~-----AD~ivlNK~Dlv~~~~l~ 164 (323)
T COG0523 116 RLDGVVTVVDAAHFLEGLDAIAELAEDQLAF-----ADVIVLNKTDLVDAEELE 164 (323)
T ss_pred eeceEEEEEeHHHhhhhHHHHHHHHHHHHHh-----CcEEEEecccCCCHHHHH
Confidence 3477888888765544222 32322222222 227889999997755444
No 341
>cd03112 CobW_like The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K.
Probab=69.05 E-value=14 Score=21.46 Aligned_cols=40 Identities=18% Similarity=0.168 Sum_probs=20.3
Q ss_pred CCcEEEEEEECCChhhHH-HHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 10 GALGALLVYDVTKSTTFE-NVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~-~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
..++++.+.|..+-...- +-..+.+++.. .+ +++-||+|+
T Consensus 118 ~~d~vv~vvDa~~~~~~~~~~~~~~~Qi~~---ad---~ivlnk~dl 158 (158)
T cd03112 118 LLDGVITLVDAKHANQHLDQQTEAQSQIAF---AD---RILLNKTDL 158 (158)
T ss_pred eeccEEEEEEhhHhHHHhhccHHHHHHHHH---CC---EEEEecccC
Confidence 467788888855433211 11222233321 11 567899886
No 342
>KOG0099 consensus G protein subunit Galphas, small G protein superfamily [Signal transduction mechanisms]
Probab=68.63 E-value=8.8 Score=25.38 Aligned_cols=51 Identities=14% Similarity=0.216 Sum_probs=29.4
Q ss_pred cchhcCCcEEEEEEECCChh-------hHHHHH---HHHHHHhhh-cCCCCeEEEEeeCCCCC
Q 038356 5 AYYNRGALGALLVYDVTKST-------TFENVS---RWLKDLGDH-ADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~-------s~~~~~---~~~~~~~~~-~~~~~~~~lvgnK~Dl~ 56 (78)
+.| .+..++|+|...++-+ +-+.++ ..++.+=.+ .-..+.+++.-||.||.
T Consensus 221 QcF-ndvtAiifv~acSsyn~vlrED~~qNRL~EaL~LFksiWnNRwL~tisvIlFLNKqDll 282 (379)
T KOG0099|consen 221 QCF-NDVTAIIFVVACSSYNMVLREDNQQNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLL 282 (379)
T ss_pred HHh-cCccEEEEEEeccchhhhhhcCCchhHHHHHHHHHHHHHhhhHHhhhheeEEecHHHHH
Confidence 457 8899999998876521 111121 122222111 11457789999999984
No 343
>PRK09489 rsmC 16S ribosomal RNA m2G1207 methyltransferase; Provisional
Probab=68.59 E-value=22 Score=23.66 Aligned_cols=42 Identities=10% Similarity=0.029 Sum_probs=30.2
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
..|.+++.+.- +-..++.++..+....+++.+++++|.|.+-
T Consensus 76 ~~d~~~~~~pk----~k~~~~~~l~~~~~~l~~g~~i~~~G~~~~g 117 (342)
T PRK09489 76 DCDTLIYYWPK----NKQEAQFQLMNLLSLLPVGTDIFVVGENRSG 117 (342)
T ss_pred CCCEEEEECCC----CHHHHHHHHHHHHHhCCCCCEEEEEEecccc
Confidence 45666666633 3344566777777777788999999999884
No 344
>cd02038 FleN-like FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by influencing FleQ activity.
Probab=67.72 E-value=20 Score=20.27 Aligned_cols=45 Identities=13% Similarity=0.170 Sum_probs=29.6
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
..+|.++++.+.+ ..++..+...++.+.+.. ...++.++.|+.+-
T Consensus 65 ~~aD~vviv~~~~-~~s~~~~~~~l~~l~~~~-~~~~~~lVvN~~~~ 109 (139)
T cd02038 65 LAADEVIVVTTPE-PTSITDAYALIKKLAKQL-RVLNFRVVVNRAES 109 (139)
T ss_pred HhCCeEEEEcCCC-hhHHHHHHHHHHHHHHhc-CCCCEEEEEeCCCC
Confidence 6889888887764 555655544455554433 44567799999974
No 345
>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=67.64 E-value=5.7 Score=24.99 Aligned_cols=44 Identities=18% Similarity=0.154 Sum_probs=21.6
Q ss_pred cEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 12 LGALLVYDVTK---STTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 12 ~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
-+++.+.|... +.+|-+ .++-...-...-+.|.+.|-||+|+..
T Consensus 124 ~~~v~LvD~~~~~~~~~f~s--~~L~s~s~~~~~~lP~vnvlsK~Dl~~ 170 (238)
T PF03029_consen 124 LVVVFLVDSSFCSDPSKFVS--SLLLSLSIMLRLELPHVNVLSKIDLLS 170 (238)
T ss_dssp -EEEEEE-GGG-SSHHHHHH--HHHHHHHHHHHHTSEEEEEE--GGGS-
T ss_pred eEEEEEEecccccChhhHHH--HHHHHHHHHhhCCCCEEEeeeccCccc
Confidence 45666777553 333433 222222111124689999999999976
No 346
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=67.47 E-value=8.3 Score=28.98 Aligned_cols=40 Identities=25% Similarity=0.205 Sum_probs=25.3
Q ss_pred cCCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTK---STTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
.-++.+|+|.|+.. +.+.+++.- + ...+.|.++.-||+|-
T Consensus 562 slC~~aIlvvdImhGlepqtiESi~l----L---R~rktpFivALNKiDR 604 (1064)
T KOG1144|consen 562 SLCDLAILVVDIMHGLEPQTIESINL----L---RMRKTPFIVALNKIDR 604 (1064)
T ss_pred cccceEEEEeehhccCCcchhHHHHH----H---HhcCCCeEEeehhhhh
Confidence 34577788877753 333333211 1 1257899999999995
No 347
>TIGR03369 cellulose_bcsE cellulose biosynthesis protein BcsE. This protein, called BcsE (bacterial cellulose synthase E) or YhjS, is required for cellulose biosynthesis in Salmonella enteritidis. Its role is this process across multiple bacterial species is implied by the partial phylogenetic profiling algorithm. Members are found in the vicinity of other cellulose biosynthesis genes. The model does not include a much less well-conserved N-terminal region about 150 amino acids in length for most members. Solano, et al. suggest this protein acts as a protease.
Probab=67.46 E-value=24 Score=23.59 Aligned_cols=48 Identities=25% Similarity=0.304 Sum_probs=40.6
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
.++.+.-+||++++.+-.+.+-.-...+++.+++...|+|.-++.-|+
T Consensus 107 ~~a~AATvvfs~~~~~qle~La~qih~LRr~~G~aLKIvVRE~~~~LR 154 (322)
T TIGR03369 107 SGAHAATVVLSCTGTTQLEQLAAQVHALRRQCGSALKIVVREMKECLR 154 (322)
T ss_pred cccceeEEEEEcCCchHHHHHHHHHHHHHHhcCccceEEEEechhHHH
Confidence 578899999999999999999777888888887888888877776664
No 348
>TIGR03677 rpl7ae 50S ribosomal protein L7Ae. Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs. Interacts with protein L15e.
Probab=66.78 E-value=8.2 Score=21.69 Aligned_cols=40 Identities=18% Similarity=0.223 Sum_probs=24.4
Q ss_pred CcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 11 ALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 11 a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
+..+|+.=|++..+.-..+..+.++ .++|++.+++|.+|.
T Consensus 43 a~LVilA~D~s~~~~~~~i~~lc~~------~~Ip~~~~~sk~eLG 82 (117)
T TIGR03677 43 AKLVVIAEDVEPPEIVAHLPALCEE------KGIPYVYVKKKEDLG 82 (117)
T ss_pred ccEEEEeCCCCcHHHHHHHHHHHHH------cCCCEEEeCCHHHHH
Confidence 4455555566554433444444322 568999999998884
No 349
>KOG2485 consensus Conserved ATP/GTP binding protein [General function prediction only]
Probab=66.64 E-value=15 Score=24.67 Aligned_cols=48 Identities=17% Similarity=0.027 Sum_probs=29.4
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
+..|++|-|-|.-=+=|-++ ..+++.. +..|-++|-||+||.+..+..
T Consensus 45 ~~~D~iiEvrDaRiPLssrn-----~~~~~~~-~~k~riiVlNK~DLad~~~~k 92 (335)
T KOG2485|consen 45 PLVDCIIEVRDARIPLSSRN-----ELFQDFL-PPKPRIIVLNKMDLADPKEQK 92 (335)
T ss_pred ccccEEEEeeccccCCcccc-----HHHHHhc-CCCceEEEEecccccCchhhh
Confidence 56678888877543322211 1233333 467889999999998754443
No 350
>COG5256 TEF1 Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]
Probab=66.60 E-value=15 Score=25.51 Aligned_cols=49 Identities=22% Similarity=0.140 Sum_probs=29.0
Q ss_pred cCCcEEEEEEECCChh---hHH---HHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 9 RGALGALLVYDVTKST---TFE---NVSRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~---s~~---~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
..||+.|+|.|..+.+ .|. ..+. ...+.+.. .--.++++-||+|+.+.+
T Consensus 107 sqAD~aVLVV~a~~~efE~g~~~~gQtrE-H~~La~tl-Gi~~lIVavNKMD~v~wd 161 (428)
T COG5256 107 SQADVAVLVVDARDGEFEAGFGVGGQTRE-HAFLARTL-GIKQLIVAVNKMDLVSWD 161 (428)
T ss_pred hhccEEEEEEECCCCccccccccCCchhH-HHHHHHhc-CCceEEEEEEcccccccC
Confidence 4789999999987763 121 1111 11122222 234578889999997643
No 351
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=66.30 E-value=22 Score=20.43 Aligned_cols=40 Identities=10% Similarity=-0.013 Sum_probs=25.9
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEee
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGN 51 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgn 51 (78)
++|.+ ..+.....+...++++.+.+++...+++++++-|+
T Consensus 54 ~~d~V--~lS~~~~~~~~~~~~~~~~L~~~~~~~~~i~vGG~ 93 (137)
T PRK02261 54 DADAI--LVSSLYGHGEIDCRGLREKCIEAGLGDILLYVGGN 93 (137)
T ss_pred CCCEE--EEcCccccCHHHHHHHHHHHHhcCCCCCeEEEECC
Confidence 34444 44555557777888999999877545666555554
No 352
>PF01656 CbiA: CobQ/CobB/MinD/ParA nucleotide binding domain; InterPro: IPR002586 This entry consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from Salmonella typhimurium []., and CobQ from Rhodobacter capsulatus []. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [].; PDB: 3K9G_A 3K9H_B 3EZ9_B 3EZF_A 3EZ2_B 3EZ6_A 3EZ7_A 1G3Q_A 1G3R_A 1DTS_A ....
Probab=64.30 E-value=16 Score=21.31 Aligned_cols=53 Identities=13% Similarity=0.085 Sum_probs=37.5
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
..+|.+|++.+.+. .+.+.+..+.+.+++.......+.+|-||.+..+.+...
T Consensus 115 ~~ad~viv~~~~~~-~~i~~~~~~~~~l~~~~~~~~~~~vv~N~v~~~~~~~~~ 167 (195)
T PF01656_consen 115 AAADYVIVPIEPDP-SSIEGAERLIELLKRLGKKLKIIGVVINRVDPGNESKLQ 167 (195)
T ss_dssp HTSSEEEEEEESSH-HHHHHHHHHHHHHHHHTHTEEEEEEEEEEETSCCHHHHH
T ss_pred HhCceeeeecCCcH-HHHHHHHHHHHHHHHhccccceEEEEEeeeCCCccchHH
Confidence 57899999988754 568888888888776542322567899999876544333
No 353
>PF09827 CRISPR_Cas2: CRISPR associated protein Cas2; InterPro: IPR019199 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. Members of this family of bacterial proteins comprise various hypothetical proteins, as well as CRISPR (clustered regularly interspaced short palindromic repeats) associated proteins, conferring resistance to infection by certain bacteriophages. ; PDB: 3EXC_X 2I0X_A 3OQ2_B 3UI3_A 1ZPW_X 2I8E_A 2IVY_A.
Probab=64.27 E-value=11 Score=19.28 Aligned_cols=25 Identities=28% Similarity=0.462 Sum_probs=18.0
Q ss_pred EEEEEEECCChhhHHHHHHHHHHHh
Q 038356 13 GALLVYDVTKSTTFENVSRWLKDLG 37 (78)
Q Consensus 13 ~~ilv~d~~~~~s~~~~~~~~~~~~ 37 (78)
-++++||+++......+.+.++...
T Consensus 3 ~~lv~YDi~~~k~~~kv~k~L~~~g 27 (78)
T PF09827_consen 3 LYLVAYDISDNKRRNKVRKILKSYG 27 (78)
T ss_dssp EEEEEEEEHSHHHHHHHHHHHHHTT
T ss_pred EEEEEEECCCcHHHHHHHHHHHHhC
Confidence 4789999998877777665554443
No 354
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=62.29 E-value=12 Score=25.52 Aligned_cols=44 Identities=27% Similarity=0.239 Sum_probs=24.6
Q ss_pred cEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 12 LGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 12 ~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
||++||.+-+.+----+.++.+-.+.-. .---++++-||+||-.
T Consensus 111 DgAlLvIaANEpcPQPQT~EHl~AleIi--gik~iiIvQNKIDlV~ 154 (415)
T COG5257 111 DGALLVIAANEPCPQPQTREHLMALEII--GIKNIIIVQNKIDLVS 154 (415)
T ss_pred cceEEEEecCCCCCCCchHHHHHHHhhh--ccceEEEEecccceec
Confidence 7888888876542222222222112211 2235789999999954
No 355
>PRK06756 flavodoxin; Provisional
Probab=60.71 E-value=29 Score=19.72 Aligned_cols=43 Identities=7% Similarity=0.011 Sum_probs=27.7
Q ss_pred cCCcEEEEEEECCChhhHH-HHHHHHHHHhhhcCCCCeEEEEee
Q 038356 9 RGALGALLVYDVTKSTTFE-NVSRWLKDLGDHADSNIVIMMIGN 51 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~-~~~~~~~~~~~~~~~~~~~~lvgn 51 (78)
.++|++++....-....+. .+..+++.+......+.++.++|+
T Consensus 48 ~~~d~vi~gspt~~~g~~p~~~~~fl~~l~~~~l~~k~~~~fgt 91 (148)
T PRK06756 48 EQYDGIILGAYTWGDGDLPDDFLDFYDAMDSIDLTGKKAAVFGS 91 (148)
T ss_pred hcCCeEEEEeCCCCCCCCcHHHHHHHHHHhcCCCCCCEEEEEeC
Confidence 5678888877554433333 356677766544336788999988
No 356
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=59.96 E-value=25 Score=18.71 Aligned_cols=35 Identities=17% Similarity=0.112 Sum_probs=25.7
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEE
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMI 49 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lv 49 (78)
..||.+|++-|..+..+...+++..+. .++|++.+
T Consensus 47 ~~aD~VIv~t~~vsH~~~~~vk~~akk------~~ip~~~~ 81 (97)
T PF10087_consen 47 KKADLVIVFTDYVSHNAMWKVKKAAKK------YGIPIIYS 81 (97)
T ss_pred CCCCEEEEEeCCcChHHHHHHHHHHHH------cCCcEEEE
Confidence 678999999999999887766543222 46787765
No 357
>PRK15478 cbiH cobalt-precorrin-3B C(17)-methyltransferase; Provisional
Probab=59.82 E-value=41 Score=21.17 Aligned_cols=45 Identities=9% Similarity=0.036 Sum_probs=29.6
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKT 53 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~ 53 (78)
.+++..+.+|.-.++.+...+..-.+.+....+++.|+.++.|=.
T Consensus 150 ~~~~~tlvlym~~~~~~~~~l~~~~~ll~~g~~~~tPvaiv~~~t 194 (241)
T PRK15478 150 GEADFVICFYNPRSRGREGHLARAFDLLAASKSAQTPVGVVKSAG 194 (241)
T ss_pred hcCCeEEEEECCcccccHHHHHHHHHHHHccCCCCCEEEEEEeCC
Confidence 456778888877766665665543444555556789998886644
No 358
>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase. Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.
Probab=59.69 E-value=37 Score=20.54 Aligned_cols=44 Identities=9% Similarity=0.068 Sum_probs=27.0
Q ss_pred CCcEEEEEEECCChhhHHHHH---HHHHHHhhhcCCCC-eEEEEeeCCCCC
Q 038356 10 GALGALLVYDVTKSTTFENVS---RWLKDLGDHADSNI-VIMMIGNKTDLK 56 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~---~~~~~~~~~~~~~~-~~~lvgnK~Dl~ 56 (78)
.||.++++... +..++..+. ++++++++. .+. ...++-||.+..
T Consensus 141 ~ad~vliv~~p-~~~sl~~~~~l~~~i~~~~~~--~~~~~~gvv~N~~~~~ 188 (212)
T cd02117 141 KADEIYIVTSG-EFMALYAANNICKGIRKYAKS--GGVRLGGLICNSRNTD 188 (212)
T ss_pred cCcEEEEEecc-cHHHHHHHHHHHHHHHHhCcc--cCCcEEEEEEeCCCCc
Confidence 78888888855 455554444 444444322 233 345899999865
No 359
>cd07379 MPP_239FB Homo sapiens 239FB and related proteins, metallophosphatase domain. 239FB (Fetal brain protein 239) is thought to play a role in central nervous system development, but its specific role in unknown. 239FB is expressed predominantly in human fetal brain from a gene located in the chromosome 11p13 region associated with the mental retardation component of the WAGR (Wilms tumor, Aniridia, Genitourinary anomalies, Mental retardation) syndrome. Orthologous brp-like (brain protein 239-like) proteins have been identified in the invertebrate amphioxus group and in vertebrates. 239FB belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzyme
Probab=58.58 E-value=28 Score=19.36 Aligned_cols=45 Identities=24% Similarity=0.273 Sum_probs=24.7
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
.++|.+++.=|+.+...........+.+.+.. ....+++.|| .|.
T Consensus 18 ~~~D~vi~~GD~~~~~~~~~~~~~~~~l~~~~-~~~~~~v~GN-HD~ 62 (135)
T cd07379 18 PDGDVLIHAGDLTERGTLEELQKFLDWLKSLP-HPHKIVIAGN-HDL 62 (135)
T ss_pred CCCCEEEECCCCCCCCCHHHHHHHHHHHHhCC-CCeEEEEECC-CCC
Confidence 46799999999887654443333332233221 1123467787 553
No 360
>PF11111 CENP-M: Centromere protein M (CENP-M); InterPro: IPR020987 The prime candidate for specifying centromere identity is the array of nucleosomes assembles associated with CENP-A []. CENP-A recruits a nucleosome associated complex (CENP-A-NAC complex) comprised of CENP-M which this entry represents, along with two other proteins []. Assembly of the CENP-A NAC at centromeres is partly dependent on CENP-M. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival [].
Probab=58.54 E-value=34 Score=20.88 Aligned_cols=28 Identities=11% Similarity=0.118 Sum_probs=22.1
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHh
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLG 37 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~ 37 (78)
..|-++++.|.++..|+..++.=+..+.
T Consensus 64 rIDlIVFvinl~sk~SL~~ve~SL~~vd 91 (176)
T PF11111_consen 64 RIDLIVFVINLHSKYSLQSVEASLSHVD 91 (176)
T ss_pred eeEEEEEEEecCCcccHHHHHHHHhhCC
Confidence 4588999999999999998866554443
No 361
>PRK15045 cellulose biosynthesis protein BcsE; Provisional
Probab=58.24 E-value=41 Score=24.01 Aligned_cols=48 Identities=23% Similarity=0.390 Sum_probs=40.6
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
.++.+.-+||++++.+-.+.+-.-...+++.+++...|+|.-++.-|+
T Consensus 255 ~~a~AATvVfs~~~~~qle~LA~qih~LRRq~G~aLKIvVRE~~~~LR 302 (519)
T PRK15045 255 RTAQAATVVFSLQQNAQIEPLARSIHTLRRQRGSAMKILVRENTASLR 302 (519)
T ss_pred cccceeEEEEEcCCchHHHHHHHHHHHHHHhcCccceEEEEechhHHH
Confidence 578899999999999999999777888888887888888877776664
No 362
>COG1358 RPL8A Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis]
Probab=57.58 E-value=15 Score=20.79 Aligned_cols=42 Identities=17% Similarity=0.291 Sum_probs=27.1
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
.+.-+++.=|++=++....+....+ ..++|++.|++|..|..
T Consensus 43 ~a~LVviA~Dv~P~~~~~~l~~lc~------~~~vpyv~V~sk~~LG~ 84 (116)
T COG1358 43 KAKLVVIAEDVSPEELVKHLPALCE------EKNVPYVYVGSKKELGK 84 (116)
T ss_pred CCcEEEEecCCCHHHHHHHHHHHHH------hcCCCEEEeCCHHHHHH
Confidence 4566677767654555444433322 26799999999998853
No 363
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=57.51 E-value=38 Score=20.59 Aligned_cols=38 Identities=16% Similarity=0.139 Sum_probs=26.8
Q ss_pred EEEEECCChhhHHHHHHHHHHHhhhcC-CCCeEEEEeeC
Q 038356 15 LLVYDVTKSTTFENVSRWLKDLGDHAD-SNIVIMMIGNK 52 (78)
Q Consensus 15 ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~lvgnK 52 (78)
++..+.+...+...++++.+.+++... +++++++-|.=
T Consensus 138 ~v~lS~~~~~~~~~~~~~i~~l~~~~~~~~v~i~vGG~~ 176 (197)
T TIGR02370 138 MLTGSALMTTTMYGQKDINDKLKEEGYRDSVKFMVGGAP 176 (197)
T ss_pred EEEEccccccCHHHHHHHHHHHHHcCCCCCCEEEEEChh
Confidence 455667777778888999999988753 45666665543
No 364
>cd05295 MDH_like Malate dehydrogenase-like. These MDH-like proteins are related to other groups in the MDH family but do not have conserved substrate and cofactor binding residues. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subgroup are uncharacterized MDH-like proteins from animals. They are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Probab=57.42 E-value=28 Score=24.32 Aligned_cols=48 Identities=13% Similarity=0.151 Sum_probs=32.4
Q ss_pred hhcCCcEEEEEEECCChhh---HHH-------HHHHHHHHhhhcCCCCeEEEEe-eCCCC
Q 038356 7 YNRGALGALLVYDVTKSTT---FEN-------VSRWLKDLGDHADSNIVIMMIG-NKTDL 55 (78)
Q Consensus 7 ~~~~a~~~ilv~d~~~~~s---~~~-------~~~~~~~~~~~~~~~~~~~lvg-nK~Dl 55 (78)
+ ++||.+|++-....... .+- ++...+.+.++.+++..++|+| |=+|.
T Consensus 197 ~-~daDvvIitag~prk~G~~R~DLL~~N~~Ifk~~g~~I~~~a~~~~~VlVv~tNPvD~ 255 (452)
T cd05295 197 F-KDAHVIVLLDDFLIKEGEDLEGCIRSRVAICQLYGPLIEKNAKEDVKVIVAGRTFLNL 255 (452)
T ss_pred h-CCCCEEEECCCCCCCcCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCeEEEEeCCcHHH
Confidence 5 79999999988754332 221 2455556666666667888888 87775
No 365
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=57.21 E-value=15 Score=20.81 Aligned_cols=40 Identities=18% Similarity=0.211 Sum_probs=24.1
Q ss_pred CcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 11 ALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 11 a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
+..+|+.=|++..+....+..+.++ .++|++.+++|.+|.
T Consensus 47 akLVilA~D~s~~~i~~~~~~lc~~------~~Vp~~~~~tk~eLG 86 (122)
T PRK04175 47 AKLVVIAEDVDPEEIVAHLPLLCEE------KKIPYVYVPSKKDLG 86 (122)
T ss_pred ccEEEEeCCCChHHHHHHHHHHHHH------cCCCEEEECCHHHHH
Confidence 4445555566544434444444322 578999999998874
No 366
>cd01832 SGNH_hydrolase_like_1 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid. Myxobacterial members of this subfamily have been reported to be involved in adventurous gliding motility.
Probab=57.18 E-value=36 Score=19.66 Aligned_cols=39 Identities=5% Similarity=-0.043 Sum_probs=24.4
Q ss_pred CCcEEEEEEECCChhh--------HHHHHHHHHHHhhhcCCCCeEEEEee
Q 038356 10 GALGALLVYDVTKSTT--------FENVSRWLKDLGDHADSNIVIMMIGN 51 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s--------~~~~~~~~~~~~~~~~~~~~~~lvgn 51 (78)
..|.+++.+-.+|... .+++...++.++ .++.++++++.
T Consensus 67 ~~d~vii~~G~ND~~~~~~~~~~~~~~~~~~i~~i~---~~~~~vil~~~ 113 (185)
T cd01832 67 RPDLVTLLAGGNDILRPGTDPDTYRADLEEAVRRLR---AAGARVVVFTI 113 (185)
T ss_pred CCCEEEEeccccccccCCCCHHHHHHHHHHHHHHHH---hCCCEEEEecC
Confidence 5688888876666533 444566666665 25667777653
No 367
>PF05783 DLIC: Dynein light intermediate chain (DLIC); InterPro: IPR022780 This entry consists of several eukaryotic dynein light intermediate chain proteins. The light intermediate chains (LICs) of cytoplasmic dynein consist of multiple isoforms, which undergo post-translational modification to produce a large number of species. DLIC1 is known to be involved in assembly, organisation, and function of centrosomes and mitotic spindles when bound to pericentrin [, ]. DLIC2 is a subunit of cytoplasmic dynein 2 that may play a role in maintaining Golgi organisation by binding cytoplasmic dynein 2 to its Golgi-associated cargo [].
Probab=57.14 E-value=24 Score=24.78 Aligned_cols=25 Identities=28% Similarity=0.550 Sum_probs=17.5
Q ss_pred cEEEEEEECCChhh-HHHHHHHHHHH
Q 038356 12 LGALLVYDVTKSTT-FENVSRWLKDL 36 (78)
Q Consensus 12 ~~~ilv~d~~~~~s-~~~~~~~~~~~ 36 (78)
-.+|+|.|++.+-+ ++.++.|+..+
T Consensus 102 t~vvIvlDlS~PW~~~esL~~W~~vl 127 (472)
T PF05783_consen 102 TLVVIVLDLSKPWNIMESLEKWLSVL 127 (472)
T ss_pred eEEEEEecCCChHHHHHHHHHHHHHH
Confidence 36788999999976 44566666543
No 368
>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=56.10 E-value=24 Score=20.85 Aligned_cols=44 Identities=20% Similarity=0.182 Sum_probs=25.5
Q ss_pred CCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 10 GALGALLVYDVTKSTTFENV-SRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
..+.+|.|.|..+-...... ..+.+++... + +++-||+|+.+..
T Consensus 113 ~~~~iI~vVDa~~~~~~~~~~~~~~~Qi~~A---D---vIvlnK~D~~~~~ 157 (178)
T PF02492_consen 113 RLDSIITVVDATNFDELENIPELLREQIAFA---D---VIVLNKIDLVSDE 157 (178)
T ss_dssp SESEEEEEEEGTTHGGHTTHCHHHHHHHCT----S---EEEEE-GGGHHHH
T ss_pred cccceeEEeccccccccccchhhhhhcchhc---C---EEEEeccccCChh
Confidence 34678888898775444444 2333333221 1 7788999986443
No 369
>cd05294 LDH-like_MDH_nadp A lactate dehydrogenases-like structure with malate dehydrogenase enzymatic activity. The LDH-like MDH proteins have a lactate dehyhydrogenase-like (LDH-like) structure and malate dehydrogenase (MDH) enzymatic activity. This subgroup is composed of some archaeal LDH-like MDHs that prefer NADP(H) rather than NAD(H) as a cofactor. One member, MJ0490 from Methanococcus jannaschii, has been observed to form dimers and tetramers during crystalization, although it is believed to exist primarilly as a tetramer in solution. In addition to its MDH activity, MJ0490 also possesses fructose-1,6-bisphosphate-activated LDH activity. Members of this subgroup have a higher sequence similarity to LDHs than to other MDHs. LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carbox
Probab=54.72 E-value=46 Score=21.73 Aligned_cols=47 Identities=17% Similarity=0.345 Sum_probs=31.1
Q ss_pred hhcCCcEEEEEEECCCh-----hhH-----HHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 7 YNRGALGALLVYDVTKS-----TTF-----ENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 7 ~~~~a~~~ilv~d~~~~-----~s~-----~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
. ++||.+++....... ..+ .-++...+.+.+.+ ++..+++++|-.|.
T Consensus 70 l-~~aDiViitag~p~~~~~~r~dl~~~n~~i~~~~~~~i~~~~-~~~~viv~~npvd~ 126 (309)
T cd05294 70 V-AGSDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQIAEFA-PDTKILVVTNPVDV 126 (309)
T ss_pred h-CCCCEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC-CCeEEEEeCCchHH
Confidence 5 799999999875332 222 22345555556555 67788888988885
No 370
>PRK15029 arginine decarboxylase; Provisional
Probab=53.34 E-value=37 Score=25.34 Aligned_cols=44 Identities=14% Similarity=0.397 Sum_probs=32.5
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTD 54 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~D 54 (78)
..|++|+=+.+.+.+.++...++++.+++.. .++|++++..+.|
T Consensus 53 ~~DlVLLD~~LPd~dG~~~~~ell~~IR~~~-~~iPIIlLTar~~ 96 (755)
T PRK15029 53 AIDCLMFSYQMEHPDEHQNVRQLIGKLHERQ-QNVPVFLLGDREK 96 (755)
T ss_pred CCcEEEEECCCCCCccchhHHHHHHHHHhhC-CCCCEEEEEcCCc
Confidence 4577777666878877766666777776543 6899999988876
No 371
>COG2895 CysN GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]
Probab=52.64 E-value=72 Score=22.13 Aligned_cols=48 Identities=21% Similarity=0.176 Sum_probs=25.9
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~ 60 (78)
.||..|++.|. ...-++..+.. ..+.... .=..+++.-||+||.+-.+
T Consensus 109 TadlAIlLVDA-R~Gvl~QTrRH-s~I~sLL-GIrhvvvAVNKmDLvdy~e 156 (431)
T COG2895 109 TADLAILLVDA-RKGVLEQTRRH-SFIASLL-GIRHVVVAVNKMDLVDYSE 156 (431)
T ss_pred cccEEEEEEec-chhhHHHhHHH-HHHHHHh-CCcEEEEEEeeecccccCH
Confidence 46888988886 22223332111 1111111 2235788899999976543
No 372
>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.
Probab=52.52 E-value=50 Score=20.05 Aligned_cols=38 Identities=16% Similarity=0.234 Sum_probs=27.3
Q ss_pred EEEEECCChhhHHHHHHHHHHHhhhcC-CCCeEEEEeeC
Q 038356 15 LLVYDVTKSTTFENVSRWLKDLGDHAD-SNIVIMMIGNK 52 (78)
Q Consensus 15 ilv~d~~~~~s~~~~~~~~~~~~~~~~-~~~~~~lvgnK 52 (78)
++..+.+...+...++.+.+.+++... +++++++-|.=
T Consensus 136 ~v~lS~~~~~~~~~~~~~i~~lr~~~~~~~~~i~vGG~~ 174 (201)
T cd02070 136 ILGLSALMTTTMGGMKEVIEALKEAGLRDKVKVMVGGAP 174 (201)
T ss_pred EEEEeccccccHHHHHHHHHHHHHCCCCcCCeEEEECCc
Confidence 455666677778889999999988752 36777766653
No 373
>PF13124 DUF3963: Protein of unknown function (DUF3963)
Probab=52.24 E-value=17 Score=16.32 Aligned_cols=15 Identities=13% Similarity=0.880 Sum_probs=11.4
Q ss_pred hhhHHHHHHHHHHHh
Q 038356 23 STTFENVSRWLKDLG 37 (78)
Q Consensus 23 ~~s~~~~~~~~~~~~ 37 (78)
+.-|+.+++|+..+.
T Consensus 10 eryfddiqkwirnit 24 (40)
T PF13124_consen 10 ERYFDDIQKWIRNIT 24 (40)
T ss_pred HHHHHHHHHHHHHHH
Confidence 356888999988764
No 374
>cd01844 SGNH_hydrolase_like_6 SGNH_hydrolase subfamily. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=51.87 E-value=46 Score=19.30 Aligned_cols=43 Identities=12% Similarity=0.089 Sum_probs=28.7
Q ss_pred CCcEEEEEEECCChh----hHHHHHHHHHHHhhhcCCCCeEEEEeeCC
Q 038356 10 GALGALLVYDVTKST----TFENVSRWLKDLGDHADSNIVIMMIGNKT 53 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~----s~~~~~~~~~~~~~~~~~~~~~~lvgnK~ 53 (78)
..+.+++.+-.+|.. -.+++...++.++... ++.|+++++-..
T Consensus 57 ~pd~vii~~G~ND~~~~~~~~~~~~~~i~~i~~~~-p~~~iil~~~~~ 103 (177)
T cd01844 57 PADLYIIDCGPNIVGAEAMVRERLGPLVKGLRETH-PDTPILLVSPRY 103 (177)
T ss_pred CCCEEEEEeccCCCccHHHHHHHHHHHHHHHHHHC-cCCCEEEEecCC
Confidence 567788877766643 2345566677776655 678888887543
No 375
>TIGR01753 flav_short flavodoxin, short chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the short chain type. Many of these are involved in sulfite reduction.
Probab=51.42 E-value=41 Score=18.55 Aligned_cols=43 Identities=12% Similarity=0.165 Sum_probs=26.1
Q ss_pred cCCcEEEEEEECCChhhH--HHHHHHHHHHhhhcCCCCeEEEEee
Q 038356 9 RGALGALLVYDVTKSTTF--ENVSRWLKDLGDHADSNIVIMMIGN 51 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~--~~~~~~~~~~~~~~~~~~~~~lvgn 51 (78)
..+|.+++...+-..... ..+..|++.+.....++.++.++|+
T Consensus 44 ~~~d~iilgspty~~g~~p~~~~~~f~~~l~~~~~~gk~~~vfgt 88 (140)
T TIGR01753 44 LSYDAVLLGCSTWGDEDLEQDDFEPFFEELEDIDLGGKKVALFGS 88 (140)
T ss_pred hcCCEEEEEcCCCCCCCCCcchHHHHHHHhhhCCCCCCEEEEEec
Confidence 567888888766443222 3556666666543335667777776
No 376
>cd01339 LDH-like_MDH L-lactate dehydrogenase-like malate dehydrogenase proteins. Members of this subfamily have an LDH-like structure and an MDH enzymatic activity. Some members, like MJ0490 from Methanococcus jannaschii, exhibit both MDH and LDH activities. Tetrameric MDHs, including those from phototrophic bacteria, are more similar to LDHs than to other MDHs. LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenas
Probab=51.23 E-value=45 Score=21.47 Aligned_cols=46 Identities=15% Similarity=0.276 Sum_probs=30.2
Q ss_pred cCCcEEEEEEECCC----------hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTK----------STTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~----------~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
++||.+|+...... .+.+.-++...+.+.+.+ ++.-+++++|=+|.
T Consensus 65 ~dADiVIit~g~p~~~~~~r~e~~~~n~~i~~~i~~~i~~~~-p~~~iIv~sNP~di 120 (300)
T cd01339 65 AGSDVVVITAGIPRKPGMSRDDLLGTNAKIVKEVAENIKKYA-PNAIVIVVTNPLDV 120 (300)
T ss_pred CCCCEEEEecCCCCCcCCCHHHHHHHHHHHHHHHHHHHHHHC-CCeEEEEecCcHHH
Confidence 78999988765433 223444456667777766 55667888887775
No 377
>TIGR01757 Malate-DH_plant malate dehydrogenase, NADP-dependent. This model represents the NADP-dependent malate dehydrogenase found in plants, mosses and green algae and localized to the chloroplast. Malate dehydrogenase converts oxaloacetate into malate, a critical step in the C4 cycle which allows circumvention of the effects of photorespiration. Malate is subsequenctly transported from the chloroplast to the cytoplasm (and then to the bundle sheath cells in C4 plants). The plant and moss enzymes are light regulated via cysteine disulfide bonds. The enzyme from Sorghum has been crystallized.
Probab=50.26 E-value=32 Score=23.50 Aligned_cols=47 Identities=21% Similarity=0.191 Sum_probs=33.0
Q ss_pred cCCcEEEEEEECCChh---hHH-------HHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKST---TFE-------NVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~---s~~-------~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
+++|.+|+.-...+.. ..+ -++.+...+.++.+++..+++|+|=+|.
T Consensus 119 kdaDIVVitAG~prkpg~tR~dll~~N~~I~k~i~~~I~~~a~~~~iviVVsNPvDv 175 (387)
T TIGR01757 119 EDADWALLIGAKPRGPGMERADLLDINGQIFADQGKALNAVASKNCKVLVVGNPCNT 175 (387)
T ss_pred CCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCeEEEEcCCcHHH
Confidence 7899999987765422 222 1356666777766688889999998875
No 378
>KOG0458 consensus Elongation factor 1 alpha [Translation, ribosomal structure and biogenesis]
Probab=50.17 E-value=70 Score=23.34 Aligned_cols=47 Identities=23% Similarity=0.116 Sum_probs=28.4
Q ss_pred CCcEEEEEEECCChhhHHH-------HHHHHHHHhhhcCCCCeEEEEeeCCCCCCCC
Q 038356 10 GALGALLVYDVTKSTTFEN-------VSRWLKDLGDHADSNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~-------~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~ 59 (78)
.||+.+||.|.+. ..|+. +++...- .+.. .-.-++++-||.|+-+..
T Consensus 278 qaD~avLvvd~s~-~~FE~gfd~~gQtrEha~l-lr~L-gi~qlivaiNKmD~V~Ws 331 (603)
T KOG0458|consen 278 QADVAVLVVDAST-GEFESGFDPGGQTREHALL-LRSL-GISQLIVAINKMDLVSWS 331 (603)
T ss_pred ccceEEEEEECCc-chhhhccCCCCchHHHHHH-HHHc-CcceEEEEeecccccCcc
Confidence 6799999999763 44442 2222212 2222 234678899999997643
No 379
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=49.74 E-value=37 Score=17.57 Aligned_cols=39 Identities=13% Similarity=0.268 Sum_probs=23.7
Q ss_pred CcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCC
Q 038356 11 ALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTD 54 (78)
Q Consensus 11 a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~D 54 (78)
.|.+++=++..+.+..+ ..+.++... ++.|++++++..|
T Consensus 44 ~d~iiid~~~~~~~~~~----~~~~i~~~~-~~~~ii~~t~~~~ 82 (112)
T PF00072_consen 44 PDLIIIDLELPDGDGLE----LLEQIRQIN-PSIPIIVVTDEDD 82 (112)
T ss_dssp ESEEEEESSSSSSBHHH----HHHHHHHHT-TTSEEEEEESSTS
T ss_pred ceEEEEEeeeccccccc----ccccccccc-ccccEEEecCCCC
Confidence 35555555555544443 334444444 7899999998776
No 380
>cd01338 MDH_choloroplast_like Chloroplast-like malate dehydrogenases. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subfamily are bacterial MDHs, and plant MDHs localized to the choloroplasts. MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Probab=49.37 E-value=47 Score=21.92 Aligned_cols=47 Identities=23% Similarity=0.256 Sum_probs=32.0
Q ss_pred cCCcEEEEEEECCChhh---HH-------HHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKSTT---FE-------NVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s---~~-------~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
.+||.+|+.....+... .+ -++.....+.++++++..+++++|=+|.
T Consensus 77 ~daDivvitaG~~~k~g~tR~dll~~N~~i~~~i~~~i~~~~~~~~iiivvsNPvD~ 133 (322)
T cd01338 77 KDADWALLVGAKPRGPGMERADLLKANGKIFTAQGKALNDVASRDVKVLVVGNPCNT 133 (322)
T ss_pred CCCCEEEEeCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHhhCCCCeEEEEecCcHHH
Confidence 78999999887754321 21 1355666666666457888999987775
No 381
>PRK13660 hypothetical protein; Provisional
Probab=49.23 E-value=55 Score=20.02 Aligned_cols=38 Identities=21% Similarity=0.300 Sum_probs=23.2
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEE
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMI 49 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lv 49 (78)
.+++++|++||-..+.+-.. -++.+++.. .++.|+..+
T Consensus 128 ~~sd~~i~~YD~e~~Ggt~y---~~~~A~k~~~~~~y~i~~I 166 (182)
T PRK13660 128 EHTDGALLVYDEENEGSPKY---FYEAAKKKQEKEDYPLDLI 166 (182)
T ss_pred HccCeEEEEEcCCCCCChHH---HHHHHHHhhhccCceEEEe
Confidence 68999999999776543322 233333332 246777766
No 382
>KOG3905 consensus Dynein light intermediate chain [Cell motility]
Probab=49.03 E-value=40 Score=23.17 Aligned_cols=26 Identities=19% Similarity=0.429 Sum_probs=19.6
Q ss_pred EEEEEEECCCh-hhHHHHHHHHHHHhh
Q 038356 13 GALLVYDVTKS-TTFENVSRWLKDLGD 38 (78)
Q Consensus 13 ~~ilv~d~~~~-~s~~~~~~~~~~~~~ 38 (78)
.+|++-|++++ .-++++++|..-+.+
T Consensus 130 lviltasms~Pw~~lesLqkWa~Vl~e 156 (473)
T KOG3905|consen 130 LVILTASMSNPWTLLESLQKWASVLRE 156 (473)
T ss_pred EEEEEEecCCcHHHHHHHHHHHHHHHH
Confidence 57789999999 557778888765443
No 383
>COG0370 FeoB Fe2+ transport system protein B [Inorganic ion transport and metabolism]
Probab=48.84 E-value=55 Score=24.12 Aligned_cols=56 Identities=14% Similarity=-0.079 Sum_probs=36.0
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCch----HHHHhccCc
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTSM----SIFQSLSGL 71 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v~----~~~~~~~~~ 71 (78)
..|.++-|.|.++.+.=-. ..-++.+ -+.|++++-|+.|..+.+.+. +..+.++.+
T Consensus 81 ~~D~ivnVvDAtnLeRnLy---ltlQLlE---~g~p~ilaLNm~D~A~~~Gi~ID~~~L~~~LGvP 140 (653)
T COG0370 81 KPDLIVNVVDATNLERNLY---LTLQLLE---LGIPMILALNMIDEAKKRGIRIDIEKLSKLLGVP 140 (653)
T ss_pred CCCEEEEEcccchHHHHHH---HHHHHHH---cCCCeEEEeccHhhHHhcCCcccHHHHHHHhCCC
Confidence 4599999999988763111 1222333 357899999999997655443 555555544
No 384
>PRK13185 chlL protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional
Probab=48.73 E-value=66 Score=20.14 Aligned_cols=45 Identities=18% Similarity=0.135 Sum_probs=28.7
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeE-EEEeeCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVI-MMIGNKTD 54 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~-~lvgnK~D 54 (78)
..||.+|++... +..++..+....+.+.+.. +.++++ -++.|+.+
T Consensus 139 ~~AD~viip~~~-~~~sl~~~~~~~~~i~~~~~~~~l~i~giv~N~~~ 185 (270)
T PRK13185 139 QYADYALIVTAN-DFDSIFAANRIAAAIQAKAKNYKVRLAGVIANRSA 185 (270)
T ss_pred hhCcEEEEEecC-chhhHHHHHHHHHHHHhhhhccCCCceEEEEeccC
Confidence 468888887743 5667777666555554322 345664 47889976
No 385
>PRK05569 flavodoxin; Provisional
Probab=48.54 E-value=48 Score=18.53 Aligned_cols=44 Identities=11% Similarity=0.138 Sum_probs=26.8
Q ss_pred cCCcEEEEEEECCChhhH--HHHHHHHHHHhhhcCCCCeEEEEeeC
Q 038356 9 RGALGALLVYDVTKSTTF--ENVSRWLKDLGDHADSNIVIMMIGNK 52 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~--~~~~~~~~~~~~~~~~~~~~~lvgnK 52 (78)
.++|++++..-+-.-.-+ ..+..+++.+.....++.+++++|+-
T Consensus 47 ~~~d~iilgsPty~~~~~~~~~~~~~~~~l~~~~~~~K~v~~f~t~ 92 (141)
T PRK05569 47 LEADAVAFGSPSMDNNNIEQEEMAPFLDQFKLTPNENKKCILFGSY 92 (141)
T ss_pred hhCCEEEEECCCcCCCcCChHHHHHHHHHhhccCcCCCEEEEEeCC
Confidence 577888887754332211 34556666665443356788888873
No 386
>COG4917 EutP Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=47.59 E-value=17 Score=21.31 Aligned_cols=19 Identities=16% Similarity=0.076 Sum_probs=14.3
Q ss_pred CeEEEEeeCCCCCCCCCch
Q 038356 44 IVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 44 ~~~~lvgnK~Dl~~~~~v~ 62 (78)
.|++=|-+|.||.+...++
T Consensus 91 k~vIgvVTK~DLaed~dI~ 109 (148)
T COG4917 91 KKVIGVVTKADLAEDADIS 109 (148)
T ss_pred cceEEEEecccccchHhHH
Confidence 3477788999998666655
No 387
>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=47.56 E-value=71 Score=20.24 Aligned_cols=46 Identities=9% Similarity=0.031 Sum_probs=23.2
Q ss_pred CCcEEEEEEECCChh-hHHHHHHHHHHHhhhcCCC--CeEEEEeeCCCCC
Q 038356 10 GALGALLVYDVTKST-TFENVSRWLKDLGDHADSN--IVIMMIGNKTDLK 56 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~-s~~~~~~~~~~~~~~~~~~--~~~~lvgnK~Dl~ 56 (78)
+.+++++|..++... +... ...+..+.+..+.+ .++++|-||+|..
T Consensus 114 ~idvIL~V~rlD~~r~~~~d-~~llk~I~e~fG~~i~~~~ivV~T~~d~~ 162 (249)
T cd01853 114 TPDVVLYVDRLDMYRRDYLD-LPLLRAITDSFGPSIWRNAIVVLTHAASS 162 (249)
T ss_pred CCCEEEEEEcCCCCCCCHHH-HHHHHHHHHHhChhhHhCEEEEEeCCccC
Confidence 456777665554322 2221 23333333332222 3578888888874
No 388
>PRK15001 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional
Probab=47.44 E-value=89 Score=21.30 Aligned_cols=43 Identities=16% Similarity=0.152 Sum_probs=29.7
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
.++|.+++-+ +.+...+..++..+.....++.++++.|++.++
T Consensus 105 ~~~d~vl~~~----PK~~~~l~~~l~~l~~~l~~~~~ii~g~~~k~i 147 (378)
T PRK15001 105 QQPGVVLIKV----PKTLALLEQQLRALRKVVTSDTRIIAGAKARDI 147 (378)
T ss_pred CCCCEEEEEe----CCCHHHHHHHHHHHHhhCCCCCEEEEEEecCCC
Confidence 4567666666 455566777777787777788887766666665
No 389
>KOG1496 consensus Malate dehydrogenase [Energy production and conversion]
Probab=47.11 E-value=42 Score=22.03 Aligned_cols=49 Identities=18% Similarity=0.260 Sum_probs=34.6
Q ss_pred chhcCCcEEEEEEECCChhhHHHHH----------HHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVS----------RWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~----------~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
-| ++.+..|+|=...+++..+.-. .--..+.+...+++.+++|||-+.-
T Consensus 77 af-kdv~~ailvGa~PR~eGMERkDll~~NvkIfk~Qg~AL~k~A~~~~KVlVVgNPaNT 135 (332)
T KOG1496|consen 77 AF-KDVDVAILVGAMPRREGMERKDLLSANVKIFKSQGAALEKYAKPNVKVLVVGNPANT 135 (332)
T ss_pred hh-ccCcEEEEeccccCcccchhhhHHhhcceeehhhhHHHHHhcCCCceEEEecCcccc
Confidence 35 7889999999988888776521 1112334455688999999998753
No 390
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=46.62 E-value=65 Score=20.56 Aligned_cols=41 Identities=17% Similarity=0.327 Sum_probs=28.8
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEee
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGN 51 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgn 51 (78)
.|+|++++.--.-...|-+.+..|++.+-+. .+.|+++-=+
T Consensus 95 ~Gad~v~v~~P~~~~~s~~~l~~y~~~ia~~--~~~pi~iYn~ 135 (289)
T PF00701_consen 95 AGADAVLVIPPYYFKPSQEELIDYFRAIADA--TDLPIIIYNN 135 (289)
T ss_dssp TT-SEEEEEESTSSSCCHHHHHHHHHHHHHH--SSSEEEEEEB
T ss_pred cCceEEEEeccccccchhhHHHHHHHHHHhh--cCCCEEEEEC
Confidence 4789998886665566777788888888754 5688876533
No 391
>COG5258 GTPBP1 GTPase [General function prediction only]
Probab=46.53 E-value=17 Score=25.40 Aligned_cols=20 Identities=10% Similarity=0.135 Sum_probs=16.0
Q ss_pred CCeEEEEeeCCCCCCCCCch
Q 038356 43 NIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 43 ~~~~~lvgnK~Dl~~~~~v~ 62 (78)
..|++++-+|+|+.++..+.
T Consensus 255 ~lPviVvvTK~D~~~ddr~~ 274 (527)
T COG5258 255 ELPVIVVVTKIDMVPDDRFQ 274 (527)
T ss_pred cCCEEEEEEecccCcHHHHH
Confidence 68999999999997654433
No 392
>PHA02763 hypothetical protein; Provisional
Probab=46.41 E-value=24 Score=19.15 Aligned_cols=18 Identities=33% Similarity=0.602 Sum_probs=14.7
Q ss_pred hhhHHHHHHHHHHHhhhc
Q 038356 23 STTFENVSRWLKDLGDHA 40 (78)
Q Consensus 23 ~~s~~~~~~~~~~~~~~~ 40 (78)
-+.|+++++|+.+.++..
T Consensus 64 ~SGFe~VEeWl~eArrLh 81 (102)
T PHA02763 64 FSGFENVEEWLNEARRLH 81 (102)
T ss_pred hcchhhHHHHHHHHHHHh
Confidence 356899999999998765
No 393
>TIGR01756 LDH_protist lactate dehydrogenase. This model represents a family of protist lactate dehydrogenases which have aparrently evolved from a recent protist malate dehydrogenase ancestor. Lactate dehydrogenase converts the hydroxyl at C-2 of lactate to a carbonyl in the product, pyruvate. The preference of this enzyme for NAD or NADP has not been determined. A critical residue in malate dehydrogenase, arginine-91 (T. vaginalis numbering) has been mutated to a leucine, eliminating the positive charge which complemeted the carboxylate in malate which is absent in lactate. Several other more subtle changes are proposed to make the active site smaller to accomadate the less bulky lactate molecule.
Probab=46.33 E-value=27 Score=22.98 Aligned_cols=47 Identities=19% Similarity=0.214 Sum_probs=31.4
Q ss_pred cCCcEEEEEEECCCh---hhHH-------HHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKS---TTFE-------NVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~---~s~~-------~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
++||.+|+.-...+. +..+ -++.....+.++++++..+++++|=+|.
T Consensus 59 ~daDiVVitaG~~~k~g~tR~dll~~N~~I~~~i~~~i~~~a~~~~ivivvtNPvDv 115 (313)
T TIGR01756 59 KDIDCAFLVASVPLKPGEVRADLLTKNTPIFKATGEALSEYAKPTVKVLVIGNPVNT 115 (313)
T ss_pred CCCCEEEECCCCCCCcCCCHHHHHHHHHHHHHHHHHHHHhhCCCCeEEEEeCCchHH
Confidence 789999987766432 2222 1345666666676556778899998875
No 394
>cd08166 MPP_Cdc1_like_1 uncharacterized subgroup related to Saccharomyces cerevisiae CDC1, metallophosphatase domain. A functionally uncharacterized subgroup related to the metallophosphatase domain of Saccharomyces cerevisiae Cdc1, S. cerevisiae Ted1 and human MPPE1. Cdc1 is an endoplasmic reticulum-localized transmembrane lipid phosphatase and is a subunit of DNA polymerase delta. TED1 (trafficking of Emp24p/Erv25p-dependent cargo disrupted 1), acts together with Emp24p and Erv25p in cargo exit from the ER. The MPPE1 gene is a candidate susceptibility gene for Bipolar disorder. Proteins in this uncharacterized subgroup belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like R
Probab=45.66 E-value=21 Score=22.04 Aligned_cols=47 Identities=11% Similarity=0.169 Sum_probs=31.1
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhc-----CCCCeEE-EEeeCCCCCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHA-----DSNIVIM-MIGNKTDLKH 57 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-----~~~~~~~-lvgnK~Dl~~ 57 (78)
..|+++++=|+.|........+|.+.+++.. +++.|++ +.|| -|...
T Consensus 42 ~PD~Vi~lGDL~D~G~~~~~~e~~e~l~Rf~~If~~~~~~~~~~VpGN-HDIG~ 94 (195)
T cd08166 42 QPDIVIFLGDLMDEGSIANDDEYYSYVQRFINIFEVPNGTKIIYLPGD-NDIGG 94 (195)
T ss_pred CCCEEEEeccccCCCCCCCHHHHHHHHHHHHHHhcCCCCCcEEEECCC-CCcCC
Confidence 6799999999999876555555666554432 2456665 4455 67654
No 395
>PF06490 FleQ: Flagellar regulatory protein FleQ; InterPro: IPR010518 This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators that are involved in regulation of flagellar motility e.g. FleQ in Pseudomonas aeruginosa. It is clearly related to IPR001789 from INTERPRO, but lacks the conserved aspartate residue that undergoes phosphorylation in the classic two-component system response regulator (IPR001789 from INTERPRO).
Probab=45.12 E-value=53 Score=18.01 Aligned_cols=25 Identities=24% Similarity=0.454 Sum_probs=16.9
Q ss_pred HHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 30 SRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 30 ~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
..+++.+.+.. +.+|++++|.+-..
T Consensus 57 ~~~l~~l~~~~-~~~Pvlllg~~~~~ 81 (109)
T PF06490_consen 57 AELLKELLKWA-PHIPVLLLGEHDSP 81 (109)
T ss_pred HHHHHHHHhhC-CCCCEEEECCCCcc
Confidence 34444454443 78999999988765
No 396
>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=43.87 E-value=17 Score=23.97 Aligned_cols=16 Identities=25% Similarity=0.171 Sum_probs=14.1
Q ss_pred chhcCCcEEEEEEECCC
Q 038356 6 YYNRGALGALLVYDVTK 22 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~ 22 (78)
++ |+||++++|+|++.
T Consensus 96 ~i-r~aD~ii~Vvd~~~ 111 (318)
T cd01899 96 DL-RDADALIHVVDASG 111 (318)
T ss_pred HH-HHCCEEEEEEeCCC
Confidence 37 99999999999974
No 397
>cd00300 LDH_like L-lactate dehydrogenase-like enzymes. Members of this subfamily are tetrameric NAD-dependent 2-hydroxycarboxylate dehydrogenases including LDHs, L-2-hydroxyisocaproate dehydrogenases (L-HicDH), and LDH-like malate dehydrogenases (MDH). Dehydrogenases catalyze the conversion of carbonyl compounds to alcohols or amino acids. LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. Vertebrate LDHs are non-allosteric, but some bacterial LDHs are activated by an allosteric effector such as fructose-1,6-bisphosphate. L-HicDH catalyzes the conversion of a variety of 2-oxo carboxylic acids with medium-sized aliphatic or aromatic side chains. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like subfamily is part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of prot
Probab=43.68 E-value=41 Score=21.83 Aligned_cols=46 Identities=11% Similarity=0.247 Sum_probs=30.6
Q ss_pred cCCcEEEEEEECCChh---hHH-------HHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKST---TFE-------NVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~---s~~-------~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
.+||.+|+.......+ ..+ -+++..+.+.+++ ++.-+++++|=.|+
T Consensus 65 ~~aDiVIitag~p~~~~~~R~~l~~~n~~i~~~~~~~i~~~~-p~~~viv~sNP~d~ 120 (300)
T cd00300 65 ADADIVVITAGAPRKPGETRLDLINRNAPILRSVITNLKKYG-PDAIILVVSNPVDI 120 (300)
T ss_pred CCCCEEEEcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC-CCeEEEEccChHHH
Confidence 7899999988753321 111 1345555666666 77888999998886
No 398
>cd00704 MDH Malate dehydrogenase. Malate dehydrogenase (MDH) is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. MDHs belong to the NAD-dependent, lactate dehydrogenase (LDH)-like, 2-hydroxycarboxylate dehydrogenase family, which also includes the GH4 family of glycoside hydrolases. They are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Probab=43.42 E-value=64 Score=21.32 Aligned_cols=47 Identities=15% Similarity=0.206 Sum_probs=31.7
Q ss_pred cCCcEEEEEEECCChh---hHH-------HHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKST---TFE-------NVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~---s~~-------~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
.++|.+|+.-...+.. ..+ -++.....+.++++++..+++++|=+|.
T Consensus 75 ~~aDiVVitAG~~~~~g~tR~dll~~N~~i~~~i~~~i~~~~~~~~iiivvsNPvD~ 131 (323)
T cd00704 75 KDVDVAILVGAFPRKPGMERADLLRKNAKIFKEQGEALNKVAKPTVKVLVVGNPANT 131 (323)
T ss_pred CCCCEEEEeCCCCCCcCCcHHHHHHHhHHHHHHHHHHHHHhCCCCeEEEEeCCcHHH
Confidence 7899999987765432 111 1355666677774467778889988875
No 399
>cd01611 GABARAP Ubiquitin domain of GABA-receptor-associated protein. GABARAP (GABA-receptor-associated protein) belongs ot a large family of proteins that mediate intracellular membrane trafficking and/or fusion. GABARAP binds not only to GABA, type A but also to tubulin, gephrin, and ULK1. Orthologues of GABARAP include Gate-16 (golgi-associated ATPase enhancer), LC3 (microtubule-associated protein light chain 3), and ATG8 (autophagy protein 8). ATG8 is a ubiquitin-like protein that is conjugated to the membrane phospholipid, phosphatidylethanolamine as part of a ubiquitin-like conjugation system essential for autophagosome-formation.
Probab=43.32 E-value=48 Score=18.54 Aligned_cols=33 Identities=18% Similarity=0.225 Sum_probs=21.7
Q ss_pred hhhHHHHHHHHHHHhhhcCCCCeEEEE-eeCCCC
Q 038356 23 STTFENVSRWLKDLGDHADSNIVIMMI-GNKTDL 55 (78)
Q Consensus 23 ~~s~~~~~~~~~~~~~~~~~~~~~~lv-gnK~Dl 55 (78)
+.||+.-..-...+++..+..+|+++- ..+.++
T Consensus 4 ~~s~e~R~~e~~~ir~kyp~~iPVIvE~~~~~~~ 37 (112)
T cd01611 4 RHPFEKRKAEVERIRAKYPDRIPVIVERYPKSDL 37 (112)
T ss_pred ccCHHHHHHHHHHHHHHCCCceEEEEEEcCCCCc
Confidence 457777766666677666678887765 344554
No 400
>COG4108 PrfC Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]
Probab=42.23 E-value=72 Score=22.73 Aligned_cols=43 Identities=23% Similarity=0.174 Sum_probs=26.9
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeEEEEeeCCCCCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~~lvgnK~Dl~~ 57 (78)
-+|++++|.|...- ++.--..+-+.| -.++||+-.-||.|-..
T Consensus 104 AvDsAvMVIDaAKG-----iE~qT~KLfeVcrlR~iPI~TFiNKlDR~~ 147 (528)
T COG4108 104 AVDSAVMVIDAAKG-----IEPQTLKLFEVCRLRDIPIFTFINKLDREG 147 (528)
T ss_pred hhheeeEEEecccC-----ccHHHHHHHHHHhhcCCceEEEeecccccc
Confidence 56888999886531 111111222333 26899999999999654
No 401
>cd07393 MPP_DR1119 Deinococcus radiodurans DR1119 and related proteins, metallophosphatase domain. DR1119 is an uncharacterized Deinococcus radiodurans protein with a metallophosphatase domain. The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordinat
Probab=42.00 E-value=68 Score=19.82 Aligned_cols=40 Identities=15% Similarity=0.097 Sum_probs=22.6
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEee
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGN 51 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgn 51 (78)
++|.+++.=|+++....+....-+..++.. +...+++.||
T Consensus 41 ~~D~viiaGDl~~~~~~~~~~~~l~~l~~l--~~~v~~V~GN 80 (232)
T cd07393 41 PEDIVLIPGDISWAMKLEEAKLDLAWIDAL--PGTKVLLKGN 80 (232)
T ss_pred CCCEEEEcCCCccCCChHHHHHHHHHHHhC--CCCeEEEeCC
Confidence 689999999998754443332222223322 2224567777
No 402
>PF00056 Ldh_1_N: lactate/malate dehydrogenase, NAD binding domain Prosite entry for lactate dehydrogenase Prosite entry for malate dehydrogenase; InterPro: IPR001236 L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis []. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate []. The enzyme participates in the citric acid cycle. This entry represents the N-terminal, and is thought to be a Rossmann NAD-binding fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1IB6_B 3HHP_C 1IE3_A 2PWZ_A 1EMD_A 2CMD_A 1EZ4_D 9LDT_B 9LDB_B 2D4A_C ....
Probab=41.75 E-value=51 Score=18.85 Aligned_cols=46 Identities=17% Similarity=0.289 Sum_probs=29.1
Q ss_pred cCCcEEEEEEECCChh------hHH----HHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKST------TFE----NVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~------s~~----~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
++||.+++.-.....+ -++ -++++.+.+.+.+ ++..++++.|=.|+
T Consensus 68 ~~aDivvitag~~~~~g~sR~~ll~~N~~i~~~~~~~i~~~~-p~~~vivvtNPvd~ 123 (141)
T PF00056_consen 68 KDADIVVITAGVPRKPGMSRLDLLEANAKIVKEIAKKIAKYA-PDAIVIVVTNPVDV 123 (141)
T ss_dssp TTESEEEETTSTSSSTTSSHHHHHHHHHHHHHHHHHHHHHHS-TTSEEEE-SSSHHH
T ss_pred ccccEEEEeccccccccccHHHHHHHhHhHHHHHHHHHHHhC-CccEEEEeCCcHHH
Confidence 7888888876554321 111 1356667777776 77788888887773
No 403
>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
Probab=41.40 E-value=86 Score=19.42 Aligned_cols=37 Identities=5% Similarity=0.166 Sum_probs=27.2
Q ss_pred EEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEee
Q 038356 14 ALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGN 51 (78)
Q Consensus 14 ~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgn 51 (78)
-++..+.....+...++++.+.+++.. .++++++-|.
T Consensus 141 ~~V~lS~~~~~~~~~~~~~i~~L~~~~-~~~~i~vGG~ 177 (213)
T cd02069 141 DIIGLSGLLVPSLDEMVEVAEEMNRRG-IKIPLLIGGA 177 (213)
T ss_pred CEEEEccchhccHHHHHHHHHHHHhcC-CCCeEEEECh
Confidence 344556777788888999999998764 5777766664
No 404
>PF08438 MMR_HSR1_C: GTPase of unknown function C-terminal; InterPro: IPR013646 This domain is found at the C terminus of IPR002917 from INTERPRO in archaeal and eukaryotic GTP-binding proteins. ; PDB: 1WXQ_A.
Probab=41.24 E-value=7.5 Score=21.81 Aligned_cols=19 Identities=21% Similarity=0.146 Sum_probs=9.6
Q ss_pred EeeCCCCC-CCCCchHHHHh
Q 038356 49 IGNKTDLK-HLPTSMSIFQS 67 (78)
Q Consensus 49 vgnK~Dl~-~~~~v~~~~~~ 67 (78)
++||+|+. ....+.++.++
T Consensus 1 AaNK~D~~~a~~ni~kl~~~ 20 (109)
T PF08438_consen 1 AANKADLPAADENIEKLKEK 20 (109)
T ss_dssp EEE-GGG-S-HHHHHHHHHH
T ss_pred CCccccccccHhHHHHHHHh
Confidence 58999984 33445554443
No 405
>cd05292 LDH_2 A subgroup of L-lactate dehydrogenases. L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed predominantly of bacterial LDHs and a few fungal LDHs. Bacterial LDHs may be non-allosteric or may be activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Probab=40.68 E-value=57 Score=21.22 Aligned_cols=46 Identities=13% Similarity=0.250 Sum_probs=30.2
Q ss_pred cCCcEEEEEEECCCh---h-------hHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKS---T-------TFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~---~-------s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
++||.+++....... + +..-++.|.+.+.+.. ++..++++.|=.|+
T Consensus 66 ~~aDiViita~~~~~~~~~r~dl~~~n~~i~~~~~~~l~~~~-~~giiiv~tNP~d~ 121 (308)
T cd05292 66 KGADVVVITAGANQKPGETRLDLLKRNVAIFKEIIPQILKYA-PDAILLVVTNPVDV 121 (308)
T ss_pred CCCCEEEEccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC-CCeEEEEecCcHHH
Confidence 788999988766322 1 2223466777777766 66677777776664
No 406
>PTZ00380 microtubule-associated protein (MAP); Provisional
Probab=40.63 E-value=57 Score=18.68 Aligned_cols=27 Identities=11% Similarity=0.073 Sum_probs=19.0
Q ss_pred hhhHHHHHHHHHHHhhhcCCCCeEEEE
Q 038356 23 STTFENVSRWLKDLGDHADSNIVIMMI 49 (78)
Q Consensus 23 ~~s~~~~~~~~~~~~~~~~~~~~~~lv 49 (78)
+.||+.-+.-...++...+..+|+++-
T Consensus 7 ~~s~e~R~~e~~~Ir~kyPdrIPVIvE 33 (121)
T PTZ00380 7 SNPVEARRAECARLQAKYPGHVAVVVE 33 (121)
T ss_pred cCCHHHHHHHHHHHHHHCCCccEEEEe
Confidence 456777666666777766778998764
No 407
>TIGR01759 MalateDH-SF1 malate dehydrogenase. This model represents a family of malate dehydrogenases in bacteria and eukaryotes which utilize either NAD or NADP depending on the species and context. MDH interconverts malate and oxaloacetate and is a part of the citric acid cycle as well as the C4 cycle in certain photosynthetic organisms.
Probab=40.42 E-value=83 Score=20.84 Aligned_cols=47 Identities=19% Similarity=0.265 Sum_probs=32.2
Q ss_pred cCCcEEEEEEECCChh---hHH-------HHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKST---TFE-------NVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~---s~~-------~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
++||.+|+.-...+.. ..+ -++.+.+.+.++++++..+++++|=+|.
T Consensus 78 ~daDvVVitAG~~~k~g~tR~dll~~Na~i~~~i~~~i~~~~~~~~iiivvsNPvDv 134 (323)
T TIGR01759 78 KDVDAALLVGAFPRKPGMERADLLSKNGKIFKEQGKALNKVAKKDVKVLVVGNPANT 134 (323)
T ss_pred CCCCEEEEeCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHhhCCCCeEEEEeCCcHHH
Confidence 7899999988775432 222 1356666777776448888899987775
No 408
>PF12327 FtsZ_C: FtsZ family, C-terminal domain; InterPro: IPR024757 The FtsZ family of proteins are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin []. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea []. This entry represents a domain of FtsZ. In most FtsZ proteins is found in the C terminus, except in some alphaproteobacteria proteins where there is an extension C-terminal domain TIGR03483 from TIGRFAMs.; PDB: 2RHO_B 2RHJ_A 2VXY_A 2RHL_B 2RHH_A 2VAM_A 1W5F_B 2R75_1 2R6R_1 1RQ7_A ....
Probab=40.39 E-value=61 Score=17.38 Aligned_cols=47 Identities=19% Similarity=0.294 Sum_probs=32.3
Q ss_pred chhcCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCC
Q 038356 6 YYNRGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTD 54 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~D 54 (78)
-+ ++|.++++-......-++..+..-.+.+++..+++.- ++.|...|
T Consensus 32 ~i-~~A~~vLvni~~~~d~~l~ev~~~~~~i~~~~~~~a~-ii~G~~id 78 (95)
T PF12327_consen 32 DI-KGAKGVLVNITGGPDLSLSEVNEAMEIIREKADPDAN-IIWGASID 78 (95)
T ss_dssp -G-GG-SEEEEEEEE-TTS-HHHHHHHHHHHHHHSSTTSE-EEEEEEE-
T ss_pred Ch-HHhceEEEEEEcCCCCCHHHHHHHHHHHHHHhhcCce-EEEEEEEC
Confidence 35 7899999888776667899998888889888765544 45676666
No 409
>COG0420 SbcD DNA repair exonuclease [DNA replication, recombination, and repair]
Probab=40.32 E-value=69 Score=21.40 Aligned_cols=47 Identities=17% Similarity=0.194 Sum_probs=29.3
Q ss_pred CCcEEEEEEECCC--hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 10 GALGALLVYDVTK--STTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 10 ~a~~~ilv~d~~~--~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
++|++|+.=|+=+ ..|...+....+.+++.+..++|++++.--=|-.
T Consensus 40 ~vD~vliAGDlFd~~~Ps~~a~~~~~~~l~~l~~~~Ipv~~I~GNHD~~ 88 (390)
T COG0420 40 KVDFVLIAGDLFDTNNPSPRALKLFLEALRRLKDAGIPVVVIAGNHDSP 88 (390)
T ss_pred cCCEEEEccccccCCCCCHHHHHHHHHHHHHhccCCCcEEEecCCCCch
Confidence 5688888544433 3456666666677776666778887554445543
No 410
>TIGR01771 L-LDH-NAD L-lactate dehydrogenase. This model represents the NAD-dependent L-lactate dehydrogenases from bacteria and eukaryotes. This enzyme function as as the final step in anaerobic glycolysis. Although lactate dehydrogenases have in some cases been mistaken for malate dehydrogenases due to the similarity of these two substrates and the apparent ease with which evolution can toggle these activities, critical residues have been identified which can discriminate between the two activities. At the time of the creation of this model no hits above the trusted cutoff contained critical residues typical of malate dehydrogenases.
Probab=40.27 E-value=50 Score=21.54 Aligned_cols=46 Identities=7% Similarity=0.085 Sum_probs=30.8
Q ss_pred cCCcEEEEEEECCCh------hhHH----HHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKS------TTFE----NVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~------~s~~----~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
++||.+|+.-..... +-+. -++++.+.+.+++ ++..+++++|=.|.
T Consensus 63 ~daDivVitag~~rk~g~~R~dll~~N~~i~~~~~~~i~~~~-p~~~vivvsNP~d~ 118 (299)
T TIGR01771 63 KDADLVVITAGAPQKPGETRLELVGRNVRIMKSIVPEVVKSG-FDGIFLVATNPVDI 118 (299)
T ss_pred CCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC-CCeEEEEeCCHHHH
Confidence 789999998776332 2222 1345666666664 77889999998875
No 411
>PLN00135 malate dehydrogenase
Probab=40.09 E-value=91 Score=20.56 Aligned_cols=47 Identities=15% Similarity=0.217 Sum_probs=31.4
Q ss_pred cCCcEEEEEEECCChh---hHHH-------HHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKST---TFEN-------VSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~---s~~~-------~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
.+||.+|+.-...... ..+. ++.....+.++..++..+++++|=+|.
T Consensus 57 ~daDiVVitAG~~~k~g~sR~dll~~N~~I~~~i~~~i~~~~~p~aivivvsNPvDv 113 (309)
T PLN00135 57 KGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAPDCKVLVVANPANT 113 (309)
T ss_pred CCCCEEEEeCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHhcCCCeEEEEeCCcHHH
Confidence 7899999988774322 2221 245555666654478889999998876
No 412
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=39.93 E-value=35 Score=17.88 Aligned_cols=15 Identities=7% Similarity=0.186 Sum_probs=12.1
Q ss_pred CCCeEEEEeeCCCCC
Q 038356 42 SNIVIMMIGNKTDLK 56 (78)
Q Consensus 42 ~~~~~~lvgnK~Dl~ 56 (78)
.++|++.+++|.+|.
T Consensus 52 ~~Vp~~~~~s~~eLG 66 (82)
T PRK13602 52 KGVPVSKVDSMKKLG 66 (82)
T ss_pred cCCCEEEECCHHHHH
Confidence 568999999887774
No 413
>PF00319 SRF-TF: SRF-type transcription factor (DNA-binding and dimerisation domain); InterPro: IPR002100 Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box [], that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. In SRF, the MADS box has been shown to be involved in DNA-binding and dimerisation []. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel beta-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see IPR002487 from INTERPRO ; GO: 0003677 DNA binding, 0046983 protein dimerization activity; PDB: 1MNM_B 1N6J_A 1TQE_S 3MU6_D 3P57_I 1EGW_A 1C7U_B 3KOV_A 1HBX_A 1K6O_C ....
Probab=39.67 E-value=34 Score=16.41 Aligned_cols=14 Identities=29% Similarity=0.299 Sum_probs=10.6
Q ss_pred cCCcEEEEEEECCC
Q 038356 9 RGALGALLVYDVTK 22 (78)
Q Consensus 9 ~~a~~~ilv~d~~~ 22 (78)
-+++++++||+.++
T Consensus 31 C~~~v~~iv~~~~g 44 (51)
T PF00319_consen 31 CGVDVALIVFSPDG 44 (51)
T ss_dssp HT-EEEEEEEETTS
T ss_pred cCCeEEEEEECCCC
Confidence 48999999998664
No 414
>COG1217 TypA Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]
Probab=39.42 E-value=67 Score=23.14 Aligned_cols=48 Identities=19% Similarity=0.138 Sum_probs=27.5
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPT 60 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~ 60 (78)
.-.|+++++.|..+-. .-..+--.+... ..+.+-++|-||+|-.+.|-
T Consensus 90 ~MVDgvlLlVDA~EGp-MPQTrFVlkKAl---~~gL~PIVVvNKiDrp~Arp 137 (603)
T COG1217 90 SMVDGVLLLVDASEGP-MPQTRFVLKKAL---ALGLKPIVVINKIDRPDARP 137 (603)
T ss_pred hhcceEEEEEEcccCC-CCchhhhHHHHH---HcCCCcEEEEeCCCCCCCCH
Confidence 4568999999875411 111111112222 23455678889999877653
No 415
>KOG1143 consensus Predicted translation elongation factor [Translation, ribosomal structure and biogenesis]
Probab=39.39 E-value=31 Score=24.16 Aligned_cols=21 Identities=24% Similarity=0.178 Sum_probs=16.8
Q ss_pred CCCeEEEEeeCCCCCCCCCch
Q 038356 42 SNIVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 42 ~~~~~~lvgnK~Dl~~~~~v~ 62 (78)
-++|.+++-+|.||.....++
T Consensus 302 L~iPfFvlvtK~Dl~~~~~~~ 322 (591)
T KOG1143|consen 302 LNIPFFVLVTKMDLVDRQGLK 322 (591)
T ss_pred hCCCeEEEEEeeccccchhHH
Confidence 469999999999998764444
No 416
>KOG0460 consensus Mitochondrial translation elongation factor Tu [Translation, ribosomal structure and biogenesis]
Probab=39.31 E-value=97 Score=21.48 Aligned_cols=49 Identities=24% Similarity=0.178 Sum_probs=28.1
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCCCCc
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHLPTS 61 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~~~v 61 (78)
.-|+.|+|..-+|-. ....++.+-..++.. --.+++.-||.|+-++.+.
T Consensus 140 qMDGaILVVaatDG~-MPQTrEHlLLArQVG--V~~ivvfiNKvD~V~d~e~ 188 (449)
T KOG0460|consen 140 QMDGAILVVAATDGP-MPQTREHLLLARQVG--VKHIVVFINKVDLVDDPEM 188 (449)
T ss_pred ccCceEEEEEcCCCC-CcchHHHHHHHHHcC--CceEEEEEecccccCCHHH
Confidence 348999999888732 112222222223332 1346788899999855443
No 417
>PLN00112 malate dehydrogenase (NADP); Provisional
Probab=38.81 E-value=58 Score=22.75 Aligned_cols=47 Identities=21% Similarity=0.258 Sum_probs=32.2
Q ss_pred cCCcEEEEEEECCChh---hHHH-------HHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKST---TFEN-------VSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~---s~~~-------~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
++||.+|+.-...... ..+- +++..+.+.++..++..+++|+|=+|.
T Consensus 175 kdaDiVVitAG~prkpG~tR~dLl~~N~~I~k~i~~~I~~~a~p~~ivIVVsNPvDv 231 (444)
T PLN00112 175 QDAEWALLIGAKPRGPGMERADLLDINGQIFAEQGKALNEVASRNVKVIVVGNPCNT 231 (444)
T ss_pred CcCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCeEEEEcCCcHHH
Confidence 7899999988764422 2221 345666666644478889999998885
No 418
>TIGR00991 3a0901s02IAP34 GTP-binding protein (Chloroplast Envelope Protein Translocase).
Probab=38.78 E-value=1.2e+02 Score=20.27 Aligned_cols=46 Identities=7% Similarity=0.040 Sum_probs=26.3
Q ss_pred CCcEEEEEEECCChhhHHHH-HHHHHHHhhhcCC--CCeEEEEeeCCCCC
Q 038356 10 GALGALLVYDVTKSTTFENV-SRWLKDLGDHADS--NIVIMMIGNKTDLK 56 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~~~--~~~~~lvgnK~Dl~ 56 (78)
+.|++++|..++.. .+... ...++.+++..+. -.+.+++-++.|..
T Consensus 118 g~DvVLyV~rLD~~-R~~~~DkqlLk~Iqe~FG~~iw~~~IVVfTh~d~~ 166 (313)
T TIGR00991 118 TIDVLLYVDRLDAY-RVDTLDGQVIRAITDSFGKDIWRKSLVVLTHAQFS 166 (313)
T ss_pred CCCEEEEEeccCcc-cCCHHHHHHHHHHHHHhhhhhhccEEEEEECCccC
Confidence 68899999655432 12222 3344444444322 23578888999865
No 419
>cd05291 HicDH_like L-2-hydroxyisocapronate dehydrogenases and some bacterial L-lactate dehydrogenases. L-2-hydroxyisocapronate dehydrogenase (HicDH) catalyzes the conversion of a variety of 2-oxo carboxylic acids with medium-sized aliphatic or aromatic side chains. This subfamily is composed of HicDHs and some bacterial L-lactate dehydrogenases (LDH). LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. Bacterial LDHs can be non-allosteric or may be activated by an allosteric effector such as fructose-1,6-bisphosphate. Members of this subfamily with known structures such as the HicDH of Lactobacillus confusus, the non-allosteric LDH of Lactobacillus pentosus, and the allosteric LDH of Bacillus stearothermophilus, show that they exist as homotetramers. The HicDH-like subfamily is part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine
Probab=38.74 E-value=78 Score=20.51 Aligned_cols=46 Identities=9% Similarity=0.135 Sum_probs=30.9
Q ss_pred cCCcEEEEEEECCCh------hhHH----HHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKS------TTFE----NVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~------~s~~----~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
.++|.+|+.-..... +-+. -++.+.+.+.+++ ++..+++++|=.|.
T Consensus 67 ~~aDIVIitag~~~~~g~~R~dll~~N~~i~~~~~~~i~~~~-~~~~vivvsNP~d~ 122 (306)
T cd05291 67 KDADIVVITAGAPQKPGETRLDLLEKNAKIMKSIVPKIKASG-FDGIFLVASNPVDV 122 (306)
T ss_pred CCCCEEEEccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC-CCeEEEEecChHHH
Confidence 688999988776422 2122 1356666667766 67788999998875
No 420
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=38.62 E-value=66 Score=17.28 Aligned_cols=35 Identities=17% Similarity=0.299 Sum_probs=21.1
Q ss_pred EEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEee
Q 038356 16 LVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGN 51 (78)
Q Consensus 16 lv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgn 51 (78)
+.++.....++.......+.+++.. +++++++-|.
T Consensus 55 V~iS~~~~~~~~~~~~l~~~~k~~~-p~~~iv~GG~ 89 (121)
T PF02310_consen 55 VGISVSMTPNLPEAKRLARAIKERN-PNIPIVVGGP 89 (121)
T ss_dssp EEEEESSSTHHHHHHHHHHHHHTTC-TTSEEEEEES
T ss_pred EEEEccCcCcHHHHHHHHHHHHhcC-CCCEEEEECC
Confidence 3445545556666666666666554 6677666554
No 421
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=38.20 E-value=86 Score=20.13 Aligned_cols=39 Identities=10% Similarity=0.225 Sum_probs=25.0
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEE
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMI 49 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lv 49 (78)
|+|+++++--.--+.+=+.+..+++.+-+.. ++.|+++-
T Consensus 96 Gad~v~~~~P~y~~~~~~~i~~~~~~v~~a~-~~lpi~iY 134 (288)
T cd00954 96 GYDAISAITPFYYKFSFEEIKDYYREIIAAA-ASLPMIIY 134 (288)
T ss_pred CCCEEEEeCCCCCCCCHHHHHHHHHHHHHhc-CCCCEEEE
Confidence 7888887654443444566777777775543 36887775
No 422
>COG4328 Predicted nuclease (RNAse H fold) [General function prediction only]
Probab=37.80 E-value=57 Score=21.02 Aligned_cols=31 Identities=23% Similarity=0.364 Sum_probs=25.0
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhc
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHA 40 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~ 40 (78)
.+|+=..++|.+.++|+..+-.|++......
T Consensus 22 ~~dg~~~i~~~~rr~s~aei~a~id~~v~ea 52 (266)
T COG4328 22 LADGGLLIGDLARRDSAAEIFAWIDYVVGEA 52 (266)
T ss_pred EcCCCceEeechhhhhHHHHHHHHHHhhccc
Confidence 3456677899999999999999998876543
No 423
>PRK11148 cyclic 3',5'-adenosine monophosphate phosphodiesterase; Provisional
Probab=37.60 E-value=66 Score=20.36 Aligned_cols=40 Identities=10% Similarity=0.042 Sum_probs=25.4
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeE-EEEeeC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVI-MMIGNK 52 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~-~lvgnK 52 (78)
.+|.+|+.=|+++..+.+....+.+.+.+. +.|+ ++.||-
T Consensus 55 ~~D~vvitGDl~~~~~~~~~~~~~~~l~~l---~~Pv~~v~GNH 95 (275)
T PRK11148 55 EFDLIVATGDLAQDHSSEAYQHFAEGIAPL---RKPCVWLPGNH 95 (275)
T ss_pred CCCEEEECCCCCCCCCHHHHHHHHHHHhhc---CCcEEEeCCCC
Confidence 478899999999876655555554444433 2455 566774
No 424
>TIGR03566 FMN_reduc_MsuE FMN reductase, MsuE subfamily. Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the NADH-dependent enzyme MsuE from Pseudomonas aeruginosa, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. The NADP-dependent enzyme from E. coli is outside the scope of this model.
Probab=37.59 E-value=70 Score=18.76 Aligned_cols=40 Identities=10% Similarity=0.040 Sum_probs=18.9
Q ss_pred cCCcEEEEEEECCC---hhhHHHHHHHHHHHhhhcCCCCeEEEEee
Q 038356 9 RGALGALLVYDVTK---STTFENVSRWLKDLGDHADSNIVIMMIGN 51 (78)
Q Consensus 9 ~~a~~~ilv~d~~~---~~s~~~~~~~~~~~~~~~~~~~~~~lvgn 51 (78)
+.||++|++.-.=+ +..+ +.|++.+....-.+.|++++++
T Consensus 67 ~~AD~iIi~tP~Y~~s~~~~L---Kn~lD~~~~~~l~~K~~~~v~~ 109 (174)
T TIGR03566 67 ESADLLVVGSPVYRGSYTGLF---KHLFDLVDPNALIGKPVLLAAT 109 (174)
T ss_pred HHCCEEEEECCcCcCcCcHHH---HHHHHhcCHhHhCCCEEEEEEe
Confidence 56788877543322 2233 3344433211113456666665
No 425
>cd00945 Aldolase_Class_I Class I aldolases. The class I aldolases use an active-site lysine which stablilzes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin.
Probab=37.02 E-value=69 Score=18.60 Aligned_cols=42 Identities=19% Similarity=0.212 Sum_probs=23.3
Q ss_pred CCcEEEEEEECCChhh--HHHHHHHHHHHhhhcCCCCeEEEEee
Q 038356 10 GALGALLVYDVTKSTT--FENVSRWLKDLGDHADSNIVIMMIGN 51 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s--~~~~~~~~~~~~~~~~~~~~~~lvgn 51 (78)
|+|++.+.-..--..+ .+.+.+++..+.+..+.+.|+++--+
T Consensus 78 Gad~i~v~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~pv~iy~~ 121 (201)
T cd00945 78 GADEIDVVINIGSLKEGDWEEVLEEIAAVVEAADGGLPLKVILE 121 (201)
T ss_pred CCCEEEEeccHHHHhCCCHHHHHHHHHHHHHHhcCCceEEEEEE
Confidence 7788877643322222 45666666666655334577665443
No 426
>PRK06242 flavodoxin; Provisional
Probab=36.90 E-value=80 Score=17.75 Aligned_cols=42 Identities=5% Similarity=-0.090 Sum_probs=25.8
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNK 52 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK 52 (78)
.++|++++...+-.-.-...++.|++.+... .+.+++++++-
T Consensus 42 ~~~d~ii~g~pvy~~~~~~~~~~fl~~~~~~--~~k~~~~f~t~ 83 (150)
T PRK06242 42 SEYDLIGFGSGIYFGKFHKSLLKLIEKLPPV--SGKKAFIFSTS 83 (150)
T ss_pred hHCCEEEEeCchhcCCcCHHHHHHHHhhhhh--cCCeEEEEECC
Confidence 5778888876543333344556666655432 45788888774
No 427
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=36.86 E-value=81 Score=20.42 Aligned_cols=46 Identities=13% Similarity=0.262 Sum_probs=30.5
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEE----eeCCCCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMI----GNKTDLK 56 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lv----gnK~Dl~ 56 (78)
|+|+++++--.--+.+-+.+..++..+-+.. ++.|+++- .++.|+.
T Consensus 95 Gad~v~v~pP~y~~~~~~~l~~~f~~ia~a~-~~lpv~iYn~P~~tg~~l~ 144 (294)
T TIGR02313 95 GADAAMVIVPYYNKPNQEALYDHFAEVADAV-PDFPIIIYNIPGRAAQEIA 144 (294)
T ss_pred CCCEEEEcCccCCCCCHHHHHHHHHHHHHhc-cCCCEEEEeCchhcCcCCC
Confidence 7888888765444555677777777776653 36888876 3455553
No 428
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=36.68 E-value=52 Score=17.81 Aligned_cols=39 Identities=18% Similarity=0.209 Sum_probs=21.6
Q ss_pred CcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEE-eeCCCCC
Q 038356 11 ALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMI-GNKTDLK 56 (78)
Q Consensus 11 a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lv-gnK~Dl~ 56 (78)
+..+++.=|. ++++-+.+..+.++ .++|++.. ++|.+|.
T Consensus 33 aklViiA~D~-~~~~~~~i~~~c~~------~~Ip~~~~~~tk~eLG 72 (99)
T PRK01018 33 AKLVIVASNC-PKDIKEDIEYYAKL------SGIPVYEYEGSSVELG 72 (99)
T ss_pred ceEEEEeCCC-CHHHHHHHHHHHHH------cCCCEEEECCCHHHHH
Confidence 3444444453 34444444444322 46898775 8998874
No 429
>PF04684 BAF1_ABF1: BAF1 / ABF1 chromatin reorganising factor; InterPro: IPR006774 ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture []. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 Saccharomyces cerevisiae (P14164 from SWISSPROT)) []. The N-terminal two thirds of the protein are necessary for DNA binding, and the N terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilise the protein structure [].; GO: 0003677 DNA binding, 0006338 chromatin remodeling, 0005634 nucleus
Probab=36.42 E-value=19 Score=25.34 Aligned_cols=26 Identities=19% Similarity=0.475 Sum_probs=19.6
Q ss_pred hhhHHHHHHHHHHHhhhc-CCCCeEEE
Q 038356 23 STTFENVSRWLKDLGDHA-DSNIVIMM 48 (78)
Q Consensus 23 ~~s~~~~~~~~~~~~~~~-~~~~~~~l 48 (78)
..+|..+..|+.-+...- ...+||+|
T Consensus 25 ~~~f~tl~~wy~v~ndyefq~rcpiil 51 (496)
T PF04684_consen 25 ARKFPTLEAWYNVINDYEFQSRCPIIL 51 (496)
T ss_pred ccCCCcHHHHHHHHhhhhhhhcCceee
Confidence 557999999999887654 46677766
No 430
>cd05293 LDH_1 A subgroup of L-lactate dehydrogenases. L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed of eukaryotic LDHs. Vertebrate LDHs are non-allosteric. This is in contrast to some bacterial LDHs that are activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Probab=35.93 E-value=39 Score=22.21 Aligned_cols=46 Identities=9% Similarity=0.214 Sum_probs=28.7
Q ss_pred cCCcEEEEEEECCCh------hhHHH----HHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKS------TTFEN----VSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~------~s~~~----~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
++||.+|+.-..... +-+.. ++...+.+.+++ ++.-+++++|=.|.
T Consensus 70 ~~adivvitaG~~~k~g~~R~dll~~N~~i~~~~~~~i~~~~-p~~~vivvsNP~d~ 125 (312)
T cd05293 70 ANSKVVIVTAGARQNEGESRLDLVQRNVDIFKGIIPKLVKYS-PNAILLVVSNPVDI 125 (312)
T ss_pred CCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC-CCcEEEEccChHHH
Confidence 788988886554322 11111 244455566665 67778999998875
No 431
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=35.72 E-value=1e+02 Score=19.92 Aligned_cols=39 Identities=8% Similarity=0.107 Sum_probs=25.0
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEE
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMI 49 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lv 49 (78)
|+|++++.--.--+.+-+.+..++..+-+.. ++.|+++-
T Consensus 96 Gad~v~v~~P~y~~~~~~~i~~yf~~v~~~~-~~lpv~lY 134 (290)
T TIGR00683 96 GYDCLSAVTPFYYKFSFPEIKHYYDTIIAET-GGLNMIVY 134 (290)
T ss_pred CCCEEEEeCCcCCCCCHHHHHHHHHHHHhhC-CCCCEEEE
Confidence 7788887654444445567777777775443 45787766
No 432
>PRK07308 flavodoxin; Validated
Probab=35.19 E-value=88 Score=17.69 Aligned_cols=43 Identities=16% Similarity=0.193 Sum_probs=24.5
Q ss_pred cCCcEEEEEEECCChhhH-HHHHHHHHHHhhhcCCCCeEEEEee
Q 038356 9 RGALGALLVYDVTKSTTF-ENVSRWLKDLGDHADSNIVIMMIGN 51 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~-~~~~~~~~~~~~~~~~~~~~~lvgn 51 (78)
...+++++.........+ ..+..|++.++....++.++.++|.
T Consensus 47 ~~~d~vi~g~~t~g~G~~p~~~~~fl~~l~~~~l~~k~~~vfG~ 90 (146)
T PRK07308 47 EDADIAIVATYTYGDGELPDEIVDFYEDLADLDLSGKIYGVVGS 90 (146)
T ss_pred ccCCEEEEEeCccCCCCCCHHHHHHHHHHhcCCCCCCEEEEEee
Confidence 456777776554432222 3456666666554335567777665
No 433
>PF08309 LVIVD: LVIVD repeat; InterPro: IPR013211 This repeat is found in bacterial and archaeal cell surface proteins, many of which are hypothetical. The secondary structure corresponding to this repeat is predicted to comprise 4 beta-strands, which may associate to form a beta-propeller. The repeat copy number varies from 2-14. This repeat is sometimes found with the PKD domain IPR000601 from INTERPRO.
Probab=34.78 E-value=30 Score=15.84 Aligned_cols=13 Identities=15% Similarity=0.544 Sum_probs=8.9
Q ss_pred EEEEEEECCChhh
Q 038356 13 GALLVYDVTKSTT 25 (78)
Q Consensus 13 ~~ilv~d~~~~~s 25 (78)
.=+.++|++|+.+
T Consensus 21 ~Gl~IvDISnPs~ 33 (42)
T PF08309_consen 21 NGLVIVDISNPSN 33 (42)
T ss_pred CCEEEEECCCCCC
Confidence 3466789988753
No 434
>KOG0085 consensus G protein subunit Galphaq/Galphay, small G protein superfamily [Signal transduction mechanisms]
Probab=34.74 E-value=85 Score=20.59 Aligned_cols=18 Identities=28% Similarity=0.314 Sum_probs=14.4
Q ss_pred CCCeEEEEeeCCCCCCCC
Q 038356 42 SNIVIMMIGNKTDLKHLP 59 (78)
Q Consensus 42 ~~~~~~lvgnK~Dl~~~~ 59 (78)
.+.++++.-||.||-++.
T Consensus 265 ~nssVIlFLNKkDlLEek 282 (359)
T KOG0085|consen 265 QNSSVILFLNKKDLLEEK 282 (359)
T ss_pred cCCceEEEechhhhhhhh
Confidence 467899999999986543
No 435
>cd00650 LDH_MDH_like NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family. Members of this family include ubiquitous enzymes like L-lactate dehydrogenases (LDH), L-2-hydroxyisocaproate dehydrogenases, and some malate dehydrogenases (MDH). LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH/MDH-like proteins are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains
Probab=34.59 E-value=69 Score=20.18 Aligned_cols=46 Identities=13% Similarity=0.200 Sum_probs=29.7
Q ss_pred cCCcEEEEEEECCChh----------hHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKST----------TFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~----------s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
++||.+++.......+ ...-+++..+.+.+.+ ++..+++++|=.|.
T Consensus 69 ~~aDiVv~t~~~~~~~g~~r~~~~~~n~~i~~~i~~~i~~~~-p~a~~i~~tNP~d~ 124 (263)
T cd00650 69 KDADVVIITAGVGRKPGMGRLDLLKRNVPIVKEIGDNIEKYS-PDAWIIVVSNPVDI 124 (263)
T ss_pred CCCCEEEECCCCCCCcCCCHHHHHHHHHHHHHHHHHHHHHHC-CCeEEEEecCcHHH
Confidence 7888888866542221 1222356666777776 77778888887775
No 436
>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [, ].; PDB: 1BAP_A 7ABP_A 6ABP_A 1ABF_A 5ABP_A 2WRZ_B 9ABP_A 1APB_A 1ABE_A 8ABP_A ....
Probab=34.50 E-value=1.1e+02 Score=19.31 Aligned_cols=38 Identities=26% Similarity=0.305 Sum_probs=21.6
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
+++||+|+. ..... .+.+.. +.+ .++|+|+++...+..
T Consensus 55 ~~vDGiI~~-s~~~~--~~~l~~----~~~---~~iPvV~~~~~~~~~ 92 (279)
T PF00532_consen 55 RRVDGIILA-SSEND--DEELRR----LIK---SGIPVVLIDRYIDNP 92 (279)
T ss_dssp TTSSEEEEE-SSSCT--CHHHHH----HHH---TTSEEEEESS-SCTT
T ss_pred cCCCEEEEe-cccCC--hHHHHH----HHH---cCCCEEEEEeccCCc
Confidence 578898887 33222 222222 111 368999999987654
No 437
>COG0329 DapA Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=34.44 E-value=92 Score=20.34 Aligned_cols=38 Identities=18% Similarity=0.323 Sum_probs=27.5
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEE
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMI 49 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lv 49 (78)
|+|+++++--.=.+.+.+.+.+|+..+-+.. +.|+++-
T Consensus 99 Gad~il~v~PyY~k~~~~gl~~hf~~ia~a~--~lPvilY 136 (299)
T COG0329 99 GADGILVVPPYYNKPSQEGLYAHFKAIAEAV--DLPVILY 136 (299)
T ss_pred CCCEEEEeCCCCcCCChHHHHHHHHHHHHhc--CCCEEEE
Confidence 7888888876666777778877777776654 6776554
No 438
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=33.72 E-value=70 Score=19.56 Aligned_cols=29 Identities=17% Similarity=0.501 Sum_probs=21.8
Q ss_pred ChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCC
Q 038356 22 KSTTFENVSRWLKDLGDHADSNIVIMMIGNKT 53 (78)
Q Consensus 22 ~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~ 53 (78)
+++--.+++.|+.+++.. .+.++++-|+.
T Consensus 44 ~~~~tpe~~~W~~e~k~~---gi~v~vvSNn~ 72 (175)
T COG2179 44 NPDATPELRAWLAELKEA---GIKVVVVSNNK 72 (175)
T ss_pred CCCCCHHHHHHHHHHHhc---CCEEEEEeCCC
Confidence 355567789999999864 47888888854
No 439
>KOG0448 consensus Mitofusin 1 GTPase, involved in mitochondrila biogenesis [Posttranslational modification, protein turnover, chaperones]
Probab=33.55 E-value=1.6e+02 Score=22.11 Aligned_cols=45 Identities=18% Similarity=0.258 Sum_probs=28.3
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
.+||.+|+|-...+.-+..+ ++++..+.+ ...-++++-||-|...
T Consensus 231 ldaDVfVlV~NaEntlt~se-k~Ff~~vs~---~KpniFIlnnkwDasa 275 (749)
T KOG0448|consen 231 LDADVFVLVVNAENTLTLSE-KQFFHKVSE---EKPNIFILNNKWDASA 275 (749)
T ss_pred hcCCeEEEEecCccHhHHHH-HHHHHHhhc---cCCcEEEEechhhhhc
Confidence 68999999876544443332 444444432 2455788889999853
No 440
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=32.57 E-value=1e+02 Score=17.61 Aligned_cols=39 Identities=13% Similarity=0.144 Sum_probs=24.9
Q ss_pred EEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCC
Q 038356 15 LLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKT 53 (78)
Q Consensus 15 ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~ 53 (78)
+++.+..+..+.+.++...+.+++...+++++++=|+..
T Consensus 56 ii~iSsl~~~~~~~~~~~~~~L~~~g~~~i~vivGG~~~ 94 (132)
T TIGR00640 56 VVGVSSLAGGHLTLVPALRKELDKLGRPDILVVVGGVIP 94 (132)
T ss_pred EEEEcCchhhhHHHHHHHHHHHHhcCCCCCEEEEeCCCC
Confidence 444456666777778888888877653455655545553
No 441
>TIGR01758 MDH_euk_cyt malate dehydrogenase, NAD-dependent. This model represents the NAD-dependent cytosolic malate dehydrogenase from eukaryotes. The enzyme from pig has been studied by X-ray crystallography
Probab=32.39 E-value=1.2e+02 Score=20.11 Aligned_cols=47 Identities=15% Similarity=0.187 Sum_probs=31.4
Q ss_pred cCCcEEEEEEECCChh--hHHH--------HHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKST--TFEN--------VSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~--s~~~--------~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
.++|.+|+.-.....+ +... ++.+.+.+.++++++..+++++|=+|.
T Consensus 74 ~~aDiVVitAG~~~~~~~tr~~ll~~N~~i~k~i~~~i~~~~~~~~iiivvsNPvDv 130 (324)
T TIGR01758 74 TDVDVAILVGAFPRKEGMERRDLLSKNVKIFKEQGRALDKLAKKDCKVLVVGNPANT 130 (324)
T ss_pred CCCCEEEEcCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHhhCCCCeEEEEeCCcHHH
Confidence 6889999887765432 1111 356666677664477888889987775
No 442
>PTZ00222 60S ribosomal protein L7a; Provisional
Probab=32.34 E-value=52 Score=21.41 Aligned_cols=41 Identities=15% Similarity=0.238 Sum_probs=26.3
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
.+..+|+.=|++..+- ..|+..+-+. .++|.+++++|.+|.
T Consensus 148 KAkLVIIA~DVsPie~----vk~LpaLCrk--~~VPY~iVktKaeLG 188 (263)
T PTZ00222 148 QARMVVIANNVDPVEL----VLWMPNLCRA--NKIPYAIVKDMARLG 188 (263)
T ss_pred CceEEEEeCCCCHHHH----HHHHHHHHHh--cCCCEEEECCHHHHH
Confidence 4566777767654432 3344444333 579999999999883
No 443
>PRK06223 malate dehydrogenase; Reviewed
Probab=32.30 E-value=94 Score=19.98 Aligned_cols=46 Identities=11% Similarity=0.198 Sum_probs=27.1
Q ss_pred cCCcEEEEEEECCC----------hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTK----------STTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~----------~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
.+||.+|+...... .+...-++...+.+.+.+ ++.-++++.|=+|+
T Consensus 69 ~~aDiVii~~~~p~~~~~~r~~~~~~n~~i~~~i~~~i~~~~-~~~~viv~tNP~d~ 124 (307)
T PRK06223 69 AGSDVVVITAGVPRKPGMSRDDLLGINAKIMKDVAEGIKKYA-PDAIVIVVTNPVDA 124 (307)
T ss_pred CCCCEEEECCCCCCCcCCCHHHHHHHHHHHHHHHHHHHHHHC-CCeEEEEecCcHHH
Confidence 68888887654332 122233355555666665 55567777776664
No 444
>KOG2455 consensus Delta-1-pyrroline-5-carboxylate dehydrogenase [Amino acid transport and metabolism]
Probab=31.52 E-value=66 Score=22.86 Aligned_cols=37 Identities=16% Similarity=0.267 Sum_probs=27.2
Q ss_pred ECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCCC
Q 038356 19 DVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 19 d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~~ 58 (78)
.+-+..+|..+++|++..+.. ++ .-+|+|-|+|-...
T Consensus 387 avIh~~sF~rl~k~le~ak~~--~~-leiL~GGk~DdS~G 423 (561)
T KOG2455|consen 387 AVIHDKSFARLKKVLEHAKKD--PE-LEILAGGKCDDSTG 423 (561)
T ss_pred hhccHHHHHHHHHHHHhhccC--cc-ceeeecCcccCCCC
Confidence 344688999999998877643 33 44789999997644
No 445
>cd01840 SGNH_hydrolase_yrhL_like yrhL-like subfamily of SGNH-hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. Most members of this sub-family appear to co-occur with N-terminal acyltransferase domains. Might be involved in lipid metabolism.
Probab=31.49 E-value=1e+02 Score=17.41 Aligned_cols=39 Identities=8% Similarity=0.100 Sum_probs=27.7
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNK 52 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK 52 (78)
..+.+++.+-.++...-++++..++.+ +++.++++++..
T Consensus 50 ~~d~vvi~lGtNd~~~~~nl~~ii~~~----~~~~~ivlv~~~ 88 (150)
T cd01840 50 LRKTVVIGLGTNGPFTKDQLDELLDAL----GPDRQVYLVNPH 88 (150)
T ss_pred CCCeEEEEecCCCCCCHHHHHHHHHHc----CCCCEEEEEECC
Confidence 468888888888876666666655544 245778888876
No 446
>PRK05442 malate dehydrogenase; Provisional
Probab=31.31 E-value=1.6e+02 Score=19.55 Aligned_cols=47 Identities=21% Similarity=0.244 Sum_probs=31.6
Q ss_pred cCCcEEEEEEECCChh---hHHH-------HHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKST---TFEN-------VSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~---s~~~-------~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
++||.+|+.....+.. ..+- +++..+.+.++.+++..+++++|=.|.
T Consensus 79 ~daDiVVitaG~~~k~g~tR~dll~~Na~i~~~i~~~i~~~~~~~~iiivvsNPvDv 135 (326)
T PRK05442 79 KDADVALLVGARPRGPGMERKDLLEANGAIFTAQGKALNEVAARDVKVLVVGNPANT 135 (326)
T ss_pred CCCCEEEEeCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHhCCCCeEEEEeCCchHH
Confidence 7899999988764422 2221 245556666666568888999998875
No 447
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=31.24 E-value=1.1e+02 Score=19.93 Aligned_cols=39 Identities=15% Similarity=0.314 Sum_probs=24.7
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEE
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMI 49 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lv 49 (78)
|+|+++++--.--+.+-+.+-.+++.+-+.. +++|+++-
T Consensus 103 Gad~vlv~~P~y~~~~~~~l~~yf~~va~a~-~~lPv~iY 141 (309)
T cd00952 103 GADGTMLGRPMWLPLDVDTAVQFYRDVAEAV-PEMAIAIY 141 (309)
T ss_pred CCCEEEECCCcCCCCCHHHHHHHHHHHHHhC-CCCcEEEE
Confidence 7888888744322334467767777776543 35888776
No 448
>PTZ00082 L-lactate dehydrogenase; Provisional
Probab=31.20 E-value=1e+02 Score=20.37 Aligned_cols=46 Identities=13% Similarity=0.212 Sum_probs=29.6
Q ss_pred cCCcEEEEEEECC-----------Chh----hHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVT-----------KST----TFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~-----------~~~----s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
++||.+|+..... +.+ ...-+++..+.+.+.+ ++..++++.|=+|+
T Consensus 73 ~~aDiVI~tag~~~~~~~~~~~~~r~~~l~~n~~i~~~i~~~i~~~~-p~a~~iv~sNP~di 133 (321)
T PTZ00082 73 AGSDVVIVTAGLTKRPGKSDKEWNRDDLLPLNAKIMDEVAEGIKKYC-PNAFVIVITNPLDV 133 (321)
T ss_pred CCCCEEEECCCCCCCCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHHC-CCeEEEEecCcHHH
Confidence 7888888865432 211 2333456667777776 66678888887775
No 449
>TIGR01573 cas2 CRISPR-associated endoribonuclease Cas2. This model describes most members of the family of Cas2, one of the first four protein families found to mark prokaryotic genomes that contain multiple CRISPR elements. It is an endoribonuclease, capable of cleaving single-stranded RNA. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. The cas genes are found near the repeats. A distinct branch of the Cas2 family shows a very low level of sequence identity and is modeled by TIGR01873 instead.
Probab=31.14 E-value=91 Score=16.64 Aligned_cols=10 Identities=40% Similarity=0.853 Sum_probs=7.9
Q ss_pred EEEEEECCCh
Q 038356 14 ALLVYDVTKS 23 (78)
Q Consensus 14 ~ilv~d~~~~ 23 (78)
++++||+++.
T Consensus 3 ~lV~YDI~~~ 12 (95)
T TIGR01573 3 VLVVYDIPTD 12 (95)
T ss_pred EEEEEECCCC
Confidence 6788888876
No 450
>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=30.96 E-value=30 Score=22.98 Aligned_cols=19 Identities=26% Similarity=0.239 Sum_probs=13.7
Q ss_pred EEEeeCCCCCCCCCchHHH
Q 038356 47 MMIGNKTDLKHLPTSMSIF 65 (78)
Q Consensus 47 ~lvgnK~Dl~~~~~v~~~~ 65 (78)
+|+.||+|+.++.++....
T Consensus 177 ~IvlnK~Dl~~~~~l~~~~ 195 (341)
T TIGR02475 177 LVILNKADLLDAAGLARVR 195 (341)
T ss_pred EEEEeccccCCHHHHHHHH
Confidence 7889999997765554433
No 451
>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=30.93 E-value=68 Score=17.92 Aligned_cols=27 Identities=22% Similarity=0.504 Sum_probs=17.3
Q ss_pred hHHHHHHHHHHHhhhcCCCCeEEEEeeCC
Q 038356 25 TFENVSRWLKDLGDHADSNIVIMMIGNKT 53 (78)
Q Consensus 25 s~~~~~~~~~~~~~~~~~~~~~~lvgnK~ 53 (78)
+.+.++.|++..-. ++++.++++|+-.
T Consensus 3 t~e~l~~f~~~~y~--p~n~~l~i~Gd~~ 29 (184)
T PF05193_consen 3 TLEDLRAFYKKFYR--PSNMTLVIVGDID 29 (184)
T ss_dssp -HHHHHHHHHHHSS--GGGEEEEEEESSG
T ss_pred CHHHHHHHHHHhcC--ccceEEEEEcCcc
Confidence 35566677666543 3578888998754
No 452
>TIGR01303 IMP_DH_rel_1 IMP dehydrogenase family protein. This model represents a family of proteins, often annotated as a putative IMP dehydrogenase, related to IMP dehydrogenase and GMP reductase and restricted to the high GC Gram-positive bacteria. All species in which a member is found so far (Corynebacterium glutamicum, Mycobacterium tuberculosis, Streptomyces coelicolor, etc.) also have IMP dehydrogenase as described by TIGRFAMs entry TIGR01302.
Probab=30.71 E-value=1.5e+02 Score=20.94 Aligned_cols=41 Identities=20% Similarity=0.192 Sum_probs=26.0
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
+++. ++.|.++..+ +.+.+..+.++... +++|+ ++||=.+.
T Consensus 237 GVd~--i~~D~a~g~~-~~~~~~i~~i~~~~-~~~~v-i~g~~~t~ 277 (475)
T TIGR01303 237 GVDV--LVIDTAHGHQ-VKMISAIKAVRALD-LGVPI-VAGNVVSA 277 (475)
T ss_pred CCCE--EEEeCCCCCc-HHHHHHHHHHHHHC-CCCeE-EEeccCCH
Confidence 4444 6779999777 45555566666554 56774 44876654
No 453
>PF11176 DUF2962: Protein of unknown function (DUF2962); InterPro: IPR021346 This eukaryotic family of proteins has no known function. ; PDB: 2KKM_A.
Probab=30.59 E-value=47 Score=19.67 Aligned_cols=18 Identities=22% Similarity=0.451 Sum_probs=12.4
Q ss_pred EEEEECCChhhHHHHHHH
Q 038356 15 LLVYDVTKSTTFENVSRW 32 (78)
Q Consensus 15 ilv~d~~~~~s~~~~~~~ 32 (78)
+.|-|++|.++++.++.|
T Consensus 121 ~~vPDLtd~~nv~~Lr~W 138 (155)
T PF11176_consen 121 FEVPDLTDEKNVKLLREW 138 (155)
T ss_dssp EEEE-S--HHHHHHHHT-
T ss_pred eeCCCCCCHHHHHHHHhc
Confidence 567899999999999999
No 454
>KOG0467 consensus Translation elongation factor 2/ribosome biogenesis protein RIA1 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=30.37 E-value=1.1e+02 Score=23.44 Aligned_cols=38 Identities=32% Similarity=0.547 Sum_probs=23.9
Q ss_pred cCCcEEEEEEECCC---hhhHHHH-HHHHHHHhhhcCCCCeEEEEeeCCC
Q 038356 9 RGALGALLVYDVTK---STTFENV-SRWLKDLGDHADSNIVIMMIGNKTD 54 (78)
Q Consensus 9 ~~a~~~ilv~d~~~---~~s~~~~-~~~~~~~~~~~~~~~~~~lvgnK~D 54 (78)
|=+|++++..|+.. ..+..-+ +.|. .+...++|-||+|
T Consensus 94 ~l~d~alvlvdvvegv~~qt~~vlrq~~~--------~~~~~~lvinkid 135 (887)
T KOG0467|consen 94 RLSDGALVLVDVVEGVCSQTYAVLRQAWI--------EGLKPILVINKID 135 (887)
T ss_pred hhcCCcEEEEeeccccchhHHHHHHHHHH--------ccCceEEEEehhh
Confidence 45677777777654 3344444 3353 3455688999999
No 455
>PRK00066 ldh L-lactate dehydrogenase; Reviewed
Probab=30.33 E-value=64 Score=21.18 Aligned_cols=46 Identities=9% Similarity=0.133 Sum_probs=28.7
Q ss_pred cCCcEEEEEEECCCh------hhHHH----HHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKS------TTFEN----VSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~------~s~~~----~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
++||.+|+.-..... +-+.. +++..+.+.+++ ++..+++++|=.|.
T Consensus 72 ~~adivIitag~~~k~g~~R~dll~~N~~i~~~i~~~i~~~~-~~~~vivvsNP~d~ 127 (315)
T PRK00066 72 KDADLVVITAGAPQKPGETRLDLVEKNLKIFKSIVGEVMASG-FDGIFLVASNPVDI 127 (315)
T ss_pred CCCCEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC-CCeEEEEccCcHHH
Confidence 789999998776332 22221 233344445454 67788899998875
No 456
>TIGR00381 cdhD CO dehydrogenase/acetyl-CoA synthase, delta subunit. This is the small subunit of a heterodimer which catalyzes the reaction CO + H2O + Acceptor = CO2 + Reduced acceptor and is involved in the synthesis of acetyl-CoA from CO2 and H2.
Probab=30.16 E-value=84 Score=21.70 Aligned_cols=43 Identities=21% Similarity=0.091 Sum_probs=28.4
Q ss_pred CCcEEEEEEECCChhhHHHH-HHHHHHHhhhc-CCCCeEEEEeeC
Q 038356 10 GALGALLVYDVTKSTTFENV-SRWLKDLGDHA-DSNIVIMMIGNK 52 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~-~~~~~~~~~~~-~~~~~~~lvgnK 52 (78)
++|.+.+.+..+|++..+.. ....+-++... ..++|++|.|+.
T Consensus 153 ~aD~Ialr~~S~DP~~~d~~~~e~a~~vk~V~~av~vPLIL~gsg 197 (389)
T TIGR00381 153 GADMVTIHLISTDPKLDDKSPSEAAKVLEDVLQAVDVPIVIGGSG 197 (389)
T ss_pred CCCEEEEEecCCCccccccCHHHHHHHHHHHHHhCCCCEEEeCCC
Confidence 88999999999999843333 22333333332 267999999773
No 457
>KOG1752 consensus Glutaredoxin and related proteins [Posttranslational modification, protein turnover, chaperones]
Probab=30.05 E-value=97 Score=17.10 Aligned_cols=35 Identities=20% Similarity=0.309 Sum_probs=20.8
Q ss_pred EEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCC
Q 038356 17 VYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKT 53 (78)
Q Consensus 17 v~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~ 53 (78)
|+.++..+--.++++++.++.. ...+|.+.+|.|.
T Consensus 43 vvELD~~~~g~eiq~~l~~~tg--~~tvP~vFI~Gk~ 77 (104)
T KOG1752|consen 43 VVELDEDEDGSEIQKALKKLTG--QRTVPNVFIGGKF 77 (104)
T ss_pred EEEccCCCCcHHHHHHHHHhcC--CCCCCEEEECCEE
Confidence 3444444444477777665532 3578888887775
No 458
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=29.97 E-value=75 Score=16.74 Aligned_cols=15 Identities=27% Similarity=0.392 Sum_probs=12.3
Q ss_pred CCCeEEEEeeCCCCC
Q 038356 42 SNIVIMMIGNKTDLK 56 (78)
Q Consensus 42 ~~~~~~lvgnK~Dl~ 56 (78)
.++|++.+++|.+|.
T Consensus 49 ~~Vpv~~~~t~~eLG 63 (82)
T PRK13601 49 KSIKIVYIDTMKELG 63 (82)
T ss_pred CCCCEEEeCCHHHHH
Confidence 578999999988874
No 459
>PHA02518 ParA-like protein; Provisional
Probab=29.60 E-value=1.3e+02 Score=17.79 Aligned_cols=45 Identities=11% Similarity=0.023 Sum_probs=24.6
Q ss_pred cCCcEEEEEEECCChhhHH---HHHHHHHHHhhhcCCCCe-EEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKSTTFE---NVSRWLKDLGDHADSNIV-IMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~---~~~~~~~~~~~~~~~~~~-~~lvgnK~Dl 55 (78)
..||.+|++...+ +.++. .+..++++.+... +..| ..++.|+.+-
T Consensus 97 ~~aD~viip~~ps-~~~~~~~~~~~~~~~~~~~~~-~~~~~~~iv~n~~~~ 145 (211)
T PHA02518 97 RIADMVLIPVQPS-PFDIWAAPDLVELIKARQEVT-DGLPKFAFIISRAIK 145 (211)
T ss_pred HHCCEEEEEeCCC-hhhHHHHHHHHHHHHHHHhhC-CCCceEEEEEeccCC
Confidence 5678888877554 33444 4444444443332 3344 4567787654
No 460
>TIGR01763 MalateDH_bact malate dehydrogenase, NAD-dependent. The annotation of Botryococcus braunii as lactate dehydrogenase appears top be in error. This was initially annotated as MDH by Swiss-Prot and then changed. The rationale for either of these annotations is not traceable.
Probab=29.49 E-value=1.7e+02 Score=19.15 Aligned_cols=46 Identities=13% Similarity=0.166 Sum_probs=31.0
Q ss_pred cCCcEEEEEEECCChh----------hHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 9 RGALGALLVYDVTKST----------TFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~----------s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
.++|.+|+........ ...-++...+.+.++. ++..++++.|=.|.
T Consensus 68 ~~aDiVIitag~p~~~~~sR~~l~~~N~~iv~~i~~~I~~~~-p~~~iIv~tNP~di 123 (305)
T TIGR01763 68 ANSDIVVITAGLPRKPGMSREDLLSMNAGIVREVTGRIMEHS-PNPIIVVVSNPLDA 123 (305)
T ss_pred CCCCEEEEcCCCCCCcCCCHHHHHHHHHHHHHHHHHHHHHHC-CCeEEEEecCcHHH
Confidence 7889999887653321 2233456666676665 67888999997775
No 461
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=29.29 E-value=1.3e+02 Score=18.14 Aligned_cols=12 Identities=8% Similarity=0.357 Sum_probs=8.8
Q ss_pred CCCeEEEEeeCC
Q 038356 42 SNIVIMMIGNKT 53 (78)
Q Consensus 42 ~~~~~~lvgnK~ 53 (78)
.++|++++++..
T Consensus 77 ~~ipvV~~~~~~ 88 (265)
T cd06299 77 RGIPVVFVDREI 88 (265)
T ss_pred CCCCEEEEeccc
Confidence 468888888754
No 462
>PRK12399 tagatose 1,6-diphosphate aldolase; Reviewed
Probab=29.19 E-value=1.4e+02 Score=20.08 Aligned_cols=40 Identities=23% Similarity=0.450 Sum_probs=28.1
Q ss_pred CCcE--EEEEEECCChhhHHHH-HHHHHHHhhhc-CCCCeEEEE
Q 038356 10 GALG--ALLVYDVTKSTTFENV-SRWLKDLGDHA-DSNIVIMMI 49 (78)
Q Consensus 10 ~a~~--~ilv~d~~~~~s~~~~-~~~~~~~~~~~-~~~~~~~lv 49 (78)
|+|+ +++-||.++.+-.+.. +.|++.+.+.| ..++|.++=
T Consensus 118 GadavK~Llyy~pD~~~~in~~k~a~vervg~eC~a~dipf~lE 161 (324)
T PRK12399 118 GADAVKFLLYYDVDEPDEINEQKKAYIERIGSECVAEDIPFFLE 161 (324)
T ss_pred CCCeEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCeEEE
Confidence 4444 4667888888877777 56888886666 467887763
No 463
>TIGR01007 eps_fam capsular exopolysaccharide family. This model describes the capsular exopolysaccharide proteins in bacteria. The exopolysaccharide gene cluster consists of several genes which encode a number of proteins which regulate the exoploysaccharide biosynthesis(EPS). Atleast 13 genes espA to espM in streptococcus species seem to direct the EPS proteins and all of which share high homology. Functional roles were characterized by gene disruption experiments which resulted in exopolysaccharide-deficient phenotypes.
Probab=29.10 E-value=1.3e+02 Score=17.87 Aligned_cols=46 Identities=20% Similarity=0.231 Sum_probs=29.0
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
+.+|++++|.+.. ..+...+..-.+.+++.. -..+-+|-||.|...
T Consensus 149 ~~~D~vilV~~~~-~~~~~~~~~~~~~l~~~~--~~~~gvVlN~~~~~~ 194 (204)
T TIGR01007 149 RACDASILVTDAG-EIKKRDVQKAKEQLEQTG--SNFLGVVLNKVDISV 194 (204)
T ss_pred HhCCeEEEEEECC-CCCHHHHHHHHHHHHhCC--CCEEEEEEeCccccc
Confidence 5689999998763 444555555555554432 234568889999754
No 464
>PHA03050 glutaredoxin; Provisional
Probab=29.10 E-value=89 Score=17.13 Aligned_cols=37 Identities=5% Similarity=0.257 Sum_probs=19.8
Q ss_pred EEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCC
Q 038356 15 LLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKT 53 (78)
Q Consensus 15 ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~ 53 (78)
.-++++...+.-..++.++.+... ...+|.++++.+.
T Consensus 43 ~~~i~i~~~~~~~~~~~~l~~~tG--~~tVP~IfI~g~~ 79 (108)
T PHA03050 43 YEIVDIKEFKPENELRDYFEQITG--GRTVPRIFFGKTS 79 (108)
T ss_pred cEEEECCCCCCCHHHHHHHHHHcC--CCCcCEEEECCEE
Confidence 335677653332333444333321 2578999888765
No 465
>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=28.93 E-value=73 Score=14.88 Aligned_cols=11 Identities=18% Similarity=0.323 Sum_probs=8.5
Q ss_pred CCCeEEEEeeC
Q 038356 42 SNIVIMMIGNK 52 (78)
Q Consensus 42 ~~~~~~lvgnK 52 (78)
..+|.++++++
T Consensus 48 ~~~P~v~i~g~ 58 (60)
T PF00462_consen 48 RTVPQVFIDGK 58 (60)
T ss_dssp SSSSEEEETTE
T ss_pred CccCEEEECCE
Confidence 67898888764
No 466
>KOG2733 consensus Uncharacterized membrane protein [Function unknown]
Probab=28.91 E-value=63 Score=22.36 Aligned_cols=18 Identities=11% Similarity=0.385 Sum_probs=15.4
Q ss_pred cEEEEEEECCChhhHHHH
Q 038356 12 LGALLVYDVTKSTTFENV 29 (78)
Q Consensus 12 ~~~ilv~d~~~~~s~~~~ 29 (78)
..+|++.|.+|++|++++
T Consensus 63 ~~~i~i~D~~n~~Sl~em 80 (423)
T KOG2733|consen 63 SSVILIADSANEASLDEM 80 (423)
T ss_pred cceEEEecCCCHHHHHHH
Confidence 445999999999999876
No 467
>COG1343 CRISPR-associated protein Cas2 [Defense mechanisms]
Probab=28.46 E-value=1.1e+02 Score=16.57 Aligned_cols=11 Identities=36% Similarity=0.797 Sum_probs=9.2
Q ss_pred EEEEEECCChh
Q 038356 14 ALLVYDVTKST 24 (78)
Q Consensus 14 ~ilv~d~~~~~ 24 (78)
+++|||+++..
T Consensus 3 vlvvYDI~~d~ 13 (89)
T COG1343 3 VLVVYDISDDG 13 (89)
T ss_pred EEEEEecCCcH
Confidence 68899999875
No 468
>TIGR03371 cellulose_yhjQ cellulose synthase operon protein YhjQ. Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (PubMed:16930487), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.
Probab=28.13 E-value=1.5e+02 Score=18.07 Aligned_cols=47 Identities=15% Similarity=0.068 Sum_probs=28.3
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLK 56 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~ 56 (78)
..||.++++... +..++..+..-...+.+......+.-++-|+.|..
T Consensus 135 ~~ad~vii~~~~-~~~s~~~~~~~~~~l~~~~~~~~~~~iv~n~~~~~ 181 (246)
T TIGR03371 135 AAADLVLVVVNA-DAACYATLHQQALALFAGSGPRIGPHFLINQFDPA 181 (246)
T ss_pred HhCCeEEEEeCC-CHHHHHHHHHHHHHHhhcccccccceEEeeccCcc
Confidence 578888888765 45566666532222222222345567889999864
No 469
>PRK04161 tagatose 1,6-diphosphate aldolase; Reviewed
Probab=27.78 E-value=1.6e+02 Score=19.94 Aligned_cols=40 Identities=23% Similarity=0.443 Sum_probs=27.9
Q ss_pred CCcE--EEEEEECCChhhHHHH-HHHHHHHhhhc-CCCCeEEEE
Q 038356 10 GALG--ALLVYDVTKSTTFENV-SRWLKDLGDHA-DSNIVIMMI 49 (78)
Q Consensus 10 ~a~~--~ilv~d~~~~~s~~~~-~~~~~~~~~~~-~~~~~~~lv 49 (78)
|+|+ +++-||.++.+-.+.. +.|++.+.+.| ..++|.++=
T Consensus 120 GadavK~Llyy~pD~~~ein~~k~a~vervg~eC~a~dipf~lE 163 (329)
T PRK04161 120 GADAVKFLLYYDVDGDEEINDQKQAYIERIGSECTAEDIPFFLE 163 (329)
T ss_pred CCCeEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCeEEE
Confidence 4444 4667788877777776 56888886666 467888764
No 470
>PF13788 DUF4180: Domain of unknown function (DUF4180)
Probab=27.72 E-value=99 Score=17.47 Aligned_cols=46 Identities=17% Similarity=0.294 Sum_probs=28.7
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHHHHHH-hhhcCCCCeEEEEee
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRWLKDL-GDHADSNIVIMMIGN 51 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~~~~~-~~~~~~~~~~~lvgn 51 (78)
.|+ .+++.+++--+.-+++=|+--.....++ |+...-++.+.+||-
T Consensus 31 ~~~-~~~~~i~l~~~~l~~dFF~L~TglAGeiLQKf~NY~iklAivGD 77 (113)
T PF13788_consen 31 AYE-HGADRIILPKEALSEDFFDLRTGLAGEILQKFVNYRIKLAIVGD 77 (113)
T ss_pred HHH-cCCCEEEEEhHHCCHHHHHhhcchHHHHHHHHHhhceeEEEEEc
Confidence 467 8888888766655555555434444455 333345688888864
No 471
>COG0012 Predicted GTPase, probable translation factor [Translation, ribosomal structure and biogenesis]
Probab=27.21 E-value=66 Score=22.02 Aligned_cols=17 Identities=6% Similarity=0.114 Sum_probs=13.9
Q ss_pred CCCeEEEEeeCCCCCCC
Q 038356 42 SNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 42 ~~~~~~lvgnK~Dl~~~ 58 (78)
...|+++++||.|....
T Consensus 205 t~KP~lyvaN~~e~~~~ 221 (372)
T COG0012 205 TAKPMLYVANVSEDDLA 221 (372)
T ss_pred hcCCeEEEEECCccccc
Confidence 45799999999998653
No 472
>PF14606 Lipase_GDSL_3: GDSL-like Lipase/Acylhydrolase family; PDB: 3SKV_B.
Probab=27.12 E-value=1.5e+02 Score=18.02 Aligned_cols=40 Identities=13% Similarity=0.214 Sum_probs=22.3
Q ss_pred CCcEEEEEEECC-ChhhHHHH-HHHHHHHhhhcCCCCeEEEEe
Q 038356 10 GALGALLVYDVT-KSTTFENV-SRWLKDLGDHADSNIVIMMIG 50 (78)
Q Consensus 10 ~a~~~ilv~d~~-~~~s~~~~-~~~~~~~~~~~~~~~~~~lvg 50 (78)
.++.+++-+-++ +.+.|..- ...++.+++.. |+.||+++-
T Consensus 59 ~a~~~~ld~~~N~~~~~~~~~~~~fv~~iR~~h-P~tPIllv~ 100 (178)
T PF14606_consen 59 DADLIVLDCGPNMSPEEFRERLDGFVKTIREAH-PDTPILLVS 100 (178)
T ss_dssp --SEEEEEESHHCCTTTHHHHHHHHHHHHHTT--SSS-EEEEE
T ss_pred CCCEEEEEeecCCCHHHHHHHHHHHHHHHHHhC-CCCCEEEEe
Confidence 345555555332 34455544 67777777655 889998885
No 473
>KOG1036 consensus Mitotic spindle checkpoint protein BUB3, WD repeat superfamily [Cell cycle control, cell division, chromosome partitioning]
Probab=26.83 E-value=50 Score=22.09 Aligned_cols=24 Identities=13% Similarity=0.458 Sum_probs=19.8
Q ss_pred cCCcEEEEEEECCChhhHHHHHHH
Q 038356 9 RGALGALLVYDVTKSTTFENVSRW 32 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~ 32 (78)
-|+||++..||.-++..+.++..+
T Consensus 250 gGsDG~V~~Wd~~~rKrl~q~~~~ 273 (323)
T KOG1036|consen 250 GGSDGIVNIWDLFNRKRLKQLAKY 273 (323)
T ss_pred cCCCceEEEccCcchhhhhhccCC
Confidence 589999999999999887765443
No 474
>PRK09602 translation-associated GTPase; Reviewed
Probab=26.78 E-value=95 Score=21.20 Aligned_cols=14 Identities=29% Similarity=0.261 Sum_probs=13.1
Q ss_pred hhcCCcEEEEEEECC
Q 038356 7 YNRGALGALLVYDVT 21 (78)
Q Consensus 7 ~~~~a~~~ilv~d~~ 21 (78)
+ |++|++++|+|..
T Consensus 100 i-r~ad~ll~Vvd~~ 113 (396)
T PRK09602 100 L-RQADALIHVVDAS 113 (396)
T ss_pred H-HHCCEEEEEEeCC
Confidence 7 8999999999997
No 475
>TIGR03567 FMN_reduc_SsuE FMN reductase, SsuE family. Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the homodimeric, NAD(P)H-dependent enzyme SsuE from Escherichia coli, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. It is induced by sulfate starvation. The NADH-dependent enzyme MsuE from Pseudomonas aeruginosa is outside the scope of this model (see model TIGR03566).
Probab=26.60 E-value=1.1e+02 Score=17.93 Aligned_cols=10 Identities=20% Similarity=0.179 Sum_probs=6.4
Q ss_pred cCCcEEEEEE
Q 038356 9 RGALGALLVY 18 (78)
Q Consensus 9 ~~a~~~ilv~ 18 (78)
+.||++|++.
T Consensus 64 ~~AD~iI~~s 73 (171)
T TIGR03567 64 AQADGVVVAT 73 (171)
T ss_pred HHCCEEEEEC
Confidence 4677777754
No 476
>COG1660 Predicted P-loop-containing kinase [General function prediction only]
Probab=26.58 E-value=2e+02 Score=19.07 Aligned_cols=29 Identities=24% Similarity=0.360 Sum_probs=25.1
Q ss_pred cEEEEEEECCChhhHHHHHHHHHHHhhhc
Q 038356 12 LGALLVYDVTKSTTFENVSRWLKDLGDHA 40 (78)
Q Consensus 12 ~~~ilv~d~~~~~s~~~~~~~~~~~~~~~ 40 (78)
+-+-++.|+-+++.|..+..++.++++..
T Consensus 52 ~kvAv~iDiRs~~~~~~l~~~l~~l~~~~ 80 (286)
T COG1660 52 TKVAVVIDVRSREFFGDLEEVLDELKDNG 80 (286)
T ss_pred ceEEEEEecccchhHHHHHHHHHHHHhcC
Confidence 55678889999999999999999998764
No 477
>TIGR01232 lacD tagatose 1,6-diphosphate aldolase. This family consists of Gram-positive proteins. Tagatose 1,6-diphosphate aldolase is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation.
Probab=26.44 E-value=1.7e+02 Score=19.71 Aligned_cols=45 Identities=22% Similarity=0.355 Sum_probs=30.3
Q ss_pred CCcE--EEEEEECCChhhHHHH-HHHHHHHhhhc-CCCCeEEEEeeCCC
Q 038356 10 GALG--ALLVYDVTKSTTFENV-SRWLKDLGDHA-DSNIVIMMIGNKTD 54 (78)
Q Consensus 10 ~a~~--~ilv~d~~~~~s~~~~-~~~~~~~~~~~-~~~~~~~lvgnK~D 54 (78)
|+|+ +++-||..+.+-.+.. +.|++.+.+.| ..++|.++=---.|
T Consensus 119 GadavK~Llyy~pD~~~ein~~k~a~vervg~ec~a~dipf~lE~ltYd 167 (325)
T TIGR01232 119 GANAVKFLLYYDVDDAEEINIQKKAYIERIGSECVAEDIPFFLEVLTYD 167 (325)
T ss_pred CCCeEEEEEEeCCCCChHHHHHHHHHHHHHHHHHHHCCCCeEEEEeccC
Confidence 4444 4667888887777777 66888887666 46788876433334
No 478
>cd02037 MRP-like MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.
Probab=26.35 E-value=1.4e+02 Score=17.21 Aligned_cols=43 Identities=12% Similarity=0.171 Sum_probs=30.1
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
.+|.++++... ++.+...+..+.+.+++.. -....++.|+.+-
T Consensus 91 ~ad~viiV~~p-~~~s~~~~~~~~~~l~~~~--~~~~gvv~N~~~~ 133 (169)
T cd02037 91 PIDGAVIVTTP-QEVALDDVRKAIDMFKKVN--IPILGVVENMSYF 133 (169)
T ss_pred CCCeEEEEECC-chhhHHHHHHHHHHHHhcC--CCeEEEEEcCCcc
Confidence 57888888744 4677888888887777653 2244578999875
No 479
>TIGR03249 KdgD 5-dehydro-4-deoxyglucarate dehydratase. 5-dehydro-4-deoxyglucarate dehydratase not only catalyzes the dehydration of the substrate (diol to ketone + water), but causes the decarboxylation of the intermediate product to yield 2-oxoglutarate semialdehyde (2,5-dioxopentanoate). The gene for the enzyme is usually observed in the vicinity of transporters and dehydratases handling D-galactarate and D-gluconate as well as aldehyde dehydrogenases which convert the product to alpha-ketoglutarate.
Probab=26.06 E-value=1.4e+02 Score=19.23 Aligned_cols=39 Identities=15% Similarity=0.212 Sum_probs=25.9
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEE
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMI 49 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lv 49 (78)
-|+|+++++-..--+.|-+.+.+|+..+.+. .+.|+++.
T Consensus 98 ~Gadav~~~pP~y~~~s~~~i~~~f~~v~~a--~~~pvilY 136 (296)
T TIGR03249 98 AGADGYLLLPPYLINGEQEGLYAHVEAVCES--TDLGVIVY 136 (296)
T ss_pred hCCCEEEECCCCCCCCCHHHHHHHHHHHHhc--cCCCEEEE
Confidence 3788887765444444567777788877654 35787775
No 480
>cd02036 MinD Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. MinD is a monomer.
Probab=25.94 E-value=1.4e+02 Score=17.02 Aligned_cols=46 Identities=22% Similarity=0.086 Sum_probs=30.6
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDLKH 57 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl~~ 57 (78)
..+|.++++.+.+ ..++..+..+.+.++.. ......++.|+.+-..
T Consensus 83 ~~ad~viiv~~~~-~~s~~~~~~~~~~~~~~--~~~~~~iv~N~~~~~~ 128 (179)
T cd02036 83 APADEALLVTTPE-ISSLRDADRVKGLLEAL--GIKVVGVIVNRVRPDM 128 (179)
T ss_pred HhCCcEEEEeCCC-cchHHHHHHHHHHHHHc--CCceEEEEEeCCcccc
Confidence 6788888887654 45666666666666542 2235678999998653
No 481
>cd02032 Bchl_like This family of proteins contains bchL and chlL. Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are involved in light-independent protochlorophyllide reduction in bacteriochlorophyll biosynthesis. In cyanobacteria, algae, and gymnosperms, three similar genes, chlL, chlN and chlB are involved in protochlorophyllide reduction during chlorophylls biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit significant sequence similarity to the nifH, nifD and nifK subunits of nitrogenase, respectively. Nitrogenase catalyzes the reductive formation of ammonia from dinitrogen.
Probab=25.86 E-value=1.7e+02 Score=18.21 Aligned_cols=46 Identities=24% Similarity=0.195 Sum_probs=26.6
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHHHHhhhc-CCCCeE-EEEeeCCCC
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLKDLGDHA-DSNIVI-MMIGNKTDL 55 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~-~~~~~~-~lvgnK~Dl 55 (78)
..||.++++... +..++..+....+.+++.. ..+.++ .++.|+.+.
T Consensus 137 ~~aD~vlip~~p-~~~~l~~~~~~~~~i~~~~~~~~l~~~giV~Nr~~~ 184 (267)
T cd02032 137 NYADYALIVTDN-DFDSIFAANRIAAAVREKAKTYKVRLAGLIANRTDK 184 (267)
T ss_pred hhcCEEEEEecC-CcccHHHHHHHHHHHHHHhhccCCceEEEEEeCCCH
Confidence 578988887654 4445555544444333221 244543 478899884
No 482
>KOG0463 consensus GTP-binding protein GP-1 [General function prediction only]
Probab=25.80 E-value=40 Score=23.62 Aligned_cols=17 Identities=12% Similarity=0.237 Sum_probs=14.6
Q ss_pred CCCeEEEEeeCCCCCCC
Q 038356 42 SNIVIMMIGNKTDLKHL 58 (78)
Q Consensus 42 ~~~~~~lvgnK~Dl~~~ 58 (78)
-.+|+++|-+|+|+...
T Consensus 272 L~VPVfvVVTKIDMCPA 288 (641)
T KOG0463|consen 272 LHVPVFVVVTKIDMCPA 288 (641)
T ss_pred hcCcEEEEEEeeccCcH
Confidence 36899999999999764
No 483
>COG0252 AnsB L-asparaginase/archaeal Glu-tRNAGln amidotransferase subunit D [Amino acid transport and metabolism / Translation, ribosomal structure and biogenesis]
Probab=25.72 E-value=1.7e+02 Score=19.84 Aligned_cols=39 Identities=13% Similarity=0.146 Sum_probs=28.4
Q ss_pred CcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 11 ALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 11 a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
+||+++.- .-+|++....++....+. +.|+|++|...-.
T Consensus 101 ~dGvVItH---GTDTmeeTA~~L~l~l~~---~kPVVlTGamr~s 139 (351)
T COG0252 101 VDGVVITH---GTDTMEETAFFLSLTLNT---PKPVVLTGAMRPA 139 (351)
T ss_pred CCeEEEeC---CCchHHHHHHHHHHHhcC---CCCEEEeCCCCCC
Confidence 48888764 567888877777766543 6899999987654
No 484
>PF10923 DUF2791: P-loop Domain of unknown function (DUF2791); InterPro: IPR021228 This is a family of proteins found in archaea and bacteria. Some of the proteins in this family are annotated as being methyl-accepting chemotaxis proteins and ATP/GTP binding proteins.
Probab=25.61 E-value=1.9e+02 Score=20.12 Aligned_cols=46 Identities=15% Similarity=0.390 Sum_probs=31.7
Q ss_pred CCcEEEEEEE-----------CCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 10 GALGALLVYD-----------VTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 10 ~a~~~ilv~d-----------~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
|-.|.++++| .++..++++++++++++..-.-++.-+++-|+-.=+
T Consensus 237 Gy~GLlI~lDE~e~l~kl~~~~~R~~~ye~lr~lidd~~~G~~~gL~~~~~gTPef~ 293 (416)
T PF10923_consen 237 GYKGLLILLDELENLYKLRNDQAREKNYEALRQLIDDIDQGRAPGLYFVFAGTPEFF 293 (416)
T ss_pred CCCceEEEEechHHHHhcCChHHHHHHHHHHHHHHHHHhcCCCCceEEEEeeCHHHh
Confidence 4467788877 224567889999988875433366777788887655
No 485
>TIGR01772 MDH_euk_gproteo malate dehydrogenase, NAD-dependent. Although malate dehydrogenases have in some cases been mistaken for lactate dehydrogenases due to the similarity of these two substrates and the apparent ease with which evolution can toggle these activities, critical residues have been identified which can discriminate between the two activities. At the time of the creation of this model no hits above the trusted cutoff contained critical residues typical of lactate dehydrogenases.
Probab=25.46 E-value=2.1e+02 Score=18.93 Aligned_cols=48 Identities=17% Similarity=0.226 Sum_probs=32.7
Q ss_pred chhcCCcEEEEEEECCCh---hhHHH-------HHHHHHHHhhhcCCCCeEEEEeeCCCC
Q 038356 6 YYNRGALGALLVYDVTKS---TTFEN-------VSRWLKDLGDHADSNIVIMMIGNKTDL 55 (78)
Q Consensus 6 y~~~~a~~~ilv~d~~~~---~s~~~-------~~~~~~~~~~~~~~~~~~~lvgnK~Dl 55 (78)
-+ ++||.+|+..-.... +..+. ++.+.+.+.+++ ++..++++.|=+|.
T Consensus 64 ~~-~daDivvitaG~~~~~g~~R~dll~~N~~I~~~i~~~i~~~~-p~~iiivvsNPvDv 121 (312)
T TIGR01772 64 AL-KGADVVVIPAGVPRKPGMTRDDLFNVNAGIVKDLVAAVAESC-PKAMILVITNPVNS 121 (312)
T ss_pred Hc-CCCCEEEEeCCCCCCCCccHHHHHHHhHHHHHHHHHHHHHhC-CCeEEEEecCchhh
Confidence 35 899999998876432 22222 245566666665 77889999999984
No 486
>PRK11340 phosphodiesterase YaeI; Provisional
Probab=25.43 E-value=1.1e+02 Score=19.37 Aligned_cols=42 Identities=21% Similarity=-0.005 Sum_probs=21.1
Q ss_pred CCcEEEEEEECCChhhHHHHHHHHHHHhhhcCCCCeE-EEEeeC
Q 038356 10 GALGALLVYDVTKSTTFENVSRWLKDLGDHADSNIVI-MMIGNK 52 (78)
Q Consensus 10 ~a~~~ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~-~lvgnK 52 (78)
+.|.+++.=|+.+..+-.....+.+.++.... ..|+ .+.||-
T Consensus 80 ~pDlVli~GD~~d~~~~~~~~~~~~~L~~L~~-~~pv~~V~GNH 122 (271)
T PRK11340 80 KPDLILLGGDYVLFDMPLNFSAFSDVLSPLAE-CAPTFACFGNH 122 (271)
T ss_pred CCCEEEEccCcCCCCccccHHHHHHHHHHHhh-cCCEEEecCCC
Confidence 56788888888763322223334333333321 2344 466664
No 487
>PF08630 Dfp1_Him1_M: Dfp1/Him1, central region; InterPro: IPR013939 This region, together with the C-terminal zinc finger (IPR006572 from INTERPRO) is essential for the mitotic and kinase activation functions of Dfp1/Him1 []. ; PDB: 3OQ0_J 3OQ4_D 3QBZ_A.
Probab=25.13 E-value=24 Score=20.30 Aligned_cols=25 Identities=24% Similarity=0.401 Sum_probs=0.0
Q ss_pred cchhcCCcEEEEEEECCChhhHHHHHHH
Q 038356 5 AYYNRGALGALLVYDVTKSTTFENVSRW 32 (78)
Q Consensus 5 ~y~~~~a~~~ilv~d~~~~~s~~~~~~~ 32 (78)
.|| + ..+|+|||+...-.=-.+++|
T Consensus 74 ~yF-k--~~yiyV~D~~q~~rPImvrEy 98 (125)
T PF08630_consen 74 HYF-K--GPYIYVYDLDQKTRPIMVREY 98 (125)
T ss_dssp ----------------------------
T ss_pred Eec-C--CCEEEEEecCcCCCcEEEEec
Confidence 355 5 558889998755433334556
No 488
>smart00432 MADS MADS domain.
Probab=25.13 E-value=78 Score=15.59 Aligned_cols=15 Identities=33% Similarity=0.271 Sum_probs=12.0
Q ss_pred cCCcEEEEEEECCCh
Q 038356 9 RGALGALLVYDVTKS 23 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~ 23 (78)
-++++++++|+.+..
T Consensus 38 c~~~v~~iv~sp~g~ 52 (59)
T smart00432 38 CDAEVALIVFSPTGK 52 (59)
T ss_pred cCCeEEEEEECCCCC
Confidence 488999999987653
No 489
>PRK06843 inosine 5-monophosphate dehydrogenase; Validated
Probab=25.09 E-value=2.1e+02 Score=19.90 Aligned_cols=36 Identities=19% Similarity=0.369 Sum_probs=19.1
Q ss_pred EEEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCC
Q 038356 15 LLVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKT 53 (78)
Q Consensus 15 ilv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~ 53 (78)
+++.|.+...+ +.+.++++.+++.. ++.+ +++||=.
T Consensus 168 vI~iD~a~g~~-~~~~~~v~~ik~~~-p~~~-vi~g~V~ 203 (404)
T PRK06843 168 ILVIDSAHGHS-TRIIELVKKIKTKY-PNLD-LIAGNIV 203 (404)
T ss_pred EEEEECCCCCC-hhHHHHHHHHHhhC-CCCc-EEEEecC
Confidence 45558888765 23444555565544 3444 4444544
No 490
>PLN00106 malate dehydrogenase
Probab=24.96 E-value=2.2e+02 Score=18.97 Aligned_cols=46 Identities=20% Similarity=0.325 Sum_probs=31.6
Q ss_pred hhcCCcEEEEEEECCCh--hhHHH--------HHHHHHHHhhhcCCCCeEEEEeeCCC
Q 038356 7 YNRGALGALLVYDVTKS--TTFEN--------VSRWLKDLGDHADSNIVIMMIGNKTD 54 (78)
Q Consensus 7 ~~~~a~~~ilv~d~~~~--~s~~~--------~~~~~~~~~~~~~~~~~~~lvgnK~D 54 (78)
+ +++|.+|+..-.... .+... +++..+.+.+++ ++..++++.|=.|
T Consensus 84 l-~~aDiVVitAG~~~~~g~~R~dll~~N~~i~~~i~~~i~~~~-p~aivivvSNPvD 139 (323)
T PLN00106 84 L-KGADLVIIPAGVPRKPGMTRDDLFNINAGIVKTLCEAVAKHC-PNALVNIISNPVN 139 (323)
T ss_pred c-CCCCEEEEeCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC-CCeEEEEeCCCcc
Confidence 5 899999998876443 12222 245556666665 7788899999988
No 491
>PRK10569 NAD(P)H-dependent FMN reductase; Provisional
Probab=24.88 E-value=1.3e+02 Score=18.19 Aligned_cols=41 Identities=17% Similarity=0.169 Sum_probs=21.9
Q ss_pred cCCcEEEEEEECC---ChhhHHHHHHHHHHHhhhcCCCCeEEEEeeC
Q 038356 9 RGALGALLVYDVT---KSTTFENVSRWLKDLGDHADSNIVIMMIGNK 52 (78)
Q Consensus 9 ~~a~~~ilv~d~~---~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK 52 (78)
+.||++|++.-+= =+..+.+.-+|.. ...-.+.|+.++++-
T Consensus 65 ~~AD~iIi~tP~Y~~s~pg~LKn~iD~l~---~~~l~~K~v~iiat~ 108 (191)
T PRK10569 65 AQADGLIVATPVYKASFSGALKTLLDLLP---ERALEHKVVLPLATG 108 (191)
T ss_pred HHCCEEEEECCccCCCCCHHHHHHHHhCC---hhhhCCCEEEEEEec
Confidence 5788888865432 2334444444442 111134577777774
No 492
>PF00975 Thioesterase: Thioesterase domain; InterPro: IPR001031 Thioesterase domains often occur integrated in or associated with peptide synthetases which are involved in the non-ribosomal synthesis of peptide antibiotics []. Thioesterases are required for the addition of the last amino acid to the peptide antibiotic, thereby forming a cyclic antibiotic. Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of vertebrates.; GO: 0016788 hydrolase activity, acting on ester bonds, 0009058 biosynthetic process; PDB: 2RON_A 2K2Q_B 3LCR_B 2HFJ_B 1MNQ_A 1MN6_B 1MNA_B 2HFK_B 2H7Y_B 2H7X_A ....
Probab=24.79 E-value=1.3e+02 Score=17.87 Aligned_cols=27 Identities=15% Similarity=0.277 Sum_probs=19.3
Q ss_pred hhHHHH-HHHHHHHhhhcCCCCeEEEEee
Q 038356 24 TTFENV-SRWLKDLGDHADSNIVIMMIGN 51 (78)
Q Consensus 24 ~s~~~~-~~~~~~~~~~~~~~~~~~lvgn 51 (78)
.|++.+ ..+.+.++... ++-|++|+|-
T Consensus 46 ~si~~la~~y~~~I~~~~-~~gp~~L~G~ 73 (229)
T PF00975_consen 46 DSIEELASRYAEAIRARQ-PEGPYVLAGW 73 (229)
T ss_dssp SSHHHHHHHHHHHHHHHT-SSSSEEEEEE
T ss_pred CCHHHHHHHHHHHhhhhC-CCCCeeehcc
Confidence 477877 66777777765 3348888885
No 493
>cd01833 XynB_like SGNH_hydrolase subfamily, similar to Ruminococcus flavefaciens XynB. Most likely a secreted hydrolase with xylanase activity. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=24.57 E-value=1.4e+02 Score=16.66 Aligned_cols=40 Identities=10% Similarity=0.122 Sum_probs=24.2
Q ss_pred CCcEEEEEEECCCh-------hhHHHHHHHHHHHhhhcCCCCeEEEEe
Q 038356 10 GALGALLVYDVTKS-------TTFENVSRWLKDLGDHADSNIVIMMIG 50 (78)
Q Consensus 10 ~a~~~ilv~d~~~~-------~s~~~~~~~~~~~~~~~~~~~~~~lvg 50 (78)
..+.+++.+-.+|. +..++++..++.++... +++++++++
T Consensus 40 ~pd~vvi~~G~ND~~~~~~~~~~~~~~~~~i~~i~~~~-p~~~ii~~~ 86 (157)
T cd01833 40 KPDVVLLHLGTNDLVLNRDPDTAPDRLRALIDQMRAAN-PDVKIIVAT 86 (157)
T ss_pred CCCEEEEeccCcccccCCCHHHHHHHHHHHHHHHHHhC-CCeEEEEEe
Confidence 45667776654443 33455566777776654 667777664
No 494
>KOG0466 consensus Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=24.50 E-value=41 Score=22.91 Aligned_cols=19 Identities=26% Similarity=0.384 Sum_probs=14.0
Q ss_pred CeEEEEeeCCCCCCCCCch
Q 038356 44 IVIMMIGNKTDLKHLPTSM 62 (78)
Q Consensus 44 ~~~~lvgnK~Dl~~~~~v~ 62 (78)
..++++-||.||-.+.+..
T Consensus 180 khiiilQNKiDli~e~~A~ 198 (466)
T KOG0466|consen 180 KHIIILQNKIDLIKESQAL 198 (466)
T ss_pred ceEEEEechhhhhhHHHHH
Confidence 3578999999997654443
No 495
>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....
Probab=24.26 E-value=1.6e+02 Score=17.45 Aligned_cols=21 Identities=19% Similarity=0.384 Sum_probs=11.4
Q ss_pred HHHHHHhhhcCCCCeEEEEee
Q 038356 31 RWLKDLGDHADSNIVIMMIGN 51 (78)
Q Consensus 31 ~~~~~~~~~~~~~~~~~lvgn 51 (78)
+..+.+++....+.|++|.|.
T Consensus 10 ~~~~~~~~~a~~~~pVlI~GE 30 (168)
T PF00158_consen 10 RLREQAKRAASSDLPVLITGE 30 (168)
T ss_dssp HHHHHHHHHTTSTS-EEEECS
T ss_pred HHHHHHHHHhCCCCCEEEEcC
Confidence 334445555555678777764
No 496
>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....
Probab=24.16 E-value=69 Score=21.20 Aligned_cols=39 Identities=18% Similarity=0.316 Sum_probs=24.8
Q ss_pred EEEECCChhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCC
Q 038356 16 LVYDVTKSTTFENVSRWLKDLGDHADSNIVIMMIGNKTD 54 (78)
Q Consensus 16 lv~d~~~~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~D 54 (78)
-+.++.+..+.+.+..|...+....+....-++|--|.|
T Consensus 78 pMlSL~k~~s~eel~~w~~r~~~~~~~~~~~~~~e~KiD 116 (315)
T PF01653_consen 78 PMLSLDKAYSEEELRKWLKRVEKALGEEEEEFVVEPKID 116 (315)
T ss_dssp -----EEESSHHHHHHHHHHHHHHCSS-SSEEEEEEEES
T ss_pred cccCccccCCHHHHHHHHHHHHHHhcccccceeEeeccc
Confidence 356777777889999999998776543333567777777
No 497
>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
Probab=24.04 E-value=1.2e+02 Score=15.73 Aligned_cols=25 Identities=12% Similarity=0.142 Sum_probs=17.5
Q ss_pred cCCcEEEEEEECCChhhHHHHHHHHH
Q 038356 9 RGALGALLVYDVTKSTTFENVSRWLK 34 (78)
Q Consensus 9 ~~a~~~ilv~d~~~~~s~~~~~~~~~ 34 (78)
..+|.++++.+. +..++..+..+.+
T Consensus 60 ~~ad~viv~~~~-~~~s~~~~~~~~~ 84 (104)
T cd02042 60 AAADLVLIPVQP-SPLDLDGLEKLLE 84 (104)
T ss_pred HHCCEEEEeccC-CHHHHHHHHHHHH
Confidence 567888887754 5667777766665
No 498
>PF09419 PGP_phosphatase: Mitochondrial PGP phosphatase; InterPro: IPR010021 This group of hypothetical proteins is a part of the IIIA subfamily of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterised members of this subfamily and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs [], all of which are found conserved here. This family consists of sequences from fungi, plants, cyanobacteria, Gram-positive bacteria and Deinococcus. There is presently no characterisation of any sequence in this family.
Probab=23.90 E-value=1.8e+02 Score=17.55 Aligned_cols=44 Identities=14% Similarity=0.277 Sum_probs=27.1
Q ss_pred CCcEEEEEEECCC-------hhhHHHHHHHHHHHhhhcCCCCeEEEEeeCCC
Q 038356 10 GALGALLVYDVTK-------STTFENVSRWLKDLGDHADSNIVIMMIGNKTD 54 (78)
Q Consensus 10 ~a~~~ilv~d~~~-------~~s~~~~~~~~~~~~~~~~~~~~~~lvgnK~D 54 (78)
....-.+++|.+| .+-...+..|++++++..+ .--++||-|-.-
T Consensus 38 ~~Gik~li~DkDNTL~~~~~~~i~~~~~~~~~~l~~~~~-~~~v~IvSNsaG 88 (168)
T PF09419_consen 38 KKGIKALIFDKDNTLTPPYEDEIPPEYAEWLNELKKQFG-KDRVLIVSNSAG 88 (168)
T ss_pred hcCceEEEEcCCCCCCCCCcCcCCHHHHHHHHHHHHHCC-CCeEEEEECCCC
Confidence 3333445666655 2224567889999987753 225788888753
No 499
>PF13692 Glyco_trans_1_4: Glycosyl transferases group 1; PDB: 3OY2_A 3OY7_B 2Q6V_A 2HY7_A 3CV3_A 3CUY_A.
Probab=23.88 E-value=1.3e+02 Score=16.11 Aligned_cols=32 Identities=25% Similarity=0.450 Sum_probs=22.2
Q ss_pred ChhhHHHHHH-HHHHHhhhcCCCCeEEEEeeCCC
Q 038356 22 KSTTFENVSR-WLKDLGDHADSNIVIMMIGNKTD 54 (78)
Q Consensus 22 ~~~s~~~~~~-~~~~~~~~~~~~~~~~lvgnK~D 54 (78)
..+.++.+-+ .++.+.+.. +++.+.++|+..|
T Consensus 13 ~~k~~~~li~~~~~~l~~~~-p~~~l~i~G~~~~ 45 (135)
T PF13692_consen 13 PDKGLEELIEAALERLKEKH-PDIELIIIGNGPD 45 (135)
T ss_dssp GGGTHHHHHH-HHHHHHHHS-TTEEEEEECESS-
T ss_pred ccccccchhhhHHHHHHHHC-cCEEEEEEeCCHH
Confidence 3456776655 777777665 6789999999654
No 500
>COG3967 DltE Short-chain dehydrogenase involved in D-alanine esterification of lipoteichoic acid and wall teichoic acid (D-alanine transfer protein) [Cell envelope biogenesis, outer membrane]
Probab=23.75 E-value=1e+02 Score=19.82 Aligned_cols=23 Identities=26% Similarity=0.367 Sum_probs=18.2
Q ss_pred EEEEEEECCChhhHHHHHHHHHH
Q 038356 13 GALLVYDVTKSTTFENVSRWLKD 35 (78)
Q Consensus 13 ~~ilv~d~~~~~s~~~~~~~~~~ 35 (78)
..-.|+|+.|++|.+.+-+|+..
T Consensus 52 ~~t~v~Dv~d~~~~~~lvewLkk 74 (245)
T COG3967 52 IHTEVCDVADRDSRRELVEWLKK 74 (245)
T ss_pred hheeeecccchhhHHHHHHHHHh
Confidence 34568999999999998888643
Done!