Query 007717
Match_columns 591
No_of_seqs 143 out of 224
Neff 5.0
Searched_HMMs 46136
Date Thu Mar 28 14:23:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007717.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007717hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0446 Vacuolar sorting prote 100.0 2.2E-55 4.8E-60 493.5 29.7 472 1-580 166-647 (657)
2 PF01031 Dynamin_M: Dynamin ce 100.0 2.1E-35 4.6E-40 303.7 23.3 269 56-388 1-278 (295)
3 KOG0447 Dynamin-like GTP bindi 99.4 1.3E-12 2.9E-17 142.4 13.4 129 1-152 446-580 (980)
4 smart00053 DYNc Dynamin, GTPas 99.4 6.7E-13 1.4E-17 134.5 5.9 77 1-91 159-236 (240)
5 COG0699 Predicted GTPases (dyn 97.7 0.00028 6.2E-09 77.5 12.7 268 2-384 88-361 (546)
6 KOG0446 Vacuolar sorting prote 96.7 0.44 9.6E-06 55.6 24.3 325 184-574 328-655 (657)
7 PF10662 PduV-EutP: Ethanolami 92.8 0.18 3.8E-06 48.2 5.1 67 5-86 64-133 (143)
8 PF02212 GED: Dynamin GTPase e 79.8 18 0.0004 31.4 9.5 83 481-568 6-88 (92)
9 TIGR03598 GTPase_YsxC ribosome 69.7 11 0.00023 35.8 5.9 41 5-46 102-142 (179)
10 PRK03003 GTP-binding protein D 58.8 46 0.001 37.3 9.1 43 3-46 293-335 (472)
11 PRK09518 bifunctional cytidyla 58.4 44 0.00095 39.5 9.2 42 4-46 533-574 (712)
12 PF12842 DUF3819: Domain of un 58.0 80 0.0017 30.2 9.3 67 134-201 2-68 (147)
13 cd00880 Era_like Era (E. coli 53.2 18 0.0004 31.4 4.0 43 3-46 75-117 (163)
14 cd04163 Era Era subfamily. Er 52.0 19 0.00042 31.9 4.0 42 4-46 83-124 (168)
15 TIGR03777 RPE4 Rickettsial pal 51.6 3.8 8.3E-05 29.7 -0.5 17 501-517 12-28 (32)
16 PRK00093 GTP-binding protein D 50.4 53 0.0012 35.9 7.8 42 4-46 256-297 (435)
17 PRK10867 signal recognition pa 50.3 97 0.0021 34.8 9.8 132 3-156 213-357 (433)
18 PRK00771 signal recognition pa 50.1 1.2E+02 0.0027 34.0 10.6 132 3-156 205-349 (437)
19 cd01849 YlqF_related_GTPase Yl 47.9 21 0.00044 33.3 3.6 40 7-46 2-42 (155)
20 cd04171 SelB SelB subfamily. 47.3 45 0.00098 30.0 5.7 42 3-46 74-117 (164)
21 cd01878 HflX HflX subfamily. 45.9 73 0.0016 30.6 7.2 43 4-46 121-166 (204)
22 PF00009 GTP_EFTU: Elongation 44.5 38 0.00082 32.5 4.9 44 2-46 92-135 (188)
23 smart00302 GED Dynamin GTPase 44.1 2.2E+02 0.0048 24.9 9.2 83 481-568 6-88 (92)
24 cd01865 Rab3 Rab3 subfamily. 42.8 83 0.0018 29.0 6.8 44 3-46 73-119 (165)
25 PF05879 RHD3: Root hair defec 42.2 6.9E+02 0.015 30.1 24.7 87 482-574 421-527 (742)
26 TIGR00450 mnmE_trmE_thdF tRNA 42.0 2.9E+02 0.0064 31.0 12.0 42 3-46 282-323 (442)
27 TIGR03594 GTPase_EngA ribosome 40.4 82 0.0018 34.2 7.3 42 4-46 255-296 (429)
28 cd01887 IF2_eIF5B IF2/eIF5B (i 40.3 34 0.00073 31.2 3.7 40 4-46 74-115 (168)
29 cd04164 trmE TrmE (MnmE, ThdF, 39.9 42 0.0009 29.8 4.2 41 3-46 80-120 (157)
30 cd01895 EngA2 EngA2 subfamily. 39.7 35 0.00075 30.8 3.7 42 4-46 85-126 (174)
31 cd04112 Rab26 Rab26 subfamily. 38.5 57 0.0012 31.2 5.1 44 3-46 73-119 (191)
32 PRK12289 GTPase RsgA; Reviewed 37.9 61 0.0013 35.3 5.7 39 5-46 91-133 (352)
33 PRK13796 GTPase YqeH; Provisio 37.9 46 0.001 36.1 4.8 43 2-46 67-109 (365)
34 cd01890 LepA LepA subfamily. 37.8 42 0.00091 31.1 4.0 43 3-46 90-132 (179)
35 cd01885 EF2 EF2 (for archaea a 37.7 43 0.00093 33.9 4.3 43 4-47 97-139 (222)
36 cd04165 GTPBP1_like GTPBP1-lik 37.6 45 0.00097 33.6 4.4 43 3-46 109-151 (224)
37 COG0486 ThdF Predicted GTPase 37.2 1.8E+02 0.004 33.0 9.3 38 7-46 299-337 (454)
38 cd04114 Rab30 Rab30 subfamily. 37.1 64 0.0014 29.5 5.0 45 2-46 78-125 (169)
39 PF06213 CobT: Cobalamin biosy 36.9 1.8E+02 0.0039 30.5 8.9 94 484-579 103-205 (282)
40 TIGR03594 GTPase_EngA ribosome 36.5 55 0.0012 35.6 5.2 68 4-86 79-147 (429)
41 cd01893 Miro1 Miro1 subfamily. 36.5 63 0.0014 29.9 4.9 44 2-46 69-116 (166)
42 TIGR00959 ffh signal recogniti 36.2 2E+02 0.0043 32.3 9.5 131 4-156 213-356 (428)
43 cd04128 Spg1 Spg1p. Spg1p (se 33.8 68 0.0015 30.8 4.8 43 3-46 72-117 (182)
44 cd01867 Rab8_Rab10_Rab13_like 33.2 80 0.0017 29.1 5.0 44 3-46 75-121 (167)
45 cd01859 MJ1464 MJ1464. This f 32.9 41 0.00089 31.1 3.0 40 7-46 15-54 (156)
46 PRK09866 hypothetical protein; 32.7 9.7E+02 0.021 29.0 16.8 39 7-46 261-302 (741)
47 cd01882 BMS1 Bms1. Bms1 is an 32.4 73 0.0016 32.0 4.9 39 7-46 106-146 (225)
48 KOG1916 Nuclear protein, conta 32.2 1.1E+03 0.024 29.6 15.3 34 461-494 965-1009(1283)
49 cd00882 Ras_like_GTPase Ras-li 31.4 93 0.002 26.4 4.8 46 3-48 68-117 (157)
50 cd04124 RabL2 RabL2 subfamily. 31.4 89 0.0019 28.8 5.0 44 2-46 71-117 (161)
51 PF10167 NEP: Uncharacterised 31.3 1.1E+02 0.0024 28.5 5.5 29 143-179 34-62 (118)
52 cd00878 Arf_Arl Arf (ADP-ribos 31.3 63 0.0014 29.2 4.0 44 3-46 66-113 (158)
53 cd01869 Rab1_Ypt1 Rab1/Ypt1 su 31.0 89 0.0019 28.6 4.9 45 2-46 73-120 (166)
54 PF01926 MMR_HSR1: 50S ribosom 30.7 73 0.0016 27.7 4.1 37 4-42 80-116 (116)
55 cd01891 TypA_BipA TypA (tyrosi 30.5 50 0.0011 31.6 3.3 43 3-46 88-130 (194)
56 cd00154 Rab Rab family. Rab G 30.2 1E+02 0.0022 27.1 5.0 61 2-62 71-134 (159)
57 PF05384 DegS: Sensor protein 30.0 1.2E+02 0.0027 29.6 5.8 68 512-579 64-134 (159)
58 PRK11058 GTPase HflX; Provisio 29.7 78 0.0017 35.3 5.0 44 3-46 276-322 (426)
59 cd01864 Rab19 Rab19 subfamily. 29.6 1E+02 0.0022 28.2 5.1 45 2-46 74-121 (165)
60 PRK01889 GTPase RsgA; Reviewed 29.5 84 0.0018 34.1 5.1 38 9-46 117-155 (356)
61 PRK00093 GTP-binding protein D 29.2 1.3E+02 0.0027 33.0 6.5 41 3-46 80-122 (435)
62 cd01884 EF_Tu EF-Tu subfamily. 28.9 69 0.0015 31.6 4.0 43 3-46 88-131 (195)
63 cd01858 NGP_1 NGP-1. Autoanti 28.5 77 0.0017 29.5 4.1 39 7-46 11-52 (157)
64 COG1160 Predicted GTPases [Gen 28.4 98 0.0021 35.0 5.4 66 7-86 86-152 (444)
65 PF04026 SpoVG: SpoVG; InterP 28.1 47 0.001 29.1 2.3 36 72-107 38-75 (84)
66 COG4026 Uncharacterized protei 27.8 3.6E+02 0.0079 28.2 8.8 93 482-580 69-176 (290)
67 cd04118 Rab24 Rab24 subfamily. 27.6 1.1E+02 0.0025 28.8 5.2 43 3-46 73-118 (193)
68 cd04113 Rab4 Rab4 subfamily. 27.6 1.1E+02 0.0024 27.7 4.9 45 2-46 71-118 (161)
69 cd01850 CDC_Septin CDC/Septin. 27.2 85 0.0018 32.7 4.5 41 4-46 115-156 (276)
70 cd04142 RRP22 RRP22 subfamily. 26.8 1.6E+02 0.0034 28.8 6.1 58 2-59 79-142 (198)
71 cd04119 RJL RJL (RabJ-Like) su 26.6 2E+02 0.0044 25.8 6.4 44 3-46 72-123 (168)
72 cd01879 FeoB Ferrous iron tran 26.3 86 0.0019 28.1 3.9 41 3-46 74-114 (158)
73 cd01860 Rab5_related Rab5-rela 26.2 1.2E+02 0.0027 27.3 5.0 45 2-46 72-119 (163)
74 cd04160 Arfrp1 Arfrp1 subfamil 26.2 93 0.002 28.3 4.2 59 2-62 72-134 (167)
75 TIGR00436 era GTP-binding prot 26.1 70 0.0015 32.8 3.6 40 5-46 81-120 (270)
76 TIGR01425 SRP54_euk signal rec 26.0 4.6E+02 0.0099 29.6 10.1 59 3-68 212-270 (429)
77 PF09763 Sec3_C: Exocyst compl 25.9 1.2E+03 0.025 27.7 14.4 266 133-532 399-689 (701)
78 cd04123 Rab21 Rab21 subfamily. 25.6 1.3E+02 0.0028 26.9 4.9 44 3-46 72-118 (162)
79 smart00174 RHO Rho (Ras homolo 25.5 1.2E+02 0.0026 27.9 4.8 44 2-46 68-115 (174)
80 PRK03003 GTP-binding protein D 25.0 1.2E+02 0.0027 33.9 5.6 69 4-86 118-186 (472)
81 cd04101 RabL4 RabL4 (Rab-like4 25.0 1.4E+02 0.0029 27.2 5.0 44 2-46 74-120 (164)
82 PF11553 DUF3231: Protein of u 24.9 2.1E+02 0.0046 27.3 6.5 57 124-180 15-73 (166)
83 cd01876 YihA_EngB The YihA (En 24.9 84 0.0018 28.0 3.5 39 8-46 85-123 (170)
84 cd01898 Obg Obg subfamily. Th 24.7 1E+02 0.0022 28.2 4.1 43 4-46 79-127 (170)
85 cd01894 EngA1 EngA1 subfamily. 24.5 89 0.0019 27.8 3.6 39 5-46 78-118 (157)
86 PRK00089 era GTPase Era; Revie 24.2 1.2E+02 0.0027 31.1 5.1 42 4-46 85-126 (292)
87 PRK13259 regulatory protein Sp 24.1 1.2E+02 0.0026 27.3 4.2 41 72-112 38-80 (94)
88 PF02421 FeoB_N: Ferrous iron 23.6 67 0.0015 31.0 2.8 41 3-46 78-118 (156)
89 cd04151 Arl1 Arl1 subfamily. 23.3 1.3E+02 0.0028 27.4 4.5 45 2-46 65-113 (158)
90 COG4917 EutP Ethanolamine util 23.0 60 0.0013 31.2 2.2 47 7-62 67-117 (148)
91 cd01862 Rab7 Rab7 subfamily. 23.0 2E+02 0.0043 26.2 5.7 61 2-62 71-138 (172)
92 COG1382 GimC Prefoldin, chaper 23.0 1.8E+02 0.004 27.2 5.3 39 542-580 69-111 (119)
93 cd01886 EF-G Elongation factor 22.9 1E+02 0.0022 32.2 4.0 41 5-46 89-129 (270)
94 cd01861 Rab6 Rab6 subfamily. 22.8 1.5E+02 0.0033 26.7 4.9 45 2-46 71-118 (161)
95 cd04169 RF3 RF3 subfamily. Pe 22.6 1.7E+02 0.0036 30.4 5.6 60 4-64 95-155 (267)
96 cd03115 SRP The signal recogni 22.3 95 0.0021 29.2 3.5 58 4-68 113-170 (173)
97 PF08700 Vps51: Vps51/Vps67; 22.2 4.7E+02 0.01 21.9 7.5 49 94-152 6-54 (87)
98 cd04172 Rnd3_RhoE_Rho8 Rnd3/Rh 22.1 1.5E+02 0.0032 28.6 4.9 44 2-46 75-122 (182)
99 cd01888 eIF2_gamma eIF2-gamma 21.9 1E+02 0.0022 30.2 3.7 42 5-46 108-150 (203)
100 cd04167 Snu114p Snu114p subfam 21.7 1.2E+02 0.0025 29.8 4.1 42 4-46 95-136 (213)
101 cd04157 Arl6 Arl6 subfamily. 21.7 1.6E+02 0.0035 26.5 4.8 45 2-46 67-117 (162)
102 cd04104 p47_IIGP_like p47 (47- 21.5 1.3E+02 0.0029 29.2 4.4 30 16-48 91-122 (197)
103 PHA02699 hypothetical protein; 21.5 8.3E+02 0.018 27.4 10.5 70 485-569 357-426 (466)
104 cd01868 Rab11_like Rab11-like. 21.0 1.8E+02 0.0039 26.5 4.9 43 4-46 76-121 (165)
105 cd04135 Tc10 TC10 subfamily. 21.0 1.7E+02 0.0037 26.8 4.9 42 4-46 72-117 (174)
106 PLN03108 Rab family protein; P 20.9 1.7E+02 0.0037 28.6 5.1 44 3-46 78-124 (210)
107 PF04583 Baculo_p74: Baculovir 20.9 7E+02 0.015 26.3 9.6 51 120-170 18-68 (249)
108 cd01874 Cdc42 Cdc42 subfamily. 20.7 1.6E+02 0.0035 27.8 4.7 43 3-46 72-118 (175)
109 cd04130 Wrch_1 Wrch-1 subfamil 20.7 1.7E+02 0.0036 27.2 4.8 44 2-46 70-117 (173)
110 smart00175 RAB Rab subfamily o 20.7 2.3E+02 0.005 25.4 5.6 59 3-61 72-133 (164)
111 cd04125 RabA_like RabA-like su 20.3 1.9E+02 0.0042 27.3 5.2 45 2-46 71-118 (188)
112 TIGR03596 GTPase_YlqF ribosome 20.3 1E+02 0.0022 31.9 3.6 38 7-46 24-61 (276)
113 COG1160 Predicted GTPases [Gen 20.3 1.9E+02 0.0041 32.8 5.7 106 7-147 263-373 (444)
114 cd04174 Rnd1_Rho6 Rnd1/Rho6 su 20.2 1.8E+02 0.0038 29.7 5.1 44 2-46 83-130 (232)
115 cd00876 Ras Ras family. The R 20.2 1.7E+02 0.0037 26.0 4.6 60 3-62 70-133 (160)
116 PRK05291 trmE tRNA modificatio 20.2 1.2E+03 0.027 26.0 13.7 40 4-46 295-334 (449)
117 cd00157 Rho Rho (Ras homology) 20.1 1.3E+02 0.0028 27.4 3.8 43 3-46 71-117 (171)
No 1
>KOG0446 consensus Vacuolar sorting protein VPS1, dynamin, and related proteins [Intracellular trafficking, secretion, and vesicular transport; General function prediction only]
Probab=100.00 E-value=2.2e-55 Score=493.53 Aligned_cols=472 Identities=17% Similarity=0.133 Sum_probs=388.2
Q ss_pred CCCCceEEEEeccCC-chhhhhHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcCCCcccCCccccCCCCceE
Q 007717 1 MQHREFIILCLEDCS-DWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLSPPACTLDGFILGGSPFFT 79 (591)
Q Consensus 1 i~~~n~IILaV~~An-D~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g~~~~L~~~llG~~pFFv 79 (591)
|++||||||||+||| |||||+|+++|++|||+|.|||||+||+|+| |+|||+.+.|.|+.|+++ +| ||
T Consensus 166 i~~~~~iILav~~an~d~ats~alkiarevDp~g~RTigvitK~Dlm----dkGt~~~~~L~g~~~~l~---~g----~v 234 (657)
T KOG0446|consen 166 IEKPNRIILAVTPANSDIATSPALVVAREVDPGGSRTLEVITKFDFM----DKGTNAVTRLVGRPITLK---VG----YV 234 (657)
T ss_pred ccccchhhhhccchhhhhhcCHHHHHHHhhCCCccchhHHhhhHHhh----hcCCcceeeecCCccccc---cc----ee
Confidence 589999999999999 9999999999999999999999999999999 999999999999999999 88 99
Q ss_pred eecCCCCCCCCccccCChHHHHHHHhhhhhhHHHHHHHHh--CCCCchhhhhhcChhHHHHHHHHHHHHHHHhhhhhhHH
Q 007717 80 SVPSGRVGTGHDSVYSSNEEFKQAIFIREMEDITSLEEKL--GRSLSKQERSRIGVSKLRSFLEELLQKRYMDSVPMIIP 157 (591)
Q Consensus 80 svp~~R~g~~~D~v~~s~~~f~~ai~~~~~~d~~~le~~~--~~~~~~~~~~~~G~~~L~~~Ln~~L~~hyr~~lP~i~~ 157 (591)
+|.| |+ |.| +..++ ++.++++.|..| +||.|+....+||++||++.|+++|+.||++++|.|+.
T Consensus 235 ~vvn-R~--q~d--i~~~k---------~~~~al~~e~~~f~~~p~y~~~~~~~g~p~La~~L~~~l~~hi~~~lP~l~~ 300 (657)
T KOG0446|consen 235 GVVN-RS--QSI--IDFKK---------SILEALNDEVPSFESVPSYPILLTISGVPYLALLLPGYLQSHIRDQLPELKT 300 (657)
T ss_pred eeec-cc--hhh--hhhhh---------hHHHHHHhhhhhhhccccccccccccCcchHHHHHHHHHHHHHHhcCcHHHH
Confidence 9988 66 666 55555 455566778777 99999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhHhhcccChHHHHHHHHHHHHHHHHHHhHhhcccccCCCcCcccchHHHhhhcCcccCCCCCCC
Q 007717 158 LLEKEYCSTTRKLNEINKELSTLDEVKLKEKGRVFHDLFLTKLSLLLKGTVVAPPDKFGETLQNERINGGAFVGTDGLQF 237 (591)
Q Consensus 158 ~L~~~~~~~~~eL~~~~~el~~~d~~~l~~~~l~~i~~F~~~~~~lI~Gt~~~~P~~~G~Tl~eEr~~~g~~~~~~g~~~ 237 (591)
+|+..|.+++.+|..++. .+. + ..-...++.++..|+..|...++|....
T Consensus 301 ~i~~~~~~~~~el~~~g~-~~~-~-~~~~~~ll~~i~~~~~~~~~~v~g~~~~--------------------------- 350 (657)
T KOG0446|consen 301 KINKLLEKYQDELNRIGA-VDV-D-LANSAALLAIIREDPRGLRTGVIGKLDL--------------------------- 350 (657)
T ss_pred HHHHHHHHHHHHHHHhcc-cCC-c-cchhhHHHHHHHHHHHHHHHhhcccccc---------------------------
Confidence 999999999999999997 222 2 2225678899999999999999998552
Q ss_pred CcccCCCCCccccchhHHHHHHHh-hHhhhccc-cCCCCCHHHHHHHhccCCCCCCCc-----hhhHHHHHHHHHHHHhh
Q 007717 238 PHKLIPNAGMRLYGGAQYHRAMAE-FRFMVGGI-KCPPITREEIVNACGVEDIHDGTN-----YSRTACVIAVAKARDTF 310 (591)
Q Consensus 238 ~~~~v~~~~~eL~GGAqi~Rif~E-F~~~v~~i-~~~~ls~eeI~~Aig~~~~~~g~~-----~~~Afe~Iak~qir~l~ 310 (591)
+| +.+|+||||++++||+ |...+..+ |+..++..+|++++. +..|+. |+.||+.||++||+.+.
T Consensus 351 ----~~--~~elsggari~~~F~~~f~~~i~~i~~~~~~~~~~i~~~i~---~~~G~~~~lf~p~~afe~lvk~~i~~l~ 421 (657)
T KOG0446|consen 351 ----VP--TKALSGGARINYPFHGGFPGVIKKLPPDRKLLGQNIEKLVS---EASGIRPSLFVPESSFESLVKGQIQSLR 421 (657)
T ss_pred ----cc--hhcccchhhhhhhhhhccchhhhcCCcchhhhHHHHHHHHH---hccCCCccccCChHHHHHHHHHHHHHHh
Confidence 33 7899999999999999 99999999 787799999999995 555553 89999999999999999
Q ss_pred cchHHHHHhhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccccCC
Q 007717 311 EPFLHQLGCRLLHILKRLLPISIYLLQKEGEYLSGHEVFLRRVASAFNNFAESTERACREKCMEDLVSTTRYVTWSLHNK 390 (591)
Q Consensus 311 ~P~L~cv~~Rl~~V~~eL~~I~~~~~~k~~~~l~ryp~l~~~v~~~~~~fi~e~~~~ck~~~~d~l~s~t~~v~w~L~~~ 390 (591)
+|+++|| ..|+++|++++.++..+ ..+.|||.|+.++.++...|++++..++++++++.++.+.+|+|++.. .
T Consensus 422 ~p~l~~v----~~v~~el~~~~~~~~~~--~~l~rfp~l~~~~~~~~~~~~~~~~~~t~~~v~~~i~~e~~yinT~h~-d 494 (657)
T KOG0446|consen 422 DPSLKCV----EEVHRELVRIVADSIRA--TELKRFPVLYSELVEIASSLIAEGLDETKKAVKNLIDLEQSYLNTDHP-D 494 (657)
T ss_pred hhHHHHH----HHHHHHHHHHHHHHhhh--HHHHHhHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhcCcCh-h
Confidence 9999999 88999999999988885 269999999999999999999999999999999999999999985442 2
Q ss_pred cchhhhhhhcccCCccchhhccccCCCCccccccccccccccCCCCCcccccccccccCCCCCCccchhhhHHHHhhhhh
Q 007717 391 NRAGLRQFLDSFGSTEQSAVLSNSLSMPLCQESSFVSVANEKHDTKPRTDVKLSQVASGVDSSSSVQTTETRLADLLDNT 470 (591)
Q Consensus 391 ~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 470 (591)
..+..++.+...... ++ ..+..+. + . .-.....+.....+.+.++
T Consensus 495 f~~~~~~al~~~~~~---~~---~~~~~~~--~--------------------------~-~~~~~~~~~~~~~~~~~~~ 539 (657)
T KOG0446|consen 495 FRSLTDSALSSVTSP---SI---AAMKLIS--A--------------------------Q-LLKEELGECNSALKAIKNA 539 (657)
T ss_pred hhhhHHHHHHHhhcc---cc---ccccccc--c--------------------------c-ccccccccccchhhhhcch
Confidence 222332222221100 00 0000000 0 0 0011122333567777788
Q ss_pred hhccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhchhhhhhhhhHHHHHHHHhhcccchhhhhchhhHHHHHHh
Q 007717 471 LWNRRLAPSSERIVYALVQQIFHGIREYFLASAELKFNCFLLMPVVDKLPALLREDLESAFEGDLDNVFDITNLRHSLSQ 550 (591)
Q Consensus 471 l~~r~l~~~s~~iV~~l~~~iF~~IR~~~~~~~~~Kfn~fFL~P~~~~l~~~lr~~l~~~~d~~l~~vF~~~~~r~~L~~ 550 (591)
.|+..+.+.......+...+.+..+...+.++....|+|+=+++++|..|..|.-.|...+.++|...|+..-.+ . .+
T Consensus 540 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~sY~~iv~~~i~d~vpk~i~~~lv~~~k~~l~~~l~~~L~~-~-~~ 617 (657)
T KOG0446|consen 540 VGSIRLDPSDIVLSRALVLKKRECKETEEISSCPESYLNIVSDKLVDTVPKALNHELLNEFKDDLPNELDQRLYA-G-DE 617 (657)
T ss_pred hhhhhhcccchhhhhhhhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-c-hh
Confidence 888888888888888888888888888888888888888888888888888888888888888888888877766 4 77
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 007717 551 QKSDTEIEMKRIKKLKEKFKLIHEQFISHH 580 (591)
Q Consensus 551 ~~~~l~~e~~~~~~~~~kF~~i~~~~~~~~ 580 (591)
+.++|..|...+++-+++++.--+.|+.+.
T Consensus 618 ~~~~ll~E~~~i~~~R~~~~~~l~~L~~a~ 647 (657)
T KOG0446|consen 618 QLESLLKEDPRIKRRRELQQKRLLALQKAL 647 (657)
T ss_pred HHHHHHccCHHHHHHHHHHHHHHHHHHHHH
Confidence 788888888888777777777666555554
No 2
>PF01031 Dynamin_M: Dynamin central region; InterPro: IPR000375 Dynamin is a microtubule-associated force-producing protein of 100 Kd which is involved in the production of microtubule bundles. At the N terminus of dynamin is a GTPase domain (see IPR001401 from INTERPRO), and at the C terminus is a PH domain (see IPR001849 from INTERPRO). Between these two domains lies a central region of unknown function, which this entry represents.; GO: 0005525 GTP binding; PDB: 3ZVR_A 2AKA_B 2X2F_D 2X2E_D 3SNH_A 3ZYS_D 3ZYC_D 1JWY_B 1JX2_B 3SZR_A ....
Probab=100.00 E-value=2.1e-35 Score=303.73 Aligned_cols=269 Identities=17% Similarity=0.190 Sum_probs=229.0
Q ss_pred HhhhcCCCcccCCccccCCCCceEeecCCCCCCCCccccCChHHHHHHHhhhhhhHHHHHHHHh--CCCCchhhhhhcCh
Q 007717 56 VEVFLSPPACTLDGFILGGSPFFTSVPSGRVGTGHDSVYSSNEEFKQAIFIREMEDITSLEEKL--GRSLSKQERSRIGV 133 (591)
Q Consensus 56 v~~~L~g~~~~L~~~llG~~pFFvsvp~~R~g~~~D~v~~s~~~f~~ai~~~~~~d~~~le~~~--~~~~~~~~~~~~G~ 133 (591)
|.++|.|++|||+ +| |++|.| | |++++. ...++++++..|+.| +||.|+..+++|||
T Consensus 1 ~~~iL~n~~~pLk---lG----y~~V~n-r----------sq~di~---~~~s~~~a~~~E~~fF~~~~~~~~~~~~~G~ 59 (295)
T PF01031_consen 1 AMDILRNKVIPLK---LG----YVGVKN-R----------SQQDIN---DGKSIEEARQKEKEFFSNHPWYSSPADRCGT 59 (295)
T ss_dssp SHHHHTTSSS--T---T-----EEEE---S-----------HHHHH---TTEEHHHHHHHHHHHHHHSTTTGGGGGGSSH
T ss_pred ChHHhCCCeeccC---CC----eEEEec-C----------Cccccc---cCCCHHHHHHHHHHHHhcccccCCcccccch
Confidence 5689999999999 99 999966 4 344444 455788889999998 99999999999999
Q ss_pred hHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHhHhhcccChHHHHHHHHHHHHHHHHHHhHhhcccccCCCc
Q 007717 134 SKLRSFLEELLQKRYMDSVPMIIPLLEKEYCSTTRKLNEINKELSTLDEVKLKEKGRVFHDLFLTKLSLLLKGTVVAPPD 213 (591)
Q Consensus 134 ~~L~~~Ln~~L~~hyr~~lP~i~~~L~~~~~~~~~eL~~~~~el~~~d~~~l~~~~l~~i~~F~~~~~~lI~Gt~~~~P~ 213 (591)
++|++.|+++|.+||+++||.|+..|++.+.+++.+|..+|....+ ++...+..+++++..|++.+.++|+|....
T Consensus 60 ~~L~~~L~~~L~~~I~~~LP~l~~~I~~~l~~~~~eL~~lG~~~~~-~~~~~~~~l~~~~~~f~~~~~~~i~G~~~~--- 135 (295)
T PF01031_consen 60 PALRKRLSELLVEHIRKSLPSLKSEIQKKLQEAEKELKRLGPPRPE-TPEEQRAYLLQIISKFSRIFKDAIDGEYSD--- 135 (295)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHCSSS-CHHHHHHHHHHHHHHHHHHHHHHHTT-------
T ss_pred HHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHHHHHHHHHHHhcCCccc---
Confidence 9999999999999999999999999999999999999999988874 455567889999999999999999998440
Q ss_pred CcccchHHHhhhcCcccCCCCCCCCcccCCCCCccccchhHHHHHHHh-hHhhhccc-cCCCCCHHHHHHHhccCCCCCC
Q 007717 214 KFGETLQNERINGGAFVGTDGLQFPHKLIPNAGMRLYGGAQYHRAMAE-FRFMVGGI-KCPPITREEIVNACGVEDIHDG 291 (591)
Q Consensus 214 ~~G~Tl~eEr~~~g~~~~~~g~~~~~~~v~~~~~eL~GGAqi~Rif~E-F~~~v~~i-~~~~ls~eeI~~Aig~~~~~~g 291 (591)
...+.+|.|||++.++|++ |...+..+ ++..++++||+++|. ++.|
T Consensus 136 -----------------------------~~~~~~l~~~ari~~~f~~~~~~~~~~~~~~~~~~~~eI~~~i~---~~~G 183 (295)
T PF01031_consen 136 -----------------------------EFSTNELRGGARIRYIFNEWFDKFLEKIDPFEDLSDEEIRTAIR---NSRG 183 (295)
T ss_dssp --------------------------------TTS--HHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHH---H--S
T ss_pred -----------------------------cccccccchhhHHHHHHHhhhhhhhhhhccccchhHHHHHHHHH---hhcc
Confidence 1267799999999999999 88888888 788899999999995 6666
Q ss_pred Cc-----hhhHHHHHHHHHHHHhhcchHHHHHhhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHH
Q 007717 292 TN-----YSRTACVIAVAKARDTFEPFLHQLGCRLLHILKRLLPISIYLLQKEGEYLSGHEVFLRRVASAFNNFAESTER 366 (591)
Q Consensus 292 ~~-----~~~Afe~Iak~qir~l~~P~L~cv~~Rl~~V~~eL~~I~~~~~~k~~~~l~ryp~l~~~v~~~~~~fi~e~~~ 366 (591)
+. |..||+.|+++++++|.+|+++|+ ..|+++|.+|+..++.+ .+.+||.|++++.+++.++++++..
T Consensus 184 ~elp~f~p~~afe~Li~~~i~~l~~Pa~~cv----~~V~~~l~~i~~~~~~~---~~~~fp~L~~~i~~~v~~~l~~~~~ 256 (295)
T PF01031_consen 184 RELPGFVPESAFESLIRKQIEKLEEPALQCV----EEVHEELQRIVEQVLEK---EFERFPNLKEAIKEAVQQLLEECRE 256 (295)
T ss_dssp -SSS-SCCHHHHHHHHHHHHHTTHHHHHHHH----HHHHHHHHHHHHHHHCH---HHTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred cccccchhHHHHHHHHHHHHHHHHhHHHHHH----HHHHHHHHHHHHhhcch---hcCCchHHHHHHHHHHHHHHHHHHH
Confidence 63 899999999999999999999999 78999999999999884 6999999999999999999999999
Q ss_pred HHHHHHHHHHhhhhhhhccccc
Q 007717 367 ACREKCMEDLVSTTRYVTWSLH 388 (591)
Q Consensus 367 ~ck~~~~d~l~s~t~~v~w~L~ 388 (591)
+|+++|.+.|+++++|||++-+
T Consensus 257 ~a~~~i~~li~~E~~~i~T~~~ 278 (295)
T PF01031_consen 257 PAKEMIENLIDMELSYINTQHP 278 (295)
T ss_dssp HHHHHHHHHHHHHTTS--TTST
T ss_pred HHHHHHHHHHHHhcccCCCCCH
Confidence 9999999999999999998764
No 3
>KOG0447 consensus Dynamin-like GTP binding protein [General function prediction only]
Probab=99.42 E-value=1.3e-12 Score=142.39 Aligned_cols=129 Identities=29% Similarity=0.418 Sum_probs=105.4
Q ss_pred CCCCceEEEEeccCC-chhhhhHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcCCCcccCCccccCCCCceE
Q 007717 1 MQHREFIILCLEDCS-DWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLSPPACTLDGFILGGSPFFT 79 (591)
Q Consensus 1 i~~~n~IILaV~~An-D~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g~~~~L~~~llG~~pFFv 79 (591)
|++||+||||+++.+ |---|..-.||.++||.|.|||+|+||.|+--+..+++.-+..+|+|+-+|.. .+| |.
T Consensus 446 M~NPNAIILCIQDGSVDAERSnVTDLVsq~DP~GrRTIfVLTKVDlAEknlA~PdRI~kIleGKLFPMK--ALG----Yf 519 (980)
T KOG0447|consen 446 MQNPNAIILCIQDGSVDAERSIVTDLVSQMDPHGRRTIFVLTKVDLAEKNVASPSRIQQIIEGKLFPMK--ALG----YF 519 (980)
T ss_pred hcCCCeEEEEeccCCcchhhhhHHHHHHhcCCCCCeeEEEEeecchhhhccCCHHHHHHHHhcCccchh--hcc----ee
Confidence 899999999999999 99999999999999999999999999999997778999999999999998865 467 99
Q ss_pred eecCCCCCCCCccccCChHHHHHHHhhhhhhHHHHHHHHh--CCCCchh---hhhhcChhHHHHHHHHHHHHHHHhhh
Q 007717 80 SVPSGRVGTGHDSVYSSNEEFKQAIFIREMEDITSLEEKL--GRSLSKQ---ERSRIGVSKLRSFLEELLQKRYMDSV 152 (591)
Q Consensus 80 svp~~R~g~~~D~v~~s~~~f~~ai~~~~~~d~~~le~~~--~~~~~~~---~~~~~G~~~L~~~Ln~~L~~hyr~~l 152 (591)
+|+.|||.+ .+ +|+.++..|+.| +....+. ..+++-+.+|.--...-.|+..|+++
T Consensus 520 aVVTGrGns--------sd---------SIdaIR~YEE~FF~nSkLl~~~vlkphQvTtRNlSLAVSDcFWkMVResi 580 (980)
T KOG0447|consen 520 AVVTGKGNS--------SE---------SIEAIREYEEEFFQNSKLLKTSMLKAHQVTTRNLSLAVSDCFWKMVRESV 580 (980)
T ss_pred EEEecCCCc--------ch---------hHHHHHHHHHHHhhhhHHHHhhccchhhhcccchhHHHHHHHHHHHHHHH
Confidence 999999842 22 455566778776 2222111 12678888888888888888777765
No 4
>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=99.36 E-value=6.7e-13 Score=134.54 Aligned_cols=77 Identities=29% Similarity=0.418 Sum_probs=71.9
Q ss_pred CCCCceEEEEeccCC-chhhhhHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcCCCcccCCccccCCCCceE
Q 007717 1 MQHREFIILCLEDCS-DWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLSPPACTLDGFILGGSPFFT 79 (591)
Q Consensus 1 i~~~n~IILaV~~An-D~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g~~~~L~~~llG~~pFFv 79 (591)
|+++++|||||.+|+ ||+|++++++|+++||.|.|||||+||+|.+ ++|+++.++|.|+.++|. +| |+
T Consensus 159 i~~~~~IIL~Vvda~~d~~~~d~l~ia~~ld~~~~rti~ViTK~D~~----~~~~~~~~~~~~~~~~l~---~g----~~ 227 (240)
T smart00053 159 ISKEECLILAVTPANVDLANSDALKLAKEVDPQGERTIGVITKLDLM----DEGTDARDILENKLLPLR---RG----YI 227 (240)
T ss_pred HhCccCeEEEEEECCCCCCchhHHHHHHHHHHcCCcEEEEEECCCCC----CccHHHHHHHhCCccccC---CC----EE
Confidence 567899999999999 9999999999999999999999999999999 999999999999999999 99 99
Q ss_pred eecCCCCCCCCc
Q 007717 80 SVPSGRVGTGHD 91 (591)
Q Consensus 80 svp~~R~g~~~D 91 (591)
+|.| |+ |+|
T Consensus 228 ~v~n-r~--~~d 236 (240)
T smart00053 228 GVVN-RS--QKD 236 (240)
T ss_pred EEEC-CC--hHH
Confidence 9977 55 555
No 5
>COG0699 Predicted GTPases (dynamin-related) [General function prediction only]
Probab=97.73 E-value=0.00028 Score=77.47 Aligned_cols=268 Identities=12% Similarity=0.094 Sum_probs=183.4
Q ss_pred CCCceEEEEeccCC-chhhhhHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcCCCcccCCccccCCCCceEe
Q 007717 2 QHREFIILCLEDCS-DWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLSPPACTLDGFILGGSPFFTS 80 (591)
Q Consensus 2 ~~~n~IILaV~~An-D~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g~~~~L~~~llG~~pFFvs 80 (591)
+.++++|.....++ |-++.++.+.+++.|| |.||.+.| +.++++...+ . .| |++
T Consensus 88 ~~~~~li~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~----~~~~~~~~~~-------~---~~----~~~ 142 (546)
T COG0699 88 EIENALILLGIAPNADEEAELSIEVIREADR-------VPTKINFL----NGGTNLTLIL-------G---NG----DVL 142 (546)
T ss_pred HHHHHHHhcchhhhhhhccchhhHhhhhhcc-------hhHHHHHH----hcCCceeeee-------c---cc----ccc
Confidence 45788999999999 9999999999999999 99999999 8777776541 1 33 555
Q ss_pred ecCCCCCCCCccccCChHHHHHHHhhhhhhHHHHHHHHhCCCCchhhhhhcChhHHHHHHHHHHHHHHHhhhhhhHHHHH
Q 007717 81 VPSGRVGTGHDSVYSSNEEFKQAIFIREMEDITSLEEKLGRSLSKQERSRIGVSKLRSFLEELLQKRYMDSVPMIIPLLE 160 (591)
Q Consensus 81 vp~~R~g~~~D~v~~s~~~f~~ai~~~~~~d~~~le~~~~~~~~~~~~~~~G~~~L~~~Ln~~L~~hyr~~lP~i~~~L~ 160 (591)
+++ +. ..+++..+... ..-..+.+....++.+......+|++++...+..++..||+...|...-+..
T Consensus 143 ~~~-~~----------~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 (546)
T COG0699 143 VVD-AL----------ETDIQLLKTAL-EALVKELEYFAEHPLLEDNEKLVLLPYLKKLLSKILELHLRLLPKYDKLQDV 210 (546)
T ss_pred ccC-ch----------hHHHHhcccch-HHHHHHHHHhhcCccccccccccCChhhhhhhhhhHHHHHHhcChhhhhHhh
Confidence 543 11 12222211111 0111222322378888888899999999999999999999998887664443
Q ss_pred HHHHHHHHHHHHHhHhhcccChHHHHHHHHHHHHHHHHHHhHhhcccccCCCcCcccchHHHhhhcCcccCCCCCCCCcc
Q 007717 161 KEYCSTTRKLNEINKELSTLDEVKLKEKGRVFHDLFLTKLSLLLKGTVVAPPDKFGETLQNERINGGAFVGTDGLQFPHK 240 (591)
Q Consensus 161 ~~~~~~~~eL~~~~~el~~~d~~~l~~~~l~~i~~F~~~~~~lI~Gt~~~~P~~~G~Tl~eEr~~~g~~~~~~g~~~~~~ 240 (591)
..+.. .+ ....++.....|+..+..+.+|
T Consensus 211 ~~~~~------~~-----------~~~~~~~~~~~~~~~~~~~~~~---------------------------------- 239 (546)
T COG0699 211 IQLSQ------DL-----------FENEVLAVIQTLLKRLSELVRG---------------------------------- 239 (546)
T ss_pred hcccc------cc-----------cchHHHHHHHHHHHHHHHHhcc----------------------------------
Confidence 32221 11 1225666777777777534333
Q ss_pred cCCCCCccccchhHHHHHHHhhHhhhccccCCCCCHHHHHHHhccCCCCCCC-----chhhHHHHHHHHHHHHhhcchHH
Q 007717 241 LIPNAGMRLYGGAQYHRAMAEFRFMVGGIKCPPITREEIVNACGVEDIHDGT-----NYSRTACVIAVAKARDTFEPFLH 315 (591)
Q Consensus 241 ~v~~~~~eL~GGAqi~Rif~EF~~~v~~i~~~~ls~eeI~~Aig~~~~~~g~-----~~~~Afe~Iak~qir~l~~P~L~ 315 (591)
+++.-..+-|. +.+.+.+..++.+..+ +.+. ....++..++..++..+..++.+
T Consensus 240 ------------~~~~~~~~~~~------~l~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~ 298 (546)
T COG0699 240 ------------ARIRLNIILFS------DLEEVSDSPVLLKELA---SKGERPSLLSGLTLLDTLVETPIGQFDTQINQ 298 (546)
T ss_pred ------------chhhhhhcccc------hHHHhhhhhhHHHHHc---ccCCCccccccccchhhhhHHHHHHHHHHHHH
Confidence 33332211121 5555666666666542 2222 25778888889999877777775
Q ss_pred HHHhhHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 007717 316 QLGCRLLHILKRLLPISIYLLQKEGEYLSGHEVFLRRVASAFNNFAESTERACREKCMEDLVSTTRYVT 384 (591)
Q Consensus 316 cv~~Rl~~V~~eL~~I~~~~~~k~~~~l~ryp~l~~~v~~~~~~fi~e~~~~ck~~~~d~l~s~t~~v~ 384 (591)
|+ ..++.+|.+++..++.. .....||.+...+...+..+......+........+....+|++
T Consensus 299 ~~----~~~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 361 (546)
T COG0699 299 LL----RKLISELVRILLKELES--ASSSPFPKLSEALEEVVNQLKNKVDSGLESGLLAIIDIEERYIN 361 (546)
T ss_pred HH----HHHHHHHHHHHHhhhcc--cccccchhhHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHh
Confidence 55 37889999986665553 45678999999999999998889999999999999999999997
No 6
>KOG0446 consensus Vacuolar sorting protein VPS1, dynamin, and related proteins [Intracellular trafficking, secretion, and vesicular transport; General function prediction only]
Probab=96.68 E-value=0.44 Score=55.57 Aligned_cols=325 Identities=14% Similarity=0.075 Sum_probs=173.6
Q ss_pred HHHHHHHHHHHHHHHHHhHhhcccccCCCcCcccchHHHhhhcCcccCCCCCCCCcccCCCCCccccchhHHHHHHHhhH
Q 007717 184 KLKEKGRVFHDLFLTKLSLLLKGTVVAPPDKFGETLQNERINGGAFVGTDGLQFPHKLIPNAGMRLYGGAQYHRAMAEFR 263 (591)
Q Consensus 184 ~l~~~~l~~i~~F~~~~~~lI~Gt~~~~P~~~G~Tl~eEr~~~g~~~~~~g~~~~~~~v~~~~~eL~GGAqi~Rif~EF~ 263 (591)
.+......+...|+..+..-.++-. . ++.+. -.|++ +.|...++.-+. .++ -.+-++|.-+.++.+++.
T Consensus 328 ~ll~~i~~~~~~~~~~v~g~~~~~~-~----~elsg-gari~-~~F~~~f~~~i~--~i~--~~~~~~~~~i~~~i~~~~ 396 (657)
T KOG0446|consen 328 ALLAIIREDPRGLRTGVIGKLDLVP-T----KALSG-GARIN-YPFHGGFPGVIK--KLP--PDRKLLGQNIEKLVSEAS 396 (657)
T ss_pred HHHHHHHHHHHHHHHhhcccccccc-h----hcccc-hhhhh-hhhhhccchhhh--cCC--cchhhhHHHHHHHHHhcc
Confidence 4566677777777777766666631 0 00000 01111 123222222111 111 128889999999999998
Q ss_pred hhhccccCCCCCHHHHHHHhccCCCCCCC--chhhHHHHHHHHHHHHhhcchHHHHHhhHHHHHHHHHHHHHHHHhhhcc
Q 007717 264 FMVGGIKCPPITREEIVNACGVEDIHDGT--NYSRTACVIAVAKARDTFEPFLHQLGCRLLHILKRLLPISIYLLQKEGE 341 (591)
Q Consensus 264 ~~v~~i~~~~ls~eeI~~Aig~~~~~~g~--~~~~Afe~Iak~qir~l~~P~L~cv~~Rl~~V~~eL~~I~~~~~~k~~~ 341 (591)
..--.+-+|+.+-+.|..-- +....+.. -.+.+.+.|++--.+.+..| .+.|+-..++++..++...++++
T Consensus 397 G~~~~lf~p~~afe~lvk~~-i~~l~~p~l~~v~~v~~el~~~~~~~~~~~----~l~rfp~l~~~~~~~~~~~~~~~-- 469 (657)
T KOG0446|consen 397 GIRPSLFVPESSFESLVKGQ-IQSLRDPSLKCVEEVHRELVRIVADSIRAT----ELKRFPVLYSELVEIASSLIAEG-- 469 (657)
T ss_pred CCCccccCChHHHHHHHHHH-HHHHhhhHHHHHHHHHHHHHHHHHHHhhhH----HHHHhHHHHHHHHHHHHHHHHHh--
Confidence 88888888888888877633 11111111 25777777777777777777 34577889999999999998853
Q ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccccCCcchhhh-hhhcccCCccchhhccccCCCCcc
Q 007717 342 YLSGHEVFLRRVASAFNNFAESTERACREKCMEDLVSTTRYVTWSLHNKNRAGLR-QFLDSFGSTEQSAVLSNSLSMPLC 420 (591)
Q Consensus 342 ~l~ryp~l~~~v~~~~~~fi~e~~~~ck~~~~d~l~s~t~~v~w~L~~~~~~~l~-~~l~~~~~~~~~~~~~~~~~~~~~ 420 (591)
++.+-.+...+.++=..|++-.-..+.......+...++- +- ++...+. .......+ +..+ ..+.+.
T Consensus 470 -~~~t~~~v~~~i~~e~~yinT~h~df~~~~~~al~~~~~~---~~--~~~~~~~~~~~~~~~~-~~~~-----~~~~~~ 537 (657)
T KOG0446|consen 470 -LDETKKAVKNLIDLEQSYLNTDHPDFRSLTDSALSSVTSP---SI--AAMKLISAQLLKEELG-ECNS-----ALKAIK 537 (657)
T ss_pred -hhHHHHHHHHHHHHHHHHhcCcChhhhhhHHHHHHHhhcc---cc--cccccccccccccccc-cccc-----hhhhhc
Confidence 3333333332222222223211111111111011111100 00 0000000 00000000 0000 000000
Q ss_pred ccccccccccccCCCCCcccccccccccCCCCCCccchhhhHHHHhhhhhhhccccCCccHHHHHHHHHHHHHHHHHHHH
Q 007717 421 QESSFVSVANEKHDTKPRTDVKLSQVASGVDSSSSVQTTETRLADLLDNTLWNRRLAPSSERIVYALVQQIFHGIREYFL 500 (591)
Q Consensus 421 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~r~l~~~s~~iV~~l~~~iF~~IR~~~~ 500 (591)
... .+ ..+. +++... .+...+.+. ......+...++..-|.-++..++
T Consensus 538 ~~~-----------~~----~~~~---------~~~~~~-~~~~~~~~~-------~~~~~~~i~~~~~sY~~iv~~~i~ 585 (657)
T KOG0446|consen 538 NAV-----------GS----IRLD---------PSDIVL-SRALVLKKR-------ECKETEEISSCPESYLNIVSDKLV 585 (657)
T ss_pred chh-----------hh----hhhc---------ccchhh-hhhhhcchh-------hhHHHHHHHHHHHHHHHHHHHHHH
Confidence 000 00 0000 000000 000000000 011356678888888888999999
Q ss_pred HHHHhhhhhhchhhhhhhhhHHHHHHHHhhcccchhhhhchhhHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q 007717 501 ASAELKFNCFLLMPVVDKLPALLREDLESAFEGDLDNVFDITNLRHSLSQQKSDTEIEMKRIKKLKEKFKLIHE 574 (591)
Q Consensus 501 ~~~~~Kfn~fFL~P~~~~l~~~lr~~l~~~~d~~l~~vF~~~~~r~~L~~~~~~l~~e~~~~~~~~~kF~~i~~ 574 (591)
-+|+.-.|++++.++-++|+.+|-.+|.. .+++++ .|-... ..+.++|+.++..++.++++++-+..+..
T Consensus 586 d~vpk~i~~~lv~~~k~~l~~~l~~~L~~-~~~~~~-~ll~E~--~~i~~~R~~~~~~l~~L~~a~~ii~~~~~ 655 (657)
T KOG0446|consen 586 DTVPKALNHELLNEFKDDLPNELDQRLYA-GDEQLE-SLLKED--PRIKRRRELQQKRLLALQKALSILATVAQ 655 (657)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh-chhHHH-HHHccC--HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999 655555 554444 77889999999999999999988887653
No 7
>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=92.85 E-value=0.18 Score=48.16 Aligned_cols=67 Identities=19% Similarity=0.205 Sum_probs=42.9
Q ss_pred ceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeecccccccCCCchhhH---hhhcCCCcccCCccccCCCCceEee
Q 007717 5 EFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDV---EVFLSPPACTLDGFILGGSPFFTSV 81 (591)
Q Consensus 5 n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv---~~~L~g~~~~L~~~llG~~pFFvsv 81 (591)
-.+|+-|.+|++=.+.-.=..++-. ..+.|||+||.|+- .+..++ ..+|..-|. ..+|+||.
T Consensus 64 ad~V~ll~dat~~~~~~pP~fa~~f---~~pvIGVITK~Dl~----~~~~~i~~a~~~L~~aG~--------~~if~vS~ 128 (143)
T PF10662_consen 64 ADVVLLLQDATEPRSVFPPGFASMF---NKPVIGVITKIDLP----SDDANIERAKKWLKNAGV--------KEIFEVSA 128 (143)
T ss_pred CCEEEEEecCCCCCccCCchhhccc---CCCEEEEEECccCc----cchhhHHHHHHHHHHcCC--------CCeEEEEC
Confidence 3578888888733333222233222 25789999999998 555555 468876553 25899999
Q ss_pred cCCCC
Q 007717 82 PSGRV 86 (591)
Q Consensus 82 p~~R~ 86 (591)
..|-+
T Consensus 129 ~~~eG 133 (143)
T PF10662_consen 129 VTGEG 133 (143)
T ss_pred CCCcC
Confidence 77443
No 8
>PF02212 GED: Dynamin GTPase effector domain; InterPro: IPR003130 Dynamin GTPase effector domain found in proteins related to dynamin. Dynamin is a GTP-hydrolysing protein that is an essential participant in clathrin-mediated endocytosis by cells. It self-assembles into 'collars' in vivo at the necks of invaginated coated pits; the self-assembly of dynamin being coordinated by the GTPase domain. Mutation studies indicate that dynamin functions as a molecular regulator of receptor-mediated endocytosis [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 3ZYS_B 3SZR_A 3LJB_B 3T35_C 3T34_A 2X2F_D 2X2E_D 3SNH_A 3ZYC_D 3ZVR_A.
Probab=79.84 E-value=18 Score=31.44 Aligned_cols=83 Identities=18% Similarity=0.306 Sum_probs=59.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhchhhhhhhhhHHHHHHHHhhcccchhhhhchhhHHHHHHhhhhhHHHHHH
Q 007717 481 ERIVYALVQQIFHGIREYFLASAELKFNCFLLMPVVDKLPALLREDLESAFEGDLDNVFDITNLRHSLSQQKSDTEIEMK 560 (591)
Q Consensus 481 ~~iV~~l~~~iF~~IR~~~~~~~~~Kfn~fFL~P~~~~l~~~lr~~l~~~~d~~l~~vF~~~~~r~~L~~~~~~l~~e~~ 560 (591)
.+.+..++..-|.-.+..|+-+|+..-..|++--+.+.|...|-.+|..-.+ +++++.=. ....++|.+|..+++
T Consensus 6 ~~~i~~~l~aY~~ia~kr~~D~Vpk~I~~~lv~~~~~~L~~~l~~~l~~~~~--~~~Ll~Ed---~~i~~kR~~l~~~~~ 80 (92)
T PF02212_consen 6 VEEIKALLRAYFEIARKRFIDSVPKAIMHFLVNKSKEQLQSELLNELYDEED--LEELLQED---PEIAEKREELKKKLE 80 (92)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGG--CCCCT--G---HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHhccchHH--HHHHHCCC---HHHHHHHHHHHHHHH
Confidence 4667888999999999999999998888887777777666666666544332 55555433 566778888888888
Q ss_pred HHHHHHHH
Q 007717 561 RIKKLKEK 568 (591)
Q Consensus 561 ~~~~~~~k 568 (591)
++++.++-
T Consensus 81 ~L~~A~~~ 88 (92)
T PF02212_consen 81 RLKKAQQI 88 (92)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 87776543
No 9
>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=69.70 E-value=11 Score=35.83 Aligned_cols=41 Identities=15% Similarity=0.080 Sum_probs=29.6
Q ss_pred ceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 5 EFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 5 n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+++|+++...+.....+ +++.+.+++.+...|+|+||.|++
T Consensus 102 ~~ii~vvd~~~~~~~~~-~~~~~~~~~~~~pviiv~nK~D~~ 142 (179)
T TIGR03598 102 KGVVLLMDIRHPLKELD-LEMLEWLRERGIPVLIVLTKADKL 142 (179)
T ss_pred cEEEEEecCCCCCCHHH-HHHHHHHHHcCCCEEEEEECcccC
Confidence 45777765544544443 456677778899999999999998
No 10
>PRK03003 GTP-binding protein Der; Reviewed
Probab=58.77 E-value=46 Score=37.26 Aligned_cols=43 Identities=12% Similarity=0.164 Sum_probs=30.4
Q ss_pred CCceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-+++||++..++-. +...++++..+-..+.-.|.|.||.|+.
T Consensus 293 ~ad~vilV~Da~~~~-s~~~~~~~~~~~~~~~piIiV~NK~Dl~ 335 (472)
T PRK03003 293 AAEVAVVLIDASEPI-SEQDQRVLSMVIEAGRALVLAFNKWDLV 335 (472)
T ss_pred cCCEEEEEEeCCCCC-CHHHHHHHHHHHHcCCCEEEEEECcccC
Confidence 346777777654432 3334566777766888999999999997
No 11
>PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed
Probab=58.40 E-value=44 Score=39.54 Aligned_cols=42 Identities=12% Similarity=0.142 Sum_probs=29.7
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
-+.+||++...... +...++++..+...+.-.|+|+||.|++
T Consensus 533 advvilViDat~~~-s~~~~~i~~~~~~~~~piIiV~NK~DL~ 574 (712)
T PRK09518 533 SELALFLFDASQPI-SEQDLKVMSMAVDAGRALVLVFNKWDLM 574 (712)
T ss_pred CCEEEEEEECCCCC-CHHHHHHHHHHHHcCCCEEEEEEchhcC
Confidence 45666666544333 3334567777777889999999999997
No 12
>PF12842 DUF3819: Domain of unknown function (DUF3819); InterPro: IPR024557 The Ccr4-Not complex is a global regulator of gene expression that is conserved from yeast to human. It affects genes positively and negatively and is thought to regulate transcription factor IID function. In Saccharomyces cerevisiae, it exists in two prominent forms and consists of at least nine core subunits: the five Not proteins (Not1p to Not5p), Caf1p, Caf40p, Caf130p and Ccr4p []. The Ccr4-Not complex regulates many different cellular functions, including RNA degradation and transcription initiation. It may be a regulatory platform that senses nutrient levels and stress []. Caf1p and Ccr4p, are directly involved in mRNA deadenylation, and Caf1p is associated with Dhh1p, a putative RNA helicase thought to be a component of the decapping complex []. Pop2, a component of the Ccr4-Not complex, functions as a deadenylase []. This entry represents a domain of unknown function found in the Not1 subunit of the CCR4-Not complex.
Probab=57.98 E-value=80 Score=30.25 Aligned_cols=67 Identities=13% Similarity=0.169 Sum_probs=52.6
Q ss_pred hHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHhHhhcccChHHHHHHHHHHHHHHHHHHh
Q 007717 134 SKLRSFLEELLQKRYMDSVPMIIPLLEKEYCSTTRKLNEINKELSTLDEVKLKEKGRVFHDLFLTKLS 201 (591)
Q Consensus 134 ~~L~~~Ln~~L~~hyr~~lP~i~~~L~~~~~~~~~eL~~~~~el~~~d~~~l~~~~l~~i~~F~~~~~ 201 (591)
|.|++.+-.-|.+-|+|.++++..+.-.....+..+|-.-.=- -+.|..++++.+.+|+.+++..+.
T Consensus 2 p~lk~~v~~Al~rai~Eii~pvveRsv~IA~~Tt~~LV~KDFa-~E~De~~~r~aa~~Mv~~LA~sLa 68 (147)
T PF12842_consen 2 PQLKRIVQNALDRAIREIISPVVERSVTIASITTEELVKKDFA-TEPDENKMRRAAHNMVRSLAGSLA 68 (147)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc-CCccHHHHHHHHHHHHHHHHHHHH
Confidence 6789999999999999999988887777767777666543211 234788899999999999998884
No 13
>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=53.21 E-value=18 Score=31.42 Aligned_cols=43 Identities=12% Similarity=0.260 Sum_probs=27.7
Q ss_pred CCceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
..+.+|+++..++. .+.....+.++.--.....|+|+||.|++
T Consensus 75 ~~d~il~v~~~~~~-~~~~~~~~~~~~~~~~~~~ivv~nK~D~~ 117 (163)
T cd00880 75 RADLILFVVDADLR-ADEEEEKLLELLRERGKPVLLVLNKIDLL 117 (163)
T ss_pred hCCEEEEEEeCCCC-CCHHHHHHHHHHHhcCCeEEEEEEccccC
Confidence 34566776666652 22222234555555677799999999998
No 14
>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=52.00 E-value=19 Score=31.94 Aligned_cols=42 Identities=10% Similarity=0.221 Sum_probs=26.8
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.+.+++++...+-... ....+.+.+.-.+...|+|+||.|+.
T Consensus 83 ~d~i~~v~d~~~~~~~-~~~~~~~~~~~~~~~~iiv~nK~Dl~ 124 (168)
T cd04163 83 VDLVLFVVDASEPIGE-GDEFILELLKKSKTPVILVLNKIDLV 124 (168)
T ss_pred CCEEEEEEECCCccCc-hHHHHHHHHHHhCCCEEEEEEchhcc
Confidence 4667777777652122 22334444444467789999999998
No 15
>TIGR03777 RPE4 Rickettsial palindromic element RPE4 domain. This model describes protein translations of a family, RPE4, of Rickettsia palindromic elements (RPE). The elements spread within a genome as selfish genetic elements, inserting into genes additional coding region that does not disrupt the reading frame. This model finds RPE-encoded regions in several Rickettsial species and, so far, no where else.
Probab=51.57 E-value=3.8 Score=29.70 Aligned_cols=17 Identities=35% Similarity=0.436 Sum_probs=13.8
Q ss_pred HHHHhhhhhhchhhhhh
Q 007717 501 ASAELKFNCFLLMPVVD 517 (591)
Q Consensus 501 ~~~~~Kfn~fFL~P~~~ 517 (591)
++.-+.|+||||+|+|-
T Consensus 12 k~~~~~~~~~~LD~VvK 28 (32)
T TIGR03777 12 KSTNNDFISCFLDPVVK 28 (32)
T ss_pred cccccchhhhhcccccc
Confidence 45567899999999973
No 16
>PRK00093 GTP-binding protein Der; Reviewed
Probab=50.43 E-value=53 Score=35.85 Aligned_cols=42 Identities=14% Similarity=0.189 Sum_probs=31.1
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
-+.+||.+........ ...++++.+.-.|..-|.|+||.|+.
T Consensus 256 ad~~ilViD~~~~~~~-~~~~i~~~~~~~~~~~ivv~NK~Dl~ 297 (435)
T PRK00093 256 ADVVLLVIDATEGITE-QDLRIAGLALEAGRALVIVVNKWDLV 297 (435)
T ss_pred CCEEEEEEeCCCCCCH-HHHHHHHHHHHcCCcEEEEEECccCC
Confidence 3567777766555443 34577777777899999999999987
No 17
>PRK10867 signal recognition particle protein; Provisional
Probab=50.25 E-value=97 Score=34.81 Aligned_cols=132 Identities=20% Similarity=0.235 Sum_probs=75.8
Q ss_pred CCceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcCCCcccCCccccCCCCceEeec
Q 007717 3 HREFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLSPPACTLDGFILGGSPFFTSVP 82 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g~~~~L~~~llG~~pFFvsvp 82 (591)
.|.-++|.|.+.. ..++...|+.......-|=.|+||+|-- .+|-.+..+..-.+.|+. |+|+.
T Consensus 213 ~p~evllVlda~~---gq~av~~a~~F~~~~~i~giIlTKlD~~----~rgG~alsi~~~~~~PI~---------fig~G 276 (433)
T PRK10867 213 NPDEILLVVDAMT---GQDAVNTAKAFNEALGLTGVILTKLDGD----ARGGAALSIRAVTGKPIK---------FIGTG 276 (433)
T ss_pred CCCeEEEEEeccc---HHHHHHHHHHHHhhCCCCEEEEeCccCc----ccccHHHHHHHHHCcCEE---------EEeCC
Confidence 4666777777533 3567778887776666788899999977 666667666554455544 77773
Q ss_pred CCCCCCCCccccCChHHHHHHHhhhhhhHHHHHHHHh-CCCCc---hhhhhh--cChhHHHHHHHHHHH-------HHHH
Q 007717 83 SGRVGTGHDSVYSSNEEFKQAIFIREMEDITSLEEKL-GRSLS---KQERSR--IGVSKLRSFLEELLQ-------KRYM 149 (591)
Q Consensus 83 ~~R~g~~~D~v~~s~~~f~~ai~~~~~~d~~~le~~~-~~~~~---~~~~~~--~G~~~L~~~Ln~~L~-------~hyr 149 (591)
- ++ .|..--+++.|.+.|- ..-|...|-++. ....+ ++...+ =|.-.|..|++|+-+ ..+.
T Consensus 277 e-~v---~DLe~f~p~~~~~~il--gmgD~~~l~e~~~~~~~~~~~~~~~~~~~~g~f~l~d~~~q~~~~~kmG~~~~~~ 350 (433)
T PRK10867 277 E-KL---DDLEPFHPDRMASRIL--GMGDVLSLIEKAQEVVDEEKAEKLAKKLKKGKFDLEDFLEQLQQMKKMGGLGSLL 350 (433)
T ss_pred C-cc---ccCccCCHHHHHHHHh--CCCChHHHHHHHHHhhCHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHH
Confidence 3 22 4433445666666554 334444443332 11111 111111 155567777776543 4566
Q ss_pred hhhhhhH
Q 007717 150 DSVPMII 156 (591)
Q Consensus 150 ~~lP~i~ 156 (591)
..+|.+-
T Consensus 351 ~m~Pg~~ 357 (433)
T PRK10867 351 GMLPGMG 357 (433)
T ss_pred HhCCCcc
Confidence 6777653
No 18
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=50.15 E-value=1.2e+02 Score=34.03 Aligned_cols=132 Identities=16% Similarity=0.233 Sum_probs=75.2
Q ss_pred CCceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcCCCcccCCccccCCCCceEeec
Q 007717 3 HREFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLSPPACTLDGFILGGSPFFTSVP 82 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g~~~~L~~~llG~~pFFvsvp 82 (591)
.|+.+||.|.+... .++...|+...+...-+-.|+||+|-- ++|--+..+..-.+.|+. |+|.=
T Consensus 205 ~pdevlLVvda~~g---q~av~~a~~F~~~l~i~gvIlTKlD~~----a~~G~~ls~~~~~~~Pi~---------fig~G 268 (437)
T PRK00771 205 KPDEVLLVIDATIG---QQAKNQAKAFHEAVGIGGIIITKLDGT----AKGGGALSAVAETGAPIK---------FIGTG 268 (437)
T ss_pred cccceeEEEecccc---HHHHHHHHHHHhcCCCCEEEEecccCC----CcccHHHHHHHHHCcCEE---------EEecC
Confidence 46677777775543 467778888777777788899999999 888888766665555544 77761
Q ss_pred CCCCCCCCccccCChHHHHHHHhhhhhhHHHHHHHHh-CCCC---chhhhhh--cChhHHHHHHHHHHH-------HHHH
Q 007717 83 SGRVGTGHDSVYSSNEEFKQAIFIREMEDITSLEEKL-GRSL---SKQERSR--IGVSKLRSFLEELLQ-------KRYM 149 (591)
Q Consensus 83 ~~R~g~~~D~v~~s~~~f~~ai~~~~~~d~~~le~~~-~~~~---~~~~~~~--~G~~~L~~~Ln~~L~-------~hyr 149 (591)
- ++ .|...-+.+.|...|-. +-|...|-++. .... .++...+ -|.-.|..|++|+-+ ..+.
T Consensus 269 e-~v---~Dle~f~~~~~~~~ilg--mgd~~~l~e~~~~~~~~~~~~~~~~~~~~~~f~l~d~~~q~~~~~kmG~~~~~~ 342 (437)
T PRK00771 269 E-KI---DDLERFDPDRFISRLLG--MGDLESLLEKVEEALDEEEEEKDVEKMMKGKFTLKDMYKQLEAMNKMGPLKQIL 342 (437)
T ss_pred C-Cc---ccCCcCCHHHHHHHHhC--CCChHHHHHHHHHhhhHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhcCCHHHHH
Confidence 1 11 34333455666554432 23333332222 0000 1111111 155567777776543 4566
Q ss_pred hhhhhhH
Q 007717 150 DSVPMII 156 (591)
Q Consensus 150 ~~lP~i~ 156 (591)
..+|.+-
T Consensus 343 ~m~pg~~ 349 (437)
T PRK00771 343 QMLPGLG 349 (437)
T ss_pred HhCcCcc
Confidence 6777653
No 19
>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=47.93 E-value=21 Score=33.32 Aligned_cols=40 Identities=25% Similarity=0.249 Sum_probs=28.2
Q ss_pred EEEEeccCCchhhhhHHHHH-HhcCCCCCceEEEeeccccc
Q 007717 7 IILCLEDCSDWSNATTRRVV-MQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 7 IILaV~~AnD~ANSdaLkla-keVDP~g~RTIgV~TKlD~m 46 (591)
+||.|-+|.|+-.+....+. ..+-..+...|.|+||.|+.
T Consensus 2 vvl~VvD~~~p~~~~~~~i~~~~~~~~~~p~IiVlNK~Dl~ 42 (155)
T cd01849 2 VILEVLDARDPLGTRSPDIERVLIKEKGKKLILVLNKADLV 42 (155)
T ss_pred EEEEEEeccCCccccCHHHHHHHHhcCCCCEEEEEechhcC
Confidence 45666677755444444555 45556678999999999996
No 20
>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=47.27 E-value=45 Score=30.02 Aligned_cols=42 Identities=17% Similarity=0.241 Sum_probs=26.2
Q ss_pred CCceEEEEeccCCchhhh--hHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCSDWSNA--TTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANS--daLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-+++|+++...++|... ..+.+++... ...-|+|+||.|+.
T Consensus 74 ~ad~ii~V~d~~~~~~~~~~~~~~~~~~~~--~~~~ilv~NK~Dl~ 117 (164)
T cd04171 74 GIDLVLLVVAADEGIMPQTREHLEILELLG--IKRGLVVLTKADLV 117 (164)
T ss_pred cCCEEEEEEECCCCccHhHHHHHHHHHHhC--CCcEEEEEECcccc
Confidence 346777777765566432 2334444432 23689999999997
No 21
>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=45.91 E-value=73 Score=30.57 Aligned_cols=43 Identities=19% Similarity=0.379 Sum_probs=30.8
Q ss_pred CceEEEEeccCC-chhh--hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 4 REFIILCLEDCS-DWSN--ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 4 ~n~IILaV~~An-D~AN--SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
-+.+|+.+...+ ++.. ..++++.+++...+..-|+|.||.|+.
T Consensus 121 ~d~ii~v~D~~~~~~~~~~~~~~~~l~~~~~~~~~viiV~NK~Dl~ 166 (204)
T cd01878 121 ADLLLHVVDASDPDYEEQIETVEKVLKELGAEDIPMILVLNKIDLL 166 (204)
T ss_pred CCeEEEEEECCCCChhhHHHHHHHHHHHcCcCCCCEEEEEEccccC
Confidence 356777776555 4432 245677778877778899999999997
No 22
>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=44.55 E-value=38 Score=32.48 Aligned_cols=44 Identities=16% Similarity=0.172 Sum_probs=28.9
Q ss_pred CCCceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+..+++||.|.+... -...+....+.+.-.+...|+|+||.|+.
T Consensus 92 ~~~D~ailvVda~~g-~~~~~~~~l~~~~~~~~p~ivvlNK~D~~ 135 (188)
T PF00009_consen 92 RQADIAILVVDANDG-IQPQTEEHLKILRELGIPIIVVLNKMDLI 135 (188)
T ss_dssp TTSSEEEEEEETTTB-STHHHHHHHHHHHHTT-SEEEEEETCTSS
T ss_pred cccccceeeeecccc-cccccccccccccccccceEEeeeeccch
Confidence 346788888877642 23344444444444455599999999999
No 23
>smart00302 GED Dynamin GTPase effector domain.
Probab=44.13 E-value=2.2e+02 Score=24.90 Aligned_cols=83 Identities=16% Similarity=0.185 Sum_probs=56.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhchhhhhhhhhHHHHHHHHhhcccchhhhhchhhHHHHHHhhhhhHHHHHH
Q 007717 481 ERIVYALVQQIFHGIREYFLASAELKFNCFLLMPVVDKLPALLREDLESAFEGDLDNVFDITNLRHSLSQQKSDTEIEMK 560 (591)
Q Consensus 481 ~~iV~~l~~~iF~~IR~~~~~~~~~Kfn~fFL~P~~~~l~~~lr~~l~~~~d~~l~~vF~~~~~r~~L~~~~~~l~~e~~ 560 (591)
.+.+..++..-|.-+|..+...||.--=+|-+.-..+.+...|-.+|-. .++++++..=. ....++|..+...++
T Consensus 6 ~~~i~~lv~sYf~iv~k~i~D~VPKaI~~~lv~~~~~~lq~~L~~~L~~--~~~~~~LL~E~---~~i~~kR~~~~~~l~ 80 (92)
T smart00302 6 LEEIKSLVKSYFTIVSKTLADQVPKAIMYLLVNESKDSLQNELLALLYK--EELLDELLEED---PEIASKRKELKKRLE 80 (92)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhC--cccHHHHHcCC---HHHHHHHHHHHHHHH
Confidence 4567888999999999999999987776666666666666666555533 44566665543 345566666666677
Q ss_pred HHHHHHHH
Q 007717 561 RIKKLKEK 568 (591)
Q Consensus 561 ~~~~~~~k 568 (591)
.+++.++.
T Consensus 81 ~L~~A~~~ 88 (92)
T smart00302 81 LLKKARQI 88 (92)
T ss_pred HHHHHHHH
Confidence 77665543
No 24
>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=42.77 E-value=83 Score=28.96 Aligned_cols=44 Identities=14% Similarity=0.048 Sum_probs=31.5
Q ss_pred CCceEEEEeccCC-c--hhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCS-D--WSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~An-D--~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-+++|+++..++ + ..-.+|++..++..|+...-|+|.||.|+.
T Consensus 73 ~~~~~l~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piivv~nK~Dl~ 119 (165)
T cd01865 73 GAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGNKCDME 119 (165)
T ss_pred CCcEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCCEEEEEECcccC
Confidence 4466777777654 1 122457777777777778899999999997
No 25
>PF05879 RHD3: Root hair defective 3 GTP-binding protein (RHD3); InterPro: IPR008803 This family consists of several eukaryotic root hair defective 3 like GTP-binding proteins. It has been speculated that the RHD3 protein is a member of a novel class of GTP-binding proteins that is widespread in eukaryotes and required for regulated cell enlargement []. The family also contains the homologous Saccharomyces cerevisiae synthetic construct enhancement of YOP1 (SEY1) protein which is involved in membrane trafficking [].; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=42.24 E-value=6.9e+02 Score=30.12 Aligned_cols=87 Identities=16% Similarity=0.146 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhhchhhhhhhhhHHHHHHHHhhcccchhh--------------------hhch
Q 007717 482 RIVYALVQQIFHGIREYFLASAELKFNCFLLMPVVDKLPALLREDLESAFEGDLDN--------------------VFDI 541 (591)
Q Consensus 482 ~iV~~l~~~iF~~IR~~~~~~~~~Kfn~fFL~P~~~~l~~~lr~~l~~~~d~~l~~--------------------vF~~ 541 (591)
.-+..|+.++...++..+...|..-|+.- -.++|..|+..+..+.+.-+.. -|..
T Consensus 421 ~el~~l~~~~eK~l~~~l~e~v~~~l~~~-----~~d~Wd~I~~~f~~~~~~~~~~~~~~~~~f~~s~~e~~~~~~~lr~ 495 (742)
T PF05879_consen 421 EELNELVARIEKKLKSELKEPVESLLENP-----SPDMWDRIRKLFESATESAVSKFSDRLKGFGLSEEENEKALKKLRR 495 (742)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHhCC-----ChhhHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHH
Confidence 44667777777888888877777777762 2667777776666555532211 1111
Q ss_pred hhHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q 007717 542 TNLRHSLSQQKSDTEIEMKRIKKLKEKFKLIHE 574 (591)
Q Consensus 542 ~~~r~~L~~~~~~l~~e~~~~~~~~~kF~~i~~ 574 (591)
.++..|+.+-++...+-.-+.++++.|....+
T Consensus 496 -~aw~~l~~ki~e~~~~~~ll~~LkdRFe~~Fr 527 (742)
T PF05879_consen 496 -KAWSVLREKIREEASEDNLLIRLKDRFEDKFR 527 (742)
T ss_pred -HHHHHHHHHHHHHHhHhHHHHHHHHHHHHHhC
Confidence 12445666666666566677888888887654
No 26
>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=42.01 E-value=2.9e+02 Score=30.97 Aligned_cols=42 Identities=19% Similarity=0.395 Sum_probs=25.9
Q ss_pred CCceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-+++|+++..++...-.+. +..++...+...|.|.||.|+.
T Consensus 282 ~aD~il~V~D~s~~~s~~~~--~l~~~~~~~~piIlV~NK~Dl~ 323 (442)
T TIGR00450 282 QADLVIYVLDASQPLTKDDF--LIIDLNKSKKPFILVLNKIDLK 323 (442)
T ss_pred hCCEEEEEEECCCCCChhHH--HHHHHhhCCCCEEEEEECccCC
Confidence 34677777776652221121 3334444567889999999986
No 27
>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=40.43 E-value=82 Score=34.24 Aligned_cols=42 Identities=21% Similarity=0.234 Sum_probs=30.0
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
-+++|+.+..++... ...+++++.+.-.|..-|.|+||.|+.
T Consensus 255 ad~~ilV~D~~~~~~-~~~~~~~~~~~~~~~~iiiv~NK~Dl~ 296 (429)
T TIGR03594 255 ADVVLLVLDATEGIT-EQDLRIAGLILEAGKALVIVVNKWDLV 296 (429)
T ss_pred CCEEEEEEECCCCcc-HHHHHHHHHHHHcCCcEEEEEECcccC
Confidence 456777776554333 334567777766789999999999997
No 28
>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=40.30 E-value=34 Score=31.15 Aligned_cols=40 Identities=13% Similarity=0.091 Sum_probs=26.1
Q ss_pred CceEEEEeccCC-c-hhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 4 REFIILCLEDCS-D-WSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 4 ~n~IILaV~~An-D-~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
-+++|+++...+ + ..+-..++.++. .+...|+|+||.|+.
T Consensus 74 ~d~il~v~d~~~~~~~~~~~~~~~~~~---~~~p~ivv~NK~Dl~ 115 (168)
T cd01887 74 TDIAILVVAADDGVMPQTIEAIKLAKA---ANVPFIVALNKIDKP 115 (168)
T ss_pred cCEEEEEEECCCCccHHHHHHHHHHHH---cCCCEEEEEEceecc
Confidence 457778877766 3 222223444444 567899999999987
No 29
>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=39.93 E-value=42 Score=29.85 Aligned_cols=41 Identities=15% Similarity=0.289 Sum_probs=26.7
Q ss_pred CCceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+.+++++++...+-....+. ++.+. ..+...|.|+||.|++
T Consensus 80 ~~~~~v~v~d~~~~~~~~~~-~~~~~--~~~~~vi~v~nK~D~~ 120 (157)
T cd04164 80 EADLVLFVIDASRGLDEEDL-EILEL--PADKPIIVVLNKSDLL 120 (157)
T ss_pred hCCEEEEEEECCCCCCHHHH-HHHHh--hcCCCEEEEEEchhcC
Confidence 45677777766653333333 33333 4568899999999998
No 30
>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=39.71 E-value=35 Score=30.76 Aligned_cols=42 Identities=21% Similarity=0.253 Sum_probs=30.2
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.+++|+++...+.+. ...+++.+.+.-.+..-|.|+||.|++
T Consensus 85 ~d~vi~v~d~~~~~~-~~~~~~~~~~~~~~~~~iiv~nK~Dl~ 126 (174)
T cd01895 85 ADVVLLVIDATEGIT-EQDLRIAGLILEEGKALVIVVNKWDLV 126 (174)
T ss_pred cCeEEEEEeCCCCcc-hhHHHHHHHHHhcCCCEEEEEeccccC
Confidence 456777776544544 344567777766678899999999998
No 31
>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=38.52 E-value=57 Score=31.20 Aligned_cols=44 Identities=11% Similarity=0.129 Sum_probs=33.1
Q ss_pred CCceEEEEeccCC-c-hhh-hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCS-D-WSN-ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~An-D-~AN-SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-+++|+++...+ + +.+ ..|+..+++..|.+..-|+|.||.|+.
T Consensus 73 ~ad~~i~v~D~~~~~s~~~~~~~~~~i~~~~~~~~piiiv~NK~Dl~ 119 (191)
T cd04112 73 DAHALLLLYDITNKASFDNIRAWLTEIKEYAQEDVVIMLLGNKADMS 119 (191)
T ss_pred CCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEEcccch
Confidence 4578888887665 2 222 237788888888888889999999996
No 32
>PRK12289 GTPase RsgA; Reviewed
Probab=37.92 E-value=61 Score=35.32 Aligned_cols=39 Identities=10% Similarity=0.045 Sum_probs=23.3
Q ss_pred ceEEEEeccCC-chhh---hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 5 EFIILCLEDCS-DWSN---ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 5 n~IILaV~~An-D~AN---SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+.|++.+...+ ++.. ..+|..| -..+...|.|+||.|+.
T Consensus 91 D~vLlV~d~~~p~~~~~~LdR~L~~a---~~~~ip~ILVlNK~DLv 133 (352)
T PRK12289 91 DQILLVFALAEPPLDPWQLSRFLVKA---ESTGLEIVLCLNKADLV 133 (352)
T ss_pred CEEEEEEECCCCCCCHHHHHHHHHHH---HHCCCCEEEEEEchhcC
Confidence 34555554444 4332 2334333 34578899999999997
No 33
>PRK13796 GTPase YqeH; Provisional
Probab=37.91 E-value=46 Score=36.14 Aligned_cols=43 Identities=12% Similarity=0.125 Sum_probs=31.3
Q ss_pred CCCceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
...+++|+.|=++.|.- +.+.+..++.-+ ....|.|+||.|+.
T Consensus 67 ~~~~~lIv~VVD~~D~~-~s~~~~L~~~~~-~kpviLViNK~DLl 109 (365)
T PRK13796 67 GDSDALVVNVVDIFDFN-GSWIPGLHRFVG-NNPVLLVGNKADLL 109 (365)
T ss_pred cccCcEEEEEEECccCC-CchhHHHHHHhC-CCCEEEEEEchhhC
Confidence 45677999999998844 445555555443 56789999999996
No 34
>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=37.79 E-value=42 Score=31.11 Aligned_cols=43 Identities=16% Similarity=-0.001 Sum_probs=27.1
Q ss_pred CCceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-+++|+++...+.+.. ..+.........+...|+|+||.|+.
T Consensus 90 ~ad~~i~v~D~~~~~~~-~~~~~~~~~~~~~~~iiiv~NK~Dl~ 132 (179)
T cd01890 90 ACEGALLLVDATQGVEA-QTLANFYLALENNLEIIPVINKIDLP 132 (179)
T ss_pred hcCeEEEEEECCCCccH-hhHHHHHHHHHcCCCEEEEEECCCCC
Confidence 34688888876553322 22333333334567799999999986
No 35
>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=37.68 E-value=43 Score=33.89 Aligned_cols=43 Identities=19% Similarity=0.201 Sum_probs=32.3
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeecccccc
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTKI 47 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~ml 47 (591)
-+++||.|.....+ ...+.++.+.+...+...|.|+||+|+.+
T Consensus 97 aD~~ilVvD~~~g~-~~~t~~~l~~~~~~~~p~ilviNKiD~~~ 139 (222)
T cd01885 97 CDGALVVVDAVEGV-CVQTETVLRQALKERVKPVLVINKIDRLI 139 (222)
T ss_pred cCeeEEEEECCCCC-CHHHHHHHHHHHHcCCCEEEEEECCCcch
Confidence 35677777655543 34567888888888899999999999873
No 36
>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=37.57 E-value=45 Score=33.65 Aligned_cols=43 Identities=14% Similarity=0.103 Sum_probs=32.1
Q ss_pred CCceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.++++||.|.....+ ....++++..+.-.|...|+|+||.|+.
T Consensus 109 ~~D~~llVvda~~g~-~~~d~~~l~~l~~~~ip~ivvvNK~D~~ 151 (224)
T cd04165 109 APDYAMLVVAANAGI-IGMTKEHLGLALALNIPVFVVVTKIDLA 151 (224)
T ss_pred CCCEEEEEEECCCCC-cHHHHHHHHHHHHcCCCEEEEEECcccc
Confidence 467777777644455 3556677777777888899999999986
No 37
>COG0486 ThdF Predicted GTPase [General function prediction only]
Probab=37.23 E-value=1.8e+02 Score=32.99 Aligned_cols=38 Identities=24% Similarity=0.285 Sum_probs=31.1
Q ss_pred EEEEeccCC-chhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 7 IILCLEDCS-DWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 7 IILaV~~An-D~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+||.|-+++ .|-..|-.-+- .=|...++|.|.||.|+.
T Consensus 299 lvL~v~D~~~~~~~~d~~~~~--~~~~~~~~i~v~NK~DL~ 337 (454)
T COG0486 299 LVLFVLDASQPLDKEDLALIE--LLPKKKPIIVVLNKADLV 337 (454)
T ss_pred EEEEEEeCCCCCchhhHHHHH--hcccCCCEEEEEechhcc
Confidence 788899998 67777765554 458889999999999999
No 38
>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=37.08 E-value=64 Score=29.50 Aligned_cols=45 Identities=20% Similarity=0.158 Sum_probs=32.7
Q ss_pred CCCceEEEEeccCC-ch--hhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS-DW--SNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An-D~--ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+.-+++|+++...+ += .-..+++..+..-+.+...|.|.||.|+-
T Consensus 78 ~~~d~~i~v~d~~~~~s~~~~~~~~~~l~~~~~~~~~~i~v~NK~D~~ 125 (169)
T cd04114 78 RSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVGNKIDLA 125 (169)
T ss_pred cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccc
Confidence 34578888888665 21 11357777777777778889999999985
No 39
>PF06213 CobT: Cobalamin biosynthesis protein CobT; InterPro: IPR006538 These proteins are CobT subunits of the aerobic cobalt chelatase (aerobic cobalamin biosynthesis pathway). Pseudomonas denitrificans CobT has been experimentally characterised [, ]. Aerobic cobalt chelatase consists of three subunits, CobT, CobN (IPR003672 from INTERPRO) and CobS (IPR006537 from INTERPRO). Cobalamin (vitamin B12) can be complexed with metal via the ATP-dependent reactions (aerobic pathway) (e.g., in P. denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in Salmonella typhimurium) [, ]. The corresponding cobalt chelatases are not homologous. However, aerobic cobalt chelatase subunits CobN and CobS are homologous to Mg-chelatase subunits BchH and BchI, respectively []. CobT, too, has been found to be remotely related to the third subunit of Mg-chelatase, BchD (involved in bacteriochlorophyll synthesis, e.g., in Rhodobacter capsulatus) []. Nomenclature note: CobT of the aerobic pathway P. denitrificans is not a homologue of CobT of the anaerobic pathway (Salmonella typhimurium, Escherichia coli). Therefore, annotation of any members of this family as nicotinate-mononucleotide--5,6-dimethylbenzimidazole phosphoribosyltransferases is erroneous.
Probab=36.90 E-value=1.8e+02 Score=30.51 Aligned_cols=94 Identities=19% Similarity=0.193 Sum_probs=70.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhch--------hhhhhhhhHHHHHHHHhhcc-cchhhhhchhhHHHHHHhhhhh
Q 007717 484 VYALVQQIFHGIREYFLASAELKFNCFLL--------MPVVDKLPALLREDLESAFE-GDLDNVFDITNLRHSLSQQKSD 554 (591)
Q Consensus 484 V~~l~~~iF~~IR~~~~~~~~~Kfn~fFL--------~P~~~~l~~~lr~~l~~~~d-~~l~~vF~~~~~r~~L~~~~~~ 554 (591)
|-++..+.|.|+|.-+-..++-+|....+ .|+..-|..+||..|....- .....+.+ ..|..|..+...
T Consensus 103 vE~~g~~~~~Gv~~NL~~~~~~~~~~~~~~~~~~~~~~~l~~al~l~lr~rl~g~~~p~~~~~~~~--~~R~~l~~~~g~ 180 (282)
T PF06213_consen 103 VEALGARRMPGVRANLDAMLEDRYARGGFDRITDREDAPLSEALALLLRERLTGQPPPESAEKVVE--LWRPWLEEKAGK 180 (282)
T ss_pred HHHHhhhcCCcHHHHHHHHHHHHHHhcCCCcccCcccccHHHHHHHHHHHHHhCCCCcHHHHHHHH--HHHHHHHHHHHH
Confidence 77888999999999998888877765544 47778888889988887665 33455555 346667766655
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q 007717 555 TEIEMKRIKKLKEKFKLIHEQFISH 579 (591)
Q Consensus 555 l~~e~~~~~~~~~kF~~i~~~~~~~ 579 (591)
--..+.++..-|..|+.+.++|...
T Consensus 181 ~L~~L~~~~~dq~afa~~~~~ll~~ 205 (282)
T PF06213_consen 181 DLDGLRDSLDDQAAFARAARDLLED 205 (282)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5666777778889999988887766
No 40
>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=36.54 E-value=55 Score=35.55 Aligned_cols=68 Identities=25% Similarity=0.362 Sum_probs=38.4
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcCCCcccCCccccC-CCCceEeec
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLSPPACTLDGFILG-GSPFFTSVP 82 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g~~~~L~~~llG-~~pFFvsvp 82 (591)
.+.||+.| ++.+--+.....+++.+...+...|+|.||.|+. .....+.++.. +| +.+|++|--
T Consensus 79 ad~vl~vv-D~~~~~~~~d~~i~~~l~~~~~piilVvNK~D~~----~~~~~~~~~~~----------lg~~~~~~vSa~ 143 (429)
T TIGR03594 79 ADVILFVV-DGREGLTPEDEEIAKWLRKSGKPVILVANKIDGK----KEDAVAAEFYS----------LGFGEPIPISAE 143 (429)
T ss_pred CCEEEEEE-eCCCCCCHHHHHHHHHHHHhCCCEEEEEECccCC----cccccHHHHHh----------cCCCCeEEEeCC
Confidence 34455555 4542223333445555555678899999999998 43333333321 22 257788775
Q ss_pred CCCC
Q 007717 83 SGRV 86 (591)
Q Consensus 83 ~~R~ 86 (591)
.|++
T Consensus 144 ~g~g 147 (429)
T TIGR03594 144 HGRG 147 (429)
T ss_pred cCCC
Confidence 5443
No 41
>cd01893 Miro1 Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
Probab=36.52 E-value=63 Score=29.88 Aligned_cols=44 Identities=14% Similarity=0.106 Sum_probs=31.5
Q ss_pred CCCceEEEEeccCC-ch-hh--hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS-DW-SN--ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An-D~-AN--SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+.-+++||++...+ +- -+ ..|.+.+++.-| ..--|+|.||.|+.
T Consensus 69 ~~ad~~ilv~d~~~~~s~~~~~~~~~~~i~~~~~-~~pviiv~nK~Dl~ 116 (166)
T cd01893 69 RKANVICLVYSVDRPSTLERIRTKWLPLIRRLGV-KVPIILVGNKSDLR 116 (166)
T ss_pred ccCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCC-CCCEEEEEEchhcc
Confidence 34578889887665 33 22 246777887655 67789999999997
No 42
>TIGR00959 ffh signal recognition particle protein. This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.
Probab=36.20 E-value=2e+02 Score=32.34 Aligned_cols=131 Identities=25% Similarity=0.267 Sum_probs=75.3
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcCCCcccCCccccCCCCceEeecC
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLSPPACTLDGFILGGSPFFTSVPS 83 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g~~~~L~~~llG~~pFFvsvp~ 83 (591)
|.-++|.|.+.. ..++...|+.......-|=.|+||+|-- .++..+..+....+.|+. |+++.-
T Consensus 213 p~e~lLVvda~t---gq~~~~~a~~f~~~v~i~giIlTKlD~~----~~~G~~lsi~~~~~~PI~---------fi~~Ge 276 (428)
T TIGR00959 213 PDEILLVVDAMT---GQDAVNTAKTFNERLGLTGVVLTKLDGD----ARGGAALSVRSVTGKPIK---------FIGVGE 276 (428)
T ss_pred CceEEEEEeccc---hHHHHHHHHHHHhhCCCCEEEEeCccCc----ccccHHHHHHHHHCcCEE---------EEeCCC
Confidence 555677776432 3577778887776666788899999977 666667766665555544 777743
Q ss_pred CCCCCCCccccCChHHHHHHHhhhhhhHHHHHHHHh-CCCCc---hhhhhh--cChhHHHHHHHHHHH-------HHHHh
Q 007717 84 GRVGTGHDSVYSSNEEFKQAIFIREMEDITSLEEKL-GRSLS---KQERSR--IGVSKLRSFLEELLQ-------KRYMD 150 (591)
Q Consensus 84 ~R~g~~~D~v~~s~~~f~~ai~~~~~~d~~~le~~~-~~~~~---~~~~~~--~G~~~L~~~Ln~~L~-------~hyr~ 150 (591)
|. .|.-.-+++.|...|- ..-|...|-++. ..... ++...+ -|.-.|..|++|+-+ ..+..
T Consensus 277 -~i---~dl~~f~p~~~~~~iL--g~gD~~~l~e~~~~~~~~~~~~~~~~~~~~~~f~l~d~~~q~~~~~kmG~~~~~~~ 350 (428)
T TIGR00959 277 -KI---DDLEPFHPERMASRIL--GMGDILSLVEKAQEVVDEEEAKKLAEKMKKGQFDLEDFLEQLRQIKKMGPLSSLLK 350 (428)
T ss_pred -Ch---hhCccCCHHHHHHHHh--CCCChHHHHHHHHHhhCHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHH
Confidence 22 3433445666665553 234444443332 11111 112222 155567777777644 56666
Q ss_pred hhhhhH
Q 007717 151 SVPMII 156 (591)
Q Consensus 151 ~lP~i~ 156 (591)
.+|.+-
T Consensus 351 ~~Pg~~ 356 (428)
T TIGR00959 351 MIPGMG 356 (428)
T ss_pred hCcCcc
Confidence 777643
No 43
>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=33.81 E-value=68 Score=30.77 Aligned_cols=43 Identities=16% Similarity=0.120 Sum_probs=30.0
Q ss_pred CCceEEEEeccCC-c-hhhh-hHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCS-D-WSNA-TTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~An-D-~ANS-daLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-+++|+++.-++ + +.+. .|+..+++..|... .|+|.||.|+.
T Consensus 72 ~a~~iilv~D~t~~~s~~~i~~~~~~~~~~~~~~~-pilVgnK~Dl~ 117 (182)
T cd04128 72 DAVAILFMFDLTRKSTLNSIKEWYRQARGFNKTAI-PILVGTKYDLF 117 (182)
T ss_pred CCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCC-EEEEEEchhcc
Confidence 4567888888766 2 2221 57777877766543 49999999986
No 44
>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=33.23 E-value=80 Score=29.15 Aligned_cols=44 Identities=20% Similarity=0.172 Sum_probs=32.0
Q ss_pred CCceEEEEeccCC-c-hhh-hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCS-D-WSN-ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~An-D-~AN-SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-+++|++....+ + +.+ ..+++..++..+.+.-.|.|.||.|+.
T Consensus 75 ~ad~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~p~iiv~nK~Dl~ 121 (167)
T cd01867 75 GAMGIILVYDITDEKSFENIRNWMRNIEEHASEDVERMLVGNKCDME 121 (167)
T ss_pred CCCEEEEEEECcCHHHHHhHHHHHHHHHHhCCCCCcEEEEEECcccc
Confidence 4467888876654 2 111 357777777778888899999999997
No 45
>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=32.94 E-value=41 Score=31.08 Aligned_cols=40 Identities=23% Similarity=0.187 Sum_probs=25.1
Q ss_pred EEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 7 IILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 7 IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+||.|-++++--.+....+...+...+...|.|+||.|+.
T Consensus 15 ~vl~V~D~~~~~~~~~~~l~~~~~~~~~p~iiv~NK~Dl~ 54 (156)
T cd01859 15 VVLEVLDARDPELTRSRKLERYVLELGKKLLIVLNKADLV 54 (156)
T ss_pred EEEEEeeCCCCcccCCHHHHHHHHhCCCcEEEEEEhHHhC
Confidence 4444555653222333455555555678899999999985
No 46
>PRK09866 hypothetical protein; Provisional
Probab=32.70 E-value=9.7e+02 Score=29.03 Aligned_cols=39 Identities=18% Similarity=0.154 Sum_probs=27.6
Q ss_pred EEEEeccCCc-hhhhhHHHHHHhcCCCCC--ceEEEeeccccc
Q 007717 7 IILCLEDCSD-WSNATTRRVVMQIDPELK--RTIIVSTKLDTK 46 (591)
Q Consensus 7 IILaV~~AnD-~ANSdaLklakeVDP~g~--RTIgV~TKlD~m 46 (591)
+||+|-++++ +...| ..+++.+=..+. ..|.|+||+|..
T Consensus 261 vVLFVVDat~~~s~~D-eeIlk~Lkk~~K~~PVILVVNKIDl~ 302 (741)
T PRK09866 261 AVLAVLDYTQLKSISD-EEVREAILAVGQSVPLYVLVNKFDQQ 302 (741)
T ss_pred EEEEEEeCCCCCChhH-HHHHHHHHhcCCCCCEEEEEEcccCC
Confidence 6888888884 44444 456665555553 789999999986
No 47
>cd01882 BMS1 Bms1. Bms1 is an essential, evolutionarily conserved, nucleolar protein. Its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. Bms1, the putative endonuclease Rc11, and the essential U3 small nucleolar RNA form a stable subcomplex that is believed to control an early step in the formation of the 40S subumit. The C-terminal domain of Bms1 contains a GTPase-activating protein (GAP) that functions intramolecularly. It is believed that Rc11 activates Bms1 by acting as a guanine-nucleotide exchange factor (GEF) to promote GDP/GTP exchange, and that activated (GTP-bound) Bms1 delivers Rc11 to the preribosomes.
Probab=32.41 E-value=73 Score=31.98 Aligned_cols=39 Identities=26% Similarity=0.191 Sum_probs=23.9
Q ss_pred EEEEeccCC-chhhhhHHHHHHhcCCCCC-ceEEEeeccccc
Q 007717 7 IILCLEDCS-DWSNATTRRVVMQIDPELK-RTIIVSTKLDTK 46 (591)
Q Consensus 7 IILaV~~An-D~ANSdaLklakeVDP~g~-RTIgV~TKlD~m 46 (591)
++|.|-+++ ++...+ .++...+...|. +.|+|+||.|+.
T Consensus 106 vVllviDa~~~~~~~~-~~i~~~l~~~g~p~vi~VvnK~D~~ 146 (225)
T cd01882 106 LVLLLIDASFGFEMET-FEFLNILQVHGFPRVMGVLTHLDLF 146 (225)
T ss_pred EEEEEEecCcCCCHHH-HHHHHHHHHcCCCeEEEEEeccccC
Confidence 345555565 665444 345555544444 467799999987
No 48
>KOG1916 consensus Nuclear protein, contains WD40 repeats [General function prediction only]
Probab=32.15 E-value=1.1e+03 Score=29.58 Aligned_cols=34 Identities=21% Similarity=0.445 Sum_probs=25.7
Q ss_pred hHHHHhhhhhhh-----------ccccCCccHHHHHHHHHHHHHH
Q 007717 461 TRLADLLDNTLW-----------NRRLAPSSERIVYALVQQIFHG 494 (591)
Q Consensus 461 ~~~~~~~e~~l~-----------~r~l~~~s~~iV~~l~~~iF~~ 494 (591)
.-+.+++|.++. +|.+.|.-...|...++++|..
T Consensus 965 ~~~~~~~e~ti~~El~~tv~P~v~rs~~p~~~q~~~s~itkl~~~ 1009 (1283)
T KOG1916|consen 965 KELNAMFEKTIKKELAKTVGPCVARSVEPVIEQTVSSAITKLFQR 1009 (1283)
T ss_pred HHHHHHHHHHHHHHHHhhcchhhhhhhHHHHHHHHHHHHHHHHHh
Confidence 345666666663 7888888888899999998864
No 49
>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=31.39 E-value=93 Score=26.36 Aligned_cols=46 Identities=20% Similarity=0.173 Sum_probs=30.3
Q ss_pred CCceEEEEeccCCchhhhhHH----HHHHhcCCCCCceEEEeeccccccc
Q 007717 3 HREFIILCLEDCSDWSNATTR----RVVMQIDPELKRTIIVSTKLDTKIP 48 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANSdaL----klakeVDP~g~RTIgV~TKlD~ml~ 48 (591)
..+.+|+++...++....+.. .......-.+...|+|.||.|+.-+
T Consensus 68 ~~~~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivv~nk~D~~~~ 117 (157)
T cd00882 68 GADGIILVYDVTDRESFENVKEWLLLILINKEGENIPIILVGNKIDLPEE 117 (157)
T ss_pred CCCEEEEEEECcCHHHHHHHHHHHHHHHHhhccCCCcEEEEEeccccccc
Confidence 456778888777632222222 3445556667999999999999833
No 50
>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=31.36 E-value=89 Score=28.79 Aligned_cols=44 Identities=20% Similarity=0.277 Sum_probs=30.9
Q ss_pred CCCceEEEEeccCC-c-hhh-hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS-D-WSN-ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An-D-~AN-SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
++-+++|+++...+ + ..+ ..|+...++..|+ ..-|.|.||.|+-
T Consensus 71 ~~~d~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~-~p~ivv~nK~Dl~ 117 (161)
T cd04124 71 HKAHACILVFDVTRKITYKNLSKWYEELREYRPE-IPCIVVANKIDLD 117 (161)
T ss_pred CCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCC-CcEEEEEECccCc
Confidence 45678899888766 2 222 3467777776554 6789999999984
No 51
>PF10167 NEP: Uncharacterised conserved protein; InterPro: IPR019320 This entry represents the uncharacterised protein family UPF0402. It contains a characteristic NEP sequence motif. Their function is not known.
Probab=31.34 E-value=1.1e+02 Score=28.52 Aligned_cols=29 Identities=28% Similarity=0.537 Sum_probs=19.2
Q ss_pred HHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHhHhhcc
Q 007717 143 LLQKRYMDSVPMIIPLLEKEYCSTTRKLNEINKELST 179 (591)
Q Consensus 143 ~L~~hyr~~lP~i~~~L~~~~~~~~~eL~~~~~el~~ 179 (591)
.|++|+|.+||.+.. ++ .++.++..++..
T Consensus 34 rlQeHvrkslP~lv~-~k-------~~v~~~~~~~~g 62 (118)
T PF10167_consen 34 RLQEHVRKSLPKLVE-LK-------KEVQELSQELQG 62 (118)
T ss_pred HHHHHHHHHhHHHHH-HH-------HHHHHHHHHhcc
Confidence 367899999999885 33 344455555543
No 52
>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=31.32 E-value=63 Score=29.24 Aligned_cols=44 Identities=11% Similarity=0.162 Sum_probs=31.7
Q ss_pred CCceEEEEeccCC-c---hhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCS-D---WSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~An-D---~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-.++|+++..++ + .+-....++.+.....+...|.|.||.|+.
T Consensus 66 ~~~~~i~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~piiiv~nK~D~~ 113 (158)
T cd00878 66 NTNGIIFVVDSSDRERIEEAKEELHKLLNEEELKGVPLLIFANKQDLP 113 (158)
T ss_pred cCCEEEEEEECCCHHHHHHHHHHHHHHHhCcccCCCcEEEEeeccCCc
Confidence 4567888887775 2 333445566666667788899999999986
No 53
>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=30.99 E-value=89 Score=28.59 Aligned_cols=45 Identities=13% Similarity=0.144 Sum_probs=31.2
Q ss_pred CCCceEEEEeccCC-c-hh-hhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS-D-WS-NATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An-D-~A-NSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
..-+++|+++..++ + .. =..+++..++....+.--|+|.||.|+.
T Consensus 73 ~~~~~ii~v~d~~~~~s~~~l~~~~~~~~~~~~~~~~~iiv~nK~Dl~ 120 (166)
T cd01869 73 RGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLT 120 (166)
T ss_pred CcCCEEEEEEECcCHHHHHhHHHHHHHHHHhCCCCCcEEEEEEChhcc
Confidence 34678899987766 3 11 1236666666665567789999999986
No 54
>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=30.67 E-value=73 Score=27.74 Aligned_cols=37 Identities=19% Similarity=0.354 Sum_probs=27.5
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeec
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTK 42 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TK 42 (591)
-+.||++|. +++-.+.+-.++.+++. .+...|.|+||
T Consensus 80 ~d~ii~vv~-~~~~~~~~~~~~~~~l~-~~~~~i~v~NK 116 (116)
T PF01926_consen 80 SDLIIYVVD-ASNPITEDDKNILRELK-NKKPIILVLNK 116 (116)
T ss_dssp ESEEEEEEE-TTSHSHHHHHHHHHHHH-TTSEEEEEEES
T ss_pred CCEEEEEEE-CCCCCCHHHHHHHHHHh-cCCCEEEEEcC
Confidence 467788888 55433455667778887 99999999998
No 55
>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=30.52 E-value=50 Score=31.65 Aligned_cols=43 Identities=19% Similarity=0.130 Sum_probs=27.8
Q ss_pred CCceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
..+++|+.+...+++.. ....+.+++.-.+...|.|+||.|+.
T Consensus 88 ~~d~~ilV~d~~~~~~~-~~~~~~~~~~~~~~p~iiv~NK~Dl~ 130 (194)
T cd01891 88 MVDGVLLLVDASEGPMP-QTRFVLKKALELGLKPIVVINKIDRP 130 (194)
T ss_pred hcCEEEEEEECCCCccH-HHHHHHHHHHHcCCCEEEEEECCCCC
Confidence 34677877776554322 22333444445678899999999986
No 56
>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=30.17 E-value=1e+02 Score=27.11 Aligned_cols=61 Identities=16% Similarity=0.171 Sum_probs=37.6
Q ss_pred CCCceEEEEeccCC-ch-hh-hhHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcCC
Q 007717 2 QHREFIILCLEDCS-DW-SN-ATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLSP 62 (591)
Q Consensus 2 ~~~n~IILaV~~An-D~-AN-SdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g 62 (591)
++-+++|+++...+ +. .. ..++...+..-..+.-.|+|.||.|+--+.-....++.++...
T Consensus 71 ~~~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~~~~~~~~~~~~~~~~~ 134 (159)
T cd00154 71 RGAHGAILVYDITNRESFENLDKWLKELKEYAPENIPIILVGNKIDLEDQRQVSTEEAQQFAKE 134 (159)
T ss_pred cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCcEEEEEEcccccccccccHHHHHHHHHH
Confidence 45678888888776 42 22 2255555555545678899999999951222234555565543
No 57
>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction
Probab=30.02 E-value=1.2e+02 Score=29.58 Aligned_cols=68 Identities=18% Similarity=0.267 Sum_probs=44.4
Q ss_pred hhhhhhhhhHHHHHHHHhhcccchhhhhchhhHH---HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 007717 512 LMPVVDKLPALLREDLESAFEGDLDNVFDITNLR---HSLSQQKSDTEIEMKRIKKLKEKFKLIHEQFISH 579 (591)
Q Consensus 512 L~P~~~~l~~~lr~~l~~~~d~~l~~vF~~~~~r---~~L~~~~~~l~~e~~~~~~~~~kF~~i~~~~~~~ 579 (591)
|+=+--+|..|=..++-.||++--+=...+...| .+|..+|++||.++++++..-++=-.+..|+..+
T Consensus 64 L~eVS~~f~~ysE~dik~AYe~A~~lQ~~L~~~re~E~qLr~rRD~LErrl~~l~~tierAE~l~sqi~vv 134 (159)
T PF05384_consen 64 LAEVSRNFDRYSEEDIKEAYEEAHELQVRLAMLREREKQLRERRDELERRLRNLEETIERAENLVSQIGVV 134 (159)
T ss_pred HHHHHhhhcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444445555555566666655443333333333 5789999999999999999888877777766544
No 58
>PRK11058 GTPase HflX; Provisional
Probab=29.66 E-value=78 Score=35.30 Aligned_cols=44 Identities=16% Similarity=0.274 Sum_probs=30.8
Q ss_pred CCceEEEEeccCC-chhhhh--HHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCS-DWSNAT--TRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~An-D~ANSd--aLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-+.||+.+..++ ++.... +.++.+++...+...|.|.||.|+.
T Consensus 276 ~ADlIL~VvDaS~~~~~e~l~~v~~iL~el~~~~~pvIiV~NKiDL~ 322 (426)
T PRK11058 276 QATLLLHVVDAADVRVQENIEAVNTVLEEIDAHEIPTLLVMNKIDML 322 (426)
T ss_pred cCCEEEEEEeCCCccHHHHHHHHHHHHHHhccCCCCEEEEEEcccCC
Confidence 3456666666555 543332 4577788876778899999999986
No 59
>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=29.61 E-value=1e+02 Score=28.24 Aligned_cols=45 Identities=9% Similarity=0.022 Sum_probs=32.9
Q ss_pred CCCceEEEEeccCC-ch-hh-hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS-DW-SN-ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An-D~-AN-SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
..-+++||++...+ +- -+ ..|+...+...+.+.--|.|.||.|+.
T Consensus 74 ~~~d~~llv~d~~~~~s~~~~~~~~~~i~~~~~~~~p~ivv~nK~Dl~ 121 (165)
T cd01864 74 RSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIGNKCDLE 121 (165)
T ss_pred ccCCEEEEEEECcCHHHHHhHHHHHHHHHHhCCCCCcEEEEEECcccc
Confidence 34578999998887 32 21 257777777666666679999999997
No 60
>PRK01889 GTPase RsgA; Reviewed
Probab=29.52 E-value=84 Score=34.07 Aligned_cols=38 Identities=18% Similarity=0.097 Sum_probs=22.6
Q ss_pred EEeccCC-chhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 9 LCLEDCS-DWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 9 LaV~~An-D~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+-|.+++ |+....--++.-.+=-.|.+-|.|+||.|+.
T Consensus 117 liV~s~~p~~~~~~ldr~L~~a~~~~i~piIVLNK~DL~ 155 (356)
T PRK01889 117 FIVCSLNHDFNLRRIERYLALAWESGAEPVIVLTKADLC 155 (356)
T ss_pred EEEEecCCCCChhHHHHHHHHHHHcCCCEEEEEEChhcC
Confidence 3344445 7776443333222222456779999999998
No 61
>PRK00093 GTP-binding protein Der; Reviewed
Probab=29.17 E-value=1.3e+02 Score=32.96 Aligned_cols=41 Identities=15% Similarity=0.282 Sum_probs=25.7
Q ss_pred CCceEEEEeccCC--chhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCS--DWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~An--D~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-++||++|...+ ....-...+..++. +...|.|+||.|+.
T Consensus 80 ~ad~il~vvd~~~~~~~~~~~~~~~l~~~---~~piilv~NK~D~~ 122 (435)
T PRK00093 80 EADVILFVVDGRAGLTPADEEIAKILRKS---NKPVILVVNKVDGP 122 (435)
T ss_pred hCCEEEEEEECCCCCCHHHHHHHHHHHHc---CCcEEEEEECccCc
Confidence 3466777777654 22222233444443 78999999999976
No 62
>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=28.86 E-value=69 Score=31.57 Aligned_cols=43 Identities=14% Similarity=0.049 Sum_probs=30.3
Q ss_pred CCceEEEEeccCCchhhhhHHHHHHhcCCCCCc-eEEEeeccccc
Q 007717 3 HREFIILCLEDCSDWSNATTRRVVMQIDPELKR-TIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANSdaLklakeVDP~g~R-TIgV~TKlD~m 46 (591)
.-+++||.|.....+ ...+.++++.++-.|.. -|+|+||+|+.
T Consensus 88 ~~D~~ilVvda~~g~-~~~~~~~~~~~~~~~~~~iIvviNK~D~~ 131 (195)
T cd01884 88 QMDGAILVVSATDGP-MPQTREHLLLARQVGVPYIVVFLNKADMV 131 (195)
T ss_pred hCCEEEEEEECCCCC-cHHHHHHHHHHHHcCCCcEEEEEeCCCCC
Confidence 346777877754454 35566677777777764 67999999986
No 63
>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=28.55 E-value=77 Score=29.46 Aligned_cols=39 Identities=15% Similarity=0.153 Sum_probs=24.8
Q ss_pred EEEEeccCC-chhh--hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 7 IILCLEDCS-DWSN--ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 7 IILaV~~An-D~AN--SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+||.|-++. -+.+ ..-.+..+.. ..+...|.|+||.|+.
T Consensus 11 ~il~VvD~~~p~~~~~~~i~~~l~~~-~~~~p~ilVlNKiDl~ 52 (157)
T cd01858 11 VVIQVLDARDPMGTRCKHVEEYLKKE-KPHKHLIFVLNKCDLV 52 (157)
T ss_pred EEEEEEECCCCccccCHHHHHHHHhc-cCCCCEEEEEEchhcC
Confidence 566666676 3332 2334444443 3357899999999996
No 64
>COG1160 Predicted GTPases [General function prediction only]
Probab=28.40 E-value=98 Score=35.02 Aligned_cols=66 Identities=23% Similarity=0.267 Sum_probs=46.7
Q ss_pred EEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcC-CCcccCCccccCCCCceEeecCCC
Q 007717 7 IILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLS-PPACTLDGFILGGSPFFTSVPSGR 85 (591)
Q Consensus 7 IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~-g~~~~L~~~llG~~pFFvsvp~~R 85 (591)
+||+|-++..=-+.+=..+|+-+=+....+|+|++|.|.. .....+.+|-+ | +| .||=||--.||
T Consensus 86 vilfvVD~~~Git~~D~~ia~~Lr~~~kpviLvvNK~D~~----~~e~~~~efyslG---------~g-~~~~ISA~Hg~ 151 (444)
T COG1160 86 VILFVVDGREGITPADEEIAKILRRSKKPVILVVNKIDNL----KAEELAYEFYSLG---------FG-EPVPISAEHGR 151 (444)
T ss_pred EEEEEEeCCCCCCHHHHHHHHHHHhcCCCEEEEEEcccCc----hhhhhHHHHHhcC---------CC-CceEeehhhcc
Confidence 5677777763234444566666668889999999999999 55555556654 3 44 68888888877
Q ss_pred C
Q 007717 86 V 86 (591)
Q Consensus 86 ~ 86 (591)
|
T Consensus 152 G 152 (444)
T COG1160 152 G 152 (444)
T ss_pred C
Confidence 7
No 65
>PF04026 SpoVG: SpoVG; InterPro: IPR007170 This is a stage V sporulation protein G. It is essential for sporulation and specific to stage V sporulation in Bacillus megaterium and Bacillus subtilis []. In B. subtilis, expression decreases after 30-60 minutes of cold shock [].; GO: 0030435 sporulation resulting in formation of a cellular spore; PDB: 2IA9_F 2I9X_B 2I9Z_A.
Probab=28.06 E-value=47 Score=29.11 Aligned_cols=36 Identities=22% Similarity=0.295 Sum_probs=22.8
Q ss_pred cCCCCceEeecCCCCC--CCCccccCChHHHHHHHhhh
Q 007717 72 LGGSPFFTSVPSGRVG--TGHDSVYSSNEEFKQAIFIR 107 (591)
Q Consensus 72 lG~~pFFvsvp~~R~g--~~~D~v~~s~~~f~~ai~~~ 107 (591)
.|++.+||+.|+.+.+ .-+|.++.-+++||+.|.+.
T Consensus 38 eg~~GlFVaMPs~k~~~g~y~Di~~Pitke~Re~i~~a 75 (84)
T PF04026_consen 38 EGEKGLFVAMPSRKSKDGEYKDICHPITKEFREQIEEA 75 (84)
T ss_dssp EETTEEEEE--EEE-TTS-EEESEEESSHHHHHHHHHH
T ss_pred ECCCCcEEECCCcCCCCCCEEEEEEECCHHHHHHHHHH
Confidence 5666689999995543 24676677788888866554
No 66
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=27.81 E-value=3.6e+02 Score=28.15 Aligned_cols=93 Identities=17% Similarity=0.335 Sum_probs=57.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhhchhhhhhhh----hHHHHHHHHhh----cccc---hhhhhchhhHHHHHHh
Q 007717 482 RIVYALVQQIFHGIREYFLASAELKFNCFLLMPVVDKL----PALLREDLESA----FEGD---LDNVFDITNLRHSLSQ 550 (591)
Q Consensus 482 ~iV~~l~~~iF~~IR~~~~~~~~~Kfn~fFL~P~~~~l----~~~lr~~l~~~----~d~~---l~~vF~~~~~r~~L~~ 550 (591)
..=..||.+.|...|.++-.--++| ||+--++ +..+|.+|.+| .=+. .-+..|+..-++.++.
T Consensus 69 ~~GReLA~kf~eeLrg~VGhiERmK------~PiGHDvEhiD~elvrkEl~nAlvRAGLktL~~v~~~~d~ke~~ee~ke 142 (290)
T COG4026 69 RVGRELAEKFFEELRGMVGHIERMK------IPIGHDVEHIDVELVRKELKNALVRAGLKTLQRVPEYMDLKEDYEELKE 142 (290)
T ss_pred chhHHHHHHHHHHHHHhhhhhheec------cCCCCCccccCHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHH
Confidence 4456899999999999998888888 4665544 34455555543 2222 2344455555555555
Q ss_pred hhhhHHHH----HHHHHHHHHHHHHHHHHHHhhh
Q 007717 551 QKSDTEIE----MKRIKKLKEKFKLIHEQFISHH 580 (591)
Q Consensus 551 ~~~~l~~e----~~~~~~~~~kF~~i~~~~~~~~ 580 (591)
+.+++..| ++.+++++.++.++.++|.+-.
T Consensus 143 kl~E~~~EkeeL~~eleele~e~ee~~erlk~le 176 (290)
T COG4026 143 KLEELQKEKEELLKELEELEAEYEEVQERLKRLE 176 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55544443 3556777777777777766544
No 67
>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=27.60 E-value=1.1e+02 Score=28.83 Aligned_cols=43 Identities=12% Similarity=0.162 Sum_probs=29.2
Q ss_pred CCceEEEEeccCC--chhh-hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCS--DWSN-ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~An--D~AN-SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-+++||++...+ .+.+ ..|++..++..| +...|+|.||.|+.
T Consensus 73 ~~d~iilv~d~~~~~s~~~~~~~~~~i~~~~~-~~piilv~nK~Dl~ 118 (193)
T cd04118 73 GAKAAIVCYDLTDSSSFERAKFWVKELQNLEE-HCKIYLCGTKSDLI 118 (193)
T ss_pred CCCEEEEEEECCCHHHHHHHHHHHHHHHhcCC-CCCEEEEEEccccc
Confidence 4567777776544 2333 246777777665 46789999999986
No 68
>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=27.58 E-value=1.1e+02 Score=27.75 Aligned_cols=45 Identities=13% Similarity=0.045 Sum_probs=30.1
Q ss_pred CCCceEEEEeccCC-c-hhh-hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS-D-WSN-ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An-D-~AN-SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
...+++|+++...+ + ..+ ..++...+..-....--|+|.||.|+.
T Consensus 71 ~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iivv~nK~D~~ 118 (161)
T cd04113 71 RGAAGALLVYDITNRTSFEALPTWLSDARALASPNIVVILVGNKSDLA 118 (161)
T ss_pred cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEEchhcc
Confidence 34578899988877 2 222 245565665544455689999999996
No 69
>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=27.19 E-value=85 Score=32.74 Aligned_cols=41 Identities=15% Similarity=0.075 Sum_probs=31.7
Q ss_pred CceEEEEeccCC-chhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 4 REFIILCLEDCS-DWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 4 ~n~IILaV~~An-D~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
-.+++.++.++. .+...| +++.+++-. +.-.|.|+||.|+.
T Consensus 115 vh~~ly~i~~~~~~l~~~D-~~~lk~l~~-~v~vi~VinK~D~l 156 (276)
T cd01850 115 VHACLYFIEPTGHGLKPLD-IEFMKRLSK-RVNIIPVIAKADTL 156 (276)
T ss_pred eEEEEEEEeCCCCCCCHHH-HHHHHHHhc-cCCEEEEEECCCcC
Confidence 357888888887 776665 667777753 67899999999997
No 70
>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=26.78 E-value=1.6e+02 Score=28.81 Aligned_cols=58 Identities=21% Similarity=0.355 Sum_probs=34.7
Q ss_pred CCCceEEEEeccCC-c-hhhh-hHHHHHHhc---CCCCCceEEEeecccccccCCCchhhHhhh
Q 007717 2 QHREFIILCLEDCS-D-WSNA-TTRRVVMQI---DPELKRTIIVSTKLDTKIPQFARASDVEVF 59 (591)
Q Consensus 2 ~~~n~IILaV~~An-D-~ANS-daLklakeV---DP~g~RTIgV~TKlD~ml~qfd~gtDv~~~ 59 (591)
+.-+++||++..++ + +.+. .+++...+. .+.+...|.|.||.|+.-.......++..+
T Consensus 79 ~~ad~iilv~D~~~~~S~~~~~~~~~~i~~~~~~~~~~~piiivgNK~Dl~~~~~~~~~~~~~~ 142 (198)
T cd04142 79 RNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQQRHRFAPRHVLSVL 142 (198)
T ss_pred ccCCEEEEEEECCCHHHHHHHHHHHHHHHHhcccCCCCCCEEEEEECccccccccccHHHHHHH
Confidence 45678899888876 2 2221 123333332 467889999999999973333334444333
No 71
>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=26.57 E-value=2e+02 Score=25.77 Aligned_cols=44 Identities=14% Similarity=0.200 Sum_probs=29.2
Q ss_pred CCceEEEEeccCC-c-hh-hhhHHHHHHhc-CC----CCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCS-D-WS-NATTRRVVMQI-DP----ELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~An-D-~A-NSdaLklakeV-DP----~g~RTIgV~TKlD~m 46 (591)
..+++|+++...+ + +. -..|++..++. .| ....-|+|.||.|+.
T Consensus 72 ~~d~~ilv~D~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~piilv~nK~Dl~ 123 (168)
T cd04119 72 DTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKIDLT 123 (168)
T ss_pred cCCEEEEEEECCCHHHHHhHHHHHHHHHHhccccccCCCceEEEEEEchhcc
Confidence 4578899987665 2 11 12355555543 33 567899999999986
No 72
>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=26.31 E-value=86 Score=28.06 Aligned_cols=41 Identities=7% Similarity=0.125 Sum_probs=25.6
Q ss_pred CCceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
..+++|+.+...+ ..+ ...+..++.-.+...|+|+||.|+.
T Consensus 74 ~~d~vi~v~d~~~-~~~--~~~~~~~~~~~~~~~iiv~NK~Dl~ 114 (158)
T cd01879 74 KPDLIVNVVDATN-LER--NLYLTLQLLELGLPVVVALNMIDEA 114 (158)
T ss_pred CCcEEEEEeeCCc-chh--HHHHHHHHHHcCCCEEEEEehhhhc
Confidence 4567777776544 222 1233334443567899999999997
No 73
>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=26.23 E-value=1.2e+02 Score=27.32 Aligned_cols=45 Identities=13% Similarity=0.073 Sum_probs=30.0
Q ss_pred CCCceEEEEeccCC--chhhhh-HHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS--DWSNAT-TRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An--D~ANSd-aLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+.-+++|+++...+ .+.+.. ++..+++......--|+|.||.|+.
T Consensus 72 ~~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iivv~nK~D~~ 119 (163)
T cd01860 72 RGAAAAIVVYDITSEESFEKAKSWVKELQRNASPNIIIALVGNKADLE 119 (163)
T ss_pred ccCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccc
Confidence 34578999998876 343332 4455555554445568899999976
No 74
>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=26.20 E-value=93 Score=28.33 Aligned_cols=59 Identities=12% Similarity=0.151 Sum_probs=34.1
Q ss_pred CCCceEEEEeccCC-chhh---hhHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcCC
Q 007717 2 QHREFIILCLEDCS-DWSN---ATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLSP 62 (591)
Q Consensus 2 ~~~n~IILaV~~An-D~AN---SdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g 62 (591)
+..+++|+++...+ +.-. ....++.+...-.+...|.|+||.|+. +. ....++..++..
T Consensus 72 ~~~~~~v~vvd~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~NK~D~~-~~-~~~~~~~~~~~~ 134 (167)
T cd04160 72 AECHAIIYVIDSTDRERFEESKSALEKVLRNEALEGVPLLILANKQDLP-DA-LSVEEIKEVFQD 134 (167)
T ss_pred CCCCEEEEEEECchHHHHHHHHHHHHHHHhChhhcCCCEEEEEEccccc-cC-CCHHHHHHHhcc
Confidence 34578888887765 3221 122333333344578899999999975 11 122345566653
No 75
>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=26.12 E-value=70 Score=32.83 Aligned_cols=40 Identities=20% Similarity=0.504 Sum_probs=24.8
Q ss_pred ceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 5 EFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 5 n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+.+|+.+ +++++...+ ..+...+...+...|.|+||.|+.
T Consensus 81 Dvvl~Vv-D~~~~~~~~-~~i~~~l~~~~~p~ilV~NK~Dl~ 120 (270)
T TIGR00436 81 DLILFVV-DSDQWNGDG-EFVLTKLQNLKRPVVLTRNKLDNK 120 (270)
T ss_pred CEEEEEE-ECCCCCchH-HHHHHHHHhcCCCEEEEEECeeCC
Confidence 4455554 555443332 444444545577899999999986
No 76
>TIGR01425 SRP54_euk signal recognition particle protein SRP54. This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.
Probab=26.03 E-value=4.6e+02 Score=29.63 Aligned_cols=59 Identities=12% Similarity=0.161 Sum_probs=35.3
Q ss_pred CCceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcCCCcccCC
Q 007717 3 HREFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLSPPACTLD 68 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g~~~~L~ 68 (591)
+|..++|.+.+.... ++...|+...-...-|-.|+||+|-- .+|--+..+..-.+.|+.
T Consensus 212 ~p~e~lLVlda~~Gq---~a~~~a~~F~~~~~~~g~IlTKlD~~----argG~aLs~~~~t~~PI~ 270 (429)
T TIGR01425 212 QPDNIIFVMDGSIGQ---AAEAQAKAFKDSVDVGSVIITKLDGH----AKGGGALSAVAATKSPII 270 (429)
T ss_pred CCcEEEEEeccccCh---hHHHHHHHHHhccCCcEEEEECccCC----CCccHHhhhHHHHCCCeE
Confidence 466777877755422 22344444433334577899999998 777766655554444433
No 77
>PF09763 Sec3_C: Exocyst complex component Sec3; InterPro: IPR019160 The exocyst complex is composed of 8 subunits: Exoc1, Exoc2, Exoc3, Exoc4, Exoc5, Exoc6, Exoc7 and Exoc8. This entry represents the subunit Exoc1 (Sec3). Sec3 binds to the C-terminal cytoplasmic domain of GLYT1 (glycine transporter protein 1). Sec3 is the exocyst component that is closest to the plasma membrane docking site and it serves as a spatial landmark in the plasma membrane for incoming secretory vesicles. Sec3 is recruited to the sites of polarised membrane growth through its interaction with Rho1p, a small GTP-binding protein.
Probab=25.92 E-value=1.2e+03 Score=27.73 Aligned_cols=266 Identities=14% Similarity=0.158 Sum_probs=0.0
Q ss_pred hhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHhHhhcccChHHHHHHHHHHHHHHHHHHhHhhcccccCCC
Q 007717 133 VSKLRSFLEELLQKRYMDSVPMIIPLLEKEYCSTTRKLNEINKELSTLDEVKLKEKGRVFHDLFLTKLSLLLKGTVVAPP 212 (591)
Q Consensus 133 ~~~L~~~Ln~~L~~hyr~~lP~i~~~L~~~~~~~~~eL~~~~~el~~~d~~~l~~~~l~~i~~F~~~~~~lI~Gt~~~~P 212 (591)
.+.|..+++..+...-..+++-+. .|...-.+++..+-+-+...+..+...+.+.|.+-|+..+..
T Consensus 399 ~~~l~~~v~~~~~~dp~~~~~~l~------------~le~~~~~~~~s~~~fl~~~L~~l~~~~k~~f~~fv~~Qi~~-- 464 (701)
T PF09763_consen 399 ENELQSFVDWAEKNDPLQCVSMLV------------YLERYIKSLEQSNQSFLSNLLQKLQVRLKRLFDKFVDEQIKS-- 464 (701)
T ss_pred HHHHHHHHHHHHccCchhHHHHHH------------HHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--
Q ss_pred cCcccchHHHhhhcCcccCCCCCCCCcccCCCCCccccchh--HHHHHHHhhHhhhccc--cCCCCCH-HHHHHHhccCC
Q 007717 213 DKFGETLQNERINGGAFVGTDGLQFPHKLIPNAGMRLYGGA--QYHRAMAEFRFMVGGI--KCPPITR-EEIVNACGVED 287 (591)
Q Consensus 213 ~~~G~Tl~eEr~~~g~~~~~~g~~~~~~~v~~~~~eL~GGA--qi~Rif~EF~~~v~~i--~~~~ls~-eeI~~Aig~~~ 287 (591)
....+..... -+--.+..|+..+..+ -+....+ .+++..+
T Consensus 465 -------------------------------ie~~k~~~k~r~GVl~~i~~fp~f~~~~E~~~~~~~~~~~~r~~v---- 509 (701)
T PF09763_consen 465 -------------------------------IEETKVSKKKRKGVLPFIKKFPEFVKRVESMFSGAERAREDRSLV---- 509 (701)
T ss_pred -------------------------------HHHhccccCCCCccchHHHHHHHHHHHHHHHHccccccchHHHHH----
Q ss_pred CCCCCchhhHHHHHHHHHHHHhhcchHHHHHhhHHHHHHHHHHHH-------------------HHHHhhhcccccccHH
Q 007717 288 IHDGTNYSRTACVIAVAKARDTFEPFLHQLGCRLLHILKRLLPIS-------------------IYLLQKEGEYLSGHEV 348 (591)
Q Consensus 288 ~~~g~~~~~Afe~Iak~qir~l~~P~L~cv~~Rl~~V~~eL~~I~-------------------~~~~~k~~~~l~ryp~ 348 (591)
+.|.+-|++. +++-|-.++ ..++. +..|-.
T Consensus 510 -------d~aY~kl~~a-------------------~~~~l~~~a~~~~~~~~~~~~~dk~~~~~~v~~-----leN~~~ 558 (701)
T PF09763_consen 510 -------DKAYEKLVRA-------------------MFDSLERIAKLSPKNSGSQDPEDKEKLNYHVVL-----LENYHH 558 (701)
T ss_pred -------HHHHHHHHHH-------------------HHHHHHHhcccCcccccccCccccccchhhHHH-----HHHHHH
Q ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHHHHHhhhhhhhcccccCCcchhhhhhhcccCCccchhhccccCCCCccccccccc
Q 007717 349 FLRRVASAFN-NFAESTERACREKCMEDLVSTTRYVTWSLHNKNRAGLRQFLDSFGSTEQSAVLSNSLSMPLCQESSFVS 427 (591)
Q Consensus 349 l~~~v~~~~~-~fi~e~~~~ck~~~~d~l~s~t~~v~w~L~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 427 (591)
|.+.+...-. .-+++..+.++....+.+. .|++|-|+ ..+.++.+=+.+.+.+-..+.+...+....=|
T Consensus 559 ~~e~l~~~~~~~~l~~~~~~A~~~~~~~~~---~Y~~~~l~----r~~~kL~~F~~gve~l~~~~~~~ei~~~~~yS--- 628 (701)
T PF09763_consen 559 FYEELSQLKINSVLEEFRKEAKQIYDEHLE---AYVTFLLR----RPFGKLLDFFEGVEALLQTVSPEEISYQAAYS--- 628 (701)
T ss_pred HHHHHhhccchhhHHHHHHHHHHHHHHHHH---HHHHHHHh----ccHHHHHHHHHHHHHHHhccCchhcccchhcc---
Q ss_pred cccccCCCCCcccccccccccCCCCCCccchhhhHHHHhhhhhhhccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 007717 428 VANEKHDTKPRTDVKLSQVASGVDSSSSVQTTETRLADLLDNTLWNRRLAPSSERIVYALVQQIFHGIREYFLASAELKF 507 (591)
Q Consensus 428 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~r~l~~~s~~iV~~l~~~iF~~IR~~~~~~~~~Kf 507 (591)
+..|-.++..- +..-|...+.+++..+-.||...+...
T Consensus 629 --------------------------------k~~l~kvl~~y---------~~kev~k~i~~l~krveKHf~~~~~~~- 666 (701)
T PF09763_consen 629 --------------------------------KQELKKVLKSY---------PSKEVRKGIEALYKRVEKHFSRDADDP- 666 (701)
T ss_pred --------------------------------HHHHHHHHHhC---------ChHHHHHHHHHHHHHHHHHcCCccccc-
Q ss_pred hhhchhhhhhhhhHHHHHHHHhhcc
Q 007717 508 NCFLLMPVVDKLPALLREDLESAFE 532 (591)
Q Consensus 508 n~fFL~P~~~~l~~~lr~~l~~~~d 532 (591)
-+=-.+.+.+|..++.++-..|+
T Consensus 667 --~~~~~Ll~~vW~~~q~~~i~~~~ 689 (701)
T PF09763_consen 667 --SFEEDLLQVVWSAMQEEFIRQYE 689 (701)
T ss_pred --cchhhHHHHHHHHHHHHHHHHHH
No 78
>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=25.62 E-value=1.3e+02 Score=26.87 Aligned_cols=44 Identities=18% Similarity=0.133 Sum_probs=30.3
Q ss_pred CCceEEEEeccCC-chhh--hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCS-DWSN--ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~An-D~AN--SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-+++|+++...+ +... ..+++-.++..+...-.|+|.||.|+.
T Consensus 72 ~~~~~i~v~d~~~~~s~~~~~~~~~~i~~~~~~~~piiiv~nK~D~~ 118 (162)
T cd04123 72 DADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKIDLE 118 (162)
T ss_pred cCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccc
Confidence 3467788877666 4322 234555666677677899999999986
No 79
>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=25.53 E-value=1.2e+02 Score=27.90 Aligned_cols=44 Identities=25% Similarity=0.380 Sum_probs=31.6
Q ss_pred CCCceEEEEeccCC--chhhh--hHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS--DWSNA--TTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An--D~ANS--daLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+.-+++||+....+ .+-+. .|++..++.-| ..-.|+|.||.|+.
T Consensus 68 ~~~d~~ilv~d~~~~~s~~~~~~~~~~~i~~~~~-~~piilv~nK~Dl~ 115 (174)
T smart00174 68 PDTDVFLICFSVDSPASFENVKEKWYPEVKHFCP-NTPIILVGTKLDLR 115 (174)
T ss_pred CCCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCC-CCCEEEEecChhhh
Confidence 34578899888766 33332 36676666655 57889999999997
No 80
>PRK03003 GTP-binding protein Der; Reviewed
Probab=25.04 E-value=1.2e+02 Score=33.91 Aligned_cols=69 Identities=20% Similarity=0.302 Sum_probs=39.4
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcCCCcccCCccccCCCCceEeecC
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLSPPACTLDGFILGGSPFFTSVPS 83 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g~~~~L~~~llG~~pFFvsvp~ 83 (591)
-+.||+.|...+-...++ ..++..+...+...|+|.||.|+. ....+...+.. +. +| .||+||--.
T Consensus 118 aD~il~VvD~~~~~s~~~-~~i~~~l~~~~~piilV~NK~Dl~----~~~~~~~~~~~-----~g---~~-~~~~iSA~~ 183 (472)
T PRK03003 118 ADAVLFVVDATVGATATD-EAVARVLRRSGKPVILAANKVDDE----RGEADAAALWS-----LG---LG-EPHPVSALH 183 (472)
T ss_pred CCEEEEEEECCCCCCHHH-HHHHHHHHHcCCCEEEEEECccCC----ccchhhHHHHh-----cC---CC-CeEEEEcCC
Confidence 456677766655322222 345555556788999999999986 22223322221 11 33 478888766
Q ss_pred CCC
Q 007717 84 GRV 86 (591)
Q Consensus 84 ~R~ 86 (591)
|++
T Consensus 184 g~g 186 (472)
T PRK03003 184 GRG 186 (472)
T ss_pred CCC
Confidence 554
No 81
>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=25.02 E-value=1.4e+02 Score=27.17 Aligned_cols=44 Identities=16% Similarity=0.204 Sum_probs=29.8
Q ss_pred CCCceEEEEeccCC-c-hhh-hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS-D-WSN-ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An-D-~AN-SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
..-+++|+++...+ + +.+ ..|+...++.+| ..-.|.|.||.|+.
T Consensus 74 ~~~d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~-~~p~ilv~nK~Dl~ 120 (164)
T cd04101 74 ESPSVFILVYDVSNKASFENCSRWVNKVRTASK-HMPGVLVGNKMDLA 120 (164)
T ss_pred CCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCC-CCCEEEEEECcccc
Confidence 34577888776655 2 221 346677776664 47889999999985
No 82
>PF11553 DUF3231: Protein of unknown function (DUF3231); InterPro: IPR021617 This bacterial family of proteins has no known function. ; PDB: 2RBD_B.
Probab=24.90 E-value=2.1e+02 Score=27.27 Aligned_cols=57 Identities=14% Similarity=0.209 Sum_probs=45.4
Q ss_pred chhhhhhcChhHHHHHHHHHHHHHHHhhh--hhhHHHHHHHHHHHHHHHHHHhHhhccc
Q 007717 124 SKQERSRIGVSKLRSFLEELLQKRYMDSV--PMIIPLLEKEYCSTTRKLNEINKELSTL 180 (591)
Q Consensus 124 ~~~~~~~~G~~~L~~~Ln~~L~~hyr~~l--P~i~~~L~~~~~~~~~eL~~~~~el~~~ 180 (591)
...+...+=..+..+++...+.++|.+.+ |++++.|+.-+...++++..+++.+.+.
T Consensus 15 ~~~Ei~~Lw~~~~~~~~~~~~~~~f~~~~~D~dik~~l~~~~~~~~~~i~~l~~ll~~e 73 (166)
T PF11553_consen 15 NASEIGNLWNNYMANYMSICLLQYFLQVAEDKDIKKLLKKGLDLSQKQIEQLEKLLKEE 73 (166)
T ss_dssp BHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 33344456667888999999999999988 8999999998888888888888877763
No 83
>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=24.87 E-value=84 Score=27.96 Aligned_cols=39 Identities=15% Similarity=0.078 Sum_probs=24.6
Q ss_pred EEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 8 ILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 8 ILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
++.|-++.+-.++...++.+.++.-+...|.|.||.|++
T Consensus 85 ~~~v~d~~~~~~~~~~~~~~~l~~~~~~vi~v~nK~D~~ 123 (170)
T cd01876 85 VVLLIDSRHGPTEIDLEMLDWLEELGIPFLVVLTKADKL 123 (170)
T ss_pred EEEEEEcCcCCCHhHHHHHHHHHHcCCCEEEEEEchhcC
Confidence 344544441123344455666666667789999999998
No 84
>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=24.67 E-value=1e+02 Score=28.16 Aligned_cols=43 Identities=21% Similarity=0.251 Sum_probs=27.8
Q ss_pred CceEEEEeccCC-c-hhh--hhHHHHHHhcCC--CCCceEEEeeccccc
Q 007717 4 REFIILCLEDCS-D-WSN--ATTRRVVMQIDP--ELKRTIIVSTKLDTK 46 (591)
Q Consensus 4 ~n~IILaV~~An-D-~AN--SdaLklakeVDP--~g~RTIgV~TKlD~m 46 (591)
-+++|+++...+ + +-. ..+.+..++..| .+...|.|+||.|+.
T Consensus 79 ~d~vi~v~D~~~~~~~~~~~~~~~~~l~~~~~~~~~~p~ivv~NK~Dl~ 127 (170)
T cd01898 79 TRLLLHVIDLSGDDDPVEDYKTIRNELELYNPELLEKPRIVVLNKIDLL 127 (170)
T ss_pred CCEEEEEEecCCCCCHHHHHHHHHHHHHHhCccccccccEEEEEchhcC
Confidence 357777776654 2 211 234555566655 467889999999986
No 85
>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=24.55 E-value=89 Score=27.77 Aligned_cols=39 Identities=15% Similarity=0.280 Sum_probs=24.6
Q ss_pred ceEEEEeccCC--chhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 5 EFIILCLEDCS--DWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 5 n~IILaV~~An--D~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+.+|+.+...+ ...+....+.+++ .+...|+|+||.|+.
T Consensus 78 d~ii~v~d~~~~~~~~~~~~~~~~~~---~~~piiiv~nK~D~~ 118 (157)
T cd01894 78 DVILFVVDGREGLTPADEEIAKYLRK---SKKPVILVVNKVDNI 118 (157)
T ss_pred CEEEEEEeccccCCccHHHHHHHHHh---cCCCEEEEEECcccC
Confidence 45566665543 2333333444544 458899999999998
No 86
>PRK00089 era GTPase Era; Reviewed
Probab=24.24 E-value=1.2e+02 Score=31.10 Aligned_cols=42 Identities=10% Similarity=0.211 Sum_probs=26.8
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
-++|++.+...+.|...+ ..+++.+-..+...|.|+||.|+.
T Consensus 85 ~D~il~vvd~~~~~~~~~-~~i~~~l~~~~~pvilVlNKiDl~ 126 (292)
T PRK00089 85 VDLVLFVVDADEKIGPGD-EFILEKLKKVKTPVILVLNKIDLV 126 (292)
T ss_pred CCEEEEEEeCCCCCChhH-HHHHHHHhhcCCCEEEEEECCcCC
Confidence 456666665444455443 444444444467899999999997
No 87
>PRK13259 regulatory protein SpoVG; Reviewed
Probab=24.06 E-value=1.2e+02 Score=27.35 Aligned_cols=41 Identities=20% Similarity=0.245 Sum_probs=27.6
Q ss_pred cCCCCceEeecCCCCC--CCCccccCChHHHHHHHhhhhhhHH
Q 007717 72 LGGSPFFTSVPSGRVG--TGHDSVYSSNEEFKQAIFIREMEDI 112 (591)
Q Consensus 72 lG~~pFFvsvp~~R~g--~~~D~v~~s~~~f~~ai~~~~~~d~ 112 (591)
.|++..||+.|+.+.+ .-+|.+..-+++||+.|...=++.|
T Consensus 38 eg~~GlFVaMPs~k~~~g~y~DI~~Pit~e~Re~i~~aVl~aY 80 (94)
T PRK13259 38 EGNNGLFIAMPSKRTPDGEFRDIAHPINSDTREKIQDAILKEY 80 (94)
T ss_pred ECCCCeEEECcCcCCCCCcEEEEEccCCHHHHHHHHHHHHHHH
Confidence 4555679999996653 2567777777888876655544444
No 88
>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=23.61 E-value=67 Score=31.05 Aligned_cols=41 Identities=15% Similarity=0.231 Sum_probs=30.9
Q ss_pred CCceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+++.||+.|.+.+ |. ..|.+..++=--|...|.|+||.|..
T Consensus 78 ~~D~ii~VvDa~~-l~--r~l~l~~ql~e~g~P~vvvlN~~D~a 118 (156)
T PF02421_consen 78 KPDLIIVVVDATN-LE--RNLYLTLQLLELGIPVVVVLNKMDEA 118 (156)
T ss_dssp SSSEEEEEEEGGG-HH--HHHHHHHHHHHTTSSEEEEEETHHHH
T ss_pred CCCEEEEECCCCC-HH--HHHHHHHHHHHcCCCEEEEEeCHHHH
Confidence 4566666665555 43 44677888888899999999999998
No 89
>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=23.32 E-value=1.3e+02 Score=27.43 Aligned_cols=45 Identities=11% Similarity=0.162 Sum_probs=27.9
Q ss_pred CCCceEEEEeccCC-chh---hhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS-DWS---NATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An-D~A---NSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+..+++|+++..++ +.- ......+.++....+.-.|+|.||.|+.
T Consensus 65 ~~~~~ii~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~piiiv~nK~Dl~ 113 (158)
T cd04151 65 SNTDAIIYVVDSTDRDRLGTAKEELHAMLEEEELKGAVLLVFANKQDMP 113 (158)
T ss_pred cCCCEEEEEEECCCHHHHHHHHHHHHHHHhchhhcCCcEEEEEeCCCCC
Confidence 34577888887555 321 1223334444443467789999999986
No 90
>COG4917 EutP Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=23.05 E-value=60 Score=31.16 Aligned_cols=47 Identities=23% Similarity=0.257 Sum_probs=29.9
Q ss_pred EEEEeccCC-chhhhhHHHHHHhcCCCCCceEEEeecccccccCCCchhhH---hhhcCC
Q 007717 7 IILCLEDCS-DWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDV---EVFLSP 62 (591)
Q Consensus 7 IILaV~~An-D~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv---~~~L~g 62 (591)
+|.-|..|| -|..-. ++-.||--.-+|||+||.|+- . ..|+ ..||.-
T Consensus 67 vi~~v~~and~~s~f~----p~f~~~~~k~vIgvVTK~DLa----e-d~dI~~~~~~L~e 117 (148)
T COG4917 67 VIIYVHAANDPESRFP----PGFLDIGVKKVIGVVTKADLA----E-DADISLVKRWLRE 117 (148)
T ss_pred eeeeeecccCccccCC----cccccccccceEEEEeccccc----c-hHhHHHHHHHHHH
Confidence 556677777 333222 233466666799999999986 3 4444 578864
No 91
>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=23.04 E-value=2e+02 Score=26.18 Aligned_cols=61 Identities=11% Similarity=0.234 Sum_probs=33.9
Q ss_pred CCCceEEEEeccCC-c-hhhh-hHH-HHHHhcC---CCCCceEEEeecccccccCCCchhhHhhhcCC
Q 007717 2 QHREFIILCLEDCS-D-WSNA-TTR-RVVMQID---PELKRTIIVSTKLDTKIPQFARASDVEVFLSP 62 (591)
Q Consensus 2 ~~~n~IILaV~~An-D-~ANS-daL-klakeVD---P~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g 62 (591)
+.-+++|+++...+ + ..+. .+. .+.+... |...-.|.|.||.|+.-+.=-...++..++..
T Consensus 71 ~~~d~~i~v~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~ilv~nK~Dl~~~~~~~~~~~~~~~~~ 138 (172)
T cd01862 71 RGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPSDPENFPFVVLGNKIDLEEKRQVSTKKAQQWCQS 138 (172)
T ss_pred cCCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCccCCCCceEEEEEECcccccccccCHHHHHHHHHH
Confidence 34578888887654 2 1222 222 2334344 45777899999999973211123445556543
No 92
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=22.97 E-value=1.8e+02 Score=27.24 Aligned_cols=39 Identities=18% Similarity=0.359 Sum_probs=31.6
Q ss_pred hhHHHHHHhhhhhHHHHHHHH----HHHHHHHHHHHHHHHhhh
Q 007717 542 TNLRHSLSQQKSDTEIEMKRI----KKLKEKFKLIHEQFISHH 580 (591)
Q Consensus 542 ~~~r~~L~~~~~~l~~e~~~~----~~~~~kF~~i~~~~~~~~ 580 (591)
..+...|+.+.+.|+.+++.+ ++++++|..+-+.+..+-
T Consensus 69 ~~~~~eL~er~E~Le~ri~tLekQe~~l~e~l~eLq~~i~~~l 111 (119)
T COG1382 69 EEAVDELEERKETLELRIKTLEKQEEKLQERLEELQSEIQKAL 111 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 467889999999999999777 668888888877776654
No 93
>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=22.87 E-value=1e+02 Score=32.16 Aligned_cols=41 Identities=17% Similarity=0.126 Sum_probs=29.6
Q ss_pred ceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 5 EFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 5 n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+++|+.|.....+ ...+.++.+.+.-.+...|+|+||+|+.
T Consensus 89 D~ailVVDa~~g~-~~~t~~~~~~~~~~~~p~ivviNK~D~~ 129 (270)
T cd01886 89 DGAVAVFDAVAGV-EPQTETVWRQADRYNVPRIAFVNKMDRT 129 (270)
T ss_pred CEEEEEEECCCCC-CHHHHHHHHHHHHcCCCEEEEEECCCCC
Confidence 4667766544455 3445677777777788999999999986
No 94
>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=22.83 E-value=1.5e+02 Score=26.66 Aligned_cols=45 Identities=11% Similarity=0.085 Sum_probs=29.5
Q ss_pred CCCceEEEEeccCC--chhhhh-HHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS--DWSNAT-TRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An--D~ANSd-aLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+.-+++|+++...+ .+.+.. ++...++.-+.+..-|.|.||.|+-
T Consensus 71 ~~~~~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilv~nK~D~~ 118 (161)
T cd01861 71 RDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLS 118 (161)
T ss_pred ccCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCEEEEEEEChhcc
Confidence 34567788776655 344433 5555444444468899999999994
No 95
>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=22.63 E-value=1.7e+02 Score=30.44 Aligned_cols=60 Identities=13% Similarity=0.082 Sum_probs=36.0
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeecccccccCCCc-hhhHhhhcCCCc
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFAR-ASDVEVFLSPPA 64 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~-gtDv~~~L~g~~ 64 (591)
-+++|+++...+.+. ..+.++.+..+-.+...|+|+||+|..-..|.+ -.++.+.|..+.
T Consensus 95 aD~~IlVvda~~g~~-~~~~~i~~~~~~~~~P~iivvNK~D~~~a~~~~~~~~l~~~l~~~~ 155 (267)
T cd04169 95 VDSAVMVIDAAKGVE-PQTRKLFEVCRLRGIPIITFINKLDREGRDPLELLDEIEEELGIDC 155 (267)
T ss_pred CCEEEEEEECCCCcc-HHHHHHHHHHHhcCCCEEEEEECCccCCCCHHHHHHHHHHHHCCCc
Confidence 467888887665443 233455555566678899999999986222221 124445555444
No 96
>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.
Probab=22.25 E-value=95 Score=29.22 Aligned_cols=58 Identities=16% Similarity=0.179 Sum_probs=34.6
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcCCCcccCC
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLSPPACTLD 68 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g~~~~L~ 68 (591)
+..+||.|.+.+. .++++.+++.-....-+-.|+||+|.. .++..+.......+.|+.
T Consensus 113 ~~~~~lVv~~~~~---~~~~~~~~~~~~~~~~~~viltk~D~~----~~~g~~~~~~~~~~~p~~ 170 (173)
T cd03115 113 PDEVLLVVDAMTG---QDAVNQAKAFNEALGITGVILTKLDGD----ARGGAALSIRAVTGKPIK 170 (173)
T ss_pred CCeEEEEEECCCC---hHHHHHHHHHHhhCCCCEEEEECCcCC----CCcchhhhhHHHHCcCeE
Confidence 5667787776432 233344444432222588899999998 777666655544445433
No 97
>PF08700 Vps51: Vps51/Vps67; InterPro: IPR014812 The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved in recycling of proteins from endosomes to the late Golgi. Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1 [].
Probab=22.19 E-value=4.7e+02 Score=21.87 Aligned_cols=49 Identities=27% Similarity=0.430 Sum_probs=34.5
Q ss_pred cCChHHHHHHHhhhhhhHHHHHHHHhCCCCchhhhhhcChhHHHHHHHHHHHHHHHhhh
Q 007717 94 YSSNEEFKQAIFIREMEDITSLEEKLGRSLSKQERSRIGVSKLRSFLEELLQKRYMDSV 152 (591)
Q Consensus 94 ~~s~~~f~~ai~~~~~~d~~~le~~~~~~~~~~~~~~~G~~~L~~~Ln~~L~~hyr~~l 152 (591)
++...-|++.+...++.+++.++.++ .-.+.....-|.+.+-++|++-|
T Consensus 6 fd~~~~~~~~l~~~s~~~i~~~~~~L----------~~~i~~~~~eLr~~V~~nY~~fI 54 (87)
T PF08700_consen 6 FDVDEYFKDLLKNSSIKEIRQLENKL----------RQEIEEKDEELRKLVYENYRDFI 54 (87)
T ss_pred CCHHHHHHHHHhhCCHHHHHHHHHHH----------HHHHHHHHHHHHHHHHhhHHHHH
Confidence 55566777777788888888887653 12345566778888888888766
No 98
>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=22.12 E-value=1.5e+02 Score=28.64 Aligned_cols=44 Identities=11% Similarity=0.354 Sum_probs=33.7
Q ss_pred CCCceEEEEeccCC--chhh--hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS--DWSN--ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An--D~AN--SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
..-+++|||..-.+ -..+ ..|.+.+++..|+ .--|.|.||.|+.
T Consensus 75 ~~ad~~ilvyDit~~~Sf~~~~~~w~~~i~~~~~~-~piilVgNK~DL~ 122 (182)
T cd04172 75 PDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPN-TKMLLVGCKSDLR 122 (182)
T ss_pred CCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCC-CCEEEEeEChhhh
Confidence 34578999998776 3444 4688888888774 6788999999987
No 99
>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=21.91 E-value=1e+02 Score=30.17 Aligned_cols=42 Identities=17% Similarity=0.148 Sum_probs=23.7
Q ss_pred ceEEEEeccCCchhhhhHHHHHHhcCCCCC-ceEEEeeccccc
Q 007717 5 EFIILCLEDCSDWSNATTRRVVMQIDPELK-RTIIVSTKLDTK 46 (591)
Q Consensus 5 n~IILaV~~AnD~ANSdaLklakeVDP~g~-RTIgV~TKlD~m 46 (591)
+++||+|......-...+......++-.+. +.|+|+||.|+.
T Consensus 108 D~~llVvd~~~~~~~~~t~~~l~~~~~~~~~~iiivvNK~Dl~ 150 (203)
T cd01888 108 DGALLLIAANEPCPQPQTSEHLAALEIMGLKHIIIVQNKIDLV 150 (203)
T ss_pred CEEEEEEECCCCCCCcchHHHHHHHHHcCCCcEEEEEEchhcc
Confidence 567777775542222233333333332333 478899999987
No 100
>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=21.71 E-value=1.2e+02 Score=29.81 Aligned_cols=42 Identities=17% Similarity=0.216 Sum_probs=28.6
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
-+++|+.+...+.+. ..+.++.+.+...+.-.|+|+||.|..
T Consensus 95 aD~~llVvD~~~~~~-~~~~~~~~~~~~~~~p~iiviNK~D~~ 136 (213)
T cd04167 95 SDGVVLVVDVVEGVT-SNTERLIRHAILEGLPIVLVINKIDRL 136 (213)
T ss_pred CCEEEEEEECCCCCC-HHHHHHHHHHHHcCCCEEEEEECcccC
Confidence 467888886655332 234455555555677899999999986
No 101
>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=21.68 E-value=1.6e+02 Score=26.45 Aligned_cols=45 Identities=9% Similarity=0.130 Sum_probs=28.4
Q ss_pred CCCceEEEEeccCC-c-hhhh-hHHHHHHhc---CCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS-D-WSNA-TTRRVVMQI---DPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An-D-~ANS-daLklakeV---DP~g~RTIgV~TKlD~m 46 (591)
..-+++|+++..++ + +.++ .+++.+.+. ...+...|+|.||.|+.
T Consensus 67 ~~~d~ii~v~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~iiv~NK~Dl~ 117 (162)
T cd04157 67 KNIQGIIFVIDSSDRLRLVVVKDELELLLNHPDIKHRRVPILFFANKMDLP 117 (162)
T ss_pred ccCCEEEEEEeCCcHHHHHHHHHHHHHHHcCcccccCCCCEEEEEeCcccc
Confidence 35577888877665 2 2222 244444332 23578899999999997
No 102
>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=21.50 E-value=1.3e+02 Score=29.15 Aligned_cols=30 Identities=20% Similarity=0.309 Sum_probs=21.6
Q ss_pred chhhhh--HHHHHHhcCCCCCceEEEeeccccccc
Q 007717 16 DWSNAT--TRRVVMQIDPELKRTIIVSTKLDTKIP 48 (591)
Q Consensus 16 D~ANSd--aLklakeVDP~g~RTIgV~TKlD~ml~ 48 (591)
++...+ +++.+++. +.+.|.|.||.|+..+
T Consensus 91 ~~~~~d~~~~~~l~~~---~~~~ilV~nK~D~~~~ 122 (197)
T cd04104 91 RFSSNDVKLAKAIQCM---GKKFYFVRTKVDRDLS 122 (197)
T ss_pred CCCHHHHHHHHHHHHh---CCCEEEEEecccchhh
Confidence 554444 55666665 7899999999999743
No 103
>PHA02699 hypothetical protein; Provisional
Probab=21.45 E-value=8.3e+02 Score=27.38 Aligned_cols=70 Identities=23% Similarity=0.265 Sum_probs=49.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhchhhhhhhhhHHHHHHHHhhcccchhhhhchhhHHHHHHhhhhhHHHHHHHHHH
Q 007717 485 YALVQQIFHGIREYFLASAELKFNCFLLMPVVDKLPALLREDLESAFEGDLDNVFDITNLRHSLSQQKSDTEIEMKRIKK 564 (591)
Q Consensus 485 ~~l~~~iF~~IR~~~~~~~~~Kfn~fFL~P~~~~l~~~lr~~l~~~~d~~l~~vF~~~~~r~~L~~~~~~l~~e~~~~~~ 564 (591)
-+|+.+--.+.|..|++.++- .|.=|.+-+++-++|-.+++..++=|=++- +|... |+.-+-+| .
T Consensus 357 ~sl~~~~l~~l~~~fa~~~e~-------~~~pdsl~~~me~dl~~~~~~~~elwd~i~----~~asd---lds~lp~c-e 421 (466)
T PHA02699 357 HSILEHGINGLFAMFAQCAEG-------TPHPDSLMARMEKDLQDLYARFSELWDDIL----EKAAD---LDSTLPRC-E 421 (466)
T ss_pred hHHHHHHHHHHHHHHhhcCCC-------CCCchHHHHHHHHHHHHHHHHHHHHHHHHH----HHHhh---hhhcCCcc-h
Confidence 456777888999999998887 788899999999999999887665443332 23333 33335555 5
Q ss_pred HHHHH
Q 007717 565 LKEKF 569 (591)
Q Consensus 565 ~~~kF 569 (591)
+-|||
T Consensus 422 ~ierf 426 (466)
T PHA02699 422 CIEKF 426 (466)
T ss_pred HHHHH
Confidence 66777
No 104
>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=20.99 E-value=1.8e+02 Score=26.48 Aligned_cols=43 Identities=12% Similarity=-0.019 Sum_probs=30.9
Q ss_pred CceEEEEeccCC-chh-h-hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 4 REFIILCLEDCS-DWS-N-ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 4 ~n~IILaV~~An-D~A-N-SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
-.++|+++..++ +-. + ..|++..++.-|.+.--|+|.||.|+.
T Consensus 76 ~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~pi~vv~nK~Dl~ 121 (165)
T cd01868 76 AVGALLVYDITKKQTFENVERWLKELRDHADSNIVIMLVGNKSDLR 121 (165)
T ss_pred CCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECcccc
Confidence 456888887776 222 2 236777778777777788999999986
No 105
>cd04135 Tc10 TC10 subfamily. TC10 is a Rho family protein that has been shown to induce microspike formation and neurite outgrowth in vitro. Its expression changes dramatically after peripheral nerve injury, suggesting an important role in promoting axonal outgrowth and regeneration. TC10 regulates translocation of insulin-stimulated GLUT4 in adipocytes and has also been shown to bind directly to Golgi COPI coat proteins. GTP-bound TC10 in vitro can bind numerous potential effectors. Depending on its subcellular localization and distinct functional domains, TC10 can differentially regulate two types of filamentous actin in adipocytes. TC10 mRNAs are highly expressed in three types of mouse muscle tissues: leg skeletal muscle, cardiac muscle, and uterus; they were also present in brain, with higher levels in adults than in newborns. TC10 has also been shown to play a role in regulating the expression of cystic fibrosis transmembrane conductance regulator (CFTR) through interacti
Probab=20.96 E-value=1.7e+02 Score=26.82 Aligned_cols=42 Identities=12% Similarity=0.292 Sum_probs=28.3
Q ss_pred CceEEEEeccCC--chhh--hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 4 REFIILCLEDCS--DWSN--ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 4 ~n~IILaV~~An--D~AN--SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
-+++||++...+ .+-+ ..|.+..++. ..+.--|+|.||.|+.
T Consensus 72 ~~~~ilv~~~~~~~s~~~~~~~~~~~l~~~-~~~~piivv~nK~Dl~ 117 (174)
T cd04135 72 TDVFLICFSVVNPASFQNVKEEWVPELKEY-APNVPYLLVGTQIDLR 117 (174)
T ss_pred CCEEEEEEECCCHHHHHHHHHHHHHHHHhh-CCCCCEEEEeEchhhh
Confidence 367888886655 2222 2366666666 4456678999999987
No 106
>PLN03108 Rab family protein; Provisional
Probab=20.93 E-value=1.7e+02 Score=28.65 Aligned_cols=44 Identities=11% Similarity=-0.026 Sum_probs=29.9
Q ss_pred CCceEEEEeccCC-chhhh--hHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCS-DWSNA--TTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~An-D~ANS--daLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-+++||++...+ +.-.. .|+..+++.......-|+|.||.|+.
T Consensus 78 ~ad~~vlv~D~~~~~s~~~l~~~~~~~~~~~~~~~piiiv~nK~Dl~ 124 (210)
T PLN03108 78 GAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKCDLA 124 (210)
T ss_pred cCCEEEEEEECCcHHHHHHHHHHHHHHHHhcCCCCcEEEEEECccCc
Confidence 3457888887776 43332 45555555555567789999999986
No 107
>PF04583 Baculo_p74: Baculoviridae p74 conserved region; InterPro: IPR007663 Baculoviruses are distinct from other virus families in that there are two viral phenotypes: budded virus (BV) and occlusion-derived virus (ODV). BVs disseminate viral infection throughout the tissues of the host and ODVs transmit baculovirus between insect hosts. GFP tagging experiments implicate p74 as an ODV envelope protein [, ].; GO: 0019058 viral infectious cycle
Probab=20.88 E-value=7e+02 Score=26.30 Aligned_cols=51 Identities=22% Similarity=0.269 Sum_probs=42.7
Q ss_pred CCCCchhhhhhcChhHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHH
Q 007717 120 GRSLSKQERSRIGVSKLRSFLEELLQKRYMDSVPMIIPLLEKEYCSTTRKL 170 (591)
Q Consensus 120 ~~~~~~~~~~~~G~~~L~~~Ln~~L~~hyr~~lP~i~~~L~~~~~~~~~eL 170 (591)
+|..+-.+.-.+|+..|-.-|...|.+-...-+|.++..|-+.-.+...+|
T Consensus 18 d~~~i~~I~~d~Gfd~l~~~lk~mlkkin~~liP~Lk~~ll~~s~~vt~rl 68 (249)
T PF04583_consen 18 DHALIMSIATDLGFDVLESALKSMLKKINTKLIPALKRMLLSTSRRVTVRL 68 (249)
T ss_pred hhHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence 577888999999999999999999999999999998887776555555444
No 108
>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=20.69 E-value=1.6e+02 Score=27.84 Aligned_cols=43 Identities=16% Similarity=0.380 Sum_probs=31.7
Q ss_pred CCceEEEEeccCC--chhhh--hHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCS--DWSNA--TTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~An--D~ANS--daLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-+++|||..-.+ ...+. .|++..++..|+ .--|.|.||.|+.
T Consensus 72 ~a~~~ilv~d~~~~~s~~~~~~~w~~~i~~~~~~-~piilvgnK~Dl~ 118 (175)
T cd01874 72 QTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPK-TPFLLVGTQIDLR 118 (175)
T ss_pred cCCEEEEEEECCCHHHHHHHHHHHHHHHHHhCCC-CCEEEEEECHhhh
Confidence 4578999998776 34444 377777766653 6779999999987
No 109
>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=20.67 E-value=1.7e+02 Score=27.23 Aligned_cols=44 Identities=18% Similarity=0.363 Sum_probs=30.7
Q ss_pred CCCceEEEEeccCC-c-hhh--hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS-D-WSN--ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An-D-~AN--SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+.-+++|++....+ + ..+ ..|++..++..| +.-.|.|.||.|+-
T Consensus 70 ~~a~~~i~v~d~~~~~sf~~~~~~~~~~~~~~~~-~~piilv~nK~Dl~ 117 (173)
T cd04130 70 PDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHNP-KAPIILVGTQADLR 117 (173)
T ss_pred CCCcEEEEEEECCCHHHHHHHHHHHHHHHHhhCC-CCCEEEEeeChhhc
Confidence 45678899887665 3 323 347777766544 46789999999985
No 110
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=20.65 E-value=2.3e+02 Score=25.40 Aligned_cols=59 Identities=12% Similarity=0.007 Sum_probs=34.5
Q ss_pred CCceEEEEeccCCchhhh---hHHHHHHhcCCCCCceEEEeecccccccCCCchhhHhhhcC
Q 007717 3 HREFIILCLEDCSDWSNA---TTRRVVMQIDPELKRTIIVSTKLDTKIPQFARASDVEVFLS 61 (591)
Q Consensus 3 ~~n~IILaV~~AnD~ANS---daLklakeVDP~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~ 61 (591)
.-+++|+++..++-++-. .|+....+.-..+.--|+|.||.|+.-+.--.-.++..+..
T Consensus 72 ~~d~~ilv~d~~~~~s~~~~~~~l~~~~~~~~~~~pivvv~nK~D~~~~~~~~~~~~~~~~~ 133 (164)
T smart00175 72 GAVGALLVYDITNRESFENLKNWLKELREYADPNVVIMLVGNKSDLEDQRQVSREEAEAFAE 133 (164)
T ss_pred CCCEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEEchhcccccCCCHHHHHHHHH
Confidence 457889999876522221 24444444443578899999999976211112344555553
No 111
>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=20.34 E-value=1.9e+02 Score=27.26 Aligned_cols=45 Identities=16% Similarity=0.046 Sum_probs=31.3
Q ss_pred CCCceEEEEeccCC-ch-hh-hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS-DW-SN-ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An-D~-AN-SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+.-+++|+.+...+ +- .+ ..|++..+..-+...--|+|.||.|+.
T Consensus 71 ~~~d~iilv~d~~~~~s~~~i~~~~~~i~~~~~~~~~~ivv~nK~Dl~ 118 (188)
T cd04125 71 RGAHGYLLVYDVTDQESFENLKFWINEINRYARENVIKVIVANKSDLV 118 (188)
T ss_pred cCCCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECCCCc
Confidence 35578888888766 32 11 236666666666666789999999986
No 112
>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=20.30 E-value=1e+02 Score=31.88 Aligned_cols=38 Identities=16% Similarity=0.043 Sum_probs=24.4
Q ss_pred EEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 7 IILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 7 IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
+||.|-+|.+.-++.-..+.+.+ .+...|+|+||.|+.
T Consensus 24 vVl~V~Dar~p~~~~~~~i~~~l--~~kp~IiVlNK~DL~ 61 (276)
T TIGR03596 24 VVIEVLDARIPLSSRNPMIDEIR--GNKPRLIVLNKADLA 61 (276)
T ss_pred EEEEEEeCCCCCCCCChhHHHHH--CCCCEEEEEEccccC
Confidence 55566667643334444444544 256789999999986
No 113
>COG1160 Predicted GTPases [General function prediction only]
Probab=20.25 E-value=1.9e+02 Score=32.84 Aligned_cols=106 Identities=24% Similarity=0.222 Sum_probs=62.8
Q ss_pred EEEEeccCC-chhhhhHHHHHHhcCCCCCceEEEeecccccccCCCc--hhhH--hhhcCCCcccCCccccCCCCceEee
Q 007717 7 IILCLEDCS-DWSNATTRRVVMQIDPELKRTIIVSTKLDTKIPQFAR--ASDV--EVFLSPPACTLDGFILGGSPFFTSV 81 (591)
Q Consensus 7 IILaV~~An-D~ANSdaLklakeVDP~g~RTIgV~TKlD~ml~qfd~--gtDv--~~~L~g~~~~L~~~llG~~pFFvsv 81 (591)
++|-|-+|. ....- =+++|.-+--.|.=.|.|++|.|++ ++ .+.. ..-|...-.-+ -+..-||||.
T Consensus 263 vvllviDa~~~~~~q-D~~ia~~i~~~g~~~vIvvNKWDl~----~~~~~~~~~~k~~i~~~l~~l----~~a~i~~iSA 333 (444)
T COG1160 263 VVLLVIDATEGISEQ-DLRIAGLIEEAGRGIVIVVNKWDLV----EEDEATMEEFKKKLRRKLPFL----DFAPIVFISA 333 (444)
T ss_pred EEEEEEECCCCchHH-HHHHHHHHHHcCCCeEEEEEccccC----CchhhHHHHHHHHHHHHhccc----cCCeEEEEEe
Confidence 455566666 44443 4678888888999999999999999 43 2111 11222211111 2234569998
Q ss_pred cCCCCCCCCccccCChHHHHHHHhhhhhhHHHHHHHHhCCCCchhhhhhcChhHHHHHHHHHHHHH
Q 007717 82 PSGRVGTGHDSVYSSNEEFKQAIFIREMEDITSLEEKLGRSLSKQERSRIGVSKLRSFLEELLQKR 147 (591)
Q Consensus 82 p~~R~g~~~D~v~~s~~~f~~ai~~~~~~d~~~le~~~~~~~~~~~~~~~G~~~L~~~Ln~~L~~h 147 (591)
-.|++- .+-|. +| . ..|+....++.|+-|-+.|+.-+..|
T Consensus 334 ~~~~~i---------~~l~~-~i-----------~-----~~~~~~~~ri~Ts~LN~~l~~a~~~~ 373 (444)
T COG1160 334 LTGQGL---------DKLFE-AI-----------K-----EIYECATRRISTSLLNRVLEDAVAKH 373 (444)
T ss_pred cCCCCh---------HHHHH-HH-----------H-----HHHHHhccccCHHHHHHHHHHHHHhC
Confidence 776651 11111 11 1 13556667999888877777766664
No 114
>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=20.25 E-value=1.8e+02 Score=29.73 Aligned_cols=44 Identities=16% Similarity=0.409 Sum_probs=33.0
Q ss_pred CCCceEEEEeccCC-c-hhh--hhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 2 QHREFIILCLEDCS-D-WSN--ATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 2 ~~~n~IILaV~~An-D-~AN--SdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
..-+++||+..-.+ + +.+ ..|.+.+++..|+ .--|+|.||.|+.
T Consensus 83 ~~ad~vIlVyDit~~~Sf~~~~~~w~~~i~~~~~~-~piilVgNK~DL~ 130 (232)
T cd04174 83 SDSDAVLLCFDISRPETVDSALKKWKAEIMDYCPS-TRILLIGCKTDLR 130 (232)
T ss_pred CCCcEEEEEEECCChHHHHHHHHHHHHHHHHhCCC-CCEEEEEECcccc
Confidence 34578899888877 3 333 3688888887774 5679999999986
No 115
>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=20.23 E-value=1.7e+02 Score=25.99 Aligned_cols=60 Identities=12% Similarity=0.113 Sum_probs=34.5
Q ss_pred CCceEEEEeccCC-chhh--hhHHHHHHhcCC-CCCceEEEeecccccccCCCchhhHhhhcCC
Q 007717 3 HREFIILCLEDCS-DWSN--ATTRRVVMQIDP-ELKRTIIVSTKLDTKIPQFARASDVEVFLSP 62 (591)
Q Consensus 3 ~~n~IILaV~~An-D~AN--SdaLklakeVDP-~g~RTIgV~TKlD~ml~qfd~gtDv~~~L~g 62 (591)
.-+++|+++..++ ++-. ..+........+ .+.-.+.|.||.|+.-...-.-.++..++..
T Consensus 70 ~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~p~ivv~nK~D~~~~~~~~~~~~~~~~~~ 133 (160)
T cd00876 70 QGDGFILVYSITDRESFEEIKGYREQILRVKDDEDIPIVLVGNKCDLENERQVSKEEGKALAKE 133 (160)
T ss_pred cCCEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCCcEEEEEECCcccccceecHHHHHHHHHH
Confidence 3467888887776 4321 223344444444 6788999999999983111122344555543
No 116
>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed
Probab=20.19 E-value=1.2e+03 Score=25.99 Aligned_cols=40 Identities=18% Similarity=0.318 Sum_probs=25.8
Q ss_pred CceEEEEeccCCchhhhhHHHHHHhcCCCCCceEEEeeccccc
Q 007717 4 REFIILCLEDCSDWSNATTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 4 ~n~IILaV~~AnD~ANSdaLklakeVDP~g~RTIgV~TKlD~m 46 (591)
-+++|+++..++.+... -.++..+ ..+...|.|.||.|+.
T Consensus 295 aD~il~VvD~s~~~s~~-~~~~l~~--~~~~piiiV~NK~DL~ 334 (449)
T PRK05291 295 ADLVLLVLDASEPLTEE-DDEILEE--LKDKPVIVVLNKADLT 334 (449)
T ss_pred CCEEEEEecCCCCCChh-HHHHHHh--cCCCCcEEEEEhhhcc
Confidence 45677766665533222 3444444 4567889999999997
No 117
>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=20.08 E-value=1.3e+02 Score=27.40 Aligned_cols=43 Identities=19% Similarity=0.249 Sum_probs=30.1
Q ss_pred CCceEEEEeccCC-chhhh---hHHHHHHhcCCCCCceEEEeeccccc
Q 007717 3 HREFIILCLEDCS-DWSNA---TTRRVVMQIDPELKRTIIVSTKLDTK 46 (591)
Q Consensus 3 ~~n~IILaV~~An-D~ANS---daLklakeVDP~g~RTIgV~TKlD~m 46 (591)
.-+++|+++...+ +.... .++....+.-| ....|+|.||.|+.
T Consensus 71 ~~~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~-~~p~ivv~nK~Dl~ 117 (171)
T cd00157 71 NTDVFLICFSVDSPSSFENVKTKWIPEIRHYCP-NVPIILVGTKIDLR 117 (171)
T ss_pred CCCEEEEEEECCCHHHHHHHHHHHHHHHHhhCC-CCCEEEEEccHHhh
Confidence 4578888888776 44333 35555555444 68889999999987
Done!