Query 033421
Match_columns 119
No_of_seqs 148 out of 1244
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 13:41:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033421.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033421hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3342 Signal peptidase I [In 99.9 3.5E-23 7.5E-28 149.0 10.5 117 1-118 1-118 (180)
2 TIGR02228 sigpep_I_arch signal 99.9 1.4E-21 3E-26 142.0 12.6 72 45-118 28-100 (158)
3 PRK10861 signal peptidase I; P 99.8 4.7E-19 1E-23 141.2 9.2 79 19-104 60-154 (324)
4 TIGR02227 sigpep_I_bact signal 99.8 2.1E-18 4.5E-23 125.2 8.8 76 22-104 1-80 (163)
5 cd06530 S26_SPase_I The S26 Ty 99.6 1.8E-15 3.9E-20 98.1 7.8 58 50-118 2-63 (85)
6 TIGR02754 sod_Ni_protease nick 99.5 4.8E-14 1E-18 92.6 8.5 61 52-118 2-66 (90)
7 PF00717 Peptidase_S24: Peptid 99.5 3.9E-14 8.5E-19 88.4 7.2 60 52-118 1-60 (70)
8 COG0681 LepB Signal peptidase 99.4 5.8E-13 1.3E-17 94.9 5.9 78 19-104 7-89 (166)
9 KOG0171 Mitochondrial inner me 99.4 7.9E-13 1.7E-17 96.5 5.9 68 30-104 22-94 (176)
10 cd06462 Peptidase_S24_S26 The 99.4 5.1E-12 1.1E-16 80.4 8.6 63 50-118 2-64 (84)
11 cd06529 S24_LexA-like Peptidas 99.1 2.8E-10 6.1E-15 72.3 7.8 52 50-104 2-53 (81)
12 KOG1568 Mitochondrial inner me 99.1 5.1E-10 1.1E-14 81.7 6.7 55 50-104 33-97 (174)
13 COG2932 Predicted transcriptio 98.8 1.8E-08 4E-13 75.5 7.4 53 50-104 125-177 (214)
14 PRK00215 LexA repressor; Valid 98.5 1.2E-06 2.5E-11 65.2 8.3 49 50-101 120-169 (205)
15 PRK10276 DNA polymerase V subu 98.4 1.6E-06 3.4E-11 61.3 6.6 48 50-100 53-101 (139)
16 PRK12423 LexA repressor; Provi 98.3 4.1E-06 8.9E-11 62.6 8.3 49 50-101 116-165 (202)
17 PRK13838 conjugal transfer pil 98.3 8.2E-06 1.8E-10 60.3 9.4 39 66-104 37-98 (176)
18 TIGR00498 lexA SOS regulatory 98.2 7.7E-06 1.7E-10 60.5 8.3 49 50-101 113-162 (199)
19 TIGR02771 TraF_Ti conjugative 98.2 7E-06 1.5E-10 60.3 7.9 48 51-104 27-94 (171)
20 PRK13884 conjugal transfer pep 97.6 0.0013 2.8E-08 48.6 10.5 30 75-104 49-98 (178)
21 COG1974 LexA SOS-response tran 97.6 0.0004 8.6E-09 52.5 7.6 53 49-103 113-166 (201)
22 PF10502 Peptidase_S26: Signal 96.0 0.0018 3.9E-08 45.8 0.0 28 77-104 22-62 (138)
23 COG0361 InfA Translation initi 86.3 0.84 1.8E-05 29.4 2.7 23 61-83 46-68 (75)
24 TIGR00008 infA translation ini 85.6 0.91 2E-05 28.7 2.6 21 63-83 46-66 (68)
25 PF01176 eIF-1a: Translation i 82.1 1.2 2.5E-05 27.5 2.0 27 62-88 22-53 (65)
26 cd05793 S1_IF1A S1_IF1A: Trans 80.5 1.6 3.6E-05 27.9 2.3 21 63-83 40-60 (77)
27 smart00652 eIF1a eukaryotic tr 77.8 2.3 4.9E-05 27.7 2.4 21 63-83 45-65 (83)
28 cd04456 S1_IF1A_like S1_IF1A_l 76.5 2.7 5.8E-05 27.1 2.4 21 63-83 40-61 (78)
29 COG3602 Uncharacterized protei 75.1 2.4 5.1E-05 29.8 2.0 42 56-97 12-56 (134)
30 PRK04012 translation initiatio 74.7 3 6.5E-05 28.2 2.4 21 63-83 61-81 (100)
31 PRK12442 translation initiatio 74.3 3.8 8.3E-05 27.1 2.8 20 64-83 49-68 (87)
32 PF07423 DUF1510: Protein of u 70.5 9 0.00019 29.3 4.4 29 16-44 8-36 (217)
33 PF10000 ACT_3: ACT domain; I 70.4 2.5 5.5E-05 26.8 1.2 35 56-90 12-49 (72)
34 PF04319 NifZ: NifZ domain; I 69.0 15 0.00032 23.6 4.5 29 58-86 1-35 (75)
35 TIGR01000 bacteriocin_acc bact 68.9 21 0.00045 29.6 6.6 36 6-42 7-42 (457)
36 PF14118 YfzA: YfzA-like prote 66.1 9.3 0.0002 25.6 3.2 26 33-67 19-44 (94)
37 PF12273 RCR: Chitin synthesis 62.0 5.6 0.00012 27.5 1.7 16 22-37 2-17 (130)
38 cd04714 BAH_BAHCC1 BAH, or Bro 61.5 19 0.0004 24.6 4.3 28 77-104 4-32 (121)
39 PF15057 DUF4537: Domain of un 59.1 7.6 0.00017 26.9 2.0 21 52-72 46-66 (124)
40 TIGR02594 conserved hypothetic 58.6 34 0.00073 23.8 5.2 15 75-89 72-86 (129)
41 KOG4146 Ubiquitin-like protein 58.6 12 0.00025 25.3 2.7 34 50-87 55-96 (101)
42 cd04712 BAH_DCM_I BAH, or Brom 58.1 24 0.00051 24.6 4.4 28 77-104 6-44 (130)
43 COG1188 Ribosome-associated he 57.2 23 0.00049 24.0 3.9 30 73-104 45-74 (100)
44 PF09285 Elong-fact-P_C: Elong 55.8 23 0.00049 21.4 3.4 38 55-97 18-56 (56)
45 PLN00208 translation initiatio 55.1 11 0.00024 27.2 2.3 27 62-88 71-97 (145)
46 PTZ00329 eukaryotic translatio 54.7 11 0.00025 27.4 2.3 26 62-87 71-96 (155)
47 COG0179 MhpD 2-keto-4-pentenoa 53.5 31 0.00066 27.1 4.7 39 60-99 223-263 (266)
48 COG4959 TraF Type IV secretory 53.4 5.2 0.00011 29.5 0.4 28 77-104 54-94 (173)
49 COG3895 Predicted periplasmic 53.1 36 0.00077 23.6 4.4 40 77-117 49-90 (112)
50 PF08802 CytB6-F_Fe-S: Cytochr 51.6 43 0.00093 18.9 4.9 32 11-42 3-34 (39)
51 PRK00276 infA translation init 51.4 17 0.00036 22.7 2.5 25 63-87 27-57 (72)
52 KOG1666 V-SNARE [Intracellular 50.4 68 0.0015 24.7 6.0 28 4-31 179-206 (220)
53 PF07423 DUF1510: Protein of u 50.2 19 0.00042 27.5 3.1 29 12-40 8-36 (217)
54 COG5131 URM1 Ubiquitin-like pr 49.9 22 0.00047 23.8 2.9 34 50-87 50-91 (96)
55 cd05792 S1_eIF1AD_like S1_eIF1 48.9 15 0.00033 23.6 2.0 10 77-86 39-48 (78)
56 cd06555 ASCH_PF0470_like ASC-1 46.8 40 0.00086 23.0 3.9 27 75-101 30-56 (109)
57 cd04466 S1_YloQ_GTPase S1_YloQ 46.3 42 0.00091 19.8 3.7 25 75-99 36-60 (68)
58 PF05382 Amidase_5: Bacterioph 45.4 24 0.00052 25.3 2.7 37 52-88 50-87 (145)
59 CHL00010 infA translation init 44.3 27 0.00059 22.2 2.7 11 77-87 47-57 (78)
60 cd04717 BAH_polybromo BAH, or 44.2 51 0.0011 22.2 4.2 28 77-104 4-32 (121)
61 PRK11372 lysozyme inhibitor; P 42.8 51 0.0011 22.4 4.0 38 80-118 50-88 (109)
62 smart00841 Elong-fact-P_C Elon 42.4 44 0.00096 20.2 3.2 38 55-97 18-56 (56)
63 TIGR00523 eIF-1A eukaryotic/ar 41.8 29 0.00063 23.3 2.6 9 77-85 58-66 (99)
64 smart00439 BAH Bromo adjacent 41.6 49 0.0011 21.5 3.7 11 62-72 2-12 (120)
65 cd05794 S1_EF-P_repeat_2 S1_EF 40.3 44 0.00095 20.2 3.0 38 55-97 18-56 (56)
66 COG4393 Predicted membrane pro 38.6 2.3E+02 0.005 23.6 9.7 11 108-118 341-351 (405)
67 PF00278 Orn_DAP_Arg_deC: Pyri 37.2 36 0.00078 22.2 2.5 30 60-89 65-95 (116)
68 PF15428 Imm14: Immunity prote 37.1 46 0.001 22.5 3.1 26 78-104 1-27 (129)
69 PRK15136 multidrug efflux syst 36.6 89 0.0019 25.4 5.2 8 76-83 82-89 (390)
70 PRK08564 5'-methylthioadenosin 36.4 25 0.00053 27.6 1.8 19 54-72 92-110 (267)
71 PF01426 BAH: BAH domain; Int 35.9 40 0.00086 22.0 2.6 28 77-104 3-31 (119)
72 cd04721 BAH_plant_1 BAH, or Br 35.1 77 0.0017 22.0 4.0 28 76-104 7-34 (130)
73 TIGR01694 MTAP 5'-deoxy-5'-met 34.9 27 0.00058 26.5 1.8 19 54-72 84-102 (241)
74 PHA03164 hypothetical protein; 34.7 47 0.001 21.6 2.6 17 20-36 62-78 (88)
75 cd04370 BAH BAH, or Bromo Adja 34.4 56 0.0012 21.1 3.1 12 92-103 22-33 (123)
76 cd04720 BAH_Orc1p_Yeast BAH, o 34.2 87 0.0019 23.0 4.3 31 74-104 50-80 (179)
77 cd04716 BAH_plantDCM_I BAH, or 33.7 1.1E+02 0.0023 21.2 4.5 27 78-104 5-31 (122)
78 PRK08666 5'-methylthioadenosin 33.3 27 0.0006 26.8 1.6 19 54-72 84-102 (261)
79 PRK11578 macrolide transporter 33.1 66 0.0014 25.7 3.8 11 94-104 71-81 (370)
80 cd04713 BAH_plant_3 BAH, or Br 32.7 62 0.0013 22.9 3.3 27 76-102 20-46 (146)
81 PRK04313 30S ribosomal protein 32.4 1.8E+02 0.004 22.6 6.0 36 53-89 128-163 (237)
82 cd04719 BAH_Orc1p_animal BAH, 32.3 38 0.00083 23.7 2.1 12 61-72 3-14 (128)
83 PF05257 CHAP: CHAP domain; I 31.1 1.6E+02 0.0035 19.5 5.2 13 74-86 60-72 (124)
84 cd04497 hPOT1_OB1_like hPOT1_O 31.0 1.4E+02 0.003 20.7 4.8 36 50-87 40-79 (138)
85 PRK09136 5'-methylthioadenosin 30.7 33 0.00072 26.4 1.7 22 51-72 81-102 (245)
86 PF11302 DUF3104: Protein of u 30.3 1.5E+02 0.0033 19.0 4.5 12 61-72 5-16 (75)
87 PRK05573 rplU 50S ribosomal pr 29.9 1E+02 0.0022 20.7 3.8 34 51-86 3-36 (103)
88 PF02362 B3: B3 DNA binding do 29.5 67 0.0014 20.2 2.8 16 74-89 71-86 (100)
89 PRK07823 5'-methylthioadenosin 29.1 38 0.00082 26.6 1.7 21 52-72 87-107 (264)
90 TIGR01697 PNPH-PUNA-XAPA inosi 29.0 41 0.00088 25.7 1.9 19 54-72 91-109 (248)
91 TIGR02219 phage_NlpC_fam putat 29.0 38 0.00082 23.4 1.6 13 75-87 75-87 (134)
92 PF06923 GutM: Glucitol operon 28.9 98 0.0021 20.9 3.6 39 63-104 35-73 (109)
93 KOG0557 Dihydrolipoamide acety 28.7 1E+02 0.0022 26.4 4.3 37 50-86 38-75 (470)
94 TIGR00998 8a0101 efflux pump m 28.6 2.8E+02 0.006 21.4 7.0 10 95-104 53-62 (334)
95 cd05790 S1_Rrp40 S1_Rrp40: Rrp 28.6 49 0.0011 21.6 2.0 18 55-72 43-60 (86)
96 PF06459 RR_TM4-6: Ryanodine R 28.6 1.5E+02 0.0032 23.5 5.0 15 28-42 176-190 (274)
97 cd04451 S1_IF1 S1_IF1: Transla 28.3 63 0.0014 19.3 2.3 12 76-87 40-51 (64)
98 TIGR01843 type_I_hlyD type I s 27.6 2.5E+02 0.0054 22.3 6.3 18 24-41 8-25 (423)
99 PF13800 Sigma_reg_N: Sigma fa 27.6 1.5E+02 0.0033 19.0 4.3 15 10-24 4-18 (96)
100 PF14085 DUF4265: Domain of un 27.5 2E+02 0.0043 19.4 5.6 30 74-104 23-52 (117)
101 PRK07432 5'-methylthioadenosin 27.3 60 0.0013 25.9 2.6 23 50-72 84-106 (290)
102 PF06940 DUF1287: Domain of un 27.3 37 0.0008 25.0 1.3 15 75-89 105-119 (164)
103 PRK14578 elongation factor P; 27.2 1E+02 0.0022 23.0 3.7 32 62-98 156-187 (187)
104 PRK04542 elongation factor P; 27.2 1.1E+02 0.0024 22.9 3.9 33 61-98 156-188 (189)
105 COG2326 Uncharacterized conser 27.2 42 0.00092 26.6 1.7 29 76-104 128-156 (270)
106 COG0690 SecE Preprotein transl 26.8 1.4E+02 0.003 18.7 3.8 23 2-24 22-47 (73)
107 COG3655 Predicted transcriptio 26.7 47 0.001 21.2 1.6 16 75-90 55-70 (73)
108 TIGR01700 PNPH purine nucleosi 26.6 43 0.00094 25.7 1.7 19 54-72 91-109 (249)
109 PF08940 DUF1918: Domain of un 26.5 52 0.0011 20.1 1.7 36 63-98 4-41 (58)
110 PF09138 Urm1: Urm1 (Ubiquitin 26.4 56 0.0012 21.8 2.0 28 60-87 56-91 (96)
111 PF13550 Phage-tail_3: Putativ 26.3 1.2E+02 0.0025 20.8 3.7 25 75-101 138-162 (164)
112 PRK08202 purine nucleoside pho 25.8 50 0.0011 25.7 1.9 20 53-72 112-131 (272)
113 PF12961 DUF3850: Domain of Un 25.7 1.4E+02 0.0031 18.9 3.7 17 71-87 23-39 (72)
114 PRK08931 5'-methylthioadenosin 25.6 46 0.001 26.5 1.7 22 51-72 85-106 (289)
115 PHA02650 hypothetical protein; 25.5 1.1E+02 0.0023 20.0 3.0 22 21-42 51-72 (81)
116 PF12751 Vac7: Vacuolar segreg 25.3 1.9E+02 0.0042 24.1 5.3 29 44-72 324-352 (387)
117 cd04709 BAH_MTA BAH, or Bromo 25.2 1.1E+02 0.0024 22.3 3.5 26 77-102 4-29 (164)
118 PRK12426 elongation factor P; 25.1 1.1E+02 0.0024 22.8 3.5 38 56-98 147-185 (185)
119 TIGR02303 HpaG-C-term 4-hydrox 24.9 1.4E+02 0.0031 22.8 4.3 30 61-90 204-235 (245)
120 TIGR00038 efp translation elon 24.9 1.1E+02 0.0024 22.5 3.5 37 57-98 147-184 (184)
121 TIGR01698 PUNP purine nucleoti 24.8 69 0.0015 24.7 2.5 23 50-72 87-109 (237)
122 cd06836 PLPDE_III_ODC_DapDC_li 24.7 1E+02 0.0022 24.9 3.6 29 61-89 328-356 (379)
123 PF00829 Ribosomal_L21p: Ribos 24.7 70 0.0015 21.1 2.2 32 53-86 5-36 (96)
124 PHA02844 putative transmembran 24.4 1.2E+02 0.0027 19.4 3.2 21 20-40 49-69 (75)
125 TIGR03794 NHPM_micro_HlyD NHPM 24.3 3.9E+02 0.0085 21.7 7.5 22 19-40 17-39 (421)
126 PF01878 EVE: EVE domain; Int 24.1 1.2E+02 0.0026 20.8 3.4 15 75-89 38-52 (143)
127 TIGR02178 yeiP elongation fact 23.9 1E+02 0.0022 23.0 3.2 37 57-98 149-186 (186)
128 PF01455 HupF_HypC: HupF/HypC 23.8 71 0.0015 19.8 2.0 16 57-72 33-48 (68)
129 cd06840 PLPDE_III_Bif_AspK_Dap 23.8 1.1E+02 0.0023 24.7 3.5 30 60-89 318-347 (368)
130 cd06843 PLPDE_III_PvsE_like Ty 23.7 1E+02 0.0022 24.6 3.4 30 60-89 326-355 (377)
131 PF13829 DUF4191: Domain of un 23.4 92 0.002 24.0 2.9 19 93-117 114-132 (224)
132 TIGR01048 lysA diaminopimelate 23.3 1.2E+02 0.0025 24.6 3.7 30 60-89 345-374 (417)
133 PRK07115 AMP nucleosidase; Pro 23.2 74 0.0016 24.7 2.4 19 54-72 94-112 (258)
134 PRK15203 4-hydroxyphenylacetat 23.1 1.4E+02 0.0031 24.9 4.2 31 60-90 164-196 (429)
135 cd04092 mtEFG2_II_like mtEFG2_ 23.0 1.1E+02 0.0024 18.8 2.9 12 75-86 59-70 (83)
136 TIGR01718 Uridine-psphlse urid 23.0 64 0.0014 24.6 2.0 19 54-72 87-105 (245)
137 PRK00529 elongation factor P; 22.9 1.4E+02 0.003 22.0 3.8 37 57-98 148-185 (186)
138 KOG2921 Intramembrane metallop 22.7 3.8E+02 0.0082 22.9 6.5 29 58-86 212-248 (484)
139 PF00877 NLPC_P60: NlpC/P60 fa 22.5 49 0.0011 21.3 1.1 13 75-87 50-62 (105)
140 cd04760 BAH_Dnmt1_I BAH, or Br 22.3 1.6E+02 0.0035 20.5 3.7 28 77-104 4-32 (124)
141 cd04088 EFG_mtEFG_II EFG_mtEFG 22.2 1.1E+02 0.0025 18.6 2.8 12 75-86 59-70 (83)
142 cd06839 PLPDE_III_Btrk_like Ty 22.1 1.3E+02 0.0027 24.0 3.6 30 60-89 331-360 (382)
143 TIGR03468 HpnG hopanoid-associ 22.0 61 0.0013 24.1 1.7 19 54-72 54-72 (212)
144 PF13150 DUF3989: Protein of u 21.7 2.4E+02 0.0052 18.3 4.8 20 6-25 14-33 (85)
145 TIGR01704 MTA/SAH-Nsdase 5'-me 21.6 85 0.0018 23.4 2.4 18 55-72 76-93 (228)
146 PF01372 Melittin: Melittin; 21.6 1E+02 0.0022 15.7 1.9 11 6-16 15-25 (26)
147 TIGR03099 dCO2ase_PEP1 pyridox 21.6 1.2E+02 0.0026 24.4 3.4 28 62-89 349-376 (398)
148 PRK13791 lysozyme inhibitor; P 21.4 2.8E+02 0.0061 19.0 4.8 37 81-118 54-95 (113)
149 PF01724 DUF29: Domain of unkn 21.4 1.8E+02 0.004 20.4 4.0 21 4-24 30-50 (139)
150 cd06829 PLPDE_III_CANSDC Type 21.3 1.2E+02 0.0027 24.0 3.4 30 60-89 295-324 (346)
151 PRK07597 secE preprotein trans 21.3 2E+02 0.0043 17.2 4.0 22 3-24 13-37 (64)
152 PLN00036 40S ribosomal protein 21.3 3.8E+02 0.0082 21.2 6.0 12 77-88 154-165 (261)
153 PF15179 Myc_target_1: Myc tar 21.2 1.6E+02 0.0035 22.2 3.7 36 8-43 10-46 (197)
154 PTZ00223 40S ribosomal protein 21.2 3.8E+02 0.0083 21.3 6.0 11 61-71 150-160 (273)
155 PRK13792 lysozyme inhibitor; P 21.2 2.7E+02 0.0058 19.5 4.7 37 82-118 69-106 (127)
156 TIGR01047 nspC carboxynorsperm 21.0 1.1E+02 0.0024 24.8 3.1 30 60-89 309-338 (380)
157 PRK10691 hypothetical protein; 20.7 1.1E+02 0.0023 23.1 2.8 29 61-89 181-211 (219)
158 PF02639 DUF188: Uncharacteriz 20.7 1.7E+02 0.0036 20.5 3.6 38 49-86 12-58 (130)
159 PRK06714 S-adenosylhomocystein 20.6 76 0.0017 24.1 2.0 18 55-72 78-95 (236)
160 PF03908 Sec20: Sec20; InterP 20.2 2.5E+02 0.0054 17.9 5.8 21 4-24 52-72 (92)
161 PF13856 Gifsy-2: ATP-binding 20.1 2.5E+02 0.0055 18.0 4.4 26 75-103 64-89 (95)
162 COG1471 RPS4A Ribosomal protei 20.1 2.6E+02 0.0056 21.9 4.7 15 76-90 152-166 (241)
163 PRK14697 bifunctional 5'-methy 20.1 80 0.0017 23.8 2.0 18 55-72 78-95 (233)
164 COG4043 Preprotein translocase 20.0 62 0.0013 22.2 1.2 14 74-87 31-44 (111)
No 1
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.90 E-value=3.5e-23 Score=149.02 Aligned_cols=117 Identities=61% Similarity=0.979 Sum_probs=108.3
Q ss_pred CcchHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCCcccccCCCEEEEee-cCCCCCc
Q 033421 1 MGWIGESIESIKSLQIRQVLTQGVSLGMIVTSALIIWKALMCITGSESPVVVVLSGSMEPGFKRGDILFLHM-SKDPIRA 79 (119)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~i~~~i~~i~~~i~i~~li~~~~~~~~~~~~~~~~V~g~SM~Pti~~GD~vlv~~-~~~~~~~ 79 (119)
|+|..+....+|+|+.|+.+.-++++++++.-|+++|..+....|+.+|+++|-++||||.++.||+++... .....+.
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 689999999999999999999999999999999999999999999999999999999999999999999874 5566899
Q ss_pred CcEEEEEeCCCCCCEEEEEEEeCCCCCCCeeEEEEcCCC
Q 033421 80 GEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGGN 118 (119)
Q Consensus 80 GDIVvf~~~~~~~~~ikRVi~~~gd~~~~~~~~~tkGD~ 118 (119)
||||+|+.++.+.+++|||+.+-+. .+++..|.|||||
T Consensus 81 GdivVf~vegR~IPiVHRviK~he~-~~~~~~~LTKGDN 118 (180)
T KOG3342|consen 81 GDIVVFKVEGREIPIVHRVIKQHEK-SNGHIKFLTKGDN 118 (180)
T ss_pred ccEEEEEECCccCchhHHHHHHhcc-cCCcEEEEecCCC
Confidence 9999999999988999999998775 3577889999997
No 2
>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=99.87 E-value=1.4e-21 Score=142.00 Aligned_cols=72 Identities=40% Similarity=0.789 Sum_probs=62.2
Q ss_pred CCCCCeEEEeCCCCcccccCCCEEEEee-cCCCCCcCcEEEEEeCCCCCCEEEEEEEeCCCCCCCeeEEEEcCCC
Q 033421 45 GSESPVVVVLSGSMEPGFKRGDILFLHM-SKDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGGN 118 (119)
Q Consensus 45 ~~~~~~~~V~g~SM~Pti~~GD~vlv~~-~~~~~~~GDIVvf~~~~~~~~~ikRVi~~~gd~~~~~~~~~tkGD~ 118 (119)
++..|.+.|.|+||+||+++||.+++++ ..+++++||||+|+.+++++.++|||+++.++ +++.+|+|||||
T Consensus 28 ~~~~p~v~V~g~SM~Ptl~~GD~vlv~~~~~~~~~~GDIVvf~~~~~~~~iihRVi~v~~~--~g~~~~~tkGDn 100 (158)
T TIGR02228 28 SGPDPVVVVLSGSMEPTFNTGDLILVTGADPNDIQVGDVITYKSPGFNTPVTHRVIEINNS--GGELGFITKGDN 100 (158)
T ss_pred cCCCcEEEEcCCCCcCCccCCCEEEEEecccCCCCCCCEEEEEECCCCccEEEEEEEEECC--CCcEEEEEEecC
Confidence 4456777799999999999999999998 35789999999999887656899999999876 356789999997
No 3
>PRK10861 signal peptidase I; Provisional
Probab=99.79 E-value=4.7e-19 Score=141.20 Aligned_cols=79 Identities=24% Similarity=0.357 Sum_probs=69.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCCcccccCCCEEEEeecC---------------CCCCcCcEE
Q 033421 19 VLTQGVSLGMIVTSALIIWKALMCITGSESPVVVVLSGSMEPGFKRGDILFLHMSK---------------DPIRAGEIV 83 (119)
Q Consensus 19 i~~~i~~i~~~i~i~~li~~~~~~~~~~~~~~~~V~g~SM~Pti~~GD~vlv~~~~---------------~~~~~GDIV 83 (119)
++.++..++.+++++++++.|++. ++.|+|+||+|||..||.++++|.. .+|++||||
T Consensus 60 ~~~~~~~~~~~l~i~~~ir~fv~~-------~~~Ips~SM~PTL~~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIV 132 (324)
T PRK10861 60 WLETGASVFPVLAIVLIVRSFIYE-------PFQIPSGSMMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIV 132 (324)
T ss_pred HHHHHHHHHHHHhHHHHHHhhEEE-------EEEECCCcCcCcccCCCEEEEEEeecCccCccccccccccCCCCCCCEE
Confidence 677777777888888899999888 6999999999999999999999931 468999999
Q ss_pred EEEeCCC-CCCEEEEEEEeCCC
Q 033421 84 VFNVDGR-EIPIVHRVIKVHER 104 (119)
Q Consensus 84 vf~~~~~-~~~~ikRVi~~~gd 104 (119)
+|+.|.+ +..|||||||+|||
T Consensus 133 VF~~P~~~~~~yIKRVIGlPGD 154 (324)
T PRK10861 133 VFKYPEDPKLDYIKRVVGLPGD 154 (324)
T ss_pred EEecCCCCCCcEEEEeeecCCc
Confidence 9998765 35799999999999
No 4
>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=2.1e-18 Score=125.17 Aligned_cols=76 Identities=29% Similarity=0.361 Sum_probs=64.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCeEEEeCCCCcccccCCCEEEEeec---CCCCCcCcEEEEEeCCC-CCCEEEE
Q 033421 22 QGVSLGMIVTSALIIWKALMCITGSESPVVVVLSGSMEPGFKRGDILFLHMS---KDPIRAGEIVVFNVDGR-EIPIVHR 97 (119)
Q Consensus 22 ~i~~i~~~i~i~~li~~~~~~~~~~~~~~~~V~g~SM~Pti~~GD~vlv~~~---~~~~~~GDIVvf~~~~~-~~~~ikR 97 (119)
|+..++++++++++++.|++. ++.|+|+||+|||++||+++++|. ..++++||+|+|+.++. .+.++||
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 355666777778888888877 599999999999999999999994 37799999999998753 3579999
Q ss_pred EEEeCCC
Q 033421 98 VIKVHER 104 (119)
Q Consensus 98 Vi~~~gd 104 (119)
|+|+|||
T Consensus 74 Vig~pGd 80 (163)
T TIGR02227 74 VIGLPGD 80 (163)
T ss_pred EEecCCC
Confidence 9999999
No 5
>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=99.62 E-value=1.8e-15 Score=98.07 Aligned_cols=58 Identities=38% Similarity=0.634 Sum_probs=51.1
Q ss_pred eEEEeCCCCcccccCCCEEEEeecCC---CCCcCcEEEEEeCCC-CCCEEEEEEEeCCCCCCCeeEEEEcCCC
Q 033421 50 VVVVLSGSMEPGFKRGDILFLHMSKD---PIRAGEIVVFNVDGR-EIPIVHRVIKVHERQDTGEVEVLTKGGN 118 (119)
Q Consensus 50 ~~~V~g~SM~Pti~~GD~vlv~~~~~---~~~~GDIVvf~~~~~-~~~~ikRVi~~~gd~~~~~~~~~tkGD~ 118 (119)
++.|+|+||+|++++||++++++... .+++||+|+|+.++. ...++|||++ |+++|||
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~~~~~~vkRv~~-----------~~~~gDn 63 (85)
T cd06530 2 PVVVPGGSMEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPGDPGKPIIKRVIG-----------YFVLGDN 63 (85)
T ss_pred eeEEcCCCCcCcccCCCEEEEEEeecccCCCCCCCEEEEeCCCCCCCEEEEEEEE-----------EEEeeCC
Confidence 58999999999999999999998533 699999999998875 4589999998 7889987
No 6
>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=99.54 E-value=4.8e-14 Score=92.57 Aligned_cols=61 Identities=23% Similarity=0.225 Sum_probs=50.1
Q ss_pred EEeCCCCcccccCCCEEEEeec---CCCCCcCcEEEEEeCCC-CCCEEEEEEEeCCCCCCCeeEEEEcCCC
Q 033421 52 VVLSGSMEPGFKRGDILFLHMS---KDPIRAGEIVVFNVDGR-EIPIVHRVIKVHERQDTGEVEVLTKGGN 118 (119)
Q Consensus 52 ~V~g~SM~Pti~~GD~vlv~~~---~~~~~~GDIVvf~~~~~-~~~~ikRVi~~~gd~~~~~~~~~tkGD~ 118 (119)
.|+|+||+|||++||+|++++. ...+++||+|+|+.+++ .+.++||+++.+++ .+...|||
T Consensus 2 ~V~g~SM~P~l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~~~~~~~~vkRv~~~~~~------~~~l~~dN 66 (90)
T TIGR02754 2 KVTGVSMSPTLPPGDRIIVVPWLKIFRVPPIGNVVVVRHPLQPYGLIIKRLAAVDDN------GLFLLGDN 66 (90)
T ss_pred EeeCCCccCccCCCCEEEEEEccccCCCCCCCeEEEEecCCCCcceEEEEeeEEcCC------eEEEeCCC
Confidence 5899999999999999999972 34456799999998763 35899999999876 45667776
No 7
>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=99.53 E-value=3.9e-14 Score=88.36 Aligned_cols=60 Identities=35% Similarity=0.506 Sum_probs=48.5
Q ss_pred EEeCCCCcccccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEEEEeCCCCCCCeeEEEEcCCC
Q 033421 52 VVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGGN 118 (119)
Q Consensus 52 ~V~g~SM~Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~~gd~~~~~~~~~tkGD~ 118 (119)
+|+|+||+|+|++||+|++++. ..++.||+|+|+.++....++||+.+.+++ .+....+|
T Consensus 1 ~V~GdSM~P~i~~Gd~v~v~~~-~~~~~gdivv~~~~~~~~~~iKrv~~~~~~------~~~~~~~n 60 (70)
T PF00717_consen 1 RVEGDSMEPTIKDGDIVLVDPS-SEPKDGDIVVVKIDGDEELYIKRVVGEPGG------IILISSNN 60 (70)
T ss_dssp EEESSTTGGTSSTTEEEEEEET-S---TTSEEEEEETTEESEEEEEEEEETTE------EEEE-SST
T ss_pred CeECcCcccCeeCCCEEEEEEc-CCCccCeEEEEEECCceeeEEEEEEEeCCC------EEEEeccC
Confidence 4899999999999999999985 579999999999987644799999999987 66666554
No 8
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.39 E-value=5.8e-13 Score=94.93 Aligned_cols=78 Identities=31% Similarity=0.350 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHHHHHHHH--HHHHHHhhCCCCCeEEEeCCCCcccccCCCEEEEeec---CCCCCcCcEEEEEeCCCCCC
Q 033421 19 VLTQGVSLGMIVTSALII--WKALMCITGSESPVVVVLSGSMEPGFKRGDILFLHMS---KDPIRAGEIVVFNVDGREIP 93 (119)
Q Consensus 19 i~~~i~~i~~~i~i~~li--~~~~~~~~~~~~~~~~V~g~SM~Pti~~GD~vlv~~~---~~~~~~GDIVvf~~~~~~~~ 93 (119)
...|+..++.++++++++ +.+.+. ++.|+|+||+||++.||+++++|. ...+..+|++.+-. .....
T Consensus 7 ~~~~~~~~~~~~~~~~~i~~~~~~~~-------~~~V~s~SM~Ptl~~GD~v~v~k~~~~~~~~~~~~~~~~~~-~~~~~ 78 (166)
T COG0681 7 FLELISSLLIAIILALIIGVRTFVFE-------PVVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDIIVLPA-VVEGD 78 (166)
T ss_pred HHHHHHHHHHHHHHhheeeeEEEEEE-------EEEECCCccccccccCCEEEEEeccccccCCccceeeecCC-CCCcc
Confidence 556777777777777776 555555 699999999999999999999994 23467777773322 22346
Q ss_pred EEEEEEEeCCC
Q 033421 94 IVHRVIKVHER 104 (119)
Q Consensus 94 ~ikRVi~~~gd 104 (119)
++||+++.+||
T Consensus 79 ~~kr~~~~~GD 89 (166)
T COG0681 79 LIKRVIGLRGD 89 (166)
T ss_pred eEEEeccCCCC
Confidence 99999999998
No 9
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.38 E-value=7.9e-13 Score=96.47 Aligned_cols=68 Identities=21% Similarity=0.278 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHHHhhCCCCCeEEEeCCCCcccccCC-CEEEEee---cCCCCCcCcEEEEEeCCC-CCCEEEEEEEeCCC
Q 033421 30 VTSALIIWKALMCITGSESPVVVVLSGSMEPGFKRG-DILFLHM---SKDPIRAGEIVVFNVDGR-EIPIVHRVIKVHER 104 (119)
Q Consensus 30 i~i~~li~~~~~~~~~~~~~~~~V~g~SM~Pti~~G-D~vlv~~---~~~~~~~GDIVvf~~~~~-~~~~ikRVi~~~gd 104 (119)
.|++.....+++. +...+|.||+||++++ |+++++| .++.+++||||+++.|.+ .+.++|||+|++||
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 3444455556666 4889999999999865 5555577 367789999999999876 36899999999999
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=99.37 E-value=5.1e-12 Score=80.44 Aligned_cols=63 Identities=32% Similarity=0.445 Sum_probs=53.8
Q ss_pred eEEEeCCCCcccccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEEEEeCCCCCCCeeEEEEcCCC
Q 033421 50 VVVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGGN 118 (119)
Q Consensus 50 ~~~V~g~SM~Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~~gd~~~~~~~~~tkGD~ 118 (119)
.+.++|+||+|+|++||++++++....++.||+++++.++ ...++||+...++. ..+.+++||
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~i~~~~~~~~~G~iv~~~~~~-~~~~ikrl~~~~~~-----~~~~l~~~N 64 (84)
T cd06462 2 ALRVEGDSMEPTIPDGDLVLVDKSSYEPKRGDIVVFRLPG-GELTVKRVIGLPGE-----GHYFLLGDN 64 (84)
T ss_pred eeEEcCCCccCcccCCCEEEEEecCCCCcCCEEEEEEcCC-CcEEEEEEEEECCC-----CEEEEECCC
Confidence 4789999999999999999999864458999999999887 34799999999872 167888886
No 11
>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=99.15 E-value=2.8e-10 Score=72.31 Aligned_cols=52 Identities=35% Similarity=0.492 Sum_probs=45.9
Q ss_pred eEEEeCCCCcccccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEEEEeCCC
Q 033421 50 VVVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHER 104 (119)
Q Consensus 50 ~~~V~g~SM~Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~~gd 104 (119)
.+.++|+||+|++++||.+++++. ..++.||++++..++ +.++||+...+++
T Consensus 2 ~~~v~g~sM~p~i~~gd~lii~~~-~~~~~g~i~~~~~~~--~~~ikr~~~~~~~ 53 (81)
T cd06529 2 ALRVKGDSMEPTIPDGDLVLVDPS-DTPRDGDIVVARLDG--ELTVKRLQRRGGG 53 (81)
T ss_pred EEEEECCCcCCccCCCCEEEEcCC-CCCCCCCEEEEEECC--EEEEEEEEECCCC
Confidence 378999999999999999999985 449999999999887 4699999988864
No 12
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.05 E-value=5.1e-10 Score=81.70 Aligned_cols=55 Identities=25% Similarity=0.410 Sum_probs=48.0
Q ss_pred eEEEeCCCCcccccCC------CEEEEeec---CCCCCcCcEEEEEeCCC-CCCEEEEEEEeCCC
Q 033421 50 VVVVLSGSMEPGFKRG------DILFLHMS---KDPIRAGEIVVFNVDGR-EIPIVHRVIKVHER 104 (119)
Q Consensus 50 ~~~V~g~SM~Pti~~G------D~vlv~~~---~~~~~~GDIVvf~~~~~-~~~~ikRVi~~~gd 104 (119)
+..|.|.||.||++++ |.|++.|. ...+.+||||+|+.|.+ ++++||||.|++||
T Consensus 33 va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~p~~~~iKRv~alegd 97 (174)
T KOG1568|consen 33 VAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPNDPDKVIIKRVAALEGD 97 (174)
T ss_pred EeEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCCChhheeeeeeeccccc
Confidence 5789999999999876 89999982 34588999999999876 47899999999998
No 13
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.80 E-value=1.8e-08 Score=75.54 Aligned_cols=53 Identities=26% Similarity=0.385 Sum_probs=43.9
Q ss_pred eEEEeCCCCcccccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEEEEeCCC
Q 033421 50 VVVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHER 104 (119)
Q Consensus 50 ~~~V~g~SM~Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~~gd 104 (119)
...|.|+||+|+|++||.++|+.. .+..+||.+++...+. +.+|||+...++.
T Consensus 125 ~i~V~GDSMeP~~~~Gd~ilVd~~-~~~~~gd~v~v~~~g~-~~~VK~l~~~~~~ 177 (214)
T COG2932 125 ALRVTGDSMEPTYEDGDTLLVDPG-VNTRRGDRVYVETDGG-ELYVKKLQREPGG 177 (214)
T ss_pred EEEEeCCcccccccCCCEEEECCC-CceeeCCEEEEEEeCC-eEEEEEEEEecCC
Confidence 478999999999999999999985 4567788666665553 3799999999987
No 14
>PRK00215 LexA repressor; Validated
Probab=98.45 E-value=1.2e-06 Score=65.16 Aligned_cols=49 Identities=29% Similarity=0.417 Sum_probs=42.0
Q ss_pred eEEEeCCCCc-ccccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEEEEe
Q 033421 50 VVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKV 101 (119)
Q Consensus 50 ~~~V~g~SM~-Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~ 101 (119)
.+.|.|+||. |+|++||++++++. ..++.||++++..++ ..++||+.-.
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 79999999999984 567899999998876 4789998765
No 15
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=98.35 E-value=1.6e-06 Score=61.32 Aligned_cols=48 Identities=29% Similarity=0.416 Sum_probs=40.6
Q ss_pred eEEEeCCCCc-ccccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEEEE
Q 033421 50 VVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIK 100 (119)
Q Consensus 50 ~~~V~g~SM~-Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~ 100 (119)
.+.|+|+||. |+|++||++++++. ..++.||++++..++. ..+||...
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 5789999998 68999999999985 4578999999987653 68999874
No 16
>PRK12423 LexA repressor; Provisional
Probab=98.31 E-value=4.1e-06 Score=62.60 Aligned_cols=49 Identities=33% Similarity=0.466 Sum_probs=41.8
Q ss_pred eEEEeCCCCc-ccccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEEEEe
Q 033421 50 VVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKV 101 (119)
Q Consensus 50 ~~~V~g~SM~-Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~ 101 (119)
.+.|.|+||. |+|.+||+|++++. ..++.||+|++..++ ..++||..-.
T Consensus 116 ~l~V~GdSM~~~~i~~Gd~viv~~~-~~~~~Gdivv~~~~~--~~~vKrl~~~ 165 (202)
T PRK12423 116 LLQVQGDSMIDDGILDGDLVGVHRS-PEARDGQIVVARLDG--EVTIKRLERS 165 (202)
T ss_pred EEEEecCcCCCCCcCCCCEEEEeCC-CcCCCCCEEEEEECC--EEEEEEEEEe
Confidence 5789999997 79999999999985 668899999998865 3689998754
No 17
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=98.29 E-value=8.2e-06 Score=60.29 Aligned_cols=39 Identities=18% Similarity=0.318 Sum_probs=28.8
Q ss_pred CEEEEee---cCCCCCcCcEEEEEeCCCC--------------------CCEEEEEEEeCCC
Q 033421 66 DILFLHM---SKDPIRAGEIVVFNVDGRE--------------------IPIVHRVIKVHER 104 (119)
Q Consensus 66 D~vlv~~---~~~~~~~GDIVvf~~~~~~--------------------~~~ikRVi~~~gd 104 (119)
+-+.+.+ ...++++||+|+|+.|... .+++|||+|+|||
T Consensus 37 ~pig~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD 98 (176)
T PRK13838 37 EPLGLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQ 98 (176)
T ss_pred CEEEEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCc
Confidence 3344444 2467999999999866432 2599999999999
No 18
>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=98.23 E-value=7.7e-06 Score=60.48 Aligned_cols=49 Identities=35% Similarity=0.495 Sum_probs=41.7
Q ss_pred eEEEeCCCCc-ccccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEEEEe
Q 033421 50 VVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKV 101 (119)
Q Consensus 50 ~~~V~g~SM~-Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~ 101 (119)
.+.|.|+||. |+|++||++++++. ..++.||+|++..++ ..++||+.-.
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 68999999999985 678999999999844 3689998754
No 19
>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=7e-06 Score=60.33 Aligned_cols=48 Identities=21% Similarity=0.375 Sum_probs=34.1
Q ss_pred EEEeCCCCcccccCCCEEEEeecCCCCCcCcEEEEEeCCCCC--------------------CEEEEEEEeCCC
Q 033421 51 VVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDGREI--------------------PIVHRVIKVHER 104 (119)
Q Consensus 51 ~~V~g~SM~Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~--------------------~~ikRVi~~~gd 104 (119)
..-.++||-+.+ .. ..+ ..++++||+|+|+.|+... .++|||+|+|||
T Consensus 27 ~~N~T~S~P~g~----Y~-~~~-~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpGD 94 (171)
T TIGR02771 27 RINTTKSLPLGL----YW-TTS-SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGD 94 (171)
T ss_pred EEECCCCCcceE----EE-eCC-CCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCCC
Confidence 344556766554 33 222 3679999999999765321 699999999999
No 20
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=97.60 E-value=0.0013 Score=48.62 Aligned_cols=30 Identities=23% Similarity=0.361 Sum_probs=22.6
Q ss_pred CCCCcCcEEEEEeCCC--------------------CCCEEEEEEEeCCC
Q 033421 75 DPIRAGEIVVFNVDGR--------------------EIPIVHRVIKVHER 104 (119)
Q Consensus 75 ~~~~~GDIVvf~~~~~--------------------~~~~ikRVi~~~gd 104 (119)
.++++||+|+|..|.. ..+++|||+|+|||
T Consensus 49 ~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD 98 (178)
T PRK13884 49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGD 98 (178)
T ss_pred CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCc
Confidence 4578888888875541 13689999999999
No 21
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=97.58 E-value=0.0004 Score=52.46 Aligned_cols=53 Identities=28% Similarity=0.408 Sum_probs=44.0
Q ss_pred CeEEEeCCCCc-ccccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEEEEeCC
Q 033421 49 PVVVVLSGSME-PGFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHE 103 (119)
Q Consensus 49 ~~~~V~g~SM~-Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~~g 103 (119)
....|.|+||. +.+.+||+|+|++. ...+.||||+...++ ++..+||..--.+
T Consensus 113 f~L~V~GdSM~~~gi~dGDlvvV~~~-~~a~~GdiVvA~i~g-~e~TvKrl~~~g~ 166 (201)
T COG1974 113 FFLRVSGDSMIDAGILDGDLVVVDPT-EDAENGDIVVALIDG-EEATVKRLYRDGN 166 (201)
T ss_pred EEEEecCCccccCcCCCCCEEEEcCC-CCCCCCCEEEEEcCC-CcEEEEEEEEeCC
Confidence 36889999997 78889999999984 678999999999888 4478888765433
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=95.98 E-value=0.0018 Score=45.84 Aligned_cols=28 Identities=32% Similarity=0.546 Sum_probs=0.0
Q ss_pred CCcCcEEEEEeCCC-------------CCCEEEEEEEeCCC
Q 033421 77 IRAGEIVVFNVDGR-------------EIPIVHRVIKVHER 104 (119)
Q Consensus 77 ~~~GDIVvf~~~~~-------------~~~~ikRVi~~~gd 104 (119)
+++||+|+|..|.. ...++|||+|+|||
T Consensus 22 ~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD 62 (138)
T PF10502_consen 22 IERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGD 62 (138)
T ss_dssp -----------------------------------------
T ss_pred ccccccccccccccccccccccccccccccccccccccccc
Confidence 67777777776531 23789999999999
No 23
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=86.28 E-value=0.84 Score=29.41 Aligned_cols=23 Identities=26% Similarity=0.507 Sum_probs=18.3
Q ss_pred cccCCCEEEEeecCCCCCcCcEE
Q 033421 61 GFKRGDILFLHMSKDPIRAGEIV 83 (119)
Q Consensus 61 ti~~GD~vlv~~~~~~~~~GDIV 83 (119)
-|.+||.|+|+....++++|||+
T Consensus 46 ~I~~GD~V~Ve~~~~d~~kg~I~ 68 (75)
T COG0361 46 RILPGDVVLVELSPYDLTKGRIV 68 (75)
T ss_pred EeCCCCEEEEEecccccccccEE
Confidence 46788888888876778888876
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=85.62 E-value=0.91 Score=28.69 Aligned_cols=21 Identities=24% Similarity=0.332 Sum_probs=12.4
Q ss_pred cCCCEEEEeecCCCCCcCcEE
Q 033421 63 KRGDILFLHMSKDPIRAGEIV 83 (119)
Q Consensus 63 ~~GD~vlv~~~~~~~~~GDIV 83 (119)
.+||.|.|..+..++.+|+|+
T Consensus 46 ~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 46 LPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred CCCCEEEEEECcccCCcEeEE
Confidence 466666666554556666654
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=82.12 E-value=1.2 Score=27.47 Aligned_cols=27 Identities=15% Similarity=0.294 Sum_probs=12.2
Q ss_pred ccCCCEEEEee-----cCCCCCcCcEEEEEeC
Q 033421 62 FKRGDILFLHM-----SKDPIRAGEIVVFNVD 88 (119)
Q Consensus 62 i~~GD~vlv~~-----~~~~~~~GDIVvf~~~ 88 (119)
+.+|..+++.- ..--+++||.|+....
T Consensus 22 ~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~~ 53 (65)
T PF01176_consen 22 CEDGEERLARIPGKFRKRIWIKRGDFVLVEPS 53 (65)
T ss_dssp ETTSEEEEEEE-HHHHTCC---TTEEEEEEES
T ss_pred eCCCCEEEEEeccceeeeEecCCCCEEEEEec
Confidence 44555555542 1223566666666643
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=80.48 E-value=1.6 Score=27.95 Aligned_cols=21 Identities=19% Similarity=0.274 Sum_probs=11.2
Q ss_pred cCCCEEEEeecCCCCCcCcEE
Q 033421 63 KRGDILFLHMSKDPIRAGEIV 83 (119)
Q Consensus 63 ~~GD~vlv~~~~~~~~~GDIV 83 (119)
..||.|++.....+..+|||+
T Consensus 40 ~~GD~V~Ve~~~~d~~kg~Iv 60 (77)
T cd05793 40 NEGDIVLVAPWDFQDDKADII 60 (77)
T ss_pred cCCCEEEEEeccccCCEEEEE
Confidence 455555555544445555554
No 27
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=77.75 E-value=2.3 Score=27.69 Aligned_cols=21 Identities=24% Similarity=0.365 Sum_probs=10.5
Q ss_pred cCCCEEEEeecCCCCCcCcEE
Q 033421 63 KRGDILFLHMSKDPIRAGEIV 83 (119)
Q Consensus 63 ~~GD~vlv~~~~~~~~~GDIV 83 (119)
+.||.|+++....+..+|||+
T Consensus 45 ~~GD~VlVe~~~~~~~kg~Iv 65 (83)
T smart00652 45 RRGDIVLVDPWDFQDVKADII 65 (83)
T ss_pred cCCCEEEEEecCCCCCEEEEE
Confidence 455555555433334555544
No 28
>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=76.51 E-value=2.7 Score=27.06 Aligned_cols=21 Identities=29% Similarity=0.488 Sum_probs=10.2
Q ss_pred cCCCEEEEeecCC-CCCcCcEE
Q 033421 63 KRGDILFLHMSKD-PIRAGEIV 83 (119)
Q Consensus 63 ~~GD~vlv~~~~~-~~~~GDIV 83 (119)
+.||.|+++.... +..+|||+
T Consensus 40 ~~GD~VlV~~~~~~~~~kg~Iv 61 (78)
T cd04456 40 KRGDFLIVDPIEEGEDVKADII 61 (78)
T ss_pred cCCCEEEEEecccCCCceEEEE
Confidence 4555555554332 34555554
No 29
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.11 E-value=2.4 Score=29.77 Aligned_cols=42 Identities=21% Similarity=0.284 Sum_probs=24.8
Q ss_pred CCCcccccCCCEEEEeec--CCCC-CcCcEEEEEeCCCCCCEEEE
Q 033421 56 GSMEPGFKRGDILFLHMS--KDPI-RAGEIVVFNVDGREIPIVHR 97 (119)
Q Consensus 56 ~SM~Pti~~GD~vlv~~~--~~~~-~~GDIVvf~~~~~~~~~ikR 97 (119)
.||.|.+.+||.|+..-. ...+ .---+-.|+.+..-..++.|
T Consensus 12 ~smtPeL~~G~yVfcT~~~ga~~~~~lePla~FRE~EG~tLiler 56 (134)
T COG3602 12 ASMTPELLDGDYVFCTVAPGALQPKNLEPLATFREREGLTLILER 56 (134)
T ss_pred HhcCccccCCceEEEEecCCcCCCcCCChHhhhccccCcEEEEeh
Confidence 389999999999998752 1111 22235566655443333433
No 30
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=74.74 E-value=3 Score=28.17 Aligned_cols=21 Identities=14% Similarity=0.286 Sum_probs=11.1
Q ss_pred cCCCEEEEeecCCCCCcCcEE
Q 033421 63 KRGDILFLHMSKDPIRAGEIV 83 (119)
Q Consensus 63 ~~GD~vlv~~~~~~~~~GDIV 83 (119)
..||.|+|.....+..+|||+
T Consensus 61 ~~GD~VlVe~~~~~~~kg~Iv 81 (100)
T PRK04012 61 REGDVVIVAPWDFQDEKADII 81 (100)
T ss_pred cCCCEEEEEecccCCCEEEEE
Confidence 355666665543345555554
No 31
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=74.30 E-value=3.8 Score=27.11 Aligned_cols=20 Identities=30% Similarity=0.404 Sum_probs=9.0
Q ss_pred CCCEEEEeecCCCCCcCcEE
Q 033421 64 RGDILFLHMSKDPIRAGEIV 83 (119)
Q Consensus 64 ~GD~vlv~~~~~~~~~GDIV 83 (119)
+||.|.|..+..++.+|+|+
T Consensus 49 ~GD~V~VE~spYDltkGRIi 68 (87)
T PRK12442 49 AGDRVTLELSPYDLTKGRIN 68 (87)
T ss_pred CCCEEEEEECcccCCceeEE
Confidence 44444444443444444443
No 32
>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=70.46 E-value=9 Score=29.35 Aligned_cols=29 Identities=21% Similarity=0.162 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033421 16 IRQVLTQGVSLGMIVTSALIIWKALMCIT 44 (119)
Q Consensus 16 ~~~i~~~i~~i~~~i~i~~li~~~~~~~~ 44 (119)
+|+-...++.+++++++++++....+.++
T Consensus 8 KrRK~N~iLNiaI~IV~lLIiiva~~lf~ 36 (217)
T PF07423_consen 8 KRRKTNKILNIAIGIVSLLIIIVAYQLFF 36 (217)
T ss_pred HhhhhhhhHHHHHHHHHHHHHHHhhhhee
Confidence 44444555666655555444444444433
No 33
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=70.44 E-value=2.5 Score=26.79 Aligned_cols=35 Identities=20% Similarity=0.303 Sum_probs=19.3
Q ss_pred CCCcccccCCCEEEEeec--CCCC-CcCcEEEEEeCCC
Q 033421 56 GSMEPGFKRGDILFLHMS--KDPI-RAGEIVVFNVDGR 90 (119)
Q Consensus 56 ~SM~Pti~~GD~vlv~~~--~~~~-~~GDIVvf~~~~~ 90 (119)
.||+|.+++|+.||+.-. ...+ .-.=+.+|+.+..
T Consensus 12 ~~m~P~L~~~~yVF~t~~~~~~~~~~l~pi~~frE~EG 49 (72)
T PF10000_consen 12 ASMSPELNPGEYVFCTVPGDLADPPGLEPIATFREAEG 49 (72)
T ss_dssp ST-EEEE-SS-EEEEEE-S-GGGGGGG--SEEEEETTE
T ss_pred hhCCcEeCCCCEEEEEecCcccCccCCcceEEEEecCc
Confidence 489999999999999753 1111 2223467776654
No 34
>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=68.97 E-value=15 Score=23.61 Aligned_cols=29 Identities=28% Similarity=0.358 Sum_probs=21.8
Q ss_pred CcccccCCCEEEEeec------CCCCCcCcEEEEE
Q 033421 58 MEPGFKRGDILFLHMS------KDPIRAGEIVVFN 86 (119)
Q Consensus 58 M~Pti~~GD~vlv~~~------~~~~~~GDIVvf~ 86 (119)
|.|.++.||.|.+.+. ...-..|++++-+
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 8899999999999872 2345667777654
No 35
>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein. This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193.
Probab=68.87 E-value=21 Score=29.63 Aligned_cols=36 Identities=14% Similarity=0.018 Sum_probs=20.6
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033421 6 ESIESIKSLQIRQVLTQGVSLGMIVTSALIIWKALMC 42 (119)
Q Consensus 6 ~~~~~~~~~~~~~i~~~i~~i~~~i~i~~li~~~~~~ 42 (119)
.|+|.+.+...... ++++.+++++++++++|.++..
T Consensus 7 ~s~~~~~~~~~~~~-~~~~~~~~~~~~~~~~WA~~~~ 42 (457)
T TIGR01000 7 ESSEFYQKRYHNFS-TLVIVPIFLLLVFLVLFSLFAK 42 (457)
T ss_pred hHHHHHHhcCCCcc-hhHHHHHHHHHHHHHHHHHhEe
Confidence 46677766654444 4544455555556667766554
No 36
>PF14118 YfzA: YfzA-like protein
Probab=66.09 E-value=9.3 Score=25.64 Aligned_cols=26 Identities=27% Similarity=0.471 Sum_probs=18.4
Q ss_pred HHHHHHHHHHhhCCCCCeEEEeCCCCcccccCCCE
Q 033421 33 ALIIWKALMCITGSESPVVVVLSGSMEPGFKRGDI 67 (119)
Q Consensus 33 ~~li~~~~~~~~~~~~~~~~V~g~SM~Pti~~GD~ 67 (119)
++++.+++|.. +.+.|+.|.+++||.
T Consensus 19 iF~i~QLlFi~---------~d~t~w~pnf~~g~~ 44 (94)
T PF14118_consen 19 IFLIVQLLFII---------FDGTGWGPNFNEGDF 44 (94)
T ss_pred HHHHHHHHHHH---------hhccccccccCCCch
Confidence 34455555543 678999999999864
No 37
>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=61.97 E-value=5.6 Score=27.50 Aligned_cols=16 Identities=19% Similarity=0.131 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHHHHHH
Q 033421 22 QGVSLGMIVTSALIIW 37 (119)
Q Consensus 22 ~i~~i~~~i~i~~li~ 37 (119)
|++.+++++++++++.
T Consensus 2 W~l~~iii~~i~l~~~ 17 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLF 17 (130)
T ss_pred eeeHHHHHHHHHHHHH
Confidence 5554444444333333
No 38
>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=61.52 E-value=19 Score=24.64 Aligned_cols=28 Identities=39% Similarity=0.733 Sum_probs=19.5
Q ss_pred CCcCcEEEEEeCCC-CCCEEEEEEEeCCC
Q 033421 77 IRAGEIVVFNVDGR-EIPIVHRVIKVHER 104 (119)
Q Consensus 77 ~~~GDIVvf~~~~~-~~~~ikRVi~~~gd 104 (119)
++.||-|.++.++. ..++|.||..+-.+
T Consensus 4 ~~vGD~V~v~~~~~~~~pyIgrI~~i~e~ 32 (121)
T cd04714 4 IRVGDCVLFKSPGRPSLPYVARIESLWED 32 (121)
T ss_pred EEcCCEEEEeCCCCCCCCEEEEEEEEEEc
Confidence 56778888776654 45788888877654
No 39
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=59.11 E-value=7.6 Score=26.92 Aligned_cols=21 Identities=24% Similarity=0.411 Sum_probs=17.2
Q ss_pred EEeCCCCcccccCCCEEEEee
Q 033421 52 VVLSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 52 ~V~g~SM~Pti~~GD~vlv~~ 72 (119)
.--+++|.|.|+.||.|++..
T Consensus 46 I~~~~~~~~~L~~GD~VLA~~ 66 (124)
T PF15057_consen 46 IALSDAMRHSLQVGDKVLAPW 66 (124)
T ss_pred EEccCcccCcCCCCCEEEEec
Confidence 344578899999999999974
No 40
>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=58.64 E-value=34 Score=23.80 Aligned_cols=15 Identities=27% Similarity=0.164 Sum_probs=11.3
Q ss_pred CCCCcCcEEEEEeCC
Q 033421 75 DPIRAGEIVVFNVDG 89 (119)
Q Consensus 75 ~~~~~GDIVvf~~~~ 89 (119)
..|++||+|+|+.++
T Consensus 72 ~~p~~GDiv~f~~~~ 86 (129)
T TIGR02594 72 SKPAYGCIAVKRRGG 86 (129)
T ss_pred CCCCccEEEEEECCC
Confidence 457899999997544
No 41
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=58.56 E-value=12 Score=25.28 Aligned_cols=34 Identities=26% Similarity=0.560 Sum_probs=25.6
Q ss_pred eEEEeCCCCcccccCCCEEEEee--------cCCCCCcCcEEEEEe
Q 033421 50 VVVVLSGSMEPGFKRGDILFLHM--------SKDPIRAGEIVVFNV 87 (119)
Q Consensus 50 ~~~V~g~SM~Pti~~GD~vlv~~--------~~~~~~~GDIVvf~~ 87 (119)
-+.++++|.+|. =++++|. ....++.||.|+|-+
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 378999988774 4666665 246789999999964
No 42
>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=58.12 E-value=24 Score=24.63 Aligned_cols=28 Identities=29% Similarity=0.538 Sum_probs=15.6
Q ss_pred CCcCcEEEEEeCCCC-----------CCEEEEEEEeCCC
Q 033421 77 IRAGEIVVFNVDGRE-----------IPIVHRVIKVHER 104 (119)
Q Consensus 77 ~~~GDIVvf~~~~~~-----------~~~ikRVi~~~gd 104 (119)
++.||+|..+.++.+ ..+|-||..+..+
T Consensus 6 i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~ 44 (130)
T cd04712 6 IRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKG 44 (130)
T ss_pred EeCCCEEEEcCCCCCccccccccccccceEEEEEEeeec
Confidence 455666666544322 3577777766444
No 43
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=57.17 E-value=23 Score=24.03 Aligned_cols=30 Identities=17% Similarity=0.475 Sum_probs=24.3
Q ss_pred cCCCCCcCcEEEEEeCCCCCCEEEEEEEeCCC
Q 033421 73 SKDPIRAGEIVVFNVDGREIPIVHRVIKVHER 104 (119)
Q Consensus 73 ~~~~~~~GDIVvf~~~~~~~~~ikRVi~~~gd 104 (119)
...+++.||++.+..+++. +.=+|.+++..
T Consensus 45 pS~~VK~GD~l~i~~~~~~--~~v~Vl~~~~~ 74 (100)
T COG1188 45 PSKEVKVGDILTIRFGNKE--FTVKVLALGEQ 74 (100)
T ss_pred cccccCCCCEEEEEeCCcE--EEEEEEecccc
Confidence 3577999999999988764 77888888776
No 44
>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=55.82 E-value=23 Score=21.44 Aligned_cols=38 Identities=21% Similarity=0.374 Sum_probs=22.1
Q ss_pred CCCCccc-ccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEE
Q 033421 55 SGSMEPG-FKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHR 97 (119)
Q Consensus 55 g~SM~Pt-i~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikR 97 (119)
++++.|. |.+|-.+-|-. -++.||.|..+..+.+ |+.|
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 3345553 45776666633 4899999999876554 8877
No 45
>PLN00208 translation initiation factor (eIF); Provisional
Probab=55.09 E-value=11 Score=27.15 Aligned_cols=27 Identities=11% Similarity=0.292 Sum_probs=19.1
Q ss_pred ccCCCEEEEeecCCCCCcCcEEEEEeC
Q 033421 62 FKRGDILFLHMSKDPIRAGEIVVFNVD 88 (119)
Q Consensus 62 i~~GD~vlv~~~~~~~~~GDIVvf~~~ 88 (119)
+..||+|+|........+||||--..+
T Consensus 71 I~~GD~VlVel~~~d~~KgdIv~ry~~ 97 (145)
T PLN00208 71 IAAGDIILVGLRDYQDDKADVILKYMP 97 (145)
T ss_pred ecCCCEEEEEccCCCCCEEEEEEEcCH
Confidence 468888888775566788888754433
No 46
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=54.71 E-value=11 Score=27.40 Aligned_cols=26 Identities=12% Similarity=0.278 Sum_probs=18.8
Q ss_pred ccCCCEEEEeecCCCCCcCcEEEEEe
Q 033421 62 FKRGDILFLHMSKDPIRAGEIVVFNV 87 (119)
Q Consensus 62 i~~GD~vlv~~~~~~~~~GDIVvf~~ 87 (119)
|.+||+|+|........+||||--..
T Consensus 71 I~~GD~VlVel~~yd~~KgdIi~Ry~ 96 (155)
T PTZ00329 71 INIGDIILVSLRDFQDSKADVILKYT 96 (155)
T ss_pred ecCCCEEEEeccCCCCCEEEEEEEcC
Confidence 46888888887656678888875443
No 47
>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=53.48 E-value=31 Score=27.14 Aligned_cols=39 Identities=15% Similarity=0.407 Sum_probs=27.7
Q ss_pred ccccCCCEEEEee--cCCCCCcCcEEEEEeCCCCCCEEEEEE
Q 033421 60 PGFKRGDILFLHM--SKDPIRAGEIVVFNVDGREIPIVHRVI 99 (119)
Q Consensus 60 Pti~~GD~vlv~~--~~~~~~~GDIVvf~~~~~~~~~ikRVi 99 (119)
=||++||+++.-. -...++.||+|.....+-. .+-.+|+
T Consensus 223 ~tL~pGDvI~TGTP~Gvg~l~~GD~v~~~iegiG-~l~n~v~ 263 (266)
T COG0179 223 MTLEPGDVILTGTPSGVGFLKPGDVVEVEIEGIG-ELENTVV 263 (266)
T ss_pred cccCCCCEEEeCCCCCcccCCCCCEEEEEeccee-EEEEEEe
Confidence 3789999999854 2456899999998877643 3444444
No 48
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=53.36 E-value=5.2 Score=29.47 Aligned_cols=28 Identities=21% Similarity=0.536 Sum_probs=19.6
Q ss_pred CCcCcEEEEEeCCC-------------CCCEEEEEEEeCCC
Q 033421 77 IRAGEIVVFNVDGR-------------EIPIVHRVIKVHER 104 (119)
Q Consensus 77 ~~~GDIVvf~~~~~-------------~~~~ikRVi~~~gd 104 (119)
+.+||.|++..|+. ..+.+|||.|+||+
T Consensus 54 vt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq 94 (173)
T COG4959 54 VTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQ 94 (173)
T ss_pred cccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCC
Confidence 46666666665542 13679999999998
No 49
>COG3895 Predicted periplasmic protein [General function prediction only]
Probab=53.08 E-value=36 Score=23.56 Aligned_cols=40 Identities=30% Similarity=0.459 Sum_probs=29.0
Q ss_pred CCcCcE-EEEEeCCCCCCEEEEEEEeCCCC-CCCeeEEEEcCC
Q 033421 77 IRAGEI-VVFNVDGREIPIVHRVIKVHERQ-DTGEVEVLTKGG 117 (119)
Q Consensus 77 ~~~GDI-Vvf~~~~~~~~~ikRVi~~~gd~-~~~~~~~~tkGD 117 (119)
.+.||+ +.|-.+++. +..+-||.-+|.. .+|--.+.||||
T Consensus 49 ~n~gd~sv~~v~Dg~t-lv~~nviSaSGAkYa~G~YvwWsKG~ 90 (112)
T COG3895 49 NNAGDISVSFVLDGKT-LVLSNVISASGAKYADGIYVWWSKGD 90 (112)
T ss_pred ecCCCceEEEEecCCE-EEEeeeeeccCccccCcEEEEEeCCC
Confidence 577999 999887764 6788888888872 123334788887
No 50
>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=51.60 E-value=43 Score=18.85 Aligned_cols=32 Identities=9% Similarity=0.170 Sum_probs=21.8
Q ss_pred HHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033421 11 IKSLQIRQVLTQGVSLGMIVTSALIIWKALMC 42 (119)
Q Consensus 11 ~~~~~~~~i~~~i~~i~~~i~i~~li~~~~~~ 42 (119)
+-+|.+|++.++++.-++++.++.+++-++..
T Consensus 3 VPdm~RR~lmN~ll~Gava~~a~~~lyP~~~f 34 (39)
T PF08802_consen 3 VPDMSRRQLMNLLLGGAVAVPAGGMLYPYVKF 34 (39)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCChhHHHHHHHHHHhhHHHHHHHHhhhheeE
Confidence 34688999999988777777666666665544
No 51
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=51.42 E-value=17 Score=22.66 Aligned_cols=25 Identities=24% Similarity=0.372 Sum_probs=15.5
Q ss_pred cCCCEEEEeec------CCCCCcCcEEEEEe
Q 033421 63 KRGDILFLHMS------KDPIRAGEIVVFNV 87 (119)
Q Consensus 63 ~~GD~vlv~~~------~~~~~~GDIVvf~~ 87 (119)
.+|......-. ...|..||.|.|..
T Consensus 27 ~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve~ 57 (72)
T PRK00276 27 ENGHEVLAHISGKMRKNYIRILPGDKVTVEL 57 (72)
T ss_pred CCCCEEEEEEccceeeCCcccCCCCEEEEEE
Confidence 45655555421 22378899999983
No 52
>KOG1666 consensus V-SNARE [Intracellular trafficking, secretion, and vesicular transport]
Probab=50.44 E-value=68 Score=24.70 Aligned_cols=28 Identities=14% Similarity=0.214 Sum_probs=17.7
Q ss_pred hHHHHHHHHhhhHHHHHHHHHHHHHHHH
Q 033421 4 IGESIESIKSLQIRQVLTQGVSLGMIVT 31 (119)
Q Consensus 4 ~~~~~~~~~~~~~~~i~~~i~~i~~~i~ 31 (119)
+++|..-++.|..|-+......-+++++
T Consensus 179 lgkS~kiL~tM~RR~~~nk~~~~aii~~ 206 (220)
T KOG1666|consen 179 LGKSRKILTTMTRRLIRNKFTLTAIIAL 206 (220)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6778888888887766554443333333
No 53
>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=50.19 E-value=19 Score=27.53 Aligned_cols=29 Identities=7% Similarity=0.093 Sum_probs=19.2
Q ss_pred HhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033421 12 KSLQIRQVLTQGVSLGMIVTSALIIWKAL 40 (119)
Q Consensus 12 ~~~~~~~i~~~i~~i~~~i~i~~li~~~~ 40 (119)
|+++...++.+++.++++++++++...|+
T Consensus 8 KrRK~N~iLNiaI~IV~lLIiiva~~lf~ 36 (217)
T PF07423_consen 8 KRRKTNKILNIAIGIVSLLIIIVAYQLFF 36 (217)
T ss_pred HhhhhhhhHHHHHHHHHHHHHHHhhhhee
Confidence 56777788888887777665555444444
No 54
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=49.92 E-value=22 Score=23.82 Aligned_cols=34 Identities=26% Similarity=0.606 Sum_probs=23.5
Q ss_pred eEEEeCCCCcccccCCCEEEEee--------cCCCCCcCcEEEEEe
Q 033421 50 VVVVLSGSMEPGFKRGDILFLHM--------SKDPIRAGEIVVFNV 87 (119)
Q Consensus 50 ~~~V~g~SM~Pti~~GD~vlv~~--------~~~~~~~GDIVvf~~ 87 (119)
.+.+..++..| |=+++++. -...++.||+|+|-+
T Consensus 50 sifie~g~lrp----GiI~LINd~DWeLleke~y~ledgDiIvfis 91 (96)
T COG5131 50 SIFIEHGELRP----GIICLINDMDWELLEKERYPLEDGDIIVFIS 91 (96)
T ss_pred eeeecCCCCcc----cEEEEEcCccHhhhhcccccCCCCCEEEEEe
Confidence 35667766555 55677765 135689999999964
No 55
>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=48.87 E-value=15 Score=23.63 Aligned_cols=10 Identities=30% Similarity=0.753 Sum_probs=4.7
Q ss_pred CCcCcEEEEE
Q 033421 77 IRAGEIVVFN 86 (119)
Q Consensus 77 ~~~GDIVvf~ 86 (119)
+++||+|+..
T Consensus 39 IkrGd~VlV~ 48 (78)
T cd05792 39 IKRGDFVLVE 48 (78)
T ss_pred EEeCCEEEEE
Confidence 3445555443
No 56
>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=46.81 E-value=40 Score=23.04 Aligned_cols=27 Identities=19% Similarity=0.444 Sum_probs=17.4
Q ss_pred CCCCcCcEEEEEeCCCCCCEEEEEEEe
Q 033421 75 DPIRAGEIVVFNVDGREIPIVHRVIKV 101 (119)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ikRVi~~ 101 (119)
..+++||.++|+.-.....+.-+|..+
T Consensus 30 ~~ikvGD~I~f~~~~~~~~l~v~V~~i 56 (109)
T cd06555 30 QQIKVGDKILFNDLDTGQQLLVKVVDI 56 (109)
T ss_pred hcCCCCCEEEEEEcCCCcEEEEEEEEE
Confidence 468999999997643233455555554
No 57
>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=46.33 E-value=42 Score=19.79 Aligned_cols=25 Identities=16% Similarity=0.421 Sum_probs=16.2
Q ss_pred CCCCcCcEEEEEeCCCCCCEEEEEE
Q 033421 75 DPIRAGEIVVFNVDGREIPIVHRVI 99 (119)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ikRVi 99 (119)
..|-.||-|.+..++.+..+|.++.
T Consensus 36 ~~~~VGD~V~~~~~~~~~~~I~~vl 60 (68)
T cd04466 36 NPPAVGDRVEFEPEDDGEGVIEEIL 60 (68)
T ss_pred CCCCCCcEEEEEECCCCcEEEEEEe
Confidence 3478999999976544333555554
No 58
>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=45.39 E-value=24 Score=25.33 Aligned_cols=37 Identities=8% Similarity=0.149 Sum_probs=25.5
Q ss_pred EEeCCCCcccccCCCEEEEeec-CCCCCcCcEEEEEeC
Q 033421 52 VVLSGSMEPGFKRGDILFLHMS-KDPIRAGEIVVFNVD 88 (119)
Q Consensus 52 ~V~g~SM~Pti~~GD~vlv~~~-~~~~~~GDIVvf~~~ 88 (119)
...+++|...|...=.-.+.+. ..++++|||+++...
T Consensus 50 ~~nT~tl~~~L~~~G~~~I~~~~~~~~q~GDI~I~g~~ 87 (145)
T PF05382_consen 50 AGNTETLHDWLKKNGFKKISENVDWNLQRGDIFIWGRR 87 (145)
T ss_pred ccCHHHHHHHHhhCCcEEeccCCcccccCCCEEEEcCC
Confidence 4677888887765555555442 246899999998654
No 59
>CHL00010 infA translation initiation factor 1
Probab=44.26 E-value=27 Score=22.17 Aligned_cols=11 Identities=27% Similarity=0.410 Sum_probs=8.6
Q ss_pred CCcCcEEEEEe
Q 033421 77 IRAGEIVVFNV 87 (119)
Q Consensus 77 ~~~GDIVvf~~ 87 (119)
|..||.|.|..
T Consensus 47 ~~vGD~V~ve~ 57 (78)
T CHL00010 47 ILPGDRVKVEL 57 (78)
T ss_pred cCCCCEEEEEE
Confidence 67788888873
No 60
>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=44.21 E-value=51 Score=22.17 Aligned_cols=28 Identities=21% Similarity=0.392 Sum_probs=16.9
Q ss_pred CCcCcEEEEEeCCC-CCCEEEEEEEeCCC
Q 033421 77 IRAGEIVVFNVDGR-EIPIVHRVIKVHER 104 (119)
Q Consensus 77 ~~~GDIVvf~~~~~-~~~~ikRVi~~~gd 104 (119)
++.||-|.+++++. ..++|.||..+--+
T Consensus 4 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~ 32 (121)
T cd04717 4 YRVGDCVYVANPEDPSKPIIFRIERLWKD 32 (121)
T ss_pred EECCCEEEEeCCCCCCCCEEEEEeEEEEC
Confidence 45666666665544 44677777766444
No 61
>PRK11372 lysozyme inhibitor; Provisional
Probab=42.82 E-value=51 Score=22.37 Aligned_cols=38 Identities=18% Similarity=0.184 Sum_probs=25.6
Q ss_pred CcEEEEEeCCCCCCEEEEEEEeCCCC-CCCeeEEEEcCCC
Q 033421 80 GEIVVFNVDGREIPIVHRVIKVHERQ-DTGEVEVLTKGGN 118 (119)
Q Consensus 80 GDIVvf~~~~~~~~~ikRVi~~~gd~-~~~~~~~~tkGD~ 118 (119)
+|.+.+..+++. +..+++++-.|-. .++.-.|.+|||.
T Consensus 50 ~~~v~l~~~~~~-~~L~~~~SASGArY~~g~~~fWtKG~e 88 (109)
T PRK11372 50 RQEVSFVYDNQL-LHLKQGISASGARYTDGIYVFWSKGDE 88 (109)
T ss_pred CCeEEEEECCEE-EEEEEeeccCcCcEeCCcEEEEEeCCe
Confidence 567777766543 6788888777762 1234579999983
No 62
>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=42.38 E-value=44 Score=20.17 Aligned_cols=38 Identities=24% Similarity=0.395 Sum_probs=24.8
Q ss_pred CCCCcc-cccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEE
Q 033421 55 SGSMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHR 97 (119)
Q Consensus 55 g~SM~P-ti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikR 97 (119)
++|+.| ++..|-.+.| +.-++.||.|..+....+ |+.|
T Consensus 18 ~~~~K~A~letG~~i~V---P~FI~~Gd~I~V~T~~g~--Y~~R 56 (56)
T smart00841 18 SGGTKPATLETGAVVQV---PLFINEGDKIKVDTRTGE--YVSR 56 (56)
T ss_pred CCCcceEEECCCCEEEc---CCcccCCCEEEEECCCCc--EEcC
Confidence 334444 4567777666 344899999988766544 6665
No 63
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=41.81 E-value=29 Score=23.29 Aligned_cols=9 Identities=44% Similarity=1.025 Sum_probs=5.2
Q ss_pred CCcCcEEEE
Q 033421 77 IRAGEIVVF 85 (119)
Q Consensus 77 ~~~GDIVvf 85 (119)
+++||.|+.
T Consensus 58 I~~GD~VlV 66 (99)
T TIGR00523 58 IREGDVVIV 66 (99)
T ss_pred ecCCCEEEE
Confidence 455666655
No 64
>smart00439 BAH Bromo adjacent homology domain.
Probab=41.61 E-value=49 Score=21.48 Aligned_cols=11 Identities=18% Similarity=0.534 Sum_probs=5.4
Q ss_pred ccCCCEEEEee
Q 033421 62 FKRGDILFLHM 72 (119)
Q Consensus 62 i~~GD~vlv~~ 72 (119)
++.||.|++..
T Consensus 2 ~~vgd~V~v~~ 12 (120)
T smart00439 2 IRVGDFVLVEP 12 (120)
T ss_pred cccCCEEEEeC
Confidence 44555555543
No 65
>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=40.30 E-value=44 Score=20.18 Aligned_cols=38 Identities=24% Similarity=0.338 Sum_probs=23.4
Q ss_pred CCCCccc-ccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEE
Q 033421 55 SGSMEPG-FKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHR 97 (119)
Q Consensus 55 g~SM~Pt-i~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikR 97 (119)
++++.|. ++.|-.+.| +.-++.||.|..+....+ |+.|
T Consensus 18 ~~~~K~A~letG~~i~V---P~FI~~Gd~I~V~T~~g~--Y~~R 56 (56)
T cd05794 18 SSGTKPATLETGAEVQV---PLFIKEGEKIKVDTRTGE--YVER 56 (56)
T ss_pred CCCcceEEECCCCEEEc---CCeecCCCEEEEECCCCc--EecC
Confidence 4455554 456654444 244788999988766544 6665
No 66
>COG4393 Predicted membrane protein [Function unknown]
Probab=38.57 E-value=2.3e+02 Score=23.55 Aligned_cols=11 Identities=18% Similarity=0.477 Sum_probs=8.7
Q ss_pred CeeEEEEcCCC
Q 033421 108 GEVEVLTKGGN 118 (119)
Q Consensus 108 ~~~~~~tkGD~ 118 (119)
|+.+|+++||.
T Consensus 341 Gd~GYv~e~dq 351 (405)
T COG4393 341 GDQGYVMEGDQ 351 (405)
T ss_pred cccceEeECCE
Confidence 56789999984
No 67
>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=37.17 E-value=36 Score=22.22 Aligned_cols=30 Identities=23% Similarity=0.482 Sum_probs=21.0
Q ss_pred ccccCCCEEEEee-cCCCCCcCcEEEEEeCC
Q 033421 60 PGFKRGDILFLHM-SKDPIRAGEIVVFNVDG 89 (119)
Q Consensus 60 Pti~~GD~vlv~~-~~~~~~~GDIVvf~~~~ 89 (119)
||-..+|.+.-+. ...+++.||.++|..-+
T Consensus 65 ptC~~~D~i~~~~~lP~~l~~GD~l~f~~~G 95 (116)
T PF00278_consen 65 PTCDSGDVIARDVMLPKELEVGDWLVFENMG 95 (116)
T ss_dssp SSSSTTSEEEEEEEEESTTTTT-EEEESS-S
T ss_pred CCcCCCceEeeeccCCCCCCCCCEEEEecCc
Confidence 6777889887554 33479999999997544
No 68
>PF15428 Imm14: Immunity protein 14
Probab=37.11 E-value=46 Score=22.48 Aligned_cols=26 Identities=23% Similarity=0.284 Sum_probs=17.6
Q ss_pred CcCcEEEEEeCCCCCCEEEEEEE-eCCC
Q 033421 78 RAGEIVVFNVDGREIPIVHRVIK-VHER 104 (119)
Q Consensus 78 ~~GDIVvf~~~~~~~~~ikRVi~-~~gd 104 (119)
|+|||..+..++. .+...||++ ....
T Consensus 1 K~GDIF~ipL~~~-~y~~G~Vi~~~~~~ 27 (129)
T PF15428_consen 1 KPGDIFCIPLDDG-KYGFGRVIGDFKKV 27 (129)
T ss_pred CCceEEEEEcCCC-CEEEEEEEeccccc
Confidence 5788888886643 467888883 4433
No 69
>PRK15136 multidrug efflux system protein EmrA; Provisional
Probab=36.62 E-value=89 Score=25.42 Aligned_cols=8 Identities=13% Similarity=0.675 Sum_probs=3.7
Q ss_pred CCCcCcEE
Q 033421 76 PIRAGEIV 83 (119)
Q Consensus 76 ~~~~GDIV 83 (119)
.++.||++
T Consensus 82 ~VkkGqvL 89 (390)
T PRK15136 82 FVKEGDVL 89 (390)
T ss_pred EECCCCEE
Confidence 34445543
No 70
>PRK08564 5'-methylthioadenosine phosphorylase II; Reviewed
Probab=36.40 E-value=25 Score=27.55 Aligned_cols=19 Identities=26% Similarity=0.510 Sum_probs=16.7
Q ss_pred eCCCCcccccCCCEEEEee
Q 033421 54 LSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 54 ~g~SM~Pti~~GD~vlv~~ 72 (119)
..+||.|.+++||+++.+.
T Consensus 92 avGsl~~~~~pGDlVv~~D 110 (267)
T PRK08564 92 AVGSLREDYKPGDFVIPDQ 110 (267)
T ss_pred cccccCCCCCCCCEEeehh
Confidence 4479999999999999875
No 71
>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=35.86 E-value=40 Score=21.96 Aligned_cols=28 Identities=29% Similarity=0.478 Sum_probs=16.2
Q ss_pred CCcCcEEEEEeCC-CCCCEEEEEEEeCCC
Q 033421 77 IRAGEIVVFNVDG-REIPIVHRVIKVHER 104 (119)
Q Consensus 77 ~~~GDIVvf~~~~-~~~~~ikRVi~~~gd 104 (119)
++.||.|..+.++ ...++|.||..+--+
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i~~~ 31 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEIWED 31 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEEEEE
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEEEcC
Confidence 3456666665544 234677777766544
No 72
>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=35.08 E-value=77 Score=22.02 Aligned_cols=28 Identities=18% Similarity=0.114 Sum_probs=17.7
Q ss_pred CCCcCcEEEEEeCCCCCCEEEEEEEeCCC
Q 033421 76 PIRAGEIVVFNVDGREIPIVHRVIKVHER 104 (119)
Q Consensus 76 ~~~~GDIVvf~~~~~~~~~ikRVi~~~gd 104 (119)
.++.||.|..+.++ +..++.+|-.+-.+
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 36677777777554 33567777666554
No 73
>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=34.94 E-value=27 Score=26.51 Aligned_cols=19 Identities=21% Similarity=0.443 Sum_probs=16.7
Q ss_pred eCCCCcccccCCCEEEEee
Q 033421 54 LSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 54 ~g~SM~Pti~~GD~vlv~~ 72 (119)
..+||.|.++.||+|+.+.
T Consensus 84 saG~l~~~l~~GDlVI~~~ 102 (241)
T TIGR01694 84 AVGSLREEYPPGDLVVPDQ 102 (241)
T ss_pred cccccCCCCCCCCEEEEhh
Confidence 3479999999999999976
No 74
>PHA03164 hypothetical protein; Provisional
Probab=34.66 E-value=47 Score=21.60 Aligned_cols=17 Identities=18% Similarity=0.520 Sum_probs=7.3
Q ss_pred HHHHHHHHHHHHHHHHH
Q 033421 20 LTQGVSLGMIVTSALII 36 (119)
Q Consensus 20 ~~~i~~i~~~i~i~~li 36 (119)
+...+.|++++++++++
T Consensus 62 vLtgLaIamILfiifvl 78 (88)
T PHA03164 62 VLTGLAIAMILFIIFVL 78 (88)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33344444444444433
No 75
>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=34.35 E-value=56 Score=21.10 Aligned_cols=12 Identities=25% Similarity=0.487 Sum_probs=6.4
Q ss_pred CCEEEEEEEeCC
Q 033421 92 IPIVHRVIKVHE 103 (119)
Q Consensus 92 ~~~ikRVi~~~g 103 (119)
.+++.||..+-.
T Consensus 22 ~~~i~~I~~i~~ 33 (123)
T cd04370 22 PPYIARIEELWE 33 (123)
T ss_pred CCEEEEEeeeeE
Confidence 355666655543
No 76
>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=34.22 E-value=87 Score=22.98 Aligned_cols=31 Identities=13% Similarity=0.182 Sum_probs=23.1
Q ss_pred CCCCCcCcEEEEEeCCCCCCEEEEEEEeCCC
Q 033421 74 KDPIRAGEIVVFNVDGREIPIVHRVIKVHER 104 (119)
Q Consensus 74 ~~~~~~GDIVvf~~~~~~~~~ikRVi~~~gd 104 (119)
...+++||.|+++.++...+++..|..+.-+
T Consensus 50 ~~~~~vGD~Vlik~~~~~~~~V~iI~ei~~~ 80 (179)
T cd04720 50 GLELSVGDTILVKDDVANSPSVYLIHEIRLN 80 (179)
T ss_pred CeEEeCCCEEEEeCCCCCCCEEEEEEEEEeC
Confidence 4568999999999876555777777776544
No 77
>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=33.73 E-value=1.1e+02 Score=21.18 Aligned_cols=27 Identities=15% Similarity=0.245 Sum_probs=14.9
Q ss_pred CcCcEEEEEeCCCCCCEEEEEEEeCCC
Q 033421 78 RAGEIVVFNVDGREIPIVHRVIKVHER 104 (119)
Q Consensus 78 ~~GDIVvf~~~~~~~~~ikRVi~~~gd 104 (119)
+.||-|..+..+.+.+||.||..+-.+
T Consensus 5 ~lgD~V~v~~~~~~~~yi~rI~~i~e~ 31 (122)
T cd04716 5 NLGDDAYVQGGEGEEPFICKITEFFEG 31 (122)
T ss_pred EcCCEEEEECCCCCCCEEEEEEEEEEc
Confidence 445555555443344677777665443
No 78
>PRK08666 5'-methylthioadenosine phosphorylase; Validated
Probab=33.25 E-value=27 Score=26.85 Aligned_cols=19 Identities=37% Similarity=0.714 Sum_probs=16.6
Q ss_pred eCCCCcccccCCCEEEEee
Q 033421 54 LSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 54 ~g~SM~Pti~~GD~vlv~~ 72 (119)
..+|+.|.+++||+|+.+.
T Consensus 84 saGsl~~~l~~GDiVi~~d 102 (261)
T PRK08666 84 AVGSLNPNMKPGDFVILDQ 102 (261)
T ss_pred cccccCCCCCCCCEEeehh
Confidence 3379999999999999976
No 79
>PRK11578 macrolide transporter subunit MacA; Provisional
Probab=33.10 E-value=66 Score=25.66 Aligned_cols=11 Identities=0% Similarity=-0.136 Sum_probs=7.0
Q ss_pred EEEEEEEeCCC
Q 033421 94 IVHRVIKVHER 104 (119)
Q Consensus 94 ~ikRVi~~~gd 104 (119)
.|.++...+|+
T Consensus 71 ~V~~v~v~~G~ 81 (370)
T PRK11578 71 QLKTLSVAIGD 81 (370)
T ss_pred EEEEEEcCCCC
Confidence 56666666666
No 80
>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=32.73 E-value=62 Score=22.86 Aligned_cols=27 Identities=11% Similarity=0.218 Sum_probs=15.8
Q ss_pred CCCcCcEEEEEeCCCCCCEEEEEEEeC
Q 033421 76 PIRAGEIVVFNVDGREIPIVHRVIKVH 102 (119)
Q Consensus 76 ~~~~GDIVvf~~~~~~~~~ikRVi~~~ 102 (119)
.++.||-|.++.++...+||.+|..+-
T Consensus 20 ~y~vgD~Vlv~~~~~~~pyI~~I~~i~ 46 (146)
T cd04713 20 KYRLEDCVLLVPEDDQKPYIAIIKDIY 46 (146)
T ss_pred EEECCCEEEEeCCCCCCCEEEEEEEEE
Confidence 356666666665443445666666553
No 81
>PRK04313 30S ribosomal protein S4e; Validated
Probab=32.41 E-value=1.8e+02 Score=22.58 Aligned_cols=36 Identities=14% Similarity=0.420 Sum_probs=15.0
Q ss_pred EeCCCCcccccCCCEEEEeecCCCCCcCcEEEEEeCC
Q 033421 53 VLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFNVDG 89 (119)
Q Consensus 53 V~g~SM~Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~ 89 (119)
++|+-.+=++++|--+++... ..++.||-|+++.++
T Consensus 128 ~~gG~~ql~~hDGrni~~~~~-~~~k~~Dtv~i~l~~ 163 (237)
T PRK04313 128 VKGGKIQLNLHDGRNILVDVE-DDYKTGDSLLISLPE 163 (237)
T ss_pred ecCCEEEEEecCCceEEccCc-cccccCCEEEEECCC
Confidence 344444444444444444210 234455555554443
No 82
>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=32.30 E-value=38 Score=23.70 Aligned_cols=12 Identities=17% Similarity=0.415 Sum_probs=6.7
Q ss_pred cccCCCEEEEee
Q 033421 61 GFKRGDILFLHM 72 (119)
Q Consensus 61 ti~~GD~vlv~~ 72 (119)
||+.||-|++..
T Consensus 3 ~i~vGd~VlI~~ 14 (128)
T cd04719 3 TIEVGDFVLIEG 14 (128)
T ss_pred EEecCCEEEEEC
Confidence 455566666654
No 83
>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=31.08 E-value=1.6e+02 Score=19.48 Aligned_cols=13 Identities=31% Similarity=0.631 Sum_probs=8.6
Q ss_pred CCCCCcCcEEEEE
Q 033421 74 KDPIRAGEIVVFN 86 (119)
Q Consensus 74 ~~~~~~GDIVvf~ 86 (119)
...|++|||++|+
T Consensus 60 ~~~P~~Gdivv~~ 72 (124)
T PF05257_consen 60 GSTPQPGDIVVWD 72 (124)
T ss_dssp CS---TTEEEEEE
T ss_pred CcccccceEEEec
Confidence 4679999999995
No 84
>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=30.98 E-value=1.4e+02 Score=20.66 Aligned_cols=36 Identities=14% Similarity=0.266 Sum_probs=21.1
Q ss_pred eEEEeCCCCcccccCCCEEEEeec----CCCCCcCcEEEEEe
Q 033421 50 VVVVLSGSMEPGFKRGDILFLHMS----KDPIRAGEIVVFNV 87 (119)
Q Consensus 50 ~~~V~g~SM~Pti~~GD~vlv~~~----~~~~~~GDIVvf~~ 87 (119)
.+.+...|+.+ ..|=.+.+.+. ...++.||||+++.
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 45677788865 33333333331 12368899999874
No 85
>PRK09136 5'-methylthioadenosine phosphorylase; Validated
Probab=30.66 E-value=33 Score=26.43 Aligned_cols=22 Identities=14% Similarity=0.264 Sum_probs=17.9
Q ss_pred EEEeCCCCcccccCCCEEEEee
Q 033421 51 VVVLSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 51 ~~V~g~SM~Pti~~GD~vlv~~ 72 (119)
.+-.-+|+.|.+++||+|+.+.
T Consensus 81 ~t~aaG~l~~~l~~Gdlvi~~d 102 (245)
T PRK09136 81 AVNTVGGIHADMGPGTLVVPDQ 102 (245)
T ss_pred EecccccCCCCCCCCCEEEEHH
Confidence 3344569999999999999875
No 86
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=30.27 E-value=1.5e+02 Score=18.99 Aligned_cols=12 Identities=25% Similarity=0.454 Sum_probs=7.4
Q ss_pred cccCCCEEEEee
Q 033421 61 GFKRGDILFLHM 72 (119)
Q Consensus 61 ti~~GD~vlv~~ 72 (119)
.+++||.|++..
T Consensus 5 ~Vk~Gd~ViV~~ 16 (75)
T PF11302_consen 5 SVKPGDTVIVQD 16 (75)
T ss_pred ccCCCCEEEEec
Confidence 346666666655
No 87
>PRK05573 rplU 50S ribosomal protein L21; Validated
Probab=29.92 E-value=1e+02 Score=20.70 Aligned_cols=34 Identities=18% Similarity=0.408 Sum_probs=25.5
Q ss_pred EEEeCCCCcccccCCCEEEEeecCCCCCcCcEEEEE
Q 033421 51 VVVLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFN 86 (119)
Q Consensus 51 ~~V~g~SM~Pti~~GD~vlv~~~~~~~~~GDIVvf~ 86 (119)
..+..++.+=-..+||.+.+++. +.+.||-|.|+
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 45677777777889999999985 25778777665
No 88
>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=29.45 E-value=67 Score=20.23 Aligned_cols=16 Identities=25% Similarity=0.727 Sum_probs=10.0
Q ss_pred CCCCCcCcEEEEEeCC
Q 033421 74 KDPIRAGEIVVFNVDG 89 (119)
Q Consensus 74 ~~~~~~GDIVvf~~~~ 89 (119)
.+.++.||+++|+..+
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 4779999999999764
No 89
>PRK07823 5'-methylthioadenosine phosphorylase; Validated
Probab=29.05 E-value=38 Score=26.57 Aligned_cols=21 Identities=19% Similarity=0.374 Sum_probs=17.0
Q ss_pred EEeCCCCcccccCCCEEEEee
Q 033421 52 VVLSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 52 ~V~g~SM~Pti~~GD~vlv~~ 72 (119)
+-..+||.|.+++||+++.+.
T Consensus 87 tnA~Gsln~~~~pGdlvi~dd 107 (264)
T PRK07823 87 PCAVGSLRPELGPGTVVVPDQ 107 (264)
T ss_pred ecccccCCCCCCCCCEEEcch
Confidence 344579999999999999654
No 90
>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=28.98 E-value=41 Score=25.70 Aligned_cols=19 Identities=32% Similarity=0.805 Sum_probs=16.7
Q ss_pred eCCCCcccccCCCEEEEee
Q 033421 54 LSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 54 ~g~SM~Pti~~GD~vlv~~ 72 (119)
..+|+.|.++.||+|+.+.
T Consensus 91 saGsl~~~l~~GDiVI~~~ 109 (248)
T TIGR01697 91 AAGGLNPDFKPGDLMIIKD 109 (248)
T ss_pred ccccCCCCCCCCCEEEEhh
Confidence 4469999999999999976
No 91
>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=28.96 E-value=38 Score=23.40 Aligned_cols=13 Identities=31% Similarity=0.726 Sum_probs=11.1
Q ss_pred CCCCcCcEEEEEe
Q 033421 75 DPIRAGEIVVFNV 87 (119)
Q Consensus 75 ~~~~~GDIVvf~~ 87 (119)
+++++||+|.|+.
T Consensus 75 ~~~qpGDlvff~~ 87 (134)
T TIGR02219 75 DAAQPGDVLVFRW 87 (134)
T ss_pred hcCCCCCEEEEee
Confidence 5689999999985
No 92
>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=28.86 E-value=98 Score=20.93 Aligned_cols=39 Identities=26% Similarity=0.271 Sum_probs=26.4
Q ss_pred cCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEEEEeCCC
Q 033421 63 KRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRVIKVHER 104 (119)
Q Consensus 63 ~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRVi~~~gd 104 (119)
+.| .|.+-+.....++|-||++-.+++. .|.+..-+.|-
T Consensus 35 ~~G-~V~iG~~~g~f~~g~Ivlla~D~~~--~I~~~~~M~G~ 73 (109)
T PF06923_consen 35 KKG-RVGIGRSKGRFRPGVIVLLAVDEDG--RIVDAEIMKGI 73 (109)
T ss_pred hCC-cEEEeeecCcccCCeEEEEEECCCC--cEEEEEEEece
Confidence 677 6666665677899999999877553 45555544443
No 93
>KOG0557 consensus Dihydrolipoamide acetyltransferase [Energy production and conversion]
Probab=28.73 E-value=1e+02 Score=26.43 Aligned_cols=37 Identities=16% Similarity=0.303 Sum_probs=30.7
Q ss_pred eEEEeCCCCcccccCCCEEEEee-cCCCCCcCcEEEEE
Q 033421 50 VVVVLSGSMEPGFKRGDILFLHM-SKDPIRAGEIVVFN 86 (119)
Q Consensus 50 ~~~V~g~SM~Pti~~GD~vlv~~-~~~~~~~GDIVvf~ 86 (119)
...+.=.+|.||...|.++--.+ -.+.++.||+++--
T Consensus 38 h~~i~MPALSPTMeeGnIvsW~kKeGdkls~GDvl~EV 75 (470)
T KOG0557|consen 38 HKTFSMPALSPTMEEGNIVSWKKKEGDKLSAGDVLLEV 75 (470)
T ss_pred ceEeecCCCCccccCCceeeEeeccCCccCCCceEEEE
Confidence 46788889999999999998776 35679999999754
No 94
>TIGR00998 8a0101 efflux pump membrane protein (multidrug resistance protein A).
Probab=28.62 E-value=2.8e+02 Score=21.44 Aligned_cols=10 Identities=20% Similarity=-0.077 Sum_probs=4.3
Q ss_pred EEEEEEeCCC
Q 033421 95 VHRVIKVHER 104 (119)
Q Consensus 95 ikRVi~~~gd 104 (119)
|.++.-.+|+
T Consensus 53 V~~i~v~~G~ 62 (334)
T TIGR00998 53 VIEVNVDDTD 62 (334)
T ss_pred EEEEEeCCCC
Confidence 4444444444
No 95
>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=28.57 E-value=49 Score=21.58 Aligned_cols=18 Identities=17% Similarity=0.541 Sum_probs=14.6
Q ss_pred CCCCcccccCCCEEEEee
Q 033421 55 SGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 55 g~SM~Pti~~GD~vlv~~ 72 (119)
+..|.|.|+.||+|.+.-
T Consensus 43 tk~~rp~L~~GDlV~ArV 60 (86)
T cd05790 43 TKRNRPNLNVGDLVYARV 60 (86)
T ss_pred cccccccCCCCCEEEEEE
Confidence 345789999999999874
No 96
>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=28.56 E-value=1.5e+02 Score=23.51 Aligned_cols=15 Identities=20% Similarity=0.122 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHHH
Q 033421 28 MIVTSALIIWKALMC 42 (119)
Q Consensus 28 ~~i~i~~li~~~~~~ 42 (119)
+++++|+.|+..+..
T Consensus 176 lALflAFaINFILLF 190 (274)
T PF06459_consen 176 LALFLAFAINFILLF 190 (274)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344445555544443
No 97
>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=28.34 E-value=63 Score=19.25 Aligned_cols=12 Identities=25% Similarity=0.351 Sum_probs=10.0
Q ss_pred CCCcCcEEEEEe
Q 033421 76 PIRAGEIVVFNV 87 (119)
Q Consensus 76 ~~~~GDIVvf~~ 87 (119)
.+..||.|.|+.
T Consensus 40 ~~~vGD~V~~~~ 51 (64)
T cd04451 40 RILPGDRVKVEL 51 (64)
T ss_pred ccCCCCEEEEEE
Confidence 378899999984
No 98
>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family. Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.
Probab=27.63 E-value=2.5e+02 Score=22.27 Aligned_cols=18 Identities=11% Similarity=0.181 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 033421 24 VSLGMIVTSALIIWKALM 41 (119)
Q Consensus 24 ~~i~~~i~i~~li~~~~~ 41 (119)
+.+++++++++++|.++.
T Consensus 8 ~~~~~~~~~~~~~~~~~~ 25 (423)
T TIGR01843 8 TWLIAGLVVIFFLWAYFA 25 (423)
T ss_pred HHHHHHHHHHHHHHHhhe
Confidence 333344444444454443
No 99
>PF13800 Sigma_reg_N: Sigma factor regulator N-terminal
Probab=27.57 E-value=1.5e+02 Score=19.00 Aligned_cols=15 Identities=20% Similarity=0.158 Sum_probs=9.7
Q ss_pred HHHhhhHHHHHHHHH
Q 033421 10 SIKSLQIRQVLTQGV 24 (119)
Q Consensus 10 ~~~~~~~~~i~~~i~ 24 (119)
.+|+-++|.++++++
T Consensus 4 i~kK~K~k~~l~~~~ 18 (96)
T PF13800_consen 4 ILKKAKRKSRLRTVV 18 (96)
T ss_pred HHHHHHHHHHHHHHH
Confidence 366667777777653
No 100
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=27.45 E-value=2e+02 Score=19.42 Aligned_cols=30 Identities=13% Similarity=0.158 Sum_probs=20.9
Q ss_pred CCCCCcCcEEEEEeCCCCCCEEEEEEEeCCC
Q 033421 74 KDPIRAGEIVVFNVDGREIPIVHRVIKVHER 104 (119)
Q Consensus 74 ~~~~~~GDIVvf~~~~~~~~~ikRVi~~~gd 104 (119)
..++..||+|.++.++ ..+...+++.-.|+
T Consensus 23 a~glA~gDvV~~~~~~-g~~~~~~~v~~sGn 52 (117)
T PF14085_consen 23 AYGLALGDVVRAEPDD-GELWFQKVVESSGN 52 (117)
T ss_pred cCCCCCCCEEEEEeCC-CeEEEEEEEecCCC
Confidence 5678999999998776 33556666555554
No 101
>PRK07432 5'-methylthioadenosine phosphorylase; Provisional
Probab=27.27 E-value=60 Score=25.88 Aligned_cols=23 Identities=17% Similarity=0.180 Sum_probs=19.1
Q ss_pred eEEEeCCCCcccccCCCEEEEee
Q 033421 50 VVVVLSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 50 ~~~V~g~SM~Pti~~GD~vlv~~ 72 (119)
+..-..+|+.|.+++||+++.+-
T Consensus 84 i~tna~Gsln~~~~pGdlvv~~D 106 (290)
T PRK07432 84 ISASAVGSLKEEAKPLDMVVPDQ 106 (290)
T ss_pred EEEeccccccCCCCCCCEEeecc
Confidence 34556679999999999999875
No 102
>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=27.27 E-value=37 Score=25.00 Aligned_cols=15 Identities=27% Similarity=0.674 Sum_probs=12.1
Q ss_pred CCCCcCcEEEEEeCC
Q 033421 75 DPIRAGEIVVFNVDG 89 (119)
Q Consensus 75 ~~~~~GDIVvf~~~~ 89 (119)
++.+.||||+|+.++
T Consensus 105 ~~~q~GDIVtw~l~~ 119 (164)
T PF06940_consen 105 EDWQPGDIVTWRLPG 119 (164)
T ss_pred hhcCCCCEEEEeCCC
Confidence 568899999998665
No 103
>PRK14578 elongation factor P; Provisional
Probab=27.19 E-value=1e+02 Score=22.96 Aligned_cols=32 Identities=16% Similarity=0.272 Sum_probs=22.0
Q ss_pred ccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEE
Q 033421 62 FKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (119)
Q Consensus 62 i~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRV 98 (119)
++.|=.|-| +.-++.||.|..+....+ |+.|+
T Consensus 156 leTG~~v~V---P~FI~~Gd~I~VdT~~g~--Y~~R~ 187 (187)
T PRK14578 156 LETGLRLQV---PPYLESGEKIKVDTRDGR--FISRA 187 (187)
T ss_pred EcCCCEEEe---CCcccCCCEEEEECCCCc--EEeeC
Confidence 455644444 344899999999876655 88885
No 104
>PRK04542 elongation factor P; Provisional
Probab=27.18 E-value=1.1e+02 Score=22.87 Aligned_cols=33 Identities=21% Similarity=0.402 Sum_probs=22.6
Q ss_pred cccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEE
Q 033421 61 GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (119)
Q Consensus 61 ti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRV 98 (119)
|++.|=.|-| +.-++.||.|..+....+ |+.|+
T Consensus 156 tLetG~~v~V---P~FI~~Gd~I~VdT~tge--Yv~R~ 188 (189)
T PRK04542 156 TLSTGLVIQV---PEYISTGEKIRINTEERK--FMGRA 188 (189)
T ss_pred EEcCCCEEEe---CCcccCCCEEEEECCCCc--EEeec
Confidence 3456654444 344899999999877655 88886
No 105
>COG2326 Uncharacterized conserved protein [Function unknown]
Probab=27.17 E-value=42 Score=26.60 Aligned_cols=29 Identities=31% Similarity=0.288 Sum_probs=24.4
Q ss_pred CCCcCcEEEEEeCCCCCCEEEEEEEeCCC
Q 033421 76 PIRAGEIVVFNVDGREIPIVHRVIKVHER 104 (119)
Q Consensus 76 ~~~~GDIVvf~~~~~~~~~ikRVi~~~gd 104 (119)
-|..|+||+|+....+...|-||.|-..+
T Consensus 128 lPa~GeiviFdRSwYnr~gVeRVmGfct~ 156 (270)
T COG2326 128 LPAAGEIVIFDRSWYNRAGVERVMGFCTP 156 (270)
T ss_pred CCCCCeEEEechhhccccCeeeccccCCH
Confidence 48999999999887777889999986554
No 106
>COG0690 SecE Preprotein translocase subunit SecE [Intracellular trafficking and secretion]
Probab=26.79 E-value=1.4e+02 Score=18.68 Aligned_cols=23 Identities=9% Similarity=0.280 Sum_probs=13.0
Q ss_pred cchHHHHHHHHhhh---HHHHHHHHH
Q 033421 2 GWIGESIESIKSLQ---IRQVLTQGV 24 (119)
Q Consensus 2 ~~~~~~~~~~~~~~---~~~i~~~i~ 24 (119)
.++.++++++++-. .++.+...+
T Consensus 22 ~f~~~~~~E~~KV~WPsrke~~~~t~ 47 (73)
T COG0690 22 NFFKEVRKELKKVVWPTRKELIRSTL 47 (73)
T ss_pred HHHHHHHHHHHhccCCCHHHHHHHHH
Confidence 35667777777753 244444433
No 107
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=26.71 E-value=47 Score=21.20 Aligned_cols=16 Identities=19% Similarity=0.320 Sum_probs=12.7
Q ss_pred CCCCcCcEEEEEeCCC
Q 033421 75 DPIRAGEIVVFNVDGR 90 (119)
Q Consensus 75 ~~~~~GDIVvf~~~~~ 90 (119)
-+.++||++.|..+..
T Consensus 55 LeCqpgDiley~~d~~ 70 (73)
T COG3655 55 LECQPGDILEYVPDSD 70 (73)
T ss_pred cCCChhheeEEecCCc
Confidence 4679999999986654
No 108
>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=26.64 E-value=43 Score=25.66 Aligned_cols=19 Identities=32% Similarity=0.782 Sum_probs=16.7
Q ss_pred eCCCCcccccCCCEEEEee
Q 033421 54 LSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 54 ~g~SM~Pti~~GD~vlv~~ 72 (119)
..+|+.|.++.||+|+.+.
T Consensus 91 saGsl~~~l~~GDiVi~~d 109 (249)
T TIGR01700 91 AAGGINPEFKVGDLMLIRD 109 (249)
T ss_pred ccccCCCCCCCCCEEEEhh
Confidence 3459999999999999976
No 109
>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=26.45 E-value=52 Score=20.12 Aligned_cols=36 Identities=33% Similarity=0.374 Sum_probs=19.0
Q ss_pred cCCCEEEEeec--CCCCCcCcEEEEEeCCCCCCEEEEE
Q 033421 63 KRGDILFLHMS--KDPIRAGEIVVFNVDGREIPIVHRV 98 (119)
Q Consensus 63 ~~GD~vlv~~~--~~~~~~GDIVvf~~~~~~~~~ikRV 98 (119)
+.||++++... ...-+.|.|+-.+.++..-+|.=|-
T Consensus 4 ~vGD~lvv~g~~vg~~~r~GeIveV~g~dG~PPY~VRw 41 (58)
T PF08940_consen 4 SVGDRLVVHGRTVGQPDRHGEIVEVRGPDGSPPYLVRW 41 (58)
T ss_dssp -TTEEEEES-TTTS--EEEEEEEE-S-SSS-S-EEEEE
T ss_pred CCCCEEEEcCCcCCCCCcEeEEEEEECCCCCCCEEEEe
Confidence 46888888752 3344668888887665544666554
No 110
>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=26.42 E-value=56 Score=21.85 Aligned_cols=28 Identities=11% Similarity=0.312 Sum_probs=18.6
Q ss_pred ccccCCCEEEEeec--------CCCCCcCcEEEEEe
Q 033421 60 PGFKRGDILFLHMS--------KDPIRAGEIVVFNV 87 (119)
Q Consensus 60 Pti~~GD~vlv~~~--------~~~~~~GDIVvf~~ 87 (119)
-++++|=+|++|.. ...++.||.|+|-+
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 45666778999862 35789999999965
No 111
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=26.28 E-value=1.2e+02 Score=20.76 Aligned_cols=25 Identities=20% Similarity=0.569 Sum_probs=17.4
Q ss_pred CCCCcCcEEEEEeCCCCCCEEEEEEEe
Q 033421 75 DPIRAGEIVVFNVDGREIPIVHRVIKV 101 (119)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ikRVi~~ 101 (119)
..+++||+|....++. ...=||..+
T Consensus 138 ~~l~pGDvi~l~~~~~--~~~~RI~~i 162 (164)
T PF13550_consen 138 LALEPGDVIALSDDGR--DMRFRITEI 162 (164)
T ss_pred ccCCCCCEEEEEeCCC--ceEEEEEEE
Confidence 3488889888887744 366677654
No 112
>PRK08202 purine nucleoside phosphorylase; Provisional
Probab=25.77 E-value=50 Score=25.70 Aligned_cols=20 Identities=25% Similarity=0.660 Sum_probs=17.1
Q ss_pred EeCCCCcccccCCCEEEEee
Q 033421 53 VLSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 53 V~g~SM~Pti~~GD~vlv~~ 72 (119)
=..+|+.|.+++||+|+.+.
T Consensus 112 gaaGsL~~~l~~GDiVi~~d 131 (272)
T PRK08202 112 NAAGGLNPDFGPGDLMLISD 131 (272)
T ss_pred cccccCCCCCCCCCEEEEch
Confidence 34569999999999999976
No 113
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=25.70 E-value=1.4e+02 Score=18.89 Aligned_cols=17 Identities=18% Similarity=0.415 Sum_probs=13.3
Q ss_pred eecCCCCCcCcEEEEEe
Q 033421 71 HMSKDPIRAGEIVVFNV 87 (119)
Q Consensus 71 ~~~~~~~~~GDIVvf~~ 87 (119)
.++.++.+.||++..+.
T Consensus 23 RkNDRdf~VGD~L~L~E 39 (72)
T PF12961_consen 23 RKNDRDFQVGDILVLRE 39 (72)
T ss_pred EecCCCCCCCCEEEEEE
Confidence 34567899999999875
No 114
>PRK08931 5'-methylthioadenosine phosphorylase; Provisional
Probab=25.63 E-value=46 Score=26.46 Aligned_cols=22 Identities=14% Similarity=0.309 Sum_probs=18.3
Q ss_pred EEEeCCCCcccccCCCEEEEee
Q 033421 51 VVVLSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 51 ~~V~g~SM~Pti~~GD~vlv~~ 72 (119)
..-..+|+.|.+++||+++.+-
T Consensus 85 ~tnA~Gsln~~~~pGd~vi~~D 106 (289)
T PRK08931 85 SLSACGSFREELPPGTFVIVDQ 106 (289)
T ss_pred EecccccCCCCCCCCCEEeehh
Confidence 4455679999999999999865
No 115
>PHA02650 hypothetical protein; Provisional
Probab=25.51 E-value=1.1e+02 Score=20.01 Aligned_cols=22 Identities=9% Similarity=-0.050 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 033421 21 TQGVSLGMIVTSALIIWKALMC 42 (119)
Q Consensus 21 ~~i~~i~~~i~i~~li~~~~~~ 42 (119)
.+++.++.+++++++.+.++..
T Consensus 51 ~~ii~i~~v~i~~l~~flYLK~ 72 (81)
T PHA02650 51 NFIFLIFSLIIVALFSFFVFKG 72 (81)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444555555555555544
No 116
>PF12751 Vac7: Vacuolar segregation subunit 7; InterPro: IPR024260 Vac7 is localised at the vacuole membrane, a location which is consistent with its involvement in vacuole morphology and inheritance []. Vac7 has been shown to function as an upstream regulator of the Fab1 lipid kinase pathway []. The Fab1 lipid pathway is important for correct regulation of membrane trafficking events.
Probab=25.28 E-value=1.9e+02 Score=24.13 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=19.2
Q ss_pred hCCCCCeEEEeCCCCcccccCCCEEEEee
Q 033421 44 TGSESPVVVVLSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 44 ~~~~~~~~~V~g~SM~Pti~~GD~vlv~~ 72 (119)
+....|+.-|.=.+|+-.|-..|.++.+-
T Consensus 324 ~AttKpL~~v~v~~I~NVlaS~qELmfdl 352 (387)
T PF12751_consen 324 FATTKPLTDVQVVSIQNVLASEQELMFDL 352 (387)
T ss_pred hhcCcccccceEEEeeeeeeccceEEEee
Confidence 34445555566667888888777777765
No 117
>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=25.22 E-value=1.1e+02 Score=22.29 Aligned_cols=26 Identities=19% Similarity=0.413 Sum_probs=14.0
Q ss_pred CCcCcEEEEEeCCCCCCEEEEEEEeC
Q 033421 77 IRAGEIVVFNVDGREIPIVHRVIKVH 102 (119)
Q Consensus 77 ~~~GDIVvf~~~~~~~~~ikRVi~~~ 102 (119)
++.||-|.+..+.+.-++|.||..+.
T Consensus 4 yrvGD~Vy~~~~~~~Py~I~rI~e~~ 29 (164)
T cd04709 4 YRVGDYVYFESSPNNPYLIRRIEELN 29 (164)
T ss_pred EecCCEEEEECCCCCCCEEEEEEEEE
Confidence 35566666654432224577776654
No 118
>PRK12426 elongation factor P; Provisional
Probab=25.14 E-value=1.1e+02 Score=22.83 Aligned_cols=38 Identities=16% Similarity=0.330 Sum_probs=24.9
Q ss_pred CCCcc-cccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEE
Q 033421 56 GSMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (119)
Q Consensus 56 ~SM~P-ti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRV 98 (119)
++..| |++.|=.|-| +.-++.||.|..+....+ |+.|+
T Consensus 147 ~~~KpAtLeTG~~V~V---P~FI~~Gd~IkVdT~~ge--Y~~R~ 185 (185)
T PRK12426 147 GGAKKALLETGVEVLV---PPFVEIGDVIKVDTRTCE--YIQRV 185 (185)
T ss_pred CCcccEEEcCCCEEEe---CCcccCCCEEEEECCCCe--EEeeC
Confidence 34444 3556655544 344899999988876554 88885
No 119
>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=24.94 E-value=1.4e+02 Score=22.83 Aligned_cols=30 Identities=17% Similarity=0.539 Sum_probs=22.5
Q ss_pred cccCCCEEEEeec--CCCCCcCcEEEEEeCCC
Q 033421 61 GFKRGDILFLHMS--KDPIRAGEIVVFNVDGR 90 (119)
Q Consensus 61 ti~~GD~vlv~~~--~~~~~~GDIVvf~~~~~ 90 (119)
||++||+|+.-.. ...++.||.|.....+-
T Consensus 204 tL~pGDvIlTGTp~g~~~l~~GD~v~~~i~gl 235 (245)
T TIGR02303 204 TLEPGDVILTGTPKGLSDVKPGDVVRLEIEGV 235 (245)
T ss_pred CcCCCCEEEcCCCCCCeEcCCCCEEEEEEcCc
Confidence 8899999988542 34578899988877653
No 120
>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=24.87 E-value=1.1e+02 Score=22.51 Aligned_cols=37 Identities=22% Similarity=0.356 Sum_probs=24.8
Q ss_pred CCccc-ccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEE
Q 033421 57 SMEPG-FKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (119)
Q Consensus 57 SM~Pt-i~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRV 98 (119)
|+.|. |++|=.|-| +.-++.||.|..+....+ |+.|+
T Consensus 147 ~~K~A~letG~~v~V---P~fi~~Gd~I~v~T~~g~--y~~R~ 184 (184)
T TIGR00038 147 GTKPATLETGAVVQV---PLFIEEGEKIKVDTRTGE--YVERA 184 (184)
T ss_pred CcccEEEcCCCEEEe---CCcccCCCEEEEECCCCc--EEecC
Confidence 55553 456654444 345899999999877655 88885
No 121
>TIGR01698 PUNP purine nucleotide phosphorylase. methylthioadenosine.
Probab=24.80 E-value=69 Score=24.72 Aligned_cols=23 Identities=9% Similarity=0.316 Sum_probs=18.9
Q ss_pred eEEEeCCCCcccccCCCEEEEee
Q 033421 50 VVVVLSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 50 ~~~V~g~SM~Pti~~GD~vlv~~ 72 (119)
+.+-..+|+.|.+++||+++.+-
T Consensus 87 i~tna~Gsl~~~~~pGdlv~~~D 109 (237)
T TIGR01698 87 ILTNAAGGLRQDWGPGTPVLISD 109 (237)
T ss_pred EEEcccccCCCCCCCCCEEeech
Confidence 34455679999999999999875
No 122
>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=24.69 E-value=1e+02 Score=24.86 Aligned_cols=29 Identities=24% Similarity=0.375 Sum_probs=18.8
Q ss_pred cccCCCEEEEeecCCCCCcCcEEEEEeCC
Q 033421 61 GFKRGDILFLHMSKDPIRAGEIVVFNVDG 89 (119)
Q Consensus 61 ti~~GD~vlv~~~~~~~~~GDIVvf~~~~ 89 (119)
+=..+|.+.-+....++++||+++|..-+
T Consensus 328 ~C~~~D~l~~~~~lp~l~~GD~l~~~~~G 356 (379)
T cd06836 328 CCFAGDVLAKERALPPLEPGDYVAVHDTG 356 (379)
T ss_pred CCCCCCEEeecccCCCCCCCCEEEEeCCC
Confidence 33456765544433458999999997654
No 123
>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=24.67 E-value=70 Score=21.15 Aligned_cols=32 Identities=13% Similarity=0.272 Sum_probs=21.7
Q ss_pred EeCCCCcccccCCCEEEEeecCCCCCcCcEEEEE
Q 033421 53 VLSGSMEPGFKRGDILFLHMSKDPIRAGEIVVFN 86 (119)
Q Consensus 53 V~g~SM~Pti~~GD~vlv~~~~~~~~~GDIVvf~ 86 (119)
|+.++=+=-..+||.+.+++. +.+.||-|.|+
T Consensus 5 i~~ggkQykV~~gd~i~v~~l--~~~~G~~i~l~ 36 (96)
T PF00829_consen 5 IEIGGKQYKVEEGDVIDVERL--DAEVGDKIELD 36 (96)
T ss_dssp EESSSEEEEESSSEEEEEEST--SSSTTSEEEET
T ss_pred EEECCEEEEEeCCCEEEECCc--CcCCCCEEEEE
Confidence 334444445678999999875 56778887774
No 124
>PHA02844 putative transmembrane protein; Provisional
Probab=24.41 E-value=1.2e+02 Score=19.43 Aligned_cols=21 Identities=10% Similarity=0.110 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 033421 20 LTQGVSLGMIVTSALIIWKAL 40 (119)
Q Consensus 20 ~~~i~~i~~~i~i~~li~~~~ 40 (119)
..|++.++.+++++++.+.++
T Consensus 49 ~~~ii~i~~v~~~~~~~flYL 69 (75)
T PHA02844 49 KIWILTIIFVVFATFLTFLYL 69 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 334444444455454444443
No 125
>TIGR03794 NHPM_micro_HlyD NHPM bacteriocin system secretion protein. Members of this protein family are homologs of the HlyD membrane fusion protein of type I secretion systems. Their occurrence in prokaryotic genomes is associated with the occurrence of a novel class of microcin (small bacteriocins) with a propeptide region related to nitrile hydratase. We designate the class of bacteriocin as Nitrile Hydratase Propeptide Microcin, or NHPM. This family, therefore, is designated as NHPM bacteriocin system secretion protein. Some but not all NHPM-class putative microcins belong to the TOMM (thiazole/oxazole modified microcin) class as assessed by the presence of the scaffolding protein and/or cyclodehydratase in the same gene clusters.
Probab=24.33 E-value=3.9e+02 Score=21.71 Aligned_cols=22 Identities=9% Similarity=0.087 Sum_probs=9.5
Q ss_pred HHHHHHHHHHH-HHHHHHHHHHH
Q 033421 19 VLTQGVSLGMI-VTSALIIWKAL 40 (119)
Q Consensus 19 i~~~i~~i~~~-i~i~~li~~~~ 40 (119)
-..|.+.++++ +++++++|.++
T Consensus 17 p~~~~~~~~~~~~~~~~l~~~~~ 39 (421)
T TIGR03794 17 PRSWLALAALGVIVVAALAWGIF 39 (421)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Confidence 34555544443 33334444433
No 126
>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=24.15 E-value=1.2e+02 Score=20.81 Aligned_cols=15 Identities=27% Similarity=0.656 Sum_probs=8.6
Q ss_pred CCCCcCcEEEEEeCC
Q 033421 75 DPIRAGEIVVFNVDG 89 (119)
Q Consensus 75 ~~~~~GDIVvf~~~~ 89 (119)
+.+++||-++|...+
T Consensus 38 ~~mk~GD~vifY~s~ 52 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSG 52 (143)
T ss_dssp HC--TT-EEEEEETS
T ss_pred hcCCCCCEEEEEEcC
Confidence 357888888877766
No 127
>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=23.94 E-value=1e+02 Score=23.01 Aligned_cols=37 Identities=22% Similarity=0.382 Sum_probs=24.2
Q ss_pred CCcc-cccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEE
Q 033421 57 SMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (119)
Q Consensus 57 SM~P-ti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRV 98 (119)
++.| +++.|=.|-| +.-++.||.|..+....+ |+.|+
T Consensus 149 ~~KpA~LeTG~~v~V---P~FI~~Gd~IkVdTrtg~--Y~~R~ 186 (186)
T TIGR02178 149 RPKPAKLITGLVVQV---PEYITTGERILINTTERA--FMGRA 186 (186)
T ss_pred CcccEEEcCCCEEEe---CCeecCCCEEEEECCCCc--EEccC
Confidence 3444 3456654444 344899999999876654 88885
No 128
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=23.83 E-value=71 Score=19.81 Aligned_cols=16 Identities=31% Similarity=0.677 Sum_probs=9.3
Q ss_pred CCcccccCCCEEEEee
Q 033421 57 SMEPGFKRGDILFLHM 72 (119)
Q Consensus 57 SM~Pti~~GD~vlv~~ 72 (119)
++-|..++||+|++.-
T Consensus 33 ~lv~~v~~Gd~VLVHa 48 (68)
T PF01455_consen 33 ALVPDVKVGDYVLVHA 48 (68)
T ss_dssp TTCTSB-TT-EEEEET
T ss_pred EEeCCCCCCCEEEEec
Confidence 5566677777777754
No 129
>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=23.75 E-value=1.1e+02 Score=24.68 Aligned_cols=30 Identities=20% Similarity=0.329 Sum_probs=20.3
Q ss_pred ccccCCCEEEEeecCCCCCcCcEEEEEeCC
Q 033421 60 PGFKRGDILFLHMSKDPIRAGEIVVFNVDG 89 (119)
Q Consensus 60 Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~ 89 (119)
|+=..+|.+.-+....++++||.++|..-+
T Consensus 318 p~C~~~D~l~~~~~lp~l~~GD~l~~~~~G 347 (368)
T cd06840 318 PICESGDVLGRDRLLPETEEGDVILIANAG 347 (368)
T ss_pred CCcCCCCEEeecccCCCCCCCCEEEEecCC
Confidence 455567766554433458999999997654
No 130
>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=23.69 E-value=1e+02 Score=24.63 Aligned_cols=30 Identities=33% Similarity=0.529 Sum_probs=19.8
Q ss_pred ccccCCCEEEEeecCCCCCcCcEEEEEeCC
Q 033421 60 PGFKRGDILFLHMSKDPIRAGEIVVFNVDG 89 (119)
Q Consensus 60 Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~ 89 (119)
|+=..+|.+.-+....++++||+++|..-+
T Consensus 326 ~~C~~~D~l~~~~~lp~~~~GD~l~i~~~G 355 (377)
T cd06843 326 QLCTPKDVLARDVPVDRLRAGDLVVFPLAG 355 (377)
T ss_pred CCCCCCCEEeeccccCCCCCCCEEEEcCCC
Confidence 344566766544433469999999997654
No 131
>PF13829 DUF4191: Domain of unknown function (DUF4191)
Probab=23.44 E-value=92 Score=24.04 Aligned_cols=19 Identities=26% Similarity=0.333 Sum_probs=16.0
Q ss_pred CEEEEEEEeCCCCCCCeeEEEEcCC
Q 033421 93 PIVHRVIKVHERQDTGEVEVLTKGG 117 (119)
Q Consensus 93 ~~ikRVi~~~gd~~~~~~~~~tkGD 117 (119)
..+||++|.||- ..+..|+
T Consensus 114 D~V~R~vGrpGV------vLVgEG~ 132 (224)
T PF13829_consen 114 DAVHRVVGRPGV------VLVGEGP 132 (224)
T ss_pred ceEEEecCCCcE------EEEecCC
Confidence 489999999997 7777776
No 132
>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=23.26 E-value=1.2e+02 Score=24.62 Aligned_cols=30 Identities=20% Similarity=0.347 Sum_probs=20.3
Q ss_pred ccccCCCEEEEeecCCCCCcCcEEEEEeCC
Q 033421 60 PGFKRGDILFLHMSKDPIRAGEIVVFNVDG 89 (119)
Q Consensus 60 Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~ 89 (119)
|+=..+|++.-+....++++||.++|..-+
T Consensus 345 ~~C~~~D~l~~~~~lp~l~~GD~l~~~~~G 374 (417)
T TIGR01048 345 PLCESGDVLARDRELPEVEPGDLLAVFDAG 374 (417)
T ss_pred CCcCCCCEEeeccCCCCCCCCCEEEEeCCC
Confidence 445567766544433468999999998654
No 133
>PRK07115 AMP nucleosidase; Provisional
Probab=23.15 E-value=74 Score=24.73 Aligned_cols=19 Identities=16% Similarity=0.392 Sum_probs=16.7
Q ss_pred eCCCCcccccCCCEEEEee
Q 033421 54 LSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 54 ~g~SM~Pti~~GD~vlv~~ 72 (119)
..+++.|.++.||+|+.+.
T Consensus 94 taGaL~~~l~~GDiVI~t~ 112 (258)
T PRK07115 94 KCGGLKSKYQVGDYFLPIA 112 (258)
T ss_pred cccCcCCCCCCCCEEEEEE
Confidence 4469999999999999986
No 134
>PRK15203 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase; Provisional
Probab=23.10 E-value=1.4e+02 Score=24.89 Aligned_cols=31 Identities=23% Similarity=0.383 Sum_probs=21.5
Q ss_pred ccccCCCEEEEeec--CCCCCcCcEEEEEeCCC
Q 033421 60 PGFKRGDILFLHMS--KDPIRAGEIVVFNVDGR 90 (119)
Q Consensus 60 Pti~~GD~vlv~~~--~~~~~~GDIVvf~~~~~ 90 (119)
=||++||+++.-.. ...++.||.|.....+.
T Consensus 164 ~tL~pGDvI~TGTP~g~~~l~~GD~v~~~i~gi 196 (429)
T PRK15203 164 ATLNPGDAILLGTPQARVEIQPGDRVRVLAEGF 196 (429)
T ss_pred CCcCCCCEEEcCCCCCceECCCCCEEEEEEeCe
Confidence 37888888887542 23478888888876653
No 135
>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n
Probab=23.04 E-value=1.1e+02 Score=18.82 Aligned_cols=12 Identities=33% Similarity=0.495 Sum_probs=8.3
Q ss_pred CCCCcCcEEEEE
Q 033421 75 DPIRAGEIVVFN 86 (119)
Q Consensus 75 ~~~~~GDIVvf~ 86 (119)
++...|||+...
T Consensus 59 ~~~~aGdI~~i~ 70 (83)
T cd04092 59 PSLSAGNIGVIT 70 (83)
T ss_pred CeeCCCCEEEEE
Confidence 456778888764
No 136
>TIGR01718 Uridine-psphlse uridine phosphorylase. Sequences from Clostridium, Streptomyces, Treponema, Halobacterium and Pyrobaculum were included above trusted on the basis of sequence homology and a PAM-based neighbor-joining tree. A clade including second sequences from Halobacterium and Vibrio was somewhat more distantly related and may represent a slightly different substrate specificity - these were placed below the noise cutoff. More distantly related is a clade of archaeal sequences which as related to the DeoD family of inosine phosphorylases (TIGR00107) as they are to these uridine phosphorylases. This clade includes a characterized protein from Sulfolobus solfataricus which has been mis-named as a methylthioadenosine phosphorylase, but which acts on inosine and guanosine - it is unclear whether uridine has been evaluated as a substrate.
Probab=23.00 E-value=64 Score=24.56 Aligned_cols=19 Identities=26% Similarity=0.618 Sum_probs=16.6
Q ss_pred eCCCCcccccCCCEEEEee
Q 033421 54 LSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 54 ~g~SM~Pti~~GD~vlv~~ 72 (119)
..+++.|.++.||+|+.+.
T Consensus 87 taG~l~~~~~~GDiVI~~~ 105 (245)
T TIGR01718 87 TTGAIQPHINVGDVLITTA 105 (245)
T ss_pred ccccCCCCCCCCCEEEeCc
Confidence 3459999999999999976
No 137
>PRK00529 elongation factor P; Validated
Probab=22.94 E-value=1.4e+02 Score=21.95 Aligned_cols=37 Identities=22% Similarity=0.341 Sum_probs=24.3
Q ss_pred CCcc-cccCCCEEEEeecCCCCCcCcEEEEEeCCCCCCEEEEE
Q 033421 57 SMEP-GFKRGDILFLHMSKDPIRAGEIVVFNVDGREIPIVHRV 98 (119)
Q Consensus 57 SM~P-ti~~GD~vlv~~~~~~~~~GDIVvf~~~~~~~~~ikRV 98 (119)
+..| +++.|=.|-| +.-++.||.|..+....+ |+.|+
T Consensus 148 ~~K~A~letG~~v~V---P~fI~~Gd~I~v~T~~g~--y~~R~ 185 (186)
T PRK00529 148 GTKPATLETGAVVQV---PLFINEGEKIKVDTRTGE--YVERA 185 (186)
T ss_pred CcccEEEcCCCEEEe---CCeecCCCEEEEECCCCc--EEeec
Confidence 3444 3456644444 345899999999876654 89886
No 138
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=22.68 E-value=3.8e+02 Score=22.89 Aligned_cols=29 Identities=10% Similarity=0.272 Sum_probs=20.8
Q ss_pred CcccccCCCEEEEeec--------CCCCCcCcEEEEE
Q 033421 58 MEPGFKRGDILFLHMS--------KDPIRAGEIVVFN 86 (119)
Q Consensus 58 M~Pti~~GD~vlv~~~--------~~~~~~GDIVvf~ 86 (119)
|.|-+..|.-|.|... .+.+.+||+|+=-
T Consensus 212 LsPfya~g~gV~Vtev~~~Spl~gprGL~vgdvitsl 248 (484)
T KOG2921|consen 212 LSPFYAHGEGVTVTEVPSVSPLFGPRGLSVGDVITSL 248 (484)
T ss_pred hchhhhcCceEEEEeccccCCCcCcccCCccceEEec
Confidence 5688888888887641 3457889988753
No 139
>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=22.47 E-value=49 Score=21.32 Aligned_cols=13 Identities=15% Similarity=0.626 Sum_probs=10.8
Q ss_pred CCCCcCcEEEEEe
Q 033421 75 DPIRAGEIVVFNV 87 (119)
Q Consensus 75 ~~~~~GDIVvf~~ 87 (119)
.++++||++.|+.
T Consensus 50 ~~~~pGDlif~~~ 62 (105)
T PF00877_consen 50 SELQPGDLIFFKG 62 (105)
T ss_dssp GG-TTTEEEEEEG
T ss_pred hcCCcccEEEEeC
Confidence 5689999999998
No 140
>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. 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=22.27 E-value=1.6e+02 Score=20.52 Aligned_cols=28 Identities=21% Similarity=0.290 Sum_probs=15.2
Q ss_pred CCcCcEEEEEeCCC-CCCEEEEEEEeCCC
Q 033421 77 IRAGEIVVFNVDGR-EIPIVHRVIKVHER 104 (119)
Q Consensus 77 ~~~GDIVvf~~~~~-~~~~ikRVi~~~gd 104 (119)
++.||-|..+.++. ..++|.||..+-.+
T Consensus 4 i~vGD~V~v~~~~~~~p~~I~rV~~mfe~ 32 (124)
T cd04760 4 LEAGDCVSVKPDDPTKPLYIARVTYMWKD 32 (124)
T ss_pred EecCCEEEEecCCCCCCcEEEEEhhheec
Confidence 45566666654322 23577777665544
No 141
>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl
Probab=22.17 E-value=1.1e+02 Score=18.64 Aligned_cols=12 Identities=25% Similarity=0.354 Sum_probs=7.9
Q ss_pred CCCCcCcEEEEE
Q 033421 75 DPIRAGEIVVFN 86 (119)
Q Consensus 75 ~~~~~GDIVvf~ 86 (119)
++...|||+...
T Consensus 59 ~~~~aGdI~~i~ 70 (83)
T cd04088 59 EEAGAGDIGAVA 70 (83)
T ss_pred CEeCCCCEEEEE
Confidence 446677777764
No 142
>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=22.14 E-value=1.3e+02 Score=23.96 Aligned_cols=30 Identities=23% Similarity=0.345 Sum_probs=19.9
Q ss_pred ccccCCCEEEEeecCCCCCcCcEEEEEeCC
Q 033421 60 PGFKRGDILFLHMSKDPIRAGEIVVFNVDG 89 (119)
Q Consensus 60 Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~ 89 (119)
|+-..+|.+.-+....+++.||.++|..-+
T Consensus 331 ~~C~~~D~~~~~~~lp~l~~GD~l~~~~~G 360 (382)
T cd06839 331 PLCTPLDLLGRNVELPPLEPGDLVAVLQSG 360 (382)
T ss_pred CCCCCCCEEeecccCCCCCCCCEEEEecCC
Confidence 444566777654433458999999997654
No 143
>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=22.03 E-value=61 Score=24.07 Aligned_cols=19 Identities=21% Similarity=0.629 Sum_probs=16.6
Q ss_pred eCCCCcccccCCCEEEEee
Q 033421 54 LSGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 54 ~g~SM~Pti~~GD~vlv~~ 72 (119)
..+++.|.+++||+++.+.
T Consensus 54 ~aG~l~~~l~~Gdvvi~~~ 72 (212)
T TIGR03468 54 TAGALDPALQPGDLVVPEE 72 (212)
T ss_pred ecccCCCCCCCCCEEeehh
Confidence 4569999999999999876
No 144
>PF13150 DUF3989: Protein of unknown function (DUF3989)
Probab=21.73 E-value=2.4e+02 Score=18.31 Aligned_cols=20 Identities=15% Similarity=-0.051 Sum_probs=10.9
Q ss_pred HHHHHHHhhhHHHHHHHHHH
Q 033421 6 ESIESIKSLQIRQVLTQGVS 25 (119)
Q Consensus 6 ~~~~~~~~~~~~~i~~~i~~ 25 (119)
+++..|.++..++-...++.
T Consensus 14 ~Lr~~c~~Lsp~~R~~vvl~ 33 (85)
T PF13150_consen 14 RLRRYCGRLSPKQRLRVVLV 33 (85)
T ss_pred HHHHHHhcCCHHHHHHHHHH
Confidence 34556677766554444443
No 145
>TIGR01704 MTA/SAH-Nsdase 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase. There are homologs of this enzyme in plants, some of which score between trusted and noise cutoffs here, but there is no experimental evidence to validate this function at this time.
Probab=21.62 E-value=85 Score=23.41 Aligned_cols=18 Identities=33% Similarity=0.632 Sum_probs=16.2
Q ss_pred CCCCcccccCCCEEEEee
Q 033421 55 SGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 55 g~SM~Pti~~GD~vlv~~ 72 (119)
.+|+.|.++.||+++.++
T Consensus 76 aG~l~~~l~~GDvvi~~~ 93 (228)
T TIGR01704 76 AGGLAPTLKVGDIVVSDE 93 (228)
T ss_pred ccCCCCCCccCCEEEEEE
Confidence 459999999999999986
No 146
>PF01372 Melittin: Melittin; InterPro: IPR002116 Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an Arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Api m 3. Melittin is the principal protein component of the venom of the honeybee, Apis mellifera. It inhibits protein kinase C, Ca2+/calmodulin-dependent protein kinase II, myosin light chain kinase and Na+/K+-ATPase (synaptosomal membrane) and is a cell membrane lytic factor. Melittin is a small peptide with no disulphide bridge; the N-terminal part of the molecule is predominantly hydrophobic and the C-terminal part is hydrophilic and strongly basic. The molecular mechanisms underlying the various effects of melittin on membranes have not been completely defined and much of the evidence indicates that different molecular mechanisms may underlie different actions of the peptide []. Extensive work with melittin has shown that the venom has multiple effects, probably, as a result of its interaction with negatively changed phospholipids. It inhibits well known transport pumps such as the Na+-K+-ATPase and the H+-K+-ATPase. Melittin increases the permeability of cell membranes to ions, particularly Na+ and indirectly Ca2+, because of the Na+-Ca2+-exchange. This effect results in marked morphological and functional changes, particularly in excitable tissues such as cardiac myocytes. In some other tissues, e.g., cornea, not only Na+ but Cl- permeability is also increased by melittin. Similar effects to melittin on H+-K+-ATPase have been found with the synthetic amphipathic polypeptide Trp-3 []. The study of melittin in model membranes has been useful for the development of methodology for determination of membrane protein structures. A molecular dynamics simulation of melittin in a hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer was carried out. The effect of melittin on the surrounding membrane was localised to its immediate vicinity, and its asymmetry with respect to the two layers may be a result of the fact that it is not fully transmembranal. Melittin's hydrophilic C terminus anchors it at the extracellular interface, leaving the N terminus "loose" in the lower layer of the membrane [].; GO: 0004860 protein kinase inhibitor activity, 0005576 extracellular region; PDB: 3QRX_B 2MLT_A 1BH1_A.
Probab=21.62 E-value=1e+02 Score=15.72 Aligned_cols=11 Identities=27% Similarity=0.132 Sum_probs=6.4
Q ss_pred HHHHHHHhhhH
Q 033421 6 ESIESIKSLQI 16 (119)
Q Consensus 6 ~~~~~~~~~~~ 16 (119)
..++|+|+.++
T Consensus 15 ~lISWIK~kr~ 25 (26)
T PF01372_consen 15 TLISWIKNKRQ 25 (26)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHhc
Confidence 45667776543
No 147
>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=21.61 E-value=1.2e+02 Score=24.44 Aligned_cols=28 Identities=21% Similarity=0.201 Sum_probs=17.1
Q ss_pred ccCCCEEEEeecCCCCCcCcEEEEEeCC
Q 033421 62 FKRGDILFLHMSKDPIRAGEIVVFNVDG 89 (119)
Q Consensus 62 i~~GD~vlv~~~~~~~~~GDIVvf~~~~ 89 (119)
=..+|.+.-+....++++||.++|..-+
T Consensus 349 C~~~D~~~~~~~lp~~~~GD~l~~~~~G 376 (398)
T TIGR03099 349 CTPLDLLAEKGTLPVAEPGDLVVIFQSG 376 (398)
T ss_pred CCCCCEEeecCcCCCCCCCCEEEEcCCC
Confidence 3455655443333458889999987544
No 148
>PRK13791 lysozyme inhibitor; Provisional
Probab=21.42 E-value=2.8e+02 Score=18.98 Aligned_cols=37 Identities=8% Similarity=0.014 Sum_probs=24.5
Q ss_pred cEEEEEeCCCCCCEEEEEEEeCCCC---C--CCeeEEEEcCCC
Q 033421 81 EIVVFNVDGREIPIVHRVIKVHERQ---D--TGEVEVLTKGGN 118 (119)
Q Consensus 81 DIVvf~~~~~~~~~ikRVi~~~gd~---~--~~~~~~~tkGD~ 118 (119)
..++++.+++ ....++++.-+|-. + ++.-.+.||||+
T Consensus 54 s~A~l~~~g~-~i~l~~v~SaSGarY~~~~~~~~y~~WtKG~~ 95 (113)
T PRK13791 54 AYAIISQVDE-MIPMRLMKMASGANYEAINKNYTYKLYTKGKT 95 (113)
T ss_pred cEEEEEECCe-EEEEEEEeecCcceeeccCCCceEEEEEcCCe
Confidence 3677776664 36788888877762 1 223458899984
No 149
>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=21.35 E-value=1.8e+02 Score=20.35 Aligned_cols=21 Identities=19% Similarity=0.145 Sum_probs=13.4
Q ss_pred hHHHHHHHHhhhHHHHHHHHH
Q 033421 4 IGESIESIKSLQIRQVLTQGV 24 (119)
Q Consensus 4 ~~~~~~~~~~~~~~~i~~~i~ 24 (119)
|-+++|+|.+..++.+.+.+.
T Consensus 30 LiEEiE~mg~se~~~l~s~L~ 50 (139)
T PF01724_consen 30 LIEEIEDMGRSEKRALESRLR 50 (139)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhHHHHHHHHHHHH
Confidence 446667777777766666553
No 150
>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=21.28 E-value=1.2e+02 Score=24.04 Aligned_cols=30 Identities=20% Similarity=0.306 Sum_probs=20.0
Q ss_pred ccccCCCEEEEeecCCCCCcCcEEEEEeCC
Q 033421 60 PGFKRGDILFLHMSKDPIRAGEIVVFNVDG 89 (119)
Q Consensus 60 Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~ 89 (119)
|+=..+|.+.-.....+++.||.++|..-+
T Consensus 295 p~C~s~D~l~~~~~~~~l~~GD~l~~~~~G 324 (346)
T cd06829 295 NSCLAGDVIGDYSFDEPLQVGDRLVFEDMA 324 (346)
T ss_pred CCCCcccEEeecccCCCCCCCCEEEEeCch
Confidence 555677877422233468899999998654
No 151
>PRK07597 secE preprotein translocase subunit SecE; Reviewed
Probab=21.28 E-value=2e+02 Score=17.21 Aligned_cols=22 Identities=5% Similarity=0.286 Sum_probs=11.8
Q ss_pred chHHHHHHHHhhh---HHHHHHHHH
Q 033421 3 WIGESIESIKSLQ---IRQVLTQGV 24 (119)
Q Consensus 3 ~~~~~~~~~~~~~---~~~i~~~i~ 24 (119)
++.+..+++|+-. +++..+...
T Consensus 13 f~~~~~~ElkkV~WPs~~e~~~~t~ 37 (64)
T PRK07597 13 FFKDVKAELKKVTWPTRKELVRSTI 37 (64)
T ss_pred HHHHHHHHHhhCcCcCHHHHHhHHH
Confidence 4455666676643 345555444
No 152
>PLN00036 40S ribosomal protein S4; Provisional
Probab=21.26 E-value=3.8e+02 Score=21.19 Aligned_cols=12 Identities=17% Similarity=0.576 Sum_probs=5.8
Q ss_pred CCcCcEEEEEeC
Q 033421 77 IRAGEIVVFNVD 88 (119)
Q Consensus 77 ~~~GDIVvf~~~ 88 (119)
++.+|.|.++.+
T Consensus 154 ~k~~Dtv~i~l~ 165 (261)
T PLN00036 154 IKANDTIKIDLE 165 (261)
T ss_pred cccCCEEEEeCC
Confidence 445555555443
No 153
>PF15179 Myc_target_1: Myc target protein 1
Probab=21.24 E-value=1.6e+02 Score=22.25 Aligned_cols=36 Identities=19% Similarity=0.382 Sum_probs=22.4
Q ss_pred HHHHHhhhH-HHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033421 8 IESIKSLQI-RQVLTQGVSLGMIVTSALIIWKALMCI 43 (119)
Q Consensus 8 ~~~~~~~~~-~~i~~~i~~i~~~i~i~~li~~~~~~~ 43 (119)
.||+|+-.+ .-|+.+.+..++.++++.++|.++.-.
T Consensus 10 ~~~~~~f~~~~lIlaF~vSm~iGLviG~li~~Lltwl 46 (197)
T PF15179_consen 10 LEWLENFDWEDLILAFCVSMAIGLVIGALIWALLTWL 46 (197)
T ss_pred ccchhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666644 335667777777777776777666543
No 154
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=21.23 E-value=3.8e+02 Score=21.32 Aligned_cols=11 Identities=36% Similarity=0.534 Sum_probs=5.3
Q ss_pred cccCCCEEEEe
Q 033421 61 GFKRGDILFLH 71 (119)
Q Consensus 61 ti~~GD~vlv~ 71 (119)
.++.||-|.++
T Consensus 150 ~~k~~Dtv~i~ 160 (273)
T PTZ00223 150 RTSRGDTLVYN 160 (273)
T ss_pred cccCCCEEEEE
Confidence 44445555444
No 155
>PRK13792 lysozyme inhibitor; Provisional
Probab=21.22 E-value=2.7e+02 Score=19.55 Aligned_cols=37 Identities=22% Similarity=0.288 Sum_probs=22.9
Q ss_pred EEEEEeCCCCCCEEEEEEEeCCCC-CCCeeEEEEcCCC
Q 033421 82 IVVFNVDGREIPIVHRVIKVHERQ-DTGEVEVLTKGGN 118 (119)
Q Consensus 82 IVvf~~~~~~~~~ikRVi~~~gd~-~~~~~~~~tkGD~ 118 (119)
.++++.++...+..++++.-+|-. ..+.-.|.||||.
T Consensus 69 ~Avl~~~dg~~~~l~~v~SaSGaRY~~~~y~wWtKG~e 106 (127)
T PRK13792 69 LAVVPVSDNSTLVFSNVISASGAKYAAGQYIWWTKGEE 106 (127)
T ss_pred eEEEEeCCCCEEEEEEeeecCcccCcCCcEEEEEcCCc
Confidence 445544443345788888888762 1234458899984
No 156
>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=20.95 E-value=1.1e+02 Score=24.75 Aligned_cols=30 Identities=20% Similarity=0.204 Sum_probs=19.7
Q ss_pred ccccCCCEEEEeecCCCCCcCcEEEEEeCC
Q 033421 60 PGFKRGDILFLHMSKDPIRAGEIVVFNVDG 89 (119)
Q Consensus 60 Pti~~GD~vlv~~~~~~~~~GDIVvf~~~~ 89 (119)
|+=..+|.+.-+....+++.||.++|..-+
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 444567777433333468899999997554
No 157
>PRK10691 hypothetical protein; Provisional
Probab=20.72 E-value=1.1e+02 Score=23.09 Aligned_cols=29 Identities=17% Similarity=0.548 Sum_probs=18.4
Q ss_pred cccCCCEEEEeec--CCCCCcCcEEEEEeCC
Q 033421 61 GFKRGDILFLHMS--KDPIRAGEIVVFNVDG 89 (119)
Q Consensus 61 ti~~GD~vlv~~~--~~~~~~GDIVvf~~~~ 89 (119)
||++||+|+.--. ...+++||.|.....+
T Consensus 181 tL~aGDvI~TGTp~g~~~l~~GD~v~~~i~g 211 (219)
T PRK10691 181 TLRAGDVVLTGTPEGVGPLQSGDELTVTFNG 211 (219)
T ss_pred ccCCCCEEEcCCCCCCEECCCCCEEEEEEeC
Confidence 7777887776441 2346777777666543
No 158
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=20.67 E-value=1.7e+02 Score=20.46 Aligned_cols=38 Identities=18% Similarity=0.273 Sum_probs=27.6
Q ss_pred CeEEEeCCCCcccc-cCCCEEEEeec--------CCCCCcCcEEEEE
Q 033421 49 PVVVVLSGSMEPGF-KRGDILFLHMS--------KDPIRAGEIVVFN 86 (119)
Q Consensus 49 ~~~~V~g~SM~Pti-~~GD~vlv~~~--------~~~~~~GDIVvf~ 86 (119)
+++.|.+.+....- .....+.|+.. .+..++||+|+=+
T Consensus 12 ~vi~Van~~h~~~~~~~~~~i~Vd~g~DaaD~~I~~~~~~gDiVITq 58 (130)
T PF02639_consen 12 PVIFVANYSHRLPRSPYVEMIVVDSGFDAADFYIVNHAKPGDIVITQ 58 (130)
T ss_pred EEEEEeCCCccCCCCCCeEEEEECCCCChHHHHHHHcCCCCCEEEEC
Confidence 46778888777665 56677777762 3568999999865
No 159
>PRK06714 S-adenosylhomocysteine nucleosidase; Validated
Probab=20.63 E-value=76 Score=24.13 Aligned_cols=18 Identities=28% Similarity=0.392 Sum_probs=16.0
Q ss_pred CCCCcccccCCCEEEEee
Q 033421 55 SGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 55 g~SM~Pti~~GD~vlv~~ 72 (119)
.+++.|.++.||+|+.++
T Consensus 78 aG~l~~~l~iGDvVi~~~ 95 (236)
T PRK06714 78 CGSLSNKVKNGHIVVALN 95 (236)
T ss_pred ccCCCCCCCCCCEEEECe
Confidence 348999999999999976
No 160
>PF03908 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membrane glycoprotein associated with secretory pathway.
Probab=20.17 E-value=2.5e+02 Score=17.93 Aligned_cols=21 Identities=19% Similarity=0.202 Sum_probs=11.1
Q ss_pred hHHHHHHHHhhhHHHHHHHHH
Q 033421 4 IGESIESIKSLQIRQVLTQGV 24 (119)
Q Consensus 4 ~~~~~~~~~~~~~~~i~~~i~ 24 (119)
+.++..-++++.++...+.++
T Consensus 52 l~~s~~ll~~l~r~~~~D~~l 72 (92)
T PF03908_consen 52 LKKSRKLLKKLERRDKTDRIL 72 (92)
T ss_pred HHHHHHHHHHHHHHHHHhHHH
Confidence 344555566666655544443
No 161
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=20.11 E-value=2.5e+02 Score=17.98 Aligned_cols=26 Identities=27% Similarity=0.303 Sum_probs=15.3
Q ss_pred CCCCcCcEEEEEeCCCCCCEEEEEEEeCC
Q 033421 75 DPIRAGEIVVFNVDGREIPIVHRVIKVHE 103 (119)
Q Consensus 75 ~~~~~GDIVvf~~~~~~~~~ikRVi~~~g 103 (119)
..|++||.|+++ ++ .++|.|+---.|
T Consensus 64 ~~P~~gd~v~~d--G~-~y~V~~~~~~~G 89 (95)
T PF13856_consen 64 PKPRRGDRVVID--GE-SYTVTRFQEEDG 89 (95)
T ss_dssp ----TT-EEEET--TE-EEEEEEEEEETT
T ss_pred CCCCCCCEEEEC--Ce-EEEEeEEecCCC
Confidence 349999999874 33 478888876655
No 162
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=20.09 E-value=2.6e+02 Score=21.89 Aligned_cols=15 Identities=13% Similarity=0.352 Sum_probs=8.0
Q ss_pred CCCcCcEEEEEeCCC
Q 033421 76 PIRAGEIVVFNVDGR 90 (119)
Q Consensus 76 ~~~~GDIVvf~~~~~ 90 (119)
.++.||.+....|+.
T Consensus 152 ~~k~~Dtv~i~lp~~ 166 (241)
T COG1471 152 NYKTGDTVKISLPEQ 166 (241)
T ss_pred ccccccEEEEeCCCh
Confidence 355555555555543
No 163
>PRK14697 bifunctional 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/phosphatase; Provisional
Probab=20.08 E-value=80 Score=23.79 Aligned_cols=18 Identities=33% Similarity=0.626 Sum_probs=16.0
Q ss_pred CCCCcccccCCCEEEEee
Q 033421 55 SGSMEPGFKRGDILFLHM 72 (119)
Q Consensus 55 g~SM~Pti~~GD~vlv~~ 72 (119)
.+++.|.++.||+|+.++
T Consensus 78 AG~l~~~l~iGDvVi~~~ 95 (233)
T PRK14697 78 AGGLHPDVKVGDIVISTN 95 (233)
T ss_pred ccCCCCCCCcCCEEEECe
Confidence 348999999999999987
No 164
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.02 E-value=62 Score=22.18 Aligned_cols=14 Identities=29% Similarity=0.717 Sum_probs=11.6
Q ss_pred CCCCCcCcEEEEEe
Q 033421 74 KDPIRAGEIVVFNV 87 (119)
Q Consensus 74 ~~~~~~GDIVvf~~ 87 (119)
.+.+++||.|+|+.
T Consensus 31 rr~ik~GD~IiF~~ 44 (111)
T COG4043 31 RRQIKPGDKIIFNG 44 (111)
T ss_pred hcCCCCCCEEEEcC
Confidence 46799999999974
Done!