Query 002054
Match_columns 974
No_of_seqs 637 out of 4689
Neff 6.9
Searched_HMMs 46136
Date Thu Mar 28 15:28:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002054.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002054hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1185 Pnp Polyribonucleotide 100.0 1E-165 2E-170 1416.0 65.2 690 55-755 1-691 (692)
2 TIGR02696 pppGpp_PNP guanosine 100.0 6E-163 1E-167 1431.1 80.0 686 57-750 6-718 (719)
3 KOG1067 Predicted RNA-binding 100.0 4E-162 8E-167 1333.0 57.9 734 13-761 6-746 (760)
4 PLN00207 polyribonucleotide nu 100.0 1E-157 3E-162 1410.9 83.0 702 57-762 78-833 (891)
5 PRK11824 polynucleotide phosph 100.0 3E-147 7E-152 1333.3 82.3 690 55-755 1-693 (693)
6 TIGR03591 polynuc_phos polyrib 100.0 7E-147 2E-151 1326.5 79.2 675 66-749 3-684 (684)
7 COG0539 RpsA Ribosomal protein 100.0 7.8E-47 1.7E-51 434.0 26.0 298 657-968 166-507 (541)
8 PRK12269 bifunctional cytidyla 100.0 7.7E-39 1.7E-43 391.8 28.4 302 658-973 468-826 (863)
9 TIGR02065 ECX1 archaeal exosom 100.0 2.4E-38 5.3E-43 338.7 25.9 224 363-605 2-228 (230)
10 PRK03983 exosome complex exonu 100.0 1E-37 2.2E-42 336.9 26.2 225 363-606 8-235 (244)
11 PRK00173 rph ribonuclease PH; 100.0 1.4E-36 3.1E-41 326.4 26.4 218 369-604 1-237 (238)
12 TIGR01966 RNasePH ribonuclease 100.0 1.4E-35 3E-40 318.6 27.0 218 370-603 1-235 (236)
13 PRK11824 polynucleotide phosph 100.0 1.4E-34 3E-39 351.5 37.5 211 380-613 14-232 (693)
14 PRK04282 exosome complex RNA-b 100.0 2.4E-35 5.2E-40 323.3 27.3 232 352-604 8-270 (271)
15 PRK06299 rpsA 30S ribosomal pr 100.0 1.7E-35 3.6E-40 356.6 27.9 281 679-972 197-530 (565)
16 TIGR03591 polynuc_phos polyrib 100.0 9.2E-35 2E-39 352.2 34.2 213 380-614 5-225 (684)
17 TIGR00717 rpsA ribosomal prote 100.0 1.1E-34 2.3E-39 346.3 27.7 300 658-971 162-515 (516)
18 COG0539 RpsA Ribosomal protein 100.0 3.2E-35 6.9E-40 338.4 21.5 286 660-966 86-426 (541)
19 TIGR02065 ECX1 archaeal exosom 100.0 8.4E-35 1.8E-39 311.4 22.5 203 67-279 18-229 (230)
20 COG0689 Rph RNase PH [Translat 100.0 1.4E-34 3.1E-39 301.4 23.1 224 365-604 4-230 (230)
21 PLN00207 polyribonucleotide nu 100.0 6.7E-35 1.4E-39 352.0 22.8 217 67-287 448-683 (891)
22 PRK13806 rpsA 30S ribosomal pr 100.0 2.2E-33 4.7E-38 330.7 28.8 277 679-971 111-448 (491)
23 PRK00173 rph ribonuclease PH; 100.0 1.6E-33 3.6E-38 302.8 22.3 201 67-277 11-237 (238)
24 PRK07899 rpsA 30S ribosomal pr 100.0 3.2E-33 6.9E-38 324.8 26.2 281 679-972 31-363 (486)
25 KOG1068 Exosomal 3'-5' exoribo 100.0 3.1E-33 6.7E-38 289.3 17.7 225 364-606 8-235 (245)
26 TIGR01966 RNasePH ribonuclease 100.0 4.9E-32 1.1E-36 291.1 22.4 203 67-276 10-235 (236)
27 PRK03983 exosome complex exonu 100.0 4E-32 8.7E-37 293.3 21.7 204 67-280 24-236 (244)
28 COG2123 RNase PH-related exori 100.0 7.2E-31 1.6E-35 275.6 26.9 228 356-604 11-271 (272)
29 PRK12269 bifunctional cytidyla 100.0 4.1E-31 8.9E-36 324.0 24.2 278 679-972 394-736 (863)
30 COG1185 Pnp Polyribonucleotide 100.0 6.7E-31 1.4E-35 303.7 23.6 344 380-756 14-382 (692)
31 COG0689 Rph RNase PH [Translat 100.0 3.4E-31 7.3E-36 276.3 18.8 200 67-276 18-229 (230)
32 PRK06299 rpsA 30S ribosomal pr 100.0 2.5E-30 5.4E-35 311.7 27.5 298 653-972 89-444 (565)
33 TIGR02696 pppGpp_PNP guanosine 100.0 1.7E-29 3.7E-34 299.8 32.6 213 380-613 17-254 (719)
34 PRK06676 rpsA 30S ribosomal pr 100.0 5.2E-30 1.1E-34 295.6 25.5 280 679-972 13-347 (390)
35 TIGR00717 rpsA ribosomal prote 100.0 4.9E-28 1.1E-32 289.2 25.8 278 679-973 96-431 (516)
36 PRK00087 4-hydroxy-3-methylbut 100.0 5.7E-28 1.2E-32 293.8 26.5 280 679-972 298-632 (647)
37 PRK13806 rpsA 30S ribosomal pr 100.0 5.4E-27 1.2E-31 276.5 25.5 277 680-973 31-364 (491)
38 PRK07400 30S ribosomal protein 100.0 3.9E-27 8.5E-32 262.4 22.1 230 659-972 11-265 (318)
39 KOG1069 Exosomal 3'-5' exoribo 99.9 2.6E-27 5.6E-32 236.2 16.7 202 378-606 4-211 (217)
40 KOG1614 Exosomal 3'-5' exoribo 99.9 3.2E-26 7E-31 233.6 22.4 233 357-613 11-279 (291)
41 PRK04282 exosome complex RNA-b 99.9 5.3E-26 1.1E-30 249.5 21.9 201 67-276 34-269 (271)
42 KOG1613 Exosomal 3'-5' exoribo 99.9 4.6E-26 1E-30 231.7 17.3 243 348-600 15-297 (298)
43 KOG1069 Exosomal 3'-5' exoribo 99.9 5.9E-25 1.3E-29 219.4 15.3 193 68-278 6-210 (217)
44 COG2123 RNase PH-related exori 99.9 2.6E-24 5.6E-29 226.3 19.1 192 68-277 34-271 (272)
45 KOG1067 Predicted RNA-binding 99.9 7.6E-23 1.6E-27 228.5 18.8 208 379-610 55-271 (760)
46 KOG1068 Exosomal 3'-5' exoribo 99.9 2.9E-23 6.2E-28 215.5 13.9 204 68-280 24-236 (245)
47 KOG1612 Exosomal 3'-5' exoribo 99.9 2.7E-21 6E-26 199.1 23.5 220 366-606 18-277 (288)
48 PF01138 RNase_PH: 3' exoribon 99.9 4.7E-22 1E-26 194.8 15.0 131 378-511 1-132 (132)
49 PRK07899 rpsA 30S ribosomal pr 99.9 2.8E-21 6.1E-26 225.2 17.0 226 653-901 97-368 (486)
50 PRK06676 rpsA 30S ribosomal pr 99.8 6.7E-20 1.5E-24 211.7 18.1 208 679-903 101-354 (390)
51 PRK00087 4-hydroxy-3-methylbut 99.8 1.4E-18 3.1E-23 211.8 16.4 228 653-902 364-638 (647)
52 COG1098 VacB Predicted RNA bin 99.7 4.4E-18 9.5E-23 158.0 5.6 81 680-760 2-82 (129)
53 PF01138 RNase_PH: 3' exoribon 99.7 2.6E-17 5.7E-22 161.2 9.4 122 68-197 3-132 (132)
54 KOG1614 Exosomal 3'-5' exoribo 99.6 1E-14 2.2E-19 149.9 17.6 204 68-286 33-279 (291)
55 PRK07400 30S ribosomal protein 99.6 4.4E-15 9.5E-20 166.0 14.9 169 653-845 93-274 (318)
56 KOG1070 rRNA processing protei 99.5 2.9E-13 6.3E-18 165.3 20.5 275 679-973 881-1233(1710)
57 KOG1070 rRNA processing protei 99.5 1.6E-13 3.5E-18 167.4 17.6 273 679-966 983-1316(1710)
58 COG2996 Predicted RNA-bindinin 99.5 8.1E-13 1.8E-17 138.9 19.7 208 681-972 3-216 (287)
59 PTZ00248 eukaryotic translatio 99.5 4.1E-14 8.9E-19 155.4 10.5 93 681-773 15-116 (319)
60 PRK08582 hypothetical protein; 99.5 1.2E-13 2.7E-18 136.0 10.5 82 680-761 2-83 (139)
61 cd05704 S1_Rrp5_repeat_hs13 S1 99.5 9E-14 1.9E-18 121.8 8.0 71 681-752 1-72 (72)
62 cd05705 S1_Rrp5_repeat_hs14 S1 99.4 2.4E-13 5.3E-18 119.6 7.9 70 681-750 1-74 (74)
63 cd05686 S1_pNO40 S1_pNO40: pNO 99.4 1.1E-12 2.4E-17 115.3 9.6 71 681-751 1-72 (73)
64 cd05698 S1_Rrp5_repeat_hs6_sc5 99.4 2E-12 4.4E-17 112.3 8.3 69 684-752 1-70 (70)
65 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.4 2E-12 4.4E-17 112.9 8.1 68 684-751 1-71 (71)
66 PF00575 S1: S1 RNA binding do 99.3 4E-12 8.7E-17 111.7 9.1 72 681-752 2-74 (74)
67 cd04461 S1_Rrp5_repeat_hs8_sc7 99.3 2.9E-12 6.3E-17 115.4 8.1 73 679-751 10-83 (83)
68 cd05703 S1_Rrp5_repeat_hs12_sc 99.3 4.4E-12 9.5E-17 111.4 8.5 69 684-752 1-72 (73)
69 cd04452 S1_IF2_alpha S1_IF2_al 99.3 6.3E-12 1.4E-16 110.9 9.3 73 681-753 1-76 (76)
70 COG1098 VacB Predicted RNA bin 99.3 1.8E-12 4E-17 120.8 5.8 67 907-973 2-75 (129)
71 cd05684 S1_DHX8_helicase S1_DH 99.3 8.8E-12 1.9E-16 111.2 10.0 74 684-758 1-78 (79)
72 PRK05807 hypothetical protein; 99.3 8.5E-12 1.8E-16 122.7 10.5 75 680-755 2-76 (136)
73 cd05706 S1_Rrp5_repeat_sc10 S1 99.3 8.7E-12 1.9E-16 109.3 9.5 72 681-752 1-73 (73)
74 PRK07252 hypothetical protein; 99.3 8.6E-12 1.9E-16 119.9 10.0 76 682-757 2-78 (120)
75 PHA02945 interferon resistance 99.3 1.1E-11 2.3E-16 109.4 9.1 74 680-756 8-86 (88)
76 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.3 7.8E-12 1.7E-16 108.5 8.2 68 684-751 1-69 (69)
77 PF03726 PNPase: Polyribonucle 99.3 1.7E-11 3.6E-16 110.5 10.3 80 294-375 1-83 (83)
78 cd05707 S1_Rrp5_repeat_sc11 S1 99.3 9.3E-12 2E-16 107.7 7.5 67 684-750 1-68 (68)
79 cd05694 S1_Rrp5_repeat_hs2_sc2 99.3 2.8E-11 6.1E-16 106.5 9.6 71 680-756 1-73 (74)
80 cd05691 S1_RPS1_repeat_ec6 S1_ 99.2 2.7E-11 6E-16 105.9 9.1 71 684-754 1-72 (73)
81 cd05692 S1_RPS1_repeat_hs4 S1_ 99.2 3.2E-11 6.9E-16 103.8 9.1 69 684-752 1-69 (69)
82 cd05690 S1_RPS1_repeat_ec5 S1_ 99.2 2.4E-11 5.3E-16 105.1 7.8 67 684-750 1-69 (69)
83 cd05708 S1_Rrp5_repeat_sc12 S1 99.2 5E-11 1.1E-15 105.3 9.4 73 682-754 1-75 (77)
84 COG1093 SUI2 Translation initi 99.2 9.2E-12 2E-16 130.6 5.3 78 680-757 8-88 (269)
85 cd05687 S1_RPS1_repeat_ec1_hs1 99.2 5.4E-11 1.2E-15 103.4 8.6 69 684-752 1-70 (70)
86 PRK08059 general stress protei 99.2 5.9E-11 1.3E-15 115.0 9.7 80 679-758 3-83 (123)
87 cd05689 S1_RPS1_repeat_ec4 S1_ 99.2 8.8E-11 1.9E-15 102.7 8.4 70 681-750 1-72 (72)
88 KOG1612 Exosomal 3'-5' exoribo 99.2 2.6E-09 5.7E-14 111.3 20.5 201 67-276 31-274 (288)
89 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.1 1.1E-10 2.4E-15 105.8 8.3 75 680-754 3-81 (86)
90 cd04472 S1_PNPase S1_PNPase: P 99.1 1.7E-10 3.6E-15 99.3 8.7 68 684-751 1-68 (68)
91 cd05694 S1_Rrp5_repeat_hs2_sc2 99.1 2.6E-10 5.7E-15 100.4 9.4 65 907-971 1-68 (74)
92 cd05685 S1_Tex S1_Tex: The C-t 99.1 1.5E-10 3.3E-15 99.3 7.4 67 684-750 1-68 (68)
93 KOG1613 Exosomal 3'-5' exoribo 99.1 3.5E-10 7.6E-15 116.6 10.9 195 68-271 47-295 (298)
94 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.1 2.4E-10 5.2E-15 98.4 7.9 65 684-750 1-66 (66)
95 cd04453 S1_RNase_E S1_RNase_E: 99.1 2.8E-10 6.1E-15 103.6 8.6 73 679-751 3-81 (88)
96 cd05705 S1_Rrp5_repeat_hs14 S1 99.1 3.2E-10 6.9E-15 99.9 8.6 59 908-966 1-69 (74)
97 cd04465 S1_RPS1_repeat_ec2_hs2 99.1 4.1E-10 9E-15 97.1 8.6 66 684-752 1-67 (67)
98 cd05693 S1_Rrp5_repeat_hs1_sc1 99.1 2.2E-10 4.7E-15 106.9 6.6 74 681-754 1-97 (100)
99 cd05703 S1_Rrp5_repeat_hs12_sc 99.0 1.1E-09 2.4E-14 96.2 9.3 62 911-972 1-72 (73)
100 PRK03987 translation initiatio 99.0 7.1E-10 1.5E-14 120.5 9.3 78 680-757 5-85 (262)
101 PF00575 S1: S1 RNA binding do 99.0 2.1E-09 4.5E-14 94.4 10.1 65 907-971 1-73 (74)
102 cd05688 S1_RPS1_repeat_ec3 S1_ 99.0 1.1E-09 2.4E-14 94.1 8.1 67 683-750 1-68 (68)
103 cd04471 S1_RNase_R S1_RNase_R: 99.0 2.6E-09 5.5E-14 95.8 9.7 69 683-751 1-82 (83)
104 smart00316 S1 Ribosomal protei 99.0 2.1E-09 4.5E-14 92.6 8.7 71 682-752 1-72 (72)
105 cd04454 S1_Rrp4_like S1_Rrp4_l 99.0 1.9E-09 4.2E-14 96.8 8.8 73 681-753 4-76 (82)
106 cd04473 S1_RecJ_like S1_RecJ_l 99.0 4.2E-09 9.1E-14 93.5 10.0 68 904-972 10-77 (77)
107 COG2183 Tex Transcriptional ac 99.0 8E-10 1.7E-14 131.8 7.0 78 680-757 655-733 (780)
108 PRK08582 hypothetical protein; 98.9 3.5E-09 7.7E-14 104.5 10.1 66 907-972 2-74 (139)
109 cd04461 S1_Rrp5_repeat_hs8_sc7 98.9 2.3E-09 5E-14 96.5 8.0 68 904-971 8-83 (83)
110 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.9 3.4E-09 7.4E-14 92.6 8.5 61 911-971 1-71 (71)
111 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.9 3.4E-09 7.5E-14 91.9 8.4 61 911-971 1-69 (69)
112 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.9 4E-09 8.8E-14 90.8 8.7 57 911-967 1-62 (66)
113 cd05704 S1_Rrp5_repeat_hs13 S1 98.9 4.2E-09 9E-14 92.3 8.2 63 908-971 1-71 (72)
114 cd05706 S1_Rrp5_repeat_sc10 S1 98.9 7.8E-09 1.7E-13 90.6 9.9 64 908-971 1-72 (73)
115 cd05702 S1_Rrp5_repeat_hs11_sc 98.9 3.6E-09 7.7E-14 92.1 7.5 64 684-747 1-66 (70)
116 cd04473 S1_RecJ_like S1_RecJ_l 98.9 8.1E-09 1.7E-13 91.7 9.5 65 679-751 12-76 (77)
117 cd05698 S1_Rrp5_repeat_hs6_sc5 98.9 6.3E-09 1.4E-13 90.4 8.2 61 911-971 1-69 (70)
118 cd05686 S1_pNO40 S1_pNO40: pNO 98.9 1.3E-08 2.8E-13 89.4 9.9 63 909-971 2-72 (73)
119 cd05707 S1_Rrp5_repeat_sc11 S1 98.9 7.3E-09 1.6E-13 89.6 8.1 56 911-966 1-63 (68)
120 PRK05807 hypothetical protein; 98.8 1.3E-08 2.8E-13 100.2 10.1 65 907-972 2-73 (136)
121 PF03725 RNase_PH_C: 3' exorib 98.8 1.1E-08 2.4E-13 88.5 8.3 65 200-264 1-68 (68)
122 cd05689 S1_RPS1_repeat_ec4 S1_ 98.8 1.4E-08 2.9E-13 88.8 8.6 59 908-966 1-67 (72)
123 cd05690 S1_RPS1_repeat_ec5 S1_ 98.8 1.4E-08 3.1E-13 87.7 7.7 56 911-966 1-64 (69)
124 cd02393 PNPase_KH Polynucleoti 98.8 6.6E-09 1.4E-13 88.0 5.1 59 615-673 1-60 (61)
125 cd00164 S1_like S1_like: Ribos 98.8 1.5E-08 3.3E-13 85.4 7.0 64 687-750 1-65 (65)
126 cd05692 S1_RPS1_repeat_hs4 S1_ 98.8 3.6E-08 7.8E-13 84.6 9.3 61 911-971 1-68 (69)
127 PRK07252 hypothetical protein; 98.8 3.8E-08 8.2E-13 94.8 9.7 65 909-973 2-74 (120)
128 cd05708 S1_Rrp5_repeat_sc12 S1 98.7 4.2E-08 9.2E-13 86.5 9.1 65 909-973 1-74 (77)
129 PTZ00248 eukaryotic translatio 98.7 2E-08 4.3E-13 111.0 8.3 70 903-972 9-89 (319)
130 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.7 5.1E-08 1.1E-12 88.3 9.0 65 908-972 4-79 (86)
131 cd05691 S1_RPS1_repeat_ec6 S1_ 98.7 5.4E-08 1.2E-12 85.0 8.6 62 911-972 1-70 (73)
132 cd05693 S1_Rrp5_repeat_hs1_sc1 98.7 2.8E-08 6.1E-13 92.7 7.2 65 908-972 1-95 (100)
133 cd04460 S1_RpoE S1_RpoE: RpoE, 98.7 6.8E-08 1.5E-12 90.0 9.3 75 685-760 1-92 (99)
134 cd05687 S1_RPS1_repeat_ec1_hs1 98.7 8.9E-08 1.9E-12 83.1 8.9 61 911-971 1-69 (70)
135 cd05684 S1_DHX8_helicase S1_DH 98.7 9.2E-08 2E-12 85.2 9.2 61 911-972 1-72 (79)
136 cd04452 S1_IF2_alpha S1_IF2_al 98.7 1.4E-07 3E-12 83.1 10.0 64 909-972 2-75 (76)
137 smart00316 S1 Ribosomal protei 98.7 1.2E-07 2.5E-12 81.6 9.2 63 909-971 1-71 (72)
138 PRK13763 putative RNA-processi 98.7 4.2E-08 9.2E-13 101.3 7.2 83 616-698 3-96 (180)
139 cd04465 S1_RPS1_repeat_ec2_hs2 98.7 1.3E-07 2.9E-12 81.4 9.2 60 911-971 1-66 (67)
140 cd05702 S1_Rrp5_repeat_hs11_sc 98.6 1.1E-07 2.4E-12 82.8 8.2 58 911-968 1-67 (70)
141 PRK08059 general stress protei 98.6 1.2E-07 2.6E-12 92.0 9.3 68 905-972 2-77 (123)
142 cd05685 S1_Tex S1_Tex: The C-t 98.6 1.1E-07 2.4E-12 81.4 8.1 58 911-968 1-66 (68)
143 cd04471 S1_RNase_R S1_RNase_R: 98.6 1.6E-07 3.4E-12 84.2 8.9 62 910-971 1-82 (83)
144 cd04453 S1_RNase_E S1_RNase_E: 98.6 1.3E-07 2.8E-12 86.2 8.2 61 906-966 3-75 (88)
145 PRK04163 exosome complex RNA-b 98.6 9.9E-08 2.2E-12 102.7 8.8 88 680-773 60-151 (235)
146 PRK09521 exosome complex RNA-b 98.6 8.8E-08 1.9E-12 99.9 8.0 73 679-753 60-142 (189)
147 TIGR03665 arCOG04150 arCOG0415 98.6 5.5E-08 1.2E-12 99.8 6.3 78 620-697 2-89 (172)
148 cd04472 S1_PNPase S1_PNPase: P 98.6 2.4E-07 5.1E-12 79.6 8.8 60 911-970 1-67 (68)
149 cd04455 S1_NusA S1_NusA: N-uti 98.5 3.9E-07 8.4E-12 78.7 7.7 63 682-751 2-67 (67)
150 cd04454 S1_Rrp4_like S1_Rrp4_l 98.5 8.3E-07 1.8E-11 79.7 9.4 65 909-973 5-76 (82)
151 TIGR02063 RNase_R ribonuclease 98.4 9.2E-07 2E-11 110.1 12.0 72 680-751 624-708 (709)
152 cd04455 S1_NusA S1_NusA: N-uti 98.4 1E-06 2.3E-11 76.0 8.8 55 909-964 2-57 (67)
153 PHA02945 interferon resistance 98.4 7.5E-07 1.6E-11 79.1 7.8 62 909-972 10-82 (88)
154 cd05688 S1_RPS1_repeat_ec3 S1_ 98.4 8.8E-07 1.9E-11 76.0 7.8 55 910-965 1-62 (68)
155 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.4 1E-06 2.2E-11 81.0 7.7 73 681-753 4-86 (92)
156 PF03725 RNase_PH_C: 3' exorib 98.4 7.9E-07 1.7E-11 76.9 6.2 67 514-591 1-68 (68)
157 PRK09521 exosome complex RNA-b 98.3 2.9E-06 6.2E-11 88.6 11.1 93 872-972 27-141 (189)
158 COG1093 SUI2 Translation initi 98.3 5.4E-07 1.2E-11 95.2 5.6 63 909-971 10-82 (269)
159 TIGR00448 rpoE DNA-directed RN 98.3 2.7E-06 5.9E-11 88.0 9.9 76 680-756 78-170 (179)
160 PRK03987 translation initiatio 98.3 2.5E-06 5.5E-11 93.0 9.0 65 908-972 6-80 (262)
161 PRK09202 nusA transcription el 98.2 2.2E-06 4.8E-11 100.5 7.2 95 871-966 86-190 (470)
162 PRK11642 exoribonuclease R; Pr 98.2 8E-06 1.7E-10 102.2 12.2 73 681-753 641-726 (813)
163 TIGR00358 3_prime_RNase VacB a 98.2 7.7E-06 1.7E-10 100.7 11.8 71 681-751 570-653 (654)
164 cd00164 S1_like S1_like: Ribos 98.2 4.1E-06 8.8E-11 70.5 6.5 52 914-965 1-59 (65)
165 COG1095 RPB7 DNA-directed RNA 98.2 4.6E-06 1E-10 84.5 7.7 76 679-755 77-169 (183)
166 PRK09202 nusA transcription el 98.1 4.4E-06 9.6E-11 98.0 7.4 68 679-753 128-200 (470)
167 PRK08563 DNA-directed RNA poly 98.1 1.4E-05 3.1E-10 83.3 9.4 75 679-754 77-168 (187)
168 cd04460 S1_RpoE S1_RpoE: RpoE, 97.9 3.8E-05 8.2E-10 71.6 8.7 52 912-964 1-70 (99)
169 PHA02858 EIF2a-like PKR inhibi 97.9 2.2E-05 4.9E-10 69.0 6.0 70 680-751 13-85 (86)
170 cd02395 SF1_like-KH Splicing f 97.9 1.5E-05 3.2E-10 76.8 5.2 54 624-677 14-93 (120)
171 PRK04163 exosome complex RNA-b 97.8 6.7E-05 1.5E-09 81.0 9.7 65 908-972 61-136 (235)
172 COG2183 Tex Transcriptional ac 97.8 2.5E-05 5.4E-10 94.2 6.3 69 904-972 652-728 (780)
173 TIGR02063 RNase_R ribonuclease 97.8 5.1E-05 1.1E-09 94.7 9.1 65 907-971 624-708 (709)
174 PF13509 S1_2: S1 domain; PDB: 97.8 8.4E-05 1.8E-09 63.0 7.6 61 683-752 1-61 (61)
175 TIGR01953 NusA transcription t 97.7 4.2E-05 9.2E-10 86.4 6.6 94 870-964 82-186 (341)
176 PRK12327 nusA transcription el 97.7 4.8E-05 1E-09 86.5 6.5 95 870-965 85-189 (362)
177 TIGR01953 NusA transcription t 97.6 0.00023 5.1E-09 80.5 10.8 66 682-754 130-199 (341)
178 PRK12327 nusA transcription el 97.6 0.00031 6.7E-09 80.0 10.6 68 679-753 128-200 (362)
179 PRK11642 exoribonuclease R; Pr 97.6 0.00019 4.2E-09 90.0 9.3 65 909-973 642-726 (813)
180 cd02394 vigilin_like_KH K homo 97.6 0.00014 3.1E-09 61.5 5.7 55 618-673 2-61 (62)
181 TIGR00757 RNaseEG ribonuclease 97.5 0.00018 3.8E-09 83.7 8.1 63 680-743 22-98 (414)
182 KOG2916 Translation initiation 97.5 4.7E-05 1E-09 80.3 2.9 78 680-757 13-93 (304)
183 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.5 0.00049 1.1E-08 62.3 8.5 73 681-754 4-76 (86)
184 cd05791 S1_CSL4 S1_CSL4: CSL4, 97.5 0.00041 8.9E-09 63.8 8.1 64 909-972 5-85 (92)
185 COG1097 RRP4 RNA-binding prote 97.5 0.00041 8.9E-09 73.4 9.0 88 680-773 61-152 (239)
186 COG2996 Predicted RNA-bindinin 97.5 0.00016 3.5E-09 77.2 5.6 94 683-788 155-248 (287)
187 TIGR00448 rpoE DNA-directed RN 97.4 0.0006 1.3E-08 70.7 8.7 53 909-962 80-150 (179)
188 PF00013 KH_1: KH domain syndr 97.4 0.00031 6.6E-09 59.1 5.2 55 618-673 2-60 (60)
189 TIGR00358 3_prime_RNase VacB a 97.4 0.00046 1E-08 85.3 8.9 59 909-967 571-648 (654)
190 PRK05054 exoribonuclease II; P 97.3 0.0014 3E-08 80.8 11.7 70 682-751 558-643 (644)
191 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.2 0.0011 2.4E-08 60.4 7.9 60 683-743 1-71 (88)
192 COG1096 Predicted RNA-binding 97.2 0.00034 7.4E-09 71.1 4.8 72 680-753 61-142 (188)
193 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.2 0.0011 2.3E-08 57.7 6.6 66 684-752 1-72 (72)
194 COG1095 RPB7 DNA-directed RNA 97.2 0.0007 1.5E-08 68.9 6.2 57 909-966 80-154 (183)
195 PRK08563 DNA-directed RNA poly 97.2 0.0016 3.4E-08 68.0 9.0 57 908-965 79-153 (187)
196 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.0 0.0036 7.7E-08 56.7 8.7 66 909-974 5-76 (86)
197 PTZ00162 DNA-directed RNA poly 97.0 0.0026 5.6E-08 65.7 8.6 74 679-753 77-165 (176)
198 cd04462 S1_RNAPII_Rpb7 S1_RNAP 96.9 0.0041 8.9E-08 56.8 8.4 55 910-965 1-73 (88)
199 TIGR02062 RNase_B exoribonucle 96.8 0.0067 1.4E-07 74.8 11.1 69 682-750 554-638 (639)
200 PF13509 S1_2: S1 domain; PDB: 96.7 0.0067 1.5E-07 51.4 7.7 60 910-971 1-60 (61)
201 cd00105 KH-I K homology RNA-bi 96.7 0.0023 5E-08 54.1 4.8 55 618-673 2-63 (64)
202 PF10447 EXOSC1: Exosome compo 96.7 0.0034 7.4E-08 56.3 5.9 61 681-741 2-82 (82)
203 COG0557 VacB Exoribonuclease R 96.7 0.0065 1.4E-07 76.0 10.6 73 680-752 619-704 (706)
204 COG1107 Archaea-specific RecJ- 96.7 0.0044 9.4E-08 72.4 7.8 71 679-755 118-189 (715)
205 PF10447 EXOSC1: Exosome compo 96.6 0.0047 1E-07 55.4 6.0 53 909-961 3-82 (82)
206 PRK05054 exoribonuclease II; P 96.5 0.0068 1.5E-07 74.8 8.4 60 909-968 558-639 (644)
207 TIGR00757 RNaseEG ribonuclease 96.3 0.0078 1.7E-07 70.2 7.6 55 906-960 21-96 (414)
208 PRK12328 nusA transcription el 96.3 0.014 3E-07 66.4 8.7 57 909-966 137-195 (374)
209 smart00322 KH K homology RNA-b 96.2 0.011 2.4E-07 49.8 6.0 60 616-676 3-67 (69)
210 cd05699 S1_Rrp5_repeat_hs7 S1_ 96.2 0.017 3.8E-07 50.3 6.8 55 911-967 1-66 (72)
211 TIGR03665 arCOG04150 arCOG0415 96.1 0.0089 1.9E-07 61.5 5.7 51 626-677 99-149 (172)
212 PRK12328 nusA transcription el 96.0 0.035 7.6E-07 63.2 10.1 87 660-753 105-206 (374)
213 PRK11712 ribonuclease G; Provi 96.0 0.015 3.3E-07 68.9 7.5 62 681-743 36-111 (489)
214 PRK13763 putative RNA-processi 95.9 0.011 2.4E-07 61.4 5.4 51 626-677 105-155 (180)
215 COG1107 Archaea-specific RecJ- 95.9 0.0064 1.4E-07 71.1 3.9 61 904-964 116-177 (715)
216 PRK10811 rne ribonuclease E; R 95.9 0.013 2.9E-07 72.7 6.8 61 681-741 36-107 (1068)
217 cd02396 PCBP_like_KH K homolog 95.9 0.015 3.4E-07 49.7 5.4 54 619-673 3-64 (65)
218 PRK12329 nusA transcription el 95.9 0.026 5.6E-07 65.3 8.7 56 909-964 151-212 (449)
219 PHA02858 EIF2a-like PKR inhibi 95.7 0.029 6.4E-07 49.8 6.4 56 908-965 14-78 (86)
220 PTZ00162 DNA-directed RNA poly 95.6 0.032 6.9E-07 57.7 7.2 55 909-964 80-153 (176)
221 COG1097 RRP4 RNA-binding prote 95.3 0.059 1.3E-06 57.4 8.1 65 909-973 63-138 (239)
222 KOG1856 Transcription elongati 95.3 0.025 5.4E-07 70.7 6.0 75 680-754 982-1060(1299)
223 TIGR02062 RNase_B exoribonucle 95.2 0.051 1.1E-06 67.2 8.4 58 911-968 558-635 (639)
224 COG0557 VacB Exoribonuclease R 95.1 0.051 1.1E-06 68.1 8.4 61 905-965 617-696 (706)
225 PRK12329 nusA transcription el 94.5 0.2 4.3E-06 58.2 10.4 67 681-753 150-225 (449)
226 KOG2191 RNA-binding protein NO 94.3 0.34 7.4E-06 53.4 10.9 120 558-688 82-213 (402)
227 PF13014 KH_3: KH domain 93.3 0.042 9.1E-07 43.0 1.4 27 627-653 2-28 (43)
228 KOG3409 Exosomal 3'-5' exoribo 92.8 0.35 7.5E-06 48.8 7.2 58 909-966 67-141 (193)
229 KOG0119 Splicing factor 1/bran 92.7 0.5 1.1E-05 54.8 9.3 88 591-679 111-230 (554)
230 COG1530 CafA Ribonucleases G a 92.5 0.14 3E-06 61.2 4.9 62 680-742 34-102 (487)
231 KOG1676 K-homology type RNA bi 91.9 0.44 9.5E-06 56.6 7.9 61 617-678 231-299 (600)
232 PRK10811 rne ribonuclease E; R 91.3 0.42 9.1E-06 60.0 7.1 55 909-963 37-109 (1068)
233 PF10246 MRP-S35: Mitochondria 90.8 1 2.3E-05 41.8 7.5 63 900-962 13-75 (104)
234 KOG1856 Transcription elongati 90.5 0.33 7.2E-06 61.3 5.3 64 905-968 980-1053(1299)
235 PRK12442 translation initiatio 90.4 1.2 2.7E-05 40.2 7.4 64 686-753 8-73 (87)
236 COG1094 Predicted RNA-binding 90.2 0.61 1.3E-05 48.4 6.1 64 614-677 6-75 (194)
237 KOG3409 Exosomal 3'-5' exoribo 90.1 0.92 2E-05 45.9 7.0 73 681-753 66-148 (193)
238 TIGR00008 infA translation ini 89.7 1.4 3.1E-05 38.2 7.0 59 686-748 6-66 (68)
239 COG1096 Predicted RNA-binding 89.2 0.91 2E-05 46.8 6.5 58 905-962 59-133 (188)
240 PRK11712 ribonuclease G; Provi 88.3 0.97 2.1E-05 54.0 6.9 55 907-961 35-110 (489)
241 TIGR03319 YmdA_YtgF conserved 88.2 1.9 4.1E-05 52.1 9.3 62 616-677 204-268 (514)
242 COG1094 Predicted RNA-binding 88.0 0.53 1.1E-05 48.9 3.9 59 627-687 113-171 (194)
243 PRK00106 hypothetical protein; 87.4 2.5 5.3E-05 51.1 9.6 62 616-677 225-289 (535)
244 KOG3298 DNA-directed RNA polym 87.2 2.5 5.4E-05 42.5 7.8 62 680-742 78-150 (170)
245 KOG2193 IGF-II mRNA-binding pr 86.8 1.2 2.5E-05 50.8 5.9 62 587-652 255-316 (584)
246 KOG1676 K-homology type RNA bi 86.1 2.2 4.8E-05 50.9 8.0 93 582-677 284-387 (600)
247 PRK12704 phosphodiesterase; Pr 85.9 2.9 6.2E-05 50.6 9.2 62 616-677 210-274 (520)
248 KOG2916 Translation initiation 85.8 0.59 1.3E-05 50.2 2.9 58 909-966 15-81 (304)
249 cd02134 NusA_KH NusA_K homolog 84.3 0.59 1.3E-05 39.6 1.7 36 616-651 25-60 (61)
250 KOG3298 DNA-directed RNA polym 83.6 4.3 9.4E-05 40.8 7.6 60 909-968 80-156 (170)
251 PF08292 RNA_pol_Rbc25: RNA po 83.3 5 0.00011 39.0 7.8 61 683-743 3-76 (122)
252 PF00313 CSD: 'Cold-shock' DNA 82.0 9.7 0.00021 32.4 8.4 55 914-969 1-61 (66)
253 PF00313 CSD: 'Cold-shock' DNA 79.4 17 0.00036 30.9 9.0 54 687-745 1-57 (66)
254 PRK09937 stationary phase/star 79.1 10 0.00022 33.6 7.6 62 688-754 3-67 (74)
255 PRK13764 ATPase; Provisional 78.7 0.99 2.1E-05 55.2 1.6 144 589-738 455-601 (602)
256 PRK15464 cold shock-like prote 78.3 9.4 0.0002 33.4 7.1 55 687-746 5-62 (70)
257 KOG2190 PolyC-binding proteins 76.7 2 4.4E-05 51.2 3.4 64 615-679 137-208 (485)
258 PRK12705 hypothetical protein; 76.6 6.1 0.00013 47.5 7.3 62 616-677 198-262 (508)
259 PRK10943 cold shock-like prote 75.6 15 0.00032 32.0 7.6 55 686-745 3-60 (69)
260 PRK09890 cold shock protein Cs 74.9 17 0.00037 31.7 7.8 55 687-746 5-62 (70)
261 PRK09507 cspE cold shock prote 74.7 15 0.00033 31.9 7.4 55 686-745 3-60 (69)
262 PRK15463 cold shock-like prote 74.6 8.8 0.00019 33.5 5.9 54 687-745 5-61 (70)
263 COG0361 InfA Translation initi 73.7 19 0.0004 32.0 7.6 65 684-752 6-72 (75)
264 PRK14998 cold shock-like prote 73.6 16 0.00035 32.2 7.4 60 688-752 3-65 (73)
265 COG1855 ATPase (PilT family) [ 73.5 3.7 7.9E-05 47.9 4.1 60 592-652 463-522 (604)
266 PRK15464 cold shock-like prote 72.3 19 0.00041 31.5 7.4 57 914-971 5-67 (70)
267 PRK12442 translation initiatio 71.5 12 0.00027 34.0 6.1 52 913-964 8-63 (87)
268 cd05700 S1_Rrp5_repeat_hs9 S1_ 70.8 14 0.00031 31.0 5.8 53 911-963 1-56 (65)
269 TIGR00008 infA translation ini 70.6 14 0.0003 32.2 6.1 53 913-965 6-62 (68)
270 PF03459 TOBE: TOBE domain; I 66.2 12 0.00026 31.4 5.0 48 912-959 5-58 (64)
271 cd05793 S1_IF1A S1_IF1A: Trans 66.0 17 0.00037 32.4 5.9 58 687-749 2-61 (77)
272 PRK10354 RNA chaperone/anti-te 65.5 35 0.00076 29.7 7.7 54 687-745 5-61 (70)
273 TIGR02381 cspD cold shock doma 65.3 25 0.00053 30.5 6.7 54 688-746 3-59 (68)
274 PF08292 RNA_pol_Rbc25: RNA po 65.2 24 0.00052 34.4 7.3 54 910-963 3-76 (122)
275 PF10246 MRP-S35: Mitochondria 64.1 29 0.00063 32.6 7.1 55 681-742 21-75 (104)
276 PRK04012 translation initiatio 63.4 23 0.00051 33.2 6.6 62 684-750 20-83 (100)
277 KOG0336 ATP-dependent RNA heli 61.7 7.1 0.00015 44.8 3.3 59 618-677 49-111 (629)
278 PRK00468 hypothetical protein; 61.5 4.3 9.4E-05 36.0 1.3 25 618-642 32-56 (75)
279 cd04458 CSP_CDS Cold-Shock Pro 61.4 41 0.00089 28.4 7.4 53 688-746 2-58 (65)
280 PRK02821 hypothetical protein; 59.8 4.9 0.00011 35.8 1.3 28 616-643 31-58 (77)
281 COG1530 CafA Ribonucleases G a 59.5 12 0.00025 45.2 4.8 60 905-964 32-104 (487)
282 KOG2191 RNA-binding protein NO 58.4 17 0.00037 40.6 5.4 60 618-677 41-109 (402)
283 KOG4078 Putative mitochondrial 58.1 20 0.00043 35.2 5.2 54 909-962 81-134 (173)
284 COG5176 MSL5 Splicing factor ( 58.0 7.5 0.00016 40.5 2.5 54 625-678 163-220 (269)
285 PF07076 DUF1344: Protein of u 56.2 36 0.00079 28.9 5.8 52 912-964 3-54 (61)
286 PF09883 DUF2110: Uncharacteri 55.3 46 0.00099 35.4 7.7 69 684-753 75-148 (225)
287 COG1278 CspC Cold shock protei 55.3 34 0.00073 29.8 5.6 57 688-749 3-62 (67)
288 PRK09937 stationary phase/star 55.2 60 0.0013 28.7 7.4 55 915-970 3-63 (74)
289 KOG2192 PolyC-binding hnRNP-K 54.2 21 0.00045 38.6 5.1 57 618-674 317-379 (390)
290 PRK10354 RNA chaperone/anti-te 53.8 68 0.0015 27.9 7.5 52 914-967 5-63 (70)
291 PRK09507 cspE cold shock prote 53.6 49 0.0011 28.8 6.5 52 913-966 3-61 (69)
292 PRK10943 cold shock-like prote 53.2 62 0.0014 28.1 7.1 54 913-967 3-62 (69)
293 KOG3013 Exosomal 3'-5' exoribo 52.8 12 0.00026 40.4 3.1 75 680-754 82-166 (301)
294 PRK13343 F0F1 ATP synthase sub 52.1 2.7E+02 0.0059 33.8 14.6 169 114-330 268-439 (502)
295 PRK09890 cold shock protein Cs 52.1 82 0.0018 27.5 7.7 56 914-970 5-66 (70)
296 COG1837 Predicted RNA-binding 51.7 7.6 0.00017 34.5 1.2 25 618-642 32-56 (76)
297 KOG1588 RNA-binding protein Sa 51.6 33 0.00072 37.5 6.2 28 625-652 107-134 (259)
298 KOG1004 Exosomal 3'-5' exoribo 51.2 62 0.0014 34.3 7.8 71 680-752 62-133 (230)
299 COG1545 Predicted nucleic-acid 50.9 57 0.0012 32.5 7.4 60 909-968 62-130 (140)
300 TIGR00638 Mop molybdenum-pteri 49.2 51 0.0011 27.9 6.0 50 911-960 6-61 (69)
301 PRK15463 cold shock-like prote 49.0 61 0.0013 28.3 6.4 54 914-968 5-64 (70)
302 TIGR03324 alt_F1F0_F1_al alter 47.9 3.2E+02 0.0069 33.1 14.2 168 113-330 267-439 (497)
303 PRK14998 cold shock-like prote 47.2 91 0.002 27.5 7.2 55 915-970 3-63 (73)
304 PF13184 KH_5: NusA-like KH do 46.5 13 0.00028 32.4 1.8 27 625-651 17-44 (69)
305 COG0361 InfA Translation initi 46.3 72 0.0016 28.4 6.3 54 911-964 6-63 (75)
306 smart00652 eIF1a eukaryotic tr 46.1 58 0.0013 29.5 6.0 60 686-750 6-67 (83)
307 PRK08406 transcription elongat 44.7 11 0.00024 37.5 1.3 58 595-652 74-135 (140)
308 KOG2814 Transcription coactiva 44.0 29 0.00063 39.0 4.4 59 619-677 60-123 (345)
309 KOG1004 Exosomal 3'-5' exoribo 43.8 1.1E+02 0.0023 32.6 8.1 66 909-974 64-135 (230)
310 cd04456 S1_IF1A_like S1_IF1A_l 42.2 69 0.0015 28.7 5.8 59 687-750 2-63 (78)
311 cd04458 CSP_CDS Cold-Shock Pro 42.0 1.1E+02 0.0023 25.9 6.8 52 915-967 2-59 (65)
312 PRK08149 ATP synthase SpaL; Va 40.3 3.9E+02 0.0084 31.8 13.2 167 114-329 255-424 (428)
313 PRK01064 hypothetical protein; 39.1 16 0.00034 32.8 1.2 25 618-642 32-56 (78)
314 COG4044 Uncharacterized protei 38.3 1.3E+02 0.0027 31.9 7.7 65 679-743 71-147 (247)
315 TIGR02381 cspD cold shock doma 38.3 1.2E+02 0.0026 26.2 6.5 54 915-969 3-62 (68)
316 TIGR03498 FliI_clade3 flagella 37.5 3.2E+02 0.007 32.4 12.0 170 113-329 243-415 (418)
317 TIGR00830 PTBA PTS system, glu 36.5 79 0.0017 30.8 5.7 49 914-962 42-102 (121)
318 cd00210 PTS_IIA_glc PTS_IIA, P 36.0 82 0.0018 30.8 5.7 49 914-962 42-102 (124)
319 PRK00276 infA translation init 35.5 2E+02 0.0044 25.1 7.7 60 686-749 8-69 (72)
320 TIGR00523 eIF-1A eukaryotic/ar 35.1 1.9E+02 0.0042 27.1 7.8 54 684-742 18-72 (99)
321 smart00357 CSP Cold shock prot 35.0 1.4E+02 0.003 24.4 6.4 51 916-966 2-55 (64)
322 PRK08406 transcription elongat 33.8 26 0.00055 35.0 1.9 33 619-651 35-67 (140)
323 PRK09099 type III secretion sy 33.7 4.4E+02 0.0095 31.5 12.4 91 116-236 269-360 (441)
324 PF13083 KH_4: KH domain; PDB: 32.9 21 0.00045 31.1 1.0 32 614-645 27-58 (73)
325 TIGR01952 nusA_arch NusA famil 32.9 29 0.00064 34.6 2.1 33 619-651 36-68 (141)
326 KOG2190 PolyC-binding proteins 32.7 24 0.00051 42.4 1.7 40 613-652 335-374 (485)
327 PF01176 eIF-1a: Translation i 32.6 53 0.0012 28.1 3.4 57 686-747 4-62 (65)
328 CHL00010 infA translation init 32.4 2.8E+02 0.006 24.8 8.1 63 687-753 9-73 (78)
329 CHL00059 atpA ATP synthase CF1 31.8 8.2E+02 0.018 29.6 14.2 86 113-225 246-332 (485)
330 TIGR01952 nusA_arch NusA famil 31.2 38 0.00082 33.9 2.6 59 594-652 74-136 (141)
331 KOG2193 IGF-II mRNA-binding pr 31.1 25 0.00053 40.5 1.4 80 621-701 204-291 (584)
332 cd04322 LysRS_N LysRS_N: N-ter 30.7 97 0.0021 29.0 5.2 52 686-737 3-59 (108)
333 TIGR02546 III_secr_ATP type II 29.5 5.6E+02 0.012 30.4 12.4 91 116-236 251-342 (422)
334 PRK07165 F0F1 ATP synthase sub 29.1 1.1E+03 0.024 28.7 15.8 83 114-225 247-329 (507)
335 COG0195 NusA Transcription elo 28.6 38 0.00082 35.6 2.2 34 618-651 78-111 (190)
336 smart00357 CSP Cold shock prot 28.3 2.4E+02 0.0051 22.9 6.7 47 689-741 2-50 (64)
337 cd05700 S1_Rrp5_repeat_hs9 S1_ 26.8 1.5E+02 0.0032 25.2 4.8 55 684-743 1-56 (65)
338 PRK08972 fliI flagellum-specif 26.2 8.1E+02 0.018 29.3 12.8 169 115-330 267-438 (444)
339 cd02414 jag_KH jag_K homology 26.2 40 0.00088 29.8 1.7 31 616-646 24-54 (77)
340 PRK06002 fliI flagellum-specif 26.1 5.9E+02 0.013 30.5 11.7 170 114-331 268-440 (450)
341 KOG2192 PolyC-binding hnRNP-K 25.6 95 0.002 33.8 4.5 63 615-677 122-191 (390)
342 PRK09280 F0F1 ATP synthase sub 24.9 4.2E+02 0.0092 31.8 10.2 91 116-236 254-345 (463)
343 PRK09281 F0F1 ATP synthase sub 24.9 1.3E+03 0.029 28.1 15.5 93 115-233 269-362 (502)
344 cd05701 S1_Rrp5_repeat_hs10 S1 24.5 1.1E+02 0.0024 26.3 3.7 58 685-742 2-60 (69)
345 PRK08472 fliI flagellum-specif 24.0 6.5E+02 0.014 30.1 11.5 165 116-328 262-429 (434)
346 PTZ00329 eukaryotic translatio 23.4 1.9E+02 0.0042 29.3 6.0 64 682-751 30-95 (155)
347 COG0195 NusA Transcription elo 23.2 58 0.0013 34.2 2.4 36 617-652 143-178 (190)
348 PF00358 PTS_EIIA_1: phosphoen 23.1 1.3E+02 0.0029 29.7 4.7 49 915-963 47-107 (132)
349 PF03459 TOBE: TOBE domain; I 23.0 1.8E+02 0.0039 24.2 5.0 47 685-738 5-57 (64)
350 TIGR03497 FliI_clade2 flagella 22.8 8.1E+02 0.018 29.0 12.0 91 116-236 243-334 (413)
351 PRK06820 type III secretion sy 22.2 1.1E+03 0.024 28.2 13.0 92 114-235 267-359 (440)
352 cd02409 KH-II KH-II (K homolo 21.5 60 0.0013 26.9 1.8 23 626-648 35-57 (68)
353 PF07076 DUF1344: Protein of u 21.3 3.2E+02 0.0069 23.4 5.9 49 686-742 4-52 (61)
354 PF01330 RuvA_N: RuvA N termin 21.3 4.1E+02 0.0088 22.3 6.8 49 913-963 4-53 (61)
355 PRK06418 transcription elongat 20.7 62 0.0013 33.3 1.9 29 622-651 67-95 (166)
356 PF14444 S1-like: S1-like 20.4 3.4E+02 0.0074 23.0 5.8 43 913-960 3-46 (58)
357 TIGR00638 Mop molybdenum-pteri 20.2 1.1E+02 0.0024 25.8 3.2 49 685-740 7-61 (69)
358 cd04322 LysRS_N LysRS_N: N-ter 20.2 2.8E+02 0.0061 25.9 6.3 45 913-957 3-59 (108)
359 KOG3273 Predicted RNA-binding 20.2 1.1E+02 0.0023 32.2 3.5 60 626-687 179-238 (252)
No 1
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.7e-166 Score=1415.99 Aligned_cols=690 Identities=47% Similarity=0.768 Sum_probs=672.4
Q ss_pred cceeeeeeEEECCeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCCCCCCCceeeEeeccccccccCCCCCcccccc
Q 002054 55 VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIPNTYMRRE 134 (974)
Q Consensus 55 ~~~~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Re 134 (974)
||+....+++||||++++|||++|+||+|||+++||+|.|||||++.+.+++.|||||||+|+||+||+|||||||+|||
T Consensus 1 ~~~~~~~~~~~~~~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~~~~~~dF~PLtV~y~Ek~yaaGkiPGgf~kRE 80 (692)
T COG1185 1 MFNKIVKTIEWGGRTLTLETGKIARQANGAVLVRYGDTVVLATVVASKPKEGQDFFPLTVNYEEKTYAAGKIPGGFFKRE 80 (692)
T ss_pred CCcceEEEEEECCeeEEEEcchhhhhcCccEEEEECCeEEEEEEeecCCCCCCCccceeEeeeeehhccCcCCCcccccC
Confidence 46778889999999999999999999999999999999999999999878899999999999999999999999999999
Q ss_pred CCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEE
Q 002054 135 GAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQF 214 (974)
Q Consensus 135 g~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~ 214 (974)
|||+++|||+|||||||||||||++|++++||+++|+|+|+.++|+++|++|||+||++|+|||.+||+|||||++||+|
T Consensus 81 Grpse~e~L~sRLIDRpiRPlFp~g~~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf~gpi~~vrvg~idg~~ 160 (692)
T COG1185 81 GRPSEKEILTSRLIDRPIRPLFPKGFRNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDGIF 160 (692)
T ss_pred CCCCccchhhhhhcccccccccchhhccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCccCccceEEEEEECCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEcCCHHHHhcCccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCCCHH
Q 002054 215 IVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQ 294 (974)
Q Consensus 215 vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~~~~~~~~~ 294 (974)
|+|||++|.+.|++||+|+||.++|+|+|+++++++|++|++||.+||+.++.++++|+++..++|++++++.....+++
T Consensus 161 vlNPt~~e~~~s~lDlvVAGT~~aV~MVE~~a~~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g~~~~~~~~~~~~~~ 240 (692)
T COG1185 161 VLNPTLEELEESKLDLVVAGTKDAVNMVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEPPSLDEE 240 (692)
T ss_pred EECCChHHhhhcceeeEecCChhhhheeecccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCccHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999988889888889999
Q ss_pred HHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhccchhhhchHHHHHHHHHHHHHHHHHHhcCCcCCCC
Q 002054 295 TLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGR 374 (974)
Q Consensus 295 ~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR 374 (974)
+...+++.+.+++.+++.+ .+|++|..+++++++++.+.|..++ .....++..+|+.++++.+|.+|++.++|+|||
T Consensus 241 l~~~i~~~~~~~l~~a~~i--~~K~eR~~~~~~~~~~i~~~~~~~e-~~~~~~~~~~~~~l~~~~vR~~Il~~~vR~DGR 317 (692)
T COG1185 241 LEAKVRDLAEDELKEAVGI--REKQERSAALDAIKEKIEEELSGEE-ESSLKEIKAILEKLEKKPVRRLILEGKVRIDGR 317 (692)
T ss_pred HHHHHHHHhHHHHHHHhcc--cchhhhhhhHHHHHHHHHHHHhhhc-cccHHHHHHHHHHHhHHHHHHHHhcCCcccCCC
Confidence 9999999999999999988 5999999999999999999997542 122578999999999999999999999999999
Q ss_pred CCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCCch
Q 002054 375 QLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRR 454 (974)
Q Consensus 375 ~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~rr 454 (974)
..+++|||.|++|+||++|||++|+||+||.++++|||++.++|.+|.+.++..++|++||||||||+||++|.++|+||
T Consensus 318 ~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNFPp~SvGE~g~~g~p~RR 397 (692)
T COG1185 318 FGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNFPPFSVGETGRMGSPGRR 397 (692)
T ss_pred CcceeeeeeEEecCCCCccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccCCCCCccccCCCCCCCcc
Confidence 99999999999999999999999999999999999999999999999999888999999999999999999999999999
Q ss_pred hhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCCcc
Q 002054 455 EVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEI 534 (974)
Q Consensus 455 e~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~~~ 534 (974)
|+|||+|++|++.+++|..+.|||+||++++|++||||++||++|+++|||||||||++.+|||++|||+.++|
T Consensus 398 EiGHG~LA~Ral~~vlp~~e~fpytiRvVsEi~eSNGSsSmaSVCg~sLaLmdAGVPIk~pVAGIAMGLI~eg~------ 471 (692)
T COG1185 398 EIGHGALAERALAPVLPSEEEFPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGD------ 471 (692)
T ss_pred cccCchhhHHHHhhhCCchhcCCceeeeeehhhcccCcccchhhhhhHHHHHhCCCcccccccchhccceecCC------
Confidence 99999999999999999989999999999999999999999999999999999999999999999999999865
Q ss_pred cceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCC
Q 002054 535 KDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNS 614 (974)
Q Consensus 535 ~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~~ 614 (974)
+|.+|+||.++|||+|||||+||||.+|||++|||+|..|++.++|.+||.||+.+|.||+..|.+++++||.++++||
T Consensus 472 -~~~vLsDI~G~EDhlGDMDFKVAGT~~GiTAlQMDiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~a 550 (692)
T COG1185 472 -KYAVLSDILGDEDHLGDMDFKVAGTDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYA 550 (692)
T ss_pred -ceEeeccccccccccCCceeEEecCCCcceeeeeeeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccC
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEE
Q 002054 615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTS 693 (974)
Q Consensus 615 p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~ 693 (974)
|++.+++|+++||+++|||||++|++|+++||++|||+ ||+|++++.+.+..++|+++|+.++ .++++|++|.|+|++
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~IdieddGtv~i~~s~~~~~~~ak~~I~~i~-~e~evg~iy~G~V~r 629 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDGTVKIAASDGESAKKAKERIEAIT-REVEVGEVYEGTVVR 629 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCCCcEEEEecchHHHHHHHHHHHHHH-hhcccccEEEEEEEE
Confidence 99999999999999999999999999999999999997 8999999999999999999999998 799999999999999
Q ss_pred EeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccC
Q 002054 694 VKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVS 755 (974)
Q Consensus 694 i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~ 755 (974)
+.+||+||+|.||.+||||+|++++.++.++++++++||.|.||++++|++||+.||+|...
T Consensus 630 i~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~~~ 691 (692)
T COG1185 630 IVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRLSIKAVL 691 (692)
T ss_pred EeecceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccCCccceehhcc
Confidence 99999999999999999999999999999999999999999999999999999999999764
No 2
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=100.00 E-value=6.2e-163 Score=1431.09 Aligned_cols=686 Identities=40% Similarity=0.643 Sum_probs=652.7
Q ss_pred eeeeeeEEECCeEEEEEeCccCcCCCcEEEEEe-CCeEEEEEEEeCCC-CCCCCceeeEeeccccccccCCCCCcccccc
Q 002054 57 ETFKEEFEIGSRLITLETGKIARFANGAVVLGM-DETKVLSTVTSSKG-DSVRDFLPLTVDYQEKQFAQGVIPNTYMRRE 134 (974)
Q Consensus 57 ~~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~-G~T~Vl~tv~~~~~-~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Re 134 (974)
+.....+++|++++.||||++|+||||||++++ |+|+|||||+..++ +.+.||+||+|+|+||+||+|||||||+|||
T Consensus 6 ~~~~~~~~~~~~~~~~etG~~A~qA~Gav~v~~~G~t~vl~t~~~~~~~~~~~dF~PLtV~y~Ek~yA~GkiPggf~kRE 85 (719)
T TIGR02696 6 EAVIDNGRFGTRTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPKDQFDFFPLTVDVEERMYAAGRIPGSFFRRE 85 (719)
T ss_pred eeEEEEEEECCEEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCCCCCCCCCcceeEeeeehhhhcCccCCceeccC
Confidence 344556777777999999999999999999999 99999999998777 7789999999999999999999999999999
Q ss_pred CCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEE
Q 002054 135 GAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQF 214 (974)
Q Consensus 135 g~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~ 214 (974)
|+|+++|||++||||||||||||++|+++|||+|+|||+|+.++||++|+||||+||++|+|||+|||+|||||++||+|
T Consensus 86 grps~~eiL~sRliDR~iRPLFp~~~~~e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiPf~gPv~~vrVg~i~g~~ 165 (719)
T TIGR02696 86 GRPSTDAILTCRLIDRPLRPSFVKGLRNEVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIDGQW 165 (719)
T ss_pred CCCChhhhHHHHhhCCCCccCCCCCCCcceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCCCCCceEEEEEEEECCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEcCCHHHHhcCccceeEeeeC----C-eEEEEEe------------cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054 215 IVNPTMDELSLSDLNLVYACTR----E-KTLMIDV------------QAREISEKDLEAGLRLAHPEAVKYLEPQIRLAE 277 (974)
Q Consensus 215 vldPt~~e~~~s~~~l~v~~t~----~-~i~mie~------------~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~ 277 (974)
|+|||++|++.|+|||+||||+ + +++|||+ +++++||++|.+||++||++++.++++|+++.+
T Consensus 166 viNPt~~~~~~s~ldLvvagt~~~~~~~~i~MiE~~a~~~~~~~~~~~a~e~~e~~~~~Ai~~a~~~i~~~~~~~~~l~~ 245 (719)
T TIGR02696 166 VAFPTHEQLEGAVFDMVVAGRVLENGDVAIMMVEAEATEKTWDLVKGGAEAPTEEVVAEGLEAAKPFIKVLCRAQADLAE 245 (719)
T ss_pred EECcCHHHHhhCeeeEEEEeeecCCCCccEEEEecCCccccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999997 6 8999998 899999999999999999999999999999999
Q ss_pred HhCCcccccc-ccCCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhccchhhhchHHHHHHHHH
Q 002054 278 KAGKQKKEYK-LSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTVR 356 (974)
Q Consensus 278 ~~g~~k~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (974)
++||+|+++. ....+++|.+.+++++.++|++++.+ .+|.+|+++++++++++.++|.+. .+.+..++..+|++++
T Consensus 246 ~~gk~k~~~~~~~~~~~~l~~~v~~~~~~~~~~~~~~--~~K~~R~~~~~~~~~~~~~~~~~~-~~~~~~~i~~~~~~~~ 322 (719)
T TIGR02696 246 KAAKPTGEFPLFPDYQDDVYEAVEGAVKDELSAALTI--AGKQEREEALDEVKALVAAKLAEQ-FEGREKEISAAYRAVT 322 (719)
T ss_pred HhCCCccccCCCCCCCHHHHHHHHHHHHHHHHHHHhc--cchHHHHHHHHHHHHHHHHHhhcc-ccccHHHHHHHHHHHH
Confidence 9999999998 77788999999999999999999987 499999999999999999999653 2123367999999999
Q ss_pred HHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEe
Q 002054 357 KRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYS 436 (974)
Q Consensus 357 ~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~ 436 (974)
++.+|+++|++|+|+|||.++|+|||+|++|++|++||||+|++|+|||+|++++|.+.++|..+.+.+++.++|+|||+
T Consensus 323 k~~~r~~il~~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~Yn 402 (719)
T TIGR02696 323 KKLVRERVLTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYN 402 (719)
T ss_pred HHHHHHHHhcCCCCCCCCCccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEe
Confidence 99999999999999999999999999999999999999999999999999999998888888888888888999999999
Q ss_pred cCCCCccccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccc
Q 002054 437 FPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHV 516 (974)
Q Consensus 437 f~p~s~~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~v 516 (974)
|||||++++++.++++|||++|++|++|+|++++|..+.|||+|+++++||++|||++|||+||++||||||||||+++|
T Consensus 403 fpPFSt~er~~~~~~~RReighg~La~rALe~vI~~~e~fP~TIrvvseVLeSdGSss~AsIcaasLALmDAGVPmkd~V 482 (719)
T TIGR02696 403 FPPYSTGETGRVGSPKRREIGHGALAERALVPVLPSREEFPYAIRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPV 482 (719)
T ss_pred CCCCcccCCCCCCCCCccHHHHHHHHHHHHHHhhCcHhhCCCEEEEEEEeeccCCcHHHHHHHHHHHHHHHcCcchhhee
Confidence 99999999999999999999999999999999999658999999999999999999999999999999999999999999
Q ss_pred cceeeeeeccCCCCCCccc-ceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHH
Q 002054 517 AGVSVGLVSEVDPSTGEIK-DYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQI 595 (974)
Q Consensus 517 agvs~gli~~~d~~~~~~~-~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I 595 (974)
|||+||++.+.+ +.. +|.+|+||++.||++|+|||+|++|.+|||++|||++..|++.++|.+||++|+++|.+|
T Consensus 483 Agis~Gli~e~~----~~~~~~~iL~Di~g~ED~~Gdmdfkvagt~~gIt~lQmd~ki~gi~~e~l~~aL~~A~~g~~~I 558 (719)
T TIGR02696 483 AGIAMGLISDEV----DGETRYVALTDILGAEDAFGDMDFKVAGTSEFVTALQLDTKLDGIPASVLASALKQARDARLAI 558 (719)
T ss_pred eEEEEEEecccc----CCCcceeEEeCCCchhhhcCCceEEEEecCCCEEEEEEEeeECCCCHHHHHHHHHHHHHHHHHH
Confidence 999999996521 011 689999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHH
Q 002054 596 LDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVD 674 (974)
Q Consensus 596 ~~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~ 674 (974)
++.|++++..| .++++|||++.+++|+|+||+++||||||+||+|+++||++|||+ +|+|.|++.+++.+++|+++|+
T Consensus 559 l~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G~V~I~a~d~~~~~~A~~~I~ 637 (719)
T TIGR02696 559 LDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDDGTVYIGAADGPSAEAARAMIN 637 (719)
T ss_pred HHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecCcEEEEEeCCHHHHHHHHHHHH
Confidence 99999999999 999999999999999999999999999999999999999999998 8999999999999999999999
Q ss_pred HHhhc-ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCC----CccccccccccccCCEEEEEEEEEccCCceEE
Q 002054 675 FIIGR-EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELS----HEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKL 749 (974)
Q Consensus 675 ~l~~~-~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels----~~~v~~~~~~~~vGd~V~vkVl~id~~gri~L 749 (974)
.++.. ++++|++|+|+|++|++||+||+|.+|.+||||+||++ +.++.++.++|++||.|+|||+++|.+||+.|
T Consensus 638 ~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~~gKI~L 717 (719)
T TIGR02696 638 AIANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGKLSL 717 (719)
T ss_pred HhhCcCcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECCCCCeee
Confidence 99843 68999999999999999999999999999999999996 46899999999999999999999998899998
Q ss_pred E
Q 002054 750 S 750 (974)
Q Consensus 750 S 750 (974)
+
T Consensus 718 ~ 718 (719)
T TIGR02696 718 V 718 (719)
T ss_pred c
Confidence 6
No 3
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=100.00 E-value=3.6e-162 Score=1333.00 Aligned_cols=734 Identities=52% Similarity=0.819 Sum_probs=701.2
Q ss_pred CCCCccccccccCccccccCCCCCCCCCCCCCCCCCcccccccc-eeeeeeEEECCeEEEEEeCccCcCCCcEEEEEeCC
Q 002054 13 NNLPPFLTWRALGFRTICSGRLGFAPCEPAPPTPAPSVAGTKVL-ETFKEEFEIGSRLITLETGKIARFANGAVVLGMDE 91 (974)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~G~ 91 (974)
-+++.++.|++.+|++.|+|+.+++++-++++ .+.+.. +...+++.+|+|.+.||||++|+||+|||++++|+
T Consensus 6 csls~l~~~~a~kf~~~~l~r~~~~~~~~~~~------~~s~t~~~~vsveipfGnR~i~~etGklaRfAngsvvv~~Ge 79 (760)
T KOG1067|consen 6 CSLSNLLARRALKFRTILLGRLRALPQLQVRA------LGSSTGPNAVSVEIPFGNREILFETGKLARFANGSVVVQMGE 79 (760)
T ss_pred eeehhhhcccccCcceeeccCccCCCCCCccc------cccccCccceeeeeccCCeEEEEecchhhhhcCCcEEEccCC
Confidence 47899999999999999999999888777664 333322 33455666699999999999999999999999999
Q ss_pred eEEEEEEEeCCCCCCCCceeeEeeccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEE
Q 002054 92 TKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVL 171 (974)
Q Consensus 92 T~Vl~tv~~~~~~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl 171 (974)
|.|++||+....|...+|+||.|+|+||+||+|+||++|+||||+|+++|+|+.|||||+|||+||++|++++|+.|++|
T Consensus 80 T~Vm~Tv~~a~~PSp~qFlPL~VdYqeK~aAvGRip~~fmRREg~tkdkEiL~~rLidrsirplfp~g~~~etqi~~n~L 159 (760)
T KOG1067|consen 80 TAVMTTVVLADKPSPPQFLPLVVDYQEKFAAVGRIPGNFMRREGRTKDKEILTGRLIDRPIRPLFPKGFYHETQILCNVL 159 (760)
T ss_pred eEEEEEEEecCCCCccccceEEEehhhhhhhhccCCCcccccccCCcchhheeeeccccccccCCcccchhHHHHHhhhe
Confidence 99999999988866667999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCeEEEEEecCCCCCH
Q 002054 172 SSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISE 251 (974)
Q Consensus 172 ~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~~~~~e 251 (974)
++||-.+||++|+|+|++||++|+|||++|+++||+|+++|+||+|||..|++.|+|||++|||++.++|+|+.++.+++
T Consensus 160 s~dG~~~pdvlainaas~Al~lsdvpw~gpig~vRigLi~Ge~vVNPT~kEmssS~Lnlvvagt~~~~vmle~~s~~i~q 239 (760)
T KOG1067|consen 160 SSDGVHDPDVLAINAASAALSLSDVPWNGPIGAVRIGLIDGEFVVNPTRKEMSSSQLNLVVAGTKSQTVMLEGSSNNILQ 239 (760)
T ss_pred ecccccCchHHHHhHHHHHhhhccCCCCCceeeeEeeeecceEEeCcchhhhhhccceeEEEeccceEEEEEcccccccH
Confidence 99999999999999999999999999999999999999999999999999999999999999998889999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccc-cccCCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHH
Q 002054 252 KDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEY-KLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQ 330 (974)
Q Consensus 252 ~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~ 330 (974)
++|.+||+.+++++++++..++.+++++||+|+++ .....++||..++++++.++|+++|++++|||.+|++|+++|+.
T Consensus 240 qdl~~Aikvg~~~~q~~i~~i~~L~k~~Gk~Kr~~~~~~~p~pel~K~v~~la~erl~~vftd~shdK~sR~eAvn~i~~ 319 (760)
T KOG1067|consen 240 QDLLHAIKVGVKEAQQIIQGIERLAKKYGKQKREPQKLFLPDPELVKHVHKLAMERLYAVFTDYSHDKISRDEAVNKIRL 319 (760)
T ss_pred HHHHHHHHhccHHHHHHHHHHHHHHHHhCccccchhhhcCCCHHHHHHHHHHHHHHHHHHhcccccccchhhhHHhhhcc
Confidence 99999999999999999999999999999999998 46778899999999999999999999999999999999999998
Q ss_pred HHHHHhhhccchhhhchHHHHHHHHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEE
Q 002054 331 DVKKALEEECDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT 410 (974)
Q Consensus 331 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vt 410 (974)
+..+++.|++++....++.+.|+.+.++.+|++|+++|+|+|||.++|+|+|+|+++++++.|||++|+||+|||+|+||
T Consensus 320 ~~e~~~~e~~pe~e~~~i~~~fn~vskkv~Rs~i~~~gkR~DGR~ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVt 399 (760)
T KOG1067|consen 320 DDEDKVKEEFPEQEPSEIIESFNTVSKKVFRSRILEEGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVT 399 (760)
T ss_pred chHHHHHhhcCCccHHHHHHHHHHHHHHHHHHHHHhcccccCCcchhhhcccceecCccccccchhhhhcCceeEEEEEE
Confidence 88888877776666778999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCCchhhhccccCCCCce-eEEEEEecCCCCccccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcC
Q 002054 411 LGAPAEAQRLESLVGPPTK-RFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMAS 489 (974)
Q Consensus 411 l~~p~~~~~~d~~~~~~~~-~~~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLes 489 (974)
|+.+..+|+.|++.+++++ +||+||+|||||++|.++.|+++|||+||++|+||||.+++| ++|||||||+++||+|
T Consensus 400 l~s~e~a~klD~l~~~~~~~~FmLhY~FPPyat~Evgkig~~nRRE~GhgaLAEkaL~~vlP--~dfPftIRv~SeVleS 477 (760)
T KOG1067|consen 400 LDSLESAQKLDSLIGPDNGINFMLHYEFPPYATNEVGKIGGLNRRELGHGALAEKALLPVLP--EDFPFTIRVTSEVLES 477 (760)
T ss_pred cCCHHHhhhhhhhccCccCceEEEEeccCCccccccccccCCcccccCchhHhhhhhhccCc--ccCceEEEEeeeeeec
Confidence 9999999999999888776 999999999999999999999999999999999999999999 7999999999999999
Q ss_pred CCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCceEEEEe
Q 002054 490 DGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQL 569 (974)
Q Consensus 490 dGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~ 569 (974)
|||++||++|++||||||||||++.++|||+|||+.+-||+.+++.+|.+|+||+|.||+.|||||+||||++|+|++
T Consensus 478 nGSsSMASvCGGslALmDaGvPv~a~vAGvaiGlvt~td~e~g~i~dyriltDIlGiEd~~GDMDFKiAGt~dGvTA~-- 555 (760)
T KOG1067|consen 478 NGSSSMASVCGGSLALMDAGVPVSAHVAGVAIGLVTKTDPEKGEIEDYRILTDILGIEDYNGDMDFKIAGTNDGVTAL-- 555 (760)
T ss_pred CCcchHHhhhcchhhhhhcCCccccccceeEEEeEeccCcccCCcccceeehhhcchhhhcCCcceeeccccCcceec--
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred eccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceE
Q 002054 570 DIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRI 649 (974)
Q Consensus 570 ~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~I 649 (974)
||+++++++++++|+.++.+|++.|.+++..||...++|+|++++++++|+|...+|||||++.|.|+.|||+.-
T Consensus 556 -----gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~ 630 (760)
T KOG1067|consen 556 -----GIPLKIVMEALQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAIS 630 (760)
T ss_pred -----CCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeecccee
Confidence 699999999999999999999999999999999999999999999999999999999999999999999999655
Q ss_pred EeeCCEEEEEecCHHHHHHHHHHHHHHhhc----ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccc
Q 002054 650 SVSDGTLTVVAKNRSVMEKVLEKVDFIIGR----EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVS 725 (974)
Q Consensus 650 di~dg~v~i~~~~~~~~~~a~~~i~~l~~~----~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~ 725 (974)
.+|+|+++|++++..+|++|++.|..++.. +++.|.+|+++|+++.++|+||+|+|+..||+|+|||+.+++.+|+
T Consensus 631 ~vDe~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakps 710 (760)
T KOG1067|consen 631 QVDEGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPS 710 (760)
T ss_pred eecCceEEEEecCHHHHHHHHHHHHHHhcCccccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChH
Confidence 578999999999999999999999999865 6889999999999999999999999999999999999999999999
Q ss_pred cccccCCEEEEEEEEEccCCceEEEEeccCCCcccc
Q 002054 726 DVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEAD 761 (974)
Q Consensus 726 ~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~~~ 761 (974)
+.+++||.|.||.++.|+.|.+.||.|+++++|...
T Consensus 711 d~levGq~I~vk~ie~d~~g~~~ls~ralLp~p~~~ 746 (760)
T KOG1067|consen 711 DLLEVGQEIQVKYIERDPRGGIMLSSRALLPDPATK 746 (760)
T ss_pred HHHhhcceeEEEEEeecCccceeehhhhhcCCcccC
Confidence 999999999999999999999999999999887554
No 4
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=100.00 E-value=1.3e-157 Score=1410.93 Aligned_cols=702 Identities=39% Similarity=0.623 Sum_probs=662.5
Q ss_pred eeeeeeEEECCeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCCCCceeeEeeccccccccCCCCCccccccC
Q 002054 57 ETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSVRDFLPLTVDYQEKQFAQGVIPNTYMRREG 135 (974)
Q Consensus 57 ~~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg 135 (974)
+.++..+++|+|++.+|||++|+||+|||++++|+|.|||||+..++ +.+.||+||+|+|+||+||+|||||||+||||
T Consensus 78 ~~~~~~~~~g~~~~~~etG~~a~qA~gav~v~~g~t~vl~t~~~~~~~~~~~dF~PLtV~y~Ek~~AaGkipggf~kREg 157 (891)
T PLN00207 78 QQFSVKIPVGDRHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSEPSDFFPLSVHYQERFSAAGRTSGGFFKREG 157 (891)
T ss_pred cceEEEEEECCEEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEeccCCCCCCCccceeEeeeeehhhcCccCCceeccCC
Confidence 34666788888899999999999999999999999999999998777 67899999999999999999999999999999
Q ss_pred CCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEE
Q 002054 136 APKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFI 215 (974)
Q Consensus 136 ~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~v 215 (974)
+|+++|||++|||||+|||+||++|++++||+++||++||+++|+++||||||+||++|||||++||+|||||++||++|
T Consensus 158 rp~d~eiL~sRlIdR~lRPlfp~~~~~etQI~i~VLsaDg~~~pd~~AInAASaAL~~SgIP~~gpVaAVrVG~idg~~V 237 (891)
T PLN00207 158 RTKDHEVLICRLIDRPLRPTMPKGFYHETQILSWVLSYDGLHSPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLIGGKFI 237 (891)
T ss_pred CCChHHHHHHHHHCccchhhccccCCCCcEEEEEEEeeCCCCChhhHHHHHHHHHHHhhCCCccCceEEEEEEEECCEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCCHHHHhcCccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCCCHHH
Q 002054 216 VNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQT 295 (974)
Q Consensus 216 ldPt~~e~~~s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~~~~~~~~~~ 295 (974)
||||++|++.|++||+|+||+++|+|||+++++++|++|.+||++||++|++++++|+++++++|++|+++.....+++|
T Consensus 238 lnPt~~E~~~s~ldLvvagt~~~IvMIE~~a~e~see~l~~Al~~a~~aik~i~~~~~el~~~~gk~k~~~~~~~~~~~l 317 (891)
T PLN00207 238 VNPTTKEMEESELDLIMAGTDSAILMIEGYCNFLPEEKLLEAVEVGQDAVRAICKEIEVLVKKCGKPKMLDAIKLPPPEL 317 (891)
T ss_pred ECCCHHHHhcCCeeEEEEEcCCeEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCCCCCCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999888889999
Q ss_pred HHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhcc---------------------chh-----------
Q 002054 296 LEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEEC---------------------DEE----------- 343 (974)
Q Consensus 296 ~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~---------------------~~~----------- 343 (974)
.+.+++++.++|++++.+ .+|++|++++++|++++.+.|.++. ..+
T Consensus 318 ~~~v~~~~~~~~~~~~~~--~~K~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 395 (891)
T PLN00207 318 YKHVKEIAGDELVKALQI--RGKIPRRKALSSLEEKVLSILTEEGYVSKDESFGTSETRADLLEDEDEDEEVVVDGEVDE 395 (891)
T ss_pred HHHHHHHHHHHHHHHHhc--cchHHHHHHHHHHHHHHHHHhhccccccccccccccccccccccccccchhccccccccc
Confidence 999999999999999988 4999999999999999999885431 000
Q ss_pred -----------------hhchHHHHHHHHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEE
Q 002054 344 -----------------SLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVL 406 (974)
Q Consensus 344 -----------------~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl 406 (974)
...++..+|++++++.+|++++++|+|+|||.++|+|||+|++|++|++||||+|++|+||||
T Consensus 396 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~k~~~R~~i~~~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVL 475 (891)
T PLN00207 396 GDVHIKPIPRKSSPLLFSEVDVKLVFKEVTSKFLRRRIVEGGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQAL 475 (891)
T ss_pred ccccccccccccccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEE
Confidence 124589999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeCCCchhhhccccCC-CCceeEEEEEecCCCCccccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEE
Q 002054 407 CTVTLGAPAEAQRLESLVG-PPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSE 485 (974)
Q Consensus 407 ~~Vtl~~p~~~~~~d~~~~-~~~~~~~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~ 485 (974)
|+|++|...+.|..+.+.+ +..++|++||+|||||+++++|.+++++||++|++|++|+|++++|..+.|||+|+|+++
T Consensus 476 atVtlGp~~~~q~~d~l~~~~~~~~f~~~y~fPPfs~ge~~r~g~psrREi~hg~L~eRALrpvip~~~~fP~tIrV~~~ 555 (891)
T PLN00207 476 AVVTLGDKQMAQRIDNLVDADEVKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFPYTIRVEST 555 (891)
T ss_pred EEEEecCccccccccccccccceeeEEEEEEcCCCCCccccCCCCCCHHHHHHHHHHHHHHHHhCCcccCCCEEEEEEEE
Confidence 9999885556666666543 567899999999999999999999999999999999999999999986689999999999
Q ss_pred EEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCceE
Q 002054 486 VMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVT 565 (974)
Q Consensus 486 VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~ 565 (974)
||++|||++||++||++||||||||||+++|+||+||++.+.++..+ .+++.+|+||++.|++.|+|||+|++|.+||+
T Consensus 556 VLesDGSssmAaV~aaSLALmDAGIPmk~~VAGvsvGli~d~~~~~~-~g~~~IL~Dp~g~Ed~~gdmDfkVAgT~~gIt 634 (891)
T PLN00207 556 ITESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGG-DGSPLILSDITGSEDASGDMDFKVAGNEDGIT 634 (891)
T ss_pred EEeCCCChHHHHHHHHHHHHHhcCCCccCceeEEEEEEEecccccCC-CCcEEEEeCCCHHHHhcCCceEEEEecccceE
Confidence 99999999999999999999999999999999999999954221111 12577999999999999999999999999999
Q ss_pred EEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhh
Q 002054 566 AIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEET 645 (974)
Q Consensus 566 alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~ 645 (974)
++||+++..+++.++|.+||++|++++.+|++.|++++++||.++++|||++.+++|+|+||+++||+||++||+|+++|
T Consensus 635 ~iqmd~k~~gis~e~l~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eet 714 (891)
T PLN00207 635 AFQMDIKVGGITLPIMERALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEET 714 (891)
T ss_pred EEEEecccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Cce-EEee-CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEE-EEEEEEeeceEEEEEcCCeEEEEecccCCCcccc
Q 002054 646 GGR-ISVS-DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYK-GVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS 722 (974)
Q Consensus 646 g~~-Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~-G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~ 722 (974)
|++ ||++ +|.|.|++.+.+.+++|+++|+.+. .++++|++|+ |+|++|.+||+||+|.+|.+||||+|+++|+++.
T Consensus 715 g~~~Idi~ddg~V~I~a~d~~~i~~A~~~I~~l~-~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~ 793 (891)
T PLN00207 715 GVEAIDTQDDGTVKITAKDLSSLEKSKAIISSLT-MVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLA 793 (891)
T ss_pred CCCccCcCCCeeEEEEeCCHHHHHHHHHHHHHHh-cCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCcccc
Confidence 999 9997 8999999999999999999999998 5899999996 6999999999999999999999999999999999
Q ss_pred ccccccccCCEEEEEEEEEccCCceEEEEeccCCCccccc
Q 002054 723 RVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADV 762 (974)
Q Consensus 723 ~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~~~~ 762 (974)
+++++|++||.|+|+|+++|.+|||.||+|+++++||.+.
T Consensus 794 ~~~dv~kvGD~V~VkVi~ID~~grI~LSlK~l~~~Pw~~~ 833 (891)
T PLN00207 794 KPEDAFKVGDRIDVKLIEVNDKGQLRLSRRALLPEANSEK 833 (891)
T ss_pred CHHHhcCCCCEEEEEEEEECCCCcEEEEEeccccCchhhh
Confidence 9999999999999999999988999999999999999874
No 5
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=100.00 E-value=3.1e-147 Score=1333.31 Aligned_cols=690 Identities=48% Similarity=0.794 Sum_probs=663.3
Q ss_pred cceeeeeeEEECCeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCCCCceeeEeeccccccccCCCCCccccc
Q 002054 55 VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSVRDFLPLTVDYQEKQFAQGVIPNTYMRR 133 (974)
Q Consensus 55 ~~~~~~~~~~~~~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~~~f~pL~v~y~e~~~a~g~ip~~~~~R 133 (974)
|++.++.++++|+|+++++||++|+||||||++++|+|+|||||+++.+ +++.+|+||+|+|+|++||+|||||||+||
T Consensus 1 ~~~~~~~~~~~~~r~i~~e~G~ia~qAdGSa~v~~G~T~VlatV~~~~~~~~~~df~pL~v~y~e~~~A~gkiP~~f~kr 80 (693)
T PRK11824 1 MFNKIVKSIEFGGRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKEGQDFFPLTVDYEEKTYAAGKIPGGFFKR 80 (693)
T ss_pred CCceEEEEEEECCccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCCCCeeeeEEEEEehhhhccCCCcccccC
Confidence 3566677888899999999999999999999999999999999999998 667899999999999999999999999999
Q ss_pred cCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCE
Q 002054 134 EGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQ 213 (974)
Q Consensus 134 eg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~ 213 (974)
||+|+++|+|++|+|||+|||+||++|++++||+|+||++||+++|++||+||||+||++|+|||++||+|||||++||+
T Consensus 81 eg~pse~eil~srlIdR~lrplfp~~~~~~i~I~~~VL~~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~i~g~ 160 (693)
T PRK11824 81 EGRPSEKETLTSRLIDRPIRPLFPKGFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDGE 160 (693)
T ss_pred CCCCChHHHHHHHHHhhhHHHhCCCCCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcCCHHHHhcCccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCCCH
Q 002054 214 FIVNPTMDELSLSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE 293 (974)
Q Consensus 214 ~vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~~~~~~~~ 293 (974)
+|+|||.+|++.|++||+|++|.+.++|+|++++++++++|.+||++||++|+++++.|+++++++| +|+++.....++
T Consensus 161 ~ivdPt~~E~~~s~~~l~va~t~~~i~mie~~~~~l~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~-~~~~~~~~~~~~ 239 (693)
T PRK11824 161 FVLNPTVEELEESDLDLVVAGTKDAVLMVESEAKELSEEVMLEAIEFGHEAIQELIDAQEELAAEAG-PKWEWQPPEVDE 239 (693)
T ss_pred EEEcCCHHHHhhCcceEEEEEccCceEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCcccCCCCCCH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999 999998888899
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhc-cchhhhchHHHHHHHHHHHHHHHHHHhcCCcCC
Q 002054 294 QTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEE-CDEESLQVLPKAVDTVRKRVIRKRIIAEGVRVD 372 (974)
Q Consensus 294 ~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R~D 372 (974)
++.+.+++++.+++++++.. ++|.+|+++++++++++.++|.++ ..+.+..++..+|++++++.+|++++++|+|+|
T Consensus 240 ~~~~~~~~~~~~~~~~~~~~--~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~g~R~D 317 (693)
T PRK11824 240 ELKAAVKELAEAKLKEAYQI--TDKQEREAALDAIKEEVLEALAAEEEEEEDEKEIKEAFKKLEKKIVRRRILEEGIRID 317 (693)
T ss_pred HHHHHHHHHHHHHHHHHHhc--cccHHHHHHHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Confidence 99999999999999999987 599999999999999999999653 233445689999999999999999999999999
Q ss_pred CCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCC
Q 002054 373 GRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLN 452 (974)
Q Consensus 373 GR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~ 452 (974)
||.++|+|||+|++|++|++||||+|++|+|||+|+||+|.|.++|..+.+.+.+.++|++||+|||||+++++|.++|+
T Consensus 318 GR~~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~~~~~ 397 (693)
T PRK11824 318 GRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDEQIIDGLEGEYKKRFMLHYNFPPYSVGETGRVGSPG 397 (693)
T ss_pred CCCcCcccceEEEeCCCCCCCceEEEEECCeEEEEEEecCCCcccccccccCCCCcEEEEEEEEcCCCCCCCcCCCCCCC
Confidence 99999999999999999999999999999999999999988888887777767788999999999999999999999999
Q ss_pred chhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCC
Q 002054 453 RREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTG 532 (974)
Q Consensus 453 rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~ 532 (974)
|||++|++|++|+|++++|.++.|||+|+|+++||++|||++|||+||+++|||||||||+++|+|++||++++++
T Consensus 398 rre~~~~~li~ral~~vi~~~~~~p~~I~v~~~VLe~dGs~~~Aai~aaslAL~dAgvP~~~~Va~vs~gli~~~~---- 473 (693)
T PRK11824 398 RREIGHGALAERALEPVLPSEEEFPYTIRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPVAGIAMGLIKEGD---- 473 (693)
T ss_pred hhHHHHHHHHHHHHHHhcCcccCCCEEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCceeEEEEEEEcCCC----
Confidence 9999999999999999999878999999999999999999999999999999999999999999999999997532
Q ss_pred cccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q 002054 533 EIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDR 612 (974)
Q Consensus 533 ~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~ 612 (974)
+|.+|+||++.||+++||||+|++|.+|||++|+++|.++++.++|.+|+++|+++|.+|++.|++++++||.++++
T Consensus 474 ---~~~il~D~~~~Ed~~~d~d~~va~t~~gi~~lq~d~k~~~i~~~~l~~al~~a~~g~~~I~~~M~~aI~~~r~~~~~ 550 (693)
T PRK11824 474 ---KYAVLTDILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREILEEALEQAKEGRLHILGKMNEAISEPRAELSP 550 (693)
T ss_pred ---ceEEEcCCChhhHhhCCceEEEEecCCceEEEEEecccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhhhcc
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEE
Q 002054 613 NSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVV 691 (974)
Q Consensus 613 ~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V 691 (974)
++|++..++|+|+||+++||+||++||+|+++||++||++ +|.+.+++.+.+.+++|+++|+.+. .++++|++|.|+|
T Consensus 551 ~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~G~v~i~~~~~~~~~~a~~~I~~~~-~~~~vG~v~~G~V 629 (693)
T PRK11824 551 YAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDDGTVKIAATDGEAAEAAKERIEGIT-AEPEVGEIYEGKV 629 (693)
T ss_pred cCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCCceEEEEcccHHHHHHHHHHHHHhc-ccCcCCeEEEEEE
Confidence 9999999999999999999999999999999999999997 8999999999999999999999988 6899999999999
Q ss_pred EEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccC
Q 002054 692 TSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVS 755 (974)
Q Consensus 692 ~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~ 755 (974)
++|.+||+||+|.++.+||+|+|++++++++++.++|++||.|+|+|+++|.+|++.||+|.++
T Consensus 630 ~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~~~ 693 (693)
T PRK11824 630 VRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAVL 693 (693)
T ss_pred EEEECCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCCCcEEEEEEecC
Confidence 9999999999999999999999999999999999999999999999999998899999999763
No 6
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=100.00 E-value=7.4e-147 Score=1326.46 Aligned_cols=675 Identities=48% Similarity=0.803 Sum_probs=648.1
Q ss_pred CCeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCCCCceeeEeeccccccccCCCCCccccccCCCCchhhhH
Q 002054 66 GSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLV 144 (974)
Q Consensus 66 ~~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~ 144 (974)
|+|+++++||++|+||||||++++|+|+|||||+++.+ +++.+|+||+|+|+|++||+|||||+|+||||+|+++|+|+
T Consensus 3 ~~R~i~ie~G~la~~AdGSa~v~~G~T~VlatV~~~~~~~~~~df~pL~vey~e~~~A~gkipg~f~kReg~p~~~eil~ 82 (684)
T TIGR03591 3 GGRTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEGQDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKETLT 82 (684)
T ss_pred CCccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCCCceEeEEEEEEehhhhccCCCCCcccCCCCCCHHHHHH
Confidence 67899999999999999999999999999999999988 66789999999999999999999999999999999999999
Q ss_pred HHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCCHHHHh
Q 002054 145 GRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELS 224 (974)
Q Consensus 145 ~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt~~e~~ 224 (974)
+|+|||+|||+||++|++++||+|+||++||+++|++||+||||+||++|+|||++||+|||||++||++|+|||.+|++
T Consensus 83 srlIdR~lrplfp~~~~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~idg~~ildPt~~E~~ 162 (684)
T TIGR03591 83 SRLIDRPIRPLFPKGFRNEVQVVATVLSYDPENDPDILAIIGASAALAISGIPFNGPIAAVRVGYIDGQYVLNPTVDELE 162 (684)
T ss_pred HHHHhhHHHHhcCCCCCceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEEEEcCCHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccccccccCCCHHHHHHHHHHHH
Q 002054 225 LSDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEKVSNLAE 304 (974)
Q Consensus 225 ~s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~~~~~~~~~~~~~~~~~~~ 304 (974)
.|++||+|+++.++++|+|++++++++++|.+||++||++|++++++|+++++++|++|+++.....+++|.+.+++++.
T Consensus 163 ~s~~~l~va~t~~~i~mie~~~~~i~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~ 242 (684)
T TIGR03591 163 KSDLDLVVAGTKDAVLMVESEAKELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKEKWEFVAPEVDEELKAKVKELAY 242 (684)
T ss_pred hCCceEEEEccCCcEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCCCCCCCHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999888889999999999999
Q ss_pred H-HHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhcc--ch--hhhchHHHHHHHHHHHHHHHHHHhcCCcCCCCCCCCc
Q 002054 305 A-HIEAVFTDPSYSKFERGEALDKIGQDVKKALEEEC--DE--ESLQVLPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEV 379 (974)
Q Consensus 305 ~-~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~~--~~--~~~~~~~~~~~~~~~~~~r~~il~~~~R~DGR~~~e~ 379 (974)
+ ++++++.. .+|.+|+++++++++++.++|.+.. .+ .+...+..+|++++++.+|++++++|+|+|||.++|+
T Consensus 243 ~~~~~~~~~~--~~k~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~il~~g~R~DGR~~~e~ 320 (684)
T TIGR03591 243 EAGLKEAYQI--TEKQERYAALDAIKEEVLEALAEEEEEEEEADREKEIKEAFKDLEKKIVRERILKEGKRIDGRDLDTI 320 (684)
T ss_pred hHHHHHHhhc--cchHHHHHHHHHHHHHHHHHhhhhcccccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCc
Confidence 9 89999987 5999999999999999999996531 11 2345799999999999999999999999999999999
Q ss_pred cCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCCchhhhHH
Q 002054 380 RPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHG 459 (974)
Q Consensus 380 R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~rre~~~~ 459 (974)
|||+|++|++|++||||+|++|+|||||+||+|.|.+.|..+.+.+...++|++||+|||||+++++|.++|+|||++|+
T Consensus 321 Rpi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~g~~~rrei~~~ 400 (684)
T TIGR03591 321 RPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEYRKRFMLHYNFPPYSVGEVGRVGGPGRREIGHG 400 (684)
T ss_pred CceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCcccccCCcccCCCccEEEEEEEEcCCCCCCCcCCCCCCChHHHHHH
Confidence 99999999999999999999999999999999988887877888778889999999999999999999999999999999
Q ss_pred HHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCCcccceEE
Q 002054 460 TLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRI 539 (974)
Q Consensus 460 ~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~~~~~~~i 539 (974)
+|++|+|++++|..+.|||+|+|+++||++|||++|||+||++||||||||||+++|+|++||++++++ .+|.+
T Consensus 401 ~l~~ral~~~i~~~~~~p~tI~v~~~VLesdGs~~~Aai~aaslAL~dAgvP~~~~Vagvs~gli~~~~------~~~~i 474 (684)
T TIGR03591 401 ALAERALKAVLPSEEEFPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGD------ERFAV 474 (684)
T ss_pred HHHHHHHHHhcCccccCCeEEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCCcCCEEEEEEEEEcCCC------cceEE
Confidence 999999999999778999999999999999999999999999999999999999999999999997521 04789
Q ss_pred EecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCccee
Q 002054 540 LTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLAT 619 (974)
Q Consensus 540 L~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~~p~~~~ 619 (974)
|+||++.||+++||+|+|++|.+|||++|++++..+++.++|.+|+++|++++.+|++.|++++.+++.++++|||++.+
T Consensus 475 l~D~~~~Ed~~~d~d~~va~t~~gI~~lq~d~k~~~i~~~~l~~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~ 554 (684)
T TIGR03591 475 LSDILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIET 554 (684)
T ss_pred EeCCChHHHhcCCceEEEEEcCCceEEEEEEcCcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeece
Q 002054 620 LKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYG 698 (974)
Q Consensus 620 ~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G 698 (974)
++|||+||+++||||||+||+|+++||++|||+ +|+|++++.+++.+++|+++|+.+. ..+++|++|.|+|++|.+||
T Consensus 555 ~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~~~~-~~~~~G~i~~G~V~~I~~~G 633 (684)
T TIGR03591 555 IKINPDKIRDVIGPGGKVIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEGIT-AEPEVGKIYEGKVVRIMDFG 633 (684)
T ss_pred EecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHHHHHHHhhh-cccccCcEEEEEEEEEeCCE
Confidence 999999999999999999999999999999998 8999999999999999999999887 57899999999999999999
Q ss_pred EEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEE
Q 002054 699 AFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKL 749 (974)
Q Consensus 699 ~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~L 749 (974)
+||++.++.+||||+|+++++++.++.++|++||.|+|||+++|.+|++.|
T Consensus 634 afVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~~gki~L 684 (684)
T TIGR03591 634 AFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKQGRIKL 684 (684)
T ss_pred EEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECCCCCccC
Confidence 999999999999999999999999999999999999999999998788765
No 7
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.8e-47 Score=434.03 Aligned_cols=298 Identities=24% Similarity=0.337 Sum_probs=272.3
Q ss_pred EEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEE
Q 002054 657 TVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSL 736 (974)
Q Consensus 657 ~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~v 736 (974)
++..+.+..++......+......+++|++++|+|++|++||+||+|. |++||||+|||||.++.+|+++|++||+|+|
T Consensus 166 ~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdig-GvdGLlHiseiS~~rv~~P~~vvkvGd~Vkv 244 (541)
T COG0539 166 NVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIG-GVDGLLHISEISWKRVDHPSEVVKVGDEVKV 244 (541)
T ss_pred cEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEec-CeeeEEehhhccccccCCHHHhcccCCEEEE
Confidence 556667778876554444333378999999999999999999999995 6999999999999999999999999999999
Q ss_pred EEEEEcc-CCceEEEEeccCCCccccc---------------CceEEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCC
Q 002054 737 RCIGQDV-RGNIKLSLKAVSPRPEADV---------------KGVVEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNE 800 (974)
Q Consensus 737 kVl~id~-~gri~LS~K~~~~~~~~~~---------------g~~~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~ 800 (974)
+|+++|. ++|+.||+|++.++||... ....+|+|+++.+|++||+|+|+++|.+... |.
T Consensus 245 kVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~-P~---- 319 (541)
T COG0539 245 KVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNV-PS---- 319 (541)
T ss_pred EEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCC-HH----
Confidence 9999997 8999999999999999972 3457899999999999999999999998655 66
Q ss_pred CCCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec------------------
Q 002054 801 TPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS------------------ 862 (974)
Q Consensus 801 ~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~------------------ 862 (974)
+.+++||+|.|.| +++|+++|||+|++|++.++| |..+.+.+++|++++|.|++
T Consensus 320 ---evv~~Gq~V~V~V---l~id~e~rRIsL~iKq~~~~p--w~~~~~~~~~g~~v~g~v~~~t~~g~fv~le~gidG~v 391 (541)
T COG0539 320 ---EVVKVGQEVEVKV---LDIDPERRRISLGLKQLKENP--WEEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLV 391 (541)
T ss_pred ---HhcccCCEEEEEE---EeeCchhceEEeeehhhhcCh--hhhhhhhcCCCCeEEEEEeeecccceEEccCCCccceE
Confidence 8999999999999 999999999999999999999 99999999999999999998
Q ss_pred -----ccCcCCC--cccccCCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCC
Q 002054 863 -----STNIQKS--TSFSQREREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGG 932 (974)
Q Consensus 863 -----~~~~~~~--~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~ 932 (974)
+|..... ..||+|++++++|+.+|+++++++ ++|++..+|| ....|++|++|+|+|+++.++|+||+|++
T Consensus 392 h~~d~sw~~~~~~~~~~k~Gd~v~~~vl~vd~~~~~isLgiKql~~~p~~~~~~~~~~~~~v~~~v~~i~~~G~~v~l~~ 471 (541)
T COG0539 392 HLSDLSWDRPGEEAEKYKKGDEVEAKVLAVDKEKERISLGIKQLEESPWEEFSEKYKKGSVVKGKVKSVKDKGAFVELGG 471 (541)
T ss_pred EHHhcCccccCcHHHhhccCcEEEEEEEEEecccceeeeehhhhccCchhhhHhhccCCCeEEEEEEEEccCceEEEecC
Confidence 8876544 389999999999999999999999 9999999999 57779999999999999999999999999
Q ss_pred CeEEEEecccCCCCCCCCCCEEEEEEEEEeCCCcee
Q 002054 933 GIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPV 968 (974)
Q Consensus 933 gv~Glih~se~~~~~f~vGd~V~vkVl~id~~~~~~ 968 (974)
++.||++.+++....|++||.|+|+|+++|+++.-+
T Consensus 472 ~v~G~i~~~~~~~~~~~~gd~v~a~v~~id~k~~ki 507 (541)
T COG0539 472 GVEGLIRLSELSRDVLKVGDEVEAVVVSIDKKNRKI 507 (541)
T ss_pred ceeeeeecchhhhhhccCCCEEEEEEEEEcCCCCEE
Confidence 999999999998889999999999999999887654
No 8
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=100.00 E-value=7.7e-39 Score=391.78 Aligned_cols=302 Identities=20% Similarity=0.254 Sum_probs=261.6
Q ss_pred EEecCHHHHHH-HHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEE
Q 002054 658 VVAKNRSVMEK-VLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSL 736 (974)
Q Consensus 658 i~~~~~~~~~~-a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~v 736 (974)
+..+.+..+++ +.+.++.+. .++++|++++|+|+++.+||+||++ +|++||||+|+++|.++.++.+.|++||+++|
T Consensus 468 iVlSrr~~l~e~~~~~~ee~~-~~l~~G~~V~G~Vk~i~~~G~fVdl-~Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~v 545 (863)
T PRK12269 468 IVINRRRYLEERARQAREEFF-NSVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHVARPREFVKKGQTIEL 545 (863)
T ss_pred EEEEHHHHHHHHHHHHHHHHH-hcCCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEchhccccccCCHHHhccCCCEEEE
Confidence 44445554443 445555555 6799999999999999999999999 68999999999999999999999999999999
Q ss_pred EEEEEcc-CCceEEEEeccCCCcccc------cCce---------EEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCC
Q 002054 737 RCIGQDV-RGNIKLSLKAVSPRPEAD------VKGV---------VEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNE 800 (974)
Q Consensus 737 kVl~id~-~gri~LS~K~~~~~~~~~------~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~ 800 (974)
+|+++|+ ++++.||+|++.++||.. .|++ .+|.|+++.+|++|++|+++++|.....+|.
T Consensus 546 kVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~---- 621 (863)
T PRK12269 546 KVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPS---- 621 (863)
T ss_pred EEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHH----
Confidence 9999998 789999999999999975 2333 4677778888999999999999954344454
Q ss_pred CCCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec------------------
Q 002054 801 TPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS------------------ 862 (974)
Q Consensus 801 ~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~------------------ 862 (974)
+.+++||.|.++| +++|+++++++||+++..++| |....+.+++|++++|+|++
T Consensus 622 ---~~~kvGd~V~vkV---l~iD~e~~rIsLS~K~l~~~P--w~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlI 693 (863)
T PRK12269 622 ---DMVKIGDEVECMI---LGYDIQAGRVSLGLKQVTANP--WEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFL 693 (863)
T ss_pred ---HcCCCCCEEEEEE---EEEecccCceEEEehhcccCc--hHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEE
Confidence 7899999999999 999999999999999999998 99999999999999999988
Q ss_pred -----ccCcC---CCcccccCCeEEEEEEEeecCCCCcC-ccccccccccc--cccCCCCCEEEEEEEEEeCCeEEEEeC
Q 002054 863 -----STNIQ---KSTSFSQREREELAECLFGTEDGDED-NKGTRVEAIVS--AKNLKLGTKVAAKVYQVRARGLVLDLG 931 (974)
Q Consensus 863 -----~~~~~---~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~~--~~~~~vG~vV~G~V~~I~~~GvFV~L~ 931 (974)
+|... .+..|++||.|+++|+++|++++++. |+|++..+||. .++|++|++|+|+|.++++||+||+|+
T Consensus 694 h~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV~GkV~~v~~~GvFVeL~ 773 (863)
T PRK12269 694 HVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVP 773 (863)
T ss_pred EhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEecccccChHHHHHhhCCCCCEEEEEEEEEecCeEEEEcC
Confidence 56543 23479999999999999999999999 99999999994 667999999999999999999999999
Q ss_pred CCeEEEEecccCCC----------CCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054 932 GGIRGMYRFENNEK----------KDFVVGDELLVKCSSFTG-KGIPVVSLVD 973 (974)
Q Consensus 932 ~gv~Glih~se~~~----------~~f~vGd~V~vkVl~id~-~~~~~~~~~~ 973 (974)
+|+.||+|.++++. +.|++||+|+|+|+++|. ++...+|+.+
T Consensus 774 ~gVeGlI~~s~lsdd~~~~~~~~~~~f~vGD~V~v~Vl~iD~~~rkI~LSlk~ 826 (863)
T PRK12269 774 GGVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFSVRD 826 (863)
T ss_pred CCeEEEEEHHHcCCcccccchhhccccCCCCEEEEEEEEEEcCCCEEEEEEec
Confidence 99999999998742 248999999999999997 4566777653
No 9
>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1. This family contains the archaeal protein orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt.
Probab=100.00 E-value=2.4e-38 Score=338.73 Aligned_cols=224 Identities=32% Similarity=0.471 Sum_probs=202.4
Q ss_pred HHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCc
Q 002054 363 RIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCI 442 (974)
Q Consensus 363 ~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~ 442 (974)
.++++|+|+|||.++|+|++.+++|.++++||||+|++|+|+|+|+|+ +|.+..... ...++++.+.++|+++||++
T Consensus 2 ~~~~~~~R~DGR~~~e~R~~~~~~g~~~~a~GSa~~~~G~T~Vl~~V~--gp~e~~~~~-~~~~~~~~l~v~~~~~~~a~ 78 (230)
T TIGR02065 2 LILEDGVRLDGRKPDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAVY--GPREMHPRH-LQLPDRAVLRVRYHMAPFST 78 (230)
T ss_pred cccCCCcCCCCCCcccccCeEEEECCCCCCCeEEEEEECCcEEEEEEe--CCCcccccc-ccCCCceEEEEEEEeCCccc
Confidence 367899999999999999999999999999999999999999999999 887643221 22367889999999999999
Q ss_pred cccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceee
Q 002054 443 NEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSV 521 (974)
Q Consensus 443 ~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~ 521 (974)
.+.++ ++++++|+.++++++|+|+++++. +.||+ +|+|.++||++|||.++|++||+++||+||||||+++|+|+++
T Consensus 79 ~~~~~-~~~~~~~~~~s~~l~~~l~~~i~~-~~~p~~~i~i~v~vl~~DG~~~~aai~aa~lAL~dagIp~~~~v~avtv 156 (230)
T TIGR02065 79 DERKR-PGPSRREIEISKVIREALEPAILL-EQFPRTAIDVFIEVLQADAGTRCAGLTAASLALADAGIPMRDLVVGVAV 156 (230)
T ss_pred CCccC-CCCCccHHHHHHHHHHHHHHHhCh-hhcCCeEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCCccccceeeEEE
Confidence 76554 568999999999999999999998 68897 4999999999999999999999999999999999999999999
Q ss_pred eeeccCCCCCCcccceEEEecCCccccccCCccEEEEe--eCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 002054 522 GLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAG--TRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHM 599 (974)
Q Consensus 522 gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~--t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m 599 (974)
|++++ .+++||+..|+..++++++|+. +.+.|+.+++++ .++++.|.+|++.|++++.++.++|
T Consensus 157 ~~~~~-----------~~v~Dpt~~Ee~~~~~~l~va~~~~~~~i~~i~~~g---~~~~e~~~~~l~~a~~~~~~l~~~~ 222 (230)
T TIGR02065 157 GKVDG-----------VVVLDLNEEEDMYGEADMPVAMMPKLGEITLLQLDG---DMTPDEFRQALDLAVKGIKIIYQIQ 222 (230)
T ss_pred EEECC-----------eEEECCCHHHhhcCCCceEEEEeCCCCCEEEEEEec---CcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 99864 6999999999999999999997 445699999985 5999999999999999999999999
Q ss_pred HHHhcC
Q 002054 600 EREISA 605 (974)
Q Consensus 600 ~~~i~~ 605 (974)
++++.+
T Consensus 223 ~~~l~~ 228 (230)
T TIGR02065 223 REALKN 228 (230)
T ss_pred HHHHHh
Confidence 999865
No 10
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=100.00 E-value=1e-37 Score=336.91 Aligned_cols=225 Identities=33% Similarity=0.522 Sum_probs=203.9
Q ss_pred HHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCc
Q 002054 363 RIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCI 442 (974)
Q Consensus 363 ~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~ 442 (974)
.++++|+|+|||.++|+|++++++|.+++++|||+|++|+|+|+|+|+ +|.+.... ....++.+.+.++|+|+||++
T Consensus 8 ~~~~~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~--gp~e~~~~-~~~~~~~~~l~v~~~~~p~~~ 84 (244)
T PRK03983 8 LILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVY--GPREMHPR-HLQLPDRAVLRVRYNMAPFSV 84 (244)
T ss_pred hhccCCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEe--cCCccccc-cccCCCcEEEEEEEEcCCCcc
Confidence 578999999999999999999999999999999999999999999999 88764322 223467899999999999999
Q ss_pred cccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCeE-EEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceee
Q 002054 443 NEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSV 521 (974)
Q Consensus 443 ~e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~t-I~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~ 521 (974)
.+.+ .+++++++++++++++++|+++++. +.||++ |+|.++||++|||+++||+||+++||+||||||+++++++++
T Consensus 85 ~~~~-~~~~~~~~~~~s~~l~~~l~~~i~~-~~~p~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp~~~~v~avtv 162 (244)
T PRK03983 85 DERK-RPGPDRRSIEISKVIREALEPAIML-ELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAV 162 (244)
T ss_pred cccc-CCCCChhHHHHHHHHHHHHHHhccH-HhCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCccccceeEEEE
Confidence 7754 4468899999999999999999997 678885 999999999999999999999999999999999999999999
Q ss_pred eeeccCCCCCCcccceEEEecCCccccccCCccEEEEee-CCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 002054 522 GLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGT-RIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHM 599 (974)
Q Consensus 522 gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t-~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m 599 (974)
|++++ .+|+||+..|+..++++++|+++ ..| |+++|+++ .++.+++.+|++.|++++.+|.+.|
T Consensus 163 ~~~~~-----------~~i~DPt~~Ee~~~~~~l~va~~~~~~~I~~l~~~G---~~~~~~~~~~i~~A~~~~~~i~~~i 228 (244)
T PRK03983 163 GKVDG-----------VIVLDLNKEEDNYGEADMPVAIMPRLGEITLLQLDG---NLTREEFLEALELAKKGIKRIYQLQ 228 (244)
T ss_pred EEECC-----------EEEECCCHHHhccCCceEEEEEECCCCCEEEEEEec---CcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 99864 69999999999999999999997 345 99999985 5999999999999999999999999
Q ss_pred HHHhcCC
Q 002054 600 EREISAP 606 (974)
Q Consensus 600 ~~~i~~~ 606 (974)
++++.+.
T Consensus 229 ~~~l~~~ 235 (244)
T PRK03983 229 REALKSK 235 (244)
T ss_pred HHHHHHH
Confidence 9998753
No 11
>PRK00173 rph ribonuclease PH; Reviewed
Probab=100.00 E-value=1.4e-36 Score=326.40 Aligned_cols=218 Identities=27% Similarity=0.373 Sum_probs=197.0
Q ss_pred CcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCceeEEEEEecCCCCccccc
Q 002054 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPTKRFMLHYSFPPFCINEVG 446 (974)
Q Consensus 369 ~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~ 446 (974)
+|+|||+++|+|++.|++|++++++|||+|++|+|+|+|+|+.. .|.. ...++++.++++|+++||++.+++
T Consensus 1 ~R~DGR~~~e~R~i~~~~g~~~~a~GSa~v~~G~T~Vla~V~~~~~~p~~------~~~~~~g~l~v~~~~~p~a~~~~~ 74 (238)
T PRK00173 1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRF------LKGQGQGWVTAEYGMLPRATHTRN 74 (238)
T ss_pred CCCCCCCcccccCeEEEeCCCCCCCeeEEEEecCcEEEEEEEcCCCCCCc------cCCCCcEEEEEEEecCCCCCcccc
Confidence 59999999999999999999999999999999999999999943 2322 224578999999999999998863
Q ss_pred c----ccCCCchhhhHHHHHHHHhhhcCCCCCCCC-eEEEEEEEEEcCCCChhhHHHHHHHHHHHHc-----------CC
Q 002054 447 K----RVGLNRREVGHGTLAEKALLAVLPPENDFP-YTVRVNSEVMASDGSTSMATVCGGSMALMDA-----------GI 510 (974)
Q Consensus 447 ~----~~~~~rre~~~~~l~eral~~vi~~~~~~p-~tI~V~v~VLesdGs~~~A~v~aa~lAL~da-----------gv 510 (974)
+ .|.++++++.++++++|+|+++++. +.|| ++|+|+++||++|||.++||++|+++||+|| ++
T Consensus 75 ~~~~~~g~~~~~~~~~sr~i~r~lr~~i~l-~~l~~~~i~v~v~VL~~DG~~~~aai~Aa~~AL~da~~~~~~~~~~~~i 153 (238)
T PRK00173 75 DREAAKGKQGGRTQEIQRLIGRSLRAVVDL-KALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKN 153 (238)
T ss_pred cccccCCCCCccHHHHHHHHHHHHHHhcCH-HHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhhccCcccCC
Confidence 2 3467888999999999999999998 4555 5799999999999999999999999999999 99
Q ss_pred CccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHH
Q 002054 511 PLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAH 589 (974)
Q Consensus 511 Pi~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~ 589 (974)
||+++|+++++|++++ .+|+||+.+|+..++++++|+.+..| |+++|+++++.+++.++|.+|++.|+
T Consensus 154 p~~~~~~~vt~~~~~~-----------~~lvDpt~~Ee~~~~~~l~v~~~~~~~i~~v~~~g~g~~~~~e~l~~~i~~A~ 222 (238)
T PRK00173 154 PLKDQVAAVSVGIVDG-----------EPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAE 222 (238)
T ss_pred cccCceeEEEEEEECC-----------EEEECCCHHHHhcCCceEEEEECCCCCEEEEEccCCCCCcCHHHHHHHHHHHH
Confidence 9999999999999964 69999999999999999999999876 99999987767899999999999999
Q ss_pred HHHHHHHHHHHHHhc
Q 002054 590 KGRLQILDHMEREIS 604 (974)
Q Consensus 590 ~~~~~I~~~m~~~i~ 604 (974)
+++.+|.+.|++++.
T Consensus 223 ~~~~~l~~~~~~~l~ 237 (238)
T PRK00173 223 KGIAELVALQKAALA 237 (238)
T ss_pred HHHHHHHHHHHHHhc
Confidence 999999999999875
No 12
>TIGR01966 RNasePH ribonuclease PH. This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans.
Probab=100.00 E-value=1.4e-35 Score=318.56 Aligned_cols=218 Identities=27% Similarity=0.381 Sum_probs=194.4
Q ss_pred cCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCcccc-ccc
Q 002054 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEV-GKR 448 (974)
Q Consensus 370 R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~-~~~ 448 (974)
|+|||+++|+|++++++|++++++|||+|++|+|+|+|+|+...+.+.. ...++++.+.++|+|+||++.+. +|.
T Consensus 1 R~DGR~~~e~R~i~i~~G~~~~A~GSa~v~~G~T~Vla~V~~~~~~p~~----~~~~~~g~l~v~~~~~p~a~~~~~~r~ 76 (236)
T TIGR01966 1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPF----LRGSGEGWITAEYGMLPRATQTRNRRE 76 (236)
T ss_pred CCCCCCCCCccCeEEEeCCcCCCCceEEEEecCCEEEEEEEccCccCCc----ccCCCcEEEEEEEecCCCCCCCCcccc
Confidence 8999999999999999999999999999999999999999955443311 11346789999999999999876 232
Q ss_pred ---cCCCchhhhHHHHHHHHhhhcCCCCCCCC-eEEEEEEEEEcCCCChhhHHHHHHHHHHHHc-----------CCCcc
Q 002054 449 ---VGLNRREVGHGTLAEKALLAVLPPENDFP-YTVRVNSEVMASDGSTSMATVCGGSMALMDA-----------GIPLQ 513 (974)
Q Consensus 449 ---~~~~rre~~~~~l~eral~~vi~~~~~~p-~tI~V~v~VLesdGs~~~A~v~aa~lAL~da-----------gvPi~ 513 (974)
|.+++++.+++++++|+|+++++. +.|| ++|+|+++||++|||.++||+||+++||+|| |+||+
T Consensus 77 ~~~g~~~~~~~e~~~~i~r~lr~~i~l-~~l~~~~i~I~v~VL~~DG~~~~aai~Aa~aAL~da~~~~~~~~~~~~ip~~ 155 (236)
T TIGR01966 77 SAKGKQSGRTQEIQRLIGRALRAVVDL-EALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIR 155 (236)
T ss_pred ccCCCCCccHHHHHHHHHHHHHHhcCH-hhcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHHHHhhhhcCcccCCCcc
Confidence 566668889999999999999998 5565 5799999999999999999999999999999 99999
Q ss_pred ccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHH
Q 002054 514 EHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGR 592 (974)
Q Consensus 514 ~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~ 592 (974)
++|+++++|++++ .+|+||+..|+..++..++++.+..+ |+.+|+++..+.+++++|.+|++.|++++
T Consensus 156 ~~~~~vt~~~~~~-----------~~v~Dpt~~Ee~~~~~~l~l~~~~~~~i~~i~~~g~~~~~~~~~l~~~i~~a~~~~ 224 (236)
T TIGR01966 156 DFVAAVSVGIVDG-----------EPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGI 224 (236)
T ss_pred CceeEEEEEEECC-----------EEEECCChhHHhccCceEEEEEcCCCCEEEEEecCCCCCcCHHHHHHHHHHHHHHH
Confidence 9999999999975 69999999999999999999988776 99999976667899999999999999999
Q ss_pred HHHHHHHHHHh
Q 002054 593 LQILDHMEREI 603 (974)
Q Consensus 593 ~~I~~~m~~~i 603 (974)
.+|.+.|++++
T Consensus 225 ~~l~~~~~~~l 235 (236)
T TIGR01966 225 RELIELQKQAL 235 (236)
T ss_pred HHHHHHHHHHh
Confidence 99999999986
No 13
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=100.00 E-value=1.4e-34 Score=351.54 Aligned_cols=211 Identities=23% Similarity=0.337 Sum_probs=186.4
Q ss_pred cCeEEEeCCCC-CCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCcc-----ccccccCCCc
Q 002054 380 RPIYCESGNLP-ILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCIN-----EVGKRVGLNR 453 (974)
Q Consensus 380 R~I~ie~g~l~-~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~-----e~~~~~~~~r 453 (974)
|++++++|.++ +|||||++++|+|+|+|+|+ +|.+++ .+.++.+++++|...+|+.+ ..+|.|.|++
T Consensus 14 r~i~~e~G~ia~qAdGSa~v~~G~T~VlatV~--~~~~~~-----~~~df~pL~v~y~e~~~A~gkiP~~f~kreg~pse 86 (693)
T PRK11824 14 RTLTLETGKLARQANGAVLVRYGDTVVLVTVV--ASKEPK-----EGQDFFPLTVDYEEKTYAAGKIPGGFFKREGRPSE 86 (693)
T ss_pred ccEEEEECCcCCCCCeEEEEEECCeEEEEEEE--cCCCCC-----CCCCeeeeEEEEEehhhhccCCCcccccCCCCCCh
Confidence 78999999996 69999999999999999999 555532 23456778889988888755 4567889999
Q ss_pred hhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChh--hHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCC
Q 002054 454 REVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTS--MATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPST 531 (974)
Q Consensus 454 re~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~--~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~ 531 (974)
+|+.++++++|+|++++| +.|.|.|+|+++||++||+.+ +||+||+++||+++|||+.++|+||++|++++
T Consensus 87 ~eil~srlIdR~lrplfp--~~~~~~i~I~~~VL~~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~i~g----- 159 (693)
T PRK11824 87 KETLTSRLIDRPIRPLFP--KGFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDG----- 159 (693)
T ss_pred HHHHHHHHHhhhHHHhCC--CCCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECC-----
Confidence 999999999999999999 469999999999999999773 48999999999999999999999999999975
Q ss_pred CcccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 002054 532 GEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDD 611 (974)
Q Consensus 532 ~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~ 611 (974)
.+++||+..|+..++++++|++|.+.+++++..+ .+++++.|.+||+.|++++.+|.+.|++.+++.. ++.
T Consensus 160 ------~~ivdPt~~E~~~s~~~l~va~t~~~i~mie~~~--~~l~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~-~~~ 230 (693)
T PRK11824 160 ------EFVLNPTVEELEESDLDLVVAGTKDAVLMVESEA--KELSEEVMLEAIEFGHEAIQELIDAQEELAAEAG-PKW 230 (693)
T ss_pred ------EEEEcCCHHHHhhCcceEEEEEccCceEEEECCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCc
Confidence 6999999999999999999999998888888654 4699999999999999999999999999998877 433
Q ss_pred CC
Q 002054 612 RN 613 (974)
Q Consensus 612 ~~ 613 (974)
++
T Consensus 231 ~~ 232 (693)
T PRK11824 231 EW 232 (693)
T ss_pred cc
Confidence 33
No 14
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=100.00 E-value=2.4e-35 Score=323.28 Aligned_cols=232 Identities=20% Similarity=0.313 Sum_probs=204.5
Q ss_pred HHHHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCce
Q 002054 352 VDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPTK 429 (974)
Q Consensus 352 ~~~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~~ 429 (974)
.++.+++.++ ..+++|+|+|||.++|+|++++++|.+++++|||+++.|+|+|+|+|+.+ .|.. ..++++
T Consensus 8 ~~~~e~~~i~-~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~~~~p~~-------~~~~~g 79 (271)
T PRK04282 8 IPEIKKDYIL-SLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFP-------DTPNEG 79 (271)
T ss_pred hhHHHHHHHH-HHHhcCCCCCCCCCccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEEEecCCC-------CCCCCC
Confidence 5567777776 56689999999999999999999999999999999999999999999954 2322 136789
Q ss_pred eEEEEEecCCCCccccccccCCCchhhhHHHHHHHHhhhcCCC--------CCCCCeEEEEEEEEEcCCCChhhHHHHHH
Q 002054 430 RFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPP--------ENDFPYTVRVNSEVMASDGSTSMATVCGG 501 (974)
Q Consensus 430 ~~~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~vi~~--------~~~~p~tI~V~v~VLesdGs~~~A~v~aa 501 (974)
++.++|+|+|++...+ +.+.+++++..++++++|+|++..+. ..++.|+|+|+++||++|||+++||++|+
T Consensus 80 ~i~~~v~~~~~a~~~~-~~~~~~~~~~~l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~daa~~Aa 158 (271)
T PRK04282 80 VLIVNAELLPLASPTF-EPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAA 158 (271)
T ss_pred EEEEEEEECCCcCccc-cCCCCCHHHHHHHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHHHHHHHHH
Confidence 9999999999998765 45678889999999999998664221 13568999999999999999999999999
Q ss_pred HHHHHHcCCC--------------------ccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeC
Q 002054 502 SMALMDAGIP--------------------LQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTR 561 (974)
Q Consensus 502 ~lAL~dagvP--------------------i~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~ 561 (974)
++||+|+++| |+++|.++++|++++ .+|+||+..|+..++..++|+.+.
T Consensus 159 ~aAL~~~~iP~~~~~~~~~~~~~~~~~~l~~~~~p~~vt~~~~~~-----------~~v~Dpt~~Ee~~~~~~l~va~~~ 227 (271)
T PRK04282 159 VAALLNTKVPAVEEGEDGVVDKLGEDFPLPVNDKPVTVTFAKIGN-----------YLIVDPTLEEESVMDARITITTDE 227 (271)
T ss_pred HHHHHhCCCCcEEEcCCceeccCCCcccCCCCCeeEEEEEEEECC-----------EEEECCCHHHHhhcCceEEEEECC
Confidence 9999999995 999999999999964 699999999999999999999999
Q ss_pred Cc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 002054 562 IG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREIS 604 (974)
Q Consensus 562 ~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~ 604 (974)
+| ++.++..+ +++++.+.|.+|+++|+++++++.+.|+++++
T Consensus 228 ~g~i~~l~~~g-~~~~~~~~l~~~i~~A~~~~~~l~~~~~~~l~ 270 (271)
T PRK04282 228 DGNIVAIQKSG-IGSFTEEEVDKAIDIALEKAKELREKLKEALG 270 (271)
T ss_pred CCcEEEEEcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 85 88998864 36799999999999999999999999999884
No 15
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=1.7e-35 Score=356.58 Aligned_cols=281 Identities=22% Similarity=0.304 Sum_probs=248.7
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR 757 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~ 757 (974)
.++++|+++.|+|+++.++|+||++. |.+||+|+||++|.++.++.+.|++||.|+|+|+++|. ++++.||+|.+.++
T Consensus 197 ~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~ 275 (565)
T PRK06299 197 ENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGED 275 (565)
T ss_pred hcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccC
Confidence 57899999999999999999999996 99999999999999999999999999999999999997 78999999999999
Q ss_pred cccc------cCce---------EEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEeecccc
Q 002054 758 PEAD------VKGV---------VEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAEC 822 (974)
Q Consensus 758 ~~~~------~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~i 822 (974)
||.. .|.. .+|.++++.+|+++|+|+++++|.....+|. ..+++||.+.+.| +++
T Consensus 276 p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~-------~~~~~G~~v~v~V---~~i 345 (565)
T PRK06299 276 PWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPS-------KVVSVGQEVEVMV---LEI 345 (565)
T ss_pred hhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCHH-------HhcCCCCEEEEEE---EEE
Confidence 9975 2433 4567777788999999999999865333443 5689999999999 999
Q ss_pred cccccccccccccccccccccccccCCCCCCCcEEEEEec-----------------------ccC---cCCCcccccCC
Q 002054 823 DEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS-----------------------STN---IQKSTSFSQRE 876 (974)
Q Consensus 823 D~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~-----------------------~~~---~~~~~~~k~Gq 876 (974)
|++++++.||+++...+| |......+++|+++.|.|.+ +|. ......|++||
T Consensus 346 d~~~~~i~ls~k~~~~~p--~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd 423 (565)
T PRK06299 346 DEEKRRISLGLKQCKENP--WEEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGD 423 (565)
T ss_pred cCCCCEEEEehHHhccch--hhhHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCC
Confidence 999999999999888888 88888888899999999987 443 22335899999
Q ss_pred eEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CC
Q 002054 877 REELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KK 946 (974)
Q Consensus 877 ~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~ 946 (974)
.|+++|+.+|++++++. |+|++..+|| ..+++++|++|.|+|+++.++|+||++++|+.||||.+++. .+
T Consensus 424 ~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~G~vV~G~V~~v~~~G~fV~l~~gi~g~i~~se~s~~~~~~~~~ 503 (565)
T PRK06299 424 EVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATE 503 (565)
T ss_pred EEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCCCCEEEEEEEEEecCceEEecCCCcEEEEEHHHhcchhccCccc
Confidence 99999999999999999 9999999999 47789999999999999999999999999999999999773 45
Q ss_pred CCCCCCEEEEEEEEEeC-CCceeeeec
Q 002054 947 DFVVGDELLVKCSSFTG-KGIPVVSLV 972 (974)
Q Consensus 947 ~f~vGd~V~vkVl~id~-~~~~~~~~~ 972 (974)
.|++||.|+|+|+++|. ++...+|+.
T Consensus 504 ~~~~Gd~v~~~V~~vd~~~~~i~LS~k 530 (565)
T PRK06299 504 VLKVGDEVEAKVINIDRKNRRISLSIK 530 (565)
T ss_pred cCCCCCEEEEEEEEEccccCEEEEEee
Confidence 79999999999999996 477777764
No 16
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=100.00 E-value=9.2e-35 Score=352.22 Aligned_cols=213 Identities=21% Similarity=0.316 Sum_probs=189.2
Q ss_pred cCeEEEeCCC-CCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCcc-----ccccccCCCc
Q 002054 380 RPIYCESGNL-PILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCIN-----EVGKRVGLNR 453 (974)
Q Consensus 380 R~I~ie~g~l-~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~-----e~~~~~~~~r 453 (974)
|++++++|.+ ++|+|||++++|+|+|+|+|+ +|.+.+ .+.++.+++++|...+|+.+ ..+|.|.|++
T Consensus 5 R~i~ie~G~la~~AdGSa~v~~G~T~VlatV~--~~~~~~-----~~~df~pL~vey~e~~~A~gkipg~f~kReg~p~~ 77 (684)
T TIGR03591 5 RTLTLETGKIARQADGAVVVRYGDTVVLVTVV--AAKEAK-----EGQDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSE 77 (684)
T ss_pred ccEEEEECCcCCCCCeEEEEEECCeEEEEEEE--cCCCCC-----CCCceEeEEEEEEehhhhccCCCCCcccCCCCCCH
Confidence 7999999999 579999999999999999999 665532 23456788889988777665 4567889999
Q ss_pred hhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCChh--hHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCC
Q 002054 454 REVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTS--MATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPST 531 (974)
Q Consensus 454 re~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~~--~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~ 531 (974)
+|+.++++++|+|++++| ..|.|.|+|+++||++||+.+ .||+||+++||+++|||++++|+||++|++++
T Consensus 78 ~eil~srlIdR~lrplfp--~~~~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~idg----- 150 (684)
T TIGR03591 78 KETLTSRLIDRPIRPLFP--KGFRNEVQVVATVLSYDPENDPDILAIIGASAALAISGIPFNGPIAAVRVGYIDG----- 150 (684)
T ss_pred HHHHHHHHHhhHHHHhcC--CCCCceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECC-----
Confidence 999999999999999999 579999999999999999974 49999999999999999999999999999965
Q ss_pred CcccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 002054 532 GEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDD 611 (974)
Q Consensus 532 ~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~ 611 (974)
.+++||+..|+..++++++|+++.+++++++..+ ..+++++|.+||+.|++++.+|++.|++.+++...++.
T Consensus 151 ------~~ildPt~~E~~~s~~~l~va~t~~~i~mie~~~--~~i~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~~~k~ 222 (684)
T TIGR03591 151 ------QYVLNPTVDELEKSDLDLVVAGTKDAVLMVESEA--KELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKEKW 222 (684)
T ss_pred ------EEEEcCCHHHHhhCCceEEEEccCCcEEEEEcCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCc
Confidence 6999999999999999999999998888888754 47999999999999999999999999999998876554
Q ss_pred CCC
Q 002054 612 RNS 614 (974)
Q Consensus 612 ~~~ 614 (974)
.+.
T Consensus 223 ~~~ 225 (684)
T TIGR03591 223 EFV 225 (684)
T ss_pred cCC
Confidence 443
No 17
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=100.00 E-value=1.1e-34 Score=346.34 Aligned_cols=300 Identities=22% Similarity=0.317 Sum_probs=253.8
Q ss_pred EEecCHHHHHHHHHH-HHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEE
Q 002054 658 VVAKNRSVMEKVLEK-VDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSL 736 (974)
Q Consensus 658 i~~~~~~~~~~a~~~-i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~v 736 (974)
+..+.+..++.+.+. ..... ..+++|++++|+|+++.++|+||++ +|.+||+|.++++|.++.++.+.|++||.++|
T Consensus 162 iv~Srk~~l~~~~~~~~~~~~-~~l~~G~~v~g~V~~i~~~G~~V~l-~g~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v 239 (516)
T TIGR00717 162 IVVSRRAYLEEERSQAREELL-ENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKV 239 (516)
T ss_pred EEEEHHHHHHHHHHHHHHHHH-HhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCCCCCCCHHHhccCCCEEEE
Confidence 334455555544322 22322 5789999999999999999999999 58999999999999999999999999999999
Q ss_pred EEEEEcc-CCceEEEEeccCCCcccc------cCce---------EEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCC
Q 002054 737 RCIGQDV-RGNIKLSLKAVSPRPEAD------VKGV---------VEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNE 800 (974)
Q Consensus 737 kVl~id~-~gri~LS~K~~~~~~~~~------~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~ 800 (974)
+|+++|. ++++.||+|.+.++||.. .|.. .+|.++++.+|+.+|+|+++++|......|.
T Consensus 240 ~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~---- 315 (516)
T TIGR00717 240 KVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPS---- 315 (516)
T ss_pred EEEEEECCCCcEEEEEEecchhHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHH----
Confidence 9999998 689999999998888864 3444 4566777778999999999999864333332
Q ss_pred CCCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec------------------
Q 002054 801 TPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS------------------ 862 (974)
Q Consensus 801 ~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~------------------ 862 (974)
..+++||.+.+.| +++|++++++.||+++...+| |......+++|++++|+|.+
T Consensus 316 ---~~~~vG~~v~v~V---~~id~~~~~i~lS~k~~~~~p--~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv 387 (516)
T TIGR00717 316 ---KVVKKGDEVEVMI---LDIDPERRRLSLGLKQCKANP--WEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLI 387 (516)
T ss_pred ---HhccCCCEEEEEE---EEEcCCCCEEEEEehhcccCc--HHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEE
Confidence 5689999999999 999999999999999888888 88887788899999999988
Q ss_pred -----ccCcC---CCcccccCCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeC
Q 002054 863 -----STNIQ---KSTSFSQREREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLG 931 (974)
Q Consensus 863 -----~~~~~---~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~ 931 (974)
+|... ....|++||.|+++|+.+|++++++. |+|++..+|| ..+++++|++++|+|++++++|+||+|+
T Consensus 388 ~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~ 467 (516)
T TIGR00717 388 HLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFGAFVELP 467 (516)
T ss_pred EHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhhccCcceEEEEEEEEEecceEEEEcC
Confidence 45432 22579999999999999999999998 9999999999 4677999999999999999999999999
Q ss_pred CCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeee
Q 002054 932 GGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSL 971 (974)
Q Consensus 932 ~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~ 971 (974)
+++.||||.++++ .+.|++||+|+|+|+++|. ++...+|+
T Consensus 468 ~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~ls~ 515 (516)
T TIGR00717 468 GGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSV 515 (516)
T ss_pred CCeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 9999999999863 4579999999999999997 46666765
No 18
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.2e-35 Score=338.36 Aligned_cols=286 Identities=19% Similarity=0.214 Sum_probs=250.2
Q ss_pred ecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEE
Q 002054 660 AKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739 (974)
Q Consensus 660 ~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl 739 (974)
+..+...++++..++ ..++.|++++|+|+...+.|+.|++. |++||+|.|+++..++++...+ +|.++.++++
T Consensus 86 S~~k~~~~~~w~~l~----~~~e~~~~V~~~v~~~vKGG~~Vdi~-gvr~FlP~S~v~~r~v~d~~~~--~Gk~~~~kii 158 (541)
T COG0539 86 SRRKAERERAWEKLE----EAFENGEIVEGKITGKVKGGLTVDIE-GVRAFLPGSLVDVRPVRDLDPL--IGKELEFKIL 158 (541)
T ss_pred eHHHHHHHHhHHHHH----HHHhcCCeEEEEEEEEecCcEEEEEC-CEEEeccHHHhccccccccccc--CCceEEEEEE
Confidence 344455555655555 35689999999999999999999995 6999999999999999887765 5999999999
Q ss_pred EEcc-CCceEEEEeccCCCccc----------ccC---------ceEEEEEeecCCcceeeEEeeccCCCCCCCCCCCCC
Q 002054 740 GQDV-RGNIKLSLKAVSPRPEA----------DVK---------GVVEGSVPVNKQATDVWASVGDVSNGQNPELPMRKN 799 (974)
Q Consensus 740 ~id~-~gri~LS~K~~~~~~~~----------~~g---------~~~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~ 799 (974)
++|. ++++.+|+|++++.... +.| .+.+|+|+++ .|++|++|+++|+|.+ ..+|.
T Consensus 159 e~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdi-gGvdGLlHiseiS~~r-v~~P~--- 233 (541)
T COG0539 159 ELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDI-GGVDGLLHISEISWKR-VDHPS--- 233 (541)
T ss_pred EEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEe-cCeeeEEehhhccccc-cCCHH---
Confidence 9998 78999999988763222 123 4556777777 4599999999999987 56777
Q ss_pred CCCCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec-----------------
Q 002054 800 ETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS----------------- 862 (974)
Q Consensus 800 ~~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~----------------- 862 (974)
+.+++||.|.|+| +++|++++|++||+|++.++| |....+.+++|+.+.|+|.+
T Consensus 234 ----~vvkvGd~VkvkV---i~~D~e~~RVsLSlK~l~~dP--w~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGl 304 (541)
T COG0539 234 ----EVVKVGDEVKVKV---ISLDEERGRVSLSLKQLEEDP--WEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGL 304 (541)
T ss_pred ----HhcccCCEEEEEE---EEEccCCCeEEEEehhcccCc--HHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccce
Confidence 8999999999999 999999999999999999999 99999999999999999988
Q ss_pred ------ccCcC--CCcccccCCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeC
Q 002054 863 ------STNIQ--KSTSFSQREREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLG 931 (974)
Q Consensus 863 ------~~~~~--~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~ 931 (974)
+|.+. .+..+++||.|+++||++|+++++++ |+|++..+|| +...|++|++++|+|+++++||+||.|+
T Consensus 305 vhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~v~g~v~~~t~~g~fv~le 384 (541)
T COG0539 305 VHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITDFGAFVELE 384 (541)
T ss_pred eechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcCCCCeEEEEEeeecccceEEccC
Confidence 78654 34699999999999999999999999 9999999999 5677999999999999999999999999
Q ss_pred CCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCc
Q 002054 932 GGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 932 ~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~ 966 (974)
+|++||+|.+++. ...|+.||+++++|+.+|.++.
T Consensus 385 ~gidG~vh~~d~sw~~~~~~~~~~k~Gd~v~~~vl~vd~~~~ 426 (541)
T COG0539 385 GGIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLAVDKEKE 426 (541)
T ss_pred CCccceEEHHhcCccccCcHHHhhccCcEEEEEEEEEecccc
Confidence 9999999999774 2379999999999999998854
No 19
>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1. This family contains the archaeal protein orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt.
Probab=100.00 E-value=8.4e-35 Score=311.43 Aligned_cols=203 Identities=19% Similarity=0.311 Sum_probs=180.7
Q ss_pred CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC----CCCceeeEeeccccccccCCCCCccccccCCCCchh
Q 002054 67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS----VRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERE 141 (974)
Q Consensus 67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~----~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~e 141 (974)
=|++++++|.+ .+|||||++++|+|+|+|+|++|++ .. ..++.+|+|+|....||. +.+|+++|+++|
T Consensus 18 ~R~~~~~~g~~-~~a~GSa~~~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~~~a~------~~~~~~~~~~~~ 90 (230)
T TIGR02065 18 LRPIKIEAGVL-KNADGSAYVEFGGTKIIAAVYGPREMHPRHLQLPDRAVLRVRYHMAPFST------DERKRPGPSRRE 90 (230)
T ss_pred ccCeEEEECCC-CCCCeEEEEEECCcEEEEEEeCCCccccccccCCCceEEEEEEEeCCccc------CCccCCCCCccH
Confidence 48899999999 8999999999999999999999876 22 246778999998877655 355568899999
Q ss_pred hhHHHhhcCCccccccCCCCC--ceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCC
Q 002054 142 LLVGRIIDRPIRPLFPAGFYH--EVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPT 219 (974)
Q Consensus 142 il~~RlidR~lrplfp~~~~~--~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt 219 (974)
++++|+|+|+|||+++.++++ .++|.++||+.||+.. ++|+|||++||++|||||+++|+||++|+++|++|+|||
T Consensus 91 ~~~s~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~DG~~~--~aai~aa~lAL~dagIp~~~~v~avtv~~~~~~~v~Dpt 168 (230)
T TIGR02065 91 IEISKVIREALEPAILLEQFPRTAIDVFIEVLQADAGTR--CAGLTAASLALADAGIPMRDLVVGVAVGKVDGVVVLDLN 168 (230)
T ss_pred HHHHHHHHHHHHHHhChhhcCCeEEEEEEEEEEcCCCHH--HHHHHHHHHHHHHcCCccccceeeEEEEEECCeEEECCC
Confidence 999999999999999988755 4555577999999754 999999999999999999999999999999999999999
Q ss_pred HHHHhcCccceeEee--eCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 002054 220 MDELSLSDLNLVYAC--TREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKA 279 (974)
Q Consensus 220 ~~e~~~s~~~l~v~~--t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~ 279 (974)
.+|++.++.+++|+. +.+.++|+|..+ .+++++|.+||++|+++|++++++|++.+++.
T Consensus 169 ~~Ee~~~~~~l~va~~~~~~~i~~i~~~g-~~~~e~~~~~l~~a~~~~~~l~~~~~~~l~~~ 229 (230)
T TIGR02065 169 EEEDMYGEADMPVAMMPKLGEITLLQLDG-DMTPDEFRQALDLAVKGIKIIYQIQREALKNK 229 (230)
T ss_pred HHHhhcCCCceEEEEeCCCCCEEEEEEec-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999997 456699999998 69999999999999999999999999988653
No 20
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-34 Score=301.45 Aligned_cols=224 Identities=34% Similarity=0.475 Sum_probs=201.6
Q ss_pred HhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccc
Q 002054 365 IAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINE 444 (974)
Q Consensus 365 l~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e 444 (974)
..+++|+|||.++|+|+|.++.|++++++||++|++|+|+|+|+|+ ||.+.. ...+.++..+.++++|++.|||+.+
T Consensus 4 ~~~~~R~dgR~~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~vs--Gp~e~~-p~~l~~~~~g~~t~ey~m~p~sT~~ 80 (230)
T COG0689 4 SEDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVS--GPREPV-PRFLRGTGKGWLTAEYGMLPRSTDE 80 (230)
T ss_pred cccCcCCCCCCcccccceEEEeccccCCCccEEEEeCCeEEEEEEe--cCCCCC-ChhhcCCCceEEEEEEecccccccc
Confidence 4689999999999999999999999999999999999999999999 888743 3345567889999999999999966
Q ss_pred cccccCCCc-hhhhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeee
Q 002054 445 VGKRVGLNR-REVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVG 522 (974)
Q Consensus 445 ~~~~~~~~r-re~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~g 522 (974)
+.+. .+.+ |++++++++.++|++++.+ +.||. +|.|+++|++.||++..|+++|+++||+|||+||+++++|+|+|
T Consensus 81 R~~~-~~~~gR~~eisrli~~al~~~i~L-~~~p~~~I~i~~dVlqaDggTrta~It~A~lAL~DAgipl~~~vaaiSvg 158 (230)
T COG0689 81 RKKR-EADRGRTKEISRLIGRALRAVIDL-ELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVG 158 (230)
T ss_pred cccc-cccccchhHHHHHHHHHHHHHhhh-hhcCccEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCchhhheeEeEEE
Confidence 5444 3444 9999999999999999999 79998 59999999999999999999999999999999999999999999
Q ss_pred eeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054 523 LVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMER 601 (974)
Q Consensus 523 li~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~ 601 (974)
++++ .+++|++..||..+..|.+|+.+.+| +.-+|.-...+.+++++|.++|+.|.+++.++.+.|++
T Consensus 159 i~~~-----------~~~lDl~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~~~~~del~~lL~la~~g~~~~~~~~~~ 227 (230)
T COG0689 159 IVDG-----------VIVLDLDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQRE 227 (230)
T ss_pred EECC-----------ceEecCcchhhcccccCceEEEEecCCeEEEEEEeccCCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9986 59999999999999888888877765 56666666667899999999999999999999999999
Q ss_pred Hhc
Q 002054 602 EIS 604 (974)
Q Consensus 602 ~i~ 604 (974)
+|.
T Consensus 228 al~ 230 (230)
T COG0689 228 ALA 230 (230)
T ss_pred HhC
Confidence 873
No 21
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=100.00 E-value=6.7e-35 Score=352.01 Aligned_cols=217 Identities=23% Similarity=0.310 Sum_probs=194.9
Q ss_pred CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEE-eCCC-CCCCCceeeEeeccccccccCCCCCccc---cccCCCCchh
Q 002054 67 SRLITLETGKIARFANGAVVLGMDETKVLSTVT-SSKG-DSVRDFLPLTVDYQEKQFAQGVIPNTYM---RREGAPKERE 141 (974)
Q Consensus 67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~-~~~~-~~~~~f~pL~v~y~e~~~a~g~ip~~~~---~Reg~p~~~e 141 (974)
-|++.+++|.++ .|+|||++++|+|+|||+|+ ++.+ ....+|+ +.++|.+++|..+++|..+. +|+|+|++||
T Consensus 448 iRpI~~e~G~Lp-~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l-~~~~~~~~f~~~y~fPPfs~ge~~r~g~psrRE 525 (891)
T PLN00207 448 IRPINSSCGLLP-RAHGSALFTRGETQALAVVTLGDKQMAQRIDNL-VDADEVKRFYLQYSFPPSCVGEVGRIGAPSRRE 525 (891)
T ss_pred cceEEEEeCCcC-CCCceEEEEECCeEEEEEEEecCcccccccccc-ccccceeeEEEEEEcCCCCCccccCCCCCCHHH
Confidence 478999999995 59999999999999999997 6655 4455666 78899999999999999765 8899999999
Q ss_pred hhHHHhhcCCccccccCC--CCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEE-C-------
Q 002054 142 LLVGRIIDRPIRPLFPAG--FYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRI-C------- 211 (974)
Q Consensus 142 il~~RlidR~lrplfp~~--~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i-~------- 211 (974)
++++||++|+|||+||.. |.+.++|+++||++||+.+ +||+||||+||++|||||+++|+||+||++ +
T Consensus 526 i~hg~L~eRALrpvip~~~~fP~tIrV~~~VLesDGSss--mAaV~aaSLALmDAGIPmk~~VAGvsvGli~d~~~~~~~ 603 (891)
T PLN00207 526 IGHGMLAERALEPILPSEDDFPYTIRVESTITESNGSSS--MASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGD 603 (891)
T ss_pred HHHHHHHHHHHHHhCCcccCCCEEEEEEEEEEeCCCChH--HHHHHHHHHHHHhcCCCccCceeEEEEEEEecccccCCC
Confidence 999999999999999976 9999999999999999966 999999999999999999999999999999 3
Q ss_pred CEE--EEcCCHHHHhcCccceeEeeeCCeEEEEEecC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccc
Q 002054 212 GQF--IVNPTMDELSLSDLNLVYACTREKTLMIDVQA--REISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYK 287 (974)
Q Consensus 212 g~~--vldPt~~e~~~s~~~l~v~~t~~~i~mie~~~--~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g~~k~~~~ 287 (974)
|++ ++||+..|+..+++||.|+||.++|+|+|+++ ++++++.|.+||++|++++..|++.|++.+.+-.++...+.
T Consensus 604 g~~~IL~Dp~g~Ed~~gdmDfkVAgT~~gIt~iqmd~k~~gis~e~l~eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~a 683 (891)
T PLN00207 604 GSPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPIMERALLQAKDGRKHILAEMSKCSPPPSKRLSKYA 683 (891)
T ss_pred CcEEEEeCCCHHHHhcCCceEEEEecccceEEEEEecccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccC
Confidence 354 46999999999999999999999999999854 56899999999999999999999999999877655444443
No 22
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=100.00 E-value=2.2e-33 Score=330.69 Aligned_cols=277 Identities=14% Similarity=0.078 Sum_probs=238.3
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR 757 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~ 757 (974)
..++.|++++|+|+++.++|++|++. |..||+|.|++++.+..++... +|+.++|+|+++|. ++++.||+|+++..
T Consensus 111 ~~~~~g~~v~g~V~~~~~~G~~V~i~-g~~~flP~s~~~~~~~~~~~~~--vG~~i~~~V~~id~~~~~v~lSrk~~~~~ 187 (491)
T PRK13806 111 EAYENGVPVEGKVTGTCKGGFNVEVL-GRRAFCPVSQIDLRYVEDPESY--VGQTFQFLITRVEENGRNIVVSRRALLER 187 (491)
T ss_pred HHHhCCCEEEEEEEEEEcCCEEEEEC-CEEEEEEHHHhccccCCChHHc--CCCeEEEEEEEEECCCCeEEEEeehhhhh
Confidence 45789999999999999999999995 8999999999999988888774 89999999999998 67999999988643
Q ss_pred ----ccc------ccCce---------EEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEee
Q 002054 758 ----PEA------DVKGV---------VEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRS 818 (974)
Q Consensus 758 ----~~~------~~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~ 818 (974)
+|. +.|.. .+|.|+++..|+++|+|+++++|.+. ..|. +.+++||.+.++|
T Consensus 188 ~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~-~~~~-------~~~~vGd~i~vkV-- 257 (491)
T PRK13806 188 EQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRV-QKAD-------EAVSVGDTVRVKV-- 257 (491)
T ss_pred hhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccc-cChh-------HhcCCCCEEEEEE--
Confidence 222 13433 45677777778999999999999753 2333 6789999999999
Q ss_pred cccccccc----cccccccccccccccccccccCCCCCCCcEEEEEec-----------------------ccCcC---C
Q 002054 819 AAECDEEE----KASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS-----------------------STNIQ---K 868 (974)
Q Consensus 819 ~l~iD~~~----r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~-----------------------~~~~~---~ 868 (974)
+++|+++ +++.||+++..++| |......+++|+++.|.|.+ +|... .
T Consensus 258 -l~id~~~~~~~~ri~lS~K~~~~~p--~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~ 334 (491)
T PRK13806 258 -LGIERAKKGKGLRISLSIKQAGGDP--WDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKP 334 (491)
T ss_pred -EEEecccCCcceEEEEEehhhhccc--chhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCH
Confidence 9999987 47999999998888 99999999999999999988 56432 2
Q ss_pred CcccccCCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-
Q 002054 869 STSFSQREREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE- 944 (974)
Q Consensus 869 ~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~- 944 (974)
...|++||.|+++|+++|++++++. |+|++..+|| ...+|++|++|+|+|+++++||+||++++|+.||||.++++
T Consensus 335 ~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~ 414 (491)
T PRK13806 335 EDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISR 414 (491)
T ss_pred HHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCc
Confidence 3479999999999999999999999 9999999999 47799999999999999999999999999999999999874
Q ss_pred ------CCCCCCCCEEEEEEEEEeCCC-ceeeee
Q 002054 945 ------KKDFVVGDELLVKCSSFTGKG-IPVVSL 971 (974)
Q Consensus 945 ------~~~f~vGd~V~vkVl~id~~~-~~~~~~ 971 (974)
.+.|++||+|+|+|+++|+++ +..+|+
T Consensus 415 ~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls~ 448 (491)
T PRK13806 415 AGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAP 448 (491)
T ss_pred ccccchhhcCCCCCEEEEEEEEEeCCCCEEEEEe
Confidence 357999999999999999765 444443
No 23
>PRK00173 rph ribonuclease PH; Reviewed
Probab=100.00 E-value=1.6e-33 Score=302.75 Aligned_cols=201 Identities=20% Similarity=0.273 Sum_probs=178.9
Q ss_pred CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC---CCCceeeEeeccccccccCCCCCccccc------cCC
Q 002054 67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS---VRDFLPLTVDYQEKQFAQGVIPNTYMRR------EGA 136 (974)
Q Consensus 67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~---~~~f~pL~v~y~e~~~a~g~ip~~~~~R------eg~ 136 (974)
=|++++++|.+ ++|+|||++++|+|+|+|+|+++.+ |. ..+..+|+|+|.-. |..+.+| .|+
T Consensus 11 ~R~i~~~~g~~-~~a~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~-------p~a~~~~~~~~~~~g~ 82 (238)
T PRK00173 11 LRPVTITRNFT-KHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGML-------PRATHTRNDREAAKGK 82 (238)
T ss_pred ccCeEEEeCCC-CCCCeeEEEEecCcEEEEEEEcCCCCCCccCCCCcEEEEEEEecC-------CCCCcccccccccCCC
Confidence 48899999998 8999999999999999999998776 42 34678999999544 4444444 378
Q ss_pred CCchhhhHHHhhcCCccccccCCCCCc--eEEEEEEEeccCCCChhhHHHHHHHHHhhcC-----------CCCCCCCeE
Q 002054 137 PKERELLVGRIIDRPIRPLFPAGFYHE--VQVMASVLSSDGKQDPDIMAANATSAALMLS-----------DIPWGGPIG 203 (974)
Q Consensus 137 p~~~eil~~RlidR~lrplfp~~~~~~--~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s-----------~iP~~~~v~ 203 (974)
|++++++++|+|+|+|||+||..++++ ++|+++||++||+.. .||+|||++||+++ ++||+++++
T Consensus 83 ~~~~~~~~sr~i~r~lr~~i~l~~l~~~~i~v~v~VL~~DG~~~--~aai~Aa~~AL~da~~~~~~~~~~~~ip~~~~~~ 160 (238)
T PRK00173 83 QGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTR--TASITGAYVALADALNKLVARGKLKKNPLKDQVA 160 (238)
T ss_pred CCccHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHH--HHHHHHHHHHHHHhhhhhhccCcccCCcccCcee
Confidence 999999999999999999999877766 899999999999985 99999999999977 999999999
Q ss_pred EEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEe--cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054 204 MIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLMIDV--QAREISEKDLEAGLRLAHPEAVKYLEPQIRLAE 277 (974)
Q Consensus 204 av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~--~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~ 277 (974)
+|++|+++|++|+|||.+|++.++.+|+|+++.++ |+|++. ++..+++++|.+|+++|++.+++++++|++.++
T Consensus 161 ~vt~~~~~~~~lvDpt~~Ee~~~~~~l~v~~~~~~~i~~v~~~g~g~~~~~e~l~~~i~~A~~~~~~l~~~~~~~l~ 237 (238)
T PRK00173 161 AVSVGIVDGEPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAALA 237 (238)
T ss_pred EEEEEEECCEEEECCCHHHHhcCCceEEEEECCCCCEEEEEccCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999865 999997 355799999999999999999999999988664
No 24
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=100.00 E-value=3.2e-33 Score=324.76 Aligned_cols=281 Identities=19% Similarity=0.166 Sum_probs=235.6
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccC-C
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVS-P 756 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~-~ 756 (974)
..++.|++++|+|+++.++|+||+|.++.+|+||.+|+++.+..++++.|++||.|+|+|+++|. +|++.||+|.+. .
T Consensus 31 ~~~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~~~~~ 110 (486)
T PRK07899 31 KYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVEVGDEVEALVLQKEDKEGRLILSKKRAQYE 110 (486)
T ss_pred hcCCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcccccCChhhcCCCCCEEEEEEEEEECCCCeEEEEehhhccc
Confidence 46899999999999999999999998889999999999999999999999999999999999986 689999999875 5
Q ss_pred Ccccc------cCceEEEEEeecCC-------cceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEeeccccc
Q 002054 757 RPEAD------VKGVVEGSVPVNKQ-------ATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECD 823 (974)
Q Consensus 757 ~~~~~------~g~~~~G~vv~i~~-------gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~iD 823 (974)
.+|.. .|..+.|+|+.+.. |+++|+|.+++++.+...+ . -.+|+.+.++| +++|
T Consensus 111 ~~w~~ie~~~e~g~~V~G~V~~v~k~G~~VdlGi~gflP~Sel~~~~~~~~---------~-~~vGq~V~vkV---leid 177 (486)
T PRK07899 111 RAWGTIEKIKEKDGVVTGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDL---------Q-PYIGQEIEAKI---IELD 177 (486)
T ss_pred chHHHHHHHhcCCCEEEEEEEEEECCeEEEEECCEEEEEhhHhcccccCCh---------h-hcCCCEEEEEE---EEEE
Confidence 66764 35555555444322 7999999999988542111 1 14899999999 9999
Q ss_pred cccccccccccccccc--ccccccccCCCCCCCcEEEEEec----------------------ccCc--CCCcccccCCe
Q 002054 824 EEEKASGFSQSSKSTL--KSTLASKSNSKPKKFTSQSDFFS----------------------STNI--QKSTSFSQRER 877 (974)
Q Consensus 824 ~~~r~i~ls~k~~~~~--~~~~~~~~~~~~~G~~v~g~V~~----------------------~~~~--~~~~~~k~Gq~ 877 (974)
++++++.||.+...+. ...|......+++|++++|.|++ +|.. +.+..|++||.
T Consensus 178 ~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~v~~~~~~~kvGd~ 257 (486)
T PRK07899 178 KNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGQE 257 (486)
T ss_pred CCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCCHHHhcCCCCE
Confidence 9999999999854321 12266777788999999999988 5643 23357999999
Q ss_pred EEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-------CC
Q 002054 878 EELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-------KD 947 (974)
Q Consensus 878 v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-------~~ 947 (974)
|+++|+.+|++++++. |+|++..+|| ...++++|++++|+|++|++||+||+|.+|+.||+|+++++. +.
T Consensus 258 V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~ 337 (486)
T PRK07899 258 VTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQV 337 (486)
T ss_pred EEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcccccCccce
Confidence 9999999999999998 9999999999 456789999999999999999999999999999999998752 35
Q ss_pred CCCCCEEEEEEEEEeC-CCceeeeec
Q 002054 948 FVVGDELLVKCSSFTG-KGIPVVSLV 972 (974)
Q Consensus 948 f~vGd~V~vkVl~id~-~~~~~~~~~ 972 (974)
|++||+|+|+|+++|. +++..+|+.
T Consensus 338 ~kvGd~V~VkIi~ID~e~rrI~LSlK 363 (486)
T PRK07899 338 VQVGDEVFVKVIDIDLERRRISLSLK 363 (486)
T ss_pred eCCCCEEEEEEEEEECCCCEEEEEEE
Confidence 8999999999999995 566667764
No 25
>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.1e-33 Score=289.34 Aligned_cols=225 Identities=27% Similarity=0.425 Sum_probs=204.2
Q ss_pred HHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCcc
Q 002054 364 IIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCIN 443 (974)
Q Consensus 364 il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~ 443 (974)
+-++|.|.|||.++|+|+|.+..|++.+++|||++++|||+|+|.|+ ||++.+..... .++...+++.|++.+|+++
T Consensus 8 ~seeg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV~--GPre~~~~~~~-~~~~a~lnc~~~~a~Fst~ 84 (245)
T KOG1068|consen 8 LSEEGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVY--GPREIRGKSAR-RPDKAVLNCEVSSAQFSTG 84 (245)
T ss_pred cCccccccCCCChhHhhhhhhhcCccccCCccchhhcCCeEEEEEEe--CCccccccccc-ccccceEEEEEeeeccccc
Confidence 45799999999999999999999999999999999999999999999 99997643333 5677889999999999999
Q ss_pred ccccccCCCchhhhHHHHHHHHhhhcCCCCCCCCe-EEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeee
Q 002054 444 EVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPY-TVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVG 522 (974)
Q Consensus 444 e~~~~~~~~rre~~~~~l~eral~~vi~~~~~~p~-tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~g 522 (974)
++++....++|+.+++.+++++|+++|.. +.||+ +|.|.++||++||+.+.||+||+++||.||||||++++.|+++|
T Consensus 85 ~r~~~~~~~rr~~e~s~~L~~afe~~I~~-~lyPrsqIDI~v~VleddG~~laa~inaatlAL~daGI~m~D~i~~~t~~ 163 (245)
T KOG1068|consen 85 DRKKRPKGDRREKELSLMLQQAFEPVILL-ELYPRSQIDIYVQVLEDDGSNLAAAINAATLALADAGIPMYDLITACTAG 163 (245)
T ss_pred hhccCCCccHHHHHHHHHHHHHHHHHHHh-hhCccccceEEEEEEECCCccHHHHHHHHHHHHHHcCCChhhhhhhceee
Confidence 98877777899999999999999999998 79999 59999999999999999999999999999999999999999999
Q ss_pred eeccCCCCCCcccceEEEecCCccccccCCccEEEE--eeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 002054 523 LVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME 600 (974)
Q Consensus 523 li~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va--~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~ 600 (974)
+.++ ..++|++..||......++|+ ++.+.|..+|++.+ ++.+.|...++.|.++|+++.+.|+
T Consensus 164 l~~~-----------~~l~Dl~~~eesa~~~~ltVa~l~~~~~i~~l~~~~~---~~~d~l~~vl~~a~~~c~~v~~~l~ 229 (245)
T KOG1068|consen 164 LADG-----------TPLLDLTSLEESARAPGLTVAALPNREEIALLQLDER---LHCDHLETVLELAIAGCKRVYERLR 229 (245)
T ss_pred ecCC-----------ccccccccchhhccCCceEEEEecCcceEEEEEecCC---CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9975 699999999998877667776 55666999999864 9999999999999999999999999
Q ss_pred HHhcCC
Q 002054 601 REISAP 606 (974)
Q Consensus 601 ~~i~~~ 606 (974)
..+.+.
T Consensus 230 ~~l~~~ 235 (245)
T KOG1068|consen 230 LVLREH 235 (245)
T ss_pred HHHHHH
Confidence 887653
No 26
>TIGR01966 RNasePH ribonuclease PH. This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans.
Probab=100.00 E-value=4.9e-32 Score=291.12 Aligned_cols=203 Identities=21% Similarity=0.250 Sum_probs=173.4
Q ss_pred CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCC---CCceeeEeeccccccccCCCCCcccccc---CCCCc
Q 002054 67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSV---RDFLPLTVDYQEKQFAQGVIPNTYMRRE---GAPKE 139 (974)
Q Consensus 67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~---~~f~pL~v~y~e~~~a~g~ip~~~~~Re---g~p~~ 139 (974)
=|++++++|.+ ++|+|||++++|+|+|||+|+++.. |.. .+..+|+|+|.-..+|.. .+.+|+ |+|++
T Consensus 10 ~R~i~i~~G~~-~~A~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~----~~~~r~~~~g~~~~ 84 (236)
T TIGR01966 10 LRPVSITRDFL-KHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQ----TRNRRESAKGKQSG 84 (236)
T ss_pred ccCeEEEeCCc-CCCCceEEEEecCCEEEEEEEccCccCCcccCCCcEEEEEEEecCCCCCC----CCccccccCCCCCc
Confidence 48899999976 9999999999999999999997665 321 245678888854443331 112444 78888
Q ss_pred hhhhHHHhhcCCccccccCCCCCce--EEEEEEEeccCCCChhhHHHHHHHHHhhcC-----------CCCCCCCeEEEE
Q 002054 140 RELLVGRIIDRPIRPLFPAGFYHEV--QVMASVLSSDGKQDPDIMAANATSAALMLS-----------DIPWGGPIGMIR 206 (974)
Q Consensus 140 ~eil~~RlidR~lrplfp~~~~~~~--~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s-----------~iP~~~~v~av~ 206 (974)
++++++|+|+|+|||+|+.+++++. +|+++||++||+.. +||+|||++||+++ +|||++++++|+
T Consensus 85 ~~~e~~~~i~r~lr~~i~l~~l~~~~i~I~v~VL~~DG~~~--~aai~Aa~aAL~da~~~~~~~~~~~~ip~~~~~~~vt 162 (236)
T TIGR01966 85 RTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTR--TASITGAFVALADAISKLHKRGILKESPIRDFVAAVS 162 (236)
T ss_pred cHHHHHHHHHHHHHHhcCHhhcCCeEEEEEEEEEeCCCCHH--HHHHHHHHHHHHHHHHhhhhcCcccCCCccCceeEEE
Confidence 9999999999999999998777666 88999999999885 99999999999977 999999999999
Q ss_pred EEEECCEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEec--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054 207 IGRICGQFIVNPTMDELSLSDLNLVYACTREK-TLMIDVQ--AREISEKDLEAGLRLAHPEAVKYLEPQIRLA 276 (974)
Q Consensus 207 vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~~--~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~ 276 (974)
+|++++++|+|||.+|++.++.+|+++.+.++ |+|+|.. +..+++++|.+|+++|+++++++++.|++.+
T Consensus 163 ~~~~~~~~v~Dpt~~Ee~~~~~~l~l~~~~~~~i~~i~~~g~~~~~~~~~l~~~i~~a~~~~~~l~~~~~~~l 235 (236)
T TIGR01966 163 VGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQAL 235 (236)
T ss_pred EEEECCEEEECCChhHHhccCceEEEEEcCCCCEEEEEecCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999998777777777655 9999973 5789999999999999999999999988754
No 27
>PRK03983 exosome complex exonuclease Rrp41; Provisional
Probab=100.00 E-value=4e-32 Score=293.31 Aligned_cols=204 Identities=18% Similarity=0.310 Sum_probs=175.8
Q ss_pred CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CCCCCc----eeeEeeccccccccCCCCCccccccCCCCchh
Q 002054 67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DSVRDF----LPLTVDYQEKQFAQGVIPNTYMRREGAPKERE 141 (974)
Q Consensus 67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~~~~f----~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~e 141 (974)
=|++++++|.+ ++|||||++++|+|+|+|+|++|++ ...... ..|.+.|.-..++. . .+++++|++++
T Consensus 24 ~R~i~i~~G~l-~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~-----~-~~~~~~~~~~~ 96 (244)
T PRK03983 24 LRPIKIEVGVL-KNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSV-----D-ERKRPGPDRRS 96 (244)
T ss_pred ccceEEEeCCC-CCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCcc-----c-cccCCCCChhH
Confidence 47899999999 8999999999999999999999887 322222 34666665443333 2 23456799999
Q ss_pred hhHHHhhcCCccccccCCCCCc--eEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCC
Q 002054 142 LLVGRIIDRPIRPLFPAGFYHE--VQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPT 219 (974)
Q Consensus 142 il~~RlidR~lrplfp~~~~~~--~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt 219 (974)
++++|+|+|+|||+++.++++. ++|.++||+.||+.. ++|+|||++||+++||||+++++||+|++++|++++|||
T Consensus 97 ~~~s~~l~~~l~~~i~~~~~p~~~I~I~i~VL~~DG~~~--~aai~Aa~lAL~dagIp~~~~v~avtv~~~~~~~i~DPt 174 (244)
T PRK03983 97 IEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTR--VAGITAASLALADAGIPMRDLVAGCAVGKVDGVIVLDLN 174 (244)
T ss_pred HHHHHHHHHHHHHhccHHhCCCeEEEEEEEEEECCCCHH--HHHHHHHHHHHHhcCCccccceeEEEEEEECCEEEECCC
Confidence 9999999999999999887777 555566999999855 999999999999999999999999999999999999999
Q ss_pred HHHHhcCccceeEeeeC--CeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 002054 220 MDELSLSDLNLVYACTR--EKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAG 280 (974)
Q Consensus 220 ~~e~~~s~~~l~v~~t~--~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g 280 (974)
.+|++.++.+|+|+++. +.|+|+|..| .+++++|.+|+++|++++++++++|++.+++..
T Consensus 175 ~~Ee~~~~~~l~va~~~~~~~I~~l~~~G-~~~~~~~~~~i~~A~~~~~~i~~~i~~~l~~~~ 236 (244)
T PRK03983 175 KEEDNYGEADMPVAIMPRLGEITLLQLDG-NLTREEFLEALELAKKGIKRIYQLQREALKSKY 236 (244)
T ss_pred HHHhccCCceEEEEEECCCCCEEEEEEec-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999983 4499999998 699999999999999999999999999776544
No 28
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=99.98 E-value=7.2e-31 Score=275.58 Aligned_cols=228 Identities=21% Similarity=0.310 Sum_probs=201.3
Q ss_pred HHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCceeEEE
Q 002054 356 RKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPTKRFML 433 (974)
Q Consensus 356 ~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~~~~~v 433 (974)
.++.+. ..++.|.|+|||.++|+|+|.+++|+++.++|||+++.|+|||+|+|+.+ .|.++ .|++|.+.+
T Consensus 11 ~~~~i~-~ll~~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~eig~Pf~D-------tP~eG~~~~ 82 (272)
T COG2123 11 KREYIL-NLLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEPFPD-------TPNEGVLVV 82 (272)
T ss_pred HHHHHH-HHhccCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEEcccCCCCCC-------CCCCceEEe
Confidence 344443 67789999999999999999999999999999999999999999999954 56664 378999999
Q ss_pred EEecCCCCccccccccCCCchhhhHHHHHHHHhhh--------cCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHH
Q 002054 434 HYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA--------VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMAL 505 (974)
Q Consensus 434 ~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~~--------vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL 505 (974)
+.++.|.++..+- .|.|+.+.+++.++++|.++. +.+...++.|.|+++++||++|||..+||..|+.+||
T Consensus 83 n~El~Plas~~fE-~Gppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aAL 161 (272)
T COG2123 83 NVELSPLASPSFE-PGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAAL 161 (272)
T ss_pred eeeeecccccccc-CCCCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHHH
Confidence 9999999887653 456677888999999999843 1222257899999999999999999999999999999
Q ss_pred HHcCCC----------------------ccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc
Q 002054 506 MDAGIP----------------------LQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG 563 (974)
Q Consensus 506 ~dagvP----------------------i~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g 563 (974)
+++++| +.+++..++++.+++ .+++||+.+|+..+|..++|..+.+|
T Consensus 162 ~~t~vP~~~~~~~~~~v~~~~~~~~pl~~~~~pi~vt~a~ig~-----------~lvvDPsleEe~v~d~~ltit~~~~~ 230 (272)
T COG2123 162 LNTRVPKAVEVGDGEIVIEVEEEPVPLPVSNPPISVTFAKIGN-----------VLVVDPSLEEELVADGRLTITVNEDG 230 (272)
T ss_pred HhcCCCceeecCCcceeecccCCCcccccCCCceEEEEEEECC-----------EEEeCCCcchhhhcCceEEEEECCCC
Confidence 999988 678999999999986 79999999999999999999999998
Q ss_pred -eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 002054 564 -VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREIS 604 (974)
Q Consensus 564 -I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~ 604 (974)
|+++|..+ ++.++++.+.+|++.|.+.+.++.+.+.++|+
T Consensus 231 ~Iv~iqK~g-~~~~~~~~~~~~~~~A~~~~~kl~~~~~~~L~ 271 (272)
T COG2123 231 EIVAIQKVG-GGSITESDLEKALKTALSKAEKLREALKEALK 271 (272)
T ss_pred cEEEEEEcC-CCcCCHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 99999976 57899999999999999999999999998875
No 29
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.97 E-value=4.1e-31 Score=324.03 Aligned_cols=278 Identities=13% Similarity=0.100 Sum_probs=234.2
Q ss_pred cccccCcEEEEEEEEEe--eceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc------CCceEEE
Q 002054 679 REIEVGGIYKGVVTSVK--EYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV------RGNIKLS 750 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~--~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~------~gri~LS 750 (974)
..++.|++++|+|+++. +.|++|++..+.+||||.||++..+..++... +|+.++++|+.+|. ++++.||
T Consensus 394 ~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~~~~~~~~--vG~~ie~~V~~~~~~~~~~~~~~iVlS 471 (863)
T PRK12269 394 DAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPESL--IGLTSKFYIERISQSKQHRGNDNIVIN 471 (863)
T ss_pred HHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhccccccchHHh--CCCeEEEEEEEEecccccCCCCeEEEE
Confidence 34689999999999985 36999999768999999999987777666643 69999999999864 3689999
Q ss_pred EeccCCC--------ccc--ccCce---------EEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCc
Q 002054 751 LKAVSPR--------PEA--DVKGV---------VEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSST 811 (974)
Q Consensus 751 ~K~~~~~--------~~~--~~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~ 811 (974)
+|.++.. -+. +.|.. .+|.|+++ +|+++|+|+++++|.+. ..|. +.+++||+
T Consensus 472 rr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl-~Gv~Gfvp~SeiS~~~v-~~~~-------~~~kvGq~ 542 (863)
T PRK12269 472 RRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHV-ARPR-------EFVKKGQT 542 (863)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEchhcccccc-CCHH-------HhccCCCE
Confidence 9876431 111 12333 34666677 68999999999999763 2333 67899999
Q ss_pred ceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec-----------------------ccCc--
Q 002054 812 PAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS-----------------------STNI-- 866 (974)
Q Consensus 812 v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~-----------------------~~~~-- 866 (974)
+.++| +++|++++++.||+++..++| |....+.+++|++++|.|.+ +|..
T Consensus 543 v~vkV---i~iD~e~~rI~LSlK~l~~~p--~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~ 617 (863)
T PRK12269 543 IELKV---IRLDQAEKRINLSLKHFQPDP--WLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKT 617 (863)
T ss_pred EEEEE---EEEecCCCeEEEEEeccccch--hhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCcccc
Confidence 99999 999999999999999998888 99988999999999999988 7743
Q ss_pred -CCCcccccCCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEeccc
Q 002054 867 -QKSTSFSQREREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFEN 942 (974)
Q Consensus 867 -~~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se 942 (974)
+....|++||+|+++|+.+|+++++++ |+|++..||| ..++|++|++|+|+|+++++||+||+|++|+.||+|.++
T Consensus 618 ~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~se 697 (863)
T PRK12269 618 SKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDD 697 (863)
T ss_pred CCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHH
Confidence 334589999999999999999999999 9999999999 467899999999999999999999999999999999997
Q ss_pred CC--------CCCCCCCCEEEEEEEEEeCC-Cceeeeec
Q 002054 943 NE--------KKDFVVGDELLVKCSSFTGK-GIPVVSLV 972 (974)
Q Consensus 943 ~~--------~~~f~vGd~V~vkVl~id~~-~~~~~~~~ 972 (974)
+. ...|++||.|+|+|+++|++ ++..+|+.
T Consensus 698 ls~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K 736 (863)
T PRK12269 698 LSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVK 736 (863)
T ss_pred hhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEec
Confidence 64 23699999999999999965 56666754
No 30
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=6.7e-31 Score=303.74 Aligned_cols=344 Identities=21% Similarity=0.272 Sum_probs=257.0
Q ss_pred cCeEEEeCCCC-CCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccc-----cccccCCCc
Q 002054 380 RPIYCESGNLP-ILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINE-----VGKRVGLNR 453 (974)
Q Consensus 380 R~I~ie~g~l~-~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e-----~~~~~~~~r 453 (974)
|++.+|+|.+. +|+||++++.|+|.||++|+...+.+ +.++.+++++|+-..|+.|. ++|.|.|+.
T Consensus 14 ~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~~~~--------~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse 85 (692)
T COG1185 14 RTLTLETGKIARQANGAVLVRYGDTVVLATVVASKPKE--------GQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSE 85 (692)
T ss_pred eeEEEEcchhhhhcCccEEEEECCeEEEEEEeecCCCC--------CCCccceeEeeeeehhccCcCCCcccccCCCCCc
Confidence 78999999998 79999999999999999999543333 56888999999999999865 689999999
Q ss_pred hhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCCh--hhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCC
Q 002054 454 REVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGST--SMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPST 531 (974)
Q Consensus 454 re~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~--~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~ 531 (974)
+|+..++|++|.++|++| +.|-+.++|.++|++.|+.. ...+++|+|+||.-+++|+..+++|+.+|++++
T Consensus 86 ~e~L~sRLIDRpiRPlFp--~g~~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf~gpi~~vrvg~idg----- 158 (692)
T COG1185 86 KEILTSRLIDRPIRPLFP--KGFRNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDG----- 158 (692)
T ss_pred cchhhhhhcccccccccc--hhhccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCccCccceEEEEEECC-----
Confidence 999999999999999999 57888999999999999865 489999999999999999999999999999976
Q ss_pred CcccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 002054 532 GEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDD 611 (974)
Q Consensus 532 ~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~ 611 (974)
.++++|+..|-+.+++|+.||||.+.|.++..+.+ .++++++.+|+..+++..+.+.+++++......+...
T Consensus 159 ------~~vlNPt~~e~~~s~lDlvVAGT~~aV~MVE~~a~--~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g~~~~ 230 (692)
T COG1185 159 ------IFVLNPTLEELEESKLDLVVAGTKDAVNMVESEAD--ELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKW 230 (692)
T ss_pred ------EEEECCChHHhhhcceeeEecCChhhhheeecccc--cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccc
Confidence 79999999999999999999999999988888765 7999999999999999999999999988776653333
Q ss_pred CCCCc--ceee-----eeccchhhhhcCCCccchhh-----hhhhhCceEEeeCCEEEEEecCHHHHHHHHHHHH-HHhh
Q 002054 612 RNSPR--LATL-----KYDNDTLRRLIGPLGALKRK-----IEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVD-FIIG 678 (974)
Q Consensus 612 ~~~p~--~~~~-----~i~~~ki~~vIg~gGk~i~~-----i~~~~g~~Idi~dg~v~i~~~~~~~~~~a~~~i~-~l~~ 678 (974)
+..|. -..+ .+-.+++.+.++..+|.-|. +.++.-.++. +. .......+......++ ..++
T Consensus 231 ~~~~~~~~~~l~~~i~~~~~~~l~~a~~i~~K~eR~~~~~~~~~~i~~~~~---~~---e~~~~~~~~~~~~~l~~~~vR 304 (692)
T COG1185 231 ELEPPSLDEELEAKVRDLAEDELKEAVGIREKQERSAALDAIKEKIEEELS---GE---EESSLKEIKAILEKLEKKPVR 304 (692)
T ss_pred cccccCccHHHHHHHHHHhHHHHHHHhcccchhhhhhhHHHHHHHHHHHHh---hh---ccccHHHHHHHHHHHhHHHHH
Confidence 32221 0111 01123355555555544442 1111111111 00 0111122222222221 1111
Q ss_pred c-ccccCcEEEE-EEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc--CCceEEEEecc
Q 002054 679 R-EIEVGGIYKG-VVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV--RGNIKLSLKAV 754 (974)
Q Consensus 679 ~-~~~~G~i~~G-~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~--~gri~LS~K~~ 754 (974)
. -+.-+-..+| ....|++.++-|.+.| ..|.|.|..+...++..+...|+...+++++... .++..|+++-.
T Consensus 305 ~~Il~~~vR~DGR~~~~VRpi~~ev~~lp----r~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNF 380 (692)
T COG1185 305 RLILEGKVRIDGRFGDEVRPIGIEVGVLP----RTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNF 380 (692)
T ss_pred HHHhcCCcccCCCCcceeeeeeEEecCCC----CccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccC
Confidence 1 1233334445 4555667777776665 4899999998888999999999999999988654 35677777765
Q ss_pred CC
Q 002054 755 SP 756 (974)
Q Consensus 755 ~~ 756 (974)
-+
T Consensus 381 Pp 382 (692)
T COG1185 381 PP 382 (692)
T ss_pred CC
Confidence 44
No 31
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=3.4e-31 Score=276.29 Aligned_cols=200 Identities=22% Similarity=0.309 Sum_probs=174.8
Q ss_pred CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC--C---CCCCceeeEeeccccccccCCCCCccccccC-CCCc-
Q 002054 67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG--D---SVRDFLPLTVDYQEKQFAQGVIPNTYMRREG-APKE- 139 (974)
Q Consensus 67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~--~---~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg-~p~~- 139 (974)
-|++.++.|++ ++|+||+++++|||+|+|+|++|++ | .+.+..|++++| ++.|.+...|.- .++.
T Consensus 18 lR~i~~~~~~~-~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey-------~m~p~sT~~R~~~~~~~g 89 (230)
T COG0689 18 LRPIKITRGVL-KHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEY-------GMLPRSTDERKKREADRG 89 (230)
T ss_pred ccceEEEeccc-cCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEE-------eccccccccccccccccc
Confidence 58999999999 8999999999999999999999988 2 256778999999 667766655532 2333
Q ss_pred hhhhHHHhhcCCccccccCCCCC--ceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEc
Q 002054 140 RELLVGRIIDRPIRPLFPAGFYH--EVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVN 217 (974)
Q Consensus 140 ~eil~~RlidR~lrplfp~~~~~--~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vld 217 (974)
|+.++||+|.|+||+.+....++ .++|.|+|+++||+++ +||||||++||+++++|+.+.|+||+||.++|++++|
T Consensus 90 R~~eisrli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTr--ta~It~A~lAL~DAgipl~~~vaaiSvgi~~~~~~lD 167 (230)
T COG0689 90 RTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTR--TASITGASLALADAGIPLRDLVAAISVGIVDGVIVLD 167 (230)
T ss_pred chhHHHHHHHHHHHHHhhhhhcCccEEEEEEEEEECCCCee--eehhhHHHHHHHHcCCchhhheeEeEEEEECCceEec
Confidence 89999999999999977755554 5566699999999999 9999999999999999999999999999999999999
Q ss_pred CCHHHHhcCccceeEeeeCCe-EEEEEe--cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054 218 PTMDELSLSDLNLVYACTREK-TLMIDV--QAREISEKDLEAGLRLAHPEAVKYLEPQIRLA 276 (974)
Q Consensus 218 Pt~~e~~~s~~~l~v~~t~~~-i~mie~--~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~ 276 (974)
|++.|++.+..|++|+++.++ ++-|++ +.+.|++++|.++|++|.++|+++++.|++++
T Consensus 168 l~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~~~~~del~~lL~la~~g~~~~~~~~~~al 229 (230)
T COG0689 168 LDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREAL 229 (230)
T ss_pred CcchhhcccccCceEEEEecCCeEEEEEEeccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999876 555554 33459999999999999999999999999875
No 32
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.97 E-value=2.5e-30 Score=311.75 Aligned_cols=298 Identities=19% Similarity=0.191 Sum_probs=244.7
Q ss_pred CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCC
Q 002054 653 DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQ 732 (974)
Q Consensus 653 dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd 732 (974)
+|.+.++.. +...+.+++.+. ..++.|++++|+|+++.++|+||++. |+.||+|.|++++.+..++. +.+||
T Consensus 89 ~~~i~lS~k-~~~~~~~~~~l~----~~~~~g~~v~g~V~~~~~~G~~V~~~-g~~gfip~s~~~~~~~~~~~--~~vG~ 160 (565)
T PRK06299 89 FGETVLSRE-KAKRLEAWDKLE----KAFENGEIVEGVINGKVKGGFTVDLN-GVEAFLPGSQVDVRPVRDTD--PLEGK 160 (565)
T ss_pred CCcEEEech-HHHHHHHHHHHH----HHhhCCCEEEEEEEEEECCEEEEEEC-CEEEEEEHHHccCcCCCChH--HhCCC
Confidence 355555432 222333444333 34678999999999999999999996 99999999999998877766 45899
Q ss_pred EEEEEEEEEcc-CCceEEEEeccCCCc----ccc------cCce---------EEEEEeecCCcceeeEEeeccCCCCCC
Q 002054 733 QLSLRCIGQDV-RGNIKLSLKAVSPRP----EAD------VKGV---------VEGSVPVNKQATDVWASVGDVSNGQNP 792 (974)
Q Consensus 733 ~V~vkVl~id~-~gri~LS~K~~~~~~----~~~------~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~ 792 (974)
.++|+|+++|. ++++.||+|.+...+ |.. .|.+ .+|.++++. |+++++|+++++|.+.
T Consensus 161 ~i~~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~- 238 (565)
T PRK06299 161 ELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRV- 238 (565)
T ss_pred EEEEEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhccccc-
Confidence 99999999998 679999999886533 221 3444 456666775 8999999999999752
Q ss_pred CCCCCCCCCCCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec----------
Q 002054 793 ELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS---------- 862 (974)
Q Consensus 793 ~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~---------- 862 (974)
.+|. +.+++||.+.++| +++|++++++.||+++..++| |......+++|+++.|.|.+
T Consensus 239 ~~~~-------~~~kvG~~v~v~V---~~~d~~~~~i~lS~k~~~~~p--~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l 306 (565)
T PRK06299 239 NHPS-------EVVNVGDEVKVKV---LKFDKEKKRVSLGLKQLGEDP--WEAIEKKYPVGSKVKGKVTNITDYGAFVEL 306 (565)
T ss_pred CCHh-------hcCCCCCEEEEEE---EEEeCCCCeEEEEEEecccCh--hHHHHhhCCCCCEEEEEEEEEeCCeEEEEe
Confidence 2333 6789999999999 999999999999999988888 98888889999999999877
Q ss_pred -------------ccCcCC---CcccccCCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeC
Q 002054 863 -------------STNIQK---STSFSQREREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRA 923 (974)
Q Consensus 863 -------------~~~~~~---~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~ 923 (974)
+|.... ...|++||.++++|+++|++++++. |+|++..+|| ...+|++|++|.|+|+++++
T Consensus 307 ~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~ 386 (565)
T PRK06299 307 EEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITD 386 (565)
T ss_pred CCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEec
Confidence 454322 2368999999999999999999998 9999999999 46679999999999999999
Q ss_pred CeEEEEeCCCeEEEEecccCC--------CCCCCCCCEEEEEEEEEeCC-Cceeeeec
Q 002054 924 RGLVLDLGGGIRGMYRFENNE--------KKDFVVGDELLVKCSSFTGK-GIPVVSLV 972 (974)
Q Consensus 924 ~GvFV~L~~gv~Glih~se~~--------~~~f~vGd~V~vkVl~id~~-~~~~~~~~ 972 (974)
+|+||+|++++.||+|.++++ .+.|++||.|+|+|+++|.+ +...+|+.
T Consensus 387 ~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k 444 (565)
T PRK06299 387 FGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIK 444 (565)
T ss_pred ceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence 999999999999999999875 24689999999999999964 66667764
No 33
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=99.97 E-value=1.7e-29 Score=299.78 Aligned_cols=213 Identities=15% Similarity=0.135 Sum_probs=187.2
Q ss_pred cCeEEEeCCCC-CCCcceEEEe-CCeEEEEEEEeC-CCchhhhccccCCCCceeEEEEEecCCCCccc-----cccccCC
Q 002054 380 RPIYCESGNLP-ILHGSSLFSR-GDTQVLCTVTLG-APAEAQRLESLVGPPTKRFMLHYSFPPFCINE-----VGKRVGL 451 (974)
Q Consensus 380 R~I~ie~g~l~-~a~GSal~~~-G~T~Vl~~Vtl~-~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e-----~~~~~~~ 451 (974)
|++.+++|-+. +|+||++++. |+|.|||||+.. .|.+ +.++.+++|+|.-..|+.|. ++|.|+|
T Consensus 17 ~~~~~etG~~A~qA~Gav~v~~~G~t~vl~t~~~~~~~~~--------~~dF~PLtV~y~Ek~yA~GkiPggf~kREgrp 88 (719)
T TIGR02696 17 RTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPKD--------QFDFFPLTVDVEERMYAAGRIPGSFFRREGRP 88 (719)
T ss_pred EEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCCCCC--------CCCCcceeEeeeehhhhcCccCCceeccCCCC
Confidence 47999999998 7999999999 999999999943 2222 45788999999999999865 5899999
Q ss_pred CchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCCh--hhHHHHHHHHHHHHcCCCccccccceeeeeeccCCC
Q 002054 452 NRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGST--SMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP 529 (974)
Q Consensus 452 ~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~--~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~ 529 (974)
+.+|+..++|++|.|+|++| +.|.|.++|.++||+.|+.. ...+++|||+||+-++||+..|++||.+|++++
T Consensus 89 s~~eiL~sRliDR~iRPLFp--~~~~~e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiPf~gPv~~vrVg~i~g--- 163 (719)
T TIGR02696 89 STDAILTCRLIDRPLRPSFV--KGLRNEVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIDG--- 163 (719)
T ss_pred ChhhhHHHHhhCCCCccCCC--CCCCcceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCCCCCceEEEEEEEECC---
Confidence 99999999999999999999 68999999999999999854 588999999999999999999999999999976
Q ss_pred CCCcccceEEEecCCccccccCCccEEEEeeC----C-ceEEEEee----------ccCCCCCHHHHHHHHHHHHHHHHH
Q 002054 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGTR----I-GVTAIQLD----------IKPAGIPLDIICECLEHAHKGRLQ 594 (974)
Q Consensus 530 ~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~----~-gI~alq~~----------~k~~~i~~e~l~~al~~A~~~~~~ 594 (974)
.++++|+..|-..+++|+.|+||. + .|+++.+. .....++++.|.+||..|+++.+.
T Consensus 164 --------~~viNPt~~~~~~s~ldLvvagt~~~~~~~~i~MiE~~a~~~~~~~~~~~a~e~~e~~~~~Ai~~a~~~i~~ 235 (719)
T TIGR02696 164 --------QWVAFPTHEQLEGAVFDMVVAGRVLENGDVAIMMVEAEATEKTWDLVKGGAEAPTEEVVAEGLEAAKPFIKV 235 (719)
T ss_pred --------EEEECcCHHHHhhCeeeEEEEeeecCCCCccEEEEecCCccccccccccCCCCCCHHHHHHHHHHHHHHHHH
Confidence 699999999999999999999997 5 78888862 133579999999999999999999
Q ss_pred HHHHHHHHhcCCCCCCCCC
Q 002054 595 ILDHMEREISAPRTQDDRN 613 (974)
Q Consensus 595 I~~~m~~~i~~~~~~~~~~ 613 (974)
+++.+++..++..+++..+
T Consensus 236 ~~~~~~~l~~~~gk~k~~~ 254 (719)
T TIGR02696 236 LCRAQADLAEKAAKPTGEF 254 (719)
T ss_pred HHHHHHHHHHHhCCCcccc
Confidence 9999999877666544443
No 34
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.97 E-value=5.2e-30 Score=295.61 Aligned_cols=280 Identities=20% Similarity=0.204 Sum_probs=231.7
Q ss_pred cccccCcEEEEEEEEEeeceEEEEE-cCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEF-NGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP 756 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l-~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~ 756 (974)
.++++|+++.|+|+++.++|+||++ .++.+|+||.+|+++.+..++...|++||.|+|+|+++|. ++++.||+|.+..
T Consensus 13 ~~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~~~~ 92 (390)
T PRK06676 13 KEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEA 92 (390)
T ss_pred hcccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccccccCcccccCCCCEEEEEEEEEECCCCCEEEEHHHhhh
Confidence 4789999999999999999999999 7799999999999999999999999999999999999987 5789999998654
Q ss_pred -Ccccc------cCceEE---------EEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEeecc
Q 002054 757 -RPEAD------VKGVVE---------GSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAA 820 (974)
Q Consensus 757 -~~~~~------~g~~~~---------G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l 820 (974)
.+|.. .|.... |+++++ +|+++|+|++++++... ..| ..+ +|+.+.++| +
T Consensus 93 ~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~-~G~~gflp~~el~~~~~-~~~--------~~~-vG~~v~~~V---l 158 (390)
T PRK06676 93 EKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDV-EGVRGFIPASLISTRFV-EDF--------SDF-KGKTLEVKI---I 158 (390)
T ss_pred hhhHHHHHHhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCCccC-CCh--------HHc-CCCEEEEEE---E
Confidence 34543 354444 555565 47899999999998642 111 122 899999999 9
Q ss_pred cccccccccccccccccccc--cccccccCCCCCCCcEEEEEec----------------------ccC--cCCCccccc
Q 002054 821 ECDEEEKASGFSQSSKSTLK--STLASKSNSKPKKFTSQSDFFS----------------------STN--IQKSTSFSQ 874 (974)
Q Consensus 821 ~iD~~~r~i~ls~k~~~~~~--~~~~~~~~~~~~G~~v~g~V~~----------------------~~~--~~~~~~~k~ 874 (974)
++|++++++.+|++...... ..|......+..|+++.|.|.+ +|. ......|++
T Consensus 159 ~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~~~~~~~~~v 238 (390)
T PRK06676 159 ELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSV 238 (390)
T ss_pred EEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCccccCCHHHhcCC
Confidence 99999999999999754321 1244555667899999999888 332 122346899
Q ss_pred CCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------
Q 002054 875 REREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------- 944 (974)
Q Consensus 875 Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------- 944 (974)
||.++++|+.+|++++++. |+|++..+|| ..+++++|++++|+|+++++||+||++++|+.||+|.++++
T Consensus 239 Gd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~~~~ 318 (390)
T PRK06676 239 GQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATP 318 (390)
T ss_pred CCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCccccCCh
Confidence 9999999999999999998 9999999999 46789999999999999999999999999999999999874
Q ss_pred CCCCCCCCEEEEEEEEEeC-CCceeeeec
Q 002054 945 KKDFVVGDELLVKCSSFTG-KGIPVVSLV 972 (974)
Q Consensus 945 ~~~f~vGd~V~vkVl~id~-~~~~~~~~~ 972 (974)
.+.|++||+|+|+|+++|+ ++...+|+.
T Consensus 319 ~~~~~~Gd~v~v~V~~id~e~~~i~ls~k 347 (390)
T PRK06676 319 SEVLEEGQEVKVKVLEVNEEEKRISLSIK 347 (390)
T ss_pred hhccCCCCEEEEEEEEEECCCCEEEEEEE
Confidence 2458999999999999995 566666654
No 35
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=99.96 E-value=4.9e-28 Score=289.17 Aligned_cols=278 Identities=18% Similarity=0.187 Sum_probs=232.1
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR 757 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~ 757 (974)
..++.|++++|+|+++.+.|++|++. |.+||+|.|+++..+.++.. ..+|+.++|+|+++|. ++++.||+|.++..
T Consensus 96 ~a~~~g~~v~g~V~~~~~~g~~V~i~-g~~~flP~s~~~~~~~~~~~--~~vG~~i~~~v~~~~~~~~~iv~Srk~~l~~ 172 (516)
T TIGR00717 96 KAYEEGSIVEGKIVGKVKGGFIVDLN-GVEAFLPGSQVDVKPIKDLD--SLIGKTLKFKIIKLDQKRNNIVVSRRAYLEE 172 (516)
T ss_pred HHhhCCCeEEEEEEEEECCEEEEEEC-CEEEEEeHHHhcCcccCchh--hhCCCEEEEEEEEEECCCCcEEEEHHHHHHH
Confidence 34689999999999999999999995 99999999999876555433 4689999999999998 56899999987543
Q ss_pred c----------ccccCceE---------EEEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEee
Q 002054 758 P----------EADVKGVV---------EGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRS 818 (974)
Q Consensus 758 ~----------~~~~g~~~---------~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~ 818 (974)
. ..+.|..+ +|.++++ +|+++|+|.++++|... ..|. +.+++||.+.+.|
T Consensus 173 ~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l-~g~~g~lp~~e~s~~~~-~~~~-------~~~~vG~~v~v~V-- 241 (516)
T TIGR00717 173 ERSQAREELLENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRV-KHPS-------EYVKVGQEVKVKV-- 241 (516)
T ss_pred HHHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCCCCC-CCHH-------HhccCCCEEEEEE--
Confidence 2 11234444 4555565 47999999999998652 2232 6789999999999
Q ss_pred cccccccccccccccccccccccccccccCCCCCCCcEEEEEec-----------------------ccCcCCC---ccc
Q 002054 819 AAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS-----------------------STNIQKS---TSF 872 (974)
Q Consensus 819 ~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~-----------------------~~~~~~~---~~~ 872 (974)
+++|++++++.+|++...++| |......++.|++++|.|.+ +|..... ..|
T Consensus 242 -l~~d~~~~~i~lS~k~~~~~p--~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~ 318 (516)
T TIGR00717 242 -IKFDKEKGRISLSLKQLGEDP--WEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVV 318 (516)
T ss_pred -EEEECCCCcEEEEEEecchhH--HHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhc
Confidence 999999999999999888888 88877788999999999888 4432222 358
Q ss_pred ccCCeEEEEEEEeecCCCCcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-----
Q 002054 873 SQREREELAECLFGTEDGDED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE----- 944 (974)
Q Consensus 873 k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~----- 944 (974)
++||.++++|+++|++++++. |+|++..+|| ..+++++|++++|+|+++++||+||+|++|++||+|.++++
T Consensus 319 ~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~ 398 (516)
T TIGR00717 319 KKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDG 398 (516)
T ss_pred cCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCcccC
Confidence 999999999999999999998 9999999999 46679999999999999999999999999999999999874
Q ss_pred ---CCCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054 945 ---KKDFVVGDELLVKCSSFTG-KGIPVVSLVD 973 (974)
Q Consensus 945 ---~~~f~vGd~V~vkVl~id~-~~~~~~~~~~ 973 (974)
...|++||+|.|+|+++|+ ++...+|+.+
T Consensus 399 ~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~ 431 (516)
T TIGR00717 399 READHLYKKGDEIEAVVLAVDKEKKRISLGVKQ 431 (516)
T ss_pred CCHhHccCCCCEEEEEEEEEeCcCCEEEEeecc
Confidence 2569999999999999996 5677787753
No 36
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.96 E-value=5.7e-28 Score=293.77 Aligned_cols=280 Identities=17% Similarity=0.199 Sum_probs=232.2
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccC-C
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVS-P 756 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~-~ 756 (974)
..+++|+++.|+|.++.+.|+||++.++.+|+||.+++++....++.+.|++||.|+|+|+++|. +|++.||+|... .
T Consensus 298 ~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~ 377 (647)
T PRK00087 298 KQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADRE 377 (647)
T ss_pred hhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEeehhcch
Confidence 46899999999999999999999998889999999999999999999999999999999999976 789999999875 3
Q ss_pred Ccccc------cCceEE---------EEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEeeccc
Q 002054 757 RPEAD------VKGVVE---------GSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAE 821 (974)
Q Consensus 757 ~~~~~------~g~~~~---------G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~ 821 (974)
.+|.. .|.... |.+++++ |+++|+|.+++++..... | .. .+|+.+.+.| ++
T Consensus 378 ~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lg-gi~gfiP~sel~~~~~~d-~--------~~-~vG~~v~v~V---l~ 443 (647)
T PRK00087 378 KAWKELEEAFENGEPVKGKVKEVVKGGLLVDYG-GVRAFLPASHVELGYVED-L--------SE-YKGQELEVKI---IE 443 (647)
T ss_pred hHHHHHHHHhhCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHhCccccCC-H--------HH-hCCCEEEEEE---EE
Confidence 45653 355544 4555553 589999999998864211 1 12 2899999999 99
Q ss_pred ccccccc-cccccccccc--cccccccccCCCCCCCcEEEEEec----------------------ccCc--CCCccccc
Q 002054 822 CDEEEKA-SGFSQSSKST--LKSTLASKSNSKPKKFTSQSDFFS----------------------STNI--QKSTSFSQ 874 (974)
Q Consensus 822 iD~~~r~-i~ls~k~~~~--~~~~~~~~~~~~~~G~~v~g~V~~----------------------~~~~--~~~~~~k~ 874 (974)
+|+++++ +.+|.+.... ....+......+.+|+++.|.|.+ +|.. +....|++
T Consensus 444 vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~~~~~~~~~~~~v 523 (647)
T PRK00087 444 FNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRVEKPSDVLKV 523 (647)
T ss_pred EEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCccccCCHHHhcCC
Confidence 9999998 9999887542 111245555667899999999887 3321 22347999
Q ss_pred CCeEEEEEEEeecCCCCcC-ccccccccccc--cccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------
Q 002054 875 REREELAECLFGTEDGDED-NKGTRVEAIVS--AKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------- 944 (974)
Q Consensus 875 Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~~--~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------- 944 (974)
||.++++|+++|++++++. |+|++..+||. .++|++|+++.|+|+++++||+||+|++|+.||+|.++++
T Consensus 524 Gd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~~~ 603 (647)
T PRK00087 524 GDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKP 603 (647)
T ss_pred CCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccCCH
Confidence 9999999999999999999 99999999993 5789999999999999999999999999999999999875
Q ss_pred CCCCCCCCEEEEEEEEEeC-CCceeeeec
Q 002054 945 KKDFVVGDELLVKCSSFTG-KGIPVVSLV 972 (974)
Q Consensus 945 ~~~f~vGd~V~vkVl~id~-~~~~~~~~~ 972 (974)
.+.|++||+|+|+|+++|. ++...+|+.
T Consensus 604 ~~~~kvGd~V~vkV~~id~e~~rI~lslk 632 (647)
T PRK00087 604 EDVLSEGEEVKAKILEVDPEEKRIRLSIK 632 (647)
T ss_pred hhcCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence 2368999999999999995 577777764
No 37
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.95 E-value=5.4e-27 Score=276.53 Aligned_cols=277 Identities=19% Similarity=0.176 Sum_probs=223.4
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCcc
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPE 759 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~ 759 (974)
.++.|++++|+|+++.+.|+||+++.+.+|++|.+|+++..- ...+++||.|+|+|++++ .+.+.||++......|
T Consensus 31 ~~~~G~~v~G~V~~v~~~~v~Vdig~k~eg~ip~~e~~~~~~---~~~~~~G~~i~~~Vi~~~-~~~~~lS~~~~~~~~~ 106 (491)
T PRK13806 31 ELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDADG---ELTVAVGDEVELYVVSVN-GQEIRLSKALSGQGGA 106 (491)
T ss_pred cCCCCCEEEEEEEEEECCEEEEEECCCcEEEEEHHHhcCccc---cccccCCCEEEEEEEEEc-CCEEEEEhHHhhhhhH
Confidence 388999999999999999999999778999999999975321 234899999999999986 4679999875544445
Q ss_pred cc------cCceEEEEEeec--------CCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEeeccccccc
Q 002054 760 AD------VKGVVEGSVPVN--------KQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECDEE 825 (974)
Q Consensus 760 ~~------~g~~~~G~vv~i--------~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~iD~~ 825 (974)
.. .|..+.|.|... ..|+.+|+|.+++++... ..| .. .+|+.+.++| +++|++
T Consensus 107 ~~l~~~~~~g~~v~g~V~~~~~~G~~V~i~g~~~flP~s~~~~~~~-~~~--------~~-~vG~~i~~~V---~~id~~ 173 (491)
T PRK13806 107 AMLEEAYENGVPVEGKVTGTCKGGFNVEVLGRRAFCPVSQIDLRYV-EDP--------ES-YVGQTFQFLI---TRVEEN 173 (491)
T ss_pred HHHHHHHhCCCEEEEEEEEEEcCCEEEEECCEEEEEEHHHhccccC-CCh--------HH-cCCCeEEEEE---EEEECC
Confidence 44 356655555443 138999999999998642 111 12 2899999999 999999
Q ss_pred cccccccccccccc--ccccccccCCCCCCCcEEEEEec-----------------------ccCc--CCCcccccCCeE
Q 002054 826 EKASGFSQSSKSTL--KSTLASKSNSKPKKFTSQSDFFS-----------------------STNI--QKSTSFSQRERE 878 (974)
Q Consensus 826 ~r~i~ls~k~~~~~--~~~~~~~~~~~~~G~~v~g~V~~-----------------------~~~~--~~~~~~k~Gq~v 878 (974)
++++.+|.++.... ...|......+..|++++|.|.. +|.. +.+..|++||.+
T Consensus 174 ~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i 253 (491)
T PRK13806 174 GRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTV 253 (491)
T ss_pred CCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEE
Confidence 99999999876432 22355556678899999999887 5542 334579999999
Q ss_pred EEEEEEeecCCC----CcC-cccccccccc--ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC------
Q 002054 879 ELAECLFGTEDG----DED-NKGTRVEAIV--SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK------ 945 (974)
Q Consensus 879 ~~~Vl~vd~e~~----~i~-slK~~~~~p~--~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~------ 945 (974)
+++|+++|.+++ ++. |+|++..+|| ..++|++|+++.|+|+++++||+||+|++|+.||+|.|+++.
T Consensus 254 ~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~ 333 (491)
T PRK13806 254 RVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNK 333 (491)
T ss_pred EEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCC
Confidence 999999999874 577 9999999999 467999999999999999999999999999999999998752
Q ss_pred --CCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054 946 --KDFVVGDELLVKCSSFTG-KGIPVVSLVD 973 (974)
Q Consensus 946 --~~f~vGd~V~vkVl~id~-~~~~~~~~~~ 973 (974)
+.|++||+|+|+|+++|+ +++..+|+..
T Consensus 334 ~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~ 364 (491)
T PRK13806 334 PEDVVAPGDAVAVKIKDIDPAKRRISLSLRD 364 (491)
T ss_pred HHHcCCCCCEEEEEEEEEEccCCEEEEEEee
Confidence 358999999999999997 4667777653
No 38
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.95 E-value=3.9e-27 Score=262.36 Aligned_cols=230 Identities=18% Similarity=0.275 Sum_probs=181.7
Q ss_pred EecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEE
Q 002054 659 VAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRC 738 (974)
Q Consensus 659 ~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkV 738 (974)
+..+.+.+++..+..+ ..++.|+++.|+|+++.++|+||+|+++.+||+|.+|+++.++.++.+.|++||.++|+|
T Consensus 11 ~~~~~~~f~~~le~~~----~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~V 86 (318)
T PRK07400 11 IGFTHEDFAALLDKYD----YHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFI 86 (318)
T ss_pred cCCCHHHHHHHHHhhH----hhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEE
Confidence 3445556665554332 348999999999999999999999987899999999999999999999999999999999
Q ss_pred EEEcc-CCceEEEEeccCC-Ccccc------cCce---------EEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCCC
Q 002054 739 IGQDV-RGNIKLSLKAVSP-RPEAD------VKGV---------VEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNET 801 (974)
Q Consensus 739 l~id~-~gri~LS~K~~~~-~~~~~------~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~ 801 (974)
+++|. +|++.||+|.+.. .+|.. .+.. ..|.|+++ +|+++|+|+++++|... .
T Consensus 87 i~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l-~Gv~gfip~s~ls~~~~----~----- 156 (318)
T PRK07400 87 LSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRI-EGLRGFIPGSHISTRKP----K----- 156 (318)
T ss_pred EEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCccCC----c-----
Confidence 99987 6899999998753 67775 1333 35667777 58999999999998531 1
Q ss_pred CCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEecccCcCCCcccccCCeEEEE
Q 002054 802 PGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFSSTNIQKSTSFSQREREELA 881 (974)
Q Consensus 802 ~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~~~~~~~~~~~k~Gq~v~~~ 881 (974)
+ ..+|+.+.++| +++|++++++.||+|+...
T Consensus 157 --~-~~vG~~i~~kV---l~id~~~~~i~lS~K~~~~------------------------------------------- 187 (318)
T PRK07400 157 --E-ELVGEELPLKF---LEVDEERNRLVLSHRRALV------------------------------------------- 187 (318)
T ss_pred --c-ccCCCEEEEEE---EEEEcccCEEEEEhhHhhh-------------------------------------------
Confidence 1 23677777777 7777776666666663321
Q ss_pred EEEeecCCCCcCccccccccccccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEE
Q 002054 882 ECLFGTEDGDEDNKGTRVEAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDEL 954 (974)
Q Consensus 882 Vl~vd~e~~~i~slK~~~~~p~~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V 954 (974)
.+ ...++++|++|.|+|++|++||+||+++ |+.||+|.++++ .+.|++||.|
T Consensus 188 -------------------~~-~~~~~k~G~vv~G~V~~I~~~G~fV~i~-gv~Gllhisels~~~~~~~~~~~~vGd~V 246 (318)
T PRK07400 188 -------------------ER-KMNRLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEM 246 (318)
T ss_pred -------------------hh-hhccCCCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcccccccChhhccCCCCEE
Confidence 11 2466899999999999999999999995 899999999775 3458999999
Q ss_pred EEEEEEEeC-CCceeeeec
Q 002054 955 LVKCSSFTG-KGIPVVSLV 972 (974)
Q Consensus 955 ~vkVl~id~-~~~~~~~~~ 972 (974)
+|+|+++|. ++...+|+.
T Consensus 247 kvkVl~iD~e~~rI~LS~K 265 (318)
T PRK07400 247 KVMIIDLDAERGRISLSTK 265 (318)
T ss_pred EEEEEEEeCCCCEEEEEEe
Confidence 999999996 667777764
No 39
>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=2.6e-27 Score=236.20 Aligned_cols=202 Identities=23% Similarity=0.328 Sum_probs=176.2
Q ss_pred CccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCCchhhh
Q 002054 378 EVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVG 457 (974)
Q Consensus 378 e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~rre~~ 457 (974)
.+|++.|+.|+|+++||||.|++|+|+|+|+|+ ||.|.+..++. ..+..+++.+.|.+.. ++++|..
T Consensus 4 ~lr~~~cei~iLsr~dGSs~fsqgdT~V~c~V~--GP~dvk~r~E~----~~katleVi~rp~~G~-------~~~~eK~ 70 (217)
T KOG1069|consen 4 RLRGIACEISILSRPDGSSEFSQGDTKVICSVY--GPIDVKARQED----PEKATLEVIWRPKSGV-------NGTVEKV 70 (217)
T ss_pred hhhhhhhhhceecCCCCccceecCCcEEEEEee--CCcchhhcccC----chhceEEEEEecccCc-------chHHHHH
Confidence 789999999999999999999999999999999 99998765543 4567899999888753 5789999
Q ss_pred HHHHHHHHhhhcCCCCCCCCeE-EEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCccccccceeeeeeccCCCCCCcccc
Q 002054 458 HGTLAEKALLAVLPPENDFPYT-VRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKD 536 (974)
Q Consensus 458 ~~~l~eral~~vi~~~~~~p~t-I~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~~~~~~~~ 536 (974)
+++++++.|.+.+.+ +.||+| |+|.++|+++|||.+.+|+|||++||.||||||+++++|+++.+.+++
T Consensus 71 ~e~iI~~tl~~~I~l-~l~Prt~iqVsiqvv~ddgs~LacaINaAclALvDaGIpl~~mfcai~~~~~~d~--------- 140 (217)
T KOG1069|consen 71 LERIIRKTLSKAIIL-ELYPRTTIQVSIQVVEDDGSTLACAINAACLALVDAGIPLRSMFCAISCALHEDG--------- 140 (217)
T ss_pred HHHHHHHHHHHhhee-eecCCceEEEEEEEEecCCcchHHHHHHHHHHHHhcCCchHHhhhhceEEEecCc---------
Confidence 999999999999998 899995 999999999999999999999999999999999999999999999863
Q ss_pred eEEEecCCcccccc--CCccEEEEeeCC---ceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 002054 537 YRILTDILGLEDHL--GDMDFKIAGTRI---GVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAP 606 (974)
Q Consensus 537 ~~iL~Dp~~~Ee~~--~d~d~~Va~t~~---gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~ 606 (974)
.+++||+..++.. +...+++.++.. +++.+ +. .+.++.++|..+++.|..++.+++.++++.+.+.
T Consensus 141 -~lv~Dpt~~qek~~~~~~~lsf~~~~~~~~~vi~s--~t-~G~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~~ 211 (217)
T KOG1069|consen 141 -VLVLDPTAKQEKISTARATLSFEGGSLGEPKVIIS--ET-NGEKSEDQLFYVLELAQAAAQSLFPFYREVLQRK 211 (217)
T ss_pred -cEEECCcHHhhhhhhceEEEEEecCCCCCcceEEE--ec-cCCCCHHHHHHHHHhhHHHHHHHHHHHHHHHHhh
Confidence 6999999999984 445666654433 34443 33 3679999999999999999999999999999764
No 40
>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=3.2e-26 Score=233.56 Aligned_cols=233 Identities=21% Similarity=0.272 Sum_probs=200.8
Q ss_pred HHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCCCCceeEEEE
Q 002054 357 KRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVGPPTKRFMLH 434 (974)
Q Consensus 357 ~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~~~~~~~~v~ 434 (974)
++++. ..|+.|.|.|||+++|+|.+.+++| .-.||+.++.|+|+|+|.|+.. .|... .|.+|.|.+.
T Consensus 11 ~~fvl-~alk~g~R~DgR~l~efR~lei~fG---ke~gs~~vt~G~Tkvm~~vt~~ia~Py~d-------RP~eG~~~I~ 79 (291)
T KOG1614|consen 11 SKFVL-NALKAGLRFDGRSLEEFRDLEIEFG---KEYGSVLVTMGNTKVMARVTAQIAQPYID-------RPHEGSFSIF 79 (291)
T ss_pred HHHHH-HHHHhcccccccchhhhhceEEEec---cccccEEEEecCeeEEEEeehhhcCcccC-------CCCCCeeeee
Confidence 44454 6778999999999999999999999 5789999999999999999943 45443 4788999999
Q ss_pred EecCCCCccccccccCCCchhhhHHHHHHHHhh----------hcCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHH
Q 002054 435 YSFPPFCINEVGKRVGLNRREVGHGTLAEKALL----------AVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMA 504 (974)
Q Consensus 435 ~~f~p~s~~e~~~~~~~~rre~~~~~l~eral~----------~vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lA 504 (974)
.++.|.+...+. .|..+..+..++++++++++ |+.- .+-.|.||+++++|+.|||+.+||..|+.+|
T Consensus 80 telsPmA~~sfE-~Gr~~~~~v~l~Rliek~~R~S~aiD~EsLCI~a--G~kvW~IRiDlhiLd~DGnlvDaA~iAviaa 156 (291)
T KOG1614|consen 80 TELSPMASPSFE-PGRKGESEVELSRLIEKALRRSKAIDTESLCIRA--GEKVWLIRIDLHILDHDGNLVDAACIAVIAA 156 (291)
T ss_pred eccccccccccC-CCCccchHHHHHHHHHHHHHhccccchHHHHhhh--CCeEEEEEEEEEEEcCCCCeehhHHHHHHHH
Confidence 999999886653 34456778899999999983 3444 3678999999999999999999999999999
Q ss_pred HHHcCCC-----------------------ccccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeC
Q 002054 505 LMDAGIP-----------------------LQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTR 561 (974)
Q Consensus 505 L~dagvP-----------------------i~~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~ 561 (974)
||+.+-| |+++|.++++|+++.+ ..+++||+..|+.++|..++|+.++
T Consensus 157 L~hFrrPdvTv~g~ev~ihp~eEr~PvPL~I~HmPIC~tf~ffnkG---------~ivviDpt~~Ee~~~dGs~vVt~Nk 227 (291)
T KOG1614|consen 157 LMHFRRPDVTVGGEEVIIHPVEEREPVPLSIHHMPICFTFGFFNKG---------EIVVIDPTEKEEAVMDGSMVVTMNK 227 (291)
T ss_pred HHhcCCCCcccccceeEecChhccCCcceeeeeccceEEEEEecCc---------eEEEeCCcHHHHhccCceEEEEEcC
Confidence 9999943 8999999999999863 2899999999999999999999999
Q ss_pred Cc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCC
Q 002054 562 IG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRN 613 (974)
Q Consensus 562 ~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~ 613 (974)
++ +|++|..++ -.+...++..|...|...+..+.+.+.+++++...+.+.+
T Consensus 228 ~rEVc~i~k~G~-~~~~~~~i~~C~k~A~~~a~~vt~ii~e~l~~d~~~r~~~ 279 (291)
T KOG1614|consen 228 NREVCAIQKSGG-EILDESVIERCYKLAKDRAVEVTGIILEALEEDQRERSAQ 279 (291)
T ss_pred CccEEEEecCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 88 999999764 5788999999999999999999999999999876655543
No 41
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional
Probab=99.94 E-value=5.3e-26 Score=249.55 Aligned_cols=201 Identities=24% Similarity=0.293 Sum_probs=172.4
Q ss_pred CeEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC--CCCceeeEeeccccccccCCCCCccccccCCCCchhhh
Q 002054 67 SRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS--VRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELL 143 (974)
Q Consensus 67 ~r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~--~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil 143 (974)
-|++.+++|.+ ++|+|||++++|+|+|+|+|+.+.. |. ..+-.-++++|.-..+|.. + .|.|+|++++++
T Consensus 34 ~R~i~i~~g~l-~~a~GSa~v~~G~T~vl~~V~~~~~~p~~~~~~~g~i~~~v~~~~~a~~-----~-~~~~~~~~~~~~ 106 (271)
T PRK04282 34 YRPIEIETGVI-KKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASP-----T-FEPGPPDENAIE 106 (271)
T ss_pred ccCeEEEeCCc-cCCCcEEEEEECCCEEEEEEEEEEecCCCCCCCCCEEEEEEEECCCcCc-----c-ccCCCCCHHHHH
Confidence 48899999999 9999999999999999999996543 21 1233446777665554432 1 256899999999
Q ss_pred HHHhhcCCccccc----------cCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCC----------------
Q 002054 144 VGRIIDRPIRPLF----------PAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIP---------------- 197 (974)
Q Consensus 144 ~~RlidR~lrplf----------p~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP---------------- 197 (974)
++|+++|+||+.+ |..+.|.++|.++||+.||+.. .||++||++||+++++|
T Consensus 107 l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~--daa~~Aa~aAL~~~~iP~~~~~~~~~~~~~~~~ 184 (271)
T PRK04282 107 LARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLL--DASMLAAVAALLNTKVPAVEEGEDGVVDKLGED 184 (271)
T ss_pred HHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHH--HHHHHHHHHHHHhCCCCcEEEcCCceeccCCCc
Confidence 9999999999963 4455779999999999999855 79999999999999995
Q ss_pred ----CCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCC-eEEEEEe-cCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 002054 198 ----WGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTRE-KTLMIDV-QAREISEKDLEAGLRLAHPEAVKYLEP 271 (974)
Q Consensus 198 ----~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~-~i~mie~-~~~~~~e~~~~~al~~a~~~~~~i~~~ 271 (974)
|++++.+|++|++++++|+|||.+|++.++.+++|+.+++ .+++++. ++..+++++|.+|+++|++.++++++.
T Consensus 185 ~~l~~~~~p~~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~va~~~~g~i~~l~~~g~~~~~~~~l~~~i~~A~~~~~~l~~~ 264 (271)
T PRK04282 185 FPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTEEEVDKAIDIALEKAKELREK 264 (271)
T ss_pred ccCCCCCeeEEEEEEEECCEEEECCCHHHHhhcCceEEEEECCCCcEEEEEcCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999988 5888885 456799999999999999999999999
Q ss_pred HHHHH
Q 002054 272 QIRLA 276 (974)
Q Consensus 272 ~~~~~ 276 (974)
+++.+
T Consensus 265 ~~~~l 269 (271)
T PRK04282 265 LKEAL 269 (271)
T ss_pred HHHHh
Confidence 98876
No 42
>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=4.6e-26 Score=231.74 Aligned_cols=243 Identities=21% Similarity=0.305 Sum_probs=191.7
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeC--CCchhhhccccCC
Q 002054 348 LPKAVDTVRKRVIRKRIIAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLG--APAEAQRLESLVG 425 (974)
Q Consensus 348 ~~~~~~~~~~~~~r~~il~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~--~p~~~~~~d~~~~ 425 (974)
-.++|+++.|+.|.+++|++|+|+|||.+.|+|.+.++.|.+++++|||+++.|+|.|+|+++.+ .|..+ .
T Consensus 15 ~p~~fkrI~Pe~~l~rhLse~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~ei~epstd-------a 87 (298)
T KOG1613|consen 15 PPEVFKRISPELYLQRHLSEGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEIAEPSTD-------A 87 (298)
T ss_pred CHHHHhhcCHHHHHHHHhhcccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeeeeecccccC-------C
Confidence 45789999999999999999999999999999999999999999999999999999999999965 45542 3
Q ss_pred CCceeEEEEEecCCCCccccccccCCCchhhhHHHHHHHHh----------hhcCCCCCCCCeEEEEEEEEEcCCCChhh
Q 002054 426 PPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKAL----------LAVLPPENDFPYTVRVNSEVMASDGSTSM 495 (974)
Q Consensus 426 ~~~~~~~v~~~f~p~s~~e~~~~~~~~rre~~~~~l~eral----------~~vi~~~~~~p~tI~V~v~VLesdGs~~~ 495 (974)
++++.+..+|.+||.|+..+ |.|.|+..+.-++..+...+ +|+.+ .+..|.++.++.||+.||+.++
T Consensus 88 pdeg~Iv~n~~lpplcs~r~-RpG~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~--gKaawvlYadIicLd~dG~~fD 164 (298)
T KOG1613|consen 88 PDEGDIVPNYALPPLCSSRF-RPGPPTDEAQVISQKLHDTILHSRIIPKKALCIKA--GKAAWVLYADIICLDYDGPVFD 164 (298)
T ss_pred CCCcceeecccCCcccccCC-CCCCCchHHHHHHHHHHHHHHhcCCcchhhheeec--cceeeEEEEEEEEEcCCCcHHH
Confidence 67899999999999999764 57777777755554443333 34444 4688999999999999999999
Q ss_pred HHHHHHHHHHHHcCCCcc---c-----------cccceee-----------eee-ccCCCCCC-cccceEEEecCCcccc
Q 002054 496 ATVCGGSMALMDAGIPLQ---E-----------HVAGVSV-----------GLV-SEVDPSTG-EIKDYRILTDILGLED 548 (974)
Q Consensus 496 A~v~aa~lAL~dagvPi~---~-----------~vagvs~-----------gli-~~~d~~~~-~~~~~~iL~Dp~~~Ee 548 (974)
||++|.++||.+-.+|.- . ..+..+. .+. .+.+.+-. -..+.-++.|||.+||
T Consensus 165 a~w~al~aAlknvklP~a~ide~~~~~~~t~e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~~li~adpT~eEE 244 (298)
T KOG1613|consen 165 ACWNALMAALKNVKLPRAFIDERASDLRMTIEEIICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDDVLIAADPTEEEE 244 (298)
T ss_pred HHHHHHHHHHhcCCCceeeecccchhhhhhHHHHHHhhhhcchhhhccccccccccCCCccHHHhhcceeEecCCCchhh
Confidence 999999999999999921 1 1111100 000 00000000 0113356699999999
Q ss_pred ccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 002054 549 HLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME 600 (974)
Q Consensus 549 ~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~ 600 (974)
++.+..++|..+..| ++.+.+-++..-++++.+++|++.|+.+.+++-+.|.
T Consensus 245 ~l~~~~lTIvldss~n~v~l~k~GG~al~~~~~iK~c~elar~Rakelk~~~~ 297 (298)
T KOG1613|consen 245 TLITSTLTIVLDSSGNYVQLTKVGGGALITPEMIKRCLELARVRAKELKTRFN 297 (298)
T ss_pred hhhhceEEEEEcCCCCEEEEEecCcccccCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999988877 8888887776778889999999999999999887764
No 43
>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=5.9e-25 Score=219.40 Aligned_cols=193 Identities=22% Similarity=0.250 Sum_probs=167.0
Q ss_pred eEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCCC----CCCCceeeEeeccccccccCCCCCccccccCCCCchhhh
Q 002054 68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGD----SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELL 143 (974)
Q Consensus 68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~~----~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil 143 (974)
|++..|.|.| +++|||+-+++|+|+|+|+|+||.+. +.-+-..|.|-||++. |-+...|..
T Consensus 6 r~~~cei~iL-sr~dGSs~fsqgdT~V~c~V~GP~dvk~r~E~~~katleVi~rp~~--------------G~~~~~eK~ 70 (217)
T KOG1069|consen 6 RGIACEISIL-SRPDGSSEFSQGDTKVICSVYGPIDVKARQEDPEKATLEVIWRPKS--------------GVNGTVEKV 70 (217)
T ss_pred hhhhhhhcee-cCCCCccceecCCcEEEEEeeCCcchhhcccCchhceEEEEEeccc--------------CcchHHHHH
Confidence 6788999999 89999999999999999999999882 2334567999999987 888999999
Q ss_pred HHHhhcCCccccccCCC--CCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEE-CCEEEEcCCH
Q 002054 144 VGRIIDRPIRPLFPAGF--YHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRI-CGQFIVNPTM 220 (974)
Q Consensus 144 ~~RlidR~lrplfp~~~--~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i-~g~~vldPt~ 220 (974)
.+|+|.+.|.+++-... +..+||+++|++.||+.. ++|||||++||.|+||||+.+.+|+.+.+. ||.+|+|||.
T Consensus 71 ~e~iI~~tl~~~I~l~l~Prt~iqVsiqvv~ddgs~L--acaINaAclALvDaGIpl~~mfcai~~~~~~d~~lv~Dpt~ 148 (217)
T KOG1069|consen 71 LERIIRKTLSKAIILELYPRTTIQVSIQVVEDDGSTL--ACAINAACLALVDAGIPLRSMFCAISCALHEDGVLVLDPTA 148 (217)
T ss_pred HHHHHHHHHHHhheeeecCCceEEEEEEEEecCCcch--HHHHHHHHHHHHhcCCchHHhhhhceEEEecCccEEECCcH
Confidence 99999999988544333 447889999999999876 999999999999999999999999999998 5699999999
Q ss_pred HHHhcCc--cceeEeee---CCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054 221 DELSLSD--LNLVYACT---REKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEK 278 (974)
Q Consensus 221 ~e~~~s~--~~l~v~~t---~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~ 278 (974)
.|++.+. ..|.+.++ ..+++|.|..| ++++++|..++++|..+++.++.++++..++
T Consensus 149 ~qek~~~~~~~lsf~~~~~~~~~vi~s~t~G-~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~ 210 (217)
T KOG1069|consen 149 KQEKISTARATLSFEGGSLGEPKVIISETNG-EKSEDQLFYVLELAQAAAQSLFPFYREVLQR 210 (217)
T ss_pred HhhhhhhceEEEEEecCCCCCcceEEEeccC-CCCHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence 9999654 44555333 34599999998 5999999999999999999999999998865
No 44
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=2.6e-24 Score=226.34 Aligned_cols=192 Identities=27% Similarity=0.350 Sum_probs=170.3
Q ss_pred eEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C----C-------CCCceeeEeeccccccccCCCCCccccccC
Q 002054 68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D----S-------VRDFLPLTVDYQEKQFAQGVIPNTYMRREG 135 (974)
Q Consensus 68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~----~-------~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg 135 (974)
|++.+++|++ +.|+|||+|++|+|+|+|+++.+.. | + +.++.||...++|. |
T Consensus 34 R~ieI~~~vi-~ka~GSa~VklG~Tqvv~gvK~eig~Pf~DtP~eG~~~~n~El~Plas~~fE~---------------G 97 (272)
T COG2123 34 RPLEIETGVI-PKANGSALVKLGNTQVVVGVKAEIGEPFPDTPNEGVLVVNVELSPLASPSFEP---------------G 97 (272)
T ss_pred cceEEEeCce-ecCCCcEEEEecCeEEEEEEEcccCCCCCCCCCCceEEeeeeeeccccccccC---------------C
Confidence 7899999999 8899999999999999999998765 2 1 13567888888777 9
Q ss_pred CCCchhhhHHHhhcCCccc----------cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCC--------
Q 002054 136 APKERELLVGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIP-------- 197 (974)
Q Consensus 136 ~p~~~eil~~RlidR~lrp----------lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP-------- 197 (974)
+|++++++++|++||.||. .+++.+.+-++++++||++||+.- .||..|+.+||+...+|
T Consensus 98 ppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~--Da~~lA~~aAL~~t~vP~~~~~~~~ 175 (272)
T COG2123 98 PPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLI--DAASLAAVAALLNTRVPKAVEVGDG 175 (272)
T ss_pred CCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHH--HHHHHHHHHHHHhcCCCceeecCCc
Confidence 9999999999999999999 566788889999999999999766 89999999999988766
Q ss_pred --------------CCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCe--EEEEEecCCCCCHHHHHHHHHHH
Q 002054 198 --------------WGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREK--TLMIDVQAREISEKDLEAGLRLA 261 (974)
Q Consensus 198 --------------~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~--i~mie~~~~~~~e~~~~~al~~a 261 (974)
+.+++-+|+++++|+.+++|||.+|+..++..++++.++++ +.|..+++..++++++.+|++.|
T Consensus 176 ~~v~~~~~~~~pl~~~~~pi~vt~a~ig~~lvvDPsleEe~v~d~~ltit~~~~~~Iv~iqK~g~~~~~~~~~~~~~~~A 255 (272)
T COG2123 176 EIVIEVEEEPVPLPVSNPPISVTFAKIGNVLVVDPSLEEELVADGRLTITVNEDGEIVAIQKVGGGSITESDLEKALKTA 255 (272)
T ss_pred ceeecccCCCcccccCCCceEEEEEEECCEEEeCCCcchhhhcCceEEEEECCCCcEEEEEEcCCCcCCHHHHHHHHHHH
Confidence 67788899999999999999999999999999999999987 45556677889999999999999
Q ss_pred HHHHHHHHHHHHHHHH
Q 002054 262 HPEAVKYLEPQIRLAE 277 (974)
Q Consensus 262 ~~~~~~i~~~~~~~~~ 277 (974)
.+...++++.+.+.++
T Consensus 256 ~~~~~kl~~~~~~~L~ 271 (272)
T COG2123 256 LSKAEKLREALKEALK 271 (272)
T ss_pred HHHHHHHHHHHHHhhc
Confidence 9999999998877653
No 45
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=99.90 E-value=7.6e-23 Score=228.51 Aligned_cols=208 Identities=21% Similarity=0.330 Sum_probs=183.7
Q ss_pred ccCeEEEeCCCC-CCCcceEEEeCCeEEEEEEEeC-CCchhhhccccCCCCceeEEEEEecCCCCccc-----cccccCC
Q 002054 379 VRPIYCESGNLP-ILHGSSLFSRGDTQVLCTVTLG-APAEAQRLESLVGPPTKRFMLHYSFPPFCINE-----VGKRVGL 451 (974)
Q Consensus 379 ~R~I~ie~g~l~-~a~GSal~~~G~T~Vl~~Vtl~-~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e-----~~~~~~~ 451 (974)
-|.|.+++|.+. .|+||+.++.|+|.|+++|++. .|.+ +.+-++++||....+++|. .+|.+++
T Consensus 55 nR~i~~etGklaRfAngsvvv~~GeT~Vm~Tv~~a~~PSp---------~qFlPL~VdYqeK~aAvGRip~~fmRREg~t 125 (760)
T KOG1067|consen 55 NREILFETGKLARFANGSVVVQMGETAVMTTVVLADKPSP---------PQFLPLVVDYQEKFAAVGRIPGNFMRREGRT 125 (760)
T ss_pred CeEEEEecchhhhhcCCcEEEccCCeEEEEEEEecCCCCc---------cccceEEEehhhhhhhhccCCCcccccccCC
Confidence 488999999998 5999999999999999999976 4555 3477899999998887764 5788999
Q ss_pred CchhhhHHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCCCh--hhHHHHHHHHHHHHcCCCccccccceeeeeeccCCC
Q 002054 452 NRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGST--SMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP 529 (974)
Q Consensus 452 ~rre~~~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdGs~--~~A~v~aa~lAL~dagvPi~~~vagvs~gli~~~d~ 529 (974)
+.+|+..++|++|.++|.+| +.|-+..++.+.+|.+||-. ...++||+++||+-+.||+..++.++.+|++++
T Consensus 126 kdkEiL~~rLidrsirplfp--~g~~~etqi~~n~Ls~dG~~~pdvlainaas~Al~lsdvpw~gpig~vRigLi~G--- 200 (760)
T KOG1067|consen 126 KDKEILTGRLIDRPIRPLFP--KGFYHETQILCNVLSSDGVHDPDVLAINAASAALSLSDVPWNGPIGAVRIGLIDG--- 200 (760)
T ss_pred cchhheeeeccccccccCCc--ccchhHHHHHhhheecccccCchHHHHhHHHHHhhhccCCCCCceeeeEeeeecc---
Confidence 99999999999999999999 57877899999999999944 467899999999999999999999999999986
Q ss_pred CCCcccceEEEecCCccccccCCccEEEEeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 002054 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQ 609 (974)
Q Consensus 530 ~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~ 609 (974)
.++++||..|.+.++.++.+|+|++.+.++.. +...|..+.|..|+.++++.+.+++..+....++..+.
T Consensus 201 --------e~vVNPT~kEmssS~Lnlvvagt~~~~vmle~--~s~~i~qqdl~~Aikvg~~~~q~~i~~i~~L~k~~Gk~ 270 (760)
T KOG1067|consen 201 --------EFVVNPTRKEMSSSQLNLVVAGTKSQTVMLEG--SSNNILQQDLLHAIKVGVKEAQQIIQGIERLAKKYGKQ 270 (760)
T ss_pred --------eEEeCcchhhhhhccceeEEEeccceEEEEEc--ccccccHHHHHHHHHhccHHHHHHHHHHHHHHHHhCcc
Confidence 69999999999999999999999877766554 44579999999999999999999999988888777654
Q ss_pred C
Q 002054 610 D 610 (974)
Q Consensus 610 ~ 610 (974)
+
T Consensus 271 K 271 (760)
T KOG1067|consen 271 K 271 (760)
T ss_pred c
Confidence 4
No 46
>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=2.9e-23 Score=215.48 Aligned_cols=204 Identities=23% Similarity=0.260 Sum_probs=168.2
Q ss_pred eEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCCCCCC-----CceeeEeeccccccccCCCCCccccccCCCCchhh
Q 002054 68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVR-----DFLPLTVDYQEKQFAQGVIPNTYMRREGAPKEREL 142 (974)
Q Consensus 68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~~~~~-----~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~ei 142 (974)
|++...+|++ .+|+||||+++|||+|||+|+||++..+. +..-+.|.|.-..|++|- .++..+-+.++.
T Consensus 24 R~i~~~~g~~-~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fst~~-----r~~~~~~~rr~~ 97 (245)
T KOG1068|consen 24 RRIYARIGVL-TQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFSTGD-----RKKRPKGDRREK 97 (245)
T ss_pred hhhhhhcCcc-ccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccccch-----hccCCCccHHHH
Confidence 6899999988 89999999999999999999999984332 345589999777776652 122234456899
Q ss_pred hHHHhhcCCccccccCCCCC--ceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCCCCCCeEEEEEEEECCEEEEcCCH
Q 002054 143 LVGRIIDRPIRPLFPAGFYH--EVQVMASVLSSDGKQDPDIMAANATSAALMLSDIPWGGPIGMIRIGRICGQFIVNPTM 220 (974)
Q Consensus 143 l~~RlidR~lrplfp~~~~~--~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP~~~~v~av~vg~i~g~~vldPt~ 220 (974)
+++.++.+.+.|.+-...++ .+.|.++||+.||++. ++|||||.+||+++||||++.|.|+++|+.+|.+++||++
T Consensus 98 e~s~~L~~afe~~I~~~lyPrsqIDI~v~VleddG~~l--aa~inaatlAL~daGI~m~D~i~~~t~~l~~~~~l~Dl~~ 175 (245)
T KOG1068|consen 98 ELSLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNL--AAAINAATLALADAGIPMYDLITACTAGLADGTPLLDLTS 175 (245)
T ss_pred HHHHHHHHHHHHHHHhhhCccccceEEEEEEECCCccH--HHHHHHHHHHHHHcCCChhhhhhhceeeecCCcccccccc
Confidence 99999999999865555544 4555578888888777 9999999999999999999999999999999999999999
Q ss_pred HHHhcCccceeEe--eeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 002054 221 DELSLSDLNLVYA--CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAG 280 (974)
Q Consensus 221 ~e~~~s~~~l~v~--~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~~~~~~g 280 (974)
-|++...-.++|+ +..+.+..+|.++. ++.+.+...|++|.++|+++.+.++..+.++-
T Consensus 176 ~eesa~~~~ltVa~l~~~~~i~~l~~~~~-~~~d~l~~vl~~a~~~c~~v~~~l~~~l~~~l 236 (245)
T KOG1068|consen 176 LEESARAPGLTVAALPNREEIALLQLDER-LHCDHLETVLELAIAGCKRVYERLRLVLREHL 236 (245)
T ss_pred chhhccCCceEEEEecCcceEEEEEecCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9988855444444 55556999999886 99999999999999999999999988776653
No 47
>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=2.7e-21 Score=199.06 Aligned_cols=220 Identities=20% Similarity=0.262 Sum_probs=179.7
Q ss_pred hcCCcCCCCCCCCccCeEEEeCCCCCCCcceEEEeCC-eEEEEEEEe--CCCchhhhccccCCCCceeEEEEEecCCCCc
Q 002054 366 AEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGD-TQVLCTVTL--GAPAEAQRLESLVGPPTKRFMLHYSFPPFCI 442 (974)
Q Consensus 366 ~~~~R~DGR~~~e~R~I~ie~g~l~~a~GSal~~~G~-T~Vl~~Vtl--~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~ 442 (974)
+..+|.|||..+++|||.+++|+||+++|||.++.|+ |-++++|+. |.|.+++ +.++.+.+.+.+.|.+.
T Consensus 18 e~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKaEvg~~~~~~-------p~egk~~~~VD~S~sas 90 (288)
T KOG1612|consen 18 EPDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKAEVGSPDDET-------PVEGKYLFFVDCSPSAS 90 (288)
T ss_pred CcccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEeeeccCccccC-------CCCCeEEEEEEecCCcC
Confidence 5689999999999999999999999999999999999 999999994 4677754 67788999999999998
Q ss_pred cccccccCCCchh--hhHHHHHHHHhhh--------cCCCCCCCCeEEEEEEEEEcCCCChhhHHHHHHHHHHHHcCCCc
Q 002054 443 NEVGKRVGLNRRE--VGHGTLAEKALLA--------VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPL 512 (974)
Q Consensus 443 ~e~~~~~~~~rre--~~~~~l~eral~~--------vi~~~~~~p~tI~V~v~VLesdGs~~~A~v~aa~lAL~dagvPi 512 (974)
.++.-+ +..| .++.+.++|+|.. -+...+.|.|.|+|++.|+++|||+++|...|+.+||.+..+|-
T Consensus 91 p~f~gR---ggde~~~eltsaLq~~l~~~~sgv~ls~L~lt~~~~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL~~T~lPk 167 (288)
T KOG1612|consen 91 PQFQGR---GGDELVEELTSALQRVLNSLGSGVDLSKLQLTPGYCWKIYVDVLVISSDGNLLDAISIAIYAALNNTRLPK 167 (288)
T ss_pred ccccCC---ChhhHHHHHHHHHHHHHhCcCcccchhheeccCCeeEEEEEeEEEEecCCCHHHHHHHHHHHHHhcccCCc
Confidence 876422 3333 2456677777755 11122469999999999999999999999999999999999992
Q ss_pred cc---------------------------cccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCceE
Q 002054 513 QE---------------------------HVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVT 565 (974)
Q Consensus 513 ~~---------------------------~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~gI~ 565 (974)
-. ++.-+++..+. +.+|+||+.+|+.+....+.|..+..|++
T Consensus 168 v~v~~dd~~~~~i~~s~~~Yd~~~~~~~~~P~ivtlskIG-----------~~~lVD~T~eEe~~a~s~l~Isv~a~giv 236 (288)
T KOG1612|consen 168 VIVAFDDDGEVEILLSDEEYDLMVKLVENVPLIVTLSKIG-----------TNMLVDPTAEEESVANSGLLISVSAGGIV 236 (288)
T ss_pred cccccccCCceeeccCcccchhhhhhcccCCEEEEEEeec-----------ceEEccCCccHHHhhhcceEEEEecCcce
Confidence 11 33333444332 47999999999999999999999999977
Q ss_pred EEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 002054 566 AIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAP 606 (974)
Q Consensus 566 alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~ 606 (974)
.+....+.+++.++.+.++++++++-...+...+.+.|.+.
T Consensus 237 s~~r~VG~G~l~~s~i~~mle~~~~~~e~l~~~l~k~L~~~ 277 (288)
T KOG1612|consen 237 SCTRSVGLGDLDPSSIPEMLEQGKAVVETLAPDLVKSLENE 277 (288)
T ss_pred EEEEEecCCCCChhhHHHHHHHHHHHHHhhhHHHHHHhhhh
Confidence 77666555669999999999999999999988888888764
No 48
>PF01138 RNase_PH: 3' exoribonuclease family, domain 1 This Prosite family only includes Ribonuclease PH; InterPro: IPR001247 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 1, which has a core 2-layer alpha/beta structure with a left-handed crossover, similar to that found in ribosomal protein S5. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; PDB: 2C38_G 2BR2_O 2C37_M 3L7Z_A 2JEB_A 2C39_A 2JEA_A 2JE6_A 3U1K_A 4AM3_B ....
Probab=99.88 E-value=4.7e-22 Score=194.81 Aligned_cols=131 Identities=31% Similarity=0.482 Sum_probs=114.6
Q ss_pred CccCeEEEeCCCCCCCcceEEEeCCeEEEEEEEeCCCchhhhccccCCCCceeEEEEEecCCCCccccccccCCCchhhh
Q 002054 378 EVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVG 457 (974)
Q Consensus 378 e~R~I~ie~g~l~~a~GSal~~~G~T~Vl~~Vtl~~p~~~~~~d~~~~~~~~~~~v~~~f~p~s~~e~~~~~~~~rre~~ 457 (974)
|+|++.+++|+++++||||+|++|+|+|+|+|+ +|.+....... ....+.+.++|+++|++..++++.+.+++++..
T Consensus 1 e~R~i~i~~~~~~~a~GSa~v~~G~T~V~~~V~--~~~~~~~~~~~-~~~~g~~~v~v~~~~~~~~~~~~~~~~~~~~~~ 77 (132)
T PF01138_consen 1 ELRPISIETGVLPRADGSARVSLGNTKVICSVK--GPIEPPPSNER-DDAEGRLTVEVEFSPFASPSFRRGGRPDEEERE 77 (132)
T ss_dssp CBEEEEEEESSSSSSSEEEEEEETTEEEEEEEE--EEEEGCSCSTT-SSSSEEEEEEEEECCCGSTSSSSSSSTHHHHHH
T ss_pred CCccEEEEeCCCCCCCeEEEEEECCeEEEEEEE--ecccccchhcc-cCCCceEEEEEEeccccccccccccccchhHHH
Confidence 789999999999999999999999999999999 55553111111 123488999999999999998777889999999
Q ss_pred HHHHHHHHhhhcCCCCCCCCeEEEEEEEEEcCCC-ChhhHHHHHHHHHHHHcCCC
Q 002054 458 HGTLAEKALLAVLPPENDFPYTVRVNSEVMASDG-STSMATVCGGSMALMDAGIP 511 (974)
Q Consensus 458 ~~~l~eral~~vi~~~~~~p~tI~V~v~VLesdG-s~~~A~v~aa~lAL~dagvP 511 (974)
++++++++|++++..+..+.|+|+|+++||++|| |+++||++|+++||+|+|||
T Consensus 78 l~~~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG~~~~~a~~~A~~~AL~~~~iP 132 (132)
T PF01138_consen 78 LSSLLERALRSSILLEGYPRWQIHVDVQVLSDDGGNLLDAAINAACLALLDAGIP 132 (132)
T ss_dssp HHHHHHHHHHHTBSTTTTSSEEEEEEEEEEECSSSSHHHHHHHHHHHHHHHHTCS
T ss_pred HHHHHhhhccccccccccCceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCC
Confidence 9999999999999984444589999999999999 99999999999999999998
No 49
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.86 E-value=2.8e-21 Score=225.20 Aligned_cols=226 Identities=16% Similarity=0.151 Sum_probs=181.2
Q ss_pred CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCC
Q 002054 653 DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQ 732 (974)
Q Consensus 653 dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd 732 (974)
+|.+.++... .....++..++.+ .+.|++++|+|+++.++|+||++ |++||+|.|++++.++.++..+ +||
T Consensus 97 ~g~liLS~k~-~~~~~~w~~ie~~----~e~g~~V~G~V~~v~k~G~~Vdl--Gi~gflP~Sel~~~~~~~~~~~--vGq 167 (486)
T PRK07899 97 EGRLILSKKR-AQYERAWGTIEKI----KEKDGVVTGTVIEVVKGGLILDI--GLRGFLPASLVEMRRVRDLQPY--IGQ 167 (486)
T ss_pred CCeEEEEehh-hcccchHHHHHHH----hcCCCEEEEEEEEEECCeEEEEE--CCEEEEEhhHhcccccCChhhc--CCC
Confidence 4566655432 2234455555432 46899999999999999999999 6899999999999888887763 899
Q ss_pred EEEEEEEEEcc-CCceEEEEeccCC----Ccccc------cCce---------EEEEEeecCCcceeeEEeeccCCCCCC
Q 002054 733 QLSLRCIGQDV-RGNIKLSLKAVSP----RPEAD------VKGV---------VEGSVPVNKQATDVWASVGDVSNGQNP 792 (974)
Q Consensus 733 ~V~vkVl~id~-~gri~LS~K~~~~----~~~~~------~g~~---------~~G~vv~i~~gv~~~~~~~~l~~~~~~ 792 (974)
.|+|+|+++|. ++++.||+|.++. .+|.. .|.+ .+|.|+++ .|+++|+|+++++|.+.
T Consensus 168 ~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdl-ggv~Glv~~Sels~~~v- 245 (486)
T PRK07899 168 EIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDL-GGVDGLVHVSELSWKHI- 245 (486)
T ss_pred EEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCccc-
Confidence 99999999998 6799999997543 23332 3433 45777777 47999999999999752
Q ss_pred CCCCCCCCCCCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec----------
Q 002054 793 ELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS---------- 862 (974)
Q Consensus 793 ~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~---------- 862 (974)
.+|. +.+++||.|.++| +++|+++++|.||+++..++| |..+.+.+++|+++.|.|.+
T Consensus 246 ~~~~-------~~~kvGd~V~vkV---l~iD~e~~rI~LSlK~~~~dP--w~~~~~~~~vG~vv~G~V~~I~~fGvFVeL 313 (486)
T PRK07899 246 DHPS-------EVVEVGQEVTVEV---LDVDMDRERVSLSLKATQEDP--WQQFARTHAIGQIVPGKVTKLVPFGAFVRV 313 (486)
T ss_pred CCHH-------HhcCCCCEEEEEE---EEEECCCCEEEEEEeeccccc--hhhhHHhcCCCCEEEEEEEEEeccEEEEEe
Confidence 3333 6789999999999 999999999999999999998 98888889999999999888
Q ss_pred -------------ccC--cCCCcccccCCeEEEEEEEeecCCCCcC-cccccccc
Q 002054 863 -------------STN--IQKSTSFSQREREELAECLFGTEDGDED-NKGTRVEA 901 (974)
Q Consensus 863 -------------~~~--~~~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~ 901 (974)
+|. ......|++||.|+++|+++|.+++++. |+|++..+
T Consensus 314 ~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~~~ 368 (486)
T PRK07899 314 EEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQANEG 368 (486)
T ss_pred CCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEEEcccC
Confidence 222 1223468999999999999999999999 99987654
No 50
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.83 E-value=6.7e-20 Score=211.72 Aligned_cols=208 Identities=19% Similarity=0.165 Sum_probs=174.0
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR 757 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~ 757 (974)
..++.|+++.|+|+++.++|+||++ +|.+||||++|+++.+..++.++ +||.++|+|+++|. ++++.||+|.+...
T Consensus 101 ~~~~~G~~v~g~V~~v~~~G~~V~~-~G~~gflp~~el~~~~~~~~~~~--vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~ 177 (390)
T PRK06676 101 EKFEEGEVVEVKVTEVVKGGLVVDV-EGVRGFIPASLISTRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAVVEE 177 (390)
T ss_pred HhccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCCccCCChHHc--CCCEEEEEEEEEECCCCEEEEEeHHHhhh
Confidence 3468999999999999999999999 57899999999999988887764 89999999999998 68999999987543
Q ss_pred ----ccc------ccCceE---------EEEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCCCcccCCCCcceEEEee
Q 002054 758 ----PEA------DVKGVV---------EGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRS 818 (974)
Q Consensus 758 ----~~~------~~g~~~---------~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~ 818 (974)
+|. ..|..+ .|.|+.+ .|+++|+|+++++|.+. ..|. +.+++||.+.++|
T Consensus 178 ~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l-~~v~g~v~~sels~~~~-~~~~-------~~~~vGd~i~~~V-- 246 (390)
T PRK06676 178 ERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSHERV-EKPS-------EVVSVGQEVEVKV-- 246 (390)
T ss_pred hhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEe-CCeEEEEEHHHcCcccc-CCHH-------HhcCCCCEEEEEE--
Confidence 222 134444 4566666 47999999999998642 2232 6689999999999
Q ss_pred cccccccccccccccccccccccccccccCCCCCCCcEEEEEec-----------------------ccCc--CCCcccc
Q 002054 819 AAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS-----------------------STNI--QKSTSFS 873 (974)
Q Consensus 819 ~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~-----------------------~~~~--~~~~~~k 873 (974)
+++|++++++.||+++..++| |......+++|++++|.|.+ +|.. +....|+
T Consensus 247 -l~vd~~~~~i~lS~k~~~~~~--~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~ 323 (390)
T PRK06676 247 -LSIDWETERISLSLKDTLPGP--WEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLE 323 (390)
T ss_pred -EEEeCCCCEEEEEEeecccCc--cccchhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCccccCChhhccC
Confidence 999999999999999988888 88888889999999999888 2221 1224689
Q ss_pred cCCeEEEEEEEeecCCCCcC-cccccccccc
Q 002054 874 QREREELAECLFGTEDGDED-NKGTRVEAIV 903 (974)
Q Consensus 874 ~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p~ 903 (974)
+||.|+++|+.+|++++++. |+|++..+||
T Consensus 324 ~Gd~v~v~V~~id~e~~~i~ls~k~~~~~~~ 354 (390)
T PRK06676 324 EGQEVKVKVLEVNEEEKRISLSIKALEEAPA 354 (390)
T ss_pred CCCEEEEEEEEEECCCCEEEEEEEecccChh
Confidence 99999999999999999999 9999999999
No 51
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.78 E-value=1.4e-18 Score=211.78 Aligned_cols=228 Identities=21% Similarity=0.181 Sum_probs=182.9
Q ss_pred CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCC
Q 002054 653 DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQ 732 (974)
Q Consensus 653 dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd 732 (974)
+|++.++.... ....+++.+. ..++.|+++.|+|+++.++|+||+++ +.+||+|.+|+++.+..++..+ +|+
T Consensus 364 ~g~i~LS~k~~-~~~~~~~~l~----~~~~~G~iv~g~V~~v~~~G~~V~lg-gi~gfiP~sel~~~~~~d~~~~--vG~ 435 (647)
T PRK00087 364 DGYVVLSKKEA-DREKAWKELE----EAFENGEPVKGKVKEVVKGGLLVDYG-GVRAFLPASHVELGYVEDLSEY--KGQ 435 (647)
T ss_pred CCcEEEEeehh-cchhHHHHHH----HHhhCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHhCccccCCHHHh--CCC
Confidence 56666665432 2334444433 34689999999999999999999995 6999999999999988887764 899
Q ss_pred EEEEEEEEEcc-CCc-eEEEEeccCC--------Ccccc--cCceE---------EEEEeecCCcceeeEEeeccCCCCC
Q 002054 733 QLSLRCIGQDV-RGN-IKLSLKAVSP--------RPEAD--VKGVV---------EGSVPVNKQATDVWASVGDVSNGQN 791 (974)
Q Consensus 733 ~V~vkVl~id~-~gr-i~LS~K~~~~--------~~~~~--~g~~~---------~G~vv~i~~gv~~~~~~~~l~~~~~ 791 (974)
.++|+|+++|+ +++ +.||+|.... ..|.. .|+.+ +|.|+++ +|+++|+|.++++|.+.
T Consensus 436 ~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l-~gv~Gll~~sels~~~~ 514 (647)
T PRK00087 436 ELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRV 514 (647)
T ss_pred EEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCcccc
Confidence 99999999998 567 9999998753 12322 34444 4566666 68999999999998652
Q ss_pred CCCCCCCCCCCCcccCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec---------
Q 002054 792 PELPMRKNETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS--------- 862 (974)
Q Consensus 792 ~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~--------- 862 (974)
..|. +.+++||.+.++| +++|++++++.||+++..++| |......+++|+++.|.|.+
T Consensus 515 -~~~~-------~~~~vGd~V~vkV---~~id~~~~~I~lS~K~~~~~p--~~~~~~~~~~G~~v~g~V~~i~~~G~fV~ 581 (647)
T PRK00087 515 -EKPS-------DVLKVGDEIKVYI---LDIDKENKKLSLSLKKLLPDP--WENVEEKYPVGSIVLGKVVRIAPFGAFVE 581 (647)
T ss_pred -CCHH-------HhcCCCCEEEEEE---EEEECCCCEEEEEeeccccCh--hhhhhhhccCCeEEEEEEEEEECCeEEEE
Confidence 2222 6789999999999 999999999999999999888 88888888899999999887
Q ss_pred --------------ccC--cCCCcccccCCeEEEEEEEeecCCCCcC-ccccccccc
Q 002054 863 --------------STN--IQKSTSFSQREREELAECLFGTEDGDED-NKGTRVEAI 902 (974)
Q Consensus 863 --------------~~~--~~~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~~p 902 (974)
+|. .+....|++||.|+++|+++|.+++++. |+|++..+|
T Consensus 582 l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~~~ 638 (647)
T PRK00087 582 LEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP 638 (647)
T ss_pred ECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence 222 1223478999999999999999999999 999998887
No 52
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.72 E-value=4.4e-18 Score=158.00 Aligned_cols=81 Identities=37% Similarity=0.722 Sum_probs=77.4
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCcc
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPE 759 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~ 759 (974)
.+++|++++|+|++|++|||||+|.+|..|||||||+++.+++++.+++++||.|+|||+++|++|+|.||+|++.+.|.
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~~~e~pe 81 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRKLEEEPE 81 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHHhhhCcc
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999988765
Q ss_pred c
Q 002054 760 A 760 (974)
Q Consensus 760 ~ 760 (974)
.
T Consensus 82 ~ 82 (129)
T COG1098 82 K 82 (129)
T ss_pred c
Confidence 4
No 53
>PF01138 RNase_PH: 3' exoribonuclease family, domain 1 This Prosite family only includes Ribonuclease PH; InterPro: IPR001247 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 1, which has a core 2-layer alpha/beta structure with a left-handed crossover, similar to that found in ribosomal protein S5. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; PDB: 2C38_G 2BR2_O 2C37_M 3L7Z_A 2JEB_A 2C39_A 2JEA_A 2JE6_A 3U1K_A 4AM3_B ....
Probab=99.71 E-value=2.6e-17 Score=161.20 Aligned_cols=122 Identities=31% Similarity=0.396 Sum_probs=105.3
Q ss_pred eEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCCC-C-CC-Ccee--eEeeccccccccCCCCCccccccCCCCchhh
Q 002054 68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGD-S-VR-DFLP--LTVDYQEKQFAQGVIPNTYMRREGAPKEREL 142 (974)
Q Consensus 68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~~-~-~~-~f~p--L~v~y~e~~~a~g~ip~~~~~Reg~p~~~ei 142 (974)
|++.+++|.+ .+|+|||++++|+|+|+|+|++|.+. + .. +..+ +++++.-..++.++. +|+|+++..+.
T Consensus 3 R~i~i~~~~~-~~a~GSa~v~~G~T~V~~~V~~~~~~~~~~~~~~~~g~~~v~v~~~~~~~~~~-----~~~~~~~~~~~ 76 (132)
T PF01138_consen 3 RPISIETGVL-PRADGSARVSLGNTKVICSVKGPIEPPPSNERDDAEGRLTVEVEFSPFASPSF-----RRGGRPDEEER 76 (132)
T ss_dssp EEEEEEESSS-SSSSEEEEEEETTEEEEEEEEEEEEGCSCSTTSSSSEEEEEEEEECCCGSTSS-----SSSSSTHHHHH
T ss_pred ccEEEEeCCC-CCCCeEEEEEECCeEEEEEEEecccccchhcccCCCceEEEEEEecccccccc-----ccccccchhHH
Confidence 8999999999 89999999999999999999999872 2 22 4333 888888777776654 56689999999
Q ss_pred hHHHhhcCCcccccc--CCCCCceEEEEEEEeccC-CCChhhHHHHHHHHHhhcCCCC
Q 002054 143 LVGRIIDRPIRPLFP--AGFYHEVQVMASVLSSDG-KQDPDIMAANATSAALMLSDIP 197 (974)
Q Consensus 143 l~~RlidR~lrplfp--~~~~~~~~i~~~vl~~dg-~~~~~~~ai~aAs~AL~~s~iP 197 (974)
++++++++.|++.+. ..+++.++|.++||+.|| +.. .+|+|||++||++++||
T Consensus 77 ~l~~~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG~~~~--~a~~~A~~~AL~~~~iP 132 (132)
T PF01138_consen 77 ELSSLLERALRSSILLEGYPRWQIHVDVQVLSDDGGNLL--DAAINAACLALLDAGIP 132 (132)
T ss_dssp HHHHHHHHHHHHTBSTTTTSSEEEEEEEEEEECSSSSHH--HHHHHHHHHHHHHHTCS
T ss_pred HHHHHHhhhccccccccccCceEEEEEEEEEecCCCCHH--HHHHHHHHHHHHhcCCC
Confidence 999999999999665 455789999999999999 666 99999999999999998
No 54
>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]
Probab=99.63 E-value=1e-14 Score=149.90 Aligned_cols=204 Identities=21% Similarity=0.249 Sum_probs=158.6
Q ss_pred eEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-C----CCCCceeeEeeccccccccCCCCCcccccc-CCCCchh
Q 002054 68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-D----SVRDFLPLTVDYQEKQFAQGVIPNTYMRRE-GAPKERE 141 (974)
Q Consensus 68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~----~~~~f~pL~v~y~e~~~a~g~ip~~~~~Re-g~p~~~e 141 (974)
|.++++.|+. . ||+.+++|+|+|+|.++.+.- | +..+-+-+..+..+-++. .-| |++++.+
T Consensus 33 R~lei~fGke-~---gs~~vt~G~Tkvm~~vt~~ia~Py~dRP~eG~~~I~telsPmA~~---------sfE~Gr~~~~~ 99 (291)
T KOG1614|consen 33 RDLEIEFGKE-Y---GSVLVTMGNTKVMARVTAQIAQPYIDRPHEGSFSIFTELSPMASP---------SFEPGRKGESE 99 (291)
T ss_pred hceEEEeccc-c---ccEEEEecCeeEEEEeehhhcCcccCCCCCCeeeeeecccccccc---------ccCCCCccchH
Confidence 5789999988 4 999999999999999998754 2 222223333333322211 112 8999999
Q ss_pred hhHHHhhcCCccc----------cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCC----------------
Q 002054 142 LLVGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSD---------------- 195 (974)
Q Consensus 142 il~~RlidR~lrp----------lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~---------------- 195 (974)
++++|+|++.+|- ..-..-.+.+.|+.++|+.||+.- .||..||.+||+-=.
T Consensus 100 v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlv--DaA~iAviaaL~hFrrPdvTv~g~ev~ihp~ 177 (291)
T KOG1614|consen 100 VELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLV--DAACIAVIAALMHFRRPDVTVGGEEVIIHPV 177 (291)
T ss_pred HHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCee--hhHHHHHHHHHHhcCCCCcccccceeEecCh
Confidence 9999999999997 223444667888899999999987 899999999998644
Q ss_pred -----CC--CCCCeEEEEEEEEC--CEEEEcCCHHHHhcCccceeEeeeCCe-EEEEEecCC-CCCHHHHHHHHHHHHHH
Q 002054 196 -----IP--WGGPIGMIRIGRIC--GQFIVNPTMDELSLSDLNLVYACTREK-TLMIDVQAR-EISEKDLEAGLRLAHPE 264 (974)
Q Consensus 196 -----iP--~~~~v~av~vg~i~--g~~vldPt~~e~~~s~~~l~v~~t~~~-i~mie~~~~-~~~e~~~~~al~~a~~~ 264 (974)
+| ++....+++.|..| +-.|+|||.+|+...|.-++|+.++.. |+.++..|+ -+++.+++.+.+.|..-
T Consensus 178 eEr~PvPL~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~~~dGs~vVt~Nk~rEVc~i~k~G~~~~~~~~i~~C~k~A~~~ 257 (291)
T KOG1614|consen 178 EEREPVPLSIHHMPICFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVTMNKNREVCAIQKSGGEILDESVIERCYKLAKDR 257 (291)
T ss_pred hccCCcceeeeeccceEEEEEecCceEEEeCCcHHHHhccCceEEEEEcCCccEEEEecCCCccccHHHHHHHHHHHHHH
Confidence 33 56778899999986 557899999999999999999999887 777776554 48999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCccccc
Q 002054 265 AVKYLEPQIRLAEKAGKQKKEY 286 (974)
Q Consensus 265 ~~~i~~~~~~~~~~~g~~k~~~ 286 (974)
+.++...+.+.+++.-+++..+
T Consensus 258 a~~vt~ii~e~l~~d~~~r~~~ 279 (291)
T KOG1614|consen 258 AVEVTGIILEALEEDQRERSAQ 279 (291)
T ss_pred HHHHHHHHHHHHHHHHHHhhhh
Confidence 9999998888887765444333
No 55
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.61 E-value=4.4e-15 Score=165.99 Aligned_cols=169 Identities=19% Similarity=0.201 Sum_probs=129.9
Q ss_pred CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCC
Q 002054 653 DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQ 732 (974)
Q Consensus 653 dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd 732 (974)
+|.+.++.... ....+++.+.. ..+.|++++|+|+++.++|+||++ +|++||||+|++++.+.. +.+ +|+
T Consensus 93 ~~~i~lS~k~~-~~~~~w~~l~~----~~~~~~~V~g~V~~~~~~G~~V~l-~Gv~gfip~s~ls~~~~~---~~~-vG~ 162 (318)
T PRK07400 93 DGQLTLSIRRI-EYMRAWERVRQ----LQKEDATVRSEVFATNRGGALVRI-EGLRGFIPGSHISTRKPK---EEL-VGE 162 (318)
T ss_pred CCeEEEehhhh-hhhhHHHHHHH----hccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcCccCCc---ccc-CCC
Confidence 46666654432 12234444332 346799999999999999999999 699999999999986433 333 999
Q ss_pred EEEEEEEEEcc-CCceEEEEeccCCCc-cc--ccCc---------eEEEEEeecCCcceeeEEeeccCCCCCCCCCCCCC
Q 002054 733 QLSLRCIGQDV-RGNIKLSLKAVSPRP-EA--DVKG---------VVEGSVPVNKQATDVWASVGDVSNGQNPELPMRKN 799 (974)
Q Consensus 733 ~V~vkVl~id~-~gri~LS~K~~~~~~-~~--~~g~---------~~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~ 799 (974)
.|.|+|+++|+ ++++.||+|....+. +. +.|. ..+|.|+++ .|++|++|+++++|.+. ..|
T Consensus 163 ~i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~fV~i-~gv~Gllhisels~~~~-~~~---- 236 (318)
T PRK07400 163 ELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHI-ETP---- 236 (318)
T ss_pred EEEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHcccccc-cCh----
Confidence 99999999998 689999999765432 21 2344 345667776 58999999999999763 223
Q ss_pred CCCCcccCCCCcceEEEeeccccccccccccccccccccccccccc
Q 002054 800 ETPGVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLAS 845 (974)
Q Consensus 800 ~~~~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~ 845 (974)
.+.+++||.+++.| +++|.+++++.||+++..++| |..
T Consensus 237 ---~~~~~vGd~VkvkV---l~iD~e~~rI~LS~K~l~~~P--~~~ 274 (318)
T PRK07400 237 ---HSVFNVNDEMKVMI---IDLDAERGRISLSTKQLEPEP--GDM 274 (318)
T ss_pred ---hhccCCCCEEEEEE---EEEeCCCCEEEEEEeccccCh--hhh
Confidence 37899999999999 999999999999999999998 644
No 56
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.53 E-value=2.9e-13 Score=165.30 Aligned_cols=275 Identities=18% Similarity=0.158 Sum_probs=202.3
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcc--ccccccccccCCEEEEEEEEEcc------------C
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP--VSRVSDVVSVGQQLSLRCIGQDV------------R 744 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~--v~~~~~~~~vGd~V~vkVl~id~------------~ 744 (974)
.++.+|.++.++|++|.++++-|.+..+..|.||+||+-+.. +.+|.+.|++||.|.|+|++.-. .
T Consensus 881 ~~~~igsiv~a~v~svKp~~L~v~l~~~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrviG~~D~k~lpith~i~k~ 960 (1710)
T KOG1070|consen 881 EDLSIGSIVRAYVKSVKPDQLNVLLAANHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRVIGGHDVKDLPITHLISKE 960 (1710)
T ss_pred cceeeeeEEEEEEeeecccceEEeccccccCceehHHhhccccccCChhhhcccCCeEEEEEEcCCccccCccccccchh
Confidence 368899999999999999999999999999999999998764 66899999999999999999621 1
Q ss_pred CceEEEEeccCCC--ccc-------ccCceEEEEEeec---------CCcceeeEEeeccCCC-CCCCCCCCCCCCCCcc
Q 002054 745 GNIKLSLKAVSPR--PEA-------DVKGVVEGSVPVN---------KQATDVWASVGDVSNG-QNPELPMRKNETPGVN 805 (974)
Q Consensus 745 gri~LS~K~~~~~--~~~-------~~g~~~~G~vv~i---------~~gv~~~~~~~~l~~~-~~~~lp~~~~~~~~~~ 805 (974)
.-..||+|....+ +.. ..|+.+.|.|... ...+++.+++.+++.. ....+| ...
T Consensus 961 ~v~ElSvkps~les~~~~t~s~~q~~~gq~vtGfV~nv~ke~~w~~isp~v~~RIplld~s~~~~~le~~-------e~~ 1033 (1710)
T KOG1070|consen 961 QVLELSVKPSELESDEFNTTSTKQFKAGQEVTGFVNNVSKEWLWVRISPFVDGRIPLLDTSLDLHVLELP-------ESL 1033 (1710)
T ss_pred hhhhhccChhhhccccccccchhhhhcCCeEEEEEEccccceeEEEccccccceeeeeeccchhhhhhCc-------hhh
Confidence 2345666643222 111 1377888877643 3457888888888843 222233 378
Q ss_pred cCCCCcceEEEeecccccccccccccccccccccccccccccCCCCCCCcEEEEEec-----------------------
Q 002054 806 SSTSSTPAVLIRSAAECDEEEKASGFSQSSKSTLKSTLASKSNSKPKKFTSQSDFFS----------------------- 862 (974)
Q Consensus 806 ~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~~~~~~~~~~~~~~~~G~~v~g~V~~----------------------- 862 (974)
|..|+.+.++| +..|.. +....++....++ ...+|++.-|+|.+
T Consensus 1034 F~~g~al~~~V---~~~~~~--~tv~~iG~~~~~k--------~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~ 1100 (1710)
T KOG1070|consen 1034 FPLGKALDEYV---VRNDKS--KTVRAIGFSKSDK--------NPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIED 1100 (1710)
T ss_pred cccccceeeEE---ecccce--eEEEecccccCCC--------CCCcchhhcceeeeeccceeEEecCCccccceEEeee
Confidence 99999999999 777732 2222222221111 11156665555544
Q ss_pred ---ccCcCCCcccccCCeEEEEEEEeecCCCCcC-ccccccc--ccc--------ccccCCCCCEEEEEEEEEeCCeEEE
Q 002054 863 ---STNIQKSTSFSQREREELAECLFGTEDGDED-NKGTRVE--AIV--------SAKNLKLGTKVAAKVYQVRARGLVL 928 (974)
Q Consensus 863 ---~~~~~~~~~~k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~--~p~--------~~~~~~vG~vV~G~V~~I~~~GvFV 928 (974)
+|.-..-..|..+|.+...+|.++..++.+. |++.... .|. ..++++.|++|.|.|.++.+.|+|+
T Consensus 1101 ~~d~~~~~P~~~f~~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi 1180 (1710)
T KOG1070|consen 1101 MSDSYSMTPVEHFTKIQIVYVCVLSVSALNKGLELSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFI 1180 (1710)
T ss_pred hhccccCChHHhcccccEEEEEEEEEecccccceeecccccccCccccccCCcccchhhcccCceeEEEEEEecCCcEEE
Confidence 4444444589999999999999999998665 7763322 221 5789999999999999999999999
Q ss_pred EeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCC-ceeeeecC
Q 002054 929 DLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKG-IPVVSLVD 973 (974)
Q Consensus 929 ~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~-~~~~~~~~ 973 (974)
.|..++.++++++++. +.+|.+|+-|.++|++++++- ..-++|..
T Consensus 1181 ~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~ 1233 (1710)
T KOG1070|consen 1181 ALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKN 1233 (1710)
T ss_pred EEccceEEEEEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEec
Confidence 9999999999998663 668999999999999999876 55566643
No 57
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=99.52 E-value=1.6e-13 Score=167.44 Aligned_cols=273 Identities=13% Similarity=0.088 Sum_probs=204.6
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCc--cccccccccccCCEEEEEEEEEccCCceEEEEecc--
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE--PVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV-- 754 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~--~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~-- 754 (974)
.+++.|+.|+|.|.++....++|.+.|.++|.+|+-+++.+ ..++|...|++|+.+++.|...|..+ +....
T Consensus 983 ~q~~~gq~vtGfV~nv~ke~~w~~isp~v~~RIplld~s~~~~~le~~e~~F~~g~al~~~V~~~~~~~----tv~~iG~ 1058 (1710)
T KOG1070|consen 983 KQFKAGQEVTGFVNNVSKEWLWVRISPFVDGRIPLLDTSLDLHVLELPESLFPLGKALDEYVVRNDKSK----TVRAIGF 1058 (1710)
T ss_pred hhhhcCCeEEEEEEccccceeEEEccccccceeeeeeccchhhhhhCchhhcccccceeeEEeccccee----EEEeccc
Confidence 36889999999999999999999999999999999999843 46789999999999999999987322 11111
Q ss_pred -CCCcccccCceEEEEEeec---------CCcceeeEEee-ccCCCCCCCCCCCCCCCCCcccCCCCcceEEEeeccccc
Q 002054 755 -SPRPEADVKGVVEGSVPVN---------KQATDVWASVG-DVSNGQNPELPMRKNETPGVNSSTSSTPAVLIRSAAECD 823 (974)
Q Consensus 755 -~~~~~~~~g~~~~G~vv~i---------~~gv~~~~~~~-~l~~~~~~~lp~~~~~~~~~~~~~G~~v~v~Ir~~l~iD 823 (974)
.......+|....|.+..+ ..++.|..++- ++++.. ..+|. ..+..++.+.+-+ +.++
T Consensus 1059 ~~~~k~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~d~~-~~~P~-------~~f~~~~~v~~~~---L~vs 1127 (1710)
T KOG1070|consen 1059 SKSDKNPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMSDSY-SMTPV-------EHFTKIQIVYVCV---LSVS 1127 (1710)
T ss_pred ccCCCCCCcchhhcceeeeeccceeEEecCCccccceEEeeehhccc-cCChH-------HhcccccEEEEEE---EEEe
Confidence 1111112455555555543 33344433333 555544 23444 6777788877777 9999
Q ss_pred ccccccccccccccc------cccccccccCCCCCCCcEEEEEec----------cc---------------CcCCCccc
Q 002054 824 EEEKASGFSQSSKST------LKSTLASKSNSKPKKFTSQSDFFS----------ST---------------NIQKSTSF 872 (974)
Q Consensus 824 ~~~r~i~ls~k~~~~------~~~~~~~~~~~~~~G~~v~g~V~~----------~~---------------~~~~~~~~ 872 (974)
..++.+.||++.... .....++..+....|+.+.|+|+| +. ...-+.+|
T Consensus 1128 ~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~ 1207 (1710)
T KOG1070|consen 1128 ALNKGLELSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHL 1207 (1710)
T ss_pred cccccceeecccccccCccccccCCcccchhhcccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhhhhhccC
Confidence 999989999984321 122356677888899999999998 00 01112489
Q ss_pred ccCCeEEEEEEEeecCCCCcC-ccccccc-ccc----ccccCCCCCEEEEEEEEEeCCeEEEEeCCCe--EEEEecccCC
Q 002054 873 SQREREELAECLFGTEDGDED-NKGTRVE-AIV----SAKNLKLGTKVAAKVYQVRARGLVLDLGGGI--RGMYRFENNE 944 (974)
Q Consensus 873 k~Gq~v~~~Vl~vd~e~~~i~-slK~~~~-~p~----~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv--~Glih~se~~ 944 (974)
.+||.|.++|+.+++..+++. ++|.... ++. .+.++++||...|+|.++.+||+||+++.++ .|+||.++..
T Consensus 1208 ~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~tv~~~g~~~~~e~~ 1287 (1710)
T KOG1070|consen 1208 PVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFIKLDVTVNMVGLCHISEEA 1287 (1710)
T ss_pred CccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhccccccceEEEecCCceEEEecCcceecccccceeec
Confidence 999999999999999999999 9887432 222 4788999999999999999999999999855 9999999653
Q ss_pred -------CCCCCCCCEEEEEEEEEeCCCc
Q 002054 945 -------KKDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 945 -------~~~f~vGd~V~vkVl~id~~~~ 966 (974)
...|..|+.|.|.|++++.++.
T Consensus 1288 d~~~e~it~~~~~~~~V~a~~lk~~~ek~ 1316 (1710)
T KOG1070|consen 1288 DDRGENITALYYAGDRVKACVLKEDSEKK 1316 (1710)
T ss_pred chhhhhcccceeccceeeeEeeeccchhh
Confidence 4568999999999999997664
No 58
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.51 E-value=8.1e-13 Score=138.92 Aligned_cols=208 Identities=16% Similarity=0.150 Sum_probs=153.8
Q ss_pred cccCcEEEEEEEEEeeceEEEEEcCCe-EEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCcc
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQ-QGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPE 759 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~-~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~ 759 (974)
..+|++....|.+..+||+|++=..+- .-++|.++...+ .+.+||+|+|.++- |.++++.++++. |.
T Consensus 3 ~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~~~-------e~evGdev~vFiY~-D~~~rl~aTt~~----p~ 70 (287)
T COG2996 3 IKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPEED-------ELEVGDEVTVFIYV-DSEDRLIATTRE----PK 70 (287)
T ss_pred ccccceEEEEEEEeeceeEEEecCCCceEEeccccCCcCC-------ccccCcEEEEEEEE-CCCCceeheeec----ce
Confidence 478999999999999999999975432 678888876433 37899999999876 889999999875 66
Q ss_pred cccCceEEEEEeecCCcceeeEEeeccCCCCCCCCCCCCCCCC--CcccCCCCcceEEEeeccccccccccccccccccc
Q 002054 760 ADVKGVVEGSVPVNKQATDVWASVGDVSNGQNPELPMRKNETP--GVNSSTSSTPAVLIRSAAECDEEEKASGFSQSSKS 837 (974)
Q Consensus 760 ~~~g~~~~G~vv~i~~gv~~~~~~~~l~~~~~~~lp~~~~~~~--~~~~~~G~~v~v~Ir~~l~iD~~~r~i~ls~k~~~ 837 (974)
..+|.-..+.|++. ....+.|.+++..+...+|..+ ... .-.+++||. ++|+ +.+|..+| |.-.+..
T Consensus 71 ~tvg~~g~~~Vv~v---~~~lGaFlD~Gl~KDl~vp~~e-lp~~~~~wpq~Gd~--l~v~--l~~Dkk~R-i~g~~a~-- 139 (287)
T COG2996 71 ATVGEYGWLKVVEV---NKDLGAFLDWGLPKDLLVPLDE-LPTLKSLWPQKGDK--LLVY--LYVDKKGR-IWGTLAI-- 139 (287)
T ss_pred EeecceeEEEEEEE---cCCcceEEecCCCcceeeehhh-cccccccCCCCCCE--EEEE--EEEccCCc-EEEEecc--
Confidence 67788888888883 2378888888877655555411 111 123678887 4443 56666653 2111110
Q ss_pred ccccccccccCCCCCCCcEEEEEecccCcCCCcccccCCeEEEEEEEeecCCCCcCccccccccccccccCC---CCCEE
Q 002054 838 TLKSTLASKSNSKPKKFTSQSDFFSSTNIQKSTSFSQREREELAECLFGTEDGDEDNKGTRVEAIVSAKNLK---LGTKV 914 (974)
Q Consensus 838 ~~~~~~~~~~~~~~~G~~v~g~V~~~~~~~~~~~~k~Gq~v~~~Vl~vd~e~~~i~slK~~~~~p~~~~~~~---vG~vV 914 (974)
. +.+.. .+..+. .+|.|
T Consensus 140 ~---------------------------------------------------------~~l~~---l~~~~~~~l~nq~v 159 (287)
T COG2996 140 E---------------------------------------------------------KILEN---LATPAYNNLKNQEV 159 (287)
T ss_pred h---------------------------------------------------------hHHHh---cCCccchhhhcCee
Confidence 0 00000 012222 59999
Q ss_pred EEEEEEEeCCeEEEEeCCCeEEEEecccCCCCCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054 915 AAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLV 972 (974)
Q Consensus 915 ~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~~f~vGd~V~vkVl~id~~~~~~~~~~ 972 (974)
.|+|+++..-|.||-+++++-||||.||. ..+++.||+++++|+.+.++|..++|+.
T Consensus 160 ~~tVYr~~~~G~fv~~e~~~~GfIh~sEr-~~~prlG~~l~~rVi~~reDg~lnLSl~ 216 (287)
T COG2996 160 DATVYRLLESGTFVITENGYLGFIHKSER-FAEPRLGERLTARVIGVREDGKLNLSLR 216 (287)
T ss_pred eeEEEEEeccceEEEEcCCeEEEEcchhh-cccccCCceEEEEEEEEccCCeeecccc
Confidence 99999999999999999999999999998 6789999999999999999999999984
No 59
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.51 E-value=4.1e-14 Score=155.42 Aligned_cols=93 Identities=25% Similarity=0.331 Sum_probs=87.4
Q ss_pred cccCcEEEEEEEEEeeceEEEEEc--CCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFN--GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR 757 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~--~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~ 757 (974)
+++|+++.|+|++|.+||+||+|. +|++||||+|||||.++.++.+++++||.|.|+|+.+|+ +|+|.||+|++.++
T Consensus 15 P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~~ 94 (319)
T PTZ00248 15 PEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSPE 94 (319)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecccc
Confidence 458999999999999999999996 689999999999999999999999999999999999998 79999999999999
Q ss_pred cccc------cCceEEEEEeec
Q 002054 758 PEAD------VKGVVEGSVPVN 773 (974)
Q Consensus 758 ~~~~------~g~~~~G~vv~i 773 (974)
||.. .|..+.|.+..+
T Consensus 95 pw~~~~e~~~~g~~v~~~V~~i 116 (319)
T PTZ00248 95 DIEACEEKFSKSKKVHSIMRHI 116 (319)
T ss_pred hHHHHHHhCcCCCEEEEEEEEc
Confidence 9987 478899988886
No 60
>PRK08582 hypothetical protein; Provisional
Probab=99.48 E-value=1.2e-13 Score=135.97 Aligned_cols=82 Identities=35% Similarity=0.672 Sum_probs=78.1
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCcc
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPE 759 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~ 759 (974)
.+++|++|.|+|++|++||+||+|.++.+||||+|++++.++.++.+.|++||.|+|+|+++|.+|+|.||+|++..+||
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~~~~~~~ 81 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRPK 81 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEEecccCch
Confidence 36899999999999999999999999999999999999999999999999999999999999988999999999999898
Q ss_pred cc
Q 002054 760 AD 761 (974)
Q Consensus 760 ~~ 761 (974)
..
T Consensus 82 ~~ 83 (139)
T PRK08582 82 RQ 83 (139)
T ss_pred hh
Confidence 65
No 61
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.48 E-value=9e-14 Score=121.81 Aligned_cols=71 Identities=25% Similarity=0.346 Sum_probs=67.2
Q ss_pred cccCcEEEEEEEEEee-ceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEe
Q 002054 681 IEVGGIYKGVVTSVKE-YGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK 752 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~-~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K 752 (974)
+++|++|.|+|+++.+ ||+||+|.++.+|++|+|+++++++.++.+.|++||.|+|+|+++|. +++.||+|
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD-GKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC-CEEEEEeC
Confidence 4689999999999986 89999999999999999999999999999999999999999999985 99999986
No 62
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.44 E-value=2.4e-13 Score=119.64 Aligned_cols=70 Identities=21% Similarity=0.375 Sum_probs=64.7
Q ss_pred cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccccc---ccccccCCEEEEEEEEEcc-CCceEEE
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRV---SDVVSVGQQLSLRCIGQDV-RGNIKLS 750 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~---~~~~~vGd~V~vkVl~id~-~gri~LS 750 (974)
+++|+++.|+|+++.+||+||++.++++||||+++++|.++.++ .+.|++||.++|+|+++|+ +++|.||
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence 47899999999999999999999999999999999999997775 5889999999999999997 6888876
No 63
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=99.40 E-value=1.1e-12 Score=115.26 Aligned_cols=71 Identities=44% Similarity=0.700 Sum_probs=65.4
Q ss_pred cccCcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEE
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSL 751 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~ 751 (974)
+++|++|+|+|+++.+||+||++.+ +.+||+|+|++++.++.++.+.|++||.|+|+|+++|..+++.||+
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~ 72 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL 72 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence 3689999999999999999999943 2699999999999999999999999999999999999877999986
No 64
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.36 E-value=2e-12 Score=112.35 Aligned_cols=69 Identities=29% Similarity=0.399 Sum_probs=66.1
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK 752 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K 752 (974)
|++|.|+|+++.++|+||+|+++.+||+|+|+++++++.++.+.|++||.++|+|+++|. ++++.||+|
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k 70 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence 789999999999999999999899999999999999999999999999999999999998 789999986
No 65
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.35 E-value=2e-12 Score=112.93 Aligned_cols=68 Identities=32% Similarity=0.488 Sum_probs=64.3
Q ss_pred CcEEE-EEEEEE-eeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEE
Q 002054 684 GGIYK-GVVTSV-KEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSL 751 (974)
Q Consensus 684 G~i~~-G~V~~i-~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~ 751 (974)
|++|+ |+|+++ .+||+||++.++.+||+|+|++++.+..++.+.|++||.++|+|+++|+ ++++.||+
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 78999 899999 6999999999999999999999999999999999999999999999998 78999985
No 66
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=99.34 E-value=4e-12 Score=111.68 Aligned_cols=72 Identities=39% Similarity=0.724 Sum_probs=68.9
Q ss_pred cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK 752 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K 752 (974)
+++|+++.|+|+++.++|+||+|.++.+||||.+++++.+..++...+++||.++|+|+++|. ++++.||+|
T Consensus 2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k 74 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK 74 (74)
T ss_dssp SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence 689999999999999999999998899999999999999999999999999999999999998 678999986
No 67
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.33 E-value=2.9e-12 Score=115.40 Aligned_cols=73 Identities=33% Similarity=0.459 Sum_probs=69.4
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEE
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSL 751 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~ 751 (974)
.++++|++|.|+|+++.++|+||++.++.+||+|+++++++++.++.+.|++||.|+|+|+++|. ++++.||+
T Consensus 10 ~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 10 SDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred HhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 46899999999999999999999999999999999999999999999999999999999999998 79999985
No 68
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.32 E-value=4.4e-12 Score=111.43 Aligned_cols=69 Identities=20% Similarity=0.344 Sum_probs=65.2
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcc--ccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP--VSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK 752 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~--v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K 752 (974)
|+++.|+|+++.++|+||+|.++++|++|++++++.+ .+++.+.|++||.|+|+|+++|+ +++|.||+|
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 7899999999999999999999999999999999864 88999999999999999999998 689999987
No 69
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=99.32 E-value=6.3e-12 Score=110.94 Aligned_cols=73 Identities=30% Similarity=0.464 Sum_probs=67.9
Q ss_pred cccCcEEEEEEEEEeeceEEEEEcC--CeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEec
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFNG--GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKA 753 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~~--g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~ 753 (974)
++.|++|.|+|+++.++|+||++.+ +.+||+|+|+++++++.++.+.|++||.|+|+|+++|. ++++.||+|+
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~ 76 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence 4689999999999999999999963 69999999999999999999999999999999999997 6899999874
No 70
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.31 E-value=1.8e-12 Score=120.85 Aligned_cols=67 Identities=24% Similarity=0.435 Sum_probs=62.2
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeeeecC
Q 002054 907 NLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVSLVD 973 (974)
Q Consensus 907 ~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~~~~ 973 (974)
.+++|++++|+|..|++||+||+|++|=.||||+|+.. ++.+++||+|+|+|+++|++|++-+|+.+
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~ 75 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRK 75 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHH
Confidence 57899999999999999999999999999999999774 56799999999999999999999999754
No 71
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=99.31 E-value=8.8e-12 Score=111.17 Aligned_cols=74 Identities=43% Similarity=0.741 Sum_probs=68.6
Q ss_pred CcEEEEEEEEEeeceEEEEEc---CCeEEEEecccCCCccc-cccccccccCCEEEEEEEEEccCCceEEEEeccCCCc
Q 002054 684 GGIYKGVVTSVKEYGAFVEFN---GGQQGLLHVSELSHEPV-SRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRP 758 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~---~g~~Glvhisels~~~v-~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~ 758 (974)
|++|.|+|+++.+||+||+|. ++.+||+|++++++++. .++.+.|++||.|+|+|+++| ++++.||+|++.++.
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k~~~~~~ 78 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ-NGKISLSMKDVDQDT 78 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe-CCEEEEEEEecccCC
Confidence 789999999999999999997 46899999999999986 899999999999999999999 999999999987653
No 72
>PRK05807 hypothetical protein; Provisional
Probab=99.31 E-value=8.5e-12 Score=122.65 Aligned_cols=75 Identities=31% Similarity=0.603 Sum_probs=71.4
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccC
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVS 755 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~ 755 (974)
.+++|++|+|+|++|.++|+||+| ++.+||||+|++++.++.++.+.|++||.|+|+|+++|.+|+|.||+|.+.
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~~~ 76 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAM 76 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence 367999999999999999999999 689999999999999999999999999999999999998899999999976
No 73
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.31 E-value=8.7e-12 Score=109.32 Aligned_cols=72 Identities=21% Similarity=0.286 Sum_probs=67.6
Q ss_pred cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK 752 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K 752 (974)
+++|+++.|+|+++.++|+||+|.++.+|++|++++++++..++.+.|++||.++|+|+++|. ++++.||+|
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~ 73 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence 368999999999999999999999999999999999999888888999999999999999998 689999975
No 74
>PRK07252 hypothetical protein; Provisional
Probab=99.31 E-value=8.6e-12 Score=119.86 Aligned_cols=76 Identities=30% Similarity=0.645 Sum_probs=72.3
Q ss_pred ccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054 682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR 757 (974)
Q Consensus 682 ~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~ 757 (974)
++|++|.|+|++|.++|+||+|.++.+||+|+|+++++++.++.+.|++||.|+|+|+++|. ++++.||+|.+.++
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~ 78 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEE 78 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccC
Confidence 57999999999999999999999899999999999999999999999999999999999998 79999999998764
No 75
>PHA02945 interferon resistance protein; Provisional
Probab=99.30 E-value=1.1e-11 Score=109.43 Aligned_cols=74 Identities=22% Similarity=0.366 Sum_probs=68.4
Q ss_pred ccccCcEEEEEEEEEeeceEEEEE--cCCeEEEEecccC--CCccccccccccccCCEEEEEEEEEcc-CCceEEEEecc
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEF--NGGQQGLLHVSEL--SHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAV 754 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l--~~g~~Glvhisel--s~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~ 754 (974)
-|++|+++.|+|+. .+||+||.| ++|.+||+|+|++ +..|+++ ++++ +||++.|||+.+|+ +|.|.||+|++
T Consensus 8 ~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK~V 84 (88)
T PHA02945 8 LPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYKRM 84 (88)
T ss_pred CCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEeeEc
Confidence 36899999999999 999999999 4689999999955 9999999 9999 99999999999998 79999999987
Q ss_pred CC
Q 002054 755 SP 756 (974)
Q Consensus 755 ~~ 756 (974)
.+
T Consensus 85 ~~ 86 (88)
T PHA02945 85 CR 86 (88)
T ss_pred cc
Confidence 54
No 76
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.29 E-value=7.8e-12 Score=108.47 Aligned_cols=68 Identities=21% Similarity=0.389 Sum_probs=64.7
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEE
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSL 751 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~ 751 (974)
|++|+|+|+++.++|+||++.++.+||+|++++++.+..++.+.|++||.++|+|+++|. ++++.||+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 789999999999999999999899999999999999999999999999999999999998 78999984
No 77
>PF03726 PNPase: Polyribonucleotide nucleotidyltransferase, RNA binding domain; InterPro: IPR015848 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents an RNA-binding phosphorolytic (PH) domain found in bacterial and organelle PNPases, but not in exosomes. It usually occurs in combination with PH domain 1 (IPR001247 from INTERPRO) and PH domain 2 (IPR015847 from INTERPRO), both of which are found in PNPases and exosomes. The core structure of the RNA-binding PH domain consists of a DNA/RNA-binding 3-helical bundle. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0000175 3'-5'-exoribonuclease activity, 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 3U1K_B 3GCM_A 3GLL_A 3GME_A 4AM3_B 4AID_C 4AIM_A 1WHU_A ....
Probab=99.29 E-value=1.7e-11 Score=110.54 Aligned_cols=80 Identities=38% Similarity=0.573 Sum_probs=72.4
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHHHHHHhhhc---cchhhhchHHHHHHHHHHHHHHHHHHhcCCc
Q 002054 294 QTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEE---CDEESLQVLPKAVDTVRKRVIRKRIIAEGVR 370 (974)
Q Consensus 294 ~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~r~~il~~~~R 370 (974)
+|.+.|++++.++|++++.+ ++|++|++++++|++++.+.|.++ .++.....+..+|+.++++.+|++||++|+|
T Consensus 1 el~~~v~~~~~~~l~~a~~~--~~K~eR~~a~~~i~~~~~~~~~~~~~e~~~~~~~~i~~~~~~l~k~~vR~~Il~~~~R 78 (83)
T PF03726_consen 1 ELKEAVKELAGEKLKEALQI--PDKQEREEALDAIKEEVIEELEEEYEEEDEEDEKEIKEAFEELEKKIVREMILEEGIR 78 (83)
T ss_dssp HHHHHHHHHHHHHHHHHHTS--SSHHHHHHHHHHHHHHHHHHHHCCCHHSTTSHHHHHHHHHHHHHHHHHHHHHHCTSBT
T ss_pred CHHHHHHHHHHHHHHHHHcc--cchHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHHHHHHHHCCCCC
Confidence 58899999999999999988 699999999999999999999843 2456677899999999999999999999999
Q ss_pred CCCCC
Q 002054 371 VDGRQ 375 (974)
Q Consensus 371 ~DGR~ 375 (974)
+|||+
T Consensus 79 ~DGR~ 83 (83)
T PF03726_consen 79 IDGRK 83 (83)
T ss_dssp TTS-B
T ss_pred CCCCC
Confidence 99995
No 78
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.27 E-value=9.3e-12 Score=107.66 Aligned_cols=67 Identities=27% Similarity=0.458 Sum_probs=64.0
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS 750 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS 750 (974)
|++|.|+|+++.++|+||+|.++.+||+|++++++++..++.+.|++||.|+|+|+++|+ ++++.||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999999999999999999999999999999999999999999998 7888876
No 79
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.25 E-value=2.8e-11 Score=106.52 Aligned_cols=71 Identities=21% Similarity=0.268 Sum_probs=64.3
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEc-CCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFN-GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP 756 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~-~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~ 756 (974)
+++.|+++.|+|++|.++|+||++. ++++||+|.+++++. +.+++||.+.|+|+++|+ ++++.||+|+..+
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~~ 73 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence 4689999999999999999999995 589999999999986 569999999999999998 6789999998653
No 80
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.24 E-value=2.7e-11 Score=105.87 Aligned_cols=71 Identities=34% Similarity=0.513 Sum_probs=67.5
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEecc
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAV 754 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~ 754 (974)
|+++.|+|+++.++|+||++.++.+|++|+++++++++.++.+.|++||.++|+|+++|. ++++.||+|.+
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~ 72 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK 72 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence 789999999999999999999999999999999999999999999999999999999998 58899999875
No 81
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.24 E-value=3.2e-11 Score=103.78 Aligned_cols=69 Identities=42% Similarity=0.815 Sum_probs=65.9
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEe
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK 752 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K 752 (974)
|++|.|+|+++.++|+||++.++.+||+|+++++++++.++.+.|++||.++|+|+++|.++++.||+|
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~k 69 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence 789999999999999999999899999999999999999999999999999999999998889999986
No 82
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.23 E-value=2.4e-11 Score=105.13 Aligned_cols=67 Identities=33% Similarity=0.654 Sum_probs=61.9
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCC-ccccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSH-EPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS 750 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~-~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS 750 (974)
|++|.|+|+++.+||+||+|.++.+||+|+++++| .+..++.+.|++||.|+|+|+++|. ++++.||
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence 78999999999999999999999999999999996 5778888999999999999999997 6788774
No 83
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.22 E-value=5e-11 Score=105.28 Aligned_cols=73 Identities=34% Similarity=0.610 Sum_probs=68.1
Q ss_pred ccCcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEecc
Q 002054 682 EVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAV 754 (974)
Q Consensus 682 ~~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~ 754 (974)
++|++|.|+|+++.++|+||+|.+ +.+|++|++++++++..++.+.|++||.|+|+|+++|. ++++.||+|..
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~ 75 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence 469999999999999999999975 79999999999999988899999999999999999998 78999999874
No 84
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.22 E-value=9.2e-12 Score=130.58 Aligned_cols=78 Identities=38% Similarity=0.613 Sum_probs=73.7
Q ss_pred ccccCcEEEEEEEEEeeceEEEEE--cCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEF--NGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP 756 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l--~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~ 756 (974)
-+++|+++-|+|++|.+||+||.| ++|.+||+|+||++..|++++.+++++||.+-||||.+|+ +|.|.||+|.+.+
T Consensus 8 ~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~ 87 (269)
T COG1093 8 YPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTE 87 (269)
T ss_pred CCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCCH
Confidence 378999999999999999999999 5799999999999999999999999999999999999999 7999999998865
Q ss_pred C
Q 002054 757 R 757 (974)
Q Consensus 757 ~ 757 (974)
+
T Consensus 88 ~ 88 (269)
T COG1093 88 H 88 (269)
T ss_pred H
Confidence 3
No 85
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.20 E-value=5.4e-11 Score=103.42 Aligned_cols=69 Identities=30% Similarity=0.531 Sum_probs=65.7
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK 752 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K 752 (974)
|+++.|+|.++.++|+||++.++.+|++|.+|+++.+..++.+.|++||.++|+|+++|+ ++++.||+|
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence 789999999999999999998899999999999999999999999999999999999996 689999986
No 86
>PRK08059 general stress protein 13; Validated
Probab=99.20 E-value=5.9e-11 Score=115.01 Aligned_cols=80 Identities=38% Similarity=0.713 Sum_probs=75.1
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR 757 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~ 757 (974)
.++++|++|.|+|+++.++|+||++.++.+|++|+++++++++.++.+.|++||.|+|+|+++|. ++++.||+|.+..+
T Consensus 3 ~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~~ 82 (123)
T PRK08059 3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEA 82 (123)
T ss_pred ccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEcccC
Confidence 45889999999999999999999999999999999999999999999999999999999999987 79999999998776
Q ss_pred c
Q 002054 758 P 758 (974)
Q Consensus 758 ~ 758 (974)
|
T Consensus 83 ~ 83 (123)
T PRK08059 83 P 83 (123)
T ss_pred c
Confidence 6
No 87
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.17 E-value=8.8e-11 Score=102.65 Aligned_cols=70 Identities=36% Similarity=0.554 Sum_probs=62.3
Q ss_pred cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCc-cccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE-PVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS 750 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~-~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS 750 (974)
+.+|++|.|+|+++.+||+||+|.++.+||+|+++++|. +..++.+.|++||.|+|+|+++|. ++++.|+
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence 368999999999999999999999899999999999875 455777889999999999999997 5777764
No 88
>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]
Probab=99.17 E-value=2.6e-09 Score=111.30 Aligned_cols=201 Identities=18% Similarity=0.220 Sum_probs=140.9
Q ss_pred CeEEEEEeCccCcCCCcEEEEEeCC-eEEEEEEEeCCC-C----CCCCceeeEeeccccccccCCCCCccccccCC--CC
Q 002054 67 SRLITLETGKIARFANGAVVLGMDE-TKVLSTVTSSKG-D----SVRDFLPLTVDYQEKQFAQGVIPNTYMRREGA--PK 138 (974)
Q Consensus 67 ~r~i~~etg~~a~~A~GSa~v~~G~-T~Vl~tv~~~~~-~----~~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~--p~ 138 (974)
=|+|.+|||++ ++++|||.|++|+ |-||++|+..-+ | +.....-+.||...... ..|-.|+|- ++
T Consensus 31 ~Rpi~vetdVl-p~tNGSaRVk~g~~tdiivgVKaEvg~~~~~~p~egk~~~~VD~S~sas------p~f~gRggde~~~ 103 (288)
T KOG1612|consen 31 FRPIEVETDVL-PGTNGSARVKLGDGTDIIVGVKAEVGSPDDETPVEGKYLFFVDCSPSAS------PQFQGRGGDELVE 103 (288)
T ss_pred cceEEEEeccc-cCCCCcEEEEecCCceEEEEEeeeccCccccCCCCCeEEEEEEecCCcC------ccccCCChhhHHH
Confidence 37999999999 9999999999999 889999998765 2 12233456677643321 124455442 33
Q ss_pred chhhhHHHhhcC-Cccc-----cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCC---------------
Q 002054 139 ERELLVGRIIDR-PIRP-----LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIP--------------- 197 (974)
Q Consensus 139 ~~eil~~RlidR-~lrp-----lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP--------------- 197 (974)
+-.-.++|+... ..-+ .|-++|.+.+.|++.|++.||+.. .|--.|+.+||.+.-+|
T Consensus 104 eltsaLq~~l~~~~sgv~ls~L~lt~~~~W~i~VDvlVi~s~gn~~--dAiS~Ai~~AL~~T~lPkv~v~~dd~~~~~i~ 181 (288)
T KOG1612|consen 104 ELTSALQRVLNSLGSGVDLSKLQLTPGYCWKIYVDVLVISSDGNLL--DAISIAIYAALNNTRLPKVIVAFDDDGEVEIL 181 (288)
T ss_pred HHHHHHHHHHhCcCcccchhheeccCCeeEEEEEeEEEEecCCCHH--HHHHHHHHHHHhcccCCccccccccCCceeec
Confidence 333344454433 1101 455669999999999999999654 55567888999887666
Q ss_pred ------------CCCCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeeeCCeE-EEE-EecCCCCCHHHHHHHHHHHHH
Q 002054 198 ------------WGGPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACTREKT-LMI-DVQAREISEKDLEAGLRLAHP 263 (974)
Q Consensus 198 ------------~~~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t~~~i-~mi-e~~~~~~~e~~~~~al~~a~~ 263 (974)
...+..=+++.+|+..+++|||.+|++.+..-+.|+-+..++ ..+ ..+.+.+..+-..++|+.|.+
T Consensus 182 ~s~~~Yd~~~~~~~~~P~ivtlskIG~~~lVD~T~eEe~~a~s~l~Isv~a~givs~~r~VG~G~l~~s~i~~mle~~~~ 261 (288)
T KOG1612|consen 182 LSDEEYDLMVKLVENVPLIVTLSKIGTNMLVDPTAEEESVANSGLLISVSAGGIVSCTRSVGLGDLDPSSIPEMLEQGKA 261 (288)
T ss_pred cCcccchhhhhhcccCCEEEEEEeecceEEccCCccHHHhhhcceEEEEecCcceEEEEEecCCCCChhhHHHHHHHHHH
Confidence 112334578899999999999999999999999998887773 333 334444777788888888888
Q ss_pred HHHHHHHHHHHHH
Q 002054 264 EAVKYLEPQIRLA 276 (974)
Q Consensus 264 ~~~~i~~~~~~~~ 276 (974)
-.+.+.....+.+
T Consensus 262 ~~e~l~~~l~k~L 274 (288)
T KOG1612|consen 262 VVETLAPDLVKSL 274 (288)
T ss_pred HHHhhhHHHHHHh
Confidence 7776665544433
No 89
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=99.15 E-value=1.1e-10 Score=105.80 Aligned_cols=75 Identities=23% Similarity=0.252 Sum_probs=68.6
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCC----ccccccccccccCCEEEEEEEEEccCCceEEEEecc
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSH----EPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV 754 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~----~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~ 754 (974)
.+++|+++.|+|+++.++|++|++.++.+|++|+|++++ .+..++.+.+++||.++|+|+++|+++++.||+|..
T Consensus 3 ~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~~ 81 (86)
T cd05789 3 IPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSL 81 (86)
T ss_pred cCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCCCEEEEeCcc
Confidence 368999999999999999999999989999999999986 455777888999999999999998889999999874
No 90
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=99.14 E-value=1.7e-10 Score=99.28 Aligned_cols=68 Identities=49% Similarity=0.824 Sum_probs=64.4
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEE
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSL 751 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~ 751 (974)
|++|.|+|+++.++|+||++.++.+||+|+++++++++.++.+.|++||.|+|+|+++|.++++.||+
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~~~~i~ls~ 68 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECCCCcEEeeC
Confidence 78999999999999999999888999999999999999888899999999999999999888999985
No 91
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.12 E-value=2.6e-10 Score=100.37 Aligned_cols=65 Identities=25% Similarity=0.371 Sum_probs=58.1
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeC-CCeEEEEecccCCC-CCCCCCCEEEEEEEEEeCCCce-eeee
Q 002054 907 NLKLGTKVAAKVYQVRARGLVLDLG-GGIRGMYRFENNEK-KDFVVGDELLVKCSSFTGKGIP-VVSL 971 (974)
Q Consensus 907 ~~~vG~vV~G~V~~I~~~GvFV~L~-~gv~Glih~se~~~-~~f~vGd~V~vkVl~id~~~~~-~~~~ 971 (974)
+++.|++|.|+|++|++||+||+++ +|+.||+|.++++. ..|++||.+.|+|+++|+++.. .+|+
T Consensus 1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~~~~~~Gq~v~~~V~~vd~~~~~v~ls~ 68 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNFSKLKVGQLLLCVVEKVKDDGRVVSLSA 68 (74)
T ss_pred CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcccccCCCCEEEEEEEEEECCCCEEEEEE
Confidence 5789999999999999999999997 69999999999975 6799999999999999987765 4444
No 92
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=99.11 E-value=1.5e-10 Score=99.27 Aligned_cols=67 Identities=46% Similarity=0.736 Sum_probs=63.3
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS 750 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS 750 (974)
|++|.|+|+++.++|+||++.++.+||+|.++++++++.++.+.|++||.++|+|+++|. ++++.||
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 789999999999999999999899999999999999998999999999999999999998 7888875
No 93
>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]
Probab=99.11 E-value=3.5e-10 Score=116.55 Aligned_cols=195 Identities=19% Similarity=0.173 Sum_probs=133.5
Q ss_pred eEEEEEeCccCcCCCcEEEEEeCCeEEEEEEEeCCC-CC--CCCceeeEeeccccccccCCCCCccccccCCCCchhhhH
Q 002054 68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKG-DS--VRDFLPLTVDYQEKQFAQGVIPNTYMRREGAPKERELLV 144 (974)
Q Consensus 68 r~i~~etg~~a~~A~GSa~v~~G~T~Vl~tv~~~~~-~~--~~~f~pL~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~ 144 (974)
|...++.|-+ ..||||++++.|+|.|+|++++..- |. ..+-.++..+|.-..--.. .-|-|+|++.+.-+
T Consensus 47 Rdt~in~g~I-sTangSal~K~G~ttvi~~Ik~ei~epstdapdeg~Iv~n~~lpplcs~------r~RpG~p~dea~vi 119 (298)
T KOG1613|consen 47 RDTAINAGNI-STANGSALLKSGKTTVICGIKAEIAEPSTDAPDEGDIVPNYALPPLCSS------RFRPGPPTDEAQVI 119 (298)
T ss_pred hhhheecCce-eccCcHHHHhcCCcEEEEEeeeeecccccCCCCCcceeecccCCccccc------CCCCCCCchHHHHH
Confidence 5678889999 8999999999999999999998753 21 1233344444421111111 12459999988777
Q ss_pred HHhhcCCccc----------cccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCCCC---CCCC----------
Q 002054 145 GRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSDIP---WGGP---------- 201 (974)
Q Consensus 145 ~RlidR~lrp----------lfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~iP---~~~~---------- 201 (974)
|.-+-.+|.. ++++.+.|-....+.+|++||..- .+|.+|+.+||..-.+| |+..
T Consensus 120 Sq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~f--Da~w~al~aAlknvklP~a~ide~~~~~~~t~e~ 197 (298)
T KOG1613|consen 120 SQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVF--DACWNALMAALKNVKLPRAFIDERASDLRMTIEE 197 (298)
T ss_pred HHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcHH--HHHHHHHHHHHhcCCCceeeecccchhhhhhHHH
Confidence 6665444443 677777777778899999999877 89999999999887777 2221
Q ss_pred ----------------eEEE-------EEE-EECCEEE-EcCCHHHHhcCccceeEeeeCCe--EEEEEe-cCCCCCHHH
Q 002054 202 ----------------IGMI-------RIG-RICGQFI-VNPTMDELSLSDLNLVYACTREK--TLMIDV-QAREISEKD 253 (974)
Q Consensus 202 ----------------v~av-------~vg-~i~g~~v-ldPt~~e~~~s~~~l~v~~t~~~--i~mie~-~~~~~~e~~ 253 (974)
.-++ +-. ..|+.++ .|||-+|+..++..+++.....+ +-+... ++.-.+.+.
T Consensus 198 ~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~~li~adpT~eEE~l~~~~lTIvldss~n~v~l~k~GG~al~~~~~ 277 (298)
T KOG1613|consen 198 IICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDDVLIAADPTEEEETLITSTLTIVLDSSGNYVQLTKVGGGALITPEM 277 (298)
T ss_pred HHHhhhhcchhhhccccccccccCCCccHHHhhcceeEecCCCchhhhhhhceEEEEEcCCCCEEEEEecCcccccCHHH
Confidence 1111 111 2355555 89999999998888877776654 333443 444466688
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 002054 254 LEAGLRLAHPEAVKYLEP 271 (974)
Q Consensus 254 ~~~al~~a~~~~~~i~~~ 271 (974)
+..++++|..-.+++-..
T Consensus 278 iK~c~elar~Rakelk~~ 295 (298)
T KOG1613|consen 278 IKRCLELARVRAKELKTR 295 (298)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 889999998877766544
No 94
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.10 E-value=2.4e-10 Score=98.37 Aligned_cols=65 Identities=23% Similarity=0.267 Sum_probs=58.8
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS 750 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS 750 (974)
|++++|+|+++.++|+||+|.++++||+|.++++..+.. .+.|++||.++|+|+++|+ ++++.||
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS 66 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence 789999999999999999998899999999999876544 7779999999999999998 6788876
No 95
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=99.10 E-value=2.8e-10 Score=103.60 Aligned_cols=73 Identities=26% Similarity=0.487 Sum_probs=63.3
Q ss_pred cccccCcEEEEEEEEEeec--eEEEEEcCCeEEEEecccCCC---ccccccccccccCCEEEEEEEEEccCC-ceEEEE
Q 002054 679 REIEVGGIYKGVVTSVKEY--GAFVEFNGGQQGLLHVSELSH---EPVSRVSDVVSVGQQLSLRCIGQDVRG-NIKLSL 751 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~--G~fV~l~~g~~Glvhisels~---~~v~~~~~~~~vGd~V~vkVl~id~~g-ri~LS~ 751 (974)
..+++|++|.|+|++|.++ |+||+|.++.+||||+||++| .++.++.+.+++||.|.|+|+....++ -..||.
T Consensus 3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~ 81 (88)
T cd04453 3 REPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTT 81 (88)
T ss_pred CcCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEE
Confidence 3578999999999999997 999999989999999999999 678888999999999999999976533 344443
No 96
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.09 E-value=3.2e-10 Score=99.90 Aligned_cols=59 Identities=25% Similarity=0.288 Sum_probs=53.1
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC----------CCCCCCCCEEEEEEEEEeCCCc
Q 002054 908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE----------KKDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~----------~~~f~vGd~V~vkVl~id~~~~ 966 (974)
+++|++|.|+|++|++||+||+|++++.|++|.+++. .+.|++||.|+|+|+++|+++.
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~ 69 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKN 69 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCC
Confidence 5799999999999999999999999999999988663 2578999999999999998654
No 97
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.08 E-value=4.1e-10 Score=97.09 Aligned_cols=66 Identities=33% Similarity=0.515 Sum_probs=60.8
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK 752 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K 752 (974)
|++++|+|+++.++|+||++ ++.+||+|.|++++.+..++.+. +||.++|+|+++|. ++++.||+|
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~~~~~~~~~--vG~~i~~~i~~vd~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCChHHh--CCCEEEEEEEEEeCCCCEEEEEcC
Confidence 78999999999999999999 79999999999999888777663 89999999999998 789999986
No 98
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.06 E-value=2.2e-10 Score=106.87 Aligned_cols=74 Identities=22% Similarity=0.395 Sum_probs=66.4
Q ss_pred cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc-------------------cccccccccCCEEEEEEEEE
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV-------------------SRVSDVVSVGQQLSLRCIGQ 741 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v-------------------~~~~~~~~vGd~V~vkVl~i 741 (974)
+++|+++.|+|++|.++|+||+|+++.+|++|++++++++. .++.+.|++||.|+|+|+++
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~ 80 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence 46899999999999999999999999999999999998753 34778899999999999999
Q ss_pred cc----CCceEEEEecc
Q 002054 742 DV----RGNIKLSLKAV 754 (974)
Q Consensus 742 d~----~gri~LS~K~~ 754 (974)
|+ +++|.||+|..
T Consensus 81 d~~~~~~~~i~LSlr~~ 97 (100)
T cd05693 81 DKSKSGKKRIELSLEPE 97 (100)
T ss_pred cCCcCCCcEEEEEecHH
Confidence 98 46999999853
No 99
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.03 E-value=1.1e-09 Score=96.24 Aligned_cols=62 Identities=19% Similarity=0.244 Sum_probs=54.5
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC---------CCCCCCCEEEEEEEEEeCCC-ceeeeec
Q 002054 911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK---------KDFVVGDELLVKCSSFTGKG-IPVVSLV 972 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~---------~~f~vGd~V~vkVl~id~~~-~~~~~~~ 972 (974)
|++|+|+|+++.++|+||+|++++.|++|.++++. +.|++||.|+|+|+++|+++ +..+|+.
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence 89999999999999999999999999999998742 24999999999999999765 5666664
No 100
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.02 E-value=7.1e-10 Score=120.49 Aligned_cols=78 Identities=37% Similarity=0.605 Sum_probs=72.6
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcC--CeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNG--GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP 756 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~--g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~ 756 (974)
-+++|+++.|+|++|.++|+||+|.. +.+||+|+|+++++++.++.+.|++||.|.|+|+++|. ++++.||+|.+.+
T Consensus 5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~ 84 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNE 84 (262)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEeccc
Confidence 37899999999999999999999964 79999999999999999999999999999999999998 6899999998765
Q ss_pred C
Q 002054 757 R 757 (974)
Q Consensus 757 ~ 757 (974)
+
T Consensus 85 ~ 85 (262)
T PRK03987 85 H 85 (262)
T ss_pred c
Confidence 4
No 101
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=99.01 E-value=2.1e-09 Score=94.40 Aligned_cols=65 Identities=29% Similarity=0.396 Sum_probs=58.6
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-------CCCCCCCEEEEEEEEEeCCCc-eeeee
Q 002054 907 NLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-------KDFVVGDELLVKCSSFTGKGI-PVVSL 971 (974)
Q Consensus 907 ~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-------~~f~vGd~V~vkVl~id~~~~-~~~~~ 971 (974)
++++|+++.|+|.++.++|+||+|++++.|++|.+++.. ..|++||+|+|+|+++|.++. ..+|+
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~ 73 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSL 73 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEES
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEE
Confidence 378999999999999999999999999999999998863 579999999999999998876 77765
No 102
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.01 E-value=1.1e-09 Score=94.12 Aligned_cols=67 Identities=37% Similarity=0.707 Sum_probs=62.4
Q ss_pred cCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054 683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS 750 (974)
Q Consensus 683 ~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS 750 (974)
+|+++.|+|+++.++|+||++. +.+|++|.+++++.++.++.+.|++||.|+|+|+++|. ++++.||
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 4899999999999999999996 79999999999998898999999999999999999997 6888875
No 103
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=98.98 E-value=2.6e-09 Score=95.82 Aligned_cols=69 Identities=33% Similarity=0.661 Sum_probs=61.0
Q ss_pred cCcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCcccc-----------ccccccccCCEEEEEEEEEcc-CCceEE
Q 002054 683 VGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVS-----------RVSDVVSVGQQLSLRCIGQDV-RGNIKL 749 (974)
Q Consensus 683 ~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v~-----------~~~~~~~vGd~V~vkVl~id~-~gri~L 749 (974)
+|++++|+|+++.++|+||++.+ +.+|++|.++++++++. +....|++||.|+|+|+++|. ++++.|
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~ 80 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEE
Confidence 48999999999999999999987 89999999999876532 345789999999999999997 789998
Q ss_pred EE
Q 002054 750 SL 751 (974)
Q Consensus 750 S~ 751 (974)
++
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
Confidence 85
No 104
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.97 E-value=2.1e-09 Score=92.56 Aligned_cols=71 Identities=39% Similarity=0.729 Sum_probs=66.0
Q ss_pred ccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054 682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK 752 (974)
Q Consensus 682 ~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K 752 (974)
++|+++.|+|+++.++|+||++.++.+|++|.+++.+.+..++.+.|++||.++|+|+++|. ++++.||++
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence 36999999999999999999998899999999999998888888889999999999999998 489999975
No 105
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.97 E-value=1.9e-09 Score=96.79 Aligned_cols=73 Identities=19% Similarity=0.172 Sum_probs=69.3
Q ss_pred cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEec
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKA 753 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~ 753 (974)
+++|+++.|+|+++.+.|++|++..+.+|++|+++++..+..++.+.|++||.+.|+|+++|..+++.||++.
T Consensus 4 p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~ 76 (82)
T cd04454 4 PDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTAD 76 (82)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCCCCEEEEECC
Confidence 6899999999999999999999988999999999999988888999999999999999999877899999986
No 106
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=98.95 E-value=4.2e-09 Score=93.53 Aligned_cols=68 Identities=28% Similarity=0.449 Sum_probs=62.8
Q ss_pred ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCCCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054 904 SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSLV 972 (974)
Q Consensus 904 ~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~~f~vGd~V~vkVl~id~~~~~~~~~~ 972 (974)
...++++|+.+.|+|+++++||+||++++++.||+|.+++ .+.|++||+++++|.++.+++...+|++
T Consensus 10 ~~~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~-~~~~~iGd~v~v~I~~i~e~~~i~l~~~ 77 (77)
T cd04473 10 TMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNL-LRDYEVGDEVIVQVTDIPENGNIDLIPV 77 (77)
T ss_pred chhhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhc-cCcCCCCCEEEEEEEEECCCCcEEEEEC
Confidence 4677999999999999999999999999999999999998 5679999999999999987888888875
No 107
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.95 E-value=8e-10 Score=131.85 Aligned_cols=78 Identities=35% Similarity=0.574 Sum_probs=73.9
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCCC
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSPR 757 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~~ 757 (974)
++++|+++.|+|+++.+||+||+|+-+.+|+||+|++++.++.+|.+++++||.|+|+|+++|. +++|.|||+.....
T Consensus 655 dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~~ 733 (780)
T COG2183 655 DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDEEE 733 (780)
T ss_pred hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccCCc
Confidence 7899999999999999999999998899999999999999999999999999999999999998 78999999976543
No 108
>PRK08582 hypothetical protein; Provisional
Probab=98.94 E-value=3.5e-09 Score=104.53 Aligned_cols=66 Identities=24% Similarity=0.390 Sum_probs=60.6
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054 907 NLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVSLV 972 (974)
Q Consensus 907 ~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~~~ 972 (974)
.+++|++|.|+|++|++||+||+|++++.||+|++++. .+.|++||+|+|+|+++|.++...+|+.
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk 74 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIK 74 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEE
Confidence 37899999999999999999999999999999999885 3579999999999999998888888874
No 109
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.94 E-value=2.3e-09 Score=96.54 Aligned_cols=68 Identities=24% Similarity=0.301 Sum_probs=59.9
Q ss_pred ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeee
Q 002054 904 SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSL 971 (974)
Q Consensus 904 ~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~ 971 (974)
.+.++++|+++.|+|+++.+||+||+|++++.||+|.++++ .+.|++||+|+|+|+++|. ++...+||
T Consensus 8 ~~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl 83 (83)
T cd04461 8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83 (83)
T ss_pred hHHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence 36779999999999999999999999999999999999874 3469999999999999997 46666664
No 110
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.93 E-value=3.4e-09 Score=92.61 Aligned_cols=61 Identities=23% Similarity=0.346 Sum_probs=52.8
Q ss_pred CCEEE-EEEEEE-eCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCC-ceeeee
Q 002054 911 GTKVA-AKVYQV-RARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKG-IPVVSL 971 (974)
Q Consensus 911 G~vV~-G~V~~I-~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~-~~~~~~ 971 (974)
|++++ |+|.++ .+||+||+|++|+.||+|.|+++ .+.|++||+++|+|+++|+++ +..+||
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~ 71 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence 78999 999999 79999999999999999999774 346999999999999999766 555553
No 111
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.93 E-value=3.4e-09 Score=91.86 Aligned_cols=61 Identities=21% Similarity=0.321 Sum_probs=53.5
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeee
Q 002054 911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSL 971 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~ 971 (974)
|++++|+|.+|.++|+||+|++++.||+|.++++ .+.|++||+++|+|+++|.+ +...+||
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence 8999999999999999999999999999999774 24699999999999999974 5555554
No 112
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.93 E-value=4e-09 Score=90.78 Aligned_cols=57 Identities=23% Similarity=0.313 Sum_probs=52.1
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-----CCCCCCCCEEEEEEEEEeCCCce
Q 002054 911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-----KKDFVVGDELLVKCSSFTGKGIP 967 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-----~~~f~vGd~V~vkVl~id~~~~~ 967 (974)
|++|+|+|.++.++|+||+|.++++|++|.+++. .+.|++||+|+|+|+++|++++.
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~~~~~~~~G~~i~~kVi~id~~~~~ 62 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSSKSTYKEGQKVRARILYVDPSTKV 62 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCcccCcCCCCEEEEEEEEEeCCCCE
Confidence 8999999999999999999988999999999885 24599999999999999987765
No 113
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.91 E-value=4.2e-09 Score=92.32 Aligned_cols=63 Identities=24% Similarity=0.192 Sum_probs=55.6
Q ss_pred CCCCCEEEEEEEEEeC-CeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeeee
Q 002054 908 LKLGTKVAAKVYQVRA-RGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVSL 971 (974)
Q Consensus 908 ~~vG~vV~G~V~~I~~-~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~~ 971 (974)
+++|++|.|+|++|.+ ||+||+|++|..|++|+|++. .+.|++||.|+|+|+++|. +..-+|+
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LSl 71 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD-GKYQLSL 71 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC-CEEEEEe
Confidence 4689999999999986 899999999999999999774 2458999999999999996 6666765
No 114
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.91 E-value=7.8e-09 Score=90.60 Aligned_cols=64 Identities=22% Similarity=0.228 Sum_probs=55.9
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeee
Q 002054 908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSL 971 (974)
Q Consensus 908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~ 971 (974)
+++|++|.|+|++++++|+||+|++++.|++|.+++. .+.|++||.|+|+|+++|.+ +...+|+
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~ 72 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSL 72 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 4789999999999999999999999999999999774 23599999999999999985 4555554
No 115
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.90 E-value=3.6e-09 Score=92.14 Aligned_cols=64 Identities=28% Similarity=0.307 Sum_probs=58.9
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcc--ccccccccccCCEEEEEEEEEccCCce
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEP--VSRVSDVVSVGQQLSLRCIGQDVRGNI 747 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~--v~~~~~~~~vGd~V~vkVl~id~~gri 747 (974)
|+++.|+|+++.++|+||++.++.+|++|++++++++ ..++.+.|++||.|+|+|+++|..+..
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~~ 66 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTH 66 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcccc
Confidence 7899999999999999999999999999999999885 788889999999999999999875443
No 116
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=98.89 E-value=8.1e-09 Score=91.72 Aligned_cols=65 Identities=37% Similarity=0.626 Sum_probs=59.0
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEE
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSL 751 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~ 751 (974)
.++++|++|.|+|+++.+||+||++.++.+||+|.|++. +.+++||.++|+|.++..+|++.||+
T Consensus 12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i~e~~~i~l~~ 76 (77)
T cd04473 12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDIPENGNIDLIP 76 (77)
T ss_pred hhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEECCCCcEEEEE
Confidence 468999999999999999999999999999999999974 34999999999999995589999985
No 117
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.88 E-value=6.3e-09 Score=90.36 Aligned_cols=61 Identities=20% Similarity=0.310 Sum_probs=54.0
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeee
Q 002054 911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSL 971 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~ 971 (974)
|+++.|+|.+++++|+||+|.+++.||+|.+++. .+.|++||+++|+|+++|++ +...+|+
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~ 69 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSC 69 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEe
Confidence 8999999999999999999999999999999874 33599999999999999984 5666665
No 118
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=98.87 E-value=1.3e-08 Score=89.44 Aligned_cols=63 Identities=21% Similarity=0.186 Sum_probs=54.3
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCC-------CCCCCCCEEEEEEEEEeCCCceeeee
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEK-------KDFVVGDELLVKCSSFTGKGIPVVSL 971 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~-------~~f~vGd~V~vkVl~id~~~~~~~~~ 971 (974)
.+|++++|+|.+|++||+||+|++ +..||+|.+++.. +.|++||+|+|+|+++|.+++.-+|+
T Consensus 2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence 589999999999999999999954 3799999998852 34799999999999999988666654
No 119
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.86 E-value=7.3e-09 Score=89.56 Aligned_cols=56 Identities=27% Similarity=0.326 Sum_probs=50.9
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCc
Q 002054 911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~ 966 (974)
|++|.|+|+++.++|+||+|.+++.||+|.++++ .+.|++||.|+|+|+++|+++.
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~ 63 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNG 63 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCC
Confidence 7899999999999999999999999999999874 3459999999999999998543
No 120
>PRK05807 hypothetical protein; Provisional
Probab=98.85 E-value=1.3e-08 Score=100.20 Aligned_cols=65 Identities=20% Similarity=0.328 Sum_probs=59.1
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054 907 NLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVSLV 972 (974)
Q Consensus 907 ~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~~~ 972 (974)
.+++|++|+|+|+.|++||+||+| ++..||+|++++. ...|++||+|+|+|+++|.++...+|+.
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk 73 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIK 73 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEE
Confidence 478999999999999999999999 6899999999885 4568999999999999999888888874
No 121
>PF03725 RNase_PH_C: 3' exoribonuclease family, domain 2 This Prosite family only includes Ribonuclease PH; InterPro: IPR015847 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 2, which has a core 3-layer alpha/beta/alpha structure. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 2NN6_E 2WNR_A 3U1K_B 2BA0_H 2BA1_H 3M85_G 3M7N_H 3H1C_K ....
Probab=98.84 E-value=1.1e-08 Score=88.53 Aligned_cols=65 Identities=31% Similarity=0.437 Sum_probs=50.8
Q ss_pred CCeEEEEEEEECCEEEEcCCHHHHhcCccceeEeee--CCeEEEEEecCCC-CCHHHHHHHHHHHHHH
Q 002054 200 GPIGMIRIGRICGQFIVNPTMDELSLSDLNLVYACT--REKTLMIDVQARE-ISEKDLEAGLRLAHPE 264 (974)
Q Consensus 200 ~~v~av~vg~i~g~~vldPt~~e~~~s~~~l~v~~t--~~~i~mie~~~~~-~~e~~~~~al~~a~~~ 264 (974)
++++|||+|++||++|+|||.+|+..++.+|+++.+ .+.+.|++.++.. +++++|.+||++|+++
T Consensus 1 ~~~~avt~~~i~~~~v~Dpt~~Ee~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~l~~~i~~A~~~ 68 (68)
T PF03725_consen 1 DPPVAVTVGIIDGELVVDPTAEEESLSDSSLTLAVDGTGNICTLQKSGGGSELSEDQLEEAIELAKKA 68 (68)
T ss_dssp SEEEEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSSEEEEEEEEESSEEEHHHHHHHHHHHHHH
T ss_pred CCeEEEEEEEECCEEEECCCHHHHhhcCCcEEEEEECCCCEEEEEEcCCCCCCCHHHHHHHHHHHhcC
Confidence 579999999999999999999998776655555544 5555666666554 9999999999999985
No 122
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.83 E-value=1.4e-08 Score=88.83 Aligned_cols=59 Identities=22% Similarity=0.318 Sum_probs=53.0
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC--------CCCCCCCEEEEEEEEEeCCCc
Q 002054 908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK--------KDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~--------~~f~vGd~V~vkVl~id~~~~ 966 (974)
|++|+++.|+|.+|++||+||+|++++.||+|.+++.. +.|++||+|+|+|+++|.+..
T Consensus 1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~ 67 (72)
T cd05689 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERR 67 (72)
T ss_pred CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcC
Confidence 68999999999999999999999999999999998741 247999999999999997654
No 123
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.80 E-value=1.4e-08 Score=87.74 Aligned_cols=56 Identities=21% Similarity=0.359 Sum_probs=50.3
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC--------CCCCCCCCEEEEEEEEEeCCCc
Q 002054 911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE--------KKDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~--------~~~f~vGd~V~vkVl~id~~~~ 966 (974)
|+++.|+|.+|++||+||+|++++.||+|.++++ .+.|++||+|+|+|+++|.+..
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~ 64 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERE 64 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcC
Confidence 7899999999999999999999999999999874 2348999999999999997643
No 124
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.79 E-value=6.6e-09 Score=87.99 Aligned_cols=59 Identities=39% Similarity=0.644 Sum_probs=55.9
Q ss_pred CcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-CCEEEEEecCHHHHHHHHHHH
Q 002054 615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-DGTLTVVAKNRSVMEKVLEKV 673 (974)
Q Consensus 615 p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v~i~~~~~~~~~~a~~~i 673 (974)
|++..++|++++++.+||+||++|++|+++||++|+++ +|.|.|++.+++.++.|++++
T Consensus 1 P~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 1 PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred CeEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCCCCEEEEEeCCHHHHHHHHHHh
Confidence 78899999999999999999999999999999999998 799999999899999998765
No 125
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.77 E-value=1.5e-08 Score=85.40 Aligned_cols=64 Identities=39% Similarity=0.693 Sum_probs=59.1
Q ss_pred EEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054 687 YKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS 750 (974)
Q Consensus 687 ~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS 750 (974)
+.|+|+++.++|+||++.++.+|++|.+++++.+..++.+.|++||.|+|+|+++|. ++++.||
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence 579999999999999999899999999999999888888899999999999999997 6788775
No 126
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.77 E-value=3.6e-08 Score=84.63 Aligned_cols=61 Identities=28% Similarity=0.480 Sum_probs=55.5
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-------CCCCCCCEEEEEEEEEeCCCceeeee
Q 002054 911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-------KDFVVGDELLVKCSSFTGKGIPVVSL 971 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-------~~f~vGd~V~vkVl~id~~~~~~~~~ 971 (974)
|+++.|+|.+++++|+||++++++.||+|.++++. +.|++||.|+|+|+++|.++...+|+
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~ 68 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSI 68 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECCCCcEEEEE
Confidence 79999999999999999999999999999998853 34899999999999999977887775
No 127
>PRK07252 hypothetical protein; Provisional
Probab=98.75 E-value=3.8e-08 Score=94.79 Aligned_cols=65 Identities=25% Similarity=0.460 Sum_probs=58.2
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSLVD 973 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~~~ 973 (974)
++|+++.|+|.+|+++|+||+|++++.||+|.+++. .+.|++||.|+|+|+++|. .+...+|+.+
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~ 74 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRT 74 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEee
Confidence 589999999999999999999999999999999874 3469999999999999998 6777788754
No 128
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.74 E-value=4.2e-08 Score=86.51 Aligned_cols=65 Identities=26% Similarity=0.410 Sum_probs=57.1
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCC-------CCCCCCCEEEEEEEEEeC-CCceeeeecC
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEK-------KDFVVGDELLVKCSSFTG-KGIPVVSLVD 973 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~-------~~f~vGd~V~vkVl~id~-~~~~~~~~~~ 973 (974)
++|+++.|+|.+++++|+||+|.+ ++.|++|.+++.. +.|++||.|+|+|+++|. ++...+|+..
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~ 74 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKA 74 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence 479999999999999999999986 8999999998853 357999999999999998 6777777754
No 129
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.74 E-value=2e-08 Score=111.00 Aligned_cols=70 Identities=20% Similarity=0.169 Sum_probs=60.3
Q ss_pred cccccCC-CCCEEEEEEEEEeCCeEEEEeC--CCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeee
Q 002054 903 VSAKNLK-LGTKVAAKVYQVRARGLVLDLG--GGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSL 971 (974)
Q Consensus 903 ~~~~~~~-vG~vV~G~V~~I~~~GvFV~L~--~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~ 971 (974)
|..++|+ +|++|.|+|++|.+||+||+|. +|+.||+|.|++. .+.+++||+|.|+|++||++ |..-+|+
T Consensus 9 ~~~~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~ 88 (319)
T PTZ00248 9 FYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSK 88 (319)
T ss_pred chhhhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEe
Confidence 4567788 8999999999999999999997 5999999999885 44699999999999999864 5566776
Q ss_pred c
Q 002054 972 V 972 (974)
Q Consensus 972 ~ 972 (974)
.
T Consensus 89 K 89 (319)
T PTZ00248 89 K 89 (319)
T ss_pred e
Confidence 4
No 130
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.72 E-value=5.1e-08 Score=88.32 Aligned_cols=65 Identities=14% Similarity=0.181 Sum_probs=58.9
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-----------CCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054 908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-----------KDFVVGDELLVKCSSFTGKGIPVVSLV 972 (974)
Q Consensus 908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-----------~~f~vGd~V~vkVl~id~~~~~~~~~~ 972 (974)
.++|++|.|+|.++.++|+||++++++.|++|.+++.. +.|++||.|+|+|+++|+++...+|+.
T Consensus 4 p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~ 79 (86)
T cd05789 4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTR 79 (86)
T ss_pred CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCCCEEEEeC
Confidence 47999999999999999999999999999999998742 148999999999999999888888864
No 131
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.71 E-value=5.4e-08 Score=84.95 Aligned_cols=62 Identities=32% Similarity=0.491 Sum_probs=55.2
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeeec
Q 002054 911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSLV 972 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~~ 972 (974)
|++|.|+|++++++|+||+|.+++.|++|.+++. .+.|++||.++|+|+++|.+ +...+|+.
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k 70 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEE
Confidence 8999999999999999999999999999999874 23589999999999999987 56777764
No 132
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.71 E-value=2.8e-08 Score=92.70 Aligned_cols=65 Identities=26% Similarity=0.290 Sum_probs=57.6
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC--------------------------CCCCCCCEEEEEEEEE
Q 002054 908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK--------------------------KDFVVGDELLVKCSSF 961 (974)
Q Consensus 908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~--------------------------~~f~vGd~V~vkVl~i 961 (974)
+++|++|.|+|++|.++|+||.|++|+.|++|.+++.. +.|++||.|+|+|+++
T Consensus 1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~ 80 (100)
T cd05693 1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL 80 (100)
T ss_pred CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence 57999999999999999999999999999999997742 4599999999999999
Q ss_pred eCC----Cceeeeec
Q 002054 962 TGK----GIPVVSLV 972 (974)
Q Consensus 962 d~~----~~~~~~~~ 972 (974)
|.+ +...+||.
T Consensus 81 d~~~~~~~~i~LSlr 95 (100)
T cd05693 81 DKSKSGKKRIELSLE 95 (100)
T ss_pred cCCcCCCcEEEEEec
Confidence 985 56677764
No 133
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=98.69 E-value=6.8e-08 Score=90.04 Aligned_cols=75 Identities=25% Similarity=0.451 Sum_probs=64.2
Q ss_pred cEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccccc-----------ccccccCCEEEEEEEEEccC------Cce
Q 002054 685 GIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRV-----------SDVVSVGQQLSLRCIGQDVR------GNI 747 (974)
Q Consensus 685 ~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~-----------~~~~~vGd~V~vkVl~id~~------gri 747 (974)
++|.|+|+++.++|+||++. +.+|++|+++++++++... ...|++||.|+|+|.++|.. +++
T Consensus 1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i 79 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI 79 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceE
Confidence 47999999999999999997 5999999999998876533 47799999999999999962 589
Q ss_pred EEEEeccCCCccc
Q 002054 748 KLSLKAVSPRPEA 760 (974)
Q Consensus 748 ~LS~K~~~~~~~~ 760 (974)
.||+|+....||.
T Consensus 80 ~ls~k~~~~g~~~ 92 (99)
T cd04460 80 GLTMRQPGLGKLE 92 (99)
T ss_pred EEEEecCCCCcHH
Confidence 9999987665544
No 134
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.68 E-value=8.9e-08 Score=83.15 Aligned_cols=61 Identities=25% Similarity=0.328 Sum_probs=54.1
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeee
Q 002054 911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSL 971 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~ 971 (974)
|++|+|+|.++.++|+||+|+.++.|++|.+++. .+.|++||.++|+|+++|++ +...+|+
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~ 69 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSK 69 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEe
Confidence 8999999999999999999998999999999884 34699999999999999954 5666665
No 135
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=98.68 E-value=9.2e-08 Score=85.25 Aligned_cols=61 Identities=21% Similarity=0.242 Sum_probs=54.5
Q ss_pred CCEEEEEEEEEeCCeEEEEeC---CCeEEEEecccCCCC--------CCCCCCEEEEEEEEEeCCCceeeeec
Q 002054 911 GTKVAAKVYQVRARGLVLDLG---GGIRGMYRFENNEKK--------DFVVGDELLVKCSSFTGKGIPVVSLV 972 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~---~gv~Glih~se~~~~--------~f~vGd~V~vkVl~id~~~~~~~~~~ 972 (974)
|+++.|+|.++++||+||+|+ +++.||+|.++++.. .|++||+|+|+|+++| ++...+|+.
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k 72 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ-NGKISLSMK 72 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe-CCEEEEEEE
Confidence 789999999999999999998 479999999988533 3699999999999999 888888874
No 136
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=98.67 E-value=1.4e-07 Score=83.14 Aligned_cols=64 Identities=22% Similarity=0.221 Sum_probs=54.8
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCC--CeEEEEecccCCCC-------CCCCCCEEEEEEEEEeCC-Cceeeeec
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGG--GIRGMYRFENNEKK-------DFVVGDELLVKCSSFTGK-GIPVVSLV 972 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~--gv~Glih~se~~~~-------~f~vGd~V~vkVl~id~~-~~~~~~~~ 972 (974)
++|+++.|+|.++.+||+||+|.+ ++.||+|.+++... .|++||.|+|+|+++|.+ +...+|+.
T Consensus 2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k 75 (76)
T cd04452 2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75 (76)
T ss_pred CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEc
Confidence 589999999999999999999975 69999999988532 379999999999999974 55666653
No 137
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.66 E-value=1.2e-07 Score=81.59 Aligned_cols=63 Identities=32% Similarity=0.500 Sum_probs=57.0
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCC-------CCCCCCEEEEEEEEEeCC-Cceeeee
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKK-------DFVVGDELLVKCSSFTGK-GIPVVSL 971 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~-------~f~vGd~V~vkVl~id~~-~~~~~~~ 971 (974)
++|+++.|+|.+++++|+||++++++.|++|.+++... .|++||.|.|+|+++|.+ +...+|+
T Consensus 1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~ 71 (72)
T smart00316 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71 (72)
T ss_pred CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEe
Confidence 47999999999999999999999999999999988643 499999999999999987 7777776
No 138
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.65 E-value=4.2e-08 Score=101.28 Aligned_cols=83 Identities=25% Similarity=0.373 Sum_probs=74.7
Q ss_pred cceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-C-CEEEEE---ecCHHHHHHHHHHHHHHhhc-ccc-----cC
Q 002054 616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D-GTLTVV---AKNRSVMEKVLEKVDFIIGR-EIE-----VG 684 (974)
Q Consensus 616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d-g~v~i~---~~~~~~~~~a~~~i~~l~~~-~~~-----~G 684 (974)
.+..++||+++++.+||+||++|+.|++++|++|+++ + |.|.|. +.+...+++|+++++.+... +++ .|
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~g 82 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLD 82 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHHHHHhC
Confidence 4678899999999999999999999999999999997 5 999999 89999999999999988742 456 79
Q ss_pred cEEEEEEEEEeece
Q 002054 685 GIYKGVVTSVKEYG 698 (974)
Q Consensus 685 ~i~~G~V~~i~~~G 698 (974)
+.|.++|.++.+|+
T Consensus 83 d~y~~~Vi~i~~~~ 96 (180)
T PRK13763 83 DDYVLEVIDLSDYG 96 (180)
T ss_pred CCceEEEEEhhhcc
Confidence 99999999998873
No 139
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.65 E-value=1.3e-07 Score=81.44 Aligned_cols=60 Identities=27% Similarity=0.340 Sum_probs=51.6
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCCC-----CCCCCEEEEEEEEEeC-CCceeeee
Q 002054 911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKD-----FVVGDELLVKCSSFTG-KGIPVVSL 971 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~~-----f~vGd~V~vkVl~id~-~~~~~~~~ 971 (974)
|++|+|+|.++.++|+||++ +|+.||+|.++++... ..+||+++|+|+++|+ ++..++|.
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~vd~~~~~i~lS~ 66 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDRERNNIVLSR 66 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEeCCCCEEEEEc
Confidence 78999999999999999999 7999999999885332 2489999999999997 56666664
No 140
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.64 E-value=1.1e-07 Score=82.78 Aligned_cols=58 Identities=19% Similarity=0.247 Sum_probs=51.9
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC---------CCCCCCCEEEEEEEEEeCCCcee
Q 002054 911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK---------KDFVVGDELLVKCSSFTGKGIPV 968 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~---------~~f~vGd~V~vkVl~id~~~~~~ 968 (974)
|++|.|+|.++.++|+||+|++++.|++|.+++.. +.|++||.|+|+|+++|..+.-.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~~~ 67 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHR 67 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccccc
Confidence 89999999999999999999999999999997742 34999999999999999877543
No 141
>PRK08059 general stress protein 13; Validated
Probab=98.63 E-value=1.2e-07 Score=91.96 Aligned_cols=68 Identities=25% Similarity=0.344 Sum_probs=59.9
Q ss_pred cccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeC-CCceeeeec
Q 002054 905 AKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTG-KGIPVVSLV 972 (974)
Q Consensus 905 ~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~-~~~~~~~~~ 972 (974)
+.++++|+++.|+|.++.++|+||++++++.||+|.++++ .+.|++||.|+|+|+++|. ++...+|+.
T Consensus 2 ~~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk 77 (123)
T PRK08059 2 MSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77 (123)
T ss_pred cccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEE
Confidence 3568999999999999999999999999999999999874 3458999999999999986 667777764
No 142
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=98.63 E-value=1.1e-07 Score=81.38 Aligned_cols=58 Identities=24% Similarity=0.290 Sum_probs=51.2
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCC-------CCCCCCEEEEEEEEEeCC-Ccee
Q 002054 911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKK-------DFVVGDELLVKCSSFTGK-GIPV 968 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~-------~f~vGd~V~vkVl~id~~-~~~~ 968 (974)
|+++.|+|.+++++|+||+++++..||+|.+++... .|++||.|+|+|+++|.+ +...
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ 66 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRIS 66 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEe
Confidence 789999999999999999999999999999988533 479999999999999984 4433
No 143
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=98.61 E-value=1.6e-07 Score=84.20 Aligned_cols=62 Identities=19% Similarity=0.304 Sum_probs=54.5
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCC------------------CCCCCCCEEEEEEEEEeC-CCceee
Q 002054 910 LGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEK------------------KDFVVGDELLVKCSSFTG-KGIPVV 969 (974)
Q Consensus 910 vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~------------------~~f~vGd~V~vkVl~id~-~~~~~~ 969 (974)
+|+++.|+|.+|+++|+||+|++ ++.|++|.++++. ..|++||+|+|+|+++|. ++...+
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~ 80 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEE
Confidence 48999999999999999999998 8999999998742 457999999999999997 466666
Q ss_pred ee
Q 002054 970 SL 971 (974)
Q Consensus 970 ~~ 971 (974)
++
T Consensus 81 ~l 82 (83)
T cd04471 81 EL 82 (83)
T ss_pred EE
Confidence 65
No 144
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=98.61 E-value=1.3e-07 Score=86.21 Aligned_cols=61 Identities=18% Similarity=0.220 Sum_probs=54.1
Q ss_pred ccCCCCCEEEEEEEEEeCC--eEEEEeCCCeEEEEecccCC----------CCCCCCCCEEEEEEEEEeCCCc
Q 002054 906 KNLKLGTKVAAKVYQVRAR--GLVLDLGGGIRGMYRFENNE----------KKDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 906 ~~~~vG~vV~G~V~~I~~~--GvFV~L~~gv~Glih~se~~----------~~~f~vGd~V~vkVl~id~~~~ 966 (974)
..+.+|+++.|+|.+|.+| |+||+|++|..||+|.+++. .+.|++||+|.|+|+....+++
T Consensus 3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K 75 (88)
T cd04453 3 REPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTK 75 (88)
T ss_pred CcCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCC
Confidence 3578999999999999997 99999999999999999874 3469999999999999876654
No 145
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.61 E-value=9.9e-08 Score=102.73 Aligned_cols=88 Identities=24% Similarity=0.302 Sum_probs=77.7
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc----cccccccccCCEEEEEEEEEccCCceEEEEeccC
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV----SRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVS 755 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v----~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~ 755 (974)
.+++|+++.|+|+++.++|+||+|.++.+|+||++++++.++ .++.+.|++||.|+|||+++++.+++.||+|+.
T Consensus 60 ~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~- 138 (235)
T PRK04163 60 IPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGK- 138 (235)
T ss_pred cCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCC-
Confidence 369999999999999999999999888999999999999987 788999999999999999999878899999752
Q ss_pred CCcccccCceEEEEEeec
Q 002054 756 PRPEADVKGVVEGSVPVN 773 (974)
Q Consensus 756 ~~~~~~~g~~~~G~vv~i 773 (974)
..|....|.+..+
T Consensus 139 -----~lG~L~~G~~~~V 151 (235)
T PRK04163 139 -----GLGKIEGGTIVEI 151 (235)
T ss_pred -----CCCccCCCEEEEE
Confidence 3566666776664
No 146
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.60 E-value=8.8e-08 Score=99.91 Aligned_cols=73 Identities=26% Similarity=0.382 Sum_probs=67.3
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEc----------CCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceE
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFN----------GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIK 748 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~----------~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~ 748 (974)
..+++|+++.|+|+++.++|+||+|. ++.+|++|++++++.+..++.+.|++||.|+|+|++++ +++.
T Consensus 60 ~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~--~~i~ 137 (189)
T PRK09521 60 PLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT--DPLQ 137 (189)
T ss_pred CCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC--CcEE
Confidence 35789999999999999999999994 36889999999999988889999999999999999998 8999
Q ss_pred EEEec
Q 002054 749 LSLKA 753 (974)
Q Consensus 749 LS~K~ 753 (974)
||+|+
T Consensus 138 LS~k~ 142 (189)
T PRK09521 138 LSTKG 142 (189)
T ss_pred EEEec
Confidence 99985
No 147
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.60 E-value=5.5e-08 Score=99.76 Aligned_cols=78 Identities=29% Similarity=0.391 Sum_probs=70.6
Q ss_pred eeeccchhhhhcCCCccchhhhhhhhCceEEee-C-CEEEE--EecCHHHHHHHHHHHHHHhhc-ccc-----cCcEEEE
Q 002054 620 LKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D-GTLTV--VAKNRSVMEKVLEKVDFIIGR-EIE-----VGGIYKG 689 (974)
Q Consensus 620 ~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d-g~v~i--~~~~~~~~~~a~~~i~~l~~~-~~~-----~G~i~~G 689 (974)
++||+++|+.+||+||++|+.|++++|++|+++ + |.|.| ...+...+++|+++|+.+... .++ .|+.|.+
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~gd~y~~ 81 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDDDYML 81 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcCCcceE
Confidence 578999999999999999999999999999998 4 99999 788999999999999988742 466 7999999
Q ss_pred EEEEEeec
Q 002054 690 VVTSVKEY 697 (974)
Q Consensus 690 ~V~~i~~~ 697 (974)
.|.++.+|
T Consensus 82 ~Vi~I~~~ 89 (172)
T TIGR03665 82 EVIDLKEY 89 (172)
T ss_pred EEEEhhhc
Confidence 99999887
No 148
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=98.58 E-value=2.4e-07 Score=79.59 Aligned_cols=60 Identities=23% Similarity=0.343 Sum_probs=53.5
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-------CCCCCCCEEEEEEEEEeCCCceeee
Q 002054 911 GTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-------KDFVVGDELLVKCSSFTGKGIPVVS 970 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-------~~f~vGd~V~vkVl~id~~~~~~~~ 970 (974)
|+++.|+|.++++||+||+++++..||+|.++++. +.|++||.|+|+|+++|+.+...+|
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~~~~i~ls 67 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLS 67 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECCCCcEEee
Confidence 78999999999999999999999999999998753 2479999999999999986676665
No 149
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=98.50 E-value=3.9e-07 Score=78.71 Aligned_cols=63 Identities=19% Similarity=0.234 Sum_probs=54.9
Q ss_pred ccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc---CCceEEEE
Q 002054 682 EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV---RGNIKLSL 751 (974)
Q Consensus 682 ~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~---~gri~LS~ 751 (974)
+.|++++|+|.++.++|+||++. +.+|+||.+|++. .+.|++||.|+|.|++++. .++|.||+
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig-~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr 67 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILSR 67 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC-CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence 47999999999999999999995 5999999999973 3468999999999999986 24788884
No 150
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.47 E-value=8.3e-07 Score=79.71 Aligned_cols=65 Identities=20% Similarity=0.176 Sum_probs=59.1
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeeeecC
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVSLVD 973 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~~~~ 973 (974)
++|++|.|+|.++.+.|++|++..+..|++|.+++. .+.|++||.+.|+|+++|.++.+.+|...
T Consensus 5 ~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~ 76 (82)
T cd04454 5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTAD 76 (82)
T ss_pred CCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCCCCEEEEECC
Confidence 699999999999999999999999999999999874 34599999999999999998888888753
No 151
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=98.43 E-value=9.2e-07 Score=110.05 Aligned_cols=72 Identities=29% Similarity=0.637 Sum_probs=63.5
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCccc-----------cccccccccCCEEEEEEEEEcc-CCc
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPV-----------SRVSDVVSVGQQLSLRCIGQDV-RGN 746 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v-----------~~~~~~~~vGd~V~vkVl~id~-~gr 746 (974)
..++|++|+|+|++|++||+||+|.+ +.+||||+|+++++++ ++....|++||.|+|+|.++|. +|+
T Consensus 624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~ 703 (709)
T TIGR02063 624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGK 703 (709)
T ss_pred hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence 45789999999999999999999987 7999999999987654 2345679999999999999997 799
Q ss_pred eEEEE
Q 002054 747 IKLSL 751 (974)
Q Consensus 747 i~LS~ 751 (974)
|.|++
T Consensus 704 I~~~l 708 (709)
T TIGR02063 704 IDFEL 708 (709)
T ss_pred EEEEE
Confidence 99985
No 152
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=98.43 E-value=1e-06 Score=76.01 Aligned_cols=55 Identities=16% Similarity=0.268 Sum_probs=50.3
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-CCCCCCCCEEEEEEEEEeCC
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-KKDFVVGDELLVKCSSFTGK 964 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-~~~f~vGd~V~vkVl~id~~ 964 (974)
+.|++|+|+|.++.++|+||+++ ++.|++|.+++. .+.|++||+|+|.|++++.+
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig-~~eg~lp~~e~~~~~~~~~Gd~v~v~v~~v~~~ 57 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKEQIPGESYRPGDRIKAYVLEVRKT 57 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC-CeEEEeeHHHCCCCCcCCCCCEEEEEEEEEecC
Confidence 47999999999999999999996 499999999884 56899999999999999964
No 153
>PHA02945 interferon resistance protein; Provisional
Probab=98.43 E-value=7.5e-07 Score=79.11 Aligned_cols=62 Identities=19% Similarity=0.218 Sum_probs=52.6
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCC--CeEEEEecccC--C------CCCCCCCCEEEEEEEEEeCCCcee-eeec
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGG--GIRGMYRFENN--E------KKDFVVGDELLVKCSSFTGKGIPV-VSLV 972 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~--gv~Glih~se~--~------~~~f~vGd~V~vkVl~id~~~~~~-~~~~ 972 (974)
.+|++|.|+|+. ++||+||.|++ |+.||+|.|+. . .+.+ +||+|.|+|+.+|+....+ +||.
T Consensus 10 ~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~rd~l-~GqkvV~KVirVd~~kg~IDlSlK 82 (88)
T PHA02945 10 NVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKYRDKL-VGKTVKVKVIRVDYTKGYIDVNYK 82 (88)
T ss_pred CCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEeeeeEe-cCCEEEEEEEEECCCCCEEEeEee
Confidence 689999999999 99999999998 99999999955 3 4456 9999999999999775443 4553
No 154
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.41 E-value=8.8e-07 Score=75.97 Aligned_cols=55 Identities=27% Similarity=0.418 Sum_probs=49.3
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCC
Q 002054 910 LGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKG 965 (974)
Q Consensus 910 vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~ 965 (974)
+|+++.|+|.+++++|+||+++ ++.|++|.+++. .+.|++||+|+|+|+++|.+.
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~ 62 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKER 62 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCC
Confidence 5899999999999999999997 799999999773 345899999999999999754
No 155
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.37 E-value=1e-06 Score=81.01 Aligned_cols=73 Identities=16% Similarity=0.179 Sum_probs=66.1
Q ss_pred cccCcEEEEEEEEEeeceEEEEE--------cCCeEEEEecccCCCcccc--ccccccccCCEEEEEEEEEccCCceEEE
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEF--------NGGQQGLLHVSELSHEPVS--RVSDVVSVGQQLSLRCIGQDVRGNIKLS 750 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l--------~~g~~Glvhisels~~~v~--~~~~~~~vGd~V~vkVl~id~~gri~LS 750 (974)
+++|+++.|+|+++....++|+| .....|++|++++...+.+ ++.+.|++||.|++||++.+....+.||
T Consensus 4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~Ls 83 (92)
T cd05791 4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYYLS 83 (92)
T ss_pred CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcEEE
Confidence 68999999999999999999999 6678999999999877776 6788899999999999999876789999
Q ss_pred Eec
Q 002054 751 LKA 753 (974)
Q Consensus 751 ~K~ 753 (974)
++.
T Consensus 84 t~~ 86 (92)
T cd05791 84 TAE 86 (92)
T ss_pred ecC
Confidence 875
No 156
>PF03725 RNase_PH_C: 3' exoribonuclease family, domain 2 This Prosite family only includes Ribonuclease PH; InterPro: IPR015847 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 2, which has a core 3-layer alpha/beta/alpha structure. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 2NN6_E 2WNR_A 3U1K_B 2BA0_H 2BA1_H 3M85_G 3M7N_H 3H1C_K ....
Probab=98.35 E-value=7.9e-07 Score=76.90 Aligned_cols=67 Identities=22% Similarity=0.331 Sum_probs=54.6
Q ss_pred ccccceeeeeeccCCCCCCcccceEEEecCCccccccCCccEEEEeeCCc-eEEEEeeccCCCCCHHHHHHHHHHHHHH
Q 002054 514 EHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLEHAHKG 591 (974)
Q Consensus 514 ~~vagvs~gli~~~d~~~~~~~~~~iL~Dp~~~Ee~~~d~d~~Va~t~~g-I~alq~~~k~~~i~~e~l~~al~~A~~~ 591 (974)
++|+++++|++++ .+++||+.+||.+++..++++.+.++ ++.++..+...+++++.|.+|++.|+++
T Consensus 1 ~~~~avt~~~i~~-----------~~v~Dpt~~Ee~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~l~~~i~~A~~~ 68 (68)
T PF03725_consen 1 DPPVAVTVGIIDG-----------ELVVDPTAEEESLSDSSLTLAVDGTGNICTLQKSGGGSELSEDQLEEAIELAKKA 68 (68)
T ss_dssp SEEEEEEEEEETT-----------EEEES--HHHHHHSSEEEEEEEETTSSEEEEEEEEESSEEEHHHHHHHHHHHHHH
T ss_pred CCeEEEEEEEECC-----------EEEECCCHHHHhhcCCcEEEEEECCCCEEEEEEcCCCCCCCHHHHHHHHHHHhcC
Confidence 5799999999975 59999999999999999999988777 6555555443459999999999999975
No 157
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.34 E-value=2.9e-06 Score=88.63 Aligned_cols=93 Identities=14% Similarity=0.125 Sum_probs=71.8
Q ss_pred cccCCeEEEEE---EEeecCCCCcCccccccccccc--cccCCCCCEEEEEEEEEeCCeEEEEeC----------CCeEE
Q 002054 872 FSQREREELAE---CLFGTEDGDEDNKGTRVEAIVS--AKNLKLGTKVAAKVYQVRARGLVLDLG----------GGIRG 936 (974)
Q Consensus 872 ~k~Gq~v~~~V---l~vd~e~~~i~slK~~~~~p~~--~~~~~vG~vV~G~V~~I~~~GvFV~L~----------~gv~G 936 (974)
|..+..+.+.+ +++|.+++++. .+||. ...+++|++|.|+|++|.++|+||+|. .++.|
T Consensus 27 y~~~~~i~as~~G~~~id~~~~~Is------v~P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G 100 (189)
T PRK09521 27 YEDNGEVYASVVGKVFIDDINRKIS------VIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLA 100 (189)
T ss_pred EeeCCEEEEEeeEEEEEcCCCCEEE------EecCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCcee
Confidence 33445555555 45566665543 25773 456789999999999999999999984 37899
Q ss_pred EEecccCC-------CCCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054 937 MYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPVVSLV 972 (974)
Q Consensus 937 lih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~~~~~ 972 (974)
++|.+++. .+.|++||.|.|+|++++ +...+|..
T Consensus 101 ~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~--~~i~LS~k 141 (189)
T PRK09521 101 YIHISQVSDGYVESLTDAFKIGDIVRAKVISYT--DPLQLSTK 141 (189)
T ss_pred eEEhhHcChhhhhhHHhccCCCCEEEEEEEecC--CcEEEEEe
Confidence 99999774 456999999999999999 67777764
No 158
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.34 E-value=5.4e-07 Score=95.21 Aligned_cols=63 Identities=22% Similarity=0.282 Sum_probs=55.9
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCC--CeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCcee-eee
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGG--GIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPV-VSL 971 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~--gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~-~~~ 971 (974)
.+|++|-|+|++|.+||+||.|++ |+.||+|+||.. .+.+++||+|.|+|+.||++...+ +||
T Consensus 10 eeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSl 82 (269)
T COG1093 10 EEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSL 82 (269)
T ss_pred CCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeeh
Confidence 489999999999999999999987 899999999885 567999999999999999876543 454
No 159
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=98.30 E-value=2.7e-06 Score=87.99 Aligned_cols=76 Identities=26% Similarity=0.472 Sum_probs=64.5
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccc-----------ccccccccCCEEEEEEEEEcc-----
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS-----------RVSDVVSVGQQLSLRCIGQDV----- 743 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~-----------~~~~~~~vGd~V~vkVl~id~----- 743 (974)
.+.+|++++|+|++++++|+||++. ..+|++|.+++.+++.. +....+++||.|++||.++|.
T Consensus 78 ~p~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~ 156 (179)
T TIGR00448 78 KPELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRP 156 (179)
T ss_pred eccCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCC
Confidence 5678999999999999999999995 59999999999876542 234679999999999999983
Q ss_pred -CCceEEEEeccCC
Q 002054 744 -RGNIKLSLKAVSP 756 (974)
Q Consensus 744 -~gri~LS~K~~~~ 756 (974)
..+|.||+|+...
T Consensus 157 ~~~~I~lt~k~~~L 170 (179)
T TIGR00448 157 EGSKIGLTMRQPLL 170 (179)
T ss_pred CcceEEEEeccCcC
Confidence 4689999998543
No 160
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.26 E-value=2.5e-06 Score=92.98 Aligned_cols=65 Identities=20% Similarity=0.277 Sum_probs=56.8
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCC--CeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCC-Cceeeeec
Q 002054 908 LKLGTKVAAKVYQVRARGLVLDLGG--GIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGK-GIPVVSLV 972 (974)
Q Consensus 908 ~~vG~vV~G~V~~I~~~GvFV~L~~--gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~-~~~~~~~~ 972 (974)
.++|++|.|+|.+|.+||+||+|.+ |+.||+|.|++. .+.|++||.|.|+|+++|.+ +...+|+.
T Consensus 6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK 80 (262)
T PRK03987 6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEE
Confidence 4689999999999999999999986 899999999875 33589999999999999985 45677764
No 161
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.20 E-value=2.2e-06 Score=100.49 Aligned_cols=95 Identities=12% Similarity=0.118 Sum_probs=75.8
Q ss_pred ccccCCeEEEEEEEeecCCCCcCcccccccccc-------ccccCC--CCCEEEEEEEEEeCCeEEEEeCCCeEEEEecc
Q 002054 871 SFSQREREELAECLFGTEDGDEDNKGTRVEAIV-------SAKNLK--LGTKVAAKVYQVRARGLVLDLGGGIRGMYRFE 941 (974)
Q Consensus 871 ~~k~Gq~v~~~Vl~vd~e~~~i~slK~~~~~p~-------~~~~~~--vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~s 941 (974)
.+++|+.++..|...+..+.-+.+.|+....-| .+..|+ +|++|+|+|+++.++|+||+|+ |+.||+|.+
T Consensus 86 ~~~vGD~ie~~I~~~~fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLg-gvea~LP~s 164 (470)
T PRK09202 86 DAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLG-RAEAILPRK 164 (470)
T ss_pred cccCCCeEEEEEccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEEC-CeEEEecHH
Confidence 578999999998777633322225555433333 377787 9999999999999999999995 899999999
Q ss_pred cC-CCCCCCCCCEEEEEEEEEeCCCc
Q 002054 942 NN-EKKDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 942 e~-~~~~f~vGd~V~vkVl~id~~~~ 966 (974)
++ +...|++||+|+|.|++|+.++.
T Consensus 165 E~ip~E~~~~GdrIka~I~~Vd~~~k 190 (470)
T PRK09202 165 EQIPRENFRPGDRVRAYVYEVRKEAR 190 (470)
T ss_pred HcCCCccCCCCCEEEEEEEEEecCCC
Confidence 87 57789999999999999998654
No 162
>PRK11642 exoribonuclease R; Provisional
Probab=98.18 E-value=8e-06 Score=102.16 Aligned_cols=73 Identities=29% Similarity=0.533 Sum_probs=63.4
Q ss_pred cccCcEEEEEEEEEeeceEEEEEcCC-eEEEEecccCCCcccc-----------ccccccccCCEEEEEEEEEcc-CCce
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFNGG-QQGLLHVSELSHEPVS-----------RVSDVVSVGQQLSLRCIGQDV-RGNI 747 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~~g-~~Glvhisels~~~v~-----------~~~~~~~vGd~V~vkVl~id~-~gri 747 (974)
-++|++|+|+|++|++||+||+|.+. ++||||++++.++++. +....|++||.|+|+|.++|. +++|
T Consensus 641 ~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI 720 (813)
T PRK11642 641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKI 720 (813)
T ss_pred ccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeE
Confidence 37899999999999999999999764 9999999999887532 234679999999999999997 7899
Q ss_pred EEEEec
Q 002054 748 KLSLKA 753 (974)
Q Consensus 748 ~LS~K~ 753 (974)
.|++-.
T Consensus 721 ~f~l~~ 726 (813)
T PRK11642 721 DFSLIS 726 (813)
T ss_pred EEEEec
Confidence 999853
No 163
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=98.18 E-value=7.7e-06 Score=100.75 Aligned_cols=71 Identities=25% Similarity=0.534 Sum_probs=62.0
Q ss_pred cccCcEEEEEEEEEeeceEEEEEc-CCeEEEEecccCCCccc-----------cccccccccCCEEEEEEEEEcc-CCce
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFN-GGQQGLLHVSELSHEPV-----------SRVSDVVSVGQQLSLRCIGQDV-RGNI 747 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~-~g~~Glvhisels~~~v-----------~~~~~~~~vGd~V~vkVl~id~-~gri 747 (974)
-++|++|+|+|++|++||+||+|. .+++||||++++.++++ ++....|++||.|+|+|.++|. +++|
T Consensus 570 ~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I 649 (654)
T TIGR00358 570 DKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSI 649 (654)
T ss_pred hCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeE
Confidence 368999999999999999999997 68999999999988752 2334679999999999999997 7899
Q ss_pred EEEE
Q 002054 748 KLSL 751 (974)
Q Consensus 748 ~LS~ 751 (974)
.+++
T Consensus 650 ~f~l 653 (654)
T TIGR00358 650 IFEL 653 (654)
T ss_pred EEEE
Confidence 8875
No 164
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=98.17 E-value=4.1e-06 Score=70.45 Aligned_cols=52 Identities=27% Similarity=0.440 Sum_probs=46.7
Q ss_pred EEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCC
Q 002054 914 VAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKG 965 (974)
Q Consensus 914 V~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~ 965 (974)
+.|+|.++.++|+||++++++.|++|.+++. ...|++||.|+|+|+++|.++
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~ 59 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEK 59 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCc
Confidence 4799999999999999999999999999874 346999999999999999744
No 165
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.16 E-value=4.6e-06 Score=84.46 Aligned_cols=76 Identities=28% Similarity=0.497 Sum_probs=64.0
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccc----------c-cccccccCCEEEEEEEEEcc----
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS----------R-VSDVVSVGQQLSLRCIGQDV---- 743 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~----------~-~~~~~~vGd~V~vkVl~id~---- 743 (974)
..+..|++++|.|+++.+||+||.+. -.+||+|+||+.++++. + ...++++||.|++||++.+.
T Consensus 77 fkP~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~ 155 (183)
T COG1095 77 FKPFRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRR 155 (183)
T ss_pred EEeccccEEEEEEEEEeecceEEEec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCc
Confidence 36788999999999999999999996 69999999999998432 2 34479999999999999875
Q ss_pred --CCceEEEEeccC
Q 002054 744 --RGNIKLSLKAVS 755 (974)
Q Consensus 744 --~gri~LS~K~~~ 755 (974)
.-+|.|+||+..
T Consensus 156 ~~~~~I~lTmrq~~ 169 (183)
T COG1095 156 PRESKIGLTMRQPG 169 (183)
T ss_pred cccceEEEEecccc
Confidence 147899999854
No 166
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.11 E-value=4.4e-06 Score=97.97 Aligned_cols=68 Identities=24% Similarity=0.272 Sum_probs=61.0
Q ss_pred cccc--cCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CC--ceEEEEec
Q 002054 679 REIE--VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RG--NIKLSLKA 753 (974)
Q Consensus 679 ~~~~--~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~g--ri~LS~K~ 753 (974)
..++ .|++++|+|.++.++|+||++ ++.+||||.++++ |.+.|++||.|+|+|+++|. ++ +|.||++.
T Consensus 128 ~eyk~~~GeIV~G~V~ri~~~giiVDL-ggvea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~ 200 (470)
T PRK09202 128 EEYKDRVGEIITGVVKRVERGNIIVDL-GRAEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTH 200 (470)
T ss_pred HHHHhhcCCEEEEEEEEEecCCEEEEE-CCeEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence 4565 999999999999999999999 6899999999995 66789999999999999987 23 79999975
No 167
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.06 E-value=1.4e-05 Score=83.29 Aligned_cols=75 Identities=28% Similarity=0.500 Sum_probs=63.8
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccc-----------ccccccccCCEEEEEEEEEccC---
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVS-----------RVSDVVSVGQQLSLRCIGQDVR--- 744 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~-----------~~~~~~~vGd~V~vkVl~id~~--- 744 (974)
..+.+|+++.|+|+++.++|+||++. ..+|++|.+++.+++.. +....+++||.|+++|.++|.+
T Consensus 77 f~P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~ 155 (187)
T PRK08563 77 FKPELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERR 155 (187)
T ss_pred EeccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCC
Confidence 35789999999999999999999996 59999999999877532 3456799999999999999862
Q ss_pred ---CceEEEEecc
Q 002054 745 ---GNIKLSLKAV 754 (974)
Q Consensus 745 ---gri~LS~K~~ 754 (974)
.++.||+|+.
T Consensus 156 ~~~~~I~ls~~~~ 168 (187)
T PRK08563 156 PRGSKIGLTMRQP 168 (187)
T ss_pred CCCCEEEEEecCC
Confidence 3788999874
No 168
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=97.93 E-value=3.8e-05 Score=71.61 Aligned_cols=52 Identities=19% Similarity=0.291 Sum_probs=46.0
Q ss_pred CEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC------------------CCCCCCCEEEEEEEEEeCC
Q 002054 912 TKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK------------------KDFVVGDELLVKCSSFTGK 964 (974)
Q Consensus 912 ~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~------------------~~f~vGd~V~vkVl~id~~ 964 (974)
+++.|+|.+|.++|+||+|+ ++.||+|.+++.. ..|++||.|+|+|.++|.+
T Consensus 1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~ 70 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLK 70 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHH
Confidence 47899999999999999998 5999999997641 3479999999999999975
No 169
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.90 E-value=2.2e-05 Score=69.01 Aligned_cols=70 Identities=17% Similarity=0.312 Sum_probs=64.2
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcC-CeEEEEe-cccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEE
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLH-VSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSL 751 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvh-isels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~ 751 (974)
-|++|+++. .|+.+.+.|++|.|.. +.+|++. .+|++.+++++..+.+ +|..+.|+|+.+|. +|-|.||.
T Consensus 13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~ 85 (86)
T PHA02858 13 FPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85 (86)
T ss_pred cCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence 478999999 8889999999999954 6899988 9999999999999999 99999999999998 89999984
No 170
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=97.89 E-value=1.5e-05 Score=76.83 Aligned_cols=54 Identities=22% Similarity=0.478 Sum_probs=50.3
Q ss_pred cchhhhhcCCCccchhhhhhhhCceEEee-C-----------------------CEEEEEecC--HHHHHHHHHHHHHHh
Q 002054 624 NDTLRRLIGPLGALKRKIEEETGGRISVS-D-----------------------GTLTVVAKN--RSVMEKVLEKVDFII 677 (974)
Q Consensus 624 ~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d-----------------------g~v~i~~~~--~~~~~~a~~~i~~l~ 677 (974)
-.+|+.+|||||+++|.|+++||++|+|. + +.|.|++.+ .+.+++|.+.|+.++
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 36899999999999999999999999997 5 789999999 999999999999887
No 171
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.83 E-value=6.7e-05 Score=80.97 Aligned_cols=65 Identities=22% Similarity=0.247 Sum_probs=58.1
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-----------CCCCCCCEEEEEEEEEeCCCceeeeec
Q 002054 908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-----------KDFVVGDELLVKCSSFTGKGIPVVSLV 972 (974)
Q Consensus 908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-----------~~f~vGd~V~vkVl~id~~~~~~~~~~ 972 (974)
.++||+|.|+|.+++++|+||+++.++.|++|.+++.. ..|++||.|.|+|+++++++.+.+|+.
T Consensus 61 P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k 136 (235)
T PRK04163 61 PKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLK 136 (235)
T ss_pred CCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEc
Confidence 37999999999999999999999999999999997642 248999999999999999888888865
No 172
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=97.80 E-value=2.5e-05 Score=94.21 Aligned_cols=69 Identities=23% Similarity=0.246 Sum_probs=59.8
Q ss_pred ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccC-------CCCCCCCCCEEEEEEEEEeCCCce-eeeec
Q 002054 904 SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENN-------EKKDFVVGDELLVKCSSFTGKGIP-VVSLV 972 (974)
Q Consensus 904 ~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~-------~~~~f~vGd~V~vkVl~id~~~~~-~~~~~ 972 (974)
...++++|+++.|+|+++.+||+||+++=..+|++|+|++ |.+.+++||.|+|+|++||.+++- -+|+.
T Consensus 652 ~i~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr 728 (780)
T COG2183 652 SITDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMR 728 (780)
T ss_pred hHhhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEee
Confidence 4669999999999999999999999999999999999966 356788999999999999976543 34544
No 173
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=97.79 E-value=5.1e-05 Score=94.68 Aligned_cols=65 Identities=23% Similarity=0.329 Sum_probs=56.4
Q ss_pred cCCCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCC------------------CCCCCCCEEEEEEEEEeC-CCc
Q 002054 907 NLKLGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEK------------------KDFVVGDELLVKCSSFTG-KGI 966 (974)
Q Consensus 907 ~~~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~------------------~~f~vGd~V~vkVl~id~-~~~ 966 (974)
.-++|++++|+|.+|++||+||+|++ ++.||+|+++++. +.|++||+|+|+|.++|. ++.
T Consensus 624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~ 703 (709)
T TIGR02063 624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGK 703 (709)
T ss_pred hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence 34689999999999999999999998 8999999997741 358999999999999997 566
Q ss_pred eeeee
Q 002054 967 PVVSL 971 (974)
Q Consensus 967 ~~~~~ 971 (974)
..++|
T Consensus 704 I~~~l 708 (709)
T TIGR02063 704 IDFEL 708 (709)
T ss_pred EEEEE
Confidence 66665
No 174
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.79 E-value=8.4e-05 Score=62.98 Aligned_cols=61 Identities=26% Similarity=0.390 Sum_probs=38.8
Q ss_pred cCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEe
Q 002054 683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK 752 (974)
Q Consensus 683 ~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K 752 (974)
+|++.+.+|+++.++|+|++...+.+-|||.+|+... +++||.|.|.|+. |.++++..|+|
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~--------~~~Gd~v~VFvY~-D~~~rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEP--------LKVGDEVEVFVYL-DKEGRLVATTK 61 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEEEE--TTS-EEEE--
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCC--------CCCCCEEEEEEEE-CCCCCEEEecC
Confidence 5889999999999999999987779999999998654 8999999999998 88899999876
No 175
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=97.74 E-value=4.2e-05 Score=86.43 Aligned_cols=94 Identities=16% Similarity=0.173 Sum_probs=69.1
Q ss_pred cccccCCeEEEEEEEeecCCCCcCcccccc-----cccc--ccccC--CCCCEEEEEEEEEeCCe-EEEEeCCCeEEEEe
Q 002054 870 TSFSQREREELAECLFGTEDGDEDNKGTRV-----EAIV--SAKNL--KLGTKVAAKVYQVRARG-LVLDLGGGIRGMYR 939 (974)
Q Consensus 870 ~~~k~Gq~v~~~Vl~vd~e~~~i~slK~~~-----~~p~--~~~~~--~vG~vV~G~V~~I~~~G-vFV~L~~gv~Glih 939 (974)
..+++||.++..+..-+..+.-+.+.|+.. ..-+ .+..| +.|++|+|+|.++.+.| +||+++ ++.|++|
T Consensus 82 ~~~~vGD~I~~~I~~~~fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG-~~ea~LP 160 (341)
T TIGR01953 82 PDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG-KTEGILP 160 (341)
T ss_pred cccccCCEEEEEecccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC-CeEEEec
Confidence 468889998877743332221111455421 1111 35566 59999999999999988 799995 9999999
Q ss_pred cccC-CCCCCCCCCEEEEEEEEEeCC
Q 002054 940 FENN-EKKDFVVGDELLVKCSSFTGK 964 (974)
Q Consensus 940 ~se~-~~~~f~vGd~V~vkVl~id~~ 964 (974)
.+++ +.+.|++||+++|.|++|+.+
T Consensus 161 ~~E~ip~E~~~~Gd~ik~~V~~V~~~ 186 (341)
T TIGR01953 161 KKEQIPGEKFRIGDRIKAYVYEVRKT 186 (341)
T ss_pred HHHcCCCcCCCCCCEEEEEEEEEEcC
Confidence 9987 467899999999999999954
No 176
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.71 E-value=4.8e-05 Score=86.47 Aligned_cols=95 Identities=12% Similarity=0.101 Sum_probs=69.2
Q ss_pred cccccCCeEEEEEEEeecCCCCcCccccccccc-------cccccC--CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEec
Q 002054 870 TSFSQREREELAECLFGTEDGDEDNKGTRVEAI-------VSAKNL--KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRF 940 (974)
Q Consensus 870 ~~~k~Gq~v~~~Vl~vd~e~~~i~slK~~~~~p-------~~~~~~--~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~ 940 (974)
...++|+.++..+-..+..+..+...|+....- -.+..| +.|++|+|+|+++.+.|+||+++ ++.|++|.
T Consensus 85 ~~~~vGD~i~~~I~~~~fgR~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg-~vEa~LP~ 163 (362)
T PRK12327 85 PAYELGDVIEIEVTPKDFGRIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG-KIEAVLPP 163 (362)
T ss_pred ccccCCCEEEEecCcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC-CeEEEecH
Confidence 356788888776644333322222333321111 136777 99999999999999999999996 69999997
Q ss_pred ccC-CCCCCCCCCEEEEEEEEEeCCC
Q 002054 941 ENN-EKKDFVVGDELLVKCSSFTGKG 965 (974)
Q Consensus 941 se~-~~~~f~vGd~V~vkVl~id~~~ 965 (974)
+++ +...|++||+++|.|++|+.+.
T Consensus 164 ~E~ip~e~~~~Gd~Ika~V~~V~~~~ 189 (362)
T PRK12327 164 AEQIPGETYKHGDRIKVYVVKVEKTT 189 (362)
T ss_pred HHcCCCCCCCCCCEEEEEEEEEecCC
Confidence 755 6788999999999999999543
No 177
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=97.65 E-value=0.00023 Score=80.50 Aligned_cols=66 Identities=24% Similarity=0.342 Sum_probs=57.8
Q ss_pred ccCcEEEEEEEEEeece-EEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc---CCceEEEEecc
Q 002054 682 EVGGIYKGVVTSVKEYG-AFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV---RGNIKLSLKAV 754 (974)
Q Consensus 682 ~~G~i~~G~V~~i~~~G-~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~---~gri~LS~K~~ 754 (974)
+.|++++|+|.++.+.| +||++ ++.+|+||.+|... .+.|++||.++|.|++++. .+.+.||++..
T Consensus 130 k~GeiV~G~V~~v~~~g~v~Vdi-G~~ea~LP~~E~ip------~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~ 199 (341)
T TIGR01953 130 KEGEIISGTVKRVNRRGNLYVEL-GKTEGILPKKEQIP------GEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP 199 (341)
T ss_pred hcCCEEEEEEEEEecCCcEEEEE-CCeEEEecHHHcCC------CcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence 59999999999999988 69999 68999999999873 4559999999999999985 24799999863
No 178
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.58 E-value=0.00031 Score=80.02 Aligned_cols=68 Identities=21% Similarity=0.317 Sum_probs=58.5
Q ss_pred ccc--ccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc--CC-ceEEEEec
Q 002054 679 REI--EVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV--RG-NIKLSLKA 753 (974)
Q Consensus 679 ~~~--~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~--~g-ri~LS~K~ 753 (974)
.++ +.|++++|+|.++.++|+||++ ++.+|+||.+++.. .+.|++||.++|.|++++. +| .|.||+..
T Consensus 128 ~ef~~k~GeiV~G~V~~~~~~~~~Vdl-g~vEa~LP~~E~ip------~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~ 200 (362)
T PRK12327 128 NEFSEREGDIVTGVVQRRDNRFVYVNL-GKIEAVLPPAEQIP------GETYKHGDRIKVYVVKVEKTTKGPQIFVSRTH 200 (362)
T ss_pred HHHHHhcCCEEEEEEEEEeCCcEEEEe-CCeEEEecHHHcCC------CCCCCCCCEEEEEEEEEecCCCCCeEEEEeCC
Confidence 346 8999999999999999999999 57999999888743 5669999999999999986 33 69999854
No 179
>PRK11642 exoribonuclease R; Provisional
Probab=97.56 E-value=0.00019 Score=90.00 Aligned_cols=65 Identities=17% Similarity=0.283 Sum_probs=55.4
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCC------------------CCCCCCCCEEEEEEEEEeC-CCcee
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNE------------------KKDFVVGDELLVKCSSFTG-KGIPV 968 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~------------------~~~f~vGd~V~vkVl~id~-~~~~~ 968 (974)
++|++++|+|.+|++||+||+|++ ++.||||.+++. .+.|++||+|+|+|.++|. ++...
T Consensus 642 ~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~ 721 (813)
T PRK11642 642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKID 721 (813)
T ss_pred cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeEE
Confidence 789999999999999999999998 599999999663 2459999999999999996 45566
Q ss_pred eeecC
Q 002054 969 VSLVD 973 (974)
Q Consensus 969 ~~~~~ 973 (974)
++++.
T Consensus 722 f~l~~ 726 (813)
T PRK11642 722 FSLIS 726 (813)
T ss_pred EEEec
Confidence 66653
No 180
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=97.56 E-value=0.00014 Score=61.53 Aligned_cols=55 Identities=31% Similarity=0.430 Sum_probs=47.4
Q ss_pred eeeeeccchhhhhcCCCccchhhhhhhhCceEEee-----CCEEEEEecCHHHHHHHHHHH
Q 002054 618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-----DGTLTVVAKNRSVMEKVLEKV 673 (974)
Q Consensus 618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-----dg~v~i~~~~~~~~~~a~~~i 673 (974)
..+.||+++++.+||++|++|++|++++|++|++. ++.|.|.++ .+.+..|..++
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP-KENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-HHHHHHHHHHh
Confidence 46789999999999999999999999999999985 378999987 56777776654
No 181
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=97.55 E-value=0.00018 Score=83.69 Aligned_cols=63 Identities=27% Similarity=0.467 Sum_probs=54.5
Q ss_pred ccccCcEEEEEEEEEeec--eEEEEEcCCeEEEEecccCCCc------------cccccccccccCCEEEEEEEEEcc
Q 002054 680 EIEVGGIYKGVVTSVKEY--GAFVEFNGGQQGLLHVSELSHE------------PVSRVSDVVSVGQQLSLRCIGQDV 743 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~--G~fV~l~~g~~Glvhisels~~------------~v~~~~~~~~vGd~V~vkVl~id~ 743 (974)
...+|.+|.|+|+++.++ ||||+|+.+..||+|++++.+. +..++.+.+++||.|.|.|.. ++
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~K-e~ 98 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVK-EP 98 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEee-CC
Confidence 456899999999999999 9999999999999999999653 234566779999999999999 54
No 182
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.54 E-value=4.7e-05 Score=80.28 Aligned_cols=78 Identities=31% Similarity=0.463 Sum_probs=73.2
Q ss_pred ccccCcEEEEEEEEEeeceEEEEE--cCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccCC
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEF--NGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVSP 756 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l--~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~~ 756 (974)
-+++++++-+.|.+|.+-|+||.| ++.++|++-.||||.+|++++..+.++|..=-|.|+.+|. +|-|.||.+.+.+
T Consensus 13 yPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs~ 92 (304)
T KOG2916|consen 13 YPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSP 92 (304)
T ss_pred CCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccCCH
Confidence 479999999999999999999999 4689999999999999999999999999999999999998 8999999998876
Q ss_pred C
Q 002054 757 R 757 (974)
Q Consensus 757 ~ 757 (974)
+
T Consensus 93 e 93 (304)
T KOG2916|consen 93 E 93 (304)
T ss_pred H
Confidence 4
No 183
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.49 E-value=0.00049 Score=62.27 Aligned_cols=73 Identities=16% Similarity=0.115 Sum_probs=63.8
Q ss_pred cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEecc
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV 754 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~ 754 (974)
+++|+.+-|+|+++....++|+|.....|++|.+++... .++....|++||-|-++|..+|+.....||+...
T Consensus 4 P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~~ 76 (86)
T cd05790 4 PAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRDMEPELSCVDS 76 (86)
T ss_pred CCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-cccccccCCCCCEEEEEEEecCCCCCeEEEEeCC
Confidence 789999999999999999999998888999999887543 4445667999999999999999888899999863
No 184
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.49 E-value=0.00041 Score=63.84 Aligned_cols=64 Identities=28% Similarity=0.307 Sum_probs=55.9
Q ss_pred CCCCEEEEEEEEEeCCeEEEEe--------CCCeEEEEecccCC---------CCCCCCCCEEEEEEEEEeCCCceeeee
Q 002054 909 KLGTKVAAKVYQVRARGLVLDL--------GGGIRGMYRFENNE---------KKDFVVGDELLVKCSSFTGKGIPVVSL 971 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L--------~~gv~Glih~se~~---------~~~f~vGd~V~vkVl~id~~~~~~~~~ 971 (974)
++|++|-|+|.+++...++|++ ...+.|++|.++.. .+.|++||-|+|+|++++......+|.
T Consensus 5 ~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~Lst 84 (92)
T cd05791 5 KVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYYLST 84 (92)
T ss_pred CCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcEEEe
Confidence 7999999999999999999999 77899999988652 356999999999999998766677776
Q ss_pred c
Q 002054 972 V 972 (974)
Q Consensus 972 ~ 972 (974)
.
T Consensus 85 ~ 85 (92)
T cd05791 85 A 85 (92)
T ss_pred c
Confidence 4
No 185
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.48 E-value=0.00041 Score=73.38 Aligned_cols=88 Identities=20% Similarity=0.305 Sum_probs=74.4
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc----cccccccccCCEEEEEEEEEccCCceEEEEeccC
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV----SRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVS 755 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v----~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~ 755 (974)
.+++||++-|+|..+...++.|+|.....+++|.|++-++.+ .+...+|++||-|.+||..+|..+...|++|..
T Consensus 61 iP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~- 139 (239)
T COG1097 61 IPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDE- 139 (239)
T ss_pred cCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeecC-
Confidence 479999999999999999999999888999999999966553 467788999999999999999999999999653
Q ss_pred CCcccccCceEEEEEeec
Q 002054 756 PRPEADVKGVVEGSVPVN 773 (974)
Q Consensus 756 ~~~~~~~g~~~~G~vv~i 773 (974)
..|....|.++.+
T Consensus 140 -----~~GkL~~G~iv~i 152 (239)
T COG1097 140 -----GLGKLKNGQIVKI 152 (239)
T ss_pred -----CCccccCCEEEEE
Confidence 3444556666663
No 186
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=97.45 E-value=0.00016 Score=77.21 Aligned_cols=94 Identities=23% Similarity=0.290 Sum_probs=71.2
Q ss_pred cCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEeccCCCccccc
Q 002054 683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAVSPRPEADV 762 (974)
Q Consensus 683 ~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~~~~~~~~~ 762 (974)
.|+.+.|+|.++...|.||-+.+++-||||-||.... .++|+.++++|+++.++|+|.||++....+.-..-
T Consensus 155 ~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~--------prlG~~l~~rVi~~reDg~lnLSl~p~~~E~l~~d 226 (287)
T COG2996 155 KNQEVDATVYRLLESGTFVITENGYLGFIHKSERFAE--------PRLGERLTARVIGVREDGKLNLSLRPRAHEMLDED 226 (287)
T ss_pred hcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhccc--------ccCCceEEEEEEEEccCCeeecccccccHHhhhhh
Confidence 4899999999999999999999999999999997655 78899999999999889999999987644332222
Q ss_pred CceEEEEEeecCCcceeeEEeeccCC
Q 002054 763 KGVVEGSVPVNKQATDVWASVGDVSN 788 (974)
Q Consensus 763 g~~~~G~vv~i~~gv~~~~~~~~l~~ 788 (974)
.++......+ ..|+.++++=+.
T Consensus 227 aq~Il~yL~~----~gG~mpf~DKSs 248 (287)
T COG2996 227 AQMILTYLES----NGGFMPFNDKSS 248 (287)
T ss_pred HHHHHHHHHH----cCCccccCCCCC
Confidence 2222222223 456666665443
No 187
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=97.38 E-value=0.0006 Score=70.68 Aligned_cols=53 Identities=23% Similarity=0.419 Sum_probs=47.2
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC------------------CCCCCCCCEEEEEEEEEe
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------------------KKDFVVGDELLVKCSSFT 962 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------------------~~~f~vGd~V~vkVl~id 962 (974)
.+|+++.|+|.+++++|+||+++ .++|++|.+++. ...|+.||+|++||.++|
T Consensus 80 ~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 150 (179)
T TIGR00448 80 ELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALS 150 (179)
T ss_pred cCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEE
Confidence 47999999999999999999995 699999999652 135899999999999998
No 188
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=97.36 E-value=0.00031 Score=59.10 Aligned_cols=55 Identities=27% Similarity=0.455 Sum_probs=48.4
Q ss_pred eeeeeccchhhhhcCCCccchhhhhhhhCceEEeeC----CEEEEEecCHHHHHHHHHHH
Q 002054 618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD----GTLTVVAKNRSVMEKVLEKV 673 (974)
Q Consensus 618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~d----g~v~i~~~~~~~~~~a~~~i 673 (974)
..+.+|++.++.+||++|.++++|++++|++|.+.+ ..+.+.+ +.+..++|+++|
T Consensus 2 ~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G-~~~~v~~A~~~I 60 (60)
T PF00013_consen 2 ERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEE-SHHHHHHHHHHH
T ss_pred EEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEe-CHHHHHHHHhhC
Confidence 467899999999999999999999999999999984 4788888 888999887754
No 189
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=97.36 E-value=0.00046 Score=85.27 Aligned_cols=59 Identities=24% Similarity=0.423 Sum_probs=51.8
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeC-CCeEEEEecccCCC------------------CCCCCCCEEEEEEEEEeCCCce
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLG-GGIRGMYRFENNEK------------------KDFVVGDELLVKCSSFTGKGIP 967 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~-~gv~Glih~se~~~------------------~~f~vGd~V~vkVl~id~~~~~ 967 (974)
++|++++|+|.+|++||+||+|+ .++.||+|.++++. ..|++||+|+|+|.++|.....
T Consensus 571 ~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~ 648 (654)
T TIGR00358 571 KVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRS 648 (654)
T ss_pred CCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence 57999999999999999999998 58999999996641 4599999999999999965543
No 190
>PRK05054 exoribonuclease II; Provisional
Probab=97.27 E-value=0.0014 Score=80.77 Aligned_cols=70 Identities=13% Similarity=0.167 Sum_probs=56.7
Q ss_pred ccC--cEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCcc--c--c--------ccccccccCCEEEEEEEEEcc-CC
Q 002054 682 EVG--GIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEP--V--S--------RVSDVVSVGQQLSLRCIGQDV-RG 745 (974)
Q Consensus 682 ~~G--~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~--v--~--------~~~~~~~vGd~V~vkVl~id~-~g 745 (974)
++| +.|.|.|+++++||+||+|.. +++||||++.|.+++ + . .-...|++||.|+|+|.++|. ++
T Consensus 558 ~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~ 637 (644)
T PRK05054 558 KAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR 637 (644)
T ss_pred ccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence 565 599999999999999999954 799999999997642 1 0 112469999999999999997 77
Q ss_pred ceEEEE
Q 002054 746 NIKLSL 751 (974)
Q Consensus 746 ri~LS~ 751 (974)
+|.++.
T Consensus 638 ~i~~~~ 643 (644)
T PRK05054 638 SIIARP 643 (644)
T ss_pred eEEEEE
Confidence 887764
No 191
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=97.25 E-value=0.0011 Score=60.45 Aligned_cols=60 Identities=22% Similarity=0.280 Sum_probs=49.2
Q ss_pred cCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCcccccc-----------ccccccCCEEEEEEEEEcc
Q 002054 683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRV-----------SDVVSVGQQLSLRCIGQDV 743 (974)
Q Consensus 683 ~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~-----------~~~~~vGd~V~vkVl~id~ 743 (974)
.|++++|+|+++.++|+||.+. ..++|+|.+++..+..-++ ...++.|+.|++||+++..
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~ 71 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRV 71 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEE
Confidence 4899999999999999999994 6889999999976543322 3348899999999998753
No 192
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=97.23 E-value=0.00034 Score=71.12 Aligned_cols=72 Identities=32% Similarity=0.409 Sum_probs=62.6
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcC----------CeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEE
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNG----------GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKL 749 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~----------g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~L 749 (974)
-++.|+++-|.|+++....+.|++.. ...|-+|+|+..+.++++.++.|++||.|+++|++.- -.+.|
T Consensus 61 ~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~--~~~~L 138 (188)
T COG1096 61 LPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG--DPIQL 138 (188)
T ss_pred CCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC--CCeEE
Confidence 47899999999999999999998852 1457799999999999999999999999999999963 46788
Q ss_pred EEec
Q 002054 750 SLKA 753 (974)
Q Consensus 750 S~K~ 753 (974)
|.+.
T Consensus 139 st~~ 142 (188)
T COG1096 139 STKG 142 (188)
T ss_pred EecC
Confidence 8664
No 193
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.18 E-value=0.0011 Score=57.69 Aligned_cols=66 Identities=24% Similarity=0.313 Sum_probs=55.5
Q ss_pred CcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCccccc---cccccccCCEE-EEEEEEEcc-CCceEEEEe
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVSR---VSDVVSVGQQL-SLRCIGQDV-RGNIKLSLK 752 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v~~---~~~~~~vGd~V-~vkVl~id~-~gri~LS~K 752 (974)
|++++|+|..-++.+++|++.+ +..|+++..+|++ .+++ ....+++||++ ++.|+ |. .+.+.||.|
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD-~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~i~lt~K 72 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD-HVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC-chhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence 7899999999999999999987 8999999999999 4433 33458999999 99999 55 567888865
No 194
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=97.16 E-value=0.0007 Score=68.91 Aligned_cols=57 Identities=21% Similarity=0.278 Sum_probs=49.9
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC------------------CCCCCCCCEEEEEEEEEeCCCc
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------------------KKDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------------------~~~f~vGd~V~vkVl~id~~~~ 966 (974)
-.|++|.|.|.++.+||+||.++ -++||+|.+++. +..+++||.|+|||++++.+..
T Consensus 80 ~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~ 154 (183)
T COG1095 80 FRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSR 154 (183)
T ss_pred ccccEEEEEEEEEeecceEEEec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccC
Confidence 47999999999999999999998 889999999653 2268999999999999987654
No 195
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=97.15 E-value=0.0016 Score=68.01 Aligned_cols=57 Identities=19% Similarity=0.274 Sum_probs=49.3
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC------------------CCCCCCCEEEEEEEEEeCCC
Q 002054 908 LKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK------------------KDFVVGDELLVKCSSFTGKG 965 (974)
Q Consensus 908 ~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~------------------~~f~vGd~V~vkVl~id~~~ 965 (974)
-.+|+++.|+|.++.++|+||+++ .++|++|.++++. ..++.||.|+++|.+++.+.
T Consensus 79 P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~ 153 (187)
T PRK08563 79 PELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKE 153 (187)
T ss_pred ccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccc
Confidence 348999999999999999999997 5999999997642 23689999999999999653
No 196
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.01 E-value=0.0036 Score=56.74 Aligned_cols=66 Identities=23% Similarity=0.260 Sum_probs=60.2
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC------CCCCCCCCEEEEEEEEEeCCCceeeeecCC
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------KKDFVVGDELLVKCSSFTGKGIPVVSLVDS 974 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------~~~f~vGd~V~vkVl~id~~~~~~~~~~~~ 974 (974)
++||.|-|+|..+...+-+|++..-..|++|.+.++ ...|++||-|-|+|.++|+...+.++.+|+
T Consensus 5 ~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~gatk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~~ 76 (86)
T cd05790 5 AKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDS 76 (86)
T ss_pred CCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccccccccccCCCCCEEEEEEEecCCCCCeEEEEeCC
Confidence 689999999999999999999998889999998763 346999999999999999999999999884
No 197
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=96.99 E-value=0.0026 Score=65.67 Aligned_cols=74 Identities=15% Similarity=0.132 Sum_probs=57.7
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccc------------cccccccccCCEEEEEEEEEcc---
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPV------------SRVSDVVSVGQQLSLRCIGQDV--- 743 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v------------~~~~~~~~vGd~V~vkVl~id~--- 743 (974)
..+-.|++++|+|+++.++|+||.+++ .++|+|.+++.++.. ++-+..++.|+.|++||.++..
T Consensus 77 FrPf~gEVv~g~V~~v~~~G~~v~~Gp-~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~ 155 (176)
T PTZ00162 77 FKPFKDEVLDAIVTDVNKLGFFAQAGP-LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDAS 155 (176)
T ss_pred EecCCCCEEEEEEEEEecceEEEEeeC-eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCC
Confidence 357899999999999999999999964 669999999975421 1123469999999999999754
Q ss_pred CCceEEEEec
Q 002054 744 RGNIKLSLKA 753 (974)
Q Consensus 744 ~gri~LS~K~ 753 (974)
+.+..+|||+
T Consensus 156 ~~~~i~T~~~ 165 (176)
T PTZ00162 156 NLFAIATINS 165 (176)
T ss_pred CcEEEEEecC
Confidence 2346667775
No 198
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=96.93 E-value=0.0041 Score=56.78 Aligned_cols=55 Identities=16% Similarity=0.074 Sum_probs=46.2
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC------------------CCCCCCCCEEEEEEEEEeCCC
Q 002054 910 LGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------------------KKDFVVGDELLVKCSSFTGKG 965 (974)
Q Consensus 910 vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------------------~~~f~vGd~V~vkVl~id~~~ 965 (974)
+|+++.|+|+++.++|+||.++ .++||+|.+.++ ...++.|+.|++||+++.-+.
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~ 73 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDA 73 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEcc
Confidence 5899999999999999999996 788999988443 123789999999999887543
No 199
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=96.75 E-value=0.0067 Score=74.78 Aligned_cols=69 Identities=12% Similarity=0.224 Sum_probs=54.8
Q ss_pred ccC--cEEEEEEEEEeeceEEEEE-cCCeEEEEecccCCC--ccc-----c---cc--ccccccCCEEEEEEEEEcc-CC
Q 002054 682 EVG--GIYKGVVTSVKEYGAFVEF-NGGQQGLLHVSELSH--EPV-----S---RV--SDVVSVGQQLSLRCIGQDV-RG 745 (974)
Q Consensus 682 ~~G--~i~~G~V~~i~~~G~fV~l-~~g~~Glvhisels~--~~v-----~---~~--~~~~~vGd~V~vkVl~id~-~g 745 (974)
++| +.|+|.|+++.+||+||+| ..+++||||++.+.+ +++ . .. ...|++||.|+|+|.++|. ++
T Consensus 554 ~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~ 633 (639)
T TIGR02062 554 KAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETR 633 (639)
T ss_pred ccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccC
Confidence 454 5999999999999999999 457999999999976 221 1 11 1269999999999999997 67
Q ss_pred ceEEE
Q 002054 746 NIKLS 750 (974)
Q Consensus 746 ri~LS 750 (974)
+|.+.
T Consensus 634 ~i~~~ 638 (639)
T TIGR02062 634 SIIAR 638 (639)
T ss_pred cEeee
Confidence 77653
No 200
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=96.74 E-value=0.0067 Score=51.41 Aligned_cols=60 Identities=25% Similarity=0.258 Sum_probs=37.1
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCCCCCCCCEEEEEEEEEeCCCceeeee
Q 002054 910 LGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPVVSL 971 (974)
Q Consensus 910 vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~~f~vGd~V~vkVl~id~~~~~~~~~ 971 (974)
+|++.+.+|.++.++|+|++-+++-.=|+|.++.+ ..+++||+|.|.| -.|.++.++++.
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~-~~~~~Gd~v~VFv-Y~D~~~rl~AT~ 60 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVP-EPLKVGDEVEVFV-YLDKEGRLVATT 60 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG-------TTSEEEEEE-EE-TTS-EEEE-
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcC-CCCCCCCEEEEEE-EECCCCCEEEec
Confidence 58999999999999999999888899999999995 6799999999976 567788887764
No 201
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=96.72 E-value=0.0023 Score=54.10 Aligned_cols=55 Identities=27% Similarity=0.443 Sum_probs=44.2
Q ss_pred eeeeeccchhhhhcCCCccchhhhhhhhCceEEeeC-------CEEEEEecCHHHHHHHHHHH
Q 002054 618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-------GTLTVVAKNRSVMEKVLEKV 673 (974)
Q Consensus 618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~d-------g~v~i~~~~~~~~~~a~~~i 673 (974)
..+.||.+.++.+||++|++|+.|++++|+.|.+.+ ..+.+.+. .+.++.|...+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~-~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT-PEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC-HHHHHHHHHHh
Confidence 467899999999999999999999999999998852 45677765 56677666543
No 202
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=96.71 E-value=0.0034 Score=56.30 Aligned_cols=61 Identities=25% Similarity=0.258 Sum_probs=42.1
Q ss_pred cccCcEEEEEEEEEeeceEEEEEcC------------------CeEEEEecccCCCccccc--cccccccCCEEEEEEEE
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFNG------------------GQQGLLHVSELSHEPVSR--VSDVVSVGQQLSLRCIG 740 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~~------------------g~~Glvhisels~~~v~~--~~~~~~vGd~V~vkVl~ 740 (974)
+++|+++.|+|+++.+.-++++|.- ...|++|.+++-...... +.+-|++||.|+++|++
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViS 81 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVIS 81 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEE
T ss_pred CCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEee
Confidence 6899999999999999999988741 356899999986654443 57789999999999997
Q ss_pred E
Q 002054 741 Q 741 (974)
Q Consensus 741 i 741 (974)
.
T Consensus 82 l 82 (82)
T PF10447_consen 82 L 82 (82)
T ss_dssp E
T ss_pred C
Confidence 3
No 203
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=96.70 E-value=0.0065 Score=75.98 Aligned_cols=73 Identities=30% Similarity=0.572 Sum_probs=61.0
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCcccc-----------ccccccccCCEEEEEEEEEcc-CCc
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVS-----------RVSDVVSVGQQLSLRCIGQDV-RGN 746 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v~-----------~~~~~~~vGd~V~vkVl~id~-~gr 746 (974)
.-.+|+.++|.|+++..||+||.|.+ +++|+||++.+.++++. .....+++||.|+|+|.++|. .++
T Consensus 619 ~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~ 698 (706)
T COG0557 619 KKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERK 698 (706)
T ss_pred HHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccc
Confidence 34789999999999999999999976 48999999999875432 234469999999999999987 678
Q ss_pred eEEEEe
Q 002054 747 IKLSLK 752 (974)
Q Consensus 747 i~LS~K 752 (974)
+.+++-
T Consensus 699 i~~~~v 704 (706)
T COG0557 699 IDFELV 704 (706)
T ss_pred eEEEec
Confidence 887753
No 204
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=96.65 E-value=0.0044 Score=72.39 Aligned_cols=71 Identities=30% Similarity=0.604 Sum_probs=61.6
Q ss_pred cccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEeccC
Q 002054 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKAVS 755 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~~~ 755 (974)
.+++.|..|.|+|.++.+||+||+|...+.||+|-++++.. .-+.+||.+-|++..+-+ +|.+.+....+.
T Consensus 118 ~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~ 189 (715)
T COG1107 118 EDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD 189 (715)
T ss_pred hhcccceeeeccccchhhhcceeecChhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCc
Confidence 47899999999999999999999999999999999999863 128899999999999977 588888776543
No 205
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=96.59 E-value=0.0047 Score=55.42 Aligned_cols=53 Identities=25% Similarity=0.347 Sum_probs=37.5
Q ss_pred CCCCEEEEEEEEEeCCeEEEEe------------------CCCeEEEEecccCC---------CCCCCCCCEEEEEEEEE
Q 002054 909 KLGTKVAAKVYQVRARGLVLDL------------------GGGIRGMYRFENNE---------KKDFVVGDELLVKCSSF 961 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L------------------~~gv~Glih~se~~---------~~~f~vGd~V~vkVl~i 961 (974)
++|++|.|+|.++++..+++++ .+.+.|++|.++.. .+.|++||-|.|+|+++
T Consensus 3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl 82 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL 82 (82)
T ss_dssp -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence 5899999999999999998876 23578999998542 44699999999999985
No 206
>PRK05054 exoribonuclease II; Provisional
Probab=96.46 E-value=0.0068 Score=74.85 Aligned_cols=60 Identities=18% Similarity=0.232 Sum_probs=50.3
Q ss_pred CCC--CEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCC-------------------CCCCCCCCEEEEEEEEEeCCCc
Q 002054 909 KLG--TKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNE-------------------KKDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 909 ~vG--~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~-------------------~~~f~vGd~V~vkVl~id~~~~ 966 (974)
++| +...|.|..+++||+||+|++ ++.||||.+.+. ...|+.||+|+|+|.++|....
T Consensus 558 ~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~ 637 (644)
T PRK05054 558 KAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR 637 (644)
T ss_pred ccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence 365 599999999999999999987 899999998552 1258999999999999996654
Q ss_pred ee
Q 002054 967 PV 968 (974)
Q Consensus 967 ~~ 968 (974)
.+
T Consensus 638 ~i 639 (644)
T PRK05054 638 SI 639 (644)
T ss_pred eE
Confidence 43
No 207
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=96.34 E-value=0.0078 Score=70.19 Aligned_cols=55 Identities=15% Similarity=0.191 Sum_probs=48.8
Q ss_pred ccCCCCCEEEEEEEEEeCC--eEEEEeCCCeEEEEecccCCC-------------------CCCCCCCEEEEEEEE
Q 002054 906 KNLKLGTKVAAKVYQVRAR--GLVLDLGGGIRGMYRFENNEK-------------------KDFVVGDELLVKCSS 960 (974)
Q Consensus 906 ~~~~vG~vV~G~V~~I~~~--GvFV~L~~gv~Glih~se~~~-------------------~~f~vGd~V~vkVl~ 960 (974)
....+|+++.|+|.+|.+. |+||+++++-.||+|.++... +.+++||+|.|.|++
T Consensus 21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~K 96 (414)
T TIGR00757 21 SRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVK 96 (414)
T ss_pred CcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEee
Confidence 3457999999999999999 999999999999999998632 148999999999998
No 208
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.25 E-value=0.014 Score=66.42 Aligned_cols=57 Identities=21% Similarity=0.297 Sum_probs=51.1
Q ss_pred CCCCEEEEEEEEEeCC-eEEEEeCCCeEEEEecccC-CCCCCCCCCEEEEEEEEEeCCCc
Q 002054 909 KLGTKVAAKVYQVRAR-GLVLDLGGGIRGMYRFENN-EKKDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~-GvFV~L~~gv~Glih~se~-~~~~f~vGd~V~vkVl~id~~~~ 966 (974)
++|++|+|+|.++... ++||+|+ ++.|++|.++. +.+.|++||+++|.|.+|+....
T Consensus 137 ~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eqip~E~~~~Gdrik~~i~~V~~~~k 195 (374)
T PRK12328 137 KVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNRIKGEKFKVGDVVKAVLKRVKIDKN 195 (374)
T ss_pred hcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHcCCCCcCCCCCEEEEEEEEEecCCC
Confidence 6999999999999875 5999996 89999999966 68899999999999999997654
No 209
>smart00322 KH K homology RNA-binding domain.
Probab=96.22 E-value=0.011 Score=49.84 Aligned_cols=60 Identities=27% Similarity=0.327 Sum_probs=48.8
Q ss_pred cceeeeeccchhhhhcCCCccchhhhhhhhCceEEeeC-----CEEEEEecCHHHHHHHHHHHHHH
Q 002054 616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVSD-----GTLTVVAKNRSVMEKVLEKVDFI 676 (974)
Q Consensus 616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~d-----g~v~i~~~~~~~~~~a~~~i~~l 676 (974)
....+.++++.++.+||++|++|+.|++.+|++|.+.. ..+.+.+. ....+.|...+...
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~-~~~v~~a~~~i~~~ 67 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGP-PENVEKAAELILEI 67 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcC-HHHHHHHHHHHHHH
Confidence 34577899999999999999999999999999998763 56777776 57777777766543
No 210
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.16 E-value=0.017 Score=50.29 Aligned_cols=55 Identities=20% Similarity=0.219 Sum_probs=47.7
Q ss_pred CCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCC---------CCCCCCCEE-EEEEEEEeCCCce
Q 002054 911 GTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEK---------KDFVVGDEL-LVKCSSFTGKGIP 967 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~---------~~f~vGd~V-~vkVl~id~~~~~ 967 (974)
|++|+|+|.+-++-+++|++++ |+.|+++..+++. ..+++||++ .+-|+ +...+.
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~ 66 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGR 66 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccE
Confidence 7899999999999999999999 9999999998853 368999999 99999 555443
No 211
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=96.10 E-value=0.0089 Score=61.54 Aligned_cols=51 Identities=31% Similarity=0.438 Sum_probs=47.7
Q ss_pred hhhhhcCCCccchhhhhhhhCceEEeeCCEEEEEecCHHHHHHHHHHHHHHh
Q 002054 626 TLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFII 677 (974)
Q Consensus 626 ki~~vIg~gGk~i~~i~~~~g~~Idi~dg~v~i~~~~~~~~~~a~~~i~~l~ 677 (974)
.++.+||+||++++.|++.||++|.+.+..|.+.+ +.+..+.|++.++.|+
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~~~v~i~G-~~~~~~~A~~~i~~li 149 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYGKTVGIIG-DPEQVQIAREAIEMLI 149 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcCCEEEEEC-CHHHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999988 7889999999998887
No 212
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.96 E-value=0.035 Score=63.21 Aligned_cols=87 Identities=20% Similarity=0.297 Sum_probs=64.8
Q ss_pred ecCHHHHHHHHHHHHHHh--------hcc--cccCcEEEEEEEEEee-ceEEEEEcCCeEEEEecccCCCcccccccccc
Q 002054 660 AKNRSVMEKVLEKVDFII--------GRE--IEVGGIYKGVVTSVKE-YGAFVEFNGGQQGLLHVSELSHEPVSRVSDVV 728 (974)
Q Consensus 660 ~~~~~~~~~a~~~i~~l~--------~~~--~~~G~i~~G~V~~i~~-~G~fV~l~~g~~Glvhisels~~~v~~~~~~~ 728 (974)
...+-+++.|++.+...+ ..+ -++|+++.|+|.++.. .++||+| ++.+|++|.++.. |.+.|
T Consensus 105 ~fgRiaaq~akq~i~Qkir~~er~~i~~ey~~~~Geiv~g~V~r~~~~~~i~vdl-g~~ea~LP~~eqi------p~E~~ 177 (374)
T PRK12328 105 NMGRTAANTLFKELEYHIQRLLEESIFEKYKKKVGKIVFGTVVRVDNEENTFIEI-DEIRAVLPMKNRI------KGEKF 177 (374)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEc-CCeEEEeCHHHcC------CCCcC
Confidence 344556666665542211 112 4799999999999986 4699999 5899999988765 44679
Q ss_pred ccCCEEEEEEEEEcc--C-C-ceEEEEec
Q 002054 729 SVGQQLSLRCIGQDV--R-G-NIKLSLKA 753 (974)
Q Consensus 729 ~vGd~V~vkVl~id~--~-g-ri~LS~K~ 753 (974)
++||.++|.|.+++. + | ++.||+..
T Consensus 178 ~~Gdrik~~i~~V~~~~k~gp~IilSRt~ 206 (374)
T PRK12328 178 KVGDVVKAVLKRVKIDKNNGILIELSRTS 206 (374)
T ss_pred CCCCEEEEEEEEEecCCCCCCEEEEEcCC
Confidence 999999999999986 3 3 68899854
No 213
>PRK11712 ribonuclease G; Provisional
Probab=95.95 E-value=0.015 Score=68.94 Aligned_cols=62 Identities=32% Similarity=0.483 Sum_probs=50.7
Q ss_pred cccCcEEEEEEEEEeec--eEEEEEcCCeEEEEecccCCCc------------cccccccccccCCEEEEEEEEEcc
Q 002054 681 IEVGGIYKGVVTSVKEY--GAFVEFNGGQQGLLHVSELSHE------------PVSRVSDVVSVGQQLSLRCIGQDV 743 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~--G~fV~l~~g~~Glvhisels~~------------~v~~~~~~~~vGd~V~vkVl~id~ 743 (974)
..+|.||.|+|.+|.+. +|||+|+.+..||+|++++... ...++.+.+++||.|-|.|.. ++
T Consensus 36 ~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~K-e~ 111 (489)
T PRK11712 36 GIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVK-DP 111 (489)
T ss_pred cccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEe-CC
Confidence 45899999999999884 8999999999999999998321 112345669999999999998 44
No 214
>PRK13763 putative RNA-processing protein; Provisional
Probab=95.91 E-value=0.011 Score=61.36 Aligned_cols=51 Identities=33% Similarity=0.460 Sum_probs=46.6
Q ss_pred hhhhhcCCCccchhhhhhhhCceEEeeCCEEEEEecCHHHHHHHHHHHHHHh
Q 002054 626 TLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFII 677 (974)
Q Consensus 626 ki~~vIg~gGk~i~~i~~~~g~~Idi~dg~v~i~~~~~~~~~~a~~~i~~l~ 677 (974)
..+.+||+||++++.|++.||++|.+++..+.+.+ +.+..+.|++.++.|.
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~~v~i~G-~~~~~~~A~~~I~~li 155 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGKTVAIIG-DPEQVEIAREAIEMLI 155 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCCEEEEEe-CHHHHHHHHHHHHHHH
Confidence 57899999999999999999999999988899986 7789999999998887
No 215
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=95.90 E-value=0.0064 Score=71.07 Aligned_cols=61 Identities=23% Similarity=0.440 Sum_probs=57.1
Q ss_pred ccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCC-CCCCCCCEEEEEEEEEeCC
Q 002054 904 SAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEK-KDFVVGDELLVKCSSFTGK 964 (974)
Q Consensus 904 ~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~-~~f~vGd~V~vkVl~id~~ 964 (974)
..+++..|....|+|.++.+||+||+|+..+.||+|.+++.. ..|.+||++-+.|..+.+.
T Consensus 116 ~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~~~~~vgdeiiV~v~~vr~~ 177 (715)
T COG1107 116 TMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGDPDYAVGDEIIVQVSDVRPE 177 (715)
T ss_pred chhhcccceeeeccccchhhhcceeecChhhhccccccccCCCCCCCCCCeEEEEeeccCCC
Confidence 478899999999999999999999999999999999999974 6899999999999999877
No 216
>PRK10811 rne ribonuclease E; Reviewed
Probab=95.90 E-value=0.013 Score=72.67 Aligned_cols=61 Identities=26% Similarity=0.511 Sum_probs=51.1
Q ss_pred cccCcEEEEEEEEEeec--eEEEEEcCCeEEEEecccCCCcccc---------ccccccccCCEEEEEEEEE
Q 002054 681 IEVGGIYKGVVTSVKEY--GAFVEFNGGQQGLLHVSELSHEPVS---------RVSDVVSVGQQLSLRCIGQ 741 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~--G~fV~l~~g~~Glvhisels~~~v~---------~~~~~~~vGd~V~vkVl~i 741 (974)
..+|.||.|+|.+|.+. ++||+|+.+..||+|++++....+. +..+.++.||.|-|.|.+-
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KE 107 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE 107 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeec
Confidence 35899999999999884 8999999999999999999654322 2355699999999999983
No 217
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=95.89 E-value=0.015 Score=49.73 Aligned_cols=54 Identities=30% Similarity=0.410 Sum_probs=42.6
Q ss_pred eeeeccchhhhhcCCCccchhhhhhhhCceEEee-C-------CEEEEEecCHHHHHHHHHHH
Q 002054 619 TLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D-------GTLTVVAKNRSVMEKVLEKV 673 (974)
Q Consensus 619 ~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d-------g~v~i~~~~~~~~~~a~~~i 673 (974)
.+.++.++++.+||.+|.+|+.|++++|++|.+. + ..+.+.+ +.+..++|..+|
T Consensus 3 r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I 64 (65)
T cd02396 3 RLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISG-KPSAVQKALLLI 64 (65)
T ss_pred EEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEe-CHHHHHHHHHhh
Confidence 5778999999999999999999999999999875 1 2455555 456677776554
No 218
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.89 E-value=0.026 Score=65.26 Aligned_cols=56 Identities=7% Similarity=0.136 Sum_probs=50.7
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeC----C-CeEEEEecccC-CCCCCCCCCEEEEEEEEEeCC
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLG----G-GIRGMYRFENN-EKKDFVVGDELLVKCSSFTGK 964 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~----~-gv~Glih~se~-~~~~f~vGd~V~vkVl~id~~ 964 (974)
++|++|+|+|.++...+++|+|+ . ++.|++|.++. +.+.|++||+|+|.|.+|+..
T Consensus 151 ~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip~E~y~~Gdrika~i~~V~~~ 212 (449)
T PRK12329 151 LEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLPNDNYRANATFKVFLKEVSEG 212 (449)
T ss_pred hcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCCCCcCCCCCEEEEEEEEeecC
Confidence 69999999999999999999994 2 49999999966 788999999999999999875
No 219
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=95.72 E-value=0.029 Score=49.81 Aligned_cols=56 Identities=16% Similarity=0.203 Sum_probs=48.4
Q ss_pred CCCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEe-cccCC-------CCCCCCCCEEEEEEEEEeCCC
Q 002054 908 LKLGTKVAAKVYQVRARGLVLDLGG-GIRGMYR-FENNE-------KKDFVVGDELLVKCSSFTGKG 965 (974)
Q Consensus 908 ~~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih-~se~~-------~~~f~vGd~V~vkVl~id~~~ 965 (974)
-.+|+++. .|+.|++.|++|.|-+ |+.|++. .+++. .+.+ +|-...|+|+.+|..+
T Consensus 14 P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~K 78 (86)
T PHA02858 14 PNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLK 78 (86)
T ss_pred CCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCC
Confidence 46899999 8999999999999987 9999998 66663 4456 9999999999999764
No 220
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=95.58 E-value=0.032 Score=57.68 Aligned_cols=55 Identities=11% Similarity=0.072 Sum_probs=46.3
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-------------------CCCCCCCCEEEEEEEEEeCC
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-------------------KKDFVVGDELLVKCSSFTGK 964 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-------------------~~~f~vGd~V~vkVl~id~~ 964 (974)
-+|+++.|+|+++.++|+||.++ =+++++|.+.++ ...++.|+.|++||.++.-+
T Consensus 80 f~gEVv~g~V~~v~~~G~~v~~G-p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~ 153 (176)
T PTZ00162 80 FKDEVLDAIVTDVNKLGFFAQAG-PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYD 153 (176)
T ss_pred CCCCEEEEEEEEEecceEEEEee-CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEec
Confidence 48999999999999999999996 667999999553 12478899999999888644
No 221
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=95.29 E-value=0.059 Score=57.44 Aligned_cols=65 Identities=22% Similarity=0.328 Sum_probs=58.7
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC-----------CCCCCCCCEEEEEEEEEeCCCceeeeecC
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE-----------KKDFVVGDELLVKCSSFTGKGIPVVSLVD 973 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~-----------~~~f~vGd~V~vkVl~id~~~~~~~~~~~ 973 (974)
++||+|-|+|..+...+-.|++..-+.+++|.|++. ...|++||-|.|+|.++|+++.+.+++.|
T Consensus 63 ~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~ 138 (239)
T COG1097 63 EVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKD 138 (239)
T ss_pred CCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeec
Confidence 699999999999999999999998899999999662 44699999999999999999999888754
No 222
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=95.27 E-value=0.025 Score=70.75 Aligned_cols=75 Identities=27% Similarity=0.329 Sum_probs=65.1
Q ss_pred ccccCcEEEEEEEEEeece---EEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCC-ceEEEEecc
Q 002054 680 EIEVGGIYKGVVTSVKEYG---AFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRG-NIKLSLKAV 754 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G---~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~g-ri~LS~K~~ 754 (974)
.+..|.++.++|++++..- +-|.+..|+.|+||.+++|+..+.+|...+++||.|.|||+++|... -+.||+|..
T Consensus 982 t~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~s 1060 (1299)
T KOG1856|consen 982 TFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTS 1060 (1299)
T ss_pred HhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhH
Confidence 4779999999999997654 56788899999999999999999999999999999999999999733 566777654
No 223
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=95.17 E-value=0.051 Score=67.16 Aligned_cols=58 Identities=16% Similarity=0.177 Sum_probs=48.6
Q ss_pred CCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCC-------------------CCCCCCCEEEEEEEEEeCCCcee
Q 002054 911 GTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEK-------------------KDFVVGDELLVKCSSFTGKGIPV 968 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~-------------------~~f~vGd~V~vkVl~id~~~~~~ 968 (974)
|+...|.|..++++|+||+|.+ |+.||||.+.+.. ..|+.||+|+|+|.++|.....+
T Consensus 558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i 635 (639)
T TIGR02062 558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSI 635 (639)
T ss_pred CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcE
Confidence 4599999999999999999965 8999999885521 13889999999999999776544
No 224
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=95.14 E-value=0.051 Score=68.08 Aligned_cols=61 Identities=23% Similarity=0.351 Sum_probs=52.8
Q ss_pred cccCCCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecccCC------------------CCCCCCCCEEEEEEEEEeCCC
Q 002054 905 AKNLKLGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFENNE------------------KKDFVVGDELLVKCSSFTGKG 965 (974)
Q Consensus 905 ~~~~~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~------------------~~~f~vGd~V~vkVl~id~~~ 965 (974)
+-.-.+|+..+|+|.++..+|+||.|++ +++|++|.+.++ ...|+.||+|+++|++++..-
T Consensus 617 ~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~ 696 (706)
T COG0557 617 YMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDE 696 (706)
T ss_pred HHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccc
Confidence 4456899999999999999999999998 699999999664 235999999999999998543
No 225
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.55 E-value=0.2 Score=58.18 Aligned_cols=67 Identities=12% Similarity=0.049 Sum_probs=55.7
Q ss_pred cccCcEEEEEEEEEeeceEEEEEc---C--CeEEEEecccCCCccccccccccccCCEEEEEEEEEcc---CC-ceEEEE
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFN---G--GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV---RG-NIKLSL 751 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~---~--g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~---~g-ri~LS~ 751 (974)
-++|+++.|+|.++...+++|++. + +.+|+||.++.. |.+.|++||.|+|.|.++.. +| +|.||+
T Consensus 150 ~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpqIilSR 223 (449)
T PRK12329 150 DLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQLFVSR 223 (449)
T ss_pred HhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEEc
Confidence 479999999999999999999983 3 389999988764 34669999999999999965 33 699998
Q ss_pred ec
Q 002054 752 KA 753 (974)
Q Consensus 752 K~ 753 (974)
-.
T Consensus 224 t~ 225 (449)
T PRK12329 224 AN 225 (449)
T ss_pred CC
Confidence 53
No 226
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=94.29 E-value=0.34 Score=53.41 Aligned_cols=120 Identities=20% Similarity=0.228 Sum_probs=72.1
Q ss_pred EeeCCceEEEEeeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCC-cce--eeeeccchhhhhcCCC
Q 002054 558 AGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMEREISAPRTQDDRNSP-RLA--TLKYDNDTLRRLIGPL 634 (974)
Q Consensus 558 a~t~~gI~alq~~~k~~~i~~e~l~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~~p-~~~--~~~i~~~ki~~vIg~g 634 (974)
-+|.+.||.+|-. .+.++..++.-.+...+..+.+.+ +..-+.+..| |.. .+-+|..--+-+||+|
T Consensus 82 PGTTeRvcli~Gt-------~eai~av~efI~dKire~p~~~~k----~v~~~~pqt~~r~kqikivvPNstag~iigkg 150 (402)
T KOG2191|consen 82 PGTTERVCLIQGT-------VEALNAVHEFIADKIREKPQAVAK----PVDILQPQTPDRIKQIKIVVPNSTAGMIIGKG 150 (402)
T ss_pred CCccceEEEEecc-------HHHHHHHHHHHHHHHHHhHHhhcC----CccccCCCCccccceeEEeccCCcccceecCC
Confidence 3677788888763 445555555433333333333222 1111122112 333 3345667789999999
Q ss_pred ccchhhhhhhhCceEEee---------CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEE
Q 002054 635 GALKRKIEEETGGRISVS---------DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYK 688 (974)
Q Consensus 635 Gk~i~~i~~~~g~~Idi~---------dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~ 688 (974)
|.+||.|+|+.|..|.|. ..+|.....+.+...+|..+|-..+..+++-+.-+.
T Consensus 151 gAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln 213 (402)
T KOG2191|consen 151 GATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLN 213 (402)
T ss_pred cchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceec
Confidence 999999999999877653 245555566777777777666443436777666543
No 227
>PF13014 KH_3: KH domain
Probab=93.26 E-value=0.042 Score=42.98 Aligned_cols=27 Identities=37% Similarity=0.655 Sum_probs=24.1
Q ss_pred hhhhcCCCccchhhhhhhhCceEEeeC
Q 002054 627 LRRLIGPLGALKRKIEEETGGRISVSD 653 (974)
Q Consensus 627 i~~vIg~gGk~i~~i~~~~g~~Idi~d 653 (974)
.+.+||++|.+|++|++++|++|.+.+
T Consensus 2 vg~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred cCeEECCCChHHHHHHHHhCcEEEECC
Confidence 577999999999999999999998753
No 228
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=92.78 E-value=0.35 Score=48.79 Aligned_cols=58 Identities=28% Similarity=0.348 Sum_probs=45.8
Q ss_pred CCCCEEEEEEEEEeCCeEEEEe--------CCCeEEEEecccCC---------CCCCCCCCEEEEEEEEEeCCCc
Q 002054 909 KLGTKVAAKVYQVRARGLVLDL--------GGGIRGMYRFENNE---------KKDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L--------~~gv~Glih~se~~---------~~~f~vGd~V~vkVl~id~~~~ 966 (974)
.+|++|+++|..|...-+-+++ .+.++|++|..+.. -+.|+|||.|.|+|++.+.+..
T Consensus 67 ~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~ 141 (193)
T KOG3409|consen 67 FVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSN 141 (193)
T ss_pred ccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCc
Confidence 4899999999999887777665 34799999998662 3469999999999999654443
No 229
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=92.68 E-value=0.5 Score=54.83 Aligned_cols=88 Identities=18% Similarity=0.356 Sum_probs=61.8
Q ss_pred HHHHHHHHHHHHhcCCCCCCCCCCCc---ceeeeecc------chhhhhcCCCccchhhhhhhhCceEEee------CC-
Q 002054 591 GRLQILDHMEREISAPRTQDDRNSPR---LATLKYDN------DTLRRLIGPLGALKRKIEEETGGRISVS------DG- 654 (974)
Q Consensus 591 ~~~~I~~~m~~~i~~~~~~~~~~~p~---~~~~~i~~------~ki~~vIg~gGk~i~~i~~~~g~~Idi~------dg- 654 (974)
.+.++++.+.+.+... +...+|-|. -..+.|+. +.++-+||+.|.|.|.++++||++|-|- +|
T Consensus 111 er~e~I~~~lk~nP~f-kpP~DYk~p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk 189 (554)
T KOG0119|consen 111 ERHEIIEEILKLNPGF-KPPADYKPPAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGK 189 (554)
T ss_pred HHHHHHHHHHHhCcCC-CCCcccCcccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccc
Confidence 3444555555544433 234444443 34455654 4689999999999999999999999763 22
Q ss_pred ----------------EEEEEecCHHHHHHHHHHHHHHhhc
Q 002054 655 ----------------TLTVVAKNRSVMEKVLEKVDFIIGR 679 (974)
Q Consensus 655 ----------------~v~i~~~~~~~~~~a~~~i~~l~~~ 679 (974)
...|++.+.+.+++|.+.|+.++..
T Consensus 190 ~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 190 GRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred cCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence 2478899999999999999988853
No 230
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=92.50 E-value=0.14 Score=61.23 Aligned_cols=62 Identities=34% Similarity=0.431 Sum_probs=52.7
Q ss_pred ccccCcEEEEEEEEEeec--eEEEEEcCCeEEEEecccCCCcccccc-----ccccccCCEEEEEEEEEc
Q 002054 680 EIEVGGIYKGVVTSVKEY--GAFVEFNGGQQGLLHVSELSHEPVSRV-----SDVVSVGQQLSLRCIGQD 742 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~--G~fV~l~~g~~Glvhisels~~~v~~~-----~~~~~vGd~V~vkVl~id 742 (974)
...+|.+|.|+|++|.+. .+||+++....||+|.+++.+ +++.+ ...++.||.+-|.|+.-.
T Consensus 34 ~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~ 102 (487)
T COG1530 34 EQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEP 102 (487)
T ss_pred EeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeec
Confidence 456899999999999886 789999988999999999988 54433 347999999999999843
No 231
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=91.93 E-value=0.44 Score=56.61 Aligned_cols=61 Identities=23% Similarity=0.398 Sum_probs=49.7
Q ss_pred ceeeeeccchhhhhcCCCccchhhhhhhhCceEEee--CC------EEEEEecCHHHHHHHHHHHHHHhh
Q 002054 617 LATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS--DG------TLTVVAKNRSVMEKVLEKVDFIIG 678 (974)
Q Consensus 617 ~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~--dg------~v~i~~~~~~~~~~a~~~i~~l~~ 678 (974)
-..++|+..+.+-|||.+|.+||.|+.+||++|-+. |+ .+.|.. ..+..+.|.+.|..|+.
T Consensus 231 ~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG-~~d~ie~Aa~lI~eii~ 299 (600)
T KOG1676|consen 231 TREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIG-TVDQIEHAAELINEIIA 299 (600)
T ss_pred eeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeec-CHHHHHHHHHHHHHHHH
Confidence 456788999999999999999999999999999874 33 345554 56788888888888883
No 232
>PRK10811 rne ribonuclease E; Reviewed
Probab=91.27 E-value=0.42 Score=60.01 Aligned_cols=55 Identities=16% Similarity=0.253 Sum_probs=46.6
Q ss_pred CCCCEEEEEEEEEeCC--eEEEEeCCCeEEEEecccCC----------------CCCCCCCCEEEEEEEEEeC
Q 002054 909 KLGTKVAAKVYQVRAR--GLVLDLGGGIRGMYRFENNE----------------KKDFVVGDELLVKCSSFTG 963 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~--GvFV~L~~gv~Glih~se~~----------------~~~f~vGd~V~vkVl~id~ 963 (974)
.+|+++.|+|.+|.+- ++||+|++|-.||+|.++.. +..+++||+|-|-|.+--.
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~ 109 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEER 109 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeeccc
Confidence 5899999999999665 89999999999999987662 2248899999999987443
No 233
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=90.84 E-value=1 Score=41.79 Aligned_cols=63 Identities=16% Similarity=0.276 Sum_probs=52.4
Q ss_pred ccccccccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCCCCCCCCEEEEEEEEEe
Q 002054 900 EAIVSAKNLKLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFT 962 (974)
Q Consensus 900 ~~p~~~~~~~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~~f~vGd~V~vkVl~id 962 (974)
.+||..-.-..|.+|.|+|..|-+--+||+++......|.......+.|..|.+|.+++.+..
T Consensus 13 ~S~fi~lG~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~~~y~~G~rV~lrLkdlE 75 (104)
T PF10246_consen 13 NSPFIQLGDPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNGEKYVRGSRVRLRLKDLE 75 (104)
T ss_pred CChhhhcCCccCCEEEEEEEEEecCceEEEeCCceeEEEecccccccccccCCEEEEEECCHh
Confidence 345532223699999999999988899999999999999998766778999999999987654
No 234
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=90.51 E-value=0.33 Score=61.29 Aligned_cols=64 Identities=20% Similarity=0.285 Sum_probs=55.1
Q ss_pred cccCCCCCEEEEEEEEEeCCe---EEEEeCCCeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCcee
Q 002054 905 AKNLKLGTKVAAKVYQVRARG---LVLDLGGGIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGIPV 968 (974)
Q Consensus 905 ~~~~~vG~vV~G~V~~I~~~G---vFV~L~~gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~~~ 968 (974)
-+.+-+|.+|.++|++++..- |=|.++.|+.|+|+.++.+ ...+++||+|.|||+++|.++.+|
T Consensus 980 ~et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v 1053 (1299)
T KOG1856|consen 980 PETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSV 1053 (1299)
T ss_pred hhHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhh
Confidence 456899999999999997665 6678999999999999664 446889999999999999988765
No 235
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=90.40 E-value=1.2 Score=40.21 Aligned_cols=64 Identities=20% Similarity=0.261 Sum_probs=51.0
Q ss_pred EEEEEEEEEeeceEE-EEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEec
Q 002054 686 IYKGVVTSVKEYGAF-VEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKA 753 (974)
Q Consensus 686 i~~G~V~~i~~~G~f-V~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~ 753 (974)
.++|+|+.+.+.+.| |.|.+|..-+.|+|= +...-.-.+-+||.|.|.+--.|. +|+|..-.|.
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isG----KmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASG----RMRKHRIRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEecc----ceeeeeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence 589999999999998 699999999999873 333223337789999999988887 7899887763
No 236
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=90.16 E-value=0.61 Score=48.40 Aligned_cols=64 Identities=27% Similarity=0.405 Sum_probs=55.1
Q ss_pred CCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee--CCEEEEEec----CHHHHHHHHHHHHHHh
Q 002054 614 SPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS--DGTLTVVAK----NRSVMEKVLEKVDFII 677 (974)
Q Consensus 614 ~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~--dg~v~i~~~----~~~~~~~a~~~i~~l~ 677 (974)
.+....+.||+++++-+||+.|.+-+.|.+.+++++.+| +|.|.+... |.-...+|.+.++.+-
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIg 75 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIG 75 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHh
Confidence 345677899999999999999999999999999998887 689998877 6678888888887665
No 237
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=90.06 E-value=0.92 Score=45.86 Aligned_cols=73 Identities=18% Similarity=0.143 Sum_probs=56.0
Q ss_pred cccCcEEEEEEEEEeeceEEEEEc--------CCeEEEEecccCCCcc--ccccccccccCCEEEEEEEEEccCCceEEE
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFN--------GGQQGLLHVSELSHEP--VSRVSDVVSVGQQLSLRCIGQDVRGNIKLS 750 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~--------~g~~Glvhisels~~~--v~~~~~~~~vGd~V~vkVl~id~~gri~LS 750 (974)
+.+|+|+.++|.++...-+-|+|. ....|++|..++-..- --++.+-|++||.|.++|++.+...+..||
T Consensus 66 P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LT 145 (193)
T KOG3409|consen 66 PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLT 145 (193)
T ss_pred CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEEE
Confidence 689999999999998887777764 2567999988874321 223455699999999999997666678888
Q ss_pred Eec
Q 002054 751 LKA 753 (974)
Q Consensus 751 ~K~ 753 (974)
.-+
T Consensus 146 tAe 148 (193)
T KOG3409|consen 146 TAE 148 (193)
T ss_pred Eec
Confidence 543
No 238
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=89.66 E-value=1.4 Score=38.17 Aligned_cols=59 Identities=25% Similarity=0.339 Sum_probs=46.1
Q ss_pred EEEEEEEEEeeceEE-EEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceE
Q 002054 686 IYKGVVTSVKEYGAF-VEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIK 748 (974)
Q Consensus 686 i~~G~V~~i~~~G~f-V~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~ 748 (974)
.+.|+|++..+.+.| |.+.+|.+-+.|+|= +...-.-.+.+||.|.|.+-..|. +|+|.
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~G----Kmr~~rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHISG----KIRMHYIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecC----cchhccEEECCCCEEEEEECcccCCcEeEE
Confidence 578999999999998 699999999999873 232223347889999999887776 67764
No 239
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=89.24 E-value=0.91 Score=46.76 Aligned_cols=58 Identities=19% Similarity=0.173 Sum_probs=46.7
Q ss_pred cccCCCCCEEEEEEEEEeCCeEEEEeCC----------CeEEEEecccCC-------CCCCCCCCEEEEEEEEEe
Q 002054 905 AKNLKLGTKVAAKVYQVRARGLVLDLGG----------GIRGMYRFENNE-------KKDFVVGDELLVKCSSFT 962 (974)
Q Consensus 905 ~~~~~vG~vV~G~V~~I~~~GvFV~L~~----------gv~Glih~se~~-------~~~f~vGd~V~vkVl~id 962 (974)
..-.+.|++|-|.|.++....+.|++-. -..|-+|.|+.. .+.|++||-|+|+|++.-
T Consensus 59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~ 133 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG 133 (188)
T ss_pred CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC
Confidence 3446889999999999999999987742 256778988552 567999999999999974
No 240
>PRK11712 ribonuclease G; Provisional
Probab=88.33 E-value=0.97 Score=54.01 Aligned_cols=55 Identities=13% Similarity=0.128 Sum_probs=46.2
Q ss_pred cCCCCCEEEEEEEEEeCC--eEEEEeCCCeEEEEecccCCC-------------------CCCCCCCEEEEEEEEE
Q 002054 907 NLKLGTKVAAKVYQVRAR--GLVLDLGGGIRGMYRFENNEK-------------------KDFVVGDELLVKCSSF 961 (974)
Q Consensus 907 ~~~vG~vV~G~V~~I~~~--GvFV~L~~gv~Glih~se~~~-------------------~~f~vGd~V~vkVl~i 961 (974)
...+|+++.|+|.+|.+- ++||+++.+-.||+|.++... +.+++||+|-|.|++=
T Consensus 35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke 110 (489)
T PRK11712 35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKD 110 (489)
T ss_pred ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeC
Confidence 346999999999999775 899999999999999997621 1288899999999863
No 241
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=88.18 E-value=1.9 Score=52.13 Aligned_cols=62 Identities=21% Similarity=0.262 Sum_probs=50.2
Q ss_pred cceeeeeccch-hhhhcCCCccchhhhhhhhCceEEeeC--CEEEEEecCHHHHHHHHHHHHHHh
Q 002054 616 RLATLKYDNDT-LRRLIGPLGALKRKIEEETGGRISVSD--GTLTVVAKNRSVMEKVLEKVDFII 677 (974)
Q Consensus 616 ~~~~~~i~~~k-i~~vIg~gGk~i~~i~~~~g~~Idi~d--g~v~i~~~~~~~~~~a~~~i~~l~ 677 (974)
.+.++.+|.|. -|.+||..|.|||.++.-||+.+=||| +.|.+++.|.---+-|+..++.|+
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~fdp~rreia~~~l~~li 268 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPVRREIARMALEKLI 268 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCCCeEEecCCchHHHHHHHHHHHHHH
Confidence 35567788865 499999999999999999999988884 688999988766666666666665
No 242
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=87.99 E-value=0.53 Score=48.86 Aligned_cols=59 Identities=34% Similarity=0.451 Sum_probs=48.5
Q ss_pred hhhhcCCCccchhhhhhhhCceEEeeCCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEE
Q 002054 627 LRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIY 687 (974)
Q Consensus 627 i~~vIg~gGk~i~~i~~~~g~~Idi~dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~ 687 (974)
.+.+||++|++-+.|++-||++|.+-+.+|.+.+. .+.++.|++.++.++ ...+.|.+|
T Consensus 113 kgRIIG~~GkTr~~IE~lt~~~I~V~g~tVaiiG~-~~~v~iAr~AVemli-~G~~h~~Vy 171 (194)
T COG1094 113 KGRIIGREGKTRRAIEELTGVYISVYGKTVAIIGG-FEQVEIAREAVEMLI-NGAPHGKVY 171 (194)
T ss_pred hceeeCCCchHHHHHHHHhCCeEEEeCcEEEEecC-hhhhHHHHHHHHHHH-cCCCchhHH
Confidence 58999999999999999999999998889999875 478888888888877 444555444
No 243
>PRK00106 hypothetical protein; Provisional
Probab=87.42 E-value=2.5 Score=51.08 Aligned_cols=62 Identities=21% Similarity=0.272 Sum_probs=51.0
Q ss_pred cceeeeeccch-hhhhcCCCccchhhhhhhhCceEEeeC--CEEEEEecCHHHHHHHHHHHHHHh
Q 002054 616 RLATLKYDNDT-LRRLIGPLGALKRKIEEETGGRISVSD--GTLTVVAKNRSVMEKVLEKVDFII 677 (974)
Q Consensus 616 ~~~~~~i~~~k-i~~vIg~gGk~i~~i~~~~g~~Idi~d--g~v~i~~~~~~~~~~a~~~i~~l~ 677 (974)
.+.++.+|.|. -|.+||..|.|||.++.-||+.+=||| +.|.+++.|.---+-|+..++.|+
T Consensus 225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~~v~lS~fdpvRReiAr~~le~Li 289 (535)
T PRK00106 225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPEVVVLSGFDPIRREIARMTLESLI 289 (535)
T ss_pred eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCCCeEEEeCCChHHHHHHHHHHHHHH
Confidence 35567788865 599999999999999999999988874 688999999777777777677665
No 244
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=87.24 E-value=2.5 Score=42.51 Aligned_cols=62 Identities=21% Similarity=0.275 Sum_probs=42.9
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCC----c-------cccccccccccCCEEEEEEEEEc
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSH----E-------PVSRVSDVVSVGQQLSLRCIGQD 742 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~----~-------~v~~~~~~~~vGd~V~vkVl~id 742 (974)
.+-.|++++|.|+++...|+|++.+| .+-++-.-.+.. . +..+-..+.++|.+|++||++.-
T Consensus 78 kpfKGEVvdgvV~~Vnk~G~F~~~GP-l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr 150 (170)
T KOG3298|consen 78 KPFKGEVVDGVVTKVNKMGVFARSGP-LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR 150 (170)
T ss_pred eecCCcEEEEEEEEEeeeeEEEeccc-eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence 45679999999999999999999965 444442211111 1 11122236899999999999964
No 245
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=86.83 E-value=1.2 Score=50.77 Aligned_cols=62 Identities=31% Similarity=0.455 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee
Q 002054 587 HAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS 652 (974)
Q Consensus 587 ~A~~~~~~I~~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~ 652 (974)
.+.++|+.|++.|.+.-...+. ..-.| ..+.-.....|.+||+.|+++++|..+||++|.|.
T Consensus 255 g~s~Ac~~ILeimqkEA~~~k~--~~e~p--Lk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 255 GTSKACKMILEIMQKEAVDDKV--AEEIP--LKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred chHHHHHHHHHHHHHhhhccch--hhhcc--hhhhhhcchhhhhhhhccccHHHHHhhcCCceeee
Confidence 5678899999999876554421 22212 22333455789999999999999999999998754
No 246
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=86.08 E-value=2.2 Score=50.88 Aligned_cols=93 Identities=17% Similarity=0.233 Sum_probs=62.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCcc---eeeeeccchhhhhcCCCccchhhhhhhhCceEEee------
Q 002054 582 CECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRL---ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS------ 652 (974)
Q Consensus 582 ~~al~~A~~~~~~I~~~m~~~i~~~~~~~~~~~p~~---~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~------ 652 (974)
.++++.|.+...+|+. ++.+.......-.+|.. ..+.|+.+|-+-+||+||.|||.|..++|+++...
T Consensus 284 ~d~ie~Aa~lI~eii~---~~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~ 360 (600)
T KOG1676|consen 284 VDQIEHAAELINEIIA---EAEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNG 360 (600)
T ss_pred HHHHHHHHHHHHHHHH---HHhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCC
Confidence 3455555544444443 34333323344455654 67789999999999999999999999999987642
Q ss_pred --CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054 653 --DGTLTVVAKNRSVMEKVLEKVDFII 677 (974)
Q Consensus 653 --dg~v~i~~~~~~~~~~a~~~i~~l~ 677 (974)
+.++.+..-++..++-|+..|+..+
T Consensus 361 ~~~ektf~IrG~~~QIdhAk~LIr~kv 387 (600)
T KOG1676|consen 361 NPKEKTFVIRGDKRQIDHAKQLIRDKV 387 (600)
T ss_pred CccceEEEEecCcccchHHHHHHHHHh
Confidence 2345555566678888887776443
No 247
>PRK12704 phosphodiesterase; Provisional
Probab=85.87 E-value=2.9 Score=50.64 Aligned_cols=62 Identities=19% Similarity=0.275 Sum_probs=49.2
Q ss_pred cceeeeeccchh-hhhcCCCccchhhhhhhhCceEEeeC--CEEEEEecCHHHHHHHHHHHHHHh
Q 002054 616 RLATLKYDNDTL-RRLIGPLGALKRKIEEETGGRISVSD--GTLTVVAKNRSVMEKVLEKVDFII 677 (974)
Q Consensus 616 ~~~~~~i~~~ki-~~vIg~gGk~i~~i~~~~g~~Idi~d--g~v~i~~~~~~~~~~a~~~i~~l~ 677 (974)
.+.++.+|.|.+ |.+||..|.|||.++.-||+.|=||| +.|.+++.+...-+-|+..++.++
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~~~~~rre~a~~~l~~l~ 274 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPIRREIARLALEKLV 274 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCCCeEEEecCChhhHHHHHHHHHHHH
Confidence 355677888665 99999999999999999999988884 688888888766566666666554
No 248
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=85.82 E-value=0.59 Score=50.22 Aligned_cols=58 Identities=19% Similarity=0.139 Sum_probs=51.6
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCC--CeEEEEecccCC-------CCCCCCCCEEEEEEEEEeCCCc
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGG--GIRGMYRFENNE-------KKDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~--gv~Glih~se~~-------~~~f~vGd~V~vkVl~id~~~~ 966 (974)
.++++|-+.|++|.+.|++|.|-+ ++.||+-.|+++ .+..++|-.=-|.|+.||++..
T Consensus 15 ev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekG 81 (304)
T KOG2916|consen 15 EVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKG 81 (304)
T ss_pred CcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCC
Confidence 589999999999999999999965 899999999996 4468899999999999997653
No 249
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=84.29 E-value=0.59 Score=39.57 Aligned_cols=36 Identities=25% Similarity=0.279 Sum_probs=32.1
Q ss_pred cceeeeeccchhhhhcCCCccchhhhhhhhCceEEe
Q 002054 616 RLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISV 651 (974)
Q Consensus 616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi 651 (974)
....+.++++.++..||++|.+|+.+..-+|.+|++
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 456778999999999999999999999999988875
No 250
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=83.61 E-value=4.3 Score=40.83 Aligned_cols=60 Identities=17% Similarity=0.098 Sum_probs=42.1
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEecc---------cC-C------CCCCCCCCEEEEEEEEEeCCCcee
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGG-GIRGMYRFE---------NN-E------KKDFVVGDELLVKCSSFTGKGIPV 968 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~-gv~Glih~s---------e~-~------~~~f~vGd~V~vkVl~id~~~~~~ 968 (974)
-.|++|.|+|+++...|+|++.++ .+-=+=|.. ++ | .+..++|.+|+++|++..-+....
T Consensus 80 fKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~~i 156 (170)
T KOG3298|consen 80 FKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDETEI 156 (170)
T ss_pred cCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEeeeeE
Confidence 389999999999999999999986 222111111 11 1 225778999999999887555443
No 251
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=83.30 E-value=5 Score=39.04 Aligned_cols=61 Identities=16% Similarity=0.178 Sum_probs=44.4
Q ss_pred cCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCc-c-----------c-cccccccccCCEEEEEEEEEcc
Q 002054 683 VGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE-P-----------V-SRVSDVVSVGQQLSLRCIGQDV 743 (974)
Q Consensus 683 ~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~-~-----------v-~~~~~~~~vGd~V~vkVl~id~ 743 (974)
+|+++.|+|.+-...|+.|.|.--.+-+||.+.|... . . ..-.-++..|+.|++||.++..
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence 6999999999999999999995556688988888642 1 1 2223347899999999999754
No 252
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=81.97 E-value=9.7 Score=32.42 Aligned_cols=55 Identities=16% Similarity=0.250 Sum_probs=40.1
Q ss_pred EEEEEEEEeC---CeEEEEeCCCeEEEEecccCCC---CCCCCCCEEEEEEEEEeCCCceee
Q 002054 914 VAAKVYQVRA---RGLVLDLGGGIRGMYRFENNEK---KDFVVGDELLVKCSSFTGKGIPVV 969 (974)
Q Consensus 914 V~G~V~~I~~---~GvFV~L~~gv~Glih~se~~~---~~f~vGd~V~vkVl~id~~~~~~~ 969 (974)
++|+|+...+ ||....-+++-+=++|.+++.. ..+.+||+|+..+.. ++++....
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~~l~~G~~V~F~~~~-~~~g~~A~ 61 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFRSLKEGDRVEFEVEE-GKKGPQAV 61 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSSTS--TTSEEEEEEEE-CTTSEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEeccccccccccccCCCCCEEEEEEEE-CCCCCEEE
Confidence 4799999964 7766555556699999998853 358999999999998 66555443
No 253
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=79.37 E-value=17 Score=30.94 Aligned_cols=54 Identities=22% Similarity=0.420 Sum_probs=38.0
Q ss_pred EEEEEEEEee---ceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCC
Q 002054 687 YKGVVTSVKE---YGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRG 745 (974)
Q Consensus 687 ~~G~V~~i~~---~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~g 745 (974)
.+|+|+...+ ||....-.++.+-|+|+|++.... ...++.|+.|+..+.. +++|
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~-~~~g 57 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE-GKKG 57 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE-CTTS
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEeccccccccc----cccCCCCCEEEEEEEE-CCCC
Confidence 3799999865 555554444558999999998764 2348899999999888 4444
No 254
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=79.11 E-value=10 Score=33.57 Aligned_cols=62 Identities=23% Similarity=0.328 Sum_probs=42.6
Q ss_pred EEEEEEEee-ceE-EEEE-cCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEecc
Q 002054 688 KGVVTSVKE-YGA-FVEF-NGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV 754 (974)
Q Consensus 688 ~G~V~~i~~-~G~-fV~l-~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K~~ 754 (974)
+|+|+...+ .|. |+.- .++.+-|+|+|.+...-. ..+..||.|+..+.. +++|+--..+..+
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~----~~l~~G~~V~f~~~~-~~~G~~A~~V~~~ 67 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGY----RTLKAGQSVQFDVHQ-GPKGNHASVIVPV 67 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCC----CCCCCCCEEEEEEEE-CCCCceeeEEEEC
Confidence 488888744 444 5655 346899999999975432 237889999999877 6677654444443
No 255
>PRK13764 ATPase; Provisional
Probab=78.69 E-value=0.99 Score=55.24 Aligned_cols=144 Identities=19% Similarity=0.184 Sum_probs=82.3
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee--CCEEEEEecCHHHH
Q 002054 589 HKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS--DGTLTVVAKNRSVM 666 (974)
Q Consensus 589 ~~~~~~I~~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~--dg~v~i~~~~~~~~ 666 (974)
+-+...|.+.+++.+.. ..+..-.-+....++++.+.|..+||.||++|++|.+..|..||+. +..- ..... ..
T Consensus 455 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~-~~~~~--~~ 530 (602)
T PRK13764 455 RLAEKEIEREIKRYLPG-PVEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP-GEEAE--EG 530 (602)
T ss_pred HHHHHHHHHHHHHhcCC-ceEEEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc-ccccc--cc
Confidence 33445666777777732 2233222345567889999999999999999999999999999975 2110 00000 00
Q ss_pred HHHHHHHHHHhhcccccCcEEEEEEEEEeeceEEEE-EcCCeEEEEecccCCCccccccccccccCCEEEEEE
Q 002054 667 EKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVE-FNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRC 738 (974)
Q Consensus 667 ~~a~~~i~~l~~~~~~~G~i~~G~V~~i~~~G~fV~-l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkV 738 (974)
.... ..+.-..--+.+|.-+.|+.+.|.-.|-|+- -.-+..|-++++.=+.- -+.+.+.++-|..|.+++
T Consensus 531 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~g~i~~~~~~~~-~~~~~~~~~~~~~i~~~~ 601 (602)
T PRK13764 531 EEVT-VEETKKHVILIVGPDYAGKTVDVYAGGEYLFTATVSRKGEIKVAKNSAI-AKELLRAIDEGEDIRVRP 601 (602)
T ss_pred Cccc-eEEeccEEEEEcChhhCCCeEEEEECCEEEEEEEcCCCceEEeccCChH-HHHHHHHHhCCCcEEEee
Confidence 0000 0000000124566667777777765555432 22356677777653321 233444577788887764
No 256
>PRK15464 cold shock-like protein CspH; Provisional
Probab=78.31 E-value=9.4 Score=33.39 Aligned_cols=55 Identities=18% Similarity=0.385 Sum_probs=40.3
Q ss_pred EEEEEEEEee-ceE-EEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCc
Q 002054 687 YKGVVTSVKE-YGA-FVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGN 746 (974)
Q Consensus 687 ~~G~V~~i~~-~G~-fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gr 746 (974)
++|+|+...+ .|. |+.-.. +.+-|+|+|.+..... ..+.+||.|+..+.. +++|.
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~----~~l~~G~~V~f~v~~-~~kG~ 62 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDA----EVLIPGLRVEFCRVN-GLRGP 62 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCC----CCCCCCCEEEEEEEE-CCCCc
Confidence 5899999855 455 676544 5789999999965432 238899999999877 55664
No 257
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=76.70 E-value=2 Score=51.25 Aligned_cols=64 Identities=28% Similarity=0.385 Sum_probs=49.2
Q ss_pred CcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee-C-------CEEEEEecCHHHHHHHHHHHHHHhhc
Q 002054 615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-D-------GTLTVVAKNRSVMEKVLEKVDFIIGR 679 (974)
Q Consensus 615 p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-d-------g~v~i~~~~~~~~~~a~~~i~~l~~~ 679 (974)
|....+-++-++++.+||+||++|++|.++||++|-+- + -.|.|.. ...+..+|...|-..+.+
T Consensus 137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG-~~~av~~al~~Is~~L~~ 208 (485)
T KOG2190|consen 137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISG-EPDAVKKALVQISSRLLE 208 (485)
T ss_pred ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcC-chHHHHHHHHHHHHHHHh
Confidence 67778889999999999999999999999999998764 2 2345544 446777777777655533
No 258
>PRK12705 hypothetical protein; Provisional
Probab=76.64 E-value=6.1 Score=47.51 Aligned_cols=62 Identities=19% Similarity=0.235 Sum_probs=47.4
Q ss_pred cceeeeeccch-hhhhcCCCccchhhhhhhhCceEEeeC--CEEEEEecCHHHHHHHHHHHHHHh
Q 002054 616 RLATLKYDNDT-LRRLIGPLGALKRKIEEETGGRISVSD--GTLTVVAKNRSVMEKVLEKVDFII 677 (974)
Q Consensus 616 ~~~~~~i~~~k-i~~vIg~gGk~i~~i~~~~g~~Idi~d--g~v~i~~~~~~~~~~a~~~i~~l~ 677 (974)
.+.++.+|.|. -|.+||..|.|||.++..||+.+-||| +.|.++..+...-+.+...++.++
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~~V~ls~fdp~rreia~~~l~~Li 262 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTPEAVVISSFNPIRREIARLTLEKLL 262 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCccchhhcccCccchHHHHHHHHHHH
Confidence 34566777765 599999999999999999999988874 567777777666666666666554
No 259
>PRK10943 cold shock-like protein CspC; Provisional
Probab=75.64 E-value=15 Score=31.97 Aligned_cols=55 Identities=22% Similarity=0.355 Sum_probs=39.3
Q ss_pred EEEEEEEEEee-ceE-EEEEc-CCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCC
Q 002054 686 IYKGVVTSVKE-YGA-FVEFN-GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRG 745 (974)
Q Consensus 686 i~~G~V~~i~~-~G~-fV~l~-~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~g 745 (974)
.++|+|+...+ .|. |++-. ++.+-|+|+|.+..... ..+.+||.|...+.. +++|
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~----~~l~~G~~V~f~~~~-~~~g 60 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGF----KTLAEGQNVEFEIQD-GQKG 60 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCC----CCCCCCCEEEEEEEE-CCCC
Confidence 57899998854 444 56553 46799999999975432 237889999998766 4444
No 260
>PRK09890 cold shock protein CspG; Provisional
Probab=74.90 E-value=17 Score=31.72 Aligned_cols=55 Identities=15% Similarity=0.289 Sum_probs=38.7
Q ss_pred EEEEEEEEee-ceE-EEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCc
Q 002054 687 YKGVVTSVKE-YGA-FVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGN 746 (974)
Q Consensus 687 ~~G~V~~i~~-~G~-fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gr 746 (974)
++|+|+...+ .|. |+.-.. +.+-|+|+|.+...-++ .+++||.|+..+.. +++|.
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~----~l~~G~~V~f~~~~-~~~G~ 62 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFR----TLNENQKVEFSIEQ-GQRGP 62 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCC----CCCCCCEEEEEEEE-CCCCc
Confidence 5899988754 343 555544 57899999999765322 37889999997655 55554
No 261
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=74.70 E-value=15 Score=31.91 Aligned_cols=55 Identities=22% Similarity=0.397 Sum_probs=38.9
Q ss_pred EEEEEEEEEee-ceE-EEEE-cCCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCC
Q 002054 686 IYKGVVTSVKE-YGA-FVEF-NGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRG 745 (974)
Q Consensus 686 i~~G~V~~i~~-~G~-fV~l-~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~g 745 (974)
.++|+|+...+ .|. |+.- .++.+-|+|+|.+..... ..+.+||.|...+.. +++|
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~-~~~G 60 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGF----KTLAEGQRVEFEITN-GAKG 60 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCC----CCCCCCCEEEEEEEE-CCCC
Confidence 47899998754 344 5555 445789999999965432 237889999998766 4455
No 262
>PRK15463 cold shock-like protein CspF; Provisional
Probab=74.58 E-value=8.8 Score=33.54 Aligned_cols=54 Identities=19% Similarity=0.363 Sum_probs=39.2
Q ss_pred EEEEEEEEee-ceE-EEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEccCC
Q 002054 687 YKGVVTSVKE-YGA-FVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRG 745 (974)
Q Consensus 687 ~~G~V~~i~~-~G~-fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~g 745 (974)
++|+|+...+ .|. |++-.. +.+-|+|+|.+...... .+++||.|...+.. +.+|
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~----~l~~G~~V~f~v~~-~~~G 61 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAE----ELTTGLRVEFCRIN-GLRG 61 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCC----CCCCCCEEEEEEEE-CCCC
Confidence 4799998855 454 666544 57899999999754222 37899999998766 5556
No 263
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=73.68 E-value=19 Score=31.99 Aligned_cols=65 Identities=23% Similarity=0.295 Sum_probs=49.0
Q ss_pred CcEEEEEEEEEeeceEE-EEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEe
Q 002054 684 GGIYKGVVTSVKEYGAF-VEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLK 752 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~f-V~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K 752 (974)
.-.+.|+|.+..+.+.| |.+.+|..-+-|++-=-.. -.-.+.+||.|.|.....|. +|+|..-.+
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~----~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRK----NRIRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchh----eeEEeCCCCEEEEEecccccccccEEEEec
Confidence 34688999999999887 8999898888888742222 12237899999999998885 678766543
No 264
>PRK14998 cold shock-like protein CspD; Provisional
Probab=73.58 E-value=16 Score=32.16 Aligned_cols=60 Identities=20% Similarity=0.301 Sum_probs=41.4
Q ss_pred EEEEEEEee-ceE-EEEEc-CCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEEEEe
Q 002054 688 KGVVTSVKE-YGA-FVEFN-GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK 752 (974)
Q Consensus 688 ~G~V~~i~~-~G~-fV~l~-~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K 752 (974)
+|+|+-... .|. |+.-. ++.+-|+|+|.+..... ..+..||.|+..+.. +++|+.-....
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~----~~l~~G~~V~f~~~~-~~~G~~A~~V~ 65 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGY----RTLKAGQSVRFDVHQ-GPKGNHASVIV 65 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCC----CCCCCCCEEEEEEEE-CCCCceeEEEE
Confidence 488888744 444 66554 46789999999965432 347889999999877 56776444443
No 265
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=73.47 E-value=3.7 Score=47.90 Aligned_cols=60 Identities=20% Similarity=0.268 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHhcCCCCCCCCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee
Q 002054 592 RLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS 652 (974)
Q Consensus 592 ~~~I~~~m~~~i~~~~~~~~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~ 652 (974)
-..|.+.+++.+.. +.+..-.-+....+++|++.|+.+||.+|++|++|.+.+|.+|++.
T Consensus 463 ~~~i~~~i~r~~p~-~~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~ 522 (604)
T COG1855 463 EEEIEREIKRYLPG-DVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVK 522 (604)
T ss_pred HHHHHHHHHHhCCC-CceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEE
Confidence 34456667777764 2333323455678889999999999999999999999999999874
No 266
>PRK15464 cold shock-like protein CspH; Provisional
Probab=72.31 E-value=19 Score=31.50 Aligned_cols=57 Identities=7% Similarity=-0.025 Sum_probs=42.6
Q ss_pred EEEEEEEEeC-CeE-EEEeCC-CeEEEEecccCC---CCCCCCCCEEEEEEEEEeCCCceeeee
Q 002054 914 VAAKVYQVRA-RGL-VLDLGG-GIRGMYRFENNE---KKDFVVGDELLVKCSSFTGKGIPVVSL 971 (974)
Q Consensus 914 V~G~V~~I~~-~Gv-FV~L~~-gv~Glih~se~~---~~~f~vGd~V~vkVl~id~~~~~~~~~ 971 (974)
++|+|+...+ .|. ||+.++ +=+-|+|++.+. .+.+.+||+|+..|.. +++|.....+
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~l~~G~~V~f~v~~-~~kG~~A~~v 67 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVN-GLRGPTAANV 67 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEEEEEEE-CCCCceeEEE
Confidence 4899999954 465 787766 579999999774 3469999999998865 4556555544
No 267
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=71.49 E-value=12 Score=33.97 Aligned_cols=52 Identities=13% Similarity=0.132 Sum_probs=42.3
Q ss_pred EEEEEEEEEeCCeEEE-EeCCCeEEEEecc-cCC--CCCCCCCCEEEEEEEEEeCC
Q 002054 913 KVAAKVYQVRARGLVL-DLGGGIRGMYRFE-NNE--KKDFVVGDELLVKCSSFTGK 964 (974)
Q Consensus 913 vV~G~V~~I~~~GvFV-~L~~gv~Glih~s-e~~--~~~f~vGd~V~vkVl~id~~ 964 (974)
.+.|+|....+.+.|. +|+||..=++|++ .+. .-...+||+|.|.+...|..
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~spYDlt 63 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELSPYDLT 63 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEECcccCC
Confidence 5899999998888886 8999999999998 332 23467999999999988844
No 268
>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=70.84 E-value=14 Score=31.02 Aligned_cols=53 Identities=21% Similarity=0.194 Sum_probs=38.1
Q ss_pred CCEEEEEEEEEeCCeEEEEeCCCeEEEEe---cccCCCCCCCCCCEEEEEEEEEeC
Q 002054 911 GTKVAAKVYQVRARGLVLDLGGGIRGMYR---FENNEKKDFVVGDELLVKCSSFTG 963 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV~L~~gv~Glih---~se~~~~~f~vGd~V~vkVl~id~ 963 (974)
|+..+=.|..+++-|-.+--++.+.|+.- .-+.....+.+|++++|.|+.||-
T Consensus 1 G~~L~LvV~~~~edgsv~fs~g~v~g~tv~AtryH~~g~nl~pGqK~kaviLhvD~ 56 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEGVNVTPGCKLKAVILHVDF 56 (65)
T ss_pred CceEEEEEeeeccCCcEEEecCCcCCcEEEEEEEEecceecCCCceeEEEEEEEee
Confidence 67777788887666665555666666622 224456678999999999999993
No 269
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=70.62 E-value=14 Score=32.18 Aligned_cols=53 Identities=15% Similarity=0.198 Sum_probs=43.0
Q ss_pred EEEEEEEEEeCCeEEE-EeCCCeEEEEecc-cCC--CCCCCCCCEEEEEEEEEeCCC
Q 002054 913 KVAAKVYQVRARGLVL-DLGGGIRGMYRFE-NNE--KKDFVVGDELLVKCSSFTGKG 965 (974)
Q Consensus 913 vV~G~V~~I~~~GvFV-~L~~gv~Glih~s-e~~--~~~f~vGd~V~vkVl~id~~~ 965 (974)
.+.|+|.+..+.|.|- ++++|..=++|++ .+. .-...+||.|.+.....|...
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve~spyd~tk 62 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDKVKVELSPYDLTR 62 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhccEEECCCCEEEEEECcccCCc
Confidence 5789999998888886 8999999999998 332 234779999999998887543
No 270
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=66.25 E-value=12 Score=31.39 Aligned_cols=48 Identities=27% Similarity=0.457 Sum_probs=35.0
Q ss_pred CEEEEEEEEEeCCe----EEEEeCCC--eEEEEecccCCCCCCCCCCEEEEEEE
Q 002054 912 TKVAAKVYQVRARG----LVLDLGGG--IRGMYRFENNEKKDFVVGDELLVKCS 959 (974)
Q Consensus 912 ~vV~G~V~~I~~~G----vFV~L~~g--v~Glih~se~~~~~f~vGd~V~vkVl 959 (974)
..+.|+|..|++.| +.++++++ +...+.......=.+++||+|.+.+-
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~~L~L~~G~~V~~~ik 58 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAEELGLKPGDEVYASIK 58 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHHHCT-STT-EEEEEE-
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHHHcCCCCCCEEEEEEe
Confidence 36899999999999 77788875 67777766443346889999998763
No 271
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=65.98 E-value=17 Score=32.40 Aligned_cols=58 Identities=14% Similarity=0.158 Sum_probs=43.7
Q ss_pred EEEEEEEEeeceEE-EEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEE
Q 002054 687 YKGVVTSVKEYGAF-VEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKL 749 (974)
Q Consensus 687 ~~G~V~~i~~~G~f-V~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~L 749 (974)
..|+|++....+.| |.+.+|..-+.|++- +++. .-.++.||.|.|.....|. +|+|..
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g~~~la~i~g----K~rk-~iwI~~GD~V~Ve~~~~d~~kg~Iv~ 61 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDGKKRLCRIRG----KMRK-RVWINEGDIVLVAPWDFQDDKADIIY 61 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCCCEEEEEEch----hhcc-cEEEcCCCEEEEEeccccCCEEEEEE
Confidence 57899999999887 788889998888873 2333 3448899999998777654 566544
No 272
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=65.47 E-value=35 Score=29.70 Aligned_cols=54 Identities=19% Similarity=0.370 Sum_probs=37.8
Q ss_pred EEEEEEEEee-ceE-EEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEccCC
Q 002054 687 YKGVVTSVKE-YGA-FVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRG 745 (974)
Q Consensus 687 ~~G~V~~i~~-~G~-fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~g 745 (974)
.+|+|+...+ .|. |+.-.. +.+-|+|+|.+..... ..+++||.|+..+.. +++|
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~-~~~G 61 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGY----KSLDEGQKVSFTIES-GAKG 61 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccCC----CCCCCCCEEEEEEEE-CCCC
Confidence 3799988743 333 555544 5789999999975422 337899999998766 4455
No 273
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=65.34 E-value=25 Score=30.50 Aligned_cols=54 Identities=17% Similarity=0.273 Sum_probs=37.4
Q ss_pred EEEEEEEee-ceE-EEEEc-CCeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCc
Q 002054 688 KGVVTSVKE-YGA-FVEFN-GGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGN 746 (974)
Q Consensus 688 ~G~V~~i~~-~G~-fV~l~-~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gr 746 (974)
+|+|+-..+ .|. |+.-. ++.+-|+|+|.+..... ..+++||.|+..+.. +++|.
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~----~~l~~G~~V~f~~~~-~~~G~ 59 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGY----RTLKAGQKVQFEVVQ-GPKGA 59 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCC----CCCCCCCEEEEEEEE-CCCCc
Confidence 488888743 444 55554 46889999999965422 337899999998766 44554
No 274
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=65.18 E-value=24 Score=34.35 Aligned_cols=54 Identities=19% Similarity=0.110 Sum_probs=38.7
Q ss_pred CCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC--------------------CCCCCCCCEEEEEEEEEeC
Q 002054 910 LGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE--------------------KKDFVVGDELLVKCSSFTG 963 (974)
Q Consensus 910 vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~--------------------~~~f~vGd~V~vkVl~id~ 963 (974)
+|+++.|+|++-.+.|+.|.|+===+=+||.+.++ .-.|..|++|+.||.++.-
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence 79999999999999999999952223456666442 0136899999999999875
No 275
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=64.15 E-value=29 Score=32.56 Aligned_cols=55 Identities=16% Similarity=0.246 Sum_probs=44.4
Q ss_pred cccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEc
Q 002054 681 IEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQD 742 (974)
Q Consensus 681 ~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id 742 (974)
...|.++.|+|..+.+.-+|++++....+.+.-.+... +.+..|..|++++....
T Consensus 21 ~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdlE 75 (104)
T PF10246_consen 21 DPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNG-------EKYVRGSRVRLRLKDLE 75 (104)
T ss_pred CccCCEEEEEEEEEecCceEEEeCCceeEEEecccccc-------cccccCCEEEEEECCHh
Confidence 35899999999999999999999888889987554422 33778999999886643
No 276
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=63.44 E-value=23 Score=33.20 Aligned_cols=62 Identities=13% Similarity=0.111 Sum_probs=46.9
Q ss_pred CcEEEEEEEEEeeceEE-EEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054 684 GGIYKGVVTSVKEYGAF-VEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS 750 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~f-V~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS 750 (974)
...+.|+|+.....+.| |.+.+|..-+.|++- +++. .-.++.||.|.|.....|. +|+|..-
T Consensus 20 e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~G----K~Rk-~IwI~~GD~VlVe~~~~~~~kg~Iv~r 83 (100)
T PRK04012 20 EGEVFGVVEQMLGANRVRVRCMDGVERMGRIPG----KMKK-RMWIREGDVVIVAPWDFQDEKADIIWR 83 (100)
T ss_pred CCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEch----hhcc-cEEecCCCEEEEEecccCCCEEEEEEE
Confidence 34588999999999987 688889999998873 3333 3458899999999877765 4555443
No 277
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=61.75 E-value=7.1 Score=44.84 Aligned_cols=59 Identities=20% Similarity=0.316 Sum_probs=43.2
Q ss_pred eeeeeccchhhhhcCCCccchhhhhhhhCceEEee--C--CEEEEEecCHHHHHHHHHHHHHHh
Q 002054 618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS--D--GTLTVVAKNRSVMEKVLEKVDFII 677 (974)
Q Consensus 618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~--d--g~v~i~~~~~~~~~~a~~~i~~l~ 677 (974)
..+.|..+..+.+||-||.+|+.|+..|+++|.|. + -.|+|++.+ ..-.+|+..++...
T Consensus 49 lcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~~-~m~~kaka~id~~~ 111 (629)
T KOG0336|consen 49 LCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGIN-HMRKKAKASIDRGQ 111 (629)
T ss_pred hhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCceeEEEEechH-HHHHHHHhhHhhhh
Confidence 46677888999999999999999999999999886 3 356776654 23334444454433
No 278
>PRK00468 hypothetical protein; Provisional
Probab=61.51 E-value=4.3 Score=35.99 Aligned_cols=25 Identities=24% Similarity=0.482 Sum_probs=21.8
Q ss_pred eeeeeccchhhhhcCCCccchhhhh
Q 002054 618 ATLKYDNDTLRRLIGPLGALKRKIE 642 (974)
Q Consensus 618 ~~~~i~~~ki~~vIg~gGk~i~~i~ 642 (974)
..+.++++.+|++||.+|++|+.|.
T Consensus 32 ~~l~v~~~D~GrVIGk~Gr~i~AIR 56 (75)
T PRK00468 32 LELKVAPEDMGKVIGKQGRIAKAIR 56 (75)
T ss_pred EEEEEChhhCcceecCCChhHHHHH
Confidence 4567899999999999999999765
No 279
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=61.42 E-value=41 Score=28.42 Aligned_cols=53 Identities=19% Similarity=0.412 Sum_probs=37.5
Q ss_pred EEEEEEEee---ceEEEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEccCCc
Q 002054 688 KGVVTSVKE---YGAFVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGN 746 (974)
Q Consensus 688 ~G~V~~i~~---~G~fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gr 746 (974)
.|+|+...+ || |+.-.. +.+-|+|.+++...- ...+++||.|...+.. +.+|.
T Consensus 2 ~G~Vk~~~~~kGfG-FI~~~~~g~diffh~~~~~~~~----~~~~~~G~~V~f~~~~-~~~g~ 58 (65)
T cd04458 2 TGTVKWFDDEKGFG-FITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEE-GDKGP 58 (65)
T ss_pred cEEEEEEECCCCeE-EEecCCCCcCEEEEhhHhhccC----CCcCCCCCEEEEEEEE-CCCCC
Confidence 588888755 44 454444 789999999997652 2347899999998776 34443
No 280
>PRK02821 hypothetical protein; Provisional
Probab=59.76 E-value=4.9 Score=35.84 Aligned_cols=28 Identities=21% Similarity=0.350 Sum_probs=23.5
Q ss_pred cceeeeeccchhhhhcCCCccchhhhhh
Q 002054 616 RLATLKYDNDTLRRLIGPLGALKRKIEE 643 (974)
Q Consensus 616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~ 643 (974)
....+.++++.+|++||.+|++|+.|..
T Consensus 31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRt 58 (77)
T PRK02821 31 RTLEVRVHPDDLGKVIGRGGRTATALRT 58 (77)
T ss_pred EEEEEEEChhhCcceeCCCCchHHHHHH
Confidence 3456678999999999999999997653
No 281
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=59.48 E-value=12 Score=45.19 Aligned_cols=60 Identities=18% Similarity=0.186 Sum_probs=49.9
Q ss_pred cccCCCCCEEEEEEEEEeCC--eEEEEeCCCeEEEEecccCCC-----------CCCCCCCEEEEEEEEEeCC
Q 002054 905 AKNLKLGTKVAAKVYQVRAR--GLVLDLGGGIRGMYRFENNEK-----------KDFVVGDELLVKCSSFTGK 964 (974)
Q Consensus 905 ~~~~~vG~vV~G~V~~I~~~--GvFV~L~~gv~Glih~se~~~-----------~~f~vGd~V~vkVl~id~~ 964 (974)
.....+|.+..|+|.+|.+- .+||+++.+=.||+|.++... ..++.||.+-|.|+.-...
T Consensus 32 ~~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G 104 (487)
T COG1530 32 AKEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVPYFRAVLEEKIKVRLRGGQATLVQVVKEPRG 104 (487)
T ss_pred CcEeeecCceEEEecccCccchhheeeccCCccceEEecccchhhhhcccccceeeecCCceEEEEEEeecCc
Confidence 34567899999999999775 799999999999999998854 4688999999888776543
No 282
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=58.39 E-value=17 Score=40.62 Aligned_cols=60 Identities=20% Similarity=0.247 Sum_probs=43.9
Q ss_pred eeeeeccchhhhhcCCCccchhhhhhhhCceEEee---------CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054 618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS---------DGTLTVVAKNRSVMEKVLEKVDFII 677 (974)
Q Consensus 618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~---------dg~v~i~~~~~~~~~~a~~~i~~l~ 677 (974)
..+-|+.-.-+.+||+||.+|.+++.++|+.|... ..+|.+..-.-+.+....+.|.+.+
T Consensus 41 ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKi 109 (402)
T KOG2191|consen 41 LKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKI 109 (402)
T ss_pred EEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHH
Confidence 34557778889999999999999999999988643 1456666666666666655554333
No 283
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=58.12 E-value=20 Score=35.18 Aligned_cols=54 Identities=15% Similarity=0.327 Sum_probs=49.4
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCCCCCCCCEEEEEEEEEe
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFT 962 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~~f~vGd~V~vkVl~id 962 (974)
..|.+|.|+|-.|-..-+|++++..+...|..-....+.|+-|-+|.-++++..
T Consensus 81 a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n~e~Y~~GaRVrlRl~DlE 134 (173)
T KOG4078|consen 81 AKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALNGEAYQKGARVRLRLIDLE 134 (173)
T ss_pred cCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcCHHHhhcCceEEEEEcChh
Confidence 479999999999988899999999999999998887889999999999998765
No 284
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=57.99 E-value=7.5 Score=40.54 Aligned_cols=54 Identities=17% Similarity=0.394 Sum_probs=40.5
Q ss_pred chhhhhcCCCccchhhhhhhhCceEEee-CCEE---EEEecCHHHHHHHHHHHHHHhh
Q 002054 625 DTLRRLIGPLGALKRKIEEETGGRISVS-DGTL---TVVAKNRSVMEKVLEKVDFIIG 678 (974)
Q Consensus 625 ~ki~~vIg~gGk~i~~i~~~~g~~Idi~-dg~v---~i~~~~~~~~~~a~~~i~~l~~ 678 (974)
..+|-+|||.|.+.+.+++.++++|.|- .|.+ ++.+...+.+..+-+.+.-++.
T Consensus 163 NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~ 220 (269)
T COG5176 163 NFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIE 220 (269)
T ss_pred ceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhh
Confidence 4689999999999999999999999986 4443 5555556666666655655553
No 285
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=56.23 E-value=36 Score=28.94 Aligned_cols=52 Identities=13% Similarity=0.178 Sum_probs=39.7
Q ss_pred CEEEEEEEEEeCCeEEEEeCCCeEEEEecccCCCCCCCCCCEEEEEEEEEeCC
Q 002054 912 TKVAAKVYQVRARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGK 964 (974)
Q Consensus 912 ~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~~~~f~vGd~V~vkVl~id~~ 964 (974)
+.++|+|.+|.+...-|.|++|=.=-+|. +..-..+++|.+|.+.-...+.+
T Consensus 3 ~~veG~I~~id~~~~titLdDGksy~lp~-ef~~~~L~~G~kV~V~yd~~~gk 54 (61)
T PF07076_consen 3 ADVEGTIKSIDPETMTITLDDGKSYKLPE-EFDFDGLKPGMKVVVFYDEVDGK 54 (61)
T ss_pred ccceEEEEEEcCCceEEEecCCCEEECCC-cccccccCCCCEEEEEEEccCCc
Confidence 45899999999999999999885444443 33356799999998877776643
No 286
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=55.27 E-value=46 Score=35.41 Aligned_cols=69 Identities=16% Similarity=0.148 Sum_probs=47.6
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCC---ccccccccccc--cCCEEEEEEEEEccCCceEEEEec
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSH---EPVSRVSDVVS--VGQQLSLRCIGQDVRGNIKLSLKA 753 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~---~~v~~~~~~~~--vGd~V~vkVl~id~~gri~LS~K~ 753 (974)
|++|.|++.+..+-|.-+++. |....+|.++|.. ..++++...|- .--.|+++++..+.....+||=++
T Consensus 75 Ge~y~G~l~s~~~~G~~~~v~-G~~~~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~~~~~rltd~q 148 (225)
T PF09883_consen 75 GETYVGTLISWDEDGYGVDVD-GIFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDGIEARLTDEQ 148 (225)
T ss_pred CceEEEEEEeecccceEEEee-cccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEcccCcccccCHHH
Confidence 999999999999988888886 7888888888832 22333333343 234566888887655555565444
No 287
>COG1278 CspC Cold shock proteins [Transcription]
Probab=55.25 E-value=34 Score=29.75 Aligned_cols=57 Identities=18% Similarity=0.317 Sum_probs=36.0
Q ss_pred EEEEEEEee-ceE-EEEEcCC-eEEEEecccCCCccccccccccccCCEEEEEEEEEccCCceEE
Q 002054 688 KGVVTSVKE-YGA-FVEFNGG-QQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKL 749 (974)
Q Consensus 688 ~G~V~~i~~-~G~-fV~l~~g-~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~~gri~L 749 (974)
.|+|+-..+ .|. |+.=.+| .+-|+|+|.+-....+. |..||+|...+.. +.+|..-.
T Consensus 3 ~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~g~~~----L~eGQ~V~f~~~~-g~kgp~A~ 62 (67)
T COG1278 3 TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRT----LREGQKVEFEVEQ-GRKGPSAA 62 (67)
T ss_pred cceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccCCCcc----cCCCCEEEEEEec-CCCCCcee
Confidence 456655532 222 4443344 78999999996554433 7889999998876 55554433
No 288
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=55.22 E-value=60 Score=28.73 Aligned_cols=55 Identities=13% Similarity=0.172 Sum_probs=39.9
Q ss_pred EEEEEEEeC-CeE-EEEeCC-CeEEEEecccCC---CCCCCCCCEEEEEEEEEeCCCceeee
Q 002054 915 AAKVYQVRA-RGL-VLDLGG-GIRGMYRFENNE---KKDFVVGDELLVKCSSFTGKGIPVVS 970 (974)
Q Consensus 915 ~G~V~~I~~-~Gv-FV~L~~-gv~Glih~se~~---~~~f~vGd~V~vkVl~id~~~~~~~~ 970 (974)
+|+|+...+ .|. ||..++ +-+-|+|+|.+. ...+.+||.|+..+.. +++|.....
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~~~l~~G~~V~f~~~~-~~~G~~A~~ 63 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQ-GPKGNHASV 63 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEE-CCCCceeeE
Confidence 588988844 454 666655 789999999874 2569999999998765 555655443
No 289
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=54.20 E-value=21 Score=38.65 Aligned_cols=57 Identities=16% Similarity=0.297 Sum_probs=43.6
Q ss_pred eeeeeccchhhhhcCCCccchhhhhhhhCceEEee---C---CEEEEEecCHHHHHHHHHHHH
Q 002054 618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS---D---GTLTVVAKNRSVMEKVLEKVD 674 (974)
Q Consensus 618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~---d---g~v~i~~~~~~~~~~a~~~i~ 674 (974)
..+.|+.|.=+.+||.||..|+.|..|.|+.|.++ + .++......++.++.|.-..+
T Consensus 317 aQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQ 379 (390)
T KOG2192|consen 317 AQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQ 379 (390)
T ss_pred eeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHH
Confidence 45679999999999999999999999999999886 2 344444445667777764444
No 290
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=53.83 E-value=68 Score=27.92 Aligned_cols=52 Identities=15% Similarity=0.158 Sum_probs=38.3
Q ss_pred EEEEEEEEe---CCeEEEEeCC-CeEEEEecccCCC---CCCCCCCEEEEEEEEEeCCCce
Q 002054 914 VAAKVYQVR---ARGLVLDLGG-GIRGMYRFENNEK---KDFVVGDELLVKCSSFTGKGIP 967 (974)
Q Consensus 914 V~G~V~~I~---~~GvFV~L~~-gv~Glih~se~~~---~~f~vGd~V~vkVl~id~~~~~ 967 (974)
++|+|+... -|| ||+-++ +-+=|+|+|.+.. ..+++||.|+..+.. +++|..
T Consensus 5 ~~G~Vk~f~~~kGfG-FI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~-~~~G~~ 63 (70)
T PRK10354 5 MTGIVKWFNADKGFG-FITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIES-GAKGPA 63 (70)
T ss_pred ceEEEEEEeCCCCcE-EEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEE-CCCCce
Confidence 489999884 455 566655 5899999998853 468999999997655 555643
No 291
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=53.59 E-value=49 Score=28.76 Aligned_cols=52 Identities=15% Similarity=0.173 Sum_probs=38.3
Q ss_pred EEEEEEEEEeC---CeEEEEeCC-CeEEEEecccCCC---CCCCCCCEEEEEEEEEeCCCc
Q 002054 913 KVAAKVYQVRA---RGLVLDLGG-GIRGMYRFENNEK---KDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 913 vV~G~V~~I~~---~GvFV~L~~-gv~Glih~se~~~---~~f~vGd~V~vkVl~id~~~~ 966 (974)
.++|+|+...+ || ||+-++ +-+=|+|+|.+.. ..+++||.|...+..=+ +|.
T Consensus 3 ~~~G~Vk~f~~~kGyG-FI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~-~G~ 61 (69)
T PRK09507 3 KIKGNVKWFNESKGFG-FITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGA-KGP 61 (69)
T ss_pred ccceEEEEEeCCCCcE-EEecCCCCeeEEEEeecccccCCCCCCCCCEEEEEEEECC-CCc
Confidence 46799999854 55 566655 5799999998853 46899999999766544 553
No 292
>PRK10943 cold shock-like protein CspC; Provisional
Probab=53.19 E-value=62 Score=28.11 Aligned_cols=54 Identities=15% Similarity=0.211 Sum_probs=39.3
Q ss_pred EEEEEEEEEeC-CeE-EEEeCC-CeEEEEecccCCC---CCCCCCCEEEEEEEEEeCCCce
Q 002054 913 KVAAKVYQVRA-RGL-VLDLGG-GIRGMYRFENNEK---KDFVVGDELLVKCSSFTGKGIP 967 (974)
Q Consensus 913 vV~G~V~~I~~-~Gv-FV~L~~-gv~Glih~se~~~---~~f~vGd~V~vkVl~id~~~~~ 967 (974)
.++|+|+...+ .|. ||+-++ +-+=|+|+|.+.. ..+.+||.|...+..=+ +|..
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~l~~G~~V~f~~~~~~-~g~~ 62 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQ-KGPA 62 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCCCCCCCEEEEEEEECC-CCce
Confidence 57899999854 343 666655 6899999998753 46899999999876533 4543
No 293
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=52.79 E-value=12 Score=40.41 Aligned_cols=75 Identities=19% Similarity=0.240 Sum_probs=61.1
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCC--c--cc------cccccccccCCEEEEEEEEEccCCceEE
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSH--E--PV------SRVSDVVSVGQQLSLRCIGQDVRGNIKL 749 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~--~--~v------~~~~~~~~vGd~V~vkVl~id~~gri~L 749 (974)
.+++|+++-|+|..|...-+-|++....++.+..|.+-- . |- .+.+++|+.||-|.+.|-.+-.+|-+.|
T Consensus 82 ~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~sL 161 (301)
T KOG3013|consen 82 APEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLSL 161 (301)
T ss_pred CCccCCEEEEEeeeeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhccCCeEEE
Confidence 479999999999999999999999888999998887632 1 11 2467789999999999888766898888
Q ss_pred EEecc
Q 002054 750 SLKAV 754 (974)
Q Consensus 750 S~K~~ 754 (974)
-.|.+
T Consensus 162 hTRS~ 166 (301)
T KOG3013|consen 162 HTRSL 166 (301)
T ss_pred Eecch
Confidence 76654
No 294
>PRK13343 F0F1 ATP synthase subunit alpha; Provisional
Probab=52.08 E-value=2.7e+02 Score=33.76 Aligned_cols=169 Identities=14% Similarity=0.175 Sum_probs=93.2
Q ss_pred eeccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhc
Q 002054 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALML 193 (974)
Q Consensus 114 v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~ 193 (974)
.-|||-.-+.|+.|| |||=|.+---+++||+.|+-+---..+ ...++..-+|+--.++
T Consensus 268 ~A~REisL~l~epPg----r~gYP~~vf~~~srLlERAg~~~~~~~-gGSITal~~V~~~~dD----------------- 325 (502)
T PRK13343 268 AAYRELSLLLRRPPG----REAYPGDIFYLHSRLLERAAKLSPELG-GGSLTALPIIETLAGE----------------- 325 (502)
T ss_pred HHHHHHHHhcCCCCC----cCCcCcchHhhhHHHHHhhccCCCCCC-CcceEEEEEEEcCCCC-----------------
Confidence 347788888888887 667777766789999998876111111 2344444334322222
Q ss_pred CCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 002054 194 SDIPWGGPIGMIRIGRICGQFIVNPTMDELSL-SDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQ 272 (974)
Q Consensus 194 s~iP~~~~v~av~vg~i~g~~vldPt~~e~~~-s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~ 272 (974)
+.+||+.-..+..||+++|+....+... .-.|...+-+. +|-. -.++ ++...-..++..+..+
T Consensus 326 ----~s~pI~~~v~sItDGqIvLsr~La~~G~~PAIDv~~SvSR---v~~~----~~~~-----~~~~~a~~lr~~la~y 389 (502)
T PRK13343 326 ----LSAYIPTNLISITDGQIYLDSDLFAAGQRPAVDVGLSVSR---VGGK----AQHP-----AIRKESGRLRLDYAQF 389 (502)
T ss_pred ----CCCcchhhhhcccceEEEECHHHHhCCCCCccCCccchhc---cCcc----ccCH-----HHHHHHHHHHHHHHHH
Confidence 2355655566778999999988877654 33454444332 1211 1222 2222233344445555
Q ss_pred HHHH--HHhCCccccccccCCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHH
Q 002054 273 IRLA--EKAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQ 330 (974)
Q Consensus 273 ~~~~--~~~g~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~ 330 (974)
+++. .+.|-. .+++....++ ...+|++.+++..++...-.+.+..+..
T Consensus 390 ~e~e~~~~~G~~--------ld~~~~~~i~--~~~~i~~~L~Q~~~~~~~~~~~~~~l~~ 439 (502)
T PRK13343 390 LELEAFTRFGGL--------LDAGTQKQIT--RGRRLRELLKQPRFSPLSVEEQIALLYA 439 (502)
T ss_pred HHHHHHHHHhhh--------cCHHHHHHHH--HHHHHHHHhcCCCCCCCCHHHHHHHHHH
Confidence 4432 334421 4555555554 3567777777665555555555555543
No 295
>PRK09890 cold shock protein CspG; Provisional
Probab=52.05 E-value=82 Score=27.46 Aligned_cols=56 Identities=9% Similarity=0.123 Sum_probs=39.6
Q ss_pred EEEEEEEEeC-CeE-EEEeCC-CeEEEEecccCCC---CCCCCCCEEEEEEEEEeCCCceeee
Q 002054 914 VAAKVYQVRA-RGL-VLDLGG-GIRGMYRFENNEK---KDFVVGDELLVKCSSFTGKGIPVVS 970 (974)
Q Consensus 914 V~G~V~~I~~-~Gv-FV~L~~-gv~Glih~se~~~---~~f~vGd~V~vkVl~id~~~~~~~~ 970 (974)
++|+|+...+ .|. ||.-++ +-+=|+|+|.+.. ..+++||+|+..+. -+++|....+
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~~~-~~~~G~~A~~ 66 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIE-QGQRGPAAAN 66 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEEEE-ECCCCceeEE
Confidence 4899999843 333 666665 5899999997752 45899999999654 4556654443
No 296
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=51.72 E-value=7.6 Score=34.49 Aligned_cols=25 Identities=20% Similarity=0.388 Sum_probs=21.4
Q ss_pred eeeeeccchhhhhcCCCccchhhhh
Q 002054 618 ATLKYDNDTLRRLIGPLGALKRKIE 642 (974)
Q Consensus 618 ~~~~i~~~ki~~vIg~gGk~i~~i~ 642 (974)
..+.+.++.+|++||.+|++|+.|.
T Consensus 32 ~~l~v~~~D~GkvIGk~GRti~AIR 56 (76)
T COG1837 32 IELRVAPEDMGKVIGKQGRTIQAIR 56 (76)
T ss_pred EEEEECcccccceecCCChhHHHHH
Confidence 4456889999999999999999875
No 297
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=51.63 E-value=33 Score=37.47 Aligned_cols=28 Identities=36% Similarity=0.709 Sum_probs=25.5
Q ss_pred chhhhhcCCCccchhhhhhhhCceEEee
Q 002054 625 DTLRRLIGPLGALKRKIEEETGGRISVS 652 (974)
Q Consensus 625 ~ki~~vIg~gGk~i~~i~~~~g~~Idi~ 652 (974)
+.+|+++||.|-++|.++++||++|.|-
T Consensus 107 NFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 107 NFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred ccccccccCCcchHHHHHHHHCCeEEEe
Confidence 4689999999999999999999998764
No 298
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=51.23 E-value=62 Score=34.25 Aligned_cols=71 Identities=17% Similarity=0.118 Sum_probs=51.8
Q ss_pred ccccCcEEEEEEEEEeeceEEEEEcCCeEEEEecccCCCc-cccccccccccCCEEEEEEEEEccCCceEEEEe
Q 002054 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHE-PVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK 752 (974)
Q Consensus 680 ~~~~G~i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~-~v~~~~~~~~vGd~V~vkVl~id~~gri~LS~K 752 (974)
-+.+|+.+-|.|+.-..-+..|+|.+..-+.++.-..... +-+.| .|++||-|.+||...+++-.-.|++-
T Consensus 62 iP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrP--nl~vGdliyakv~~a~~~~Epel~Ci 133 (230)
T KOG1004|consen 62 IPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRP--NLQVGDLIYAKVVDANKDMEPELTCI 133 (230)
T ss_pred cCCCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCC--ccccccEEEEEEEecCCCcCcceEEE
Confidence 3789999999999999999999997656677776555433 22233 39999999999998765433444443
No 299
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=50.93 E-value=57 Score=32.51 Aligned_cols=60 Identities=17% Similarity=0.147 Sum_probs=46.0
Q ss_pred CCCCEEEEEEEEEeCCe---------EEEEeCCCeEEEEecccCCCCCCCCCCEEEEEEEEEeCCCcee
Q 002054 909 KLGTKVAAKVYQVRARG---------LVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSSFTGKGIPV 968 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~G---------vFV~L~~gv~Glih~se~~~~~f~vGd~V~vkVl~id~~~~~~ 968 (974)
..|.+.+=+|..+.+.| +.|+|+++-..+.|......+.+++|++|+++...+.+++-..
T Consensus 62 ~~G~V~t~Tv~~~~~~~~~~~~P~viaiV~l~~~~~i~~~i~~~~p~~v~iGm~V~~v~~~~~~~~~~~ 130 (140)
T COG1545 62 GEGKVETYTVVYVKPPGFSLEEPYVIAIVELEEGGRILGQLVDVDPDDVEIGMKVEAVFRKREEDGGRG 130 (140)
T ss_pred CCeEEEEEEEEeeCCCCcccCCCEEEEEEEeCCCCceEEEEEecCcccccCCCEEEEEEEEccccCCce
Confidence 47778888888877765 6778887668888887633568999999999999887666443
No 300
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=49.22 E-value=51 Score=27.90 Aligned_cols=50 Identities=18% Similarity=0.305 Sum_probs=34.9
Q ss_pred CCEEEEEEEEEeCCeEEE----EeCCC--eEEEEecccCCCCCCCCCCEEEEEEEE
Q 002054 911 GTKVAAKVYQVRARGLVL----DLGGG--IRGMYRFENNEKKDFVVGDELLVKCSS 960 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvFV----~L~~g--v~Glih~se~~~~~f~vGd~V~vkVl~ 960 (974)
-..+.|+|.++.+.|.++ +++++ +...++.+....-.+++|+.|.+.+-.
T Consensus 6 ~N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~~l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 6 RNQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVAELGLKPGKEVYAVIKA 61 (69)
T ss_pred ccEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHhhCCCCCCCEEEEEEEC
Confidence 357899999997776554 44444 555666554445578999999998754
No 301
>PRK15463 cold shock-like protein CspF; Provisional
Probab=48.97 E-value=61 Score=28.33 Aligned_cols=54 Identities=7% Similarity=0.021 Sum_probs=39.8
Q ss_pred EEEEEEEEeC-CeE-EEEeCC-CeEEEEecccCC---CCCCCCCCEEEEEEEEEeCCCcee
Q 002054 914 VAAKVYQVRA-RGL-VLDLGG-GIRGMYRFENNE---KKDFVVGDELLVKCSSFTGKGIPV 968 (974)
Q Consensus 914 V~G~V~~I~~-~Gv-FV~L~~-gv~Glih~se~~---~~~f~vGd~V~vkVl~id~~~~~~ 968 (974)
++|+|+...+ .|. ||+-++ +=+-|+|++.+. ...+++||+|...+.. +++|...
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~-~~~G~~A 64 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRIN-GLRGPTA 64 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEE-CCCCcee
Confidence 4899999955 454 777765 679999999774 3569999999997554 5556433
No 302
>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.
Probab=47.91 E-value=3.2e+02 Score=33.12 Aligned_cols=168 Identities=15% Similarity=0.174 Sum_probs=93.4
Q ss_pred EeeccccccccCCCCCccccccCCCCchhhhHHHhhcCCcc--ccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHH
Q 002054 113 TVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIR--PLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAA 190 (974)
Q Consensus 113 ~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lr--plfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~A 190 (974)
..-|||-.-+.|+.|| |||=|.+-=-+++||+.|+=+ ..... ..++..-+|+--.++
T Consensus 267 A~A~REisL~lgepPg----r~gYPg~vF~~~srLlERag~~~~~~~~---GSITal~~V~~~~dD-------------- 325 (497)
T TIGR03324 267 ARAYRELSLLLRRPPG----REAFPGDIFYVHSRLLERSTHLNEELGG---GSLTALPIIETEAQN-------------- 325 (497)
T ss_pred HHHHHHHHhhccCCCc----cCcCCccHHHHhHHHHHhhhhccCCCCC---cceeEEEEEEcCCCC--------------
Confidence 4457888888888887 567777766789999999866 22122 234443333333222
Q ss_pred hhcCCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHH
Q 002054 191 LMLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSL-SDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYL 269 (974)
Q Consensus 191 L~~s~iP~~~~v~av~vg~i~g~~vldPt~~e~~~-s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~ 269 (974)
+.+||+.-..+..||+++++....+... .-.|...+-+. +| +.-.++ ++...-...+..+
T Consensus 326 -------~s~pI~d~v~sItDGqIvLsr~La~~G~~PAIDv~~SvSR---v~----~~~~~~-----~~~~~a~~lr~~l 386 (497)
T TIGR03324 326 -------ISAYIPTNLISITDGQIYLSPTLFELGVLPAVDVGKSVSR---VG----GKAQLA-----AYRAVAGDLKLAY 386 (497)
T ss_pred -------CCCcchHhheeccceEEEEcHHHHhCCCCCcCCCcccccc---CC----ccccCH-----HHHHHHHHHHHHH
Confidence 2345555556778999999988777654 33454444333 11 111222 2222223333444
Q ss_pred HHHHHHH--HHhCCccccccccCCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHH
Q 002054 270 EPQIRLA--EKAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQ 330 (974)
Q Consensus 270 ~~~~~~~--~~~g~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~ 330 (974)
..++++. ...|- + .+++....++ ...+|++.++++......-.+.+..+..
T Consensus 387 a~y~e~e~~~~~G~----~----ld~~~~~~i~--~~~~i~~fL~Q~~~~~~~~~~~~~~l~~ 439 (497)
T TIGR03324 387 AQFEELETFARFGA----R----LDENTRKTIE--HGRRIRACLKQTQSSPLTVPQQIAILLA 439 (497)
T ss_pred HHHHHHHHHHHhhh----h----cCHHHHHHHH--hHHHHHHHhCCCCCCCCCHHHHHHHHHH
Confidence 4444432 22331 1 4556666664 4677888887765555555666655543
No 303
>PRK14998 cold shock-like protein CspD; Provisional
Probab=47.17 E-value=91 Score=27.49 Aligned_cols=55 Identities=13% Similarity=0.174 Sum_probs=39.4
Q ss_pred EEEEEEEeC-CeE-EEEeCC-CeEEEEecccCC---CCCCCCCCEEEEEEEEEeCCCceeee
Q 002054 915 AAKVYQVRA-RGL-VLDLGG-GIRGMYRFENNE---KKDFVVGDELLVKCSSFTGKGIPVVS 970 (974)
Q Consensus 915 ~G~V~~I~~-~Gv-FV~L~~-gv~Glih~se~~---~~~f~vGd~V~vkVl~id~~~~~~~~ 970 (974)
+|+|+...+ .|. ||.-++ +-+=|+|+|.+. ...+.+||+|...+.. +++|.....
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g~~~l~~G~~V~f~~~~-~~~G~~A~~ 63 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQ-GPKGNHASV 63 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccCCCCCCCCCEEEEEEEE-CCCCceeEE
Confidence 589998844 344 666655 689999999774 2569999999999765 444544433
No 304
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=46.49 E-value=13 Score=32.41 Aligned_cols=27 Identities=37% Similarity=0.539 Sum_probs=21.7
Q ss_pred chhhhhcCCCccchhhhhhhh-CceEEe
Q 002054 625 DTLRRLIGPLGALKRKIEEET-GGRISV 651 (974)
Q Consensus 625 ~ki~~vIg~gGk~i~~i~~~~-g~~Idi 651 (974)
|-++..||.+|..|+.|.+++ |.+|++
T Consensus 17 d~vG~~iG~~G~rik~i~~~L~gekIdv 44 (69)
T PF13184_consen 17 DPVGACIGKKGSRIKAISEELNGEKIDV 44 (69)
T ss_dssp -HHHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred CcceecCccccHHHHHHHHHhCCCeEEE
Confidence 448999999999999999999 888774
No 305
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=46.33 E-value=72 Score=28.39 Aligned_cols=54 Identities=17% Similarity=0.293 Sum_probs=42.3
Q ss_pred CCEEEEEEEEEeCCeEE-EEeCCCeEEEEecc-cCC--CCCCCCCCEEEEEEEEEeCC
Q 002054 911 GTKVAAKVYQVRARGLV-LDLGGGIRGMYRFE-NNE--KKDFVVGDELLVKCSSFTGK 964 (974)
Q Consensus 911 G~vV~G~V~~I~~~GvF-V~L~~gv~Glih~s-e~~--~~~f~vGd~V~vkVl~id~~ 964 (974)
.-.+.|+|.+.-+.+-| |.+++|..=+.|++ .+. .-...+||.|.+.....|.+
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~~d~~ 63 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRKNRIRILPGDVVLVELSPYDLT 63 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchheeEEeCCCCEEEEEecccccc
Confidence 45689999999777655 78999999999987 221 22477999999999999843
No 306
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=46.09 E-value=58 Score=29.51 Aligned_cols=60 Identities=12% Similarity=0.114 Sum_probs=44.1
Q ss_pred EEEEEEEEEeeceEE-EEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEE
Q 002054 686 IYKGVVTSVKEYGAF-VEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLS 750 (974)
Q Consensus 686 i~~G~V~~i~~~G~f-V~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS 750 (974)
.+.|+|++....+.| |.+.+|..-++|++- ++++ .-.++.||.|.|.....|. +|+|..-
T Consensus 6 q~~g~V~~~lG~~~~~V~~~dG~~~la~ipg----K~Rk-~iwI~~GD~VlVe~~~~~~~kg~Iv~r 67 (83)
T smart00652 6 QEIAQVVKMLGNGRLEVMCADGKERLARIPG----KMRK-KVWIRRGDIVLVDPWDFQDVKADIIYK 67 (83)
T ss_pred cEEEEEEEEcCCCEEEEEECCCCEEEEEEch----hhcc-cEEEcCCCEEEEEecCCCCCEEEEEEE
Confidence 478999999999887 688889998888864 2332 3348899999998766554 4555443
No 307
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=44.71 E-value=11 Score=37.51 Aligned_cols=58 Identities=9% Similarity=0.131 Sum_probs=40.7
Q ss_pred HHHHHHHHhcCCCCC---C-CCCCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee
Q 002054 595 ILDHMEREISAPRTQ---D-DRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS 652 (974)
Q Consensus 595 I~~~m~~~i~~~~~~---~-~~~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~ 652 (974)
..+++++++...... . ...--+...+.++++..+..||++|+|++.+..=++.+++++
T Consensus 74 ~~~fI~n~l~Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 74 PEEFIKNIFAPAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred HHHHHHHHcCCCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 445666666544321 1 111124456678999999999999999999999999888764
No 308
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=43.97 E-value=29 Score=39.05 Aligned_cols=59 Identities=24% Similarity=0.422 Sum_probs=51.1
Q ss_pred eeeeccchhhhhcCCCccchhhhhhhhCceEEee-----CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054 619 TLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS-----DGTLTVVAKNRSVMEKVLEKVDFII 677 (974)
Q Consensus 619 ~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~-----dg~v~i~~~~~~~~~~a~~~i~~l~ 677 (974)
++.+.+..|+-+||..|++-+.|+++|+++|-+. .+.+.+....+..+.+|.++|..++
T Consensus 60 si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~i 123 (345)
T KOG2814|consen 60 SILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLI 123 (345)
T ss_pred hhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHH
Confidence 4456778899999999999999999999998653 5789999999999999999988776
No 309
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=43.78 E-value=1.1e+02 Score=32.62 Aligned_cols=66 Identities=21% Similarity=0.255 Sum_probs=53.5
Q ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEecccCC------CCCCCCCCEEEEEEEEEeCCCceeeeecCC
Q 002054 909 KLGTKVAAKVYQVRARGLVLDLGGGIRGMYRFENNE------KKDFVVGDELLVKCSSFTGKGIPVVSLVDS 974 (974)
Q Consensus 909 ~vG~vV~G~V~~I~~~GvFV~L~~gv~Glih~se~~------~~~f~vGd~V~vkVl~id~~~~~~~~~~~~ 974 (974)
.+||.|-|+|..-..-+.-|+|++.-.++++.--++ .-.+++||-|-|+|..-+++-.|-+.-+||
T Consensus 64 ~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrPnl~vGdliyakv~~a~~~~Epel~Cids 135 (230)
T KOG1004|consen 64 VKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRPNLQVGDLIYAKVVDANKDMEPELTCIDS 135 (230)
T ss_pred CCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCCccccccEEEEEEEecCCCcCcceEEEcc
Confidence 589999999999877788999987566666655332 226999999999999999888888877775
No 310
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=42.17 E-value=69 Score=28.67 Aligned_cols=59 Identities=17% Similarity=0.156 Sum_probs=43.1
Q ss_pred EEEEEEEEeeceEE-EEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEE-cc-CCceEEE
Q 002054 687 YKGVVTSVKEYGAF-VEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQ-DV-RGNIKLS 750 (974)
Q Consensus 687 ~~G~V~~i~~~G~f-V~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~i-d~-~gri~LS 750 (974)
.-|+|++....+.| |++.+|..-++|++-= ++.- -.++.||.|.|..... |. +|.|..-
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg~~~l~~i~gK----~Rk~-iwI~~GD~VlV~~~~~~~~~kg~Iv~r 63 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADGQRRLVSIPGK----LRKN-IWIKRGDFLIVDPIEEGEDVKADIIFV 63 (78)
T ss_pred eEEEEEEECCCCEEEEEECCCCEEEEEEchh----hccC-EEEcCCCEEEEEecccCCCceEEEEEE
Confidence 35889999999887 7888899999988742 2221 3488999999988776 33 5665543
No 311
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=41.99 E-value=1.1e+02 Score=25.85 Aligned_cols=52 Identities=17% Similarity=0.159 Sum_probs=37.4
Q ss_pred EEEEEEEeC---CeEEEEeCCCeEEEEecccCCC---CCCCCCCEEEEEEEEEeCCCce
Q 002054 915 AAKVYQVRA---RGLVLDLGGGIRGMYRFENNEK---KDFVVGDELLVKCSSFTGKGIP 967 (974)
Q Consensus 915 ~G~V~~I~~---~GvFV~L~~gv~Glih~se~~~---~~f~vGd~V~vkVl~id~~~~~ 967 (974)
+|+|+...+ ||....-+.+=+=++|.+.+.. ..+++||.|...+..- .+|..
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~-~~g~~ 59 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEG-DKGPQ 59 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEEC-CCCCe
Confidence 588888854 6654443338889999998753 5799999999987766 34433
No 312
>PRK08149 ATP synthase SpaL; Validated
Probab=40.31 E-value=3.9e+02 Score=31.82 Aligned_cols=167 Identities=15% Similarity=0.181 Sum_probs=93.9
Q ss_pred eeccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhc
Q 002054 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALML 193 (974)
Q Consensus 114 v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~ 193 (974)
--|+|-.-+.|+.|+ |+|=|..=-..++||+.|+=+- . ...++.+-+|+--.++
T Consensus 255 ~A~rEi~l~~ge~P~----~~Gyp~~vfs~l~~l~ERag~~--~---~GSIT~~~tVl~~~dD----------------- 308 (428)
T PRK08149 255 RALRDVALAAGELPA----RRGYPASVFDSLPRLLERPGAT--L---AGSITAFYTVLLESEE----------------- 308 (428)
T ss_pred HHHHHhHhhcCCCCc----ccccCccHHHHHHHHHHhccCC--C---CCCceEEEEEEecCCC-----------------
Confidence 346777778888887 3466666566788888887753 1 2355555555543333
Q ss_pred CCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 002054 194 SDIPWGGPIGMIRIGRICGQFIVNPTMDELSL-SDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQ 272 (974)
Q Consensus 194 s~iP~~~~v~av~vg~i~g~~vldPt~~e~~~-s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~ 272 (974)
+++||+--..+..||+++++-...+... .-.|..-+.+. +|- .-.+++. .++. ..+++++..+
T Consensus 309 ----~~dpi~d~~~~ilDg~ivLsr~La~~g~yPAIDvl~S~SR---~~~----~~~~~~~-~~~a----~~~r~~l~~y 372 (428)
T PRK08149 309 ----EPDPIGDEIRSILDGHIYLSRKLAAKGHYPAIDVLKSVSR---VFG----QVTDPKH-RQLA----AAFRKLLTRL 372 (428)
T ss_pred ----CCCCchhhhheeccEEEEEcHHHHhCCCCCcccCcccccc---chh----hhcCHHH-HHHH----HHHHHHHHHH
Confidence 2367777777788999999998877654 44555544433 111 1133332 2222 2233333333
Q ss_pred HHHHH--HhCCccccccccCCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHH
Q 002054 273 IRLAE--KAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIG 329 (974)
Q Consensus 273 ~~~~~--~~g~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~ 329 (974)
+++.. +.|-.+ . -.++++...++. ..+|++.+++...+.....+.+..|.
T Consensus 373 ~e~e~li~~G~y~----~-g~~~~~d~ai~~--~~~i~~fl~Q~~~~~~~~~~~~~~l~ 424 (428)
T PRK08149 373 EELQLFIDLGEYR----R-GENADNDRAMDK--RPALEAFLKQDVAEKSSFSDTLERLN 424 (428)
T ss_pred HHHHHHHHcCCCC----C-CCCHHHHHHHHh--HHHHHHHhCCCCCCCCCHHHHHHHHH
Confidence 33221 234221 1 235566666654 67788888776556665555555543
No 313
>PRK01064 hypothetical protein; Provisional
Probab=39.13 E-value=16 Score=32.76 Aligned_cols=25 Identities=20% Similarity=0.325 Sum_probs=21.2
Q ss_pred eeeeeccchhhhhcCCCccchhhhh
Q 002054 618 ATLKYDNDTLRRLIGPLGALKRKIE 642 (974)
Q Consensus 618 ~~~~i~~~ki~~vIg~gGk~i~~i~ 642 (974)
..+.++++.++.+||.+|++++.|.
T Consensus 32 ~~l~v~~~D~g~vIGk~G~~i~air 56 (78)
T PRK01064 32 YELTVAKPDIGKIIGKEGRTIKAIR 56 (78)
T ss_pred EEEEECcccceEEECCCCccHHHHH
Confidence 3456888999999999999998765
No 314
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=38.31 E-value=1.3e+02 Score=31.92 Aligned_cols=65 Identities=17% Similarity=0.288 Sum_probs=45.0
Q ss_pred cccccCcEEEEEEEEEee--ceEEEEEcC----CeEEEEecccCCCccc----ccccccc--ccCCEEEEEEEEEcc
Q 002054 679 REIEVGGIYKGVVTSVKE--YGAFVEFNG----GQQGLLHVSELSHEPV----SRVSDVV--SVGQQLSLRCIGQDV 743 (974)
Q Consensus 679 ~~~~~G~i~~G~V~~i~~--~G~fV~l~~----g~~Glvhisels~~~v----~~~~~~~--~vGd~V~vkVl~id~ 743 (974)
.+++.|++|-|+.....+ ||++|+++- -.++|+|.-+|....- +++...| -.--.++|.|.++|.
T Consensus 71 ~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk 147 (247)
T COG4044 71 SKVEEGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNK 147 (247)
T ss_pred ccCCCCcEEEEEEeeeccceeEEEccccccCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccc
Confidence 468999999999999855 677888742 3678999888865443 3333333 234567888888765
No 315
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=38.30 E-value=1.2e+02 Score=26.24 Aligned_cols=54 Identities=11% Similarity=0.138 Sum_probs=38.0
Q ss_pred EEEEEEEeC-CeE-EEEeCC-CeEEEEecccCC---CCCCCCCCEEEEEEEEEeCCCceee
Q 002054 915 AAKVYQVRA-RGL-VLDLGG-GIRGMYRFENNE---KKDFVVGDELLVKCSSFTGKGIPVV 969 (974)
Q Consensus 915 ~G~V~~I~~-~Gv-FV~L~~-gv~Glih~se~~---~~~f~vGd~V~vkVl~id~~~~~~~ 969 (974)
+|+|+...+ .|. ||.-++ +-+-++|+|.+. ...+++||+|+..+.. +++|-...
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g~~~l~~G~~V~f~~~~-~~~G~~A~ 62 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQ-GPKGAHAT 62 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcCCCCCCCCCEEEEEEEE-CCCCceeE
Confidence 589998743 344 666655 789999999774 2568999999996543 44554433
No 316
>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=37.47 E-value=3.2e+02 Score=32.38 Aligned_cols=170 Identities=14% Similarity=0.131 Sum_probs=95.8
Q ss_pred EeeccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhh
Q 002054 113 TVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALM 192 (974)
Q Consensus 113 ~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~ 192 (974)
.--|||-.-+.|+.|+ |+|=|..--.+++||+.|+=+- +. -...++.+-+|+ .+|+.
T Consensus 243 A~A~REisl~~gepP~----~~gyp~~vf~~l~~L~ERag~~-~~--~~GSIT~~~tVl-~~gdd--------------- 299 (418)
T TIGR03498 243 AMAQREIGLAAGEPPV----ARGYTPSVFSELPRLLERAGPG-AE--GKGSITGIFTVL-VDGDD--------------- 299 (418)
T ss_pred HHHHHHHHHhcCCCCc----cccCCchhhhhhhHHHHHhccC-CC--CCcceeeeEEEe-ccCCC---------------
Confidence 3446787788888887 4576766667889999998763 21 123555555565 34332
Q ss_pred cCCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 002054 193 LSDIPWGGPIGMIRIGRICGQFIVNPTMDELSL-SDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEP 271 (974)
Q Consensus 193 ~s~iP~~~~v~av~vg~i~g~~vldPt~~e~~~-s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~ 271 (974)
|++||+--..+..||+++|+-...+... .-.|...+.+.- | ..-++++... ....+++++..
T Consensus 300 -----~~dpi~d~~~si~DG~ivLsr~la~~g~~PAIDv~~S~SR~---~----~~~~~~~~~~-----~a~~~r~~l~~ 362 (418)
T TIGR03498 300 -----HNEPVADAVRGILDGHIVLDRAIAERGRYPAINVLASVSRL---A----PRVWSPEERK-----LVRRLRALLAR 362 (418)
T ss_pred -----CCCcchhhhheeeeeEEEECHHHHhCCCCCccCCccccccc---c----hhhcCHHHHH-----HHHHHHHHHHh
Confidence 2356666666778999999887776654 445655554432 2 1123443222 12224444444
Q ss_pred HHHHH--HHhCCccccccccCCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHH
Q 002054 272 QIRLA--EKAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIG 329 (974)
Q Consensus 272 ~~~~~--~~~g~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~ 329 (974)
++++. .+.|-.+ .-.++++.+.++ ...+|++.+++...+.....+.+++|.
T Consensus 363 y~e~~~~~~~g~y~-----~g~d~~~d~ai~--~~~~i~~fl~Q~~~~~~~~~~~~~~l~ 415 (418)
T TIGR03498 363 YEETEDLIRLGAYR-----KGSDPELDEAIR--LVPKIYEFLTQGPDEPTSLQDPFADLA 415 (418)
T ss_pred hHHHHHHHHhhCCc-----CCCCHHHHHHHH--hHHHHHHHhCCCCCCCCCHHHHHHHHH
Confidence 44332 2233211 124556666665 356777777765555555555555543
No 317
>TIGR00830 PTBA PTS system, glucose subfamily, IIA component. These are part of the The PTS Glucose-Glucoside (Glc) SuperFamily. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). The IIA, IIB and IIC domains of all of the permeases listed below are demonstrably homologous. These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-c
Probab=36.47 E-value=79 Score=30.78 Aligned_cols=49 Identities=10% Similarity=0.167 Sum_probs=38.0
Q ss_pred EEEEEEEEeC--CeEEEEeCCCeEEEEecc----cCC----CCCCCCCCEEEE--EEEEEe
Q 002054 914 VAAKVYQVRA--RGLVLDLGGGIRGMYRFE----NNE----KKDFVVGDELLV--KCSSFT 962 (974)
Q Consensus 914 V~G~V~~I~~--~GvFV~L~~gv~Glih~s----e~~----~~~f~vGd~V~v--kVl~id 962 (974)
+.|+|..+-+ +-+-++.++|+.-|+|+. ++. ....+.||+|++ .+.++|
T Consensus 42 ~~G~v~~v~~T~HA~gi~~~~G~evLiHiGidTV~L~G~gF~~~v~~Gd~V~~G~~l~~~D 102 (121)
T TIGR00830 42 VDGKIGKIFPTKHAFGIESDSGVEILIHIGIDTVKLNGEGFTSHVEEGQRVKKGDPLLEFD 102 (121)
T ss_pred CCeEEEEEccCCCEEEEEeCCCcEEEEEeeeceeecCCCceEEEecCCCEEcCCCEEEEEc
Confidence 5789999966 556678888999999998 232 224778999998 788888
No 318
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=35.96 E-value=82 Score=30.79 Aligned_cols=49 Identities=12% Similarity=0.207 Sum_probs=37.9
Q ss_pred EEEEEEEEeC--CeEEEEeCCCeEEEEecc----cCC----CCCCCCCCEEEE--EEEEEe
Q 002054 914 VAAKVYQVRA--RGLVLDLGGGIRGMYRFE----NNE----KKDFVVGDELLV--KCSSFT 962 (974)
Q Consensus 914 V~G~V~~I~~--~GvFV~L~~gv~Glih~s----e~~----~~~f~vGd~V~v--kVl~id 962 (974)
+.|+|..+.+ +-+-++.++|+.-|+|.. ++. ....+.||+|++ .+.++|
T Consensus 42 ~~G~v~~i~~T~HA~~i~~~~G~eiLiHiGidTv~l~g~gF~~~vk~Gd~V~~G~~l~~~D 102 (124)
T cd00210 42 VDGTIVQIFPTKHAIGIESDSGVEILIHIGIDTVKLNGEGFTSHVEEGQRVKQGDKLLEFD 102 (124)
T ss_pred CCeEEEEEccCCCEEEEEeCCCcEEEEEeeeeeeecCCCceEEEecCCCEEcCCCEEEEEc
Confidence 5799999955 555578888999999998 222 224678999998 788888
No 319
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=35.49 E-value=2e+02 Score=25.07 Aligned_cols=60 Identities=20% Similarity=0.281 Sum_probs=37.0
Q ss_pred EEEEEEEEEeece-EEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEE
Q 002054 686 IYKGVVTSVKEYG-AFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKL 749 (974)
Q Consensus 686 i~~G~V~~i~~~G-~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~L 749 (974)
.+.|.|++....+ ..|.+.+|..-.+|+.- .++.......+||.|.+.+-..|. +|.|..
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~G----klr~~~i~i~vGD~V~ve~~~~~~~~g~Iv~ 69 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELENGHEVLAHISG----KMRKNYIRILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEEcc----ceeeCCcccCCCCEEEEEEcccCCCeEEEEE
Confidence 4679999988774 45666566555555432 222212236789999998755544 566654
No 320
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=35.08 E-value=1.9e+02 Score=27.11 Aligned_cols=54 Identities=15% Similarity=0.173 Sum_probs=40.7
Q ss_pred CcEEEEEEEEEeeceEE-EEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEc
Q 002054 684 GGIYKGVVTSVKEYGAF-VEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQD 742 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~f-V~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id 742 (974)
-..+.|+|+.....+.| |.+.+|..-+.|++- ++++ .-.++.||.|.|...+..
T Consensus 18 e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~G----K~Rk-~iwI~~GD~VlVsp~d~~ 72 (99)
T TIGR00523 18 EGEILGVIEQMLGAGRVKVRCLDGKTRLGRIPG----KLKK-RIWIREGDVVIVKPWEFQ 72 (99)
T ss_pred CCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEch----hhcc-cEEecCCCEEEEEEccCC
Confidence 45589999999999887 688889988888863 2333 344889999999655543
No 321
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=34.96 E-value=1.4e+02 Score=24.37 Aligned_cols=51 Identities=24% Similarity=0.173 Sum_probs=31.6
Q ss_pred EEEEEEe-CCeEEEEeCCCeEEEEecccC--CCCCCCCCCEEEEEEEEEeCCCc
Q 002054 916 AKVYQVR-ARGLVLDLGGGIRGMYRFENN--EKKDFVVGDELLVKCSSFTGKGI 966 (974)
Q Consensus 916 G~V~~I~-~~GvFV~L~~gv~Glih~se~--~~~~f~vGd~V~vkVl~id~~~~ 966 (974)
|+|.... .||.++..+++-+=++|.+.+ ....+..||.|.+++..-+..+.
T Consensus 2 G~i~~~~~g~gfv~~~~~~~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~~~~~~~ 55 (64)
T smart00357 2 GVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPRGGGK 55 (64)
T ss_pred eEEEEEcCCeeEEecCCCCccEEEEhHHhhcCCCcCCCCCEEEEEEEEccCCCC
Confidence 5666554 456544432334778887763 12457889999999987544343
No 322
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=33.82 E-value=26 Score=34.99 Aligned_cols=33 Identities=21% Similarity=0.330 Sum_probs=28.3
Q ss_pred eeeeccchhhhhcCCCccchhhhhhhhCceEEe
Q 002054 619 TLKYDNDTLRRLIGPLGALKRKIEEETGGRISV 651 (974)
Q Consensus 619 ~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi 651 (974)
.+-+++...|..||++|.+|+.|++..|.+|++
T Consensus 35 i~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdV 67 (140)
T PRK08406 35 IFVVKEGDMGLAIGKGGENVKRLEEKLGKDIEL 67 (140)
T ss_pred EEEEeCCCccccCCcCchHHHHHHHHhCCceEE
Confidence 344678899999999999999999999988874
No 323
>PRK09099 type III secretion system ATPase; Provisional
Probab=33.74 E-value=4.4e+02 Score=31.52 Aligned_cols=91 Identities=20% Similarity=0.271 Sum_probs=61.2
Q ss_pred ccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCC
Q 002054 116 YQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSD 195 (974)
Q Consensus 116 y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~ 195 (974)
|||-.-+.|..|+ |+|=|..--.+++|++.|+=+. . ...++.+-+|+.-+++
T Consensus 269 ~REisl~~gepP~----~~gyP~~vf~~l~~l~ERag~~--~---~GSIT~i~tVl~~~dd------------------- 320 (441)
T PRK09099 269 QREIGLAAGEPPA----RRGFPPSVFAELPRLLERAGMG--E---TGSITALYTVLAEDES------------------- 320 (441)
T ss_pred HHHHHHhcCCCCc----cccCCccHHHHhHHHHHhhcCC--C---CcchheeEEEEecCCC-------------------
Confidence 6788888888887 4576777777889999888531 1 3355555555543333
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CccceeEeeeC
Q 002054 196 IPWGGPIGMIRIGRICGQFIVNPTMDELSL-SDLNLVYACTR 236 (974)
Q Consensus 196 iP~~~~v~av~vg~i~g~~vldPt~~e~~~-s~~~l~v~~t~ 236 (974)
+++||+--..+..||+++|+-...+... .-.|...+.+.
T Consensus 321 --~~dpI~d~~~~i~DG~ivLsr~La~~g~yPAIDvl~S~SR 360 (441)
T PRK09099 321 --GSDPIAEEVRGILDGHMILSREIAARNQYPAIDVLGSLSR 360 (441)
T ss_pred --cCCcchhhhheecceEEEEcHHHHhCCCCCccCCccccCc
Confidence 2367777677788999999988877655 44566555544
No 324
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=32.90 E-value=21 Score=31.15 Aligned_cols=32 Identities=19% Similarity=0.236 Sum_probs=25.9
Q ss_pred CCcceeeeeccchhhhhcCCCccchhhhhhhh
Q 002054 614 SPRLATLKYDNDTLRRLIGPLGALKRKIEEET 645 (974)
Q Consensus 614 ~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~ 645 (974)
-.....+.++++..+.+||..|++++.|+-=.
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~ 58 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLV 58 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHH
Confidence 34556778899999999999999999876433
No 325
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=32.89 E-value=29 Score=34.64 Aligned_cols=33 Identities=21% Similarity=0.319 Sum_probs=28.6
Q ss_pred eeeeccchhhhhcCCCccchhhhhhhhCceEEe
Q 002054 619 TLKYDNDTLRRLIGPLGALKRKIEEETGGRISV 651 (974)
Q Consensus 619 ~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi 651 (974)
.+-+++..++..||++|.+|+.+++..|.+|++
T Consensus 36 ifvV~~g~vG~~IG~~G~rIk~i~el~gekIdV 68 (141)
T TIGR01952 36 VFVVKEGEMGAAIGKGGENVKRLEELIGKSIEL 68 (141)
T ss_pred EEEEcCCCccccCCCCchHHHHHHHhcCCeeEE
Confidence 445778899999999999999998888888874
No 326
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=32.72 E-value=24 Score=42.44 Aligned_cols=40 Identities=28% Similarity=0.321 Sum_probs=34.0
Q ss_pred CCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee
Q 002054 613 NSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS 652 (974)
Q Consensus 613 ~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~ 652 (974)
+.-....+.++.+.|+.+||++|.+|-+|++.+|+.|.|-
T Consensus 335 ~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~ 374 (485)
T KOG2190|consen 335 TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISIL 374 (485)
T ss_pred cceeeeeeccCccccceeecccccchHHHHHhcCCceEEc
Confidence 3334456778999999999999999999999999998764
No 327
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=32.63 E-value=53 Score=28.13 Aligned_cols=57 Identities=21% Similarity=0.193 Sum_probs=37.4
Q ss_pred EEEEEEEEEeeceEE-EEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCce
Q 002054 686 IYKGVVTSVKEYGAF-VEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNI 747 (974)
Q Consensus 686 i~~G~V~~i~~~G~f-V~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri 747 (974)
.+.|+|++....+.| |.+.+|..-++|++-= +-+ .-.++.||.|.|.+-..|. +|+|
T Consensus 4 e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK---~r~--~iwI~~GD~V~V~~~~~d~~kG~I 62 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECEDGEERLARIPGK---FRK--RIWIKRGDFVLVEPSPYDKVKGRI 62 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETTSEEEEEEE-HH---HHT--CC---TTEEEEEEESTTCTTEEEE
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccc---eee--eEecCCCCEEEEEecccCCCeEEE
Confidence 567999999998887 8888898888887642 111 1238899999887744443 3444
No 328
>CHL00010 infA translation initiation factor 1
Probab=32.40 E-value=2.8e+02 Score=24.77 Aligned_cols=63 Identities=25% Similarity=0.309 Sum_probs=39.6
Q ss_pred EEEEEEEEeeceE-EEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEEec
Q 002054 687 YKGVVTSVKEYGA-FVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSLKA 753 (974)
Q Consensus 687 ~~G~V~~i~~~G~-fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~K~ 753 (974)
+.|.|+++...|. .|.+.+|..-.+|+.- .+++-.-...+||.|.+.+-..+. +|.|..-.+.
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~g~~~~c~~rG----klr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDNGCQVLGYISG----KIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCCCCEEEEEecc----ceecCCcccCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 6799999886554 4666666555666442 222222336789999999655444 5777665554
No 329
>CHL00059 atpA ATP synthase CF1 alpha subunit
Probab=31.76 E-value=8.2e+02 Score=29.63 Aligned_cols=86 Identities=17% Similarity=0.227 Sum_probs=54.4
Q ss_pred EeeccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccC-CCCCceEEEEEEEeccCCCChhhHHHHHHHHHh
Q 002054 113 TVDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPA-GFYHEVQVMASVLSSDGKQDPDIMAANATSAAL 191 (974)
Q Consensus 113 ~v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~-~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL 191 (974)
..-|||-.-+.|+.|| |||=|.+---+++||+.|+=+- -.. + ...++..-.|+--+++
T Consensus 246 A~A~REisl~l~epPg----r~gYP~~vF~~~srLlERag~~-~~~~~-~GSITal~~V~~~~dD--------------- 304 (485)
T CHL00059 246 AQAYRQMSLLLRRPPG----REAYPGDVFYLHSRLLERAAKL-SSQLG-EGSMTALPIVETQAGD--------------- 304 (485)
T ss_pred HHHHHHHHHhcCCCCC----cCCcCchHHHHhHHHHHhhhcc-cCCCC-CcceEEEEEEEccCCC---------------
Confidence 4557888888888887 4566766667899999888752 111 1 2344444444332222
Q ss_pred hcCCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc
Q 002054 192 MLSDIPWGGPIGMIRIGRICGQFIVNPTMDELSL 225 (974)
Q Consensus 192 ~~s~iP~~~~v~av~vg~i~g~~vldPt~~e~~~ 225 (974)
+.+||+.-..+..||+++++...-+...
T Consensus 305 ------~s~pI~~~v~sItDGqIvLsr~La~~G~ 332 (485)
T CHL00059 305 ------VSAYIPTNVISITDGQIFLSADLFNAGI 332 (485)
T ss_pred ------CCCcchHhhhhhcceEEEEcHHHHhCCC
Confidence 2345555556677999999987776644
No 330
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=31.19 E-value=38 Score=33.86 Aligned_cols=59 Identities=10% Similarity=0.143 Sum_probs=41.4
Q ss_pred HHHHHHHHHhcCCCC-CC--CC-CCCcceeeeeccchhhhhcCCCccchhhhhhhhCceEEee
Q 002054 594 QILDHMEREISAPRT-QD--DR-NSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS 652 (974)
Q Consensus 594 ~I~~~m~~~i~~~~~-~~--~~-~~p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~ 652 (974)
.+-+++++++...+. .. .. .-.+...+.++++..+..||.+|+|++....=++-++||+
T Consensus 74 D~~~fI~N~l~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 74 NLEEFVANKLAPAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CHHHHHHHcCCCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 445667776665441 11 11 1234556779999999999999999998888888877764
No 331
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=31.13 E-value=25 Score=40.55 Aligned_cols=80 Identities=19% Similarity=0.204 Sum_probs=52.0
Q ss_pred eeccchhhhhcCCCccchhhhhhhhCceEEee--------CCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEEEEEEE
Q 002054 621 KYDNDTLRRLIGPLGALKRKIEEETGGRISVS--------DGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVT 692 (974)
Q Consensus 621 ~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~--------dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~~G~V~ 692 (974)
-++....+.+||+.|.+||.|...|..+||+- |..+++-+ ..+..-+|..+|-+++.++...-++-.-++-
T Consensus 204 lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~-tpEg~s~Ac~~ILeimqkEA~~~k~~~e~pL 282 (584)
T KOG2193|consen 204 LVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHS-TPEGTSKACKMILEIMQKEAVDDKVAEEIPL 282 (584)
T ss_pred eeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEec-CccchHHHHHHHHHHHHHhhhccchhhhcch
Confidence 35566679999999999999999999999974 12345544 4466777777777776444433333333444
Q ss_pred EEeeceEEE
Q 002054 693 SVKEYGAFV 701 (974)
Q Consensus 693 ~i~~~G~fV 701 (974)
++....-||
T Consensus 283 k~lAHN~lv 291 (584)
T KOG2193|consen 283 KILAHNNLV 291 (584)
T ss_pred hhhhhcchh
Confidence 444433333
No 332
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=30.67 E-value=97 Score=29.05 Aligned_cols=52 Identities=15% Similarity=0.326 Sum_probs=32.4
Q ss_pred EEEEEEEEEeece--EEEEEcCC---eEEEEecccCCCccccccccccccCCEEEEE
Q 002054 686 IYKGVVTSVKEYG--AFVEFNGG---QQGLLHVSELSHEPVSRVSDVVSVGQQLSLR 737 (974)
Q Consensus 686 i~~G~V~~i~~~G--~fV~l~~g---~~Glvhisels~~~v~~~~~~~~vGd~V~vk 737 (974)
.+.|.|.+++..| +|++|..+ ++.++...+.....+.+....++.|+.|.|.
T Consensus 3 ~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~ 59 (108)
T cd04322 3 SVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVT 59 (108)
T ss_pred EEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEE
Confidence 4789999998765 79999654 3445544443222222222337889988774
No 333
>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase.
Probab=29.51 E-value=5.6e+02 Score=30.43 Aligned_cols=91 Identities=18% Similarity=0.260 Sum_probs=60.7
Q ss_pred ccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCC
Q 002054 116 YQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSD 195 (974)
Q Consensus 116 y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~ 195 (974)
|+|-.-+.|..|+ |+|=|..--..++||+.|+=+. + ...++.+-+|+--.++
T Consensus 251 ~rei~l~~ge~P~----~~gyp~~~f~~l~~l~ERag~~----~-~GSIT~~~tv~~~~dd------------------- 302 (422)
T TIGR02546 251 LREIGLAAGEPPA----RGGYPPSVFSSLPRLLERAGNG----E-KGSITALYTVLVEGDD------------------- 302 (422)
T ss_pred HHHHHHhcCCCCc----ccccChhHHHHhHHHHHHhcCC----C-CCceeEEEEEeccCCC-------------------
Confidence 4566667788886 4576776667889999998762 1 3456666555544333
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CccceeEeeeC
Q 002054 196 IPWGGPIGMIRIGRICGQFIVNPTMDELSL-SDLNLVYACTR 236 (974)
Q Consensus 196 iP~~~~v~av~vg~i~g~~vldPt~~e~~~-s~~~l~v~~t~ 236 (974)
+++||+--..+..||+++|+-...+... .-.|...+.+.
T Consensus 303 --~~~pi~~~~~~i~dg~i~Lsr~la~~g~yPAId~~~S~SR 342 (422)
T TIGR02546 303 --MNDPIADEVRSILDGHIVLSRALAERNHYPAIDVLASLSR 342 (422)
T ss_pred --CCCCchhhhhccccEEEEEcHHHHhCCCCCccCCcccccc
Confidence 2367777777788999999988877654 44566555544
No 334
>PRK07165 F0F1 ATP synthase subunit alpha; Validated
Probab=29.14 E-value=1.1e+03 Score=28.66 Aligned_cols=83 Identities=12% Similarity=0.112 Sum_probs=54.8
Q ss_pred eeccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhc
Q 002054 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALML 193 (974)
Q Consensus 114 v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~ 193 (974)
.-|||-..+.|+.|| |||=|.+-=-+++||+.|+-+- . + ...++-.-.|+--+++.
T Consensus 247 ~A~REisLllgepPg----regYPg~vF~~~srLlERAg~~--~-g-~GSITalpiV~t~~dDi---------------- 302 (507)
T PRK07165 247 NIYREIALLTNKPVG----KEAFPGDMFFAHSKLLERAGKF--K-N-RKTITALPILQTVDNDI---------------- 302 (507)
T ss_pred HHHHHHHhhccCCCC----ccCCCchHHHHhHHHHHhccCC--C-C-CCceEEEEEEECCCCCC----------------
Confidence 457888888899886 5788888778999999998872 2 1 12222222233222222
Q ss_pred CCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc
Q 002054 194 SDIPWGGPIGMIRIGRICGQFIVNPTMDELSL 225 (974)
Q Consensus 194 s~iP~~~~v~av~vg~i~g~~vldPt~~e~~~ 225 (974)
.+||+.-.....||+++++.+.-+...
T Consensus 303 -----s~pIpdnv~sItDGqIvLsr~L~~~G~ 329 (507)
T PRK07165 303 -----TSLISSNIISITDGQIVTSSDLFASGK 329 (507)
T ss_pred -----CCcchhhhccccCeEEEEcHHHHhCCC
Confidence 245665566777999999998876654
No 335
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=28.57 E-value=38 Score=35.59 Aligned_cols=34 Identities=26% Similarity=0.359 Sum_probs=28.7
Q ss_pred eeeeeccchhhhhcCCCccchhhhhhhhCceEEe
Q 002054 618 ATLKYDNDTLRRLIGPLGALKRKIEEETGGRISV 651 (974)
Q Consensus 618 ~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi 651 (974)
...-...+.++..||++|.+++.+.+++|.+||+
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdV 111 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDV 111 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEE
Confidence 3444566789999999999999999999988875
No 336
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=28.27 E-value=2.4e+02 Score=22.92 Aligned_cols=47 Identities=19% Similarity=0.503 Sum_probs=28.7
Q ss_pred EEEEEEee-ceEEEEEcCC-eEEEEecccCCCccccccccccccCCEEEEEEEEE
Q 002054 689 GVVTSVKE-YGAFVEFNGG-QQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQ 741 (974)
Q Consensus 689 G~V~~i~~-~G~fV~l~~g-~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~i 741 (974)
|+|....+ || |+.-... .+-++|.+++.. .. ..+..||.|.+++..-
T Consensus 2 G~i~~~~~g~g-fv~~~~~~~~i~v~~~~~~~-~~----~~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 2 GVVKWFNKGFG-FIRPDDGGKDVFVHPSQIQG-GL----KSLREGDEVEFKVVSP 50 (64)
T ss_pred eEEEEEcCCee-EEecCCCCccEEEEhHHhhc-CC----CcCCCCCEEEEEEEEc
Confidence 55554443 44 4444333 578889887532 11 1267799999999873
No 337
>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=26.78 E-value=1.5e+02 Score=25.22 Aligned_cols=55 Identities=27% Similarity=0.268 Sum_probs=33.0
Q ss_pred CcEEEEEEEEEeeceEEEEEcCCeEEE-EecccCCCccccccccccccCCEEEEEEEEEcc
Q 002054 684 GGIYKGVVTSVKEYGAFVEFNGGQQGL-LHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV 743 (974)
Q Consensus 684 G~i~~G~V~~i~~~G~fV~l~~g~~Gl-vhisels~~~v~~~~~~~~vGd~V~vkVl~id~ 743 (974)
|+..+-.|..+++.|--+--.+.+.|+ +-.+. +..-...+-+|+++++.|+.+|.
T Consensus 1 G~~L~LvV~~~~edgsv~fs~g~v~g~tv~Atr-----yH~~g~nl~pGqK~kaviLhvD~ 56 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASR-----YHKEGVNVTPGCKLKAVILHVDF 56 (65)
T ss_pred CceEEEEEeeeccCCcEEEecCCcCCcEEEEEE-----EEecceecCCCceeEEEEEEEee
Confidence 566677777766555433333444444 22222 22223347889999999999996
No 338
>PRK08972 fliI flagellum-specific ATP synthase; Validated
Probab=26.21 E-value=8.1e+02 Score=29.33 Aligned_cols=169 Identities=16% Similarity=0.200 Sum_probs=92.6
Q ss_pred eccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcC
Q 002054 115 DYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLS 194 (974)
Q Consensus 115 ~y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s 194 (974)
-|+|-.-+.|+.|+ |+|=|..---+++||..|+=+- .. + ...++.+-+|+--.++
T Consensus 267 A~REIsl~~gepP~----~~GYPpsvfs~l~~L~ERAg~~-~~-~-~GSITai~tVl~~gdD------------------ 321 (444)
T PRK08972 267 AQREIALAVGEPPA----TKGYPPSVFAKLPALVERAGNG-GP-G-QGSITAFYTVLTEGDD------------------ 321 (444)
T ss_pred HHHHHHHhcCCCCc----cccCCchHHHHhHHHHHHhcCC-CC-C-CceeeeEEEEEEeCCC------------------
Confidence 35777778888886 3466666666788888887641 11 1 1345555555443222
Q ss_pred CCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 002054 195 DIPWGGPIGMIRIGRICGQFIVNPTMDELSL-SDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQI 273 (974)
Q Consensus 195 ~iP~~~~v~av~vg~i~g~~vldPt~~e~~~-s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~ 273 (974)
|++||+.-..+..||+++|+-...+... --.|..-+.+.- | ..-.++++..-| ..+++++..++
T Consensus 322 ---~~dpI~d~~~silDGhIvLsr~La~~g~yPAIDvl~S~SR~---~----~~i~~~~h~~~a-----~~~r~~ls~y~ 386 (444)
T PRK08972 322 ---LQDPIADASRAILDGHIVLSRELADSGHYPAIDIEASISRV---M----PMVISEEHLEAM-----RRVKQVYSLYQ 386 (444)
T ss_pred ---CCcchHHhhhhhcceEEEEcHHHHhCCCCCeeCCccccccC---c----hhcCcHHHHHHH-----HHHHHHHHHHH
Confidence 2356666666778999999988877654 335555444432 1 111333332222 22333444444
Q ss_pred HHHH--HhCCccccccccCCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHH
Q 002054 274 RLAE--KAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQ 330 (974)
Q Consensus 274 ~~~~--~~g~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~ 330 (974)
+... ..|. |.. -.++++.++++ ...+|++.+++...+.....+.+++|.+
T Consensus 387 ~~e~li~~g~----y~~-g~d~~~d~ai~--~~~~i~~fl~Q~~~~~~~~~~~~~~l~~ 438 (444)
T PRK08972 387 QNRDLISIGA----YKQ-GSDPRIDNAIR--LQPAMNAFLQQTMKEAVPYDMSVNMLKQ 438 (444)
T ss_pred HHHHHHHHhC----ccC-CCCHHHHHHHH--hhHHHHHHhCCCCCCCCCHHHHHHHHHH
Confidence 3321 2332 222 34667777776 3577888887755555655555555543
No 339
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=26.18 E-value=40 Score=29.76 Aligned_cols=31 Identities=16% Similarity=0.210 Sum_probs=24.5
Q ss_pred cceeeeeccchhhhhcCCCccchhhhhhhhC
Q 002054 616 RLATLKYDNDTLRRLIGPLGALKRKIEEETG 646 (974)
Q Consensus 616 ~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g 646 (974)
....+.++++..+.+||..|+++..|+-=++
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~ 54 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLAN 54 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHH
Confidence 3456788899999999999999987764333
No 340
>PRK06002 fliI flagellum-specific ATP synthase; Validated
Probab=26.14 E-value=5.9e+02 Score=30.51 Aligned_cols=170 Identities=13% Similarity=0.130 Sum_probs=95.2
Q ss_pred eeccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhc
Q 002054 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALML 193 (974)
Q Consensus 114 v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~ 193 (974)
--|+|-.-+.|+.|+ |+|-|..---+++||+.|+=+- +. + ...++.+-+|+--.++.
T Consensus 268 ~A~rEisl~~ge~P~----~~gyp~~vf~~l~~l~ERag~~-~~-~-~GSIT~~~tvl~~~dd~---------------- 324 (450)
T PRK06002 268 HAAREVALAAGEPPV----ARGYPPSVFSELPRLLERAGPG-AE-G-GGSITGIFSVLVDGDDH---------------- 324 (450)
T ss_pred HHHHHHHHhcCCCCc----cccCCccHHHHhhHHHHHhccC-CC-C-CeeeeEEEEEEecCCCC----------------
Confidence 345777777888886 4576766667889999998873 22 1 23455555555433332
Q ss_pred CCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 002054 194 SDIPWGGPIGMIRIGRICGQFIVNPTMDELSL-SDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQ 272 (974)
Q Consensus 194 s~iP~~~~v~av~vg~i~g~~vldPt~~e~~~-s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~ 272 (974)
++||+--..+..||+++|+-...+... .-+|..-+.+.-. -. -++++ ..++. ..++.++..+
T Consensus 325 -----~dpI~d~~~~i~Dg~ivLsr~la~~g~~PAIDv~~S~SR~~---~~----~~~~~-~~~~a----~~~r~~la~y 387 (450)
T PRK06002 325 -----NDPVADSIRGTLDGHIVLDRAIAEQGRYPAVDPLASISRLA---RH----AWTPE-QRKLV----SRLKSMIARF 387 (450)
T ss_pred -----CCccHHHHHhhcceEEEEcHHHHhCCCCCccCCccccCccc---cc----ccCHH-HHHHH----HHHHHHHHHH
Confidence 245555555677999999887777655 4466665554422 11 13332 22222 2233344444
Q ss_pred HHHHH--HhCCccccccccCCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHHHHH
Q 002054 273 IRLAE--KAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQD 331 (974)
Q Consensus 273 ~~~~~--~~g~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~~~~ 331 (974)
+++.. ..|- |. .-.++++-+.++. ..+|++.+++...++.. .+.+..|.+-
T Consensus 388 ~e~e~li~ig~----y~-~G~d~~~D~ai~~--~~~i~~fL~Q~~~~~~~-~~~~~~l~~~ 440 (450)
T PRK06002 388 EETRDLRLIGG----YR-AGSDPDLDQAVDL--VPRIYEALRQSPGDPPS-DDAFADLAAA 440 (450)
T ss_pred HHHHHHHHhhc----cc-cCCChHHHHHHHh--HHHHHHHhCCCCCCCCC-HHHHHHHHHH
Confidence 44322 1221 11 1244556666664 77888888876556666 6666655443
No 341
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=25.65 E-value=95 Score=33.83 Aligned_cols=63 Identities=13% Similarity=0.234 Sum_probs=43.9
Q ss_pred CcceeeeeccchhhhhcCCCccchhhhhhhhCceEEe--e-----CCEEEEEecCHHHHHHHHHHHHHHh
Q 002054 615 PRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRISV--S-----DGTLTVVAKNRSVMEKVLEKVDFII 677 (974)
Q Consensus 615 p~~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi--~-----dg~v~i~~~~~~~~~~a~~~i~~l~ 677 (974)
|-...+-|..+.-+.+||..|..|+++.|...+.+.| + ..+|-+.......+-...+.+-.++
T Consensus 122 pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i 191 (390)
T KOG2192|consen 122 PCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLI 191 (390)
T ss_pred chhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHh
Confidence 4445566778888999999999999999998887654 2 2456666655555555555544444
No 342
>PRK09280 F0F1 ATP synthase subunit beta; Validated
Probab=24.91 E-value=4.2e+02 Score=31.85 Aligned_cols=91 Identities=12% Similarity=0.180 Sum_probs=60.7
Q ss_pred ccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCC
Q 002054 116 YQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSD 195 (974)
Q Consensus 116 y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~ 195 (974)
|||-.-+.|+.|+ |+|=|..---.++||+.|+-. .. ...++.+-+|+--.++.
T Consensus 254 ~REisl~~gepP~----~~GYPpsvfs~l~~L~ERag~----~~-~GSITai~tVl~~gdD~------------------ 306 (463)
T PRK09280 254 GSEVSALLGRMPS----AVGYQPTLATEMGQLQERITS----TK-KGSITSVQAVYVPADDL------------------ 306 (463)
T ss_pred HHHHHHhcCCCCc----ccCcCchHHHHHHHHHHHhcC----CC-CCceeEEEEEECcCCCC------------------
Confidence 4777788888887 356555555678888888743 12 34666666666554443
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CccceeEeeeC
Q 002054 196 IPWGGPIGMIRIGRICGQFIVNPTMDELSL-SDLNLVYACTR 236 (974)
Q Consensus 196 iP~~~~v~av~vg~i~g~~vldPt~~e~~~-s~~~l~v~~t~ 236 (974)
++||+-...+..||+++|+....+... .-.|...+.+.
T Consensus 307 ---~dPI~d~~~silDGhIvLsr~La~~g~yPAIDvl~S~SR 345 (463)
T PRK09280 307 ---TDPAPATTFAHLDATTVLSRQIAELGIYPAVDPLDSTSR 345 (463)
T ss_pred ---CCcchHhhhhhcceEEEEcHHHHhCCCCCccCCcccccc
Confidence 357776667778999999998877755 44666655544
No 343
>PRK09281 F0F1 ATP synthase subunit alpha; Validated
Probab=24.89 E-value=1.3e+03 Score=28.05 Aligned_cols=93 Identities=16% Similarity=0.188 Sum_probs=56.4
Q ss_pred eccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcC
Q 002054 115 DYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLS 194 (974)
Q Consensus 115 ~y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s 194 (974)
-|||-.-+.|+.|| |+|=|.+--.+++||+.|+=+ +-...-...++..-.|+--+++
T Consensus 269 A~REisl~~gepPg----r~gyP~~vf~~~s~LlERag~-~~~~~~~GSITal~~V~~~~dD------------------ 325 (502)
T PRK09281 269 AYRQLSLLLRRPPG----REAYPGDVFYLHSRLLERAAK-LSDELGGGSLTALPIIETQAGD------------------ 325 (502)
T ss_pred HHHHHHHhcCCCCC----CCCcCccHHHHhHHHHHHhhh-ccCCCCCccEEEEEEEECCCCC------------------
Confidence 37888888899998 567777666789999988876 2111002244433333322222
Q ss_pred CCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CccceeEe
Q 002054 195 DIPWGGPIGMIRIGRICGQFIVNPTMDELSL-SDLNLVYA 233 (974)
Q Consensus 195 ~iP~~~~v~av~vg~i~g~~vldPt~~e~~~-s~~~l~v~ 233 (974)
+.+||+.-..+..||+++++....+... .-.|...+
T Consensus 326 ---~s~pI~d~~~sItDGqIvLsr~La~~G~~PAIdv~~S 362 (502)
T PRK09281 326 ---VSAYIPTNVISITDGQIFLESDLFNAGIRPAINVGIS 362 (502)
T ss_pred ---CCCcchHhhhcccceEEEEcHHHHhCCCCCccCCccc
Confidence 2345554455667999999998877654 33444433
No 344
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=24.46 E-value=1.1e+02 Score=26.35 Aligned_cols=58 Identities=17% Similarity=0.152 Sum_probs=37.1
Q ss_pred cEEEEEEEEEeeceEEEEEcC-CeEEEEecccCCCccccccccccccCCEEEEEEEEEc
Q 002054 685 GIYKGVVTSVKEYGAFVEFNG-GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQD 742 (974)
Q Consensus 685 ~i~~G~V~~i~~~G~fV~l~~-g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id 742 (974)
..+.++|..+.+.-+.|.|.. +.-..+|.+.=-++-+..-.+.+++|+.+.|++....
T Consensus 2 S~htA~VQh~~kdfAvvSL~~t~~L~a~p~~sHLNdtfrf~seklkvG~~l~v~lk~~~ 60 (69)
T cd05701 2 SRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPN 60 (69)
T ss_pred CccchhhhhhhhceEEEEeeccccEEEEEchhhccccccccceeeeccceEEEEEecCc
Confidence 346667777777777777754 3335555533223334444566999999999987754
No 345
>PRK08472 fliI flagellum-specific ATP synthase; Validated
Probab=24.01 E-value=6.5e+02 Score=30.07 Aligned_cols=165 Identities=16% Similarity=0.236 Sum_probs=90.9
Q ss_pred ccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCC
Q 002054 116 YQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSD 195 (974)
Q Consensus 116 y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~ 195 (974)
|||-.-+.|..|+ |+|=|..--.+++||..|+=+ +. + ...++.+-+|+ .+|+.
T Consensus 262 ~REi~l~~ge~P~----~~Gyp~~vf~~l~~l~ERag~--~~-g-~GSIT~~~tVl-v~gdD------------------ 314 (434)
T PRK08472 262 QREIGLALGEPPT----SKGYPPSVLSLLPQLMERAGK--EE-G-KGSITAFFTVL-VEGDD------------------ 314 (434)
T ss_pred HHHHHHhcCCCCC----ccCcCchHHHHHHHHHHHhcc--CC-C-CceeeEeEEEE-ecCCC------------------
Confidence 5777788888887 456666666788899888776 22 1 23555555555 44332
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CccceeEeeeCCeEEEEEecCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 002054 196 IPWGGPIGMIRIGRICGQFIVNPTMDELSL-SDLNLVYACTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIR 274 (974)
Q Consensus 196 iP~~~~v~av~vg~i~g~~vldPt~~e~~~-s~~~l~v~~t~~~i~mie~~~~~~~e~~~~~al~~a~~~~~~i~~~~~~ 274 (974)
|++||+--..+..||+++|+-...+... .-.|..-+.+. +|- .-.++++.. +...+++++..+++
T Consensus 315 --~~dpi~d~~~~i~Dg~ivLsr~la~~g~~PAIDvl~S~SR---~~~----~~~~~~~~~-----~a~~~r~~l~~y~e 380 (434)
T PRK08472 315 --MSDPIADQSRSILDGHIVLSRELTDFGIYPPINILNSASR---VMN----DIISPEHKL-----AARKFKRLYSLLKE 380 (434)
T ss_pred --CCCCchHHhhhhcceEEEEcHHHHhCCCCCccCCccccCc---cch----hcCCHHHHH-----HHHHHHHHHHhchh
Confidence 2356666566778999999998877754 44555544442 121 113332222 12223334444433
Q ss_pred H--HHHhCCccccccccCCCHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHHHHH
Q 002054 275 L--AEKAGKQKKEYKLSMISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKI 328 (974)
Q Consensus 275 ~--~~~~g~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~r~~~~~~~ 328 (974)
. +-+.|-.+ . -.++++...|+ ...+|++.++++..+.....+.++.+
T Consensus 381 ~e~li~~G~y~----~-g~d~~~d~ai~--~~~~i~~fL~Q~~~~~~~~~~~~~~l 429 (434)
T PRK08472 381 NEVLIRIGAYQ----K-GNDKELDEAIS--KKEFMEQFLKQNPNELFPFEQTFEQL 429 (434)
T ss_pred HHHHHHhhCcc----C-CCCHHHHHHHH--hHHHHHHHhCCCCCCCCCHHHHHHHH
Confidence 2 22344222 1 23445555554 35677777776544555445544444
No 346
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=23.43 E-value=1.9e+02 Score=29.34 Aligned_cols=64 Identities=14% Similarity=0.168 Sum_probs=46.4
Q ss_pred ccCcEEEEEEEEEeeceEE-EEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEcc-CCceEEEE
Q 002054 682 EVGGIYKGVVTSVKEYGAF-VEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDV-RGNIKLSL 751 (974)
Q Consensus 682 ~~G~i~~G~V~~i~~~G~f-V~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id~-~gri~LS~ 751 (974)
+.|+ .-|+|++....|.| |.+.+|..-+.|++-= ++. .-.+..||.|.|..-..+. +|+|..-.
T Consensus 30 eegq-~~g~V~~~LGn~~f~V~c~dG~~rLa~I~GK----mRK-~IWI~~GD~VlVel~~yd~~KgdIi~Ry 95 (155)
T PTZ00329 30 EEGQ-EYAQVLRMLGNGRLEAYCFDGVKRLCHIRGK----MRK-RVWINIGDIILVSLRDFQDSKADVILKY 95 (155)
T ss_pred CCCc-EEEEEEEEcCCCEEEEEECCCCEEEEEeecc----cee-eEEecCCCEEEEeccCCCCCEEEEEEEc
Confidence 4565 56999999999887 7888899999998742 222 2348899999998755544 56666544
No 347
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=23.22 E-value=58 Score=34.24 Aligned_cols=36 Identities=28% Similarity=0.257 Sum_probs=32.3
Q ss_pred ceeeeeccchhhhhcCCCccchhhhhhhhCceEEee
Q 002054 617 LATLKYDNDTLRRLIGPLGALKRKIEEETGGRISVS 652 (974)
Q Consensus 617 ~~~~~i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi~ 652 (974)
...+.++++.++.+||.+|.|++-+..=||.+++|.
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~ 178 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIE 178 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEE
Confidence 455668999999999999999999999999999886
No 348
>PF00358 PTS_EIIA_1: phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1; InterPro: IPR001127 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. ; GO: 0005351 sugar:hydrogen symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane; PDB: 3OUR_D 1GPR_A 1F3G_A 2F3G_B 1F3Z_A 1O2F_A 1GLB_F 1GGR_A 1GLA_F 1GLE_F ....
Probab=23.13 E-value=1.3e+02 Score=29.69 Aligned_cols=49 Identities=10% Similarity=0.078 Sum_probs=33.8
Q ss_pred EEEEEEEeC--CeEEEEeCCCeEEEEeccc----CC----CCCCCCCCEEEE--EEEEEeC
Q 002054 915 AAKVYQVRA--RGLVLDLGGGIRGMYRFEN----NE----KKDFVVGDELLV--KCSSFTG 963 (974)
Q Consensus 915 ~G~V~~I~~--~GvFV~L~~gv~Glih~se----~~----~~~f~vGd~V~v--kVl~id~ 963 (974)
.|+|..+-+ +-+-++.++|+.-|+|+-- +. ...++.||+|++ .++++|.
T Consensus 47 ~G~v~~i~~T~HAi~i~s~~G~eiLiHiGidTv~L~G~gF~~~v~~G~~V~~G~~L~~~D~ 107 (132)
T PF00358_consen 47 DGTVTMIFPTKHAIGIRSDNGVEILIHIGIDTVKLNGEGFETLVKEGDKVKAGQPLIEFDL 107 (132)
T ss_dssp SEEEEEE-TTSSEEEEEETTSEEEEEE-SBSGGGGTTTTEEESS-TTSEE-TTEEEEEE-H
T ss_pred eEEEEEEcCCCCEEEEEeCCCCEEEEEEccchhhcCCcceEEEEeCCCEEECCCEEEEEcH
Confidence 599999955 6677788899999999982 22 335779999987 6777774
No 349
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=22.96 E-value=1.8e+02 Score=24.16 Aligned_cols=47 Identities=15% Similarity=0.282 Sum_probs=27.8
Q ss_pred cEEEEEEEEEeece----EEEEEcCCe--EEEEecccCCCccccccccccccCCEEEEEE
Q 002054 685 GIYKGVVTSVKEYG----AFVEFNGGQ--QGLLHVSELSHEPVSRVSDVVSVGQQLSLRC 738 (974)
Q Consensus 685 ~i~~G~V~~i~~~G----~fV~l~~g~--~Glvhisels~~~v~~~~~~~~vGd~V~vkV 738 (974)
-.+.|+|..+.+.| +.+++.++. .+.+..... . +-.+++||.|.+.+
T Consensus 5 N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~-----~--~L~L~~G~~V~~~i 57 (64)
T PF03459_consen 5 NQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESA-----E--ELGLKPGDEVYASI 57 (64)
T ss_dssp EEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHH-----H--HCT-STT-EEEEEE
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHH-----H--HcCCCCCCEEEEEE
Confidence 36899999999999 455555443 233332221 1 11277899998875
No 350
>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Probab=22.82 E-value=8.1e+02 Score=29.03 Aligned_cols=91 Identities=16% Similarity=0.243 Sum_probs=60.6
Q ss_pred ccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhcCC
Q 002054 116 YQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALMLSD 195 (974)
Q Consensus 116 y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~s~ 195 (974)
|+|-.-+.|+.|+. +|=|..--..++||..|+=.. + ...++.+-+|+--.++
T Consensus 243 ~rEisl~~ge~P~~----~gyp~~~f~~l~~l~ERag~~----~-~GSIT~~~tVl~~gdD------------------- 294 (413)
T TIGR03497 243 QREIGLAVGEPPTT----RGYTPSVFSLLPKLLERSGNS----Q-KGSITGFYTVLVDGDD------------------- 294 (413)
T ss_pred HHHHHHhcCCCCCC----CCcCchHHHHhHHHHHHhcCC----C-CcceeEEEEEEccCCC-------------------
Confidence 57878888888873 465666666778888887651 2 3456666555544332
Q ss_pred CCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CccceeEeeeC
Q 002054 196 IPWGGPIGMIRIGRICGQFIVNPTMDELSL-SDLNLVYACTR 236 (974)
Q Consensus 196 iP~~~~v~av~vg~i~g~~vldPt~~e~~~-s~~~l~v~~t~ 236 (974)
+.+||+--..+..||+++|+-...+... .-.|...+.+.
T Consensus 295 --~~dpi~~~~~si~dg~ivLsr~la~~g~~PAId~~~S~SR 334 (413)
T TIGR03497 295 --MNEPIADAVRGILDGHIVLSRELAAKNHYPAIDVLASVSR 334 (413)
T ss_pred --CCCcchhhccccccEEEEECHHHHhCCCCCccCCcccccc
Confidence 2356666666778999999998877755 44666655554
No 351
>PRK06820 type III secretion system ATPase; Validated
Probab=22.20 E-value=1.1e+03 Score=28.17 Aligned_cols=92 Identities=12% Similarity=0.166 Sum_probs=60.1
Q ss_pred eeccccccccCCCCCccccccCCCCchhhhHHHhhcCCccccccCCCCCceEEEEEEEeccCCCChhhHHHHHHHHHhhc
Q 002054 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMAANATSAALML 193 (974)
Q Consensus 114 v~y~e~~~a~g~ip~~~~~Reg~p~~~eil~~RlidR~lrplfp~~~~~~~~i~~~vl~~dg~~~~~~~ai~aAs~AL~~ 193 (974)
--|||-..+.|..|+ |+|=|..--..++||..|+=+- . ...++.+-+|+--.++
T Consensus 267 ~A~REisl~~gepP~----~~GYP~~vf~~l~~L~ERag~~--~---~GSIT~i~tVl~~gdD----------------- 320 (440)
T PRK06820 267 RAAREIGLAAGEPPA----AGSFPPSVFANLPRLLERTGNS--D---RGSITAFYTVLVEGDD----------------- 320 (440)
T ss_pred HHHHHHHHhcCCCCc----cccCCccHHHHHHHHHHhhccC--C---CcceeEEEEEEccCCC-----------------
Confidence 345777778888876 3465665556788999988762 2 3356666555544332
Q ss_pred CCCCCCCCeEEEEEEEECCEEEEcCCHHHHhc-CccceeEeee
Q 002054 194 SDIPWGGPIGMIRIGRICGQFIVNPTMDELSL-SDLNLVYACT 235 (974)
Q Consensus 194 s~iP~~~~v~av~vg~i~g~~vldPt~~e~~~-s~~~l~v~~t 235 (974)
|++||+--..+..||+++++-...+... .-.|..-+.+
T Consensus 321 ----~~dpI~d~~~~ilDg~ivLsr~La~~g~yPAIDvl~S~S 359 (440)
T PRK06820 321 ----MNEPVADEVRSLLDGHIVLSRRLAGAGHYPAIDIAASVS 359 (440)
T ss_pred ----CCCcchhhhccccceEEEECHHHHhCCCCCccCCccccc
Confidence 2356666666788999999998877755 4455554444
No 352
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=21.51 E-value=60 Score=26.94 Aligned_cols=23 Identities=17% Similarity=0.105 Sum_probs=19.9
Q ss_pred hhhhhcCCCccchhhhhhhhCce
Q 002054 626 TLRRLIGPLGALKRKIEEETGGR 648 (974)
Q Consensus 626 ki~~vIg~gGk~i~~i~~~~g~~ 648 (974)
..+.+||.+|++++.++..++..
T Consensus 35 ~~g~lIGk~G~~l~~l~~l~~~~ 57 (68)
T cd02409 35 QPGLVIGKKGQNIRALQKLLQKL 57 (68)
T ss_pred CCceEECCCCccHHHHHHHHHHH
Confidence 58999999999999998888743
No 353
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=21.33 E-value=3.2e+02 Score=23.45 Aligned_cols=49 Identities=16% Similarity=0.184 Sum_probs=35.8
Q ss_pred EEEEEEEEEeeceEEEEEcCCeEEEEecccCCCccccccccccccCCEEEEEEEEEc
Q 002054 686 IYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQD 742 (974)
Q Consensus 686 i~~G~V~~i~~~G~fV~l~~g~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~id 742 (974)
-++|+|++|.+...-+.|..|..=-+| .+.. -+-+++|.+|.|..-..|
T Consensus 4 ~veG~I~~id~~~~titLdDGksy~lp-~ef~-------~~~L~~G~kV~V~yd~~~ 52 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSYKLP-EEFD-------FDGLKPGMKVVVFYDEVD 52 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEEECC-Cccc-------ccccCCCCEEEEEEEccC
Confidence 578999999999999999877665444 2222 123899998887765543
No 354
>PF01330 RuvA_N: RuvA N terminal domain; InterPro: IPR013849 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. This entry represents domain I of RuvA, which has an OB-fold structure. This domain forms the RuvA tetramer contacts [].; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJP_A 1D8L_B 1CUK_A 1C7Y_A 1IXR_B 2ZTC_A 2ZTD_B 2H5X_A 2ZTE_A 1BVS_E ....
Probab=21.30 E-value=4.1e+02 Score=22.26 Aligned_cols=49 Identities=16% Similarity=0.190 Sum_probs=36.0
Q ss_pred EEEEEEEEEeCCeEEEEeCC-CeEEEEecccCCCCCCCCCCEEEEEEEEEeC
Q 002054 913 KVAAKVYQVRARGLVLDLGG-GIRGMYRFENNEKKDFVVGDELLVKCSSFTG 963 (974)
Q Consensus 913 vV~G~V~~I~~~GvFV~L~~-gv~Glih~se~~~~~f~vGd~V~vkVl~id~ 963 (974)
-++|+|..+.+.-+.++.++ |+.=+++.+.. ..+..+++++.-+--+-+
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~~--~~l~~~~~v~l~t~~~vr 53 (61)
T PF01330_consen 4 YLKGKVVEKNPDYVVIDVNGVGYEVFVPSNTL--SELPEGGEVKLYTYLIVR 53 (61)
T ss_dssp EEEEEEEEEESSEEEEEETTEEEEEEE-HHHH--HTS-TTSEEEEEEEEEEE
T ss_pred EEEEEEEEEcCCEEEEEECCEEEEEEeCCchH--HhCCCCCEEEEEEEEEEe
Confidence 47899999999999999997 78888887644 456667778776654443
No 355
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=20.71 E-value=62 Score=33.27 Aligned_cols=29 Identities=21% Similarity=0.395 Sum_probs=25.0
Q ss_pred eccchhhhhcCCCccchhhhhhhhCceEEe
Q 002054 622 YDNDTLRRLIGPLGALKRKIEEETGGRISV 651 (974)
Q Consensus 622 i~~~ki~~vIg~gGk~i~~i~~~~g~~Idi 651 (974)
+.+.. +..||++|++++.+++.+|.+|.+
T Consensus 67 V~~gd-g~aIGk~G~~ik~l~~~lgk~Vev 95 (166)
T PRK06418 67 VTSGP-RIPIGKGGKIAKALSRKLGKKVRV 95 (166)
T ss_pred EeCCC-cccccccchHHHHHHHHhCCcEEE
Confidence 45566 999999999999999999988764
No 356
>PF14444 S1-like: S1-like
Probab=20.36 E-value=3.4e+02 Score=23.03 Aligned_cols=43 Identities=16% Similarity=0.261 Sum_probs=25.1
Q ss_pred EEEEEEEEE-eCCeEEEEeCCCeEEEEecccCCCCCCCCCCEEEEEEEE
Q 002054 913 KVAAKVYQV-RARGLVLDLGGGIRGMYRFENNEKKDFVVGDELLVKCSS 960 (974)
Q Consensus 913 vV~G~V~~I-~~~GvFV~L~~gv~Glih~se~~~~~f~vGd~V~vkVl~ 960 (974)
+++|.|.+. .+||+. ++.+ +.+.+-.....+++||+|.|.-+.
T Consensus 3 ~~~GvVTkl~~~yG~I---De~v--FF~~~vv~G~~P~vGdrV~v~A~~ 46 (58)
T PF14444_consen 3 VFTGVVTKLCDDYGFI---DEDV--FFQTDVVKGNVPKVGDRVLVEAIY 46 (58)
T ss_pred eEEEEEEEEeCCcceE---cccE--EEEcccEecCCCccCCEEEEEEEe
Confidence 578999998 566652 2221 111111123456899999987654
No 357
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=20.25 E-value=1.1e+02 Score=25.77 Aligned_cols=49 Identities=16% Similarity=0.254 Sum_probs=29.1
Q ss_pred cEEEEEEEEEeeceEEEEEc----CC--eEEEEecccCCCccccccccccccCCEEEEEEEE
Q 002054 685 GIYKGVVTSVKEYGAFVEFN----GG--QQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIG 740 (974)
Q Consensus 685 ~i~~G~V~~i~~~G~fV~l~----~g--~~Glvhisels~~~v~~~~~~~~vGd~V~vkVl~ 740 (974)
-.+.|+|.++.+.|.++++. ++ ....++.+. .. +-.+++|+.|.+.+-.
T Consensus 7 N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~-----~~--~l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 7 NQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLES-----VA--ELGLKPGKEVYAVIKA 61 (69)
T ss_pred cEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHH-----Hh--hCCCCCCCEEEEEEEC
Confidence 46899999998887766552 22 112222211 11 1227899999887644
No 358
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=20.24 E-value=2.8e+02 Score=25.87 Aligned_cols=45 Identities=27% Similarity=0.288 Sum_probs=31.9
Q ss_pred EEEEEEEEEeCCe--EEEEeCCC---eEEEEecccCC-------CCCCCCCCEEEEE
Q 002054 913 KVAAKVYQVRARG--LVLDLGGG---IRGMYRFENNE-------KKDFVVGDELLVK 957 (974)
Q Consensus 913 vV~G~V~~I~~~G--vFV~L~~g---v~Glih~se~~-------~~~f~vGd~V~vk 957 (974)
.+.|.|++++..| +|++|-+| +..++..++.. ...+..|+-|.+.
T Consensus 3 ~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~ 59 (108)
T cd04322 3 SVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVT 59 (108)
T ss_pred EEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEE
Confidence 5889999998775 99999874 56666554321 1228889988774
No 359
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=20.20 E-value=1.1e+02 Score=32.18 Aligned_cols=60 Identities=23% Similarity=0.306 Sum_probs=43.4
Q ss_pred hhhhhcCCCccchhhhhhhhCceEEeeCCEEEEEecCHHHHHHHHHHHHHHhhcccccCcEE
Q 002054 626 TLRRLIGPLGALKRKIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIY 687 (974)
Q Consensus 626 ki~~vIg~gGk~i~~i~~~~g~~Idi~dg~v~i~~~~~~~~~~a~~~i~~l~~~~~~~G~i~ 687 (974)
.||.+.|.|||+--.|++-+-..|-+.|-+++|.+.= ..+.-|+..+-.++ ..-.+|.+|
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVlad~kIHiLG~~-~niriAR~avcsLI-lGsppgkVy 238 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVLADSKIHILGAF-QNIRIARDAVCSLI-LGSPPGKVY 238 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEecCceEEEeecc-hhhHHHHHhhHhhh-ccCCchhHH
Confidence 5899999999998888888888888778899988753 45666666555444 233455444
Done!