Query 033489
Match_columns 118
No_of_seqs 156 out of 1198
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 02:51:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033489.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033489hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10861 signal peptidase I; P 99.8 1.5E-19 3.3E-24 144.5 11.0 90 18-114 59-168 (324)
2 KOG3342 Signal peptidase I [In 99.8 7.4E-19 1.6E-23 127.3 9.5 103 1-103 1-104 (180)
3 TIGR02227 sigpep_I_bact signal 99.8 1.8E-18 3.9E-23 125.8 8.5 81 22-109 1-85 (163)
4 TIGR02228 sigpep_I_arch signal 99.7 1.9E-17 4.1E-22 120.7 11.4 75 32-107 16-91 (158)
5 PF00717 Peptidase_S24: Peptid 99.5 1.8E-13 4E-18 85.5 6.5 54 52-106 1-54 (70)
6 cd06530 S26_SPase_I The S26 Ty 99.4 6.1E-13 1.3E-17 86.3 6.8 51 50-100 2-56 (85)
7 TIGR02754 sod_Ni_protease nick 99.4 8.4E-13 1.8E-17 86.8 7.4 54 52-105 2-59 (90)
8 COG0681 LepB Signal peptidase 99.4 2.9E-13 6.3E-18 96.6 5.2 84 19-110 7-95 (166)
9 KOG0171 Mitochondrial inner me 99.4 2E-12 4.4E-17 94.8 7.3 73 30-109 22-99 (176)
10 cd06462 Peptidase_S24_S26 The 99.2 3.5E-10 7.6E-15 72.0 8.7 53 50-103 2-54 (84)
11 KOG1568 Mitochondrial inner me 99.1 2.8E-10 6.1E-15 83.4 6.0 56 50-105 33-98 (174)
12 cd06529 S24_LexA-like Peptidas 99.0 2.1E-09 4.7E-14 68.3 7.9 51 50-103 2-52 (81)
13 COG2932 Predicted transcriptio 98.8 1.5E-08 3.4E-13 76.1 7.5 55 50-106 125-179 (214)
14 PRK00215 LexA repressor; Valid 98.4 1E-06 2.2E-11 65.6 7.3 49 50-101 120-169 (205)
15 PRK10276 DNA polymerase V subu 98.4 9.4E-07 2E-11 62.6 6.6 48 50-100 53-101 (139)
16 PRK13838 conjugal transfer pil 98.4 3.4E-06 7.3E-11 62.5 8.7 35 74-108 48-102 (176)
17 PRK12423 LexA repressor; Provi 98.3 2.7E-06 5.9E-11 63.7 7.1 50 50-102 116-166 (202)
18 TIGR02771 TraF_Ti conjugative 98.2 7.5E-06 1.6E-10 60.4 8.1 52 52-109 28-99 (171)
19 TIGR00498 lexA SOS regulatory 98.2 6.6E-06 1.4E-10 61.0 7.4 49 50-101 113-162 (199)
20 PRK13884 conjugal transfer pep 97.7 0.00062 1.3E-08 50.5 10.1 35 75-109 49-103 (178)
21 COG1974 LexA SOS-response tran 97.7 0.00017 3.7E-09 54.6 7.1 51 50-102 114-165 (201)
22 PF10502 Peptidase_S26: Signal 96.1 0.0016 3.4E-08 46.3 0.0 33 76-108 21-66 (138)
23 COG0361 InfA Translation initi 87.6 0.6 1.3E-05 30.2 2.6 29 55-83 37-68 (75)
24 TIGR00008 infA translation ini 87.2 0.62 1.4E-05 29.6 2.5 22 62-83 45-66 (68)
25 PF01176 eIF-1a: Translation i 83.5 0.93 2E-05 28.0 2.0 11 77-87 42-52 (65)
26 cd05793 S1_IF1A S1_IF1A: Trans 81.2 1.4 3E-05 28.4 2.2 21 63-83 40-60 (77)
27 COG0681 LepB Signal peptidase 79.8 2.6 5.7E-05 29.4 3.4 17 93-109 139-155 (166)
28 PRK12442 translation initiatio 77.9 2.5 5.4E-05 28.1 2.6 22 62-83 47-68 (87)
29 smart00652 eIF1a eukaryotic tr 77.6 2.1 4.6E-05 27.9 2.2 21 63-83 45-65 (83)
30 TIGR02594 conserved hypothetic 76.9 9.2 0.0002 26.8 5.5 15 75-89 72-86 (129)
31 cd04456 S1_IF1A_like S1_IF1A_l 76.5 2.5 5.3E-05 27.3 2.3 21 63-83 40-61 (78)
32 PRK04012 translation initiatio 75.0 2.7 5.9E-05 28.5 2.3 21 63-83 61-81 (100)
33 cd04720 BAH_Orc1p_Yeast BAH, o 73.0 15 0.00033 27.1 6.0 43 75-117 51-94 (179)
34 COG1188 Ribosome-associated he 71.9 11 0.00024 25.7 4.6 38 73-112 45-88 (100)
35 PF04319 NifZ: NifZ domain; I 69.7 13 0.00028 24.0 4.4 29 58-86 1-35 (75)
36 PF09285 Elong-fact-P_C: Elong 66.6 12 0.00025 22.8 3.5 38 55-97 18-56 (56)
37 COG5131 URM1 Ubiquitin-like pr 65.4 8.4 0.00018 25.9 2.9 33 51-87 51-91 (96)
38 PF10000 ACT_3: ACT domain; I 64.6 3.8 8.3E-05 26.0 1.2 17 56-72 12-28 (72)
39 PF05257 CHAP: CHAP domain; I 61.9 36 0.00077 22.8 5.7 28 74-101 60-88 (124)
40 KOG4146 Ubiquitin-like protein 60.9 8.2 0.00018 26.1 2.3 34 50-87 55-96 (101)
41 PF14118 YfzA: YfzA-like prote 60.8 11 0.00024 25.4 2.8 16 52-67 29-44 (94)
42 PF05382 Amidase_5: Bacterioph 60.0 9.5 0.00021 27.5 2.7 38 51-88 49-87 (145)
43 cd05794 S1_EF-P_repeat_2 S1_EF 59.3 14 0.0003 22.5 2.9 38 55-97 18-56 (56)
44 COG3602 Uncharacterized protei 58.6 5.5 0.00012 28.1 1.2 17 56-72 12-28 (134)
45 PF15057 DUF4537: Domain of un 58.5 7.8 0.00017 26.9 2.0 20 53-72 47-66 (124)
46 cd04712 BAH_DCM_I BAH, or Brom 58.5 28 0.00062 24.3 4.8 37 76-112 5-54 (130)
47 smart00841 Elong-fact-P_C Elon 57.4 16 0.00034 22.3 2.9 38 55-97 18-56 (56)
48 PLN00208 translation initiatio 56.4 10 0.00022 27.5 2.3 24 62-85 71-94 (145)
49 cd04714 BAH_BAHCC1 BAH, or Bro 55.9 35 0.00076 23.3 4.9 28 77-104 4-32 (121)
50 PTZ00329 eukaryotic translatio 55.4 11 0.00023 27.6 2.3 24 62-85 71-94 (155)
51 COG4959 TraF Type IV secretory 53.7 4.2 9.1E-05 30.1 -0.1 19 92-110 82-100 (173)
52 COG0179 MhpD 2-keto-4-pentenoa 52.9 33 0.00072 27.0 4.9 30 61-90 224-255 (266)
53 PRK00276 infA translation init 52.4 15 0.00032 23.0 2.3 10 77-86 47-56 (72)
54 cd06555 ASCH_PF0470_like ASC-1 52.0 32 0.0007 23.6 4.1 28 75-102 30-57 (109)
55 PF12273 RCR: Chitin synthesis 47.2 13 0.00028 25.8 1.6 10 22-31 2-11 (130)
56 cd04370 BAH BAH, or Bromo Adja 47.0 39 0.00084 21.9 3.9 28 77-104 4-34 (123)
57 PF14085 DUF4265: Domain of un 46.4 92 0.002 21.2 5.9 38 65-103 11-51 (117)
58 CHL00010 infA translation init 45.5 24 0.00051 22.5 2.5 10 77-86 47-56 (78)
59 cd04466 S1_YloQ_GTPase S1_YloQ 45.5 47 0.001 19.6 3.8 24 76-99 37-60 (68)
60 PF00278 Orn_DAP_Arg_deC: Pyri 45.2 21 0.00045 23.5 2.3 31 60-90 65-96 (116)
61 TIGR00523 eIF-1A eukaryotic/ar 43.4 25 0.00054 23.7 2.4 9 77-85 58-66 (99)
62 cd04709 BAH_MTA BAH, or Bromo 43.1 51 0.0011 24.1 4.3 28 77-104 4-31 (164)
63 cd04719 BAH_Orc1p_animal BAH, 42.0 32 0.0007 24.2 3.0 28 78-105 5-32 (128)
64 smart00439 BAH Bromo adjacent 41.8 69 0.0015 20.8 4.5 24 78-101 3-27 (120)
65 cd05792 S1_eIF1AD_like S1_eIF1 41.5 21 0.00045 23.1 1.7 11 77-87 39-49 (78)
66 PF09138 Urm1: Urm1 (Ubiquitin 41.2 26 0.00057 23.5 2.3 28 60-87 56-91 (96)
67 PF07423 DUF1510: Protein of u 40.8 33 0.00072 26.3 3.1 11 18-28 14-24 (217)
68 cd04717 BAH_polybromo BAH, or 40.6 70 0.0015 21.6 4.4 27 77-103 4-31 (121)
69 TIGR02219 phage_NlpC_fam putat 38.9 21 0.00046 24.8 1.6 13 75-87 75-87 (134)
70 PF09874 DUF2101: Predicted me 38.5 1.2E+02 0.0026 23.2 5.7 67 20-88 116-193 (206)
71 cd04713 BAH_plant_3 BAH, or Br 38.2 59 0.0013 23.0 3.9 27 76-102 20-46 (146)
72 PRK14578 elongation factor P; 38.1 64 0.0014 24.2 4.2 37 57-98 150-187 (187)
73 PRK08564 5'-methylthioadenosin 37.7 23 0.00049 27.8 1.8 19 54-72 92-110 (267)
74 PF02362 B3: B3 DNA binding do 37.6 42 0.00091 21.2 2.8 16 74-89 71-86 (100)
75 PF01426 BAH: BAH domain; Int 37.4 40 0.00086 22.0 2.7 26 77-102 3-29 (119)
76 TIGR02178 yeiP elongation fact 36.8 56 0.0012 24.5 3.7 38 56-98 148-186 (186)
77 PF06923 GutM: Glucitol operon 36.6 67 0.0015 21.8 3.8 38 63-103 35-72 (109)
78 PRK12426 elongation factor P; 36.0 68 0.0015 24.0 4.0 39 55-98 146-185 (185)
79 PRK04542 elongation factor P; 35.4 83 0.0018 23.6 4.4 37 57-98 151-188 (189)
80 TIGR00038 efp translation elon 35.4 55 0.0012 24.2 3.4 38 56-98 146-184 (184)
81 PRK05573 rplU 50S ribosomal pr 35.3 75 0.0016 21.4 3.8 34 51-86 3-36 (103)
82 PF11302 DUF3104: Protein of u 35.1 83 0.0018 20.3 3.8 12 61-72 5-16 (75)
83 COG3655 Predicted transcriptio 34.9 29 0.00063 22.3 1.7 16 75-90 55-70 (73)
84 PF02559 CarD_CdnL_TRCF: CarD- 34.9 40 0.00087 21.8 2.4 12 77-88 2-13 (98)
85 PF10030 DUF2272: Uncharacteri 34.9 1.9E+02 0.0042 21.5 6.3 34 51-86 85-131 (183)
86 PF04970 LRAT: Lecithin retino 34.8 1.2E+02 0.0027 20.3 5.0 13 76-88 6-18 (125)
87 PRK08666 5'-methylthioadenosin 33.9 26 0.00057 27.0 1.6 19 54-72 84-102 (261)
88 COG1792 MreC Cell shape-determ 33.8 2.1E+02 0.0045 22.6 6.7 43 74-116 210-256 (284)
89 cd04497 hPOT1_OB1_like hPOT1_O 33.2 1.2E+02 0.0026 21.0 4.8 36 50-87 40-79 (138)
90 PF13550 Phage-tail_3: Putativ 33.1 85 0.0018 21.5 4.0 25 76-102 139-163 (164)
91 TIGR01694 MTAP 5'-deoxy-5'-met 32.2 31 0.00067 26.2 1.7 19 54-72 84-102 (241)
92 PF13800 Sigma_reg_N: Sigma fa 32.1 1.2E+02 0.0025 19.7 4.3 14 11-24 5-18 (96)
93 PF15428 Imm14: Immunity prote 32.1 71 0.0015 21.6 3.4 27 78-105 1-28 (129)
94 PRK07432 5'-methylthioadenosin 32.1 31 0.00068 27.5 1.8 23 50-72 84-106 (290)
95 PRK07823 5'-methylthioadenosin 32.0 31 0.00067 27.1 1.7 21 52-72 87-107 (264)
96 PRK09136 5'-methylthioadenosin 31.9 31 0.00067 26.7 1.7 22 51-72 81-102 (245)
97 PF08802 CytB6-F_Fe-S: Cytochr 31.8 1E+02 0.0022 17.4 5.0 30 13-42 5-34 (39)
98 PF06890 Phage_Mu_Gp45: Bacter 31.5 82 0.0018 23.1 3.8 28 75-103 73-103 (162)
99 cd04721 BAH_plant_1 BAH, or Br 31.3 84 0.0018 21.9 3.7 28 76-104 7-34 (130)
100 TIGR01698 PUNP purine nucleoti 31.0 34 0.00074 26.5 1.8 23 50-72 87-109 (237)
101 PRK15136 multidrug efflux syst 29.8 1.4E+02 0.0031 24.3 5.3 11 75-85 81-91 (390)
102 PRK00529 elongation factor P; 29.6 89 0.0019 23.1 3.8 37 57-98 148-185 (186)
103 COG1935 Uncharacterized conser 29.3 30 0.00065 24.3 1.1 20 61-80 38-58 (122)
104 PRK13884 conjugal transfer pep 29.3 1.1E+02 0.0023 22.5 4.1 19 50-72 43-61 (178)
105 TIGR01048 lysA diaminopimelate 29.2 80 0.0017 25.6 3.7 30 60-89 345-374 (417)
106 PF06940 DUF1287: Domain of un 29.1 34 0.00074 25.3 1.4 15 75-89 105-119 (164)
107 KOG1666 V-SNARE [Intracellular 29.0 2.3E+02 0.0051 21.9 6.0 17 4-20 179-195 (220)
108 PRK08931 5'-methylthioadenosin 28.8 37 0.00081 27.1 1.7 22 51-72 85-106 (289)
109 KOG0557 Dihydrolipoamide acety 28.7 87 0.0019 26.9 3.9 36 50-85 38-74 (470)
110 cd04451 S1_IF1 S1_IF1: Transla 28.6 57 0.0012 19.5 2.2 12 76-87 40-51 (64)
111 cd06836 PLPDE_III_ODC_DapDC_li 28.3 83 0.0018 25.4 3.7 29 62-90 329-357 (379)
112 PF00877 NLPC_P60: NlpC/P60 fa 28.2 34 0.00073 22.2 1.2 34 51-87 29-62 (105)
113 PF07423 DUF1510: Protein of u 28.1 1.2E+02 0.0026 23.3 4.3 29 16-44 8-36 (217)
114 TIGR00219 mreC rod shape-deter 27.7 3E+02 0.0066 21.6 6.8 44 74-117 213-260 (283)
115 PF06459 RR_TM4-6: Ryanodine R 27.6 1.7E+02 0.0036 23.2 5.2 15 28-42 176-190 (274)
116 PRK13922 rod shape-determining 27.2 1.8E+02 0.0039 22.3 5.3 44 74-117 212-259 (276)
117 TIGR01700 PNPH purine nucleosi 27.2 43 0.00094 25.7 1.8 19 54-72 91-109 (249)
118 cd06843 PLPDE_III_PvsE_like Ty 27.0 83 0.0018 25.2 3.5 30 61-90 327-356 (377)
119 TIGR01697 PNPH-PUNA-XAPA inosi 26.9 45 0.00098 25.5 1.8 19 54-72 91-109 (248)
120 cd06839 PLPDE_III_Btrk_like Ty 26.7 94 0.002 24.7 3.7 31 60-90 331-361 (382)
121 COG2326 Uncharacterized conser 26.7 43 0.00094 26.6 1.7 29 76-104 128-156 (270)
122 PF02285 COX8: Cytochrome oxid 26.7 35 0.00076 19.8 0.9 13 2-14 31-43 (44)
123 COG0690 SecE Preprotein transl 26.6 1.7E+02 0.0037 18.4 4.8 26 2-27 22-50 (73)
124 PF00957 Synaptobrevin: Synapt 26.6 1.7E+02 0.0038 18.4 5.5 17 15-31 58-74 (89)
125 PF04085 MreC: rod shape-deter 26.5 1.7E+02 0.0038 20.6 4.7 44 74-117 91-138 (152)
126 cd06840 PLPDE_III_Bif_AspK_Dap 26.3 91 0.002 25.1 3.6 31 60-90 318-348 (368)
127 PF04322 DUF473: Protein of un 26.1 1.7E+02 0.0037 20.4 4.5 22 61-82 38-60 (119)
128 PRK11507 ribosome-associated p 25.9 28 0.00061 22.1 0.4 14 74-87 50-63 (70)
129 COG4043 Preprotein translocase 25.7 44 0.00094 23.0 1.4 14 74-87 31-44 (111)
130 PRK08202 purine nucleoside pho 25.6 50 0.0011 25.8 1.9 21 52-72 111-131 (272)
131 PRK10691 hypothetical protein; 25.3 86 0.0019 23.6 3.1 27 61-87 181-209 (219)
132 TIGR03099 dCO2ase_PEP1 pyridox 25.2 94 0.002 25.1 3.5 28 63-90 350-377 (398)
133 PF09926 DUF2158: Uncharacteri 25.2 1.4E+02 0.003 17.8 3.4 23 78-101 2-24 (53)
134 PRK10838 spr outer membrane li 24.8 54 0.0012 24.6 1.8 13 75-87 127-139 (190)
135 PF00829 Ribosomal_L21p: Ribos 24.5 1E+02 0.0023 20.4 3.0 33 52-86 4-36 (96)
136 PF02639 DUF188: Uncharacteriz 24.3 99 0.0022 21.7 3.0 40 48-87 11-59 (130)
137 KOG1535 Predicted fumarylaceto 24.0 92 0.002 24.0 3.0 29 61-89 176-206 (217)
138 cd06829 PLPDE_III_CANSDC Type 23.7 1.1E+02 0.0023 24.5 3.5 31 60-90 295-325 (346)
139 KOG4544 Uncharacterized conser 23.2 3E+02 0.0064 19.9 5.5 34 4-37 32-70 (144)
140 TIGR01047 nspC carboxynorsperm 22.9 98 0.0021 25.1 3.2 30 60-89 309-338 (380)
141 cd05790 S1_Rrp40 S1_Rrp40: Rrp 22.8 78 0.0017 20.7 2.1 15 57-71 45-59 (86)
142 PF13759 2OG-FeII_Oxy_5: Putat 22.1 1.1E+02 0.0024 19.7 2.8 24 76-104 69-92 (101)
143 CHL00075 rpl21 ribosomal prote 22.0 1.9E+02 0.0042 19.7 4.0 34 51-86 5-38 (108)
144 TIGR03468 HpnG hopanoid-associ 21.6 64 0.0014 24.0 1.7 21 52-72 52-72 (212)
145 PF13640 2OG-FeII_Oxy_3: 2OG-F 21.5 2.2E+02 0.0047 17.8 4.3 21 77-101 66-86 (100)
146 cd06810 PLPDE_III_ODC_DapDC_li 21.4 1.3E+02 0.0028 23.8 3.5 30 61-90 319-348 (368)
147 KOG2921 Intramembrane metallop 21.4 4.2E+02 0.0091 22.7 6.5 29 58-86 212-248 (484)
148 PF05708 DUF830: Orthopoxvirus 21.1 72 0.0016 22.0 1.8 12 77-88 2-13 (158)
149 PLN02537 diaminopimelate decar 21.1 1.4E+02 0.0031 24.3 3.8 30 60-89 335-364 (410)
150 PRK15203 4-hydroxyphenylacetat 21.1 1E+02 0.0022 25.8 3.0 30 61-90 165-196 (429)
151 TIGR01699 XAPA xanthosine phos 21.0 39 0.00085 26.2 0.5 21 52-72 89-109 (248)
152 PF01878 EVE: EVE domain; Int 20.9 1.7E+02 0.0037 20.1 3.7 14 76-89 39-52 (143)
153 cd04716 BAH_plantDCM_I BAH, or 20.9 2.9E+02 0.0063 19.0 5.0 25 78-102 5-29 (122)
154 PF07883 Cupin_2: Cupin domain 20.9 1.8E+02 0.004 16.7 3.7 30 76-110 40-69 (71)
155 PF08940 DUF1918: Domain of un 20.9 74 0.0016 19.6 1.6 35 63-97 4-40 (58)
156 cd06841 PLPDE_III_MccE_like Ty 20.7 1.4E+02 0.0031 23.9 3.7 31 60-90 326-356 (379)
157 cd06828 PLPDE_III_DapDC Type I 20.7 1.5E+02 0.0032 23.5 3.7 30 61-90 324-353 (373)
158 TIGR00061 L21 ribosomal protei 20.6 1.9E+02 0.0042 19.4 3.8 33 52-86 3-35 (101)
159 PF01079 Hint: Hint module; I 20.5 1.2E+02 0.0025 23.2 3.0 36 51-86 19-56 (217)
160 cd06541 ASCH ASC-1 homology or 20.5 2.1E+02 0.0045 18.8 3.9 26 75-101 29-54 (105)
161 TIGR02303 HpaG-C-term 4-hydrox 20.4 1.2E+02 0.0026 23.3 3.1 30 61-90 204-235 (245)
162 PF02311 AraC_binding: AraC-li 20.3 2E+02 0.0042 18.2 3.8 36 75-115 43-78 (136)
163 cd05828 Sortase_D_4 Sortase D 20.3 2.9E+02 0.0062 18.7 5.1 16 75-90 60-75 (127)
164 PF01724 DUF29: Domain of unkn 20.2 2.5E+02 0.0053 19.8 4.4 24 4-27 30-53 (139)
165 TIGR03027 pepcterm_export puta 20.1 75 0.0016 22.6 1.8 16 57-72 147-162 (165)
No 1
>PRK10861 signal peptidase I; Provisional
Probab=99.81 E-value=1.5e-19 Score=144.45 Aligned_cols=90 Identities=26% Similarity=0.328 Sum_probs=76.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCccccCcCCCEEEEecc---------------CCCCCCCcE
Q 033489 18 QVLTQGVSLGMIVTSALIIWKALMCITGSESPVVVVLSGSMEPGFKRGDILFLHMS---------------KDPIRAGEI 82 (118)
Q Consensus 18 ~i~~~i~~i~~~~~i~~li~~~~~~~~g~~~~~~~V~g~SM~Ptl~~GD~vlv~k~---------------~~~~~~GDI 82 (118)
.+++++..++.+++++++++.|++. ++.|+|+||+|||++||.++++|. ..+|+||||
T Consensus 59 ~~~~~~~~~~~~l~i~~~ir~fv~~-------~~~Ips~SM~PTL~~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDI 131 (324)
T PRK10861 59 GWLETGASVFPVLAIVLIVRSFIYE-------PFQIPSGSMMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDI 131 (324)
T ss_pred hHHHHHHHHHHHHhHHHHHHhhEEE-------EEEECCCcCcCcccCCCEEEEEEeecCccCccccccccccCCCCCCCE
Confidence 3678888888888889999999887 599999999999999999999992 146899999
Q ss_pred EEEEeCCC-CcCEEEEEEEECCCceEEE----EEEee
Q 033489 83 VVFNVDGR-EIPIVHRVIKVNILLTLFF----ELTIQ 114 (118)
Q Consensus 83 Vvf~~~~~-~~~~ikRVI~~~g~~~~~~----~~~~~ 114 (118)
|+|+.|.+ +..+||||||+|||..++- +|.|.
T Consensus 132 VVF~~P~~~~~~yIKRVIGlPGD~I~~~~~~~~l~iN 168 (324)
T PRK10861 132 VVFKYPEDPKLDYIKRVVGLPGDKVTYDPVSKEVTIQ 168 (324)
T ss_pred EEEecCCCCCCcEEEEeeecCCcEEEEEeCCCEEEEc
Confidence 99998764 4579999999999999884 55554
No 2
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.79 E-value=7.4e-19 Score=127.31 Aligned_cols=103 Identities=61% Similarity=0.962 Sum_probs=96.3
Q ss_pred CcchHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCccccCcCCCEEEEec-cCCCCCC
Q 033489 1 MGWIGESIESIKSLQIRQVLTQGVSLGMIVTSALIIWKALMCITGSESPVVVVLSGSMEPGFKRGDILFLHM-SKDPIRA 79 (118)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~i~~~i~~i~~~~~i~~li~~~~~~~~g~~~~~~~V~g~SM~Ptl~~GD~vlv~k-~~~~~~~ 79 (118)
|.|..|....+|+|++|+.+.-++.++.++..++.+|..+....|+++|+++|.|+||||.++.||+++... ..+..+.
T Consensus 1 ~~~~~~~~~~~k~mn~Rq~l~Q~ln~~mivssA~MiwK~l~vvt~seSPiVVVLSgSMePaF~RGDlLfL~N~~~~p~~v 80 (180)
T KOG3342|consen 1 MLVSLEMFDDLKRMNIRQLLYQVLNFAMIVSSAYMIWKGLMVVTGSESPIVVVLSGSMEPAFHRGDLLFLTNRNEDPIRV 80 (180)
T ss_pred CcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhheeeeCCCCCEEEEEcCCcCcccccccEEEEecCCCCccee
Confidence 689999999999999999999999999999999999999999999999999999999999999999999875 5566899
Q ss_pred CcEEEEEeCCCCcCEEEEEEEECC
Q 033489 80 GEIVVFNVDGREIPIVHRVIKVNI 103 (118)
Q Consensus 80 GDIVvf~~~~~~~~~ikRVI~~~g 103 (118)
||||+|+.++++.+.+|||+.+-+
T Consensus 81 GdivVf~vegR~IPiVHRviK~he 104 (180)
T KOG3342|consen 81 GDIVVFKVEGREIPIVHRVIKQHE 104 (180)
T ss_pred ccEEEEEECCccCchhHHHHHHhc
Confidence 999999999998899999998765
No 3
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=99.77 E-value=1.8e-18 Score=125.83 Aligned_cols=81 Identities=28% Similarity=0.305 Sum_probs=67.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCccccCcCCCEEEEecc---CCCCCCCcEEEEEeCCC-CcCEEEE
Q 033489 22 QGVSLGMIVTSALIIWKALMCITGSESPVVVVLSGSMEPGFKRGDILFLHMS---KDPIRAGEIVVFNVDGR-EIPIVHR 97 (118)
Q Consensus 22 ~i~~i~~~~~i~~li~~~~~~~~g~~~~~~~V~g~SM~Ptl~~GD~vlv~k~---~~~~~~GDIVvf~~~~~-~~~~ikR 97 (118)
|+..++++++++++++.+++. ++.|+|+||+|||++||+++++|. ..++++||+|+|+.+++ +..++||
T Consensus 1 ~~~~~~~~~~~~~~i~~~~~~-------~~~v~g~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~~~~~~iKR 73 (163)
T TIGR02227 1 LILSLLIAILLALLIRTFVFF-------PYKIPGGSMEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKDPDDNKNIYVKR 73 (163)
T ss_pred CHHHHHHHHHHHHHHHhhEEE-------EEEECCcccccchhCCCEEEEEEeEcCCCCCCCCcEEEEecCCCCCceeEEE
Confidence 355566677777788888776 599999999999999999999983 36799999999998653 4579999
Q ss_pred EEEECCCceEEE
Q 033489 98 VIKVNILLTLFF 109 (118)
Q Consensus 98 VI~~~g~~~~~~ 109 (118)
|+|+|||..+.-
T Consensus 74 Vig~pGd~v~i~ 85 (163)
T TIGR02227 74 VIGLPGDKVEFR 85 (163)
T ss_pred EEecCCCEEEEE
Confidence 999999877653
No 4
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=99.75 E-value=1.9e-17 Score=120.65 Aligned_cols=75 Identities=33% Similarity=0.613 Sum_probs=58.1
Q ss_pred HHHHHHHHHHHhhCCCCCeEEEeCCCccccCcCCCEEEEec-cCCCCCCCcEEEEEeCCCCcCEEEEEEEECCCceE
Q 033489 32 SALIIWKALMCITGSESPVVVVLSGSMEPGFKRGDILFLHM-SKDPIRAGEIVVFNVDGREIPIVHRVIKVNILLTL 107 (118)
Q Consensus 32 i~~li~~~~~~~~g~~~~~~~V~g~SM~Ptl~~GD~vlv~k-~~~~~~~GDIVvf~~~~~~~~~ikRVI~~~g~~~~ 107 (118)
+++++..+.+. .+++.|.+.|.|+||+||+++||.+++++ ..+++++||+|+|+.++++..++|||+++.+++++
T Consensus 16 ~~~~~~~l~~~-~~~~~p~v~V~g~SM~Ptl~~GD~vlv~~~~~~~~~~GDIVvf~~~~~~~~iihRVi~v~~~~g~ 91 (158)
T TIGR02228 16 VILLLYGLVSK-ASGPDPVVVVLSGSMEPTFNTGDLILVTGADPNDIQVGDVITYKSPGFNTPVTHRVIEINNSGGE 91 (158)
T ss_pred HHHHHHHheee-ccCCCcEEEEcCCCCcCCccCCCEEEEEecccCCCCCCCEEEEEECCCCccEEEEEEEEECCCCc
Confidence 33334343333 34555667799999999999999999998 45679999999999887656899999999876543
No 5
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=99.46 E-value=1.8e-13 Score=85.45 Aligned_cols=54 Identities=35% Similarity=0.481 Sum_probs=44.3
Q ss_pred EEeCCCccccCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEEEEECCCce
Q 033489 52 VVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVNILLT 106 (118)
Q Consensus 52 ~V~g~SM~Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRVI~~~g~~~ 106 (118)
.|.|+||+|++++||++++++. .+++.||+|+|+.++....++||+.+.+++..
T Consensus 1 ~V~GdSM~P~i~~Gd~v~v~~~-~~~~~gdivv~~~~~~~~~~iKrv~~~~~~~~ 54 (70)
T PF00717_consen 1 RVEGDSMEPTIKDGDIVLVDPS-SEPKDGDIVVVKIDGDEELYIKRVVGEPGGII 54 (70)
T ss_dssp EEESSTTGGTSSTTEEEEEEET-S---TTSEEEEEETTEESEEEEEEEEETTEEE
T ss_pred CeECcCcccCeeCCCEEEEEEc-CCCccCeEEEEEECCceeeEEEEEEEeCCCEE
Confidence 4899999999999999999984 47999999999988764479999999987443
No 6
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=99.42 E-value=6.1e-13 Score=86.32 Aligned_cols=51 Identities=39% Similarity=0.660 Sum_probs=44.6
Q ss_pred eEEEeCCCccccCcCCCEEEEeccCC---CCCCCcEEEEEeCCC-CcCEEEEEEE
Q 033489 50 VVVVLSGSMEPGFKRGDILFLHMSKD---PIRAGEIVVFNVDGR-EIPIVHRVIK 100 (118)
Q Consensus 50 ~~~V~g~SM~Ptl~~GD~vlv~k~~~---~~~~GDIVvf~~~~~-~~~~ikRVI~ 100 (118)
.+.|.|+||+|++++||++++++... ++++||+|+|+.++. ...++||+++
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~~~~~~vkRv~~ 56 (85)
T cd06530 2 PVVVPGGSMEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRVIG 56 (85)
T ss_pred eeEEcCCCCcCcccCCCEEEEEEeecccCCCCCCCEEEEeCCCCCCCEEEEEEEE
Confidence 48999999999999999999998433 699999999998874 4579999977
No 7
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=99.42 E-value=8.4e-13 Score=86.82 Aligned_cols=54 Identities=22% Similarity=0.125 Sum_probs=45.0
Q ss_pred EEeCCCccccCcCCCEEEEec---cCCCCCCCcEEEEEeCCC-CcCEEEEEEEECCCc
Q 033489 52 VVLSGSMEPGFKRGDILFLHM---SKDPIRAGEIVVFNVDGR-EIPIVHRVIKVNILL 105 (118)
Q Consensus 52 ~V~g~SM~Ptl~~GD~vlv~k---~~~~~~~GDIVvf~~~~~-~~~~ikRVI~~~g~~ 105 (118)
.|.|+||+|+|++||.+++++ ....+++||+|+|+.+++ ++.++||++++++++
T Consensus 2 ~V~g~SM~P~l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~~~~ 59 (90)
T TIGR02754 2 KVTGVSMSPTLPPGDRIIVVPWLKIFRVPPIGNVVVVRHPLQPYGLIIKRLAAVDDNG 59 (90)
T ss_pred EeeCCCccCccCCCCEEEEEEccccCCCCCCCeEEEEecCCCCcceEEEEeeEEcCCe
Confidence 689999999999999999997 234457899999997763 367999999998754
No 8
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.41 E-value=2.9e-13 Score=96.63 Aligned_cols=84 Identities=30% Similarity=0.339 Sum_probs=61.7
Q ss_pred HHHHHHHHHHHHHHHHHH--HHHHHHhhCCCCCeEEEeCCCccccCcCCCEEEEecc---CCCCCCCcEEEEEeCCCCcC
Q 033489 19 VLTQGVSLGMIVTSALII--WKALMCITGSESPVVVVLSGSMEPGFKRGDILFLHMS---KDPIRAGEIVVFNVDGREIP 93 (118)
Q Consensus 19 i~~~i~~i~~~~~i~~li--~~~~~~~~g~~~~~~~V~g~SM~Ptl~~GD~vlv~k~---~~~~~~GDIVvf~~~~~~~~ 93 (118)
...|+..++.++++++++ ..+.+. ++.|+|+||+||++.||+++++|. ...++.+|++.+... ....
T Consensus 7 ~~~~~~~~~~~~~~~~~i~~~~~~~~-------~~~V~s~SM~Ptl~~GD~v~v~k~~~~~~~~~~~~~~~~~~~-~~~~ 78 (166)
T COG0681 7 FLELISSLLIAIILALIIGVRTFVFE-------PVVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDIIVLPAV-VEGD 78 (166)
T ss_pred HHHHHHHHHHHHHHhheeeeEEEEEE-------EEEECCCccccccccCCEEEEEeccccccCCccceeeecCCC-CCcc
Confidence 556677777777777666 455554 699999999999999999999993 234677777633222 2346
Q ss_pred EEEEEEEECCCceEEEE
Q 033489 94 IVHRVIKVNILLTLFFE 110 (118)
Q Consensus 94 ~ikRVI~~~g~~~~~~~ 110 (118)
++||+++.+||...|-.
T Consensus 79 ~~kr~~~~~GD~i~~~~ 95 (166)
T COG0681 79 LIKRVIGLRGDIVVFKD 95 (166)
T ss_pred eEEEeccCCCCEEEEEC
Confidence 99999999998887763
No 9
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.36 E-value=2e-12 Score=94.77 Aligned_cols=73 Identities=21% Similarity=0.233 Sum_probs=55.1
Q ss_pred HHHHHHHHHHHHHhhCCCCCeEEEeCCCccccCcCC-CEEEEec---cCCCCCCCcEEEEEeCCC-CcCEEEEEEEECCC
Q 033489 30 VTSALIIWKALMCITGSESPVVVVLSGSMEPGFKRG-DILFLHM---SKDPIRAGEIVVFNVDGR-EIPIVHRVIKVNIL 104 (118)
Q Consensus 30 ~~i~~li~~~~~~~~g~~~~~~~V~g~SM~Ptl~~G-D~vlv~k---~~~~~~~GDIVvf~~~~~-~~~~ikRVI~~~g~ 104 (118)
.|++.....+++. +...+|.||+||++++ |+++.+| .++.+++||||+++.|.+ .+.++|||+|++||
T Consensus 22 ~~f~h~t~~yl~e-------~~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~~~~~~cKRIva~eGD 94 (176)
T KOG0171|consen 22 AAFTHVTHEYLGE-------FVMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPDPKEHICKRIVAMEGD 94 (176)
T ss_pred HHHHHHHHHHhcc-------eeeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCCCchhhhhheeeccCCc
Confidence 3444455556665 5889999999999865 5555476 456789999999998866 56799999999998
Q ss_pred ceEEE
Q 033489 105 LTLFF 109 (118)
Q Consensus 105 ~~~~~ 109 (118)
-.+..
T Consensus 95 ~v~v~ 99 (176)
T KOG0171|consen 95 LVEVH 99 (176)
T ss_pred eEEEe
Confidence 55544
No 10
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=99.16 E-value=3.5e-10 Score=71.97 Aligned_cols=53 Identities=34% Similarity=0.473 Sum_probs=46.5
Q ss_pred eEEEeCCCccccCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEEEEECC
Q 033489 50 VVVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVNI 103 (118)
Q Consensus 50 ~~~V~g~SM~Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRVI~~~g 103 (118)
.+.|.|+||+|++++||.+++++....++.||+++++.++ ...++||+...++
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~i~~~~~~~~~G~iv~~~~~~-~~~~ikrl~~~~~ 54 (84)
T cd06462 2 ALRVEGDSMEPTIPDGDLVLVDKSSYEPKRGDIVVFRLPG-GELTVKRVIGLPG 54 (84)
T ss_pred eeEEcCCCccCcccCCCEEEEEecCCCCcCCEEEEEEcCC-CcEEEEEEEEECC
Confidence 3789999999999999999999854459999999999876 3579999999986
No 11
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.07 E-value=2.8e-10 Score=83.42 Aligned_cols=56 Identities=25% Similarity=0.404 Sum_probs=47.7
Q ss_pred eEEEeCCCccccCcCC------CEEEEec-c--CCCCCCCcEEEEEeCCC-CcCEEEEEEEECCCc
Q 033489 50 VVVVLSGSMEPGFKRG------DILFLHM-S--KDPIRAGEIVVFNVDGR-EIPIVHRVIKVNILL 105 (118)
Q Consensus 50 ~~~V~g~SM~Ptl~~G------D~vlv~k-~--~~~~~~GDIVvf~~~~~-~~~~ikRVI~~~g~~ 105 (118)
...|.|.||.||++++ |.|++.| . .....+||||+|++|.+ +++++|||.|++|+-
T Consensus 33 va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~p~~~~iKRv~alegd~ 98 (174)
T KOG1568|consen 33 VAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPNDPDKVIIKRVAALEGDI 98 (174)
T ss_pred EeEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCCChhheeeeeeecccccE
Confidence 6899999999999876 8899998 2 24488999999998876 568999999999953
No 12
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=99.02 E-value=2.1e-09 Score=68.31 Aligned_cols=51 Identities=33% Similarity=0.468 Sum_probs=45.3
Q ss_pred eEEEeCCCccccCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEEEEECC
Q 033489 50 VVVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVNI 103 (118)
Q Consensus 50 ~~~V~g~SM~Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRVI~~~g 103 (118)
.+.+.|+||+|++++||.+++++.. .++.||+++++.++ +.++||+...++
T Consensus 2 ~~~v~g~sM~p~i~~gd~lii~~~~-~~~~g~i~~~~~~~--~~~ikr~~~~~~ 52 (81)
T cd06529 2 ALRVKGDSMEPTIPDGDLVLVDPSD-TPRDGDIVVARLDG--ELTVKRLQRRGG 52 (81)
T ss_pred EEEEECCCcCCccCCCCEEEEcCCC-CCCCCCEEEEEECC--EEEEEEEEECCC
Confidence 3789999999999999999999854 49999999999876 469999999886
No 13
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.82 E-value=1.5e-08 Score=76.11 Aligned_cols=55 Identities=27% Similarity=0.346 Sum_probs=45.4
Q ss_pred eEEEeCCCccccCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEEEEECCCce
Q 033489 50 VVVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVNILLT 106 (118)
Q Consensus 50 ~~~V~g~SM~Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRVI~~~g~~~ 106 (118)
...|.|+||+|++++||.++|+.. .+..+||.+++...+. ..++||+...++...
T Consensus 125 ~i~V~GDSMeP~~~~Gd~ilVd~~-~~~~~gd~v~v~~~g~-~~~VK~l~~~~~~~~ 179 (214)
T COG2932 125 ALRVTGDSMEPTYEDGDTLLVDPG-VNTRRGDRVYVETDGG-ELYVKKLQREPGGLL 179 (214)
T ss_pred EEEEeCCcccccccCCCEEEECCC-CceeeCCEEEEEEeCC-eEEEEEEEEecCCeE
Confidence 479999999999999999999984 4578899777766653 469999999998444
No 14
>PRK00215 LexA repressor; Validated
Probab=98.42 E-value=1e-06 Score=65.58 Aligned_cols=49 Identities=29% Similarity=0.417 Sum_probs=42.1
Q ss_pred eEEEeCCCcc-ccCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEEEEE
Q 033489 50 VVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKV 101 (118)
Q Consensus 50 ~~~V~g~SM~-Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRVI~~ 101 (118)
.+.|.|+||. |++++||.+++++. .+++.||+|++..++ +.++||+...
T Consensus 120 ~~~V~GdSM~~~~i~~Gd~v~v~~~-~~~~~G~ivv~~~~~--~~~vKrl~~~ 169 (205)
T PRK00215 120 LLRVRGDSMIDAGILDGDLVIVRKQ-QTARNGQIVVALIDD--EATVKRFRRE 169 (205)
T ss_pred EEEEccCCCCCCCcCCCCEEEEeCC-CCCCCCCEEEEEECC--EEEEEEEEEe
Confidence 5789999995 79999999999974 468999999998876 4699999865
No 15
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.41 E-value=9.4e-07 Score=62.64 Aligned_cols=48 Identities=29% Similarity=0.416 Sum_probs=40.7
Q ss_pred eEEEeCCCcc-ccCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEEEE
Q 033489 50 VVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIK 100 (118)
Q Consensus 50 ~~~V~g~SM~-Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRVI~ 100 (118)
.+.|.|+||+ |++++||.+++++. ..++.||++++..+++ ..+||...
T Consensus 53 ~l~V~GdSM~~~~I~~GD~liVd~~-~~~~~Gdivv~~~~g~--~~vKrl~~ 101 (139)
T PRK10276 53 FVKASGDSMIDAGISDGDLLIVDSA-ITASHGDIVIAAVDGE--FTVKKLQL 101 (139)
T ss_pred EEEEecCCCCCCCCCCCCEEEEECC-CCCCCCCEEEEEECCE--EEEEEEEE
Confidence 5899999998 68999999999984 4589999999987653 58999875
No 16
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=98.35 E-value=3.4e-06 Score=62.53 Aligned_cols=35 Identities=14% Similarity=0.272 Sum_probs=27.8
Q ss_pred CCCCCCCcEEEEEeCCCC--------------------cCEEEEEEEECCCceEE
Q 033489 74 KDPIRAGEIVVFNVDGRE--------------------IPIVHRVIKVNILLTLF 108 (118)
Q Consensus 74 ~~~~~~GDIVvf~~~~~~--------------------~~~ikRVI~~~g~~~~~ 108 (118)
..++++||+|+|+.|+.. ..++|||+|+|||..+.
T Consensus 48 ~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i 102 (176)
T PRK13838 48 DRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEI 102 (176)
T ss_pred CCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEE
Confidence 467999999999865431 25999999999988763
No 17
>PRK12423 LexA repressor; Provisional
Probab=98.30 E-value=2.7e-06 Score=63.72 Aligned_cols=50 Identities=32% Similarity=0.460 Sum_probs=42.4
Q ss_pred eEEEeCCCcc-ccCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEEEEEC
Q 033489 50 VVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVN 102 (118)
Q Consensus 50 ~~~V~g~SM~-Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRVI~~~ 102 (118)
.+.|.|+||. |++.+||.+++++. .+++.||+|++..++ +.++||.....
T Consensus 116 ~l~V~GdSM~~~~i~~Gd~viv~~~-~~~~~Gdivv~~~~~--~~~vKrl~~~~ 166 (202)
T PRK12423 116 LLQVQGDSMIDDGILDGDLVGVHRS-PEARDGQIVVARLDG--EVTIKRLERSG 166 (202)
T ss_pred EEEEecCcCCCCCcCCCCEEEEeCC-CcCCCCCEEEEEECC--EEEEEEEEEeC
Confidence 5899999997 79999999999974 578999999998764 46899987653
No 18
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.
Probab=98.23 E-value=7.5e-06 Score=60.35 Aligned_cols=52 Identities=19% Similarity=0.245 Sum_probs=36.3
Q ss_pred EEeCCCccccCcCCCEEEEeccCCCCCCCcEEEEEeCCCC--------------------cCEEEEEEEECCCceEEE
Q 033489 52 VVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGRE--------------------IPIVHRVIKVNILLTLFF 109 (118)
Q Consensus 52 ~V~g~SM~Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~--------------------~~~ikRVI~~~g~~~~~~ 109 (118)
.=.++||-..+- . ..+ ..++++||+|+|+.+++. ..++|||+|+|||..+.-
T Consensus 28 ~N~T~S~P~g~Y----~-~~~-~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpGD~V~i~ 99 (171)
T TIGR02771 28 INTTKSLPLGLY----W-TTS-SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVR 99 (171)
T ss_pred EECCCCCcceEE----E-eCC-CCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCCCEEEEE
Confidence 344556665543 2 322 457999999999976532 169999999999887653
No 19
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=98.20 E-value=6.6e-06 Score=60.97 Aligned_cols=49 Identities=35% Similarity=0.495 Sum_probs=41.7
Q ss_pred eEEEeCCCcc-ccCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEEEEE
Q 033489 50 VVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKV 101 (118)
Q Consensus 50 ~~~V~g~SM~-Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRVI~~ 101 (118)
.+.|.|+||+ |.+++||.+++++. .+++.||+|++..++ +.++||....
T Consensus 113 ~~~V~GdSM~~~~i~~Gd~v~v~~~-~~~~~G~ivvv~~~~--~~~vKrl~~~ 162 (199)
T TIGR00498 113 LLKVMGDSMVDAGICDGDLLIVRSQ-KDARNGEIVAAMIDG--EVTVKRFYKD 162 (199)
T ss_pred EEEecCCCCCCCCCCCCCEEEEecC-CCCCCCCEEEEEECC--EEEEEEEEEE
Confidence 5899999996 68999999999974 579999999999843 4689998754
No 20
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=97.70 E-value=0.00062 Score=50.45 Aligned_cols=35 Identities=20% Similarity=0.190 Sum_probs=25.8
Q ss_pred CCCCCCcEEEEEeCCC--------------------CcCEEEEEEEECCCceEEE
Q 033489 75 DPIRAGEIVVFNVDGR--------------------EIPIVHRVIKVNILLTLFF 109 (118)
Q Consensus 75 ~~~~~GDIVvf~~~~~--------------------~~~~ikRVI~~~g~~~~~~ 109 (118)
.++++||+|+|..|.. ..+++|||+|+|||..+.-
T Consensus 49 ~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD~V~~~ 103 (178)
T PRK13884 49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGDAVSVT 103 (178)
T ss_pred CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCcEEEEE
Confidence 3578888888875431 1268999999999887664
No 21
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=97.69 E-value=0.00017 Score=54.59 Aligned_cols=51 Identities=29% Similarity=0.445 Sum_probs=43.1
Q ss_pred eEEEeCCCcc-ccCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEEEEEC
Q 033489 50 VVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVN 102 (118)
Q Consensus 50 ~~~V~g~SM~-Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRVI~~~ 102 (118)
...|.|+||. +.+.+||.|+|++ ..+.+.||||+...++ ++..+||...-.
T Consensus 114 ~L~V~GdSM~~~gi~dGDlvvV~~-~~~a~~GdiVvA~i~g-~e~TvKrl~~~g 165 (201)
T COG1974 114 FLRVSGDSMIDAGILDGDLVVVDP-TEDAENGDIVVALIDG-EEATVKRLYRDG 165 (201)
T ss_pred EEEecCCccccCcCCCCCEEEEcC-CCCCCCCCEEEEEcCC-CcEEEEEEEEeC
Confidence 5899999998 6788999999997 5679999999999887 457888876654
No 22
>PF10502 Peptidase_S26: Signal peptidase, peptidase S26 ; InterPro: IPR019533 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents a conserved region found in the S26A family of serine endopeptidases, which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes. ; PDB: 3S04_B 1KN9_C 1B12_D 3IIQ_B 1T7D_A.
Probab=96.06 E-value=0.0016 Score=46.28 Aligned_cols=33 Identities=27% Similarity=0.345 Sum_probs=0.0
Q ss_pred CCCCCcEEEEEeCCC-------------CcCEEEEEEEECCCceEE
Q 033489 76 PIRAGEIVVFNVDGR-------------EIPIVHRVIKVNILLTLF 108 (118)
Q Consensus 76 ~~~~GDIVvf~~~~~-------------~~~~ikRVI~~~g~~~~~ 108 (118)
.+++||+|+|..|.. +..++|||+|+|||....
T Consensus 21 ~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v 66 (138)
T PF10502_consen 21 KIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEV 66 (138)
T ss_dssp ----------------------------------------------
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccc
Confidence 378888888876541 236899999999987543
No 23
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=87.65 E-value=0.6 Score=30.23 Aligned_cols=29 Identities=31% Similarity=0.551 Sum_probs=20.5
Q ss_pred CCCccc---cCcCCCEEEEeccCCCCCCCcEE
Q 033489 55 SGSMEP---GFKRGDILFLHMSKDPIRAGEIV 83 (118)
Q Consensus 55 g~SM~P---tl~~GD~vlv~k~~~~~~~GDIV 83 (118)
++.|.= -+.+||.|+|..+..++++|||+
T Consensus 37 ~GKmr~~~i~I~~GD~V~Ve~~~~d~~kg~I~ 68 (75)
T COG0361 37 SGKMRKNRIRILPGDVVLVELSPYDLTKGRIV 68 (75)
T ss_pred cCcchheeEEeCCCCEEEEEecccccccccEE
Confidence 345544 45788888888766678888876
No 24
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=87.18 E-value=0.62 Score=29.57 Aligned_cols=22 Identities=23% Similarity=0.332 Sum_probs=13.7
Q ss_pred CcCCCEEEEeccCCCCCCCcEE
Q 033489 62 FKRGDILFLHMSKDPIRAGEIV 83 (118)
Q Consensus 62 l~~GD~vlv~k~~~~~~~GDIV 83 (118)
+.+||+|.|..+..++.+|||+
T Consensus 45 I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 45 ILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred ECCCCEEEEEECcccCCcEeEE
Confidence 3566766666655566666665
No 25
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=83.53 E-value=0.93 Score=28.03 Aligned_cols=11 Identities=27% Similarity=0.631 Sum_probs=5.8
Q ss_pred CCCCcEEEEEe
Q 033489 77 IRAGEIVVFNV 87 (118)
Q Consensus 77 ~~~GDIVvf~~ 87 (118)
+++||.|+...
T Consensus 42 I~~GD~V~V~~ 52 (65)
T PF01176_consen 42 IKRGDFVLVEP 52 (65)
T ss_dssp --TTEEEEEEE
T ss_pred cCCCCEEEEEe
Confidence 56666666664
No 26
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=81.22 E-value=1.4 Score=28.39 Aligned_cols=21 Identities=19% Similarity=0.274 Sum_probs=10.8
Q ss_pred cCCCEEEEeccCCCCCCCcEE
Q 033489 63 KRGDILFLHMSKDPIRAGEIV 83 (118)
Q Consensus 63 ~~GD~vlv~k~~~~~~~GDIV 83 (118)
.+||.|+++.+..+..+|||+
T Consensus 40 ~~GD~V~Ve~~~~d~~kg~Iv 60 (77)
T cd05793 40 NEGDIVLVAPWDFQDDKADII 60 (77)
T ss_pred cCCCEEEEEeccccCCEEEEE
Confidence 455555555543445555554
No 27
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=79.76 E-value=2.6 Score=29.41 Aligned_cols=17 Identities=24% Similarity=0.178 Sum_probs=14.1
Q ss_pred CEEEEEEEECCCceEEE
Q 033489 93 PIVHRVIKVNILLTLFF 109 (118)
Q Consensus 93 ~~ikRVI~~~g~~~~~~ 109 (118)
.+++|+++.+|++..+.
T Consensus 139 ~~~~~~~~~~gd~~~~~ 155 (166)
T COG0681 139 DYIKRVIGLPGDNILYT 155 (166)
T ss_pred ccccceEEeeccceeec
Confidence 48999999999887765
No 28
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=77.95 E-value=2.5 Score=28.11 Aligned_cols=22 Identities=27% Similarity=0.351 Sum_probs=14.4
Q ss_pred CcCCCEEEEeccCCCCCCCcEE
Q 033489 62 FKRGDILFLHMSKDPIRAGEIV 83 (118)
Q Consensus 62 l~~GD~vlv~k~~~~~~~GDIV 83 (118)
+.+||.|.|..+..++.+|+|+
T Consensus 47 Il~GD~V~VE~spYDltkGRIi 68 (87)
T PRK12442 47 ILAGDRVTLELSPYDLTKGRIN 68 (87)
T ss_pred ecCCCEEEEEECcccCCceeEE
Confidence 4567777776655666777765
No 29
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=77.63 E-value=2.1 Score=27.93 Aligned_cols=21 Identities=24% Similarity=0.365 Sum_probs=9.3
Q ss_pred cCCCEEEEeccCCCCCCCcEE
Q 033489 63 KRGDILFLHMSKDPIRAGEIV 83 (118)
Q Consensus 63 ~~GD~vlv~k~~~~~~~GDIV 83 (118)
..||.|+++....+..+|||+
T Consensus 45 ~~GD~VlVe~~~~~~~kg~Iv 65 (83)
T smart00652 45 RRGDIVLVDPWDFQDVKADII 65 (83)
T ss_pred cCCCEEEEEecCCCCCEEEEE
Confidence 345555554433334444433
No 30
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=76.93 E-value=9.2 Score=26.77 Aligned_cols=15 Identities=27% Similarity=0.164 Sum_probs=11.2
Q ss_pred CCCCCCcEEEEEeCC
Q 033489 75 DPIRAGEIVVFNVDG 89 (118)
Q Consensus 75 ~~~~~GDIVvf~~~~ 89 (118)
++|++||+|+|+..+
T Consensus 72 ~~p~~GDiv~f~~~~ 86 (129)
T TIGR02594 72 SKPAYGCIAVKRRGG 86 (129)
T ss_pred CCCCccEEEEEECCC
Confidence 357899999997544
No 31
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=76.55 E-value=2.5 Score=27.33 Aligned_cols=21 Identities=29% Similarity=0.488 Sum_probs=9.4
Q ss_pred cCCCEEEEeccCC-CCCCCcEE
Q 033489 63 KRGDILFLHMSKD-PIRAGEIV 83 (118)
Q Consensus 63 ~~GD~vlv~k~~~-~~~~GDIV 83 (118)
.+||.|+++.... +..+|||+
T Consensus 40 ~~GD~VlV~~~~~~~~~kg~Iv 61 (78)
T cd04456 40 KRGDFLIVDPIEEGEDVKADII 61 (78)
T ss_pred cCCCEEEEEecccCCCceEEEE
Confidence 4455555544222 34445444
No 32
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=74.95 E-value=2.7 Score=28.47 Aligned_cols=21 Identities=14% Similarity=0.286 Sum_probs=10.1
Q ss_pred cCCCEEEEeccCCCCCCCcEE
Q 033489 63 KRGDILFLHMSKDPIRAGEIV 83 (118)
Q Consensus 63 ~~GD~vlv~k~~~~~~~GDIV 83 (118)
..||.|++..+..+..+|||+
T Consensus 61 ~~GD~VlVe~~~~~~~kg~Iv 81 (100)
T PRK04012 61 REGDVVIVAPWDFQDEKADII 81 (100)
T ss_pred cCCCEEEEEecccCCCEEEEE
Confidence 355555555433334555544
No 33
>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=72.99 E-value=15 Score=27.10 Aligned_cols=43 Identities=14% Similarity=0.074 Sum_probs=30.7
Q ss_pred CCCCCCcEEEEEeCCCCcCEEEEEEEECCCce-EEEEEEeeecC
Q 033489 75 DPIRAGEIVVFNVDGREIPIVHRVIKVNILLT-LFFELTIQPCC 117 (118)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ikRVI~~~g~~~-~~~~~~~~~~~ 117 (118)
..++.||.|+++.++.+.+++..|..+..+.. ++.++.+.-++
T Consensus 51 ~~~~vGD~Vlik~~~~~~~~V~iI~ei~~~~~~~~v~i~v~Wy~ 94 (179)
T cd04720 51 LELSVGDTILVKDDVANSPSVYLIHEIRLNTLNNEVELWVMWFL 94 (179)
T ss_pred eEEeCCCEEEEeCCCCCCCEEEEEEEEEeCCCCCEEEEEEEEcC
Confidence 45899999999987665678888877765443 66677665443
No 34
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=71.92 E-value=11 Score=25.68 Aligned_cols=38 Identities=18% Similarity=0.413 Sum_probs=27.4
Q ss_pred cCCCCCCCcEEEEEeCCCCcCEEEEEEEECC------CceEEEEEE
Q 033489 73 SKDPIRAGEIVVFNVDGREIPIVHRVIKVNI------LLTLFFELT 112 (118)
Q Consensus 73 ~~~~~~~GDIVvf~~~~~~~~~ikRVI~~~g------~~~~~~~~~ 112 (118)
..++++.||++.+..+.+. +.=+|.+++. +.+.+|+..
T Consensus 45 pS~~VK~GD~l~i~~~~~~--~~v~Vl~~~~~r~~~~~a~~ly~~~ 88 (100)
T COG1188 45 PSKEVKVGDILTIRFGNKE--FTVKVLALGEQRRPAEEARLLYEET 88 (100)
T ss_pred cccccCCCCEEEEEeCCcE--EEEEEEecccccCchhhhccEEEec
Confidence 4567999999999877653 7788888776 445555443
No 35
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=69.72 E-value=13 Score=24.04 Aligned_cols=29 Identities=28% Similarity=0.369 Sum_probs=22.5
Q ss_pred ccccCcCCCEEEEec------cCCCCCCCcEEEEE
Q 033489 58 MEPGFKRGDILFLHM------SKDPIRAGEIVVFN 86 (118)
Q Consensus 58 M~Ptl~~GD~vlv~k------~~~~~~~GDIVvf~ 86 (118)
|+|.++.||.|.+.+ +..+-..|++.+-+
T Consensus 1 ~~p~f~~G~~V~a~~~irNDGt~Pg~~~g~lLv~~ 35 (75)
T PF04319_consen 1 MPPRFEWGDKVRARKDIRNDGTFPGKEIGELLVRK 35 (75)
T ss_pred CCCccCCCCEEEEEEEeEcCCCCCCCCCCCEEEcC
Confidence 899999999999987 23346778887754
No 36
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=66.56 E-value=12 Score=22.82 Aligned_cols=38 Identities=21% Similarity=0.360 Sum_probs=22.6
Q ss_pred CCCccc-cCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEE
Q 033489 55 SGSMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHR 97 (118)
Q Consensus 55 g~SM~P-tl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikR 97 (118)
++++.| +|..|=.+-|-. -++.||.|..+..+.. |+.|
T Consensus 18 ~~~~K~A~letG~~i~VP~---FI~~Gd~I~VdT~~g~--Yv~R 56 (56)
T PF09285_consen 18 SSSYKPATLETGAEIQVPL---FIEEGDKIKVDTRDGS--YVER 56 (56)
T ss_dssp STTEEEEEETTS-EEEEET---T--TT-EEEEETTTTE--EEEE
T ss_pred CCCccEEEEcCCCEEEccc---eecCCCEEEEECCCCe--EeCC
Confidence 445666 456777766643 3899999999866543 8877
No 37
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=65.36 E-value=8.4 Score=25.89 Aligned_cols=33 Identities=24% Similarity=0.572 Sum_probs=22.7
Q ss_pred EEEeCCCccccCcCCCEEEEec--------cCCCCCCCcEEEEEe
Q 033489 51 VVVLSGSMEPGFKRGDILFLHM--------SKDPIRAGEIVVFNV 87 (118)
Q Consensus 51 ~~V~g~SM~Ptl~~GD~vlv~k--------~~~~~~~GDIVvf~~ 87 (118)
+.+..++. .+|=.+++|. ....++.||+|+|-+
T Consensus 51 ifie~g~l----rpGiI~LINd~DWeLleke~y~ledgDiIvfis 91 (96)
T COG5131 51 IFIEHGEL----RPGIICLINDMDWELLEKERYPLEDGDIIVFIS 91 (96)
T ss_pred eeecCCCC----cccEEEEEcCccHhhhhcccccCCCCCEEEEEe
Confidence 55666554 4566677775 235689999999964
No 38
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=64.57 E-value=3.8 Score=26.05 Aligned_cols=17 Identities=29% Similarity=0.649 Sum_probs=12.6
Q ss_pred CCccccCcCCCEEEEec
Q 033489 56 GSMEPGFKRGDILFLHM 72 (118)
Q Consensus 56 ~SM~Ptl~~GD~vlv~k 72 (118)
.||+|.+++|+.||..-
T Consensus 12 ~~m~P~L~~~~yVF~t~ 28 (72)
T PF10000_consen 12 ASMSPELNPGEYVFCTV 28 (72)
T ss_dssp ST-EEEE-SS-EEEEEE
T ss_pred hhCCcEeCCCCEEEEEe
Confidence 48999999999999975
No 39
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=61.94 E-value=36 Score=22.81 Aligned_cols=28 Identities=25% Similarity=0.266 Sum_probs=14.2
Q ss_pred CCCCCCCcEEEEEeCCC-CcCEEEEEEEE
Q 033489 74 KDPIRAGEIVVFNVDGR-EIPIVHRVIKV 101 (118)
Q Consensus 74 ~~~~~~GDIVvf~~~~~-~~~~ikRVI~~ 101 (118)
...|++|||++|+.... ..=.|-=|.++
T Consensus 60 ~~~P~~Gdivv~~~~~~~~~GHVaIV~~v 88 (124)
T PF05257_consen 60 GSTPQPGDIVVWDSGSGGGYGHVAIVESV 88 (124)
T ss_dssp CS---TTEEEEEEECTTTTT-EEEEEEEE
T ss_pred CcccccceEEEeccCCCCCCCeEEEEEEE
Confidence 45799999999953222 11145555555
No 40
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=60.87 E-value=8.2 Score=26.13 Aligned_cols=34 Identities=26% Similarity=0.560 Sum_probs=25.5
Q ss_pred eEEEeCCCccccCcCCCEEEEec--------cCCCCCCCcEEEEEe
Q 033489 50 VVVVLSGSMEPGFKRGDILFLHM--------SKDPIRAGEIVVFNV 87 (118)
Q Consensus 50 ~~~V~g~SM~Ptl~~GD~vlv~k--------~~~~~~~GDIVvf~~ 87 (118)
-+.+.++|..|. =++++|. ...+++.||.|+|-+
T Consensus 55 ~lFi~~gsvrpG----ii~lINd~DWEllekedy~ledgD~ivfiS 96 (101)
T KOG4146|consen 55 SLFIHHGSVRPG----IIVLINDMDWELLEKEDYPLEDGDHIVFIS 96 (101)
T ss_pred ceEeeCCcCcCc----EEEEEeccchhhhcccccCcccCCEEEEEE
Confidence 378899987774 4667765 246799999999964
No 41
>PF14118 YfzA: YfzA-like protein
Probab=60.75 E-value=11 Score=25.43 Aligned_cols=16 Identities=25% Similarity=0.534 Sum_probs=13.7
Q ss_pred EEeCCCccccCcCCCE
Q 033489 52 VVLSGSMEPGFKRGDI 67 (118)
Q Consensus 52 ~V~g~SM~Ptl~~GD~ 67 (118)
.+++.|+.|.+++||.
T Consensus 29 ~~d~t~w~pnf~~g~~ 44 (94)
T PF14118_consen 29 IFDGTGWGPNFNEGDF 44 (94)
T ss_pred HhhccccccccCCCch
Confidence 5679999999999875
No 42
>PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 This entry is represented by Bacteriophage SFi21, lysin (Cell wall hydrolase; 3.5.1.28 from EC). At least one of proteins in this entry, the Pal protein from the pneumococcal bacteriophage Dp-1 (O03979 from SWISSPROT) has been shown to be an N-acetylmuramoyl-L-alanine amidase []. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside within this domain while a C-terminal domain binds to the choline residues of the cell wall teichoic acids [, ].
Probab=60.04 E-value=9.5 Score=27.49 Aligned_cols=38 Identities=8% Similarity=0.136 Sum_probs=26.5
Q ss_pred EEEeCCCccccCcCCCEEEEecc-CCCCCCCcEEEEEeC
Q 033489 51 VVVLSGSMEPGFKRGDILFLHMS-KDPIRAGEIVVFNVD 88 (118)
Q Consensus 51 ~~V~g~SM~Ptl~~GD~vlv~k~-~~~~~~GDIVvf~~~ 88 (118)
....++||...|...=.-.+.+. ..++|+|||+++...
T Consensus 49 ~~~nT~tl~~~L~~~G~~~I~~~~~~~~q~GDI~I~g~~ 87 (145)
T PF05382_consen 49 SAGNTETLHDWLKKNGFKKISENVDWNLQRGDIFIWGRR 87 (145)
T ss_pred CccCHHHHHHHHhhCCcEEeccCCcccccCCCEEEEcCC
Confidence 35677899887765555555542 247999999998654
No 43
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=59.35 E-value=14 Score=22.49 Aligned_cols=38 Identities=24% Similarity=0.334 Sum_probs=23.5
Q ss_pred CCCcccc-CcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEE
Q 033489 55 SGSMEPG-FKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHR 97 (118)
Q Consensus 55 g~SM~Pt-l~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikR 97 (118)
++|+.|. |..|=.+-|- .-++.||.|..+..... |+.|
T Consensus 18 ~~~~K~A~letG~~i~VP---~FI~~Gd~I~V~T~~g~--Y~~R 56 (56)
T cd05794 18 SSGTKPATLETGAEVQVP---LFIKEGEKIKVDTRTGE--YVER 56 (56)
T ss_pred CCCcceEEECCCCEEEcC---CeecCCCEEEEECCCCc--EecC
Confidence 4466664 4566544442 23789999988765443 6665
No 44
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.62 E-value=5.5 Score=28.09 Aligned_cols=17 Identities=35% Similarity=0.638 Sum_probs=15.0
Q ss_pred CCccccCcCCCEEEEec
Q 033489 56 GSMEPGFKRGDILFLHM 72 (118)
Q Consensus 56 ~SM~Ptl~~GD~vlv~k 72 (118)
.||.|.+.+||.|+..-
T Consensus 12 ~smtPeL~~G~yVfcT~ 28 (134)
T COG3602 12 ASMTPELLDGDYVFCTV 28 (134)
T ss_pred HhcCccccCCceEEEEe
Confidence 48999999999999864
No 45
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=58.54 E-value=7.8 Score=26.94 Aligned_cols=20 Identities=25% Similarity=0.380 Sum_probs=16.5
Q ss_pred EeCCCccccCcCCCEEEEec
Q 033489 53 VLSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 53 V~g~SM~Ptl~~GD~vlv~k 72 (118)
-.+++|.|.|+.||.|++.-
T Consensus 47 ~~~~~~~~~L~~GD~VLA~~ 66 (124)
T PF15057_consen 47 ALSDAMRHSLQVGDKVLAPW 66 (124)
T ss_pred EccCcccCcCCCCCEEEEec
Confidence 34578899999999999974
No 46
>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=58.53 E-value=28 Score=24.30 Aligned_cols=37 Identities=24% Similarity=0.345 Sum_probs=21.8
Q ss_pred CCCCCcEEEEEeCCCC-----------cCEEEEEEEECCC--ceEEEEEE
Q 033489 76 PIRAGEIVVFNVDGRE-----------IPIVHRVIKVNIL--LTLFFELT 112 (118)
Q Consensus 76 ~~~~GDIVvf~~~~~~-----------~~~ikRVI~~~g~--~~~~~~~~ 112 (118)
.++.||+|..+.++.+ ..+|-||..+..+ +...|++.
T Consensus 5 ~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~ 54 (130)
T cd04712 5 TIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGR 54 (130)
T ss_pred EEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEE
Confidence 3566777777654432 3578888777654 34455443
No 47
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970.
Probab=57.39 E-value=16 Score=22.27 Aligned_cols=38 Identities=24% Similarity=0.391 Sum_probs=24.9
Q ss_pred CCCccc-cCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEE
Q 033489 55 SGSMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHR 97 (118)
Q Consensus 55 g~SM~P-tl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikR 97 (118)
++|+.| +|..|-.+-|- .-++.||.|..+..... |+.|
T Consensus 18 ~~~~K~A~letG~~i~VP---~FI~~Gd~I~V~T~~g~--Y~~R 56 (56)
T smart00841 18 SGGTKPATLETGAVVQVP---LFINEGDKIKVDTRTGE--YVSR 56 (56)
T ss_pred CCCcceEEECCCCEEEcC---CcccCCCEEEEECCCCc--EEcC
Confidence 445565 45677766663 23899999988765443 6665
No 48
>PLN00208 translation initiation factor (eIF); Provisional
Probab=56.45 E-value=10 Score=27.50 Aligned_cols=24 Identities=13% Similarity=0.335 Sum_probs=17.3
Q ss_pred CcCCCEEEEeccCCCCCCCcEEEE
Q 033489 62 FKRGDILFLHMSKDPIRAGEIVVF 85 (118)
Q Consensus 62 l~~GD~vlv~k~~~~~~~GDIVvf 85 (118)
+.+||.|+|.....+..+||||--
T Consensus 71 I~~GD~VlVel~~~d~~KgdIv~r 94 (145)
T PLN00208 71 IAAGDIILVGLRDYQDDKADVILK 94 (145)
T ss_pred ecCCCEEEEEccCCCCCEEEEEEE
Confidence 468888888765556788887744
No 49
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=55.88 E-value=35 Score=23.32 Aligned_cols=28 Identities=36% Similarity=0.582 Sum_probs=19.3
Q ss_pred CCCCcEEEEEeCCC-CcCEEEEEEEECCC
Q 033489 77 IRAGEIVVFNVDGR-EIPIVHRVIKVNIL 104 (118)
Q Consensus 77 ~~~GDIVvf~~~~~-~~~~ikRVI~~~g~ 104 (118)
++.||-|.+++++. +.++|-||..+-.+
T Consensus 4 ~~vGD~V~v~~~~~~~~pyIgrI~~i~e~ 32 (121)
T cd04714 4 IRVGDCVLFKSPGRPSLPYVARIESLWED 32 (121)
T ss_pred EEcCCEEEEeCCCCCCCCEEEEEEEEEEc
Confidence 56788888876654 44688888876543
No 50
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=55.38 E-value=11 Score=27.64 Aligned_cols=24 Identities=13% Similarity=0.321 Sum_probs=16.9
Q ss_pred CcCCCEEEEeccCCCCCCCcEEEE
Q 033489 62 FKRGDILFLHMSKDPIRAGEIVVF 85 (118)
Q Consensus 62 l~~GD~vlv~k~~~~~~~GDIVvf 85 (118)
+.+||+|+|.....+..+||||--
T Consensus 71 I~~GD~VlVel~~yd~~KgdIi~R 94 (155)
T PTZ00329 71 INIGDIILVSLRDFQDSKADVILK 94 (155)
T ss_pred ecCCCEEEEeccCCCCCEEEEEEE
Confidence 468888888775556777887643
No 51
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=53.65 E-value=4.2 Score=30.07 Aligned_cols=19 Identities=16% Similarity=0.307 Sum_probs=15.4
Q ss_pred cCEEEEEEEECCCceEEEE
Q 033489 92 IPIVHRVIKVNILLTLFFE 110 (118)
Q Consensus 92 ~~~ikRVI~~~g~~~~~~~ 110 (118)
.+.+|||.++||+.+--+.
T Consensus 82 ~pllK~i~Alpgq~Vci~~ 100 (173)
T COG4959 82 IPLLKRILALPGQHVCITS 100 (173)
T ss_pred cHHHHHHhcCCCCcEEEec
Confidence 3579999999998877663
No 52
>COG0179 MhpD 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=52.92 E-value=33 Score=27.00 Aligned_cols=30 Identities=17% Similarity=0.476 Sum_probs=23.3
Q ss_pred cCcCCCEEEEec--cCCCCCCCcEEEEEeCCC
Q 033489 61 GFKRGDILFLHM--SKDPIRAGEIVVFNVDGR 90 (118)
Q Consensus 61 tl~~GD~vlv~k--~~~~~~~GDIVvf~~~~~ 90 (118)
||++||+++.-. ....++.||+|..+.++-
T Consensus 224 tL~pGDvI~TGTP~Gvg~l~~GD~v~~~iegi 255 (266)
T COG0179 224 TLEPGDVILTGTPSGVGFLKPGDVVEVEIEGI 255 (266)
T ss_pred ccCCCCEEEeCCCCCcccCCCCCEEEEEecce
Confidence 789999988865 234689999998887664
No 53
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=52.36 E-value=15 Score=23.00 Aligned_cols=10 Identities=30% Similarity=0.458 Sum_probs=9.1
Q ss_pred CCCCcEEEEE
Q 033489 77 IRAGEIVVFN 86 (118)
Q Consensus 77 ~~~GDIVvf~ 86 (118)
+..||.|.|+
T Consensus 47 i~vGD~V~ve 56 (72)
T PRK00276 47 ILPGDKVTVE 56 (72)
T ss_pred cCCCCEEEEE
Confidence 7889999998
No 54
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=51.97 E-value=32 Score=23.58 Aligned_cols=28 Identities=18% Similarity=0.432 Sum_probs=18.0
Q ss_pred CCCCCCcEEEEEeCCCCcCEEEEEEEEC
Q 033489 75 DPIRAGEIVVFNVDGREIPIVHRVIKVN 102 (118)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ikRVI~~~ 102 (118)
.+++.||.++|+.-..+....-+|..+.
T Consensus 30 ~~ikvGD~I~f~~~~~~~~l~v~V~~i~ 57 (109)
T cd06555 30 QQIKVGDKILFNDLDTGQQLLVKVVDIR 57 (109)
T ss_pred hcCCCCCEEEEEEcCCCcEEEEEEEEEE
Confidence 4699999999976432223555555543
No 55
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=47.17 E-value=13 Score=25.76 Aligned_cols=10 Identities=20% Similarity=-0.071 Sum_probs=4.2
Q ss_pred HHHHHHHHHH
Q 033489 22 QGVSLGMIVT 31 (118)
Q Consensus 22 ~i~~i~~~~~ 31 (118)
|++.++++++
T Consensus 2 W~l~~iii~~ 11 (130)
T PF12273_consen 2 WVLFAIIIVA 11 (130)
T ss_pred eeeHHHHHHH
Confidence 4444443333
No 56
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=47.01 E-value=39 Score=21.92 Aligned_cols=28 Identities=18% Similarity=0.246 Sum_probs=15.7
Q ss_pred CCCCcEEEEEeCCC---CcCEEEEEEEECCC
Q 033489 77 IRAGEIVVFNVDGR---EIPIVHRVIKVNIL 104 (118)
Q Consensus 77 ~~~GDIVvf~~~~~---~~~~ikRVI~~~g~ 104 (118)
.+.||.|.++.++. +.+++-||..+-.+
T Consensus 4 y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~ 34 (123)
T cd04370 4 YEVGDSVYVEPDDSIKSDPPYIARIEELWED 34 (123)
T ss_pred EecCCEEEEecCCcCCCCCCEEEEEeeeeEC
Confidence 34556555554442 34677777766554
No 57
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=46.45 E-value=92 Score=21.19 Aligned_cols=38 Identities=16% Similarity=0.103 Sum_probs=24.2
Q ss_pred CCEEEEec---cCCCCCCCcEEEEEeCCCCcCEEEEEEEECC
Q 033489 65 GDILFLHM---SKDPIRAGEIVVFNVDGREIPIVHRVIKVNI 103 (118)
Q Consensus 65 GD~vlv~k---~~~~~~~GDIVvf~~~~~~~~~ikRVI~~~g 103 (118)
+|..-+.. ...++..||+|.++.++ +.+...+++.-.|
T Consensus 11 ~~~y~l~n~Pf~a~glA~gDvV~~~~~~-g~~~~~~~v~~sG 51 (117)
T PF14085_consen 11 DDTYRLDNIPFFAYGLALGDVVRAEPDD-GELWFQKVVESSG 51 (117)
T ss_pred CCEEEEEecccccCCCCCCCEEEEEeCC-CeEEEEEEEecCC
Confidence 34444544 24679999999998776 3455555555554
No 58
>CHL00010 infA translation initiation factor 1
Probab=45.51 E-value=24 Score=22.54 Aligned_cols=10 Identities=30% Similarity=0.391 Sum_probs=8.3
Q ss_pred CCCCcEEEEE
Q 033489 77 IRAGEIVVFN 86 (118)
Q Consensus 77 ~~~GDIVvf~ 86 (118)
|..||.|.|+
T Consensus 47 ~~vGD~V~ve 56 (78)
T CHL00010 47 ILPGDRVKVE 56 (78)
T ss_pred cCCCCEEEEE
Confidence 6778888887
No 59
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=45.51 E-value=47 Score=19.64 Aligned_cols=24 Identities=17% Similarity=0.408 Sum_probs=15.7
Q ss_pred CCCCCcEEEEEeCCCCcCEEEEEE
Q 033489 76 PIRAGEIVVFNVDGREIPIVHRVI 99 (118)
Q Consensus 76 ~~~~GDIVvf~~~~~~~~~ikRVI 99 (118)
.+-.||.|.++.++.+...|.++.
T Consensus 37 ~~~VGD~V~~~~~~~~~~~I~~vl 60 (68)
T cd04466 37 PPAVGDRVEFEPEDDGEGVIEEIL 60 (68)
T ss_pred CCCCCcEEEEEECCCCcEEEEEEe
Confidence 478999999976444333555554
No 60
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=45.20 E-value=21 Score=23.45 Aligned_cols=31 Identities=23% Similarity=0.460 Sum_probs=21.0
Q ss_pred ccCcCCCEEEEec-cCCCCCCCcEEEEEeCCC
Q 033489 60 PGFKRGDILFLHM-SKDPIRAGEIVVFNVDGR 90 (118)
Q Consensus 60 Ptl~~GD~vlv~k-~~~~~~~GDIVvf~~~~~ 90 (118)
||-..+|.+.-+. ...+++.||.++|.+-|.
T Consensus 65 ptC~~~D~i~~~~~lP~~l~~GD~l~f~~~GA 96 (116)
T PF00278_consen 65 PTCDSGDVIARDVMLPKELEVGDWLVFENMGA 96 (116)
T ss_dssp SSSSTTSEEEEEEEEESTTTTT-EEEESS-SS
T ss_pred CCcCCCceEeeeccCCCCCCCCCEEEEecCcc
Confidence 6777889886544 233799999999986553
No 61
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=43.41 E-value=25 Score=23.71 Aligned_cols=9 Identities=44% Similarity=1.025 Sum_probs=5.1
Q ss_pred CCCCcEEEE
Q 033489 77 IRAGEIVVF 85 (118)
Q Consensus 77 ~~~GDIVvf 85 (118)
+++||+|+.
T Consensus 58 I~~GD~VlV 66 (99)
T TIGR00523 58 IREGDVVIV 66 (99)
T ss_pred ecCCCEEEE
Confidence 455555555
No 62
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=43.11 E-value=51 Score=24.12 Aligned_cols=28 Identities=21% Similarity=0.374 Sum_probs=16.9
Q ss_pred CCCCcEEEEEeCCCCcCEEEEEEEECCC
Q 033489 77 IRAGEIVVFNVDGREIPIVHRVIKVNIL 104 (118)
Q Consensus 77 ~~~GDIVvf~~~~~~~~~ikRVI~~~g~ 104 (118)
++.||-|.++.+...-++|.||..+...
T Consensus 4 yrvGD~Vy~~~~~~~Py~I~rI~e~~~~ 31 (164)
T cd04709 4 YRVGDYVYFESSPNNPYLIRRIEELNKT 31 (164)
T ss_pred EecCCEEEEECCCCCCCEEEEEEEEEeC
Confidence 4567777776543323567888776543
No 63
>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=41.95 E-value=32 Score=24.17 Aligned_cols=28 Identities=18% Similarity=0.262 Sum_probs=12.3
Q ss_pred CCCcEEEEEeCCCCcCEEEEEEEECCCc
Q 033489 78 RAGEIVVFNVDGREIPIVHRVIKVNILL 105 (118)
Q Consensus 78 ~~GDIVvf~~~~~~~~~ikRVI~~~g~~ 105 (118)
+.||-|..++++.+..|+-|+..+-+++
T Consensus 5 ~vGd~VlI~~~d~~~~yVAkI~~i~e~~ 32 (128)
T cd04719 5 EVGDFVLIEGEDADGPDVARILHLYEDG 32 (128)
T ss_pred ecCCEEEEECCCCCCCcEeeehhhhccc
Confidence 3444444443332234555555544443
No 64
>smart00439 BAH Bromo adjacent homology domain.
Probab=41.81 E-value=69 Score=20.80 Aligned_cols=24 Identities=25% Similarity=0.445 Sum_probs=11.9
Q ss_pred CCCcEEEEEeCCC-CcCEEEEEEEE
Q 033489 78 RAGEIVVFNVDGR-EIPIVHRVIKV 101 (118)
Q Consensus 78 ~~GDIVvf~~~~~-~~~~ikRVI~~ 101 (118)
+.||-|.+++++. ..+++-||..+
T Consensus 3 ~vgd~V~v~~~~~~~~~~i~~I~~i 27 (120)
T smart00439 3 RVGDFVLVEPDDADEPYYIGRIEEI 27 (120)
T ss_pred ccCCEEEEeCCCCCCCCEEEEEEEE
Confidence 4455555554431 23455555554
No 65
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=41.46 E-value=21 Score=23.14 Aligned_cols=11 Identities=27% Similarity=0.631 Sum_probs=6.4
Q ss_pred CCCCcEEEEEe
Q 033489 77 IRAGEIVVFNV 87 (118)
Q Consensus 77 ~~~GDIVvf~~ 87 (118)
+++||+|+...
T Consensus 39 IkrGd~VlV~p 49 (78)
T cd05792 39 IKRGDFVLVEP 49 (78)
T ss_pred EEeCCEEEEEe
Confidence 46666666653
No 66
>PF09138 Urm1: Urm1 (Ubiquitin related modifier); InterPro: IPR015221 Ubiquitin related modifier 1 (Urm1) is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like urmylation pathway []. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily []. ; GO: 0034227 tRNA thio-modification, 0005737 cytoplasm; PDB: 2AX5_A 2QJL_A 2PKO_A 1WGK_A 1XO3_A 2K9X_A.
Probab=41.21 E-value=26 Score=23.55 Aligned_cols=28 Identities=11% Similarity=0.312 Sum_probs=18.7
Q ss_pred ccCcCCCEEEEecc--------CCCCCCCcEEEEEe
Q 033489 60 PGFKRGDILFLHMS--------KDPIRAGEIVVFNV 87 (118)
Q Consensus 60 Ptl~~GD~vlv~k~--------~~~~~~GDIVvf~~ 87 (118)
.++++|=+|++|.. ...++.||.|+|-+
T Consensus 56 ~~vrPGILvLINd~DwEl~g~~~y~l~~~D~I~FiS 91 (96)
T PF09138_consen 56 GSVRPGILVLINDADWELLGEEDYVLKDGDNITFIS 91 (96)
T ss_dssp SSB-TTEEEEETTCEHHHHTCCCSB--TTEEEEEEE
T ss_pred CeEcCcEEEEEcCccceeecCcceEcCCCCEEEEEc
Confidence 45666778999861 35699999999965
No 67
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=40.82 E-value=33 Score=26.35 Aligned_cols=11 Identities=9% Similarity=0.283 Sum_probs=4.8
Q ss_pred HHHHHHHHHHH
Q 033489 18 QVLTQGVSLGM 28 (118)
Q Consensus 18 ~i~~~i~~i~~ 28 (118)
.++.+++.+++
T Consensus 14 ~iLNiaI~IV~ 24 (217)
T PF07423_consen 14 KILNIAIGIVS 24 (217)
T ss_pred hhHHHHHHHHH
Confidence 34444444433
No 68
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=40.57 E-value=70 Score=21.56 Aligned_cols=27 Identities=22% Similarity=0.335 Sum_probs=15.7
Q ss_pred CCCCcEEEEEeCCC-CcCEEEEEEEECC
Q 033489 77 IRAGEIVVFNVDGR-EIPIVHRVIKVNI 103 (118)
Q Consensus 77 ~~~GDIVvf~~~~~-~~~~ikRVI~~~g 103 (118)
++.||-|.++++++ ...++-||..+-.
T Consensus 4 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~ 31 (121)
T cd04717 4 YRVGDCVYVANPEDPSKPIIFRIERLWK 31 (121)
T ss_pred EECCCEEEEeCCCCCCCCEEEEEeEEEE
Confidence 45666666665543 4456666666543
No 69
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=38.94 E-value=21 Score=24.77 Aligned_cols=13 Identities=31% Similarity=0.726 Sum_probs=11.2
Q ss_pred CCCCCCcEEEEEe
Q 033489 75 DPIRAGEIVVFNV 87 (118)
Q Consensus 75 ~~~~~GDIVvf~~ 87 (118)
+++++||+|.|+.
T Consensus 75 ~~~qpGDlvff~~ 87 (134)
T TIGR02219 75 DAAQPGDVLVFRW 87 (134)
T ss_pred hcCCCCCEEEEee
Confidence 5689999999985
No 70
>PF09874 DUF2101: Predicted membrane protein (DUF2101); InterPro: IPR018663 This family of conserved hypothetical proteins has no known function.
Probab=38.47 E-value=1.2e+02 Score=23.23 Aligned_cols=67 Identities=16% Similarity=0.252 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhCCCCC-----------eEEEeCCCccccCcCCCEEEEeccCCCCCCCcEEEEEeC
Q 033489 20 LTQGVSLGMIVTSALIIWKALMCITGSESP-----------VVVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVD 88 (118)
Q Consensus 20 ~~~i~~i~~~~~i~~li~~~~~~~~g~~~~-----------~~~V~g~SM~Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~ 88 (118)
......++++++++++++..+..-.|..++ ..+...+.+..+.++|-- .+++ ..+.+.||+|--.-.
T Consensus 116 ~~y~~yL~~v~laVl~fr~~Fr~ky~RdyTyG~VeEv~~~~v~V~V~dDI~ANVkPg~Y-wV~~-~~d~~~G~vVKl~VE 193 (206)
T PF09874_consen 116 YPYYTYLGFVFLAVLAFRYYFRSKYGRDYTYGVVEEVKENLVRVFVHDDIAANVKPGYY-WVEA-VPDVEEGDVVKLLVE 193 (206)
T ss_pred hhHHHHHHHHHHHHHHHhhheeeeecccceeEEEEEecCCEEEEEEccchhhcCCCCeE-EecC-CCCCCCCceEEEEEe
Confidence 334444444444444454444444666554 223334445555555544 3333 236777777765543
No 71
>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=38.23 E-value=59 Score=23.04 Aligned_cols=27 Identities=11% Similarity=0.228 Sum_probs=17.7
Q ss_pred CCCCCcEEEEEeCCCCcCEEEEEEEEC
Q 033489 76 PIRAGEIVVFNVDGREIPIVHRVIKVN 102 (118)
Q Consensus 76 ~~~~GDIVvf~~~~~~~~~ikRVI~~~ 102 (118)
.++.||-|.+++++...+||-+|..+-
T Consensus 20 ~y~vgD~Vlv~~~~~~~pyI~~I~~i~ 46 (146)
T cd04713 20 KYRLEDCVLLVPEDDQKPYIAIIKDIY 46 (146)
T ss_pred EEECCCEEEEeCCCCCCCEEEEEEEEE
Confidence 467788888876544446666766654
No 72
>PRK14578 elongation factor P; Provisional
Probab=38.13 E-value=64 Score=24.16 Aligned_cols=37 Identities=14% Similarity=0.205 Sum_probs=23.9
Q ss_pred Cccc-cCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEE
Q 033489 57 SMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (118)
Q Consensus 57 SM~P-tl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRV 98 (118)
+..| ++..|=.|-|- .-++.||.|..+..... |+.|+
T Consensus 150 ~~KpA~leTG~~v~VP---~FI~~Gd~I~VdT~~g~--Y~~R~ 187 (187)
T PRK14578 150 QTKEAVLETGLRLQVP---PYLESGEKIKVDTRDGR--FISRA 187 (187)
T ss_pred CcceEEEcCCCEEEeC---CcccCCCEEEEECCCCc--EEeeC
Confidence 3454 34566544442 23899999999876544 88885
No 73
>PRK08564 5'-methylthioadenosine phosphorylase II; Reviewed
Probab=37.69 E-value=23 Score=27.82 Aligned_cols=19 Identities=26% Similarity=0.510 Sum_probs=16.6
Q ss_pred eCCCccccCcCCCEEEEec
Q 033489 54 LSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 54 ~g~SM~Ptl~~GD~vlv~k 72 (118)
..+||.|.+++||.++.+-
T Consensus 92 avGsl~~~~~pGDlVv~~D 110 (267)
T PRK08564 92 AVGSLREDYKPGDFVIPDQ 110 (267)
T ss_pred cccccCCCCCCCCEEeehh
Confidence 3479999999999999876
No 74
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=37.55 E-value=42 Score=21.24 Aligned_cols=16 Identities=25% Similarity=0.727 Sum_probs=9.9
Q ss_pred CCCCCCCcEEEEEeCC
Q 033489 74 KDPIRAGEIVVFNVDG 89 (118)
Q Consensus 74 ~~~~~~GDIVvf~~~~ 89 (118)
.++++.||+++|+..+
T Consensus 71 ~n~L~~GD~~~F~~~~ 86 (100)
T PF02362_consen 71 DNGLKEGDVCVFELIG 86 (100)
T ss_dssp HCT--TT-EEEEEE-S
T ss_pred HcCCCCCCEEEEEEec
Confidence 4679999999999654
No 75
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=37.39 E-value=40 Score=22.01 Aligned_cols=26 Identities=27% Similarity=0.437 Sum_probs=14.8
Q ss_pred CCCCcEEEEEeCC-CCcCEEEEEEEEC
Q 033489 77 IRAGEIVVFNVDG-REIPIVHRVIKVN 102 (118)
Q Consensus 77 ~~~GDIVvf~~~~-~~~~~ikRVI~~~ 102 (118)
++.||.|..+.++ ...+++.||..+-
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i~ 29 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEIW 29 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEEE
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEEE
Confidence 3456666666554 2345677776654
No 76
>TIGR02178 yeiP elongation factor P-like protein YeiP. This model represents the family of Escherichia coli protein YeiP, a close homolog of elongation factor P (TIGR00038) and probably itself a translation factor. Member of this family are found only in some Gammaproteobacteria, including E. coli and Vibrio cholerae.
Probab=36.84 E-value=56 Score=24.46 Aligned_cols=38 Identities=21% Similarity=0.358 Sum_probs=25.0
Q ss_pred CCccc-cCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEE
Q 033489 56 GSMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (118)
Q Consensus 56 ~SM~P-tl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRV 98 (118)
+++.| +|..|=.|-|- .-++.||.|..+..... |+.|+
T Consensus 148 ~~~KpA~LeTG~~v~VP---~FI~~Gd~IkVdTrtg~--Y~~R~ 186 (186)
T TIGR02178 148 KRPKPAKLITGLVVQVP---EYITTGERILINTTERA--FMGRA 186 (186)
T ss_pred CCcccEEEcCCCEEEeC---CeecCCCEEEEECCCCc--EEccC
Confidence 34565 45666555442 23899999999876544 88885
No 77
>PF06923 GutM: Glucitol operon activator protein (GutM); InterPro: IPR009693 This family consists of several glucitol operon activator (GutM) proteins. Expression of the glucitol (gut) operon in Escherichia coli is regulated by an unusual, complex system, which consists of an activator (encoded by the gutM gene) and a repressor (encoded by the gutR gene) in addition to the cAMP-CRP complex (CRP, cAMP receptor protein). Synthesis of the mRNA, which initiates at the promoter specific to the gutR gene, occurs within the gutM gene. Expressional control of the gut operon appears to occur as a consequence of the antagonistic action of the products of the autogenously regulated gutM and gutR genes [].
Probab=36.60 E-value=67 Score=21.84 Aligned_cols=38 Identities=26% Similarity=0.268 Sum_probs=27.3
Q ss_pred cCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEEEEECC
Q 033489 63 KRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVNI 103 (118)
Q Consensus 63 ~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRVI~~~g 103 (118)
+.| .|.+-+.....++|-||++-.++++ .|.+.--+.|
T Consensus 35 ~~G-~V~iG~~~g~f~~g~Ivlla~D~~~--~I~~~~~M~G 72 (109)
T PF06923_consen 35 KKG-RVGIGRSKGRFRPGVIVLLAVDEDG--RIVDAEIMKG 72 (109)
T ss_pred hCC-cEEEeeecCcccCCeEEEEEECCCC--cEEEEEEEec
Confidence 777 6777665667899999999877554 5666555555
No 78
>PRK12426 elongation factor P; Provisional
Probab=36.02 E-value=68 Score=24.01 Aligned_cols=39 Identities=18% Similarity=0.336 Sum_probs=25.9
Q ss_pred CCCccc-cCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEE
Q 033489 55 SGSMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (118)
Q Consensus 55 g~SM~P-tl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRV 98 (118)
+++..| +|..|=.|-|- .-++.||.|..+..... |+.|+
T Consensus 146 t~~~KpAtLeTG~~V~VP---~FI~~Gd~IkVdT~~ge--Y~~R~ 185 (185)
T PRK12426 146 SGGAKKALLETGVEVLVP---PFVEIGDVIKVDTRTCE--YIQRV 185 (185)
T ss_pred CCCcccEEEcCCCEEEeC---CcccCCCEEEEECCCCe--EEeeC
Confidence 345566 45677555552 23899999998866543 88885
No 79
>PRK04542 elongation factor P; Provisional
Probab=35.45 E-value=83 Score=23.60 Aligned_cols=37 Identities=22% Similarity=0.426 Sum_probs=24.7
Q ss_pred Cccc-cCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEE
Q 033489 57 SMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (118)
Q Consensus 57 SM~P-tl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRV 98 (118)
+..| +|..|=.|-|- .-++.||.|..+..... |+.|+
T Consensus 151 ~~KpAtLetG~~v~VP---~FI~~Gd~I~VdT~tge--Yv~R~ 188 (189)
T PRK04542 151 RTKPATLSTGLVIQVP---EYISTGEKIRINTEERK--FMGRA 188 (189)
T ss_pred CCccEEEcCCCEEEeC---CcccCCCEEEEECCCCc--EEeec
Confidence 4455 45666555442 24899999999876543 88886
No 80
>TIGR00038 efp translation elongation factor P. function: involved in peptide bond synthesis. stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity). The trusted cutoff of this model is set high enough to exclude members of TIGR02178, an EFP-like protein of certain Gammaproteobacteria.
Probab=35.35 E-value=55 Score=24.20 Aligned_cols=38 Identities=24% Similarity=0.386 Sum_probs=25.6
Q ss_pred CCccc-cCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEE
Q 033489 56 GSMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (118)
Q Consensus 56 ~SM~P-tl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRV 98 (118)
+|+.| +|..|=.|-|- .-++.||.|..+..... |+.|+
T Consensus 146 ~~~K~A~letG~~v~VP---~fi~~Gd~I~v~T~~g~--y~~R~ 184 (184)
T TIGR00038 146 GGTKPATLETGAVVQVP---LFIEEGEKIKVDTRTGE--YVERA 184 (184)
T ss_pred CCcccEEEcCCCEEEeC---CcccCCCEEEEECCCCc--EEecC
Confidence 36666 44666555542 24899999999876544 88885
No 81
>PRK05573 rplU 50S ribosomal protein L21; Validated
Probab=35.29 E-value=75 Score=21.43 Aligned_cols=34 Identities=18% Similarity=0.408 Sum_probs=26.7
Q ss_pred EEEeCCCccccCcCCCEEEEeccCCCCCCCcEEEEE
Q 033489 51 VVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFN 86 (118)
Q Consensus 51 ~~V~g~SM~Ptl~~GD~vlv~k~~~~~~~GDIVvf~ 86 (118)
..|..++.+=-..+||.+.+++. +.+.||.|.|+
T Consensus 3 AIi~~gGkQykV~~Gd~i~v~~l--~~~~G~~i~l~ 36 (103)
T PRK05573 3 AIIKTGGKQYKVEEGDVIKVEKL--DAEVGDTVEFD 36 (103)
T ss_pred EEEEECCEEEEEeCCCEEEEccc--CCCCCCEEEEe
Confidence 46677777777889999999984 36788888776
No 82
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=35.06 E-value=83 Score=20.32 Aligned_cols=12 Identities=25% Similarity=0.454 Sum_probs=8.1
Q ss_pred cCcCCCEEEEec
Q 033489 61 GFKRGDILFLHM 72 (118)
Q Consensus 61 tl~~GD~vlv~k 72 (118)
..++||.|++..
T Consensus 5 ~Vk~Gd~ViV~~ 16 (75)
T PF11302_consen 5 SVKPGDTVIVQD 16 (75)
T ss_pred ccCCCCEEEEec
Confidence 356777777765
No 83
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=34.94 E-value=29 Score=22.27 Aligned_cols=16 Identities=19% Similarity=0.320 Sum_probs=12.8
Q ss_pred CCCCCCcEEEEEeCCC
Q 033489 75 DPIRAGEIVVFNVDGR 90 (118)
Q Consensus 75 ~~~~~GDIVvf~~~~~ 90 (118)
-+.++||++.|..+.+
T Consensus 55 LeCqpgDiley~~d~~ 70 (73)
T COG3655 55 LECQPGDILEYVPDSD 70 (73)
T ss_pred cCCChhheeEEecCCc
Confidence 4689999999986654
No 84
>PF02559 CarD_CdnL_TRCF: CarD-like/TRCF domain; InterPro: IPR003711 The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. A single gene, carD, is required for the activation of both light- and starvation-inducible genes []. The predicted protein contains four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3MLQ_H 2EYQ_A.
Probab=34.93 E-value=40 Score=21.83 Aligned_cols=12 Identities=25% Similarity=0.432 Sum_probs=7.1
Q ss_pred CCCCcEEEEEeC
Q 033489 77 IRAGEIVVFNVD 88 (118)
Q Consensus 77 ~~~GDIVvf~~~ 88 (118)
++.||.|++...
T Consensus 2 f~~GD~VVh~~~ 13 (98)
T PF02559_consen 2 FKIGDYVVHPNH 13 (98)
T ss_dssp --TTSEEEETTT
T ss_pred CCCCCEEEECCC
Confidence 567888887544
No 85
>PF10030 DUF2272: Uncharacterized protein conserved in bacteria (DUF2272); InterPro: IPR019262 This is a domain of unknown function found in proteins of unknown function.
Probab=34.90 E-value=1.9e+02 Score=21.54 Aligned_cols=34 Identities=18% Similarity=0.210 Sum_probs=24.2
Q ss_pred EEEeCCCccccCcCCCEEEEeccC-------------CCCCCCcEEEEE
Q 033489 51 VVVLSGSMEPGFKRGDILFLHMSK-------------DPIRAGEIVVFN 86 (118)
Q Consensus 51 ~~V~g~SM~Ptl~~GD~vlv~k~~-------------~~~~~GDIVvf~ 86 (118)
....-+.-.| +.||+|+..|.. .-+++-||||-.
T Consensus 85 ~~~~~~~y~P--~~GDlIc~~R~~~~~~~~~~~~~~~~~~~HcdIVVa~ 131 (183)
T PF10030_consen 85 RARDPAEYKP--RPGDLICYDRGRSKTYDFASLPTSGGFPSHCDIVVAV 131 (183)
T ss_pred cccCcCCCCC--CCCCEEEecCCCCcccchhhhccCCCCCCceeEEEee
Confidence 3444556666 789999999832 246888999984
No 86
>PF04970 LRAT: Lecithin retinol acyltransferase; InterPro: IPR007053 This entry represents a conserved sequence region found in proteins from viruses, bacteria and eukaryotes. It contains a well-conserved NCEHF motif, though its function in these proteins is unknown.; PDB: 2KYT_A 4DOT_A 4FA0_A.
Probab=34.79 E-value=1.2e+02 Score=20.28 Aligned_cols=13 Identities=8% Similarity=0.271 Sum_probs=5.0
Q ss_pred CCCCCcEEEEEeC
Q 033489 76 PIRAGEIVVFNVD 88 (118)
Q Consensus 76 ~~~~GDIVvf~~~ 88 (118)
.+++||+|.++..
T Consensus 6 ~~~~GD~I~~~r~ 18 (125)
T PF04970_consen 6 RLKPGDHIEVPRG 18 (125)
T ss_dssp S--TT-EEEEEET
T ss_pred CCCCCCEEEEecC
Confidence 3555555555443
No 87
>PRK08666 5'-methylthioadenosine phosphorylase; Validated
Probab=33.92 E-value=26 Score=27.02 Aligned_cols=19 Identities=37% Similarity=0.714 Sum_probs=16.7
Q ss_pred eCCCccccCcCCCEEEEec
Q 033489 54 LSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 54 ~g~SM~Ptl~~GD~vlv~k 72 (118)
..+|+.|.+++||+|+.+.
T Consensus 84 saGsl~~~l~~GDiVi~~d 102 (261)
T PRK08666 84 AVGSLNPNMKPGDFVILDQ 102 (261)
T ss_pred cccccCCCCCCCCEEeehh
Confidence 3479999999999999976
No 88
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=33.76 E-value=2.1e+02 Score=22.60 Aligned_cols=43 Identities=23% Similarity=0.247 Sum_probs=29.6
Q ss_pred CCCCCCCcEEEEEeCCC---CcCEEEEEEEECCCceEEE-EEEeeec
Q 033489 74 KDPIRAGEIVVFNVDGR---EIPIVHRVIKVNILLTLFF-ELTIQPC 116 (118)
Q Consensus 74 ~~~~~~GDIVvf~~~~~---~~~~ikRVI~~~g~~~~~~-~~~~~~~ 116 (118)
..+++.||.|+-..-+. .+..+.+|-.+..++...+ ++.+.|+
T Consensus 210 ~~~i~~GD~vvTSGlgg~fP~Gl~Vg~V~~v~~~~~~~~~~v~~~P~ 256 (284)
T COG1792 210 NSDIKEGDLVVTSGLGGVFPAGLPVGEVSSVKLDDYGLFKVVIVKPA 256 (284)
T ss_pred CCCccCCCEEEecCCCCcCCCCcEEEEEEEEEeCCCceeEEEEEecc
Confidence 46789999888764332 3578888888888775555 4555554
No 89
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=33.19 E-value=1.2e+02 Score=20.98 Aligned_cols=36 Identities=14% Similarity=0.270 Sum_probs=21.2
Q ss_pred eEEEeCCCccccCcCCCEEEEec-c---CCCCCCCcEEEEEe
Q 033489 50 VVVVLSGSMEPGFKRGDILFLHM-S---KDPIRAGEIVVFNV 87 (118)
Q Consensus 50 ~~~V~g~SM~Ptl~~GD~vlv~k-~---~~~~~~GDIVvf~~ 87 (118)
.+++..+|+.+ ..|=.+-+-+ . ...++.||||.++.
T Consensus 40 tl~i~D~S~~~--~~~l~v~~F~~~~~~LP~v~~GDVIll~~ 79 (138)
T cd04497 40 TLTITDPSLAN--SDGLTVKLFRPNEESLPIVKVGDIILLRR 79 (138)
T ss_pred EEEEECCCCCC--CCcEEEEEECCChhhCCCCCCCCEEEEEE
Confidence 46778888865 2332232322 1 12368999999974
No 90
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=33.10 E-value=85 Score=21.49 Aligned_cols=25 Identities=20% Similarity=0.634 Sum_probs=18.4
Q ss_pred CCCCCcEEEEEeCCCCcCEEEEEEEEC
Q 033489 76 PIRAGEIVVFNVDGREIPIVHRVIKVN 102 (118)
Q Consensus 76 ~~~~GDIVvf~~~~~~~~~ikRVI~~~ 102 (118)
.+++||+|....++. ...=||.++.
T Consensus 139 ~l~pGDvi~l~~~~~--~~~~RI~~i~ 163 (164)
T PF13550_consen 139 ALEPGDVIALSDDGR--DMRFRITEIE 163 (164)
T ss_pred cCCCCCEEEEEeCCC--ceEEEEEEEe
Confidence 588999999887744 3777777654
No 91
>TIGR01694 MTAP 5'-deoxy-5'-methylthioadenosine phosphorylase. In between the trusted and noise cutoffs are: 1) several archaeal sequences which appear to contain several residues characteristic of phosphorylases which act on guanosine or inosine (according to the crystal structure of MTAP and alignments). In any case, these residues are not conserved. 2) sequences from Mycobacterium tuberculosis and Streptomyces coelicolor which have better, although not perfect retention of the active site residues, but considering the general observation that bacteria utilize the MTA/SAH nucleotidase enzyme and a kinase to do this reaction, these have been excluded pending stronger evidence of their function, and 3) a sequence from Drosophila which appears to be a recent divergence (long branch in neighbor-joining trees) and lacks some of the conserved active site residues.
Probab=32.19 E-value=31 Score=26.23 Aligned_cols=19 Identities=21% Similarity=0.443 Sum_probs=16.6
Q ss_pred eCCCccccCcCCCEEEEec
Q 033489 54 LSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 54 ~g~SM~Ptl~~GD~vlv~k 72 (118)
..+||.|.++.||+|+.+.
T Consensus 84 saG~l~~~l~~GDlVI~~~ 102 (241)
T TIGR01694 84 AVGSLREEYPPGDLVVPDQ 102 (241)
T ss_pred cccccCCCCCCCCEEEEhh
Confidence 3479999999999999976
No 92
>PF13800 Sigma_reg_N: Sigma factor regulator N-terminal
Probab=32.14 E-value=1.2e+02 Score=19.67 Aligned_cols=14 Identities=21% Similarity=0.211 Sum_probs=9.0
Q ss_pred HHhhhHHHHHHHHH
Q 033489 11 IKSLQIRQVLTQGV 24 (118)
Q Consensus 11 ~~~~~~~~i~~~i~ 24 (118)
+|+.+++..++++.
T Consensus 5 ~kK~K~k~~l~~~~ 18 (96)
T PF13800_consen 5 LKKAKRKSRLRTVV 18 (96)
T ss_pred HHHHHHHHHHHHHH
Confidence 56666777776643
No 93
>PF15428 Imm14: Immunity protein 14
Probab=32.13 E-value=71 Score=21.59 Aligned_cols=27 Identities=22% Similarity=0.228 Sum_probs=18.9
Q ss_pred CCCcEEEEEeCCCCcCEEEEEEE-ECCCc
Q 033489 78 RAGEIVVFNVDGREIPIVHRVIK-VNILL 105 (118)
Q Consensus 78 ~~GDIVvf~~~~~~~~~ikRVI~-~~g~~ 105 (118)
|+|||..+.-++. .+...||++ ....+
T Consensus 1 K~GDIF~ipL~~~-~y~~G~Vi~~~~~~~ 28 (129)
T PF15428_consen 1 KPGDIFCIPLDDG-KYGFGRVIGDFKKVG 28 (129)
T ss_pred CCceEEEEEcCCC-CEEEEEEEecccccc
Confidence 6899999985533 478899994 44433
No 94
>PRK07432 5'-methylthioadenosine phosphorylase; Provisional
Probab=32.08 E-value=31 Score=27.55 Aligned_cols=23 Identities=17% Similarity=0.180 Sum_probs=19.2
Q ss_pred eEEEeCCCccccCcCCCEEEEec
Q 033489 50 VVVVLSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 50 ~~~V~g~SM~Ptl~~GD~vlv~k 72 (118)
..+-..+|+.|.+++||.++.+-
T Consensus 84 i~tna~Gsln~~~~pGdlvv~~D 106 (290)
T PRK07432 84 ISASAVGSLKEEAKPLDMVVPDQ 106 (290)
T ss_pred EEEeccccccCCCCCCCEEeecc
Confidence 45556679999999999999876
No 95
>PRK07823 5'-methylthioadenosine phosphorylase; Validated
Probab=32.02 E-value=31 Score=27.12 Aligned_cols=21 Identities=19% Similarity=0.374 Sum_probs=16.8
Q ss_pred EEeCCCccccCcCCCEEEEec
Q 033489 52 VVLSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 52 ~V~g~SM~Ptl~~GD~vlv~k 72 (118)
+=..+|+.|.+++||+++.+-
T Consensus 87 tnA~Gsln~~~~pGdlvi~dd 107 (264)
T PRK07823 87 PCAVGSLRPELGPGTVVVPDQ 107 (264)
T ss_pred ecccccCCCCCCCCCEEEcch
Confidence 334479999999999999654
No 96
>PRK09136 5'-methylthioadenosine phosphorylase; Validated
Probab=31.87 E-value=31 Score=26.68 Aligned_cols=22 Identities=14% Similarity=0.264 Sum_probs=18.0
Q ss_pred EEEeCCCccccCcCCCEEEEec
Q 033489 51 VVVLSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 51 ~~V~g~SM~Ptl~~GD~vlv~k 72 (118)
.+=.-+|+.|.+++||+++.+.
T Consensus 81 ~t~aaG~l~~~l~~Gdlvi~~d 102 (245)
T PRK09136 81 AVNTVGGIHADMGPGTLVVPDQ 102 (245)
T ss_pred EecccccCCCCCCCCCEEEEHH
Confidence 3444569999999999999876
No 97
>PF08802 CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit ; InterPro: IPR014909 The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The cytochrome b6-f complex has 4 large subunits, these are: cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are: PetG, PetL, PetM and PetN. The complex functions as a dimer. This protein corresponds to the alpha helical transmembrane domain of the cytochrome b6-f complex Rieske iron-sulphur subunit. ; GO: 0009496 plastoquinol-plastocyanin reductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process, 0042651 thylakoid membrane; PDB: 1Q90_R 1VF5_D 2E75_D 2E74_D 2E76_D 2D2C_Q 2ZT9_D.
Probab=31.83 E-value=1e+02 Score=17.41 Aligned_cols=30 Identities=10% Similarity=0.153 Sum_probs=20.4
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033489 13 SLQIRQVLTQGVSLGMIVTSALIIWKALMC 42 (118)
Q Consensus 13 ~~~~~~i~~~i~~i~~~~~i~~li~~~~~~ 42 (118)
+|.+|++++++..-.+++.++..+.-++..
T Consensus 5 dm~RR~lmN~ll~Gava~~a~~~lyP~~~f 34 (39)
T PF08802_consen 5 DMSRRQLMNLLLGGAVAVPAGGMLYPYVKF 34 (39)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ChhHHHHHHHHHHhhHHHHHHHHhhhheeE
Confidence 578899999987776666666555555543
No 98
>PF06890 Phage_Mu_Gp45: Bacteriophage Mu Gp45 protein; InterPro: IPR014462 This entry is represented by the Bacteriophage Mu, Gp45. The characteristics of the protein distribution suggest prophage matches.
Probab=31.52 E-value=82 Score=23.07 Aligned_cols=28 Identities=21% Similarity=0.592 Sum_probs=18.2
Q ss_pred CCCCCCcEEEEEeCCCCcCEEE---EEEEECC
Q 033489 75 DPIRAGEIVVFNVDGREIPIVH---RVIKVNI 103 (118)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ik---RVI~~~g 103 (118)
..+++||+++|+..+.. .++| |+|...+
T Consensus 73 ~~L~~GEvalY~~~G~~-I~L~~~G~ii~~~~ 103 (162)
T PF06890_consen 73 KGLKPGEVALYDDEGQK-IHLKRDGRIIEVTC 103 (162)
T ss_pred cCCCCCcEEEEcCCCCE-EEEEecceEEeccC
Confidence 45889999999866653 3444 4655544
No 99
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=31.34 E-value=84 Score=21.91 Aligned_cols=28 Identities=14% Similarity=0.005 Sum_probs=17.5
Q ss_pred CCCCCcEEEEEeCCCCcCEEEEEEEECCC
Q 033489 76 PIRAGEIVVFNVDGREIPIVHRVIKVNIL 104 (118)
Q Consensus 76 ~~~~GDIVvf~~~~~~~~~ikRVI~~~g~ 104 (118)
.++.||.|..+.++ +..++-+|-.+-.+
T Consensus 7 ~i~vGD~V~v~~~~-~~~~va~Ie~i~ed 34 (130)
T cd04721 7 TISVHDFVYVLSEE-EDRYVAYIEDLYED 34 (130)
T ss_pred EEECCCEEEEeCCC-CCcEEEEEEEEEEc
Confidence 36777877777655 33466666665554
No 100
>TIGR01698 PUNP purine nucleotide phosphorylase. methylthioadenosine.
Probab=31.02 E-value=34 Score=26.50 Aligned_cols=23 Identities=9% Similarity=0.316 Sum_probs=18.9
Q ss_pred eEEEeCCCccccCcCCCEEEEec
Q 033489 50 VVVVLSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 50 ~~~V~g~SM~Ptl~~GD~vlv~k 72 (118)
..+=..+|+.|.+++||+++++.
T Consensus 87 i~tna~Gsl~~~~~pGdlv~~~D 109 (237)
T TIGR01698 87 ILTNAAGGLRQDWGPGTPVLISD 109 (237)
T ss_pred EEEcccccCCCCCCCCCEEeech
Confidence 34555679999999999999976
No 101
>PRK15136 multidrug efflux system protein EmrA; Provisional
Probab=29.82 E-value=1.4e+02 Score=24.31 Aligned_cols=11 Identities=27% Similarity=0.670 Sum_probs=6.5
Q ss_pred CCCCCCcEEEE
Q 033489 75 DPIRAGEIVVF 85 (118)
Q Consensus 75 ~~~~~GDIVvf 85 (118)
..++.||+++-
T Consensus 81 d~VkkGqvL~~ 91 (390)
T PRK15136 81 DFVKEGDVLVT 91 (390)
T ss_pred CEECCCCEEEE
Confidence 34677776544
No 102
>PRK00529 elongation factor P; Validated
Probab=29.64 E-value=89 Score=23.07 Aligned_cols=37 Identities=22% Similarity=0.337 Sum_probs=24.5
Q ss_pred Cccc-cCcCCCEEEEeccCCCCCCCcEEEEEeCCCCcCEEEEE
Q 033489 57 SMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (118)
Q Consensus 57 SM~P-tl~~GD~vlv~k~~~~~~~GDIVvf~~~~~~~~~ikRV 98 (118)
+..| +|..|=.+-|- .-++.||.|..+..... |+.|+
T Consensus 148 ~~K~A~letG~~v~VP---~fI~~Gd~I~v~T~~g~--y~~R~ 185 (186)
T PRK00529 148 GTKPATLETGAVVQVP---LFINEGEKIKVDTRTGE--YVERA 185 (186)
T ss_pred CcccEEEcCCCEEEeC---CeecCCCEEEEECCCCc--EEeec
Confidence 4555 44566544442 24899999999876543 99886
No 103
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=29.30 E-value=30 Score=24.29 Aligned_cols=20 Identities=30% Similarity=0.635 Sum_probs=13.3
Q ss_pred cCcCCCEEEEec-cCCCCCCC
Q 033489 61 GFKRGDILFLHM-SKDPIRAG 80 (118)
Q Consensus 61 tl~~GD~vlv~k-~~~~~~~G 80 (118)
.+++||.||+.. ..+++.+|
T Consensus 38 rl~~GDlVFlT~~~~~Dl~~G 58 (122)
T COG1935 38 RLHEGDLVFLTSTSLEDLTKG 58 (122)
T ss_pred cCCCCCEEEEehhHhhHhhcC
Confidence 468899998876 33445555
No 104
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=29.28 E-value=1.1e+02 Score=22.46 Aligned_cols=19 Identities=5% Similarity=0.085 Sum_probs=13.5
Q ss_pred eEEEeCCCccccCcCCCEEEEec
Q 033489 50 VVVVLSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 50 ~~~V~g~SM~Ptl~~GD~vlv~k 72 (118)
.|.+. .. .++.||.|.+..
T Consensus 43 lY~~~---~~-~~~~Gd~V~f~~ 61 (178)
T PRK13884 43 LYWTS---SA-PVEKGAYVLFCP 61 (178)
T ss_pred EEEEe---CC-CCCCCCEEEEeC
Confidence 56654 22 488999999974
No 105
>TIGR01048 lysA diaminopimelate decarboxylase. This family consists of diaminopimelate decarboxylase, an enzyme which catalyzes the conversion of diaminopimelic acid into lysine during the last step of lysine biosynthesis.
Probab=29.19 E-value=80 Score=25.61 Aligned_cols=30 Identities=20% Similarity=0.347 Sum_probs=20.2
Q ss_pred ccCcCCCEEEEeccCCCCCCCcEEEEEeCC
Q 033489 60 PGFKRGDILFLHMSKDPIRAGEIVVFNVDG 89 (118)
Q Consensus 60 Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~ 89 (118)
|+=.++|.+.-+....++++||.++|.+-|
T Consensus 345 ~~C~~~D~l~~~~~lp~l~~GD~l~~~~~G 374 (417)
T TIGR01048 345 PLCESGDVLARDRELPEVEPGDLLAVFDAG 374 (417)
T ss_pred CCcCCCCEEeeccCCCCCCCCCEEEEeCCC
Confidence 344567765544433469999999998655
No 106
>PF06940 DUF1287: Domain of unknown function (DUF1287); InterPro: IPR009706 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=29.13 E-value=34 Score=25.29 Aligned_cols=15 Identities=27% Similarity=0.674 Sum_probs=11.6
Q ss_pred CCCCCCcEEEEEeCC
Q 033489 75 DPIRAGEIVVFNVDG 89 (118)
Q Consensus 75 ~~~~~GDIVvf~~~~ 89 (118)
++.+.||||+|+-++
T Consensus 105 ~~~q~GDIVtw~l~~ 119 (164)
T PF06940_consen 105 EDWQPGDIVTWRLPG 119 (164)
T ss_pred hhcCCCCEEEEeCCC
Confidence 568899999997554
No 107
>KOG1666 consensus V-SNARE [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.01 E-value=2.3e+02 Score=21.91 Aligned_cols=17 Identities=18% Similarity=0.366 Sum_probs=10.7
Q ss_pred hHHHHHHHHhhhHHHHH
Q 033489 4 IGESIESIKSLQIRQVL 20 (118)
Q Consensus 4 ~~~~~~~~~~~~~~~i~ 20 (118)
++|+...++.|..|-+.
T Consensus 179 lgkS~kiL~tM~RR~~~ 195 (220)
T KOG1666|consen 179 LGKSRKILTTMTRRLIR 195 (220)
T ss_pred hhHHHHHHHHHHHHHHH
Confidence 46666667777665554
No 108
>PRK08931 5'-methylthioadenosine phosphorylase; Provisional
Probab=28.79 E-value=37 Score=27.07 Aligned_cols=22 Identities=14% Similarity=0.309 Sum_probs=18.3
Q ss_pred EEEeCCCccccCcCCCEEEEec
Q 033489 51 VVVLSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 51 ~~V~g~SM~Ptl~~GD~vlv~k 72 (118)
.+=..+|+.|.+++||.++.+-
T Consensus 85 ~tnA~Gsln~~~~pGd~vi~~D 106 (289)
T PRK08931 85 SLSACGSFREELPPGTFVIVDQ 106 (289)
T ss_pred EecccccCCCCCCCCCEEeehh
Confidence 4445579999999999999876
No 109
>KOG0557 consensus Dihydrolipoamide acetyltransferase [Energy production and conversion]
Probab=28.70 E-value=87 Score=26.88 Aligned_cols=36 Identities=17% Similarity=0.332 Sum_probs=29.5
Q ss_pred eEEEeCCCccccCcCCCEEEEec-cCCCCCCCcEEEE
Q 033489 50 VVVVLSGSMEPGFKRGDILFLHM-SKDPIRAGEIVVF 85 (118)
Q Consensus 50 ~~~V~g~SM~Ptl~~GD~vlv~k-~~~~~~~GDIVvf 85 (118)
...+.=.+|.||+..|.++--.+ ..+.+..||++.=
T Consensus 38 h~~i~MPALSPTMeeGnIvsW~kKeGdkls~GDvl~E 74 (470)
T KOG0557|consen 38 HKTFSMPALSPTMEEGNIVSWKKKEGDKLSAGDVLLE 74 (470)
T ss_pred ceEeecCCCCccccCCceeeEeeccCCccCCCceEEE
Confidence 46777889999999999987766 4566999999864
No 110
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=28.62 E-value=57 Score=19.53 Aligned_cols=12 Identities=25% Similarity=0.351 Sum_probs=10.1
Q ss_pred CCCCCcEEEEEe
Q 033489 76 PIRAGEIVVFNV 87 (118)
Q Consensus 76 ~~~~GDIVvf~~ 87 (118)
.+..||.|.|+.
T Consensus 40 ~~~vGD~V~~~~ 51 (64)
T cd04451 40 RILPGDRVKVEL 51 (64)
T ss_pred ccCCCCEEEEEE
Confidence 388999999984
No 111
>cd06836 PLPDE_III_ODC_DapDC_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Uncharacterized Proteins with similarity to Ornithine and Diaminopimelate Decarboxylases. This subfamily contains uncharacterized proteins with similarity to ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarbo
Probab=28.28 E-value=83 Score=25.45 Aligned_cols=29 Identities=24% Similarity=0.391 Sum_probs=18.9
Q ss_pred CcCCCEEEEeccCCCCCCCcEEEEEeCCC
Q 033489 62 FKRGDILFLHMSKDPIRAGEIVVFNVDGR 90 (118)
Q Consensus 62 l~~GD~vlv~k~~~~~~~GDIVvf~~~~~ 90 (118)
=.++|.+.-+....++++||+++|.+-|.
T Consensus 329 C~~~D~l~~~~~lp~l~~GD~l~~~~~GA 357 (379)
T cd06836 329 CFAGDVLAKERALPPLEPGDYVAVHDTGA 357 (379)
T ss_pred CCCCCEEeecccCCCCCCCCEEEEeCCCc
Confidence 34566555443334589999999986553
No 112
>PF00877 NLPC_P60: NlpC/P60 family; InterPro: IPR000064 The Escherichia coli NLPC/Listeria P60 domain occurs at the C terminus of a number of different bacterial and viral proteins. The viral proteins are either described as tail assembly proteins or Gp19. In bacteria, the proteins are variously described as being putative tail component of prophage, invasin, invasion associated protein, putative lipoprotein, cell wall hydrolase, or putative endopeptidase. The E. coli NLPC/Listeria P60 domain is contained within the boundaries of the cysteine peptidase domain that defines the MEROPS peptidase family C40 (clan C-). A type example being dipeptidyl-peptidase VI from Bacillus sphaericus and gamma-glutamyl-diamino acid-endopeptidase precursor from Lactococcus lactis 3.4.19.11 from EC. This group also contains proteins classified as non-peptidase homologues in that they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the C40 family. ; PDB: 3PVQ_B 3GT2_A 3NPF_B 2K1G_A 3I86_A 3S0Q_A 2XIV_A 3PBC_A 3NE0_A 3M1U_B ....
Probab=28.23 E-value=34 Score=22.18 Aligned_cols=34 Identities=12% Similarity=0.284 Sum_probs=18.6
Q ss_pred EEEeCCCccccCcCCCEEEEeccCCCCCCCcEEEEEe
Q 033489 51 VVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNV 87 (118)
Q Consensus 51 ~~V~g~SM~Ptl~~GD~vlv~k~~~~~~~GDIVvf~~ 87 (118)
..++..|... ...+....++. +++++||++.|+.
T Consensus 29 i~l~~~~~~~-~~~~~~~~~~~--~~~~pGDlif~~~ 62 (105)
T PF00877_consen 29 INLPRTSADQ-YSVGFQKRVPI--SELQPGDLIFFKG 62 (105)
T ss_dssp EE--SSHHHH-TTSSEEEHEEG--GG-TTTEEEEEEG
T ss_pred CCCCcccccc-cccccccccch--hcCCcccEEEEeC
Confidence 3455444433 33344434443 5699999999997
No 113
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=28.15 E-value=1.2e+02 Score=23.32 Aligned_cols=29 Identities=21% Similarity=0.162 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033489 16 IRQVLTQGVSLGMIVTSALIIWKALMCIT 44 (118)
Q Consensus 16 ~~~i~~~i~~i~~~~~i~~li~~~~~~~~ 44 (118)
+|+=...++.+++++++++++......++
T Consensus 8 KrRK~N~iLNiaI~IV~lLIiiva~~lf~ 36 (217)
T PF07423_consen 8 KRRKTNKILNIAIGIVSLLIIIVAYQLFF 36 (217)
T ss_pred HhhhhhhhHHHHHHHHHHHHHHHhhhhee
Confidence 34445666777776666555544444433
No 114
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=27.72 E-value=3e+02 Score=21.61 Aligned_cols=44 Identities=20% Similarity=0.304 Sum_probs=31.5
Q ss_pred CCCCCCCcEEEEEeCCC---CcCEEEEEEEECCC-ceEEEEEEeeecC
Q 033489 74 KDPIRAGEIVVFNVDGR---EIPIVHRVIKVNIL-LTLFFELTIQPCC 117 (118)
Q Consensus 74 ~~~~~~GDIVvf~~~~~---~~~~ikRVI~~~g~-~~~~~~~~~~~~~ 117 (118)
..+++.||.|+=..-+. .+..|.+|..+..+ .+.|.++.+.|+-
T Consensus 213 ~~~v~~GD~VvTSGlgg~fP~Gl~VG~V~~v~~~~~~~~~~v~v~P~a 260 (283)
T TIGR00219 213 EKDIKKGDLIVTSGLGGRFPEGYPIGVVTSVHIDSYNSLLVIEVKPAA 260 (283)
T ss_pred CCCCCCCCEEEECCCCCcCCCCCEEEEEEEEEeCCCCceEEEEEEECC
Confidence 45799999988754332 35789999998664 4556688888864
No 115
>PF06459 RR_TM4-6: Ryanodine Receptor TM 4-6; InterPro: IPR009460 The release of Ca2+ ions from intracellular stores is a key step in a wide variety of cellular functions. In striated muscle, the release of Ca2+ from the sarcoplasmic reticulum (SR) leads to muscle contraction. Ca2+ release occurs through large, high-conductance Ca2+ release channels, also known as ryanodine receptors (RyRs) because they bind the plant alkaloid ryanodine with high affinity and specificity []. This region covers TM regions 4-6 of the ryanodine receptor 1 family.; GO: 0005219 ryanodine-sensitive calcium-release channel activity, 0006874 cellular calcium ion homeostasis, 0016021 integral to membrane
Probab=27.56 E-value=1.7e+02 Score=23.25 Aligned_cols=15 Identities=20% Similarity=0.122 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHHHHH
Q 033489 28 MIVTSALIIWKALMC 42 (118)
Q Consensus 28 ~~~~i~~li~~~~~~ 42 (118)
+++.++|.|+.++.+
T Consensus 176 lALflAFaINFILLF 190 (274)
T PF06459_consen 176 LALFLAFAINFILLF 190 (274)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344555556555443
No 116
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=27.23 E-value=1.8e+02 Score=22.31 Aligned_cols=44 Identities=23% Similarity=0.186 Sum_probs=30.4
Q ss_pred CCCCCCCcEEEEEeCCC---CcCEEEEEEEECCCceE-EEEEEeeecC
Q 033489 74 KDPIRAGEIVVFNVDGR---EIPIVHRVIKVNILLTL-FFELTIQPCC 117 (118)
Q Consensus 74 ~~~~~~GDIVvf~~~~~---~~~~ikRVI~~~g~~~~-~~~~~~~~~~ 117 (118)
..+++.||.|+=..-+. .+..|.||..+..++.. |.+..+.|+-
T Consensus 212 ~~~i~~GD~VvTSGl~g~fP~Gi~VG~V~~v~~~~~~~~~~~~v~p~~ 259 (276)
T PRK13922 212 SADIKVGDLVVTSGLGGIFPAGLPVGKVTSVERDDYGLFKTVYVKPAA 259 (276)
T ss_pred CCCCCCCCEEEECCCCCcCCCCCEEEEEEEEEeCCCCCeeEEEEEECc
Confidence 35699999988754322 35688999888654433 6788888863
No 117
>TIGR01700 PNPH purine nucleoside phosphorylase I, inosine and guanosine-specific. Several metazoan enzymes (PNPH) are well characterized including the human and bovine enzymes which have been crystallized.
Probab=27.21 E-value=43 Score=25.73 Aligned_cols=19 Identities=32% Similarity=0.782 Sum_probs=16.6
Q ss_pred eCCCccccCcCCCEEEEec
Q 033489 54 LSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 54 ~g~SM~Ptl~~GD~vlv~k 72 (118)
..+|+.|.++.||.|+.+.
T Consensus 91 saGsl~~~l~~GDiVi~~d 109 (249)
T TIGR01700 91 AAGGINPEFKVGDLMLIRD 109 (249)
T ss_pred ccccCCCCCCCCCEEEEhh
Confidence 3459999999999999987
No 118
>cd06843 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE. This subfamily is composed of PvsE from Vibrio parahaemolyticus and similar proteins. PvsE is a vibrioferrin biosynthesis protein which is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. It has been suggested that PvsE may be involved in the biosynthesis of the polycarboxylate siderophore vibrioferrin. It may catalyze the decarboxylation of serine to yield ethanolamine. PvsE may require homodimer formation and the presence of the PLP cofactor for activity.
Probab=27.05 E-value=83 Score=25.20 Aligned_cols=30 Identities=33% Similarity=0.524 Sum_probs=20.1
Q ss_pred cCcCCCEEEEeccCCCCCCCcEEEEEeCCC
Q 033489 61 GFKRGDILFLHMSKDPIRAGEIVVFNVDGR 90 (118)
Q Consensus 61 tl~~GD~vlv~k~~~~~~~GDIVvf~~~~~ 90 (118)
+=..+|.+.-+....++++||+++|.+-|.
T Consensus 327 ~C~~~D~l~~~~~lp~~~~GD~l~i~~~GA 356 (377)
T cd06843 327 LCTPKDVLARDVPVDRLRAGDLVVFPLAGA 356 (377)
T ss_pred CCCCCCEEeeccccCCCCCCCEEEEcCCCc
Confidence 345667655444334699999999986654
No 119
>TIGR01697 PNPH-PUNA-XAPA inosine guanosine and xanthosine phosphorylase family. Sequences from Clostridium and Thermotoga fall between these last two clades and are uncharacterized with respect to substrate range and operon.
Probab=26.90 E-value=45 Score=25.50 Aligned_cols=19 Identities=32% Similarity=0.805 Sum_probs=16.7
Q ss_pred eCCCccccCcCCCEEEEec
Q 033489 54 LSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 54 ~g~SM~Ptl~~GD~vlv~k 72 (118)
..+|+.|.++.||.|+.+.
T Consensus 91 saGsl~~~l~~GDiVI~~~ 109 (248)
T TIGR01697 91 AAGGLNPDFKPGDLMIIKD 109 (248)
T ss_pred ccccCCCCCCCCCEEEEhh
Confidence 3469999999999999986
No 120
>cd06839 PLPDE_III_Btrk_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase. This subfamily is composed of Bacillus circulans BtrK decarboxylase and similar proteins. These proteins are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases, eukaryotic ornithine decarboxylases and diaminopimelate decarboxylases. BtrK is presumed to function as a PLP-dependent decarboxylase involved in the biosynthesis of the aminoglycoside antibiotic butirosin. Homodimer formation and the presence of the PLP cofactor may be required for catalytic activity.
Probab=26.73 E-value=94 Score=24.73 Aligned_cols=31 Identities=23% Similarity=0.327 Sum_probs=20.8
Q ss_pred ccCcCCCEEEEeccCCCCCCCcEEEEEeCCC
Q 033489 60 PGFKRGDILFLHMSKDPIRAGEIVVFNVDGR 90 (118)
Q Consensus 60 Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~~ 90 (118)
|+=..+|.+.-+....+++.||.++|.+-|.
T Consensus 331 ~~C~~~D~~~~~~~lp~l~~GD~l~~~~~GA 361 (382)
T cd06839 331 PLCTPLDLLGRNVELPPLEPGDLVAVLQSGA 361 (382)
T ss_pred CCCCCCCEEeecccCCCCCCCCEEEEecCCC
Confidence 3445667766544334689999999986654
No 121
>COG2326 Uncharacterized conserved protein [Function unknown]
Probab=26.70 E-value=43 Score=26.64 Aligned_cols=29 Identities=31% Similarity=0.260 Sum_probs=23.8
Q ss_pred CCCCCcEEEEEeCCCCcCEEEEEEEECCC
Q 033489 76 PIRAGEIVVFNVDGREIPIVHRVIKVNIL 104 (118)
Q Consensus 76 ~~~~GDIVvf~~~~~~~~~ikRVI~~~g~ 104 (118)
-|.+|+||+|+....+..-|-||.|-..+
T Consensus 128 lPa~GeiviFdRSwYnr~gVeRVmGfct~ 156 (270)
T COG2326 128 LPAAGEIVIFDRSWYNRAGVERVMGFCTP 156 (270)
T ss_pred CCCCCeEEEechhhccccCeeeccccCCH
Confidence 48999999999876666789999986654
No 122
>PF02285 COX8: Cytochrome oxidase c subunit VIII; InterPro: IPR003205 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits.This family is composed of cytochrome c oxidase subunit VIII. ; GO: 0004129 cytochrome-c oxidase activity; PDB: 3AG3_Z 3ABM_M 1OCC_Z 3ASO_Z 3AG2_Z 3ABL_M 3AG4_M 3AG1_M 3ASN_M 1OCZ_M ....
Probab=26.67 E-value=35 Score=19.82 Aligned_cols=13 Identities=38% Similarity=0.731 Sum_probs=10.9
Q ss_pred cchHHHHHHHHhh
Q 033489 2 GWIGESIESIKSL 14 (118)
Q Consensus 2 ~~~~~~~~~~~~~ 14 (118)
+|++-++|+.|+.
T Consensus 31 gWVLshL~~YKk~ 43 (44)
T PF02285_consen 31 GWVLSHLESYKKR 43 (44)
T ss_dssp HHHHHTHHHHHT-
T ss_pred HHHHHHHHHhhcc
Confidence 6999999999873
No 123
>COG0690 SecE Preprotein translocase subunit SecE [Intracellular trafficking and secretion]
Probab=26.59 E-value=1.7e+02 Score=18.36 Aligned_cols=26 Identities=8% Similarity=0.199 Sum_probs=15.2
Q ss_pred cchHHHHHHHHhhhH---HHHHHHHHHHH
Q 033489 2 GWIGESIESIKSLQI---RQVLTQGVSLG 27 (118)
Q Consensus 2 ~~~~~~~~~~~~~~~---~~i~~~i~~i~ 27 (118)
+++.+..+++++-.+ ++.+...+.++
T Consensus 22 ~f~~~~~~E~~KV~WPsrke~~~~t~~Vl 50 (73)
T COG0690 22 NFFKEVRKELKKVVWPTRKELIRSTLIVL 50 (73)
T ss_pred HHHHHHHHHHHhccCCCHHHHHHHHHHHH
Confidence 345667777777743 55555544443
No 124
>PF00957 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis. Vesicle function is mediated by proteins in their membranes, although the precise nature of the protein-protein interactions underlying this are still uncertain []. Synaptobrevin may play a role in the molecular events underlying neurotransmitter release and vesicle recycling and may be involved in the regulation of membrane flow in the nerve terminal, a process mediated by interaction with low molecular weight GTP-binding proteins []. Synaptic vesicle-associated membrane proteins (VAMPs) from Torpedo californica (Pacific electric ray) and SNC1 from yeast are related to synaptobrevin.; GO: 0016192 vesicle-mediated transport, 0016021 integral to membrane; PDB: 3EGX_C 2NUP_C 3EGD_C 2NUT_C 1IOU_A 1H8M_A 3B5N_A 3ZYM_A 2NPS_A 1SFC_E ....
Probab=26.57 E-value=1.7e+02 Score=18.41 Aligned_cols=17 Identities=6% Similarity=-0.101 Sum_probs=7.0
Q ss_pred hHHHHHHHHHHHHHHHH
Q 033489 15 QIRQVLTQGVSLGMIVT 31 (118)
Q Consensus 15 ~~~~i~~~i~~i~~~~~ 31 (118)
+.+.+++.....+++++
T Consensus 58 ~r~~~~~~~k~~~i~~~ 74 (89)
T PF00957_consen 58 KRKMWWRNYKLYIIIII 74 (89)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhHHh
Confidence 33444444444433333
No 125
>PF04085 MreC: rod shape-determining protein MreC; InterPro: IPR007221 MreC (murein formation C) is involved in the rod shape determination in Escherichia coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.; GO: 0008360 regulation of cell shape; PDB: 2J5U_B 2QF4_B 2QF5_A.
Probab=26.47 E-value=1.7e+02 Score=20.57 Aligned_cols=44 Identities=30% Similarity=0.283 Sum_probs=26.9
Q ss_pred CCCCCCCcEEEEEeCCC---CcCEEEEEEEECCCce-EEEEEEeeecC
Q 033489 74 KDPIRAGEIVVFNVDGR---EIPIVHRVIKVNILLT-LFFELTIQPCC 117 (118)
Q Consensus 74 ~~~~~~GDIVvf~~~~~---~~~~ikRVI~~~g~~~-~~~~~~~~~~~ 117 (118)
..+++.||.|+-..-+. ....+.||.....+.. .|.++.+.|+.
T Consensus 91 ~~~i~~GD~V~TSG~~~~fP~Gi~VG~V~~v~~~~~~~~~~~~v~p~~ 138 (152)
T PF04085_consen 91 DADIKKGDIVVTSGLGGIFPPGIPVGTVSSVEPDKSGLFKEVYVKPAV 138 (152)
T ss_dssp TS---TT-EEEEE-TTSSS-CCEEEEEEEEEECTTTCCCEEEEEEESS
T ss_pred CCCCCCCCEEEECCCCCcCCCCCEEEEEEEEEeCCCCcEEEEEEEECC
Confidence 46799999988753332 3468999998877555 45577777764
No 126
>cd06840 PLPDE_III_Bif_AspK_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bifunctional Aspartate Kinase/Diaminopimelate Decarboxylase. Bifunctional aspartate kinase/diaminopimelate decarboxylase (AspK/DapDC, EC 4.1.1.20/EC 2.7.2.4) typically exists in bacteria. These proteins contain an N-terminal AspK region and a C-terminal DapDC region, which contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, characteristic of fold type III PLP-dependent enzymes. Members of this subfamily have not been fully characterized. Based on their sequence, these proteins may catalyze both reactions catalyzed by AspK and DapDC. AspK catalyzes the phosphorylation of L-aspartate to produce 4-phospho-L-aspartate while DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine.
Probab=26.27 E-value=91 Score=25.13 Aligned_cols=31 Identities=19% Similarity=0.312 Sum_probs=20.5
Q ss_pred ccCcCCCEEEEeccCCCCCCCcEEEEEeCCC
Q 033489 60 PGFKRGDILFLHMSKDPIRAGEIVVFNVDGR 90 (118)
Q Consensus 60 Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~~ 90 (118)
|+=..+|.+--+....++++||.++|.+-+.
T Consensus 318 p~C~~~D~l~~~~~lp~l~~GD~l~~~~~GA 348 (368)
T cd06840 318 PICESGDVLGRDRLLPETEEGDVILIANAGA 348 (368)
T ss_pred CCcCCCCEEeecccCCCCCCCCEEEEecCCc
Confidence 4445677655444333589999999987653
No 127
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=26.09 E-value=1.7e+02 Score=20.40 Aligned_cols=22 Identities=27% Similarity=0.468 Sum_probs=15.4
Q ss_pred cCcCCCEEEEec-cCCCCCCCcE
Q 033489 61 GFKRGDILFLHM-SKDPIRAGEI 82 (118)
Q Consensus 61 tl~~GD~vlv~k-~~~~~~~GDI 82 (118)
.+++||.||... ...++.+|+-
T Consensus 38 ~~~~Gd~VFlT~~~~~Dl~~Gt~ 60 (119)
T PF04322_consen 38 SLDPGDRVFLTSVSLEDLTPGTE 60 (119)
T ss_pred cCCCCCEEEEecCCHHHCCCCCC
Confidence 458899999876 4456766663
No 128
>PRK11507 ribosome-associated protein; Provisional
Probab=25.92 E-value=28 Score=22.13 Aligned_cols=14 Identities=36% Similarity=0.401 Sum_probs=11.5
Q ss_pred CCCCCCCcEEEEEe
Q 033489 74 KDPIRAGEIVVFNV 87 (118)
Q Consensus 74 ~~~~~~GDIVvf~~ 87 (118)
.+.+.+||+|.|+.
T Consensus 50 gkKl~~GD~V~~~g 63 (70)
T PRK11507 50 RCKIVAGQTVSFAG 63 (70)
T ss_pred CCCCCCCCEEEECC
Confidence 46799999999953
No 129
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.72 E-value=44 Score=23.03 Aligned_cols=14 Identities=29% Similarity=0.717 Sum_probs=11.6
Q ss_pred CCCCCCCcEEEEEe
Q 033489 74 KDPIRAGEIVVFNV 87 (118)
Q Consensus 74 ~~~~~~GDIVvf~~ 87 (118)
...+++||.|+|+.
T Consensus 31 rr~ik~GD~IiF~~ 44 (111)
T COG4043 31 RRQIKPGDKIIFNG 44 (111)
T ss_pred hcCCCCCCEEEEcC
Confidence 45699999999974
No 130
>PRK08202 purine nucleoside phosphorylase; Provisional
Probab=25.58 E-value=50 Score=25.75 Aligned_cols=21 Identities=24% Similarity=0.629 Sum_probs=17.5
Q ss_pred EEeCCCccccCcCCCEEEEec
Q 033489 52 VVLSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 52 ~V~g~SM~Ptl~~GD~vlv~k 72 (118)
+=..+|+.|.+++||+|+.+.
T Consensus 111 tgaaGsL~~~l~~GDiVi~~d 131 (272)
T PRK08202 111 TNAAGGLNPDFGPGDLMLISD 131 (272)
T ss_pred ecccccCCCCCCCCCEEEEch
Confidence 334469999999999999986
No 131
>PRK10691 hypothetical protein; Provisional
Probab=25.34 E-value=86 Score=23.64 Aligned_cols=27 Identities=15% Similarity=0.480 Sum_probs=14.3
Q ss_pred cCcCCCEEEEecc--CCCCCCCcEEEEEe
Q 033489 61 GFKRGDILFLHMS--KDPIRAGEIVVFNV 87 (118)
Q Consensus 61 tl~~GD~vlv~k~--~~~~~~GDIVvf~~ 87 (118)
+|++||+|+.-.. ...+++||.|...-
T Consensus 181 tL~aGDvI~TGTp~g~~~l~~GD~v~~~i 209 (219)
T PRK10691 181 TLRAGDVVLTGTPEGVGPLQSGDELTVTF 209 (219)
T ss_pred ccCCCCEEEcCCCCCCEECCCCCEEEEEE
Confidence 5666666665431 12356666665544
No 132
>TIGR03099 dCO2ase_PEP1 pyridoxal-dependent decarboxylase, exosortase system type 1 associated. The sequences in this family contain the pyridoxal binding domain (pfam02784) and C-terminal sheet domain (pfam00278) of a family of Pyridoxal-dependent decarboxylases. Characterized enzymes in this family decarboxylate substrates such as ornithine, diaminopimelate and arginine. The genes of the family modeled here, with the exception of those observed in certain Burkholderia species, are all found in the context of exopolysaccharide biosynthesis loci containing the exosortase/PEP-CTERM protein sorting system. More specifically, these are characteristic of the type 1 exosortase system represented by the Genome Property GenProp0652. The substrate of these enzymes may be a precursor of the carrier or linker which is hypothesized to release the PEP-CTERM protein from the exosortase enzyme. These enzymes are apparently most closely related to the diaminopimelate decarboxylase modeled by TIGR01048
Probab=25.16 E-value=94 Score=25.07 Aligned_cols=28 Identities=21% Similarity=0.203 Sum_probs=17.9
Q ss_pred cCCCEEEEeccCCCCCCCcEEEEEeCCC
Q 033489 63 KRGDILFLHMSKDPIRAGEIVVFNVDGR 90 (118)
Q Consensus 63 ~~GD~vlv~k~~~~~~~GDIVvf~~~~~ 90 (118)
..+|.+.-+....++++||.++|.+-|.
T Consensus 350 ~~~D~~~~~~~lp~~~~GD~l~~~~~GA 377 (398)
T TIGR03099 350 TPLDLLAEKGTLPVAEPGDLVVIFQSGA 377 (398)
T ss_pred CCCCEEeecCcCCCCCCCCEEEEcCCCC
Confidence 4556554433333589999999986553
No 133
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=25.15 E-value=1.4e+02 Score=17.79 Aligned_cols=23 Identities=22% Similarity=0.262 Sum_probs=14.4
Q ss_pred CCCcEEEEEeCCCCcCEEEEEEEE
Q 033489 78 RAGEIVVFNVDGREIPIVHRVIKV 101 (118)
Q Consensus 78 ~~GDIVvf~~~~~~~~~ikRVI~~ 101 (118)
+.||+|.-++.+. ...|..+-..
T Consensus 2 ~~GDvV~LKSGGp-~MTV~~v~~~ 24 (53)
T PF09926_consen 2 KIGDVVQLKSGGP-RMTVTEVGPN 24 (53)
T ss_pred CCCCEEEEccCCC-CeEEEEcccc
Confidence 5788888876655 3555555444
No 134
>PRK10838 spr outer membrane lipoprotein; Provisional
Probab=24.84 E-value=54 Score=24.57 Aligned_cols=13 Identities=31% Similarity=0.838 Sum_probs=9.7
Q ss_pred CCCCCCcEEEEEe
Q 033489 75 DPIRAGEIVVFNV 87 (118)
Q Consensus 75 ~~~~~GDIVvf~~ 87 (118)
+++++||+|.|+.
T Consensus 127 ~~lqpGDLVfF~~ 139 (190)
T PRK10838 127 SKLRTGDLVLFRA 139 (190)
T ss_pred CCCCCCcEEEECC
Confidence 4578888888864
No 135
>PF00829 Ribosomal_L21p: Ribosomal prokaryotic L21 protein; InterPro: IPR001787 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L21 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L21 is known to bind to the 23S rRNA in the presence of L20. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Bacterial L21. Marchantia polymorpha chloroplast L21. Cyanelle L21. Plant chloroplast L21 (nuclear-encoded). Bacterial L21 is a protein of about 100 amino-acid residues, the mature form of the spinach chloroplast L21 has 200 residues.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XG0_V 2X9S_V 2XG2_V 3UZ1_2 2Y19_V 2WDL_V 3V23_V 2WRO_V 2WRL_V 2Y11_V ....
Probab=24.45 E-value=1e+02 Score=20.35 Aligned_cols=33 Identities=12% Similarity=0.295 Sum_probs=23.5
Q ss_pred EEeCCCccccCcCCCEEEEeccCCCCCCCcEEEEE
Q 033489 52 VVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFN 86 (118)
Q Consensus 52 ~V~g~SM~Ptl~~GD~vlv~k~~~~~~~GDIVvf~ 86 (118)
.|..++=+=-..+||.+.+++. +.+.||-|.|+
T Consensus 4 Ii~~ggkQykV~~gd~i~v~~l--~~~~G~~i~l~ 36 (96)
T PF00829_consen 4 IIEIGGKQYKVEEGDVIDVERL--DAEVGDKIELD 36 (96)
T ss_dssp EEESSSEEEEESSSEEEEEEST--SSSTTSEEEET
T ss_pred EEEECCEEEEEeCCCEEEECCc--CcCCCCEEEEE
Confidence 3444444445679999999974 57889988885
No 136
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=24.28 E-value=99 Score=21.66 Aligned_cols=40 Identities=18% Similarity=0.221 Sum_probs=28.2
Q ss_pred CCeEEEeCCCccccC-cCCCEEEEecc--------CCCCCCCcEEEEEe
Q 033489 48 SPVVVVLSGSMEPGF-KRGDILFLHMS--------KDPIRAGEIVVFNV 87 (118)
Q Consensus 48 ~~~~~V~g~SM~Ptl-~~GD~vlv~k~--------~~~~~~GDIVvf~~ 87 (118)
.+.+.|.+.+....- .....+.|+.. .+..++||+|+=++
T Consensus 11 i~vi~Van~~h~~~~~~~~~~i~Vd~g~DaaD~~I~~~~~~gDiVITqD 59 (130)
T PF02639_consen 11 IPVIFVANYSHRLPRSPYVEMIVVDSGFDAADFYIVNHAKPGDIVITQD 59 (130)
T ss_pred CEEEEEeCCCccCCCCCCeEEEEECCCCChHHHHHHHcCCCCCEEEECC
Confidence 346778888877655 56677888762 24589999998754
No 137
>KOG1535 consensus Predicted fumarylacetoacetate hydralase [General function prediction only]
Probab=23.96 E-value=92 Score=24.02 Aligned_cols=29 Identities=10% Similarity=0.376 Sum_probs=20.8
Q ss_pred cCcCCCEEEEec--cCCCCCCCcEEEEEeCC
Q 033489 61 GFKRGDILFLHM--SKDPIRAGEIVVFNVDG 89 (118)
Q Consensus 61 tl~~GD~vlv~k--~~~~~~~GDIVvf~~~~ 89 (118)
||.+||+++.-. ....++.||+|-..-.+
T Consensus 176 tL~~GDvILTGTP~GVg~v~~Gd~i~~ei~~ 206 (217)
T KOG1535|consen 176 TLEPGDVILTGTPEGVGEVKPGDVIQCELLE 206 (217)
T ss_pred eecCCCEEEecCCCccccccCCCEEEecccc
Confidence 677899888865 23457889988876544
No 138
>cd06829 PLPDE_III_CANSDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase. Carboxynorspermidine decarboxylase (CANSDC) catalyzes the decarboxylation of carboxynorspermidine, the last step in the biosynthesis of norspermidine. It is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC), which are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. Based on this similarity, CANSDC may require homodimer formation and the presence of the PLP cofactor for its catalytic activity.
Probab=23.70 E-value=1.1e+02 Score=24.47 Aligned_cols=31 Identities=19% Similarity=0.303 Sum_probs=20.2
Q ss_pred ccCcCCCEEEEeccCCCCCCCcEEEEEeCCC
Q 033489 60 PGFKRGDILFLHMSKDPIRAGEIVVFNVDGR 90 (118)
Q Consensus 60 Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~~ 90 (118)
|+=.++|.+.=+....+++.||.++|.+-|.
T Consensus 295 p~C~s~D~l~~~~~~~~l~~GD~l~~~~~GA 325 (346)
T cd06829 295 NSCLAGDVIGDYSFDEPLQVGDRLVFEDMAH 325 (346)
T ss_pred CCCCcccEEeecccCCCCCCCCEEEEeCchh
Confidence 4455678763222333589999999987653
No 139
>KOG4544 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.22 E-value=3e+02 Score=19.92 Aligned_cols=34 Identities=12% Similarity=0.162 Sum_probs=21.8
Q ss_pred hHHHHHHHHhhhH-----HHHHHHHHHHHHHHHHHHHHH
Q 033489 4 IGESIESIKSLQI-----RQVLTQGVSLGMIVTSALIIW 37 (118)
Q Consensus 4 ~~~~~~~~~~~~~-----~~i~~~i~~i~~~~~i~~li~ 37 (118)
+|.++.+-+++.. |..++|+..+.....+.+...
T Consensus 32 im~~l~~~rq~A~~Ia~~RE~f~w~~~f~~~avv~laa~ 70 (144)
T KOG4544|consen 32 IMAHLQERRQIAFKIAEEREKFNWIACFGSLAVVLLAAS 70 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677777777643 678888877765554444433
No 140
>TIGR01047 nspC carboxynorspermidine decarboxylase. This protein is related to diaminopimelate decarboxylase. It is the last enzyme in norspermidine biosynthesis by an unusual pathway shown in Vibrio alginolyticus.
Probab=22.91 E-value=98 Score=25.14 Aligned_cols=30 Identities=20% Similarity=0.204 Sum_probs=19.2
Q ss_pred ccCcCCCEEEEeccCCCCCCCcEEEEEeCC
Q 033489 60 PGFKRGDILFLHMSKDPIRAGEIVVFNVDG 89 (118)
Q Consensus 60 Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~ 89 (118)
|+=.++|.+.-+....+++.||.++|.+-|
T Consensus 309 ~~C~s~D~l~~~~~lp~l~~GD~l~~~~~G 338 (380)
T TIGR01047 309 CTCLAGDVMGEYAFDEPLKVGDKLVFLDMI 338 (380)
T ss_pred CCCCcccEEeecccCCCCCCCCEEEEcCcC
Confidence 344556766432333468999999998654
No 141
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=22.80 E-value=78 Score=20.70 Aligned_cols=15 Identities=20% Similarity=0.605 Sum_probs=10.1
Q ss_pred CccccCcCCCEEEEe
Q 033489 57 SMEPGFKRGDILFLH 71 (118)
Q Consensus 57 SM~Ptl~~GD~vlv~ 71 (118)
.|.|.|+.||+|+..
T Consensus 45 ~~rp~L~~GDlV~Ar 59 (86)
T cd05790 45 RNRPNLNVGDLVYAR 59 (86)
T ss_pred cccccCCCCCEEEEE
Confidence 456777777777665
No 142
>PF13759 2OG-FeII_Oxy_5: Putative 2OG-Fe(II) oxygenase; PDB: 3BVC_B 2RG4_A.
Probab=22.06 E-value=1.1e+02 Score=19.74 Aligned_cols=24 Identities=25% Similarity=0.220 Sum_probs=12.6
Q ss_pred CCCCCcEEEEEeCCCCcCEEEEEEEECCC
Q 033489 76 PIRAGEIVVFNVDGREIPIVHRVIKVNIL 104 (118)
Q Consensus 76 ~~~~GDIVvf~~~~~~~~~ikRVI~~~g~ 104 (118)
+++.||+|+|... .-|+|.--.++
T Consensus 69 ~p~~G~lvlFPs~-----l~H~v~p~~~~ 92 (101)
T PF13759_consen 69 EPEEGDLVLFPSW-----LWHGVPPNNSD 92 (101)
T ss_dssp ---TTEEEEEETT-----SEEEE----SS
T ss_pred CCCCCEEEEeCCC-----CEEeccCcCCC
Confidence 5899999999643 56776655554
No 143
>CHL00075 rpl21 ribosomal protein L21
Probab=22.03 E-value=1.9e+02 Score=19.71 Aligned_cols=34 Identities=15% Similarity=0.343 Sum_probs=25.2
Q ss_pred EEEeCCCccccCcCCCEEEEeccCCCCCCCcEEEEE
Q 033489 51 VVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFN 86 (118)
Q Consensus 51 ~~V~g~SM~Ptl~~GD~vlv~k~~~~~~~GDIVvf~ 86 (118)
..|..++=+=-..+||.+.+++. +.+.||-|.|+
T Consensus 5 AIi~~gGkQykV~~Gd~i~vekl--~~~~G~~i~l~ 38 (108)
T CHL00075 5 AIIEAGGKQLWVEPGRFYDINHF--PLEPGTKILLN 38 (108)
T ss_pred EEEEECCEEEEEeCCCEEEEEEc--CCCCCCEEEEE
Confidence 45666666667789999999984 35678887775
No 144
>TIGR03468 HpnG hopanoid-associated phosphorylase. The sequences in this family are members of the pfam01048 family of phosphorylases typically acting on nucleotide-sugar substrates. The genes of the family modeled here are generally in the same locus with genes involved in the biosynthesis and elaboration of hopene, the cyclization product of the polyisoprenoid squalene. This gene is adjacent to the genes PhnA-E and squalene-hopene cyclase (which would be HpnF) in Zymomonas mobilis and their association with hopene biosynthesis has been noted in the literature. Extending the gene symbol sequence, we suggest the symbol HpnG for the product of this gene. Hopanoids are known to be components of the plasma membrane and to have polar sugar head groups in Z. mobilis and other species.
Probab=21.60 E-value=64 Score=23.99 Aligned_cols=21 Identities=19% Similarity=0.518 Sum_probs=17.3
Q ss_pred EEeCCCccccCcCCCEEEEec
Q 033489 52 VVLSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 52 ~V~g~SM~Ptl~~GD~vlv~k 72 (118)
.=..+|+.|.+++||.++.+.
T Consensus 52 ~G~aG~l~~~l~~Gdvvi~~~ 72 (212)
T TIGR03468 52 FGTAGALDPALQPGDLVVPEE 72 (212)
T ss_pred EEecccCCCCCCCCCEEeehh
Confidence 334569999999999999875
No 145
>PF13640 2OG-FeII_Oxy_3: 2OG-Fe(II) oxygenase superfamily; PDB: 3DKQ_B 3GZE_D 3HQR_A 2Y34_A 2G1M_A 2G19_A 3OUI_A 3OUJ_A 2HBU_A 2Y33_A ....
Probab=21.51 E-value=2.2e+02 Score=17.78 Aligned_cols=21 Identities=29% Similarity=0.502 Sum_probs=16.6
Q ss_pred CCCCcEEEEEeCCCCcCEEEEEEEE
Q 033489 77 IRAGEIVVFNVDGREIPIVHRVIKV 101 (118)
Q Consensus 77 ~~~GDIVvf~~~~~~~~~ikRVI~~ 101 (118)
|+.|++|+|.. . ...|+|-.+
T Consensus 66 p~~g~~v~F~~-~---~~~H~v~~v 86 (100)
T PF13640_consen 66 PKPGRLVIFPS-D---NSLHGVTPV 86 (100)
T ss_dssp -BTTEEEEEES-C---TCEEEEEEE
T ss_pred CCCCEEEEEeC-C---CCeecCccc
Confidence 89999999987 2 278888888
No 146
>cd06810 PLPDE_III_ODC_DapDC_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Ornithine and Diaminopimelate Decarboxylases, and Related Enzymes. This family includes eukaryotic ornithine decarboxylase (ODC, EC 4.1.1.17), diaminopimelate decarboxylase (DapDC, EC 4.1.1.20), plant and prokaryotic biosynthetic arginine decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine decarboxylase (CANSDC), and ODC-like enzymes from diverse bacterial species. These proteins are fold type III PLP-dependent enzymes that catalyze essential steps in the biosynthesis of polyamine and lysine. ODC and ADC participate in alternative pathways of the biosynthesis of putrescine, which is the precursor of aliphatic polyamines in many organisms. ODC catalyzes the direct synthesis of putrescine from L-ornithine, while ADC converts L-arginine to agmatine, which is hydrolysed to putrescine by agmatinase in a pathway that exists only in plants and bacteria. DapDC converts meso-2,6-diaminoheptanedioate to
Probab=21.37 E-value=1.3e+02 Score=23.79 Aligned_cols=30 Identities=20% Similarity=0.299 Sum_probs=19.5
Q ss_pred cCcCCCEEEEeccCCCCCCCcEEEEEeCCC
Q 033489 61 GFKRGDILFLHMSKDPIRAGEIVVFNVDGR 90 (118)
Q Consensus 61 tl~~GD~vlv~k~~~~~~~GDIVvf~~~~~ 90 (118)
+=..+|.+.-+....+++.||.++|.+-|.
T Consensus 319 ~C~~~D~~~~~~~lp~l~~GD~l~~~~~GA 348 (368)
T cd06810 319 LCDSGDVIGRDRLLPELEVGDLLVFEDMGA 348 (368)
T ss_pred CCCCCcEEeecccCCCCCCCCEEEEcCCCC
Confidence 444566655444334689999999986553
No 147
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=21.36 E-value=4.2e+02 Score=22.73 Aligned_cols=29 Identities=10% Similarity=0.288 Sum_probs=19.2
Q ss_pred ccccCcCCCEEEEec--------cCCCCCCCcEEEEE
Q 033489 58 MEPGFKRGDILFLHM--------SKDPIRAGEIVVFN 86 (118)
Q Consensus 58 M~Ptl~~GD~vlv~k--------~~~~~~~GDIVvf~ 86 (118)
|.|-+..|.-|.|.. ....+..||+|+=-
T Consensus 212 LsPfya~g~gV~Vtev~~~Spl~gprGL~vgdvitsl 248 (484)
T KOG2921|consen 212 LSPFYAHGEGVTVTEVPSVSPLFGPRGLSVGDVITSL 248 (484)
T ss_pred hchhhhcCceEEEEeccccCCCcCcccCCccceEEec
Confidence 558888888777754 12346788888653
No 148
>PF05708 DUF830: Orthopoxvirus protein of unknown function (DUF830); PDB: 2IF6_B 3KW0_C.
Probab=21.13 E-value=72 Score=22.01 Aligned_cols=12 Identities=17% Similarity=0.512 Sum_probs=5.6
Q ss_pred CCCCcEEEEEeC
Q 033489 77 IRAGEIVVFNVD 88 (118)
Q Consensus 77 ~~~GDIVvf~~~ 88 (118)
++.|||+.++.+
T Consensus 2 l~~GDIil~~~~ 13 (158)
T PF05708_consen 2 LQTGDIILTRGK 13 (158)
T ss_dssp --TT-EEEEEE-
T ss_pred CCCeeEEEEECC
Confidence 566777777654
No 149
>PLN02537 diaminopimelate decarboxylase
Probab=21.10 E-value=1.4e+02 Score=24.25 Aligned_cols=30 Identities=20% Similarity=0.132 Sum_probs=20.1
Q ss_pred ccCcCCCEEEEeccCCCCCCCcEEEEEeCC
Q 033489 60 PGFKRGDILFLHMSKDPIRAGEIVVFNVDG 89 (118)
Q Consensus 60 Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~ 89 (118)
|+=..+|.+.-+....++++||.++|.+-|
T Consensus 335 ~~C~~~D~l~~~~~lp~~~~GD~l~~~~~G 364 (410)
T PLN02537 335 PVCESADFLGKDRELPTPPKGAGLVVHDAG 364 (410)
T ss_pred CccCCCCEEEEcccCCCCCCCCEEEEeCCC
Confidence 455567766544433358999999998654
No 150
>PRK15203 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase; Provisional
Probab=21.08 E-value=1e+02 Score=25.82 Aligned_cols=30 Identities=23% Similarity=0.392 Sum_probs=22.4
Q ss_pred cCcCCCEEEEecc--CCCCCCCcEEEEEeCCC
Q 033489 61 GFKRGDILFLHMS--KDPIRAGEIVVFNVDGR 90 (118)
Q Consensus 61 tl~~GD~vlv~k~--~~~~~~GDIVvf~~~~~ 90 (118)
||.+||+++.-.. ...++.||.|...-.+.
T Consensus 165 tL~pGDvI~TGTP~g~~~l~~GD~v~~~i~gi 196 (429)
T PRK15203 165 TLNPGDAILLGTPQARVEIQPGDRVRVLAEGF 196 (429)
T ss_pred CcCCCCEEEcCCCCCceECCCCCEEEEEEeCe
Confidence 7889999888652 23488999998877654
No 151
>TIGR01699 XAPA xanthosine phosphorylase. (TIGR01698, TIGR01700).
Probab=21.05 E-value=39 Score=26.23 Aligned_cols=21 Identities=24% Similarity=0.412 Sum_probs=17.3
Q ss_pred EEeCCCccccCcCCCEEEEec
Q 033489 52 VVLSGSMEPGFKRGDILFLHM 72 (118)
Q Consensus 52 ~V~g~SM~Ptl~~GD~vlv~k 72 (118)
+=..+|+.|.+++||.++.+.
T Consensus 89 t~aaG~l~~~l~~Gdlvi~~d 109 (248)
T TIGR01699 89 TNAAGSLRPEVGAGSLVALKD 109 (248)
T ss_pred ecceeccCCCCCCCCEECHHH
Confidence 334569999999999999876
No 152
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=20.94 E-value=1.7e+02 Score=20.07 Aligned_cols=14 Identities=29% Similarity=0.691 Sum_probs=7.8
Q ss_pred CCCCCcEEEEEeCC
Q 033489 76 PIRAGEIVVFNVDG 89 (118)
Q Consensus 76 ~~~~GDIVvf~~~~ 89 (118)
.+++||-++|...+
T Consensus 39 ~mk~GD~vifY~s~ 52 (143)
T PF01878_consen 39 RMKPGDKVIFYHSG 52 (143)
T ss_dssp C--TT-EEEEEETS
T ss_pred cCCCCCEEEEEEcC
Confidence 57777777777665
No 153
>cd04716 BAH_plantDCM_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=20.92 E-value=2.9e+02 Score=19.01 Aligned_cols=25 Identities=12% Similarity=0.190 Sum_probs=13.1
Q ss_pred CCCcEEEEEeCCCCcCEEEEEEEEC
Q 033489 78 RAGEIVVFNVDGREIPIVHRVIKVN 102 (118)
Q Consensus 78 ~~GDIVvf~~~~~~~~~ikRVI~~~ 102 (118)
+.||-|..+..+.+.+|+-||..+-
T Consensus 5 ~lgD~V~v~~~~~~~~yi~rI~~i~ 29 (122)
T cd04716 5 NLGDDAYVQGGEGEEPFICKITEFF 29 (122)
T ss_pred EcCCEEEEECCCCCCCEEEEEEEEE
Confidence 4455555554433345677766543
No 154
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=20.91 E-value=1.8e+02 Score=16.65 Aligned_cols=30 Identities=13% Similarity=0.224 Sum_probs=21.7
Q ss_pred CCCCCcEEEEEeCCCCcCEEEEEEEECCCceEEEE
Q 033489 76 PIRAGEIVVFNVDGREIPIVHRVIKVNILLTLFFE 110 (118)
Q Consensus 76 ~~~~GDIVvf~~~~~~~~~ikRVI~~~g~~~~~~~ 110 (118)
.+++||.+.+..+ .-|++....++...++.
T Consensus 40 ~l~~Gd~~~i~~~-----~~H~~~n~~~~~~~~l~ 69 (71)
T PF07883_consen 40 ELKPGDAIYIPPG-----VPHQVRNPGDEPARFLV 69 (71)
T ss_dssp EEETTEEEEEETT-----SEEEEEEESSSEEEEEE
T ss_pred EccCCEEEEECCC-----CeEEEEECCCCCEEEEE
Confidence 4788998888654 45788777777666654
No 155
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=20.86 E-value=74 Score=19.55 Aligned_cols=35 Identities=34% Similarity=0.410 Sum_probs=18.8
Q ss_pred cCCCEEEEecc--CCCCCCCcEEEEEeCCCCcCEEEE
Q 033489 63 KRGDILFLHMS--KDPIRAGEIVVFNVDGREIPIVHR 97 (118)
Q Consensus 63 ~~GD~vlv~k~--~~~~~~GDIVvf~~~~~~~~~ikR 97 (118)
+.||++++... ...-+.|.|+-.+.++..-+|.=|
T Consensus 4 ~vGD~lvv~g~~vg~~~r~GeIveV~g~dG~PPY~VR 40 (58)
T PF08940_consen 4 SVGDRLVVHGRTVGQPDRHGEIVEVRGPDGSPPYLVR 40 (58)
T ss_dssp -TTEEEEES-TTTS--EEEEEEEE-S-SSS-S-EEEE
T ss_pred CCCCEEEEcCCcCCCCCcEeEEEEEECCCCCCCEEEE
Confidence 47899999762 234578888888765543345544
No 156
>cd06841 PLPDE_III_MccE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme MccE. This subfamily is composed of uncharacterized proteins with similarity to Escherichia coli MccE, a hypothetical protein that is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Most members of this subfamily share the same domain architecture as ODC and DapDC. A few members, including Escherichia coli MccE, contain an additional acetyltransferase domain at the C-terminus.
Probab=20.74 E-value=1.4e+02 Score=23.89 Aligned_cols=31 Identities=23% Similarity=0.434 Sum_probs=20.5
Q ss_pred ccCcCCCEEEEeccCCCCCCCcEEEEEeCCC
Q 033489 60 PGFKRGDILFLHMSKDPIRAGEIVVFNVDGR 90 (118)
Q Consensus 60 Ptl~~GD~vlv~k~~~~~~~GDIVvf~~~~~ 90 (118)
|+-.++|.+.-+....++++||.++|.+-|.
T Consensus 326 ~~C~~~D~~~~~~~lp~l~~GD~l~~~~~GA 356 (379)
T cd06841 326 FNCMESDVLFPNVPLPPLNVGDILAIRNVGA 356 (379)
T ss_pred CCcCCCCEEeeCCcCCCCCCCCEEEEeCCCC
Confidence 4555677654443333599999999986653
No 157
>cd06828 PLPDE_III_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase. Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20) participates in the last step of lysine biosynthesis. It converts meso-2,6-diaminoheptanedioate to L-lysine. It is a fold type III PLP-dependent enzyme that contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. DapDC exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity.
Probab=20.73 E-value=1.5e+02 Score=23.49 Aligned_cols=30 Identities=13% Similarity=0.288 Sum_probs=19.2
Q ss_pred cCcCCCEEEEeccCCCCCCCcEEEEEeCCC
Q 033489 61 GFKRGDILFLHMSKDPIRAGEIVVFNVDGR 90 (118)
Q Consensus 61 tl~~GD~vlv~k~~~~~~~GDIVvf~~~~~ 90 (118)
+=.++|.+.-+....++++||.++|.+-|.
T Consensus 324 ~C~~~D~l~~~~~lp~l~~GD~l~~~~~GA 353 (373)
T cd06828 324 ICESGDVFAKDRELPEVEEGDLLAIHDAGA 353 (373)
T ss_pred CCCCCCEEeecccCCCCCCCCEEEEeCCCc
Confidence 444566554333334699999999986653
No 158
>TIGR00061 L21 ribosomal protein L21. Eubacterial and chloroplast.
Probab=20.62 E-value=1.9e+02 Score=19.39 Aligned_cols=33 Identities=18% Similarity=0.299 Sum_probs=22.6
Q ss_pred EEeCCCccccCcCCCEEEEeccCCCCCCCcEEEEE
Q 033489 52 VVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFN 86 (118)
Q Consensus 52 ~V~g~SM~Ptl~~GD~vlv~k~~~~~~~GDIVvf~ 86 (118)
.|..++=+=...+||.+.+++. +.+.||-|.|+
T Consensus 3 Ii~~gGkQykV~~Gd~i~Ve~l--~~~~G~~i~l~ 35 (101)
T TIGR00061 3 IVEIGGKQYKVEEGQTVRIEKL--DAAPGDTVEFD 35 (101)
T ss_pred EEEECCEEEEEeCCCEEEEccc--CCCCCCEEEEE
Confidence 3444444445678999999974 35788888775
No 159
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B ....
Probab=20.53 E-value=1.2e+02 Score=23.17 Aligned_cols=36 Identities=19% Similarity=0.283 Sum_probs=17.1
Q ss_pred EEEeCCCccc--cCcCCCEEEEeccCCCCCCCcEEEEE
Q 033489 51 VVVLSGSMEP--GFKRGDILFLHMSKDPIRAGEIVVFN 86 (118)
Q Consensus 51 ~~V~g~SM~P--tl~~GD~vlv~k~~~~~~~GDIVvf~ 86 (118)
+...+++..+ .|+.||+|+.-....++..-+|+.|-
T Consensus 19 V~~~~G~~k~m~~L~iGD~Vla~d~~G~~~yS~V~~fl 56 (217)
T PF01079_consen 19 VTLEDGGRKRMSDLKIGDRVLAVDSDGKLVYSPVIMFL 56 (217)
T ss_dssp EEBTTS-EEEGGG--TT-EEEEE-TTS-EEEEEEEEEE
T ss_pred EEeCCCCEeEHHHCCCCCEEEEecCCCcEEEEeEEEEe
Confidence 4555554443 67788877775433345555666664
No 160
>cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=20.52 E-value=2.1e+02 Score=18.83 Aligned_cols=26 Identities=19% Similarity=0.266 Sum_probs=14.2
Q ss_pred CCCCCCcEEEEEeCCCCcCEEEEEEEE
Q 033489 75 DPIRAGEIVVFNVDGREIPIVHRVIKV 101 (118)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ikRVI~~ 101 (118)
..|++||.++|.+.+ ....+=|+.++
T Consensus 29 ~~~k~Gd~~i~~~~~-~~~~~i~v~~V 54 (105)
T cd06541 29 QLPKAGDYLIILDGQ-QPLAIAEVVKV 54 (105)
T ss_pred cCCCCCCEEEEecCC-CcEEEEEEEEE
Confidence 457888888876543 22234444443
No 161
>TIGR02303 HpaG-C-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit. This model represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation. In E. coli and some other species this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (TIGR02305). In other species such as Pasteurella multocida these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
Probab=20.42 E-value=1.2e+02 Score=23.30 Aligned_cols=30 Identities=17% Similarity=0.539 Sum_probs=20.9
Q ss_pred cCcCCCEEEEecc--CCCCCCCcEEEEEeCCC
Q 033489 61 GFKRGDILFLHMS--KDPIRAGEIVVFNVDGR 90 (118)
Q Consensus 61 tl~~GD~vlv~k~--~~~~~~GDIVvf~~~~~ 90 (118)
||++||+|+.=.. ...++.||.+...-.+-
T Consensus 204 tL~pGDvIlTGTp~g~~~l~~GD~v~~~i~gl 235 (245)
T TIGR02303 204 TLEPGDVILTGTPKGLSDVKPGDVVRLEIEGV 235 (245)
T ss_pred CcCCCCEEEcCCCCCCeEcCCCCEEEEEEcCc
Confidence 7888888887641 23478888887776543
No 162
>PF02311 AraC_binding: AraC-like ligand binding domain; InterPro: IPR003313 This entry defines the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The crystal structure of the arabinose-binding and dimerization domain of the Escherichia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1XJA_B 2ARA_A 2AAC_B 2ARC_A.
Probab=20.32 E-value=2e+02 Score=18.22 Aligned_cols=36 Identities=11% Similarity=0.206 Sum_probs=16.9
Q ss_pred CCCCCCcEEEEEeCCCCcCEEEEEEEECCCceEEEEEEeee
Q 033489 75 DPIRAGEIVVFNVDGREIPIVHRVIKVNILLTLFFELTIQP 115 (118)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ikRVI~~~g~~~~~~~~~~~~ 115 (118)
..+++||++.+..+ ..|+....++..-.++-+-+.|
T Consensus 43 ~~l~~g~~~li~p~-----~~H~~~~~~~~~~~~~~i~~~~ 78 (136)
T PF02311_consen 43 YPLKPGDLFLIPPG-----QPHSYYPDSNEPWEYYWIYFSP 78 (136)
T ss_dssp EEE-TT-EEEE-TT-----S-EEEEE-TTSEEEEEEEEE--
T ss_pred EEEECCEEEEecCC-----ccEEEecCCCCCEEEEEEEECH
Confidence 34788888887643 3456555555555555544443
No 163
>cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.
Probab=20.31 E-value=2.9e+02 Score=18.67 Aligned_cols=16 Identities=19% Similarity=0.497 Sum_probs=12.8
Q ss_pred CCCCCCcEEEEEeCCC
Q 033489 75 DPIRAGEIVVFNVDGR 90 (118)
Q Consensus 75 ~~~~~GDIVvf~~~~~ 90 (118)
.+++.||.|.+...+.
T Consensus 60 ~~l~~Gd~i~v~~~~~ 75 (127)
T cd05828 60 GELEPGDIITLQTLGG 75 (127)
T ss_pred hcCCCCCEEEEEECCE
Confidence 4689999999987744
No 164
>PF01724 DUF29: Domain of unknown function DUF29; InterPro: IPR002636 This entry is represented by Ralstonia phage RSS1, Orf11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of various hypothetical proteins from cyanobacteria, none of which are functionally described. The aligned region is approximately 120-140 amino acids long corresponding to almost the entire length of the proteins in the family.; PDB: 3FCN_A.
Probab=20.23 E-value=2.5e+02 Score=19.77 Aligned_cols=24 Identities=21% Similarity=0.108 Sum_probs=17.0
Q ss_pred hHHHHHHHHhhhHHHHHHHHHHHH
Q 033489 4 IGESIESIKSLQIRQVLTQGVSLG 27 (118)
Q Consensus 4 ~~~~~~~~~~~~~~~i~~~i~~i~ 27 (118)
|.+++|+|.+..++.+.+.+..++
T Consensus 30 LiEEiE~mg~se~~~l~s~L~~ll 53 (139)
T PF01724_consen 30 LIEEIEDMGRSEKRALESRLRVLL 53 (139)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHH
Confidence 567788888888777776665443
No 165
>TIGR03027 pepcterm_export putative polysaccharide export protein, PEP-CTERM sytem-associated. This protein family belongs to the larger set of polysaccharide biosynthesis/export proteins described by Pfam model pfam02563. Members of this family are variable in either containing of lacking a 78-residue insert, but appear to fall within a single clade, nevertheless, where the regions in which the gene is found encode components of the PEP-CTERM/EpsH proposed exosortase protein sorting system.
Probab=20.05 E-value=75 Score=22.62 Aligned_cols=16 Identities=25% Similarity=0.470 Sum_probs=8.5
Q ss_pred CccccCcCCCEEEEec
Q 033489 57 SMEPGFKRGDILFLHM 72 (118)
Q Consensus 57 SM~Ptl~~GD~vlv~k 72 (118)
+..+.|++||.|+|.+
T Consensus 147 ~~n~~L~~gD~I~Vp~ 162 (165)
T TIGR03027 147 TANVELKPGDVLIIPE 162 (165)
T ss_pred cCCceeCCCCEEEEec
Confidence 3445556666665543
Done!