Query psy800
Match_columns 204
No_of_seqs 296 out of 2005
Neff 5.9
Searched_HMMs 46136
Date Sat Aug 17 00:15:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy800.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/800hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1774|consensus 99.9 1.2E-26 2.6E-31 168.0 3.2 79 78-189 8-86 (88)
2 cd01732 LSm5 The eukaryotic Sm 99.9 8.8E-23 1.9E-27 148.1 10.5 74 116-189 2-75 (76)
3 PRK00737 small nuclear ribonuc 99.9 9E-22 2E-26 141.1 9.8 70 116-188 3-72 (72)
4 cd01731 archaeal_Sm1 The archa 99.9 2.1E-21 4.6E-26 137.5 9.6 68 118-188 1-68 (68)
5 PTZ00138 small nuclear ribonuc 99.9 1.3E-21 2.8E-26 145.9 8.3 78 79-189 11-88 (89)
6 cd01730 LSm3 The eukaryotic Sm 99.9 3.6E-21 7.8E-26 141.2 9.6 72 117-188 1-82 (82)
7 cd01726 LSm6 The eukaryotic Sm 99.8 8.5E-21 1.8E-25 134.2 9.6 67 118-187 1-67 (67)
8 cd01720 Sm_D2 The eukaryotic S 99.8 8.7E-21 1.9E-25 141.0 10.1 74 116-189 1-86 (87)
9 cd01718 Sm_E The eukaryotic Sm 99.8 6.6E-21 1.4E-25 139.2 8.3 51 136-188 29-79 (79)
10 cd01722 Sm_F The eukaryotic Sm 99.8 4.2E-20 9E-25 131.1 8.9 68 117-187 1-68 (68)
11 cd01729 LSm7 The eukaryotic Sm 99.8 8.3E-20 1.8E-24 133.9 9.8 71 118-189 4-79 (81)
12 cd01719 Sm_G The eukaryotic Sm 99.8 7.8E-20 1.7E-24 131.3 9.1 67 120-189 3-69 (72)
13 cd01728 LSm1 The eukaryotic Sm 99.8 2.4E-19 5.1E-24 129.5 10.4 71 118-188 3-73 (74)
14 cd01727 LSm8 The eukaryotic Sm 99.8 4.5E-19 9.9E-24 127.7 9.5 70 121-190 3-73 (74)
15 COG1958 LSM1 Small nuclear rib 99.8 6.2E-19 1.3E-23 128.2 10.2 73 115-188 5-79 (79)
16 cd01723 LSm4 The eukaryotic Sm 99.8 7.9E-19 1.7E-23 127.1 9.6 71 117-189 1-71 (76)
17 cd01721 Sm_D3 The eukaryotic S 99.8 1.4E-18 3E-23 124.1 9.6 69 118-189 1-69 (70)
18 cd01717 Sm_B The eukaryotic Sm 99.8 1.9E-18 4E-23 125.9 9.1 68 121-188 4-78 (79)
19 smart00651 Sm snRNP Sm protein 99.8 4.1E-18 8.9E-23 119.2 9.5 66 121-188 2-67 (67)
20 PF01423 LSM: LSM domain ; In 99.8 5.2E-18 1.1E-22 118.8 9.4 67 120-188 1-67 (67)
21 cd01732 LSm5 The eukaryotic Sm 99.7 5.8E-18 1.3E-22 122.8 8.8 62 13-74 2-66 (76)
22 KOG3482|consensus 99.7 4.4E-18 9.5E-23 121.1 5.6 67 10-76 4-73 (79)
23 PRK00737 small nuclear ribonuc 99.7 1.6E-17 3.6E-22 119.0 8.2 62 13-74 3-64 (72)
24 cd01731 archaeal_Sm1 The archa 99.7 2.6E-17 5.6E-22 116.5 8.2 60 15-74 1-60 (68)
25 cd01724 Sm_D1 The eukaryotic S 99.7 7.2E-17 1.6E-21 120.6 9.7 69 118-189 2-70 (90)
26 cd01726 LSm6 The eukaryotic Sm 99.7 4.2E-17 9.2E-22 115.2 7.9 60 15-74 1-60 (67)
27 KOG1775|consensus 99.7 1.4E-17 2.9E-22 119.6 5.0 78 112-189 2-79 (84)
28 cd06168 LSm9 The eukaryotic Sm 99.7 1.2E-16 2.5E-21 115.8 9.7 69 120-188 3-74 (75)
29 cd01730 LSm3 The eukaryotic Sm 99.7 5.1E-17 1.1E-21 119.2 7.9 61 14-74 1-74 (82)
30 cd00600 Sm_like The eukaryotic 99.7 1.3E-16 2.8E-21 110.1 8.9 63 122-187 1-63 (63)
31 cd01725 LSm2 The eukaryotic Sm 99.7 1.4E-16 3E-21 116.8 9.2 71 117-189 1-72 (81)
32 cd01719 Sm_G The eukaryotic Sm 99.7 8.2E-17 1.8E-21 115.6 7.5 60 15-74 1-60 (72)
33 cd01733 LSm10 The eukaryotic S 99.7 1.9E-16 4.1E-21 115.4 9.4 71 115-188 7-77 (78)
34 cd01722 Sm_F The eukaryotic Sm 99.7 2E-16 4.3E-21 112.2 8.2 61 14-74 1-61 (68)
35 cd01718 Sm_E The eukaryotic Sm 99.7 5.7E-16 1.2E-20 113.2 8.9 65 10-74 2-71 (79)
36 cd01720 Sm_D2 The eukaryotic S 99.6 6.7E-16 1.5E-20 114.8 8.5 61 14-74 2-77 (87)
37 KOG1780|consensus 99.6 3.4E-16 7.4E-21 111.8 6.2 66 121-189 8-73 (77)
38 cd01729 LSm7 The eukaryotic Sm 99.6 9.1E-16 2E-20 112.5 8.1 59 15-74 4-70 (81)
39 COG1958 LSM1 Small nuclear rib 99.6 1.6E-15 3.4E-20 110.3 8.6 65 10-74 3-71 (79)
40 KOG3460|consensus 99.6 1.3E-16 2.9E-21 116.2 2.5 76 114-189 2-87 (91)
41 KOG1780|consensus 99.6 1.8E-15 3.8E-20 108.2 4.5 66 18-84 8-73 (77)
42 cd01721 Sm_D3 The eukaryotic S 99.6 8.9E-15 1.9E-19 104.4 7.9 60 15-74 1-60 (70)
43 cd01728 LSm1 The eukaryotic Sm 99.6 1.5E-14 3.3E-19 104.4 7.9 60 15-74 3-65 (74)
44 cd01723 LSm4 The eukaryotic Sm 99.6 1.3E-14 2.9E-19 105.0 7.3 61 14-74 1-62 (76)
45 cd01727 LSm8 The eukaryotic Sm 99.5 1.5E-14 3.3E-19 104.1 7.4 67 17-84 2-72 (74)
46 cd01717 Sm_B The eukaryotic Sm 99.5 2.7E-14 5.8E-19 104.0 7.5 56 18-73 4-69 (79)
47 KOG3482|consensus 99.5 2.4E-14 5.1E-19 102.1 6.8 73 113-188 4-76 (79)
48 KOG1781|consensus 99.5 1.2E-15 2.5E-20 114.4 0.1 81 119-199 19-106 (108)
49 PF01423 LSM: LSM domain ; In 99.5 4.6E-14 1E-18 98.7 8.2 58 17-74 1-59 (67)
50 KOG1775|consensus 99.5 4.1E-15 9E-20 106.8 2.7 76 8-84 1-79 (84)
51 PTZ00138 small nuclear ribonuc 99.5 7.4E-14 1.6E-18 104.2 8.8 68 7-74 7-79 (89)
52 smart00651 Sm snRNP Sm protein 99.5 7.2E-14 1.6E-18 97.7 7.1 58 17-74 1-59 (67)
53 cd01724 Sm_D1 The eukaryotic S 99.5 2.1E-13 4.5E-18 102.0 8.0 60 15-74 2-61 (90)
54 cd06168 LSm9 The eukaryotic Sm 99.5 2E-13 4.4E-18 98.8 7.3 58 17-74 3-66 (75)
55 KOG1783|consensus 99.5 1.4E-14 3E-19 103.3 1.1 73 114-189 3-75 (77)
56 cd01733 LSm10 The eukaryotic S 99.4 5.1E-13 1.1E-17 97.4 8.2 64 11-74 6-69 (78)
57 cd00600 Sm_like The eukaryotic 99.4 4.2E-13 9.1E-18 92.5 6.9 56 19-74 1-56 (63)
58 KOG1784|consensus 99.4 2.2E-13 4.9E-18 100.9 4.3 70 121-190 4-74 (96)
59 KOG1783|consensus 99.4 7.8E-14 1.7E-18 99.4 0.5 64 11-74 3-66 (77)
60 cd01725 LSm2 The eukaryotic Sm 99.3 2.9E-12 6.3E-17 93.9 7.4 61 14-74 1-63 (81)
61 KOG1782|consensus 99.3 1.5E-13 3.2E-18 106.9 -0.2 72 121-192 13-84 (129)
62 KOG1774|consensus 99.3 2.5E-12 5.5E-17 93.6 4.0 68 7-74 5-77 (88)
63 KOG3460|consensus 99.3 9.6E-13 2.1E-17 96.1 1.1 49 11-59 2-50 (91)
64 KOG3293|consensus 99.2 1.9E-11 4.2E-16 95.2 6.6 72 116-189 1-72 (134)
65 KOG3448|consensus 99.1 3E-10 6.4E-15 84.0 8.2 72 117-189 2-73 (96)
66 KOG3168|consensus 99.1 1.1E-11 2.3E-16 101.3 0.2 69 121-189 8-83 (177)
67 KOG1781|consensus 99.1 8E-12 1.7E-16 93.8 -1.3 65 19-84 22-94 (108)
68 KOG3172|consensus 99.0 1.5E-09 3.3E-14 82.9 6.9 71 115-188 3-73 (119)
69 KOG3459|consensus 99.0 7.9E-11 1.7E-15 90.1 -0.4 74 116-189 23-108 (114)
70 KOG3428|consensus 98.7 1.1E-07 2.4E-12 72.9 8.7 71 119-193 4-75 (109)
71 KOG1784|consensus 98.6 8.5E-08 1.8E-12 71.4 4.4 55 18-72 4-62 (96)
72 KOG3293|consensus 98.5 2.2E-07 4.9E-12 72.6 4.9 49 14-62 2-50 (134)
73 KOG3168|consensus 98.3 7.1E-08 1.5E-12 79.1 -1.3 58 14-72 5-72 (177)
74 KOG1782|consensus 98.2 6.8E-08 1.5E-12 75.4 -2.7 41 19-59 14-54 (129)
75 KOG3448|consensus 98.2 2.3E-06 5E-11 63.5 5.0 43 16-58 4-46 (96)
76 PRK14091 RNA-binding protein H 98.0 0.00013 2.8E-09 60.1 11.5 111 16-154 14-131 (165)
77 cd01739 LSm11_C The eukaryotic 97.9 7.3E-06 1.6E-10 57.7 3.0 25 139-163 24-48 (66)
78 KOG3459|consensus 97.7 5.6E-06 1.2E-10 63.7 -1.3 49 11-59 21-71 (114)
79 cd01739 LSm11_C The eukaryotic 97.6 7.8E-05 1.7E-09 52.6 3.2 37 25-61 9-49 (66)
80 KOG3172|consensus 97.4 0.00025 5.4E-09 54.5 5.1 63 12-74 3-65 (119)
81 PF14438 SM-ATX: Ataxin 2 SM d 97.2 0.0011 2.5E-08 47.4 5.6 65 120-184 5-76 (77)
82 KOG3428|consensus 96.7 0.0032 7E-08 48.5 5.2 46 16-61 4-49 (109)
83 cd01716 Hfq Hfq, an abundant, 96.0 0.014 3.1E-07 40.7 4.6 28 127-154 11-38 (61)
84 PF14438 SM-ATX: Ataxin 2 SM d 95.8 0.025 5.5E-07 40.4 5.5 44 18-61 6-52 (77)
85 TIGR02383 Hfq RNA chaperone Hf 95.7 0.021 4.6E-07 39.9 4.5 29 127-155 15-43 (61)
86 PF02237 BPL_C: Biotin protein 95.4 0.1 2.2E-06 34.2 6.6 33 126-159 2-34 (48)
87 cd01716 Hfq Hfq, an abundant, 95.3 0.056 1.2E-06 37.8 5.5 33 18-50 3-37 (61)
88 TIGR02383 Hfq RNA chaperone Hf 95.3 0.06 1.3E-06 37.6 5.6 35 17-51 6-42 (61)
89 PF12701 LSM14: Scd6-like Sm d 95.2 0.12 2.6E-06 39.1 7.3 63 124-188 5-76 (96)
90 PRK00395 hfq RNA-binding prote 95.2 0.039 8.4E-07 40.5 4.4 31 127-157 19-49 (79)
91 PRK00395 hfq RNA-binding prote 94.6 0.11 2.4E-06 38.1 5.5 35 17-51 10-46 (79)
92 COG1923 Hfq Uncharacterized ho 94.4 0.09 1.9E-06 38.3 4.7 30 127-157 19-48 (77)
93 cd01736 LSm14_N LSm14 (also kn 94.0 0.29 6.2E-06 35.5 6.6 62 124-185 3-72 (74)
94 COG1923 Hfq Uncharacterized ho 93.7 0.32 6.9E-06 35.4 6.3 30 24-54 19-48 (77)
95 PF11095 Gemin7: Gem-associate 91.5 1.1 2.5E-05 32.8 6.9 63 118-188 15-78 (80)
96 PRK14091 RNA-binding protein H 90.6 0.84 1.8E-05 37.8 6.1 35 16-50 94-130 (165)
97 PF03614 Flag1_repress: Repres 90.6 2 4.3E-05 35.3 8.1 110 24-150 29-143 (165)
98 cd01735 LSm12_N LSm12 belongs 90.4 0.71 1.5E-05 32.2 4.7 36 125-160 4-39 (61)
99 PF02237 BPL_C: Biotin protein 87.8 1.4 3E-05 28.7 4.5 32 23-55 2-33 (48)
100 PRK14638 hypothetical protein; 87.8 1.1 2.4E-05 36.3 4.9 40 115-155 85-127 (150)
101 PRK02001 hypothetical protein; 85.9 1.6 3.5E-05 35.6 4.9 40 115-155 75-117 (152)
102 PRK14639 hypothetical protein; 85.6 1.7 3.7E-05 34.8 4.9 35 120-155 81-115 (140)
103 PF10842 DUF2642: Protein of u 85.5 5.2 0.00011 28.3 6.7 53 119-188 13-66 (66)
104 PF06372 Gemin6: Gemin6 protei 84.1 1.8 3.8E-05 36.0 4.4 59 118-187 9-68 (166)
105 PRK14639 hypothetical protein; 83.8 1.9 4.2E-05 34.5 4.4 33 20-53 84-116 (140)
106 PF12701 LSM14: Scd6-like Sm d 83.7 2.4 5.1E-05 32.1 4.6 38 21-58 5-43 (96)
107 cd01735 LSm12_N LSm12 belongs 83.4 2.7 5.9E-05 29.3 4.5 34 22-55 4-37 (61)
108 PF06372 Gemin6: Gemin6 protei 82.5 2 4.3E-05 35.7 4.1 43 13-57 7-50 (166)
109 PRK14638 hypothetical protein; 82.1 2.2 4.7E-05 34.6 4.1 36 15-52 92-127 (150)
110 PRK14644 hypothetical protein; 80.3 3.9 8.5E-05 32.7 5.0 35 121-156 79-117 (136)
111 PRK02001 hypothetical protein; 79.1 3.2 6.9E-05 33.9 4.2 36 15-52 82-117 (152)
112 PRK14644 hypothetical protein; 78.7 4.7 0.0001 32.2 5.0 34 19-53 80-117 (136)
113 cd01734 YlxS_C YxlS is a Bacil 77.9 6.8 0.00015 28.3 5.2 30 121-150 19-52 (83)
114 cd01734 YlxS_C YxlS is a Bacil 75.6 7 0.00015 28.2 4.8 31 15-46 17-51 (83)
115 PRK14640 hypothetical protein; 75.6 6.4 0.00014 31.9 5.0 40 115-155 82-128 (152)
116 PRK14633 hypothetical protein; 74.5 7.2 0.00016 31.5 5.0 41 115-156 79-126 (150)
117 PRK14645 hypothetical protein; 74.1 6.7 0.00015 32.0 4.8 39 115-155 87-128 (154)
118 cd01736 LSm14_N LSm14 (also kn 74.0 9.1 0.0002 27.8 4.9 61 20-91 2-63 (74)
119 PRK14642 hypothetical protein; 73.8 7.5 0.00016 33.1 5.1 40 115-155 85-140 (197)
120 PRK06955 biotin--protein ligas 73.0 15 0.00033 32.7 7.2 33 125-157 247-279 (300)
121 PF11095 Gemin7: Gem-associate 72.8 9.1 0.0002 28.1 4.7 40 16-55 16-56 (80)
122 PF02576 DUF150: Uncharacteris 72.5 6.4 0.00014 31.1 4.2 34 116-149 73-113 (141)
123 PRK14643 hypothetical protein; 71.5 9.5 0.00021 31.4 5.1 40 116-155 90-137 (164)
124 PRK14634 hypothetical protein; 71.4 9.7 0.00021 31.0 5.1 39 116-155 86-131 (155)
125 PRK14636 hypothetical protein; 70.9 9.6 0.00021 31.8 5.1 35 120-155 91-129 (176)
126 PRK14646 hypothetical protein; 70.0 11 0.00024 30.6 5.2 40 115-155 85-131 (155)
127 PRK14636 hypothetical protein; 69.6 9 0.00019 31.9 4.6 31 15-46 90-124 (176)
128 PRK14640 hypothetical protein; 69.4 14 0.00031 29.8 5.7 37 15-53 89-129 (152)
129 KOG1073|consensus 69.3 11 0.00024 35.0 5.5 64 123-186 5-76 (361)
130 COG0779 Uncharacterized protei 68.8 19 0.00042 29.4 6.3 39 116-155 85-130 (153)
131 PRK14632 hypothetical protein; 68.5 12 0.00026 31.0 5.1 41 115-156 83-133 (172)
132 PRK14643 hypothetical protein; 68.1 10 0.00022 31.2 4.7 36 16-52 97-137 (164)
133 PF02576 DUF150: Uncharacteris 67.5 8.8 0.00019 30.3 4.0 38 9-46 69-113 (141)
134 PRK14642 hypothetical protein; 66.7 10 0.00022 32.4 4.4 31 21-52 97-140 (197)
135 PRK14633 hypothetical protein; 66.7 10 0.00022 30.7 4.3 31 21-52 91-125 (150)
136 PRK14632 hypothetical protein; 66.6 11 0.00025 31.1 4.7 32 21-53 95-133 (172)
137 PRK14647 hypothetical protein; 66.1 15 0.00032 29.9 5.2 34 116-149 85-130 (159)
138 PRK14645 hypothetical protein; 64.8 11 0.00023 30.8 4.1 30 16-47 95-124 (154)
139 PRK11886 bifunctional biotin-- 64.6 29 0.00063 30.8 7.2 49 125-181 270-318 (319)
140 COG0779 Uncharacterized protei 64.5 20 0.00043 29.3 5.6 42 10-52 82-130 (153)
141 PRK00092 ribosome maturation p 63.7 16 0.00035 29.4 5.0 30 120-149 91-124 (154)
142 PRK00092 ribosome maturation p 63.1 14 0.00031 29.7 4.5 28 19-46 93-124 (154)
143 PRK13325 bifunctional biotin-- 62.3 27 0.00059 34.3 7.1 33 125-157 276-308 (592)
144 PRK14637 hypothetical protein; 61.9 16 0.00035 29.6 4.6 40 115-155 83-126 (151)
145 PRK14631 hypothetical protein; 61.2 19 0.00042 29.9 5.1 34 115-148 102-142 (174)
146 PRK14641 hypothetical protein; 57.7 22 0.00048 29.6 4.8 34 115-148 89-129 (173)
147 PRK14634 hypothetical protein; 56.1 22 0.00047 29.0 4.5 36 15-52 92-131 (155)
148 TIGR00121 birA_ligase birA, bi 56.0 45 0.00098 28.4 6.7 31 125-156 191-221 (237)
149 PRK14647 hypothetical protein; 55.0 23 0.0005 28.8 4.5 27 20-46 95-130 (159)
150 PRK14631 hypothetical protein; 53.5 42 0.00092 27.9 5.9 26 20-45 113-142 (174)
151 PRK14646 hypothetical protein; 53.1 27 0.00058 28.4 4.5 36 16-53 93-132 (155)
152 PRK14637 hypothetical protein; 48.3 27 0.00059 28.3 3.9 33 20-53 94-127 (151)
153 PRK08330 biotin--protein ligas 47.8 75 0.0016 27.0 6.8 32 125-157 186-218 (236)
154 PF10842 DUF2642: Protein of u 44.0 63 0.0014 22.8 4.7 32 13-45 8-41 (66)
155 PRK14641 hypothetical protein; 43.1 40 0.00086 28.1 4.1 26 20-45 100-129 (173)
156 PRK10898 serine endoprotease; 43.0 42 0.0009 30.6 4.7 32 128-159 102-133 (353)
157 PRK10898 serine endoprotease; 41.6 40 0.00088 30.7 4.4 31 25-55 102-132 (353)
158 PRK14630 hypothetical protein; 40.7 55 0.0012 26.2 4.5 39 115-155 82-123 (143)
159 TIGR02038 protease_degS peripl 39.0 46 0.001 30.2 4.3 30 25-54 102-131 (351)
160 TIGR02038 protease_degS peripl 38.7 52 0.0011 29.9 4.6 32 128-159 102-133 (351)
161 PRK14635 hypothetical protein; 38.5 74 0.0016 25.9 5.0 36 115-150 84-127 (162)
162 PF03614 Flag1_repress: Repres 38.0 45 0.00097 27.5 3.6 34 126-159 28-61 (165)
163 PF14563 DUF4444: Domain of un 35.3 42 0.00091 21.8 2.4 22 140-161 10-31 (42)
164 PRK11625 Rho-binding antitermi 35.2 1.8E+02 0.004 21.4 6.4 49 127-187 23-72 (84)
165 PF11607 DUF3247: Protein of u 34.8 50 0.0011 25.1 3.1 19 127-145 28-46 (101)
166 PRK10942 serine endoprotease; 34.7 62 0.0014 30.8 4.6 31 128-158 136-166 (473)
167 PRK10942 serine endoprotease; 34.5 57 0.0012 31.0 4.3 30 25-54 136-165 (473)
168 PRK10139 serine endoprotease; 34.4 66 0.0014 30.5 4.7 32 128-159 115-146 (455)
169 PRK10139 serine endoprotease; 34.3 60 0.0013 30.7 4.4 31 25-55 115-145 (455)
170 PTZ00275 biotin-acetyl-CoA-car 33.9 79 0.0017 28.0 4.9 31 126-157 236-266 (285)
171 COG0340 BirA Biotin-(acetyl-Co 31.5 1.9E+02 0.0041 25.0 6.7 34 125-158 188-221 (238)
172 PRK06955 biotin--protein ligas 30.0 90 0.0019 27.7 4.6 32 22-53 247-278 (300)
173 PRK09618 flgD flagellar basal 28.8 1.6E+02 0.0035 23.8 5.4 26 123-148 88-113 (142)
174 KOG1708|consensus 28.8 1.2E+02 0.0026 26.3 4.8 97 44-140 67-173 (236)
175 PRK13325 bifunctional biotin-- 28.6 1.6E+02 0.0034 29.1 6.3 32 22-53 276-307 (592)
176 PF06257 DUF1021: Protein of u 28.4 1.3E+02 0.0028 21.8 4.3 28 120-147 10-41 (76)
177 TIGR02037 degP_htrA_DO peripla 27.6 89 0.0019 28.9 4.3 31 25-55 82-112 (428)
178 TIGR02037 degP_htrA_DO peripla 27.5 99 0.0021 28.6 4.6 32 128-159 82-113 (428)
179 COG5316 Uncharacterized conser 27.5 1.5E+02 0.0034 28.0 5.7 48 12-60 70-117 (421)
180 PRK05163 rpsL 30S ribosomal pr 27.0 1.5E+02 0.0032 23.6 4.8 24 125-148 48-71 (124)
181 PRK14630 hypothetical protein; 25.0 1.1E+02 0.0023 24.6 3.8 30 21-52 94-123 (143)
182 PF11607 DUF3247: Protein of u 23.7 97 0.0021 23.6 3.0 19 24-42 28-46 (101)
183 PRK14635 hypothetical protein; 22.8 1.5E+02 0.0033 24.1 4.3 33 14-47 90-127 (162)
184 PF05071 NDUFA12: NADH ubiquin 22.2 48 0.001 25.1 1.2 17 142-158 1-17 (105)
185 PRK08477 biotin--protein ligas 21.2 2.8E+02 0.006 23.6 5.8 35 125-160 173-207 (211)
186 PRK09618 flgD flagellar basal 21.0 2.8E+02 0.0061 22.4 5.5 26 20-45 88-113 (142)
No 1
>KOG1774|consensus
Probab=99.93 E-value=1.2e-26 Score=167.96 Aligned_cols=79 Identities=28% Similarity=0.500 Sum_probs=70.7
Q ss_pred cceeeccccccceeecccEeEEEeeeccCCcccCCCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcc
Q psy800 78 LPMITPITCAYSRSHQYRTLTHLLYTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLED 157 (204)
Q Consensus 78 ~~~~~PI~~~f~~~~~~~~v~~~l~~~~~~~~~~~~~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~d 157 (204)
-+|++|||+||+|||++.+|++||||+ -+.+++|.+.|||+|||+||||
T Consensus 8 kvmv~Pin~Ifr~Lq~~t~VqIWl~eq-------------------------------~~~rieG~IvGFDEyMNvVlD~ 56 (88)
T KOG1774|consen 8 KVMVQPINLIFRFLQNRTRVQIWLFEQ-------------------------------VGLRIEGRIVGFDEYMNLVLDD 56 (88)
T ss_pred ceecCcHHHHHHHHhcCCceEEEEEec-------------------------------cCcEEeEEEechHHhhhhhhcc
Confidence 378999999999999999999999997 4669999999999999999999
Q ss_pred eEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800 158 VTEYESTPEGRRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 158 a~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
|+|...+. +..+.+|+++++||||.+|...
T Consensus 57 aeev~~k~--~~rk~lGRilLKGDnItli~~~ 86 (88)
T KOG1774|consen 57 AEEVHSKT--KSRKELGRILLKGDNITLIQSA 86 (88)
T ss_pred hhhccccc--cCCCccccEEEcCCcEEEEeec
Confidence 99998653 2356999999999999999654
No 2
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.89 E-value=8.8e-23 Score=148.12 Aligned_cols=74 Identities=81% Similarity=1.207 Sum_probs=68.3
Q ss_pred CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800 116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
.+|+++|+++++++|+|++++|+++.|+|+|||+|||+||+||+|++..++++..+.+|.++|||+||++|+|.
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p~ 75 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVPG 75 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEECC
Confidence 57999999999999999999999999999999999999999999998655555678899999999999999975
No 3
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.87 E-value=9e-22 Score=141.14 Aligned_cols=70 Identities=24% Similarity=0.600 Sum_probs=64.8
Q ss_pred CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800 116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~ 188 (204)
..|+++|+++++++|.|+|+||+.|+|+|.|||+|||++|+||+|.+ +++..+++|.++|||++|++|+|
T Consensus 3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~lg~v~iRG~~V~~i~~ 72 (72)
T PRK00737 3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQ---DGEVVRKLGKVVIRGDNVVYVSP 72 (72)
T ss_pred cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEc---CCCeEeEcCcEEEeCCEEEEEcC
Confidence 57999999999999999999999999999999999999999999975 34467899999999999999975
No 4
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.86 E-value=2.1e-21 Score=137.48 Aligned_cols=68 Identities=24% Similarity=0.588 Sum_probs=63.1
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~ 188 (204)
|+++|+++++++|+|+|++|+.|.|+|.|||+|||++|+||+|++. + ...+.+|.++|||++|++|+|
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~--~-~~~~~lg~~~iRG~~I~~i~~ 68 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDD--G-EPVRKYGRVVIRGDNVLFISP 68 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEec--C-CeEeEcCcEEEeCCEEEEEcC
Confidence 8899999999999999999999999999999999999999999863 2 256889999999999999986
No 5
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.86 E-value=1.3e-21 Score=145.90 Aligned_cols=78 Identities=29% Similarity=0.478 Sum_probs=70.2
Q ss_pred ceeeccccccceeecccEeEEEeeeccCCcccCCCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcce
Q psy800 79 PMITPITCAYSRSHQYRTLTHLLYTMTAPSVATNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV 158 (204)
Q Consensus 79 ~~~~PI~~~f~~~~~~~~v~~~l~~~~~~~~~~~~~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da 158 (204)
.|++||+++|+|++.+.+|.+|++++ ++++++|+|.|||+|||+||+||
T Consensus 11 ~~~~P~~~~~~~~~~~~~V~i~l~~~-------------------------------~~r~~~G~L~gfD~~mNlVL~d~ 59 (89)
T PTZ00138 11 IMTQPINQIFRFFTEKTRVQIWLYDH-------------------------------PNLRIEGKILGFDEYMNMVLDDA 59 (89)
T ss_pred eecCCHHHHHHHhcCCcEEEEEEEeC-------------------------------CCcEEEEEEEEEcccceEEEccE
Confidence 68899999999999999999999885 68999999999999999999999
Q ss_pred EEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800 159 TEYESTPEGRRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 159 ~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
+|+.. +++..+.+|.++||||||++|++.
T Consensus 60 ~E~~~--~~~~~~~lG~ilIRGnnV~~I~~~ 88 (89)
T PTZ00138 60 EEVYT--KKNTRKDLGRILLKGDNITLIMAA 88 (89)
T ss_pred EEEec--CCceeeEcCeEEEcCCEEEEEEcC
Confidence 99863 234578999999999999999764
No 6
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.85 E-value=3.6e-21 Score=141.24 Aligned_cols=72 Identities=25% Similarity=0.539 Sum_probs=64.2
Q ss_pred CcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCC-C---------eeeeeeCeEEEeCCcEEEE
Q psy800 117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE-G---------RRITKLDQILLNGNNITML 186 (204)
Q Consensus 117 ~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~-~---------~~~~~lg~ilIRGdnI~~I 186 (204)
.|+++|+.+++++|.|+|++||.+.|+|+|||+||||+|+||+|.+.... + ...+.+|.++||||+|++|
T Consensus 1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i 80 (82)
T cd01730 1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV 80 (82)
T ss_pred CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence 38999999999999999999999999999999999999999999975311 1 2467899999999999999
Q ss_pred cc
Q psy800 187 GL 188 (204)
Q Consensus 187 ~~ 188 (204)
+|
T Consensus 81 ~~ 82 (82)
T cd01730 81 SP 82 (82)
T ss_pred CC
Confidence 85
No 7
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.85 E-value=8.5e-21 Score=134.20 Aligned_cols=67 Identities=25% Similarity=0.515 Sum_probs=62.2
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEc
Q psy800 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLG 187 (204)
Q Consensus 118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~ 187 (204)
|+++|+++++++|+|+|++|++|+|+|.|||+|||++|+||+|.. ++.....+|.++|||++|.+|+
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~---~~~~~~~~~~v~IRG~~I~~I~ 67 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYV---NGQLKNKYGDAFIRGNNVLYIS 67 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEe---CCceeeEeCCEEEECCEEEEEC
Confidence 899999999999999999999999999999999999999999864 3446789999999999999985
No 8
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.84 E-value=8.7e-21 Score=140.97 Aligned_cols=74 Identities=24% Similarity=0.492 Sum_probs=65.1
Q ss_pred CCcHHHHHhhc--CCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCC--C--------eeeeeeCeEEEeCCcE
Q psy800 116 LLPLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE--G--------RRITKLDQILLNGNNI 183 (204)
Q Consensus 116 ~~Pl~~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~--~--------~~~~~lg~ilIRGdnI 183 (204)
.+|+++|.+++ +++|.|+|++|+.+.|+|.|||+||||+|+||+|.+...+ + ...+++|.+|||||+|
T Consensus 1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~V 80 (87)
T cd01720 1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSV 80 (87)
T ss_pred CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEE
Confidence 37999999997 8999999999999999999999999999999999875421 1 2356799999999999
Q ss_pred EEEccc
Q psy800 184 TMLGLH 189 (204)
Q Consensus 184 ~~I~~~ 189 (204)
++|++.
T Consensus 81 v~Is~~ 86 (87)
T cd01720 81 ILVLRN 86 (87)
T ss_pred EEEecC
Confidence 999875
No 9
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.84 E-value=6.6e-21 Score=139.23 Aligned_cols=51 Identities=35% Similarity=0.642 Sum_probs=45.7
Q ss_pred CCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800 136 NDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 136 ~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~ 188 (204)
+|+.+.|+|.|||+|||+||+||+|+... ++..+.+|.++||||||++|+|
T Consensus 29 ~g~~~~G~L~gfD~~mNlvL~d~~E~~~~--~~~~~~lG~iliRGnnV~~I~p 79 (79)
T cd01718 29 TDLRIEGVIIGFDEYMNLVLDDAEEVHLK--TKTRKPLGRILLKGDNITLIQN 79 (79)
T ss_pred CCcEEEEEEEEEccceeEEEcCEEEEecC--CceEeEcCcEEEeCCEEEEEcC
Confidence 89999999999999999999999998632 3456789999999999999985
No 10
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.82 E-value=4.2e-20 Score=131.08 Aligned_cols=68 Identities=25% Similarity=0.469 Sum_probs=62.1
Q ss_pred CcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEc
Q psy800 117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLG 187 (204)
Q Consensus 117 ~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~ 187 (204)
.|+++|+++++++|+|+|+||+.|+|+|.|||+|||++|+||+|.. ++.....+|.++|||++|.+|+
T Consensus 1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~---~~~~~~~lg~~~IRG~~I~~i~ 68 (68)
T cd01722 1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI---DGKSTGNLGEVLIRCNNVLYIR 68 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEe---CCccccCcCcEEEECCEEEEEC
Confidence 3899999999999999999999999999999999999999999974 3335678999999999999984
No 11
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.82 E-value=8.3e-20 Score=133.92 Aligned_cols=71 Identities=23% Similarity=0.588 Sum_probs=62.1
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCC-----CeeeeeeCeEEEeCCcEEEEccc
Q psy800 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE-----GRRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~-----~~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
+++ |.++++++|.|+|++||++.|+|.|||+||||||+||+|+...++ .+..+.+|.++|||+||++|++.
T Consensus 4 ~~~-L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~ 79 (81)
T cd01729 4 ILD-LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPV 79 (81)
T ss_pred hhh-HHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecC
Confidence 344 899999999999999999999999999999999999999875321 12568899999999999999875
No 12
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.82 E-value=7.8e-20 Score=131.30 Aligned_cols=67 Identities=25% Similarity=0.585 Sum_probs=61.3
Q ss_pred HHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800 120 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 120 ~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
..|+++++|+|.|+|++|+++.|+|.|||+||||+|+||+|+. ++...+.+|.++|||++|++|++.
T Consensus 3 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~---~~~~~~~lg~v~IRG~~I~~i~~~ 69 (72)
T cd01719 3 PELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVN---SGGEKNNIGMVVIRGNSIVMLEAL 69 (72)
T ss_pred hhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEc---cCCceeEeceEEECCCEEEEEEcc
Confidence 4789999999999999999999999999999999999999986 233578999999999999999875
No 13
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.81 E-value=2.4e-19 Score=129.55 Aligned_cols=71 Identities=18% Similarity=0.414 Sum_probs=62.5
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~ 188 (204)
++..|+++++++|.|.|++|+++.|+|+|||+|||++|+||.|.....+....+.+|.++|||++|++|+.
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~ 73 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE 73 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence 35578999999999999999999999999999999999999998754333346889999999999999975
No 14
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.79 E-value=4.5e-19 Score=127.68 Aligned_cols=70 Identities=29% Similarity=0.523 Sum_probs=62.6
Q ss_pred HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecC-CCeeeeeeCeEEEeCCcEEEEcccc
Q psy800 121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP-EGRRITKLDQILLNGNNITMLGLHT 190 (204)
Q Consensus 121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~-~~~~~~~lg~ilIRGdnI~~I~~~~ 190 (204)
.|+++++++|.|++++|+.+.|+|+|||+|||++|+||.|+.... ++...+.+|.++|||++|++|++.+
T Consensus 3 ~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d 73 (74)
T cd01727 3 TLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEID 73 (74)
T ss_pred hHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccC
Confidence 588999999999999999999999999999999999999986532 3445778999999999999999864
No 15
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.79 E-value=6.2e-19 Score=128.24 Aligned_cols=73 Identities=34% Similarity=0.638 Sum_probs=63.0
Q ss_pred CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCee--eeeeCeEEEeCCcEEEEcc
Q psy800 115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRR--ITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 115 ~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~--~~~lg~ilIRGdnI~~I~~ 188 (204)
...|+++|+++++++|.|+|++|+++.|+|+|||+|||++|+||+|.... ++.. .+..|.++|||++|.+|++
T Consensus 5 ~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-~~~~~~~~~~~~~~IRG~~I~~I~~ 79 (79)
T COG1958 5 GPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH-DGEKNVRRLGGEVLIRGDNIVLISP 79 (79)
T ss_pred cCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEecc-CCccccceeccEEEEECCcEEEEeC
Confidence 45789999999999999999999999999999999999999999998741 3333 3344599999999999864
No 16
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.79 E-value=7.9e-19 Score=127.09 Aligned_cols=71 Identities=25% Similarity=0.446 Sum_probs=63.9
Q ss_pred CcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800 117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 117 ~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
.|+++|+++.+++|.|+||+|++++|+|.+||+|||++|+||+|.. .+|+....++.++|||++|.+|+..
T Consensus 1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~--~~g~~~~~~~~v~IRG~~I~~i~~p 71 (76)
T cd01723 1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTS--KDGDKFWKMPECYIRGNTIKYLRVP 71 (76)
T ss_pred CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEEC--CCCcEeeeCCcEEEeCCEEEEEEcC
Confidence 4999999999999999999999999999999999999999999864 3565556789999999999999743
No 17
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.78 E-value=1.4e-18 Score=124.06 Aligned_cols=69 Identities=28% Similarity=0.484 Sum_probs=62.4
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
|+++|+++.+++|+|+||||..|+|+|.++|+|||++|+||++.. .+| +..++|.++|||++|.+|...
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~--~~g-~~~~~~~v~IRG~nI~~v~lP 69 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTA--RDG-RVSQLEQVYIRGSKIRFFILP 69 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEEC--CCC-cEeEcCcEEEeCCEEEEEEeC
Confidence 889999999999999999999999999999999999999998854 345 357789999999999999654
No 18
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.77 E-value=1.9e-18 Score=125.88 Aligned_cols=68 Identities=25% Similarity=0.501 Sum_probs=60.3
Q ss_pred HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecC-------CCeeeeeeCeEEEeCCcEEEEcc
Q psy800 121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTP-------EGRRITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~-------~~~~~~~lg~ilIRGdnI~~I~~ 188 (204)
.|.++++++|.|.|+|||.+.|+|.|||+||||||+||+|++... .+.+.+.+|.++|||++|++|+.
T Consensus 4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v 78 (79)
T cd01717 4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV 78 (79)
T ss_pred hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence 688999999999999999999999999999999999999987532 12356889999999999999863
No 19
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.76 E-value=4.1e-18 Score=119.24 Aligned_cols=66 Identities=42% Similarity=0.726 Sum_probs=60.3
Q ss_pred HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800 121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~ 188 (204)
+|+++++++|+|+|+||+.+.|+|.+||+|||++|+||.|.... +...+++|.++|||++|++|++
T Consensus 2 ~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~--~~~~~~~~~~~IrG~~I~~i~~ 67 (67)
T smart00651 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKD--GEKKRKLGLVFIRGNNIVYIIL 67 (67)
T ss_pred hhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecC--CcEEeEeCCEEEcCCEEEEEeC
Confidence 68899999999999999999999999999999999999998732 2468999999999999999864
No 20
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.76 E-value=5.2e-18 Score=118.82 Aligned_cols=67 Identities=36% Similarity=0.640 Sum_probs=60.8
Q ss_pred HHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800 120 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 120 ~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~ 188 (204)
.+|+++++++|+|+|+||+.++|+|.+||+|||++|+||.|.... +...+++|.++|||++|++|++
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~--~~~~~~~~~~~irG~~I~~I~~ 67 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKN--GPEKRSLGLVFIRGSNIRYISL 67 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETT--ESEEEEEEEEEEEGGGEEEEEE
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECC--CCcEeECcEEEEECCEEEEEEC
Confidence 368999999999999999999999999999999999999998732 2268899999999999999975
No 21
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.75 E-value=5.8e-18 Score=122.84 Aligned_cols=62 Identities=61% Similarity=0.974 Sum_probs=57.0
Q ss_pred CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee---cCccccccccEEEee
Q psy800 13 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH---DSHLLSYFASDLINF 74 (204)
Q Consensus 13 ~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~---~~~~~~~lG~vlIn~ 74 (204)
..|+++|+++++++|+|++++|+++.|+|+|||+|||++|+||+|+. +++....+|.++|+.
T Consensus 2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG 66 (76)
T cd01732 2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNG 66 (76)
T ss_pred cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeC
Confidence 47999999999999999999999999999999999999999999998 555667899999954
No 22
>KOG3482|consensus
Probab=99.73 E-value=4.4e-18 Score=121.08 Aligned_cols=67 Identities=21% Similarity=0.360 Sum_probs=62.7
Q ss_pred CCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEE---eeec
Q psy800 10 PSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLI---NFIW 76 (204)
Q Consensus 10 ~~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlI---n~~~ 76 (204)
..+.+|.+||+.+.+|+|.|+||||.+|+|+|.+.|.||||.|.+|+|++++...+.+|+++| |++|
T Consensus 4 ~~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvly 73 (79)
T KOG3482|consen 4 KQPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLY 73 (79)
T ss_pred cccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEE
Confidence 345699999999999999999999999999999999999999999999999999999999999 5553
No 23
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=99.73 E-value=1.6e-17 Score=119.03 Aligned_cols=62 Identities=21% Similarity=0.477 Sum_probs=58.1
Q ss_pred CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800 13 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF 74 (204)
Q Consensus 13 ~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~ 74 (204)
..|+++|+++++++|.|+|+||++|.|+|.|||+|||++|+||.|+.+++..+.+|.++|+.
T Consensus 3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG 64 (72)
T PRK00737 3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRG 64 (72)
T ss_pred cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeC
Confidence 47999999999999999999999999999999999999999999998877778899999954
No 24
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=99.72 E-value=2.6e-17 Score=116.53 Aligned_cols=60 Identities=23% Similarity=0.504 Sum_probs=56.8
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF 74 (204)
Q Consensus 15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~ 74 (204)
|+++|+++++|+|+|+|++|++|.|+|.|||+|||++|+||+|+.++.....+|.++|+.
T Consensus 1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG 60 (68)
T cd01731 1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRG 60 (68)
T ss_pred ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeC
Confidence 899999999999999999999999999999999999999999998777778899999955
No 25
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.71 E-value=7.2e-17 Score=120.62 Aligned_cols=69 Identities=29% Similarity=0.395 Sum_probs=62.4
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
|+++|+++.+++|+|+|++|..|+|+|.++|.|||++|+||+|.. ++.....+|.++|||++|.+|...
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~---~~~~~~~~~~v~IRG~nI~yi~lP 70 (90)
T cd01724 2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTL---KGRNPVPLDTLSIRGNNIRYFILP 70 (90)
T ss_pred HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEc---CCCceeEcceEEEeCCEEEEEEcC
Confidence 678999999999999999999999999999999999999999875 233567899999999999999644
No 26
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.71 E-value=4.2e-17 Score=115.25 Aligned_cols=60 Identities=20% Similarity=0.405 Sum_probs=56.7
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF 74 (204)
Q Consensus 15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~ 74 (204)
|+++|+++++++|.|+|++|++|+|+|.|||.|||++|+||+|..+++....+|.++|+.
T Consensus 1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG 60 (67)
T cd01726 1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRG 60 (67)
T ss_pred CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEEC
Confidence 899999999999999999999999999999999999999999988777778899999954
No 27
>KOG1775|consensus
Probab=99.70 E-value=1.4e-17 Score=119.60 Aligned_cols=78 Identities=85% Similarity=1.235 Sum_probs=73.1
Q ss_pred CCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800 112 NPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 112 ~~~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
.++..+|++++.++++.+|+|.+|+++++.|+|.|||.|.|+||+|+.|+...++|+...+++++++.|++|.+..|.
T Consensus 2 n~~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPG 79 (84)
T KOG1775|consen 2 NPSTLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPG 79 (84)
T ss_pred ChhhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecC
Confidence 356789999999999999999999999999999999999999999999998878888889999999999999998876
No 28
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.70 E-value=1.2e-16 Score=115.78 Aligned_cols=69 Identities=20% Similarity=0.415 Sum_probs=61.4
Q ss_pred HHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCC---CeeeeeeCeEEEeCCcEEEEcc
Q psy800 120 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE---GRRITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 120 ~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~---~~~~~~lg~ilIRGdnI~~I~~ 188 (204)
+.|+++++++|.|.|+|||.+.|+|.+||+||||+|+||.|+....+ +...+.+|.++|||++|+.|..
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v 74 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV 74 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence 46889999999999999999999999999999999999999975422 2368899999999999999863
No 29
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.70 E-value=5.1e-17 Score=119.23 Aligned_cols=61 Identities=23% Similarity=0.443 Sum_probs=54.1
Q ss_pred CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCc-------------cccccccEEEee
Q psy800 14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH-------------LLSYFASDLINF 74 (204)
Q Consensus 14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~-------------~~~~lG~vlIn~ 74 (204)
.|+++|+.+++|+|.|+++|||++.|+|+|||+||||+|+||+|++.+. ..+.+|.++|..
T Consensus 1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG 74 (82)
T cd01730 1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRG 74 (82)
T ss_pred CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeC
Confidence 4999999999999999999999999999999999999999999998432 355788888843
No 30
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.69 E-value=1.3e-16 Score=110.07 Aligned_cols=63 Identities=24% Similarity=0.553 Sum_probs=57.3
Q ss_pred HHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEc
Q psy800 122 VDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLG 187 (204)
Q Consensus 122 L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~ 187 (204)
|+++++++|+|+|+||+.+.|+|.+||+|||++|+||.|.+.. ....++|.++|||++|.+|.
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~---~~~~~~~~~~irG~~I~~I~ 63 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKE---GKKRVLGLVLIRGDNVRLVT 63 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecC---CcEEECCeEEEECCEEEEEC
Confidence 4678999999999999999999999999999999999998732 36789999999999999873
No 31
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.69 E-value=1.4e-16 Score=116.81 Aligned_cols=71 Identities=23% Similarity=0.482 Sum_probs=61.8
Q ss_pred CcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCC-eeeeeeCeEEEeCCcEEEEccc
Q psy800 117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEG-RRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 117 ~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~-~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
+|+++|+++.|++|+|+||+|..|.|+|.++|.|||++|+||++.. +++ .....++.++|||++|.+|..+
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~--~~~~~~~~~~~~v~IRG~~I~~I~lp 72 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTD--PEKYPHMLSVKNCFIRGSVVRYVQLP 72 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEc--CCCcccccccCeEEEECCEEEEEEeC
Confidence 4889999999999999999999999999999999999999998764 222 1245679999999999999755
No 32
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.69 E-value=8.2e-17 Score=115.60 Aligned_cols=60 Identities=18% Similarity=0.400 Sum_probs=55.8
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF 74 (204)
Q Consensus 15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~ 74 (204)
|.+.|+++++|+|+|+|++|++|.|+|.|||+||||+|+||+|+.++...+.+|.++|+.
T Consensus 1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG 60 (72)
T cd01719 1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRG 60 (72)
T ss_pred CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECC
Confidence 567899999999999999999999999999999999999999998777778899999954
No 33
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.69 E-value=1.9e-16 Score=115.41 Aligned_cols=71 Identities=21% Similarity=0.454 Sum_probs=62.8
Q ss_pred CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800 115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 115 ~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~ 188 (204)
...+..+|+.+.|+.|.|+||||..|.|+|.++|.|||++|+||++.. +++ ...++|.++|||++|.+|..
T Consensus 7 ~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~--~~~-~~~~~~~v~IRG~nI~yI~l 77 (78)
T cd01733 7 ENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIID--RNG-KQVQVEEIMVTGRNIRYVHI 77 (78)
T ss_pred hchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEc--CCC-ceeECCcEEEECCEEEEEEc
Confidence 346788999999999999999999999999999999999999999864 233 45689999999999999864
No 34
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=99.68 E-value=2e-16 Score=112.20 Aligned_cols=61 Identities=21% Similarity=0.326 Sum_probs=57.1
Q ss_pred CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800 14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF 74 (204)
Q Consensus 14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~ 74 (204)
.|+++|+++++++|.|+|++|++|.|+|.|||+|||++|+||+|+.++.....+|.++|+.
T Consensus 1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG 61 (68)
T cd01722 1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRC 61 (68)
T ss_pred CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEEC
Confidence 5999999999999999999999999999999999999999999998777778899999954
No 35
>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.66 E-value=5.7e-16 Score=113.23 Aligned_cols=65 Identities=25% Similarity=0.466 Sum_probs=57.6
Q ss_pred CCCCCcHHHHHhhcCC--EEEEEEe--CCeEEEEEEEeecCeeeeEecceEEeec-CccccccccEEEee
Q psy800 10 PSTLLPLELVDKCIGS--RIHIIMK--NDKEIVGTLNGFDDFVNMLLEDVTDCHD-SHLLSYFASDLINF 74 (204)
Q Consensus 10 ~~~~~P~~~L~~~~~k--~V~V~l~--~g~~~~G~L~gfD~~mNlvL~~~~E~~~-~~~~~~lG~vlIn~ 74 (204)
+....|++.+.+++++ +|.|+++ +|+++.|+|.|||+||||+|+||+|+.+ ++....+|.++|+.
T Consensus 2 ~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRG 71 (79)
T cd01718 2 KVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKG 71 (79)
T ss_pred ccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeC
Confidence 4678999999999998 7888777 8999999999999999999999999985 55677899999944
No 36
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.65 E-value=6.7e-16 Score=114.78 Aligned_cols=61 Identities=23% Similarity=0.449 Sum_probs=54.2
Q ss_pred CcHHHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCc-------------cccccccEEEee
Q psy800 14 LPLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH-------------LLSYFASDLINF 74 (204)
Q Consensus 14 ~P~~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~-------------~~~~lG~vlIn~ 74 (204)
.|+++|++++ +++|+|+|++|+++.|+|.|||+||||+|+||+|+..+. ..+++|.+||..
T Consensus 2 gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRG 77 (87)
T cd01720 2 GPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRG 77 (87)
T ss_pred ChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeC
Confidence 6999999998 899999999999999999999999999999999987543 244689999943
No 37
>KOG1780|consensus
Probab=99.64 E-value=3.4e-16 Score=111.81 Aligned_cols=66 Identities=23% Similarity=0.561 Sum_probs=59.7
Q ss_pred HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800 121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
-|++|++|++.++|..||.+.|+|+|||.|||+||+|+.|... ++ ....+|.++|||++|+.+.+.
T Consensus 8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~--~~-~~~~ig~~vIrgnsiv~~eaL 73 (77)
T KOG1780|consen 8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNG--DG-DKNNIGMVVIRGNSIVMVEAL 73 (77)
T ss_pred hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecC--cC-CcceeeeEEEeccEEEEEeec
Confidence 7999999999999999999999999999999999999999752 22 468899999999999998654
No 38
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.63 E-value=9.1e-16 Score=112.51 Aligned_cols=59 Identities=19% Similarity=0.421 Sum_probs=51.9
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC--------ccccccccEEEee
Q psy800 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS--------HLLSYFASDLINF 74 (204)
Q Consensus 15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~--------~~~~~lG~vlIn~ 74 (204)
+++ |+++++|+|.|+|+|||+|+|+|.|||+||||+|++|+|+..+ ...+.+|.++|+.
T Consensus 4 ~~~-L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG 70 (81)
T cd01729 4 ILD-LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRG 70 (81)
T ss_pred hhh-HHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcC
Confidence 455 7899999999999999999999999999999999999999854 2457789999943
No 39
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=99.63 E-value=1.6e-15 Score=110.32 Aligned_cols=65 Identities=32% Similarity=0.529 Sum_probs=56.4
Q ss_pred CCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee--cCcc-ccccc-cEEEee
Q psy800 10 PSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH--DSHL-LSYFA-SDLINF 74 (204)
Q Consensus 10 ~~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~--~~~~-~~~lG-~vlIn~ 74 (204)
.....|+++|+++++++|.|+|++|++|.|+|+|||+|||++|+||+|+. ++.. ...+| +++|+.
T Consensus 3 ~~~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG 71 (79)
T COG1958 3 MLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRG 71 (79)
T ss_pred cccCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEEC
Confidence 44567999999999999999999999999999999999999999999998 5554 34445 888854
No 40
>KOG3460|consensus
Probab=99.62 E-value=1.3e-16 Score=116.21 Aligned_cols=76 Identities=26% Similarity=0.505 Sum_probs=67.1
Q ss_pred CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCC----------eeeeeeCeEEEeCCcE
Q psy800 114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEG----------RRITKLDQILLNGNNI 183 (204)
Q Consensus 114 ~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~----------~~~~~lg~ilIRGdnI 183 (204)
+..-|+++|+-+++++|.|++|++|++.|+|.|||+|+|++|.||+|....-++ ..++.+..+|+|||+|
T Consensus 2 ~v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~V 81 (91)
T KOG3460|consen 2 TVEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGV 81 (91)
T ss_pred cccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeE
Confidence 346799999999999999999999999999999999999999999998764111 1467889999999999
Q ss_pred EEEccc
Q psy800 184 TMLGLH 189 (204)
Q Consensus 184 ~~I~~~ 189 (204)
++|+|.
T Consensus 82 ilvspp 87 (91)
T KOG3460|consen 82 ILVSPP 87 (91)
T ss_pred EEEcCc
Confidence 999986
No 41
>KOG1780|consensus
Probab=99.58 E-value=1.8e-15 Score=108.16 Aligned_cols=66 Identities=17% Similarity=0.375 Sum_probs=58.1
Q ss_pred HHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEeeecccceeecc
Q psy800 18 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINFIWGLPMITPI 84 (204)
Q Consensus 18 ~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~~~g~~~~~PI 84 (204)
=|++|++|++.++|++||.+.|+|+|||.|||+||+||.|...++....+|.++|... +++++.+.
T Consensus 8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgn-siv~~eaL 73 (77)
T KOG1780|consen 8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGN-SIVMVEAL 73 (77)
T ss_pred hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEecc-EEEEEeec
Confidence 5889999999999999999999999999999999999999998888899999999553 33555544
No 42
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.57 E-value=8.9e-15 Score=104.38 Aligned_cols=60 Identities=23% Similarity=0.269 Sum_probs=54.1
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF 74 (204)
Q Consensus 15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~ 74 (204)
|+++|+++.+++|.|+||||.+|+|+|.+||.|||++|+||+|...++....+|+++|+.
T Consensus 1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG 60 (70)
T cd01721 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRG 60 (70)
T ss_pred ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeC
Confidence 899999999999999999999999999999999999999998876554456789999944
No 43
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.55 E-value=1.5e-14 Score=104.43 Aligned_cols=60 Identities=15% Similarity=0.243 Sum_probs=52.2
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCc---cccccccEEEee
Q psy800 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH---LLSYFASDLINF 74 (204)
Q Consensus 15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~---~~~~lG~vlIn~ 74 (204)
+...|+++++|+|.|++++|++|.|+|+|||+|||++|+||.|+...+ .+..+|.++|+.
T Consensus 3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG 65 (74)
T cd01728 3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRG 65 (74)
T ss_pred chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEEC
Confidence 467799999999999999999999999999999999999999987322 356789998844
No 44
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.55 E-value=1.3e-14 Score=104.95 Aligned_cols=61 Identities=23% Similarity=0.315 Sum_probs=54.1
Q ss_pred CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee-cCccccccccEEEee
Q psy800 14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH-DSHLLSYFASDLINF 74 (204)
Q Consensus 14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~-~~~~~~~lG~vlIn~ 74 (204)
.|++||+++.+++|.|+||||+++.|+|.+||.|||++|+||.|.. +++....+|+++|+.
T Consensus 1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG 62 (76)
T cd01723 1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRG 62 (76)
T ss_pred CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeC
Confidence 4999999999999999999999999999999999999999999985 444445678999954
No 45
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.55 E-value=1.5e-14 Score=104.07 Aligned_cols=67 Identities=21% Similarity=0.344 Sum_probs=54.8
Q ss_pred HHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeec----CccccccccEEEeeecccceeecc
Q psy800 17 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD----SHLLSYFASDLINFIWGLPMITPI 84 (204)
Q Consensus 17 ~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~----~~~~~~lG~vlIn~~~g~~~~~PI 84 (204)
+-|+++++++|+|++++|+.+.|+|+|||+|||++|++|+|+.. +.....+|.++|+.- +.++..|+
T Consensus 2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~-~I~~i~~~ 72 (74)
T cd01727 2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGD-NIAVVGEI 72 (74)
T ss_pred hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCC-EEEEEEcc
Confidence 35789999999999999999999999999999999999999863 224667899999552 33444454
No 46
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.53 E-value=2.7e-14 Score=103.96 Aligned_cols=56 Identities=18% Similarity=0.364 Sum_probs=49.1
Q ss_pred HHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC----------ccccccccEEEe
Q psy800 18 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS----------HLLSYFASDLIN 73 (204)
Q Consensus 18 ~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~----------~~~~~lG~vlIn 73 (204)
-|.++++++|.|+++|||++.|+|.|||+||||+|+||+|+... ...+.+|.++|.
T Consensus 4 ~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iR 69 (79)
T cd01717 4 KMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLR 69 (79)
T ss_pred hhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEc
Confidence 46789999999999999999999999999999999999998742 234678999883
No 47
>KOG3482|consensus
Probab=99.53 E-value=2.4e-14 Score=102.06 Aligned_cols=73 Identities=25% Similarity=0.422 Sum_probs=67.0
Q ss_pred CCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800 113 PSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 113 ~~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~ 188 (204)
..+..|--+|+.+.+|+|.|+||-|.+|+|+|.+.|.|||+.|.+|+|+. +|.....+|.++||.+||.+|..
T Consensus 4 ~~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~i---dG~~~g~lGEilIRCNNvlyi~g 76 (79)
T KOG3482|consen 4 KQPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYI---DGVSTGNLGEILIRCNNVLYIRG 76 (79)
T ss_pred cccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhh---cccccccceeEEEEeccEEEEec
Confidence 34458889999999999999999999999999999999999999999986 67778899999999999999964
No 48
>KOG1781|consensus
Probab=99.53 E-value=1.2e-15 Score=114.40 Aligned_cols=81 Identities=22% Similarity=0.522 Sum_probs=67.4
Q ss_pred HHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCC-----eeeeeeCeEEEeCCcEEEEccccCCC
Q psy800 119 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEG-----RRITKLDQILLNGNNITMLGLHTHCG 193 (204)
Q Consensus 119 l~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~-----~~~~~lg~ilIRGdnI~~I~~~~~~~ 193 (204)
+=-|.+|++++|+|++.+||...|+|+|||+.|||||+|+.|+-..++. ...|++|.+++||..+++|+|.+..-
T Consensus 19 ilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e 98 (108)
T KOG1781|consen 19 ILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSE 98 (108)
T ss_pred HhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchh
Confidence 3358899999999999999999999999999999999999998654322 24699999999999999999985331
Q ss_pred --CCcccc
Q psy800 194 --MRPYIQ 199 (204)
Q Consensus 194 --~~~~~~ 199 (204)
.+|.+|
T Consensus 99 ~I~npf~~ 106 (108)
T KOG1781|consen 99 EIANPFVQ 106 (108)
T ss_pred hhccchhc
Confidence 156555
No 49
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=99.53 E-value=4.6e-14 Score=98.72 Aligned_cols=58 Identities=31% Similarity=0.483 Sum_probs=54.1
Q ss_pred HHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCc-cccccccEEEee
Q psy800 17 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH-LLSYFASDLINF 74 (204)
Q Consensus 17 ~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~-~~~~lG~vlIn~ 74 (204)
.+|+++++++|+|.+++|++++|+|.+||+|||++|+||.|..... ...++|.++|+.
T Consensus 1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG 59 (67)
T PF01423_consen 1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRG 59 (67)
T ss_dssp HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEG
T ss_pred ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEEC
Confidence 4799999999999999999999999999999999999999999776 888899999965
No 50
>KOG1775|consensus
Probab=99.52 E-value=4.1e-15 Score=106.82 Aligned_cols=76 Identities=61% Similarity=0.930 Sum_probs=67.3
Q ss_pred CCCCCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee---cCccccccccEEEeeecccceeecc
Q psy800 8 TNPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH---DSHLLSYFASDLINFIWGLPMITPI 84 (204)
Q Consensus 8 ~~~~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~---~~~~~~~lG~vlIn~~~g~~~~~PI 84 (204)
++++...|++++.++++.+|||.+|+++++.|+|.|||.|.|++|+|+.||- ++....+++++++|.. ++.|+.|-
T Consensus 1 ~n~~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGN-ni~mLvPG 79 (84)
T KOG1775|consen 1 TNPSTLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGN-NITMLVPG 79 (84)
T ss_pred CChhhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCC-cEEEEecC
Confidence 3567889999999999999999999999999999999999999999999987 4456778899999884 66777664
No 51
>PTZ00138 small nuclear ribonucleoprotein; Provisional
Probab=99.51 E-value=7.4e-14 Score=104.22 Aligned_cols=68 Identities=19% Similarity=0.355 Sum_probs=58.2
Q ss_pred CCCCCCCCcHHHHHhhcCC--EEEEEEeC--CeEEEEEEEeecCeeeeEecceEEeec-CccccccccEEEee
Q psy800 7 ATNPSTLLPLELVDKCIGS--RIHIIMKN--DKEIVGTLNGFDDFVNMLLEDVTDCHD-SHLLSYFASDLINF 74 (204)
Q Consensus 7 ~~~~~~~~P~~~L~~~~~k--~V~V~l~~--g~~~~G~L~gfD~~mNlvL~~~~E~~~-~~~~~~lG~vlIn~ 74 (204)
...+....|++++.+++.+ +|.|.+.+ +++++|+|.|||+|||++|+||+|+.. ++..+.+|.++|+.
T Consensus 7 ~~~~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRG 79 (89)
T PTZ00138 7 KLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKG 79 (89)
T ss_pred ccceeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcC
Confidence 5667788999999999975 67777766 589999999999999999999999975 44667899999943
No 52
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=99.50 E-value=7.2e-14 Score=97.66 Aligned_cols=58 Identities=34% Similarity=0.559 Sum_probs=53.0
Q ss_pred HHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC-ccccccccEEEee
Q psy800 17 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS-HLLSYFASDLINF 74 (204)
Q Consensus 17 ~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~-~~~~~lG~vlIn~ 74 (204)
.+|+++++++|+|.|++|+++.|+|.|||+|||++|+||.|+..+ .....+|.++|+.
T Consensus 1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG 59 (67)
T smart00651 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRG 59 (67)
T ss_pred ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcC
Confidence 378999999999999999999999999999999999999999866 6778889999954
No 53
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.46 E-value=2.1e-13 Score=101.96 Aligned_cols=60 Identities=20% Similarity=0.172 Sum_probs=56.1
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF 74 (204)
Q Consensus 15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~ 74 (204)
|..||+++.|++|.|+|+||.+|.|+|.++|.|||++|+||+|..+++....+|+++|+.
T Consensus 2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG 61 (90)
T cd01724 2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRG 61 (90)
T ss_pred HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeC
Confidence 678999999999999999999999999999999999999999998887778899999944
No 54
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.46 E-value=2e-13 Score=98.84 Aligned_cols=58 Identities=16% Similarity=0.216 Sum_probs=51.4
Q ss_pred HHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC------ccccccccEEEee
Q psy800 17 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS------HLLSYFASDLINF 74 (204)
Q Consensus 17 ~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~------~~~~~lG~vlIn~ 74 (204)
+-|+++++++|.|+++|||.|.|+|.|||+||||+|+||.|+... ...+.+|.++|..
T Consensus 3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG 66 (75)
T cd06168 3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPG 66 (75)
T ss_pred hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeC
Confidence 468899999999999999999999999999999999999999843 4567889888844
No 55
>KOG1783|consensus
Probab=99.46 E-value=1.4e-14 Score=103.29 Aligned_cols=73 Identities=25% Similarity=0.468 Sum_probs=67.9
Q ss_pred CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800 114 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 114 ~~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
....|-++|++.++++|.|+|.+|-.|+|+|...|.|||+.|+.++|.. +|+..+++|..||||++|.+|+..
T Consensus 3 ~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~---ngql~n~ygdaFirGnnVlyIs~~ 75 (77)
T KOG1783|consen 3 EGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYV---NGQLKNKYGDAFIRGNNVLYISTQ 75 (77)
T ss_pred cccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHh---cCcccccccceeeccccEEEEEec
Confidence 3467899999999999999999999999999999999999999999985 677889999999999999999865
No 56
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=99.44 E-value=5.1e-13 Score=97.36 Aligned_cols=64 Identities=16% Similarity=0.207 Sum_probs=56.9
Q ss_pred CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800 11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF 74 (204)
Q Consensus 11 ~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~ 74 (204)
.-..+..||+.+.|++|.|+||||.+|.|+|.++|.|||++|+||++...++....+|+++|..
T Consensus 6 ~~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG 69 (78)
T cd01733 6 LENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTG 69 (78)
T ss_pred hhchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEEC
Confidence 3456789999999999999999999999999999999999999999887666666789999943
No 57
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.43 E-value=4.2e-13 Score=92.46 Aligned_cols=56 Identities=21% Similarity=0.420 Sum_probs=51.4
Q ss_pred HHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800 19 VDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF 74 (204)
Q Consensus 19 L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~ 74 (204)
|+++++++|+|++++|+.|.|+|.+||+|||++|+||.|...+.....+|.++|+.
T Consensus 1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~irG 56 (63)
T cd00600 1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVLIRG 56 (63)
T ss_pred ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEEEEC
Confidence 46789999999999999999999999999999999999998777778889999854
No 58
>KOG1784|consensus
Probab=99.40 E-value=2.2e-13 Score=100.92 Aligned_cols=70 Identities=24% Similarity=0.519 Sum_probs=64.1
Q ss_pred HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeec-CCCeeeeeeCeEEEeCCcEEEEcccc
Q psy800 121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYEST-PEGRRITKLDQILLNGNNITMLGLHT 190 (204)
Q Consensus 121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~-~~~~~~~~lg~ilIRGdnI~~I~~~~ 190 (204)
-|+.|++++|.|.+.|||.+.|.|+|||+..||+|+|+.|+.++ ..+..+..+|..+|||+||..|.+.+
T Consensus 4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iD 74 (96)
T KOG1784|consen 4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEID 74 (96)
T ss_pred hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecc
Confidence 48899999999999999999999999999999999999998875 34567889999999999999998875
No 59
>KOG1783|consensus
Probab=99.38 E-value=7.8e-14 Score=99.45 Aligned_cols=64 Identities=20% Similarity=0.375 Sum_probs=61.1
Q ss_pred CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800 11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF 74 (204)
Q Consensus 11 ~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~ 74 (204)
....|.+||++.++|+|.|||.+|..|+|+|...|.|||+.||.++|+.+++..+++|+.||+.
T Consensus 3 ~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirG 66 (77)
T KOG1783|consen 3 EGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRG 66 (77)
T ss_pred cccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeecc
Confidence 5678999999999999999999999999999999999999999999999999999999999954
No 60
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=99.35 E-value=2.9e-12 Score=93.92 Aligned_cols=61 Identities=21% Similarity=0.364 Sum_probs=52.4
Q ss_pred CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCc--cccccccEEEee
Q psy800 14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH--LLSYFASDLINF 74 (204)
Q Consensus 14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~--~~~~lG~vlIn~ 74 (204)
.|+.||+++.|++|.|+||+|..|+|+|.++|.|||++|+||++...+. ....+++++|+.
T Consensus 1 l~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG 63 (81)
T cd01725 1 LFFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRG 63 (81)
T ss_pred ChhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEEC
Confidence 4789999999999999999999999999999999999999998775332 234568899844
No 61
>KOG1782|consensus
Probab=99.34 E-value=1.5e-13 Score=106.88 Aligned_cols=72 Identities=18% Similarity=0.381 Sum_probs=64.7
Q ss_pred HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccccCC
Q psy800 121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHTHC 192 (204)
Q Consensus 121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~~~~ 192 (204)
-|-+++++++.|.|+|||.+.|.|++||||-|++|++|.|+.+..+.......|.++|||+||++++..+..
T Consensus 13 sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~d 84 (129)
T KOG1782|consen 13 SLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLD 84 (129)
T ss_pred HHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcc
Confidence 378899999999999999999999999999999999999988765555678889999999999999877655
No 62
>KOG1774|consensus
Probab=99.29 E-value=2.5e-12 Score=93.57 Aligned_cols=68 Identities=19% Similarity=0.408 Sum_probs=57.1
Q ss_pred CCCCCCCCcHHHHHhhcCC----EEEEEEeCCeEEEEEEEeecCeeeeEecceEEee-cCccccccccEEEee
Q psy800 7 ATNPSTLLPLELVDKCIGS----RIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH-DSHLLSYFASDLINF 74 (204)
Q Consensus 7 ~~~~~~~~P~~~L~~~~~k----~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~-~~~~~~~lG~vlIn~ 74 (204)
-.++....|.+++.+|+.. +||..-+-|..++|.+.|||+|||+||+||+|.. +.+..+.+|+++++.
T Consensus 5 kv~kvmv~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKG 77 (88)
T KOG1774|consen 5 KVQKVMVQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKG 77 (88)
T ss_pred cccceecCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcC
Confidence 3456678999999998864 5777777799999999999999999999999987 455666999999954
No 63
>KOG3460|consensus
Probab=99.27 E-value=9.6e-13 Score=96.11 Aligned_cols=49 Identities=33% Similarity=0.637 Sum_probs=46.9
Q ss_pred CCCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee
Q psy800 11 STLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH 59 (204)
Q Consensus 11 ~~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~ 59 (204)
.+..|+++|+-+++.+|.||++++|++.|+|.|||+|+|++|.||+|.+
T Consensus 2 ~v~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eeti 50 (91)
T KOG3460|consen 2 TVEEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETI 50 (91)
T ss_pred cccccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheE
Confidence 4678999999999999999999999999999999999999999999987
No 64
>KOG3293|consensus
Probab=99.23 E-value=1.9e-11 Score=95.21 Aligned_cols=72 Identities=22% Similarity=0.447 Sum_probs=66.3
Q ss_pred CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800 116 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 116 ~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
++||.+|+.+-++++.|+||||..|.|.|..+|.+|||.|.++.+.. +||.+--.+..++|||.+|.|+...
T Consensus 1 mlPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts--~Dgdkf~r~pEcYirGttIkylri~ 72 (134)
T KOG3293|consen 1 MLPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTS--EDGDKFFRMPECYIRGTTIKYLRIP 72 (134)
T ss_pred CcchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEec--cCCCceeecceeEEecceeEEEecc
Confidence 47999999999999999999999999999999999999999999975 5777778889999999999999654
No 65
>KOG3448|consensus
Probab=99.13 E-value=3e-10 Score=84.01 Aligned_cols=72 Identities=21% Similarity=0.421 Sum_probs=60.8
Q ss_pred CcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEccc
Q psy800 117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 117 ~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
+-+++++.++|++|.|+|||+-.+.|+|.|.|+|+|+-|+|......++- ..-..+..++|||+.|.||..+
T Consensus 2 LFysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~ky-Phm~Sv~ncfIRGSvvrYv~l~ 73 (96)
T KOG3448|consen 2 LFYSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKY-PHMLSVKNCFIRGSVVRYVQLP 73 (96)
T ss_pred chHHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccC-CCeeeeeeEEEeccEEEEEEeC
Confidence 34678999999999999999999999999999999999999998653211 1356678999999999999654
No 66
>KOG3168|consensus
Probab=99.12 E-value=1.1e-11 Score=101.33 Aligned_cols=69 Identities=23% Similarity=0.526 Sum_probs=60.7
Q ss_pred HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeec-------CCCeeeeeeCeEEEeCCcEEEEccc
Q psy800 121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYEST-------PEGRRITKLDQILLNGNNITMLGLH 189 (204)
Q Consensus 121 ~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~-------~~~~~~~~lg~ilIRGdnI~~I~~~ 189 (204)
.|-+.+|.+..|.++|||.+.|.+++||.|||+||.||+|.... .++++.+-+|.+++||++|++.+..
T Consensus 8 kml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVe 83 (177)
T KOG3168|consen 8 KMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVE 83 (177)
T ss_pred HHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEecc
Confidence 46678999999999999999999999999999999999996532 3456789999999999999998654
No 67
>KOG1781|consensus
Probab=99.09 E-value=8e-12 Score=93.85 Aligned_cols=65 Identities=20% Similarity=0.395 Sum_probs=53.1
Q ss_pred HHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC--------ccccccccEEEeeecccceeecc
Q psy800 19 VDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS--------HLLSYFASDLINFIWGLPMITPI 84 (204)
Q Consensus 19 L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~--------~~~~~lG~vlIn~~~g~~~~~PI 84 (204)
|.+|++|+|+|++.+||+..|+|+|||+.|||||+||+|+..+ ...+.+|-+++.. .+++.+.|-
T Consensus 22 Lsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RG-Talvlisp~ 94 (108)
T KOG1781|consen 22 LSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRG-TALVLISPA 94 (108)
T ss_pred HHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcc-cEEEEEcCC
Confidence 5689999999999999999999999999999999999999732 1347788888766 344555443
No 68
>KOG3172|consensus
Probab=98.98 E-value=1.5e-09 Score=82.85 Aligned_cols=71 Identities=27% Similarity=0.471 Sum_probs=64.2
Q ss_pred CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800 115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 115 ~~~Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~ 188 (204)
...|+++|++.-++.|++++..|..|+|+|.-.|++||+.|+|+.... .|| ...++.+++|||+.|.++..
T Consensus 3 ~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~--~dg-~vs~le~V~IRGS~IRFlvl 73 (119)
T KOG3172|consen 3 VGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTA--RDG-RVSQLEQVFIRGSKIRFLVL 73 (119)
T ss_pred cccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEc--cCC-cceeeeeEEEecCeEEEEEC
Confidence 467999999999999999999999999999999999999999999875 455 57789999999999998743
No 69
>KOG3459|consensus
Probab=98.97 E-value=7.9e-11 Score=90.12 Aligned_cols=74 Identities=22% Similarity=0.460 Sum_probs=64.2
Q ss_pred CCcHHHHHhhcC--CEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeec----CCCe------eeeeeCeEEEeCCcE
Q psy800 116 LLPLELVDKCIG--SRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYEST----PEGR------RITKLDQILLNGNNI 183 (204)
Q Consensus 116 ~~Pl~~L~~~i~--k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~----~~~~------~~~~lg~ilIRGdnI 183 (204)
.+|++++...+. .+|.|.+||++.+.|+++|||.|.|++|+++.|.|.. .+|+ ..+.+|+++||||+|
T Consensus 23 ~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsv 102 (114)
T KOG3459|consen 23 TGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSV 102 (114)
T ss_pred cCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeE
Confidence 479999999885 5799999999999999999999999999999999875 1333 268899999999999
Q ss_pred EEEccc
Q psy800 184 TMLGLH 189 (204)
Q Consensus 184 ~~I~~~ 189 (204)
+++...
T Consensus 103 I~v~r~ 108 (114)
T KOG3459|consen 103 ILVLRN 108 (114)
T ss_pred EEEEec
Confidence 998644
No 70
>KOG3428|consensus
Probab=98.70 E-value=1.1e-07 Score=72.88 Aligned_cols=71 Identities=25% Similarity=0.351 Sum_probs=62.0
Q ss_pred HHHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEE-ccccCCC
Q psy800 119 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITML-GLHTHCG 193 (204)
Q Consensus 119 l~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I-~~~~~~~ 193 (204)
+.+|+++.+++|+|+|++|..+.|++.+.|-+||..|.++.-.. .| +..++..+.+||++|.|+ -|++.++
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~---~~-~pv~l~~lsirgnniRy~~lpD~l~l 75 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTV---KG-EPVRLDTLSIRGNNIRYYILPDSLNL 75 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEec---CC-CceeEEEEEeecceEEEEEccCCcCc
Confidence 56899999999999999999999999999999999999988764 24 567899999999999997 5666553
No 71
>KOG1784|consensus
Probab=98.55 E-value=8.5e-08 Score=71.37 Aligned_cols=55 Identities=22% Similarity=0.419 Sum_probs=46.4
Q ss_pred HHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC----ccccccccEEE
Q psy800 18 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS----HLLSYFASDLI 72 (204)
Q Consensus 18 ~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~----~~~~~lG~vlI 72 (204)
-|+.|+|++|.|...|||.+.|.|+|||+-.||+|+++-|++-+ .....+|--+|
T Consensus 4 ~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyii 62 (96)
T KOG1784|consen 4 TLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYII 62 (96)
T ss_pred hHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEE
Confidence 47899999999999999999999999999999999999998733 34445564444
No 72
>KOG3293|consensus
Probab=98.47 E-value=2.2e-07 Score=72.62 Aligned_cols=49 Identities=24% Similarity=0.419 Sum_probs=46.4
Q ss_pred CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCc
Q psy800 14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSH 62 (204)
Q Consensus 14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~ 62 (204)
.|+.+|+.+-+.++.|.||+|.+|.|.|..+|.+|||.|.++.++.++.
T Consensus 2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dg 50 (134)
T KOG3293|consen 2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDG 50 (134)
T ss_pred cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCC
Confidence 6999999999999999999999999999999999999999999988543
No 73
>KOG3168|consensus
Probab=98.31 E-value=7.1e-08 Score=79.08 Aligned_cols=58 Identities=16% Similarity=0.407 Sum_probs=46.9
Q ss_pred CcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeec----------CccccccccEEE
Q psy800 14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD----------SHLLSYFASDLI 72 (204)
Q Consensus 14 ~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~----------~~~~~~lG~vlI 72 (204)
.+.++| +.+|.++.|.++|||.|.|.+.+||.||||+|.||+|+.. .++++.+|-+++
T Consensus 5 ~sskml-~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvll 72 (177)
T KOG3168|consen 5 KSSKML-QHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLL 72 (177)
T ss_pred chhHHH-HhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEe
Confidence 344555 5789999999999999999999999999999999999752 234555666665
No 74
>KOG1782|consensus
Probab=98.24 E-value=6.8e-08 Score=75.44 Aligned_cols=41 Identities=20% Similarity=0.618 Sum_probs=39.4
Q ss_pred HHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee
Q psy800 19 VDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH 59 (204)
Q Consensus 19 L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~ 59 (204)
+-++++|++.|-|+|||.+.|.|++||+|-|++|++|.|++
T Consensus 14 l~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi 54 (129)
T KOG1782|consen 14 LVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERI 54 (129)
T ss_pred HHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhhe
Confidence 66899999999999999999999999999999999999987
No 75
>KOG3448|consensus
Probab=98.21 E-value=2.3e-06 Score=63.51 Aligned_cols=43 Identities=28% Similarity=0.553 Sum_probs=40.3
Q ss_pred HHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEe
Q psy800 16 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDC 58 (204)
Q Consensus 16 ~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~ 58 (204)
.+|.+.++++.|.|.||++..+.|+|.|.|+|+|+-|+|..-.
T Consensus 4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~ 46 (96)
T KOG3448|consen 4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVT 46 (96)
T ss_pred HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEee
Confidence 5789999999999999999999999999999999999997654
No 76
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=97.99 E-value=0.00013 Score=60.11 Aligned_cols=111 Identities=19% Similarity=0.292 Sum_probs=66.9
Q ss_pred HHHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeEec-ceEEeecCccccccccEEE--eeecccceeeccccccce
Q psy800 16 LELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLE-DVTDCHDSHLLSYFASDLI--NFIWGLPMITPITCAYSR 90 (204)
Q Consensus 16 ~~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~-~~~E~~~~~~~~~lG~vlI--n~~~g~~~~~PI~~~f~~ 90 (204)
-.||+.+- +.+|.|.|.+|-.++|.+.|||.|. +.|+ +.. ..+| .-+.-+....|++..+ .
T Consensus 14 D~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ft-VlL~~~gk------------qqLIYKHAISTI~p~~~i~~~~-~ 79 (165)
T PRK14091 14 DIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFS-ILLRRDGQ------------SQLVYKHAISTIMPAHPLDLSR-F 79 (165)
T ss_pred HHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceE-EEEEeCCc------------eEEEEeeeeeeecccCCcchhh-h
Confidence 45665554 3589999999999999999999999 4443 221 2222 2222223334444211 1
Q ss_pred eecccEeEEEeeeccCCcccCCCCCCCcHHHHHhhc--CCEEEEEEeCCeEEEEEEEEEcCccceE
Q psy800 91 SHQYRTLTHLLYTMTAPSVATNPSTLLPLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNML 154 (204)
Q Consensus 91 ~~~~~~v~~~l~~~~~~~~~~~~~~~~Pl~~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~mNlV 154 (204)
+ + .|.. +.++..+-=.+|..+. ..+|+|.|.||-.+.|.+.|||.|.=|.
T Consensus 80 -~-~------~~~~------~~~~~nlQd~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL 131 (165)
T PRK14091 80 -S-K------SLDA------NKKSRLLQDVFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLL 131 (165)
T ss_pred -c-c------hhhh------cccccccHHHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEE
Confidence 1 1 1111 1111122223555554 3569999999999999999999998444
No 77
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=97.94 E-value=7.3e-06 Score=57.75 Aligned_cols=25 Identities=44% Similarity=0.470 Sum_probs=23.4
Q ss_pred EEEEEEEEEcCccceEEcceEEEee
Q psy800 139 EIVGTLNGFDDFVNMLLEDVTEYES 163 (204)
Q Consensus 139 ~i~G~L~gfD~~mNlVL~da~E~~~ 163 (204)
.++|.|.+||.|+||+|.|+.|.+.
T Consensus 24 ~~~G~lvAFDK~wNm~L~DV~E~y~ 48 (66)
T cd01739 24 VCSGFLVAFDKFWNMALVDVDETYR 48 (66)
T ss_pred EEEEEEEeeeeehhheehhhhhhhc
Confidence 7899999999999999999999874
No 78
>KOG3459|consensus
Probab=97.67 E-value=5.6e-06 Score=63.66 Aligned_cols=49 Identities=24% Similarity=0.478 Sum_probs=44.6
Q ss_pred CCCCcHHHHHhhcC--CEEEEEEeCCeEEEEEEEeecCeeeeEecceEEee
Q psy800 11 STLLPLELVDKCIG--SRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH 59 (204)
Q Consensus 11 ~~~~P~~~L~~~~~--k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~ 59 (204)
-...|++++...+. .+|+|.+++++.+.|++.|||.|.|++|+++.|..
T Consensus 21 f~~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelw 71 (114)
T KOG3459|consen 21 FNTGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELW 71 (114)
T ss_pred cCcCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHC
Confidence 34589999998884 69999999999999999999999999999999976
No 79
>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=97.55 E-value=7.8e-05 Score=52.57 Aligned_cols=37 Identities=30% Similarity=0.437 Sum_probs=30.2
Q ss_pred CEEEEEEeC--C--eEEEEEEEeecCeeeeEecceEEeecC
Q psy800 25 SRIHIIMKN--D--KEIVGTLNGFDDFVNMLLEDVTDCHDS 61 (204)
Q Consensus 25 k~V~V~l~~--g--~~~~G~L~gfD~~mNlvL~~~~E~~~~ 61 (204)
++|.|.++. | -.+.|.|.+||.|+||+|.|+.|....
T Consensus 9 ~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y~~ 49 (66)
T cd01739 9 IRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETYRK 49 (66)
T ss_pred cEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhhcc
Confidence 566666664 3 378999999999999999999997644
No 80
>KOG3172|consensus
Probab=97.45 E-value=0.00025 Score=54.53 Aligned_cols=63 Identities=21% Similarity=0.233 Sum_probs=55.9
Q ss_pred CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEee
Q psy800 12 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLINF 74 (204)
Q Consensus 12 ~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~ 74 (204)
...|.++|.+.-+.-|.+.+..|..|.|+|.-.|.+||.+|+|..-...+.....+-.++|..
T Consensus 3 ~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRG 65 (119)
T KOG3172|consen 3 VGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRG 65 (119)
T ss_pred cccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEec
Confidence 457999999999999999999999999999999999999999998887766666777788843
No 81
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=97.16 E-value=0.0011 Score=47.43 Aligned_cols=65 Identities=9% Similarity=0.238 Sum_probs=40.9
Q ss_pred HHHHhhcCCEEEEEEeCCeEEEEEEEEEcC---ccceEEcceEEEeecCC--C--eeeeeeCeEEEeCCcEE
Q psy800 120 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDD---FVNMLLEDVTEYESTPE--G--RRITKLDQILLNGNNIT 184 (204)
Q Consensus 120 ~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~---~mNlVL~da~E~~~~~~--~--~~~~~lg~ilIRGdnI~ 184 (204)
-++..++|++|.|.++||..|+|.|.+++. -+-++|+-|........ . .......+++|.++.|+
T Consensus 5 ~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv 76 (77)
T PF14438_consen 5 YLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV 76 (77)
T ss_dssp HHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred HHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence 356778999999999999999999999997 89999999988643211 1 12334566677766654
No 82
>KOG3428|consensus
Probab=96.74 E-value=0.0032 Score=48.51 Aligned_cols=46 Identities=24% Similarity=0.364 Sum_probs=41.5
Q ss_pred HHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecC
Q psy800 16 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61 (204)
Q Consensus 16 ~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~ 61 (204)
..||+++.+.+|.|.|++|....|++.+.|.+||..|.++.=...+
T Consensus 4 vr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~ 49 (109)
T KOG3428|consen 4 VRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG 49 (109)
T ss_pred HHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC
Confidence 4689999999999999999999999999999999999988755543
No 83
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=96.01 E-value=0.014 Score=40.75 Aligned_cols=28 Identities=25% Similarity=0.532 Sum_probs=24.8
Q ss_pred CCEEEEEEeCCeEEEEEEEEEcCccceE
Q psy800 127 GSRIHIIMKNDKEIVGTLNGFDDFVNML 154 (204)
Q Consensus 127 ~k~V~V~Lk~gr~i~G~L~gfD~~mNlV 154 (204)
..+|+|.|.||-.+.|.+.|||+|+=++
T Consensus 11 ~~~Vtv~L~NG~~l~G~I~~fD~ftVll 38 (61)
T cd01716 11 KIPVTIYLVNGVQLKGQIESFDNFTVLL 38 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEcceEEEE
Confidence 4569999999999999999999998444
No 84
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=95.85 E-value=0.025 Score=40.39 Aligned_cols=44 Identities=16% Similarity=0.274 Sum_probs=34.6
Q ss_pred HHHhhcCCEEEEEEeCCeEEEEEEEeecC---eeeeEecceEEeecC
Q psy800 18 LVDKCIGSRIHIIMKNDKEIVGTLNGFDD---FVNMLLEDVTDCHDS 61 (204)
Q Consensus 18 ~L~~~~~k~V~V~l~~g~~~~G~L~gfD~---~mNlvL~~~~E~~~~ 61 (204)
++..++|++|.|.++||..|+|.|.+++. =+.++|.-|....++
T Consensus 6 l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~ 52 (77)
T PF14438_consen 6 LLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKS 52 (77)
T ss_dssp HHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS-
T ss_pred HHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeecccc
Confidence 56678899999999999999999999999 789999988876543
No 85
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=95.72 E-value=0.021 Score=39.90 Aligned_cols=29 Identities=21% Similarity=0.492 Sum_probs=25.3
Q ss_pred CCEEEEEEeCCeEEEEEEEEEcCccceEE
Q psy800 127 GSRIHIIMKNDKEIVGTLNGFDDFVNMLL 155 (204)
Q Consensus 127 ~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL 155 (204)
..+|+|.|.||-.+.|.+.|||+|+=++-
T Consensus 15 ~~~Vti~L~nG~~l~G~I~~fD~ftVll~ 43 (61)
T TIGR02383 15 RIPVTVFLVNGVQLKGVIESFDNFTVLLE 43 (61)
T ss_pred CCcEEEEEeCCcEEEEEEEEEeeeEEEEE
Confidence 45799999999999999999999985543
No 86
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=95.37 E-value=0.1 Score=34.16 Aligned_cols=33 Identities=27% Similarity=0.455 Sum_probs=29.0
Q ss_pred cCCEEEEEEeCCeEEEEEEEEEcCccceEEcceE
Q psy800 126 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 159 (204)
Q Consensus 126 i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~ 159 (204)
++++|+|.+ ++..++|+..|+|+.-.|+++...
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~ 34 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTED 34 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETT
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECC
Confidence 689999999 677889999999999999997644
No 87
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=95.34 E-value=0.056 Score=37.76 Aligned_cols=33 Identities=18% Similarity=0.448 Sum_probs=27.1
Q ss_pred HHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeee
Q psy800 18 LVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNM 50 (204)
Q Consensus 18 ~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNl 50 (204)
||+.+- +.+|.|.|.||-.++|.+.|||.|+=+
T Consensus 3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVl 37 (61)
T cd01716 3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVL 37 (61)
T ss_pred HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEE
Confidence 444443 458999999999999999999999933
No 88
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=95.31 E-value=0.06 Score=37.63 Aligned_cols=35 Identities=17% Similarity=0.471 Sum_probs=28.2
Q ss_pred HHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeE
Q psy800 17 ELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNML 51 (204)
Q Consensus 17 ~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlv 51 (204)
.||+.+- +.+|.|.|.+|-.++|.+.|||.|+=|.
T Consensus 6 ~fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll 42 (61)
T TIGR02383 6 QFLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLL 42 (61)
T ss_pred HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEE
Confidence 3555444 4689999999999999999999999333
No 89
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=95.16 E-value=0.12 Score=39.13 Aligned_cols=63 Identities=30% Similarity=0.464 Sum_probs=51.1
Q ss_pred hhcCCEEEEEEeCCeEEEEEEEEEcC-ccceEEcceEEEeecCCCe--------eeeeeCeEEEeCCcEEEEcc
Q psy800 124 KCIGSRIHIIMKNDKEIVGTLNGFDD-FVNMLLEDVTEYESTPEGR--------RITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 124 ~~i~k~V~V~Lk~gr~i~G~L~gfD~-~mNlVL~da~E~~~~~~~~--------~~~~lg~ilIRGdnI~~I~~ 188 (204)
.|+|++|.+..+++-+|+|+|...|. --.|.|.++.-.-++ +. ...-+..++.||..|.-+..
T Consensus 5 ~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE--~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v 76 (96)
T PF12701_consen 5 PYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTE--GRPTDREIPPSDEVYDYIVFRGSDIKDLKV 76 (96)
T ss_dssp CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTET--TSS-SS---C-CSSSSEEEEETTTEEEEEE
T ss_pred cccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcC--CCCcCcccCCCCceeeEEEEEccccceEEE
Confidence 58999999999999999999999994 788999998875432 21 13457899999999987644
No 90
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=95.15 E-value=0.039 Score=40.47 Aligned_cols=31 Identities=26% Similarity=0.505 Sum_probs=26.2
Q ss_pred CCEEEEEEeCCeEEEEEEEEEcCccceEEcc
Q psy800 127 GSRIHIIMKNDKEIVGTLNGFDDFVNMLLED 157 (204)
Q Consensus 127 ~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~d 157 (204)
..+|+|.|.||-.+.|.+.|||+|+=++-.+
T Consensus 19 ~~~VtifL~NG~~l~G~I~~fD~ftVll~~~ 49 (79)
T PRK00395 19 RVPVTIYLVNGIKLQGQIESFDNFVVLLRNT 49 (79)
T ss_pred CCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence 4569999999999999999999998555333
No 91
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=94.59 E-value=0.11 Score=38.13 Aligned_cols=35 Identities=23% Similarity=0.471 Sum_probs=28.3
Q ss_pred HHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeeeE
Q psy800 17 ELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNML 51 (204)
Q Consensus 17 ~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNlv 51 (204)
.||+.+- +.+|.|.|.+|-.++|.+.|||.|+=|.
T Consensus 10 ~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll 46 (79)
T PRK00395 10 PFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLL 46 (79)
T ss_pred HHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEE
Confidence 4555444 4689999999999999999999999443
No 92
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=94.41 E-value=0.09 Score=38.28 Aligned_cols=30 Identities=30% Similarity=0.614 Sum_probs=25.5
Q ss_pred CCEEEEEEeCCeEEEEEEEEEcCccceEEcc
Q psy800 127 GSRIHIIMKNDKEIVGTLNGFDDFVNMLLED 157 (204)
Q Consensus 127 ~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~d 157 (204)
..+|+|.|.||-.+.|.+.|||+|. +.|++
T Consensus 19 ~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~ 48 (77)
T COG1923 19 KIPVTIFLVNGFKLQGQVESFDNFV-VLLKN 48 (77)
T ss_pred CCeEEEEEEcCEEEEEEEEeeeeEE-EEEEc
Confidence 4679999999999999999999998 44443
No 93
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=93.99 E-value=0.29 Score=35.50 Aligned_cols=62 Identities=26% Similarity=0.416 Sum_probs=46.5
Q ss_pred hhcCCEEEEEEeCCeEEEEEEEEEc-CccceEEcceEEEeecC---CCe----eeeeeCeEEEeCCcEEE
Q psy800 124 KCIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDVTEYESTP---EGR----RITKLDQILLNGNNITM 185 (204)
Q Consensus 124 ~~i~k~V~V~Lk~gr~i~G~L~gfD-~~mNlVL~da~E~~~~~---~~~----~~~~lg~ilIRGdnI~~ 185 (204)
+++++++.+..+.+-+|+|+|.++| +---+.|.|+...-++. ++. ...-+..++.||+.|.-
T Consensus 3 ~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIkD 72 (74)
T cd01736 3 PYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIKD 72 (74)
T ss_pred cccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCcccc
Confidence 5899999999999999999999999 44668899987654321 111 23446788899987753
No 94
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=93.65 E-value=0.32 Score=35.43 Aligned_cols=30 Identities=30% Similarity=0.614 Sum_probs=26.0
Q ss_pred CCEEEEEEeCCeEEEEEEEeecCeeeeEecc
Q psy800 24 GSRIHIIMKNDKEIVGTLNGFDDFVNMLLED 54 (204)
Q Consensus 24 ~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~ 54 (204)
+.+|.|.|.||-.+.|.+.|||+|. +.|++
T Consensus 19 ~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~ 48 (77)
T COG1923 19 KIPVTIFLVNGFKLQGQVESFDNFV-VLLKN 48 (77)
T ss_pred CCeEEEEEEcCEEEEEEEEeeeeEE-EEEEc
Confidence 5689999999999999999999998 44443
No 95
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=91.46 E-value=1.1 Score=32.85 Aligned_cols=63 Identities=14% Similarity=0.324 Sum_probs=46.2
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEc-CccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD-~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~ 188 (204)
-|..|....|++|.+.|.++.++.|++.|+| .-.|+..+|-.- +=| ....-+||..-|+.++-
T Consensus 15 fLr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~T----PlG----v~~eAlLR~~DVi~~~f 78 (80)
T PF11095_consen 15 FLRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQT----PLG----VQPEALLRCSDVISISF 78 (80)
T ss_dssp HHHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEET----TTT----EEEEEEEEGGGEEEEEE
T ss_pred HHHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcCC----Ccc----cChhheeecCCEEEEEe
Confidence 3566777889999999999999999999999 556766655431 223 24688999999998864
No 96
>PRK14091 RNA-binding protein Hfq; Provisional
Probab=90.61 E-value=0.84 Score=37.82 Aligned_cols=35 Identities=17% Similarity=0.337 Sum_probs=28.7
Q ss_pred HHHHHhhc--CCEEEEEEeCCeEEEEEEEeecCeeee
Q psy800 16 LELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNM 50 (204)
Q Consensus 16 ~~~L~~~~--~k~V~V~l~~g~~~~G~L~gfD~~mNl 50 (204)
-.||+.+- +.+|.|.|.+|-.++|.+.|||.|+=|
T Consensus 94 d~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvl 130 (165)
T PRK14091 94 DVFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCML 130 (165)
T ss_pred HHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEE
Confidence 45665554 358999999999999999999999933
No 97
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=90.57 E-value=2 Score=35.33 Aligned_cols=110 Identities=16% Similarity=0.191 Sum_probs=66.0
Q ss_pred CCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeecCccccccccEEEe--eecccceeeccccccceeecccEeE-EE
Q psy800 24 GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLIN--FIWGLPMITPITCAYSRSHQYRTLT-HL 100 (204)
Q Consensus 24 ~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~~~~~~~lG~vlIn--~~~g~~~~~PI~~~f~~~~~~~~v~-~~ 100 (204)
+-+|.|.+.||+.+.|.+.||+.-=|.+|.-+. .++.. ++-+. .+..+... |.+-.+..+ .|. ..
T Consensus 29 ~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~--~~~~n-----Ri~~plE~I~t~Ee~-~~~d~~g~~----ti~~d~ 96 (165)
T PF03614_consen 29 DIPVRVVSENGQVFCMYVSGFMSKENKILAPDP--FKKEN-----RIRLPLERISTIEEL-IVSDFKGRL----TIHPDY 96 (165)
T ss_pred CCceEEEecCCcEEEEEEeccCcccCEEeccCC--CCCCc-----eEEEEhHHhhhHhhh-ccccccccE----Eechhh
Confidence 568999999999999999999999999987554 12211 12111 11111111 111111111 110 11
Q ss_pred eeeccCCcccCCCCCCCcHHHHHhhc--CCEEEEEEeCCeEEEEEEEEEcCc
Q psy800 101 LYTMTAPSVATNPSTLLPLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDF 150 (204)
Q Consensus 101 l~~~~~~~~~~~~~~~~Pl~~L~~~i--~k~V~V~Lk~gr~i~G~L~gfD~~ 150 (204)
+-.+ ...|+...-+++-+++. ++-|.|.+.|||.++|+-.|.|..
T Consensus 97 ~~~q-----~~~psrrDFF~Icrka~qqg~sIrVyM~DgR~ieG~stGvnac 143 (165)
T PF03614_consen 97 FNNQ-----PYKPSRRDFFSICRKAHQQGKSIRVYMADGREIEGKSTGVNAC 143 (165)
T ss_pred cccc-----cCCCccchHHHHHHHHHHCCCeEEEEEcCCcEEEeeecccceE
Confidence 1111 13344455567777765 778999999999999999998753
No 98
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=90.38 E-value=0.71 Score=32.21 Aligned_cols=36 Identities=19% Similarity=0.306 Sum_probs=30.6
Q ss_pred hcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEE
Q psy800 125 CIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTE 160 (204)
Q Consensus 125 ~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E 160 (204)
.+|..|.+++..|.+++|.+.+||.-.++++-.+.+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~s 39 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCPS 39 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEECcc
Confidence 478999999999999999999999888877655443
No 99
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=87.82 E-value=1.4 Score=28.70 Aligned_cols=32 Identities=28% Similarity=0.469 Sum_probs=28.3
Q ss_pred cCCEEEEEEeCCeEEEEEEEeecCeeeeEecce
Q psy800 23 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV 55 (204)
Q Consensus 23 ~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~ 55 (204)
+|++|.+.. ++..+.|+..|.|..=.|+++..
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~ 33 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTE 33 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEET
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEEC
Confidence 689999999 77778999999999999998653
No 100
>PRK14638 hypothetical protein; Provisional
Probab=87.79 E-value=1.1 Score=36.34 Aligned_cols=40 Identities=23% Similarity=0.334 Sum_probs=31.4
Q ss_pred CCCcHH---HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEE
Q psy800 115 TLLPLE---LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLL 155 (204)
Q Consensus 115 ~~~Pl~---~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL 155 (204)
...||. -+.+++|++|.|++++++.++|+|.++|+- ++.|
T Consensus 85 ldRpL~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l 127 (150)
T PRK14638 85 LDRPLRGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITI 127 (150)
T ss_pred CCCCCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 345544 466778999999999999999999999964 3444
No 101
>PRK02001 hypothetical protein; Validated
Probab=85.92 E-value=1.6 Score=35.59 Aligned_cols=40 Identities=33% Similarity=0.512 Sum_probs=31.6
Q ss_pred CCCcHH---HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEE
Q psy800 115 TLLPLE---LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLL 155 (204)
Q Consensus 115 ~~~Pl~---~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL 155 (204)
...||. -+.+++|+.|.|.+.+++.++|+|.++|+- +++|
T Consensus 75 ldRpL~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 75 LTSPLKVPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred CCCcCCCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 345544 466778999999999999999999999874 3444
No 102
>PRK14639 hypothetical protein; Provisional
Probab=85.61 E-value=1.7 Score=34.82 Aligned_cols=35 Identities=29% Similarity=0.438 Sum_probs=29.4
Q ss_pred HHHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEE
Q psy800 120 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLL 155 (204)
Q Consensus 120 ~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL 155 (204)
+-+.+++|+.|.|++++++.+.|+|.++|+- ++.|
T Consensus 81 ~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l 115 (140)
T PRK14639 81 EHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL 115 (140)
T ss_pred HHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 3566788999999999999999999999883 4544
No 103
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=85.54 E-value=5.2 Score=28.34 Aligned_cols=53 Identities=19% Similarity=0.342 Sum_probs=40.3
Q ss_pred HHHHHhhcCCEEEEEEeCCeEEEEEEEEEc-CccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEcc
Q psy800 119 LELVDKCIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLGL 188 (204)
Q Consensus 119 l~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD-~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~~ 188 (204)
++.|++++|++|.|.+..| .++|+|.+.. +|. +|+.. + ..++||=..|+.|.|
T Consensus 13 yq~lq~liG~~vvV~T~~g-~v~G~L~~V~pDhI--vl~~~--------~------~~~~IR~~~IV~v~p 66 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTRG-SVRGILVDVKPDHI--VLEEN--------G------TPFFIRIAQIVWVMP 66 (66)
T ss_pred HHHHHHhcCCEEEEEEcCC-cEEEEEEeecCCEE--EEEeC--------C------cEEEEEeeeEEEEcC
Confidence 5689999999999999776 5599999985 554 44432 1 368888888888754
No 104
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=84.06 E-value=1.8 Score=35.99 Aligned_cols=59 Identities=20% Similarity=0.431 Sum_probs=39.7
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEEEc-CccceEEcceEEEeecCCCeeeeeeCeEEEeCCcEEEEc
Q psy800 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITMLG 187 (204)
Q Consensus 118 Pl~~L~~~i~k~V~V~Lk~gr~i~G~L~gfD-~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGdnI~~I~ 187 (204)
|++ +.+|++|.|.|.+.| +++.|.|..+| ..-|+||-+..| +++ .. --+|=|-.|..|.
T Consensus 9 p~~-~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e-----~~~--~s--v~~I~ghaVk~ve 68 (166)
T PF06372_consen 9 PLE-WQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE-----DGK--RS--VKVIMGHAVKSVE 68 (166)
T ss_dssp HHH-HHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T-----TS---EE--EEEE-GGGEEEEE
T ss_pred HHH-HHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc-----CCc--ee--EEEEEccceEEEE
Confidence 444 678999999999999 99999999999 567899986664 332 22 3566777777664
No 105
>PRK14639 hypothetical protein; Provisional
Probab=83.79 E-value=1.9 Score=34.52 Aligned_cols=33 Identities=30% Similarity=0.483 Sum_probs=27.8
Q ss_pred HhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEec
Q psy800 20 DKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLE 53 (204)
Q Consensus 20 ~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~ 53 (204)
++++|+.|.|++++++.+.|+|.++|.- ++.|+
T Consensus 84 ~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l~ 116 (140)
T PRK14639 84 AKSIGELVKITTNEKEKFEGKIVSVDDE-NITLE 116 (140)
T ss_pred HHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence 3688999999999999999999999983 45543
No 106
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=83.65 E-value=2.4 Score=32.11 Aligned_cols=38 Identities=32% Similarity=0.433 Sum_probs=34.3
Q ss_pred hhcCCEEEEEEeCCeEEEEEEEeecC-eeeeEecceEEe
Q psy800 21 KCIGSRIHIIMKNDKEIVGTLNGFDD-FVNMLLEDVTDC 58 (204)
Q Consensus 21 ~~~~k~V~V~l~~g~~~~G~L~gfD~-~mNlvL~~~~E~ 58 (204)
.|+|++|.+..+.+-.|+|+|...|. --.+.|.++.-+
T Consensus 5 ~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~ 43 (96)
T PF12701_consen 5 PYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSF 43 (96)
T ss_dssp CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEET
T ss_pred cccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeec
Confidence 68999999999999999999999998 567999998764
No 107
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=83.43 E-value=2.7 Score=29.28 Aligned_cols=34 Identities=21% Similarity=0.321 Sum_probs=29.6
Q ss_pred hcCCEEEEEEeCCeEEEEEEEeecCeeeeEecce
Q psy800 22 CIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV 55 (204)
Q Consensus 22 ~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~ 55 (204)
++|..|.++.-.|.+++|.+.+||.-.++..=.+
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~ 37 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKC 37 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEEC
Confidence 4689999999999999999999999998764443
No 108
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=82.48 E-value=2 Score=35.68 Aligned_cols=43 Identities=21% Similarity=0.416 Sum_probs=32.6
Q ss_pred CCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCee-eeEecceEE
Q psy800 13 LLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFV-NMLLEDVTD 57 (204)
Q Consensus 13 ~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~m-NlvL~~~~E 57 (204)
..|+.+. .|++|+|.|.+.+ +++.|.|-.+|.-- |+||-+-.|
T Consensus 7 ~~p~~~~-~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e 50 (166)
T PF06372_consen 7 KSPLEWQ-DYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE 50 (166)
T ss_dssp S-HHHHH-CTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T
T ss_pred CCHHHHH-HhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc
Confidence 5688777 6999999999999 99999999999865 788875543
No 109
>PRK14638 hypothetical protein; Provisional
Probab=82.10 E-value=2.2 Score=34.63 Aligned_cols=36 Identities=25% Similarity=0.510 Sum_probs=28.6
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEe
Q psy800 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLL 52 (204)
Q Consensus 15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL 52 (204)
|.+|. ++.|+.|.|++++++.+.|+|.++|.- ++.|
T Consensus 92 ~~~f~-r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l 127 (150)
T PRK14638 92 PKDYV-RFTGKLAKIVTKDGKTFIGRIESFVDG-TITI 127 (150)
T ss_pred HHHHH-HhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence 33444 678999999999999999999999963 3444
No 110
>PRK14644 hypothetical protein; Provisional
Probab=80.29 E-value=3.9 Score=32.68 Aligned_cols=35 Identities=20% Similarity=0.298 Sum_probs=29.4
Q ss_pred HHHhhcCCEEEEEEeCC----eEEEEEEEEEcCccceEEc
Q psy800 121 LVDKCIGSRIHIIMKND----KEIVGTLNGFDDFVNMLLE 156 (204)
Q Consensus 121 ~L~~~i~k~V~V~Lk~g----r~i~G~L~gfD~~mNlVL~ 156 (204)
-+.+++|+.|.|+|++. +.++|+|.++|+- ++.|+
T Consensus 79 ~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 79 ELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred HHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 57888999999999887 8999999999974 35554
No 111
>PRK02001 hypothetical protein; Validated
Probab=79.07 E-value=3.2 Score=33.86 Aligned_cols=36 Identities=33% Similarity=0.564 Sum_probs=28.9
Q ss_pred cHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEe
Q psy800 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLL 52 (204)
Q Consensus 15 P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL 52 (204)
|.+|- +++|+.|.|++.+++++.|+|.++|.- +++|
T Consensus 82 ~~~f~-r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l 117 (152)
T PRK02001 82 PRQYK-KNIGRELEVLTKNGKKIEGELKSADEN-DITL 117 (152)
T ss_pred HHHHH-HhCCCEEEEEECCCCEEEEEEEEEeCC-EEEE
Confidence 34444 678999999999999999999999974 3444
No 112
>PRK14644 hypothetical protein; Provisional
Probab=78.68 E-value=4.7 Score=32.21 Aligned_cols=34 Identities=21% Similarity=0.334 Sum_probs=28.1
Q ss_pred HHhhcCCEEEEEEeCC----eEEEEEEEeecCeeeeEec
Q psy800 19 VDKCIGSRIHIIMKND----KEIVGTLNGFDDFVNMLLE 53 (204)
Q Consensus 19 L~~~~~k~V~V~l~~g----~~~~G~L~gfD~~mNlvL~ 53 (204)
+.+++|+.|.|++++. +++.|.|.++|.- ++.|+
T Consensus 80 f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~ 117 (136)
T PRK14644 80 LENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK 117 (136)
T ss_pred HHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 5578899999999876 8999999999984 35553
No 113
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=77.90 E-value=6.8 Score=28.27 Aligned_cols=30 Identities=33% Similarity=0.564 Sum_probs=25.2
Q ss_pred HHHhhcCCEEEEEEe---CC-eEEEEEEEEEcCc
Q psy800 121 LVDKCIGSRIHIIMK---ND-KEIVGTLNGFDDF 150 (204)
Q Consensus 121 ~L~~~i~k~V~V~Lk---~g-r~i~G~L~gfD~~ 150 (204)
-+..++|+.|.|+++ +| +.+.|.|.++|+-
T Consensus 19 ~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~ 52 (83)
T cd01734 19 DFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD 52 (83)
T ss_pred HHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC
Confidence 566778999999998 55 5899999999873
No 114
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=75.58 E-value=7 Score=28.19 Aligned_cols=31 Identities=32% Similarity=0.619 Sum_probs=25.3
Q ss_pred cHHHHHhhcCCEEEEEEe---CC-eEEEEEEEeecC
Q psy800 15 PLELVDKCIGSRIHIIMK---ND-KEIVGTLNGFDD 46 (204)
Q Consensus 15 P~~~L~~~~~k~V~V~l~---~g-~~~~G~L~gfD~ 46 (204)
|.+|- +++|+.|.|+++ +| +++.|.|.++|.
T Consensus 17 ~~~~~-r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~ 51 (83)
T cd01734 17 EADFE-RAVGKYVHVKLYQPIDGQKEFEGTLLGVDD 51 (83)
T ss_pred HHHHH-HhCCCEEEEEEEcccCCeEEEEEEEEeEeC
Confidence 44444 678999999998 55 699999999988
No 115
>PRK14640 hypothetical protein; Provisional
Probab=75.56 E-value=6.4 Score=31.87 Aligned_cols=40 Identities=18% Similarity=0.301 Sum_probs=30.2
Q ss_pred CCCcHH---HHHhhcCCEEEEEE----eCCeEEEEEEEEEcCccceEE
Q psy800 115 TLLPLE---LVDKCIGSRIHIIM----KNDKEIVGTLNGFDDFVNMLL 155 (204)
Q Consensus 115 ~~~Pl~---~L~~~i~k~V~V~L----k~gr~i~G~L~gfD~~mNlVL 155 (204)
...||. -+.+++|+.|.|++ .+.+.++|+|.++|+- ++.|
T Consensus 82 l~RpL~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l 128 (152)
T PRK14640 82 LDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITL 128 (152)
T ss_pred CCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEE
Confidence 345544 56677899999999 4678999999999874 3444
No 116
>PRK14633 hypothetical protein; Provisional
Probab=74.49 E-value=7.2 Score=31.54 Aligned_cols=41 Identities=12% Similarity=0.219 Sum_probs=30.5
Q ss_pred CCCcHH---HHHhhcCCEEEEEEe----CCeEEEEEEEEEcCccceEEc
Q psy800 115 TLLPLE---LVDKCIGSRIHIIMK----NDKEIVGTLNGFDDFVNMLLE 156 (204)
Q Consensus 115 ~~~Pl~---~L~~~i~k~V~V~Lk----~gr~i~G~L~gfD~~mNlVL~ 156 (204)
...||. -+.+++|++|.|+++ +.+.++|+|.++|+- ++.|+
T Consensus 79 ldRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~ 126 (150)
T PRK14633 79 MNRQIFNIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN 126 (150)
T ss_pred CCCCCCCHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence 345644 566678999999984 668999999999875 34443
No 117
>PRK14645 hypothetical protein; Provisional
Probab=74.15 E-value=6.7 Score=31.99 Aligned_cols=39 Identities=10% Similarity=0.169 Sum_probs=29.3
Q ss_pred CCCcHH---HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEE
Q psy800 115 TLLPLE---LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLL 155 (204)
Q Consensus 115 ~~~Pl~---~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL 155 (204)
...||. -+.+++|++|.|.+ +++++.|+|.++|+-. +.|
T Consensus 87 ldRpL~~~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~~-i~l 128 (154)
T PRK14645 87 PKRPLFTARHFERFAGLKAKVRG-PGENFTGRIKAVSGDQ-VTF 128 (154)
T ss_pred CCCCCCCHHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCCE-EEE
Confidence 345544 45667899999986 7899999999998742 444
No 118
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=74.01 E-value=9.1 Score=27.75 Aligned_cols=61 Identities=26% Similarity=0.314 Sum_probs=43.1
Q ss_pred HhhcCCEEEEEEeCCeEEEEEEEeecCee-eeEecceEEeecCccccccccEEEeeecccceeecccccccee
Q psy800 20 DKCIGSRIHIIMKNDKEIVGTLNGFDDFV-NMLLEDVTDCHDSHLLSYFASDLINFIWGLPMITPITCAYSRS 91 (204)
Q Consensus 20 ~~~~~k~V~V~l~~g~~~~G~L~gfD~~m-NlvL~~~~E~~~~~~~~~lG~vlIn~~~g~~~~~PI~~~f~~~ 91 (204)
..++++++.+..+.+-.|+|+|.++|..= -+.|.|+..+=.+...+ ++ +-++|.+.+|.+.
T Consensus 2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~----------~~-~~ipp~~~vyd~I 63 (74)
T cd01736 2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPT----------DG-PEIPPSDEVYDYI 63 (74)
T ss_pred ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCC----------CC-CccCCCCcceeEE
Confidence 36899999999999999999999999765 46788876653222211 11 2356777777664
No 119
>PRK14642 hypothetical protein; Provisional
Probab=73.82 E-value=7.5 Score=33.15 Aligned_cols=40 Identities=28% Similarity=0.334 Sum_probs=30.6
Q ss_pred CCCcHH---HHHhhcCCEEEEEEe-------------CCeEEEEEEEEEcCccceEE
Q psy800 115 TLLPLE---LVDKCIGSRIHIIMK-------------NDKEIVGTLNGFDDFVNMLL 155 (204)
Q Consensus 115 ~~~Pl~---~L~~~i~k~V~V~Lk-------------~gr~i~G~L~gfD~~mNlVL 155 (204)
...||. -+.+++|+.|.|+|+ +.+.++|+|.++|+. ++.|
T Consensus 85 ldRPLk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 85 IDRPLRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred CCCCCCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 345654 456678999999998 779999999999874 3434
No 120
>PRK06955 biotin--protein ligase; Provisional
Probab=72.99 E-value=15 Score=32.66 Aligned_cols=33 Identities=18% Similarity=0.372 Sum_probs=28.0
Q ss_pred hcCCEEEEEEeCCeEEEEEEEEEcCccceEEcc
Q psy800 125 CIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLED 157 (204)
Q Consensus 125 ~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~d 157 (204)
+++++|.|...+++.++|+++|+|+.-.|++++
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~ 279 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDT 279 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEEe
Confidence 468999997667778999999999999999853
No 121
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=72.78 E-value=9.1 Score=28.13 Aligned_cols=40 Identities=13% Similarity=0.270 Sum_probs=31.2
Q ss_pred HHHHHhhcCCEEEEEEeCCeEEEEEEEeecCee-eeEecce
Q psy800 16 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFV-NMLLEDV 55 (204)
Q Consensus 16 ~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~m-NlvL~~~ 55 (204)
+.+|..+.+|+|.+.|.++.++.|+..|+|... |+..++-
T Consensus 16 Lr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L 56 (80)
T PF11095_consen 16 LRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNL 56 (80)
T ss_dssp HHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEE
T ss_pred HHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhc
Confidence 556777789999999999999999999999765 6665543
No 122
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=72.49 E-value=6.4 Score=31.11 Aligned_cols=34 Identities=29% Similarity=0.498 Sum_probs=24.5
Q ss_pred CCcH---HHHHhhcCCEEEEEEe----CCeEEEEEEEEEcC
Q psy800 116 LLPL---ELVDKCIGSRIHIIMK----NDKEIVGTLNGFDD 149 (204)
Q Consensus 116 ~~Pl---~~L~~~i~k~V~V~Lk----~gr~i~G~L~gfD~ 149 (204)
..|| +.+..++|+.|.|.++ +.+.+.|+|.++|+
T Consensus 73 ~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~ 113 (141)
T PF02576_consen 73 DRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE 113 (141)
T ss_dssp SS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred CCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence 4565 4678889999999994 55689999999998
No 123
>PRK14643 hypothetical protein; Provisional
Probab=71.51 E-value=9.5 Score=31.41 Aligned_cols=40 Identities=13% Similarity=0.161 Sum_probs=30.0
Q ss_pred CCcHH---HHHhhcCCEEEEEEeC----CeEEEEEEEEEcCc-cceEE
Q psy800 116 LLPLE---LVDKCIGSRIHIIMKN----DKEIVGTLNGFDDF-VNMLL 155 (204)
Q Consensus 116 ~~Pl~---~L~~~i~k~V~V~Lk~----gr~i~G~L~gfD~~-mNlVL 155 (204)
..||. -+..++|++|.|+|+. .+.++|+|.++|+- ..+.|
T Consensus 90 eRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l 137 (164)
T PRK14643 90 EKQIRSQEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRF 137 (164)
T ss_pred CCCCCCHHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEE
Confidence 44544 5667899999999976 68999999999854 44443
No 124
>PRK14634 hypothetical protein; Provisional
Probab=71.45 E-value=9.7 Score=30.99 Aligned_cols=39 Identities=13% Similarity=0.140 Sum_probs=28.8
Q ss_pred CCcHH---HHHhhcCCEEEEEEeCC----eEEEEEEEEEcCccceEE
Q psy800 116 LLPLE---LVDKCIGSRIHIIMKND----KEIVGTLNGFDDFVNMLL 155 (204)
Q Consensus 116 ~~Pl~---~L~~~i~k~V~V~Lk~g----r~i~G~L~gfD~~mNlVL 155 (204)
..||. -+.+++|++|.|++++. +.+.|+|.++|+- ++.|
T Consensus 86 dRpL~~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 86 GDQLSSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred CCcCCCHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 44544 56677899999999743 6999999999874 3444
No 125
>PRK14636 hypothetical protein; Provisional
Probab=70.93 E-value=9.6 Score=31.75 Aligned_cols=35 Identities=20% Similarity=0.358 Sum_probs=27.4
Q ss_pred HHHHhhcCCEEEEEEe---CC-eEEEEEEEEEcCccceEE
Q psy800 120 ELVDKCIGSRIHIIMK---ND-KEIVGTLNGFDDFVNMLL 155 (204)
Q Consensus 120 ~~L~~~i~k~V~V~Lk---~g-r~i~G~L~gfD~~mNlVL 155 (204)
+-+.+++|++|.|+|+ +| ++++|+|.++|+- +++|
T Consensus 91 ~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l 129 (176)
T PRK14636 91 KDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI 129 (176)
T ss_pred HHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence 3566788999999997 55 6999999999873 3444
No 126
>PRK14646 hypothetical protein; Provisional
Probab=70.03 E-value=11 Score=30.63 Aligned_cols=40 Identities=13% Similarity=0.058 Sum_probs=29.6
Q ss_pred CCCcHH---HHHhhcCCEEEEEEeCC----eEEEEEEEEEcCccceEE
Q psy800 115 TLLPLE---LVDKCIGSRIHIIMKND----KEIVGTLNGFDDFVNMLL 155 (204)
Q Consensus 115 ~~~Pl~---~L~~~i~k~V~V~Lk~g----r~i~G~L~gfD~~mNlVL 155 (204)
...||. -+.+++|++|.|+|++. +.+.|+|.++|+- ++.|
T Consensus 85 ldRpL~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l 131 (155)
T PRK14646 85 VSDELTSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAI 131 (155)
T ss_pred CCCcCCCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEE
Confidence 345544 56678899999999643 5889999999974 4555
No 127
>PRK14636 hypothetical protein; Provisional
Probab=69.57 E-value=9 Score=31.92 Aligned_cols=31 Identities=26% Similarity=0.556 Sum_probs=25.4
Q ss_pred cHHHHHhhcCCEEEEEEe---CC-eEEEEEEEeecC
Q psy800 15 PLELVDKCIGSRIHIIMK---ND-KEIVGTLNGFDD 46 (204)
Q Consensus 15 P~~~L~~~~~k~V~V~l~---~g-~~~~G~L~gfD~ 46 (204)
|.+|. +++|+.|.|+++ +| +++.|+|.++|.
T Consensus 90 ~~df~-r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~ 124 (176)
T PRK14636 90 PKDFA-DWAGHEARIALSEPLDGRKQFRGELKGIDG 124 (176)
T ss_pred HHHHH-HhCCCeEEEEEecccCCeEEEEEEEEEEeC
Confidence 34444 688999999998 45 799999999987
No 128
>PRK14640 hypothetical protein; Provisional
Probab=69.36 E-value=14 Score=29.83 Aligned_cols=37 Identities=14% Similarity=0.301 Sum_probs=28.1
Q ss_pred cHHHHHhhcCCEEEEEE----eCCeEEEEEEEeecCeeeeEec
Q psy800 15 PLELVDKCIGSRIHIIM----KNDKEIVGTLNGFDDFVNMLLE 53 (204)
Q Consensus 15 P~~~L~~~~~k~V~V~l----~~g~~~~G~L~gfD~~mNlvL~ 53 (204)
|.+|. +++|+.|.|++ .+.+++.|+|.++|.- ++.|+
T Consensus 89 ~~~f~-r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~ 129 (152)
T PRK14640 89 VAQFE-KYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT 129 (152)
T ss_pred HHHHH-HhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence 34444 68899999999 4669999999999984 34443
No 129
>KOG1073|consensus
Probab=69.26 E-value=11 Score=34.99 Aligned_cols=64 Identities=30% Similarity=0.411 Sum_probs=48.8
Q ss_pred HhhcCCEEEEEEeCCeEEEEEEEEEc-CccceEEcceEEEeec---CCCe----eeeeeCeEEEeCCcEEEE
Q psy800 123 DKCIGSRIHIIMKNDKEIVGTLNGFD-DFVNMLLEDVTEYEST---PEGR----RITKLDQILLNGNNITML 186 (204)
Q Consensus 123 ~~~i~k~V~V~Lk~gr~i~G~L~gfD-~~mNlVL~da~E~~~~---~~~~----~~~~lg~ilIRGdnI~~I 186 (204)
..+|+++|.+.-|...+|+|+|.-.| +=.-|-|.++-..-++ .++. ..+-+..|+.||+.|.-+
T Consensus 5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL 76 (361)
T KOG1073|consen 5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDL 76 (361)
T ss_pred cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCccccee
Confidence 45899999999999999999999998 6678899996443221 1110 223678999999999854
No 130
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.80 E-value=19 Score=29.43 Aligned_cols=39 Identities=21% Similarity=0.388 Sum_probs=31.3
Q ss_pred CCcHH---HHHhhcCCEEEEEE----eCCeEEEEEEEEEcCccceEE
Q psy800 116 LLPLE---LVDKCIGSRIHIIM----KNDKEIVGTLNGFDDFVNMLL 155 (204)
Q Consensus 116 ~~Pl~---~L~~~i~k~V~V~L----k~gr~i~G~L~gfD~~mNlVL 155 (204)
..||. -+..++|+.|.|.| .+++.+.|+|.++|+-. +++
T Consensus 85 dRpL~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 85 DRPLKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred CCCcCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 45544 56667899999999 78999999999999876 444
No 131
>PRK14632 hypothetical protein; Provisional
Probab=68.49 E-value=12 Score=31.04 Aligned_cols=41 Identities=15% Similarity=0.299 Sum_probs=30.6
Q ss_pred CCCcHH---HHHhhcCCEEEEEEeC-------CeEEEEEEEEEcCccceEEc
Q psy800 115 TLLPLE---LVDKCIGSRIHIIMKN-------DKEIVGTLNGFDDFVNMLLE 156 (204)
Q Consensus 115 ~~~Pl~---~L~~~i~k~V~V~Lk~-------gr~i~G~L~gfD~~mNlVL~ 156 (204)
...||. -+.+++|+.|.|++++ .+.+.|+|.++|+- +++|+
T Consensus 83 ldRpL~~~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 83 LERPFFRAEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred CCCcCCCHHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 345544 5667789999999986 57999999999863 34443
No 132
>PRK14643 hypothetical protein; Provisional
Probab=68.09 E-value=10 Score=31.19 Aligned_cols=36 Identities=22% Similarity=0.316 Sum_probs=27.4
Q ss_pred HHHHHhhcCCEEEEEEeC----CeEEEEEEEeecC-eeeeEe
Q psy800 16 LELVDKCIGSRIHIIMKN----DKEIVGTLNGFDD-FVNMLL 52 (204)
Q Consensus 16 ~~~L~~~~~k~V~V~l~~----g~~~~G~L~gfD~-~mNlvL 52 (204)
.+|. +++|++|.|+++. .+.+.|+|.++|. ...+.|
T Consensus 97 ~df~-r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l 137 (164)
T PRK14643 97 EELV-KALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRF 137 (164)
T ss_pred HHHH-HhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEE
Confidence 3444 6889999999975 5899999999986 344443
No 133
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=67.48 E-value=8.8 Score=30.31 Aligned_cols=38 Identities=29% Similarity=0.518 Sum_probs=24.8
Q ss_pred CCCCCCcH---HHHHhhcCCEEEEEEe----CCeEEEEEEEeecC
Q psy800 9 NPSTLLPL---ELVDKCIGSRIHIIMK----NDKEIVGTLNGFDD 46 (204)
Q Consensus 9 ~~~~~~P~---~~L~~~~~k~V~V~l~----~g~~~~G~L~gfD~ 46 (204)
||-...|+ .=+.+++|+.|.|+++ +.+++.|+|.++|.
T Consensus 69 SPG~~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~ 113 (141)
T PF02576_consen 69 SPGIDRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE 113 (141)
T ss_dssp --SSSS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET
T ss_pred CCCCCCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC
Confidence 33445554 3455788999999994 45799999999999
No 134
>PRK14642 hypothetical protein; Provisional
Probab=66.71 E-value=10 Score=32.35 Aligned_cols=31 Identities=29% Similarity=0.387 Sum_probs=25.8
Q ss_pred hhcCCEEEEEEe-------------CCeEEEEEEEeecCeeeeEe
Q psy800 21 KCIGSRIHIIMK-------------NDKEIVGTLNGFDDFVNMLL 52 (204)
Q Consensus 21 ~~~~k~V~V~l~-------------~g~~~~G~L~gfD~~mNlvL 52 (204)
+++|+.|.|+++ +.+.++|+|.++|.- ++.|
T Consensus 97 rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l 140 (197)
T PRK14642 97 RFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI 140 (197)
T ss_pred HhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence 577999999998 679999999999884 3444
No 135
>PRK14633 hypothetical protein; Provisional
Probab=66.71 E-value=10 Score=30.67 Aligned_cols=31 Identities=16% Similarity=0.362 Sum_probs=25.3
Q ss_pred hhcCCEEEEEEe----CCeEEEEEEEeecCeeeeEe
Q psy800 21 KCIGSRIHIIMK----NDKEIVGTLNGFDDFVNMLL 52 (204)
Q Consensus 21 ~~~~k~V~V~l~----~g~~~~G~L~gfD~~mNlvL 52 (204)
+++|++|.|+++ ++++++|+|.++|.- ++.|
T Consensus 91 r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l 125 (150)
T PRK14633 91 ALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVIL 125 (150)
T ss_pred HhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEE
Confidence 678999999994 568999999999984 3444
No 136
>PRK14632 hypothetical protein; Provisional
Probab=66.62 E-value=11 Score=31.14 Aligned_cols=32 Identities=16% Similarity=0.383 Sum_probs=25.7
Q ss_pred hhcCCEEEEEEeC-------CeEEEEEEEeecCeeeeEec
Q psy800 21 KCIGSRIHIIMKN-------DKEIVGTLNGFDDFVNMLLE 53 (204)
Q Consensus 21 ~~~~k~V~V~l~~-------g~~~~G~L~gfD~~mNlvL~ 53 (204)
+++|+.|.|++++ .+++.|+|.++|.- +++|+
T Consensus 95 r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~ 133 (172)
T PRK14632 95 PYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR 133 (172)
T ss_pred HhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence 6789999999986 57999999999863 34443
No 137
>PRK14647 hypothetical protein; Provisional
Probab=66.06 E-value=15 Score=29.93 Aligned_cols=34 Identities=24% Similarity=0.404 Sum_probs=27.1
Q ss_pred CCcHH---HHHhhcCCEEEEEEe---------CCeEEEEEEEEEcC
Q psy800 116 LLPLE---LVDKCIGSRIHIIMK---------NDKEIVGTLNGFDD 149 (204)
Q Consensus 116 ~~Pl~---~L~~~i~k~V~V~Lk---------~gr~i~G~L~gfD~ 149 (204)
..||. -+.+++|+.|.|+++ +.+.+.|+|.++|+
T Consensus 85 ~RpL~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 85 DRPLKKEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred CCcCCCHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 44544 566778999999996 35899999999986
No 138
>PRK14645 hypothetical protein; Provisional
Probab=64.82 E-value=11 Score=30.81 Aligned_cols=30 Identities=7% Similarity=0.142 Sum_probs=24.5
Q ss_pred HHHHHhhcCCEEEEEEeCCeEEEEEEEeecCe
Q psy800 16 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDF 47 (204)
Q Consensus 16 ~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~ 47 (204)
.+|. +++|++|.|++ ++++++|+|.++|.-
T Consensus 95 ~df~-r~~G~~v~v~~-~~k~~~G~L~~~~d~ 124 (154)
T PRK14645 95 RHFE-RFAGLKAKVRG-PGENFTGRIKAVSGD 124 (154)
T ss_pred HHHH-HhCCCEEEEEc-CCeEEEEEEEEEeCC
Confidence 3444 67799999986 789999999999884
No 139
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=64.56 E-value=29 Score=30.81 Aligned_cols=49 Identities=31% Similarity=0.424 Sum_probs=34.9
Q ss_pred hcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEeecCCCeeeeeeCeEEEeCC
Q psy800 125 CIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGN 181 (204)
Q Consensus 125 ~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~~~~~~~~~~~lg~ilIRGd 181 (204)
+++++|.+.. ++..++|++.|+|+...|++++. ++.+....|.+.+|+.
T Consensus 270 ~~g~~v~~~~-~~~~~~G~~~gi~~~G~L~i~~~-------g~~~~~~~gev~~~~~ 318 (319)
T PRK11886 270 FLGREVKLII-GDKEISGIARGIDEQGALLLEDD-------GVEKPFNGGEISLRSW 318 (319)
T ss_pred ccCCeEEEEe-CCcEEEEEEEEECCCceEEEEeC-------CcEEEEEEeEEEEecC
Confidence 4689999987 45679999999999999999621 1223344566666653
No 140
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.45 E-value=20 Score=29.35 Aligned_cols=42 Identities=21% Similarity=0.414 Sum_probs=31.8
Q ss_pred CCCCCcHH---HHHhhcCCEEEEEE----eCCeEEEEEEEeecCeeeeEe
Q psy800 10 PSTLLPLE---LVDKCIGSRIHIIM----KNDKEIVGTLNGFDDFVNMLL 52 (204)
Q Consensus 10 ~~~~~P~~---~L~~~~~k~V~V~l----~~g~~~~G~L~gfD~~mNlvL 52 (204)
|-...|+. =...+.|+.|.|+| .+++.++|+|.++|+=. +++
T Consensus 82 PGldRpL~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~ 130 (153)
T COG0779 82 PGLDRPLKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL 130 (153)
T ss_pred CCCCCCcCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence 33355543 33467899999999 78899999999999976 444
No 141
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=63.68 E-value=16 Score=29.38 Aligned_cols=30 Identities=20% Similarity=0.371 Sum_probs=25.7
Q ss_pred HHHHhhcCCEEEEEE----eCCeEEEEEEEEEcC
Q psy800 120 ELVDKCIGSRIHIIM----KNDKEIVGTLNGFDD 149 (204)
Q Consensus 120 ~~L~~~i~k~V~V~L----k~gr~i~G~L~gfD~ 149 (204)
+-+.+++|+.|.|++ .+++.++|+|.++|+
T Consensus 91 ~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 91 RDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 356778999999997 577899999999987
No 142
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=63.13 E-value=14 Score=29.70 Aligned_cols=28 Identities=21% Similarity=0.440 Sum_probs=24.0
Q ss_pred HHhhcCCEEEEEE----eCCeEEEEEEEeecC
Q psy800 19 VDKCIGSRIHIIM----KNDKEIVGTLNGFDD 46 (204)
Q Consensus 19 L~~~~~k~V~V~l----~~g~~~~G~L~gfD~ 46 (204)
+.+++|+.|.|++ .+++++.|+|.++|.
T Consensus 93 f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~ 124 (154)
T PRK00092 93 FRRFIGREVKVKLYEPIDGRKKFQGILLAVDG 124 (154)
T ss_pred HHHhCCCeEEEEEEcccCCceEEEEEEEEeeC
Confidence 3468899999997 467899999999988
No 143
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=62.31 E-value=27 Score=34.30 Aligned_cols=33 Identities=21% Similarity=0.308 Sum_probs=28.2
Q ss_pred hcCCEEEEEEeCCeEEEEEEEEEcCccceEEcc
Q psy800 125 CIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLED 157 (204)
Q Consensus 125 ~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~d 157 (204)
+++++|.+...++..++|+..|+|+.-.|+|+.
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~~ 308 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLET 308 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEEE
Confidence 468999987667778999999999999999963
No 144
>PRK14637 hypothetical protein; Provisional
Probab=61.86 E-value=16 Score=29.62 Aligned_cols=40 Identities=15% Similarity=0.251 Sum_probs=28.7
Q ss_pred CCCcHH---HHHhhcCCEEEEEEeCCeEE-EEEEEEEcCccceEE
Q psy800 115 TLLPLE---LVDKCIGSRIHIIMKNDKEI-VGTLNGFDDFVNMLL 155 (204)
Q Consensus 115 ~~~Pl~---~L~~~i~k~V~V~Lk~gr~i-~G~L~gfD~~mNlVL 155 (204)
...||. -+.+++|+.|.|++.+.+.+ +|+|.++|+- ++.|
T Consensus 83 ldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l 126 (151)
T PRK14637 83 IERVIKNAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVL 126 (151)
T ss_pred CCCCCCCHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEE
Confidence 345644 56667899999999544556 7999999874 3444
No 145
>PRK14631 hypothetical protein; Provisional
Probab=61.19 E-value=19 Score=29.89 Aligned_cols=34 Identities=18% Similarity=0.247 Sum_probs=27.2
Q ss_pred CCCcHH---HHHhhcCCEEEEEEe----CCeEEEEEEEEEc
Q psy800 115 TLLPLE---LVDKCIGSRIHIIMK----NDKEIVGTLNGFD 148 (204)
Q Consensus 115 ~~~Pl~---~L~~~i~k~V~V~Lk----~gr~i~G~L~gfD 148 (204)
...||. -+.+++|+.|.|+++ +.+.++|+|.++|
T Consensus 102 ldRpL~~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 102 WDRPFFQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred CCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 345544 566788999999996 5589999999998
No 146
>PRK14641 hypothetical protein; Provisional
Probab=57.65 E-value=22 Score=29.58 Aligned_cols=34 Identities=15% Similarity=0.361 Sum_probs=26.7
Q ss_pred CCCcHH---HHHhhcCCEEEEEEeC----CeEEEEEEEEEc
Q psy800 115 TLLPLE---LVDKCIGSRIHIIMKN----DKEIVGTLNGFD 148 (204)
Q Consensus 115 ~~~Pl~---~L~~~i~k~V~V~Lk~----gr~i~G~L~gfD 148 (204)
...||. -+.+++|+.|.|++++ .+.+.|+|.++|
T Consensus 89 ldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 89 LGEPIILPRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred CCCcCCCHHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 345544 5667789999999976 568999999995
No 147
>PRK14634 hypothetical protein; Provisional
Probab=56.14 E-value=22 Score=28.96 Aligned_cols=36 Identities=8% Similarity=0.205 Sum_probs=27.2
Q ss_pred cHHHHHhhcCCEEEEEEeC----CeEEEEEEEeecCeeeeEe
Q psy800 15 PLELVDKCIGSRIHIIMKN----DKEIVGTLNGFDDFVNMLL 52 (204)
Q Consensus 15 P~~~L~~~~~k~V~V~l~~----g~~~~G~L~gfD~~mNlvL 52 (204)
|.+|- +++|+.|.|++++ .+.+.|+|.++|.- ++.|
T Consensus 92 ~~~f~-r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~-~v~l 131 (155)
T PRK14634 92 DRDFQ-TFRGFPVEVSHRDDDGSEQRLEGLLLERNED-HLQI 131 (155)
T ss_pred HHHHH-HhCCCeEEEEEecCCCCeEEEEEEEEEEeCC-EEEE
Confidence 44444 6789999999974 27999999999984 3444
No 148
>TIGR00121 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] ligase region. The protein name suggests that this enzyme transfers biotin only to acetyl-CoA-carboxylase but it also transfers the biotin moiety to other proteins. The apparent orthologs among the eukaryotes are larger proteins that contain a single copy of this domain.
Probab=56.02 E-value=45 Score=28.36 Aligned_cols=31 Identities=35% Similarity=0.490 Sum_probs=26.6
Q ss_pred hcCCEEEEEEeCCeEEEEEEEEEcCccceEEc
Q psy800 125 CIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLE 156 (204)
Q Consensus 125 ~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~ 156 (204)
.++++|.|...+ ..+.|++.|+|+.-.|+++
T Consensus 191 ~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~ 221 (237)
T TIGR00121 191 HIGREVSLTTGN-GEIEGIARGIDKDGALLLE 221 (237)
T ss_pred ccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence 458999998744 5799999999999999996
No 149
>PRK14647 hypothetical protein; Provisional
Probab=55.04 E-value=23 Score=28.80 Aligned_cols=27 Identities=22% Similarity=0.490 Sum_probs=23.1
Q ss_pred HhhcCCEEEEEEe---------CCeEEEEEEEeecC
Q psy800 20 DKCIGSRIHIIMK---------NDKEIVGTLNGFDD 46 (204)
Q Consensus 20 ~~~~~k~V~V~l~---------~g~~~~G~L~gfD~ 46 (204)
.+++|+.|.|+++ +.+++.|+|.++|.
T Consensus 95 ~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~ 130 (159)
T PRK14647 95 ERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLAD 130 (159)
T ss_pred HHhCCcEEEEEEeccccccccCCceEEEEEEEeecC
Confidence 3678999999996 34899999999996
No 150
>PRK14631 hypothetical protein; Provisional
Probab=53.49 E-value=42 Score=27.88 Aligned_cols=26 Identities=19% Similarity=0.371 Sum_probs=22.8
Q ss_pred HhhcCCEEEEEEe----CCeEEEEEEEeec
Q psy800 20 DKCIGSRIHIIMK----NDKEIVGTLNGFD 45 (204)
Q Consensus 20 ~~~~~k~V~V~l~----~g~~~~G~L~gfD 45 (204)
.+++|+.|.|+++ +.+.++|+|.++|
T Consensus 113 ~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~ 142 (174)
T PRK14631 113 QGYIGQQVALRLIAAVENRRKFQAKLLAVD 142 (174)
T ss_pred HHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence 3688999999996 4589999999998
No 151
>PRK14646 hypothetical protein; Provisional
Probab=53.11 E-value=27 Score=28.42 Aligned_cols=36 Identities=11% Similarity=0.136 Sum_probs=27.0
Q ss_pred HHHHHhhcCCEEEEEEeC---C-eEEEEEEEeecCeeeeEec
Q psy800 16 LELVDKCIGSRIHIIMKN---D-KEIVGTLNGFDDFVNMLLE 53 (204)
Q Consensus 16 ~~~L~~~~~k~V~V~l~~---g-~~~~G~L~gfD~~mNlvL~ 53 (204)
.+|. +++|+.|.|+++. | +.+.|+|.++|.- ++.|+
T Consensus 93 ~df~-r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~ 132 (155)
T PRK14646 93 RDFK-TFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN 132 (155)
T ss_pred HHHH-HhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence 3443 6789999999964 3 6899999999984 35553
No 152
>PRK14637 hypothetical protein; Provisional
Probab=48.34 E-value=27 Score=28.30 Aligned_cols=33 Identities=18% Similarity=0.364 Sum_probs=24.9
Q ss_pred HhhcCCEEEEEEeCCeEE-EEEEEeecCeeeeEec
Q psy800 20 DKCIGSRIHIIMKNDKEI-VGTLNGFDDFVNMLLE 53 (204)
Q Consensus 20 ~~~~~k~V~V~l~~g~~~-~G~L~gfD~~mNlvL~ 53 (204)
.+++|+.|.|++.+.+++ +|+|.++|.- ++.|+
T Consensus 94 ~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~ 127 (151)
T PRK14637 94 SIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT 127 (151)
T ss_pred HHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence 367899999999655566 7999999984 34443
No 153
>PRK08330 biotin--protein ligase; Provisional
Probab=47.84 E-value=75 Score=27.00 Aligned_cols=32 Identities=25% Similarity=0.486 Sum_probs=26.3
Q ss_pred hcCCEEEEEEeCCeEE-EEEEEEEcCccceEEcc
Q psy800 125 CIGSRIHIIMKNDKEI-VGTLNGFDDFVNMLLED 157 (204)
Q Consensus 125 ~i~k~V~V~Lk~gr~i-~G~L~gfD~~mNlVL~d 157 (204)
.++++|.+.. ++..+ +|+..|+|+.-.|+++.
T Consensus 186 ~~g~~v~~~~-~~~~~~~G~~~gI~~~G~L~v~~ 218 (236)
T PRK08330 186 ILGKRVKIIG-DGEILVEGIAEDIDEFGALILRL 218 (236)
T ss_pred hcCCeEEEEE-CCcEEEEEEEEEECCCCEEEEEE
Confidence 4689999875 56665 79999999999999874
No 154
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=44.00 E-value=63 Score=22.80 Aligned_cols=32 Identities=19% Similarity=0.361 Sum_probs=26.0
Q ss_pred CCc--HHHHHhhcCCEEEEEEeCCeEEEEEEEeec
Q psy800 13 LLP--LELVDKCIGSRIHIIMKNDKEIVGTLNGFD 45 (204)
Q Consensus 13 ~~P--~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD 45 (204)
.+| ...|++++|++|.|..-.|. +.|+|.+..
T Consensus 8 vdpyvyq~lq~liG~~vvV~T~~g~-v~G~L~~V~ 41 (66)
T PF10842_consen 8 VDPYVYQTLQSLIGQRVVVQTTRGS-VRGILVDVK 41 (66)
T ss_pred cCHHHHHHHHHhcCCEEEEEEcCCc-EEEEEEeec
Confidence 455 67899999999999996665 499999864
No 155
>PRK14641 hypothetical protein; Provisional
Probab=43.08 E-value=40 Score=28.06 Aligned_cols=26 Identities=15% Similarity=0.516 Sum_probs=22.0
Q ss_pred HhhcCCEEEEEEeC----CeEEEEEEEeec
Q psy800 20 DKCIGSRIHIIMKN----DKEIVGTLNGFD 45 (204)
Q Consensus 20 ~~~~~k~V~V~l~~----g~~~~G~L~gfD 45 (204)
.+++|+.|.|++++ .+.+.|+|.++|
T Consensus 100 ~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~ 129 (173)
T PRK14641 100 GRHVGRLLRVTYRDEEGSEHEVTGHLQEVS 129 (173)
T ss_pred HHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence 36779999999975 469999999995
No 156
>PRK10898 serine endoprotease; Provisional
Probab=43.03 E-value=42 Score=30.59 Aligned_cols=32 Identities=13% Similarity=0.330 Sum_probs=27.5
Q ss_pred CEEEEEEeCCeEEEEEEEEEcCccceEEcceE
Q psy800 128 SRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 159 (204)
Q Consensus 128 k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~ 159 (204)
..+.|.+.||+.+.+++.++|....|.+=.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v~ 133 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKIN 133 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEEc
Confidence 46888899999999999999999999775553
No 157
>PRK10898 serine endoprotease; Provisional
Probab=41.63 E-value=40 Score=30.68 Aligned_cols=31 Identities=13% Similarity=0.335 Sum_probs=27.2
Q ss_pred CEEEEEEeCCeEEEEEEEeecCeeeeEecce
Q psy800 25 SRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV 55 (204)
Q Consensus 25 k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~ 55 (204)
..+.|.+.+|+.+.+++.++|...+|.|=.+
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvl~v 132 (353)
T PRK10898 102 DQIIVALQDGRVFEALLVGSDSLTDLAVLKI 132 (353)
T ss_pred CEEEEEeCCCCEEEEEEEEEcCCCCEEEEEE
Confidence 5799999999999999999999999966433
No 158
>PRK14630 hypothetical protein; Provisional
Probab=40.66 E-value=55 Score=26.25 Aligned_cols=39 Identities=13% Similarity=0.127 Sum_probs=27.8
Q ss_pred CCCcHH---HHHhhcCCEEEEEEeCCeEEEEEEEEEcCccceEE
Q psy800 115 TLLPLE---LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLL 155 (204)
Q Consensus 115 ~~~Pl~---~L~~~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL 155 (204)
...||. -+.+++|++|.|++... ..+|+|.++|+-. +.|
T Consensus 82 ldRpL~~~~df~r~~G~~v~V~l~~~-~~~G~L~~~~d~~-i~l 123 (143)
T PRK14630 82 INRKIKSDREFKIFEGKKIKLMLDND-FEEGFILEAKADS-FIF 123 (143)
T ss_pred CCCcCCCHHHHHHhCCCEEEEEEcCc-ceEEEEEEEeCCE-EEE
Confidence 345544 56677899999999654 4599999998743 444
No 159
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=38.97 E-value=46 Score=30.19 Aligned_cols=30 Identities=13% Similarity=0.348 Sum_probs=26.8
Q ss_pred CEEEEEEeCCeEEEEEEEeecCeeeeEecc
Q psy800 25 SRIHIIMKNDKEIVGTLNGFDDFVNMLLED 54 (204)
Q Consensus 25 k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~ 54 (204)
..+.|.+.+|+.+.+++.++|...+|.|=.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlk 131 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLK 131 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEE
Confidence 478999999999999999999999997733
No 160
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=38.71 E-value=52 Score=29.85 Aligned_cols=32 Identities=13% Similarity=0.358 Sum_probs=27.5
Q ss_pred CEEEEEEeCCeEEEEEEEEEcCccceEEcceE
Q psy800 128 SRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 159 (204)
Q Consensus 128 k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~ 159 (204)
..+.|.+.||+.+.+++.++|...+|.+=.+.
T Consensus 102 ~~i~V~~~dg~~~~a~vv~~d~~~DlAvlkv~ 133 (351)
T TIGR02038 102 DQIVVALQDGRKFEAELVGSDPLTDLAVLKIE 133 (351)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEec
Confidence 35788899999999999999999999885544
No 161
>PRK14635 hypothetical protein; Provisional
Probab=38.49 E-value=74 Score=25.95 Aligned_cols=36 Identities=14% Similarity=0.169 Sum_probs=26.7
Q ss_pred CCCcHH---HHHhhcCCEEEEEEe--CCeEEEE---EEEEEcCc
Q psy800 115 TLLPLE---LVDKCIGSRIHIIMK--NDKEIVG---TLNGFDDF 150 (204)
Q Consensus 115 ~~~Pl~---~L~~~i~k~V~V~Lk--~gr~i~G---~L~gfD~~ 150 (204)
...||. -+.+++|+.|.|++. ++..+.| +|.++|+-
T Consensus 84 ldRpL~~~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~ 127 (162)
T PRK14635 84 AERKLRLPEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD 127 (162)
T ss_pred CCCcCCCHHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC
Confidence 345544 466778999999886 4678887 99999864
No 162
>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella. The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent
Probab=37.96 E-value=45 Score=27.53 Aligned_cols=34 Identities=15% Similarity=0.175 Sum_probs=30.2
Q ss_pred cCCEEEEEEeCCeEEEEEEEEEcCccceEEcceE
Q psy800 126 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 159 (204)
Q Consensus 126 i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~ 159 (204)
-+-+|.|.+.||..+.|.+.||+.-=|.+|.-+.
T Consensus 28 ~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~ 61 (165)
T PF03614_consen 28 NDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP 61 (165)
T ss_pred cCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence 3568999999999999999999999999987655
No 163
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=35.35 E-value=42 Score=21.76 Aligned_cols=22 Identities=36% Similarity=0.508 Sum_probs=14.8
Q ss_pred EEEEEEEEcCccceEEcceEEE
Q psy800 140 IVGTLNGFDDFVNMLLEDVTEY 161 (204)
Q Consensus 140 i~G~L~gfD~~mNlVL~da~E~ 161 (204)
..|+..|.|+...+.|.+....
T Consensus 10 ~tGtFlGvDE~FGmLLr~~~~T 31 (42)
T PF14563_consen 10 LTGTFLGVDEDFGMLLRDDDTT 31 (42)
T ss_dssp EEEEEEEE-TT--EEEE-SS-E
T ss_pred cceeEEeeccccceEEEeCCcc
Confidence 5899999999999999886654
No 164
>PRK11625 Rho-binding antiterminator; Provisional
Probab=35.22 E-value=1.8e+02 Score=21.40 Aligned_cols=49 Identities=14% Similarity=0.150 Sum_probs=32.6
Q ss_pred CCEEEEEEeCCeEEEEEEEEEcCccceEEcceEEEe-ecCCCeeeeeeCeEEEeCCcEEEEc
Q psy800 127 GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYE-STPEGRRITKLDQILLNGNNITMLG 187 (204)
Q Consensus 127 ~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E~~-~~~~~~~~~~lg~ilIRGdnI~~I~ 187 (204)
+-+|.++++||..++|+. .|=+.+ +-.|+. ...+| +...||=|.|..++
T Consensus 23 ~~~l~l~l~dGe~~~g~A--~D~~~~----~k~EyL~l~~~g------~~~~iRLD~I~s~~ 72 (84)
T PRK11625 23 HLMLTLELKDGEVLQAKA--SDLVSR----KNVEYLVVEAAG------ETRELRLDKIASFS 72 (84)
T ss_pred CCeEEEEECCCCEEEEEE--EeeecC----CceEEEEEEcCC------CEEEEEeeeEeecc
Confidence 567999999999999954 565533 333433 22223 46677888888776
No 165
>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions []. ; PDB: 2E12_B.
Probab=34.83 E-value=50 Score=25.15 Aligned_cols=19 Identities=16% Similarity=0.401 Sum_probs=14.9
Q ss_pred CCEEEEEEeCCeEEEEEEE
Q psy800 127 GSRIHIIMKNDKEIVGTLN 145 (204)
Q Consensus 127 ~k~V~V~Lk~gr~i~G~L~ 145 (204)
+.+|.+.|+||+.+.|++.
T Consensus 28 e~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 28 EERVELELDDGSMLRGTVA 46 (101)
T ss_dssp T-EEEEEETTS-EEEEEEC
T ss_pred cceEEEEEcCCCeeeeeec
Confidence 4679999999999999863
No 166
>PRK10942 serine endoprotease; Provisional
Probab=34.70 E-value=62 Score=30.78 Aligned_cols=31 Identities=13% Similarity=0.303 Sum_probs=27.5
Q ss_pred CEEEEEEeCCeEEEEEEEEEcCccceEEcce
Q psy800 128 SRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV 158 (204)
Q Consensus 128 k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da 158 (204)
..+.|.+.||+++.+++.++|...+|.|=..
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlki 166 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQL 166 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEEe
Confidence 4689999999999999999999999887644
No 167
>PRK10942 serine endoprotease; Provisional
Probab=34.47 E-value=57 Score=31.04 Aligned_cols=30 Identities=13% Similarity=0.293 Sum_probs=26.7
Q ss_pred CEEEEEEeCCeEEEEEEEeecCeeeeEecc
Q psy800 25 SRIHIIMKNDKEIVGTLNGFDDFVNMLLED 54 (204)
Q Consensus 25 k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~ 54 (204)
..+.|.+.+|+++.+++.++|...+|.|=.
T Consensus 136 ~~i~V~~~dg~~~~a~vv~~D~~~DlAvlk 165 (473)
T PRK10942 136 TKIKVQLSDGRKFDAKVVGKDPRSDIALIQ 165 (473)
T ss_pred CEEEEEECCCCEEEEEEEEecCCCCEEEEE
Confidence 478999999999999999999999996643
No 168
>PRK10139 serine endoprotease; Provisional
Probab=34.44 E-value=66 Score=30.48 Aligned_cols=32 Identities=25% Similarity=0.410 Sum_probs=27.6
Q ss_pred CEEEEEEeCCeEEEEEEEEEcCccceEEcceE
Q psy800 128 SRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 159 (204)
Q Consensus 128 k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~ 159 (204)
.++.|.+.||+++.+++.|+|....|.+=.+.
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv~ 146 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQIQ 146 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEec
Confidence 46888899999999999999999998875543
No 169
>PRK10139 serine endoprotease; Provisional
Probab=34.26 E-value=60 Score=30.75 Aligned_cols=31 Identities=26% Similarity=0.423 Sum_probs=27.4
Q ss_pred CEEEEEEeCCeEEEEEEEeecCeeeeEecce
Q psy800 25 SRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV 55 (204)
Q Consensus 25 k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~ 55 (204)
..+.|.+.+|+++.+++.|+|....|.+=.+
T Consensus 115 ~~i~V~~~dg~~~~a~vvg~D~~~DlAvlkv 145 (455)
T PRK10139 115 QKISIQLNDGREFDAKLIGSDDQSDIALLQI 145 (455)
T ss_pred CEEEEEECCCCEEEEEEEEEcCCCCEEEEEe
Confidence 5899999999999999999999999976433
No 170
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=33.88 E-value=79 Score=27.99 Aligned_cols=31 Identities=26% Similarity=0.288 Sum_probs=26.7
Q ss_pred cCCEEEEEEeCCeEEEEEEEEEcCccceEEcc
Q psy800 126 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLED 157 (204)
Q Consensus 126 i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~d 157 (204)
++++|.|.. ++..+.|++.|+|+...|+++.
T Consensus 236 ~g~~V~v~~-~~~~~~G~~~gId~~G~L~i~~ 266 (285)
T PTZ00275 236 KDKKVLIDQ-DNELIVGYLQGLLHDGSLLLLR 266 (285)
T ss_pred CCCEEEEEe-CCCEEEEEEEEECCCCeEEEEe
Confidence 689999875 6788999999999999998864
No 171
>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]
Probab=31.46 E-value=1.9e+02 Score=25.05 Aligned_cols=34 Identities=21% Similarity=0.348 Sum_probs=30.6
Q ss_pred hcCCEEEEEEeCCeEEEEEEEEEcCccceEEcce
Q psy800 125 CIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV 158 (204)
Q Consensus 125 ~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da 158 (204)
.++++|++...++....|+..|+|+...|+++..
T Consensus 188 ~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~ 221 (238)
T COG0340 188 SLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD 221 (238)
T ss_pred cCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence 4789999999888888889999999999999876
No 172
>PRK06955 biotin--protein ligase; Provisional
Probab=30.00 E-value=90 Score=27.74 Aligned_cols=32 Identities=19% Similarity=0.384 Sum_probs=27.1
Q ss_pred hcCCEEEEEEeCCeEEEEEEEeecCeeeeEec
Q psy800 22 CIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLE 53 (204)
Q Consensus 22 ~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~ 53 (204)
+++++|.+...++..+.|+..|.|..=.|+++
T Consensus 247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~ 278 (300)
T PRK06955 247 YAGREVVLLEDGAELARGVAHGIDETGQLLLD 278 (300)
T ss_pred cCCCeEEEEECCCcEEEEEEeeECCCceEEEE
Confidence 34789998766778899999999999999885
No 173
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=28.85 E-value=1.6e+02 Score=23.79 Aligned_cols=26 Identities=15% Similarity=0.300 Sum_probs=23.3
Q ss_pred HhhcCCEEEEEEeCCeEEEEEEEEEc
Q psy800 123 DKCIGSRIHIIMKNDKEIVGTLNGFD 148 (204)
Q Consensus 123 ~~~i~k~V~V~Lk~gr~i~G~L~gfD 148 (204)
..++||.|.+...+|..+.|++.+..
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 46789999999999999999999885
No 174
>KOG1708|consensus
Probab=28.76 E-value=1.2e+02 Score=26.31 Aligned_cols=97 Identities=10% Similarity=0.112 Sum_probs=56.3
Q ss_pred ecCeeeeEecceEEeecCccccccccEEEeee-cccceeeccccccceeecccE-eEEEeeeccCCcccCC------CCC
Q psy800 44 FDDFVNMLLEDVTDCHDSHLLSYFASDLINFI-WGLPMITPITCAYSRSHQYRT-LTHLLYTMTAPSVATN------PST 115 (204)
Q Consensus 44 fD~~mNlvL~~~~E~~~~~~~~~lG~vlIn~~-~g~~~~~PI~~~f~~~~~~~~-v~~~l~~~~~~~~~~~------~~~ 115 (204)
.|.=+-+...|.+|.+.++.++..|.++=-+- .+-+.+.=.|.=|++.-.... ..-.+.-+-||...+. +.-
T Consensus 67 ~d~dw~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~~gsekeg~pgtivk~EaPlhvsk~VmLvdp~d 146 (236)
T KOG1708|consen 67 IDEDWHFFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRHMGSEKEGEPGTIVKSEAPLHVSKQVMLVDPED 146 (236)
T ss_pred cccceeEecCCEEEEEecccCCccceEEEEeecCceEEEcccchhhhhhcccccCCCceEEeecCCceecceeEEECccc
Confidence 46667788899999998888888897764111 122444455555555543332 2223333445553322 222
Q ss_pred CCcHHHHHhhc--CCEEEEEEeCCeEE
Q psy800 116 LLPLELVDKCI--GSRIHIIMKNDKEI 140 (204)
Q Consensus 116 ~~Pl~~L~~~i--~k~V~V~Lk~gr~i 140 (204)
..|-++=-++. |.+|+|.+|.|+.|
T Consensus 147 ~q~te~~wr~~e~GekVRvstrSG~iI 173 (236)
T KOG1708|consen 147 DQPTEVEWRFTEDGEKVRVSTRSGRII 173 (236)
T ss_pred cCCceeeEEEcCCCcEEEEEecccccc
Confidence 33444333333 68899999999866
No 175
>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed
Probab=28.62 E-value=1.6e+02 Score=29.07 Aligned_cols=32 Identities=22% Similarity=0.317 Sum_probs=27.3
Q ss_pred hcCCEEEEEEeCCeEEEEEEEeecCeeeeEec
Q psy800 22 CIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLE 53 (204)
Q Consensus 22 ~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~ 53 (204)
+++++|.+...++.++.|+..|.|..=.|+|+
T Consensus 276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~ 307 (592)
T PRK13325 276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE 307 (592)
T ss_pred cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence 34788988766777899999999999999986
No 176
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=28.41 E-value=1.3e+02 Score=21.84 Aligned_cols=28 Identities=18% Similarity=0.383 Sum_probs=21.0
Q ss_pred HHHHhhcCCEEEEEEeCCe----EEEEEEEEE
Q psy800 120 ELVDKCIGSRIHIIMKNDK----EIVGTLNGF 147 (204)
Q Consensus 120 ~~L~~~i~k~V~V~Lk~gr----~i~G~L~gf 147 (204)
+.|...+|++|.++...|| +-+|+|..-
T Consensus 10 ~~l~~~vG~~V~l~a~~GRkK~~~r~GvL~~t 41 (76)
T PF06257_consen 10 KELESHVGKRVKLKANKGRKKIIEREGVLEET 41 (76)
T ss_dssp HHHHHTTTSEEEEEE--SSS--S-EEEEEEEE
T ss_pred HHHHHcCCCEEEEEEcCCceEEEEEEEEEEee
Confidence 3678899999999999999 568998764
No 177
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=27.62 E-value=89 Score=28.93 Aligned_cols=31 Identities=16% Similarity=0.329 Sum_probs=27.1
Q ss_pred CEEEEEEeCCeEEEEEEEeecCeeeeEecce
Q psy800 25 SRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV 55 (204)
Q Consensus 25 k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~ 55 (204)
..+.|.+.+|+++.+++.++|...+|.|=..
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv 112 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKI 112 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEe
Confidence 4788999999999999999999999977433
No 178
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=27.54 E-value=99 Score=28.62 Aligned_cols=32 Identities=16% Similarity=0.319 Sum_probs=27.6
Q ss_pred CEEEEEEeCCeEEEEEEEEEcCccceEEcceE
Q psy800 128 SRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 159 (204)
Q Consensus 128 k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~ 159 (204)
..+.|.+.||+.+.+++.++|...+|.|=...
T Consensus 82 ~~i~V~~~~~~~~~a~vv~~d~~~DlAllkv~ 113 (428)
T TIGR02037 82 DEITVTLSDGREFKAKLVGKDPRTDIAVLKID 113 (428)
T ss_pred CeEEEEeCCCCEEEEEEEEecCCCCEEEEEec
Confidence 46888899999999999999999998875554
No 179
>COG5316 Uncharacterized conserved protein [Function unknown]
Probab=27.49 E-value=1.5e+02 Score=28.02 Aligned_cols=48 Identities=25% Similarity=0.242 Sum_probs=41.6
Q ss_pred CCCcHHHHHhhcCCEEEEEEeCCeEEEEEEEeecCeeeeEecceEEeec
Q psy800 12 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHD 60 (204)
Q Consensus 12 ~~~P~~~L~~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL~~~~E~~~ 60 (204)
-..|-.++.++++|.|+- -++|++..++|.+-|.-.=+.+.|-.|...
T Consensus 70 l~s~~~l~~~~~GK~v~~-~kdG~~~t~tl~a~d~gv~~~~~~~~~v~~ 117 (421)
T COG5316 70 LLSPGKLVEKSLGKVVRT-RKDGRQTTATLLAGDYGVVLRTGDGVEVLG 117 (421)
T ss_pred ccCchhHHhhhhCcEEEe-cCCCceeEEEEEecCceEEEecCCcEEEEe
Confidence 456889999999999999 899999999999999988888887777653
No 180
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=27.00 E-value=1.5e+02 Score=23.57 Aligned_cols=24 Identities=13% Similarity=0.202 Sum_probs=19.9
Q ss_pred hcCCEEEEEEeCCeEEEEEEEEEc
Q psy800 125 CIGSRIHIIMKNDKEIVGTLNGFD 148 (204)
Q Consensus 125 ~i~k~V~V~Lk~gr~i~G~L~gfD 148 (204)
++.|-+.|.|+||+++...+=|-.
T Consensus 48 A~RKvarVrL~ngk~v~AyIPGeG 71 (124)
T PRK05163 48 ALRKVARVRLTNGFEVTAYIPGEG 71 (124)
T ss_pred hhheEEEEEeCCCCEEEEEcCCCC
Confidence 467789999999999988877655
No 181
>PRK14630 hypothetical protein; Provisional
Probab=24.99 E-value=1.1e+02 Score=24.56 Aligned_cols=30 Identities=17% Similarity=0.243 Sum_probs=23.1
Q ss_pred hhcCCEEEEEEeCCeEEEEEEEeecCeeeeEe
Q psy800 21 KCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLL 52 (204)
Q Consensus 21 ~~~~k~V~V~l~~g~~~~G~L~gfD~~mNlvL 52 (204)
+++|++|.|++.... .+|+|.++|.- ++.|
T Consensus 94 r~~G~~v~V~l~~~~-~~G~L~~~~d~-~i~l 123 (143)
T PRK14630 94 IFEGKKIKLMLDNDF-EEGFILEAKAD-SFIF 123 (143)
T ss_pred HhCCCEEEEEEcCcc-eEEEEEEEeCC-EEEE
Confidence 678999999996644 59999999883 3444
No 182
>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions []. ; PDB: 2E12_B.
Probab=23.68 E-value=97 Score=23.59 Aligned_cols=19 Identities=16% Similarity=0.401 Sum_probs=15.2
Q ss_pred CCEEEEEEeCCeEEEEEEE
Q psy800 24 GSRIHIIMKNDKEIVGTLN 42 (204)
Q Consensus 24 ~k~V~V~l~~g~~~~G~L~ 42 (204)
+.+|.+.|+||+.+.|++.
T Consensus 28 e~~V~l~L~DGs~l~Gtv~ 46 (101)
T PF11607_consen 28 EERVELELDDGSMLRGTVA 46 (101)
T ss_dssp T-EEEEEETTS-EEEEEEC
T ss_pred cceEEEEEcCCCeeeeeec
Confidence 3599999999999999974
No 183
>PRK14635 hypothetical protein; Provisional
Probab=22.79 E-value=1.5e+02 Score=24.09 Aligned_cols=33 Identities=18% Similarity=0.291 Sum_probs=24.8
Q ss_pred CcHHHHHhhcCCEEEEEEe--CCeEEEE---EEEeecCe
Q psy800 14 LPLELVDKCIGSRIHIIMK--NDKEIVG---TLNGFDDF 47 (204)
Q Consensus 14 ~P~~~L~~~~~k~V~V~l~--~g~~~~G---~L~gfD~~ 47 (204)
.|.+|. ++.|+.|.|++. ++..+.| +|.++|.-
T Consensus 90 ~~~~~~-r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~ 127 (162)
T PRK14635 90 LPEDLD-RFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD 127 (162)
T ss_pred CHHHHH-HhCCCEEEEEEecCCCcEEEecceEEEEEcCC
Confidence 344444 678999999886 4678888 99999873
No 184
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=22.22 E-value=48 Score=25.09 Aligned_cols=17 Identities=47% Similarity=0.643 Sum_probs=15.6
Q ss_pred EEEEEEcCccceEEcce
Q psy800 142 GTLNGFDDFVNMLLEDV 158 (204)
Q Consensus 142 G~L~gfD~~mNlVL~da 158 (204)
|+|+|.|.|.|.--++-
T Consensus 1 G~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 1 GTLVGTDEFGNKYYENP 17 (105)
T ss_pred CCEeeEeCCCCEEEeec
Confidence 78999999999998876
No 185
>PRK08477 biotin--protein ligase; Provisional
Probab=21.22 E-value=2.8e+02 Score=23.58 Aligned_cols=35 Identities=6% Similarity=-0.105 Sum_probs=29.0
Q ss_pred hcCCEEEEEEeCCeEEEEEEEEEcCccceEEcceEE
Q psy800 125 CIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTE 160 (204)
Q Consensus 125 ~i~k~V~V~Lk~gr~i~G~L~gfD~~mNlVL~da~E 160 (204)
.+++.|.|. .+++.++|+..+.|+..-|++..-..
T Consensus 173 ~~~~~v~v~-~~~~~~~g~a~~I~~~G~L~v~~~~~ 207 (211)
T PRK08477 173 EKSKSFSFH-IDGKLVSLKDAELLEDGSILINGKKV 207 (211)
T ss_pred HcCCEEEEE-ECCEEEEEEEeeECCCCeEEECCEEe
Confidence 468999986 57899999999999999888876544
No 186
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=21.00 E-value=2.8e+02 Score=22.40 Aligned_cols=26 Identities=15% Similarity=0.300 Sum_probs=23.1
Q ss_pred HhhcCCEEEEEEeCCeEEEEEEEeec
Q psy800 20 DKCIGSRIHIIMKNDKEIVGTLNGFD 45 (204)
Q Consensus 20 ~~~~~k~V~V~l~~g~~~~G~L~gfD 45 (204)
..++||.|.+...+|..+.|++.+..
T Consensus 88 ~slVGk~V~~~~~~g~~~tG~V~~V~ 113 (142)
T PRK09618 88 SELIGKEVEWEGEDGEIVSGTVTSVK 113 (142)
T ss_pred HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence 46889999999899999999999875
Done!