Query psy104
Match_columns 86
No_of_seqs 106 out of 514
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 16:54:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy104.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/104hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1547|consensus 100.0 7.4E-33 1.6E-37 199.0 9.1 78 8-85 83-161 (336)
2 KOG2655|consensus 100.0 4.5E-31 9.7E-36 196.7 8.9 82 4-85 54-135 (366)
3 COG5019 CDC3 Septin family pro 100.0 7.8E-30 1.7E-34 189.8 9.9 77 9-85 62-139 (373)
4 PF00735 Septin: Septin; Inte 99.9 6.4E-27 1.4E-31 169.5 9.6 80 6-85 40-119 (281)
5 KOG3859|consensus 99.9 6.6E-26 1.4E-30 165.9 5.6 84 2-85 68-153 (406)
6 cd01850 CDC_Septin CDC/Septin. 99.9 6.9E-22 1.5E-26 142.5 10.1 78 8-85 42-120 (276)
7 cd01852 AIG1 AIG1 (avrRpt2-ind 95.1 0.032 7E-07 37.7 3.6 31 10-44 34-64 (196)
8 cd01853 Toc34_like Toc34-like 95.0 0.059 1.3E-06 38.6 4.9 15 29-43 79-93 (249)
9 PF04548 AIG1: AIG1 family; I 94.9 0.028 6.1E-07 38.8 3.0 29 12-44 36-64 (212)
10 TIGR03596 GTPase_YlqF ribosome 94.5 0.042 9E-07 39.5 3.2 42 30-71 164-226 (276)
11 TIGR00991 3a0901s02IAP34 GTP-b 93.9 0.11 2.4E-06 38.8 4.4 14 29-42 86-99 (313)
12 smart00053 DYNc Dynamin, GTPas 93.4 0.14 3E-06 36.7 4.0 40 29-69 125-164 (240)
13 cd01876 YihA_EngB The YihA (En 93.0 0.42 9.2E-06 29.9 5.5 15 30-44 46-60 (170)
14 cd01894 EngA1 EngA1 subfamily. 92.0 0.91 2E-05 28.3 6.1 16 29-44 45-60 (157)
15 PF00350 Dynamin_N: Dynamin fa 91.2 0.099 2.2E-06 33.8 1.0 15 28-42 100-114 (168)
16 PF01926 MMR_HSR1: 50S ribosom 90.9 0.26 5.7E-06 30.2 2.6 14 31-44 49-62 (116)
17 COG0218 Predicted GTPase [Gene 90.5 0.29 6.4E-06 34.5 2.9 38 31-72 72-109 (200)
18 TIGR00993 3a0901s04IAP86 chlor 90.1 0.63 1.4E-05 38.5 4.8 15 29-43 166-180 (763)
19 cd01855 YqeH YqeH. YqeH is an 89.4 0.44 9.5E-06 31.9 3.0 10 30-39 181-190 (190)
20 cd01879 FeoB Ferrous iron tran 86.0 1 2.3E-05 28.2 3.1 15 29-43 43-57 (158)
21 TIGR03597 GTPase_YqeH ribosome 84.5 0.75 1.6E-05 34.5 2.1 34 31-71 206-239 (360)
22 PTZ00099 rab6; Provisional 83.5 5 0.00011 26.8 5.7 34 7-40 7-40 (176)
23 cd01861 Rab6 Rab6 subfamily. 83.1 5.5 0.00012 25.0 5.5 29 12-40 32-60 (161)
24 COG4659 RnfG Predicted NADH:ub 82.1 1.9 4E-05 30.4 3.2 28 22-49 109-140 (195)
25 cd04164 trmE TrmE (MnmE, ThdF, 81.8 1.3 2.8E-05 27.5 2.1 16 29-44 49-64 (157)
26 cd01857 HSR1_MMR1 HSR1/MMR1. 81.5 0.94 2E-05 29.0 1.5 11 30-40 129-139 (141)
27 COG3596 Predicted GTPase [Gene 81.0 1.7 3.8E-05 32.3 2.9 18 29-46 87-104 (296)
28 cd04167 Snu114p Snu114p subfam 80.9 2.6 5.6E-05 28.7 3.6 18 25-42 67-84 (213)
29 cd01868 Rab11_like Rab11-like. 80.4 7.6 0.00016 24.6 5.5 30 11-40 34-63 (165)
30 cd00154 Rab Rab family. Rab G 80.2 6.6 0.00014 24.0 5.0 31 10-40 30-60 (159)
31 TIGR03598 GTPase_YsxC ribosome 80.1 3.4 7.4E-05 27.1 3.8 15 30-44 65-79 (179)
32 PRK00454 engB GTP-binding prot 80.0 3.7 8.1E-05 26.9 4.0 15 29-43 70-84 (196)
33 cd01897 NOG NOG1 is a nucleola 79.2 1.7 3.6E-05 27.7 2.1 14 28-41 46-59 (168)
34 cd00877 Ran Ran (Ras-related n 78.4 8.9 0.00019 24.8 5.4 32 9-40 29-60 (166)
35 cd01864 Rab19 Rab19 subfamily. 78.1 8.5 0.00018 24.5 5.2 19 21-39 44-62 (165)
36 cd01869 Rab1_Ypt1 Rab1/Ypt1 su 78.0 8.6 0.00019 24.4 5.2 20 21-40 43-62 (166)
37 PRK04213 GTP-binding protein; 77.4 9.6 0.00021 25.2 5.4 15 30-44 53-67 (201)
38 cd04119 RJL RJL (RabJ-Like) su 77.1 8.2 0.00018 24.1 4.9 20 21-40 41-60 (168)
39 cd00880 Era_like Era (E. coli 77.1 1.8 3.8E-05 26.3 1.7 19 28-46 44-62 (163)
40 cd04142 RRP22 RRP22 subfamily. 76.8 13 0.00028 25.2 6.0 20 21-40 41-60 (198)
41 cd04113 Rab4 Rab4 subfamily. 76.6 11 0.00024 23.7 5.4 30 11-40 31-60 (161)
42 cd04168 TetM_like Tet(M)-like 76.5 4.8 0.0001 28.3 3.9 28 13-42 50-77 (237)
43 TIGR00436 era GTP-binding prot 76.3 11 0.00025 26.6 5.9 13 30-42 49-61 (270)
44 cd04122 Rab14 Rab14 subfamily. 76.0 11 0.00023 24.1 5.2 18 22-39 44-61 (166)
45 cd04106 Rab23_lke Rab23-like s 75.8 7.1 0.00015 24.5 4.3 23 17-39 39-61 (162)
46 cd04108 Rab36_Rab34 Rab34/Rab3 75.8 12 0.00026 24.3 5.5 31 10-40 30-60 (170)
47 cd04163 Era Era subfamily. Er 75.2 2.6 5.7E-05 26.0 2.1 16 28-43 50-65 (168)
48 cd01895 EngA2 EngA2 subfamily. 74.9 5.7 0.00012 24.8 3.7 14 30-43 51-64 (174)
49 smart00175 RAB Rab subfamily o 74.6 15 0.00032 22.9 5.5 29 11-39 31-59 (164)
50 cd04112 Rab26 Rab26 subfamily. 73.9 9.6 0.00021 25.2 4.7 17 22-38 43-59 (191)
51 KOG0462|consensus 73.6 5 0.00011 32.7 3.7 30 12-41 107-137 (650)
52 PF03193 DUF258: Protein of un 73.1 0.59 1.3E-05 31.7 -1.4 11 32-42 90-100 (161)
53 COG0481 LepA Membrane GTPase L 72.9 5.8 0.00013 32.0 3.9 31 11-41 55-88 (603)
54 cd01866 Rab2 Rab2 subfamily. 72.5 15 0.00031 23.6 5.2 20 20-39 44-63 (168)
55 cd01884 EF_Tu EF-Tu subfamily. 72.4 4.8 0.0001 27.5 3.0 28 12-41 50-77 (195)
56 TIGR00231 small_GTP small GTP- 72.2 13 0.00028 22.3 4.7 19 22-40 43-61 (161)
57 cd01856 YlqF YlqF. Proteins o 71.6 2.7 5.9E-05 27.6 1.6 12 29-40 160-171 (171)
58 cd04124 RabL2 RabL2 subfamily. 71.5 18 0.00039 23.0 5.5 29 12-40 32-60 (161)
59 cd01849 YlqF_related_GTPase Yl 71.3 2.7 5.8E-05 27.2 1.5 10 30-39 146-155 (155)
60 TIGR01394 TypA_BipA GTP-bindin 71.0 4.6 0.0001 32.5 3.0 29 12-42 49-77 (594)
61 cd04116 Rab9 Rab9 subfamily. 70.9 18 0.0004 22.9 5.4 27 12-38 37-63 (170)
62 TIGR00157 ribosome small subun 70.9 5.1 0.00011 28.4 3.0 10 32-41 174-183 (245)
63 cd00882 Ras_like_GTPase Ras-li 70.6 9.1 0.0002 22.6 3.7 29 15-43 31-59 (157)
64 smart00176 RAN Ran (Ras-relate 70.2 19 0.00042 24.5 5.7 31 10-40 25-55 (200)
65 cd01886 EF-G Elongation factor 70.1 9.1 0.0002 27.5 4.2 30 11-42 48-77 (270)
66 cd01890 LepA LepA subfamily. 69.8 9.7 0.00021 24.4 3.9 17 25-41 63-79 (179)
67 PLN03071 GTP-binding nuclear p 69.6 16 0.00034 25.1 5.1 32 10-41 43-74 (219)
68 TIGR03594 GTPase_EngA ribosome 69.1 8.2 0.00018 28.9 3.9 12 30-41 48-59 (429)
69 PLN03118 Rab family protein; P 68.9 18 0.00039 24.3 5.3 19 21-39 54-72 (211)
70 PRK00089 era GTPase Era; Revie 68.8 23 0.00049 25.2 6.0 15 29-43 53-67 (292)
71 cd01881 Obg_like The Obg-like 68.5 3.3 7.3E-05 26.3 1.5 13 29-41 44-56 (176)
72 cd04104 p47_IIGP_like p47 (47- 68.5 2.7 5.9E-05 28.4 1.1 14 29-42 52-65 (197)
73 cd01889 SelB_euk SelB subfamil 68.2 6.3 0.00014 26.1 2.8 13 28-40 67-79 (192)
74 PRK00093 GTP-binding protein D 68.0 17 0.00037 27.3 5.4 13 29-41 49-61 (435)
75 COG0480 FusA Translation elong 67.9 7.9 0.00017 32.0 3.8 32 10-42 58-89 (697)
76 cd04130 Wrch_1 Wrch-1 subfamil 67.8 20 0.00043 23.1 5.1 21 20-40 39-59 (173)
77 cd01862 Rab7 Rab7 subfamily. 67.7 22 0.00047 22.4 5.2 19 22-40 42-60 (172)
78 cd04118 Rab24 Rab24 subfamily. 67.7 21 0.00046 23.3 5.3 20 21-40 42-61 (193)
79 cd04169 RF3 RF3 subfamily. Pe 67.5 9 0.00019 27.5 3.7 28 12-41 56-83 (267)
80 cd04115 Rab33B_Rab33A Rab33B/R 67.4 24 0.00052 22.6 5.5 20 21-40 43-62 (170)
81 cd01859 MJ1464 MJ1464. This f 67.2 10 0.00022 24.2 3.6 10 30-39 147-156 (156)
82 cd01867 Rab8_Rab10_Rab13_like 66.8 19 0.00041 23.0 4.8 19 21-39 44-62 (167)
83 PF04784 DUF547: Protein of un 66.5 3.6 7.8E-05 26.1 1.3 19 67-85 65-86 (117)
84 cd04117 Rab15 Rab15 subfamily. 66.4 26 0.00057 22.3 5.4 31 10-40 30-60 (161)
85 cd00881 GTP_translation_factor 66.2 4.2 9.2E-05 26.1 1.6 14 28-41 61-74 (189)
86 cd01863 Rab18 Rab18 subfamily. 65.9 21 0.00046 22.3 4.9 17 24-40 44-60 (161)
87 cd01865 Rab3 Rab3 subfamily. 65.3 29 0.00063 22.0 5.5 20 21-40 42-61 (165)
88 COG1162 Predicted GTPases [Gen 64.8 3.3 7.1E-05 30.9 1.0 9 32-40 219-227 (301)
89 cd01860 Rab5_related Rab5-rela 64.7 24 0.00052 22.0 5.0 19 21-39 42-60 (163)
90 cd04170 EF-G_bact Elongation f 64.6 6.1 0.00013 27.9 2.3 20 21-42 58-77 (268)
91 PRK10218 GTP-binding protein; 64.6 18 0.00038 29.4 5.1 30 12-43 53-82 (607)
92 cd01885 EF2 EF2 (for archaea a 64.4 5.5 0.00012 27.9 2.0 17 26-42 70-86 (222)
93 cd04171 SelB SelB subfamily. 64.2 9.9 0.00021 23.7 3.1 12 29-40 51-62 (164)
94 TIGR01631 Trypano_RHS trypanos 63.9 5.8 0.00012 33.1 2.3 37 28-71 279-315 (760)
95 PF07999 RHSP: Retrotransposon 63.5 5.3 0.00011 31.2 1.9 36 28-70 124-159 (439)
96 PTZ00209 retrotransposon hot s 63.4 5.9 0.00013 32.7 2.3 37 28-71 172-208 (693)
97 cd01878 HflX HflX subfamily. 63.3 13 0.00028 24.7 3.7 13 30-42 90-102 (204)
98 cd01898 Obg Obg subfamily. Th 63.3 5.7 0.00012 25.2 1.8 13 29-41 48-60 (170)
99 PF12075 KN_motif: KN motif; 62.0 5.4 0.00012 21.1 1.2 19 34-58 4-22 (39)
100 cd04136 Rap_like Rap-like subf 61.9 19 0.00041 22.5 4.1 19 22-40 42-60 (163)
101 PF00009 GTP_EFTU: Elongation 61.8 5.6 0.00012 26.4 1.6 14 28-41 69-82 (188)
102 cd01851 GBP Guanylate-binding 60.9 6.4 0.00014 27.4 1.8 17 28-44 59-75 (224)
103 cd01858 NGP_1 NGP-1. Autoanti 60.6 5.8 0.00013 25.6 1.5 9 31-39 149-157 (157)
104 cd04110 Rab35 Rab35 subfamily. 60.6 29 0.00063 23.1 5.0 19 21-39 47-65 (199)
105 PLN03127 Elongation factor Tu; 60.3 9.3 0.0002 29.6 2.8 30 11-42 108-137 (447)
106 TIGR03594 GTPase_EngA ribosome 60.2 24 0.00051 26.4 4.9 23 21-45 214-236 (429)
107 TIGR00503 prfC peptide chain r 59.9 13 0.00028 29.6 3.5 29 12-42 65-93 (527)
108 COG5256 TEF1 Translation elong 59.7 6.8 0.00015 30.7 1.9 29 13-43 71-99 (428)
109 PRK00741 prfC peptide chain re 59.6 14 0.0003 29.4 3.7 29 12-42 64-92 (526)
110 TIGR03134 malonate_gamma malon 59.2 16 0.00034 26.3 3.6 37 26-65 66-102 (238)
111 cd01893 Miro1 Miro1 subfamily. 58.8 15 0.00034 23.4 3.3 17 25-41 43-59 (166)
112 cd04101 RabL4 RabL4 (Rab-like4 58.6 35 0.00076 21.3 4.9 15 25-39 48-62 (164)
113 cd04145 M_R_Ras_like M-Ras/R-R 58.5 25 0.00054 21.9 4.2 15 25-39 46-60 (164)
114 cd04141 Rit_Rin_Ric Rit/Rin/Ri 58.5 31 0.00067 22.4 4.8 19 22-40 43-61 (172)
115 cd01883 EF1_alpha Eukaryotic e 57.7 13 0.00028 25.5 2.9 26 13-40 63-88 (219)
116 cd01887 IF2_eIF5B IF2/eIF5B (i 57.3 6.3 0.00014 24.8 1.2 13 28-40 49-61 (168)
117 PF00063 Myosin_head: Myosin h 57.1 15 0.00033 29.7 3.6 37 27-65 362-399 (689)
118 PF00071 Ras: Ras family; Int 56.6 30 0.00066 21.6 4.4 30 11-40 30-59 (162)
119 cd04121 Rab40 Rab40 subfamily. 56.2 51 0.0011 22.2 5.6 20 21-40 47-66 (189)
120 PRK12288 GTPase RsgA; Reviewed 56.1 17 0.00036 27.3 3.5 11 32-42 260-270 (347)
121 KOG0458|consensus 56.0 16 0.00035 29.8 3.5 20 27-46 253-272 (603)
122 cd04123 Rab21 Rab21 subfamily. 55.8 46 0.001 20.5 5.2 14 25-38 45-58 (162)
123 cd04175 Rap1 Rap1 subgroup. T 55.6 28 0.00061 21.9 4.1 19 21-39 41-59 (164)
124 cd04166 CysN_ATPS CysN_ATPS su 55.4 14 0.00031 25.0 2.8 26 13-40 63-88 (208)
125 PLN03110 Rab GTPase; Provision 55.3 50 0.0011 22.4 5.5 29 11-39 43-71 (216)
126 COG1159 Era GTPase [General fu 55.3 11 0.00025 28.1 2.4 15 28-42 53-67 (298)
127 cd04135 Tc10 TC10 subfamily. 55.0 38 0.00082 21.5 4.7 21 21-41 40-60 (174)
128 cd04107 Rab32_Rab38 Rab38/Rab3 54.9 50 0.0011 21.9 5.4 14 26-39 47-60 (201)
129 TIGR03156 GTP_HflX GTP-binding 54.9 18 0.00039 27.1 3.5 26 11-39 222-247 (351)
130 cd04114 Rab30 Rab30 subfamily. 54.6 51 0.0011 20.7 5.6 19 22-40 49-67 (169)
131 cd04178 Nucleostemin_like Nucl 54.1 7.6 0.00017 26.1 1.3 10 30-39 163-172 (172)
132 cd04120 Rab12 Rab12 subfamily. 53.4 53 0.0012 22.4 5.4 29 11-39 31-59 (202)
133 cd04176 Rap2 Rap2 subgroup. T 53.4 30 0.00065 21.7 4.0 18 22-39 42-59 (163)
134 smart00173 RAS Ras subfamily o 53.2 31 0.00068 21.6 4.0 19 22-40 41-59 (164)
135 PLN00043 elongation factor 1-a 53.0 8.7 0.00019 29.8 1.6 31 10-42 68-98 (447)
136 TIGR01393 lepA GTP-binding pro 52.8 21 0.00046 28.7 3.8 31 12-42 50-83 (595)
137 cd04132 Rho4_like Rho4-like su 52.6 50 0.0011 21.3 5.0 15 25-39 45-59 (187)
138 cd04146 RERG_RasL11_like RERG/ 52.5 30 0.00065 21.9 3.9 17 25-41 43-59 (165)
139 TIGR02034 CysN sulfate adenyly 52.5 18 0.00038 27.5 3.1 28 12-41 65-92 (406)
140 COG1084 Predicted GTPase [Gene 52.2 13 0.00028 28.4 2.3 28 13-41 198-227 (346)
141 cd04125 RabA_like RabA-like su 52.0 55 0.0012 21.3 5.2 17 25-41 45-61 (188)
142 smart00174 RHO Rho (Ras homolo 51.9 49 0.0011 20.9 4.8 19 21-39 38-56 (174)
143 PRK12289 GTPase RsgA; Reviewed 50.9 7.8 0.00017 29.2 1.0 10 32-41 227-236 (352)
144 TIGR00485 EF-Tu translation el 50.1 18 0.00039 27.2 2.8 29 11-41 59-87 (394)
145 TIGR01938 nqrC NADH:ubiquinone 49.8 8.3 0.00018 28.0 0.9 20 27-46 162-184 (251)
146 PTZ00141 elongation factor 1- 49.7 13 0.00028 28.8 2.0 29 12-42 70-98 (446)
147 cd04160 Arfrp1 Arfrp1 subfamil 49.1 28 0.00061 21.9 3.3 14 28-41 49-62 (167)
148 cd04128 Spg1 Spg1p. Spg1p (se 48.6 71 0.0015 21.0 5.3 30 10-39 30-59 (182)
149 cd01854 YjeQ_engC YjeQ/EngC. 48.5 28 0.0006 25.2 3.5 10 32-41 216-225 (287)
150 PF02421 FeoB_N: Ferrous iron 48.4 65 0.0014 21.5 5.1 27 10-40 32-58 (156)
151 cd04144 Ras2 Ras2 subfamily. 48.3 39 0.00083 22.2 4.0 18 23-40 41-58 (190)
152 cd04111 Rab39 Rab39 subfamily. 47.9 58 0.0013 22.1 4.9 15 25-39 48-62 (211)
153 TIGR00484 EF-G translation elo 47.9 26 0.00057 28.5 3.6 29 13-43 61-89 (689)
154 cd04127 Rab27A Rab27a subfamil 47.5 72 0.0016 20.3 5.3 14 26-39 60-73 (180)
155 cd00157 Rho Rho (Ras homology) 47.3 62 0.0013 20.2 4.7 20 22-41 41-60 (171)
156 TIGR00450 mnmE_trmE_thdF tRNA 47.3 46 0.001 25.8 4.7 16 25-42 249-264 (442)
157 cd04109 Rab28 Rab28 subfamily. 46.7 78 0.0017 21.3 5.4 30 10-39 30-60 (215)
158 CHL00189 infB translation init 46.6 24 0.00052 29.4 3.2 27 15-41 281-307 (742)
159 PF00448 SRP54: SRP54-type pro 46.5 36 0.00079 23.3 3.7 12 29-40 84-95 (196)
160 PLN03108 Rab family protein; P 46.0 57 0.0012 22.0 4.6 18 22-39 48-65 (210)
161 KOG2486|consensus 45.1 43 0.00093 25.3 4.1 28 21-48 175-202 (320)
162 COG1217 TypA Predicted membran 45.0 31 0.00067 28.0 3.5 30 11-42 52-81 (603)
163 PRK12317 elongation factor 1-a 44.7 26 0.00056 26.6 3.0 27 13-41 70-96 (425)
164 TIGR00490 aEF-2 translation el 44.6 23 0.0005 29.1 2.8 14 28-41 85-98 (720)
165 cd01888 eIF2_gamma eIF2-gamma 44.5 16 0.00034 24.7 1.6 12 29-40 83-94 (203)
166 PLN03126 Elongation factor Tu; 44.4 37 0.00081 26.7 3.9 29 11-41 128-156 (478)
167 PRK05433 GTP-binding protein L 44.2 23 0.0005 28.6 2.7 18 25-42 70-87 (600)
168 cd04154 Arl2 Arl2 subfamily. 44.2 34 0.00073 22.0 3.1 13 28-40 57-69 (173)
169 cd04148 RGK RGK subfamily. Th 44.2 57 0.0012 22.3 4.4 16 25-40 46-61 (221)
170 cd01385 MYSc_type_IX Myosin mo 44.1 38 0.00083 27.9 4.0 36 28-64 375-411 (692)
171 cd01871 Rac1_like Rac1-like su 44.0 53 0.0011 21.4 4.1 20 21-40 41-60 (174)
172 PRK03003 GTP-binding protein D 43.6 1.5E+02 0.0033 22.9 7.2 11 30-40 87-97 (472)
173 cd04147 Ras_dva Ras-dva subfam 43.6 48 0.001 22.0 3.9 17 23-39 41-57 (198)
174 cd01870 RhoA_like RhoA-like su 43.5 54 0.0012 20.8 4.0 18 22-39 42-59 (175)
175 cd04157 Arl6 Arl6 subfamily. 43.3 20 0.00043 22.4 1.9 13 28-40 44-56 (162)
176 cd00876 Ras Ras family. The R 43.2 63 0.0014 19.8 4.2 18 23-40 41-58 (160)
177 cd01874 Cdc42 Cdc42 subfamily. 42.8 56 0.0012 21.3 4.1 20 21-40 41-60 (175)
178 CHL00071 tufA elongation facto 42.7 43 0.00093 25.4 3.9 29 11-41 59-87 (409)
179 PRK13796 GTPase YqeH; Provisio 42.6 25 0.00055 26.4 2.6 28 32-66 213-240 (365)
180 cd04140 ARHI_like ARHI subfami 42.6 59 0.0013 20.6 4.1 19 22-40 42-60 (165)
181 PTZ00369 Ras-like protein; Pro 42.5 60 0.0013 21.3 4.2 17 25-41 49-65 (189)
182 PRK05291 trmE tRNA modificatio 42.4 44 0.00096 25.8 4.0 26 12-41 250-275 (449)
183 PRK00049 elongation factor Tu; 42.3 35 0.00077 25.8 3.4 29 10-40 58-86 (396)
184 cd01891 TypA_BipA TypA (tyrosi 42.0 20 0.00044 23.7 1.9 14 28-41 64-77 (194)
185 cd04137 RheB Rheb (Ras Homolog 41.8 57 0.0012 20.8 4.0 19 22-40 42-60 (180)
186 cd01875 RhoG RhoG subfamily. 41.7 1E+02 0.0022 20.3 5.4 18 22-39 44-61 (191)
187 TIGR02584 cas_NE0113 CRISPR-as 41.4 17 0.00038 25.8 1.5 11 75-85 116-126 (209)
188 PRK09518 bifunctional cytidyla 41.3 1.7E+02 0.0036 24.1 7.2 13 29-41 323-335 (712)
189 smart00242 MYSc Myosin. Large 41.3 47 0.001 27.2 4.1 36 27-64 367-403 (677)
190 PRK05724 acetyl-CoA carboxylas 41.2 17 0.00037 27.4 1.5 15 25-40 150-164 (319)
191 PF12508 DUF3714: Protein of u 41.0 57 0.0012 22.9 4.0 29 11-39 101-129 (200)
192 PRK05124 cysN sulfate adenylyl 40.9 34 0.00073 26.7 3.1 27 12-40 92-118 (474)
193 PTZ00132 GTP-binding nuclear p 40.8 98 0.0021 20.7 5.1 30 10-39 39-68 (215)
194 PRK12736 elongation factor Tu; 40.8 33 0.00071 25.9 3.0 27 11-39 59-85 (394)
195 cd04139 RalA_RalB RalA/RalB su 40.7 64 0.0014 19.9 4.0 17 23-39 42-58 (164)
196 TIGR02836 spore_IV_A stage IV 40.5 19 0.00042 28.7 1.7 26 18-43 79-105 (492)
197 cd04177 RSR1 RSR1 subgroup. R 40.4 63 0.0014 20.5 4.0 17 24-40 44-60 (168)
198 PRK07560 elongation factor EF- 40.3 29 0.00064 28.5 2.8 15 27-41 85-99 (731)
199 PRK09563 rbgA GTPase YlqF; Rev 39.9 17 0.00037 26.2 1.3 13 30-42 167-179 (287)
200 TIGR00483 EF-1_alpha translati 39.8 44 0.00094 25.4 3.5 26 12-39 70-95 (426)
201 PRK05346 Na(+)-translocating N 39.7 13 0.00029 27.0 0.7 20 27-46 160-182 (256)
202 cd04165 GTPBP1_like GTPBP1-lik 39.5 21 0.00044 24.9 1.6 11 29-39 84-94 (224)
203 PRK00098 GTPase RsgA; Reviewed 39.4 32 0.00069 25.0 2.7 9 32-40 219-227 (298)
204 cd04161 Arl2l1_Arl13_like Arl2 39.4 53 0.0011 21.1 3.5 12 28-39 42-53 (167)
205 cd04133 Rop_like Rop subfamily 38.9 66 0.0014 21.3 4.0 20 21-40 41-60 (176)
206 cd04152 Arl4_Arl7 Arl4/Arl7 su 38.8 46 0.00099 21.8 3.2 16 25-40 48-63 (183)
207 TIGR00475 selB selenocysteine- 38.7 61 0.0013 26.0 4.4 12 29-40 50-61 (581)
208 PRK12740 elongation factor G; 38.3 41 0.00089 27.1 3.3 27 13-41 46-72 (668)
209 PRK12735 elongation factor Tu; 38.1 43 0.00093 25.3 3.3 27 12-40 60-86 (396)
210 PRK00007 elongation factor G; 37.9 43 0.00092 27.4 3.4 28 12-41 60-87 (693)
211 PF09140 MipZ: ATPase MipZ; I 37.5 15 0.00033 27.0 0.7 14 29-42 99-112 (261)
212 KOG1030|consensus 37.2 95 0.0021 21.4 4.5 52 17-68 56-107 (168)
213 cd04134 Rho3 Rho3 subfamily. 37.1 81 0.0017 20.7 4.2 18 22-39 41-58 (189)
214 KOG0465|consensus 36.9 39 0.00084 28.1 3.0 27 13-41 90-116 (721)
215 cd04174 Rnd1_Rho6 Rnd1/Rho6 su 36.5 1.2E+02 0.0026 21.3 5.2 20 20-39 52-71 (232)
216 TIGR00513 accA acetyl-CoA carb 36.4 22 0.00049 26.7 1.5 14 26-40 151-164 (316)
217 TIGR00487 IF-2 translation ini 36.2 48 0.001 26.8 3.4 11 30-40 136-146 (587)
218 cd04138 H_N_K_Ras_like H-Ras/N 36.0 94 0.002 19.0 4.2 15 25-39 45-59 (162)
219 KOG0446|consensus 35.7 24 0.00053 28.9 1.7 44 28-72 131-174 (657)
220 TIGR00437 feoB ferrous iron tr 35.6 1.6E+02 0.0034 23.8 6.2 27 14-42 28-54 (591)
221 CHL00198 accA acetyl-CoA carbo 35.5 23 0.0005 26.7 1.5 15 26-41 154-168 (322)
222 COG0532 InfB Translation initi 35.5 57 0.0012 26.2 3.6 29 10-39 37-65 (509)
223 PTZ00416 elongation factor 2; 35.2 31 0.00068 28.9 2.3 15 28-42 91-105 (836)
224 cd04105 SR_beta Signal recogni 35.2 55 0.0012 22.1 3.2 14 28-41 47-60 (203)
225 cd01387 MYSc_type_XV Myosin mo 35.1 72 0.0015 26.3 4.3 36 28-65 360-396 (677)
226 cd01378 MYSc_type_I Myosin mot 35.0 66 0.0014 26.4 4.1 36 27-64 364-400 (674)
227 PRK12739 elongation factor G; 34.6 38 0.00083 27.6 2.6 28 12-41 58-85 (691)
228 cd01900 YchF YchF subfamily. 34.4 35 0.00076 24.9 2.2 14 27-40 60-73 (274)
229 KOG1954|consensus 34.2 20 0.00044 28.3 0.9 33 29-61 147-183 (532)
230 PRK05306 infB translation init 34.1 55 0.0012 27.5 3.5 14 29-42 337-350 (787)
231 cd01380 MYSc_type_V Myosin mot 34.0 66 0.0014 26.5 3.9 35 28-64 367-402 (691)
232 cd01379 MYSc_type_III Myosin m 33.8 72 0.0016 26.2 4.1 35 28-64 372-407 (653)
233 PRK12319 acetyl-CoA carboxylas 33.4 27 0.00059 25.3 1.5 16 25-41 97-112 (256)
234 PF15016 DUF4520: Domain of un 33.4 29 0.00063 21.2 1.4 13 73-85 19-31 (85)
235 TIGR03779 Bac_Flav_CT_M Bacter 33.3 71 0.0015 25.0 3.8 29 11-39 304-332 (410)
236 PF08189 Meleagrin: Meleagrin/ 33.3 29 0.00062 18.2 1.2 11 75-85 25-35 (39)
237 cd04172 Rnd3_RhoE_Rho8 Rnd3/Rh 33.2 1.5E+02 0.0032 19.7 5.2 19 21-39 45-63 (182)
238 PF00460 Flg_bb_rod: Flagella 33.2 14 0.00031 18.2 0.0 6 34-39 25-30 (31)
239 cd04131 Rnd Rnd subfamily. Th 33.1 1.4E+02 0.0031 19.5 5.4 19 21-39 41-59 (178)
240 PRK11058 GTPase HflX; Provisio 33.1 46 0.00099 25.7 2.7 26 11-39 230-255 (426)
241 cd01383 MYSc_type_VIII Myosin 33.0 83 0.0018 25.9 4.3 34 29-64 365-399 (677)
242 cd01382 MYSc_type_VI Myosin mo 32.5 67 0.0014 26.6 3.7 34 29-64 397-431 (717)
243 PRK12685 flgB flagellar basal 32.3 18 0.00039 23.0 0.3 8 33-40 32-39 (116)
244 cd00878 Arf_Arl Arf (ADP-ribos 32.1 70 0.0015 19.8 3.1 14 28-41 42-55 (158)
245 PRK07182 flgB flagellar basal 32.0 19 0.00041 23.8 0.5 7 34-40 33-39 (148)
246 PHA02857 monoglyceride lipase; 31.9 54 0.0012 22.4 2.8 18 29-46 53-70 (276)
247 PF11567 PfUIS3: Plasmodium fa 31.4 51 0.0011 20.6 2.3 18 51-68 83-100 (101)
248 cd04151 Arl1 Arl1 subfamily. 31.3 40 0.00086 21.2 1.9 13 28-40 42-54 (158)
249 KOG2655|consensus 31.2 39 0.00084 26.0 2.0 74 11-84 217-292 (366)
250 cd01381 MYSc_type_VII Myosin m 31.1 87 0.0019 25.8 4.1 35 28-64 361-396 (671)
251 cd01386 MYSc_type_XVIII Myosin 31.0 83 0.0018 26.4 4.0 36 29-64 373-413 (767)
252 TIGR01947 rnfG electron transp 31.0 31 0.00067 23.5 1.4 20 25-44 106-128 (186)
253 cd04158 ARD1 ARD1 subfamily. 30.8 78 0.0017 20.2 3.2 14 28-41 42-55 (169)
254 cd04173 Rnd2_Rho7 Rnd2/Rho7 su 30.7 99 0.0021 21.5 3.9 21 20-40 40-60 (222)
255 TIGR03319 YmdA_YtgF conserved 30.7 41 0.00089 26.8 2.2 33 28-64 235-267 (514)
256 PF09439 SRPRB: Signal recogni 30.4 18 0.00039 24.9 0.1 15 28-42 48-62 (181)
257 PLN03230 acetyl-coenzyme A car 30.3 32 0.00069 27.1 1.5 14 26-40 221-234 (431)
258 cd01873 RhoBTB RhoBTB subfamil 30.3 54 0.0012 22.1 2.5 16 24-39 61-76 (195)
259 cd04153 Arl5_Arl8 Arl5/Arl8 su 30.1 75 0.0016 20.4 3.1 13 28-40 58-70 (174)
260 PRK13351 elongation factor G; 29.1 35 0.00076 27.7 1.6 15 28-42 72-86 (687)
261 PLN00116 translation elongatio 29.0 29 0.00062 29.1 1.1 15 28-42 97-111 (843)
262 TIGR03874 4cys_cytochr c-type 29.0 41 0.00088 22.5 1.6 26 35-60 91-116 (143)
263 cd01384 MYSc_type_XI Myosin mo 28.7 1E+02 0.0023 25.4 4.2 35 28-64 366-401 (674)
264 PF14038 YqzE: YqzE-like prote 28.3 65 0.0014 18.1 2.1 17 50-66 3-19 (54)
265 PRK06003 flgB flagellar basal 28.2 23 0.00051 22.7 0.4 7 34-40 31-37 (126)
266 KOG1145|consensus 28.2 66 0.0014 26.6 2.9 32 5-39 180-211 (683)
267 KOG0095|consensus 27.8 1.6E+02 0.0034 20.5 4.4 26 12-39 41-66 (213)
268 PRK12298 obgE GTPase CgtA; Rev 27.6 44 0.00095 25.5 1.8 12 30-41 208-219 (390)
269 COG4604 CeuD ABC-type enteroch 27.5 33 0.00071 24.9 1.1 51 23-73 82-142 (252)
270 cd04159 Arl10_like Arl10-like 27.3 1.1E+02 0.0024 18.4 3.4 12 29-40 44-55 (159)
271 PF02089 Palm_thioest: Palmito 27.2 49 0.0011 24.4 1.9 29 33-61 8-36 (279)
272 COG0825 AccA Acetyl-CoA carbox 27.0 37 0.00079 25.6 1.3 11 30-40 153-163 (317)
273 PF14149 YhfH: YhfH-like prote 26.7 53 0.0012 17.1 1.5 14 53-66 20-33 (37)
274 PF01797 Y1_Tnp: Transposase I 26.7 29 0.00063 21.1 0.6 12 48-59 110-121 (121)
275 PLN00223 ADP-ribosylation fact 26.6 1E+02 0.0022 20.2 3.3 12 28-39 60-71 (181)
276 PRK15494 era GTPase Era; Provi 26.3 44 0.00096 24.7 1.6 12 30-41 101-112 (339)
277 PRK09866 hypothetical protein; 25.5 43 0.00093 28.1 1.5 27 15-41 215-242 (741)
278 cd04156 ARLTS1 ARLTS1 subfamil 25.5 1E+02 0.0022 19.0 3.1 13 28-40 43-55 (160)
279 PRK01908 electron transport co 25.4 41 0.00088 23.5 1.2 12 34-45 122-133 (205)
280 KOG0464|consensus 25.2 82 0.0018 25.5 2.9 29 11-41 86-114 (753)
281 PTZ00133 ADP-ribosylation fact 25.0 1E+02 0.0022 20.2 3.1 13 28-40 60-72 (182)
282 KOG0078|consensus 24.9 2.6E+02 0.0056 19.9 5.4 32 9-40 41-72 (207)
283 cd04143 Rhes_like Rhes_like su 24.7 1.5E+02 0.0032 20.9 4.0 16 25-40 44-59 (247)
284 PF11144 DUF2920: Protein of u 24.6 48 0.0011 25.8 1.6 33 28-61 33-65 (403)
285 cd01896 DRG The developmentall 24.5 56 0.0012 22.8 1.8 12 29-40 47-58 (233)
286 KOG0395|consensus 24.5 1.8E+02 0.0038 19.9 4.2 27 11-38 34-60 (196)
287 PRK11126 2-succinyl-6-hydroxy- 24.2 1.4E+02 0.0029 19.8 3.6 16 29-44 28-43 (242)
288 PRK09554 feoB ferrous iron tra 24.1 1.4E+02 0.0031 25.0 4.3 14 29-42 50-63 (772)
289 PF10662 PduV-EutP: Ethanolami 23.7 36 0.00078 22.6 0.6 7 32-38 39-45 (143)
290 PHA02130 hypothetical protein 23.5 37 0.00081 20.1 0.6 20 47-66 14-33 (81)
291 TIGR03100 hydr1_PEP hydrolase, 23.3 2.3E+02 0.005 19.8 4.8 33 29-61 58-90 (274)
292 COG1160 Predicted GTPases [Gen 23.3 1.3E+02 0.0028 23.8 3.7 32 29-65 51-82 (444)
293 TIGR03680 eif2g_arch translati 23.2 55 0.0012 24.8 1.6 12 28-39 79-90 (406)
294 PLN02824 hydrolase, alpha/beta 23.1 2E+02 0.0043 19.9 4.4 12 31-42 58-69 (294)
295 KOG0468|consensus 22.8 1E+02 0.0022 26.3 3.1 31 10-40 175-208 (971)
296 PF07885 Ion_trans_2: Ion chan 22.7 58 0.0013 18.5 1.4 17 34-50 36-52 (79)
297 PRK04000 translation initiatio 22.7 57 0.0012 24.9 1.6 13 29-41 85-97 (411)
298 PF06500 DUF1100: Alpha/beta h 22.5 1.1E+02 0.0024 23.9 3.1 30 29-58 219-254 (411)
299 cd01899 Ygr210 Ygr210 subfamil 22.2 54 0.0012 24.3 1.4 11 29-39 69-79 (318)
300 PRK15467 ethanolamine utilizat 22.2 35 0.00077 22.0 0.4 9 33-41 41-49 (158)
301 KOG0097|consensus 22.1 1.3E+02 0.0028 20.7 3.1 30 10-39 41-70 (215)
302 PF09623 Cas_NE0113: CRISPR-as 22.1 58 0.0013 23.2 1.5 10 76-85 111-120 (224)
303 COG1161 Predicted GTPases [Gen 22.1 51 0.0011 24.4 1.2 10 31-40 179-188 (322)
304 PF11342 DUF3144: Protein of u 21.8 1E+02 0.0023 18.5 2.4 19 49-67 55-73 (78)
305 COG2869 NqrC Na+-transporting 21.8 51 0.0011 24.2 1.1 16 34-50 176-191 (264)
306 PF04670 Gtr1_RagA: Gtr1/RagA 21.7 64 0.0014 22.9 1.6 35 9-46 31-65 (232)
307 PTZ00014 myosin-A; Provisional 21.6 1.5E+02 0.0033 25.1 4.0 35 28-64 461-496 (821)
308 KOG4742|consensus 21.5 36 0.00078 25.4 0.4 11 33-43 234-244 (286)
309 KOG0079|consensus 21.5 1.7E+02 0.0037 20.3 3.6 25 12-38 42-66 (198)
310 PF01039 Carboxyl_trans: Carbo 21.3 72 0.0016 25.0 2.0 36 26-64 329-364 (493)
311 TIGR02729 Obg_CgtA Obg family 21.1 70 0.0015 23.7 1.8 12 29-40 205-216 (329)
312 PRK09601 GTP-binding protein Y 21.1 60 0.0013 24.8 1.5 15 27-41 64-78 (364)
313 PRK12297 obgE GTPase CgtA; Rev 21.0 68 0.0015 24.9 1.8 13 29-41 206-218 (424)
314 PRK06004 flgB flagellar basal 20.9 38 0.00083 21.8 0.3 7 34-40 23-29 (127)
315 cd00879 Sar1 Sar1 subfamily. 20.7 1.3E+02 0.0029 19.3 3.0 12 29-40 63-74 (190)
316 COG1815 FlgB Flagellar basal b 20.6 40 0.00087 22.2 0.4 8 33-40 31-38 (133)
317 COG4108 PrfC Peptide chain rel 20.6 1E+02 0.0022 24.8 2.7 29 12-42 66-94 (528)
318 TIGR03695 menH_SHCHC 2-succiny 20.5 2.3E+02 0.0051 17.8 4.1 27 29-55 28-58 (251)
319 PF09547 Spore_IV_A: Stage IV 20.5 73 0.0016 25.5 1.8 17 24-40 86-102 (492)
320 PRK12620 flgB flagellar basal 20.3 41 0.00088 21.5 0.4 7 34-40 33-39 (132)
321 TIGR02240 PHA_depoly_arom poly 20.2 2.4E+02 0.0053 19.3 4.3 29 29-57 52-82 (276)
No 1
>KOG1547|consensus
Probab=100.00 E-value=7.4e-33 Score=198.98 Aligned_cols=78 Identities=44% Similarity=0.710 Sum_probs=75.9
Q ss_pred CCCcceEEEEEEEEEeecCeEEEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhhhcCCccC-CCCCCeeEEeec
Q psy104 8 RQGKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGLNRK-NIVDNREVVDKS 85 (86)
Q Consensus 8 ~~~~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~eE~~i~R~-~~~D~RVH~Cl~ 85 (86)
+++||.+|...+..++|+|++++|||||||||||++||++||+||++||.+||++||++|..+.|+ .++|+||||||.
T Consensus 83 p~pkT~eik~~thvieE~gVklkltviDTPGfGDqInN~ncWePI~kyIneQye~yL~eElni~R~kripDTRVHccly 161 (336)
T KOG1547|consen 83 PIPKTTEIKSITHVIEEKGVKLKLTVIDTPGFGDQINNDNCWEPIEKYINEQYEQYLREELNIAREKRIPDTRVHCCLY 161 (336)
T ss_pred cccceEEEEeeeeeeeecceEEEEEEecCCCcccccCccchhHHHHHHHHHHHHHHHHHHHhHHhhhcCCCceEEEEEE
Confidence 789999999999999999999999999999999999999999999999999999999999999996 899999999984
No 2
>KOG2655|consensus
Probab=99.97 E-value=4.5e-31 Score=196.70 Aligned_cols=82 Identities=48% Similarity=0.790 Sum_probs=78.8
Q ss_pred cCCCCCCcceEEEEEEEEEeecCeEEEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhhhcCCccCCCCCCeeEEe
Q psy104 4 RGNNRQGKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGLNRKNIVDNREVVD 83 (86)
Q Consensus 4 ~~~~~~~~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~eE~~i~R~~~~D~RVH~C 83 (86)
.|+.++.+|+.|..+++.|+|+|++++|||||||||||.+||+.||.||++||++||++||.+|++++|.++.|+|||||
T Consensus 54 ~~~~~~~~t~~i~~~~~~iee~g~~l~LtvidtPGfGD~vdns~~w~pi~~yi~~q~~~yl~~E~~~~R~~~~D~RVH~c 133 (366)
T KOG2655|consen 54 GASERIKETVEIESTKVEIEENGVKLNLTVIDTPGFGDAVDNSNCWRPIVNYIDSQFDQYLDEESRLNRSKIKDNRVHCC 133 (366)
T ss_pred CcccCccccceeeeeeeeecCCCeEEeeEEeccCCCcccccccccchhhhHHHHHHHHHHHhhhccCCcccccCCceEEE
Confidence 36678888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ec
Q psy104 84 KS 85 (86)
Q Consensus 84 l~ 85 (86)
|.
T Consensus 134 LY 135 (366)
T KOG2655|consen 134 LY 135 (366)
T ss_pred EE
Confidence 94
No 3
>COG5019 CDC3 Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]
Probab=99.96 E-value=7.8e-30 Score=189.81 Aligned_cols=77 Identities=39% Similarity=0.689 Sum_probs=75.0
Q ss_pred CCcceEEEEEEEEEeecCeEEEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhhhcCCccC-CCCCCeeEEeec
Q psy104 9 QGKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGLNRK-NIVDNREVVDKS 85 (86)
Q Consensus 9 ~~~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~eE~~i~R~-~~~D~RVH~Cl~ 85 (86)
.++++.|..++..|.|+|++++|||||||||||.+||+.||.||++||++||++||.+|+++.|+ ++.|+||||||.
T Consensus 62 ~~~~~~i~~~~~~l~e~~~~~~l~vIDtpGfGD~idNs~~we~I~~yI~~q~d~yl~~E~~~~R~~~~~D~RVH~cLY 139 (373)
T COG5019 62 TSPTLEIKITKAELEEDGFHLNLTVIDTPGFGDFIDNSKCWEPIVDYIDDQFDQYLDEEQKIKRNPKFKDTRVHACLY 139 (373)
T ss_pred CCcceEEEeeeeeeecCCeEEEEEEeccCCccccccccccHHHHHHHHHHHHHHHHHHhhccccccccccCceEEEEE
Confidence 67899999999999999999999999999999999999999999999999999999999999998 999999999994
No 4
>PF00735 Septin: Septin; InterPro: IPR000038 Septins constitute a eukaryotic family of guanine nucleotide-binding proteins, most of which polymerise to form filaments []. Members of the family were first identified by genetic screening for Saccharomyces cerevisiae (Baker's yeast) mutants defective in cytokinesis []. Temperature-sensitive mutations in four genes, CDC3, CDC10, CDC11 and CDC12, were found to cause cell-cycle arrest and defects in bud growth and cytokinesis. The protein products of these genes localise at the division plane between mother and daughter cells, indicating a role in mother-daughter separation during cytokinesis []. Members of the family were therefore termed septins to reflect their role in septation and cell division. The identification of septin homologues in higher eukaryotes, which localise to the cleavage furrow in dividing cells, supports an orthologous function in cytokinesis. Septins have since been identified in most eukaryotes, except plants []. Septins are approximately 40-50 kDa in molecular mass, and typically comprise a conserved central core domain (more than 35% sequence identity between mammalian and yeast homologues) flanked by more divergent N- and C-termini. Most septins possess a P-loop motif in their N-terminal domain (which is characteristic of GTP-binding proteins), and a predicted C-terminal coiled-coil domain []. A number of septin interaction partners have been identified in yeast, many of which are components of the budding site selection machinery, kinase cascades or of the ubiquitination pathway. It has been proposed that septins may act as a scaffold that provides an interaction matrix for other proteins [, ]. In mammals, septins have been shown to regulate vesicle dynamics []. Mammalian septins have also been implicated in a variety of other cellular processes, including apoptosis, carcinogenesis and neurodegeneration []. This entry represents a variety of septins and homologous sequences involved in the cell division process.; GO: 0005525 GTP binding, 0007049 cell cycle; PDB: 2QAG_B 3FTQ_D 2QA5_A 2QNR_B 3TW4_A 3T5D_C.
Probab=99.94 E-value=6.4e-27 Score=169.47 Aligned_cols=80 Identities=40% Similarity=0.751 Sum_probs=67.2
Q ss_pred CCCCCcceEEEEEEEEEeecCeEEEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhhhcCCccCCCCCCeeEEeec
Q psy104 6 NNRQGKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGLNRKNIVDNREVVDKS 85 (86)
Q Consensus 6 ~~~~~~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~eE~~i~R~~~~D~RVH~Cl~ 85 (86)
.++..++..|..+++.++|++++++|+|||||||||.++|+.+|.+|++||++||+.||.+|.++.|..+.|+||||||.
T Consensus 40 ~~~~~~~~~i~~~~~~l~e~~~~l~LtiiDTpGfGd~i~n~~~~~~I~~yI~~qf~~~l~eE~~~~R~~~~D~RVH~cLY 119 (281)
T PF00735_consen 40 SASISRTLEIEERTVELEENGVKLNLTIIDTPGFGDNIDNSDCWEPIVDYIESQFDSYLEEESKINRPRIEDTRVHACLY 119 (281)
T ss_dssp -----SCEEEEEEEEEEEETCEEEEEEEEEEC-CSSSSTHCHHHHHHHHHHHHHHHHHHHHHTSSS-TTS----EEEEEE
T ss_pred ccccccccceeeEEEEeccCCcceEEEEEeCCCccccccchhhhHHHHHHHHHHHHHHHHHhhcccccCcCCCCcceEEE
Confidence 34677889999999999999999999999999999999999999999999999999999999999999999999999994
No 5
>KOG3859|consensus
Probab=99.92 E-value=6.6e-26 Score=165.94 Aligned_cols=84 Identities=33% Similarity=0.571 Sum_probs=79.1
Q ss_pred CccCCCCCCcceEEEEEEEEEeecCeEEEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhhhcCCccC--CCCCCe
Q psy104 2 EKRGNNRQGKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGLNRK--NIVDNR 79 (86)
Q Consensus 2 ~~~~~~~~~~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~eE~~i~R~--~~~D~R 79 (86)
+..++.|.-+++.+...++++.|.+++++|||+||.||||++|.+.|++||++||++||+.||++|.+|.|. .+.|+|
T Consensus 68 ~~~p~~H~~~~V~L~~~TyelqEsnvrlKLtiv~tvGfGDQinK~~Syk~iVdyidaQFEaYLQEELKi~Rsl~~~hDsR 147 (406)
T KOG3859|consen 68 ESEPSTHTLPNVKLQANTYELQESNVRLKLTIVDTVGFGDQINKEDSYKPIVDYIDAQFEAYLQEELKIRRSLFTYHDSR 147 (406)
T ss_pred CCCCCccCCCCceeecchhhhhhcCeeEEEEEEeecccccccCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhccCc
Confidence 345677888899999999999999999999999999999999999999999999999999999999999997 789999
Q ss_pred eEEeec
Q psy104 80 EVVDKS 85 (86)
Q Consensus 80 VH~Cl~ 85 (86)
||+||.
T Consensus 148 iH~CLY 153 (406)
T KOG3859|consen 148 IHVCLY 153 (406)
T ss_pred eEEEEE
Confidence 999994
No 6
>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=99.87 E-value=6.9e-22 Score=142.52 Aligned_cols=78 Identities=47% Similarity=0.791 Sum_probs=73.8
Q ss_pred CCCcceEEEEEEEEEeecCeEEEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhhhcCCcc-CCCCCCeeEEeec
Q psy104 8 RQGKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGLNR-KNIVDNREVVDKS 85 (86)
Q Consensus 8 ~~~~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~eE~~i~R-~~~~D~RVH~Cl~ 85 (86)
+..+|+.+..+...++++|++++|+|+|||||||.++|+.+|++|++||++||+.||.+|.++.| ..+.|+||||||.
T Consensus 42 ~~~~T~~i~~~~~~i~~~g~~~~l~iiDTpGfgd~~~~~~~~~~i~~yi~~q~~~~l~~e~~~~r~~~~~d~rvh~~ly 120 (276)
T cd01850 42 HIDKTVEIKSSKAEIEENGVKLKLTVIDTPGFGDNINNSDCWKPIVDYIDDQFDQYLREESRIKRNPRIPDTRVHACLY 120 (276)
T ss_pred ccCCceEEEEEEEEEEECCEEEEEEEEecCCccccccchhhHHHHHHHHHHHHHHHHHHHhhhcccccCCCCceEEEEE
Confidence 46788899999999999999999999999999999999999999999999999999999999999 5899999999984
No 7
>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=95.05 E-value=0.032 Score=37.66 Aligned_cols=31 Identities=39% Similarity=0.502 Sum_probs=20.4
Q ss_pred CcceEEEEEEEEEeecCeEEEEEEEeCCCCCCccC
Q psy104 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSIN 44 (86)
Q Consensus 10 ~~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~i~ 44 (86)
+.|...+.+...+. + ..++|||||||++...
T Consensus 34 ~~T~~~~~~~~~~~--~--~~i~viDTPG~~d~~~ 64 (196)
T cd01852 34 SVTKTCQKESAVWD--G--RRVNVIDTPGLFDTSV 64 (196)
T ss_pred CcccccceeeEEEC--C--eEEEEEECcCCCCccC
Confidence 34555555555442 2 4689999999998754
No 8
>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=94.99 E-value=0.059 Score=38.61 Aligned_cols=15 Identities=40% Similarity=0.941 Sum_probs=12.5
Q ss_pred EEEEEEeCCCCCCcc
Q psy104 29 LRLTVVDTPGFGDSI 43 (86)
Q Consensus 29 l~LtIidTpGfGd~i 43 (86)
.++++|||||||+..
T Consensus 79 ~~i~vIDTPGl~~~~ 93 (249)
T cd01853 79 FKLNIIDTPGLLESV 93 (249)
T ss_pred eEEEEEECCCcCcch
Confidence 457999999999773
No 9
>PF04548 AIG1: AIG1 family; InterPro: IPR006703 This entry represents a domain found in Arabidopsis protein AIG1 which 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 (avrRpt2-induced gene) exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2 []. The domain is also apparently found in a number of mammalian proteins, for example the rat immune-associated nucleotide 4 protein. ; GO: 0005525 GTP binding; PDB: 3LXX_A 3BB4_A 3DEF_A 3BB3_A 2J3E_A 3V70_B 3BB1_A 1H65_B 2XTP_A 3P1J_C ....
Probab=94.92 E-value=0.028 Score=38.84 Aligned_cols=29 Identities=45% Similarity=0.491 Sum_probs=15.6
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCCCccC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFGDSIN 44 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~i~ 44 (86)
|.....+.. ..+| ..++|||||||+|.-.
T Consensus 36 t~~~~~~~~--~~~g--~~v~VIDTPGl~d~~~ 64 (212)
T PF04548_consen 36 TQECQKYSG--EVDG--RQVTVIDTPGLFDSDG 64 (212)
T ss_dssp -SS-EEEEE--EETT--EEEEEEE--SSEETTE
T ss_pred ccccceeee--eecc--eEEEEEeCCCCCCCcc
Confidence 344444444 3334 5678999999987654
No 10
>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=94.52 E-value=0.042 Score=39.52 Aligned_cols=42 Identities=21% Similarity=0.430 Sum_probs=31.3
Q ss_pred EEEEEeCCCC-----CCc----------------cCCccchhHHHHHHHHHHHHhhhhhcCCc
Q psy104 30 RLTVVDTPGF-----GDS----------------INSEESWRACCSYIDDQFRQYFNDESGLN 71 (86)
Q Consensus 30 ~LtIidTpGf-----Gd~----------------i~n~~~~~~i~~yI~~qf~~yl~eE~~i~ 71 (86)
.+.++||||+ ++. ++....+..+..||..++..++.+.-++.
T Consensus 164 ~~~l~DtPG~~~~~~~~~~~~~~l~~~g~i~~~~~~~~~~~~~~~~~l~~~~~~~l~~~y~i~ 226 (276)
T TIGR03596 164 GLELLDTPGILWPKFEDQEVGLKLAATGAIKDEALDLEDVALFLLEYLLEHYPERLKERYKLD 226 (276)
T ss_pred CEEEEECCCcccCCCCchHHHHHHHHhCCcccccCChHHHHHHHHHHHHhhCHHHHHHHhCcC
Confidence 5689999999 443 55566677888899998887777665543
No 11
>TIGR00991 3a0901s02IAP34 GTP-binding protein (Chloroplast Envelope Protein Translocase).
Probab=93.93 E-value=0.11 Score=38.82 Aligned_cols=14 Identities=36% Similarity=0.821 Sum_probs=12.1
Q ss_pred EEEEEEeCCCCCCc
Q psy104 29 LRLTVVDTPGFGDS 42 (86)
Q Consensus 29 l~LtIidTpGfGd~ 42 (86)
.+|+||||||+.+.
T Consensus 86 ~~l~VIDTPGL~d~ 99 (313)
T TIGR00991 86 FTLNIIDTPGLIEG 99 (313)
T ss_pred eEEEEEECCCCCch
Confidence 57899999999874
No 12
>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=93.37 E-value=0.14 Score=36.69 Aligned_cols=40 Identities=25% Similarity=0.367 Sum_probs=27.6
Q ss_pred EEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhhhcC
Q psy104 29 LRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESG 69 (86)
Q Consensus 29 l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~eE~~ 69 (86)
..|++||||||-..-. ...-..+...+.++.+.|++++..
T Consensus 125 ~~ltLIDlPGl~~~~~-~~~~~~~~~~i~~lv~~yi~~~~~ 164 (240)
T smart00053 125 LNLTLIDLPGITKVAV-GDQPPDIEEQIKDMIKQFISKEEC 164 (240)
T ss_pred CceEEEeCCCcccccc-CCccHHHHHHHHHHHHHHHhCccC
Confidence 6899999999953211 111234677888899999887653
No 13
>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=92.96 E-value=0.42 Score=29.86 Aligned_cols=15 Identities=33% Similarity=0.733 Sum_probs=13.1
Q ss_pred EEEEEeCCCCCCccC
Q psy104 30 RLTVVDTPGFGDSIN 44 (86)
Q Consensus 30 ~LtIidTpGfGd~i~ 44 (86)
.+.++||||||+...
T Consensus 46 ~~~~~D~~g~~~~~~ 60 (170)
T cd01876 46 KFRLVDLPGYGYAKV 60 (170)
T ss_pred eEEEecCCCcccccc
Confidence 899999999998754
No 14
>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=92.01 E-value=0.91 Score=28.29 Aligned_cols=16 Identities=19% Similarity=0.289 Sum_probs=13.0
Q ss_pred EEEEEEeCCCCCCccC
Q psy104 29 LRLTVVDTPGFGDSIN 44 (86)
Q Consensus 29 l~LtIidTpGfGd~i~ 44 (86)
..|.++||||+++...
T Consensus 45 ~~~~i~DtpG~~~~~~ 60 (157)
T cd01894 45 REFILIDTGGIEPDDE 60 (157)
T ss_pred eEEEEEECCCCCCchh
Confidence 5789999999987543
No 15
>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=91.24 E-value=0.099 Score=33.83 Aligned_cols=15 Identities=47% Similarity=0.744 Sum_probs=12.2
Q ss_pred EEEEEEEeCCCCCCc
Q psy104 28 KLRLTVVDTPGFGDS 42 (86)
Q Consensus 28 ~l~LtIidTpGfGd~ 42 (86)
...+++|||||+++.
T Consensus 100 ~~~~~lvDtPG~~~~ 114 (168)
T PF00350_consen 100 LRNLTLVDTPGLNST 114 (168)
T ss_dssp SCSEEEEEEEEBHSS
T ss_pred ccceEEEeCCccccc
Confidence 356789999999873
No 16
>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=90.86 E-value=0.26 Score=30.20 Aligned_cols=14 Identities=43% Similarity=0.778 Sum_probs=10.8
Q ss_pred EEEEeCCCCCCccC
Q psy104 31 LTVVDTPGFGDSIN 44 (86)
Q Consensus 31 LtIidTpGfGd~i~ 44 (86)
+.++|||||++...
T Consensus 49 ~~~vDtpG~~~~~~ 62 (116)
T PF01926_consen 49 FILVDTPGINDGES 62 (116)
T ss_dssp EEEEESSSCSSSSH
T ss_pred EEEEeCCCCcccch
Confidence 36999999986544
No 17
>COG0218 Predicted GTPase [General function prediction only]
Probab=90.48 E-value=0.29 Score=34.47 Aligned_cols=38 Identities=21% Similarity=0.412 Sum_probs=22.9
Q ss_pred EEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhhhcCCcc
Q psy104 31 LTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGLNR 72 (86)
Q Consensus 31 LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~eE~~i~R 72 (86)
+.+||-||||-.--.. ...+-...-..+||+....+.+
T Consensus 72 ~~lVDlPGYGyAkv~k----~~~e~w~~~i~~YL~~R~~L~~ 109 (200)
T COG0218 72 LRLVDLPGYGYAKVPK----EVKEKWKKLIEEYLEKRANLKG 109 (200)
T ss_pred EEEEeCCCcccccCCH----HHHHHHHHHHHHHHhhchhheE
Confidence 7799999999654332 2344444455556665444544
No 18
>TIGR00993 3a0901s04IAP86 chloroplast protein import component Toc86/159, G and M domains. The long precursor of the 86K protein originally described is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation. The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M.
Probab=90.14 E-value=0.63 Score=38.50 Aligned_cols=15 Identities=40% Similarity=0.840 Sum_probs=12.8
Q ss_pred EEEEEEeCCCCCCcc
Q psy104 29 LRLTVVDTPGFGDSI 43 (86)
Q Consensus 29 l~LtIidTpGfGd~i 43 (86)
..|+|||||||++..
T Consensus 166 ~~L~VIDTPGL~dt~ 180 (763)
T TIGR00993 166 VKIRVIDTPGLKSSA 180 (763)
T ss_pred ceEEEEECCCCCccc
Confidence 468999999999874
No 19
>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=89.36 E-value=0.44 Score=31.86 Aligned_cols=10 Identities=40% Similarity=0.670 Sum_probs=8.8
Q ss_pred EEEEEeCCCC
Q psy104 30 RLTVVDTPGF 39 (86)
Q Consensus 30 ~LtIidTpGf 39 (86)
.+.|+|||||
T Consensus 181 ~~~~~DtPG~ 190 (190)
T cd01855 181 GKKLYDTPGI 190 (190)
T ss_pred CCEEEeCcCC
Confidence 5789999997
No 20
>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=85.98 E-value=1 Score=28.18 Aligned_cols=15 Identities=27% Similarity=0.346 Sum_probs=11.9
Q ss_pred EEEEEEeCCCCCCcc
Q psy104 29 LRLTVVDTPGFGDSI 43 (86)
Q Consensus 29 l~LtIidTpGfGd~i 43 (86)
..+.++||||+.+..
T Consensus 43 ~~~~liDtpG~~~~~ 57 (158)
T cd01879 43 KEIEIVDLPGTYSLS 57 (158)
T ss_pred eEEEEEECCCccccC
Confidence 478999999987543
No 21
>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=84.50 E-value=0.75 Score=34.47 Aligned_cols=34 Identities=24% Similarity=0.464 Sum_probs=22.6
Q ss_pred EEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhhhcCCc
Q psy104 31 LTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGLN 71 (86)
Q Consensus 31 LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~eE~~i~ 71 (86)
+.++|||||+.. ..+.++++.+-..++.....++
T Consensus 206 ~~l~DtPG~~~~-------~~~~~~l~~~~l~~~~~~~~i~ 239 (360)
T TIGR03597 206 HSLYDTPGIINS-------HQMAHYLDKKDLKYITPKKEIK 239 (360)
T ss_pred CEEEECCCCCCh-------hHhhhhcCHHHHhhcCCCCccC
Confidence 469999999854 2346677766666665544444
No 22
>PTZ00099 rab6; Provisional
Probab=83.54 E-value=5 Score=26.79 Aligned_cols=34 Identities=26% Similarity=0.170 Sum_probs=22.5
Q ss_pred CCCCcceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 7 NRQGKTTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 7 ~~~~~t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
+...+|+.+.-+...+.-++-.++|.|.||||..
T Consensus 7 ~~~~~Tig~~~~~~~~~~~~~~v~l~iwDt~G~e 40 (176)
T PTZ00099 7 NNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQE 40 (176)
T ss_pred CCCCCccceEEEEEEEEECCEEEEEEEEECCChH
Confidence 3445566555544444445668999999999964
No 23
>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=83.05 E-value=5.5 Score=25.01 Aligned_cols=29 Identities=28% Similarity=0.223 Sum_probs=19.1
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
+.........+..++..++|.+.||||-.
T Consensus 32 ~~~~~~~~~~~~~~~~~~~l~~~D~~G~~ 60 (161)
T cd01861 32 TIGIDFLSKTMYLEDKTVRLQLWDTAGQE 60 (161)
T ss_pred ceeeeEEEEEEEECCEEEEEEEEECCCcH
Confidence 33333344445556677899999999954
No 24
>COG4659 RnfG Predicted NADH:ubiquinone oxidoreductase, subunit RnfG [Energy production and conversion]
Probab=82.14 E-value=1.9 Score=30.35 Aligned_cols=28 Identities=43% Similarity=0.812 Sum_probs=21.2
Q ss_pred EeecCeEEEEEEE---eCCCCCCccCCccc-h
Q psy104 22 IEERGVKLRLTVV---DTPGFGDSINSEES-W 49 (86)
Q Consensus 22 l~e~~~~l~LtIi---dTpGfGd~i~n~~~-~ 49 (86)
+..+|.-+.++|+ +|||+||.|+-+-| |
T Consensus 109 i~~~G~vlGvRVi~h~ETPGLGdKI~~~~s~W 140 (195)
T COG4659 109 IDFDGTVLGVRVIEHHETPGLGDKIELRISDW 140 (195)
T ss_pred EcCCCeEEEEEEEeccCCCCchhhhcchhhcc
Confidence 4567766777777 59999999998643 5
No 25
>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=81.83 E-value=1.3 Score=27.54 Aligned_cols=16 Identities=19% Similarity=0.547 Sum_probs=12.6
Q ss_pred EEEEEEeCCCCCCccC
Q psy104 29 LRLTVVDTPGFGDSIN 44 (86)
Q Consensus 29 l~LtIidTpGfGd~i~ 44 (86)
.+++++||||+++...
T Consensus 49 ~~~~i~DtpG~~~~~~ 64 (157)
T cd04164 49 IPVRLIDTAGIRETED 64 (157)
T ss_pred EEEEEEECCCcCCCcc
Confidence 4678999999986543
No 26
>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=81.46 E-value=0.94 Score=28.95 Aligned_cols=11 Identities=36% Similarity=0.727 Sum_probs=9.5
Q ss_pred EEEEEeCCCCC
Q psy104 30 RLTVVDTPGFG 40 (86)
Q Consensus 30 ~LtIidTpGfG 40 (86)
.+.++|||||-
T Consensus 129 ~~~i~DtpG~~ 139 (141)
T cd01857 129 TITLCDCPGLV 139 (141)
T ss_pred CEEEEECCCcC
Confidence 57899999984
No 27
>COG3596 Predicted GTPase [General function prediction only]
Probab=81.04 E-value=1.7 Score=32.31 Aligned_cols=18 Identities=39% Similarity=0.717 Sum_probs=15.1
Q ss_pred EEEEEEeCCCCCCccCCc
Q psy104 29 LRLTVVDTPGFGDSINSE 46 (86)
Q Consensus 29 l~LtIidTpGfGd~i~n~ 46 (86)
=.|++-||||+||...-+
T Consensus 87 ~~l~lwDtPG~gdg~~~D 104 (296)
T COG3596 87 ENLVLWDTPGLGDGKDKD 104 (296)
T ss_pred cceEEecCCCcccchhhh
Confidence 367899999999987765
No 28
>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=80.94 E-value=2.6 Score=28.71 Aligned_cols=18 Identities=28% Similarity=0.586 Sum_probs=14.5
Q ss_pred cCeEEEEEEEeCCCCCCc
Q psy104 25 RGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 25 ~~~~l~LtIidTpGfGd~ 42 (86)
++-.+.++++||||..+.
T Consensus 67 ~~~~~~i~iiDtpG~~~f 84 (213)
T cd04167 67 KGKSYLFNIIDTPGHVNF 84 (213)
T ss_pred CCCEEEEEEEECCCCcch
Confidence 355789999999998754
No 29
>cd01868 Rab11_like Rab11-like. Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP
Probab=80.36 E-value=7.6 Score=24.58 Aligned_cols=30 Identities=23% Similarity=0.306 Sum_probs=19.8
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
+|.........+.-++..+++.+.||||-.
T Consensus 34 ~t~~~~~~~~~~~~~~~~~~~~l~D~~g~~ 63 (165)
T cd01868 34 STIGVEFATRSIQIDGKTIKAQIWDTAGQE 63 (165)
T ss_pred CccceEEEEEEEEECCEEEEEEEEeCCChH
Confidence 344343344455556778899999999954
No 30
>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=80.23 E-value=6.6 Score=23.99 Aligned_cols=31 Identities=32% Similarity=0.384 Sum_probs=22.1
Q ss_pred CcceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 10 ~~t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
.+|.........+.-.+..+.++++|+||.-
T Consensus 30 ~~t~~~~~~~~~~~~~~~~~~~~l~D~~g~~ 60 (159)
T cd00154 30 KSTIGVDFKSKTIEIDGKTVKLQIWDTAGQE 60 (159)
T ss_pred CCceeeeeEEEEEEECCEEEEEEEEecCChH
Confidence 3455566665666656677899999999963
No 31
>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=80.11 E-value=3.4 Score=27.13 Aligned_cols=15 Identities=33% Similarity=0.651 Sum_probs=12.2
Q ss_pred EEEEEeCCCCCCccC
Q psy104 30 RLTVVDTPGFGDSIN 44 (86)
Q Consensus 30 ~LtIidTpGfGd~i~ 44 (86)
.+.++||||||....
T Consensus 65 ~~~liDtpG~~~~~~ 79 (179)
T TIGR03598 65 GFRLVDLPGYGYAKV 79 (179)
T ss_pred cEEEEeCCCCccccC
Confidence 588999999987543
No 32
>PRK00454 engB GTP-binding protein YsxC; Reviewed
Probab=79.98 E-value=3.7 Score=26.87 Aligned_cols=15 Identities=40% Similarity=0.738 Sum_probs=12.5
Q ss_pred EEEEEEeCCCCCCcc
Q psy104 29 LRLTVVDTPGFGDSI 43 (86)
Q Consensus 29 l~LtIidTpGfGd~i 43 (86)
..|.++||||++...
T Consensus 70 ~~l~l~DtpG~~~~~ 84 (196)
T PRK00454 70 DKLRLVDLPGYGYAK 84 (196)
T ss_pred CeEEEeCCCCCCCcC
Confidence 679999999998643
No 33
>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=79.23 E-value=1.7 Score=27.71 Aligned_cols=14 Identities=57% Similarity=0.859 Sum_probs=11.6
Q ss_pred EEEEEEEeCCCCCC
Q psy104 28 KLRLTVVDTPGFGD 41 (86)
Q Consensus 28 ~l~LtIidTpGfGd 41 (86)
.++++++||||+.+
T Consensus 46 ~~~~~i~Dt~G~~~ 59 (168)
T cd01897 46 YLRWQVIDTPGLLD 59 (168)
T ss_pred ceEEEEEECCCcCC
Confidence 36899999999864
No 34
>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=78.39 E-value=8.9 Score=24.78 Aligned_cols=32 Identities=28% Similarity=0.316 Sum_probs=23.4
Q ss_pred CCcceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 9 QGKTTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 9 ~~~t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
..+|..+......+..++-.+.|.+.||||-.
T Consensus 29 ~~~t~~~~~~~~~~~~~~~~~~l~i~Dt~G~~ 60 (166)
T cd00877 29 YVATLGVEVHPLDFHTNRGKIRFNVWDTAGQE 60 (166)
T ss_pred CCCceeeEEEEEEEEECCEEEEEEEEECCCCh
Confidence 34566666666666667778999999999864
No 35
>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=78.14 E-value=8.5 Score=24.46 Aligned_cols=19 Identities=32% Similarity=0.566 Sum_probs=14.3
Q ss_pred EEeecCeEEEEEEEeCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGf 39 (86)
.+.-++..+.|.+.||||.
T Consensus 44 ~~~~~~~~~~l~i~D~~G~ 62 (165)
T cd01864 44 TLEIEGKRVKLQIWDTAGQ 62 (165)
T ss_pred EEEECCEEEEEEEEECCCh
Confidence 3444566789999999995
No 36
>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=77.98 E-value=8.6 Score=24.41 Aligned_cols=20 Identities=35% Similarity=0.504 Sum_probs=14.9
Q ss_pred EEeecCeEEEEEEEeCCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGfG 40 (86)
.+.-++..+.+.++||||.-
T Consensus 43 ~~~~~~~~~~~~i~D~~G~~ 62 (166)
T cd01869 43 TIELDGKTIKLQIWDTAGQE 62 (166)
T ss_pred EEEECCEEEEEEEEECCCcH
Confidence 34445678899999999943
No 37
>PRK04213 GTP-binding protein; Provisional
Probab=77.41 E-value=9.6 Score=25.21 Aligned_cols=15 Identities=33% Similarity=0.596 Sum_probs=12.2
Q ss_pred EEEEEeCCCCCCccC
Q psy104 30 RLTVVDTPGFGDSIN 44 (86)
Q Consensus 30 ~LtIidTpGfGd~i~ 44 (86)
.++++||||+|+...
T Consensus 53 ~~~l~Dt~G~~~~~~ 67 (201)
T PRK04213 53 DFILTDLPGFGFMSG 67 (201)
T ss_pred ceEEEeCCccccccc
Confidence 588999999986544
No 38
>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=77.11 E-value=8.2 Score=24.12 Aligned_cols=20 Identities=20% Similarity=0.405 Sum_probs=15.1
Q ss_pred EEeecCeEEEEEEEeCCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGfG 40 (86)
.+.-++..+.|++.||||..
T Consensus 41 ~~~~~~~~~~l~i~Dt~G~~ 60 (168)
T cd04119 41 KVSVRNKEVRVNFFDLSGHP 60 (168)
T ss_pred EEEECCeEEEEEEEECCccH
Confidence 34444678999999999964
No 39
>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=77.08 E-value=1.8 Score=26.30 Aligned_cols=19 Identities=21% Similarity=0.328 Sum_probs=14.9
Q ss_pred EEEEEEEeCCCCCCccCCc
Q psy104 28 KLRLTVVDTPGFGDSINSE 46 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~n~ 46 (86)
...+.++||||+++.....
T Consensus 44 ~~~~~~~Dt~g~~~~~~~~ 62 (163)
T cd00880 44 LGPVVLIDTPGIDEAGGLG 62 (163)
T ss_pred CCcEEEEECCCCCccccch
Confidence 4688999999999765444
No 40
>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=76.82 E-value=13 Score=25.19 Aligned_cols=20 Identities=20% Similarity=0.375 Sum_probs=15.4
Q ss_pred EEeecCeEEEEEEEeCCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGfG 40 (86)
.+.-++..++|.++||||..
T Consensus 41 ~i~~~~~~~~l~i~Dt~G~~ 60 (198)
T cd04142 41 AVVLSGRVYDLHILDVPNMQ 60 (198)
T ss_pred EEEECCEEEEEEEEeCCCcc
Confidence 34446778999999999965
No 41
>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=76.64 E-value=11 Score=23.69 Aligned_cols=30 Identities=30% Similarity=0.329 Sum_probs=18.8
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
++.........+.-++..++|.+.||||-.
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~l~l~D~~G~~ 60 (161)
T cd04113 31 HTIGVEFGSKIIRVGGKRVKLQIWDTAGQE 60 (161)
T ss_pred CceeeeEEEEEEEECCEEEEEEEEECcchH
Confidence 344443333444444667899999999953
No 42
>cd04168 TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria. Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site. This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative. Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G. EF-G and Tet(M) compete for binding on the ribosomes. Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind. Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity. These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB.
Probab=76.51 E-value=4.8 Score=28.31 Aligned_cols=28 Identities=25% Similarity=0.331 Sum_probs=18.2
Q ss_pred eEEEEEEEEEeecCeEEEEEEEeCCCCCCc
Q psy104 13 TTIEKKSMDIEERGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 13 ~~I~~~~~~l~e~~~~l~LtIidTpGfGd~ 42 (86)
.++......++.++ .+++++||||+.+.
T Consensus 50 ~ti~~~~~~~~~~~--~~i~liDTPG~~~f 77 (237)
T cd04168 50 ITIFSAVASFQWED--TKVNLIDTPGHMDF 77 (237)
T ss_pred CceeeeeEEEEECC--EEEEEEeCCCccch
Confidence 34444444555444 56889999999764
No 43
>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=76.31 E-value=11 Score=26.63 Aligned_cols=13 Identities=38% Similarity=0.940 Sum_probs=10.8
Q ss_pred EEEEEeCCCCCCc
Q psy104 30 RLTVVDTPGFGDS 42 (86)
Q Consensus 30 ~LtIidTpGfGd~ 42 (86)
.+.++||||+...
T Consensus 49 qii~vDTPG~~~~ 61 (270)
T TIGR00436 49 QIIFIDTPGFHEK 61 (270)
T ss_pred EEEEEECcCCCCC
Confidence 5889999999754
No 44
>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=76.00 E-value=11 Score=24.10 Aligned_cols=18 Identities=44% Similarity=0.663 Sum_probs=13.9
Q ss_pred EeecCeEEEEEEEeCCCC
Q psy104 22 IEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGf 39 (86)
+.-++..++|.+.||||-
T Consensus 44 ~~~~~~~~~l~i~Dt~G~ 61 (166)
T cd04122 44 IEVNGQKIKLQIWDTAGQ 61 (166)
T ss_pred EEECCEEEEEEEEECCCc
Confidence 344566889999999984
No 45
>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=75.84 E-value=7.1 Score=24.52 Aligned_cols=23 Identities=26% Similarity=0.387 Sum_probs=16.5
Q ss_pred EEEEEEeecCeEEEEEEEeCCCC
Q psy104 17 KKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 17 ~~~~~l~e~~~~l~LtIidTpGf 39 (86)
...+.+...+..++|.+.||||-
T Consensus 39 ~~~~~~~~~~~~~~~~i~D~~G~ 61 (162)
T cd04106 39 EKQIFLRQSDEDVRLMLWDTAGQ 61 (162)
T ss_pred EEEEEEcCCCCEEEEEEeeCCch
Confidence 34445554467899999999993
No 46
>cd04108 Rab36_Rab34 Rab34/Rab36 subfamily. Rab34, found primarily in the Golgi, interacts with its effector, Rab-interacting lysosomal protein (RILP). This enables its participation in microtubular dynenin-dynactin-mediated repositioning of lysosomes from the cell periphery to the Golgi. A Rab34 (Rah) isoform that lacks the consensus GTP-binding region has been identified in mice. This isoform is associated with membrane ruffles and promotes macropinosome formation. Rab36 has been mapped to human chromosome 22q11.2, a region that is homozygously deleted in malignant rhabdoid tumors (MRTs). However, experimental assessments do not implicate Rab36 as a tumor suppressor that would enable tumor formation through a loss-of-function mechanism. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further re
Probab=75.76 E-value=12 Score=24.34 Aligned_cols=31 Identities=26% Similarity=0.261 Sum_probs=19.4
Q ss_pred CcceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 10 ~~t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
..|.........+.-+|..++|.+.||||.-
T Consensus 30 ~~t~~~~~~~~~~~~~~~~~~l~i~Dt~G~~ 60 (170)
T cd04108 30 KATIGVDFEMERFEILGVPFSLQLWDTAGQE 60 (170)
T ss_pred CCceeeEEEEEEEEECCEEEEEEEEeCCChH
Confidence 3444333333334445778999999999954
No 47
>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=75.22 E-value=2.6 Score=26.03 Aligned_cols=16 Identities=31% Similarity=0.549 Sum_probs=12.6
Q ss_pred EEEEEEEeCCCCCCcc
Q psy104 28 KLRLTVVDTPGFGDSI 43 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i 43 (86)
...+.++||||+++..
T Consensus 50 ~~~~~liDtpG~~~~~ 65 (168)
T cd04163 50 DAQIIFVDTPGIHKPK 65 (168)
T ss_pred CeEEEEEECCCCCcch
Confidence 4678899999998543
No 48
>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=74.91 E-value=5.7 Score=24.81 Aligned_cols=14 Identities=29% Similarity=0.465 Sum_probs=11.2
Q ss_pred EEEEEeCCCCCCcc
Q psy104 30 RLTVVDTPGFGDSI 43 (86)
Q Consensus 30 ~LtIidTpGfGd~i 43 (86)
.++++||||+++..
T Consensus 51 ~~~iiDtpG~~~~~ 64 (174)
T cd01895 51 KYTLIDTAGIRRKG 64 (174)
T ss_pred eEEEEECCCCcccc
Confidence 36799999998664
No 49
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=74.58 E-value=15 Score=22.95 Aligned_cols=29 Identities=31% Similarity=0.463 Sum_probs=19.0
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
++.........+.-++-.+++.++||||-
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~l~D~~G~ 59 (164)
T smart00175 31 STIGVDFKTKTIEVDGKRVKLQIWDTAGQ 59 (164)
T ss_pred CceeeEEEEEEEEECCEEEEEEEEECCCh
Confidence 34444444444555666788999999995
No 50
>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=73.92 E-value=9.6 Score=25.21 Aligned_cols=17 Identities=41% Similarity=0.728 Sum_probs=13.7
Q ss_pred EeecCeEEEEEEEeCCC
Q psy104 22 IEERGVKLRLTVVDTPG 38 (86)
Q Consensus 22 l~e~~~~l~LtIidTpG 38 (86)
+.-++..+.|+|.||||
T Consensus 43 ~~~~~~~~~~~i~Dt~G 59 (191)
T cd04112 43 VTVDGVKVKLQIWDTAG 59 (191)
T ss_pred EEECCEEEEEEEEeCCC
Confidence 44456789999999999
No 51
>KOG0462|consensus
Probab=73.56 E-value=5 Score=32.74 Aligned_cols=30 Identities=33% Similarity=0.509 Sum_probs=20.2
Q ss_pred ceEEEEEEEEE-eecCeEEEEEEEeCCCCCC
Q psy104 12 TTTIEKKSMDI-EERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 12 t~~I~~~~~~l-~e~~~~l~LtIidTpGfGd 41 (86)
.+.|...+..+ =.+|-...|++|||||=-|
T Consensus 107 GITIkaQtasify~~~~~ylLNLIDTPGHvD 137 (650)
T KOG0462|consen 107 GITIKAQTASIFYKDGQSYLLNLIDTPGHVD 137 (650)
T ss_pred CcEEEeeeeEEEEEcCCceEEEeecCCCccc
Confidence 44555555533 2448889999999999543
No 52
>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis. RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.
Probab=73.15 E-value=0.59 Score=31.72 Aligned_cols=11 Identities=45% Similarity=0.890 Sum_probs=8.7
Q ss_pred EEEeCCCCCCc
Q psy104 32 TVVDTPGFGDS 42 (86)
Q Consensus 32 tIidTpGfGd~ 42 (86)
-|||||||.+.
T Consensus 90 ~iIDTPGf~~~ 100 (161)
T PF03193_consen 90 YIIDTPGFRSF 100 (161)
T ss_dssp EEECSHHHHT-
T ss_pred EEEECCCCCcc
Confidence 59999999754
No 53
>COG0481 LepA Membrane GTPase LepA [Cell envelope biogenesis, outer membrane]
Probab=72.90 E-value=5.8 Score=31.99 Aligned_cols=31 Identities=29% Similarity=0.557 Sum_probs=22.4
Q ss_pred cceEEEEEEEEEe---ecCeEEEEEEEeCCCCCC
Q psy104 11 KTTTIEKKSMDIE---ERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 11 ~t~~I~~~~~~l~---e~~~~l~LtIidTpGfGd 41 (86)
....|....+.+. .+|-.+.|++|||||==|
T Consensus 55 RGITIKaq~v~l~Yk~~~g~~Y~lnlIDTPGHVD 88 (603)
T COG0481 55 RGITIKAQAVRLNYKAKDGETYVLNLIDTPGHVD 88 (603)
T ss_pred cCceEEeeEEEEEEEeCCCCEEEEEEcCCCCccc
Confidence 3456666666553 677899999999999643
No 54
>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=72.47 E-value=15 Score=23.59 Aligned_cols=20 Identities=30% Similarity=0.403 Sum_probs=14.8
Q ss_pred EEEeecCeEEEEEEEeCCCC
Q psy104 20 MDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 20 ~~l~e~~~~l~LtIidTpGf 39 (86)
..+.-++..+.+++.||||-
T Consensus 44 ~~~~~~~~~~~~~i~Dt~G~ 63 (168)
T cd01866 44 RMITIDGKQIKLQIWDTAGQ 63 (168)
T ss_pred EEEEECCEEEEEEEEECCCc
Confidence 34444566789999999993
No 55
>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=72.39 E-value=4.8 Score=27.49 Aligned_cols=28 Identities=29% Similarity=0.430 Sum_probs=17.2
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
..++......++.++ -.++++||||+.+
T Consensus 50 g~Ti~~~~~~~~~~~--~~i~~iDtPG~~~ 77 (195)
T cd01884 50 GITINTAHVEYETAN--RHYAHVDCPGHAD 77 (195)
T ss_pred CccEEeeeeEecCCC--eEEEEEECcCHHH
Confidence 344444444454443 3678999999864
No 56
>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=72.20 E-value=13 Score=22.35 Aligned_cols=19 Identities=37% Similarity=0.622 Sum_probs=14.2
Q ss_pred EeecCeEEEEEEEeCCCCC
Q psy104 22 IEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGfG 40 (86)
+..++..+.+.++||||..
T Consensus 43 ~~~~~~~~~~~~~D~~G~~ 61 (161)
T TIGR00231 43 IEEDGKTYKFNLLDTAGQE 61 (161)
T ss_pred EEECCEEEEEEEEECCCcc
Confidence 4445556889999999954
No 57
>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=71.57 E-value=2.7 Score=27.65 Aligned_cols=12 Identities=33% Similarity=0.534 Sum_probs=9.9
Q ss_pred EEEEEEeCCCCC
Q psy104 29 LRLTVVDTPGFG 40 (86)
Q Consensus 29 l~LtIidTpGfG 40 (86)
..+.|+||||+.
T Consensus 160 ~~~~~iDtpG~~ 171 (171)
T cd01856 160 PGIYLLDTPGIL 171 (171)
T ss_pred CCEEEEECCCCC
Confidence 467899999983
No 58
>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=71.48 E-value=18 Score=23.00 Aligned_cols=29 Identities=17% Similarity=0.154 Sum_probs=18.2
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
+.....+...+.-++..+.|.+.||||.-
T Consensus 32 ~~~~~~~~~~~~~~~~~~~~~i~Dt~G~~ 60 (161)
T cd04124 32 TYALTLYKHNAKFEGKTILVDFWDTAGQE 60 (161)
T ss_pred ceeeEEEEEEEEECCEEEEEEEEeCCCch
Confidence 33333333333444667899999999953
No 59
>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=71.32 E-value=2.7 Score=27.18 Aligned_cols=10 Identities=40% Similarity=1.052 Sum_probs=8.8
Q ss_pred EEEEEeCCCC
Q psy104 30 RLTVVDTPGF 39 (86)
Q Consensus 30 ~LtIidTpGf 39 (86)
.+.++||||+
T Consensus 146 ~~~liDtPG~ 155 (155)
T cd01849 146 KIKLLDTPGI 155 (155)
T ss_pred CEEEEECCCC
Confidence 5789999997
No 60
>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=71.02 E-value=4.6 Score=32.48 Aligned_cols=29 Identities=38% Similarity=0.556 Sum_probs=19.8
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCCCc
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~ 42 (86)
..+|......+.-++ .+++++||||..|.
T Consensus 49 GiTI~~~~~~v~~~~--~kinlIDTPGh~DF 77 (594)
T TIGR01394 49 GITILAKNTAIRYNG--TKINIVDTPGHADF 77 (594)
T ss_pred CccEEeeeEEEEECC--EEEEEEECCCHHHH
Confidence 455555555555554 67889999998764
No 61
>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=70.88 E-value=18 Score=22.95 Aligned_cols=27 Identities=33% Similarity=0.396 Sum_probs=17.6
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPG 38 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpG 38 (86)
+.........+.-++-.++|.+.||||
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~i~D~~G 63 (170)
T cd04116 37 TIGVEFLNKDLEVDGHFVTLQIWDTAG 63 (170)
T ss_pred ceeeEEEEEEEEECCeEEEEEEEeCCC
Confidence 333333333444566788999999998
No 62
>TIGR00157 ribosome small subunit-dependent GTPase A. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option).
Probab=70.88 E-value=5.1 Score=28.37 Aligned_cols=10 Identities=50% Similarity=1.112 Sum_probs=8.5
Q ss_pred EEEeCCCCCC
Q psy104 32 TVVDTPGFGD 41 (86)
Q Consensus 32 tIidTpGfGd 41 (86)
-|+|||||-.
T Consensus 174 ~liDtPG~~~ 183 (245)
T TIGR00157 174 LIADTPGFNE 183 (245)
T ss_pred EEEeCCCccc
Confidence 5999999964
No 63
>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=70.56 E-value=9.1 Score=22.57 Aligned_cols=29 Identities=34% Similarity=0.344 Sum_probs=20.8
Q ss_pred EEEEEEEEeecCeEEEEEEEeCCCCCCcc
Q psy104 15 IEKKSMDIEERGVKLRLTVVDTPGFGDSI 43 (86)
Q Consensus 15 I~~~~~~l~e~~~~l~LtIidTpGfGd~i 43 (86)
+..........+....++++||||..+..
T Consensus 31 ~~~~~~~~~~~~~~~~~~l~D~~g~~~~~ 59 (157)
T cd00882 31 IDFYSKTIEVDGKKVKLQIWDTAGQERFR 59 (157)
T ss_pred hheeeEEEEECCEEEEEEEEecCChHHHH
Confidence 55555555655667899999999977544
No 64
>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=70.21 E-value=19 Score=24.54 Aligned_cols=31 Identities=23% Similarity=0.222 Sum_probs=21.1
Q ss_pred CcceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 10 ~~t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
.+|+.+...+..+.-++-.++|.|.||+|-.
T Consensus 25 ~~Tig~~~~~~~~~~~~~~~~l~iwDt~G~e 55 (200)
T smart00176 25 VATLGVEVHPLVFHTNRGPIRFNVWDTAGQE 55 (200)
T ss_pred CCceeEEEEEEEEEECCEEEEEEEEECCCch
Confidence 3455555555555545568999999999964
No 65
>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=70.14 E-value=9.1 Score=27.55 Aligned_cols=30 Identities=27% Similarity=0.391 Sum_probs=19.2
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCCCCc
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~ 42 (86)
...++......++-++ .+++++||||..+.
T Consensus 48 rgiti~~~~~~~~~~~--~~i~liDTPG~~df 77 (270)
T cd01886 48 RGITIQSAATTCFWKD--HRINIIDTPGHVDF 77 (270)
T ss_pred CCcCeeccEEEEEECC--EEEEEEECCCcHHH
Confidence 3455555555555554 46778999998653
No 66
>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=69.83 E-value=9.7 Score=24.42 Aligned_cols=17 Identities=41% Similarity=0.704 Sum_probs=13.3
Q ss_pred cCeEEEEEEEeCCCCCC
Q psy104 25 RGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 25 ~~~~l~LtIidTpGfGd 41 (86)
++-.+.|+++||||.-+
T Consensus 63 ~~~~~~~~l~Dt~G~~~ 79 (179)
T cd01890 63 DGQEYLLNLIDTPGHVD 79 (179)
T ss_pred CCCcEEEEEEECCCChh
Confidence 34467899999999864
No 67
>PLN03071 GTP-binding nuclear protein Ran; Provisional
Probab=69.59 E-value=16 Score=25.12 Aligned_cols=32 Identities=25% Similarity=0.255 Sum_probs=22.0
Q ss_pred CcceEEEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 10 ~~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
.+|+.+..+...+.-++-.++|.+.||||-..
T Consensus 43 ~~tig~~~~~~~~~~~~~~~~l~i~Dt~G~~~ 74 (219)
T PLN03071 43 EPTIGVEVHPLDFFTNCGKIRFYCWDTAGQEK 74 (219)
T ss_pred CCccceeEEEEEEEECCeEEEEEEEECCCchh
Confidence 45555555555555555679999999999653
No 68
>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=69.12 E-value=8.2 Score=28.92 Aligned_cols=12 Identities=25% Similarity=0.606 Sum_probs=10.2
Q ss_pred EEEEEeCCCCCC
Q psy104 30 RLTVVDTPGFGD 41 (86)
Q Consensus 30 ~LtIidTpGfGd 41 (86)
.++++||||++.
T Consensus 48 ~~~liDTpG~~~ 59 (429)
T TIGR03594 48 EFILIDTGGIEE 59 (429)
T ss_pred EEEEEECCCCCC
Confidence 589999999963
No 69
>PLN03118 Rab family protein; Provisional
Probab=68.94 E-value=18 Score=24.29 Aligned_cols=19 Identities=37% Similarity=0.588 Sum_probs=14.1
Q ss_pred EEeecCeEEEEEEEeCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGf 39 (86)
.+.-++..++|.++||||.
T Consensus 54 ~~~~~~~~~~l~l~Dt~G~ 72 (211)
T PLN03118 54 QLTVGGKRLKLTIWDTAGQ 72 (211)
T ss_pred EEEECCEEEEEEEEECCCc
Confidence 3344456788999999995
No 70
>PRK00089 era GTPase Era; Reviewed
Probab=68.76 E-value=23 Score=25.17 Aligned_cols=15 Identities=33% Similarity=0.574 Sum_probs=12.1
Q ss_pred EEEEEEeCCCCCCcc
Q psy104 29 LRLTVVDTPGFGDSI 43 (86)
Q Consensus 29 l~LtIidTpGfGd~i 43 (86)
..+.++||||+.+..
T Consensus 53 ~qi~~iDTPG~~~~~ 67 (292)
T PRK00089 53 AQIIFVDTPGIHKPK 67 (292)
T ss_pred ceEEEEECCCCCCch
Confidence 678999999997543
No 71
>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=68.53 E-value=3.3 Score=26.30 Aligned_cols=13 Identities=38% Similarity=0.726 Sum_probs=10.5
Q ss_pred EEEEEEeCCCCCC
Q psy104 29 LRLTVVDTPGFGD 41 (86)
Q Consensus 29 l~LtIidTpGfGd 41 (86)
..+.++||||+.+
T Consensus 44 ~~~~i~DtpG~~~ 56 (176)
T cd01881 44 ARIQVADIPGLIE 56 (176)
T ss_pred CeEEEEeccccch
Confidence 4578999999964
No 72
>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=68.52 E-value=2.7 Score=28.36 Aligned_cols=14 Identities=36% Similarity=0.684 Sum_probs=11.9
Q ss_pred EEEEEEeCCCCCCc
Q psy104 29 LRLTVVDTPGFGDS 42 (86)
Q Consensus 29 l~LtIidTpGfGd~ 42 (86)
-.++++||||+|+.
T Consensus 52 ~~l~l~DtpG~~~~ 65 (197)
T cd04104 52 PNVTLWDLPGIGST 65 (197)
T ss_pred CCceEEeCCCCCcc
Confidence 37899999999964
No 73
>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=68.22 E-value=6.3 Score=26.14 Aligned_cols=13 Identities=46% Similarity=0.912 Sum_probs=11.0
Q ss_pred EEEEEEEeCCCCC
Q psy104 28 KLRLTVVDTPGFG 40 (86)
Q Consensus 28 ~l~LtIidTpGfG 40 (86)
...++++||||..
T Consensus 67 ~~~~~i~DtpG~~ 79 (192)
T cd01889 67 NLQITLVDCPGHA 79 (192)
T ss_pred CceEEEEECCCcH
Confidence 5688999999974
No 74
>PRK00093 GTP-binding protein Der; Reviewed
Probab=68.00 E-value=17 Score=27.33 Aligned_cols=13 Identities=23% Similarity=0.416 Sum_probs=11.6
Q ss_pred EEEEEEeCCCCCC
Q psy104 29 LRLTVVDTPGFGD 41 (86)
Q Consensus 29 l~LtIidTpGfGd 41 (86)
..+.++||||+.+
T Consensus 49 ~~~~liDT~G~~~ 61 (435)
T PRK00093 49 REFILIDTGGIEP 61 (435)
T ss_pred cEEEEEECCCCCC
Confidence 6789999999986
No 75
>COG0480 FusA Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]
Probab=67.89 E-value=7.9 Score=31.97 Aligned_cols=32 Identities=28% Similarity=0.459 Sum_probs=22.9
Q ss_pred CcceEEEEEEEEEeecCeEEEEEEEeCCCCCCc
Q psy104 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 10 ~~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~ 42 (86)
....+|+.....+.=++ ..++++|||||-=|.
T Consensus 58 eRGITI~saa~s~~~~~-~~~iNlIDTPGHVDF 89 (697)
T COG0480 58 ERGITITSAATTLFWKG-DYRINLIDTPGHVDF 89 (697)
T ss_pred hcCCEEeeeeeEEEEcC-ceEEEEeCCCCcccc
Confidence 44667777777665444 688999999997443
No 76
>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=67.80 E-value=20 Score=23.07 Aligned_cols=21 Identities=29% Similarity=0.398 Sum_probs=15.6
Q ss_pred EEEeecCeEEEEEEEeCCCCC
Q psy104 20 MDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 20 ~~l~e~~~~l~LtIidTpGfG 40 (86)
..+.-++..+++.+.||||..
T Consensus 39 ~~~~~~~~~~~~~i~Dt~G~~ 59 (173)
T cd04130 39 VVVLVDGKPVRLQLCDTAGQD 59 (173)
T ss_pred EEEEECCEEEEEEEEECCCCh
Confidence 344445678999999999964
No 77
>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=67.74 E-value=22 Score=22.39 Aligned_cols=19 Identities=21% Similarity=0.246 Sum_probs=14.3
Q ss_pred EeecCeEEEEEEEeCCCCC
Q psy104 22 IEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGfG 40 (86)
+.-++..+.|+++||||..
T Consensus 42 ~~~~~~~~~~~~~D~~g~~ 60 (172)
T cd01862 42 VTVDDKLVTLQIWDTAGQE 60 (172)
T ss_pred EEECCEEEEEEEEeCCChH
Confidence 3444567899999999964
No 78
>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=67.67 E-value=21 Score=23.29 Aligned_cols=20 Identities=20% Similarity=0.142 Sum_probs=15.6
Q ss_pred EEeecCeEEEEEEEeCCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGfG 40 (86)
.+.-++..++|.+.||||--
T Consensus 42 ~~~~~~~~~~l~i~D~~G~~ 61 (193)
T cd04118 42 RMVVGERVVTLGIWDTAGSE 61 (193)
T ss_pred EEEECCEEEEEEEEECCCch
Confidence 44556778999999999953
No 79
>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=67.54 E-value=9 Score=27.50 Aligned_cols=28 Identities=29% Similarity=0.507 Sum_probs=18.6
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
..+|......++-++ .+++++||||..+
T Consensus 56 g~si~~~~~~~~~~~--~~i~liDTPG~~d 83 (267)
T cd04169 56 GISVTSSVMQFEYRD--CVINLLDTPGHED 83 (267)
T ss_pred CCCeEEEEEEEeeCC--EEEEEEECCCchH
Confidence 445555555565554 5678899999764
No 80
>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=67.44 E-value=24 Score=22.58 Aligned_cols=20 Identities=25% Similarity=0.473 Sum_probs=14.8
Q ss_pred EEeecCeEEEEEEEeCCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGfG 40 (86)
.+.-++..+.|.|+||||-.
T Consensus 43 ~~~~~~~~~~~~i~Dt~G~~ 62 (170)
T cd04115 43 TVEIDGERIKVQLWDTAGQE 62 (170)
T ss_pred EEEECCeEEEEEEEeCCChH
Confidence 34445667899999999954
No 81
>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=67.23 E-value=10 Score=24.20 Aligned_cols=10 Identities=40% Similarity=0.956 Sum_probs=8.8
Q ss_pred EEEEEeCCCC
Q psy104 30 RLTVVDTPGF 39 (86)
Q Consensus 30 ~LtIidTpGf 39 (86)
.+.++||||+
T Consensus 147 ~~~~~DtpGi 156 (156)
T cd01859 147 KIYLLDTPGV 156 (156)
T ss_pred CEEEEECcCC
Confidence 5889999996
No 82
>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=66.79 E-value=19 Score=22.97 Aligned_cols=19 Identities=42% Similarity=0.599 Sum_probs=14.4
Q ss_pred EEeecCeEEEEEEEeCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGf 39 (86)
.+.-++..+.|.+.||||-
T Consensus 44 ~~~~~~~~~~l~l~D~~g~ 62 (167)
T cd01867 44 TIELDGKKIKLQIWDTAGQ 62 (167)
T ss_pred EEEECCEEEEEEEEeCCch
Confidence 3444566789999999993
No 83
>PF04784 DUF547: Protein of unknown function, DUF547; InterPro: IPR006869 This is a conserved region found in uncharacterised proteins from Caenorhabditis elegans and Arabidopsis thaliana (Mouse-ear cress).
Probab=66.49 E-value=3.6 Score=26.09 Aligned_cols=19 Identities=32% Similarity=0.282 Sum_probs=15.7
Q ss_pred hcCCccCC---CCCCeeEEeec
Q psy104 67 ESGLNRKN---IVDNREVVDKS 85 (86)
Q Consensus 67 E~~i~R~~---~~D~RVH~Cl~ 85 (86)
|.++-|.+ ..|.|||.+|+
T Consensus 65 e~~ILR~~~~~~~DprihFaL~ 86 (117)
T PF04784_consen 65 EHGILRGNRPPWPDPRIHFALN 86 (117)
T ss_pred HHhhccCCCCCCCCCceeeeee
Confidence 66777766 89999999986
No 84
>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=66.37 E-value=26 Score=22.30 Aligned_cols=31 Identities=32% Similarity=0.411 Sum_probs=20.6
Q ss_pred CcceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 10 ~~t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
.+|.....+...+.-++..++|.+.||||-.
T Consensus 30 ~~t~~~~~~~~~~~~~~~~~~l~i~D~~g~~ 60 (161)
T cd04117 30 ISTIGVDFKMKTIEVDGIKVRIQIWDTAGQE 60 (161)
T ss_pred CCceeeEEEEEEEEECCEEEEEEEEeCCCcH
Confidence 3444444444455556778999999999854
No 85
>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=66.16 E-value=4.2 Score=26.07 Aligned_cols=14 Identities=43% Similarity=0.802 Sum_probs=11.7
Q ss_pred EEEEEEEeCCCCCC
Q psy104 28 KLRLTVVDTPGFGD 41 (86)
Q Consensus 28 ~l~LtIidTpGfGd 41 (86)
...+.++||||+++
T Consensus 61 ~~~~~liDtpG~~~ 74 (189)
T cd00881 61 DRRVNFIDTPGHED 74 (189)
T ss_pred CEEEEEEeCCCcHH
Confidence 46789999999874
No 86
>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=65.86 E-value=21 Score=22.28 Aligned_cols=17 Identities=35% Similarity=0.515 Sum_probs=13.2
Q ss_pred ecCeEEEEEEEeCCCCC
Q psy104 24 ERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 24 e~~~~l~LtIidTpGfG 40 (86)
-++..++|.++||||..
T Consensus 44 ~~~~~~~~~l~D~~g~~ 60 (161)
T cd01863 44 VDGKKVKLAIWDTAGQE 60 (161)
T ss_pred ECCEEEEEEEEECCCch
Confidence 34567889999999953
No 87
>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=65.32 E-value=29 Score=22.03 Aligned_cols=20 Identities=20% Similarity=0.346 Sum_probs=14.9
Q ss_pred EEeecCeEEEEEEEeCCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGfG 40 (86)
.+.-++-.+.|.+.||||..
T Consensus 42 ~~~~~~~~~~~~l~Dt~g~~ 61 (165)
T cd01865 42 TVFRNDKRVKLQIWDTAGQE 61 (165)
T ss_pred EEEECCEEEEEEEEECCChH
Confidence 34445667899999999964
No 88
>COG1162 Predicted GTPases [General function prediction only]
Probab=64.85 E-value=3.3 Score=30.93 Aligned_cols=9 Identities=56% Similarity=1.114 Sum_probs=7.8
Q ss_pred EEEeCCCCC
Q psy104 32 TVVDTPGFG 40 (86)
Q Consensus 32 tIidTpGfG 40 (86)
-|||||||.
T Consensus 219 ~iiDTPGf~ 227 (301)
T COG1162 219 WIIDTPGFR 227 (301)
T ss_pred EEEeCCCCC
Confidence 389999996
No 89
>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=64.75 E-value=24 Score=22.02 Aligned_cols=19 Identities=16% Similarity=0.344 Sum_probs=14.1
Q ss_pred EEeecCeEEEEEEEeCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGf 39 (86)
.+.-++..++|.++||||-
T Consensus 42 ~v~~~~~~~~~~i~D~~G~ 60 (163)
T cd01860 42 TVNLDDTTVKFEIWDTAGQ 60 (163)
T ss_pred EEEECCEEEEEEEEeCCch
Confidence 3344466789999999994
No 90
>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=64.64 E-value=6.1 Score=27.90 Aligned_cols=20 Identities=35% Similarity=0.810 Sum_probs=13.7
Q ss_pred EEeecCeEEEEEEEeCCCCCCc
Q psy104 21 DIEERGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGfGd~ 42 (86)
.+.-++ .+++++||||+++.
T Consensus 58 ~~~~~~--~~i~liDtPG~~~f 77 (268)
T cd04170 58 PLEWKG--HKINLIDTPGYADF 77 (268)
T ss_pred EEEECC--EEEEEEECcCHHHH
Confidence 444344 46788999999753
No 91
>PRK10218 GTP-binding protein; Provisional
Probab=64.57 E-value=18 Score=29.36 Aligned_cols=30 Identities=37% Similarity=0.443 Sum_probs=20.1
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCCCcc
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFGDSI 43 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~i 43 (86)
..++......++.++ .+++++||||..+..
T Consensus 53 GiTi~~~~~~i~~~~--~~inliDTPG~~df~ 82 (607)
T PRK10218 53 GITILAKNTAIKWND--YRINIVDTPGHADFG 82 (607)
T ss_pred ceEEEEEEEEEecCC--EEEEEEECCCcchhH
Confidence 455555555555544 678899999987653
No 92
>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=64.42 E-value=5.5 Score=27.95 Aligned_cols=17 Identities=29% Similarity=0.598 Sum_probs=13.2
Q ss_pred CeEEEEEEEeCCCCCCc
Q psy104 26 GVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 26 ~~~l~LtIidTpGfGd~ 42 (86)
+-...++++||||.-+.
T Consensus 70 ~~~~~i~iiDTPG~~~f 86 (222)
T cd01885 70 GNEYLINLIDSPGHVDF 86 (222)
T ss_pred CCceEEEEECCCCcccc
Confidence 34688999999997543
No 93
>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=64.17 E-value=9.9 Score=23.69 Aligned_cols=12 Identities=42% Similarity=0.742 Sum_probs=9.9
Q ss_pred EEEEEEeCCCCC
Q psy104 29 LRLTVVDTPGFG 40 (86)
Q Consensus 29 l~LtIidTpGfG 40 (86)
..++++||||..
T Consensus 51 ~~~~~~DtpG~~ 62 (164)
T cd04171 51 KRLGFIDVPGHE 62 (164)
T ss_pred cEEEEEECCChH
Confidence 478999999963
No 94
>TIGR01631 Trypano_RHS trypanosome RHS (retrotransposon hot spot) family. This model describes full-length and part-length members of the RHS (retrotransposon hot spot) family in Trypanosoma brucei and Trypanosoma cruzi. Members of this family are frequently interrupted by non-LTR retrotransposons inserted at exactly the same relative position.
Probab=63.93 E-value=5.8 Score=33.14 Aligned_cols=37 Identities=24% Similarity=0.372 Sum_probs=29.1
Q ss_pred EEEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhhhcCCc
Q psy104 28 KLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGLN 71 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~eE~~i~ 71 (86)
|..--+|.|||+|.+.+-. +|+--|+..|-.+..++-
T Consensus 279 p~~~vlIGTPGIGKS~~aG-------SyLLYqLLHydae~L~vV 315 (760)
T TIGR01631 279 PERRVLIGTPGIGKSFGVG-------SFLLYQLLHYDAEKLQVV 315 (760)
T ss_pred CCCeEEECCCCccccccch-------HHHHHHHHhccHhhCcEE
Confidence 4444599999999998866 599999998887776653
No 95
>PF07999 RHSP: Retrotransposon hot spot protein; InterPro: IPR006518 These sequences are full-length and part-length members of the RHS (retrotransposon hot spot) family in Trypanosoma brucei and Trypanosoma cruzi. Members of this family are frequently interrupted by non-LTR retrotransposons inserted at exactly the same relative position.
Probab=63.46 E-value=5.3 Score=31.16 Aligned_cols=36 Identities=25% Similarity=0.437 Sum_probs=26.8
Q ss_pred EEEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhhhcCC
Q psy104 28 KLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGL 70 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~eE~~i 70 (86)
+.-..+|.|||.|.+.+-. +|+-.|...|=.+..++
T Consensus 124 ~~p~vlIGTPGIGKS~~~G-------S~LLyqLLHy~~~~L~v 159 (439)
T PF07999_consen 124 PRPFVLIGTPGIGKSFGTG-------SYLLYQLLHYDAEKLPV 159 (439)
T ss_pred CCceEEEecCCcCccccch-------hhhhhhhhcCChhhccE
Confidence 3445899999999888765 48888887776665544
No 96
>PTZ00209 retrotransposon hot spot protein; Provisional
Probab=63.38 E-value=5.9 Score=32.70 Aligned_cols=37 Identities=14% Similarity=0.223 Sum_probs=29.7
Q ss_pred EEEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhhhcCCc
Q psy104 28 KLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGLN 71 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~eE~~i~ 71 (86)
|..--+|.|||+|.+.+-. +||--|+..|=.+..++-
T Consensus 172 P~~~vLIGTPGIGKSm~aG-------SyLLYqLLHyDae~L~vV 208 (693)
T PTZ00209 172 PPTHIVIGISGIGKSCGVG-------SFLLHSLLHFHEGMLDVV 208 (693)
T ss_pred CCceEEECCCCccccccch-------HHHHHHHHccCHhHCcEE
Confidence 5556699999999998866 599999998877776653
No 97
>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=63.35 E-value=13 Score=24.66 Aligned_cols=13 Identities=31% Similarity=0.447 Sum_probs=10.8
Q ss_pred EEEEEeCCCCCCc
Q psy104 30 RLTVVDTPGFGDS 42 (86)
Q Consensus 30 ~LtIidTpGfGd~ 42 (86)
.++++||||+.+.
T Consensus 90 ~~~i~Dt~G~~~~ 102 (204)
T cd01878 90 EVLLTDTVGFIRD 102 (204)
T ss_pred eEEEeCCCccccC
Confidence 6889999999654
No 98
>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=63.28 E-value=5.7 Score=25.16 Aligned_cols=13 Identities=31% Similarity=0.554 Sum_probs=10.8
Q ss_pred EEEEEEeCCCCCC
Q psy104 29 LRLTVVDTPGFGD 41 (86)
Q Consensus 29 l~LtIidTpGfGd 41 (86)
..++++||||+.+
T Consensus 48 ~~~~l~DtpG~~~ 60 (170)
T cd01898 48 RSFVVADIPGLIE 60 (170)
T ss_pred CeEEEEecCcccC
Confidence 4789999999854
No 99
>PF12075 KN_motif: KN motif; InterPro: IPR021939 This small motif is found at the N terminus of Kank proteins and has been called the KN (for Kank N-terminal) motif. This protein is found in eukaryotes. Proteins in this family are typically between 413 to 1202 amino acids in length. This protein is found associated with PF00023 from PFAM. This protein has two conserved sequence motifs: TPYG and LDLDF. Kank1 was obtained by positional cloning of a tumor suppressor gene in renal cell carcinoma, while the other members were found by homology search. The family is involved in the regulation of actin polymerisation and cell motility through signaling pathways containing PI3K/Akt and/or unidentified modulators/effectors [].
Probab=61.99 E-value=5.4 Score=21.10 Aligned_cols=19 Identities=37% Similarity=0.810 Sum_probs=13.9
Q ss_pred EeCCCCCCccCCccchhHHHHHHHH
Q psy104 34 VDTPGFGDSINSEESWRACCSYIDD 58 (86)
Q Consensus 34 idTpGfGd~i~n~~~~~~i~~yI~~ 58 (86)
+.|| ||-++|..+ ++|+++
T Consensus 4 v~tP-YGyhiDLDF-----vkyve~ 22 (39)
T PF12075_consen 4 VETP-YGYHIDLDF-----VKYVED 22 (39)
T ss_pred ccCC-cceeecchH-----HHHHHH
Confidence 3564 888899887 777765
No 100
>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=61.95 E-value=19 Score=22.47 Aligned_cols=19 Identities=37% Similarity=0.504 Sum_probs=14.7
Q ss_pred EeecCeEEEEEEEeCCCCC
Q psy104 22 IEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGfG 40 (86)
+.-++..+.|.+.||||.-
T Consensus 42 ~~~~~~~~~l~i~Dt~G~~ 60 (163)
T cd04136 42 IEVDGQQCMLEILDTAGTE 60 (163)
T ss_pred EEECCEEEEEEEEECCCcc
Confidence 4445678899999999953
No 101
>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=61.78 E-value=5.6 Score=26.38 Aligned_cols=14 Identities=43% Similarity=0.873 Sum_probs=11.6
Q ss_pred EEEEEEEeCCCCCC
Q psy104 28 KLRLTVVDTPGFGD 41 (86)
Q Consensus 28 ~l~LtIidTpGfGd 41 (86)
...++++||||..+
T Consensus 69 ~~~i~~iDtPG~~~ 82 (188)
T PF00009_consen 69 NRKITLIDTPGHED 82 (188)
T ss_dssp SEEEEEEEESSSHH
T ss_pred ccceeecccccccc
Confidence 57889999999854
No 102
>cd01851 GBP Guanylate-binding protein (GBP), N-terminal domain. Guanylate-binding proteins (GBPs) define a group of proteins that are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. Furthermore, two unique regions around the base and the phosphate-binding areas, the guanine and the phosphate caps, respectively, give the nucleotide-binding site a unique appearance not found in the canonical GTP-binding proteins. The phosphate cap, which constitutes the region analogous to switch I, completely shields the phosphate-binding site from solvent such that a potential GTPase-activating protein
Probab=60.88 E-value=6.4 Score=27.44 Aligned_cols=17 Identities=18% Similarity=0.227 Sum_probs=13.9
Q ss_pred EEEEEEEeCCCCCCccC
Q psy104 28 KLRLTVVDTPGFGDSIN 44 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~ 44 (86)
...+-++||||+++.-.
T Consensus 59 ~~~v~~lDteG~~~~~~ 75 (224)
T cd01851 59 EHAVLLLDTEGTDGRER 75 (224)
T ss_pred cceEEEEecCCcCcccc
Confidence 36789999999997654
No 103
>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=60.65 E-value=5.8 Score=25.60 Aligned_cols=9 Identities=33% Similarity=0.899 Sum_probs=7.9
Q ss_pred EEEEeCCCC
Q psy104 31 LTVVDTPGF 39 (86)
Q Consensus 31 LtIidTpGf 39 (86)
+.++||||+
T Consensus 149 ~~liDtPGi 157 (157)
T cd01858 149 IYLIDCPGV 157 (157)
T ss_pred EEEEECcCC
Confidence 679999995
No 104
>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=60.62 E-value=29 Score=23.10 Aligned_cols=19 Identities=32% Similarity=0.566 Sum_probs=14.1
Q ss_pred EEeecCeEEEEEEEeCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGf 39 (86)
.+.-++..+.|.+.||||-
T Consensus 47 ~~~~~~~~~~l~l~D~~G~ 65 (199)
T cd04110 47 TVEINGERVKLQIWDTAGQ 65 (199)
T ss_pred EEEECCEEEEEEEEeCCCc
Confidence 3444566788999999994
No 105
>PLN03127 Elongation factor Tu; Provisional
Probab=60.28 E-value=9.3 Score=29.61 Aligned_cols=30 Identities=27% Similarity=0.383 Sum_probs=18.9
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCCCCc
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~ 42 (86)
+...+......++.++ -.++++||||..+.
T Consensus 108 rGiTi~~~~~~~~~~~--~~i~~iDtPGh~~f 137 (447)
T PLN03127 108 RGITIATAHVEYETAK--RHYAHVDCPGHADY 137 (447)
T ss_pred cCceeeeeEEEEcCCC--eEEEEEECCCccch
Confidence 4445555555555443 36789999998654
No 106
>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=60.23 E-value=24 Score=26.45 Aligned_cols=23 Identities=22% Similarity=0.364 Sum_probs=15.3
Q ss_pred EEeecCeEEEEEEEeCCCCCCccCC
Q psy104 21 DIEERGVKLRLTVVDTPGFGDSINS 45 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGfGd~i~n 45 (86)
.++.++. .++++||||+......
T Consensus 214 ~~~~~~~--~~~liDT~G~~~~~~~ 236 (429)
T TIGR03594 214 PFERNGK--KYLLIDTAGIRRKGKV 236 (429)
T ss_pred EEEECCc--EEEEEECCCccccccc
Confidence 3443443 6789999999765543
No 107
>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=59.90 E-value=13 Score=29.56 Aligned_cols=29 Identities=28% Similarity=0.407 Sum_probs=19.0
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCCCc
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~ 42 (86)
..++......++-++ .+++++||||..+.
T Consensus 65 gisi~~~~~~~~~~~--~~inliDTPG~~df 93 (527)
T TIGR00503 65 GISITTSVMQFPYRD--CLVNLLDTPGHEDF 93 (527)
T ss_pred CCcEEEEEEEEeeCC--eEEEEEECCChhhH
Confidence 445555555555554 56788999998643
No 108
>COG5256 TEF1 Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]
Probab=59.69 E-value=6.8 Score=30.65 Aligned_cols=29 Identities=31% Similarity=0.550 Sum_probs=17.3
Q ss_pred eEEEEEEEEEeecCeEEEEEEEeCCCCCCcc
Q psy104 13 TTIEKKSMDIEERGVKLRLTVVDTPGFGDSI 43 (86)
Q Consensus 13 ~~I~~~~~~l~e~~~~l~LtIidTpGfGd~i 43 (86)
+.|......++-+ +..+||+|+||--|.+
T Consensus 71 vTi~~~~~~fet~--k~~~tIiDaPGHrdFv 99 (428)
T COG5256 71 VTIDVAHSKFETD--KYNFTIIDAPGHRDFV 99 (428)
T ss_pred eEEEEEEEEeecC--CceEEEeeCCchHHHH
Confidence 4444444433322 4589999999965543
No 109
>PRK00741 prfC peptide chain release factor 3; Provisional
Probab=59.57 E-value=14 Score=29.36 Aligned_cols=29 Identities=24% Similarity=0.408 Sum_probs=18.5
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCCCc
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~ 42 (86)
..+|......+.-++ .+++++||||..|.
T Consensus 64 giSi~~~~~~~~~~~--~~inliDTPG~~df 92 (526)
T PRK00741 64 GISVTSSVMQFPYRD--CLINLLDTPGHEDF 92 (526)
T ss_pred CCceeeeeEEEEECC--EEEEEEECCCchhh
Confidence 344555545555454 56789999998653
No 110
>TIGR03134 malonate_gamma malonate decarboxylase, gamma subunit. Members of this protein family are the gamma subunit of malonate decarboxylase. Malonate decarboxylase may be a soluble enzyme, or linked to membrane subunits and active as a sodium pump. In the malonate decarboxylase complex, the beta subunit appears to act as a malonyl-CoA decarboxylase, while the gamma subunit appears either to mediate subunit interaction or to act as a co-decarboxylase with the beta subunit. The beta and gamma subunits exhibit some local sequence similarity.
Probab=59.15 E-value=16 Score=26.28 Aligned_cols=37 Identities=14% Similarity=0.090 Sum_probs=23.4
Q ss_pred CeEEEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhh
Q psy104 26 GVKLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFN 65 (86)
Q Consensus 26 ~~~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~ 65 (86)
++|| |++||||||-- ....-+.-+..++..-+..|..
T Consensus 66 ~~PI-v~lvDtpG~~~--g~~aE~~G~~~a~A~l~~a~a~ 102 (238)
T TIGR03134 66 KRPI-VVLVDTPSQAY--GRREELLGINQALAHLAKALAL 102 (238)
T ss_pred CCCE-EEEEeCCCCCC--CHHHHHHHHHHHHHHHHHHHHH
Confidence 4454 89999999973 3333345567777665555543
No 111
>cd01893 Miro1 Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
Probab=58.82 E-value=15 Score=23.41 Aligned_cols=17 Identities=24% Similarity=0.231 Sum_probs=13.9
Q ss_pred cCeEEEEEEEeCCCCCC
Q psy104 25 RGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 25 ~~~~l~LtIidTpGfGd 41 (86)
++..+++.++||||.+.
T Consensus 43 ~~~~~~~~i~Dt~G~~~ 59 (166)
T cd01893 43 TPERVPTTIVDTSSRPQ 59 (166)
T ss_pred cCCeEEEEEEeCCCchh
Confidence 45678999999999874
No 112
>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=58.64 E-value=35 Score=21.34 Aligned_cols=15 Identities=20% Similarity=0.346 Sum_probs=12.4
Q ss_pred cCeEEEEEEEeCCCC
Q psy104 25 RGVKLRLTVVDTPGF 39 (86)
Q Consensus 25 ~~~~l~LtIidTpGf 39 (86)
.+-.+.|.+.||||-
T Consensus 48 ~~~~~~l~i~Dt~G~ 62 (164)
T cd04101 48 TDNTVELFIFDSAGQ 62 (164)
T ss_pred CCCEEEEEEEECCCH
Confidence 456789999999983
No 113
>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=58.49 E-value=25 Score=21.92 Aligned_cols=15 Identities=33% Similarity=0.404 Sum_probs=12.4
Q ss_pred cCeEEEEEEEeCCCC
Q psy104 25 RGVKLRLTVVDTPGF 39 (86)
Q Consensus 25 ~~~~l~LtIidTpGf 39 (86)
++-.+++.++||||.
T Consensus 46 ~~~~~~~~i~Dt~G~ 60 (164)
T cd04145 46 DGQWAILDILDTAGQ 60 (164)
T ss_pred CCEEEEEEEEECCCC
Confidence 455789999999994
No 114
>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=58.46 E-value=31 Score=22.40 Aligned_cols=19 Identities=21% Similarity=0.212 Sum_probs=14.7
Q ss_pred EeecCeEEEEEEEeCCCCC
Q psy104 22 IEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGfG 40 (86)
+.-++-.+.|++.||||..
T Consensus 43 ~~~~~~~~~l~i~Dt~G~~ 61 (172)
T cd04141 43 ARIDNEPALLDILDTAGQA 61 (172)
T ss_pred EEECCEEEEEEEEeCCCch
Confidence 4445678899999999954
No 115
>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=57.72 E-value=13 Score=25.47 Aligned_cols=26 Identities=31% Similarity=0.519 Sum_probs=15.7
Q ss_pred eEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 13 TTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 13 ~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
..+......++-++ .+++++||||..
T Consensus 63 ~T~d~~~~~~~~~~--~~i~liDtpG~~ 88 (219)
T cd01883 63 VTIDVGLAKFETEK--YRFTILDAPGHR 88 (219)
T ss_pred cCeecceEEEeeCC--eEEEEEECCChH
Confidence 33444334444444 578999999974
No 116
>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=57.28 E-value=6.3 Score=24.85 Aligned_cols=13 Identities=38% Similarity=0.606 Sum_probs=10.8
Q ss_pred EEEEEEEeCCCCC
Q psy104 28 KLRLTVVDTPGFG 40 (86)
Q Consensus 28 ~l~LtIidTpGfG 40 (86)
...++++||||..
T Consensus 49 ~~~~~iiDtpG~~ 61 (168)
T cd01887 49 IPGITFIDTPGHE 61 (168)
T ss_pred cceEEEEeCCCcH
Confidence 4678999999975
No 117
>PF00063 Myosin_head: Myosin head (motor domain); InterPro: IPR001609 Muscle contraction is caused by sliding between the thick and thin filaments of the myofibril. Myosin is a major component of thick filaments and exists as a hexamer of 2 heavy chains [], 2 alkali light chains, and 2 regulatory light chains. The heavy chain can be subdivided into the N-terminal globular head and the C-terminal coiled-coil rod-like tail, although some forms have a globular region in their C-terminal. There are many cell-specific isoforms of myosin heavy chains, coded for by a multi-gene family []. Myosin interacts with actin to convert chemical energy, in the form of ATP, to mechanical energy []. The 3-D structure of the head portion of myosin has been determined [] and a model for actin-myosin complex has been constructed []. The globular head is well conserved, some highly-conserved regions possibly relating to functional and structural domains []. The rod-like tail starts with an invariant proline residue, and contains many repeats of a 28 residue region, interrupted at 4 regularly-spaced points known as skip residues. Although the sequence of the tail is not well conserved, the chemical character is, hydrophobic, charged and skip residues occuring in a highly ordered and repeated fashion [].; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 1LKX_A 2V26_A 2BKI_A 3L9I_A 2BKH_A 2X51_A 2VB6_A 2VAS_A 1OE9_A 1W8J_A ....
Probab=57.12 E-value=15 Score=29.74 Aligned_cols=37 Identities=27% Similarity=0.610 Sum_probs=23.0
Q ss_pred eEEEEEEEeCCCCCCccCCccchh-HHHHHHHHHHHHhhh
Q psy104 27 VKLRLTVVDTPGFGDSINSEESWR-ACCSYIDDQFRQYFN 65 (86)
Q Consensus 27 ~~l~LtIidTpGfGd~i~n~~~~~-~i~~yI~~qf~~yl~ 65 (86)
..-.+.|+|.|||-.. ..++++ -.++|..++...|+.
T Consensus 362 ~~~~IgILDi~GFE~~--~~N~fEQLciNyanErLq~~f~ 399 (689)
T PF00063_consen 362 NSSSIGILDIFGFENF--SVNSFEQLCINYANERLQQFFN 399 (689)
T ss_dssp -SEEEEEEEEE-B-----SSB-HHHHHHHHHHHHHHHHHH
T ss_pred ccccCcccCccccccc--cccccccceeeeccccccceee
Confidence 3456789999999866 444566 458999988877743
No 118
>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=56.64 E-value=30 Score=21.58 Aligned_cols=30 Identities=27% Similarity=0.338 Sum_probs=21.7
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
+|..+..+...+.-++.++.|.+.||+|-.
T Consensus 30 ~t~~~~~~~~~~~~~~~~~~l~i~D~~g~~ 59 (162)
T PF00071_consen 30 PTIGIDSYSKEVSIDGKPVNLEIWDTSGQE 59 (162)
T ss_dssp TTSSEEEEEEEEEETTEEEEEEEEEETTSG
T ss_pred cccccccccccccccccccccccccccccc
Confidence 344455555566666889999999999853
No 119
>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=56.16 E-value=51 Score=22.15 Aligned_cols=20 Identities=35% Similarity=0.523 Sum_probs=15.7
Q ss_pred EEeecCeEEEEEEEeCCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGfG 40 (86)
.+.-++-.++|.+.||+|-.
T Consensus 47 ~i~~~~~~~~l~iwDt~G~~ 66 (189)
T cd04121 47 TILLDGRRVKLQLWDTSGQG 66 (189)
T ss_pred EEEECCEEEEEEEEeCCCcH
Confidence 34446678999999999965
No 120
>PRK12288 GTPase RsgA; Reviewed
Probab=56.07 E-value=17 Score=27.33 Aligned_cols=11 Identities=27% Similarity=0.736 Sum_probs=8.7
Q ss_pred EEEeCCCCCCc
Q psy104 32 TVVDTPGFGDS 42 (86)
Q Consensus 32 tIidTpGfGd~ 42 (86)
.|||||||...
T Consensus 260 ~liDTPGir~~ 270 (347)
T PRK12288 260 DLIDSPGVREF 270 (347)
T ss_pred EEEECCCCCcc
Confidence 39999999643
No 121
>KOG0458|consensus
Probab=56.02 E-value=16 Score=29.80 Aligned_cols=20 Identities=30% Similarity=0.423 Sum_probs=16.2
Q ss_pred eEEEEEEEeCCCCCCccCCc
Q psy104 27 VKLRLTVVDTPGFGDSINSE 46 (86)
Q Consensus 27 ~~l~LtIidTpGfGd~i~n~ 46 (86)
-+-.+|++|+||-+|.+.|-
T Consensus 253 ~~~~~tliDaPGhkdFi~nm 272 (603)
T KOG0458|consen 253 KSKIVTLIDAPGHKDFIPNM 272 (603)
T ss_pred CceeEEEecCCCccccchhh
Confidence 36788999999988887664
No 122
>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=55.81 E-value=46 Score=20.45 Aligned_cols=14 Identities=36% Similarity=0.674 Sum_probs=11.9
Q ss_pred cCeEEEEEEEeCCC
Q psy104 25 RGVKLRLTVVDTPG 38 (86)
Q Consensus 25 ~~~~l~LtIidTpG 38 (86)
.+..+.+.+.||||
T Consensus 45 ~~~~~~~~~~D~~g 58 (162)
T cd04123 45 GGKRIDLAIWDTAG 58 (162)
T ss_pred CCEEEEEEEEECCc
Confidence 35678999999999
No 123
>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=55.65 E-value=28 Score=21.91 Aligned_cols=19 Identities=32% Similarity=0.518 Sum_probs=14.8
Q ss_pred EEeecCeEEEEEEEeCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGf 39 (86)
.+.-++..+.|.+.||||.
T Consensus 41 ~~~~~~~~~~l~i~Dt~G~ 59 (164)
T cd04175 41 QVEVDGQQCMLEILDTAGT 59 (164)
T ss_pred EEEECCEEEEEEEEECCCc
Confidence 3444567899999999996
No 124
>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=55.41 E-value=14 Score=25.00 Aligned_cols=26 Identities=23% Similarity=0.322 Sum_probs=14.8
Q ss_pred eEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 13 TTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 13 ~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
..+......++-++. +++++||||+-
T Consensus 63 ~T~~~~~~~~~~~~~--~~~liDTpG~~ 88 (208)
T cd04166 63 ITIDVAYRYFSTPKR--KFIIADTPGHE 88 (208)
T ss_pred cCeecceeEEecCCc--eEEEEECCcHH
Confidence 334433334443443 56789999974
No 125
>PLN03110 Rab GTPase; Provisional
Probab=55.27 E-value=50 Score=22.41 Aligned_cols=29 Identities=21% Similarity=0.312 Sum_probs=18.5
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
.|..+......+.-++..+.|.+.||||-
T Consensus 43 ~t~g~~~~~~~v~~~~~~~~l~l~Dt~G~ 71 (216)
T PLN03110 43 STIGVEFATRTLQVEGKTVKAQIWDTAGQ 71 (216)
T ss_pred CceeEEEEEEEEEECCEEEEEEEEECCCc
Confidence 34444433334444567789999999995
No 126
>COG1159 Era GTPase [General function prediction only]
Probab=55.26 E-value=11 Score=28.10 Aligned_cols=15 Identities=33% Similarity=0.638 Sum_probs=11.5
Q ss_pred EEEEEEEeCCCCCCc
Q psy104 28 KLRLTVVDTPGFGDS 42 (86)
Q Consensus 28 ~l~LtIidTpGfGd~ 42 (86)
.-.+..+|||||=..
T Consensus 53 ~~QiIfvDTPGih~p 67 (298)
T COG1159 53 NAQIIFVDTPGIHKP 67 (298)
T ss_pred CceEEEEeCCCCCCc
Confidence 456789999999543
No 127
>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=55.01 E-value=38 Score=21.45 Aligned_cols=21 Identities=29% Similarity=0.379 Sum_probs=15.8
Q ss_pred EEeecCeEEEEEEEeCCCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGfGd 41 (86)
.+.-++..+.++++||||-.+
T Consensus 40 ~~~~~~~~~~~~i~Dt~G~~~ 60 (174)
T cd04135 40 SVTVGGKQYLLGLYDTAGQED 60 (174)
T ss_pred EEEECCEEEEEEEEeCCCccc
Confidence 344456678899999999754
No 128
>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=54.95 E-value=50 Score=21.89 Aligned_cols=14 Identities=29% Similarity=0.401 Sum_probs=12.2
Q ss_pred CeEEEEEEEeCCCC
Q psy104 26 GVKLRLTVVDTPGF 39 (86)
Q Consensus 26 ~~~l~LtIidTpGf 39 (86)
+..+.|.+.||||-
T Consensus 47 ~~~~~l~l~Dt~G~ 60 (201)
T cd04107 47 NTVVRLQLWDIAGQ 60 (201)
T ss_pred CCEEEEEEEECCCc
Confidence 56889999999995
No 129
>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=54.91 E-value=18 Score=27.10 Aligned_cols=26 Identities=27% Similarity=0.452 Sum_probs=17.0
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
.|.......+.+. ++. .+.++|||||
T Consensus 222 tT~d~~~~~i~~~-~~~--~i~l~DT~G~ 247 (351)
T TIGR03156 222 ATLDPTTRRLDLP-DGG--EVLLTDTVGF 247 (351)
T ss_pred cccCCEEEEEEeC-CCc--eEEEEecCcc
Confidence 4555555655553 333 6788999999
No 130
>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=54.64 E-value=51 Score=20.66 Aligned_cols=19 Identities=37% Similarity=0.620 Sum_probs=14.0
Q ss_pred EeecCeEEEEEEEeCCCCC
Q psy104 22 IEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGfG 40 (86)
+.-++.++++.+.||||..
T Consensus 49 ~~~~~~~~~~~~~D~~g~~ 67 (169)
T cd04114 49 VEIKGEKIKLQIWDTAGQE 67 (169)
T ss_pred EEECCEEEEEEEEECCCcH
Confidence 3344667889999999853
No 131
>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=54.06 E-value=7.6 Score=26.08 Aligned_cols=10 Identities=30% Similarity=0.986 Sum_probs=8.5
Q ss_pred EEEEEeCCCC
Q psy104 30 RLTVVDTPGF 39 (86)
Q Consensus 30 ~LtIidTpGf 39 (86)
.+.++||||+
T Consensus 163 ~~~l~DtPGi 172 (172)
T cd04178 163 KVKLLDSPGI 172 (172)
T ss_pred CEEEEECcCC
Confidence 4779999996
No 132
>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=53.42 E-value=53 Score=22.37 Aligned_cols=29 Identities=34% Similarity=0.468 Sum_probs=18.1
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
.|..+.-+.-.+.-++-.++|.+.||+|-
T Consensus 31 ~Ti~~~~~~~~i~~~~~~v~l~iwDtaGq 59 (202)
T cd04120 31 SGVGVDFKIKTVELRGKKIRLQIWDTAGQ 59 (202)
T ss_pred CcceeEEEEEEEEECCEEEEEEEEeCCCc
Confidence 34433333233444567899999999984
No 133
>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=53.41 E-value=30 Score=21.68 Aligned_cols=18 Identities=33% Similarity=0.386 Sum_probs=14.0
Q ss_pred EeecCeEEEEEEEeCCCC
Q psy104 22 IEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGf 39 (86)
+.-++.++.|.+.||||.
T Consensus 42 ~~~~~~~~~l~i~Dt~G~ 59 (163)
T cd04176 42 IEVDSSPSVLEILDTAGT 59 (163)
T ss_pred EEECCEEEEEEEEECCCc
Confidence 334567889999999995
No 134
>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=53.20 E-value=31 Score=21.58 Aligned_cols=19 Identities=37% Similarity=0.413 Sum_probs=14.2
Q ss_pred EeecCeEEEEEEEeCCCCC
Q psy104 22 IEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGfG 40 (86)
+.-++-.+.|.++||||--
T Consensus 41 ~~~~~~~~~l~i~Dt~g~~ 59 (164)
T smart00173 41 IEIDGEVCLLDILDTAGQE 59 (164)
T ss_pred EEECCEEEEEEEEECCCcc
Confidence 3344568999999999953
No 135
>PLN00043 elongation factor 1-alpha; Provisional
Probab=52.98 E-value=8.7 Score=29.75 Aligned_cols=31 Identities=29% Similarity=0.362 Sum_probs=19.7
Q ss_pred CcceEEEEEEEEEeecCeEEEEEEEeCCCCCCc
Q psy104 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 10 ~~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~ 42 (86)
.+...|......++.++ .+++++||||..+.
T Consensus 68 ~rGiTi~~~~~~~~~~~--~~i~liDtPGh~df 98 (447)
T PLN00043 68 ERGITIDIALWKFETTK--YYCTVIDAPGHRDF 98 (447)
T ss_pred hcCceEEEEEEEecCCC--EEEEEEECCCHHHH
Confidence 44555555545555443 57889999997544
No 136
>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=52.78 E-value=21 Score=28.71 Aligned_cols=31 Identities=29% Similarity=0.498 Sum_probs=20.2
Q ss_pred ceEEEEEEEEEe---ecCeEEEEEEEeCCCCCCc
Q psy104 12 TTTIEKKSMDIE---ERGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 12 t~~I~~~~~~l~---e~~~~l~LtIidTpGfGd~ 42 (86)
...|....+.+. .++-.+.|+++||||.-+.
T Consensus 50 GiTi~~~~v~~~~~~~~g~~~~l~liDTPG~~dF 83 (595)
T TIGR01393 50 GITIKAQAVRLNYKAKDGETYVLNLIDTPGHVDF 83 (595)
T ss_pred CCCeeeeEEEEEEEcCCCCEEEEEEEECCCcHHH
Confidence 344554444442 1455789999999999764
No 137
>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=52.63 E-value=50 Score=21.30 Aligned_cols=15 Identities=33% Similarity=0.481 Sum_probs=12.7
Q ss_pred cCeEEEEEEEeCCCC
Q psy104 25 RGVKLRLTVVDTPGF 39 (86)
Q Consensus 25 ~~~~l~LtIidTpGf 39 (86)
++..+.|.+.||||-
T Consensus 45 ~~~~~~l~i~Dt~G~ 59 (187)
T cd04132 45 NGKIIELALWDTAGQ 59 (187)
T ss_pred CCcEEEEEEEECCCc
Confidence 367889999999994
No 138
>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=52.52 E-value=30 Score=21.86 Aligned_cols=17 Identities=29% Similarity=0.544 Sum_probs=13.9
Q ss_pred cCeEEEEEEEeCCCCCC
Q psy104 25 RGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 25 ~~~~l~LtIidTpGfGd 41 (86)
++-.+++.++||||...
T Consensus 43 ~~~~~~~~i~D~~g~~~ 59 (165)
T cd04146 43 DGEQVSLEILDTAGQQQ 59 (165)
T ss_pred CCEEEEEEEEECCCCcc
Confidence 45678999999999873
No 139
>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=52.46 E-value=18 Score=27.52 Aligned_cols=28 Identities=25% Similarity=0.305 Sum_probs=17.2
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
.+++......++-++ .+++++||||..+
T Consensus 65 giTid~~~~~~~~~~--~~~~liDtPGh~~ 92 (406)
T TIGR02034 65 GITIDVAYRYFSTDK--RKFIVADTPGHEQ 92 (406)
T ss_pred CcCeEeeeEEEccCC--eEEEEEeCCCHHH
Confidence 444555444554444 3678999999543
No 140
>COG1084 Predicted GTPase [General function prediction only]
Probab=52.24 E-value=13 Score=28.38 Aligned_cols=28 Identities=43% Similarity=0.744 Sum_probs=16.2
Q ss_pred eEEEEEEEEEe--ecCeEEEEEEEeCCCCCC
Q psy104 13 TTIEKKSMDIE--ERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 13 ~~I~~~~~~l~--e~~~~l~LtIidTpGfGd 41 (86)
..++++.+.+- |.+ -++..||||||+=|
T Consensus 198 YPFTTK~i~vGhfe~~-~~R~QvIDTPGlLD 227 (346)
T COG1084 198 YPFTTKGIHVGHFERG-YLRIQVIDTPGLLD 227 (346)
T ss_pred CCccccceeEeeeecC-CceEEEecCCcccC
Confidence 34455555442 211 24677999999954
No 141
>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=51.96 E-value=55 Score=21.27 Aligned_cols=17 Identities=24% Similarity=0.319 Sum_probs=13.4
Q ss_pred cCeEEEEEEEeCCCCCC
Q psy104 25 RGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 25 ~~~~l~LtIidTpGfGd 41 (86)
++-.+.|.+.||||...
T Consensus 45 ~~~~~~~~i~Dt~g~~~ 61 (188)
T cd04125 45 ENKIIKLQIWDTNGQER 61 (188)
T ss_pred CCEEEEEEEEECCCcHH
Confidence 44578999999999753
No 142
>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=51.90 E-value=49 Score=20.92 Aligned_cols=19 Identities=37% Similarity=0.515 Sum_probs=14.6
Q ss_pred EEeecCeEEEEEEEeCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGf 39 (86)
.+.-++-.+.|.+.||||-
T Consensus 38 ~~~~~~~~~~~~i~Dt~G~ 56 (174)
T smart00174 38 DVEVDGKPVELGLWDTAGQ 56 (174)
T ss_pred EEEECCEEEEEEEEECCCC
Confidence 3444567889999999994
No 143
>PRK12289 GTPase RsgA; Reviewed
Probab=50.90 E-value=7.8 Score=29.23 Aligned_cols=10 Identities=50% Similarity=1.009 Sum_probs=8.3
Q ss_pred EEEeCCCCCC
Q psy104 32 TVVDTPGFGD 41 (86)
Q Consensus 32 tIidTpGfGd 41 (86)
-++|||||-.
T Consensus 227 ~liDTPG~~~ 236 (352)
T PRK12289 227 LLADTPGFNQ 236 (352)
T ss_pred EEEeCCCccc
Confidence 4999999963
No 144
>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=50.08 E-value=18 Score=27.24 Aligned_cols=29 Identities=28% Similarity=0.457 Sum_probs=17.8
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
+...+......++.++ .+++++||||.-+
T Consensus 59 rG~Ti~~~~~~~~~~~--~~~~liDtpGh~~ 87 (394)
T TIGR00485 59 RGITINTAHVEYETEN--RHYAHVDCPGHAD 87 (394)
T ss_pred cCcceeeEEEEEcCCC--EEEEEEECCchHH
Confidence 3444555444554443 4678999999753
No 145
>TIGR01938 nqrC NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit. This model represents the NqrC subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria. This oxidoreductase complex functions primarily as a sodium ion pump.
Probab=49.81 E-value=8.3 Score=28.01 Aligned_cols=20 Identities=35% Similarity=0.627 Sum_probs=14.4
Q ss_pred eEEEEEEE---eCCCCCCccCCc
Q psy104 27 VKLRLTVV---DTPGFGDSINSE 46 (86)
Q Consensus 27 ~~l~LtIi---dTpGfGd~i~n~ 46 (86)
.-.-+.+. +|||+|..+.+.
T Consensus 162 tI~Gi~~~~h~ETPGLG~~I~~~ 184 (251)
T TIGR01938 162 TVLGITYYQQGETPGLGAEIENP 184 (251)
T ss_pred EEEEEEEeecCcCCCCccccCCH
Confidence 34445555 899999999765
No 146
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=49.66 E-value=13 Score=28.79 Aligned_cols=29 Identities=28% Similarity=0.393 Sum_probs=18.0
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCCCc
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~ 42 (86)
..++......++.++ .++++|||||.-+.
T Consensus 70 GiTid~~~~~~~~~~--~~i~lIDtPGh~~f 98 (446)
T PTZ00141 70 GITIDIALWKFETPK--YYFTIIDAPGHRDF 98 (446)
T ss_pred CEeEEeeeEEEccCC--eEEEEEECCChHHH
Confidence 444544444555443 57889999996544
No 147
>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=49.14 E-value=28 Score=21.86 Aligned_cols=14 Identities=29% Similarity=0.273 Sum_probs=11.2
Q ss_pred EEEEEEEeCCCCCC
Q psy104 28 KLRLTVVDTPGFGD 41 (86)
Q Consensus 28 ~l~LtIidTpGfGd 41 (86)
...+.++||||...
T Consensus 49 ~~~~~l~Dt~G~~~ 62 (167)
T cd04160 49 NARLKFWDLGGQES 62 (167)
T ss_pred CEEEEEEECCCChh
Confidence 46889999999653
No 148
>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=48.63 E-value=71 Score=21.05 Aligned_cols=30 Identities=20% Similarity=0.242 Sum_probs=19.2
Q ss_pred CcceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 10 ~~t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
.+|.....+...+.-++.++.|.|.||+|-
T Consensus 30 ~~T~g~~~~~~~i~~~~~~~~l~iwDt~G~ 59 (182)
T cd04128 30 IQTLGVNFMEKTISIRGTEITFSIWDLGGQ 59 (182)
T ss_pred CCccceEEEEEEEEECCEEEEEEEEeCCCc
Confidence 445544433333444567899999999984
No 149
>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=48.46 E-value=28 Score=25.18 Aligned_cols=10 Identities=50% Similarity=1.122 Sum_probs=8.4
Q ss_pred EEEeCCCCCC
Q psy104 32 TVVDTPGFGD 41 (86)
Q Consensus 32 tIidTpGfGd 41 (86)
.++|||||..
T Consensus 216 ~liDtPG~~~ 225 (287)
T cd01854 216 LLIDTPGFRE 225 (287)
T ss_pred EEEECCCCCc
Confidence 4999999954
No 150
>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=48.41 E-value=65 Score=21.52 Aligned_cols=27 Identities=22% Similarity=0.398 Sum_probs=13.1
Q ss_pred CcceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 10 ~~t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
..|++.....+.+. + -.+.++|+||.=
T Consensus 32 G~Tv~~~~g~~~~~--~--~~~~lvDlPG~y 58 (156)
T PF02421_consen 32 GTTVEKKEGIFKLG--D--QQVELVDLPGIY 58 (156)
T ss_dssp TSSSEEEEEEEEET--T--EEEEEEE----S
T ss_pred CCCeeeeeEEEEec--C--ceEEEEECCCcc
Confidence 34555555444443 3 567899999963
No 151
>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=48.30 E-value=39 Score=22.23 Aligned_cols=18 Identities=33% Similarity=0.316 Sum_probs=13.8
Q ss_pred eecCeEEEEEEEeCCCCC
Q psy104 23 EERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 23 ~e~~~~l~LtIidTpGfG 40 (86)
.-++..+.|.+.||||.-
T Consensus 41 ~~~~~~~~l~i~Dt~G~~ 58 (190)
T cd04144 41 VVDGQPCMLEVLDTAGQE 58 (190)
T ss_pred EECCEEEEEEEEECCCch
Confidence 345667899999999953
No 152
>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=47.87 E-value=58 Score=22.06 Aligned_cols=15 Identities=40% Similarity=0.711 Sum_probs=12.6
Q ss_pred cCeEEEEEEEeCCCC
Q psy104 25 RGVKLRLTVVDTPGF 39 (86)
Q Consensus 25 ~~~~l~LtIidTpGf 39 (86)
++..++|.+.||||-
T Consensus 48 ~~~~~~l~i~Dt~G~ 62 (211)
T cd04111 48 PGVRIKLQLWDTAGQ 62 (211)
T ss_pred CCCEEEEEEEeCCcc
Confidence 467889999999993
No 153
>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=47.86 E-value=26 Score=28.45 Aligned_cols=29 Identities=31% Similarity=0.481 Sum_probs=18.3
Q ss_pred eEEEEEEEEEeecCeEEEEEEEeCCCCCCcc
Q psy104 13 TTIEKKSMDIEERGVKLRLTVVDTPGFGDSI 43 (86)
Q Consensus 13 ~~I~~~~~~l~e~~~~l~LtIidTpGfGd~i 43 (86)
..+......++-++ .+++++||||..+..
T Consensus 61 iti~~~~~~~~~~~--~~i~liDTPG~~~~~ 89 (689)
T TIGR00484 61 ITITSAATTVFWKG--HRINIIDTPGHVDFT 89 (689)
T ss_pred CCEecceEEEEECC--eEEEEEECCCCcchh
Confidence 34444444454444 467899999997643
No 154
>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=47.52 E-value=72 Score=20.29 Aligned_cols=14 Identities=36% Similarity=0.617 Sum_probs=11.9
Q ss_pred CeEEEEEEEeCCCC
Q psy104 26 GVKLRLTVVDTPGF 39 (86)
Q Consensus 26 ~~~l~LtIidTpGf 39 (86)
+..+.|.+.||||-
T Consensus 60 ~~~~~~~i~Dt~G~ 73 (180)
T cd04127 60 GQRIHLQLWDTAGQ 73 (180)
T ss_pred CCEEEEEEEeCCCh
Confidence 56789999999993
No 155
>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=47.31 E-value=62 Score=20.22 Aligned_cols=20 Identities=25% Similarity=0.415 Sum_probs=15.3
Q ss_pred EeecCeEEEEEEEeCCCCCC
Q psy104 22 IEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGfGd 41 (86)
+.-.+..+.|.++||||...
T Consensus 41 ~~~~~~~~~l~~~D~~g~~~ 60 (171)
T cd00157 41 VTVDGKQVNLGLWDTAGQEE 60 (171)
T ss_pred EEECCEEEEEEEEeCCCccc
Confidence 34456788999999999763
No 156
>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=47.30 E-value=46 Score=25.77 Aligned_cols=16 Identities=25% Similarity=0.646 Sum_probs=11.8
Q ss_pred cCeEEEEEEEeCCCCCCc
Q psy104 25 RGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 25 ~~~~l~LtIidTpGfGd~ 42 (86)
+|.+ ++++||||+.+.
T Consensus 249 ~g~~--v~l~DTaG~~~~ 264 (442)
T TIGR00450 249 NGIL--IKLLDTAGIREH 264 (442)
T ss_pred CCEE--EEEeeCCCcccc
Confidence 4544 589999999754
No 157
>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=46.68 E-value=78 Score=21.30 Aligned_cols=30 Identities=20% Similarity=0.202 Sum_probs=18.3
Q ss_pred CcceEEEEEEEEEe-ecCeEEEEEEEeCCCC
Q psy104 10 GKTTTIEKKSMDIE-ERGVKLRLTVVDTPGF 39 (86)
Q Consensus 10 ~~t~~I~~~~~~l~-e~~~~l~LtIidTpGf 39 (86)
.+|..+..+...+. .++..++|.|.||||-
T Consensus 30 ~~T~~~d~~~~~i~~~~~~~~~~~i~Dt~G~ 60 (215)
T cd04109 30 KQTIGLDFFSKRVTLPGNLNVTLQVWDIGGQ 60 (215)
T ss_pred CCceeEEEEEEEEEeCCCCEEEEEEEECCCc
Confidence 44554444333333 2336789999999994
No 158
>CHL00189 infB translation initiation factor 2; Provisional
Probab=46.61 E-value=24 Score=29.44 Aligned_cols=27 Identities=22% Similarity=0.431 Sum_probs=16.7
Q ss_pred EEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 15 IEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 15 I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
+..+.+.+.-++-...++++||||..+
T Consensus 281 i~~~~v~~~~~~~~~kItfiDTPGhe~ 307 (742)
T CHL00189 281 IGAYEVEFEYKDENQKIVFLDTPGHEA 307 (742)
T ss_pred cceEEEEEEecCCceEEEEEECCcHHH
Confidence 334444443333357899999999753
No 159
>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....
Probab=46.55 E-value=36 Score=23.28 Aligned_cols=12 Identities=33% Similarity=0.553 Sum_probs=8.7
Q ss_pred EEEEEEeCCCCC
Q psy104 29 LRLTVVDTPGFG 40 (86)
Q Consensus 29 l~LtIidTpGfG 40 (86)
..+-+|||||..
T Consensus 84 ~D~vlIDT~Gr~ 95 (196)
T PF00448_consen 84 YDLVLIDTAGRS 95 (196)
T ss_dssp SSEEEEEE-SSS
T ss_pred CCEEEEecCCcc
Confidence 346799999986
No 160
>PLN03108 Rab family protein; Provisional
Probab=45.96 E-value=57 Score=21.99 Aligned_cols=18 Identities=28% Similarity=0.381 Sum_probs=13.5
Q ss_pred EeecCeEEEEEEEeCCCC
Q psy104 22 IEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGf 39 (86)
+.-++..+.|++.||||-
T Consensus 48 i~~~~~~i~l~l~Dt~G~ 65 (210)
T PLN03108 48 ITIDNKPIKLQIWDTAGQ 65 (210)
T ss_pred EEECCEEEEEEEEeCCCc
Confidence 333456789999999984
No 161
>KOG2486|consensus
Probab=45.10 E-value=43 Score=25.30 Aligned_cols=28 Identities=29% Similarity=0.258 Sum_probs=18.8
Q ss_pred EEeecCeEEEEEEEeCCCCCCccCCccc
Q psy104 21 DIEERGVKLRLTVVDTPGFGDSINSEES 48 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGfGd~i~n~~~ 48 (86)
.|+-..+..++.++|-||||..--+...
T Consensus 175 ~in~f~v~~~~~~vDlPG~~~a~y~~~~ 202 (320)
T KOG2486|consen 175 AINHFHVGKSWYEVDLPGYGRAGYGFEL 202 (320)
T ss_pred eeeeeeccceEEEEecCCcccccCCccC
Confidence 3444556778999999997755444433
No 162
>COG1217 TypA Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]
Probab=44.99 E-value=31 Score=27.97 Aligned_cols=30 Identities=37% Similarity=0.585 Sum_probs=19.8
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCCCCc
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~ 42 (86)
....|-.+..-+.=++ .+++|+||||=.|.
T Consensus 52 RGITILaKnTav~~~~--~~INIvDTPGHADF 81 (603)
T COG1217 52 RGITILAKNTAVNYNG--TRINIVDTPGHADF 81 (603)
T ss_pred cCcEEEeccceeecCC--eEEEEecCCCcCCc
Confidence 3455555555555454 67889999996654
No 163
>PRK12317 elongation factor 1-alpha; Reviewed
Probab=44.70 E-value=26 Score=26.56 Aligned_cols=27 Identities=33% Similarity=0.493 Sum_probs=16.2
Q ss_pred eEEEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 13 TTIEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 13 ~~I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
..+......++.++ .+++++||||.-+
T Consensus 70 ~T~d~~~~~~~~~~--~~i~liDtpG~~~ 96 (425)
T PRK12317 70 VTIDLAHKKFETDK--YYFTIVDCPGHRD 96 (425)
T ss_pred ccceeeeEEEecCC--eEEEEEECCCccc
Confidence 33444334444443 5789999999643
No 164
>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=44.62 E-value=23 Score=29.05 Aligned_cols=14 Identities=36% Similarity=0.712 Sum_probs=12.0
Q ss_pred EEEEEEEeCCCCCC
Q psy104 28 KLRLTVVDTPGFGD 41 (86)
Q Consensus 28 ~l~LtIidTpGfGd 41 (86)
...++++||||+-+
T Consensus 85 ~~~i~liDTPG~~~ 98 (720)
T TIGR00490 85 EYLINLIDTPGHVD 98 (720)
T ss_pred ceEEEEEeCCCccc
Confidence 57889999999865
No 165
>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=44.47 E-value=16 Score=24.72 Aligned_cols=12 Identities=33% Similarity=0.631 Sum_probs=10.2
Q ss_pred EEEEEEeCCCCC
Q psy104 29 LRLTVVDTPGFG 40 (86)
Q Consensus 29 l~LtIidTpGfG 40 (86)
.+++++||||..
T Consensus 83 ~~i~~iDtPG~~ 94 (203)
T cd01888 83 RHVSFVDCPGHE 94 (203)
T ss_pred cEEEEEECCChH
Confidence 678999999954
No 166
>PLN03126 Elongation factor Tu; Provisional
Probab=44.42 E-value=37 Score=26.65 Aligned_cols=29 Identities=28% Similarity=0.477 Sum_probs=17.3
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
+...+......++.++ .+++++||||.-+
T Consensus 128 rGiTi~~~~~~~~~~~--~~i~liDtPGh~~ 156 (478)
T PLN03126 128 RGITINTATVEYETEN--RHYAHVDCPGHAD 156 (478)
T ss_pred CCeeEEEEEEEEecCC--cEEEEEECCCHHH
Confidence 3444554444444343 3678999999643
No 167
>PRK05433 GTP-binding protein LepA; Provisional
Probab=44.22 E-value=23 Score=28.57 Aligned_cols=18 Identities=39% Similarity=0.582 Sum_probs=14.2
Q ss_pred cCeEEEEEEEeCCCCCCc
Q psy104 25 RGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 25 ~~~~l~LtIidTpGfGd~ 42 (86)
++-.++|+++||||.-+.
T Consensus 70 dg~~~~lnLiDTPGh~dF 87 (600)
T PRK05433 70 DGETYILNLIDTPGHVDF 87 (600)
T ss_pred CCCcEEEEEEECCCcHHH
Confidence 344688999999998764
No 168
>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=44.20 E-value=34 Score=21.95 Aligned_cols=13 Identities=23% Similarity=0.325 Sum_probs=10.5
Q ss_pred EEEEEEEeCCCCC
Q psy104 28 KLRLTVVDTPGFG 40 (86)
Q Consensus 28 ~l~LtIidTpGfG 40 (86)
.+.|.++||||-.
T Consensus 57 ~~~l~l~D~~G~~ 69 (173)
T cd04154 57 GYKLNIWDVGGQK 69 (173)
T ss_pred CEEEEEEECCCCH
Confidence 3678999999954
No 169
>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=44.19 E-value=57 Score=22.31 Aligned_cols=16 Identities=25% Similarity=0.189 Sum_probs=13.2
Q ss_pred cCeEEEEEEEeCCCCC
Q psy104 25 RGVKLRLTVVDTPGFG 40 (86)
Q Consensus 25 ~~~~l~LtIidTpGfG 40 (86)
++....|.++||||..
T Consensus 46 ~~~~~~l~i~Dt~G~~ 61 (221)
T cd04148 46 DGEESTLVVIDHWEQE 61 (221)
T ss_pred CCEEEEEEEEeCCCcc
Confidence 3457889999999986
No 170
>cd01385 MYSc_type_IX Myosin motor domain, type IX myosins. Myosin IX is a processive single-headed motor, which might play a role in signalling. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the hea
Probab=44.15 E-value=38 Score=27.91 Aligned_cols=36 Identities=31% Similarity=0.575 Sum_probs=25.5
Q ss_pred EEEEEEEeCCCCCCccCCccchhHH-HHHHHHHHHHhh
Q psy104 28 KLRLTVVDTPGFGDSINSEESWRAC-CSYIDDQFRQYF 64 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~n~~~~~~i-~~yI~~qf~~yl 64 (86)
...+.|.|.+||=. ..+.++++.+ ++|..++...++
T Consensus 375 ~~~IgiLDI~GFE~-f~~~NsfEQLcINyaNEkLQ~~f 411 (692)
T cd01385 375 GLSIGVLDIFGFED-FGRCNSFEQLCINYANEQLQYYF 411 (692)
T ss_pred ceEEEEEecCcccc-CCCCCCHHHHhhHHHHHHHHHHH
Confidence 35688999999943 3333566744 889888877764
No 171
>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=43.97 E-value=53 Score=21.37 Aligned_cols=20 Identities=25% Similarity=0.340 Sum_probs=15.1
Q ss_pred EEeecCeEEEEEEEeCCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGfG 40 (86)
.+.-++-.++|.+.||||-.
T Consensus 41 ~~~~~~~~~~l~i~Dt~G~~ 60 (174)
T cd01871 41 NVMVDGKPVNLGLWDTAGQE 60 (174)
T ss_pred EEEECCEEEEEEEEECCCch
Confidence 33445678999999999854
No 172
>PRK03003 GTP-binding protein Der; Reviewed
Probab=43.63 E-value=1.5e+02 Score=22.88 Aligned_cols=11 Identities=64% Similarity=0.939 Sum_probs=9.3
Q ss_pred EEEEEeCCCCC
Q psy104 30 RLTVVDTPGFG 40 (86)
Q Consensus 30 ~LtIidTpGfG 40 (86)
.+.++||||+.
T Consensus 87 ~~~l~DT~G~~ 97 (472)
T PRK03003 87 RFTVVDTGGWE 97 (472)
T ss_pred EEEEEeCCCcC
Confidence 47789999986
No 173
>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=43.59 E-value=48 Score=21.97 Aligned_cols=17 Identities=47% Similarity=0.685 Sum_probs=13.4
Q ss_pred eecCeEEEEEEEeCCCC
Q psy104 23 EERGVKLRLTVVDTPGF 39 (86)
Q Consensus 23 ~e~~~~l~LtIidTpGf 39 (86)
.-++..++|+++||||.
T Consensus 41 ~~~~~~~~l~i~D~~G~ 57 (198)
T cd04147 41 EVGGVSLTLDILDTSGS 57 (198)
T ss_pred EECCEEEEEEEEECCCc
Confidence 33456789999999995
No 174
>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=43.46 E-value=54 Score=20.77 Aligned_cols=18 Identities=39% Similarity=0.543 Sum_probs=13.6
Q ss_pred EeecCeEEEEEEEeCCCC
Q psy104 22 IEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGf 39 (86)
+.-++-.+.|.+.||||-
T Consensus 42 ~~~~~~~~~l~i~Dt~G~ 59 (175)
T cd01870 42 IEVDGKQVELALWDTAGQ 59 (175)
T ss_pred EEECCEEEEEEEEeCCCc
Confidence 343456789999999994
No 175
>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=43.26 E-value=20 Score=22.36 Aligned_cols=13 Identities=38% Similarity=0.626 Sum_probs=11.0
Q ss_pred EEEEEEEeCCCCC
Q psy104 28 KLRLTVVDTPGFG 40 (86)
Q Consensus 28 ~l~LtIidTpGfG 40 (86)
.++++++||||..
T Consensus 44 ~~~~~l~Dt~G~~ 56 (162)
T cd04157 44 NLSFTAFDMSGQG 56 (162)
T ss_pred CEEEEEEECCCCH
Confidence 5778999999975
No 176
>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=43.24 E-value=63 Score=19.76 Aligned_cols=18 Identities=28% Similarity=0.374 Sum_probs=13.6
Q ss_pred eecCeEEEEEEEeCCCCC
Q psy104 23 EERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 23 ~e~~~~l~LtIidTpGfG 40 (86)
.-++..+++.++|+||-.
T Consensus 41 ~~~~~~~~~~l~D~~g~~ 58 (160)
T cd00876 41 VVDGETYTLDILDTAGQE 58 (160)
T ss_pred EECCEEEEEEEEECCChH
Confidence 344567889999999954
No 177
>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=42.78 E-value=56 Score=21.26 Aligned_cols=20 Identities=25% Similarity=0.282 Sum_probs=15.2
Q ss_pred EEeecCeEEEEEEEeCCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGfG 40 (86)
.+.-++-+++|.|.||+|-.
T Consensus 41 ~~~~~~~~~~l~i~Dt~G~~ 60 (175)
T cd01874 41 TVMIGGEPYTLGLFDTAGQE 60 (175)
T ss_pred EEEECCEEEEEEEEECCCcc
Confidence 34445678999999999864
No 178
>CHL00071 tufA elongation factor Tu
Probab=42.68 E-value=43 Score=25.42 Aligned_cols=29 Identities=28% Similarity=0.457 Sum_probs=17.0
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
+...+......++.++ .+++++||||..+
T Consensus 59 rg~T~~~~~~~~~~~~--~~~~~iDtPGh~~ 87 (409)
T CHL00071 59 RGITINTAHVEYETEN--RHYAHVDCPGHAD 87 (409)
T ss_pred CCEeEEccEEEEccCC--eEEEEEECCChHH
Confidence 3444554444444333 3567999999653
No 179
>PRK13796 GTPase YqeH; Provisional
Probab=42.63 E-value=25 Score=26.36 Aligned_cols=28 Identities=18% Similarity=0.292 Sum_probs=16.8
Q ss_pred EEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhh
Q psy104 32 TVVDTPGFGDSINSEESWRACCSYIDDQFRQYFND 66 (86)
Q Consensus 32 tIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~e 66 (86)
.++||||+-. .. .+.+|++.+-...+..
T Consensus 213 ~l~DTPGi~~----~~---~~~~~l~~~~l~~~~p 240 (365)
T PRK13796 213 FLYDTPGIIH----RH---QMAHYLSAKDLKIISP 240 (365)
T ss_pred EEEECCCccc----cc---hhhhcCCHHHHhhcCC
Confidence 6999999941 11 2456666555544433
No 180
>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=42.63 E-value=59 Score=20.56 Aligned_cols=19 Identities=26% Similarity=0.190 Sum_probs=14.2
Q ss_pred EeecCeEEEEEEEeCCCCC
Q psy104 22 IEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGfG 40 (86)
+.-++-.+.|.+.||||.-
T Consensus 42 ~~~~~~~~~l~i~Dt~G~~ 60 (165)
T cd04140 42 ISCSKNICTLQITDTTGSH 60 (165)
T ss_pred EEECCEEEEEEEEECCCCC
Confidence 3334457899999999964
No 181
>PTZ00369 Ras-like protein; Provisional
Probab=42.46 E-value=60 Score=21.28 Aligned_cols=17 Identities=24% Similarity=0.309 Sum_probs=13.2
Q ss_pred cCeEEEEEEEeCCCCCC
Q psy104 25 RGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 25 ~~~~l~LtIidTpGfGd 41 (86)
++-.+.|.+.||||.-+
T Consensus 49 ~~~~~~l~i~Dt~G~~~ 65 (189)
T PTZ00369 49 DEETCLLDILDTAGQEE 65 (189)
T ss_pred CCEEEEEEEEeCCCCcc
Confidence 45578899999999543
No 182
>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed
Probab=42.42 E-value=44 Score=25.81 Aligned_cols=26 Identities=23% Similarity=0.595 Sum_probs=16.1
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
|..+....+.+ +|. .++++||||+.+
T Consensus 250 T~d~~~~~i~~--~g~--~i~l~DT~G~~~ 275 (449)
T PRK05291 250 TRDVIEEHINL--DGI--PLRLIDTAGIRE 275 (449)
T ss_pred ccccEEEEEEE--CCe--EEEEEeCCCCCC
Confidence 44444444444 444 468999999964
No 183
>PRK00049 elongation factor Tu; Reviewed
Probab=42.25 E-value=35 Score=25.78 Aligned_cols=29 Identities=24% Similarity=0.392 Sum_probs=17.4
Q ss_pred CcceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 10 ~~t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
.....+......++.++ ..++++||||..
T Consensus 58 ~rg~Ti~~~~~~~~~~~--~~i~~iDtPG~~ 86 (396)
T PRK00049 58 ARGITINTAHVEYETEK--RHYAHVDCPGHA 86 (396)
T ss_pred hcCeEEeeeEEEEcCCC--eEEEEEECCCHH
Confidence 34445555444554443 356899999974
No 184
>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=42.03 E-value=20 Score=23.67 Aligned_cols=14 Identities=43% Similarity=0.909 Sum_probs=11.2
Q ss_pred EEEEEEEeCCCCCC
Q psy104 28 KLRLTVVDTPGFGD 41 (86)
Q Consensus 28 ~l~LtIidTpGfGd 41 (86)
..+++++||||..+
T Consensus 64 ~~~~~l~DtpG~~~ 77 (194)
T cd01891 64 DTKINIVDTPGHAD 77 (194)
T ss_pred CEEEEEEECCCcHH
Confidence 36789999999754
No 185
>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=41.83 E-value=57 Score=20.83 Aligned_cols=19 Identities=37% Similarity=0.573 Sum_probs=14.3
Q ss_pred EeecCeEEEEEEEeCCCCC
Q psy104 22 IEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGfG 40 (86)
+.-++..+.+.++||||..
T Consensus 42 ~~~~~~~~~~~l~D~~g~~ 60 (180)
T cd04137 42 IRYKGQDYHLEIVDTAGQD 60 (180)
T ss_pred EEECCEEEEEEEEECCChH
Confidence 3444567889999999964
No 186
>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=41.74 E-value=1e+02 Score=20.33 Aligned_cols=18 Identities=28% Similarity=0.348 Sum_probs=13.9
Q ss_pred EeecCeEEEEEEEeCCCC
Q psy104 22 IEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGf 39 (86)
+.-++-.++|.|.||+|-
T Consensus 44 ~~~~~~~~~l~i~Dt~G~ 61 (191)
T cd01875 44 TAVDGRTVSLNLWDTAGQ 61 (191)
T ss_pred EEECCEEEEEEEEECCCc
Confidence 333567899999999983
No 187
>TIGR02584 cas_NE0113 CRISPR-associated protein, NE0113 family. Members of this minor CRISPR-associated (Cas) protein family are found in cas gene clusters in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, Mannheimia succiniciproducens MBEL55E, and Verrucomicrobium spinosum.
Probab=41.41 E-value=17 Score=25.82 Aligned_cols=11 Identities=9% Similarity=-0.000 Sum_probs=9.1
Q ss_pred CCCCeeEEeec
Q psy104 75 IVDNREVVDKS 85 (86)
Q Consensus 75 ~~D~RVH~Cl~ 85 (86)
-+|.|+|+||+
T Consensus 116 d~~~~lH~sIA 126 (209)
T TIGR02584 116 AQDHQLHASIA 126 (209)
T ss_pred CCCCEEEEEec
Confidence 35789999997
No 188
>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed
Probab=41.32 E-value=1.7e+02 Score=24.07 Aligned_cols=13 Identities=31% Similarity=0.524 Sum_probs=10.5
Q ss_pred EEEEEEeCCCCCC
Q psy104 29 LRLTVVDTPGFGD 41 (86)
Q Consensus 29 l~LtIidTpGfGd 41 (86)
..++++||||+..
T Consensus 323 ~~~~liDT~G~~~ 335 (712)
T PRK09518 323 TDFKLVDTGGWEA 335 (712)
T ss_pred EEEEEEeCCCcCC
Confidence 3577899999974
No 189
>smart00242 MYSc Myosin. Large ATPases. ATPase; molecular motor. Muscle contraction consists of a cyclical interaction between myosin and actin. The core of the myosin structure is similar in fold to that of kinesin.
Probab=41.25 E-value=47 Score=27.20 Aligned_cols=36 Identities=22% Similarity=0.390 Sum_probs=26.3
Q ss_pred eEEEEEEEeCCCCCCccCCccchhHH-HHHHHHHHHHhh
Q psy104 27 VKLRLTVVDTPGFGDSINSEESWRAC-CSYIDDQFRQYF 64 (86)
Q Consensus 27 ~~l~LtIidTpGfGd~i~n~~~~~~i-~~yI~~qf~~yl 64 (86)
....+.|+|.|||=..-. ++|+.+ ++|..+++..++
T Consensus 367 ~~~~IgiLDifGFE~f~~--NsfEQLcINyaNEkLq~~f 403 (677)
T smart00242 367 STYFIGVLDIYGFEIFEV--NSFEQLCINYANEKLQQFF 403 (677)
T ss_pred CceEEEEEeccccccccc--CCHHHHHhHhhHHHHHHHH
Confidence 456789999999954433 467754 899998887764
No 190
>PRK05724 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated
Probab=41.17 E-value=17 Score=27.35 Aligned_cols=15 Identities=40% Similarity=0.689 Sum_probs=11.4
Q ss_pred cCeEEEEEEEeCCCCC
Q psy104 25 RGVKLRLTVVDTPGFG 40 (86)
Q Consensus 25 ~~~~l~LtIidTpGfG 40 (86)
.++|+ ++++|||||-
T Consensus 150 f~lPI-VtlvDTpGa~ 164 (319)
T PRK05724 150 FGLPI-ITFIDTPGAY 164 (319)
T ss_pred cCCCE-EEEEeCCCCC
Confidence 34554 8999999995
No 191
>PF12508 DUF3714: Protein of unknown function (DUF3714) ; InterPro: IPR022187 Proteins in this entry are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage.
Probab=40.99 E-value=57 Score=22.93 Aligned_cols=29 Identities=21% Similarity=0.240 Sum_probs=22.9
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
+-+.|...++.+..+=+|+.|++.|+.|.
T Consensus 101 ~Rl~i~I~SI~~~~~IipV~L~vYD~DG~ 129 (200)
T PF12508_consen 101 QRLLITITSIEYGGNIIPVELSVYDLDGQ 129 (200)
T ss_pred cEEEEEEEEEEECCEEEEEEEEEECCCCC
Confidence 34667777777766668999999999875
No 192
>PRK05124 cysN sulfate adenylyltransferase subunit 1; Provisional
Probab=40.86 E-value=34 Score=26.73 Aligned_cols=27 Identities=22% Similarity=0.310 Sum_probs=16.1
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
.++|......++.++ ..++++||||.-
T Consensus 92 giTid~~~~~~~~~~--~~i~~iDTPGh~ 118 (474)
T PRK05124 92 GITIDVAYRYFSTEK--RKFIIADTPGHE 118 (474)
T ss_pred CCCeEeeEEEeccCC--cEEEEEECCCcH
Confidence 344554444444443 367899999953
No 193
>PTZ00132 GTP-binding nuclear protein Ran; Provisional
Probab=40.80 E-value=98 Score=20.69 Aligned_cols=30 Identities=20% Similarity=0.139 Sum_probs=20.3
Q ss_pred CcceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 10 ~~t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
..|+.+..+...+..++-.+.+.+.||||-
T Consensus 39 ~~t~~~~~~~~~~~~~~~~i~i~~~Dt~g~ 68 (215)
T PTZ00132 39 IPTLGVEVHPLKFYTNCGPICFNVWDTAGQ 68 (215)
T ss_pred CCccceEEEEEEEEECCeEEEEEEEECCCc
Confidence 345555555555555566789999999984
No 194
>PRK12736 elongation factor Tu; Reviewed
Probab=40.76 E-value=33 Score=25.92 Aligned_cols=27 Identities=26% Similarity=0.409 Sum_probs=16.1
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
+..++......++.++ -.++++||||.
T Consensus 59 rg~T~~~~~~~~~~~~--~~i~~iDtPGh 85 (394)
T PRK12736 59 RGITINTAHVEYETEK--RHYAHVDCPGH 85 (394)
T ss_pred cCccEEEEeeEecCCC--cEEEEEECCCH
Confidence 3444544444444433 35689999995
No 195
>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=40.74 E-value=64 Score=19.88 Aligned_cols=17 Identities=29% Similarity=0.479 Sum_probs=13.3
Q ss_pred eecCeEEEEEEEeCCCC
Q psy104 23 EERGVKLRLTVVDTPGF 39 (86)
Q Consensus 23 ~e~~~~l~LtIidTpGf 39 (86)
.-++-.+.+.++||||.
T Consensus 42 ~~~~~~~~~~i~D~~g~ 58 (164)
T cd04139 42 VLDGEDVQLNILDTAGQ 58 (164)
T ss_pred EECCEEEEEEEEECCCh
Confidence 34556788999999994
No 196
>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=40.47 E-value=19 Score=28.65 Aligned_cols=26 Identities=23% Similarity=0.511 Sum_probs=19.4
Q ss_pred EEEEEe-ecCeEEEEEEEeCCCCCCcc
Q psy104 18 KSMDIE-ERGVKLRLTVVDTPGFGDSI 43 (86)
Q Consensus 18 ~~~~l~-e~~~~l~LtIidTpGfGd~i 43 (86)
..++|. .+++..++.+|||+||.+.-
T Consensus 79 kAvEI~~~~~~~~~VrlIDcvG~~v~G 105 (492)
T TIGR02836 79 EAVEININEGTKFKVRLVDCVGYTVKG 105 (492)
T ss_pred cceEEeccCCCcccEEEEECCCcccCC
Confidence 334553 45788999999999998753
No 197
>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=40.44 E-value=63 Score=20.49 Aligned_cols=17 Identities=29% Similarity=0.417 Sum_probs=13.2
Q ss_pred ecCeEEEEEEEeCCCCC
Q psy104 24 ERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 24 e~~~~l~LtIidTpGfG 40 (86)
-++..+++.++||||.-
T Consensus 44 ~~~~~~~~~i~Dt~G~~ 60 (168)
T cd04177 44 IDGRQCDLEILDTAGTE 60 (168)
T ss_pred ECCEEEEEEEEeCCCcc
Confidence 34566899999999954
No 198
>PRK07560 elongation factor EF-2; Reviewed
Probab=40.25 E-value=29 Score=28.47 Aligned_cols=15 Identities=33% Similarity=0.627 Sum_probs=12.1
Q ss_pred eEEEEEEEeCCCCCC
Q psy104 27 VKLRLTVVDTPGFGD 41 (86)
Q Consensus 27 ~~l~LtIidTpGfGd 41 (86)
-...+++|||||+-+
T Consensus 85 ~~~~i~liDtPG~~d 99 (731)
T PRK07560 85 KEYLINLIDTPGHVD 99 (731)
T ss_pred CcEEEEEEcCCCccC
Confidence 357889999999765
No 199
>PRK09563 rbgA GTPase YlqF; Reviewed
Probab=39.93 E-value=17 Score=26.16 Aligned_cols=13 Identities=38% Similarity=0.506 Sum_probs=10.2
Q ss_pred EEEEEeCCCCCCc
Q psy104 30 RLTVVDTPGFGDS 42 (86)
Q Consensus 30 ~LtIidTpGfGd~ 42 (86)
.+.++||||+-..
T Consensus 167 ~~~l~DtPGi~~~ 179 (287)
T PRK09563 167 GLELLDTPGILWP 179 (287)
T ss_pred cEEEEECCCcCCC
Confidence 4679999999644
No 200
>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=39.78 E-value=44 Score=25.37 Aligned_cols=26 Identities=31% Similarity=0.487 Sum_probs=16.4
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
+..+......+..++ ..++++||||.
T Consensus 70 g~Tid~~~~~~~~~~--~~i~iiDtpGh 95 (426)
T TIGR00483 70 GVTIDVAHWKFETDK--YEVTIVDCPGH 95 (426)
T ss_pred CceEEEEEEEEccCC--eEEEEEECCCH
Confidence 444444444454443 57899999995
No 201
>PRK05346 Na(+)-translocating NADH-quinone reductase subunit C; Provisional
Probab=39.70 E-value=13 Score=26.97 Aligned_cols=20 Identities=35% Similarity=0.572 Sum_probs=14.4
Q ss_pred eEEEEEEE---eCCCCCCccCCc
Q psy104 27 VKLRLTVV---DTPGFGDSINSE 46 (86)
Q Consensus 27 ~~l~LtIi---dTpGfGd~i~n~ 46 (86)
.-.-+.+. +|||+|+.+.+.
T Consensus 160 tI~gi~v~~h~ETPGLG~~i~~~ 182 (256)
T PRK05346 160 TVKGLTFYEHGETPGLGGEIENP 182 (256)
T ss_pred EEEEEEeeccCCCccccccccCh
Confidence 44455555 899999998765
No 202
>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=39.52 E-value=21 Score=24.93 Aligned_cols=11 Identities=27% Similarity=0.407 Sum_probs=9.2
Q ss_pred EEEEEEeCCCC
Q psy104 29 LRLTVVDTPGF 39 (86)
Q Consensus 29 l~LtIidTpGf 39 (86)
-.++++||||.
T Consensus 84 ~~i~liDtpG~ 94 (224)
T cd04165 84 KLVTFIDLAGH 94 (224)
T ss_pred cEEEEEECCCc
Confidence 46889999995
No 203
>PRK00098 GTPase RsgA; Reviewed
Probab=39.44 E-value=32 Score=24.99 Aligned_cols=9 Identities=56% Similarity=1.198 Sum_probs=8.1
Q ss_pred EEEeCCCCC
Q psy104 32 TVVDTPGFG 40 (86)
Q Consensus 32 tIidTpGfG 40 (86)
.|+|||||-
T Consensus 219 ~~~DtpG~~ 227 (298)
T PRK00098 219 LLIDTPGFS 227 (298)
T ss_pred EEEECCCcC
Confidence 699999996
No 204
>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=39.35 E-value=53 Score=21.08 Aligned_cols=12 Identities=25% Similarity=0.315 Sum_probs=10.0
Q ss_pred EEEEEEEeCCCC
Q psy104 28 KLRLTVVDTPGF 39 (86)
Q Consensus 28 ~l~LtIidTpGf 39 (86)
.++++++||||-
T Consensus 42 ~~~~~i~D~~G~ 53 (167)
T cd04161 42 KYEVCIFDLGGG 53 (167)
T ss_pred CEEEEEEECCCc
Confidence 477899999994
No 205
>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=38.93 E-value=66 Score=21.29 Aligned_cols=20 Identities=25% Similarity=0.380 Sum_probs=15.3
Q ss_pred EEeecCeEEEEEEEeCCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGfG 40 (86)
.+.-++-.++|.|.||+|-.
T Consensus 41 ~~~~~~~~v~l~i~Dt~G~~ 60 (176)
T cd04133 41 NVSVDGNTVNLGLWDTAGQE 60 (176)
T ss_pred EEEECCEEEEEEEEECCCCc
Confidence 34446778999999999843
No 206
>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=38.84 E-value=46 Score=21.78 Aligned_cols=16 Identities=13% Similarity=0.127 Sum_probs=12.4
Q ss_pred cCeEEEEEEEeCCCCC
Q psy104 25 RGVKLRLTVVDTPGFG 40 (86)
Q Consensus 25 ~~~~l~LtIidTpGfG 40 (86)
++-.+.|.+.||||-.
T Consensus 48 ~~~~~~l~l~Dt~G~~ 63 (183)
T cd04152 48 NSKGITFHFWDVGGQE 63 (183)
T ss_pred CCCceEEEEEECCCcH
Confidence 3456889999999963
No 207
>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=38.74 E-value=61 Score=26.00 Aligned_cols=12 Identities=42% Similarity=0.800 Sum_probs=10.2
Q ss_pred EEEEEEeCCCCC
Q psy104 29 LRLTVVDTPGFG 40 (86)
Q Consensus 29 l~LtIidTpGfG 40 (86)
..++++||||.-
T Consensus 50 ~~v~~iDtPGhe 61 (581)
T TIGR00475 50 YRLGFIDVPGHE 61 (581)
T ss_pred EEEEEEECCCHH
Confidence 788999999953
No 208
>PRK12740 elongation factor G; Reviewed
Probab=38.32 E-value=41 Score=27.09 Aligned_cols=27 Identities=30% Similarity=0.547 Sum_probs=16.9
Q ss_pred eEEEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 13 TTIEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 13 ~~I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
..+......+.-++ ..++++||||..+
T Consensus 46 iTi~~~~~~~~~~~--~~i~liDtPG~~~ 72 (668)
T PRK12740 46 ISITSAATTCEWKG--HKINLIDTPGHVD 72 (668)
T ss_pred CCeeeceEEEEECC--EEEEEEECCCcHH
Confidence 33444434444444 6788999999865
No 209
>PRK12735 elongation factor Tu; Reviewed
Probab=38.12 E-value=43 Score=25.29 Aligned_cols=27 Identities=26% Similarity=0.394 Sum_probs=15.8
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
...+......++.++ -.++++||||.-
T Consensus 60 GiT~~~~~~~~~~~~--~~i~~iDtPGh~ 86 (396)
T PRK12735 60 GITINTSHVEYETAN--RHYAHVDCPGHA 86 (396)
T ss_pred CceEEEeeeEEcCCC--cEEEEEECCCHH
Confidence 344444444444333 356899999974
No 210
>PRK00007 elongation factor G; Reviewed
Probab=37.95 E-value=43 Score=27.37 Aligned_cols=28 Identities=29% Similarity=0.399 Sum_probs=17.1
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
..++......+.-++ .++++|||||+-+
T Consensus 60 g~ti~~~~~~~~~~~--~~~~liDTPG~~~ 87 (693)
T PRK00007 60 GITITSAATTCFWKD--HRINIIDTPGHVD 87 (693)
T ss_pred CCCEeccEEEEEECC--eEEEEEeCCCcHH
Confidence 344544444444443 4788899999743
No 211
>PF09140 MipZ: ATPase MipZ; InterPro: IPR015223 Cell division in bacteria is facilitated by a polymeric ring structure, the Z ring, composed of tubulin-like FtsZ protofilaments. Correct positioning of the division plane is a prerequisite for the generation of daughter cells with a normal chromosome complement. In Caulobacter crescentus MipZ, an essential protein, coordinates and regulates the assembly of the FtsZ cytokinetic ring during cell division. MipZ, forms a complex with the partitioning protein ParB near the origin of replication and localizes with the duplicated origin regions to the cell poles. MipZ also directly interferes with FtsZ polymerisation, thereby restricting FtsZ ring formation to mid-cell, the region of lowest MipZ concentration. In eukaryotes members of this entry belong to the Mrp/NBP35 ATP-binding protein family, and specifically the NUBP2/CFD1 subfamily. This includes the cytosolic Fe-S cluster assembly factor Cfd1, which is a component of the cytosolic iron-sulphur (Fe/S) protein assembly machinery. This protein is required for maturation of extra-mitochondrial Fe/S proteins. It may bind and transfer a labile 4Fe-4S cluster to target apoproteins. Cfd1 is also required for biogenesis and export of both ribosomal subunits, suggesting a role in assembly of the Fe/S clusters in RLI1, a protein which performs rRNA processing and ribosome export. ; PDB: 2XIT_B 2XJ4_A 2XJ9_A.
Probab=37.50 E-value=15 Score=26.97 Aligned_cols=14 Identities=50% Similarity=0.826 Sum_probs=8.7
Q ss_pred EEEEEEeCCCCCCc
Q psy104 29 LRLTVVDTPGFGDS 42 (86)
Q Consensus 29 l~LtIidTpGfGd~ 42 (86)
+-+-||||||.++.
T Consensus 99 ~DfLVID~PGtd~~ 112 (261)
T PF09140_consen 99 LDFLVIDTPGTDDR 112 (261)
T ss_dssp -SEEEEEE-SSS-H
T ss_pred CCEEEEeCCCCCcH
Confidence 44569999998764
No 212
>KOG1030|consensus
Probab=37.25 E-value=95 Score=21.38 Aligned_cols=52 Identities=17% Similarity=0.199 Sum_probs=36.0
Q ss_pred EEEEEEeecCeEEEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhhhc
Q psy104 17 KKSMDIEERGVKLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDES 68 (86)
Q Consensus 17 ~~~~~l~e~~~~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~eE~ 68 (86)
..++.+.+...+++|+|-|-..|-..---...=-+|..|++.+...||..|.
T Consensus 56 ~ltf~v~d~~~~lkv~VyD~D~fs~dD~mG~A~I~l~p~~~~~~~~~l~~~~ 107 (168)
T KOG1030|consen 56 ELTFTVKDPNTPLKVTVYDKDTFSSDDFMGEATIPLKPLLEAQKMDYLKLEL 107 (168)
T ss_pred eEEEEecCCCceEEEEEEeCCCCCcccccceeeeccHHHHHHhhhhcccccc
Confidence 3455667778899999999988853322222335778899998888866443
No 213
>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=37.13 E-value=81 Score=20.69 Aligned_cols=18 Identities=33% Similarity=0.488 Sum_probs=14.1
Q ss_pred EeecCeEEEEEEEeCCCC
Q psy104 22 IEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 22 l~e~~~~l~LtIidTpGf 39 (86)
+.-++..+.|.+.||||-
T Consensus 41 i~~~~~~~~l~i~Dt~G~ 58 (189)
T cd04134 41 IFVDGLHIELSLWDTAGQ 58 (189)
T ss_pred EEECCEEEEEEEEECCCC
Confidence 344567789999999985
No 214
>KOG0465|consensus
Probab=36.92 E-value=39 Score=28.12 Aligned_cols=27 Identities=33% Similarity=0.540 Sum_probs=16.3
Q ss_pred eEEEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 13 TTIEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 13 ~~I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
+.|+..-....-. ..++++|||||==|
T Consensus 90 ITiqSAAt~~~w~--~~~iNiIDTPGHvD 116 (721)
T KOG0465|consen 90 ITIQSAATYFTWR--DYRINIIDTPGHVD 116 (721)
T ss_pred ceeeeceeeeeec--cceeEEecCCCcee
Confidence 4444443333322 67889999999643
No 215
>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=36.52 E-value=1.2e+02 Score=21.30 Aligned_cols=20 Identities=25% Similarity=0.415 Sum_probs=15.7
Q ss_pred EEEeecCeEEEEEEEeCCCC
Q psy104 20 MDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 20 ~~l~e~~~~l~LtIidTpGf 39 (86)
..+.-++..++|.|.||+|-
T Consensus 52 ~~i~~~~~~v~l~iwDTaG~ 71 (232)
T cd04174 52 AGLETEEQRVELSLWDTSGS 71 (232)
T ss_pred EEEEECCEEEEEEEEeCCCc
Confidence 34555677899999999984
No 216
>TIGR00513 accA acetyl-CoA carboxylase, carboxyl transferase, alpha subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the alpha chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=36.38 E-value=22 Score=26.67 Aligned_cols=14 Identities=36% Similarity=0.627 Sum_probs=10.9
Q ss_pred CeEEEEEEEeCCCCC
Q psy104 26 GVKLRLTVVDTPGFG 40 (86)
Q Consensus 26 ~~~l~LtIidTpGfG 40 (86)
++|+ ++++|||||-
T Consensus 151 ~iPv-VtlvDTpGa~ 164 (316)
T TIGR00513 151 KMPI-ITFIDTPGAY 164 (316)
T ss_pred CCCE-EEEEECCCCC
Confidence 4443 8999999985
No 217
>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=36.15 E-value=48 Score=26.75 Aligned_cols=11 Identities=45% Similarity=0.788 Sum_probs=9.5
Q ss_pred EEEEEeCCCCC
Q psy104 30 RLTVVDTPGFG 40 (86)
Q Consensus 30 ~LtIidTpGfG 40 (86)
.++++||||--
T Consensus 136 ~i~~iDTPGhe 146 (587)
T TIGR00487 136 MITFLDTPGHE 146 (587)
T ss_pred EEEEEECCCCc
Confidence 78999999964
No 218
>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=36.02 E-value=94 Score=18.98 Aligned_cols=15 Identities=33% Similarity=0.472 Sum_probs=11.8
Q ss_pred cCeEEEEEEEeCCCC
Q psy104 25 RGVKLRLTVVDTPGF 39 (86)
Q Consensus 25 ~~~~l~LtIidTpGf 39 (86)
++-.+.+.++||||-
T Consensus 45 ~~~~~~~~i~Dt~G~ 59 (162)
T cd04138 45 DGETCLLDILDTAGQ 59 (162)
T ss_pred CCEEEEEEEEECCCC
Confidence 445677899999995
No 219
>KOG0446|consensus
Probab=35.73 E-value=24 Score=28.94 Aligned_cols=44 Identities=18% Similarity=0.260 Sum_probs=32.2
Q ss_pred EEEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhhhhcCCcc
Q psy104 28 KLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFNDESGLNR 72 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~eE~~i~R 72 (86)
-.+||+||.||+= .+-..+....|..-|..-...|+..+..+-.
T Consensus 131 v~~lTLvDlPG~t-kvpv~dqp~di~~qI~~mi~~yi~~~~~iIL 174 (657)
T KOG0446|consen 131 VANLTLVDLPGLT-KVPVADQPDDIEEEIKSMIEEYIEKPNRIIL 174 (657)
T ss_pred CchhhhcCCCCCc-ccccCCCCccHHHHHHHHHHHhccccchhhh
Confidence 4689999999994 4555557777888888888888776655443
No 220
>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=35.64 E-value=1.6e+02 Score=23.81 Aligned_cols=27 Identities=33% Similarity=0.482 Sum_probs=15.6
Q ss_pred EEEEEEEEEeecCeEEEEEEEeCCCCCCc
Q psy104 14 TIEKKSMDIEERGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 14 ~I~~~~~~l~e~~~~l~LtIidTpGfGd~ 42 (86)
.+......++-++. +++++||||.-+.
T Consensus 28 Tv~~~~~~i~~~~~--~i~lvDtPG~~~~ 54 (591)
T TIGR00437 28 TVEKKEGKLGFQGE--DIEIVDLPGIYSL 54 (591)
T ss_pred EEEEEEEEEEECCe--EEEEEECCCcccc
Confidence 33333333333443 4689999998653
No 221
>CHL00198 accA acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional
Probab=35.54 E-value=23 Score=26.69 Aligned_cols=15 Identities=47% Similarity=0.780 Sum_probs=11.3
Q ss_pred CeEEEEEEEeCCCCCC
Q psy104 26 GVKLRLTVVDTPGFGD 41 (86)
Q Consensus 26 ~~~l~LtIidTpGfGd 41 (86)
++|+ ++++||||+--
T Consensus 154 ~lPI-ItlvDTpGA~~ 168 (322)
T CHL00198 154 GLPI-LTFIDTPGAWA 168 (322)
T ss_pred CCCE-EEEEeCCCcCc
Confidence 4443 89999999953
No 222
>COG0532 InfB Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=35.53 E-value=57 Score=26.23 Aligned_cols=29 Identities=28% Similarity=0.381 Sum_probs=18.7
Q ss_pred CcceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 10 ~~t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
.-|-.|-.|.+.+...+ .-.|+++||||=
T Consensus 37 GITQhIGA~~v~~~~~~-~~~itFiDTPGH 65 (509)
T COG0532 37 GITQHIGAYQVPLDVIK-IPGITFIDTPGH 65 (509)
T ss_pred ceeeEeeeEEEEeccCC-CceEEEEcCCcH
Confidence 34566777777665221 126889999984
No 223
>PTZ00416 elongation factor 2; Provisional
Probab=35.20 E-value=31 Score=28.88 Aligned_cols=15 Identities=27% Similarity=0.585 Sum_probs=12.0
Q ss_pred EEEEEEEeCCCCCCc
Q psy104 28 KLRLTVVDTPGFGDS 42 (86)
Q Consensus 28 ~l~LtIidTpGfGd~ 42 (86)
...++++||||+-+.
T Consensus 91 ~~~i~liDtPG~~~f 105 (836)
T PTZ00416 91 PFLINLIDSPGHVDF 105 (836)
T ss_pred ceEEEEEcCCCHHhH
Confidence 467899999998653
No 224
>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=35.19 E-value=55 Score=22.12 Aligned_cols=14 Identities=29% Similarity=0.577 Sum_probs=11.2
Q ss_pred EEEEEEEeCCCCCC
Q psy104 28 KLRLTVVDTPGFGD 41 (86)
Q Consensus 28 ~l~LtIidTpGfGd 41 (86)
..++.|+||||-..
T Consensus 47 ~~~~~l~D~pG~~~ 60 (203)
T cd04105 47 GKKFRLVDVPGHPK 60 (203)
T ss_pred CceEEEEECCCCHH
Confidence 46788999999763
No 225
>cd01387 MYSc_type_XV Myosin motor domain, type XV myosins. In vertebrates, myosin XV appears to be expressed in sensory tissue and play a role in hearing. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis caus
Probab=35.09 E-value=72 Score=26.29 Aligned_cols=36 Identities=25% Similarity=0.494 Sum_probs=25.3
Q ss_pred EEEEEEEeCCCCCCccCCccchhHH-HHHHHHHHHHhhh
Q psy104 28 KLRLTVVDTPGFGDSINSEESWRAC-CSYIDDQFRQYFN 65 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~n~~~~~~i-~~yI~~qf~~yl~ 65 (86)
...+.|.|.+||=..- .++|+.+ ++|..++...++.
T Consensus 360 ~~~IgILDIfGFE~f~--~NsfEQLcINyaNEkLQ~~f~ 396 (677)
T cd01387 360 TLSIAILDIYGFEDLS--FNSFEQLCINYANENLQYLFN 396 (677)
T ss_pred CceEEEEecCccccCC--CCCHHHHHhHHHHHHHHHHHH
Confidence 3468899999995433 3567744 8888887776643
No 226
>cd01378 MYSc_type_I Myosin motor domain, type I myosins. Myosin I generates movement at the leading edge in cell motility, and class I myosins have been implicated in phagocytosis and vesicle transport. Myosin I, an unconventional myosin, does not form dimers. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 picon
Probab=34.98 E-value=66 Score=26.43 Aligned_cols=36 Identities=22% Similarity=0.409 Sum_probs=26.4
Q ss_pred eEEEEEEEeCCCCCCccCCccchhHH-HHHHHHHHHHhh
Q psy104 27 VKLRLTVVDTPGFGDSINSEESWRAC-CSYIDDQFRQYF 64 (86)
Q Consensus 27 ~~l~LtIidTpGfGd~i~n~~~~~~i-~~yI~~qf~~yl 64 (86)
....+.|.|.+||=..- .++|+.+ ++|..+++..++
T Consensus 364 ~~~~IgILDIfGFE~f~--~NsfEQLcINyaNEkLQ~~f 400 (674)
T cd01378 364 KNKVIGVLDIYGFEIFQ--KNSFEQFCINYVNEKLQQIF 400 (674)
T ss_pred CcceEEEEecccccccc--cccHHHHHhHHHHHHHHHHH
Confidence 35568999999996543 3467754 899998887774
No 227
>PRK12739 elongation factor G; Reviewed
Probab=34.56 E-value=38 Score=27.59 Aligned_cols=28 Identities=32% Similarity=0.476 Sum_probs=17.0
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
...+......++-++ .+++++||||+-+
T Consensus 58 giti~~~~~~~~~~~--~~i~liDTPG~~~ 85 (691)
T PRK12739 58 GITITSAATTCFWKG--HRINIIDTPGHVD 85 (691)
T ss_pred CCCccceeEEEEECC--EEEEEEcCCCHHH
Confidence 344444444444444 4678899999754
No 228
>cd01900 YchF YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated with the ribosome. Several members of the family, including YchF, possess the TGS domain related to the RNA-binding proteins. Experimental data and genomic analysis suggest that YchF may be part of a nucleoprotein complex and may function as a GTP-dependent translational factor.
Probab=34.38 E-value=35 Score=24.87 Aligned_cols=14 Identities=29% Similarity=0.413 Sum_probs=11.4
Q ss_pred eEEEEEEEeCCCCC
Q psy104 27 VKLRLTVVDTPGFG 40 (86)
Q Consensus 27 ~~l~LtIidTpGfG 40 (86)
++-.+.++||||+-
T Consensus 60 ~~~~i~lvD~pGl~ 73 (274)
T cd01900 60 VPATIEFVDIAGLV 73 (274)
T ss_pred eeeEEEEEECCCcC
Confidence 35579999999985
No 229
>KOG1954|consensus
Probab=34.17 E-value=20 Score=28.32 Aligned_cols=33 Identities=21% Similarity=0.422 Sum_probs=19.8
Q ss_pred EEEEEEeCCCCC--Cc--cCCccchhHHHHHHHHHHH
Q psy104 29 LRLTVVDTPGFG--DS--INSEESWRACCSYIDDQFR 61 (86)
Q Consensus 29 l~LtIidTpGfG--d~--i~n~~~~~~i~~yI~~qf~ 61 (86)
=+++||||||.= .. +.....|.-+..+..++-+
T Consensus 147 e~vtiVdtPGILsgeKQrisR~ydF~~v~~WFaeR~D 183 (532)
T KOG1954|consen 147 ESVTIVDTPGILSGEKQRISRGYDFTGVLEWFAERVD 183 (532)
T ss_pred hheeeeccCcccccchhcccccCChHHHHHHHHHhcc
Confidence 368999999983 22 3333446666665555433
No 230
>PRK05306 infB translation initiation factor IF-2; Validated
Probab=34.08 E-value=55 Score=27.55 Aligned_cols=14 Identities=36% Similarity=0.546 Sum_probs=11.2
Q ss_pred EEEEEEeCCCCCCc
Q psy104 29 LRLTVVDTPGFGDS 42 (86)
Q Consensus 29 l~LtIidTpGfGd~ 42 (86)
..++++||||..+.
T Consensus 337 ~~ItfiDTPGhe~F 350 (787)
T PRK05306 337 GKITFLDTPGHEAF 350 (787)
T ss_pred EEEEEEECCCCccc
Confidence 56899999997654
No 231
>cd01380 MYSc_type_V Myosin motor domain, type V myosins. Myosins V transport a variety of intracellular cargo processively along actin filaments, such as membraneous organelles and mRNA. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an act
Probab=34.05 E-value=66 Score=26.52 Aligned_cols=35 Identities=23% Similarity=0.401 Sum_probs=25.5
Q ss_pred EEEEEEEeCCCCCCccCCccchhHH-HHHHHHHHHHhh
Q psy104 28 KLRLTVVDTPGFGDSINSEESWRAC-CSYIDDQFRQYF 64 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~n~~~~~~i-~~yI~~qf~~yl 64 (86)
...+.|.|.+||=..- .++|+.+ ++|..+++..|+
T Consensus 367 ~~~IgiLDI~GFE~f~--~NsfEQLcINyaNEkLQ~~f 402 (691)
T cd01380 367 TSFIGVLDIYGFETFE--KNSFEQFCINYANEKLQQQF 402 (691)
T ss_pred cceEEEEecCcccccC--CCCHHHHhhhhhhHHHHHHH
Confidence 4567899999995443 3467754 899998887764
No 232
>cd01379 MYSc_type_III Myosin motor domain, type III myosins. Myosin III has been shown to play a role in the vision process in insects and in hearing in mammals. Myosin III, an unconventional myosin, does not form dimers. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the
Probab=33.85 E-value=72 Score=26.19 Aligned_cols=35 Identities=26% Similarity=0.596 Sum_probs=25.0
Q ss_pred EEEEEEEeCCCCCCccCCccchhH-HHHHHHHHHHHhh
Q psy104 28 KLRLTVVDTPGFGDSINSEESWRA-CCSYIDDQFRQYF 64 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~n~~~~~~-i~~yI~~qf~~yl 64 (86)
...+.|+|.+||=..-. ++++. .++|..++...++
T Consensus 372 ~~~IgiLDI~GFE~f~~--NsfEQLcINyaNEkLQ~~f 407 (653)
T cd01379 372 QLNVGILDIFGFENFKK--NSFEQLCINIANEQIQYYF 407 (653)
T ss_pred cceEEEEeccccccCCC--CCHHHHHhhhhHHHHHHHH
Confidence 45689999999964433 45664 4888888877663
No 233
>PRK12319 acetyl-CoA carboxylase subunit alpha; Provisional
Probab=33.43 E-value=27 Score=25.33 Aligned_cols=16 Identities=25% Similarity=0.308 Sum_probs=12.2
Q ss_pred cCeEEEEEEEeCCCCCC
Q psy104 25 RGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 25 ~~~~l~LtIidTpGfGd 41 (86)
.++|+ ++++||||+-.
T Consensus 97 ~~lPv-V~lvDtpGa~~ 112 (256)
T PRK12319 97 FGRPV-VTFINTAGAYP 112 (256)
T ss_pred cCCCE-EEEEECCCcCC
Confidence 35554 89999999964
No 234
>PF15016 DUF4520: Domain of unknown function (DUF4520)
Probab=33.36 E-value=29 Score=21.24 Aligned_cols=13 Identities=23% Similarity=0.130 Sum_probs=10.3
Q ss_pred CCCCCCeeEEeec
Q psy104 73 KNIVDNREVVDKS 85 (86)
Q Consensus 73 ~~~~D~RVH~Cl~ 85 (86)
.-+.|.||||.+.
T Consensus 19 ~AysDgrVr~~F~ 31 (85)
T PF15016_consen 19 TAYSDGRVRVHFD 31 (85)
T ss_pred EEEcCCeEEEEEc
Confidence 3678999999874
No 235
>TIGR03779 Bac_Flav_CT_M Bacteroides conjugative transposon TraM protein. Members of this protein family are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage.
Probab=33.30 E-value=71 Score=24.97 Aligned_cols=29 Identities=24% Similarity=0.308 Sum_probs=23.7
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
+-+.|...++...++=+|++|+|.|+.|-
T Consensus 304 ~R~~i~I~si~~~g~iipV~L~vyD~DG~ 332 (410)
T TIGR03779 304 ERLDIKISSIEYNGTILPVELSVYDTDGQ 332 (410)
T ss_pred ceEEEEEEEEEECCEEEEEEEEEEcCCCC
Confidence 34677778887777778999999999885
No 236
>PF08189 Meleagrin: Meleagrin/Cygnin family; InterPro: IPR012573 This family consists of meleagrin and cygnin basic peptides that are isolated from turkey and black swan respectively. Both peptides are low in molecular weight and contain three disulphide bonds with high concentrations of aromatic residues. These peptides show similarity to transferrins and probably play some vital role in avian eggs but the exact function is still unknown [].
Probab=33.28 E-value=29 Score=18.17 Aligned_cols=11 Identities=9% Similarity=-0.170 Sum_probs=8.9
Q ss_pred CCCCeeEEeec
Q psy104 75 IVDNREVVDKS 85 (86)
Q Consensus 75 ~~D~RVH~Cl~ 85 (86)
-+|..+||||-
T Consensus 25 s~~CK~yCClP 35 (39)
T PF08189_consen 25 SQDCKMYCCLP 35 (39)
T ss_pred cCCccEEEeCC
Confidence 36889999984
No 237
>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=33.24 E-value=1.5e+02 Score=19.67 Aligned_cols=19 Identities=26% Similarity=0.379 Sum_probs=15.0
Q ss_pred EEeecCeEEEEEEEeCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGf 39 (86)
.+.-++..++|.|.||+|-
T Consensus 45 ~~~~~~~~~~l~iwDtaG~ 63 (182)
T cd04172 45 SFEIDTQRIELSLWDTSGS 63 (182)
T ss_pred EEEECCEEEEEEEEECCCc
Confidence 4455677899999999984
No 238
>PF00460 Flg_bb_rod: Flagella basal body rod protein; InterPro: IPR001444 Many bacterial species swim actively by means of flagella. The flagella organelle is made of three parts: the basal body, the hook and the filament. The basal body consists of four rings (L,P,S, and M) mounted on a central rod []. In Salmonella typhimurium and related organisms the rod has been shown to consist of four different, yet evolutionary related proteins: in the distal portion of the rod there are about 26 subunits of protein flgG and in the proximal portion there are about six subunits each of proteins flgB, flgC, and flgF. These four proteins contain a highly conserved asparagine-rich domain at their N terminus.; GO: 0003774 motor activity, 0005198 structural molecule activity, 0001539 ciliary or flagellar motility, 0009288 bacterial-type flagellum; PDB: 3A69_A.
Probab=33.18 E-value=14 Score=18.20 Aligned_cols=6 Identities=50% Similarity=1.337 Sum_probs=0.0
Q ss_pred EeCCCC
Q psy104 34 VDTPGF 39 (86)
Q Consensus 34 idTpGf 39 (86)
++||||
T Consensus 25 ~nT~Gy 30 (31)
T PF00460_consen 25 ANTPGY 30 (31)
T ss_dssp ------
T ss_pred cCCCCC
Confidence 578887
No 239
>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=33.11 E-value=1.4e+02 Score=19.52 Aligned_cols=19 Identities=26% Similarity=0.384 Sum_probs=14.6
Q ss_pred EEeecCeEEEEEEEeCCCC
Q psy104 21 DIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 21 ~l~e~~~~l~LtIidTpGf 39 (86)
.+.-++-.++|.+.||+|-
T Consensus 41 ~~~~~~~~~~l~iwDt~G~ 59 (178)
T cd04131 41 SFEIDEQRIELSLWDTSGS 59 (178)
T ss_pred EEEECCEEEEEEEEECCCc
Confidence 3444567899999999985
No 240
>PRK11058 GTPase HflX; Provisional
Probab=33.05 E-value=46 Score=25.70 Aligned_cols=26 Identities=27% Similarity=0.464 Sum_probs=15.3
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
.|.......+.+...+ .+.++|||||
T Consensus 230 tTld~~~~~i~l~~~~---~~~l~DTaG~ 255 (426)
T PRK11058 230 ATLDPTLRRIDVADVG---ETVLADTVGF 255 (426)
T ss_pred CCcCCceEEEEeCCCC---eEEEEecCcc
Confidence 3444444555443221 4568999999
No 241
>cd01383 MYSc_type_VIII Myosin motor domain, plant-specific type VIII myosins, a subgroup which has been associated with endocytosis, cytokinesis, cell-to-cell coupling and gating at plasmodesmata. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates f
Probab=33.03 E-value=83 Score=25.94 Aligned_cols=34 Identities=21% Similarity=0.448 Sum_probs=24.8
Q ss_pred EEEEEEeCCCCCCccCCccchhHH-HHHHHHHHHHhh
Q psy104 29 LRLTVVDTPGFGDSINSEESWRAC-CSYIDDQFRQYF 64 (86)
Q Consensus 29 l~LtIidTpGfGd~i~n~~~~~~i-~~yI~~qf~~yl 64 (86)
-.+.|+|.+||=..-. ++|+.+ ++|-.++...++
T Consensus 365 ~~IgiLDI~GFE~f~~--NsfEQLcINyaNEkLQ~~f 399 (677)
T cd01383 365 RSISILDIYGFESFDK--NSFEQFCINYANERLQQHF 399 (677)
T ss_pred ceEEEeeccccccCCC--CCHHHHHHHHHHHHHHHHH
Confidence 4678999999965443 467744 889988877763
No 242
>cd01382 MYSc_type_VI Myosin motor domain, type VI myosins. Myosin VI is a monomeric myosin, which moves towards the minus-end of actin filaments, in contrast to most other myosins. It has been implicated in endocytosis, secretion, and cell migration. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the minus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of
Probab=32.52 E-value=67 Score=26.65 Aligned_cols=34 Identities=24% Similarity=0.465 Sum_probs=24.7
Q ss_pred EEEEEEeCCCCCCccCCccchhHH-HHHHHHHHHHhh
Q psy104 29 LRLTVVDTPGFGDSINSEESWRAC-CSYIDDQFRQYF 64 (86)
Q Consensus 29 l~LtIidTpGfGd~i~n~~~~~~i-~~yI~~qf~~yl 64 (86)
-.+.|.|.+||=..- .++++.+ ++|..++...++
T Consensus 397 ~~IgiLDIfGFE~f~--~NsfEQLcINyaNEkLQ~~f 431 (717)
T cd01382 397 NFIGVLDIAGFEYFE--HNSFEQFCINYCNEKLQQFF 431 (717)
T ss_pred cEEEEEeccccccCC--CCCHHHHhhhhhHHHHHHHH
Confidence 358899999995443 3467744 899888887774
No 243
>PRK12685 flgB flagellar basal body rod protein FlgB; Reviewed
Probab=32.26 E-value=18 Score=22.99 Aligned_cols=8 Identities=38% Similarity=0.887 Sum_probs=6.7
Q ss_pred EEeCCCCC
Q psy104 33 VVDTPGFG 40 (86)
Q Consensus 33 IidTpGfG 40 (86)
=+|||||-
T Consensus 32 NadTPgYk 39 (116)
T PRK12685 32 NAETPGYK 39 (116)
T ss_pred ccCCCCcC
Confidence 47999995
No 244
>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=32.13 E-value=70 Score=19.83 Aligned_cols=14 Identities=29% Similarity=0.368 Sum_probs=11.4
Q ss_pred EEEEEEEeCCCCCC
Q psy104 28 KLRLTVVDTPGFGD 41 (86)
Q Consensus 28 ~l~LtIidTpGfGd 41 (86)
.+.+.+.||||...
T Consensus 42 ~~~~~i~D~~G~~~ 55 (158)
T cd00878 42 NVSFTVWDVGGQDK 55 (158)
T ss_pred CEEEEEEECCCChh
Confidence 47899999999754
No 245
>PRK07182 flgB flagellar basal body rod protein FlgB; Reviewed
Probab=32.04 E-value=19 Score=23.81 Aligned_cols=7 Identities=57% Similarity=1.051 Sum_probs=6.1
Q ss_pred EeCCCCC
Q psy104 34 VDTPGFG 40 (86)
Q Consensus 34 idTpGfG 40 (86)
+|||||-
T Consensus 33 adTPGYk 39 (148)
T PRK07182 33 VNTPNFQ 39 (148)
T ss_pred cCCCCCC
Confidence 6999995
No 246
>PHA02857 monoglyceride lipase; Provisional
Probab=31.90 E-value=54 Score=22.43 Aligned_cols=18 Identities=22% Similarity=0.242 Sum_probs=13.9
Q ss_pred EEEEEEeCCCCCCccCCc
Q psy104 29 LRLTVVDTPGFGDSINSE 46 (86)
Q Consensus 29 l~LtIidTpGfGd~i~n~ 46 (86)
+++-..|-||+|.+-...
T Consensus 53 ~~via~D~~G~G~S~~~~ 70 (276)
T PHA02857 53 ILVFSHDHIGHGRSNGEK 70 (276)
T ss_pred CEEEEccCCCCCCCCCcc
Confidence 567789999999875443
No 247
>PF11567 PfUIS3: Plasmodium falciparum UIS3 membrane protein; InterPro: IPR021626 UIS3 is a membrane protein essential for sporozoite development in infected hepatocytes. This family is 130-229 of the Plasmodium falciparum UIS3 protein which is compact and has an all alpha-helical structure.PfUIS3(130-229) interacts with lipids, phospholipid lysosomes, the human liver fatty acid-binding protein and with the lipid phosphatidylethanolamine. The interaction with liver fatty acid-binding protein provides the parasite with a method to import essential fatty acids/lipids during rapid growth phases of sporozoites []. ; PDB: 2VWA_C.
Probab=31.35 E-value=51 Score=20.60 Aligned_cols=18 Identities=22% Similarity=0.656 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHhhhhhc
Q psy104 51 ACCSYIDDQFRQYFNDES 68 (86)
Q Consensus 51 ~i~~yI~~qf~~yl~eE~ 68 (86)
-+..|+.++|..||.+|.
T Consensus 83 ~~e~fLq~~y~~~~~~~~ 100 (101)
T PF11567_consen 83 NVEHFLQEQYQQYLSQEE 100 (101)
T ss_dssp HHHHHHHHHHHHHHHHH-
T ss_pred hHHHHHHHHHHHHHhhhc
Confidence 346799999999999875
No 248
>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=31.25 E-value=40 Score=21.15 Aligned_cols=13 Identities=31% Similarity=0.386 Sum_probs=10.9
Q ss_pred EEEEEEEeCCCCC
Q psy104 28 KLRLTVVDTPGFG 40 (86)
Q Consensus 28 ~l~LtIidTpGfG 40 (86)
.+++.++||||..
T Consensus 42 ~~~~~i~Dt~G~~ 54 (158)
T cd04151 42 NLKFQVWDLGGQT 54 (158)
T ss_pred CEEEEEEECCCCH
Confidence 4688999999975
No 249
>KOG2655|consensus
Probab=31.15 E-value=39 Score=26.02 Aligned_cols=74 Identities=16% Similarity=0.007 Sum_probs=50.0
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCCCCccCCc--cchhHHHHHHHHHHHHhhhhhcCCccCCCCCCeeEEee
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSE--ESWRACCSYIDDQFRQYFNDESGLNRKNIVDNREVVDK 84 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~i~n~--~~~~~i~~yI~~qf~~yl~eE~~i~R~~~~D~RVH~Cl 84 (86)
-+..|......++.+|-.....--...|+.+--|-+ +.|..-.-+|...++.+..-...+...++...++++|.
T Consensus 217 ~PFAIigs~~~~e~~G~~~vrgR~YpWG~veien~~h~DF~~Lr~~Li~thl~dLk~~T~~~~YEnYR~~~L~~~~ 292 (366)
T KOG2655|consen 217 IPFAIIGSNTEIEEKGKKRVRGRKYPWGTVEIENPEHCDFKKLRNLLIRTHLEDLKDTTNNLLYENYRTEKLEGLL 292 (366)
T ss_pred CCeEEEecCceeecCCceEeeceecCCceeeccCCCcchHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhhcc
Confidence 346777777778888877666678899999776644 44666666777777777666666655555555555554
No 250
>cd01381 MYSc_type_VII Myosin motor domain, type VII myosins. Myosins in this group have been associated with functions in sensory systems such as vision and hearing. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydr
Probab=31.07 E-value=87 Score=25.78 Aligned_cols=35 Identities=20% Similarity=0.445 Sum_probs=25.3
Q ss_pred EEEEEEEeCCCCCCccCCccchhHH-HHHHHHHHHHhh
Q psy104 28 KLRLTVVDTPGFGDSINSEESWRAC-CSYIDDQFRQYF 64 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~n~~~~~~i-~~yI~~qf~~yl 64 (86)
...+.|.|.+||=..- .++|+.+ ++|..++...++
T Consensus 361 ~~~IgiLDIfGFE~f~--~NsfEQLcINy~NEkLQ~~f 396 (671)
T cd01381 361 RNSIGVLDIFGFENFD--VNSFEQLCINFANENLQQFF 396 (671)
T ss_pred cceEEEEecCCcccCC--CCCHHHHHHHHHHHHHHHHH
Confidence 4568899999995443 3467744 899998877663
No 251
>cd01386 MYSc_type_XVIII Myosin motor domain, type XVIII myosins. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the
Probab=30.99 E-value=83 Score=26.40 Aligned_cols=36 Identities=22% Similarity=0.598 Sum_probs=26.6
Q ss_pred EEEEEEeCCCCCCccCC----ccchhHH-HHHHHHHHHHhh
Q psy104 29 LRLTVVDTPGFGDSINS----EESWRAC-CSYIDDQFRQYF 64 (86)
Q Consensus 29 l~LtIidTpGfGd~i~n----~~~~~~i-~~yI~~qf~~yl 64 (86)
..+.|.|.+||=..-.| .++|+.+ ++|..+++..++
T Consensus 373 ~~IgiLDIfGFE~f~~n~~~~~NsfEQLcINyaNEkLQq~f 413 (767)
T cd01386 373 ASIMLVDTPGFQNPASQGKDRAATFEELCHNYLQERLQLLF 413 (767)
T ss_pred cEEEEEecccccccccccccCCCCHHHHhhhhhHHHHHHHH
Confidence 46789999999654332 2578854 899999888775
No 252
>TIGR01947 rnfG electron transport complex, RnfABCDGE type, G subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the A subunit.
Probab=30.98 E-value=31 Score=23.52 Aligned_cols=20 Identities=45% Similarity=0.861 Sum_probs=12.6
Q ss_pred cCeEEEEEEE---eCCCCCCccC
Q psy104 25 RGVKLRLTVV---DTPGFGDSIN 44 (86)
Q Consensus 25 ~~~~l~LtIi---dTpGfGd~i~ 44 (86)
+|.-..+.|+ +|||+|+.+.
T Consensus 106 dg~I~gv~v~~~~ETpGlG~~i~ 128 (186)
T TIGR01947 106 DGTILGVRVLSHKETPGLGDKIE 128 (186)
T ss_pred CCeEEEEEEeecCCCcccccccc
Confidence 3443344443 6999998876
No 253
>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=30.76 E-value=78 Score=20.22 Aligned_cols=14 Identities=29% Similarity=0.430 Sum_probs=11.4
Q ss_pred EEEEEEEeCCCCCC
Q psy104 28 KLRLTVVDTPGFGD 41 (86)
Q Consensus 28 ~l~LtIidTpGfGd 41 (86)
.+++.++||||...
T Consensus 42 ~~~i~l~Dt~G~~~ 55 (169)
T cd04158 42 NLKFTIWDVGGKHK 55 (169)
T ss_pred CEEEEEEECCCChh
Confidence 47889999999754
No 254
>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=30.74 E-value=99 Score=21.51 Aligned_cols=21 Identities=24% Similarity=0.311 Sum_probs=15.8
Q ss_pred EEEeecCeEEEEEEEeCCCCC
Q psy104 20 MDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 20 ~~l~e~~~~l~LtIidTpGfG 40 (86)
..+.-++..++|.+.||+|-.
T Consensus 40 ~~~~~~~~~v~L~iwDt~G~e 60 (222)
T cd04173 40 ASFEIDKRRIELNMWDTSGSS 60 (222)
T ss_pred EEEEECCEEEEEEEEeCCCcH
Confidence 344456778999999999953
No 255
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=30.73 E-value=41 Score=26.75 Aligned_cols=33 Identities=15% Similarity=0.128 Sum_probs=23.1
Q ss_pred EEEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhh
Q psy104 28 KLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYF 64 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl 64 (86)
-+.|-|=|||+. +-. .||.||..-|...=..-|
T Consensus 235 gvd~iiddtp~~---v~l-s~fdp~rreia~~~l~~l 267 (514)
T TIGR03319 235 GVDLIIDDTPEA---VIL-SGFDPVRREIARMALEKL 267 (514)
T ss_pred CceEEEcCCCCe---EEe-cCCchHHHHHHHHHHHHH
Confidence 466888899976 333 489999888876544433
No 256
>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=30.37 E-value=18 Score=24.89 Aligned_cols=15 Identities=33% Similarity=0.505 Sum_probs=10.7
Q ss_pred EEEEEEEeCCCCCCc
Q psy104 28 KLRLTVVDTPGFGDS 42 (86)
Q Consensus 28 ~l~LtIidTpGfGd~ 42 (86)
.-.+.+||+||-+.-
T Consensus 48 ~~~~~lvD~PGH~rl 62 (181)
T PF09439_consen 48 GKKLRLVDIPGHPRL 62 (181)
T ss_dssp GTCECEEEETT-HCC
T ss_pred CCEEEEEECCCcHHH
Confidence 346789999998754
No 257
>PLN03230 acetyl-coenzyme A carboxylase carboxyl transferase; Provisional
Probab=30.35 E-value=32 Score=27.07 Aligned_cols=14 Identities=57% Similarity=0.809 Sum_probs=10.9
Q ss_pred CeEEEEEEEeCCCCC
Q psy104 26 GVKLRLTVVDTPGFG 40 (86)
Q Consensus 26 ~~~l~LtIidTpGfG 40 (86)
++|+ |++|||||+-
T Consensus 221 ~lPI-VtLVDTpGA~ 234 (431)
T PLN03230 221 GFPI-LTFVDTPGAY 234 (431)
T ss_pred CCCE-EEEEeCCCcC
Confidence 4443 8999999985
No 258
>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=30.26 E-value=54 Score=22.08 Aligned_cols=16 Identities=38% Similarity=0.376 Sum_probs=13.6
Q ss_pred ecCeEEEEEEEeCCCC
Q psy104 24 ERGVKLRLTVVDTPGF 39 (86)
Q Consensus 24 e~~~~l~LtIidTpGf 39 (86)
-+|.+++|.+.||+|-
T Consensus 61 ~~~~~v~l~iwDTaG~ 76 (195)
T cd01873 61 VDGVSVSLRLWDTFGD 76 (195)
T ss_pred eCCEEEEEEEEeCCCC
Confidence 3567899999999995
No 259
>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=30.12 E-value=75 Score=20.43 Aligned_cols=13 Identities=23% Similarity=0.353 Sum_probs=10.8
Q ss_pred EEEEEEEeCCCCC
Q psy104 28 KLRLTVVDTPGFG 40 (86)
Q Consensus 28 ~l~LtIidTpGfG 40 (86)
.++|.++||||..
T Consensus 58 ~~~~~l~D~~G~~ 70 (174)
T cd04153 58 NIRFLMWDIGGQE 70 (174)
T ss_pred CeEEEEEECCCCH
Confidence 4778999999974
No 260
>PRK13351 elongation factor G; Reviewed
Probab=29.14 E-value=35 Score=27.66 Aligned_cols=15 Identities=40% Similarity=0.678 Sum_probs=11.8
Q ss_pred EEEEEEEeCCCCCCc
Q psy104 28 KLRLTVVDTPGFGDS 42 (86)
Q Consensus 28 ~l~LtIidTpGfGd~ 42 (86)
..+++++||||..+.
T Consensus 72 ~~~i~liDtPG~~df 86 (687)
T PRK13351 72 NHRINLIDTPGHIDF 86 (687)
T ss_pred CEEEEEEECCCcHHH
Confidence 357899999998653
No 261
>PLN00116 translation elongation factor EF-2 subunit; Provisional
Probab=29.04 E-value=29 Score=29.12 Aligned_cols=15 Identities=27% Similarity=0.581 Sum_probs=12.0
Q ss_pred EEEEEEEeCCCCCCc
Q psy104 28 KLRLTVVDTPGFGDS 42 (86)
Q Consensus 28 ~l~LtIidTpGfGd~ 42 (86)
..++++|||||.-|.
T Consensus 97 ~~~inliDtPGh~dF 111 (843)
T PLN00116 97 EYLINLIDSPGHVDF 111 (843)
T ss_pred ceEEEEECCCCHHHH
Confidence 567899999998544
No 262
>TIGR03874 4cys_cytochr c-type cytochrome, methanol metabolism-related. This family represents a c-type cytochrome related to (but excluding) cytochrome c-555 of Methylococcus capsulatus. Members contain four invariant Cys residues, including two from a heme-binding motif shared with c-555, and two others.
Probab=29.02 E-value=41 Score=22.48 Aligned_cols=26 Identities=23% Similarity=0.247 Sum_probs=19.7
Q ss_pred eCCCCCCccCCccchhHHHHHHHHHH
Q psy104 35 DTPGFGDSINSEESWRACCSYIDDQF 60 (86)
Q Consensus 35 dTpGfGd~i~n~~~~~~i~~yI~~qf 60 (86)
-.|+|+...+....+..|..||..+-
T Consensus 91 ~MPaF~~~LsD~~eIa~L~~YLR~~~ 116 (143)
T TIGR03874 91 VMPAFGDNPNVMCYLDDLYVYLRARG 116 (143)
T ss_pred CCCCccccCCcHHHHHHHHHHHHhcc
Confidence 38999988876556788888887653
No 263
>cd01384 MYSc_type_XI Myosin motor domain, plant-specific type XI myosin, involved in organelle transport. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new act
Probab=28.71 E-value=1e+02 Score=25.36 Aligned_cols=35 Identities=26% Similarity=0.484 Sum_probs=25.7
Q ss_pred EEEEEEEeCCCCCCccCCccchhH-HHHHHHHHHHHhh
Q psy104 28 KLRLTVVDTPGFGDSINSEESWRA-CCSYIDDQFRQYF 64 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~n~~~~~~-i~~yI~~qf~~yl 64 (86)
...+.|.|.+||=..-. ++++. .++|..++...++
T Consensus 366 ~~~IgiLDI~GFE~f~~--NsfEQLcINyaNEkLQ~~f 401 (674)
T cd01384 366 KSLIGVLDIYGFESFKT--NSFEQFCINLTNEKLQQHF 401 (674)
T ss_pred CeEEEEEecccccccCc--CCHHHHHhhhhHHHHHHHH
Confidence 35688999999965543 36664 4889888887764
No 264
>PF14038 YqzE: YqzE-like protein
Probab=28.26 E-value=65 Score=18.14 Aligned_cols=17 Identities=24% Similarity=0.620 Sum_probs=14.5
Q ss_pred hHHHHHHHHHHHHhhhh
Q psy104 50 RACCSYIDDQFRQYFND 66 (86)
Q Consensus 50 ~~i~~yI~~qf~~yl~e 66 (86)
+..++|+.+|+=.|+..
T Consensus 3 nDyVKy~Tqq~V~Ymdt 19 (54)
T PF14038_consen 3 NDYVKYMTQQFVKYMDT 19 (54)
T ss_pred hHHHHHHHHHHHHHhhC
Confidence 35699999999999875
No 265
>PRK06003 flgB flagellar basal body rod protein FlgB; Reviewed
Probab=28.24 E-value=23 Score=22.70 Aligned_cols=7 Identities=43% Similarity=1.099 Sum_probs=6.0
Q ss_pred EeCCCCC
Q psy104 34 VDTPGFG 40 (86)
Q Consensus 34 idTpGfG 40 (86)
+|||||-
T Consensus 31 ~~TPgyk 37 (126)
T PRK06003 31 ANTPGYR 37 (126)
T ss_pred cCCCCcc
Confidence 6999995
No 266
>KOG1145|consensus
Probab=28.16 E-value=66 Score=26.62 Aligned_cols=32 Identities=28% Similarity=0.463 Sum_probs=23.0
Q ss_pred CCCCCCcceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 5 GNNRQGKTTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 5 ~~~~~~~t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
|.++..-|-.|-..++.+. +| =++|..||||=
T Consensus 180 A~E~GGITQhIGAF~V~~p-~G--~~iTFLDTPGH 211 (683)
T KOG1145|consen 180 AGEAGGITQHIGAFTVTLP-SG--KSITFLDTPGH 211 (683)
T ss_pred hhhcCCccceeceEEEecC-CC--CEEEEecCCcH
Confidence 3444455667778888777 66 57899999994
No 267
>KOG0095|consensus
Probab=27.82 E-value=1.6e+02 Score=20.54 Aligned_cols=26 Identities=27% Similarity=0.491 Sum_probs=19.4
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
.+.+..++++++ |-+++|.|-||.|=
T Consensus 41 gvdfmiktvev~--gekiklqiwdtagq 66 (213)
T KOG0095|consen 41 GVDFMIKTVEVN--GEKIKLQIWDTAGQ 66 (213)
T ss_pred eeeEEEEEEEEC--CeEEEEEEeeccch
Confidence 466677776654 56899999999884
No 268
>PRK12298 obgE GTPase CgtA; Reviewed
Probab=27.61 E-value=44 Score=25.50 Aligned_cols=12 Identities=33% Similarity=0.661 Sum_probs=10.2
Q ss_pred EEEEEeCCCCCC
Q psy104 30 RLTVVDTPGFGD 41 (86)
Q Consensus 30 ~LtIidTpGfGd 41 (86)
++.++||||+..
T Consensus 208 ~i~~vDtPGi~~ 219 (390)
T PRK12298 208 SFVVADIPGLIE 219 (390)
T ss_pred EEEEEeCCCccc
Confidence 578999999964
No 269
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=27.53 E-value=33 Score=24.95 Aligned_cols=51 Identities=31% Similarity=0.393 Sum_probs=38.6
Q ss_pred eecCeEEEEEEEeCCCCCCc-----cCCccchhHHHHHHHH-----HHHHhhhhhcCCccC
Q psy104 23 EERGVKLRLTVVDTPGFGDS-----INSEESWRACCSYIDD-----QFRQYFNDESGLNRK 73 (86)
Q Consensus 23 ~e~~~~l~LtIidTpGfGd~-----i~n~~~~~~i~~yI~~-----qf~~yl~eE~~i~R~ 73 (86)
++|.+..+|||-|-.|||.. .-+..+|.-|...|+- --++||.+=++..|+
T Consensus 82 Q~N~i~~rlTV~dLv~FGRfPYSqGRlt~eD~~~I~~aieyl~L~~l~dryLd~LSGGQrQ 142 (252)
T COG4604 82 QENHINSRLTVRDLVGFGRFPYSQGRLTKEDRRIINEAIEYLHLEDLSDRYLDELSGGQRQ 142 (252)
T ss_pred hhchhhheeEHHHHhhcCCCcccCCCCchHHHHHHHHHHHHhcccchHHHhHHhcccchhh
Confidence 37788999999999999965 4456678888665553 346788887888775
No 270
>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=27.30 E-value=1.1e+02 Score=18.39 Aligned_cols=12 Identities=33% Similarity=0.299 Sum_probs=10.2
Q ss_pred EEEEEEeCCCCC
Q psy104 29 LRLTVVDTPGFG 40 (86)
Q Consensus 29 l~LtIidTpGfG 40 (86)
+.+.++||||..
T Consensus 44 ~~~~~~D~~g~~ 55 (159)
T cd04159 44 VTLKVWDLGGQP 55 (159)
T ss_pred EEEEEEECCCCH
Confidence 679999999963
No 271
>PF02089 Palm_thioest: Palmitoyl protein thioesterase; InterPro: IPR002472 Neuronal ceroid lipofuscinoses (NCL) represent a group of encephalopathies that occur in 1 in 12,500 children. Mutations in the palmitoyl protein thioesterase gene causing infantile neuronal ceroid lipofuscinosis []. The most common mutation results in intracellular accumulation of the polypeptide and undetectable enzyme activity in the brain. Direct sequencing of cDNAs derived from brain RNA of INCL patients has shown a mis-sense transversion of A to T at nucleotide position 364, which results in substitution of Trp for Arg at position 122 in the protein - Arg 122 is immediately adjacent to a lipase consensus sequence that contains the putative active site Ser of PPT. The occurrence of this and two other independent mutations in the PPT gene strongly suggests that defects in this gene cause INCL.; GO: 0008474 palmitoyl-(protein) hydrolase activity, 0006464 protein modification process; PDB: 3GRO_B 1PJA_A 1EXW_A 1EH5_A 1EI9_A.
Probab=27.17 E-value=49 Score=24.45 Aligned_cols=29 Identities=31% Similarity=0.306 Sum_probs=18.3
Q ss_pred EEeCCCCCCccCCccchhHHHHHHHHHHH
Q psy104 33 VVDTPGFGDSINSEESWRACCSYIDDQFR 61 (86)
Q Consensus 33 IidTpGfGd~i~n~~~~~~i~~yI~~qf~ 61 (86)
||--.|+||+-.|..++..|.++|++.+-
T Consensus 8 vViwHGmGD~~~~~~~m~~i~~~i~~~~P 36 (279)
T PF02089_consen 8 VVIWHGMGDSCCNPSSMGSIKELIEEQHP 36 (279)
T ss_dssp EEEE--TT--S--TTTHHHHHHHHHHHST
T ss_pred EEEEEcCccccCChhHHHHHHHHHHHhCC
Confidence 56678999999888889999888887653
No 272
>COG0825 AccA Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]
Probab=26.98 E-value=37 Score=25.64 Aligned_cols=11 Identities=45% Similarity=0.643 Sum_probs=8.3
Q ss_pred EEEEEeCCCCC
Q psy104 30 RLTVVDTPGFG 40 (86)
Q Consensus 30 ~LtIidTpGfG 40 (86)
-+|+|||||-=
T Consensus 153 iitfIDT~GAy 163 (317)
T COG0825 153 IITFIDTPGAY 163 (317)
T ss_pred EEEEecCCCCC
Confidence 37899998853
No 273
>PF14149 YhfH: YhfH-like protein
Probab=26.71 E-value=53 Score=17.09 Aligned_cols=14 Identities=29% Similarity=0.295 Sum_probs=11.5
Q ss_pred HHHHHHHHHHhhhh
Q psy104 53 CSYIDDQFRQYFND 66 (86)
Q Consensus 53 ~~yI~~qf~~yl~e 66 (86)
-+.|++|.+.|+.+
T Consensus 20 G~~i~EQ~E~Y~n~ 33 (37)
T PF14149_consen 20 GKEIEEQAECYGNE 33 (37)
T ss_pred HHHHHHHHHHHhCc
Confidence 46799999999865
No 274
>PF01797 Y1_Tnp: Transposase IS200 like; InterPro: IPR002686 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This entry represents a domain found in transposases for IS200 from Escherichia coli []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2F5G_B 2F4F_B 2EC2_F 2XM3_C 2XQC_D 2XO6_A 2XMA_E 2VJV_B 2VIH_B 2VJU_A ....
Probab=26.67 E-value=29 Score=21.10 Aligned_cols=12 Identities=25% Similarity=0.473 Sum_probs=9.4
Q ss_pred chhHHHHHHHHH
Q psy104 48 SWRACCSYIDDQ 59 (86)
Q Consensus 48 ~~~~i~~yI~~q 59 (86)
+...+.+||..|
T Consensus 110 ~~~~~~~YI~~n 121 (121)
T PF01797_consen 110 SLDNVIRYIENN 121 (121)
T ss_dssp BHHHHHHHHHHH
T ss_pred hHHHHHHHHhhC
Confidence 777888888765
No 275
>PLN00223 ADP-ribosylation factor; Provisional
Probab=26.64 E-value=1e+02 Score=20.22 Aligned_cols=12 Identities=33% Similarity=0.440 Sum_probs=10.0
Q ss_pred EEEEEEEeCCCC
Q psy104 28 KLRLTVVDTPGF 39 (86)
Q Consensus 28 ~l~LtIidTpGf 39 (86)
.+.|.+.||||-
T Consensus 60 ~~~~~i~D~~Gq 71 (181)
T PLN00223 60 NISFTVWDVGGQ 71 (181)
T ss_pred CEEEEEEECCCC
Confidence 467999999994
No 276
>PRK15494 era GTPase Era; Provisional
Probab=26.27 E-value=44 Score=24.74 Aligned_cols=12 Identities=33% Similarity=0.648 Sum_probs=9.8
Q ss_pred EEEEEeCCCCCC
Q psy104 30 RLTVVDTPGFGD 41 (86)
Q Consensus 30 ~LtIidTpGfGd 41 (86)
++.++||||+..
T Consensus 101 qi~~~DTpG~~~ 112 (339)
T PRK15494 101 QVILYDTPGIFE 112 (339)
T ss_pred EEEEEECCCcCC
Confidence 568999999853
No 277
>PRK09866 hypothetical protein; Provisional
Probab=25.52 E-value=43 Score=28.10 Aligned_cols=27 Identities=30% Similarity=0.437 Sum_probs=16.3
Q ss_pred EEEEEEEEee-cCeEEEEEEEeCCCCCC
Q psy104 15 IEKKSMDIEE-RGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 15 I~~~~~~l~e-~~~~l~LtIidTpGfGd 41 (86)
|.+...++.+ ....-.+.++||||+-.
T Consensus 215 iev~f~hl~g~l~~~~QIIFVDTPGIhk 242 (741)
T PRK09866 215 IEVEFVHLAGLESYPGQLTLLDTPGPNE 242 (741)
T ss_pred eeeeeeeccccccccCCEEEEECCCCCC
Confidence 3344445542 22345778999999964
No 278
>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=25.50 E-value=1e+02 Score=19.03 Aligned_cols=13 Identities=46% Similarity=0.463 Sum_probs=11.0
Q ss_pred EEEEEEEeCCCCC
Q psy104 28 KLRLTVVDTPGFG 40 (86)
Q Consensus 28 ~l~LtIidTpGfG 40 (86)
.+.|.+.||||..
T Consensus 43 ~~~l~i~D~~G~~ 55 (160)
T cd04156 43 HLSLTVWDVGGQE 55 (160)
T ss_pred ceEEEEEECCCCH
Confidence 4789999999964
No 279
>PRK01908 electron transport complex protein RnfG; Validated
Probab=25.43 E-value=41 Score=23.49 Aligned_cols=12 Identities=50% Similarity=0.933 Sum_probs=9.1
Q ss_pred EeCCCCCCccCC
Q psy104 34 VDTPGFGDSINS 45 (86)
Q Consensus 34 idTpGfGd~i~n 45 (86)
-+|||+|+.+..
T Consensus 122 ~ETpGLG~~i~~ 133 (205)
T PRK01908 122 HETPGLGDKIEL 133 (205)
T ss_pred CCCcccchhhhh
Confidence 369999987754
No 280
>KOG0464|consensus
Probab=25.19 E-value=82 Score=25.51 Aligned_cols=29 Identities=31% Similarity=0.646 Sum_probs=18.7
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCCCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPGFGD 41 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd 41 (86)
..+.|+..-+.+.=.| .++++|||||-=|
T Consensus 86 rgitiqsaav~fdwkg--~rinlidtpghvd 114 (753)
T KOG0464|consen 86 RGITIQSAAVNFDWKG--HRINLIDTPGHVD 114 (753)
T ss_pred cCceeeeeeeeccccc--ceEeeecCCCcce
Confidence 3455666666555444 4567899999644
No 281
>PTZ00133 ADP-ribosylation factor; Provisional
Probab=24.96 E-value=1e+02 Score=20.16 Aligned_cols=13 Identities=31% Similarity=0.468 Sum_probs=10.8
Q ss_pred EEEEEEEeCCCCC
Q psy104 28 KLRLTVVDTPGFG 40 (86)
Q Consensus 28 ~l~LtIidTpGfG 40 (86)
.+.+.+.||||-.
T Consensus 60 ~~~~~l~D~~G~~ 72 (182)
T PTZ00133 60 NLKFTMWDVGGQD 72 (182)
T ss_pred CEEEEEEECCCCH
Confidence 4789999999964
No 282
>KOG0078|consensus
Probab=24.89 E-value=2.6e+02 Score=19.87 Aligned_cols=32 Identities=34% Similarity=0.319 Sum_probs=22.5
Q ss_pred CCcceEEEEEEEEEeecCeEEEEEEEeCCCCC
Q psy104 9 QGKTTTIEKKSMDIEERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 9 ~~~t~~I~~~~~~l~e~~~~l~LtIidTpGfG 40 (86)
..+|+-|.-+.-.++-+|.+++|.+.||-|=.
T Consensus 41 ~~sTiGIDFk~kti~l~g~~i~lQiWDtaGQe 72 (207)
T KOG0078|consen 41 FISTIGIDFKIKTIELDGKKIKLQIWDTAGQE 72 (207)
T ss_pred ccceEEEEEEEEEEEeCCeEEEEEEEEcccch
Confidence 44555555554455667799999999998843
No 283
>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=24.70 E-value=1.5e+02 Score=20.88 Aligned_cols=16 Identities=38% Similarity=0.580 Sum_probs=13.1
Q ss_pred cCeEEEEEEEeCCCCC
Q psy104 25 RGVKLRLTVVDTPGFG 40 (86)
Q Consensus 25 ~~~~l~LtIidTpGfG 40 (86)
++-.+.|.|.||+|..
T Consensus 44 ~~~~~~l~I~Dt~G~~ 59 (247)
T cd04143 44 RGEVYQLDILDTSGNH 59 (247)
T ss_pred CCEEEEEEEEECCCCh
Confidence 4567999999999953
No 284
>PF11144 DUF2920: Protein of unknown function (DUF2920); InterPro: IPR022605 This bacterial family of proteins has no known function.
Probab=24.63 E-value=48 Score=25.81 Aligned_cols=33 Identities=30% Similarity=0.506 Sum_probs=21.8
Q ss_pred EEEEEEEeCCCCCCccCCccchhHHHHHHHHHHH
Q psy104 28 KLRLTVVDTPGFGDSINSEESWRACCSYIDDQFR 61 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~ 61 (86)
.++--|+-.||||...|... ..-+.+|+..+|.
T Consensus 33 e~kaIvfiI~GfG~dan~~~-~d~~r~~iA~~fn 65 (403)
T PF11144_consen 33 EIKAIVFIIPGFGADANSNY-LDFMREYIAKKFN 65 (403)
T ss_pred CceEEEEEeCCcCCCcchHH-HHHHHHHHHHhCC
Confidence 55556777899999888653 2455555555554
No 285
>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=24.54 E-value=56 Score=22.76 Aligned_cols=12 Identities=25% Similarity=0.612 Sum_probs=9.7
Q ss_pred EEEEEEeCCCCC
Q psy104 29 LRLTVVDTPGFG 40 (86)
Q Consensus 29 l~LtIidTpGfG 40 (86)
..+.++||||+-
T Consensus 47 ~~i~l~DtpG~~ 58 (233)
T cd01896 47 AKIQLLDLPGII 58 (233)
T ss_pred eEEEEEECCCcc
Confidence 467899999983
No 286
>KOG0395|consensus
Probab=24.48 E-value=1.8e+02 Score=19.89 Aligned_cols=27 Identities=22% Similarity=0.325 Sum_probs=18.8
Q ss_pred cceEEEEEEEEEeecCeEEEEEEEeCCC
Q psy104 11 KTTTIEKKSMDIEERGVKLRLTVVDTPG 38 (86)
Q Consensus 11 ~t~~I~~~~~~l~e~~~~l~LtIidTpG 38 (86)
+|.+ ..|.-.+.-++-...|.|.||+|
T Consensus 34 ptie-d~y~k~~~v~~~~~~l~ilDt~g 60 (196)
T KOG0395|consen 34 PTIE-DSYRKELTVDGEVCMLEILDTAG 60 (196)
T ss_pred CCcc-ccceEEEEECCEEEEEEEEcCCC
Confidence 3443 44444555557889999999999
No 287
>PRK11126 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase; Provisional
Probab=24.17 E-value=1.4e+02 Score=19.75 Aligned_cols=16 Identities=31% Similarity=0.478 Sum_probs=13.2
Q ss_pred EEEEEEeCCCCCCccC
Q psy104 29 LRLTVVDTPGFGDSIN 44 (86)
Q Consensus 29 l~LtIidTpGfGd~i~ 44 (86)
.++-.+|-||+|.+-.
T Consensus 28 ~~vi~~D~~G~G~S~~ 43 (242)
T PRK11126 28 YPRLYIDLPGHGGSAA 43 (242)
T ss_pred CCEEEecCCCCCCCCC
Confidence 6788999999997644
No 288
>PRK09554 feoB ferrous iron transport protein B; Reviewed
Probab=24.11 E-value=1.4e+02 Score=25.02 Aligned_cols=14 Identities=36% Similarity=0.451 Sum_probs=10.9
Q ss_pred EEEEEEeCCCCCCc
Q psy104 29 LRLTVVDTPGFGDS 42 (86)
Q Consensus 29 l~LtIidTpGfGd~ 42 (86)
.+++++||||.-+.
T Consensus 50 ~~i~lvDtPG~ysl 63 (772)
T PRK09554 50 HQVTLVDLPGTYSL 63 (772)
T ss_pred eEEEEEECCCcccc
Confidence 45789999998653
No 289
>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=23.71 E-value=36 Score=22.62 Aligned_cols=7 Identities=57% Similarity=1.189 Sum_probs=5.8
Q ss_pred EEEeCCC
Q psy104 32 TVVDTPG 38 (86)
Q Consensus 32 tIidTpG 38 (86)
.+|||||
T Consensus 39 ~~IDTPG 45 (143)
T PF10662_consen 39 NTIDTPG 45 (143)
T ss_pred cEEECCh
Confidence 4799997
No 290
>PHA02130 hypothetical protein
Probab=23.46 E-value=37 Score=20.13 Aligned_cols=20 Identities=25% Similarity=0.747 Sum_probs=16.8
Q ss_pred cchhHHHHHHHHHHHHhhhh
Q psy104 47 ESWRACCSYIDDQFRQYFND 66 (86)
Q Consensus 47 ~~~~~i~~yI~~qf~~yl~e 66 (86)
.+|+.+.++++++|+.+=..
T Consensus 14 ks~~sl~~wl~~~~dswddd 33 (81)
T PHA02130 14 KSWESLREWLDERFDSWDDD 33 (81)
T ss_pred HHHHHHHHHHHhcccccccc
Confidence 58999999999999987544
No 291
>TIGR03100 hydr1_PEP hydrolase, ortholog 1, exosortase system type 1 associated. This group of proteins are members of the alpha/beta hydrolase superfamily. These proteins are generally found in genomes containing the exosortase/PEP-CTERM protein expoert system, specifically the type 1 variant of this system described by the Genome Property GenProp0652. When found in this context they are invariably present in the vicinity of a second, relatively unrelated enzyme (ortholog 2, TIGR03101) of the same superfamily.
Probab=23.29 E-value=2.3e+02 Score=19.80 Aligned_cols=33 Identities=18% Similarity=0.225 Sum_probs=20.6
Q ss_pred EEEEEEeCCCCCCccCCccchhHHHHHHHHHHH
Q psy104 29 LRLTVVDTPGFGDSINSEESWRACCSYIDDQFR 61 (86)
Q Consensus 29 l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~ 61 (86)
+..-.+|.||+|++......|.....-+.+-++
T Consensus 58 ~~v~~~Dl~G~G~S~~~~~~~~~~~~d~~~~~~ 90 (274)
T TIGR03100 58 FPVLRFDYRGMGDSEGENLGFEGIDADIAAAID 90 (274)
T ss_pred CEEEEeCCCCCCCCCCCCCCHHHHHHHHHHHHH
Confidence 567799999999876544445444333444433
No 292
>COG1160 Predicted GTPases [General function prediction only]
Probab=23.28 E-value=1.3e+02 Score=23.82 Aligned_cols=32 Identities=19% Similarity=0.204 Sum_probs=19.5
Q ss_pred EEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhhh
Q psy104 29 LRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYFN 65 (86)
Q Consensus 29 l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl~ 65 (86)
..+.+|||+|+-+.-+ .++..-+.+|=+.-+.
T Consensus 51 ~~f~lIDTgGl~~~~~-----~~l~~~i~~Qa~~Ai~ 82 (444)
T COG1160 51 REFILIDTGGLDDGDE-----DELQELIREQALIAIE 82 (444)
T ss_pred ceEEEEECCCCCcCCc-----hHHHHHHHHHHHHHHH
Confidence 4588999999964332 2345555555554443
No 293
>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=23.17 E-value=55 Score=24.82 Aligned_cols=12 Identities=42% Similarity=0.739 Sum_probs=10.1
Q ss_pred EEEEEEEeCCCC
Q psy104 28 KLRLTVVDTPGF 39 (86)
Q Consensus 28 ~l~LtIidTpGf 39 (86)
..+++++||||-
T Consensus 79 ~~~i~liDtPGh 90 (406)
T TIGR03680 79 LRRVSFVDAPGH 90 (406)
T ss_pred ccEEEEEECCCH
Confidence 457899999995
No 294
>PLN02824 hydrolase, alpha/beta fold family protein
Probab=23.08 E-value=2e+02 Score=19.86 Aligned_cols=12 Identities=33% Similarity=0.609 Sum_probs=6.3
Q ss_pred EEEEeCCCCCCc
Q psy104 31 LTVVDTPGFGDS 42 (86)
Q Consensus 31 LtIidTpGfGd~ 42 (86)
+-.+|-||+|.+
T Consensus 58 vi~~DlpG~G~S 69 (294)
T PLN02824 58 VYAIDLLGYGYS 69 (294)
T ss_pred EEEEcCCCCCCC
Confidence 344555555544
No 295
>KOG0468|consensus
Probab=22.82 E-value=1e+02 Score=26.35 Aligned_cols=31 Identities=19% Similarity=0.502 Sum_probs=22.0
Q ss_pred CcceEEEEEEEEE---eecCeEEEEEEEeCCCCC
Q psy104 10 GKTTTIEKKSMDI---EERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 10 ~~t~~I~~~~~~l---~e~~~~l~LtIidTpGfG 40 (86)
....+|......+ ..+|...-++++||||==
T Consensus 175 eRg~sIK~~p~Tl~l~D~~~KS~l~nilDTPGHV 208 (971)
T KOG0468|consen 175 ERGCSIKSTPVTLVLSDSKGKSYLMNILDTPGHV 208 (971)
T ss_pred hcCceEeecceEEEEecCcCceeeeeeecCCCcc
Confidence 4456666655533 367889999999999963
No 296
>PF07885 Ion_trans_2: Ion channel; InterPro: IPR013099 This entry includes the two membrane helix type ion channels found in bacteria []. ; PDB: 1KKD_A 2A0L_A 1ORQ_C 3UKM_C 1LNQ_E 3OUS_A 3LDC_A 3LDD_A 3RBZ_A 3LDE_A ....
Probab=22.73 E-value=58 Score=18.50 Aligned_cols=17 Identities=29% Similarity=0.561 Sum_probs=9.7
Q ss_pred EeCCCCCCccCCccchh
Q psy104 34 VDTPGFGDSINSEESWR 50 (86)
Q Consensus 34 idTpGfGd~i~n~~~~~ 50 (86)
+-|-||||-...+...+
T Consensus 36 ~tTvGyGDi~p~t~~gr 52 (79)
T PF07885_consen 36 ITTVGYGDIVPQTPAGR 52 (79)
T ss_dssp HTT---SSSSTSSHHHH
T ss_pred HhcccCCCccCCccchH
Confidence 46899999988864433
No 297
>PRK04000 translation initiation factor IF-2 subunit gamma; Validated
Probab=22.72 E-value=57 Score=24.89 Aligned_cols=13 Identities=38% Similarity=0.715 Sum_probs=10.5
Q ss_pred EEEEEEeCCCCCC
Q psy104 29 LRLTVVDTPGFGD 41 (86)
Q Consensus 29 l~LtIidTpGfGd 41 (86)
.+++++||||..+
T Consensus 85 ~~i~liDtPG~~~ 97 (411)
T PRK04000 85 RRVSFVDAPGHET 97 (411)
T ss_pred cEEEEEECCCHHH
Confidence 5789999999643
No 298
>PF06500 DUF1100: Alpha/beta hydrolase of unknown function (DUF1100); InterPro: IPR010520 Proteins in this entry display esterase activity toward pNP-butyrate []. This entry also includes 2,6-dihydropseudooxynicotine hydrolase which has a role in nicotine catabolism by cleaving a C-C bond in 2,6-dihydroxypseudooxyicotine [, ].; PDB: 3OUR_A 3MVE_B 2JBW_C.
Probab=22.53 E-value=1.1e+02 Score=23.93 Aligned_cols=30 Identities=30% Similarity=0.529 Sum_probs=17.1
Q ss_pred EEEEEEeCCCCCCcc------CCccchhHHHHHHHH
Q psy104 29 LRLTVVDTPGFGDSI------NSEESWRACCSYIDD 58 (86)
Q Consensus 29 l~LtIidTpGfGd~i------~n~~~~~~i~~yI~~ 58 (86)
+..-++|-||.|++. |-+.-|.+|++|+..
T Consensus 219 iA~LtvDmPG~G~s~~~~l~~D~~~l~~aVLd~L~~ 254 (411)
T PF06500_consen 219 IAMLTVDMPGQGESPKWPLTQDSSRLHQAVLDYLAS 254 (411)
T ss_dssp -EEEEE--TTSGGGTTT-S-S-CCHHHHHHHHHHHH
T ss_pred CEEEEEccCCCcccccCCCCcCHHHHHHHHHHHHhc
Confidence 345579999999863 222237777777655
No 299
>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=22.22 E-value=54 Score=24.31 Aligned_cols=11 Identities=18% Similarity=0.640 Sum_probs=9.9
Q ss_pred EEEEEEeCCCC
Q psy104 29 LRLTVVDTPGF 39 (86)
Q Consensus 29 l~LtIidTpGf 39 (86)
+.+.++||||+
T Consensus 69 v~i~l~D~aGl 79 (318)
T cd01899 69 VPVELIDVAGL 79 (318)
T ss_pred ceEEEEECCCC
Confidence 56999999999
No 300
>PRK15467 ethanolamine utilization protein EutP; Provisional
Probab=22.18 E-value=35 Score=22.03 Aligned_cols=9 Identities=44% Similarity=0.342 Sum_probs=7.4
Q ss_pred EEeCCCCCC
Q psy104 33 VVDTPGFGD 41 (86)
Q Consensus 33 IidTpGfGd 41 (86)
++||||+..
T Consensus 41 ~iDtpG~~~ 49 (158)
T PRK15467 41 DIDTPGEYF 49 (158)
T ss_pred cccCCcccc
Confidence 699999863
No 301
>KOG0097|consensus
Probab=22.14 E-value=1.3e+02 Score=20.71 Aligned_cols=30 Identities=33% Similarity=0.372 Sum_probs=20.1
Q ss_pred CcceEEEEEEEEEeecCeEEEEEEEeCCCC
Q psy104 10 GKTTTIEKKSMDIEERGVKLRLTVVDTPGF 39 (86)
Q Consensus 10 ~~t~~I~~~~~~l~e~~~~l~LtIidTpGf 39 (86)
+.|+-+.--+-.|+-.|-+++|.|-||.|-
T Consensus 41 phtigvefgtriievsgqkiklqiwdtagq 70 (215)
T KOG0097|consen 41 PHTIGVEFGTRIIEVSGQKIKLQIWDTAGQ 70 (215)
T ss_pred CcccceecceeEEEecCcEEEEEEeecccH
Confidence 344444444445566678999999999874
No 302
>PF09623 Cas_NE0113: CRISPR-associated protein NE0113 (Cas_NE0113); InterPro: IPR019092 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. This entry represents a Cas protein family found in both bacteria and arachaea. The function of these proteins is unknown.
Probab=22.12 E-value=58 Score=23.22 Aligned_cols=10 Identities=20% Similarity=0.049 Sum_probs=8.2
Q ss_pred CCCeeEEeec
Q psy104 76 VDNREVVDKS 85 (86)
Q Consensus 76 ~D~RVH~Cl~ 85 (86)
.+.||||||+
T Consensus 111 ~~~~lh~sIA 120 (224)
T PF09623_consen 111 PGRRLHVSIA 120 (224)
T ss_pred CCCeEEEEec
Confidence 3588999997
No 303
>COG1161 Predicted GTPases [General function prediction only]
Probab=22.06 E-value=51 Score=24.38 Aligned_cols=10 Identities=40% Similarity=0.747 Sum_probs=8.9
Q ss_pred EEEEeCCCCC
Q psy104 31 LTVVDTPGFG 40 (86)
Q Consensus 31 LtIidTpGfG 40 (86)
+-++||||+-
T Consensus 179 i~LlDtPGii 188 (322)
T COG1161 179 IYLLDTPGII 188 (322)
T ss_pred eEEecCCCcC
Confidence 7799999985
No 304
>PF11342 DUF3144: Protein of unknown function (DUF3144); InterPro: IPR021490 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=21.81 E-value=1e+02 Score=18.45 Aligned_cols=19 Identities=16% Similarity=0.503 Sum_probs=15.7
Q ss_pred hhHHHHHHHHHHHHhhhhh
Q psy104 49 WRACCSYIDDQFRQYFNDE 67 (86)
Q Consensus 49 ~~~i~~yI~~qf~~yl~eE 67 (86)
=+.+++|..+||+..|.+-
T Consensus 55 ke~~i~~f~~qy~~mL~~n 73 (78)
T PF11342_consen 55 KEEAIDYFTEQYRKMLEEN 73 (78)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3578999999999998763
No 305
>COG2869 NqrC Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrC [Energy production and conversion]
Probab=21.76 E-value=51 Score=24.19 Aligned_cols=16 Identities=38% Similarity=0.960 Sum_probs=12.9
Q ss_pred EeCCCCCCccCCccchh
Q psy104 34 VDTPGFGDSINSEESWR 50 (86)
Q Consensus 34 idTpGfGd~i~n~~~~~ 50 (86)
-+|||+|-.|.|- .|+
T Consensus 176 GETPGLGgeI~NP-~Wq 191 (264)
T COG2869 176 GETPGLGGEIENP-KWQ 191 (264)
T ss_pred CCCCCCccccCCH-HHH
Confidence 3799999999987 455
No 306
>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=21.69 E-value=64 Score=22.95 Aligned_cols=35 Identities=26% Similarity=0.312 Sum_probs=19.8
Q ss_pred CCcceEEEEEEEEEeecCeEEEEEEEeCCCCCCccCCc
Q psy104 9 QGKTTTIEKKSMDIEERGVKLRLTVVDTPGFGDSINSE 46 (86)
Q Consensus 9 ~~~t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~i~n~ 46 (86)
...|..++...+.... -+.|+|.|.||-.+-..+.
T Consensus 31 L~~T~~ve~~~v~~~~---~~~l~iwD~pGq~~~~~~~ 65 (232)
T PF04670_consen 31 LEPTIDVEKSHVRFLS---FLPLNIWDCPGQDDFMENY 65 (232)
T ss_dssp -----SEEEEEEECTT---SCEEEEEEE-SSCSTTHTT
T ss_pred cCCcCCceEEEEecCC---CcEEEEEEcCCcccccccc
Confidence 4566666655543222 3689999999998777763
No 307
>PTZ00014 myosin-A; Provisional
Probab=21.55 E-value=1.5e+02 Score=25.10 Aligned_cols=35 Identities=17% Similarity=0.261 Sum_probs=25.3
Q ss_pred EEEEEEEeCCCCCCccCCccchhHH-HHHHHHHHHHhh
Q psy104 28 KLRLTVVDTPGFGDSINSEESWRAC-CSYIDDQFRQYF 64 (86)
Q Consensus 28 ~l~LtIidTpGfGd~i~n~~~~~~i-~~yI~~qf~~yl 64 (86)
...+.|.|.+||=..- .++|+.+ ++|-.+++.+++
T Consensus 461 ~~~IGiLDI~GFE~f~--~NSfEQLcINy~NEkLQq~F 496 (821)
T PTZ00014 461 KVFIGMLDIFGFEVFK--NNSLEQLFINITNEMLQKNF 496 (821)
T ss_pred CceEEEEecccccccC--cchHHHHHHHHHHHHHHHHH
Confidence 3468899999995443 3467744 889888877774
No 308
>KOG4742|consensus
Probab=21.54 E-value=36 Score=25.35 Aligned_cols=11 Identities=55% Similarity=1.047 Sum_probs=8.7
Q ss_pred EEeCCCCCCcc
Q psy104 33 VVDTPGFGDSI 43 (86)
Q Consensus 33 IidTpGfGd~i 43 (86)
-.||||||.++
T Consensus 234 ~~~~~gFGaTt 244 (286)
T KOG4742|consen 234 AYDTPGFGATT 244 (286)
T ss_pred cccCCCcchhh
Confidence 36899999773
No 309
>KOG0079|consensus
Probab=21.47 E-value=1.7e+02 Score=20.34 Aligned_cols=25 Identities=28% Similarity=0.586 Sum_probs=18.8
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCC
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPG 38 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpG 38 (86)
.+.+..+++++. |-+++|-|-||.|
T Consensus 42 GvDfkirTv~i~--G~~VkLqIwDtAG 66 (198)
T KOG0079|consen 42 GVDFKIRTVDIN--GDRVKLQIWDTAG 66 (198)
T ss_pred eeeEEEEEeecC--CcEEEEEEeeccc
Confidence 355666666666 6788899999987
No 310
>PF01039 Carboxyl_trans: Carboxyl transferase domain; InterPro: IPR000022 Members in this domain include biotin dependent carboxylases [, ]. The carboxyl transferase domain carries out the following reaction; transcarboxylation from biotin to an acceptor molecule. There are two recognised types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxo acid as the acceptor molecule of carbon dioxide. All of the members in this family utilise acyl-CoA as the acceptor molecule.; GO: 0016874 ligase activity; PDB: 2F9Y_B 1XO6_B 1XNV_B 3MFM_C 3IBB_A 1XNW_F 3IAV_B 1XNY_A 3IB9_A 3U9S_F ....
Probab=21.35 E-value=72 Score=25.05 Aligned_cols=36 Identities=25% Similarity=0.261 Sum_probs=21.6
Q ss_pred CeEEEEEEEeCCCCCCccCCccchhHHHHHHHHHHHHhh
Q psy104 26 GVKLRLTVVDTPGFGDSINSEESWRACCSYIDDQFRQYF 64 (86)
Q Consensus 26 ~~~l~LtIidTpGfGd~i~n~~~~~~i~~yI~~qf~~yl 64 (86)
++|| |+++|||||= ...+.-+.-+.+++..-+..|-
T Consensus 329 ~iPl-v~l~dtpGf~--~g~~~E~~g~~~~ga~~~~a~~ 364 (493)
T PF01039_consen 329 NIPL-VTLVDTPGFM--PGPEAERAGIIRAGARLLYALA 364 (493)
T ss_dssp T--E-EEEEEECEB----SHHHHHTTHHHHHHHHHHHHH
T ss_pred CCce-EEEeeccccc--ccchhhhcchHHHHHHHHHHHH
Confidence 4553 7899999994 4444445567777776666553
No 311
>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=21.15 E-value=70 Score=23.71 Aligned_cols=12 Identities=25% Similarity=0.517 Sum_probs=10.2
Q ss_pred EEEEEEeCCCCC
Q psy104 29 LRLTVVDTPGFG 40 (86)
Q Consensus 29 l~LtIidTpGfG 40 (86)
.+++++||||+.
T Consensus 205 ~~~~i~D~PGli 216 (329)
T TIGR02729 205 RSFVIADIPGLI 216 (329)
T ss_pred eEEEEEeCCCcc
Confidence 567899999984
No 312
>PRK09601 GTP-binding protein YchF; Reviewed
Probab=21.07 E-value=60 Score=24.81 Aligned_cols=15 Identities=27% Similarity=0.397 Sum_probs=11.7
Q ss_pred eEEEEEEEeCCCCCC
Q psy104 27 VKLRLTVVDTPGFGD 41 (86)
Q Consensus 27 ~~l~LtIidTpGfGd 41 (86)
++-.+.++||||+-.
T Consensus 64 ~~a~i~lvD~pGL~~ 78 (364)
T PRK09601 64 VPATIEFVDIAGLVK 78 (364)
T ss_pred cCceEEEEECCCCCC
Confidence 345789999999853
No 313
>PRK12297 obgE GTPase CgtA; Reviewed
Probab=21.03 E-value=68 Score=24.88 Aligned_cols=13 Identities=23% Similarity=0.508 Sum_probs=10.7
Q ss_pred EEEEEEeCCCCCC
Q psy104 29 LRLTVVDTPGFGD 41 (86)
Q Consensus 29 l~LtIidTpGfGd 41 (86)
.+++++||||++.
T Consensus 206 ~~~~laD~PGlie 218 (424)
T PRK12297 206 RSFVMADIPGLIE 218 (424)
T ss_pred ceEEEEECCCCcc
Confidence 4688999999963
No 314
>PRK06004 flgB flagellar basal body rod protein FlgB; Reviewed
Probab=20.85 E-value=38 Score=21.81 Aligned_cols=7 Identities=71% Similarity=1.308 Sum_probs=6.2
Q ss_pred EeCCCCC
Q psy104 34 VDTPGFG 40 (86)
Q Consensus 34 idTpGfG 40 (86)
+|||||-
T Consensus 23 ~~Tpgyk 29 (127)
T PRK06004 23 ADTPGFR 29 (127)
T ss_pred cCCCCcc
Confidence 6999996
No 315
>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=20.74 E-value=1.3e+02 Score=19.30 Aligned_cols=12 Identities=17% Similarity=0.423 Sum_probs=9.8
Q ss_pred EEEEEEeCCCCC
Q psy104 29 LRLTVVDTPGFG 40 (86)
Q Consensus 29 l~LtIidTpGfG 40 (86)
+.+.++||||..
T Consensus 63 ~~~~l~D~~G~~ 74 (190)
T cd00879 63 IKFKTFDLGGHE 74 (190)
T ss_pred EEEEEEECCCCH
Confidence 568899999964
No 316
>COG1815 FlgB Flagellar basal body protein [Cell motility and secretion]
Probab=20.64 E-value=40 Score=22.24 Aligned_cols=8 Identities=50% Similarity=0.970 Sum_probs=6.5
Q ss_pred EEeCCCCC
Q psy104 33 VVDTPGFG 40 (86)
Q Consensus 33 IidTpGfG 40 (86)
=+|||||-
T Consensus 31 NadTP~yK 38 (133)
T COG1815 31 NADTPGYK 38 (133)
T ss_pred cCCCCCCC
Confidence 37999995
No 317
>COG4108 PrfC Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]
Probab=20.55 E-value=1e+02 Score=24.82 Aligned_cols=29 Identities=21% Similarity=0.377 Sum_probs=18.4
Q ss_pred ceEEEEEEEEEeecCeEEEEEEEeCCCCCCc
Q psy104 12 TTTIEKKSMDIEERGVKLRLTVVDTPGFGDS 42 (86)
Q Consensus 12 t~~I~~~~~~l~e~~~~l~LtIidTpGfGd~ 42 (86)
.++|+++-..++=+ ...+++.||||=-|.
T Consensus 66 GISVtsSVMqF~Y~--~~~iNLLDTPGHeDF 94 (528)
T COG4108 66 GISVTSSVMQFDYA--DCLVNLLDTPGHEDF 94 (528)
T ss_pred CceEEeeEEEeccC--CeEEeccCCCCcccc
Confidence 45555555444433 356789999997654
No 318
>TIGR03695 menH_SHCHC 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase. This protein catalyzes the formation of SHCHC, or (1 R,6 R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate, by elmination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC). Note that SHCHC synthase activity previously was attributed to MenD, which in fact is SEPHCHC synthase.
Probab=20.52 E-value=2.3e+02 Score=17.84 Aligned_cols=27 Identities=22% Similarity=0.420 Sum_probs=17.6
Q ss_pred EEEEEEeCCCCCCccCC----ccchhHHHHH
Q psy104 29 LRLTVVDTPGFGDSINS----EESWRACCSY 55 (86)
Q Consensus 29 l~LtIidTpGfGd~i~n----~~~~~~i~~y 55 (86)
+.+-.+|-||+|.+-.. ..+|..+++.
T Consensus 28 ~~v~~~d~~g~G~s~~~~~~~~~~~~~~~~~ 58 (251)
T TIGR03695 28 FRCLAIDLPGHGSSQSPDEIERYDFEEAAQD 58 (251)
T ss_pred CeEEEEcCCCCCCCCCCCccChhhHHHHHHH
Confidence 45678999999987442 2345555544
No 319
>PF09547 Spore_IV_A: Stage IV sporulation protein A (spore_IV_A); InterPro: IPR014201 This entry is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=20.49 E-value=73 Score=25.49 Aligned_cols=17 Identities=24% Similarity=0.724 Sum_probs=15.2
Q ss_pred ecCeEEEEEEEeCCCCC
Q psy104 24 ERGVKLRLTVVDTPGFG 40 (86)
Q Consensus 24 e~~~~l~LtIidTpGfG 40 (86)
++++.+++++||+.||-
T Consensus 86 ~~~~~~kVRLiDCVGy~ 102 (492)
T PF09547_consen 86 DDGIKVKVRLIDCVGYM 102 (492)
T ss_pred cCCceEEEEEEeeccee
Confidence 67899999999999984
No 320
>PRK12620 flgB flagellar basal body rod protein FlgB; Provisional
Probab=20.35 E-value=41 Score=21.54 Aligned_cols=7 Identities=71% Similarity=1.369 Sum_probs=6.0
Q ss_pred EeCCCCC
Q psy104 34 VDTPGFG 40 (86)
Q Consensus 34 idTpGfG 40 (86)
+|||||-
T Consensus 33 adTPgYk 39 (132)
T PRK12620 33 VDTPGYK 39 (132)
T ss_pred cCCCCcC
Confidence 6999995
No 321
>TIGR02240 PHA_depoly_arom poly(3-hydroxyalkanoate) depolymerase. This family consists of the polyhydroxyalkanoic acid (PHA) depolymerase of Pseudomonas oleovorans, Pseudomonas putida BM01, and related species. This enzyme is part of polyester storage and mobilization system as in many bacteria. However, species containing this enzyme are unusual in their capacity to produce aromatic polyesters when grown on carbon sources such as benzoic acid or phenylacetic acid.
Probab=20.23 E-value=2.4e+02 Score=19.25 Aligned_cols=29 Identities=21% Similarity=0.363 Sum_probs=17.2
Q ss_pred EEEEEEeCCCCCCccCCc--cchhHHHHHHH
Q psy104 29 LRLTVVDTPGFGDSINSE--ESWRACCSYID 57 (86)
Q Consensus 29 l~LtIidTpGfGd~i~n~--~~~~~i~~yI~ 57 (86)
.++-.+|-||+|.+-... .++..+.+.+.
T Consensus 52 ~~vi~~Dl~G~G~S~~~~~~~~~~~~~~~~~ 82 (276)
T TIGR02240 52 LEVIAFDVPGVGGSSTPRHPYRFPGLAKLAA 82 (276)
T ss_pred ceEEEECCCCCCCCCCCCCcCcHHHHHHHHH
Confidence 567788999999774322 23444444443
Done!